Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013347.1 Corchorus capsularis cultivar CVL-1 contig13368, 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: 35043
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Found at i:1665 original size:3 final size:3
Alignment explanation
Indices: 1657--1687 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1647 CAAAAGAGTC
1657 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG A
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG A
1688 AACAAAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:2876 original size:2 final size:2
Alignment explanation
Indices: 2869--2895 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2859 ATATTTAGTG
2869 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
2896 TATCTTCGGA
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:3016 original size:15 final size:15
Alignment explanation
Indices: 2996--3027 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2986 AAACCAGCAA
2996 CATTGGAGGGTGAAT
1 CATTGGAGGGTGAAT
3011 CATTGGAGGGTGAAT
1 CATTGGAGGGTGAAT
3026 CA
1 CA
3028 GAGGTTGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.09, G:0.38, T:0.25
Consensus pattern (15 bp):
CATTGGAGGGTGAAT
Found at i:5536 original size:54 final size:54
Alignment explanation
Indices: 5467--5576 Score: 211
Period size: 54 Copynumber: 2.0 Consensus size: 54
5457 TAAGACAGGA
*
5467 AATATGATAGTGAGTATAATAAAAGTGGGGAGAAAATGCAAAACCCTACATGAT
1 AATACGATAGTGAGTATAATAAAAGTGGGGAGAAAATGCAAAACCCTACATGAT
5521 AATACGATAGTGAGTATAATAAAAGTGGGGAGAAAATGCAAAACCCTACATGAT
1 AATACGATAGTGAGTATAATAAAAGTGGGGAGAAAATGCAAAACCCTACATGAT
5575 AA
1 AA
5577 GTTCATAAAA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.47, C:0.10, G:0.22, T:0.21
Consensus pattern (54 bp):
AATACGATAGTGAGTATAATAAAAGTGGGGAGAAAATGCAAAACCCTACATGAT
Found at i:7690 original size:46 final size:46
Alignment explanation
Indices: 7632--7720 Score: 126
Period size: 46 Copynumber: 1.9 Consensus size: 46
7622 ATTATTTTTC
* *
7632 CCTTTATTAAGAACAATTACTACTGTTCTTAGAAACATTTTAACCA
1 CCTTTATTAAGAACAAATACTACTGTTCTTAAAAACATTTTAACCA
* *
7678 CCTTT-TTCAAGAACAAATACTATTGTTTTTAAAAACATTTTAA
1 CCTTTATT-AAGAACAAATACTACTGTTCTTAAAAACATTTTAA
7721 ACACAAATCC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
45 2 0.05
46 36 0.95
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.39
Consensus pattern (46 bp):
CCTTTATTAAGAACAAATACTACTGTTCTTAAAAACATTTTAACCA
Found at i:12221 original size:3 final size:3
Alignment explanation
Indices: 12213--12253 Score: 64
Period size: 3 Copynumber: 13.0 Consensus size: 3
12203 TTCAAACTCC
12213 ATT ATT ATT ATT ATT ATT ATT ATTT ATT ATTT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT A-TT ATT A-TT ATT ATT ATT
12254 CCTGCCTCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 30 0.83
4 6 0.17
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:14100 original size:23 final size:23
Alignment explanation
Indices: 14070--14124 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
14060 AGGCGCGAGT
* *
14070 GACCGGCCAGGCGACTTGGAGAA
1 GACCGGCCACGCGACTCGGAGAA
*
14093 GACCGGCCACGCGACTCGGAGAT
1 GACCGGCCACGCGACTCGGAGAA
*
14116 GCCCGGCCA
1 GACCGGCCA
14125 TCACCGGCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.22, C:0.35, G:0.36, T:0.07
