Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold421
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: 441760
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 3
Found at i:170750 original size:15 final size:17
Alignment explanation
Indices: 170730--170768 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
170720 ATCATAGCAT
170730 TGCATTAT-CATC-ATA
1 TGCATTATGCATCAATA
170745 TGCATT-TGCATCAATA
1 TGCATTATGCATCAATA
170761 TGCATTAT
1 TGCATTAT
170769 TCATAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 1 0.05
15 10 0.48
16 9 0.43
17 1 0.05
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.41
Consensus pattern (17 bp):
TGCATTATGCATCAATA
Found at i:170880 original size:46 final size:48
Alignment explanation
Indices: 170813--170936 Score: 146
Period size: 47 Copynumber: 2.6 Consensus size: 48
170803 TTCTGACTCA
* * *
170813 AAAAGTCCTAAACTCATAAAGAACT-TAGGTACAGACTTCTAA-TTTT
1 AAAAGTCCTAAACTTAAAAAGAACTCTAGGTACAGACTCCTAACTTTT
* * *
170859 AAAAGTCCTAAACTTAAAAAGAACTCCAGGAATAGACTCCTAACTTTT
1 AAAAGTCCTAAACTTAAAAAGAACTCTAGGTACAGACTCCTAACTTTT
** *
170907 AAATTTCC-AAACTTAAAAAGAACTGTAGGT
1 AAAAGTCCTAAACTTAAAAAGAACTCTAGGT
170937 GAGAACTCTT
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
46 23 0.35
47 32 0.49
48 10 0.15
ACGTcount: A:0.44, C:0.18, G:0.11, T:0.27
Consensus pattern (48 bp):
AAAAGTCCTAAACTTAAAAAGAACTCTAGGTACAGACTCCTAACTTTT
Found at i:171276 original size:52 final size:52
Alignment explanation
Indices: 171090--171710 Score: 402
Period size: 52 Copynumber: 12.0 Consensus size: 52
171080 TGTCTAATAG
* * * * * * *
171090 AACCTAAAGTCCACTTTAGCTGGTACCTATATAGGGAGATTAAGCCTTATAGA
1 AACCTAAAGTCCACATTAGCTGGCACCTGTATAAGGAGGTCAAGCCCTATA-A
* * * * * *
171143 ATCC--ACGTCAACACTAGCTGGAACCTGTATAAGGAGGTCAAGCACTATAA
1 AACCTAAAGTCCACATTAGCTGGCACCTGTATAAGGAGGTCAAGCCCTATAA
* * *
171193 AATCT-AAGTCCACACTAGCTAGCA-CTCGTATAAGGAGGTCAAGCCCTATAA
1 AACCTAAAGTCCACATTAGCTGGCACCT-GTATAAGGAGGTCAAGCCCTATAA
* * * *
171244 AACCTAAAGTCCACACTAGCTGGCACCTGTATAGGGAGGTCAAACCCTATAG
1 AACCTAAAGTCCACATTAGCTGGCACCTGTATAAGGAGGTCAAGCCCTATAA
* * * * * * * *
171296 AATCTAAAGTCTATATTAGCTAGCACTTGTAT-AGAGAGGTCAGGCCATATAG
1 AACCTAAAGTCCACATTAGCTGGCACCTGTATAAG-GAGGTCAAGCCCTATAA
* * * ** * *
171348 AACCCAAAGTCAATATTATTTGGCACCTGTATAAGGAGGTTAAGCCTTATAGA
1 AACCTAAAGTCCACATTAGCTGGCACCTGTATAAGGAGGTCAAGCCCTATA-A
* * * * * * * * *
171401 ATCC--AAGCCCATAATAACTAGCATCTATATAAAGAGGTCAAGCCCTATAA
1 AACCTAAAGTCCACATTAGCTGGCACCTGTATAAGGAGGTCAAGCCCTATAA
** * * *
171451 AACCCGAAGTCCACATTAGCT-ACACTTATATAAGGAGGTCAAGCCCTATAA
1 AACCTAAAGTCCACATTAGCTGGCACCTGTATAAGGAGGTCAAGCCCTATAA
** * * * * * *
171502 AGTC-AAAGTCTAAACTAGCTGGCACCTGTATAGGGGGGTCAAGCGCTATAGA
1 AACCTAAAGTCCACATTAGCTGGCACCTGTATAAGGAGGTCAAGCCCTATA-A
* * * * * * *
171554 ACCCT-AAGTCCATATTAACTGGCACTTGTAT-AGAGAGGTTAAGCCTTATAT
1 AACCTAAAGTCCACATTAGCTGGCACCTGTATAAG-GAGGTCAAGCCCTATAA
* * * * *
171605 AA-CTCAAAGTCCACAGTAGCTGACACCTGTATAGGGAGGTTAAGCCTTATAA
1 AACCT-AAAGTCCACATTAGCTGGCACCTGTATAAGGAGGTCAAGCCCTATAA
* * * * * * * *
171657 AACTTAAAGTCTACAATAGCTAGCACCTATATAGGGAGGTCAAACCTTATAA
1 AACCTAAAGTCCACATTAGCTGGCACCTGTATAAGGAGGTCAAGCCCTATAA
171709 AA
1 AA
171711 TCGAAGTCCA
Statistics
Matches: 444, Mismatches: 107, Indels: 35
0.76 0.18 0.06
Matches are distributed among these distances:
50 23 0.05
51 164 0.37
52 245 0.55
53 12 0.03
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (52 bp):
AACCTAAAGTCCACATTAGCTGGCACCTGTATAAGGAGGTCAAGCCCTATAA
Found at i:171594 original size:205 final size:207
Alignment explanation
Indices: 171160--171712 Score: 530
Period size: 207 Copynumber: 2.7 Consensus size: 207
171150 TCAACACTAG
* * * * * * * * *
171160 CTGGAACCTGTATAAGGAGGTCAAGCAC-TATAAAATCTAAGTCCACACTAGCTAGCA-CTCGTA
1 CTGGCACCTGTATAAGGAGGTTAAGC-CTTATAGAATCCAAGCCCATAATAACTAGCATCT-ATA
* * * * *
171223 TAAGGAGGTCAAGCCCTATAAAACCTAAAGTCCACACTAGCTGGCACCTGTATAGGGAGGTCAAA
64 TAAAGAGGTCAAGCCCTATAAAACCCAAAGTCCACACTAGCTGACACCTATATAAGGAGGTCAAA
* * * *
171288 CCCTATAGAATCTAAAGTCTATATTAGCTAGCACTTGTATAGAGAGGTCAGGCCATATAGAACCC
129 CCCTATAGAATCTAAAGTCTAAACTAGCTAGCACCTGTATAGAGAGGTCAAGCCATATAGAACCC
*
171353 AAAGTCAATATTAT
194 AAAGTCAATATTAA
*
171367 TTGGCACCTGTATAAGGAGGTTAAGCCTTATAGAATCCAAGCCCATAATAACTAGCATCTATATA
1 CTGGCACCTGTATAAGGAGGTTAAGCCTTATAGAATCCAAGCCCATAATAACTAGCATCTATATA
* * * *
171432 AAGAGGTCAAGCCCTATAAAACCCGAAGTCCACATTAGCT-ACACTTATATAAGGAGGTCAAGCC
66 AAGAGGTCAAGCCCTATAAAACCCAAAGTCCACACTAGCTGACACCTATATAAGGAGGTCAAACC
* * *
171496 CTATA-AAGTC-AAAGTCTAAACTAGCTGGCACCTGTATAGGGGGGTCAAGCGC-TATAGAACCC
131 CTATAGAA-TCTAAAGTCTAAACTAGCTAGCACCTGTATAGAGAGGTCAAGC-CATATAGAACCC
* *
171558 TAAGTCCATATTAA
194 AAAGTCAATATTAA
* * * * * * * * *
171572 CTGGCACTTGTAT-AGAGAGGTTAAGCCTTATATAACTCAAAGTCCACAGTAGCT-GACACCTGT
1 CTGGCACCTGTATAAG-GAGGTTAAGCCTTATAGAA-TCCAAGCCCATAATAACTAG-CATCTAT
** * * ** * * *
171635 ATAGGGAGGTTAAGCCTTATAAAACTTAAAGTCTACAATAGCT-AGCACCTATATAGGGAGGTCA
63 ATAAAGAGGTCAAGCCCTATAAAACCCAAAGTCCACACTAGCTGA-CACCTATATAAGGAGGTCA
* *
171699 AACCTTATAAAATC
127 AACCCTATAGAATC
171713 GAAGTCCACG
Statistics
Matches: 285, Mismatches: 52, Indels: 18
0.80 0.15 0.05
Matches are distributed among these distances:
204 2 0.01
205 86 0.30
206 81 0.28
207 112 0.39
208 4 0.01
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (207 bp):
CTGGCACCTGTATAAGGAGGTTAAGCCTTATAGAATCCAAGCCCATAATAACTAGCATCTATATA
AAGAGGTCAAGCCCTATAAAACCCAAAGTCCACACTAGCTGACACCTATATAAGGAGGTCAAACC
CTATAGAATCTAAAGTCTAAACTAGCTAGCACCTGTATAGAGAGGTCAAGCCATATAGAACCCAA
AGTCAATATTAA
Found at i:171634 original size:257 final size:258
Alignment explanation
Indices: 171170--171655 Score: 663
Period size: 257 Copynumber: 1.9 Consensus size: 258
171160 CTGGAACCTG
* * * *
171170 TATAAGGAGGTCAAGCACTATAAAATCTAAGTCCACACTAGCTAGCACTCGTATAAGGAGGTCAA
1 TATAAAGAGGTCAAGCACTATAAAACCGAAGTCCACACTAGCTAGCACTCATATAAGGAGGTCAA
* *
171235 GCCCTATAAAACCTAAAGTCCACACTAGCTGGCACCTGTATAGGGAGGTCAAACCCTATAGAATC
66 GCCCTATAAAACCTAAAGTCCAAACTAGCTGGCACCTGTATAGGGAGGTCAAACCCTATAGAACC
* * * * *
171300 TAAAGTCTATATTAGCTAGCACTTGTATAGAGAGGTCAGGCCATATAGAACCCAAAGTCAATATT
131 TAAAGTCCATATTAACTAGCACTTGTATAGAGAGGTCAAGCCATATAGAACCCAAAGTCAACAGT
** *
171365 ATTTGGCACCTGTATAAGGAGGTTAAGCCTTATAGAATCCAAGCCCATAATAACTAGCATCTA
196 AGCTGACACCTGTATAAGGAGGTTAAGCCTTATAGAATCCAAGCCCATAATAACTAGCATCTA
* * *
171428 TATAAAGAGGTCAAGCCCTATAAAACCCGAAGTCCACATTAGCTA-CACTTATATAAGGAGGTCA
1 TATAAAGAGGTCAAGCACTATAAAA-CCGAAGTCCACACTAGCTAGCACTCATATAAGGAGGTCA
** * * * *
171492 AGCCCTATAAAGTC-AAAGTCTAAACTAGCTGGCACCTGTATAGGGGGGTCAAGCGCTATAGAAC
65 AGCCCTATAAAACCTAAAGTCCAAACTAGCTGGCACCTGTATAGGGAGGTCAAACCCTATAGAA-
* * * * * *
171556 CCT-AAGTCCATATTAACTGGCACTTGTATAGAGAGGTTAAGCCTTATATAACTCAAAGTCCACA
129 CCTAAAGTCCATATTAACTAGCACTTGTATAGAGAGGTCAAGCCATATAGAACCCAAAGTCAACA
*
171620 GTAGCTGACACCTGTATAGGGAGGTTAAGCCTTATA
194 GTAGCTGACACCTGTATAAGGAGGTTAAGCCTTATA
171656 AAACTTAAAG
Statistics
Matches: 196, Mismatches: 30, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
257 126 0.64
258 54 0.28
259 16 0.08
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (258 bp):
TATAAAGAGGTCAAGCACTATAAAACCGAAGTCCACACTAGCTAGCACTCATATAAGGAGGTCAA
GCCCTATAAAACCTAAAGTCCAAACTAGCTGGCACCTGTATAGGGAGGTCAAACCCTATAGAACC
TAAAGTCCATATTAACTAGCACTTGTATAGAGAGGTCAAGCCATATAGAACCCAAAGTCAACAGT
AGCTGACACCTGTATAAGGAGGTTAAGCCTTATAGAATCCAAGCCCATAATAACTAGCATCTA
Found at i:171638 original size:104 final size:103
Alignment explanation
Indices: 171086--171721 Score: 460
Period size: 104 Copynumber: 6.2 Consensus size: 103
171076 CACCTGTCTA
* ** * * * * * * * *
171086 ATAGAACCTAAAGTCCACTTTAGCTGGTACCTATATAGGGAGATTAAGCCTTATAGAATCC-ACG
1 ATAGAATC-AAAGTCCACACTAGCTAGCACCTGTATAGGGAGGTCAAGCCCTATAGAACCCTAAG
* * * *
171150 TCAACACTAGCTGGAACCTGTATAAGGAGGTCAAGCACT
65 TCCACATTAGCTGGCACCTGTATAAGGAGGTCAAGCCCT
* * * *
171189 ATAAAATCTAAGTCCACACTAGCTAGCA-CTCGTATAAGGAGGTCAAGCCCTATA-AAACCTAAA
1 ATAGAATCAAAGTCCACACTAGCTAGCACCT-GTATAGGGAGGTCAAGCCCTATAGAACCCT-AA
* * *
171252 GTCCACACTAGCTGGCACCTGTATAGGGAGGTCAAACCCT
64 GTCCACATTAGCTGGCACCTGTATAAGGAGGTCAAGCCCT
* * * * * * * *
171292 ATAGAATCTAAAGTCTATATTAGCTAGCACTTGTATAGAGAGGTCAGGCCATATAGAACCCAAAG
1 ATAGAATC-AAAGTCCACACTAGCTAGCACCTGTATAGGGAGGTCAAGCCCTATAGAACCCTAAG
* * ** * *
171357 TCAATATTATTTGGCACCTGTATAAGGAGGTTAAGCCTT
65 TCCACATTAGCTGGCACCTGTATAAGGAGGTCAAGCCCT
* * * * * * * ** * *
171396 ATAGAATCCAAGCCCATAATAACTAGCATCTATATAAAGAGGTCAAGCCCTATAAAACCCGAAGT
1 ATAGAATCAAAGTCCACACTAGCTAGCACCTGTATAGGGAGGTCAAGCCCTATAGAACCCTAAGT
* * *
171461 CCACATTAGCT-ACACTTATATAAGGAGGTCAAGCCCT
66 CCACATTAGCTGGCACCTGTATAAGGAGGTCAAGCCCT
* * * * *
171498 ATA-AAGTCAAAGTCTAAACTAGCTGGCACCTGTATAGGGGGGTCAAGCGCTATAGAACCCTAAG
1 ATAGAA-TCAAAGTCCACACTAGCTAGCACCTGTATAGGGAGGTCAAGCCCTATAGAACCCTAAG
* * * * *
171562 TCCATATTAACTGGCACTTGTAT-AGAGAGGTTAAGCCTT
65 TCCACATTAGCTGGCACCTGTATAAG-GAGGTCAAGCCCT
* * * * * *
171601 ATATAACTCAAAGTCCACAGTAGCT-GACACCTGTATAGGGAGGTTAAGCCTTATA-AAACTTAA
1 ATAGAA-TCAAAGTCCACACTAGCTAG-CACCTGTATAGGGAGGTCAAGCCCTATAGAACCCT-A
* * * * * * *
171664 AGTCTACAATAGCTAGCACCTATATAGGGAGGTCAAACCTT
63 AGTCCACATTAGCTGGCACCTGTATAAGGAGGTCAAGCCCT
* *
171705 ATAAAATCGAAGTCCAC
1 ATAGAATCAAAGTCCAC
171722 GTTAATTGAC
Statistics
Matches: 415, Mismatches: 105, Indels: 26
0.76 0.19 0.05
Matches are distributed among these distances:
101 8 0.02
102 112 0.27
103 137 0.33
104 152 0.37
105 6 0.01
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (103 bp):
ATAGAATCAAAGTCCACACTAGCTAGCACCTGTATAGGGAGGTCAAGCCCTATAGAACCCTAAGT
CCACATTAGCTGGCACCTGTATAAGGAGGTCAAGCCCT
Found at i:172711 original size:387 final size:387
Alignment explanation
Indices: 171997--172760 Score: 1510
Period size: 387 Copynumber: 2.0 Consensus size: 387
171987 AGGGCATCAT
171997 CAATGCTGAATATATATGCTCAGATCCAATCCCATCATTCTAGCTAAGGTAAGGTCATTATTTAT
1 CAATGCTGAATATATATGCTCAGATCCAATCCCATCATTCTAGCTAAGGTAAGGTCATTATTTAT
172062 TTAATTTAAGGTCAAGTTTTATAAAAATATATATATTAGATAGAATATGTTCAATGTGCATCTTT
66 TTAATTTAAGGTCAAGTTTTATAAAAATATATATATTAGATAGAATATGTTCAATGTGCATCTTT
172127 AATAATTTTATTTGGGCCTATTTTATTTAACTATGTTGAGTTATAAATTTTTTAACTTAAGATCA
131 AATAATTTTATTTGGGCCTATTTTATTTAACTATGTTGAGTTATAAATTTTTTAACTTAAGATCA
172192 AACCCCATAAAAAATACATCAGATAAAATAAGGCCCAGTGCCATATTTAATTAATTTATTCGAGG
196 AACCCCATAAAAAATACATCAGATAAAATAAGGCCCAGTGCCATATTTAATTAATTTATTCGAGG
172257 CCTATTTTACTTAATTATGTTAGGCCAATCTTTTAAATGTTTTAAATTCACGTTGGGCCTCAGTA
261 CCTATTTTACTTAATTATGTTAGGCCAATCTTTTAAATGTTTTAAATTCACGTTGGGCCTCAGTA
172322 TTATTATTTGATCTATTACTTAATTAATTTTAGGCCCACTGGGTTAGATTAAAGGTCGGATC
326 TTATTATTTGATCTATTACTTAATTAATTTTAGGCCCACTGGGTTAGATTAAAGGTCGGATC
*
172384 CAATGCTGAATATATATGCTCGGATCCAATCCCATCATTCTAGCTAAGGTAAGGTCATTATTTAT
1 CAATGCTGAATATATATGCTCAGATCCAATCCCATCATTCTAGCTAAGGTAAGGTCATTATTTAT
172449 TTAATTTAAGGTCAAGTTTTATAAAAATATATATATTAGATAGAATATGTTCAATGTGCATCTTT
66 TTAATTTAAGGTCAAGTTTTATAAAAATATATATATTAGATAGAATATGTTCAATGTGCATCTTT
172514 AATAATTTTATTTGGGCCTATTTTATTTAACTATGTTGAGTTATAAATTTTTTAACTTAAGATCA
131 AATAATTTTATTTGGGCCTATTTTATTTAACTATGTTGAGTTATAAATTTTTTAACTTAAGATCA
*
172579 AACCCCATAAAAAATACATTAGATAAAATAAGGCCCAGTGCCATATTTAATTAATTTATTCGAGG
196 AACCCCATAAAAAATACATCAGATAAAATAAGGCCCAGTGCCATATTTAATTAATTTATTCGAGG
172644 CCTATTTTACTTAATTATGTTAGGCCAATCTTTTAAATGTTTTAAATTCACGTTGGGCCTCAGTA
261 CCTATTTTACTTAATTATGTTAGGCCAATCTTTTAAATGTTTTAAATTCACGTTGGGCCTCAGTA
172709 TTATTATTTGATCTATTACTTAATTAATTTTAGGCCCACTGGGTTAGATTAA
326 TTATTATTTGATCTATTACTTAATTAATTTTAGGCCCACTGGGTTAGATTAA
172761 TATTTTTTTA
Statistics
Matches: 375, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
387 375 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (387 bp):
CAATGCTGAATATATATGCTCAGATCCAATCCCATCATTCTAGCTAAGGTAAGGTCATTATTTAT
TTAATTTAAGGTCAAGTTTTATAAAAATATATATATTAGATAGAATATGTTCAATGTGCATCTTT
