Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020274.1 Corchorus olitorius cultivar O-4 contig20307, 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: 5270
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.35
Found at i:35 original size:13 final size:13
Alignment explanation
Indices: 17--251 Score: 107
Period size: 13 Copynumber: 16.5 Consensus size: 13
7 AAAAAATTTT
17 TAATTTCTAAATA
1 TAATTTCTAAATA
* *
30 TTATTTTCTAATTA
1 -TAATTTCTAAATA
44 TAATTTCAATACATATA
1 TAATTTC--TA-A-ATA
61 TAATTTCTAAATA
1 TAATTTCTAAATA
74 -ATATTTCATTACATATA
1 TA-ATTTC--TA-A-ATA
*
91 TAATTTAT-AATA
1 TAATTTCTAAATA
* *
103 TAATTCCTAATTA
1 TAATTTCTAAATA
116 TAATTTCTTCACATATA
1 TAATTTC-T-A-A-ATA
*
133 TAGTTTCTAAATA
1 TAATTTCTAAATA
*
146 TCATTTCTAAATA
1 TAATTTCTAAATA
159 -ATATTTCATTACATATA
1 TA-ATTTC--TA-A-ATA
*
176 TAATTTATAAATA
1 TAATTTCTAAATA
* *
189 TAATTCCTAATTA
1 TAATTTCTAAATA
202 TAATTTCATTACATATA
1 TAATTTC--TA-A-ATA
*
219 TCATTTCTAAATA
1 TAATTTCTAAATA
* * *
232 TTATTTTCTCATTA
1 -TAATTTCTAAATA
246 TAATTT
1 TAATTT
252 ATGACCTATT
Statistics
Matches: 169, Mismatches: 26, Indels: 53
0.68 0.10 0.21
Matches are distributed among these distances:
12 10 0.06
13 70 0.41
14 25 0.15
15 17 0.10
16 6 0.04
17 39 0.23
18 2 0.01
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (13 bp):
TAATTTCTAAATA
Found at i:70 original size:30 final size:30
Alignment explanation
Indices: 34--193 Score: 126
Period size: 30 Copynumber: 5.5 Consensus size: 30
24 TAAATATTAT
* *
34 TTTCTAATTATAATTTCAATACATATATAA
1 TTTCTAAATATAATTTCATTACATATATAA
64 TTTCTAAATA-ATATTTCATTACATATATAA
1 TTTCTAAATATA-ATTTCATTACATATATAA
* *
94 TTTAT-AATATAA-TTC-CTA-AT-TATAA
1 TTTCTAAATATAATTTCATTACATATATAA
* *
119 TTTCTTCACATATATAGTTTC--TA-A-ATATCA
1 TTTC-T-A-A-ATATAATTTCATTACATATATAA
149 TTTCTAAATA-ATATTTCATTACATATATAA
1 TTTCTAAATATA-ATTTCATTACATATATAA
*
179 TTTATAAATATAATT
1 TTTCTAAATATAATT
194 CCTAATTATA
Statistics
Matches: 105, Mismatches: 10, Indels: 30
0.72 0.07 0.21
Matches are distributed among these distances:
25 9 0.09
26 10 0.10
27 3 0.03
28 6 0.06
29 9 0.09
30 64 0.61
31 4 0.04
ACGTcount: A:0.42, C:0.10, G:0.01, T:0.47
Consensus pattern (30 bp):
TTTCTAAATATAATTTCATTACATATATAA
Found at i:165 original size:43 final size:43
Alignment explanation
Indices: 58--251 Score: 216
Period size: 43 Copynumber: 4.5 Consensus size: 43
48 TTCAATACAT
58 ATATAATTTCTAAATAAT-ATTTCATTACATATATAATTTAT-A
1 ATATAATTTCT-AATAATAATTTCATTACATATATAATTTATAA
* * * *
100 ATATAATTCCTAATTATAATTTC-TTCACATATATAGTTTCTAA
1 ATATAATTTCTAATAATAATTTCATT-ACATATATAATTTATAA
*
143 ATATCATTTCTAAATAAT-ATTTCATTACATATATAATTTATAA
1 ATATAATTTCT-AATAATAATTTCATTACATATATAATTTATAA
* * * *
186 ATATAATTCCTAATTATAATTTCATTACATATATCATTTCTAA
1 ATATAATTTCTAATAATAATTTCATTACATATATAATTTATAA
* * *
229 ATATTATTTTCTCATTATAATTT
1 ATA-TAATTTCTAATAATAATTT
252 ATGACCTATT
Statistics
Matches: 128, Mismatches: 17, Indels: 12
0.82 0.11 0.08
Matches are distributed among these distances:
41 7 0.05
42 33 0.26
43 65 0.51
44 23 0.18
ACGTcount: A:0.40, C:0.11, G:0.01, T:0.48
Consensus pattern (43 bp):
ATATAATTTCTAATAATAATTTCATTACATATATAATTTATAA
Found at i:738 original size:20 final size:21
Alignment explanation
Indices: 701--740 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
691 CTTTAAAGTC
* *
701 TCGATTTGTTGTTGTAGGTCT
1 TCGATTTATGGTTGTAGGTCT
722 TCGATTTATGGTT-TAGGTC
1 TCGATTTATGGTTGTAGGTC
741 GAAAATCCCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.12, C:0.10, G:0.28, T:0.50
Consensus pattern (21 bp):
TCGATTTATGGTTGTAGGTCT
Done.