Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007987.1 Corchorus capsularis cultivar CVL-1 contig08008, 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: 70023
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:3226 original size:12 final size:12
Alignment explanation
Indices: 3204--3242 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3194 CATGACCGGC
*
3204 CAACTCATGGAG
1 CAACGCATGGAG
*
3216 CATCGCATGGAG
1 CAACGCATGGAG
*
3228 CAACGCATGGGG
1 CAACGCATGGAG
3240 CAA
1 CAA
3243 TCGGCCACAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.31, C:0.26, G:0.31, T:0.13
Consensus pattern (12 bp):
CAACGCATGGAG
Found at i:11461 original size:33 final size:33
Alignment explanation
Indices: 11424--11487 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
11414 CCTAATTTGA
*
11424 GTGTTGTTTGCAATGACACTAAATCTGTTTTAG
1 GTGTTGTTTGCAATGAAACTAAATCTGTTTTAG
**
11457 GTGTTGTTTGTGATGAAACTAAATCTGTTTT
1 GTGTTGTTTGCAATGAAACTAAATCTGTTTT
11488 GGATGCTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.23, C:0.09, G:0.22, T:0.45
Consensus pattern (33 bp):
GTGTTGTTTGCAATGAAACTAAATCTGTTTTAG
Found at i:11506 original size:33 final size:32
Alignment explanation
Indices: 11436--11521 Score: 93
Period size: 33 Copynumber: 2.6 Consensus size: 32
11426 GTTGTTTGCA
* * ** *
11436 ATGACACTAAATCTGTTTTAGGTGTTGTTTGTG
1 ATGAAACTAAATCTGTTTT-GGTGCTAATTGTC
11469 ATGAAACTAAATCTGTTTTGGATGCTAATTGTC
1 ATGAAACTAAATCTGTTTTGG-TGCTAATTGTC
11502 ATGAAAAC-AAATCTGTTTTG
1 ATG-AAACTAAATCTGTTTTG
11522 CTTGATCATA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
32 2 0.04
33 40 0.87
34 4 0.09
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (32 bp):
ATGAAACTAAATCTGTTTTGGTGCTAATTGTC
Found at i:11554 original size:33 final size:33
Alignment explanation
Indices: 11517--11593 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 33
11507 AACAAATCTG
* * *
11517 TTTTGCTTGATCATAGCATTGCAAAAAATTCTA
1 TTTTGGTTGATCATAACATTGCAAAAAATTATA
* *
11550 TTTTGGTTGATCATAACATTGCAAATAATTATG
1 TTTTGGTTGATCATAACATTGCAAAAAATTATA
11583 TTTTGGTTGAT
1 TTTTGGTTGAT
11594 GGCATTGAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.30, C:0.10, G:0.16, T:0.44
Consensus pattern (33 bp):
TTTTGGTTGATCATAACATTGCAAAAAATTATA
Found at i:15117 original size:10 final size:10
Alignment explanation
Indices: 15102--15128 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
15092 CACGGGCCAT
15102 CCGGCCACAA
1 CCGGCCACAA
15112 CCGGCCACAA
1 CCGGCCACAA
15122 CCGGCCA
1 CCGGCCA
15129 TTCGACCCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.26, C:0.52, G:0.22, T:0.00
Consensus pattern (10 bp):
CCGGCCACAA
Found at i:18626 original size:16 final size:17
Alignment explanation
Indices: 18595--18627 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
18585 TTGTAAACAT
18595 AAGTTGAGTTGATTATTA
1 AAGTTGAG-TGATTATTA
18613 AAGTTGAG-GATTATT
1 AAGTTGAGTGATTATT
18628 TTCCCAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.42
Consensus pattern (17 bp):
AAGTTGAGTGATTATTA
Found at i:33266 original size:33 final size:34
Alignment explanation
Indices: 33224--33353 Score: 106
Period size: 33 Copynumber: 3.9 Consensus size: 34
33214 AATTAGTATC
* *
33224 CAAAACAGATTTAGTTTCATCACAAACAACACCT
1 CAAATCAGATTTAGTATCATCACAAACAACACCT
* ** *
33258 -AAATCAGATTTAGTGTCATTGCAAAAAACA-CT
1 CAAATCAGATTTAGTATCATCACAAACAACACCT
* *
33290 CAAATTAGGTTTAGTATCATCA-AAACCAACA-CT
1 CAAATCAGATTTAGTATCATCACAAA-CAACACCT
* * ** *
33323 CAAATTAGGTTTAGTATTTTCGCAAACAACA
1 CAAATCAGATTTAGTATCATCACAAACAACA
33354 TCTAAAACAC
Statistics
Matches: 79, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
32 5 0.06
33 71 0.90
34 3 0.04
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (34 bp):
CAAATCAGATTTAGTATCATCACAAACAACACCT
Found at i:34765 original size:10 final size:9
Alignment explanation
Indices: 34745--34779 Score: 52
Period size: 10 Copynumber: 3.7 Consensus size: 9
34735 CTGGTCGAAA
34745 ATTTTTTTT
1 ATTTTTTTT
34754 ATTTTATTTT
1 ATTTT-TTTT
