Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 151 of 172
Found at i:49426404 original size:17 final size:18
Alignment explanation
Indices: 49426368--49426405 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
49426358 TTGGGCCGGG
49426368 CACTAGTCTCTTCATAAA
1 CACTAGTCTCTTCATAAA
* *
49426386 CACTAGT-TTTTCTTAAA
1 CACTAGTCTCTTCATAAA
49426403 CAC
1 CAC
49426406 AAGCACTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.32, C:0.26, G:0.05, T:0.37
Consensus pattern (18 bp):
CACTAGTCTCTTCATAAA
Found at i:49428288 original size:92 final size:92
Alignment explanation
Indices: 49428157--49428525 Score: 720
Period size: 92 Copynumber: 4.0 Consensus size: 92
49428147 AGCAATCCTT
*
49428157 TTCTTCGCCTTTATTTACTTTTGTTAGGATTGAGCTCTGATTAGAGATTTTGTTTTGGGTTTAAT
1 TTCTTCGCCTTTATTTAC-TTTGTTAGGATTGAGCTCTGATTAGAGGTTTTGTTTTGGGTTTAAT
49428222 TGTTGATTCATCTTTTTTCTATTATTTC
65 TGTTGATTCATCTTTTTTCTATTATTTC
49428250 TTCTTCGCCTTTATTTACTTTGTTAGGATTGAGCTCTGATTAGAGGTTTTGTTTTGGGTTTAATT
1 TTCTTCGCCTTTATTTACTTTGTTAGGATTGAGCTCTGATTAGAGGTTTTGTTTTGGGTTTAATT
49428315 GTTGATTCATCTTTTTTCTATTATTTC
66 GTTGATTCATCTTTTTTCTATTATTTC
49428342 TTCTTCGCCTTTATTTACTTTGTTAGGATTGAGCTCTGATTAGAGGTTTTGTTTTGGGTTTAATT
1 TTCTTCGCCTTTATTTACTTTGTTAGGATTGAGCTCTGATTAGAGGTTTTGTTTTGGGTTTAATT
49428407 GTTGATTCATCTTTTTTCTATTATTTC
66 GTTGATTCATCTTTTTTCTATTATTTC
49428434 TTCTTCGCCTTTATTTACTTTGTTAGGATTGAGCTCTGATTAGAGGTTTTGTTTTGGGTTTAATT
1 TTCTTCGCCTTTATTTACTTTGTTAGGATTGAGCTCTGATTAGAGGTTTTGTTTTGGGTTTAATT
49428499 GTTGATTCATCTTTTTTCTATTATTTC
66 GTTGATTCATCTTTTTTCTATTATTTC
49428526 CTGGCAGCTC
Statistics
Matches: 275, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
92 257 0.93
93 18 0.07
ACGTcount: A:0.15, C:0.12, G:0.17, T:0.56
Consensus pattern (92 bp):
TTCTTCGCCTTTATTTACTTTGTTAGGATTGAGCTCTGATTAGAGGTTTTGTTTTGGGTTTAATT
GTTGATTCATCTTTTTTCTATTATTTC
Found at i:49429414 original size:21 final size:21
Alignment explanation
Indices: 49429388--49429432 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
49429378 AGGTGGTAAT
*
49429388 TCTGAAGGTTCCTTGAACTCA
1 TCTGAAGATTCCTTGAACTCA
49429409 TCTGAAGATTCCTTGAACTCA
1 TCTGAAGATTCCTTGAACTCA
49429430 TCT
1 TCT
49429433 AAGTAGGAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (21 bp):
TCTGAAGATTCCTTGAACTCA
Found at i:49434724 original size:20 final size:21
Alignment explanation
Indices: 49434696--49434736 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
49434686 TTCAATTCTA
49434696 AAATATTAAAT-GATTTATTT
1 AAATATTAAATCGATTTATTT
* *
49434716 AAATTTTAAATCTATTTATTT
1 AAATATTAAATCGATTTATTT
49434737 TTAAGTCCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (21 bp):
AAATATTAAATCGATTTATTT
Found at i:49435296 original size:21 final size:21
Alignment explanation
Indices: 49435271--49435319 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
49435261 ACTCTAGTGG
*
49435271 ATATTTTGAGAAAATAAAA-AA
1 ATATTTT-AAAAAATAAAATAA
49435292 ATA-TTTAAAAAATAAAATAA
1 ATATTTTAAAAAATAAAATAA
*
49435312 AAATTTTA
1 ATATTTTA
49435320 TTTTAGGTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 10 0.42
20 7 0.29
21 7 0.29
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (21 bp):
ATATTTTAAAAAATAAAATAA
Found at i:49435511 original size:29 final size:30
Alignment explanation
Indices: 49435479--49435540 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
49435469 CAATTTGATG
*
49435479 CATGAAA-TTTGATTTG-ATACAATTATACA
1 CATGAAACTTTGATTTGAAT-CAAATATACA
*
49435508 CATGAAACTTTTATTTGAATCAAATATACA
1 CATGAAACTTTGATTTGAATCAAATATACA
49435538 CAT
1 CAT
49435541 TTAAAGGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 7 0.24
30 20 0.69
31 2 0.07
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.37
Consensus pattern (30 bp):
CATGAAACTTTGATTTGAATCAAATATACA
Found at i:49441359 original size:35 final size:35
Alignment explanation
Indices: 49441291--49441368 Score: 88
Period size: 35 Copynumber: 2.2 Consensus size: 35
49441281 GTAAACAACA
* * *
49441291 TAATATTATTAAAATCACAATACATTTATATTATG
1 TAATATTATTAAAATCACAATACATTAAAATTATC
49441326 TAATATTATTAAAATCA-AATA-ATAGTAAAATTATC
1 TAATATTATTAAAATCACAATACAT--TAAAATTATC
*
49441361 AAATATTA
1 TAATATTA
49441369 AATTATAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
33 2 0.05
34 4 0.11
35 31 0.84
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (35 bp):
TAATATTATTAAAATCACAATACATTAAAATTATC
Found at i:49442897 original size:156 final size:157
Alignment explanation
Indices: 49442612--49442923 Score: 608
Period size: 156 Copynumber: 2.0 Consensus size: 157
49442602 AAAGCAGCCC
49442612 ATTTTCAGCCAATTTAAACCCAAAAACTACAAGCCCAAATGCCCAATATTAATAAAAACCCTAGA
1 ATTTTCAGCCAATTTAAACCCAAAAACTACAAGCCCAAATGCCCAATATTAATAAAAACCCTAGA
49442677 GGCCCGAATGGCCCAAAACTACACCAACTTTCAAACACAAAAAGAAACCCCAGCCGCATGTTGTT
66 GGCCCGAATGGCCCAAAACTACACCAACTTTCAAACACAAAAAGAAACCCCAGCCGCATGTTGTT
49442742 GCTGCCACCTCCTGCGCACGCCCACCA
131 GCTGCCACCTCCTGCGCACGCCCACCA
49442769 ATTTTCAGCCAATTTAAACCCAAAAACTACAAGCCCAAAT-CCCAATATTAATAAAAACCCTAGA
1 ATTTTCAGCCAATTTAAACCCAAAAACTACAAGCCCAAATGCCCAATATTAATAAAAACCCTAGA
*
49442833 GGCCCGAATGGCCCAAAACTACACCAACTTTCAAACACAAAAAGAAACCCCAGCCTCATGTTGTT
66 GGCCCGAATGGCCCAAAACTACACCAACTTTCAAACACAAAAAGAAACCCCAGCCGCATGTTGTT
49442898 GCTGCCACCTCCTGCGCACGCCCACC
131 GCTGCCACCTCCTGCGCACGCCCACC
49442924 GCCGCTACTC
Statistics
Matches: 154, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
156 114 0.74
157 40 0.26
ACGTcount: A:0.37, C:0.34, G:0.12, T:0.18
Consensus pattern (157 bp):
ATTTTCAGCCAATTTAAACCCAAAAACTACAAGCCCAAATGCCCAATATTAATAAAAACCCTAGA
GGCCCGAATGGCCCAAAACTACACCAACTTTCAAACACAAAAAGAAACCCCAGCCGCATGTTGTT
GCTGCCACCTCCTGCGCACGCCCACCA
Found at i:49455635 original size:6 final size:7
Alignment explanation
Indices: 49455618--49455643 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
49455608 CTTTGCCTAA
49455618 AAAAAAT
1 AAAAAAT
49455625 AAAAAAT
1 AAAAAAT
49455632 AAAAAAT
1 AAAAAAT
49455639 AAAAA
1 AAAAA
49455644 GGGAGAGGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:49456552 original size:43 final size:45
Alignment explanation
Indices: 49456482--49456574 Score: 127
Period size: 43 Copynumber: 2.1 Consensus size: 45
49456472 ATTGATTTTA
* *
49456482 TAGATCGAAGGTAGCAGATCCTATCTTCCTATATTGGTAG-GAAG
1 TAGATCGAAGATAGCAGATCCTATCTTCCCATATTGGTAGCGAAG
* * *
49456526 TAGATCGAAGAT-GCAGATCTTGTCTTCCCATATTGGTGGCGAAG
1 TAGATCGAAGATAGCAGATCCTATCTTCCCATATTGGTAGCGAAG
49456570 TAGAT
1 TAGAT
49456575 NNNNNNNNNN
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
43 23 0.53
44 20 0.47
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (45 bp):
TAGATCGAAGATAGCAGATCCTATCTTCCCATATTGGTAGCGAAG
Found at i:49466935 original size:2 final size:2
Alignment explanation
Indices: 49466928--49466960 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
49466918 GGAGTAATAT
49466928 TC TC TC 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 TC TC TC T
49466961 TTTTTTTTTA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:49477275 original size:13 final size:14
Alignment explanation
Indices: 49477250--49477282 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
49477240 TTTTCTCATC
49477250 TTCT-TCCCAAAAA
1 TTCTATCCCAAAAA
49477263 TTCTATCCCAAAAA
1 TTCTATCCCAAAAA
49477277 TTCTAT
1 TTCTAT
49477283 GGAGACTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.36, C:0.27, G:0.00, T:0.36
Consensus pattern (14 bp):
TTCTATCCCAAAAA
Found at i:49481799 original size:22 final size:22
Alignment explanation
Indices: 49481771--49481814 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
49481761 TCTTCTATCA
49481771 AGGTCTACAGCAAAATCAACAT
1 AGGTCTACAGCAAAATCAACAT
49481793 AGGTCTACAGCAAAATCAACAT
1 AGGTCTACAGCAAAATCAACAT
49481815 CAACATACCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.23, G:0.14, T:0.18
Consensus pattern (22 bp):
AGGTCTACAGCAAAATCAACAT
Found at i:49483531 original size:13 final size:13
Alignment explanation
Indices: 49483515--49483546 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
49483505 CTCCGTAATA
49483515 GTTCTGTTGATTC
1 GTTCTGTTGATTC
*
49483528 GTTCTATTGATTC
1 GTTCTGTTGATTC
49483541 GTTCTG
1 GTTCTG
49483547 CAACGCCATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.09, C:0.16, G:0.22, T:0.53
Consensus pattern (13 bp):
GTTCTGTTGATTC
Found at i:49485286 original size:5 final size:5
Alignment explanation
Indices: 49485276--49485303 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
49485266 CAATTTGTGA
49485276 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
49485304 GAACACACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:49496644 original size:52 final size:51
Alignment explanation
Indices: 49496583--49496690 Score: 182
Period size: 52 Copynumber: 2.1 Consensus size: 51
49496573 ATAAATAATA
49496583 ATAATAAAATTATAGA-AATTGTTGCATATGAACATGAAATGTATTAAATTC
1 ATAATAAAATTATAGAGAA-TGTTGCATATGAACATGAAATGTATTAAATTC
*
49496634 ATAAGTAAAATTATAGAGAATGTTGCATATGAACATGAAATGTATTAAATTG
1 ATAA-TAAAATTATAGAGAATGTTGCATATGAACATGAAATGTATTAAATTC
49496686 ATAAT
1 ATAAT
49496691 TAATATATTT
Statistics
Matches: 54, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
51 5 0.09
52 47 0.87
53 2 0.04
ACGTcount: A:0.47, C:0.05, G:0.14, T:0.34
Consensus pattern (51 bp):
ATAATAAAATTATAGAGAATGTTGCATATGAACATGAAATGTATTAAATTC
Found at i:49505567 original size:42 final size:42
Alignment explanation
Indices: 49505511--49505651 Score: 122
Period size: 42 Copynumber: 3.4 Consensus size: 42
49505501 TTGTCTTTAC
* * * *
49505511 TTTCCGTTTAGCTCTCACAAGCTTTTGTTTAACTCATATGAG
1 TTTCCGTTCAGCTCTTACAAGCTTTTATTTAACCCATATGAG
* ** *
49505553 TTTTCGTTCAGCTCTTTTGAA-CTTTTATTTAACCCTTATGAG
1 TTTCCGTTCAGCTC-TTACAAGCTTTTATTTAACCCATATGAG
* * * * * *
49505595 TTTCCGTTCAGCTCTTACGAGCTTTCATTCAACACTTATGGG
1 TTTCCGTTCAGCTCTTACAAGCTTTTATTTAACCCATATGAG
* *
49505637 TTTCTGTTTAGCTCT
1 TTTCCGTTCAGCTCT
