Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold4
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: 5986281
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.33
Warning! 213817 characters in sequence are not A, C, G, or T
File 3 of 31
Found at i:661116 original size:84 final size:84
Alignment explanation
Indices: 661028--661190 Score: 308
Period size: 84 Copynumber: 1.9 Consensus size: 84
661018 AAATATAATT
*
661028 ATAATATAATAAAATATATAAATATAAGAATTATGGAATCTAAGTATAACCGGCCAATAATCATA
1 ATAATATAATAAAATATATAAATATAAAAATTATGGAATCTAAGTATAACCGGCCAATAATCATA
661093 AATTCAACTAGGAGATTCA
66 AATTCAACTAGGAGATTCA
*
661112 ATAATATAATAAAATATATAAATATAAAAATTATGGAATCTAAGTATAACCGGCCAATAATTATA
1 ATAATATAATAAAATATATAAATATAAAAATTATGGAATCTAAGTATAACCGGCCAATAATCATA
661177 AATTCAACTAGGAG
66 AATTCAACTAGGAG
661191 TGTTCTCTAC
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 77 1.00
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.29
Consensus pattern (84 bp):
ATAATATAATAAAATATATAAATATAAAAATTATGGAATCTAAGTATAACCGGCCAATAATCATA
AATTCAACTAGGAGATTCA
Found at i:662151 original size:2 final size:2
Alignment explanation
Indices: 662144--662171 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
662134 AATGAAAAAT
662144 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
662172 TGGAAAATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:668919 original size:33 final size:33
Alignment explanation
Indices: 668875--668985 Score: 100
Period size: 39 Copynumber: 3.2 Consensus size: 33
668865 TAATTTTAAC
668875 ATAATAT--ATAAAATATATTATAAATAAAATT
1 ATAATATAAATAAAATATATTATAAATAAAATT
* * * *
668906 ATACTATAAATAAAATAAATAATAGATAAACAAAAAAT
1 ATAATATAAATAAAAT--AT-AT-TATAAA-TAAAATT
668944 ATAAATATAAATATATAATATATTATAAATAAAATT
1 AT-AATATAAATA-A-AATATATTATAAATAAAATT
668980 ATAATA
1 ATAATA
668986 ATCGTTTTCC
Statistics
Matches: 62, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
31 6 0.10
33 7 0.11
35 6 0.10
36 9 0.15
37 10 0.16
38 9 0.15
39 11 0.18
40 1 0.02
41 3 0.05
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.33
Consensus pattern (33 bp):
ATAATATAAATAAAATATATTATAAATAAAATT
Found at i:669069 original size:2 final size:2
Alignment explanation
Indices: 668996--669051 Score: 62
Period size: 2 Copynumber: 29.0 Consensus size: 2
668986 ATCGTTTTCC
* * *
668996 AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AC AA AT AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
669037 AT AT AA AT A- AT AT AT
1 AT AT AT AT AT AT AT AT
669052 TGCAATAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
1 2 0.04
2 43 0.96
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:669069 original size:47 final size:44
Alignment explanation
Indices: 668998--669142 Score: 113
Period size: 47 Copynumber: 3.2 Consensus size: 44
668988 CGTTTTCCAT
* *
668998 ATATATATATATATAATATATATATATACAAATATATAAATATAAATA
1 ATATAT-TATAAATAA-A-ATATATATACAAATA-ATAAATTTAAATA
*
669046 ATATATTGCAATAAA-AAAATATAT-TA-AAATAAT--ATTTATATA
1 ATATATT---ATAAATAAAATATATATACAAATAATAAATTTAAATA
669088 ATATATTATAAATAAAAT-TATACTACAAATGAAATAATATTTAAATA
1 ATATATTATAAATAAAATATATA-TACAAAT--AATAA-ATTTAAATA
*
669135 ATTTATTA
1 ATATATTA
669143 AACTATCCAT
Statistics
Matches: 80, Mismatches: 5, Indels: 25
0.73 0.05 0.23
Matches are distributed among these distances:
39 8 0.10
40 5 0.06
41 2 0.03
42 18 0.22
44 5 0.06
45 5 0.06
46 2 0.03
47 22 0.28
48 7 0.09
49 2 0.03
50 4 0.05
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (44 bp):
ATATATTATAAATAAAATATATATACAAATAATAAATTTAAATA
Found at i:669077 original size:18 final size:17
Alignment explanation
Indices: 669027--669073 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
669017 ATATATATAC
669027 AAATATA-TAAATATAAA
1 AAATATATTAAATA-AAA
* *
669044 TAATATATTGCAATAAAA
1 AAATATATT-AAATAAAA
669062 AAATATATTAAA
1 AAATATATTAAA
669074 ATAATATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
17 8 0.33
18 12 0.50
19 4 0.17
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (17 bp):
AAATATATTAAATAAAA
Found at i:670795 original size:2 final size:2
Alignment explanation
Indices: 670788--670821 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
670778 TAATCTTAAA
* *
670788 AT AT AT AT AT AA AA AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
670822 TAAAAGCACT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:670804 original size:14 final size:14
Alignment explanation
Indices: 670785--670812 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
670775 AAATAATCTT
670785 AAAATATATATATA
1 AAAATATATATATA
670799 AAAATATATATATA
1 AAAATATATATATA
670813 TATATATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AAAATATATATATA
Found at i:673609 original size:2 final size:2
Alignment explanation
Indices: 673602--673635 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
673592 ACCCTTCTTG
673602 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
673636 TTGTATTTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:675656 original size:2 final size:2
Alignment explanation
Indices: 675649--675690 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
675639 AATCAGGATA
*
675649 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT GT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
675689 AT
1 AT
675691 GCCATCATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:680378 original size:15 final size:15
Alignment explanation
Indices: 680358--680391 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
680348 GAAACTAAGG
680358 CTTTTTTGC-TCTTTT
1 CTTTTTT-CTTCTTTT
680373 CTTTTTTCTTCTTTT
1 CTTTTTTCTTCTTTT
680388 CTTT
1 CTTT
680392 CTATGGACGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 1 0.06
15 17 0.94
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
CTTTTTTCTTCTTTT
Found at i:686101 original size:26 final size:27
Alignment explanation
Indices: 686049--686102 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
686039 AACAAAAGTC
**
686049 GTATTTATAAAAAATAATGGTTATTTT
1 GTATTTATAAAAAATAATGAATATTTT
* * *
686076 GTATTTGTAAAAAATGATGAATTTTTT
1 GTATTTATAAAAAATAATGAATATTTT
686103 TTTTTACAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (27 bp):
GTATTTATAAAAAATAATGAATATTTT
Found at i:687030 original size:19 final size:19
Alignment explanation
Indices: 687006--687042 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
686996 GAGTTTGAGT
687006 TTTTTGAAACAACTCTACG
1 TTTTTGAAACAACTCTACG
687025 TTTTTGAAACAACTCTAC
1 TTTTTGAAACAACTCTAC
687043 TGCATGAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38
Consensus pattern (19 bp):
TTTTTGAAACAACTCTACG
Found at i:689287 original size:16 final size:16
Alignment explanation
Indices: 689236--689290 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
689226 CTGGTAGCAC
689236 AGTTAAATTTGGAGCT
1 AGTTAAATTTGGAGCT
689252 AGCTT-AATTT-GA--T
1 AG-TTAAATTTGGAGCT
689265 -G-TAAATTTGGAGCT
1 AGTTAAATTTGGAGCT
689279 AGTTAAATTTGG
1 AGTTAAATTTGG
689291 CCCTGGTAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 14
0.70 0.00 0.30
Matches are distributed among these distances:
10 1 0.03
11 5 0.16
12 3 0.09
13 1 0.03
14 1 0.03
15 3 0.09
16 16 0.50
17 2 0.06
ACGTcount: A:0.31, C:0.05, G:0.24, T:0.40
Consensus pattern (16 bp):
AGTTAAATTTGGAGCT
Found at i:690653 original size:27 final size:28
Alignment explanation
Indices: 690622--690690 Score: 95
Period size: 27 Copynumber: 2.5 Consensus size: 28
690612 CCACTATTTG
* *
690622 TATTTGTCAAAAATGGTGGTTACT-TTA
1 TATTTGTCAAAAATGGTAGATACTGTTA
* *
690649 TATTTGTCAAAAATGGTAGATCCTGTTT
1 TATTTGTCAAAAATGGTAGATACTGTTA
690677 TATTTGTCAAAAAT
1 TATTTGTCAAAAAT
690691 TGTGATTTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 21 0.57
28 16 0.43
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (28 bp):
TATTTGTCAAAAATGGTAGATACTGTTA
Found at i:694515 original size:2 final size:2
Alignment explanation
Indices: 694508--694534 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
694498 TAATTTTATT
694508 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
