Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012235.1 Corchorus capsularis cultivar CVL-1 contig12256, 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: 73490
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1262 original size:118 final size:118
Alignment explanation
Indices: 1072--1395 Score: 490
Period size: 118 Copynumber: 2.7 Consensus size: 118
1062 CCTGAACCTA
* *
1072 ATATAGATGTGTACGGGGGAAGGAATCCAAGCCGCATTAAGGCGATTTCACAGACCCAGTTGAAA
1 ATATAGATGTGTACAGGGGAAGGAATCCAGGCCGCATTAAGGCGATTTCACAGACCCAGTTGAAA
* * * *
1137 GAAAAAGGCGCTAAAAAAGAGAGTGCTGAAAAAATGGCTCTTGAACCTAATAT
66 GAAAAAGGCGCTAAAAAAGAGAGCGCTGAAAAAATGACTCCTAAACCTAATAT
* *
1190 ATATAGATGTGTACATGGGAAGGAATCCAGGCCGCATTATGGCGATTTCACAGACCCAGTTGAAA
1 ATATAGATGTGTACAGGGGAAGGAATCCAGGCCGCATTAAGGCGATTTCACAGACCCAGTTGAAA
1255 GAAAAAGGCGCTAAAAAAGAGAGCGCTGAAAAAATGACTCCTAAACCTAATAT
66 GAAAAAGGCGCTAAAAAAGAGAGCGCTGAAAAAATGACTCCTAAACCTAATAT
*
1308 AAAT-G-TGTGTACAGGGGAAGGAATCCAGGCCGCATTAAGGCGATTTCACACACAGACCCAGTT
1 ATATAGATGTGTACAGGGGAAGGAATCCAGGCCGCATTAAGGCGATTT----CACAGACCCAGTT
* * *
1371 GAAAGAAAAAGACACTCAAAAAGAG
62 GAAAGAAAAAGGCGCTAAAAAAGAG
1396 TGGACACCTA
Statistics
Matches: 188, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
116 39 0.21
117 1 0.01
118 113 0.60
120 35 0.19
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (118 bp):
ATATAGATGTGTACAGGGGAAGGAATCCAGGCCGCATTAAGGCGATTTCACAGACCCAGTTGAAA
GAAAAAGGCGCTAAAAAAGAGAGCGCTGAAAAAATGACTCCTAAACCTAATAT
Found at i:5163 original size:167 final size:167
Alignment explanation
Indices: 4969--5324 Score: 687
Period size: 167 Copynumber: 2.1 Consensus size: 167
4959 CTTTCAACCA
4969 ACACTTGAACAACCTCAATCGGACAAGTCGACCGAAAATTATACAATATTAGATAGACCGACAAT
1 ACACTTGAACAACCTCAATCGGACAAGTCGACCGAAAATTATACAATATTAGATAGACCGACAAT
5034 TGAGACCACAAAATTTTAGAAGCATTTTTTAGAATCAAAACATCAAAATTGGCTTTTGATTCCTT
66 TGAGACCACAAAATTTTAGAAGCATTTTTTAGAATCAAAACATCAAAATTGGCTTTTGATTCCTT
5099 CATGAAAGTTGTAGACCATGGAATTACCTTTAAATAG
131 CATGAAAGTTGTAGACCATGGAATTACCTTTAAATAG
5136 ACACTTGAACAACCTCAATCGGACAAGTCGACCGAAAATTATACAATATTAGATAGACCGACAAT
1 ACACTTGAACAACCTCAATCGGACAAGTCGACCGAAAATTATACAATATTAGATAGACCGACAAT
5201 TGAGACCACAAAATTTTAGAAGCATTTTTTAGAATCAAAACATCAAAATTGGCTTTTGATTCCTT
66 TGAGACCACAAAATTTTAGAAGCATTTTTTAGAATCAAAACATCAAAATTGGCTTTTGATTCCTT
5266 CATGAAAGTTGTAGACCATGGAATTACCTTTAAATAG
131 CATGAAAGTTGTAGACCATGGAATTACCTTTAAATAG
*
5303 ACACTTGAATC-ACCTTAATCGG
1 ACACTTGAA-CAACCTCAATCGG
5325 TCAAATAGAA
Statistics
Matches: 187, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
167 186 0.99
168 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (167 bp):
ACACTTGAACAACCTCAATCGGACAAGTCGACCGAAAATTATACAATATTAGATAGACCGACAAT
TGAGACCACAAAATTTTAGAAGCATTTTTTAGAATCAAAACATCAAAATTGGCTTTTGATTCCTT
CATGAAAGTTGTAGACCATGGAATTACCTTTAAATAG
Found at i:5609 original size:178 final size:181
Alignment explanation
Indices: 5274--5627 Score: 599
Period size: 178 Copynumber: 2.0 Consensus size: 181
5264 TTCATGAAAG
* *
5274 TTGTAGACCATGGAATTACCTTTAAATAGACACTTGAATCACCTTAATCGGTCAAATAGAAAAAA
1 TTGTAGACCATGAAATTACCTTTAAATAGACACCTGAATCACCTTAATCGGTCAAATAGAAAAAA
* * * *
5339 AATAAAAGAATTAAAGCCGAAACATTCAATCGTCCAACCCATAATTGTAAGTGATTAAATAGTAT
66 AATAAAACAATTAAAGCCGAAACATTCAATCATCCAACACATAATTGTAAGTGATTAAATAGCAT
5404 AAATTATAAAAGTATGAGGATCATTTAATAAATAATCCAACAAAAAAAATGA
131 AAATTATAAAAGTATGAGGATCATTTAATAAATAATCCAA-AAAAAAAATGA
*
5456 TTGTAGACCATGAAATTACCTTTAAATAGACACCT-AATCACCTTGATCGGTCAAATAG-AAAAA
1 TTGTAGACCATGAAATTACCTTTAAATAGACACCTGAATCACCTTAATCGGTCAAATAGAAAAAA
*
5519 AA-AAAACAATTAAAGCCGAAACATTCAATCATCCAACATATAATTGTAAG-GATTAAATAGCAT
66 AATAAAACAATTAAAGCCGAAACATTCAATCATCCAACACATAATTGTAAGTGATTAAATAGCAT
