Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015303.1 Corchorus capsularis cultivar CVL-1 contig15324, 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: 24451
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3786 original size:16 final size:16
Alignment explanation
Indices: 3762--3817 Score: 71
Period size: 16 Copynumber: 3.6 Consensus size: 16
3752 GACAGTTTCC
3762 TCGGGTCATTCGGGTT
1 TCGGGTCATTCGGGTT
*
3778 TCAGGTCA-TCTGGG-T
1 TCGGGTCATTC-GGGTT
*
3793 TCGGGTTATTCGGGTT
1 TCGGGTCATTCGGGTT
3809 TCGGGTCAT
1 TCGGGTCAT
3818 CCGAGCTCAG
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 12 0.36
16 21 0.64
ACGTcount: A:0.09, C:0.18, G:0.36, T:0.38
Consensus pattern (16 bp):
TCGGGTCATTCGGGTT
Found at i:4137 original size:42 final size:42
Alignment explanation
Indices: 4077--4158 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
4067 TAGATATTAA
* *
4077 TTTTGAATATTAAGTACATAATTGATTATCAGGTGAGGTAGG
1 TTTTGAATATTAAATACATAATTAATTATCAGGTGAGGTAGG
* *
4119 TTTTGAATATTAAATACATAATTAATTATTAGGTGGGGTA
1 TTTTGAATATTAAATACATAATTAATTATCAGGTGAGGTA
4159 TGTGTCAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.35, C:0.04, G:0.21, T:0.40
Consensus pattern (42 bp):
TTTTGAATATTAAATACATAATTAATTATCAGGTGAGGTAGG
Found at i:5369 original size:16 final size:16
Alignment explanation
Indices: 5350--5401 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
5340 CAGATCACTC
5350 GGGTTACGGGTCATTT
1 GGGTTACGGGTCATTT
** * *
5366 GGGTTTTGGGTCGTCT
1 GGGTTACGGGTCATTT
5382 GGGTTACGGGTCATTT
1 GGGTTACGGGTCATTT
5398 GGGT
1 GGGT
5402 CTCGGGGGCG
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.08, C:0.12, G:0.42, T:0.38
Consensus pattern (16 bp):
GGGTTACGGGTCATTT
Found at i:5407 original size:16 final size:15
Alignment explanation
Indices: 5350--5407 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 15
5340 CAGATCACTC
5350 GGGTTACGGGTCATTT
1 GGGTT-CGGGTCATTT
* * *
5366 GGGTTTTGGGTCGTCT
1 GGG-TTCGGGTCATTT
5382 GGGTTACGGGTCATTT
1 GGGTT-CGGGTCATTT
5398 GGGTCTCGGG
1 GGGT-TCGGG
5408 GGCGGATTCG
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
15 2 0.06
16 28 0.85
17 3 0.09
ACGTcount: A:0.07, C:0.14, G:0.43, T:0.36
Consensus pattern (15 bp):
GGGTTCGGGTCATTT
Found at i:7690 original size:31 final size:31
Alignment explanation
Indices: 7645--7785 Score: 167
Period size: 31 Copynumber: 4.5 Consensus size: 31
7635 ACGGTATCCG
7645 ACGTGGCATGCCACGTGTATCC-AAAAGTGAC
1 ACGTGGCATGCCACGTGTA-CCAAAAAGTGAC
* **
7676 ATGTGGCACACCACGTGTACCAAAAAGTGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
* * *
7707 ACATGTCATGCCACATGTACCAAAAAGTGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
* ** *
7738 ACGTGGCATGCCACATGTTTCAAAATGTGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
*
7769 ATGTGGCATGCCACGTG
1 ACGTGGCATGCCACGTG
7786 CACAAAAGGA
Statistics
Matches: 93, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
30 2 0.02
31 91 0.98
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.21
Consensus pattern (31 bp):
ACGTGGCATGCCACGTGTACCAAAAAGTGAC
Found at i:8288 original size:15 final size:15
Alignment explanation
Indices: 8229--8291 Score: 72
Period size: 16 Copynumber: 4.1 Consensus size: 15
8219 AACCCTCTTG
*
8229 AACCTGAACCCGAAAA
1 AACCCGAACCCG-AAA
8245 AACCCGAACCCGAAA
1 AACCCGAACCCGAAA
* *
8260 AAGCTCAAACCCGAAA
1 AA-CCCGAACCCGAAA
*
8276 AACCCGAATCCGAAA
1 AACCCGAACCCGAAA
8291 A
1 A
8292 TTTATGAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
15 16 0.40
16 24 0.60
