Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold405
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: 649601
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.31
Warning! 46917 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:476666 original size:253 final size:253
Alignment explanation
Indices: 476218--476965 Score: 1408
Period size: 253 Copynumber: 3.0 Consensus size: 253
476208 ACAGGAAGAG
* *
476218 GAGTAGGAGGATGAAGTAAAACGGTAAGTGAAAACCCATTTGCGTTGTTATTTGGTTTGAGGGAA
1 GAGTAGGAGGATGAAGTAAAGCGGTAAGTGAAAACCCATTTGCGTTGTTATTTTGTTTGAGGGAA
*
476283 ATCAATGAAGATTTAAAGAAACAAAGGATGTTTGAGTGAGAAGCAAATGAAAAGTATTTGGTCAC
66 ATGAATGAAGATTTAAAGAAACAAAGGATGTTTGAGTGAGAAGCAAATGAAAAGTATTTGGTCAC
476348 ACTTTCCTTGAAGTTCCAGTATAAGTGCATTTGATTTGAGAATAATTCATTAATTTGCAAAGACT
131 ACTTTCCTTGAAGTTCCAGTATAAGTGCATTTGATTTGAGAATAATTCATTAATTTGCAAAGACT
476413 GTTGGATACAATTTTCCAGCT-CACGTAAGAGGGTCTCCATTCAAAGAAATAAAGGGAA
196 GTTGGATACAATTTTCCAGCTACACGTAAGA-GGTCTCCATTCAAAGAAATAAAGGGAA
476471 GAGTAGGAGGATGAAGTAAAGCGGTAAGTGAAAACCCATTTGCGTTGTTATTTTGTTTGAGGGAA
1 GAGTAGGAGGATGAAGTAAAGCGGTAAGTGAAAACCCATTTGCGTTGTTATTTTGTTTGAGGGAA
476536 ATGAATGAAGATTTAAAGAAACAAAGGATGTTTGAGTGAGAAGCAAATGAAAAGTATTTGGTCAC
66 ATGAATGAAGATTTAAAGAAACAAAGGATGTTTGAGTGAGAAGCAAATGAAAAGTATTTGGTCAC
476601 ACTTTCCTTGAAGTTCCAGTATAAGTGCATTTGATTTGAGAATAATTCATTAATTTGCAAAGACT
131 ACTTTCCTTGAAGTTCCAGTATAAGTGCATTTGATTTGAGAATAATTCATTAATTTGCAAAGACT
476666 GTTGGATACAATTTTCCAGCTACACGTAAGAGGTCTCCATTCAAAGAAATAAAGGGAA
196 GTTGGATACAATTTTCCAGCTACACGTAAGAGGTCTCCATTCAAAGAAATAAAGGGAA
*
476724 GAGTAGGAGGATGAAGTAAAGCGGTAAGTGAAAACCCATTTGCGTTGTTATTTTGTTTGAGGGGA
1 GAGTAGGAGGATGAAGTAAAGCGGTAAGTGAAAACCCATTTGCGTTGTTATTTTGTTTGAGGGAA
* *
476789 ATGAATGAAGATTTAAAGAAACAAAGGATGTTTGAGTGAGAAGCAAATGAAAAGAATTTGCTCAC
66 ATGAATGAAGATTTAAAGAAACAAAGGATGTTTGAGTGAGAAGCAAATGAAAAGTATTTGGTCAC
*
476854 ACTTTCCTTGAAGTTCCAGTGTAAGTGCATTTGATTTGAGAATAATTCATTAATTTGCAAAGACT
131 ACTTTCCTTGAAGTTCCAGTATAAGTGCATTTGATTTGAGAATAATTCATTAATTTGCAAAGACT
*
476919 GTTGGATACAATTTTCCAGCTACACGTAAGTGGTCTCCATTCAAAGA
196 GTTGGATACAATTTTCCAGCTACACGTAAGAGGTCTCCATTCAAAGA
476966 GTAGGTTACG
Statistics
Matches: 486, Mismatches: 8, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
253 477 0.98
254 9 0.02
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.29
Consensus pattern (253 bp):
GAGTAGGAGGATGAAGTAAAGCGGTAAGTGAAAACCCATTTGCGTTGTTATTTTGTTTGAGGGAA
ATGAATGAAGATTTAAAGAAACAAAGGATGTTTGAGTGAGAAGCAAATGAAAAGTATTTGGTCAC
ACTTTCCTTGAAGTTCCAGTATAAGTGCATTTGATTTGAGAATAATTCATTAATTTGCAAAGACT
GTTGGATACAATTTTCCAGCTACACGTAAGAGGTCTCCATTCAAAGAAATAAAGGGAA
Found at i:477679 original size:14 final size:17
Alignment explanation
Indices: 477643--477679 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
477633 TGAGACAACC
477643 TTTTTACATCATTCAAT
1 TTTTTACATCATTCAAT
477660 TGTTTT-CAT-ATTCAAT
1 T-TTTTACATCATTCAAT
477676 TTTT
1 TTTT
477680 ACAAATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 3 0.16
16 8 0.42
17 4 0.21
18 4 0.21
ACGTcount: A:0.24, C:0.14, G:0.03, T:0.59
Consensus pattern (17 bp):
TTTTTACATCATTCAAT
Found at i:497163 original size:23 final size:24
Alignment explanation
Indices: 497133--497181 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
497123 TTGAATCGTA
*
497133 TTTTATAA-TTGTTAATATTTTAT
1 TTTTATAACTTGTTAATAATTTAT
*
497156 TTTTATAACTTTTTAATAATTTAT
1 TTTTATAACTTGTTAATAATTTAT
497180 TT
1 TT
497182 GATTTGCACT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (24 bp):
TTTTATAACTTGTTAATAATTTAT
Found at i:497802 original size:3 final size:3
Alignment explanation
Indices: 497473--497785 Score: 545
Period size: 3 Copynumber: 104.3 Consensus size: 3
497463 ATTTATATCT
*
497473 GAA GAA GAA GAA GAA GAA GAA GAA GAA AAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* *
497521 GAA GAA GAA AAA GAA GAA GAA GAA GAA GAA GAA GAA GAA AAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
*
497569 GAA GAA GAA GAA GAA GAA GAA AAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* *
497617 GAA AAA GAA GAA GAA GAA GAA GAA GAA GAA GAA AAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
*
497665 GAA GAA GAA GAA GAA AAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* *
497713 GAA GAA AAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA AAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
497761 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
497786 GTCAAGGATG
Statistics
Matches: 292, Mismatches: 18, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 292 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:499057 original size:12 final size:12
Alignment explanation
Indices: 499036--499067 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
499026 TTTTATAGCC
*
499036 TTATTCATTTCT
1 TTATTTATTTCT
499048 TTATTTATTTCT
1 TTATTTATTTCT
499060 TTATTTAT
1 TTATTTAT
499068 ATTTTCATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (12 bp):
TTATTTATTTCT
Found at i:501039 original size:19 final size:18
Alignment explanation
Indices: 500998--501040 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
500988 CGTCTCTTTT
500998 TGCATTCATTTCATGCATC
1 TGCATTCATTTCATGCA-C
501017 TGCATTACATTTCATTGCA-
1 TGCATT-CATTTCA-TGCAC
501036 TGCAT
1 TGCAT
501041 CAAATTTCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 11 0.50
20 7 0.32
21 4 0.18
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.42
Consensus pattern (18 bp):
TGCATTCATTTCATGCAC
Found at i:503274 original size:15 final size:15
Alignment explanation
Indices: 503251--503320 Score: 72
Period size: 15 Copynumber: 4.7 Consensus size: 15
503241 AAGAATGTTC
503251 AAAAAAAAAGAAAGA
1 AAAAAAAAAGAAAGA
*
503266 AACAAAAAAGAGAAGA
1 AAAAAAAAAGA-AAGA
503282 AAAAAGAAAAG-AAGA
1 AAAAA-AAAAGAAAGA
* *
503297 AAAGAAGAA-AAAGA
1 AAAAAAAAAGAAAGA
*
503311 AAAGAAAAAG
1 AAAAAAAAAG
503321 GAGAGGCCAA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
14 15 0.33
15 18 0.39
16 8 0.17
17 5 0.11
ACGTcount: A:0.80, C:0.01, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAGAAAGA
Found at i:503284 original size:11 final size:11
Alignment explanation
Indices: 503261--503320 Score: 61
Period size: 11 Copynumber: 5.4 Consensus size: 11
503251 AAAAAAAAAG
503261 AAAGAAACA-AA
1 AAAGAAA-AGAA
*
503272 AAAGAGAAGAAA
1 AAAGAAAAG-AA
503284 AAAGAAAAGAA
1 AAAGAAAAGAA
*
503295 GAAA-AGAAGAA
1 -AAAGAAAAGAA
503306 AAAGAAAAGAA
1 AAAGAAAAGAA
503317 AAAG
1 AAAG
503321 GAGAGGCCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
10 4 0.10
11 24 0.59
12 13 0.32
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAGAAAAGAA
Found at i:503298 original size:8 final size:8
Alignment explanation
Indices: 503276--503316 Score: 61
Period size: 8 Copynumber: 5.5 Consensus size: 8
503266 AACAAAAAAG
503276 AGAAGAAA
1 AGAAGAAA
503284 A-AAGAAA
1 AGAAGAAA
503291 AGAAGAAA
1 AGAAGAAA
503299 AGAAG-AA
1 AGAAGAAA
503306 A-AAGAAA
1 AGAAGAAA
503313 AGAA
1 AGAA
503317 AAAGGAGAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
6 3 0.10
7 13 0.43
8 14 0.47
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (8 bp):
AGAAGAAA
Found at i:503299 original size:27 final size:27
Alignment explanation
Indices: 503251--503318 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 27
503241 AAGAATGTTC
503251 AAAAAAAAAG-AAAGAAACAAAA-AAG
1 AAAAAAAAAGAAAAGAAACAAAAGAAG
*
503276 AGAAGAAAAAAGAAAAG-AAGAAAAGAAG
1 A-AA-AAAAAAGAAAAGAAACAAAAGAAG
503304 AAAAAGAAAAGAAAA
1 AAAAA-AAAAGAAAA
503319 AGGAGAGGCC
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
25 1 0.03
26 4 0.11
27 24 0.65
28 8 0.22
ACGTcount: A:0.81, C:0.01, G:0.18, T:0.00
Consensus pattern (27 bp):
AAAAAAAAAGAAAAGAAACAAAAGAAG
Found at i:503763 original size:97 final size:97
Alignment explanation
Indices: 503597--504078 Score: 795
Period size: 97 Copynumber: 5.0 Consensus size: 97
503587 TTTCATTTCG
* *
503597 TATCTTAGTAAAATTTGCTATCTTGATTAATTTATTCATTTCGAGCCGTGCTCTCAATAAATTTT
1 TATCTTAGCAAAATTTGCTATCTTGATTAATTTATTCATTTCGAGCCTTGCTCTCAATAAATTTT
503662 CATCTTATCCATTGTGATAATCTTTTTCATCT
66 CATCTTATCCATTGTGATAATCTTTTTCATCT
* *
503694 TATCTTAGCAAAATTTGCTATCTTGATTAATTTATTCATTTCGAGCCGTGATCTCAATAAATTTT
1 TATCTTAGCAAAATTTGCTATCTTGATTAATTTATTCATTTCGAGCCTTGCTCTCAATAAATTTT
503759 CATCTTATCCATTGTGATAATCTTTTTCATCT
66 CATCTTATCCATTGTGATAATCTTTTTCATCT
* * *
503791 TATCTTAGCAAAATTTGCTATCTTGATTAATTTATTCATTTTGAGCTTTGCTTTCAATAAATTTT
1 TATCTTAGCAAAATTTGCTATCTTGATTAATTTATTCATTTCGAGCCTTGCTCTCAATAAATTTT
*
503856 TATCTTATCCATTGTGATAATCTTTTTCATCT
66 CATCTTATCCATTGTGATAATCTTTTTCATCT
* *
503888 TATCTTAGCAAAATTTGCTATCTTGATTAATTTATTCATTTTGAGCTTTGCTCTCAATAAATTTT
1 TATCTTAGCAAAATTTGCTATCTTGATTAATTTATTCATTTCGAGCCTTGCTCTCAATAAATTTT
*
503953 TATCTTATCCATTGTGATAATCTTTTTCATCT
66 CATCTTATCCATTGTGATAATCTTTTTCATCT
* *
503985 TATCTTAGCAAAATTTGCTATCTTGATTAATTTATTCATCTT-GAGCCTTGTTCTCAATAAAATT
1 TATCTTAGCAAAATTTGCTATCTTGATTAATTTATTCAT-TTCGAGCCTTGCTCTCAATAAATTT
* * * *
504049 TCATATTGTCCATTGTAATAATCTCTTTCA
65 TCATCTTATCCATTGTGATAATCTTTTTCA
504079 AGCTTTTTTT
Statistics
Matches: 367, Mismatches: 17, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
97 365 0.99
98 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.48
Consensus pattern (97 bp):
TATCTTAGCAAAATTTGCTATCTTGATTAATTTATTCATTTCGAGCCTTGCTCTCAATAAATTTT
CATCTTATCCATTGTGATAATCTTTTTCATCT
Found at i:503861 original size:47 final size:47
Alignment explanation
Indices: 503809--503958 Score: 137
Period size: 47 Copynumber: 3.1 Consensus size: 47
503799 CAAAATTTGC
503809 TATCTTGATTAATTTATTCATTTTGAGCTTTGCTTTCAATAAATTTT
1 TATCTTGATTAATTTATTCATTTTGAGCTTTGCTTTCAATAAATTTT
** * * * * *
503856 TATCTT-ATCCATTGTGATAATCTTTTTCATCTTAT-CTTAGC-A-AAATTTGC
1 TATCTTGATTAATT-T-AT--TCATTTTGAGCTT-TGCTT-TCAATAAATTT-T
*
503906 TATCTTGATTAATTTATTCATTTTGAGCTTTGCTCTCAATAAATTTT
1 TATCTTGATTAATTTATTCATTTTGAGCTTTGCTTTCAATAAATTTT
503953 TATCTT
1 TATCTT
503959 ATCCATTGTG
Statistics
Matches: 77, Mismatches: 15, Indels: 22
0.68 0.13 0.19
Matches are distributed among these distances:
46 7 0.09
47 26 0.34
