Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007065.1 Hibiscus syriacus cultivar Beakdansim tig00018354_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: 56184
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:4964 original size:21 final size:21
Alignment explanation
Indices: 4940--4985 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
4930 ATACAACTGT
4940 TTTAATTGTACTTACCTGTAC
1 TTTAATTGTACTTACCTGTAC
*
4961 TTTAGTTGTACTTACCTGTAC
1 TTTAATTGTACTTACCTGTAC
4982 TTTA
1 TTTA
4986 TTTAGCTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.17, G:0.11, T:0.50
Consensus pattern (21 bp):
TTTAATTGTACTTACCTGTAC
Found at i:8359 original size:22 final size:22
Alignment explanation
Indices: 8316--8359 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
8306 CTATCTTTAA
* *
8316 TTTTGATTTAAAAATCTGATTC
1 TTTTGATTGAAAAATCTAATTC
8338 TTTTG-TTGAAAAATTCTAATTC
1 TTTTGATTGAAAAA-TCTAATTC
8360 AAAATTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.50
Consensus pattern (22 bp):
TTTTGATTGAAAAATCTAATTC
Found at i:12214 original size:41 final size:40
Alignment explanation
Indices: 12139--12215 Score: 100
Period size: 41 Copynumber: 1.9 Consensus size: 40
12129 CTTATATTTA
* * *
12139 ATTATTACCCTTGTTTATCTTGTCTTTATTCTTCTTTAAT
1 ATTATTACCCTTGTTTATATTATCTTTAATCTTCTTTAAT
* *
12179 ATTATTACCCTTATTTTTTATTATCTTTAATCTTCTT
1 ATTATTACCCTT-GTTTATATTATCTTTAATCTTCTT
12216 CCTTTTCCTG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
40 12 0.39
41 19 0.61
ACGTcount: A:0.19, C:0.17, G:0.03, T:0.61
Consensus pattern (40 bp):
ATTATTACCCTTGTTTATATTATCTTTAATCTTCTTTAAT
Found at i:19074 original size:4 final size:4
Alignment explanation
Indices: 19059--19093 Score: 61
Period size: 4 Copynumber: 8.5 Consensus size: 4
19049 CATGTAACAA
19059 ATAC ACTAC ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC A-TAC ATAC ATAC ATAC ATAC ATAC ATAC AT
19094 GTCATTATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:19480 original size:18 final size:18
Alignment explanation
Indices: 19457--19522 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 18
19447 ACTGAATATT
* *
19457 TGTCCCGAATAACCACTA
1 TGTCCCGAAGAACAACTA
*
19475 TGTCCCGAAGGACAACTGA
1 TGTCCCGAAGAACAACT-A
* *
19494 TTGTTCCGAAGAACTACTA
1 -TGTCCCGAAGAACAACTA
19513 TGTCCCGAAG
1 TGTCCCGAAG
19523 GACCACTGAT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
18 23 0.59
19 2 0.05
20 14 0.36
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (18 bp):
TGTCCCGAAGAACAACTA
Found at i:19503 original size:38 final size:38
Alignment explanation
Indices: 19456--19532 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
19446 CACTGAATAT
*
19456 TTGTCCCGAATAACCACTATGTCCCGAAGGACAACTGA
1 TTGTCCCGAAGAACCACTATGTCCCGAAGGACAACTGA
* * *
19494 TTGTTCCGAAGAACTACTATGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGAACCACTATGTCCCGAAGGACAACTGA
19532 T
1 T
19533 AATCCCTCGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.23
Consensus pattern (38 bp):
TTGTCCCGAAGAACCACTATGTCCCGAAGGACAACTGA
Found at i:19504 original size:20 final size:20
Alignment explanation
Indices: 19475--19532 Score: 66
Period size: 18 Copynumber: 3.0 Consensus size: 20
19465 ATAACCACTA
19475 TGTCCCGAAGGACAACTGAT
1 TGTCCCGAAGGACAACTGAT
* * *
19495 TGTTCCGAAGAACTACT-A-
1 TGTCCCGAAGGACAACTGAT
*
19513 TGTCCCGAAGGACCACTGAT
1 TGTCCCGAAGGACAACTGAT
19533 AATCCCTCGA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
18 14 0.47
19 2 0.07
20 14 0.47
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.22
Consensus pattern (20 bp):
TGTCCCGAAGGACAACTGAT
Found at i:37634 original size:30 final size:28
Alignment explanation
Indices: 37593--37691 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 28
37583 CTTTAGATGA
37593 AATATTTTATCTATAGTTTAGGGGTTAAATT
1 AATA-TTTATCTA-AGTTTA-GGGTTAAATT
*
37624 AATATTTATCTAAGTTTTAGGGTTAAACT
1 AATATTTATCTAAG-TTTAGGGTTAAATT
* * *
37653 AGTATTCTATCTAAAATTTCAGGGTTAAGTT
1 AATATT-TATCT-AAGTTT-AGGGTTAAATT
*
37684 AAAATTTA
1 AATATTTA
37692 ACCATTTTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
29 16 0.28
30 22 0.39
31 19 0.33
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.44
Consensus pattern (28 bp):
AATATTTATCTAAGTTTAGGGTTAAATT
Found at i:37679 original size:31 final size:29
Alignment explanation
Indices: 37614--37680 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
37604 TATAGTTTAG
* * *
37614 GGGTTAAATTAATATTTATCTAAGTTTTA
1 GGGTTAAACTAATATTTATCTAAATTTCA
*
37643 GGGTTAAACTAGTATTCTATCTAAAATTTCA
1 GGGTTAAACTAATATT-TATCT-AAATTTCA
37674 GGGTTAA
1 GGGTTAA
37681 GTTAAAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 14 0.44
30 5 0.16
31 13 0.41
ACGTcount: A:0.34, C:0.07, G:0.16, T:0.42
Consensus pattern (29 bp):
GGGTTAAACTAATATTTATCTAAATTTCA
Found at i:42673 original size:50 final size:50
Alignment explanation
Indices: 42613--42722 Score: 157
Period size: 50 Copynumber: 2.2 Consensus size: 50
42603 TTAGCAGGAA
* * * *
42613 AGCGTGCCCCCTGCATCGCGTTATATGCTTATTTGGCGTCACATGGGTAT
1 AGCGCGCCCCCTGCACCGCGTTATATGCTGATTTGGCGCCACATGGGTAT
* * *
42663 AGCGCGCCCCCTGCCCCGTGTTATATGCTGATTTGGCGCCACGTGGGTAT
1 AGCGCGCCCCCTGCACCGCGTTATATGCTGATTTGGCGCCACATGGGTAT
42713 AGCGCGCCCC
1 AGCGCGCCCC
42723 TGAATCAGGG
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.14, C:0.32, G:0.28, T:0.26
Consensus pattern (50 bp):
AGCGCGCCCCCTGCACCGCGTTATATGCTGATTTGGCGCCACATGGGTAT
Found at i:48361 original size:19 final size:19
Alignment explanation
Indices: 48339--48381 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
48329 GAGAAAAGGT
*
48339 AAAAGTTAAAATGAAAGAG
1 AAAAGCTAAAATGAAAGAG
* * *
48358 AAAAACTATAATGAAAGAT
1 AAAAGCTAAAATGAAAGAG
48377 AAAAG
1 AAAAG
48382 AAAAAGTTAA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.65, C:0.02, G:0.16, T:0.16
Consensus pattern (19 bp):
AAAAGCTAAAATGAAAGAG
Done.