ACGTcount: A:0.49, C:0.33, G:0.13, T:0.05
Consensus pattern (15 bp):
AACCCGAACCCGAAA
Found at i:8460 original size:16 final size:16
Alignment explanation
Indices: 8439--8527 Score: 110
Period size: 16 Copynumber: 5.6 Consensus size: 16
8429 ACCCAAACAG
8439 AACCTGAACCCGAATT
1 AACCTGAACCCGAATT
*
8455 AACCTG-ACCCAAATT
1 AACCTGAACCCGAATT
*
8470 CAACCCGAACCCGAATT
1 -AACCTGAACCCGAATT
*
8487 AACCTG-ACCCAAATT
1 AACCTGAACCCGAATT
*
8502 AACCCGAACCCGAATT
1 AACCTGAACCCGAATT
*
8518 AACATGAACC
1 AACCTGAACC
8528 AAATCCAACC
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
15 21 0.34
16 32 0.52
17 8 0.13
ACGTcount: A:0.39, C:0.35, G:0.10, T:0.16
Consensus pattern (16 bp):
AACCTGAACCCGAATT
Found at i:8465 original size:32 final size:31
Alignment explanation
Indices: 8439--8546 Score: 162
Period size: 32 Copynumber: 3.4 Consensus size: 31
8429 ACCCAAACAG
*
8439 AACCTGAACCCGAATTAACCTGACCCAAATTC
1 AACCCGAACCCGAATTAACCTGACCCAAA-TC
*
8471 AACCCGAACCCGAATTAACCTGACCCAAATT
1 AACCCGAACCCGAATTAACCTGACCCAAATC
* *
8502 AACCCGAACCCGAATTAACATGAACCAAATCC
1 AACCCGAACCCGAATTAACCTGACCCAAAT-C
8534 AACCCGAACCCGA
1 AACCCGAACCCGA
8547 CTCAAACCCG
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
31 29 0.41
32 41 0.59
ACGTcount: A:0.40, C:0.36, G:0.10, T:0.14
Consensus pattern (31 bp):
AACCCGAACCCGAATTAACCTGACCCAAATC
Found at i:8543 original size:6 final size:6
Alignment explanation
Indices: 8534--8585 Score: 54
Period size: 6 Copynumber: 8.7 Consensus size: 6
8524 AACCAAATCC
* *
8534 AACCCG AACCCG -ACTCA AACCCG AACCCG ATAACCCG AACCCG AACCC-
1 AACCCG AACCCG AACCCG AACCCG AACCCG --AACCCG AACCCG AACCCG
8582 AACC
1 AACC
8586 TGACCCGCCC
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
5 7 0.18
6 26 0.67
8 6 0.15
ACGTcount: A:0.37, C:0.48, G:0.12, T:0.04
Consensus pattern (6 bp):
AACCCG
Found at i:8568 original size:63 final size:63
Alignment explanation
Indices: 8439--8578 Score: 176
Period size: 63 Copynumber: 2.2 Consensus size: 63
8429 ACCCAAACAG
* * * * * *
8439 AACCTGAACCCGAATTAACCTGACCCAAATTCAACCCGAACCCGAATTAACCTGACCCAAATT
1 AACCCGAACCCGAATTAACATGAACCAAATCCAACCCGAACCCGAATAAACCCGACCCAAATT
* *
8502 AACCCGAACCCGAATTAACATGAACCAAATCCAACCCGAACCCGACTCAAACCCGAACCC-GA-T
1 AACCCGAACCCGAATTAACATGAACCAAATCCAACCCGAACCCGAAT-AAACCCG-ACCCAAATT
8565 AACCCGAACCCGAA
1 AACCCGAACCCGAA
8579 CCCAACCTGA
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
63 57 0.85
64 6 0.09
65 4 0.06
ACGTcount: A:0.39, C:0.38, G:0.11, T:0.12
Consensus pattern (63 bp):
AACCCGAACCCGAATTAACATGAACCAAATCCAACCCGAACCCGAATAAACCCGACCCAAATT
Found at i:10934 original size:26 final size:25
Alignment explanation
Indices: 10900--10948 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
10890 TTAATGTGTA
*
10900 AATTTTATTT-TTTATTAAAAAATTT
1 AATTTTATTTAATTA-TAAAAAATTT
10925 AATTATTATTTAATTATAAAAAAT
1 AATT-TTATTTAATTATAAAAAAT
10949 ATATATGGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 4 0.19
26 14 0.67
27 3 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
AATTTTATTTAATTATAAAAAATTT
Found at i:11148 original size:24 final size:25
Alignment explanation
Indices: 11116--11167 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 25
11106 TACCTTGTCC
11116 TTTCTCTTTTTTT-TTAAATTTTCCT
1 TTTCTCTTTTTTTCTT-AATTTTCCT
*
11141 TTTC-CTTTTTTTCTTATTTTTCCT
1 TTTCTCTTTTTTTCTTAATTTTCCT
11165 TTT
1 TTT
11168 TTTATTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (25 bp):
TTTCTCTTTTTTTCTTAATTTTCCT
Found at i:11152 original size:9 final size:9
