Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012986.1 Corchorus capsularis cultivar CVL-1 contig13007, 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: 29523
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Found at i:268 original size:32 final size:32
Alignment explanation
Indices: 182--260 Score: 140
Period size: 32 Copynumber: 2.5 Consensus size: 32
172 GCATCCTATG
*
182 GTGAAGCCGCCCTAGGAGGGCGGCCTGACCAT
1 GTGAAGCCGCCCTAGGAGGGCGGCATGACCAT
*
214 GTGAAACCGCCCTAGGAGGGCGGCATGACCAT
1 GTGAAGCCGCCCTAGGAGGGCGGCATGACCAT
246 GTGAAGCCGCCCTAG
1 GTGAAGCCGCCCTAG
261 TTGGGCGGTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.22, C:0.30, G:0.35, T:0.13
Consensus pattern (32 bp):
GTGAAGCCGCCCTAGGAGGGCGGCATGACCAT
Found at i:2687 original size:15 final size:14
Alignment explanation
Indices: 2667--2700 Score: 59
Period size: 15 Copynumber: 2.4 Consensus size: 14
2657 TTTAGGCAAC
2667 TGTTTTTAACTCAA
1 TGTTTTTAACTCAA
2681 TTGTTTTTAACTCAA
1 -TGTTTTTAACTCAA
2696 TGTTT
1 TGTTT
2701 AACATTATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.24, C:0.12, G:0.09, T:0.56
Consensus pattern (14 bp):
TGTTTTTAACTCAA
Found at i:6233 original size:290 final size:290
Alignment explanation
Indices: 5713--6293 Score: 1162
Period size: 290 Copynumber: 2.0 Consensus size: 290
5703 CAATTATAGG
5713 TTTATATGGGCTGAGTATATTCCCATATAAATAATCCAAAAAACCTCAACTTCAGGGCTTCATCT
1 TTTATATGGGCTGAGTATATTCCCATATAAATAATCCAAAAAACCTCAACTTCAGGGCTTCATCT
5778 GGTCTTGCCTTCAATCCTTTGCAAATAAACTCCAAATCTTCAATTCTTACTTCTTGAATTAACTC
66 GGTCTTGCCTTCAATCCTTTGCAAATAAACTCCAAATCTTCAATTCTTACTTCTTGAATTAACTC
5843 TTCAATTGTCTTCAAATCTTCAAAATATCTTCAATCACGAACTTCGCATCTTCAAATCTTCATTC
131 TTCAATTGTCTTCAAATCTTCAAAATATCTTCAATCACGAACTTCGCATCTTCAAATCTTCATTC
5908 CAAATGGCTAAATCCATAGTTGAGTAAAAAGTCACTAAAATAGCTCCAAAAAGAGTGAAAAACAA
196 CAAATGGCTAAATCCATAGTTGAGTAAAAAGTCACTAAAATAGCTCCAAAAAGAGTGAAAAACAA
5973 TAAGTTTTCACTTTTCTTGTCTTCAAGACC
261 TAAGTTTTCACTTTTCTTGTCTTCAAGACC
6003 TTTATATGGGCTGAGTATATTCCCATATAAATAATCCAAAAAACCTCAACTTCAGGGCTTCATCT
1 TTTATATGGGCTGAGTATATTCCCATATAAATAATCCAAAAAACCTCAACTTCAGGGCTTCATCT
6068 GGTCTTGCCTTCAATCCTTTGCAAATAAACTCCAAATCTTCAATTCTTACTTCTTGAATTAACTC
66 GGTCTTGCCTTCAATCCTTTGCAAATAAACTCCAAATCTTCAATTCTTACTTCTTGAATTAACTC
6133 TTCAATTGTCTTCAAATCTTCAAAATATCTTCAATCACGAACTTCGCATCTTCAAATCTTCATTC
131 TTCAATTGTCTTCAAATCTTCAAAATATCTTCAATCACGAACTTCGCATCTTCAAATCTTCATTC
6198 CAAATGGCTAAATCCATAGTTGAGTAAAAAGTCACTAAAATAGCTCCAAAAAGAGTGAAAAACAA
196 CAAATGGCTAAATCCATAGTTGAGTAAAAAGTCACTAAAATAGCTCCAAAAAGAGTGAAAAACAA
6263 TAAGTTTTCACTTTTCTTGTCTTCAAGACC
261 TAAGTTTTCACTTTTCTTGTCTTCAAGACC
6293 T
1 T
6294 ACAAACACAA
Statistics
Matches: 291, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
290 291 1.00
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.34
Consensus pattern (290 bp):
TTTATATGGGCTGAGTATATTCCCATATAAATAATCCAAAAAACCTCAACTTCAGGGCTTCATCT
GGTCTTGCCTTCAATCCTTTGCAAATAAACTCCAAATCTTCAATTCTTACTTCTTGAATTAACTC
