Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006384.1 Hibiscus syriacus cultivar Beakdansim tig00015373_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: 83782
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:10719 original size:24 final size:24
Alignment explanation
Indices: 10694--10743 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
10684 GAAATTTCTT
10694 AAAATATATTATT-TCTTTATTATTA
1 AAAATATA-TATTAT-TTTATTATTA
*
10719 AAAATATATATTATTTTCTTATTA
1 AAAATATATATTATTTTATTATTA
10743 A
1 A
10744 TTAGATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (24 bp):
AAAATATATATTATTTTATTATTA
Found at i:35259 original size:2 final size:2
Alignment explanation
Indices: 35252--35277 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35242 AACCCATCTA
35252 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
35278 GTATTTCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:35505 original size:23 final size:23
Alignment explanation
Indices: 35479--35525 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
35469 TTATTAACAA
*
35479 TTTTAATAATATAATATTGTATT
1 TTTTAATAATATAATATTATATT
* *
35502 TTTTAGTATTATAATATTATATT
1 TTTTAATAATATAATATTATATT
35525 T
1 T
35526 AATTATATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (23 bp):
TTTTAATAATATAATATTATATT
Found at i:35534 original size:23 final size:23
Alignment explanation
Indices: 35488--35534 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
35478 ATTTTAATAA
* *
35488 TATAATATTGTATTTTTTAGTAT
1 TATAATATTATATTTATTAGTAT
35511 TATAATATTATATTTAATTA-TAT
1 TATAATATTATATTT-ATTAGTAT
35534 T
1 T
35535 CTTAGATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 18 0.86
24 3 0.14
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (23 bp):
TATAATATTATATTTATTAGTAT
Found at i:35909 original size:18 final size:18
Alignment explanation
Indices: 35868--35966 Score: 58
Period size: 19 Copynumber: 5.3 Consensus size: 18
35858 TTTTTCAAAA
35868 ATAATATTATTTATTTTT
1 ATAATATTATTTATTTTT
* *
35886 AAAATATTTTTTAATTTTT
1 ATAATATTATTT-ATTTTT
** *
35905 -TAATAATCTATAAATTATT
1 ATAAT-AT-TATTTATTTTT
* *
35924 ATGAATAGTATATATTTTT
1 AT-AATATTATTTATTTTT
* *
35943 AAAATATTTTTTAATTTTT
1 ATAATATTATTT-ATTTTT
35962 -TAATA
1 ATAATA
35967 ATCTATAAAT
Statistics
Matches: 60, Mismatches: 15, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
18 24 0.40
19 29 0.48
20 4 0.07
21 3 0.05
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (18 bp):
ATAATATTATTTATTTTT
Found at i:36001 original size:56 final size:57
Alignment explanation
Indices: 35870--36036 Score: 300
Period size: 57 Copynumber: 2.9 Consensus size: 57
35860 TTTCAAAAAT
* *
35870 AATATTATTTATTTTTAAAATATTTTTTAATTTTTTAATAATCTATAAATTATTATG
1 AATAGTATATATTTTTAAAATATTTTTTAATTTTTTAATAATCTATAAATTATTATG
35927 AATAGTATATATTTTTAAAATATTTTTTAATTTTTTAATAATCTATAAATTATTATG
1 AATAGTATATATTTTTAAAATATTTTTTAATTTTTTAATAATCTATAAATTATTATG
*
35984 AATAGTATATATTTTAAAAATATTTTTTAA-TTTTTAATAATCTATAAATTATT
1 AATAGTATATATTTTTAAAATATTTTTTAATTTTTTAATAATCTATAAATTATT
36037 GTTTATAATT
Statistics
Matches: 107, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
56 23 0.21
57 84 0.79
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (57 bp):
AATAGTATATATTTTTAAAATATTTTTTAATTTTTTAATAATCTATAAATTATTATG
Found at i:56690 original size:31 final size:31
Alignment explanation
Indices: 56624--56690 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 31
56614 ATGGTTCTGA
* *
56624 AAAATTAAAAGTTTAGATACTAAAATGAACC
1 AAAATTAAAAGTTTAGATAATAAAACGAACC
* * *
56655 AAAATTAATAGTTTA-AGTAATAAAACGGACT
1 AAAATTAAAAGTTTAGA-TAATAAAACGAACC
56686 AAAAT
1 AAAAT
56691 ATTCAAGGGA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 1 0.03
31 29 0.97
ACGTcount: A:0.55, C:0.07, G:0.10, T:0.27
Consensus pattern (31 bp):
AAAATTAAAAGTTTAGATAATAAAACGAACC
Found at i:59175 original size:33 final size:34
Alignment explanation
Indices: 59129--59224 Score: 101
Period size: 33 Copynumber: 2.9 Consensus size: 34
59119 GTTTAAGTTT
* * *
59129 TTTCAAGTTCGAGTCGAGCTTGAAAATTTTAAGC
1 TTTCGAGTTCGAGTCGAGCTTGACAATTTTAAGA
* * *
59163 TTTTGAG-TCGAGTTGAGCTT--CAATTTT-TGA
1 TTTCGAGTTCGAGTCGAGCTTGACAATTTTAAGA
*
59193 TTTCGAGTTCGATTCGAGCTTGACAATTTTAA
1 TTTCGAGTTCGAGTCGAGCTTGACAATTTTAA
59225 ACACGTGAGC
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
30 7 0.15
31 17 0.35
33 19 0.40
34 5 0.10
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.41
Consensus pattern (34 bp):
TTTCGAGTTCGAGTCGAGCTTGACAATTTTAAGA
Found at i:74787 original size:10 final size:10
Alignment explanation
Indices: 74772--74797 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
74762 TAATTAATAA
74772 AAAAATAAAT
1 AAAAATAAAT
74782 AAAAATAAAT
1 AAAAATAAAT
74792 AAAAAT
1 AAAAAT
74798 GATGTAAGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (10 bp):
AAAAATAAAT
Done.