Inverted Repeats Finder Program written by:
Gary Benson
Department of Biomathematical Sciences
Mount Sinai School of Medicine
Version 3.05
Sequence: NFA 2003-09-04
Parameters: 2 3 5 80 10 40 100000 500000 -t7 600000 -d
Length: 6021225
ACGTcount: A:0.15, C:0.35, G:0.35, T:0.15, N:0.00
File 3 of 3
Found at i: 4922605 center: 9427323 interval size: 300 g: 3
Alignment explanation
Indices: 4504672--4505216,4922122--4922651 Loop: 416905 Score: 148
Left Length: 545 Right Length: 530 Average length: 537.5
3 most common centers (desc): 9427323 9427338 9427335
4504662 >> (LF) CATGCTCGCC
4922661 << (RF) GCGCCACAAC
4504672 >> GAGGGCACCGTGCGCGGCACCGGCGGCAT-CGACGTGGTGGACGACGACTGCGCCACCACCGTGCCCGGTCTGTT >> 4504745
4922651 << *****************A*****A***G*C**G*AGTGG**-**G*********C*********C*C**C****T << 4922578
4504746 >> CGCCGCGGGCGACGCCGCCACCCGTGAGCGCATCTGCGGCGGATTCACCGGCGGCGGCAGCCACAACTCCGCGTG >> 4504820
4922577 << **************A****CT***C**T*TC***T******GCCGC*C***TAGC**AC*****G**C****G** << 4922503
4504821 >> GGCGATGTCCTCTGGCAGC-TGGGCCGGGCGCGGCG-CGGCCCGGTTCGCGCTGAGCTCCG-GGCGACCGGCCGA >> 4504892
4922502 << ******GC****G***-**C*****-**********C*****C*T*T*****-*G-*C***G***-*A*--**-- << 4922437
4504893 >> CGCCCGGCTGCGGGGCGCGGGCC-GG-GTCGGGTTGCGGCCCAGCGGTTCCGGCGCGGTGGACGCCGC-CGAGGT >> 4504964
4922436 << ****-*-*C***AAG*G**A***G**G*G****G**-*G*T*G-***C-*CTT*-*--*****-****C**GG** << 4922371
4504965 >> GGT-GGCG-GCCGC-GCAGCGCGAGCTGATCCCGTTCGAGAAGAACTACCTGCGCCACGGCGACCGGTTGCGCC- >> 4505037
4922370 << ***G***GA*CA**T*C***T*TG****G-***-*C**-*GCG*C***A******TC**G****T*GG*****CT << 4922299
4505036 >> CGGCGCTGTCCGAGCTCGACGCGCTGTGGACCGCGGCGGC-G-TCCGGCCTGGGCGGGCACACCGGCGAACAG-C >> 4505107
4922298 << *T**TAG*-****T***************-***-****G*G*G*A**TT**G******A**C--***-*-*C*T* << 4922231
4505108 >> GGGTGCGCGCCCGGCAGGCCGCCGCCATCACCGCCGTGGGCAGGCTGATGT-ACCGCTCGGCGCTGGCGCGTCCG >> 4505181
4922230 << ****GT*******GC**********CG*CGAC*****G*-*CG****CCGGC***T*C*G*****G*****GT*G << 4922157
4505182 >> GAGACACGCGGCATGAACAAGC-GGGCCGATCACCC >> 4505216
4922156 << ****CG**C**A***G**G-**T**********A** << 4922122
Statistics
Matches: 385 (68.63%), Mismatches: 129 (22.99%), Indels: 47 (8.38%)
ATpairs: 16.62%, CGpairs: 83.38%, GTpairs: 0.00%
:i = 4922605
tupleindex: 3
intervalindex: 1
matches_in_interval: 97.0000
lowcenter: 9427299
highcenter: 9427347
testcenter: 9427323
im3: 38.0000
frequent_center_ratio*rnkp: 25.9200
Found at i: 4923031 center: 9427302 interval size: 600 g: 3
Alignment explanation
Indices: 4504136--4504393,4922909--4923169 Loop: 418515 Score: 139
Left Length: 258 Right Length: 261 Average length: 259.5
3 most common centers (desc): 9427302 9427305 9427306
4504126 >> (LF) CTCAAGCGGA
4923179 << (RF) GACGCCGACG
4504136 >> TCGGCGTGCGCATCCTCGACCACTCCCCCG-CGCTGGAGCTGCTCGTCGACGACGCCGGGGTGGTGCGC-GGCGC >> 4504208
4923169 << **********CC*C*******C-**TA***C*G***G*G*****CTG****GC**T***G*****-***G***** << 4923097
4504209 >> GGCCGGCCATCAGCGCCAGCTCGGCCGC-GACTACCG-G-ATCACC-GCG-GGCG-CGGTGGTACTGGCCACCGG >> 4504277
4923096 << ***C***CAC*-**T**C**--*T***CA*G**C***A*C*G*C**G***G**C*C****G**G*********** << 4923025
4504278 >> CGGGTGCGCGTTCCTGTCCCGCGCGCTGGGCACCAACGTCGACACCGGCGACGGCGC-GTTGATGGCCGCCGAGG >> 4504351
4923024 << ***G*********CCG***C*****CG*******CGC*C**G******A**C**-**A*G*******C******* << 4922951
4504352 >> TCGGGGCCCGGTTCTCCGGTATGGAGTTCTCCAACGCCTACG >> 4504393
4922950 << GC*****C***G*C**C**G*****T******AC**C***** << 4922909
Statistics
Matches: 194 (72.66%), Mismatches: 58 (21.72%), Indels: 15 (5.62%)
ATpairs: 20.62%, CGpairs: 79.38%, GTpairs: 0.00%
:i = 4923031
tupleindex: 3
intervalindex: 2
matches_in_interval: 234.0000
lowcenter: 9427268
highcenter: 9427336
testcenter: 9427302
im3: 57.0000
frequent_center_ratio*rnkp: 41.4200
Found at i: 4923037 center: 9819784 interval size: 600 g: 3
Alignment explanation
Indices: 4896747--4896797,4922984--4923037 Loop: 26186 Score: 40
Left Length: 51 Right Length: 54 Average length: 52.5
3 most common centers (desc): 9819784 9819781 9819785
4896737 >> (LF) TACCTGGCGA
4923047 << (RF) CCCCGCCAGC
4896747 >> TCCTGGCCACCGTGCTGG-GCGCGGGCGCGTTCGGCGCGGC---CACCGCGGGCG >> 4896797
4923037 << ************-**C*GA*****AA**CG*G*********CCC*********** << 4922984
Statistics
Matches: 43 (78.18%), Mismatches: 7 (12.73%), Indels: 5 (9.09%)
ATpairs: 11.63%, CGpairs: 88.37%, GTpairs: 0.00%
:i = 4923037
tupleindex: 3
intervalindex: 2
matches_in_interval: 237.0000
lowcenter: 9819750
highcenter: 9819818
testcenter: 9819784
im3: 43.0000
frequent_center_ratio*rnkp: 41.4200
Found at i: 5000325 center: 9808697 interval size: 300 g: 3
Alignment explanation
Indices: 4808362--4808397,5000301--5000334 Loop: 191903 Score: 43
Left Length: 36 Right Length: 34 Average length: 35.0
3 most common centers (desc): 9808697 9808696 9808698
4808352 >> (LF) GACGCCGGGC
5000344 << (RF) CGCTGTAGGC
4808362 >> ACCTCGGCGGTGTCGGTGGTGTGGATCAGCCAGCCG >> 4808397
5000334 << **T*****T-**********G*********-***** << 5000301
Statistics
Matches: 31 (86.11%), Mismatches: 3 (8.33%), Indels: 2 (5.56%)
ATpairs: 35.48%, CGpairs: 64.52%, GTpairs: 0.00%
:i = 5000325
tupleindex: 3
intervalindex: 1
matches_in_interval: 96.0000
lowcenter: 9808673
highcenter: 9808721
testcenter: 9808697
im3: 27.0000
frequent_center_ratio*rnkp: 25.9200
Found at i: 5001707 center: 9979036 interval size: 300 g: 3
Alignment explanation
Indices: 4977328--4977369,5001667--5001708 Loop: 24297 Score: 42
Left Length: 42 Right Length: 42 Average length: 42.0
3 most common centers (desc): 9979036 9979035 0
4977318 >> (LF) AGCGGGGCGC
5001718 << (RF) GCGTCCGCAA
4977328 >> GGCGGCGGCGGGGGTGGCGGAGGCG-GTGACGCCCAGGGCGGC >> 4977369
5001708 << **********G*********G**C*G**G-**C*C******** << 5001667
Statistics
Matches: 35 (81.40%), Mismatches: 6 (13.95%), Indels: 2 (4.65%)
ATpairs: 8.57%, CGpairs: 91.43%, GTpairs: 0.00%
:i = 5001707
tupleindex: 3
intervalindex: 1
matches_in_interval: 103.0000
lowcenter: 9979012
highcenter: 9979060
testcenter: 9979036
im3: 26.0000
frequent_center_ratio*rnkp: 25.9200
Found at i: 5001735 center: 9638928 interval size: 300 g: 3
Alignment explanation
Indices: 4637193--4637240,5001688--5001735 Loop: 364447 Score: 41
Left Length: 48 Right Length: 48 Average length: 48.0
3 most common centers (desc): 9638928 0 0
4637183 >> (LF) CGTGGAAATC
5001745 << (RF) CCTGCTTGTC
4637193 >> GGCGGCGGCGCGGCGGGCGCGCGGGGCGTCGCCGGCGCGGGCGGCCGC >> 4637240
5001735 << **********AA********TC*G*AA*C**C*********A***C** << 5001688
Statistics
Matches: 37 (77.08%), Mismatches: 11 (22.92%), Indels: 0 (0.00%)
ATpairs: 0.00%, CGpairs: 100.00%, GTpairs: 0.00%
:i = 5001735
tupleindex: 3
intervalindex: 1
matches_in_interval: 115.0000
lowcenter: 9638904
highcenter: 9638952
testcenter: 9638928
im3: 35.0000
frequent_center_ratio*rnkp: 25.9200
Found at i: 5050613 center: 10039528 interval size: 300 g: 3
Alignment explanation
Indices: 4987931--4988989,5050540--5051596 Loop: 61550 Score: 2009
Left Length: 1059 Right Length: 1057 Average length: 1058.0
3 most common centers (desc): 10039528 10039527 10039529
4987921 >> (LF) CCTCGCGACC
5051606 << (RF) AGGTCTTGCT
4987931 >> CTAGGCGGTGTCTCGAAGTAGTGCCGCAGGTGTGGGACTGTTTGGCAGGCTGGGGGTTTGAGATATGGCGAGGTC >> 4988005
5051596 << ******T**************G**A*CA*********************************************** << 5051522
4988006 >> TCCGGTAGTTGGTTGATCGACCAAGATTCAACTGAACACCGGAGACCTCGTGACCACCCTAGCGGTGACCGCGCG >> 4988080
5051521 << *********************************************************A***************** << 5051447
4988081 >> AGCGGATCTGTCCGATGCCCAATGGGCACGGCTGGAACCGCTGCTCCCCACCCCGAAACGACCCGGCCGCCCCTC >> 4988155
5051446 << *********************************************T***************************** << 5051372
4988156 >> GAGATGGACCCGACGCCGACTCCTGGACGGGATCCGCTGGCGGATCCGGGTCGGCTGCCCGTGGCGGGACATCCC >> 4988230
5051371 << ******************G**C***************************************************** << 5051297
4988231 >> ACCGCAGTACGGGTCCTGGCAGGCGATCTACGCACTGTTCCGCCGCTGGAGTCGGGCCGGGGTGTGGGCACATGT >> 4988305
5051296 << *************************************************************************** << 5051222
4988306 >> GCTGCGGCAACTTCAGGCGATCGCCGACGCCGCCGAACAGATCGGATGGATGGTCAGCGTGGACTCCACGATCAT >> 4988380
5051221 << *************************************************************************** << 5051147
4988381 >> GCGTGCCCACCCCCACGCCGCCGGGGGCCCGCCGCGATGGCGACCGCCAGGCCGAACCACCCGGCGGCTACCGCA >> 4988455
