Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008142.1 Corchorus capsularis cultivar CVL-1 contig08163, 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: 46148
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:5778 original size:18 final size:17
Alignment explanation
Indices: 5751--5786 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
5741 TTTCTCTTCA
5751 TCTATTTTTCTTCTAGT
1 TCTATTTTTCTTCTAGT
5768 TCTAGTTTTTCTTCTAGT
1 TCTA-TTTTTCTTCTAGT
5786 T
1 T
5787 TTAGGTTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.11, C:0.17, G:0.08, T:0.64
Consensus pattern (17 bp):
TCTATTTTTCTTCTAGT
Found at i:9867 original size:13 final size:13
Alignment explanation
Indices: 9849--9875 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
9839 GAGGTGAATA
9849 CTAAATTAGCCTC
1 CTAAATTAGCCTC
9862 CTAAATTAGCCTC
1 CTAAATTAGCCTC
9875 C
1 C
9876 ATAGATGGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.33, G:0.07, T:0.30
Consensus pattern (13 bp):
CTAAATTAGCCTC
Found at i:11607 original size:14 final size:15
Alignment explanation
Indices: 11588--11617 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
11578 CCAAAAAAAA
11588 AAAATAATTTG-TAT
1 AAAATAATTTGATAT
11602 AAAATAATTTGATAT
1 AAAATAATTTGATAT
11617 A
1 A
11618 CGAAAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (15 bp):
AAAATAATTTGATAT
Found at i:13439 original size:11 final size:10
Alignment explanation
Indices: 13421--13454 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
13411 ATTTGTCTTC
13421 AAATCTTCAA
1 AAATCTTCAA
13431 AATATCTTCAA
1 AA-ATCTTCAA
13442 GAAATCTTCAA
1 -AAATCTTCAA
13453 AA
1 AA
13455 CACGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Found at i:14054 original size:26 final size:25
Alignment explanation
Indices: 13999--14069 Score: 99
Period size: 26 Copynumber: 2.8 Consensus size: 25
13989 GAAGTCACCT
13999 AGGGGCA-TTTTGGTCATTTTGAACC
1 AGGGGCACTTTT-GTCATTTTGAACC
*
14024 AGGGGCACTTTTGTCATTTTGAACT
1 AGGGGCACTTTTGTCATTTTGAACC
*
14049 AGGGGGCACTTTAGTCATTTT
1 A-GGGGCACTTTTGTCATTTT
14070 TAGTTCCTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
25 20 0.48
26 22 0.52
ACGTcount: A:0.20, C:0.15, G:0.27, T:0.38
Consensus pattern (25 bp):
AGGGGCACTTTTGTCATTTTGAACC
Found at i:17832 original size:40 final size:38
Alignment explanation
Indices: 17737--17832 Score: 104
Period size: 38 Copynumber: 2.5 Consensus size: 38
17727 AAAGATAAAA
* * *
17737 AAAAGTAGTAATCAGTCAATTGGTAATTAAAAGGAAGT
1 AAAAGTAGTAATCAGTAAATTGATAACTAAAAGGAAGT
* *
17775 AAAA-TGATTAATTAGTAAATTGATAACTAAGAGAGGAAGT
1 AAAAGT-AGTAATCAGTAAATTGATAACTAA-A-AGGAAGT
*
17815 AAAAGTAGCAATCAGTAA
1 AAAAGTAGTAATCAGTAA
17833 GTAAGGGTCA
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
