Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010511.1 Corchorus capsularis cultivar CVL-1 contig10532, 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: 148180
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:12801 original size:3 final size:3
Alignment explanation
Indices: 12795--12820 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
12785 GCCTCTTCTT
12795 CTC CTC CTC CTC CTC CTC CTC CTC CT
1 CTC CTC CTC CTC CTC CTC CTC CTC CT
12821 TTCTAGCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (3 bp):
CTC
Found at i:17294 original size:13 final size:14
Alignment explanation
Indices: 17276--17305 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
17266 GTCTAGAAGG
17276 AAAAAAAAAA-GAA
1 AAAAAAAAAAGGAA
17289 AAAAAAAAAAGGAA
1 AAAAAAAAAAGGAA
17303 AAA
1 AAA
17306 GTAACATGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAGGAA
Found at i:17295 original size:14 final size:14
Alignment explanation
Indices: 17276--17305 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
17266 GTCTAGAAGG
17276 AAAAAAAAAAGAAA
1 AAAAAAAAAAGAAA
*
17290 AAAAAAAAAGGAAA
1 AAAAAAAAAAGAAA
17304 AA
1 AA
17306 GTAACATGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAGAAA
Found at i:17304 original size:12 final size:12
Alignment explanation
Indices: 17272--17305 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
17262 CCTGGTCTAG
17272 AAGGAAAAAAAA
1 AAGGAAAAAAAA
*
17284 AAGAAAAAAAAAA
1 AAG-GAAAAAAAA
17297 AAGGAAAAA
1 AAGGAAAAA
17306 GTAACATGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAGGAAAAAAAA
Found at i:24659 original size:1 final size:1
Alignment explanation
Indices: 24655--24679 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
24645 GAAAAATGTG
24655 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
24680 CCTAGCTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:26101 original size:64 final size:64
Alignment explanation
Indices: 25999--26127 Score: 231
Period size: 64 Copynumber: 2.0 Consensus size: 64
25989 TTATAGTGCA
* *
25999 ACCATTTTGGATAACAATGCCAAGAATTTGTCTTTCAGACAAAACCAAGGAAGAAAGACGATAT
1 ACCATCTTGGATAACAATGCCAAGAATTTGTCTCTCAGACAAAACCAAGGAAGAAAGACGATAT
*
26063 ACCATCTTGGATAACAATGCCAAGAATTTGTCTCTCAGACAAAACCAAGGAAGAAAGGCGATAT
1 ACCATCTTGGATAACAATGCCAAGAATTTGTCTCTCAGACAAAACCAAGGAAGAAAGACGATAT
26127 A
1 A
26128 TGCATATTAT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.22
Consensus pattern (64 bp):
ACCATCTTGGATAACAATGCCAAGAATTTGTCTCTCAGACAAAACCAAGGAAGAAAGACGATAT
Found at i:29435 original size:21 final size:23
Alignment explanation
Indices: 29401--29444 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
29391 TTGATCGATC
*
29401 TAAAGAATCTAAA-CAAGAAAAA
1 TAAAGAATCTAAACCAACAAAAA
*
29423 TAAAGGAT-TAAACCAACAAAAA
1 TAAAGAATCTAAACCAACAAAAA
29445 CAGGAGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.66, C:0.11, G:0.09, T:0.14
Consensus pattern (23 bp):
TAAAGAATCTAAACCAACAAAAA
Found at i:42575 original size:16 final size:16
Alignment explanation
Indices: 42554--42584 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
42544 TTTCCCCCTT
42554 AATTTCCTAAGGTCAA
1 AATTTCCTAAGGTCAA
42570 AATTTCCTAAGGTCA
1 AATTTCCTAAGGTCA
42585 GGGACACTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (16 bp):
AATTTCCTAAGGTCAA
Found at i:50317 original size:2 final size:2
Alignment explanation
Indices: 50310--50338 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
50300 GGGTGGGTAC
50310 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
50339 CAACAACATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:51142 original size:7 final size:7
Alignment explanation
Indices: 51132--51165 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
51122 TCCCTTCATT
51132 TTGAAAG
1 TTGAAAG
51139 TTGAAAG
1 TTGAAAG
51146 TTGAAAG
1 TTGAAAG
51153 TTGAAAG
1 TTGAAAG
