Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold500
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: 2046043
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 10
Found at i:1090825 original size:20 final size:20
Alignment explanation
Indices: 1090703--1090825 Score: 85
Period size: 20 Copynumber: 6.0 Consensus size: 20
1090693 ATATTTATTA
*
1090703 ATATAAATATATTAA-AATTT
1 ATATAAATATA-TAATATTTT
1090723 ATATAAATATATAATATTTT
1 ATATAAATATATAATATTTT
* ***
1090743 AAATATAAT-TATAATATAAAA
1 ATATA-AATATATAATAT-TTT
*
1090764 ATAATTAAATAT-T-ATATTAAT
1 AT-A-TAAATATATAATATT-TT
*
1090785 ATATAAATATATTAA-AATTT
1 ATATAAATATA-TAATATTTT
1090805 ATATAAATATATAATATTTT
1 ATATAAATATATAATATTTT
1090825 A
1 A
1090826 AATATGATTA
Statistics
Matches: 81, Mismatches: 11, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
19 13 0.16
20 45 0.56
21 14 0.17
22 6 0.07
23 3 0.04
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATAAATATATAATATTTT
Found at i:1105710 original size:13 final size:13
Alignment explanation
Indices: 1105692--1105717 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1105682 TGGGAGGCAA
1105692 TTGCTTGATATTT
1 TTGCTTGATATTT
1105705 TTGCTTGATATTT
1 TTGCTTGATATTT
1105718 CGTCTGAGCA
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:0.15, C:0.08, G:0.15, T:0.62
Consensus pattern (13 bp):
TTGCTTGATATTT
Found at i:1108544 original size:19 final size:19
Alignment explanation
Indices: 1108520--1108559 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1108510 TCGACCAAAA
1108520 AACAAAAGTGTGTATAAGT
1 AACAAAAGTGTGTATAAGT
1108539 AACAAAAGTGTGTATAAGT
1 AACAAAAGTGTGTATAAGT
1108558 AA
1 AA
1108560 AAGCAAAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.50, C:0.05, G:0.20, T:0.25
Consensus pattern (19 bp):
AACAAAAGTGTGTATAAGT
Found at i:1110037 original size:15 final size:15
Alignment explanation
Indices: 1110019--1110064 Score: 60
Period size: 13 Copynumber: 3.1 Consensus size: 15
1110009 TTTTATATTT
1110019 TTTAATATATTTATA
1 TTTAATATATTTATA
1110034 TTT-A-ATATTTATA
1 TTTAATATATTTATA
1110047 TTTCACATATATTTATA
1 TTT-A-ATATATTTATA
1110064 T
1 T
1110065 ATAAATATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 12 0.44
14 1 0.04
15 3 0.11
16 1 0.04
17 10 0.37
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTAATATATTTATA
Found at i:1112679 original size:2 final size:2
Alignment explanation
Indices: 1112672--1112701 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1112662 ACACAAAACC
*
1112672 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1112702 CTTGAAGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1113676 original size:3 final size:3
Alignment explanation
Indices: 1113670--1113696 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1113660 TTCTTCCTCC
1113670 ACG ACG ACG ACG ACG ACG ACG ACG ACG
1 ACG ACG ACG ACG ACG ACG ACG ACG ACG
1113697 TTTCGTTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.33, T:0.00
Consensus pattern (3 bp):
ACG
Found at i:1118401 original size:17 final size:18
Alignment explanation
Indices: 1118379--1118420 Score: 63
Period size: 16 Copynumber: 2.5 Consensus size: 18
1118369 AGGCTGAATG
1118379 AGAAAG-AACAAAGAAAA
1 AGAAAGAAACAAAGAAAA
1118396 AGAAAGAAACAAAG--AA
1 AGAAAGAAACAAAGAAAA
1118412 AGAAAGAAA
1 AGAAAGAAA
1118421 AAAAAGAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.46
17 6 0.25
18 7 0.29
ACGTcount: A:0.76, C:0.05, G:0.19, T:0.00
Consensus pattern (18 bp):
AGAAAGAAACAAAGAAAA
Found at i:1118409 original size:25 final size:25
Alignment explanation
Indices: 1118381--1118428 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
1118371 GCTGAATGAG
1118381 AAAG-AACAAAGAAAAAGAAAGAAAC
1 AAAGAAACAAAGAAAAA-AAAGAAAC
*
1118406 AAAGAAAGAAAGAAAAAAAAGAA
1 AAAGAAACAAAGAAAAAAAAGAA
1118429 GGTAAAGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.79, C:0.04, G:0.17, T:0.00
Consensus pattern (25 bp):
AAAGAAACAAAGAAAAAAAAGAAAC
Found at i:1118428 original size:17 final size:17
Alignment explanation
Indices: 1118379--1118428 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
1118369 AGGCTGAATG
*
1118379 AGAAAGAACAAAGAA-AA
1 AGAAAGAA-AAAAAAGAA
*
1118396 AGAAAG-AAACAAAGAA
1 AGAAAGAAAAAAAAGAA
1118412 AGAAAGAAAAAAAAGAA
1 AGAAAGAAAAAAAAGAA
1118429 GGTAAAGGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 4 0.14
16 9 0.32
17 15 0.54
ACGTcount: A:0.78, C:0.04, G:0.18, T:0.00
Consensus pattern (17 bp):
AGAAAGAAAAAAAAGAA
Found at i:1120989 original size:16 final size:16
Alignment explanation
Indices: 1120970--1121003 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1120960 TTATTATAAA
1120970 AAAATAAT-TAAAATAT
1 AAAATAATATAAAA-AT
1120986 AAAATAATATAAAAAT
1 AAAATAATATAAAAAT
1121002 AA
1 AA
1121004 TATGATCACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAATAATATAAAAAT
Found at i:1124807 original size:26 final size:26
Alignment explanation
Indices: 1124778--1124841 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 26
1124768 AAGTAAATAA
1124778 AAAATTAAATTAAAT-TCACATATATT
1 AAAATTAAATTAAATAT-ACATATATT
* *
1124804 AAAATT-AATATATATATATATATATT
1 AAAATTAAAT-TAAATATACATATATT
1124830 AAAATTTAAATT
1 AAAA-TTAAATT
1124842 TTACATCTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
25 3 0.09
26 22 0.69
27 4 0.12
28 3 0.09
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (26 bp):
AAAATTAAATTAAATATACATATATT
Found at i:1126244 original size:2 final size:2
Alignment explanation
Indices: 1126237--1126263 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1126227 TCTCCATCAG
1126237 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 A
1126264 CTCATCTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1127608 original size:14 final size:15
Alignment explanation
Indices: 1127578--1127623 Score: 67
Period size: 14 Copynumber: 3.1 Consensus size: 15
1127568 ATAATAAAAA
1127578 AAAATTATAAATATT
1 AAAATTATAAATATT
*
1127593 AAAATTA-AAATTTT
1 AAAATTATAAATATT
1127607 AAAATTATTAAATATT
1 AAAATTA-TAAATATT
1127623 A
1 A
1127624 TTTTTAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 13 0.48
15 7 0.26
16 7 0.26
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAATTATAAATATT
Found at i:1128219 original size:26 final size:26
Alignment explanation
Indices: 1128181--1128232 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
1128171 AATAAAAAAA
1128181 TAAAAAAATTATAAAT-ATTAAATTT
1 TAAAAAAATTATAAATCATTAAATTT
*
1128206 TAAATAAATATATAAATCGATTAAATT
1 TAAAAAAAT-TATAAATC-ATTAAATT
1128233 AAGATTCGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 8 0.35
26 7 0.30
28 8 0.35
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (26 bp):
TAAAAAAATTATAAATCATTAAATTT
Found at i:1129785 original size:13 final size:13
Alignment explanation
Indices: 1129764--1129801 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
1129754 CTAAACAAAG
1129764 ATTTATTATTATT
1 ATTTATTATTATT
*
1129777 ATTTTTTATTATT
1 ATTTATTATTATT
*
1129790 A-GTATTATTATT
1 ATTTATTATTATT
1129802 GTCCTAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 9 0.41
13 13 0.59
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (13 bp):
ATTTATTATTATT
Found at i:1129786 original size:16 final size:16
Alignment explanation
Indices: 1129765--1129795 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1129755 TAAACAAAGA
