Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008718.1 Corchorus capsularis cultivar CVL-1 contig08739, 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: 39970
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:2538 original size:432 final size:428
Alignment explanation
Indices: 1688--2718 Score: 1599
Period size: 432 Copynumber: 2.4 Consensus size: 428
1678 TCGAGTAAGA
*
1688 AAATAAGAAAATAG-TTGTTAATGGAGATCTTGAAACATAAAAA-TTCTGTTTTAATCCCTCCAT
1 AAATAAGAAAAT-GTTTGTTAATGGAGATCTTGAAACATAAAAATTTC-CTTTTAA-CCCTCC-T
* * * * *
1751 AAAACCCGTAGATCAAATTAACTTTTGGGTTCTTCATGAAAG-TCGTAGACCCGTAACCTTTTAA
62 GAAACTCGTAGATCAAATTAACTTTCGGGTTCTTCATGAAAGTTTGTAGACCAGTAACCTTTTAA
*
1815 CCGACACTTGAATAACTTCAATTGGACATGTGGATCAAAAGTTATATGGTATTAAATAGACCAAC
127 CCGACACTTGAATAACTTCAATTGGACATGTGGATCAAAAGGTATATGGTATTAAATAGACCAAC
1880 AATCAAAACAACCAAATTTAGGAAGCATTTTTTTTTGAATTGAAACATAAAAAATTACTTTTGAG
192 AATCAAAACAACCAAATTTAGGAAGCA-TTTTTTTTGAATTGAAACATAAAAAATTACTTTTGAG
* * *
1945 TCCTGAAAGTTGTAAATCATGAAATTACCTTTTAATATACACATGAATCAACTTAATCGGACAAA
256 TCCTGAAAGTTGTAAATAATGAAATTACCTTTTAATAGACACATGAATCAACTTAATCGAACAAA
2010 TATAACAAAGAATAAAAAAATAAAGCTTAAACGTCAGATTAGATAGAATTTGTAAAGGACTAAGT
321 TATAACAAAGAATAAAAAAATAAAGCTTAAACGTCAGATTAGATAGAATTTGTAAAGGACTAAGT
*
2075 AGTATAAAGTAGAAAAGTATGAGGGTCATTTGATAAATAATCC
386 AGTATAAAATAGAAAAGTATGAGGGTCATTTGATAAATAATCC
2118 AAATAAGAAAATGTTTGTTAATGGAGATCTTGAAACATAAAAATTTCCTTTTGAACCCTCCTGAA
1 AAATAAGAAAATGTTTGTTAATGGAGATCTTGAAACATAAAAATTTCCTTTT-AACCCTCCTGAA
2183 ACTCGTAGATCAAATTAACTTTCGGGTTCTTCATGAAAGTTTGTAGACCAGTAACCTTTTAACCG
65 ACTCGTAGATCAAATTAACTTTCGGGTTCTTCATGAAAGTTTGTAGACCAGTAACCTTTTAACCG
*
2248 ACACTTGAATAACTTCAATTGGACATGTGGATCGAAAGGTATATGGTATTAAATAGACCAACAAT
130 ACACTTGAATAACTTCAATTGGACATGTGGATCAAAAGGTATATGGTATTAAATAGACCAACAAT
* *
2313 CGAAACAACCAAATTTAGGAAGCA-TTTTTTTGAATTGAAACATAATAAATTACTTTTGAGTCAT
195 CAAAACAACCAAATTTAGGAAGCATTTTTTTTGAATTGAAACATAAAAAATTACTTTTGAG----
2377 TCCTGAAAGTTGTAAATAATGAAATTACCTTTTAATAGACACATGAATCAACTTAATCGAACAAA
256 TCCTGAAAGTTGTAAATAATGAAATTACCTTTTAATAGACACATGAATCAACTTAATCGAACAAA
* *
2442 TATAACAAAGAATAAAAAAATAAAGCTTAAACGTCAGATTGGATAGAATTTGTAAAGGACTGAGT
321 TATAACAAAGAATAAAAAAATAAAGCTTAAACGTCAGATTAGATAGAATTTGTAAAGGACTAAGT
*
2507 AGTATAAAATGGAAAAGTATGAGGGTCATTTGATAAATAATCC
386 AGTATAAAATAGAAAAGTATGAGGGTCATTTGATAAATAATCC
* * *
2550 AAATAAGAAAATGTTTATTAATGGAGATCTTGAAACATAAAAATTCCCTTTTAACCCTTAC-GAA
1 AAATAAGAAAATGTTTGTTAATGGAGATCTTGAAACATAAAAATTTCCTTTTAACCC-TCCTGAA
* * * * * *
2614 ACTCATAGATCAAATTTAGCTTTCGGGTCCTTCATGAAAGTCT-TAAATCATGCAATAACCTTTT
65 ACTCGTAGATCAAA-TTAACTTTCGGGTTCTTCATGAAAGTTTGTAGA-C---CAGTAACCTTTT
* * * *
2678 AACCTACACTTCAATAACTTCAATCGGACATATGGA-CAAAA
125 AACCGACACTTGAATAACTTCAATTGGACATGTGGATCAAAA
2719 AATTATACGA
Statistics
Matches: 556, Mismatches: 31, Indels: 24
0.91 0.05 0.04
