Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008586.1 Corchorus capsularis cultivar CVL-1 contig08607, 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: 5680
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Found at i:163 original size:22 final size:22
Alignment explanation
Indices: 79--727 Score: 163
Period size: 22 Copynumber: 29.5 Consensus size: 22
69 ATATTCATAC
*
79 GAAATTATGATAACCTTCCTAT
1 GAAATTTTGATAACCTTCCTAT
*
101 GAAATTATGATAA--TTACACTAT
1 GAAATTTTGATAACCTT-C-CTAT
** * *
123 ----TTTTGATAATGTACTTAT
1 GAAATTTTGATAACCTTCCTAT
141 GAAATTTTGATAACCTTCCTAT
1 GAAATTTTGATAACCTTCCTAT
** ** *
163 GAAATTTCAATAACGATACTAT
1 GAAATTTTGATAACCTTCCTAT
* * * *
185 GGAATTTCGAGAACCTT-TTAT
1 GAAATTTTGATAACCTTCCTAT
* *
206 -AAATTTTGTTTTAACCTTCTTAT
1 GAAATTTTG--ATAACCTTCCTAT
* * * *
229 GAAATTTTGTTTACCTCCCTAA
1 GAAATTTTGATAACCTTCCTAT
* *
251 GGAATTTTGA-AGATCTCACCTCACTAT
1 GAAATTTTGATA-A---C-CTTC-CTAT
*
278 GAAATTTTGATAA-CTTCCAAAT
1 GAAATTTTGATAACCTTCC-TAT
* **
300 GGAATTTTGATAACCAACACTAT
1 GAAATTTTGATAACCTTC-CTAT
* *
323 -AAGATGTTGATAGCC-TCCATAT
1 GAA-ATTTTGATAACCTTCC-TAT
* * *
345 GATATATTGATAATCACGT--TAT
1 GAAATTTTGATAA-C-CTTCCTAT
* * *
367 GAAAATTTAAAAACC-TCCATAT
1 GAAATTTTGATAACCTTCC-TAT
* * * * *
389 G-AATTGTCAGTAATC-ACACTCT
1 GAAATTTTGA-TAACCTTC-CTAT
* *
411 GAAATTTTGATAATC-ACACTAT
1 GAAATTTTGATAACCTTC-CTAT
*
433 GAAATTGTGATAACC-TCGCTAT
1 GAAATTTTGATAACCTTC-CTAT
455 GAAATTTTGATAAACCTTCCTAT
1 GAAATTTTGAT-AACCTTCCTAT
* * *
478 AAAATTCTGATAA-ATCTCCTTAT
1 GAAATTTTGATAACCT-TCC-TAT
*
501 AAAATTTTGATAACC-TCCTTAT
1 GAAATTTTGATAACCTTCC-TAT
*
523 GAAATCTTGATAA-----CTA-
1 GAAATTTTGATAACCTTCCTAT
* * *
539 CAAATTTTGATAATCTCCCTAT
1 GAAATTTTGATAACCTTCCTAT
** *
561 GATTTTTTGATAACC-TCATTAT
1 GAAATTTTGATAACCTTC-CTAT
* * * *
583 GAGATTTTGTTAATCTCCCTAT
1 GAAATTTTGATAACCTTCCTAT
** *
605 GAAATTTTGATTTACATATATACTAT
1 GAAATTTTGA--TA-ACCT-TCCTAT
* *
631 GAAATTTTGATAACCCTCTTAT
1 GAAATTTTGATAACCTTCCTAT
* * **
653 GAAATTTT-AAAAACTAAACTAT
1 GAAATTTTGATAACCT-TCCTAT
* *
675 GATATTTTGATAACCTTCATAT
1 GAAATTTTGATAACCTTCCTAT
* *
697 GAAATTTTGATATCC-TCC-CT
1 GAAATTTTGATAACCTTCCTAT
717 GAAATTTTGAT
1 GAAATTTTGAT
728 TACTCCATAA
Statistics
Matches: 461, Mismatches: 113, Indels: 108
0.68 0.17 0.16
Matches are distributed among these distances:
16 11 0.02
17 2 0.00
18 12 0.03
19 2 0.00
20 22 0.05
21 23 0.05
22 272 0.59
23 66 0.14
24 16 0.03
25 5 0.01
26 16 0.03
27 13 0.03
28 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (22 bp):
GAAATTTTGATAACCTTCCTAT
Found at i:241 original size:23 final size:22
Alignment explanation
Indices: 196--240 Score: 72
Period size: 24 Copynumber: 2.0 Consensus size: 22
186 GAATTTCGAG
196 AACCTTTTATAAATTTTGTTTT
1 AACCTTTTATAAATTTTGTTTT
218 AACCTTCTTATGAAATTTTGTTT
1 AACCTT-TTAT-AAATTTTGTTT
241 ACCTCCCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.29
23 4 0.19
24 11 0.52
ACGTcount: A:0.27, C:0.11, G:0.07, T:0.56
Consensus pattern (22 bp):
AACCTTTTATAAATTTTGTTTT
Found at i:858 original size:22 final size:22
