Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024801.1 Corchorus olitorius cultivar O-4 contig24834, 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: 42991
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:171 original size:3 final size:3
Alignment explanation
Indices: 163--239 Score: 145
Period size: 3 Copynumber: 25.7 Consensus size: 3
153 TAATCCAAAT
*
163 ATA ATA ATA ATA ATA ATG ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
211 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
240 GTACATTTTG
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:656 original size:109 final size:109
Alignment explanation
Indices: 465--682 Score: 400
Period size: 109 Copynumber: 2.0 Consensus size: 109
455 CTATTATATA
465 TATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATA
1 TATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATA
*
530 CAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
66 CAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAACACC
*
574 TATTATTATTAATTGTGTTGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATA
1 TATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATA
* *
639 GAAAGTGCAATGAACTATTGGATTTAAAGAAAAATACAAACACC
66 CAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAACACC
683 AAATTGACTA
Statistics
Matches: 105, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
109 105 1.00
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.31
Consensus pattern (109 bp):
TATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATA
CAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAACACC
Found at i:5235 original size:2 final size:2
Alignment explanation
Indices: 5228--5254 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5218 ACTTACTTAA
5228 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 A
5255 CTAGTTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7330 original size:2 final size:2
Alignment explanation
Indices: 7323--7350 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
7313 TTCGTACTTT
7323 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
7351 ATAATTGCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10868 original size:21 final size:21
Alignment explanation
Indices: 10821--10870 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
10811 GCGGAAATCT
* *
10821 AAAACGACTGCATCAATGGCG
1 AAAAAGACTGCATCAATGCCG
10842 AAAAAGACTGCATCAATGCCG
1 AAAAAGACTGCATCAATGCCG
*
10863 AGAAAGAC
1 AAAAAGAC
10871 GGACTATCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (21 bp):
AAAAAGACTGCATCAATGCCG
Found at i:11693 original size:390 final size:391
Alignment explanation
Indices: 11153--11938 Score: 1367
Period size: 390 Copynumber: 2.0 Consensus size: 391
11143 TTCAAGGAAA
*
11153 ATTTGAAAATAGAGAAATTAAAAGAGAAAATTCAAAGTCGTGGAATAGAAACAATGTCCTAAAAC
1 ATTTGAAAATAGAGAAATTAAAAGAGAAAATTCAAAGTCATGGAATAGAAACAATGTCCTAAAAC
11218 ATCTTTTTTTTTTGGTATTGAGGAAATCAAACCTTTTTCCCATTAAAAGGACTCCCGTGAGACCT
66 ATCTTTTTTTTTTGGTATTGAGGAAATCAAACCTTTTTCCCATTAAAAGGACTCCCGTGAGACCT
