Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014415.1 Corchorus capsularis cultivar CVL-1 contig14436, 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: 30934
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1041 original size:47 final size:44
Alignment explanation
Indices: 942--1080 Score: 185
Period size: 42 Copynumber: 3.1 Consensus size: 44
932 GGGTCGTCAA
942 TTTTGAATTCTGAGATTTAGGGTTTTGTCATTGATTTGGG-GTTT
1 TTTTG-ATTCTGAGATTTAGGGTTTTGTCATTGATTTGGGTGTTT
* *
986 TTTT-ATTCTGAGAATTAGGGTTTTGTCATTGATGTGGGTGTTCTAT
1 TTTTGATTCTGAGATTTAGGGTTTTGTCATTGATTTGGGTG-T-T-T
*
1032 TTTTGATTCTCAGATTTAGGGTTTTGTCATTGATTTGGGT-TTT
1 TTTTGATTCTGAGATTTAGGGTTTTGTCATTGATTTGGGTGTTT
1075 GTTTTG
1 -TTTTG
1081 TTTTGATTTG
Statistics
Matches: 84, Mismatches: 5, Indels: 12
0.83 0.05 0.12
Matches are distributed among these distances:
42 32 0.38
43 2 0.02
44 11 0.13
45 2 0.02
46 5 0.06
47 32 0.38
ACGTcount: A:0.15, C:0.06, G:0.26, T:0.53
Consensus pattern (44 bp):
TTTTGATTCTGAGATTTAGGGTTTTGTCATTGATTTGGGTGTTT
Found at i:4869 original size:31 final size:31
Alignment explanation
Indices: 4802--4879 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
4792 AAACGGCTAA
4802 ATGCTCAATTTGGGGCCAAACGTTTGCCGCG
1 ATGCTCAATTTGGGGCCAAACGTTTGCCGCG
* * *
4833 ATGCTCGATTTGGGGCCAAACGTTT-TCGGG
1 ATGCTCAATTTGGGGCCAAACGTTTGCCGCG
*
4863 ACTGCTCAATTCGGGGC
1 A-TGCTCAATTTGGGGC
4880 TTTTTTGGAT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
30 4 0.10
31 37 0.90
ACGTcount: A:0.18, C:0.24, G:0.31, T:0.27
Consensus pattern (31 bp):
ATGCTCAATTTGGGGCCAAACGTTTGCCGCG
Found at i:5859 original size:12 final size:11
Alignment explanation
Indices: 5835--5871 Score: 56
Period size: 12 Copynumber: 3.2 Consensus size: 11
5825 CTATTGACCG
5835 AAGAAAAAAAA
1 AAGAAAAAAAA
5846 AAGAAAACAAAA
1 AAGAAAA-AAAA
5858 AAGAAAAAAGAA
1 AAGAAAAAA-AA
5870 AA
1 AA
5872 TATATCAACG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.86, C:0.03, G:0.11, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:5959 original size:27 final size:27
Alignment explanation
Indices: 5906--5959 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
5896 AGGAATGTAT
* **
5906 AAATAAGGAGGTATTTTTGGCCAAAAA
1 AAATAAGGAGGTATTTATGAACAAAAA
*
5933 AAATAAGGAGGTATTTAT-AACAGAAA
1 AAATAAGGAGGTATTTATGAACAAAAA
5959 A
1 A
5960 GAAGAAAGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.50, C:0.06, G:0.20, T:0.24
Consensus pattern (27 bp):
AAATAAGGAGGTATTTATGAACAAAAA
Found at i:8306 original size:2 final size:2
Alignment explanation
Indices: 8299--8328 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
8289 TATAATCACC
8299 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
8329 TACTAGCCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10695 original size:15 final size:15
Alignment explanation
Indices: 10671--10701 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
10661 GGAGACCTTG
*
10671 ACCACTCCAAATGAA
1 ACCACGCCAAATGAA
10686 ACCACGCCAAATGAA
1 ACCACGCCAAATGAA
10701 A
1 A
10702 GGATTTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.32, G:0.10, T:0.10
Consensus pattern (15 bp):
ACCACGCCAAATGAA
Found at i:13717 original size:124 final size:123
Alignment explanation
Indices: 13466--13691 Score: 319
Period size: 124 Copynumber: 1.8 Consensus size: 123
13456 TTAGAAGTAG
*
13466 TATTAGTTTTTGGTAGTCGCCGCCATTTACAAGTCAAATATAAAGGATTTTGTTCATGAATTTGC
1 TATTAATTTTTGGTAGTCGCCGCCATTTACAAGTCAAATATAAAGGATTTTGTTCATGAATTTGC
* * * *
13531 ATTTAAAACACTTTTAAGATTAATCCATGAAGACTTGAAGAGTATACTGGAGTACCATT
66 ATTTAAAACACTTTTAAGATTAATCCATAAAAACTT-AAGACTATACTGGAGTAACATT
* * *
13590 TATTAATTTTTGGTAGTGGCCGCCATTTACAAGTCAAATATAGAGGATTTTGTTCATGAATTTGG
1 TATTAATTTTTGGTAGTCGCCGCCATTTACAAGTCAAATATAAAGGATTTTGTTCATGAATTTGC
* * * *
13655 ATTTAAAACGCTTTCTGAGATTAGTCGA-AAAAACTTA
66 ATTTAAAACACTTT-TAAGATTAATCCATAAAAACTTA
13692 TCTATTGTGG
Statistics
Matches: 91, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
123 1 0.01
124 80 0.88
125 10 0.11
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.37
Consensus pattern (123 bp):
TATTAATTTTTGGTAGTCGCCGCCATTTACAAGTCAAATATAAAGGATTTTGTTCATGAATTTGC
ATTTAAAACACTTTTAAGATTAATCCATAAAAACTTAAGACTATACTGGAGTAACATT
Done.