Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024480.1 Corchorus olitorius cultivar O-4 contig24513, 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: 9605
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1643 original size:12 final size:12
Alignment explanation
Indices: 1626--1669 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 12
1616 TTTGACCTTT
1626 AATTATTAAAAA
1 AATTATTAAAAA
1638 AATTATATAAAAATA
1 AATTAT-T-AAAA-A
1653 AATT-TTAAAAA
1 AATTATTAAAAA
1664 AATTAT
1 AATTAT
1670 GTTTTGATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
11 5 0.18
12 11 0.39
13 2 0.07
14 5 0.18
15 5 0.18
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
AATTATTAAAAA
Found at i:2371 original size:22 final size:22
Alignment explanation
Indices: 2337--2556 Score: 178
Period size: 22 Copynumber: 10.1 Consensus size: 22
2327 AGTTTCATTC
* * *
2337 TCATAGGGAGGTTATCGAAATT
1 TCATAGTGTGGTTATCAAAATT
2359 TCAT-GATGTGGTTATCAAAATTT
1 TCATAG-TGTGGTTATCAAAA-TT
* *
2382 TCATAGTGCGGTTA-C-CAATT
1 TCATAGTGTGGTTATCAAAATT
* * * *
2402 TTATTGTGTGATTATCAAAACT
1 TCATAGTGTGGTTATCAAAATT
* * *
2424 TCACATTGAGGTTATCAAAATT
1 TCATAGTGTGGTTATCAAAATT
2446 TCATAGTGTGGTTATCAAAATT
1 TCATAGTGTGGTTATCAAAATT
* *
2468 TCACAGTGTGGTTATCAAATTT
1 TCATAGTGTGGTTATCAAAATT
* * **
2490 TCATAAT-AGGTTATTGAAATT
1 TCATAGTGTGGTTATCAAAATT
** * *
2511 TCATAACGAGGTTATCAAATTT
1 TCATAGTGTGGTTATCAAAATT
* *
2533 TCACAGTGTGGTTATCAATATT
1 TCATAGTGTGGTTATCAAAATT
2555 TC
1 TC
2557 TACGTTAGCA
Statistics
Matches: 153, Mismatches: 39, Indels: 12
0.75 0.19 0.06
Matches are distributed among these distances:
20 12 0.08
21 20 0.13
22 107 0.70
23 13 0.08
24 1 0.01
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (22 bp):
TCATAGTGTGGTTATCAAAATT
Found at i:2490 original size:87 final size:86
Alignment explanation
Indices: 2344--2556 Score: 225
Period size: 87 Copynumber: 2.5 Consensus size: 86
2334 TTCTCATAGG
* * * *
2344 GAGGTTATCGAAATTTCAT-GATGTGGTTATCAAAATTTTCATAGTGCGGTTACCAATTTT-ATT
1 GAGGTTATCAAAATTTCATAG-TGTGGTTATCAAAA-TTTCACAGTGCGGTTACAAATTTTCATA
* **
2407 GT-GTGATTATCAAAACTTCACATT
64 ATAG-G-TTATCAAAACTTCACAAC
*
2431 GAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCACAGTGTGGTTATCAAATTTTCATAA
1 GAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCACAGTGCGGTTA-CAAATTTTCATAA
** * *
2496 TAGGTTATTGAAATTTCATAAC
65 TAGGTTATCAAAACTTCACAAC
* * *
2518 GAGGTTATCAAATTTTCACAGTGTGGTTATCAATATTTC
1 GAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTC
2557 TACGTTAGCA
Statistics
Matches: 107, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
86 14 0.13
87 87 0.81
88 5 0.05
89 1 0.01
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (86 bp):
GAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCACAGTGCGGTTACAAATTTTCATAAT
