Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010153.1 Corchorus capsularis cultivar CVL-1 contig10174, 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: 20066
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Found at i:364 original size:13 final size:12
Alignment explanation
Indices: 341--383 Score: 77
Period size: 12 Copynumber: 3.5 Consensus size: 12
331 TAAATACAGG
341 TATCGACGGATA
1 TATCGACGGATA
353 TATCGAACGGATA
1 TATCG-ACGGATA
366 TATCGACGGATA
1 TATCGACGGATA
378 TATCGA
1 TATCGA
384 GGTATCGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 18 0.60
13 12 0.40
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (12 bp):
TATCGACGGATA
Found at i:559 original size:10 final size:9
Alignment explanation
Indices: 543--567 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
533 ATATGTAGAC
543 ATTTTTTTT
1 ATTTTTTTT
552 ATTTTTTTT
1 ATTTTTTTT
561 ATTTTTT
1 ATTTTTT
568 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:1413 original size:10 final size:10
Alignment explanation
Indices: 1398--1433 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
1388 AATTTAATAT
1398 GGATATTTAC
1 GGATATTTAC
*
1408 GGATATTTAT
1 GGATATTTAC
1418 GGATATTTAC
1 GGATATTTAC
1428 GGATAT
1 GGATAT
1434 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:1420 original size:20 final size:20
Alignment explanation
Indices: 1395--1433 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1385 TTTAATTTAA
1395 TATGGATATTTACGGATATT
1 TATGGATATTTACGGATATT
1415 TATGGATATTTACGGATAT
1 TATGGATATTTACGGATAT
1434 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:1638 original size:34 final size:34
Alignment explanation
Indices: 1595--1660 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
1585 AATTCCATGA
* *
1595 TGGTAGGACAAGGTTCTA-GAGCTTGAGGAATAGG
1 TGGTAGGACAAGGCTCTAGGA-CTTGAGAAATAGG
1629 TGGTAGGACAAGGCTCTAGGACTTGAGAAATA
1 TGGTAGGACAAGGCTCTAGGACTTGAGAAATA
1661 AGTTTACTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 27 0.93
35 2 0.07
ACGTcount: A:0.32, C:0.11, G:0.35, T:0.23
Consensus pattern (34 bp):
TGGTAGGACAAGGCTCTAGGACTTGAGAAATAGG
Found at i:12394 original size:1 final size:1
Alignment explanation
Indices: 12388--12424 Score: 56
Period size: 1 Copynumber: 37.0 Consensus size: 1
12378 ACAATATTTC
**
12388 AAAAAAAAATTAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
12425 CCTTAAAGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.95, C:0.00, G:0.00, T:0.05
Consensus pattern (1 bp):
A
Found at i:13573 original size:9 final size:9
Alignment explanation
Indices: 13559--13592 Score: 68
Period size: 9 Copynumber: 3.8 Consensus size: 9
13549 TCTTCTTTTT
13559 TTTTTTTAA
1 TTTTTTTAA
13568 TTTTTTTAA
1 TTTTTTTAA
13577 TTTTTTTAA
1 TTTTTTTAA
13586 TTTTTTT
1 TTTTTTT
13593 TAATATTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:13573 original size:10 final size:10
Alignment explanation
Indices: 13558--13596 Score: 64
Period size: 9 Copynumber: 4.1 Consensus size: 10
13548 ATCTTCTTTT
13558 TTTTTTTTAA
1 TTTTTTTTAA
13568 -TTTTTTTAA
1 TTTTTTTTAA
13577 -TTTTTTTAA
1 TTTTTTTTAA
13586 TTTTTTTTAA
1 TTTTTTTTAA
13596 T
1 T
13597 ATTAATTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 18 0.64
10 10 0.36
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTTTTAA
Found at i:13677 original size:26 final size:26
Alignment explanation
Indices: 13648--13715 Score: 93
Period size: 26 Copynumber: 2.6 Consensus size: 26
13638 TACTTAGTTT
*
13648 ATTAGTTTATGTTTAATTAGTATCTA
1 ATTAGTTTATGTTTAATTAATATCTA
*
13674 ATTAGTTTAT-TATTAATTAATATTTA
1 ATTAGTTTATGT-TTAATTAATATCTA
*
13700 ATTAGTTTATGATTAA
1 ATTAGTTTATGTTTAA
13716 AATGAAGGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 1 0.03
26 36 0.97
ACGTcount: A:0.35, C:0.01, G:0.09, T:0.54
Consensus pattern (26 bp):
ATTAGTTTATGTTTAATTAATATCTA
Found at i:13763 original size:24 final size:25
Alignment explanation
Indices: 13724--13783 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 25
13714 AAAATGAAGG
*
13724 AAAATGAA-TTTGAAG-ATTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
