Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008370.1 Corchorus capsularis cultivar CVL-1 contig08391, 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: 28020
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Found at i:2425 original size:31 final size:32
Alignment explanation
Indices: 2381--2445 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 32
2371 TTGTTATTTC
** *
2381 ATATAAGTTTTAAGGGCAATTTGGGCA-TCCA
1 ATATAAGACTTAAGGACAATTTGGGCATTCCA
* *
2412 ATATAAGACTTAAGGATAATTTGGGTATTCCA
1 ATATAAGACTTAAGGACAATTTGGGCATTCCA
2444 AT
1 AT
2446 TCTTTTTTGC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 22 0.79
32 6 0.21
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.34
Consensus pattern (32 bp):
ATATAAGACTTAAGGACAATTTGGGCATTCCA
Found at i:16595 original size:20 final size:18
Alignment explanation
Indices: 16559--16613 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 18
16549 TAGAGATGGC
16559 TTTTCAAAAGGATTTTTAAAAT
1 TTTTCAAAA--ATTTTT--AAT
*
16581 TTTTCAAAAATTTTTGAT
1 TTTTCAAAAATTTTTAAT
16599 TTTTCAAAAAATTTT
1 TTTTC-AAAAATTTT
16614 GCTTCTCTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
18 7 0.23
19 9 0.29
20 6 0.19
22 9 0.29
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.51
Consensus pattern (18 bp):
TTTTCAAAAATTTTTAAT
Found at i:16602 original size:18 final size:18
Alignment explanation
Indices: 16579--16614 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
16569 GATTTTTAAA
*
16579 ATTTTTCAAAAATTTTTG
1 ATTTTTCAAAAAATTTTG
16597 ATTTTTCAAAAAATTTTG
1 ATTTTTCAAAAAATTTTG
16615 CTTCTCTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.53
Consensus pattern (18 bp):
ATTTTTCAAAAAATTTTG
Found at i:20356 original size:2 final size:2
Alignment explanation
Indices: 20349--20374 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20339 ATTATTCGTC
20349 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
20375 GTACTAGTTT
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):
TA
Found at i:20544 original size:22 final size:22
Alignment explanation
Indices: 20499--20551 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
20489 TGATCTCATC
* *
20499 ATGAAATTTTAATAACTTTTCT
1 ATGAAATTTTAATAACTATACT
20521 ATGAAATTTTAATAA-TGATACT
1 ATGAAATTTTAATAACT-ATACT
*
20543 ATGGAATTT
1 ATGAAATTT
20552 CGATAACCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 1 0.04
22 26 0.96
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.45
Consensus pattern (22 bp):
ATGAAATTTTAATAACTATACT
Found at i:20581 original size:22 final size:22
Alignment explanation
Indices: 20555--20604 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
20545 GGAATTTCGA
* * * *
20555 TAACCTTTTTATTAATTTTTTT
1 TAACCTTCTTATGAAATTTTGT
20577 TAACCTTCTTATGAAATTTTGT
1 TAACCTTCTTATGAAATTTTGT
20599 TAACCT
1 TAACCT
20605 CCCTAAGGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.14, G:0.04, T:0.56
Consensus pattern (22 bp):
TAACCTTCTTATGAAATTTTGT
Found at i:20837 original size:23 final size:23
Alignment explanation
Indices: 20767--20868 Score: 93
Period size: 23 Copynumber: 4.5 Consensus size: 23
