Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold40
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: 3440810
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 28138 characters in sequence are not A, C, G, or T
File 8 of 24
Found at i:1043540 original size:27 final size:28
Alignment explanation
Indices: 1043510--1043571 Score: 65
Period size: 32 Copynumber: 2.1 Consensus size: 28
1043500 AATTATTATT
1043510 TTTA-ATATTATTAAA-TTAAAAATAATA
1 TTTATATATTATTAAATTTAAAAA-AATA
1043537 TTTATTTTTATATTATTAAATTTAAAAAAATA
1 TTTA----TATATTATTAAATTTAAAAAAATA
1043569 TTT
1 TTT
1043572 TTTATCATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
27 4 0.14
32 18 0.62
33 7 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
TTTATATATTATTAAATTTAAAAAAATA
Found at i:1043555 original size:32 final size:34
Alignment explanation
Indices: 1043491--1043571 Score: 116
Period size: 33 Copynumber: 2.5 Consensus size: 34
1043481 TTTAAAATAT
*
1043491 TTTAATAATAAT-TATTATTTTTAATATTATTAAA
1 TTTAAAAATAATAT-TTATTTTTAATATTATTAAA
1043525 -TTAAAAATAATATTTATTTTT-ATATTATTAAA
1 TTTAAAAATAATATTTATTTTTAATATTATTAAA
1043557 TTTAAAAA-AATATTT
1 TTTAAAAATAATATTT
1043572 TTTATCATTA
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
32 18 0.41
33 25 0.57
34 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (34 bp):
TTTAAAAATAATATTTATTTTTAATATTATTAAA
Found at i:1043572 original size:27 final size:31
Alignment explanation
Indices: 1043492--1043583 Score: 109
Period size: 33 Copynumber: 2.9 Consensus size: 31
1043482 TTAAAATATT
*
1043492 TTAATAATAATTATTATTTTTAATATTATTAAA
1 TTAAAAATAA-TATTATTTTT-ATATTATTAAA
1043525 TTAAAAATAATATTTATTTTTATATTATTAAA
1 TTAAAAATAATA-TTATTTTTATATTATTAAA
1043557 TTTAAAAA-AATA-T-TTTTTATCATTATT
1 -TTAAAAATAATATTATTTTTAT-ATTATT
1043584 TTAATCGATA
Statistics
Matches: 55, Mismatches: 1, Indels: 9
0.85 0.02 0.14
Matches are distributed among these distances:
29 7 0.13
30 7 0.13
32 17 0.31
33 24 0.44
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (31 bp):
TTAAAAATAATATTATTTTTATATTATTAAA
Found at i:1043670 original size:15 final size:16
Alignment explanation
Indices: 1043629--1043670 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
1043619 TAATTATGTG
1043629 AATATATTTTTAAAAAA
1 AATAT-TTTTTAAAAAA
*
1043646 AATATTTTTTAAAATA
1 AATATTTTTTAAAAAA
1043662 AAT-TTTTTT
1 AATATTTTTT
1043671 GAATATATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 6 0.25
16 13 0.54
17 5 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATATTTTTTAAAAAA
Found at i:1043832 original size:31 final size:33
Alignment explanation
Indices: 1043770--1043836 Score: 93
Period size: 31 Copynumber: 2.1 Consensus size: 33
1043760 TAAATTTAAT
* *
1043770 AAATAATATATTAATTATTATTTTTATAAAATTA
1 AAATAATATATTAATTA-TAATTTTAAAAAATTA
1043804 AAATAATAT-TTAATTA-AATTTTAAAAAATTA
1 AAATAATATATTAATTATAATTTTAAAAAATTA
1043835 AA
1 AA
1043837 GTATGATTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
31 15 0.48
33 7 0.23
34 9 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (33 bp):
AAATAATATATTAATTATAATTTTAAAAAATTA
Found at i:1044127 original size:11 final size:11
Alignment explanation
Indices: 1044111--1044147 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
1044101 TTATTACTTT
1044111 TTATTTATAAA
1 TTATTTATAAA
* *
1044122 TTATTTTTAAT
1 TTATTTATAAA
1044133 TTATTTATAAA
1 TTATTTATAAA
1044144 TTAT
1 TTAT
1044148 ACAAAATTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTATTTATAAA
Found at i:1044155 original size:22 final size:22
Alignment explanation
Indices: 1044110--1044159 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
1044100 ATTATTACTT
****
1044110 TTTATTTATAAATTATTTTTAA
1 TTTATTTATAAATTATACAAAA
1044132 TTTATTTATAAATTATACAAAA
1 TTTATTTATAAATTATACAAAA
1044154 -TTATTT
1 TTTATTT
1044160 TTATTAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTATTTATAAATTATACAAAA
Found at i:1044423 original size:11 final size:11
Alignment explanation
Indices: 1044407--1044443 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
1044397 TTATTACTTT
1044407 TTATTTATAAA
1 TTATTTATAAA
* *
1044418 TTATTTTTAAT
1 TTATTTATAAA
1044429 TTATTTATAAA
1 TTATTTATAAA
1044440 TTAT
1 TTAT
1044444 ACAAATTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTATTTATAAA
Found at i:1044524 original size:296 final size:295
Alignment explanation
Indices: 1043990--1044645 Score: 1116
Period size: 296 Copynumber: 2.2 Consensus size: 295
1043980 TTTACATGTA
** * * * *
1043990 TTATTTTTTAGTAACGACTTAAATATGAATTTTTTTATCTATAAAATGACTAAGAAAAAATTTAT
1 TTATTTTTCGGTAACAACTTAAATATGAGTTTTTTTATCTGTAAAATGACCAAGAAAAAA-TTAT
* * *
1044055 TGTACATGTATTATTTTTATTAAAATTAATTAATATTATACATGTATTATTACTTTTTATTTATA
65 TATACATATATTATTTTTATTAAAATTAATTAATATTATACATATATTATTACTTTTTATTTATA
1044120 AATTATTTTTAATTTATTTATAAATTATACAAAATTATTTTTATTAAAATTAATTAATATTGTAC
130 AATTATTTTTAATTTATTTATAAATTATACAAAATTATTTTTATTAAAATTAATTAATATTGTAC
1044185 ATGTATTATTTTTATAATTGATAGAACTTAAATTTATGTTAGCTAACAATAAATTACTTTTTTCG
195 ATGTATTATTTTTATAATTGATAGAACTTAAATTTATGTTAGCTAACAATAAATTACTTTTTTCG
1044250 ATAACGACTTATTTCGGATTTATAGACGCACACATT
260 ATAACGACTTATTTCGGATTTATAGACGCACACATT
*
1044286 TTATTTTTCGGTAATAACTTAAATATGAGCTTTCTTTTATCTGT-AAATGACCAAGAAAAAATTA
1 TTATTTTTCGGTAACAACTTAAATATGAG-TTT-TTTTATCTGTAAAATGACCAAGAAAAAATTA
*
1044350 TTATACATATATTATTTTTATTAAAATTAATTAATATTATGCATATATTATTACTTTTTATTTAT
64 TTATACATATATTATTTTTATTAAAATTAATTAATATTATACATATATTATTACTTTTTATTTAT
*
1044415 AAATTATTTTTAATTTATTTATAAATTATACAAATTTATTTTTATTAAAATTAATTAATATTGTA
129 AAATTATTTTTAATTTATTTATAAATTATACAAAATTATTTTTATTAAAATTAATTAATATTGTA
*
1044480 CATGTATTATTTTTATAATTGATAGAACTTAAATTTATGTTAGCTAACAATAAATTATTTTTTTC
194 CATGTATTATTTTTATAATTGATAGAACTTAAATTTATGTTAGCTAACAATAAATTACTTTTTTC
*
1044545 GATAACGACTTATTTCGGATTTATAGACGTACACATT
259 GATAACGACTTATTTCGGATTTATAGACGCACACATT
* *
1044582 TTATTTTTCGGTAACAACTTAAATACGAGTTTTTCTTTATCTGTAAAATAACCAAGAAAAAATT
1 TTATTTTTCGGTAACAACTTAAATATGAG-TTTT-TTTATCTGTAAAATGACCAAGAAAAAATT
1044646 TTTCTCTAAC
Statistics
Matches: 338, Mismatches: 18, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
295 1 0.00
296 291 0.86
297 37 0.11
298 9 0.03
ACGTcount: A:0.38, C:0.08, G:0.07, T:0.47
Consensus pattern (295 bp):
TTATTTTTCGGTAACAACTTAAATATGAGTTTTTTTATCTGTAAAATGACCAAGAAAAAATTATT
ATACATATATTATTTTTATTAAAATTAATTAATATTATACATATATTATTACTTTTTATTTATAA
ATTATTTTTAATTTATTTATAAATTATACAAAATTATTTTTATTAAAATTAATTAATATTGTACA
TGTATTATTTTTATAATTGATAGAACTTAAATTTATGTTAGCTAACAATAAATTACTTTTTTCGA
TAACGACTTATTTCGGATTTATAGACGCACACATT
Found at i:1048362 original size:92 final size:93
Alignment explanation
Indices: 1048247--1048426 Score: 317
Period size: 92 Copynumber: 1.9 Consensus size: 93
1048237 CCTTACAGTT
* *
1048247 TTTCTTTTTTTTTTATAAAAAAGAATTCGATTCTCAGATATAATTCATGCATTAGTCTAATCCTT
1 TTTCTTTTTTTTCTATAAAAAAGAATCCGATTCTCAGATATAATTCATGCATTAGTCTAATCCTT
1048312 GAAGTCTGACATTTACAATCAATTAGTC
66 GAAGTCTGACATTTACAATCAATTAGTC
*
1048340 TTTC-TTTTTTTCTATAACAAAGAATCCGATTCTCAGATATAATTCATGCATTAGTCTAATCCTT
1 TTTCTTTTTTTTCTATAAAAAAGAATCCGATTCTCAGATATAATTCATGCATTAGTCTAATCCTT
*
1048404 GCAGTCTGACATTTACAATCAAT
66 GAAGTCTGACATTTACAATCAAT
1048427 CACTAATCCT
Statistics
Matches: 83, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
92 79 0.95
93 4 0.05
ACGTcount: A:0.32, C:0.17, G:0.09, T:0.42
Consensus pattern (93 bp):
TTTCTTTTTTTTCTATAAAAAAGAATCCGATTCTCAGATATAATTCATGCATTAGTCTAATCCTT
GAAGTCTGACATTTACAATCAATTAGTC
Found at i:1048433 original size:34 final size:34
Alignment explanation
Indices: 1048395--1048462 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
1048385 ATGCATTAGT
1048395 CTAATCCTTGCAGTCTGACATTTACAATCAATCA
1 CTAATCCTTGCAGTCTGACATTTACAATCAATCA
* *
1048429 CTAATCCTTGCAGTCTGATATTTACAATTAATCA
1 CTAATCCTTGCAGTCTGACATTTACAATCAATCA
1048463 GTCTTTCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.32, C:0.24, G:0.09, T:0.35
Consensus pattern (34 bp):
CTAATCCTTGCAGTCTGACATTTACAATCAATCA
Found at i:1048528 original size:127 final size:126
Alignment explanation
Indices: 1048303--1048551 Score: 408
Period size: 127 Copynumber: 2.0 Consensus size: 126
1048293 ATGCATTAGT
* *
1048303 CTAATCCTTGAAGTCTGACATTTACAATCAATTAGTCTTTCTTTTTTTCTATAACAAAGAATCCG
1 CTAATCCTTGAAGTCTGACATTTACAATCAATCAGTCTTTCTTTTTTTCTATAAAAAAGAATCCG
*
1048368 ATTCTCAGATATAATTCATGCATTAGTCTAATCCTTGCAGTCTGACATTTACAATCAATCA
66 ATTCTCAGATATAATTCATGCATTAGTCTAATCCTTACAGTCTGACATTTACAATCAATCA
* * * *
1048429 CTAATCCTTGCAGTCTGATATTTACAATTAATCAGTCTTTCTTTTTTTTCTATAAAAAAGAATCT
1 CTAATCCTTGAAGTCTGACATTTACAATCAATCAGTCTTTC-TTTTTTTCTATAAAAAAGAATCC
* *
1048494 GATTCTCATATATAATTTATGCATTAGTCTAATCCTTACAGTCTGACATTTACAATCA
65 GATTCTCAGATATAATTCATGCATTAGTCTAATCCTTACAGTCTGACATTTACAATCA
1048552 GTCAACTTTT
Statistics
Matches: 113, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
126 37 0.33
127 76 0.67
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.40
Consensus pattern (126 bp):
CTAATCCTTGAAGTCTGACATTTACAATCAATCAGTCTTTCTTTTTTTCTATAAAAAAGAATCCG
ATTCTCAGATATAATTCATGCATTAGTCTAATCCTTACAGTCTGACATTTACAATCAATCA
Found at i:1048974 original size:92 final size:92
Alignment explanation
Indices: 1048429--1049054 Score: 771
Period size: 93 Copynumber: 6.9 Consensus size: 92
1048419 CAATCAATCA
* * * *
1048429 CTAATCCTTGCAGTCTGATATTTACAATTAATC-AGTCTTTCTTTTTTTTCTATAAAAAAGAATC
1 CTAATCCTTACAGTCTGACATTTACAATCAATCAACT-TTTC-TTTTTTTCTATAAAAAAGAATC
* *
1048493 TGATTCTCATATATAATTTATGCATTAGT
64 TGATTCTCAGATATAATTCATGCATTAGT
*
1048522 CTAATCCTTACAGTCTGACATTTACAATCAGTCAAC---T-TTTTTTTCTATAAAAAAGAAT-TC
1 CTAATCCTTACAGTCTGACATTTACAATCAATCAACTTTTCTTTTTTTCTATAAAAAAGAATCT-
*
1048582 AATTCTCAGATATAATTCATGCATTAGT
65 GATTCTCAGATATAATTCATGCATTAGT
* * *
1048610 CTAATCCTT---G-CTGACATTTACAATCAATCAGTCTTTCTGTTTTTTTTATATAAAAAAGAAT
1 CTAATCCTTACAGTCTGACATTTACAATCAATCA-ACTTT-T-CTTTTTTTCTATAAAAAAGAAT
* *
1048671 CCGATTCTTAGATATAATTCATGCATTAGT
63 CTGATTCTCAGATATAATTCATGCATTAGT
**
1048701 CTAAT-CTCTACAGTCTGACATTTACAATCTGTCAACTTTTCTTTTTTTCTATAAAAAAAGAATC
1 CTAATCCT-TACAGTCTGACATTTACAATCAATCAACTTTTCTTTTTTTCTAT-AAAAAAGAATC
*
1048765 TGATTCTCAGATATAATTCATGTATTAGT
64 TGATTCTCAGATATAATTCATGCATTAGT
* ** * *
1048794 CTAATTCTTGTAGTTTGACATTTATAATCAATCAACTTTTCTCTTTTTTCCTATAAAAAAGAATC
1 CTAATCCTTACAGTCTGACATTTACAATCAATCAACTTTTCT-TTTTTT-CTATAAAAAAGAATC
* *
1048859 CGATTCTCAGATATAATTCATGCATTTGT
64 TGATTCTCAGATATAATTCATGCATTAGT
* * * *
1048888 CTAATCCTTGCAGTCTGACATTTATAATCAATCAACTTTTCTTTTTTTCCATAAAAAATAATCTG
