Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014521.1 Corchorus capsularis cultivar CVL-1 contig14542, 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: 23123
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:4782 original size:1 final size:1
Alignment explanation
Indices: 4776--4812 Score: 65
Period size: 1 Copynumber: 37.0 Consensus size: 1
4766 CTCTTTCTGC
*
4776 AAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4813 CTATAGTTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.97, C:0.00, G:0.00, T:0.03
Consensus pattern (1 bp):
A
Found at i:7540 original size:27 final size:27
Alignment explanation
Indices: 7509--7569 Score: 113
Period size: 27 Copynumber: 2.2 Consensus size: 27
7499 TCTGGAAAAT
7509 AAGGGAAAGGGACAATTAAAAAGGAAC
1 AAGGGAAAGGGACAATTAAAAAGGAAC
7536 AAGGGAAAGGGACAATTAAAAAGGAAC
1 AAGGGAAAGGGACAATTAAAAAGGAAC
7563 AGAGGGA
1 A-AGGGA
7570 GTATATGGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 28 0.85
28 5 0.15
ACGTcount: A:0.54, C:0.07, G:0.33, T:0.07
Consensus pattern (27 bp):
AAGGGAAAGGGACAATTAAAAAGGAAC
Found at i:16446 original size:2 final size:2
Alignment explanation
Indices: 16439--16471 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
16429 ATGCTTTGAC
16439 TA TA 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 TA TA T
16472 CCGAAGAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17418 original size:21 final size:21
Alignment explanation
Indices: 17394--17435 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
17384 CCTCATTCCC
*
17394 ATATTATCTGTCCACTTCTAT
1 ATATTATCTATCCACTTCTAT
*
17415 ATATTATCTATCCGCTTCTAT
1 ATATTATCTATCCACTTCTAT
17436 TAGGGGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.05, T:0.48
Consensus pattern (21 bp):
ATATTATCTATCCACTTCTAT
Found at i:21036 original size:2 final size:2
Alignment explanation
Indices: 21024--21056 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
21014 CGATCATTGG
21024 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21057 TATTGTTGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21168 original size:2 final size:2
Alignment explanation
Indices: 21163--21193 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
21153 TAAAGTATTG
21163 TA 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 TA T
21194 CCATTTGACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22590 original size:19 final size:19
Alignment explanation
Indices: 22563--22605 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
22553 CATGTTGAGC
*
22563 TTTTCATAAGTATATAAAT
1 TTTTTATAAGTATATAAAT
22582 TTTTTATAAGTATATAAAT
1 TTTTTATAAGTATATAAAT
22601 TTTTT
1 TTTTT
22606 TTTACGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (19 bp):
TTTTTATAAGTATATAAAT
Done.