*
1129765 TTTATTATTATTATTT
1 TTTATTATTAGTATTT
1129781 TTTATTATTAGTATT
1 TTTATTATTAGTATT
1129796 ATTATTGTCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (16 bp):
TTTATTATTAGTATTT
Found at i:1131982 original size:34 final size:34
Alignment explanation
Indices: 1131943--1132007 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
1131933 TGTTATAATC
1131943 ATATA-TAAT-ATTATATATTTATATAAATTTTGGT
1 ATATATTAATAATT-TAT-TTTATATAAATTTTGGT
*
1131977 ATATATTAATAATTTATTTTATATAGATTTT
1 ATATATTAATAATTTATTTTATATAAATTTT
1132008 AACATATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 18 0.64
35 7 0.25
36 3 0.11
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (34 bp):
ATATATTAATAATTTATTTTATATAAATTTTGGT
Found at i:1134447 original size:12 final size:12
Alignment explanation
Indices: 1134430--1134454 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1134420 GAAAAAAAAA
1134430 AAACACACACAC
1 AAACACACACAC
1134442 AAACACACACAC
1 AAACACACACAC
1134454 A
1 A
1134455 CAAAAAAGGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.40, G:0.00, T:0.00
Consensus pattern (12 bp):
AAACACACACAC
Found at i:1134451 original size:14 final size:14
Alignment explanation
Indices: 1134432--1134458 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1134422 AAAAAAAAAA
1134432 ACACACACACAAAC
1 ACACACACACAAAC
1134446 ACACACACACAAA
1 ACACACACACAAA
1134459 AAAGGGCTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.41, G:0.00, T:0.00
Consensus pattern (14 bp):
ACACACACACAAAC
Found at i:1140183 original size:15 final size:17
Alignment explanation
Indices: 1140163--1140203 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
1140153 TTATTTTAGC
1140163 TTAATTTTTTG-T-ACA
1 TTAATTTTTTGATGACA
*
1140178 TTAATTTATTTGATGACC
1 TTAATTT-TTTGATGACA
1140196 TTAATTTT
1 TTAATTTT
1140204 CTAATACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 7 0.32
16 4 0.18
17 2 0.09
18 9 0.41
ACGTcount: A:0.27, C:0.07, G:0.07, T:0.59
Consensus pattern (17 bp):
TTAATTTTTTGATGACA
Found at i:1141632 original size:24 final size:23
Alignment explanation
Indices: 1141600--1141655 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 23
1141590 GATGTTTTTC
* * *
1141600 TTTTAAAAATTTATTTACATTATT
1 TTTTAAAAATATATATACATT-TA
*
1141624 TTTTAAAAATATATATATATTTA
1 TTTTAAAAATATATATACATTTA
1141647 TTTTAAAAA
1 TTTTAAAAA
1141656 AATCATTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 10 0.36
24 18 0.64
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTTAAAAATATATATACATTTA
Found at i:1141731 original size:32 final size:33
Alignment explanation
Indices: 1141685--1141768 Score: 116
Period size: 32 Copynumber: 2.5 Consensus size: 33
1141675 ATTCACTTAC
*
1141685 AAAACTATTTATTTTTTATTTATAAATATTTTT
1 AAAACTATTAATTTTTTATTTATAAATATTTTT
* *
1141718 AAAA-TATTCATTTTTTATTTGTAAATATTTTT
1 AAAACTATTAATTTTTTATTTATAAATATTTTT
*
1141750 AAAATTATTAAATTTTTTA
1 AAAACTATT-AATTTTTTA
1141769 CTTTCATGAT
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
32 30 0.65
33 8 0.17
34 8 0.17
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.58
Consensus pattern (33 bp):
AAAACTATTAATTTTTTATTTATAAATATTTTT
Found at i:1142230 original size:17 final size:15
Alignment explanation
Indices: 1142210--1142253 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 15
1142200 TTATAACCTT
1142210 TTTAATTTTGAATTTAA
1 TTTAATTTT-AATTT-A
1142227 TTTAATTAATTAATTTA
1 TTTAATT--TTAATTTA
1142244 TTTAATTTTA
1 TTTAATTTTA
1142254 TAATATAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 3 0.12
17 15 0.60
18 5 0.20
19 2 0.08
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (15 bp):
TTTAATTTTAATTTA
Found at i:1146324 original size:2 final size:2
Alignment explanation
Indices: 1146317--1146343 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1146307 GAAGATGGAA
1146317 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1146344 TTCGCTTTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1147084 original size:37 final size:35
Alignment explanation
Indices: 1147039--1147108 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 35
1147029 TTTTTTAAAA
1147039 AAATTATATATTTAA-TATATTATTTTTATCAAATTC
1 AAATTATATA-TTAATTATATTATTTTTAT-AAATTC
*
1147075 AAATATATATATTAATTATATTTTTTTTATAAAT
1 AAAT-TATATATTAATTATATTATTTTTATAAAT
1147109 ATCATCATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 12 0.39
37 19 0.61
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (35 bp):
AAATTATATATTAATTATATTATTTTTATAAATTC
Found at i:1150766 original size:3 final size:3
Alignment explanation
Indices: 1150758--1150807 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
1150748 GTTCCTGCTG
*
1150758 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AGT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1150806 AT
1 AT
1150808 CTTCCATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1151836 original size:5 final size:5
Alignment explanation
Indices: 1151816--1151866 Score: 54
Period size: 5 Copynumber: 10.6 Consensus size: 5
1151806 AACCCTTCGC
* *
1151816 AACAA AATCCA AACAA AACAA AACAA AACAA AGCAA AA-AA AA-AA AA-AA
1 AACAA AA-CAA AACAA AACAA AACAA AACAA AACAA AACAA AACAA AACAA
1151864 AAC
1 AAC
1151867 CCTTACTTGT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
4 12 0.30
5 24 0.60
6 4 0.10
ACGTcount: A:0.78, C:0.18, G:0.02, T:0.02
Consensus pattern (5 bp):
AACAA
Found at i:1152064 original size:13 final size:13
Alignment explanation
Indices: 1152020--1152056 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1152010 GATTAGTGTT
1152020 AGAGAAAGAGAAAG
1 AGAGAAAG-GAAAG
*
1152034 AGAGAAAGGAAAA
1 AGAGAAAGGAAAG
1152047 AGAGAAAGGA
1 AGAGAAAGGA
1152057 GGGAGAGATG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 14 0.64
14 8 0.36
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (13 bp):
AGAGAAAGGAAAG
Found at i:1152644 original size:5 final size:6
Alignment explanation
Indices: 1152614--1152641 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1152604 TTGATGTATT
1152614 ATTTTA ATTTTA ATTTTA ATTTTA ATTT
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTT
1152642 AATAAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
ATTTTA
Found at i:1156604 original size:20 final size:21
Alignment explanation
Indices: 1156576--1156615 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1156566 ATTAATCAGT
**
1156576 GAAACAAAATTTTAAAAAAAG
1 GAAACAAAACCTTAAAAAAAG
1156597 GAAA-AAAACCTTAAAAAAA
1 GAAACAAAACCTTAAAAAAA
1156616 ACGAAATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.70, C:0.07, G:0.07, T:0.15
Consensus pattern (21 bp):
GAAACAAAACCTTAAAAAAAG
Found at i:1161729 original size:4 final size:4
Alignment explanation
Indices: 1161720--1161754 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
1161710 CAGCACTTCG
1161720 AATA AATA AATA AATA AATA AATA AATA AATA AAT
1 AATA AATA AATA AATA AATA AATA AATA AATA AAT
1161755 GCATTCAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:1162523 original size:22 final size:23
Alignment explanation
Indices: 1162497--1162557 Score: 56
Period size: 22 Copynumber: 2.7 Consensus size: 23
1162487 CTTTCTTTAG
1162497 TTAATTTTTACTTTT-TTATCAT
1 TTAATTTTTACTTTTATTATCAT
* *
1162519 TTAA--TATAATTTTAATTATCAT
1 TTAATTTTTACTTTT-ATTATCAT
1162541 TGATAATTTTTACTTTT