Matches are distributed among these distances:
428 35 0.06
429 41 0.07
430 160 0.29
431 29 0.05
432 244 0.44
434 4 0.01
435 43 0.08
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (428 bp):
AAATAAGAAAATGTTTGTTAATGGAGATCTTGAAACATAAAAATTTCCTTTTAACCCTCCTGAAA
CTCGTAGATCAAATTAACTTTCGGGTTCTTCATGAAAGTTTGTAGACCAGTAACCTTTTAACCGA
CACTTGAATAACTTCAATTGGACATGTGGATCAAAAGGTATATGGTATTAAATAGACCAACAATC
AAAACAACCAAATTTAGGAAGCATTTTTTTTGAATTGAAACATAAAAAATTACTTTTGAGTCCTG
AAAGTTGTAAATAATGAAATTACCTTTTAATAGACACATGAATCAACTTAATCGAACAAATATAA
CAAAGAATAAAAAAATAAAGCTTAAACGTCAGATTAGATAGAATTTGTAAAGGACTAAGTAGTAT
AAAATAGAAAAGTATGAGGGTCATTTGATAAATAATCC
Found at i:3323 original size:22 final size:22
Alignment explanation
Indices: 3295--3357 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 22
3285 GTAGTTAATC
3295 ATAAATTAACTAATTAAA-ACTA
1 ATAAATTAA-TAATTAAATACTA
*
3317 ATAAATTAAGTAATTAAATGCTA
1 ATAAATTAA-TAATTAAATACTA
* *
3340 ATTAATTAAAAATTAAAT
1 ATAAATTAATAATTAAAT
3358 TTTTTTTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
22 25 0.69
23 11 0.31
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (22 bp):
ATAAATTAATAATTAAATACTA
Found at i:3493 original size:33 final size:33
Alignment explanation
Indices: 3374--3481 Score: 182
Period size: 33 Copynumber: 3.3 Consensus size: 33
3364 TAAAGAAAAT
* *
3374 TGGCTTTGCCGCCCATTTTGGGCGGCATG-CCA
1 TGGCCTTGCCGCCCATTTTGGGCGGCTTGCCCA
*
3406 TGGCCTTGCCGCCCATTTTGGGTGGCTTGCCCA
1 TGGCCTTGCCGCCCATTTTGGGCGGCTTGCCCA
3439 TGGCCTTGCCGCCCATTTTGGGCGGCTTGCCCA
1 TGGCCTTGCCGCCCATTTTGGGCGGCTTGCCCA
3472 TGGCCTTGCC
1 TGGCCTTGCC
3482 ACCTAGTTTG
Statistics
Matches: 71, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
32 26 0.37
33 45 0.63
ACGTcount: A:0.06, C:0.34, G:0.31, T:0.29
Consensus pattern (33 bp):
TGGCCTTGCCGCCCATTTTGGGCGGCTTGCCCA
Found at i:3691 original size:21 final size:21
Alignment explanation
Indices: 3665--3708 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3655 CAAAAGTGTA
3665 AAAAGGGGAGCGATATTTAGC
1 AAAAGGGGAGCGATATTTAGC
* * *
3686 AAAAGGGGGGCGGTGTTTAGC
1 AAAAGGGGAGCGATATTTAGC
3707 AA
1 AA
3709 TCCAGATAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.09, G:0.39, T:0.18
Consensus pattern (21 bp):
AAAAGGGGAGCGATATTTAGC
Found at i:7796 original size:20 final size:20
Alignment explanation
Indices: 7755--7808 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
7745 CGCTCATAGC
*
7755 CTTTTTTTTTTTAT-CTCTCT
1 CTTTTTTTTTTT-TCCTCCCT
7775 CTTTTTTTTTTTTCCTCCCT
1 CTTTTTTTTTTTTCCTCCCT
* *
7795 CTTTCTTTCTTTTC
1 CTTTTTTTTTTTTC
7809 ACTTTTTGTC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (20 bp):
CTTTTTTTTTTTTCCTCCCT
Found at i:7832 original size:31 final size:31
Alignment explanation
Indices: 7797--7862 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
7787 TCCTCCCTCT
** * *
7797 TTCTTTCTTTTCACTTTTTGTCTTTTTCTAG
