Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 2 of 203
Found at i:308165 original size:12 final size:12
Alignment explanation
Indices: 308148--308172 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
308138 CGAACAAGAG
308148 TCATTTGCAAAT
1 TCATTTGCAAAT
308160 TCATTTGCAAAT
1 TCATTTGCAAAT
308172 T
1 T
308173 ATGTCAAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (12 bp):
TCATTTGCAAAT
Found at i:311159 original size:17 final size:17
Alignment explanation
Indices: 311116--311166 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
311106 TTGGTAGAGT
*
311116 GGATAGGAAAATTGGAAA
1 GGATAGAAAAATT-GAAA
311134 -GAT-GAAAAATTGAAA
1 GGATAGAAAAATTGAAA
*
311149 GGATAGAAAAATAGAAA
1 GGATAGAAAAATTGAAA
311166 G
1 G
311167 AAGGAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
15 4 0.14
16 10 0.34
17 15 0.52
ACGTcount: A:0.57, C:0.00, G:0.27, T:0.16
Consensus pattern (17 bp):
GGATAGAAAAATTGAAA
Found at i:326964 original size:21 final size:21
Alignment explanation
Indices: 326918--326961 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
326908 TATTAGAAAA
326918 TAAA-TATCGATACCCAACTG
1 TAAATTATCGATACCCAACTG
*
326938 TAAATTATCGATA-CCAACTT
1 TAAATTATCGATACCCAACTG
326958 TAAA
1 TAAA
326962 ATTTTGAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.30
Consensus pattern (21 bp):
TAAATTATCGATACCCAACTG
Found at i:328560 original size:131 final size:129
Alignment explanation
Indices: 328326--328878 Score: 581
Period size: 131 Copynumber: 4.3 Consensus size: 129
328316 AGCGATTGGA
* * * *
328326 AAATCAACTAACACAAATGAGATTGTTCATGATATTAAATCGAATGAACTTAAGTTGTGATATTA
1 AAATCAACTAACTCAAATAAGATTGTTCATGATATTAAATCAAATGAACTT-AGTTGTGATCTTA
*
328391 AATCAGTGAACCTTAACGATATCAACTGTGATCTTAAATCAACGAGTTTTTTGGAGTAGCGATCT
65 AATCAGTGAACCTTAACGATATC-ACTGTGATCTTAAATCAACGAGTTGTTTGGAGTAGCGATCT
328456 T
129 T
*
328457 AAATCAACTAACTCAAATAAGATTGTTCATGATGTTAAATCAAATGAACTTAGTTTGTGATCTTA
1 AAATCAACTAACTCAAATAAGATTGTTCATGATATTAAATCAAATGAACTTAG-TTGTGATCTTA
** * * * *
328522 AATTTGTGAACCTTAACGATATCACTTGTGATCTTAAATCATCGAGATGTTTGGAGTAGCGGTAT
65 AATCAGTGAACCTTAACGATATCAC-TGTGATCTTAAATCAACGAGTTGTTTGGAGTAGCGATCT
328587 T
129 T
** ** *
328588 AAATCAA-TGAACTCAAATAAGATTGTTCACAATATTAAATTGAATGAACTTAGGTTGTAATCTT
1 AAATCAACT-AACTCAAATAAGATTGTTCATGATATTAAATCAAATGAACTTA-GTTGTGATCTT
** ** ** * *
328652 AAATCAACGAACCTTAACGATATTGGCTGCAATCTTAAATCAACAAATTGTTTGGAGTAGC-ACT
64 AAATCAGTGAACCTTAACGATA-TCACTGTGATCTTAAATCAACGAGTTGTTTGGAGTAGCGA-T
328716 CTT
127 CTT
* * *
328719 AAATCAACTAACTAAAATAAGATTGTTCATGATATTAAATC-AA-CAA---A----TGATATTAA
1 AAATCAACTAACTCAAATAAGATTGTTCATGATATTAAATCAAATGAACTTAGTTGTGATCTTAA
* * * * * * ** *
328775 ATCAGCGAATCTCAA-TATATCAACTGTGATATTAAATCAGCGAACTATTTGGAGTAGCGATCTT
66 ATCAGTGAACCTTAACGATATC-ACTGTGATCTTAAATCAACGAGTTGTTTGGAGTAGCGATCTT
* *
328839 AAATCAGCTAACTCAAATAAGATTTTTCATGATATATAAA
1 AAATCAACTAACTCAAATAAGATTGTTCATGATAT-TAAA
328879 GTAAACAATA
Statistics
Matches: 357, Mismatches: 55, Indels: 30
0.81 0.12 0.07
Matches are distributed among these distances:
119 1 0.00
120 67 0.19
121 24 0.07
126 1 0.00
129 2 0.01
130 7 0.02
131 251 0.70
132 4 0.01
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (129 bp):
AAATCAACTAACTCAAATAAGATTGTTCATGATATTAAATCAAATGAACTTAGTTGTGATCTTAA
ATCAGTGAACCTTAACGATATCACTGTGATCTTAAATCAACGAGTTGTTTGGAGTAGCGATCTT
Found at i:334057 original size:19 final size:20
Alignment explanation
Indices: 334025--334062 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
334015 CAAGCTGATT
334025 TTAGCTCAATTTCAGCTCCC
1 TTAGCTCAATTTCAGCTCCC
334045 TTAGCTC-ATTTCAGCTCC
1 TTAGCTCAATTTCAGCTCC
334063 AACCAGCTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.18, C:0.34, G:0.11, T:0.37
Consensus pattern (20 bp):
TTAGCTCAATTTCAGCTCCC
Found at i:340267 original size:72 final size:72
Alignment explanation
Indices: 340150--340339 Score: 283
Period size: 72 Copynumber: 2.6 Consensus size: 72
340140 GTTGAATAAT
* * * *
340150 CAGCTTAGAAAAATGCAACAGCAGCCTCCTCTCTT-AATGCCGTCCCAAATCCCATGCACACATT
1 CAGCTTGGAAAAATGCAGCAGCAACCTTCTCT-TTAAATGCCGTCCCAAATCCCATGCACACATT
340214 AAATTCGG
65 AAATTCGG
* * *
340222 CAGCTTGGAAAAAGGCAGCACCAACCTTCTCTTTAAATGCCGTCCCAAGTCCCATGCACACATTA
1 CAGCTTGGAAAAATGCAGCAGCAACCTTCTCTTTAAATGCCGTCCCAAATCCCATGCACACATTA
*
340287 AATTTGG
66 AATTCGG
340294 CAGCTTGGAAAAATGCAGCAGCAACCTTTCTCTTTAAATGCCGTCC
1 CAGCTTGGAAAAATGCAGCAGCAACC-TTCTCTTTAAATGCCGTCC
340340 ATGTACCTGC
Statistics
Matches: 106, Mismatches: 10, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
71 2 0.02
72 85 0.80
73 19 0.18
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.24
Consensus pattern (72 bp):
CAGCTTGGAAAAATGCAGCAGCAACCTTCTCTTTAAATGCCGTCCCAAATCCCATGCACACATTA
AATTCGG
Found at i:345704 original size:30 final size:28
Alignment explanation
Indices: 345670--345725 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 28
345660 GTGATTAAAT
345670 AAAATCGACA-CAAGCAGAATTTAAAAGAAA
1 AAAATCGACAGCAAG-A-AA-TTAAAAGAAA
*
345700 AAAATTGACAGCAAGAAATTAAAAGA
1 AAAATCGACAGCAAGAAATTAAAAGA
345726 TAAGTCCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 8 0.33
29 2 0.08
30 10 0.42
31 4 0.17
ACGTcount: A:0.61, C:0.11, G:0.14, T:0.14
Consensus pattern (28 bp):
AAAATCGACAGCAAGAAATTAAAAGAAA
Found at i:347513 original size:33 final size:33
Alignment explanation
Indices: 347475--347546 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
347465 GATTACTCTC
347475 TTCACTCG-TTTCTTTTACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTT-CAGACTCTCTTTCTTT
* *
347508 TTCACTCGATTTCTTTTCAGGCTCTTTTTCTTT
1 TTCACTCGATTTCTTTTCAGACTCTCTTTCTTT
*
347541 TCCACT
1 TTCACT
347547 TTTGTTTTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
33 27 0.77
34 8 0.23
ACGTcount: A:0.11, C:0.28, G:0.07, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAGACTCTCTTTCTTT
Found at i:348737 original size:2 final size:2
Alignment explanation
Indices: 348732--348762 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
348722 TTCCAAAATT
348732 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 T
348763 TTTTAATACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:349945 original size:72 final size:73
Alignment explanation
Indices: 349862--350016 Score: 222
Period size: 72 Copynumber: 2.1 Consensus size: 73
349852 CTCCTCCCTT
* * * * *
349862 AATGCCATCCCAAATCCCATGCACACATTAAATTTGGCAGCTTGGAAAAAGGCAACATCAAC-CT
1 AATGCCGTCCCAAATCCCATCCACACATTAAATTCGGCAGCTTGAAAAAAGGCAACAGCAACTCT
349926 TCTCTTTA
66 TCTCTTTA
* * *
349934 AATGCCGTCCCAAGTCCCATCCACACATTAAATTCGGCAGCTTGAAAAAATGCAACAGCAACTTT
1 AATGCCGTCCCAAATCCCATCCACACATTAAATTCGGCAGCTTGAAAAAAGGCAACAGCAACTCT
349999 TCTCTTTA
66 TCTCTTTA
*
350007 AATGCTGTCC
1 AATGCCGTCC
350017 ATGTACCTGC
Statistics
Matches: 73, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
72 55 0.75
73 18 0.25
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (73 bp):
AATGCCGTCCCAAATCCCATCCACACATTAAATTCGGCAGCTTGAAAAAAGGCAACAGCAACTCT
TCTCTTTA
Found at i:353404 original size:41 final size:40
Alignment explanation
Indices: 353308--353407 Score: 100
Period size: 41 Copynumber: 2.5 Consensus size: 40
353298 CTTATTAAAC
* *
353308 AAAGAT-A-AAAAATAGAAATGAAACAACAGTAAATAATT
1 AAAGATAACAAAAATAAAAATGAAACAACAGTAAACAATT
*
353346 AATGATAACAAATAATAAAAATGAAATCAA-AGTAAAGCAATT
1 AAAGATAACAAA-AATAAAAATGAAA-CAACAGTAAA-CAATT
*
353388 AAAGA-AAGGAAAAATAAAAA
1 AAAGATAA-CAAAAATAAAAA
353408 CAAAAATACT
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
38 5 0.10
39 1 0.02
40 3 0.06
41 28 0.55
42 14 0.27
ACGTcount: A:0.67, C:0.05, G:0.11, T:0.17
Consensus pattern (40 bp):
AAAGATAACAAAAATAAAAATGAAACAACAGTAAACAATT
Found at i:357604 original size:58 final size:58
Alignment explanation
Indices: 357534--357644 Score: 195
Period size: 58 Copynumber: 1.9 Consensus size: 58
357524 AAGTGTGGCG
* * *
357534 TTTGCTATACCTTTGGTTCTTATCTCGTTAGATAGTGGGTCAAGGTTTATTTGTTGAT
1 TTTGCTATACCTTTGGTTCCTATCTCGTTAAATAGTGAGTCAAGGTTTATTTGTTGAT
357592 TTTGCTATACCTTTGGTTCCTATCTCGTTAAATAGTGAGTCAAGGTTTATTTG
1 TTTGCTATACCTTTGGTTCCTATCTCGTTAAATAGTGAGTCAAGGTTTATTTG
357645 ATAATTTCAC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 50 1.00
ACGTcount: A:0.19, C:0.14, G:0.21, T:0.47
Consensus pattern (58 bp):
TTTGCTATACCTTTGGTTCCTATCTCGTTAAATAGTGAGTCAAGGTTTATTTGTTGAT
Found at i:361235 original size:21 final size:21
Alignment explanation
Indices: 361211--361252 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
361201 TAAATTTAAC
361211 TCAATTCAATACAATTCACAT
1 TCAATTCAATACAATTCACAT
* *
361232 TCAATTTAATCCAATTCACAT
1 TCAATTCAATACAATTCACAT
361253 CTTAGGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (21 bp):
TCAATTCAATACAATTCACAT
Found at i:364573 original size:19 final size:18
Alignment explanation
Indices: 364537--364576 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
364527 TTTCCACTCA
*
364537 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
364555 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
364574 TTT
1 TTT
364577 GTTTGTTGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:365425 original size:14 final size:15
Alignment explanation
Indices: 365405--365443 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
365395 AGCTTCTTCT
365405 TTTTTTTTCACGAAA
1 TTTTTTTTCACGAAA
*
365420 TTTTTTTTCACG-AT
1 TTTTTTTTCACGAAA
365434 TTTTTTTTCA
1 TTTTTTTTCA
365444 ACTTGATATC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.18, C:0.13, G:0.05, T:0.64
Consensus pattern (15 bp):
TTTTTTTTCACGAAA
Found at i:365500 original size:13 final size:13
Alignment explanation
Indices: 365480--365538 Score: 95
Period size: 13 Copynumber: 4.7 Consensus size: 13
365470 AATGGAAACT
365480 AATTTTTTTTTG-
1 AATTTTTTTTTGA
*
365492 AATTTTTTTTTCA
1 AATTTTTTTTTGA
365505 AATTTTTTTTTGA
1 AATTTTTTTTTGA
365518 AATTTTTTTTTG-
1 AATTTTTTTTTGA
365530 AATTTTTTT
1 AATTTTTTT
365539 CGAAGATGTT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
12 20 0.45
13 24 0.55
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.73
Consensus pattern (13 bp):
AATTTTTTTTTGA
Found at i:365514 original size:25 final size:25
Alignment explanation
Indices: 365480--365538 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
365470 AATGGAAACT
365480 AATTTTTTTTTG-AATTTTTTTTTCA
1 AATTTTTTTTTGAAATTTTTTTTT-A
*
365505 AATTTTTTTTTGAAATTTTTTTTTG
1 AATTTTTTTTTGAAATTTTTTTTTA
365530 AATTTTTTT
1 AATTTTTTT
365539 CGAAGATGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 21 0.66
26 11 0.34
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.73
Consensus pattern (25 bp):
AATTTTTTTTTGAAATTTTTTTTTA
Found at i:368335 original size:21 final size:21
Alignment explanation
Indices: 368311--368368 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 21
368301 TCGATTTTAC
368311 CTCACTTTTTCTTTTTGTTTT
1 CTCACTTTTTCTTTTTGTTTT
* *
368332 CTCACTCTTT-TTTCT-TTTT
1 CTCACTTTTTCTTTTTGTTTT
368351 CT-A-TCTTTTCTTTTTGTT
1 CTCACT-TTTTCTTTTTGTT
368369 CTTTTGCTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
17 1 0.03
18 4 0.13
19 10 0.33
20 6 0.20
21 9 0.30
ACGTcount: A:0.05, C:0.21, G:0.03, T:0.71
Consensus pattern (21 bp):
CTCACTTTTTCTTTTTGTTTT
Found at i:369462 original size:22 final size:22
Alignment explanation