Alignment explanation
Indices: 833--953 Score: 91
Period size: 22 Copynumber: 5.5 Consensus size: 22
823 AATCGCATTT
*
833 TGAAAATTTGATAACCTTTTTA
1 TGAAATTTTGATAACCTTTTTA
* ** *
855 TGAAATTTTGGTAACCGCTCTA
1 TGAAATTTTGATAACCTTTTTA
* * * **
877 TAAAATTTTGTTGACCCCTTTA
1 TGAAATTTTGATAACCTTTTTA
* * *
899 TGAAATTTTGATAATCATATTA
1 TGAAATTTTGATAACCTTTTTA
* *
921 TGTAATTTTGATAACCTTGCTT-
1 TGAAATTTTGATAACCTT-TTTA
943 TGAAATTTTGA
1 TGAAATTTTGA
954 AATCGGACAA
Statistics
Matches: 76, Mismatches: 22, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
22 74 0.97
23 2 0.03
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (22 bp):
TGAAATTTTGATAACCTTTTTA
Found at i:859 original size:44 final size:44
Alignment explanation
Indices: 809--952 Score: 132
Period size: 44 Copynumber: 3.3 Consensus size: 44
799 TAAGTACCAC
*
809 TATGAAATTTTGGTAATCGCATTTTGAAAATTTGATAACCTTTT
1 TATGAAATTTTGGTAATCGCATTATGAAAATTTGATAACCTTTT
* * * **
853 TATGAAATTTTGGTAACCGC-TCTAT-AAAATTTTGTTGACCCCTT
1 TATGAAATTTTGGTAATCGCAT-TATGAAAA-TTTGATAACCTTTT
* ** * * *
897 TATGAAATTTTGATAATCATATTATGTAATTTTGATAACCTTGCT
1 TATGAAATTTTGGTAATCGCATTATGAAAATTTGATAACCTT-TT
942 T-TGAAATTTTG
1 TATGAAATTTTG
953 AAATCGGACA
Statistics
Matches: 78, Mismatches: 17, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
43 5 0.06
44 68 0.87
45 5 0.06
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.45
Consensus pattern (44 bp):
TATGAAATTTTGGTAATCGCATTATGAAAATTTGATAACCTTTT
Found at i:1101 original size:37 final size:37
Alignment explanation
Indices: 1013--1106 Score: 116
Period size: 38 Copynumber: 2.5 Consensus size: 37
1003 CTAAGCTCGG
* * *
1013 ATAGAACGTTGGAGACGAAGACAAAAAGCAAAATTAA
1 ATAGAACGTTGGAAACAAAGACAAAAAGAAAAATTAA
* * *
1050 ATATAACGACTGGAAACAAAGACAAAAGGAAAAATTAA
1 ATAGAACG-TTGGAAACAAAGACAAAAAGAAAAATTAA
*
1088 ATAGGACGTTGGAAACAAA
1 ATAGAACGTTGGAAACAAA
1107 AAGTTAAATT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
37 17 0.36
38 30 0.64
ACGTcount: A:0.55, C:0.11, G:0.20, T:0.14
Consensus pattern (37 bp):
ATAGAACGTTGGAAACAAAGACAAAAAGAAAAATTAA
Found at i:1330 original size:2 final size:2
Alignment explanation
Indices: 1323--1361 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
1313 TTCGTACTTT
1323 TA TA TA TA GTA 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 TA TA TA
1362 CTAGTTTTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1507 original size:22 final size:22
Alignment explanation
Indices: 1482--2054 Score: 176
Period size: 22 Copynumber: 26.5 Consensus size: 22
1472 ATGATCCCAT
1482 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* ** *
1504 TATGAAATTTTAATAACGATAC
1 TATGAAATTTTGATAACCTTCC
* * * *
1526 TATGGAATTTCGAGAACCATT-T
1 TATGAAATTTTGATAACC-TTCC
** *
1548 TAT-AAATTTTTTTAACCTTCT
1 TATGAAATTTTGATAACCTTCC
* *
1569 TATGAAATTTGGTTAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
* * *
1591 TAAGGAATTTTGA-AGACC-TCAA
1 TATGAAATTTTGATA-ACCTTC-C
*
1613 TATTAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
* * * **
1635 AATAAAATTTTGATGACCAACAC
