Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010592.1 Corchorus capsularis cultivar CVL-1 contig10613, 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: 57546
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:173 original size:14 final size:14
Alignment explanation
Indices: 154--180 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
144 TGCAGCTAAA
154 AAAATAGAATATTC
1 AAAATAGAATATTC
168 AAAATAGAATATT
1 AAAATAGAATATT
181 TTTCTACAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (14 bp):
AAAATAGAATATTC
Found at i:198 original size:22 final size:23
Alignment explanation
Indices: 168--226 Score: 93
Period size: 22 Copynumber: 2.6 Consensus size: 23
158 TAGAATATTC
*
168 AAAATAGAATATTTTTCTAC-AA
1 AAAAAAGAATATTTTTCTACAAA
190 AAAAAAGAATATTTTTCTACAAA
1 AAAAAAGAATATTTTTCTACAAA
213 AAAAATAGAATATT
1 AAAAA-AGAATATT
227 CAAAATAACT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
22 19 0.56
23 7 0.21
24 8 0.24
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.32
Consensus pattern (23 bp):
AAAAAAGAATATTTTTCTACAAA
Found at i:8127 original size:6 final size:6
Alignment explanation
Indices: 8116--8140 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
8106 TGCAGGGTGC
8116 AGCAAA AGCAAA AGCAAA AGCAAA A
1 AGCAAA AGCAAA AGCAAA AGCAAA A
8141 CTAGAAGAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.16, G:0.16, T:0.00
Consensus pattern (6 bp):
AGCAAA
Found at i:9214 original size:3 final size:3
Alignment explanation
Indices: 9206--9249 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
9196 TATATTCATC
9206 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
9250 CTAGTTCGGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:19474 original size:26 final size:26
Alignment explanation
Indices: 19445--19503 Score: 118
Period size: 26 Copynumber: 2.3 Consensus size: 26
19435 TATTATCTTC
19445 ATTTGAAAATTTGGATTCTTATGGTA
1 ATTTGAAAATTTGGATTCTTATGGTA
19471 ATTTGAAAATTTGGATTCTTATGGTA
1 ATTTGAAAATTTGGATTCTTATGGTA
19497 ATTTGAA
1 ATTTGAA
19504 TCTGTTTGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.32, C:0.03, G:0.19, T:0.46
Consensus pattern (26 bp):
ATTTGAAAATTTGGATTCTTATGGTA
Found at i:28431 original size:9 final size:9
Alignment explanation
Indices: 28417--28470 Score: 55
Period size: 9 Copynumber: 6.6 Consensus size: 9
28407 TTTTTAATAT
28417 TGTTGTTAA
1 TGTTGTTAA
28426 TGTTGTTAA
1 TGTTGTTAA
28435 TGTTGTTAA
1 TGTTGTTAA
28444 -GTT-TTAA
1 TGTTGTTAA
**
28451 -CAT-TTAA
1 TGTTGTTAA
28458 -GTTGTTAA
1 TGTTGTTAA
28466 TGTTG
1 TGTTG
28471 AACAATTTGC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 10 0.26
8 7 0.18
9 22 0.56
ACGTcount: A:0.24, C:0.02, G:0.20, T:0.54
Consensus pattern (9 bp):
TGTTGTTAA
Found at i:28434 original size:21 final size:20
Alignment explanation
Indices: 28402--28441 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
28392 TCATAAACAT
*
28402 TTAAGTTTTTAATATTGTTG
1 TTAAGTTGTTAATATTGTTG
*
28422 TTAATGTTGTTAATGTTGTT
1 TTAA-GTTGTTAATATTGTT
28442 AAGTTTTAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.23, C:0.00, G:0.17, T:0.60
Consensus pattern (20 bp):
TTAAGTTGTTAATATTGTTG
Found at i:28474 original size:22 final size:23
Alignment explanation
Indices: 28431--28474 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
28421 GTTAATGTTG
*
28431 TTAATGTTGTTAAGTTTTAACAT
1 TTAATGTTGTTAAGTTTGAACAT
28454 TTAA-GTTGTTAA-TGTTGAACA
1 TTAATGTTGTTAAGT-TTGAACA
28475 ATTTGCAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 1 0.05
22 14 0.74
23 4 0.21
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.48
Consensus pattern (23 bp):
TTAATGTTGTTAAGTTTGAACAT
Found at i:38084 original size:3 final size:3
Alignment explanation
Indices: 38076--38112 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
38066 CTTTATATAT
38076 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
38113 CTTTCAATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:39956 original size:3 final size:3
Alignment explanation
Indices: 39948--39972 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
39938 TGGCCACTAA
39948 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
39973 TATCTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:41826 original size:12 final size:12
Alignment explanation
Indices: 41802--41839 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
