Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001071.1 Hibiscus syriacus cultivar Beakdansim tig00002120_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: 71307
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:6449 original size:3 final size:3
Alignment explanation
Indices: 6436--6475 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
6426 TGAGCGTTTG
6436 TTC TCTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TC TTC T
1 TTC T-TC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
6476 CTTGTTTTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:16645 original size:27 final size:23
Alignment explanation
Indices: 16590--16641 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
16580 TAATTACATG
16590 TAATTATATATAATTACAAACTT
1 TAATTATATATAATTACAAACTT
*
16613 TAATTATATATAATTACATACTT
1 TAATTATATATAATTACAAACTT
*
16636 AAATTA
1 TAATTA
16642 ATTAAACTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (23 bp):
TAATTATATATAATTACAAACTT
Found at i:18359 original size:15 final size:15
Alignment explanation
Indices: 18339--18368 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18329 AGAGTGAATC
*
18339 AAATTAATCATAATT
1 AAATTAATCAAAATT
18354 AAATTAATCAAAATT
1 AAATTAATCAAAATT
18369 TTTAATCATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATTAATCAAAATT
Found at i:19781 original size:13 final size:13
Alignment explanation
Indices: 19763--19790 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
19753 ACGATCCAAC
19763 TTTATTAAATATA
1 TTTATTAAATATA
19776 TTTATTAAATATA
1 TTTATTAAATATA
19789 TT
1 TT
19791 AAATTATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTATTAAATATA
Found at i:40196 original size:27 final size:27
Alignment explanation
Indices: 40096--40225 Score: 109
Period size: 27 Copynumber: 4.7 Consensus size: 27
40086 TTCTTTATAA
* *
40096 TTTTATAAATTACAATAATACTATAACT
1 TTTTATAAATTATAATAA-AATATAACT
* * * *
40124 TTTTAAAAATTATAGTAAAGAAGAAAACT
1 TTTTATAAATTATAAT-AA-AATATAACT
* * * *
40153 TTTTAGAAAGTACAATAAAATATATCT
1 TTTTATAAATTATAATAAAATATAACT
**
40180 TTTTATAAATTATAAT-AAATGATATTT
1 TTTTATAAATTATAATAAAAT-ATAACT
40207 TTTTATAAATTATAATAAA
1 TTTTATAAATTATAATAAA
40226 GAATAATTAT
Statistics
Matches: 81, Mismatches: 18, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
26 4 0.05
27 40 0.49
28 17 0.21
29 20 0.25
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.42
Consensus pattern (27 bp):
TTTTATAAATTATAATAAAATATAACT
Found at i:40251 original size:30 final size:27
Alignment explanation
Indices: 40152--40256 Score: 106
Period size: 27 Copynumber: 3.8 Consensus size: 27
40142 AGAAGAAAAC
* * * *
40152 TTTTTAGAAAGTACAATAAAAT-ATATC
1 TTTTTATAAATTATAAT-AAATGATATT
40179 TTTTTATAAATTATAATAAATGATATT
1 TTTTTATAAATTATAATAAATGATATT
40206 TTTTTATAAATTATAATAAA-GAATAATT
1 TTTTTATAAATTATAATAAATG-AT-ATT
*
40234 ATTTTTATAAAAATATAATAAAT
1 -TTTTTAT-AAATTATAATAAAT
40257 ATCAAAATTT
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
26 5 0.07
27 40 0.60
28 3 0.04
29 7 0.10
30 12 0.18
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.45
Consensus pattern (27 bp):
TTTTTATAAATTATAATAAATGATATT
Found at i:40258 original size:83 final size:84
Alignment explanation
Indices: 40096--40255 Score: 182
Period size: 83 Copynumber: 1.9 Consensus size: 84
40086 TTCTTTATAA
* *
40096 TTTTATAAATTACAATAATACTATAACTTTTTAAAAATTATAGTAAAGAAGAAAACTTTTTAGAA
1 TTTTATAAATTACAATAATACTATAACTTTTTAAAAATTATAATAAAGAAGAAAACTTTTTAAAA
*
40161 AGTACAATAAAATATATCT
66 AATACAATAAAATATATCT
* ** * * *
40180 TTTTATAAATTATAATAA-A-TGATATTTTTTTATAAATTATAATAAAGAATAATTA-TTTTTAT
1 TTTTATAAATTACAATAATACT-ATAACTTTTTAAAAATTATAATAAAGAAGAA-AACTTTTTA-
*
40242 AAAAATATAATAAA
63 AAAAATACAATAAA
40256 TATCAAAATT
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
82 1 0.02
83 33 0.52
84 29 0.46
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (84 bp):
TTTTATAAATTACAATAATACTATAACTTTTTAAAAATTATAATAAAGAAGAAAACTTTTTAAAA
AATACAATAAAATATATCT
Found at i:47067 original size:14 final size:15
Alignment explanation
Indices: 47037--47075 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
47027 ATTATTTTAA
47037 ATATTTTAAACAAAT
1 ATATTTTAAACAAAT
*
47052 ATATTTTATA-AAAT
1 ATATTTTAAACAAAT
47066 ATATTTTAAA
1 ATATTTTAAA
47076 ATTACTTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (15 bp):
ATATTTTAAACAAAT
Found at i:53807 original size:53 final size:54
Alignment explanation
Indices: 53725--53839 Score: 169
Period size: 53 Copynumber: 2.1 Consensus size: 54
53715 GTGGTAGGAA
* * * *
53725 GTTTCCTGATTTTTCTCAAATGAACTTTCAAAGAAATGAAGCCTATTTTTATGG
1 GTTTCTTGATGTTTCTCAAATGAACTTTCAAAGAAATGAAGCCTAATTTTAGGG
* *
53779 GTTTCTTGATGTTT-TCAAATGAATTTTCAAAGAAATTAAGCCTAATTTTAGGG
1 GTTTCTTGATGTTTCTCAAATGAACTTTCAAAGAAATGAAGCCTAATTTTAGGG
53832 GTTTCTTG
1 GTTTCTTG
53840 GGGATATTAT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
53 43 0.78
54 12 0.22
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.43
Consensus pattern (54 bp):
GTTTCTTGATGTTTCTCAAATGAACTTTCAAAGAAATGAAGCCTAATTTTAGGG
Found at i:69007 original size:13 final size:13
Alignment explanation
Indices: 68986--69015 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
68976 CCAGACACCG
*
68986 AAGCGCTAAGCGA
1 AAGCACTAAGCGA
68999 AAGCACTAAGCGA
1 AAGCACTAAGCGA
69012 AAGC
1 AAGC
69016 GCTCGCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.23, G:0.27, T:0.07
Consensus pattern (13 bp):
AAGCACTAAGCGA
Done.