48 8 0.10
49 8 0.10
50 21 0.27
51 7 0.09
ACGTcount: A:0.25, C:0.14, G:0.08, T:0.53
Consensus pattern (47 bp):
TATCTTGATTAATTTATTCATTTTGAGCTTTGCTTTCAATAAATTTT
Found at i:504928 original size:46 final size:46
Alignment explanation
Indices: 504861--505326 Score: 722
Period size: 46 Copynumber: 10.1 Consensus size: 46
504851 ACAGATAAAT
*
504861 GAAGATAGCAGATCTTGTCTTCCTGTATTTGACAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATC
*
504907 GAAGATAGCAAATCTTGTCTTCCTGTATTTGGCAGC-AGAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGA-AGTAGATC
*
504953 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGGCAG-TAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTT-GGCAGCGAAGTAGATC
* *
504999 GAAGATAGCAGATCTTGTCTTCCTATATTTGGCAGCGGAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATC
*
505045 AAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATC
* *
505091 GAAGATAGCAGATCTTGTCTTCTTGTATTTGGCAGCGGAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATC
*
505137 GAAAATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATC
* * *
505183 AAAGATTGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATC
* * *
505229 AAAGATAGCATATCTTGTCTTCCTGTATTTGGAAGC-AGAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGA-AGTAGATC
* * *
505275 GAAGATAGCAAATCTTGTCTTTCTGTATTTGGCAGCGAATTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATC
505321 GAAGAT
1 GAAGAT
505327 TACAGATTCT
Statistics
Matches: 386, Mismatches: 28, Indels: 12
0.91 0.07 0.03
Matches are distributed among these distances:
45 6 0.02
46 373 0.97
47 7 0.02
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (46 bp):
GAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATC
Found at i:505815 original size:88 final size:88
Alignment explanation
Indices: 505700--505861 Score: 206
Period size: 88 Copynumber: 1.8 Consensus size: 88
505690 CTTTGTCTCT
* *
505700 CTGAAGTTGCAGTAGAGCAGGTTAAAAT-A-GCAAACCTTATC-CCCATGAAGTTGCAGTGGGGC
1 CTGAAGTTGCAGTAGAACAGGTTAAAATGATG-AAACC-TATCTCCC-TAAAGTTGCAGTGGGGC
*
505762 AAGTTGAAGATACAAATTCCACCTCC
63 AAGTCGAAGATACAAATTCCACCTCC
* * *
505788 CTGAAGTTGCAGTGGAAC-GGATTAAAATGATGGATCCTATCTCCCTAAAGTTGCAGTGGGGCAA
1 CTGAAGTTGCAGTAGAACAGG-TTAAAATGATGAAACCTATCTCCCTAAAGTTGCAGTGGGGCAA
505852 GTCGAAGATA
65 GTCGAAGATA
505862 GCAAGTCTTA
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
87 2 0.03
88 54 0.84
89 7 0.11
90 1 0.02
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.23
Consensus pattern (88 bp):
CTGAAGTTGCAGTAGAACAGGTTAAAATGATGAAACCTATCTCCCTAAAGTTGCAGTGGGGCAAG
TCGAAGATACAAATTCCACCTCC
Found at i:508108 original size:12 final size:12
Alignment explanation
Indices: 508087--508118 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
508077 TTTTATAGCC
*
508087 TTATTCATTTCT
1 TTATTTATTTCT
508099 TTATTTATTTCT
1 TTATTTATTTCT
508111 TTATTTAT
1 TTATTTAT
508119 ATTTTCATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (12 bp):
TTATTTATTTCT
Found at i:510802 original size:84 final size:84
Alignment explanation
Indices: 510661--510825 Score: 294
Period size: 84 Copynumber: 2.0 Consensus size: 84
510651 AAAATATAAT
*
510661 AGCCCATTTTCAGTGAAGTTGGAATAGTAGTTTCGGGACCACAAATTCGAGTCCGGAAGAAAAAT
1 AGCCCATTTTCAGTGAAGTTAGAATAGTAGTTTCGGGACCACAAATTCGAGTCCGGAAGAAAAAT
510726 TATTTTAATATTATTTAAC
66 TATTTTAATATTATTTAAC
* * *
510745 AGCCCGTTTTCAGTGAAGTTAGAATAGTAGTTTTGGGACCACAAATTTGAGTCCGGAAGAAAAAT
1 AGCCCATTTTCAGTGAAGTTAGAATAGTAGTTTCGGGACCACAAATTCGAGTCCGGAAGAAAAAT
510810 TATTTTAATATTATTT
66 TATTTTAATATTATTT
510826 CATGGTCTGC
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 77 1.00
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (84 bp):
AGCCCATTTTCAGTGAAGTTAGAATAGTAGTTTCGGGACCACAAATTCGAGTCCGGAAGAAAAAT
TATTTTAATATTATTTAAC
Found at i:511633 original size:16 final size:16
Alignment explanation
Indices: 511595--511633 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
511585 AATTAAATTA
*
511595 ATTAAAAGTAAATTTT
1 ATTAAATGTAAATTTT
511611 ATTAAATGTAAATTTT
1 ATTAAATGTAAATTTT
511627 ATTAAAT
1 ATTAAAT
511634 TGATGTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (16 bp):
ATTAAATGTAAATTTT
Found at i:512102 original size:25 final size:25
Alignment explanation
Indices: 512074--512167 Score: 86
Period size: 25 Copynumber: 3.8 Consensus size: 25
512064 ATACACCGTA
512074 GCTCTTATGAGCTTCCCGATATATG
1 GCTCTTATGAGCTTCCCGATATATG
* * * *
512099 GCTCTCCA-GAGCTTCCTGTTATATA
1 GCTCT-TATGAGCTTCCCGATATATG
* **
512124 GTTCTTGCGAGCTTCCC-AT-TATG
1 GCTCTTATGAGCTTCCCGATATATG
*
512147 GCTCTTATGAGCTTCTCGATA
1 GCTCTTATGAGCTTCCCGATA
512168 ATTAGCTCTT
Statistics
Matches: 51, Mismatches: 14, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
23 16 0.31
24 3 0.06
25 31 0.61
26 1 0.02
ACGTcount: A:0.18, C:0.26, G:0.19, T:0.37
Consensus pattern (25 bp):
GCTCTTATGAGCTTCCCGATATATG
Found at i:512111 original size:105 final size:106
Alignment explanation
Indices: 511929--512129 Score: 280
Period size: 105 Copynumber: 1.9 Consensus size: 106
511919 ACAGGGTTCC
*
511929 CGATTGGCTGTGATCCTGCATGTGTTACAGACACACCATAGCTCTTACGAGCGTCCCAATATTTG
1 CGATTGGCTGTGATCCTGCATGTGTTACAGACACACCATAGCTCTTACGAGCGTCCCAATATATG
511994 GCTCTCACGAGCTTCCCGTTA-ATAGCTCTTCGAAGCATCT
66 GCTCTCACGAGCTTCCCGTTATATAGCTCTTCGAAGCATCT
* ** * * * * *
512034 CGATTGGTTGTGATCCTGCATGTGTTTTAGATACACCGTAGCTCTTATGAGCTTCCCGATATATG
1 CGATTGGCTGTGATCCTGCATGTGTTACAGACACACCATAGCTCTTACGAGCGTCCCAATATATG
* *
512099 GCTCTC-CAGAGCTTCCTGTTATATAGTTCTT
66 GCTCTCAC-GAGCTTCCCGTTATATAGCTCTT
512130 GCGAGCTTCC
Statistics
Matches: 83, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
104 1 0.01
105 74 0.89
106 8 0.10
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.34
Consensus pattern (106 bp):
CGATTGGCTGTGATCCTGCATGTGTTACAGACACACCATAGCTCTTACGAGCGTCCCAATATATG
GCTCTCACGAGCTTCCCGTTATATAGCTCTTCGAAGCATCT
Found at i:512193 original size:25 final size:25
Alignment explanation
Indices: 512165--512212 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
512155 GAGCTTCTCG
*
512165 ATAATTAGCTCTTCAGAGCTTCCTA
1 ATAACTAGCTCTTCAGAGCTTCCTA
**
512190 ATAACTAGCTCTTTTGAGCTTCC
1 ATAACTAGCTCTTCAGAGCTTCC
512213 CATTATATTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (25 bp):
ATAACTAGCTCTTCAGAGCTTCCTA
Found at i:512209 original size:73 final size:73
Alignment explanation
Indices: 512074--512218 Score: 186
Period size: 73 Copynumber: 2.0 Consensus size: 73
512064 ATACACCGTA
* ** *
512074 GCTCTTATGAGCTTCCCGATATATGGCTCTCCAGAGCTTCCTGTTATATAGTTCTTGCGAGCTTC
1 GCTCTTATGAGCTTCCCGATATATAGCTCTCCAGAGCTTCCTAATATATAGCTCTTGCGAGCTTC
512139 CCATTATG
66 CCATTATG
* * **
512147 GCTCTTATGAGCTTCTCGATA-ATTAGCTCTTCAGAGCTTCCTAATA-ACTAGCTCTTTTGAGCT
1 GCTCTTATGAGCTTCCCGATATA-TAGCTCTCCAGAGCTTCCTAATATA-TAGCTCTTGCGAGCT
512210 TCCCATTAT
64 TCCCATTAT
512219 ATTGCTCGAC
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
72 2 0.03
73 60 0.97
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.38
Consensus pattern (73 bp):
GCTCTTATGAGCTTCCCGATATATAGCTCTCCAGAGCTTCCTAATATATAGCTCTTGCGAGCTTC
CCATTATG
Found at i:512263 original size:26 final size:25
Alignment explanation
Indices: 512204--512251 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
512194 CTAGCTCTTT
512204 TGAGCTTCCCATTATATTGCTCGAC
1 TGAGCTTCCCATTATATTGCTCGAC
*
512229 AGAGCTTCCCATT-TATGTGCTCG
1 TGAGCTTCCCATTATAT-TGCTCG
512252 TATGAGCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 3 0.14
25 18 0.86
ACGTcount: A:0.19, C:0.27, G:0.19, T:0.35
Consensus pattern (25 bp):
TGAGCTTCCCATTATATTGCTCGAC
Found at i:524064 original size:69 final size:69
Alignment explanation
Indices: 523953--524178 Score: 353
Period size: 69 Copynumber: 3.3 Consensus size: 69
523943 CAGGGTTAAG
* * *
523953 TAGCACCACGAGATATAAATTATAATTCTTAAAGTAGCACCACTAGTGATTTTCTTTTGTTTTTA
1 TAGCACCACTAAATGTAAATTATAATTCTTAAAGTAGCACCACTAGTGATTTTCTTTTGTTTTTA
*
524018 TAAT
66 AAAT
524022 TAGCACCACTAAATGTAAATTATAATTCTTAAAGTAGCACCACTAGTGATTTTCTTTTGTTTTTA
1 TAGCACCACTAAATGTAAATTATAATTCTTAAAGTAGCACCACTAGTGATTTTCTTTTGTTTTTA
524087 AAAT
66 AAAT
* * * *
524091 TAGCACCACTAAATGTAACTTATAATTCTTAAAGCAGCACCACTAGTGTTTTTCTTTTCTTTTTA
1 TAGCACCACTAAATGTAAATTATAATTCTTAAAGTAGCACCACTAGTGATTTTCTTTTGTTTTTA
524156 AAAT
66 AAAT
** *
524160 TATTACCACTAGATGTAAA
1 TAGCACCACTAAATGTAAA
524179 AATAAATTAT
Statistics
Matches: 145, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 145 1.00
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (69 bp):
TAGCACCACTAAATGTAAATTATAATTCTTAAAGTAGCACCACTAGTGATTTTCTTTTGTTTTTA
AAAT
Found at i:524065 original size:34 final size:34
Alignment explanation
Indices: 523950--524135 Score: 101
Period size: 34 Copynumber: 5.4 Consensus size: 34
523940 AAGCAGGGTT
* * *
523950 AAGTAGCACCACGAGATATAAATTATAATTCTTA
1 AAGTAGCACCACTAAATGTAAATTATAATTCTTA
* ** * ** *
523984 AAGTAGCACCACT-AGTG-ATTTTCTTTTGTTTTTA
1 AAGTAGCACCACTAAATGTA-AAT-TATAATTCTTA
*
524018 TAATTAGCACCACTAAATGTAAATTATAATTCTTA
1 -AAGTAGCACCACTAAATGTAAATTATAATTCTTA
* ** * ** *
524053 AAGTAGCACCACT-AGTG-ATTTTCTTTTGTTTTTAA
1 AAGTAGCACCACTAAATGTA-AAT-TATAATTCTT-A
* *
524088 AATTAGCACCACTAAATGTAACTTATAATTCTTA
1 AAGTAGCACCACTAAATGTAAATTATAATTCTTA
*
524122 AAGCAGCACCACTA
1 AAGTAGCACCACTA
524136 GTGTTTTTCT
Statistics
Matches: 106, Mismatches: 36, Indels: 20
0.65 0.22 0.12
Matches are distributed among these distances:
32 2 0.02
33 6 0.06
34 50 0.47
35 38 0.36
36 8 0.08
37 2 0.02
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.37
Consensus pattern (34 bp):
AAGTAGCACCACTAAATGTAAATTATAATTCTTA
Found at i:524100 original size:35 final size:35
Alignment explanation
Indices: 523987--524101 Score: 110
Period size: 35 Copynumber: 3.3 Consensus size: 35
523977 ATTCTTAAAG
*
523987 TAGCACCACTAGTGATTTTCTTTTGTTTTTATAAT
1 TAGCACCACTAGTGATTTTCTTTTGTTTTTAAAAT
* ** * ** * *
524022 TAGCACCACTAAATG-TAAAT-TATAATTCTT-AAAG
1 TAGCACCACT-AGTGAT-TTTCTTTTGTTTTTAAAAT
524056 TAGCACCACTAGTGATTTTCTTTTGTTTTTAAAAT
1 TAGCACCACTAGTGATTTTCTTTTGTTTTTAAAAT
524091 TAGCACCACTA
1 TAGCACCACTA
524102 AATGTAACTT
Statistics