49505652 CATGAGCTTC
Statistics
Matches: 79, Mismatches: 18, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
41 3 0.04
42 73 0.92
43 3 0.04
ACGTcount: A:0.18, C:0.22, G:0.14, T:0.45
Consensus pattern (42 bp):
TTTCCGTTCAGCTCTTACAAGCTTTTATTTAACCCATATGAG
Found at i:49508220 original size:31 final size:31
Alignment explanation
Indices: 49508185--49508245 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
49508175 TGCACTACTG
49508185 TACTTTCTCAACTTAATTTTACTAGTCCAAT
1 TACTTTCTCAACTTAATTTTACTAGTCCAAT
49508216 TACTTTCTCAACTTAATTTTACTAGTCCAA
1 TACTTTCTCAACTTAATTTTACTAGTCCAA
49508246 GGCTTATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.30, C:0.23, G:0.03, T:0.44
Consensus pattern (31 bp):
TACTTTCTCAACTTAATTTTACTAGTCCAAT
Found at i:49511617 original size:16 final size:17
Alignment explanation
Indices: 49511596--49511641 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
49511586 AGCAGGGGTG
49511596 GAGAAAGGGAGAGGA-A
1 GAGAAAGGGAGAGGAGA
*
49511612 GAGAAAGAGAGA-GAGA
1 GAGAAAGGGAGAGGAGA
49511628 GAGAAAAGGGAGAG
1 GAG-AAAGGGAGAG
49511642 AGGGTTTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 2 0.08
16 15 0.60
17 8 0.32
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (17 bp):
GAGAAAGGGAGAGGAGA
Found at i:49525562 original size:10 final size:10
Alignment explanation
Indices: 49525549--49525592 Score: 70
Period size: 10 Copynumber: 4.4 Consensus size: 10
49525539 TATGTGTATG
49525549 TATATATTTT
1 TATATATTTT
*
49525559 TATATATTTA
1 TATATATTTT
49525569 TATATATTTT
1 TATATATTTT
*
49525579 TATATATATT
1 TATATATTTT
49525589 TATA
1 TATA
49525593 CATATTTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TATATATTTT
Found at i:49525574 original size:12 final size:12
Alignment explanation
Indices: 49525549--49525619 Score: 64
Period size: 10 Copynumber: 6.4 Consensus size: 12
49525539 TATGTGTATG
49525549 TATATATTT-T-
1 TATATATTTATA
49525559 TATATATTTATA
1 TATATATTTATA
49525571 TATAT-TTT-TA
1 TATATATTTATA
49525581 TATATATTTATA
1 TATATATTTATA
*
49525593 CATAT-TTTA-A
1 TATATATTTATA
* * *
49525603 TACATATCTACA
1 TATATATTTATA
49525615 TATAT
1 TATAT
49525620 CTAAATACCC
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
10 20 0.40
11 14 0.28
12 16 0.32
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (12 bp):
TATATATTTATA
Found at i:49525584 original size:22 final size:22
Alignment explanation
Indices: 49525549--49525619 Score: 83
Period size: 22 Copynumber: 3.3 Consensus size: 22
49525539 TATGTGTATG
49525549 TATATA-TTTT-TATATATTTA
1 TATATATTTTTATATATATTTA
49525569 TATATATTTTTATATATATTTA
1 TATATATTTTTATATATATTTA
* * * *
49525591 TACATATTTTAATACATATCTA
1 TATATATTTTTATATATATTTA
*
49525613 CATATAT
1 TATATAT
49525620 CTAAATACCC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.14
21 4 0.09
22 33 0.77
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (22 bp):
TATATATTTTTATATATATTTA
Found at i:49525597 original size:10 final size:10
Alignment explanation
Indices: 49525549--49525599 Score: 66
Period size: 10 Copynumber: 4.9 Consensus size: 10
49525539 TATGTGTATG
*
49525549 TATATATTTT
1 TATATATTTA
49525559 TATATATTTA
1 TATATATTTA
49525569 TATATATTTTTA
1 TATATA--TTTA
49525581 TATATATTTA
1 TATATATTTA
*
49525591 TACATATTT
1 TATATATTT
49525600 TAATACATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
10 27 0.73
12 10 0.27
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (10 bp):
TATATATTTA
Found at i:49527962 original size:23 final size:23
Alignment explanation
Indices: 49527934--49527980 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
49527924 AGAACACCGT
49527934 AAGAATTTATTATTGACAATAAG
1 AAGAATTTATTATTGACAATAAG
*
49527957 AAGAATTTATTATTGACCATAAG
1 AAGAATTTATTATTGACAATAAG
49527980 A
1 A
49527981 GAAAAACTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.47, C:0.06, G:0.13, T:0.34
Consensus pattern (23 bp):
AAGAATTTATTATTGACAATAAG
Found at i:49529862 original size:39 final size:38
Alignment explanation
Indices: 49529819--49529907 Score: 90
Period size: 39 Copynumber: 2.3 Consensus size: 38
49529809 TATTGGCATC
** *
49529819 TTAATATTTTTTTTAATGTTTATGTTATAATATTATAT-A
1 TTAATATTTTTAGT-ATGTTTATGTTATAA-ATTACATAA
* *
49529858 TTAATATGATTTAGTATTTTTATGTTATAAATTACATAA
1 TTAATAT-TTTTAGTATGTTTATGTTATAAATTACATAA
49529897 TATAATATTTT
1 T-TAATATTTT
49529908 AACAAATTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
38 6 0.15
39 25 0.61
40 10 0.24
ACGTcount: A:0.36, C:0.01, G:0.06, T:0.57
Consensus pattern (38 bp):
TTAATATTTTTAGTATGTTTATGTTATAAATTACATAA
Found at i:49534336 original size:32 final size:30
Alignment explanation
Indices: 49534288--49534357 Score: 79
Period size: 32 Copynumber: 2.3 Consensus size: 30
49534278 AAATTTTAAA
* *
49534288 TTAATAAA-AATAAAATTATATTTTTATCTCTT
1 TTAA-AAATAATAAAATTATAATTTAAT-T-TT
*
49534320 TTAAAAATAATAAAATTTTAATTTAATTTT
1 TTAAAAATAATAAAATTATAATTTAATTTT
49534350 TTAAAAAT
1 TTAAAAAT
49534358 TATATTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 10 0.29
31 4 0.12
32 20 0.59
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (30 bp):
TTAAAAATAATAAAATTATAATTTAATTTT
Found at i:49534870 original size:19 final size:19
Alignment explanation
Indices: 49534846--49534884 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
49534836 CAAGATTAGC
49534846 TGCAACATGCTTTCCTTCG
1 TGCAACATGCTTTCCTTCG
49534865 TGCAACATGCTTTCCTTCG
1 TGCAACATGCTTTCCTTCG
49534884 T
1 T
49534885 ACGGGGGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.31, G:0.15, T:0.38
Consensus pattern (19 bp):
TGCAACATGCTTTCCTTCG
Found at i:49535784 original size:28 final size:28
Alignment explanation
Indices: 49535739--49535794 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
49535729 GGGCTTGAAT
* * *
49535739 AATATTATTTTATAAATTATAAATTATA
1 AATATTATTTTAAAAATTAAAAAATATA
49535767 AATA-TATTTTAAATAATTAAAAAATATA
1 AATATTATTTTAAA-AATTAAAAAATATA
49535795 TTAAATTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
AATATTATTTTAAAAATTAAAAAATATA
Found at i:49535798 original size:20 final size:21
Alignment explanation
Indices: 49535760--49535800 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
49535750 ATAAATTATA
* *
49535760 AATTATAAATATATTTTAAAT
1 AATTATAAAAATATATTAAAT
49535781 AATTA-AAAAATATATTAAAT
1 AATTATAAAAATATATTAAAT
49535801 TAAAATTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AATTATAAAAATATATTAAAT
Found at i:49541255 original size:4 final size:4
Alignment explanation
Indices: 49541246--49541276 Score: 53
Period size: 4 Copynumber: 7.5 Consensus size: 4
49541236 TCTTTTTCTC
49541246 TTTA TTTA TTTA TTTA TTTA TTTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TT
49541277 ATTATTAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 22 0.85
5 4 0.15
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:49541263 original size:12 final size:13
Alignment explanation
Indices: 49541246--49541276 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
49541236 TCTTTTTCTC
49541246 TTTATTTA-TTTA
1 TTTATTTATTTTA
49541258 TTTATTTATTTTA
1 TTTATTTATTTTA
49541271 TTTATT
1 TTTATT
49541277 ATTATTAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTATTTATTTTA
Found at i:49541311 original size:22 final size:23
Alignment explanation
Indices: 49541286--49541334 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
49541276 TATTATTAAC
49541286 TTTAAAA-ATTTTGA-AATATATA
1 TTTAAAATATTTT-ATAATATATA
49541308 TTTAAAATATTTTATTAATATATA
1 TTTAAAATATTTTA-TAATATATA
49541332 TTT
1 TTT
49541335 TGAAATTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.33
23 5 0.21
24 11 0.46
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TTTAAAATATTTTATAATATATA
Found at i:49541372 original size:21 final size:21
Alignment explanation
Indices: 49541347--49541435 Score: 78
Period size: 23 Copynumber: 4.1 Consensus size: 21
49541337 AAATTACTTT
49541347 TTTTTTAAT-TTTAAATATTA
1 TTTTTTAATATTTAAATATTA
49541367 TTTTTTAATATTTAAATATT-
1 TTTTTTAATATTTAAATATTA
* *
49541387 TTAAACTTTCAA-ATTT-ATTATTA
1 TT----TTTTAATATTTAAATATTA
49541410 TTTTTATAATAATTTAAATATTA
1 TTTTT-TAAT-ATTTAAATATTA
49541433 TTT
1 TTT
49541436 AATTTGTTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 17
0.72 0.05 0.22
Matches are distributed among these distances:
19 3 0.05
20 13 0.24
21 10 0.18
22 9 0.16
23 15 0.27
24 5 0.09
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTTTAATATTTAAATATTA
Found at i:49541471 original size:20 final size:21
Alignment explanation
Indices: 49541422--49541472 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
49541412 TTTATAATAA
*
49541422 TTTAAATATTATTTAATTTGT
1 TTTAAATATTATTAAATTTGT
49541443 TTTATAATATT-TTAAATTAT-T
1 TTTA-AATATTATTAAATT-TGT
49541464 TTTAAATAT
1 TTTAAATAT
49541473 ATTCAAACCA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 5 0.19
21 15 0.56
22 7 0.26
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
TTTAAATATTATTAAATTTGT
Found at i:49541681 original size:4 final size:4
Alignment explanation
Indices: 49541672--49541697 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
49541662 TTTTATTTTG
49541672 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
49541698 GTTATTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:49541775 original size:19 final size:22
Alignment explanation
Indices: 49541738--49541780 Score: 65
Period size: 19 Copynumber: 2.1 Consensus size: 22
49541728 ATTTGAAATG
49541738 TTTTATAATATATATTTTTAAA
1 TTTTATAATATATATTTTTAAA
49541760 TTTTA-AATAT-TA-TTTTAAA
1 TTTTATAATATATATTTTTAAA
49541779 TT
1 TT
49541781 ATTTTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 9 0.43
20 2 0.10
21 5 0.24
22 5 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTTATAATATATATTTTTAAA
Found at i:49541785 original size:22 final size:22
Alignment explanation
Indices: 49541705--49541778 Score: 62
Period size: 23 Copynumber: 3.4 Consensus size: 22
