Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013256.1 Corchorus capsularis cultivar CVL-1 contig13277, 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: 27351
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:110 original size:23 final size:22
Alignment explanation
Indices: 47--116 Score: 74
Period size: 19 Copynumber: 3.1 Consensus size: 22
37 ATATATTTTT
47 AATATATATTTATATTATTAGTA
1 AATATATATTTAT-TTATTAGTA
70 AATTAGTAAATATTTATTTATTAGT-
1 AA-TA-T--ATATTTATTTATTAGTA
95 -ATATATA-TTATTTATTAGTA
1 AATATATATTTATTTATTAGTA
115 AA
1 AA
117 ACATATCTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
19 12 0.29
20 3 0.07
21 1 0.02
22 1 0.02
23 4 0.10
24 3 0.07
25 1 0.02
26 8 0.20
27 8 0.20
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (22 bp):
AATATATATTTATTTATTAGTA
Found at i:191 original size:2 final size:2
Alignment explanation
Indices: 186--228 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
176 TAAAAAAAAC
*
186 AT AT AT AT -T A- AT AT AT AT AT AT AT AT AT AT AC AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
225 AT AT
1 AT AT
229 TTCAGGGCCG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
1 3 0.08
2 33 0.92
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6126 original size:1 final size:1
Alignment explanation
Indices: 6122--6156 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
6112 AAAATATAGG
6122 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
6157 CTCACCCAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:21587 original size:15 final size:15
Alignment explanation
Indices: 21569--21600 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
21559 ATATTTTTCC
21569 TTAATGTATTATTAA
1 TTAATGTATTATTAA
*
21584 TTAATTTATTATTAA
1 TTAATGTATTATTAA
21599 TT
1 TT
21601 CGGCGTTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (15 bp):
TTAATGTATTATTAA
Found at i:22688 original size:32 final size:32
Alignment explanation
Indices: 22642--22726 Score: 125
Period size: 32 Copynumber: 2.7 Consensus size: 32
22632 AAAAATTTGG
* *
22642 TGCCGTGGCAAAGCCACCCCATGAAGGCGGCC
1 TGCCGTGGCGAAGCCGCCCCATGAAGGCGGCC
* *
22674 TGCCGTGGCGAAGCCGCCTCATGAGGGCGGCC
1 TGCCGTGGCGAAGCCGCCCCATGAAGGCGGCC
*
22706 TGCTGTGGCGAAGCCGCCCCA
1 TGCCGTGGCGAAGCCGCCCCA
22727 GTGGGGAGGC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.16, C:0.36, G:0.35, T:0.12
Consensus pattern (32 bp):
TGCCGTGGCGAAGCCGCCCCATGAAGGCGGCC
Found at i:23306 original size:22 final size:22
Alignment explanation
Indices: 23281--23903 Score: 392