5051146 << **************************-**********G**********************************T** << 5051073
4988456 >> ACGAACCGGCCGATCACGCGCTCGGGCGGTCGAGGGGCGGATGGGGAACCAAACTCCATCTGGCCTGCGAACACC >> 4988530
5051072 << *******************T******************************************************* << 5050998
4988531 >> GCCTGCGTCCGTTGTCGTTGCTGCTCACCGCCGGTCAAGCCGGTGACAGCCCCCAGTTCGCCGGGGTCCTCGACG >> 4988605
5050997 << T***************************************************************T********** << 5050923
4988606 >> GCATCCGGGTCCCGCGCCTGGGTCGTGGACGGGCACGCGTGCGTCCGGACCGGGTACTGGCGGACAAGGCGTATT >> 4988680
5050922 << *************************************************************************** << 5050848
4988681 >> CCTCGGCCGCCAACCGCACCTACCTGCGCGAGCGTGGTATCCCCGCCACGATCCCGGTCCCGTCAGATCAAGCAG >> 4988755
5050847 << *************************************************************************** << 5050773
4988756 >> GACACCGCCGCAATCGTGGCCGCGCGGGCGGGCGACCACCAGCGTTCGACCGTGAGATCTACCGGCACCGCAACA >> 4988830
5050772 << ***********************GC***************C********************************** << 5050698
4988831 >> CCATCGAACGCGGCATCAACCGACTCAAACAACACCGCGCCGTCGCCACCCGCTACGAGAAACTCGCCACCCGCT >> 4988905
5050697 << *************************************************************************** << 5050623
4988906 >> ACCTCGCCGTCATCCAGATCGCCGCCATCGACCAATGGCTGTGACCTCGACACCTACTTCGAGACACCGCCTAGG >> 4988980
5050622 << **************************************************************************- << 5050549
4988981 >> TGCCCGGCG >> 4988989
5050548 << *G*C***** << 5050540
Statistics
Matches: 1038 (98.02%), Mismatches: 19 (1.79%), Indels: 2 (0.19%)
ATpairs: 31.98%, CGpairs: 68.02%, GTpairs: 0.00%
:i = 5050613
tupleindex: 3
intervalindex: 1
matches_in_interval: 96.0000
lowcenter: 10039504
highcenter: 10039552
testcenter: 10039528
im3: 65.0000
frequent_center_ratio*rnkp: 25.9200
Found at i: 5067484 center: 9941143 interval size: 300 g: 3
Alignment explanation
Indices: 4873634--4873764,5067381--5067509 Loop: 193616 Score: 213
Left Length: 131 Right Length: 129 Average length: 130.0
3 most common centers (desc): 9941143 9941144 9941145
4873624 >> (LF) CTTTTTCGTC
5067519 << (RF) CTCGCCCCGC
4873634 >> GCCTGCGTGGTGACGCTGCGCTACCGCCTCCGGCCGCTGACCCGCTCAGGCGGTGCCCGATTGCGCCCGAGCGGG >> 4873708
5067509 << ***************************************************A***AAC****A****A******* << 5067435
4873709 >> GCGGCCTGCGTGGTGACGCTGCGCTACCGTCTCCGGCCGCTGACCCGCTCAGGCGG >> 4873764
5067434 << *******************-*********G***************-********** << 5067381
Statistics
Matches: 122 (93.13%), Mismatches: 7 (5.34%), Indels: 2 (1.53%)
ATpairs: 22.95%, CGpairs: 77.05%, GTpairs: 0.00%
:i = 5067484
tupleindex: 3
intervalindex: 1
matches_in_interval: 96.0000
lowcenter: 9941119
highcenter: 9941167
testcenter: 9941143
im3: 52.0000
frequent_center_ratio*rnkp: 25.9200
Found at i: 5067628 center: 10014020 interval size: 300 g: 3
Alignment explanation
Indices: 4946370--4946640,5067381--5067651 Loop: 120740 Score: 224
Left Length: 271 Right Length: 271 Average length: 271.0
3 most common centers (desc): 10014020 10014021 0
4946360 >> (LF) GCTGACCCGC
5067661 << (RF) GACGCCCCAT
4946370 >> ACGCTCCGCTCCC-CCTCCGGGCGCTGACCCGCTCAGGCTGTGTCCAATTCCGCCCGAGCGGGACGCCCTACGCG >> 4946443
5067651 << *****C****T**C*******G**********************ACC***A-***A*******C**C***C**A* << 5067578
4946444 >> GCCACGCTCCGCTCCCAC-TCCGGGCGCTGACCCGCTCAGGCGGTACCCAATTCCGCCCGAGCGGGACGCCCTAC >> 4946517
5067577 << *AC*****C****T**C*G*****G*****************A**CAACC***A-***A*******C**C***C* << 5067504
4946518 >> GCGGCCACGCTCCGCTCCCAC-TCCGGGCGCTGACCCGCTCAGGCGGTACCCAATTCCGCCCGAGCGGGACGCCC >> 4946591
5067503 << *A**AC*****C****T**C*G*****G*****************A**CAACC***A****A*******C**C** << 5067429
4946592 >> TACGCGGCCACGCTCCGCTCCCAC-TCCGGGCGCTGACCCGCTCAGGCGG >> 4946640
5067428 << *C**A**AC****C*-***T**C*G*****G********-********** << 5067381
Statistics
Matches: 213 (77.45%), Mismatches: 54 (19.64%), Indels: 8 (2.91%)
ATpairs: 23.94%, CGpairs: 76.06%, GTpairs: 0.00%
:i = 5067628
tupleindex: 3
intervalindex: 1
matches_in_interval: 96.0000
lowcenter: 10013996
highcenter: 10014044
testcenter: 10014020
im3: 70.0000
frequent_center_ratio*rnkp: 25.9200
Found at i: 5072496 center: 10004709 interval size: 300 g: 3
Alignment explanation
Indices: 4932054--4932365,5072344--5072658 Loop: 139978 Score: 184
Left Length: 312 Right Length: 315 Average length: 313.5
3 most common centers (desc): 10004709 10004712 10004706
4932044 >> (LF) TGCCACATGC
5072668 << (RF) ACGCCGTAGC
4932054 >> CCTGGACCATGCTGGCCGGTATCGGCCGGGTGGAGTCCACGCACGCGTTCGGCGGCAAGGCCGA-C-GC-CGACG >> 4932125
5072658 << *********G******C**G****G*T*A******TC**T*****CGTG*GT*G**C**A****A*A**T**G** << 5072584
4932126 >> GCAACCCGATCAAGCCGGTC-T-A-CGGCCCGGTGCTCGACGGCTCGCTCGCGGGCAACAACGTCATCCACGACA >> 4932197
5072583 << T*CC*CA*C*CGCG***GG*T*G*A****CA**G***C**********-**C*G*ACC*C--*******C***** << 5072512
4932198 >> GCGACAACGGCGCGCTCGACGGACTCGACG-GCTACGACCGCGCGGTCGGCCCGATGCAGTTCCTGCCCGAGACC >> 4932271
5072511 << G****CC***************GCT*GG**T**-****************T***A********T*A********* << 5072438
4932272 >> TGGCAGCGCTACGCCGCCGACGGCAACGGTGACGGCATCGC-CGACCCGCAGAACCTCTTCGACGCGGCGCTGAC >> 4932345
5072437 << **********CC*CA*A*****G******G*****CC*-**A***********C*T**CT******G*****G** << 5072364
4932346 >> CGCGGGCAAGTACCTGTGCG >> 4932365
5072363 << ***G*G*GC*********** << 5072344
Statistics
Matches: 234 (73.12%), Mismatches: 73 (22.81%), Indels: 13 (4.06%)
ATpairs: 23.50%, CGpairs: 76.50%, GTpairs: 0.00%
:i = 5072496
tupleindex: 3
intervalindex: 1
matches_in_interval: 101.0000
lowcenter: 10004685
highcenter: 10004733
testcenter: 10004709
im3: 86.0000
frequent_center_ratio*rnkp: 25.9200
Found at i: 5118677 center: 9809760 interval size: 300 g: 3
Alignment explanation
Indices: 4691069--4691193,5118567--5118691 Loop: 427373 Score: 119
Left Length: 125 Right Length: 125 Average length: 125.0
3 most common centers (desc): 9809760 9809759 0
4691059 >> (LF) CCACCCACAA
5118701 << (RF) TGCCGCGCTA
4691069 >> CTGGGACGGCG-TCGCGCAGTGTGAGAGCGGCGGCAACTGGGGCATCAACACCGGCAACGGCTACTACGGCGGCC >> 4691142
5118691 << ********-**G*C********G**TAG*TT***********G*******************************T << 5118618
4691143 >> TGCAGTTCTCGCACAGCACCTGGGT-CGCCAACGGCGGCACCG-GTTACGCCC >> 4691193
5118617 << *G******CTG**C**********TT**C**C-******-*A*G*G******* << 5118567
Statistics
Matches: 103 (80.47%), Mismatches: 19 (14.84%), Indels: 6 (4.69%)
ATpairs: 30.10%, CGpairs: 69.90%, GTpairs: 0.00%
:i = 5118677
tupleindex: 3
intervalindex: 1
matches_in_interval: 96.0000
lowcenter: 9809736
highcenter: 9809784
testcenter: 9809760
im3: 66.0000
frequent_center_ratio*rnkp: 25.9200
Found at i: 5178087 center: 10120474 interval size: 300 g: 3
Alignment explanation
Indices: 4942013--4942468,5178006--5178464 Loop: 235537 Score: 159
Left Length: 456 Right Length: 459 Average length: 457.5
3 most common centers (desc): 10120486 10120474 10120489
4942003 >> (LF) CGGCTCGACC
5178474 << (RF) GCTCCCCCTC
4942013 >> GGCTCCGGCGTGGT-CA-TCGACGGCGCGGGCTACATCGTCACCAACAACCACGTGATCTCGATGGCCGCGCAGG >> 4942085
5178464 << ********C*****C*AC**GA***T-***T**C-***G*****************C-**---*--***-**-** << 5178400
4942086 >> ACAAGAGCGGCCGG-GCGAGCATCCAGGTCACCTTCTCCGACGGCAGCCGGGTGCCCGCGAACATCGTCGGGCGC >> 4942159
5178400 << -*--*-**T-****G**GG****CC*T***GT****C****A***AG*TGG*G******G*G*C****-****** << 5178331
4942161 >> -GACCCGAAGACCGATCTGGCCGTGCTCAAGGTGGATGT--GAAAA-ACCTCACCGTGGCCCGGCTCGGCCGCTC >> 4942230
5178330 << G******CAGA*C**G*****C***T******G*G*C*CGG*G*GGC*A******GG*TA*CT***C**ATG*** << 5178256
4942231 >> CGACGA-CGTGCAGGTCGGCGACGACGTGC-TCGCCATCGGCTCGCCGCTCGGCCTGAGCAAG-ACCGTGACCTC >> 4942302
5178255 << C*-***C*G***********G*-*G**CA*T**************************-**CC*G**C******T* << 5178184
4942303 >> CGGCATCGTCAGCGCACTGCACCGGCCGGTGAAGCTCTCCGGCGAGGGCAGCGACA--CC-AACGC-C-G----- >> 4942369
5178183 << ***A******AG***C**GT*A**G*****GAGGTG*TC***A*******G*G*C*TA**C*****A*G*GTCGG << 5178109
4942369 >> --TGATCGACGCGGTGCAGACCGACGCCTCGATCAACCCGGGCAACTCCGGTGGTGCGCTGGTGGACATGGACGG >> 4942440
5178108 << CC**********GT*G************C*G*****A**G*****A********G************ATG**C** << 5178034
4942441 >> CCAGGTCATCGGCATCAACTCCGCCATC >> 4942468
5178033 << *T*TG*C************T******** << 5178006
Statistics