1 CTAATCCTTACAGTCTGACATTTACAATCAATCAACTTTTCTTTTTTTCTATAAAAAAGAATCTG
1048953 ATTCTCAGATATAATTCATGCATTAGT
66 ATTCTCAGATATAATTCATGCATTAGT
* * *
1048980 CTAATCTTTACAGTTTGACATTTACAATCAATCAACTTTTC--TTTTTCTAT-AAAAAG--TCCG
1 CTAATCCTTACAGTCTGACATTTACAATCAATCAACTTTTCTTTTTTTCTATAAAAAAGAATCTG
*
1049040 ATTCTCAAATATAAT
66 ATTCTCAGATATAAT
1049055 CACATTTATT
Statistics
Matches: 468, Mismatches: 46, Indels: 44
0.84 0.08 0.08
Matches are distributed among these distances:
84 19 0.04
85 2 0.00
87 18 0.04
88 55 0.12
89 6 0.01
90 11 0.02
91 52 0.11
92 87 0.19
93 106 0.23
94 90 0.19
95 22 0.05
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (92 bp):
CTAATCCTTACAGTCTGACATTTACAATCAATCAACTTTTCTTTTTTTCTATAAAAAAGAATCTG
ATTCTCAGATATAATTCATGCATTAGT
Found at i:1049713 original size:27 final size:28
Alignment explanation
Indices: 1049654--1049719 Score: 75
Period size: 30 Copynumber: 2.4 Consensus size: 28
1049644 ATTTAATAAA
*
1049654 TTTAATAAATAATAATGTATTAATTATTAT
1 TTTAATAAA-AATAATATATTAATTA-TAT
1049684 TTTAATAAAAATAATAT-TTAATTA-ACT
1 TTTAATAAAAATAATATATTAATTATA-T
1049711 TTTAA-AAAA
1 TTTAATAAAA
1049720 TTTATATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
26 5 0.15
27 6 0.18
28 7 0.21
29 7 0.21
30 9 0.26
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (28 bp):
TTTAATAAAAATAATATATTAATTATAT
Found at i:1049943 original size:13 final size:14
Alignment explanation
Indices: 1049925--1049959 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1049915 TAATATTTTT
*
1049925 TATTTTTTA-AATA
1 TATTTTTTAGAAAA
1049938 TATTTTTTAGAAAA
1 TATTTTTTAGAAAA
1049952 TATTTTTT
1 TATTTTTT
1049960 TGTTAGGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (14 bp):
TATTTTTTAGAAAA
Found at i:1050330 original size:13 final size:13
Alignment explanation
Indices: 1050312--1050337 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1050302 ATAATAAACC
1050312 TTTTTTATTTTAA
1 TTTTTTATTTTAA
1050325 TTTTTTATTTTAA
1 TTTTTTATTTTAA
1050338 AAAAATAATT
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTTATTTTAA
Found at i:1050384 original size:25 final size:27
Alignment explanation
Indices: 1050356--1050432 Score: 70
Period size: 27 Copynumber: 2.9 Consensus size: 27
1050346 TTAATATTTT
*
1050356 AATTTATT-AATATAAATTTTT-TTAA
1 AATTAATTAAATATAAATTTTTATTAA
* *
1050381 AATTAATTAAATATTATTTTTTATTAA
1 AATTAATTAAATATAAATTTTTATTAA
* * *
1050408 AAATAA-TAATTAATATATTTTTATT
1 AATTAATTAAAT-ATAAATTTTTATT
1050433 TATTAAATTT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
25 7 0.17
26 15 0.37
27 19 0.46
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
AATTAATTAAATATAAATTTTTATTAA
Found at i:1050414 original size:27 final size:27
Alignment explanation
Indices: 1050371--1050432 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
1050361 ATTAATATAA
* *
1050371 ATTTTT-TTAAAATTAATTAAATATTAT
1 ATTTTTATTAAAAATAA-TAAATAATAT
*
1050398 -TTTTTATTAAAAATAATAATTAATAT
1 ATTTTTATTAAAAATAATAAATAATAT
1050424 ATTTTTATT
1 ATTTTTATT
1050433 TATTAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 13 0.43
27 17 0.57
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
ATTTTTATTAAAAATAATAAATAATAT
Found at i:1050445 original size:28 final size:28
Alignment explanation
Indices: 1050387--1050449 Score: 67
Period size: 31 Copynumber: 2.2 Consensus size: 28
1050377 TTAAAATTAA
*
1050387 TTAA-ATATTATTTTTTATTAAAAATAATAA
1 TTAATATATTATTTTTTATT--AAAT-TTAA
1050417 TTAATATATT-TTTATTTATTAAATTTAA
1 TTAATATATTATTT-TTTATTAAATTTAA
1050445 TTAAT
1 TTAAT
1050450 TTATAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
28 8 0.27
29 4 0.13
30 7 0.23
31 11 0.37
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
TTAATATATTATTTTTTATTAAATTTAA
Found at i:1052517 original size:2 final size:2
Alignment explanation
Indices: 1052505--1052534 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1052495 ACAAGTAACC
*
1052505 TA TA AA 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
1052535 AGTATTTCCC
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1052688 original size:17 final size:17
Alignment explanation
Indices: 1052668--1052731 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 17
1052658 ATAAATTATA
1052668 AATTATTATTTAAATTT
1 AATTATTATTTAAATTT
*
1052685 AATTAATA-TTAAATATT
1 AATTATTATTTAAAT-TT
* *
1052702 AATAATT-TTTAAATTA
1 AATTATTATTTAAATTT
* *
1052718 AAATATTTTTTAAA
1 AATTATTATTTAAA
1052732 ATTATTAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
16 12 0.32
17 26 0.68
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AATTATTATTTAAATTT
Found at i:1052733 original size:18 final size:17
Alignment explanation
Indices: 1052649--1052772 Score: 57
Period size: 16 Copynumber: 7.5 Consensus size: 17
1052639 TAAAATTAAA
*
1052649 AAAATAA-TTATAAATT
1 AAAATAATTTTTAAATT
*
1052665 ATAAATTATTATTTAAATT
1 A-AAATAATT-TTTAAATT
* * *
1052684 TAATTAA-TATTAAA-T
1 AAAATAATTTTTAAATT
*
1052699 ATTAATAATTTTTAAATT
1 A-AAATAATTTTTAAATT
*
1052717 AAAATATTTTTTAAAATT
1 AAAATAATTTTT-AAATT
* * *
1052735 --ATTAA-ATTT-ATTT
1 AAAATAATTTTTAAATT
*
1052748 AAAATATTTTTTAAA-T
1 AAAATAATTTTTAAATT
1052764 AAAATAATT
1 AAAATAATT
1052773 AATACAATAA
Statistics
Matches: 76, Mismatches: 21, Indels: 22
0.64 0.18 0.18
Matches are distributed among these distances:
13 3 0.04
15 7 0.09
16 25 0.33
17 22 0.29
18 12 0.16
19 7 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AAAATAATTTTTAAATT
Found at i:1053215 original size:15 final size:15
Alignment explanation
Indices: 1053197--1053265 Score: 59
Period size: 15 Copynumber: 4.3 Consensus size: 15
1053187 TCTTAAATAT
1053197 AATTTTTTTAATTTA
1 AATTTTTTTAATTTA
* *
1053212 AATTTATTTAACTTA
1 AATTTTTTTAATTTA
1053227 AATTATTATTTAATAATATA
1 AATT-TT-TTTAAT--T-TA
*
1053247 AATATTTTT-ATTTA
1 AATTTTTTTAATTTA
1053261 AATTT
1 AATTT
1053266 AATTATAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
14 6 0.14
15 18 0.42
16 1 0.02
17 7 0.16
18 3 0.07
19 3 0.07
20 5 0.12
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (15 bp):
AATTTTTTTAATTTA
Found at i:1070311 original size:12 final size:12
Alignment explanation
Indices: 1070294--1070319 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1070284 GCTCGAAAGA
1070294 TAAAGTTGGATT
1 TAAAGTTGGATT
1070306 TAAAGTTGGATT
1 TAAAGTTGGATT
1070318 TA
1 TA
1070320 GAGAAAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (12 bp):
TAAAGTTGGATT
Found at i:1071131 original size:22 final size:22
Alignment explanation
Indices: 1071089--1071132 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1071079 ATTGTATTGG
*
1071089 AGTATTTAGTTTCTGAATATTT
1 AGTATTTAGTTTATGAATATTT
*
1071111 AGTATTT-GATTTATGACTATTT
1 AGTATTTAG-TTTATGAATATTT
1071133 GATTTATCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.27, C:0.05, G:0.14, T:0.55
Consensus pattern (22 bp):
AGTATTTAGTTTATGAATATTT
Found at i:1071332 original size:8 final size:8
Alignment explanation
Indices: 1071315--1071364 Score: 50
Period size: 8 Copynumber: 6.2 Consensus size: 8
1071305 ATATTATTAG
1071315 AATT-ATA
1 AATTAATA
1071322 AATTAATA
1 AATTAATA
*
1071330 AATAAATA
1 AATTAATA
1071338 AA-TAATA
1 AATTAATA
*
1071345 AATTATTAA
1 AATTAAT-A
1071354 AATATAATA
1 AAT-TAATA
1071363 AA
1 AA
1071365 CTATGACTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
7 10 0.29
8 15 0.43
9 7 0.20
10 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
AATTAATA
Found at i:1074688 original size:28 final size:28
Alignment explanation
Indices: 1074635--1074693 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
1074625 CATTTCTCAT
*
1074635 TAATTCAAACATATTTTCAAGTCCAT-G
1 TAATTCAAACATATTTTCAACTCCATAG
*
1074662 TAATTCAAATGCAT-TTTTTAACTCCATAG
1 TAATTCAAA--CATATTTTCAACTCCATAG
1074691 TAA
1 TAA
1074694 AGTACTCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 9 0.33
28 11 0.41
29 7 0.26
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (28 bp):
TAATTCAAACATATTTTCAACTCCATAG
Found at i:1075320 original size:15 final size:16
Alignment explanation
Indices: 1075281--1075320 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
1075271 GTAAACAACG
1075281 AACAAAAATAGCAATA
1 AACAAAAATAGCAATA
*
1075297 AA-AACAATA-CAATA
1 AACAAAAATAGCAATA
1075311 AACAAAAATA
1 AACAAAAATA
1075321 TCTACAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 7 0.33
15 12 0.57
16 2 0.10
ACGTcount: A:0.72, C:0.12, G:0.03, T:0.12
Consensus pattern (16 bp):
AACAAAAATAGCAATA
Found at i:1078724 original size:2 final size:2
Alignment explanation
Indices: 1078717--1078741 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1078707 AAATATTAAA
1078717 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
1078742 ATATCGGTAC
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1079126 original size:14 final size:14
Alignment explanation
Indices: 1079107--1079133 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1079097 ATGATGAATA
1079107 GGAGAGAGGCAGGG
1 GGAGAGAGGCAGGG
1079121 GGAGAGAGGCAGG
1 GGAGAGAGGCAGG
1079134 AGAAATGGAA
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:0.30, C:0.07, G:0.63, T:0.00
Consensus pattern (14 bp):
GGAGAGAGGCAGGG
Found at i:1079344 original size:24 final size:24
Alignment explanation
Indices: 1079295--1079347 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 24
1079285 AGATATTAAG
* *
1079295 TATTTTTTATTATTAAAATATAAA
1 TATTTTATATTATTAAAACATAAA
1079319 TATTTTATATTATTAAATACATAATA
1 TATTTTATATTATTAAA-ACATAA-A
1079345 TAT
1 TAT
1079348 AATATTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 16 0.64
25 5 0.20
26 4 0.16
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
TATTTTATATTATTAAAACATAAA
Found at i:1079352 original size:24 final size:24
Alignment explanation
Indices: 1079302--1079353 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
1079292 AAGTATTTTT
* * *
1079302 TATTATTAAAATATAAATATTTTA
1 TATTATTAAAACATAAATATATAA
1079326 TATTATTAAATACAT-AATATATAA
1 TATTATTAAA-ACATAAATATATAA
1079350 TATT
1 TATT
1079354 TTATTATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
TATTATTAAAACATAAATATATAA
Found at i:1079834 original size:20 final size:19
Alignment explanation
Indices: 1079800--1079849 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 19
1079790 ACAAATAAAT
*
1079800 ATAATATTTTATGTAATTA
1 ATAATGTTTTATGTAATTA
*
1079819 ATAATGTTTATATGTAATTT
1 ATAATGTTT-TATGTAATTA
*
1079839 TTAATGTTTTA
1 ATAATGTTTTA
1079850 ATAATTACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 10 0.37