TTCAATTGTCTTCAAATCTTCAAAATATCTTCAATCACGAACTTCGCATCTTCAAATCTTCATTC
CAAATGGCTAAATCCATAGTTGAGTAAAAAGTCACTAAAATAGCTCCAAAAAGAGTGAAAAACAA
TAAGTTTTCACTTTTCTTGTCTTCAAGACC
Found at i:7045 original size:19 final size:20
Alignment explanation
Indices: 7010--7048 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
7000 CCTCTTACAT
7010 GAAAAACACTTTATTTTTAA
1 GAAAAACACTTTATTTTTAA
*
7030 GAAAAAGACTTT-TTTTTAA
1 GAAAAACACTTTATTTTTAA
7049 CTACCCTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.41
Consensus pattern (20 bp):
GAAAAACACTTTATTTTTAA
Found at i:11680 original size:35 final size:34
Alignment explanation
Indices: 11636--11703 Score: 100
Period size: 35 Copynumber: 2.0 Consensus size: 34
11626 ATCGCAAATA
* *
11636 TTTTTTTTTAGAAAAATCAGAAAAAGGAAAAACTT
1 TTTTTTTTTAGAAAAAACAGAAAAA-CAAAAACTT
*
11671 TTTTTTTTTAGAAAAAACGGAAAAACAAAAACT
1 TTTTTTTTTAGAAAAAACAGAAAAACAAAAACT
11704 AATTCTTGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 7 0.23
35 23 0.77
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.32
Consensus pattern (34 bp):
TTTTTTTTTAGAAAAAACAGAAAAACAAAAACTT
Found at i:13245 original size:40 final size:40
Alignment explanation
Indices: 13190--13269 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
13180 TGCTGGTGAT
13190 ACGAATCTAGTTGTATATCGGACAAAATCCACCTTAGAGA
1 ACGAATCTAGTTGTATATCGGACAAAATCCACCTTAGAGA
* *
13230 ACGAATCTAGTTGTATATCGGGCCAAATCCACCTTAGAGA
1 ACGAATCTAGTTGTATATCGGACAAAATCCACCTTAGAGA
13270 CCCACCTAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (40 bp):
ACGAATCTAGTTGTATATCGGACAAAATCCACCTTAGAGA
Found at i:14052 original size:30 final size:30
Alignment explanation
Indices: 14018--14080 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
14008 AATGGGTCGA
*
14018 ATGGCTGGTTGTGGCCGGATGGCCCGTGCG
1 ATGGCCGGTTGTGGCCGGATGGCCCGTGCG
*
14048 ATGGCCGGTTGTGGCCGGATGGCTCGTGCG
1 ATGGCCGGTTGTGGCCGGATGGCCCGTGCG
14078 ATG
1 ATG
14081 TCCCATGCGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.08, C:0.22, G:0.46, T:0.24
Consensus pattern (30 bp):
ATGGCCGGTTGTGGCCGGATGGCCCGTGCG
Found at i:17941 original size:30 final size:30
Alignment explanation
Indices: 17907--17969 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
17897 AATGGGTCGA
* *
17907 ATGGCCGGTTGTGGCCGGATGGCCCGTGCG
1 ATGGCCGATTGTGGCCGGATGGCCCGAGCG
*
17937 ATGGCCGATTGTGGCCGGATGGCTCGAGCG
1 ATGGCCGATTGTGGCCGGATGGCCCGAGCG
17967 ATG
1 ATG
17970 TCCCGTCCGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.11, C:0.24, G:0.44, T:0.21
Consensus pattern (30 bp):
ATGGCCGATTGTGGCCGGATGGCCCGAGCG
Found at i:28690 original size:10 final size:10
Alignment explanation
Indices: 28675--28700 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
28665 AGTTGCTGCC
28675 AAATTCCAGA
1 AAATTCCAGA
28685 AAATTCCAGA
1 AAATTCCAGA
28695 AAATTC
1 AAATTC
28701 TAGAGTCCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23
Consensus pattern (10 bp):
AAATTCCAGA
Done.