49541695 ATTGTTATTA
* * *
49541705 ATTTTAAAAAATTTAAAATGTAT
1 ATTTT-AAAATTTTATAATATAT
* *
49541728 ATTTGAAATGTTTTATAATATAT
1 ATTTTAAA-ATTTTATAATATAT
*
49541751 ATTTTTAAATTTTA-AATAT-T
1 ATTTTAAAATTTTATAATATAT
49541771 ATTTTAAA
1 ATTTTAAA
49541779 TTATTTTTAA
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
20 8 0.20
21 5 0.12
22 8 0.20
23 20 0.49
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (22 bp):
ATTTTAAAATTTTATAATATAT
Found at i:49541831 original size:21 final size:22
Alignment explanation
Indices: 49541779--49541848 Score: 79
Period size: 23 Copynumber: 3.1 Consensus size: 22
49541769 TTATTTTAAA
* *
49541779 TTATTTTTAAAATTTTGAATAT
1 TTATTTTTAAAATATTAAATAT
*
49541801 TATTTTTTTAAAA-ATTAAATAT
1 T-TATTTTTAAAATATTAAATAT
*
49541823 TTATTTTTAATAATATAAAATAT
1 TTATTTTTAA-AATATTAAATAT
49541846 TTA
1 TTA
49541849 AATATTTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
21 8 0.20
22 11 0.28
23 21 0.52
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (22 bp):
TTATTTTTAAAATATTAAATAT
Found at i:49542215 original size:14 final size:15
Alignment explanation
Indices: 49542196--49542228 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
49542186 ATCTTTAAAA
49542196 ATAATTTAAAA-ATT
1 ATAATTTAAAATATT
49542210 ATAATTTAAAATATT
1 ATAATTTAAAATATT
49542225 ATAA
1 ATAA
49542229 AACAAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATAATTTAAAATATT
Found at i:49542316 original size:31 final size:31
Alignment explanation
Indices: 49542203--49542319 Score: 96
Period size: 31 Copynumber: 3.6 Consensus size: 31
49542193 AAAATAATTT
* *
49542203 AAAAATTATAATTTAAAATATTATAAAA-CAA
1 AAAAATAAT-ATTTAAAATATTATAAAATTAA
* *
49542234 ATTAAATAATATTTAAATTATTATAAAATTAA
1 A-AAAATAATATTTAAAATATTATAAAATTAA
49542266 TAATAAATTTGAA-AGTTTAAAATATT-TAAATATTAA
1 -AA-AAA--T-AATA-TTTAAAATATTATAAA-ATTAA
49542302 AAAAATAATATTTAAAAT
1 AAAAATAATATTTAAAAT
49542320 TAAAAAAGTA
Statistics
Matches: 70, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
31 28 0.40
32 10 0.14
33 4 0.06
34 3 0.04
35 8 0.11
36 17 0.24
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (31 bp):
AAAAATAATATTTAAAATATTATAAAATTAA
Found at i:49542323 original size:21 final size:21
Alignment explanation
Indices: 49542286--49542339 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
49542276 GAAAGTTTAA
49542286 AATATTTAAATATTAAAAAAAT
1 AATATTTAAA-ATTAAAAAAAT
*
49542308 AATATTTAAAATTAAAAAAGT
1 AATATTTAAAATTAAAAAAAT
*
49542329 AAT-TTCAAAAT
1 AATATTTAAAAT
49542340 ATATATTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 7 0.23
21 13 0.43
22 10 0.33
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (21 bp):
AATATTTAAAATTAAAAAAAT
Found at i:49542403 original size:4 final size:4
Alignment explanation
Indices: 49542394--49542433 Score: 53
Period size: 4 Copynumber: 9.5 Consensus size: 4
49542384 AGTTAATAAT
*
49542394 AATA AATA AATA AGTAA AATA AATA AATAA AATA AATA AA
1 AATA AATA AATA AAT-A AATA AATA AAT-A AATA AATA AA
49542434 AATACAAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 25 0.78
5 7 0.22
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:49542415 original size:13 final size:13
Alignment explanation
Indices: 49542397--49542433 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
49542387 TAATAATAAT
*
49542397 AAATAAATAAGTA
1 AAATAAATAAATA
49542410 AAATAAATAAATA
1 AAATAAATAAATA
49542423 AAATAAATAAA
1 AAATAAATAAA
49542434 AATACAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.22
Consensus pattern (13 bp):
AAATAAATAAATA
Found at i:49542430 original size:17 final size:17
Alignment explanation
Indices: 49542388--49542433 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
49542378 TTTTAAAGTT
49542388 AATAATAATAAATAAATA
1 AATAA-AATAAATAAATA
*
49542406 AGTAAAATAAATAAATA
1 AATAAAATAAATAAATA
49542423 AA-ATAAATAAA
1 AATA-AAATAAA
49542434 AATACAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 1 0.04
17 20 0.80
18 4 0.16
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (17 bp):
AATAAAATAAATAAATA
Found at i:49558449 original size:25 final size:25
Alignment explanation
Indices: 49558419--49558471 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
49558409 TTGAAGTCAA
49558419 AATTATGTACTCAACCTAAATAAAT
1 AATTATGTACTCAACCTAAATAAAT
49558444 AATTATGTACTCAACCTAAATAAAT
1 AATTATGTACTCAACCTAAATAAAT
49558469 AAT
1 AAT
49558472 AAGGTTTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.49, C:0.15, G:0.04, T:0.32
Consensus pattern (25 bp):
AATTATGTACTCAACCTAAATAAAT
Found at i:49572074 original size:24 final size:24
Alignment explanation
Indices: 49572047--49572092 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
49572037 TACAATTTTA
49572047 AAAAT-CAAGTAATAGAAAGAATTC
1 AAAATGCAAGT-ATAGAAAGAATTC
* *
49572071 AAAATGTAAGTATAGAATGAAT
1 AAAATGCAAGTATAGAAAGAAT
49572093 CTGAACAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.57, C:0.04, G:0.15, T:0.24
Consensus pattern (24 bp):
AAAATGCAAGTATAGAAAGAATTC
Found at i:49572294 original size:53 final size:53
Alignment explanation
Indices: 49572232--49572391 Score: 320
Period size: 53 Copynumber: 3.0 Consensus size: 53
49572222 GAGCAACTAC
49572232 GAATAATTACATTCAATTTAGAATTATTAAATATCCAAATATGAGTAATACAA
1 GAATAATTACATTCAATTTAGAATTATTAAATATCCAAATATGAGTAATACAA
49572285 GAATAATTACATTCAATTTAGAATTATTAAATATCCAAATATGAGTAATACAA
1 GAATAATTACATTCAATTTAGAATTATTAAATATCCAAATATGAGTAATACAA
49572338 GAATAATTACATTCAATTTAGAATTATTAAATATCCAAATATGAGTAATACAA
1 GAATAATTACATTCAATTTAGAATTATTAAATATCCAAATATGAGTAATACAA
49572391 G
1 G
49572392 CGTGTAATAT
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 107 1.00
ACGTcount: A:0.49, C:0.09, G:0.08, T:0.34
Consensus pattern (53 bp):
GAATAATTACATTCAATTTAGAATTATTAAATATCCAAATATGAGTAATACAA
Found at i:49574768 original size:14 final size:15
Alignment explanation
Indices: 49574749--49574781 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
49574739 GTTAATTAGG
49574749 TTTAATTAT-AATAA
1 TTTAATTATGAATAA
49574763 TTTAATTATGAATAA
1 TTTAATTATGAATAA
49574778 TTTA
1 TTTA
49574782 TCATTGGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (15 bp):
TTTAATTATGAATAA
Found at i:49575472 original size:24 final size:24
Alignment explanation
Indices: 49575445--49575496 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
49575435 GAGTAAAGAT
49575445 TATTAAAAATT-GTAAATATTAAAA
1 TATTAAAAATTAG-AAATATTAAAA
* *
49575469 TATTAATAATTAGAAATTTTAAAA
1 TATTAAAAATTAGAAATATTAAAA
49575493 -ATTA
1 TATTA
49575497 TAGTAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 4 0.16
24 20 0.80
25 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (24 bp):
TATTAAAAATTAGAAATATTAAAA
Found at i:49577724 original size:27 final size:27
Alignment explanation
Indices: 49577652--49577722 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 27
49577642 AAATAAGTAA
49577652 AAATA-ATAAAATTTTAAAATTTAAATT
1 AAATATAT-AAATTTTAAAATTTAAATT
*
49577679 AAATATATATATTTT-AAATTTAAGATT
1 AAATATATAAATTTTAAAATTTAA-ATT
49577706 AAAT-T-TAAATTTTAAAA
1 AAATATATAAATTTTAAAA
49577723 ATATTAACTT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
25 7 0.18
26 12 0.31
27 18 0.46
28 2 0.05
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (27 bp):
AAATATATAAATTTTAAAATTTAAATT
Found at i:49577930 original size:13 final size:12
Alignment explanation
Indices: 49577907--49577941 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
49577897 CATGTATCTC
49577907 TATTTTTTTAAA
1 TATTTTTTTAAA
49577919 TATTTATTTTAAA
1 TATTT-TTTTAAA
*
49577932 TAGTTTTTTA
1 TATTTTTTTA
49577942 TACTCCTACG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (12 bp):
TATTTTTTTAAA
Found at i:49578124 original size:11 final size:10
Alignment explanation
Indices: 49578099--49578128 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
49578089 TTTGCACTTG
49578099 TATTTTTAAT
1 TATTTTTAAT
49578109 TATTTTTAAT
1 TATTTTTAAT
49578119 TAATTTTTAA
1 T-ATTTTTAA
49578129 GATTTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.58
11 8 0.42
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TATTTTTAAT
Found at i:49578141 original size:22 final size:22
Alignment explanation
Indices: 49578116--49578167 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 22
49578106 AATTATTTTT
49578116 AATTAATTTT-TAAGATTTTAAA
1 AATTAATTTTATAA-ATTTTAAA
* *
49578138 AATTCAGTTTTATAATTTTTAAA
1 AATT-AATTTTATAAATTTTAAA
49578161 AACTTAA
1 AA-TTAA
49578168 AAAAAATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
22 4 0.17
23 15 0.62
24 5 0.21
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (22 bp):
AATTAATTTTATAAATTTTAAA
Found at i:49578323 original size:22 final size:22
Alignment explanation
Indices: 49578295--49578338 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
49578285 TCAATACTTT
49578295 GACACATGACATATTCTTATTG
1 GACACATGACATATTCTTATTG
49578317 GACACATGACATATTCTTATTG
1 GACACATGACATATTCTTATTG
49578339 ATTGAATGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (22 bp):
GACACATGACATATTCTTATTG
Found at i:49584221 original size:15 final size:15
Alignment explanation
Indices: 49584197--49584235 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
49584187 CTCCGCTCAA
49584197 TTATTCTTCTCTCACT
1 TTATTCTTCTCT-ACT
49584213 TTATT-TTCTCTACT
1 TTATTCTTCTCTACT
49584227 TT-TTCTTCT
1 TTATTCTTCT
49584236 TTTCTCTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 2 0.09
14 9 0.41
15 6 0.27
16 5 0.23
ACGTcount: A:0.10, C:0.26, G:0.00, T:0.64
Consensus pattern (15 bp):
TTATTCTTCTCTACT
Found at i:49584251 original size:19 final size:19
Alignment explanation
Indices: 49584216--49584252 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
49584206 TCTCACTTTA
* *
49584216 TTTTCTCTACTTTTTCTTC
1 TTTTCTCTAATTCTTCTTC
49584235 TTTTCTCTAATTCTTCTT
1 TTTTCTCTAATTCTTCTT
49584253 TCTTGAATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTCTCTAATTCTTCTTC
Found at i:49589675 original size:14 final size:14
Alignment explanation
Indices: 49589635--49589664 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
49589625 CCGTTAGTGA
*
49589635 ATAAATACATAAAT
1 ATAAATAAATAAAT
49589649 ATAAATAAATAAAT
1 ATAAATAAATAAAT
49589663 AT
1 AT
49589665 TTATATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (14 bp):
ATAAATAAATAAAT
Found at i:49597407 original size:47 final size:48
Alignment explanation
Indices: 49597296--49597520 Score: 182
Period size: 47 Copynumber: 4.8 Consensus size: 48
49597286 TTTGTTTGTA
** *
49597296 AGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCAACCA-T-ATTATGAG
1 AGCTAGTGTAAGACCATGTCTGGGACATGGCATC-GGCATTGA-GATGAG
* *
49597342 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGAG
1 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGATGAG
** * *
49597390 AGCTAGTGTAAGA-CATGTCTGGGGTAT-GCATCGGC-TACGAGATGAT
1 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT-TGAGATGAG
* * * * *
49597436 AG-TCAGTATAAGACCGTGTCTGGGATATGGCATCGAC-TTTAGAT-ATG
1 AGCT-AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGATGA-G
* * *
49597483 AGCTAGTGTAAGACCATATTTGGGACATGGCATGGGCA
1 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
49597521 CCTTACCCAC
Statistics
Matches: 143, Mismatches: 25, Indels: 20
0.76 0.13 0.11
Matches are distributed among these distances:
45 2 0.01
46 37 0.26
47 72 0.50
48 31 0.22
49 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.25
Consensus pattern (48 bp):
AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGATGAG
Found at i:49597457 original size:94 final size:93
Alignment explanation
Indices: 49597296--49597511 Score: 229
Period size: 94 Copynumber: 2.3 Consensus size: 93
49597286 TTTGTTTGTA
* * *
49597296 AGCTAGTGTAAGACATGTCTGGGACATGCATCAACCATATTATGAGAGCCAGTGTAAGACCATGT
1 AGCTAGTGTAAGACATGTCTGGGACATGCATCAACCAGATGATGAGAGCCAGTATAAGACCATGT
*
49597361 CTGGGACATGGCATCGGCATTGAGACGA-G
66 CTGGGACATGGCATCGAC-TTGAGA-GATG
** ** * * * *
49597390 AGCTAGTGTAAGACATGTCTGGGGTATGCATCGGCTACGA-GATGATAGTCAGTATAAGACCGTG
1 AGCTAGTGTAAGACATGTCTGGGACATGCATCAACCA-GATGATGAGAGCCAGTATAAGACCATG
* * *
49597454 TCTGGGATATGGCATCGACTTTAGATATG
65 TCTGGGACATGGCATCGACTTGAGAGATG
* *
49597483 AGCTAGTGTAAGACCATATTTGGGACATG
1 AGCTAGTGTAAGA-CATGTCTGGGACATG
49597512 GCATGGGCAC
Statistics
Matches: 100, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
92 1 0.01
93 19 0.19
94 79 0.79
95 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (93 bp):
AGCTAGTGTAAGACATGTCTGGGACATGCATCAACCAGATGATGAGAGCCAGTATAAGACCATGT
CTGGGACATGGCATCGACTTGAGAGATG
Found at i:49603745 original size:19 final size:19
Alignment explanation
Indices: 49603703--49603745 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
49603693 TGTAATTCCT
* *
49603703 AAAATACATACATCACATG
1 AAAATACATACAGCACAAG
*
49603722 AAAATACATCCAGCACAAG
1 AAAATACATACAGCACAAG
*
49603741 TAAAT
1 AAAAT
49603746 TATTATATCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.53, C:0.21, G:0.07, T:0.19
Consensus pattern (19 bp):
AAAATACATACAGCACAAG
Found at i:49605363 original size:6 final size:6
Alignment explanation
Indices: 49605356--49605387 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
49605346 GTGGCCATGG
*
49605356 AAATGG AAATGC AAATGC AAATGC AAATGC AA
1 AAATGC AAATGC AAATGC AAATGC AAATGC AA
49605388 CATTAGACTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.53, C:0.12, G:0.19, T:0.16
Consensus pattern (6 bp):
AAATGC
Found at i:49605608 original size:20 final size:20
Alignment explanation
Indices: 49605559--49605609 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
49605549 TTGGGTCAAA
49605559 TATATTTATATTTTTTATTAAT
1 TATA-TTATATTTTTTA-TAAT
*
49605581 TA-ATTATATTTTTTA-AGT
1 TATATTATATTTTTTATAAT
49605599 TATATATATAT
1 TATAT-TATAT
49605610 GTAATTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 4 0.15
19 2 0.08
20 17 0.65
21 1 0.04
22 2 0.08
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (20 bp):
TATATTATATTTTTTATAAT
Found at i:49606347 original size:13 final size:11
Alignment explanation
Indices: 49606298--49606340 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
49606288 TCTAAAATTC
49606298 AAAATATTTAT
1 AAAATATTTAT
*
49606309 AAAATATTTTTT
1 AAAATA-TTTAT
49606321 AAAA-ATTCTAT
1 AAAATATT-TAT
49606332 AAAATATTT
1 AAAATATTT
49606341 GTATAAATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
10 2 0.07
11 14 0.52
12 11 0.41
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (11 bp):
AAAATATTTAT
Found at i:49606357 original size:22 final size:23
Alignment explanation
Indices: 49606309--49606359 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
49606299 AAATATTTAT
* * *
49606309 AAAATATTTTTTAAAAATTCTAT
1 AAAATATTTTGTAAAAATTCAAA
*
49606332 AAAATA-TTTGTATAAATTCAAA
1 AAAATATTTTGTAAAAATTCAAA
49606354 AAAATA
1 AAAATA
49606360 AAAATATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (23 bp):
AAAATATTTTGTAAAAATTCAAA
Found at i:49614510 original size:46 final size:46
Alignment explanation
Indices: 49614441--49614530 Score: 135
Period size: 46 Copynumber: 2.0 Consensus size: 46
49614431 AGTCGTGAGA
* * *
49614441 TACTATATTATATGCATAGTATTTGTTTGTATAAAAGACAATGTCT
1 TACTATATTATACGCATAATATTTGTTTCTATAAAAGACAATGTCT
* *
49614487 TACTATATTGTACGCATAATATTTGTTTCTGTAAAAGACAATGT
1 TACTATATTATACGCATAATATTTGTTTCTATAAAAGACAATGT
49614531 ATTGATTTTC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.42
Consensus pattern (46 bp):
TACTATATTATACGCATAATATTTGTTTCTATAAAAGACAATGTCT
Found at i:49614628 original size:18 final size:18
Alignment explanation
Indices: 49614596--49614642 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
49614586 TTTATACTGA
49614596 GTTAATTTTAATT-AATT
1 GTTAATTTTAATTAAATT
49614613 GTTAATTTTGAATTAAATT
1 GTTAATTTT-AATTAAATT
49614632 G-TAA-TTTAATT
1 GTTAATTTTAATT
49614643 TCAAATTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 4 0.14
17 12 0.43
18 7 0.25
19 5 0.18
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (18 bp):
GTTAATTTTAATTAAATT
Found at i:49634323 original size:5 final size:5
Alignment explanation
Indices: 49634313--49634339 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
49634303 TATTGTTAAT
49634313 AACAC AACAC AACAC AACAC AACAC AA
1 AACAC AACAC AACAC AACAC AACAC AA
49634340 ACCATACCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.63, C:0.37, G:0.00, T:0.00
Consensus pattern (5 bp):
AACAC
Found at i:49640832 original size:875 final size:875
Alignment explanation
Indices: 49639142--49640891 Score: 3500
Period size: 875 Copynumber: 2.0 Consensus size: 875
49639132 TTTCTATGTG
49639142 CAAACTATTTTTAATTTACCTTATTTATTAGAAGTGAGACATTAAGTTGATGGTTTCTTTTCATA
1 CAAACTATTTTTAATTTACCTTATTTATTAGAAGTGAGACATTAAGTTGATGGTTTCTTTTCATA
49639207 TTAAAATGTGGAAAAAACCTTTTTATTAAAAGTGAAGATAATGATTTTTTATATTGTTAATGGAT
66 TTAAAATGTGGAAAAAACCTTTTTATTAAAAGTGAAGATAATGATTTTTTATATTGTTAATGGAT
49639272 AGAATATTAATGGTTGATACATGCCAGAACACTCAATTCCTTTGATTTGACTCTTTCCAAAAACA
131 AGAATATTAATGGTTGATACATGCCAGAACACTCAATTCCTTTGATTTGACTCTTTCCAAAAACA
49639337 TGCAATTAGTAGCTTTTGTAACACCCCTTGCCTAACCCGATCGTCGAGTCCAAGCTACAAGATGC
196 TGCAATTAGTAGCTTTTGTAACACCCCTTGCCTAACCCGATCGTCGAGTCCAAGCTACAAGATGC
49639402 TACATTCGTTACCGAAGTAACTACTGCAAATAAATTGTAAATAAATCAATTAAACATTCACACTT
261 TACATTCGTTACCGAAGTAACTACTGCAAATAAATTGTAAATAAATCAATTAAACATTCACACTT
49639467 GTAACACCCCAAGCCTGGCCTAGAAGTTTAGACCGAATTCAGAACGTTACATTGATCACCGAAGT
326 GTAACACCCCAAGCCTGGCCTAGAAGTTTAGACCGAATTCAGAACGTTACATTGATCACCGAAGT
49639532 GACCGCGAGAAAATATTATAAAATCATCCTTTATTCAATTTTCAAAAGCATTAATATCACATATT
391 GACCGCGAGAAAATATTATAAAATCATCCTTTATTCAATTTTCAAAAGCATTAATATCACATATT
49639597 TAAAATCAGAATAATAAAGCGATTAAATCGCCAGACAACATTATACCACAGTGTTTAAAAACCTT
456 TAAAATCAGAATAATAAAGCGATTAAATCGCCAGACAACATTATACCACAGTGTTTAAAAACCTT
49639662 ACATTCGAAATTAAATAACAAAAAAATCTGAAATCATGTGCTAATAATTTATTTGCCTCAAAACT
521 ACATTCGAAATTAAATAACAAAAAAATCTGAAATCATGTGCTAATAATTTATTTGCCTCAAAACT
49639727 GCCTGAGTCCTCCGTATACCGAGTCCAACATCCAAAATCCCGAAATGTACCTGAAAGGGGAAACA
586 GCCTGAGTCCTCCGTATACCGAGTCCAACATCCAAAATCCCGAAATGTACCTGAAAGGGGAAACA
49639792 GAAGAGGGGGTAAGCTATACGAGCTTAGTGTGTGATCAAACTAACTAGCTACCGAAGAAGAAACA
651 GAAGAGGGGGTAAGCTATACGAGCTTAGTGTGTGATCAAACTAACTAGCTACCGAAGAAGAAACA
49639857 GATACAATAAACCTGAAAATAGTTCAACAACGGGACATAGTTACAGAGCGACTATAACAAAATAG
716 GATACAATAAACCTGAAAATAGTTCAACAACGGGACATAGTTACAGAGCGACTATAACAAAATAG
49639922 ACCATGTGTAACTTTAAAGTCATATGGCTCTGTTAAACATAATATCGAAAATTTCCAGTAGTCAC
781 ACCATGTGTAACTTTAAAGTCATATGGCTCTGTTAAACATAATATCGAAAATTTCCAGTAGTCAC
49639987 AAACTGGCCTAAGCCCATTTCCAGAATCAA
846 AAACTGGCCTAAGCCCATTTCCAGAATCAA
49640017 CAAACTATTTTTAATTTACCTTATTTATTAGAAGTGAGACATTAAGTTGATGGTTTCTTTTCATA
1 CAAACTATTTTTAATTTACCTTATTTATTAGAAGTGAGACATTAAGTTGATGGTTTCTTTTCATA
49640082 TTAAAATGTGGAAAAAACCTTTTTATTAAAAGTGAAGATAATGATTTTTTATATTGTTAATGGAT
66 TTAAAATGTGGAAAAAACCTTTTTATTAAAAGTGAAGATAATGATTTTTTATATTGTTAATGGAT
49640147 AGAATATTAATGGTTGATACATGCCAGAACACTCAATTCCTTTGATTTGACTCTTTCCAAAAACA
131 AGAATATTAATGGTTGATACATGCCAGAACACTCAATTCCTTTGATTTGACTCTTTCCAAAAACA
49640212 TGCAATTAGTAGCTTTTGTAACACCCCTTGCCTAACCCGATCGTCGAGTCCAAGCTACAAGATGC
196 TGCAATTAGTAGCTTTTGTAACACCCCTTGCCTAACCCGATCGTCGAGTCCAAGCTACAAGATGC
49640277 TACATTCGTTACCGAAGTAACTACTGCAAATAAATTGTAAATAAATCAATTAAACATTCACACTT
261 TACATTCGTTACCGAAGTAACTACTGCAAATAAATTGTAAATAAATCAATTAAACATTCACACTT
49640342 GTAACACCCCAAGCCTGGCCTAGAAGTTTAGACCGAATTCAGAACGTTACATTGATCACCGAAGT
326 GTAACACCCCAAGCCTGGCCTAGAAGTTTAGACCGAATTCAGAACGTTACATTGATCACCGAAGT
49640407 GACCGCGAGAAAATATTATAAAATCATCCTTTATTCAATTTTCAAAAGCATTAATATCACATATT
391 GACCGCGAGAAAATATTATAAAATCATCCTTTATTCAATTTTCAAAAGCATTAATATCACATATT
49640472 TAAAATCAGAATAATAAAGCGATTAAATCGCCAGACAACATTATACCACAGTGTTTAAAAACCTT
456 TAAAATCAGAATAATAAAGCGATTAAATCGCCAGACAACATTATACCACAGTGTTTAAAAACCTT
