Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013780.1 Corchorus olitorius cultivar O-4 contig13813, 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: 28794
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:610 original size:23 final size:23
Alignment explanation
Indices: 577--668 Score: 80
Period size: 23 Copynumber: 4.0 Consensus size: 23
567 AAATTGTGAT
* *
577 AACCTCGCTATAAAATTTGGATA
1 AACCTCCCTATAAAATTTAGATA
* * **
600 AACCTTCCTATAAAATATATTTA
1 AACCTCCCTATAAAATTTAGATA
*
623 AACCTCCCTATAAAATTTTGAT-
1 AACCTCCCTATAAAATTTAGATA
* *
645 AACCTCCTTATGAAATCTT-GATA
1 AACCTCCCTATAAAAT-TTAGATA
668 A
1 A
669 CTACAAATTT
Statistics
Matches: 54, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
22 17 0.31
23 37 0.69
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.35
Consensus pattern (23 bp):
AACCTCCCTATAAAATTTAGATA
Found at i:669 original size:22 final size:22
Alignment explanation
Indices: 368--834 Score: 207
Period size: 22 Copynumber: 21.5 Consensus size: 22
358 TTTTTCTATA
* * *
368 AAATTTTGTTAACCTCCCTAAG
1 AAATTTTGATAACCTCCTTATG
* **
390 GAATTTTGA-ATACCTCAATATG
1 AAATTTTGATA-ACCTCCTTATG
* ** *
412 AAATTTTGATAACTTCCAAATA
1 AAATTTTGATAACCTCCTTATG
* *
434 AAATTTTCATAACCAACAC-TATG
1 AAATTTTGATAACC-TC-CTTATG
* * *
457 AGATGTTGATAACCTCCATATG
1 AAATTTTGATAACCTCCTTATG
* * * *
479 ATATATTGATAACCACGTTATG
1 AAATTTTGATAACCTCCTTATG
* * * *
501 AAAATTTAAAAACCTCCATATG
1 AAATTTTGATAACCTCCTTATG
* * *
523 -AATTGTT-AGTAATCACAC-TCTG
1 AAATT-TTGA-TAACCTC-CTTATG
* *
545 AAATTTTGATAATCACACTT-TG
1 AAATTTTGATAACCTC-CTTATG
* *
567 AAATTGTGATAACCTCGC-TATA
1 AAATTTTGATAACCTC-CTTATG
* *
589 AAATTTGGATAAACCTTCC-TATA
1 AAATTTTGAT-AACC-TCCTTATG
* * *
612 AAATATATTTA-AACCTCCCTATA
1 AAAT-T-TTGATAACCTCCTTATG
635 AAATTTTGATAACCTCCTTATG
1 AAATTTTGATAACCTCCTTATG
* *
657 AAATCTTGATAA----C-TA-C
1 AAATTTTGATAACCTCCTTATG
* *
673 AAATTTTGATAACCTCATTATA
1 AAATTTTGATAACCTCCTTATG
* * *
695 AAATTTTGTTAATCTCCCTATG
1 AAATTTTGATAACCTCCTTATG
* * *
717 AAATTTTGATCTACATAC-TATG
1 AAATTTTGAT-AACCTCCTTATG
739 AAATTTTGATAACC-CTCTTATG
1 AAATTTTGATAACCTC-CTTATG
* **
761 AAATTTTGATAACCTTCACATG
1 AAATTTTGATAACCTCCTTATG
* *
783 AAATTTTGATAACCTTCATATG
1 AAATTTTGATAACCTCCTTATG
* *
805 AAATTTTGATATCCTCC--CTG
1 AAATTTTGATAACCTCCTTATG
825 AAATTTTGAT
1 AAATTTTGAT
835 TACTGCATAA
Statistics
Matches: 343, Mismatches: 74, Indels: 58
0.72 0.16 0.12
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
18 1 0.00
20 12 0.03
21 15 0.04
22 246 0.72
23 50 0.15
24 4 0.01
25 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (22 bp):
AAATTTTGATAACCTCCTTATG
Found at i:990 original size:22 final size:22
Alignment explanation
Indices: 940--1358 Score: 175
Period size: 22 Copynumber: 18.9 Consensus size: 22
930 AATCACATTT
* *
940 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTCTA
*