Matches: 58, Mismatches: 17, Indels: 10
0.68 0.20 0.12
Matches are distributed among these distances:
33 4 0.07
34 19 0.33
35 31 0.53
36 4 0.07
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (35 bp):
TAGCACCACTAGTGATTTTCTTTTGTTTTTAAAAT
Found at i:524123 original size:35 final size:35
Alignment explanation
Indices: 524019--524123 Score: 99
Period size: 35 Copynumber: 3.0 Consensus size: 35
524009 TTGTTTTTAT
*
524019 AATTAGCACCACTAAATGTAAATTATAATTCTT-A
1 AATTAGCACCACTAAATGTAACTTATAATTCTTAA
* * ** ** *
524053 AAGTAGCACCACT-AGTGATTTTCTT-TTGTTTTTAA
1 AATTAGCACCACTAAATG--TAACTTATAATTCTTAA
524088 AATTAGCACCACTAAATGTAACTTATAATTCTTAA
1 AATTAGCACCACTAAATGTAACTTATAATTCTTAA
524123 A
1 A
524124 GCAGCACCAC
Statistics
Matches: 51, Mismatches: 15, Indels: 9
0.68 0.20 0.12
Matches are distributed among these distances:
33 3 0.06
34 21 0.41
35 24 0.47
36 3 0.06
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (35 bp):
AATTAGCACCACTAAATGTAACTTATAATTCTTAA
Found at i:528311 original size:23 final size:24
Alignment explanation
Indices: 528281--528329 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
528271 TTGAATCGTA
*
528281 TTTTATAA-TTGTTAATATTTTAT
1 TTTTATAACTTGTTAATAATTTAT
*
528304 TTTTATAACTTTTTAATAATTTAT
1 TTTTATAACTTGTTAATAATTTAT
528328 TT
1 TT
528330 GATTTGCACT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (24 bp):
TTTTATAACTTGTTAATAATTTAT
Found at i:528743 original size:3 final size:3
Alignment explanation
Indices: 528621--528726 Score: 194
Period size: 3 Copynumber: 35.3 Consensus size: 3
528611 ATTTATATCT
*
528621 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA AAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
*
528669 GAA GAA GAA GAA GAA GAA GAA GAA AAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
528717 GAA GAA GAA G
1 GAA GAA GAA G
528727 GTCAAGGATG
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 99 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:537413 original size:78 final size:78
Alignment explanation
Indices: 537284--537439 Score: 303
Period size: 78 Copynumber: 2.0 Consensus size: 78
537274 GGCAGTTTTG
537284 GTGCAATTTACTTTAAACCAGTCATTGGAATCATCCTTGTCCTCCATGCTAAAAGGGTAGTGAAA
1 GTGCAATTTACTTTAAACCAGTCATTGGAATCATCCTTGTCCTCCATGCTAAAAGGGTAGTGAAA
537349 TTTAACATTCCCA
66 TTTAACATTCCCA
*
537362 GTGCAATTTACTTTAAACCAGTCATTGGAATCATCTTTGTCCTCCATGCTAAAAGGGTAGTGAAA
1 GTGCAATTTACTTTAAACCAGTCATTGGAATCATCCTTGTCCTCCATGCTAAAAGGGTAGTGAAA
537427 TTTAACATTCCCA
66 TTTAACATTCCCA
537440 CAGTTCTCCA
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (78 bp):
GTGCAATTTACTTTAAACCAGTCATTGGAATCATCCTTGTCCTCCATGCTAAAAGGGTAGTGAAA
TTTAACATTCCCA
Found at i:538225 original size:41 final size:41
Alignment explanation
Indices: 538136--538230 Score: 97
Period size: 41 Copynumber: 2.3 Consensus size: 41
538126 CGTTTTTAAT
* * * *
538136 TGAAAGCATTTTCAAGTGATTTGTAGAAAAATGTTTCCCAC
1 TGAAAGCATTTTCAAGTGATTTGCAAAAAAATGCTTCCAAC
538177 T-AGAAGCATTTTCAACGT-A-TTGACAAAAAAATGCTTCCAAC
1 TGA-AAGCATTTTCAA-GTGATTTG-CAAAAAAATGCTTCCAAC
538218 TGAAAGCACTTTT
1 TGAAAGCA-TTTT
538231 GTCACATCAA
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
40 4 0.09
41 34 0.76
42 7 0.16
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.32
Consensus pattern (41 bp):
TGAAAGCATTTTCAAGTGATTTGCAAAAAAATGCTTCCAAC
Found at i:538500 original size:3 final size:3
Alignment explanation
Indices: 538492--538549 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
538482 TTGGTTTCTT
538492 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
538540 TTA TTA TTA T
1 TTA TTA TTA T
538550 CTTCTTTTAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:540469 original size:25 final size:25
Alignment explanation
Indices: 540405--540471 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 25
540395 CTTCCGTCAA
* *
540405 TGGCTCTTATGAGCTTCTCGATAAT
1 TGGCTCTTATGAGCTTCCCGATAAC
* * *
540430 TAGCTTTTCA-AAGCTTCCCGATAAC
1 TGGCTCTT-ATGAGCTTCCCGATAAC
540455 TGGCTCTTATGAGCTTC
1 TGGCTCTTATGAGCTTC
540472 TTGTTATATG
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
24 1 0.03
25 30 0.94
26 1 0.03
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.37
Consensus pattern (25 bp):
TGGCTCTTATGAGCTTCCCGATAAC
Found at i:540495 original size:50 final size:50
Alignment explanation
Indices: 540405--540499 Score: 120
Period size: 50 Copynumber: 1.9 Consensus size: 50
540395 CTTCCGTCAA
**
540405 TGGCTCTTATGAGCTTCTCGATAATTAGCTTTTCAAAGCTTCCCGATAAC
1 TGGCTCTTATGAGCTTCTCGATAATTAGCTTGACAAAGCTTCCCGATAAC
* * * *
540455 TGGCTCTTATGAGCTTCTTG-TTATATGGCTTGACAGAGCTTCCCG
1 TGGCTCTTATGAGCTTCTCGATAAT-TAGCTTGACAAAGCTTCCCG
540500 TTTATGTGCT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
49 3 0.08
50 35 0.92
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.37
Consensus pattern (50 bp):
TGGCTCTTATGAGCTTCTCGATAATTAGCTTGACAAAGCTTCCCGATAAC
Found at i:541337 original size:21 final size:21
Alignment explanation
Indices: 541313--541388 Score: 98
Period size: 21 Copynumber: 3.6 Consensus size: 21
541303 ATAATTAAGA
*
541313 ATTGAGGATTGAGGATTGAGG
1 ATTGAGAATTGAGGATTGAGG
* **
541334 ATTGAGAAATGAAAATTGAGG
1 ATTGAGAATTGAGGATTGAGG
*
541355 ATTGAGAATTTAGGATTGAGG
1 ATTGAGAATTGAGGATTGAGG
*
541376 ATTGAGTATTGAG
1 ATTGAGAATTGAG
541389 TTGAAAAGAA
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.36, C:0.00, G:0.34, T:0.30
Consensus pattern (21 bp):
ATTGAGAATTGAGGATTGAGG
Found at i:541389 original size:7 final size:7
Alignment explanation
Indices: 541313--541388 Score: 89
Period size: 7 Copynumber: 10.9 Consensus size: 7
541303 ATAATTAAGA
541313 ATTGAGG
1 ATTGAGG
541320 ATTGAGG
1 ATTGAGG
541327 ATTGAGG
1 ATTGAGG
*
541334 ATTGAGA
1 ATTGAGG
* **
541341 AATGAAA
1 ATTGAGG
541348 ATTGAGG
1 ATTGAGG
*
541355 ATTGAGA
1 ATTGAGG
*
541362 ATTTAGG
1 ATTGAGG
541369 ATTGAGG
1 ATTGAGG
*
541376 ATTGAGT
1 ATTGAGG
541383 ATTGAG
1 ATTGAG
541389 TTGAAAAGAA
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 58 1.00
ACGTcount: A:0.36, C:0.00, G:0.34, T:0.30
Consensus pattern (7 bp):
ATTGAGG
Found at i:545205 original size:29 final size:29
Alignment explanation
Indices: 545172--545227 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
545162 AAACGGATTT
*
545172 GATCAAATTAGTTTTTATATTATTAAATA
1 GATCAAATTAGTCTTTATATTATTAAATA
*
545201 GATCAATTTAGTCTTTATATTATTAAA
1 GATCAAATTAGTCTTTATATTATTAAA
545228 AAGAATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.48
Consensus pattern (29 bp):
GATCAAATTAGTCTTTATATTATTAAATA
Found at i:547916 original size:20 final size:21
Alignment explanation
Indices: 547893--547942 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
547883 AATTAAAGAT
**
547893 ATAAAAATTA-TTAAATTTTA
1 ATAAAAATTATTTAAAAGTTA
547913 ATAAAAA-TATTTAAAAGTTA
1 ATAAAAATTATTTAAAAGTTA
*
547933 TTAAAAATTA
1 ATAAAAATTA
547943 GAAAAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.84
21 2 0.08
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
ATAAAAATTATTTAAAAGTTA
Found at i:554006 original size:25 final size:25
Alignment explanation
Indices: 553978--554128 Score: 98
Period size: 25 Copynumber: 6.1 Consensus size: 25
553968 TACACCGCAA
*
553978 CTCTTATGAGCGTCCCGATATATGG
1 CTCTTATGAGCTTCCCGATATATGG
* *
554003 CTCTCCA-GAGCTTCCCGTTATATGG
1 CTCT-TATGAGCTTCCCGATATATGG
* ** *
554028 TTCTTGCGAGCTTCCTG-T-TATGG
1 CTCTTATGAGCTTCCCGATATATGG
* *
554051 CTCTTATGAGCTTCTCGATA-ATTAG
1 CTCTTATGAGCTTCCCGATATA-TGG
*
554076 CTCTTCA-GAGCTTCCCGGTA-ACTGG
1 CTCTT-ATGAGCTTCCCGATATA-TGG
* * * *
554101 ATCTTTTGAGCTTCCCGTTATACGG
1 CTCTTATGAGCTTCCCGATATATGG
554126 CTC
1 CTC
554129 GACAGAGCTT
Statistics
Matches: 96, Mismatches: 22, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
23 17 0.18
24 3 0.03
25 73 0.76
26 3 0.03
ACGTcount: A:0.17, C:0.26, G:0.21, T:0.36
Consensus pattern (25 bp):
CTCTTATGAGCTTCCCGATATATGG
Found at i:554014 original size:104 final size:104
Alignment explanation
Indices: 553832--554024 Score: 271
Period size: 104 Copynumber: 1.9 Consensus size: 104
553822 TATGGGTTTT
* * * *
553832 CCGATTGGCTGTGATCCTGTATGTGTTACAGACACACCATAGCTCTTACGAGCGTCCCAATATTT
1 CCGATTGGCTGTGATCCTGCATGTGTTACAGACACACCACAACTCTTACGAGCGTCCCAATATAT
553897 GGCTCTCACGAGCTTCCCGTTATAGCTCTTCGGAGCATC
66 GGCTCTCACGAGCTTCCCGTTATAGCTCTTCGGAGCATC
* ** * * * *
553936 CCGATTGGTTGTGATCCTGCATGTGTTTTAGATACACCGCAACTCTTATGAGCGTCCCGATATAT
1 CCGATTGGCTGTGATCCTGCATGTGTTACAGACACACCACAACTCTTACGAGCGTCCCAATATAT
554001 GGCTCTC-CAGAGCTTCCCGTTATA
66 GGCTCTCAC-GAGCTTCCCGTTATA
554025 TGGTTCTTGC
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
103 1 0.01
104 76 0.99
ACGTcount: A:0.20, C:0.27, G:0.21, T:0.31
Consensus pattern (104 bp):
CCGATTGGCTGTGATCCTGCATGTGTTACAGACACACCACAACTCTTACGAGCGTCCCAATATAT
GGCTCTCACGAGCTTCCCGTTATAGCTCTTCGGAGCATC
Found at i:554112 original size:73 final size:73
Alignment explanation
Indices: 553978--554121 Score: 175
Period size: 73 Copynumber: 2.0 Consensus size: 73
553968 TACACCGCAA
* * *
553978 CTCTTATGAGCGTCCCGATATATGGCTCTCCAGAGCTTCCCGTTATATGGTTCTTGCGAGCTTCC
1 CTCTTATGAGCGTCCCGATATATAGCTCTCCAGAGCTTCCCGGTATATGGATCTTGCGAGCTTCC
*
554043 TGTTATGG
66 CGTTATGG
* * * **
554051 CTCTTATGAGCTTCTCGATA-ATTAGCTCTTCAGAGCTTCCCGGTA-ACTGGATCTTTTGAGCTT
1 CTCTTATGAGCGTCCCGATATA-TAGCTCTCCAGAGCTTCCCGGTATA-TGGATCTTGCGAGCTT
554114 CCCGTTAT
64 CCCGTTAT
554122 ACGGCTCGAC
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
72 2 0.03
73 58 0.97
ACGTcount: A:0.17, C:0.26, G:0.21, T:0.37
Consensus pattern (73 bp):
CTCTTATGAGCGTCCCGATATATAGCTCTCCAGAGCTTCCCGGTATATGGATCTTGCGAGCTTCC
CGTTATGG
Found at i:556368 original size:20 final size:19
Alignment explanation
Indices: 556340--556387 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
556330 CAAAATATTG
556340 TTTTT-TTTTATGCTTTCA
1 TTTTTCTTTTATGCTTTCA
*
556358 TCTTTTCTTTTATTCTTTCA
1 T-TTTTCTTTTATGCTTTCA
*
556378 TTTTTGTTTT
1 TTTTTCTTTT
556388 GGGAATATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 1 0.04
19 12 0.46
20 13 0.50
ACGTcount: A:0.08, C:0.12, G:0.04, T:0.75
