Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010901.1 Corchorus capsularis cultivar CVL-1 contig10922, whole genome shotgun sequence
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: 157504
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--33 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1 TA TA 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 TA TA T
34 CAAAATTGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5949 original size:28 final size:28
Alignment explanation
Indices: 5914--5970 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
5904 TCTCGTTTTT
5914 AAAAGTTAA-GCGCCAATTTGTCCCCAAA
1 AAAAGTTAAGGCGCCAATTTGT-CCCAAA
*
5942 AAAAGTTAAGGGGCCAATTTGTCCCAAA
1 AAAAGTTAAGGCGCCAATTTGTCCCAAA
5970 A
1 A
5971 TGGATAGTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 16 0.59
29 11 0.41
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (28 bp):
AAAAGTTAAGGCGCCAATTTGTCCCAAA
Found at i:11290 original size:31 final size:31
Alignment explanation
Indices: 11227--11387 Score: 142
Period size: 31 Copynumber: 5.5 Consensus size: 31
11217 TTTTGTGCAC
* * * **
11227 GTGGCATGCCACGTGCCATTTTTTTGAAACAT
1 GTGGCGTGCCACGTGTCA-CTTTTTGGTACAT
*
11259 GTGGCATGCCACGTGTCACTTTTTGGTACAT
1 GTGGCGTGCCACGTGTCACTTTTTGGTACAT
* *
11290 GTGGCGTGACATGTGTCACTTTTTGGTACAT
1 GTGGCGTGCCACGTGTCACTTTTTGGTACAT
*
11321 GT---G-G-CAC--G--ACTTTTTGATACAT
1 GTGGCGTGCCACGTGTCACTTTTTGGTACAT
* * *
11343 GTGGCGTGCCACATATCACTTTTTGGTACAC
1 GTGGCGTGCCACGTGTCACTTTTTGGTACAT
11374 GTGGCGTGCCACGT
1 GTGGCGTGCCACGT
11388 CGGACACCGT
Statistics
Matches: 107, Mismatches: 13, Indels: 19
0.77 0.09 0.14
Matches are distributed among these distances:
22 15 0.14
24 1 0.01
25 1 0.01
26 3 0.03
27 4 0.04
28 1 0.01
31 65 0.61
32 17 0.16
ACGTcount: A:0.18, C:0.22, G:0.26, T:0.34
Consensus pattern (31 bp):
GTGGCGTGCCACGTGTCACTTTTTGGTACAT
Found at i:11362 original size:53 final size:53
Alignment explanation
Indices: 11276--11378 Score: 152
Period size: 53 Copynumber: 1.9 Consensus size: 53
11266 GCCACGTGTC
* ** * *
11276 ACTTTTTGGTACATGTGGCGTGACATGTGTCACTTTTTGGTACATGTGGCACG
1 ACTTTTTGATACATGTGGCGTGACACATATCACTTTTTGGTACACGTGGCACG
*
11329 ACTTTTTGATACATGTGGCGTGCCACATATCACTTTTTGGTACACGTGGC
1 ACTTTTTGATACATGTGGCGTGACACATATCACTTTTTGGTACACGTGGC
11379 GTGCCACGTC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.37
Consensus pattern (53 bp):
ACTTTTTGATACATGTGGCGTGACACATATCACTTTTTGGTACACGTGGCACG
Found at i:12224 original size:32 final size:32
Alignment explanation
Indices: 12147--12230 Score: 132
Period size: 32 Copynumber: 2.6 Consensus size: 32
12137 TAGTCACGGG
* * *
12147 AGCCTCCCCACTAAGACGGTTCTGCCACGGCT
1 AGCCGCCCCACTAGGACGGCTCTGCCACGGCT
12179 AGCCGCCCCACTAGGACGGCTCTGCCACGGCT
1 AGCCGCCCCACTAGGACGGCTCTGCCACGGCT
*
12211 AGCCGCCCCACTAGGGCGGC
1 AGCCGCCCCACTAGGACGGC
12231 AAGGCTTTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.17, C:0.43, G:0.27, T:0.13
Consensus pattern (32 bp):
AGCCGCCCCACTAGGACGGCTCTGCCACGGCT
Found at i:12338 original size:33 final size:33
Alignment explanation
Indices: 12296--12390 Score: 109
Period size: 33 Copynumber: 2.9 Consensus size: 33
12286 TAGTACCGGT
* *
12296 GCCGCCCCAGGGGGGCGGTCTATCCATGGTAGG
1 GCCGCCCCAGGGGGGCGGCCTAGCCATGGTAGG
* * *
12329 GCCGCCCCAGGGAGGCGGCCTGGCCATGGTAGT
1 GCCGCCCCAGGGGGGCGGCCTAGCCATGGTAGG
* * * *
12362 GCCGCCCCAAGAGGGCGGCTTGGCCATGG
1 GCCGCCCCAGGGGGGCGGCCTAGCCATGG
12391 CTCAGTCGCC
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.13, C:0.33, G:0.42, T:0.13
Consensus pattern (33 bp):