962 TGCAATTTTGATAACCTCTCTA
1 TGAAATTTTGATAACCTCTCTA
* * * * *
984 TAAAATTGTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTCTA
* ***
1006 TGAAATTGTGATATTTTCAT-TA
1 TGAAATTTTGATAACCTC-TCTA
* * * *
1028 TGTAATTTTGATAATCTCGCTT
1 TGAAATTTTGATAACCTCTCTA
* *
1050 TGAAATTTTGATAACAATAT-TA
1 TGAAATTTTGATAAC-CTCTCTA
* *
1072 TGAAATTTTGATGATCT-TCCTA
1 TGAAATTTTGATAACCTCT-CTA
1094 T-AAATTTTGATAACTCGATCTCTA
1 TGAAATTTTGATAAC-C--TCTCTA
* * *
1118 TGAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAACCTCTCTA
* *
1140 AGAGA-TTTGATAACCT-TCTA
1 TGAAATTTTGATAACCTCTCTA
* *
1160 TCAAATTTTGGT-A-CTC-CTTA
1 TGAAATTTTGATAACCTCTC-TA
*
1180 TGAAATTGAGACTTTTATAACCT-TCATA
1 TGAAA-T-----TTTGATAACCTCTC-TA
* *
1208 TGAAATTTTGATAACCACACTA
1 TGAAATTTTGATAACCTCTCTA
** * *
1230 AAAAATTTTAATAACCAT-ACTA
1 TGAAATTTTGATAACC-TCTCTA
1252 TGAAATTTTGATAACCTCTCTA
1 TGAAATTTTGATAACCTCTCTA
*
1274 TGAAATATT-AGTAACCTC-CTTA
1 TGAAATTTTGA-TAACCTCTC-TA
* * * *
1296 TAAAATTTTGTTAACCACACTA
1 TGAAATTTTGATAACCTCTCTA
*
1318 TAAAATTCTT-ATAACCTCGT-TA
1 TGAAATT-TTGATAACCTC-TCTA
* * *
1340 GGATATTTTGATAATCTCT
1 TGAAATTTTGATAACCTCT
1359 TTGATAACCT
Statistics
Matches: 293, Mismatches: 72, Indels: 65
0.68 0.17 0.15
Matches are distributed among these distances:
19 3 0.01
20 14 0.05
21 32 0.11
22 204 0.70
23 6 0.02
24 6 0.02
25 12 0.04
26 4 0.01
27 2 0.01
28 10 0.03
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTCTA
Found at i:1254 original size:44 final size:44
Alignment explanation
Indices: 1206--1592 Score: 171
Period size: 44 Copynumber: 8.5 Consensus size: 44
1196 ATAACCTTCA
*
1206 TATGAAATTTTGATAACCACACTAAAAAATTTTAATAACCATAC
1 TATGAAATTTTGATAACCACACTATAAAATTTTAATAACCATAC
* * * * * *
1250 TATGAAATTTTGATAACCTCTCTATGAAATATTAGTAACC-TCC
1 TATGAAATTTTGATAACCACACTATAAAATTTTAATAACCATAC
* * *
1293 TTATAAAATTTTGTTAACCACACTATAAAATTCTT-ATAACCTCGTTAGGATAT
1 -TATGAAATTTTGATAACCACACTATAAAATT-TTAATAA-C-C------ATAC
* *** * * *
1346 TTTGATAATCTCTTTGATAACCTTTCTATAAAATTGTGATAACCACAC
1 TATGA-AA--T-TTTGATAACCACACTATAAAATTTTAATAACCATAC
** * *
1394 TATGAAATTTCAATAACCTTC-CT-TAAAAATTTTAATAACCTGATCC
1 TATGAAATTTTGATAACC-ACACTAT-AAAATTTTAATAACC--ATAC
* * * * * *
1440 TATGAAATTTTG-GAACCACACAATGAAATTTTGATAACCTTTC
1 TATGAAATTTTGATAACCACACTATAAAATTTTAATAACCATAC
* * ** **
1483 CATGAAATTTTGATAA-CATCTA-TATGAAATTTTGGTAACCGCAC
1 TATGAAATTTTGATAACCA-C-ACTATAAAATTTTAATAACCATAC
* * * * *
1527 TATGGAATTTTGATAACCTC-CTCATTAAATTATAATAATCAT-C
1 TATGAAATTTTGATAACCACACT-ATAAAATTTTAATAACCATAC
1570 TTATGAAATTTTGATAACCACAC
1 -TATGAAATTTTGATAACCACAC
1593 AGAGACAAGA
Statistics
Matches: 252, Mismatches: 61, Indels: 59
0.68 0.16 0.16
Matches are distributed among these distances:
43 20 0.08
44 151 0.60
45 26 0.10
46 14 0.06
47 2 0.01
48 6 0.02
52 3 0.01
53 3 0.01
54 1 0.00
55 3 0.01
56 23 0.09
