Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011198.1 Corchorus capsularis cultivar CVL-1 contig11219, 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: 27045
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:983 original size:35 final size:35
Alignment explanation
Indices: 944--1439 Score: 462
Period size: 35 Copynumber: 14.2 Consensus size: 35
934 TCCAGTGCGG
* *
944 TCATTTTCAGAAGTTTTCAGA-GGTCAGAGTTGATC
1 TCATTTTCAGTAGTTTTCA-ACGATCAGAGTTGATC
* * *
979 TCA-TTCCAAGCAGTTTTCAGA-GGTCAGAGTTGATC
1 TCATTTTC-AGTAGTTTTCA-ACGATCAGAGTTGATC
* *
1014 TCA-TTTCAAGCAGTTTTCAGA-GGTCAGAGTTGATC
1 TCATTTTC-AGTAGTTTTCA-ACGATCAGAGTTGATC
* * *
1049 TCA-TTCCAAGCAGTTTTCAGA-GGTCAGAGTTGATC
1 TCATTTTC-AGTAGTTTTCA-ACGATCAGAGTTGATC
* * *
1084 TCA-TTCCAAGAAGTTTTCAGA-GGTCAGAGTTGATC
1 TCATTTTC-AGTAGTTTTCA-ACGATCAGAGTTGATC
* *
1119 TCA-TTTCAAGAAGTTTTCAGA-GGTCAGAGTTGATC
1 TCATTTTC-AGTAGTTTTCA-ACGATCAGAGTTGATC
1154 TCATTTTCAGTA-TTTTCCAACGATCAGAGTTGATC
1 TCATTTTCAGTAGTTTT-CAACGATCAGAGTTGATC
* *
1189 GCATTTTCAGTA-TTTCCCAACGATCAGAGTTGATC
1 TCATTTTCAGTAGTTT-TCAACGATCAGAGTTGATC
* * * *
1224 ACATTTTCAGAAGTTTCCAACGATCAAAGTTGATC
1 TCATTTTCAGTAGTTTTCAACGATCAGAGTTGATC
* *
1259 GCATTTTCAGTAGTTTCCAACGATCAGAGTTGATC
1 TCATTTTCAGTAGTTTTCAACGATCAGAGTTGATC
* *
1294 ACATTTTCAGTAGTTTCCAACGATCAGAGTTGATC
1 TCATTTTCAGTAGTTTTCAACGATCAGAGTTGATC
* *
1329 ACATTTTCAGTAGTTTCCAACGATCAGAGTTGATC
1 TCATTTTCAGTAGTTTTCAACGATCAGAGTTGATC
* * *
1364 GCATTTTCAATA-TTTTGCAACGATTAGAGTTGATC
1 TCATTTTCAGTAGTTTT-CAACGATCAGAGTTGATC
* * * *
1399 ACATTTTCAGTAGTTTCCAACAATCAGAGGTGATC
1 TCATTTTCAGTAGTTTTCAACGATCAGAGTTGATC
1434 TCATTT
1 TCATTT
1440 CAAGAAATTC
Statistics
Matches: 425, Mismatches: 28, Indels: 16
0.91 0.06 0.03
Matches are distributed among these distances:
34 11 0.03
35 404 0.95
36 10 0.02
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (35 bp):
TCATTTTCAGTAGTTTTCAACGATCAGAGTTGATC
Found at i:4920 original size:53 final size:53
Alignment explanation
Indices: 4849--4966 Score: 166
Period size: 53 Copynumber: 2.2 Consensus size: 53
4839 TGTTTGAATG
* * * *
4849 TTTTGAAAAATTTGATGGGAACTTTCCCACTTTGAAGAGACCTAAATTGAACAC
1 TTTTG-AAAACTTAATGGGAACTTTCCCAATTTGAAAAGACCTAAATTGAACAC
**
4903 TTTTGAAAACTTAATGGGAACTTTCCCAATTTGAAAAGACCTAAATTGAATGC
1 TTTTGAAAACTTAATGGGAACTTTCCCAATTTGAAAAGACCTAAATTGAACAC
4956 -TTTGAAAACTT
1 TTTTGAAAACTT
4967 GATGAAAATT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
52 11 0.19
53 42 0.72
54 5 0.09
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (53 bp):
TTTTGAAAACTTAATGGGAACTTTCCCAATTTGAAAAGACCTAAATTGAACAC
Found at i:5023 original size:7 final size:7
Alignment explanation
Indices: 4978--5007 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
4968 ATGAAAATTC
4978 TTTTGAT
1 TTTTGAT
4985 TTTTGAT