37 1 0.02
38 23 0.50
39 1 0.02
40 20 0.43
41 1 0.02
ACGTcount: A:0.50, C:0.05, G:0.20, T:0.25
Consensus pattern (38 bp):
AAAAGTAGTAATCAGTAAATTGATAACTAAAAGGAAGT
Found at i:18067 original size:40 final size:40
Alignment explanation
Indices: 18017--18125 Score: 182
Period size: 40 Copynumber: 2.7 Consensus size: 40
18007 CAGTAGAATG
* **
18017 GAGTGAAAGTAAAAGAAGTAATCAGTAAGTTGGTAATTAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAATTAA
*
18057 GAGTAAAAGTAGAAGAAGTAATCAGTAAAATGGTAATTAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAATTAA
18097 GAGTAAAAGTAAAAGAAGTAATCAGTAAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAA
18126 TCGGTAAAGA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 64 1.00
ACGTcount: A:0.52, C:0.03, G:0.23, T:0.22
Consensus pattern (40 bp):
GAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAATTAA
Found at i:18149 original size:16 final size:17
Alignment explanation
Indices: 18123--18156 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
18113 AGTAATCAGT
*
18123 AAATCGGTAAAGAGTAA
1 AAATCGGTAAAAAGTAA
18140 AAAT-GGTAAAAAGTAA
1 AAATCGGTAAAAAGTAA
18156 A
1 A
18157 GAGTAATCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.59, C:0.03, G:0.21, T:0.18
Consensus pattern (17 bp):
AAATCGGTAAAAAGTAA
Found at i:18150 original size:40 final size:39
Alignment explanation
Indices: 18017--18141 Score: 166
Period size: 40 Copynumber: 3.2 Consensus size: 39
18007 CAGTAGAATG
* * *
18017 GAGTGAAAGTAAAAGAAGTAATCAGTAAGTTGGTAATTAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAATCGGTAA-TAA
*
18057 GAGTAAAAGTAGAAGAAGTAATCAGTAAAAT-GGTAATTAA
1 GAGTAAAAGTAAAAGAAGTAATCAGT-AAATCGGTAA-TAA
18097 GAGTAAAAGTAAAAGAAGTAATCAGTAAATCGGT-A-AA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAATCGGTAATAA
18134 GAGTAAAA
1 GAGTAAAA
18142 ATGGTAAAAA
Statistics
Matches: 79, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
37 10 0.13
39 5 0.06
40 61 0.77
41 3 0.04
ACGTcount: A:0.52, C:0.03, G:0.23, T:0.22
Consensus pattern (39 bp):
GAGTAAAAGTAAAAGAAGTAATCAGTAAATCGGTAATAA
Found at i:18228 original size:32 final size:33
Alignment explanation
Indices: 18168--18250 Score: 107
Period size: 32 Copynumber: 2.5 Consensus size: 33
18158 AGTAATCAGT
*
18168 AAAGAGTAAAATGGTAAAATGGTAATTAAATTC
1 AAAGAGTAAAATGGTAAAATGGCAATTAAATTC
*
18201 AAAGAGTAAAAT-G-ACAAATGGCGATTAAATTC
1 AAAGAGTAAAATGGTA-AAATGGCAATTAAATTC
*
18233 AAAGAGTGAAAATAGTAA
1 AAAGAGT-AAAATGGTAA
18251 TTAAATTCAA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
31 1 0.02
32 23 0.52
33 17 0.39
34 2 0.05
35 1 0.02
ACGTcount: A:0.53, C:0.05, G:0.19, T:0.23
Consensus pattern (33 bp):
AAAGAGTAAAATGGTAAAATGGCAATTAAATTC
