Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011403.1 Corchorus capsularis cultivar CVL-1 contig11424, 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: 29277
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:8934 original size:171 final size:171
Alignment explanation
Indices: 8649--8961 Score: 599
Period size: 171 Copynumber: 1.8 Consensus size: 171
8639 GAGAATCCTT
* *
8649 CATTAGCTCAGTATTTGAATGCAGTGCAACGCCTGCGGCATAAGGCAAGGCAAGGTAAAGCAAAC
1 CATTAGCTCAGTATTTGAATGCAGTGCAACGCCTGCGGCATAAGGCAAGCCAAGATAAAGCAAAC
8714 TAGCTTTTCTTGACATTTCTTATACCGCATGCGCCACACTGTATTAAAACAGAGCTTTCCATGTA
66 TAGCTTTTCTTGACATTTCTTATACCGCATGCGCCACACTGTATTAAAACAGAGCTTTCCATGTA
8779 ATTTGCTTCATTAGCTCTCAGTATTTGTTTTTTTGGTATAA
131 ATTTGCTTCATTAGCTCTCAGTATTTGTTTTTTTGGTATAA
8820 CATTAGCTCAGTATTTGAATGCAGTGCAACGCCTGCGGCATAAGGCAAGCCAAGATAAAGCAAAC
1 CATTAGCTCAGTATTTGAATGCAGTGCAACGCCTGCGGCATAAGGCAAGCCAAGATAAAGCAAAC
*
8885 TAGCTTTTCTTGACATTTCTTATACCGCATGCGCCACACTGTATTAAAACAGAGCTTTCTATGTA
66 TAGCTTTTCTTGACATTTCTTATACCGCATGCGCCACACTGTATTAAAACAGAGCTTTCCATGTA
8950 ATTTGCTTCATT
131 ATTTGCTTCATT
8962 TTAGCTCAGT
Statistics
Matches: 139, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
171 139 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.32
Consensus pattern (171 bp):
CATTAGCTCAGTATTTGAATGCAGTGCAACGCCTGCGGCATAAGGCAAGCCAAGATAAAGCAAAC
TAGCTTTTCTTGACATTTCTTATACCGCATGCGCCACACTGTATTAAAACAGAGCTTTCCATGTA
ATTTGCTTCATTAGCTCTCAGTATTTGTTTTTTTGGTATAA
Found at i:9083 original size:145 final size:144
Alignment explanation
Indices: 8822--9228 Score: 590
Period size: 140 Copynumber: 2.9 Consensus size: 144
8812 TGGTATAACA
*
8822 TTAGCTCAGTATTTGAATGCAGTGCAACGCCTGCGGCATAAGGCAAGCCAAGATAAAGC-AA-AC
1 TTAGCTCAGTATTTGAATGCAGTGCAACGCCTGCGGCATAA-GCAAG-CAAGCTAAAGCAAATAC
* * * *
8885 ----TAGCTTTTCTT-GACATTTCTTATACCGCATGCGCCACACTGTATTAAAACAGAGC-TTTC
64 TAATTAGCTTTGCTTAAAC-TTTCTCATGCCGCATGCGCCACACTGTATTAAAACAGAGCTTTTC
8944 TATGTAATTTGCTTCATT
128 -ATGTAATTTGCTTCATT
8962 TTAGCTCAGTATTTGAATGCAGTGCAACGCCTGCGGCATAAGCAAGGCAAGCTAAAGCAAATACT
1 TTAGCTCAGTATTTGAATGCAGTGCAACGCCTGCGGCATAAGCAA-GCAAGCTAAAGCAAATACT
9027 AATTAGCTTTGCTTAAACTTTCTCATGCCGCATGCGCCACACTGTATTAAAACAGAGCTTTTCAT
65 AATTAGCTTTGCTTAAACTTTCTCATGCCGCATGCGCCACACTGTATTAAAACAGAGCTTTTCAT
9092 GTAATTTGCTTCATT
130 GTAATTTGCTTCATT
*
9107 TTAGCTCAGTATTTGAATGCAGTGTAACGCCTGCGGCAT--G-AA--AAGGCTAAAGCAAATACT
1 TTAGCTCAGTATTTGAATGCAGTGCAACGCCTGCGGCATAAGCAAGCAA-GCTAAAGCAAATACT
*
9167 AATTAGCTTTGCTTGAAA-TTTCTCATGCCACATGCGCCACACTGTATTAAAACAGAGCTTTT
65 AATTAGCTTTGCTT-AAACTTTCTCATGCCGCATGCGCCACACTGTATTAAAACAGAGCTTTT
9229 AGTGCTTCTT
Statistics
Matches: 249, Mismatches: 7, Indels: 22
0.90 0.03 0.08
Matches are distributed among these distances:
139 16 0.06
140 116 0.47
141 5 0.02
142 2 0.01
143 1 0.00
145 103 0.41
146 6 0.02
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (144 bp):
TTAGCTCAGTATTTGAATGCAGTGCAACGCCTGCGGCATAAGCAAGCAAGCTAAAGCAAATACTA
ATTAGCTTTGCTTAAACTTTCTCATGCCGCATGCGCCACACTGTATTAAAACAGAGCTTTTCATG
TAATTTGCTTCATT
Found at i:9918 original size:47 final size:46
Alignment explanation
Indices: 9866--10133 Score: 171
Period size: 47 Copynumber: 5.8 Consensus size: 46
9856 TTATATAAGG
* *
9866 CCGTTAAGATTTTATTAACTAGATTAATCAATAACCATTCTGCAAGA
