Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012022.1 Corchorus capsularis cultivar CVL-1 contig12043, 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: 34127
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Found at i:357 original size:20 final size:20
Alignment explanation
Indices: 334--371 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
324 TAGTCCAAGG
334 GGGGGCGGTGGTTAGTAAAA
1 GGGGGCGGTGGTTAGTAAAA
*
354 GGGGGCGGTGTTTAGTAA
1 GGGGGCGGTGGTTAGTAA
372 TCCAGTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.05, G:0.50, T:0.24
Consensus pattern (20 bp):
GGGGGCGGTGGTTAGTAAAA
Found at i:822 original size:18 final size:19
Alignment explanation
Indices: 782--827 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
772 CTGATGTGGC
782 AATGCCACGTCAGACCAAA
1 AATGCCACGTCAGACCAAA
**
801 AATGCCACGTTGGACC-AA
1 AATGCCACGTCAGACCAAA
819 AATGCCACG
1 AATGCCACG
828 GGGCAAGGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 11 0.44
19 14 0.56
ACGTcount: A:0.37, C:0.30, G:0.20, T:0.13
Consensus pattern (19 bp):
AATGCCACGTCAGACCAAA
Found at i:3599 original size:84 final size:84
Alignment explanation
Indices: 3502--3669 Score: 309
Period size: 84 Copynumber: 2.0 Consensus size: 84
3492 AGGATAAAAT
*
3502 GTCTAAAATTGATATATTAATTAAAAAGAATGAGAGAAATAATTAGGGGATTCTTGTCATTTAAT
1 GTCTAAAATTGATATATTAATTAAAAAGAAAGAGAGAAATAATTAGGGGATTCTTGTCATTTAAT
*
3567 GTTCAAAAACACTTTTAAA
66 GTCCAAAAACACTTTTAAA
*
3586 GTCTAAAATTGATATATTAATTAAAAAGAAAGAGAGAAATAATTAGGGGATTTTTGTCATTTAAT
1 GTCTAAAATTGATATATTAATTAAAAAGAAAGAGAGAAATAATTAGGGGATTCTTGTCATTTAAT
3651 GTCCAAAAACACTTTTAAA
66 GTCCAAAAACACTTTTAAA
3670 ACGCAAAAGC
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 81 1.00
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (84 bp):
GTCTAAAATTGATATATTAATTAAAAAGAAAGAGAGAAATAATTAGGGGATTCTTGTCATTTAAT
GTCCAAAAACACTTTTAAA
Found at i:6646 original size:30 final size:31
Alignment explanation
Indices: 6562--6648 Score: 81
Period size: 30 Copynumber: 2.9 Consensus size: 31
6552 TGTGTTTGGG
* * * *
6562 GACTTTAGTATAGATGCCTCTGTG-TTTAGG
1 GACTTTAATGTAGATGCCTCTGTGCTTGAGA
* *
6592 GACTTTAATGTAGGTACC-CTTGTGCTTGA-A
1 GACTTTAATGTAGATGCCTC-TGTGCTTGAGA
*
6622 GACTTTGATGTAGATGCCTCTGTGCTT
1 GACTTTAATGTAGATGCCTCTGTGCTT
6649 AGGGATGAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
29 1 0.02
30 40 0.89
31 4 0.09
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.39
Consensus pattern (31 bp):
GACTTTAATGTAGATGCCTCTGTGCTTGAGA
Found at i:6704 original size:53 final size:54
Alignment explanation
Indices: 6606--6736 Score: 144
Period size: 57 Copynumber: 2.4 Consensus size: 54
6596 TTAATGTAGG
* * *
6606 TACCCTTGTGCTTGAAGAC-TTTGATGTAGATGCCTCTGTGCTTAGGG-ATGAA
1 TACCCTTGTGTTTGAGGACTTTTGATGTAGATGCCTCTGTGCTTAGGGTATAAA
*
6658 TACCCTTGTGTTTGAGGACTTTTGA-G-AGAGGTGCCTCTGTGTTTAGGGACTTATAAA
1 TACCCTTGTGTTTGAGGACTTTTGATGTAGA--TGCCTCTGTGCTTAGGG---TATAAA
*
6715 TGCCCTTGTGTTTGAGGACTTT
1 TACCCTTGTGTTTGAGGACTTT
6737 AATTATTGGG
Statistics
Matches: 67, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
51 3 0.04
52 18 0.27
53 21 0.31
57 25 0.37
ACGTcount: A:0.19, C:0.16, G:0.27, T:0.37
Consensus pattern (54 bp):
TACCCTTGTGTTTGAGGACTTTTGATGTAGATGCCTCTGTGCTTAGGGTATAAA
Found at i:14871 original size:30 final size:30
Alignment explanation
Indices: 14835--14894 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
