Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019430.1 Corchorus olitorius cultivar O-4 contig19463, 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: 12735
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:34 original size:19 final size:18
Alignment explanation
Indices: 8--86 Score: 86
Period size: 19 Copynumber: 4.1 Consensus size: 18
1 TTTTTTA
*
8 ACTATTATCTATCTATTT
1 ACTATTATCTATTTATTT
*
26 ACTATTTATCTTTTATTTTTTT
1 ACTA-TTATC---TATTTATTT
48 AACTATTATCTATTTATTT
1 -ACTATTATCTATTTATTT
67 ACTATTTATCTATTTATTT
1 ACTA-TTATCTATTTATTT
86 A
1 A
87 TTAATTTAAC
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
18 8 0.15
19 28 0.54
22 12 0.23
23 4 0.08
ACGTcount: A:0.27, C:0.11, G:0.00, T:0.62
Consensus pattern (18 bp):
ACTATTATCTATTTATTT
Found at i:40 original size:7 final size:8
Alignment explanation
Indices: 17--88 Score: 60
Period size: 8 Copynumber: 9.0 Consensus size: 8
7 AACTATTATC
17 TATCTATT
1 TATCTATT
25 TA-CTATT
1 TATCTATT
32 TATCT-TT
1 TATCTATT
* *
39 TATTTTTT
1 TATCTATT
*
47 TAACTA-T
1 TATCTATT
54 TATCTATT
1 TATCTATT
62 TATTTACTATT
1 TA--T-CTATT
73 TATCTATT
1 TATCTATT
*
81 TATTTATT
1 TATCTATT
89 AATTTAACTA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
7 19 0.37
8 24 0.46
9 1 0.02
10 1 0.02
11 7 0.13
ACGTcount: A:0.25, C:0.10, G:0.00, T:0.65
Consensus pattern (8 bp):
TATCTATT
Found at i:63 original size:15 final size:15
Alignment explanation
Indices: 4--109 Score: 66
Period size: 15 Copynumber: 7.3 Consensus size: 15
1 TTT
4 TTTAACTATTATCTA
1 TTTAACTATTATCTA
*
19 TCT-A-T-TTA-CTA
1 TTTAACTATTATCTA
* * * *
30 TTTATCTTTTATTTT
1 TTTAACTATTATCTA
45 TTTAACTATTATCTA
1 TTTAACTATTATCTA
60 TTTATTTACTATTTATCTA
1 TTTA---ACTA-TTATCTA
79 TTT-A-T-TTAT-TAA
1 TTTAACTATTATCT-A
91 TTTAACTATTATCTA
1 TTTAACTATTATCTA
106 TTTA
1 TTTA
110 CTTACTATCT
Statistics
Matches: 69, Mismatches: 9, Indels: 26
0.66 0.09 0.25
Matches are distributed among these distances:
11 6 0.09
12 11 0.16
13 3 0.04
14 6 0.09
15 28 0.41
16 1 0.01
18 4 0.06
19 10 0.14
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTAACTATTATCTA
Found at i:83 original size:27 final size:27
Alignment explanation
Indices: 53--109 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
43 TTTTTAACTA
*
53 TTATCTATTTATTT-ACTATTTATCTAT
1 TTATCTATTAATTTAACTA-TTATCTAT
*
80 TTATTTATTAATTTAACTATTATCTAT
1 TTATCTATTAATTTAACTATTATCTAT
107 TTA
1 TTA
110 CTTACTATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 23 0.85
28 4 0.15
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (27 bp):
TTATCTATTAATTTAACTATTATCTAT
Found at i:122 original size:19 final size:17
Alignment explanation
Indices: 8--122 Score: 64
Period size: 19 Copynumber: 6.5 Consensus size: 17
1 TTTTTTA
*
8 ACTATTATCTATCTATTT
1 ACTATTATCTATTTA-TT
*
26 ACTATTTATCTTTTATTTTTTT
1 ACTA-TTATC---TA-TTTATT
48 AACTATTATCTATTTATTT
1 -ACTATTATCTATTTA-TT
67 ACTATTTATCTATTTATT
1 ACTA-TTATCTATTTATT
85 --TATTA---ATTTA--
1 ACTATTATCTATTTATT
95 ACTATTATCTATTTACTT
1 ACTATTATCTATTTA-TT
113 ACTATCTATC
1 ACTAT-TATC
123 GTTTTTATTT
Statistics
Matches: 77, Mismatches: 3, Indels: 33
0.68 0.03 0.29
Matches are distributed among these distances:
12 10 0.13
15 8 0.10
16 2 0.03
18 18 0.23
19 24 0.31
22 9 0.12
23 6 0.08
ACGTcount: A:0.28, C:0.13, G:0.00, T:0.59
Consensus pattern (17 bp):
ACTATTATCTATTTATT
Found at i:219 original size:16 final size:16
Alignment explanation
Indices: 179--232 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
169 TTTTAGCTAC
179 CTATTTATCTAT-TATT
1 CTATTTATCTATATA-T
* *
195 CTCTGTATCTATATAT
1 CTATTTATCTATATAT
* *
211 CTATTTATCTCTATAC
1 CTATTTATCTATATAT
227 CTATTT
1 CTATTT
233 TTTATTATTA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
16 29 0.94
17 2 0.06
ACGTcount: A:0.24, C:0.19, G:0.02, T:0.56
Consensus pattern (16 bp):
CTATTTATCTATATAT
Found at i:230 original size:24 final size:24
Alignment explanation
Indices: 176--230 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
166 TTTTTTTAGC
* *
176 TACCTATTTATCTATTATTCTCTG
1 TACCTATATATCTATTATTCTCTA
*
200 TATCTATATATCTATT-TATCTCTA
1 TACCTATATATCTATTAT-TCTCTA
224 TACCTAT
1 TACCTAT
231 TTTTTATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 1 0.04
24 25 0.96
ACGTcount: A:0.25, C:0.20, G:0.02, T:0.53
Consensus pattern (24 bp):
TACCTATATATCTATTATTCTCTA
Found at i:9959 original size:21 final size:21
Alignment explanation
Indices: 9916--9959 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
9906 CCAATTTAGG
*
9916 TTTAGATTTAAATTTCTTGTT
1 TTTAGATTTAAATTTATTGTT
9937 TTTAGATTTAAGATTTATT-TT
1 TTTAGATTTAA-ATTTATTGTT
9958 TT
1 TT
9960 ATGCATCTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.25, C:0.02, G:0.09, T:0.64
Consensus pattern (21 bp):
TTTAGATTTAAATTTATTGTT
Found at i:10409 original size:38 final size:37
Alignment explanation
Indices: 10365--10453 Score: 90
Period size: 40 Copynumber: 2.3 Consensus size: 37
10355 CTCAATTTTT
*
10365 CAAAATTGATTTTCGACAAAAATTTT-AATTTTTGATG
1 CAAAATTGATTTTC-ACAAAAATTTTGAATTTTTCATG
* **
10402 CTAAAATTTTGATTTTCTCAAACTTTTTGAATTTTTCATG
1 C-AAAA--TTGATTTTCACAAAAATTTTGAATTTTTCATG
10442 CATAAATTGATT
1 CA-AAATTGATT
10454 AATTGATTTG
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
37 1 0.02
38 10 0.23
39 9 0.21
40 23 0.53
ACGTcount: A:0.34, C:0.10, G:0.09, T:0.47
Consensus pattern (37 bp):
CAAAATTGATTTTCACAAAAATTTTGAATTTTTCATG
Done.