Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007023.1 Hibiscus syriacus cultivar Beakdansim tig00018159_pilon, 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: 97834
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:977 original size:35 final size:35
Alignment explanation
Indices: 938--1008 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
928 TAATAAATAA
938 TCAAAATAAAATAAAAAGTCGATATATTTTTGTTT
1 TCAAAATAAAATAAAAAGTCGATATATTTTTGTTT
973 TCAAAATAAAATAAAAAGTCGATATATTTTTGTTT
1 TCAAAATAAAATAAAAAGTCGATATATTTTTGTTT
1008 T
1 T
1009 TCTTGTTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (35 bp):
TCAAAATAAAATAAAAAGTCGATATATTTTTGTTT
Found at i:7317 original size:25 final size:26
Alignment explanation
Indices: 7283--7337 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 26
7273 TTGTGAAAAG
7283 AAAATCTGGGTTTGAAAAGAATC-AA
1 AAAATCTGGGTTTGAAAAGAATCGAA
* *
7308 AAAATTTGGGTTTGAAAGGAATCGAA
1 AAAATCTGGGTTTGAAAAGAATCGAA
7334 AAAA
1 AAAA
7338 GAAGAAGAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 21 0.78
26 6 0.22
ACGTcount: A:0.49, C:0.05, G:0.22, T:0.24
Consensus pattern (26 bp):
AAAATCTGGGTTTGAAAAGAATCGAA
Found at i:13454 original size:21 final size:21
Alignment explanation
Indices: 13412--13469 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
13402 GATATATTAG
* **
13412 AAATATATTATTAAATTTTATT
1 AAAT-TATTATAAAATAATATT
13434 AAATTATTATAAAATAATATT
1 AAATTATTATAAAATAATATT
**
13455 GTATTATTATAAAAT
1 AAATTATTATAAAAT
13470 GACCATTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
21 27 0.87
22 4 0.13
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
AAATTATTATAAAATAATATT
Found at i:13532 original size:21 final size:21
Alignment explanation
Indices: 13508--13574 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
13498 TTAGATGACT
* *
13508 AAATTTTATCAAATTATTATA
1 AAATTATATAAAATTATTATA
13529 AAATTATATAAAATTATTATA
1 AAATTATATAAAATTATTATA
**
13550 AAATTATATTGAATTATTATA
1 AAATTATATAAAATTATTATA
13571 AAAT
1 AAAT
13575 GATCATTAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (21 bp):
AAATTATATAAAATTATTATA
Found at i:13538 original size:10 final size:11
Alignment explanation
Indices: 13508--13574 Score: 86
Period size: 11 Copynumber: 6.4 Consensus size: 11
13498 TTAGATGACT
*
13508 AAATT-TTATC
1 AAATTATTATA
13518 AAATTATTATA
1 AAATTATTATA
13529 AAATTA-TATA
1 AAATTATTATA
13539 AAATTATTATA
1 AAATTATTATA
*
13550 AAATTA-TATT
1 AAATTATTATA
*
13560 GAATTATTATA
1 AAATTATTATA
13571 AAAT
1 AAAT
13575 GATCATTAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
10 23 0.47
11 26 0.53
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (11 bp):
AAATTATTATA
Found at i:14293 original size:21 final size:20
Alignment explanation
Indices: 14225--14293 Score: 70
Period size: 20 Copynumber: 3.4 Consensus size: 20
14215 ATCGTTGAGT
*
14225 TAAAGTATCGAAACTT-TGGG
1 TAAAGTTTCGAAACTTCT-GG
* *
14245 GAAAGTTTCGAAAC-TCTTG
1 TAAAGTTTCGAAACTTCTGG
14264 TAGAAGTTTCGAAACTTCTGG
1 TA-AAGTTTCGAAACTTCTGG
14285 TCAAAGTTT
1 T-AAAGTTT
14294 GTTTAAAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
19 3 0.08
20 25 0.62
21 11 0.28
22 1 0.03
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.33
Consensus pattern (20 bp):
TAAAGTTTCGAAACTTCTGG
Found at i:16202 original size:60 final size:60
Alignment explanation
Indices: 16110--16224 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
16100 ATAGTTGGGT
* * * * ** *
16110 GATCATTTTGTAACTTTTAACAGTCGAGAGACTCAATAAAGTAACGTCCTATAGTAAGAG
1 GATCATTTTATAACTTTTAACAGTCAAAAGACTCAACAAAACAACATCCTATAGTAAGAG
*
16170 GATCATTTTATAACTTTTAATAGTCAAAAGACTCAACAAAACAACATCCTATAGT
1 GATCATTTTATAACTTTTAACAGTCAAAAGACTCAACAAAACAACATCCTATAGT
16225 CAGTGACCAT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 47 1.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (60 bp):
GATCATTTTATAACTTTTAACAGTCAAAAGACTCAACAAAACAACATCCTATAGTAAGAG
Found at i:28509 original size:40 final size:38
Alignment explanation
