Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016047.1 Corchorus capsularis cultivar CVL-1 contig16068, 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: 35803
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--39 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
40 GCCTTTGCCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:183 original size:41 final size:42
Alignment explanation
Indices: 118--398 Score: 220
Period size: 41 Copynumber: 6.6 Consensus size: 42
108 AAGTTGCCCT
* * * *
118 TGTGTTATCATTGTGTTT-AGGGACTTTAGTATAG-GTGCCTC
1 TGTGTTATAAATGTGTTTGA-GGACTTTAGAATAGAATGCCTC
* *
159 TGTGTTATAAATGTGCTTGAGGACTTT-GAAATAGAGATGTCC-A
1 TGTGTTATAAATGTGTTTGAGGACTTTAG-AATAGA-ATG-CCTC
* * *
202 TGTGTTATAATTGTGCTTGGGGACTTT-GAAATAG-ATGCCTC
1 TGTGTTATAAATGTGTTTGAGGACTTTAG-AATAGAATGCCTC
* * *
243 TGTGTTATAAATGTGTTTGAGAACTTTCAAAAGAGAATTG-CTCC
1 TGTGTTATAAATGTGTTTGAGGACTTT-AGAATAGAA-TGCCT-C
* * *
287 TGTGTTATAAATGTGTTTGGGGACTTTGGTAT-GAATGCCTC
1 TGTGTTATAAATGTGTTTGAGGACTTTAGAATAGAATGCCTC
** * *
328 TGTGTTATAAATGTGTTTGAGGACTTCCTA-AGGAGAGTTGCCCC
1 TGTGTTATAAATGTGTTTGAGGACTT--TAGAATAGA-ATGCCTC
*
372 TGTGTTATAAATGTGTTTGGGGACTTT
1 TGTGTTATAAATGTGTTTGAGGACTTT
399 GATTATTGGG
Statistics
Matches: 195, Mismatches: 29, Indels: 31
0.76 0.11 0.12
Matches are distributed among these distances:
40 3 0.02
41 80 0.41
42 11 0.06
43 41 0.21
44 60 0.31
ACGTcount: A:0.23, C:0.11, G:0.26, T:0.39
Consensus pattern (42 bp):
TGTGTTATAAATGTGTTTGAGGACTTTAGAATAGAATGCCTC
Found at i:329 original size:85 final size:86
Alignment explanation
Indices: 104--399 Score: 354
Period size: 85 Copynumber: 3.5 Consensus size: 86
94 TTTGCCATAT
* * * * * *
104 AGAGAAGTTGC-CCTTGTGTTATCATTGTGTTTAGGGACTTTAGTATAGGTGCCTCTGTGTTATA
1 AGAGAA-TTGCTCCATGTGTTATAAATGTGTTTGGGGACTTTGGTATAGATGCCTCTGTGTTATA
* *
168 AATGTGCTTGAGGACTTTGAAA
65 AATGTGTTTGAGGACTTTCAAA
* * **
190 TAGAG-A-TG-TCCATGTGTTATAATTGTGCTTGGGGACTTTGAAATAGATGCCTCTGTGTTATA
1 -AGAGAATTGCTCCATGTGTTATAAATGTGTTTGGGGACTTTGGTATAGATGCCTCTGTGTTATA
*
252 AATGTGTTTGAGAACTTTCAAA
65 AATGTGTTTGAGGACTTTCAAA
274 AGAGAATTGCTCC-TGTGTTATAAATGTGTTTGGGGACTTTGGTAT-GAATGCCTCTGTGTTATA
1 AGAGAATTGCTCCATGTGTTATAAATGTGTTTGGGGACTTTGGTATAG-ATGCCTCTGTGTTATA
* *
337 AATGTGTTTGAGGACTTCCTAA
65 AATGTGTTTGAGGACTTTCAAA
* * *
359 GGAGAGTTGC-CCCTGTGTTATAAATGTGTTTGGGGACTTTG
1 AGAGAATTGCTCCATGTGTTATAAATGTGTTTGGGGACTTTG
400 ATTATTGGGT
Statistics
Matches: 183, Mismatches: 20, Indels: 14
0.84 0.09 0.06
Matches are distributed among these distances:
83 4 0.02
84 70 0.38
85 101 0.55
86 4 0.02
87 4 0.02
ACGTcount: A:0.24, C:0.11, G:0.27, T:0.38
Consensus pattern (86 bp):
AGAGAATTGCTCCATGTGTTATAAATGTGTTTGGGGACTTTGGTATAGATGCCTCTGTGTTATAA
ATGTGTTTGAGGACTTTCAAA
Found at i:7328 original size:2 final size:2
Alignment explanation
Indices: 7321--7346 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
7311 CCAATCTGGA
7321 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
7347 GTATGTATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13614 original size:18 final size:17