AATAATTTTATTTGGGCCTATTTTATTTAACTATGTTGAGTTATAAATTTTTTAACTTAAGATCA
AACCCCATAAAAAATACATCAGATAAAATAAGGCCCAGTGCCATATTTAATTAATTTATTCGAGG
CCTATTTTACTTAATTATGTTAGGCCAATCTTTTAAATGTTTTAAATTCACGTTGGGCCTCAGTA
TTATTATTTGATCTATTACTTAATTAATTTTAGGCCCACTGGGTTAGATTAAAGGTCGGATC
Found at i:173966 original size:168 final size:171
Alignment explanation
Indices: 173638--173981 Score: 595
Period size: 168 Copynumber: 2.0 Consensus size: 171
173628 TTATGTGCTT
*
173638 GTTAAGATGCTTTGGATGATGACATTTTCATGCTTGCAGATGCTTGATGTTTTTGATATGATTTT
1 GTTAAGATGCTTTGGATGATGACATTTTCATGCTTGCAGATGCTTGATGTTTTTGATATAATTTT
*
173703 AGTTCATGACATGTTTGATAATATGCTTGTTTGATGTGTGCTGAAATTTGATTTTGTAAAACCAA
66 AGTTCATGACATG-TT-AT-ATATGCTTGTTTGATGTGTGCTCAAATTTGATTTTGTAAAACCAA
173768 ACCAAGTTAGACTAAAATTGACCCAAATAATAGGATTAATCTTG
128 ACCAAGTTAGACTAAAATTGACCCAAATAATAGGATTAATCTTG
* * *
173812 GTTAAGATGCTTTGGATGATGACATTTTCATGCTTGTAGATGCTTGATGTTTTTTATGTAATTTT
1 GTTAAGATGCTTTGGATGATGACATTTTCATGCTTGCAGATGCTTGATGTTTTTGATATAATTTT
173877 AGTTCATGACATG-T-T-TATGCTTGTTTGATGTGTGCTCAAATTTGATTTTGTAAAACCAAACC
66 AGTTCATGACATGTTATATATGCTTGTTTGATGTGTGCTCAAATTTGATTTTGTAAAACCAAACC
173939 AAGTTAGACTAAAATTGACCCAAATAATAGGATTAATCTTG
131 AAGTTAGACTAAAATTGACCCAAATAATAGGATTAATCTTG
173980 GT
1 GT
173982 CTATTATTTT
Statistics
Matches: 165, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
168 89 0.54
170 1 0.01
172 1 0.01
174 74 0.45
ACGTcount: A:0.29, C:0.11, G:0.19, T:0.40
Consensus pattern (171 bp):
GTTAAGATGCTTTGGATGATGACATTTTCATGCTTGCAGATGCTTGATGTTTTTGATATAATTTT
AGTTCATGACATGTTATATATGCTTGTTTGATGTGTGCTCAAATTTGATTTTGTAAAACCAAACC
AAGTTAGACTAAAATTGACCCAAATAATAGGATTAATCTTG
Found at i:177450 original size:79 final size:78
Alignment explanation
Indices: 177338--177539 Score: 210
Period size: 79 Copynumber: 2.6 Consensus size: 78
177328 AATAACGAGG
* * * * * * * * *
177338 TTGGAGTGTCCCCTTGAAAATGACAGGGCTGGAGTGTCCCCGATTGTGAGAAATCGATGA-TT-A
1 TTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-ATTTGA
177401 GAAAAAAACATCGGGA
65 GAAAAAAAC--CGGGA
* *
177417 TTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGG
1 TTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATA-TTTGA
* * *
177482 GAATAAAGCCGGGG
65 GAAAAAAACCGGGA
**
177496 TTGGAGTATCCCCTCGGAGGTAACGGGGTTGGAGTATCCCCGAT
1 TTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGAT
177540 GAAATAACGA
Statistics
Matches: 103, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
78 1 0.01
79 93 0.90
80 2 0.02
81 7 0.07
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (78 bp):
TTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTGAG
AAAAAAACCGGGA
Found at i:177547 original size:28 final size:28
Alignment explanation
Indices: 177491--177568 Score: 93
Period size: 28 Copynumber: 2.8 Consensus size: 28
177481 GGAATAAAGC
*** **
177491 CGGGGTTGGAGTATCCCCTCGGAGGTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
177519 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
* *
177547 CGAGGTTGGAGTATCCTCGATG
1 CGGGGTTGGAGTATCCCCGATG
177569 GTAAAAAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:177793 original size:134 final size:132
Alignment explanation
Indices: 177523--177793 Score: 368
Period size: 131 Copynumber: 2.0 Consensus size: 132
177513 AGGTAACGGG
* *
177523 GTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATGGTAAAAAATTGGTGTTTTT
1 GTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCCCAATGGTAAAAAATTGGTGTTTTT
* *
177588 GGAAATAAAATCGGAGCCGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAATCG
66 AGAAATAAAATCGGAGCCGGAGTATCCCCGATTAAAGGAAAATTAGTGTTTTGAAAATAAAATCG
*
177653 GG
131 GA
* * * *
177655 GTTGGAGTATCCCCGATG-ATTAACGGGGTTGGAGTATCCCCAATTGTGAAAAATTGGTGTTTTT
1 GTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCCCAATGGTAAAAAATTGGTG-----
** *
177719 TTTTTAGAAATAAAATCGGAGTTGGAGTAT-CCCGATTATA-GAAAATTAGTGTTTTGAAAATAA
61 TTTTTAGAAATAAAATCGGAGCCGGAGTATCCCCGATTAAAGGAAAATTAGTGTTTTGAAAATAA
177782 AATCGGA
126 AATCGGA
177789 GTTGG
1 GTTGG
177794 GATACCCCCG
Statistics
Matches: 122, Mismatches: 12, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
131 35 0.29
132 18 0.15
134 33 0.27
135 9 0.07
136 27 0.22
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.31
Consensus pattern (132 bp):
GTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCCCAATGGTAAAAAATTGGTGTTTTT
AGAAATAAAATCGGAGCCGGAGTATCCCCGATTAAAGGAAAATTAGTGTTTTGAAAATAAAATCG
GA
Found at i:177803 original size:134 final size:132
Alignment explanation
Indices: 177523--177805 Score: 358
Period size: 134 Copynumber: 2.1 Consensus size: 132
177513 AGGTAACGGG
* * *
177523 GTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATGGTAAAAAATTGGTGTTTTT
1 GTTGGAGTACCCCCGATGAAATAACGAGGTTGGAGTATCCCCAATGGTAAAAAATTGGTGTTTTT
* *
177588 GGAAATAAAATCGGAGCCGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAATCG
66 AGAAATAAAATCGGAGCCGGAGTATCCCCGATTAAAGGAAAATTAGTGTTTTGAAAATAAAATCG
*
177653 GG
131 GA
* * * * *
177655 GTTGGAGTATCCCCGATG-ATTAACGGGGTTGGAGTATCCCCAATTGTGAAAAATTGGTGTTTTT
1 GTTGGAGTACCCCCGATGAAATAACGAGGTTGGAGTATCCCCAATGGTAAAAAATTGGTG-----
** *
177719 TTTTTAGAAATAAAATCGGAGTTGGAGTAT-CCCGATTATA-GAAAATTAGTGTTTTGAAAATAA
61 TTTTTAGAAATAAAATCGGAGCCGGAGTATCCCCGATTAAAGGAAAATTAGTGTTTTGAAAATAA
177782 AATCGGA
126 AATCGGA
177789 GTTGG-GATACCCCCGAT
1 GTTGGAG-TACCCCCGAT
177806 TAAGAAGAAT
Statistics
Matches: 132, Mismatches: 13, Indels: 10
0.85 0.08 0.06
Matches are distributed among these distances:
131 35 0.27
132 18 0.14
133 1 0.01
134 42 0.32
135 9 0.07
136 27 0.20
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (132 bp):
GTTGGAGTACCCCCGATGAAATAACGAGGTTGGAGTATCCCCAATGGTAAAAAATTGGTGTTTTT
AGAAATAAAATCGGAGCCGGAGTATCCCCGATTAAAGGAAAATTAGTGTTTTGAAAATAAAATCG
GA
Found at i:179448 original size:20 final size:20
Alignment explanation
Indices: 179422--179474 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
179412 GTAGCCAAAC
* *
179422 TTGTATCGATACAC-CAAAG
1 TTGTATCGATACACAAAAAA
179441 TATGTATCGATACACAAAAAA
1 T-TGTATCGATACACAAAAAA
179462 TTGTATCGATACA
1 TTGTATCGATACA
179475 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 1 0.03
20 25 0.83
21 4 0.13
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:185639 original size:13 final size:13
Alignment explanation
Indices: 185621--185659 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
185611 ACATTTTTCT
185621 TTGTATCGATACA
1 TTGTATCGATACA
185634 TTGTATCGATACA
1 TTGTATCGATACA
*
185647 CTGTATCGATACA
1 TTGTATCGATACA
185660 GGGGGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:185814 original size:20 final size:20
Alignment explanation
Indices: 185771--185816 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
185761 AAATCTTTTG
185771 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
185792 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
185812 CAAAA
1 CAAAA
185817 CCAGCATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:187310 original size:22 final size:20
Alignment explanation
Indices: 187268--187310 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
187258 GTGTTTAATG
*
187268 TATTTGCTTGACTTTGTATT
1 TATTTGCTTGACTTTGAATT
187288 TATTTGCATTGTACTTTGAATT
1 TATTTGC-TTG-ACTTTGAATT
187310 T
1 T
187311 TAATCTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 3 0.15
22 10 0.50
ACGTcount: A:0.19, C:0.09, G:0.14, T:0.58
Consensus pattern (20 bp):
TATTTGCTTGACTTTGAATT
Found at i:188236 original size:20 final size:20
Alignment explanation
Indices: 188210--188262 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
188200 GTAGCCAAAC
* *
188210 TTGTATCGATACAC-CAAAG
1 TTGTATCGATACACAAAAAA
188229 TATGTATCGATACACAAAAAA
1 T-TGTATCGATACACAAAAAA
188250 TTGTATCGATACA
1 TTGTATCGATACA
188263 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 1 0.03
20 25 0.83
21 4 0.13
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:189595 original size:10 final size:10
Alignment explanation
Indices: 189582--189610 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
189572 CAATGGAATA
189582 GTGTTTTTTT
1 GTGTTTTTTT
189592 GTGTTTTTTT
1 GTGTTTTTTT
189602 G-GTTTTTTT
1 GTGTTTTTTT
189611 TGCTAAAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 8 0.42
10 11 0.58
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (10 bp):
GTGTTTTTTT
Found at i:190149 original size:20 final size:20
Alignment explanation
Indices: 190124--190176 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
190114 AACTTCCTAG
190124 ATGTATCGATACACAGAAAA
1 ATGTATCGATACACAGAAAA
190144 ATGTATCGATACACAGAAAA
1 ATGTATCGATACACAGAAAA
190164 ATGTATCGATACA
1 ATGTATCGATACA
190177 TTTCCTTGGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.23
Consensus pattern (20 bp):
ATGTATCGATACACAGAAAA
Found at i:190218 original size:13 final size:13
Alignment explanation
Indices: 190200--190251 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
190190 AGCTTCCTAG
190200 CGATACATTGTAT
1 CGATACATTGTAT
190213 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
190232 CGATACATTGTAT
1 CGATACATTGTAT
190245 CGATACA
1 CGATACA
190252 ATACTTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 17 0.52
15 2 0.06
16 2 0.06
17 2 0.06
19 10 0.30
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:190232 original size:19 final size:19
Alignment explanation
Indices: 190208--190272 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
190198 AGCGATACAT
190208 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
190227 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
*
190240 TGTATCGATACAATACTTA
1 TGTATCGATACAAAACTTA
190259 TGTATCGATACAAA
1 TGTATCGATACAAA
190273 TCGCTGAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
13 11 0.28
14 1 0.03
16 2 0.05
18 1 0.03
19 24 0.62
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.34
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:190241 original size:32 final size:32
Alignment explanation
Indices: 190200--190270 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
190190 AGCTTCCTAG
190200 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
190232 CGATACATTGTATCGATACAATACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
190264 CGATACA
1 CGATACA
190271 AATCGCTGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:190334 original size:21 final size:22
Alignment explanation
Indices: 190308--190365 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
190298 GTTGGGACCT
* *
190308 TGTATCGATACATTTGTA-GAA
1 TGTATCGATACATTTGCACAAA
*
190329 TGTATCGATACA-TTCCACAAA
1 TGTATCGATACATTTGCACAAA
190350 TGTATCGATACATTTG
1 TGTATCGATACATTTG
190366 GATAAAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 3 0.10
21 26 0.84
22 2 0.06
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (22 bp):
TGTATCGATACATTTGCACAAA
Found at i:191582 original size:20 final size:20
Alignment explanation
Indices: 191559--191633 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
191549 AAGTACCTAG
* *
191559 ATGTATCAATATATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
191579 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
191599 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
191619 ATGTATCGATACATT
1 ATGTATCGATACATT
191634 CTGTCTTTTT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:203368 original size:15 final size:16
Alignment explanation
Indices: 203348--203377 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
203338 TCTGTCAAAC
203348 CCGCCAGTG-TTGGTA
1 CCGCCAGTGCTTGGTA
203363 CCGCCAGTGCTTGGT
1 CCGCCAGTGCTTGGT
203378 CGTCCTTTAA
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:0.10, C:0.30, G:0.33, T:0.27
Consensus pattern (16 bp):
CCGCCAGTGCTTGGTA
Found at i:205627 original size:8 final size:8
Alignment explanation
Indices: 205614--205665 Score: 54
