Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013679.1 Corchorus olitorius cultivar O-4 contig13712, 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: 25783
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:4427 original size:2 final size:2
Alignment explanation
Indices: 4414--4498 Score: 58
Period size: 2 Copynumber: 44.5 Consensus size: 2
4404 TATTATTATC
* *
4414 TA TA TA -A T- TA TA TA TA T- TT TT TA TA TA TCA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA
* *
4454 TA TA TCA T- TA -A TT TA CTA TA TA TA T- TA TA -A TA TA TA AA TA
1 TA TA T-A TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
4494 TA TA T
1 TA TA T
4499 TTGTTACGTC
Statistics
Matches: 68, Mismatches: 5, Indels: 20
0.73 0.05 0.22
Matches are distributed among these distances:
1 7 0.10
2 55 0.81
3 6 0.09
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4456 original size:30 final size:31
Alignment explanation
Indices: 4406--4489 Score: 83
Period size: 30 Copynumber: 2.8 Consensus size: 31
4396 TTATAAATTA
*
4406 TTAT-TATC-TATATA-ATTATATATATT-TT
1 TTATATATCATATATATA-TATATATATTAAT
4434 TTATATATCATATATATATATATATCATTAAT
1 TTATATATCATATATATATATATAT-ATTAAT
4466 TTACTATAT-ATAT-TATA-ATATATA
1 TTA-TATATCATATATATATATATATA
4490 AATATATATT
Statistics
Matches: 49, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
28 4 0.08
29 5 0.10
30 19 0.39
31 8 0.16
32 8 0.16
33 5 0.10
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.54
Consensus pattern (31 bp):
TTATATATCATATATATATATATATATTAAT
Found at i:4466 original size:44 final size:45
Alignment explanation
Indices: 4372--4498 Score: 117
Period size: 44 Copynumber: 2.9 Consensus size: 45
4362 TTTAGCCTTT
* * *
4372 TATAT-ATTTTCTA-ATTTTTTATATTTATAAAT-TAT-TATTATC
1 TATATAATTTACTATATTTTTTATATATATATATATATATA-TATC
4414 TATATAATTATA-TATATTTTTTATATATCATATATATATATATATC
1 TATATAATT-TACTATATTTTTTATATAT-ATATATATATATATATC
* * *
4460 -AT-TAATTTACTATATATATTATA-ATATATAAATATATAT
1 TATATAATTTACTATATTTTTTATATATATATATATATATAT
4499 TTGTTACGTC
Statistics
Matches: 72, Mismatches: 6, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
42 18 0.25
43 9 0.12
44 29 0.40
45 7 0.10
46 7 0.10
47 2 0.03
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (45 bp):
TATATAATTTACTATATTTTTTATATATATATATATATATATATC
Found at i:15511 original size:206 final size:201
Alignment explanation
Indices: 15162--15562 Score: 649
Period size: 206 Copynumber: 2.0 Consensus size: 201
15152 GCACTCATTG
*
15162 AGTGTAGAAATTAAAAGATAGTTTATAATATATTTTTTTTGATACATTTAAATTGGTAGTTTTTT
1 AGTGTAGAAATTAAAAGATAGTTTATAATATATTTTTTTTGATACATTTAAATTGATAGTTTTTT
*
15227 TGAAATGATATAAATAAAAATTAATTAATATATATCTCTGGTAGACAGTGATTTTATTATGGAAT
66 TGAAATGATATAAATAAAAATTAATTAATATATATCTCTGATAGACAGTGATTTTATTATGGAAT
* *
15292 GGATAGGTTTTATTTTTGGTTTTTAATTTTTTAAAAACTGATTTTGTGTCATAATCAACTCGTGA
131 GGATAGGTTTTATTTTTGGTTTTTAATCTTTTAAAAACTGAGTTTGTGTCATAATCAACTCGTGA
15357 CACAAA
196 CACAAA
* *
15363 AGTGTAGAAATTAAAAGGTAGTTTATAATAATTTTCTTTTTTGATACATTTAAATTGATAGTCTT
1 AGTGTAGAAATTAAAAGATAGTTTATAAT-ATATT-TTTTTTGATACATTTAAATTGATAGT-TT
* * * * *
15428 TTTTTAAATGATATAAATAAAAATTAATTACTATATATATCTCTGATGGACGGTGGTTTTATTCT
63 TTTTGAAATGATATAAATAAAAATTAATTA--ATATATATCTCTGATAGACAGTGATTTTATTAT
*
15493 GGAATGGATAGGTTTTATTTTTGGTTTTTAATCTTTTAAAAACTGAGTTTGTGTCCTAATCAACT
126 GGAATGGATAGGTTTTATTTTTGGTTTTTAATCTTTTAAAAACTGAGTTTGTGTCATAATCAACT
15558 CGTGA
191 CGTGA
15563 GTCGTGACAC
Statistics
Matches: 183, Mismatches: 12, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
201 28 0.15
202 4 0.02
203 25 0.14
204 31 0.17
206 95 0.52
ACGTcount: A:0.34, C:0.06, G:0.15, T:0.45
Consensus pattern (201 bp):