AGGTTATCAAAACTTCACAAC
Found at i:2501 original size:65 final size:66
Alignment explanation
Indices: 2346--2555 Score: 203
Period size: 65 Copynumber: 3.2 Consensus size: 66
2336 CTCATAGGGA
* * * * * **
2346 GGTTATCGAAA-TTTCATGATGTGGTTATCAAAATTTTCATAGTGCGGTTA-C-CAATTTTATTG
1 GGTTATC-AAATTTTCATAATGAGGTTATCAAAA-TTTCATAGTGAGGTTATCAAAATTTCACAG
2408 TGT
64 TGT
* ** * * *
2411 GATTATCAAAACTTCACATTGAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCACAGTG
1 GGTTATCAAATTTTCATAATGAGGTTATCAAAATTTCATAGTGAGGTTATCAAAATTTCACAGTG
2476 T
66 T
** ** *
2477 GGTTATCAAATTTTCATAAT-AGGTTATTGAAATTTCATAACGAGGTTATCAAATTTTCACAGTG
1 GGTTATCAAATTTTCATAATGAGGTTATCAAAATTTCATAGTGAGGTTATCAAAATTTCACAGTG
2541 T
66 T
2542 GGTTATCAATATTT
1 GGTTATCAA-ATTT
2556 CTACGTTAGC
Statistics
Matches: 119, Mismatches: 22, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
64 18 0.15
65 72 0.61
66 29 0.24
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.40
Consensus pattern (66 bp):
GGTTATCAAATTTTCATAATGAGGTTATCAAAATTTCATAGTGAGGTTATCAAAATTTCACAGTG
T
Found at i:2800 original size:28 final size:26
Alignment explanation
Indices: 2753--2805 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 26
2743 CGGGAAAACT
2753 CTAATTTCAAATACATTGTTTGCAAAA
1 CTAATTTCAAATACATTGTTT-CAAAA
*
2780 CTAATGTTCAAAT-GATGTGTTTCAAA
1 CTAAT-TTCAAATACAT-TGTTTCAAA
2806 GTGAGTAACC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (26 bp):
CTAATTTCAAATACATTGTTTCAAAA
Found at i:2891 original size:50 final size:50
Alignment explanation
Indices: 2837--2932 Score: 174
Period size: 50 Copynumber: 1.9 Consensus size: 50
2827 TGGGCTAGCC
* *
2837 AAAAATAACTTTCTTCAAAACCTAAAATTTGAACTTCACGATTTTGAGAA
1 AAAAAAAACTTTCTTCAAAACCTAAAACTTGAACTTCACGATTTTGAGAA
2887 AAAAAAAACTTTCTTCAAAACCTAAAACTTGAACTTCACGATTTTG
1 AAAAAAAACTTTCTTCAAAACCTAAAACTTGAACTTCACGATTTTG
2933 CATGTTTGTA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.31
Consensus pattern (50 bp):
AAAAAAAACTTTCTTCAAAACCTAAAACTTGAACTTCACGATTTTGAGAA
Found at i:4814 original size:29 final size:30
Alignment explanation
Indices: 4782--4841 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
4772 TTATTTTTAG
4782 TTTTTTACC-TAAAAAAAATTCTATATATA
1 TTTTTTACCTTAAAAAAAATTCTATATATA
* *
4811 -TTTTTACCTTAAGAAAAATTCTATATTTA
1 TTTTTTACCTTAAAAAAAATTCTATATATA
4840 TT
1 TT
4842 GGAAAAAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 8 0.30
29 18 0.67
30 1 0.04
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (30 bp):
TTTTTTACCTTAAAAAAAATTCTATATATA
Found at i:6573 original size:18 final size:19
Alignment explanation
Indices: 6550--6587 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
6540 TAAGACCCAT
6550 AAATTT-TGCTGATGTGGC
1 AAATTTATGCTGATGTGGC
6568 AAATTTATGCTGATGTGGC
1 AAATTTATGCTGATGTGGC
6587 A
1 A