49640537 ACATTCGAAATTAAATAACAAAAAAATCTGAAATCATGTGCTAATAATTTATTTGCCTCAAAACT
521 ACATTCGAAATTAAATAACAAAAAAATCTGAAATCATGTGCTAATAATTTATTTGCCTCAAAACT
49640602 GCCTGAGTCCTCCGTATACCGAGTCCAACATCCAAAATCCCGAAATGTACCTGAAAGGGGAAACA
586 GCCTGAGTCCTCCGTATACCGAGTCCAACATCCAAAATCCCGAAATGTACCTGAAAGGGGAAACA
49640667 GAAGAGGGGGTAAGCTATACGAGCTTAGTGTGTGATCAAACTAACTAGCTACCGAAGAAGAAACA
651 GAAGAGGGGGTAAGCTATACGAGCTTAGTGTGTGATCAAACTAACTAGCTACCGAAGAAGAAACA
49640732 GATACAATAAACCTGAAAATAGTTCAACAACGGGACATAGTTACAGAGCGACTATAACAAAATAG
716 GATACAATAAACCTGAAAATAGTTCAACAACGGGACATAGTTACAGAGCGACTATAACAAAATAG
49640797 ACCATGTGTAACTTTAAAGTCATATGGCTCTGTTAAACATAATATCGAAAATTTCCAGTAGTCAC
781 ACCATGTGTAACTTTAAAGTCATATGGCTCTGTTAAACATAATATCGAAAATTTCCAGTAGTCAC
49640862 AAACTGGCCTAAGCCCATTTCCAGAATCAA
846 AAACTGGCCTAAGCCCATTTCCAGAATCAA
49640892 AATCGGTTGG
Statistics
Matches: 875, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
875 875 1.00
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (875 bp):
CAAACTATTTTTAATTTACCTTATTTATTAGAAGTGAGACATTAAGTTGATGGTTTCTTTTCATA
TTAAAATGTGGAAAAAACCTTTTTATTAAAAGTGAAGATAATGATTTTTTATATTGTTAATGGAT
AGAATATTAATGGTTGATACATGCCAGAACACTCAATTCCTTTGATTTGACTCTTTCCAAAAACA
TGCAATTAGTAGCTTTTGTAACACCCCTTGCCTAACCCGATCGTCGAGTCCAAGCTACAAGATGC
TACATTCGTTACCGAAGTAACTACTGCAAATAAATTGTAAATAAATCAATTAAACATTCACACTT
GTAACACCCCAAGCCTGGCCTAGAAGTTTAGACCGAATTCAGAACGTTACATTGATCACCGAAGT
GACCGCGAGAAAATATTATAAAATCATCCTTTATTCAATTTTCAAAAGCATTAATATCACATATT
TAAAATCAGAATAATAAAGCGATTAAATCGCCAGACAACATTATACCACAGTGTTTAAAAACCTT
ACATTCGAAATTAAATAACAAAAAAATCTGAAATCATGTGCTAATAATTTATTTGCCTCAAAACT
GCCTGAGTCCTCCGTATACCGAGTCCAACATCCAAAATCCCGAAATGTACCTGAAAGGGGAAACA
GAAGAGGGGGTAAGCTATACGAGCTTAGTGTGTGATCAAACTAACTAGCTACCGAAGAAGAAACA
GATACAATAAACCTGAAAATAGTTCAACAACGGGACATAGTTACAGAGCGACTATAACAAAATAG
ACCATGTGTAACTTTAAAGTCATATGGCTCTGTTAAACATAATATCGAAAATTTCCAGTAGTCAC
AAACTGGCCTAAGCCCATTTCCAGAATCAA
Found at i:49642832 original size:12 final size:12
Alignment explanation
Indices: 49642815--49642845 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
49642805 CGTGCCTAGT
49642815 AAAATAAAATTA
1 AAAATAAAATTA
49642827 AAAATAAAATTA
1 AAAATAAAATTA
*
49642839 ATAATAA
1 AAAATAA
49642846 TTAATAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
AAAATAAAATTA
Found at i:49643589 original size:6 final size:6
Alignment explanation
Indices: 49643578--49643807 Score: 460
Period size: 6 Copynumber: 38.3 Consensus size: 6
49643568 TTACCCAAAC
49643578 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
49643626 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
49643674 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
49643722 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
49643770 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT AT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT AT
49643808 GGGAATTAAC
Statistics
Matches: 224, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 224 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
ATACAT
Found at i:49651413 original size:5 final size:6
Alignment explanation
Indices: 49651376--49651440 Score: 60
Period size: 6 Copynumber: 10.2 Consensus size: 6
49651366 CTTATACTTA
*
49651376 TATTTT TAATTTTT TATATAT T-TTTT TATTTT TATTTT GCTATTTT TATTTT
1 TATTTT T-A-TTTT TAT-TTT TATTTT TATTTT TATTTT --TATTTT TATTTT
*
49651428 TATTTC TATTTT T
1 TATTTT TATTTT T
49651441 TTCGTATTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
5 3 0.06
6 30 0.61
7 5 0.10
8 11 0.22
ACGTcount: A:0.18, C:0.03, G:0.02, T:0.77
Consensus pattern (6 bp):
TATTTT
Found at i:49651441 original size:20 final size:22
Alignment explanation
Indices: 49651394--49651442 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 22
49651384 ATTTTTTATA
49651394 TATTTTTTTATTTTTATTTTGC
1 TATTTTTTTATTTTTATTTTGC
49651416 TA--TTTTTATTTTTA-TTT-C
1 TATTTTTTTATTTTTATTTTGC
49651434 TATTTTTTT
1 TATTTTTTT
49651443 CGTATTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 3 0.12
19 3 0.12
20 17 0.68
22 2 0.08
ACGTcount: A:0.14, C:0.04, G:0.02, T:0.80
Consensus pattern (22 bp):
TATTTTTTTATTTTTATTTTGC
Found at i:49651454 original size:40 final size:40
Alignment explanation
Indices: 49651376--49651458 Score: 98
Period size: 40 Copynumber: 2.1 Consensus size: 40
49651366 CTTATACTTA
*
49651376 TATTTTTAATTTTTTATATATTTTTTTATTTTTATTTTGC
1 TATTTTTAATTTTTTATATATTTTTTTATATTTATTTTGC
* * *
49651416 TATTTTT-ATTTTTATTTCTATTTTTTTCGTATTT-TTTTGC
1 TATTTTTAATTTTT-TATATATTTTTTT-ATATTTATTTTGC
49651456 TAT
1 TAT
49651459 AATCATTACA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
39 6 0.16
40 27 0.73
41 4 0.11
ACGTcount: A:0.17, C:0.05, G:0.04, T:0.75
Consensus pattern (40 bp):
TATTTTTAATTTTTTATATATTTTTTTATATTTATTTTGC
Found at i:49652548 original size:11 final size:10
Alignment explanation
Indices: 49652532--49652561 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
49652522 CCATTGTTCT
49652532 AAAAAAAATG
1 AAAAAAAATG
*
49652542 AAAAAAAGTG
1 AAAAAAAATG
49652552 AAAAAAAATG
1 AAAAAAAATG
49652562 CATTTATGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (10 bp):
AAAAAAAATG
Found at i:49663247 original size:5 final size:6
Alignment explanation
Indices: 49663220--49663246 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
49663210 GCTAACCCAA
49663220 TTTTAT TTTTAT TTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTT
49663247 ACATTTTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:49664363 original size:34 final size:34
Alignment explanation
Indices: 49664320--49664386 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
49664310 TGAGAAGTCA
49664320 TTACTCCCTCACTCATTTGTTTTCATAATTGTCG
1 TTACTCCCTCACTCATTTGTTTTCATAATTGTCG
49664354 TTACTCCCTCACTCATTTGTTTTCATAATTGTC
1 TTACTCCCTCACTCATTTGTTTTCATAATTGTC
49664387 TTTATATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.18, C:0.27, G:0.07, T:0.48
Consensus pattern (34 bp):
TTACTCCCTCACTCATTTGTTTTCATAATTGTCG
Found at i:49666637 original size:23 final size:25
Alignment explanation
Indices: 49666611--49666657 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
49666601 TATCATTCAT
*
49666611 TTCATTATAT-CA-ATATTTTATGC
1 TTCATCATATCCATATATTTTATGC
*
49666634 TTCATCATTTCCATATATTTTATG
1 TTCATCATATCCATATATTTTATG
49666658 TATATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (25 bp):
TTCATCATATCCATATATTTTATGC
Found at i:49667178 original size:46 final size:44
Alignment explanation
Indices: 49666918--49667381 Score: 484
Period size: 46 Copynumber: 11.0 Consensus size: 44
49666908 TTTGACGTGA
* * * * * *
49666918 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTA-ACA-TTTCTATCAGGT
* * * *
49666964 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTA-ACATTTC-TATCAGGT
* * * *
49667010 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTA-ACATTTC-TATCAGGT
49667056 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTA-ACATTTC-TATCAGGT
49667102 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTA-ACATTTC-TATCAGGT
49667148 TGCCATGGTATCTTTCAACCATGGTCTT-ACA---C-A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTAACATTTCTATCAGGT
49667186 TGCCATGGTATCTTTCAACCATGGTCTT-ACA---C-A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTAACATTTCTATCAGGT
49667224 TGCCATGGTATCTTTCAACCATGGTCTT-ACA---C-A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTAACATTTCTATCAGGT
49667262 TGCCATGGTATCTTTCAACCATGGTCTT-ACA---C-A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTAACATTTCTATCAGGT
49667300 TGCCATGGTATCTTTCAACCATGGTCTT-ACA---C-A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTAACATTTCTATCAGGT
49667338 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTA-ACATTTC-TATCAG
49667382 NNNNNNNNNN
Statistics
Matches: 398, Mismatches: 11, Indels: 18
0.93 0.03 0.04
Matches are distributed among these distances:
38 185 0.46
39 1 0.00
40 3 0.01
41 1 0.00
43 1 0.00
44 3 0.01
45 5 0.01
46 199 0.50
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.37
Consensus pattern (44 bp):
TGCCATGGTATCTTTCAACCATGGTCTTAACATTTCTATCAGGT
Found at i:49667194 original size:38 final size:38
Alignment explanation
Indices: 49667143--49667370 Score: 456
Period size: 38 Copynumber: 6.0 Consensus size: 38
49667133 CATTTCATAT
49667143 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
49667181 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
49667219 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
49667257 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
49667295 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
49667333 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
49667371 TTTCATATCA
Statistics
Matches: 190, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 190 1.00
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (38 bp):
CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
Found at i:49668741 original size:27 final size:28
Alignment explanation
Indices: 49668711--49668787 Score: 72
Period size: 27 Copynumber: 2.8 Consensus size: 28
49668701 TATATACTAA
49668711 TAAAATAATAATAATAAAATATCTTAT-
1 TAAAATAATAATAATAAAATATCTTATC
* *
49668738 TAAAGTATTAATAA-AATAATAT-TTATC
1 TAAAATAATAATAATAA-AATATCTTATC
* *
49668765 T-AATTAAATAATTATAAAATATC
1 TAAAAT-AATAATAATAAAATATC
49668788 AAAATATCTC
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
26 9 0.22
27 29 0.73
28 2 0.05
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (28 bp):
TAAAATAATAATAATAAAATATCTTATC
Found at i:49669842 original size:5 final size:5
Alignment explanation
Indices: 49669832--49669863 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
49669822 CATTCTGTGA
49669832 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
49669864 GAACACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:49669857 original size:9 final size:9
Alignment explanation
Indices: 49669833--49669863 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