1 T--TAATTTTTACTTTT
1162558 CTTCTTCTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
20 7 0.24
22 12 0.41
24 3 0.10
26 7 0.24
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.62
Consensus pattern (23 bp):
TTAATTTTTACTTTTATTATCAT
Found at i:1165207 original size:17 final size:16
Alignment explanation
Indices: 1165179--1165222 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
1165169 ATTCGCTTTC
*
1165179 TTTTTCTCTTTAATTTTT
1 TTTTTCT-TTTAA-TGTT
1165197 TTTTTCTTTTAATGTT
1 TTTTTCTTTTAATGTT
*
1165213 CTTTTCTTTT
1 TTTTTCTTTT
1165223 GGTTCTTCGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 12 0.50
17 5 0.21
18 7 0.29
ACGTcount: A:0.09, C:0.11, G:0.02, T:0.77
Consensus pattern (16 bp):
TTTTTCTTTTAATGTT
Found at i:1165217 original size:18 final size:18
Alignment explanation
Indices: 1165175--1165217 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1165165 TCTCATTCGC
1165175 TTTC-TTTTTCTCTTTAA
1 TTTCTTTTTTCTCTTTAA
*
1165192 TTTTTTTTTTCT-TTTAA
1 TTTCTTTTTTCTCTTTAA
1165209 TGTTCTTTT
1 T-TTCTTTT
1165218 CTTTTGGTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.09, C:0.12, G:0.02, T:0.77
Consensus pattern (18 bp):
TTTCTTTTTTCTCTTTAA
Found at i:1171145 original size:2 final size:2
Alignment explanation
Indices: 1171138--1171168 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1171128 GCTATAATTT
1171138 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1171169 TATGGAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1172477 original size:24 final size:24
Alignment explanation
Indices: 1172453--1172502 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
1172443 TAAATATTTA
1172453 TATAAGTT-TTTATTTAATTTA-T
1 TATAAGTTATTTATTTAATTTATT
*
1172475 TATAATTTAATTTATTTAATTTATT
1 TATAAGTT-ATTTATTTAATTTATT
1172500 TAT
1 TAT
1172503 GTTTATTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 7 0.29
24 13 0.54
25 4 0.17
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (24 bp):
TATAAGTTATTTATTTAATTTATT
Found at i:1172509 original size:10 final size:9
Alignment explanation
Indices: 1172461--1172501 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
1172451 TATATAAGTT
1172461 TTTATTTAA
1 TTTATTTAA
1172470 TTTA-TT-A
1 TTTATTTAA
*
1172477 -TAATTTAA
1 TTTATTTAA
1172485 TTTATTTAA
1 TTTATTTAA
1172494 TTTATTTA
1 TTTATTTA
1172502 TGTTTATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
6 2 0.07
7 3 0.11
8 3 0.11
9 19 0.70
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
TTTATTTAA
Found at i:1178869 original size:134 final size:134
Alignment explanation
Indices: 1178629--1178898 Score: 450
Period size: 134 Copynumber: 2.0 Consensus size: 134
1178619 GTGATCTGGT
* * * *
1178629 TCTTTTCCTGGATGTTCGATAAAGAACAAAACGAAAGTGAATAACTGAACTAGGCCTATGTGTAG
1 TCTTTTCCCGGATGTTAGATAAAGAACAAAACAAAAGTGAACAACTGAACTAGGCCTATGTGTAG
* * *
1178694 AGCTGTCAAGGAGGATTCAGACCGATTTACAGAGCTCTTCAGGAGTTATCAGCTTCCTTAAGGCC
66 ACCTATCAAGGAGGATTCAGACCAATTTACAGAGCTCTTCAGGAGTTATCAGCTTCCTTAAGGCC
1178759 GTGC
131 GTGC
* *
1178763 TCTTTTCCCGGATGTTAGATAAAGAACAAATCAAAAGTGAACAACTGAACTAGGCCTATGTGTAT
1 TCTTTTCCCGGATGTTAGATAAAGAACAAAACAAAAGTGAACAACTGAACTAGGCCTATGTGTAG
*
1178828 ACCTATCAAGGAGGATTCAGAGCAATTTACAGAGCTCTTCAGGAGTTATCAGCTTCCTTAAGGCC
66 ACCTATCAAGGAGGATTCAGACCAATTTACAGAGCTCTTCAGGAGTTATCAGCTTCCTTAAGGCC
1178893 GTGC
131 GTGC
1178897 TC
1 TC
1178899 GAAGCAAGCA
Statistics
Matches: 126, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
134 126 1.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (134 bp):
TCTTTTCCCGGATGTTAGATAAAGAACAAAACAAAAGTGAACAACTGAACTAGGCCTATGTGTAG
ACCTATCAAGGAGGATTCAGACCAATTTACAGAGCTCTTCAGGAGTTATCAGCTTCCTTAAGGCC
GTGC
Found at i:1183952 original size:20 final size:20
Alignment explanation
Indices: 1183927--1183968 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
1183917 TTAATTAGGT
1183927 TTATGATTTTGCTCATGATA
1 TTATGATTTTGCTCATGATA
*
1183947 TTATGATTTTGTTCATGATA
1 TTATGATTTTGCTCATGATA
1183967 TT
1 TT
1183969 TATAAATCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.07, G:0.14, T:0.55
Consensus pattern (20 bp):
TTATGATTTTGCTCATGATA
Found at i:1186922 original size:18 final size:18
Alignment explanation
Indices: 1186899--1186936 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1186889 AATTTTGAGC
1186899 TGAAATTTATCAAATCTG
1 TGAAATTTATCAAATCTG
1186917 TGAAATTTATCAAATCTG
1 TGAAATTTATCAAATCTG
1186935 TG
1 TG
1186937 TAACCAGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (18 bp):
TGAAATTTATCAAATCTG
Found at i:1197020 original size:2 final size:2
Alignment explanation
Indices: 1197013--1197058 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1197003 CTTTGCCATG
1197013 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
1197055 AT AT
1 AT AT
1197059 TTGAACCGAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1199203 original size:66 final size:65
Alignment explanation
Indices: 1199095--1199223 Score: 168
Period size: 66 Copynumber: 2.0 Consensus size: 65
1199085 TCACTTTTTG
* * * ** * *
1199095 CTTTTTATATCGAAATTTGATTATTTGGTTTGATCATCTTTATTTTACATATTAAAATTTGATCA
1 CTTTTCATATCAAAATTTAATTATTTAATTTAATCATCTTTATTTTACATATCAAAATTTGATCA
* *
1199160 CTTTTCATATCAAAATTATAATTATTTAATTTAATCATTTTTATTTTATATATCAAAATTTGAT
1 CTTTTCATATCAAAATT-TAATTATTTAATTTAATCATCTTTATTTTACATATCAAAATTTGAT
1199224 TATCACTTTA
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
65 15 0.28
66 39 0.72
ACGTcount: A:0.33, C:0.09, G:0.05, T:0.53
Consensus pattern (65 bp):
CTTTTCATATCAAAATTTAATTATTTAATTTAATCATCTTTATTTTACATATCAAAATTTGATCA
Found at i:1199249 original size:24 final size:26
Alignment explanation
Indices: 1199204--1199251 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
1199194 TCATTTTTAT
*
1199204 TTTATATATCAAAATTTGATTATCAC
1 TTTATATATCAAAATATGATTATCAC
1199230 TTTATATATCAAAA-AT-ATTATC
1 TTTATATATCAAAATATGATTATC
1199252 CATTTTCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.29
25 1 0.05
26 14 0.67
ACGTcount: A:0.42, C:0.10, G:0.02, T:0.46
Consensus pattern (26 bp):
TTTATATATCAAAATATGATTATCAC
Found at i:1204725 original size:16 final size:16
Alignment explanation
Indices: 1204704--1204736 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1204694 ATTGCATGGC
1204704 CTTGAAGATCCATATT
1 CTTGAAGATCCATATT
1204720 CTTGAAGATCCATATT
1 CTTGAAGATCCATATT
1204736 C
1 C
1204737 AACTAGCACG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.36
Consensus pattern (16 bp):
CTTGAAGATCCATATT
Found at i:1206814 original size:37 final size:37
Alignment explanation
Indices: 1206771--1206848 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
1206761 ATATAATATG
*
1206771 ATATATTTTTTAAAAAATA-ATTAAAAAATTAAATAAA
1 ATATATTTTTTAAAAAATATA-TAAAAAATAAAATAAA
*
1206808 ATATATTTTTTAAAAAATATATAAAAAATAAAATATA
1 ATATATTTTTTAAAAAATATATAAAAAATAAAATAAA
1206845 ATAT
1 ATAT
1206849 GGTTGTAGTG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (37 bp):
ATATATTTTTTAAAAAATATATAAAAAATAAAATAAA
Found at i:1212209 original size:12 final size:12
Alignment explanation
Indices: 1212192--1212218 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1212182 GGTTGATACC
1212192 TCTGTGTTTGTT
1 TCTGTGTTTGTT
1212204 TCTGTGTTTGTT
1 TCTGTGTTTGTT
1212216 TCT
1 TCT
1212219 TTCCTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.11, G:0.22, T:0.67