5582 AAATTATAAAAGTATGAGGATCATTTAATAAATAATCCAAAAAAAA
131 AAATTATAAAAGTATGAGGATCATTTAATAAATAATCCAAAAAAAA
5628 TGATTTGTTT
Statistics
Matches: 164, Mismatches: 8, Indels: 5
0.93 0.05 0.03
Matches are distributed among these distances:
177 6 0.04
178 52 0.32
179 44 0.27
180 7 0.04
181 22 0.13
182 33 0.20
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.26
Consensus pattern (181 bp):
TTGTAGACCATGAAATTACCTTTAAATAGACACCTGAATCACCTTAATCGGTCAAATAGAAAAAA
AATAAAACAATTAAAGCCGAAACATTCAATCATCCAACACATAATTGTAAGTGATTAAATAGCAT
AAATTATAAAAGTATGAGGATCATTTAATAAATAATCCAAAAAAAAAATGA
Found at i:9180 original size:14 final size:13
Alignment explanation
Indices: 9153--9192 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
9143 TAGAAAAGCA
*
9153 AAAAAAATAAAAT
1 AAAATAATAAAAT
9166 AAAATAATAATAAT
1 AAAATAATAA-AAT
*
9180 AAAATAAAAAAAT
1 AAAATAATAAAAT
9193 CAACAAAAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAATAATAAAAT
Found at i:10579 original size:60 final size:60
Alignment explanation
Indices: 10486--10669 Score: 233
Period size: 60 Copynumber: 3.1 Consensus size: 60
10476 TCAGAAACAG
* * *
10486 CAGGTGCTTCCTCTGCATCCTCAGAAGGAGCAAAGGAGATGACACCGGCTCCCGGTAGCT
1 CAGGTACTCCCTCTGCATCCTCAGAAGGAGCAAAGGAGATGACACCGGATCCCGGTAGCT
* * * **
10546 CAGGTACTCCTTCTGCATCCTCACAAGGAGCAAAGGAGGTGACACCGGATCTTGGTAGCT
1 CAGGTACTCCCTCTGCATCCTCAGAAGGAGCAAAGGAGATGACACCGGATCCCGGTAGCT
** ** * * *
10606 CAGGTACTCCCTCTGCATCCTCAGAAACAGCAAAGGATTTGACAACGGTTCCCGATAGCT
1 CAGGTACTCCCTCTGCATCCTCAGAAGGAGCAAAGGAGATGACACCGGATCCCGGTAGCT
10666 CAGG
1 CAGG
10670 CTCTCCAGTG
Statistics
Matches: 105, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 105 1.00
ACGTcount: A:0.26, C:0.29, G:0.26, T:0.20
Consensus pattern (60 bp):
CAGGTACTCCCTCTGCATCCTCAGAAGGAGCAAAGGAGATGACACCGGATCCCGGTAGCT
Found at i:10994 original size:12 final size:13
Alignment explanation
Indices: 10972--10997 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10962 GCTTCCATTC
10972 TTTGTTTTTTTTT
1 TTTGTTTTTTTTT
10985 TTTGTTTTTTTTT
1 TTTGTTTTTTTTT
10998 CCTCTTTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (13 bp):
TTTGTTTTTTTTT
Found at i:15058 original size:24 final size:24
Alignment explanation
Indices: 15026--15073 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
15016 ATGTAAACGA
15026 ATTGAACAATTATTATTCCTTGTC
1 ATTGAACAATTATTATTCCTTGTC
15050 ATTGAACAATTATTATTCCTTGTC
1 ATTGAACAATTATTATTCCTTGTC
15074 GAGCTCGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.17, G:0.08, T:0.46
Consensus pattern (24 bp):
ATTGAACAATTATTATTCCTTGTC
Found at i:15166 original size:23 final size:21
Alignment explanation
Indices: 15135--15178 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
15125 ATTTAGGGAT
*
15135 TGTTTCCAATTGTTTCTGTTTTC
1 TGTTGCCAATT-TTT-TGTTTTC
15158 TGTTGCCAATTTTTTGTTTTC
1 TGTTGCCAATTTTTTGTTTTC
15179 GGAAACAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 3 0.15
23 10 0.50
ACGTcount: A:0.09, C:0.16, G:0.14, T:0.61
Consensus pattern (21 bp):
TGTTGCCAATTTTTTGTTTTC
Found at i:16567 original size:18 final size:18
Alignment explanation
Indices: 16544--16580 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
16534 CAAACAAAGT
* *
16544 TGATGAATATGTTGTTGA
1 TGATGAAGATGATGTTGA
16562 TGATGAAGATGATGTTGA
1 TGATGAAGATGATGTTGA
16580 T
1 T
16581 CTGACACCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.30, T:0.41
Consensus pattern (18 bp):
TGATGAAGATGATGTTGA
Found at i:18954 original size:17 final size:16
Alignment explanation
Indices: 18914--18964 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
18904 CATTTAATCT
*
18914 TTGATCACCGGTGATC
1 TTGATCACTGGTGATC
18930 TTGCATCACTGGTGATC
1 TTG-ATCACTGGTGATC
*
18947 TTAGATCACTAGTGATC
1 TT-GATCACTGGTGATC