Matches: 335 (70.08%), Mismatches: 102 (21.34%), Indels: 41 (8.58%)
ATpairs: 28.96%, CGpairs: 71.04%, GTpairs: 0.00%
:i = 5178087
tupleindex: 3
intervalindex: 1
matches_in_interval: 97.0000
lowcenter: 10120450
highcenter: 10120498
testcenter: 10120474
im3: 47.0000
frequent_center_ratio*rnkp: 25.9200
Found at i: 5210607 center: 10066635 interval size: 300 g: 3
Alignment explanation
Indices: 4856025--4856063,5210572--5210610 Loop: 354508 Score: 56
Left Length: 39 Right Length: 39 Average length: 39.0
3 most common centers (desc): 10066635 10066634 0
4856015 >> (LF) AGACGGCGTG
5210620 << (RF) CGCGTCGTGG
4856025 >> GCGGCGGGCG-CGGCGGGCGCGGGCGCGCGGCGCAGTTGC >> 4856063
5210610 << **********A******-********C*********C*** << 5210572
Statistics
Matches: 36 (90.00%), Mismatches: 2 (5.00%), Indels: 2 (5.00%)
ATpairs: 5.56%, CGpairs: 94.44%, GTpairs: 0.00%
:i = 5210607
tupleindex: 3
intervalindex: 1
matches_in_interval: 113.0000
lowcenter: 10066611
highcenter: 10066659
testcenter: 10066635
im3: 33.0000
frequent_center_ratio*rnkp: 25.9200
Found at i: 5215217 center: 9985688 interval size: 300 g: 3
Alignment explanation
Indices: 4770463--4770675,5215013--5215225 Loop: 444337 Score: 47
Left Length: 213 Right Length: 213 Average length: 213.0
3 most common centers (desc): 9985688 9985689 9985687
4770453 >> (LF) CCGGGGTGGA
5215235 << (RF) GGGCCGACGC
4770463 >> CAAGATCGCCTTCACCGGCTCCACCGCCACCGGCAAGCGGATCATGGCCGCCGCCG-CGGAGAACCTGACCCCGG >> 4770536
5215225 << ****G**T******************TCCA*******TT*G*CC***T-**T*A**C**T*G**C***-*AC**G << 5215153
4770537 >> TGCT-GCTCGAGTGCGGCGGCAAGGACGCGGTCATCGTCG-CGCCCGACGCCGACGTGAAGGCCGCCGC-C-GA- >> 4770608
5215152 << TGC*G*T*C**TGA******T**G*G*G**A**C*C**CAA**T*-***********GC*G*******AT*T*CC << 5215079
4770607 >> CGCCATCGCCTGGGGCGCCACCG-GCAACAGCGGCCAGACCTGCGCCGGTGTCGAGCGCGTCTACGTGCA >> 4770675
5215078 << ***C**-**-***--**TT**A*G*****C*****C**C*C***T***GG*G*T*G***A**G******* << 5215013
Statistics
Matches: 147 (66.82%), Mismatches: 59 (26.82%), Indels: 14 (6.36%)
ATpairs: 27.89%, CGpairs: 72.11%, GTpairs: 0.00%
:i = 5215217
tupleindex: 3
intervalindex: 1
matches_in_interval: 104.0000
lowcenter: 9985664
highcenter: 9985712
testcenter: 9985688
im3: 51.0000
frequent_center_ratio*rnkp: 25.9200
Found at i: 5230535 center: 10010154 interval size: 300 g: 3
Alignment explanation
Indices: 4779619--4779719,5230434--5230535 Loop: 450714 Score: 43
Left Length: 101 Right Length: 102 Average length: 101.5
3 most common centers (desc): 10010154 10010153 10010155
4779609 >> (LF) GGCCGAAGGT
5230545 << (RF) TGCGGCGGGC
4779619 >> GTCGAGTTCGGGGGCG-AGGGCGCGCAGCGGCGCGAGCAGTTCG--GCGGCGTGCTCGTCGGTG-GCCAG-GATC >> 4779688
5230535 << *******C**AG*T**G*********G*-*******--***-**AT******-**G**CA**G*A***C*G*C** << 5230466
4779689 >> GCGCCGTCGACGATGACGACG-T-CG-CGGCCGG >> 4779719
5230465 << *T*******-***G*-**G**C*C**C******* << 5230434
Statistics
Matches: 80 (73.39%), Mismatches: 14 (12.84%), Indels: 15 (13.76%)
ATpairs: 13.75%, CGpairs: 86.25%, GTpairs: 0.00%
:i = 5230535
tupleindex: 3
intervalindex: 1
matches_in_interval: 101.0000
lowcenter: 10010130
highcenter: 10010178
testcenter: 10010154
im3: 28.0000
frequent_center_ratio*rnkp: 25.9200
Found at i: 5233884 center: 10066979 interval size: 300 g: 3
Alignment explanation
Indices: 4832991--4833358,5233612--5233988 Loop: 400253 Score: 186
Left Length: 368 Right Length: 377 Average length: 372.5
3 most common centers (desc): 10066979 10066970 10066980
4832981 >> (LF) CACGGTGGTG
5233998 << (RF) CGGGGTCAGG
4832991 >> GCGGGTGGGCTCTGCGCGATGGCCTTG-TGGAACAGGCCGGCCGCGGCGGGCGCGGTCAGCAGCGCGGTCACGCA >> 4833064
5233988 << *****G********C******-**CG*T*****C**T***AC*********C*A**G**T***A***TC****C- << 5233916
4833065 >> CCCG-GCGCCGGAGGACTCGCCGAACAGGGTGACGTTGTCCGGGTCACCGCCGAATGCCGCGATGTTCTCCCGCA >> 4833138
5233915 << *CA*G**T****G***A********C*A******************C********G**C********CGC***** << 5233841
4833139 >> CCCATTCCAGCGCCCGGATCTGGTCGTGTAGACCGAGGTTCGGGGT-GCA-G-CCGTCCAC-CAC--CGAG---G >> 4833204
5233840 << ****G*****C***CGG*G*******G*G**C********-*AA**G*T*G*C**A*C*CCC*CACC***TAAG* << 5233767
4833205 >> A-GAGGTCGAGGAAGCCGAGGACGCCGATGCGGTAGTTGACCGTGACCACCACCGCGTCGCCGGTCTCGGCGAGC >> 4833278
5233766 << GA**T*****G*A******T*C******CG********G*C***G**C******T****T***GC*TCG**G**- << 5233693
4833279 >> TTGCG-GCCGTCGTAGATCTTCTGCGCGGCGGTGCCGAGGCA-GTAGGCGCCGCCGTGCAACCACACCAGCACCG >> 4833351
5233692 << *G***G****CT***G*CCGGCT******T******G*A-**G****G**********C*ACT******A***** << 5233619
4833352 >> GGCGCGG >> 4833358
5233618 << *T**A** << 5233612
Statistics
Matches: 274 (71.73%), Mismatches: 89 (23.30%), Indels: 19 (4.97%)
ATpairs: 27.37%, CGpairs: 72.63%, GTpairs: 0.00%
:i = 5233884
tupleindex: 3
intervalindex: 1
matches_in_interval: 96.0000
lowcenter: 10066955
highcenter: 10067003
testcenter: 10066979
im3: 55.0000
frequent_center_ratio*rnkp: 25.9200
Found at i: 5241453 center: 10320996 interval size: 300 g: 3
Alignment explanation
Indices: 5079501--5079705,5241294--5241495 Loop: 161588 Score: 121
Left Length: 205 Right Length: 202 Average length: 203.5
3 most common centers (desc): 10320996 10320999 10321000
5079491 >> (LF) GACGTTGACC
5241505 << (RF) CTGCCTCTAT
5079501 >> CCGTAGTCGCGGGCGATGCCGGCCAGGCCCGAGGCGTAGCCCTGGCCGATGGCGCGGAACTTCCACTCGCC--GC >> 5079573
5241495 << ***T*T***CA***G*CT*******TA**C***A***************G****************C****GA** << 5241421
5079574 >> CGTGCCGGTACAGCTCGCCGAAGATCATCGCGGTCTCGGTGGAGGCGTCCTCGGTCAGGTCGTAGCGGGCCAGCT >> 5079648
5241420 << *-***-******T********CA*GC*TC************GAG***-**--***CGA****T*G*******G** << 5241351
5079649 >> CGGCGCCGGTCTGCTGA-TCGACGACCCGGATGAAGGCGTTGC-GGATCTGGCCGAAGG >> 5079705
5241350 << ****T***A**-**G*GC**G*CG*****G*G*A*GT-**GG*A***T*********** << 5241294
Statistics
Matches: 154 (73.68%), Mismatches: 44 (21.05%), Indels: 11 (5.26%)
ATpairs: 26.62%, CGpairs: 73.38%, GTpairs: 0.00%
:i = 5241453
tupleindex: 3
intervalindex: 1
matches_in_interval: 97.0000
lowcenter: 10320972
highcenter: 10321020
testcenter: 10320996
im3: 50.0000
frequent_center_ratio*rnkp: 25.9200
Found at i: 5251989 center: 10503411 interval size: 80 g: 2
Alignment explanation
Indices: 5251419--5251500,5251913--5251992 Loop: 412 Score: 51
Left Length: 82 Right Length: 80 Average length: 81.0
3 most common centers (desc): 10503411 10503410 10503412
5251409 >> (LF) GGGCCTGGGC
5252002 << (RF) CGTAGCTCGA
5251419 >> GGGCGAGAGCGGGATC-CGCTCCGGGCGCGGACCCGCGACCAGCGCGGGCCGG-GCCCGGCCGGTGCCGGTCTTG >> 5251491
5251992 << ********A**T**G*C****C*A*****T*-*******A****-*T*****AG**C*A*CA*******-**G*- << 5251922
5251492 >> CGCTCGGCG >> 5251500
5251921 << ****C**** << 5251913
Statistics
Matches: 63 (75.00%), Mismatches: 15 (17.86%), Indels: 6 (7.14%)
ATpairs: 15.87%, CGpairs: 84.13%, GTpairs: 0.00%
:i = 5251989
tupleindex: 2
intervalindex: 1
matches_in_interval: 41.0000
lowcenter: 10503399
highcenter: 10503423
testcenter: 10503411
im3: 19.0000
frequent_center_ratio*rnkp: 12.7600
Found at i: 5276766 center: 10552922 interval size: 80 g: 2
Alignment explanation
Indices: 5276155--5276175,5276747--5276767 Loop: 571 Score: 42
Left Length: 21 Right Length: 21 Average length: 21.0
3 most common centers (desc): 10552922 0 0
5276145 >> (LF) CTCGCCGGGC
5276777 << (RF) GGCGAGTGGC
5276155 >> ACGCCGACCGGCACCGGCCGC >> 5276175
5276767 << ********************* << 5276747
Statistics
Matches: 21 (100.00%), Mismatches: 0 (0.00%), Indels: 0 (0.00%)
ATpairs: 14.29%, CGpairs: 85.71%, GTpairs: 0.00%
:i = 5276766
tupleindex: 2
intervalindex: 1
matches_in_interval: 54.0000
lowcenter: 10552910
highcenter: 10552934
testcenter: 10552922
im3: 20.0000
frequent_center_ratio*rnkp: 12.7600
Found at i: 5317357 center: 10248097 interval size: 300 g: 3
Alignment explanation
Indices: 4930177--4930848,5317249--5317914 Loop: 386400 Score: 892
Left Length: 672 Right Length: 666 Average length: 669.0
3 most common centers (desc): 10248097 10248091 10248098
4930167 >> (LF) CTTCGGCGAC
5317924 << (RF) GGCGGCTGGC
4930177 >> CACGGTTGGCCTCTTGCCGGTCACCCCGGACAGTCCCCGCAAACTTCG-AGCTATGACGCCGCCCGCCGACGGGC >> 4930250
5317914 << ***G**G*****C***T*G***C*CA******GC**C***CGC**C**G***-*GG**G**T**********G-* << 5317842
4930251 >> TGCCGCCGTTCGGCGG-CACGGTCCCACTGCGCGACATCGCCCTGCCGAACACCGGGGGCGTGCTCGGCATCCCG >> 4930324
5317842 << -**-*--**-**-***T******C**C********C*****C**T**G*CT*C***A*GC**G**C*****A*** << 5317773