34764 ATTTTTTTAT
1 ATTTTTTT-T
34774 ATTTTT
1 ATTTTT
34780 CGATATAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:36458 original size:30 final size:30
Alignment explanation
Indices: 36422--36487 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
36412 AAAGGGTCAA
*
36422 ATGGCCGGTTGTGCCCGGATG-TCCCATGCG
1 ATGGCCGGTTGTGCCCGGATGCT-CCATCCG
* *
36452 ATGGCCGGTTGTGGCCGGTTGCTCCATCCG
1 ATGGCCGGTTGTGCCCGGATGCTCCATCCG
36482 ATGGCC
1 ATGGCC
36488 CATGCGATGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 31 0.97
31 1 0.03
ACGTcount: A:0.09, C:0.30, G:0.36, T:0.24
Consensus pattern (30 bp):
ATGGCCGGTTGTGCCCGGATGCTCCATCCG
Found at i:38804 original size:10 final size:8
Alignment explanation
Indices: 38783--38807 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
38773 CTGAGGAGGC
38783 AGAGAGTA
1 AGAGAGTA
38791 AGAGAGTA
1 AGAGAGTA
38799 AGAGAGTA
1 AGAGAGTA
38807 A
1 A
38808 CATCAAGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.36, T:0.12
Consensus pattern (8 bp):
AGAGAGTA
Found at i:39805 original size:17 final size:17
Alignment explanation
Indices: 39785--39817 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
39775 GCAGCCTATC
39785 ACCTCATACTACCTAGT
1 ACCTCATACTACCTAGT
39802 ACCTCATACTACCTAG
1 ACCTCATACTACCTAG
39818 GTACTATGAG
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:42987 original size:19 final size:18
Alignment explanation
Indices: 42963--42998 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
42953 TGAAGATTTC
42963 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
42982 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
42999 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:45428 original size:9 final size:10
Alignment explanation
Indices: 45395--45428 Score: 59
Period size: 10 Copynumber: 3.3 Consensus size: 10
45385 TTCTGGTCAA
45395 TTTTTTTAAT
1 TTTTTTTAAT
45405 TTTTTTTAAT
1 TTTTTTTAAT
45415 TTTTTTTATAT
1 TTTTTTTA-AT
45426 TTT
1 TTT
45429 AAGGACCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 18 0.78
11 5 0.22
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTTTAAT
Found at i:48688 original size:24 final size:24
Alignment explanation
Indices: 48642--48690 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
48632 GGATTTAGCA
* * *
48642 GCAAATGACGACCCAATTGAGGCT
1 GCAAAAGACGACCCAACTAAGGCT
*
48666 GCAAAAGACGACCCCACTAAGGCT
1 GCAAAAGACGACCCAACTAAGGCT
48690 G
1 G
48691 GAAATGGATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.35, C:0.29, G:0.24, T:0.12
Consensus pattern (24 bp):
GCAAAAGACGACCCAACTAAGGCT
Found at i:48760 original size:27 final size:27
Alignment explanation
Indices: 48723--48839 Score: 200
Period size: 27 Copynumber: 4.3 Consensus size: 27
48713 TCCGGCCCTC
*
48723 CCCACTTCGACCCCAGAAGTGGATCCT
1 CCCACTTCGACCCCAGCAGTGGATCCT
*
48750 CCCA-TTGCGACCCAAGCAGTGGATCCT
1 CCCACTT-CGACCCCAGCAGTGGATCCT
48777 CCCACTTCGACCCCAGCAGTGGATCCT
1 CCCACTTCGACCCCAGCAGTGGATCCT
48804 CCCACTTCGACCCCAGCAGTGGATCCT
1 CCCACTTCGACCCCAGCAGTGGATCCT
48831 CCCACTTCG
1 CCCACTTCG
48840 CCTCGGGTCG
Statistics
Matches: 85, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
26 2 0.02
27 81 0.95
28 2 0.02
ACGTcount: A:0.20, C:0.43, G:0.19, T:0.19
Consensus pattern (27 bp):
CCCACTTCGACCCCAGCAGTGGATCCT
Found at i:50857 original size:6 final size:6
Alignment explanation
Indices: 50846--50872 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
50836 GTGAATACTA
50846 GTGGCG GTGGCG GTGGCG GTGGCG GTG
1 GTGGCG GTGGCG GTGGCG GTGGCG GTG
50873 ATGATGGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.67, T:0.19
Consensus pattern (6 bp):
GTGGCG
Found at i:51285 original size:32 final size:32
Alignment explanation
Indices: 51242--51332 Score: 139
Period size: 32 Copynumber: 2.8 Consensus size: 32
51232 ATAACCTTAG
51242 ATAGCGGCGTCTAAAGAACAAAGCGCCCATAT
1 ATAGCGGCGTCTAAAGAACAAAGCGCCCATAT
* * *
51274 ATAGCGACGTCTGAAGAACAAAGCGCCCTTAT
1 ATAGCGGCGTCTAAAGAACAAAGCGCCCATAT
51306 ATAGCGGCGTCTAAAGAAACAAA-CGCC
