Inverted Repeats Finder Program written by:
Gary Benson
Department of Biomathematical Sciences
Mount Sinai School of Medicine
Version 3.05
Sequence: pNF1 2003-09-03
Parameters: 2 3 5 80 10 40 100000 500000 -t7 600000 -d
Length: 184026
ACGTcount: A:0.16, C:0.33, G:0.34, T:0.17, N:0.00
Found at i: 1967 center: 3836 interval size: 40 g: 1
Alignment explanation
Indices: 1869--1888,1948--1967 Loop: 59 Score: 40
Left Length: 20 Right Length: 20 Average length: 20.0
3 most common centers (desc): 3836 0 0
1859 >> (LF) ACCACAACGC
1977 << (RF) TCCGAGTGTA
1869 >> GGGTAAACCGCGGTTTACCC >> 1888
1967 << ******************** << 1948
Statistics
Matches: 20 (100.00%), Mismatches: 0 (0.00%), Indels: 0 (0.00%)
ATpairs: 40.00%, CGpairs: 60.00%, GTpairs: 0.00%
:i = 1967
tupleindex: 1
intervalindex: 2
matches_in_interval: 20.0000
lowcenter: 3828
highcenter: 3844
testcenter: 3836
im3: 20.0000
frequent_center_ratio*rnkp: 7.6500
Found at i: 2034 center: 3982 interval size: 40 g: 1
Alignment explanation
Indices: 1948--1967,2015--2034 Loop: 47 Score: 40
Left Length: 20 Right Length: 20 Average length: 20.0
3 most common centers (desc): 3982 0 0
1938 >> (LF) CAAGGAACAT
2044 << (RF) CCGCTCCACC
1948 >> GGGTAAACCGCGGTTTACCC >> 1967
2034 << ******************** << 2015
Statistics
Matches: 20 (100.00%), Mismatches: 0 (0.00%), Indels: 0 (0.00%)
ATpairs: 40.00%, CGpairs: 60.00%, GTpairs: 0.00%
:i = 2034
tupleindex: 1
intervalindex: 2
matches_in_interval: 20.0000
lowcenter: 3974
highcenter: 3990
testcenter: 3982
im3: 20.0000
frequent_center_ratio*rnkp: 7.6500
Found at i: 2034 center: 3903 interval size: 80 g: 2
Alignment explanation
Indices: 1869--1888,2015--2034 Loop: 126 Score: 40
Left Length: 20 Right Length: 20 Average length: 20.0
3 most common centers (desc): 3903 0 0
1859 >> (LF) ACCACAACGC
2044 << (RF) CCGCTCCACC
1869 >> GGGTAAACCGCGGTTTACCC >> 1888
2034 << ******************** << 2015
Statistics
Matches: 20 (100.00%), Mismatches: 0 (0.00%), Indels: 0 (0.00%)
ATpairs: 40.00%, CGpairs: 60.00%, GTpairs: 0.00%
:i = 2034
tupleindex: 2
intervalindex: 1
matches_in_interval: 35.0000
lowcenter: 3891
highcenter: 3915
testcenter: 3903
im3: 20.0000
frequent_center_ratio*rnkp: 12.7600
Found at i: 8487 center: 16928 interval size: 40 g: 1
Alignment explanation
Indices: 8441--8460,8468--8487 Loop: 7 Score: 40
Left Length: 20 Right Length: 20 Average length: 20.0
3 most common centers (desc): 16928 0 0
8431 >> (LF) GACGAGAGAG
8497 << (RF) GGCTGCCGCA
8441 >> GAAGGCCAGGGAGGGGGCCC >> 8460
8487 << ******************** << 8468
Statistics
Matches: 20 (100.00%), Mismatches: 0 (0.00%), Indels: 0 (0.00%)
ATpairs: 20.00%, CGpairs: 80.00%, GTpairs: 0.00%
:i = 8487
tupleindex: 1
intervalindex: 2
matches_in_interval: 36.0000
lowcenter: 16920
highcenter: 16936
testcenter: 16928
im3: 20.0000
frequent_center_ratio*rnkp: 7.6500
Found at i: 97690 center: 138910 interval size: 300 g: 3
Alignment explanation
Indices: 41192--41466,97444--97718 Loop: 55977 Score: 129
Left Length: 275 Right Length: 275 Average length: 275.0
3 most common centers (desc): 138910 138907 138909
41182 >> (LF) ATCGATCGGT
97728 << (RF) CAGCGGCGCG
41192 >> TGCACG-CCTTGG-GTATTCGTGTGTCGATGCTCACCGGTGACAAC-ACCCGCACCGCTGC-CGCCCTGGCTACC >> 41262
97718 << ******T***G**G**GCTC***-***-***********G******C*TC*-******CTTT***TAG*G*C*C* << 97647
41263 >> GAGGCCGGGATCGAGGACGTGCA-CGCGGACCTGCGCCCCGAAGACAAGGCCCGCATCGTGGGCGAACTACG-CG >> 41335
97646 << *-*GA***G*****GTG***-**A***G**TC*T*AC****CG*****T***TG**TCT*G*G********TT** << 97574
41336 >> C--CGACCGGTTCACCGCGATGGTCGGCGACGGCGTCAACGACGCCCCCGCACTGGCCACCGCCGACCTCGGTGT >> 41408
97573 << *TC**C***GGTCCA***G********************************G**G***GTT***********GT* << 97499
41409 >> GGCGATGGGTGCGATGGGTACCGACGTCGCCATCGAAACCGCCGACGTCGCCCTGATG >> 41466
97498 << G**G**G**G**G--**G-**************************A****AC**G*** << 97444
Statistics
Matches: 202 (71.38%), Mismatches: 65 (22.97%), Indels: 16 (5.65%)
ATpairs: 29.21%, CGpairs: 70.79%, GTpairs: 0.00%
:i = 97690
tupleindex: 3
intervalindex: 1
matches_in_interval: 97.0000
lowcenter: 138886
highcenter: 138934
testcenter: 138910
im3: 43.0000
frequent_center_ratio*rnkp: 25.9200
Done.