4930325 >> GAGATCGTGCTGGCCGCCTACCGCAATGCCGAACTGGCCCTGGCCTCCTCGATGCCCGGCTGCGGACTGAGCTGG >> 4930399
5317772 << *************************************************************************** << 5317698
4930400 >> CACCTGCTCGCCGGCATCGGCCGCATCGAATCCGCACACGCGAGCAGCGGTCGCACCGACGCCGCGGGCACCACC >> 4930474
5317697 << ***********************************C*********C*A**G************************ << 5317623
4930475 >> GTCTCGCCGATCTTCGGTCCCGCGCTGGACGGCACACTGCCCGGCAACGAGATCATCAAGGCCGCCGACGGCGGC >> 4930549
5317622 << ***********************************G*********************C***************** << 5317548
4930550 >> TACGTCCGGGCCGTCGGCCCCATGCAGTTCCTGCCCAGCACCTGGTCGCTGTACTCCGCCGACGGCAACGGCGAC >> 4930624
5317547 << ********************C****************************************************** << 5317473
4930625 >> GGCGTCGCCGACCCGCACAACGTGTTCGACGCCTCGCTGGCCGCGGGCAAATACCTCTGCTCCGGGGGCCTGAAC >> 4930699
5317472 << ********************************A***********************C**A**C**G**TTG*C*A << 5317398
4930700 >> CTGCGTGATCCGCAGC-AGGAACTGCGCGCGGTGCTGCGCTACAACAACTCGATGGCCTACGCCGCCGACGTGCT >> 4930773
5317397 << *****G****-**AG*G**********T********************A**GCGGA****A************A* << 5317324
4930774 >> GAGCTGGTCGGCGGCCTACCGCACCGGCGGCACCCCGCGCCA-GGTCACCGTCGA-CCCGAACCTCGTCCCGCCG >> 4930846
5317323 << *******************************C****-****GG***********GA*****A*C-***A****** << 5317251
4930847 >> GG >> 4930848
5317250 << ** << 5317249
Statistics
Matches: 591 (87.30%), Mismatches: 70 (10.34%), Indels: 16 (2.36%)
ATpairs: 27.07%, CGpairs: 72.93%, GTpairs: 0.00%
:i = 5317357
tupleindex: 3
intervalindex: 1
matches_in_interval: 98.0000
lowcenter: 10248073
highcenter: 10248121
testcenter: 10248097
im3: 70.0000
frequent_center_ratio*rnkp: 25.9200
Found at i: 5317483 center: 10249777 interval size: 300 g: 3
Alignment explanation
Indices: 4931878--4932429,5317348--5317875 Loop: 384918 Score: 220
Left Length: 552 Right Length: 528 Average length: 540.0
3 most common centers (desc): 10249777 10249756 10249751
4931868 >> (LF) ACCTCACCCA
5317885 << (RF) TGTGCGGCGC
4931878 >> CGCACT-CGCCGC-CCAGCACACC-GCC-ACCCCGCCGGTCGTGAAAAGCGTTGC-GCTGTCGAGTGATCGAGCG >> 4931947
5317875 << ***C**C***T**T***G*G****G***C**C****-*****G*C*G*-**C***G****-**G*T*****G**A << 5317804
4931948 >> CCCGCCGACCTGCCCGCGGGGCCGTTGGGCATGCCAGGCATCGCCGAGGCGGCCTACCGCAACGCCGAGGAGAAG >> 4932022
5317803 << T**-*T**TCG*CA-****A-**-*-******A**C*TC****ACGA***G***********A*****TGA*CGG << 5317734
4932023 >> CTGCACGCGGAGAACCCGCAG-TGCC-ACATGCCCTGG-ACCATGCTGGCCGGTATCGGCCGGGTGGAGTCCACG >> 4932094
5317733 << ***CG*A*GAG**AC**-*C*G***CC**-**TC****G***-****G*****G********GT*G**T***C** << 5317662
4932095 >> CACGCGTTCGGCGGCAAGGCCGACGCCGACGGCAAC-CCGATCAAGCCGGTCTACGGCCCGGTGCTCGACGGCTC >> 4932168
5317661 << ******TC***A***GCGT*********GC****G*T***-**AG****T***A***A**G*G***C******T* << 5317588
4932169 >> GCTCGCGGGCAACAACGTCATCCACGACAGCGACAACGGCGCGCTCGACGGACTCGACGGCTACGACCGCGCGGT >> 4932243
5317587 << G**CG*G******C*-*--***-*A--*-*--*----***-***-******-*--*--*-*****A***C**G** << 5317534
4932244 >> CGGCCCGATGCAGTTCCTGCCCGAG-ACCTGGCAGCGCTACGCCGCCGACGGCAACGGTGACGGCATCGCCGACC >> 4932317
5317533 << **********************-**G******AG**AC***A****************G******C********* << 5317460
4932318 >> CGCAGAACCTCTTCGACGCGGCGCTGACCGCGGGCAAGTACCTGTG--CGA-CGGCAATCTGGACATGCGCGATC >> 4932389
5317459 << ****G***C*C********AA*****C**********T********AA**CC***-**-*-***AG********* << 5317388
4932390 >> TCTCCCAGCAGAGCCGCGCCATCCTGCGCTACAACAACTC >> 4932429
5317387 << C*******C*TGAC**T**CC*C**************A** << 5317348
Statistics
Matches: 403 (71.33%), Mismatches: 112 (19.82%), Indels: 50 (8.85%)
ATpairs: 26.05%, CGpairs: 73.95%, GTpairs: 0.00%
:i = 5317483
tupleindex: 3
intervalindex: 1
matches_in_interval: 97.0000
lowcenter: 10249753
highcenter: 10249801
testcenter: 10249777
im3: 76.0000
frequent_center_ratio*rnkp: 25.9200
Found at i: 5423422 center: 10490881 interval size: 300 g: 3
Alignment explanation
Indices: 5067382--5067665,5423214--5423503 Loop: 355548 Score: 281
Left Length: 284 Right Length: 290 Average length: 287.0
3 most common centers (desc): 10490881 10490880 10490879
5067372 >> (LF) TGCCGGTCCC
5423513 << (RF) AGCTTGCTCA
5067382 >> CGCCTGAGC-GG-TCAGCGGCC-GGAGGCGGTAGCGC-GCGTCACCACGCAGGCCGCCCCG-CTCAGGCGAAATC >> 5067451
5423503 << **C******G**C**C***G**G********G*****T*A**C******C***C*******C***C***GCC-** << 5423430
5067452 >> CAACACAGCCTGAGCGGGTCAGCGGCCGGAGGCGGTAGCGCAGCGTCACCACGCAGGCCGCCCCG-CTCAGGCAA >> 5067525
5423429 << CC*A**C*****************G**********G*******A**C******C***C*******C***C***G* << 5423355
5067526 >> ATCCAACACAGCCTGAGCGGGTCAGCGGCCGGAGGCGGTAGCGCAGCGTCACCACGCAGGCCGCCCCG-CTCAGG >> 5067599
5423354 << C**CC*A**C*****************G**********G*******A**C******C***C*******C***C** << 5423280
5067600 >> CAAATCCAACACAGCCTGAGCGGGTCAGCGGCCGGAGGCGGTAGCGCAGCGTTACCCCGCAGGCCG >> 5067665
5423279 << *GCC**CC****C*****************G**********G*******A**C***T**C***C** << 5423214
Statistics
Matches: 234 (80.41%), Mismatches: 49 (16.84%), Indels: 8 (2.75%)
ATpairs: 23.08%, CGpairs: 76.92%, GTpairs: 0.00%
:i = 5423422
tupleindex: 3
intervalindex: 1
matches_in_interval: 116.0000
lowcenter: 10490857
highcenter: 10490905
testcenter: 10490881
im3: 41.0000
frequent_center_ratio*rnkp: 25.9200
Found at i: 5515522 center: 10749337 interval size: 300 g: 3
Alignment explanation
Indices: 5233801--5233875,5515461--5515536 Loop: 281585 Score: 78
Left Length: 75 Right Length: 76 Average length: 75.5
3 most common centers (desc): 10749337 10749336 10749338
5233791 >> (LF) GTTCGACAAC
5515546 << (RF) CAGGCTCCCC
5233801 >> AACCTCGGCCTGCGCGACCAGGTGGCGGCCCTGGAGTGGGTGCGGCGC-AACATCGCCGCGTTCGGCGGCGA-CC >> 5233873
5515536 << **A**********A*******G*G**G**C****C*********-**TC******GC***G***********A** << 5515463
5233874 >> CG >> 5233875
5515462 << ** << 5515461
Statistics
Matches: 63 (81.82%), Mismatches: 11 (14.29%), Indels: 3 (3.90%)
ATpairs: 26.98%, CGpairs: 73.02%, GTpairs: 0.00%
:i = 5515522
tupleindex: 3
intervalindex: 1
matches_in_interval: 113.0000
lowcenter: 10749313
highcenter: 10749361
testcenter: 10749337
im3: 27.0000
frequent_center_ratio*rnkp: 25.9200
Found at i: 5547030 center: 10830401 interval size: 300 g: 3
Alignment explanation
Indices: 5283371--5283405,5546996--5547030 Loop: 263590 Score: 40
Left Length: 35 Right Length: 35 Average length: 35.0
3 most common centers (desc): 10830401 0 0
5283361 >> (LF) GGCACGTAGC
5547040 << (RF) GTCAGGCCAA
5283371 >> CGCCGCCCGCGGCCACCGCCGCGTACACCGCGACC >> 5283405
5547030 << *******CG******C*******TA*******C** << 5546996
Statistics
Matches: 29 (82.86%), Mismatches: 6 (17.14%), Indels: 0 (0.00%)
ATpairs: 6.90%, CGpairs: 93.10%, GTpairs: 0.00%
:i = 5547030
tupleindex: 3
intervalindex: 1
matches_in_interval: 110.0000
lowcenter: 10830377
highcenter: 10830425
testcenter: 10830401
im3: 28.0000
frequent_center_ratio*rnkp: 25.9200
Found at i: 5575196 center: 10998456 interval size: 300 g: 3
Alignment explanation
Indices: 5423242--5423503,5574955--5575213 Loop: 151451 Score: 231
Left Length: 262 Right Length: 259 Average length: 260.5
3 most common centers (desc): 10998456 10998455 10998457
5423232 >> (LF) TGCGCTGCCG
5575223 << (RF) CCTGACTTTG
5423242 >> CCTCCGGGCGCTGACCCGCTCAGGCCGTGTCCGACCG-GCCCGAGCCGGGGCGCCCTCCGTGGTCACACTGCGCT >> 5423315
5575213 << ****-**G*****************C***GAC**AA*A***A*A**C******C***C******C*AC******* << 5575140
5423316 >> GCCGCCTCCGGGCGCTGACCCGCTCAGGCCGTATCCGACTGGCCCGAGCCGGGGCGCCCTCCGTGGTCACACTGC >> 5423390
5575139 << ***A*******G*****************A**C*AA**A*A***A*A**-******C***C******C*AC**** << 5575066
5423391 >> GCTGCCGCCTCCGGGCGCTGACCCGCTCAGGCCGTATCCGACCGGCCCGAGCCGGGGCGCCCTCCGTGGTCACAC >> 5423465
5575065 << **********A***G*****************C**C*AA**AAA***A*A**C******C***C******C*AC* << 5574991
5423466 >> TGCGCTGCCGCCTCCGGGGCGCCGACCCGGCTCAGCCG >> 5423503
5574990 << *********A***A***G-***A******-*****C** << 5574955
Statistics
Matches: 206 (78.33%), Mismatches: 52 (19.77%), Indels: 5 (1.90%)
ATpairs: 22.33%, CGpairs: 77.67%, GTpairs: 0.00%
:i = 5575196
tupleindex: 3
intervalindex: 1
matches_in_interval: 96.0000
lowcenter: 10998432
highcenter: 10998480
testcenter: 10998456
im3: 55.0000
frequent_center_ratio*rnkp: 25.9200
Found at i: 5575196 center: 10998378 interval size: 300 g: 3
Alignment explanation