49669823 ATTCTGTGAA
49669833 AAATAAAAT
1 AAATAAAAT
49669842 AAAATAAAAT
1 -AAATAAAAT
49669852 AAATAAAAT
1 AAATAAAAT
49669861 AAA
1 AAA
49669864 GAACACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:49673856 original size:263 final size:263
Alignment explanation
Indices: 49673382--49673903 Score: 1026
Period size: 263 Copynumber: 2.0 Consensus size: 263
49673372 CACCATCGCT
* *
49673382 GTAGTCTTCTACAACATCAGCTTCACCGGAATTTTCTGGTTGTTTTCCCTTTTGATTCGCAGCCT
1 GTAGTCATCTACAACATCAGCTTCACCGAAATTTTCTGGTTGTTTTCCCTTTTGATTCGCAGCCT
49673447 CCCTTTTAATCTTATTTTGTAGCTTATAGCACTCAGATTTAATGTGCCCTTTCTTCTTGCAGAAG
66 CCCTTTTAATCTTATTTTGTAGCTTATAGCACTCAGATTTAATGTGCCCTTTCTTCTTGCAGAAG
49673512 TTACAAGTTTTACCTCTGTTTGAAGACTTCGATCTACCCTTAGATTTACCACGAGGATTCCGTTC
131 TTACAAGTTTTACCTCTGTTTGAAGACTTCGATCTACCCTTAGATTTACCACGAGGATTCCGTTC
49673577 CTGTGTCCTACCACGATCATCATCAGCATTCCGATCTTGTCTCCCACGAACAATGAGACCCTCTT
196 CTGTGTCCTACCACGATCATCATCAGCATTCCGATCTTGTCTCCCACGAACAATGAGACCCTCTT
49673642 CCA
261 CCA
49673645 GTAGTCATCTACAACATCAGCTTCACCGAAATTTTCTGGTTGTTTTCCCTTTTGATTCGCAGCCT
1 GTAGTCATCTACAACATCAGCTTCACCGAAATTTTCTGGTTGTTTTCCCTTTTGATTCGCAGCCT
49673710 CCCTTTTAATCTTATTTTGTAGCTTATAGCACTCAGATTTAATGTGCCCTTTCTTCTTGCAGAAG
66 CCCTTTTAATCTTATTTTGTAGCTTATAGCACTCAGATTTAATGTGCCCTTTCTTCTTGCAGAAG
49673775 TTACAAGTTTTACCTCTGTTTGAAGACTTCGATCTACCCTTAGATTTACCACGAGGATTCCGTTC
131 TTACAAGTTTTACCTCTGTTTGAAGACTTCGATCTACCCTTAGATTTACCACGAGGATTCCGTTC
49673840 CTGTGTCCTACCACGATCATCATCAGCATTCCGATCTTGTCTCCCACGAACAATGAGACCCTCT
196 CTGTGTCCTACCACGATCATCATCAGCATTCCGATCTTGTCTCCCACGAACAATGAGACCCTCT
49673904 CCCTGAGAGT
Statistics
Matches: 257, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
263 257 1.00
ACGTcount: A:0.22, C:0.27, G:0.15, T:0.36
Consensus pattern (263 bp):
GTAGTCATCTACAACATCAGCTTCACCGAAATTTTCTGGTTGTTTTCCCTTTTGATTCGCAGCCT
CCCTTTTAATCTTATTTTGTAGCTTATAGCACTCAGATTTAATGTGCCCTTTCTTCTTGCAGAAG
TTACAAGTTTTACCTCTGTTTGAAGACTTCGATCTACCCTTAGATTTACCACGAGGATTCCGTTC
CTGTGTCCTACCACGATCATCATCAGCATTCCGATCTTGTCTCCCACGAACAATGAGACCCTCTT
CCA
Found at i:49677598 original size:18 final size:18
Alignment explanation
Indices: 49677575--49677626 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
49677565 AAAATGTGAG
*
49677575 AAATGATATTCACATTTT
1 AAATGATATTCACATTTC
* *
49677593 AAATGATGTTCAGATTTC
1 AAATGATATTCACATTTC
*
49677611 AAATGATTTTCACATT
1 AAATGATATTCACATT
49677627 GATGGGAACG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.42
Consensus pattern (18 bp):
AAATGATATTCACATTTC
Found at i:49678167 original size:72 final size:72
Alignment explanation
Indices: 49678050--49678361 Score: 344
Period size: 72 Copynumber: 4.3 Consensus size: 72
49678040 CAATGCTAAA
*
49678050 CTAGTTTTATCAATAGTTA-TTTATGTTTGGTTTTTGGATATTGAATTTTTGTTCTACTTATTTA
1 CTAGTTTTATCAATAG-TAGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTA
49678114 TGTGTAAT
65 TGTGTAAT
* * * *
49678122 CTAGTTTTATCAATGGCAGTTTATGTTTGGTTTTTAGATATTGAATTTATATTCTACTTATTTAT
1 CTAGTTTTATCAATAGTAGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
49678187 GTGTAAT
66 GTGTAAT
* * * * * * * *
49678194 CTAGTTTTATTAATAGTTGTTTATGTTTGGTCTTTGGATGTTGAAGTGATGGTCTAATTATTTAT
1 CTAGTTTTATCAATAGTAGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
**
49678259 GCT-TAGGG
66 G-TGTA-AT
* * * * * *
49678267 CTAGTTTTATCAATAATTGTTTATGGTTGATTTTGGGATATTAAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTAGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
* *
49678332 ACT-AAAT
66 -GTGTAAT
*
49678339 -TAGTTTTATCAATAGTTGTTTAT
1 CTAGTTTTATCAATAGTAGTTTAT
49678362 ATATGATTTT
Statistics
Matches: 200, Mismatches: 36, Indels: 9
0.82 0.15 0.04
Matches are distributed among these distances:
71 23 0.12
72 121 0.61
73 56 0.28
ACGTcount: A:0.24, C:0.06, G:0.17, T:0.53
Consensus pattern (72 bp):
CTAGTTTTATCAATAGTAGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
GTGTAAT
Found at i:49679739 original size:9 final size:9
Alignment explanation
Indices: 49679725--49679780 Score: 76
Period size: 9 Copynumber: 6.2 Consensus size: 9
49679715 GTCAAGAAAG
*
49679725 TGATAATGA
1 TGATAACGA
49679734 TGATAACGA
1 TGATAACGA
*
49679743 TGATGACGA
1 TGATAACGA
*
49679752 TGATAATGA
1 TGATAACGA
49679761 TGATAACGA
1 TGATAACGA
*
49679770 TGATGACGA
1 TGATAACGA
49679779 TG
1 TG
49679781 CAGATTTTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 41 1.00
ACGTcount: A:0.39, C:0.07, G:0.27, T:0.27
Consensus pattern (9 bp):
TGATAACGA
Found at i:49679755 original size:27 final size:27
Alignment explanation
Indices: 49679725--49679780 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
49679715 GTCAAGAAAG
49679725 TGATAATGATGATAACGATGATGACGA
1 TGATAATGATGATAACGATGATGACGA
49679752 TGATAATGATGATAACGATGATGACGA
1 TGATAATGATGATAACGATGATGACGA
49679779 TG
1 TG
49679781 CAGATTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.39, C:0.07, G:0.27, T:0.27
Consensus pattern (27 bp):
TGATAATGATGATAACGATGATGACGA
Found at i:49679884 original size:135 final size:135
Alignment explanation
Indices: 49679642--49679890 Score: 482
Period size: 135 Copynumber: 1.8 Consensus size: 135
49679632 CGGTCGAAAT
49679642 GATGCAGATTTTATGGAATACGAAGATATTAATAGGGCATATGAGAATATTATTGATTCAGAAAA
1 GATGCAGATTTTATGGAATACGAAGATATTAATAGGGCATATGAGAATATTATTGATTCAGAAAA
49679707 TGCGCATGGTCAAGAAAGTGATAATGATGATAACGATGATGACGATGATAATGATGATAACGATG
66 TGCGCATGGTCAAGAAAGTGATAATGATGATAACGATGATGACGATGATAATGATGATAACGATG
49679772 ATGAC
131 ATGAC
49679777 GATGCAGATTTTATGGAATACGAAGATATTAATAGGGCATATGAGAATATTATTGATTCAGAAAA
1 GATGCAGATTTTATGGAATACGAAGATATTAATAGGGCATATGAGAATATTATTGATTCAGAAAA
49679842 TGCGCATGGT-ATAGAAAGTGATAATGATGATAACGATGATGACGATGAT
66 TGCGCATGGTCA-AGAAAGTGATAATGATGATAACGATGATGACGATGAT
49679891 GATGGTAATG
Statistics
Matches: 113, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
134 1 0.01
135 112 0.99
ACGTcount: A:0.40, C:0.08, G:0.24, T:0.28
Consensus pattern (135 bp):
GATGCAGATTTTATGGAATACGAAGATATTAATAGGGCATATGAGAATATTATTGATTCAGAAAA
TGCGCATGGTCAAGAAAGTGATAATGATGATAACGATGATGACGATGATAATGATGATAACGATG
ATGAC
Found at i:49682891 original size:27 final size:27
Alignment explanation
Indices: 49682861--49683002 Score: 70
Period size: 27 Copynumber: 5.3 Consensus size: 27
49682851 CGACTTGTAA
49682861 AATTACCAAAGTACTCC-CGATTTACAG
1 AATTACCAAAGTAC-CCTCGATTTACAG
****
49682888 AATTACCGTTTTACCCTCGATTTACAG
1 AATTACCAAAGTACCCTCGATTTACAG
**** * ** *
49682915 AATTACCGTTTTACCCTCAATTTTTAA
1 AATTACCAAAGTACCCTCGATTTACAG
*****
49682942 AATTACTGTTTTACCCTCGATTTACAG
1 AATTACCAAAGTACCCTCGATTTACAG
**** *
49682969 AATTACCGTTTTACCCTCGACTTACAG
1 AATTACCAAAGTACCCTCGATTTACAG
49682996 AATTACC
1 AATTACC
49683003 GTTTTACCCT
Statistics
Matches: 99, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
26 2 0.02
27 97 0.98
ACGTcount: A:0.30, C:0.25, G:0.09, T:0.36
Consensus pattern (27 bp):
AATTACCAAAGTACCCTCGATTTACAG
Found at i:49682969 original size:81 final size:81
Alignment explanation
Indices: 49682878--49683117 Score: 329
Period size: 81 Copynumber: 3.0 Consensus size: 81
49682868 AAAGTACTCC
*
49682878 CGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCAATTTTTAAA
1 CGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCAATTTATAAA
*
49682943 ATTACTGTTTTACCCT
66 ATTACCGTTTTACCCT
* *
49682959 CGATTTACAGAATTACCGTTTTACCCTCGACTTACAGAATTACCGTTTTACCCTCAATTTGTAAA
1 CGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCAATTTATAAA
*
49683024 ATTACCATTTTACCCT
66 ATTACCGTTTTACCCT
** * * * * * * * *
49683040 TAATTTACAGAATTACTGGTTTACCTTC-AGTTTACAAAATTATCGTTTTACCCTTAATTTACAG
1 CGATTTACAGAATTACCGTTTTACCCTCGA-TTTACAGAATTACCGTTTTACCCTCAATTTATAA
49683104 AATTACCGTTTTAC
65 AATTACCGTTTTAC
49683118 ACTTGATTGT
Statistics
Matches: 141, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
80 1 0.01
81 140 0.99
ACGTcount: A:0.29, C:0.23, G:0.09, T:0.40
Consensus pattern (81 bp):
CGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCAATTTATAAA
ATTACCGTTTTACCCT
Found at i:49683003 original size:27 final size:27
Alignment explanation
Indices: 49682880--49683117 Score: 296
Period size: 27 Copynumber: 8.8 Consensus size: 27
49682870 AGTACTCCCG
*
49682880 ATTTACAGAATTACCGTTTTACCCTCG
1 ATTTACAGAATTACCGTTTTACCCTCA
49682907 ATTTACAGAATTACCGTTTTACCCTCA
1 ATTTACAGAATTACCGTTTTACCCTCA
** * * *
49682934 ATTTTTAAAATTACTGTTTTACCCTCG
1 ATTTACAGAATTACCGTTTTACCCTCA
*
49682961 ATTTACAGAATTACCGTTTTACCCTCG
1 ATTTACAGAATTACCGTTTTACCCTCA
*
49682988 ACTTACAGAATTACCGTTTTACCCTCA
1 ATTTACAGAATTACCGTTTTACCCTCA
** * * *
49683015 ATTTGTAAAATTACCATTTTACCCTTA
1 ATTTACAGAATTACCGTTTTACCCTCA
* * *
49683042 ATTTACAGAATTACTGGTTTACCTTCA
1 ATTTACAGAATTACCGTTTTACCCTCA
* * * *
49683069 GTTTACAAAATTATCGTTTTACCCTTA
1 ATTTACAGAATTACCGTTTTACCCTCA
49683096 ATTTACAGAATTACCGTTTTAC
1 ATTTACAGAATTACCGTTTTAC
49683118 ACTTGATTGT
Statistics
Matches: 175, Mismatches: 36, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 175 1.00
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.40
Consensus pattern (27 bp):
ATTTACAGAATTACCGTTTTACCCTCA
Found at i:49683168 original size:27 final size:27
Alignment explanation
Indices: 49683130--49683325 Score: 248
Period size: 27 Copynumber: 7.3 Consensus size: 27
49683120 TTGATTGTGA
*
49683130 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
49683157 AATTTCTGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
49683184 AATTACTGAAATACCCTTATAGGATAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
49683211 AATTACCAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
49683238 AATTATCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
49683265 AAATACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
49683292 AATTACCGAGATACCCTTGTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
49683319 AATTACC
1 AATTACC
49683326 ATTTTGCCCC
Statistics
Matches: 148, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 148 1.00