Indices: 369432--369475 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
369422 TTTGGTATTT
369432 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
369454 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
369476 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:370605 original size:30 final size:30
Alignment explanation
Indices: 370547--370605 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
370537 TTGAAAATGT
* *
370547 TTGAGCTGAAGTTGAGCTAATTCGAGCTCA
1 TTGAGCTGAAATGGAGCTAATTCGAGCTCA
*
370577 TTGAGCTGAAATGGAAGTTAATTC-AGCTC
1 TTGAGCTGAAATGG-AGCTAATTCGAGCTC
370606 GTATTAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (30 bp):
TTGAGCTGAAATGGAGCTAATTCGAGCTCA
Found at i:378500 original size:20 final size:20
Alignment explanation
Indices: 378451--378493 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
378441 ACATGTATAA
378451 GTATGTGTATTAATCAAAAT
1 GTATGTGTATTAATCAAAAT
378471 GTATGTGTATT-AT-AAAAT
1 GTATGTGTATTAATCAAAAT
378489 GTATG
1 GTATG
378494 CATGTATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 10 0.43
19 2 0.09
20 11 0.48
ACGTcount: A:0.37, C:0.02, G:0.19, T:0.42
Consensus pattern (20 bp):
GTATGTGTATTAATCAAAAT
Found at i:379993 original size:41 final size:43
Alignment explanation
Indices: 379931--380047 Score: 157
Period size: 41 Copynumber: 2.7 Consensus size: 43
379921 TGGTAAATTT
* * *
379931 AATCCGCTCCACTGCAACTTCAGGGAGATAGGATT-T-GCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTAGATTC
*
379972 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATATTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GTAGATTC
* *
380016 AAGCTGCTCCACAGCAACTTCAGGGAGATAAG
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAG
380048 GTTTGATATG
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
41 33 0.49
43 1 0.01
44 33 0.49
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (43 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTAGATTC
Found at i:380033 original size:44 final size:41
Alignment explanation
Indices: 379936--380054 Score: 157
Period size: 44 Copynumber: 2.8 Consensus size: 41
379926 AATTTAATCC
* * *
379936 GCTCCACTGCAACTTCAGGGAGATAGGATTTGCTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTTGATTCAAGCT
*
379977 GCTCCACTGCAACTTCAGGGAGATAAGATTGGTATATTCAAGCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATT--T-GATTCAAGCT
* *
380021 GCTCCACAGCAACTTCAGGGAGATAAGGTTTGAT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTTGAT
380055 ATGGTGTGAT
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
41 31 0.46
42 1 0.01
43 1 0.01
44 35 0.51
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.27
Consensus pattern (41 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATTTGATTCAAGCT
Found at i:380190 original size:50 final size:50
Alignment explanation
Indices: 380136--380886 Score: 353
Period size: 50 Copynumber: 15.1 Consensus size: 50
380126 TGCGATGTCG
* * * * *
380136 GGGAAGCAAGATTCGCTGTTGTAGCTTTAATCTGCTTCACTGCACTACCA
1 GGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTTCACTGCAATGCCA
* * * * * * * *
380186 GGGAAGTAAGATTCGCTGTTGTGGCTTCAATCT-TTTAAATTGCAATGTCA
1 GGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTT-CACTGCAATGCCA
* * *
380236 GGGAA-CAAGATTCACCGTTGTACCTTCAATCTGATCCACTGC-ATCGCCA
1 GGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTTCACTGCAAT-GCCA
* * ** * * * *
380285 GGAAAGTAAGATTCACCGTTGCGGCTTCAATCTTCTT-ATTGCAATGTCG
1 GGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTTCACTGCAATGCCA
* * ***
380334 GGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGCTCCACTGTGCTGCCA
1 GGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTTCACTGCAATGCCA
* * * * * * * *
380384 GGGAAGTAAGATTCGCTGTTGTGGCTTTAATCT--TTAACTGCGATGTC-
1 GGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTTCACTGCAATGCCA
* *** * * **
380431 GAGGAA-TAAGATTTTTCATTGTAGCTTTAATCTG-TTCCACTGCACCGCCA
1 G-GGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTT-CACTGCAATGCCA
* ** ** * * *
380481 GGGAAGTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATGTC-
1 GGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTTCACTGCAATGCCA
* * * * * *
380530 GGGGAGACAAGATTCACTGTTATGGCTTCAATCTGCTCCACTGCACTGCCA
1 GGGAAG-CAAGATTCACCGTTGTAGCTTCAATCTGCTTCACTGCAATGCCA
* ** ** * * * *
380581 GGGAAGTAAGATTTGCCGTTGCGGCTTCAATCT-TTTCAATTGCAATGTCG
1 GGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTTC-ACTGCAATGCCA
* *
380631 GGGAAACAAGATTCACCGTTGTAGCTTCAATCTGGC-CCACTGC-ATCGCCTA
1 GGGAAGCAAGATTCACCGTTGTAGCTTCAATCT-GCTTCACTGCAAT-GCC-A
* * * * ** * * * * *
380682 -GAAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGTAATGTCG
1 GGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTTCACTGCAATGCCA
* * ** * * ** *
380731 GGGAAACAAAATTCGTCGTCGTAACTTCAATCTAATCCACTGC-ATCGCCA
1 GGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTTCACTGCAAT-GCCA
* * * ** ** * * *
380781 GGAAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCA
1 GGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTTCACTGCAATGCCA
* * * * *
380831 GGGAAGCAAGATTCACCGTCGTAACTTTAATCTGCTCCACTGCACTGCCA
1 GGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTTCACTGCAATGCCA
*
380881 AGGAAG
1 GGGAAG
380887 GTAACTTCAT
Statistics
Matches: 503, Mismatches: 174, Indels: 48
0.69 0.24 0.07
Matches are distributed among these distances:
47 22 0.04
48 17 0.03
49 93 0.18
50 359 0.71
51 12 0.02
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (50 bp):
GGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTTCACTGCAATGCCA
Found at i:380584 original size:100 final size:99
Alignment explanation
Indices: 380108--380886 Score: 890
Period size: 100 Copynumber: 7.8 Consensus size: 99
380098 GTGATTTATA
* * * * * * *
380108 GCTTCAAACTTTTTAAACTGCGATGTCGGGGAAGCAAGATTCGCTGTTGTAGCTTTAATCTGCTT
1 GCTTCAATCTTTTT-AATTGCAATGTCGGGGAA-CAAGATTCACCGTTGTAGCTTCAATCTGCTC
* * *
380173 CACTGCACTACCAGGGAAGTAAGATTCGCTGTTGTG
64 CACTGCACTGCCAGGGAAGTAAGATTCGCCGTTGCG
* * * *
380209 GCTTCAATCTTTTAAATTGCAATGTCAGGGAACAAGATTCACCGTTGTACCTTCAATCTGATCCA
1 GCTTCAATCTTTTTAATTGCAATGTCGGGGAACAAGATTCACCGTTGTAGCTTCAATCTGCTCCA
* *
380274 CTGCA-TCGCCAGGAAAGTAAGATTCACCGTTGCG
66 CTGCACT-GCCAGGGAAGTAAGATTCGCCGTTGCG
* *
380308 GCTTCAATCTTCTT-ATTGCAATGTCGGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGCTCC
1 GCTTCAATCTTTTTAATTGCAATGTCGGGGAA-CAAGATTCACCGTTGTAGCTTCAATCTGCTCC
** * *
380372 ACTGTGCTGCCAGGGAAGTAAGATTCGCTGTTGTG
65 ACTGCACTGCCAGGGAAGTAAGATTCGCCGTTGCG
* * * * * *** * * *
380407 GCTTTAATC--TTTAACTGCGATGTCGAGGAATAAGATTTTTCATTGTAGCTTTAATCTGTTCCA
1 GCTTCAATCTTTTTAATTGCAATGTCGGGGAACAAGATTCACCGTTGTAGCTTCAATCTGCTCCA
* *
380470 CTGCACCGCCAGGGAAGTAAGATTCACCGTTGCG
66 CTGCACTGCCAGGGAAGTAAGATTCGCCGTTGCG
* * *
380504 GCTTCAATCTTTTTAATTGCAATGTCGGGGAGACAAGATTCACTGTTATGGCTTCAATCTGCTCC
1 GCTTCAATCTTTTTAATTGCAATGTCGGGGA-ACAAGATTCACCGTTGTAGCTTCAATCTGCTCC
*
380569 ACTGCACTGCCAGGGAAGTAAGATTTGCCGTTGCG
65 ACTGCACTGCCAGGGAAGTAAGATTCGCCGTTGCG
*
380604 GCTTCAATCTTTTCAATTGCAATGTCGGGGAAACAAGATTCACCGTTGTAGCTTCAATCTGGC-C
1 GCTTCAATCTTTTTAATTGCAATGTCGGGG-AACAAGATTCACCGTTGTAGCTTCAATCT-GCTC
* *
380668 CACTGCA-TCGCCTA-GAAAGTAAGATTCGCCGTTGTG
64 CACTGCACT-GCC-AGGGAAGTAAGATTCGCCGTTGCG
* * ** * * **
380704 GCTTCAATCTTTTTAATTGTAATGTCGGGGAAACAAAATTCGTCGTCGTAACTTCAATCTAATCC
1 GCTTCAATCTTTTTAATTGCAATGTCGGGG-AACAAGATTCACCGTTGTAGCTTCAATCTGCTCC
*
380769 ACTGCA-TCGCCAGGAAAGTAAGATTCGCCGTTGCG
65 ACTGCACT-GCCAGGGAAGTAAGATTCGCCGTTGCG
* * * *
380804 GCTTCAATCTTTTTAATTGCAATGTCAGGGAAGCAAGATTCACCGTCGTAACTTTAATCTGCTCC
1 GCTTCAATCTTTTTAATTGCAATGTCGGGGAA-CAAGATTCACCGTTGTAGCTTCAATCTGCTCC
*
380869 ACTGCACTGCCAAGGAAG
65 ACTGCACTGCCAGGGAAG
380887 GTAACTTCAT
Statistics
Matches: 572, Mismatches: 91, Indels: 31
0.82 0.13 0.04
Matches are distributed among these distances:
97 63 0.11
98 31 0.05
99 151 0.26
100 310 0.54
101 17 0.03
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.30
Consensus pattern (99 bp):
GCTTCAATCTTTTTAATTGCAATGTCGGGGAACAAGATTCACCGTTGTAGCTTCAATCTGCTCCA
CTGCACTGCCAGGGAAGTAAGATTCGCCGTTGCG
Found at i:382156 original size:5 final size:5
Alignment explanation
Indices: 382133--382179 Score: 51
Period size: 5 Copynumber: 9.0 Consensus size: 5
382123 GGCCTCTCCT
*
382133 TTTTC TTTTTC GTTCTTC TTTTC TTTTC TTTTC TTTTG TTTT- TTTTC
1 TTTTC -TTTTC -TT-TTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
382180 AAGTTAAGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
4 4 0.11
5 21 0.57
6 9 0.24
7 3 0.08
ACGTcount: A:0.00, C:0.17, G:0.04, T:0.79
Consensus pattern (5 bp):
TTTTC
Found at i:385402 original size:19 final size:20
Alignment explanation
Indices: 385368--385424 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
385358 AGGGTCACTT
* *
385368 CATGAAAATCTAATGCATATG
1 CATG-AAATGTAATGCAAATG
*
385389 -ATGCAATGTAATGCAAATG
1 CATGAAATGTAATGCAAATG
385408 CATGAAATG-AATGCAAA
1 CATGAAATGTAATGCAAA
385425 AAGAGACGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 21 0.68
20 10 0.32
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.25
Consensus pattern (20 bp):
CATGAAATGTAATGCAAATG
Found at i:387762 original size:18 final size:20
Alignment explanation
Indices: 387725--387767 Score: 72
Period size: 18 Copynumber: 2.2 Consensus size: 20
387715 ACATGTATAA
387725 GTATGTGTATTAATTAAAAT
1 GTATGTGTATTAATTAAAAT
387745 GTATGTGTATT-A-TAAAAT
1 GTATGTGTATTAATTAAAAT
387763 GTATG
1 GTATG
387768 CATGTATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 11 0.48
19 1 0.04
20 11 0.48
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.44
Consensus pattern (20 bp):
GTATGTGTATTAATTAAAAT
Found at i:398679 original size:14 final size:13
Alignment explanation
Indices: 398657--398690 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
398647 AGTCATTGTG
*
398657 AAAAAAAATTGGA
1 AAAAAAAATTCGA
398670 AAAAACAAATTCGA
1 AAAAA-AAATTCGA
398684 AAAAAAA
1 AAAAAAA
398691 TTCAAGGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.74, C:0.06, G:0.09, T:0.12
Consensus pattern (13 bp):
AAAAAAAATTCGA
Found at i:398779 original size:15 final size:16
Alignment explanation
Indices: 398767--398796 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
398757 AAACAAAAGA
398767 AATTCGAAA-AAAAAT
1 AATTCGAAAGAAAAAT
398782 AATTCGAAAGAAAAA
1 AATTCGAAAGAAAAA
398797 AAAGAGAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.67, C:0.07, G:0.10, T:0.17
Consensus pattern (16 bp):
AATTCGAAAGAAAAAT
Found at i:398780 original size:16 final size:15
Alignment explanation
Indices: 398756--398799 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
398746 AAAAATTGAA
398756 AAAACAAAAGAAATTCG
1 AAAA-AAAA-AAATTCG
*
398773 AAAAAAAATAATTCG
1 AAAAAAAAAAATTCG
398788 AAAGAAAAAAAA
1 AAA-AAAAAAAA
398800 GAGAGGAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 9 0.38
16 11 0.46
17 4 0.17
ACGTcount: A:0.73, C:0.07, G:0.09, T:0.11
Consensus pattern (15 bp):
AAAAAAAAAAATTCG
Found at i:406219 original size:102 final size:102
Alignment explanation
Indices: 406043--406250 Score: 398
Period size: 102 Copynumber: 2.0 Consensus size: 102
406033 CATCATCTAT
406043 TGTGTGCAAATACTTGCTATTGTTTTGATACTTAGTTTTTGAATAAGGTAATGAAATTTGCCAAA
1 TGTGTGCAAATACTTGCTATTGTTTTGATACTTAGTTTTTGAATAAGGTAATGAAATTTGCCAAA
406108 ATTTTTTTCAATTTATATTCGTGCCTTAAACAGTTCC
