Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004887.1 Corchorus capsularis cultivar CVL-1 contig04905, 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: 19031
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--45 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
43 TC T
1 TC T
46 ATATATATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:50 original size:2 final size:2
Alignment explanation
Indices: 45--73 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
35 TCTCTCTCTC
45 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
74 GTAATGGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4928 original size:44 final size:43
Alignment explanation
Indices: 4865--4950 Score: 118
Period size: 44 Copynumber: 2.0 Consensus size: 43
4855 GATCTGTCGA
* *
4865 AAAATATGTGTCCACAATTGGGTTTTGGATTGAATGGATGCAAC
1 AAAATATGTGTCCACAATTGGG-CTTGAATTGAATGGATGCAAC
* * *
4909 AAAATATGTGTCTACAATTGTGCTTGAATTGAATGGCTGCAA
1 AAAATATGTGTCCACAATTGGGCTTGAATTGAATGGATGCAA
4951 AGCGAGATCA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
43 17 0.46
44 20 0.54
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.33
Consensus pattern (43 bp):
AAAATATGTGTCCACAATTGGGCTTGAATTGAATGGATGCAAC
Found at i:5189 original size:2 final size:2
Alignment explanation
Indices: 5177--5210 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
5167 TTATAACATG
5177 AT AT AT A- AT AT AT AT AT AT AT AT AGT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
5211 TTTACCACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 27 0.90
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5197 original size:17 final size:17
Alignment explanation
Indices: 5177--5210 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5167 TTATAACATG
5177 ATATATAATATATATAT
1 ATATATAATATATATAT
*
5194 ATATATAGTATATATAT
1 ATATATAATATATATAT
5211 TTTACCACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
ATATATAATATATATAT
Found at i:6171 original size:17 final size:17
Alignment explanation
Indices: 6137--6174 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
6127 ACCCCTCAGG
*
6137 TCACCAGTGATCTTAGA
1 TCACCAGTGATCTAAGA
6154 TCACCAGTGATGC-AAGA
1 TCACCAGTGAT-CTAAGA
6171 TCAC
1 TCAC
6175 TGGTAATCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 18 0.95
18 1 0.05
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (17 bp):
TCACCAGTGATCTAAGA
Found at i:7299 original size:20 final size:20
Alignment explanation
Indices: 7261--7299 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
7251 AGTTTTTCTA
***
7261 GTGTGTTTTCTTTCTATTAT
1 GTGTGTTTTCTTGAGATTAT
7281 GTGTGTTTTCTTGAGATTA
1 GTGTGTTTTCTTGAGATTA
7300 GTTTAGCCTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.08, G:0.21, T:0.59
Consensus pattern (20 bp):
GTGTGTTTTCTTGAGATTAT
Found at i:9900 original size:2 final size:2
Alignment explanation
Indices: 9893--9923 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
9883 ATTTGAAAGA
*
9893 AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9924 GTAGTACTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:11020 original size:2 final size:2
Alignment explanation
Indices: 11015--11041 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11005 TGTGTGTGTG
11015 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
11042 CTGCTCTACC
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:12433 original size:1 final size:1
Alignment explanation
Indices: 12427--12467 Score: 55
Period size: 1 Copynumber: 41.0 Consensus size: 1
12417 TTGCTTTCTG
* * *
12427 TTTTTTTGTTTTTGTTTTTTTTTTGTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
12468 GAGAATGGAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (1 bp):
T
Found at i:12449 original size:11 final size:11
Alignment explanation
Indices: 12429--12467 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
12419 GCTTTCTGTT
12429 TTTTTGTTTTTG
1 TTTTT-TTTTTG
12441 TTTTTTTTTTG
1 TTTTTTTTTTG
12452 TTTTTTTTTT-
1 TTTTTTTTTTG
12462 TTTTTT
1 TTTTTT
12468 GAGAATGGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 6 0.22
11 16 0.59
12 5 0.19
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:12449 original size:17 final size:17
Alignment explanation
Indices: 12427--12468 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
12417 TTGCTTTCTG
12427 TTTTTTTGTTTTTGTTT
1 TTTTTTTGTTTTTGTTT
*
12444 TTTTTTTGTTTTTTTTT
1 TTTTTTTGTTTTTGTTT
12461 TTTTTTTG
1 TTTTTTTG
12469 AGAATGGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (17 bp):
TTTTTTTGTTTTTGTTT
Found at i:13026 original size:14 final size:14
Alignment explanation
Indices: 13007--13035 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
12997 CCACGGAAAC
13007 CATCAGACCAAGTA
1 CATCAGACCAAGTA
13021 CATCAGACCAAGTA
1 CATCAGACCAAGTA
13035 C
1 C
13036 CCGATGACGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.31, G:0.14, T:0.14
Consensus pattern (14 bp):
CATCAGACCAAGTA
Found at i:18968 original size:12 final size:12
Alignment explanation
Indices: 18953--18988 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
18943 GAGGAGGAAC
18953 TGGAGGTGGTGG
1 TGGAGGTGGTGG
*
18965 TGGAGGTGGAGG
1 TGGAGGTGGTGG
*
18977 TGGTGGTGGTGG
1 TGGAGGTGGTGG
18989 AGGCGGCAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.08, C:0.00, G:0.67, T:0.25
Consensus pattern (12 bp):
TGGAGGTGGTGG
Found at i:18980 original size:15 final size:15
Alignment explanation
Indices: 18960--18991 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
18950 AACTGGAGGT
18960 GGTGGTGGAGGTGGA
1 GGTGGTGGAGGTGGA
*
18975 GGTGGTGGTGGTGGA
1 GGTGGTGGAGGTGGA
18990 GG
1 GG
18992 CGGCAGTGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.09, C:0.00, G:0.69, T:0.22
Consensus pattern (15 bp):
GGTGGTGGAGGTGGA
Done.