20 17 0.63
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (19 bp):
ATAATGTTTTATGTAATTA
Found at i:1079896 original size:27 final size:28
Alignment explanation
Indices: 1079850--1079910 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 28
1079840 TAATGTTTTA
*
1079850 ATAATTACATGTAAAAGTAA-ATTTTAT
1 ATAATTACATGTAAAAGTAATATTATAT
* * *
1079877 GTAATTACATGTGAAGGTAATATTATAT
1 ATAATTACATGTAAAAGTAATATTATAT
1079905 ATAATT
1 ATAATT
1079911 TGTAAAATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 17 0.61
28 11 0.39
ACGTcount: A:0.44, C:0.03, G:0.11, T:0.41
Consensus pattern (28 bp):
ATAATTACATGTAAAAGTAATATTATAT
Found at i:1079924 original size:20 final size:20
Alignment explanation
Indices: 1079893--1080061 Score: 110
Period size: 20 Copynumber: 8.2 Consensus size: 20
1079883 ACATGTGAAG
1079893 GTAATA-TTATATATAATTT
1 GTAATATTTATATATAATTT
* *
1079912 GTAAAATTTATATATAATTA
1 GTAATATTTATATATAATTT
*
1079932 GAAATTATTTATATAATTATATATAT
1 GTAA-TATTTATAT-A-TA-AT-T-T
** *
1079958 AAAAATATTT-TATATAACTT
1 -GTAATATTTATATATAATTT
* * *
1079978 ATAATGTTTATATATAATTG
1 GTAATATTTATATATAATTT
* *
1079998 GTAATGTTTATATGTAATTT
1 GTAATATTTATATATAATTT
* * *
1080018 ATAATATTT-TATGTAATTG
1 GTAATATTTATATATAATTT
* *
1080037 GTAATATTTATTTTTAATTT
1 GTAATATTTATATATAATTT
1080057 GTAAT
1 GTAAT
1080062 GTTTTAAGTA
Statistics
Matches: 119, Mismatches: 21, Indels: 19
0.75 0.13 0.12
Matches are distributed among these distances:
19 29 0.24
20 60 0.50
21 9 0.08
22 2 0.02
23 4 0.03
24 3 0.03
25 4 0.03
26 5 0.04
27 3 0.03
ACGTcount: A:0.41, C:0.01, G:0.07, T:0.51
Consensus pattern (20 bp):
GTAATATTTATATATAATTT
Found at i:1080037 original size:39 final size:39
Alignment explanation
Indices: 1079961--1080074 Score: 131
Period size: 39 Copynumber: 2.9 Consensus size: 39
1079951 TATATATAAA
* * *
1079961 AATATTT-TATATAACTTATAATGTTTATATATAATTGGT
1 AATATTTATATGTAATTTATAATGTTT-TATGTAATTGGT
* *
1080000 AATGTTTATATGTAATTTATAATATTTTATGTAATTGGT
1 AATATTTATATGTAATTTATAATGTTTTATGTAATTGGT
* * * *
1080039 AATATTTATTTTTAATTTGTAATGTTTTAAGTAATT
1 AATATTTATATGTAATTTATAATGTTTTATGTAATT
1080075 ATATATAAAG
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
39 47 0.75
40 16 0.25
ACGTcount: A:0.35, C:0.01, G:0.10, T:0.54
Consensus pattern (39 bp):
AATATTTATATGTAATTTATAATGTTTTATGTAATTGGT
Found at i:1080047 original size:59 final size:59
Alignment explanation
Indices: 1079961--1080079 Score: 143
Period size: 59 Copynumber: 2.0 Consensus size: 59
1079951 TATATATAAA
* *
1079961 AATATTTTATATAACTTATAATGTTTATATATAATTGGTAATGTTTATATGTAATT-TAT
1 AATATTTTATATAACTTATAATATTTATATATAATTGGTAATGTTT-TAAGTAATTATAT
* * * * *
1080020 AATATTTTATGTAA-TTGGTAATATTTATTTTTAATTTGTAATGTTTTAAGTAATTATAT
1 AATATTTTATATAACTT-ATAATATTTATATATAATTGGTAATGTTTTAAGTAATTATAT
1080079 A
1 A
1080080 TAAAGATAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
58 10 0.20
59 41 0.80
ACGTcount: A:0.36, C:0.01, G:0.09, T:0.54
Consensus pattern (59 bp):
AATATTTTATATAACTTATAATATTTATATATAATTGGTAATGTTTTAAGTAATTATAT
Found at i:1080128 original size:21 final size:20
Alignment explanation
Indices: 1080085--1080135 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
1080075 ATATATAAAG
* *
1080085 ATAATATTTT-ATGTAATTT
1 ATAATATTTTAATATAATTA
1080104 ATAATATTTTAAATATAATTA
1 ATAATATTTT-AATATAATTA
1080125 ATAATATTTTA
1 ATAATATTTTA
1080136 TGTAATTACA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 10 0.36
20 1 0.04
21 17 0.61
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
ATAATATTTTAATATAATTA
Found at i:1080143 original size:19 final size:19
Alignment explanation
Indices: 1080085--1080143 Score: 82
Period size: 19 Copynumber: 3.0 Consensus size: 19
1080075 ATATATAAAG
*
1080085 ATAATATTTTATGTAATTT
1 ATAATATTTTATGTAATTA
*
1080104 ATAATATTTTAAATATAATTA
1 ATAATATTTT--ATGTAATTA
1080125 ATAATATTTTATGTAATTA
1 ATAATATTTTATGTAATTA
1080144 CATATAAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 18 0.51
21 17 0.49
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (19 bp):
ATAATATTTTATGTAATTA
Found at i:1080143 original size:68 final size:67
Alignment explanation
Indices: 1080018--1080151 Score: 169
Period size: 68 Copynumber: 2.0 Consensus size: 67
1080008 TATGTAATTT
* ** * ** * *
1080018 ATAATATTTTATGTAATTGGTAATATTTATTTTTAATTTGTAATGTTTTAAGTAATTATATATAA
1 ATAATATTTTATGTAATTGATAATATTTAAATATAATTAATAATATTTTAAGTAATTACATATAA
1080083 AG
66 AG
* *
1080085 ATAATATTTTATGTAATTTATAATATTTTAAATATAATTAATAATATTTTATGTAATTACATATA
1 ATAATATTTTATGTAATTGATAATA-TTTAAATATAATTAATAATATTTTAAGTAATTACATATA
1080150 AA
65 AA
1080152 AGTAATGATA
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
67 23 0.41
68 33 0.59
ACGTcount: A:0.42, C:0.01, G:0.07, T:0.51
Consensus pattern (67 bp):
ATAATATTTTATGTAATTGATAATATTTAAATATAATTAATAATATTTTAAGTAATTACATATAA
AG
Found at i:1080726 original size:25 final size:25
Alignment explanation
Indices: 1080698--1080745 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
1080688 CAATTATGGT
*
1080698 ATTTTATATTTTTA-AATTAAATCAA
1 ATTTTAT-TTTTTATAAATAAATCAA
1080723 ATTTTATTTTTTATAAATAAATC
1 ATTTTATTTTTTATAAATAAATC
1080746 GAAAAAGGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (25 bp):
ATTTTATTTTTTATAAATAAATCAA
Found at i:1081206 original size:47 final size:48
Alignment explanation
Indices: 1081137--1081235 Score: 146
Period size: 51 Copynumber: 2.0 Consensus size: 48
1081127 GCATGAGTGC
*
1081137 TAATACTTTATTCATG-AATAAATGTACTCTCAAAACTAATTTTGTTT
1 TAATACTTTATTCATGAAATAAATGTACTCTCAAAACTAATTCTGTTT
*
1081184 TAATACTTTATTCATGAATAAATAAATGTACTCTCAAAATTAATTCTGTTT
1 TAATACTTTATTCATG---AAATAAATGTACTCTCAAAACTAATTCTGTTT
1081235 T
1 T
1081236 CTTAGAGAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
47 16 0.35
51 30 0.65
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.44
Consensus pattern (48 bp):
TAATACTTTATTCATGAAATAAATGTACTCTCAAAACTAATTCTGTTT
Found at i:1084538 original size:16 final size:16
Alignment explanation
Indices: 1084506--1084549 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
1084496 AAATAGCTCA
* *
1084506 AACCCAAAAGAACCCG
1 AACCCAAAAAAATCCG
*
1084522 AACTCAAAAAAATCCG
1 AACCCAAAAAAATCCG
1084538 AACCCAAAAAAA
1 AACCCAAAAAAA
1084550 CTTAAACCTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.59, C:0.30, G:0.07, T:0.05
Consensus pattern (16 bp):
AACCCAAAAAAATCCG
Found at i:1084765 original size:22 final size:22
Alignment explanation
Indices: 1084740--1084793 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
1084730 ATATATGATG
* *
1084740 AAATAATAAT-TTATTAAAATGT
1 AAATAAT-ATCTTATCAAAAAGT
*
1084762 AAATTATATCTTATCAAAAAGT
1 AAATAATATCTTATCAAAAAGT
*
1084784 AAATTATATC
1 AAATAATATC
1084794 ATGAGCTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 2 0.07
22 26 0.93
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.39
Consensus pattern (22 bp):
AAATAATATCTTATCAAAAAGT
Found at i:1085245 original size:15 final size:15
Alignment explanation
Indices: 1085222--1085251 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1085212 AACTACATTC
*
1085222 AATATTATTTTAATT
1 AATAGTATTTTAATT
1085237 AATAGTATTTTAATT
1 AATAGTATTTTAATT
1085252 GACATATCTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (15 bp):
AATAGTATTTTAATT
Found at i:1085326 original size:2 final size:2
Alignment explanation
Indices: 1085321--1085353 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1085311 ATAACTAAAG
1085321 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
1085354 CACTAAACCA
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:1085755 original size:13 final size:14
Alignment explanation
Indices: 1085718--1085777 Score: 50
Period size: 13 Copynumber: 4.2 Consensus size: 14
1085708 TTACAATATA
*
1085718 TAATATTATAATAAT
1 TAATATT-TAAAAAT
*
1085733 AAATTATTTAAAAAT
1 TAA-TATTTAAAAAT
*
1085748 TAAT-TTTATAAAT
1 TAATATTTAAAAAT
* *
1085761 AAATATTTTAAAAT
1 TAATATTTAAAAAT
1085775 TAA
1 TAA
1085778 CATATTAGAA
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
13 11 0.31
14 10 0.29
15 10 0.29
16 4 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TAATATTTAAAAAT
Found at i:1085956 original size:16 final size:16
Alignment explanation
Indices: 1085935--1085968 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1085925 CCCGAACTAG
1085935 AAAAGTTTGAACCCGA
1 AAAAGTTTGAACCCGA
1085951 AAAAGTTTGAACCCGA
1 AAAAGTTTGAACCCGA
1085967 AA
1 AA
1085969 GGCTTGAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.18
Consensus pattern (16 bp):
AAAAGTTTGAACCCGA
Found at i:1085977 original size:15 final size:16
Alignment explanation
Indices: 1085935--1085977 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
1085925 CCCGAACTAG
*
1085935 AAAAGTTTGAACCCGA
1 AAAAGCTTGAACCCGA
*
1085951 AAAAGTTTGAACCCG-
1 AAAAGCTTGAACCCGA
*
1085966 AAAGGCTTGAAC
1 AAAAGCTTGAAC
1085978 TCAAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 10 0.40
16 15 0.60
ACGTcount: A:0.42, C:0.19, G:0.21, T:0.19
Consensus pattern (16 bp):
AAAAGCTTGAACCCGA
Found at i:1090964 original size:28 final size:28
Alignment explanation
Indices: 1090902--1090964 Score: 65
Period size: 28 Copynumber: 2.2 Consensus size: 28
1090892 TTATTTTATA
*
1090902 TTAATATATTTTTATAATTAAATTTAAAT
1 TTAA-ATATTTTTATAATTAAATATAAAT
** *
1090931 AAAAATATTTTTATTATTAAATA-ATAAT
1 TTAAATATTTTTATAATTAAATATA-AAT
1090959 TTAAAT
1 TTAAAT
1090965 TAAATCAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
27 1 0.04
28 24 0.89
29 2 0.07
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
TTAAATATTTTTATAATTAAATATAAAT
Found at i:1091647 original size:17 final size:18
Alignment explanation
Indices: 1091627--1091660 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1091617 AGGGGACTGT
*
1091627 AATTTTAAA-ATTAAAAA
1 AATTATAAATATTAAAAA
1091644 AATTATAAATATTAAAA
1 AATTATAAATATTAAAA
1091661 TTTAAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AATTATAAATATTAAAAA
Found at i:1093635 original size:21 final size:20
Alignment explanation
Indices: 1093597--1093645 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
1093587 TAAAAGATAC
1093597 AAATTCAATAATTAAAATTTT
1 AAATT-AATAATTAAAATTTT
*
1093618 AAATTAATAATTTCAAATTTT
1 AAATTAATAA-TTAAAATTTT
1093639 AAATTAA
1 AAATTAA
1093646 ATTAATATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 5 0.19
21 21 0.81
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (20 bp):
AAATTAATAATTAAAATTTT
Found at i:1097014 original size:17 final size:19
Alignment explanation
