Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015922.1 Corchorus capsularis cultivar CVL-1 contig15943, 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: 50721
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:6119 original size:114 final size:112
Alignment explanation
Indices: 5916--6145 Score: 322
Period size: 114 Copynumber: 2.0 Consensus size: 112
5906 AGGCTGTTAA
** *
5916 TAGCCATTCTTCTTGTTGATGGCTCATTTATTTTGTTGATAACTAATTTGGTATATCCTTTAAAA
1 TAGCCATTCTTCTTGTAAATGGCACATTTATTTTGTTGATAACTAATTTGGTATATCCTTTAAAA
* *
5981 CTATATTCTGCTATCATGTATGTAAAGAAGTGTAAAGGGTTAGCTATT
66 CTATATTCTGCTATCATG-ATGTAAAGAAGTGTAAAGGGTTACCTACT
*
6029 TAGCCATTCTTTTTTGTAAATGGCACATTCT-TTTTGTTGATAACTAATTTGGTATATCCTTT-A
1 TAGCCATTC-TTCTTGTAAATGGCACATT-TATTTTGTTGATAACTAATTTGGTATATCCTTTAA
*
6092 AACTATATATTTCTGCTATCATG-TGTAAAGCAGTGTAAAGGGTTACCTACT
64 AAC--TATA-TTCTGCTATCATGATGTAAAGAAGTGTAAAGGGTTACCTACT
6143 TAG
1 TAG
6146 ACTTATTACT
Statistics
Matches: 105, Mismatches: 7, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
113 13 0.12
114 74 0.70
115 5 0.05
116 13 0.12
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.43
Consensus pattern (112 bp):
TAGCCATTCTTCTTGTAAATGGCACATTTATTTTGTTGATAACTAATTTGGTATATCCTTTAAAA
CTATATTCTGCTATCATGATGTAAAGAAGTGTAAAGGGTTACCTACT
Found at i:8475 original size:14 final size:14
Alignment explanation
Indices: 8453--8482 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
8443 ACACAGTTCT
8453 ATCTCTTTCTTTTC
1 ATCTCTTTCTTTTC
*
8467 ATCTTTTTCTTTTC
1 ATCTCTTTCTTTTC
8481 AT
1 AT
8483 TTATTTTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.10, C:0.23, G:0.00, T:0.67
Consensus pattern (14 bp):
ATCTCTTTCTTTTC
Found at i:15399 original size:22 final size:22
Alignment explanation
Indices: 15352--15400 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
15342 GTGAGGGAGG
*
15352 AAGAAAGAAAGAAAAAAGAAAG
1 AAGAAAGAAAGAAAAAAGAAAA
**
15374 AAGAAAG-AAGAAGAAGTGAAAA
1 AAGAAAGAAAGAA-AAAAGAAAA
15396 AAGAA
1 AAGAA
15401 TAAAATAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.02
Consensus pattern (22 bp):
AAGAAAGAAAGAAAAAAGAAAA
Found at i:17004 original size:26 final size:26
Alignment explanation
Indices: 16968--17040 Score: 101
Period size: 27 Copynumber: 2.7 Consensus size: 26
16958 TATATTCCTA
*
16968 TGTTTCTTTTTAATTTTCCAAACTTT
1 TGTTTTTTTTTAATTTTCCAAACTTT
*
16994 TGTTTTTTTTTAATTATCACAAACTTT
1 TGTTTTTTTTTAATTTTC-CAAACTTT
*
17021 TGTTCTTTTTTAATTGTTCC
1 TGTTTTTTTTTAATT-TTCC
17041 TCTTTATTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
26 16 0.39
27 23 0.56
28 2 0.05
ACGTcount: A:0.19, C:0.14, G:0.05, T:0.62
Consensus pattern (26 bp):
TGTTTTTTTTTAATTTTCCAAACTTT
Found at i:17275 original size:28 final size:28
Alignment explanation
Indices: 17235--17295 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
17225 AAAAAGGAAC
* *
17235 AGAGAGAGTATAATATATATATATATAT
1 AGAGGGAGTATAATATATATATATATAG