1 TTTTGAT
4992 TTTTGAT
1 TTTTGAT
4999 TTTTGAT
1 TTTTGAT
5006 TT
1 TT
5008 GATTTTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.13, C:0.00, G:0.13, T:0.73
Consensus pattern (7 bp):
TTTTGAT
Found at i:6750 original size:1 final size:1
Alignment explanation
Indices: 6744--6778 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
6734 ATCGTCATTC
6744 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
6779 CAGGAAAAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:14621 original size:14 final size:14
Alignment explanation
Indices: 14602--14631 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
14592 AAACCTCATA
14602 CTCACAATTCATGT
1 CTCACAATTCATGT
14616 CTCACAATTCATGT
1 CTCACAATTCATGT
14630 CT
1 CT
14632 GAAATTTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.30, G:0.07, T:0.37
Consensus pattern (14 bp):
CTCACAATTCATGT
Found at i:16293 original size:17 final size:17
Alignment explanation
Indices: 16271--16304 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
16261 AAAGAAGTTT
16271 TTGTAGTTAGCCTATGC
1 TTGTAGTTAGCCTATGC
16288 TTGTAGTTAGCCTATGC
1 TTGTAGTTAGCCTATGC
16305 GCATAGAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.41
Consensus pattern (17 bp):
TTGTAGTTAGCCTATGC
Found at i:19940 original size:19 final size:19
Alignment explanation
Indices: 19916--19956 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
19906 TTGCACTTCA
19916 ATTATTATTGATTGTTTAT
1 ATTATTATTGATTGTTTAT
19935 ATTATTATTGATTGTTTAT
1 ATTATTATTGATTGTTTAT
19954 ATT
1 ATT
19957 TATCAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (19 bp):
ATTATTATTGATTGTTTAT
Found at i:20893 original size:130 final size:131
Alignment explanation
Indices: 20480--21038 Score: 696
Period size: 131 Copynumber: 4.3 Consensus size: 131
20470 AGGATGGTGA
* * * * *
20480 TGTAAATATACCATCAAAATCACTTAGAAAAC-ATTTTTTTAAAATTGTTACCAATAGTGTATGA
1 TGTAAA-ATACCATCAAAATCACTTAGACAACGA-CTTTATAAAATTGTTACGAATAGTTTATGA
* * * * * * *
20544 TTTCGCAACAACTTAAGAAGTTGTTGTTAGGAATACTGTAAACATTGGCAACTACTAAAAAAATG
64 TTTCACAACAACTTAAGAATTTGTTGTTACGAAAACTATAAACATTGGCAACAACTAAAAAAGTG
20609 TTG
129 TTG
* * *** *
20612 TGTAAAATACCATCAGAATCACTTAGGCAACTTTTTTATAAAGTTGTTACGAATAGTTTATGATT
1 TGTAAAATACCATCAAAATCACTTAGACAACGACTTTATAAAATTGTTACGAATAGTTTATGATT
* * * * *
20677 TCACAACAACTTAAGAATTTGTTGTTACGAATATTGTAAACATCGTCAACAACTAAAAAAGTGTT
66 TCACAACAACTTAAGAATTTGTTGTTACGAAAACTATAAACATTGGCAACAACTAAAAAAGTGTT
20742 G
131 G
20743 TGTAAAATACCATCAAAATCACTTAGACAACGACTTTATAAAATTGTTACGAATA-TATTATGAT
1 TGTAAAATACCATCAAAATCACTTAGACAACGACTTTATAAAATTGTTACGAATAGT-TTATGAT
* * ** * *
20807 TTCACAACGACTT-TGTTTTTGTTGTTACGAAAACTATAAGCATTGGCAACGACTAAAAAAGTGT
65 TTCACAACAACTTAAGAATTTGTTGTTACGAAAACTATAAACATTGGCAACAACTAAAAAAGTGT
20871 TG
130 TG
*