Indices: 1096981--1097016 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1096971 CGATTCATAC
1096981 CATATTATATAATTATATT
1 CATATTATATAATTATATT
1097000 CATATTATA-AA-TATATT
1 CATATTATATAATTATATT
1097017 AAGATATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 2 0.12
19 9 0.53
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (19 bp):
CATATTATATAATTATATT
Found at i:1102481 original size:7 final size:7
Alignment explanation
Indices: 1102469--1102493 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1102459 TCGATGAATT
1102469 AGAAAAG
1 AGAAAAG
1102476 AGAAAAG
1 AGAAAAG
1102483 AGAAAAG
1 AGAAAAG
1102490 AGAA
1 AGAA
1102494 GCATCTAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (7 bp):
AGAAAAG
Found at i:1108907 original size:16 final size:16
Alignment explanation
Indices: 1108886--1108920 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1108876 TTTAATTATA
1108886 ATTATTATAATTAATT
1 ATTATTATAATTAATT
* *
1108902 ATTATTATTATTATTT
1 ATTATTATAATTAATT
1108918 ATT
1 ATT
1108921 CTTTTTTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
ATTATTATAATTAATT
Found at i:1111939 original size:14 final size:13
Alignment explanation
Indices: 1111920--1111967 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
1111910 AATTTTTTTT
1111920 ATTTTTATAAATAA
1 ATTTTT-TAAATAA
*
1111934 ATTTTTTTAAA-AT
1 A-TTTTTTAAATAA
1111947 ATTTTTTAAAATAA
1 ATTTTTT-AAATAA
1111961 ATTTTTT
1 ATTTTTT
1111968 TATAAATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 6 0.21
13 5 0.17
14 13 0.45
15 5 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
ATTTTTTAAATAA
Found at i:1111949 original size:27 final size:28
Alignment explanation
Indices: 1111921--1111974 Score: 92
Period size: 27 Copynumber: 1.9 Consensus size: 28
1111911 ATTTTTTTTA
1111921 TTTTTATAAATAAATTTTTTTA-AAATAT
1 TTTTTA-AAATAAATTTTTTTATAAATAT
1111949 TTTTTAAAATAAATTTTTTTATAAAT
1 TTTTTAAAATAAATTTTTTTATAAAT
1111975 TAATTAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 15 0.60
28 10 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
TTTTTAAAATAAATTTTTTTATAAATAT
Found at i:1112057 original size:24 final size:24
Alignment explanation
Indices: 1111984--1112074 Score: 67
Period size: 27 Copynumber: 3.4 Consensus size: 24
1111974 TTAATTAAAT
*
1111984 TTAATAAATTTAATAAATAATACTATA
1 TTAATAAATTT--TAAAAAATA-TATA
*
1112011 TTAATTATTATTTTTAATAAAA-ATAATA
1 TTAA-TA--AATTTTAA-AAAATAT-ATA
1112039 TTTAATTAAATTTTAAAAAATATATA
1 -TTAA-TAAATTTTAAAAAATATATA
1112065 TTAATAAATT
1 TTAATAAATT
1112075 AAAATATTAA
Statistics
Matches: 54, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
24 6 0.11
25 4 0.07
26 7 0.13
27 14 0.26
28 9 0.17
29 10 0.19
30 4 0.07
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (24 bp):
TTAATAAATTTTAAAAAATATATA
Found at i:1112076 original size:22 final size:24
Alignment explanation
Indices: 1112029--1112078 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
1112019 TATTTTTAAT
1112029 AAAAATAATATTTAATTAAATTTTA
1 AAAAATAATATTTAATTAAA-TTTA
1112054 AAAAAT-ATATATTAA-TAAA-TTA
1 AAAAATAATAT-TTAATTAAATTTA
1112076 AAA
1 AAA
1112079 TATTAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 6 0.25
24 8 0.33
25 10 0.42
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
AAAAATAATATTTAATTAAATTTA
Found at i:1112552 original size:22 final size:22
Alignment explanation
Indices: 1112472--1112555 Score: 73
Period size: 22 Copynumber: 3.8 Consensus size: 22
1112462 TAATTATATA
* *
1112472 AATTTAATTTAATTTTT-TAAGT
1 AATTTAATTT-ATTTTTAAAATT
** *
1112494 AATTTAA-AAATGTTTAAAATCT
1 AATTTAATTTATTTTTAAAAT-T
*
1112516 AATTTATTTTTATTTTTAAAATT
1 AATTTA-ATTTATTTTTAAAATT
1112539 AATTTAATTTATTTTTA
1 AATTTAATTTATTTTTA
1112556 TGAAATTTAT
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
20 5 0.10
21 2 0.04
22 24 0.50
23 7 0.15
24 10 0.21
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.57
Consensus pattern (22 bp):
AATTTAATTTATTTTTAAAATT
Found at i:1112568 original size:199 final size:198
Alignment explanation
Indices: 1112204--1112570 Score: 544
Period size: 199 Copynumber: 1.8 Consensus size: 198
1112194 ATATTTAATT
*
1112204 AAATTTTAAAAAATTAAAGTATGATTTGTAAAATTAATTGTTAAAATATTTTTAATACGATTATA
1 AAATTTTAAAAAATTAAAGTATGATTTGTAAAATTAATTGTTAAAATATTTTTAATACAATTATA
* * * * *
1112269 TAAATTTAATTTAACTTTTTTTAGATAATTTAAAACTTTTTTAAAGTATGATTTTTTTTATTTAT
66 TAAATTTAATTTAACTTTTTTAAGATAATTTAAAACATGTTTAAAATATAATTTTTTTTATTTAT
*
1112334 AAAATTAATTTAATTTATTTTTACATGTATTATTTTTTGGTAACGACTTAAATATAAATTTTTTT
131 AAAATTAATTTAATTTATTTTTA-ATGAATTATTTTTTGGTAACGACTTAAATATAAATTTTTTT
1112399 AAAA
195 AAAA
* * *
1112403 AAATTTTAAAAAAATTAAGGTATGATTTGTAAAATTAATTGTTAAAATATTTTTTGATATAATTA
1 AAATTTT-AAAAAATTAAAGTATGATTTGTAAAATTAATTGTTAAAATA-TTTTTAATACAATTA
*
1112468 TATAAATTTAATTTAA-TTTTTTAAG-TAATTTAAAA-ATGTTTAAAATCTAATTTATTTTTATT
64 TATAAATTTAATTTAACTTTTTTAAGATAATTTAAAACATGTTTAAAATATAATTT-TTTTTATT
*
1112530 TTTAAAATTAATTTAATTTATTTTT-ATGAAATTTATTTTTT
128 TATAAAATTAATTTAATTTATTTTTAATG-AA-TTATTTTTT
1112571 ATTTTATTAT
Statistics
Matches: 151, Mismatches: 12, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
197 3 0.02
198 14 0.09
199 58 0.38
200 48 0.32
201 28 0.19
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.52
Consensus pattern (198 bp):
AAATTTTAAAAAATTAAAGTATGATTTGTAAAATTAATTGTTAAAATATTTTTAATACAATTATA
TAAATTTAATTTAACTTTTTTAAGATAATTTAAAACATGTTTAAAATATAATTTTTTTTATTTAT
AAAATTAATTTAATTTATTTTTAATGAATTATTTTTTGGTAACGACTTAAATATAAATTTTTTTA
AAA
Found at i:1116027 original size:20 final size:21
Alignment explanation
Indices: 1116002--1116040 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1115992 ATTAAAAAAT
*
1116002 TATTTTAT-ATTAATTTTATA
1 TATTTTATAATTAAATTTATA
1116022 TATTTTATAATTAAATTTA
1 TATTTTATAATTAAATTTA
1116041 AATAATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTTTATAATTAAATTTATA
Found at i:1116101 original size:36 final size:34
Alignment explanation
Indices: 1116034--1116111 Score: 86
Period size: 36 Copynumber: 2.2 Consensus size: 34
1116024 TTTTATAATT
* *
1116034 AAATTTAAATAATAAATTTATTTTATTAATAAATAA
1 AAATTTAAAT-ATAAATTAAATTTATTAATAAA-AA
*
1116070 TAATTTAAAT-TAAATTAAATTTATTCAAATAAAAA
1 AAATTTAAATATAAATTAAATTTATT--AATAAAAA
1116105 AAATTTA
1 AAATTTA
1116112 TCTAACTATA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
34 13 0.36
35 8 0.22
36 15 0.42
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (34 bp):
AAATTTAAATATAAATTAAATTTATTAATAAAAA
Found at i:1117319 original size:16 final size:16
Alignment explanation
Indices: 1117273--1117325 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 16
1117263 TTAATATTAC
*
1117273 ATATTTTTA-TAATTA
1 ATATTTTTATTAAATA
*
1117288 A-A-TTTAATTAAA-A
1 ATATTTTTATTAAATA
1117301 ATATTTTTATTAAATA
1 ATATTTTTATTAAATA
*
1117317 ATAATTTTA
1 ATATTTTTA
1117326 AATAATAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
13 6 0.20
14 5 0.17
15 10 0.33
16 9 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATTTTTATTAAATA
Found at i:1117373 original size:26 final size:25
Alignment explanation
Indices: 1117326--1117392 Score: 84
Period size: 26 Copynumber: 2.7 Consensus size: 25
1117316 AATAATTTTA
*
1117326 AATAATAA-AAATAAAAAATTATTAT
1 AATAATAATTAATAAAAAATTA-TAT
*
1117351 AAT-CTAATTAATAATAAAATTATAT
1 AATAATAATTAATAA-AAAATTATAT
1117376 AATAATAATTAATAAAA
1 AATAATAATTAATAAAA
1117393 CTAATTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
24 3 0.08
25 16 0.44
26 17 0.47
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (25 bp):
AATAATAATTAATAAAAAATTATAT
Found at i:1117398 original size:13 final size:13
Alignment explanation
Indices: 1117355--1117390 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1117345 TATTATAATC
1117355 TAATTAATAATAA
1 TAATTAATAATAA
1117368 -AATTATATAATAA
1 TAATTA-ATAATAA
1117381 TAATTAATAA
1 TAATTAATAA
1117391 AACTAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 5 0.24
13 11 0.52
14 5 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
TAATTAATAATAA
Found at i:1122139 original size:21 final size:20
Alignment explanation
Indices: 1122105--1122176 Score: 72
Period size: 22 Copynumber: 3.4 Consensus size: 20
1122095 CTACCAATAA
*
1122105 ATATTATAATTATATAAATT
1 ATATTATAATTATAAAAATT
*
1122125 ATATTATTTATTATAAAAATT
1 ATATTA-TAATTATAAAAATT
* *
1122146 ATTATAATAAATAATAAAAATT
1 A-TATTAT-AATTATAAAAATT
1122168 AATATTATA
1 -ATATTATA
1122177 CATTTTTATT
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
20 6 0.14
21 15 0.36
22 20 0.48
23 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATATTATAATTATAAAAATT
Found at i:1124961 original size:24 final size:24
Alignment explanation
Indices: 1124934--1125010 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
1124924 TTGCAATAGA
1124934 TAATTGCTAAATAATTCTAAAAAT
1 TAATTGCTAAATAATTCTAAAAAT
* *
1124958 TAATTAC-AAAGTCATT-TCAATAAA-
1 TAATTGCTAAA-TAATTCT-AA-AAAT
* *
1124982 TAATTGTTGAATAATTCTAAAAAT
1 TAATTGCTAAATAATTCTAAAAAT
*
1125006 CAATT
1 TAATT
1125011 ACAAAGTCAT
Statistics
Matches: 40, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
23 7 0.17
24 27 0.68
25 6 0.15
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.38
Consensus pattern (24 bp):
TAATTGCTAAATAATTCTAAAAAT
Found at i:1124979 original size:48 final size:48
Alignment explanation
Indices: 1124927--1125020 Score: 152
Period size: 48 Copynumber: 2.0 Consensus size: 48
1124917 TAAGCAATTG
* *
1124927 CAATAGATAATTGCTAAATAATTCTAAAAATTAATTACAAAGTCATTT
1 CAATAAATAATTGCTAAATAATTCTAAAAATCAATTACAAAGTCATTT
* *
1124975 CAATAAATAATTGTTGAATAATTCTAAAAATCAATTACAAAGTCAT
1 CAATAAATAATTGCTAAATAATTCTAAAAATCAATTACAAAGTCAT
1125021 ATCTAGGGCT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.34
Consensus pattern (48 bp):
CAATAAATAATTGCTAAATAATTCTAAAAATCAATTACAAAGTCATTT
Found at i:1126995 original size:18 final size:19
Alignment explanation
Indices: 1126972--1127008 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1126962 TAGATAATTA
1126972 TATTTATT-AAATAAATAT
1 TATTTATTGAAATAAATAT
1126990 TATTTATTGAAATAAATAT
1 TATTTATTGAAATAAATAT
1127009 GTAATTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
TATTTATTGAAATAAATAT
Found at i:1127229 original size:27 final size:28
Alignment explanation
Indices: 1127188--1127240 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
1127178 AGAATATTGA
*
1127188 AAAAAATTTTGT-AAATAGGTTTTTTGT
1 AAAAAATTTTGTAAAATAGATTTTTTGT
* *
1127215 AAAATATTTTTTAAAATAGATTTTTT
1 AAAAAATTTTGTAAAATAGATTTTTT