694535 TTGAGGTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:694712 original size:20 final size:20
Alignment explanation
Indices: 694687--694727 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
694677 TGTTCATGAG
694687 TATGCATGCTCATGAACTAT
1 TATGCATGCTCATGAACTAT
*
694707 TATGCATGCTGATGAACTAT
1 TATGCATGCTCATGAACTAT
694727 T
1 T
694728 CAATCTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (20 bp):
TATGCATGCTCATGAACTAT
Found at i:700131 original size:2 final size:2
Alignment explanation
Indices: 700089--700121 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
700079 CTCTTTCAAT
700089 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
700122 GGGATATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:705974 original size:1 final size:1
Alignment explanation
Indices: 705968--705992 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
705958 TCTTTGTTCT
705968 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
705993 AATTGTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:707888 original size:33 final size:35
Alignment explanation
Indices: 707851--707921 Score: 103
Period size: 33 Copynumber: 2.1 Consensus size: 35
707841 TAATAAATAT
*
707851 ATATTTAAAAATTATAT-AATATAAATTA-TTAAA
1 ATATTTAAAAATTATATAAATATAAAATATTTAAA
*
707884 ATA-TTAAAATTTATATAAATATAAAATATTTAAA
1 ATATTTAAAAATTATATAAATATAAAATATTTAAA
707918 ATAT
1 ATAT
707922 AATATCGTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 12 0.36
33 13 0.39
34 8 0.24
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (35 bp):
ATATTTAAAAATTATATAAATATAAAATATTTAAA
Found at i:707898 original size:25 final size:26
Alignment explanation
Indices: 707869--707919 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 26
707859 AAATTATATA
707869 ATATAAATTATTAAAATA-TTAAAATTT
1 ATATAAA-TA-TAAAATATTTAAAATTT
707896 ATATAAATATAAAATATTTAAAAT
1 ATATAAATATAAAATATTTAAAAT
707920 ATAATATCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 7 0.30
26 9 0.39
27 7 0.30
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
ATATAAATATAAAATATTTAAAATTT
Found at i:707898 original size:32 final size:34
Alignment explanation
Indices: 707855--707921 Score: 102
Period size: 32 Copynumber: 2.0 Consensus size: 34
707845 AAATATATAT
*
707855 TTAAAAATTATAT-AATATAAATTA-TTAAAATA
1 TTAAAAATTATATAAATATAAAATATTTAAAATA
*
707887 TTAAAATTTATATAAATATAAAATATTTAAAATA
1 TTAAAAATTATATAAATATAAAATATTTAAAATA
707921 T
1 T
707922 AATATCGTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 12 0.39
33 10 0.32
34 9 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (34 bp):
TTAAAAATTATATAAATATAAAATATTTAAAATA
Found at i:720298 original size:2 final size:2
Alignment explanation
Indices: 720288--720321 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
720278 ATATATAAAA
*
720288 AG AG GG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
720322 GCAATGACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:722479 original size:2 final size:2
Alignment explanation
Indices: 722474--722503 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
722464 CTCTGTCTGC
722474 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
722504 TCATTCCCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:723831 original size:4 final size:4
Alignment explanation
Indices: 723822--723846 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
723812 ATTATCATTT
723822 TTAA TTAA TTAA TTAA TTAA TTAA T
1 TTAA TTAA TTAA TTAA TTAA TTAA T
723847 ATGGATCCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:726408 original size:3 final size:3
Alignment explanation
Indices: 726400--726426 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
726390 ATACAAGAAG
726400 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
726427 ATAAATCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:728551 original size:23 final size:24
Alignment explanation
Indices: 728525--728569 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
728515 AATCACATAA
728525 TAATATAAT-TTAAAAA-TAAATTT
1 TAATA-AATATTAAAAATTAAATTT
*
728548 TAATAATTATTAAAAATTAAAT
1 TAATAAATATTAAAAATTAAAT
728570 CAGATAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 2 0.11
23 12 0.63
24 5 0.26
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
TAATAAATATTAAAAATTAAATTT
Found at i:729129 original size:2 final size:2
Alignment explanation
Indices: 729087--729118 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
729077 TAGCAAAAGA
729087 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
729119 GATTTTATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:733191 original size:97 final size:96
Alignment explanation
Indices: 733021--733317 Score: 443
Period size: 97 Copynumber: 3.1 Consensus size: 96
733011 TCCTGCATAA
*
733021 GATTATAGCATTTAAAAGACATAGCTAAAGCAAATTTTTGAAAGAACATATAGATTCTTAACAAC
1 GATTATAGCATTTAAAAGACATAGCTAAAGCAAATTTTTGAAAGAACATATAGATTCTTAACAAA
733086 AGAGAAAGAGTAGAAGACAGACATGAAATGAT
66 AGAGAAAGAGTAGAAGACA-ACATGAAATGAT
* * * * * *
733118 GATCATAGCATTTAAAAGGCATAGCTAAAGTAAATTGTTGAAAGAACATACAGATTCTCAACAAA
1 GATTATAGCATTTAAAAGACATAGCTAAAGCAAATTTTTGAAAGAACATATAGATTCTTAACAAA
* *
733183 AGAGAAAGAGTAGAAGGCACAGATGAAATGAT
66 AGAGAAAGAGTAGAAGACA-ACATGAAATGAT
* * * *
733215 GATTGTAGCATTTAAAAGACACAGCTAAAGCAAATTTTTGAACGAACATATAAATTCTTAACAAA
1 GATTATAGCATTTAAAAGACATAGCTAAAGCAAATTTTTGAAAGAACATATAGATTCTTAACAAA
*
733280 AAAGAAAGAGTAGAAGAC-ACATGAAATGAT
66 AGAGAAAGAGTAGAAGACAACATGAAATGAT
733310 GATTATAG
1 GATTATAG
733318 TGCCCTACCG
Statistics
Matches: 176, Mismatches: 24, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
95 18 0.10
97 158 0.90
ACGTcount: A:0.48, C:0.11, G:0.18, T:0.23
Consensus pattern (96 bp):
GATTATAGCATTTAAAAGACATAGCTAAAGCAAATTTTTGAAAGAACATATAGATTCTTAACAAA
AGAGAAAGAGTAGAAGACAACATGAAATGAT
Found at i:745282 original size:2 final size:2
Alignment explanation
Indices: 745275--745303 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
745265 TTAGCACGCC
745275 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
745304 GACCCATTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:747767 original size:2 final size:2
Alignment explanation
Indices: 747760--747789 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
747750 CCTATTTGTT
*
747760 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
747790 CACGCACACG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:749256 original size:2 final size:2
Alignment explanation
Indices: 749249--749274 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
749239 ATGACCTGAT
749249 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
749275 GCTCATCCAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:754490 original size:82 final size:82
Alignment explanation
Indices: 754397--754558 Score: 270
Period size: 82 Copynumber: 2.0 Consensus size: 82
754387 CAAATTCCCA
* * * *
754397 TTTTTTTTCTGGTTTAGGTAGTGAATTAGAATTCACTTTGACTCTGTTTCATCTTATATTTTCTG
1 TTTTTTTTCTGGTTTAGGTAGTGAACTAGAATTCACTTTGACTCTCTTTCATCCTACATTTTCTG
754462 AGCCACCAAACAGAATT
66 AGCCACCAAACAGAATT
* *
754479 TTTTTTTTCTGGTTTAGGTAGTGAACTAGAATTCACTTTGACTCTCTTTCGTCCTACGTTTTCTG
1 TTTTTTTTCTGGTTTAGGTAGTGAACTAGAATTCACTTTGACTCTCTTTCATCCTACATTTTCTG
754544 AGCCACCAAACAGAA
66 AGCCACCAAACAGAA
754559 CATAATGTAA
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
82 74 1.00
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.43
Consensus pattern (82 bp):
TTTTTTTTCTGGTTTAGGTAGTGAACTAGAATTCACTTTGACTCTCTTTCATCCTACATTTTCTG
AGCCACCAAACAGAATT
Found at i:755229 original size:6 final size:6
Alignment explanation
Indices: 755218--755245 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
755208 TCCCTTCACT
755218 CACTTC CACTTC CACTTC CACTTC CACT
1 CACTTC CACTTC CACTTC CACTTC CACT
755246 GGCATTCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.50, G:0.00, T:0.32
Consensus pattern (6 bp):
CACTTC
Found at i:756599 original size:13 final size:13
Alignment explanation