Consensus pattern (19 bp):
TTTTTCTTTTATGCTTTCA
Found at i:559705 original size:21 final size:21
Alignment explanation
Indices: 559662--559705 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
559652 ACATGCCTAT
* *
559662 TGAAAGAAGCACACGACCGTG
1 TGAAAGAAACACACGACCATG
* *
559683 TGAAGGAAACACACGCCCATG
1 TGAAAGAAACACACGACCATG
559704 TG
1 TG
559706 TTCGAGCTGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.25, G:0.27, T:0.11
Consensus pattern (21 bp):
TGAAAGAAACACACGACCATG
Found at i:563762 original size:34 final size:34
Alignment explanation
Indices: 563719--563836 Score: 114
Period size: 34 Copynumber: 3.4 Consensus size: 34
563709 AAGCAGGGTT
*
563719 AAGTAGCACCACGAGATGTAAATTATAATTCTTA
1 AAGTAGCACCACTAGATGTAAATTATAATTCTTA
*** ** *
563753 AAGTAGCACCACTACTGAT-TTTCTT-TTCTTTTTAA
1 AAGTAGCACCACTA--GATGTAAATTATAATTCTT-A
* *
563788 AATTAGCACCACTAAATGTAAATTATAATTCTTA
1 AAGTAGCACCACTAGATGTAAATTATAATTCTTA
563822 AAGTAGCACCACTAG
1 AAGTAGCACCACTAG
563837 TGTTTTTCTT
Statistics
Matches: 62, Mismatches: 17, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
33 2 0.03
34 35 0.56
35 22 0.35
36 3 0.05
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (34 bp):
AAGTAGCACCACTAGATGTAAATTATAATTCTTA
Found at i:563833 original size:69 final size:69
Alignment explanation
Indices: 563722--563875 Score: 263
Period size: 69 Copynumber: 2.2 Consensus size: 69
563712 CAGGGTTAAG
*
563722 TAGCACCACGAGATGTAAATTATAATTCTTAAAGTAGCACCACTACTGATTTTCTTTTCTTTTTA
1 TAGCACCACTAGATGTAAATTATAATTCTTAAAGTAGCACCACTACTGATTTTCTTTTCTTTTTA
563787 AAAT
66 AAAT
* * *
563791 TAGCACCACTAAATGTAAATTATAATTCTTAAAGTAGCACCACTAGTGTTTTTCTTTTCTTTTTA
1 TAGCACCACTAGATGTAAATTATAATTCTTAAAGTAGCACCACTACTGATTTTCTTTTCTTTTTA
563856 AAAT
66 AAAT
*
563860 TAGCGCCACTAGATGT
1 TAGCACCACTAGATGT
563876 CAAAATAAAT
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 79 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (69 bp):
TAGCACCACTAGATGTAAATTATAATTCTTAAAGTAGCACCACTACTGATTTTCTTTTCTTTTTA
AAAT
Found at i:563857 original size:34 final size:35
Alignment explanation
Indices: 563752--563871 Score: 100
Period size: 35 Copynumber: 3.5 Consensus size: 35
563742 TATAATTCTT
* *
563752 AAAGTAGCACCACTACTGATTTTCTTTTCTTTTTA
1 AAAGTAGCACCACTAGTGTTTTTCTTTTCTTTTTA
* * *** * ** *
563787 AAATTAGCACCACTAAATGTAAAT-TATAATTCTT-
1 AAAGTAGCACCACT-AGTGTTTTTCTTTTCTTTTTA
563821 AAAGTAGCACCACTAGTGTTTTTCTTTTCTTTTTA
1 AAAGTAGCACCACTAGTGTTTTTCTTTTCTTTTTA
* *
563856 AAATTAGCGCCACTAG
1 AAAGTAGCACCACTAG
563872 ATGTCAAAAT
Statistics
Matches: 61, Mismatches: 21, Indels: 6
0.69 0.24 0.07
Matches are distributed among these distances:
33 5 0.08
34 19 0.31
35 33 0.54
36 4 0.07
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.40
Consensus pattern (35 bp):
AAAGTAGCACCACTAGTGTTTTTCTTTTCTTTTTA
Found at i:568296 original size:14 final size:14
Alignment explanation
Indices: 568279--568308 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
568269 AGAGGCTGAT
568279 CTTAAGGTATTCAA
1 CTTAAGGTATTCAA
568293 CTTAAGGTATTCAA
1 CTTAAGGTATTCAA
568307 CT
1 CT
568309 GTAACCTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (14 bp):
CTTAAGGTATTCAA
Found at i:569818 original size:125 final size:125
Alignment explanation
Indices: 569596--569848 Score: 488
Period size: 125 Copynumber: 2.0 Consensus size: 125
569586 TTAGGGTTTT
*
569596 TAGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
1 TAGGTCATGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
*
569661 AGGATGCTATTTGAGAAGAATTTGTGAAAGTGCGCCCTCGTGGACGCGCTTTTGCTACAG
66 AGGATGCTATTTGAGAAGAATTTGTGAAAGTGCGCCCTCGTGGACGCGCCTTTGCTACAG
569721 TAGGTCATGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
1 TAGGTCATGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
569786 AGGATGCTATTTGAGAAGAATTTGTGAAAGTGCGCCCTCGTGGACGCGCCTTTGCTACAG
66 AGGATGCTATTTGAGAAGAATTTGTGAAAGTGCGCCCTCGTGGACGCGCCTTTGCTACAG
569846 TAG
1 TAG
569849 CATGTTTGGG
Statistics
Matches: 126, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
125 126 1.00
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (125 bp):
TAGGTCATGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
AGGATGCTATTTGAGAAGAATTTGTGAAAGTGCGCCCTCGTGGACGCGCCTTTGCTACAG
Found at i:570850 original size:18 final size:18
Alignment explanation
Indices: 570812--570851 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
570802 GACTCGGAAA
* * *
570812 AGGATATATATAAGGGTT
1 AGGATACATATAAAGGCT
570830 AGGATACATATAAAGGCT
1 AGGATACATATAAAGGCT
570848 AGGA
1 AGGA
570852 AATGCACCTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.28, T:0.25
Consensus pattern (18 bp):
AGGATACATATAAAGGCT
Found at i:572626 original size:38 final size:38
Alignment explanation
Indices: 572575--572649 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
572565 TTCTCCGGCC
* *
572575 ATTGCTGAAATCGTACAAATTTTTACGGTTTAAAAAAA
1 ATTGCTGAAATCGTACAAAATTTTACGGTATAAAAAAA
572613 ATTGCTGAAATCGTACAAAATTTTACGGTATAAAAAA
1 ATTGCTGAAATCGTACAAAATTTTACGGTATAAAAAA
572650 TTTGAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (38 bp):
ATTGCTGAAATCGTACAAAATTTTACGGTATAAAAAAA
Found at i:572744 original size:51 final size:51
Alignment explanation
Indices: 572683--572780 Score: 144
Period size: 51 Copynumber: 1.9 Consensus size: 51
572673 AATTATTTAA
572683 AAATAGGGATTTAAGAGAAATTTAAGAA-GAACTTGAGAGCAAATTGAAATT
1 AAATAGGGATTTAAGAGAAATTT-AGAAGGAACTTGAGAGCAAATTGAAATT
* * * *
572734 AAATATGGATTTGAGAGAAATTTTGAAGGAATTTGAGAGCAAATTGA
1 AAATAGGGATTTAAGAGAAATTTAGAAGGAACTTGAGAGCAAATTGA
572781 GAGGAAATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
50 3 0.07
51 39 0.93
ACGTcount: A:0.46, C:0.03, G:0.23, T:0.28
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAGAAGGAACTTGAGAGCAAATTGAAATT
Found at i:572778 original size:12 final size:11
Alignment explanation
Indices: 572742--572796 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
572732 TTAAATATGG
572742 ATTTGAGAGAA
1 ATTTGAGAGAA
*
572753 ATTTTGA-AGGA
1 A-TTTGAGAGAA
572764 ATTTGAGAGCAA
1 ATTTGAGAG-AA
572776 A-TTGAGAGGAA
1 ATTTGAGA-GAA
572787 ATTTGAGAGA
1 ATTTGAGAGA
572797 GGATTAGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
10 5 0.14
11 18 0.49
12 14 0.38
ACGTcount: A:0.42, C:0.02, G:0.29, T:0.27
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:572789 original size:23 final size:21
Alignment explanation
Indices: 572742--572796 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 21
572732 TTAAATATGG
572742 ATTTGAGAGAAATTTTGAAGGA
1 ATTTGAGAGAAA-TTTGAAGGA
572764 ATTTGAGAGCAAA-TTGAGAGGAA
1 ATTTGAGAG-AAATTTGA-AGG-A
572787 ATTTGAGAGA
1 ATTTGAGAGA
572797 GGATTAGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
21 4 0.13
22 13 0.43
23 13 0.43
ACGTcount: A:0.42, C:0.02, G:0.29, T:0.27
Consensus pattern (21 bp):
ATTTGAGAGAAATTTGAAGGA
Found at i:573291 original size:88 final size:89
Alignment explanation
Indices: 573182--573353 Score: 247
Period size: 89 Copynumber: 1.9 Consensus size: 89
573172 AAATTGAAGG
* * * * * *
573182 GGTAGAAAAATAGAAATATGG-AGAATATAAATTTTCTTTCCATGTGTGTGCTTGGTAGGAAAGA
1 GGTAGAAAAATAGAAAGATGGAAAAATATAAATTTTCTTTCCATATGTGTGCTTAGCAGGAAACA
**
573246 TGGAAAAATTGAAAGAAAAGAAAA
66 TGGAAAAATCAAAAGAAAAGAAAA
* *
573270 GGTAGAAAGATAGAAAGATGGAAAAATATAAATTTTCTTTTCATATGTGTGCTTAGCAGGAAACA
1 GGTAGAAAAATAGAAAGATGGAAAAATATAAATTTTCTTTCCATATGTGTGCTTAGCAGGAAACA
573335 TGGAAAAATCAAAAGAAAA
66 TGGAAAAATCAAAAGAAAA
573354 AATATTTTTT
Statistics
Matches: 73, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
88 19 0.26
89 54 0.74
ACGTcount: A:0.47, C:0.06, G:0.22, T:0.26
Consensus pattern (89 bp):
GGTAGAAAAATAGAAAGATGGAAAAATATAAATTTTCTTTCCATATGTGTGCTTAGCAGGAAACA
TGGAAAAATCAAAAGAAAAGAAAA
Found at i:574225 original size:164 final size:164
Alignment explanation
Indices: 573945--574250 Score: 417
Period size: 164 Copynumber: 1.9 Consensus size: 164
573935 TGTTGTAACA
* * *
573945 GTCAACATTAGTCAAAGGGCCTATTTGGCCAATTTTTTAAGTTTAGTGGCTCAATTGGGTGCAAA
1 GTCAACATTAGTCAAAGGGCCTATTTGACCAATTTGTTAAGTTTAGGGGCTCAATTGGGTGCAAA
* * * *
574010 AAGTTCGTAGGGGTTTAATTAATTTTTTTTTTGAATTCGAGGACCAAAAATACCATTAAGCCCTT
66 AAGTTCATAGGGGCTTAATTAATTTTTTTTTTGAATTCGAGGACAAAAAATACCATTAAGCCATT
574075 CTTTAACTATTGATATATCCTTTTCTATGTATTG
131 CTTTAACTATTGATATATCCTTTTCTATGTATTG
* *
574109 GTCAACATTAGTCAAATGGCCTATTTGACCAATTTGTT-AGTTTAGGGGCTCAATTGGGTGTAAA
1 GTCAACATTAGTCAAAGGGCCTATTTGACCAATTTGTTAAGTTTAGGGGCTCAATTGGGTGCAAA
*
574173 AAGTTCATAGGGGCTTAATTGATTTTTTGAAAATGTTTG-A-T-GA-GA-AAAAAATACCATTAA
66 AAGTTCATAGGGGCTTAATTAATTTTTT-----T-TTTGAATTCGAGGACAAAAAATACCATTAA
*
574233 GTCATTCTTTAACTATTG
125 GCCATTCTTTAACTATTG
574251 TTATGTCTTT
Statistics
Matches: 125, Mismatches: 11, Indels: 12
0.84 0.07 0.08
Matches are distributed among these distances:
163 49 0.39
164 65 0.52
165 2 0.02
166 2 0.02
167 1 0.01
168 2 0.02
169 4 0.03
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.38
Consensus pattern (164 bp):
GTCAACATTAGTCAAAGGGCCTATTTGACCAATTTGTTAAGTTTAGGGGCTCAATTGGGTGCAAA
AAGTTCATAGGGGCTTAATTAATTTTTTTTTTGAATTCGAGGACAAAAAATACCATTAAGCCATT
CTTTAACTATTGATATATCCTTTTCTATGTATTG
Found at i:577166 original size:34 final size:35
Alignment explanation
Indices: 577123--577188 Score: 107
Period size: 34 Copynumber: 1.9 Consensus size: 35
577113 AATCTAAATA
*
577123 TGTATCATTAACATTATCGAGATC-ATTTTTTATC
1 TGTATCATTAACATTATCAAGATCTATTTTTTATC
*
577157 TGTATCATTAATATTATCAAGATCTATTTTTT
1 TGTATCATTAACATTATCAAGATCTATTTTTT
577189 TATGTACTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 22 0.76
35 7 0.24
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.50
Consensus pattern (35 bp):
TGTATCATTAACATTATCAAGATCTATTTTTTATC
Found at i:582346 original size:5 final size:5
Alignment explanation
Indices: 582336--582361 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
582326 ACAAAGGATA
582336 ATAAT ATAAT ATAAT ATAAT ATAAT A
1 ATAAT ATAAT ATAAT ATAAT ATAAT A
582362 ATCTCTTCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:594295 original size:45 final size:46
Alignment explanation