18964 T
1 T
18965 GGGGGTGATC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 3 0.10
17 27 0.87
18 1 0.03
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:19513 original size:64 final size:64
Alignment explanation
Indices: 19434--19563 Score: 260
Period size: 64 Copynumber: 2.0 Consensus size: 64
19424 ATTCATAGTA
19434 TGAATTTGATGTTTTGCATACATATATATATTGTGTAATGTTGTTTGTTGTATGAGGTAACAAT
1 TGAATTTGATGTTTTGCATACATATATATATTGTGTAATGTTGTTTGTTGTATGAGGTAACAAT
19498 TGAATTTGATGTTTTGCATACATATATATATTGTGTAATGTTGTTTGTTGTATGAGGTAACAAT
1 TGAATTTGATGTTTTGCATACATATATATATTGTGTAATGTTGTTTGTTGTATGAGGTAACAAT
19562 TG
1 TG
19564 CATCACTTTA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.28, C:0.05, G:0.21, T:0.47
Consensus pattern (64 bp):
TGAATTTGATGTTTTGCATACATATATATATTGTGTAATGTTGTTTGTTGTATGAGGTAACAAT
Found at i:20376 original size:1 final size:1
Alignment explanation
Indices: 20370--20398 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
20360 ATAAAGCTGG
20370 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
20399 ATCTTGGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:22755 original size:4 final size:4
Alignment explanation
Indices: 22746--22771 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
22736 TTTCTGGGTT
22746 TTTC TTTC TTTC TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TT
22772 CATCTTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:24187 original size:20 final size:20
Alignment explanation
Indices: 24164--24205 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
24154 AAATGTATGG
24164 TACACCCATAAAACTTGGTA
1 TACACCCATAAAACTTGGTA
*
24184 TACAGCCATAAAACTTGGTA
1 TACACCCATAAAACTTGGTA
24204 TA
1 TA
24206 GTTCGATGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.26
Consensus pattern (20 bp):
TACACCCATAAAACTTGGTA
Found at i:27581 original size:156 final size:154
Alignment explanation
Indices: 27350--27695 Score: 355
Period size: 156 Copynumber: 2.2 Consensus size: 154
27340 TCATACCTCA
* *
27350 AACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCTCCTCAAGTCTGAATGAGCTGAAACTTTT
1 AACTGTCCTTAAATGAAAAACTAGCATAAG-TTTTCTCCTCAAGTCTCAACGAGCTG-AACTTTT
* * *
27415 CCAAGGGACTTA-AGTTCTCTCCACAAAACTATCGAAAAAATTCTAAGTAAAACCGAGCTCCCCT
64 CCAAGAGACTTAGA-TTATCCCCACAAAACTATCGAAAAAATTCTAAGTAAAACCGAGCT-CCCT
* ** *
27479 TG-ATAGTGAACTAGGTTTCTCTCCCC-
127 AGCATAGTGAACTAGGTTTAACACCCCG
**
27505 AGGTTGTCCTTAAATGAAAAACTAGCATAAGTTTTC-CACTCTAAGTC-CAACGAAGCTG-A-TT
1 A-ACTGTCCTTAAATGAAAAACTAGCATAAGTTTTCTC-CTC-AAGTCTCAACG-AGCTGAACTT
** * * * *
27566 TTCCACCAGTAGACTTAGATTATCCCCATGAAGCTATGGGAAAAATTCTAAGTAAAACTGAGCTC
62 TTCCA--AG-AGACTTAGATTATCCCCACAAAACTATCGAAAAAATTCTAAGTAAAACCGAGCTC
* * *
27631 TCTAGCATAGTGAAGTGGGTTTAACACCCCG
124 CCTAGCATAGTGAACTAGGTTTAACACCCCG
*
27662 AACTGTCCTTAACTGAAAAACTAGCATAAGTTTT
1 AACTGTCCTTAAATGAAAAACTAGCATAAGTTTT
27696 TCATACGAAG
Statistics
Matches: 158, Mismatches: 23, Indels: 19
0.79 0.12 0.09
Matches are distributed among these distances:
153 7 0.04
154 2 0.01
155 18 0.11
156 129 0.82
157 2 0.01
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.29
Consensus pattern (154 bp):
AACTGTCCTTAAATGAAAAACTAGCATAAGTTTTCTCCTCAAGTCTCAACGAGCTGAACTTTTCC
AAGAGACTTAGATTATCCCCACAAAACTATCGAAAAAATTCTAAGTAAAACCGAGCTCCCTAGCA
TAGTGAACTAGGTTTAACACCCCG
Found at i:29162 original size:15 final size:15
Alignment explanation
Indices: 29124--29162 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
29114 GAATCACTCT
29124 TCTTCCCTTCCCTTC
1 TCTTCCCTTCCCTTC
* *
29139 CCTCCCCTTCCCTTC
1 TCTTCCCTTCCCTTC
*
29154 TCTTTCCTT
1 TCTTCCCTT
29163 TGTCTTCTCC
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (15 bp):
TCTTCCCTTCCCTTC
Found at i:32467 original size:2 final size:2
