Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold71
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5741892
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.33
Warning! 121862 characters in sequence are not A, C, G, or T
File 8 of 33
Found at i:1259544 original size:30 final size:30
Alignment explanation
Indices: 1259488--1259546 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
1259478 ATTAAAAATT
*
1259488 ATATAATTATTAATATAAAATAATATTTTA
1 ATATAATTATAAATATAAAATAATATTTTA
*
1259518 ATATTATTATAAATAATAAAAT-ATATTTT
1 ATATAATTATAAAT-ATAAAATAATATTTT
1259547 CAAATTGCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 19 0.73
31 7 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (30 bp):
ATATAATTATAAATATAAAATAATATTTTA
Found at i:1268490 original size:3 final size:3
Alignment explanation
Indices: 1268482--1268506 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1268472 ATCTCCACAT
1268482 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
1268507 AAGCCAAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:1271221 original size:10 final size:10
Alignment explanation
Indices: 1271208--1271234 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1271198 TTCTTTTTTT
1271208 TTTTTTTGAA
1 TTTTTTTGAA
1271218 TTTTTTTGAA
1 TTTTTTTGAA
1271228 TTTTTTT
1 TTTTTTT
1271235 TAGAAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:1272170 original size:22 final size:22
Alignment explanation
Indices: 1272142--1272194 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
1272132 TTATAAAATA
1272142 ATTATA-TTATATATATCTTTT-T
1 ATTATATTTAT-TATAT-TTTTAT
*
1272164 ATTATATTTATTTTATTTTTAT
1 ATTATATTTATTATATTTTTAT
1272186 ATTATATTT
1 ATTATATTT
1272195 TAATTATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 4 0.14
22 20 0.71
23 4 0.14
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (22 bp):
ATTATATTTATTATATTTTTAT
Found at i:1272184 original size:11 final size:11
Alignment explanation
Indices: 1272148--1272205 Score: 57
Period size: 11 Copynumber: 5.2 Consensus size: 11
1272138 AATAATTATA
1272148 TTATATATATCTT
1 TTATAT-TAT-TT
*
1272161 TT-TATTATAT
1 TTATATTATTT
*
1272171 TTATTTTATTT
1 TTATATTATTT
1272182 TTATATTATATT
1 TTATATTAT-TT
1272194 TTA-ATTATTT
1 TTATATTATTT
1272204 TT
1 TT
1272206 GTTATGTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
10 7 0.18
11 22 0.56
12 8 0.21
13 2 0.05
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATATTATTT
Found at i:1273019 original size:15 final size:15
Alignment explanation
Indices: 1272999--1273029 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1272989 AAGTTAATTT
*
1272999 ATTTTTTAATAAATA
1 ATTTTTTAAAAAATA
1273014 ATTTTTTAAAAAATA
1 ATTTTTTAAAAAATA
1273029 A
1 A
1273030 ATAATTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTTTTTAAAAAATA
Found at i:1273040 original size:20 final size:19
Alignment explanation
Indices: 1273006--1273048 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
1272996 TTTATTTTTT
1273006 AATAAATAATTTTTTAAAA
1 AATAAATAATTTTTTAAAA
*
1273025 AATAAATAATTTTTTTAAA
1 AATAAATAATTTTTTAAAA
1273044 AATAA
1 AATAA
1273049 TGTTTGTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AATAAATAATTTTTTAAAA
Found at i:1273046 original size:15 final size:16
Alignment explanation
Indices: 1273000--1273049 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 16
1272990 AGTTAATTTA
1273000 TTTTTTAATAAATAAT
1 TTTTTTAATAAATAAT
*
1273016 TTTTTAAAAAATAAATAAT
1 TTTTT---TAATAAATAAT
1273035 TTTTTTAA-AAATAAT
1 TTTTTTAATAAATAAT
1273050 GTTTGTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
15 7 0.24
16 7 0.24
19 15 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTTTTAATAAATAAT
Found at i:1275293 original size:6 final size:7
Alignment explanation
Indices: 1275275--1275301 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1275265 TTTAAACAAC
1275275 ATTTTTA
1 ATTTTTA
1275282 ATTTTTA
1 ATTTTTA
1275289 ATTTTTA
1 ATTTTTA
1275296 ATTTTT
1 ATTTTT
1275302 TTTTTATAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
ATTTTTA
Found at i:1276578 original size:6 final size:7
Alignment explanation
Indices: 1276559--1276584 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1276549 AGTTCAAATA
1276559 AATTTTT
1 AATTTTT
1276566 AATTTTT
1 AATTTTT
1276573 AATTTTT
1 AATTTTT
1276580 AATTT
1 AATTT
1276585 GTTCTCAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
AATTTTT
Found at i:1276605 original size:37 final size:36
Alignment explanation
Indices: 1276532--1276614 Score: 96
Period size: 37 Copynumber: 2.3 Consensus size: 36
1276522 TATAACTAAC
***
1276532 TTTTTAATTTTTAATTAAGTTCAAATAAATTTTTAA
1 TTTTTAATTTTTAATTAAGTTCAAATAAAGCCTTAA
*
1276568 TTTTTAATTTTTAATT-TGTTCTCAAATAAAGCCTTAA
1 TTTTTAATTTTTAATTAAG-T-TCAAATAAAGCCTTAA
*
1276605 TATTTAATTT
1 TTTTTAATTT
1276615 ATATCTAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
35 1 0.03
36 17 0.43
37 22 0.55
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (36 bp):
TTTTTAATTTTTAATTAAGTTCAAATAAAGCCTTAA
Found at i:1276611 original size:30 final size:30
Alignment explanation
Indices: 1276571--1276627 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1276561 TTTTTAATTT
* *
1276571 TTAATTTTTAATTTGT-TCTCAAATAAAGCC
1 TTAATATTTAATTTATATCT-AAATAAAGCC
1276601 TTAATATTTAATTTATATCTAAATAAA
1 TTAATATTTAATTTATATCTAAATAAA
1276628 TTTTATCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 21 0.88
31 3 0.12
ACGTcount: A:0.40, C:0.09, G:0.04, T:0.47
Consensus pattern (30 bp):
TTAATATTTAATTTATATCTAAATAAAGCC
Found at i:1276639 original size:16 final size:16
Alignment explanation
Indices: 1276610--1276660 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
1276600 CTTAATATTT
1276610 AATTTATATC-TAAATA
1 AATTT-TATCATAAATA
1276626 AATTTTATCATAAATTA
1 AATTTTATCATAAA-TA
*
1276643 ACTTTTTAT-ATAAATA
1 A-ATTTTATCATAAATA
1276659 AA
1 AA
1276661 AATTTATTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
15 4 0.13
16 12 0.40
17 8 0.27
18 6 0.20
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTTTATCATAAATA
Found at i:1276648 original size:17 final size:18
Alignment explanation
Indices: 1276610--1276657 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 18
1276600 CTTAATATTT
*
1276610 AATTTATATC-TAAA-TA
1 AATTTTTATCATAAATTA
1276626 AA-TTTTATCATAAATTA
1 AATTTTTATCATAAATTA
*
1276643 ACTTTTTAT-ATAAAT
1 AATTTTTATCATAAAT
1276658 AAAAATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 6 0.22
16 6 0.22
17 9 0.33
18 6 0.22
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (18 bp):
AATTTTTATCATAAATTA
Found at i:1277692 original size:18 final size:17
Alignment explanation
Indices: 1277658--1277710 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
1277648 TATTTAAAAT
1277658 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
1277675 ATTTTAATATATTA-AT-A
1 ATTTT-ATAT-TTATATAA
1277692 A-TTTATATTT-TATAA
1 ATTTTATATTTATATAA
1277707 ATTT
1 ATTT
1277711 AAAAAATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
14 4 0.13
15 6 0.19
16 5 0.16
17 7 0.23
18 6 0.19
19 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:1277709 original size:15 final size:15
Alignment explanation
Indices: 1277660--1277711 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
1277650 TTTAAAATAT
1277660 TTTATATTTATATAAA
1 TTTATATTT-TATAAA
*
1277676 TTTTAATATATTA-ATAA
1 -TTT-ATATTTTATA-AA
1277693 TTTATATTTTATAAA
1 TTTATATTTTATAAA
1277708 TTTA
1 TTTA
1277712 AAAAATTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
15 13 0.43
16 5 0.17
17 7 0.23
18 5 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTATATTTTATAAA
Found at i:1278013 original size:21 final size:21
Alignment explanation
Indices: 1277987--1278027 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1277977 CACTTGGGAT
1277987 TTTACAACAGCTGAAGCTACA
1 TTTACAACAGCTGAAGCTACA
1278008 TTTACAACAGCTGAAGCTAC
1 TTTACAACAGCTGAAGCTAC
1278028 CGTAACTCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (21 bp):
TTTACAACAGCTGAAGCTACA
Found at i:1279720 original size:16 final size:16
Alignment explanation
Indices: 1279699--1279732 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1279689 GTTTTGATAA
1279699 TAATT-ATTAAATATTT
1 TAATTAATTAAA-ATTT
1279715 TAATTAATTAAAATTT
1 TAATTAATTAAAATTT
1279731 TA
1 TA
1279733 TAATATTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAATTAATTAAAATTT
Found at i:1280081 original size:22 final size:21
Alignment explanation
Indices: 1280046--1280086 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1280036 TATTTTTATT
*
1280046 TAAATTTATTATAAAAATATA
1 TAAATTTAATATAAAAATATA
1280067 TAAATATTAATATAAAAATA
1 TAAAT-TTAATATAAAAATA
1280087 AATTTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TAAATTTAATATAAAAATATA
Found at i:1280659 original size:20 final size:19
Alignment explanation
Indices: 1280626--1280664 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
1280616 TATCTGATAA
*
1280626 TTTATTTATCATATTATTT
1 TTTATTTATAATATTATTT
1280645 TTTATATTATAATATTATTT
1 TTTAT-TTATAATATTATTT
1280665 AAAATATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTATTTATAATATTATTT
Found at i:1280696 original size:20 final size:18
Alignment explanation
Indices: 1280650--1280699 Score: 52
Period size: 20 Copynumber: 2.8 Consensus size: 18
1280640 TATTTTTTAT
1280650 ATTA-TAATATTATTTAAA
1 ATTATTAATA-TATTTAAA
1280668 A-TATT-ATATATTTATATA
1 ATTATTAATATATTTA-A-A
1280686 ATTATTAATATATT
1 ATTATTAATATATT
1280700 AATAATTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
16 6 0.22
17 6 0.22
18 4 0.15
19 4 0.15
20 7 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTATTAATATATTTAAA
Found at i:1280777 original size:10 final size:11
Alignment explanation
Indices: 1280744--1280782 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
1280734 TACTTATCTC
*
1280744 ATTTTTGTATT
1 ATTTTTATATT
1280755 AATTTTTATATT
1 -ATTTTTATATT
1280767 ATTTTTA-ATT
1 ATTTTTATATT
1280777 ATTTTT
1 ATTTTT
1280783 TTGAATCATG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 9 0.35
11 7 0.27
12 10 0.38
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (11 bp):