Period size: 22 Copynumber: 28.8 Consensus size: 22
23271 TGTCACATTT
*
23281 TATGAAATTTTGATAA-CTACAC
1 TATGAAATTTTGGTAACCT-CAC
**
23303 TATGAAATTTTGGTAACCTGTC
1 TATGAAATTTTGGTAACCTCAC
* *
23325 TATGGAATTTTGGTAACCTGAC
1 TATGAAATTTTGGTAACCTCAC
* *
23347 TATGAAATTTTGGTAATCTCAT
1 TATGAAATTTTGGTAACCTCAC
* *
23369 TATGAAATTTGGGTAACGTCGACAC
1 TATGAAATTTTGGTAAC--C-TCAC
* * *
23394 TATGAAAATTCTGGCAACCTTC-T
1 TATG-AAATTTTGGTAACC-TCAC
*
23417 TATGAAA-TTTGAGTAACATC-C
1 TATGAAATTTTG-GTAACCTCAC
*
23438 TATGAAATTTTGGAAACCTC-C
1 TATGAAATTTTGGTAACCTCAC
* *
23459 ATAGGAAATTTTGGTTACC-C-C
1 -TATGAAATTTTGGTAACCTCAC
23480 TATGAAATTTTGGTAA-CTGCAC
1 TATGAAATTTTGGTAACCT-CAC
*
23502 TATGAAATTTTTGTAACCTCAC
1 TATGAAATTTTGGTAACCTCAC
* ** * *
23524 TATGGAATTCAGATAACC-C-T
1 TATGAAATTTTGGTAACCTCAC
* *
23544 TATGAAATTTCGATAACCTCAC
1 TATGAAATTTTGGTAACCTCAC
* * * *
23566 AATTAAATTTTTGTAAGCTCAC
1 TATGAAATTTTGGTAACCTCAC
* *
23588 TATGAAATTTTTGTAGCCTTC-C
1 TATGAAATTTTGGTAACC-TCAC
** *
23610 TAAAAAATATTGGTAACC-C-C
1 TATGAAATTTTGGTAACCTCAC
*
23630 TATGAAATATTGGTAACCTCAC
1 TATGAAATTTTGGTAACCTCAC
* * *
23652 AATGAAATTTTGGTCATC-CA-
1 TATGAAATTTTGGTAACCTCAC
*
23672 TATGAAATTTCT-GTAACCTCCC
1 TATGAAATTT-TGGTAACCTCAC
* * * **
23694 TGTGAAATTTTTGTAGCCGGAC
1 TATGAAATTTTGGTAACCTCAC
*
23716 TATGAAATTGAT-GTAACCTCAC
1 TATGAAATT-TTGGTAACCTCAC
* ** *
23738 TATGAAAATTTCATAAACTCAC
1 TATGAAATTTTGGTAACCTCAC
* * * *
23760 --TGTAATGTTGATAACCT-AT
1 TATGAAATTTTGGTAACCTCAC
* * *
23779 TTTGAAATATTGGTAACC-CAT
1 TATGAAATTTTGGTAACCTCAC
*
23800 TATGAAATTTTGGTAACCTCCC
1 TATGAAATTTTGGTAACCTCAC
* *
23822 TATGAAATTTTGGTAA-ATCCC
1 TATGAAATTTTGGTAACCTCAC
* * * *
23843 TATGAGATTTTAGTAACCCCAG
1 TATGAAATTTTGGTAACCTCAC
* *
23865 TAT-AAAATTTAGTAACCTCAC
1 TATGAAATTTTGGTAACCTCAC
*
23886 CATGAAATTTTGGTAACC
1 TATGAAATTTTGGTAACC
23904 CCCACTATTC
Statistics
Matches: 465, Mismatches: 107, Indels: 58
0.74 0.17 0.09
Matches are distributed among these distances:
19 2 0.00
20 72 0.15
21 96 0.21
22 265 0.57
23 11 0.02
24 3 0.01
25 6 0.01
26 10 0.02
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.35
Consensus pattern (22 bp):
TATGAAATTTTGGTAACCTCAC
Found at i:23349 original size:44 final size:42
Alignment explanation
Indices: 23301--23665 Score: 141
Period size: 42 Copynumber: 8.4 Consensus size: 42
23291 TGATAACTAC
23301 ACTATGAAATTTTGGTAACCTGTCTATGGAATTTTGGTAACCT
1 ACTATGAAATTTTGGTAACCT-TCTATGGAATTTTGGTAACCT
* * * *
23344 GACTATGAAATTTTGGTAATC-TCATTATGAAATTTGGGTAACGTCGAC