1 CCGTTAAGATTTTATTAACTAGATTAACCAATAACCATTATG-AAGA
* **
9913 CCGTTAAGATTTTATTAACTACTAGTAGATTAACCAATAACCATTTTGTGTGA
1 CCGTTAAGATTTTATT-A--AC---TAGATTAACCAATAACCATTATG-AAGA
** * * * *
9966 CTATCAAGATTTTATTAACTAAATTAA-CAAT---TA-TAT-AAGG
1 CCGTTAAGATTTTATTAACTAGATTAACCAATAACCATTATGAAGA
* * * * *
10006 CCGTTGAGATTTTATTAAATAGTTTAACCAATAACCATTTTGTATGA
1 CCGTTAAGATTTTATTAACTAGATTAACCAATAACCATTATG-AAGA
* * * * *
10053 TCGTTACA-ATTTTATTAACTAAATTAA-CAATTA-TA-TAT-AAGG
1 CCGTTA-AGATTTTATTAACTAGATTAACCAATAACCATTATGAAGA
*
10095 CCGTTAAAATTTTATTAACTAGATTAACCAATAACCATT
1 CCGTTAAGATTTTATTAACTAGATTAACCAATAACCATT
10134 CTGTATGACT
Statistics
Matches: 164, Mismatches: 39, Indels: 38
0.68 0.16 0.16
Matches are distributed among these distances:
40 21 0.13
41 5 0.03
42 27 0.16
43 6 0.04
44 4 0.02
45 4 0.02
46 9 0.05
47 45 0.27
48 2 0.01
50 4 0.02
52 1 0.01
53 36 0.22
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.38
Consensus pattern (46 bp):
CCGTTAAGATTTTATTAACTAGATTAACCAATAACCATTATGAAGA
Found at i:10139 original size:89 final size:87
Alignment explanation
Indices: 9938--10143 Score: 292
Period size: 89 Copynumber: 2.3 Consensus size: 87
9928 TAACTACTAG
*
9938 TAGATTAACCAATAACCATTTTGTGTGACTATCAAGATTTTATTAACTAAATTAACAATTATATA
1 TAGATTAACCAATAACCATTTTGTATGACTATCAAGATTTTATTAACTAAATTAACAATTATATA
* *
10003 AGGCCGTTGAGATTTTATTAAA
66 AGGCCGTTAAAATTTTATTAAA
*
10025 TAGTTTAACCAATAACCATTTTGTATGATCGT-T-ACA-ATTTTATTAACTAAATTAACAATTAT
1 TAGATTAACCAATAACCATTTTGTATGA-C-TATCA-AGATTTTATTAACTAAATTAACAA-T-T
*
10087 ATATAAGGCCGTTAAAATTTTATTAAC
61 ATATAAGGCCGTTAAAATTTTATTAAA
*
10114 TAGATTAACCAATAACCATTCTGTATGACT
1 TAGATTAACCAATAACCATTTTGTATGACT
10144 GTTATAGATT
Statistics
Matches: 107, Mismatches: 7, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
87 50 0.47
88 5 0.05
89 52 0.49
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (87 bp):
TAGATTAACCAATAACCATTTTGTATGACTATCAAGATTTTATTAACTAAATTAACAATTATATA
AGGCCGTTAAAATTTTATTAAA
Found at i:10167 original size:27 final size:26
Alignment explanation
Indices: 10126--10179 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
10116 GATTAACCAA
* * *
10126 TAACCATTCTGTATGACTGTTATAGAT
1 TAACCATTATATATGACCGTTA-AGAT
10153 TAACCATTATATATGACCGTTAAGAT
1 TAACCATTATATATGACCGTTAAGAT
10179 T
1 T
10180 TTATTAACTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 5 0.21
27 19 0.79
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (26 bp):
TAACCATTATATATGACCGTTAAGAT
Found at i:10198 original size:74 final size:75
Alignment explanation
Indices: 10075--10234 Score: 261
Period size: 74 Copynumber: 2.1 Consensus size: 75
10065 TATTAACTAA
* *
10075 ATTAACAATTATATATAAGGCCGTTAAAATTTTATTAACTAGATTAACCAATAACCATTCTGTAT
1 ATTAACCATTATATAT-AGACCGTTAAAATTTTATTAACTAGATTAACCAATAACCATTCTGTAT
10140 GA-CTGTTATAG
65 GATC-GTTATAG
*
10151 ATTAACCATTATATAT-GACCGTTAAGATTTTATTAACTAGATTAACCAATAACCATTCTGTATG
1 ATTAACCATTATATATAGACCGTTAAAATTTTATTAACTAGATTAACCAATAACCATTCTGTATG
10215 ATCGTTATAG
66 ATCGTTATAG
10225 ATTAACCATT
1 ATTAACCATT
10235 CTGTATGGCG
Statistics
Matches: 80, Mismatches: 3, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
74 64 0.80
75 1 0.01
76 15 0.19
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (75 bp):