Consensus pattern (12 bp):
TCTGTGTTTGTT
Found at i:1212514 original size:100 final size:100
Alignment explanation
Indices: 1212341--1212542 Score: 404
Period size: 100 Copynumber: 2.0 Consensus size: 100
1212331 GCATGCTGGA
1212341 TTGAAACTAGTGGATTTGCTGATAGAGAGGCTTTTTACAAGTCAATAATCTCTCAGTAGTTCCTT
1 TTGAAACTAGTGGATTTGCTGATAGAGAGGCTTTTTACAAGTCAATAATCTCTCAGTAGTTCCTT
1212406 TTTTGGAATTTTTTTGGTTCCTTTTTCTTTAACAT
66 TTTTGGAATTTTTTTGGTTCCTTTTTCTTTAACAT
1212441 TTGAAACTAGTGGATTTGCTGATAGAGAGGCTTTTTACAAGTCAATAATCTCTCAGTAGTTCCTT
1 TTGAAACTAGTGGATTTGCTGATAGAGAGGCTTTTTACAAGTCAATAATCTCTCAGTAGTTCCTT
1212506 TTTTGGAATTTTTTTGGTTCCTTTTTCTTTAACAT
66 TTTTGGAATTTTTTTGGTTCCTTTTTCTTTAACAT
1212541 TT
1 TT
1212543 TATTACGGAT
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 102 1.00
ACGTcount: A:0.23, C:0.14, G:0.17, T:0.47
Consensus pattern (100 bp):
TTGAAACTAGTGGATTTGCTGATAGAGAGGCTTTTTACAAGTCAATAATCTCTCAGTAGTTCCTT
TTTTGGAATTTTTTTGGTTCCTTTTTCTTTAACAT
Found at i:1212821 original size:2 final size:2
Alignment explanation
Indices: 1212814--1212847 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1212804 TTAATTGTTA
1212814 AT AT AT 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 AT AT AT
1212848 GCTAGTTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1216079 original size:14 final size:14
Alignment explanation
Indices: 1216062--1216104 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
1216052 ATTTGTTATT
1216062 TATTATAAATTAAA
1 TATTATAAATTAAA
1216076 TATT-TAAATTTAAA
1 TATTATAAA-TTAAA
*
1216090 TAATATAAATGTAAA
1 TATTATAAAT-TAAA
1216105 ATAAAATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 4 0.16
14 13 0.52
15 8 0.32
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (14 bp):
TATTATAAATTAAA
Found at i:1223976 original size:13 final size:14
Alignment explanation
Indices: 1223948--1224023 Score: 56
Period size: 14 Copynumber: 5.9 Consensus size: 14
1223938 ATTTGATTGA
1223948 ATAAAAATTAAAAT
1 ATAAAAATTAAAAT
1223962 ATAAAAA-T--AAT
1 ATAAAAATTAAAAT
****
1223973 ATATTTTTTAAAAT
1 ATAAAAATTAAAAT
*
1223987 AT-TAAATTAAAA-
1 ATAAAAATTAAAAT
*
1223999 AT-CAAATTAAAAT
1 ATAAAAATTAAAAT
1224012 ATAAAAATTAAA
1 ATAAAAATTAAA
1224024 TAAATATATT
Statistics
Matches: 48, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
11 6 0.12
12 12 0.25
13 10 0.21
14 20 0.42
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAAAAATTAAAAT
Found at i:1224005 original size:12 final size:13
Alignment explanation
Indices: 1223980--1224023 Score: 54
Period size: 12 Copynumber: 3.4 Consensus size: 13
1223970 AATATATTTT
*
1223980 TTAAAATATTAAA
1 TTAAAATATCAAA
1223993 TTAAAA-ATCAAA
1 TTAAAATATCAAA
*
1224005 TTAAAATATAAAAA
1 TTAAAATAT-CAAA
1224019 TTAAA
1 TTAAA
1224024 TAAATATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 11 0.41
13 8 0.30
14 8 0.30
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (13 bp):
TTAAAATATCAAA
Found at i:1224030 original size:17 final size:18
Alignment explanation
Indices: 1223987--1224031 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
1223977 TTTTTAAAAT
1223987 ATTAAAT-TAAAAATCAA
1 ATTAAATATAAAAATCAA
*
1224004 ATTAAAATATAAAAATTAA
1 ATT-AAATATAAAAATCAA
1224023 A-TAAATATA
1 ATTAAATATA
1224032 TTATTTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 10 0.40
18 5 0.20
19 10 0.40
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (18 bp):
ATTAAATATAAAAATCAA
Found at i:1234811 original size:31 final size:31
Alignment explanation
Indices: 1234787--1234888 Score: 95
Period size: 31 Copynumber: 3.4 Consensus size: 31
1234777 AATTTACATG
*
1234787 ATAAATTTTAAAAAATTATTTAATTATAAAT
1 ATAAAATTTAAAAAATTATTTAATTATAAAT
* *
1234818 TTAAAATTTAAAAAATTA-TTAA-AATAAAT
1 ATAAAATTTAAAAAATTATTTAATTATAAAT
* * * *
1234847 A-AAAATATAACAATTTATTTAA-AATAAAAT
1 ATAAAATTTAAAAAATTATTTAATTAT-AAAT
1234877 GATAAAATTTAA
1 -ATAAAATTTAA
1234889 TAATTTTCTG
Statistics
Matches: 59, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
28 13 0.22
29 13 0.22
30 8 0.14
31 17 0.29
32 8 0.14
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (31 bp):
ATAAAATTTAAAAAATTATTTAATTATAAAT
Found at i:1239762 original size:20 final size:21
Alignment explanation
Indices: 1239710--1239762 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1239700 ATAAAAATTG
* *
1239710 ATTAAGTTTGTAAATTATTTAA
1 ATTAAATTT-TAAAATATTTAA
1239732 ATTAAATTTTAAAATATTTAA
1 ATTAAATTTTAAAATATTTAA
*
1239753 A-TATATTTTA
1 ATTAAATTTTA
1239763 TTTGATAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 8 0.29
21 12 0.43
22 8 0.29
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (21 bp):
ATTAAATTTTAAAATATTTAA
Found at i:1239789 original size:15 final size:15
Alignment explanation
Indices: 1239746--1239789 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 15
1239736 AATTTTAAAA
* *
1239746 TATTTAAATATATTT
1 TATTTAAATTTATAT
1239761 TATTTGATAATTTATAT
1 TATTT-A-AATTTATAT
1239778 TATTTAAATTTA
1 TATTTAAATTTA
1239790 ATTTAATTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 11 0.44
16 2 0.08
17 12 0.48
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (15 bp):
TATTTAAATTTATAT
Found at i:1253000 original size:19 final size:21
Alignment explanation
Indices: 1252978--1253025 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1252968 TTTTAATATG
1252978 TAAATTTA-TATATTA-TAAA
1 TAAATTTATTATATTATTAAA
*
1252997 TAAATTATATTATTTTATTAAA
1 TAAATT-TATTATATTATTAAA
1253019 -AAATTTA
1 TAAATTTA
1253026 AAAATAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 6 0.24
20 4 0.16
21 11 0.44
22 4 0.16
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TAAATTTATTATATTATTAAA
Found at i:1256656 original size:3 final size:3
Alignment explanation
Indices: 1256648--1256674 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1256638 AAAGCTATGC
1256648 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1256675 TTGCATTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1257188 original size:2 final size:2
Alignment explanation
Indices: 1257181--1257212 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1257171 AAGATAGAAT
1257181 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
1257213 AAGGATATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1258353 original size:2 final size:2
Alignment explanation
Indices: 1258346--1258384 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
1258336 TCTTTTATTT
* *
1258346 TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA GA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1258385 TTTCAGAACG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1265388 original size:14 final size:14
Alignment explanation
Indices: 1265369--1265430 Score: 81
Period size: 14 Copynumber: 4.5 Consensus size: 14
1265359 ACAACACTAA
*
1265369 ATAATAATTAAAAT
1 ATAATAATAAAAAT
1265383 ATAATAATAAAAAT
1 ATAATAATAAAAAT
*
1265397 ATAATTATAAAAAT
1 ATAATAATAAAAAT
*
1265411 ATAAT-ATAAATAT
1 ATAATAATAAAAAT
*
1265424 AAAATAA
1 ATAATAA
1265431 ATTATTAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
13 11 0.26
14 32 0.74
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
ATAATAATAAAAAT
Found at i:1265400 original size:25 final size:25
Alignment explanation
Indices: 1265367--1265425 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 25
1265357 ATACAACACT
