Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014953.1 Corchorus capsularis cultivar CVL-1 contig14974, 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: 13846
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.28
Found at i:438 original size:23 final size:23
Alignment explanation
Indices: 412--463 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
402 CTAAATGGAG
412 ATGCAACAATACCAAATTACTAA
1 ATGCAACAATACCAAATTACTAA
** *
435 ATGCAGTAATACCAAGTTACTAA
1 ATGCAACAATACCAAATTACTAA
458 ATGCAA
1 ATGCAA
464 ATATGCAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.48, C:0.19, G:0.10, T:0.23
Consensus pattern (23 bp):
ATGCAACAATACCAAATTACTAA
Found at i:607 original size:27 final size:26
Alignment explanation
Indices: 571--663 Score: 114
Period size: 27 Copynumber: 3.5 Consensus size: 26
561 AAACCCAAAG
* *
571 AATGACCAAAATGCCCCTGAGTGTCAA
1 AATGACCAAAATACCCCTGAATG-CAA
*
598 AATGACCAAAATACCCCTGAATGCCAG
1 AATGACCAAAATACCCCTGAATG-CAA
*
625 AATGACCAAAATACCCCTAAATGCAA
1 AATGACCAAAATACCCCTGAATGCAA
*
651 AGAAGACCAAAAT
1 A-ATGACCAAAAT
664 GCTAATTCGA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
26 3 0.05
27 55 0.95
ACGTcount: A:0.45, C:0.26, G:0.14, T:0.15
Consensus pattern (26 bp):
AATGACCAAAATACCCCTGAATGCAA
Found at i:964 original size:2 final size:2
Alignment explanation
Indices: 957--985 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
947 TGGAATAAAG
957 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
986 ACCTAGGCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2484 original size:41 final size:41
Alignment explanation
Indices: 2427--2602 Score: 201
Period size: 41 Copynumber: 4.1 Consensus size: 41
2417 CAGTAGTTAA
**
2427 CAGTTTTCGGTTGCTCACAAGGGGGGCATGCCAACAGTTTT
1 CAGTTTTCAATTGCTCACAAGGGGGGCATGCCAACAGTTTT
* **
2468 CAGTTTTCAATTGCTCACAAGGGGGGCATTCCAGTAGTTTTCAGTT
1 CAGTTTTCAATTGCTCACAAGGGGGGCATGCCAACAG--TT---TT
*
2514 CAGTAGTTTTCGATTGCTCACAA-GGGGGCATGCCAACAGTTTT
1 C---AGTTTTCAATTGCTCACAAGGGGGGCATGCCAACAGTTTT
* *
2557 CAGTTTTCAATTGCTCACAAGGGGGGCATTCCAGCAGTTTT
1 CAGTTTTCAATTGCTCACAAGGGGGGCATGCCAACAGTTTT
2598 CAGTT
1 CAGTT
2603 GCTCACGATG
Statistics
Matches: 114, Mismatches: 12, Indels: 18
0.79 0.08 0.12
Matches are distributed among these distances:
40 18 0.16
41 55 0.48
43 5 0.04
46 5 0.04
48 13 0.11
49 18 0.16
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.32
Consensus pattern (41 bp):
CAGTTTTCAATTGCTCACAAGGGGGGCATGCCAACAGTTTT
Found at i:2532 original size:49 final size:46
Alignment explanation
Indices: 2466--2602 Score: 169
Period size: 40 Copynumber: 3.0 Consensus size: 46
2456 GCCAACAGTT
*
2466 TTCAGTTTTCAATTGCTCACAAGGGGGGCATTCCAGTAGTTTTCAG
1 TTCAGTTTTCAATTGCTCACAAGGGGGGCATTCCAGCAGTTTTCAG
* * *
2512 TTCAGTAGTTTTCGATTGCTCACAA-GGGGGCATGCCAACAG--TT---
1 TTC---AGTTTTCAATTGCTCACAAGGGGGGCATTCCAGCAGTTTTCAG
2555 TTCAGTTTTCAATTGCTCACAAGGGGGGCATTCCAGCAGTTTTCAG
1 TTCAGTTTTCAATTGCTCACAAGGGGGGCATTCCAGCAGTTTTCAG
2601 TT
1 TT
2603 GCTCACGATG
Statistics
Matches: 75, Mismatches: 7, Indels: 18
0.75 0.07 0.18
Matches are distributed among these distances:
40 18 0.24
41 14 0.19
43 5 0.07
46 7 0.09
48 13 0.17
49 18 0.24
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (46 bp):
TTCAGTTTTCAATTGCTCACAAGGGGGGCATTCCAGCAGTTTTCAG
Found at i:2580 original size:89 final size:90
Alignment explanation
Indices: 2428--2602 Score: 325
Period size: 89 Copynumber: 2.0 Consensus size: 90
2418 AGTAGTTAAC
*
2428 AGTTTTCGGTTGCTCACAAGGGGGGCATGCCAACAGTTTTCAGTTTTCAATTGCTCACAAGGGGG
1 AGTTTTCGATTGCTCACAAGGGGGGCATGCCAACAGTTTTCAGTTTTCAATTGCTCACAAGGGGG
