Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009585.1 Corchorus olitorius cultivar O-4 contig09617, 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: 6563
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Found at i:58 original size:22 final size:22
Alignment explanation
Indices: 29--177 Score: 128
Period size: 22 Copynumber: 6.8 Consensus size: 22
19 TGAATTTTTT
29 TATGAAATTTTGATAACTACCC
1 TATGAAATTTTGATAACTACCC
* * *
51 TATTAAATTTTGATAACCACGC
1 TATGAAATTTTGATAACTACCC
*
73 TATGAAATTTTGATAATTTA-CC
1 TATGAAATTTTGATAA-CTACCC
* *
95 TATGAAATTGTGATAAACT-CCA
1 TATGAAATTTTGAT-AACTACCC
* *
117 TATGAAACTTTGATAACTTA-AC
1 TATGAAATTTTGATAAC-TACCC
* *
139 TATGAAATTTTAATAAACCT-TCC
1 TATGAAATTTTGAT-AA-CTACCC
162 TATGAAATTTTG-TAAC
1 TATGAAATTTTGATAAC
178 CTTCATATGA
Statistics
Matches: 101, Mismatches: 18, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
20 1 0.01
21 5 0.05
22 76 0.75
23 18 0.18
24 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACTACCC
Found at i:97 original size:44 final size:42
Alignment explanation
Indices: 29--201 Score: 156
Period size: 44 Copynumber: 4.0 Consensus size: 42
19 TGAATTTTTT
* * *
29 TATGAAATTTTGATAACTACCCTATTAAATTTTGATAACCACGC
1 TATGAAATTTTGATAATTA-CCTATGAAATTTTGATAACCTC-C
* *
73 TATGAAATTTTGATAATTTACCTATGAAATTGTGATAAACTCC
1 TATGAAATTTTGATAA-TTACCTATGAAATTTTGATAACCTCC
* * *
116 ATATGAAACTTTGATAACTTAACTATGAAATTTTAATAAACCTTCC
1 -TATGAAATTTTGATAA-TTACCTATGAAATTTTGAT-AACC-TCC
*
162 TATGAAATTTTG-TAACCTT-CATATG--ATTTTGATAACCTCC
1 TATGAAATTTTGATAA--TTACCTATGAAATTTTGATAACCTCC
202 ATGTGAGATT
Statistics
Matches: 109, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
40 3 0.03
41 4 0.04
42 7 0.06
43 1 0.01
44 72 0.66
45 19 0.17
46 3 0.03
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (42 bp):
TATGAAATTTTGATAATTACCTATGAAATTTTGATAACCTCC
Found at i:142 original size:66 final size:66
Alignment explanation
Indices: 29--154 Score: 157
Period size: 66 Copynumber: 1.9 Consensus size: 66
19 TGAATTTTTT
* * * * * *
29 TATGAAATTTTGATAACTACCCTATTAAATTTTGATAACCACGCTATGAAATTTTGATAATTTAC
1 TATGAAATTGTGATAACTACCATATGAAACTTTGATAACCACACTATGAAATTTTAATAATTTAC
94 C
66 C
*
95 TATGAAATTGTGATAAACT-CCATATGAAACTTTGATAACTTA-ACTATGAAATTTTAATAA
1 TATGAAATTGTGAT-AACTACCATATGAAACTTTGATAAC-CACACTATGAAATTTTAATAA
155 ACCTTCCTAT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
66 46 0.90
67 5 0.10
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.38
Consensus pattern (66 bp):
TATGAAATTGTGATAACTACCATATGAAACTTTGATAACCACACTATGAAATTTTAATAATTTAC
C
Found at i:192 original size:19 final size:21
Alignment explanation
Indices: 56--213 Score: 74
Period size: 22 Copynumber: 7.3 Consensus size: 21
46 TACCCTATTA
* *
56 AATTTTGATAACC-ACGCTATG
1 AATTTTGATAACCTTC-ATATG
* *
