Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018692.1 Corchorus olitorius cultivar O-4 contig18725, 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: 60770
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.31
Found at i:8555 original size:21 final size:21
Alignment explanation
Indices: 8512--8557 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
8502 CCAATTTAGG
* *
8512 TTTAGATTTCAATTTCTTGTT
1 TTTAGATTTAAATTTATTGTT
8533 TTTAGATTTAAGATTTATT-TT
1 TTTAGATTTAA-ATTTATTGTT
8554 TTTA
1 TTTA
8558 TGCATCTTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.24, C:0.04, G:0.09, T:0.63
Consensus pattern (21 bp):
TTTAGATTTAAATTTATTGTT
Found at i:9907 original size:15 final size:16
Alignment explanation
Indices: 9878--9907 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9868 GTGTGAATTC
9878 AAATTGATCTTTTGAA
1 AAATTGATCTTTTGAA
9894 AAATTGAT-TTTTGA
1 AAATTGATCTTTTGA
9908 TAAACTTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.03, G:0.13, T:0.47
Consensus pattern (16 bp):
AAATTGATCTTTTGAA
Found at i:22370 original size:19 final size:19
Alignment explanation
Indices: 22348--22395 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
22338 AGGCTGAAAT
22348 TAATTAATTATTAATTAAA
1 TAATTAATTATTAATTAAA
* *
22367 TAA-TAATTATTTTATTGAA
1 TAATTAATTA-TTAATTAAA
22386 TAATT-ATTAT
1 TAATTAATTAT
22396 CAAAAATAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 7 0.28
19 17 0.68
20 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TAATTAATTATTAATTAAA
Found at i:28166 original size:21 final size:21
Alignment explanation
Indices: 28142--28188 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
28132 TTTGGTTTCC
28142 AGAGATTGTTGAAGTGCTAAT
1 AGAGATTGTTGAAGTGCTAAT
28163 AGAGATTGTTGAAGTGCTAAT
1 AGAGATTGTTGAAGTGCTAAT
*
28184 TGAGA
1 AGAGA
28189 AGCACGCAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.04, G:0.30, T:0.32
Consensus pattern (21 bp):
AGAGATTGTTGAAGTGCTAAT
Found at i:37226 original size:16 final size:16
Alignment explanation
Indices: 37205--37244 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
37195 TAATGATTAG
37205 AAAAGACAAAAAAAGA
1 AAAAGACAAAAAAAGA
*
37221 AAAAGA-AAAAAAAGG
1 AAAAGACAAAAAAAGA
*
37236 AAAGGACAA
1 AAAAGACAA
37245 TCTGAGGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.78, C:0.05, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAGACAAAAAAAGA
Found at i:40481 original size:10 final size:10
Alignment explanation
Indices: 40468--40494 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
40458 CCAAAAGTTT
40468 AAAAAAAGAA
1 AAAAAAAGAA
40478 AAAAAAAGAA
1 AAAAAAAGAA
40488 AAAAAAA
1 AAAAAAA
40495 AGAGTGAGAG
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:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:40482 original size:11 final size:11
Alignment explanation
Indices: 40468--40497 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
40458 CCAAAAGTTT
40468 AAAAAAAG-AA
1 AAAAAAAGAAA
40478 AAAAAAAGAAA
1 AAAAAAAGAAA
40489 AAAAAAAGA
1 AAAAAAAGA
40498 GTGAGAGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.42
11 11 0.58
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:51222 original size:23 final size:23
Alignment explanation
Indices: 51191--51275 Score: 84
Period size: 22 Copynumber: 3.7 Consensus size: 23
51181 CCGTTTAGTA
*
51191 ATATTTATAATTAAATATATTAT
1 ATATATATAATTAAATATATTAT
*
51214 ATATATAT-ATAAAATAATATTAGAT
1 ATATATATAATTAAAT-ATATT--AT
* * *
51239 ATATATATAGTTACATATATAAT
1 ATATATATAATTAAATATATTAT
51262 A-ATATATAATTAAA
1 ATATATATAATTAAA
51276 CTGTATAGTC
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
22 17 0.34
23 15 0.30
25 14 0.28
26 4 0.08
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (23 bp):
ATATATATAATTAAATATATTAT
Found at i:51266 original size:10 final size:11
Alignment explanation
Indices: 51204--51271 Score: 54
Period size: 12 Copynumber: 6.3 Consensus size: 11
51194 TTTATAATTA
51204 AATATAT-TAT
1 AATATATATAT
51214 -ATATATATAT
1 AATATATATAT
*
51224 AAAATA-ATATT
1 AATATATATA-T
51235 AGATATATATAT
1 A-ATATATATAT
* *
51247 AGTTACATATAT
1 A-ATATATATAT
51259 AATA-ATATAT
1 AATATATATAT
51269 AAT
1 AAT
51272 TAAACTGTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
9 6 0.12
10 15 0.31
11 8 0.17
12 16 0.33
13 3 0.06
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (11 bp):
AATATATATAT
Done.