Alignment explanation
Indices: 32413--32458 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
32403 AAATATAGTG
* *
32413 TA TA TA TA TA T- TA TA CA TA TA TA TA TA TA TA TA TA TA TA TC
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
32454 TA TA T
1 TA TA T
32459 GGATATATAG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:33038 original size:16 final size:17
Alignment explanation
Indices: 33001--33038 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
32991 CAAAACAAAC
33001 TAAACAAACTGACATCT
1 TAAACAAACTGACATCT
*
33018 T-AACAAACTGAGA-CT
1 TAAACAAACTGACATCT
33033 TAAACA
1 TAAACA
33039 TCCAAAATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 3 0.16
16 15 0.79
17 1 0.05
ACGTcount: A:0.50, C:0.21, G:0.08, T:0.21
Consensus pattern (17 bp):
TAAACAAACTGACATCT
Found at i:34130 original size:424 final size:424
Alignment explanation
Indices: 33445--34261 Score: 1054
Period size: 422 Copynumber: 1.9 Consensus size: 424
33435 CCGATTAAGA
* *
33445 TGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAATTTTCATTAAGAACTCAAAAGTCA
1 TGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCATGAAGAACTCAAAAGTCA
** * * * * * *
33510 ATTTTAATGTTTTGATTCTAAAAAACGCTTCCGAAATTTTGTGGTTTTGATTGCCGGTTTATTAA
66 ATTTTAATGTTTCAATTCAAAAAAACGCTCCCGAAATTTGGTCGTTTCGATTGCCGGTCTATTAA
* * * * * * * * * *
33575 TATCGTATATTTTTTGTTCACATGTCCGATTGAAGTTATTGAGGTGTCGGTTAAAAGGTTATTGC
131 TACCATATATTTTTCGTCCACATGTCCAATTAAAGTTATTCAAGTGTCGGTTAAAAGGCTACTGC
* * * * *
33640 ATGATTTACGACTTCCATGAAGGACCCGAAAGCTAAATTTGATCTACGAGTTTCGTGAAGGGTTC
196 ATAATTTACGACTTCCATGAAGAAACCAAAAGCTAAATTTGATCTACGAGTTTCATGAAGGGTTC
* *
33705 AAAAGGGAATTTTCATGTTTCAAGATCTCTAT-TAACAAATATTTTCTTATTT-AGATTATTTAT
261 AAAAGGGAATTTTCATGTTTCAAGATCTCCATATAACAAATATTTTCTTATTTGA-ATTAGTTAT
* *
33768 CAAATGACCC-TCATACTTTTATACTTTATACTACTTAGTCCTTTACAAATTCTATCTTAATCGC
325 CAAATCACCCATCATACTTTTATACTTTATACTACTTAGTCCTTTACAAATTCTATCTTAATCGA
33832 TTTATTTTTTTATTCTTTGTTTTATTTGTCCGAGT
390 TTTATTTTTTTATTCTTTGTTTTATTTGTCCGAGT
* * * *
33867 TGATTCATA-TGTCTATTAAAAGGTGATTTCATGATCTACAACTTTCATGAAGGATTCGAAAG-C
1 TGATTCA-AGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCATGAAGAACTCAAAAGTC
* * * **
33930 AAATTTTTATGTTTCAATTCAAAAAAATGCTCCCTAAATTTGGTCGTTTCGATTGTTGGTCTATT
65 -AATTTTAATGTTTCAATTCAAAAAAACGCTCCCGAAATTTGGTCGTTTCGATTGCCGGTCTA-T
*
33995 TAATACCATATCA-TTTTCGATCCACATGTCCAATTAAAGTTATTCAAGTTTCGGTTAAAAAGGC
128 TAATACCATAT-ATTTTTCG-TCCACATGTCCAATTAAAGTTATTCAAGTGTCGGTT-AAAAGGC
* * *
34059 TACTGTATAATTTACGACTTTCATGAAGAAACCAAAAG-TTAATTTGATCTACGAGTTTCATGAA
190 TACTGCATAATTTACGACTTCCATGAAGAAACCAAAAGCTAAATTTGATCTACGAGTTTCATGAA
* * *
34123 TGGTTCAAAAGGGAATTTTTATGTTTCAAGATCTCCATATAACAACTATTTTCTTATTTGAATTA
255 GGGTTCAAAAGGGAATTTTCATGTTTCAAGATCTCCATATAACAAATATTTTCTTATTTGAATTA
* * * * * *
34188 GTTATCAAATCACCCATCATACTTTTCTATTTTATGCTACTTAGTTCTTTACAGATTTTATCTTA
320 GTTATCAAATCACCCATCATACTTTTATACTTTATACTACTTAGTCCTTTACAAATTCTATCTTA
*
34253 CTCGATTTA
385 ATCGATTTA
34262 ATACTTCATT
Statistics
Matches: 334, Mismatches: 52, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
421 1 0.00
422 103 0.31
423 16 0.05
424 90 0.27
425 73 0.22
426 51 0.15
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (424 bp):
TGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCATGAAGAACTCAAAAGTCA
ATTTTAATGTTTCAATTCAAAAAAACGCTCCCGAAATTTGGTCGTTTCGATTGCCGGTCTATTAA
TACCATATATTTTTCGTCCACATGTCCAATTAAAGTTATTCAAGTGTCGGTTAAAAGGCTACTGC
ATAATTTACGACTTCCATGAAGAAACCAAAAGCTAAATTTGATCTACGAGTTTCATGAAGGGTTC
AAAAGGGAATTTTCATGTTTCAAGATCTCCATATAACAAATATTTTCTTATTTGAATTAGTTATC
AAATCACCCATCATACTTTTATACTTTATACTACTTAGTCCTTTACAAATTCTATCTTAATCGAT
TTATTTTTTTATTCTTTGTTTTATTTGTCCGAGT
