Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015663.1 Corchorus capsularis cultivar CVL-1 contig15684, 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: 16690
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2155 original size:18 final size:18
Alignment explanation
Indices: 2127--2181 Score: 83
Period size: 18 Copynumber: 3.1 Consensus size: 18
2117 TAGTGAGGAA
* *
2127 AATGGAGAACCTGACGGT
1 AATGAAGAACCTGACAGT
*
2145 GATGAAGAACCTGACAGT
1 AATGAAGAACCTGACAGT
2163 AATGAAGAACCTGACAGT
1 AATGAAGAACCTGACAGT
2181 A
1 A
2182 GTAGTGATGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.40, C:0.16, G:0.27, T:0.16
Consensus pattern (18 bp):
AATGAAGAACCTGACAGT
Found at i:3387 original size:28 final size:27
Alignment explanation
Indices: 3333--3524 Score: 248
Period size: 28 Copynumber: 7.0 Consensus size: 27
3323 CGCACTGCCA
*
3333 GGGAGTCTCCCTTGGCGCG-CTGCTGG
1 GGGAGTCTCCCCTGGCGCGCCTGCTGG
*
3359 GGGAGCCTCCCCTGGCGCGCACTGCTGG
1 GGGAGTCTCCCCTGGCGCGC-CTGCTGG
* *
3387 GGGAGTCTCCCATGGCGCGCGCTGC-CG
1 GGGAGTCTCCCCTGGCGCGC-CTGCTGG
*
3414 GGGAGCCTCCCCTGGCGCG-CTGCTGG
1 GGGAGTCTCCCCTGGCGCGCCTGCTGG
3440 GGGAGTCTCCCCTGGCGCGCGCTGCTGG
1 GGGAGTCTCCCCTGGCGCGC-CTGCTGG
*
3468 GGGAGTCTCCCTTGGCGCACGCGCTGCTGG
1 GGGAGTCTCCCCTGGCG--CGC-CTGCTGG
3498 GGGAGTCTCCCCTGGCGCG-CTGCTGG
1 GGGAGTCTCCCCTGGCGCGCCTGCTGG
3524 G
1 G
3525 CCTCCTTTAA
Statistics
Matches: 147, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
25 4 0.03
26 44 0.30
27 18 0.12
28 54 0.37
30 27 0.18
ACGTcount: A:0.05, C:0.35, G:0.42, T:0.18
Consensus pattern (27 bp):
GGGAGTCTCCCCTGGCGCGCCTGCTGG
Found at i:3450 original size:81 final size:81
Alignment explanation
Indices: 3312--3524 Score: 309
Period size: 81 Copynumber: 2.6 Consensus size: 81
3302 CTAGGGAGAC
* * * * *
3312 CTCCCCTGGCTCGCACTGCCAGGGAGTCTCCCTTGGCGCGCTGCTGGGGGAGCCTCCCCTGGCGC
1 CTCCCATGGCGCGCGCTGCCGGGGAGTCTCCCCTGGCGCGCTGCTGGGGGAGCCTCCCCTGGCGC
3377 GCACTGCTGGGGGAGT
66 GCACTGCTGGGGGAGT
* *
3393 CTCCCATGGCGCGCGCTGCCGGGGAGCCTCCCCTGGCGCGCTGCTGGGGGAGTCTCCCCTGGCGC
1 CTCCCATGGCGCGCGCTGCCGGGGAGTCTCCCCTGGCGCGCTGCTGGGGGAGCCTCCCCTGGCGC
*
3458 GCGCTGCTGGGGGAGT
66 GCACTGCTGGGGGAGT
* *
3474 CTCCCTTGGCGCACGCGCTGCTGGGGGAGTCTCCCCTGGCGCGCTGCTGGG
1 CTCCCATGGCG--CGCGCTGC-CGGGGAGTCTCCCCTGGCGCGCTGCTGGG
3525 CCTCCTTTAA
Statistics
Matches: 118, Mismatches: 11, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
81 83 0.70
83 8 0.07
84 27 0.23
ACGTcount: A:0.06, C:0.37, G:0.39, T:0.18
Consensus pattern (81 bp):
CTCCCATGGCGCGCGCTGCCGGGGAGTCTCCCCTGGCGCGCTGCTGGGGGAGCCTCCCCTGGCGC
GCACTGCTGGGGGAGT
Found at i:3749 original size:2 final size:2
Alignment explanation
Indices: 3742--3773 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3732 AACATAAGTA