Period size: 8 Copynumber: 6.6 Consensus size: 8
205604 CATACACCAA
205614 AAAAAAAC
1 AAAAAAAC
205622 -AAAAAAC
1 AAAAAAAC
205629 AAAAAAAC
1 AAAAAAAC
* *
205637 CAAGAAA-
1 AAAAAAAC
*
205644 AAAATAAC
1 AAAAAAAC
205652 AAAAAAAC
1 AAAAAAAC
205660 AGAAAA
1 A-AAAA
205666 TGGTCTAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
7 11 0.31
8 20 0.57
9 4 0.11
ACGTcount: A:0.83, C:0.12, G:0.04, T:0.02
Consensus pattern (8 bp):
AAAAAAAC
Found at i:207023 original size:84 final size:84
Alignment explanation
Indices: 206880--207039 Score: 248
Period size: 84 Copynumber: 1.9 Consensus size: 84
206870 CGTTCATCTC
* **
206880 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGACACTTTTTCAAAGCC
1 TTCAAAGCCCACAAGTCAATGGCACCCTTTCAAAGCCCACAAGTCAGTGACACACTTTCAAAGCC
206945 CACAAGTTAGTGGCACATT
66 CACAAGTTAGTGGCACATT
* * *
206964 TTCAAAGCCCATAAGTCAATGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACACTTTCAAAGCC
1 TTCAAAGCCCACAAGTCAATGGCACCCTTTCAAAGCCCACAAGTCAGTGACACACTTTCAAAGCC
* *
207029 TATAAGTTAGT
66 CACAAGTTAGT
207040 AGCCCACAAG
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
84 68 1.00
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (84 bp):
TTCAAAGCCCACAAGTCAATGGCACCCTTTCAAAGCCCACAAGTCAGTGACACACTTTCAAAGCC
CACAAGTTAGTGGCACATT
Found at i:207110 original size:36 final size:37
Alignment explanation
Indices: 207045--207115 Score: 126
Period size: 36 Copynumber: 1.9 Consensus size: 37
207035 TTAGTAGCCC
*
207045 ACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCT
1 ACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCT
207082 ACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGT
1 ACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGT
207116 TAGTGGCACC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 19 0.58
37 14 0.42
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.23
Consensus pattern (37 bp):
ACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCT
Found at i:207221 original size:32 final size:34
Alignment explanation
Indices: 207141--207231 Score: 106
Period size: 32 Copynumber: 2.9 Consensus size: 34
207131 AAAGCTCACA
* *
207141 AGTCAGTGGC-ACTCTTTTCAAAGCCCACAAGCT
1 AGTCGGTGGCAACTCTTTTCAAAGCCCACAAGCG
207174 AGT-GGT---AACTCTTTTCAAAGCCCA-AA-CG
1 AGTCGGTGGCAACTCTTTTCAAAGCCCACAAGCG
*
207202 AGTCGGTGGCAACTCTTTTCAAAGGCCACA
1 AGTCGGTGGCAACTCTTTTCAAAGCCCACA
207232 CAAGTTAGTG
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
28 4 0.08
29 5 0.10
30 17 0.35
32 19 0.39
33 4 0.08
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (34 bp):
AGTCGGTGGCAACTCTTTTCAAAGCCCACAAGCG
Found at i:207243 original size:32 final size:29
Alignment explanation
Indices: 206880--207250 Score: 225
Period size: 28 Copynumber: 13.1 Consensus size: 29
206870 CGTTCATCTC
*
206880 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
*
206908 TTCAAAGCCCACAAGTCAGTGACACT-TT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
* *
206936 TTCAAAGCCCACAAGTTAGTGGCAC-ATT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
* * *
206964 TTCAAAGCCCATAAGTCAATGGCA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
*
206992 TTCAAAGCCCACAAGTCAGTGGCACAC-T
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
* * * * * * **
207020 TTCAAAGCCTATAAGTTAGTAGCCCACAA
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
* ** * * *** **
207049 GTCAGTGGCACTCTTTTCA-AAGC-C-C--
1 TTCA-AAGCCCACAAGTCAGTGGCACTCTT
* * * *
207074 -AC-AAGTCTACAAGTCAGTGGCA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
* *
207100 TTCAAAGCCCACAAGTTAGTGGCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
*
207128 TTCAAAGCTCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTT
*
207157 TTCAAAGCCCACAAG-CTAGTGGTAACTCTT
1 TTCAAAGCCCACAAGTC-AGTGG-CACTCTT
* *
207187 TTCAAAGCCCAAACGAGTCGGTGGCAACTCTT
1 TTCAAAGCCC--ACAAGTCAGTGGC-ACTCTT
*
207219 TTCAAAGGCCACACAAGTTAGTGGCAC-CTT
1 TTCAAA-GCC-CACAAGTCAGTGGCACTCTT
207249 TT
1 TT
207251 AAAAAAAAAC
Statistics
Matches: 263, Mismatches: 57, Indels: 44
0.72 0.16 0.12
Matches are distributed among these distances:
22 5 0.02
23 2 0.01
24 2 0.01
27 2 0.01
28 162 0.62
29 28 0.11
30 25 0.10
31 2 0.01
32 30 0.11
33 4 0.02
34 1 0.00
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.24
Consensus pattern (29 bp):
TTCAAAGCCCACAAGTCAGTGGCACTCTT
Found at i:208119 original size:20 final size:20
Alignment explanation
Indices: 208096--208170 Score: 105
Period size: 20 Copynumber: 3.8 Consensus size: 20
208086 AAGTACCCAG
208096 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
208116 ATGTATTGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
208136 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
208156 ATGTATCGATACATT
1 ATGTATCGATACATT
208171 CTGTCTTTTT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:212308 original size:19 final size:19
Alignment explanation
Indices: 212284--212340 Score: 69
Period size: 19 Copynumber: 3.0 Consensus size: 19
212274 CTACCAGTTT
* *
212284 CATGTATCAATACAATGTG
1 CATGTATCGATACAATGTA
* **
212303 CATGTATCGATATAATAAA
1 CATGTATCGATACAATGTA
212322 CATGTATCGATACAATGTA
1 CATGTATCGATACAATGTA
212341 TCGATACAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGTA
Found at i:212341 original size:13 final size:13
Alignment explanation
Indices: 212323--212349 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
212313 TATAATAAAC
212323 ATGTATCGATACA
1 ATGTATCGATACA
212336 ATGTATCGATACA
1 ATGTATCGATACA
212349 A
1 A
212350 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:212954 original size:22 final size:23
Alignment explanation
Indices: 212929--212973 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
212919 GCTCTCGTTT
*
212929 AAAATTTTCT-TCCCCTTGATAA
1 AAAATTTTCTCCCCCCTTGATAA
212951 AAAATTTTCTCCCCCCTTGATAA
1 AAAATTTTCTCCCCCCTTGATAA
212974 TCATTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.31, C:0.27, G:0.04, T:0.38
Consensus pattern (23 bp):
AAAATTTTCTCCCCCCTTGATAA
Found at i:213011 original size:31 final size:31
Alignment explanation
Indices: 212948--213011 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
212938 TTCCCCTTGA
**
212948 TAAAAAATTTTCTCCCCCCTTGATAATCATT
1 TAAAAAATTTTCTCCCCCCTTGATAAAAATT
212979 TAAAAAATTTTCT-CCCCCTTGATAAAAAATT
1 TAAAAAATTTTCTCCCCCCTTGAT-AAAAATT
213010 TA
1 TA
213012 TTTTCAAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 10 0.33
31 20 0.67
ACGTcount: A:0.38, C:0.22, G:0.03, T:0.38
Consensus pattern (31 bp):
TAAAAAATTTTCTCCCCCCTTGATAAAAATT
Found at i:213369 original size:33 final size:33
Alignment explanation
Indices: 213332--213395 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
213322 TGCACCAAAG
*
213332 TGCTCACCCATGTGCTGCGAAAGTGATGTGAAA
1 TGCTCACCCATGTGCTGCGAAAGTGACGTGAAA
* * *
213365 TGCTCACTCATGTGTTGTGAAAGTGACGTGA
1 TGCTCACCCATGTGCTGCGAAAGTGACGTGA
213396 TCAACTCTCG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (33 bp):
TGCTCACCCATGTGCTGCGAAAGTGACGTGAAA
Found at i:219439 original size:3 final size:3
Alignment explanation
Indices: 219431--219455 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
219421 TCCGAGTCAG
219431 CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT C
219456 TTCTTCATCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:221190 original size:13 final size:13
Alignment explanation
Indices: 221172--221196 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
221162 CAATTGTGCA
221172 TGTATCGATACAG
1 TGTATCGATACAG
221185 TGTATCGATACA
1 TGTATCGATACA
221197 AAGCGTAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:221778 original size:21 final size:21
Alignment explanation
Indices: 221754--221796 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
221744 GCTCTCGTTT
221754 AAAAA-TTTCTCCCTCTTGATA
1 AAAAATTTTCTCCC-CTTGATA
221775 AAAAATTTTCTCCCCTTGATA
1 AAAAATTTTCTCCCCTTGATA
221796 A
1 A
221797 TCGTTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.35, C:0.23, G:0.05, T:0.37
Consensus pattern (21 bp):
AAAAATTTTCTCCCCTTGATA
Found at i:223716 original size:13 final size:13
Alignment explanation
Indices: 223698--223724 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
223688 ATAATAACCC
223698 ATGTATCGATACA
1 ATGTATCGATACA
223711 ATGTATCGATACA
1 ATGTATCGATACA
223724 A
1 A
223725 AGAATATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:230163 original size:22 final size:22
Alignment explanation
Indices: 230116--230168 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
230106 TATTTTTACT
** *
230116 TAAAAACATTTGATTTAAGGTT
1 TAAAAACATTTGATTTAAACTC
230138 TAAAAACATTTG-TTTATAACTC
1 TAAAAACATTTGATTTA-AACTC
230160 T-AAAACATT
1 TAAAAACATT
230169 CATTGATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 12 0.44
22 15 0.56
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (22 bp):
TAAAAACATTTGATTTAAACTC
Found at i:231845 original size:20 final size:20
Alignment explanation
Indices: 231822--231859 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
231812 CTTAATACAT
231822 TTAAAATATAAAAAATAACA
1 TTAAAATATAAAAAATAACA
* *
231842 TTAATATATAAAATATAA
1 TTAAAATATAAAAAATAA
231860 AATATAATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (20 bp):
TTAAAATATAAAAAATAACA
Found at i:231857 original size:7 final size:7
Alignment explanation
Indices: 231823--231866 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
231813 TTAATACATT
231823 TAAAATA
1 TAAAATA
*
231830 TAAAAAA
1 TAAAATA
*
231837 TAACAT-
1 TAAAATA
*
231843 TAATATA
1 TAAAATA
231850 TAAAATA
1 TAAAATA
231857 TAAAATA
1 TAAAATA
231864 TAA
1 TAA
231867 TTCAATTAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
6 5 0.16
7 26 0.84
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (7 bp):
TAAAATA
Found at i:234335 original size:24 final size:24
Alignment explanation
Indices: 234286--234337 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
234276 GATTATTAAT
* * *
234286 TTTTACTTTCATTTTTTATTTTAA
1 TTTTAATTTCATTTTTAATTTGAA
234310 TTTTAATTTCA-TTTTAATTGTGAA
1 TTTTAATTTCATTTTTAATT-TGAA
234334 TTTT
1 TTTT
234338 TCTACTAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.23, C:0.06, G:0.04, T:0.67
Consensus pattern (24 bp):
TTTTAATTTCATTTTTAATTTGAA
Found at i:236016 original size:155 final size:155
Alignment explanation
Indices: 235732--236044 Score: 344
Period size: 155 Copynumber: 2.0 Consensus size: 155
235722 TTGAAAGTAC
* * *
235732 ACCTTAGGAGCTTTTGGTCATTTTCCCTAGAATCCAGTCCTAGGTAGTCATCGGGTCACTTTTAT
1 ACCTTAGGAGATTTTGGTCAATTTCCCTAAAATCCAGTCCTAGGTAGTCATCGGGTCACTTTTAT
* * * * *
235797 GACAAAAGTGTGCATTTAGGATAGGTTGACCTTTTTATGATCTTGTCGTGTCCTTTAAGGGTTAC
66 GACAAAAGTGTGCATTTAGGATAGATTGACCCTTTTAAGATCTTGTCGAGTCCTTTAAGAGTTAC
*
235862 CGAGATACCTTCACATCAAAGGTAT
131 CGAAATACCTTCACATCAAAGGTAT
* * ** * *
235887 ACCTTAGGAGTATTTTGGT-AATTTCTCTAAAATCGAGTTTTAGGTTGTCATTGGGTCACTTTTA
1 ACCTTAGGAG-ATTTTGGTCAATTTCCCTAAAATCCAGTCCTAGGTAGTCATCGGGTCACTTTTA
* ** * * *
235951 TG-CTAAAGATGTGTGTTTAGGATAGATTTACCCTTTTAAGATCATTTTTGAGTCCTTT-AGAGT
65 TGACAAAAG-TGTGCATTTAGGATAGATTGACCCTTTTAAGATC-TTGTCGAGTCCTTTAAGAGT
* * * * *
236014 TACTGAAATACTTTCACGTTAAATGTAT
128 TACCGAAATACCTTCACATCAAAGGTAT
236042 ACC
1 ACC
236045 CCATGGTATT
Statistics
Matches: 129, Mismatches: 26, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
154 5 0.04
155 106 0.82
156 18 0.14
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (155 bp):
ACCTTAGGAGATTTTGGTCAATTTCCCTAAAATCCAGTCCTAGGTAGTCATCGGGTCACTTTTAT
GACAAAAGTGTGCATTTAGGATAGATTGACCCTTTTAAGATCTTGTCGAGTCCTTTAAGAGTTAC
CGAAATACCTTCACATCAAAGGTAT
Found at i:239481 original size:17 final size:17
Alignment explanation
Indices: 239455--239493 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
239445 TCCGTTGATT
239455 TTTTAAATTTTTTTTAA
1 TTTTAAATTTTTTTTAA
* *
239472 TTTTAGATTTTTTTTAG