ATTTTTATATT
Found at i:1281893 original size:24 final size:25
Alignment explanation
Indices: 1281858--1281904 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
1281848 CAACTGTACT
*
1281858 AAAATAATATATATTA-TATTATTC
1 AAAATAATATATATAATTATTATTC
1281882 AAAAT-ATAATATATAATTATTAT
1 AAAATAAT-ATATATAATTATTAT
1281905 AAAAAAATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 2 0.10
24 12 0.60
25 6 0.30
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
AAAATAATATATATAATTATTATTC
Found at i:1281909 original size:24 final size:26
Alignment explanation
Indices: 1281861--1281910 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
1281851 CTGTACTAAA
* *
1281861 ATAATATATATTATATTATTCAAAAT
1 ATAATATATAATATATTATTAAAAAT
*
1281887 ATAATATATAAT-TATTATAAAAAA
1 ATAATATATAATATATTATTAAAAA
1281911 ATACACTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (26 bp):
ATAATATATAATATATTATTAAAAAT
Found at i:1282549 original size:21 final size:21
Alignment explanation
Indices: 1282523--1282562 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1282513 TTCCATCATT
1282523 TATCAATTTTATAG-CATAATG
1 TATCAATTTT-TAGACATAATG
1282544 TATCAATTTTTAGACATAA
1 TATCAATTTTTAGACATAA
1282563 GCAATCAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.42
Consensus pattern (21 bp):
TATCAATTTTTAGACATAATG
Found at i:1282569 original size:21 final size:21
Alignment explanation
Indices: 1282524--1282570 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
1282514 TCCATCATTT
*
1282524 ATCAATTTTATAGCATAATGT
1 ATCAATTTTATAGCATAATGA
1282545 ATCAATTTT-TAGACATAA-GCA
1 ATCAATTTTATAG-CATAATG-A
1282566 ATCAA
1 ATCAA
1282571 GTTGGTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.36
Consensus pattern (21 bp):
ATCAATTTTATAGCATAATGA
Found at i:1283177 original size:23 final size:22
Alignment explanation
Indices: 1283151--1283195 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1283141 ATAAGTATTA
1283151 TTTAATAAATTTAAAATTTTAAT
1 TTTAAT-AATTTAAAATTTTAAT
* *
1283174 TTTAATAATTTTAATTTTTAAT
1 TTTAATAATTTAAAATTTTAAT
1283196 CTATTTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTAATAATTTAAAATTTTAAT
Found at i:1283185 original size:15 final size:14
Alignment explanation
Indices: 1283160--1283191 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
1283150 ATTTAATAAA
1283160 TTTAAAATTTTAAT
1 TTTAAAATTTTAAT
1283174 TTTAATAATTTTAAT
1 TTTAA-AATTTTAAT
1283189 TTT
1 TTT
1283192 TAATCTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTAAAATTTTAAT
Found at i:1283651 original size:3 final size:3
Alignment explanation
Indices: 1283643--1283685 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
1283633 CGACAACATC
1283643 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1283686 CTTTAAATGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1283854 original size:3 final size:3
Alignment explanation
Indices: 1283846--1283870 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1283836 GCAAACCTTT
1283846 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
1283871 AAAAAATGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1284450 original size:29 final size:26
Alignment explanation
Indices: 1284402--1284457 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 26
1284392 TTAATTAAAA
*
1284402 TATTTTTATTAAATGATAATATCTAT
1 TATTTTTATTAAATGATAATAACTAT
*
1284428 TATTATTTATTACATGATTTAATAACTAT
1 TATT-TTTATTAAATGA--TAATAACTAT
1284457 T
1 T
1284458 GAAATAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 4 0.16
27 11 0.44
29 10 0.40
ACGTcount: A:0.38, C:0.05, G:0.04, T:0.54
Consensus pattern (26 bp):
TATTTTTATTAAATGATAATAACTAT
Found at i:1285500 original size:7 final size:8
Alignment explanation
Indices: 1285484--1285558 Score: 50
Period size: 8 Copynumber: 9.9 Consensus size: 8
1285474 AATGATAATA
1285484 TATATTAT
1 TATATTAT
1285492 TAT-TTAT
1 TATATTAT
1285499 TATATTAT
1 TATATTAT
*
1285507 T-TAATA-
1 TATATTAT
** *
1285513 TCCATTAG
1 TATATTAT
* *
1285521 AATAATAT
1 TATATTAT
*
1285529 TTTATTAT
1 TATATTAT
1285537 TATATTA-
1 TATATTAT
1285544 TATATTAT
1 TATATTAT
*
1285552 AATATTA
1 TATATTA
1285559 GGATTATATT
Statistics
Matches: 50, Mismatches: 13, Indels: 8
0.70 0.18 0.11
Matches are distributed among these distances:
6 1 0.02
7 21 0.42
8 28 0.56
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (8 bp):
TATATTAT
Found at i:1285551 original size:15 final size:15
Alignment explanation
Indices: 1285482--1285558 Score: 50
Period size: 15 Copynumber: 5.1 Consensus size: 15
1285472 TAAATGATAA
1285482 TATATATTATTAT-T
1 TATATATTATTATAT
*
1285496 TATTATATTATT-TAA
1 TA-TATATTATTATAT
** ** *
1285511 TATCCATTAGAATAA
1 TATATATTATTATAT
*
1285526 TATTTTATTATTATAT
1 TA-TATATTATTATAT
*
1285542 TATATATTATAATAT
1 TATATATTATTATAT
1285557 TA
1 TA
1285559 GGATTATATT
Statistics
Matches: 47, Mismatches: 12, Indels: 7
0.71 0.18 0.11
Matches are distributed among these distances:
14 8 0.17
15 29 0.62
16 10 0.21
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (15 bp):
TATATATTATTATAT
Found at i:1287836 original size:16 final size:15
Alignment explanation
Indices: 1287771--1287836 Score: 53
Period size: 16 Copynumber: 4.1 Consensus size: 15
1287761 TTTTTTAAAT
1287771 ATTTTATATTTATATA
1 ATTTTATATTTAT-TA
* *
1287787 AATTTA-ATATATTA
1 ATTTTATATTTATTA
*
1287801 ATAATTTATATTATTTTA
1 AT--TTTATATT-TATTA
1287819 ATTTTATATTTATGTA
1 ATTTTATATTTAT-TA
1287835 AT
1 AT
1287837 ATTGAAGCTT
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
14 3 0.08
15 7 0.18
16 21 0.54
17 2 0.05
18 6 0.15
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (15 bp):
ATTTTATATTTATTA
Found at i:1292871 original size:2 final size:2
Alignment explanation
Indices: 1292808--1292859 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
1292798 ATTAAAAAGG
* * *
1292808 AT AT AC AT AT AT GT GT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1292850 AT AT AT AT AT
1 AT AT AT AT AT
1292860 TAAGTTATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1294333 original size:2 final size:2
Alignment explanation
Indices: 1294326--1294353 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1294316 CATAAAATTC
1294326 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1294354 TTAAAAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1296294 original size:2 final size:2
Alignment explanation
Indices: 1296287--1296319 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1296277 TATAGATACA
1296287 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1296320 GAGAGAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1296324 original size:2 final size:2
Alignment explanation
Indices: 1296319--1296356 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1296309 ATATATATAT
1296319 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1296357 GCAACATAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1298266 original size:23 final size:23
Alignment explanation
Indices: 1298235--1298304 Score: 113
Period size: 23 Copynumber: 3.0 Consensus size: 23
1298225 AGTATTCCTA
1298235 GTATTAATGTAAAGTGAAAGATT
1 GTATTAATGTAAAGTGAAAGATT
* *
1298258 GTATCAATGGAAAGTGAAAGATT
1 GTATTAATGTAAAGTGAAAGATT
*
1298281 GTATTAATGTGAAGTGAAAGATT
1 GTATTAATGTAAAGTGAAAGATT
1298304 G
1 G
1298305 CATGGCATGC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.41, C:0.01, G:0.26, T:0.31
Consensus pattern (23 bp):
GTATTAATGTAAAGTGAAAGATT
Found at i:1299676 original size:27 final size:27
Alignment explanation
Indices: 1299643--1299697 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
1299633 ATATCACAAA
*
1299643 ATAATATTAATTTAATGCTAATAAAAT
1 ATAATATTAATTTAATACTAATAAAAT
*
1299670 ATAATATTAATTTAATATTAATAAAAT
1 ATAATATTAATTTAATACTAATAAAAT
1299697 A
1 A
1299698 AAAAAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (27 bp):
ATAATATTAATTTAATACTAATAAAAT
Found at i:1300582 original size:21 final size:20
Alignment explanation
Indices: 1300554--1300592 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1300544 TATTTTATTT
1300554 AAATTTAAT-TATAAAATATA
1 AAATTTAATAT-TAAAATATA
1300574 AAATATTAATATTAAAATA
1 AAAT-TTAATATTAAAATA
1300593 ATTTTTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 12 0.71
22 1 0.06
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATTTAATATTAAAATATA
Found at i:1301172 original size:17 final size:17
Alignment explanation
Indices: 1301132--1301174 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
1301122 AAAATTGTAT
* *
1301132 TTTTATA-TTCTATTTA
1 TTTTATATTTCAATTCA
*
1301148 TGTTATATTTCAATTCA
1 TTTTATATTTCAATTCA
1301165 TTTTATATTT
1 TTTTATATTT
1301175 TACATAATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.65
Consensus pattern (17 bp):
TTTTATATTTCAATTCA
Found at i:1301378 original size:23 final size:22
Alignment explanation
Indices: 1301352--1301399 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
1301342 TTATTTCTCA
*
1301352 TTTTGTATCATGTTTTG-ATTATT
1 TTTTATATCAT-TTTTGTATT-TT
*
1301375 TTTTATATTATTTTTGTATTTT
1 TTTTATATCATTTTTGTATTTT
1301397 TTT
1 TTT
1301400 ATTTCATCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.17, C:0.02, G:0.08, T:0.73
Consensus pattern (22 bp):
TTTTATATCATTTTTGTATTTT
Found at i:1301729 original size:7 final size:7
Alignment explanation
Indices: 1301714--1301751 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
1301704 AGTAGAGGGC
1301714 TTTTT-T
1 TTTTTAT
1301720 TTTTTAT
1 TTTTTAT
1301727 TTTTTAT
1 TTTTTAT
1301734 TTTTT-T
1 TTTTTAT
1301740 ATTTTTAT
1 -TTTTTAT
1301748 TTTT
1 TTTT
1301752 AAATTTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
6 6 0.21
7 22 0.76
8 1 0.03
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTAT
Found at i:1301731 original size:8 final size:8
Alignment explanation
Indices: 1301714--1301745 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
1301704 AGTAGAGGGC
1301714 TTTT-TTT
1 TTTTATTT
1301721 TTTTA-TT
1 TTTTATTT
1301728 TTTTATTT
1 TTTTATTT
1301736 TTTTATTT
1 TTTTATTT
1301744 TT
1 TT
1301746 ATTTTTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 11 0.48
8 12 0.52