Indices: 28403--28532 Score: 167
Period size: 40 Copynumber: 3.4 Consensus size: 38
28393 ACTGCGAAGC
* * *
28403 AGGGACCAAAACTCCAAATTCCGGAGATTGTGTGCTAAGC
1 AGGGACCAAAACT-C-AATTCCCGAGATTGTGTGCCAAGT
28443 AGGGA-CAATAAC-C-ATTCCCGAGATTGTGTGCCAAGT
1 AGGGACCAA-AACTCAATTCCCGAGATTGTGTGCCAAGT
28479 AGGGACCAAAACTACAAGTTCCCGAGATTGTGTGCCAAGT
1 AGGGACCAAAACT-CAA-TTCCCGAGATTGTGTGCCAAGT
28519 AGGGACCAAAACTC
1 AGGGACCAAAACTC
28533 CGAATTATCC
Statistics
Matches: 81, Mismatches: 3, Indels: 13
0.84 0.03 0.13
Matches are distributed among these distances:
36 28 0.35
37 3 0.04
38 2 0.02
39 5 0.06
40 43 0.53
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.19
Consensus pattern (38 bp):
AGGGACCAAAACTCAATTCCCGAGATTGTGTGCCAAGT
Found at i:43676 original size:24 final size:24
Alignment explanation
Indices: 43644--43691 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
43634 TATCTAACCG
*
43644 AAAATATTATGATTTTTATAATAT
1 AAAATATTATAATTTTTATAATAT
43668 AAAATATTATAATTTTTATAATAT
1 AAAATATTATAATTTTTATAATAT
43692 TTTTATTTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
AAAATATTATAATTTTTATAATAT
Found at i:62475 original size:31 final size:31
Alignment explanation
Indices: 62439--62498 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
62429 AACTTAAAAG
* *
62439 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
62470 AGTTTTACAGTACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
62499 CATACAACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:63024 original size:14 final size:14
Alignment explanation
Indices: 63007--63053 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
62997 ATCTATAATA
63007 TAATATTAAAAAAT
1 TAATATTAAAAAAT
*
63021 TAATATT---TAAT
1 TAATATTAAAAAAT
63032 T-AT-TTAAAAAAT
1 TAATATTAAAAAAT
63044 TAATATTAAA
1 TAATATTAAA
63054 TTATATCTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
9 2 0.08
10 2 0.08
11 4 0.15
12 4 0.15
13 2 0.08
14 12 0.46
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TAATATTAAAAAAT
Found at i:63026 original size:19 final size:21
Alignment explanation
Indices: 63002--63049 Score: 64
Period size: 23 Copynumber: 2.3 Consensus size: 21
62992 TAAATATCTA
63002 TAATATAA-TA-TTAAAAAAT
1 TAATATAATTATTTAAAAAAT
63021 TAATATTTAATTATTTAAAAAAT
1 TAATA--TAATTATTTAAAAAAT
63044 TAATAT
1 TAATAT
63050 TAAATTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 5 0.20
21 4 0.16
22 2 0.08
23 14 0.56
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TAATATAATTATTTAAAAAAT
Found at i:63042 original size:23 final size:23
Alignment explanation
Indices: 63012--63057 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
63002 TAATATAATA
*
63012 TTAAAAAATTAATATTTAATTAT
1 TTAAAAAATTAATATTAAATTAT
63035 TTAAAAAATTAATATTAAATTAT
1 TTAAAAAATTAATATTAAATTAT
63058 ATCTATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
TTAAAAAATTAATATTAAATTAT
Found at i:63073 original size:61 final size:62
Alignment explanation
Indices: 62995--63115 Score: 210
Period size: 61 Copynumber: 2.0 Consensus size: 62
62985 TATAAATTAA
*
62995 ATATCTATAATATAATATTAAAAAATTAATATTTAA-TTATTT-AAAAAATTAATATTAAATT
1 ATATCTATAATACAATATT-AAAAATTAATATTTAATTTATTTAAAAAAATTAATATTAAATT
63056 ATATCTATAATACAATATTAAAAATTAATATTTAATTTATTTAAAAAAATTAATATTAAA
1 ATATCTATAATACAATATTAAAAATTAATATTTAATTTATTTAAAAAAATTAATATTAAA
63116 ATTAAAATCA
Statistics
Matches: 57, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
60 16 0.28
61 24 0.42
62 17 0.30
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (62 bp):
ATATCTATAATACAATATTAAAAATTAATATTTAATTTATTTAAAAAAATTAATATTAAATT
Found at i:80638 original size:17 final size:17
Alignment explanation
Indices: 80616--80652 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
80606 TTTCCAGCAT
*
80616 GGGGCTTTTGTGGTTGA
1 GGGGCTTTTGTGGATGA
80633 GGGGCTTTTGTGGATGA
1 GGGGCTTTTGTGGATGA
80650 GGG
1 GGG
80653 CAGATTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.08, C:0.05, G:0.51, T:0.35
Consensus pattern (17 bp):
GGGGCTTTTGTGGATGA
Done.