Alignment explanation
Indices: 11140--11207 Score: 61
Period size: 9 Copynumber: 7.7 Consensus size: 9
11130 TAAATTTTCC
11140 TTTTCCTTT
1 TTTTCCTTT
11149 TTTT-CTTAT
1 TTTTCCTT-T
11158 TTTTCCTTT
1 TTTTCCTTT
*
11167 TTTT-ATTT
1 TTTTCCTTT
*
11175 TTTTCCCTTC
1 TTTT-CCTTT
**
11185 TCAT-CTTT
1 TTTTCCTTT
11193 TTTTCCTTT
1 TTTTCCTTT
11202 TTTTCC
1 TTTTCC
11208 CATATATGTT
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
8 15 0.33
9 24 0.52
10 7 0.15
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTTCCTTT
Found at i:11161 original size:18 final size:17
Alignment explanation
Indices: 11140--11206 Score: 80
Period size: 18 Copynumber: 3.8 Consensus size: 17
11130 TAAATTTTCC
11140 TTTTCCTTTTTTTCTTAT
1 TTTTCCTTTTTTTCTT-T
*
11158 TTTTCCTTTTTTTATTT
1 TTTTCCTTTTTTTCTTT
* **
11175 TTTTCCCTTCTCATCTTT
1 TTTT-CCTTTTTTTCTTT
11193 TTTTCCTTTTTTTC
1 TTTTCCTTTTTTTC
11207 CCATATATGT
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
17 12 0.30
18 28 0.70
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTCCTTTTTTTCTTT
Found at i:13950 original size:2 final size:2
Alignment explanation
Indices: 13943--13969 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13933 ATTAAGCCTC
13943 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
13970 GGTAATGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15938 original size:78 final size:78
Alignment explanation
Indices: 15850--16000 Score: 248
Period size: 78 Copynumber: 1.9 Consensus size: 78
15840 GTTTTTTAAT
* * *
15850 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTATATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTATATTTAATTAAATAAAAATAGA
15915 GTTATTAGTTGAG
66 GTTATTAGTTGAG
* *
15928 TAAAATAGTAAAATGGTAAAATAAAATATTTATAAAGATATTATTTTTAATTAAATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTATATTTAATTAAATAAAAATAGA
*
15993 GTTTTTAG
66 GTTATTAG
16001 GTAAAATAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
78 67 1.00
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (78 bp):
TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTATATTTAATTAAATAAAAATAGA
GTTATTAGTTGAG
Found at i:16010 original size:58 final size:58
Alignment explanation
Indices: 15942--16058 Score: 207
Period size: 58 Copynumber: 2.0 Consensus size: 58
15932 ATAGTAAAAT
* *
15942 GGTAAAATAAAATATTTATAAAGATATTATTTTTAATTAAATAAAAATAGAGTTTTTA
1 GGTAAAATAAAATAGTTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTTA
*
16000 GGTAAAATAAAGTAGTTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTTA
1 GGTAAAATAAAATAGTTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTTA
16058 G
1 G
16059 TTAAGTAAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (58 bp):
GGTAAAATAAAATAGTTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTTA
Found at i:16443 original size:11 final size:11
Alignment explanation
Indices: 16429--16459 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
16419 AATCTACTTA
16429 AATCTTCAGAT
1 AATCTTCAGAT
*
16440 AATCTACAGAT
1 AATCTTCAGAT
16451 AATCTTCAG
1 AATCTTCAG
16460 TTGAAATCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (11 bp):
AATCTTCAGAT
Found at i:16490 original size:13 final size:13
Alignment explanation
Indices: 16452--16491 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
16442 TCTACAGATA
* *
16452 ATCTTCAGTTGAA
1 ATCTTCTGTTGAT
*
16465 ATCTTCTGATGAT
1 ATCTTCTGTTGAT
16478 ATCTTCTGTTGAT
1 ATCTTCTGTTGAT
16491 A
1 A
16492 ATATTCTCTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (13 bp):
ATCTTCTGTTGAT
Done.