Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013912.1 Corchorus olitorius cultivar O-4 contig13945, 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: 13539
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32
Found at i:5374 original size:2 final size:2
Alignment explanation
Indices: 5369--5401 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5359 AAAAGGAGTT
5369 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
5402 CAAAAGACGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:11226 original size:21 final size:21
Alignment explanation
Indices: 11202--11243 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
11192 CCCTGTACTC
* *
11202 ATCATTTATGTATCTATCTCT
1 ATCATTTATGAATCGATCTCT
*
11223 ATCATTTTTGAATCGATCTCT
1 ATCATTTATGAATCGATCTCT
11244 TCTTTGGCCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.19, G:0.07, T:0.50
Consensus pattern (21 bp):
ATCATTTATGAATCGATCTCT
Found at i:13309 original size:22 final size:21
Alignment explanation
Indices: 13276--13333 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
13266 ATCATTTATT
13276 ATAATTAATAATAACAATTTAA
1 ATAATTAATAATAACAA-TTAA
*
13298 ATTAA-TAATAATTAATAATTAA
1 A-TAATTAATAA-TAACAATTAA
13320 ATAATTAATAATAA
1 ATAATTAATAATAA
13334 TTAAAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
21 6 0.19
22 18 0.56
23 8 0.25
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
ATAATTAATAATAACAATTAA
Found at i:13312 original size:10 final size:10
Alignment explanation
Indices: 13257--13337 Score: 50
Period size: 10 Copynumber: 8.7 Consensus size: 10
13247 TTTTGTTTTT
*
13257 TAATTATTAA
1 TAATTAATAA
* * *
13267 TCATTTATTA
1 TAATTAATAA
13277 TAATTAATAA
1 TAATTAATAA
* *
13287 TAA-CAAT-T
1 TAATTAATAA
13295 TAAATTAATAA
1 T-AATTAATAA
13306 TAA-T--TAA
1 TAATTAATAA
13313 TAATT-A-AA
1 TAATTAATAA
13321 TAATTAATAA
1 TAATTAATAA
13331 TAATTAA
1 TAATTAA
13338 AAAAATAAAA
Statistics
Matches: 53, Mismatches: 11, Indels: 14
0.68 0.14 0.18
Matches are distributed among these distances:
7 6 0.11
8 9 0.17
9 7 0.13
10 30 0.57
11 1 0.02
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (10 bp):
TAATTAATAA
Found at i:13315 original size:7 final size:7
Alignment explanation
Indices: 13276--13331 Score: 53
Period size: 7 Copynumber: 7.7 Consensus size: 7
13266 ATCATTTATT
13276 ATAATTA
1 ATAATTA
13283 ATAA-TA
1 ATAATTA
*
13289 ACAATTTAA
1 ATAA-TT-A
13298 ATTAA-TA
1 A-TAATTA
13305 ATAATTA
1 ATAATTA
13312 ATAATTAA
1 ATAATT-A
13320 ATAATTA
1 ATAATTA
13327 ATAAT
1 ATAAT
13332 AATTAAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
6 8 0.20
7 20 0.49
8 9 0.22
9 2 0.05
10 2 0.05
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (7 bp):
ATAATTA
Found at i:13345 original size:15 final size:17
Alignment explanation
Indices: 13297--13338 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
13287 TAACAATTTA
13297 AATT-AATAATAATTAAT
1 AATTAAATAATAA-TAAT
13314 AATTAAATAATTAATAAT
1 AATTAAATAA-TAATAAT
13332 AATTAAA
1 AATTAAA
13339 AAAATAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.17
18 16 0.70
19 3 0.13
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AATTAAATAATAATAAT
Found at i:13449 original size:11 final size:11
Alignment explanation
Indices: 13433--13470 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
13423 AACTTAGATT
*
13433 ATTATTTTTTA
1 ATTATTTATTA
13444 ATTA-TTATTA
1 ATTATTTATTA
*
13454 ATTATTTAATA
1 ATTATTTATTA
13465 ATTATT
1 ATTATT
13471 AATTTAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
ATTATTTATTA
Found at i:13463 original size:18 final size:18
Alignment explanation
Indices: 13430--13474 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
13420 TACAACTTAG
* *
13430 ATTATT-ATTTTTTAATT
1 ATTATTAATTATTTAATA
13447 ATTATTAATTATTTAATA
1 ATTATTAATTATTTAATA
13465 ATTATTAATT
1 ATTATTAATT
13475 TAAATTGTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 6 0.24
18 19 0.76
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTATTAATTATTTAATA
Found at i:13515 original size:37 final size:36
Alignment explanation
Indices: 13445--13515 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 36
13435 TATTTTTTAA
*
13445 TTATTATTAATTATTTAATAATTATTAATTTAAATTG
1 TTATTATTAATTA-TTAATAATAATTAATTTAAATTG
13482 TTATTATTAATTA-TAATAAATAATTAATATTAAA
1 TTATTATTAATTATTAAT-AATAATTAAT-TTAAA
13516 AACAAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
35 4 0.13
36 9 0.29
37 18 0.58
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (36 bp):
TTATTATTAATTATTAATAATAATTAATTTAAATTG
Done.