Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold733
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1111331
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.28
Warning! 184803 characters in sequence are not A, C, G, or T
File 4 of 3
Found at i:782197 original size:12 final size:12
Alignment explanation
Indices: 782180--782204 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
782170 TACATTGTAC
782180 TACTTTAATGCA
1 TACTTTAATGCA
782192 TACTTTAATGCA
1 TACTTTAATGCA
782204 T
1 T
782205 TAATCTCTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (12 bp):
TACTTTAATGCA
Found at i:785814 original size:200 final size:200
Alignment explanation
Indices: 785471--785870 Score: 800
Period size: 200 Copynumber: 2.0 Consensus size: 200
785461 GTCGGGGGTT
785471 GGGTAGCTGTAGGTCTGTAGCTCCCGGTCTAAAAAAAAATTCGGATGGACGACCTGTCGACCTGC
1 GGGTAGCTGTAGGTCTGTAGCTCCCGGTCTAAAAAAAAATTCGGATGGACGACCTGTCGACCTGC
785536 AGCTGGGAGGGGGGAGCGCGTTGGCTGCAGGTCTGTACTTCCCGGTCTGAACAAATTCGGATGGA
66 AGCTGGGAGGGGGGAGCGCGTTGGCTGCAGGTCTGTACTTCCCGGTCTGAACAAATTCGGATGGA
785601 CGACTTGGGAGCTACAGTGCCACCCATTGAAAAAAAAGTGTATTGTATAGTTTTGGACACATCAA
131 CGACTTGGGAGCTACAGTGCCACCCATTGAAAAAAAAGTGTATTGTATAGTTTTGGACACATCAA
785666 TGATA
196 TGATA
785671 GGGTAGCTGTAGGTCTGTAGCTCCCGGTCTAAAAAAAAATTCGGATGGACGACCTGTCGACCTGC
1 GGGTAGCTGTAGGTCTGTAGCTCCCGGTCTAAAAAAAAATTCGGATGGACGACCTGTCGACCTGC
785736 AGCTGGGAGGGGGGAGCGCGTTGGCTGCAGGTCTGTACTTCCCGGTCTGAACAAATTCGGATGGA
66 AGCTGGGAGGGGGGAGCGCGTTGGCTGCAGGTCTGTACTTCCCGGTCTGAACAAATTCGGATGGA
785801 CGACTTGGGAGCTACAGTGCCACCCATTGAAAAAAAAGTGTATTGTATAGTTTTGGACACATCAA
131 CGACTTGGGAGCTACAGTGCCACCCATTGAAAAAAAAGTGTATTGTATAGTTTTGGACACATCAA
785866 TGATA
196 TGATA
785871 AAGAAAGTTG
Statistics
Matches: 200, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
200 200 1.00
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (200 bp):
GGGTAGCTGTAGGTCTGTAGCTCCCGGTCTAAAAAAAAATTCGGATGGACGACCTGTCGACCTGC
AGCTGGGAGGGGGGAGCGCGTTGGCTGCAGGTCTGTACTTCCCGGTCTGAACAAATTCGGATGGA
CGACTTGGGAGCTACAGTGCCACCCATTGAAAAAAAAGTGTATTGTATAGTTTTGGACACATCAA
TGATA
Found at i:788388 original size:4 final size:4
Alignment explanation
Indices: 788387--788458 Score: 99
Period size: 4 Copynumber: 18.0 Consensus size: 4
788377 GGGACAGACA
* * *
788387 GACG GACG GACA GACG GACG GACG GACG GACG GACA GACG GACG GACA
1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG
* *
788435 GACG GACA GACG GACT GACG GACG
1 GACG GACG GACG GACG GACG GACG
788459 CAGAGGAAAG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 58 1.00
ACGTcount: A:0.31, C:0.25, G:0.43, T:0.01
Consensus pattern (4 bp):
GACG
Found at i:788404 original size:8 final size:8
Alignment explanation
Indices: 788378--788457 Score: 87
Period size: 8 Copynumber: 10.5 Consensus size: 8
788368 AACTGAAGTG
788378 GGACAGAC
1 GGACAGAC
* *
788386 AGACGGAC
1 GGACAGAC
788394 GGACAGAC
1 GGACAGAC
*
788402 GGACGGAC
1 GGACAGAC
*
788410 GGACGGAC
1 GGACAGAC
788418 GGACAGAC
1 GGACAGAC
788426 -G---GAC
1 GGACAGAC
788430 GGACAGAC
1 GGACAGAC
788438 GGACAGAC
1 GGACAGAC
*
788446 GGACTGAC
1 GGACAGAC
788454 GGAC
1 GGAC
788458 GCAGAGGAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
4 3 0.05
5 1 0.02
7 1 0.02
8 56 0.92
ACGTcount: A:0.33, C:0.25, G:0.41, T:0.01
Consensus pattern (8 bp):
GGACAGAC
Found at i:788458 original size:12 final size:12
Alignment explanation
Indices: 788378--788457 Score: 115
Period size: 12 Copynumber: 6.7 Consensus size: 12
788368 AACTGAAGTG
*
788378 GGACAGACAGAC
1 GGACGGACAGAC
788390 GGACGGACAGAC
1 GGACGGACAGAC
*
788402 GGACGGACGGAC
1 GGACGGACAGAC
788414 GGACGGACAGAC
1 GGACGGACAGAC
788426 GGACGGACAGAC
1 GGACGGACAGAC
* *
788438 GGACAGACGGAC
1 GGACGGACAGAC
*
788450 TGACGGAC
1 GGACGGAC
788458 GCAGAGGAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 61 1.00
ACGTcount: A:0.33, C:0.25, G:0.41, T:0.01
Consensus pattern (12 bp):
GGACGGACAGAC
Found at i:788862 original size:179 final size:177
Alignment explanation
Indices: 788549--788869 Score: 529
Period size: 179 Copynumber: 1.8 Consensus size: 177
788539 TCACACAACC
*
788549 AGTAAGAGGCTTAGCTAGCTGGCGAAAACGGGACATTTCATATAATACAGTTATAATGGGATTTC
1 AGTAAGAGGCTAAGCTAGCTGGCGAAAACGGGACATTTCATATAATACAGTTATAATGGGATTTC
* *
788614 TTCCAAGGGCTGGCTAACACTCTGTATCCCATATTTGGGCCTTCATATTTGGTGATGATGGGACC
66 TTCCAAGGGCTGGCGAACACTCTGTATCCCATATTTGGGCCTTCATATTTGGTGAGGATGGGACC
788679 CCGGGACAGCCCGGTCGACCCTCAAAAGGAATTAGGTTTACACGACA
131 CCGGGACAGCCCGGTCGACCCTCAAAAGGAATTAGGTTTACACGACA
* *
788726 AGTAAGAGGCTAAGCTAGCCTTGCGAAAACGGGACATTTCGTATAATACAGTTATAATGGGATTT
1 AGTAAGAGGCTAAGCTAG-CTGGCGAAAACGGGACATTTCATATAATACAGTTATAATGGGATTT
*
788791 C-TCTCAGGGGGCTGGCGAACAC-CATGTATCCCATATTTGGGCCTTCATATTTGGTGAGGATGG
65 CTTC-CA-AGGGCTGGCGAACACTC-TGTATCCCATATTTGGGCCTTCATATTTGGTGAGGATGG
*
788854 GGCCCCGGGACAGCCC
127 GACCCCGGGACAGCCC
788870 TGTCTTTTGT
Statistics
Matches: 133, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
177 19 0.14
178 48 0.36
179 66 0.50
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (177 bp):
AGTAAGAGGCTAAGCTAGCTGGCGAAAACGGGACATTTCATATAATACAGTTATAATGGGATTTC
TTCCAAGGGCTGGCGAACACTCTGTATCCCATATTTGGGCCTTCATATTTGGTGAGGATGGGACC
CCGGGACAGCCCGGTCGACCCTCAAAAGGAATTAGGTTTACACGACA
Found at i:793381 original size:11 final size:11
Alignment explanation
Indices: 793365--793390 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
793355 ATTGAGTTGC
793365 TGATCTACATT
1 TGATCTACATT
793376 TGATCTACATT
1 TGATCTACATT
793387 TGAT
1 TGAT
793391 GCCAGGAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (11 bp):
TGATCTACATT
Found at i:805849 original size:2 final size:2
Alignment explanation
Indices: 805842--805891 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
805832 TGCTTCTGAT
805842 GA GA GA GA GA GA GA GA GA 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 GA GA GA
805884 GA GA GA GA
1 GA GA GA GA
805892 TGGCCAGGGG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:808627 original size:9 final size:9
Alignment explanation
Indices: 808613--808641 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
808603 AATGATAAAC
808613 AAATCAAAT
1 AAATCAAAT
808622 AAATCAAAT
1 AAATCAAAT
808631 AAATC-AAT
1 AAATCAAAT
808639 AAA
1 AAA
808642 CCTATTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.30
9 14 0.70
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.21
Consensus pattern (9 bp):
AAATCAAAT
Found at i:818021 original size:70 final size:70
Alignment explanation
Indices: 817908--818206 Score: 463
Period size: 70 Copynumber: 4.3 Consensus size: 70
817898 ACAGGGTCGA
* * *
817908 TGTCAATGGTTCAGCACATTGAAATTGCCACATCAAAATTCGTCACTTATTCATGTGTAGGATTT
1 TGTCAATGGTTCAGCACATTGAAATTGCCACATCAAAATTCGTCACTGATTCATGTGTAAGATTG
*
817973 AACTG
66 AACCG
* * *
817978 TGTCAATGGTTCAGCTCATTGAAATTGCCACATCAAAATTCGTCACTGATTCATGTGTAGGATTA
1 TGTCAATGGTTCAGCACATTGAAATTGCCACATCAAAATTCGTCACTGATTCATGTGTAAGATTG
*
818043 AACCA
66 AACCG
*
818048 TGTCAATGGTTCAGCACATTGAAATTGCCACATCAAAATTTGTCACTGATTCATGTGTAAGATTG
1 TGTCAATGGTTCAGCACATTGAAATTGCCACATCAAAATTCGTCACTGATTCATGTGTAAGATTG
818113 AACCG
66 AACCG
* ** *
818118 GGTCAATGGTTTGGCACATTGAAATTGCCACATCAAAATTTGTCACTGATTTCATGTGTAAGATT
1 TGTCAATGGTTCAGCACATTGAAATTGCCACATCAAAATTCGTCACTGA-TTCATGTGTAAGATT
818183 GAACCG
65 GAACCG
*
818189 GGTCAATGGTTCAGCACA
1 TGTCAATGGTTCAGCACA
818207 AGGCACTGGT
Statistics
Matches: 213, Mismatches: 15, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
70 176 0.83
71 37 0.17
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (70 bp):
TGTCAATGGTTCAGCACATTGAAATTGCCACATCAAAATTCGTCACTGATTCATGTGTAAGATTG
AACCG
Found at i:822947 original size:2 final size:2
Alignment explanation
Indices: 822940--822980 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
822930 TTTGGGGGTT
*
822940 GA GA GA GA GA GA GA GA GA GA AA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
822981 CTCTCAAGGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:823674 original size:2 final size:2
Alignment explanation
Indices: 823667--823734 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