GCCGCCCCAGGGGGGCGGCCTAGCCATGGTAGG
Found at i:12521 original size:32 final size:32
Alignment explanation
Indices: 12480--12551 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 32
12470 AAAATAGCCG
* *
12480 AGCCGCCCCACCGGGCCGGCCTGCCGTGGCGA
1 AGCCGCCCCACCGGGACGGCCTGCCCTGGCGA
*
12512 AGCCGCCCCACCGGGACGGCCTGCCCTGGCTA
1 AGCCGCCCCACCGGGACGGCCTGCCCTGGCGA
12544 AGCCGCCC
1 AGCCGCCC
12552 TAGTGGGGCG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.11, C:0.49, G:0.33, T:0.07
Consensus pattern (32 bp):
AGCCGCCCCACCGGGACGGCCTGCCCTGGCGA
Found at i:12628 original size:32 final size:32
Alignment explanation
Indices: 12496--12629 Score: 117
Period size: 32 Copynumber: 4.2 Consensus size: 32
12486 CCCACCGGGC
* * ** *
12496 CGGCCTGCCGTGGCGAAGCCGCCCCACCGGGA
1 CGGCTTGCCGTGGCGAAGCCGCCCTAGTGGGG
* * *
12528 CGGCCTGCCCTGGCTAAGCCGCCCTAGTGGGG
1 CGGCTTGCCGTGGCGAAGCCGCCCTAGTGGGG
** * **
12560 CGGCCTTTTCATGG-GAAGCCGCCCTCTTGGGG
1 CGG-CTTGCCGTGGCGAAGCCGCCCTAGTGGGG
* *
12592 CGGCTTGCCGTGGCGAAGCCTCCCAAGTGGGG
1 CGGCTTGCCGTGGCGAAGCCGCCCTAGTGGGG
12624 CGGCTT
1 CGGCTT
12630 CGCCACGGTA
Statistics
Matches: 80, Mismatches: 20, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
31 7 0.09
32 67 0.84
33 6 0.08
ACGTcount: A:0.10, C:0.36, G:0.37, T:0.16
Consensus pattern (32 bp):
CGGCTTGCCGTGGCGAAGCCGCCCTAGTGGGG
Found at i:14856 original size:64 final size:64
Alignment explanation
Indices: 14775--14894 Score: 163
Period size: 64 Copynumber: 1.9 Consensus size: 64
14765 TCAAATAGGT
* * * *
14775 TCCTAATGTATGTGAAAATGCTCAAT-T-TAGGACCCATGCTTTTAATTTGGTTAAATTAAATGG
1 TCCTAACGTATGCGAAAATACTCAATATATA-G-CCCATGCTTTGAATTTGGTTAAATTAAATGG
14838 G
64 G
*
14839 TCCTAACGTATGCGAAAATACTCAATATATAGCTCATGCTTTGAATTTGGTTAAAT
1 TCCTAACGTATGCGAAAATACTCAATATATAGCCCATGCTTTGAATTTGGTTAAAT
14895 AGGGCCTAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
64 45 0.92
65 2 0.04
66 2 0.04
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.37
Consensus pattern (64 bp):
TCCTAACGTATGCGAAAATACTCAATATATAGCCCATGCTTTGAATTTGGTTAAATTAAATGGG
Found at i:15073 original size:60 final size:60
Alignment explanation
Indices: 15008--15124 Score: 171
Period size: 60 Copynumber: 1.9 Consensus size: 60
14998 GTTAGGGTCA
* * * * *
15008 TATTTAACCAAATTAAAAGTATGGGTCTTAAATTGAGCATTTTCACATATATTAGGGCTT
1 TATTTAACCAAATGAAAAGCATGAGCCCTAAATTGAGCATTTTCACATATATTAGGGCTT
* *
15068 TATTTAACTAAATGAAAAGCATGAGCCCTAAATTGAGCATTTTCATATATATTAGGG
1 TATTTAACCAAATGAAAAGCATGAGCCCTAAATTGAGCATTTTCACATATATTAGGG
15125 ACCTATTTGA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (60 bp):
TATTTAACCAAATGAAAAGCATGAGCCCTAAATTGAGCATTTTCACATATATTAGGGCTT
Found at i:18545 original size:266 final size:266
Alignment explanation
Indices: 18063--18602 Score: 1028
Period size: 266 Copynumber: 2.0 Consensus size: 266
18053 ACCATCTTTC
* * *
18063 AAACATT-GCAATTCTCTCCTTCGGACATAGCAAATGTTTCGCTTGTTGTATAACAATTCCGTAT
1 AAACATTATCAATTCTCTCCTTCGGACATAGCAAATGTTTCACTTGTTGCATAACAATTCCGTAT
18127 ATTTTTGTAATTTGCTATTAGTTTCACAGTATAAAAGCAAAACAAATACATTTAACAACACACAT
66 ATTTTTGTAATTTGCTATTAGTTTCACAGTATAAAAGCAAAACAAATACATTTAACAACACACAT
18192 CAGTCATAGTAAGACACAGTAAATTTACTTACTTTTCATCAATTTTCTTTAATAGGACATAATAG
131 CAGTCATAGTAAGACACAGTAAATTTACTTACTTTTCATCAATTTTCTTTAATAGGACATAATAG
*
18257 CACAAGGCTCTATCAATTTCACCCTCAAAGTTGTCTTCAATTTTCCTCCGGATAGCCTCAGACTT
196 CACAAGGCTCTATCAATTTCACCCTCAAAGTAGTCTTCAATTTTCCTCCGGATAGCCTCAGACTT
18322 GAACTT
261 GAACTT
18328 AAACATTATCAATTCTCTCCTTCGGACATAGCAAATGTTTCACTTGTTGCATAACAATTCCGTAT