Indices: 756566--756607 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 13
756556 TCTCAAAATT
756566 AAATTTGATGATAATA
1 AAATTTGA--ATAA-A
756582 AAATTTGAATAAA
1 AAATTTGAATAAA
756595 AAATTTG-ATAAA
1 AAATTTGAATAAA
756607 A
1 A
756608 TTAATTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 6 0.23
13 8 0.31
14 4 0.15
16 8 0.31
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (13 bp):
AAATTTGAATAAA
Found at i:756716 original size:16 final size:15
Alignment explanation
Indices: 756681--756726 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
756671 TCTAAAATAT
*
756681 ATATATTATAT-GAA
1 ATATATTATATAAAA
756695 AT-TATTAGTATAAAA
1 ATATATTA-TATAAAA
*
756710 ATATATTAAATAAAA
1 ATATATTATATAAAA
756725 AT
1 AT
756727 TAATTATCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 5 0.19
14 5 0.19
15 12 0.44
16 5 0.19
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (15 bp):
ATATATTATATAAAA
Found at i:756758 original size:19 final size:19
Alignment explanation
Indices: 756711--756758 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
756701 AGTATAAAAA
756711 TATATTAAATAAAAATTAAT
1 TATA-TAAATAAAAATTAAT
**
756731 TATCA-AAATAATTATTAAT
1 TAT-ATAAATAAAAATTAAT
756750 TATATAAAT
1 TATATAAAT
756759 TTAATATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 1 0.04
19 19 0.79
20 3 0.12
21 1 0.04
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
TATATAAATAAAAATTAAT
Found at i:757214 original size:14 final size:14
Alignment explanation
Indices: 757186--757236 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
757176 CTCAATACTA
**
757186 TTTAATTTATTTAT
1 TTTAATTTAAATAT
757200 TTTAATTTAAATAT
1 TTTAATTTAAATAT
*
757214 TATAAATTTAAATA-
1 T-TTAATTTAAATAT
757228 TTTAATTTA
1 TTTAATTTA
757237 CTATTTATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
13 7 0.22
14 14 0.44
15 11 0.34
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTAATTTAAATAT
Found at i:757743 original size:21 final size:19
Alignment explanation
Indices: 757717--757766 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 19
757707 ATAAGTAAAT
*
757717 AATAAATAAATTTAAATTTTA
1 AATAAATAAA--TAAATTTAA
757738 AATAAATTAAATAAATTTAA
1 AATAAA-TAAATAAATTTAA
757758 ATATAAATA
1 A-ATAAATA
757767 GTTAAAACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 11 0.42
21 11 0.42
22 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AATAAATAAATAAATTTAA
Found at i:757759 original size:10 final size:10
Alignment explanation
Indices: 757719--757760 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
757709 AAGTAAATAA
757719 TAAATAAATT
1 TAAATAAATT
757729 TAAAT---TT
1 TAAATAAATT
757736 TAAATAAA-T
1 TAAATAAATT
757745 TAAATAAATT
1 TAAATAAATT
757755 TAAATA
1 TAAATA
757761 TAAATAGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
7 7 0.25
9 9 0.32
10 12 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
TAAATAAATT
Found at i:759871 original size:20 final size:22
Alignment explanation
Indices: 759818--759871 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 22
759808 TAAAGTTATT
759818 TTAA-ATATATTTTTGAATTAA
1 TTAATATATATTTTTGAATTAA
759839 TTAATATATTATTTTT-AA-TAA
1 TTAATATA-TATTTTTGAATTAA
759860 -TAATATTATATT
1 TTAATA-TATATT
759872 AATTATAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
20 9 0.30
21 9 0.30
22 5 0.17
23 7 0.23
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TTAATATATATTTTTGAATTAA
Found at i:759873 original size:17 final size:18
Alignment explanation
Indices: 759834--759881 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
759824 ATATTTTTGA
759834 ATTAATTAAT-ATATTATT
1 ATTAA-TAATAATATTATT
*
759852 TTTAATAATAATATTA-T
1 ATTAATAATAATATTATT
*
759869 ATTAATTATAATA
1 ATTAATAATAATA
759882 ATTAAAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 16 0.62
18 10 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATTAATAATAATATTATT
Found at i:760192 original size:2 final size:2
Alignment explanation
Indices: 760180--760231 Score: 95
Period size: 2 Copynumber: 25.5 Consensus size: 2
760170 TACTTGCTTT
760180 TA TA GTA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
760223 TA TA TA TA T
1 TA TA TA TA T
760232 GTGTGTAATT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 47 0.96
3 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:760646 original size:21 final size:21
Alignment explanation
Indices: 760622--760665 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
760612 TTTATAAAAA
*
760622 TTTAA-AAAATATTTTTAAATT
1 TTTAATAAAA-ATTATTAAATT
*
760643 TTTAATAAAAATTATTATATT
1 TTTAATAAAAATTATTAAATT
760664 TT
1 TT
760666 AATCACCGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTAATAAAAATTATTAAATT
Found at i:763918 original size:3 final size:3
Alignment explanation
Indices: 763910--763945 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
763900 TAAATGTTAA
763910 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
763946 CATGCTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:764457 original size:18 final size:17
Alignment explanation
Indices: 764434--764467 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
764424 TATCATCTTT
764434 TAAAAAATATTTAAAAAA
1 TAAAAAAT-TTTAAAAAA
764452 TAAAAAATTTTAAAAA
1 TAAAAAATTTTAAAAA
764468 TATATTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAAAAATTTTAAAAAA
Found at i:764461 original size:16 final size:17
Alignment explanation
Indices: 764436--764469 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
764426 TCATCTTTTA
764436 AAAAATATTTAAAAAAT
1 AAAAATATTTAAAAAAT
*
764453 AAAAA-ATTTTAAAAAT
1 AAAAATATTTAAAAAAT
764469 A
1 A
764470 TATTTATATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAAATATTTAAAAAAT
Found at i:764472 original size:2 final size:2
Alignment explanation
Indices: 764467--764502 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
764457 AATTTTAAAA
*
764467 AT AT AT TT AT AT CAT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT A
764503 ATTTTAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:769495 original size:2 final size:2
Alignment explanation
Indices: 769488--769513 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
769478 CCAGCCACCC
769488 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
769514 CATGCAATTA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:774470 original size:26 final size:26
Alignment explanation
Indices: 774441--774490 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
774431 AATCAAATCA
*
774441 ATTTTTACATTGCATAATAGCATAAC
1 ATTTTTACATTGCATAATAACATAAC
774467 ATTTTTACATTGCATAATAACATA
1 ATTTTTACATTGCATAATAACATA
774491 TCTATAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.40, C:0.14, G:0.06, T:0.40
Consensus pattern (26 bp):
ATTTTTACATTGCATAATAACATAAC
Found at i:774521 original size:3 final size:3
Alignment explanation
Indices: 774513--774542 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
774503 AAATTAATGA
774513 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
774543 TTGCAAATGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:774920 original size:21 final size:19
Alignment explanation
Indices: 774880--774922 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
774870 ATGTTTTTTG
* *
774880 AATTTTAAAATTTATTATT
1 AATTTTAAAAATAATTATT
774899 AATTTATAAAAATAATTAATT
1 AATTT-TAAAAATAATT-ATT
774920 AAT
1 AAT
774923 ATGTATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 9 0.45
21 6 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AATTTTAAAAATAATTATT
Found at i:775447 original size:13 final size:12
Alignment explanation
Indices: 775414--775472 Score: 50
Period size: 12 Copynumber: 4.6 Consensus size: 12
775404 AACAAAACTT
775414 TAATTTTAAAAA
1 TAATTTTAAAAA
775426 T-ATCTTTAAAAA
1 TAAT-TTTAAAAA
775438 TAATTGTTAATAAA
1 TAATT-TTAA-AAA
775452 -AATTTTATAATATA
1 TAATTTTA-AA-A-A
775466 TAATTTT
1 TAATTTT
775473 TACTAAATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
11 2 0.05
12 15 0.38
13 12 0.31
14 4 0.10
15 6 0.15
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (12 bp):
TAATTTTAAAAA