Found at i:34384 original size:16 final size:16
Alignment explanation
Indices: 34363--34440 Score: 106
Period size: 16 Copynumber: 4.9 Consensus size: 16
34353 GGCAGTTTTC
34363 TCGGGTCATTCGGGTT
1 TCGGGTCATTCGGGTT
*
34379 TCGGGTCA-TC-TGTGT
1 TCGGGTCATTCGGGT-T
*
34394 TCGGGTTATTCGGGTT
1 TCGGGTCATTCGGGTT
34410 TCGGGTCATTCGGGTT
1 TCGGGTCATTCGGGTT
*
34426 ACGGGTCATTCGGGT
1 TCGGGTCATTCGGGT
34441 CTCAGGTTGG
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
14 2 0.04
15 10 0.19
16 40 0.74
17 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.37, T:0.37
Consensus pattern (16 bp):
TCGGGTCATTCGGGTT
Found at i:34399 original size:31 final size:31
Alignment explanation
Indices: 34363--34440 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
34353 GGCAGTTTTC
*
34363 TCGGGTCATTCGGGTTTCGGGTCA-TCTGTGT
1 TCGGGTCATTCGGGTTTCGGGTCATTC-GGGT
*
34394 TCGGGTTATTCGGGTTTCGGGTCATTCGGGT
1 TCGGGTCATTCGGGTTTCGGGTCATTCGGGT
34425 TACGGGTCATTCGGGT
1 T-CGGGTCATTCGGGT
34441 CTCAGGTTGG
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
31 27 0.64
32 15 0.36
ACGTcount: A:0.08, C:0.18, G:0.37, T:0.37
Consensus pattern (31 bp):
TCGGGTCATTCGGGTTTCGGGTCATTCGGGT
Found at i:34460 original size:47 final size:47
Alignment explanation
Indices: 34363--34462 Score: 114
Period size: 47 Copynumber: 2.1 Consensus size: 47
34353 GGCAGTTTTC
* * * **
34363 TCGGGTCATTCGGGTTTCGGGTCATCTGTGTTCGGGTTATTCGGGTT
1 TCGGGTCATTCGGGTTACGGGTCATCTGGGTTCAGGTTAGGCGGGTT
*
34410 TCGGGTCATTCGGGTTACGGGTCAT-TCGGGTCTCAGGTTGGGCGGG-T
1 TCGGGTCATTCGGGTTACGGGTCATCT-GGGT-TCAGGTTAGGCGGGTT
34457 TCGGGT
1 TCGGGT
34463 TTTGGCATCG
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
46 1 0.02
47 34 0.76
48 10 0.22
ACGTcount: A:0.07, C:0.18, G:0.40, T:0.35
Consensus pattern (47 bp):
TCGGGTCATTCGGGTTACGGGTCATCTGGGTTCAGGTTAGGCGGGTT
Found at i:35319 original size:16 final size:15
Alignment explanation
Indices: 35300--35346 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
35290 CGGATCACTC
35300 GGGTTATGGGTCATT
1 GGGTTATGGGTCATT
35315 AGGGTT-TCGGGTCATCT
1 -GGGTTAT-GGGTCAT-T
*
35332 GGGTTACGGGTCATT
1 GGGTTATGGGTCATT
35347 CAGGTCTCGG
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
15 2 0.07
16 24 0.89
17 1 0.04
ACGTcount: A:0.13, C:0.13, G:0.38, T:0.36
Consensus pattern (15 bp):
GGGTTATGGGTCATT
Found at i:35320 original size:32 final size:32
Alignment explanation
Indices: 35274--35368 Score: 95
Period size: 32 Copynumber: 3.0 Consensus size: 32
35264 GTTAACTTCT
* *
35274 CGGGTTATTCGGGTTTCGGATCA-CTCGGGTTA
1 CGGGTCATTAGGGTTTCGGATCATCT-GGGTTA
* *
35306 TGGGTCATTAGGGTTTCGGGTCATCTGGGTTA
1 CGGGTCATTAGGGTTTCGGATCATCTGGGTTA
* * *
35338 CGGGTCATTCA-GGTCTCGGGTCATATGGGTT
1 CGGGTCATT-AGGGTTTCGGATCATCTGGGTT
35369 GCAGGTCACT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
32 51 0.94
33 3 0.06
ACGTcount: A:0.13, C:0.17, G:0.36, T:0.35
Consensus pattern (32 bp):
CGGGTCATTAGGGTTTCGGATCATCTGGGTTA
Found at i:35376 original size:32 final size:32
Alignment explanation
Indices: 35308--35388 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 32
35298 TCGGGTTATG
* * *
35308 GGTCATT-AGGGTTTCGGGTCATCTGGGTTACG
1 GGTCATTCA-GGTCTCGGGTCATATGGGTTACA
*
35340 GGTCATTCAGGTCTCGGGTCATATGGGTTGCA
1 GGTCATTCAGGTCTCGGGTCATATGGGTTACA
* *
35372 GGTCACTCGGGTCTCGG
1 GGTCATTCAGGTCTCGG
35389 TCGGACGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
32 41 0.98
33 1 0.02
ACGTcount: A:0.12, C:0.20, G:0.37, T:0.31
Consensus pattern (32 bp):
GGTCATTCAGGTCTCGGGTCATATGGGTTACA
Found at i:36466 original size:33 final size:33
Alignment explanation
Indices: 36429--36501 Score: 146
Period size: 33 Copynumber: 2.2 Consensus size: 33
36419 ATTACTCGAC
36429 AGTAAATGACTCTTTACTTATTTTTTTGGCGAA