Alignment explanation
Indices: 13581--13615 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
13571 AAAAAATATT
*
13581 TAAAAAATTTTGAAAAA
1 TAAAAAATTTTAAAAAA
13598 TAAAAAATATTTAAAAAA
1 TAAAAAAT-TTTAAAAAA
13616 GCCATGTAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (17 bp):
TAAAAAATTTTAAAAAA
Found at i:13746 original size:40 final size:40
Alignment explanation
Indices: 13702--13830 Score: 111
Period size: 41 Copynumber: 3.1 Consensus size: 40
13692 TTTCAAACGT
13702 TTGGTACCTAATAATTCGAAATTATAGATTTGGTACCAAG
1 TTGGTACCTAATAATTCGAAATTATAGATTTGGTACCAAG
* * * ** * * *
13742 TTGGTACATAAAAAAGTACTTAATTAGACGAAATT--T-CAAACG
1 TTGGTACCT-AATAA-TTCGAAATTATA-G-ATTTGGTACCAA-G
13784 TTTGGTACCTAATAATTCGAAATTATAGATTTGGTACCAAG
1 -TTGGTACCTAATAATTCGAAATTATAGATTTGGTACCAAG
13825 TTGGTA
1 TTGGTA
13831 TTTTCATACC
Statistics
Matches: 64, Mismatches: 16, Indels: 18
0.65 0.16 0.18
Matches are distributed among these distances:
39 3 0.05
40 15 0.23
41 17 0.27
42 17 0.27
43 9 0.14
44 3 0.05
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (40 bp):
TTGGTACCTAATAATTCGAAATTATAGATTTGGTACCAAG
Found at i:13755 original size:83 final size:83
Alignment explanation
Indices: 13665--13830 Score: 332
Period size: 83 Copynumber: 2.0 Consensus size: 83
13655 GATTGCACTT
13665 CATAAAAAAGTACTTAATTAGACGAAATTTCAAACGTTTGGTACCTAATAATTCGAAATTATAGA
1 CATAAAAAAGTACTTAATTAGACGAAATTTCAAACGTTTGGTACCTAATAATTCGAAATTATAGA
13730 TTTGGTACCAAGTTGGTA
66 TTTGGTACCAAGTTGGTA
13748 CATAAAAAAGTACTTAATTAGACGAAATTTCAAACGTTTGGTACCTAATAATTCGAAATTATAGA
1 CATAAAAAAGTACTTAATTAGACGAAATTTCAAACGTTTGGTACCTAATAATTCGAAATTATAGA
13813 TTTGGTACCAAGTTGGTA
66 TTTGGTACCAAGTTGGTA
13831 TTTTCATACC
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 83 1.00
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.33
Consensus pattern (83 bp):
CATAAAAAAGTACTTAATTAGACGAAATTTCAAACGTTTGGTACCTAATAATTCGAAATTATAGA
TTTGGTACCAAGTTGGTA
Found at i:13790 original size:43 final size:43
Alignment explanation
Indices: 13665--13791 Score: 113
Period size: 41 Copynumber: 3.0 Consensus size: 43
13655 GATTGCACTT
13665 CATAAAAAAGTACTTAATTAGACGAAATTTCAAACGTTTGGTA
1 CATAAAAAAGTACTTAATTAGACGAAATTTCAAACGTTTGGTA
* * * ** * * *
13708 CCT-AATAA-TTCGAAATTATA-G-ATTTGGTACCAA-G-TTGGTA
1 CATAAAAAAGTACTTAATTAGACGAAATT--T-CAAACGTTTGGTA
13748 CATAAAAAAGTACTTAATTAGACGAAATTTCAAACGTTTGGTA
1 CATAAAAAAGTACTTAATTAGACGAAATTTCAAACGTTTGGTA
13791 C
1 C
13792 CTAATAATTC
Statistics
Matches: 59, Mismatches: 16, Indels: 18
0.63 0.17 0.19
Matches are distributed among these distances:
39 3 0.05
40 9 0.15
41 17 0.29
42 17 0.29
43 10 0.17
44 3 0.05
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (43 bp):
CATAAAAAAGTACTTAATTAGACGAAATTTCAAACGTTTGGTA
Found at i:21356 original size:18 final size:18
Alignment explanation
Indices: 21318--21361 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
21308 ATCATCGCAT
**
21318 TCATCATCTTCATAATCC
1 TCATCATCTTCATAAGAC
*
21336 TCATCATCTTCATAGGAC
1 TCATCATCTTCATAAGAC
21354 TCATCATC
1 TCATCATC
