Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011402.1 Corchorus capsularis cultivar CVL-1 contig11423, 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: 41472
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:3756 original size:30 final size:29
Alignment explanation
Indices: 3660--3766 Score: 115
Period size: 29 Copynumber: 3.6 Consensus size: 29
3650 TAATTTACCA
**
3660 TTTTGCCCCCTGAACTTGTAGCGTTTAGACG
1 TTTTGCCCCCTGAACTT-TA-ATTTTAGACG
* * * *
3691 TTTTGCCCCCCGAACTTTAATCTTGGACA
1 TTTTGCCCCCTGAACTTTAATTTTAGACG
*
3720 TTTTGCCCCCTGAACTTCAATTTTATGACG
1 TTTTGCCCCCTGAACTTTAATTTTA-GACG
*
3750 TTTTGCCCCCTCAACTT
1 TTTTGCCCCCTGAACTT
3767 AACGGATCCG
Statistics
Matches: 63, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
29 26 0.41
30 21 0.33
31 16 0.25
ACGTcount: A:0.18, C:0.30, G:0.15, T:0.37
Consensus pattern (29 bp):
TTTTGCCCCCTGAACTTTAATTTTAGACG
Found at i:3842 original size:29 final size:30
Alignment explanation
Indices: 3787--3858 Score: 94
Period size: 29 Copynumber: 2.4 Consensus size: 30
3777 TTAAGTTGAG
3787 GGGGCAAAACGTCCCAAAATTGAAGTTCAT
1 GGGGCAAAACGTCCCAAAATTGAAGTTCAT
* *
3817 GGGGCAAAATGT-CCAAGATTGAAGTTCGA-
1 GGGGCAAAACGTCCCAAAATTGAAGTTC-AT
*
3846 GGGACAAAACGTC
1 GGGGCAAAACGTC
3859 TAAACGCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 24 0.67
30 12 0.33
ACGTcount: A:0.36, C:0.18, G:0.28, T:0.18
Consensus pattern (30 bp):
GGGGCAAAACGTCCCAAAATTGAAGTTCAT
Found at i:20127 original size:16 final size:18
Alignment explanation
Indices: 20096--20128 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
20086 ACTAATGTCA
20096 AAACTCAAAAAGGAAACC
1 AAACTCAAAAAGGAAACC
20114 AAAC-CAAAAA-GAAAC
1 AAACTCAAAAAGGAAAC
20129 ATTAATCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 6 0.40
18 4 0.27
ACGTcount: A:0.67, C:0.21, G:0.09, T:0.03
Consensus pattern (18 bp):
AAACTCAAAAAGGAAACC
Found at i:31513 original size:7 final size:7
Alignment explanation
Indices: 31503--31538 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
31493 AAAGTTGAAA
31503 GAAAAGG
1 GAAAAGG
31510 GAAAAGG
1 GAAAAGG
31517 GAAAAGG
1 GAAAAGG
31524 GAAAAGG
1 GAAAAGG
31531 GAAAAGG
1 GAAAAGG
31538 G
1 G
31539 CTCAGTTAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (7 bp):
GAAAAGG
Found at i:40007 original size:24 final size:24
Alignment explanation
Indices: 39975--40022 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
39965 TATTTTTTTT
39975 TTTTGGTTGGAAATTAAGATGAAA
1 TTTTGGTTGGAAATTAAGATGAAA
39999 TTTTGGTTGGAAATTAAGATGAAA
1 TTTTGGTTGGAAATTAAGATGAAA
40023 GTGAGTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.25, T:0.38
Consensus pattern (24 bp):
TTTTGGTTGGAAATTAAGATGAAA
Found at i:40235 original size:2 final size:2
Alignment explanation
Indices: 40228--40265 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
40218 TGAGGAATGA
* *
40228 AT AT AT AT AA AT AT AT AT AA 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 AT AT
40266 TTGATAGCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:40242 original size:10 final size:10
Alignment explanation
Indices: 40227--40265 Score: 69
Period size: 10 Copynumber: 3.9 Consensus size: 10
40217 ATGAGGAATG
40227 AATATATATA
1 AATATATATA
40237 AATATATATA
1 AATATATATA
40247 AATATATATA
1 AATATATATA
*
40257 TATATATAT
1 AATATATAT
40266 TTGATAGCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
AATATATATA
Found at i:41439 original size:2 final size:2
Alignment explanation
Indices: 41432--41470 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
41422 GTAGGTGGAG
41432 AT 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 AT A
41471 AT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.