1127241 TTTTTACAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 10 0.45
28 12 0.55
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (28 bp):
AAAAAATTTTGTAAAATAGATTTTTTGT
Found at i:1127692 original size:23 final size:22
Alignment explanation
Indices: 1127686--1127739 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
1127676 CTAATTTATT
1127686 TTTATTTTTAAAAATTAATTTAA
1 TTTA-TTTTAAAAATTAATTTAA
*
1127709 TTTATTTTTATAAAATTTATTT--
1 TTTA-TTTTA-AAAATTAATTTAA
1127731 TTTATTTTA
1 TTTATTTTA
1127740 TTACATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 5 0.17
22 4 0.14
23 10 0.34
24 10 0.34
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTATTTTAAAAATTAATTTAA
Found at i:1127704 original size:24 final size:23
Alignment explanation
Indices: 1127667--1127738 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 23
1127657 TTTAAAAAAA
*
1127667 TTTT-AAAATCTAATTTATTTTTAT
1 TTTTAAAAAT-TAATTTA-ATTTAT
1127691 TTTTAAAAATTAATTTAATTTAT
1 TTTTAAAAATTAATTTAATTTAT
*
1127714 TTTTATAAAATTTATTT--TTTAT
1 TTTTA-AAAATTAATTTAATTTAT
1127736 TTT
1 TTT
1127739 ATTACATATA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
22 8 0.18
23 10 0.23
24 21 0.48
25 5 0.11
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTTAAAAATTAATTTAATTTAT
Found at i:1127753 original size:195 final size:196
Alignment explanation
Indices: 1127373--1127732 Score: 555
Period size: 195 Copynumber: 1.8 Consensus size: 196
1127363 TTTAATTAAA
*
1127373 TTTAAAAAATTTAAGGTATGATTTGTAAAATTAATTGTTAAAATATTTTTGATATGATTATATAA
1 TTTAAAAAATTTAAGGTATGATTTGTAAAATTAATTGTTAAAATATTTTTGATATAATTATATAA
* *** *
1127438 ATTTAATTTAATTTTTTTAGATAATTTAAAACTTTTTTAAAGTATAATTTTTTTATTTATAAAAT
66 ATTTAATTTAATTTTTTAAGATAATTTAAAAAAATTTTAAAATATAATTTTTTTATTTATAAAAT
**
1127503 TAATTTAATTTATTTTTATATGTATTATTTTTCGATAACGACTTAAATATAAATTTTCTTTAAAA
131 TAATTTAATTTATTTTTATAAATATTATTTTTCGATAACGACTTAAATATAAATTTTCTTTAAAA
1127568 T
196 T
1127569 TTTAAAAAA-TTAAGGTATGATTTGTAAAATTAATTGTTAAAATAATTTTTGATATAATTATATA
1 TTTAAAAAATTTAAGGTATGATTTGTAAAATTAATTGTTAAAAT-ATTTTTGATATAATTATATA
* * *
1127633 AATTTACTTTAATTTTTTAAG-TAATTTAAAAAAATTTTAAAATCTAATTTATTTTTATTTTTAA
65 AATTTAATTTAATTTTTTAAGATAATTTAAAAAAATTTTAAAATATAA-TT-TTTTTATTTAT-A
1127697 AAATTAATTTAATTTATTTTTATAAA-ATTTATTTTT
127 AAATTAATTTAATTTATTTTTATAAATA-TTATTTTT
1127733 TATTTTATTA
Statistics
Matches: 148, Mismatches: 11, Indels: 8
0.89 0.07 0.05
Matches are distributed among these distances:
195 55 0.37
196 49 0.33
197 11 0.07
198 33 0.22
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (196 bp):
TTTAAAAAATTTAAGGTATGATTTGTAAAATTAATTGTTAAAATATTTTTGATATAATTATATAA
ATTTAATTTAATTTTTTAAGATAATTTAAAAAAATTTTAAAATATAATTTTTTTATTTATAAAAT
TAATTTAATTTATTTTTATAAATATTATTTTTCGATAACGACTTAAATATAAATTTTCTTTAAAA
T
Found at i:1127779 original size:22 final size:21
Alignment explanation
Indices: 1127754--1127799 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
1127744 ATATAAATTT
1127754 AAAATATT-AATTATAAAAATAA
1 AAAATATTAAATT-TAAAAA-AA
*
1127776 AAAATTTTAAATTTAAAAAAA
1 AAAATATTAAATTTAAAAAAA
1127797 AAA
1 AAA
1127800 GAATCATGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 5 0.23
22 13 0.59
23 4 0.18
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (21 bp):
AAAATATTAAATTTAAAAAAA
Found at i:1129913 original size:18 final size:19
Alignment explanation
Indices: 1129890--1129930 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
1129880 ATCGATACAG
1129890 TACAT-AGTGTTGTATCGA
1 TACATAAGTGTTGTATCGA
*
1129908 TACATAAGTTTTGTATCGA
1 TACATAAGTGTTGTATCGA
1129927 TACA
1 TACA
1129931 ATTTAAGCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (19 bp):
TACATAAGTGTTGTATCGA
Found at i:1129991 original size:13 final size:13
Alignment explanation
Indices: 1129973--1129997 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1129963 ATTACTCAAA
1129973 TGTATCGATACAT
1 TGTATCGATACAT
1129986 TGTATCGATACA
1 TGTATCGATACA
1129998 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1130050 original size:52 final size:52
Alignment explanation
Indices: 1130006--1130134 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
1129996 CACTGATCTT
1130006 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1130058 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1130110 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1130135 TCATATTTCG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 76 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1134944 original size:16 final size:17
Alignment explanation
Indices: 1134925--1134957 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1134915 TTAATCATTA
1134925 CAAATTTT-ATAGCTTT
1 CAAATTTTAATAGCTTT
1134941 CAAATTTTAATAGCTTT
1 CAAATTTTAATAGCTTT
1134958 TTTGAACATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.33, C:0.12, G:0.06, T:0.48
Consensus pattern (17 bp):
CAAATTTTAATAGCTTT
Found at i:1135424 original size:119 final size:116
Alignment explanation
Indices: 1135099--1135425 Score: 391
Period size: 116 Copynumber: 2.8 Consensus size: 116
1135089 ATTAATAAAA
* *
1135099 TTTTAATTTAAAATTTTTTATTTTAAAAACATAATAATTAATATTTTTATTTGTTAATGTAAATT
1 TTTTAATTT-AAATTTTTTATTTTAAAAACATAATAATTAATATTTTAATTTGTTAATATAAATT
* **
1135164 TTTTAAACTTAATTAAATA-TTTTTT-ATTTTATTGAAAATTATAATAATTT
65 TTTTAAACTTAATTAAATATTTTTTTAATTTTATTAAAAATTATAATAACCT
* *
1135214 TTTTATTTTAAATTTTTTATTTTATAAAAACATAATAATTAGTATTTTAATTTGTTAATAT-AAT
1 TTTTAATTTAAATTTTTTA-TTT-TAAAAACATAATAATTAATATTTTAATTTGTTAATATAAAT
1135278 TTTTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAAAATAATAATAATAAACCCT
64 TTTTTAAACTTAATTAAATATT-TTTTTAATTTTATT-AAAAAT--T-ATAAT-AA-CCT
*
1135338 TTTTAATTT-AA-TTTTTATTTT-AAAA-A-AATAATTAATATTTTAATTTATTAATATAAATTC
1 TTTTAATTTAAATTTTTTATTTTAAAAACATAATAATTAATATTTTAATTTGTTAATATAAATT-
* * *
1135398 GTTTAAAGTTAATTAACTATTCTTTTTA
65 TTTTAAACTTAATTAAATATT-TTTTTA
1135426 TTAAAAAATA
Statistics
Matches: 185, Mismatches: 14, Indels: 22
0.84 0.06 0.10
Matches are distributed among these distances:
114 10 0.05
115 34 0.18
116 35 0.19
117 31 0.17
118 13 0.07
119 33 0.18
120 1 0.01
121 4 0.02
122 11 0.06
123 4 0.02
124 9 0.05
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (116 bp):
TTTTAATTTAAATTTTTTATTTTAAAAACATAATAATTAATATTTTAATTTGTTAATATAAATTT
TTTAAACTTAATTAAATATTTTTTTAATTTTATTAAAAATTATAATAACCT
Found at i:1139733 original size:13 final size:13
Alignment explanation
Indices: 1139715--1139739 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1139705 TACAATGATC
1139715 AATGTATCGATAT
1 AATGTATCGATAT
1139728 AATGTATCGATA
1 AATGTATCGATA
1139740 CATTTCCTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (13 bp):
AATGTATCGATAT
Found at i:1139865 original size:21 final size:20
Alignment explanation
Indices: 1139839--1139877 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1139829 ATTGGGACCT
*
1139839 TGTATCGATATATTCTAGAAA
1 TGTATCGATACATT-TAGAAA
1139860 TGTATCGATACATTTAGA
1 TGTATCGATACATTTAGA
1139878 TAAAAATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATTTAGAAA
Found at i:1140372 original size:23 final size:25
Alignment explanation
Indices: 1140324--1140372 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
1140314 TATTTTAATT
* *
1140324 TTTTAAAATTTTTATAAATTAGATC
1 TTTTAAAATTTTTATAAATAACATC
1140349 TTTT-AAATTTTT-TAAATAACATC
1 TTTTAAAATTTTTATAAATAACATC
1140372 T
1 T
1140373 AAAATATTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 10 0.45
24 8 0.36
25 4 0.18
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (25 bp):
TTTTAAAATTTTTATAAATAACATC
Found at i:1141565 original size:20 final size:19
Alignment explanation
Indices: 1141515--1141591 Score: 73
Period size: 20 Copynumber: 3.9 Consensus size: 19
1141505 TTTTACCTTG
*
1141515 ATGTATCGATACATTTTTCA
1 ATGTATCGATACA-TTATCA
* * *
1141535 ATATATTGATACATGTATGA
1 ATGTATCGATACAT-TATCA
* *
1141555 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTAT-CA
1141575 ATGTATCGATACATTAT
1 ATGTATCGATACATTAT
1141592 GTCTTTTTAC
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
19 3 0.07
20 41 0.93
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.42
Consensus pattern (19 bp):
ATGTATCGATACATTATCA
Found at i:1141586 original size:40 final size:39
Alignment explanation
Indices: 1141515--1141592 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
1141505 TTTTACCTTG
* * *
1141515 ATGTATCGATACATTTTTCAATATATTGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
1141555 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
1141593 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:0.35, C:0.12, G:0.13, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:1148718 original size:22 final size:23
Alignment explanation
Indices: 1148689--1148740 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
1148679 AATGAAAAGA
* *
1148689 AAAAAAAAGTGCAA-AAGCAAAAT
1 AAAAAAAAGAG-AACAAGAAAAAT
1148712 AAAAAAAAGAGAACAAGAAAAAT
1 AAAAAAAAGAGAACAAGAAAAAT
1148735 AAAAAA
1 AAAAAA
1148741 CGAGGACATG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 2 0.08
23 24 0.92
ACGTcount: A:0.77, C:0.06, G:0.12, T:0.06
Consensus pattern (23 bp):
AAAAAAAAGAGAACAAGAAAAAT
Found at i:1148719 original size:40 final size:40
Alignment explanation
Indices: 1148651--1148738 Score: 108
Period size: 39 Copynumber: 2.2 Consensus size: 40
1148641 TCAAAATGAC
* *
1148651 AAAAAAAGTCAAAAGCAAAAGCACAAAAAA-TGAA-AAGAA
1 AAAAAAAGTCAAAAGCAAAAG-AAAAAAAAGAGAACAAGAA
*
1148690 AAAAAAAGTGCAAAAGCAAAATAAAAAAAAGAGAACAAGAA
1 AAAAAAAGT-CAAAAGCAAAAGAAAAAAAAGAGAACAAGAA
1148731 AAATAAAA
1 AAA-AAAA
1148739 AACGAGGACA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
39 16 0.38
40 14 0.33
41 8 0.19
42 4 0.10
ACGTcount: A:0.74, C:0.08, G:0.12, T:0.06
Consensus pattern (40 bp):
AAAAAAAGTCAAAAGCAAAAGAAAAAAAAGAGAACAAGAA
Found at i:1149016 original size:11 final size:12
Alignment explanation
Indices: 1148983--1149015 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
1148973 ACCCAATCCT
1148983 AAAAAAAAAACA
1 AAAAAAAAAACA
1148995 AAAAAAAAAACA
1 AAAAAAAAAACA
1149007 AAAAAAAAA
1 AAAAAAAAA
1149016 CCCTTTTCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAACA
Found at i:1150061 original size:27 final size:27
Alignment explanation
Indices: 1150025--1150681 Score: 956
Period size: 27 Copynumber: 24.0 Consensus size: 27
1150015 ACTGTGACCA
*
1150025 CTTTTAAGTCCACAACTCCGTGGCACA
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1150052 CTTTTAAGTCCACAACTCCGTAGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* **