Indices: 594185--594317 Score: 171
Period size: 46 Copynumber: 2.9 Consensus size: 46
594175 CTAAAAGGTG
*
594185 GGACCAAGGTGAAAGCCTGCAAAGGGCGCTTTGAGTCAAAAAAAAA
1 GGACCAAGGTGAAAGCCTACAAAGGGCGCTTTGAGTCAAAAAAAAA
* * * *
594231 GGGCCAAGGTTAAAGCCTACAAAGGGCTCTTTGGGTCAAAAAAAAA
1 GGACCAAGGTGAAAGCCTACAAAGGGCGCTTTGAGTCAAAAAAAAA
* * * *
594277 -GACCAGGGTGAAACCCTACAAAGGGAGCCTTGAGT-AAAAAA
1 GGACCAAGGTGAAAGCCTACAAAGGGCGCTTTGAGTCAAAAAA
594318 GGAAAAAAAA
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
44 6 0.08
45 27 0.36
46 41 0.55
ACGTcount: A:0.41, C:0.18, G:0.27, T:0.14
Consensus pattern (46 bp):
GGACCAAGGTGAAAGCCTACAAAGGGCGCTTTGAGTCAAAAAAAAA
Found at i:595710 original size:50 final size:50
Alignment explanation
Indices: 595636--595910 Score: 212
Period size: 50 Copynumber: 5.5 Consensus size: 50
595626 GCAATGGAAC
* * *
595636 AGATTGAAGCTACGACGGCAGATCTGGTTTCCCTGATATTGCAATTTAAA
1 AGATTGAAGCCACAACGGCAGATCTGGTTTCCCTGATATTGCAATTAAAA
* * *** * * * **** *
595686 AGATTGAAGCCACAATGGCGGATCTTACTT-CCTTAGCAGTGCAGCGGAAC
1 AGATTGAAGCCACAACGGCAGATCTGGTTTCCCTGA-TATTGCAATTAAAA
* * *
595736 AGATTGAAGCTACGACGGCAGATCTGGTTTCCCTGATATTGCCATTAAAA
1 AGATTGAAGCCACAACGGCAGATCTGGTTTCCCTGATATTGCAATTAAAA
*** * * * * ** *
595786 AGATTGAAGCCACAACGGCAGATCTTACTT-CCTTAGCAGTGCAGTGGAAT
1 AGATTGAAGCCACAACGGCAGATCTGGTTTCCCTGA-TATTGCAATTAAAA
* * * *
595836 AGATTAAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAA
1 AGATTGAAGCCACAACGGCAGATCTGGTTTCCCTGATATTGCAATTAAAA
*
595886 AGATTGAAGCCACAACGACAGATCT
1 AGATTGAAGCCACAACGGCAGATCT
595911 TACTTCTCTA
Statistics
Matches: 158, Mismatches: 63, Indels: 8
0.69 0.28 0.03
Matches are distributed among these distances:
49 8 0.05
50 142 0.90
51 8 0.05
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (50 bp):
AGATTGAAGCCACAACGGCAGATCTGGTTTCCCTGATATTGCAATTAAAA
Found at i:595994 original size:100 final size:100
Alignment explanation
Indices: 595605--595978 Score: 579
Period size: 100 Copynumber: 3.7 Consensus size: 100
595595 GTGAAACCAT
* *
595605 AGATTTTACTTCCTTAGCAGTGCAATGGAACAGATTGAAGCTACGACGGCAGATCTGGTTTCCCT
1 AGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCAGATCTGGTTTCCCT
* *
595670 GATATTGCAATTTAAAAGATTGAAGCCACAATGGC
66 GATATTGCAATTAAAAAGATTGAAGCCACAACGGC
* *
595705 GGATCTTACTTCCTTAGCAGTGCAGCGGAACAGATTGAAGCTACGACGGCAGATCTGGTTTCCCT
1 AGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCAGATCTGGTTTCCCT
*
595770 GATATTGCCATTAAAAAGATTGAAGCCACAACGGC
66 GATATTGCAATTAAAAAGATTGAAGCCACAACGGC
* * *
595805 AGATCTTACTTCCTTAGCAGTGCAGTGGAATAGATTAAAGCTACGACGGCGGATCTGGTTTCCCT
1 AGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCAGATCTGGTTTCCCT
*
595870 GATATTGCAATTAAAAAGATTGAAGCCACAACGAC
66 GATATTGCAATTAAAAAGATTGAAGCCACAACGGC
* * * *
595905 AGATCTTACTT-CTCTAACGGTGCGGTGGAACAGATTGAAGCCACGACGGCAGATCTGGTTTCCC
1 AGATCTTACTTCCT-TAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCAGATCTGGTTTCCC
* *
595969 CGACATTGCA
65 TGATATTGCA
595979 GTTGAGCAAA
Statistics
Matches: 250, Mismatches: 23, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
99 2 0.01
100 248 0.99
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (100 bp):
AGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCAGATCTGGTTTCCCT
GATATTGCAATTAAAAAGATTGAAGCCACAACGGC
Found at i:596265 original size:44 final size:43
Alignment explanation
Indices: 596131--596281 Score: 131
Period size: 44 Copynumber: 3.4 Consensus size: 43
596121 TTGAAAAAGC
* * *
596131 AGATCTTGTCCTCATATATTGGCGTGAAGTAGATCGAAGAAAGC
1 AGATCTTGTCTTCATATACTGGCGTGAAGTAGATCGAAGAAA-T
* ** * * *
596175 AGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCGAATAAAAT
1 AGATCTTGTCTTCATATACTGG-CGTGAAGTAGATCGAA-GAAAT
* * *
596220 AGATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGATAAT
1 AGATCTTGTCTTCATATACTGGCGTGAAGTAGATCGAAGA-AAT
* * *
596264 AGGTCCTGTCTTCCTATA
1 AGATCTTGTCTTCATATA
596282 TCGGTAGCGA
Statistics
Matches: 81, Mismatches: 23, Indels: 6
0.74 0.21 0.05
Matches are distributed among these distances:
43 1 0.01
44 46 0.57
45 31 0.38
46 3 0.04
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (43 bp):
AGATCTTGTCTTCATATACTGGCGTGAAGTAGATCGAAGAAAT
Found at i:597814 original size:241 final size:240
Alignment explanation
Indices: 597392--597872 Score: 944
Period size: 241 Copynumber: 2.0 Consensus size: 240
597382 ATCGGAGCAT
597392 CGGCGCGCGGTTGAACGGCGGCGCGGAGAACGAGTTGAAAACCCTAGCAGAGCTTTTGCTCTCTT
1 CGGCGCGCGGTTGAACGGCGGCGCGGAGAACGAGTTGAAAACCCTAGCAGAGCTTTTGCTCTCTT
597457 TTTTTTCTTTCCTTATGCTACAAATGAAAATTTTTTAAAAAATTTTGTTTTAAATTGTATTAGCA
66 TTTTTTCTTTCCTTATGCTACAAATGAAAATTTTTTAAAAAATTTTGTTTTAAATTGTATTAGCA
597522 AAACGGCGCCGTTTAGGTGGCCATGACCCGCGCGGTGACCCGACCCGGAGGGGAGGATCCGCGCA
131 AAACGGCGCCGTTTAGGTGGCCATGACCCGCGCGGTGACCCGACCCGGAGGGGAGGATCCGCGCA
597587 TTCTGGCCTTGAATGGGAAATTTGCGCATCTGGTCCTTCAATTTC
196 TTCTGGCCTTGAATGGGAAATTTGCGCATCTGGTCCTTCAATTTC
597632 CGGCGCGCGGTTGAACGGCGGCGCGGAGAACGAGTTGAAAACCCTAGCAGAGCTTTTGCTCTCTT
1 CGGCGCGCGGTTGAACGGCGGCGCGGAGAACGAGTTGAAAACCCTAGCAGAGCTTTTGCTCTC-T
597697 TTTTTTTCTTTCCTTATGCTACAAATGAAAATTTTTTAAAAAATTTTGTTTTAAATTGTATTAGC
65 TTTTTTTCTTTCCTTATGCTACAAATGAAAATTTTTTAAAAAATTTTGTTTTAAATTGTATTAGC
*
597762 AAAACGGCGCCGTTTAGGTGGCCATGACCCGCGCGGTGACCCGACCCGGAGGGGTGGATCCGCGC
130 AAAACGGCGCCGTTTAGGTGGCCATGACCCGCGCGGTGACCCGACCCGGAGGGGAGGATCCGCGC
597827 ATTCTGGCCTTGAATGGGAAATTTGCGCATCTGGTCCTTCAATTTC
195 ATTCTGGCCTTGAATGGGAAATTTGCGCATCTGGTCCTTCAATTTC
597873 TAAAATCGTT
Statistics
Matches: 239, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
240 63 0.26
241 176 0.74
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (240 bp):
CGGCGCGCGGTTGAACGGCGGCGCGGAGAACGAGTTGAAAACCCTAGCAGAGCTTTTGCTCTCTT
TTTTTTCTTTCCTTATGCTACAAATGAAAATTTTTTAAAAAATTTTGTTTTAAATTGTATTAGCA
AAACGGCGCCGTTTAGGTGGCCATGACCCGCGCGGTGACCCGACCCGGAGGGGAGGATCCGCGCA
TTCTGGCCTTGAATGGGAAATTTGCGCATCTGGTCCTTCAATTTC
Found at i:598219 original size:18 final size:18
Alignment explanation
Indices: 598187--598221 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
598177 CTTTTATAAA
* *
598187 TACATACATATATTTTTG
1 TACATACAAACATTTTTG
598205 TACATACAAACATTTTT
1 TACATACAAACATTTTT
598222 ATATATATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.14, G:0.03, T:0.46
Consensus pattern (18 bp):
TACATACAAACATTTTTG
Found at i:600652 original size:3 final size:3
Alignment explanation
Indices: 600644--600682 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
600634 NNNNNNNNNN
600644 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
600683 GGTTGAGCTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:604244 original size:165 final size:159
Alignment explanation
Indices: 603964--604278 Score: 384
Period size: 165 Copynumber: 1.9 Consensus size: 159
603954 CATTGTAATA
*
603964 GTCAACATTAGTCAAAGGGCCTATTTAGCAAATTTTATTAGTTCAGGGCAATTGGGTGCAAAAAG
1 GTCAACATTAGTCAAAGGGCCTATTTAGCAAATTTTATTAGTTAAGGGCAATTGGGTGCAAAAAG
* * *
604029 TTCACAAGGGTTAATTGATTTTTTGATAAAGTTCGAGGACCAAAAATACCATTAAACCCTTCTTT
66 TTCACAAGGGTTAATTGATTTTTCGATAAAGTTCGAGGA-CAAAAATACCAATAAACCCTACTTT
*
604094 AACTATTGGTATATCTTTTTCTAAGTATCG
130 AACTATTGATATATCTTTTTCTAAGTATCG
* * * * *
604124 GTCAACATTAGTCAAATGGCTTATTTGGTC-AATTTTGTTAGTTTAAGGGCTTAGTTGGGTGCAA
1 GTCAACATTAGTCAAAGGGCCTATTTAG-CAAATTTTATTAG-TTAAGGGC--AATTGGGTGCAA
* * * *
604188 AAAGTTCGCAGGGGCTTAATTGACTTTTTCGA-AATAGTTCGACAGTA-AAAAATACCAATAAGC
62 AAAGTTCACAAGGG-TTAATTGA-TTTTTCGATAA-AGTTCG--AGGACAAAAATACCAATAAAC
*
604251 CCTACTTTAACTATTGATATGTCTTTTT
122 CCTACTTTAACTATTGATATATCTTTTT
604279 TAATTAATTT
Statistics
Matches: 131, Mismatches: 15, Indels: 13
0.82 0.09 0.08
Matches are distributed among these distances:
160 35 0.27
161 8 0.06
163 23 0.18
164 10 0.08
165 52 0.40
167 3 0.02
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (159 bp):
GTCAACATTAGTCAAAGGGCCTATTTAGCAAATTTTATTAGTTAAGGGCAATTGGGTGCAAAAAG
TTCACAAGGGTTAATTGATTTTTCGATAAAGTTCGAGGACAAAAATACCAATAAACCCTACTTTA
ACTATTGATATATCTTTTTCTAAGTATCG
Found at i:609150 original size:16 final size:14
Alignment explanation
Indices: 609127--609173 Score: 58
Period size: 16 Copynumber: 3.1 Consensus size: 14
609117 GACAACCCAA
609127 TTTTATTTTTATTT
1 TTTTATTTTTATTT
609141 TATGTTATTTATATATTT
1 T-T-TTATTT-T-TATTT
609159 TTTTATTTTTATTT
1 TTTTATTTTTATTT
609173 T
1 T
609174 CTCGAATGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
14 7 0.24
15 2 0.07
16 12 0.41
17 2 0.07
18 6 0.21
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (14 bp):
TTTTATTTTTATTT
Found at i:617830 original size:66 final size:67
Alignment explanation
Indices: 617723--617858 Score: 265
Period size: 66 Copynumber: 2.0 Consensus size: 67
617713 TAAAATATTT
617723 TTTAATTTAAAAAAGTTTTAAGCTTCGAAACGAATGAACTTGGTACTGCAACATCATCAACTATT
1 TTTAATTTAAAAAAGTTTTAAGCTTCGAAACGAATGAACTTGGTACTGCAACATCATCAACTATT
617788 CC
66 CC
617790 TTTAATTT-AAAAAGTTTTAAGCTTCGAAACGAATGAACTTGGTACTGCAACATCATCAACTATT
1 TTTAATTTAAAAAAGTTTTAAGCTTCGAAACGAATGAACTTGGTACTGCAACATCATCAACTATT
617854 CC
66 CC
617856 TTT
1 TTT
617859 TAAAAATTAA
Statistics
Matches: 69, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
66 61 0.88
67 8 0.12
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.35
Consensus pattern (67 bp):
TTTAATTTAAAAAAGTTTTAAGCTTCGAAACGAATGAACTTGGTACTGCAACATCATCAACTATT
CC
Found at i:618282 original size:164 final size:166
Alignment explanation
Indices: 617972--618290 Score: 453
Period size: 165 Copynumber: 1.9 Consensus size: 166
617962 ACGTCAATAT
* ** * * *
617972 TGTAACGGTCAACATTAGTCAAATGGCCTATTTGGTCAATTTTGTTAGTTAAGTGACTCAATTGG
1 TGTAACGGTCAACATTAGTCAAAGGGCCTATTTGACCAATTTTATTAGTTAAGGGACTCAATTGA
* *
618037 GTGCAAAAAATTCATAGGGGTTTAATTAATTTTTTTTGAAAAAGTTCGAGGACCAAAAATACCAT
66 GTGCAAAAAATTCACAGGGGCTTAATTAATTTTTTTTGAAAAAGTTCGAGGACCAAAAATACCAT
618102 TAAGCCCTTCTTTAACTATTGATATATCCTTTTCTA
131 TAAGCCCTTCTTTAACTATTGATATATCCTTTTCTA
* * *
618138 TGTATCGGTCAACATTAGTCAAAGGGCCTATTTGACCAA-TTTATTAGTTCAGGGGCTCAATTGA
1 TGTAACGGTCAACATTAGTCAAAGGGCCTATTTGACCAATTTTATTAGTTAAGGGACTCAATTGA
* * *** * * *