* * *
11283 CCTCTATCTACCACGTTGCCCCATCCTTTTATACCACCTGGATTTTTCGCAATGACTCTTATGGG
131 CCTCTATCTACCACGTTGCCCCATCCTTTTATACCACATGGATTTTTCACAATGACTCTTATGAG
11348 CTGACACGTTAGCAA-TTTTTTTTTTCACTTTTTTTGGGCAAACGGGGTCATATCGGGTTTATTT
196 CTGACACGTTAGCAATTTTTTTTTTTCACTTTTTTTGGGCAAACGGGGTCATATCGGGTTTATTT
*
11412 GCGAGAACATTCTAGAGAGAGAAAAAATATCGGTGGCAAGGAGAGGAAGGAACAGGAAAGAGAGG
261 GCGAGAACATTCTAGAGAGAGAAAAAATATCGGAGGCAAGGAGAGGAAGGAACAGGAAAGAGAGG
* *
11477 AGGGACCAAGGGAGAAATGAGAGGAAAAGCAAGAGGAAGAAGGCCTGACGACTGCTTCCGCCGCC
326 AGGGACCAAGGGAGAAAGGAGAGGAAAAGCAAGAGGAAGAAGGCCCGACGACTGCTTCCGCCGCC
11542 G
391 G
* * *
11543 ATTTGAAAATAGAGAAATTAAAAGAGAAAATTCAAAGTCATGGATTGGAAACAGTGTCCTAAAAC
1 ATTTGAAAATAGAGAAATTAAAAGAGAAAATTCAAAGTCATGGAATAGAAACAATGTCCTAAAAC
* *
11608 ATCTTTTTTTTTTGGTATTTAGGAAATCAAACCTTTTTCCCATTAAAAGGACTCCTGTGAGACCT
66 ATCTTTTTTTTTTGGTATTGAGGAAATCAAACCTTTTTCCCATTAAAAGGACTCCCGTGAGACCT
* *
11673 CCTCTATCTGCCACGTTGCCCCATCCTTTTATACCACATGTATTTTTCACAATGACTCTTATGAG
131 CCTCTATCTACCACGTTGCCCCATCCTTTTATACCACATGGATTTTTCACAATGACTCTTATGAG
* * *
11738 CTGACACGTTAGCAATTTTTTTTTTTCAGTTTTTTTTGGCAAACGGGGTCATATCGGTTTTATTT
196 CTGACACGTTAGCAATTTTTTTTTTTCACTTTTTTTGGGCAAACGGGGTCATATCGGGTTTATTT
*
11803 GCGAGAACATTCTAGAGAGAGAAAAAATATCGGAGGCAAGGAGAGGAAGGAACGGGAAAGAGAGG
261 GCGAGAACATTCTAGAGAGAGAAAAAATATCGGAGGCAAGGAGAGGAAGGAACAGGAAAGAGAGG
* * * *
11868 AGGGACCGAGGGAGAAAGGAGAGGAAGAGGAAGAGGAAGAAGGCCCGACGACTGCTTCCGTCGCC
326 AGGGACCAAGGGAGAAAGGAGAGGAAAAGCAAGAGGAAGAAGGCCCGACGACTGCTTCCGCCGCC
11933 G
391 G
11934 ATTTG
1 ATTTG
11939 GAAGAGAGAA
Statistics
Matches: 373, Mismatches: 22, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
390 199 0.53
391 174 0.47
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (391 bp):
ATTTGAAAATAGAGAAATTAAAAGAGAAAATTCAAAGTCATGGAATAGAAACAATGTCCTAAAAC
ATCTTTTTTTTTTGGTATTGAGGAAATCAAACCTTTTTCCCATTAAAAGGACTCCCGTGAGACCT
CCTCTATCTACCACGTTGCCCCATCCTTTTATACCACATGGATTTTTCACAATGACTCTTATGAG
CTGACACGTTAGCAATTTTTTTTTTTCACTTTTTTTGGGCAAACGGGGTCATATCGGGTTTATTT
GCGAGAACATTCTAGAGAGAGAAAAAATATCGGAGGCAAGGAGAGGAAGGAACAGGAAAGAGAGG
AGGGACCAAGGGAGAAAGGAGAGGAAAAGCAAGAGGAAGAAGGCCCGACGACTGCTTCCGCCGCC
G
Found at i:12107 original size:23 final size:23
Alignment explanation
Indices: 12080--12129 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
12070 TTTATGTTTG
**
12080 TTTTCATTCCTAATT-TCTCTCTA
1 TTTTCATGACTAATTCTCTCT-TA
*
12103 TTTTCCTGACTAATTCTCTCTTA
1 TTTTCATGACTAATTCTCTCTTA
12126 TTTT
1 TTTT
12130 TTCTCTACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.16, C:0.24, G:0.02, T:0.58
Consensus pattern (23 bp):
TTTTCATGACTAATTCTCTCTTA
Found at i:17917 original size:4 final size:4
Alignment explanation
Indices: 17908--17932 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
17898 AAAAAATAAA
17908 AAAC AAAC AAAC AAAC AAAC AAAC A
1 AAAC AAAC AAAC AAAC AAAC AAAC A
17933 GTACTAAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.24, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:23551 original size:10 final size:10
