Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012285.1 Corchorus capsularis cultivar CVL-1 contig12306, 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: 19093
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:24 original size:10 final size:10
Alignment explanation
Indices: 9--35 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1 TTCTTTCT
9 TTTTTTTTAA
1 TTTTTTTTAA
19 TTTTTTTTAA
1 TTTTTTTTAA
29 TTTTTTT
1 TTTTTTT
36 AATATTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTTTAA
Found at i:64 original size:21 final size:20
Alignment explanation
Indices: 40--83 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
30 TTTTTTAATA
*
40 TTAATTAGTTTATGATTAGCT
1 TTAATTAGTTAATGATTAG-T
*
61 TTAATTAGTTAATTATTAGT
1 TTAATTAGTTAATGATTAGT
81 TTA
1 TTA
84 TGTTTAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.32, C:0.02, G:0.11, T:0.55
Consensus pattern (20 bp):
TTAATTAGTTAATGATTAGT
Found at i:92 original size:26 final size:26
Alignment explanation
Indices: 60--142 Score: 100
Period size: 26 Copynumber: 3.2 Consensus size: 26
50 TATGATTAGC
60 TTTAATTAGTTAATT-ATTAGTTTATG
1 TTTAATTAG-TAATTAATTAGTTTATG
86 TTTAATTAGT-ATCTAATTAGTTTAT-
1 TTTAATTAGTAAT-TAATTAGTTTATG
*
111 TATTAATTAGTATTTAATTAGTTTATG
1 T-TTAATTAGTAATTAATTAGTTTATG
*
138 ATTAA
1 TTTAA
143 AATGAAGGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
24 2 0.04
25 3 0.06
26 44 0.88
27 1 0.02
ACGTcount: A:0.34, C:0.01, G:0.10, T:0.55
Consensus pattern (26 bp):
TTTAATTAGTAATTAATTAGTTTATG
Found at i:113 original size:37 final size:37
Alignment explanation
Indices: 34--132 Score: 100
Period size: 37 Copynumber: 2.7 Consensus size: 37
24 TTTAATTTTT
*
34 TTAA-TATTAATTAGT-TTATGATTAGCT-T-TAATTAG
1 TTAATTATTAATTAGTATT-TAATTAG-TATCTAATTAG
* *
69 TTAATTATTAGTTTA-TGTTTAATTAGTATCTAATTAG
1 TTAATTATTA-ATTAGTATTTAATTAGTATCTAATTAG
*
106 TTTATTATTAATTAGTATTTAATTAGT
1 TTAATTATTAATTAGTATTTAATTAGT
133 TTATGATTAA
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
35 5 0.09
36 16 0.30
37 32 0.60
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (37 bp):
TTAATTATTAATTAGTATTTAATTAGTATCTAATTAG
Found at i:142 original size:15 final size:13
Alignment explanation
Indices: 60--136 Score: 58
Period size: 11 Copynumber: 6.1 Consensus size: 13
50 TATGATTAGC
60 TTTAATTAG-TTA
1 TTTAATTAGTTTA
*
72 ATT-ATTAGTTTA
1 TTTAATTAGTTTA
84 TGTTTAATTAG--TA
1 --TTTAATTAGTTTA
*
97 TCTAATTAGTTTA
1 TTTAATTAGTTTA
110 TTATTAATTAG--TA
1 -T-TTAATTAGTTTA
123 TTTAATTAGTTTA
1 TTTAATTAGTTTA
136 T
1 T
137 GATTAAAATG
Statistics
Matches: 51, Mismatches: 4, Indels: 19
0.69 0.05 0.26
Matches are distributed among these distances:
11 21 0.41
12 6 0.12
13 9 0.18
14 3 0.06
15 12 0.24
ACGTcount: A:0.32, C:0.01, G:0.09, T:0.57
Consensus pattern (13 bp):
TTTAATTAGTTTA
Found at i:1814 original size:16 final size:16
Alignment explanation
Indices: 1778--1876 Score: 62
Period size: 16 Copynumber: 6.4 Consensus size: 16
1768 CCGTTTGTTA
* *
1778 CTTTCCAAAGAGAGCG
1 CTTTCCAAGGAGAGTG
1794 CTTTCCAAGGAGAGTG
1 CTTTCCAAGGAGAGTG
* *
1810 TTTTCCATGGAGAGTG
1 CTTTCCAAGGAGAGTG
* * *
1826 -ATTCCAAGAAGAATG
1 CTTTCCAAGGAGAGTG
* *
1841 -ATTCTC-AGGAGAGTA
1 CTTTC-CAAGGAGAGTG
* *
1856 CTTTCCATGGAAAGT-
1 CTTTCCAAGGAGAGTG
1871 CTTTCC
1 CTTTCC
1877 CTACTCCCTC
Statistics
Matches: 66, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
15 28 0.42
16 38 0.58
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.28
Consensus pattern (16 bp):
CTTTCCAAGGAGAGTG
Done.