1 AGTAAATGACTCTTTACTTATTTTTTTGGCGAA
36462 AGTAAATGACTCTTTACTTATTTTTTTGGCGAA
1 AGTAAATGACTCTTTACTTATTTTTTTGGCGAA
36495 AGTAAAT
1 AGTAAAT
36502 AGTAGTACCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.44
Consensus pattern (33 bp):
AGTAAATGACTCTTTACTTATTTTTTTGGCGAA
Found at i:36682 original size:27 final size:27
Alignment explanation
Indices: 36644--36709 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 27
36634 AGCACTCAAG
36644 AAAGGCCTAATTTT-TTACCTTT-AAAAA
1 AAAGGCCTAATTTTCTT--CTTTAAAAAA
*
36671 AAAGGCCTAATTTTCTTGTTTAAAAAA
1 AAAGGCCTAATTTTCTTCTTTAAAAAA
36698 AAACGGCCTAAT
1 AAA-GGCCTAAT
36710 AATAATTTGC
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
26 3 0.09
27 22 0.63
28 10 0.29
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (27 bp):
AAAGGCCTAATTTTCTTCTTTAAAAAA
Found at i:39116 original size:25 final size:24
Alignment explanation
Indices: 39068--39116 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
39058 TTAAATGATT
* *
39068 GAGATTTGAAAGTTTGAAGGTTGA
1 GAGAATTGAAAGTTTGAAAGTTGA
*
39092 GAGAATTGAAAAGTTTGAAATTTGA
1 GAGAATTG-AAAGTTTGAAAGTTGA
39117 TGGAAAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.33
Consensus pattern (24 bp):
GAGAATTGAAAGTTTGAAAGTTGA
Found at i:44687 original size:22 final size:22
Alignment explanation
Indices: 44645--44688 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
44635 TATTCATATG
*
44645 AAATTATGATAATCTCTCTATT
1 AAATTATGATAATCTCACTATT
44667 AAATTATGATAAT-TACACTATT
1 AAATTATGATAATCT-CACTATT
44689 TTTTATGATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (22 bp):
AAATTATGATAATCTCACTATT
Found at i:44964 original size:22 final size:22
Alignment explanation
Indices: 44939--44981 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
44929 TGTTAGTAAC
* *
44939 CACACTCTGAAATTTTGATAAT
1 CACACTATGAAATTATGATAAT
44961 CACACTATGAAATTATGATAA
1 CACACTATGAAATTATGATAA
44982 CCTTGCTATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (22 bp):
CACACTATGAAATTATGATAAT
Found at i:45003 original size:22 final size:23
Alignment explanation
Indices: 44965--45051 Score: 77
Period size: 23 Copynumber: 3.7 Consensus size: 23
44955 GATAATCACA
* * *
44965 CTATGAAATTATGAT-AACCTTG
1 CTATGAAATTTTAATAAACCTTC
*
44987 CTATGAAATTTTAATAAATCTTC
1 CTATGAAATTTTAATAAACCTTC
* *
45010 CTATAAAATTTTGATATAAACCTCC
1 CTATGAAATTTT-A-ATAAACCTTC
* *
45035 CTATAAAATTTTGATAA
1 CTATGAAATTTTAATAA
45052 CTTTTTTTAT
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
22 13 0.24
23 20 0.37
24 1 0.02
25 20 0.37
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.39
Consensus pattern (23 bp):
CTATGAAATTTTAATAAACCTTC
Found at i:45037 original size:25 final size:25
Alignment explanation
Indices: 44987--45050 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
44977 GATAACCTTG
* * *
44987 CTATGAAATTTT-A-ATAAATCTTC
1 CTATAAAATTTTGATATAAACCTCC
45010 CTATAAAATTTTGATATAAACCTCC
1 CTATAAAATTTTGATATAAACCTCC
45035 CTATAAAATTTTGATA
1 CTATAAAATTTTGATA
45051 ACTTTTTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 11 0.31
24 1 0.03
25 24 0.67
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.41
Consensus pattern (25 bp):
CTATAAAATTTTGATATAAACCTCC
Found at i:45166 original size:22 final size:22
Alignment explanation
Indices: 45107--45175 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
45097 TATGATTTTA
* *
45107 TGATAACCTCATTATGAAATTT
1 TGATAATCTCCTTATGAAATTT
* *
45129 TGTTAATCTCCCTATGAAATTT
1 TGATAATCTCCTTATGAAATTT
*
45151 TGATAATC-CTTTTATGAAATTT
1 TGATAATCTC-CTTATGAAATTT
45173 TGA
1 TGA
45176 AAACTAAACT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
21 1 0.03
22 38 0.97
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.45
