Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007869.1 Corchorus capsularis cultivar CVL-1 contig07890, 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: 22606
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.34
Found at i:1270 original size:19 final size:21
Alignment explanation
Indices: 1248--1292 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
1238 AATTCGTAGG
1248 AATTTT-TATAT-TTTCATTA
1 AATTTTCTATATATTTCATTA
*
1267 AATTTTTCTATGTATTTCATTA
1 AA-TTTTCTATATATTTCATTA
1289 AATT
1 AATT
1293 ATATATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 2 0.09
20 4 0.18
21 6 0.27
22 10 0.45
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.60
Consensus pattern (21 bp):
AATTTTCTATATATTTCATTA
Found at i:2234 original size:85 final size:84
Alignment explanation
Indices: 2136--2308 Score: 240
Period size: 85 Copynumber: 2.0 Consensus size: 84
2126 TATTTTTATC
*
2136 TAATTAAATCTAATCTCTTTATAACTATTTTATCTTTAACA-TTTACTATATTAATTTGAAAAAA
1 TAATTAAATCTAATCTCTTTATAAATATTTTATCTTTAACATTTTACTATATTAA-TT-AAAAAA
2200 CTTAGATATATTAGAAATTTT
64 CTTAGATATATTAGAAATTTT
* * * * *
2221 TAATTAAATCTAATCTCTTTATAAATATTTTATTTTTACCATTTTTAGTATTTTAATTACAAAAC
1 TAATTAAATCTAATCTCTTTATAAATATTTTATCTTTAACA-TTTTACTATATTAATTAAAAAAC
* *
2286 TTAGATATATTATAATTTTT
65 TTAGATATATTAGAAATTTT
2306 TAA
1 TAA
2309 ATTTATTTCT
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
85 65 0.83
86 2 0.03
87 11 0.14
ACGTcount: A:0.39, C:0.09, G:0.03, T:0.50
Consensus pattern (84 bp):
TAATTAAATCTAATCTCTTTATAAATATTTTATCTTTAACATTTTACTATATTAATTAAAAAACT
TAGATATATTAGAAATTTT
Found at i:5316 original size:65 final size:65
Alignment explanation
Indices: 5240--5371 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 65
5230 CTAGCTCCAA
* *
5240 AAGCAAGCCTTGGTAGGGAT-TTTTAGTAATTCCACTACTCTATTAAAGTCAATTGAGAAATGAC
1 AAGCAAGCCTTGATAGGGATCTTTTAGTAATTCCACTACTCCATTAAAGTCAATTGA-AAATGAC
5304 C
65 C
5305 AAGCAAGCCTTGATAGGGATCTTTTAGTAATTCCACTACTCCATTAAAGTCAATTGAAAATGACC
1 AAGCAAGCCTTGATAGGGATCTTTTAGTAATTCCACTACTCCATTAAAGTCAATTGAAAATGACC
5370 AA
1 AA
5372 AACGTCAAGT
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
65 29 0.45
66 35 0.55
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.30
Consensus pattern (65 bp):
AAGCAAGCCTTGATAGGGATCTTTTAGTAATTCCACTACTCCATTAAAGTCAATTGAAAATGACC
Found at i:7395 original size:29 final size:29
Alignment explanation
Indices: 7337--7405 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 29
7327 ACCGAACCGT
****
7337 CAAATAAGCCCCTGAACTATTATTTCAGC
1 CAAATAAGCCCCTGAACTATTAAAAAAGC
*
7366 CAAATAAGCCCCTGAACTCTTAAAAAAGC
1 CAAATAAGCCCCTGAACTATTAAAAAAGC
7395 CAAATAAGCCC
1 CAAATAAGCCC
7406 TGTTGCCAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.41, C:0.29, G:0.10, T:0.20
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACTATTAAAAAAGC
Found at i:9732 original size:22 final size:21
Alignment explanation
Indices: 9692--9732 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
9682 CCATTACTCA
**
9692 ATTTTTCTTCATATTAATTTC
1 ATTTTTCTTCATAAAAATTTC
9713 ATTTTTACTTCATAAAAATT
1 ATTTTT-CTTCATAAAAATT