13747 AAAATGAAGTTTGAAGAAGTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
* *
13772 GAAATTAAGTTT
1 AAAATGAAGTTT
13784 AGGGTTTGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 8 0.25
24 7 0.22
25 17 0.53
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (25 bp):
AAAATGAAGTTTGAAGAAGTTGTTA
Found at i:14427 original size:12 final size:11
Alignment explanation
Indices: 14404--14490 Score: 54
Period size: 11 Copynumber: 7.5 Consensus size: 11
14394 TCTTCCCCAA
14404 TTTCTTAATTT
1 TTTCTTAATTT
14415 TTTCTTAAGTTT
1 TTTCTTAA-TTT
14427 TTATACGTTGTATATTT
1 TT-T-C--T-TA-ATTT
*
14444 TTTCTTAAATT
1 TTTCTTAATTT
14455 TTTCTTAA-TT
1 TTTCTTAATTT
** *
14465 TCACCT--TTT
1 TTTCTTAATTT
14474 TTTCTTAATTT
1 TTTCTTAATTT
14485 TTTCTT
1 TTTCTT
14491 TTCTTTTTCC
Statistics
Matches: 59, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
9 5 0.08
10 5 0.08
11 28 0.47
12 7 0.12
13 2 0.03
14 1 0.02
15 1 0.02
16 2 0.03
17 7 0.12
18 1 0.02
ACGTcount: A:0.18, C:0.11, G:0.03, T:0.67
Consensus pattern (11 bp):
TTTCTTAATTT
Found at i:14492 original size:16 final size:16
Alignment explanation
Indices: 14473--14518 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
14463 TTTCACCTTT
14473 TTTTCTTAATTTTTTC
1 TTTTCTTAATTTTTTC
*
14489 TTTTC----TTTTTCC
1 TTTTCTTAATTTTTTC
14501 TTTTCTTAATTTTTTC
1 TTTTCTTAATTTTTTC
14517 TT
1 TT
14519 AAATTTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 8
0.71 0.06 0.24
Matches are distributed among these distances:
12 11 0.46
16 13 0.54
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTCTTAATTTTTTC
Found at i:14683 original size:24 final size:23
Alignment explanation
Indices: 14639--14685 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
14629 TTTCTAAAGA
*
14639 ATTTGGGAATGGTGCATATGATT
1 ATTTGGGAATGGTGCAAATGATT
* *
14662 ATTTGGGGATGGTGAGAAATGATT
1 ATTTGGGAATGGTG-CAAATGATT
14686 TGGGTATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.28, C:0.02, G:0.34, T:0.36
Consensus pattern (23 bp):
ATTTGGGAATGGTGCAAATGATT
Found at i:16805 original size:183 final size:182
Alignment explanation
Indices: 16470--16877 Score: 432
Period size: 183 Copynumber: 2.2 Consensus size: 182
16460 TAAACTCCCT
** * * *
16470 ATTTTTGGCTTAATTAA-CTAATTTTTCCTAAATCACAAAAACCCTAATTCACCAAGCAAGCTAA
1 ATTTTTGG-TTAATTAATC-AATTTGGCCAAAATCACAAGAACCCTAATTCACCAAGCAAGCCAA
* * *
16534 TTTGCCGCCTATGTTGCAATTTTTGCAAAGAAGGACTCGGCTCATTAGGAGTAGCTTGGTTCATT
64 TTTGCCGCCTAAGTTGCAATTTTTGCAAAGAAGGACACGGCTCATTAGGAGTAGCTTGGTTCATC
* * * *
16599 AAATTGGGCTTATATTTATGTGATATAACCTAGTTTT-AAGGGTTTAACCTACTG
129 AAATTAGGCTTATATTCATGTGATATAACCTAATTTTCAAAGGTTT-ACCTACTG
* * *
16653 ATTTTTGGTTTAATTAATCAATTTGGCCAAAATCACAAGAACCCTAATTTATCAAGCTAGCCAAT
1 ATTTTTGG-TTAATTAATCAATTTGGCCAAAATCACAAGAACCCTAATTCACCAAGCAAGCCAAT
* * * * * *
16718 TTGCCGCC-AAGTTGCAATTTTTGCAAA-ATGGGTCACGGC-CTATT-GGGGATTGCTTGATTTT
65 TTGCCGCCTAAGTTGCAATTTTTGCAAAGA-AGGACACGGCTC-ATTAGGAG-TAGCTTG-GTTC
* * *
16779 ATCAAATTAGGTTTATGTTCATGTGATATGACCTAATTTTCAAAGGTTTACCTACTG
126 ATCAAATTAGGCTTATATTCATGTGATATAACCTAATTTTCAAAGGTTTACCTACTG
* * * *
16836 ATTTTTGGCTAATTTAGTCAATTAGGCCGAAAATTACAAGAA
1 ATTTTTGGTTAA-TTAATCAATTTGGCC-AAAATCACAAGAA
16878 AATTACTAAA
Statistics
Matches: 188, Mismatches: 29, Indels: 15
0.81 0.12 0.06
Matches are distributed among these distances:
181 5 0.03
182 37 0.20
183 126 0.67
184 20 0.11
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (182 bp):
ATTTTTGGTTAATTAATCAATTTGGCCAAAATCACAAGAACCCTAATTCACCAAGCAAGCCAATT
TGCCGCCTAAGTTGCAATTTTTGCAAAGAAGGACACGGCTCATTAGGAGTAGCTTGGTTCATCAA
ATTAGGCTTATATTCATGTGATATAACCTAATTTTCAAAGGTTTACCTACTG
Found at i:19260 original size:17 final size:18
Alignment explanation
Indices: 19240--19275 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
19230 AGCCTATCAC
19240 CTCATACTACCTA-GTAT
1 CTCATACTACCTAGGTAT
19257 CTCATACTACCTAGGTAT
1 CTCATACTACCTAGGTAT
19275 C
1 C
19276 ATGAGGAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.28, C:0.31, G:0.08, T:0.33
Consensus pattern (18 bp):
CTCATACTACCTAGGTAT
Done.