41792 CTCTTTGGCC
41802 AAAAAA-AAA-A
1 AAAAAAGAAACA
41812 AAAAAAGAAACA
1 AAAAAAGAAACA
41824 AAAAAAGAAACA
1 AAAAAAGAAACA
41836 AAAA
1 AAAA
41840 GAGAGTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 6 0.23
11 3 0.12
12 17 0.65
ACGTcount: A:0.89, C:0.05, G:0.05, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAACA
Found at i:41838 original size:22 final size:21
Alignment explanation
Indices: 41801--41841 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
41791 GCTCTTTGGC
41801 CAAAAAAAAAAAAAAAAGAAA
1 CAAAAAAAAAAAAAAAAGAAA
*
41822 CAAAAAAAGAAACAAAAAGA
1 CAAAAAAA-AAAAAAAAAGA
41842 GAGTATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.85, C:0.07, G:0.07, T:0.00
Consensus pattern (21 bp):
CAAAAAAAAAAAAAAAAGAAA
Found at i:46631 original size:16 final size:18
Alignment explanation
Indices: 46610--46645 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
46600 ATTTTGGGTC
46610 TTTTCTTTT-C-ATTTTT
1 TTTTCTTTTGCAATTTTT
46626 TTTTCTTTTGCAATTTTT
1 TTTTCTTTTGCAATTTTT
46644 TT
1 TT
46646 ATTGGATTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
17 1 0.06
18 8 0.44
ACGTcount: A:0.08, C:0.11, G:0.03, T:0.78
Consensus pattern (18 bp):
TTTTCTTTTGCAATTTTT
Found at i:48799 original size:15 final size:15
Alignment explanation
Indices: 48781--48812 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
48771 ATATTTTTCC
48781 TTAATGTATTATTAA
1 TTAATGTATTATTAA
*
48796 TTAATTTATTATTAA
1 TTAATGTATTATTAA
48811 TT
1 TT
48813 CAACGGCGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (15 bp):
TTAATGTATTATTAA
Found at i:51199 original size:24 final size:24
Alignment explanation
Indices: 51172--51254 Score: 62
Period size: 24 Copynumber: 3.3 Consensus size: 24
51162 ACAACAAAAA
51172 AAAATAAAATAATTACACGTTAGG
1 AAAATAAAATAATTACACGTTAGG
* * *
51196 AAAATAACAAATTTAAATA-A-TTATAAGT
1 AAAAT-A-AAA--TAATTACACGT-T-AGG
*
51224 CAAATAAAATAATTACACGTTAGG
1 AAAATAAAATAATTACACGTTAGG
51248 AAAATAA
1 AAAATAA
51255 CAAATTTTAA
Statistics
Matches: 43, Mismatches: 8, Indels: 16
0.64 0.12 0.24
Matches are distributed among these distances:
24 18 0.42
25 3 0.07
26 8 0.19
27 3 0.07
28 11 0.26
ACGTcount: A:0.58, C:0.07, G:0.08, T:0.27
Consensus pattern (24 bp):
AAAATAAAATAATTACACGTTAGG
Found at i:51492 original size:114 final size:114
Alignment explanation
Indices: 51358--51625 Score: 491
Period size: 114 Copynumber: 2.4 Consensus size: 114
51348 TAAAATATTG
* * *
51358 AATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGAAAAAATTTTAATA
1 AATTTAATTGAATAAAAATAGAGTTTCTAGTAGAATAAAATTGTATATTAGAAAAAATTTTAATA
*
51423 TATCCAAATTTTTTGGTAAAAATAAAGTAATTATAAAGATATTAGATTT
66 TATCCAAAATTTTTGGTAAAAATAAAGTAATTATAAAGATATTAGATTT
*
51472 AATTTAATTGAATAAAAATAGAGTTTCTAGTAGAATAAAATTGTATATTAGAAAAAATTTTAGTA
1 AATTTAATTGAATAAAAATAGAGTTTCTAGTAGAATAAAATTGTATATTAGAAAAAATTTTAATA
51537 TATCCAAAATTTTTGGTAAAAATAAAGTAATTATAAAGATATTAGATTT
66 TATCCAAAATTTTTGGTAAAAATAAAGTAATTATAAAGATATTAGATTT
51586 AATTTAATTGAATAAAAATAGAGTTTCTAGTAGAATAAAA
1 AATTTAATTGAATAAAAATAGAGTTTCTAGTAGAATAAAA
51626 CTATAATAGT
Statistics
Matches: 149, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
114 149 1.00
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (114 bp):
AATTTAATTGAATAAAAATAGAGTTTCTAGTAGAATAAAATTGTATATTAGAAAAAATTTTAATA
TATCCAAAATTTTTGGTAAAAATAAAGTAATTATAAAGATATTAGATTT
Found at i:52128 original size:21 final size:21
Alignment explanation
Indices: 52104--52147 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
52094 AAATTTTTCA
52104 TAATTTA-CTAAATATGTATTT
1 TAATTTATCTAAAT-TGTATTT
*
52125 TAATTTATTTAAATTGTATTT
1 TAATTTATCTAAATTGTATTT
52146 TA
1 TA
52148 GGACCCTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (21 bp):
TAATTTATCTAAATTGTATTT
Found at i:54671 original size:31 final size:31
Alignment explanation
Indices: 54624--54698 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
54614 TAAAATGTCT
* *
54624 TGAATTTGAGAAGTTTAGGAGGCAAGATGTTC
1 TGAATTTG-GAAGTTTAGGAGGCAAAATATTC
*
54656 TGAATTTGGAAGTTTAGGTGGCAAAATATTC
1 TGAATTTGGAAGTTTAGGAGGCAAAATATTC
54687 TG-ATTT-GAAGTT
1 TGAATTTGGAAGTT
54699 CATAATGTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
29 6 0.15
30 4 0.10
31 22 0.55
32 8 0.20
ACGTcount: A:0.31, C:0.05, G:0.28, T:0.36
Consensus pattern (31 bp):
TGAATTTGGAAGTTTAGGAGGCAAAATATTC
Done.