3742 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3774 GATCATGCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9455 original size:17 final size:17
Alignment explanation
Indices: 9433--9472 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
9423 GTTCCCACCC
9433 TACTCACCCAATACAAA
1 TACTCACCCAATACAAA
***
9450 TACTCACCTGGTACAAA
1 TACTCACCCAATACAAA
9467 TACTCA
1 TACTCA
9473 TTTGGTCCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.40, C:0.33, G:0.05, T:0.23
Consensus pattern (17 bp):
TACTCACCCAATACAAA
Found at i:9478 original size:17 final size:17
Alignment explanation
Indices: 9444--9539 Score: 99
Period size: 16 Copynumber: 5.8 Consensus size: 17
9434 ACTCACCCAA
9444 TACAAATACTCACCTGG
1 TACAAATACTCACCTGG
**
9461 TACAAATACTCATTTGG
1 TACAAATACTCACCTGG
*
9478 TCCAAATACTCACCTGG
1 TACAAATACTCACCTGG
*
9495 TGC-AATACTCACCTGG
1 TACAAATACTCACCTGG
* * **
9511 T-GAGATACTCACCCAG
1 TACAAATACTCACCTGG
9527 TAC-AATACTCACC
1 TACAAATACTCACC
9540 CGGTGAGGTC
Statistics
Matches: 65, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
16 34 0.52
17 31 0.48
ACGTcount: A:0.32, C:0.30, G:0.12, T:0.25
Consensus pattern (17 bp):
TACAAATACTCACCTGG
Found at i:9533 original size:32 final size:32
Alignment explanation
Indices: 9483--9546 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
9473 TTTGGTCCAA
** * *
9483 ATACTCACCTGGTGCAATACTCACCTGGTGAG
1 ATACTCACCCAGTACAATACTCACCCGGTGAG
9515 ATACTCACCCAGTACAATACTCACCCGGTGAG
1 ATACTCACCCAGTACAATACTCACCCGGTGAG
9547 GTCACCAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.22
Consensus pattern (32 bp):
ATACTCACCCAGTACAATACTCACCCGGTGAG
Found at i:11292 original size:55 final size:55
Alignment explanation
Indices: 11205--11381 Score: 216
Period size: 55 Copynumber: 3.2 Consensus size: 55
11195 ATTAAATATT
*
11205 ACACCATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAAGTTGAAGGCA
1 ACACCATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAAATTGAAGGCA
* * * * * * * *
11260 ACACCATCAGGATCAATTTATTAGTCCTGATGATTTG-A-G-TAATTTTTAATTGACA
1 ACACCATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAA-ATTGAA--GGCA
*
11315 ACACTATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAAATTGAAGGCA
1 ACACCATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAAATTGAAGGCA
11370 ACACCATCAGGA
1 ACACCATCAGGA
11382 TCAAGCTATT
Statistics
Matches: 98, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
52 3 0.03
53 5 0.05
54 1 0.01
55 80 0.82
56 1 0.01
57 5 0.05
58 3 0.03
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.30
Consensus pattern (55 bp):
ACACCATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAAATTGAAGGCA
Found at i:12462 original size:28 final size:29
Alignment explanation
Indices: 12404--12462 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 29
12394 ACCTCTCTCT
*** *
12404 TTCCCCAAAGAGATTCAACGTCTTTCCCC
1 TTCCCCAAAGAGATTCAACGTCAAACACC
*
12433 TTCCCCAAAGAGATTC-ACGTCAAAGACC
1 TTCCCCAAAGAGATTCAACGTCAAACACC
12461 TT
1 TT
12463 TTTGGGCGCA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.29, C:0.34, G:0.12, T:0.25
Consensus pattern (29 bp):
TTCCCCAAAGAGATTCAACGTCAAACACC
Found at i:14760 original size:16 final size:16
Alignment explanation
Indices: 14739--14775 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
14729 AATATATAAT
14739 ACATATTATTTGAATA
1 ACATATTATTTGAATA
14755 ACATATTATTTGAATA
1 ACATATTATTTGAATA
14771 A-ATAT
1 ACATAT
14776 ATGGAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.43
Consensus pattern (16 bp):
ACATATTATTTGAATA
Found at i:15008 original size:45 final size:45
Alignment explanation
Indices: 14944--15033 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
14934 TAGTAGAGTA
14944 GTGGAATTACTAAAAGATCCCTACCCC-GAGTTAATGATAAGCTGG
1 GTGGAATTACTAAAAGATCCCTACCCCGGA-TTAATGATAAGCTGG
*
14989 GTGGAATTACTAAAAGATCCCTACCCCGGATTAATGATGAGCTGG
1 GTGGAATTACTAAAAGATCCCTACCCCGGATTAATGATAAGCTGG
15034 AGAAGTAATC
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
45 41 0.95
46 2 0.05
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.24
Consensus pattern (45 bp):
GTGGAATTACTAAAAGATCCCTACCCCGGATTAATGATAAGCTGG
Found at i:15426 original size:315 final size:316
Alignment explanation
Indices: 14849--15603 Score: 1124
Period size: 315 Copynumber: 2.4 Consensus size: 316
14839 GTCTTTTCCC
* * * * *
14849 ACTTGGCCGATTACTTAAATG-CCATAACTTTTGATTCTCGAGGTGATTAAATAACTAGACTTTT
1 ACTTGGCAGATTACTTAAATGTCC-TAACTTTTGATTCTTGAGGGGATTAAATAAGTA-TCTTTT
* * * *
14913 TGGTCATTTCTCATTTGAATTT-AGTAGAGTAGTGGAATTACTAAAAGATCCCTACCCCGAGTTA
64 TGGTCATTTCTCA-ATGGATTTGAATAGAGTAGTGGAATTACTAAAAGATCCCTACCCCGAATTA
* *
14977 ATGATAAGCTGGGTGGAATTACTAAAAGATCCCTACCCCGGATTAATGATGAGCTGGAGAAGTAA
128 ATGATAAGCTGGATGGAATTACTAAAAGATCCCTACCCCCGATTAATGATGAGCTGGAGAAGTAA
*
15042 TCTTTTTGTCTTTACCTACCTAGCAGATTACTTAAATGTCCTAAACTTTAATAGAGTAGTGGAAT
193 TCTTTTTGTCTTTACCTACCTAGCAAATTACTTAAATGTCCTAAACTTTAATAGAGTAGTGGAAT
* * *
15107 TACTAAAAGATCCCTAATAAGACTTGCTTTTGAAGTTAGAGAACTTA-TTTTTTCG-CT
258 TACTAAAAGACCCCTAACAAGACTTGATTTTGAAGTTAGAGAACTTATTTTTTTCGTCT
15164 ACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAAGTATCTTTTTG
1 ACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAAGTATCTTTTTG
* * * *
15229 GTTATTTCTCAATGGATTTGAATAGAGTAGTGGAATTAATAAATGATCCCTACCCTGAATTAATG
66 GTCATTTCTCAATGGATTTGAATAGAGTAGTGGAATTACTAAAAGATCCCTACCCCGAATTAATG
* * *