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (8 bp):
TTTTATTT
Found at i:1301736 original size:14 final size:14
Alignment explanation
Indices: 1301714--1301751 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
1301704 AGTAGAGGGC
1301714 TTTT-TTTTTTTATT
1 TTTTATTTTTTTA-T
1301728 TTTTATTTTTTTAT
1 TTTTATTTTTTTAT
1301742 TTTTATTTTT
1 TTTTATTTTT
1301752 AAATTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 15 0.65
15 8 0.35
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (14 bp):
TTTTATTTTTTTAT
Found at i:1301757 original size:14 final size:14
Alignment explanation
Indices: 1301714--1301758 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
1301704 AGTAGAGGGC
*
1301714 TTTTT-TTTTTTAT
1 TTTTTATTTTTTAA
*
1301727 TTTTTATTTTTTTA
1 TTTTTATTTTTTAA
*
1301741 TTTTTATTTTTAAA
1 TTTTTATTTTTTAA
1301755 TTTT
1 TTTT
1301759 AAACTATTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
13 5 0.19
14 22 0.81
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTATTTTTTAA
Found at i:1302588 original size:30 final size:29
Alignment explanation
Indices: 1302554--1302619 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 29
1302544 AGAGCTTTCA
1302554 TAAATATAAATCAAAAATA-AATAATTTATT
1 TAAATA-AAAT-AAAAATATAATAATTTATT
* *
1302584 TAAATACAATAAAAATATAATTATTTATT
1 TAAATAAAATAAAAATATAATAATTTATT
1302613 TAAATAA
1 TAAATAA
1302620 TTCGAGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 7 0.22
29 19 0.59
30 6 0.19
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (29 bp):
TAAATAAAATAAAAATATAATAATTTATT
Found at i:1304802 original size:2 final size:2
Alignment explanation
Indices: 1304795--1304846 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
1304785 TTCACAGTCA
1304795 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1304837 AG AG A- AG AG A
1 AG AG AG AG AG A
1304847 CCTATGGGTA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1310621 original size:22 final size:22
Alignment explanation
Indices: 1310576--1310617 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1310566 TTAATTGGAT
*
1310576 TTATTTGATTAAATTTAAATTA
1 TTATTTGATTAAATTAAAATTA
*
1310598 TTATTT-ATTATATTAAAATT
1 TTATTTGATTAAATTAAAATT
1310618 TATTTTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
TTATTTGATTAAATTAAAATTA
Found at i:1311394 original size:17 final size:18
Alignment explanation
Indices: 1311349--1311393 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
1311339 TTTATTCTTT
*
1311349 TATTTTATTTTAATAAAT
1 TATTTTATTTTAATAAAA
*
1311367 TA-TATATTTTAATAAAA
1 TATTTTATTTTAATAAAA
1311384 TATTTTATTT
1 TATTTTATTT
1311394 ATATTCTCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TATTTTATTTTAATAAAA
Found at i:1311617 original size:22 final size:22
Alignment explanation
Indices: 1311554--1311617 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 22
1311544 AAATTTTTAT
1311554 AAATTTTAATATAAATAATAATATCA
1 AAATTTTAAT-T--ATAA-AATATCA
* *
1311580 AAATATTT-ATTTTAAAATATTA
1 AAAT-TTTAATTATAAAATATCA
1311602 AAATTTTAATTATAAA
1 AAATTTTAATTATAAA
1311618 TAATATAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
21 3 0.09
22 17 0.52
23 3 0.09
25 1 0.03
26 6 0.18
27 3 0.09
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
AAATTTTAATTATAAAATATCA
Found at i:1312166 original size:28 final size:28
Alignment explanation
Indices: 1312105--1312167 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
1312095 CTTTGGTCTG
* *
1312105 ATTTCTTAATTTGTTGATTTTTACGTTT
1 ATTTTTTAATTCGTTGATTTTTACGTTT
* *
1312133 AATTTTTAATTCGTTGATTTTTGC-TTCT
1 ATTTTTTAATTCGTTGATTTTTACGTT-T
1312161 ATTTTTT
1 ATTTTTT
1312168 TTTTGCTCTC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 2 0.07
28 27 0.93
ACGTcount: A:0.17, C:0.08, G:0.10, T:0.65
Consensus pattern (28 bp):
ATTTTTTAATTCGTTGATTTTTACGTTT
Found at i:1312172 original size:17 final size:17
Alignment explanation
Indices: 1312150--1312193 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
1312140 AATTCGTTGA
1312150 TTTTTGCTTCTATTTTT
1 TTTTTGCTTCTATTTTT
*
1312167 TTTTTGC-TCTCTTTTT
1 TTTTTGCTTCTATTTTT
*
1312183 TTTTTCCTTCT
1 TTTTTGCTTCT
1312194 TTTATGTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.02, C:0.18, G:0.05, T:0.75
Consensus pattern (17 bp):
TTTTTGCTTCTATTTTT
Found at i:1323095 original size:26 final size:24
Alignment explanation
Indices: 1323012--1323114 Score: 93
Period size: 24 Copynumber: 4.2 Consensus size: 24
1323002 TAAATCAAAA
* *
1323012 AAATAATATTTTTAAGTAAAAATT
1 AAATAATTTTTTTAAATAAAAATT
* **
1323036 AAA-AAGTTTTTTTAAATAGAAGGT
1 AAATAA-TTTTTTTAAATAAAAATT
* * *
1323060 GAGTAA-TTTTTTACATGTAAAAATT
1 AAATAATTTTTTTA-A-ATAAAAATT
1323085 AAATAATTTTTTTAAATAAAAATT
1 AAATAATTTTTTTAAATAAAAATT
1323109 AAATAA
1 AAATAA
1323115 ATTATTATTA
Statistics
Matches: 60, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
23 9 0.15
24 32 0.53
25 12 0.20
26 7 0.12
ACGTcount: A:0.50, C:0.01, G:0.08, T:0.41
Consensus pattern (24 bp):
AAATAATTTTTTTAAATAAAAATT
Found at i:1324374 original size:20 final size:20
Alignment explanation
Indices: 1324337--1324376 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1324327 AATTAAATAA
*
1324337 TAAATAATTTATTTAAGAGT
1 TAAATAATTTATTAAAGAGT
1324357 TAAATAATTT-TTAAAAGAGT
1 TAAATAATTTATT-AAAGAGT
1324377 AATTTGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.42
Consensus pattern (20 bp):
TAAATAATTTATTAAAGAGT
Found at i:1324397 original size:17 final size:16
Alignment explanation
Indices: 1324365--1324407 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
1324355 GTTAAATAAT
1324365 TTTTAAAAGAGTAATT-
1 TTTTAAAA-AGTAATTC
1324381 TGTTTAAAAAGTAAATTC
1 T-TTTAAAAAGT-AATTC
1324399 TTTTAAAAA
1 TTTTAAAAA
1324408 TAAGATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 4 0.17
17 19 0.79
18 1 0.04
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (16 bp):
TTTTAAAAAGTAATTC
Found at i:1328696 original size:22 final size:22
Alignment explanation
Indices: 1328668--1328718 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
1328658 TATAAATATC
*
1328668 AATACTTTTTTCA-CAAGGTATT
1 AATACTTTTAT-ATCAAGGTATT
1328690 AATAC-TTTATATCAAGGTATT
1 AATACTTTTATATCAAGGTATT
*
1328711 GATACTTT
1 AATACTTT
1328719 GCTCCTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 1 0.04
21 17 0.68
22 7 0.28
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (22 bp):
AATACTTTTATATCAAGGTATT
Found at i:1331168 original size:24 final size:22
Alignment explanation
Indices: 1331112--1331160 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
1331102 TGGACATGTT
1331112 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
1331134 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
1331156 AAAAA
1 AAAAA
1331161 AATGCATGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.67, C:0.08, G:0.08, T:0.16
Consensus pattern (22 bp):
AAAAATGCATGAAACATAATAA
Found at i:1332128 original size:20 final size:20
Alignment explanation
Indices: 1332081--1332155 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
1332071 AAAAAAACAT
* ** *
1332081 AATGTATTGATACATTGTAG
1 AATGTATCGATACATTCAAA
* *
1332101 AATATATCGATACATTCATA
1 AATGTATCGATACATTCAAA
* * *
1332121 TATGTATCGATATATTGAAA
1 AATGTATCGATACATTCAAA
1332141 AATGTATCGATACAT
1 AATGTATCGATACAT
1332156 CAAGGTAAAA
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.37
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:1332149 original size:40 final size:39
Alignment explanation
Indices: 1332078--1332155 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
1332068 GGTAAAAAAA
* * *
1332078 CATAATGTATTGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
1332117 CATATATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
1332156 CAAGGTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:1332866 original size:28 final size:28
Alignment explanation
Indices: 1332785--1335441 Score: 2531
Period size: 28 Copynumber: 92.8 Consensus size: 28
1332775 AAAGAGTGTT
* * *
1332785 ACTGACTTGCGTGAGCTTTAAAAGGGTGCC
1 ACTGACTT--GTGGGCTTTGAAAGGATGCC
*
1332815 ACTGACTTGCGTGGGCTTTAAAAGGATGCC
1 ACTGACTT--GTGGGCTTTGAAAGGATGCC
* *
1332845 ACTGACTCGTGGGCTTTGAAA-GAGTGCT
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
*
1332873 ACTAACTTGTGGGCTTTGAAAGG-TGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
* *
1332900 ACTGACTCGTGGGCTTTGAAAAGG-TACC
1 ACTGACTTGTGGGCTTTG-AAAGGATGCC
* * *
1332928 ACTGACTCGTGGGC-CTGAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
1332955 ACTGACTTGTGGGCTTTGAAA-GAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
*
1332983 ACTGACTCGTGGGCTTTGAAAAGG-TGCC
1 ACTGACTTGTGGGCTTTG-AAAGGATGCC
* *
1333011 ATTGACTTGCGTGGGCTTTGAAAGGAGTGTC
1 ACTGACTT--GTGGGCTTTGAAAGGA-TGCC
* *
1333042 ACTGACTTGTGTGGGCTTTGAAAGGGTGTC
1 ACTGAC-T-TGTGGGCTTTGAAAGGATGCC
* *
1333072 ACTAACTCGTGGGCTTTGAAAGGATGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
1333100 ACTGACTTGTGGGCTTTGAAA-GAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
* *
1333128 ACTGACTCGTGGGCTTTGAAAAGG-TACC
1 ACTGACTTGTGGGCTTTG-AAAGGATGCC
* *
1333156 ACTGACTTGCGTGAGCTTTAAAAGGAGTGCC
1 ACTGACTT--GTGGGCTTTGAAAGGA-TGCC
** *
1333187 ACTGACTTGTGTGGGCTTCAAAAGGGTGCC
1 ACTGAC-T-TGTGGGCTTTGAAAGGATGCC
1333217 ACTGACTTGTGGGCTTTGAAA-GAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
* * *
1333245 ACTGAATTGTGGGCTTCGCAATGG-TGCC
1 ACTGACTTGTGGGCTTTG-AAAGGATGCC
** *
1333273 ACTGACTTGTGGGCTTCAAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
1333301 ACTGACTTGTGGGCTTTGAAAAGG-TGCC
1 ACTGACTTGTGGGCTTTG-AAAGGATGCC
* *
1333329 ACTAACTTGTGGGCTTTGAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
* *
1333357 ACTGATTTGTGGGCTTTGAAAAGAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
* *
1333386 ACTGATTTGTGGGCTTTGAAAAGAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
*
1333415 ACTAACTTGTGGGCTTTGAAAGGAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
1333444 ACTGACTTGTGGGCTTTGAAAGGAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
* *
1333473 ACTGACTTGTGTGGGCTTTAAAAGGGTGCC
1 ACTGAC-T-TGTGGGCTTTGAAAGGATGCC