1 AAACATTATCAATTCTCTCCTTCGGACATAGCAAATGTTTCACTTGTTGCATAACAATTCCGTAT
18393 ATTTTTGTAATTTGCTATTAGTTTCACAGTATAAAAGCAAAACAAATACATTTAACAACACACAT
66 ATTTTTGTAATTTGCTATTAGTTTCACAGTATAAAAGCAAAACAAATACATTTAACAACACACAT
*
18458 CAGTCATAGTAAGACACAGTAAATTTATTTACTTTTCATCAATTTTCTTTAATAGGACATAATAG
131 CAGTCATAGTAAGACACAGTAAATTTACTTACTTTTCATCAATTTTCTTTAATAGGACATAATAG
18523 CACAAGGCTCTATCAATTTCACCCTCAAAGTAGTCTTCAATTTTCCTCCGGATAGCCTCAGACTT
196 CACAAGGCTCTATCAATTTCACCCTCAAAGTAGTCTTCAATTTTCCTCCGGATAGCCTCAGACTT
18588 GAACTT
261 GAACTT
18594 AAACATTAT
1 AAACATTAT
18603 TATTTTGCAA
Statistics
Matches: 269, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
265 7 0.03
266 262 0.97
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.35
Consensus pattern (266 bp):
AAACATTATCAATTCTCTCCTTCGGACATAGCAAATGTTTCACTTGTTGCATAACAATTCCGTAT
ATTTTTGTAATTTGCTATTAGTTTCACAGTATAAAAGCAAAACAAATACATTTAACAACACACAT
CAGTCATAGTAAGACACAGTAAATTTACTTACTTTTCATCAATTTTCTTTAATAGGACATAATAG
CACAAGGCTCTATCAATTTCACCCTCAAAGTAGTCTTCAATTTTCCTCCGGATAGCCTCAGACTT
GAACTT
Found at i:19229 original size:22 final size:22
Alignment explanation
Indices: 19204--19251 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
19194 TGATCTCATT
19204 GCGACCAGGCCATGGCCCAGTC
1 GCGACCAGGCCATGGCCCAGTC
* *
19226 GCGACCAGTCCATGGCCCATTC
1 GCGACCAGGCCATGGCCCAGTC
19248 GCGA
1 GCGA
19252 TAAGGTCGCG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.19, C:0.40, G:0.29, T:0.12
Consensus pattern (22 bp):
GCGACCAGGCCATGGCCCAGTC
Found at i:39958 original size:17 final size:17
Alignment explanation
Indices: 39936--39972 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
39926 ATGGTGAGTA
*
39936 TAAAATTTCATCTATAT
1 TAAAATTTCATCCATAT
39953 TAAAATTTCATCCATAT
1 TAAAATTTCATCCATAT
39970 TAA
1 TAA
39973 TGTATAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAAATTTCATCCATAT
Found at i:40211 original size:109 final size:106
Alignment explanation
Indices: 40029--40242 Score: 324
Period size: 109 Copynumber: 2.0 Consensus size: 106
40019 ATTAATCGGA
* * *
40029 TATATTAATTTTTCAACAAAATAATCCGACTTTACATTATAAATTTTAAGGCTGGGATATTCGGA
1 TATATTAATTCTTCAACAAAATAATCCGACTTTACATTATAAATTATAAGGCTGAGATATTCGG-
40094 AAAAAAAAAACAAAAAAATTGATTTAAGGATATTGTTAATTAAG
65 AAAAAAAAAACAAAAAAATTGA--TAAGGATATTGTTAATTAAG
* *
40138 TATATTAATTCTTGAACAAAATAAT-CGTACTTTATATTATAAATTAT-AGGTCTGAGATATTCG
1 TATATTAATTCTTCAACAAAATAATCCG-ACTTTACATTATAAATTATAAGG-CTGAGATATTCG
40201 GAAAAAAAAAACAAAAAAATTGATAAGGATATTGTTAATTAA
64 GAAAAAAAAAACAAAAAAATTGATAAGGATATTGTTAATTAA
40243 TTTTTACATT
Statistics
Matches: 98, Mismatches: 5, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
106 19 0.19
108 27 0.28
109 52 0.53
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.34
Consensus pattern (106 bp):
TATATTAATTCTTCAACAAAATAATCCGACTTTACATTATAAATTATAAGGCTGAGATATTCGGA
AAAAAAAAACAAAAAAATTGATAAGGATATTGTTAATTAAG
Found at i:40696 original size:31 final size:31
Alignment explanation
Indices: 40659--40717 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
40649 GTTAGATAAG
*
40659 TAAGGATATAATAGGTATTTTAAAAGTTAAA
1 TAAGGATATAATAGGTATTTCAAAAGTTAAA
40690 TAAGGATATAATAGGTATTTCAAAAGTT
1 TAAGGATATAATAGGTATTTCAAAAGTT
40718 TCTCAAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.46, C:0.02, G:0.17, T:0.36
Consensus pattern (31 bp):
TAAGGATATAATAGGTATTTCAAAAGTTAAA
Found at i:40852 original size:16 final size:16
Alignment explanation
Indices: 40815--40852 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
40805 ATCCCATGAC
*
40815 TCAGAATAAATAAATA
1 TCAGAATAAATAAAAA