*
1265367 AAATAATAATTA-AAATATAATAATAA
1 AAAT-ATAATTATAAAAAT-ATAATAA
*
1265393 AAATATAATTATAAAAATATAATAT
1 AAATATAATTATAAAAATATAATAA
1265418 AAATATAA
1 AAATATAA
1265426 AATAAATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 21 0.70
26 9 0.30
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (25 bp):
AAATATAATTATAAAAATATAATAA
Found at i:1266822 original size:26 final size:26
Alignment explanation
Indices: 1266788--1266841 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
1266778 TCATAATGTA
*
1266788 AAAATAGCATCAACACGTTTCCTAGT
1 AAAATAGCATCAACACGTTTCCCAGT
1266814 AAAATAGCATCAACACGTTTCCCAGT
1 AAAATAGCATCAACACGTTTCCCAGT
1266840 AA
1 AA
1266842 TCAAAGATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.41, C:0.24, G:0.11, T:0.24
Consensus pattern (26 bp):
AAAATAGCATCAACACGTTTCCCAGT
Found at i:1267163 original size:75 final size:75
Alignment explanation
Indices: 1267011--1267167 Score: 174
Period size: 75 Copynumber: 2.1 Consensus size: 75
1267001 TATTCATCAC
* * * * * * * *
1267011 ATAAATTTTAATCATTAAAAAAATAAAATTTTGATAATTAATATTTATTCTGACTGTTAGATCTG
1 ATAAATTTTAATCATCAAAAAAATAAAATCTTGACAATAAACATTAATTCTGACTGTCAAATCTG
* *
1267076 TACTTGTTAT
66 TACTCGTCAT
* *
1267086 ATAAATTTTAATCA-CAAAAAAGATAAAATCTTGACAATAAACATTAATTCTGATTGTCAAATTT
1 ATAAATTTTAATCATCAAAAAA-ATAAAATCTTGACAATAAACATTAATTCTGACTGTCAAATCT
1267150 GTGA-TCGTCAT
65 GT-ACTCGTCAT
1267161 ATAAATT
1 ATAAATT
1267168 CTGATCGTGA
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
74 6 0.09
75 61 0.90
76 1 0.01
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (75 bp):
ATAAATTTTAATCATCAAAAAAATAAAATCTTGACAATAAACATTAATTCTGACTGTCAAATCTG
TACTCGTCAT
Found at i:1267397 original size:18 final size:18
Alignment explanation
Indices: 1267374--1267422 Score: 59
Period size: 16 Copynumber: 2.9 Consensus size: 18
1267364 CATTAAAATA
1267374 TTTATATATTTATATTAT
1 TTTATATATTTATATTAT
*
1267392 TTTATAT-TTTA-ATAAT
1 TTTATATATTTATATTAT
*
1267408 TTTTTATA-TTATATT
1 TTTATATATTTATATT
1267423 TATATAATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 13 0.50
17 6 0.23
18 7 0.27
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTATATATTTATATTAT
Found at i:1267399 original size:16 final size:16
Alignment explanation
Indices: 1267372--1267422 Score: 52
Period size: 18 Copynumber: 3.1 Consensus size: 16
1267362 TACATTAAAA
1267372 TATTTATATATTTATAT
1 TATTT-TATATTTATAT
1267389 TATTTTATATTTTAATAAT
1 TATTTTATA-TTT-AT-AT
1267408 T-TTTTATA-TTATAT
1 TATTTTATATTTATAT
1267422 T
1 T
1267423 TATATAATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
14 3 0.10
15 2 0.06
16 6 0.19
17 8 0.26
18 9 0.29
19 3 0.10
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTTTATATTTATAT
Found at i:1267419 original size:23 final size:23
Alignment explanation
Indices: 1267371--1267431 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 23
1267361 TTACATTAAA
*
1267371 ATATTTATAT-ATTTATATTATTTT
1 ATATTTATATAATTT-T-TTATATT
1267395 ATATTT-TAATAATTTTTTATATT
1 ATATTTAT-ATAATTTTTTATATT
1267418 ATATTTATATAATT
1 ATATTTATATAATT
1267432 GTGTTAATCA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
23 19 0.58
24 10 0.30
25 4 0.12
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
ATATTTATATAATTTTTTATATT
Found at i:1273701 original size:24 final size:24
Alignment explanation
Indices: 1273658--1273740 Score: 96
Period size: 27 Copynumber: 3.3 Consensus size: 24
1273648 ATATAAAATG
* *
1273658 TATTATATTAATTATGTTATTTTTA
1 TATT-TATTAAATATATTATTTTTA
1273683 TATTTATTAAATATATTATTATTTTCA
1 TATTTATTAAATATATTA-T-TTTT-A
*
1273710 TATTTATTAAATATATTATTATT-
1 TATTTATTAAATATATTATTTTTA
1273733 TATTTATT
1 TATTTATT
1273741 TTTATTTTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
23 8 0.15
24 12 0.23
25 8 0.15
26 5 0.10
27 19 0.37
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (24 bp):
TATTTATTAAATATATTATTTTTA
Found at i:1273712 original size:27 final size:27
Alignment explanation
Indices: 1273674--1273733 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
1273664 ATTAATTATG
*
1273674 TTATTTTTATATTTATTAAATATATTA
1 TTATTTTCATATTTATTAAATATATTA
1273701 TTATTTTCATATTTATTAAATATATTA
1 TTATTTTCATATTTATTAAATATATTA
1273728 TTATTT
1 TTATTT
1273734 ATTTATTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (27 bp):
TTATTTTCATATTTATTAAATATATTA
Found at i:1273740 original size:27 final size:26
Alignment explanation
Indices: 1273674--1273741 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 26
1273664 ATTAATTATG
1273674 TTATTTTTATATTTATTAAATATATTA
1 TTATTTTT-TATTTATTAAATATATTA
*
1273701 TTATTTTCATATTTATTAAATATATTA
1 TTATTTT-TTATTTATTAAATATATTA
1273728 TTATTTATTTATTT
1 TTATTT-TTTATTT
1273742 TTATTTTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
27 36 0.97
28 1 0.03
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (26 bp):
TTATTTTTTATTTATTAAATATATTA
Found at i:1273788 original size:15 final size:16
Alignment explanation
Indices: 1273750--1273793 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
1273740 TTTTATTTTT
1273750 TATAAATTAA-ATATGA
1 TATAAA-TAATATATGA
1273766 TATAAATAATATAT-A
1 TATAAATAATATATGA
*
1273781 TATTAATAATATA
1 TATAAATAATATA
1273794 ATAAATACGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 16 0.62
16 10 0.38
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (16 bp):
TATAAATAATATATGA
Found at i:1274992 original size:32 final size:33
Alignment explanation
Indices: 1274944--1275024 Score: 119
Period size: 32 Copynumber: 2.5 Consensus size: 33
1274934 CATATTATTT
*
1274944 TATATTTTTATTTATATAAATTTTAAAATATTAA
1 TATATTTATA-TTATATAAATTTTAAAATATTAA
*
1274978 TA-ATTTATATTATATAAATTTTAAAATATTTA
1 TATATTTATATTATATAAATTTTAAAATATTAA
*
1275010 TATATTCATATTATA
1 TATATTTATATTATA
1275025 ATTATATTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
32 24 0.56
33 17 0.40
34 2 0.05
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (33 bp):
TATATTTATATTATATAAATTTTAAAATATTAA
Found at i:1275044 original size:23 final size:20
Alignment explanation
Indices: 1275017--1275066 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 20
1275007 TTATATATTC
1275017 ATATTATAATTATATTAATTTTT
1 ATATTATAA-T-T-TTAATTTTT
1275040 ATATTAT-ATTTTAATTTTT
1 ATATTATAATTTTAATTTTT
*
1275059 TTATTATA
1 ATATTATA
1275067 TCATATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 15 0.60
20 1 0.04
21 1 0.04
22 1 0.04
23 7 0.28
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
ATATTATAATTTTAATTTTT
Found at i:1275055 original size:19 final size:19
Alignment explanation
Indices: 1275031--1275067 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1275021 TATAATTATA
1275031 TTAATTTTTATATTATATT
1 TTAATTTTTATATTATATT
*
1275050 TTAATTTTTTTATTATAT
1 TTAATTTTTATATTATAT
1275068 CATATTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTAATTTTTATATTATATT
Found at i:1282957 original size:2 final size:2
Alignment explanation
Indices: 1282950--1282993 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
1282940 TTGTAACTAC
* * *
1282950 AT AT AT AT AT AT AT AT AT CT AT AT AT AT AA AT AT AA 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
1282992 AT
1 AT
1282994 TTATGTTGGT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1283987 original size:32 final size:32
Alignment explanation