1 TTCTTTCTTTTCACCGTTTGTCCTTTTCTAC
* *
7828 TTCTTTTTTTTGACCGTTTGTCCTTTTCTAC
1 TTCTTTCTTTTCACCGTTTGTCCTTTTCTAC
7859 TTCT
1 TTCT
7863 AACCCTTCTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.06, C:0.21, G:0.08, T:0.65
Consensus pattern (31 bp):
TTCTTTCTTTTCACCGTTTGTCCTTTTCTAC
Found at i:11269 original size:15 final size:15
Alignment explanation
Indices: 11249--11296 Score: 78
Period size: 15 Copynumber: 3.2 Consensus size: 15
11239 TGAAAGTTCC
11249 TATGAATATTGTTTT
1 TATGAATATTGTTTT
11264 TATGAATATTGTTTT
1 TATGAATATTGTTTT
* *
11279 TATGAACATGGTTTT
1 TATGAATATTGTTTT
11294 TAT
1 TAT
11297 AATGCTATCC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.27, C:0.02, G:0.15, T:0.56
Consensus pattern (15 bp):
TATGAATATTGTTTT
Found at i:13734 original size:37 final size:39
Alignment explanation
Indices: 13692--13792 Score: 145
Period size: 37 Copynumber: 2.6 Consensus size: 39
13682 AATTTTATTA
13692 ATTTCCAAAAGTCTTCTCTTGGATTTT-T-AAAACATTT
1 ATTTCCAAAAGTCTTCTCTTGGATTTTCTAAAAACATTT
*
13729 ATTTCCAAAAGTCTTCTTTTGG-TTTTGCTAAAAAACATTT
1 ATTTCCAAAAGTCTTCTCTTGGATTTT-CT-AAAAACATTT
13769 ATTTTCCAAAAGTCTTCTCTTGGA
1 A-TTTCCAAAAGTCTTCTCTTGGA
13793 ATTGCTTAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
36 4 0.07
37 21 0.38
38 1 0.02
40 10 0.18
41 20 0.36
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.45
Consensus pattern (39 bp):
ATTTCCAAAAGTCTTCTCTTGGATTTTCTAAAAACATTT
Found at i:13798 original size:41 final size:39
Alignment explanation
Indices: 13692--13798 Score: 137
Period size: 41 Copynumber: 2.7 Consensus size: 39
13682 AATTTTATTA
**
13692 ATTTCCAAAAGTCTTCTCTTGGATT--TTTAAAACATTT
1 ATTTCCAAAAGTCTTCTCTTGGATTGCTAAAAAACATTT
* *
13729 ATTTCCAAAAGTCTTCTTTTGGTTTTGCTAAAAAACATTT
1 ATTTCCAAAAGTCTTCTCTTGG-ATTGCTAAAAAACATTT
13769 ATTTTCCAAAAGTCTTCTCTTGGAATTGCT
1 A-TTTCCAAAAGTCTTCTCTTGG-ATTGCT
13799 TAAATAGAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
37 21 0.36
38 2 0.03
40 11 0.19
41 25 0.42
ACGTcount: A:0.28, C:0.17, G:0.10, T:0.45
Consensus pattern (39 bp):
ATTTCCAAAAGTCTTCTCTTGGATTGCTAAAAAACATTT
Found at i:16186 original size:17 final size:18
Alignment explanation
Indices: 16158--16192 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
16148 CCACCTGGAA
16158 TTTCTATTTTTTTTCTTT
1 TTTCTATTTTTTTTCTTT
16176 TTTCT-TTTTTTTTCTTT
1 TTTCTATTTTTTTTCTTT
16193 AACCGATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (18 bp):
TTTCTATTTTTTTTCTTT
Found at i:21174 original size:53 final size:52
Alignment explanation
Indices: 21066--21256 Score: 260
Period size: 52 Copynumber: 3.7 Consensus size: 52
21056 TAAAAAAGAA
* * **
21066 GTTCAATTTAAG--TTTTCAAAGTGGGAAAATTCCCAACAAGTTTAAAAAGT
1 GTTCAATTTAGGTCTTTTCAAAGTGGGAAAGTTCCCAACAAGTTTTCAAAGT
*
21116 ATTCAATTTAGGTCTTTTCAAAGTGGGAAAGTTCCCCAACAAGTTTTCAAAGT
1 GTTCAATTTAGGTCTTTTCAAAGTGGGAAAGTT-CCCAACAAGTTTTCAAAGT
* * * *