823657 TTTGTGTTTA
823667 AG AG AG AG AG AG AG 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 AG AG AG AG
823709 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
823735 CACTTTATGG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:826044 original size:51 final size:52
Alignment explanation
Indices: 825873--826008 Score: 254
Period size: 52 Copynumber: 2.6 Consensus size: 52
825863 GGAGGGGGGG
*
825873 GGGGGAAAAAAAGCTGCAATAAAATCCATGTATAAGAGTAATTGCAGGTAGA
1 GGGGGCAAAAAAGCTGCAATAAAATCCATGTATAAGAGTAATTGCAGGTAGA
825925 GGGGGCAAAAAAGCTGCAATAAAATCCATGTATAAGAGTAATTGCAGGTAGA
1 GGGGGCAAAAAAGCTGCAATAAAATCCATGTATAAGAGTAATTGCAGGTAGA
*
825977 GGGGGCACAAAAGCTGCAATAAAATCCATGTA
1 GGGGGCAAAAAAGCTGCAATAAAATCCATGTA
826009 AAGTATTATT
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 82 1.00
ACGTcount: A:0.43, C:0.12, G:0.26, T:0.18
Consensus pattern (52 bp):
GGGGGCAAAAAAGCTGCAATAAAATCCATGTATAAGAGTAATTGCAGGTAGA
Found at i:826602 original size:36 final size:37
Alignment explanation
Indices: 826484--826614 Score: 180
Period size: 36 Copynumber: 3.6 Consensus size: 37
826474 CCGGGTTCTT
* *
826484 TATTGGCTCAA-CTACTTCTTATTGGGTGGTAAGTTA
1 TATTGACTCAACCTACTTCTTACTGGGTGGTAAGTTA
* * *
826520 TATTGACTC-AGCTAATTCTAACTGGGTGGTAAGTTA
1 TATTGACTCAACCTACTTCTTACTGGGTGGTAAGTTA
*
826556 TATTGACTCAACCT-CTTCATACTGGGTGGTAAGTTA
1 TATTGACTCAACCTACTTCTTACTGGGTGGTAAGTTA
826592 TATTGACTCAACC-ACTTCTTACT
1 TATTGACTCAACCTACTTCTTACT
826615 AAGTAGTAAC
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
35 1 0.01
36 79 0.95
37 3 0.04
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.38
Consensus pattern (37 bp):
TATTGACTCAACCTACTTCTTACTGGGTGGTAAGTTA
Found at i:828040 original size:166 final size:166
Alignment explanation
Indices: 827765--828545 Score: 1395
Period size: 166 Copynumber: 4.7 Consensus size: 166
827755 GGTATTTTTC
* ** * * * ** * *
827765 AAAAATCTTCTTCTCAAAAACTGTTCGGCCGGAAAAACTTAAACTT-GTATTGAGGCATCCTCAG
1 AAAAATCTTCTTCTCAAAAACTATTAAGCCAGAAAAGCTCAAA-TTAAAATGGAAGCATCCTCAG
* * *
827829 GTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCAT-GGGTAGGGTGGGGCCAAAATAGGGG
65 GTATTGTAGAATCAAGTTTGTTCAAATCATGGTCCCC-TGGGGTAGGGTGGGGCCACAATAGGGG
*
827893 GATCAAGTTTACCATAGGAATATATAGAGAACATCTTT
129 GATCAAGTTTACCATAGGAATATATAGAGAAAATCTTT
827931 AAAAATCTTCTTCTCAAAAACTATTAAGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAAAAACTATTAAGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGG
827996 TATTGTAGAATCAAGTTTGTTCAAATCATGGTCCCCTGGGGTAGGGTGGGGCCACAATAGGGGGA
66 TATTGTAGAATCAAGTTTGTTCAAATCATGGTCCCCTGGGGTAGGGTGGGGCCACAATAGGGGGA
828061 TCAAGTTTACCATAGGAATATATAGAGAAAATCTTT
131 TCAAGTTTACCATAGGAATATATAGAGAAAATCTTT
828097 AAAAATCTTCTTCTCAAAAACTATTAAGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAAAAACTATTAAGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGG
828162 TATTGTAGAATCAAGTTTGTTCAAATCATGGTCCCCTGGGGTAGGGTGGGGCCACAATAGGGGGA
66 TATTGTAGAATCAAGTTTGTTCAAATCATGGTCCCCTGGGGTAGGGTGGGGCCACAATAGGGGGA
828227 TCAAGTTTACCATAGGAATATATAGAGAAAATCTTT
131 TCAAGTTTACCATAGGAATATATAGAGAAAATCTTT
828263 AAAAATCTTCTTCTCAAAAACTATTAAGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAAAAACTATTAAGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGG
*
828328 TATTGTAGAATCAAGTTTGTTCAAATCATGGTCCCCTGGGGTAGGGTGGGGCCACAATGGGGGGA
66 TATTGTAGAATCAAGTTTGTTCAAATCATGGTCCCCTGGGGTAGGGTGGGGCCACAATAGGGGGA
828393 TCAAGTTTACCATAGGAATATATAGAGAAAATCTTT
131 TCAAGTTTACCATAGGAATATATAGAGAAAATCTTT
828429 AAAAATCTTCTTCTCAAAAACTATTAAGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAAAAACTATTAAGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGG
828494 TATTGTAGAATCAAGTTTGTTCAAATCATGGTCCCCTGGGGTAGGGTGGGGC
66 TATTGTAGAATCAAGTTTGTTCAAATCATGGTCCCCTGGGGTAGGGTGGGGC
828546 NGTGGAAACA
Statistics
Matches: 598, Mismatches: 15, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
165 3 0.01
166 595 0.99
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.27
Consensus pattern (166 bp):
AAAAATCTTCTTCTCAAAAACTATTAAGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGG
TATTGTAGAATCAAGTTTGTTCAAATCATGGTCCCCTGGGGTAGGGTGGGGCCACAATAGGGGGA
TCAAGTTTACCATAGGAATATATAGAGAAAATCTTT
Found at i:854006 original size:2 final size:2
Alignment explanation
Indices: 853999--854037 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
853989 NNNNNNNNNN
853999 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
854038 TAAGGTTTAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:854323 original size:10 final size:9
Alignment explanation
Indices: 854304--854370 Score: 72
Period size: 8 Copynumber: 7.8 Consensus size: 9
854294 GCAAATGAAA
854304 TCTCT-TTC
1 TCTCTCTTC
*
854312 TCTCTATT-
1 TCTCTCTTC
854320 TCTCT-TTC
1 TCTCTCTTC
854328 TCTCTCTT-
1 TCTCTCTTC
854336 TCTCTC-TC
1 TCTCTCTTC
854344 TCTCTCTCTC
1 TCTCTCT-TC
854354 TCTCTCTCTC
1 TCTCTCT-TC
854364 TCTCTCT
1 TCTCTCT
854371 CAGTATCTTC
Statistics
Matches: 53, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
7 3 0.06
8 27 0.51
9 4 0.08
10 19 0.36
ACGTcount: A:0.01, C:0.42, G:0.00, T:0.57
Consensus pattern (9 bp):
TCTCTCTTC
Found at i:854325 original size:16 final size:16
Alignment explanation
Indices: 854304--854371 Score: 91
Period size: 16 Copynumber: 4.2 Consensus size: 16
854294 GCAAATGAAA
* *
854304 TCTCTTTCTCTCTATT
1 TCTCTTTCTCTCTCTC
*
854320 TCTCTTTCTCTCTCTT
1 TCTCTTTCTCTCTCTC
*
854336 TCTCTCTCTCTCTCTC
1 TCTCTTTCTCTCTCTC
*
854352 TCTCTCTCTCTCTCTC
1 TCTCTTTCTCTCTCTC
854368 TCTC
1 TCTC
854372 AGTATCTTCA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.01, C:0.43, G:0.00, T:0.56
Consensus pattern (16 bp):
TCTCTTTCTCTCTCTC
Found at i:854327 original size:6 final size:6
Alignment explanation
Indices: 854304--854371 Score: 91
Period size: 6 Copynumber: 11.3 Consensus size: 6
854294 GCAAATGAAA
* * * * *
854304 TCTCTT TCTCTC TATTTC TCTTTC TCTCTC TTTCTC TCTCTC TCTCTC
1 TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC
854352 TCTCTC TCTCTC TCTCTC TC
1 TCTCTC TCTCTC TCTCTC TC
854372 AGTATCTTCA
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 55 1.00
ACGTcount: A:0.01, C:0.43, G:0.00, T:0.56
Consensus pattern (6 bp):
TCTCTC
Found at i:854371 original size:10 final size:10
Alignment explanation
Indices: 854304--854371 Score: 91
Period size: 10 Copynumber: 6.8 Consensus size: 10
854294 GCAAATGAAA
*
854304 TCTCTTTCTC
1 TCTCTCTCTC
* *
854314 TCTATTTCTC
1 TCTCTCTCTC
*
854324 TTTCTCTCTC
1 TCTCTCTCTC
*
854334 TTTCTCTCTC
1 TCTCTCTCTC
854344 TCTCTCTCTC
1 TCTCTCTCTC
854354 TCTCTCTCTC
1 TCTCTCTCTC
854364 TCTCTCTC
1 TCTCTCTC
854372 AGTATCTTCA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 53 1.00
ACGTcount: A:0.01, C:0.43, G:0.00, T:0.56
Consensus pattern (10 bp):
TCTCTCTCTC
Found at i:854551 original size:71 final size:71
Alignment explanation
Indices: 854425--854575 Score: 196
Period size: 71 Copynumber: 2.1 Consensus size: 71
854415 TTCGATAAAT
* * * ** * *
854425 ATCACGGAA-TAAACTCTATCTTAATGTTTAAAGTGTCTGATAAAGATGAGGTCAAAAGCCTTAT
1 ATCACGGAAGAAAACTCTATCTGAACGTTTAAAGTGTCTGATAAAGATGAAATCAAAAACCTTAA
854489 GACAAG
66 GACAAG
* * * *
854495 ATCATGGAAGAAAACTCTATCTGAACGTTTAAAGTGTCTTATAAAGATTAAATCAAAAACTTTAA
1 ATCACGGAAGAAAACTCTATCTGAACGTTTAAAGTGTCTGATAAAGATGAAATCAAAAACCTTAA
854560 GACAAG
66 GACAAG
854566 ATCACGGAAG
1 ATCACGGAAG
854576 GAACTTTATA
Statistics
Matches: 68, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
70 8 0.12
71 60 0.88
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (71 bp):
ATCACGGAAGAAAACTCTATCTGAACGTTTAAAGTGTCTGATAAAGATGAAATCAAAAACCTTAA
GACAAG
Found at i:855025 original size:2 final size:2
Alignment explanation
Indices: 855012--855046 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
855002 AATCTACACG
* *
855012 GA GA GC GA GA GA GA GA GA CA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
855047 GTTTACACGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.06, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:855316 original size:2 final size:2