20757 TCACACTCTG
* * * *
20767 AAATTTTGATAATCA-CACTCTG
1 AAATTTTGATAAACATCCCTATA
* * * *
20789 AAATTGTGAT-AACCTCGCTATG
1 AAATTTTGATAAACATCCCTATA
*
20811 AAATTTTGATAAATC-TTCCTATA
1 AAATTTTGATAAA-CATCCCTATA
20834 AAATTTTGATAAACATCCCTATA
1 AAATTTTGATAAACATCCCTATA
20857 AAATTTTGATAA
1 AAATTTTGATAA
20869 CTTTTTTATG
Statistics
Matches: 66, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
21 2 0.03
22 24 0.36
23 39 0.59
24 1 0.02
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (23 bp):
AAATTTTGATAAACATCCCTATA
Found at i:20945 original size:22 final size:22
Alignment explanation
Indices: 20586--21013 Score: 191
Period size: 22 Copynumber: 19.6 Consensus size: 22
20576 TTAACCTTCT
* *
20586 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTCAC
* * * * *
20608 TAAGGAATTTTGA-AGAGCTTAA
1 TATGAAATTTTGATA-ACCTCAC
* *
20630 TATGAAATTTTGATAACTTCCC
1 TATGAAATTTTGATAACCTCAC
* *
20652 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACC-TCAC
* ** *
20675 TATGAGACGTTGTTAACCTC-C
1 TATGAAATTTTGATAACCTCAC
* * * **
20696 ATATGATATATTGATAACCACGT
1 -TATGAAATTTTGATAACCTCAC
* * *
20719 TATGAAAATTTAAAAACCTC-C
1 TATGAAATTTTGATAACCTCAC
* *
20740 ATATG-AATTGTT-AGTAATCACAC
1 -TATGAAATT-TTGA-TAACCTCAC
* * *
20763 TCTGAAATTTTGATAATCACAC
1 TATGAAATTTTGATAACCTCAC
* * *
20785 TCTGAAATTGTGATAACCTCGC
1 TATGAAATTTTGATAACCTCAC
*
20807 TATGAAATTTTGATAAATCTTC-C
1 TATGAAATTTTGAT-AA-CCTCAC
* * *
20830 TATAAAATTTTGATAAACATCCC
1 TATGAAATTTTGAT-AACCTCAC
* * ***
20853 TATAAAATTTTGATAACTTTTT
1 TATGAAATTTTGATAACCTCAC
*
20875 TATGAAATCTTGATAA-CT-AC
1 TATGAAATTTTGATAACCTCAC
*
20895 ----AAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCAC
** *
20913 TATGATTTTTTGATAACCTCAT
1 TATGAAATTTTGATAACCTCAC
* ** *
20935 TATGAAATTTTGTTAATTTCCC
1 TATGAAATTTTGATAACCTCAC
* *
20957 TATGAAATTTTGATCTACAT-AC
1 TATGAAATTTTGAT-AACCTCAC
*
20979 TATGAAATTTTGATAACCCTC-T
1 TATGAAATTTTGATAA-CCTCAC
21001 TATGAAATTTTGA
1 TATGAAATTTTGA
21014 AAATTAAACT
Statistics
Matches: 302, Mismatches: 81, Indels: 46
0.70 0.19 0.11
Matches are distributed among these distances:
16 11 0.04
17 2 0.01
18 1 0.00
21 8 0.03
22 219 0.73
23 58 0.19
24 3 0.01
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCAC
Found at i:21219 original size:44 final size:44
Alignment explanation
Indices: 21166--21250 Score: 111
Period size: 44 Copynumber: 1.9 Consensus size: 44
21156 TTGTTGACCC
* *
21166 CTCTATGAAA-TTCTGATAATC-ACATTATGTAATTTTGATAACCT
1 CTCTATGAAATTTC-GATAA-CAACACTATGAAATTTTGATAACCT
*
21210 CTCTTTGAAATTTCGATAACAACACTATGAAATTTTGATAA
1 CTCTATGAAATTTCGATAACAACACTATGAAATTTTGATAA
21251 TCTTATTATA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
43 1 0.03
44 32 0.89
45 3 0.08
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.39
Consensus pattern (44 bp):
CTCTATGAAATTTCGATAACAACACTATGAAATTTTGATAACCT
Found at i:21259 original size:66 final size:67
Alignment explanation
Indices: 21168--21296 Score: 172
Period size: 66 Copynumber: 1.9 Consensus size: 67
21158 GTTGACCCCT
* * *
21168 CTATGAAATTCTGATAATCACATTATGTAATTTTGATAA-C-CTCTCTTTGAAATTTCGATAACA