Found at i:775730 original size:2 final size:2
Alignment explanation
Indices: 775720--775751 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
775710 TTTTTTTTAA
*
775720 CT CT GT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
775752 ATACTGTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (2 bp):
CT
Found at i:776132 original size:2 final size:2
Alignment explanation
Indices: 776125--776161 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
776115 AGTATCTTTT
776125 GA GA GA GA GA TGA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA -GA GA GA GA GA GA GA GA GA GA GA GA GA
776162 AGCTACTCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.49, T:0.03
Consensus pattern (2 bp):
GA
Found at i:777669 original size:18 final size:18
Alignment explanation
Indices: 777646--777680 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
777636 ATTTAGGCTT
*
777646 TAAATAAGCACTCCTTTG
1 TAAATAAACACTCCTTTG
777664 TAAATAAACACTCCTTT
1 TAAATAAACACTCCTTT
777681 TACATCTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.34
Consensus pattern (18 bp):
TAAATAAACACTCCTTTG
Found at i:778869 original size:2 final size:2
Alignment explanation
Indices: 778862--778890 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
778852 TTTTTGCTCG
778862 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
778891 CCCTTTCTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:791511 original size:39 final size:39
Alignment explanation
Indices: 791426--791522 Score: 117
Period size: 39 Copynumber: 2.5 Consensus size: 39
791416 CTGGGGTCAA
*
791426 CAACTGAGATTTTTCTTCAGTGTATGCAATTGGCGTCAG
1 CAACTGAGATTTTTCTTCAGTGTATGCAATTGGCGCCAG
** *
791465 CAACTGAGATTTTTCTTCAGTGTACT-CTTTTGGTGCCA-
1 CAACTGAGATTTTTCTTCAGTGTA-TGCAATTGGCGCCAG
*
791503 CACCCTGAGATTTTTCTTCA
1 CA-ACTGAGATTTTTCTTCA
791523 ACGTTCTCCA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
38 2 0.04
39 48 0.94
40 1 0.02
ACGTcount: A:0.21, C:0.22, G:0.19, T:0.39
Consensus pattern (39 bp):
CAACTGAGATTTTTCTTCAGTGTATGCAATTGGCGCCAG
Found at i:791550 original size:39 final size:38
Alignment explanation
Indices: 791416--791561 Score: 100
Period size: 39 Copynumber: 3.8 Consensus size: 38
791406 TCTGAGTCCT
* * *
791416 CTGGGGTCAACAACTGAGATTTTTCTTC-AGTGTATGCAA
1 CTGGTGTCAGCAACTGAGATTTTTCTTCAAGT-TCT-CAA
* * **
791455 TTGGCGTCAGCAACTGAGATTTTTCTTC-AGTGTACTCTT
1 CTGGTGTCAGCAACTGAGATTTTTCTTCAAGT-T-CTCAA
* * * *
791494 TTGGTGCCA-CACCCTGAGATTTTTCTTCAACGTTCTCCA
1 CTGGTGTCAGCA-ACTGAGATTTTTCTTCAA-GTTCTCAA
* *
791533 CTGGTGTCAGCAACTGAGGTTTCTCTTCA
1 CTGGTGTCAGCAACTGAGATTTTTCTTCA
791562 CTGTATTGAA
Statistics
Matches: 86, Mismatches: 16, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
38 2 0.02
39 77 0.90
40 5 0.06
41 2 0.02
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (38 bp):
CTGGTGTCAGCAACTGAGATTTTTCTTCAAGTTCTCAA
Found at i:797186 original size:28 final size:27
Alignment explanation
Indices: 797130--797195 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 27
797120 ATTGTCATCC
*
797130 ACATTTATCTATTTTTTATTTTTCATAT
1 ACATTTATTTATTTTTTATTTTT-ATAT
797158 ACATTTATTTATTTATTTATATTTT-TAT
1 ACATTTATTTATTT-TTTAT-TTTTATAT
*
797186 AAATTTATTT
1 ACATTTATTT
797196 TATCAATCGT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 25 0.74
29 5 0.15
30 4 0.12
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (27 bp):
ACATTTATTTATTTTTTATTTTTATAT
Found at i:801513 original size:12 final size:12
Alignment explanation
Indices: 801496--801520 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
801486 AGGAAGAAGG
801496 AAAGACCAATGA
1 AAAGACCAATGA
801508 AAAGACCAATGA
1 AAAGACCAATGA
801520 A
1 A
801521 TTTTTCTTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.16, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAGACCAATGA
Found at i:802941 original size:3 final size:3
Alignment explanation
Indices: 802933--802960 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
802923 GACCTGATCG
802933 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
802961 GGGTTCTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:803126 original size:3 final size:3
Alignment explanation
Indices: 803118--803162 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
803108 ATTTTATTGG
803118 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
803163 GGGATACGGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:804670 original size:2 final size:2
Alignment explanation
Indices: 804663--804691 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
804653 TCCACATTCC
804663 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
804692 TGATATTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:807716 original size:31 final size:32
Alignment explanation
Indices: 807655--807718 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
807645 GAGAATATAA
*
807655 AATTATATCAAAGATTACGAATTAAAAATCAC
1 AATTATATCAAAGATTACGAATCAAAAATCAC
* * *
807687 AATTATATGAAA-ATTCCTAATCAAAAATCAC
1 AATTATATCAAAGATTACGAATCAAAAATCAC
807718 A
1 A
807719 TTAAATGTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 17 0.61
32 11 0.39
ACGTcount: A:0.53, C:0.14, G:0.05, T:0.28
Consensus pattern (32 bp):
AATTATATCAAAGATTACGAATCAAAAATCAC
Found at i:807780 original size:26 final size:23
Alignment explanation
Indices: 807709--807780 Score: 54
Period size: 26 Copynumber: 2.9 Consensus size: 23
807699 ATTCCTAATC
*
807709 AAAAATCACATTAAATGTTATAT
1 AAAAATCACATTAAATATTATAT
* * *
807732 GAAAATTACTATATCAAAGATTATCAATT
1 AAAAATCAC-AT-T-AAATATTAT--A-T
807761 AAAAATCACATTAAATATTA
1 AAAAATCACATTAAATATTA
807781 CATGAAGATT
Statistics
Matches: 36, Mismatches: 7, Indels: 9
0.69 0.13 0.17
Matches are distributed among these distances:
23 7 0.19
24 2 0.06
25 1 0.03
26 14 0.39
27 1 0.03
28 3 0.08
29 8 0.22
ACGTcount: A:0.53, C:0.10, G:0.04, T:0.33
Consensus pattern (23 bp):
AAAAATCACATTAAATATTATAT
Found at i:807868 original size:11 final size:10
Alignment explanation
Indices: 807852--807894 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
807842 AATCATAACT
807852 AAGATTATATA
1 AAGATTAT-TA
807863 AAGATTATTA
1 AAGATTATTA
* *
807873 AATAATATTA
1 AAGATTATTA
*
807883 AAAATTATTA
1 AAGATTATTA
807893 AA
1 AA
807895 TTAAATTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
10 20 0.71
11 8 0.29
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (10 bp):
AAGATTATTA
Found at i:810062 original size:2 final size:2
Alignment explanation
Indices: 810057--810086 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
810047 CGTTTTAACC
*
810057 AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
810087 TTCTCTCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:813582 original size:52 final size:52
Alignment explanation
Indices: 813497--813621 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
813487 ATATGAAAAG
* * *
813497 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGAGCAAAT
*
813549 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGAGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGAGCAAAT
813601 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
813622 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGAGCAAAT
Found at i:813634 original size:52 final size:51
Alignment explanation
Indices: 813497--813641 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 51
813487 ATATGAAAAG
* *
813497 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGAGCAAAT
* *
813549 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGAGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGAGCAAAT
*
813601 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
813642 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 82 0.98
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGAGCAAAT
Found at i:813648 original size:13 final size:13
Alignment explanation
Indices: 813630--813654 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
813620 CAAAGATCAG
813630 TGTATCGATACAA
1 TGTATCGATACAA
813643 TGTATCGATACA
1 TGTATCGATACA