21169 GTTCAATTTAGATCTTTTCGAAGTGGGAAAGTTCCCATCAGGTTTTCAAAGT
1 GTTCAATTTAGGTCTTTTCAAAGTGGGAAAGTTCCCAACAAGTTTTCAAAGT
* *
21221 GTTCAATTTAGGTCTTCTCGAAGTGGGAAAGTTCCC
1 GTTCAATTTAGGTCTTTTCAAAGTGGGAAAGTTCCC
21257 GTCAACATTG
Statistics
Matches: 126, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
50 10 0.08
52 69 0.55
53 47 0.37
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (52 bp):
GTTCAATTTAGGTCTTTTCAAAGTGGGAAAGTTCCCAACAAGTTTTCAAAGT
Found at i:21311 original size:34 final size:32
Alignment explanation
Indices: 21267--21367 Score: 105
Period size: 35 Copynumber: 3.0 Consensus size: 32
21257 GTCAACATTG
21267 GTTTTAGTTTTCAAATTGGGAAAGTTCCCATCA
1 GTTTTAGTTTT-AAATTGGGAAAGTTCCCATCA
* *
21300 GATTTTAGTTTTTAACTTAGGGAAAGTTCCCGTTCA
1 G-TTTTAG-TTTTAAATT-GGGAAAGTTCCC-ATCA
**
21336 GTTTCCGTTCTTAAA-TGGGAAAGTTCCCATCA
1 GTTTTAGTT-TTAAATTGGGAAAGTTCCCATCA
21368 AATAACAGTT
Statistics
Matches: 57, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
32 3 0.05
33 13 0.23
34 13 0.23
35 24 0.42
36 4 0.07
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.39
Consensus pattern (32 bp):
GTTTTAGTTTTAAATTGGGAAAGTTCCCATCA
Found at i:28597 original size:102 final size:103
Alignment explanation
Indices: 28421--28639 Score: 309
Period size: 102 Copynumber: 2.1 Consensus size: 103
28411 TTATTATTAA
* *
28421 ATTGAAAT-TTAAAACGGAAACTTATTCAATACATCATCAGTAGAGTTTATCAGACTGCACGTGC
1 ATTGAAATATTAAAACGGAAAATTATTCAATACATCATCAGTAGAGTTTAACAGACTGCACGTGC
**
28485 GGATCTAAAAGAGTGACATGTGTCCTTTTAGGAACTAG
66 GGATCTAAAAGAGTGACATGTGTCCCCTTAGGAACTAG
* * * * *
28523 ATTGAAATATTAAAA-GGAAAATTATTTAATACA-CTGTTAGTGGAGTTTAACAGACTGCATGTG
1 ATTGAAATATTAAAACGGAAAATTATTCAATACATC-ATCAGTAGAGTTTAACAGACTGCACGTG
* *
28586 CGGATCTAAAAGGGTGACATGTGTCCCCTTAGGGACTAG
65 CGGATCTAAAAGAGTGACATGTGTCCCCTTAGGAACTAG
28625 ATTGAAATATTAAAA
1 ATTGAAATATTAAAA
28640 TTCTAACTAA
Statistics
Matches: 104, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
101 1 0.01
102 97 0.93
103 6 0.06
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.30
Consensus pattern (103 bp):
ATTGAAATATTAAAACGGAAAATTATTCAATACATCATCAGTAGAGTTTAACAGACTGCACGTGC
GGATCTAAAAGAGTGACATGTGTCCCCTTAGGAACTAG
Found at i:29374 original size:6 final size:6
Alignment explanation
Indices: 29357--29386 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
29347 TTACCTTTTA
*
29357 TATATT TTTATT TATATT TATATT TATATT
1 TATATT TATATT TATATT TATATT TATATT
29387 AAATTCTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TATATT
Found at i:29863 original size:144 final size:143
Alignment explanation
Indices: 29603--29863 Score: 479
Period size: 144 Copynumber: 1.8 Consensus size: 143
29593 GATTAACAAC
29603 AAAAAAATTAGAAAAGATATACCATTAAATAAGTACAGATACCAAACAATACAAAATGCAATGAA
1 AAAAAAATTAGAAAAGATATACCATTAAATAAGTACAGATACCAAACAATACAAAATGCAATGAA
*