1 CTATGAAATTCTGATAATCACATTAT-AAATTTTGATAATCGATCTCTATGAAATTTCGATAACA
21231 ACA
65 ACA
* **
21234 CTATGAAATTTTGATAATCTTATTATAAATTTTGATAATCTGATCTCTATGAAATTTCGATAA
1 CTATGAAATTCTGATAATCACATTATAAATTTTGATAATC-GATCTCTATGAAATTTCGATAA
21297 TCACTCAATG
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
65 11 0.20
66 24 0.44
68 19 0.35
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.41
Consensus pattern (67 bp):
CTATGAAATTCTGATAATCACATTATAAATTTTGATAATCGATCTCTATGAAATTTCGATAACAA
CA
Found at i:21288 original size:25 final size:23
Alignment explanation
Indices: 21167--21298 Score: 87
Period size: 22 Copynumber: 5.9 Consensus size: 23
21157 TGTTGACCCC
* **
21167 TCTATGAAATTCTGATAATCACA
1 TCTATGAAATTTTGATAATCTTA
* * *
21190 T-TATGTAATTTTGATAA-CCTC
1 TCTATGAAATTTTGATAATCTTA
* * *
21211 TCTTTGAAATTTCGATAA-C-AA
1 TCTATGAAATTTTGATAATCTTA
*
21232 CACTATGAAATTTTGATAATCTTA
1 -TCTATGAAATTTTGATAATCTTA
*
21256 T-TAT-AAATTTTGATAATCTGATC
1 TCTATGAAATTTTGATAATCT--TA
*
21279 TCTATGAAATTTCGATAATC
1 TCTATGAAATTTTGATAATC
21299 ACTCAATGAG
Statistics
Matches: 84, Mismatches: 17, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
21 17 0.20
22 46 0.55
23 4 0.05
24 4 0.05
25 13 0.15
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.42
Consensus pattern (23 bp):
TCTATGAAATTTTGATAATCTTA
Found at i:21386 original size:22 final size:22
Alignment explanation
Indices: 21169--21496 Score: 78
Period size: 22 Copynumber: 14.7 Consensus size: 22
21159 TTGACCCCTC
* * *
21169 TATGAAATTCTGATAATC-ACA
1 TATGAAATTTTGATAACCTTCA
*
21190 TTATGTAATTTTGATAACCTCTC-
1 -TATGAAATTTTGATAACCT-TCA
* * **
21213 TTTGAAATTTCGATAA-CAACA
1 TATGAAATTTTGATAACCTTCA
*
21234 CTATGAAATTTTGATAATCTT-A
1 -TATGAAATTTTGATAACCTTCA
* *
21256 TTAT-AAATTTTGATAATCTGATCTC
1 -TATGAAATTTTGATAACCT--TC-A
*
21281 TATGAAATTTCGATAATCAC-TCA
1 TATGAAATTTTGATAA-C-CTTCA
*
21304 -ATGAGA-TTTGATAACCTTC-
1 TATGAAATTTTGATAACCTTCA
* * *
21323 TATCAAATTTTGGTACTCCTT-A
1 TATGAAATTTTGATA-ACCTTCA
*
21345 TGAAATTGAGACTTTT-ATAACCTTCA
1 T---A-TGA-AATTTTGATAACCTTCA
*
21371 TATGAAATTTTGATAACC-ACA
1 TATGAAATTTTGATAACCTTCA
* * * *
21392 CTATAAAATTTTAATAACCTCCC
1 -TATGAAATTTTGATAACCTTCA
* * * *
21415 CATGAAA-TATCAGTAACC-TCC
1 TATGAAATTTTGA-TAACCTTCA
* *
21436 TAATGAAATTTTGTTAACC-ACA
1 T-ATGAAATTTTGATAACCTTCA
21458 CTATGAAATTCTT-ATAACC-TCA
1 -TATGAAATT-TTGATAACCTTCA
* *
21480 CTATGACATTTTAATAA
1 -TATGAAATTTTGATAA
21497 TCTCTTTGAT
Statistics
Matches: 226, Mismatches: 48, Indels: 64
0.67 0.14 0.19
Matches are distributed among these distances:
19 1 0.00
20 8 0.04
21 43 0.19
22 131 0.58
23 9 0.04
24 6 0.03
25 16 0.07
26 6 0.03
27 6 0.03
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCA
Found at i:21615 original size:22 final size:21
Alignment explanation
Indices: 21540--21673 Score: 115
Period size: 22 Copynumber: 6.0 Consensus size: 21
21530 AATCAATTAC
**
21540 CCTATGAAATTTCAATAACCAA
1 CCTATGAAATTTTGATAACC-A
* * *
21562 CCTAAGAAATTTTAATAACTTGA
1 CCTATGAAATTTTGATAAC--CA
*
21585 TCCTATGAAATTTTGGTAACCA
1 -CCTATGAAATTTTGATAACCA
*
21607 CACTATGAAATTTTGATAACCT
