Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006785.1 Corchorus capsularis cultivar CVL-1 contig06806, 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: 24086
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Found at i:3589 original size:31 final size:31
Alignment explanation
Indices: 3546--3612 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
3536 GATATTTATT
3546 TATTTTTGTTTGGCACACAATAAGAATAAGA
1 TATTTTTGTTTGGCACACAATAAGAATAAGA
3577 TATTTTCT-TTTGGCACACAATAAGAATAAGA
1 TATTTT-TGTTTGGCACACAATAAGAATAAGA
3608 TATTT
1 TATTT
3613 AACTATGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
31 34 0.97
32 1 0.03
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.39
Consensus pattern (31 bp):
TATTTTTGTTTGGCACACAATAAGAATAAGA
Found at i:6232 original size:147 final size:147
Alignment explanation
Indices: 5965--6254 Score: 562
Period size: 147 Copynumber: 2.0 Consensus size: 147
5955 TGGCTATTGT
5965 TAATGTGATTCTGTAGGAGCTCATTAAGGAAACCTTGTAACCGGTAGGTAATATAATTTAATTAG
1 TAATGTGATTCTGTAGGAGCTCATTAAGGAAACCTTGTAACCGGTAGGTAATATAATTTAATTAG
*
6030 GACAGTGTGCAAAATCGAACTGTCCTACAATCATAAAGAACGAAGGCCGACATGTAGAAAGAGAG
66 GACAGTGTGCAAAATCGAACTGTCCTACAATCATAAAGAACAAAGGCCGACATGTAGAAAGAGAG
6095 AAAGAAGACTCCAATCA
131 AAAGAAGACTCCAATCA
6112 TAATGTGATTCTGTAGGAGCTCATTAAGGAAACCTTGTAACCGGTAGGTAATATAATTTAATTAG
1 TAATGTGATTCTGTAGGAGCTCATTAAGGAAACCTTGTAACCGGTAGGTAATATAATTTAATTAG
*
6177 GACGGTGTGCAAAATCGAACTGTCCTACAATCATAAAGAACAAAGGCCGACATGTAGAAAGAGAG
66 GACAGTGTGCAAAATCGAACTGTCCTACAATCATAAAGAACAAAGGCCGACATGTAGAAAGAGAG
6242 AAAGAAGACTCCA
131 AAAGAAGACTCCA
6255 CTCAGTAGAC
Statistics
Matches: 141, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
147 141 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (147 bp):
TAATGTGATTCTGTAGGAGCTCATTAAGGAAACCTTGTAACCGGTAGGTAATATAATTTAATTAG
GACAGTGTGCAAAATCGAACTGTCCTACAATCATAAAGAACAAAGGCCGACATGTAGAAAGAGAG
AAAGAAGACTCCAATCA
Found at i:11768 original size:45 final size:45
Alignment explanation
Indices: 11717--11811 Score: 183
Period size: 45 Copynumber: 2.1 Consensus size: 45
11707 GTCCATGTGC
11717 AATGCTGGTGTTATTAACGACATTAAGCTTCTGAGAAGGCATTAG
1 AATGCTGGTGTTATTAACGACATTAAGCTTCTGAGAAGGCATTAG
11762 AATGCTGGTGTTATTAACGACATTAAGCTTCTGAGAAGGCATTAG
1 AATGCTGGTGTTATTAACGACATTAAGCTTCTGAGAAGGCATTAG
11807 -ATGCT
1 AATGCT
11812 TCTATCATCA
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 5 0.10
45 45 0.90
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.32
Consensus pattern (45 bp):
AATGCTGGTGTTATTAACGACATTAAGCTTCTGAGAAGGCATTAG
Found at i:16758 original size:177 final size:177
Alignment explanation
Indices: 16462--16818 Score: 714
Period size: 177 Copynumber: 2.0 Consensus size: 177
16452 TTCGTTTCTT
16462 GAATTAGAAAAGATTTGGCTCCTTTAGATCCTTTAGATGAAATGATTCTAGATTGAGTAGAAAGG
1 GAATTAGAAAAGATTTGGCTCCTTTAGATCCTTTAGATGAAATGATTCTAGATTGAGTAGAAAGG
16527 AGATAAAGGTTTCATTTTTGCAGATGTTGGAAGGCCGGGGCTTACTTGTCTTAAAGTGTATCTTA
