Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010136.1 Corchorus capsularis cultivar CVL-1 contig10157, 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: 18190
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:85 original size:18 final size:17
Alignment explanation
Indices: 62--104 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
52 TGTTTCAATT
62 AACTAATAAACTAAACTA
1 AACTAAT-AACTAAACTA
*
80 AACTAACTAATTAAACTA
1 AACTAA-TAACTAAACTA
*
98 AATTAAT
1 AACTAAT
105 TGGACAATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 1 0.05
18 20 0.91
19 1 0.05
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.28
Consensus pattern (17 bp):
AACTAATAACTAAACTA
Found at i:319 original size:18 final size:19
Alignment explanation
Indices: 290--327 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
280 ACTTCACTCA
*
290 CCCAATCAAATTCATTAAG
1 CCCAATCAAATTAATTAAG
309 CCCAATC-AATTAATTAAG
1 CCCAATCAAATTAATTAAG
327 C
1 C
328 TATCACATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.42, C:0.26, G:0.05, T:0.26
Consensus pattern (19 bp):
CCCAATCAAATTAATTAAG
Found at i:1968 original size:109 final size:109
Alignment explanation
Indices: 1777--1998 Score: 345
Period size: 109 Copynumber: 2.0 Consensus size: 109
1767 ACTTACACAT
* *
1777 TTAAGGTGCCTTGCATACTCGTAATTTTGGGTCATGACTGACGCGAAGGTTGATATTTGTGATAC
1 TTAAGATGCCTTGCATACTCATAATTTTGGGTCATGACTGACGCGAAGGTTGATATTTGTGATAC
*
1842 CGAACCTCGTGTACTCCAATTACCAAAAACAACGGAGTAATTTA
66 CGAACCCCGTGTACTCCAATTACCAAAAACAACGGAGTAATTTA
* * *
1886 TTAAGATGCTTTGCATACTCATAATTTTGGTTCGTGACTGACGCGAAGGTTGATATTTGTGATAC
1 TTAAGATGCCTTGCATACTCATAATTTTGGGTCATGACTGACGCGAAGGTTGATATTTGTGATAC
* * * * *
1951 CGAACCCCGTGTGCTCCACTTTCCAAAAACAGCGGAGTAGTTTA
66 CGAACCCCGTGTACTCCAATTACCAAAAACAACGGAGTAATTTA
1995 TTAA
1 TTAA
1999 ATTCCCTTTT
Statistics
Matches: 102, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
109 102 1.00
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (109 bp):
TTAAGATGCCTTGCATACTCATAATTTTGGGTCATGACTGACGCGAAGGTTGATATTTGTGATAC
CGAACCCCGTGTACTCCAATTACCAAAAACAACGGAGTAATTTA
Found at i:4075 original size:13 final size:14
Alignment explanation
Indices: 4052--4080 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
4042 TTAACTAATA
4052 AACTAAATTAAACT
1 AACTAAATTAAACT
4066 AACT-AATTAAACT
1 AACTAAATTAAACT
4079 AA
1 AA
4081 ATTAATTGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.28
Consensus pattern (14 bp):
AACTAAATTAAACT
Found at i:4080 original size:23 final size:22
Alignment explanation
Indices: 4043--4085 Score: 77
Period size: 23 Copynumber: 1.9 Consensus size: 22
4033 TTGTTTCAAT
4043 TAACTAATAAACTAAATTAAAC
1 TAACTAATAAACTAAATTAAAC
4065 TAACTAATTAAACTAAATTAA
1 TAACTAA-TAAACTAAATTAA
4086 TTGGACAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (22 bp):
TAACTAATAAACTAAATTAAAC
Found at i:4301 original size:18 final size:19
Alignment explanation
Indices: 4272--4309 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
4262 ACTTCACTCA
*
4272 CCCAATCAAATTCATTAAG
1 CCCAATCAAATTAATTAAG
4291 CCCAATC-AATTAATTAAG
1 CCCAATCAAATTAATTAAG
4309 C
1 C
4310 TATCACATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.42, C:0.26, G:0.05, T:0.26
Consensus pattern (19 bp):
CCCAATCAAATTAATTAAG
Found at i:10897 original size:18 final size:18
Alignment explanation
Indices: 10856--10905 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
10846 ATTTATTTGC
*
10856 TTGTCTTTAG-TTTTGTT
1 TTGTTTTTAGCTTTTGTT
*
10873 TAAGTTTTTAGCTTTTGTT
1 T-TGTTTTTAGCTTTTGTT
10892 TTGTTTTCTAGCTT
1 TTGTTTT-TAGCTT
10906 GCTAGGGACT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 1 0.04
18 12 0.44
19 14 0.52
ACGTcount: A:0.10, C:0.08, G:0.16, T:0.66
Consensus pattern (18 bp):
TTGTTTTTAGCTTTTGTT
Found at i:18161 original size:2 final size:2
Alignment explanation
Indices: 18154--18189 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
18144 ATGATTTTGA
18154 AT AT AT AT AT AT AT AT AT 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
18190 T
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.