1 TTTTAAATTTTTTTTAA
239489 TTTTA
1 TTTTA
239494 TTTTATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (17 bp):
TTTTAAATTTTTTTTAA
Found at i:239514 original size:22 final size:23
Alignment explanation
Indices: 239466--239514 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 23
239456 TTTAAATTTT
* * *
239466 TTTTAATTTTAGATTTTTTTTAG
1 TTTTAATTTTAGATATTTTTGAA
*
239489 TTTT-ATTTTATATATTTTTGAA
1 TTTTAATTTTAGATATTTTTGAA
239511 TTTT
1 TTTT
239515 TATAATTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.71
Consensus pattern (23 bp):
TTTTAATTTTAGATATTTTTGAA
Found at i:241985 original size:208 final size:210
Alignment explanation
Indices: 241616--242039 Score: 573
Period size: 208 Copynumber: 2.0 Consensus size: 210
241606 CATTAAACCG
* *
241616 TTTATTATTGCAGAAATTAGTTTCTAATGCTTTCTACGGACTTCATTACGGTAAATGCCATGCGG
1 TTTATTATTGCAGAAATTAGTTGCTAATGCTTTCTACGGACTTCATTACAGTAAATGCCATGCGG
* * ** * * *
241681 AGCATGTCAATCCGTTGGTTGTGATTGGCAGAAGCGCTTGCTGCCTTCTTGTTGGACAACTCCTA
66 AGCATGTCAATCCGTTGGTTGTGACTGCCAGAAGCGCTCACTACCTTCTTGCTGGACAACTCCCA
* * * *
241746 TTAAAGCATTAAATCATTCTAATTATATTATTTTACGTTT-ATTGAATTAGTTTCCAGTTATAAG
131 TCAAAACATTAAATCATTCTAATGATATTATTTTACGTTTGATTGAATTAGTTTCCAATTATAAG
241810 TTTGCAGAAATTAAT
196 TTTGCAGAAATTAAT
* * * * * *
241825 TTTATTGTTTCAGAAATTAGTTGCTAATGTTTTGTACGGGCTTCATTACAG-AAATGTCATGCGG
1 TTTATTATTGCAGAAATTAGTTGCTAATGCTTTCTACGGACTTCATTACAGTAAATGCCATGCGG
*** * * *
241889 AGCATGTCAATTTTTTGGTTGTGGCTGCCAGACGTGCTCACTACCTTCTTGCTGGACAACTCCCA
66 AGCATGTCAATCCGTTGGTTGTGACTGCCAGAAGCGCTCACTACCTTCTTGCTGGACAACTCCCA
* * * *
241954 TCAAAACATTAAATCATTCTAATGGTATTATTTTACGTTTGCTTTAATTAGTTTCTAATTATAAG
131 TCAAAACATTAAATCATTCTAATGATATTATTTTACGTTTGATTGAATTAGTTTCCAATTATAAG
242019 TTTGCAGAAATTAAT
196 TTTGCAGAAATTAAT
242034 TTTATT
1 TTTATT
242040 TGTCTTAATT
Statistics
Matches: 185, Mismatches: 29, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
208 100 0.54
209 85 0.46
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (210 bp):
TTTATTATTGCAGAAATTAGTTGCTAATGCTTTCTACGGACTTCATTACAGTAAATGCCATGCGG
AGCATGTCAATCCGTTGGTTGTGACTGCCAGAAGCGCTCACTACCTTCTTGCTGGACAACTCCCA
TCAAAACATTAAATCATTCTAATGATATTATTTTACGTTTGATTGAATTAGTTTCCAATTATAAG
TTTGCAGAAATTAAT
Found at i:254362 original size:2 final size:2
Alignment explanation
Indices: 254355--254414 Score: 52
Period size: 2 Copynumber: 31.0 Consensus size: 2
254345 CCTTAATTAA
* * * * *
254355 AT AT AT AT AT -T AT AT -T AT AC AT GT GT AG AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
254395 AT AC AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
254415 GCAAATATAA
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
1 2 0.04
2 44 0.96
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (2 bp):
AT
Found at i:254440 original size:15 final size:15
Alignment explanation
Indices: 254420--254471 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
254410 TATATGCAAA
254420 TATAAATTTTAAAAT
1 TATAAATTTTAAAAT
*
254435 TATAAATTTTTAATAT
1 TATAAA-TTTTAAAAT
*
254451 CTA-ATATTTTAAAAT
1 -TATAAATTTTAAAAT
*
254466 AATAAA
1 TATAAA
254472 AAATAAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
14 1 0.03
15 16 0.55
16 10 0.34
17 2 0.07
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
TATAAATTTTAAAAT
Found at i:254485 original size:17 final size:17
Alignment explanation
Indices: 254461--254494 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
254451 CTAATATTTT
254461 AAAATAATA-AAAAATA
1 AAAATAATATAAAAATA
254477 AAAATTAATATAAAAATA
1 AAAA-TAATATAAAAATA
254495 TTTAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 5 0.31
18 7 0.44
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAATAATATAAAAATA
Found at i:255048 original size:35 final size:36
Alignment explanation
Indices: 255000--255078 Score: 90
Period size: 35 Copynumber: 2.2 Consensus size: 36
254990 TTAAGTATTA
* * *
255000 ATTATCTTAATATTAAAAGT-ATTATTATTATTAAAAT
1 ATTAT-TTAATATTAAAA-TAATAATAATTATTAAAAC
*
255037 ATTATTT-ATATTAATATAATAATAATTATTAAAAC
1 ATTATTTAATATTAAAATAATAATAATTATTAAAAC
255072 ATTATTT
1 ATTATTT
255079 TTCATTTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
34 1 0.03
35 29 0.78
36 2 0.05
37 5 0.14
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (36 bp):
ATTATTTAATATTAAAATAATAATAATTATTAAAAC
Found at i:255065 original size:20 final size:20
Alignment explanation
Indices: 254998--255065 Score: 50
Period size: 20 Copynumber: 3.4 Consensus size: 20
254988 ATTTAAGTAT
*
254998 TAATTATCTTAATATTAA-AA
1 TAATTATATTAATA-TAATAA
* * *
255018 GT-ATTATTATTATTAAAATAT
1 -TAATTA-TATTAATATAATAA
*
255039 TATTTATATTAATATAATAA
1 TAATTATATTAATATAATAA
255059 TAATTAT
1 TAATTAT
255066 TAAAACATTA
Statistics
Matches: 35, Mismatches: 9, Indels: 7
0.69 0.18 0.14
Matches are distributed among these distances:
20 24 0.69
21 11 0.31
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (20 bp):
TAATTATATTAATATAATAA
Found at i:256598 original size:21 final size:21
Alignment explanation
Indices: 256548--256600 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
256538 TAAAAATTTC
* *
256548 AATATTAAAAAAAATTATAAA
1 AATATTAAATATAATTATAAA
*
256569 AAT-TTAAATATAATTTTAAA
1 AATATTAAATATAATTATAAA
*
256589 TATATTAAATAT
1 AATATTAAATAT
256601 TATGTTTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AATATTAAATATAATTATAAA
Found at i:258300 original size:23 final size:23
Alignment explanation
Indices: 258270--258319 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
258260 GAGCATTTGT
258270 TAAAAAATAAT-TAAAATATAATA
1 TAAAAAATAATAT-AAATATAATA
*
258293 TAAAAAATAATATAAATATTATA
1 TAAAAAATAATATAAATATAATA
258316 TAAA
1 TAAA
258320 TTAATAAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 24 0.96
24 1 0.04
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (23 bp):
TAAAAAATAATATAAATATAATA
Found at i:258302 original size:12 final size:12
Alignment explanation
Indices: 258270--258308 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
258260 GAGCATTTGT
258270 TAAAAAATAAT-
1 TAAAAAATAATA
*
258281 TAAAATATAATA
1 TAAAAAATAATA
258293 TAAAAAATAATA
1 TAAAAAATAATA
258305 TAAA
1 TAAA
258309 TATTATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
TAAAAAATAATA
Found at i:258315 original size:21 final size:21
Alignment explanation
Indices: 258270--258334 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
258260 GAGCATTTGT
258270 TAAAAAATAAT-TAAAATATAATA
1 TAAAAAATAATAT-AAATAT--TA
258293 TAAAAAATAATATAAATATTA
1 TAAAAAATAATATAAATATTA
* *
258314 TATAAATTAATA-AACATATTA
1 TAAAAAATAATATAA-ATATTA
258335 AAATTTTATA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
20 2 0.05
21 18 0.47
23 17 0.45
24 1 0.03
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (21 bp):
TAAAAAATAATATAAATATTA
Found at i:258318 original size:11 final size:11
Alignment explanation
Indices: 258283--258325 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
258273 AAAATAATTA
258283 AAATATAATAT
1 AAATATAATAT
*
258294 AAAAAATAATAT
1 -AAATATAATAT
*
258306 AAATATTATAT
1 AAATATAATAT
258317 AAAT-TAATA
1 AAATATAATA
258326 AACATATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
10 4 0.15
11 13 0.48
12 10 0.37
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AAATATAATAT
Found at i:258408 original size:20 final size:20
Alignment explanation
Indices: 258357--258396 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
258347 AAAAAAATTT
*
258357 TAAATAT-TAA-ATTTTATA
1 TAAATATATAATATTTTAAA
258375 TAAATATATAATATTTTAAA
1 TAAATATATAATATTTTAAA
258395 TA
1 TA
258397 TAATTATGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 3 0.16
20 9 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TAAATATATAATATTTTAAA
Found at i:266784 original size:22 final size:22
Alignment explanation
Indices: 266759--266803 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
266749 ATAATTGAGA
266759 TATGAATAGATTTATTTAAAAG
1 TATGAATAGATTTATTTAAAAG
266781 TATGAATAGATTTATTTAAAAG
1 TATGAATAGATTTATTTAAAAG
266803 T
1 T
266804 CAAATTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.42
Consensus pattern (22 bp):
TATGAATAGATTTATTTAAAAG
Found at i:271296 original size:19 final size:20
Alignment explanation
Indices: 271252--271288 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
271242 ATATAATAAA
271252 AAATTTATTTGAATTTGAAT
1 AAATTTATTTGAATTTGAAT
271272 AAATTTATTT-AATTTGA
1 AAATTTATTTGAATTTGA
271289 CTTGATTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (20 bp):
AAATTTATTTGAATTTGAAT
Found at i:274315 original size:15 final size:15
Alignment explanation
Indices: 274297--274334 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
274287 GGGAGATCAG
274297 CTCCTCCTGCAGCAC
1 CTCCTCCTGCAGCAC
274312 CTCCTCCTGCAGCAC
1 CTCCTCCTGCAGCAC
*
274327 CACCTCCT
1 CTCCTCCT
274335 CCTCCTCCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.13, C:0.55, G:0.11, T:0.21
Consensus pattern (15 bp):
CTCCTCCTGCAGCAC
Found at i:274318 original size:18 final size:18
Alignment explanation
Indices: 274297--274340 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
274287 GGGAGATCAG
*
274297 CTCCTCCTGCAGCACCTC
1 CTCCTCCTGCACCACCTC
* *
274315 CTCCTGCAGCACCACCTC
1 CTCCTCCTGCACCACCTC
274333 CTCCTCCT
1 CTCCTCCT
274341 CCTCGTTCTA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.11, C:0.57, G:0.09, T:0.23
Consensus pattern (18 bp):
CTCCTCCTGCACCACCTC
Found at i:277336 original size:11 final size:11
Alignment explanation
Indices: 277317--277350 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
277307 TTAACCATAT
*
277317 AAAACAAGAAA
1 AAAAAAAGAAA
277328 AAAAAAAGAAA
1 AAAAAAAGAAA
277339 AAGAAAAAGAAA
1 AA-AAAAAGAAA
277351 CTGAGTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 12 0.57
12 9 0.43
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:277339 original size:6 final size:6
Alignment explanation
Indices: 277322--277350 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
277312 CATATAAAAC
277322 AAGAAA AA-AAA AAGAAA AAGAAA AAGAAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
277351 CTGAGTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:278088 original size:2 final size:2
Alignment explanation
Indices: 278081--278106 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
278071 GCAAATATTT
278081 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
278107 AAACACAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:284265 original size:13 final size:13
Alignment explanation
Indices: 284247--284271 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
284237 CATAAAATGT
284247 TGTATCGATACAA
1 TGTATCGATACAA
284260 TGTATCGATACA
1 TGTATCGATACA
284272 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:284269 original size:33 final size:33
Alignment explanation
Indices: 284227--284296 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
284217 TTCAACGATT
284227 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
284260 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
284293 TGTA
1 TGTA
284297 AGCTACTGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:284355 original size:13 final size:13
Alignment explanation
Indices: 284337--284361 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
284327 ATTACTCACA
284337 TGTATCGATACAT
1 TGTATCGATACAT
284350 TGTATCGATACA
1 TGTATCGATACA
284362 CTAATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:288077 original size:34 final size:35
Alignment explanation
Indices: 288039--288105 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
288029 CCTTACAACA
288039 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
288073 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
288106 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:288568 original size:20 final size:20