Indices: 5423167--5423425,5574953--5575210 Loop: 151527 Score: 249
Left Length: 259 Right Length: 258 Average length: 258.5
3 most common centers (desc): 10998378 10998377 0
5423157 >> (LF) ACCGGAGTTC
5575220 << (RF) GACTTTGGGA
5423167 >> CGGGCGCCGACCCGGCTCAGGCTGCGTTCGACTG-GCCCGAGCCGGGGCGCCCTCCGTGGTCACACTGCGCTGCC >> 5423240
5575210 << ***G***A******-*******C*A*G*C**A**A***A*A**C******C***C******C*AC********** << 5575137
5423241 >> GCCTCCGGGCGCTGACCCGCTCAGGCCGTGTCCGACCGGCCCGAGCCGGGGCGCCCTCCGTGGTCACACTGCGCT >> 5423315
5575136 << A*******G*****************A****AA**AAA***A*A**-******C***C******C*AC******* << 5575063
5423316 >> GCCGCCTCCGGGCGCTGACCCGCTCAGGCCGTATCCGACTGGCCCGAGCCGGGGCGCCCTCCGTGGTCACACTGC >> 5423390
5575062 << *******A***G*****************C**C*AA**A*A***A*A**C******C***C******C*AC**** << 5574988
5423391 >> GCTGCCGCCTCCGGGCGCTGACCCGCTCAGGCCGT >> 5423425
5574987 << ******A***A***G*****************C** << 5574953
Statistics
Matches: 207 (79.62%), Mismatches: 50 (19.23%), Indels: 3 (1.15%)
ATpairs: 22.71%, CGpairs: 77.29%, GTpairs: 0.00%
:i = 5575196
tupleindex: 3
intervalindex: 1
matches_in_interval: 106.0000
lowcenter: 10998354
highcenter: 10998402
testcenter: 10998378
im3: 72.0000
frequent_center_ratio*rnkp: 25.9200
Found at i: 5579269 center: 11158491 interval size: 40 g: 1
Alignment explanation
Indices: 5579190--5579244,5579246--5579300 Loop: 1 Score: 43
Left Length: 55 Right Length: 55 Average length: 55.0
3 most common centers (desc): 11158490 0 0
5579180 >> (LF) GCGGTGATGA
5579310 << (RF) AGGCGTCGCG
5579190 >> GGTCGTCGAGACGGATCTGCGGTGTGGTCATGCGTCAACTGTAGGTTGACG-ACCT >> 5579244
5579300 << ***C****G*C***CT*****G**TGG-*C*G*******************G**** << 5579246
Statistics
Matches: 43 (76.79%), Mismatches: 11 (19.64%), Indels: 2 (3.57%)
ATpairs: 37.21%, CGpairs: 62.79%, GTpairs: 0.00%
:i = 5579269
tupleindex: 1
intervalindex: 2
matches_in_interval: 27.0000
lowcenter: 11158483
highcenter: 11158499
testcenter: 11158491
im3: 19.0000
frequent_center_ratio*rnkp: 7.6500
Found at i: 5632048 center: 10926069 interval size: 300 g: 3
Alignment explanation
Indices: 5291434--5294085,5631987--5634584 Loop: 337901 Score: 596
Left Length: 2652 Right Length: 2598 Average length: 2625.0
3 most common centers (desc): 10926045 10926033 10926090
5291424 >> (LF) CCCCGGCAGC
5634594 << (RF) GCTCCTGAGC
5291434 >> CCGTTCCTGGAGCTGTCGCCGCTGGCGGCCACCGGGATGTACGGCGACGAGTGCCCGG-GG-GCGGGCATCATCA >> 5291506
5634584 << ****************CG********G***A--***--*G*-*-***--*A*G*T**AG**A**GT**C*C***C << 5634518
5291507 >> CCGGCATCGGACGGGTGTCCGGGCGCGAA-TGCGTGATCGTGGCCAACGACGCGACGGT-CAAGGGCGGCACCTA >> 5291579
5634517 << ****C*****GTAG***CT-*****A*C*C***T*******G**CGG****G*******C*CG***-*******G << 5634445
5291580 >> CTACCCGATGACGGTCAAGAAGCATCTGCGCGCGCAGGAAGTGGCGTTGCAGAACAACCTGCCG-TGCATCTACC >> 5291653
5634444 << *T*****AC****A*CGCG***T*G******TA*T*G**GT*G**GT**C*****GCC******C**-***CC** << 5634371
5291654 >> TGGTCGATTCGGGCGGCGCGTTCCTGCCGCGCCAGGACGAGGTGTTCCCCGATCGCGAGCACTTCGGCCGCATCT >> 5291728
5634370 << *******T**G*********CT******GTG****T*C*****G***---*-**-*---*-*CC***C**C**C* << 5634305
5291729 >> TCTACAACCAGGCCACCATGAGCGCGGCGGGCATCGCGCAG-ATCGCCGCCG-TGCTCGGCTCGTGCACCGCGGG >> 5291801
5634304 << **GC*C***AGT***TCG*GAG****TA******AG*-**GG*****-**A*C**A*****TTA*G********* << 5634232
5291802 >> CGGCGCGTACGTGCCCGCGATGAGCGACGAGGCGGTGATCGTGCGCAACCAGGGCACGATCTTCCTCGGCGGTCC >> 5291876
5634231 << ***A**G***T*G****CG***AG****A*GT*******CT*GTTCC*C*CGAG**T*C*C***********G** << 5634157
5291877 >> GCCGCTGGTGAAGGCGGCGACCGGCGAGGTGGTCACGGCCGAGGAA-C--TCGGTGGCGGCGAACTGCATTCGCG >> 5291948
5634156 << *************TA***G*****C****TT-**-**T*-**G***A*GG****G****G***CT*****C*G** << 5634085
5291949 >> CACCTCCGGAGTCACCGACCACCTGGCCGAGGACGACCAGGACGCACTGCGCATCGTGCGCCGCATCGTGGCCAC >> 5292023
5634084 << ******C**AG*CC*****A****G****GG*****C********GT*G**C****CG***AG******GTT-** << 5634011
5292024 >> C-CTGGGGCCGCGACCGCAGGCCCCCTGGGAGGTGCTGCCCAC-GATCGAGCC-CGCCGCGCCCACCGAGGAGCT >> 5292095
5634010 << CC***TTGAC***GTT*****C***C-*G*GG*G**C*A**CCA*G*******C***AT**T**-*******TA* << 5633938
5292097 >> -CTACGACGTGGTGCCGGTGGACCTGCGCACGCCCTACGACGTGCGCGAGGTGATCGAGCGCCTGGTCGACGGCG >> 5292169
5633937 << C**-**C*T*G*****G*GG******TTC*AG**C*A****GG**************G****C*********--- << 5633867
5292170 >> CACCGGGCGGCGAGTCCGGTTTCCACGAGTTCAAGGCCGAG-TACGGCAAGACGCTGGTCACCGGGTTCGCGCGC >> 5292243
5633867 << -**A---*--***--*---**-*C***********-***GAG*******CG*CG***********G*CC****TT << 5633805
5292244 >> ATCCACGGCCATCCGGTGGGCATCGTCGCCAACAA-CG-G-CGTGCTGTTCGCCGAATCCGC-CATGAAGGGCGC >> 5292314
5633804 << G*C******A*G*****G******G********CGC**G*C**********A****CCTC**T**-*****G*** << 5633731
5292315 >> GCATTTCATCGAGCTGTGCGACAAGCGCAGCATCCCGCTGCTGTTCCTGCAGAACATCACCGGCTTCATGGTCGG >> 5292389
5633730 << ***C******G****GCG*T**G**AG*CT**GC**T**************G****G********T********* << 5633656
5292390 >> GCGTGACTACGAGGCGGGCGGCATCGCCAAGCACGGCGCCAAGATGGTGACGGCGGTGGCGTGCGCGCGGGTGCC >> 5292464
5633655 << GTTC**C*A****GT*TTC******TA************C*A****T*G*TG******A**TT*A**TT****** << 5633581
5292465 >> GAAGCTGACGGTGGTGATCGGCGGCTCCTACGGCGCGGGCAACTACTCCATGTGCGGGCGCGCGTATTCGCCGCG >> 5292539
5633580 << *G*GT*GA**G**G****C****G****************G*****CC*********G*****G**GCTA***** << 5633506
5292540 >> CTTCCTGTGGATGTGGCCGAACGCGCGGATCT-CGGTGATGGGCGGCGAGCAGGCCGCCTCGGTGCTGGCGACTG >> 5292613
5633505 << ****C*G*AGCGG*****G*C****TT-***GC****G*****A**A*G****GAC***CCA***T*GA***AG* << 5633432
5292614 >> TGCG-CGGCGAC-CAGCTCGACA-GCAGCGGCAACCCGTG-GTCGGCCGAGGACGAGGAGAAGTTCAAGGCCCCG >> 5292684
5633431 << *GC*A***-*G*C*G**-***CCG**-*******C****AG*T**TC-****G***G*G*CC*T*CGCG**CTA* << 5633361
5292685 >> ATCCGCGAACAGTACGAGCACCAGG-GCAACCCCTACTACTCCACCGCACGACTGTGGGACGACGGCGTCATCGA >> 5292758
5633360 << ***CTC*GC***TA****CG*C**AG**AC**CT*CA*GT*CAG*C***C*-**G*TG***********C***** << 5633287
5292760 >> -CCCCGCCGACACCAGAACGGTGCTCGGCCTCGCACTCTCGGTGTGCGGGCAGGCGCCGCTGGAACCGGTCTCCT >> 5292832
5633286 << A******-**A***G*G******A*C***T*C**C*******GGTA*GTGT*G**G***T*G-**C-**-*C**C << 5633216
5292833 >> ACGGCGTCTTCCGGATGTGAGCGCGATGATGATGAACAACTCCCACCCCATCGGCTTCGACACCGTGCTGGTCGC >> 5292907
5633215 << *-**-*-****C*GC*G*AG-**-****-***C*--**-*C*C-*AC--*-**TA***--***A*********** << 5633156
5292908 >> CAACCGCGGCGAGATCGCGGTGCGGGTCATCCGCACGCTGC-GCGCGCTCGGCGTGCGCTCGGTCGCCGTCTACA >> 5292981
5633155 << C**A**T***********GGC***G**CA**CG***-****G**GC*T*C**TG**C**T*G*****C**C***A << 5633082
5292982 >> GCGACGCCGACGCCGGTGCGCGGCACGTGCGCGAGGCCGACGTCGCGGTGCGGCT-CGGACCCGC-CCCCGCCCG >> 5293054
5633081 << G*********A****GG**T*GG**A*****C**********GC*****G*****C*G*CC*TT*T*****C*** << 5633007
5293055 >> CGAGAGCTACCT-CGACATCGACAAGGTGGTCGACGCCGCGGTGCGCACCGGG-GCACAGGCCGTGCATCCGGGC >> 5293127
5633007 << --***G***A**C**-*CCC**CGA*T*GT****C**C***G*-***GC****G**GC*G**C*****G**G*** << 5632936
5293128 >> TACGGATTCCTCTCCGAGAACGCCGCCTTCGC--GA-CCGCGCTGGACAAGGCGGGCATCGTCTTCCTCGGCCCG >> 5293199
5632935 << *****G*******************TC*****GG*GC***A*******--*G*****-*C**C*CCC****C*** << 5632864
5293200 >> CCCG-CGCGGGCGATCGAGATCATGGGCGACAAGATCGCGGCGAAGAACACCGTCTCGGCCTTCGGCGTGCCGGT >> 5293273
5632863 << **C*A***G*-********CTC******AGC***C****GA*******C-*A*T-*-**T*CG**-**-*--*-* << 5632798
5293274 >> GGTGCCCGGCATCGCCGAGCCCGGCCTCAGCGACGACGACCTGATCGCCGCGGCCGCCGAGGTCGGCTATCCCGT >> 5293348
5632797 << *-****C*ACA*C*****T*A**TA*-*C**--***-*----*-**T***T***-**--*--**A**---*C-** << 5632742
5293349 >> GCTGGTGAAGCCCTCCGCGGGCGGCGGCGGCAAGGGCATGCGCCGCGT-CGACGACCCCGCCGACCT-GC-CCGC >> 5293420
5632741 << ****T*G***C****************A***GCG********CCAC**C**-***C*AC*****A**G*TT**** << 5632668
5293421 >> CGCCCTGGTGAGCGCCCGGCGCGAGGCGGGGGCGGCCTTCGGCGAC--GACACGCTGTTCCTG-GAGCGTTTCGT >> 5293492
5632667 << T*TA*-*GG*G-******G**C*****G*TTA*G************GG***-**-*****-**G*****G*T*G* << 5632598
5293493 >> CACCAATCCGC-GCCACATCGAGGTGCAGGTGCTGGCCGACCGGCACGGCAACGTCCTGCACC-TGGGCGAACGC >> 5293565
5632597 << *CTC*G-*C**G**********************G******TG********G*T**-**CC**C*G*****C**C << 5632525
5293566 >> GAGTGCAGCCTGCAGCGCAGGCACCAGAAGGTGATCGAGGAGGCGCCCTCGCCGCTGCTGGA-CGC--CGA-GAC >> 5293636
5632524 << **T***AG*T*G*****CG*************GC****************G**T***C*G**T***TA***G*C* << 5632450
5293637 >> CCGCGCGCGCATCGG--CG-CGGCGGCCTGCGACACCGCGCGCAGCG-TCGACTACGTGGGCGCGGGCACGGTGG >> 5293707
