Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015624.1 Corchorus capsularis cultivar CVL-1 contig15645, 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: 19876
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1055 original size:3 final size:3
Alignment explanation
Indices: 1047--1075 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1037 GTTAATTAAT
1047 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1076 TTCTCGTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:9192 original size:16 final size:16
Alignment explanation
Indices: 9173--9206 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
9163 TTAAACTAGC
9173 TTAAAGAAAAACTCAA
1 TTAAAGAAAAACTCAA
9189 TTAAAGAAAAACTCAA
1 TTAAAGAAAAACTCAA
9205 TT
1 TT
9207 TTCAAGATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.06, T:0.24
Consensus pattern (16 bp):
TTAAAGAAAAACTCAA
Found at i:15375 original size:6 final size:6
Alignment explanation
Indices: 15358--15387 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
15348 GTTCATATAA
*
15358 TGCGAC TACGAC TGCGAC TGCGAC TGCGAC
1 TGCGAC TGCGAC TGCGAC TGCGAC TGCGAC
15388 GACTGGGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.20, C:0.33, G:0.30, T:0.17
Consensus pattern (6 bp):
TGCGAC
Found at i:15681 original size:6 final size:6
Alignment explanation
Indices: 15672--15710 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
15662 ATCAAGAAGA
*
15672 AGAATC AGAAAC AGAAAC AGAAAC AGAAAC AGAAAC AGA
1 AGAAAC AGAAAC AGAAAC AGAAAC AGAAAC AGAAAC AGA
15711 GAGCTTTTGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.64, C:0.15, G:0.18, T:0.03
Consensus pattern (6 bp):
AGAAAC
Found at i:16874 original size:138 final size:139
Alignment explanation
Indices: 16556--16884 Score: 513
Period size: 139 Copynumber: 2.4 Consensus size: 139
16546 TACAACTTTG
* * * *
16556 ATTAGATAATCATCAATCAATTACAACTTTGATTGGCAAAATTAATTAACAACATGTTCAATAAT
1 ATTAAATAATCATCAATCAATTACAACTTTGATTGGAAAAATTAACTAACGACATGTTCAATAAT
* * *
16621 TTTTTTTTGGTAACATAATTACTAATTGATTTATTTATTTATGGTAATCTTTTTGGTGGCGATTT
66 TTTTTTTTGGTAACATAATTACTAATTGATTGATTTATTTATAGTAATCTTTTTGGTAGCGATTT
16686 TATGGTAAA
131 TATGGTAAA
*
16695 ATTATATAATCATCAATCAATTACAACTTTGATT-GACAAAATTAACTAACGACATGTTCAATAA
1 ATTAAATAATCATCAATCAATTACAACTTTGATTGGA-AAAATTAACTAACGACATGTTCAATAA
*
16759 TTTATTTTTTTGGTAACATAATTACTAATTGATTGATTTATTTATATTAAT-TTTTT-GTAGCGA
65 -TT-TTTTTTTGGTAACATAATTACTAATTGATTGATTTATTTATAGTAATCTTTTTGGTAGCGA
16822 -TTTATGGTAAA
128 TTTTATGGTAAA
*
16833 ATTAAATAATTATCAATCAATTACAACTTTGATTGGAAAAATTAACTAACGA
1 ATTAAATAATCATCAATCAATTACAACTTTGATTGGAAAAATTAACTAACGA
16885 TCACTAACTT
Statistics
Matches: 176, Mismatches: 10, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
138 59 0.34
139 66 0.38
140 7 0.04
141 44 0.25
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (139 bp):
ATTAAATAATCATCAATCAATTACAACTTTGATTGGAAAAATTAACTAACGACATGTTCAATAAT
TTTTTTTTGGTAACATAATTACTAATTGATTGATTTATTTATAGTAATCTTTTTGGTAGCGATTT
TATGGTAAA
Found at i:17433 original size:138 final size:139
Alignment explanation
Indices: 17169--17560 Score: 504
Period size: 138 Copynumber: 2.8 Consensus size: 139
17159 TTTTTGGCAA
* * * ** * * *
17169 TTAATTAACGACTGATTTGATTCCCTAATTTATTTAGTATGTTCAATCAATCTATTTTTTTGCTA
1 TTAACTAACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAATCAAT-T-TTTTTTTGGTA
*
17234 ACATAATTACTAATTGATTCATTTATTTAT-GACAAAATCAAATAATCATCAATCAATTATAACT
64 ACATAATTACTAATTGATTCATTTATTTATGGA-AAAAT-TAATAATCATCAATCAATTATAACT
17298 TTGATTGACAAAG
127 TTGATTGACAAAG
*
17311 TTGA-TCAACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAATCAA-TTTTTTTTGGTAA
1 TTAACT-AACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAATCAATTTTTTTTTGGTAA
* * *
17374 TATAATTACTAATTGATTTATTTATTTATGGAAAAATTAATAATCATCCATCAATTATAACTTTG
65 CATAATTACTAATTGATTCATTTATTTATGGAAAAATTAATAATCATCAATCAATTATAACTTTG
*
17439 ATTGGCAAAG
130 ATTGACAAAG
* * * * *
17449 TTAACTAAGGACTAACTTGATTCATTTACTTATTTTGGATGTTCAATCAATTTATTTTTTTGTAA
1 TTAACTAACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAATCAATTT-TTTTTTGGTAA
* *
17514 CATAA-TACTAATTGATTCATTTATTTGTGGCAAAATTAAATAATCAT
65 CATAATTACTAATTGATTCATTTATTTATGGAAAAATT-AATAATCAT
17561 TAGCTTTTGG
Statistics
Matches: 221, Mismatches: 23, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
138 78 0.35
139 75 0.34
140 26 0.12
141 1 0.00
142 41 0.19
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (139 bp):
TTAACTAACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAATCAATTTTTTTTTGGTAAC
ATAATTACTAATTGATTCATTTATTTATGGAAAAATTAATAATCATCAATCAATTATAACTTTGA
TTGACAAAG
Found at i:18952 original size:16 final size:16
Alignment explanation
Indices: 18931--18964 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
18921 TCTGAAATAT
18931 TTCAGAGCTTTTATGC
1 TTCAGAGCTTTTATGC
*
18947 TTCAGAGCTTTTCTGC
1 TTCAGAGCTTTTATGC
18963 TT
1 TT
18965 TCTGAATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.47
Consensus pattern (16 bp):
TTCAGAGCTTTTATGC
Found at i:19800 original size:64 final size:63
Alignment explanation
Indices: 19721--19851 Score: 226
Period size: 64 Copynumber: 2.1 Consensus size: 63
19711 ACGTAGTTCA
* *
19721 TTTTTTTTTGTGCTCTAAGTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGCCT
1 TTTTTTTTTGTGCTCTAACTTTTGCCTAAGCCGTCCATTGCAGGATTTTCAACTTAGCGAG-CT
*
19785 TTTTTTTTTTTGCTCTAACTTTTGCCTAAGCCGTCCATTGCAGGATTTTCAACTTAGCGAGCT
1 TTTTTTTTTGTGCTCTAACTTTTGCCTAAGCCGTCCATTGCAGGATTTTCAACTTAGCGAGCT
19848 TTTT
1 TTTT
19852 ATTTATTTAT
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
63 6 0.09
64 58 0.91
ACGTcount: A:0.16, C:0.21, G:0.17, T:0.46
Consensus pattern (63 bp):
TTTTTTTTTGTGCTCTAACTTTTGCCTAAGCCGTCCATTGCAGGATTTTCAACTTAGCGAGCT
Done.