Consensus pattern (23 bp):
GACCGGCCACGCGACTCGGAGAA
Found at i:14136 original size:33 final size:33
Alignment explanation
Indices: 14094--14167 Score: 98
Period size: 33 Copynumber: 2.2 Consensus size: 33
14084 CTTGGAGAAG
*
14094 ACCGGCCACGCGAC-TCGGAGATGCCCGGCCATC-
1 ACCGGCCACGCGACAT-GGACATGCCCGGCCA-CA
*
14127 ACCGGCCACGCGACATGGACATGTCCGGCCACA
1 ACCGGCCACGCGACATGGACATGCCCGGCCACA
14160 ACCGGCCA
1 ACCGGCCA
14168 TCGCTTGGCG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
32 1 0.03
33 35 0.95
34 1 0.03
ACGTcount: A:0.22, C:0.42, G:0.28, T:0.08
Consensus pattern (33 bp):
ACCGGCCACGCGACATGGACATGCCCGGCCACA
Found at i:24311 original size:2 final size:2
Alignment explanation
Indices: 24306--24332 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
24296 AAATCCAAAT
24306 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
24333 CGATTGAACG
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:25330 original size:22 final size:22
Alignment explanation
Indices: 25302--25473 Score: 73
Period size: 22 Copynumber: 7.8 Consensus size: 22
25292 ATGATCCTAT
25302 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* *** *
25324 TATGAAATTTTAATAATGATAC
1 TATGAAATTTTGATAACCTTCC
* ** **
25346 TATGAAATTTCGGGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
** * *
25368 TAT-AAATTTTTTTTAACATTCT
1 TATGAAA-TTTTGATAACCTTCC
* * *
25390 TAGGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* * ** *
25412 TAAGGAATTTTG--AAGGTCTCAA
1 TATGAAATTTTGATAACCT-TC-C
25434 TATGAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
*
25456 AATGAAATTTTGATAACC
1 TATGAAATTTTGATAACC
25474 AACACTATGT
Statistics
Matches: 106, Mismatches: 36, Indels: 15
0.68 0.23 0.10
Matches are distributed among these distances:
20 3 0.03
21 4 0.04
22 91 0.86
23 6 0.06
24 2 0.02
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:26094 original size:10 final size:9
Alignment explanation
Indices: 26079--26127 Score: 66
Period size: 8 Copynumber: 5.6 Consensus size: 9
26069 ATGAAATTCC
26079 TTTTTTGAA
1 TTTTTTGAA
26088 TTTTTTTGAA
1 -TTTTTTGAA
26098 -TTTTTGAA
1 TTTTTTGAA
26106 -TTTTTGAA
1 TTTTTTGAA
*
26114 TTTTTTGGA
1 TTTTTTGAA
26123 TTTTT
1 TTTTT
26128 GGAAAACCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
8 16 0.43
9 12 0.32
10 9 0.24
ACGTcount: A:0.18, C:0.00, G:0.12, T:0.69
Consensus pattern (9 bp):
TTTTTTGAA
Found at i:26101 original size:18 final size:16
Alignment explanation
Indices: 26080--26128 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
26070 TGAAATTCCT
26080 TTTTTGAATTTTTTTGAA
1 TTTTTGAA--TTTTTGAA
26098 TTTTTGAATTTTTGAA
1 TTTTTGAATTTTTGAA
*
26114 TTTTTTGGATTTTTG
1 -TTTTTGAATTTTTG
26129 GAAAACCTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 8 0.28
17 13 0.45
18 8 0.28
ACGTcount: A:0.18, C:0.00, G:0.14, T:0.67
Consensus pattern (16 bp):
TTTTTGAATTTTTGAA
Found at i:26116 original size:26 final size:25
Alignment explanation
Indices: 26080--26128 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
26070 TGAAATTCCT
26080 TTTTTGAATTTTTTTGAATTTTTGAA
1 TTTTTGAA-TTTTTTGAATTTTTGAA
*
26106 TTTTTGAATTTTTTGGATTTTTG
1 TTTTTGAATTTTTTGAATTTTTG
26129 GAAAACCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.18, C:0.00, G:0.14, T:0.67
Consensus pattern (25 bp):
TTTTTGAATTTTTTGAATTTTTGAA
