Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007846.1 Corchorus capsularis cultivar CVL-1 contig07867, 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: 17428
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Found at i:5468 original size:21 final size:21
Alignment explanation
Indices: 5427--5469 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
5417 TGATTGAGTG
*
5427 ATATAATTTAACTAAATCTAA
1 ATATAATTTAAATAAATCTAA
*
5448 ATATGATTTAAATCAAA-CTAA
1 ATATAATTTAAAT-AAATCTAA
5469 A
1 A
5470 ATTAAACATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.35
Consensus pattern (21 bp):
ATATAATTTAAATAAATCTAA
Found at i:5497 original size:197 final size:196
Alignment explanation
Indices: 5156--5552 Score: 566
Period size: 197 Copynumber: 2.0 Consensus size: 196
5146 AAAGAGACAA
* * *
5156 AAAAGAATGATTCTAATTTAAGGCAACCATGATTCTAGTTAATATAACTCTAATGTAAGTTGAGT
1 AAAAGAATAATTCTAATTTAAGGCAACCATGATTCTAATTAATATAACTCCAATGTAAGTTGAGT
* *
5221 GATATGTAATTTAACCAAATCTAAATCTAAATATGATTTAAATCAAACTAATAGTAAATATCAAT
66 GATA-GTAATTT----AAATCTAAATCTAAATATGATTTAAATCAAACTAAAAGTAAACATCAAT
* *
5286 AACCAAACCAAACTAAAATTAACAACTAAACTATCGAAACATCCACCTTTCTAAATACTAAGCAA
126 AACCAAACCAAACTAAAATTAACAACTAAACTATCGAAACATCCACCTCTCTAAATACCAAGCAA
5351 CATCAG
191 CATCAG
* *
5357 AAAAGAATAATTTTAATTTAAGGCAACCATGATTTTAATTAATATAACTCCAATGTAGATTGATT
1 AAAAGAATAATTCTAATTTAAGGCAACCATGATTCTAATTAATATAACTCCAATGTA-A--G-TT
*
5422 GAGTGATA-TAATTT-AA-CTAAATCTAAATATGATTTAAATCAAACTAAAATTAAACATCAATA
62 GAGTGATAGTAATTTAAATCTAAATCTAAATATGATTTAAATCAAACTAAAAGTAAACATCAATA
* * * *
5484 ACCAAATCAAACTAAAATTAACAACTAAACTGTCTAAACATTCACCTCTCTAAATACCAAGCAAC
127 ACCAAACCAAACTAAAATTAACAACTAAACTATCGAAACATCCACCTCTCTAAATACCAAGCAAC
5549 ATCA
192 ATCA
5553 AATAATGGCC
Statistics
Matches: 178, Mismatches: 14, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
197 106 0.60
198 2 0.01
201 52 0.29
202 1 0.01
203 6 0.03
204 1 0.01
205 10 0.06
ACGTcount: A:0.47, C:0.16, G:0.08, T:0.29
Consensus pattern (196 bp):
AAAAGAATAATTCTAATTTAAGGCAACCATGATTCTAATTAATATAACTCCAATGTAAGTTGAGT
GATAGTAATTTAAATCTAAATCTAAATATGATTTAAATCAAACTAAAAGTAAACATCAATAACCA
AACCAAACTAAAATTAACAACTAAACTATCGAAACATCCACCTCTCTAAATACCAAGCAACATCA
G
Found at i:5695 original size:25 final size:24
Alignment explanation
Indices: 5609--5701 Score: 79
Period size: 25 Copynumber: 4.0 Consensus size: 24
5599 CAAAAAATGA
*
5609 CATGACATGAAACCAAACCCTAAA
1 CATGACATGAAACCAAACCCTAAT
*
5633 CATGAAATG--A-CAAACCCTAA-
1 CATGACATGAAACCAAACCCTAAT
* * * *
5653 -GTGAGATGAAGGCTAAACCCTAAT
1 CATGACATGAA-ACCAAACCCTAAT
5677 CATGACATGAAAGCCAAACCCTAAT
1 CATGACATGAAA-CCAAACCCTAAT
5702 ATGTTATAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
19 6 0.11
21 10 0.19
22 1 0.02
23 9 0.17
24 8 0.15
25 19 0.36
ACGTcount: A:0.45, C:0.25, G:0.14, T:0.16
Consensus pattern (24 bp):
CATGACATGAAACCAAACCCTAAT
Found at i:5794 original size:31 final size:32
Alignment explanation
Indices: 5732--5794 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 32
5722 TAAAAAAAAT
* **
5732 TTGGAATGCCCAAATTATCCTCAAGGATTATA
1 TTGGAATGCCCAAATTACCCTCAACCATTATA
* *
5764 TTGG-ATGCCCAAATTACCCTCGACCCTTATA
1 TTGGAATGCCCAAATTACCCTCAACCATTATA
5795 CGAAATAACA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.30
Consensus pattern (32 bp):
TTGGAATGCCCAAATTACCCTCAACCATTATA
Found at i:5931 original size:2 final size:2
Alignment explanation
Indices: 5924--5962 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
5914 TGTTATTTGT
5924 TA TA TA TA TA -A TA TA TA -A 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 TA TA TA TA TA T
5963 TCTCTCTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:6842 original size:32 final size:32
Alignment explanation
Indices: 6781--6856 Score: 80
Period size: 32 Copynumber: 2.4 Consensus size: 32
6771 TTTTCAACTG
* * * * **
6781 ATTATATGCAAATAAAGCCAAATTTACAAGGT
1 ATTAAATGCAAATAAAGACAAAATAACAAGCC
*
6813 ATTAAATGCAAATTAAGACAAAATAACAAGCC
1 ATTAAATGCAAATAAAGACAAAATAACAAGCC
*
6845 ATTAATTGCAAA
1 ATTAAATGCAAA
6857 AAATGTCAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.51, C:0.13, G:0.11, T:0.25
Consensus pattern (32 bp):
ATTAAATGCAAATAAAGACAAAATAACAAGCC
Found at i:9821 original size:22 final size:22
Alignment explanation
Indices: 9793--9838 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
9783 ATAGTATAAT
9793 CAAAATTTAAGGAAATCAAAGA
1 CAAAATTTAAGGAAATCAAAGA
9815 CAAAATTTAAGGAAATCAAAGA
1 CAAAATTTAAGGAAATCAAAGA
9837 CA
1 CA
9839 GTTAAACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.59, C:0.11, G:0.13, T:0.17
Consensus pattern (22 bp):
CAAAATTTAAGGAAATCAAAGA
Done.