Consensus pattern (22 bp):
TGATAATCTCCTTATGAAATTT
Found at i:45375 original size:22 final size:22
Alignment explanation
Indices: 45325--45376 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
45315 TCACATTTTG
45325 AAAA-TTTGATAACCTCTTTAT
1 AAAATTTTGATAACCTCTTTAT
*
45346 GAAATTTTGATAACCTCTTTAT
1 AAAATTTTGATAACCTCTTTAT
45368 AAAATTTTG
1 AAAATTTTG
45377 TACGTTGACC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 3 0.11
22 25 0.89
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.44
Consensus pattern (22 bp):
AAAATTTTGATAACCTCTTTAT
Found at i:45488 original size:21 final size:24
Alignment explanation
Indices: 45457--45539 Score: 88
Period size: 21 Copynumber: 3.7 Consensus size: 24
45447 ATAACAACAT
*
45457 TATGGAATTTTGATAATCT-TC-C
1 TATGAAATTTTGATAATCTATCTC
45479 TAT-AAATTTTGATAATCTGATCTC
1 TATGAAATTTTGATAATCT-ATCTC
*
45503 TATGAAATTTCGATAATC-A-CTC
1 TATGAAATTTTGATAATCTATCTC
*
45525 TATGAGA-TTTGATAA
1 TATGAAATTTTGATAA
45540 CCTTCTATTA
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
21 21 0.40
22 12 0.23
23 3 0.06
24 4 0.08
25 13 0.25
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (24 bp):
TATGAAATTTTGATAATCTATCTC
Found at i:45556 original size:21 final size:23
Alignment explanation
Indices: 45299--45556 Score: 79
Period size: 22 Copynumber: 11.5 Consensus size: 23
45289 GAAATACCAT
45299 TATGAAATTTTTG-TAATCACATT-
1 TATGAAA-TTTTGATAATCAC-TTC
* * *
45322 T-TGAAAATTTGATAACCTCTT-
1 TATGAAATTTTGATAATCACTTC
* *
45343 TATGAAATTTTGATAACCTCTT-
1 TATGAAATTTTGATAATCACTTC
* * * *
45365 TATAAAATTTTG-TACGTTGACCCCTC
1 TATGAAATTTTGATA--AT--CACTTC
* * *
45391 TATAAAATTCTGATAATCACAT-
1 TATGAAATTTTGATAATCACTTC
* * *
45413 TATGTAATTTTGATAACCTCGCGT-
1 TATGAAATTTTGATAA--TCACTTC
*
45437 TATG--ATTTTGATAA-CAACAT-
1 TATGAAATTTTGATAATC-ACTTC
*
45457 TATGGAATTTTGATAAT--CTTCC
1 TATGAAATTTTGATAATCACTT-C
45479 TAT-AAATTTTGATAATCTGA-TCTC
1 TATGAAATTTTGATAATC--ACT-TC
*
45503 TATGAAATTTCGATAATCAC-TC
1 TATGAAATTTTGATAATCACTTC
*
45525 TATGAGA-TTTGATAA-C-CTTC
1 TATGAAATTTTGATAATCACTTC
*
45545 TATTAAATTTTG
1 TATGAAATTTTG
45557 GTACTCCTTA
Statistics
Matches: 183, Mismatches: 27, Indels: 52
0.70 0.10 0.20
Matches are distributed among these distances:
19 2 0.01
20 16 0.09
21 32 0.17
22 84 0.46
23 5 0.03
24 13 0.07
25 18 0.10
26 11 0.06
27 2 0.01
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (23 bp):
TATGAAATTTTGATAATCACTTC
Found at i:45807 original size:31 final size:31
Alignment explanation
Indices: 45771--45836 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
45761 TGACAATTTA
* *
45771 GAAATATGTTTTGAAAAA-AAGAATACAATTG
1 GAAATATATTTT-AAAAATAAGAATACAATCG
**
45802 GAAATATATTTTAAAAATAAGGGTACAATCG
1 GAAATATATTTTAAAAATAAGAATACAATCG
45833 GAAA
1 GAAA
45837 ACATAAAGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 5 0.17
31 25 0.83
ACGTcount: A:0.52, C:0.05, G:0.17, T:0.27
Consensus pattern (31 bp):
GAAATATATTTTAAAAATAAGAATACAATCG
Found at i:47561 original size:23 final size:23
Alignment explanation
Indices: 47535--47590 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
47525 GGGTCGACCT
47535 CGAGCTCGAGTAGCTAACCGAGC
1 CGAGCTCGAGTAGCTAACCGAGC
47558 CGAGCTCGAGTAGCTAACCGAGC
1 CGAGCTCGAGTAGCTAACCGAGC
47581 CGAGCTCGAG
1 CGAGCTCGAG
47591 CTTGAGCTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.25, C:0.30, G:0.32, T:0.12
Consensus pattern (23 bp):
CGAGCTCGAGTAGCTAACCGAGC
Found at i:48135 original size:18 final size:19
Alignment explanation
Indices: 48104--48141 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
48094 TTCAACTTCA
48104 TCTTTTTCAATTTT-ATTT
1 TCTTTTTCAATTTTCATTT
**
48122 TCTTTTTCTTTTTTCATTT
1 TCTTTTTCAATTTTCATTT
48141 T
1 T