9733 ATCTAATGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTTTTCTTCATAAAAATTTC
Found at i:16772 original size:199 final size:199
Alignment explanation
Indices: 16455--17468 Score: 1345
Period size: 199 Copynumber: 5.1 Consensus size: 199
16445 TTGTATGTGT
* * * * * * * *
16455 AGTCCGCTAAATTCGACTGATGGTGTATAGTATAATTTTTCGTATAAGATCATTATACAATCCAC
1 AGTCTGCTAAACTCCACTGACGGTGTATAGTATAATTTTTCTTATAGGATTATTATACAATACAC
* *
16520 TGTCAGTGTAAATTTTGGACTCCATAAACGGGTTAAGAAGTTGACATATACCTCATTTCATAATT
66 TGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCTCATTTCATAATT
* * *
16585 AATTAAATATTTAATATTAATACACATTCCCTAAGGGGACACATGCCAACCCTTAAACCCCGCAT
131 AATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGCAC
16650 GTGC
196 GTGC
* * * ** * * * *
16654 AGTCTGATAAAATCCACTAACGGTGTATCCTATAATTTTTCTTATAGAATTATCATACAACACGC
1 AGTCTGCTAAACTCCACTGACGGTGTATAGTATAATTTTTCTTATAGGATTATTATACAATACAC
* * * * * * *
16719 CGCCAGTGTAAATTTTAGACTCTATAAGAGGGTTAAGAAGTTGACACATACCTCATTTCATCATC
66 TGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCTCATTTCATAATT
* * * * *
16784 AATTAAATATATAATATTAATACATATTCCCTAAGGAGACACATTTCAACCCTTAAAACCTGCAC
131 AATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGCAC
16849 GTGC
196 GTGC
* * *
16853 AGTCTGCTAAACTCCACTTATGGTGTATAGTATAATTTTTCTTATAGGATTATTATACAATAAAC
1 AGTCTGCTAAACTCCACTGACGGTGTATAGTATAATTTTTCTTATAGGATTATTATACAATACAC
* * * * *
16918 TATCACTGTAAATTTTGGAATCCAAAAGCGGGTTAAGAAATTGACACATACCTCATTTCATAATT
66 TGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCTCATTTCATAATT
*
16983 -A--AAATATTTAATATTAATACATATTCCTTAAGGGGACACATGTCAACCCTTAAACCCCGCAC
131 AATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGCAC
17045 GTGC
196 GTGC
* * * * *
17049 AGTCTACTAAACTCGATTGACGGTATATAGTACAATTTTTCTTATAGGATTATTATACAATACAC
1 AGTCTGCTAAACTCCACTGACGGTGTATAGTATAATTTTTCTTATAGGATTATTATACAATACAC
* * * * * *
17114 AT-TAAGTGTAAATTTTGGAATCAATAAGCGGGTTAAGAAGTTGAAATATACCTTATTTCATAAT
66 -TGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCTCATTTCATAAT
* *
17178 TAATCAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCTGCA
130 TAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGCA
17243 CGTGC
195 CGTGC
* * * * **
17248 AGTCTGCTAAACTCCATTGACGGTTTATGGTATAATTTTTGTTTTATTTGATTATTATACAATAC
1 AGTCTGCTAAACTCCACTGACGGTGTATAGTATAA-TTTT-TCTTATAGGATTATTATACAATAC
* * *
17313 ACTGTCAGTGTAAATTTTGGACTCCAAAAGCGGGTTAAGAAGTTGACACATACCCCATTTTATAA
64 ACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCTCATTTCATAA
* * *
17378 TTAGTTAAATATTTAATATTAATACATATTCCCTAAGGGGATACATGTCAA-CCTTAAACCTCGC
129 TTAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGC
*
17442 ACCTGC
194 ACGTGC
17448 AGTCTGCTAAACTCCACTGAC
1 AGTCTGCTAAACTCCACTGAC
17469 TCCATAAACG
Statistics
Matches: 704, Mismatches: 104, Indels: 13
0.86 0.13 0.02
Matches are distributed among these distances:
196 171 0.24
197 2 0.00
198 1 0.00
199 366 0.52
200 41 0.06
201 123 0.17
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (199 bp):
AGTCTGCTAAACTCCACTGACGGTGTATAGTATAATTTTTCTTATAGGATTATTATACAATACAC
TGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCTCATTTCATAATT
AATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGCAC
GTGC
Found at i:17174 original size:395 final size:396
Alignment explanation
Indices: 16429--17465 Score: 1366
Period size: 395 Copynumber: 2.6 Consensus size: 396
16419 TTCCTTAACT
* * * * * * * *
16429 TGTCAACCCTT-AAACTTTGTATGTGTAGTCCGCTAAATTCGACTGATGGTGTATAGTATAATTT
1 TGTCAACCCTTAAAAC-CTGCACGTGCAGTCTGCTAAACTCCACTTATGGTGTATAGTATAATTT
* * *
16493 TTCGTATAAGATCATTATACAATCCACTGTCAGTGTAAATTTTGGACTCCATAAA-CGGGTTAAG
65 TTCTTATAAGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCA-AAAGCGGGTTAAG
* *
16557 AAGTTGACATATACCTCATTTCATAATTAATTAAATATTTAATATTAATACACATTCCCTAAGGG
129 AAGTTGACACATACCTCATTTCATAATT-A-TAAATATTTAATATTAATACATATTCCCTAAGGG
* * * * *
16622 GACACATGCCAACCCTTAAACCCCGCATGTGCAGTCTGA-TAAAATCCACTAACGGTGTATCCTA
192 GACACATGTCAACCCTTAAACCCCGCACGTGCAGTCT-ACTAAACTCCACTAACGGTATATACTA
* * * * * *
16686 TAATTTTTCTTATAGAATTATCATACAACACGCCGCCAGTGTAAATTTTAGACTCTATAAGAGGG
256 CAATTTTTCTTATAGAATTATCATACAACACACAGCAAGTGTAAATTTTAGAATCAATAAGAGGG
* * *
16751 TTAAGAAGTTGACACATACCTCATTTCATCATCAATTAAATATATAATATTAATACATATTCCCT
321 TTAAGAAGTTGAAACATACCTCATTTCATAATCAATCAAATATATAATATTAATACATATTCCCT
16816 AAGGAGACACA
386 AAGGAGACACA
*
16827 TTTCAACCCTTAAAACCTGCACGTGCAGTCTGCTAAACTCCACTTATGGTGTATAGTATAATTTT
1 TGTCAACCCTTAAAACCTGCACGTGCAGTCTGCTAAACTCCACTTATGGTGTATAGTATAATTTT
* * * * *
16892 TCTTATAGGATTATTATACAATAAACTATCACTGTAAATTTTGGAATCCAAAAGCGGGTTAAGAA
66 TCTTATAAGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCAAAAGCGGGTTAAGAA
* *
16957 ATTGACACATACCTCATTTCATAATTA-AAATATTTAATATTAATACATATTCCTTAAGGGGACA
131 GTTGACACATACCTCATTTCATAATTATAAATATTTAATATTAATACATATTCCCTAAGGGGACA
* * * *
17021 CATGTCAACCCTTAAACCCCGCACGTGCAGTCTACTAAACTCGATTGACGGTATATAGTACAATT
196 CATGTCAACCCTTAAACCCCGCACGTGCAGTCTACTAAACTCCACTAACGGTATATACTACAATT
* * * ** * *
17086 TTTCTTATAGGATTATTATACAATACACATTAAGTGTAAATTTTGGAATCAATAAGCGGGTTAAG
261 TTTCTTATAGAATTATCATACAACACACAGCAAGTGTAAATTTTAGAATCAATAAGAGGGTTAAG
* * * * *
17151 AAGTTGAAATATACCTTATTTCATAATTAATCAAATATTTAATATTAATACATATTCCCTAAGGG
326 AAGTTGAAACATACCTCATTTCATAATCAATCAAATATATAATATTAATACATATTCCCTAAGGA
17216 GACACA
391 GACACA
* * * *
17222 TGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTCCA-TTGACGGTTTATGGTATAATTT
1 TGTCAACCCTTAAAACCTGCACGTGCAGTCTGCTAAACTCCACTT-ATGGTGTATAGTATAA-TT
* **
17286 TTGTTTTATTTGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCAAAAGCGGGTTAA
64 TT-TCTTATAAGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCAAAAGCGGGTTAA
* *
17351 GAAGTTGACACATACCCCATTTTATAATTAGTTAAATATTTAATATTAATACATATTCCCTAAGG
128 GAAGTTGACACATACCTCATTTCATAATTA--TAAATATTTAATATTAATACATATTCCCTAAGG
* * * *
17416 GGATACATGTCAA-CCTTAAACCTCGCACCTGCAGTCTGCTAAACTCCACT
191 GGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTACTAAACTCCACT
17466 GACTCCATAA
Statistics
Matches: 557, Mismatches: 73, Indels: 17
0.86 0.11 0.03
Matches are distributed among these distances:
394 3 0.01
395 257 0.46
396 4 0.01
397 86 0.15
398 128 0.23
399 36 0.06
400 43 0.08
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (396 bp):
TGTCAACCCTTAAAACCTGCACGTGCAGTCTGCTAAACTCCACTTATGGTGTATAGTATAATTTT
TCTTATAAGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCAAAAGCGGGTTAAGAA
GTTGACACATACCTCATTTCATAATTATAAATATTTAATATTAATACATATTCCCTAAGGGGACA
CATGTCAACCCTTAAACCCCGCACGTGCAGTCTACTAAACTCCACTAACGGTATATACTACAATT
TTTCTTATAGAATTATCATACAACACACAGCAAGTGTAAATTTTAGAATCAATAAGAGGGTTAAG
AAGTTGAAACATACCTCATTTCATAATCAATCAAATATATAATATTAATACATATTCCCTAAGGA
GACACA
Found at i:18184 original size:199 final size:200
Alignment explanation
Indices: 17830--18191 Score: 582
Period size: 199 Copynumber: 1.8 Consensus size: 200
17820 TAACTTCATC
* * * *
17830 TTTTTCTTAATAGAATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGTGGGTT
1 TTTTTCTTAATAGAATTATTACACAAAACACTGTCAGTATAAATTTTGGACTCCATAAGCGGGTT
* * * *
17895 AAGAAGTTGACACATACCCCATTTTATAATTAATTAAATATTTAATATTAATAGATATTCCCTAA
66 AAGAAGTTGACACATACCCCATTTCATAATTAATTAAAAACTTAATATTAATACATATTCCCTAA
* *
17960 GGGAAAACAAGTCAACCCTTAAACCCCGAACGTACAGTATACTAAACTTGACTAACGGTGTATTG
131 GGGAAAACAAGACAACCCTTAAACCCCAAACGTACAGTATACTAAACTTGACTAACGGTGTATTG
18025 TATAA
196 TATAA
*
18030 TTTTTCTT-ATAGGATTATTACACAAAACACTGTCAGTATAAATTTTGGACTCCATAAGCGGGTT
1 TTTTTCTTAATAGAATTATTACACAAAACACTGTCAGTATAAATTTTGGACTCCATAAGCGGGTT
*
18094 AAGAAGTTGACACATACCTCATTTCATAATTAATTAAAAACTTAATATTAATACATATTCCCTAA
66 AAGAAGTTGACACATACCCCATTTCATAATTAATTAAAAACTTAATATTAATACATATTCCCTAA
* * *
18159 GGGGACACATGACAACCCTTAAACCCCAAACGT
131 GGGAAAACAAGACAACCCTTAAACCCCAAACGT
18192 GAAGTCTGTT
Statistics
Matches: 147, Mismatches: 15, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
199 139 0.95
200 8 0.05
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (200 bp):
TTTTTCTTAATAGAATTATTACACAAAACACTGTCAGTATAAATTTTGGACTCCATAAGCGGGTT
AAGAAGTTGACACATACCCCATTTCATAATTAATTAAAAACTTAATATTAATACATATTCCCTAA
GGGAAAACAAGACAACCCTTAAACCCCAAACGTACAGTATACTAAACTTGACTAACGGTGTATTG
TATAA
Found at i:18394 original size:26 final size:26
Alignment explanation
Indices: 18358--18411 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
18348 GTAAGTTCCC
18358 AAATTTGAGATATTACTGGGATAGTA
1 AAATTTGAGATATTACTGGGATAGTA
18384 AAATTTGAGATATTACTGGGATAGTA
1 AAATTTGAGATATTACTGGGATAGTA
18410 AA
1 AA
18412 CCTTGATTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.33
Consensus pattern (26 bp):
AAATTTGAGATATTACTGGGATAGTA
Found at i:18417 original size:26 final size:26
Alignment explanation
Indices: 18362--18417 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
18352 GTTCCCAAAT
*
18362 TTGAGATATTACTGGGATAGTAAAAT
1 TTGAGATATTACTGGGATAGTAAAAC
*
18388 TTGAGATATTACTGGGATAGTAAACC
1 TTGAGATATTACTGGGATAGTAAAAC
18414 TTGA
1 TTGA
18418 TTAGAATCTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.36, C:0.07, G:0.23, T:0.34
Consensus pattern (26 bp):
TTGAGATATTACTGGGATAGTAAAAC
Found at i:22524 original size:22 final size:22
Alignment explanation
Indices: 22499--22540 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
22489 AGGAAATAAA
*
22499 TTAAATTCAGGTTTAGCCCCCC
1 TTAAATCCAGGTTTAGCCCCCC
22521 TTAAATCCAGGTTTAGCCCC
1 TTAAATCCAGGTTTAGCCCC
22541 TAGTTATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.24, C:0.31, G:0.14, T:0.31
Consensus pattern (22 bp):
TTAAATCCAGGTTTAGCCCCCC
Done.