Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014305.1 Corchorus capsularis cultivar CVL-1 contig14326, 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: 14365
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:476 original size:8 final size:8
Alignment explanation
Indices: 463--496 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
453 ACCCTTCTTG
463 AAAAATTC
1 AAAAATTC
471 AAAAATTC
1 AAAAATTC
*
479 AGAAACTTC
1 A-AAAATTC
488 AAAAATTC
1 AAAAATTC
496 A
1 A
497 TAGCCGATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24
Consensus pattern (8 bp):
AAAAATTC
Found at i:7243 original size:203 final size:203
Alignment explanation
Indices: 6894--7303 Score: 820
Period size: 203 Copynumber: 2.0 Consensus size: 203
6884 AGTGTAATTT
6894 CATAAGTGTAATTTCAATAAAAATTAAACACAAGTTCTAGAAATAGGCAGTCATAGAAGCAATAA
1 CATAAGTGTAATTTCAATAAAAATTAAACACAAGTTCTAGAAATAGGCAGTCATAGAAGCAATAA
6959 ACAATAAACTCTTATCACAGACTTCAATTATACCTAATTCTAAGAAATAAGATATCATGCTATAA
66 ACAATAAACTCTTATCACAGACTTCAATTATACCTAATTCTAAGAAATAAGATATCATGCTATAA
7024 ATCAATTAATGAATCAAACATTCTTAAAAATTCTAAGTATGCATTAATCATAAATCAAATCAATA
131 ATCAATTAATGAATCAAACATTCTTAAAAATTCTAAGTATGCATTAATCATAAATCAAATCAATA
7089 GCTCAATA
196 GCTCAATA
7097 CATAAGTGTAATTTCAATAAAAATTAAACACAAGTTCTAGAAATAGGCAGTCATAGAAGCAATAA
1 CATAAGTGTAATTTCAATAAAAATTAAACACAAGTTCTAGAAATAGGCAGTCATAGAAGCAATAA
7162 ACAATAAACTCTTATCACAGACTTCAATTATACCTAATTCTAAGAAATAAGATATCATGCTATAA
66 ACAATAAACTCTTATCACAGACTTCAATTATACCTAATTCTAAGAAATAAGATATCATGCTATAA
7227 ATCAATTAATGAATCAAACATTCTTAAAAATTCTAAGTATGCATTAATCATAAATCAAATCAATA
131 ATCAATTAATGAATCAAACATTCTTAAAAATTCTAAGTATGCATTAATCATAAATCAAATCAATA
7292 GCTCAATA
196 GCTCAATA
7300 CATA
1 CATA
7304 TATGAAAAAT
Statistics
Matches: 207, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
203 207 1.00
ACGTcount: A:0.47, C:0.15, G:0.08, T:0.29
Consensus pattern (203 bp):
CATAAGTGTAATTTCAATAAAAATTAAACACAAGTTCTAGAAATAGGCAGTCATAGAAGCAATAA
ACAATAAACTCTTATCACAGACTTCAATTATACCTAATTCTAAGAAATAAGATATCATGCTATAA
ATCAATTAATGAATCAAACATTCTTAAAAATTCTAAGTATGCATTAATCATAAATCAAATCAATA
GCTCAATA
Found at i:9114 original size:23 final size:22
Alignment explanation
Indices: 9084--9166 Score: 64
Period size: 23 Copynumber: 3.8 Consensus size: 22
9074 GGAAAATAAT
9084 TTTTTTTTAAGAGAAAAACGCAA
1 TTTTTTTTAA-AGAAAAACGCAA
* * *
9107 TTTTTTTTAATCG-CAAACCCTAA
1 TTTTTTTTAA-AGAAAAACGC-AA
*
9130 TTTTTTTT--AGAACAACGCAA
1 TTTTTTTTAAAGAAAAACGCAA
**
9150 TTTTTTTTTTAGAAAAA
1 TTTTTTTTAAAGAAAAA
9167 ACAGAGAAAC
Statistics
Matches: 47, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
20 11 0.23
21 4 0.09
22 11 0.23
23 21 0.45
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.43
Consensus pattern (22 bp):
TTTTTTTTAAAGAAAAACGCAA
Done.