618202 GTGTAAAAAGTTCACAGGGGCTTAATTAATTTTTTTT-TTTAAGTTTGATGAGCAAAAATACCAT
66 GTGCAAAAAATTCACAGGGGCTTAATTAATTTTTTTTGAAAAAGTTCGAGGACCAAAAATACCAT
618266 TAAGCCCTTCTTTAACTATTGATAT
131 TAAGCCCTTCTTTAACTATTGATAT
618291 GTCTTTTTTA
Statistics
Matches: 134, Mismatches: 19, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
164 46 0.34
165 53 0.40
166 35 0.26
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.37
Consensus pattern (166 bp):
TGTAACGGTCAACATTAGTCAAAGGGCCTATTTGACCAATTTTATTAGTTAAGGGACTCAATTGA
GTGCAAAAAATTCACAGGGGCTTAATTAATTTTTTTTGAAAAAGTTCGAGGACCAAAAATACCAT
TAAGCCCTTCTTTAACTATTGATATATCCTTTTCTA
Found at i:620054 original size:29 final size:29
Alignment explanation
Indices: 619992--620057 Score: 123
Period size: 29 Copynumber: 2.3 Consensus size: 29
619982 TTTTTTTACA
*
619992 TTATCTATAATAATTCAATTTGATTTAGT
1 TTATTTATAATAATTCAATTTGATTTAGT
620021 TTATTTATAATAATTCAATTTGATTTAGT
1 TTATTTATAATAATTCAATTTGATTTAGT
620050 TTATTTAT
1 TTATTTAT
620058 TTTTATATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.33, C:0.05, G:0.06, T:0.56
Consensus pattern (29 bp):
TTATTTATAATAATTCAATTTGATTTAGT
Found at i:622691 original size:13 final size:13
Alignment explanation
Indices: 622673--622697 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
622663 AGTTCTTCAT
622673 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
622686 TGCTTTTGAGAA
1 TGCTTTTGAGAA
622698 CTTTGAGTGT
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:0.24, C:0.08, G:0.28, T:0.40
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:622949 original size:20 final size:19
Alignment explanation
Indices: 622924--622970 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
622914 ATTAATTATT
622924 TATAAAATTTAATTAGAATA
1 TATAAAATTTAATTA-AATA
* * *
622944 TATAAACTATATTTAAATA
1 TATAAAATTTAATTAAATA
622963 TA-AAAATT
1 TATAAAATT
622971 AAATATTATC
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
18 4 0.18
19 6 0.27
20 12 0.55
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (19 bp):
TATAAAATTTAATTAAATA
Found at i:629001 original size:9 final size:9
Alignment explanation
Indices: 628987--629017 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
628977 GTTAAACGAA
628987 TCGAGTTAT
1 TCGAGTTAT
*
628996 TCGAGTTAA
1 TCGAGTTAT
629005 TCGAGTTAT
1 TCGAGTTAT
629014 TCGA
1 TCGA
629018 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:629745 original size:42 final size:42
Alignment explanation
Indices: 629686--629769 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
629676 GATTCGATTC
629686 GAATTCCATCTCACTCGACTCGATTCGAGAAAACTTCAAATA
1 GAATTCCATCTCACTCGACTCGATTCGAGAAAACTTCAAATA
*
629728 GAATTCTATCTCACTCGACTCGATTCGAGAAAACTTCAAATA
1 GAATTCCATCTCACTCGACTCGATTCGAGAAAACTTCAAATA
629770 AAGTTAATAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.36, C:0.25, G:0.12, T:0.27
Consensus pattern (42 bp):
GAATTCCATCTCACTCGACTCGATTCGAGAAAACTTCAAATA
Found at i:631345 original size:19 final size:18
Alignment explanation
Indices: 631316--631365 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
631306 GAATATTTTT
* *
631316 AAAAATGTAAAAGTTATA
1 AAAAATATAAAAATTATA
*
631334 AAAAATTATAAAAATTATT
1 AAAAA-TATAAAAATTATA
*
631353 ACAAATATAAAAA
1 AAAAATATAAAAA
631366 ATAAAATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (18 bp):
AAAAATATAAAAATTATA
Found at i:633111 original size:22 final size:19
Alignment explanation
Indices: 633083--633131 Score: 53
Period size: 23 Copynumber: 2.4 Consensus size: 19
633073 TAAAATATTT
*
633083 TATTTTTAGAACATATATTTTA
1 TATTTTTA-AA-ATATA-ATTA
633105 TATTTTTTAAAATATAATTA
1 TA-TTTTTAAAATATAATTA
633125 TATTTTT
1 TATTTTT
633132 TAGGTCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.20
20 5 0.20
21 5 0.20
22 4 0.16
23 6 0.24
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (19 bp):
TATTTTTAAAATATAATTA
Found at i:633132 original size:22 final size:23
Alignment explanation
Indices: 633085--633134 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 23
633075 AAATATTTTA
*
633085 TTTTTAGAACATATATTTTATAT
1 TTTTTAGAACATATATTATATAT
*
633108 TTTTTA-AA-ATATAAT-TATAT
1 TTTTTAGAACATATATTATATAT
633128 TTTTTAG
1 TTTTTAG
633135 GTCAAAATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 11 0.44
21 6 0.24
22 2 0.08
23 6 0.24
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (23 bp):
TTTTTAGAACATATATTATATAT
Found at i:633492 original size:20 final size:22
Alignment explanation
Indices: 633451--633508 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
633441 TAATAATAAA
633451 ATATTTTA-A-TTTTAGAACAT
1 ATATTTTATATTTTTAGAACAT
633471 ATATTTTATATTTTTA-AA-AT
1 ATATTTTATATTTTTAGAACAT
*
633491 ATAATTATATATTTTTAG
1 AT-ATTTTATATTTTTAG
633509 GTCAAAATTG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 12 0.36
21 16 0.48
22 5 0.15
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (22 bp):
ATATTTTATATTTTTAGAACAT
Found at i:633508 original size:374 final size:375
Alignment explanation
Indices: 632810--633536 Score: 1217
Period size: 374 Copynumber: 1.9 Consensus size: 375
632800 ATGAATTAAT
* * * * * ** * *
632810 TATTAGATTTGAGTGTAATTACTTGCTATTACAAAAGTATAGTATGTTTGGCTAACTATTGTTAT
1 TATTAGATTTGAGTGCAATTACTTGCGATTACAAAAGTATAGCATGATTAGAAAACCATTGTGAT
* * *
632875 TGATGGGTCCATTAAATTAAATGTAATTATAGCACCTCAATTATACTATTCAATTTTTAGGGAGT
66 TGATGGGTCCACTAAATTAAATGTAATTATAGCACCTCAATTATAATATTCAATTCTTAGGGAGT
632940 TGAGAGTTGGGGTAATTACGCGAGTAATTACAATAAATTACTAATTACCCTATAGTTTTTCAAAC
131 TGAGAGTTGGGGTAATTACGCGAGTAATTACAATAAATTACTAATTACCCTATAGTTTTTCAAAC
*
633005 ACATGTACATGATTTAAGAATTTATTTTTTTATACAAGTTTATAAAATTTATTTTAATACAATAA
196 ACATGTACATGATTTAAGAATTTATTTTTTTATACAAGTTTATAAAAGTTATTTTAATACAATAA
*
633070 TAATAAAATATTTTATTTTTAGAACATATATTTTATATTTTTTAAAATATAATTATATTTTTTAG
261 TAATAAAATATTTTAATTTTAGAACATATATTTTATATTTTTTAAAATATAATTATATTTTTTAG
*
633135 GTCAAAATTGCTTTGCTATTAGACATATAAATTCAAATATTTCGTGCAAA
326 GTCAAAATTGCTTTGATATTAGACATATAAATTCAAATATTTCGTGCAAA
* * * *
633185 TATTAGATTTGAGTGCAATTACTTGCGATTGCAAAGGTGTGGCATGATTAGAAAACCATTGTGAT
1 TATTAGATTTGAGTGCAATTACTTGCGATTACAAAAGTATAGCATGATTAGAAAACCATTGTGA-
* *
633250 TTG-TGGGTTCACTAAATTGAATGTAATTATAGCACCTCAATTATAATATTCAATTCTTAGGG-G
65 TTGATGGGTCCACTAAATTAAATGTAATTATAGCACCTCAATTATAATATTCAATTCTTAGGGAG
*
633313 TTGAGAGTTGGGGTAATTACTCGAGTAATTACAATAAATTACTAATTACCCTATAGTTTTTCAAA
130 TTGAGAGTTGGGGTAATTACGCGAGTAATTACAATAAATTACTAATTACCCTATAGTTTTTCAAA
633378 CACATGTACATGATTTAAGAATTTATTTTTTTATACAAGTTTATAAAAGTTATTTTAATACAATA
195 CACATGTACATGATTTAAGAATTTATTTTTTTATACAAGTTTATAAAAGTTATTTTAATACAATA
633443 ATAATAAAATATTTTAATTTTAGAACATATATTTTATA-TTTTTAAAATATAATTATATATTTTT
260 ATAATAAAATATTTTAATTTTAGAACATATATTTTATATTTTTTAAAATATAATTATAT-TTTTT
633507 AGGTCAAAATTGCTTTGATATTAGACATAT
324 AGGTCAAAATTGCTTTGATATTAGACATAT
633537 GTGGGAGCCT
Statistics
Matches: 328, Mismatches: 22, Indels: 5
0.92 0.06 0.01
Matches are distributed among these distances:
373 20 0.06
374 200 0.61
375 105 0.32
376 3 0.01
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (375 bp):
TATTAGATTTGAGTGCAATTACTTGCGATTACAAAAGTATAGCATGATTAGAAAACCATTGTGAT
TGATGGGTCCACTAAATTAAATGTAATTATAGCACCTCAATTATAATATTCAATTCTTAGGGAGT
TGAGAGTTGGGGTAATTACGCGAGTAATTACAATAAATTACTAATTACCCTATAGTTTTTCAAAC
ACATGTACATGATTTAAGAATTTATTTTTTTATACAAGTTTATAAAAGTTATTTTAATACAATAA
TAATAAAATATTTTAATTTTAGAACATATATTTTATATTTTTTAAAATATAATTATATTTTTTAG
GTCAAAATTGCTTTGATATTAGACATATAAATTCAAATATTTCGTGCAAA
Found at i:633633 original size:43 final size:43
Alignment explanation
Indices: 633539--633683 Score: 177
Period size: 43 Copynumber: 3.4 Consensus size: 43
633529 AGACATATGT
* ** * *
633539 GGGAGCCTCGGGCACCATCGGC-ACCTCGGTGCTTGCAT-GTGT
1 GGGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTG-GTCGTGA
* * * *
633581 GGGAGCCTCGGACACCATCGGGAACCTAGGCCCTTTGTCGTGC
1 GGGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGA
633624 GGGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGA
1 GGGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGA
*
633667 GAGAGCCTCGGGCACCA
1 GGGAGCCTCGGGCACCA
633684 ACATATATTT
Statistics
Matches: 88, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
42 21 0.24
43 67 0.76
ACGTcount: A:0.16, C:0.32, G:0.34, T:0.17
Consensus pattern (43 bp):
GGGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGA
Found at i:634488 original size:34 final size:36
Alignment explanation
Indices: 634435--634504 Score: 108
Period size: 34 Copynumber: 2.0 Consensus size: 36
634425 AGTAAATGAA
*
634435 AAAAACATAGATCTTGATAATCTTAATGATACATAT
1 AAAAACATAGATCTCGATAATCTTAATGATACATAT
*
634471 AAAAA-AT-GATCTCGATAATCTTAATGATGCATAT
1 AAAAACATAGATCTCGATAATCTTAATGATACATAT
634505 TCAGATTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 25 0.78
35 2 0.06
36 5 0.16
ACGTcount: A:0.46, C:0.11, G:0.10, T:0.33
Consensus pattern (36 bp):
AAAAACATAGATCTCGATAATCTTAATGATACATAT
Found at i:636487 original size:165 final size:165
Alignment explanation
Indices: 636214--636535 Score: 473
Period size: 165 Copynumber: 2.0 Consensus size: 165
636204 AAATTAATTA
* * * *
636214 AAAAAGACATATCAATAGTTAAAGCAGGGCTTAAAGGTATTTTTGATAGTCGAACTTTTTCGAAA
1 AAAAAGAAATATCAATAGTTAAAGAAGGGCTTAAAGGTATTTTTGATAGTCAAACTTTTTCAAAA
* * *
636279 AAATCAATTAGGCCCCTGTGAACTTTTTGCACCCAACTGAGCCCTTAAACTAACAAAATTGACAA
66 AAATCAATTAAGCCCCTGCGAACTTTTTGCACCCAACTGAGCCCATAAACTAACAAAATTGACAA
*
636344 AATAAGCCCATTAACTAATGTTGACCGATACTTAG
131 AATAAGCCCATTAACTAATATTGACCGATACTTAG
* * * *
636379 AAAAAGAAATATCAATAGTTAAAGAAGGGTTTAATGGTATTTTTGGTCGTCAAACTTTTTCAAAA
1 AAAAAGAAATATCAATAGTTAAAGAAGGGCTTAAAGGTATTTTTGATAGTCAAACTTTTTCAAAA
* * * *
636444 AAATCAATTAAGCCCCTGCGAACTTTTTGCACCCAATTGAGCCCATGAACTAACAAAATTGGCCA
66 AAATCAATTAAGCCCCTGCGAACTTTTTGCACCCAACTGAGCCCATAAACTAACAAAATTGACAA
* * *
636509 AATAGGCCCTTTGACTAATATTGACCG
131 AATAAGCCCATTAACTAATATTGACCG
636536 TTACAACGTT
Statistics
Matches: 138, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
165 138 1.00
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.28
Consensus pattern (165 bp):