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:49683562 original size:27 final size:26
Alignment explanation
Indices: 49683524--49683606 Score: 112
Period size: 27 Copynumber: 3.1 Consensus size: 26
49683514 CGGAGGAAGC
*
49683524 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCAC-AATATCT
49683551 GTTCTGGTGGCTCTGCCACAATATCT
1 GTTCTGGTGGCTCTGCCACAATATCT
* * *
49683577 GTATTTGGTGACTCTGTCACAATATCT
1 GT-TCTGGTGGCTCTGCCACAATATCT
49683604 GTT
1 GTT
49683607 GACCGATCGA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
26 10 0.20
27 41 0.80
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.37
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACAATATCT
Found at i:49683688 original size:6 final size:6
Alignment explanation
Indices: 49683677--49683868 Score: 148
Period size: 6 Copynumber: 31.8 Consensus size: 6
49683667 TTCGTGCCGA
49683677 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG -TTACTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG
* * * *
49683725 TTTCTG -TCACCTA ATTCTG ATTCTG ATTCTG -TTACTA ATAT-TG ATTCTG
1 ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATT-CTG AT-TCTG ATTCTG
* * * * *
49683774 ATTTTG ATTCTG -TTACTA ATACTG ATTTTG ATTCTG ATTCTG -TTACTA
1 ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG ATTCTG ATTCTG ATT-CTG
* *
49683822 ATAT-TG ATTCTG AGTCTG ATTCTG -TTATTG ATTCTG ATTCTG ATTCT
1 AT-TCTG ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG ATTCT
49683869 CATTTTGGTT
Statistics
Matches: 148, Mismatches: 21, Indels: 34
0.73 0.10 0.17
Matches are distributed among these distances:
5 13 0.09
6 123 0.83
7 9 0.06
8 3 0.02
ACGTcount: A:0.20, C:0.15, G:0.15, T:0.51
Consensus pattern (6 bp):
ATTCTG
Found at i:49685460 original size:31 final size:29
Alignment explanation
Indices: 49685387--49685460 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
49685377 ACAAAATAAT
49685387 AACATAAGTGACTAAAACGTAACATTTCA
1 AACATAAGTGACTAAAACGTAACATTTCA
* *
49685416 AACATAAGAGACTAAAATGTAAC-TTGATGCA
1 AACATAAGTGACTAAAACGTAACATT--T-CA
*
49685447 AACAAAAGTGACTA
1 AACATAAGTGACTA
49685461 TTTTTGTAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 2 0.05
29 21 0.55
30 1 0.03
31 14 0.37
ACGTcount: A:0.50, C:0.15, G:0.14, T:0.22
Consensus pattern (29 bp):
AACATAAGTGACTAAAACGTAACATTTCA
Found at i:49685771 original size:13 final size:13
Alignment explanation
Indices: 49685755--49685805 Score: 75
Period size: 13 Copynumber: 3.9 Consensus size: 13
49685745 TTTAAACCAA
49685755 ACTTTTCAAAAAC
1 ACTTTTCAAAAAC
* *
49685768 ACTTTTCAATATC
1 ACTTTTCAAAAAC
*
49685781 ACTTTTCAAAATC
1 ACTTTTCAAAAAC
49685794 ACTTTTCAAAAA
1 ACTTTTCAAAAA
49685806 TATTGCCCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.41, C:0.22, G:0.00, T:0.37
Consensus pattern (13 bp):
ACTTTTCAAAAAC
Found at i:49694248 original size:43 final size:43
Alignment explanation
Indices: 49694187--49694274 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
49694177 ATATCTTCGA
49694187 TGTTAGCTCAGAAGTATGTGAGAATGGGTTGTGAAGCTTACTT
1 TGTTAGCTCAGAAGTATGTGAGAATGGGTTGTGAAGCTTACTT
*
49694230 TGTTAGCTCAGAAGTATGTGATAATGGGTTGTGAAGCTTACTT
1 TGTTAGCTCAGAAGTATGTGAGAATGGGTTGTGAAGCTTACTT
49694273 TG
1 TG
49694275 CATATGTGCT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.25, C:0.09, G:0.30, T:0.36
Consensus pattern (43 bp):
TGTTAGCTCAGAAGTATGTGAGAATGGGTTGTGAAGCTTACTT
Found at i:49696015 original size:21 final size:21
Alignment explanation
Indices: 49695977--49696016 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
49695967 AGAGCACCAA
*
49695977 GAGCCAAAAGGAGCCAAAAAC
1 GAGCCAAAAGGAGACAAAAAC
49695998 GAGCCAAAAAGG-GACAAAA
1 GAGCC-AAAAGGAGACAAAA
49696017 CAGACCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.55, C:0.20, G:0.25, T:0.00
Consensus pattern (21 bp):
GAGCCAAAAGGAGACAAAAAC
Found at i:49698430 original size:45 final size:46
Alignment explanation
Indices: 49698366--49698457 Score: 159
Period size: 45 Copynumber: 2.0 Consensus size: 46
49698356 AATTAAATTA
* *
49698366 ACCATTATTAGCAGGTTTAGTTTCA-TTTAAGTCATGCATATATAT
1 ACCATTATTAGCAGGTTTAGCTTCATTTTAAGTCAAGCATATATAT
49698411 ACCATTATTAGCAGGTTTAGCTTCATTTTAAGTCAAGCATATATAT
1 ACCATTATTAGCAGGTTTAGCTTCATTTTAAGTCAAGCATATATAT
49698457 A
1 A
49698458 TTAATGCATA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
45 24 0.55
46 20 0.45
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (46 bp):
ACCATTATTAGCAGGTTTAGCTTCATTTTAAGTCAAGCATATATAT
Found at i:49709072 original size:19 final size:21
Alignment explanation
Indices: 49709043--49709084 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
49709033 AGCTTATCGA
49709043 AAAAGAAGAAAAA-AGAAGGG
1 AAAAGAAGAAAAAGAGAAGGG
*
49709063 AAAA-AAGAAAAAGAGAATGG
1 AAAAGAAGAAAAAGAGAAGGG
49709083 AA
1 AA
49709085 TTTTCGGCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.71, C:0.00, G:0.26, T:0.02
Consensus pattern (21 bp):
AAAAGAAGAAAAAGAGAAGGG
Found at i:49713557 original size:45 final size:42
Alignment explanation
Indices: 49713508--49713662 Score: 134
Period size: 41 Copynumber: 3.6 Consensus size: 42
49713498 TGTTTTCATG
* *
49713508 TAAGACCACGTCTGGGACGTTGGCATCGATATATGTGGTTACGTA
1 TAAGACCATGTCTGGGACGTTGGCATCGATAT-T-T-GTTACATA
* * *
49713553 TAAGACCATGTCTGGGACATTGGCATC-ATATTTGTTTCATG
1 TAAGACCATGTCTGGGACGTTGGCATCGATATTTGTTACATA
* ** * *
49713594 TAAGACCTTGTCTGGGACAG-TGGCATCGATATGAGATAGCATG
1 TAAGACCATGTCTGGGAC-GTTGGCATCGATATTTGTTA-CATA
* * *
49713637 TAAGACCACGTTTGGAACGTTGGCAT
1 TAAGACCATGTCTGGGACGTTGGCAT
49713663 TGTACGATAT
Statistics
Matches: 91, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
41 29 0.32
42 8 0.09
43 25 0.27
44 4 0.04
45 25 0.27
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (42 bp):
TAAGACCATGTCTGGGACGTTGGCATCGATATTTGTTACATA
Found at i:49713610 original size:41 final size:45
Alignment explanation
Indices: 49713493--49713625 Score: 166
Period size: 45 Copynumber: 3.0 Consensus size: 45
49713483 ACATAGTTTG
* * *
49713493 ATATGTGTTTTCATGTAAGACCACGTCTGGGACGTTGGCATCGAT
1 ATATGTGGTTTCATGTAAGACCATGTCTGGGACATTGGCATCGAT
* * *
49713538 ATATGTGGTTACGTATAAGACCATGTCTGGGACATTGGCATC-AT
1 ATATGTGGTTTCATGTAAGACCATGTCTGGGACATTGGCATCGAT
* *
49713582 AT-T-T-GTTTCATGTAAGACCTTGTCTGGGACAGTGGCATCGAT
1 ATATGTGGTTTCATGTAAGACCATGTCTGGGACATTGGCATCGAT
49713624 AT
1 AT
49713626 GAGATAGCAT
Statistics
Matches: 76, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
41 30 0.39
42 5 0.07
43 1 0.01
44 4 0.05
45 36 0.47
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.34
Consensus pattern (45 bp):
ATATGTGGTTTCATGTAAGACCATGTCTGGGACATTGGCATCGAT
Found at i:49715150 original size:13 final size:14
Alignment explanation
Indices: 49715123--49715153 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
49715113 AAGTGGACAA
49715123 TTGTTAAAGCATAT
1 TTGTTAAAGCATAT
49715137 TTGTTAAA-CATAT
1 TTGTTAAAGCATAT
49715150 TTGT
1 TTGT
49715154 AATCGGCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.48
Consensus pattern (14 bp):
TTGTTAAAGCATAT
Found at i:49727590 original size:10 final size:10
Alignment explanation
Indices: 49727577--49727601 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
49727567 AAATTTTTTC
49727577 AAAGTTCGTG
1 AAAGTTCGTG
49727587 AAAGTTCGTG
1 AAAGTTCGTG
49727597 AAAGT
1 AAAGT
49727602 ACCTTAAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.08, G:0.28, T:0.28
Consensus pattern (10 bp):
AAAGTTCGTG
Found at i:49728606 original size:21 final size:21
Alignment explanation
Indices: 49728571--49728626 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
49728561 AAAACAAGTT
* *
49728571 TTTAGAGGCGCTTTTTAGGCC
1 TTTAGCGGCGTTTTTTAGGCC
* * *
49728592 TTTAGCGGCTTTTTTTGGGCT
1 TTTAGCGGCGTTTTTTAGGCC
49728613 TTTAGCGGCGTTTT
1 TTTAGCGGCGTTTT
49728627 GATAAGCGCT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.09, C:0.16, G:0.29, T:0.46
Consensus pattern (21 bp):
TTTAGCGGCGTTTTTTAGGCC
Found at i:49728789 original size:85 final size:86
Alignment explanation
Indices: 49728674--49728860 Score: 277
Period size: 85 Copynumber: 2.2 Consensus size: 86
49728664 GTTTATGTGG
* * * *
49728674 AAAAACGCCACTATAGAACATGACCCTTAGCGGCGCTTCTCTCACAAATGCCGCTAAAGAACATG
1 AAAAACGCCGCTAAAGAACATGACCCTTAGCGGCACTTCTCCCACAAATGCCGCTAAAGAACATG
49728739 ACCTTTAG-CGCGCTTCTCCC
66 ACCTTTAGTCGCGCTTCTCCC
* * *
49728759 AAAAATGCCGCTAAAGAACATGACCTTTAGCGGCACTTCTCCCTCAAATGCCGCTAAAGAACATG
1 AAAAACGCCGCTAAAGAACATGACCCTTAGCGGCACTTCTCCCACAAATGCCGCTAAAGAACATG
*
49728824 ACCTTTAGTGGCGCTTCTCCC
66 ACCTTTAGTCGCGCTTCTCCC
* *
49728845 ACAAACGCTGCTAAAG
1 AAAAACGCCGCTAAAG
49728861 GTTATTAAAA
Statistics
Matches: 90, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
85 66 0.73
86 24 0.27
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.21
Consensus pattern (86 bp):
AAAAACGCCGCTAAAGAACATGACCCTTAGCGGCACTTCTCCCACAAATGCCGCTAAAGAACATG
ACCTTTAGTCGCGCTTCTCCC
Found at i:49728812 original size:43 final size:43
Alignment explanation
Indices: 49728688--49728860 Score: 267
Period size: 43 Copynumber: 4.0 Consensus size: 43
49728678 ACGCCACTAT
* *
49728688 AGAACATGACCCTTAGCGGCGCTTCTCTCACAAATGCCGCTAA
1 AGAACATGACCTTTAGCGGCGCTTCTCCCACAAATGCCGCTAA
*
49728731 AGAACATGACCTTTAGC-GCGCTTCTCCCAAAAATGCCGCTAA
1 AGAACATGACCTTTAGCGGCGCTTCTCCCACAAATGCCGCTAA
* *
49728773 AGAACATGACCTTTAGCGGCACTTCTCCCTCAAATGCCGCTAA
1 AGAACATGACCTTTAGCGGCGCTTCTCCCACAAATGCCGCTAA
* * *
49728816 AGAACATGACCTTTAGTGGCGCTTCTCCCACAAACGCTGCTAA
1 AGAACATGACCTTTAGCGGCGCTTCTCCCACAAATGCCGCTAA
49728859 AG
1 AG
49728861 GTTATTAAAA
Statistics
Matches: 118, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
42 40 0.34
43 78 0.66
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (43 bp):
AGAACATGACCTTTAGCGGCGCTTCTCCCACAAATGCCGCTAA
Found at i:49730372 original size:32 final size:31
Alignment explanation
Indices: 49730327--49730420 Score: 136