Found at i:18253 original size:26 final size:26
Alignment explanation
Indices: 18224--18277 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
18214 ACAAATGGCG
18224 ATTAAATTCAA-AGAGTGAAAATAGTA
1 ATTAAATTCAAGAGAGT-AAAATAGTA
18250 ATTAAATTCAAGAGAGTAAAATAGTA
1 ATTAAATTCAAGAGAGTAAAATAGTA
18276 AT
1 AT
18278 CATTAAAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 22 0.81
27 5 0.19
ACGTcount: A:0.54, C:0.04, G:0.15, T:0.28
Consensus pattern (26 bp):
ATTAAATTCAAGAGAGTAAAATAGTA
Found at i:18312 original size:14 final size:14
Alignment explanation
Indices: 18272--18395 Score: 96
Period size: 14 Copynumber: 9.0 Consensus size: 14
18262 AGAGTAAAAT
*
18272 AGTAATCATTAAAG
1 AGTAATCAGTAAAG
* ** *
18286 AGAAAAGAATAAAG
1 AGTAATCAGTAAAG
18300 AGTAATCAGTAAAG
1 AGTAATCAGTAAAG
*
18314 AGTAATCAGTAAAA
1 AGTAATCAGTAAAG
* *
18328 AGTAA-AAATGACAA-
1 AGTAATCAGT-A-AAG
* *
18342 AG-AGT-AGTAAAA
1 AGTAATCAGTAAAG
18354 AGTAATCAGGTAAA-
1 AGTAATCA-GTAAAG
18368 AGTAATCAGTAAAG
1 AGTAATCAGTAAAG
18382 AGTAATCAGTAAAG
1 AGTAATCAGTAAAG
18396 GAAGAATGGT
Statistics
Matches: 88, Mismatches: 14, Indels: 16
0.75 0.12 0.14
Matches are distributed among these distances:
11 2 0.02
12 3 0.03
13 12 0.14
14 64 0.73
15 7 0.08
ACGTcount: A:0.56, C:0.06, G:0.19, T:0.19
Consensus pattern (14 bp):
AGTAATCAGTAAAG
Found at i:18331 original size:21 final size:21
Alignment explanation
Indices: 18262--18599 Score: 155
Period size: 21 Copynumber: 16.0 Consensus size: 21
18252 TAAATTCAAG
* *
18262 AGAGTAAAATAGTAATCATTAA
1 AGAGT-AAAGAGTAATCAGTAA
* * **
18284 AGAGAAAAGAATAAAGAGTAA
1 AGAGTAAAGAGTAATCAGTAA
**
18305 TCAGTAAAGAGTAATCAGTAA
1 AGAGTAAAGAGTAATCAGTAA
* * *
18326 AAAGTAAA-AATGA-CA--AA
1 AGAGTAAAGAGTAATCAGTAA
*
18343 GAGTAGTAAAAAGTAATCAGGTAA
1 -AG-AGTAAAGAGTAATCA-GTAA
** **
18367 A-AGTAATCAGTAAAGAGTAA
1 AGAGTAAAGAGTAATCAGTAA
** *
18387 TCAGTAAAGGAAG-AAT-GGTAA
1 AGAGTAAA-G-AGTAATCAGTAA
*
18408 AGAGTAAAGGGTAATCAGT-A
1 AGAGTAAAGAGTAATCAGTAA
* *
18428 AGAGCAAA-ATGGTAATTAGTAA
1 AGAGTAAAGA--GTAATCAGTAA
*
18450 AGAGTAAAATAGTAATCAGTAA
1 AGAGT-AAAGAGTAATCAGTAA
* *
18472 AAACT-AAGAAGGTAATCAGTAA
1 AGAGTAAAG-A-GTAATCAGTAA
18494 AGAGTAAAGTAGTAATCAGT-A
1 AGAGTAAAG-AGTAATCAGTAA
*
18515 AGAGTAAAACAGTAATCAGT-A
1 AGAGT-AAAGAGTAATCAGTAA
* * *
18536 AGAGCAAAGTGGTAATTAGT-A
1 AGAGTAAAG-AGTAATCAGTAA
*
18557 AGAGTAAAATAGTAATCAGTAA
1 AGAGT-AAAGAGTAATCAGTAA
*
18579 AGAGTAAA-AGGTGATCAGTAA
1 AGAGTAAAGA-GTAATCAGTAA
18600 TTCAAAGAAT
Statistics
Matches: 238, Mismatches: 53, Indels: 51
0.70 0.15 0.15
Matches are distributed among these distances:
17 2 0.01
18 1 0.00
19 9 0.04
20 28 0.12
21 126 0.53
22 59 0.25
23 10 0.04
24 3 0.01
ACGTcount: A:0.52, C:0.05, G:0.22, T:0.20
Consensus pattern (21 bp):