5632449 << TA***C*T**CC*A*AA**T**G**G**C**ACC-*****C**-***T**AG****TGG***********G**** << 5632377
5293708 >> AGTTCATCGTCTCGGCCGGCCGGCCCGACGAGTTCTTCTTCATGGAGATGAACACCCGCCTCCAGGTGGAGCATC >> 5293782
5632376 << *T***G*C*-*-**T*-*T*-*-*CC*-********T****G****************C**C********T**** << 5632308
5293783 >> CGGTGACCGAGATGGTG-ACCGGGGTGGACCTGGTGGAG-TGCCAGGTGCG-GATCGCGGCCGG-GCAGCAGCTG >> 5293853
5632307 << ****G******-**GTGG******A***********GC*G***T*G-*-**T******G**C**G**C**G-*** << 5632237
5293854 >> GGCGT--GGAC-CAGGGGCAGATCCGGC-T-C-ACCG-GGCACGCCG-T--G--GAGGCCCGGGTGTACGCCGAG >> 5293916
5632236 << GG**GGG**G*C*GG*G**A*GC*C*T*T*A*C*A**T**AC****AG*TG*GG****T**G**GGG***T-*A* << 5632163
5293917 >> G-ACCCGGGGCGCGGCTTCCTGCCCACCGG-CGGCA--CCG-TGCT-CG-ACCTGCG-CGAGCCG---GAA-GGG >> 5293979
5632162 << *G*C***GT*T*****TG*C***T*-*C**A**T**AA***G**C*C**G***CTTAA***A*A*GAG**GG*** << 5632089
5293980 >> CCGGGGGTGCGGGTGGATTCGGGCCTGCGGGTGGGCACGGTGGTCGGCA-GCGACTACGACCCGATGCTGTCGAA >> 5294053
5632088 << ****G*-*****G****GT*G**AC**CA**TG**AA***********CA**-********************** << 5632016
5294054 >> GGTGATCGCGCACGGCCCGGACCGCGCGTCCG >> 5294085
5632015 << *******A*GA***-**CT****-****-*** << 5631987
Statistics
Matches: 1844 (67.50%), Mismatches: 674 (24.67%), Indels: 214 (7.83%)
ATpairs: 27.87%, CGpairs: 72.13%, GTpairs: 0.00%
:i = 5632048
tupleindex: 3
intervalindex: 1
matches_in_interval: 97.0000
lowcenter: 10926045
highcenter: 10926093
testcenter: 10926069
im3: 36.0000
frequent_center_ratio*rnkp: 25.9200
Found at i: 5667023 center: 11054947 interval size: 600 g: 3
Alignment explanation
Indices: 5387808--5388418,5666529--5667139 Loop: 278110 Score: 186
Left Length: 611 Right Length: 611 Average length: 611.0
3 most common centers (desc): 11054950 11054947 11054949
5387798 >> (LF) GCGCCATGAA
5667149 << (RF) CGAGCGCGTC
5387808 >> CTCCGGCGTGGTGTAGGCGGCCTGCAGCGGTCCGCGGCGGCCGAGCACCACGACCTCG-CGGATGTTGCTCGCCC >> 5387881
5667139 << ****T***C****T*GAA******CCG***C*************T***CACG******T***GG-***A*C***A << 5667066
5387882 >> GCAACGCCGCC-AGCGCGTG-GTCGGCGATGTCGGTCTTGGC-G-AGTTCGTCGG-GGTCGACGGTGAGCACGCG >> 5387951
5667065 << A**CCG****CA**T-***AG*C***-***G*****C--***T*G********TGG****AA-**G********* << 5666996
5387952 >> GGCCACGTCGAGGGCGACGTTGCCGTTGCCGACGATCACGGCGCGCT-CGCC-CGAC-AGATCGAAGGTGCGGTC >> 5388023
5666995 << G********G**G************TG*****-*--***G***TG**A*A**C**A*G**GCCGG********-- << 5666926
5388024 >> GGCGAAATCGGGATGGCCGTTGTACCAGGCCACGAACTCGGTCGCGGAGTGGCTGCCGGGCAGGTCCTCGCCGGG >> 5388098
5666925 << ***-*GC**G**C**T****G********TC*****C****G****GG**T*CT****AG******CTA****** << 5666852
5388099 >> GATGTTCATCCGGCGGTCCGAGGCGGCGCCGACGGCGTAGATCACCGCGTGGTGGTGGGCGAGCAGTTCCTCGTG >> 5388173
5666851 << ********C*CG******C*G*AA*******CA**T*T************G**T*TT*GC*G****C******T* << 5666777
5388174 >> CGAGATGTGCGTGCCCACCTCGACGTTGAGGTAGTACT-GCAGGGTG-TCGCGGCGGAAGGCCGACTCGAACATG >> 5388246
5666776 << C*A*****GC*****CATC****A****GG*-**G*CCG***GG-**G**GAA*AG**-*GT*--**A*AC**C* << 5666707
5388248 >> -CGC-GA-GACGGTCTTGGTGCCGGGGTGGTCCGGGGCGACGCCCGCGCGCACCAGGCCCCACGGGGTGGGCAGC >> 5388318
5666706 << C**CA**A**A*GG****T***CG**T**T**C**G********CAT***C*A***G**CT****A*G*****AC << 5666632
5388319 >> CGGTCGAACATCTCGAC-CTCGACATCG-CAGCGC-CG-CAGCAGTTCCTCGGCGGCGTAGCAGGCGGCCGGCCC >> 5388389
5666631 << **G***A*C*CC****AC***-**C***C**A**CT*AA**A**TGC*C************TAAG********** << 5666558
5388390 >> GGCGCCGACGATCGCGACCCGCAGCGTGC >> 5388418
5666557 << G****************AC**C****C** << 5666529
Statistics
Matches: 429 (68.20%), Mismatches: 164 (26.07%), Indels: 36 (5.72%)
ATpairs: 26.34%, CGpairs: 73.66%, GTpairs: 0.00%
:i = 5667023
tupleindex: 3
intervalindex: 2
matches_in_interval: 228.0000
lowcenter: 11054913
highcenter: 11054981
testcenter: 11054947
im3: 82.0000
frequent_center_ratio*rnkp: 41.4200
Found at i: 5686439 center: 11106707 interval size: 300 g: 3
Alignment explanation
Indices: 5419504--5420483,5686224--5687208 Loop: 265740 Score: 343
Left Length: 980 Right Length: 985 Average length: 982.5
3 most common centers (desc): 11106713 11106707 11106704
5419494 >> (LF) AGGGCCACTC
5687218 << (RF) CCGCCTCACT
5419504 >> GTCCAGGTCAGGACAGCTGCACCGTCGCCG-TCGCCCGGCCGAAGATCTTCTTGCCCGCCG-ACTTGGCGACGAT >> 5419576
5687208 << ****-********C***G*C***-***C**T*C**C**********CA**CGC***-****C*CC****TG*G*C << 5687137
5419577 >> CGCCACCACCGCGGTGCGGGTCTCGGGATCCATCGACTTCACCTTGCCGGTGTACTCGACCTCG-GC-CGCCGCG >> 5419649
5687136 << *T****CCAC**G*G****GCC********C*CC**A**C*A**********T******--*C*A**A**C*A*G << 5687064
5419650 >> TCGGCGGGCACGAACACGGGGCTGGTGAAGCGCACGTTGTACTCCTTCACCGCGCCGGGGTCGCCCAGCCACGAG >> 5419724
5687063 << ***T***A***GCCC***TT**GG*G***A**C***G**T***A*C***AC***CA*********C******GG* << 5686989
5419725 >> GTGACGAAGCCGCCGCCCAGGCCCATCGTGAGCATGCCGTGCGCGACCACG-TCGTCGAGGCCGACGAGCTTGAC >> 5419798
5686988 << ****C*A**A**C**CA************G***********C*****C***C*C*C*-*************C*C* << 5686915
5419799 >> CACCTCGT-CGCTCCAGTGGATCGGGTTCGCGTCACCGGAGACACCGGCGTAGTTCACCAGGTCGCCGCGGGTCA >> 5419872
5686914 << CC*C-***A****CT*************C*C***C**G*G***C**G********C******************* << 5686841
5419873 >> GCCGCACCACGCGCGTGGGCAGCTCGTCGCCGACCGAGACGCTGTCGAAGGCCAGGGCATGCT-TGCTC-GG-C- >> 5419945
5686840 << *A**CC*CCA**GC*GG**C**A*****G**GAA**G**C**C******G*--****C***C*C***T*G**C*G << 5686768
5419944 >> GTGGCCTCGGGCACCGAGACCACCGGC-G--CGGACGCGGAGA-CG--ATC-GG-CGCC--TCGGTGCGCGGGTG >> 5420008
5686767 << *C**T*CCG***C*-*A*-**CC****T*CA***G*A**AG**A**CC***T**T*A**GC**A*****T*TAGA << 5686695
5420009 >> GTGATCCGGCTCCTCCGGGCCGATGCCGTGCATGAGCACGTTGTGCACCGCGTCGGTGAGATTCGGGTCGATGTC >> 5420083
5686694 << *G*C**-*****CT*-******C-*A-********TC*A*G**G*****T*G*CG*G**TC*****T****GG** << 5686624
5420084 >> GGCGCCGCTGCGGCCCACCAGCGTGGTGTAGGTGGTGAGCACCAGCTCGTCGTTCTGGGCG-G--TGACGATGTT >> 5420155
5686623 << ********C***GC*C**C*A******GC*G*G*T*GA**C*C*A********C****AA*T*GT*GA**CG*GC << 5686549
5420156 >> CTTGGTGACGATGAT-GTCGCCGCCGAACGCCTGCCGGAACGAGTGCAGGTACA-CATCGCAGGTCAGC-TGG-- >> 5420227
5686548 << CTGT*******T-**G**A*A*******-**-***-***A***G*-*-*T*-**C**G*-*C***CA*CT***GC << 5686482
5420226 >> TCGCCGACCTTGATCGGCCGGTGGAACTCCAGGATCTGGTCGGTCTGCATGATCTGGCTCAGGTCGTAGCCGGTG >> 5420300
5686481 << ******C**TC**T***C***G*G*C***C*T******T**********CG*G****C**********AA***** << 5686407
5420301 >> ACGACCGTCTCGAACAGCTTGCGCTGGGC-CAGG-ATCCCGACCAGGGAGATGAAGGTGAGCGGGGCCACCAGGC >> 5420373
5686406 << *CG****TT**G*C****--***A***A*C*G*GG**C****A**GG***CT*******C*******C**C*G*A << 5686334
5420374 >> CGTCGTAGCCGTACTCCTG-GGCGACGTCCTCGTCCCAGTGCACCGGGTGGTAGTCCTGGACGGCGCGGGCGTAC >> 5420447
5686333 << C**********-*CC*CC*G****A**C*****GCCAC****C*CGG***GGC**A***G************T*A << 5686260
5420448 >> TCGCGGACCTTCTCGCGGCCGACCTCGTAGTAGTCG >> 5420483
5686259 << *****G************************GC**** << 5686224
Statistics
Matches: 698 (69.04%), Mismatches: 256 (25.32%), Indels: 57 (5.64%)
ATpairs: 28.94%, CGpairs: 71.06%, GTpairs: 0.00%
:i = 5686439
tupleindex: 3
intervalindex: 1
matches_in_interval: 98.0000
lowcenter: 11106683
highcenter: 11106731
testcenter: 11106707
im3: 77.0000
frequent_center_ratio*rnkp: 25.9200
Found at i: 5700401 center: 11284608 interval size: 300 g: 3
Alignment explanation
Indices: 5583628--5584356,5700252--5700998 Loop: 115895 Score: 332
Left Length: 729 Right Length: 747 Average length: 738.0
3 most common centers (desc): 11284626 11284608 11284611
5583618 >> (LF) CCCACCTGCT
5701008 << (RF) CGACCGAGTT
5583628 >> GCTCACCCCGGCCGCGGCCCCGCGCATCGCCACCGAACTCGGCATGAACGGCGCTGCCGCCTTCGACATCTCCGC >> 5583702
5700998 << **********GT**CG******TG*C*C***A****AA*C**C*********TAG************G**T**A* << 5700924
5583703 >> CGGGTGCGCGGGCTTCTGCCACGCGCTGGCGCTGGCCTCCGACCTGGTGCGCGCGGGCACCTC-GAAGAACGTCC >> 5583776
5700923 << ***G****CG******C**A***CG**G*C*C*****C*A**A***T*G*********A*CC*G***A*-***C* << 5700850
5583777 >> TGGTGATCGGCGTGGAGAAACTGACCGACACCATCGACATGACCGACCGCTCCACGGCGTTCCTGTTCGCCGACG >> 5583851
5700849 << ************GG****GCT******A*CC*G*****GG**********CC***G**GT*CT*G****C***** << 5700775
5583852 >> GCGCGGGCGCGGTGGTGGTCGGCCCG-GCAGAGGAGCCGGGCATCGGCCCGACGGTGTGGGGCTCCGACGGCACC >> 5583925
5700774 << *A***********G***********GT**-******TTG******AG****************TC*******CTC << 5700701
5583926 >> CAGCACC-ACGCGATCCGCCAGAACAAGGACTGGATCGAGTTCTTCA-C----CG-AGATC--G-AGG--A--GA >> 5583986