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (44 bp):
TATGAAATTTTGATAACCACACTATAAAATTTTAATAACCATAC
Found at i:1487 original size:22 final size:22
Alignment explanation
Indices: 1358--1588 Score: 139
Period size: 22 Copynumber: 10.5 Consensus size: 22
1348 TGATAATCTC
* *
1358 TTTGATAACCTTTCTATAAAAT
1 TTTGATAACCTCTCTATGAAAT
* * *
1380 TGTGATAACCACACTATGAAAT
1 TTTGATAACCTCTCTATGAAAT
** *
1402 TTCAATAACCT-TCCT-TAAAAAT
1 TTTGATAACCTCT-CTAT-GAAAT
* *
1424 TTTAATAACCTGATCCTATGAAAT
1 TTTGATAACCT-CT-CTATGAAAT
* * * *
1448 TTTG-GAACCACACAATGAAAT
1 TTTGATAACCTCTCTATGAAAT
* *
1469 TTTGATAACCTTTCCATGAAAT
1 TTTGATAACCTCTCTATGAAAT
* *
1491 TTTGATAACATCTATATGAAAT
1 TTTGATAACCTCTCTATGAAAT
* * * *
1513 TTTGGTAACCGCACTATGGAAT
1 TTTGATAACCTCTCTATGAAAT
*
1535 TTTGATAACCTC-CTCATTAAAT
1 TTTGATAACCTCTCT-ATGAAAT
* * *
1557 TATAATAATCATCT-TATGAAAT
1 TTTGATAA-CCTCTCTATGAAAT
1579 TTTGATAACC
1 TTTGATAACC
1589 ACACAGAGAC
Statistics
Matches: 155, Mismatches: 45, Indels: 19
0.71 0.21 0.09
Matches are distributed among these distances:
21 16 0.10
22 119 0.77
23 8 0.05
24 11 0.07
25 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (22 bp):
TTTGATAACCTCTCTATGAAAT
Found at i:1499 original size:67 final size:67
Alignment explanation
Indices: 1376--1592 Score: 205
Period size: 66 Copynumber: 3.3 Consensus size: 67
1366 CCTTTCTATA
* * ** *
1376 AAATTGTGATAACCACACTATGAAATTTCAATAACC-TTCCTTAAAAATTTTAATAACCTGATC-
1 AAATTTTGGTAACCACACTATGAAATTTTGATAACCTTTCCATAAAAATTTTAATAA-C--ATCT
*
1439 CTATG
63 ATATG
* * *
1444 AAATTTTGG-AACCACACAATGAAATTTTGATAACCTTTCCAT-GAAATTTTGATAACATCTATA
1 AAATTTTGGTAACCACACTATGAAATTTTGATAACCTTTCCATAAAAATTTTAATAACATCTATA
1507 TG
66 TG
* * * * *
1509 AAATTTTGGTAACCGCACTATGGAATTTTGATAACC-TCCTCAT-TAAATTATAATAATCATCT-
1 AAATTTTGGTAACCACACTATGAAATTTTGATAACCTTTC-CATAAAAATTTTAATAA-CATCTA
1571 TATG
64 TATG
*
1575 AAATTTTGATAACCACAC
1 AAATTTTGGTAACCACAC
1593 AGAGACAAGA
Statistics
Matches: 126, Mismatches: 18, Indels: 12
0.81 0.12 0.08
Matches are distributed among these distances:
64 3 0.02
65 15 0.12
66 57 0.45
67 39 0.31
68 12 0.10
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (67 bp):
AAATTTTGGTAACCACACTATGAAATTTTGATAACCTTTCCATAAAAATTTTAATAACATCTATA
TG
Found at i:1793 original size:20 final size:20
Alignment explanation
Indices: 1755--1793 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1745 TATTGACATT
1755 TAAAAAATTGAAATTAAAAG
1 TAAAAAATTGAAATTAAAAG
*
1775 TAAAATATT-AAATTCAAAA
1 TAAAAAATTGAAATT-AAAA
1794 AATAATAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
TAAAAAATTGAAATTAAAAG
Found at i:2361 original size:22 final size:22
Alignment explanation
Indices: 2336--2386 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
2326 TCAGTAATTA
*
2336 TGATGCAGTAATGATTCAGCCT
1 TGATGCAGTAATGATTCAGCCC
2358 TGATGCAGTAATGATTCAGCCC
1 TGATGCAGTAATGATTCAGCCC
2380 TGATGCA