20873 TGTAAAATACCATCAAAATCACTTAGGCAACGACTTTATAAAATTGTTACGAATA-TATTATGAT
1 TGTAAAATACCATCAAAATCACTTAGACAACGACTTTATAAAATTGTTACGAATAGT-TTATGAT
* * ** * *
20937 TTCACAACGACTT-TGTTTTTGTTGTTACGAAAACTATAAGCATTGGCAACAATTAAAAAAGTTG
65 TTCACAACAACTTAAGAATTTGTTGTTACGAAAACTATAAACATTGGCAACAACTAAAAAAG-TG
21001 TTG
129 TTG
* *
21004 GGTAAAATACCATCAAAATCACTAAGACAACGACT
1 TGTAAAATACCATCAAAATCACTTAGACAACGACT
21039 ATTAATTATT
Statistics
Matches: 385, Mismatches: 39, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
130 166 0.43
131 213 0.55
132 6 0.02
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (131 bp):
TGTAAAATACCATCAAAATCACTTAGACAACGACTTTATAAAATTGTTACGAATAGTTTATGATT
TCACAACAACTTAAGAATTTGTTGTTACGAAAACTATAAACATTGGCAACAACTAAAAAAGTGTT
G
Found at i:21011 original size:261 final size:262
Alignment explanation
Indices: 20481--21038 Score: 721
Period size: 261 Copynumber: 2.1 Consensus size: 262
20471 GGATGGTGAT
* * *
20481 GTAAATATACCATCAAAATCACTTAGAAAAC-ATTTTTTTAAAATTGTTACCAATAGTGTATGAT
1 GTAAA-ATACCATCAAAATCACTTAGACAACGA-CTTTATAAAATTGTTACCAATAGTGTATGAT
* * * * *
20545 TTCGCAACAACTTAAGAAGTTGTTGTTAGGAATACTGTAAACATTGGCAACTACTAAAAAAATGT
64 TTCACAACAACTTAAGAAGTTGTTGTTACGAAAACTATAAACATTGGCAACGACTAAAAAAATGT
* *** *
20610 TGTGTAAAATACCATCAGAATCACTTAGGCAACTTTTTTATAAAGTTGTTACGAATAGTTTATGA
129 TGTGTAAAATACCATCAAAATCACTTAGGCAACGACTTTATAAAATTGTTACGAATAGTTTATGA
* * * *
20675 TTTCACAACAACTTAAGAATTTGTTGTTACGAATATTGTAAACATCGTCAACAACTAAAAAAGTG
194 TTTCACAACAACTTAAGAATTTGTTGTTACGAAAACTATAAACATCGGCAACAACTAAAAAAGTG
*
20740 TTGT
259 TTGG
* *
20744 GTAAAATACCATCAAAATCACTTAGACAACGACTTTATAAAATTGTTACGAATA-TATTATGATT
1 GTAAAATACCATCAAAATCACTTAGACAACGACTTTATAAAATTGTTACCAATAGT-GTATGATT
* * *** * *
20808 TCACAACGACTT-TGTTTTTGTTGTTACGAAAACTATAAGCATTGGCAACGACTAAAAAAGTGTT
65 TCACAACAACTTAAGAAGTTGTTGTTACGAAAACTATAAACATTGGCAACGACTAAAAAAATGTT
20872 GTGTAAAATACCATCAAAATCACTTAGGCAACGACTTTATAAAATTGTTACGAATA-TATTATGA
130 GTGTAAAATACCATCAAAATCACTTAGGCAACGACTTTATAAAATTGTTACGAATAGT-TTATGA
* * ** * * *
20936 TTTCACAACGACTT-TGTTTTTGTTGTTACGAAAACTATAAGCATTGGCAACAATTAAAAAAGTT
194 TTTCACAACAACTTAAGAATTTGTTGTTACGAAAACTATAAACATCGGCAACAACTAAAAAAG-T
21000 GTTGG
258 GTTGG
*
21005 GTAAAATACCATCAAAATCACTAAGACAACGACT
1 GTAAAATACCATCAAAATCACTTAGACAACGACT
21039 ATTAATTATT
Statistics
Matches: 256, Mismatches: 35, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
260 39 0.15
261 151 0.59
262 60 0.23
263 6 0.02
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (262 bp):
GTAAAATACCATCAAAATCACTTAGACAACGACTTTATAAAATTGTTACCAATAGTGTATGATTT
CACAACAACTTAAGAAGTTGTTGTTACGAAAACTATAAACATTGGCAACGACTAAAAAAATGTTG
TGTAAAATACCATCAAAATCACTTAGGCAACGACTTTATAAAATTGTTACGAATAGTTTATGATT
TCACAACAACTTAAGAATTTGTTGTTACGAAAACTATAAACATCGGCAACAACTAAAAAAGTGTT
GG
Done.