Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016223.1 Corchorus capsularis cultivar CVL-1 contig16244, 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: 72296
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:10117 original size:27 final size:27
Alignment explanation
Indices: 10087--10141 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
10077 CGGTTCCGGA
*
10087 TAGGATTAGTTAGAGTTTTGTCTCAGG
1 TAGGATTAGTTAGAGCTTTGTCTCAGG
10114 TAGGATTAGTTAGAGCTTTGTCTCAGG
1 TAGGATTAGTTAGAGCTTTGTCTCAGG
10141 T
1 T
10142 TCGAGATCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.22, C:0.09, G:0.29, T:0.40
Consensus pattern (27 bp):
TAGGATTAGTTAGAGCTTTGTCTCAGG
Found at i:10224 original size:42 final size:42
Alignment explanation
Indices: 10156--10236 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
10146 GATCTTGTCG
*
10156 TACGCAACTGCCTCCACCGGTGGACTCACCACCAAAACTGCA
1 TACGCAACTGCCTCCACCGGTAGACTCACCACCAAAACTGCA
* **
10198 TACGCAGCTGCCTCCATTGGTAGACTCACCACCAAAACT
1 TACGCAACTGCCTCCACCGGTAGACTCACCACCAAAACT
10237 AGATGCACGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.28, C:0.38, G:0.16, T:0.17
Consensus pattern (42 bp):
TACGCAACTGCCTCCACCGGTAGACTCACCACCAAAACTGCA
Found at i:10636 original size:19 final size:19
Alignment explanation
Indices: 10612--10650 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
10602 CCTTTTAAAT
10612 ACAAAATTAATTAAGAAAC
1 ACAAAATTAATTAAGAAAC
10631 ACAAAATTAATTAAGAAAC
1 ACAAAATTAATTAAGAAAC
10650 A
1 A
10651 GGATTATGCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.64, C:0.10, G:0.05, T:0.21
Consensus pattern (19 bp):
ACAAAATTAATTAAGAAAC
Found at i:18167 original size:2 final size:2
Alignment explanation
Indices: 18162--18194 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
18152 AAAACATCTT
18162 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18195 GTACACAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24540 original size:30 final size:30
Alignment explanation
Indices: 24495--24558 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
24485 CATTGCATGC
24495 GCCATCACATGGGGCAACCG-GCCACAACCG
1 GCCATCACATGGGGCAACCGCG-CACAACCG
* * *
24525 GCCATCGCATTGGGCATCCGCGCACAACCG
1 GCCATCACATGGGGCAACCGCGCACAACCG
24555 GCCA
1 GCCA
24559 ATGGATCCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 29 0.97
31 1 0.03
ACGTcount: A:0.23, C:0.41, G:0.27, T:0.09
Consensus pattern (30 bp):
GCCATCACATGGGGCAACCGCGCACAACCG
Found at i:25874 original size:28 final size:28
Alignment explanation
Indices: 25834--25896 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
25824 AATTTGGTTC
25834 AGGCCAAGTCTAAGTTTACTATGGAAAA
1 AGGCCAAGTCTAAGTTTACTATGGAAAA
25862 AGGCCAAGTCTAAGTTTACTATGGAAAA
1 AGGCCAAGTCTAAGTTTACTATGGAAAA
*
25890 AGTCCAA
1 AGGCCAA
25897 TGATGTGGCC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.24
Consensus pattern (28 bp):
AGGCCAAGTCTAAGTTTACTATGGAAAA
Found at i:27053 original size:75 final size:75
Alignment explanation
Indices: 26930--27163 Score: 271
Period size: 75 Copynumber: 3.0 Consensus size: 75
26920 AAATTAATAA
26930 TGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAATATA
1 TGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAATATA
26995 ATAATAAAGT
66 ATAATAAAGT
* **
27005 TGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTATAAGATATTTTAAGAAACAAATAA
1 TGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAG----AAAT-A
*
27070 ATAATAAAAATTGAATAGT
61 AT-ATAATAA-T-AA-AGT
*
27089 AATGAGAATATTTCTCTAAATCTTGCCAGATTGTGGGAGATTTAGGAGATA--TTAA-ATAATAA
1 --TGAGAATATTT-TCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGA-AATAA
27151 TA-AATAA-AAAGT
62 TATAATAATAAAGT
27163 T
1 T
27164 AAGATTAATA
Statistics
Matches: 137, Mismatches: 9, Indels: 29
0.78 0.05 0.17