Alignment explanation
Indices: 23536--23561 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
23526 TTAAAGATAC
23536 AAAAAAAACA
1 AAAAAAAACA
23546 AAAAAAAACA
1 AAAAAAAACA
23556 AAAAAA
1 AAAAAA
23562 TTACCTCATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:24284 original size:22 final size:22
Alignment explanation
Indices: 24256--24304 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
24246 GAATAAAAAC
* * *
24256 ATCATGTCAGGCTGATGATCAT
1 ATCATGTCAAGCTCATAATCAT
24278 ATCATGTCAAGCTCATAATCAT
1 ATCATGTCAAGCTCATAATCAT
24300 ATCAT
1 ATCAT
24305 ATTAATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (22 bp):
ATCATGTCAAGCTCATAATCAT
Found at i:28247 original size:23 final size:21
Alignment explanation
Indices: 28205--28247 Score: 50
Period size: 23 Copynumber: 2.0 Consensus size: 21
28195 GTGATGAACA
*
28205 AGAGAAAAATAGCGCAGAGCC
1 AGAGAAAAATAGCACAGAGCC
*
28226 AGAGAGAAAATAAGCACGGAGC
1 AGAGA-AAAAT-AGCACAGAGC
28248 TTGGTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.28
22 5 0.28
23 8 0.44
ACGTcount: A:0.49, C:0.16, G:0.30, T:0.05
Consensus pattern (21 bp):
AGAGAAAAATAGCACAGAGCC
Found at i:30245 original size:3 final size:3
Alignment explanation
Indices: 30237--30273 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
30227 TAGTTGTGTT
30237 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
30274 ATCTATTAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:30766 original size:18 final size:18
Alignment explanation
Indices: 30743--30779 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
30733 ATCCATGGTT
**
30743 CAAGCTATCTGATCCCTC
1 CAAGCTATCAAATCCCTC
30761 CAAGCTATCAAATCCCTC
1 CAAGCTATCAAATCCCTC
30779 C
1 C
30780 CCAAGGGCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.27, C:0.41, G:0.08, T:0.24
Consensus pattern (18 bp):
CAAGCTATCAAATCCCTC
Found at i:34945 original size:179 final size:180
Alignment explanation
Indices: 34645--35007 Score: 620
Period size: 179 Copynumber: 2.0 Consensus size: 180
34635 TAAGTTGTCG
34645 AGGGTGGATCTTCATTGGAGAGAGGTTGCTGCTCAGGGGCGAAGTTTATAGCTTCTGTTGGCTGC
1 AGGGTGGATCTTCATTGGAGAGAGGTTGCTGCTCAGGGGCGAAGTTTATAGCTTCTGTTGGCTGC
* * *
34710 ACCAAACTAACATTTATTGAATTAGGAGTGGAAATAGATGTAATAACAGGAACTTCAAATAGAGA
66 ACCAAACTAACATTCATTGAAGTAGGAGTGGAAATAGATGTAATAACAAGAACTTCAAATAGAGA
*
34775 AGGTGATAAAGGATCTAGACC-AGAGTGTGTGCAGTAATTTGTATGGAAA
131 AGGTGATAAAGGATCTAGACCGACAGTGTGTGCAGTAATTTGTATGGAAA
* *
34824 AGGGTGGATCTTCATTGGAGAGAGGTTGCTGCTCAGGGGCGGAGTTTATAGCTTTTGTTGGCTGC
1 AGGGTGGATCTTCATTGGAGAGAGGTTGCTGCTCAGGGGCGAAGTTTATAGCTTCTGTTGGCTGC
* * * *
34889 ACCAGACTGACATTCGTTGAAGTAGGAGTGGAAATAGATGTACTAACAAGAACTTCAAATAGAGA
66 ACCAAACTAACATTCATTGAAGTAGGAGTGGAAATAGATGTAATAACAAGAACTTCAAATAGAGA
*
34954 AGGTGATAAAGGATCTAGACCGACAGTGTGTGCAGTAATTTGTGTGGAAA
131 AGGTGATAAAGGATCTAGACCGACAGTGTGTGCAGTAATTTGTATGGAAA
35004 AGGG
1 AGGG
35008 AAACTGTAAT
Statistics
Matches: 172, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
179 142 0.83