1 TGATGCA
2387 ACATTGTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (22 bp):
TGATGCAGTAATGATTCAGCCC
Found at i:12499 original size:23 final size:23
Alignment explanation
Indices: 12473--12522 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
12463 CAAATTGTCC
12473 TTTTAATTCT-CATTTAATTTTAT
1 TTTTAATTCTACATTTAATTTT-T
* * *
12496 TTTTATTTCTAGATTTCATTTTT
1 TTTTAATTCTACATTTAATTTTT
12519 TTTT
1 TTTT
12523 CTAGTAGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.20, C:0.08, G:0.02, T:0.70
Consensus pattern (23 bp):
TTTTAATTCTACATTTAATTTTT
Found at i:12516 original size:19 final size:19
Alignment explanation
Indices: 12489--12526 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
12479 TTCTCATTTA
*
12489 ATTTTATTTTTATTTCTAG
1 ATTTCATTTTTATTTCTAG
*
12508 ATTTCATTTTTTTTTCTAG
1 ATTTCATTTTTATTTCTAG
12527 TAGATTTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.18, C:0.08, G:0.05, T:0.68
Consensus pattern (19 bp):
ATTTCATTTTTATTTCTAG
Found at i:27509 original size:2 final size:2
Alignment explanation
Indices: 27497--27585 Score: 59
Period size: 2 Copynumber: 48.5 Consensus size: 2
27487 TTAGGATTTT
* * *
27497 TA TA TA T- TA TA TA AA TA TT TA TA -A TA TA TA -A TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
27536 -A TA TA TA TA AA AA TA T- TA -A TA TA TA TA TA TA T- TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
27573 TT TA TA AA TA TA T
1 TA TA TA TA TA TA T
27586 CAGAAAACAT
Statistics
Matches: 67, Mismatches: 12, Indels: 16
0.71 0.13 0.17
Matches are distributed among these distances:
1 8 0.12
2 59 0.88
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:27522 original size:9 final size:9
Alignment explanation
Indices: 27495--27545 Score: 54
Period size: 9 Copynumber: 5.8 Consensus size: 9
27485 GATTAGGATT
27495 TTTAT-ATA
1 TTTATAATA
27503 TTATATAAATA
1 TT-TAT-AATA
27514 TTTATAATA
1 TTTATAATA
27523 --TATAATA
1 TTTATAATA
27530 TTTATAATA
1 TTTATAATA
*
27539 TATATAA
1 TTTATAA
27546 AAATATTAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
7 7 0.19
8 2 0.05
9 20 0.54
10 3 0.08
11 5 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
TTTATAATA
Found at i:27543 original size:18 final size:18
Alignment explanation
Indices: 27499--27648 Score: 91
Period size: 18 Copynumber: 8.3 Consensus size: 18
27489 AGGATTTTTA
*
27499 TATATTATATA-AATATT
1 TATAATATATATAATATT
27516 TAT-A-ATATATAATATT
1 TATAATATATATAATATT
**
27532 TATAATATATATAA-AAA
1 TATAATATATATAATATT
27549 TATTAATATATAT-ATATAT
1 TA-TAATATATATAATAT-T
*
27568 TATAATTTATA-AATATAT
1 TATAATATATATAATAT-T
* * * *
27586 CAGAAAACATA-AATCATT
1 TATAATATATATAAT-ATT
27604 TAT-ATATATATAATATT
1 TATAATATATATAATATT
*
27621 ATATAATAAATACTATTATATT
1 -TATAAT--ATA-TATAATATT
27643 TATAAT
1 TATAAT
27649 TACTTTAATA
Statistics
Matches: 103, Mismatches: 16, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