ATTAACCATTATATATAGACCGTTAAAATTTTATTAACTAGATTAACCAATAACCATTCTGTATG
ATCGTTATAG
Found at i:11445 original size:14 final size:14
Alignment explanation
Indices: 11422--11451 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
11412 AACTTTAAAC
11422 AAAAACAAAAAGAA
1 AAAAACAAAAAGAA
*
11436 AAAAAGAAAAAGAA
1 AAAAACAAAAAGAA
11450 AA
1 AA
11452 GAAAATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.87, C:0.03, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAACAAAAAGAA
Found at i:16151 original size:7 final size:7
Alignment explanation
Indices: 16139--16167 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
16129 TATCGTTTGT
16139 AAAGAAA
1 AAAGAAA
16146 AAAGAAA
1 AAAGAAA
16153 AAAGAAA
1 AAAGAAA
16160 AAAGAAA
1 AAAGAAA
16167 A
1 A
16168 GAGATATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:24899 original size:2 final size:2
Alignment explanation
Indices: 24892--24922 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
24882 ATGTTTTTCC
24892 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 T
24923 CCGAATAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:26397 original size:24 final size:24
Alignment explanation
Indices: 26370--26450 Score: 117
Period size: 24 Copynumber: 3.2 Consensus size: 24
26360 TGATGATTCA
26370 GATGAGAAAGGAGCCCCTGAAGTT
1 GATGAGAAAGGAGCCCCTGAAGTT
* *
26394 GATGAGTCAAATGAAGACCCTGAAGTT
1 GATGAG--AAA-GGAGCCCCTGAAGTT
26421 GATGAGAAAGGAGCCCCTGAAGTT
1 GATGAGAAAGGAGCCCCTGAAGTT
26445 GATGAG
1 GATGAG
26451 TCAAATGAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
24 25 0.50
25 3 0.06
26 3 0.06
27 19 0.38
ACGTcount: A:0.35, C:0.15, G:0.32, T:0.19
Consensus pattern (24 bp):
GATGAGAAAGGAGCCCCTGAAGTT
Found at i:26416 original size:27 final size:27
Alignment explanation
Indices: 26384--26459 Score: 113
Period size: 24 Copynumber: 2.9 Consensus size: 27
26374 AGAAAGGAGC
26384 CCCTGAAGTTGATGAGTCAAATGAAGA
1 CCCTGAAGTTGATGAGTCAAATGAAGA
* *
26411 CCCTGAAGTTGATGAG--AAA-GGAGC
1 CCCTGAAGTTGATGAGTCAAATGAAGA
26435 CCCTGAAGTTGATGAGTCAAATGAA
1 CCCTGAAGTTGATGAGTCAAATGAA
26460 AAAGGAGACC
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
24 19 0.44
25 3 0.07
26 3 0.07
27 18 0.42
ACGTcount: A:0.36, C:0.16, G:0.28, T:0.21
Consensus pattern (27 bp):
CCCTGAAGTTGATGAGTCAAATGAAGA
Found at i:26566 original size:27 final size:27
Alignment explanation
Indices: 26535--26589 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
26525 TGACGATTCA
* *
26535 AATGAACACGTAGCCCCCGCTGGATGC
1 AATGAAAACGTAGCCCCCACTGGATGC
26562 AATGAAAACGTAGCCCCCACTGGATGC
1 AATGAAAACGTAGCCCCCACTGGATGC
26589 A
1 A
26590 GTATCTGCTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.15
Consensus pattern (27 bp):
AATGAAAACGTAGCCCCCACTGGATGC
Found at i:28305 original size:30 final size:29
Alignment explanation
Indices: 28243--28312 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
28233 ACCGAACCGT
****
28243 CAAATAAGCCCCTGAACTATTATTTCGGC
1 CAAATAAGCCCCTGAACTATTAAAAAGGC
*
28272 CAAATAAGCCCCTGAACTCTTAAAAAAGGC
1 CAAATAAGCCCCTGAACTATT-AAAAAGGC
28302 CAAATAAGCCC
1 CAAATAAGCCC
28313 TGTTGCCAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 20 0.57
30 15 0.43
ACGTcount: A:0.39, C:0.29, G:0.13, T:0.20
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACTATTAAAAAGGC
Done.