Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013892.1 Corchorus capsularis cultivar CVL-1 contig13913, 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: 44642
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Found at i:7694 original size:166 final size:166
Alignment explanation
Indices: 7420--7748 Score: 563
Period size: 166 Copynumber: 2.0 Consensus size: 166
7410 ATAAAATCTA
7420 GAGGAAAGGAAGAGGAAGAGATGAAGCTATTATTCTTAGCTCTCTCCTCTCTAATTCATCAATAT
1 GAGGAAAGGAAGAGGAAGAGATGAAGCTATTATTCTTAGCTCTCTCCTCTCTAATTCATCAATAT
*
7485 ATATAGTCATAATATTCAAATACATAAAGACAGGTGTCAAACATGCAAAGCATCATCACATGCAA
66 ATATAGTCATAATATTCAAATACATAAAGACAGATGTCAAACATGCAAAGCATCATCACATGCAA
* *
7550 GACAGTAAAAGTAAAATCTGGACCTATCAAATTGTT
131 GACAGCAAAAGTAAAATCCGGACCTATCAAATTGTT
* *
7586 GAGGAAAGGAAGAGGAAGAGATGAAGCTATTTTTCTTATAGCTCTCTCCTCTCTAATTCAT-TA-
1 GAGGAAAGGAAGAGGAAGAGATGAAGCTATTATTC-T-TAGCTCTCTCCTCTCTAATTCATCAAT
* *
7649 ATATATAGTCATAATATTCAAATACATAAAGATAGATGTCAAACATGCAAAGCCTCATCACATGC
64 ATATATAGTCATAATATTCAAATACATAAAGACAGATGTCAAACATGCAAAGCATCATCACATGC
7714 AAGACAGCAAAAGTAAAATCCGGACCTATCAAATT
129 AAGACAGCAAAAGTAAAATCCGGACCTATCAAATT
7749 TTTTTGAAAA
Statistics
Matches: 154, Mismatches: 7, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
166 129 0.84
167 2 0.01
168 23 0.15
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.26
Consensus pattern (166 bp):
GAGGAAAGGAAGAGGAAGAGATGAAGCTATTATTCTTAGCTCTCTCCTCTCTAATTCATCAATAT
ATATAGTCATAATATTCAAATACATAAAGACAGATGTCAAACATGCAAAGCATCATCACATGCAA
GACAGCAAAAGTAAAATCCGGACCTATCAAATTGTT
Found at i:16616 original size:2 final size:2
Alignment explanation
Indices: 16609--16637 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
16599 TAATGATGTG
16609 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
16638 TCAATGGTTA
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:17745 original size:22 final size:22
Alignment explanation
Indices: 17719--17760 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
17709 AAGAAAGTTA
17719 TACCAATCTTCTTATTCAAGGT
1 TACCAATCTTCTTATTCAAGGT
*
17741 TACCATTCTTCTTATTCAAG
1 TACCAATCTTCTTATTCAAG
17761 TTAAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.24, G:0.07, T:0.43
Consensus pattern (22 bp):
TACCAATCTTCTTATTCAAGGT
Found at i:17898 original size:18 final size:19
Alignment explanation
Indices: 17875--17910 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
17865 AACACTGTAA
17875 ATGTTATCAA-AAATTAAG
1 ATGTTATCAACAAATTAAG
17893 ATGTTATCAACAAATTAA
1 ATGTTATCAACAAATTAA
17911 ATAATAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.33
Consensus pattern (19 bp):
ATGTTATCAACAAATTAAG
Found at i:39505 original size:27 final size:27
Alignment explanation
Indices: 39455--39506 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
39445 GCCAAAAAGA
* * **
39455 ATCACACGTGAAATCTATTTTTTTTGG
1 ATCAAACGTGAAATATATGATTTTTGG
39482 ATCAAACGTGAAATATATGATTTTT
1 ATCAAACGTGAAATATATGATTTTT
39507 ATATATTCTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (27 bp):
ATCAAACGTGAAATATATGATTTTTGG
Found at i:44578 original size:2 final size:2
Alignment explanation
Indices: 44571--44607 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
44561 ACATAAGCCA
44571 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
44608 GAGAGAGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:44612 original size:2 final size:2
Alignment explanation
Indices: 44607--44642 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
44597 ATATATATAT
44607 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.