1333503 ACTGACTTGTGGGCTTTGAAA-GAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
* * *
1333531 ACTGAATTGTGGGCTTCGCAATGG-TGCC
1 ACTGACTTGTGGGCTTTG-AAAGGATGCC
* *
1333559 ACTGACTTGTGGGCTTCGAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
*
1333587 ACTGACTTGCGTGGGCTTTGAAAAGGGTGCC
1 ACTGACTT--GTGGGCTTTG-AAAGGATGCC
*
1333618 ACTGACTTGTGGGCTTTGAAAAGGGTGCC
1 ACTGACTTGTGGGCTTTG-AAAGGATGCC
* *
1333647 ATTGACTTGTGGGCTTTGAAAAGAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
* * *
1333676 ACTAACTTGTGGGCTTTAAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
* *
1333704 ACTAACTTGCGTGGGCTTTGAAAGGGGTGCC
1 ACTGACTT--GTGGGCTTTGAAA-GGATGCC
*
1333735 ACTGACTTGTGGGCTTTGAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
*
1333763 ACCGACTTGTGTGGGCTTTGAAAGGATGCC
1 ACTGAC-T-TGTGGGCTTTGAAAGGATGCC
1333793 ACTGACTTGTGGGCTTTGAAA-GAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
*
1333821 ACTGACTTGTGGGCTTTGAAAAGG-TACC
1 ACTGACTTGTGGGCTTTG-AAAGGATGCC
* * * *
1333849 ACTGACTTGCGTGAGTTTTAAAAAGAGTGCC
1 ACTGACTT--GTGGGCTTTGAAAGGA-TGCC
* * *
1333880 AATGACTTGTGTGGGCTTTAAAAGGGTGCC
1 ACTGAC-T-TGTGGGCTTTGAAAGGATGCC
1333910 ACTGACTTGTGGGCTTTGAAA-GAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
* * * *
1333938 ACTAAATTGTGGGCTTCGCAATGG-TGCC
1 ACTGACTTGTGGGCTTTG-AAAGGATGCC
* * *
1333966 ACTGACTTGTGGGCTTCGAAAGGGTGCT
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
* *
1333994 ACTGACTTATGGGCTCTGAAAAGG-TGCC
1 ACTGACTTGTGGGCTTTG-AAAGGATGCC
* * *
1334022 ACTAACTTGTGGGCTTTGAAAGGGTGCT
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
* *
1334050 ACTGACTTGTGGGCTTTGAAAAGAGTGGC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
* *
1334079 ACTGATTTGTGGGCTTTGAAAAGAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
1334108 ACTGACTTGTGGGCTTTGAAAGGAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
* *
1334137 ACTGACTTGTGTGGGCTTTAAAAGGGTGCC
1 ACTGAC-T-TGTGGGCTTTGAAAGGATGCC
1334167 ACTGACTTGTGGGCTTTGAAA-GAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
* * *
1334195 ACTGAATTGTGGGCTTCGCAATGG-TGCC
1 ACTGACTTGTGGGCTTTG-AAAGGATGCC
* *
1334223 ACTGACTTGTGGGCTTCGAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
*
1334251 ACTGACTTGCGTGGGCTTTGAAAAGGGTGCC
1 ACTGACTT--GTGGGCTTTG-AAAGGATGCC
*
1334282 ACTGACTTGTGGGCTTTGAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
*
1334310 ACTGACTTGTGGGCTTTGAAAAGAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
* * *
1334339 ACTAACTTGTGGGCTTTAAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
* *
1334367 ACTAACTTGCGTGGGCTTTGAAAGGGGTGCC
1 ACTGACTT--GTGGGCTTTGAAA-GGATGCC
1334398 ACTGACTTGTGGGCTTTGAAAGGATGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
*
1334426 ACCGACTTGTGTGGGCTTTGAAAGGATGCC
1 ACTGAC-T-TGTGGGCTTTGAAAGGATGCC
*
1334456 ACTGACTTGTGGGCTTTGAAAAGAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
* *
1334485 ACTGATTTGTGGGCTTTGAAAAGAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
*
1334514 ACTGACTTTTGGGCTTTGAAAGGAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
1334543 ACTGACTTGTGGGCTTTGAAAGGAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
* *
1334572 ACTGACTTGTGTGGGCTTTAAAAGGGTGCC
1 ACTGAC-T-TGTGGGCTTTGAAAGGATGCC
1334602 ACTGACTTGTGGGCTTTGAAA-GAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
* * **
1334630 ACTGAATTGTGGGCTTCGCATTGG-TGCC
1 ACTGACTTGTGGGCTTTG-AAAGGATGCC
* *
1334658 ACTGACTTGTGGGCTTCGAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
*
1334686 ACTGACTTGCGTGGGCTTTGAAAAGGGTGCC
1 ACTGACTT--GTGGGCTTTG-AAAGGATGCC
*
1334717 ACTGACTTGTGGGCTTTGAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
*
1334745 ACTGACTTGTGGGCTTTGAAAAGAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
* * *
1334774 ACTAACTTGTGGGCTTTAAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
* *
1334802 ACTAACTTGCGTGGGCTTTGAAAGGGGTGCC
1 ACTGACTT--GTGGGCTTTGAAA-GGATGCC
*
1334833 ACTGACTTGTGGGCTTTGAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
*
1334861 ACCGACTTGTGTGGGCTTTGAAAGGATGCC
1 ACTGAC-T-TGTGGGCTTTGAAAGGATGCC
*
1334891 ACTGACTTGTGGGCTTTGAAAAGAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
* *
1334920 ACTGATTTGTGGGCTTTGAAAAGAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
*
1334949 ACTAACTTGTGGGCTTTGAAAGGAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
*
1334978 ACTGACTTGTGGGCTTTGAAAGGAGTTCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
* * *
1335007 ACTGACTTGTGTGGGCTTTAAAAGGGTGCT
1 ACTGAC-T-TGTGGGCTTTGAAAGGATGCC
1335037 ACTGACTTGTGGGCTTTGAAA-GAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
* * *
1335065 ACTGAATTGTGGGCTTCGCAATGG-TGCC
1 ACTGACTTGTGGGCTTTG-AAAGGATGCC
* *
1335093 ACTGACTTGTGGGCTTCGAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
* * * *
1335121 ACTGAGTTGT-GGATTTAAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
* * * * *
1335148 ACAGAGTTGTGGAC-TTAAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
* * * ** *
1335175 ACGGAGTTGTGGAC-TAAAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
* * * * *
1335202 ACGGAGTTGTGGACTTTAAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
* * * *
1335230 ACAGAGTTGTGGAC-TTAAAAGAGATGCC
1 ACTGACTTGTGGGCTTTGAAAG-GATGCC
* * * * * *
1335258 ACGGAGTTATGGAC-TTAAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
* * * * *
1335285 ACGGAGTTGTGGAC-TTAAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
* * * *
1335312 ACGGAGTTGTGGTC-TTAAAAGGGATGCC
1 ACTGACTTGTGGGCTTTGAAA-GGATGCC
* * * * *
1335340 ACGGAGTTGTGGAC-TTAAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
* * * * *
1335367 ACGGAGTTGTGGAC-TTAAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
* * * * *
1335394 ACGGAGTTGTGGAC-TTAAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
* *
1335421 ACGGAGTTGTGGGCTTT-AAAG
1 ACTGACTTGTGGGCTTTGAAAG
1335442 AGGTCACACT
Statistics
Matches: 2314, Mismatches: 209, Indels: 211
0.85 0.08 0.08
Matches are distributed among these distances:
26 5 0.00
27 292 0.13
28 948 0.41
29 564 0.24
30 278 0.12
31 221 0.10
32 3 0.00
33 3 0.00
ACGTcount: A:0.22, C:0.18, G:0.33, T:0.28
Consensus pattern (28 bp):
ACTGACTTGTGGGCTTTGAAAGGATGCC
Found at i:1333118 original size:145 final size:141
Alignment explanation
Indices: 1332735--1335445 Score: 2761
Period size: 145 Copynumber: 18.9 Consensus size: 141
1332725 AGCTTGTGTA
** * * * ** *
1332735 GGCTTTGAAAAAAGTTGCCACTGAAACATGTGGGCTTTAAAAAGAGTGTTACTGACTTGCGTGAG
1 GGCTTTGAAAGGAG-TGCCACTG--ACTTGTGGGCTTT-GAAAGGGTGCCACTGACTT--GTGGG
* * * *
1332800 CTTTAAAAGGGTGCCACTGACTTGCGTGGGCTTTAAAAG-GATGCCACTGACTCGTGGGCTTTG-
60 CTTTGAAAGGATGCCACTGACTT--GTGGGCTTTGAAAGAG-TGCCACTGACTTGTGGGCTTTGA
* *
1332863 AAAGAGTGCTACTAACTTGTG
122 AAAG-GTGCCACTGACTTGTG
* * * * *
1332884 GGCTTTGAAA-G-GTGCCACTGACTCGTGGGCTTTGAAAAGGTACCACTGACTCGTGGGC-CTGA
1 GGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGA
* *
1332946 AAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCC
66 AAGGATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCC
*
1333011 ATTGACTTGCGTG
131 ACTGACTT--GTG
* * * *
1333024 GGCTTTGAAAGGAGTGTCACTGACTTGTGTGGGCTTTGAAAGGGTGTCACTAACTCGTGGGCTTT
1 GGCTTTGAAAGGAGTGCCACTGAC-T-TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTT
* *
1333089 GAAAGGATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTA
64 GAAAGGATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTG
1333154 CCACTGACTTGCGTG
129 CCACTGACTT--GTG
* * **
1333169 AGCTTTAAAAGGAGTGCCACTGACTTGTGTGGGCTTCAAAAGGGTGCCACTGACTTGTGGGCTTT
1 GGCTTTGAAAGGAGTGCCACTGAC-T-TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTT
* * * *
1333234 GAAA-GAGTGCCACTGAATTGTGGGCTTCGCAATG-GTGCCACTGACTTGTGGGC-TTCAAAAGG
64 GAAAGGA-TGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTGAAAA-G
1333296 GTGCCACTGACTTGTG
126 GTGCCACTGACTTGTG
* * *
1333312 GGCTTTGAAAAG-GTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGATTTGTGGGCTTTGA
1 GGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGA
* * * *
1333376 AAAGAGTGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGAGT
66 AAGGA-TGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTGAAAAG-GT
1333441 GCCACTGACTTGTG
128 GCCACTGACTTGTG
*
1333455 GGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTT
1 GGCTTTGAAAGGAGTGCCACTGAC-T-TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTT
* * * * *
1333520 GAAA-GAGTGCCACTGAATTGTGGGCTTCGCAATG-GTGCCACTGACTTGTGGGCTTCGAAAGGG
64 GAAAGGA-TGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGG
1333583 TGCCACTGACTTGCGTG
127 TGCCACTGACTT--GTG
*
1333600 GGCTTTGAAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCATTGACTTGTGGGCTTT
1 GGCTTTG-AAAGGAGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTT
* * * * * *
1333664 GAAAAGAGTGCCACTAACTTGTGGGCTTTAAAAGGGTGCCACTAACTTGCGTGGGCTTTGAAAGG
64 GAAAGGA-TGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTT--GTGGGCTTTGAAA-A
1333729 GGTGCCACTGACTTGTG
125 GGTGCCACTGACTTGTG
* *
1333746 GGCTTTGAAAGG-GTGCCACCGACTTGTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTT
1 GGCTTTGAAAGGAGTGCCACTGAC-T-TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTT
* * * *
1333810 GAAA-GAGTGCCACTGACTTGTGGGCTTTGAAA-AGGTACCACTGACTTGCGTGAGTTTTAAAAA
64 GAAAGGA-TGCCACTGACTTGTGGGCTTTGAAAGA-GTGCCACTGACTT--GTGGGCTTTGAAAA
*
1333873 GAGTGCCAATGACTTGTGTG
125 G-GTGCCACTGAC-T-TGTG
* * * * *
1333893 GGCTTTAAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTAAATTGTGGGCTTCGC
1 GGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-
* * * * * *
1333957 AATGG-TGCCACTGACTTGTGGGCTTCGAAAGGGTGCTACTGACTTATGGGCTCTGAAAAGGTGC
65 AAAGGATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGC
*
1334021 CACTAACTTGTG
130 CACTGACTTGTG
* * * *
1334033 GGCTTTGAAAGG-GTGCTACTGACTTGTGGGCTTTGAAAAGAGTGGCACTGATTTGTGGGCTTTG
1 GGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTG
*
1334097 AAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTT-AAAAG
65 AAAGGA-TGCCACTGACTTGTGGGCTTTGAAA-GAGTGCCACTGAC-T-TGTGGGCTTTGAAAA-
1334161 GGTGCCACTGACTTGTG
125 GGTGCCACTGACTTGTG
* * * * *
1334178 GGCTTTGAAA-GAGTGCCACTGAATTGTGGGCTTCGCAATGGTGCCACTGACTTGTGGGCTTCGA