6588 CTTCCACGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.37
Consensus pattern (19 bp):
AAATTTATGCTGATGTGGC
Found at i:6815 original size:29 final size:30
Alignment explanation
Indices: 6761--6842 Score: 80
Period size: 32 Copynumber: 2.7 Consensus size: 30
6751 TTGGCCTGAT
*
6761 TTTACAAA-TTCAGGGGGCAAAGTGG-CACAA
1 TTTA-AAAGTTCAGGGGGCAAACTGGCCA-AA
* *
6791 TTT-AAAGTTCAGGGGTCAATCTGGCCTAAA
1 TTTAAAAGTTCAGGGGGCAAACTGGCC-AAA
6821 TTTACAAAGTTCAGGGGGCAAA
1 TTTA-AAAGTTCAGGGGGCAAA
6843 AGGGCTCTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
28 3 0.07
29 14 0.33
30 9 0.21
31 1 0.02
32 15 0.36
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (30 bp):
TTTAAAAGTTCAGGGGGCAAACTGGCCAAA
Found at i:7474 original size:5 final size:5
Alignment explanation
Indices: 7466--7495 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
7456 ACTTCCCTCC
*
7466 CCTTT CCTTT CCTTT CCTTC CCTTT CCTTT
1 CCTTT CCTTT CCTTT CCTTT CCTTT CCTTT
7496 AATTACTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (5 bp):
CCTTT
Found at i:8263 original size:12 final size:12
Alignment explanation
Indices: 8246--8271 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
8236 ACGTACAAAA
8246 TTTTCAATAAAT
1 TTTTCAATAAAT
8258 TTTTCAATAAAT
1 TTTTCAATAAAT
8270 TT
1 TT
8272 GTATGTCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (12 bp):
TTTTCAATAAAT
Found at i:8330 original size:22 final size:22
Alignment explanation
Indices: 8299--8775 Score: 154
Period size: 22 Copynumber: 21.4 Consensus size: 22
8289 GATAATGATG
* * *
8299 TGAAAATTTGATAACATCATTA
1 TGAAATTTTGATAACCTCACTA
8321 TGAAATTTTGATAA---C-CTA
1 TGAAATTTTGATAACCTCACTA
* *
8339 TGAAAATTTGATAACCAT-ACTG
1 TGAAATTTTGATAACC-TCACTA
* *
8361 TGAAATTTTGATAATCTCCCTA
1 TGAAATTTTGATAACCTCACTA
* *
8383 TGAAATTTTGATAATCACACTA
1 TGAAATTTTGATAACCTCACTA
* * * *
8405 T-AAA-ATTGGTAATCGCACTA
1 TGAAATTTTGATAACCTCACTA
* * *
8425 TAAAAATTTGGATAACCTC-TTCA
1 T-GAAATTTTGATAACCTCACT-A
* * *
8448 TAAAATTTTGATAACCACACCA
1 TGAAATTTTGATAACCTCACTA
* * * *
8470 TTAAGTTTCGATAACCTCCCTA
1 TGAAATTTTGATAACCTCACTA
** * **
8492 TGAGAATGAAACAATGATATCCTCTTTA
1 TGA-AAT-----TTTGATAACCTCACTA
** * * *
8520 TTTAATTTTGATAACATCTCCA
1 TGAAATTTTGATAACCTCACTA
* *
8542 TAAAATTTTTG-TAACCTTC-CAA
1 TGAAA-TTTTGATAACC-TCACTA
* *
8564 TGAAATTTTGTTAACCTCCCTA
1 TGAAATTTTGATAACCTCACTA
* * *
8586 GGAAACTTTGATAACCTCCCTCCCTA
1 TGAAATTTTGATAA----CCTCACTA
*
8612 TGAAATTTTGATAACCACACTA
1 TGAAATTTTGATAACCTCACTA
*
8634 T-AAATTTTGATAACCTTC-GTA
1 TGAAATTTTGATAACC-TCACTA
* * * *
8655 TAAAATTTTGTTAACGACACTCTA
1 TGAAATTTTGATAAC--CTCACTA
* * ***
8679 AGAAAATTTGATAACCTTTTTA
1 TGAAATTTTGATAACCTCACTA
* * **
8701 TGAAATTTTGGTAACGTCTGTA
1 TGAAATTTTGATAACCTCACTA
*
8723 TGGAATTTTGATAA-CTGCACTA
1 TGAAATTTTGATAACCT-CACTA
**
8745 TGACGTTTTGATAACCTCTA-TA