14825 TTAAATCGTG
14835 GAAGGGCATTACCGTGTAGTAGAAATTGCC
1 GAAGGGCATTACCGTGTAGTAGAAATTGCC
14865 GAAGGGCATTACCGTGTAGTAGAAATTGCC
1 GAAGGGCATTACCGTGTAGTAGAAATTGCC
14895 AATAGGTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (30 bp):
GAAGGGCATTACCGTGTAGTAGAAATTGCC
Found at i:19280 original size:30 final size:31
Alignment explanation
Indices: 19196--19282 Score: 81
Period size: 30 Copynumber: 2.9 Consensus size: 31
19186 TGTGTTTGGG
* * * *
19196 GACTTTAGTATAGATGCCTCTGTG-TTTAGG
1 GACTTTAATGTAGATGCCTCTGTGCTTGAGA
* *
19226 GACTTTAATGTAGGTACC-CTTGTGCTTGA-A
1 GACTTTAATGTAGATGCCTC-TGTGCTTGAGA
*
19256 GACTTTGATGTAGATGCCTCTGTGCTT
1 GACTTTAATGTAGATGCCTCTGTGCTT
19283 AGGGATGAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
29 1 0.02
30 40 0.89
31 4 0.09
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.39
Consensus pattern (31 bp):
GACTTTAATGTAGATGCCTCTGTGCTTGAGA
Found at i:19359 original size:26 final size:26
Alignment explanation
Indices: 19294--19427 Score: 96
Period size: 26 Copynumber: 4.7 Consensus size: 26
19284 GGGATGAATA
*
19294 CCCTTGTGTTTGAGGACTTTTGAGAGAGGTG
1 CCCTTGTGTTTGAGGACTTAT-A-A-A--TG
19325 -CCTCTGTGTTT-AGGGACTTATAAATG
1 CCCT-TGTGTTTGA-GGACTTATAAATG
19351 CCCTTGTGTTTGAGGACTTTGATATAGAATTG
1 CCCTTGTGTTTGAGGAC--T--TATA-AA-TG
19383 -CCTCTGTGTTT-AGGGACTTATAAATG
1 CCCT-TGTGTTTGA-GGACTTATAAATG
19409 CCCTTGTGTTTGAGGACTT
1 CCCTTGTGTTTGAGGACTT
19428 TAATTATTGG
Statistics
Matches: 88, Mismatches: 1, Indels: 33
0.72 0.01 0.27
Matches are distributed among these distances:
26 28 0.32
27 10 0.11
28 6 0.07
29 1 0.01
30 10 0.11
31 20 0.23
32 13 0.15
ACGTcount: A:0.19, C:0.15, G:0.27, T:0.39
Consensus pattern (26 bp):
CCCTTGTGTTTGAGGACTTATAAATG
Found at i:19400 original size:58 final size:55
Alignment explanation
Indices: 19186--19429 Score: 248
Period size: 58 Copynumber: 4.3 Consensus size: 55
19176 CTGTGTTATA
*
19186 TGTGTTTGGGGACTTTAGTATAGATGCCTCTGTGTTTAGGGACTT-TAATGTAGGTACCCT
1 TGTGTTTGAGGACTTTA-TATAGATGCCTCTGTGTTTAGGGACTTATAA---A--TACCCT
* * * * *
19246 TGTGCTTGAAGACTTTGATGTAGATGCCTCTGTGCTTAGGG----ATGAATACCCT
1 TGTGTTTGAGGACTTT-ATATAGATGCCTCTGTGTTTAGGGACTTATAAATACCCT
* *
19298 TGTGTTTGAGGACTTT-TGAGAGAGGTGCCTCTGTGTTTAGGGACTTATAAATGCCCT
1 TGTGTTTGAGGACTTTAT-ATAGA--TGCCTCTGTGTTTAGGGACTTATAAATACCCT
*
19355 TGTGTTTGAGGACTTTGATATAGAATTGCCTCTGTGTTTAGGGACTTATAAATGCCCT
1 TGTGTTTGAGGACTTT-ATATAG-A-TGCCTCTGTGTTTAGGGACTTATAAATACCCT
19413 TGTGTTTGAGGACTTTA
1 TGTGTTTGAGGACTTTA
19430 ATTATTGGGT
Statistics
Matches: 157, Mismatches: 15, Indels: 27
0.79 0.08 0.14
Matches are distributed among these distances:
50 1 0.01
51 3 0.02
52 20 0.13
53 16 0.10
54 1 0.01
57 28 0.18
58 51 0.32
59 2 0.01
60 34 0.22
61 1 0.01
ACGTcount: A:0.20, C:0.14, G:0.27, T:0.39
Consensus pattern (55 bp):
TGTGTTTGAGGACTTTATATAGATGCCTCTGTGTTTAGGGACTTATAAATACCCT
Found at i:20851 original size:54 final size:52
Alignment explanation
Indices: 20785--20942 Score: 192
Period size: 54 Copynumber: 2.9 Consensus size: 52
20775 AAAAAGCATT
* * *
20785 TCATTGTACATGCATGGTCCAACCCCAAAGTTTATTAGTCAAACCACAAAAACGA
1 TCATTGTACATGCATGGTCAAACCCCAAAATTTA-TA-TCAAACCACAAAAA-AA
*
20840 -CATTGTACATGCATGGTCAAACTCCAAAATTTGATAATCAAACCACAAAAAAA
1 TCATTGTACATGCATGGTCAAACCCCAAAATTT-AT-ATCAAACCACAAAAAAA
* *
20893 TCATTGTAGATGCATGGTCAAACCCCAAATTTTAATATGCAAACCACAAA
1 TCATTGTACATGCATGGTCAAACCCCAAAATTT-ATAT-CAAACCACAAA