AGAGTAAAGAGTAATCAGTAA
Found at i:18414 original size:35 final size:35
Alignment explanation
Indices: 18375--18456 Score: 112
Period size: 35 Copynumber: 2.3 Consensus size: 35
18365 AAAAGTAATC
*
18375 AGTAAAGAGTAATCAGTAA-AGGAAGAATGGTAAAG
1 AGTAAAGAGTAATCAGTAAGAGCAA-AATGGTAAAG
* **
18410 AGTAAAGGGTAATCAGTAAGAGCAAAATGGTAATT
1 AGTAAAGAGTAATCAGTAAGAGCAAAATGGTAAAG
18445 AGTAAAGAGTAA
1 AGTAAAGAGTAA
18457 AATAGTAATC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
35 37 0.90
36 4 0.10
ACGTcount: A:0.50, C:0.04, G:0.27, T:0.20
Consensus pattern (35 bp):
AGTAAAGAGTAATCAGTAAGAGCAAAATGGTAAAG
Found at i:18450 original size:42 final size:42
Alignment explanation
Indices: 18404--18599 Score: 198
Period size: 42 Copynumber: 4.6 Consensus size: 42
18394 AGGAAGAATG
* *
18404 GTAAAGAGTAAAGGGTAATCAGTAAGAGCAAAATGGTAATTA
1 GTAAAGAGTAAAGGGTAATCAGTAAGAGCAAAATAGTAATCA
** * * *
18446 GTAAAGAGTAAAATAGTAATCAGTAAAAACTAAGAA-GGTAATCA
1 GTAAAGAGT-AAAGGGTAATCAGTAAGAGC-AA-AATAGTAATCA
* * *
18490 GTAAAGAGTAAAGTAGTAATCAGTAAGAGTAAAACAGTAATCA
1 GTAAAGAGTAAAG-GGTAATCAGTAAGAGCAAAATAGTAATCA
* * *
18533 GT-AAGAGCAAAGTGGTAATTAGTAAGAGTAAAATAGTAATCA
1 GTAAAGAGTAAAG-GGTAATCAGTAAGAGCAAAATAGTAATCA
* *
18575 GTAAAGAGTAAAAGGTGATCAGTAA
1 GTAAAGAGTAAAGGGTAATCAGTAA
18600 TTCAAAGAAT
Statistics
Matches: 130, Mismatches: 18, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
42 59 0.45
43 38 0.29
44 31 0.24
45 2 0.02
ACGTcount: A:0.50, C:0.06, G:0.23, T:0.21
Consensus pattern (42 bp):
GTAAAGAGTAAAGGGTAATCAGTAAGAGCAAAATAGTAATCA
Found at i:18458 original size:22 final size:22
Alignment explanation
Indices: 18433--18587 Score: 174
Period size: 22 Copynumber: 7.2 Consensus size: 22
18423 CAGTAAGAGC
* *
18433 AAAATGGTAATTAGTAAAGAGT
1 AAAATAGTAATCAGTAAAGAGT
* *
18455 AAAATAGTAATCAGTAAAAACT
1 AAAATAGTAATCAGTAAAGAGT
*
18477 AAGAA-GGTAATCAGTAAAGAGT
1 AA-AATAGTAATCAGTAAAGAGT
*
18499 AAAGTAGTAATCAGT-AAGAGT
1 AAAATAGTAATCAGTAAAGAGT
* *
18520 AAAACAGTAATCAGT-AAGAGC
1 AAAATAGTAATCAGTAAAGAGT
* * *
18541 AAAGTGGTAATTAGT-AAGAGT
1 AAAATAGTAATCAGTAAAGAGT
18562 AAAATAGTAATCAGTAAAGAGT
1 AAAATAGTAATCAGTAAAGAGT
18584 AAAA
1 AAAA
18588 GGTGATCAGT
Statistics
Matches: 110, Mismatches: 20, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
21 53 0.48
22 55 0.50
23 2 0.02
ACGTcount: A:0.52, C:0.05, G:0.21, T:0.22
Consensus pattern (22 bp):
AAAATAGTAATCAGTAAAGAGT
Found at i:18677 original size:13 final size:13
Alignment explanation
Indices: 18659--18705 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
18649 GGTAATCAAT
18659 AAAAGAGAGTAAG
1 AAAAGAGAGTAAG
* *
18672 AAAAGAGTAATTAG
1 AAAAGAG-AGTAAG
18686 TAAAA-AGAGTAAG
1 -AAAAGAGAGTAAG
18699 AAAAGAG
1 AAAAGAG