5700700 << T*-*C**C*T**G***CG****C**CAG****AGG********T*C*T*TTCC**G**CG*GA*G***CG*GG** << 5700627
5583987 >> AG-GGCC-TCGACGCGGTGCGCCCC-TACCTCA-CG-ATGGAGGGCACGGCGGTGTTCCGCTGGGCGGC-G-CAC >> 5584054
5700626 << GGG****C*C**CG*****C***CCT*CA*C*AC**G********AG**GC*********C********G*A*** << 5700552
5584055 >> TC-GCTGGAGAAGGTCTGCCGCGACGCCATCGACCGGGCCGGGCTGTCCACCGACGACCTGCGCGCGATGA-TCC >> 5584127
5700551 << G*A**G*G-*GCG*-***C*GT*-****G****CCAGA****AC*G****TC**C***T*-**T*CAG*AGC*** << 5700481
5584128 >> CGCACCAGGCCAACGGCCGGATCATCGAGATCATGGCGCGGGTGCTGAAACTGCCCGAGGACTGCGCGCTGGCCA >> 5584202
5700480 << ***************G***G****T****A*C***TT*TT*TTG**GCCC**GC****G***TA*G**T****** << 5700406
5584203 >> ACGACATCGAGGAGACCGGCAACACCTCCGCGGCCTCGATCCCGCTCGCGATGGAGGCGCTGCTGCGCAAGGGCG >> 5584277
5700405 << ***********T*G*****************G*****G********C**G*******T*T*****CA**GG***T << 5700331
5584278 >> AGTCGAAGCCCGGCGA-CACGGCGCTGTTGATCGCCTTCGGCGCCGGGCTCTCCTACGCGGCCCAGGTGGTATCG >> 5584351
5700330 << **C*G***CC***AG*C*A**-*****G**G***C***************CTC********C******G**GT*G << 5700257
5584352 >> CTGCC >> 5584356
5700256 << ***** << 5700252
Statistics
Matches: 533 (70.60%), Mismatches: 188 (24.90%), Indels: 34 (4.50%)
ATpairs: 28.14%, CGpairs: 71.86%, GTpairs: 0.00%
:i = 5700401
tupleindex: 3
intervalindex: 1
matches_in_interval: 100.0000
lowcenter: 11284584
highcenter: 11284632
testcenter: 11284608
im3: 69.0000
frequent_center_ratio*rnkp: 25.9200
Found at i: 5709935 center: 11419193 interval size: 160 g: 2
Alignment explanation
Indices: 5709167--5709308,5709885--5710026 Loop: 576 Score: 71
Left Length: 142 Right Length: 142 Average length: 142.0
3 most common centers (desc): 11419193 11419191 11419192
5709157 >> (LF) GACGGTGACG
5710036 << (RF) CGGTTTGCCT
5709167 >> AGGTGGTCATGATCGCCGGTGGCACCGGGCTGGCGCCGATGCGCGCGCAGATT-CTGGAGCTGGC-CAG-GGCGC >> 5709238
5710026 << **T**G*C*******CAA*G**A*****AT*G******A**********-***C*****TT****C***G***** << 5709953
5709239 >> CGGAGCCGCCGCGCACCTACCTGTTCGTCGGCGGGCACAGTCCGCGCGACCTGTATGCCTC-GGACATGCT >> 5709308
5709952 << T*A*TA*-**TT*CAC*-****************A***GTG***A****A**G**G*T-**A***C***** << 5709885
Statistics
Matches: 105 (71.92%), Mismatches: 33 (22.60%), Indels: 8 (5.48%)
ATpairs: 32.38%, CGpairs: 67.62%, GTpairs: 0.00%
:i = 5709935
tupleindex: 2
intervalindex: 2
matches_in_interval: 83.0000
lowcenter: 11419175
highcenter: 11419211
testcenter: 11419193
im3: 43.0000
frequent_center_ratio*rnkp: 21.3900
Found at i: 5710076 center: 11418385 interval size: 300 g: 3
Alignment explanation
Indices: 5708178--5708743,5709633--5710207 Loop: 889 Score: 242
Left Length: 566 Right Length: 575 Average length: 570.5
3 most common centers (desc): 11418385 11418376 11418384
5708168 >> (LF) GCGGCCGAAA
5710217 << (RF) GGCCGGTGCC
5708178 >> ATGTGGCGTTACTTCTCCCCCGCGATTCCCTCGAACCCGTACGGCGAGATCGAATTCCATGTGCGGAAGGTGCGC >> 5708252
5710207 << ********C**AG****C*****GC****CC****A***G*C*****************G**G**G*CGT*G*A* << 5710133
5708253 >> GGCGGCTGGGTGAGTCCGGCCATCGTCAACGAAACCCAGGTCGGGGACCGCTGGCTGATCGGCGGACCGTTGGGC >> 5708327
5710132 << **A***********G**G**CC*C**C*CAG*C****CG*****G****TC************AG****G***** << 5710058
5708328 >> GGGCTGCACGTGGATCGCAACAGCGGCAAGGACG-TGCTGATGATCGGC-GCGGGGACCGGTATCGCGCCGCTGC >> 5708400
5710057 << ******CC***GGGC*****A-**GTT*G***T*T*************AA****A-***************A*** << 5709985
5708401 >> GCGCCCAGTTGATCGAGATGAGC-CAGCG-CGGGGTGAACCCGCGGGTGCATTTCTTCATCGGCGGCCGCTACCC >> 5708473
5709984 << ****C**T***G*C**T***-**C*****C**GT**T*A***TT**-****GG*C***C*******A*T*G**** << 5709912
5708474 >> GTGCGATCTCTACGACGTGGAGAACATGTGGCAGCTTT-CGCAGAGCAATCCCTGGCTGACGATCGTGCCGGTGT >> 5708547
5709911 << ***************AG******ACG*GT*-**G*G*CC**CA**GC**GTTC*****G***C**TG******GT << 5709838
5708548 >> GTGAGCA-GAAGACCAATCCCTGGTGGTA-T-CCGCA-TCCGG-CGA-CCGACGCCCCC-TACG--GCA-T-GCA >> 5708611
5709837 << GG*****G**C**C-*************AG*T****CG*****T***C***CT***CCAC*A*GGG**CG*G*T* << 5709764
5708612 >> CCGCACGTTGATCGGCAATCTCGGCGCGGTGGTGGCCAGTTTCGGGGC-GTGGGAGGACCGCCAGATCCAGATCG >> 5708685
5709763 << ****C-*G***G***AG*C******TT***G**G***-*TCC******G*****GG*****AC*GC*C******* << 5709691
5708686 >> CCGGATCGGCGCCGATGATCGCCGAC-ACCC-GCCGCGCGCTGATCGCGGTCGGCACCCC >> 5708743
5709690 << ****G***G*GA*****C*-**T***G***TT*AAG***-*****C**G*GC****A*** << 5709633
Statistics
Matches: 411 (70.26%), Mismatches: 145 (24.79%), Indels: 29 (4.96%)
ATpairs: 32.36%, CGpairs: 67.64%, GTpairs: 0.00%
:i = 5710076
tupleindex: 3
intervalindex: 1
matches_in_interval: 107.0000
lowcenter: 11418361
highcenter: 11418409
testcenter: 11418385
im3: 92.0000
frequent_center_ratio*rnkp: 25.9200
Found at i: 5748797 center: 11172051 interval size: 300 g: 3
Alignment explanation
Indices: 5423201--5423425,5748625--5748850 Loop: 325199 Score: 288
Left Length: 225 Right Length: 226 Average length: 225.5
3 most common centers (desc): 11172051 11172050 0
5423191 >> (LF) CGTTCGACTG
5748860 << (RF) ACGACAGAAA
5423201 >> GCCCGAGCCGGGGCGCCCTCCGTGGTCACACTGCGCTGCCGCCTCCGGGCGCTGACCCGCTCAGGCCGTGTCCGA >> 5423275
5748850 << ***A****C**A***C***C******C*********************G*****************A*****C** << 5748776
5423276 >> CCG-GCCCGAGCCGGGGCGCCCTCCGTGGTCACACTGCGCTGCCGCCTCCGGGCGCTGACCCGCTCAGGCCGTAT >> 5423349
5748775 << AAAG***A****-******C***C******C*********************G*****************A**C* << 5748702
5423350 >> CCGACTG-GCCCGAGCCGGGGCGCCCTCCGTGGTCACACTGCGCTGCCGCCTCCGGGCGCTGACCCGCTCAGGCC >> 5423423
5748701 << *C**A*AG***C****C******C***C******C*********************G*****************A << 5748627
5423424 >> GT >> 5423425
5748626 << ** << 5748625
Statistics
Matches: 195 (85.90%), Mismatches: 29 (12.78%), Indels: 3 (1.32%)
ATpairs: 24.10%, CGpairs: 75.90%, GTpairs: 0.00%
:i = 5748797
tupleindex: 3
intervalindex: 1
matches_in_interval: 96.0000
lowcenter: 11172027
highcenter: 11172075
testcenter: 11172051
im3: 58.0000
frequent_center_ratio*rnkp: 25.9200
Found at i: 5748815 center: 11172129 interval size: 300 g: 3
Alignment explanation
Indices: 5423279--5423500,5748630--5748850 Loop: 325129 Score: 263
Left Length: 222 Right Length: 221 Average length: 221.5
3 most common centers (desc): 11172129 11172128 11172130
5423269 >> (LF) TGTCCGACCG
5748860 << (RF) ACGACAGAAA
5423279 >> GCCCGAGCCGGGGCGCCCTCCGTGGTCACACTGCGCTGCCGCCTCCGGGCGCTGACCCGCTCAGGCCGTATCCGA >> 5423353
5748850 << ***A****C**A***C***C******C*********************G*****************A**C**C** << 5748776
5423354 >> CTG-GCCCGAGCCGGGGCGCCCTCCGTGGTCACACTGCGCTGCCGCCTCCGGGCGCTGACCCGCTCAGGCCGTAT >> 5423427
5748775 << A*AG***A****-******C***C******C*********************G*****************A**C* << 5748702
5423428 >> CCGACCG-GCCCGAGCCGGGGCGCCCTCCGTGGTCACACTGCGCTGCCGCCTCCGGGGCGCCGACCCGGCTCAG >> 5423500
5748701 << *C**AAAG***C****C******C***C******C*********************G-***A******-***** << 5748630
Statistics
Matches: 189 (84.38%), Mismatches: 30 (13.39%), Indels: 5 (2.23%)
ATpairs: 23.81%, CGpairs: 76.19%, GTpairs: 0.00%
:i = 5748815
tupleindex: 3
intervalindex: 1
matches_in_interval: 96.0000
lowcenter: 11172105
highcenter: 11172153
testcenter: 11172129
im3: 75.0000
frequent_center_ratio*rnkp: 25.9200
Found at i: 5814808 center: 11629571 interval size: 40 g: 1
Alignment explanation
Indices: 5814739--5814785,5814786--5814829 Loop: 0 Score: 48
Left Length: 47 Right Length: 44 Average length: 45.5
3 most common centers (desc): 11629571 11629568 11629570
5814729 >> (LF) CGGTCGCTCC
5814839 << (RF) GCCCGTGGCC
5814739 >> GCACCGGCGGAACCGCAACCCGGCCCTTCGGCGCAGCCGCCCCACCC >> 5814785
5814829 << ***C*****GC-****G-*******-**************A****** << 5814786
Statistics
Matches: 39 (82.98%), Mismatches: 5 (10.64%), Indels: 3 (6.38%)
ATpairs: 12.82%, CGpairs: 87.18%, GTpairs: 0.00%
:i = 5814808
tupleindex: 1
intervalindex: 2
matches_in_interval: 26.0000
lowcenter: 11629563
highcenter: 11629579
testcenter: 11629571
im3: 22.0000
frequent_center_ratio*rnkp: 7.6500
Found at i: 5823163 center: 11344342 interval size: 300 g: 3
Alignment explanation
Indices: 5521175--5521367,5822975--5823167 Loop: 301607 Score: 62
Left Length: 193 Right Length: 193 Average length: 193.0
3 most common centers (desc): 11344342 11344345 11344343
5521165 >> (LF) GTTGCGGGTG
5823177 << (RF) GGACCGCTAG
5521175 >> CTCGGGGTGCC-CTCGGCGCTGGCGCTGGCACT-GTGGGTCGGCGTGGTGTCGCAGTTCATTCCGACCGTCGGCA >> 5521247