1 TGAAATTTTGATAACCTC-ACTA
8767 TGAAATTTT
1 TGAAATTTT
8776 AGTAACCACA
Statistics
Matches: 336, Mismatches: 86, Indels: 66
0.69 0.18 0.14
Matches are distributed among these distances:
18 15 0.04
19 1 0.00
20 14 0.04
21 29 0.09
22 207 0.62
23 22 0.07
24 14 0.04
26 20 0.06
27 3 0.01
28 11 0.03
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.37
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCACTA
Found at i:8345 original size:40 final size:40
Alignment explanation
Indices: 8299--8411 Score: 120
Period size: 40 Copynumber: 2.7 Consensus size: 40
8289 GATAATGATG
*
8299 TGAAAATTTGATAA-CATCATTATGAAATTTTGATAACCTA
1 TGAAAATTTGATAACCAT-ACTATGAAATTTTGATAACCTA
*
8339 TGAAAATTTGATAACCATACTGTGAAATTTTGATAATCTCCCTA
1 TGAAAATTTGATAACCATACTATGAAATTTTGATAA----CCTA
* * * *
8383 TGAAATTTTGATAATCACACTATAAAATT
1 TGAAAATTTGATAACCATACTATGAAATT
8412 GGTAATCGCA
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
40 30 0.49
41 3 0.05
44 28 0.46
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (40 bp):
TGAAAATTTGATAACCATACTATGAAATTTTGATAACCTA
Found at i:8616 original size:26 final size:26
Alignment explanation
Indices: 8578--8627 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
8568 ATTTTGTTAA
8578 CCTCCCTAGGAAACTTTGATAACCTC
1 CCTCCCTAGGAAACTTTGATAACCTC
* *
8604 CCTCCCTATGAAATTTTGATAACC
1 CCTCCCTAGGAAACTTTGATAACC
8628 ACACTATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.28, C:0.32, G:0.10, T:0.30
Consensus pattern (26 bp):
CCTCCCTAGGAAACTTTGATAACCTC
Found at i:8707 original size:46 final size:44
Alignment explanation
Indices: 8549--8716 Score: 117
Period size: 46 Copynumber: 3.7 Consensus size: 44
8539 CCATAAAATT
** * * * *
8549 TTTG-TAACCTTCCAATGAAATTTTGTTAAC-CTCCCTAGGAAAC
1 TTTGATAACCTTCGTATGAAATTTTGATAACGCACACTA-GAAAA
* * *
8592 TTTGATAACCTCCCTCCCTATGAAATTTTGATAAC-CACACTATAAAT
1 TTTGATAACCT---T-CGTATGAAATTTTGATAACGCACACTAGAAAA
* * *
8639 TTTGATAACCTTCGTATAAAATTTTGTTAACGACACTCTAAGAAAA
1 TTTGATAACCTTCGTATGAAATTTTGATAACG-CACACT-AGAAAA
** *
8685 TTTGATAACCTTTTTATGAAATTTTGGTAACG
1 TTTGATAACCTTCGTATGAAATTTTGATAACG
8717 TCTGTATGGA
Statistics
Matches: 101, Mismatches: 16, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
43 20 0.20
44 7 0.07
45 5 0.05
46 32 0.32
47 15 0.15
48 22 0.22
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (44 bp):
TTTGATAACCTTCGTATGAAATTTTGATAACGCACACTAGAAAA
Found at i:9108 original size:17 final size:17
Alignment explanation
Indices: 9086--9121 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
9076 TATAGGGTAA
*
9086 TTGAAACTGAGTTTAGT
1 TTGAAACTGAGTTAAGT
9103 TTGAAACTGAGTTAAGT
1 TTGAAACTGAGTTAAGT
9120 TT
1 TT
9122 CCATTATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.06, G:0.22, T:0.42
Consensus pattern (17 bp):
TTGAAACTGAGTTAAGT
Done.