Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008622.1 Corchorus capsularis cultivar CVL-1 contig08643, 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: 43908
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:1596 original size:33 final size:33
Alignment explanation
Indices: 1529--1644 Score: 123
Period size: 33 Copynumber: 3.6 Consensus size: 33
1519 TTCTCGTCAC
1529 CCAAAACA-GATTTATTTTCAATGC--T-ATCAA
1 CCAAAACAGGA-TTATTTTCAATGCTATGATCAA
*
1559 CCAAAACAGGATTATTTGCAATGCTATGATCAA
1 CCAAAACAGGATTATTTTCAATGCTATGATCAA
* ** * *
1592 CCAAAATAAAATTATTTTTAATGCTATGTTCAA
1 CCAAAACAGGATTATTTTCAATGCTATGATCAA
* *
1625 CCAAAACAGAATTGTTTTCA
1 CCAAAACAGGATTATTTTCA
1645 TCACAATTAG
Statistics
Matches: 71, Mismatches: 11, Indels: 5
0.82 0.13 0.06
Matches are distributed among these distances:
30 20 0.28
31 2 0.03
32 1 0.01
33 48 0.68
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (33 bp):
CCAAAACAGGATTATTTTCAATGCTATGATCAA
Found at i:1697 original size:33 final size:33
Alignment explanation
Indices: 1660--1764 Score: 122
Period size: 33 Copynumber: 3.2 Consensus size: 33
1650 ATTAGCATCC
* *
1660 AAAACAGATTTAGTTTCATCACAAACAACACTT
1 AAAACAGATTTAGTATCATCGCAAACAACACTT
* * *
1693 AAAACAGATTTAGTGTCATTGCAAACAACACTC
1 AAAACAGATTTAGTATCATCGCAAACAACACTT
** *
1726 AAATTAGGTTTAGTATCATCGCAAACAACA-TCT
1 AAAACAGATTTAGTATCATCGCAAACAACACT-T
1759 AAAACA
1 AAAACA
1765 CTCTTTTCAA
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
32 1 0.02
33 58 0.98
ACGTcount: A:0.45, C:0.20, G:0.10, T:0.26
Consensus pattern (33 bp):
AAAACAGATTTAGTATCATCGCAAACAACACTT
Found at i:3248 original size:16 final size:17
Alignment explanation
Indices: 3227--3259 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
3217 TCTGGTCGAA
3227 ATTTTTTTTAT-TTTTT
1 ATTTTTTTTATATTTTT
3243 ATTTTTTTTATATTTTT
1 ATTTTTTTTATATTTTT
3260 CGATATAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (17 bp):
ATTTTTTTTATATTTTT
Found at i:3360 original size:8 final size:8
Alignment explanation
Indices: 3332--3365 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
3322 GAATCGGCTA
3332 TGAATTTT
1 TGAATTTT
*
3340 TGAAGTTTC
1 TGAA-TTTT
3349 TGAATTTT
1 TGAATTTT
3357 TGAATTTT
1 TGAATTTT
3365 T
1 T
3366 CAAGAAGGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:4787 original size:31 final size:31
Alignment explanation
Indices: 4751--4809 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
4741 AATTGGAATC
* *
4751 GACCAGTTATGCCGCGACAAGACTGGAACAT
1 GACCAGGTATGCAGCGACAAGACTGGAACAT
*
4782 GACCAGGTATTCAGCGACAAGACTGGAA
1 GACCAGGTATGCAGCGACAAGACTGGAA
4810 AATGGCCAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.34, C:0.24, G:0.27, T:0.15
Consensus pattern (31 bp):
GACCAGGTATGCAGCGACAAGACTGGAACAT
Found at i:6463 original size:13 final size:13
Alignment explanation
Indices: 6445--6479 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
6435 GATCTAAATC
*
6445 TAAAGCAGATTAA
1 TAAAGCAAATTAA
6458 TAAAGCAAATTAA
1 TAAAGCAAATTAA
6471 TAAAGCAAA
1 TAAAGCAAA
6480 CAATAATTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.60, C:0.09, G:0.11, T:0.20
Consensus pattern (13 bp):
TAAAGCAAATTAA
Found at i:13617 original size:7 final size:7
Alignment explanation
Indices: 13605--13630 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
13595 TGAATTTATT
13605 TGGCATG
1 TGGCATG
13612 TGGCATG
1 TGGCATG
13619 TGGCATG
1 TGGCATG
13626 TGGCA
1 TGGCA
13631 CATCACACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.15, G:0.42, T:0.27
Consensus pattern (7 bp):
TGGCATG
Found at i:13781 original size:32 final size:31
Alignment explanation
Indices: 13732--13800 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 31
13722 ATTTATGAAT
*
13732 TGAATTGAACATGTTAAGGCTATATGTAACA
1 TGAATTGAAAATGTTAAGGCTATATGTAACA
13763 TGAATTGGAAAATGTTAAGGCTATATGTAACA
1 TGAATT-GAAAATGTTAAGGCTATATGTAACA
13795 TGAATT