29668 CTATTGGATTTAAAGGAAAATACAAGCACCAAAATGAATATAAATAGACAATGAACAAAAGAGTA
66 CTATTAGATTTAAAGGAAAATACAAGCACCAAAATGAATATAAATAGACAATGAACAAAAGAGTA
29733 CAGATACCAAACA
131 CAGATACCAAACA
*
29746 AAAAAAATTAGAAGAGATGA-ACCCATTAAATAAGTACAGATACCAAACAATACAAAATGCAATG
1 AAAAAAATTAGAAAAGAT-ATA-CCATTAAATAAGTACAGATACCAAACAATACAAAATGCAATG
29810 AACTATTAGATTTAAAGGAAAATACAAGCACCAAAATGAATATAAATAGACAAT
64 AACTATTAGATTTAAAGGAAAATACAAGCACCAAAATGAATATAAATAGACAAT
29864 AGTTTTCAGA
Statistics
Matches: 114, Mismatches: 2, Indels: 3
0.96 0.02 0.03
Matches are distributed among these distances:
143 18 0.16
144 96 0.84
ACGTcount: A:0.56, C:0.13, G:0.12, T:0.19
Consensus pattern (143 bp):
AAAAAAATTAGAAAAGATATACCATTAAATAAGTACAGATACCAAACAATACAAAATGCAATGAA
CTATTAGATTTAAAGGAAAATACAAGCACCAAAATGAATATAAATAGACAATGAACAAAAGAGTA
CAGATACCAAACA
Found at i:33031 original size:3 final size:3
Alignment explanation
Indices: 33025--33077 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
33015 TTCTTCTTTT
*
33025 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTT TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
33073 TTA TT
1 TTA TT
33078 TGCTTATACT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:34994 original size:2 final size:2
Alignment explanation
Indices: 34979--35031 Score: 62
Period size: 2 Copynumber: 29.0 Consensus size: 2
34969 TCTGTATGTC
34979 TA TA T- TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA -A T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
35017 -A TA TA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA
35032 AGGTATAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
1 5 0.11
2 39 0.89
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:37548 original size:21 final size:22
Alignment explanation
Indices: 37517--37606 Score: 85
Period size: 21 Copynumber: 4.1 Consensus size: 22
37507 ACTCACAAAG
* * *
37517 AAAAGAGGAAGTGATTTAGACA
1 AAAAGACGAAGTAACTTAGACA
* *
37539 AAAAGA-GAAGCAACTTGGACA
1 AAAAGACGAAGTAACTTAGACA
*
37560 AAAAGA-GAAGTAACTTGGACA
1 AAAAGACGAAGTAACTTAGACA
*
37581 AAAAGAAACGAAGTGACTTAGACA
1 AAAAG--ACGAAGTAACTTAGACA
37605 AA
1 AA
37607 TCTTTTTGGT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
21 36 0.62
22 6 0.10
23 1 0.02
24 15 0.26
ACGTcount: A:0.53, C:0.10, G:0.23, T:0.13
Consensus pattern (22 bp):
AAAAGACGAAGTAACTTAGACA
Found at i:37599 original size:24 final size:21
Alignment explanation
Indices: 37517--37586 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
37507 ACTCACAAAG
* * *
37517 AAAAGAGGAAGTGATTTAGACA
1 AAAAGA-GAAGTAACTTGGACA
*
37539 AAAAGAGAAGCAACTTGGACA
1 AAAAGAGAAGTAACTTGGACA
37560 AAAAGAGAAGTAACTTGGACA
1 AAAAGAGAAGTAACTTGGACA
37581 AAAAGA
1 AAAAGA
37587 AACGAAGTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 37 0.86
22 6 0.14
ACGTcount: A:0.54, C:0.09, G:0.24, T:0.13
Consensus pattern (21 bp):
AAAAGAGAAGTAACTTGGACA
Done.