AGTGTAGAAATTAAAAGATAGTTTATAATATATTTTTTTTGATACATTTAAATTGATAGTTTTTT
TGAAATGATATAAATAAAAATTAATTAATATATATCTCTGATAGACAGTGATTTTATTATGGAAT
GGATAGGTTTTATTTTTGGTTTTTAATCTTTTAAAAACTGAGTTTGTGTCATAATCAACTCGTGA
CACAAA
Found at i:20149 original size:23 final size:23
Alignment explanation
Indices: 20116--20176 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
20106 TGAATATTTT
*
20116 TATG-AAATTTTGATAACTACCC
1 TATGTAAATTTTGATAACCACCC
* *
20138 TATTTAAATTTTGATAACCACGC
1 TATGTAAATTTTGATAACCACCC
20161 TATGT-AATTTTGATAA
1 TATGTAAATTTTGATAA
20177 TTTATCTATG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 14 0.41
23 20 0.59
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (23 bp):
TATGTAAATTTTGATAACCACCC
Found at i:20272 original size:21 final size:21
Alignment explanation
Indices: 20227--20304 Score: 68
Period size: 21 Copynumber: 3.6 Consensus size: 21
20217 ATGACATAAT
* *
20227 TATGAAATTTTAATAAACTTTCC
1 TATGAAATTTT-GT-AACCTTCC
20250 TATGAAATTTTGTAACCTTCC
1 TATGAAATTTTGTAACCTTCC
* *
20271 TATG-ATTTTTGATAACCTCCC
1 TATGAAATTTTG-TAACCTTCC
* *
20292 TGTGAGATTTTGT
1 TATGAAATTTTGT
20305 TAATCTCCCT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
20 6 0.13
21 23 0.50
22 6 0.13
23 11 0.24
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.45
Consensus pattern (21 bp):
TATGAAATTTTGTAACCTTCC
Found at i:23624 original size:32 final size:32
Alignment explanation
Indices: 23565--23625 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
23555 AAATTTGTTT
* *
23565 GAAAAATAAGGGTATAATGGATGATTCAATTA
1 GAAAAATAAGGGTATAATAGATAATTCAATTA
23597 GAAAAATAAGGGTATAATAG-TCAATTCAA
1 GAAAAATAAGGGTATAATAGAT-AATTCAA
23626 AAGTTTTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 1 0.04
32 25 0.96
ACGTcount: A:0.49, C:0.05, G:0.20, T:0.26
Consensus pattern (32 bp):
GAAAAATAAGGGTATAATAGATAATTCAATTA
Found at i:24987 original size:16 final size:16
Alignment explanation
Indices: 24966--24997 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
24956 ATTATTATTT
24966 TTATTAATAATATATA
1 TTATTAATAATATATA
*
24982 TTATTATTAATATATA
1 TTATTAATAATATATA
24998 AATAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATTAATAATATATA
Found at i:24987 original size:25 final size:27
Alignment explanation
Indices: 24940--24989 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
24930 AATTTAAATA
24940 TATTAGATAATAGAATATTATTATTTT
1 TATTAGATAATAGAATATTATTATTTT
*
24967 TATTA-ATAATA-TATATTATTATT
1 TATTAGATAATAGAATATTATTATT
24990 AATATATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 11 0.50
26 6 0.27
27 5 0.23
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (27 bp):
TATTAGATAATAGAATATTATTATTTT
Found at i:24988 original size:19 final size:19
Alignment explanation
Indices: 24961--25013 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
24951 AGAATATTAT
*
24961 TATTTTTATTAATAATATA
1 TATTATTATTAATAATATA
24980 TATTATTATTAAT-ATATA
1 TATTATTATTAATAATATA
* *
24998 AATAATTATATAATAA
1 TATTATTAT-TAATAA
25014 ACGAACACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 12 0.41
19 16 0.55
20 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTATTATTAATAATATA
Found at i:25055 original size:35 final size:35
Alignment explanation
Indices: 25016--25090 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 35
25006 TATAATAAAC
*
25016 GAACACTTAAATGAACAATAAACGAGTCTGTTCGT
1 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
25051 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
1 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
25086 GAACA
1 GAACA
25091 TAAACGAACT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (35 bp):
GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
Done.