*
2493 GCATTCCAGTAGTTTTCAGTTCAGT
66 GCATTCCAGCAGTTTTCAGTTCAGT
2518 AGTTTTCGATTGCTCACAA-GGGGGCATGCCAACAGTTTTCAGTTTTCAATTGCTCACAAGGGGG
1 AGTTTTCGATTGCTCACAAGGGGGGCATGCCAACAGTTTTCAGTTTTCAATTGCTCACAAGGGGG
2582 GCATTCCAGCAGTTTTCAGTT
66 GCATTCCAGCAGTTTTCAGTT
2603 GCTCACGATG
Statistics
Matches: 83, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
89 65 0.78
90 18 0.22
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.32
Consensus pattern (90 bp):
AGTTTTCGATTGCTCACAAGGGGGGCATGCCAACAGTTTTCAGTTTTCAATTGCTCACAAGGGGG
GCATTCCAGCAGTTTTCAGTTCAGT
Found at i:9153 original size:35 final size:35
Alignment explanation
Indices: 9107--9190 Score: 159
Period size: 35 Copynumber: 2.4 Consensus size: 35
9097 TCACACAAAA
9107 AGAGGTGCTTGCTTTCCACCTAGGCTCAGTGTTGG
1 AGAGGTGCTTGCTTTCCACCTAGGCTCAGTGTTGG
*
9142 AGAGGTGCTTGCTTTCCACCTAGGCTTAGTGTTGG
1 AGAGGTGCTTGCTTTCCACCTAGGCTCAGTGTTGG
9177 AGAGGTGCTTGCTT
1 AGAGGTGCTTGCTT
9191 GGCTCCACGT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 48 1.00
ACGTcount: A:0.14, C:0.20, G:0.32, T:0.33
Consensus pattern (35 bp):
AGAGGTGCTTGCTTTCCACCTAGGCTCAGTGTTGG
Found at i:9612 original size:20 final size:21
Alignment explanation
Indices: 9571--9613 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
9561 AAGATAGCAC
*
9571 TAATTAGACATGGAAAATGGG
1 TAATTAGACATGGAAAAGGGG
9592 TAATTAGACAT-GAAAAGGGG
1 TAATTAGACATGGAAAAGGGG
9612 TA
1 TA
9614 CTTCCCTACT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.44, C:0.05, G:0.28, T:0.23
Consensus pattern (21 bp):
TAATTAGACATGGAAAAGGGG
Found at i:11702 original size:16 final size:16
Alignment explanation
Indices: 11681--11714 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
11671 GCTTATCTTT
11681 CAGAACTCGA-AGAGGA
1 CAGAACTC-ACAGAGGA
11697 CAGAACTCACAGAGGA
1 CAGAACTCACAGAGGA
11713 CA
1 CA
11715 AAACCAGGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 1 0.06
16 16 0.94
ACGTcount: A:0.44, C:0.24, G:0.26, T:0.06
Consensus pattern (16 bp):
CAGAACTCACAGAGGA
Found at i:11938 original size:32 final size:32
Alignment explanation
Indices: 11901--12001 Score: 112
Period size: 32 Copynumber: 3.2 Consensus size: 32
11891 CAAAACCCAG
*
11901 CCCGAACCCGAATTAACCTGAACCAAAATTGA
1 CCCGAACCCGAATTAACCTGAACCAAAATTAA
* * * *
11933 CCCGAACCCGAATCAATCTGACCCAAATTTAA
1 CCCGAACCCGAATTAACCTGAACCAAAATTAA
* ** * *
11965 CCCGAACCTGAATTAATTTGACCCAAATTTAA
1 CCCGAACCCGAATTAACCTGAACCAAAATTAA
11997 CCCGA
1 CCCGA
12002 CCTGACTCAA
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 61 1.00
ACGTcount: A:0.38, C:0.32, G:0.11, T:0.20
Consensus pattern (32 bp):
CCCGAACCCGAATTAACCTGAACCAAAATTAA
Found at i:12023 original size:17 final size:17
Alignment explanation
Indices: 11997--12029 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
11987 CCAAATTTAA
11997 CCCGACCTG-ACTCAAG
1 CCCGACCTGAACTCAAG
12013 CCCGAACCTGAACTCAA
1 CCCG-ACCTGAACTCAA
12030 CCTGACTCGC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 5 0.33
18 6 0.40
ACGTcount: A:0.30, C:0.42, G:0.15, T:0.12
Consensus pattern (17 bp):
CCCGACCTGAACTCAAG
Found at i:13166 original size:27 final size:27
Alignment explanation
Indices: 13149--13215 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
13139 CCAAGGGTAC
13149 TTTGGTCATTTTTGCACCCAGGGGCAT
1 TTTGGTCATTTTTGCACCCAGGGGCAT
*
13176 TTTGGTCATTTTTGCACTCAGGGGCAT
1 TTTGGTCATTTTTGCACCCAGGGGCAT
*
13203 TTTAGTCATTTTT
1 TTTGGTCATTTTT
13216 TTAGTTCACC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.15, C:0.18, G:0.22, T:0.45
Consensus pattern (27 bp):
TTTGGTCATTTTTGCACCCAGGGGCAT
Done.