Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014652.1 Corchorus capsularis cultivar CVL-1 contig14673, 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: 18257
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:10 original size:2 final size:2
Alignment explanation
Indices: 4--30 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1 TAT
4 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 T
31 TTACATATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1905 original size:21 final size:21
Alignment explanation
Indices: 1879--1918 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1869 CAAAATTCAG
1879 GGGGCAAAAGGGCTATTTAAC
1 GGGGCAAAAGGGCTATTTAAC
1900 GGGGCAAAAGGGCTATTTA
1 GGGGCAAAAGGGCTATTTA
1919 GCCATTCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.12, G:0.35, T:0.20
Consensus pattern (21 bp):
GGGGCAAAAGGGCTATTTAAC
Found at i:2957 original size:19 final size:20
Alignment explanation
Indices: 2907--2965 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 20
2897 GCTGCTCTAA
* *
2907 TAATCTCATTTGTACAGTACT
1 TAATCTCATCTGTACAGTA-G
* *
2928 TAATTTGATCTGTACAGT-G
1 TAATCTCATCTGTACAGTAG
2947 TAATCTCATCTGTACAGTA
1 TAATCTCATCTGTACAGTA
2966 CCTAAATAGT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
19 16 0.52
21 15 0.48
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.41
Consensus pattern (20 bp):
TAATCTCATCTGTACAGTAG
Found at i:8190 original size:41 final size:41
Alignment explanation
Indices: 8140--8275 Score: 186
Period size: 41 Copynumber: 3.3 Consensus size: 41
8130 CTTCTATTGC
*
8140 CAAAGGTAATTTTAATTTACCAAAGGGACAACTTTTGGTGT
1 CAAAGGTAATTTTAATTTACCAAAGGGACAACTTCTGGTGT
* *
8181 CAAAGGTAATTTCAATTTACC-AAGGTGACAACTTCTAGTGT
1 CAAAGGTAATTTTAATTTACCAAAGG-GACAACTTCTGGTGT
* * *
8222 CACCA-GTAATTTTAATTTGCCAAAGTGACAACTTCTGGTGT
1 CA-AAGGTAATTTTAATTTACCAAAGGGACAACTTCTGGTGT
8263 CAAAGGTAATTTT
1 CAAAGGTAATTTT
8276 CAATATTATT
Statistics
Matches: 82, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
40 5 0.06
41 73 0.89
42 4 0.05
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (41 bp):
CAAAGGTAATTTTAATTTACCAAAGGGACAACTTCTGGTGT
Found at i:9484 original size:17 final size:18
Alignment explanation
Indices: 9456--9489 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
9446 TACAAATTAA
9456 AAAAAGTCTAAAAGACTT
1 AAAAAGTCTAAAAGACTT
9474 AAAAAGT-TAAAAGACT
1 AAAAAGTCTAAAAGACT
9490 AAATAAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.59, C:0.09, G:0.12, T:0.21
Consensus pattern (18 bp):
AAAAAGTCTAAAAGACTT
Found at i:10182 original size:7 final size:7
Alignment explanation
Indices: 10170--10199 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
10160 TTTTTTTCTT
10170 CTTGTTG
1 CTTGTTG
10177 CTTGTTG
1 CTTGTTG
10184 CTTGTTG
1 CTTGTTG
*
10191 CTTGATG
1 CTTGTTG
10198 CT
1 CT
10200 CGATTACTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.03, C:0.17, G:0.27, T:0.53
Consensus pattern (7 bp):
CTTGTTG
Found at i:12268 original size:14 final size:14
Alignment explanation
Indices: 12249--12276 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12239 ATTTGTCGGA
12249 TTATTATTATTATT
1 TTATTATTATTATT
12263 TTATTATTATTATT
1 TTATTATTATTATT
12277 ATTTTTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTATTATTATTATT
Found at i:12270 original size:17 final size:17
Alignment explanation
Indices: 12248--12281 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
12238 TATTTGTCGG
12248 ATTATTATTATTATTTT
1 ATTATTATTATTATTTT
12265 ATTATTATTATTATTTT
1 ATTATTATTATTATTTT
12282 TATTTACCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
ATTATTATTATTATTTT
Found at i:12305 original size:3 final size:3
Alignment explanation
Indices: 12248--12285 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
12238 TATTTGTCGG
*
12248 ATT ATT ATT ATT ATT -TT ATT ATT ATT ATT ATT TTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12286 TACCCACATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
ATT
Done.