Alignment explanation
Indices: 288543--288594 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
288533 TATAAGCCAA
**
288543 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATACTTTG
288563 TGTATCGATAC-ATACTTTG
1 TGTATCGATACAATACTTTG
288582 TGTATCGATACAA
1 TGTATCGATACAA
288595 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.42
Consensus pattern (20 bp):
TGTATCGATACAATACTTTG
Found at i:289393 original size:53 final size:53
Alignment explanation
Indices: 289312--289418 Score: 196
Period size: 53 Copynumber: 2.0 Consensus size: 53
289302 AAAAAATCTC
* *
289312 CCCCTTAATCAAGTAATTCATATCAAAAATTTATTTGCACATATTTATTTTCT
1 CCCCTTAATCAAGTAATTCATATAAAAAATTTATTTGCACATATCTATTTTCT
289365 CCCCTTAATCAAGTAATTCATATAAAAAATTTATTTGCACATATCTATTTTCT
1 CCCCTTAATCAAGTAATTCATATAAAAAATTTATTTGCACATATCTATTTTCT
289418 C
1 C
289419 TCCCCCTTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.35, C:0.20, G:0.04, T:0.42
Consensus pattern (53 bp):
CCCCTTAATCAAGTAATTCATATAAAAAATTTATTTGCACATATCTATTTTCT
Found at i:289794 original size:20 final size:21
Alignment explanation
Indices: 289751--289796 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
289741 AGGTTTATGC
289751 AAGTTCTCCCCCTTAATACGA
1 AAGTTCTCCCCCTTAATACGA
* *
289772 AAGTTCTTCCCTTTAATAC-A
1 AAGTTCTCCCCCTTAATACGA
289792 AAGTT
1 AAGTT
289797 TATACAAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.35
Consensus pattern (21 bp):
AAGTTCTCCCCCTTAATACGA
Found at i:290652 original size:13 final size:13
Alignment explanation
Indices: 290634--290658 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
290624 ACTGAAGCAA
290634 TGTATCGATACAT
1 TGTATCGATACAT
290647 TGTATCGATACA
1 TGTATCGATACA
290659 ATTTGGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:293872 original size:34 final size:35
Alignment explanation
Indices: 293834--293900 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
293824 CCTTACAACA
293834 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
293868 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
293901 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:294363 original size:20 final size:20
Alignment explanation
Indices: 294338--294389 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
294328 TATAAGCCAA
**
294338 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATACTTTG
294358 TGTATCGATAC-ATACTTTG
1 TGTATCGATACAATACTTTG
294377 TGTATCGATACAA
1 TGTATCGATACAA
294390 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.42
Consensus pattern (20 bp):
TGTATCGATACAATACTTTG
Found at i:295520 original size:33 final size:32
Alignment explanation
Indices: 295457--295521 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
295447 ATAATTATGT
* * *
295457 ATGTATCCATACAATGATCATGTATTGATACA
1 ATGTATCCATACAAAGATAATGTATCGATACA
*
295489 ATGTATCGATACAAAGCATAATGTATCGATACA
1 ATGTATCCATACAAAG-ATAATGTATCGATACA
295522 TCTGGATGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (32 bp):
ATGTATCCATACAAAGATAATGTATCGATACA
Found at i:301166 original size:33 final size:33
Alignment explanation
Indices: 301129--301195 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
301119 TTCAACGATT
301129 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
301162 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
301195 T
1 T
301196 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:301167 original size:13 final size:13
Alignment explanation
Indices: 301149--301173 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
301139 CATAAAATGT
301149 TGTATCGATACAA
1 TGTATCGATACAA
301162 TGTATCGATACA
1 TGTATCGATACA
301174 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:301258 original size:13 final size:13
Alignment explanation
Indices: 301240--301264 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
301230 ATTACTCACA
301240 TGTATCGATACAT
1 TGTATCGATACAT
301253 TGTATCGATACA
1 TGTATCGATACA
301265 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:301401 original size:52 final size:52
Alignment explanation
Indices: 301273--301393 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
301263 CACTGATCTT
*
301273 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
301325 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
301377 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
301394 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:308733 original size:1 final size:1
Alignment explanation
Indices: 308695--308724 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
308685 TACTCTTCAC
*
308695 AAAAAAAAAAAAAAAAAAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
308725 GGGGAAAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.97, C:0.03, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:309748 original size:30 final size:30
Alignment explanation
Indices: 309695--310133 Score: 202
Period size: 34 Copynumber: 13.9 Consensus size: 30
309685 TGGCATTTTT
309695 TCTTTAAAGCCCACAATTCCGTGGCACCTCA
1 TCTTT-AAGCCCACAATTCCGTGGCACCTCA
*
309726 TCTTTAAGTCCACAACTT-CGTGGCACC-C-
1 TCTTTAAGCCCACAA-TTCCGTGGCACCTCA
309754 T-TTTACAGCCCACAATTCCGTGGCACCTCA
1 TCTTTA-AGCCCACAATTCCGTGGCACCTCA
*
309784 TCTTTAAGCCCACAACTCCGTGGCACTCTTTTTC-
1 TCTTTAAGCCCACAATTCCGTGGCAC-C----TCA
* *
309818 TCTTTTCAAAGCCCACGACTCCGTGGCA-CTC-
1 TC-TTT--AAGCCCACAATTCCGTGGCACCTCA
* * *
309849 T-TTAAAGCCCACAACTCCGTGGCACCTTCT
1 TCTTTAAGCCCACAATTCCGTGGCACC-TCA
* * *
309879 TCTTTTCAAAGCCCACAACTCTGTGGCACCTTCT
1 TC-TTT--AAGCCCACAATTCCGTGGCACC-TCA
* * *
309913 TCTTTTCAAAGCCCACAACTCTGTGGCACCTTCT
1 TC-TTT--AAGCCCACAATTCCGTGGCACC-TCA
* *
309947 TCTGTTCAAAGCCCACGACTCCGTGGCA-CTC-
1 TCT-TT--AAGCCCACAATTCCGTGGCACCTCA
* * *
309978 T-TTAAAGCCCACAACTCCGTGGCACCTTCT
1 TCTTTAAGCCCACAATTCCGTGGCACC-TCA
* * *
310008 TCTTTTCAAAGCCCACAACTCTGTGGCACCTTCT
1 TC-TTT--AAGCCCACAATTCCGTGGCACC-TCA
* * *
310042 TCTTTTCAAAGCCCACAACTCTGTGGCACCTTCT
1 TC-TTT--AAGCCCACAATTCCGTGGCACC-TCA
* *
310076 TCTGTTCAAAGCCCACGACTCCGTGGCA-CTC-
1 TCT-TT--AAGCCCACAATTCCGTGGCACCTCA
* * *
310107 TTTTTAAAGCCCACAACTCTGTGGCAC
1 TCTTT-AAGCCCACAATTCCGTGGCAC
310134 TCTTTTTCCT
Statistics
Matches: 358, Mismatches: 19, Indels: 63
0.81 0.04 0.14
Matches are distributed among these distances:
27 44 0.12
28 20 0.06
29 28 0.08
30 43 0.12
31 18 0.05
32 8 0.02
33 4 0.01
34 168 0.47
35 6 0.02
37 19 0.05
ACGTcount: A:0.21, C:0.36, G:0.14, T:0.29
Consensus pattern (30 bp):
TCTTTAAGCCCACAATTCCGTGGCACCTCA
Found at i:309771 original size:58 final size:58
Alignment explanation
Indices: 309697--310228 Score: 263
Period size: 68 Copynumber: 8.4 Consensus size: 58
309687 GCATTTTTTC
* *
309697 TTTAAAGCCCACAATTCCGTGGCACCTCATCTTTAAGTCCACAACTTCGTGGCACCCT
1 TTTAAAGCCCACAATTCCGTGGCACCTCATCTTTAAGCCCACAACTCCGTGGCACCCT
*
309755 TTTACAGCCCACAATTCCGTGGCACCTCATCTTTAAGCCCACAACTCCGTGGCACTCTTTTTCTC
1 TTTAAAGCCCACAATTCCGTGGCACCTCATCTTTAAGCCCACAACTCCGTGGCA--C-----C-C
309820 T
58 T
* * *
309821 TTTCAAAGCCCACGACTCCGTGGCA-CTC-T-TTAAAGCCCACAACTCCGTGGCACCTTCTTCT
1 TTT-AAAGCCCACAATTCCGTGGCACCTCATCTTTAAGCCCACAACTCCGTGGCA-C--C--CT
* * * *
309882 TTTCAAAGCCCACAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTCT
1 TTT-AAAGCCCACAATTCCGTGGCACC-TCATC-TTT--AAGCCCACAACTCCGTGGCACC--C-
309947 T
58 T
* * *
309948 CTGTTCAAAGCCCACGACTCCGTGGCA-CTC-T-TTAAAGCCCACAACTCCGTGGCACCTTCTTC
1 -T-TT-AAAGCCCACAATTCCGTGGCACCTCATCTTTAAGCCCACAACTCCGTGGCA-C--C--C
310010 T
58 T
* * * *
310011 TTTCAAAGCCCACAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTCT
1 TTT-AAAGCCCACAATTCCGTGGCACC-TCATC-TTT--AAGCCCACAACTCCGTGGCACC--C-
310076 T
58 T
* * * * *
310077 CTGTTCAAAGCCCACGACTCCGTGGCA-CTC-TTTTTAAAGCCCACAACTCTGTGGCACTCTTT
1 -T-TT-AAAGCCCACAATTCCGTGGCACCTCATCTTT-AAGCCCACAACTCCGTGGCAC-C-CT
* * * ** *
310139 TTCCTCCTAAGCCCACAACTCTGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCATCC
1 TT--T--AAAGCCCACAATTCCGTGGCAC-C-TCAT-CTT-TAAGCCCACAACTCCGTGGCACCC
310204 T
58 T
* *
310205 TTT-AAGCCCATAACTCCGTGGCAC
1 TTTAAAGCCCACAATTCCGTGGCAC
310229 TTTTTTCATC
Statistics
Matches: 397, Mismatches: 34, Indels: 83
0.77 0.07 0.16
Matches are distributed among these distances:
58 51 0.13
60 5 0.01
61 87 0.22
62 6 0.02
63 50 0.13
64 33 0.08
65 13 0.03
66 22 0.06
67 26 0.07
68 103 0.26
69 1 0.00
ACGTcount: A:0.21, C:0.36, G:0.14, T:0.29
Consensus pattern (58 bp):
TTTAAAGCCCACAATTCCGTGGCACCTCATCTTTAAGCCCACAACTCCGTGGCACCCT
Found at i:309890 original size:34 final size:34
Alignment explanation
Indices: 309852--310334 Score: 449
Period size: 34 Copynumber: 14.6 Consensus size: 34
309842 GGCACTCTTT
309852 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTC
1 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTC
*
309886 AAAGCCCACAACTCTGTGGCACCTTCTTCTTTTC
1 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTC
* *
309920 AAAGCCCACAACTCTGTGGCACCTTCTTCTGTTC
1 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTC
*
309954 AAAGCCCACGACTCCGTGGCA----C-TC-TTT-
1 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTC
309981 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTC
1 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTC
*
310015 AAAGCCCACAACTCTGTGGCACCTTCTTCTTTTC
1 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTC
* *
310049 AAAGCCCACAACTCTGTGGCACCTTCTTCTGTTC
1 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTC
*
310083 AAAGCCCACGACTCCGTGGCA-C-TC-T-TTTT-
1 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTC
* * * *
310112 AAAGCCCACAACTCTGTGGCACTCTTTTTC-CTCC
1 AAAGCCCACAACTCCGTGGCAC-CTTCTTCTTTTC
* * * *
310146 TAAGCCCACAACTCTGTGGCACTCTTTTTC-CTTC
1 AAAGCCCACAACTCCGTGGCAC-CTTCTTCTTTTC
*
310180 TAAGCCCACAACTCCGTGGCA---TC--CTTTT-
1 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTC
* * *
310208 -AAGCCCATAACTCCGTGGCACTTTTTTCATCTTT-
1 AAAGCCCACAACTCCGTGGCACCTTCTTC-T-TTTC
* * * * *
310242 -GAGTCCATAACTCCGTGGCACCTTTTTTTTTTC
1 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTC
*
310275 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT-
1 ----AAAGCCCACAACTCCGTGGCAC-CTTCTT--CTTTTC
*
310315 -AAGTCCACAACTCCGTGGCA
1 AAAGCCCACAACTCCGTGGCA
310335 TCTTTCTCCC
Statistics
Matches: 387, Mismatches: 32, Indels: 59
0.81 0.07 0.12
Matches are distributed among these distances:
27 39 0.10
28 3 0.01
29 23 0.06
30 6 0.02
31 3 0.01
32 9 0.02
33 8 0.02
34 249 0.64
35 19 0.05
38 18 0.05
39 6 0.02
41 4 0.01
ACGTcount: A:0.20, C:0.35, G:0.13, T:0.31
Consensus pattern (34 bp):
AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTC
Found at i:309920 original size:95 final size:93
Alignment explanation
Indices: 309694--310205 Score: 446
Period size: 95 Copynumber: 5.3 Consensus size: 93
309684 GTGGCATTTT
* * * *
309694 TTCTTTAAAGCCCACAATTCCGTGGCACC-TCATC-TTT--AAGTCCACAACT-TCGTGGCACCC
1 TTCTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCT-GTGGCACTC
* * *
309754 TTTTACAGCCCACAATTCCGTGGCACCTC
65 TTTCAAAGCCCACAACTCCGTGGCACCTC
* * * *
309783 ATCTTT-AAGCCCACAACTCCGTGGCACTCTTTTTCTCTTTTCAAAGCCCACGACTCCGTGGCAC
1 TTCTTTAAAGCCCACAACTCCGTGGCAC-C-TTCT-TCTTTTCAAAGCCCACAACTCTGTGGCAC
309847 TCTTT-AAAGCCCACAACTCCGTGGCACCTTC
63 TCTTTCAAAGCCCACAACTCCGTGGCACC-TC
*
309878 TTCTTTTCAAAGCCCACAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACC
1 TTC-TTT-AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCA--
*
309943 TTCTTCTGTTCAAAGCCCACGACTCCGTGGCA---C
62 --C-TCT-TTCAAAGCCCACAACTCCGTGGCACCTC
309976 -TCTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTT
1 TTCTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCA----
*
310040 CTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTC
62 C-TC-TTTCAAAGCCCACAACTCCGTGGCACC-TC
*
310075 TTCTGTTCAAAGCCCACGACTCCGTGGCA-C-TC-T-TTTT-AAAGCCCACAACTCTGTGGCACT
1 TTCT-TT-AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACT
* * *
310135 CTTTTTCCTCCTAAGCCCACAACTCTGTGGCACTCTTT
64 C---TT--T-CAAAGCCCACAACTCCGTGGCAC-C-TC
310173 TTCCTTCT-AAGCCCACAACTCCGTGGCATCCTT
1 TT-CTT-TAAAGCCCACAACTCCGTGGCA-CCTT
310206 TTAAGCCCAT
Statistics
Matches: 362, Mismatches: 23, Indels: 65
0.80 0.05 0.14
Matches are distributed among these distances:
88 20 0.06
89 6 0.02
91 1 0.00
92 4 0.01
93 4 0.01
94 24 0.07
95 135 0.37
96 11 0.03
97 65 0.18
98 31 0.09
99 7 0.02
100 9 0.02
101 5 0.01
102 40 0.11
ACGTcount: A:0.21, C:0.36, G:0.13, T:0.30
Consensus pattern (93 bp):
TTCTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACTCT
TTCAAAGCCCACAACTCCGTGGCACCTC
Found at i:309967 original size:129 final size:128
Alignment explanation
Indices: 309760--310205 Score: 639
Period size: 129 Copynumber: 3.4 Consensus size: 128
309750 ACCCTTTTAC
* * * * *
309760 AGCCCACAATTCCGTGGCACC-TCATCTTT--AAGCCCACAACTCCGTGGCACTCTTTTTCTCTT
1 AGCCCACAACTCTGTGGCACCTTCTTCTTTCAAAGCCCACAACTCCGTGGCAC-C-TTCT-TCTG
309822 TTCAAAGCCCACGACTCCGTGGCACTCTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCA
63 TTCAAAGCCCACGACTCCGTGGCACTCTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCA
309887 A
128 A
*
309888 AGCCCACAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTCTTCTGTT
1 AGCCCACAACTCTGTGGCACCTTCTTC-TTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTGTT
309953 CAAAGCCCACGACTCCGTGGCACTCTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAA
65 CAAAGCCCACGACTCCGTGGCACTCTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAA
*
310017 AGCCCACAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTCTTCTGTT
1 AGCCCACAACTCTGTGGCACCTTCTTC-TTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTGTT
* * * *
310082 CAAAGCCCACGACTCCGTGGCACTCTTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTC-CTCC
65 CAAAGCCCACGACTCCGTGGCACTC--TTTAAAGCCCACAACTCCGTGGCAC-CTTCTTCTTTTC
*
310146 TA
127 AA
* * *
310148 AGCCCACAACTCTGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCATCCTT
1 AGCCCACAACTCTGTGGCAC-CTTCTTCTTTCAAAGCCCACAACTCCGTGGCA-CCTT
310206 TTAAGCCCAT
Statistics
Matches: 294, Mismatches: 15, Indels: 14
0.91 0.05 0.04
Matches are distributed among these distances:
128 19 0.06
129 163 0.55
130 6 0.02
131 70 0.24
132 36 0.12
ACGTcount: A:0.20, C:0.37, G:0.14, T:0.29
Consensus pattern (128 bp):
AGCCCACAACTCTGTGGCACCTTCTTCTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTGTTC
AAAGCCCACGACTCCGTGGCACTCTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAA
Found at i:310226 original size:61 final size:60
Alignment explanation
Indices: 310146--310336 Score: 177
Period size: 61 Copynumber: 2.9 Consensus size: 60
310136 TTTTTCCTCC
* *
310146 TAAGCCCACAACTCTGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCATCCTTT
1 TAAGCCCACAACTCCGTGGCACTCTTTTTCCTT-TAAGTCCACAACTCCGTGGCATCCTTT
* * *
310207 TAAGCCCATAACTCCGTGGCACT-TTTTTCATCTTTGAGTCCATAACTCCGTGGCACCTTTTTTT
1 TAAGCCCACAACTCCGTGGCACTCTTTTTC--CTTTAAGTCCACAACTCCGTGGCA---------
*
310271 TTTCTTT
55 -TCCTTT
310278 TAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAGTCCACAACTCCGTGGCATC
1 T-AAGCCCACAACTCCGTGGCACTCTTTTT-CC-TTTAAGTCCACAACTCCGTGGCATC
310337 TTTCTCCCTT
Statistics
Matches: 104, Mismatches: 10, Indels: 30
0.72 0.07 0.21
Matches are distributed among these distances:
60 6 0.06
61 39 0.38
62 3 0.03
63 1 0.01
71 6 0.06
72 22 0.21
73 26 0.25
74 1 0.01
ACGTcount: A:0.19, C:0.32, G:0.13, T:0.35
Consensus pattern (60 bp):
TAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTAAGTCCACAACTCCGTGGCATCCTTT
Found at i:310234 original size:27 final size:27
Alignment explanation
Indices: 310174--310227 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
310164 GCACTCTTTT
*
310174 TCCTTCTAAGCCCACAACTCCGTGGCA
1 TCCTTTTAAGCCCACAACTCCGTGGCA
*
310201 TCCTTTTAAGCCCATAACTCCGTGGCA
1 TCCTTTTAAGCCCACAACTCCGTGGCA
310228 CTTTTTTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.22, C:0.37, G:0.15, T:0.26
Consensus pattern (27 bp):
TCCTTTTAAGCCCACAACTCCGTGGCA
Found at i:310269 original size:95 final size:97
Alignment explanation
Indices: 309819--310307 Score: 315
Period size: 95 Copynumber: 5.1 Consensus size: 97
309809 CTCTTTTTCT
* *
309819 CTTTTCAAAGCCCACGACTCCGTGGCACTC--TTT-A----AAGCCCACAACTCCGTGGCACCTT
1 CTTTT-AAAGCCCACAACTCCGTGGCACTCTTTTTCATCCTAAGCCCACAACTCTGTGGCACCTT
* *
309877 CTTCTT--TTCAAAGCCCACAACTCTGTGGCACCTTC
65 -TT-TTCCTTCTAAGCCCACAACTCCGTGGCA-C-TC
* * * * * * *
309912 TTCTTTTCAAAGCCCACAACTCTGTGGCAC-CTTCTTCTGTTCAAAGCCCACGACTCCGTGGCA-
1 --CTTTT-AAAGCCCACAACTCCGTGGCACTCTTTTTC-ATCCTAAGCCCACAACTCTGTGGCAC
309975 C-----T-CTT-TAAAGCCCACAACTCCGTGGCACCTTC
62 CTTTTTTCCTTCT-AAGCCCACAACTCCGTGGCA-C-TC
* * * * *
310007 TTCTTTTCAAAGCCCACAACTCTGTGGCAC-CTTCTTCTTTTCAAAGCCCACAACTCTGTGGCAC
1 --CTTTT-AAAGCCCACAACTCCGTGGCACTCTTTTTC-ATCCTAAGCCCACAACTCTGTGGCAC
* * * *
310071 C-TTCTTCTGTTCAAAGCCCACGACTCCGTGGCACTC
62 CTTTTTTC-CTTCTAAGCCCACAACTCCGTGGCACTC
* * *
310107 TTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCTCCTAAGCCCACAACTCTGTGGCA-CTCT
1 CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCATCCTAAGCCCACAACTCTGTGGCACCT-T
310171 TTTTCCTTCTAAGCCCACAACTCCGTGGCA-TC
65 TTTTCCTTCTAAGCCCACAACTCCGTGGCACTC
* * * * * *
310203 CTTTT-AAGCCCATAACTCCGTGGCACT-TTTTTCATCTTTGAGTCCATAACTCCGTGGCACCTT
1 CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCATC-CTAAGCCCACAACTCTGTGGCACC--
* *
310266 TTTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTC
63 -TTTTTTCCTTCT-AAGCCCACAACTCCGTGGCACTC
*
310303 TTTTT
1 CTTTT
310308 CCCTTTTAAG
Statistics
Matches: 332, Mismatches: 34, Indels: 51
0.80 0.08 0.12
Matches are distributed among these distances:
94 10 0.03
95 149 0.45
96 11 0.03
97 66 0.20
98 24 0.07
99 21 0.06
100 9 0.03
101 2 0.01
102 40 0.12
ACGTcount: A:0.20, C:0.35, G:0.13, T:0.32
Consensus pattern (97 bp):
CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCATCCTAAGCCCACAACTCTGTGGCACCTTT
TTTCCTTCTAAGCCCACAACTCCGTGGCACTC
Found at i:310293 original size:72 final size:72
Alignment explanation
Indices: 310203--310339 Score: 197
Period size: 73 Copynumber: 1.9 Consensus size: 72
310193 CCGTGGCATC
* * * *
310203 CTTTTAAGCCCATAACTCCGTGGCACT-TTTTT-CATCTTTGAGTCCATAACTCCGTGGCACCTT
1 CTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCCT-TTTAAGTCCACAACTCCGTGGCACCTT
310266 TTTTTTTT
65 TTTTTTTT
*
310274 CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAGTCCACAACTCCGTGGCATCTT
1 CTTTT-AAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAGTCCACAACTCCGTGGCACCTT
310339 T
65 T
310340 CTCCCTTCCT
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
71 5 0.09
72 21 0.36
73 30 0.52
74 2 0.03
ACGTcount: A:0.18, C:0.30, G:0.12, T:0.39
Consensus pattern (72 bp):
CTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAGTCCACAACTCCGTGGCACCTTT
TTTTTTT
Found at i:310362 original size:73 final size:71
Alignment explanation
Indices: 310208--310359 Score: 173
Period size: 73 Copynumber: 2.1 Consensus size: 71
310198 GCATCCTTTT
* * * * ***
310208 AAGCCCATAACTCCGTGGCACTTTTTTCATCTTTGAGTCCATAACTCCGTGGCACCTTTTTTTTT
1 AAGCCCACAACTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTTTCTCCCT
*
310273 TCTTTTA
66 TC-TCTA
* *
310280 AAGCCCACAACTCCGTGGCACTCTTTTTC-CCTTTTAAGTCCACAACTCCGTGGCATCTTTCTCC
1 AAGCCCACAACTCCGTGGCACT-TTTTTCATC-TTTAAGTCCACAACTCCGTGGCACCTTTCTCC
310344 CTTC-CTA
64 CTTCTCTA
310351 AAGCCCACA
1 AAGCCCACA
310360 CAAGTCGGTG
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
71 11 0.16
72 22 0.32
73 35 0.51
ACGTcount: A:0.20, C:0.33, G:0.12, T:0.36
Consensus pattern (71 bp):
AAGCCCACAACTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTTTCTCCCT
TCTCTA
Found at i:310387 original size:33 final size:35
Alignment explanation
Indices: 310344--310413 Score: 126
Period size: 33 Copynumber: 2.1 Consensus size: 35
310334 ATCTTTCTCC
310344 CTTCCTAAAGCCCACACAAGTCGGTGGCAA-CCTT
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCCTT
310378 CTTCC-AAAGCCCACACAAGTCGGTGGCAACCCTT
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCCTT
310412 CT
1 CT
310414 AAGCCCAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 24 0.69
34 11 0.31
ACGTcount: A:0.26, C:0.37, G:0.17, T:0.20
Consensus pattern (35 bp):
CTTCCTAAAGCCCACACAAGTCGGTGGCAACCCTT
Found at i:310477 original size:49 final size:49
Alignment explanation
Indices: 310413--310973 Score: 661
Period size: 49 Copynumber: 11.6 Consensus size: 49
310403 GCAACCCTTC
*
310413 TAAGCCCAATATAGCTGGCCTTGAATCAGCATCTTGGCATCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATCTTGGCATCTTCATCTT
*
310462 TAAGTCCAATGTAGCTGGCCTTGAATCAGCA-CATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATC-TTGGCATCTTCATCTT
* * * *
310505 TAAGCCCAATATAGCTGGCCCTGAATCAGCATATTGGCATCTTCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATCTTGGCATCTTCATCTT
*
310554 TAAGTCCAATATCGCTGGCCTTGAATCAGCA-CATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATC-TTGGCATCTTCATCTT
* * *
310597 TAAGTCCAATATCGCTGGCATTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATCTTGGCATCTTCATCTT
* * * *
310646 TAAGTCCAATGTAGCTGGCCTTGACTCAGCA-CATTGGCACCTTCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATC-TTGGCATCTTCATCTT
* * *
310695 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATCTTGGCATCTTCATCTT
* * *
310744 TAAGTCCAATGTAGCTGGCCTTGACTCAGCA-CATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATC-TTGGCATCTTCATCTT
* *
310793 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATCTTGGCATCTTCATCTT
* * * *
310842 TAAGACCAATGTAGCTGGCCTTGACTCAGCA-CATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATC-TTGGCATCTTCATCTT
* *
310891 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATCTTGG--CATCTT-CATCTT
* *
310943 TAAGTTCAATGTAGCTGGCCTTGAATCAGCA
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCA
310974 CGTTGACATC
Statistics
Matches: 436, Mismatches: 51, Indels: 47
0.82 0.10 0.09
Matches are distributed among these distances:
43 76 0.17
45 2 0.00
47 2 0.00
48 1 0.00
49 316 0.72
51 4 0.01
52 35 0.08
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (49 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATCTTGGCATCTTCATCTT
Found at i:310721 original size:98 final size:98
Alignment explanation
Indices: 310408--310974 Score: 834
Period size: 98 Copynumber: 5.9 Consensus size: 98
310398 CGGTGGCAAC
* *
310408 CCTTCTAAGCCCAATATAGCTGGCCTTGAATCAGCATCTTGGCATCTTCATCTTTAAGTCCAATG
1 CCTT-TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATG
310473 TAGCTGGCCTTGAATCAGCACATTGG------CA
65 TAGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * * *
310501 CCTTTAAGCCCAATATAGCTGGCCCTGAATCAGCATATTGGCATCTTCACCTTTAAGTCCAATAT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
*
310566 CGCTGGCCTTGAATCAGCACATTGG------CA
66 AGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* *
310593 CCTTTAAGTCCAATATCGCTGGCATTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
*
310658 AGCTGGCCTTGACTCAGCACATTGGCACCTTCA
66 AGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* *
310691 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
*
310756 AGCTGGCCTTGACTCAGCACATTGGCACCTTCA
66 AGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * *
310789 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGACCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
*
310854 AGCTGGCCTTGACTCAGCACATTGGCACCTTCA
66 AGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * *
310887 TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAA
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG--CATCTT-CATCTTTAAGTCCAA
310952 TGTAGCTGGCCTTGAATCAGCAC
63 TGTAGCTGGCCTTGAATCAGCAC
310975 GTTGACATCT
Statistics
Matches: 442, Mismatches: 23, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
92 165 0.37
93 4 0.01
98 233 0.53