17263 AGAGGGAGTATAATATATATATATATAG
1 AGAGGGAGTATAATATATATATATATAG
17291 AGAGG
1 AGAGG
17296 ATAATTCAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.21, T:0.31
Consensus pattern (28 bp):
AGAGGGAGTATAATATATATATATATAG
Found at i:17299 original size:24 final size:25
Alignment explanation
Indices: 17249--17300 Score: 79
Period size: 26 Copynumber: 2.1 Consensus size: 25
17239 AGAGTATAAT
*
17249 ATATATATATATATAGAGGGAGTATA
1 ATATATATATATATAGA-GGAGGATA
17275 ATATATATATATATAGA-GAGGATA
1 ATATATATATATATAGAGGAGGATA
17299 AT
1 AT
17301 TCAGTTCCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 8 0.32
26 17 0.68
ACGTcount: A:0.48, C:0.00, G:0.17, T:0.35
Consensus pattern (25 bp):
ATATATATATATATAGAGGAGGATA
Found at i:20502 original size:11 final size:11
Alignment explanation
Indices: 20488--20517 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
20478 CAATATGTAA
20488 AGAATTAGTCC
1 AGAATTAGTCC
20499 AGAATTAGTCC
1 AGAATTAGTCC
*
20510 AAAATTAG
1 AGAATTAG
20518 GATATTATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (11 bp):
AGAATTAGTCC
Found at i:30321 original size:35 final size:35
Alignment explanation
Indices: 30277--30352 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 35
30267 TTAAAAAATC
* * *
30277 TAAACAAATAAACAGTATAGAAAGAGGTTTACTAA
1 TAAAAAAATAAACAGTATAGAAAGAAGTTTACCAA
* *
30312 TAAAAAAATAAAGAGTCTAGAAAGAAGTTTACCAA
1 TAAAAAAATAAACAGTATAGAAAGAAGTTTACCAA
30347 TAAAAA
1 TAAAAA
30353 CAATTACATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.58, C:0.08, G:0.13, T:0.21
Consensus pattern (35 bp):
TAAAAAAATAAACAGTATAGAAAGAAGTTTACCAA
Found at i:32242 original size:29 final size:29
Alignment explanation
Indices: 32202--32257 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
32192 ACTTTCCCCA
32202 AAATAGCTTTAAGTTCCTCCTTCATCTCC
1 AAATAGCTTTAAGTTCCTCCTTCATCTCC
32231 AAATAGCTTTAAGTTCCTCCTTCATCT
1 AAATAGCTTTAAGTTCCTCCTTCATCT
32258 TACATGTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.25, C:0.29, G:0.07, T:0.39
Consensus pattern (29 bp):
AAATAGCTTTAAGTTCCTCCTTCATCTCC
Found at i:37794 original size:16 final size:15
Alignment explanation
Indices: 37771--37861 Score: 83
Period size: 16 Copynumber: 5.7 Consensus size: 15
37761 CAACCCGAGA
37771 CCGAACCCGAGAATAC
1 CCGAACCCGA-AATAC
* *
37787 CTGAACCCGACATAGC
1 CCGAACCCGAAATA-C
*
37803 CCGAGCCCGAAAATAC
1 CCGAACCCG-AAATAC
*
37819 CCGAACCCGACATAAC
1 CCGAACCCGAAAT-AC
*
37835 CCGAGCCCGAAAATAC
1 CCGAACCCG-AAATAC
*
37851 CTGAACCCGAA
1 CCGAACCCGAA
37862 CCCGCCCAAT
Statistics
Matches: 60, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
15 8 0.13
16 45 0.75
17 7 0.12
ACGTcount: A:0.36, C:0.38, G:0.18, T:0.08
Consensus pattern (15 bp):
CCGAACCCGAAATAC
Found at i:37818 original size:32 final size:32
Alignment explanation
Indices: 37771--37860 Score: 144
Period size: 32 Copynumber: 2.8 Consensus size: 32
37761 CAACCCGAGA
* * *
37771 CCGAACCCGAGAATACCTGAACCCGACATAGC
1 CCGAGCCCGAAAATACCTGAACCCGACATAAC