1 ATAGCGGCGTCTAAAG-AACAAAGCGCC
51333 GCAATATTTA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
32 47 0.89
33 6 0.11
ACGTcount: A:0.37, C:0.25, G:0.22, T:0.15
Consensus pattern (32 bp):
ATAGCGGCGTCTAAAGAACAAAGCGCCCATAT
Found at i:51460 original size:24 final size:24
Alignment explanation
Indices: 51387--51461 Score: 87
Period size: 24 Copynumber: 3.1 Consensus size: 24
51377 AGGTAGCGGC
* * * *
51387 GTCTGGATGCCCCCAAATAGTGGC
1 GTCTGGACGCCGCCAAATAGGGGT
* * *
51411 GTCTGGACGCAGCGAAATAGGAGT
1 GTCTGGACGCCGCCAAATAGGGGT
51435 GTCTGGACGCCGCCAAATAGGGGT
1 GTCTGGACGCCGCCAAATAGGGGT
51459 GTC
1 GTC
51462 CCGACCCCGC
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.23, C:0.24, G:0.35, T:0.19
Consensus pattern (24 bp):
GTCTGGACGCCGCCAAATAGGGGT
Found at i:51471 original size:24 final size:24
Alignment explanation
Indices: 51425--51471 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
51415 GGACGCAGCG
** *
51425 AAATAGGAGTGTCTGGACGCCGCC
1 AAATAGGAGTGTCCCGACCCCGCC
*
51449 AAATAGGGGTGTCCCGACCCCGC
1 AAATAGGAGTGTCCCGACCCCGC
51472 AATATGCTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.23, C:0.30, G:0.32, T:0.15
Consensus pattern (24 bp):
AAATAGGAGTGTCCCGACCCCGCC
Found at i:56101 original size:11 final size:10
Alignment explanation
Indices: 56080--56120 Score: 59
Period size: 9 Copynumber: 4.3 Consensus size: 10
56070 ACTAGTAGTT
56080 ATATCAAAAA
1 ATATCAAAAA
56090 ATATCAAAAA
1 ATATCAAAAA
56100 A-ATCAAAAA
1 ATATCAAAAA
*
56109 AGAT-AAAAA
1 ATATCAAAAA
56118 ATA
1 ATA
56121 AAATAAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 16 0.55
10 13 0.45
ACGTcount: A:0.73, C:0.07, G:0.02, T:0.17
Consensus pattern (10 bp):
ATATCAAAAA
Found at i:56106 original size:19 final size:18
Alignment explanation
Indices: 56082--56118 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
56072 TAGTAGTTAT
*
56082 ATCAAAAAATATCAAAAAA
1 ATCAAAAAAGAT-AAAAAA
56101 ATCAAAAAAGATAAAAAA
1 ATCAAAAAAGATAAAAAA
56119 TAAAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.76, C:0.08, G:0.03, T:0.14
Consensus pattern (18 bp):
ATCAAAAAAGATAAAAAA
Found at i:57531 original size:30 final size:30
Alignment explanation
Indices: 57475--57539 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
57465 CATCGCATGC
* *
57475 GCCATCGCATGGAGCAACCGGCCACAACTG
1 GCCATCGCATGGAGCAACAGGCCACAACCG
* *
57505 GCCATCGCATGGGGCATCA-GCGCACAACCG
1 GCCATCGCATGGAGCAACAGGC-CACAACCG
57535 GCCAT
1 GCCAT
57540 TTGATCCTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 2 0.07
30 28 0.93
ACGTcount: A:0.25, C:0.37, G:0.28, T:0.11
Consensus pattern (30 bp):
GCCATCGCATGGAGCAACAGGCCACAACCG
Found at i:59399 original size:15 final size:15
Alignment explanation
Indices: 59381--59419 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
59371 CCAACTCCTC
*
59381 CCCCTCCCTACCACA
1 CCCCTCCCCACCACA
*
59396 CCCCTCCCCACCCCA
1 CCCCTCCCCACCACA
59411 CCCCTCCCC
1 CCCCTCCCC
59420 CATTTCAACC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.13, C:0.77, G:0.00, T:0.10
Consensus pattern (15 bp):
CCCCTCCCCACCACA
Found at i:67805 original size:19 final size:18
Alignment explanation
Indices: 67772--67807 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
67762 TTGAAATAAT
67772 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
67790 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
67808 GAAATCATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:70023 original size:34 final size:33
Alignment explanation
Indices: 69944--70023 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
69934 TCTTGTTAGA
*
69944 TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
1 TGAAAATAATTCTGTTTTGGTTGATCATAACAT
*
69977 TGCAAATAATTCTGTTTTGGTTGATCATAACAT
1 TGAAAATAATTCTGTTTTGGTTGATCATAACAT
70010 TGAAAAATAATTCT
1 TG-AAAATAATTCT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
33 33 0.77
34 10 0.23
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (33 bp):
TGAAAATAATTCTGTTTTGGTTGATCATAACAT
Done.