15 5 0.05
16 9 0.09
17 16 0.16
18 50 0.49
19 6 0.06
21 9 0.09
22 8 0.08
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (18 bp):
TATAATATATATAATATT
Found at i:27559 original size:20 final size:19
Alignment explanation
Indices: 27496--27564 Score: 65
Period size: 20 Copynumber: 3.7 Consensus size: 19
27486 ATTAGGATTT
*
27496 TTATATAT-TATATAAATA
1 TTATATATATATAAAAATA
*
27514 TT-TATA-ATAT-ATAATA
1 TTATATATATATAAAAATA
27530 TTTATAATATATATAAAAATA
1 -TTAT-ATATATATAAAAATA
27551 TTAATATATATATA
1 TT-ATATATATATA
27565 TATTATAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
16 4 0.10
17 9 0.22
18 3 0.07
19 3 0.07
20 15 0.37
21 7 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TTATATATATATAAAAATA
Found at i:27625 original size:10 final size:11
Alignment explanation
Indices: 27497--27628 Score: 55
Period size: 11 Copynumber: 12.0 Consensus size: 11
27487 TTAGGATTTT
*
27497 TATATATTATA
1 TATATATAATA
* *
27508 TAAATAT-TTA
1 TATATATAATA
27518 TAATATATAATA
1 T-ATATATAATA
27530 T-T-TATAATA
1 TATATATAATA
27539 TATATA-AA-A
1 TATATATAATA
27548 -ATAT-TAATA
1 TATATATAATA
27557 TATATATATATTA
1 TATATATA-A-TA
*
27570 TAATTTATAAATA
1 T-ATATAT-AATA
* * *
27583 TATCAGAAAACA
1 TAT-ATATAATA
* *
27595 TAAATCATTTATA
1 TATAT-A-TAATA
27608 TATATATAATA
1 TATATATAATA
27619 T-TATATAATA
1 TATATATAATA
27629 AATACTATTA
Statistics
Matches: 90, Mismatches: 16, Indels: 31
0.66 0.12 0.23
Matches are distributed among these distances:
8 6 0.07
9 10 0.11
10 20 0.22
11 21 0.23
12 13 0.14
13 13 0.14
14 6 0.07
15 1 0.01
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (11 bp):
TATATATAATA
Found at i:27639 original size:17 final size:16
Alignment explanation
Indices: 27504--27641 Score: 57
Period size: 17 Copynumber: 8.2 Consensus size: 16
27494 TTTTATATAT
* *
27504 TATATAAATATTTATAA
1 TATATAAATA-ATATTA
* *
27521 TATATAATATTTATAATA
1 TATATAA-A-TAATATTA
27539 TATATAAA-AATATTA
1 TATATAAATAATATTA
*
27554 -ATATATATATATATTA
1 TATATAAATA-ATATTA
**
27570 TAATTTATAAATATATCAGAA
1 T-A--TATAAATA-AT-ATTA
* * *
27591 AACATAAATCAT-TTA
1 TATATAAATAATATTA
*
27606 TATATATATAATATTA
1 TATATAAATAATATTA
*
27622 TATAATAAATACTATTA
1 TAT-ATAAATAATATTA
27639 TAT
1 TAT
27642 TTATAATTAC
Statistics
Matches: 89, Mismatches: 21, Indels: 22
0.67 0.16 0.17
Matches are distributed among these distances:
14 6 0.07
15 15 0.17
16 12 0.13
17 24 0.27
18 18 0.20
19 1 0.01
20 11 0.12
21 2 0.02
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (16 bp):
TATATAAATAATATTA
Found at i:28203 original size:2 final size:2
Alignment explanation
Indices: 28196--28227 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
28186 TTCTCTAATG
28196 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28228 GTATGTATCA
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):
TA
Done.