Alignment explanation
Indices: 855309--855356 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
855299 GAAAATGAAA
* *
855309 TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC TC TC TC TT TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
855351 TC TC TC
1 TC TC TC
855357 AGTATCTTCA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:868270 original size:19 final size:19
Alignment explanation
Indices: 868246--868288 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
868236 TCTTTCTCTC
868246 TATTTCTTTTTCTCCTTTT
1 TATTTCTTTTTCTCCTTTT
868265 TATTTCTTTTTCTCCTTTT
1 TATTTCTTTTTCTCCTTTT
868284 TATTT
1 TATTT
868289 AAGGATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.07, C:0.19, G:0.00, T:0.74
Consensus pattern (19 bp):
TATTTCTTTTTCTCCTTTT
Found at i:872960 original size:180 final size:180
Alignment explanation
Indices: 872636--872963 Score: 577
Period size: 180 Copynumber: 1.8 Consensus size: 180
872626 GGCTGCCAAA
872636 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAAATAGGAAGTTGTTCTTTTGCA
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAAATAGGAAGTTGTTCTTTTGCA
* * *
872701 GATCAATTGTACACATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAGTTTATCGA
66 GATCAATTGTACACATATCAGAGGTGTGCATATTGCTAGAATTTTGATTTCCAATAATTTATCGA
872766 AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
131 AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
* *
872816 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCT
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAAATAGGAAGTTGTTCTTTTGCA
*
872881 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGAATTTTGATTTCCAATAATTTAT-GA
66 GATCAATTGTACACATATCAGAGGTGTGCATATTGCTAGAATTTTGATTTCCAATAATTTATCGA
*
872945 AACAAATATCAGCTTTTGA
131 AA-AAATACCAGCTTTTGA
872964 CCATCTTTAA
Statistics
Matches: 140, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
179 4 0.03
180 136 0.97
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (180 bp):
AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAAATAGGAAGTTGTTCTTTTGCA
GATCAATTGTACACATATCAGAGGTGTGCATATTGCTAGAATTTTGATTTCCAATAATTTATCGA
AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
Found at i:878159 original size:33 final size:33
Alignment explanation
Indices: 878122--878254 Score: 248
Period size: 33 Copynumber: 4.0 Consensus size: 33
878112 TGTTTTTTGT
* *
878122 AGAATAATGTGATGATGACCCTTTTGATTTAGC
1 AGAATCATGTGATGATGACCATTTTGATTTAGC
878155 AGAATCATGTGATGATGACCATTTTGATTTAGC
1 AGAATCATGTGATGATGACCATTTTGATTTAGC
878188 AGAATCATGTGATGATGACCATTTTGATTTAGC
1 AGAATCATGTGATGATGACCATTTTGATTTAGC
878221 AGAATCATGTGATGATGACCATTTTGATTTAGC
1 AGAATCATGTGATGATGACCATTTTGATTTAGC
878254 A
1 A
878255 CCTGGAAGAA
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 98 1.00
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (33 bp):
AGAATCATGTGATGATGACCATTTTGATTTAGC
Found at i:881868 original size:86 final size:84
Alignment explanation
Indices: 881719--881888 Score: 313
Period size: 86 Copynumber: 2.0 Consensus size: 84
881709 TAGAAAGTTT
*
881719 CTAGTGAAGGAAAATACTTCATTTAAGCAGTGTCTAGCTATCTACATGTAATATTAGTTTGCATT
1 CTAGTGAAGGAAAATACTTCATTTAAGCAGTGTCTAGCTATCTACATGTAATATTAGTATGCATT
881784 GTAAGGGAGTTGCATTTAA
66 GTAAGGGAGTTGCATTTAA
881803 NCTAGTGAAGGAAAAATACTTCATTTAAGCAGTGTCTAGCTATCTACATGTAATATTAGTATGCA
1 -CTAGTGAAGG-AAAATACTTCATTTAAGCAGTGTCTAGCTATCTACATGTAATATTAGTATGCA
881868 TTGTAAGGGAGTTGCATTTAA
64 TTGTAAGGGAGTTGCATTTAA
881889 TGCCTGGTAG
Statistics
Matches: 83, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
85 10 0.12
86 73 0.88
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (84 bp):
CTAGTGAAGGAAAATACTTCATTTAAGCAGTGTCTAGCTATCTACATGTAATATTAGTATGCATT
GTAAGGGAGTTGCATTTAA
Found at i:882278 original size:2 final size:2
Alignment explanation
Indices: 882271--882313 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
882261 GTCTAGCTGT
882271 TC TC TC TC TC TC TC TC 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 TC TC TC TC TC TC TC TC
882313 T
1 T
882314 GTGAGTTTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:884509 original size:43 final size:43
Alignment explanation
Indices: 884448--884535 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
884438 GGAGCTATGA
884448 ACCGGAACGTTTACATTACCGCCTAAGGAAAATGCATCAGTGG
1 ACCGGAACGTTTACATTACCGCCTAAGGAAAATGCATCAGTGG
*
884491 ACCGGAACGTTTACATTACCGCCTATGGAAAATGCATCAGTGG
1 ACCGGAACGTTTACATTACCGCCTAAGGAAAATGCATCAGTGG
884534 AC
1 AC
884536 TATACTCAGG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.32, C:0.24, G:0.23, T:0.22
Consensus pattern (43 bp):
ACCGGAACGTTTACATTACCGCCTAAGGAAAATGCATCAGTGG
Found at i:888513 original size:12 final size:13
Alignment explanation
Indices: 888494--888524 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
888484 CGAAATTATT
888494 ATTTTTTTTTTTC
1 ATTTTTTTTTTTC
888507 ATTTTTTTTTTTC
1 ATTTTTTTTTTTC
888520 ATTTT
1 ATTTT
888525 CACAATCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.10, C:0.06, G:0.00, T:0.84
Consensus pattern (13 bp):
ATTTTTTTTTTTC
Found at i:890948 original size:165 final size:166
Alignment explanation
Indices: 890222--891014 Score: 1146
Period size: 166 Copynumber: 4.8 Consensus size: 166
890212 GTCGCATTTA
*
890222 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAATATTTGTATAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATAT
* * **
890287 CTTAGGATATATTTTTGTACCAATTAGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTT
*
890352 TAGCCAAAATTTTCAAACAAATTTTTGTCAAAGAAT
131 TAGCCAAAATTTTCAAACAAATTTTCGTCAAAGAAT
*
890388 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATAT
*
890453 CGTGGGATGTATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTT
*
890518 TAGCCAAAATTTTCAAACAAATTTTTGTCAAAGAAT
131 TAGCCAAAATTTTCAAACAAATTTTCGTCAAAGAAT
* * * * *
890554 TCTCAGCAACTGTTTACCACAGATGCTTGAAATTTTTACACAGTATTTGTATAGGTATGCTATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATAT
* * *
890619 CGTGGGATATATTTTTGTATCAATCGGACGTCAACGTT-CTGTTAAATAATGACTTTGTTTATTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAAC-TTCCTGTTAAATGACGACTTTGTTTATTT
* *
890683 TTAGCCAAAATTTTCAAACAAATTGTCGTCAAAGATT
130 TTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGAAT
* * * * *
890720 TCTCAGCAGCTATTTATCGCAGATCCTTGAAATTTTTACACAGTGTTTAT-TAAGGCGTGCCATA
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTAT-AGGCATGCCATA
890784 TCGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGA-GTACTTTGTTTA-T
65 TCGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACG-ACTTTGTTTATT
* * *
890847 TTCAGCCAAAATTTTCAAACAAATTTTCCTCAAAGATT
129 TTTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGAAT
* * * * * *
890885 TCTCAGGAGCTATTTATCGCAGATGCTTAAAATTTTAACACACTATTTGCT-TAGGTATGCCATA
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTG-TATAGGCATGCCATA
* * * * * * * *
890949 TTGTGGGATATATTTCTGTACCAATCGGATGCCAGCTTTCTGTTAAATGTCGACTTTGCTTATTT
65 TCGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTT
891014 T
130 T
891015 GCATATTCAC
Statistics
Matches: 570, Mismatches: 50, Indels: 14
0.90 0.08 0.02
Matches are distributed among these distances:
165 144 0.25
166 424 0.74
167 2 0.00
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (166 bp):
TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATAT
CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTT
TAGCCAAAATTTTCAAACAAATTTTCGTCAAAGAAT
Found at i:892597 original size:146 final size:146
Alignment explanation
Indices: 892291--892952 Score: 909
Period size: 146 Copynumber: 4.5 Consensus size: 146
892281 TAACTGTTGA
*
892291 TCATAAGCAATTTTTGTGTGAAGTAAGAACATT-CAATGCTTCTCCATAAGAAAGATAATGACCG
1 TCATAAGCAATCTTTGTGTGAAGTAAGAAC-TTCCAATGCTTCTCCATAAGAAAGAT-AT----G
* **
892355 GACACCAGACACGAATTTTGCACTTTTTCTGTCAGTGACCTTGACCTTGCCCAAATGACCTTGGG
60 G--ACCGGACACGAATTTTGCACTTTTTCTCCCAGTGACCTTGACCTTGCCCAAATGACCTTGGG
* * *
892420 TCATGGTCATGACACACGCTTTGG
123 TCAAGGTCATGACACACCCTTAGG
* * * * *
892444 TCCTAAGCAATATTTGTATGAAGTTAGAACATT-CATTGCTTCTCCATAAGAAAGATAAT-GACC