Indices: 1283949--1284014 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
1283939 TTTTCCCGCG
1283949 TTAAAGTTATTTTAATTTTGATTACCTAAATT
1 TTAAAGTTATTTTAATTTTGATTACCTAAATT
*
1283981 TTAAAGTTATTTTAATTTTGATTTCCTAAATT
1 TTAAAGTTATTTTAATTTTGATTACCTAAATT
1284013 TT
1 TT
1284015 CTTAGTTACC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.56
Consensus pattern (32 bp):
TTAAAGTTATTTTAATTTTGATTACCTAAATT
Found at i:1292080 original size:27 final size:28
Alignment explanation
Indices: 1292021--1292080 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 28
1292011 TGATTGAAAA
* * * *
1292021 ATAAAAAAAACTTAATTCATAAATTATT
1 ATAATAAAAACTGAATTCAAAAATTAAT
*
1292049 TTAATAAAAACTGAATT-AAAAATTAAT
1 ATAATAAAAACTGAATTCAAAAATTAAT
1292076 ATAAT
1 ATAAT
1292081 TATATTTTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
27 12 0.46
28 14 0.54
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (28 bp):
ATAATAAAAACTGAATTCAAAAATTAAT
Found at i:1292170 original size:50 final size:48
Alignment explanation
Indices: 1292116--1292212 Score: 115
Period size: 50 Copynumber: 2.0 Consensus size: 48
1292106 ATGACTTTAT
*
1292116 TAATTTAAATCT-AAACTTACCCAAATTCAAAAAAAAAAAAAAACTCAAAC
1 TAATTTAAAT-TAAAAATT-CCCAAATTCAAAAAAAAAAAAAAA-TCAAAC
* * *
1292166 TAATTTCAATTAAAAAATTTCCAAATTCAGAAAAAAAAAAAAATCAA
1 TAATTTAAATT-AAAAATTCCCAAATTCAAAAAAAAAAAAAAATCAA
1292213 GAACATGCCT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
49 5 0.12
50 31 0.76
51 5 0.12
ACGTcount: A:0.61, C:0.14, G:0.01, T:0.24
Consensus pattern (48 bp):
TAATTTAAATTAAAAATTCCCAAATTCAAAAAAAAAAAAAAATCAAAC
Found at i:1292393 original size:13 final size:14
Alignment explanation
Indices: 1292364--1292475 Score: 57
Period size: 13 Copynumber: 8.5 Consensus size: 14
1292354 ATTTTTAATA
1292364 ATTTAT-ATAT-TT
1 ATTTATAATATATT
1292376 ATTTATAATATATT
1 ATTTATAATATATT
*
1292390 -TTTATATTATAATCGT
1 ATTTATAATAT-AT--T
1292406 ATTTA-AA-ATATT
1 ATTTATAATATATT
* * *
1292418 ATATATTATATA-A
1 ATTTATAATATATT
1292431 ATTT-TAATA-A-T
1 ATTTATAATATATT
*
1292442 -TTAATAATATATT
1 ATTTATAATATATT
*
1292455 ATATATTAATATATT
1 ATTTA-TAATATATT
1292470 -TTTATA
1 ATTTATA
1292476 TTAAAATTAT
Statistics
Matches: 75, Mismatches: 12, Indels: 25
0.67 0.11 0.22
Matches are distributed among these distances:
10 2 0.03
11 6 0.08
12 16 0.21
13 20 0.27
14 14 0.19
15 11 0.15
16 2 0.03
17 4 0.05
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (14 bp):
ATTTATAATATATT
Found at i:1292409 original size:30 final size:29
Alignment explanation
Indices: 1292366--1292510 Score: 99
Period size: 30 Copynumber: 5.2 Consensus size: 29
1292356 TTTTAATAAT
*
1292366 TTATATATTTATTTATAATATATTTTTATA
1 TTATA-ATATATTTATAATATATTTTTATA
* *
1292396 TTATAATCGTATTTA-AA-ATA-TTATATA
1 TTATAAT-ATATTTATAATATATTTTTATA
* *
1292423 TTAT-ATAAATTT-TAATA-A-TTTAATA
1 TTATAATATATTTATAATATATTTTTATA
* * *
1292448 ATATATTATATAT-TAATATATTTTTATA
1 TTATAATATATTTATAATATATTTTTATA
* * * *
1292476 TTAAAATTATGTTTATATTATTTTTTTATA
1 TTATAA-TATATTTATAATATATTTTTATA
1292506 TTATA
1 TTATA
1292511 TTATGTTGGT
Statistics
Matches: 88, Mismatches: 19, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
25 15 0.17
26 13 0.15
27 11 0.12
28 12 0.14
29 9 0.10
30 28 0.32
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (29 bp):
TTATAATATATTTATAATATATTTTTATA
Found at i:1292492 original size:17 final size:16
Alignment explanation
Indices: 1292442--1292495 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
1292432 TTTTAATAAT
*
1292442 TTAATAATATATTATATA
1 TTAA-AATATGTT-TATA
* *
1292460 TTAATATATTTTTATA
1 TTAAAATATGTTTATA
1292476 TTAAAATTATGTTTATA
1 TTAAAA-TATGTTTATA
1292493 TTA
1 TTA
1292496 TTTTTTTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
16 9 0.29
17 18 0.58
18 4 0.13
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (16 bp):
TTAAAATATGTTTATA
Found at i:1296292 original size:2 final size:2
Alignment explanation
Indices: 1296227--1296275 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
1296217 GTGGTGTGTG
* *
1296227 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1296269 TA TA TA T
1 TA TA TA T
1296276 TGGAGATTGT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:1307341 original size:76 final size:77
Alignment explanation
Indices: 1307207--1307358 Score: 297
Period size: 76 Copynumber: 2.0 Consensus size: 77
1307197 ATATTAATAT
1307207 AAAATATCATCTTTTAAATATATCAAAAAATTTTAAAAATTAAATATACTCATATCCATATCCAG
1 AAAATATCATCTTTTAAATATATCAAAAAATTTTAAAAATTAAATATACTCATATCCATATCCAG
1307272 TATTCATCCTAA
66 TATTCATCCTAA
1307284 AAAATATCATCTTTTAAATATATCAAAAAA-TTTAAAAATTAAATATACTCATATCCATATCCAG
1 AAAATATCATCTTTTAAATATATCAAAAAATTTTAAAAATTAAATATACTCATATCCATATCCAG
1307348 TATTCATCCTA
66 TATTCATCCTA
1307359 GATCTTTATT
Statistics
Matches: 75, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
76 45 0.60
77 30 0.40
ACGTcount: A:0.47, C:0.16, G:0.01, T:0.36
Consensus pattern (77 bp):
AAAATATCATCTTTTAAATATATCAAAAAATTTTAAAAATTAAATATACTCATATCCATATCCAG
TATTCATCCTAA
Found at i:1307430 original size:23 final size:24
Alignment explanation
Indices: 1307389--1307434 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
1307379 CTTTGGTTCT
* *
1307389 TAAAATTTATATTTTTTTACTTTC
1 TAAAAATTATATTTATTTACTTTC
1307413 TAAAAATT-TATTTATTTACTTT
1 TAAAAATTATATTTATTTACTTT
1307435 TGTTTTACTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.61
Consensus pattern (24 bp):
TAAAAATTATATTTATTTACTTTC
Found at i:1307850 original size:2 final size:2
Alignment explanation
Indices: 1307843--1307886 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1307833 ATACATATGC
*
1307843 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1307885 AT
1 AT
1307887 CAGCCTATTG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1314384 original size:3 final size:3
Alignment explanation
Indices: 1314376--1314412 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1314366 TTGGATTAGA
1314376 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 A
1314413 TTGGACTGAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1317253 original size:19 final size:19
Alignment explanation
Indices: 1317215--1317252 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
1317205 TAGTCTCTAG
1317215 TGCTTTGAGGGTTTTTTTT
1 TGCTTTGAGGGTTTTTTTT
1317234 TGCTTTGA-GGTTTTTTTT
1 TGCTTTGAGGGTTTTTTTT
1317252 T
1 T
1317253 TATTTACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.05, C:0.05, G:0.24, T:0.66
Consensus pattern (19 bp):
TGCTTTGAGGGTTTTTTTT
Found at i:1317526 original size:1 final size:1
Alignment explanation
Indices: 1317520--1317544 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1317510 TAAGCCTAGG
1317520 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
1317545 GCGCCCAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1325753 original size:18 final size:18
Alignment explanation
Indices: 1325730--1325764 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1325720 TTTCAAATAA
1325730 ATTATTCTTATATTTAAT
1 ATTATTCTTATATTTAAT
* *
1325748 ATTATTTTTATTTTTAA
1 ATTATTCTTATATTTAA
1325765 AATAGTGTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (18 bp):
ATTATTCTTATATTTAAT
Found at i:1335612 original size:34 final size:33
Alignment explanation
Indices: 1335569--1335633 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 33