1 TGAATT
13801 TATGTAGTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
31 6 0.17
32 30 0.83
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.33
Consensus pattern (31 bp):
TGAATTGAAAATGTTAAGGCTATATGTAACA
Found at i:22916 original size:35 final size:35
Alignment explanation
Indices: 22870--22944 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 35
22860 TTTTCACTTA
22870 CCCACTAATGGAGCCAAATTAGAACCCAAAATTTT
1 CCCACTAATGGAGCCAAATTAGAACCCAAAATTTT
*
22905 CCCACTAATGGAGTCAAATTAGAACCCAAAATTTT
1 CCCACTAATGGAGCCAAATTAGAACCCAAAATTTT
22940 CCCAC
1 CCCAC
22945 GAAACAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.39, C:0.28, G:0.11, T:0.23
Consensus pattern (35 bp):
CCCACTAATGGAGCCAAATTAGAACCCAAAATTTT
Found at i:23336 original size:13 final size:13
Alignment explanation
Indices: 23318--23350 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
23308 TACCTAAAGA
23318 CTTCTCTTTGTTC
1 CTTCTCTTTGTTC
*
23331 CTTCTC-TTGTTG
1 CTTCTCTTTGTTC
23343 CTTCTCTT
1 CTTCTCTT
23351 CCTCAAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.00, C:0.30, G:0.09, T:0.61
Consensus pattern (13 bp):
CTTCTCTTTGTTC
Found at i:25156 original size:30 final size:30
Alignment explanation
Indices: 25107--25221 Score: 142
Period size: 30 Copynumber: 3.8 Consensus size: 30
25097 TGCCCTTGAT
* *
25107 GAGGGTGCTCAACCTACTGCTCCTCCCGAC
1 GAGGGTCCTCAACCCACTGCTCCTCCCGAC
* *
25137 GAGGGTCCTCAGCCCACTGCTCCTCCCAAC
1 GAGGGTCCTCAACCCACTGCTCCTCCCGAC
* *
25167 GAGGGTCCTCAACCCACTGCAT-TTCCCGAG
1 GAGGGTCCTCAACCCACTGC-TCCTCCCGAC
* *
25197 GAGGATGCTCAACCCACTGCTCCTC
1 GAGGGTCCTCAACCCACTGCTCCTC
25222 TTGACAAGAG
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
29 1 0.01
30 70 0.97
31 1 0.01
ACGTcount: A:0.18, C:0.41, G:0.22, T:0.19
Consensus pattern (30 bp):
GAGGGTCCTCAACCCACTGCTCCTCCCGAC
Found at i:28051 original size:12 final size:11
Alignment explanation
Indices: 28020--28052 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
28010 GATCAAATGG
28020 CCGG-TTGTGC
1 CCGGCTTGTGC
28030 CCGGCTTGTGC
1 CCGGCTTGTGC
28041 CCGGCCTTGTGC
1 CCGG-CTTGTGC
28053 GATTGTGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 4 0.19
11 10 0.48
12 7 0.33
ACGTcount: A:0.00, C:0.36, G:0.36, T:0.27
Consensus pattern (11 bp):
CCGGCTTGTGC
Found at i:33137 original size:17 final size:17
Alignment explanation
Indices: 33117--33149 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
33107 GCAGCCTATC
33117 ACCTCATACTACCTAGT
1 ACCTCATACTACCTAGT
33134 ACCTCATACTACCTAG
1 ACCTCATACTACCTAG
33150 GTACTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.36, G:0.06, T:0.27
Consensus pattern (17 bp):
ACCTCATACTACCTAGT
Found at i:33321 original size:21 final size:21
Alignment explanation
Indices: 33297--33337 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
33287 CAGAAGAGTT
33297 CGCCTTCCTCAGCAAGTAAAA
1 CGCCTTCCTCAGCAAGTAAAA
33318 CGCCTTCCTCAGCAAGTAAA
1 CGCCTTCCTCAGCAAGTAAA
33338 GCCCGCCAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.34, G:0.15, T:0.20
Consensus pattern (21 bp):
CGCCTTCCTCAGCAAGTAAAA
Found at i:33561 original size:55 final size:55
Alignment explanation
Indices: 33489--33650 Score: 243
Period size: 55 Copynumber: 2.9 Consensus size: 55
33479 TCTGTTAATT
* * *
33489 TTCAATGCTGACGCTCGCTTGAGATCTCCGTGATTTCCCAGTCTTCCTTGAAAGC
1 TTCAATGCTGACACTCGCTTGAGATCTCCGTGATCTCCCAGTGTTCCTTGAAAGC
* *
33544 TTCAATGCTGGCACTCGCTTGAGATCTCCATGATCTCCCAGTGTTCCTTGAAAGC
1 TTCAATGCTGACACTCGCTTGAGATCTCCGTGATCTCCCAGTGTTCCTTGAAAGC
* * * *
33599 TTCAATGCTGACACTCGCCTGAAATCTTCGTGATCTCCAAGTGTTCCTTGAA
1 TTCAATGCTGACACTCGCTTGAGATCTCCGTGATCTCCCAGTGTTCCTTGAA
33651 GAAGATTCCG
Statistics
Matches: 96, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 96 1.00
ACGTcount: A:0.20, C:0.28, G:0.19, T:0.32
Consensus pattern (55 bp):
TTCAATGCTGACACTCGCTTGAGATCTCCGTGATCTCCCAGTGTTCCTTGAAAGC
Done.