1150079 CTTTTAAGTCCACAACTCTGTGGCATAT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
1150107 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1150134 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
1150162 CTTTTAAGTTCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1150189 CTTTTAAGTCCACAACTCCGTGACATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* *
1150217 CTTTTAAGTCCACAACTTCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1150244 TTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1150271 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1150298 CTTTTAAGTCCACAACTCCGCGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1150325 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
1150353 CTTTTAAGACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1150380 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * *
1150407 CTTTTAAGTCCATAACTCCATGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
1150435 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1150462 CTTTTTAA-TCCATAATTCCGTGGCACC
1 C-TTTTAAGTCCACAACTCCGTGGCACC
1150489 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1150516 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1150543 CTTTTAAGACCACAACTCCGTGACACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1150570 CTTTTAAGTCCATAACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* *
1150598 CTTTTAAGTCCATAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * *
1150625 CTTTTAAAATCCACAACTCTGTGGCACT
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
1150653 CTTTTAAAATCCACAACTCTGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
1150681 C
1 C
1150682 ATTTCAAAGC
Statistics
Matches: 574, Mismatches: 47, Indels: 17
0.90 0.07 0.03
Matches are distributed among these distances:
26 6 0.01
27 364 0.63
28 204 0.36
ACGTcount: A:0.24, C:0.34, G:0.14, T:0.29
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:1150193 original size:82 final size:82
Alignment explanation
Indices: 1150025--1150678 Score: 965
Period size: 82 Copynumber: 8.0 Consensus size: 82
1150015 ACTGTGACCA
* *
1150025 CTTTTAAGTCCACAACTCCGTGGCACACTTTTAAGTCCACAACTCCGTAGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
* **
1150090 ACAACTCTGTGGCATAT
66 ACAACTCCGTGGCATCC
* *
1150107 CTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTT
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTC
*
1150172 CACAACTCTGTGGCA-CC
65 CACAACTCCGTGGCATCC
* * * *
1150189 CTTTTAAGTCCACAACTCCGTGACATCCCTTTTAAGTCCACAACTTCGTGGCATCTTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1150254 CACAACTCCGTGGCA-CC
65 CACAACTCCGTGGCATCC
*
1150271 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGCGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1150336 ACAACTCCGTGGCATCC
66 ACAACTCCGTGGCATCC
*
1150353 CTTTTAAGACCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
* * *
1150418 ATAACTCCATGGCATCT
66 ACAACTCCGTGGCATCC
* *
1150435 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTTAA-TCCATAATTCCGTGGCACCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCC-TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1150499 CACAACTCCGTGGCA-CC
65 CACAACTCCGTGGCATCC
* *
1150516 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGACCACAACTCCGTGACACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
* *
1150581 ATAACTCCGTGGCATCT
66 ACAACTCCGTGGCATCC
* * * * * *
1150598 CTTTTAAGTCCATAACTCTGTGGCACCCTTTTAAAATCCACAACTCTGTGGCACTCTTTTAAAAT
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTT-AAGT
*
1150663 CCACAACTCTGTGGCA
64 CCACAACTCCGTGGCA
1150679 CCCATTTCAA
Statistics
Matches: 519, Mismatches: 45, Indels: 14
0.90 0.08 0.02
Matches are distributed among these distances:
80 6 0.01
81 118 0.23
82 298 0.57
83 80 0.15
84 17 0.03
ACGTcount: A:0.24, C:0.33, G:0.14, T:0.29
Consensus pattern (82 bp):
CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
ACAACTCCGTGGCATCC
Found at i:1150297 original size:109 final size:108
Alignment explanation
Indices: 1150026--1150680 Score: 934
Period size: 109 Copynumber: 6.0 Consensus size: 108
1150016 CTGTGACCAC
* *
1150026 TTTTAAGTCCACAACTCCGTGGCACACTTTTAAGTCCACAACTCCGTAGCACCCTTTTAAGTCCA
1 TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCA
* ** *
1150091 CAACTCTGTGGCATATCTTTTAAGTCCACAACTCTGTGGCACCCT
66 CAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCA-CCT
* * *
1150136 TTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTTCACAACTCTGTGGCACCCTTTTAAGTCCA
1 TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCA
* * *
1150201 CAACTCCGTGACATCCCTTTTAAGTCCACAACTTCGTGGCATCT
66 CAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCT
1150245 TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCA
1 TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCA
* *
1150310 CAACTCCGCGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCC
66 CAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCT
*
1150354 TTTTAAGACCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCA
1 TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCA
* * *
1150419 TAACTCCATGGCATCTCTTTTAAGTCCACAACTCCGTGGCACCCT
66 CAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCA-CCT
* *
1150464 TTTTAA-TCCATAATTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCA
1 TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCA
* * *
1150528 CAACTCCGTGGCACCCTTTTAAGACCACAACTCCGTGACACCC
66 CAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCT
* * * * *
1150571 TTTTAAGTCCATAACTCCGTGGCATCTCTTTTAAGTCCATAACTCTGTGGCACCCTTTTAAAATC
1 TTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTC
* * * *
1150636 CACAACTCTGTGGCACTCTTTTAAAATCCACAACTCTGTGGCACC
64 CACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACC
1150681 CATTTCAAAG
Statistics
Matches: 492, Mismatches: 47, Indels: 11
0.89 0.09 0.02
Matches are distributed among these distances:
107 8 0.02
108 66 0.13
109 247 0.50
110 153 0.31
111 18 0.04
ACGTcount: A:0.24, C:0.33, G:0.14, T:0.29
Consensus pattern (108 bp):
TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCA
CAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCT
Found at i:1151285 original size:32 final size:32
Alignment explanation
Indices: 1150664--1151277 Score: 993
Period size: 32 Copynumber: 19.2 Consensus size: 32
1150654 TTTTAAAATC
* *
1150664 CACAACTCTGTGGC-ACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1150695 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1150727 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
1150759 CACAAGTTGGTGGCAACCCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1150791 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1150823 CACAAGTCGGTGGCAA-CCATTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCA-TTTCAAAGCCCA
*
1150855 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1150887 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
** *
1150919 CACAAGTCAATGGCAACCCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1150951 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1150983 CACAAGTCGGTGGCAA-CCATTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCA-TTTCAAAGCCCA
*
1151015 CACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1151047 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1151079 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1151111 CACAAGTTGGTGGCAA-CCATTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCA-TTTCAAAGCCCA
*
1151143 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1151175 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1151207 CACAAGTCGGTGGCAACCCATTTCAAAGTCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * ** * *
1151239 CACGAGTCAGTGGCAATTCTTTTCAAGGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1151271 CATAAGT
1 CACAAGT
1151278 TAGTGGCACC
Statistics
Matches: 544, Mismatches: 32, Indels: 13
0.92 0.05 0.02
Matches are distributed among these distances:
31 21 0.04
32 516 0.95
33 7 0.01
ACGTcount: A:0.31, C:0.33, G:0.18, T:0.18
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
Found at i:1151909 original size:20 final size:19
Alignment explanation
Indices: 1151859--1151935 Score: 73
Period size: 20 Copynumber: 3.9 Consensus size: 19
1151849 TTTTACCTTG
*
1151859 ATGTATCGATACATTTTTCA
1 ATGTATCGATACA-TTATCA
* * *
1151879 ATATATTGATACATGTATGA
1 ATGTATCGATACAT-TATCA
* *
1151899 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTAT-CA
1151919 ATGTATCGATACATTAT
1 ATGTATCGATACATTAT
1151936 GTCTTTTTAC
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
19 3 0.07
20 41 0.93
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.42
Consensus pattern (19 bp):
ATGTATCGATACATTATCA
Found at i:1151930 original size:40 final size:39
Alignment explanation
Indices: 1151859--1151936 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
1151849 TTTTACCTTG
* * *
1151859 ATGTATCGATACATTTTTCAATATATTGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
1151899 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
1151937 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:0.35, C:0.12, G:0.13, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:1157074 original size:23 final size:21
Alignment explanation
Indices: 1157014--1157081 Score: 68
Period size: 23 Copynumber: 3.2 Consensus size: 21
1157004 TCTAATATCT
1157014 TAAATAAA-ATTATT-ATAAA
1 TAAATAAATATTATTAATAAA
* *
1157033 TAAATAAATAATATAAATATAA
1 TAAATAAATATTATTAATA-AA
*
1157055 TATAATAAATATTTTTAATAAA
1 TA-AATAAATATTATTAATAAA
*
1157077 AAAAT
1 TAAAT
1157082 CTCTCAAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 8 0.21
20 4 0.10
21 6 0.15
22 7 0.18
23 14 0.36
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
TAAATAAATATTATTAATAAA
Found at i:1160922 original size:13 final size:13
Alignment explanation
Indices: 1160904--1160928 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1160894 TACAATGATC
1160904 AATGTATCGATAT
1 AATGTATCGATAT
1160917 AATGTATCGATA
1 AATGTATCGATA
1160929 CATTTCCTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (13 bp):
AATGTATCGATAT
Found at i:1161052 original size:21 final size:20
Alignment explanation
Indices: 1161028--1161066 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
1161018 ATTGGGACCT
1161028 TGTATCGATACATTCTAGAAA
1 TGTATCGATACATT-TAGAAA
1161049 TGTATCGATACATTTAGA
1 TGTATCGATACATTTAGA