18706 TAAAAATGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 4 0.15
13 13 0.48
14 6 0.22
15 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.26, T:0.13
Consensus pattern (13 bp):
AAAAGAGAGTAAG
Found at i:18681 original size:28 final size:27
Alignment explanation
Indices: 18650--18708 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 27
18640 GTAAAAAGTG
18650 GTAATCAATAAAAGAGAGTAAGAAAAGA
1 GTAATCAATAAAA-AGAGTAAGAAAAGA
* *
18678 GTAATTAGTAAAAAGAGTAAGAAAAGA
1 GTAATCAATAAAAAGAGTAAGAAAAGA
18705 GTAA
1 GTAA
18709 AAATGATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 18 0.62
28 11 0.38
ACGTcount: A:0.59, C:0.02, G:0.22, T:0.17
Consensus pattern (27 bp):
GTAATCAATAAAAAGAGTAAGAAAAGA
Found at i:21018 original size:9 final size:9
Alignment explanation
Indices: 21004--21042 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
20994 ATTTTCAACA
21004 TAATTTAAT
1 TAATTTAAT
**
21013 TAATTTCTT
1 TAATTTAAT
21022 TAATTTAAT
1 TAATTTAAT
*
21031 TAATTAAAT
1 TAATTTAAT
21040 TAA
1 TAA
21043 AAGAAATTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (9 bp):
TAATTTAAT
Found at i:26404 original size:29 final size:30
Alignment explanation
Indices: 26340--26404 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 30
26330 AAGTTTTTCC
* *
26340 TTTTTCCGATTTTTCTAAAAAAAAAATTAG
1 TTTTTCCGATTTTTCGAAAAAAAAAATTAA
*
26370 TGTTTCCGATTTTT-GAAAAAAAAAATTAA
1 TTTTTCCGATTTTTCGAAAAAAAAAATTAA
26399 TTTTTC
1 TTTTTC
26405 TTTTCGTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 18 0.58
30 13 0.42
ACGTcount: A:0.38, C:0.09, G:0.08, T:0.45
Consensus pattern (30 bp):
TTTTTCCGATTTTTCGAAAAAAAAAATTAA
Found at i:33848 original size:19 final size:18
Alignment explanation
Indices: 33824--33860 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
33814 TTGAAGATTT
33824 CTTGAAGATAATTTGAAGA
1 CTTGAAGATAA-TTGAAGA
*
33843 CTTGAAGATCATTGAAGA
1 CTTGAAGATAATTGAAGA
33861 ATTATTTCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30
Consensus pattern (18 bp):
CTTGAAGATAATTGAAGA
Found at i:38040 original size:15 final size:16
Alignment explanation
Indices: 38020--38050 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
38010 TCTGGTCGAA
38020 ATTTTTTTTAT-TTTT
1 ATTTTTTTTATATTTT
38035 ATTTTTTTTATATTTT
1 ATTTTTTTTATATTTT
38051 TCGATATAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (16 bp):
ATTTTTTTTATATTTT
Found at i:38158 original size:9 final size:8
Alignment explanation
Indices: 38124--38157 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
38114 GAATCGGCTA
38124 TGAATTTT
1 TGAATTTT
*
38132 TGAAGTTTC
1 TGAA-TTTT
38141 TGAATTTT
1 TGAATTTT
38149 TGAATTTT
1 TGAATTTT
38157 T
1 T
38158 TCAAGAAGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Done.