1 TCATAAGCAATCTTTGTGTGAAGTAAGAAC-TTCCAATGCTTCTCCATAAGAAAGAT-ATGGACC
* ** *
892507 GGACACGAATATTGCACTATTTT-TCCCAACGACCTTGACCTTGCCCAAATGACCTTGGATCAAG
64 GGACACGAATTTTGCACT-TTTTCTCCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAG
892571 GTCATGACACACCCTTAGG
128 GTCATGACACACCCTTAGG
* * *
892590 TCATAAGCAATCTTTGTGTGAATTAAGAACTTCCAATGTTTCTCCATTAGAAAGATATGGACCGG
1 TCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGCTTCTCCATAAGAAAGATATGGACCGG
* *
892655 ACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTC
66 ACACGAATTTTGCACTTTTTCTCCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTC
*
892720 ATGCCACACCCTTAGG
131 ATGACACACCCTTAGG
** *
892736 TCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATAATTCTCCATAAGAAAGATATGGACCAG
1 TCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGCTTCTCCATAAGAAAGATATGGACCGG
* * * *
892801 ACACGAATTTTGTATTTTTTCTGCCAGTGACATTGACCTTGCCCAAATGACCTTGGGTCAAGGTC
66 ACACGAATTTTGCACTTTTTCTCCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTC
892866 ATGACACACCCTTAGG
131 ATGACACACCCTTAGG
* * *
892882 TCATAACCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGAGCGG
1 TCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGCTTCTCCATAAGAAAGATATGGACCGG
892947 ACACGA
66 ACACGA
892953 TTGCACAGAC
Statistics
Matches: 460, Mismatches: 45, Indels: 15
0.88 0.09 0.03
Matches are distributed among these distances:
145 8 0.02
146 393 0.85
147 4 0.01
148 1 0.00
153 54 0.12
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.29
Consensus pattern (146 bp):
TCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGCTTCTCCATAAGAAAGATATGGACCGG
ACACGAATTTTGCACTTTTTCTCCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTC
ATGACACACCCTTAGG
Found at i:892981 original size:8 final size:8
Alignment explanation
Indices: 892957--892991 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
892947 ACACGATTGC
*
892957 ACAGACAG
1 ACAGACGG
*
892965 ACGGACGG
1 ACAGACGG
892973 ACAGACGG
1 ACAGACGG
892981 ACAGACGG
1 ACAGACGG
892989 ACA
1 ACA
892992 AGGTGATTCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.40, C:0.26, G:0.34, T:0.00
Consensus pattern (8 bp):
ACAGACGG
Found at i:913080 original size:11 final size:11
Alignment explanation
Indices: 913053--913084 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
913043 ATATGTTAAG
913053 AAATTACTATT
1 AAATTACTATT
913064 --ATTACTATT
1 AAATTACTATT
913073 AAATTACTATT
1 AAATTACTATT
913084 A
1 A
913085 TTTCACATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 9 0.47
11 10 0.53
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (11 bp):
AAATTACTATT
Found at i:931043 original size:14 final size:15
Alignment explanation
Indices: 931024--931062 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
931014 CCCCCCCCCC
931024 AAAAAAAAACAA-AA
1 AAAAAAAAACAACAA
931038 AAAAAAAAACAACAA
1 AAAAAAAAACAACAA
*
931053 AAAACAAAAC
1 AAAAAAAAAC
931063 GTCAATCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAAAAACAACAA
Found at i:931044 original size:17 final size:18
Alignment explanation
Indices: 931024--931061 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
931014 CCCCCCCCCC
931024 AAAAAAAAACAAAAAA-A
1 AAAAAAAAACAAAAAACA
*
931041 AAAAAACAACAAAAAACA
1 AAAAAAAAACAAAAAACA
931059 AAA
1 AAA
931062 CGTCAATCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (18 bp):
AAAAAAAAACAAAAAACA
Found at i:937083 original size:15 final size:17
Alignment explanation
Indices: 937051--937087 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
937041 ACAAATGGAC
937051 ATAACAATGTTATATAT
1 ATAACAATGTTATATAT
937068 ATAACAATGTTATATAT
1 ATAACAATGTTATATAT
937085 ATA
1 ATA
937088 TATATANNNN
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (17 bp):
ATAACAATGTTATATAT
Found at i:938987 original size:164 final size:157
Alignment explanation
Indices: 938378--939115 Score: 549
Period size: 164 Copynumber: 4.5 Consensus size: 157
938368 ACACATTCTA
* * * * **
938378 TATGTATTTCTATGTTAAACTTTTAACCCGGCCTGGGGCTCAACTTTTGGTCCGGGGGACACGGC
1 TATGTATTTC--TGTTAAACTTTAAACCC-G-CTGGGGC-CCAGTTTTGGTCC-GGGGTCACGAT
* * * * *
938443 TTTTACAATTTGGAATCTTCACTACATATTCTAGCTTTTATGTAAATATTGGCATTTCTGGTGCA
60 TTTTACAATTTAGAATCTTCACTATATATACAAGCGTTTATGTAAATATTGGCATTTCTGGTGCA
*
938508 GTGGTTCTTGAGAAGAACATTTTAAAACATTTTC
125 GTGGTTCTTGAGAAGAAAATTTTAAAA-ATTTTC
* * *
938542 TAATGTATTTCTGTTAAACTTTAAACTCCGCCCGGGCCCCAGTTTTTGGTCCGGGGTCACAATTT
1 T-ATGTATTTCTGTTAAACTTTAAAC-CCG-CTGGGGCCCAG-TTTTGGTCCGGGGTCACGATTT
* * * *
938607 TTACAATTTACAATGTTCGA-TATATATACAAGCGTTTGTGTAAATATTGGCATTTCTGGTTCAG
62 TTACAATTTAGAATCTTC-ACTATATATACAAGCGTTTATGTAAATATTGGCATTTCTGGTGCAG
* *
938671 TGCTTCTTG-GAAAGAAAATTTTTAAACATTTTTC
126 TGGTTCTTGAG-AAGAAAA-TTTTAAA-AATTTTC
* * * ** * *
938705 TTACGTATTTCTTTGTTAAATTTTAAACCCCACATGGGGCCCTAGTTTTAATTCGGGGGTCACGG
1 -TATGTATTTC--TGTTAAACTTTAAA-CCCGC-TGGGGCCC-AGTTTT-GGTCCGGGGTCACGA
** * * *
938770 TTTTTACAATTTAGAATCTTCTTTATATATGCAAGC-TTT-TGTATAAGTATTGGTATTTTTGGT
59 TTTTTACAATTTAGAATCTTCACTATATATACAAGCGTTTATGTA-AA-TATTGGCATTTCTGGT
* * ** * *
938833 GCATTGGTTCTTTAGAAGAGGATTTTGAAAGTTTTC
122 GCAGTGGTTCTTGAGAAGAAAATTTTAAAAATTTTC
* * **
938869 ATATGTATTTCAATGTTCAACTTTGAACCACGCGTGGGGCCTCAGTTTTGGTCTAGGGT-AGCGA
1 -TATGTATTTC--TGTTAAACTTTAAACC-CGC-TGGGGCC-CAGTTTTGGTCCGGGGTCA-CGA
* *
938933 TTTTTACAATTTAGAATCTTCACTATACTATACAAGCGTTTATGTATATATTGGTATTTCTGGTG
59 TTTTTACAATTTAGAATCTTCACTATA-TATACAAGCGTTTATGTAAATATTGGCATTTCTGGTG
* **
938998 CAGTGGTTCTTGAGAAG---A-TTCAACCATTTTCC
123 CAGTGGTTCTTGAGAAGAAAATTTTAAAAATTTT-C
* * * * * * * *
939030 TGTGGATTTCAATGTTAAACTTTGAACACTGTCCGAGGCTCCAGTTTTGCTCCGGGGGTCATGAT
1 TATGTATTTC--TGTTAAACTTTAAAC-CCG-CTGGGGC-CCAGTTTTGGTCC-GGGGTCACGAT
*
939095 TTTTACAATATAGAATCTTCA
60 TTTTACAATTTAGAATCTTCA
939116 TTGTCCAGGT
Statistics
Matches: 462, Mismatches: 82, Indels: 63
0.76 0.14 0.10
Matches are distributed among these distances:
160 46 0.10
161 33 0.07
162 80 0.17
163 86 0.19
164 90 0.19
165 50 0.11
166 76 0.16
167 1 0.00
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (157 bp):
TATGTATTTCTGTTAAACTTTAAACCCGCTGGGGCCCAGTTTTGGTCCGGGGTCACGATTTTTAC
AATTTAGAATCTTCACTATATATACAAGCGTTTATGTAAATATTGGCATTTCTGGTGCAGTGGTT
CTTGAGAAGAAAATTTTAAAAATTTTC
Found at i:939077 original size:160 final size:163
Alignment explanation
Indices: 938443--939115 Score: 425
Period size: 166 Copynumber: 4.1 Consensus size: 163
938433 GGGACACGGC
* * * * * * * *
938443 TTTTACAATTTGGAATCTTCACTACATATTCTAGCTTTTATGTAAATATTGGCATTTCTGGTGCA
1 TTTTACAATTTAGAATCTTCACTATATATACAAGCTTTTGTATAAGTATTGGTATTTCTGGTGCA
* * * * * *
938508 GTGGTTCTTGAGAAGAACATTTTAAAACATTTTC-TAATGTATTTC--TGTTAAACTTTAAACTC
66 GTGGTTCTTTAGAAGAAGA-TTTCAAA-GTTTTCAT-ATGGATTTCAATGTTAAACTTTGAAC-C
* * * *
938570 -CGCCCG-GGCCCCAGTTTTTGGTCCG-GGGTCACAAT
127 ACGCGCGAGGCCTCAG-TTTTGCTCCGAGGGTCACGAT
* * * * * * *
938605 TTTTACAATTTACAATGTTCGA-TATATATACAAGCGTTTGTGTAAATATTGGCATTTCTGGTTC
1 TTTTACAATTTAGAATCTTC-ACTATATATACAAGCTTTTGTATAAGTATTGGTATTTCTGGTGC
* * * * * * * * ** * *
938669 AGTGCTTC-TTGGAAAGAAAATTTTTAAACATTTTTCTTACGTATTTCTTTGTTAAATTTTAAAC
65 AGTGGTTCTTTAG-AAGAAGA--TTTCAA-AGTTTTCATATGGATTTCAATGTTAAACTTTGAAC
* * ** * ** * * *
938733 CCCACATGGGGCC-CTAGTTTTAATTCGGGGGTCACGGT
126 CACGCGCGAGGCCTC-AGTTTTGCTCCGAGGGTCACGAT
** * *
938771 TTTTACAATTTAGAATCTTCTTTATATATGCAAGCTTTTGTATAAGTATTGGTATTTTTGGTGCA
1 TTTTACAATTTAGAATCTTCACTATATATACAAGCTTTTGTATAAGTATTGGTATTTCTGGTGCA
* * * * *
938836 TTGGTTCTTTAGAAGAGGATTTTGAAAGTTTTCATATGTATTTCAATGTTCAACTTTGAACCACG
66 GTGGTTCTTTAGAAGAAGA-TTTCAAAGTTTTCATATGGATTTCAATGTTAAACTTTGAACCACG
* * * *
938901 CGTGGGGCCTCAGTTTTGGT-CTAGGGT-AGCGAT
130 CGCGAGGCCTCAGTTTTGCTCCGAGGGTCA-CGAT
938934 TTTTACAATTTAGAATCTTCACTATACTATACAAGCGTTTATGTAT-A-TATTGGTATTTCTGGT
1 TTTTACAATTTAGAATCTTCACTATA-TATACAAGC-TTT-TGTATAAGTATTGGTATTTCTGGT
* *
938997 GCAGTGGTTC-TT-G-AGAAGA-TTCAACCA-TTTTCCTGTGGATTTCAATGTTAAACTTTGAA-
63 GCAGTGGTTCTTTAGAAGAAGATTTCAA--AGTTTTCATATGGATTTCAATGTTAAACTTTGAAC
* *
939056 CACTGTC-CGAGG-CTCCAGTTTTGCTCCGGGGGTCATGAT
126 CAC-G-CGCGAGGCCT-CAGTTTTGCTCCGAGGGTCACGAT