1161067 TAAAAATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATTTAGAAA
Found at i:1163516 original size:2 final size:2
Alignment explanation
Indices: 1163509--1163535 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1163499 TTAGAAACAT
1163509 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 T
1163536 TCTAAAAAAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1170695 original size:16 final size:16
Alignment explanation
Indices: 1170671--1170736 Score: 55
Period size: 16 Copynumber: 4.1 Consensus size: 16
1170661 TATTTAATTT
*
1170671 ATTAAAATAAAATAAA
1 ATTATAATAAAATAAA
* *
1170687 ATTATAATATAATAATT
1 ATTATAATAAAATAA-A
* *
1170704 ATT-TTATAAAATCAA
1 ATTATAATAAAATAAA
1170719 A-TATAATTAAAATAAA
1 ATTATAA-TAAAATAAA
1170735 AT
1 AT
1170737 AAAATAATTG
Statistics
Matches: 37, Mismatches: 9, Indels: 7
0.70 0.17 0.13
Matches are distributed among these distances:
14 1 0.03
15 3 0.08
16 30 0.81
17 3 0.08
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (16 bp):
ATTATAATAAAATAAA
Found at i:1175515 original size:34 final size:35
Alignment explanation
Indices: 1175477--1175554 Score: 90
Period size: 34 Copynumber: 2.3 Consensus size: 35
1175467 TATTATTTTT
** *
1175477 TATTTTTTAAAAAATTTAATTTCT-AATAATTTAA
1 TATTTTTTAAAAAATTTAAAATATAAATAATTTAA
*
1175511 TATTTTATT--AAATTTTAAAATATAAATAATTTAA
1 TATTTT-TTAAAAAATTTAAAATATAAATAATTTAA
1175545 TATTTTTTAA
1 TATTTTTTAA
1175555 TATTTACATC
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
33 12 0.33
34 22 0.61
35 2 0.06
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (35 bp):
TATTTTTTAAAAAATTTAAAATATAAATAATTTAA
Found at i:1175734 original size:17 final size:19
Alignment explanation
Indices: 1175712--1175752 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1175702 TCTTAAAAAT
*
1175712 AATTT-ATTTTT-TATCTA
1 AATTTAATTTTTAAATCTA
1175729 AATTTAATTTTTAAATCTA
1 AATTTAATTTTTAAATCTA
1175748 AATTT
1 AATTT
1175753 TTTAAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
18 6 0.29
19 10 0.48
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (19 bp):
AATTTAATTTTTAAATCTA
Found at i:1179095 original size:57 final size:58
Alignment explanation
Indices: 1178978--1179125 Score: 151
Period size: 57 Copynumber: 2.6 Consensus size: 58
1178968 CTAAATTATG
* ** * *
1178978 AAAAA-TAACCTAAATGACATCAAAATACATACATTTGCATAAAAATCTAAGAACATT
1 AAAAAGTAACCTAAATAACCCCAACATACATAAATTTGCATAAAAATCTAAGAACATT
* * * * * *
1179035 AAAAA-TGATCTAAATGATCCCAACATACATAAATTTGCATAAAAGTTCATAA-ATCA-T
1 AAAAAGTAACCTAAATAACCCCAACATACATAAATTTGCATAAAA-ATC-TAAGAACATT
1179092 AAAAAGTAACCTAAATAACCCCAACATACATAAA
1 AAAAAGTAACCTAAATAACCCCAACATACATAAA
1179126 ATTACAATAA
Statistics
Matches: 75, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
57 43 0.57
58 29 0.39
59 3 0.04
ACGTcount: A:0.53, C:0.18, G:0.05, T:0.24
Consensus pattern (58 bp):
AAAAAGTAACCTAAATAACCCCAACATACATAAATTTGCATAAAAATCTAAGAACATT
Found at i:1179122 original size:58 final size:55
Alignment explanation
Indices: 1178934--1179125 Score: 159
Period size: 58 Copynumber: 3.3 Consensus size: 55
1178924 ATCATAAAAT
* * * * * *
1178934 TAACCTCAATATAGATAAATTTGTATAATAATCCCTAAATTATGAAAAATAACCTAAA
1 TAACCCCAACATACATAAATTTGCATAA-AAT-TCTAAATCAT-AAAAATAACCTAAA
* ** * * * * * *
1178992 TGACATCAAAATACATACATTTGCATAAAAATCTAAGAACATTAAAAATGATCTAAA
1 TAACCCCAACATACATAAATTTGCATAAAATTCTAA-ATCA-TAAAAATAACCTAAA
* *
1179049 TGATCCCAACATACATAAATTTGCATAAAAGTTCATAAATCATAAAAAGTAACCTAAA
1 TAACCCCAACATACATAAATTTGCATAAAA-TTC-TAAATCATAAAAA-TAACCTAAA
1179107 TAACCCCAACATACATAAA
1 TAACCCCAACATACATAAA
1179126 ATTACAATAA
Statistics
Matches: 106, Mismatches: 23, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
56 4 0.04
57 47 0.44
58 52 0.49
59 3 0.03
ACGTcount: A:0.51, C:0.17, G:0.06, T:0.27
Consensus pattern (55 bp):
TAACCCCAACATACATAAATTTGCATAAAATTCTAAATCATAAAAATAACCTAAA
Found at i:1179194 original size:29 final size:31
Alignment explanation
Indices: 1179120--1179195 Score: 74
Period size: 29 Copynumber: 2.6 Consensus size: 31
1179110 CCCCAACATA
* *
1179120 CATAAAATTACAATAAA-GTCCATTAAATATG
1 CATAAAATTAC-ATAAATGACCACTAAATATG
1179151 -AT-AAATTAC-TAAAATGACC-CTAAA-ATG
1 CATAAAATTACAT-AAATGACCACTAAATATG
1179178 CATAAAATTACATAAATG
1 CATAAAATTACATAAATG
1179196 GTCTCAAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
27 4 0.11
28 9 0.24
29 22 0.58
30 3 0.08
ACGTcount: A:0.53, C:0.13, G:0.07, T:0.28
Consensus pattern (31 bp):
CATAAAATTACATAAATGACCACTAAATATG
Found at i:1179237 original size:29 final size:28
Alignment explanation
Indices: 1179144--1179237 Score: 70
Period size: 29 Copynumber: 3.2 Consensus size: 28
1179134 AAAGTCCATT
*
1179144 AAATAT-GATAAATTACTAAAATGACCCTA
1 AAATATAG-TAAATTACT-AAATGACTCTA
*
1179173 AAATGCATA--AAATTACATAAATG-GTCTCA
1 AAAT--ATAGTAAATTAC-TAAATGACTCT-A
*
1179202 AATTATAGTAAATTACTAGAATGACTCTA
1 AAATATAGTAAATTACTA-AATGACTCTA
1179231 AAATATA
1 AAATATA
1179238 TGAGCATACA
Statistics
Matches: 51, Mismatches: 5, Indels: 18
0.69 0.07 0.24
Matches are distributed among these distances:
27 3 0.06
28 4 0.08
29 38 0.75
30 4 0.08
31 2 0.04
ACGTcount: A:0.50, C:0.12, G:0.09, T:0.30
Consensus pattern (28 bp):
AAATATAGTAAATTACTAAATGACTCTA
Found at i:1179300 original size:111 final size:111
Alignment explanation
Indices: 1179174--1179376 Score: 268
Period size: 111 Copynumber: 1.8 Consensus size: 111
1179164 ATGACCCTAA
* * * * *
1179174 AATGCATAAAATTACATAAATGGTCTCAAATTATAGTAAATTACTAGAATGACTC-TAAAATATA
1 AATGCATAAAATTACATAAATGATCTCAAA-AATAGCAAATTACTAAAATGA-TCATAAAATACA
*
1179238 TGAGCA-TACAT-AATGATCCTAAATCATGAAAAAAATACTAGAATGAT
64 TG-GAATTACATAAATGATCCTAAATCATGAAAAAAATACTAGAATGAT
* * *
1179285 AATGCATAAAATTACATAAATGATCTTAAAAATGGCAAATTACTAAAATGATCATAAAATGCATG
1 AATGCATAAAATTACATAAATGATCTCAAAAATAGCAAATTACTAAAATGATCATAAAATACATG
*
1179350 GAATTGCATAAATGATCCTAAATCATG
66 GAATTACATAAATGATCCTAAATCATG
1179377 GAATTTTTTA
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
109 4 0.05
110 30 0.38
111 45 0.57
ACGTcount: A:0.48, C:0.12, G:0.11, T:0.29
Consensus pattern (111 bp):
AATGCATAAAATTACATAAATGATCTCAAAAATAGCAAATTACTAAAATGATCATAAAATACATG
GAATTACATAAATGATCCTAAATCATGAAAAAAATACTAGAATGAT
Found at i:1180314 original size:10 final size:10
Alignment explanation
Indices: 1180289--1180335 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
1180279 AAACTCACTC
1180289 TTTTTTC-TT
1 TTTTTTCTTT
*
1180298 TTCTTTCTTT
1 TTTTTTCTTT
1180308 TTTTTTCTTT
1 TTTTTTCTTT
*
1180318 TTTTCTCTAGTT
1 TTTTTTCT--TT
1180330 TTTTTT
1 TTTTTT
1180336 GCTAAGAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
9 6 0.19
10 18 0.58
12 7 0.23
ACGTcount: A:0.02, C:0.13, G:0.02, T:0.83
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:1180331 original size:19 final size:19
Alignment explanation
Indices: 1180290--1180332 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1180280 AACTCACTCT
**
1180290 TTTTTCTTTTCTTTCTTTT
1 TTTTTCTTTTCTTTCTTAG
1180309 TTTTTCTTTT-TTTCTCTAG
1 TTTTTCTTTTCTTTCT-TAG
1180328 TTTTT
1 TTTTT
1180333 TTTGCTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.81
Consensus pattern (19 bp):
TTTTTCTTTTCTTTCTTAG
Found at i:1184958 original size:52 final size:52
Alignment explanation
Indices: 1184810--1184938 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
1184800 CGAAATATGA
1184810 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATATGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATATGGGC
* *
1184862 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATATGGGC
1184914 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1184939 AAGATCAGTG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATATGGGC
Found at i:1184965 original size:13 final size:13
Alignment explanation
Indices: 1184947--1184971 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1184937 CAAAGATCAG
1184947 TGTATCGATACAA
1 TGTATCGATACAA
1184960 TGTATCGATACA
1 TGTATCGATACA
1184972 TTTGAGTAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1185038 original size:19 final size:17
Alignment explanation
Indices: 1185013--1185111 Score: 70
Period size: 19 Copynumber: 5.9 Consensus size: 17
1185003 GTAGCTTACA
1185013 TTGTATCGATACAAAACT
1 TTGTATCGATAC-AAACT
1185031 TATGTATCGATAC--A--
1 T-TGTATCGATACAAACT
1185045 TTGTATCGATACAACACT
1 TTGTATCGATACAA-ACT
*
1185063 TATATATCGATAC--A--
1 T-TGTATCGATACAAACT
1185077 TTGTATCGATACAACACTTT
1 TTGTATCGATACAA-AC--T
1185097 TTGTATCGATACAAA
1 TTGTATCGATACAAA
1185112 TTGTTGAAAT
Statistics
Matches: 65, Mismatches: 2, Indels: 27
0.69 0.02 0.29
Matches are distributed among these distances:
13 21 0.32
14 2 0.03
16 4 0.06
18 2 0.03
19 22 0.34
20 14 0.22
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.35
Consensus pattern (17 bp):
TTGTATCGATACAAACT
Found at i:1185050 original size:32 final size:32
Alignment explanation
Indices: 1185009--1185109 Score: 166
Period size: 32 Copynumber: 3.1 Consensus size: 32
1184999 GGCAGTAGCT
*
1185009 TACATTGTATCGATACAAAACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
*
1185041 TACATTGTATCGATACAACACTTATATATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
*
1185073 TACATTGTATCGATACAACACTTTTTGTATCGA
1 TACATTGTATCGATACAACAC-TTATGTATCGA
1185106 TACA
1 TACA
1185110 AATTGTTGAA
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 51 0.80
33 13 0.20
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.36
Consensus pattern (32 bp):
TACATTGTATCGATACAACACTTATGTATCGA
Found at i:1185051 original size:13 final size:13
Alignment explanation
Indices: 1185033--1185089 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
1185023 ACAAAACTTA
1185033 TGTATCGATACAT
1 TGTATCGATACAT
1185046 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
*
1185064 ATATATCGATACAT
1 -TGTATCGATACAT
1185078 TGTATCGATACA
1 TGTATCGATACA
1185090 ACACTTTTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 20 0.56
14 1 0.03
16 6 0.17
18 1 0.03
19 8 0.22
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1185867 original size:43 final size:43
Alignment explanation
Indices: 1185802--1186455 Score: 588
Period size: 43 Copynumber: 14.1 Consensus size: 43
1185792 TAAATATGGA
*
1185802 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
* * * *
1185845 AAAGGTGCCAATGTGCTAATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1185888 AAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 -----A-AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
* * *