Period size: 30 Copynumber: 3.0 Consensus size: 31
49730317 AAGAAAGAAT
*
49730327 AACAATCCATTAGATTAAATTCATTAAAAAA
1 AACAATTCATTAGATTAAATTCATTAAAAAA
* *
49730358 TAATAATTCGTTAGATTAAATTCATT-AAAAA
1 -AACAATTCATTAGATTAAATTCATTAAAAAA
*
49730389 AACAATTCATTAGATTAGATTCATTAAAAAA
1 AACAATTCATTAGATTAAATTCATTAAAAAA
49730420 A
1 A
49730421 GAATAACAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
30 22 0.40
31 11 0.20
32 22 0.40
ACGTcount: A:0.52, C:0.10, G:0.05, T:0.33
Consensus pattern (31 bp):
AACAATTCATTAGATTAAATTCATTAAAAAA
Found at i:49734074 original size:8 final size:8
Alignment explanation
Indices: 49734063--49734149 Score: 72
Period size: 8 Copynumber: 10.9 Consensus size: 8
49734053 GACTAAAATA
49734063 TTAAATTT
1 TTAAATTT
*
49734071 TTAAGTTT
1 TTAAATTT
*
49734079 TTAAGTTT
1 TTAAATTT
49734087 TT-AATTT
1 TTAAATTT
*
49734094 TT-TATTT
1 TTAAATTT
49734101 TTAAA-TT
1 TTAAATTT
49734108 TTAAATTT
1 TTAAATTT
* *
49734116 TCAATTTT
1 TTAAATTT
49734124 TTGAAGATTT
1 TT-AA-ATTT
*
49734134 TTATCATTT
1 TTA-AATTT
49734143 TTAAATT
1 TTAAATT
49734150 AACATATAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
7 19 0.30
8 30 0.47
9 10 0.16
10 5 0.08
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (8 bp):
TTAAATTT
Found at i:49735448 original size:40 final size:39
Alignment explanation
Indices: 49735403--49735547 Score: 182
Period size: 40 Copynumber: 3.6 Consensus size: 39
49735393 GCGTTTTCTG
*
49735403 AAAAGCACCGCTAATGCTCGATCTTTCGCAGCGTTTTTCA
1 AAAAGCGCCGCTAATGCTCGATCTTT-GCAGCGTTTTTCA
* ** * * *
49735443 AAAAGCGCCGCTAATTCTCGATCTATTGTGGCATTTTCCT
1 AAAAGCGCCGCTAATGCTCGATCT-TTGCAGCGTTTTTCA
* *
49735483 AAAAGCGCCGCTAGTGCTCGATCTTTAGCTGCGTTTTTCA
1 AAAAGCGCCGCTAATGCTCGATCTTT-GCAGCGTTTTTCA
49735523 AAAAGCGCCGCTAATGCTCGATCTT
1 AAAAGCGCCGCTAATGCTCGATCTT
49735548 AAAAATACCG
Statistics
Matches: 88, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
39 2 0.02
40 84 0.95
41 2 0.02
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.31
Consensus pattern (39 bp):
AAAAGCGCCGCTAATGCTCGATCTTTGCAGCGTTTTTCA
Found at i:49736107 original size:27 final size:27
Alignment explanation
Indices: 49736054--49736108 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
49736044 GATTTTTAAT
*
49736054 TATTAAAATAATAAAAATATAATTATA
1 TATTAAAATAATAAAAATATAAATATA
*
49736081 TATTAAAATACTATAAAAT-TAAATATA
1 TATTAAAATAATA-AAAATATAAATATA
49736108 T
1 T
49736109 TTGTCTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 20 0.80
28 5 0.20
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (27 bp):
TATTAAAATAATAAAAATATAAATATA
Found at i:49739565 original size:31 final size:29
Alignment explanation
Indices: 49739530--49739598 Score: 77
Period size: 34 Copynumber: 2.2 Consensus size: 29
49739520 CCCATATCAT
*
49739530 TTTTTA-AAAAATTTAAAATATATTTATATTA
1 TTTTTATAAAAATTTAAAAT-T-TTAATA-TA
49739561 TTTTTAATTAAAAATTTAAAATTTTAATATA
1 TTTTT-A-TAAAAATTTAAAATTTTAATATA
49739592 TTTTTAT
1 TTTTTAT
49739599 TTATTAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
29 1 0.03
30 1 0.03
31 12 0.35
32 6 0.18
33 1 0.03
34 13 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (29 bp):
TTTTTATAAAAATTTAAAATTTTAATATA
Found at i:49739607 original size:34 final size:34
Alignment explanation
Indices: 49739536--49739597 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
49739526 TCATTTTTTA
49739536 AAAAATTTAAAATATATTTATATTATTTTTAATT
1 AAAAATTTAAAATATATTTATATTATTTTTAATT
*
49739570 AAAAATTTAAAAT-T-TTAATA-TATTTTTA
1 AAAAATTTAAAATATATTTATATTATTTTTA
49739598 TTTATTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 8 0.30
32 5 0.19
33 1 0.04
34 13 0.48
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (34 bp):
AAAAATTTAAAATATATTTATATTATTTTTAATT
Found at i:49741120 original size:58 final size:58
Alignment explanation
Indices: 49740981--49741124 Score: 148
Period size: 58 Copynumber: 2.5 Consensus size: 58
49740971 ATTCATTACA
** * * * *
49740981 TAAATTCGGGTCGAGTAATCTTGGCTGATAG-TAGTGATTTGACACAGTTTTCATCATG
1 TAAATTCAAGTCGAGTAAACTTGGTTGAAAGCTA-TGATTCGACACAGTTTTCATCATG
* ** *
49741039 TAAGTTCAAGTCGAGTAGGCTTGGTTGAAAGCTATGATTCGACAC-GATTTTCATTATG
1 TAAATTCAAGTCGAGTAAACTTGGTTGAAAGCTATGATTCGACACAG-TTTTCATCATG
* *
49741097 TAAATTCAAGTTGATTAAACTTGGTTGA
1 TAAATTCAAGTCGAGTAAACTTGGTTGA
49741125 CGTGATTTGA
Statistics
Matches: 70, Mismatches: 14, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
57 1 0.01
58 67 0.96
59 2 0.03
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.36
Consensus pattern (58 bp):
TAAATTCAAGTCGAGTAAACTTGGTTGAAAGCTATGATTCGACACAGTTTTCATCATG
Found at i:49741446 original size:98 final size:95
Alignment explanation
Indices: 49741342--49741560 Score: 215
Period size: 98 Copynumber: 2.2 Consensus size: 95
49741332 TAGGGTTATC
* * *
49741342 TTATTACCTTCTGTAAGCCTCCCCTTATACATCTGGGAGTAACGTCATGTTATCACTTTTCGTAA
1 TTATTACCTT-TGTAAGCCTCCCC-T-TACATCTAGGAATAACGTCATATTATCACTTTTCGTAA
*
49741407 GCGTCCCCCTATACGTTTAGGAGCA-AGGTCACT
63 GCCTCCCCCTATACGTTTAGGAGCAGA-GTCACT
* * * * * * * *
49741440 TTATTACTTTTTTTAAGTCTTACCCCTTGCGTCTAGGAATAAGGTTATATTATTACTTTTCGTAA
1 TTATTAC-CTTTGTAAG-CCT-CCCCTTACATCTAGGAATAACGTCATATTATCACTTTTCGTAA
** * *
49741505 GCCTCCCCCTATGTGTTTGGGAGCAGAGTTACT
63 GCCTCCCCCTATACGTTTAGGAGCAGAGTCACT
49741538 TTATTACCTTTCGTAAGCCTCCC
1 TTATTACCTTT-GTAAGCCTCCC
49741561 TCTATGCTAT
Statistics
Matches: 97, Mismatches: 19, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
96 3 0.03
97 5 0.05
98 79 0.81
99 6 0.06
100 4 0.04
ACGTcount: A:0.21, C:0.24, G:0.16, T:0.38
Consensus pattern (95 bp):
TTATTACCTTTGTAAGCCTCCCCTTACATCTAGGAATAACGTCATATTATCACTTTTCGTAAGCC
TCCCCCTATACGTTTAGGAGCAGAGTCACT
Found at i:49741449 original size:49 final size:49
Alignment explanation
Indices: 49741209--49741610 Score: 195
Period size: 49 Copynumber: 8.3 Consensus size: 49
49741199 GTGACTTTTA
* * *
49741209 TCGTAAGCCT-CCCCTATGTGTCTT-GAAGCAA-GAT-CTTT-TTACTTT
1 TCGTAAGCCTCCCCCTATGCGT-TTAGGAGCAAGGTTACTTTATTACTTT
* * * * * * *
49741254 CCGTAAGCTTCCATCC-ATGCGTTTGGGAGTAGGGTCACTTTATTACTTT
1 TCGTAAGCCTCC-CCCTATGCGTTTAGGAGCAAGGTTACTTTATTACTTT
* * ** ** * *
49741303 CCATAAGCCTCCCTCC-ATGTATTTAGGAATAGGGTTA-TCTTATTAC-CT
1 TCGTAAGCCTCCC-CCTATGCGTTTAGGAGCAAGGTTACT-TTATTACTTT
* * * * * * * * *
49741351 TCTGTAAGCCTCCCCTTATACATCTGGGAGTAACGTCA-TGTTATCACTTT
1 TC-GTAAGCCTCCCCCTATGCGTTTAGGAGCAAGGTTACT-TTATTACTTT
* * *
49741401 TCGTAAGCGTCCCCCTATACGTTTAGGAGCAAGGTCACTTTATTACTTT
1 TCGTAAGCCTCCCCCTATGCGTTTAGGAGCAAGGTTACTTTATTACTTT
** * * * **
49741450 TTTTAAGTCTTACCCCT-TGCGTCTAGGAATAAGGTTA-TATTATTACTTT
1 TCGTAAG-CCTCCCCCTATGCGTTTAGGAGCAAGGTTACT-TTATTACTTT
* * *
49741499 TCGTAAGCCTCCCCCTATGTGTTTGGGAGC-AGAGTTACTTTATTACCTT
1 TCGTAAGCCTCCCCCTATGCGTTTAGGAGCAAG-GTTACTTTATTACTTT
* * * *
49741548 TCGTAAGCCTCCCTCTATGC-TATTAGAAGCAGGGTTATTTTATTAC-TT
1 TCGTAAGCCTCCCCCTATGCGT-TTAGGAGCAAGGTTACTTTATTACTTT
*
49741596 ACTGTAAGCCTCCCC
1 TC-GTAAGCCTCCCC
49741611 TGTGCATTTG
Statistics
Matches: 270, Mismatches: 67, Indels: 36
0.72 0.18 0.10
Matches are distributed among these distances:
45 10 0.04
46 10 0.04
47 3 0.01
48 22 0.08
49 212 0.79
50 13 0.05
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (49 bp):
TCGTAAGCCTCCCCCTATGCGTTTAGGAGCAAGGTTACTTTATTACTTT
Found at i:49741697 original size:19 final size:18
Alignment explanation
Indices: 49741668--49741708 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 18
49741658 TTGCAATAGA
49741668 TACAGAATACAATAGACC
1 TACAGAATACAATAGACC
49741686 TACAGTAATACAATAGACC
1 TACAG-AATACAATAGACC
49741705 TACA
1 TACA
49741709 TTTGAGCCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.49, C:0.22, G:0.10, T:0.20
Consensus pattern (18 bp):
TACAGAATACAATAGACC
Found at i:49747016 original size:17 final size:17
Alignment explanation
Indices: 49746957--49747016 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
49746947 TAATAAATTT
49746957 AAAATATAATATATAATAA
1 AAAATATAAT-TAT-ATAA
49746976 AAAATAT-ATT-TAT-A
1 AAAATATAATTATATAA
*
49746990 AGAATAATAATTATATAA
1 AAAAT-ATAATTATATAA
49747008 AAAATATAA
1 AAAATATAA
49747017 AATATATTGG
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 5 0.14
15 4 0.11
16 4 0.11
17 8 0.23
18 7 0.20
19 7 0.20
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (17 bp):
AAAATATAATTATATAA
Found at i:49747551 original size:17 final size:18
Alignment explanation
Indices: 49747498--49747623 Score: 175
Period size: 19 Copynumber: 6.9 Consensus size: 18
49747488 AATCATATCT
*
49747498 TCTAAGATTGTATATCATA
1 TCTAAGATTG-CTATCATA
*
49747517 TCTAAGATTGCAATCATA
1 TCTAAGATTGCTATCATA
49747535 TCTAAGATTG-TATCATA
1 TCTAAGATTGCTATCATA
*
49747552 TCTAAGATTGCAATCATA
1 TCTAAGATTGCTATCATA
49747570 TCTAAGATTG-TATCATA
1 TCTAAGATTGCTATCATA
*
49747587 TCTAAGATTGCATATCACA
1 TCTAAGATTGC-TATCATA
49747606 TCTAAGATTGCATATCAT
1 TCTAAGATTGC-TATCAT
49747624 TGAAGATTAT
Statistics
Matches: 97, Mismatches: 7, Indels: 6
0.88 0.06 0.05
Matches are distributed among these distances:
17 32 0.33
18 32 0.33
19 33 0.34
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (18 bp):
TCTAAGATTGCTATCATA
Found at i:49747556 original size:35 final size:35
Alignment explanation
Indices: 49747498--49747615 Score: 200
Period size: 35 Copynumber: 3.3 Consensus size: 35
49747488 AATCATATCT
49747498 TCTAAGATTGTATATCATATCTAAGATTGCAATCATA
1 TCTAAGATTG--TATCATATCTAAGATTGCAATCATA
49747535 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
1 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
*
49747570 TCTAAGATTGTATCATATCTAAGATTGCATATCACA
1 TCTAAGATTGTATCATATCTAAGATTGCA-ATCATA
49747606 TCTAAGATTG
1 TCTAAGATTG
49747616 CATATCATTG
Statistics
Matches: 79, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
35 54 0.68
36 15 0.19
37 10 0.13
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.37
Consensus pattern (35 bp):
TCTAAGATTGTATCATATCTAAGATTGCAATCATA
Done.