66 AGATAAAGGTTTCATTTTTGCAGATGTTGGAAGGCCGGGGCTTACTTGTCTTAAAGTGTATCTTA
16592 TACATCTAAAGCTTTTCAATTATTAGTAGTCATTAATATCATATCTA
131 TACATCTAAAGCTTTTCAATTATTAGTAGTCATTAATATCATATCTA
16639 GAATTAGAAAAGATTTGGCTCCTTTAGATCCTTTAGATGAAATGATTCTAGATTGAGTAGAAAGG
1 GAATTAGAAAAGATTTGGCTCCTTTAGATCCTTTAGATGAAATGATTCTAGATTGAGTAGAAAGG
16704 AGATAAAGGTTTCATTTTTGCAGATGTTGGAAGGCCGGGGCTTACTTGTCTTAAAGTGTATCTTA
66 AGATAAAGGTTTCATTTTTGCAGATGTTGGAAGGCCGGGGCTTACTTGTCTTAAAGTGTATCTTA
16769 TACATCTAAAGCTTTTCAATTATTAGTAGTCATTAATATCATATCTA
131 TACATCTAAAGCTTTTCAATTATTAGTAGTCATTAATATCATATCTA
16816 GAA
1 GAA
16819 CTTGGTTTTG
Statistics
Matches: 180, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
177 180 1.00
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (177 bp):
GAATTAGAAAAGATTTGGCTCCTTTAGATCCTTTAGATGAAATGATTCTAGATTGAGTAGAAAGG
AGATAAAGGTTTCATTTTTGCAGATGTTGGAAGGCCGGGGCTTACTTGTCTTAAAGTGTATCTTA
TACATCTAAAGCTTTTCAATTATTAGTAGTCATTAATATCATATCTA
Found at i:17875 original size:30 final size:30
Alignment explanation
Indices: 17841--17928 Score: 97
Period size: 34 Copynumber: 2.8 Consensus size: 30
17831 GGAGGAAGAT
*
17841 TCTGATCTCTTTTCTTGTGAAGGAGAACAA
1 TCTGATTTCTTTTCTTGTGAAGGAGAACAA
*
17871 TCTGATTTTGTTCTTTGCTTGTGAAGGAGAACAA
1 TCTGA---T-TTCTTTTCTTGTGAAGGAGAACAA
*
17905 TCTGATTTC-CTTCTTGATGAAGGA
1 TCTGATTTCTTTTCTTG-TGAAGGA
17929 TTTGTTTGTG
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
29 5 0.10
30 15 0.31
31 1 0.02
33 1 0.02
34 27 0.55
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.40
Consensus pattern (30 bp):
TCTGATTTCTTTTCTTGTGAAGGAGAACAA
Found at i:17892 original size:34 final size:34
Alignment explanation
Indices: 17848--17912 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
17838 GATTCTGATC
*
17848 TCTTTTCTTGTGAAGGAGAACAATCTGATTTTGT
1 TCTTTGCTTGTGAAGGAGAACAATCTGATTTTGT
17882 TCTTTGCTTGTGAAGGAGAACAATCTGATTT
1 TCTTTGCTTGTGAAGGAGAACAATCTGATTT
17913 CCTTCTTGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.25, C:0.12, G:0.22, T:0.42
Consensus pattern (34 bp):
TCTTTGCTTGTGAAGGAGAACAATCTGATTTTGT
Found at i:19590 original size:1 final size:1
Alignment explanation
Indices: 19584--19614 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
19574 TACGGTTTCC
19584 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
19615 CTGAACTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:19915 original size:41 final size:46
Alignment explanation
Indices: 19843--19929 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 46
19833 GAGCCTTTTA
*
19843 ACATCCAAAGGTTCAATGATACTAAGTCTCAATATGGATACAAGGG
1 ACATCCAAAGGTTCAATGATACTAAGCCTCAATATGGATACAAGGG
19889 ACATCCAAAGGTTCAAT-A-A-T-A-CCTCAATATGGATACAAGGG
1 ACATCCAAAGGTTCAATGATACTAAGCCTCAATATGGATACAAGGG
19930 GATGCATACA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
41 19 0.47
42 1 0.03
43 1 0.03
44 1 0.03
45 1 0.03
46 17 0.43
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.23
Consensus pattern (46 bp):
ACATCCAAAGGTTCAATGATACTAAGCCTCAATATGGATACAAGGG
Done.