66 ATTTTTTTCAATTTATATTCGTGCCTTAAACAGTTCC
*
406145 TGTGTGCAAATACTTTCTATTGTTTTGATACTTAGTTTTTGAATAAGGTAATGAAATTTGCCAAA
1 TGTGTGCAAATACTTGCTATTGTTTTGATACTTAGTTTTTGAATAAGGTAATGAAATTTGCCAAA
*
406210 TTTTTTTTCAATTTATATTCGTGCCTTAAACAGTTCC
66 ATTTTTTTCAATTTATATTCGTGCCTTAAACAGTTCC
406247 TGTG
1 TGTG
406251 GTTGTACTTG
Statistics
Matches: 104, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
102 104 1.00
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.45
Consensus pattern (102 bp):
TGTGTGCAAATACTTGCTATTGTTTTGATACTTAGTTTTTGAATAAGGTAATGAAATTTGCCAAA
ATTTTTTTCAATTTATATTCGTGCCTTAAACAGTTCC
Found at i:415010 original size:33 final size:33
Alignment explanation
Indices: 414928--415013 Score: 93
Period size: 33 Copynumber: 2.5 Consensus size: 33
414918 GAAAGAAAAC
* *
414928 GAAAAGAAAACGAAAGTGGAAAAGAAAAAGAGCCT
1 GAAAAGAAATCG--AGTGAAAAAGAAAAAGAGCCT
* **
414963 GAAAAGAAATCGAGTGAAAAAGAAAGAGAGTTT
1 GAAAAGAAATCGAGTGAAAAAGAAAAAGAGCCT
414996 GTAAAAGAAA-CGAGTGAA
1 G-AAAAGAAATCGAGTGAA
415014 GAGAGTAATC
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
33 26 0.58
34 8 0.18
35 11 0.24
ACGTcount: A:0.57, C:0.06, G:0.27, T:0.10
Consensus pattern (33 bp):
GAAAAGAAATCGAGTGAAAAAGAAAAAGAGCCT
Found at i:429985 original size:45 final size:45
Alignment explanation
Indices: 429900--429985 Score: 104
Period size: 45 Copynumber: 1.9 Consensus size: 45
429890 TCTTCTTTCT
** *
429900 TCAATTTCTTTTTCGATTTTCTCTTTTTCACATCCTTTTTCAATC
1 TCAATTTCTTTTTCGATTTTCTCACTTTCACATCCATTTTCAATC
*
429945 TCAATTTCCTTTTTC-TTTTTCTCACTTTCAC-TCTCATTTTC
1 TCAATTT-CTTTTTCGATTTTCTCACTTTCACATC-CATTTTC
429986 TTTTTTGATT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
44 2 0.06
45 26 0.74
46 7 0.20
ACGTcount: A:0.14, C:0.27, G:0.01, T:0.58
Consensus pattern (45 bp):
TCAATTTCTTTTTCGATTTTCTCACTTTCACATCCATTTTCAATC
Found at i:430026 original size:12 final size:12
Alignment explanation
Indices: 429978--430052 Score: 55
Period size: 12 Copynumber: 6.2 Consensus size: 12
429968 ACTTTCACTC
429978 TCATTTTCTTTTT
1 TCATTTTC-TTTT
* *
429991 TGA-TTTCTTGT
1 TCATTTTCTTTT
*
430002 TC-TCTTTCATTT
1 TCAT-TTTCTTTT
*
430014 TCATTTTATTTT
1 TCATTTTCTTTT
*
430026 TCAATTTCTTTT
1 TCATTTTCTTTT
**
430038 TGTTTTTCTTTT
1 TCATTTTCTTTT
430050 TCA
1 TCA
430053 CATGCTGTTT
Statistics
Matches: 45, Mismatches: 14, Indels: 7
0.68 0.21 0.11
Matches are distributed among these distances:
11 4 0.09
12 38 0.84
13 3 0.07
ACGTcount: A:0.11, C:0.15, G:0.04, T:0.71
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:430027 original size:18 final size:18
Alignment explanation
Indices: 430006--430052 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
429996 TCTTGTTCTC
430006 TTTCATTTTCATTTTATT
1 TTTCATTTTCATTTTATT
* * *
430024 TTTCAATTTCTTTTTGTT
1 TTTCATTTTCATTTTATT
*
430042 TTTCTTTTTCA
1 TTTCATTTTCA
430053 CATGCTGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.13, C:0.13, G:0.02, T:0.72
Consensus pattern (18 bp):
TTTCATTTTCATTTTATT
Found at i:431009 original size:19 final size:19
Alignment explanation
Indices: 430967--431014 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
430957 TACTTCACCT
*
430967 TTTTTTTTAAATATACTCAA
1 TTTTTTTT-AATATACACAA
* *
430987 TTTTTTTTAATATTCACAC
1 TTTTTTTTAATATACACAA
431006 TTTTTTTTA
1 TTTTTTTTA
431015 TACTCTCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.27, C:0.10, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTTTTTAATATACACAA
Found at i:438182 original size:79 final size:81
Alignment explanation
Indices: 438046--438230 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
438036 TTGAATGATG
* *
438046 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
438110 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
438125 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
438187 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
438205 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
438231 AACGAGGAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:438244 original size:40 final size:40
Alignment explanation
Indices: 438047--438230 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
438037 TGAATGATGT
* * * *
438047 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
438087 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
438127 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
438165 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
438206 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
438231 AACGAGGAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:438252 original size:79 final size:79
Alignment explanation
Indices: 438047--438263 Score: 192
Period size: 79 Copynumber: 2.7 Consensus size: 79
438037 TGAATGATGT
** * * * ** *
438047 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAG-CCCGAAGGCATTTGAAC-GAGTGACTAAATCCGGGTTAA-ATCCCGAAGGCAAT
*
438110 TGTGCGAGATACTAATT
63 TGTGCGAGATACTAATA
** * *
438127 CCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCAATTGT
1 CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCAATTGT
*
438192 GCGAGTTACT-ATAA
66 GCGAGATACTAAT-A
* * *
438206 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-CTAAATCCGGGTTAAATCCCGAAGG
438264 TACGTGATTT
Statistics
Matches: 115, Mismatches: 17, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
78 3 0.03
79 70 0.61
80 42 0.37
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (79 bp):
CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCAATTGT
GCGAGATACTAATA
Found at i:448988 original size:20 final size:20
Alignment explanation
Indices: 448940--448988 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
448930 TTTAACTTAG
448940 TTCAGCTCACTCGAGCTCAA
1 TTCAGCTCACTCGAGCTCAA
* *
448960 GTCAGCTCATTCGAGCTCAA
1 TTCAGCTCACTCGAGCTCAA
*
448980 TTCAACTCA
1 TTCAGCTCA
448989 ATCTTAACCC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.27, C:0.33, G:0.14, T:0.27
Consensus pattern (20 bp):
TTCAGCTCACTCGAGCTCAA
Found at i:456644 original size:44 final size:46
Alignment explanation
Indices: 456558--456661 Score: 142
Period size: 44 Copynumber: 2.3 Consensus size: 46
456548 GCTACAAACA
* *
456558 AGACAAATTAAATTAGTTTAAGACAACTTAATTTGTTGTAATAATCT
1 AGACAAATTAAA-TAGTTTAAGACAACTTAAATTGCTGTAATAATCT
*
456605 AGACAAATTAAATA-TCTTAA-AC-ACTTAAATTGCTGTAATAATTT
1 AGACAAATTAAATAGT-TTAAGACAACTTAAATTGCTGTAATAATCT
456649 AGACAAATTAAAT
1 AGACAAATTAAAT
456662 GACTTAGCTT
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
44 32 0.60
45 3 0.06
46 6 0.11
47 12 0.23
ACGTcount: A:0.46, C:0.10, G:0.09, T:0.36
Consensus pattern (46 bp):
AGACAAATTAAATAGTTTAAGACAACTTAAATTGCTGTAATAATCT
Found at i:459801 original size:6 final size:6
Alignment explanation
Indices: 459786--459863 Score: 54
Period size: 6 Copynumber: 12.8 Consensus size: 6
459776 ACTTTCTCAC
* *
459786 TTTT-T TTTTCT TTTTCT CATTATTC- TTTTCT TTTTCT TTTTCAA CTTT-T
1 TTTTCT TTTTCT TTTTCT --TT-TTCT TTTTCT TTTTCT TTTTC-T TTTTCT
* * *
459835 TTTTCT TATTCC TTTTCA TTTTCT TTTTC
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTC
459864 CAAGGACTCT
Statistics
Matches: 57, Mismatches: 9, Indels: 13
0.72 0.11 0.16
Matches are distributed among these distances:
5 10 0.18
6 39 0.68
7 3 0.05
8 2 0.04
9 3 0.05
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (6 bp):
TTTTCT
Found at i:459801 original size:20 final size:20
Alignment explanation
Indices: 459778--459822 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
459768 TTACCTCCAC
*
459778 TTTCTCACTT-TTTTTTTCTT
1 TTTCTCA-TTATTCTTTTCTT
459798 TTTCTCATTATTCTTTTCTT
1 TTTCTCATTATTCTTTTCTT
459818 TTTCT
1 TTTCT
459823 TTTTCAACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTCTCATTATTCTTTTCTT
Found at i:459861 original size:24 final size:24
Alignment explanation
Indices: 459802--459863 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
459792 TTTCTTTTTC
* *
459802 TCATTATTC-TTTTCTTTTTCTTTT
1 TCATT-TTCTTTTTCTTATTCCTTT
*
459826 TCAACTTT-TTTTTCTTATTCCTTT
1 TC-ATTTTCTTTTTCTTATTCCTTT
459850 TCATTTTCTTTTTC
1 TCATTTTCTTTTTC
459864 CAAGGACTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
23 4 0.13
24 25 0.81
25 2 0.06
ACGTcount: A:0.10, C:0.19, G:0.00, T:0.71
Consensus pattern (24 bp):
TCATTTTCTTTTTCTTATTCCTTT
Found at i:461397 original size:306 final size:306
Alignment explanation
Indices: 460844--461455 Score: 1179
Period size: 306 Copynumber: 2.0 Consensus size: 306
460834 CTGAATAGTC
460844 AGTTTGGAAAAGGTGCAACAGCAGCCACCTCTTTTAATGCCGACCCAAGTCCCATGCACGTATTA
1 AGTTTGGAAAAGGTGCAACAGCAGCCACCTCTTTTAATGCCGACCCAAGTCCCATGCACGTATTA
460909 AATTCGACAGCTTGGAAAAGTGCAGAAGCGCATTAATGGACGTCCCTTGCATGCTGGACAGCTCC
66 AATTCGACAGCTTGGAAAAGTGCAGAAGCGCATTAATGGACGTCCCTTGCATGCTGGACAGCTCC
460974 CTTAATACATGTCTTGCTGTTCATTAAATTCGGCCAACATGCCTCATTTAAATGCTGTCCCATGT
131 CTTAATACATGTCTTGCTGTTCATTAAATTCGGCCAACATGCCTCATTTAAATGCTGTCCCATGT
461039 CCATGTACCTGCACCCATTAAAATTCAGCCTTTAATTCACATTTTCAAACACATTAAAAATGGTC
196 CCATGTACCTGCACCCATTAAAATTCAGCCTTTAATTCACATTTTCAAACACATTAAAAATGGTC
461104 AACAGACATATTAAATTCGGCAGCCACAATTAACTTCAGCTGGACA
261 AACAGACATATTAAATTCGGCAGCCACAATTAACTTCAGCTGGACA
* *
461150 AGTTTGGAAAAGGTGCAACAGCAGCCACCTCTTTTAATGCCGACCCAAGTCCCATGCACTTATTT
1 AGTTTGGAAAAGGTGCAACAGCAGCCACCTCTTTTAATGCCGACCCAAGTCCCATGCACGTATTA
*
461215 AATTCGGCAGCTTGGAAAAGTGCAGAAGCGCATTAATGGACGTCCCTTGCATGCTGGACAGCTCC
66 AATTCGACAGCTTGGAAAAGTGCAGAAGCGCATTAATGGACGTCCCTTGCATGCTGGACAGCTCC
461280 CTTAATACATGTCTTGCTGTTCATTAAATTCGGCCAACATGCCTCATTTAAATGCTGTCCCATGT
131 CTTAATACATGTCTTGCTGTTCATTAAATTCGGCCAACATGCCTCATTTAAATGCTGTCCCATGT
* *
461345 CCATGTACCTGCACCGATTAAAATTTAGCCTTTAATTCACATTTTCAAACACATTAAAAATGGTC
196 CCATGTACCTGCACCCATTAAAATTCAGCCTTTAATTCACATTTTCAAACACATTAAAAATGGTC
461410 AACAGACATATTAAATTCGGCAGCCACAATTAACTTCAGCTGGACA
261 AACAGACATATTAAATTCGGCAGCCACAATTAACTTCAGCTGGACA
461456 CCATTTAAGA
Statistics
Matches: 301, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
306 301 1.00
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (306 bp):
AGTTTGGAAAAGGTGCAACAGCAGCCACCTCTTTTAATGCCGACCCAAGTCCCATGCACGTATTA
AATTCGACAGCTTGGAAAAGTGCAGAAGCGCATTAATGGACGTCCCTTGCATGCTGGACAGCTCC
CTTAATACATGTCTTGCTGTTCATTAAATTCGGCCAACATGCCTCATTTAAATGCTGTCCCATGT
CCATGTACCTGCACCCATTAAAATTCAGCCTTTAATTCACATTTTCAAACACATTAAAAATGGTC
AACAGACATATTAAATTCGGCAGCCACAATTAACTTCAGCTGGACA
Found at i:463440 original size:54 final size:52
Alignment explanation
Indices: 463369--463497 Score: 140
Period size: 48 Copynumber: 2.5 Consensus size: 52
463359 ATATCACTCA
* * * *
463369 TTTCTTTTGCACTCTCGTTTCTTTCTTCATTCTCAATCTCTTTTTCAGTTTTCT
1 TTTCTTTTTCACACTCGTTTCTTT-TT-ATTCTCAATCTCATTTTCAATTTTCT
463423 TTTCTTTTTCACACTCG----TTTTTATTCTCAATCTCATTTTCAATTTTCT
1 TTTCTTTTTCACACTCGTTTCTTTTTATTCTCAATCTCATTTTCAATTTTCT
* * *
463471 TTTCTATCTCACACTCATCTTCTTTTT
1 TTTCTTTTTCACACTCGT-TTCTTTTT
463498 CTTTCATTTC
Statistics
Matches: 63, Mismatches: 7, Indels: 11
0.78 0.09 0.14
Matches are distributed among these distances:
48 38 0.60
49 2 0.03
50 3 0.05
53 5 0.08
54 15 0.24
ACGTcount: A:0.13, C:0.26, G:0.03, T:0.58
Consensus pattern (52 bp):
TTTCTTTTTCACACTCGTTTCTTTTTATTCTCAATCTCATTTTCAATTTTCT
Found at i:463510 original size:15 final size:16
Alignment explanation
Indices: 463485--463516 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