Found at i:32184 original size:30 final size:30
Alignment explanation
Indices: 32148--32263 Score: 124
Period size: 33 Copynumber: 3.7 Consensus size: 30
32138 TTCTCGTCAC
*
32148 CCAAAACAGATTTATTTTCAATGCTATCAA
1 CCAAAACAGAATTATTTTCAATGCTATCAA
* *
32178 CCAAAACAGGATTATTTGCAATGCTATAATCAA
1 CCAAAACAGAATTATTTTCAATGC--T-ATCAA
* *
32211 CCAAAACAGAATTGTTTTTAATGCTATGTTCAA
1 CCAAAACAGAATTATTTTCAATGCTA---TCAA
*
32244 CCAAAACAGAATTGTTTTCA
1 CCAAAACAGAATTATTTTCA
32264 TCACAATTAG
Statistics
Matches: 72, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
30 22 0.31
31 1 0.01
32 1 0.01
33 48 0.67
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (30 bp):
CCAAAACAGAATTATTTTCAATGCTATCAA
Found at i:32296 original size:66 final size:63
Alignment explanation
Indices: 32148--32296 Score: 142
Period size: 66 Copynumber: 2.3 Consensus size: 63
32138 TTCTCGTCAC
* * * *
32148 CCAAAACAGATTTA-TTTTCAATGCTATCAACCAAAACAGGATTATTTGCAATGCTATAATCAA
1 CCAAAACAGATTTAGTTTT-AATGCTATCAACCAAAACAGAATTATTTGCAATACAATAAGCAA
* * * *
32211 CCAAAACAGAATT-GTTTTTAATGCTATGTTCAACCAAAACAGAATTGTTTTC-ATCACAATTAG
1 CCAAAACAGATTTAG-TTTTAATGCTA---TCAACCAAAACAGAATTATTTGCAAT-ACAATAAG
*
32274 CAT
61 CAA
32277 CCAAAACAGATTTAGTTTTA
1 CCAAAACAGATTTAGTTTTA
32297 TTGCAAACAA
Statistics
Matches: 69, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
63 19 0.28
64 4 0.06
65 2 0.03
66 43 0.62
67 1 0.01
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (63 bp):
CCAAAACAGATTTAGTTTTAATGCTATCAACCAAAACAGAATTATTTGCAATACAATAAGCAA
Found at i:32324 original size:33 final size:33
Alignment explanation
Indices: 32299--32407 Score: 157
Period size: 33 Copynumber: 3.3 Consensus size: 33
32289 TAGTTTTATT
32299 GCAAACAACACTCAAATTAGGTTTAGTATCATC
1 GCAAACAACACTCAAATTAGGTTTAGTATCATC
** * * *
32332 GCAAACAACA-TCTAAAACAGATTTAGTGTCATT
1 GCAAACAACACTC-AAATTAGGTTTAGTATCATC
32365 GCAAACAACACTCAAATTAGGTTTAGTATCATC
1 GCAAACAACACTCAAATTAGGTTTAGTATCATC
32398 GCAAACAACA
1 GCAAACAACA
32408 TCTAAAACAC
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
32 2 0.03
33 60 0.94
34 2 0.03
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.25
Consensus pattern (33 bp):
GCAAACAACACTCAAATTAGGTTTAGTATCATC
Found at i:32331 original size:66 final size:66
Alignment explanation
Indices: 32274--32416 Score: 232
Period size: 66 Copynumber: 2.2 Consensus size: 66
32264 TCACAATTAG
* * *
32274 CATCCAAAACAGATTTAGTTTTATTGCAAACAACACTCAAATTAGGTTTAGTATCATCGCAAACA
1 CATCCAAAACAGATTTAGTGTCATTGCAAACAACACTCAAATTAGGTTTAGTATCATCACAAACA
32339 A
66 A
* *
32340 CATCTAAAACAGATTTAGTGTCATTGCAAACAACACTCAAATTAGGTTTAGTATCATCGCAAACA
1 CATCCAAAACAGATTTAGTGTCATTGCAAACAACACTCAAATTAGGTTTAGTATCATCACAAACA
32405 A
66 A
*
32406 CATCTAAAACA
1 CATCCAAAACA
32417 CTCTTTTCAA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 74 1.00
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.27
Consensus pattern (66 bp):
CATCCAAAACAGATTTAGTGTCATTGCAAACAACACTCAAATTAGGTTTAGTATCATCACAAACA
A
Found at i:33792 original size:5 final size:5
Alignment explanation
Indices: 33782--33812 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
33772 TCTGGTCGAA
33782 ATTTT ATTTT ATTTT ATTTT ATTTT -TTTT AT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT AT
33813 ATTTTTTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
ATTTT
Done.