813655 TGTGAGTAAT
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:813736 original size:13 final size:13
Alignment explanation
Indices: 813718--813742 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
813708 CAAAAAAACA
813718 TGTATCGATACAT
1 TGTATCGATACAT
813731 TGTATCGATACA
1 TGTATCGATACA
813743 ACATTTTATG
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:814425 original size:12 final size:12
Alignment explanation
Indices: 814387--814425 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
814377 GGTTTTTAAT
814387 TTCTTCTACATC
1 TTCTTCTACATC
* *
814399 TTCATCTTCATC
1 TTCTTCTACATC
*
814411 TTCTTCTACAGC
1 TTCTTCTACATC
814423 TTC
1 TTC
814426 GGATGTTAGA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.15, C:0.33, G:0.03, T:0.49
Consensus pattern (12 bp):
TTCTTCTACATC
Found at i:819101 original size:17 final size:17
Alignment explanation
Indices: 819055--819101 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
819045 TTATGATTAA
819055 TATATTATATATATAATT
1 TATATTATATA-ATAATT
* *
819073 TTTA-AATAATAATAATT
1 TATATTAT-ATAATAATT
819090 TATATTATATAA
1 TATATTATATAA
819102 ATTTTAAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 5
0.72 0.12 0.16
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TATATTATATAATAATT
Found at i:819112 original size:16 final size:16
Alignment explanation
Indices: 819064--819113 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
819054 ATATATTATA
*
819064 TATATAATTTTTAAA-
1 TATATAAATTTTAAAT
* *
819079 TA-ATAATAATTTATAT
1 TATATAA-ATTTTAAAT
819095 TATATAAATTTTAAAT
1 TATATAAATTTTAAAT
819111 TAT
1 TAT
819114 TTATGTATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
14 4 0.15
15 7 0.26
16 12 0.44
17 4 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TATATAAATTTTAAAT
Found at i:819139 original size:17 final size:16
Alignment explanation
Indices: 819082--819189 Score: 52
Period size: 16 Copynumber: 6.9 Consensus size: 16
819072 TTTTAAATAA
*
819082 TAATAATTTATATTATA
1 TAAT-ATTTATATTATT
*
819099 TAA-ATTTTAAATTATT
1 TAATA-TTTATATTATT
*
819115 TATGTATTTATATTATGT
1 TA-ATATTTATATTAT-T
*
819133 TAATA-TTATTTTA-T
1 TAATATTTATATTATT
819147 T-ATATTT-TATTATAT
1 TAATATTTATATTAT-T
* *
819162 T-TTAATTAT-TT-TT
1 TAATATTTATATTATT
*
819175 TATTATTTATATTAT
1 TAATATTTATATTAT
819190 ATCTGAAATT
Statistics
Matches: 70, Mismatches: 10, Indels: 23
0.68 0.10 0.22
Matches are distributed among these distances:
13 9 0.13
14 12 0.17
15 11 0.16
16 20 0.29
17 14 0.20
18 4 0.06
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
TAATATTTATATTATT
Found at i:819146 original size:21 final size:20
Alignment explanation
Indices: 819121--819189 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 20
819111 TATTTATGTA
*
819121 TTTATATTATGTTAATATTAT
1 TTTATATTAT-TTATTATTAT
819142 TTTAT-TATATTTTATTA-TAT
1 TTTATAT-TA-TTTATTATTAT
*
819162 TTTA-ATTATTTTTTATTA-
1 TTTATATTATTTATTATTAT
819180 TTTATATTAT
1 TTTATATTAT
819190 ATCTGAAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
18 10 0.24
19 9 0.22
20 9 0.22
21 12 0.29
22 1 0.02
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.68
Consensus pattern (20 bp):
TTTATATTATTTATTATTAT
Found at i:819154 original size:10 final size:10
Alignment explanation
Indices: 819139--819191 Score: 72
Period size: 10 Copynumber: 5.3 Consensus size: 10
819129 ATGTTAATAT
819139 TATTTTATTA
1 TATTTTATTA
819149 TATTTTATTA
1 TATTTTATTA
819159 TATTTTAATTA
1 TATTTT-ATTA
*
819170 TTTTTTATTA
1 TATTTTATTA
*
819180 T-TTATATTA
1 TATTTTATTA
819189 TAT
1 TAT
819192 CTGAAATTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
9 8 0.21
10 22 0.56
11 9 0.23
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TATTTTATTA
Found at i:819191 original size:5 final size:5
Alignment explanation
Indices: 819122--819191 Score: 56
Period size: 5 Copynumber: 14.2 Consensus size: 5
819112 ATTTATGTAT
* * * *
819122 TTATA TTATG TTAATA TTAT- TT-TA TTATA TTTTA TTATA TTTTAA TTATT
1 TTATA TTATA TT-ATA TTATA TTATA TTATA TTATA TTATA TTAT-A TTATA
*
819172 TTTTA TTAT- TTATA TTATA T
1 TTATA TTATA TTATA TTATA T
819192 CTGAAATTAT
Statistics
Matches: 50, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
3 1 0.02
4 8 0.16
5 33 0.66
6 8 0.16
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.67
Consensus pattern (5 bp):
TTATA
Found at i:822768 original size:2 final size:2
Alignment explanation
Indices: 822761--822791 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
822751 ATTTGTTTAC
*
822761 AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
822792 AAAACTTAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:823535 original size:14 final size:14
Alignment explanation
Indices: 823516--823542 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
823506 ATTTGTTTAC
823516 ATATATATGTATAT
1 ATATATATGTATAT
823530 ATATATATGTATA
1 ATATATATGTATA
823543 AACTTAGTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (14 bp):
ATATATATGTATAT
Found at i:823907 original size:750 final size:750
Alignment explanation
Indices: 822322--824100 Score: 2845
Period size: 755 Copynumber: 2.4 Consensus size: 750
822312 TAAAAAATTT
* * * * *
822322 TATTTATAGTAGTCTATTAAATAAATTTAAATTAATATTTTTTGTGAGATATGGAAAGAAAATTA
1 TATTTACAGTAGTCTATTAAATCAATTTAATTTAATA--TTTTGTGAGAT-TTGAAAAAAAATT-
* * * * * *
822387 AAATTGTATT-TATTTATTATATATAAGGCAAGTCAATTAAAAGTATGAAAAAAATAAATATAAT
62 -ATTTGT-TTATATATA-TATATATAAAGTACGTCAATTAAAAGTAT-AAAAAAATAAAT-TATT
** * * * * * * * *
822451 TAATCGTATGAAATATTTTGATATTAATTTAAATTAAATCAAAATAATTAAATATATGACACATG
122 TAATTATATAAAATATTTTAATATTAAATTAAATTAAGTTAAAATAATTAAA-ATGTAACATATG
* * * ** * *
822516 ATGACTATTTATAGCTAAC-CATTTGTGAATAATATATGCTATTTACATTAGATAATTACTTTTT
186 ATAACTTTTTAT-GATTGCTTATATGTGAATAATATATGCTATTTACATTAGATAATTACTTTTT
*
822580 TTATAAAAAATTTTAACTTTTATTCATTTACTATTTAGTATCTAAATTTGATTTATTTTTAAAGT
250 TTATAAAAAATTTTGACTTTTATTCATTTACTATTTAGTATCTAAATTTGATTTATTTTTAAAGT
*
822645 TGAATTTTAATGACTCCAAATTATAGAAAACCTTTATTTATGGCAGTCTATTAAATAAATTTAAA
315 TGAATTTTAATGACTCCAAATTATAGAAAACCTTTATTTATGACAGTCTATTAAATAAATTTAAA
* *
822710 TTAATATTTTTGGTGAGATATGGAAAGAAAATTAAAATTTTATTTGTTTACATATATATATATAT
380 TTAATATTTTTGGTGAGATATGAAAACAAAATTAAAATTTTATTTGTTTACA-ATATATATATAT
822775 ATATGTATATATATATAAAAACTTAGTCAACTAAAAGTTTAAAAAGAAATAAATATAATTAATTA
444 ATA-GTATATATATAT-AAAACTTAGTCAACTAAAAGTTTAAAAAGAAATAAATATAATTAATTA
*
822840 TATGAAATATTTTAATAAAATTTAAATCAGGTTGAAATAATTAAATATGTGTATATTAATTATAT
507 TATGAAATATTTTAATAAAAATTAAATCAGGTTGAAATAATTAAATATGTGTATATTAATTATAT
822905 GAATATCCACATTGAAAAATTATTTTTTTGTAAAAAGTTTGGTTTTTATTCATTTATTAAATAAG
572 GAATATCCACATTGAAAAATTATTTTTTTGTAAAAAGTTTGGTTTTTATTCATTTATTAAATAAG
822970 ATTTTTGTATTTTTAATTATTAAAATTATTATCGGTTATTGTTTACTATTTAAACTTAATGTATT
637 ATTTTTGTATTTTTAATTATTAAAATTATTATCGGTTATTGTTTACTATTTAAACTTAATGTATT
*
823035 TTTAAAATTAAATTTAAATGATTTTAAATTATCATTTATAAAAAAGCCC
702 TTTAAAATTAAATTTAAATGATTTTAAATTATCATTTATAAAAAAACCC
*
823084 TATTTACAGTATTCTATTAAATCAATTTAATTTAATATTTTGTGAGATTTGAAAAAAAATTATTT
1 TATTTACAGTAGTCTATTAAATCAATTTAATTTAATATTTTGTGAGATTTGAAAAAAAATTATTT
823149 GTTTATATATATATATATAAAGTACGTCAATTAAAAGTATAAAAAGAATTAAATTATTTAATTAT
66 GTTTATATATATATATATAAAGTACGTCAATTAAAAGTATAAAAA-AA-TAAATTATTTAATTAT
823214 ATAAAATATTTTAATATTAAATTAAATTAAGTTAAAATAATTAAAATGTAACATATGATAACTTT
129 ATAAAATATTTTAATATTAAATTAAATTAAGTTAAAATAATTAAAATGTAACATATGATAACTTT
*
823279 TTATGATTGCTTATACGTGAATAATATATGCTATTTACATTAGATAATTACTTTTTTTATAAAAA
194 TTATGATTGCTTATATGTGAATAATATATGCTATTTACATTAGATAATTACTTTTTTTATAAAAA
* *
823344 ATTTTGACTTTTATTCATTTACTATTTAGTATTTGAATTTGATTTATTTTTAAAGTTGAATTTTA
259 ATTTTGACTTTTATTCATTTACTATTTAGTATCTAAATTTGATTTATTTTTAAAGTTGAATTTTA
*
823409 ATGACTCCAAATTATAGAAAACTTTTATTTATGACAGTCTATTAAATAAATTTAAATTAATATTT
324 ATGACTCCAAATTATAGAAAACCTTTATTTATGACAGTCTATTAAATAAATTTAAATTAATATTT
*
823474 TTGGTGAGATATGAAAACAAAATTAAAATTTTATTTGTTTAC-ATATATATGTATATA-TATATA
389 TTGGTGAGATATGAAAACAAAATTAAAATTTTATTTGTTTACAATATATATATATATAGTATATA
* * * *
823537 TGTAT-AAACTTAGTCAATTAAAAGTTTAAAAGGAAATAAATATAATTATTTATATGAAATATTT
