Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011653.1 Corchorus capsularis cultivar CVL-1 contig11674, 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: 28039
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:2965 original size:17 final size:16
Alignment explanation
Indices: 2943--2975 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
2933 TTCTTTTATC
2943 TTTATAATATATAAATA
1 TTTATAATATA-AAATA
2960 TTTATAATATAAAATA
1 TTTATAATATAAAATA
2976 ATGATGATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTTATAATATAAAATA
Found at i:5983 original size:2 final size:2
Alignment explanation
Indices: 5976--6008 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5966 AATCAAAATT
*
5976 TA TA TA TA TA TA TA TA TA CA 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
6009 TATTTTCAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:6453 original size:29 final size:31
Alignment explanation
Indices: 6403--6460 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 31
6393 AACTTCTGCA
**
6403 TTGTATTTTGACACATTTAACAGCAACCATT
1 TTGTATTTTGACACATCCAACAGCAACCATT
6434 TTGT-TTTTGACA-ATCCAACAGCAACCA
1 TTGTATTTTGACACATCCAACAGCAACCA
6461 ATTTACCCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 13 0.52
30 8 0.32
31 4 0.16
ACGTcount: A:0.33, C:0.22, G:0.10, T:0.34
Consensus pattern (31 bp):
TTGTATTTTGACACATCCAACAGCAACCATT
Found at i:12410 original size:20 final size:20
Alignment explanation
Indices: 12385--12427 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
12375 AGCCTAAGCT
12385 ACAGGATTCCAGGATTTGGA
1 ACAGGATTCCAGGATTTGGA
12405 ACAGGATTCCAGGATTTGGA
1 ACAGGATTCCAGGATTTGGA
12425 ACA
1 ACA
12428 CATTCACTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.23
Consensus pattern (20 bp):
ACAGGATTCCAGGATTTGGA
Found at i:17302 original size:27 final size:28
Alignment explanation
Indices: 17271--17324 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
17261 CCAAATTTAA
* *
17271 TTTTGA-TATTTATTTGTGTATCATTTC
1 TTTTGACTATGTATTTGTGCATCATTTC
17298 TTTTGAGCTATGTATTTGTGCATCATT
1 TTTTGA-CTATGTATTTGTGCATCATT
17325 AAATTTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 6 0.26
29 17 0.74
ACGTcount: A:0.19, C:0.09, G:0.15, T:0.57
Consensus pattern (28 bp):
TTTTGACTATGTATTTGTGCATCATTTC
Found at i:18355 original size:29 final size:30
Alignment explanation
Indices: 18322--18382 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
18312 AAAGTTAAAG
*
18322 AAATAAAAA-TTAAAGGATTAAATTGTATA
1 AAATAAAAAGTTAAAGGATTAAATTGCATA
**
18351 AAATAAAAAGTTTGAGGATTAAATTGCATA
1 AAATAAAAAGTTAAAGGATTAAATTGCATA
18381 AA
1 AA
18383 TGATACATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 9 0.32
30 19 0.68
ACGTcount: A:0.56, C:0.02, G:0.13, T:0.30
Consensus pattern (30 bp):
AAATAAAAAGTTAAAGGATTAAATTGCATA
Found at i:19077 original size:32 final size:33
Alignment explanation
Indices: 19018--19085 Score: 111
Period size: 32 Copynumber: 2.1 Consensus size: 33
19008 ATCATCCCGA
* *
19018 ATTCGTCATGAAGATTCTGATTTTGATGGTGGT
1 ATTCGTCATGAAGATTCTGATTCTGATGGTAGT
19051 ATTCGTCATGAAGATT-TGATTCTGATGGTAGT
1 ATTCGTCATGAAGATTCTGATTCTGATGGTAGT
19083 ATT
1 ATT
19086 GGTTTTGTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 17 0.52
33 16 0.48
ACGTcount: A:0.24, C:0.09, G:0.25, T:0.43
Consensus pattern (33 bp):
ATTCGTCATGAAGATTCTGATTCTGATGGTAGT
Found at i:19453 original size:21 final size:21
Alignment explanation
Indices: 19429--19475 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
19419 CCGCAGGTAT
*
19429 GCCACTTGACAGAGGCAAGGC
1 GCCACTAGACAGAGGCAAGGC
* * *
19450 GCCACTAGGCGGAGGCGAGGC
1 GCCACTAGACAGAGGCAAGGC
19471 GCCAC
1 GCCAC
19476 CTGGCGGAGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.32, G:0.38, T:0.06
Consensus pattern (21 bp):
GCCACTAGACAGAGGCAAGGC
Found at i:19481 original size:21 final size:21
Alignment explanation
Indices: 19440--19519 Score: 99
Period size: 21 Copynumber: 3.8 Consensus size: 21
19430 CCACTTGACA
19440 GAGGCAAGGCGCCA-CTAGGCG
1 GAGGCAAGGCGCCACCT-GGCG
*
19461 GAGGCGAGGCGCCACCTGGCG
1 GAGGCAAGGCGCCACCTGGCG
** *
19482 GAGGCGTGGCGCCGCCTGGCG
1 GAGGCAAGGCGCCACCTGGCG
*
19503 GAGGTAAGGCGCCACCT
1 GAGGCAAGGCGCCACCT
19520 AACGAATTGT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
21 49 0.96
22 2 0.04
ACGTcount: A:0.16, C:0.31, G:0.45, T:0.07
Consensus pattern (21 bp):
GAGGCAAGGCGCCACCTGGCG
Found at i:25600 original size:19 final size:18
Alignment explanation
Indices: 25576--25611 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
25566 TGAAGATTTC
25576 TTGAAGATAATTTGAAGAG
1 TTGAAGATAA-TTGAAGAG
*
25595 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
25612 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.25, T:0.31
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAG
Found at i:26924 original size:22 final size:21
Alignment explanation
Indices: 26886--26927 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
26876 AATTTTCTTG
26886 ATTGTTTTCTTAGTTAATTTT
1 ATTGTTTTCTTAGTTAATTTT
26907 ATTGTTTT-TTAGATTTAATTT
1 ATTGTTTTCTTAG--TTAATTT
26928 CAAACTCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 8 0.42
22 7 0.37
ACGTcount: A:0.21, C:0.02, G:0.10, T:0.67
Consensus pattern (21 bp):
ATTGTTTTCTTAGTTAATTTT
Done.