463475 TATCTCACAC
463485 TCATCTTCTTTTTCTT
1 TCATCTTCTTTTTCTT
463501 TCAT-TTCTTTTTCTT
1 TCATCTTCTTTTTCTT
463516 T
1 T
463517 TTCATTTGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (16 bp):
TCATCTTCTTTTTCTT
Found at i:464477 original size:12 final size:12
Alignment explanation
Indices: 464460--464513 Score: 63
Period size: 12 Copynumber: 4.4 Consensus size: 12
464450 GAATACAAAC
464460 TTTTTTTTTAAT
1 TTTTTTTTTAAT
*
464472 TTTTTTTTCGAAT
1 TTTTTTTT-TAAT
* *
464485 TTTTTTTTCAAA
1 TTTTTTTTTAAT
*
464497 TTTTTTTTTGAT
1 TTTTTTTTTAAT
464509 TTTTT
1 TTTTT
464514 ACAATACCGT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
12 24 0.69
13 11 0.31
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.78
Consensus pattern (12 bp):
TTTTTTTTTAAT
Found at i:464478 original size:13 final size:13
Alignment explanation
Indices: 464455--464505 Score: 70
Period size: 13 Copynumber: 4.0 Consensus size: 13
464445 GAATTGAATA
464455 CAAACTTTTTTTTT
1 CAAA-TTTTTTTTT
464469 --AATTTTTTTTT
1 CAAATTTTTTTTT
*
464480 CGAATTTTTTTTT
1 CAAATTTTTTTTT
464493 CAAATTTTTTTTT
1 CAAATTTTTTTTT
464506 GATTTTTTAC
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
11 9 0.26
12 2 0.06
13 23 0.68
ACGTcount: A:0.20, C:0.08, G:0.02, T:0.71
Consensus pattern (13 bp):
CAAATTTTTTTTT
Found at i:466239 original size:13 final size:13
Alignment explanation
Indices: 466223--466255 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
466213 AAAAAAACTC
466223 AAAAAAAATTCGA
1 AAAAAAAATTCGA
466236 AAAAAAAATTCGA
1 AAAAAAAATTCGA
466249 AAAAAAA
1 AAAAAAA
466256 CTAGTTTCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.76, C:0.06, G:0.06, T:0.12
Consensus pattern (13 bp):
AAAAAAAATTCGA
Found at i:466310 original size:27 final size:27
Alignment explanation
Indices: 466293--466345 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
466283 GGATATCAAG
466293 TTGTGAAAAAAAAAATTGAAAAAAAAA
1 TTGTGAAAAAAAAAATTGAAAAAAAAA
466320 TTGTGAAAAAAAAAATTGAAAAAAAA
1 TTGTGAAAAAAAAAATTGAAAAAAAA
466346 GAGAGAGCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.70, C:0.00, G:0.11, T:0.19
Consensus pattern (27 bp):
TTGTGAAAAAAAAAATTGAAAAAAAAA
Found at i:466314 original size:13 final size:13
Alignment explanation
Indices: 466296--466345 Score: 82
Period size: 13 Copynumber: 3.8 Consensus size: 13
466286 TATCAAGTTG
466296 TGAAAAAAAAAAT
1 TGAAAAAAAAAAT
*
466309 TGAAAAAAAAATT
1 TGAAAAAAAAAAT
466322 GTGAAAAAAAAAAT
1 -TGAAAAAAAAAAT
466336 TGAAAAAAAA
1 TGAAAAAAAA
466346 GAGAGAGCTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
13 22 0.65
14 12 0.35
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.16
Consensus pattern (13 bp):
TGAAAAAAAAAAT
Found at i:466316 original size:12 final size:12
Alignment explanation
Indices: 466299--466345 Score: 67
Period size: 12 Copynumber: 3.7 Consensus size: 12
466289 CAAGTTGTGA
466299 AAAAAAAAATTG
1 AAAAAAAAATTG
466311 AAAAAAAAATTGTG
1 AAAAAAAAA-T-TG
466325 AAAAAAAAAATTG
1 -AAAAAAAAATTG
466338 AAAAAAAA
1 AAAAAAAA
466346 GAGAGAGCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
12 17 0.53
13 3 0.09
14 3 0.09
15 9 0.28
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.15
Consensus pattern (12 bp):
AAAAAAAAATTG
Found at i:468071 original size:46 final size:46
Alignment explanation
Indices: 468019--468110 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
468009 TTATTTTTCC
*
468019 CTACATCTTCTTTATTTGGCATGTGTGATGTCTTGGTGAAAGTGAA
1 CTACATCTTCTTTATTTGGCATGCGTGATGTCTTGGTGAAAGTGAA
468065 CTACATCTTCTTTATTTGGCATGCGTGATGTCTTGGTGAAAGTGAA
1 CTACATCTTCTTTATTTGGCATGCGTGATGTCTTGGTGAAAGTGAA
468111 GTTTTTGTTA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.22, C:0.14, G:0.24, T:0.40
Consensus pattern (46 bp):
CTACATCTTCTTTATTTGGCATGCGTGATGTCTTGGTGAAAGTGAA
Found at i:471718 original size:250 final size:250
Alignment explanation
Indices: 471277--471773 Score: 985
Period size: 250 Copynumber: 2.0 Consensus size: 250
471267 NNNNNNNNNN
471277 AATTTATCTATTTTAGGGTTTTTCATGCATATTCCTACCTTTCATGTACGACAGAATCACGTACC
1 AATTTATCTATTTTAGGGTTTTTCATGCATATTCCTACCTTTCATGTACGACAGAATCACGTACC
471342 GAGGGTTCTTACCGAATTGGGCCCGTTGGCCCATCATTCCAATTTTGGCCCATTAAGCCCAAAAA
66 GAGGGTTCTTACCGAATTGGGCCCGTTGGCCCATCATTCCAATTTTGGCCCATTAAGCCCAAAAA
471407 TATCGAAGGCGCAGAAATCATGCACTTTGCAGTCCAAATTTTGCAGCTTACCAAAAACATTAATC
131 TATCGAAGGCGCAGAAATCATGCACTTTGCAGTCCAAATTTTGCAGCTTACCAAAAACATTAATC
*
471472 GATTTACCTCACGAGCATTCGCACACTCGCAAATCTACAAAATACCGGTTTTTGT
196 GATTTACCTCACGAGCATTCGCACACTCGCAAATCTACAAAATACCGATTTTTGT
471527 AATTTATCTATTTTAGGGTTTTTCATGCATATTCCTACCTTTCATGTACGACAGAATCACGTACC
1 AATTTATCTATTTTAGGGTTTTTCATGCATATTCCTACCTTTCATGTACGACAGAATCACGTACC
471592 GAGGGTTCTTACCGAATTGGGCCCGTTGGCCCATCATTCCAATTTTGGCCCATTAAGCCCAAAAA
66 GAGGGTTCTTACCGAATTGGGCCCGTTGGCCCATCATTCCAATTTTGGCCCATTAAGCCCAAAAA
471657 TATCGAAGGCGCAGAAATCATGCACTTTGCAGTCCAAATTTTGCAGCTTACCAAAAACATTAATC
131 TATCGAAGGCGCAGAAATCATGCACTTTGCAGTCCAAATTTTGCAGCTTACCAAAAACATTAATC
471722 GATTTACCTCACGAGCATTCGCACACTCGCAAATCTACAAAATACCGATTTT
196 GATTTACCTCACGAGCATTCGCACACTCGCAAATCTACAAAATACCGATTTT
471774 CGGCATTTCG
Statistics
Matches: 246, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
250 246 1.00
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (250 bp):
AATTTATCTATTTTAGGGTTTTTCATGCATATTCCTACCTTTCATGTACGACAGAATCACGTACC
GAGGGTTCTTACCGAATTGGGCCCGTTGGCCCATCATTCCAATTTTGGCCCATTAAGCCCAAAAA
TATCGAAGGCGCAGAAATCATGCACTTTGCAGTCCAAATTTTGCAGCTTACCAAAAACATTAATC
GATTTACCTCACGAGCATTCGCACACTCGCAAATCTACAAAATACCGATTTTTGT
Found at i:473011 original size:26 final size:26
Alignment explanation
Indices: 472975--473085 Score: 168
Period size: 26 Copynumber: 4.3 Consensus size: 26
472965 ACATGAAATT
472975 ATTATCATGAAACATTTACCTAACCC
1 ATTATCATGAAACATTTACCTAACCC
*
473001 ATTATCATGAAACATTTACCTAAGCC
1 ATTATCATGAAACATTTACCTAACCC
* * *
473027 ATTATCATGGAACATTTACCTAATCT
1 ATTATCATGAAACATTTACCTAACCC
* *
473053 ATTATCATGGAACATTTACCTAACCT
1 ATTATCATGAAACATTTACCTAACCC
473079 ATTATCA
1 ATTATCA
473086 ATTTGTATCA
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 80 1.00
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.34
Consensus pattern (26 bp):
ATTATCATGAAACATTTACCTAACCC
Found at i:474638 original size:27 final size:25
Alignment explanation
Indices: 474606--474658 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 25
474596 ATTTTATATG
474606 TTATTTACTTTAAAAATTTCTTGTACA
1 TTATTTA-TTT-AAAATTTCTTGTACA
* *
474633 TTATTTATTTTAAATTTCTTTTACA
1 TTATTTATTTAAAATTTCTTGTACA
474658 T
1 T
474659 ATTGTTACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 14 0.58
26 3 0.12
27 7 0.29
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.58
Consensus pattern (25 bp):
TTATTTATTTAAAATTTCTTGTACA
Found at i:475005 original size:26 final size:26
Alignment explanation
Indices: 474954--475006 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
474944 CATTTTAAAA
* *
474954 TTGTTTTACATCTTATTCATTTTTAT
1 TTGTTTTACATCTTATTAATTATTAT
*
474980 TTGTTTTACA-CTTTTTAAATTATTAT
1 TTGTTTTACATCTTATT-AATTATTAT
475006 T
1 T
475007 AAATTTGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.23, C:0.09, G:0.04, T:0.64
Consensus pattern (26 bp):
TTGTTTTACATCTTATTAATTATTAT
Found at i:481881 original size:16 final size:16
Alignment explanation
Indices: 481860--481890 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
481850 TGTAATCCCC
481860 AAAAATCCCGAAATCG
1 AAAAATCCCGAAATCG
*
481876 AAAAATCTCGAAATC
1 AAAAATCCCGAAATC
481891 TTGAATTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.23, G:0.10, T:0.16
Consensus pattern (16 bp):
AAAAATCCCGAAATCG
Found at i:483147 original size:16 final size:16
Alignment explanation
Indices: 483126--483168 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
483116 GTAGATCGAC
* *
483126 AAAAGCCGAAATGCCG
1 AAAAGCTGAAATACCG
483142 AAAAGCTGAAATACCG
1 AAAAGCTGAAATACCG
483158 AAAAGCTGAAA
1 AAAAGCTGAAA
483169 GTTTGGCTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.51, C:0.19, G:0.21, T:0.09
Consensus pattern (16 bp):
AAAAGCTGAAATACCG
Found at i:483470 original size:29 final size:29
Alignment explanation
Indices: 483393--483454 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
483383 TAAAGGTGAT
* ** *
483393 TTGGGCCTAATGGTGCATATGAATATTAA
1 TTGGCCCTAATGGACCATATGAATATGAA
*
483422 TTGGCCCTAATGGACCATATGAATGTGAA
1 TTGGCCCTAATGGACCATATGAATATGAA
483451 TTGG
1 TTGG
483455 GCCTGATAGG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (29 bp):
TTGGCCCTAATGGACCATATGAATATGAA
Found at i:487648 original size:16 final size:16
Alignment explanation
Indices: 487623--487665 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
487613 GTAGATCGGC
*
487623 AAAAGTCGAAATG-CGA
1 AAAAGACGAAATGTC-A
487639 AAAAGACGAAATGTCA
1 AAAAGACGAAATGTCA
*
487655 AAAAGCCGAAA
1 AAAAGACGAAA
487666 GTTTGGCTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 23 0.96
17 1 0.04
ACGTcount: A:0.56, C:0.14, G:0.21, T:0.09
Consensus pattern (16 bp):
AAAAGACGAAATGTCA
Found at i:487924 original size:29 final size:29
Alignment explanation
Indices: 487891--487997 Score: 103
Period size: 29 Copynumber: 3.7 Consensus size: 29
487881 TAAAGGTGAT
*
487891 TTGGGCCTAATGGGGCATATGAATATGAA
1 TTGGGCCTAATGGGCCATATGAATATGAA
* * *
487920 TTGGGCTTGATGGGCCATATGAATGTGAA
1 TTGGGCCTAATGGGCCATATGAATATGAA
* ** *
487949 TTAGGCCTGTTAGGCCATAT-AA-ATGAGA
1 TTGGGCCTAATGGGCCATATGAATATGA-A
487977 TTGGGCC-AAGTGGGCCATATG
1 TTGGGCCTAA-TGGGCCATATG
487998 CATGTATGTA
Statistics
Matches: 62, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
27 3 0.05
28 18 0.29
29 41 0.66
ACGTcount: A:0.27, C:0.13, G:0.32, T:0.28
Consensus pattern (29 bp):
TTGGGCCTAATGGGCCATATGAATATGAA
Found at i:494483 original size:11 final size:12
Alignment explanation
Indices: 494456--494481 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
494446 GAGCTGTAGC
494456 AAACTAAATTAA
1 AAACTAAATTAA
494468 AAACTAAATTAA
1 AAACTAAATTAA
494480 AA
1 AA
494482 CTTAGTTTAT
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:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (12 bp):
AAACTAAATTAA
Found at i:496185 original size:17 final size:19
Alignment explanation
Indices: 496163--496200 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
496153 TTTATCTCAA
496163 TTTCTT-TTC-CACTCTTT
1 TTTCTTGTTCACACTCTTT
*
496180 TTTCTTGTTCACATTCTTT
1 TTTCTTGTTCACACTCTTT
496199 TT
1 TT
496201 CTCTCTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 3 0.17
19 9 0.50
ACGTcount: A:0.08, C:0.24, G:0.03, T:0.66
Consensus pattern (19 bp):
TTTCTTGTTCACACTCTTT
Found at i:496238 original size:30 final size:30
Alignment explanation
Indices: 496194--496252 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
496184 TTGTTCACAT
**
496194 TCTTTTTCTCTCTCAAACTCTTTTTCATTC
1 TCTTTTTCAATCTCAAACTCTTTTTCATTC
***
496224 TCTTTTTCAATCTCATTTTCTTTTTCATT
1 TCTTTTTCAATCTCAAACTCTTTTTCATT
496253 TTGTTTTTGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.14, C:0.25, G:0.00, T:0.61
Consensus pattern (30 bp):
TCTTTTTCAATCTCAAACTCTTTTTCATTC
Found at i:496352 original size:29 final size:29
Alignment explanation
Indices: 496320--496379 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
496310 CTTACTTGCC
496320 TTTTGCCTCTCTTTT-CTTTTTATTTTATT
