Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009121.1 Corchorus capsularis cultivar CVL-1 contig09142, 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: 33869
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:4876 original size:31 final size:32
Alignment explanation
Indices: 4838--4902 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 32
4828 TTTACTCCCT
4838 ATCGTTTTTG-TTTGTCAACATTTGTTTAAAA
1 ATCGTTTTTGTTTTGTCAACATTTGTTTAAAA
4869 ATCGTTTTTGTTTTTGTCAACATTTGTTTAAAA
1 ATCGTTTTTG-TTTTGTCAACATTTGTTTAAAA
4902 A
1 A
4903 GTTAGGGTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 10 0.31
33 22 0.69
ACGTcount: A:0.26, C:0.09, G:0.12, T:0.52
Consensus pattern (32 bp):
ATCGTTTTTGTTTTGTCAACATTTGTTTAAAA
Found at i:9376 original size:33 final size:32
Alignment explanation
Indices: 9324--9410 Score: 99
Period size: 30 Copynumber: 2.8 Consensus size: 32
9314 ATCCCGGCCG
*
9324 TGCAGAATCGGCTGA-TAAGGTTAATAAAGAAGT
1 TGCAGAATCGGCT-ATTAAGGTT-ATAAACAAGT
* *
9357 TGCAGAATTGGCTATTAAGG-T-TGAACAAGT
1 TGCAGAATCGGCTATTAAGGTTATAAACAAGT
*
9387 TGCAGAATCGGCTGTTAAGGTTAT
1 TGCAGAATCGGCTATTAAGGTTAT
9411 GGGAAAAGCT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
30 25 0.54
31 1 0.02
32 3 0.07
33 17 0.37
ACGTcount: A:0.33, C:0.10, G:0.28, T:0.29
Consensus pattern (32 bp):
TGCAGAATCGGCTATTAAGGTTATAAACAAGT
Found at i:23569 original size:107 final size:105
Alignment explanation
Indices: 23340--23602 Score: 377
Period size: 107 Copynumber: 2.5 Consensus size: 105
23330 AATTTTTCTA
* ** *
23340 ACCCTTAAAATAAAATTTTAATTTTAATCT-GGGCTAAACTTAGTG-AATTAATTATATATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTTA
*
23403 TTTCTAAAACCCTATAACAATATTATTAATTATGGAATTT
66 TTTCTAAAACCCTATAACAATATTATTAATTATGAAATTT
* * * * *
23443 ACCCTTAAAATGAAAATAAAATTCTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTTA
*
23508 TTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
66 TTTCTAAAACCCTATAACAAT--ATTATTAATTATGAAATTT
* *
23550 ACCCTTAAAATAAAAATAAAATTTTAATTTGAGGTTAAACTTAGTGAAATTAA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAA
23603 GGCTAAACTT
Statistics
Matches: 140, Mismatches: 16, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
103 24 0.17
104 15 0.11
105 36 0.26
107 65 0.46
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (105 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTTA
TTTCTAAAACCCTATAACAATATTATTAATTATGAAATTT
Found at i:28321 original size:16 final size:15
Alignment explanation
Indices: 28272--28324 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 15
28262 AATGAAGCAA
28272 ATATATATAT-ATAT
1 ATATATATATGATAT
* *
28286 ATATATATATGGTCTT
1 ATATATATATGAT-AT
*
28302 ATATACATATGATAT
1 ATATATATATGATAT
28317 GATATATA
1 -ATATATA
28325 ATTTTGTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
14 10 0.33
15 2 0.07
16 18 0.60
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (15 bp):
ATATATATATGATAT
Found at i:28454 original size:2 final size:2
Alignment explanation
Indices: 28415--28443 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
28405 AACCGCATGC
28415 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 T
28444 GGATAATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29297 original size:5 final size:4
Alignment explanation
Indices: 29219--29319 Score: 50
Period size: 4 Copynumber: 25.0 Consensus size: 4
29209 CAAAAGCAGG
* *
29219 GAAA -AAA GCAAA GAAA GAAAA GAAA -AACA TAAAA GAAA GGAA GAAA
1 GAAA GAAA G-AAA GAAA G-AAA GAAA GAA-A -GAAA GAAA GAAA GAAA
* * * *
29265 GAAA -AAG GCAAA GCAA TAAA GAAA GAAA GGAAA -AAA GAAA TAAA -AAA
1 GAAA GAAA G-AAA GAAA GAAA GAAA GAAA -GAAA GAAA GAAA GAAA GAAA
*
29312 GAGA GAAA
1 GAAA GAAA
29320 AACAAAGTTT
Statistics
Matches: 74, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
3 13 0.18
4 43 0.58
5 16 0.22
6 2 0.03
ACGTcount: A:0.72, C:0.04, G:0.21, T:0.03
Consensus pattern (4 bp):
GAAA
Found at i:29813 original size:12 final size:12
Alignment explanation
Indices: 29796--29827 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
29786 TACACCCCAA
29796 CTTCTTCTTCCT
1 CTTCTTCTTCCT
*
29808 CTTCTTCCTCCT
1 CTTCTTCTTCCT
29820 CTTCTTCT
1 CTTCTTCT
29828 CTTCCTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (12 bp):
CTTCTTCTTCCT
Found at i:33126 original size:18 final size:18
Alignment explanation
Indices: 33103--33145 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
33093 ATTTCAATAA
*
33103 TATTATTGAATATATATG
1 TATTATTGAAGATATATG
*
33121 TATTATTGAAGATATGTG
1 TATTATTGAAGATATATG
*
33139 TAATATT
1 TATTATT
33146 TTATCTTCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (18 bp):
TATTATTGAAGATATATG
Done.