Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017585.1 Corchorus olitorius cultivar O-4 contig17618, 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: 29507
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:915 original size:11 final size:11
Alignment explanation
Indices: 898--933 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
888 GGAATTTGGT
898 CACATCAACGC
1 CACATCAACGC
* *
909 CATATCAATGC
1 CACATCAACGC
920 CACATCAACGC
1 CACATCAACGC
931 CAC
1 CAC
934 GTCAGTATGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.36, C:0.42, G:0.08, T:0.14
Consensus pattern (11 bp):
CACATCAACGC
Found at i:3654 original size:8 final size:9
Alignment explanation
Indices: 3629--3661 Score: 50
Period size: 8 Copynumber: 3.7 Consensus size: 9
3619 TTAGGTAATG
3629 TATATTATAT
1 TATATTAT-T
3639 TATATTATT
1 TATATTATT
3648 TAT-TTATT
1 TATATTATT
3656 TATATT
1 TATATT
3662 TATATATGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.36
9 6 0.27
10 8 0.36
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TATATTATT
Found at i:5420 original size:21 final size:19
Alignment explanation
Indices: 5377--5434 Score: 89
Period size: 21 Copynumber: 2.9 Consensus size: 19
5367 TGTTTAGCAT
*
5377 CTGTACAGATGAGATTATA
1 CTGTACATATGAGATTATA
5396 CTGTACATATGAGATTAGTTA
1 CTGTACATATGAGATTA--TA
5417 CTGTACATATGAGATTAT
1 CTGTACATATGAGATTAT
5435 TATAACAGCG
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
19 17 0.47
21 19 0.53
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.36
Consensus pattern (19 bp):
CTGTACATATGAGATTATA
Found at i:6730 original size:27 final size:27
Alignment explanation
Indices: 6699--6752 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
6689 TAGATTTTCA
6699 ATAAATACTACTACTAATTTATAAAAT
1 ATAAATACTACTACTAATTTATAAAAT
6726 ATAAATACTACTACTAATTTATAAAAT
1 ATAAATACTACTACTAATTTATAAAAT
6753 TTGCAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (27 bp):
ATAAATACTACTACTAATTTATAAAAT
Found at i:7451 original size:45 final size:45
Alignment explanation
Indices: 7391--7481 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
7381 CTAACAACCC
7391 ATCTCTTCATGATGTGGATATTCCCTCACATATAAATCCTCAACA
1 ATCTCTTCATGATGTGGATATTCCCTCACATATAAATCCTCAACA
7436 ATCTCTTCATGATGTGGATATTCCCTCACATATAAATCCTCAACA
1 ATCTCTTCATGATGTGGATATTCCCTCACATATAAATCCTCAACA
7481 A
1 A
7482 GAATCACAAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.33
Consensus pattern (45 bp):
ATCTCTTCATGATGTGGATATTCCCTCACATATAAATCCTCAACA
Found at i:19435 original size:12 final size:12
Alignment explanation
Indices: 19418--19442 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19408 GCTCGTCAAG
19418 GAACAACCAGAA
1 GAACAACCAGAA
19430 GAACAACCAGAA
1 GAACAACCAGAA
19442 G
1 G
19443 CGACAGAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.24, G:0.20, T:0.00
Consensus pattern (12 bp):
GAACAACCAGAA
Found at i:21434 original size:2 final size:2
Alignment explanation
Indices: 21427--21462 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
21417 TATAGACATC
21427 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
21463 ACAGCCGCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:27416 original size:34 final size:34
Alignment explanation
Indices: 27372--27440 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
27362 GATCAAGAGG
* *
27372 TCTTAGGTTCAACTCTCACGGAATGTGAGTTTGT
1 TCTTAAGTTCAACTCTCACAGAATGTGAGTTTGT
27406 TCTTAAGTTCAACTCTCACAGAATGTGAGTTTGT
1 TCTTAAGTTCAACTCTCACAGAATGTGAGTTTGT
27440 T
1 T
27441 TGTAATTTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.39
Consensus pattern (34 bp):
TCTTAAGTTCAACTCTCACAGAATGTGAGTTTGT
Found at i:27492 original size:16 final size:16
Alignment explanation
Indices: 27471--27527 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
27461 GGTAGGTATG
27471 TAGTTTATTTATGGTA
1 TAGTTTATTTATGGTA
* *
27487 TAGTTTCTAGTTT-GGGTTG
1 TAG-TT-TA-TTTATGG-TA
27506 TAGTTTATTTATGGTA
1 TAGTTTATTTATGGTA
27522 TAGTTT
1 TAGTTT
27528 CTAGTTTGGG
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
16 13 0.41
17 6 0.19
18 6 0.19
19 7 0.22
ACGTcount: A:0.19, C:0.02, G:0.23, T:0.56
Consensus pattern (16 bp):
TAGTTTATTTATGGTA
Found at i:27513 original size:35 final size:35
Alignment explanation
Indices: 27469--27540 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
27459 TTGGTAGGTA
27469 TGTAGTTTATTTATGGTATAGTTTCTAGTTTGGGT
1 TGTAGTTTATTTATGGTATAGTTTCTAGTTTGGGT
27504 TGTAGTTTATTTATGGTATAGTTTCTAGTTTGGGT
1 TGTAGTTTATTTATGGTATAGTTTCTAGTTTGGGT
27539 TG
1 TG
27541 AATTCTCATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (35 bp):
TGTAGTTTATTTATGGTATAGTTTCTAGTTTGGGT
Done.