Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013254.1 Corchorus capsularis cultivar CVL-1 contig13275, 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: 74636
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:7774 original size:30 final size:31
Alignment explanation
Indices: 7730--7788 Score: 102
Period size: 30 Copynumber: 1.9 Consensus size: 31
7720 AAAAACAAAC
*
7730 TCACACCAATAAATAGTAAATTAATGATATT
1 TCACACCAAAAAATAGTAAATTAATGATATT
7761 TCAC-CCAAAAAATAGTAAATTAATGATA
1 TCACACCAAAAAATAGTAAATTAATGATA
7789 ACTCAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.51, C:0.14, G:0.07, T:0.29
Consensus pattern (31 bp):
TCACACCAAAAAATAGTAAATTAATGATATT
Found at i:7801 original size:30 final size:30
Alignment explanation
Indices: 7740--7802 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
7730 TCACACCAAT
** ***
7740 AAATAGTAAATTAATGATATTTCACCCAAA
1 AAATAGTAAATTAATGATAACTCAAAAAAA
7770 AAATAGTAAATTAATGATAACTCAAAAAAA
1 AAATAGTAAATTAATGATAACTCAAAAAAA
7800 AAA
1 AAA
7803 CTTTGATTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.59, C:0.10, G:0.06, T:0.25
Consensus pattern (30 bp):
AAATAGTAAATTAATGATAACTCAAAAAAA
Found at i:13267 original size:6 final size:6
Alignment explanation
Indices: 13258--13285 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
13248 AGAAAATCTA
13258 AAATAG AAATAG AAATAG AAATAG AAAT
1 AAATAG AAATAG AAATAG AAATAG AAAT
13286 TTTTATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.14, T:0.18
Consensus pattern (6 bp):
AAATAG
Found at i:25980 original size:4 final size:4
Alignment explanation
Indices: 25971--25995 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
25961 TGCATTTCGC
25971 TCTT TCTT TCTT TCTT TCTT TCTT T
1 TCTT TCTT TCTT TCTT TCTT TCTT T
25996 TTTTGGTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TCTT
Found at i:41828 original size:48 final size:48
Alignment explanation
Indices: 41746--41842 Score: 158
Period size: 48 Copynumber: 2.0 Consensus size: 48
41736 AGACTAGATC
** *
41746 TGGAGGAAGTGGGAATTCCCTTGGGAGATGAAGAAAAGATTTGCAAGA
1 TGGAGGAAGTGGGAATTCCCTTGAAAGATAAAGAAAAGATTTGCAAGA
*
41794 TGGAGGAAGTGGGAATTCCCTTGAAAGATAAAGAAAAGTTTTGCAAGA
1 TGGAGGAAGTGGGAATTCCCTTGAAAGATAAAGAAAAGATTTGCAAGA
41842 T
1 T
41843 ACTGCTGACG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.37, C:0.08, G:0.32, T:0.23
Consensus pattern (48 bp):
TGGAGGAAGTGGGAATTCCCTTGAAAGATAAAGAAAAGATTTGCAAGA
Found at i:53643 original size:25 final size:24
Alignment explanation
Indices: 53606--53672 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 24
53596 CTCTCAACTT
*
53606 CAAACCCT-AAACTTCATTTCTAA
1 CAAACCTTCAAACTTCATTTCTAA
*
53629 C-AACTTCTTCAAACTTCATTTTTAA
1 CAAAC--CTTCAAACTTCATTTCTAA
53654 CAAACCTTCAAA-TTCATTT
1 CAAACCTTCAAACTTCATTT
53673 TCCTTCATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
22 3 0.08
23 8 0.21
24 9 0.24
25 15 0.39
26 3 0.08
ACGTcount: A:0.36, C:0.27, G:0.00, T:0.37
Consensus pattern (24 bp):
CAAACCTTCAAACTTCATTTCTAA
Found at i:53712 original size:15 final size:15
Alignment explanation
Indices: 53682--53749 Score: 62
Period size: 15 Copynumber: 5.1 Consensus size: 15
53672 TTCCTTCATT
53682 TTAATCATAAACTAA
1 TTAATCATAAACTAA
53697 TTAA--AT--ACTAA
1 TTAATCATAAACTAA
53708 TTAATCATAAACTAA
1 TTAATCATAAACTAA
*
53723 TT-A-GAT--ACTAA
1 TTAATCATAAACTAA
*
53734 TTAAACATAAACTAA
1 TTAATCATAAACTAA
53749 T
1 T
53750 AAACTAAGTA
Statistics
Matches: 43, Mismatches: 2, Indels: 16
0.70 0.03 0.26
Matches are distributed among these distances:
11 16 0.37
12 1 0.02
13 8 0.19
14 1 0.02
15 17 0.40
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (15 bp):
TTAATCATAAACTAA
Found at i:53718 original size:26 final size:26
Alignment explanation
Indices: 53682--53799 Score: 120
Period size: 26 Copynumber: 4.7 Consensus size: 26
53672 TTCCTTCATT
53682 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
53708 TTAATCATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
53734 TTAAACATAAACTAA-T-AA-ACTAA
1 TTAATCATAAACTAATTAAATACTAA
* * * * * *
53757 GTAAT-TTTAATTAACTAAATA-AAA
1 TTAATCATAAACTAATTAAATACTAA
*
53781 CTAATCATAAACTAATTAA
1 TTAATCATAAACTAATTAA
53800 TATAAAACAA
Statistics
Matches: 74, Mismatches: 14, Indels: 9
0.76 0.14 0.09
Matches are distributed among these distances:
22 6 0.08
23 9 0.12
24 9 0.12
25 11 0.15
26 39 0.53
ACGTcount: A:0.54, C:0.11, G:0.02, T:0.33
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:54002 original size:21 final size:21
Alignment explanation
Indices: 53973--54017 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
53963 AAAAATTATA
*
53973 AAAATGGGGGCGGTGTTTAGC
1 AAAAGGGGGGCGGTGTTTAGC
53994 AAAAGGGGGGCGGTGTTTAGC
1 AAAAGGGGGGCGGTGTTTAGC
54015 AAA
1 AAA
54018 CCCCTTTAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.29, C:0.09, G:0.42, T:0.20
Consensus pattern (21 bp):
AAAAGGGGGGCGGTGTTTAGC
Done.