*
939095 TTTTACAATATAGAATCTTCA
1 TTTTACAATTTAGAATCTTCA
939116 TTGTCCAGGT
Statistics
Matches: 412, Mismatches: 74, Indels: 51
0.77 0.14 0.09
Matches are distributed among these distances:
159 9 0.02
160 41 0.10
161 37 0.09
162 69 0.17
163 55 0.13
164 79 0.19
165 36 0.09
166 83 0.20
167 3 0.01
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (163 bp):
TTTTACAATTTAGAATCTTCACTATATATACAAGCTTTTGTATAAGTATTGGTATTTCTGGTGCA
GTGGTTCTTTAGAAGAAGATTTCAAAGTTTTCATATGGATTTCAATGTTAAACTTTGAACCACGC
GCGAGGCCTCAGTTTTGCTCCGAGGGTCACGAT
Found at i:954340 original size:5 final size:5
Alignment explanation
Indices: 954330--954377 Score: 89
Period size: 5 Copynumber: 9.8 Consensus size: 5
954320 TTTGGGGTTT
954330 TTTTG TTTTG TTTT- TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
954378 TTTGTTACCT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 4 0.10
5 38 0.90
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (5 bp):
TTTTG
Found at i:954991 original size:21 final size:21
Alignment explanation
Indices: 954965--955007 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
954955 ACCATTTTAA
954965 ATTTTACCCGATTAAGATCAT
1 ATTTTACCCGATTAAGATCAT
*
954986 ATTTTACCGGATTAAGATCAT
1 ATTTTACCCGATTAAGATCAT
955007 A
1 A
955008 AATTCACAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (21 bp):
ATTTTACCCGATTAAGATCAT
Found at i:957938 original size:40 final size:40
Alignment explanation
Indices: 957858--958010 Score: 225
Period size: 40 Copynumber: 3.7 Consensus size: 40
957848 AGTGATATTG
*
957858 AATATTGTTATATAGGTTGATTACATCATTACATTACATTACATT
1 AATATTGGTATATAGGTTGATT--A-CATT--ATTACATTACATT
* *
957903 AATATTGTTATATAGGTTGATTACATTATTACATTATATT
1 AATATTGGTATATAGGTTGATTACATTATTACATTACATT
957943 AATATTGGTATATAGGTTGATTACATTATTACATTACATT
1 AATATTGGTATATAGGTTGATTACATTATTACATTACATT
*
957983 AATATTGGTATAAAGGTTGATTACATTA
1 AATATTGGTATATAGGTTGATTACATTA
958011 AAAGTTACAA
Statistics
Matches: 104, Mismatches: 4, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
40 77 0.74
42 4 0.04
43 1 0.01
45 22 0.21
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.45
Consensus pattern (40 bp):
AATATTGGTATATAGGTTGATTACATTATTACATTACATT
Found at i:963905 original size:2 final size:2
Alignment explanation
Indices: 963898--963978 Score: 63
Period size: 2 Copynumber: 45.0 Consensus size: 2
963888 ACTCTATGAC
*
963898 AT AT AT AT A- AT A- AT AC AT AT AT AT A- AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
963936 AC AT A- AT A- AT AC AT AT AT AT AT A- AT A- AT GT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
963973 AT AT AT
1 AT AT AT
963979 GTCATCGAGT
Statistics
Matches: 62, Mismatches: 8, Indels: 18
0.70 0.09 0.20
Matches are distributed among these distances:
1 9 0.15
2 53 0.85
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (2 bp):
AT
Found at i:963926 original size:25 final size:25
Alignment explanation
Indices: 963896--963978 Score: 102
Period size: 25 Copynumber: 3.4 Consensus size: 25
963886 ACACTCTATG
963896 ACATATATATAATAATACATATATAT
1 ACATATATAT-ATAATACATATATAT
963922 A-ATATATATATAATACATA-ATAAT
1 ACATATATATATAATACATATAT-AT
*
963946 ACATATATATATAATA-ATGTAT-T
1 ACATATATATATAATACATATATAT
*
963969 ATATATATAT
1 ACATATATAT
963979 GTCATCGAGT
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
23 12 0.23
24 15 0.29
25 24 0.46
26 1 0.02
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (25 bp):
ACATATATATATAATACATATATAT
Found at i:963944 original size:21 final size:21
Alignment explanation
Indices: 963898--963977 Score: 72
Period size: 21 Copynumber: 3.5 Consensus size: 21
963888 ACTCTATGAC
963898 ATATATATAATAATACATATATATA
1 ATATATAT-ATAATAC--ATA-ATA
963923 ATATATATATAATACATAATA
1 ATATATATATAATACATAATA
*
963944 ATACATATATATATA-ATAATGTA
1 ATATATATATA-ATACATAA--TA
*
963967 TTATATATATA
1 ATATATATATA
963978 TGTCATCGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
21 17 0.35
22 6 0.12
23 11 0.22
24 7 0.14
25 8 0.16
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (21 bp):
ATATATATATAATACATAATA
Found at i:964418 original size:2 final size:2
Alignment explanation
Indices: 964411--964517 Score: 187
Period size: 2 Copynumber: 53.0 Consensus size: 2
964401 TTGAATCATT
964411 GA GA GA GA GA GA GA GA GA 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 GA GA GA
* *
964453 GA GA GA GA GC GA GA GA GA GC GA GCA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA G-A GA GA GA GA GA GA GA GA GA
964496 GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA
964518 TTTTCTTTTC
Statistics
Matches: 100, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
2 98 0.98
3 2 0.02
ACGTcount: A:0.48, C:0.03, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:965369 original size:2 final size:2
Alignment explanation
Indices: 965364--965395 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
965354 CGCGCGCGTG
965364 CT CT CT 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
965396 GCAAATATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:966178 original size:2 final size:2
Alignment explanation
Indices: 966171--966229 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
966161 TCCATACATA
966171 CT CT CT CT CT CT CT CT 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 CT
966213 CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT C
966230 AGAGGGTGTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:977037 original size:24 final size:22
Alignment explanation
Indices: 976979--977134 Score: 174
Period size: 24 Copynumber: 7.0 Consensus size: 22
976969 GGTAAAAAAG
*
976979 AGTACTGTTTACAGTTAGAC-A
1 AGTACTGTTTACAGTCAGACAA
*
977000 AGTACTGTTAACAGTCAGACAATA
1 AGTACTGTTTACAGTCAGAC-A-A
* *
977024 AGTACAGTTTACAGTTAGAC-A
1 AGTACTGTTTACAGTCAGACAA
*
977045 AGTACTGTTAACAGTCAGACAATA
1 AGTACTGTTTACAGTCAGAC-A-A
*
977069 AGTACTGTTTACAGTTAGAC-A
1 AGTACTGTTTACAGTCAGACAA
*
977090 AGTACTGTTAACAGTCAGACAATA
1 AGTACTGTTTACAGTCAGAC-A-A
977114 AGTACTGTTTACAGTCAGACA
1 AGTACTGTTTACAGTCAGACA
977135 TTTAAGATGA
Statistics
Matches: 113, Mismatches: 13, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
21 55 0.49
23 1 0.01
24 57 0.50
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (22 bp):
AGTACTGTTTACAGTCAGACAA
Found at i:977043 original size:45 final size:45
Alignment explanation
Indices: 976979--977134 Score: 294
Period size: 45 Copynumber: 3.5 Consensus size: 45
976969 GGTAAAAAAG
976979 AGTACTGTTTACAGTTAGACAAGTACTGTTAACAGTCAGACAATA
1 AGTACTGTTTACAGTTAGACAAGTACTGTTAACAGTCAGACAATA
*
977024 AGTACAGTTTACAGTTAGACAAGTACTGTTAACAGTCAGACAATA
1 AGTACTGTTTACAGTTAGACAAGTACTGTTAACAGTCAGACAATA
977069 AGTACTGTTTACAGTTAGACAAGTACTGTTAACAGTCAGACAATA
1 AGTACTGTTTACAGTTAGACAAGTACTGTTAACAGTCAGACAATA
*
977114 AGTACTGTTTACAGTCAGACA
1 AGTACTGTTTACAGTTAGACA
977135 TTTAAGATGA
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 108 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (45 bp):
AGTACTGTTTACAGTTAGACAAGTACTGTTAACAGTCAGACAATA
Found at i:989275 original size:36 final size:36
Alignment explanation
Indices: 989173--989262 Score: 180
Period size: 36 Copynumber: 2.5 Consensus size: 36
989163 TAATTTGGTT
989173 TGAGTAAACTAAAAGACACAGCTTTGCAAATTTCTA
1 TGAGTAAACTAAAAGACACAGCTTTGCAAATTTCTA
989209 TGAGTAAACTAAAAGACACAGCTTTGCAAATTTCTA
1 TGAGTAAACTAAAAGACACAGCTTTGCAAATTTCTA
989245 TGAGTAAACTAAAAGACA
1 TGAGTAAACTAAAAGACA
989263 ACGGTCTGCA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.26
Consensus pattern (36 bp):
TGAGTAAACTAAAAGACACAGCTTTGCAAATTTCTA
Found at i:1009158 original size:20 final size:20
Alignment explanation
Indices: 1009133--1009174 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1009123 GAAACATAAA
1009133 CACGTTGGAGGATTATCTTT
1 CACGTTGGAGGATTATCTTT
1009153 CACGTTGGAGGATTATCTTT
1 CACGTTGGAGGATTATCTTT
1009173 CA
1 CA
1009175 GCTGTTCGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (20 bp):
CACGTTGGAGGATTATCTTT
Found at i:1011958 original size:32 final size:32
Alignment explanation
Indices: 1011883--1012214 Score: 195