1 TTTTGCCT-TCTTTTGCTTTTTATTTTATT
** * *
496349 TTTTTTCTTCTTTTGCTTTTTCTTTTCTT
1 TTTTGCCTTCTTTTGCTTTTTATTTTATT
496378 TT
1 TT
496380 CTTTGTTTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.77
Consensus pattern (29 bp):
TTTTGCCTTCTTTTGCTTTTTATTTTATT
Found at i:501631 original size:12 final size:12
Alignment explanation
Indices: 501616--501640 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
501606 AATAGATTCA
501616 TAAATATTAAAT
1 TAAATATTAAAT
501628 TAAATATTAAAT
1 TAAATATTAAAT
501640 T
1 T
501641 CATTATCTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAATATTAAAT
Found at i:506711 original size:57 final size:57
Alignment explanation
Indices: 506620--506749 Score: 149
Period size: 57 Copynumber: 2.3 Consensus size: 57
506610 GAAACACACT
* * * *
506620 TCGCATACTCAGTGCC-C-ACTAACTGATTTTGCACACATAGTGCTC-GATTAAAGAAC
1 TCGCACACACAGTGCCTCAACT-ACTGATCTGGCACACATAGTGCTCAG-TTAAAGAAC
* * *
506676 TCGCACACATAGTGCCTCAACTACTGATCTGGCACACATAGTGCTCAGTTGAAGAGC
1 TCGCACACACAGTGCCTCAACTACTGATCTGGCACACATAGTGCTCAGTTAAAGAAC
*
506733 TTGCACACACAGTGCCT
1 TCGCACACACAGTGCCT
506750 TATAATTCCA
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
56 13 0.21
57 45 0.73
58 4 0.06
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.25
Consensus pattern (57 bp):
TCGCACACACAGTGCCTCAACTACTGATCTGGCACACATAGTGCTCAGTTAAAGAAC
Found at i:506739 original size:28 final size:27
Alignment explanation
Indices: 506648--506747 Score: 76
Period size: 28 Copynumber: 3.6 Consensus size: 27
506638 CTAACTGATT
506648 TTGCACACATAGTGCTC-GATTAAAGAAC
1 TTGCACACATAGTGCTCAG-TT-AAGAAC
* ** * *
506676 TCGCACACATAGTGCCTCAACTACTGATC
1 TTGCACACATAGTG-CTCAGTTA-AGAAC
* *
506705 TGGCACACATAGTGCTCAGTTGAAGAGC
1 TTGCACACATAGTGCTCAGTT-AAGAAC
*
506733 TTGCACACACAGTGC
1 TTGCACACATAGTGC
506748 CTTATAATTC
Statistics
Matches: 56, Mismatches: 12, Indels: 8
0.74 0.16 0.11
Matches are distributed among these distances:
28 35 0.62
29 21 0.38
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (27 bp):
TTGCACACATAGTGCTCAGTTAAGAAC
Found at i:506830 original size:40 final size:40
Alignment explanation
Indices: 506759--507753 Score: 1841
Period size: 40 Copynumber: 24.9 Consensus size: 40
506749 TTATAATTCC
* *
506759 AGCACGAATGC-CTTCGAGG-TTTAGCCCGGATATATCACC
1 AGCACGAATGCTCTTCG-GGACTTAGCCCGGATATATCACT
* * * *
506798 AGCACTAATGCTCTTCAGGACTTAGCCCGGATATAACACC
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
* * *
506838 AGCACGAATGCTCTTCGGGACTTAGGCCGGATATAACACC
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
* *
506878 CGCACGAATGCTCTTCGGGACTTAGGCCGGATATATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
506918 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
506958 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
506998 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
507038 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
507078 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
507118 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
507158 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
507198 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
507238 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
507278 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
507318 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
507358 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
507398 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
507438 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
507478 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
507518 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
507558 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
507598 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
* *
507638 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACACC
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
*
507678 AGCACTAATGCTCTTCGGGACTTAGCCCGGATATATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
507718 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATAT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATAT
507754 AACTCTCAAT
Statistics
Matches: 936, Mismatches: 18, Indels: 3
0.98 0.02 0.00
Matches are distributed among these distances:
39 12 0.01
40 924 0.99
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
Found at i:509316 original size:47 final size:47
Alignment explanation
Indices: 509257--509993 Score: 1237
Period size: 47 Copynumber: 15.7 Consensus size: 47
509247 CATACATATC
* **
509257 TCACATTAGCCATTCGG-CTTCGCCACATATATACACTTCCACGTTTA
1 TCACATTGGCCATTCGGCCTT-ATCACATATATACACTTCCACGTTTA
** * * * * *
509304 TCACATTGGCCATTCTACCTTATCACACATATGCA-TGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATACACT-TCCACGTTTA
509351 TCACATTGGCCATTCGGCCTTATCACATATATACACTTCCACGTTTA
1 TCACATTGGCCATTCGGCCTTATCACATATATACACTTCCACGTTTA
509398 TCACATTGGCCATTCGGCCTTATCACATATATACACTTCCACGTTTA
1 TCACATTGGCCATTCGGCCTTATCACATATATACACTTCCACGTTTA
509445 TCACATTGGCCATTCGGCCTTATCACATATATACACTTCCACGTTTA
1 TCACATTGGCCATTCGGCCTTATCACATATATACACTTCCACGTTTA
509492 TCACATTGGCCATTCGGCCTTATCACATATATACACTTCCACGTTTA
1 TCACATTGGCCATTCGGCCTTATCACATATATACACTTCCACGTTTA
*
509539 TCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACGTTTA
1 TCACATTGGCCATTCGGCCTTATCACATATATACACTTCCACGTTTA
* * ** * ** **
509586 TCACATTGGCCATTCGGCCATATCACACATATGTA-TGTTCATATTCC
1 TCACATTGGCCATTCGGCCTTATCACATATATACACT-TCCACGTTTA
509633 TCACATTGGCCATTCGGCCTTATCACATATATACACTTCCACGTTTA
1 TCACATTGGCCATTCGGCCTTATCACATATATACACTTCCACGTTTA
509680 TCACATTGGCCATTCGGCCTTATCACATATATACACTTCCACGTTTA
1 TCACATTGGCCATTCGGCCTTATCACATATATACACTTCCACGTTTA
509727 TCACATTGGCCATTCGGCCTTATCACATATATACACTTCCACGTTTA
1 TCACATTGGCCATTCGGCCTTATCACATATATACACTTCCACGTTTA
509774 TCACATTGGCCATTCGGCCTTATCACATATATACACTTCCACGTTTA
1 TCACATTGGCCATTCGGCCTTATCACATATATACACTTCCACGTTTA
509821 TCACATTGGCCATTCGGCCTTATCACATATATACACTTCCACGTTTA
1 TCACATTGGCCATTCGGCCTTATCACATATATACACTTCCACGTTTA
509868 TCACATTGGCCATTCGGCCTTATCACATATATACACTTCCACGTTTA
1 TCACATTGGCCATTCGGCCTTATCACATATATACACTTCCACGTTTA
509915 TCACATTGGCCATTCGGCCTTATCACATATATACACTTCCACGTTTA
1 TCACATTGGCCATTCGGCCTTATCACATATATACACTTCCACGTTTA
*
509962 TCACATTGGCCATTCGGCCTTATCACACATAT
1 TCACATTGGCCATTCGGCCTTATCACATATAT
509994 GCATGTTCAC
Statistics
Matches: 649, Mismatches: 36, Indels: 10
0.93 0.05 0.01
Matches are distributed among these distances:
46 2 0.00
47 642 0.99
48 5 0.01
ACGTcount: A:0.26, C:0.30, G:0.11, T:0.34
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATACACTTCCACGTTTA
Found at i:517664 original size:49 final size:49
Alignment explanation
Indices: 517584--517938 Score: 615
Period size: 49 Copynumber: 7.3 Consensus size: 49
517574 CCCTTCGGGA
* * * * *
517584 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
517631 CCTGTCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
517680 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
517729 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
517778 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
517827 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
517876 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
517925 CTTATCTCATATAT
1 CTTATCACATATAT
517939 GCATGTTCAC
Statistics
Matches: 294, Mismatches: 12, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
47 8 0.03
48 1 0.00
49 285 0.97
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:520272 original size:85 final size:85
Alignment explanation
Indices: 520143--520321 Score: 340
Period size: 85 Copynumber: 2.1 Consensus size: 85
520133 TATTTTATTG
*
520143 CCCATGCCCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
520208 TAACCATAACATCTTGTCCA
66 TAACCATAACATCTTGTCCA
520228 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
*
520293 TAGCCATAACATCTTGTCCA
66 TAACCATAACATCTTGTCCA
520313 CCCATGCTC
1 CCCATGCTC
520322 ATGGCCGACC
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 92 1.00
ACGTcount: A:0.27, C:0.28, G:0.08, T:0.37
Consensus pattern (85 bp):
CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
TAACCATAACATCTTGTCCA
Found at i:521847 original size:57 final size:58
Alignment explanation
Indices: 521771--521879 Score: 157
Period size: 57 Copynumber: 1.9 Consensus size: 58
521761 GCCCACTGAT
* * *
521771 CGATCTCGTACACATAGTGCTTGGTT-GAAGAACTCGCACACACAGTGCCTCAATTAC
1 CGATCTCGCACACATAGTGCTCGGTTAAAAGAACTCGCACACACAGTGCCTCAATTAC
* * *
521828 CGATTTCGCACACATAGTGCTCGGTTAAAAGAATTTGCACACACAGTGCCTC
1 CGATCTCGCACACATAGTGCTCGGTTAAAAGAACTCGCACACACAGTGCCTC
521880 TAATCATTCG
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
57 23 0.51
58 22 0.49
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (58 bp):
CGATCTCGCACACATAGTGCTCGGTTAAAAGAACTCGCACACACAGTGCCTCAATTAC
Found at i:522135 original size:40 final size:40
Alignment explanation
Indices: 522091--522602 Score: 873
Period size: 40 Copynumber: 12.8 Consensus size: 40
522081 CCAGCATGAT
* * * *
522091 TGCTCTTCGGGACCTAGCCCAGATATAACACCAGCACGAA
1 TGCTCCTCGGGACTTAGCCCAGATATATCACTAGCACGAA
* * * *
522131 TGCTCTTCGAGG-TTTAGCACGGATATATCACTAGCACGAA
1 TGCTCCTCG-GGACTTAGCCCAGATATATCACTAGCACGAA
* * *
522171 TGCTCTTCGGAACTTAGCCCAGATACATCACTAGCACGAA
1 TGCTCCTCGGGACTTAGCCCAGATATATCACTAGCACGAA
522211 TGCTCCTCGGGACTTAGCCCAGATATATCACTAGCACGAA
1 TGCTCCTCGGGACTTAGCCCAGATATATCACTAGCACGAA
522251 TGCTCCTCGGGACTTAGCCCAGATATATCACTAGCACGAA
1 TGCTCCTCGGGACTTAGCCCAGATATATCACTAGCACGAA
522291 TGCTCCTCGGGACTTAGCCCAGATATATCACTAGCACGAA
1 TGCTCCTCGGGACTTAGCCCAGATATATCACTAGCACGAA
522331 TGCTCCTCGGGACTTAGCCCAGATATATCACTAGCACGAA
1 TGCTCCTCGGGACTTAGCCCAGATATATCACTAGCACGAA
522371 TGCTCCTCGGGACTTAGCCCAGATATATCACTAGCACGAA
1 TGCTCCTCGGGACTTAGCCCAGATATATCACTAGCACGAA
522411 TGCTCCTCGGGACTTAGCCCAGATATATCACTAGCACGAA
1 TGCTCCTCGGGACTTAGCCCAGATATATCACTAGCACGAA
522451 TGCTCCTCGGGACTTAGCCCAGATATATCACTAGCACGAA
1 TGCTCCTCGGGACTTAGCCCAGATATATCACTAGCACGAA
522491 TGCTCCTCGGGACTTAGCCCAGATATATCACTAGCACGAA
1 TGCTCCTCGGGACTTAGCCCAGATATATCACTAGCACGAA
* *
522531 TGCTCCTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCCTCGGGACTTAGCCCAGATATATCACTAGCACGAA
* *
522571 TGCTCTTCGGGACTTAGCCCGGATATATCACT
1 TGCTCCTCGGGACTTAGCCCAGATATATCACT
522603 CTCAATTCTC
Statistics
Matches: 452, Mismatches: 18, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
39 1 0.00
40 449 0.99
41 2 0.00
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.23
Consensus pattern (40 bp):
TGCTCCTCGGGACTTAGCCCAGATATATCACTAGCACGAA
Found at i:523902 original size:37 final size:37
Alignment explanation
Indices: 523852--523926 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
523842 ACCTTTAGCT
* * *
523852 CAGACGAAATCTCCACATGAAGTTATCGGGTCTTACC
1 CAGACAAAATCTCCACACGAAGTCATCGGGTCTTACC
*
523889 CAGACAAAATCTCCACACGTAGTCATCGGGTCTTACC
1 CAGACAAAATCTCCACACGAAGTCATCGGGTCTTACC
523926 C
1 C
523927 GGAATATATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (37 bp):
CAGACAAAATCTCCACACGAAGTCATCGGGTCTTACC
Found at i:524200 original size:47 final size:47
Alignment explanation
Indices: 524138--524375 Score: 422
Period size: 47 Copynumber: 5.1 Consensus size: 47
524128 ACACGTTTCG
* * * **
524138 CATTAGCCATTCGGCCTTACCACATATATTCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