*
40831 TAAGAATAAATAAAAA
1 TCAGAATAAATAAAAA
40847 TCAGAA
1 TCAGAA
40853 GGGAACAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.66, C:0.05, G:0.08, T:0.21
Consensus pattern (16 bp):
TCAGAATAAATAAAAA
Found at i:46844 original size:20 final size:20
Alignment explanation
Indices: 46816--46853 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
46806 GTGCTTGTAT
*
46816 TATTATTATTATTATTATAC
1 TATTATTATCATTATTATAC
*
46836 TATTCTTATCATTATTAT
1 TATTATTATCATTATTAT
46854 GGTGTACATT
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:0.32, C:0.08, G:0.00, T:0.61
Consensus pattern (20 bp):
TATTATTATCATTATTATAC
Found at i:47419 original size:19 final size:18
Alignment explanation
Indices: 47394--47441 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
47384 GCTATAAGTT
*
47394 CAGAGTTGAAGCTATTTTGA
1 CAGAGTTGAAG-TATATT-A
47414 -AGAGTTGCAAGTATATTA
1 CAGAGTTG-AAGTATATTA
47432 CAGAGTTGAA
1 CAGAGTTGAA
47442 TTTACGGGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 3 0.12
19 19 0.76
20 3 0.12
ACGTcount: A:0.35, C:0.08, G:0.25, T:0.31
Consensus pattern (18 bp):
CAGAGTTGAAGTATATTA
Found at i:77705 original size:14 final size:14
Alignment explanation
Indices: 77686--77716 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
77676 ATGTTAATTT
77686 TTTTTCTTTGTTTA
1 TTTTTCTTTGTTTA
77700 TTTTTCTTTGTTTA
1 TTTTTCTTTGTTTA
77714 TTT
1 TTT
77717 CTCTGAGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.06, C:0.06, G:0.06, T:0.81
Consensus pattern (14 bp):
TTTTTCTTTGTTTA
Found at i:79179 original size:117 final size:117
Alignment explanation
Indices: 79005--79707 Score: 818
Period size: 117 Copynumber: 6.0 Consensus size: 117
78995 CGTGATGATG
* * * * *
79005 ATGATGATGATAGGAGGA-G-G-AGAGATAAA--GCAGCA-AATTCTGGATCCTCTGACGAGGAC
1 ATGATGATGATAGGAGCAGGCGTAGAGATAAAGTGGAGGAGAATTCTGAATCCTCTGATGAGGA-
* * * *
79064 A-AGAAACGAGACC-AGAGAGATGGGAGGGGAGAAAGGGATCGAAGTACTAGGC
65 AGAGAAGCGAG-CCAAGAGAGATAGGAGGGGAGAAAGGGATAGAAGTACAAGGC
* * * * * * *
79116 ATGATAATGCTAAGAGTACAAG-G-AGAGATATAGTGGAGAAGAATTCTGAATCCTCTAATGAGG
1 ATGATGATGATAGGAG--CAGGCGTAGAGATAAAGTGGAGGAGAATTCTGAATCCTC---TGATG
* *
79179 AGGAAGAGAA-CGGAGCCAAGGGAGATAGGATGGGAGAAAGGGATAGAAGTACAAGGC
61 AGGAAGAGAAGC-GAGCCAAGAGAGATAGGAGGGGAGAAAGGGATAGAAGTACAAGGC
** * * * * * *
79236 ATGGCGGTGATAAGAGCAGGCGAAGAGACAAAGTGGAGGAGAAGTCTGAATCTTCTGATGAGGAA
1 ATGATGATGATAGGAGCAGGCGTAGAGATAAAGTGGAGGAGAATTCTGAATCCTCTGATGAGGAA
* * * * * *
79301 AAGAAGCGAGCCCAGGGAGATAGCATGGGAGAAAGGGATGGAAGTACAAGGC
66 GAGAAGCGAGCCAAGAGAGATAGGAGGGGAGAAAGGGATAGAAGTACAAGGC
* * * **
79353 ATGACGATGATAGGAGCTGGCGGAGAGATAAAGTGGAGGAGAATTCTGAATCCTCCCATGAGGAA
1 ATGATGATGATAGGAGCAGGCGTAGAGATAAAGTGGAGGAGAATTCTGAATCCTCTGATGAGGAA
*
79418 GAGAAGCGAGCCAAGAGAGATAGGAGGGGAGAAAGGGATAGAAGTTCAAGGC
66 GAGAAGCGAGCCAAGAGAGATAGGAGGGGAGAAAGGGATAGAAGTACAAGGC
* *
79470 ATGATGATGATAGGAGCAGGCGTAGAGATAAAGTGGAGGAGAAATCTGAATCCTCGGATGAGGAA
1 ATGATGATGATAGGAGCAGGCGTAGAGATAAAGTGGAGGAGAATTCTGAATCCTCTGATGAGGAA
* * *
79535 GAGAAGCGAGCCGAGAGAGATAGGAGGAGAGAAAGGGATAGAAGTTCAAGGC
66 GAGAAGCGAGCCAAGAGAGATAGGAGGGGAGAAAGGGATAGAAGTACAAGGC
* *
79587 ATGATGATGATAGGAGCAGGCGTAGAGATAAAGCGGAGGAGAATTCTGAATCCTCCGATGAGGAA
1 ATGATGATGATAGGAGCAGGCGTAGAGATAAAGTGGAGGAGAATTCTGAATCCTCTGATGAGGAA
* *
79652 GAGAAGCAAGCCAAGAGAGATAGGAGGGAAGAAAGGGATAGAAGTACTAA-GC
66 GAGAAGCGAGCCAAGAGAGATAGGAGGGGAGAAAGGGATAGAAGTAC-AAGGC
79704 ATGA
1 ATGA
79708 CCATGGACAT
Statistics
Matches: 513, Mismatches: 63, Indels: 26
0.85 0.10 0.04
Matches are distributed among these distances:
111 13 0.03
113 1 0.00
114 10 0.02
116 4 0.01
117 387 0.75
118 6 0.01
119 5 0.01
120 87 0.17
ACGTcount: A:0.39, C:0.11, G:0.37, T:0.14
Consensus pattern (117 bp):
ATGATGATGATAGGAGCAGGCGTAGAGATAAAGTGGAGGAGAATTCTGAATCCTCTGATGAGGAA
GAGAAGCGAGCCAAGAGAGATAGGAGGGGAGAAAGGGATAGAAGTACAAGGC
Found at i:89973 original size:15 final size:16
Alignment explanation
Indices: 89953--89982 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
89943 ACAGTTTCAG
89953 TTTTTT-CCTTTTTTT
1 TTTTTTCCCTTTTTTT
89968 TTTTTTCCCTTTTTT
1 TTTTTTCCCTTTTTT
89983 CTTCCTTGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTTCCCTTTTTTT
Found at i:95361 original size:1 final size:1
Alignment explanation
Indices: 95355--95379 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
95345 TCCTCTAAAG
95355 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
95380 GTGAGGAAGA
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:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:103036 original size:18 final size:19
Alignment explanation
Indices: 103013--103048 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
103003 GAGGAAAGAC
103013 AAATGAATAGTAT-AATAT
1 AAATGAATAGTATGAATAT
103031 AAATGAATAGTATGAATA
1 AAATGAATAGTATGAATA
103049 GACATGAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.56, C:0.00, G:0.14, T:0.31
Consensus pattern (19 bp):
AAATGAATAGTATGAATAT
Found at i:106796 original size:1 final size:1
Alignment explanation
Indices: 106790--106816 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
106780 TCTTGGATAT
106790 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
106817 GCAATGACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:113570 original size:1 final size:1
Alignment explanation
Indices: 113564--113608 Score: 90
Period size: 1 Copynumber: 45.0 Consensus size: 1
113554 ACTTTGTGGG
113564 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
113609 GCTCCTCATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:114295 original size:19 final size:20
Alignment explanation
Indices: 114267--114305 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
114257 TAGCTTCCAG
114267 AAATTGA-TTTCTGGAAAAT
1 AAATTGATTTTCTGGAAAAT
*
114286 AAATTTATTTTCTGGAAAAT
1 AAATTGATTTTCTGGAAAAT
114306 CTTCTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.41, C:0.05, G:0.13, T:0.41
Consensus pattern (20 bp):
AAATTGATTTTCTGGAAAAT
Found at i:115633 original size:11 final size:11
Alignment explanation
Indices: 115617--115658 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
115607 ATTTATGCAT
115617 TATTAATTAAC
1 TATTAATTAAC
*
115628 TATTAATTAGC
1 TATTAATTAAC
*
115639 TATTAATTAAA
1 TATTAATTAAC
115650 TATTAATTA
1 TATTAATTA
115659 GATATAGTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (11 bp):
TATTAATTAAC
Found at i:115643 original size:22 final size:22
Alignment explanation
Indices: 115617--115659 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
115607 ATTTATGCAT
*
115617 TATTAATTAACTATTAATTAGC
1 TATTAATTAAATATTAATTAGC
115639 TATTAATTAAATATTAATTAG
1 TATTAATTAAATATTAATTAG
115660 ATATAGTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.47
Consensus pattern (22 bp):
TATTAATTAAATATTAATTAGC
Found at i:115663 original size:11 final size:11
Alignment explanation
Indices: 115617--115663 Score: 60
Period size: 11 Copynumber: 4.3 Consensus size: 11
115607 ATTTATGCAT
115617 TATTAATTA-A
1 TATTAATTAGA
*
115627 CTATTAATTAGC
1 -TATTAATTAGA
*
115639 TATTAATTAAA
1 TATTAATTAGA
115650 TATTAATTAGA
1 TATTAATTAGA
115661 TAT