454 TATATAAAACTTAGTCAACTAAAAGTTTAAAAAGAAATAAATATAATTAATTATATGAAATATTT
823601 TAATAAAAATTAAATCAGGTTGAAATAATTAAATATGTGTATATTAATTATATGAATATCCACAT
519 TAATAAAAATTAAATCAGGTTGAAATAATTAAATATGTGTATATTAATTATATGAATATCCACAT
* *
823666 TGAAAAATTATTTTTTTTGTAAAAATTTTGGTTTTTATTTATTTATTAAATAAGATTTTTGTATT
584 TGAAAAATTA-TTTTTTTGTAAAAAGTTTGGTTTTTATTCATTTATTAAATAAGATTTTTGTATT
823731 TTTAATTATTAAAATTATTATCGGTTATTGTTTACTATTTAAACTTAATGTATTTTTAAAATTAA
648 TTTAATTATTAAAATTATTATCGGTTATTGTTTACTATTTAAACTTAATGTATTTTTAAAATTAA
823796 ATTTAAATGATTTTAAATTATCATTTATAAAAAAACCC
713 ATTTAAATGATTTTAAATTATCATTTATAAAAAAACCC
823834 TATTTACAGTAGTCTATTAAATCAATTTAATTTAATATTTTGTGAGATTTGAAAAAAAATTATTT
1 TATTTACAGTAGTCTATTAAATCAATTTAATTTAATATTTTGTGAGATTTGAAAAAAAATTATTT
823899 GTTTATATATATATATATATAAAGTACGTCAATTAAAAGTAT-AAAAAA-AAATTATTTAATTAT
66 G-TT-TATATATATATATATAAAGTACGTCAATTAAAAGTATAAAAAAATAAATTATTTAATTAT
823962 ATAAAATATTTTAATATTAAATTAAATTAAGTTAAAATAATTAAAATGTAACATATGATAACTTT
129 ATAAAATATTTTAATATTAAATTAAATTAAGTTAAAATAATTAAAATGTAACATATGATAACTTT
* * ** *
824027 TTATGATTGCTTATATGTGAATAATATAGGGTATCCATATTAGATAATTA-TCTTTTTTATAAAA
194 TTATGATTGCTTATATGTGAATAATATATGCTATTTACATTAGATAATTACT-TTTTTTATAAAA
**
824091 GGTTTTGACT
258 AATTTTGACT
824101 ATTAAATATT
Statistics
Matches: 954, Mismatches: 55, Indels: 30
0.92 0.05 0.03
Matches are distributed among these distances:
747 1 0.00
748 144 0.15
749 130 0.14
750 221 0.23
751 16 0.02
752 37 0.04
753 14 0.01
754 3 0.00
755 240 0.25
756 78 0.08
757 15 0.02
759 11 0.01
760 11 0.01
762 33 0.03
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.44
Consensus pattern (750 bp):
TATTTACAGTAGTCTATTAAATCAATTTAATTTAATATTTTGTGAGATTTGAAAAAAAATTATTT
GTTTATATATATATATATAAAGTACGTCAATTAAAAGTATAAAAAAATAAATTATTTAATTATAT
AAAATATTTTAATATTAAATTAAATTAAGTTAAAATAATTAAAATGTAACATATGATAACTTTTT
ATGATTGCTTATATGTGAATAATATATGCTATTTACATTAGATAATTACTTTTTTTATAAAAAAT
TTTGACTTTTATTCATTTACTATTTAGTATCTAAATTTGATTTATTTTTAAAGTTGAATTTTAAT
GACTCCAAATTATAGAAAACCTTTATTTATGACAGTCTATTAAATAAATTTAAATTAATATTTTT
GGTGAGATATGAAAACAAAATTAAAATTTTATTTGTTTACAATATATATATATATAGTATATATA
TATAAAACTTAGTCAACTAAAAGTTTAAAAAGAAATAAATATAATTAATTATATGAAATATTTTA
ATAAAAATTAAATCAGGTTGAAATAATTAAATATGTGTATATTAATTATATGAATATCCACATTG
AAAAATTATTTTTTTGTAAAAAGTTTGGTTTTTATTCATTTATTAAATAAGATTTTTGTATTTTT
AATTATTAAAATTATTATCGGTTATTGTTTACTATTTAAACTTAATGTATTTTTAAAATTAAATT
TAAATGATTTTAAATTATCATTTATAAAAAAACCC
Found at i:824874 original size:153 final size:153
Alignment explanation
Indices: 824567--824926 Score: 419
Period size: 153 Copynumber: 2.3 Consensus size: 153
824557 TTTATATAAG
* * *
824567 ATATAAAATAACTTGGATTGAATTTGAAATTCAAATACTATCTTATTTATACTTATGTTGAAAAC
1 ATATATAATAATTTGGATTGAATTTGAAATTCAAATACTATCTTATTTATACATATGTTGAAAAC
* * * *
824632 TCAAAATTATCAAATGTGAAAACTGAAAGTATTTTCACGTCTTTATTAGCAAAAGATTTAATTAA
66 TCAAAATTATCAAACGTAAAAACTGAAAGTATTTTCACGTATTAATTAGCAAAAGATTTAATTAA
*
824697 GAAAATGAAACATAATAACTTTT
131 GAAAATGAAACATAATAAATTTT
* * *
824720 ATATATAATAATTTGGATTGAACTTGGAATTCAAATACTATCATATTTATACATATGTTGAAAAC
1 ATATATAATAATTTGGATTGAATTTGAAATTCAAATACTATCTTATTTATACATATGTTGAAAAC
* * * * *
824785 TCAAGATTATCAAACGTAAAAACT-AAGAGTATTTTTATGTATTAA-TATGTAAGAGATTTAATT
66 TCAAAATTATCAAACGTAAAAACTGAA-AGTATTTTCACGTATTAATTA-GCAAAAGATTTAATT
824848 AA-AAAAT-AAGA-ATCAATAAATATTT
129 AAGAAAATGAA-ACAT-AATAAAT-TTT
* * *
824873 ATGTACTAAT-ATCTAATAG-TTGAATTTGAAATTCAAATATTATCTTATTTATAC
1 ATATA-TAATAAT-T--TGGATTGAATTTGAAATTCAAATACTATCTTATTTATAC
824927 TTAAAAGCTT
Statistics
Matches: 176, Mismatches: 22, Indels: 16
0.82 0.10 0.07
Matches are distributed among these distances:
151 4 0.02
152 16 0.09
153 118 0.67
154 5 0.03
155 31 0.18
156 2 0.01
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.38
Consensus pattern (153 bp):
ATATATAATAATTTGGATTGAATTTGAAATTCAAATACTATCTTATTTATACATATGTTGAAAAC
TCAAAATTATCAAACGTAAAAACTGAAAGTATTTTCACGTATTAATTAGCAAAAGATTTAATTAA
GAAAATGAAACATAATAAATTTT
Found at i:826062 original size:20 final size:20
Alignment explanation
Indices: 826027--826064 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
826017 AAATAAAAAA
* *
826027 TTAAAATTTGATTTTAATAT
1 TTAAAATTTAAATTTAATAT
826047 TTAAAATTTAAATTTAAT
1 TTAAAATTTAAATTTAAT
826065 TTGATTATAT
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:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
TTAAAATTTAAATTTAATAT
Found at i:829346 original size:134 final size:138
Alignment explanation
Indices: 829079--829351 Score: 387
Period size: 134 Copynumber: 2.0 Consensus size: 138
829069 TGTGCTTTGA
*
829079 CGTATAAAGTTGGAACTATTCATAAATTTACTTGTATTTTGGTCTCTTTCTTTTATAGGAGCTGA
1 CGTATAAAGTTGGAACTATTCATAAATTTACTTGTA--TT-GTCTCTTTCTTTCATAGGAGCTGA
* *
829144 CATGATTGCCAGTTTCCATTGTGGTACCTTCTGGTTTTCTAATTTTAAGAACTTCTGTTTTCTTA
63 CATGATTGCCAGTTTCCATTGTGGTACCCTCTGATTTTCTAATTTTAAGAACTTCTGTTTTCTTA
829209 AATGGAATTGG
128 AATGGAATTGG
* *
829220 CGTATAAAGTTGGAACTATTCATAAATTTACTT-TA-T-TCTGTTTC-TTCATAGGAGCTGATAT
1 CGTATAAAGTTGGAACTATTCATAAATTTACTTGTATTGTCTCTTTCTTTCATAGGAGCTGACAT
* * *
829281 GATTGTCGGTTTCCATTGCT-GTACCCTCTGATTTTCT-ATTTTAAGAAGTTCTGTTTTCTTAAA
66 GATTGCCAGTTTCCATTG-TGGTACCCTCTGATTTTCTAATTTTAAGAACTTCTGTTTTCTT-AA
829344 ATGGAATT
129 ATGGAATT
829352 TAATCCTTGG
Statistics
Matches: 122, Mismatches: 8, Indels: 11
0.87 0.06 0.08
Matches are distributed among these distances:
133 22 0.18
134 56 0.46
135 8 0.07
137 1 0.01
140 2 0.02
141 33 0.27
ACGTcount: A:0.24, C:0.14, G:0.17, T:0.45
Consensus pattern (138 bp):
CGTATAAAGTTGGAACTATTCATAAATTTACTTGTATTGTCTCTTTCTTTCATAGGAGCTGACAT
GATTGCCAGTTTCCATTGTGGTACCCTCTGATTTTCTAATTTTAAGAACTTCTGTTTTCTTAAAT
GGAATTGG
Found at i:832432 original size:179 final size:179
Alignment explanation
Indices: 832132--832486 Score: 701
Period size: 179 Copynumber: 2.0 Consensus size: 179
832122 TCTATGGGGA
832132 AAGATGGGACCCAACTGTTGCGCCATTGTGCTCGTCTTCTTGTGCTTGTTTCAACTGATCTACTT
1 AAGATGGGACCCAACTGTTGCGCCATTGTGCTCGTCTTCTTGTGCTTGTTTCAACTGATCTACTT
832197 GCAGTTCGTTCATCGGGTATTGGTTTATTTTATGCATGTATTATGTATTGTATCATTCGTAATGT
66 GCAGTTCGTTCATCGGGTATTGGTTTATTTTATGCATGTATTATGTATTGTATCATTCGTAATGT
832262 ATTTGCATGGCATGTGTGAAGTTTTTGTTTGTACATGCATTTCTGTGTG
131 ATTTGCATGGCATGTGTGAAGTTTTTGTTTGTACATGCATTTCTGTGTG
832311 AAGATGGGACCCAACTGTTGCGCCATTGTGCTCGTCTTCTTGTGCTTGTTTCAACTGATCTACTT
1 AAGATGGGACCCAACTGTTGCGCCATTGTGCTCGTCTTCTTGTGCTTGTTTCAACTGATCTACTT
*
832376 GCAGTTTGTTCATCGGGTATTGGTTTATTTTATGCATGTATTATGTATTGTATCATTCGTAATGT
66 GCAGTTCGTTCATCGGGTATTGGTTTATTTTATGCATGTATTATGTATTGTATCATTCGTAATGT
832441 ATTTGCATGGCATGTGTGAAGTTTTTGTTTGTACATGCATTTCTGT
131 ATTTGCATGGCATGTGTGAAGTTTTTGTTTGTACATGCATTTCTGT
832487 TTGCTTTTCC
Statistics
Matches: 175, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
179 175 1.00
ACGTcount: A:0.18, C:0.15, G:0.23, T:0.44
Consensus pattern (179 bp):
AAGATGGGACCCAACTGTTGCGCCATTGTGCTCGTCTTCTTGTGCTTGTTTCAACTGATCTACTT
GCAGTTCGTTCATCGGGTATTGGTTTATTTTATGCATGTATTATGTATTGTATCATTCGTAATGT
ATTTGCATGGCATGTGTGAAGTTTTTGTTTGTACATGCATTTCTGTGTG
Found at i:854473 original size:19 final size:17
Alignment explanation
Indices: 854441--854476 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
854431 CCAATTACGG
854441 CTTTTTTTTTTTCTTTT
1 CTTTTTTTTTTTCTTTT
854458 CTTTTATTTGTTTTCTTTT
1 CTTTT-TTT-TTTTCTTTT
854477 TGTTTTACGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 3 0.18
19 9 0.53
ACGTcount: A:0.03, C:0.11, G:0.03, T:0.83
Consensus pattern (17 bp):
CTTTTTTTTTTTCTTTT
Found at i:855263 original size:16 final size:16
Alignment explanation
Indices: 855229--855272 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
855219 TAGTACAAAT
*
855229 ATTATAAAATTAAATAA
1 ATTATAAAA-TAAAAAA
*
855246 ATTATAGAATAAAAAA
1 ATTATAAAATAAAAAA
*
855262 ATTATATAATA
1 ATTATAAAATA
855273 TCTTTTACGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (16 bp):
ATTATAAAATAAAAAA
Found at i:855328 original size:20 final size:21
Alignment explanation
Indices: 855282--855329 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