1 -ACTATGAAATTTTGGTAACCTTC--TATGGAATTTTGGTAAC--C--T
* * * *
23392 ACTATGAAAATTCTGGCAACCTTCTTAT-GAAATTTGAGTAACAT
1 ACTATG-AAATTTTGGTAACCTTC-TATGGAATTTTG-GTAACCT
* * * *
23436 CCTATGAAATTTTGGAAACC-TCCATAGGAAATTTTGGTTACC-
1 ACTATGAAATTTTGGTAACCTTCTAT-GG-AATTTTGGTAACCT
* * * *
23478 CCTATGAAATTTTGGTAA-CTGCACTATGAAATTTTTGTAACCT
1 ACTATGAAATTTTGGTAACCT--TCTATGGAATTTTGGTAACCT
* ** * * * * *
23521 CACTATGGAATTCAGATAACCCT-TATGAAATTTCGATAACCT
1 -ACTATGAAATTTTGGTAACCTTCTATGGAATTTTGGTAACCT
* * * * * * * *
23563 CACAATTAAATTTTTGTAAGCTCACTATGAAATTTTTGTAGCCTT
1 -ACTATGAAATTTTGGTAACCT-TCTATGGAATTTTGGTAACC-T
* ** * * * *
23608 CCTAAAAAATATTGGTAACC-CCTATGAAATATTGGTAACCT
1 ACTATGAAATTTTGGTAACCTTCTATGGAATTTTGGTAACCT
*
23649 CACAATGAAATTTTGGT
1 -ACTATGAAATTTTGGT
23666 CATCCATATG
Statistics
Matches: 234, Mismatches: 65, Indels: 46
0.68 0.19 0.13
Matches are distributed among these distances:
41 4 0.02
42 88 0.38
43 18 0.08
44 88 0.38
45 2 0.01
46 1 0.00
47 11 0.05
48 20 0.09
49 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (42 bp):
ACTATGAAATTTTGGTAACCTTCTATGGAATTTTGGTAACCT
Found at i:23467 original size:91 final size:91
Alignment explanation
Indices: 23299--23469 Score: 206
Period size: 91 Copynumber: 1.9 Consensus size: 91
23289 TTTGATAACT
* * * * * *
23299 ACACTATGAAATTTTGGTAACCTGTCTATGGAATTTTGGTAACCTGACTATGAAATTTTGGTAAT
1 ACACTATGAAATTCTGGCAACCTGTCTATGGAAATTTGGTAACATGACTATGAAATTTTGGAAAC
*
23364 CTCATTATGAAATTTGGGTAACGTCG
66 CTCATTAGGAAATTTGGGTAACGTCG
*
23390 ACACTATGAAAATTCTGGCAACCT-TCTTAT-GAAATTTGAGTAACAT-CCTATGAAATTTTGGA
1 ACACTATG-AAATTCTGGCAACCTGTC-TATGGAAATTTG-GTAACATGACTATGAAATTTTGGA
23452 AACCTCCA-TAGGAAATTT
63 AACCT-CATTAGGAAATTT
23470 TGGTTACCCC
Statistics
Matches: 68, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
91 44 0.65
92 24 0.35
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (91 bp):
ACACTATGAAATTCTGGCAACCTGTCTATGGAAATTTGGTAACATGACTATGAAATTTTGGAAAC
CTCATTAGGAAATTTGGGTAACGTCG
Found at i:23548 original size:64 final size:63
Alignment explanation
Indices: 23280--23903 Score: 270
Period size: 64 Copynumber: 9.6 Consensus size: 63
23270 TTGTCACATT
* ** *
23280 TTATGAAATTTTGATAACTACACTATGAAATTTTGGTAACCTGTCTATGGAATTTTGGTAA-CC
1 TTATGAAATTTTGGTAACT-CACTATGAAATTTTGGTAACCTCACTATGGAATTCTGGTAACCC
* * * *
23343 TGACTATGAAATTTTGGTAATCTCATTATGAAATTTGGGTAACGTCGACACTATGAAAATTCTGG
1 T---TATGAAATTTTGGTAA-CTCACTATGAAATTTTGGTAAC--C-TCACTATG-GAATTCTGG
*
23408 CAACCTTC
58 TAACC--C
* * *
23416 TTATGAAA-TTTGAGTAACATC-CTATGAAATTTTGGAAACCTC-C-ATAGGAAATTTTGGTTAC