1 GGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGA
* * *
1334242 AAGGGTGCCACTGACTTGCGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGT
66 AAGGATGCCACTGACTT--GTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGT
1334307 GCCACTGACTTGTG
128 GCCACTGACTTGTG
* * * *
1334321 GGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTAAAAGGGTGCCACTAACTTGCGTGGGCTTT
1 GGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTT--GTGGGCTTT
* *
1334386 GAAAGGGGTGCCACTGACTTGTGGGCTTTGAAAG-GATGCCACCGACTTGTGTGGGCTTTG-AAA
64 GAAA-GGATGCCACTGACTTGTGGGCTTTGAAAGAG-TGCCACTGAC-T-TGTGGGCTTTGAAAA
1334449 GGATGCCACTGACTTGTG
125 GG-TGCCACTGACTTGTG
* * * *
1334467 GGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGACTTTTGGGCTTTG
1 GGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTG
1334532 AAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTT-AAAAG
65 AAAGGA-TGCCACTGACTTGTGGGCTTTGAAA-GAGTGCCACTGAC-T-TGTGGGCTTTGAAAA-
1334596 GGTGCCACTGACTTGTG
125 GGTGCCACTGACTTGTG
* * * ** *
1334613 GGCTTTGAAA-GAGTGCCACTGAATTGTGGGCTTCGCATTGGTGCCACTGACTTGTGGGCTTCGA
1 GGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGA
* * *
1334677 AAGGGTGCCACTGACTTGCGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGT
66 AAGGATGCCACTGACTT--GTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGT
1334742 GCCACTGACTTGTG
128 GCCACTGACTTGTG
* * * *
1334756 GGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTAAAAGGGTGCCACTAACTTGCGTGGGCTTT
1 GGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTT--GTGGGCTTT
* * *
1334821 GAAAGGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACCGACTTGTGTGGGCTTTG-AAAG
64 GAAA-GGATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGAC-T-TGTGGGCTTTGAAAAG
1334885 GATGCCACTGACTTGTG
126 G-TGCCACTGACTTGTG
* * * *
1334902 GGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTG
1 GGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTG
*
1334967 AAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTTCCACTGACTTGTGTGGGCTTT-AAAAG
65 AAAGGA-TGCCACTGACTTGTGGGCTTTGAAA-GAGTGCCACTGAC-T-TGTGGGCTTTGAAAA-
*
1335031 GGTGCTACTGACTTGTG
125 GGTGCCACTGACTTGTG
* * * * *
1335048 GGCTTTGAAA-GAGTGCCACTGAATTGTGGGCTTCGCAATGGTGCCACTGACTTGTGGGCTTCGA
1 GGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGA
* * * * * * * *
1335112 AAGGGTGCCACTGAGTTGT-GGATTTAAAAGGGTGCCACAGAGTTGTGGAC-TT-AAAAGGGTGC
66 AAGGATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAA-GGTGC
* *
1335174 CACGGAGTTGTG
130 CACTGACTTGTG
* ** * * * * * * * *
1335186 GAC-TAAAAAGG-GTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGAC-TTAA
1 GGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGA
* * * * * * * * *
1335248 AAGAGATGCCACGGAGTTATGGAC-TTAAAAGGGTGCCACGGAGTTGTGGAC-TT-AAAAGGGTG
66 AAG-GATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAA-GGTG
* *
1335310 CCACGGAGTTGTG
129 CCACTGACTTGTG
* * * * * * * * * *
1335323 GTC-TTAAAAGG-GATGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGAC-TTA
1 GGCTTTGAAAGGAG-TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
* * * * * * * *
1335384 AAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGGCTTT-AAAGAGGT
65 AAAGGATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAA-AGGT
1335446 CACACTACTA
Statistics
Matches: 2249, Mismatches: 228, Indels: 182
0.85 0.09 0.07
Matches are distributed among these distances:
136 49 0.02
137 155 0.07
138 89 0.04
139 11 0.00
140 112 0.05
141 67 0.03
142 80 0.04
143 213 0.09
144 318 0.14
145 663 0.29
146 349 0.16
147 118 0.05
148 15 0.01
149 10 0.00
ACGTcount: A:0.22, C:0.18, G:0.33, T:0.28
Consensus pattern (141 bp):
GGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGA
AAGGATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCC
ACTGACTTGTG
Found at i:1336787 original size:23 final size:24
Alignment explanation
Indices: 1336761--1336812 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
1336751 TTTTATTTTG
*
1336761 TTTTTGCACTTTTTCTTTTCA-TT
1 TTTTTGCACTTTTGCTTTTCAGTT
** *
1336784 TTTTTGTGCTTTTGCTTTTGAGTT
1 TTTTTGCACTTTTGCTTTTCAGTT
1336808 TTTTT
1 TTTTT
1336813 TTGTCATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.06, C:0.12, G:0.12, T:0.71
Consensus pattern (24 bp):
TTTTTGCACTTTTGCTTTTCAGTT
Found at i:1342973 original size:24 final size:22
Alignment explanation
Indices: 1342917--1342965 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
1342907 TGGACATGTT
1342917 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
1342939 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
1342961 AAAAA
1 AAAAA
1342966 AATGCATGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.67, C:0.08, G:0.08, T:0.16
Consensus pattern (22 bp):
AAAAATGCATGAAACATAATAA
Found at i:1343933 original size:20 final size:20
Alignment explanation
Indices: 1343886--1343960 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
1343876 AAAAAAACAT
* ** *
1343886 AATGTATTGATACATTGTAG
1 AATGTATCGATACATTCAAA
* *
1343906 AATATATCGATACATTCATA
1 AATGTATCGATACATTCAAA
* * *
1343926 TATGTATCGATATATTGAAA
1 AATGTATCGATACATTCAAA
1343946 AATGTATCGATACAT
1 AATGTATCGATACAT
1343961 CAAGGTAAAA
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.37
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:1343954 original size:40 final size:39
Alignment explanation
Indices: 1343883--1343960 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
1343873 GGTAAAAAAA
* * *
1343883 CATAATGTATTGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
1343922 CATATATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
1343961 CAAGGTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:1357002 original size:223 final size:224
Alignment explanation
Indices: 1356587--1357028 Score: 672
Period size: 223 Copynumber: 2.0 Consensus size: 224
1356577 AGACGGCACC
*
1356587 AAATTGTTGATATCCTTCCTCAGCCGGAGCTCGAACTGGGAGTTCTGCAAAAAGAAAAGGTCAGA
1 AAATTGTTGATATCCTTCCTCAGCCGGAGCTCGAACTGGGAGTTCTACAAAAAGAAAAGGTCAGA
* * * *
1356652 GGGGTCGCAGGAGTTTAGGACTTCAGTGCACTCTCCGATGCTTAAGTCAGAATTTTCTTGGGAGA
66 GGGGTAGCAGGAGTTTAGGACTTCAGCGCACTCTCCGATACTTAAGTCAGAATTTTCTTAGGAGA
* * * *
1356717 ACAGAATCCTCTCTACTTACACGAGCTGAGGGTTTTGCTCCTTACTTGCCTTGCGGGTGTTTCTC
131 ACAGAATCCTCTCTACTTACACGAGCTCAGGGTTTCGCTCCTTACCTCCCTTGCGGGTGTTTCTC
1356782 CCTTCTCCTATCATATCATGCACGACTCA
196 CCTTCTCCTATCATATCATGCACGACTCA
* * *
1356811 AAATTGTTGATGTCCTTCCTCAGTCGGAGCTCGAACTGGGAGTTCTACAAAAAGAAAATGTCAGA
1 AAATTGTTGATATCCTTCCTCAGCCGGAGCTCGAACTGGGAGTTCTACAAAAAGAAAAGGTCAGA
* * * *
1356876 GGGGTAGCTGGAGTTT-GGACTTCGGCGCA-TGCTCTGATACTTAAGTTAGAATTTTCTTAGGAG
66 GGGGTAGCAGGAGTTTAGGACTTCAGCGCACT-CTCCGATACTTAAGTCAGAATTTTCTTAGGAG
* *
1356939 AACAGAATCCTCTCTACTTACACGAGCTCAGGGTTTCGCTCGTTACCTCCCTTGTGGGTGTTTCT
130 AACAGAATCCTCTCTACTTACACGAGCTCAGGGTTTCGCTCCTTACCTCCCTTGCGGGTGTTTCT
* * *
1357004 CCTTTCTCTTATTATATCATGCACG
195 CCCTTCTCCTATCATATCATGCACG
1357029 GCTCTTCCTG
Statistics
Matches: 196, Mismatches: 21, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
222 1 0.01
223 120 0.61
224 75 0.38
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (224 bp):
AAATTGTTGATATCCTTCCTCAGCCGGAGCTCGAACTGGGAGTTCTACAAAAAGAAAAGGTCAGA
GGGGTAGCAGGAGTTTAGGACTTCAGCGCACTCTCCGATACTTAAGTCAGAATTTTCTTAGGAGA
ACAGAATCCTCTCTACTTACACGAGCTCAGGGTTTCGCTCCTTACCTCCCTTGCGGGTGTTTCTC
CCTTCTCCTATCATATCATGCACGACTCA
Found at i:1358725 original size:2 final size:2
Alignment explanation
Indices: 1358718--1358742 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1358708 TGATACATAA
1358718 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1358743 ATTATCTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1364069 original size:13 final size:13
Alignment explanation
Indices: 1364051--1364076 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1364041 TACACCAAGT
1364051 ATGTATCGATACA
1 ATGTATCGATACA
1364064 ATGTATCGATACA
1 ATGTATCGATACA
1364077 CCAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1364074 original size:32 final size:33
Alignment explanation
Indices: 1364033--1364096 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1364023 TAGCCAAACT
**
1364033 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACCAAAAATTGTATCGATACAA
1364065 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
1364097 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:1366322 original size:22 final size:22
Alignment explanation
Indices: 1366295--1366350 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
1366285 TTACAAGTTG
1366295 AAATAAAGAACTTGGCTAATG-A
1 AAATAAAGAACTTGGCTAA-GAA
* *
1366317 AAATAATGAA-TTAGCTAAGAA
1 AAATAAAGAACTTGGCTAAGAA
1366338 AAATAAA-AACTTG
1 AAATAAAGAACTTG
1366351 CATGATTCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
20 3 0.11
21 16 0.57
22 9 0.32
ACGTcount: A:0.55, C:0.07, G:0.14, T:0.23
Consensus pattern (22 bp):
AAATAAAGAACTTGGCTAAGAA
Found at i:1370274 original size:13 final size:13
Alignment explanation
Indices: 1370256--1370281 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1370246 ACATTTTTCT
1370256 TTGTATCGATACA
1 TTGTATCGATACA
1370269 TTGTATCGATACA
1 TTGTATCGATACA
1370282 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1372149 original size:17 final size:18
Alignment explanation
Indices: 1372102--1372146 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
1372092 GAATTACTTG
1372102 TTTAAGGGGGAGATTTTT
1 TTTAAGGGGGAGATTTTT
1372120 TTTAAGGGGGAGATTTTT
1 TTTAAGGGGGAGATTTTT
1372138 TTTAAGGGG
1 TTTAAGGGG
1372147 AGAATGCGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.22, C:0.00, G:0.36, T:0.42
Consensus pattern (18 bp):
TTTAAGGGGGAGATTTTT
Found at i:1372744 original size:18 final size:19
Alignment explanation
Indices: 1372723--1372763 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
1372713 AATTGTCAAA
1372723 ACAC-TTAAAAGTATCGAT
1 ACACATTAAAAGTATCGAT
*
1372741 ACACAATTCAAAGTATCGAT
1 ACAC-ATTAAAAGTATCGAT
1372761 ACA
1 ACA
1372764 TGTTGCAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
20 16 0.80
ACGTcount: A:0.46, C:0.20, G:0.10, T:0.24
Consensus pattern (19 bp):
ACACATTAAAAGTATCGAT