855272 ATCTTTTACG
*
855282 AAAAAATTATCAATTTAATTA
1 AAAAAATCATCAATTTAATTA
** *
855303 TTAAAATCATC-ATTTATTTA
1 AAAAAATCATCAATTTAATTA
855323 AAAAAAT
1 AAAAAAT
855330 TACTTATATA
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAAAATCATCAATTTAATTA
Found at i:859696 original size:2 final size:2
Alignment explanation
Indices: 859689--859726 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
859679 TGGAATTAGC
*
859689 AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
859727 GTAATAAGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:860501 original size:2 final size:2
Alignment explanation
Indices: 860494--860518 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
860484 AGCAAACTTT
860494 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
860519 TCAAAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:862694 original size:6 final size:6
Alignment explanation
Indices: 862683--862804 Score: 78
Period size: 6 Copynumber: 20.8 Consensus size: 6
862673 TGGTCGTGGG
* *
862683 GGAGGT GGAGGT GGAGGT GGTGGT GGAGGC GGAGGT GGAGGT GGA---
1 GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT
* * * *
862728 GGAGGT GGTGGT GGCAGTTTT GGA--T GG-GGAT GG-GGT GGAGGA GGTGGT
1 GGAGGT GGAGGT GG-AG--GT GGAGGT GGAGG-T GGAGGT GGAGGT GGAGGT
* * *
862776 GGAGGG GGAGGG GGAGGA GGAGGT GGAGG
1 GGAGGT GGAGGT GGAGGT GGAGGT GGAGG
862805 ATGGGGATGG
Statistics
Matches: 92, Mismatches: 14, Indels: 20
0.73 0.11 0.16
Matches are distributed among these distances:
3 3 0.03
4 3 0.03
5 3 0.03
6 78 0.85
7 1 0.01
8 1 0.01
9 3 0.03
ACGTcount: A:0.16, C:0.02, G:0.66, T:0.16
Consensus pattern (6 bp):
GGAGGT
Found at i:862705 original size:24 final size:24
Alignment explanation
Indices: 862678--862726 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
862668 GGAGTTGGTC
*
862678 GTGGGGGAGGTGGAGGTGGAGGTG
1 GTGGGGGAGGCGGAGGTGGAGGTG
*
862702 GTGGTGGAGGCGGAGGTGGAGGTG
1 GTGGGGGAGGCGGAGGTGGAGGTG
862726 G
1 G
862727 AGGAGGTGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.02, G:0.69, T:0.16
Consensus pattern (24 bp):
GTGGGGGAGGCGGAGGTGGAGGTG
Found at i:862778 original size:27 final size:27
Alignment explanation
Indices: 862748--862831 Score: 132
Period size: 27 Copynumber: 3.1 Consensus size: 27
862738 GTGGCAGTTT
*
862748 TGGATGGGGATGGGGTGGAGGAGGTGG
1 TGGATGGGGATGGGGAGGAGGAGGTGG
* *
862775 TGGAGGGGGAGGGGGAGGAGGAGGTGG
1 TGGATGGGGATGGGGAGGAGGAGGTGG
*
862802 AGGATGGGGATGGGGAGGAGGAGGTGG
1 TGGATGGGGATGGGGAGGAGGAGGTGG
862829 TGG
1 TGG
862832 TTGGTACAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.18, C:0.00, G:0.69, T:0.13
Consensus pattern (27 bp):
TGGATGGGGATGGGGAGGAGGAGGTGG
Found at i:862779 original size:9 final size:9
Alignment explanation
Indices: 862761--862828 Score: 59
Period size: 9 Copynumber: 7.6 Consensus size: 9
862751 ATGGGGATGG
862761 GGTGGAGGA
1 GGTGGAGGA
*
862770 GGTGGTGGA
1 GGTGGAGGA
* *
862779 GGGGGAGGG
1 GGTGGAGGA
*
862788 GGAGGAGGA
1 GGTGGAGGA
862797 GGTGGAGGA
1 GGTGGAGGA
862806 TGG-GGATGG-
1 -GGTGGA-GGA
*
862815 GGAGGAGGA
1 GGTGGAGGA
862824 GGTGG
1 GGTGG
862829 TGGTTGGTAC
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
8 4 0.09
9 39 0.83
10 4 0.09
ACGTcount: A:0.19, C:0.00, G:0.71, T:0.10
Consensus pattern (9 bp):
GGTGGAGGA
Found at i:862805 original size:12 final size:12
Alignment explanation
Indices: 862683--862828 Score: 82
Period size: 12 Copynumber: 11.7 Consensus size: 12
862673 TGGTCGTGGG
*
862683 GGAGGTGGAGGT
1 GGAGGTGGAGGA
* *
862695 GGAGGTGGTGGT
1 GGAGGTGGAGGA
* *
862707 GGAGGCGGAGGT
1 GGAGGTGGAGGA
862719 GGAGGTGGAGGA
1 GGAGGTGGAGGA
* *
862731 GGTGGTGGTGGCA
1 GGAGGTGGAGG-A
**
862744 GTTTTGGATGG-GGA
1 G--GAGG-TGGAGGA
862758 TGG-GGTGGAGGA
1 -GGAGGTGGAGGA
* *
862770 GGTGGTGGAGGG
1 GGAGGTGGAGGA
*
862782 GGAGGGGGAGGA
1 GGAGGTGGAGGA
862794 GGAGGTGGAGGA
1 GGAGGTGGAGGA
862806 TGG-GGATGGGGAGGA
1 -GGAGG-T--GGAGGA
862821 GGAGGTGG
1 GGAGGTGG
862829 TGGTTGGTAC
Statistics
Matches: 108, Mismatches: 14, Indels: 24
0.74 0.10 0.16
Matches are distributed among these distances:
11 5 0.05
12 77 0.71
13 5 0.05
14 4 0.04
15 14 0.13
16 3 0.03
ACGTcount: A:0.16, C:0.01, G:0.66, T:0.16
Consensus pattern (12 bp):
GGAGGTGGAGGA
Found at i:863322 original size:19 final size:19
Alignment explanation
Indices: 863287--863328 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
863277 GGAACTGAGA
*
863287 TTTTGTGTTTCTTTTTTCC
1 TTTTGTGTTACTTTTTTCC
*
863306 TTTTG-GTTACTTGTTTTGC
1 TTTTGTGTTACTT-TTTTCC
863325 TTTT
1 TTTT
863329 TCAATGGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.02, C:0.12, G:0.14, T:0.71
Consensus pattern (19 bp):
TTTTGTGTTACTTTTTTCC
Found at i:864602 original size:18 final size:18
Alignment explanation
Indices: 864569--864653 Score: 61
Period size: 19 Copynumber: 4.7 Consensus size: 18
864559 AGATATATTT
864569 AAAAAATAA-A-AA-ATA
1 AAAAAATAATATAATATA
864584 AAAAAATAATATAATATA
1 AAAAAATAATATAATATA
864602 AAATATAA-ATATATAAATATA
1 AAA-A-AATA-ATAT-AATATA
** *
864623 TTAAAATATATATAACATA
1 AAAAAATA-ATATAATATA
*
864642 AAAAAATTATAT
1 AAAAAATAATAT
864654 TTAAAATATT
Statistics
Matches: 56, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
15 9 0.16
16 1 0.02
17 2 0.04
18 10 0.18
19 14 0.25
20 13 0.23
21 7 0.12
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAAAATAATATAATATA
Found at i:864635 original size:20 final size:20
Alignment explanation
Indices: 864610--864674 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 20
864600 TAAAATATAA
864610 ATATATAAATATATTAAAAT
1 ATATATAAATATATTAAAAT
*
864630 ATATATAACATA-A-AAAAATT
1 ATATATAA-ATATATTAAAA-T
*
864650 ATATTTAAA-ATATTAATAAT
1 ATATATAAATATATTAA-AAT
864670 ATATA
1 ATATA
864675 AATCTATATA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
18 1 0.03
19 6 0.17
20 24 0.67
21 5 0.14
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (20 bp):
ATATATAAATATATTAAAAT
Found at i:864643 original size:16 final size:16
Alignment explanation
Indices: 864571--864644 Score: 55
Period size: 15 Copynumber: 4.6 Consensus size: 16
864561 ATATATTTAA
* *
864571 AAAATAAAAAATA-AA
1 AAAATAAAATATATAT
*
864586 AAAATAATATA-ATAT
1 AAAATAAAATATATAT
864601 AAAATATAAATATATA-
1 AAAATA-AAATATATAT
864617 AATATATTAAAATATATAT
1 AA-A-A-TAAAATATATAT
*
864636 AACATAAAA
1 AAAATAAAA
864645 AAATTATATT
Statistics
Matches: 47, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
14 1 0.02
15 16 0.34
16 11 0.23
17 5 0.11
18 10 0.21
19 4 0.09
ACGTcount: A:0.70, C:0.01, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAATAAAATATATAT
Found at i:867564 original size:19 final size:18
Alignment explanation
Indices: 867540--867575 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
867530 TTAGCATTCA
867540 ATTTCTTTCTCATATTAAT
1 ATTTCTTTCTCA-ATTAAT
867559 ATTTCTTTCTCAATTAA
1 ATTTCTTTCTCAATTAA
867576 ATGTTTTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.28, C:0.17, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTCTTTCTCAATTAAT
Found at i:870768 original size:2 final size:2
Alignment explanation
Indices: 870761--870795 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
870751 TAATCTATTT
*
870761 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
870796 CTAAATTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:880630 original size:36 final size:36
Alignment explanation
Indices: 880556--880632 Score: 86
Period size: 36 Copynumber: 2.1 Consensus size: 36
880546 TATATATATG
* * *
880556 AATAAATCAGATAATATTATTTTATTAAAATTATAA
1 AATAAATCAGATAATATTATTTTAATAAAAATAAAA
*
880592 AATAAATATAGATAAT-TTA-TTTAATAATAAATAAAA
1 AATAAAT-CAGATAATATTATTTTAATAA-AAATAAAA
880628 AATAA
1 AATAA
880633 TGAGATTAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
35 7 0.20
36 21 0.60
37 7 0.20
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (36 bp):
AATAAATCAGATAATATTATTTTAATAAAAATAAAA
Found at i:882991 original size:23 final size:22
Alignment explanation
Indices: 882956--883002 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
882946 GAGATGAATA