AAAAAGAAATATCAATAGTTAAAGAAGGGCTTAAAGGTATTTTTGATAGTCAAACTTTTTCAAAA
AAATCAATTAAGCCCCTGCGAACTTTTTGCACCCAACTGAGCCCATAAACTAACAAAATTGACAA
AATAAGCCCATTAACTAATATTGACCGATACTTAG
Found at i:637018 original size:675 final size:676
Alignment explanation
Indices: 636051--637402 Score: 2652
Period size: 675 Copynumber: 2.0 Consensus size: 676
636041 CAAATGCATC
636051 TAGAAAATTATAATTCTTTGCAATTACTAGAAGGTGACATTACTACCTTAATAATCACATTTTCA
1 TAGAAAATTATAATTCTTTGCAATTACTAGAAGGTGACATTACTACCTTAATAATCACATTTTCA
636116 TCTAATTCCTTTGTGGCATCAAAATACGCTTTACATGTATACGTGGAAACACCCCGTACATCGTG
66 TCTAATTCCTTTGTGGCATCAAAATACGCTTTACATGTATACGTGGAAACACCCCGTACATCGTG
636181 TGCCTATACTATGCGCGAATGTAAAATTAATTAAAAAAGACATATCAATAGTTAAAGCAGGGCTT
131 TGCCTATACTATGCGCGAATGTAAAATTAATTAAAAAAGACATATCAATAGTTAAAGCAGGGCTT
636246 AAAGGTATTTTTGATAGTCGAACTTTTTCGAAAAAATCAATTAGGCCCCTGTGAACTTTTTGCAC
196 AAAGGTATTTTTGATAGTCGAACTTTTTCGAAAAAATCAATTAGGCCCCTGTGAACTTTTTGCAC
636311 CCAACTGAGCCCTTAAACTAACAAAATTGACAAAATAAGCCCATTAACTAATGTTGACCGATACT
261 CCAACTGAGCCCTTAAACTAACAAAATTGACAAAATAAGCCCATTAACTAATGTTGACCGATACT
636376 TAGAAAAAGAAATATCAATAGTTAAAGAAGGGTTTAATGGTATTTTTGGTCGTCAAACTTTTTCA
326 TAGAAAAAGAAATATCAATAGTTAAAGAAGGGTTTAATGGTATTTTTGGTCGTCAAACTTTTTCA
636441 AAAAAATCAATTAAGCCCCTGCGAACTTTTTGCACCCAATTGAGCCCATGAACTAACAAAATTGG
391 AAAAAATCAATTAAGCCCCTGCGAACTTTTTGCACCCAATTGAGCCCATGAACTAACAAAATTGG
636506 CCAAATAGGCCCTTTGACTAATATTGACCGTTACAACGTTGACGTGGCCATTAACGGCGCTAACG
456 CCAAATAGGCCCTTTGACTAATATTGACCGTTACAACGTTGACGTGGCCATTAACGGCGCTAACG
636571 TGGTGCTTCATGTTAGAGATAGTTGCTTATGTGGCAATACCACGTCAACTGCCATGTCAACAAAA
521 TGGTGCTTCATGTTAGAGATAGTTGCTTATGTGGCAATACCACGTCAACTGCCATGTCAACAAAA
* * *
636636 ATAAAAAATTAAAAGGAATGTTTAAATTTTTTTACAAGGAATAGTTGTTGATGTCGCAGTACCAA
586 ATAAAAAATGAAAAGGAATATTTAAATTTTTTTACAAGGAATAGTTGCTGATGTCGCAGTACCAA
636701 GTTCATTCGTTT-CGAAGCTTAATTT
651 GTTCATTCGTTTCCGAAGCTTAATTT
636726 TAGAAAATTATAATTCTTTGCAATTACTAGAAGGTGACATTACTACCTTAATAATCACATTTTCA
1 TAGAAAATTATAATTCTTTGCAATTACTAGAAGGTGACATTACTACCTTAATAATCACATTTTCA
636791 TCTAATTCCTTTGTGGCATCAAAATACGCTTTACATGTATACGTGGAAACACCCCGTACATCGTG
66 TCTAATTCCTTTGTGGCATCAAAATACGCTTTACATGTATACGTGGAAACACCCCGTACATCGTG
636856 TGCCTATACTATGCGCGAATGTAAAATTAATTAAAAAAGACATATCAATAGTTAAAGCAGGGCTT
131 TGCCTATACTATGCGCGAATGTAAAATTAATTAAAAAAGACATATCAATAGTTAAAGCAGGGCTT
636921 AAAGGTATTTTTGATAGTCGAACTTTTTCGAAAAAATCAATTAGGCCCCTGTGAACTTTTTGCAC
196 AAAGGTATTTTTGATAGTCGAACTTTTTCGAAAAAATCAATTAGGCCCCTGTGAACTTTTTGCAC
636986 CCAACTGAGCCCTTAAACTAACAAAATTGACAAAATAAGCCCATTAACTAATGTTGACCGATACT
261 CCAACTGAGCCCTTAAACTAACAAAATTGACAAAATAAGCCCATTAACTAATGTTGACCGATACT
637051 TAGAAAAAGAAATATCAATAGTTAAAGAAGGGTTTAATGGTATTTTTGGTCGTCAAACTTTTTCA
326 TAGAAAAAGAAATATCAATAGTTAAAGAAGGGTTTAATGGTATTTTTGGTCGTCAAACTTTTTCA
637116 AAAAAATCAATTAAGCCCCTGCGAACTTTTTGCACCCAATTGAGCCCATGAACTAACAAAATTGG
391 AAAAAATCAATTAAGCCCCTGCGAACTTTTTGCACCCAATTGAGCCCATGAACTAACAAAATTGG
637181 CCAAATAGGCCCTTTGACTAATATTGACCGTTACAACGTTGACGTGGCCATTAACGGCGCTAACG
456 CCAAATAGGCCCTTTGACTAATATTGACCGTTACAACGTTGACGTGGCCATTAACGGCGCTAACG
*
637246 TGGTGCTTCATGTTAGAGATAGTTGCTTATGTGGCAATACCACGTCAACTGCCATGTCAACACAA
521 TGGTGCTTCATGTTAGAGATAGTTGCTTATGTGGCAATACCACGTCAACTGCCATGTCAACAAAA
*
637311 ATAAAAAATGAAAAGGAGTATTTAAATTTTTTTACAAGGAATAGTTGCTGATGTCGCAGTACCAA
586 ATAAAAAATGAAAAGGAATATTTAAATTTTTTTACAAGGAATAGTTGCTGATGTCGCAGTACCAA
637376 GTTCATTCGTTTCCGAAGCTTAATTT
651 GTTCATTCGTTTCCGAAGCTTAATTT
637402 T
1 T
637403 TTTAATTTAA
Statistics
Matches: 671, Mismatches: 5, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
675 657 0.98
676 14 0.02
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (676 bp):
TAGAAAATTATAATTCTTTGCAATTACTAGAAGGTGACATTACTACCTTAATAATCACATTTTCA
TCTAATTCCTTTGTGGCATCAAAATACGCTTTACATGTATACGTGGAAACACCCCGTACATCGTG
TGCCTATACTATGCGCGAATGTAAAATTAATTAAAAAAGACATATCAATAGTTAAAGCAGGGCTT
AAAGGTATTTTTGATAGTCGAACTTTTTCGAAAAAATCAATTAGGCCCCTGTGAACTTTTTGCAC
CCAACTGAGCCCTTAAACTAACAAAATTGACAAAATAAGCCCATTAACTAATGTTGACCGATACT
TAGAAAAAGAAATATCAATAGTTAAAGAAGGGTTTAATGGTATTTTTGGTCGTCAAACTTTTTCA
AAAAAATCAATTAAGCCCCTGCGAACTTTTTGCACCCAATTGAGCCCATGAACTAACAAAATTGG
CCAAATAGGCCCTTTGACTAATATTGACCGTTACAACGTTGACGTGGCCATTAACGGCGCTAACG
TGGTGCTTCATGTTAGAGATAGTTGCTTATGTGGCAATACCACGTCAACTGCCATGTCAACAAAA
ATAAAAAATGAAAAGGAATATTTAAATTTTTTTACAAGGAATAGTTGCTGATGTCGCAGTACCAA
GTTCATTCGTTTCCGAAGCTTAATTT
Found at i:637162 original size:165 final size:165
Alignment explanation
Indices: 636889--637210 Score: 473
Period size: 165 Copynumber: 2.0 Consensus size: 165
636879 AAATTAATTA
* * * *
636889 AAAAAGACATATCAATAGTTAAAGCAGGGCTTAAAGGTATTTTTGATAGTCGAACTTTTTCGAAA
1 AAAAAGAAATATCAATAGTTAAAGAAGGGCTTAAAGGTATTTTTGATAGTCAAACTTTTTCAAAA
* * *
636954 AAATCAATTAGGCCCCTGTGAACTTTTTGCACCCAACTGAGCCCTTAAACTAACAAAATTGACAA
66 AAATCAATTAAGCCCCTGCGAACTTTTTGCACCCAACTGAGCCCATAAACTAACAAAATTGACAA
*
637019 AATAAGCCCATTAACTAATGTTGACCGATACTTAG
131 AATAAGCCCATTAACTAATATTGACCGATACTTAG
* * * *
637054 AAAAAGAAATATCAATAGTTAAAGAAGGGTTTAATGGTATTTTTGGTCGTCAAACTTTTTCAAAA
1 AAAAAGAAATATCAATAGTTAAAGAAGGGCTTAAAGGTATTTTTGATAGTCAAACTTTTTCAAAA
* * * *
637119 AAATCAATTAAGCCCCTGCGAACTTTTTGCACCCAATTGAGCCCATGAACTAACAAAATTGGCCA
66 AAATCAATTAAGCCCCTGCGAACTTTTTGCACCCAACTGAGCCCATAAACTAACAAAATTGACAA
* * *
637184 AATAGGCCCTTTGACTAATATTGACCG
131 AATAAGCCCATTAACTAATATTGACCG
637211 TTACAACGTT
Statistics
Matches: 138, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
165 138 1.00
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.28
Consensus pattern (165 bp):
AAAAAGAAATATCAATAGTTAAAGAAGGGCTTAAAGGTATTTTTGATAGTCAAACTTTTTCAAAA
AAATCAATTAAGCCCCTGCGAACTTTTTGCACCCAACTGAGCCCATAAACTAACAAAATTGACAA
AATAAGCCCATTAACTAATATTGACCGATACTTAG
Found at i:637455 original size:10 final size:10
Alignment explanation
Indices: 637437--637507 Score: 51
Period size: 10 Copynumber: 7.3 Consensus size: 10
637427 AAACTAATAT
637437 TTTTA-AAAA
1 TTTTATAAAA
637446 TTTTATAAAA
1 TTTTATAAAA
637456 -TTT-TAAAA
1 TTTTATAAAA
*
637464 TATTATTAAAA
1 TTTTA-TAAAA
637475 -TTTATAAAA
1 TTTTATAAAA
* *
637484 TATTAAATAAA
1 TTTTATA-AAA
* *
637495 TTTAAAAAAA
1 TTTTATAAAA
637505 TTT
1 TTT
637508 AAAAATTAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
8 5 0.10
9 15 0.30
10 17 0.34
11 13 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
TTTTATAAAA
Found at i:637478 original size:28 final size:30
Alignment explanation
Indices: 637432--637490 Score: 86
Period size: 28 Copynumber: 2.0 Consensus size: 30
637422 TTAAAAAACT
* *
637432 AATATTTTTAAAAATTTTATAAAATTTTAA
1 AATATTATTAAAAATTTTATAAAATATTAA
637462 AATATTATT-AAAA-TTTATAAAATATTAA
1 AATATTATTAAAAATTTTATAAAATATTAA
637490 A
1 A
637491 TAAATTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 15 0.56
29 4 0.15
30 8 0.30
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (30 bp):
AATATTATTAAAAATTTTATAAAATATTAA
Found at i:637484 original size:9 final size:9
Alignment explanation
Indices: 637438--637521 Score: 66
Period size: 9 Copynumber: 9.0 Consensus size: 9
637428 AACTAATATT
637438 TTTA-AAAA
1 TTTATAAAA
637446 TTTTATAAAA
1 -TTTATAAAA
637456 TTT-TAAAA
1 TTTATAAAA
637464 TATTATTAAAA
1 T-TTA-TAAAA
637475 TTTATAAAA
1 TTTATAAAA
*
637484 TATTAAATAAA
1 T-TTATA-AAA
*
637495 TTTAAAAAAA
1 TTT-ATAAAA
637505 TTTA-AAAA
1 TTTATAAAA
*
637513 TTAATAAAA
1 TTTATAAAA
637522 ACCATTTACA
Statistics
Matches: 65, Mismatches: 2, Indels: 16
0.78 0.02 0.19
Matches are distributed among these distances:
8 13 0.20
9 20 0.31
10 19 0.29
11 13 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
TTTATAAAA
Found at i:637484 original size:20 final size:19
Alignment explanation
Indices: 637438--637521 Score: 77
Period size: 19 Copynumber: 4.5 Consensus size: 19
637428 AACTAATATT
*
637438 TTTA-AAAATTTTATAAAA
1 TTTATAAAATATTATAAAA
637456 TTT-TAAAATATTATTAAAA
1 TTTATAAAATATTA-TAAAA
*
637475 TTTATAAAATATTAAATAAA
1 TTTATAAAATATTATA-AAA
*
637495 TTTA-AAAAAATT-TAAAAA
1 TTTATAAAATATTAT-AAAA
*
637513 TTAATAAAA
1 TTTATAAAA
637522 ACCATTTACA
Statistics
Matches: 55, Mismatches: 5, Indels: 11
0.77 0.07 0.15
Matches are distributed among these distances:
18 17 0.31
19 21 0.38
20 17 0.31
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TTTATAAAATATTATAAAA
Found at i:637502 original size:28 final size:28
Alignment explanation
Indices: 637438--637502 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
637428 AACTAATATT
* *
637438 TTTAAAAATTTTATAAAATTTTAAAATA
1 TTTAAAAATTTTATAAAATATTAAAAAA
*
637466 TTATTAAAA-TTTATAAAATATTAAATAAA
1 TT-TAAAAATTTTATAAAATATTAAA-AAA
637495 TTTAAAAA
1 TTTAAAAA
637503 AATTTAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
28 22 0.71
29 9 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (28 bp):
TTTAAAAATTTTATAAAATATTAAAAAA
Found at i:637508 original size:10 final size:10
Alignment explanation
Indices: 637471--637512 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
637461 AAATATTATT
*
637471 AAAATTT-AT
1 AAAATTTAAA
637480 AAAATATTAAA
1 AAAAT-TTAAA
*
637491 TAAATTTAAA
1 AAAATTTAAA
637501 AAAATTTAAA
1 AAAATTTAAA
637511 AA
1 AA
637513 TTAATAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
9 5 0.18
10 18 0.64
11 5 0.18
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:638032 original size:10 final size:10
Alignment explanation
Indices: 638014--638084 Score: 51
Period size: 10 Copynumber: 7.3 Consensus size: 10
638004 AAACTAATAT
638014 TTTTA-AAAA
1 TTTTATAAAA
638023 TTTTATAAAA
1 TTTTATAAAA
638033 -TTT-TAAAA
1 TTTTATAAAA
*
638041 TATTATTAAAA
1 TTTTA-TAAAA
638052 -TTTATAAAA
1 TTTTATAAAA
* *
638061 TATTAAATAAA
1 TTTTATA-AAA
* *
638072 TTTAAAAAAA
1 TTTTATAAAA
638082 TTT
1 TTT
638085 AAAAATTAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
8 5 0.10
9 15 0.30
10 17 0.34
11 13 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
TTTTATAAAA
Found at i:638055 original size:28 final size:30
Alignment explanation
Indices: 638009--638067 Score: 86
Period size: 28 Copynumber: 2.0 Consensus size: 30
637999 TTAAAAAACT
* *
638009 AATATTTTTAAAAATTTTATAAAATTTTAA
1 AATATTATTAAAAATTTTATAAAATATTAA