Matches are distributed among these distances:
72 1 0.01
74 3 0.02
75 54 0.39
78 4 0.03
79 5 0.04
80 7 0.05
81 9 0.07
82 1 0.01
83 2 0.01
84 3 0.02
85 4 0.03
86 11 0.08
87 33 0.24
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.35
Consensus pattern (75 bp):
TGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAATATA
ATAATAAAGT
Found at i:32391 original size:37 final size:38
Alignment explanation
Indices: 32322--32398 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 38
32312 GAATGAAACC
** *
32322 TTCCTCAAAGTGTGATATTTTCAAAAG-GAAAAATGTT
1 TTCCTCAAAGTGCAATATTTTCAAAAGAAAAAAATGTT
* * *
32359 TTCCTCAAAGTGCAATCTTTTGAAACGAAAAAAATGTT
1 TTCCTCAAAGTGCAATATTTTCAAAAGAAAAAAATGTT
32397 TT
1 TT
32399 TTCAAAAAGT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
37 22 0.67
38 11 0.33
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (38 bp):
TTCCTCAAAGTGCAATATTTTCAAAAGAAAAAAATGTT
Found at i:32471 original size:10 final size:10
Alignment explanation
Indices: 32456--32498 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
32446 AGTGCATGGC
32456 AAAAAAA-AA
1 AAAAAAAGAA
*
32465 AAAAAAAGGA
1 AAAAAAAGAA
*
32475 AAAAAGAGAA
1 AAAAAAAGAA
32485 AAAAAAAGAA
1 AAAAAAAGAA
32495 AAAA
1 AAAA
32499 GAAATGATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
9 7 0.24
10 22 0.76
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:32486 original size:20 final size:19
Alignment explanation
Indices: 32463--32500 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 19
32453 GGCAAAAAAA
32463 AAAAAAAAAGGAAAAAAGAG
1 AAAAAAAAA-GAAAAAAGAG
32483 AAAAAAAAAGAAAAAAGA
1 AAAAAAAAAGAAAAAAGA
32501 AATGATAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAGAAAAAAGAG
Found at i:35457 original size:35 final size:35
Alignment explanation
Indices: 35411--36463 Score: 1455
Period size: 35 Copynumber: 29.9 Consensus size: 35
35401 CTGTGCGGTC
35411 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
35446 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
* *
35481 TTTGAAGAAGTTTTCAGAGGTCAGAGTTAATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
* *
35516 TTCCAAGAAGTTTTCAGAGATCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
*
35551 TTTCAAGAAGTTTTCCGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
* *
35586 TTCCAAGAAGTTTTCTGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
* * * *
35621 TTCCAAGAAGTTTCCA-ACGATCAAAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGA-GGTCAGAGTTGATCTCA
* *
35656 TTCCAAAAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
35691 TTTCAAGAAG-TTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
* *
35725 TTTCAAGAGGTTTTCAGAGGTCAAAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
*
35760 TTTCAAGAAGTTTTCAGAGGTCAGAGTCGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
*
35795 TTTCAAGAAGTTTTCACAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
*
35830 TTTCAAGAAGCTTTT-AGAGGTCAGAGTCGATCTCA
1 TTTCAAGAAG-TTTTCAGAGGTCAGAGTTGATCTCA
*
35865 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATGTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
35900 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
35935 TTTCATATTAAGAAGTATTT-AGAGGTCAGAGTTGATCTCA
1 TTTC-----AAGAAGT-TTTCAGAGGTCAGAGTTGATCTCA
* * * ** *
35975 TTCCAAGAAG-CTTCAAACAATCAGAGTTGATATCA
1 TTTCAAGAAGTTTTCAGA-GGTCAGAGTTGATCTCA
*
36010 TTTTAAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 -TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
36046 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
* *
36081 TTCCAAGAAGTTTTCCGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
* *
36116 TTTCAAGAAGTTTTTAGAGGTTAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
*
36151 TATCAAGAAG-TTTCAAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTC-AGAGGTCAGAGTTGATCTCA