1 TAT
115664 AGTATAATGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (11 bp):
TATTAATTAGA
Found at i:123327 original size:16 final size:16
Alignment explanation
Indices: 123308--123342 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
123298 TATTTTCCTT
123308 TCTCTCCCCAAATCTC
1 TCTCTCCCCAAATCTC
**
123324 TCTCTCCCTGAATCTC
1 TCTCTCCCCAAATCTC
123340 TCT
1 TCT
123343 TATCTCTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.14, C:0.46, G:0.03, T:0.37
Consensus pattern (16 bp):
TCTCTCCCCAAATCTC
Found at i:130362 original size:23 final size:23
Alignment explanation
Indices: 130336--130381 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
130326 TTTTACTTCA
130336 AGGTTTGAGATTGAAATCACTTT
1 AGGTTTGAGATTGAAATCACTTT
*
130359 AGGTTTGAGATTGGAATCACTTT
1 AGGTTTGAGATTGAAATCACTTT
130382 TCCTGTACAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.28, C:0.09, G:0.24, T:0.39
Consensus pattern (23 bp):
AGGTTTGAGATTGAAATCACTTT
Found at i:133462 original size:30 final size:30
Alignment explanation
Indices: 133420--133476 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
133410 CTTTTGGGTA
133420 AAAATACAAAATTGGTCCCTCAAGTGAGTG
1 AAAATACAAAATTGGTCCCTCAAGTGAGTG
*
133450 AAAATAGC-AAATTGGTCTCTCAAGTGA
1 AAAATA-CAAAATTGGTCCCTCAAGTGA
133477 AAAAATATGC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (30 bp):
AAAATACAAAATTGGTCCCTCAAGTGAGTG
Found at i:133490 original size:28 final size:29
Alignment explanation
Indices: 133419--133488 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
133409 ACTTTTGGGT
133419 AAAAATA-CAAAATTGGTCCCTCAAGTGAG
1 AAAAATAGC-AAATTGGTCCCTCAAGTGAG
* *
133448 TGAAAATAGCAAATTGGTCTCTCAAGTGA-
1 -AAAAATAGCAAATTGGTCCCTCAAGTGAG
133477 AAAAATATGCAA
1 AAAAATA-GCAA
133489 TTTAGCCCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 6 0.17
29 4 0.11
30 24 0.69
31 1 0.03
ACGTcount: A:0.46, C:0.14, G:0.17, T:0.23
Consensus pattern (29 bp):
AAAAATAGCAAATTGGTCCCTCAAGTGAG
Found at i:134579 original size:30 final size:31
Alignment explanation
Indices: 134543--134608 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
134533 GTGCAAATGG
134543 GTCCCTGAAG-TGAACTT-AGTGAGCAATTGA
1 GTCCCTGAAGTTG-ACTTAAGTGAGCAATTGA
* *
134573 GTCCCTGAAGTTGAGTTAATTGAGCAATTGA
1 GTCCCTGAAGTTGACTTAAGTGAGCAATTGA
134604 GTCCC
1 GTCCC
134609 CCACCAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
30 13 0.41
31 19 0.59
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (31 bp):
GTCCCTGAAGTTGACTTAAGTGAGCAATTGA
Found at i:135076 original size:36 final size:36
Alignment explanation
Indices: 135032--135100 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
135022 ACTTAATTTC
135032 AAATATTATTTTAATATTCATGTGATTTAAACATAA
1 AAATATTATTTTAATATTCATGTGATTTAAACATAA
* *
135068 AAATATTATTTTAATATTTATTTGATTTAAACA
1 AAATATTATTTTAATATTCATGTGATTTAAACA
135101 CAACGGATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.48
Consensus pattern (36 bp):
AAATATTATTTTAATATTCATGTGATTTAAACATAA
Found at i:139473 original size:90 final size:88
Alignment explanation
Indices: 139343--139521 Score: 236
Period size: 90 Copynumber: 2.0 Consensus size: 88
139333 TATGTAATTT
* * *
139343 TTCTTCGTTTTCTTTAGTTCTTGCGTGAGGACATCGCATAAAGATACATGAG-AATGACACATTA
1 TTCTTCGTTTTCGTTAGTTCTTGCGTGAAGACATCGCATAAAGATACATGAGAAAAG-CACATTA
*
139407 TCTTTTATGTAAAAATGAATTCCATA
65 TCTTTTATGT--AAATAAATTCCATA
* * * *
139433 TTCTTTGTTTTCGTTAGTTCTTGTGTGACAG-CATCTCATAAAGATACATGAGAAAAGCTCATTA
1 TTCTTCGTTTTCGTTAGTTCTTGCGTGA-AGACATCGCATAAAGATACATGAGAAAAGCACATTA
