Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015476.1 Corchorus capsularis cultivar CVL-1 contig15497, 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: 30881
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:9138 original size:11 final size:11
Alignment explanation
Indices: 9122--9164 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
9112 TATACTATAT
9122 CTAATTAATAG
1 CTAATTAATAG
*
9133 CTAATTAATAT
1 CTAATTAATAG
9144 CTAATTAATAG
1 CTAATTAATAG
*
9155 TTAATTAATA
1 CTAATTAATA
9165 ATGAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:9143 original size:22 final size:22
Alignment explanation
Indices: 9118--9164 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
9108 CCATTATACT
9118 ATATCTAATTAATAGCTAATTA
1 ATATCTAATTAATAGCTAATTA
*
9140 ATATCTAATTAATAGTTAATTA
1 ATATCTAATTAATAGCTAATTA
9162 ATA
1 ATA
9165 ATGAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (22 bp):
ATATCTAATTAATAGCTAATTA
Found at i:11968 original size:40 final size:40
Alignment explanation
Indices: 11924--12007 Score: 159
Period size: 40 Copynumber: 2.1 Consensus size: 40
11914 CATAATATTT
11924 TAATATTTTGATATTGATTCATGAATGTTATGATTTGCTC
1 TAATATTTTGATATTGATTCATGAATGTTATGATTTGCTC
*
11964 TAATATTTTGATATTGTTTCATGAATGTTATGATTTGCTC
1 TAATATTTTGATATTGATTCATGAATGTTATGATTTGCTC
12004 TAAT
1 TAAT
12008 CTCATAATAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.27, C:0.07, G:0.14, T:0.51
Consensus pattern (40 bp):
TAATATTTTGATATTGATTCATGAATGTTATGATTTGCTC
Found at i:11969 original size:48 final size:45
Alignment explanation
Indices: 11922--12026 Score: 130
Period size: 40 Copynumber: 2.4 Consensus size: 45
11912 CTCATAATAT
11922 TTTAATATTTTGATATTGATTCATGAATGTTATGATTTGCTC---
1 TTTAATATTTTGATATTGATTCATGAATGTTATGATTTGCTCTAA
*
11964 --TAATATTTTGATATTGTTTCATGAATGTTATGATTTGCTCTAA
1 TTTAATATTTTGATATTGATTCATGAATGTTATGATTTGCTCTAA
*
12007 TCTCATAATATTTTGGTATT
1 T-T--TAATATTTTGATATT
12027 AAATTAACAT
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
40 39 0.74
48 14 0.26
ACGTcount: A:0.27, C:0.08, G:0.13, T:0.52
Consensus pattern (45 bp):
TTTAATATTTTGATATTGATTCATGAATGTTATGATTTGCTCTAA
Found at i:22976 original size:20 final size:21
Alignment explanation
Indices: 22937--22976 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
22927 GATAGCATCA
22937 TAAAGTCTTTATAATAACCTC
1 TAAAGTCTTTATAATAACCTC
* *
22958 TAAAGT-TTTTTACTAACCT
1 TAAAGTCTTTATAATAACCT
22977 TAGATAAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.35, C:0.17, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAGTCTTTATAATAACCTC
Found at i:23904 original size:109 final size:109
Alignment explanation
Indices: 23680--23881 Score: 350
Period size: 109 Copynumber: 1.9 Consensus size: 109
23670 AACCTTGATT
23680 TGAAATATTTAAAATACCCTTTTTAATTTTAAAATTTTAGTATTCCTTAAAAGGATAAACATGTA
1 TGAAATATTTAAAATACCCTTTTTAATTTTAAAATTTTAGTATTCCTTAAAAGGATAAACATGTA
* *
23745 TTTTTATTTCATTTATATTAATTAATTATTCAAAAATGTTGAAC
66 TTTTTATTTCATTTAGATTAATCAATTATTCAAAAATGTTGAAC
* * *
23789 TGAAATATTTAAAATACCCTTTTTAATTTTTAAATTTTAGTATTCCTTTAAAGGGTAAACATGTA
1 TGAAATATTTAAAATACCCTTTTTAATTTTAAAATTTTAGTATTCCTTAAAAGGATAAACATGTA
*
23854 TTTTTATTTTATTTAGATTAATCAATTA
66 TTTTTATTTCATTTAGATTAATCAATTA
23882 ATTATGGAGT
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
109 87 1.00
ACGTcount: A:0.38, C:0.08, G:0.07, T:0.48
Consensus pattern (109 bp):
TGAAATATTTAAAATACCCTTTTTAATTTTAAAATTTTAGTATTCCTTAAAAGGATAAACATGTA
TTTTTATTTCATTTAGATTAATCAATTATTCAAAAATGTTGAAC
Found at i:24229 original size:11 final size:11
Alignment explanation
Indices: 24213--24246 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
24203 ACCTTCTAGA
24213 TAATCTCCTTG
1 TAATCTCCTTG
*
24224 TAATCTGCTTG
1 TAATCTCCTTG
24235 TAATCTTCCTTG
1 TAATC-TCCTTG
24247 ATTCTCTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 15 0.75
12 5 0.25
ACGTcount: A:0.18, C:0.24, G:0.12, T:0.47
Consensus pattern (11 bp):
TAATCTCCTTG
Found at i:27345 original size:20 final size:20
Alignment explanation
Indices: 27320--27360 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
27310 AGTATTATAA
27320 TTGTTTTGA-TAACCTTTAAT
1 TTGTTTTGAGTAACC-TTAAT
*
27340 TTGTTTTTAGTAACCTTAAT
1 TTGTTTTGAGTAACCTTAAT
27360 T
1 T
27361 AGATAGGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.24, C:0.10, G:0.10, T:0.56
Consensus pattern (20 bp):
TTGTTTTGAGTAACCTTAAT
Done.