5823167 << **C********C**-*******G*******-**G*GA***CAA*T*GT-*-***-******G****A*T*****C << 5823098
5521248 >> CCTATCTCGCCGG-TGCGATCCCGATCGTCGTGGCCCTCGTC-C-ACGATCCGGGCT-CGGCGCTG-TGGTTGCT >> 5521317
5823097 << *C*A***C*****G*A*-***C**C*CA**T*G*****C***T*G*T*CC**A**ACT********T*G**-*** << 5823025
5521318 >> CGGATTCATCGTCCTCTACCAGCAATTCGAGAACTACGTGCTGCAACCGC >> 5521367
5823024 << ***GT*****T**CG*CA*TA***CG*C**T*C*G*A************* << 5822975
Statistics
Matches: 138 (69.00%), Mismatches: 48 (24.00%), Indels: 14 (7.00%)
ATpairs: 31.16%, CGpairs: 68.84%, GTpairs: 0.00%
:i = 5823163
tupleindex: 3
intervalindex: 1
matches_in_interval: 105.0000
lowcenter: 11344318
highcenter: 11344366
testcenter: 11344342
im3: 57.0000
frequent_center_ratio*rnkp: 25.9200
Found at i: 5841143 center: 11682223 interval size: 40 g: 1
Alignment explanation
Indices: 5841074--5841109,5841114--5841149 Loop: 4 Score: 42
Left Length: 36 Right Length: 36 Average length: 36.0
3 most common centers (desc): 11682223 0 0
5841064 >> (LF) CGGCGACGTG
5841159 << (RF) CGTCCGCCCG
5841074 >> TGACCGCCCCGGCGCACGAGAACATGCCCCACGGGT >> 5841109
5841149 << ***A*T*****G***C***GC*************** << 5841114
Statistics
Matches: 30 (83.33%), Mismatches: 6 (16.67%), Indels: 0 (0.00%)
ATpairs: 26.67%, CGpairs: 73.33%, GTpairs: 0.00%
:i = 5841143
tupleindex: 1
intervalindex: 2
matches_in_interval: 37.0000
lowcenter: 11682215
highcenter: 11682231
testcenter: 11682223
im3: 20.0000
frequent_center_ratio*rnkp: 7.6500
Found at i: 5842296 center: 11287652 interval size: 300 g: 3
Alignment explanation
Indices: 5444814--5445450,5842202--5842841 Loop: 396751 Score: 371
Left Length: 637 Right Length: 640 Average length: 638.5
3 most common centers (desc): 11287655 11287652 11287654
5444804 >> (LF) ACCGCCTGGT
5842851 << (RF) CGCCCGACTC
5444814 >> CAAG-GTGTTCGGACAGCAGCGGGCCGTGGACGGCGTCAGCCTGACCGTGCCGCAGGGTGCGGTCTACGGCGTGC >> 5444887
5842841 << ****T**-*****AC*****CA**ACG*G******T**CT***GC****GC***GG**GT*GT***A**G*G*** << 5842768
5444888 >> TCGGACCGAACGGGGCGGGCAAGACCACCACCATCCGCATGCTCTCGACCCTGCTGCGCCCCGACGGCGGC-AGC >> 5444961
5842767 << ****G**G*****G******************C*C*TC**G***T*G**TA**T*****C*C****G***AC**- << 5842694
5444962 >> GCCAGGATCTTCGGCCACGACGTGGTCGCCGAGCCCACCGCGGTGCGCTCGCTGCTCGGGCTCACCGGCCAGTAC >> 5445036
5842693 << *A****C**CC***AAA********GC*****T*C*C***TT**G***CC*TG*T*****C*C**********A* << 5842619
5445037 >> GCCTCGGTGGACGAGGATCTCACCG-CCGTGGAGAACCTGGTGATCTTCGCCAGGCTGCTCGGCCTGACCCGTGC >> 5445110
5842618 << ***C****G*****TGAC*******C***-**********G*GG**T*C***CTG****T*GT****G****G** << 5842545
5445111 >> CGCGGCCC-GCACCCGCGCCGCCGACCTGCTCGAGGAG-TTCGACCTCACCGAGGCGGCGAACAAG-CCGTTGAA >> 5445182
5842544 << **T**C*TT**CC*A*-****T***T******-*GGG*G********************GC*****T***GG*GG << 5842472
5445183 >> AAACTTCTCCGGCGGTATGCGCCGCAGGCTCGACCTGGCCGCCAGCCTGATCTCCACCCCGCCGCTGC-TGTTCC >> 5445256
5842471 << *G-**T******A**G***TG****G*A***********CTAC*G****C**CC*CT*****-**TA*T*G**** << 5842399
5445257 >> TCGACGAGCCCACCACCGGCCTGGACCCGCGCACCCGCGCCC-AGATGTGGGACACCATCCGCAGAC-TCGTCGC >> 5445329
5842398 << **********C***********G**********C*T*-**C*C*G******G*C*A****-**G***G*C***T* << 5842326
5445330 >> CGACG-GCGCG--ACCGTGCTGCTGACCACCCAGTACCTCGACGAAGCCGATCAGCTGGCCGACCGGATCGCGGT >> 5445401
5842325 << ****TA*C***AG*****GA*G**G*****************C**C***********G********G******** << 5842251
5445402 >> GATCGACCGCGGCCGGGTGATCGCCGACGGCACCGCCGACGAACTGAAG >> 5445450
5842250 << *G*CT***T*******T*GC*C*****C**********GC**C**G*** << 5842202
Statistics
Matches: 472 (72.73%), Mismatches: 156 (24.04%), Indels: 21 (3.24%)
ATpairs: 28.39%, CGpairs: 71.61%, GTpairs: 0.00%
:i = 5842296
tupleindex: 3
intervalindex: 1
matches_in_interval: 96.0000
lowcenter: 11287628
highcenter: 11287676
testcenter: 11287652
im3: 58.0000
frequent_center_ratio*rnkp: 25.9200
Found at i: 5842761 center: 11674509 interval size: 300 g: 3
Alignment explanation
Indices: 5831738--5831785,5842724--5842771 Loop: 10938 Score: 61
Left Length: 48 Right Length: 48 Average length: 48.0
3 most common centers (desc): 11674509 0 0
5831728 >> (LF) GGTACTCACG
5842781 << (RF) GTAGAAGCGG
5831738 >> CTGCTGGGCCCCAACGGAGCGGGCAAATCCACCACCATCGAGATCCTC >> 5831785
5842771 << *****G***********G********CT********C*CG******** << 5842724
Statistics
Matches: 41 (85.42%), Mismatches: 7 (14.58%), Indels: 0 (0.00%)
ATpairs: 31.71%, CGpairs: 68.29%, GTpairs: 0.00%
:i = 5842761
tupleindex: 3
intervalindex: 1
matches_in_interval: 101.0000
lowcenter: 11674485
highcenter: 11674533
testcenter: 11674509
im3: 41.0000
frequent_center_ratio*rnkp: 25.9200
Found at i: 5909252 center: 11818464 interval size: 40 g: 1
Alignment explanation
Indices: 5909212--5909231,5909233--5909252 Loop: 1 Score: 40
Left Length: 20 Right Length: 20 Average length: 20.0
3 most common centers (desc): 11818464 0 0
5909202 >> (LF) GATTCTCTCC
5909262 << (RF) TGCCTCGCGT
5909212 >> GCCGTCATCACCCCCGTGTC >> 5909231
5909252 << ******************** << 5909233
Statistics
Matches: 20 (100.00%), Mismatches: 0 (0.00%), Indels: 0 (0.00%)
ATpairs: 30.00%, CGpairs: 70.00%, GTpairs: 0.00%
:i = 5909252
tupleindex: 1
intervalindex: 2
matches_in_interval: 28.0000
lowcenter: 11818456
highcenter: 11818472
testcenter: 11818464
im3: 20.0000
frequent_center_ratio*rnkp: 7.6500
Found at i: 5991360 center: 11679407 interval size: 300 g: 3
Alignment explanation
Indices: 5687229--5688147,5991260--5992175 Loop: 303112 Score: 676
Left Length: 919 Right Length: 916 Average length: 917.5
3 most common centers (desc): 11679407 11679404 11679403
5687219 >> (LF) AGTTCGGCGT
5992185 << (RF) TGGCCGCTTG
5687229 >> GCATGAGATACACGTTGTAGTCGCTCCAGGTCGTGATGTTGAAGTAGAGATCG-CGCCCACTCGACCAGGGATGG >> 5687302
5992175 << **********C*********GA*AG*****G**TG***C*******G**G***A****CC-*C************ << 5992102
5687303 >> ATGAAACCGCCGTACAGCTCGGGATAGTCC-AGCACCGAGACCGTCGGCGTCGGGGCCGACCAGGCGCCCTGGGG >> 5687376
5992101 << *****C********CCG**AG*****T***C**CA*-**G***TC****TG*GG*A*C*A***G********G** << 5992028
5687377 >> CGTGGTCGCCTCCCGGACGACGATGGCGGCGCGCGCGGTGTCGAGGTAGCTCATCTGCCACACCCCCCG-GCTCG >> 5687450
5992027 << C***********C**G*TG*****G***G*********T***G******TG*********C-*CAA*C*A**G** << 5991954
5687451 >> CGTCGAAGCGCACCGACAGCTCGCCCGCGGGGGCGTCGA-CGACGGGTGTGGCGCTGGCGGCCCCGCCGACCGGC >> 5687524
5991953 << *****A******************AC***TATG**TC**T*T*****-*****-****AA-*A******-*C**T << 5991883
5687525 >> GTCCACTGCCCGTCCCGCCAGTACTGGTAGGCGGTCTTGTTGAGCAGTTGGTCGGCCGGGACGCGGGCGAGGCCG >> 5687599
5991882 << *G***C*GT****A*TG*****************T***********GC**G**GAAC**G**G*A***G**G**G << 5991808
5687600 >> ACCGCGCCGAGGCGGGTGTTGGGGGTGCCGAACATGTAGACGTGGTCGCCGTGCGGGACCATCGCGCTCACCTGG >> 5687674
5991807 << ***T******GG**GGG***G**********************T******G*****G*********CGC****** << 5991733
5687675 >> AAGTTGGCGAGGCCGAAGATGTTGTCCCAGCGGGCGTGCGGGTCCTTGGTCCAGGTCTGGCCGCGGTCGTCGGAG >> 5687749
5991732 << **GGC*G****G*****G*C*********GAA*******A****A**GTG******CCTT***AA********** << 5991658
5687750 >> TAGGCGATCCCGCCGTAGTTGGTGTAGAAGGTGCCGGGCCCGCTGTTCCAGGTGCGAATCGACATGTAGCTCAGG >> 5687824
5991657 << ********C**************GG*GG*GT*******CTA**C*G*****GC*AAG*G**************A* << 5991583
5687825 >> TACTGCCGGTCGCCGAGGGCGAAGCCGGAGGTGGGGATGGTGGTGATCTCCACGTTGTCGAGTTTGCGGCTCGAC >> 5687899
5991582 << **********A*********************G******TGG***C*****GT***G*A**AG************ << 5991508
5687900 >> AGCACCTCCGCGGCATGGCAGCGACTGTCGGTG-ACCATGCGGTCGTAGGTCATCCCGTCGCTCAGGTCACGGTC >> 5687973
5991507 << ****C***C**G**C*****G**C*****G-**G*****G******TA*GC**GC******CTC*****CCA*** << 5991434
5687974 >> GGTACTGAAGGCCAGCACATTGCTGCGCCAGTCC---CCGCCCATGCCGCCGGGCGGGTGGAACCCGCGTCCGAC >> 5688045
5991433 << ***C***A****C***C*C***************CTA******CG*******AT*AGGGT*--**AA**-****T << 5991362
5688046 >> GGTGTCGCCGAACGCCACCGCGACCTCCCCGGGCCCGCTCTCCCACATGATCCCCAGGTCGGTGCCGTCCACCTG >> 5688120
5991361 << ************CT***A***G*****C******AA*C*************C**C*************AC*A*CG << 5991287
5688121 >> CCACCGCTTGTCGGTGCGGTTCACCGA >> 5688147
5991286 << ***C***TG*************A**** << 5991260
Statistics
Matches: 699 (75.40%), Mismatches: 209 (22.55%), Indels: 19 (2.05%)
ATpairs: 31.62%, CGpairs: 68.38%, GTpairs: 0.00%
:i = 5991360
tupleindex: 3
intervalindex: 1
matches_in_interval: 96.0000
lowcenter: 11679383
highcenter: 11679431
testcenter: 11679407
im3: 50.0000
frequent_center_ratio*rnkp: 25.9200
Done.