1 TTATGAAATTTTG-GTAAC-TCACTATGAAATTTTGGTAACCTCACTAT-GG-AATTCTGGTAAC
23477 CC
62 CC
* * * *
23479 CTATGAAATTTTGGTAACTGCACTATGAAATTTTTGTAACCTCACTATGGAATTCAGATAACCC
1 TTATGAAATTTTGGTAACT-CACTATGAAATTTTGGTAACCTCACTATGGAATTCTGGTAACCC
* * * * * * * * * *
23543 TTATGAAATTTCGATAACCTCACAATTAAATTTTTGTAAGCTCACTATGAAATTTTTGTAGCCTT
1 TTATGAAATTTTGGTAA-CTCACTATGAAATTTTGGTAACCTCACTATGGAATTCTGGTAACC--
23608 C
63 C
* ** * * * * * * * *
23609 CTAAAAAATATTGGTAAC-CCCTATGAAATATTGGTAACCTCACAATGAAATTTTGGTCATCC
1 TTATGAAATTTTGGTAACTCACTATGAAATTTTGGTAACCTCACTATGGAATTCTGGTAACCC
* * * * * ** * *
23671 ATATGAAATTTCT-GTAACCTCCCTGTGAAATTTTTGTAGCCGGACTATGAAATTGAT-GTAACC
1 TTATGAAATTT-TGGTAA-CTCACTATGAAATTTTGGTAACCTCACTATGGAATT-CTGGTAACC
23734 TC
63 -C
* * ** * * * * * *
23736 ACTATGAAAATTTCATAAACTCAC--TGTAATGTTGATAACCT-ATTTTGAAATAT-TGGTAACC
1 -TTATGAAATTTTGGT-AACTCACTATGAAATTTTGGTAACCTCACTATGGAAT-TCTGGTAACC
23797 C
63 C
* * * * *
23798 ATTATGAAATTTTGGTAACCTCCCTATGAAATTTTGGTAA-ATCCCTAT-GAGATTTTAGTAACC
1 -TTATGAAATTTTGGTAA-CTCACTATGAAATTTTGGTAACCTCACTATGGA-ATTCTGGTAA-C
23861 CC
62 CC
* * * *
23863 AGTAT-AAAATTTAGTAACCTCACCATGAAATTTTGGTAACC
1 -TTATGAAATTTTGGTAA-CTCACTATGAAATTTTGGTAACC
23904 CCCACTATTC
Statistics
Matches: 421, Mismatches: 99, Indels: 80
0.70 0.17 0.13
Matches are distributed among these distances:
61 2 0.00
62 31 0.07
63 34 0.08
64 208 0.49
65 28 0.07
66 62 0.15
67 5 0.01
68 1 0.00
69 25 0.06
70 22 0.05
71 1 0.00
73 2 0.00
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (63 bp):
TTATGAAATTTTGGTAACTCACTATGAAATTTTGGTAACCTCACTATGGAATTCTGGTAACCC
Found at i:23805 original size:21 final size:21
Alignment explanation
Indices: 23771--23904 Score: 94
Period size: 21 Copynumber: 6.3 Consensus size: 21
23761 GTAATGTTGA
* * *
23771 TAACCTATTTTGAAATATTGG
1 TAACCCATTATGAAATTTTGG
23792 TAACCCATTATGAAATTTTGG
1 TAACCCATTATGAAATTTTGG
**
23813 TAACCTCCCTATGAAATTTTGG
1 TAACC-CATTATGAAATTTTGG
* *
23835 TAAATCCC--TATGAGATTTTAG
1 T-AA-CCCATTATGAAATTTTGG
* * *
23856 TAACCCCAGTAT-AAAATTTAG
1 TAA-CCCATTATGAAATTTTGG
**
23877 TAACCTCACCATGAAATTTTGG
1 TAACC-CATTATGAAATTTTGG
23899 TAACCC
1 TAACCC
23905 CCACTATTCG
Statistics
Matches: 92, Mismatches: 14, Indels: 14
0.77 0.12 0.12
Matches are distributed among these distances:
20 7 0.08
21 50 0.54
22 30 0.33
23 3 0.03
24 2 0.02
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.35
Consensus pattern (21 bp):
TAACCCATTATGAAATTTTGG
Found at i:23904 original size:43 final size:42