77 AAATTTTGATAA-TTTACCTATG
1 -AATTTTGATAACCTT-CATATG
* * *
99 AAATTGTGATAAACTCCATATG
1 -AATTTTGATAACCTTCATATG
* *
121 AAACTTTGATAA-CTTAACTATG
1 -AATTTTGATAACCTTCA-TATG
* *
143 AAATTTTAATAAACCTTCCTATG
1 -AATTTTGAT-AACCTTCATATG
166 AAATTTTG-TAACCTTCATATG
1 -AATTTTGATAACCTTCATATG
* *
187 -ATTTTGATAACCTCCATGTG
1 AATTTTGATAACCTTCATATG
207 AGATTTT
1 A-ATTTT
214 TTGTTAATCT
Statistics
Matches: 109, Mismatches: 18, Indels: 18
0.75 0.12 0.12
Matches are distributed among these distances:
19 6 0.06
20 11 0.10
21 14 0.13
22 60 0.55
23 15 0.14
24 3 0.03
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (21 bp):
AATTTTGATAACCTTCATATG
Found at i:199 original size:20 final size:20
Alignment explanation
Indices: 154--213 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
144 AATTTTAATA
*
154 AACCTTCCTATGAAATTTTGT
1 AACCTTCATATG-AATTTTGT
175 AACCTTCATATG-ATTTTGAT
1 AACCTTCATATGAATTTTG-T
* *
195 AACCTCCATGTGAGATTTT
1 AACCTTCATATGA-ATTTT
214 TTGTTAATCT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
19 6 0.18
20 11 0.33
21 11 0.33
22 5 0.15
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.42
Consensus pattern (20 bp):
AACCTTCATATGAATTTTGT
Found at i:2497 original size:35 final size:35
Alignment explanation
Indices: 2425--2498 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 35
2415 AAAATCCTTG
* * **
2425 AAAATAATAAGAGATGAAAAATGTTTAAATACTTT
1 AAAATAATAAGAGATGAAAAATATTCAAATAAATT
* *
2460 AAAATAATAAGAGATGACAAATATTCAATTAAATT
1 AAAATAATAAGAGATGAAAAATATTCAAATAAATT
2495 AAAA
1 AAAA
2499 GTGGGAGCTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.58, C:0.04, G:0.09, T:0.28
Consensus pattern (35 bp):
AAAATAATAAGAGATGAAAAATATTCAAATAAATT
Found at i:3880 original size:2 final size:2
Alignment explanation
Indices: 3875--3910 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3865 GTAAATATGA
*
3875 AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3911 GTATGTATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4958 original size:441 final size:438
Alignment explanation
Indices: 4136--5079 Score: 1509
Period size: 441 Copynumber: 2.1 Consensus size: 438
4126 TTTGTTTATG
* * * * * *
4136 TATCAAATGATTCAT-ATACTTTTATACTTTATGATATTTAGTCCCTCACAATTTATGGATTGGA
1 TATCAAATGA-TCCTCAGACTTTTATGCTTTATGCTATTTAATCCCTCACAA-TTATGGGTTGGA
* * * *
4200 CGACTGAACGTTTCGGCTTTAATTCTTTTATTTTTTTTGTTTTGCTTCTCTGATCAAGGTGATTC
64 CGACTGAACGTTTCAGCTTTAATTCTTTTATCTTTTTTCTTTTGCTTCTCCGATCAAGGTGATTC
* *
4265 AAGTGTCTATTAAAACGTAATTTCGTGATCTACAACTTCCATGAAAGACTCAAAACCAATTTTAA
129 AAGTGTCTATTAAAACGTAATTTCATGATCTACAACTTCCATGAAAGACTCAAAACCAAATTTAA
* * *
4330 TGTTTTGATTTTAAAAAATGCTTTTGAAATTTTGTGGTCTTGATTGTCGGTCTATTTGATATTGT
194 TGTTTTGATTTTAAAAAATGCTTTTGAAATTTTATGGTCTTGATTGCCGGTCTATTTGATATCGT
*