36186 TATT-AAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 T-TTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
* * * *
36221 TTCCAAGAAG-CTTCTA-ACGATCAAAGTTGATCTCA
1 TTTCAAGAAGTTTTC-AGA-GGTCAGAGTTGATCTCA
* * *
36256 TTCCAAGAAG-CTTCTA-ACGATCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTC-AGA-GGTCAGAGTTGATCTCA
* *
36291 TTTTAAAGAAGTTTTCAGAGGTCAAAGTTGATCTCA
1 -TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
*
36327 TTTCAAGAAATTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
*
36362 TTTCAGGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
*
36397 TATCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
* *
36432 TTTCAAGAAATTTTC-GATGATCAGAGTTGATC
1 TTTCAAGAAGTTTTCAGA-GGTCAGAGTTGATC
36464 CAGTGCGGCT
Statistics
Matches: 916, Mismatches: 77, Indels: 50
0.88 0.07 0.05
Matches are distributed among these distances:
33 2 0.00
34 50 0.05
35 766 0.84
36 56 0.06
37 9 0.01
40 30 0.03
41 3 0.00
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.33
Consensus pattern (35 bp):
TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
Found at i:37919 original size:87 final size:86
Alignment explanation
Indices: 37696--37927 Score: 360
Period size: 86 Copynumber: 2.7 Consensus size: 86
37686 AGATTAACAA
* *
37696 AATTAATAATGAGAATATTTTCTAAATCTTGTCAAATTGTGGAAGGTTTAGGAGATATTTTAAGA
1 AATTAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATATTTTAAGA
37761 AAACAAATAAATGAAAAATAG
66 AAACAAATAAATGAAAAATAG
37782 AATTAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATATTTTAAG-
1 AATTAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATATTTTAAGA
* *
37846 AAACAAATAAATAATAAAAATTG
66 AAACAAATAAAT--GAAAAATAG
* * *
37869 AA-TAGTAATGAGAATATTTCTCTAAATCTTGCCAGATTGTGGGAGATTTAGGAGATATT
1 AATTAATAATGAGAATATTT-TCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATATT
37928 AAATAATAAT
Statistics
Matches: 136, Mismatches: 7, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
85 12 0.09
86 78 0.57
87 46 0.34
ACGTcount: A:0.44, C:0.06, G:0.17, T:0.34
Consensus pattern (86 bp):
AATTAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATATTTTAAGA
AAACAAATAAATGAAAAATAG
Found at i:39263 original size:12 final size:13
Alignment explanation
Indices: 39246--39274 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
39236 TTCTGGTCGA
39246 TTTTTTTTTA-AT
1 TTTTTTTTTATAT
39258 TTTTTTTTTATAT
1 TTTTTTTTTATAT
39271 TTTT
1 TTTT
39275 CGATATAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTTTTTATAT
Found at i:56095 original size:21 final size:21
Alignment explanation
Indices: 56082--56123 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
56072 TTTAGCTTTG
*
56082 GGGGTAATTCCTTTTGAATTA
1 GGGGTAATTCCTTTAGAATTA
*
56103 GGGGTAATTCCTTTTGAATTA
1 GGGGTAATTCCTTTAGAATTA
56124 TAGCAGAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.10, G:0.24, T:0.43
Consensus pattern (21 bp):
GGGGTAATTCCTTTAGAATTA
Found at i:71290 original size:31 final size:31
Alignment explanation
Indices: 71255--71338 Score: 159
Period size: 31 Copynumber: 2.7 Consensus size: 31
71245 CATATTTTTT
*
71255 CACTTGAGGGACCAATTTGCTATGGTCGGTC
1 CACTTGAGGGACCAATTTGCTATGATCGGTC
71286 CACTTGAGGGACCAATTTGCTATGATCGGTC
1 CACTTGAGGGACCAATTTGCTATGATCGGTC
71317 CACTTGAGGGACCAATTTGCTA
1 CACTTGAGGGACCAATTTGCTA
71339 CTTTTACCGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.29
Consensus pattern (31 bp):
CACTTGAGGGACCAATTTGCTATGATCGGTC
Found at i:72233 original size:2 final size:2
Alignment explanation
Indices: 72226--72262 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
72216 GACTTACATC
72226 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
72263 GTAATGACAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.