100 5 0.01
101 35 0.08
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.31
Consensus pattern (98 bp):
CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
AGCTGGCCTTGAATCAGCACATTGGCACCTTCA
Found at i:311039 original size:55 final size:55
Alignment explanation
Indices: 310594--311103 Score: 351
Period size: 49 Copynumber: 9.8 Consensus size: 55
310584 ACATTGGCAC
* *
310594 CTTTAAGTCCAATATCGCTGGCATTGAATCAGCATATTGGCATC-----T-TCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTTTTTCTCAT
* * * * *
310643 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA-C----CT-TCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTTTTTCTCAT
* *
310692 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATC------ATCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTTTTTCTCAT
* * * *
310741 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA-C----CT-TCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTTTTTCTCAT
*
310790 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATC-----T-TCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTTTTTCTCAT
* * * * *
310839 CTTTAAGACCAATGTAGCTGGCCTTGACTCAGCACATTGGCA-C----CT-TCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTTTTTCTCAT
*
310888 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-C-ATTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTTTTTCTCAT
* * ** *
310940 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCTTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTTTTTCTCAT
* * * * * *
310995 CTTCAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCTTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG---C---AT--CTTTT-T--TC-TC
311060 AT
54 AT
*
311062 CTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA
311104 CCTTCATCAT
Statistics
Matches: 383, Mismatches: 52, Indels: 40
0.81 0.11 0.08
Matches are distributed among these distances:
48 3 0.01
49 248 0.65
50 2 0.01
52 41 0.11
53 1 0.00
54 5 0.01
55 32 0.08
58 1 0.00
61 3 0.01
63 5 0.01
64 2 0.01
66 2 0.01
67 38 0.10
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (55 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTTTTTCTCAT
Found at i:311938 original size:33 final size:33
Alignment explanation
Indices: 311901--311967 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
311891 TTCAACGATT
311901 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
311934 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
311967 T
1 T
311968 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:311939 original size:13 final size:13
Alignment explanation
Indices: 311921--311945 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
311911 CATAAAATGT
311921 TGTATCGATACAA
1 TGTATCGATACAA
311934 TGTATCGATACA
1 TGTATCGATACA
311946 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:312030 original size:13 final size:13
Alignment explanation
Indices: 312012--312036 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
312002 ATTACTCACA
312012 TGTATCGATACAT
1 TGTATCGATACAT
312025 TGTATCGATACA
1 TGTATCGATACA
312037 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:312173 original size:52 final size:52
Alignment explanation
Indices: 312045--312165 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
312035 CACTGATCTT
*
312045 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
312097 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
312149 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
312166 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:319107 original size:1 final size:1
Alignment explanation
Indices: 319101--319134 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
319091 AGTAAACACC
* *
319101 AAAAAAACAAAAAAAAAAAAAAAAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
319135 GTGCAAAGGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.94, C:0.03, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:319399 original size:16 final size:16
Alignment explanation
Indices: 319378--319413 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
319368 TTCCAAACAC
*
319378 AAAAAAAAGAAAAAAG
1 AAAAAAAACAAAAAAG
*
319394 AAAAAAAACAAAACAG
1 AAAAAAAACAAAAAAG
319410 AAAA
1 AAAA
319414 TCTCGGTGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.86, C:0.06, G:0.08, T:0.00
Consensus pattern (16 bp):
AAAAAAAACAAAAAAG
Found at i:319473 original size:15 final size:16
Alignment explanation
Indices: 319453--319484 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
319443 CCTACTCTTC
319453 ACAAAAA-AAAAAAAA
1 ACAAAAACAAAAAAAA
319468 ACAAAAACAAAAAAAA
1 ACAAAAACAAAAAAAA
319484 A
1 A
319485 AAGGGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (16 bp):
ACAAAAACAAAAAAAA
Found at i:320511 original size:30 final size:30
Alignment explanation
Indices: 320458--320572 Score: 157
Period size: 30 Copynumber: 3.9 Consensus size: 30
320448 TGGCATTTTT
320458 TCTTTAAAGCCCACAATTCCGTGGCACCTCA
1 TCTTT-AAGCCCACAATTCCGTGGCACCTCA
*
320489 TCTTTAAGTCCACAACTT-CGTGGCACC-C-
1 TCTTTAAGCCCACAA-TTCCGTGGCACCTCA
320517 T-TTTACAGCCCACAATTCCGTGGCACCTCA
1 TCTTTA-AGCCCACAATTCCGTGGCACCTCA
*
320547 TCTTTAAGCCCACAACTCCGTGGCAC
1 TCTTTAAGCCCACAATTCCGTGGCAC
320573 TGGCACTCTT
Statistics
Matches: 75, Mismatches: 3, Indels: 13
0.82 0.03 0.14
Matches are distributed among these distances:
27 6 0.08
28 18 0.24
29 2 0.03
30 38 0.51
31 11 0.15
ACGTcount: A:0.23, C:0.37, G:0.14, T:0.26
Consensus pattern (30 bp):
TCTTTAAGCCCACAATTCCGTGGCACCTCA
Found at i:320534 original size:58 final size:58
Alignment explanation
Indices: 320460--320572 Score: 199
Period size: 58 Copynumber: 1.9 Consensus size: 58
320450 GCATTTTTTC
* *
320460 TTTAAAGCCCACAATTCCGTGGCACCTCATCTTTAAGTCCACAACTTCGTGGCACCCT
1 TTTAAAGCCCACAATTCCGTGGCACCTCATCTTTAAGCCCACAACTCCGTGGCACCCT
*
320518 TTTACAGCCCACAATTCCGTGGCACCTCATCTTTAAGCCCACAACTCCGTGGCAC
1 TTTAAAGCCCACAATTCCGTGGCACCTCATCTTTAAGCCCACAACTCCGTGGCAC
320573 TGGCACTCTT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.24, C:0.36, G:0.14, T:0.26
Consensus pattern (58 bp):
TTTAAAGCCCACAATTCCGTGGCACCTCATCTTTAAGCCCACAACTCCGTGGCACCCT
Found at i:320659 original size:34 final size:34
Alignment explanation
Indices: 320621--320973 Score: 439
Period size: 34 Copynumber: 10.7 Consensus size: 34
320611 GGCACTCTTT
*
320621 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTC
1 AAAGCCCACAACTCTGTGGCACCTTCTTCTTTTC
320655 AAAGCCCACAACTCTGTGGCACCTTCTTCTTTTC
1 AAAGCCCACAACTCTGTGGCACCTTCTTCTTTTC
*
320689 AAAGCCCACAACTCTGTGGCACCTTCTTCTGTTC
1 AAAGCCCACAACTCTGTGGCACCTTCTTCTTTTC
* *
320723 AAAGCCCACGACTCCGTGGCA----C-TC-TTT-
1 AAAGCCCACAACTCTGTGGCACCTTCTTCTTTTC
*
320750 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTC
1 AAAGCCCACAACTCTGTGGCACCTTCTTCTTTTC
320784 AAAGCCCACAACTCTGTGGCACCTTCTTCTTTTC
1 AAAGCCCACAACTCTGTGGCACCTTCTTCTTTTC
*
320818 AAAGCCCACAACTCTGTGGCACCTTCTTCTGTTC
1 AAAGCCCACAACTCTGTGGCACCTTCTTCTTTTC
* *
320852 AAAGCCCACGACTCCGTGGCA-C-TC-T-TTTT-
1 AAAGCCCACAACTCTGTGGCACCTTCTTCTTTTC
* *
320881 AAAGCCCACAACTCTGTGGCACTCTT-TTC-CTCC
1 AAAGCCCACAACTCTGTGGCAC-CTTCTTCTTTTC
* * *
320914 TAAGCCCACAACTCTGTGGCACTCTTTTTC-CTTC
1 AAAGCCCACAACTCTGTGGCAC-CTTCTTCTTTTC
* *
320948 TAAGCCCACAACTCCGTGGCATCCTT
1 AAAGCCCACAACTCTGTGGCA-CCTT
320974 TTAAGCCCAT
Statistics
Matches: 286, Mismatches: 18, Indels: 30
0.86 0.05 0.09
Matches are distributed among these distances:
27 20 0.07
28 2 0.01
29 21 0.07
30 4 0.01
31 3 0.01
32 7 0.02
33 29 0.10
34 199 0.70
35 1 0.00
ACGTcount: A:0.21, C:0.37, G:0.14, T:0.29
Consensus pattern (34 bp):
AAAGCCCACAACTCTGTGGCACCTTCTTCTTTTC
Found at i:320708 original size:95 final size:93
Alignment explanation
Indices: 320457--320973 Score: 411
Period size: 95 Copynumber: 5.3 Consensus size: 93
320447 GTGGCATTTT
* * * *
320457 TTCTTTAAAGCCCACAATTCCGTGGCACC-TCATC-TTT--AAGTCCACAACT-TCGTGGCACCC
1 TTCTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCT-GTGGCACTC
* * *
320517 TTTTACAGCCCACAATTCCGTGGCACCTC
65 TTTCAAAGCCCACAACTCCGTGGCACCTC
* * * *
320546 ATCTTT-AAGCCCACAACTCCGTGGCACTGGCACTCTTTTTCTCTTTTCAAAGCCCACGACTCCG
1 TTCTTTAAAGCCCACAACTCC---G---TGGCAC-C-TTCT-TCTTTTCAAAGCCCACAACTCTG
320610 TGGCACTCTTT-AAAGCCCACAACTCCGTGGCACCTTC
57 TGGCACTCTTTCAAAGCCCACAACTCCGTGGCACC-TC
*
320647 TTCTTTTCAAAGCCCACAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACC
1 TTC-TTT-AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCA--
*
320712 TTCTTCTGTTCAAAGCCCACGACTCCGTGGCA---C
62 --C-TCT-TTCAAAGCCCACAACTCCGTGGCACCTC
320745 -TCTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTT
1 TTCTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCA----
*
320809 CTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTC
62 C-TC-TTTCAAAGCCCACAACTCCGTGGCACC-TC
*
320844 TTCTGTTCAAAGCCCACGACTCCGTGGCA-C-TC-T-TTTT-AAAGCCCACAACTCTGTGGCACT
1 TTCT-TT-AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACT
* * *
320904 CTTTTCCTCCTAAGCCCACAACTCTGTGGCACTCTTT
64 C--TT--T-CAAAGCCCACAACTCCGTGGCAC-C-TC
320941 TTCCTTCT-AAGCCCACAACTCCGTGGCATCCTT
1 TT-CTT-TAAAGCCCACAACTCCGTGGCA-CCTT
320974 TTAAGCCCAT
Statistics
Matches: 362, Mismatches: 23, Indels: 76
0.79 0.05 0.16
Matches are distributed among these distances:
88 13 0.04
89 5 0.01
91 1 0.00
92 2 0.01
93 4 0.01
94 6 0.02
95 112 0.31
96 48 0.13
97 31 0.09
98 17 0.05
99 7 0.02
100 29 0.08
101 31 0.09
102 43 0.12
104 13 0.04
ACGTcount: A:0.21, C:0.36, G:0.14, T:0.29
Consensus pattern (93 bp):
TTCTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACTCT
TTCAAAGCCCACAACTCCGTGGCACCTC
Found at i:320737 original size:129 final size:129
Alignment explanation
Indices: 320591--320973 Score: 628
Period size: 129 Copynumber: 3.0 Consensus size: 129
320581 TTTTTCTCTT
320591 TTCAAAGCCCACGACTCCGTGGCACTCTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCA
1 TTCAAAGCCCACGACTCCGTGGCACTCTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCA
320656 AAGCCCACAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTCTTCTG
66 AAGCCCACAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTCTTCTG
320720 TTCAAAGCCCACGACTCCGTGGCACTCTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCA
1 TTCAAAGCCCACGACTCCGTGGCACTCTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCA
320785 AAGCCCACAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTCTTCTG
66 AAGCCCACAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTCTTCTG
* *
320849 TTCAAAGCCCACGACTCCGTGGCACTCTTTTTAAAGCCCACAACTCTGTGGCACTCTT-TTC-CT
1 TTCAAAGCCCACGACTCCGTGGCACTC--TTTAAAGCCCACAACTCCGTGGCAC-CTTCTTCTTT
* * * * * *
320912 CCTAAGCCCACAACTCTGTGGCACTCTTTTTC-CTTCTAAGCCCACAACTCCGTGGCATCCTT
63 TCAAAGCCCACAACTCTGTGGCAC-CTTCTTCTTTTCAAAGCCCACAACTCTGTGGCA-CCTT
320974 TTAAGCCCAT
Statistics
Matches: 241, Mismatches: 8, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
129 156 0.65
130 45 0.19
131 37 0.15
132 3 0.01
ACGTcount: A:0.21, C:0.37, G:0.14, T:0.29
Consensus pattern (129 bp):
TTCAAAGCCCACGACTCCGTGGCACTCTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCA
AAGCCCACAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTCTTCTG
Found at i:320975 original size:34 final size:33
Alignment explanation
Indices: 320622--321101 Score: 307
Period size: 34 Copynumber: 14.6 Consensus size: 33
320612 GCACTCTTTA
* * *
320622 AAGCCCACAACTCCGTGGCACCTTCTTCTTTTCA
1 AAGCCCACAACTCCGTGGCACCTTTTTC-CTTCT
* * * *
320656 AAGCCCACAACTCTGTGGCACCTTCTTCTTTTCA
1 AAGCCCACAACTCCGTGGCACCTTTTTC-CTTCT
* * * *
320690 AAGCCCACAACTCTGTGGCACCTTCTTCTGTTCA
1 AAGCCCACAACTCCGTGGCACCTTTTTC-CTTCT
*
320724 AAGCCCACGACTCCGTGGCA-C----T-CTT-T
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTCT
* * *
320750 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCA
1 -AAGCCCACAACTCCGTGGCACCTTTTTC-CTTCT
* * * *
320785 AAGCCCACAACTCTGTGGCACCTTCTTCTTTTCA