51160 TTGAAA
1 TTGAAA
51166 CCCCCTTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.44, C:0.00, G:0.26, T:0.29
Consensus pattern (7 bp):
TTGAAAG
Found at i:52524 original size:13 final size:13
Alignment explanation
Indices: 52508--52532 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52498 GGCCTCTTTC
52508 TTTTTATTTTTGT
1 TTTTTATTTTTGT
52521 TTTTTATTTTTG
1 TTTTTATTTTTG
52533 CCTATAATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.84
Consensus pattern (13 bp):
TTTTTATTTTTGT
Found at i:55609 original size:29 final size:30
Alignment explanation
Indices: 55563--55620 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
55553 TTGAGGGGGC
55563 AAAATGTCACAAAATTGAAATTCAGGGGAT
1 AAAATGTCACAAAATTGAAATTCAGGGGAT
* * *
55593 AAAATGTC-CAAGATTGAAGTTCATGGGA
1 AAAATGTCACAAAATTGAAATTCAGGGGA
55621 CAACACGTCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.43, C:0.10, G:0.22, T:0.24
Consensus pattern (30 bp):
AAAATGTCACAAAATTGAAATTCAGGGGAT
Found at i:61426 original size:7 final size:7
Alignment explanation
Indices: 61414--61438 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
61404 TTGTTAACTT
61414 CGGTTAG
1 CGGTTAG
61421 CGGTTAG
1 CGGTTAG
61428 CGGTTAG
1 CGGTTAG
61435 CGGT
1 CGGT
61439 GGTACTTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.16, G:0.44, T:0.28
Consensus pattern (7 bp):
CGGTTAG
Found at i:66999 original size:2 final size:2
Alignment explanation
Indices: 66992--67026 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
66982 TTTCTCCTTA
66992 AT AT AT 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 AT AT AT A
67027 GATGCCAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:85178 original size:11 final size:11
Alignment explanation
Indices: 85164--85201 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
85154 ATTCATAACA
85164 AATTTATAATT
1 AATTTATAATT
85175 AATTTATAATT
1 AATTTATAATT
85186 -ATTTGATAATT
1 AATTT-ATAATT
*
85197 TATTT
1 AATTT
85202 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:101511 original size:21 final size:21
Alignment explanation
Indices: 101482--101521 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
101472 GGGAAAGTAC
101482 ATGAATTGT-TTGTGTATGAAT
1 ATGAATTGTATT-TGTATGAAT
*
101503 ATGATTTGTATTTGTATGA
1 ATGAATTGTATTTGTATGA
101522 TCCAAAGCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.28, C:0.00, G:0.23, T:0.50
Consensus pattern (21 bp):
ATGAATTGTATTTGTATGAAT
Found at i:102443 original size:13 final size:13
Alignment explanation
Indices: 102425--102449 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
102415 TTCTTCCTTT
102425 CTCTCTCTCTCTC
1 CTCTCTCTCTCTC
102438 CTCTCTCTCTCT
1 CTCTCTCTCTCT
102450 GTTTTTTTGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (13 bp):
CTCTCTCTCTCTC
Found at i:112565 original size:56 final size:56
Alignment explanation
Indices: 112479--112589 Score: 195
Period size: 56 Copynumber: 2.0 Consensus size: 56
112469 AGTCCACAAC
112479 TAACAATAGAAAGGTTAAATGAACAAACTTTCAAACCCTGCAGTTCTAGAATGAAT
1 TAACAATAGAAAGGTTAAATGAACAAACTTTCAAACCCTGCAGTTCTAGAATGAAT
* * *
112535 TAACAATAGAAAGGTTACATGAGCAAACTTTCCAACCCTGCAGTTCTAGAATGAA
1 TAACAATAGAAAGGTTAAATGAACAAACTTTCAAACCCTGCAGTTCTAGAATGAA
112590 ATGCCAAATG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.24
Consensus pattern (56 bp):
TAACAATAGAAAGGTTAAATGAACAAACTTTCAAACCCTGCAGTTCTAGAATGAAT
Found at i:115613 original size:31 final size:32
Alignment explanation
Indices: 115565--115625 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
115555 TTTTAAGAGA
* *
115565 ATATATTTACTATATTTATTTATTAAAAAATT
1 ATATATGTACTATATTTAATTATTAAAAAATT
*
115597 ATATATGTAC-ATATTTAATTATTAGAAAA
1 ATATATGTACTATATTTAATTATTAAAAAA
115626 CTCAAATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 17 0.65
32 9 0.35
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (32 bp):