524185 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
524232 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
524279 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
*
524326 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
524373 CAT
1 CAT
524376 AAAATCCTAA
Statistics
Matches: 185, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 185 1.00
ACGTcount: A:0.26, C:0.32, G:0.12, T:0.30
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
Found at i:525024 original size:69 final size:69
Alignment explanation
Indices: 524936--525073 Score: 249
Period size: 69 Copynumber: 2.0 Consensus size: 69
524926 ATCAAATTTC
*
524936 TCATTTTACAGAATTCAAAATGTGTTGTATTTGATTTCATTTGAAACTAGACTCATTAAGGAGTA
1 TCATTTTAAAGAATTCAAAATGTGTTGTATTTGATTTCATTTGAAACTAGACTCATTAAGGAGTA
525001 TAAG
66 TAAG
* *
525005 TCATTTTAAAGAATTCAAAATGTGTTGTATTTGATTTCATTTGAAACTAGGCTCATTAAGGAGTC
1 TCATTTTAAAGAATTCAAAATGTGTTGTATTTGATTTCATTTGAAACTAGACTCATTAAGGAGTA
525070 TAAG
66 TAAG
525074 CATATAAATT
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (69 bp):
TCATTTTAAAGAATTCAAAATGTGTTGTATTTGATTTCATTTGAAACTAGACTCATTAAGGAGTA
TAAG
Found at i:526027 original size:85 final size:85
Alignment explanation
Indices: 525898--526756 Score: 1709
Period size: 85 Copynumber: 10.1 Consensus size: 85
525888 TATTTTATTG
*
525898 CCCATGCCCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
525963 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
525983 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
526048 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
526068 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
526133 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
526153 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
526218 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
526238 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
526303 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
526323 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
526388 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
526408 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
526473 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
526493 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
526558 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
526578 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
526643 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
526663 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
526728 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
526748 CCCATGCTC
1 CCCATGCTC
526757 ATGGCCGGCC
Statistics
Matches: 773, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 773 1.00
ACGTcount: A:0.27, C:0.26, G:0.08, T:0.39
Consensus pattern (85 bp):
CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
TAGCCATAACATCTTGTCCA
Found at i:531108 original size:26 final size:26
Alignment explanation
Indices: 531079--531138 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
531069 TCCCTTTGAA
* * *
531079 TCATTCGATATTTTGCACACTAAGTG
1 TCATTCAATATCTCGCACACTAAGTG
531105 TCATTCTCAATATCTCGCACACTAAGTG
1 TCA-T-TCAATATCTCGCACACTAAGTG
*
531133 CCATTC
1 TCATTC
531139 TCAATATTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 5 0.18
27 2 0.07
28 21 0.75
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35
Consensus pattern (26 bp):
TCATTCAATATCTCGCACACTAAGTG
Found at i:531124 original size:28 final size:28
Alignment explanation
Indices: 531093--531164 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
531083 TCGATATTTT
*
531093 GCACACTAAGTGTCATTCTCAATATCTC
1 GCACACTAAGTGCCATTCTCAATATCTC
*
531121 GCACACTAAGTGCCATTCTCAATATTTC
1 GCACACTAAGTGCCATTCTCAATATCTC
* * *
531149 GTACACTGAGTACCAT
1 GCACACTAAGTGCCAT
531165 ATTTGATTGC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.31
Consensus pattern (28 bp):
GCACACTAAGTGCCATTCTCAATATCTC
Found at i:533096 original size:48 final size:47
Alignment explanation
Indices: 533025--533334 Score: 271
Period size: 48 Copynumber: 6.5 Consensus size: 47
533015 GTGAATTGAT
* * * * *
533025 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATGTAGAGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATA-AGGCC
* * *
533073 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTCTCAATGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAT-AAGGCC
* * * * *
533121 GATGCCATGTCCTAGACATGGTCTTACACTGGCTCTTATAATATGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAT-ATAAGGCC
* * * ** *
533169 GATGCCATGTCCCAAACATGGTCTTACACTAGCACACATATCAATACT
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAT-AAGGCC
* * * * *
533217 GATGTCATGTCCTAGACATGGTCTTACACTAGCTCTCACA-ACATCGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATA-A-GGCC
* * * * ** *
533265 GATTCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATTGTGGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATA-TAAGGCC
533313 GATGCCATGTCCCAGACATGGT
1 GATGCCATGTCCCAGACATGGT
533335 ACTAAACTGG
Statistics
Matches: 208, Mismatches: 47, Indels: 14
0.77 0.17 0.05
Matches are distributed among these distances:
46 1 0.00
47 3 0.01
48 202 0.97
49 2 0.01
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.29
Consensus pattern (47 bp):
GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAGGCC
Found at i:533189 original size:96 final size:96
Alignment explanation
Indices: 533025--533305 Score: 341
Period size: 96 Copynumber: 2.9 Consensus size: 96
533015 GTGAATTGAT
* * * * * *
533025 GATGCCATGTTCC-AAACATGGTCTTACACTGGCTCACAT-GTAGAGGCCGATGCCATGTCCCAG
1 GATGCCATG-TCCTAGACATGGTCTTACACTGGCTCTCATAATA-TGGCTGATGCCATGTCCCAA
* * *
533088 ACATGGTCTTACACTAGCTCTCGTCTCAATGCC
64 ACATGGTCTTACACTAGCTCTCATATCAATACC
*
533121 GATGCCATGTCCTAGACATGGTCTTACACTGGCTCTTATAATATGGCTGATGCCATGTCCCAAAC
1 GATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCATAATATGGCTGATGCCATGTCCCAAAC
* * *
533186 ATGGTCTTACACTAGCACACATATCAATACT
66 ATGGTCTTACACTAGCTCTCATATCAATACC
* * * * * * *
533217 GATGTCATGTCCTAGACATGGTCTTACACTAGCTCTCACAACATCGCTGATTCCATGTTCCAAAC
1 GATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCATAATATGGCTGATGCCATGTCCCAAAC
*
533282 ATGGTCTTACACTGGCTCTCATAT
66 ATGGTCTTACACTAGCTCTCATAT
533306 TGTGGTCGAT
Statistics
Matches: 159, Mismatches: 24, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
95 3 0.02
96 154 0.97
97 2 0.01
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (96 bp):
GATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCATAATATGGCTGATGCCATGTCCCAAAC
ATGGTCTTACACTAGCTCTCATATCAATACC
Found at i:533284 original size:144 final size:143
Alignment explanation
Indices: 533024--533334 Score: 378
Period size: 144 Copynumber: 2.2 Consensus size: 143
533014 GGTGAATTGA
* * * * *
533024 TGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATGTAGAGGCCGATGCCATGTCCCAGA
1 TGATGCCATGTCCCAAACATGGTCTTACACTAGCACACATATAGAGACCGATGCCATGTCCCAGA
* * *
533089 CATGGTCTTACACTAGCTCTCGTCTCAATGCCGATGCCATGTCCTAGACATGGTCTTACACTGGC
66 CATGGTCTTACACTAGCTCTCGACACAATGCCGATGCCATGTCCTAAACATGGTCTTACACTGGC
*
533154 TCTTATAATATGG
131 TCTCATAATATGG
* * * *
533167 CTGATGCCATGTCCCAAACATGGTCTTACACTAGCACACATATCA-ATACTGATGTCATGTCCTA
1 -TGATGCCATGTCCCAAACATGGTCTTACACTAGCACACATAT-AGAGACCGATGCCATGTCCCA
* *
533231 GACATGGTCTTACACTAGCTCTC-ACA-ACATCGCTGATTCCATGTTCC-AAACATGGTCTTACA
64 GACATGGTCTTACACTAGCTCTCGACACA-AT-GCCGATGCCATG-TCCTAAACATGGTCTTACA
* *
533293 CTGGCTCTCATATTGTGG
126 CTGGCTCTCATAATATGG
*
533311 TCGATGCCATGTCCCAGACATGGT
1 T-GATGCCATGTCCCAAACATGGT
533335 ACTAAACTGG
Statistics
Matches: 144, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
142 1 0.01
143 4 0.03
144 135 0.94
145 4 0.03
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (143 bp):
TGATGCCATGTCCCAAACATGGTCTTACACTAGCACACATATAGAGACCGATGCCATGTCCCAGA
CATGGTCTTACACTAGCTCTCGACACAATGCCGATGCCATGTCCTAAACATGGTCTTACACTGGC
TCTCATAATATGG
Found at i:533322 original size:96 final size:97
Alignment explanation
Indices: 533073--533334 Score: 305
Period size: 96 Copynumber: 2.7 Consensus size: 97
533063 TGTAGAGGCC
* * * * * *
533073 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTCTCAATGC-CGATGCCATGTCCTAGA
1 GATGCCATGTCCCAAACATGGTCTTACACTAGCACACATATCAATACTCGATGCCATGTCCTAGA
* * * * *
533137 CATGGTCTTACACTGGCTCTTATAATATGGCT
66 CATGGTCTTACACTAGCTCTCACAACATCGCT
*
533169 GATGCCATGTCCCAAACATGGTCTTACACTAGCACACATATCAATACT-GATGTCATGTCCTAGA
1 GATGCCATGTCCCAAACATGGTCTTACACTAGCACACATATCAATACTCGATGCCATGTCCTAGA
533233 CATGGTCTTACACTAGCTCTCACAACATCGCT
66 CATGGTCTTACACTAGCTCTCACAACATCGCT
* * * * * ** ** *
533265 GATTCCATGTTCCAAACATGGTCTTACACTGGCTCTCATAT-TGTGGTCGATGCCATGTCCCAGA
1 GATGCCATGTCCCAAACATGGTCTTACACTAGCACACATATCAATACTCGATGCCATGTCCTAGA
533329 CATGGT
66 CATGGT
533335 ACTAAACTGG
Statistics
Matches: 141, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
95 2 0.01
96 139 0.99
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.29
Consensus pattern (97 bp):
GATGCCATGTCCCAAACATGGTCTTACACTAGCACACATATCAATACTCGATGCCATGTCCTAGA
CATGGTCTTACACTAGCTCTCACAACATCGCT
Found at i:539506 original size:47 final size:46
Alignment explanation
Indices: 539394--539657 Score: 211
Period size: 46 Copynumber: 5.7 Consensus size: 46
539384 GGTAAGATGT
* * *
539394 CGATGCCATGTCCCAGACACAGTCTTACACGGGC-TCATATC-TCAAGT
1 CGATGCCATGTCCCAGACA-TGTCTTACACTGGCTTCATATCGT--AGC
* * *
539441 CGATGCCATGTCCTAGACACGGTCTTACACTGACTATCATATCGTAGC
1 CGATGCCATGTCCCAGACA-TGTCTTACACTGGCT-TCATATCGTAGC
* *
539489 CGATG-CATATCCCAGACATGTCTTACACTGGCTTACGTATCG-AGGC
1 CGATGCCATGTCCCAGACATGTCTTACACTGGCTT-CATATCGTA-GC
* * * *
539535 CGATG-CATGTCCCAGACATGTCTTACACTAGCTTTCGTCTC-AATGC
1 CGATGCCATGTCCCAGACATGTCTTACACTGGC-TTCATATCGTA-GC
* * * *
539581 CGATACCATGTCCCAGACATGGTCTTACACTAGCTCTCATAAT-GTGGT
1 CGATGCCATGTCCCAGACAT-GTCTTACACTGGCT-TCAT-ATCGTAGC
*
539629 CGATG-CATGTCCCAAACATGTCTTACACT
1 CGATGCCATGTCCCAGACATGTCTTACACT
539658 AGCTCACAAA
Statistics
Matches: 183, Mismatches: 22, Indels: 25
0.80 0.10 0.11
Matches are distributed among these distances:
45 2 0.01
46 73 0.40
47 71 0.39
48 28 0.15
49 8 0.04
50 1 0.01
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.27
Consensus pattern (46 bp):
CGATGCCATGTCCCAGACATGTCTTACACTGGCTTCATATCGTAGC
Found at i:545739 original size:29 final size:29
Alignment explanation
Indices: 545705--545790 Score: 78
Period size: 23 Copynumber: 3.2 Consensus size: 29
545695 TCGTTTTATT
*
545705 TTACCCTAACCTCTTTAATTCTTTTACAA
1 TTACCCTAACATCTTTAATTCTTTTACAA
* **
545734 TTACCCTAA-AT-TTT--CT-TTTTA-TT
1 TTACCCTAACATCTTTAATTCTTTTACAA
*
545757 TTACCCTAACTTCTTTAATTC-TTTACAA
1 TTACCCTAACATCTTTAATTCTTTTACAA
545785 TTACCC
1 TTACCC
545791 AAAATTTTCT
Statistics
Matches: 43, Mismatches: 8, Indels: 13
0.67 0.12 0.20
Matches are distributed among these distances:
23 9 0.21
24 6 0.14
25 4 0.09
27 8 0.19
28 7 0.16
29 9 0.21
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.49
Consensus pattern (29 bp):
TTACCCTAACATCTTTAATTCTTTTACAA
Found at i:545755 original size:52 final size:51
Alignment explanation
Indices: 545698--545802 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 51
545688 TATGTCATCG
*
545698 TTTTATTTTACCCTAACCTCTTTAATTCTTTTACAATTACCCTAAATTTTCT