1 C-CTATGAAATTTTGATAACCA
* *
21629 CCTCATGAAATTATAATAACCA
1 CCT-ATGAAATTTTGATAACCA
*
21651 TCTTATGAAATTTTGATAACCA
1 -CCTATGAAATTTTGATAACCA
21673 C
1 C
21674 ATATAGACAA
Statistics
Matches: 91, Mismatches: 15, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
21 4 0.04
22 68 0.75
23 3 0.03
24 16 0.18
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.34
Consensus pattern (21 bp):
CCTATGAAATTTTGATAACCA
Found at i:21619 original size:68 final size:66
Alignment explanation
Indices: 21541--21674 Score: 162
Period size: 68 Copynumber: 2.0 Consensus size: 66
21531 ATCAATTACC
* * *
21541 CTATGAAATTTCAATAACCAACCT-AAGAAATTTTAATAACTTGATCCTATGAAATTTTGGTAAC
1 CTATGAAATTTCAATAACC-ACCTCAAGAAATTATAATAAC--CATCCTATGAAATTTTGATAAC
21605 CACA
63 CACA
** * * *
21609 CTATGAAATTTTGATAACCTCCTCATGAAATTATAATAACCATCTTATGAAATTTTGATAACCAC
1 CTATGAAATTTCAATAACCACCTCAAGAAATTATAATAACCATCCTATGAAATTTTGATAACCAC
21674 A
66 A
21675 TATAGACAAG
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
66 23 0.40
67 3 0.05
68 31 0.54
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.34
Consensus pattern (66 bp):
CTATGAAATTTCAATAACCACCTCAAGAAATTATAATAACCATCCTATGAAATTTTGATAACCAC
A
Found at i:21868 original size:19 final size:20
Alignment explanation
Indices: 21837--21874 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
21827 TATTGACATT
21837 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
21856 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
21875 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:22248 original size:32 final size:32
Alignment explanation
Indices: 22212--22278 Score: 84
Period size: 31 Copynumber: 2.1 Consensus size: 32
22202 TTAGTAATGG
*
22212 CAATTTAGAAATATGTTTTTAAAAA-AAGGATA
1 CAATTTAGAAATAT-ATTTTAAAAATAAGGATA
* *
22244 CAA-TTGGAAATATATTTTAAAAATAAGGGTA
1 CAATTTAGAAATATATTTTAAAAATAAGGATA
22275 CAAT
1 CAAT
22279 CGGAAAACAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
30 9 0.30
31 18 0.60
32 3 0.10
ACGTcount: A:0.49, C:0.04, G:0.13, T:0.33
Consensus pattern (32 bp):
CAATTTAGAAATATATTTTAAAAATAAGGATA
Found at i:22264 original size:30 final size:32
Alignment explanation
Indices: 22219--22284 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 32
22209 TGGCAATTTA
* *
22219 GAAATATGTTTTTAAAAA-AAGGATACAATTG
1 GAAATATGATTTTAAAAATAAGGATACAATCG
*
22250 GAAATAT-ATTTTAAAAATAAGGGTACAATCG
1 GAAATATGATTTTAAAAATAAGGATACAATCG
22281 GAAA
1 GAAA
22285 ACATAAAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 9 0.29
31 22 0.71
ACGTcount: A:0.50, C:0.05, G:0.17, T:0.29
Consensus pattern (32 bp):
GAAATATGATTTTAAAAATAAGGATACAATCG
Found at i:23734 original size:27 final size:27
Alignment explanation
Indices: 23677--23734 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
23667 AGTTTGGTGT
** * * *
23677 AGTTTGGTGTTGTTAAGGAGTAGCAAC
1 AGTTTGGTAATGTAAAGGAGTAGAAAA
23704 AGTTTGGTAATGTAAAGGAGTAGAAAA
1 AGTTTGGTAATGTAAAGGAGTAGAAAA
23731 AGTT
1 AGTT
23735 GAGTAGCAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.34, C:0.03, G:0.31, T:0.31
Consensus pattern (27 bp):
AGTTTGGTAATGTAAAGGAGTAGAAAA
Done.