Inverted Repeats Finder Program written by:
Gary Benson
Department of Biomathematical Sciences
Mount Sinai School of Medicine
Version 3.05
Sequence: pNF2 2003-09-03
Parameters: 2 3 5 80 10 40 100000 500000 -t7 600000 -d
Length: 87093
ACGTcount: A:0.16, C:0.35, G:0.34, T:0.16, N:0.00
Found at i: 1607 center: 3155 interval size: 40 g: 1
Alignment explanation
Indices: 1548--1570,1585--1607 Loop: 14 Score: 41
Left Length: 23 Right Length: 23 Average length: 23.0
3 most common centers (desc): 3155 0 0
1538 >> (LF) CAGCACCCCC
1617 << (RF) ACTCGTCCGC
1548 >> GACGACGTCGTCGAGCAGCTGCG >> 1570
1607 << ******G**************** << 1585
Statistics
Matches: 22 (95.65%), Mismatches: 1 (4.35%), Indels: 0 (0.00%)
ATpairs: 31.82%, CGpairs: 68.18%, GTpairs: 0.00%
:i = 1607
tupleindex: 1
intervalindex: 2
matches_in_interval: 35.0000
lowcenter: 3147
highcenter: 3163
testcenter: 3155
im3: 22.0000
frequent_center_ratio*rnkp: 7.6500
Found at i: 84551 center: 168614 interval size: 300 g: 3
Alignment explanation
Indices: 84032--84125,84488--84582 Loop: 362 Score: 60
Left Length: 94 Right Length: 95 Average length: 94.5
3 most common centers (desc): 168614 168615 168612
84022 >> (LF) GGCCGTGCCC
84592 << (RF) GGCGCGCGCC
84032 >> ACCGAGTCGCGCGCGCGGGGCGGGTTCG-GTCGCGCGCGCGAGCGCCCCC-TCGATCACT-GTCGATCGCGCGCG >> 84103
84582 << *****-****A******G**A*T*CT**T**********--****TA**CC******C*CG************** << 84511
84104 >> GCCCG--CGCGCGATGGGCGCGCG >> 84125
84510 << TC***TA******A*G*-****** << 84488
Statistics
Matches: 75 (75.76%), Mismatches: 15 (15.15%), Indels: 9 (9.09%)
ATpairs: 16.00%, CGpairs: 84.00%, GTpairs: 0.00%
:i = 84551
tupleindex: 3
intervalindex: 1
matches_in_interval: 181.0000
lowcenter: 168590
highcenter: 168638
testcenter: 168614
im3: 28.0000
frequent_center_ratio*rnkp: 25.9200
Found at i: 84572 center: 168668 interval size: 160 g: 2
Alignment explanation
Indices: 83969--84176,84488--84698 Loop: 311 Score: 52
Left Length: 208 Right Length: 211 Average length: 209.5
3 most common centers (desc): 168668 168664 168667
83959 >> (LF) TGCGATCGAC
84708 << (RF) TCGCGCTTGA
83969 >> GACCGCGCGCGCGATCACCGTCGCCTCCGCGCGCGACAACGCGCGATCGAACGGGCC-GTGC-C-CA-CCGAGTC >> 84039
84698 << ******G*******-**C*GG***-**-*******C*C***T*-****-*-**G***A****T*C*CC******* << 84630
84041 >> -GCG--CG--CGCGGG-GCGGGTTCGGTCGCGCGCGCGAGCGCCCCCTCGATCACTGTCGATCGCGCGCGGCCCG >> 84108
84629 << G***TA**TA****G*G***T*C-****C**GC***-*AG***C*C*C-**-*-*CT***G**********ACT* << 84560
84109 >> CGCGCGATGGGCGCGCGCGATCGGCGTCC-TCGCGCG-CGATCG-GCGAGACCGGCTT-CG-GATCGCGCGCG >> 84176
84559 << CT**T*AG*G*****T******G*-***CT*******A******G***G**C*G*T*GC**G*A********* << 84488
Statistics
Matches: 155 (69.51%), Mismatches: 41 (18.39%), Indels: 27 (12.11%)
ATpairs: 15.48%, CGpairs: 84.52%, GTpairs: 0.00%
:i = 84572
tupleindex: 2
intervalindex: 2
matches_in_interval: 322.0000
lowcenter: 168650
highcenter: 168686
testcenter: 168668
im3: 27.0000
frequent_center_ratio*rnkp: 21.3900
Found at i: 84618 center: 168737 interval size: 80 g: 2
Alignment explanation
Indices: 84188--84241,84495--84550 Loop: 253 Score: 51
Left Length: 54 Right Length: 56 Average length: 55.0
3 most common centers (desc): 168736 168738 168737
84178 >> (LF) TCGACACCAC
84560 << (RF) CCTGCTCAGC
84188 >> CGCGCGC-CGATCGCGATCGA-CGCCC-TCGGTCGCGCGCGCGACGCTCGCGCGTTC >> 84241
84550 << ******TC*****-**C****A***C*C***T*********T*G**T********** << 84495
Statistics
Matches: 46 (80.70%), Mismatches: 7 (12.28%), Indels: 4 (7.02%)
ATpairs: 19.57%, CGpairs: 80.43%, GTpairs: 0.00%
:i = 84618
tupleindex: 2
intervalindex: 1
matches_in_interval: 140.0000
lowcenter: 168725
highcenter: 168749
testcenter: 168737
im3: 14.0000
frequent_center_ratio*rnkp: 12.7600
Done.