139497 TCTTTTATGTAAATAAATTCCATA
65 TCTTTTATGTAAATAAATTCCATA
139521 T
1 T
139522 GTAGGATGTT
Statistics
Matches: 79, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
88 14 0.18
90 61 0.77
91 4 0.05
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.40
Consensus pattern (88 bp):
TTCTTCGTTTTCGTTAGTTCTTGCGTGAAGACATCGCATAAAGATACATGAGAAAAGCACATTAT
CTTTTATGTAAATAAATTCCATA
Found at i:141279 original size:150 final size:150
Alignment explanation
Indices: 141084--141365 Score: 510
Period size: 150 Copynumber: 1.9 Consensus size: 150
141074 TTTTAGAGTG
* * *
141084 TCTCTATTTGTAGAACTTCCATTTTCTCACCATGTAAAGAATGCATGATATGGATGGATTTTTCA
1 TCTCTATTTGTAGAACTTCCATTTTCTCACCATGTAAAAAATGCATGATACGGATAGATTTTTCA
* *
141149 CTTCTTCAATTTCTTCTCTGTGATCATATGCTTGGGTTGTCCTCTATCTGTTGGATTCACTAAAT
66 CTTCTTCAATATCTTCTCTGAGATCATATGCTTGGGTTGTCCTCTATCTGTTGGATTCACTAAAT
141214 GTTATCAAATTTGTTTAGTA
131 GTTATCAAATTTGTTTAGTA
*
141234 TCTCTATTTGTAGAACTTCCGTTTTCTCACCATGTAAAAAATGCATGATACGGATAGATTTTTCA
1 TCTCTATTTGTAGAACTTCCATTTTCTCACCATGTAAAAAATGCATGATACGGATAGATTTTTCA
141299 CTTCTTCAATATCTTCTCTGAGATCATATGCTTGGGTTGTCCTCTATCTGTTGGATTCACTAAAT
66 CTTCTTCAATATCTTCTCTGAGATCATATGCTTGGGTTGTCCTCTATCTGTTGGATTCACTAAAT
141364 GT
131 GT
141366 ATATATATCA
Statistics
Matches: 126, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
150 126 1.00
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.43
Consensus pattern (150 bp):
TCTCTATTTGTAGAACTTCCATTTTCTCACCATGTAAAAAATGCATGATACGGATAGATTTTTCA
CTTCTTCAATATCTTCTCTGAGATCATATGCTTGGGTTGTCCTCTATCTGTTGGATTCACTAAAT
GTTATCAAATTTGTTTAGTA
Found at i:147129 original size:15 final size:15
Alignment explanation
Indices: 147109--147145 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
147099 AATTCTCCTA
147109 GGAGAGTGATTCTTG
1 GGAGAGTGATTCTTG
147124 GGAGAGTGATTCTTG
1 GGAGAGTGATTCTTG
147139 GGAGAGT
1 GGAGAGT
147146 AACTCTAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.22, C:0.05, G:0.43, T:0.30
Consensus pattern (15 bp):
GGAGAGTGATTCTTG
Found at i:151132 original size:44 final size:45
Alignment explanation
Indices: 151064--151159 Score: 131
Period size: 44 Copynumber: 2.1 Consensus size: 45
151054 TCCAAAAGTT
151064 ACAAATTCAAAGGGGAAAATGGTAG-TTTAGTCAAATTGAAATTG
1 ACAAATTCAAAGGGGAAAATGGTAGATTTAGTCAAATTGAAATTG
* * *
151108 ACAAGTTCAAGGGGGAAAATGGTAGTTAATTTAGTCAGATTGAAATTG
1 ACAAATTCAAAGGGGAAAATGGTAG---ATTTAGTCAAATTGAAATTG
151156 ACAA
1 ACAA
151160 TTAAGCAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
44 23 0.51
48 22 0.49
ACGTcount: A:0.42, C:0.07, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAAATTCAAAGGGGAAAATGGTAGATTTAGTCAAATTGAAATTG
Found at i:152294 original size:18 final size:18
Alignment explanation
Indices: 152271--152309 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
152261 TTCCTGTACA
152271 GATAATCATAGGCTACCT
1 GATAATCATAGGCTACCT
152289 GATAATCATAGGCTACCT
1 GATAATCATAGGCTACCT
152307 GAT
1 GAT
152310 CATGCCTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (18 bp):
GATAATCATAGGCTACCT
Found at i:152430 original size:54 final size:54
Alignment explanation
Indices: 152348--152459 Score: 190
Period size: 54 Copynumber: 2.1 Consensus size: 54
152338 TAGGTGGCCA
*
152348 TGGTGGAGGAGGTGCTCAGTCTAACTCTCCAAGGACAAGGGCATC-GACTAGTAG
1 TGGTGGAGGAGGTGCTCAATCTAACTCTCCAAGGACAAGGGCATCAG-CTAGTAG
*
152402 TGGTGGAGGAGGTGCTCAATCTAACTCTCCAGGGACAAGGGCATCAGCTAGTAG
1 TGGTGGAGGAGGTGCTCAATCTAACTCTCCAAGGACAAGGGCATCAGCTAGTAG
152456 TGGT
1 TGGT
152460 CTAGGTGACC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