638039 AATATTATT-AAAA-TTTATAAAATATTAA
1 AATATTATTAAAAATTTTATAAAATATTAA
638067 A
1 A
638068 TAAATTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 15 0.56
29 4 0.15
30 8 0.30
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (30 bp):
AATATTATTAAAAATTTTATAAAATATTAA
Found at i:638061 original size:9 final size:9
Alignment explanation
Indices: 638015--638098 Score: 66
Period size: 9 Copynumber: 9.0 Consensus size: 9
638005 AACTAATATT
638015 TTTA-AAAA
1 TTTATAAAA
638023 TTTTATAAAA
1 -TTTATAAAA
638033 TTT-TAAAA
1 TTTATAAAA
638041 TATTATTAAAA
1 T-TTA-TAAAA
638052 TTTATAAAA
1 TTTATAAAA
*
638061 TATTAAATAAA
1 T-TTATA-AAA
*
638072 TTTAAAAAAA
1 TTT-ATAAAA
638082 TTTA-AAAA
1 TTTATAAAA
*
638090 TTAATAAAA
1 TTTATAAAA
638099 ACCATTTACA
Statistics
Matches: 65, Mismatches: 2, Indels: 16
0.78 0.02 0.19
Matches are distributed among these distances:
8 13 0.20
9 20 0.31
10 19 0.29
11 13 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
TTTATAAAA
Found at i:638061 original size:20 final size:19
Alignment explanation
Indices: 638015--638098 Score: 77
Period size: 19 Copynumber: 4.5 Consensus size: 19
638005 AACTAATATT
*
638015 TTTA-AAAATTTTATAAAA
1 TTTATAAAATATTATAAAA
638033 TTT-TAAAATATTATTAAAA
1 TTTATAAAATATTA-TAAAA
*
638052 TTTATAAAATATTAAATAAA
1 TTTATAAAATATTATA-AAA
*
638072 TTTA-AAAAAATT-TAAAAA
1 TTTATAAAATATTAT-AAAA
*
638090 TTAATAAAA
1 TTTATAAAA
638099 ACCATTTACA
Statistics
Matches: 55, Mismatches: 5, Indels: 11
0.77 0.07 0.15
Matches are distributed among these distances:
18 17 0.31
19 21 0.38
20 17 0.31
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TTTATAAAATATTATAAAA
Found at i:638079 original size:28 final size:28
Alignment explanation
Indices: 638015--638079 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
638005 AACTAATATT
* *
638015 TTTAAAAATTTTATAAAATTTTAAAATA
1 TTTAAAAATTTTATAAAATATTAAAAAA
*
638043 TTATTAAAA-TTTATAAAATATTAAATAAA
1 TT-TAAAAATTTTATAAAATATTAAA-AAA
638072 TTTAAAAA
1 TTTAAAAA
638080 AATTTAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
28 22 0.71
29 9 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (28 bp):
TTTAAAAATTTTATAAAATATTAAAAAA
Found at i:638085 original size:10 final size:10
Alignment explanation
Indices: 638048--638089 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
638038 AAATATTATT
*
638048 AAAATTT-AT
1 AAAATTTAAA
638057 AAAATATTAAA
1 AAAAT-TTAAA
*
638068 TAAATTTAAA
1 AAAATTTAAA
638078 AAAATTTAAA
1 AAAATTTAAA
638088 AA
1 AA
638090 TTAATAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
9 5 0.18
10 18 0.64
11 5 0.18
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:645001 original size:162 final size:163
Alignment explanation
Indices: 644677--645001 Score: 447
Period size: 162 Copynumber: 2.0 Consensus size: 163
644667 AATGCAAAAT
* * ** *
644677 TAATTAAAAAAGACATATAAATAGTTAAAGTAGGGCTTAAAGGTATTTTTGATTGTCGAACTTTT
1 TAATTAAAAAAGAAATATAAATAGTTAAAGAAGGGCTTAAAGGTATTTTTGATCCTCAAACTTTT
** * *
644742 TTGAAAAAATCAATTAAGCCCCTGCGAACTTTTTGCACCCAATTGAGCCCTTAAACTAACAAAAC
66 TCAAAAAAATCAATTAAGCCCCT-CGAACTTCTTGCACCCAATTGAGCCCATAAACTAACAAAAC
*
644807 TGACAAAATAAGCCCTTTAACTAATGTTGACCGA
130 TGACAAAATAAGCCCTTTAACTAATATTGACCGA
* * *
644841 TAATTAGAAAAAGAAATATCAATAGTTAAAGAAGGG-TTAATGGTATTTTTGGTCCTCAAACTTT
1 TAATTA-AAAAAGAAATATAAATAGTTAAAGAAGGGCTTAAAGGTATTTTTGATCCTCAAACTTT
* *
644905 TTCAAAAAAATCAATTAAGCCCCT-GAACTTCTTGCACCCAATTGAGCCCATGAACTAACAAAAT
65 TTCAAAAAAATCAATTAAGCCCCTCGAACTTCTTGCACCCAATTGAGCCCATAAACTAACAAAAC
* * * *
644969 TGGCCAAATAGGCCCTTTGACTAATATTGACCG
130 TGACAAAATAAGCCCTTTAACTAATATTGACCG
645002 TTACAACGTT
Statistics
Matches: 141, Mismatches: 19, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
162 64 0.45
164 51 0.36
165 26 0.18
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.29
Consensus pattern (163 bp):
TAATTAAAAAAGAAATATAAATAGTTAAAGAAGGGCTTAAAGGTATTTTTGATCCTCAAACTTTT
TCAAAAAAATCAATTAAGCCCCTCGAACTTCTTGCACCCAATTGAGCCCATAAACTAACAAAACT
GACAAAATAAGCCCTTTAACTAATATTGACCGA
Found at i:645278 original size:20 final size:19
Alignment explanation
Indices: 645244--645296 Score: 79
Period size: 20 Copynumber: 2.7 Consensus size: 19
645234 TTTAAATTTT
645244 ATAAAATTTTAAAATATTA
1 ATAAAATTTTAAAATATTA
*
645263 TTAAAATTTATAAAATATTA
1 ATAAAATTT-TAAAATATTA
*
645283 AAAAAATTTTAAAA
1 ATAAAATTTTAAAA
645297 AAATTAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
ATAAAATTTTAAAATATTA
Found at i:645294 original size:28 final size:27
Alignment explanation
Indices: 645233--645296 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 27
645223 TAATGTTTTT
* * *
645233 TTTTAAATTTTATAAAATTTTAAAATA
1 TTTTAAAATTTATAAAATTTAAAAAAA
645260 TTATTAAAATTTATAAAATATTAAAAAAA
1 TT-TTAAAATTTATAAAAT-TTAAAAAAA
645289 TTTTAAAA
1 TTTTAAAA
645297 AAATTAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 2 0.06
28 21 0.66
29 9 0.28
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
TTTTAAAATTTATAAAATTTAAAAAAA
Found at i:645297 original size:20 final size:20
Alignment explanation
Indices: 645246--645306 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
645236 TAAATTTTAT
**
645246 AAAATTTT-AAAATATTATT
1 AAAATTTTAAAAATATTAAA
645265 AAAA-TTTATAAAATATTAAA
1 AAAATTTTA-AAAATATTAAA
*
645285 AAAATTTTAAAAAAATTAAA
1 AAAATTTTAAAAATATTAAA
645305 AA
1 AA
645307 TTAATAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
18 3 0.08
19 4 0.11
20 25 0.69
21 4 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAATTTTAAAAATATTAAA
Found at i:645676 original size:10 final size:9
Alignment explanation
Indices: 645657--645729 Score: 62
Period size: 9 Copynumber: 8.0 Consensus size: 9
645647 AATAATATTT
645657 TTTA-AAAA
1 TTTATAAAA
645665 TTGTATAAAA
1 TT-TATAAAA
645675 TTT-TAAAA
1 TTTATAAAA
645683 TATTATTAAAA
1 T-TTA-TAAAA
645694 TTTATAAAA
1 TTTATAAAA
*
645703 TATTAAAAAA
1 T-TTATAAAA
*
645713 ATTA-AAAA
1 TTTATAAAA
*
645721 TTAATAAAA
1 TTTATAAAA
645730 ACCATTTACA
Statistics
Matches: 54, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
8 14 0.26
9 18 0.33
10 16 0.30
11 6 0.11
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (9 bp):
TTTATAAAA
Found at i:645703 original size:20 final size:19
Alignment explanation
Indices: 645656--645707 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
645646 AAATAATATT
*
645656 TTTTAAAA-ATTGTATAAAA
1 TTTTAAAATATTAT-TAAAA
645675 TTTTAAAATATTATTAAAA
1 TTTTAAAATATTATTAAAA
645694 TTTATAAAATATTA
1 TTT-TAAAATATTA
645708 AAAAAATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
TTTTAAAATATTATTAAAA
Found at i:645713 original size:20 final size:19
Alignment explanation
Indices: 645671--645715 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
645661 AAAATTGTAT
**
645671 AAAATTTTAAAATATTATT
1 AAAATTTTAAAATATTAAA
645690 AAAATTTATAAAATATTAAA
1 AAAATTT-TAAAATATTAAA
645710 AAAATT
1 AAAATT
645716 AAAAATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAATTTTAAAATATTAAA
Found at i:645729 original size:16 final size:17
Alignment explanation
Indices: 645698--645730 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
645688 TTAAAATTTA
645698 TAAAATATTAAAAAAAT
1 TAAAATATTAAAAAAAT
645715 TAAAA-ATTAATAAAAA
1 TAAAATATTAA-AAAAA
645731 CCATTTACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAAATATTAAAAAAAT
Found at i:647235 original size:9 final size:9
Alignment explanation
Indices: 647223--647262 Score: 62
Period size: 9 Copynumber: 4.2 Consensus size: 9
647213 TTTTTATCAA
647223 TTTTAAATT
1 TTTTAAATT
647232 TTTTAAATT
1 TTTTAAATT
647241 TATTTAATATT
1 T-TTTAA-ATT
647252 TTTTAAATT
1 TTTTAAATT
647261 TT
1 TT
647263 AATAATATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 15 0.52
10 10 0.34
11 4 0.14
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTTAAATT
Found at i:647245 original size:20 final size:21
Alignment explanation
Indices: 647222--647288 Score: 77
Period size: 20 Copynumber: 3.2 Consensus size: 21
647212 GTTTTTATCA
647222 ATTTTAA-ATTTTTTAAATTT
1 ATTTTAATATTTTTTAAATTT
647242 A-TTTAATATTTTTTAAATTT
1 ATTTTAATATTTTTTAAATTT
**
647262 -TAATAATATTTTTTTAAATATT
1 ATTTTAATA-TTTTTTAAAT-TT
647284 ATTTT
1 ATTTT
647289 TAATTTAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
19 5 0.13
20 19 0.50
21 10 0.26
22 2 0.05
23 2 0.05
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTTTAATATTTTTTAAATTT
Found at i:647263 original size:21 final size:21
Alignment explanation
Indices: 647224--647287 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
647214 TTTTATCAAT
647224 TTTAA-ATTTTTTAAA-TTTA
1 TTTAATATTTTTTAAATTTTA
647243 TTTAATATTTTTTAAATTTTA
1 TTTAATATTTTTTAAATTTTA
* *
647264 -ATAATATTTTTTTAAATATTA
1 TTTAATA-TTTTTTAAATTTTA
647285 TTT
1 TTT
647288 TTAATTTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
19 5 0.13
20 15 0.39
21 17 0.45
22 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTAATATTTTTTAAATTTTA
Found at i:647296 original size:32 final size:30
Alignment explanation
Indices: 647223--647305 Score: 80
Period size: 31 Copynumber: 2.7 Consensus size: 30
647213 TTTTTATCAA
** *
647223 TTTTAAATTTT-TTAAATTTATTTAATATT
1 TTTTAAATTTTAAAAAATTTTTTTAATATT
*
647252 TTTTAAATTTTAATAATATTTTTTTAAATATT
1 TTTTAAATTTTAA-AAAATTTTTTT-AATATT
*
647284 ATTTTTAA-TTTAAAAAATTTTT
1 -TTTTAAATTTTAAAAAATTTTT
647306 AAGCTTCGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
29 11 0.25
31 16 0.36
32 11 0.25
33 6 0.14
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (30 bp):
TTTTAAATTTTAAAAAATTTTTTTAATATT
Found at i:648547 original size:34 final size:36
Alignment explanation
Indices: 648503--648572 Score: 108
Period size: 34 Copynumber: 2.0 Consensus size: 36
648493 CAAAATCTGA
*
648503 ATATGCATCATTAAGATTATCGAGATC-AT-TTTTT
1 ATATGCATCATTAAGATTATCAAGATCTATGTTTTT
*
648537 ATATGTATCATTAAGATTATCAAGATCTATGTTTTT
1 ATATGCATCATTAAGATTATCAAGATCTATGTTTTT
648573 TTCATTTACT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 25 0.78
35 2 0.06
36 5 0.16
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (36 bp):
ATATGCATCATTAAGATTATCAAGATCTATGTTTTT
Done.