180 30 0.17
ACGTcount: A:0.31, C:0.12, G:0.30, T:0.27
Consensus pattern (180 bp):
AGGGTGGATCTTCATTGGAGAGAGGTTGCTGCTCAGGGGCGAAGTTTATAGCTTCTGTTGGCTGC
ACCAAACTAACATTCATTGAAGTAGGAGTGGAAATAGATGTAATAACAAGAACTTCAAATAGAGA
AGGTGATAAAGGATCTAGACCGACAGTGTGTGCAGTAATTTGTATGGAAA
Found at i:39623 original size:51 final size:52
Alignment explanation
Indices: 39562--39664 Score: 129
Period size: 53 Copynumber: 2.0 Consensus size: 52
39552 TATTAATTAC
* *
39562 TACAACAAGACACGTG-ACTCCTTCACGGATAGGGA-ATAAGGTGGGCGCAAG
1 TACAAAAAGACACGTGAACTCCTTCACGGAT-GGGACACAAGGTGGGCGCAAG
* * *
39613 TACAAAAAGACATGTGACACTTCTTCATGGATGGGACACAAGGTGGGCGCAA
1 TACAAAAAGACACGTGA-ACTCCTTCACGGATGGGACACAAGGTGGGCGCAA
39665 ATATACACGA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
51 14 0.32
52 4 0.09
53 26 0.59
ACGTcount: A:0.34, C:0.20, G:0.28, T:0.17
Consensus pattern (52 bp):
TACAAAAAGACACGTGAACTCCTTCACGGATGGGACACAAGGTGGGCGCAAG
Found at i:41051 original size:2 final size:2
Alignment explanation
Indices: 41044--41077 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
41034 AAATAATTCG
41044 TA TA TA 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
41078 GCAAAACACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41182 original size:45 final size:42
Alignment explanation
Indices: 41119--41212 Score: 118
Period size: 45 Copynumber: 2.2 Consensus size: 42
41109 AGTGCATAAC
*
41119 CTAA-ATTCTACTTCATCTCTAAGTAATTCATTAAAATAAAA
1 CTAATATTCTACTTCATCTCTAAGTAATTCATCAAAATAAAA
* * *
41160 CTAATATTCTACTCCTCTATCTCTAGGTAATTCATCGAAATAAAG
1 CTAATATTCTACT--TC-ATCTCTAAGTAATTCATCAAAATAAAA
41205 CTAATATT
1 CTAATATT
41213 AACTGTTGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
41 4 0.09
42 8 0.18
44 2 0.04
45 31 0.69
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.37
Consensus pattern (42 bp):
CTAATATTCTACTTCATCTCTAAGTAATTCATCAAAATAAAA
Found at i:42362 original size:19 final size:19
Alignment explanation
Indices: 42340--42376 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
42330 TTTCAAAATT
42340 AATTATTTTACCACGTGGA
1 AATTATTTTACCACGTGGA
* *
42359 AATTGTTTTGCCACGTGG
1 AATTATTTTACCACGTGG
42377 CCTGATGACG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (19 bp):
AATTATTTTACCACGTGGA
Found at i:42576 original size:4 final size:4
Alignment explanation
Indices: 42567--42600 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
42557 ATAAGGATCT
*
42567 TTTC TTTC TTTC TTTC TTTC TTT- TTTC TTCC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
42601 TTCTGTAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:42584 original size:12 final size:11
Alignment explanation
Indices: 42566--42602 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
42556 TATAAGGATC
42566 TTTTCTTTCTT
1 TTTTCTTTCTT
42577 TCTTTCTTTCTT
1 T-TTTCTTTCTT
*
42589 TTTTCTTCCTT
1 TTTTCTTTCTT
42600 TTT
1 TTT
42603 CTGTAATGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 13 0.54
12 11 0.46
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTCTTTCTT
Done.