882956 AAAATTAAATTTT-ATTATTAAT
1 AAAATTAAATTTTAATT-TTAAT
882978 AAAATTAAATTTTTAATTTTAAT
1 AAAATTAAA-TTTTAATTTTAAT
883001 AA
1 AA
883003 TCAAATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 9 0.39
23 11 0.48
24 3 0.13
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AAAATTAAATTTTAATTTTAAT
Found at i:893619 original size:6 final size:6
Alignment explanation
Indices: 893608--893633 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
893598 GAGAGGGGTC
893608 GGTCAG GGTCAG GGTCAG GGTCAG GG
1 GGTCAG GGTCAG GGTCAG GGTCAG GG
893634 GTAGATATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.54, T:0.15
Consensus pattern (6 bp):
GGTCAG
Found at i:898100 original size:31 final size:31
Alignment explanation
Indices: 898062--898133 Score: 105
Period size: 28 Copynumber: 2.4 Consensus size: 31
898052 CAAGGCTAGC
898062 TAATCCCTGATGTGATCATGTCATCATGTGA
1 TAATCCCTGATGTGATCATGTCATCATGTGA
898093 TAATCCCT--T-TGATCATGTCATCATGTGA
1 TAATCCCTGATGTGATCATGTCATCATGTGA
* *
898121 AAATCCGTGATGT
1 TAATCCCTGATGT
898134 TTTTCATACA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
28 25 0.69
29 1 0.03
30 1 0.03
31 9 0.25
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.36
Consensus pattern (31 bp):
TAATCCCTGATGTGATCATGTCATCATGTGA
Found at i:900663 original size:2 final size:2
Alignment explanation
Indices: 900658--900689 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
900648 AGAAAAACAT
900658 TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
900690 CTTACAAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:908110 original size:16 final size:16
Alignment explanation
Indices: 908065--908098 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
908055 TCTTTTTCTC
*
908065 AAAAA-AAAAAAAAAG
1 AAAAAGAAAAAGAAAG
908080 AAAAAGAAAAAGAAAG
1 AAAAAGAAAAAGAAAG
908096 AAA
1 AAA
908099 GAGAGAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAAGAAAG
Found at i:908514 original size:9 final size:9
Alignment explanation
Indices: 908502--908539 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
908492 ATAATTTAAA
908502 TATTTATAT
1 TATTTATAT
908511 TATTTATATT
1 TATTTATA-T
908521 TATTTATTAT
1 TATTTA-TAT
908531 TA-TTATAT
1 TATTTATAT
908539 T
1 T
908540 TTAAAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 4 0.15
9 11 0.41
10 10 0.37
11 2 0.07
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TATTTATAT
Found at i:908526 original size:19 final size:19
Alignment explanation
Indices: 908502--908540 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
908492 ATAATTTAAA
908502 TATTTA-TATTATTTATATT
1 TATTTATTATTA-TTATATT
908521 TATTTATTATTATTATATT
1 TATTTATTATTATTATATT
908540 T
1 T
908541 TAAAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TATTTATTATTATTATATT
Found at i:908621 original size:5 final size:5
Alignment explanation
Indices: 908613--908646 Score: 50
Period size: 5 Copynumber: 6.4 Consensus size: 5
908603 ATTTTTATTT
908613 TTATA TTATA TTATA TTTTATA TTATA TTATA TT
1 TTATA TTATA TTATA --TTATA TTATA TTATA TT
908647 TAAATTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 22 0.81
7 5 0.19
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (5 bp):
TTATA
Found at i:908633 original size:17 final size:17
Alignment explanation
Indices: 908607--908647 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
908597 TAATATATTT
908607 TTAT-TTTTATATTATA
1 TTATATTTTATATTATA
908623 TTATATTTTATATTATA
1 TTATATTTTATATTATA
908640 TTATATTT
1 TTATATTT
908648 AAATTATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 4 0.17
17 20 0.83
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTATATTTTATATTATA
Found at i:908635 original size:12 final size:12
Alignment explanation
Indices: 908600--908641 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
908590 TAAAAATTAA
908600 TATATTTT-TATT
1 TATATTTTATA-T
* *
908612 TTTATATTATAT
1 TATATTTTATAT
908624 TATATTTTATAT
1 TATATTTTATAT
908636 TATATT
1 TATATT
908642 ATATTTAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
12 23 0.92
13 2 0.08
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TATATTTTATAT
Found at i:910348 original size:2 final size:2
Alignment explanation
Indices: 910338--910375 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
910328 TCCCTCCCCC
910338 CT CT C- CT CT CT C- CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
910376 AGTGATGGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:914998 original size:16 final size:16
Alignment explanation
Indices: 914953--914998 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
914943 TTAAATTAAA
914953 AAATTT-AT-TTAATT
1 AAATTTGATATTAATT
*
914967 TAATTTG-TATTAAATT
1 AAATTTGATATT-AATT
914983 AAATTTGATATTAATT
1 AAATTTGATATTAATT
914999 TTTTTAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 6 0.23
15 2 0.08
16 14 0.54
17 4 0.15
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (16 bp):
AAATTTGATATTAATT
Found at i:915013 original size:25 final size:26
Alignment explanation
Indices: 914953--915023 Score: 76
Period size: 25 Copynumber: 2.8 Consensus size: 26
914943 TTAAATTAAA
*
914953 AAATTT-ATTTAATTTAATTTGTATT
1 AAATTTAATTTGATTTAATTTGTATT
*
914978 AAATTAAATTTGATATTAATTT-T-TT
1 AAATTTAATTTGAT-TTAATTTGTATT
*
915003 TAATTTAATTTGATTTGAATT
1 AAATTTAATTTGATTT-AATT
915024 ACTACTTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
24 2 0.05
25 23 0.59
26 7 0.18
27 7 0.18
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.58
Consensus pattern (26 bp):
AAATTTAATTTGATTTAATTTGTATT
Found at i:929854 original size:15 final size:16
Alignment explanation
Indices: 929834--929870 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
929824 ATATAACTAT
929834 TTTATTTTTATTT-TA
1 TTTATTTTTATTTGTA
*
929849 TTTA-TTTTATTTGTT
1 TTTATTTTTATTTGTA
929864 TTTATTT
1 TTTATTT
929871 AAATTAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 8 0.42
15 9 0.47
16 2 0.11
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (16 bp):
TTTATTTTTATTTGTA
Found at i:929856 original size:20 final size:19
Alignment explanation
Indices: 929831--929871 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
929821 ATAATATAAC
*
929831 TATTTTATTTTTATTTTATT
1 TATTTTATTTGT-TTTTATT
929851 TATTTTATTTGTTTTTATT
1 TATTTTATTTGTTTTTATT
929870 TA
1 TA
929872 AATTAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (19 bp):
TATTTTATTTGTTTTTATT
Found at i:935668 original size:154 final size:154
Alignment explanation
Indices: 935384--935692 Score: 528
Period size: 154 Copynumber: 2.0 Consensus size: 154
935374 AGGAATACGC
** *
935384 AGAGTTGGGGCCGCAAGACCATCACGCAATTGAGAATTAAACCAACCACGGCATCAACATTGCCA
1 AGAGTTGGGGCAACAAGACCATCACGCAATTGAGAATTAAACCAACCACGGCATCAACATAGCCA
935449 CCACGTTTTGCATTACACCGGCTACTCTTACGAAGTTCCAATAACGTGCCTTTTCCTTCAGCAGC
66 CCACGTTTTGCATTACACCGGCTACTCTTACGAAGTTCCAATAACGTGCCTTTTCCTTCAGCAGC
935514 ATAAATCATTACATTTCCACGATG
131 ATAAATCATTACATTTCCACGATG
* *
935538 AGAGTTGGGGCAACAAGACCATCACGCAATTGAGAATTAGACCAACCATGGCATCAACATAGCCA
1 AGAGTTGGGGCAACAAGACCATCACGCAATTGAGAATTAAACCAACCACGGCATCAACATAGCCA
* * * * *
935603 CCACGTTTTGCTTTATACCGGCTATTCTTATGAAGTTCCAATAACGTGCCTTTTCCTTCATCAGC
66 CCACGTTTTGCATTACACCGGCTACTCTTACGAAGTTCCAATAACGTGCCTTTTCCTTCAGCAGC
935668 ATAAATCATTACATTTCCACGATG
131 ATAAATCATTACATTTCCACGATG
935692 A
1 A
935693 CCACCCATTG
Statistics
Matches: 145, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
154 145 1.00
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (154 bp):
AGAGTTGGGGCAACAAGACCATCACGCAATTGAGAATTAAACCAACCACGGCATCAACATAGCCA
CCACGTTTTGCATTACACCGGCTACTCTTACGAAGTTCCAATAACGTGCCTTTTCCTTCAGCAGC
ATAAATCATTACATTTCCACGATG
Found at i:940022 original size:21 final size:22
Alignment explanation
Indices: 939985--940028 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
939975 ATAACATGGA
* *
939985 TTAAAAATTATTTATTTATTAT
1 TTAAAAATTATTAATTTAATAT
940007 TTAAAAATT-TTAATTTAATAT
1 TTAAAAATTATTAATTTAATAT
940028 T
1 T
940029 ATTTTTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTAAAAATTATTAATTTAATAT
Done.