*
37803 CCGAGCCCGAAAATACCCGAACCCGACATAAC
1 CCGAGCCCGAAAATACCTGAACCCGACATAAC
37835 CCGAGCCCGAAAATACCTGAACCCGA
1 CCGAGCCCGAAAATACCTGAACCCGA
37861 ACCCGCCCAA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.36, C:0.39, G:0.18, T:0.08
Consensus pattern (32 bp):
CCGAGCCCGAAAATACCTGAACCCGACATAAC
Found at i:42502 original size:25 final size:25
Alignment explanation
Indices: 42474--42523 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
42464 TCCAATCCTT
42474 AATTTCTTAAATACATTAGTAGGCA
1 AATTTCTTAAATACATTAGTAGGCA
42499 AATTTCTTAAATACATTAGTAGGCA
1 AATTTCTTAAATACATTAGTAGGCA
42524 CAAAGCATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (25 bp):
AATTTCTTAAATACATTAGTAGGCA
Found at i:44304 original size:41 final size:41
Alignment explanation
Indices: 44259--44506 Score: 338
Period size: 41 Copynumber: 6.0 Consensus size: 41
44249 TCATATGCAT
* * *
44259 AAGTAAACATAGTCAAAGTCTTAATTCAGTGTAATTAAGAA
1 AAGTAAACACAGTCAAGGTCTTAATTCAGGGTAATTAAGAA
44300 AAGTAAACACAGTCAAGGTCTTAATTCAGGGTAATTAAG-A
1 AAGTAAACACAGTCAAGGTCTTAATTCAGGGTAATTAAGAA
* * * *
44340 GAGCAAACACAGTCATGGTCTTAATTTAGGGTAATTAAGAA
1 AAGTAAACACAGTCAAGGTCTTAATTCAGGGTAATTAAGAA
* * *
44381 AAGCAAACACAGTTAAGGTCTTAATTCAGGGCAATTAAGAA
1 AAGTAAACACAGTCAAGGTCTTAATTCAGGGTAATTAAGAA
*
44422 AAGTAAACACAGTTAAGGTCTTAATTCAGGGTAATTAAGAA
1 AAGTAAACACAGTCAAGGTCTTAATTCAGGGTAATTAAGAA
* * *
44463 AAGTAAA-AGCTGTCAAAGACTTAATTCAGGGTAATTAAGTAA
1 AAGTAAACA-CAGTCAAGGTCTTAATTCAGGGTAATTAAG-AA
44505 AA
1 AA
44507 TCACTAAAGG
Statistics
Matches: 186, Mismatches: 18, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
40 37 0.20
41 145 0.78
42 4 0.02
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.26
Consensus pattern (41 bp):
AAGTAAACACAGTCAAGGTCTTAATTCAGGGTAATTAAGAA
Found at i:45997 original size:19 final size:18
Alignment explanation
Indices: 45964--45999 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
45954 CTCCAATAAT
45964 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
45982 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
46000 GAAATCTTCA
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:46196 original size:20 final size:21
Alignment explanation
Indices: 46158--46196 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
46148 TAGAAAATAA
*
46158 GGTAAAAATGCATATAAAAGT
1 GGTAAAAATGCATAGAAAAGT
*
46179 GGTAAAAA-GTATAGAAAA
1 GGTAAAAATGCATAGAAAA
46197 ATAGCTATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.56, C:0.03, G:0.21, T:0.21
Consensus pattern (21 bp):
GGTAAAAATGCATAGAAAAGT
Found at i:48280 original size:19 final size:18
Alignment explanation
Indices: 48256--48292 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
48246 TTGAAGATTT
48256 CTTGAAGACAATTTGAAGA
1 CTTGAAGACAA-TTGAAGA
*
48275 CTTGAAGACCATTGAAGA
1 CTTGAAGACAATTGAAGA
48293 ATTATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.24
Consensus pattern (18 bp):
CTTGAAGACAATTGAAGA
Done.