1 TATGAAATTTTGATAACCTTC-C
* *
1658 TATGAGATGTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * * *
1679 ATATGATATATTGATAACC-ACAT
1 -TATGAAATTTTGATAACCTTC-C
* *
1702 TATGAAAATTT-A-AACACCTCC
1 TATGAAATTTTGATAAC-CTTCC
* * *
1723 AAATG-AATTGTT-AGTAATC-ACAC
1 -TATGAAATT-TTGA-TAACCTTC-C
* * * *
1746 TCTGAAATTTTGATAATC-ACGG
1 TATGAAATTTTGATAACCTTC-C
* *
1768 TATGAAATTGTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
*
1790 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AACCTTCC
* * *
1813 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAACCTTCC
*
1835 TATGAAATCTTGATAA-----C
1 TATGAAATTTTGATAACCTTCC
*
1852 TA-CAAATTTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
** * *
1872 ATATGATTTTTTGATAATC-TCAT
1 -TATGAAATTTTGATAACCTTC-C
* * *
1895 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
*** * *
1917 TATGAAATTTTGATCTGCATAC
1 TATGAAATTTTGATAACCTTCC
* *
1939 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCTTCC
* * * **
1961 TGTAAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-TCC
*
1983 TATGAAATTTTGATAACCTTCA
1 TATGAAATTTTGATAACCTTCC
*
2005 TATGAAATTTTGATATCC-TCC
1 TATGAAATTTTGATAACCTTCC
* *
2026 -CTG-AATTTTGATATCC-TCC
1 TATGAAATTTTGATAACCTTCC
2045 T-TGAAATTTT
1 TATGAAATTTT
2055 TTTTTGATGC
Statistics
Matches: 402, Mismatches: 112, Indels: 76
0.68 0.19 0.13
Matches are distributed among these distances:
16 11 0.03
17 2 0.00
19 18 0.04
20 14 0.03
21 32 0.08
22 272 0.68
23 51 0.13
24 2 0.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:2034 original size:19 final size:20
Alignment explanation
Indices: 2007--2054 Score: 80
Period size: 19 Copynumber: 2.5 Consensus size: 20
1997 AACCTTCATA
2007 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
*
2027 TG-AATTTTGATATCCTCCT
1 TGAAATTTTGATATCCTCCC
2046 TGAAATTTT
1 TGAAATTTT
2055 TTTTTGATGC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 18 0.69
20 8 0.31
ACGTcount: A:0.25, C:0.19, G:0.10, T:0.46
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:2328 original size:22 final size:22
Alignment explanation
Indices: 2297--2481 Score: 137
Period size: 22 Copynumber: 8.3 Consensus size: 22
2287 AATCACATTT
*
2297 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
2319 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
* * * * *
2341 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTTTA
* * * *
2363 TGAAATTCTGATAATCACATTA
1 TGAAATTTTGATAACCTCTTTA
* *
2385 TGTAATTTTGATAACCTCGCTT-
1 TGAAATTTTGATAACCTC-TTTA
*
2407 TGAAATTTTGATAACAATAC--TA
1 TGAAATTTTGATAAC-CT-CTTTA
*
2429 TGAAATTTTGATAATCT-TTCTA
1 TGAAATTTTGATAACCTCTT-TA
*
2451 T-AAATTTTGATAATCCGATCTCTA
1 TGAAATTTTGATAA-CC--TCTTTA
2475 TGAAATT
1 TGAAATT
2482 GCGACAATCA
Statistics
Matches: 126, Mismatches: 25, Indels: 21
0.73 0.15 0.12
Matches are distributed among these distances:
21 14 0.11
22 98 0.78
23 3 0.02
24 5 0.04
25 6 0.05
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:2365 original size:44 final size:44
Alignment explanation
Indices: 2272--2442 Score: 121