1 TTTTATTTTACCCTAACCTCTTTAATTC-TTTACAATTACCCAAAATTTTCT
*
545750 TTTTATTTTACCCTAACTTCTTTAATTCTTTACAATTACCCAAAATTTTCT
1 TTTTATTTTACCCTAACCTCTTTAATTCTTTACAATTACCCAAAATTTTCT
545801 TT
1 TT
545803 CTCTCCACTT
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
51 24 0.47
52 27 0.53
ACGTcount: A:0.26, C:0.22, G:0.00, T:0.52
Consensus pattern (51 bp):
TTTTATTTTACCCTAACCTCTTTAATTCTTTACAATTACCCAAAATTTTCT
Found at i:547726 original size:42 final size:43
Alignment explanation
Indices: 547626--547785 Score: 162
Period size: 43 Copynumber: 3.7 Consensus size: 43
547616 CAATGCTAAC
* * * * * *
547626 GTCCCAAACGTGGTCTTACATGTAATCAAATATCGATGCCACT
1 GTCCCAGACATGGTCTTACACGAAATCACATATCGATGCCAAT
* * *
547669 GTCCTAGACAGGGTCTTACACGAAATCACATA-CGAAGCCAAT
1 GTCCCAGACATGGTCTTACACGAAATCACATATCGATGCCAAT
* * *
547711 GTCCCAGACATGGTCTTACACGTAAATCTCAAATCGATGCCAAC
1 GTCCCAGACATGGTCTTACACG-AAATCACATATCGATGCCAAT
* *
547755 GTCCCA-AAAGTGGTCTTACACGATATCACAT
1 GTCCCAGACA-TGGTCTTACACGAAATCACAT
547786 CTCAAAATCA
Statistics
Matches: 95, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
42 28 0.29
43 41 0.43
44 26 0.27
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.24
Consensus pattern (43 bp):
GTCCCAGACATGGTCTTACACGAAATCACATATCGATGCCAAT
Found at i:550317 original size:50 final size:49
Alignment explanation
Indices: 550141--550370 Score: 230
Period size: 50 Copynumber: 4.6 Consensus size: 49
550131 ATTGTGAATA
* * * * *
550141 CACGTGTATAGTACTAAGTGCAGGCTACTACGTGTACCATACTGTTAAGT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGA-TGTGAGGT
* * * * ** *
550191 CGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACTCA-ATGACTTCGAT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTA-TCAGATG--TGAGGT
*
550242 CACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTATCAGATGATGAGGT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATG-TGAGGT
* *
550292 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGGAT-TGTTGGT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGTG-AGGT
* * *
550341 CGCATGTGTAGTACTAAGTACAGGCTACTA
1 CACGTGTGTAGTACTAAGTGCAGGCTACTA
550371 TTCGTATCAA
Statistics
Matches: 151, Mismatches: 24, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
48 2 0.01
49 32 0.21
50 78 0.52
51 39 0.26
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (49 bp):
CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGTGAGGT
Found at i:557690 original size:50 final size:49
Alignment explanation
Indices: 557615--557842 Score: 221
Period size: 50 Copynumber: 4.6 Consensus size: 49
557605 TGTGAATACA
* * * *
557615 CATGTATACTACTAAGTGCAAGCTACTACGTGTACCATACTGTTAAGTCG
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGA-TGTTAAGTCG
* * *
557665 CATGTGTAGTACTAAGTGCAGGCTACTATGCGTACTCA-ATG--AATTCG
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTAC-CAGATGTTAAGTCG
* * * *
557712 ATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTGAGGTCA
1 --CA--TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGAT-GTTAAGTCG
* * * *
557766 CGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGGATTGTT-GGTCG
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGA-TGTTAAGTCG
557815 CATGTGTAGTACTAAGTGCAGGCTACTA
1 CATGTGTAGTACTAAGTGCAGGCTACTA
557843 TGCGTATCAG
Statistics
Matches: 151, Mismatches: 17, Indels: 21
0.80 0.09 0.11
Matches are distributed among these distances:
47 5 0.03
49 35 0.23
50 71 0.47
51 35 0.23
52 2 0.01
54 3 0.02
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (49 bp):
CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGTTAAGTCG
Found at i:557972 original size:27 final size:26
Alignment explanation
Indices: 557942--557993 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
557932 GGGAAAATCG
557942 ATAAAGTGGTAATATGTG-AAAGTTATT
1 ATAAAGTGG--ATATGTGCAAAGTTATT
* *
557969 ATAAGGTGGATATGTGCAAATTTAT
1 ATAAAGTGGATATGTGCAAAGTTAT
557994 GTTTTTGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 7 0.32
26 7 0.32
27 8 0.36
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (26 bp):
ATAAAGTGGATATGTGCAAAGTTATT
Found at i:565904 original size:42 final size:42
Alignment explanation
Indices: 565847--566012 Score: 174
Period size: 42 Copynumber: 3.9 Consensus size: 42
565837 TAGGGTTATG
*
565847 TGTGATTTCGTGTAAGACCATATCTGGGATATGGCATCGATA
1 TGTGATTTCGTGTAAGACCATATCTAGGATATGGCATCGATA
* * *
565889 TGTGATTTCGTGTAAGACCATGTCTAGGACATGGTATCGATA
1 TGTGATTTCGTGTAAGACCATATCTAGGATATGGCATCGATA
* * * * *
565931 TGGGACATT-GTGTAAGCCCATATCTGGGCTATCGGCATCGATATA
1 TGTGA-TTTCGTGTAAGACCATATCTAGGATAT-GGCATCG--ATA
* *
565976 TGTGA-TCCTATGTAAGACCATATCTAGGATATGGCAT
1 TGTGATTTC-GTGTAAGACCATATCTAGGATATGGCAT
566013 TGGCATCTTA
Statistics
Matches: 100, Mismatches: 18, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
42 60 0.60
43 9 0.09
44 5 0.05
45 26 0.26
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (42 bp):
TGTGATTTCGTGTAAGACCATATCTAGGATATGGCATCGATA
Found at i:567398 original size:49 final size:49
Alignment explanation
Indices: 567273--567415 Score: 198
Period size: 49 Copynumber: 2.9 Consensus size: 49
567263 ACTCATTTTG
* * *
567273 CCAAATATGCAA-GATCAAATATATCATCACATAAATACTTACCCATATGT
1 CCAAATATACAAGGATC-AATATATCATCACATAAATACTTA-CCTTATGA
* *
567323 CCAAATATACGAGGTTCAATATATCATCACATAAATACTTACCTTATGA
1 CCAAATATACAAGGATCAATATATCATCACATAAATACTTACCTTATGA
* *
567372 CCGAATATACAAGGATCAATATATCATCACATAAATACCTACCT
1 CCAAATATACAAGGATCAATATATCATCACATAAATACTTACCT
567416 ACATAGCCAA
Statistics
Matches: 83, Mismatches: 9, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
49 46 0.55
50 34 0.41
51 3 0.04
ACGTcount: A:0.43, C:0.22, G:0.07, T:0.28
Consensus pattern (49 bp):
CCAAATATACAAGGATCAATATATCATCACATAAATACTTACCTTATGA
Found at i:567498 original size:49 final size:50
Alignment explanation
Indices: 567317--567522 Score: 127
Period size: 49 Copynumber: 4.2 Consensus size: 50
567307 ATACTTACCC
* * * * ** * *
567317 ATATGTCCAAATATACGAGGTTCAATA-TATCATCACATAAATACTTACCT
1 ATATGGCCAAAAATACAAGATTCAATAGTA-CATCACATATGTACCTAACT
* * * ** *
567367 -TATGACCGAATATACAAGGA-TCAATA-TATCATCACATAAATACCTACCT
1 ATATGGCCAAAAATACAA-GATTCAATAGTA-CATCACATATGTACCTAACT
* * * *
567416 ACATAGCCAAAAATACAAGATTCAATAGTACATCATATATGTACGTAACT
1 ATATGGCCAAAAATACAAGATTCAATAGTACATCACATATGTACCTAACT
* * * * *
567466 ATGTGGCCAAACATTCAAG-TTCAATA-TAACATCACATTTGTACCTACCT
1 ATATGGCCAAAAATACAAGATTCAATAGT-ACATCACATATGTACCTAACT
567515 ATATGGCC
1 ATATGGCC
567523 GATTATACAA
Statistics
Matches: 126, Mismatches: 25, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
48 1 0.01
49 75 0.60
50 48 0.38
51 2 0.02
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.29
Consensus pattern (50 bp):
ATATGGCCAAAAATACAAGATTCAATAGTACATCACATATGTACCTAACT
Found at i:568426 original size:30 final size:31
Alignment explanation
Indices: 568351--568435 Score: 129
Period size: 31 Copynumber: 2.8 Consensus size: 31
568341 TCAATCTCAA
*
568351 CATAT-ACTAGGCCGAAGCCTTTACATTATT
1 CATATCACTGGGCCGAAGCCTTTACATTATT
* *
568381 CATGTCACTGGGCCGAAGCCTTTTCATTATT
1 CATATCACTGGGCCGAAGCCTTTACATTATT
568412 CATATCAC-GGGCCGAAGCCTTTAC
1 CATATCACTGGGCCGAAGCCTTTAC
568436 TGTAAACGAT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
30 19 0.39
31 30 0.61
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.31
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTACATTATT
Found at i:568689 original size:25 final size:25
Alignment explanation
Indices: 568654--568723 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
568644 CTCTTTTAAT
**
568654 AACTGGGGCAAAGCCCTTTTTGGTA
1 AACTGGGGCAAAGCCCTTTTCAGTA
*
568679 AACTGGAGCAAAGCCCTTTTCAGTA
1 AACTGGGGCAAAGCCCTTTTCAGTA
* *
568704 AACTGGGGTAAAGTCCTTTT
1 AACTGGGGCAAAGCCCTTTT
568724 GCACTTCCTC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCAGTA
Found at i:568796 original size:20 final size:20
Alignment explanation
Indices: 568771--568878 Score: 189
Period size: 20 Copynumber: 5.4 Consensus size: 20
568761 TATATGAATT
568771 TATCATGTGCATATCATACA
1 TATCATGTGCATATCATACA
568791 TATCATGTGCATATCATACA
1 TATCATGTGCATATCATACA
* *
568811 TATCATATACATATCATACA
1 TATCATGTGCATATCATACA
*
568831 TATCATGTGCATATCATACG
1 TATCATGTGCATATCATACA
568851 TATCATGTGCATATCATACA
1 TATCATGTGCATATCATACA
568871 TATCATGT
1 TATCATGT
568879 ATATCAAAAT
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 82 1.00
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.36
Consensus pattern (20 bp):
TATCATGTGCATATCATACA
Found at i:571156 original size:39 final size:39
Alignment explanation
Indices: 571106--571185 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
571096 ATTTTATAAA
* *
571106 CATATTTAATAATAAAAATTTCCAATACCAATAATACAG
1 CATATCTAATAATAAAAAATTCCAATACCAATAATACAG
571145 CATATCTAATAATAAAAAATTCCAATACCAATAATACAG
1 CATATCTAATAATAAAAAATTCCAATACCAATAATACAG
571184 CA
1 CA
571186 AATAATAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.53, C:0.17, G:0.03, T:0.28
Consensus pattern (39 bp):
CATATCTAATAATAAAAAATTCCAATACCAATAATACAG
Found at i:573181 original size:30 final size:31
Alignment explanation
Indices: 573106--573188 Score: 116
Period size: 31 Copynumber: 2.7 Consensus size: 31
573096 TCAATCTCAG
**
573106 CATAT-ACTGGGCTAAAGCCTTTGCATTATT
1 CATATCACTGGGCCGAAGCCTTTGCATTATT
* *
573136 CATGTCACTGGGCCGAAGCCTTTTCATTATT
1 CATATCACTGGGCCGAAGCCTTTGCATTATT
573167 CATATCAC-GGGCCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
573189 ACTGTAAACG
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 18 0.38
31 29 0.62
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTGCATTATT
Found at i:573442 original size:25 final size:25
Alignment explanation
Indices: 573409--573503 Score: 129
Period size: 25 Copynumber: 3.8 Consensus size: 25
573399 CTCTTTTAAT
* *
573409 AACTCGGGCAAAGCCCGTTTCGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
573434 AACTGGGGCAAAGCCCTTTTC-AGTA
1 AACTGGGGCAAAGCCCTTTTCGA-TA
*
573459 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
* *
573484 AACTGGAGCAAAGCTCTTTT
1 AACTGGGGCAAAGCCCTTTT
573504 GCACTTCCTC
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
24 1 0.02
25 62 0.98
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:573474 original size:50 final size:50
Alignment explanation
Indices: 573409--573503 Score: 145
Period size: 50 Copynumber: 1.9 Consensus size: 50
573399 CTCTTTTAAT
*
573409 AACTCGGGCAAAGCCCGTTTCGATAAACTGGGGCAAAGCCCTTTTCAGTA
1 AACTCGGGCAAAGCCCGTTTCGATAAACTGGAGCAAAGCCCTTTTCAGTA
* * * *
573459 AACTGGGGCAAAGCCCTTTTCGGTAAACTGGAGCAAAGCTCTTTT
1 AACTCGGGCAAAGCCCGTTTCGATAAACTGGAGCAAAGCCCTTTT
573504 GCACTTCCTC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (50 bp):
AACTCGGGCAAAGCCCGTTTCGATAAACTGGAGCAAAGCCCTTTTCAGTA
Found at i:573565 original size:11 final size:11
Alignment explanation
Indices: 573551--573587 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
573541 TATATGTATT
573551 TATCATGTGCA
1 TATCATGTGCA
*
573562 TATCA--TACA
1 TATCATGTGCA
573571 TATCATGTGCA
1 TATCATGTGCA
573582 TATCAT
1 TATCAT
573588 ACGTAACATG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 8 0.36
11 14 0.64
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (11 bp):
TATCATGTGCA
Found at i:573576 original size:20 final size:20
Alignment explanation