4395 ATAATTTTTGTTCCACTAGTCTGATTGAGGTTATTCAAGTGTCGGTTAAAAGGTTATTGTGTGAT
259 ATAATTTTTGTTCCACTAGTCCGATTGAGGTTATTCAAGTGTCGGTTAAAAGGTTATTGTGTGAT
*** *
4460 CTATGGCTTTCGTTAAGGGCTTCAAAGCTGAATTTGATTAAAGAGTTTTGTGGAGGGTTCAAGAG
324 CTACAACTTTCGTTAAGGGCTTCAAAGCTGAATTTGATTAAAGAGTTTCGTGGAGGGTTCAAGAG
4525 GGAATTTTTATATTTGGTCTCCATAAACAAATATTTTTTTCGCTGGATAATT
389 GGAATTTTTATATTTGGTCTCCATAAACAAAT-TTTTTTT-GCTGGATAATT
*
4577 TATCAAATGATCCTCAGACTTTTATGCTTTATGCTATTTAATCCCTCACAAGTTCTGGGTTGGAC
1 TATCAAATGATCCTCAGACTTTTATGCTTTATGCTATTTAATCCCTCACAA-TTATGGGTTGGAC
*
4642 GACTGAACGTTTCAGCTTTAATTCTTTT-TCTTTTTTCTTTTGCTTGTCCGATCAAGGTGATTCA
65 GACTGAACGTTTCAGCTTTAATTCTTTTATCTTTTTTCTTTTGCTTCTCCGATCAAGGTGATTCA
* *
4706 AGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTCCATGAAGGACTCAAAAGCCAAATTTAA
130 AGTGTCTATTAAAACGTAATTTCATGATCTACAACTTCCATGAAAGACTCAAAA-CCAAATTTAA
4771 TGTTTTGATTTTAAAAAATGCTTTTGAAATTTTATGGTCTTGATTGCCGGTCTATTTGATATCGT
194 TGTTTTGATTTTAAAAAATGCTTTTGAAATTTTATGGTCTTGATTGCCGGTCTATTTGATATCGT
* *
4836 ATAATTTTT-TGTCCACTTGTCCGATTGAGGTTATTCAAGTGTCGGTTAGAAGGTTATTGTGTGA
259 ATAATTTTTGT-TCCACTAGTCCGATTGAGGTTATTCAAGTGTCGGTTAAAAGGTTATTGTGTGA
*
4900 TCTACAACTTTCGTTAAGGG-TCTCAAAGCTGAATTTGATTAATGAGTTTCGTGGAGGGTTCAAG
323 TCTACAACTTTCGTTAAGGGCT-TCAAAGCTGAATTTGATTAAAGAGTTTCGTGGAGGGTTCAAG
* *
4964 AGGGAATTTTTATGTTTGGTCTCCATAAACAAATTTTTTTTGCTGGATTATT
387 AGGGAATTTTTATATTTGGTCTCCATAAACAAATTTTTTTTGCTGGATAATT
* *
5016 TATCAAATGATCCTCAGATTTTTATGCTTTATGCTATTTAATCCCTCATAATTATGGGTTGGAC
1 TATCAAATGATCCTCAGACTTTTATGCTTTATGCTATTTAATCCCTCACAATTATGGGTTGGAC
5080 CATTTAATGT
Statistics
Matches: 466, Mismatches: 33, Indels: 11
0.91 0.06 0.02
Matches are distributed among these distances:
438 12 0.03
439 59 0.13
440 95 0.20
441 300 0.64
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (438 bp):
TATCAAATGATCCTCAGACTTTTATGCTTTATGCTATTTAATCCCTCACAATTATGGGTTGGACG
ACTGAACGTTTCAGCTTTAATTCTTTTATCTTTTTTCTTTTGCTTCTCCGATCAAGGTGATTCAA
GTGTCTATTAAAACGTAATTTCATGATCTACAACTTCCATGAAAGACTCAAAACCAAATTTAATG
TTTTGATTTTAAAAAATGCTTTTGAAATTTTATGGTCTTGATTGCCGGTCTATTTGATATCGTAT
AATTTTTGTTCCACTAGTCCGATTGAGGTTATTCAAGTGTCGGTTAAAAGGTTATTGTGTGATCT
ACAACTTTCGTTAAGGGCTTCAAAGCTGAATTTGATTAAAGAGTTTCGTGGAGGGTTCAAGAGGG
AATTTTTATATTTGGTCTCCATAAACAAATTTTTTTTGCTGGATAATT
Found at i:5902 original size:29 final size:27
Alignment explanation
Indices: 5860--5931 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 27
5850 ACCTCACTCT
* *
5860 AATTCTCTACCTTTGTTTTCACCAAAAAA
1 AATTCTCTGCCTTTGTTCTCACC--AAAA
*
5889 AATTCTCTGCCTTTATTCTCACCAAAA
1 AATTCTCTGCCTTTGTTCTCACCAAAA
*
5916 AATTCTCCGCCTTTGT
1 AATTCTCTGCCTTTGT
5932 GAATATACGA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
27 18 0.47
29 20 0.53
ACGTcount: A:0.28, C:0.28, G:0.06, T:0.39
Consensus pattern (27 bp):
AATTCTCTGCCTTTGTTCTCACCAAAA
Done.