Found at i:1372862 original size:13 final size:13
Alignment explanation
Indices: 1372844--1372869 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1372834 TACACCAAGT
1372844 ATGTATCGATACA
1 ATGTATCGATACA
1372857 ATGTATCGATACA
1 ATGTATCGATACA
1372870 CCAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1372867 original size:32 final size:33
Alignment explanation
Indices: 1372826--1372889 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1372816 TAGCCAAACT
**
1372826 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACCAAAAATTGTATCGATACAA
1372858 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
1372890 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:1377449 original size:2 final size:2
Alignment explanation
Indices: 1377444--1377479 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1377434 ATTAAAACAT
1377444 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1377480 AAAGATGAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1379026 original size:2 final size:2
Alignment explanation
Indices: 1379019--1379059 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1379009 ACAAAATCTA
*
1379019 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1379060 AATGAGCTAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1379192 original size:112 final size:114
Alignment explanation
Indices: 1379076--1379281 Score: 267
Period size: 114 Copynumber: 1.8 Consensus size: 114
1379066 CTAGTTATTA
* * * *
1379076 AATTTTAAAAAAT-GAA-ATTATTATTTTATTCATAACTGGATATTTGGATAAAAGTTTAAAAA-
1 AATTTTAAAAAATAAAATATTATTATCTTATT-ATAACTGAATATTTGAATAAAAG-TTAAAAAT
* * *
1379138 ATATAATTTTAATTTTGTAATATA-TAATAATATATAAATTAATGAAAATT
64 ATATAATTCTAATATTATAATATATTAATAATATATAAATTAATGAAAATT
* * *
1379188 AATTTTAAAAAATAAAAATATTATTATCTTATTTTAATTGAATATTTTAATAAAAGTTAAAAATA
1 AATTTTAAAAAAT-AAAATATTATTATCTTATTATAACTGAATATTTGAATAAAAGTTAAAAATA
1379253 TATAATTCTAATATTATAATATATTAATA
65 TATAATTCTAATATTATAATATATTAATA
1379282 CATTATCATT
Statistics
Matches: 79, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
112 13 0.16
113 7 0.09
114 41 0.52
115 18 0.23
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.44
Consensus pattern (114 bp):
AATTTTAAAAAATAAAATATTATTATCTTATTATAACTGAATATTTGAATAAAAGTTAAAAATAT
ATAATTCTAATATTATAATATATTAATAATATATAAATTAATGAAAATT
Found at i:1381105 original size:15 final size:16
Alignment explanation
Indices: 1381078--1381109 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1381068 AATTAAAGGT
1381078 AATTAATAAAAATTAA
1 AATTAATAAAAATTAA
1381094 AATTAA-AAAAATTAA
1 AATTAATAAAAATTAA
1381109 A
1 A
1381110 GTAACTCTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AATTAATAAAAATTAA
Found at i:1381146 original size:34 final size:34
Alignment explanation
Indices: 1381085--1381163 Score: 99
Period size: 34 Copynumber: 2.3 Consensus size: 34
1381075 GGTAATTAAT
*
1381085 AAAAATTAAAATTAAAAAAATTAAAGTAACTC-TCA
1 AAAAATT-AAATTAAAAAAACTAAAGTAACTCAT-A
*
1381120 AAACAATTAAATT-AATAAACTAAAGTAACTCATA
1 AAA-AATTAAATTAAAAAAACTAAAGTAACTCATA
1381154 AAAAATTAAA
1 AAAAATTAAA
1381164 AATCATATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
33 7 0.17
34 20 0.50
35 9 0.22
36 4 0.10
ACGTcount: A:0.63, C:0.09, G:0.03, T:0.25
Consensus pattern (34 bp):
AAAAATTAAATTAAAAAAACTAAAGTAACTCATA
Found at i:1383960 original size:9 final size:9
Alignment explanation
Indices: 1383913--1383963 Score: 61
Period size: 9 Copynumber: 5.8 Consensus size: 9
1383903 CATTGATTTG
1383913 TTAATTTT-
1 TTAATTTTA
1383921 TTAATTTTA
1 TTAATTTTA
* *
1383930 ATATTTTTA
1 TTAATTTTA
1383939 TT-ATTTATA
1 TTAATTT-TA
1383948 TTAATTTTA
1 TTAATTTTA
1383957 TTAATTT
1 TTAATTT
1383964 AATTTTTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
8 11 0.31
9 21 0.58
10 4 0.11
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TTAATTTTA
Found at i:1383969 original size:33 final size:32
Alignment explanation
Indices: 1383913--1384013 Score: 86
Period size: 33 Copynumber: 3.1 Consensus size: 32
1383903 CATTGATTTG
1383913 TTAATTTT-TTAATTTTAATATTTTTATTATTTATA
1 TTAATTTTATTAA-TTT-A-ATTTTTATTATTTA-A
1383948 TTAATTTTATTAATTTAATTTTTA--ATTTAAA
1 TTAATTTTATTAATTTAATTTTTATTATTT-AA
**
1383979 TATAATATTTAAGAATTT-ATTTTTATT-TTTAA
1 T-TAAT-TTTATTAATTTAATTTTTATTATTTAA
1384011 TTA
1 TTA
1384014 TTATTTAATA
Statistics
Matches: 58, Mismatches: 2, Indels: 16
0.76 0.03 0.21
Matches are distributed among these distances:
31 8 0.14
32 15 0.26
33 19 0.33
34 1 0.02
35 11 0.19
36 4 0.07
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (32 bp):
TTAATTTTATTAATTTAATTTTTATTATTTAA
Found at i:1384238 original size:16 final size:16
Alignment explanation
Indices: 1384214--1384311 Score: 88
Period size: 16 Copynumber: 6.1 Consensus size: 16
1384204 ATCCGAACTT
* *
1384214 GAAATAGCCTGAACCC
1 GAAACAGCCCGAACCC
**
1384230 GAGGCAGCCCGAACCC
1 GAAACAGCCCGAACCC
* * *
1384246 AAAAAAGCCTGAACCC
1 GAAACAGCCCGAACCC
**
1384262 GAGGCAGCCCGAACCC
1 GAAACAGCCCGAACCC
* * *
1384278 AAAAAAGCCTGAACCC
1 GAAACAGCCCGAACCC
1384294 GAAACAGCCCGAACCC
1 GAAACAGCCCGAACCC
1384310 GA
1 GA
1384312 GAAAGCTTGA
Statistics
Matches: 60, Mismatches: 22, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
16 60 1.00
ACGTcount: A:0.38, C:0.37, G:0.21, T:0.04
Consensus pattern (16 bp):
GAAACAGCCCGAACCC
Found at i:1384242 original size:32 final size:32
Alignment explanation
Indices: 1384219--1384309 Score: 164
Period size: 32 Copynumber: 2.8 Consensus size: 32
1384209 AACTTGAAAT
1384219 AGCCTGAACCCGAGGCAGCCCGAACCCAAAAA
1 AGCCTGAACCCGAGGCAGCCCGAACCCAAAAA
1384251 AGCCTGAACCCGAGGCAGCCCGAACCCAAAAA
1 AGCCTGAACCCGAGGCAGCCCGAACCCAAAAA
**
1384283 AGCCTGAACCCGAAACAGCCCGAACCC
1 AGCCTGAACCCGAGGCAGCCCGAACCC
1384310 GAGAAAGCTT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 57 1.00
ACGTcount: A:0.36, C:0.40, G:0.21, T:0.03
Consensus pattern (32 bp):
AGCCTGAACCCGAGGCAGCCCGAACCCAAAAA
Found at i:1384317 original size:32 final size:32
Alignment explanation
Indices: 1384219--1384361 Score: 162
Period size: 32 Copynumber: 4.5 Consensus size: 32
1384209 AACTTGAAAT
**
1384219 AGCCTGAACCCGAGGCAGCCCGAACCCAAAAA
1 AGCCTGAACCCGAAACAGCCCGAACCCAAAAA
**
1384251 AGCCTGAACCCGAGGCAGCCCGAACCCAAAAA
1 AGCCTGAACCCGAAACAGCCCGAACCCAAAAA
* *
1384283 AGCCTGAACCCGAAACAGCCCGAACCCGAGAA
1 AGCCTGAACCCGAAACAGCCCGAACCCAAAAA
* * *
1384315 AGCTTGAATCCGGAAA-AGCCCAAACCCAAAAA
1 AGCCTGAA-CCCGAAACAGCCCGAACCCAAAAA
* * *
1384347 AACTTGAATCCGAAA
1 AGCCTGAACCCGAAA
1384362 GAATCCGAAC
Statistics
Matches: 98, Mismatches: 12, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
31 5 0.05
32 87 0.89
33 6 0.06
ACGTcount: A:0.41, C:0.34, G:0.20, T:0.06
Consensus pattern (32 bp):
AGCCTGAACCCGAAACAGCCCGAACCCAAAAA
Found at i:1384317 original size:64 final size:65
Alignment explanation
Indices: 1384219--1384393 Score: 176
Period size: 64 Copynumber: 2.7 Consensus size: 65
1384209 AACTTGAAAT
** * * ** *
1384219 AGCCTGAACCCGAGGCAGCCCGAACCCAAAAAAGCCTGAACCCGAG-GCAGCCCGAACCCAAAAA
1 AGCCTGAACCCGAAACAGCCCGAACCCGAGAAAGCCTGAACCCGAGAAAAGCCCAAACCCAAAAA
* *
1384283 AGCCTGAACCCGAAACAGCCCGAACCCGAGAAAGCTTGAATCCG-GAAAAGCCCAAACCCAAAAA
1 AGCCTGAACCCGAAACAGCCCGAACCCGAGAAAGCCTGAACCCGAGAAAAGCCCAAACCCAAAAA
* * * * ** *
1384347 AACTTGAATCCGAAAGAATCCGAACCCGAGAGAA-CCCGAACCCGAGA
1 AGCCTGAACCCGAAACAGCCCGAACCCGAGA-AAGCCTGAACCCGAGA
1384394 TGACCCAAAC
Statistics
Matches: 90, Mismatches: 18, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
63 1 0.01
64 85 0.94
65 4 0.04
ACGTcount: A:0.40, C:0.34, G:0.21, T:0.06
Consensus pattern (65 bp):
AGCCTGAACCCGAAACAGCCCGAACCCGAGAAAGCCTGAACCCGAGAAAAGCCCAAACCCAAAAA
Found at i:1384399 original size:16 final size:16
Alignment explanation
Indices: 1384356--1384393 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1384346 AAACTTGAAT
* *
1384356 CCGAAAGAATCCGAAC
1 CCGAGAGAACCCGAAC
1384372 CCGAGAGAACCCGAAC
1 CCGAGAGAACCCGAAC
1384388 CCGAGA
1 CCGAGA
1384394 TGACCCAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.34, G:0.24, T:0.03
Consensus pattern (16 bp):
CCGAGAGAACCCGAAC
Found at i:1384800 original size:21 final size:21
Alignment explanation
Indices: 1384763--1384802 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1384753 ATCAGAGTTT
*
1384763 AAAATAATATAATAAAATAAC
1 AAAATAATATAAAAAAATAAC
1384784 AAAATAA-ATTAAAAAAATA
1 AAAATAATA-TAAAAAAATA
1384803 TAAAAGCTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAATAATATAAAAAAATAAC
Found at i:1385794 original size:16 final size:16
Alignment explanation
Indices: 1385775--1385817 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
1385765 ACTTGAACCC
*
1385775 AAACCTGAACTCGAAT
1 AAACCTGAACCCGAAT
1385791 AAACCTGAACCCGAAT
1 AAACCTGAACCCGAAT
1385807 AAACCTGAACC
1 AAACCTGAACC
1385818 TAAATAAGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.44, C:0.30, G:0.12, T:0.14
Consensus pattern (16 bp):
AAACCTGAACCCGAAT
Found at i:1385823 original size:16 final size:16
Alignment explanation
Indices: 1385775--1385824 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
1385765 ACTTGAACCC
1385775 AAACCTGAA-CTCGAAT
1 AAACCTGAACCT-GAAT
*
1385791 AAACCTGAACCCGAAT
1 AAACCTGAACCTGAAT
*
1385807 AAACCTGAACCTAAAT
1 AAACCTGAACCTGAAT
1385823 AA
1 AA
1385825 GCACGAACCC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
16 29 0.97
17 1 0.03
ACGTcount: A:0.48, C:0.26, G:0.10, T:0.16
Consensus pattern (16 bp):
AAACCTGAACCTGAAT
Found at i:1385874 original size:32 final size:31
Alignment explanation
Indices: 1385788--1385874 Score: 93
Period size: 32 Copynumber: 2.7 Consensus size: 31
1385778 CCTGAACTCG
* * * * *
1385788 AATAAACCTGAACCCGAATAAACCTGAACCTA
1 AATAAACC-GAACCCAAAAAAATCTAAACCCA
*
1385820 AATAAGCACGAACCCAAAAAAATCTAAACCCA
1 AATAAAC-CGAACCCAAAAAAATCTAAACCCA
1385852 AATAAACTCGAACCCAAAAAAAT
1 AATAAAC-CGAACCCAAAAAAAT
1385875 TCGAACTCGA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
32 45 0.98
33 1 0.02
ACGTcount: A:0.54, C:0.26, G:0.07, T:0.13
Consensus pattern (31 bp):
AATAAACCGAACCCAAAAAAATCTAAACCCA
Found at i:1385878 original size:16 final size:15
Alignment explanation