Indices: 573551--573607 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
573541 TATATGTATT
573551 TATCATGTGCATATCATACA
1 TATCATGTGCATATCATACA
*
573571 TATCATGTGCATATCATACG
1 TATCATGTGCATATCATACA
* *
573591 TAACATGTGCTTATCAT
1 TATCATGTGCATATCAT
573608 GTCAAATCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (20 bp):
TATCATGTGCATATCATACA
Found at i:576595 original size:40 final size:40
Alignment explanation
Indices: 576551--576738 Score: 292
Period size: 40 Copynumber: 4.7 Consensus size: 40
576541 GCTACTTGCT
576551 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCACA
*
576591 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCACA
*
576631 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCACA
* * *
576671 CAAATGCCTTCAGG-CTTAGCCCGG-AATTAGTCACT-AGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCA-CA
576710 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
576739 CATCCGAATA
Statistics
Matches: 136, Mismatches: 8, Indels: 8
0.89 0.05 0.05
Matches are distributed among these distances:
38 2 0.01
39 32 0.24
40 101 0.74
41 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCACA
Found at i:605345 original size:55 final size:53
Alignment explanation
Indices: 605257--605510 Score: 234
Period size: 55 Copynumber: 4.8 Consensus size: 53
605247 ATTAAGGTTT
* * *
605257 AAGGATACCATGTAAGAACATGCCAAGGCATGGCAATTGGTAAGGTTTCTCAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGC-ATTGGTAA-GTTTCTAAGGC
* * * * * *
605312 AAGGAAATCATGTATGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTT--TCTAAGGC
* *
605367 AAAGG-TCCCATGTAAGACCATGCCAAGGA-ATGGCATTGGTGAG-TTCATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAA-GACATGGCATTGGTAAGTTTC-TAAGGC
* *
605420 AAGGATACCATGTAAGACCATGTCAAGACATGGCAATGGTAAGTTTC-AA---
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTTCTAAGGC
* * * * *
605469 AAGGATACCACGTAAGACCATGACAAGTCATGGTAATGGTAA
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAA
605511 AGTACCCGGG
Statistics
Matches: 166, Mismatches: 25, Indels: 22
0.78 0.12 0.10
Matches are distributed among these distances:
49 38 0.23
52 9 0.05
53 40 0.24
54 11 0.07
55 62 0.37
56 6 0.04
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTTCTAAGGC
Found at i:605463 original size:108 final size:110
Alignment explanation
Indices: 605264--605464 Score: 291
Period size: 108 Copynumber: 1.8 Consensus size: 110
605254 TTTAAGGATA
* * * *
605264 CCATGTAAGAACATGCCAAGGCATGGCAATTGGTAAGGTTTCTCAGGCAAGGAAATCATGTATGA
1 CCATGTAAGAACATGCCAAGGAATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
*
605329 CCATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTC
66 CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
* * *
605374 CCATGTAAGACCATGCCAAGGAATGGC-ATTGGTGA-G-TTCATAAGGCAAGGATACCATGTAAG
1 CCATGTAAGAACATGCCAAGGAATGGCAATTGGTAAGGTTTC-TAAGGCAAGGAAACCATGTAAG
*
605436 ACCATGTCAAGACATGGCAATGGTAAGTT
65 ACCATGTCAAGACATGGCAATGATAAGTT
605465 TCAAAAGGAT
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
107 3 0.04
108 46 0.57
109 7 0.09
110 25 0.31
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.23
Consensus pattern (110 bp):
CCATGTAAGAACATGCCAAGGAATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
Found at i:605606 original size:23 final size:24
Alignment explanation
Indices: 605580--605624 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
605570 AAGGTAAGAT
*
605580 AAGGTAAGACGAGTT-ATGCTAAA
1 AAGGTAAGACAAGTTCATGCTAAA
605603 AAGGTAAGACAAGTTCATGCTA
1 AAGGTAAGACAAGTTCATGCTA
605625 GAAGAGCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.42, C:0.11, G:0.24, T:0.22
Consensus pattern (24 bp):
AAGGTAAGACAAGTTCATGCTAAA
Found at i:605724 original size:16 final size:16
Alignment explanation
Indices: 605703--605733 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
605693 ATAAATTTGA
605703 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
605719 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
605734 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:611730 original size:50 final size:50
Alignment explanation
Indices: 611645--611749 Score: 158
Period size: 50 Copynumber: 2.1 Consensus size: 50
611635 GTAACATCCC
* * *
611645 GAAATAGGGCCTAAATGGAATAGTGGTTGCAAAACCACAAAT-TCGAGGTA
1 GAAAAAGGGCCTAAACGGAATAGTGGTAGCAAAACCACAAATCT-GAGGTA
*
611695 GAAAAAGGGCCTAAACGGAATAGTGGTAGCGAAACCACAAATCTGAGGTA
1 GAAAAAGGGCCTAAACGGAATAGTGGTAGCAAAACCACAAATCTGAGGTA
611745 GAAAA
1 GAAAA
611750 TTTTATTTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
50 49 0.98
51 1 0.02
ACGTcount: A:0.43, C:0.14, G:0.27, T:0.16
Consensus pattern (50 bp):
GAAAAAGGGCCTAAACGGAATAGTGGTAGCAAAACCACAAATCTGAGGTA
Found at i:617744 original size:43 final size:43
Alignment explanation
Indices: 617689--617775 Score: 117
Period size: 43 Copynumber: 2.0 Consensus size: 43
617679 ATATCGTACA
*
617689 ATGCCAACGTCCCAGAC-GTGGTCTTACAT-GTAACCACATATCG
1 ATGCCAACGTCCCAGACAG-GGTCTTAC-TCGTAAACACATATCG
617732 ATGCC-ACTGTCCCAGACAGGGTCTTACTCGTAAACACATATCG
1 ATGCCAAC-GTCCCAGACAGGGTCTTACTCGTAAACACATATCG
617775 A
1 A
617776 AATCACATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
42 3 0.08
43 36 0.90
44 1 0.03
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACAGGGTCTTACTCGTAAACACATATCG
Found at i:624595 original size:42 final size:42
Alignment explanation
Indices: 624538--624702 Score: 170
Period size: 42 Copynumber: 3.9 Consensus size: 42
624528 TAGCGTTATG
* *
624538 TGTGATTTTGTGTAAGACCATATCTGGGATATGGCATCGATA
1 TGTGATCTCGTGTAAGACCATATCTGGGATATGGCATCGATA
* * * ** *
624580 TGTGATTTCGTGTAAGACCATGTTTGATACATGGCATCGATA
1 TGTGATCTCGTGTAAGACCATATCTGGGATATGGCATCGATA
* * * *
624622 TGAGA-CACGTGTAAGACCATAGCTGGGCTATTGGCATCGATATA
1 TGTGATCTCGTGTAAGACCATATCTGGGATA-TGGCATCG--ATA
* *
624666 TGTGATCCCATGTAAGACCATATCTGGGATATGGCAT
1 TGTGATCTCGTGTAAGACCATATCTGGGATATGGCAT
624703 TGGCATCTTA
Statistics
Matches: 98, Mismatches: 21, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
41 16 0.16
42 48 0.49
44 13 0.13
45 21 0.21
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (42 bp):
TGTGATCTCGTGTAAGACCATATCTGGGATATGGCATCGATA
Found at i:624700 original size:86 final size:83
Alignment explanation
Indices: 624547--624702 Score: 195
Period size: 86 Copynumber: 1.8 Consensus size: 83
624537 GTGTGATTTT
* ** * * * *
624547 GTGTAAGACCATATCTGGGATATGGCATCGATATGTGATTTCGTGTAAGACCATGTTTGATACAT
1 GTGTAAGACCATAGCTGGGATATGGCATCGATATGTGATCCCATGTAAGACCATATCTGAGACAT
624612 GGCATCGATATGAGACAC
66 GGCATCGATATGAGACAC
* *
624630 GTGTAAGACCATAGCTGGGCTATTGGCATCGATATATGTGATCCCATGTAAGACCATATCTGGGA
1 GTGTAAGACCATAGCTGGGATA-TGGCATCG--ATATGTGATCCCATGTAAGACCATATCTGAGA
*
624695 TATGGCAT
63 CATGGCAT
624703 TGGCATCTTA
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
83 20 0.33
84 8 0.13
86 32 0.53
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (83 bp):
GTGTAAGACCATAGCTGGGATATGGCATCGATATGTGATCCCATGTAAGACCATATCTGAGACAT
GGCATCGATATGAGACAC
Found at i:624875 original size:16 final size:17
Alignment explanation
Indices: 624854--624885 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
624844 AAGCATTGGC
624854 TTCATGAT-ATTATGAG
1 TTCATGATCATTATGAG
624870 TTCATGATCATTATGA
1 TTCATGATCATTATGA
624886 AAGTGCCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.31, C:0.09, G:0.16, T:0.44
Consensus pattern (17 bp):
TTCATGATCATTATGAG
Found at i:634006 original size:47 final size:47
Alignment explanation
Indices: 633928--634380 Score: 690
Period size: 47 Copynumber: 9.6 Consensus size: 47
633918 CCCTTCGGGA
* * ** * * *
633928 CTTATCACATTTATACACTTTCACATCCATCATGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
633975 CCTGTCACATATATACACTTTCATATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* **
634022 CTCATCACATATATACACTTTCACATTCATCACATCGGCTTTTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
634069 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
634116 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
634163 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
634212 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
634259 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
634308 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
634355 CTTATCACATATATATACATTCACAT
1 CTTATCACATATATACACTTTCACAT
634381 CACAATTATC
Statistics
Matches: 374, Mismatches: 28, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
47 284 0.76
49 90 0.24
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:634205 original size:96 final size:96
Alignment explanation
Indices: 633928--634380 Score: 702
Period size: 96 Copynumber: 4.8 Consensus size: 96
633918 CCCTTCGGGA
* * ** * * * * *
633928 CTTATCACATTTATACACTTTCACATCCATCATGTTGGCCACTCGGCCCTGTCAC--ATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
*
633991 ACTTTCATATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
* **
634022 CTCATCACATATATACACTTTCACATTCATCACATCGGCTTTTAGGCCTTATCAC--ATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
634085 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
634116 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
* *
634181 ACTTTCACATTCATCACATTGGCCATTCGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
634212 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
* *
634277 ACTTTCACATTCATCACATTGGCCATTCGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
*
634308 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
634373 A--TTCACAT
66 ACTTTCACAT
634381 CACAATTATC
Statistics
Matches: 338, Mismatches: 19, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
94 140 0.41
96 198 0.59
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (96 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:634241 original size:143 final size:141
Alignment explanation
Indices: 633928--634380 Score: 699
Period size: 143 Copynumber: 3.2 Consensus size: 141
633918 CCCTTCGGGA
* * ** * * * * *
633928 CTTATCACATTTATACACTTTCACATCCATCATGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
* * *
633993 TTTCATATTCATCACATCGGCCATTAGGCCTCATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATT
**
634058 GGCTTTTAGGC
131 GGCCATTAGGC
634069 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
634134 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCACA
*
634199 TTGGCCATTCGGC
129 TTGGCCATTAGGC
634212 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
* *
634277 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACA
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
634342 TTGGCCATTAGGC
129 TTGGCCATTAGGC
* *
634355 CTTATCACATATATATACATTCACAT
1 CTTATCACATATATACACTTTCACAT
634381 CACAATTATC
Statistics
Matches: 288, Mismatches: 20, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
141 91 0.32
143 152 0.53
145 45 0.16
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (141 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATT
GGCCATTAGGC
Found at i:637201 original size:6 final size:6
Alignment explanation
Indices: 637163--637194 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
637153 TTAAGAAACC
*
637163 AAAATA AAATTA AAAATA AAAATA AAAATA AA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AA
637195 TAAAAATCGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
AAAATA
Done.