Period size: 32 Copynumber: 10.2 Consensus size: 32
1011873 AATTATATAT
*
1011883 CATATATCATATGTCAATATCGGGTGATGTAA
1 CATATATCATAGGTCAATATCGGGTGATGTAA
* *
1011915 CACATACCATAGGTCAATAATCGGAG-G-TGTAA
1 CATATATCATAGGTCAAT-ATCGG-GTGATGTAA
* * * * *
1011947 CATAAATCATAGTTTAATATTGGGTGGA-GTAG
1 CATATATCATAGGTCAATATCGGGT-GATGTAA
* * * *
1011979 TATATACCATGGGTTCACAT-TC-GGTGATGTAT
1 CATATATCATAGG-TCA-ATATCGGGTGATGTAA
* * *
1012011 CAAACATCATAAGTCAATATCGGATGATTGATGTAA
1 CATATATCATAGGTCAATATCGG--G--TGATGTAA
* *
1012047 CACACAATTCATAGGTCAATATCGGGTTG-TGTAA
1 CATA-TA-TCATAGGTCAATATCGGG-TGATGTAA
*
1012081 CATCTA-CAATAGGTCAATATCGGGTTG-TGTAA
1 CATATATC-ATAGGTCAATATCGGG-TGATGTAA
*
1012113 CATCTA-CAATAGGTCAATATCGGGTTG-TGTAA
1 CATATATC-ATAGGTCAATATCGGG-TGATGTAA
*
1012145 CATCTA-CAATAGGTCAATATCGGGTTG-TGTAA
1 CATATATC-ATAGGTCAATATCGGG-TGATGTAA
* * *
1012177 CATCTA-CAATAGGTCAATATCGGATGGTGTAA
1 CATATATC-ATAGGTCAATATCGGGTGATGTAA
1012209 CATATA
1 CATATA
1012215 CCTTTTGTTT
Statistics
Matches: 249, Mismatches: 33, Indels: 36
0.78 0.10 0.11
Matches are distributed among these distances:
30 3 0.01
31 14 0.06
32 180 0.72
33 10 0.04
34 11 0.04
35 3 0.01
36 11 0.04
37 1 0.00
38 16 0.06
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.31
Consensus pattern (32 bp):
CATATATCATAGGTCAATATCGGGTGATGTAA
Found at i:1012133 original size:64 final size:64
Alignment explanation
Indices: 1012057--1012211 Score: 292
Period size: 64 Copynumber: 2.4 Consensus size: 64
1012047 CACACAATTC
1012057 ATAGGTCAATATCGGGTTGTGTAACATCTACAATAGGTCAATATCGGGTTGTGTAACATCTACA
1 ATAGGTCAATATCGGGTTGTGTAACATCTACAATAGGTCAATATCGGGTTGTGTAACATCTACA
1012121 ATAGGTCAATATCGGGTTGTGTAACATCTACAATAGGTCAATATCGGGTTGTGTAACATCTACA
1 ATAGGTCAATATCGGGTTGTGTAACATCTACAATAGGTCAATATCGGGTTGTGTAACATCTACA
* *
1012185 ATAGGTCAATATCGGATGGTGTAACAT
1 ATAGGTCAATATCGGGTTGTGTAACAT
1012212 ATACCTTTTG
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 89 1.00
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.31
Consensus pattern (64 bp):
ATAGGTCAATATCGGGTTGTGTAACATCTACAATAGGTCAATATCGGGTTGTGTAACATCTACA
Found at i:1019494 original size:112 final size:107
Alignment explanation
Indices: 1019372--1019589 Score: 373
Period size: 112 Copynumber: 2.0 Consensus size: 107
1019362 GTATATTATC
*
1019372 AGGCCGTTGAAAATTTGAAAAATGATCATCATTTTTCAAGGAACGTTTCGTCTGACTTTAACAAA
1 AGGCCGTTGAAAATTTGAAAAATAATCATCATTTTTCAAGGAACGTTTCGTCTGACTTTAACAAA
1019437 AATATACATGTACATAAAAAATGTTGACATTTGTGTTACTTTTGATG
66 AATATACA--T--A-AAAAAATGTTGACATTTGTGTTACTTTTGATG
1019484 AGGCCGTTGAAAATTTGAAAAATAATCATCATTTTTCAAGGAACGTTTCGTCTGACTTTAACAAA
1 AGGCCGTTGAAAATTTGAAAAATAATCATCATTTTTCAAGGAACGTTTCGTCTGACTTTAACAAA
*
1019549 AATATACATAAGAAAATGTTGACATTTGTGTTACTTTTGAT
66 AATATACATAAAAAAATGTTGACATTTGTGTTACTTTTGAT
1019590 TGATTTACAT
Statistics
Matches: 104, Mismatches: 2, Indels: 5
0.94 0.02 0.05
Matches are distributed among these distances:
107 30 0.29
108 1 0.01
110 1 0.01
112 72 0.69
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (107 bp):
AGGCCGTTGAAAATTTGAAAAATAATCATCATTTTTCAAGGAACGTTTCGTCTGACTTTAACAAA
AATATACATAAAAAAATGTTGACATTTGTGTTACTTTTGATG
Found at i:1022679 original size:25 final size:25
Alignment explanation
Indices: 1022645--1022692 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
1022635 ATTATCCGGA
*
1022645 ATTTGTTTATTCGTACTATAAATCT
1 ATTTGTTTATTCGTACCATAAATCT
1022670 ATTTGTTTATTCGTACCATAAAT
1 ATTTGTTTATTCGTACCATAAAT
1022693 TTTATATAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.50
Consensus pattern (25 bp):
ATTTGTTTATTCGTACCATAAATCT
Found at i:1027185 original size:1 final size:1
Alignment explanation
Indices: 1027129--1027168 Score: 71
Period size: 1 Copynumber: 40.0 Consensus size: 1
1027119 CAAAAAGTGT
*
1027129 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1027169 GAGGGAGACA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:1028895 original size:56 final size:56
Alignment explanation
Indices: 1028723--1028913 Score: 321
Period size: 56 Copynumber: 3.4 Consensus size: 56
1028713 GAGATGAATA
* * * *
1028723 CAATGAATATGATCCAATGTTATTGATAAAGAAAATGTAAGATAAATAATTAAATG
1 CAATGAATATGATCCAATGGTATTGTTAAAGAAAATGTAATATAAATAATTAATTG
* *
1028779 CAATGAATATGATACAATGGTATTGTTAAA-AAAATGTAATATAAACAATTAATTG
1 CAATGAATATGATCCAATGGTATTGTTAAAGAAAATGTAATATAAATAATTAATTG
1028834 CAATGAATATGATCCAATGGTATTGTTAAAGAAAATGTAATATAAATAATTAATTG
1 CAATGAATATGATCCAATGGTATTGTTAAAGAAAATGTAATATAAATAATTAATTG
1028890 CAATGAATATGATCCAATGGTATT
1 CAATGAATATGATCCAATGGTATT
1028914 AATATTGATT
Statistics
Matches: 126, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
55 51 0.40
56 75 0.60
ACGTcount: A:0.47, C:0.06, G:0.14, T:0.32
Consensus pattern (56 bp):
CAATGAATATGATCCAATGGTATTGTTAAAGAAAATGTAATATAAATAATTAATTG
Found at i:1031054 original size:11 final size:11
Alignment explanation
Indices: 1031025--1031123 Score: 74
Period size: 11 Copynumber: 8.9 Consensus size: 11
1031015 ACTAAACCCC
1031025 GGGTTTACTTTT
1 GGGTTTAC-TTT
1031037 GGGGTTTACTTT
1 -GGGTTTACTTT
*
1031049 GGGTTTACTCT
1 GGGTTTACTTT
1031060 GGGTTTACTTT
1 GGGTTTACTTT
** ** *
1031071 TTG-AAAATTT
1 GGGTTTACTTT
** **
1031081 GGGTCCACTCG
1 GGGTTTACTTT
1031092 GGGTTTACTTT
1 GGGTTTACTTT
*
1031103 GGGCTTACTTT
1 GGGTTTACTTT
1031114 GGGTTTACTT
1 GGGTTTACTT
1031124 GGATATTGCT
Statistics
Matches: 65, Mismatches: 20, Indels: 4
0.73 0.22 0.04
Matches are distributed among these distances:
10 5 0.08
11 49 0.75
12 3 0.05
13 8 0.12
ACGTcount: A:0.12, C:0.13, G:0.27, T:0.47
Consensus pattern (11 bp):
GGGTTTACTTT
Found at i:1031342 original size:11 final size:12
Alignment explanation
Indices: 1031328--1031362 Score: 54
Period size: 11 Copynumber: 2.9 Consensus size: 12
1031318 GTTCAACTCT
1031328 AGTAAACCCAG-
1 AGTAAACCCAGA
1031339 AGTAAACCCAGAA
1 AGTAAACCCAG-A
1031352 AGTAAACCCAG
1 AGTAAACCCAG
1031363 GGTTAAGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.50
13 11 0.50
ACGTcount: A:0.49, C:0.26, G:0.17, T:0.09
Consensus pattern (12 bp):
AGTAAACCCAGA
Found at i:1032695 original size:167 final size:166
Alignment explanation
Indices: 1032500--1032953 Score: 592
Period size: 168 Copynumber: 2.7 Consensus size: 166
1032490 CCCCCCATGT
* * *
1032500 CCTGAACCCCTGACCCAGAGGCCATGAATTTCACAATTTAGGTAGA-GGATT-ATTGGACATCAT
1 CCTGAACCCCTGA-CCAGGGGCCATGAATTTCACAATTTTGGTAGAGGGCTTCA-TGGACATCAT
* * * *
1032563 AACCATGTATTCAGTTTTTTGCCCACATGTTTGGGAGTAAAGAAGAAGATTTTTTAAGACTTAAT
64 AACCATGCATTCAGTTTTTT-CCCAAATGTATGGGAGTAGAGAAGAAGATTTTTTAAGACTTAAT
*
1032628 ACATTTTTA-TTATATGGCCATATTGGCCCCACCCTAGAG
128 ACATTTGTACTT-TATGGCCATATTGGCCCCACCCTAGAG
*
1032667 CCTGAACCCCTGACACAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCTTCATGGACATCATA
1 CCTGAACCCCTGAC-CAGGGGCCATGAATTTCACAATTTTGGTAGAGGGCTTCATGGACATCATA
* * ** * * *
1032732 ATCATGCATTTAG-TTTTTAACAAATATACATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAAT
65 ACCATGCATTCAGTTTTTTCCCAAATGT--ATGGGAGTAGAGAAGAAGATTTTTTAAGACTTAAT
1032796 ACATTTGTACTTTATGGCCATATTGGCCCCACCCTAGAG
128 ACATTTGTACTTTATGGCCATATTGGCCCCACCCTAGAG
* *
1032835 CCAGAACCCCTGATCCAAGGGGCCATGAATTTCACAATTTTGGTAGAGGGCTTCATGGATATCAT
1 CCTGAACCCCTGA-CC-AGGGGCCATGAATTTCACAATTTTGGTAGAGGGCTTCATGGACATCAT
** * *
1032900 AACCATGCAACCAGTTTTTTCCTCAAATGTGTGGGAGTAGAGCAGAAGATTTTT
64 AACCATGCATTCAGTTTTTTCC-CAAATGTATGGGAGTAGAGAAGAAGATTTTT
1032954 GAAAATTTGG
Statistics
Matches: 248, Mismatches: 29, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
166 6 0.02
167 46 0.19
168 104 0.42
169 81 0.33
170 5 0.02
171 6 0.02
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (166 bp):
CCTGAACCCCTGACCAGGGGCCATGAATTTCACAATTTTGGTAGAGGGCTTCATGGACATCATAA
CCATGCATTCAGTTTTTTCCCAAATGTATGGGAGTAGAGAAGAAGATTTTTTAAGACTTAATACA
TTTGTACTTTATGGCCATATTGGCCCCACCCTAGAG
Found at i:1054957 original size:146 final size:147
Alignment explanation
Indices: 1054692--1054996 Score: 576
Period size: 146 Copynumber: 2.1 Consensus size: 147
1054682 TACTTCCTCA
*
1054692 ATGGACCGGACACGAATTTTGCCTTTTTTTCTGCCAGTGACCTTGCCCTTGCCCAAATGACCTTG