15294 ATAAGTTGGATGGAATTACTAAAAGATCTCTACCCCCGATTAATGATGAGCTGGAGAATTAATCT
131 ATAAGCTGGATGGAATTACTAAAAGATCCCTACCCCCGATTAATGATGAGCTGGAGAAGTAATCT
15359 TTTTCGTCTTTACCTACCT-GACAAATTACTTAAATGTCCTAAACTTTAATAGAGTAGTGGAATT
196 TTTT-GTCTTTACCTACCTAG-CAAATTACTTAAATGTCCTAAACTTTAATAGAGTAGTGGAATT
* * *
15423 ACTAAACGACCCCTAACAAGGCTTGATTTTGGAGTTAGAGAACTTATTTTTTTTCGTCTTTTCCT
259 ACTAAAAGACCCCTAACAAGACTTGATTTTGAAGTTAGAGAACTTA-TTTTTTTCG-----T-CT
*
15488 ACTTGGTAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAAGTAATCTTTTT
1 ACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAAGT-ATCTTTTT
15553 GGTCATTTCTCAATGGATTTGAATAGAGTAGTGGAATTACTAAAAGATCCC
65 GGTCATTTCTCAATGGATTTGAATAGAGTAGTGGAATTACTAAAAGATCCC
15604 CATCAAGGAT
Statistics
Matches: 397, Mismatches: 29, Indels: 18
0.89 0.07 0.04
Matches are distributed among these distances:
313 6 0.02
314 122 0.31
315 146 0.37
316 2 0.01
317 8 0.02
324 57 0.14
325 56 0.14
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (316 bp):
ACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAAGTATCTTTTTG
GTCATTTCTCAATGGATTTGAATAGAGTAGTGGAATTACTAAAAGATCCCTACCCCGAATTAATG
ATAAGCTGGATGGAATTACTAAAAGATCCCTACCCCCGATTAATGATGAGCTGGAGAAGTAATCT
TTTTGTCTTTACCTACCTAGCAAATTACTTAAATGTCCTAAACTTTAATAGAGTAGTGGAATTAC
TAAAAGACCCCTAACAAGACTTGATTTTGAAGTTAGAGAACTTATTTTTTTCGTCT
Found at i:15667 original size:166 final size:168
Alignment explanation
Indices: 15406--15732 Score: 473
Period size: 166 Copynumber: 2.0 Consensus size: 168
15396 CCTAAACTTT
* * ** **
15406 AATAGAGTAGTGGAATTACTAAACGACCCCTAACAAGGCTTGATTTTGGAGTTAGAGAACTTATT
1 AATAGAGTAGTGGAATTACTAAAAGACCCCTAACAAGGATTGATGATGGAGTTAGAGAACTTAAC
* * *
15471 TTTTTTCGTCTTTTCCTACTTGGTAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATT
66 ATTTTTCGTCTTTACCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATT
*
15536 AAATAAGT-AATCTTTTTGGTCATTTCTCAATGGATTTG
131 AAATAACTAAAT-TTTTTGGTCATTTCTCAATGGATTTG
*
15574 AATAGAGTAGTGGAATTACTAAAAGATCCCC-ATCAAGGATTGATGAT-GAGTTAGAGAAC-TAA
1 AATAGAGTAGTGGAATTACTAAAAGA-CCCCTAACAAGGATTGATGATGGAGTTAGAGAACTTAA
* * * *
15636 CATTTTTCGTCTTTACTTACTTGGCAGATTACTTAAATGTCCTAATTTTTTATTTTTGAGGGGAT
65 CATTTTTCGTCTTTACCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGAT
15701 TAAATAACTAAATTTTTTGGTCATTTCTCAAT
130 TAAATAACTAAATTTTTTGGTCATTTCTCAAT
15733 TGACAAATGA
Statistics
Matches: 142, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
166 86 0.61
167 15 0.11
168 37 0.26
169 4 0.03
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (168 bp):
AATAGAGTAGTGGAATTACTAAAAGACCCCTAACAAGGATTGATGATGGAGTTAGAGAACTTAAC
ATTTTTCGTCTTTACCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATT
AAATAACTAAATTTTTTGGTCATTTCTCAATGGATTTG
Done.