Alignment explanation
Indices: 23800--23906 Score: 110
Period size: 43 Copynumber: 2.5 Consensus size: 42
23790 GGTAACCCAT
* *
23800 TATGAAATTTTGGTAACCTCCCTATGAAATTTTGGTAAATCCC
1 TATGAAATTTTGGTAACC-CCCTATGAAAATTTAGTAAATCCC
* * * *
23843 TATGAGATTTTAGTAACCCCAGTAT-AAAATTTAGTAACCTCACC
1 TATGAAATTTTGGTAACCCC-CTATGAAAATTTAGTAA-ATC-CC
23887 -ATGAAATTTTGGTAACCCCC
1 TATGAAATTTTGGTAACCCCC
23907 ACTATTCGTG
Statistics
Matches: 52, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
42 12 0.23
43 38 0.73
44 2 0.04
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.34
Consensus pattern (42 bp):
TATGAAATTTTGGTAACCCCCTATGAAAATTTAGTAAATCCC
Found at i:24313 original size:22 final size:21
Alignment explanation
Indices: 24288--24553 Score: 89
Period size: 22 Copynumber: 12.2 Consensus size: 21
24278 TCAATTTTAC
24288 TAACCTCCTTATGAAATTTTGG
1 TAACCTCC-TATGAAATTTTGG
* * *
24310 TAACCTTACTAT-CAATTTTGT
1 TAACC-TCCTATGAAATTTTGG
* * *
24331 TAATCCCCCAATGGAATTTTGG
1 TAA-CCTCCTATGAAATTTTGG
* * * *
24353 TAATCCCCCTATGAGATGTTGA
1 TAA-CCTCCTATGAAATTTTGG
**
24375 TAACCTAACTTCCTTATGAAATTTCAG
1 TAA-C---C-TCC-TATGAAATTTTGG
** *
24402 TAACCTTAATATGAAAATTTGG
1 TAACC-TCCTATGAAATTTTGG
24424 TAACCTCACTATGAAATTTTGG
1 TAACCTC-CTATGAAATTTTGG
24446 TAA------ATGAAATTTTGG
1 TAACCTCCTATGAAATTTTGG
* * * *
24461 TAACATCCCGATGAAATTCTGA
1 TAACCT-CCTATGAAATTTTGG
**
24483 TAACAC-CCTATGAAATTTCAG
1 TAAC-CTCCTATGAAATTTTGG
* * *
24504 TAATCCTCATTGTGAAATTTTAG
1 TAA-CCTC-CTATGAAATTTTGG
*
24527 TAACCCCCTATGAAAATTTTGGG
1 TAACCTCCTATG-AAATTTT-GG
24550 TAAC
1 TAAC
24554 TCTATATTTT
Statistics
Matches: 179, Mismatches: 43, Indels: 43
0.68 0.16 0.16
Matches are distributed among these distances:
15 15 0.08
21 31 0.17
22 94 0.53
23 24 0.13
25 1 0.01
26 3 0.02
27 11 0.06
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (21 bp):
TAACCTCCTATGAAATTTTGG
Found at i:24454 original size:15 final size:15
Alignment explanation
Indices: 24434--24463 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
24424 TAACCTCACT
24434 ATGAAATTTTGGTAA
1 ATGAAATTTTGGTAA
24449 ATGAAATTTTGGTAA
1 ATGAAATTTTGGTAA
24464 CATCCCGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (15 bp):
ATGAAATTTTGGTAA
Found at i:27224 original size:3 final size:3
Alignment explanation
Indices: 27216--27250 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
27206 AAAGAAAGAC
27216 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
27251 TTGACAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Done.