Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009806.1 Corchorus capsularis cultivar CVL-1 contig09827, 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, 636
Length: 1060
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Found at i:134 original size:43 final size:44
Alignment explanation
Indices: 41--154 Score: 128
Period size: 43 Copynumber: 2.6 Consensus size: 44
31 TTTTGAATAA
* * *
41 TGAAATGCAAATTTTGAACTTTGA-TTTTCGAAGAATAGAATGC
1 TGAAATGCAAGTTTTGAAATTTGATTTTTCGAAGAATAGAATCC
* *
84 TGAAATGCAAGTTTTGAATTTTGATTGTTTTGAAGAATA-AA-CC
1 TGAAATGCAAGTTTTGAAATTTGATT-TTTCGAAGAATAGAATCC
*
127 ATG-AATGCAGGTTTTGAAATTTGATTTT
1 -TGAAATGCAAGTTTTGAAATTTGATTTT
155 GAGCCAAGAA
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
42 2 0.03
43 44 0.71
44 5 0.08
45 11 0.18
ACGTcount: A:0.34, C:0.07, G:0.19, T:0.39
Consensus pattern (44 bp):
TGAAATGCAAGTTTTGAAATTTGATTTTTCGAAGAATAGAATCC
Found at i:346 original size:37 final size:37
Alignment explanation
Indices: 304--666 Score: 310
Period size: 37 Copynumber: 9.8 Consensus size: 37
294 TGGTTTTCGA
* *
304 ACACCTAAATAGGGATCATT-AACAAGATTTTGATGAG
1 ACACCTAAACAGGGATC-TTAAACAAGATTTTGATAAG
* *
341 ACACCTAAATAGGGA-CTTTAAATAAGGA-TTTGATAAG
1 ACACCTAAACAGGGATC-TTAAACAA-GATTTTGATAAG
* ** * * * * *
378 AAACCTAAACAGACATCTTGAAGAAGGTTTTGATGAC
1 ACACCTAAACAGGGATCTTAAACAAGATTTTGATAAG
* *
415 ACACCTAAACAGGTATCTTAAATAAAGATTTTGATAAG
1 ACACCTAAACAGGGATCTTAAA-CAAGATTTTGATAAG
* * * *
453 AAACCTAAATAGGAATCTTGAACAAGATTTTGAT--G
1 ACACCTAAACAGGGATCTTAAACAAGATTTTGATAAG
* *
488 ACACCTAAACAGGGACCTTAAACAAGGA-TTTAATAAG
1 ACACCTAAACAGGGATCTTAAACAA-GATTTTGATAAG
* * * *
525 AAACCTAAACAGGAATCTTGAACAAGATTTTGATGAG
1 ACACCTAAACAGGGATCTTAAACAAGATTTTGATAAG
*
562 ACACCTAAACAGGGACCTTAAACAAGGA-TTTGATAAG
1 ACACCTAAACAGGGATCTTAAACAA-GATTTTGATAAG
* * * *
599 AAATCTAAACAGGAATCTTGAACAAGATTTTGATGAA-
1 ACACCTAAACAGGGATCTTAAACAAGATTTTGAT-AAG
* * *
636 ACACCTAAATAGGGACCTTAAATAAGGATTT
1 ACACCTAAACAGGGATCTTAAACAA-GATTT
667 GTCATGAAAA
Statistics
Matches: 259, Mismatches: 54, Indels: 25
0.77 0.16 0.07
Matches are distributed among these distances:
35 26 0.10
36 10 0.04
37 182 0.70
38 41 0.16
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.25
Consensus pattern (37 bp):
ACACCTAAACAGGGATCTTAAACAAGATTTTGATAAG
Found at i:436 original size:74 final size:74
Alignment explanation
Indices: 306--667 Score: 516
Period size: 74 Copynumber: 4.9 Consensus size: 74
296 GTTTTCGAAC
* * * *
306 ACCTAAATAGGGATCATT-AACAAGATTTTGATGAGACACCTAAATAGGGACTTTAAATAAGGAT
1 ACCTAAACAGGAATC-TTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGAT
370 TTGATAAGAA
65 TTGATAAGAA
* * * * * *
380 ACCTAAACA-GACATCTTGAAGAAGGTTTTGATGACACACCTAAACAGGTATCTTAAATAAAGAT
1 ACCTAAACAGGA-ATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGA-
444 TTTGATAAGAA
64 TTTGATAAGAA
* *
455 ACCTAAATAGGAATCTTGAACAAGATTTTGAT--GACACCTAAACAGGGACCTTAAACAAGGATT
1 ACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATT
*
518 TAATAAGAA
66 TGATAAGAA
*
527 ACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATT
1 ACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATT
592 TGATAAGAA
66 TGATAAGAA
* * *
601 ATCTAAACAGGAATCTTGAACAAGATTTTGATGAAACACCTAAATAGGGACCTTAAATAAGGATT
1 ACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATT
666 TG
66 TG
668 TCATGAAAAA
Statistics
Matches: 257, Mismatches: 25, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
72 41 0.16
73 27 0.11
74 150 0.58
75 37 0.14
76 2 0.01
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (74 bp):
ACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATT
TGATAAGAA
Done.