Period size: 44 Copynumber: 3.9 Consensus size: 44
2262 AGAAATACCA
* * * * *
2272 CTATCAAATTTTTG-TAATCACATTTTGAAAA-TTTGATAACCTCT
1 CTATGAAA-TTTTGATAACCACATTAT-AAAATTTTGATAACCCCG
* * * * * *
2316 TTATGAAATTTTGATAACCTCTTTATAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAACCACATTATAAAATTTTGATAACCCCG
* * ** *
2360 CTATGAAATTCTGATAATCACATTATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAACCACATTATAAAATTTTGATAACCCCG
* * * * *
2404 CTTTGAAATTTTGATAACAATACTATGAAATTTTGATAA
1 CTATGAAATTTTGATAACCACATTATAAAATTTTGATAA
2443 TCTTTCTATA
Statistics
Matches: 98, Mismatches: 27, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
43 9 0.09
44 89 0.91
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (44 bp):
CTATGAAATTTTGATAACCACATTATAAAATTTTGATAACCCCG
Found at i:2782 original size:24 final size:22
Alignment explanation
Indices: 2718--2880 Score: 107
Period size: 22 Copynumber: 7.3 Consensus size: 22
2708 TTGTGATAAT
* *
2718 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTTAA
* *
2740 TAACCAACCTAAGAGATTTTAA
1 TAACCAACCTATGAAATTTTAA
* **
2762 TAACCTGATCCTATGAAATTTTGG
1 TAACC--AACCTATGAAATTTTAA
**
2786 TAACC-ACACTATGAAATTTTTGG
1 TAACCAAC-CTATGAAA-TTTTAA
* *
2809 TAACC-ACACTATGGAATTTTGA
1 TAACCAAC-CTATGAAATTTTAA
* *
2831 TAACC-TCCTCATGAAATTATAA
1 TAACCAACCT-ATGAAATTTTAA
* * *
2853 TAACCATCTTATGAAATTTTGA
1 TAACCAACCTATGAAATTTTAA
2875 TAACCA
1 TAACCA
2881 CTTAGAGACT
Statistics
Matches: 116, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
21 3 0.03
22 72 0.62
23 24 0.21
24 17 0.15
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.33
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:2810 original size:23 final size:23
Alignment explanation
Indices: 2772--2828 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
2762 TAACCTGATC
2772 CTATGAAA-TTTTGGTAACCACA
1 CTATGAAATTTTTGGTAACCACA
2794 CTATGAAATTTTTGGTAACCACA
1 CTATGAAATTTTTGGTAACCACA
*
2817 CTATGGAATTTT
1 CTATGAAATTTT
2829 GATAACCTCC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 8 0.24
23 25 0.76
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (23 bp):
CTATGAAATTTTTGGTAACCACA
Found at i:3695 original size:31 final size:31
Alignment explanation
Indices: 3630--3700 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
3620 TGGCAATTTA
* * *
3630 GAAATATGTTTTAAAGAAAATGGTACAATTG
1 GAAATATATTTTAAAGAAAAGGGTACAATCG
*
3661 GAAATATATTTTAAA-AATAAGGGTATAATCG
1 GAAATATATTTTAAAGAA-AAGGGTACAATCG
3692 GAAAATATA
1 G-AAATATA
3701 ATAGTATAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 2 0.06
31 25 0.74
32 7 0.21
ACGTcount: A:0.49, C:0.03, G:0.17, T:0.31
Consensus pattern (31 bp):
GAAATATATTTTAAAGAAAAGGGTACAATCG
Found at i:5459 original size:10 final size:10
Alignment explanation
Indices: 5444--5470 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
5434 TAAACGTTAG
5444 CAAATTGCAC
1 CAAATTGCAC
5454 CAAATTGCAC
1 CAAATTGCAC
5464 CAAATTG
1 CAAATTG
5471 GGGCTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.26, G:0.11, T:0.22
Consensus pattern (10 bp):
CAAATTGCAC
Done.