1335559 GCAAATGGAG
1335569 GTGGGTTCCTCTTTTCTTTTTCTTTTTTTTTTTT
1 GTGGGTTCCTCTTTTC-TTTTCTTTTTTTTTTTT
1335603 GTGGGTTCCTCTTTTCTTTTCTTTTTTTTTT
1 GTGGGTTCCTCTTTTCTTTTCTTTTTTTTTT
1335634 CCTTCTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 15 0.48
34 16 0.52
ACGTcount: A:0.00, C:0.15, G:0.12, T:0.72
Consensus pattern (33 bp):
GTGGGTTCCTCTTTTCTTTTCTTTTTTTTTTTT
Found at i:1343294 original size:2 final size:2
Alignment explanation
Indices: 1343287--1343328 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1343277 TACATAGCTG
1343287 TA TA TA 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 TA TA TA
1343329 GCAAAACATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1345705 original size:10 final size:10
Alignment explanation
Indices: 1345682--1345727 Score: 56
Period size: 11 Copynumber: 4.3 Consensus size: 10
1345672 AAAATTATTA
1345682 AATAATATAAT
1 AATAATA-AAT
1345693 AATAATAAAT
1 AATAATAAAT
1345703 AATAATAAAT
1 AATAATAAAT
*
1345713 ATATTATAATAT
1 A-ATAATAA-AT
1345725 AAT
1 AAT
1345728 TTAAAATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
10 14 0.44
11 15 0.47
12 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
AATAATAAAT
Found at i:1345706 original size:13 final size:14
Alignment explanation
Indices: 1345682--1345727 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
1345672 AAAATTATTA
1345682 AATAATATAATAAT
1 AATAATATAATAAT
1345696 AATAA-ATAATAAT
1 AATAATATAATAAT
*
1345709 AA-ATATATTATAAT
1 AATA-ATATAATAAT
1345723 -ATAAT
1 AATAAT
1345728 TTAAAATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
12 1 0.04
13 14 0.50
14 13 0.46
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AATAATATAATAAT
Found at i:1345756 original size:16 final size:15
Alignment explanation
Indices: 1345732--1345775 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
1345722 TATAATTTAA
*
1345732 AATATTTTATAT-TT
1 AATAATTTATATATT
1345746 ATATAACTTTATATATT
1 A-ATAA-TTTATATATT
1345763 AATAATTTATATA
1 AATAATTTATATA
1345776 CTCAGCATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 1 0.04
15 11 0.42
16 11 0.42
17 3 0.12
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (15 bp):
AATAATTTATATATT
Found at i:1348716 original size:2 final size:2
Alignment explanation
Indices: 1348709--1348737 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1348699 ATATAAAAGA
1348709 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1348738 ATATACATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1349213 original size:2 final size:2
Alignment explanation
Indices: 1349206--1349237 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1349196 GAAAATAGCC
1349206 AT AT 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 AT AT
1349238 CATTCAGCAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1349886 original size:19 final size:19
Alignment explanation
Indices: 1349862--1349906 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1349852 AATAAATTAA
1349862 ATATATTCATATTAAATAT
1 ATATATTCATATTAAATAT
* *
1349881 ATATATTCGTATTTAATAT
1 ATATATTCATATTAAATAT
*
1349900 TTATATT
1 ATATATT
1349907 TTAATTTAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (19 bp):
ATATATTCATATTAAATAT
Found at i:1350286 original size:16 final size:16
Alignment explanation
Indices: 1350265--1350295 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1350255 TTTATATTTT
1350265 TAAAAATATATTTAAA
1 TAAAAATATATTTAAA
*
1350281 TAAAAATATTTTTAA
1 TAAAAATATATTTAA
1350296 TTAGTGAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAAAATATATTTAAA
Found at i:1354967 original size:12 final size:12
Alignment explanation
Indices: 1354936--1354969 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1354926 TGGTCCGCCT
*
1354936 TGCTCCCACTCC
1 TGCTCCCGCTCC
*
1354948 CGCTCCCGCTCC
1 TGCTCCCGCTCC
1354960 TGCTCCCGCT
1 TGCTCCCGCT
1354970 TGCATCACCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.03, C:0.59, G:0.15, T:0.24
Consensus pattern (12 bp):
TGCTCCCGCTCC
Found at i:1361497 original size:26 final size:26
Alignment explanation
Indices: 1361466--1361531 Score: 91
Period size: 26 Copynumber: 2.5 Consensus size: 26
1361456 TAGATAATAA
1361466 ATAAATTTAAATTTTAAAATATT-TAT
1 ATAAATTTAAATTTT-AAATATTATAT
1361492 ATAAATTTAAA-TTTAAATATTATAT
1 ATAAATTTAAATTTTAAATATTATAT
*
1361517 ATAAATATTTAATTT
1 ATAAAT-TTAAATTT
1361532 ATTGTGATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
24 7 0.19
25 12 0.33
26 15 0.42
27 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
ATAAATTTAAATTTTAAATATTATAT
Found at i:1361523 original size:13 final size:13
Alignment explanation
Indices: 1361482--1361525 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
1361472 TTAAATTTTA
1361482 AAATATT-TATAT
1 AAATATTATATAT
* *
1361494 AAAT-TTAAATTT
1 AAATATTATATAT
1361506 AAATATTATATAT
1 AAATATTATATAT
1361519 AAATATT
1 AAATATT
1361526 TAATTTATTG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
11 2 0.08
12 11 0.42
13 13 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AAATATTATATAT
Found at i:1361601 original size:19 final size:18
Alignment explanation
Indices: 1361558--1361602 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
1361548 AAAAAATTAT
*
1361558 TATATATTTTATTTTTAA
1 TATATATTTTATTTTAAA
1361576 T-TGATATTTATATTTTAAA
1 TAT-ATATTT-TATTTTAAA
1361595 TATATATT
1 TATATATT
1361603 ATTTTATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 1 0.04
18 7 0.30
19 14 0.61
20 1 0.04
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
TATATATTTTATTTTAAA
Found at i:1361883 original size:18 final size:18
Alignment explanation
Indices: 1361860--1361896 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1361850 AGGTTGAGAC
1361860 TTCCGTAGCACCGATGAA
1 TTCCGTAGCACCGATGAA
1361878 TTCCGTAGCACCGATGAA
1 TTCCGTAGCACCGATGAA
1361896 T
1 T
1361897 CATGGACACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (18 bp):
TTCCGTAGCACCGATGAA
Found at i:1362890 original size:25 final size:25
Alignment explanation
Indices: 1362862--1362912 Score: 86
Period size: 25 Copynumber: 2.0 Consensus size: 25
1362852 TTTTTTTTTC
1362862 AACTATT-TATTTTAATATTATGTTA
1 AACTATTAT-TTTTAATATTATGTTA
1362887 AACTATTATTTTTAATATTATGTTA
1 AACTATTATTTTTAATATTATGTTA
1362912 A
1 A
1362913 TATATGTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 24 0.96
26 1 0.04
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (25 bp):
AACTATTATTTTTAATATTATGTTA
Found at i:1362895 original size:13 final size:12
Alignment explanation
Indices: 1362875--1362927 Score: 56
Period size: 12 Copynumber: 4.4 Consensus size: 12
1362865 TATTTATTTT
1362875 AATATTATGTTA
1 AATATTATGTTA
* *
1362887 AACTATTATTTTT
1 AA-TATTATGTTA
1362900 AATATTATGTT-
1 AATATTATGTTA
1362911 AATA-TATGTTTA
1 AATATTATG-TTA
1362923 AATAT
1 AATAT
1362928 AAATATAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
10 4 0.12
11 6 0.18
12 14 0.41
13 10 0.29
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.53
Consensus pattern (12 bp):
AATATTATGTTA
Found at i:1362920 original size:10 final size:11
Alignment explanation
Indices: 1362868--1362920 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
1362858 TTTCAACTAT
*
1362868 TTATTTTAATA
1 TTATGTTAATA
1362879 TTATGTTAAACTA
1 TTATGTT-AA-TA
*
1362892 TTATTTTTAATA
1 TTA-TGTTAATA
1362904 TTATGTTAATA
