Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018136.1 Corchorus olitorius cultivar O-4 contig18169, 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: 51282
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:13954 original size:2 final size:2
Alignment explanation
Indices: 13947--13980 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
13937 ATTAGTAGTA
*
13947 AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13981 GCTTAGTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16220 original size:2 final size:2
Alignment explanation
Indices: 16213--16249 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
16203 TCTCTATTTC
16213 TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16250 CACGTATAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:16235 original size:15 final size:15
Alignment explanation
Indices: 16215--16249 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
16205 TCTATTTCTA
16215 TATATATATATATAT
1 TATATATATATATAT
16230 TATATATATATATAT
1 TATATATATATATAT
16245 TATAT
1 TATAT
16250 CACGTATAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TATATATATATATAT
Found at i:19999 original size:7 final size:6
Alignment explanation
Indices: 19968--19997 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
19958 TATTCTTGGC
19968 GTGAAT GTGAAT GTGAAT GTGAAGT GTGAA
1 GTGAAT GTGAAT GTGAAT GTGAA-T GTGAA
19998 GTAAGCAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.33, C:0.00, G:0.37, T:0.30
Consensus pattern (6 bp):
GTGAAT
Found at i:22863 original size:15 final size:13
Alignment explanation
Indices: 22829--22857 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
22819 TATAGTAGTA
22829 CTATATTTTTTTT
1 CTATATTTTTTTT
22842 CTATATTTTTTTT
1 CTATATTTTTTTT
22855 CTA
1 CTA
22858 CATATTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.72
Consensus pattern (13 bp):
CTATATTTTTTTT
Found at i:31591 original size:21 final size:19
Alignment explanation
Indices: 31536--31594 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 19
31526 CTGCTTAACA
31536 ACTGTACAGATGAGATTAT
1 ACTGTACAGATGAGATTAT
* *
31555 ATTGTACAGATTAGATTAGGT
1 ACTGTACAGATGAGATTA--T
*
31576 ACTGTACAGACGAGATTAT
1 ACTGTACAGATGAGATTAT
31595 TAAAACAGCG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
19 17 0.52
21 16 0.48
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.32
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAT
Found at i:32950 original size:2 final size:2
Alignment explanation
Indices: 32945--32971 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
32935 AGCTAGCAAC
32945 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
32972 CAATCGATCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35059 original size:3 final size:3
Alignment explanation
Indices: 35051--35080 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
35041 TCAAATCATT
35051 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
35081 TAGTAACCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:37448 original size:13 final size:13
Alignment explanation
Indices: 37438--37471 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
37428 GGGAAGGACC
37438 AAAAAGAAGGAAA
1 AAAAAGAAGGAAA
*
37451 AAAAAGAAAGAAA
1 AAAAAGAAGGAAA
37464 AGAAAAGA
1 A-AAAAGA
37472 GCAAATATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAAAGAAGGAAA
Found at i:38002 original size:12 final size:12
Alignment explanation
Indices: 37953--38008 Score: 55
Period size: 12 Copynumber: 4.9 Consensus size: 12
37943 TTGAAAAATT
37953 TAAAAA-AAAAA
1 TAAAAAGAAAAA
*
37964 T-TAAA-AAAAA
1 TAAAAAGAAAAA
* *
37974 TAAGAAGAAGAA
1 TAAAAAGAAAAA
*
37986 GAAAAAGAAAAA
1 TAAAAAGAAAAA
37998 TAAAAAGAAAA
1 TAAAAAGAAAA
38009 CACCTTAGTT
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
10 9 0.26
11 3 0.09
12 23 0.66
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (12 bp):
TAAAAAGAAAAA
Found at i:42542 original size:17 final size:17
Alignment explanation
Indices: 42505--42552 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
42495 GTAGTCTTTG
*
42505 ATCACCGGTGATCTTGC
1 ATCACTGGTGATCTTGC
*
42522 ATCATTGGTGATCTTAG-
1 ATCACTGGTGATCTT-GC
*
42539 ATCACTAGTGATCT
1 ATCACTGGTGATCT
42553 GGGGGTGATC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 25 0.96
18 1 0.04
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (17 bp):
ATCACTGGTGATCTTGC
Found at i:45718 original size:21 final size:21
Alignment explanation
Indices: 45672--45719 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
45662 GTCATGGACA
45672 ATTATGATTATGATTATTGTT
1 ATTATGATTATGATTATTGTT
*
45693 GTTATGATCT-TGATTA-TGATT
1 ATTATGAT-TATGATTATTG-TT
45714 ATTATG
1 ATTATG
45720 GATAAATGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 2 0.09
21 20 0.87
22 1 0.04
ACGTcount: A:0.27, C:0.02, G:0.17, T:0.54
Consensus pattern (21 bp):
ATTATGATTATGATTATTGTT
Done.