Indices: 1385828--1385880 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 15
1385818 TAAATAAGCA
1385828 CGAACCCAAAAAAAT
1 CGAACCCAAAAAAAT
* *
1385843 CTAAACCCAAATAAACT
1 C-GAACCCAAA-AAAAT
1385860 CGAACCCAAAAAAATT
1 CGAACCCAAAAAAA-T
1385876 CGAAC
1 CGAAC
1385881 TCGAATGAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
15 4 0.13
16 22 0.71
17 5 0.16
ACGTcount: A:0.55, C:0.28, G:0.06, T:0.11
Consensus pattern (15 bp):
CGAACCCAAAAAAAT
Found at i:1385904 original size:16 final size:16
Alignment explanation
Indices: 1385883--1385913 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1385873 ATTCGAACTC
1385883 GAATGAACCCAAATCT
1 GAATGAACCCAAATCT
1385899 GAATGAACCCAAATC
1 GAATGAACCCAAATC
1385914 CGAACCTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.26, G:0.13, T:0.16
Consensus pattern (16 bp):
GAATGAACCCAAATCT
Found at i:1386411 original size:11 final size:11
Alignment explanation
Indices: 1386395--1386522 Score: 59
Period size: 11 Copynumber: 11.5 Consensus size: 11
1386385 AAATTATTTA
1386395 TATATTTATAT
1 TATATTTATAT
1386406 TATATTT-TAT
1 TATATTTATAT
* * *
1386416 ATATTTTTTAAAA
1 -TA-TATTTATAT
* *
1386429 TATATTTTTAA
1 TATATTTATAT
*
1386440 TATATTAATAAT
1 TATATTTAT-AT
1386452 T-TATATTATA-
1 TATAT-TTATAT
* *
1386462 TAAATTT-TAA
1 TATATTTATAT
1386472 TATATTTATAT
1 TATATTTATAT
*
1386483 TATA-TAATATT
1 TATATTTATA-T
* * *
1386494 TTTAATTATTTT
1 TATATTTA-TAT
1386506 TATATTTATAT
1 TATATTTATAT
1386517 TATATT
1 TATATT
1386523 ATTAGATCAT
Statistics
Matches: 86, Mismatches: 20, Indels: 22
0.67 0.16 0.17
Matches are distributed among these distances:
9 2 0.02
10 16 0.19
11 46 0.53
12 20 0.23
13 2 0.02
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1386470 original size:45 final size:44
Alignment explanation
Indices: 1386394--1386491 Score: 103
Period size: 45 Copynumber: 2.2 Consensus size: 44
1386384 TAAATTATTT
* * ** *
1386394 ATATATTTAT-ATTATATTTTATATATTTTTTAAAATATATTTTTA
1 ATATATTAATAATTATATATTATATAAATTTT--AATATATTTATA
1386439 ATATATTAATAATT-TATATTATATAAATTTTAATATATTTATA
1 ATATATTAATAATTATATATTATATAAATTTTAATATATTTATA
*
1386482 TTATA-TAATA
1 ATATATTAATA
1386492 TTTTTAATTA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
42 5 0.11
43 15 0.33
45 23 0.50
46 3 0.07
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (44 bp):
ATATATTAATAATTATATATTATATAAATTTTAATATATTTATA
Found at i:1386474 original size:32 final size:31
Alignment explanation
Indices: 1386428--1386521 Score: 99
Period size: 32 Copynumber: 3.1 Consensus size: 31
1386418 ATTTTTTAAA
* *
1386428 ATATATTTTTAATATATTAATAATTTATATT
1 ATATAATTTTAATATATTTATAATTTATATT
1386459 ATATAAATTTTAATATATTTAT-A-TTATA-T
1 ATAT-AATTTTAATATATTTATAATTTATATT
* *
1386488 A-ATATTTTTAAT-TATTTTTATATTTATATT
1 ATATAATTTTAATATATTTATA-ATTTATATT
1386518 ATAT
1 ATAT
1386522 TATTAGATCA
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
26 6 0.11
27 8 0.15
28 3 0.06
29 7 0.13
30 7 0.13
31 7 0.13
32 15 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (31 bp):
ATATAATTTTAATATATTTATAATTTATATT
Found at i:1386482 original size:25 final size:27
Alignment explanation
Indices: 1386444--1386537 Score: 104
Period size: 25 Copynumber: 3.4 Consensus size: 27
1386434 TTTTAATATA
1386444 TTAATA-ATTTATATTATATAA-A-TT
1 TTAATATATTTATATTATATAATATTT
1386468 TTAATATATTTATATTATATAATATTT
1 TTAATATATTTATATTATATAATATTT
* * *
1386495 TTAATTATTTTTATATTTATATTATATTA
1 TTAA-TATATTTATA-TTATATAATATTT
1386524 TTAGATCATATTTA
1 TTA-AT-ATATTTA
1386538 AAATTAAAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
24 6 0.10
25 15 0.25
26 1 0.02
27 6 0.10
28 9 0.15
29 15 0.25
30 7 0.12
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (27 bp):
TTAATATATTTATATTATATAATATTT
Found at i:1386994 original size:19 final size:19
Alignment explanation
Indices: 1386985--1387025 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1386975 TTATGAAATA
1386985 TAAATATAATATAAATTAT
1 TAAATATAATATAAATTAT
*
1387004 TAAATATATTA-AAATT-T
1 TAAATATAATATAAATTAT
1387021 TAAAT
1 TAAAT
1387026 TAAAAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.29
18 5 0.24
19 10 0.48
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TAAATATAATATAAATTAT
Found at i:1387016 original size:17 final size:19
Alignment explanation
Indices: 1386985--1387025 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
1386975 TTATGAAATA
1386985 TAAATATAATAT-AAATTAT
1 TAAATATAATATAAAATT-T
1387004 TAAATAT-AT-TAAAATTT
1 TAAATATAATATAAAATTT
1387021 TAAAT
1 TAAAT
1387026 TAAAAATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 7 0.33
18 7 0.33
19 7 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TAAATATAATATAAAATTT
Found at i:1393717 original size:19 final size:19
Alignment explanation
Indices: 1393678--1393719 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1393668 GAGGAAGGGC
*
1393678 CATTTTTTTTATTGATGTT
1 CATTTTTTTTATTGATATT
* *
1393697 CATTTTTTTTCTTGCTATT
1 CATTTTTTTTATTGATATT
1393716 CATT
1 CATT
1393720 CCCATTATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.14, C:0.12, G:0.07, T:0.67
Consensus pattern (19 bp):
CATTTTTTTTATTGATATT
Found at i:1403415 original size:9 final size:9
Alignment explanation
Indices: 1403401--1403461 Score: 74
Period size: 8 Copynumber: 7.0 Consensus size: 9
1403391 CTTTTACACC
1403401 CAAAAAAAA
1 CAAAAAAAA
1403410 C-AAAAAAA
1 CAAAAAAAA
*
1403418 -TAAAAAAA
1 CAAAAAAAA
*
1403426 -AAACAAAA
1 CAAAAAAAA
1403434 CAAAAAAAA
1 CAAAAAAAA
1403443 CAAAAAAAA
1 CAAAAAAAA
1403452 CAAGAAAAAA
1 CAA-AAAAAA
1403462 TAGCAAAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
8 20 0.43
9 20 0.43
10 6 0.13
ACGTcount: A:0.87, C:0.10, G:0.02, T:0.02
Consensus pattern (9 bp):
CAAAAAAAA
Found at i:1403426 original size:19 final size:18
Alignment explanation
Indices: 1403402--1403478 Score: 75
Period size: 19 Copynumber: 4.2 Consensus size: 18
1403392 TTTTACACCC
1403402 AAAAAAAACAAAAAAATAA
1 AAAAAAAACAAAAAAA-AA
1403421 AAAAAAAACAAAACAAAAA
1 AAAAAAAACAAAA-AAAAA
* * *
1403440 AAACAAAA-AAAACAAGA
1 AAAAAAAACAAAAAAAAA
* *
1403457 AAAAATAGCAAAAAAAAGA
1 AAAAAAAACAAAAAAAA-A
1403476 AAA
1 AAA
1403479 GGGTCTAGAT
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
17 8 0.17
18 10 0.21
19 26 0.55
20 3 0.06
ACGTcount: A:0.86, C:0.08, G:0.04, T:0.03
Consensus pattern (18 bp):
AAAAAAAACAAAAAAAAA
Found at i:1403472 original size:13 final size:11
Alignment explanation
Indices: 1403402--1403473 Score: 67
Period size: 12 Copynumber: 6.4 Consensus size: 11
1403392 TTTTACACCC
*
1403402 AAAAAA-AACA
1 AAAAAACAAAA
*
1403412 AAAAAATAAAA
1 AAAAAACAAAA
1403423 AAAAAACAAAA
1 AAAAAACAAAA
1403434 CAAAAAA-AACAA
1 -AAAAAACAA-AA
1403446 AAAAAACAAGAA
1 AAAAAACAA-AA
*
1403458 AAAATAGCAAAA
1 AAAA-AACAAAA
1403470 AAAA
1 AAAA
1403474 GAAAAGGGTC
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
10 6 0.11
11 21 0.40
12 22 0.42
13 4 0.08
ACGTcount: A:0.86, C:0.08, G:0.03, T:0.03
Consensus pattern (11 bp):
AAAAAACAAAA
Found at i:1403473 original size:1 final size:1
Alignment explanation
Indices: 1403402--1403461 Score: 57
Period size: 1 Copynumber: 60.0 Consensus size: 1
1403392 TTTTACACCC
* * * * * * *
1403402 AAAAAAAACAAAAAAATAAAAAAAAAACAAAACAAAAAAAACAAAAAAAACAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1403462 TAGCAAAAAA
Statistics
Matches: 45, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.88, C:0.08, G:0.02, T:0.02
Consensus pattern (1 bp):
A
Found at i:1403478 original size:9 final size:9
Alignment explanation
Indices: 1403402--1403478 Score: 59
Period size: 9 Copynumber: 8.4 Consensus size: 9
1403392 TTTTACACCC
*
1403402 AAAAAAAAC
1 AAAAAAAAG
*
1403411 AAAAAAATAA
1 AAAAAAA-AG
*
1403421 AAAAAAAAC
1 AAAAAAAAG
1403430 AAAACAAAA-
1 AAAA-AAAAG
*
1403439 AAAACAAA-
1 AAAAAAAAG
*
1403447 AAAAACAAG
1 AAAAAAAAG
*
1403456 AAAAAATAG
1 AAAAAAAAG
1403465 CAAAAAAAAG
1 -AAAAAAAAG
1403475 AAAA
1 AAAA
1403479 GGGTCTAGAT
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
8 9 0.16
9 27 0.48
10 20 0.36
ACGTcount: A:0.86, C:0.08, G:0.04, T:0.03
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:1404729 original size:29 final size:29
Alignment explanation
Indices: 1404689--1405529 Score: 987
Period size: 28 Copynumber: 29.5 Consensus size: 29
1404679 TGTTCATCCC
* *
1404689 TTTCAAAGCCCACGAGTCAGTGGCATTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
1404718 TTTCAAAGCCCACGAGTCAGTGGCA-TCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
1404746 TTTCAAAGCCCACATGTCAGTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
1404775 TTTCAAAGCCAACAAGTTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1404804 TTTCAAAGCCCACAAGTTAGTGGCAC-CT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
1404832 TTTCAAAGCCTAAAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1404860 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1404888 TTTCAAAGCCCACAAGTCAGTGGCACTC-
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1404916 TTTCAAAGCCCACAAGTTAGTGGCACTC-
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
1404944 TTTCAAAGCCCATAAGTCAGGGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1404972 TTTCAAAGCCCACAAGTCAGTGGCAC-CT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1405000 TTTC-AAGCCCACAAGTCAGTGGCATTC-
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
1405027 TTTCCAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
1405055 TTTCAGAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
1405083 TTTCGAAGCCCACAAGTCAGTGGCACTTT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
1405112 TTTCAAAGCCCATAATTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1405141 TTTCAAAGCCCACAAGTCAGTGGCACTC-
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1405169 TTTCAAAGCCCACAAGTCAGTGGCAC-CT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1405197 TTTC-AAGCCCACGAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1405225 TTT-AAAGCCCACAAGTCAGTGGCA-TCCT
1 TTTCAAAGCCCACAAGTCAGTGGCACT-CT
* *
1405253 TTT-AAAGCCCACACAAGTTAGTGGCACTCC
1 TTTCAAAG-CC-CACAAGTCAGTGGCACTCT
* * *
1405283 TTTCAAAGCCTATACAAGTCGGTGGCAACTCA