1 ATGGACCGGACACGAATTTTGCCATTTTTTCTGCCAGTGACCTTGCCCTTGCCCAAATGACCTTG
*
1054757 GGTCAAGGTCATGATACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATAT
66 GGTCAAGGTCATGATACACCCTTAGGTCATAAGCAATATTTGTGTGAAGTAAGAACTTCCAATAT
1054822 TTCTCCATAAGAAAGAT
131 TTCTCCATAAGAAAGAT
1054839 ATGGACCGGACACGAATTTTG-CATTTTTTCTGCCAGTGACCTTGCCCTTGCCCAAATGACCTTG
1 ATGGACCGGACACGAATTTTGCCATTTTTTCTGCCAGTGACCTTGCCCTTGCCCAAATGACCTTG
*
1054903 GGTCAAGGTCATGATACACCCTTAGGTCATAAGCAATATTTGTGTGAAGTAAGAACTTCCAATGT
66 GGTCAAGGTCATGATACACCCTTAGGTCATAAGCAATATTTGTGTGAAGTAAGAACTTCCAATAT
1054968 TTCTCCATAAGAAAGAT
131 TTCTCCATAAGAAAGAT
1054985 ATGGACCGGACA
1 ATGGACCGGACA
1054997 TGATTGCACA
Statistics
Matches: 155, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
146 134 0.86
147 21 0.14
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (147 bp):
ATGGACCGGACACGAATTTTGCCATTTTTTCTGCCAGTGACCTTGCCCTTGCCCAAATGACCTTG
GGTCAAGGTCATGATACACCCTTAGGTCATAAGCAATATTTGTGTGAAGTAAGAACTTCCAATAT
TTCTCCATAAGAAAGAT
Found at i:1059971 original size:437 final size:437
Alignment explanation
Indices: 1059155--1060662 Score: 2449
Period size: 437 Copynumber: 3.5 Consensus size: 437
1059145 TGTTTAGAAA
1059155 ATTTTTGGCCCCTAAAAACCCTTAATTACGTAACACATGATAAAATCATTACATTGCTTGAATAC
1 ATTTTTGGCCCCTAAAAACCCTTAATTACGTAACACATGATAAAATCATTACATTGCTTGAATAC
* * * *
1059220 ATAACTATAAGATAAACACATTTGCTTCTAGAACATTTCACAAAATATTTCTCAGTAAAGGGCTA
66 AGAACTATAAGATAAACACATTTGCTTCTATAATATTTCACAAAATATCTCTCAGTAAAGGGCTA
* *
1059285 CAGATTAAAGACTTTAGAGCCCTTTGGTCCCCT-TTTATTAGGGGCCAGCCCCTTTTTCTTGATA
131 CAGATTAAAGACTTTAGAGCCCTTTGGTCCCCTAATT-TGAGGGGCCAGCCCCTTTTTCTTGATA
** * * * *
1059349 TGGAATGAAAGGTCATTAAATTCTAAACAAATTTTGTTCAACACA-TGTTTAGTAATTCGTTACC
195 TCAAATAAAAGGTCATTTAATTCTACACAAATTTTGTTCAACA-AGTGTTTAGAAATTCGTTACC
* * *
1059413 GTTTTGGAGATAGATGAGAAAGAAGGTTTAAGGGGCCGGTCCCTTTTCTCCTTTTAGAGGCCGTT
259 GTTTTGGAGATAAATGAGAAAGAAGGTTTTAGGGGCCGGTCCCTTTTCTCCTTTTAGGGGCCGTT
1059478 CAACGAAATTTTGACGGTTGCAATTTGTTGAGAACATCATTTTGAACAACTTTTCTTTTATACTG
324 CAACGAAATTTTGACGGTTGCAATTTGTTGAGAACATCATTTTGAACAACTTTTCTTTTATACTG
*
1059543 CATTACAAAATATTTTTCCTTTCTGAGATAAGGGTGATCAAATTTTTGG
389 CATTACAAAATATTTTTCCTTTCTGAGATATGGGTGATCAAATTTTTGG
*
1059592 ACTTTTGGCCCCT-AAAACTCCTTAATTACGTAACACATGATAAAATCATTACATTGCTTGAATA
1 ATTTTTGGCCCCTAAAAAC-CCTTAATTACGTAACACATGATAAAATCATTACATTGCTTGAATA
1059656 CAGAACTATAAGATAAACACATTTGCTTCTATAATATTTCACAAAATATCTCTCAGTAAAGGGCT
65 CAGAACTATAAGATAAACACATTTGCTTCTATAATATTTCACAAAATATCTCTCAGTAAAGGGCT
* *
1059721 ACAGATTAAAGATTTTAGAGTCCTTTGGTCCCCTAATTTGAGGGGCCAGCCCCTTTTTCTTGATA
130 ACAGATTAAAGACTTTAGAGCCCTTTGGTCCCCTAATTTGAGGGGCCAGCCCCTTTTTCTTGATA
1059786 TCAAATAAAAGGTCATTTAATTCTACACAAATTTTGTTCAACAAGTGTTTAGAAATTCGTTACCG
195 TCAAATAAAAGGTCATTTAATTCTACACAAATTTTGTTCAACAAGTGTTTAGAAATTCGTTACCG
*
1059851 TTTTGGAGATAAATGAGAAAGAAGGTTTTAGGGGCCGGTCCCTTATT-TTCTTTTAGGGGCCGTT
260 TTTTGGAGATAAATGAGAAAGAAGGTTTTAGGGGCCGGTCCCTT-TTCTCCTTTTAGGGGCCGTT
1059915 CAACGAAATTTTGACGGTTGCAATTTGTTGAGAACATCATTTTGAACAACTTTTCTTTTATACTG
324 CAACGAAATTTTGACGGTTGCAATTTGTTGAGAACATCATTTTGAACAACTTTTCTTTTATACTG
*
1059980 CATTACAAAATATTTTTCCTTTCTGAGATATGGGTGATCAATTTTTTGG
389 CATTACAAAATATTTTTCCTTTCTGAGATATGGGTGATCAAATTTTTGG
*
1060029 ATTTTTGGCCCCTAAAAACCCTTAATTACGTAACACATGATAAACTCATTACATTGCTTGAATAC
1 ATTTTTGGCCCCTAAAAACCCTTAATTACGTAACACATGATAAAATCATTACATTGCTTGAATAC
*
1060094 AGAACTTTAAGATAAACACATTTGCTTCTATAATATTTCACAAAATATCTCTCAGTAAAGGGCTA
66 AGAACTATAAGATAAACACATTTGCTTCTATAATATTTCACAAAATATCTCTCAGTAAAGGGCTA
* * *
1060159 CAGATTAAAGATTTTTGAACCCTTTGGTCCCCTAATTTGAGGGGCCAGCCCCTTTTTCTTGATAT
131 CAGATTAAAGACTTTAGAGCCCTTTGGTCCCCTAATTTGAGGGGCCAGCCCCTTTTTCTTGATAT
* *
1060224 CAAATAAAAGGTCATTTACTTCTACACAAATTTTGTTCAATAAGTGTTTAGAAATTCGTTACCGT
196 CAAATAAAAGGTCATTTAATTCTACACAAATTTTGTTCAACAAGTGTTTAGAAATTCGTTACCGT
* * *
1060289 TTTGGAGATATATGAGAAAGAAGGTTTTAGGGGCCAGTCCCTTTTCTCCTTTTAGGGGCCGTTTA
261 TTTGGAGATAAATGAGAAAGAAGGTTTTAGGGGCCGGTCCCTTTTCTCCTTTTAGGGGCCGTTCA
*
1060354 ACGAAATTTTGACGGTTGCATTTTGTT-AGGAACATCATTTTGAACAACTTTTCTTTTATACTGC
326 ACGAAATTTTGACGGTTGCAATTTGTTGA-GAACATCATTTTGAACAACTTTTCTTTTATACTGC
*
1060418 ATTACAAAATATTTTTCCTTTCTGAGATATGGGTGATCAAATTTTTTG
390 ATTACAAAATATTTTTCCTTTCTGAGATATGGGTGATCAAATTTTTGG
1060466 ATTTTTGGCCCCTAAAAACCCTTAATTACGTAACACATGATAAAATCATTACATTGCTTGAATAC
1 ATTTTTGGCCCCTAAAAACCCTTAATTACGTAACACATGATAAAATCATTACATTGCTTGAATAC
* * * * * * * *
1060531 ATAACTGA-GAGATAAACATATTTGCTTCTATAATCTATT-ACAAAATATCCCTCGGTGAAGAGC
66 AGAACT-ATAAGATAAACACATTTGCTTCTATAATAT-TTCACAAAATATCTCTCAGTAAAGGGC
** * * * *
1060594 TATGGGTAAAAGACTTTAGAG-CCTTCTAGGT-CCCTAATTTTAGGGGCCAGCCCCTTTTTCCTG
129 TACAGATTAAAGACTTTAGAGCCCTT-T-GGTCCCCTAATTTGAGGGGCCAGCCCCTTTTTCTTG
1060657 ATATCA
192 ATATCA
1060663 GCCGAAAGGT
Statistics
Matches: 1005, Mismatches: 55, Indels: 22
0.93 0.05 0.02
Matches are distributed among these distances:
436 13 0.01
437 978 0.97
438 14 0.01
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.36
Consensus pattern (437 bp):
ATTTTTGGCCCCTAAAAACCCTTAATTACGTAACACATGATAAAATCATTACATTGCTTGAATAC
AGAACTATAAGATAAACACATTTGCTTCTATAATATTTCACAAAATATCTCTCAGTAAAGGGCTA
CAGATTAAAGACTTTAGAGCCCTTTGGTCCCCTAATTTGAGGGGCCAGCCCCTTTTTCTTGATAT
CAAATAAAAGGTCATTTAATTCTACACAAATTTTGTTCAACAAGTGTTTAGAAATTCGTTACCGT
TTTGGAGATAAATGAGAAAGAAGGTTTTAGGGGCCGGTCCCTTTTCTCCTTTTAGGGGCCGTTCA
ACGAAATTTTGACGGTTGCAATTTGTTGAGAACATCATTTTGAACAACTTTTCTTTTATACTGCA
TTACAAAATATTTTTCCTTTCTGAGATATGGGTGATCAAATTTTTGG
Found at i:1061526 original size:4 final size:4
Alignment explanation
Indices: 1061525--1061580 Score: 58
Period size: 4 Copynumber: 14.0 Consensus size: 4
1061515 GGGACAGACA
* * * * * *
1061525 GACG GACT GACG GACG GACG GACA GACA GACG GACG GACA GACT GACT
1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG
1061573 GACG GACG
1 GACG GACG
1061581 CAGAGGAAAG
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.30, C:0.25, G:0.39, T:0.05
Consensus pattern (4 bp):
GACG
Found at i:1061546 original size:16 final size:16
Alignment explanation
Indices: 1061517--1061579 Score: 81
Period size: 16 Copynumber: 3.9 Consensus size: 16
1061507 ACTAAAGTGG
* *
1061517 GACAGACAGACGGACT
1 GACAGACGGACGGACA
*
1061533 GACGGACGGACGGACA
1 GACAGACGGACGGACA
1061549 GACAGACGGACGGACA
1 GACAGACGGACGGACA
* *
1061565 GACTGACTGACGGAC
1 GACAGACGGACGGAC
1061580 GCAGAGGAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.33, C:0.25, G:0.37, T:0.05
Consensus pattern (16 bp):
GACAGACGGACGGACA
Found at i:1061556 original size:20 final size:20
Alignment explanation
Indices: 1061516--1061580 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
1061506 AACTAAAGTG
* * *
1061516 GGACAGACAGACGGACTGAC
1 GGACGGACAGACAGACAGAC
*
1061536 GGACGGACGGACAGACAGAC
1 GGACGGACAGACAGACAGAC
* *
1061556 GGACGGACAGACTGACTGAC
1 GGACGGACAGACAGACAGAC
1061576 GGACG
1 GGACG
1061581 CAGAGGAAAG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.32, C:0.25, G:0.38, T:0.05
Consensus pattern (20 bp):
GGACGGACAGACAGACAGAC
Found at i:1062539 original size:12 final size:12
Alignment explanation
Indices: 1062522--1062548 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1062512 TAAATAAGAA
1062522 TAATCTGTGTCT
1 TAATCTGTGTCT
1062534 TAATCTGTGTCT
1 TAATCTGTGTCT
1062546 TAA
1 TAA
1062549 ATGCCTCCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.15, G:0.15, T:0.48
Consensus pattern (12 bp):
TAATCTGTGTCT
Found at i:1070225 original size:166 final size:164
Alignment explanation
Indices: 1069863--1070322 Score: 584
Period size: 166 Copynumber: 2.8 Consensus size: 164
1069853 GTGAATATGC
* * * * * * * * *
1069863 AAAATAAGCCAAGTCGACATTTAACAGAAAGCTGGCATCCGAATGGTACAGAAATATATCCCAC-
1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
* * * * * *
1069927 AGTATGGCATGCCTTTACATATAGTGTGTTAAAATTTCAAGCATCT-AGATAAATAGCTGCTAAG
66 A-TATGGCATGCC-TTACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG
**
1069991 AAATCTTTGAGGAAAATTTGTTTGAAAATTTTGGCA
129 AAATCTTTGACAAAAATTTGTTTGAAAATTTTGGCA
* *
1070027 CAAATAAACAAAGTAC-TCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATACATCCCAC
1 AAAATAAACAAAGT-CGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCAC
* *
1070091 GATATGGAATGCCTATACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAACAGTTGCTGAG
65 GATATGGCATGCCT-TACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG
* *
1070156 AATTCTTTGACAAAAATTTGTTTGAAAATTTTTGCTA
129 AAATCTTTGACAAAAATTTGTTTGAAAATTTTGGC-A
* *
1070193 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCTGATTCGTACAAAAATATATCCCACG
1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
* * * *
1070258 ATATGGCATGCCTTAACAAACACTGTGTAAATATTTCAAGCATTTGCGATAAATGGTTGCTGAGA
66 ATATGGCATGCCTT-ACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
1070323 TAAATGCGAC
Statistics
Matches: 256, Mismatches: 33, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
163 1 0.00
164 89 0.35
165 49 0.19
166 117 0.46
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (164 bp):
AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
ATATGGCATGCCTTACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGAA
ATCTTTGACAAAAATTTGTTTGAAAATTTTGGCA
Found at i:1070362 original size:4 final size:4
Alignment explanation
Indices: 1070353--1070408 Score: 67
Period size: 4 Copynumber: 14.0 Consensus size: 4
1070343 GTTACGGGCG
* * * * *
1070353 GACA GACA GACG GACG GACG GACA GACA GACG GACA GACA GGCA GACA
1 GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA
1070401 GACA GACA
1 GACA GACA
1070409 CACAAGGGTA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 46 1.00
ACGTcount: A:0.41, C:0.25, G:0.34, T:0.00
Consensus pattern (4 bp):
GACA
Found at i:1070370 original size:16 final size:16
Alignment explanation
Indices: 1070351--1070408 Score: 80
Period size: 16 Copynumber: 3.6 Consensus size: 16
1070341 TTGTTACGGG
*
1070351 CGGACAGACAGACGGA
1 CGGACAGACAGACAGA
*
1070367 CGGACGGACAGACAGA
1 CGGACAGACAGACAGA
*
1070383 CGGACAGACAGGCAGA
1 CGGACAGACAGACAGA
*
1070399 CAGACAGACA
1 CGGACAGACA
1070409 CACAAGGGTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.40, C:0.26, G:0.34, T:0.00
Consensus pattern (16 bp):
CGGACAGACAGACAGA
Found at i:1070374 original size:20 final size:20
Alignment explanation
Indices: 1070346--1070403 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
1070336 AGTTTTTGTT
*
1070346 ACGGGCGGACAGACAGACGG
1 ACGGACGGACAGACAGACGG
1070366 ACGGACGGACAGACAGACGG
1 ACGGACGGACAGACAGACGG
*
1070386 ACAGACAGG-CAGACAGAC
1 ACGGAC-GGACAGACAGAC
1070404 AGACACACAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 33 0.94
21 2 0.06
ACGTcount: A:0.36, C:0.26, G:0.38, T:0.00
Consensus pattern (20 bp):
ACGGACGGACAGACAGACGG
Found at i:1073320 original size:2 final size:2
Alignment explanation
Indices: 1073313--1073356 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1073303 GTTTTTATCT
1073313 GA GA GA GA GA GA GA GA GA 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 GA GA GA
1073355 GA
1 GA
1073357 TTTTACCTGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1075948 original size:14 final size:14
Alignment explanation
Indices: 1075910--1075941 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1075900 AACCCCCAAC
1075910 AACACAAATTTGAA
1 AACACAAATTTGAA
1075924 AACACAAATTT-AA
1 AACACAAATTTGAA
1075937 AACAC
1 AACAC
1075942 CATATTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.59, C:0.19, G:0.03, T:0.19
Consensus pattern (14 bp):
AACACAAATTTGAA
Found at i:1078366 original size:14 final size:13
Alignment explanation
Indices: 1078347--1078376 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1078337 TGTATTTTGT
*
1078347 AAAAAAAAAACCA
1 AAAAAAAAAAACA
1078360 AAAAAAAAAAACA
1 AAAAAAAAAAACA
1078373 AAAA
1 AAAA
1078377 CACGACGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAACA
Found at i:1078715 original size:2 final size:2
Alignment explanation
Indices: 1078708--1078755 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1078698 TAACCAGATA
1078708 TC TC TC TC TC TC TC TC 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 TC TC TC TC TC TC TC TC
1078750 TC TC TC
1 TC TC TC
1078756 CNNNNNNNNN
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1104327 original size:21 final size:21
Alignment explanation
Indices: 1104301--1104533 Score: 303
Period size: 21 Copynumber: 11.1 Consensus size: 21
1104291 AAAATATTTT
*
1104301 TTTCGCGAATAAACGCGAAAG
1 TTTCGCGAATAAACGCGAAAC
*
1104322 TTTCGCGATTAAACGCGAAAC
1 TTTCGCGAATAAACGCGAAAC
** *
1104343 TTTCGCGAATAAACGCTTATC
1 TTTCGCGAATAAACGCGAAAC
1104364 TTTCGCGAATAAACGCGAAAC
1 TTTCGCGAATAAACGCGAAAC
** *
1104385 TTTCGCG-ATATAACGCGTTAG
1 TTTCGCGAATA-AACGCGAAAC
1104406 TTTCGCGAATAAACGCGAAAC
1 TTTCGCGAATAAACGCGAAAC
*
1104427 ATTCGCGAATAAACGCGAAAC
1 TTTCGCGAATAAACGCGAAAC
**
1104448 TTTCGCG-ATATAACGCGTTAC
1 TTTCGCGAATA-AACGCGAAAC
1104469 TTTCGCGAATAAACGCGAAAC
1 TTTCGCGAATAAACGCGAAAC
1104490 TTTCGCG-ATATAACGCGAAAC
1 TTTCGCGAATA-AACGCGAAAC
1104511 TTTCGC-AATTAAACGCGAAAC
1 TTTCGCGAA-TAAACGCGAAAC
1104532 TT
1 TT
1104534 AAATATAAAT
Statistics
Matches: 184, Mismatches: 21, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
20 9 0.05
21 167 0.91
22 8 0.04
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (21 bp):
TTTCGCGAATAAACGCGAAAC
Found at i:1105412 original size:21 final size:21
Alignment explanation
Indices: 1105383--1105572 Score: 235
Period size: 21 Copynumber: 9.0 Consensus size: 21
1105373 TTTATATAAT
1105383 AGTTTCGCG-TTATATCGCGAA
1 AGTTTCGCGTTTAT-TCGCGAA
*
1105404 AGTTACGCGTTTATTCGCGAA
1 AGTTTCGCGTTTATTCGCGAA
1105425 AGTTTCGCGTTTATTCGCGAA
1 AGTTTCGCGTTTATTCGCGAA
1105446 AGTTTCGCG-TTATATCGCGAA
1 AGTTTCGCGTTTAT-TCGCGAA
**
1105467 AGTAACGCG-TTATATCGCGAA
1 AGTTTCGCGTTTAT-TCGCGAA
1105488 AGTTTCGCGTTTATTCGCGAA
1 AGTTTCGCGTTTATTCGCGAA
*
1105509 AGTTTCGCGTTTATTTGCGAA
1 AGTTTCGCGTTTATTCGCGAA
* ** * *
1105530 ACTAACGC-ATTATATCACGAA
1 AGTTTCGCGTTTAT-TCGCGAA
1105551 AGTTTCGCGTTTATTCGCGAA
1 AGTTTCGCGTTTATTCGCGAA
1105572 A
1 A
1105573 TTTTTTTTTT
Statistics
Matches: 146, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
20 8 0.05
21 126 0.86
22 12 0.08
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (21 bp):
AGTTTCGCGTTTATTCGCGAA
Found at i:1105485 original size:63 final size:63
Alignment explanation
Indices: 1105383--1105572 Score: 303
Period size: 63 Copynumber: 3.0 Consensus size: 63
1105373 TTTATATAAT
*
1105383 AGTTTCGCGTTATATCGCGAAAGTTACGCGTT-TATTCGCGAAAGTTTCGCGTTTATTCGCGAA
1 AGTTTCGCGTTATATCGCGAAAGTAACGCGTTATA-TCGCGAAAGTTTCGCGTTTATTCGCGAA
1105446 AGTTTCGCGTTATATCGCGAAAGTAACGCGTTATATCGCGAAAGTTTCGCGTTTATTCGCGAA
1 AGTTTCGCGTTATATCGCGAAAGTAACGCGTTATATCGCGAAAGTTTCGCGTTTATTCGCGAA
* * * *
1105509 AGTTTCGCGTT-TATTTGCGAAACTAACGCATTATATCACGAAAGTTTCGCGTTTATTCGCGAA
1 AGTTTCGCGTTATA-TCGCGAAAGTAACGCGTTATATCGCGAAAGTTTCGCGTTTATTCGCGAA
1105572 A
1 A
1105573 TTTTTTTTTT
Statistics
Matches: 120, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
62 2 0.02
63 116 0.97
64 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (63 bp):
AGTTTCGCGTTATATCGCGAAAGTAACGCGTTATATCGCGAAAGTTTCGCGTTTATTCGCGAA
Found at i:1110401 original size:24 final size:23
Alignment explanation
Indices: 1110374--1110425 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 23
1110364 AATAAGTCAA
*
1110374 ATATCGAAAAATTCTACCCCTACT
1 ATATAGAAAAATTCTA-CCCTACT
*
1110398 ATATATAAAAATTCTACCCTACT
1 ATATAGAAAAATTCTACCCTACT
1110421 ATATA
1 ATATA
1110426 TAAATATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 12 0.46
24 14 0.54
ACGTcount: A:0.42, C:0.23, G:0.02, T:0.33
Consensus pattern (23 bp):
ATATAGAAAAATTCTACCCTACT
Found at i:1110407 original size:23 final size:23
Alignment explanation
Indices: 1110380--1110429 Score: 91
Period size: 23 Copynumber: 2.1 Consensus size: 23
1110370 TCAAATATCG
1110380 AAAAATTCTACCCCTACTATATAT
1 AAAAATTCTA-CCCTACTATATAT
1110404 AAAAATTCTACCCTACTATATAT
1 AAAAATTCTACCCTACTATATAT
1110427 AAA
1 AAA
1110430 TATAAAGTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 16 0.62
24 10 0.38
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (23 bp):
AAAAATTCTACCCTACTATATAT
Done.