20943 GTTTAATAGG
Statistics
Matches: 91, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
53 3 0.03
54 86 0.95
55 2 0.02
ACGTcount: A:0.42, C:0.23, G:0.11, T:0.24
Consensus pattern (52 bp):
TCATTGTACATGCATGGTCAAACCCCAAAATTTATATCAAACCACAAAAAAA
Found at i:20937 original size:21 final size:21
Alignment explanation
Indices: 20911--20950 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
20901 GATGCATGGT
* *
20911 CAAACCCCAAATTTTAATATG
1 CAAACCACAAAGTTTAATATG
20932 CAAACCACAAAGTTTAATA
1 CAAACCACAAAGTTTAATA
20951 GGATGAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.23, G:0.05, T:0.25
Consensus pattern (21 bp):
CAAACCACAAAGTTTAATATG
Found at i:21899 original size:12 final size:13
Alignment explanation
Indices: 21861--21901 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
21851 TAAAAACTAT
*
21861 TTTTATATATA-A
1 TTTTAAATATATA
21873 TTATTAAATATATA
1 TT-TTAAATATATA
21887 TTTTAAA-ATATA
1 TTTTAAATATATA
21899 TTT
1 TTT
21902 AATATACATC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 10 0.38
13 13 0.50
14 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTTAAATATATA
Found at i:22354 original size:17 final size:17
Alignment explanation
Indices: 22332--22367 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
22322 GTCATGCTAT
22332 CTGACACATCAAATCAA
1 CTGACACATCAAATCAA
22349 CTGACACATCAAATCAA
1 CTGACACATCAAATCAA
22366 CT
1 CT
22368 CTTAAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.31, G:0.06, T:0.19
Consensus pattern (17 bp):
CTGACACATCAAATCAA
Found at i:30043 original size:27 final size:26
Alignment explanation
Indices: 30009--30068 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
29999 TCTATATAAA
* *
30009 TTTAGTAATCTCACATTCTTAGAATT
1 TTTAGTAACCTCACATTCTTAGAAAT
* *
30035 TTTGAGTAACCTTATATTCTTAGAAAT
1 TTT-AGTAACCTCACATTCTTAGAAAT
30062 TTTAGTA
1 TTTAGTA
30069 TAGTAATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 7 0.24
27 22 0.76
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.47
Consensus pattern (26 bp):
TTTAGTAACCTCACATTCTTAGAAAT
Found at i:33234 original size:25 final size:25
Alignment explanation
Indices: 33200--33300 Score: 130
Period size: 25 Copynumber: 3.7 Consensus size: 25
33190 AATTTGCATA
33200 TAGCGGCGTCTAGACGCCACTATTT
1 TAGCGGCGTCTAGACGCCACTATTT
33225 TAGCGGCGTCTAGACGCCACTATTT
1 TAGCGGCGTCTAGACGCCACTATTT
33250 TAGCGGCGTCAGGACTTCAGGACGCCACTATTT
1 TAGCGGCGT-----C-T-A-GACGCCACTATTT
33283 TAGCGGCGTCTAGACGCC
1 TAGCGGCGTCTAGACGCC
33301 GCTACTTATG
Statistics
Matches: 68, Mismatches: 0, Indels: 16
0.81 0.00 0.19
Matches are distributed among these distances:
25 40 0.59
26 1 0.01
27 1 0.01
28 1 0.01
30 1 0.01
31 1 0.01
32 1 0.01
33 22 0.32
ACGTcount: A:0.20, C:0.29, G:0.27, T:0.25
Consensus pattern (25 bp):
TAGCGGCGTCTAGACGCCACTATTT
Found at i:33410 original size:32 final size:31
Alignment explanation
Indices: 33374--33444 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 31
33364 ACTATGGCGC
33374 GGCGTTTGGATATTTAGACGCCACTAAATA-AG
1 GGCGTTT-GATATTTAGACGCCACTAAA-AGAG
* * *
33406 GGCGTCTTGTTCTTTAGACGCCGCTAAAAGAG
1 GGCGT-TTGATATTTAGACGCCACTAAAAGAG
33438 GGCGTTT
1 GGCGTTT
33445 TCTTTTCATG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
31 3 0.09
32 29 0.85
33 2 0.06
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (31 bp):
GGCGTTTGATATTTAGACGCCACTAAAAGAG
Done.