1 AAGCCCACAACTCCGTGGCACCTTTTTC-CTTCT
* * * *
320819 AAGCCCACAACTCTGTGGCACCTTCTTCTGTTCA
1 AAGCCCACAACTCCGTGGCACCTTTTTC-CTTCT
* * *
320853 AAGCCCACGACTCCGTGGCA-CTCTTT--TT-A
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTCT
* *
320882 AAGCCCACAACTCTGTGGCA-CTCTTTTCCTCCT
1 AAGCCCACAACTCCGTGGCACCT-TTTTCCTTCT
*
320915 AAGCCCACAACTCTGTGGCACTCTTTTTCCTTCT
1 AAGCCCACAACTCCGTGGCAC-CTTTTTCCTTCT
*
320949 AAGCCCACAACTCCGTGGCA------TCCTTTT
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTCT
* * *
320976 AAGCCCATAACTCCGTGGCACTTTTTTCCTACTT
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTC-T
* * * *
321010 GAGTCCCAATAACTCCGTGGC-CCTTTTTTTTTTCTTTT
1 AAG-CCC-ACAACTCCGTGGCACC----TTTTTCCTTCT
*
321048 AAGCCCACAACTCCGTGGCACTCTTTTCCCTT-T
1 AAGCCCACAACTCCGTGGCAC-CTTTTTCCTTCT
*
321081 AAGTCCAACAACTCCGTGGCA
1 AAG-CCCACAACTCCGTGGCA
321102 TCTTCCTCCC
Statistics
Matches: 379, Mismatches: 36, Indels: 62
0.79 0.08 0.13
Matches are distributed among these distances:
27 46 0.12
28 1 0.00
29 22 0.06
30 5 0.01
32 2 0.01
33 33 0.09
34 224 0.59
35 6 0.02
36 25 0.07
37 4 0.01
38 4 0.01
39 7 0.02
ACGTcount: A:0.20, C:0.35, G:0.14, T:0.31
Consensus pattern (33 bp):
AAGCCCACAACTCCGTGGCACCTTTTTCCTTCT
Found at i:321002 original size:27 final size:27
Alignment explanation
Indices: 320942--320995 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
320932 GCACTCTTTT
*
320942 TCCTTCTAAGCCCACAACTCCGTGGCA
1 TCCTTTTAAGCCCACAACTCCGTGGCA
*
320969 TCCTTTTAAGCCCATAACTCCGTGGCA
1 TCCTTTTAAGCCCACAACTCCGTGGCA
320996 CTTTTTTCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.22, C:0.37, G:0.15, T:0.26
Consensus pattern (27 bp):
TCCTTTTAAGCCCACAACTCCGTGGCA
Found at i:321060 original size:36 final size:36
Alignment explanation
Indices: 320971--321101 Score: 119
Period size: 36 Copynumber: 3.7 Consensus size: 36
320961 CCGTGGCATC
320971 CTTTTAAGCCCATAACTCCGTGGCACTTTTTTCCTA
1 CTTTTAAGCCCATAACTCCGTGGCACTTTTTTCCTA
* * ** *
321007 C--TTGAGTCCCAATAACTCCGTGGCCCTTTTTTTTTT
1 CTTTTAAG-CCC-ATAACTCCGTGGCACTTTTTTCCTA
* *
321043 CTTTTAAGCCCACAACTCCGTGGCACTCTTTTCC--
1 CTTTTAAGCCCATAACTCCGTGGCACTTTTTTCCTA
* *
321077 C-TTTAAGTCCAACAACTCCGTGGCA
1 CTTTTAAG-CCCATAACTCCGTGGCA
321102 TCTTCCTCCC
Statistics
Matches: 78, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
33 6 0.08
34 21 0.27
35 3 0.04
36 41 0.53
37 3 0.04
38 4 0.05
ACGTcount: A:0.19, C:0.32, G:0.13, T:0.36
Consensus pattern (36 bp):
CTTTTAAGCCCATAACTCCGTGGCACTTTTTTCCTA
Found at i:321179 original size:32 final size:36
Alignment explanation
Indices: 321111--321181 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 36
321101 ATCTTCCTCC
321111 CTTCCTAAAGCCCACACAAGTCCGGTGGCAACCCTT
1 CTTCCTAAAGCCCACACAAGTCCGGTGGCAACCCTT
321147 CTTCC-AAAG-CCACACAAGT-CGGT-GCAACCCTT
1 CTTCCTAAAGCCCACACAAGTCCGGTGGCAACCCTT
321179 CTT
1 CTT
321182 AAGCCCAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
32 12 0.34
33 4 0.11
34 10 0.29
35 4 0.11
36 5 0.14
ACGTcount: A:0.25, C:0.38, G:0.15, T:0.21
Consensus pattern (36 bp):
CTTCCTAAAGCCCACACAAGTCCGGTGGCAACCCTT
Found at i:321354 original size:49 final size:49
Alignment explanation
Indices: 321180--321802 Score: 618
Period size: 49 Copynumber: 12.9 Consensus size: 49
321170 GCAACCCTTC
* *
321180 TTAAGCCCAATATAGCTGGCCTTGAATCAGCATCTTGGCATCTTCATCT
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCT
* * *
321229 TTAAGGCC-ATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CT
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCT
* * * *
321271 TTAAGCCCAATATAGCTGCCCTACATGCATCAGCATATTGGCAATCTTCA-CC
1 TTAAGTCCAATATAGCTGGCCT---TGAATCAGCATATTGGC-ATCTTCATCT
* * *
321323 TTAAGTCCACTATCGCTGGCCTTGAATCAGCACATTGGCA----C--C-
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCT
* * **
321365 TTAAGTCCAATATCGCTTGCAGTGAATCAGCATATTGGCATCTTCATCT
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCT
* * * * * * *
321414 TTACGTCCACTGTAGCTGGGCC-TGACTCAGCACATTGGCACCTTCACCT
1 TTAAGTCCAATATAGCT-GGCCTTGAATCAGCATATTGGCATCTTCATCT
* *
321463 TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG-ATCATCATCT
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCT
* * * *
321511 TTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCT
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCT
*
321560 TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCT
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCT
* * * * *
321609 TTAAGACCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCT
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCT
*
321658 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCT
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG--CATCTT-CATCT
* * ** *
321710 TTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCTTTTCATC-
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATC--TTCATCT
* * * *
321760 TTAAG-CCAATATCGTTGGCCATGAATCAACATATTGGCATCTT
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTT
321803 TATCACTTTT
Statistics
Matches: 471, Mismatches: 78, Indels: 52
0.78 0.13 0.09
Matches are distributed among these distances:
42 44 0.09
43 12 0.03
44 2 0.00
46 16 0.03
47 3 0.01
48 75 0.16
49 241 0.51
50 10 0.02
51 9 0.02
52 59 0.13
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.31
Consensus pattern (49 bp):
TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCT
Found at i:321497 original size:98 final size:98
Alignment explanation
Indices: 321180--321802 Score: 717
Period size: 98 Copynumber: 6.4 Consensus size: 98
321170 GCAACCCTTC
* * * *
321180 TTAAGCCCAATATAGCTGGCCTTGAATCAGCATCTTGGCATCTTCATCTTTAAGGCC-ATGTAGC
1 TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGC
321244 TGGCCTTGAATCAGCACATTGG------CACCT
66 TGGCCTTGAATCAGCACATTGGCACCTTCACCT
* * * * * * *
321271 TTAAGCCCAATATAGCTGCCCTACATGCATCAGCATATTGGCAATCTTCA-CCTTAAGTCCACTA
1 TTAAGTCCAATATCGCTGGCCT---TGAATCAGCATATTGGC-ATCTTCATCTTTAAGTCCAATG
*
321335 TCGCTGGCCTTGAATCAGCACATTGG------CACC-
62 TAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCT
* ** * *
321365 TTAAGTCCAATATCGCTTGCAGTGAATCAGCATATTGGCATCTTCATCTTTACGTCCACTGTAGC
1 TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGC
*
321430 TGGGCC-TGACTCAGCACATTGGCACCTTCACCT
66 T-GGCCTTGAATCAGCACATTGGCACCTTCACCT
*
321463 TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG-ATCATCATCTTTAAGTCCAATGTAGC
1 TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGC
* *
321527 TGGCCTTGACTCAGCACATTGGCACCTTCATCT
66 TGGCCTTGAATCAGCACATTGGCACCTTCACCT
*
321560 TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGACCAATGTAGC
1 TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGC
* *
321625 TGGCCTTGACTCAGCACATTGGCACCTTCATCT
66 TGGCCTTGAATCAGCACATTGGCACCTTCACCT
* * *
321658 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAATGT
1 TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG--CATCTT-CATCTTTAAGTCCAATGT
* * * *
321723 AGCTGGCCTTGAATCAGCACGTTGACATCTTTTCATC-
63 AGCTGGCCTTGAATCAGCACATTGGCA-C-CTTCACCT
* * *
321760 TTAAG-CCAATATCGTTGGCCATGAATCAACATATTGGCATCTT
1 TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTT
321803 TATCACTTTT
Statistics
Matches: 469, Mismatches: 42, Indels: 34
0.86 0.08 0.06
Matches are distributed among these distances:
90 7 0.01
91 67 0.14
92 4 0.01
94 39 0.08
95 37 0.08
96 4 0.01
97 92 0.20
98 129 0.28
99 5 0.01
100 5 0.01
101 68 0.14
102 6 0.01
103 6 0.01
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.31
Consensus pattern (98 bp):
TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGC
TGGCCTTGAATCAGCACATTGGCACCTTCACCT
Found at i:321602 original size:195 final size:193
Alignment explanation
Indices: 321178--321802 Score: 751
Period size: 195 Copynumber: 3.2 Consensus size: 193
321168 GTGCAACCCT
* * * *
321178 TCTTAAGCCCAATATAGCTGGCCTTGAATCAGCATCTTGGCATCTTCATCTTTAAGGCCATGTAG
1 TCTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGACCATGTAG
* * * *
321243 CTGGCCTTGAATCAGCACATTGG------CACCTTTAAGCCCAATATAGCTGCCCTACATGCATC
66 CTGGCCTTGACTCAGCACATTGGCACCTTCACCTTTAAGTCCAATATAGCTGGCCT---TGAATC
* * * * *
321302 AGCATATTGGCAATCTTCA-CCTTAAGTCCACTATCGCTGGCCTTGAATCAGCACATTGGCA---
128 AGCATATTGGC-ATCATCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACTT
321363 C-
192 CA
* ** * *
321364 -CTTAAGTCCAATATCGCTTGCAGTGAATCAGCATATTGGCATCTTCATCTTTACGTCCACTGTA
1 TCTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGACCA-TGTA
*
321428 GCTGGGCC-TGACTCAGCACATTGGCACCTTCACCTTTAAGTCCAATATCGCTGGCCTTGAATCA
65 GCT-GGCCTTGACTCAGCACATTGGCACCTTCACCTTTAAGTCCAATATAGCTGGCCTTGAATCA
*
321492 GCATATTGG-ATCATCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTC
129 GCATATTGGCATCATCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CTTC
321556 A
193 A
321557 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGACCAATGT
1 TC-TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGACC-ATGT
*
321622 AGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCA
64 AGCTGGCCTTGACTCAGCACATTGGCACCTTCACCTTTAAGTCCAATATAGCTGGCCTTGAATCA
* * *
321687 GCATATTGGCA-CATTTTCCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACAT
129 GCATATTGGCATCA---T-CATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-
321751 CTTTTCA
189 C--TTCA
* * *
321758 TCTTAAG-CCAATATCGTTGGCCATGAATCAACATATTGGCATCTT
1 TCTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTT
321803 TATCACTTTT
Statistics
Matches: 380, Mismatches: 34, Indels: 37
0.84 0.08 0.08
Matches are distributed among these distances:
185 51 0.13
186 22 0.06
187 10 0.03
188 37 0.10
189 15 0.04
192 25 0.07
194 5 0.01
195 124 0.33
196 2 0.01
198 1 0.00
199 77 0.20
200 5 0.01
201 6 0.02
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.31
Consensus pattern (193 bp):
TCTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGACCATGTAG
CTGGCCTTGACTCAGCACATTGGCACCTTCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGC
ATATTGGCATCATCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACTTCA
Found at i:322709 original size:33 final size:33
Alignment explanation
Indices: 322672--322738 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
322662 TTCAACGATT
322672 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
322705 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
322738 T
1 T
322739 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:322710 original size:13 final size:13
Alignment explanation
Indices: 322692--322716 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
322682 CATAAAATGT
322692 TGTATCGATACAA
1 TGTATCGATACAA
322705 TGTATCGATACA
1 TGTATCGATACA
322717 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:322798 original size:13 final size:13
Alignment explanation
Indices: 322780--322804 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
322770 ATTACTCACA
322780 TGTATCGATACAT
1 TGTATCGATACAT
322793 TGTATCGATACA
1 TGTATCGATACA
322805 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:322941 original size:52 final size:52
Alignment explanation
Indices: 322813--322933 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
322803 CACTGATCTT
*
322813 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
322865 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
322917 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
322934 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:329919 original size:20 final size:20
Alignment explanation
Indices: 329873--329911 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
329863 CACAAACAAA
*
329873 AGTCAAAAACAAAAAAAGAG
1 AGTCAAAAACAAAAAAAAAG
329893 AGTCAAAAA-AAAAAAAAAG
1 AGTCAAAAACAAAAAAAAAG
329912 GGTGCAAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.74, C:0.08, G:0.13, T:0.05
Consensus pattern (20 bp):
AGTCAAAAACAAAAAAAAAG
Done.