21362 ATCAGTTGCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.32, G:0.05, T:0.36
Consensus pattern (18 bp):
TCATCATCTTCATAAGAC
Found at i:26059 original size:16 final size:14
Alignment explanation
Indices: 26030--26063 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
26020 CCAAATCAGA
26030 AAAATAATAATAAT
1 AAAATAATAATAAT
26044 AAAATAAATAAATAAT
1 AAAAT-AAT-AATAAT
26060 AAAA
1 AAAA
26064 GGAGACAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 3 0.17
16 10 0.56
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
AAAATAATAATAAT
Found at i:28587 original size:236 final size:236
Alignment explanation
Indices: 28169--28638 Score: 931
Period size: 236 Copynumber: 2.0 Consensus size: 236
28159 TCCCCCTTAA
*
28169 AAGTGATAAAAGCAAAAAAAACATATTCTCAACACAACTTCTCCTTTAAAAATCAGAACTTATGG
1 AAGTAATAAAAGCAAAAAAAACATATTCTCAACACAACTTCTCCTTTAAAAATCAGAACTTATGG
28234 TTCAAAAAGAGGAATGCAAATTGATCTACACCTGTTGTCCTTGAGGCGGCTCTTCCTTTTTGGAA
66 TTCAAAAAGAGGAATGCAAATTGATCTACACCTGTTGTCCTTGAGGCGGCTCTTCCTTTTTGGAA
28299 GGCATCTTCTGCTGACAAAATTACACCACAAACCATCAGGGGAAAAAAAGAAAGAGAAAAAAAAT
131 GGCATCTTCTGCTGACAAAATTACACCACAAACCATCAGGGGAAAAAAAGAAAGAGAAAAAAAAT
28364 CAATTGAATTTCCTTAAAACCATATATAAATGTCAGTTTAT
196 CAATTGAATTTCCTTAAAACCATATATAAATGTCAGTTTAT
28405 AAGTAATAAAAGCAAAAAAAACATATTCTCAACACAACTTCTCCTTTAAAAATCAGAACTTATGG
1 AAGTAATAAAAGCAAAAAAAACATATTCTCAACACAACTTCTCCTTTAAAAATCAGAACTTATGG
28470 TTCAAAAAGAGGAATGCAAATTGATCTACACCTGTTGTCCTTGAGGCGGCTCTTCCTTTTTGGAA
66 TTCAAAAAGAGGAATGCAAATTGATCTACACCTGTTGTCCTTGAGGCGGCTCTTCCTTTTTGGAA
28535 GGCATCTTCTGCTGACAAAATTACACCACAAACCATCAGGGGAAAAAAAGAAAGAGAAAAAAAAT
131 GGCATCTTCTGCTGACAAAATTACACCACAAACCATCAGGGGAAAAAAAGAAAGAGAAAAAAAAT
28600 CAATTGAATTTCCTTAAAACCATATATAAATGTCAGTTT
196 CAATTGAATTTCCTTAAAACCATATATAAATGTCAGTTT
28639 TTAAAAAAAA
Statistics
Matches: 233, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
236 233 1.00
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.26
Consensus pattern (236 bp):
AAGTAATAAAAGCAAAAAAAACATATTCTCAACACAACTTCTCCTTTAAAAATCAGAACTTATGG
TTCAAAAAGAGGAATGCAAATTGATCTACACCTGTTGTCCTTGAGGCGGCTCTTCCTTTTTGGAA
GGCATCTTCTGCTGACAAAATTACACCACAAACCATCAGGGGAAAAAAAGAAAGAGAAAAAAAAT
CAATTGAATTTCCTTAAAACCATATATAAATGTCAGTTTAT
Found at i:35772 original size:60 final size:60
Alignment explanation
Indices: 35635--35777 Score: 207
Period size: 60 Copynumber: 2.4 Consensus size: 60
35625 AACGTTTGCC
* * * * *
35635 AAAATACTCAAATAAGGATCCGATCTTTTAATTTGGTCAAATAAGGGTCTAACGTTATCG
1 AAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGCCAAATAAGGGTCTAACATTATCG
35695 AAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGCCAAATAAGGG-CATAACATTATCG
1 AAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGCCAAATAAGGGTC-TAACATTATCG
* *
35755 AAAATGCTTAAATAAGGGCCTGA
1 AAAATGCTCAAATAAGGGTCTGA
35778 CGTCAGTTTG
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
59 1 0.01
60 74 0.99
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (60 bp):
AAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGCCAAATAAGGGTCTAACATTATCG
Done.