1 TTATGTTAATA
1362915 -TATGTT
1 TTATGTT
1362921 TAAATATAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
10 6 0.17
11 13 0.36
12 7 0.19
13 7 0.19
14 3 0.08
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.58
Consensus pattern (11 bp):
TTATGTTAATA
Found at i:1371974 original size:107 final size:106
Alignment explanation
Indices: 1371815--1372026 Score: 370
Period size: 107 Copynumber: 2.0 Consensus size: 106
1371805 TCCAATCAAC
* * *
1371815 ATCATCTTGGTCAATTATGCATTTCAATAGTTTAACCAGAAGGTTGAGGGAGACAACAGGGGCAA
1 ATCAACTTGGTCAATCATGCATTTCAATAGTTTAACCAGAAGGTTGAGGGAGACAACAAGGGCAA
*
1371880 ATTTTCAACAACACTGTGTATATGAAGAACTCACTCCATGT
66 ATTTTCAACAACACTATGTATATGAAGAACTCACTCCATGT
*
1371921 ATCAACTTGGTCAATCGTGCATTTCAATAGCTTTAACCAGAAGGTTGAGGGAGACAACAAGGGCA
1 ATCAACTTGGTCAATCATGCATTTCAATAG-TTTAACCAGAAGGTTGAGGGAGACAACAAGGGCA
1371986 AATTTTCAACAACACTATGTATATGAAGAACTCACTCCATG
65 AATTTTCAACAACACTATGTATATGAAGAACTCACTCCATG
1372027 GCTATAACCC
Statistics
Matches: 100, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
106 27 0.27
107 73 0.73
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (106 bp):
ATCAACTTGGTCAATCATGCATTTCAATAGTTTAACCAGAAGGTTGAGGGAGACAACAAGGGCAA
ATTTTCAACAACACTATGTATATGAAGAACTCACTCCATGT
Found at i:1373221 original size:3 final size:3
Alignment explanation
Indices: 1373209--1373246 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
1373199 TTGTTAGGAA
1373209 CTT C-T CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1373247 TGTAGAAATC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:1373997 original size:14 final size:14
Alignment explanation
Indices: 1373980--1374012 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1373970 TTAAAAGGGC
1373980 AAAAATAAAAAAAT
1 AAAAATAAAAAAAT
*
1373994 AAAATTAAAAAAAT
1 AAAAATAAAAAAAT
1374008 AAAAA
1 AAAAA
1374013 GGAAGAATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (14 bp):
AAAAATAAAAAAAT
Found at i:1376323 original size:4 final size:4
Alignment explanation
Indices: 1376314--1376359 Score: 92
Period size: 4 Copynumber: 11.5 Consensus size: 4
1376304 TTGCTGAGTT
1376314 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GA
1376360 AGCAGCCTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.26, T:0.24
Consensus pattern (4 bp):
GATA
Found at i:1376606 original size:2 final size:2
Alignment explanation
Indices: 1376599--1376627 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1376589 AGCTTCAGTG
1376599 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1376628 CCCCATACGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1376728 original size:3 final size:3
Alignment explanation
Indices: 1376720--1376747 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1376710 GTTTTCTTTG
1376720 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1376748 TCTAAAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1378086 original size:19 final size:18
Alignment explanation
Indices: 1378059--1378100 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1378049 AATTCGATTG
*
1378059 ATTATATAAAAATTTTAAT
1 ATTAAATAAAAA-TTTAAT
*
1378078 ATTAAATAAATATTTAAT
1 ATTAAATAAAAATTTAAT
1378096 ATTAA
1 ATTAA
1378101 TATATATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATTAAATAAAAATTTAAT
Found at i:1378102 original size:17 final size:18
Alignment explanation
Indices: 1378068--1378112 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
1378058 GATTATATAA
1378068 AAAT-TTTAATATTAAAT
1 AAATATTTAATATTAAAT
1378085 AAATATTTAATATT-AAT
1 AAATATTTAATATTAAAT
*
1378102 ATATATTTAAT
1 AAATATTTAAT
1378113 TAAATATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 17 0.65
18 9 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AAATATTTAATATTAAAT
Found at i:1378116 original size:29 final size:30
Alignment explanation
Indices: 1378079--1378141 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 30
1378069 AATTTTAATA
1378079 TTAAATAAATATT-T-AATATTAATATATAT
1 TTAAATAAATATTATAAATATTAATAT-TAT
* *
1378108 TTAATTAAATATTATAAATTTTAATATTAT
1 TTAAATAAATATTATAAATATTAATATTAT
1378138 TTAA
1 TTAA
1378142 GAAAATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 12 0.40
30 8 0.27
31 10 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (30 bp):
TTAAATAAATATTATAAATATTAATATTAT
Found at i:1378123 original size:17 final size:16
Alignment explanation
Indices: 1378078--1378119 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
1378068 AAATTTTAAT
*
1378078 ATTAAATAAATATTTA
1 ATTAAATATATATTTA
*
1378094 ATATTAATATATATTTA
1 AT-TAAATATATATTTA
1378111 ATTAAATAT
1 ATTAAATAT
1378120 TATAAATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTAAATATATATTTA
Found at i:1378480 original size:16 final size:17
Alignment explanation
Indices: 1378461--1378501 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
1378451 TAAATATTTT
1378461 TTAAATTTAATA-ATAA
1 TTAAATTTAATATATAA
1378477 TTAAA--TAATATATAA
1 TTAAATTTAATATATAA
1378492 TT-AATTTAAT
1 TTAAATTTAAT
1378502 TTTTAATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 7 0.32
15 6 0.27
16 9 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TTAAATTTAATATATAA
Found at i:1378790 original size:14 final size:15
Alignment explanation
Indices: 1378771--1378803 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1378761 TACGCCACTG
1378771 TTTTTTCTTTTGT-T
1 TTTTTTCTTTTGTCT
*
1378785 TTTTTTTTTTTGTCT
1 TTTTTTCTTTTGTCT
1378800 TTTT
1 TTTT
1378804 GTAATTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.88
Consensus pattern (15 bp):
TTTTTTCTTTTGTCT
Found at i:1380654 original size:31 final size:31
Alignment explanation
Indices: 1380618--1380684 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
1380608 AATACATAAA
*
1380618 ATAAAATA-AAT-TATTAATATGTAAAAAATAT
1 ATAAAATATAATATATTAA-ATATAAAAAA-AT
*
1380649 ATAAAATATAATATTTTAAATATAAAAAAAT
1 ATAAAATATAATATATTAAATATAAAAAAAT
1380680 ATAAA
1 ATAAA
1380685 TACAAACATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 15 0.47
32 12 0.38
33 5 0.16
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (31 bp):
ATAAAATATAATATATTAAATATAAAAAAAT
Found at i:1380654 original size:36 final size:32
Alignment explanation
Indices: 1380598--1380684 Score: 88
Period size: 36 Copynumber: 2.7 Consensus size: 32
1380588 CTCTCATATA
* *
1380598 TAAA-ATAACAAATACATAAAATAAAATAAATTAT
1 TAAATATAAAAAATATATAAAATAAAAT--ATT-T
* *
1380632 TAATATGTAAAAAATATATAAAATATAATATTT
1 TAA-ATATAAAAAATATATAAAATAAAATATTT
1380665 TAAATATAAAAAA-ATATAAA
1 TAAATATAAAAAATATATAAA
1380685 TACAAACATA
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
31 7 0.15
32 9 0.20
33 4 0.09
34 6 0.13
35 1 0.02
36 19 0.41
ACGTcount: A:0.66, C:0.02, G:0.01, T:0.31
Consensus pattern (32 bp):
TAAATATAAAAAATATATAAAATAAAATATTT
Found at i:1381959 original size:26 final size:25
Alignment explanation
Indices: 1381930--1381987 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 25
1381920 TATACATAAA
1381930 AATATTAAAAAATA-AAATAAAATATT
1 AATATTAAAAAATATAAA-AAAATA-T
* *
1381956 AATATATAAAAGATATACAAAAATAT
1 AATAT-TAAAAAATATAAAAAAATAT
1381982 AATATT
1 AATATT
1381988 TTAAATACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
25 1 0.04
26 11 0.39
27 14 0.50
28 2 0.07
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (25 bp):
AATATTAAAAAATATAAAAAAATAT
Done.