54 54 0.98
55 1 0.02
ACGTcount: A:0.25, C:0.20, G:0.34, T:0.21
Consensus pattern (54 bp):
TGGTGGAGGAGGTGCTCAATCTAACTCTCCAAGGACAAGGGCATCAGCTAGTAG
Found at i:152483 original size:69 final size:69
Alignment explanation
Indices: 152402--152621 Score: 323
Period size: 69 Copynumber: 3.1 Consensus size: 69
152392 CGACTAGTAG
* *
152402 TGGTGGAGGAGGTGCTCAATCTAACTCTCCAGGGACAAGGGCATCAGCTAGTAGTGGTCTAGGTG
1 TGGTGGAGGAGGTGCTCAATCTAACTCTCCAGGGACAAGGCCATCAACTAGTAGTGGTCTAGGTG
152467 ACCA
66 ACCA
* * * *
152471 TGATGGAGGAGGTACTCAATCTAATTACTCTTCAAGGACAAGGCCATCAACTAGTAGTGGTCTAG
1 TGGTGGAGGAGGTGCTCAATCT-A--ACTCTCCAGGGACAAGGCCATCAACTAGTAGTGGTCTAG
152536 GTGACCA
63 GTGACCA
* * * *
152543 TGGTGGAGGAGGTGCTCAGTCTAACACTCCAGGGACAAGGCCATCAACTAGTAGTGGTCAAGCTG
1 TGGTGGAGGAGGTGCTCAATCTAACTCTCCAGGGACAAGGCCATCAACTAGTAGTGGTCTAGGTG
152608 ACCA
66 ACCA
152612 TGGTGGAGGA
1 TGGTGGAGGA
152622 TCCGGTGCTC
Statistics
Matches: 134, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
69 71 0.53
70 1 0.01
71 1 0.01
72 61 0.46
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.22
Consensus pattern (69 bp):
TGGTGGAGGAGGTGCTCAATCTAACTCTCCAGGGACAAGGCCATCAACTAGTAGTGGTCTAGGTG
ACCA
Found at i:152674 original size:75 final size:69
Alignment explanation
Indices: 152402--152637 Score: 274
Period size: 72 Copynumber: 3.3 Consensus size: 69
152392 CGACTAGTAG
* * * * * * *
152402 TGGTGGAGGAGGTGCTCAATCTAACTCTCCAGGGACAAGGGCATCAGCTAGTAGTGGTCTAGGTG
1 TGGTGGAGGAGGTGCTCAGTCGAACACTCCAGGGACAAGGCCATCAACTAGTAGTGGTCAAGCTG
152467 ACCA
66 ACCA
* * * * * * *
152471 TGATGGAGGAGGTACTCAATCTAATTACTCTTCAAGGACAAGGCCATCAACTAGTAGTGGTCTAG
1 TGGTGGAGGAGGTGCTCAGTCGAA-CACTC--CAGGGACAAGGCCATCAACTAGTAGTGGTCAAG
*
152536 GTGACCA
63 CTGACCA
*
152543 TGGTGGAGGAGGTGCTCAGTCTAACACTCCAGGGACAAGGCCATCAACTAGTAGTGGTCAAGCTG
1 TGGTGGAGGAGGTGCTCAGTCGAACACTCCAGGGACAAGGCCATCAACTAGTAGTGGTCAAGCTG
152608 ACCA
66 ACCA
152612 TGGTGGAGGATCCGGTGCTCAGTCGA
1 TGGTGGAGGA---GGTGCTCAGTCGA
152638 CCAATTCTCT
Statistics
Matches: 146, Mismatches: 15, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
69 69 0.47
70 3 0.02
71 4 0.03
72 70 0.48
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.22
Consensus pattern (69 bp):
TGGTGGAGGAGGTGCTCAGTCGAACACTCCAGGGACAAGGCCATCAACTAGTAGTGGTCAAGCTG
ACCA
Found at i:153366 original size:10 final size:10
Alignment explanation
Indices: 153347--153383 Score: 51
Period size: 9 Copynumber: 3.9 Consensus size: 10
153337 ATTTTGATGT
153347 AAAA-AAAAA
1 AAAACAAAAA
153356 AAAAC-AAAA
1 AAAACAAAAA
*
153365 AAAACAAAAC
1 AAAACAAAAA
153375 AAAACAAAA
1 AAAACAAAA
153384 CTATCTGTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
9 13 0.52
10 12 0.48
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAACAAAAA
Found at i:153366 original size:14 final size:14
Alignment explanation
Indices: 153347--153383 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
153337 ATTTTGATGT
153347 AAAAAAAAAAAAAC
1 AAAAAAAAAAAAAC
*
153361 AAAAAAAACAAAAC
1 AAAAAAAAAAAAAC
153375 AAAACAAAA
1 AAAA-AAAA
153384 CTATCTGTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAAC
Found at i:153384 original size:5 final size:5
Alignment explanation
Indices: 153347--153384 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
153337 ATTTTGATGT
*
153347 AAAA- AAAAA AAAAC AAAA- AAAAC AAAAC AAAAC AAAAC
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC
153385 TATCTGTAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
4 8 0.26
5 23 0.74
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Done.