1185937 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
*
1185980 AAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGAT
1 ----A--AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T
* *
1186035 GACAAAGGCGCCAATATGATGATTCAAGGCCAGCGATATTGGACTT
1 ---AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
* * * *
1186081 AAAGGTGCCAATGTGCTAATTCAAGGCCAGCGACATTGGGCTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
*
1186124 AAAAGATGGGGGTGCCAATATGCTGATTTAAGGCCAGCGATATTGGACTT
1 --AA-A----GGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
* * * * * *
1186174 AGAGTTACCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1186217 AAAGATGATGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 --A-A--A-GGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
* * **
1186266 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACGTTGGACTTAAGAT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T----T
* *
1186314 AAAGGTGCCAATCTGCTGATTCAAGGCCAACGATATTGGACTTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-TT
* * **
1186358 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACGTTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
*
1186401 AAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT
1 ----A--AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1186450 AGAAGG
1 A-AAGG
1186456 GTTGCCAGCG
Statistics
Matches: 507, Mismatches: 62, Indels: 83
0.78 0.10 0.13
Matches are distributed among these distances:
43 186 0.37
44 45 0.09
45 4 0.01
46 3 0.01
47 4 0.01
48 42 0.08
49 146 0.29
50 36 0.07
51 1 0.00
52 37 0.07
54 2 0.00
55 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (43 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
Found at i:1185930 original size:92 final size:92
Alignment explanation
Indices: 1185768--1186032 Score: 433
Period size: 92 Copynumber: 2.8 Consensus size: 92
1185758 CACTGTGTTG
* *
1185768 ATTCAAGGCCATCTACATTGAACTTAAATATGGAA-AAGGTGCCAATATGCTGATTCAAGGCCAG
1 ATTCAAGGCCAGCTACATTGGACTT-AA-A--GAAGAAGGTGCCAATATGCTGATTCAAGGCCAG
*
1185832 CTATATTGGACTTAAAGGTGCCAATGTGCTA
62 CGATATTGGACTTAAAGGTGCCAATGTGCTA
1185863 ATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGAT
1 ATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGAT
*
1185928 ATTGGACTTAAAGGTGCCAATGTGCTG
66 ATTGGACTTAAAGGTGCCAATGTGCTA
* *
1185955 ATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAACGAT
1 ATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGAT
1186020 ATTGGACTTAAAG
66 ATTGGACTTAAAG
1186033 ATGACAAAGG
Statistics
Matches: 163, Mismatches: 6, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
91 3 0.02
92 134 0.82
93 1 0.01
94 2 0.01
95 23 0.14
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.25
Consensus pattern (92 bp):
ATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGAT
ATTGGACTTAAAGGTGCCAATGTGCTA
Found at i:1186234 original size:237 final size:236
Alignment explanation
Indices: 1185766--1186269 Score: 812
Period size: 237 Copynumber: 2.1 Consensus size: 236
1185756 GTCACTGTGT
* * * * * * *
1185766 TGATTCAAGGCCATCTACATTGAACTTAAATATGGAAAAGGTGCCAATATGCTGATTCAAGGCCA
1 TGATTCAAGGCCAACGATATTGGACTTAAAGATGGAAAAGGCGCCAATATGATGATTCAAGGCCA
* *
1185831 GCTATATTGGACTTAAAGGTGCCAATGTGCTAATTCAAGGCCAGCTACATTGGACTTAAAGAAGA
66 GCGATATTGGACTTAAAGGTGCCAATGTGCTAATTCAAGGCCAGCGACATTGGACTTAAAGAAGA
*
1185896 AGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAA
131 AGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTACCAATGTGCTGATTCAA
1185961 GGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
196 GGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1186002 TGATTCAAGGCCAACGATATTGGACTTAAAGAT-GACAAAGGCGCCAATATGATGATTCAAGGCC
1 TGATTCAAGGCCAACGATATTGGACTTAAAGATGGA-AAAGGCGCCAATATGATGATTCAAGGCC
* *
1186066 AGCGATATTGGACTTAAAGGTGCCAATGTGCTAATTCAAGGCCAGCGACATTGGGCTTAAAAGAT
65 AGCGATATTGGACTTAAAGGTGCCAATGTGCTAATTCAAGGCCAGCGACATTGGACTT-AAAGAA
** * * *
1186131 GGGGGTGCCAATATGCTGATTTAAGGCCAGCGATATTGGACTTAGAGTTACCAATGTGCTGATTC
129 GAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTACCAATGTGCTGATTC
*
1186196 AAGGCCAGCTACATTGGACTTAAAGATGATGGTGCCAATATGC
194 AAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
1186239 TGATTCAAGGCCAGCGATATTGGACTTAAAG
1 TGATTCAAGGCCAACGATATTGGACTTAAAG
1186270 GTGCCAATGT
Statistics
Matches: 247, Mismatches: 19, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
235 2 0.01
236 109 0.44
237 136 0.55
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (236 bp):
TGATTCAAGGCCAACGATATTGGACTTAAAGATGGAAAAGGCGCCAATATGATGATTCAAGGCCA
GCGATATTGGACTTAAAGGTGCCAATGTGCTAATTCAAGGCCAGCGACATTGGACTTAAAGAAGA
AGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTACCAATGTGCTGATTCAA
GGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
Found at i:1186277 original size:92 final size:92
Alignment explanation
Indices: 1185802--1186455 Score: 749
Period size: 92 Copynumber: 7.1 Consensus size: 92
1185792 TAAATATGGA
* * *
1185802 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGCCAATGTGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
* * *
1185861 TAATTCAAGGCCAGCTACATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
* * *
1185888 AAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCA
1 -----A-AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCA
* * *
1185947 ATGTGCTGATTCAAGGCCAGCTACATTGGACTT
60 ATATGCTGATTCAAGGCCAGCGATATTGGACTT
* * * * *
1185980 AAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGACAAAGGCG
1 ----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG---AAGGTG
*
1186045 CCAATATGATGATTCAAGGCCAGCGATATTGGACTT
57 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
* * * **
1186081 AAAGGTGCCAATGTGCTAATTCAAGGCCAGCGACATTGGGCTTAAAAGATGGGGGTGCCAATATG
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT-AAAGATGAAGGTGCCAATATG
*
1186146 CTGATTTAAGGCCAGCGATATTGGACTT
65 CTGATTCAAGGCCAGCGATATTGGACTT
* * * *
1186174 AGAGTTACCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGATGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1186239 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
* * *
1186266 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACGTTGGACTT-AAGATAAAGGTGCCAATCTGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
1186330 TGATTCAAGGCCAACGATATTGGACTTT
66 TGATTCAAGGCCAGCGATATTGGAC-TT
*
1186358 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACGTTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
1186423 TGATTCAAGGCCAGCGATATTGGGCTT
66 TGATTCAAGGCCAGCGATATTGGACTT
1186450 AGAAGG
1 A-AAGG
1186456 GTTGCCAGCG
Statistics
Matches: 507, Mismatches: 41, Indels: 28
0.88 0.07 0.05
Matches are distributed among these distances:
91 46 0.09
92 258 0.51
93 120 0.24
95 37 0.07
96 8 0.02
97 1 0.00
101 37 0.07
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
TGATTCAAGGCCAGCGATATTGGACTT
Found at i:1186494 original size:33 final size:33
Alignment explanation
Indices: 1186450--1186707 Score: 373
Period size: 33 Copynumber: 7.9 Consensus size: 33
1186440 TATTGGGCTT
*
1186450 AGAAGGGTTGCCAGCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
1186483 AGAATGGTTGCCACCAACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
1186516 AG-AGGGTTGCCACCGGCTTGTGTGGGCTTT-G
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
1186547 ATAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* **
1186580 AGAATGGTTGCCACTAACTTGTGTGGGCTTT-G
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1186612 AG-AGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
1186644 AAGAA-GGTTGCCACCGACTTGTGTGAGCTTTAG
1 -AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
1186677 AGAAGGGTTGCCACCAACTTGTGTGAGCTTT
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTT
1186708 TGAAGAGGAG
Statistics
Matches: 202, Mismatches: 17, Indels: 12
0.87 0.07 0.05
Matches are distributed among these distances:
31 27 0.13
32 60 0.30
33 114 0.56
34 1 0.00
ACGTcount: A:0.19, C:0.18, G:0.34, T:0.29
Consensus pattern (33 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:1186568 original size:64 final size:65
Alignment explanation
Indices: 1186443--1186707 Score: 369
Period size: 64 Copynumber: 4.1 Consensus size: 65
1186433 CCAGCGATAT
* *
1186443 TGGGC-TTAGA-AGGGTTGCCAGCGACTTGTGTGGGCTTTAGAGAATGGTTGCCACCAACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGCCACCAACTTGTG
* * *
1186506 TGGGCTTTAGAGAGGGTTGCCACCGGCTTGTGTGGGCTTT-GATAAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGCCACCAACTTGTG
* ** *
1186570 TGGGCTTTAGAGAATGGTTGCCACTAACTTGTGTGGGCTTT-GAG-AGGGTTGCCACCGACTTGT
1 TGGGCTTTAGAG-AGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGCCACCAACTTGT
1186633 G
65 G
* *
1186634 TGGGCTTTAGAAGAAGGTTGCCACCGACTTGTGTGAGCTTTAGAGAAGGGTTGCCACCAACTTGT
1 TGGGCTTTAG-AGAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGCCACCAACTTGT
1186699 G
65 G
*
1186700 TGAGCTTT
1 TGGGCTTT
1186708 TGAAGAGGAG
Statistics
Matches: 180, Mismatches: 16, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
63 5 0.03
64 92 0.51
65 57 0.32
66 26 0.14
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.30
Consensus pattern (65 bp):
TGGGCTTTAGAGAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGCCACCAACTTGTG
Found at i:1186653 original size:97 final size:97
Alignment explanation
Indices: 1186443--1186707 Score: 421
Period size: 97 Copynumber: 2.8 Consensus size: 97
1186433 CCAGCGATAT
*
1186443 TGGGC-TTAGAAG-GGTTGCCAGCGACTTGTGTGGGCTTTAGAGAATGGTTGCCACCAACTTGTG
1 TGGGCTTTAGAAGAGGTTGCCACCGACTTGTGTGGGCTTTAGAGAATGGTTGCCACCAACTTGTG
*
1186506 TGGGCTTTAGAGAGGGTTGCCACCGGCTTGTG
66 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
* *
1186538 TGGGCTTTGATAAG-GGTTGCCACCGACTTGTGTGGGCTTTAGAGAATGGTTGCCACTAACTTGT
1 TGGGCTTT-AGAAGAGGTTGCCACCGACTTGTGTGGGCTTTAGAGAATGGTTGCCACCAACTTGT
1186602 GTGGGCTTT-GAGAGGGTTGCCACCGACTTGTG
65 GTGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
* *
1186634 TGGGCTTTAGAAGAAGGTTGCCACCGACTTGTGTGAGCTTTAGAGAAGGGTTGCCACCAACTTGT
1 TGGGCTTTAGAAG-AGGTTGCCACCGACTTGTGTGGGCTTTAGAGAATGGTTGCCACCAACTTGT
*
1186699 GTGAGCTTT
65 GTGGGCTTT
1186708 TGAAGAGGAG
Statistics
Matches: 157, Mismatches: 9, Indels: 6
0.91 0.05 0.03
Matches are distributed among these distances:
95 9 0.06
96 32 0.20
97 116 0.74
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.30
Consensus pattern (97 bp):
TGGGCTTTAGAAGAGGTTGCCACCGACTTGTGTGGGCTTTAGAGAATGGTTGCCACCAACTTGTG
TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
Done.