1 TTTCAAAGCC--CACAAGTCAGTGGC-ACTCT
*
1405315 TTTCAAAGCCCACGAGTCAGTGGCACTC-
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
** * * *
1405343 TTTCAAAGCTAACAAGTCACTAGCA-TCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1405371 TTTCAAAGCCCAAGCAAGTCAGTGGCACCCT
1 TTTCAAAGCCC-A-CAAGTCAGTGGCACTCT
1405402 TTT-AAAGCCCACACAAGTCAGTGGCACT-T
1 TTTCAAAG-CC-CACAAGTCAGTGGCACTCT
**
1405431 TTTC-AAGCCCATGAGTCAGTGGCACTC-
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
1405458 TTTCAAAGCCCACAAGTTAGTGGCA-TCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
**
1405486 TTTCAAAGCCCACAAG-CTAGTAGTAACTCT
1 TTTCAAAGCCCACAAGTC-AGT-GGCACTCT
1405516 TTTCAAAGCCCACA
1 TTTCAAAGCCCACA
1405530 CGTGTCGGTG
Statistics
Matches: 713, Mismatches: 69, Indels: 59
0.85 0.08 0.07
Matches are distributed among these distances:
27 71 0.10
28 383 0.54
29 144 0.20
30 76 0.11
31 24 0.03
32 15 0.02
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.23
Consensus pattern (29 bp):
TTTCAAAGCCCACAAGTCAGTGGCACTCT
Found at i:1406163 original size:20 final size:20
Alignment explanation
Indices: 1406135--1406209 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
1406125 TTTTACCCAT
1406135 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1406155 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
1406175 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
*
1406195 ATGTATCAATACATT
1 ATGTATCGATACATT
1406210 ATGTCTTTTT
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1406207 original size:40 final size:39
Alignment explanation
Indices: 1406135--1406212 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
1406125 TTTTACCCAT
* * *
1406135 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCAATACAT-TATGA
* *
1406175 ATGTATCGATATATTCTACAATGTATCAATACATTATG
1 ATGTATCGATACATTCTACAATATATCAATACATTATG
1406213 TCTTTTTACC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCAATACATTATGA
Found at i:1414435 original size:158 final size:156
Alignment explanation
Indices: 1414204--1414636 Score: 476
Period size: 157 Copynumber: 2.8 Consensus size: 156
1414194 TAAGTCCAAG
* * * * * * * *
1414204 AAAAATTACAAAAATATCTTTATGGGATACTTTCAACATAGAAGTA-CCTGATACCCTTAAAGGA
1 AAAAATTACAAAAATACCTCTAAGGGATACTTTCGACGTAAAAGTATCCCGATACCCCTAAAGGA
* * * * * *
1414268 CTTATAAAAGACTATAGATGAGACGAACCTATCCTAAATATCTACCATT-AGCATTAAAGCA-GA
66 CTTAAAAAAGACTATAAATG-GATGAACCTATCCTAAATACCCACC-TTCAGCATAAAAGCAGGA
* * *
1414331 CCTGGTGATAACCTAGTACTTGATTCTAAA
129 CCTGATGATAACCTAGGACTCGATTCT--A
* *
1414361 AAAAATTACCAAAATACCTCTAAGGGATACCTTCGACGTAAAAGTATCCCGATACCCCTAAAGGA
1 AAAAATTACAAAAATACCTCTAAGGGATACTTTCGACGTAAAAGTATCCCGATACCCCTAAAGGA
* * *
1414426 CTTAAAAAAGACTATAAAAGGGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCAGGAT
66 CTTAAAAAAGACTAT-AAATGGATGAACCTATCCTAAATACCCACCTTCAGCATAAAAGCAGGAC
*
1414491 CTGATGATAACTTAGGACTCGATTCTA
130 CTGATGATAACCTAGGACTCGATTCTA
* * * * * *
1414518 AAAAATTATAAAAATACCCCTAAGGGATACTTTCGACGTGAAAGTATTCCGATACCTCTAAAAGA
1 AAAAATTACAAAAATACCTCTAAGGGATACTTTCGACGTAAAAGTATCCCGATACCCCTAAAGGA
* * * * * *
1414583 CGTAAAAATGACCATAAAATGGGTGAACCTATCCTAAATACCCACATTCGGCAT
66 CTTAAAAAAGACTAT-AAATGGATGAACCTATCCTAAATACCCACCTTCAGCAT
1414637 CAAACTTAGG
Statistics
Matches: 235, Mismatches: 37, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
157 146 0.62
158 62 0.26
159 27 0.11
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (156 bp):
AAAAATTACAAAAATACCTCTAAGGGATACTTTCGACGTAAAAGTATCCCGATACCCCTAAAGGA
CTTAAAAAAGACTATAAATGGATGAACCTATCCTAAATACCCACCTTCAGCATAAAAGCAGGACC
TGATGATAACCTAGGACTCGATTCTA
Found at i:1416242 original size:19 final size:19
Alignment explanation
Indices: 1416210--1416246 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1416200 TGCTGCTGTT
*
1416210 GTTGCTATTCTTCACCTTG
1 GTTGCCATTCTTCACCTTG
*
1416229 GTTGCCATTTTTCACCTT
1 GTTGCCATTCTTCACCTT
1416247 TTTTTTTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.11, C:0.27, G:0.14, T:0.49
Consensus pattern (19 bp):
GTTGCCATTCTTCACCTTG
Found at i:1416403 original size:23 final size:23
Alignment explanation
Indices: 1416369--1416436 Score: 120
Period size: 23 Copynumber: 3.0 Consensus size: 23
1416359 GCTTGCTGGT
1416369 CTCGTTGCTTTCTTTTTCACGTTA
1 CTCG-TGCTTTCTTTTTCACGTTA
1416393 CTCGTGCTTTCTTTTTCACGTTA
1 CTCGTGCTTTCTTTTTCACGTTA
1416416 CTCGTGCTTTCTTTTT-ACGTT
1 CTCGTGCTTTCTTTTTCACGTT
1416437 GCTGCTGTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
22 5 0.11
23 35 0.80
24 4 0.09
ACGTcount: A:0.07, C:0.25, G:0.13, T:0.54
Consensus pattern (23 bp):
CTCGTGCTTTCTTTTTCACGTTA
Found at i:1417281 original size:10 final size:10
Alignment explanation
Indices: 1417266--1417304 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
1417256 TCTTTATTTC
1417266 ATTTTTTATT
1 ATTTTTTATT
1417276 ATTTTTTATT
1 ATTTTTTATT
1417286 A--TTTTATT
1 ATTTTTTATT
*
1417294 ATTTTTAATT
1 ATTTTTTATT
1417304 A
1 A
1417305 ATAATAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
8 8 0.31
10 18 0.69
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (10 bp):
ATTTTTTATT
Found at i:1417292 original size:18 final size:18
Alignment explanation
Indices: 1417269--1417304 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1417259 TTATTTCATT
*
1417269 TTTTATTATTTTTTATTA
1 TTTTATTATTTTTAATTA
1417287 TTTTATTATTTTTAATTA
1 TTTTATTATTTTTAATTA
1417305 ATAATAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTATTATTTTTAATTA
Found at i:1417373 original size:19 final size:19
Alignment explanation
Indices: 1417325--1417374 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1417315 TAATTTTTTA
*
1417325 TTTTACATTTTTTTTCGAT
1 TTTTATATTTTTTTTCGAT
* *
1417344 TTTT-TGTTTTTTTGTTGAT
1 TTTTATATTTTTTT-TCGAT
1417363 TTTTATATTTTT
1 TTTTATATTTTT
1417375 AATTTTTTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 7 0.28
19 12 0.48
20 6 0.24
ACGTcount: A:0.12, C:0.04, G:0.08, T:0.76
Consensus pattern (19 bp):
TTTTATATTTTTTTTCGAT
Found at i:1418000 original size:43 final size:43
Alignment explanation
Indices: 1417952--1418104 Score: 134
Period size: 44 Copynumber: 3.6 Consensus size: 43
1417942 AGTTTACCTA
*
1417952 GGACAAAGCCGACAAGTAAACAAAGAAAGGAATGGTTGACCAG
1 GGACAAAGCAGACAAGTAAACAAAGAAAGGAATGGTTGACCAG
* * **
1417995 GGACAAAGCAGACAGGTAAAAAAAGAGTAAGG-ATGGTTGACTGG
1 GGACAAAGCAGACAAGTAAACAAAGA--AAGGAATGGTTGACCAG
* * * * * *
1418039 GGACAAAGCAGACAGGTCACCAAGGGTAAGAAAT--TT-ACCAG
1 GGACAAAGCAGACAAGTAAACAA-AGAAAGGAATGGTTGACCAG
* *
1418080 GGACATAGCTGACAAGTAAACAAAG
1 GGACAAAGCAGACAAGTAAACAAAG
1418105 GGTAAGAAAG
Statistics
Matches: 87, Mismatches: 19, Indels: 11
0.74 0.16 0.09
Matches are distributed among these distances:
40 1 0.01
41 21 0.24
42 2 0.02
43 26 0.30
44 32 0.37
45 5 0.06
ACGTcount: A:0.44, C:0.15, G:0.29, T:0.12
Consensus pattern (43 bp):
GGACAAAGCAGACAAGTAAACAAAGAAAGGAATGGTTGACCAG
Found at i:1418046 original size:44 final size:43
Alignment explanation
Indices: 1417952--1418055 Score: 138
Period size: 44 Copynumber: 2.4 Consensus size: 43
1417942 AGTTTACCTA
* * *
1417952 GGACAAAGCCGACAAGTAAACAAAGAAAGGAATGGTTGACCAG
1 GGACAAAGCAGACAGGTAAAAAAAGAAAGGAATGGTTGACCAG
**
1417995 GGACAAAGCAGACAGGTAAAAAAAGAGTAAGG-ATGGTTGACTGG
1 GGACAAAGCAGACAGGTAAAAAAAGA--AAGGAATGGTTGACCAG
1418039 GGACAAAGCAGACAGGT
1 GGACAAAGCAGACAGGT
1418056 CACCAAGGGT
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
43 23 0.43
44 27 0.50
45 4 0.07
ACGTcount: A:0.44, C:0.13, G:0.32, T:0.11
Consensus pattern (43 bp):
GGACAAAGCAGACAGGTAAAAAAAGAAAGGAATGGTTGACCAG
Found at i:1418107 original size:42 final size:42
Alignment explanation
Indices: 1418060--1418199 Score: 122
Period size: 42 Copynumber: 3.3 Consensus size: 42
1418050 ACAGGTCACC
*
1418060 AAGGGTAAGAAATTTACCAGGGACATAGCTGACAAGTAAACA
1 AAGGGTAAGAAATTTACCAGGGACATAGCCGACAAGTAAACA
* * * * * * * * *
1418102 AAGGGTAAGAAAGGCTGACCAGCGACAAAGCCAATAGGT-CACC
1 AAGGGTAAGAAA--TTTACCAGGGACATAGCCGACAAGTAAACA
* *
1418145 AAGGGATAAGAAGTTTACCAAGGACATAGCCGAC-AGCTAAACA
1 AAGGG-TAAGAAATTTACCAGGGACATAGCCGACAAG-TAAACA
1418188 AAGGGTAAGAAA
1 AAGGGTAAGAAA
1418200 GGTCGACTAG
Statistics
Matches: 71, Mismatches: 22, Indels: 10
0.69 0.21 0.10
Matches are distributed among these distances:
41 1 0.01
42 33 0.46
43 14 0.20
44 23 0.32
ACGTcount: A:0.44, C:0.17, G:0.26, T:0.13
Consensus pattern (42 bp):
AAGGGTAAGAAATTTACCAGGGACATAGCCGACAAGTAAACA
Found at i:1418186 original size:86 final size:85
Alignment explanation
Indices: 1417990--1418455 Score: 404
Period size: 85 Copynumber: 5.4 Consensus size: 85
1417980 GGAATGGTTG
* * * * * * ** *
1417990 ACCAGGGACAAAGCAGACAGGTAAAAAAAGAGTAAGGATGGTTGACTGGGGACAAAGCAGACAGG
1 ACCAGGGACATAGCTGACA-GTAAACAAAGGGTAAGAAAGGTTGACCAGGGACAAAGCCGACAGG
*
1418055 TCACCAAGGG-TAAGAAATTT
65 TCACCAAGGGATAAGAAGTTT
* * * *
1418075 ACCAGGGACATAGCTGACAAGTAAACAAAGGGTAAGAAAGGCTGACCAGCGACAAAGCCAATAGG
1 ACCAGGGACATAGCTGAC-AGTAAACAAAGGGTAAGAAAGGTTGACCAGGGACAAAGCCGACAGG
1418140 TCACCAAGGGATAAGAAGTTT
65 TCACCAAGGGATAAGAAGTTT
* * * * * **
1418161 ACCAAGGACATAGCCGACAGCTAAACAAAGGGTAAGAAAGGTCGACTAGGGATAAAATCGACAGG
1 ACCAGGGACATAGCTGACAG-TAAACAAAGGGTAAGAAAGGTTGACCAGGGACAAAGCCGACAGG
*
1418226 TCACCAAGAGG-TAAAAAGTTT
65 TCACCAAG-GGATAAGAAGTTT
* * * * * * * * *
1418247 ATCAGGGACAT-GGTGACAGGTAAACAAAAGGTAATAATGGTTGATCGGGGACAAAGCTGATAGG
1 ACCAGGGACATAGCTGACA-GTAAACAAAGGGTAAGAAAGGTTGACCAGGGACAAAGCCGACAGG
* *
1418311 TCACTAAGCGATAAGAAGTTT
65 TCACCAAGGGATAAGAAGTTT
* * * * * * * * *
1418332 ACCGGGGACATAGCTAACAAGTAAAAAAAAGATAAGAATA-GTTGATC-GAGGACATAGTCGGCA
1 ACCAGGGACATAGCTGAC-AGTAAACAAAGGGTAAGAA-AGGTTGACCAG-GGACAAAGCCGACA
*
1418395 GGTCACCAAGGAATAAGAAGTTT
63 GGTCACCAAGGGATAAGAAGTTT
* *
1418418 ACTA-GGACATAGCCGACAGGTAAACAAAGGGTAAGAAA
1 ACCAGGGACATAGCTGACA-GTAAACAAAGGGTAAGAAA
1418456 AGATAAAAAA
Statistics
Matches: 302, Mismatches: 68, Indels: 23
0.77 0.17 0.06
Matches are distributed among these distances:
84 3 0.01
85 151 0.50
86 145 0.48
87 3 0.01
ACGTcount: A:0.42, C:0.15, G:0.27, T:0.15
Consensus pattern (85 bp):
ACCAGGGACATAGCTGACAGTAAACAAAGGGTAAGAAAGGTTGACCAGGGACAAAGCCGACAGGT
CACCAAGGGATAAGAAGTTT
Done.