48142 TTCTGGTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (19 bp):
TCTTTTTCAATTTTCATTT
Found at i:53512 original size:38 final size:36
Alignment explanation
Indices: 53455--53562 Score: 184
Period size: 38 Copynumber: 3.0 Consensus size: 36
53445 GCACGAACTC
53455 AAAAATCTTAATTAG-TCAATTACTAAAATACCCTT
1 AAAAATCTTAATTAGTTCAATTACTAAAATACCCTT
53490 AAAAATCTTAATTAGTCATCAATTACTAAAATACCCTT
1 AAAAATCTTAATTAGT--TCAATTACTAAAATACCCTT
53528 AAAAATCTTAATTAGTT-AATTACTAAAATACCCTT
1 AAAAATCTTAATTAGTTCAATTACTAAAATACCCTT
53563 GATATTATAT
Statistics
Matches: 70, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
35 33 0.47
36 1 0.01
38 36 0.51
ACGTcount: A:0.45, C:0.17, G:0.03, T:0.35
Consensus pattern (36 bp):
AAAAATCTTAATTAGTTCAATTACTAAAATACCCTT
Found at i:53749 original size:30 final size:30
Alignment explanation
Indices: 53715--53776 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
53705 TATAATTTTT
*
53715 AATCATTAAATTTTTATCTATTAATTATAA
1 AATCATTAAACTTTTATCTATTAATTATAA
*
53745 AATCATTAAACTTTTATTTATTAATTATAA
1 AATCATTAAACTTTTATCTATTAATTATAA
53775 AA
1 AA
53777 AGATATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (30 bp):
AATCATTAAACTTTTATCTATTAATTATAA
Found at i:54473 original size:30 final size:30
Alignment explanation
Indices: 54437--54498 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
54427 TAAAAATTAT
54437 AATCATTAAACTTTTATCTATTAATTATAA
1 AATCATTAAACTTTTATCTATTAATTATAA
*
54467 AATCATTAAACTTTTATTTATTAATTATAA
1 AATCATTAAACTTTTATCTATTAATTATAA
54497 AA
1 AA
54499 AGATATTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (30 bp):
AATCATTAAACTTTTATCTATTAATTATAA
Found at i:58481 original size:19 final size:19
Alignment explanation
Indices: 58457--58501 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
58447 TTTCTTATTT
58457 AATTAT-GATTACTAAAAAC
1 AATTATAGATTA-TAAAAAC
* *
58476 AATTATAGGTTATCAAAAC
1 AATTATAGATTATAAAAAC
58495 AATTATA
1 AATTATA
58502 AGGTTATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.33
Consensus pattern (19 bp):
AATTATAGATTATAAAAAC
Found at i:58505 original size:20 final size:19
Alignment explanation
Indices: 58471--58508 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 19
58461 ATGATTACTA
58471 AAAACAATTATAGGTTATC
1 AAAACAATTATAGGTTATC
58490 AAAACAATTATAAGGTTAT
1 AAAACAATTAT-AGGTTAT
58509 TTATAAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.32
Consensus pattern (19 bp):
AAAACAATTATAGGTTATC
Found at i:71090 original size:15 final size:15
Alignment explanation
Indices: 71070--71105 Score: 63
Period size: 15 Copynumber: 2.3 Consensus size: 15
71060 TCAAATCTCT
71070 CAAAATTAAAACCGA
1 CAAAATTAAAACCGA
71085 CAAAATTAAAACCGA
1 CAAAATTAAAACCGA
71100 CTAAAA
1 C-AAAA
71106 ACCGACTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.61, C:0.19, G:0.06, T:0.14
Consensus pattern (15 bp):
CAAAATTAAAACCGA
Found at i:71108 original size:11 final size:12
Alignment explanation
Indices: 71092--71122 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
71082 CGACAAAATT
71092 AAAACCGACT-A
1 AAAACCGACTAA
71103 AAAACCGACTAA
1 AAAACCGACTAA
71115 AAAACCGA
1 AAAACCGA
71123 AAACCGACCG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.58, C:0.26, G:0.10, T:0.06
Consensus pattern (12 bp):
AAAACCGACTAA
Found at i:73145 original size:3 final size:3
Alignment explanation
Indices: 73137--73186 Score: 75
Period size: 3 Copynumber: 16.7 Consensus size: 3
73127 TTGTATTAGT
*
73137 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATC ATA TATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
73185 AT
1 AT
73187 CGGGGTAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 2 0.05
3 38 0.88
4 3 0.07
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Done.