ATATATGTACTATATTTAATTATTAAAAAATT
Found at i:117335 original size:32 final size:32
Alignment explanation
Indices: 117288--117370 Score: 96
Period size: 32 Copynumber: 2.6 Consensus size: 32
117278 AACTCATTCA
* * *
117288 TAATGAGTTGCAAATTTGTCTTTATTAATAAT
1 TAATCAGTTGTAAATTTGTCTTCATTAATAAT
* **
117320 TAAT-ATGTTGTAAATTTGGCTTCATTCTTAAT
1 TAATCA-GTTGTAAATTTGTCTTCATTAATAAT
117352 TAATCAGTTGTAAATTTGT
1 TAATCAGTTGTAAATTTGT
117371 GTTAAAGCAA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
31 1 0.02
32 41 0.95
33 1 0.02
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.48
Consensus pattern (32 bp):
TAATCAGTTGTAAATTTGTCTTCATTAATAAT
Found at i:118832 original size:32 final size:32
Alignment explanation
Indices: 118795--118866 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 32
118785 AATGAATTGC
118795 AAATTTGTCTCTATTCATAATTAATACGTTGT
1 AAATTTGTCTCTATTCATAATTAATACGTTGT
* * *
118827 AAATTTGACTTTATTCTTAATTAATACGTTGT
1 AAATTTGTCTCTATTCATAATTAATACGTTGT
118859 AAATTTGT
1 AAATTTGT
118867 GTTGAAATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.49
Consensus pattern (32 bp):
AAATTTGTCTCTATTCATAATTAATACGTTGT
Found at i:134294 original size:13 final size:13
Alignment explanation
Indices: 134271--134301 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
134261 TAAACACAGG
134271 TATCG-ACGGATA
1 TATCGAACGGATA
134283 TATCGAACGGATA
1 TATCGAACGGATA
134296 TATCGA
1 TATCGA
134302 GGTATCGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (13 bp):
TATCGAACGGATA
Found at i:134477 original size:10 final size:9
Alignment explanation
Indices: 134461--134485 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
134451 ATATGTAGAC
134461 ATTTTTTTT
1 ATTTTTTTT
134470 ATTTTTTTT
1 ATTTTTTTT
134479 ATTTTTT
1 ATTTTTT
134486 GTACTGCGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:135317 original size:10 final size:10
Alignment explanation
Indices: 135302--135337 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
135292 AATTTAATAT
135302 GGATATTTAC
1 GGATATTTAC
*
135312 GGATATTTAT
1 GGATATTTAC
135322 GGATATTTAC
1 GGATATTTAC
135332 GGATAT
1 GGATAT
135338 ATCGAGATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.31, C:0.06, G:0.22, T:0.42
Consensus pattern (10 bp):
GGATATTTAC
Found at i:135324 original size:20 final size:20
Alignment explanation
Indices: 135299--135337 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
135289 TTTAATTTAA
135299 TATGGATATTTACGGATATT
1 TATGGATATTTACGGATATT
135319 TATGGATATTTACGGATAT
1 TATGGATATTTACGGATAT
135338 ATCGAGATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.44
Consensus pattern (20 bp):
TATGGATATTTACGGATATT
Found at i:135465 original size:12 final size:12
Alignment explanation
Indices: 135448--135486 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
135438 GTACAGATAT
135448 CGGATATATCGA
1 CGGATATATCGA
135460 CGGATATATCGA
1 CGGATATATCGA
135472 -GG---TATCGA
1 CGGATATATCGA
135480 CGGATAT
1 CGGATAT
135487 TTAATTCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
8 6 0.26
9 2 0.09
11 2 0.09
12 13 0.57
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (12 bp):
CGGATATATCGA
Found at i:146537 original size:15 final size:15
Alignment explanation
Indices: 146517--146546 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
146507 GTTTCTGGCC
146517 AAAAAATAAAAAAAT
1 AAAAAATAAAAAAAT
*
146532 AAAAAATAAATAAAT
1 AAAAAATAAAAAAAT
146547 CATCCATTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAAAATAAAAAAAT
Found at i:147862 original size:2 final size:2
Alignment explanation
Indices: 147855--147893 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
147845 GATAATAGTA
147855 AT AT AT AT AT 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 AT AT AT AT AT A
147894 AAGCTAAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.