Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004220.1 Hibiscus syriacus cultivar Beakdansim tig00009240_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: 45320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:4967 original size:21 final size:22
Alignment explanation
Indices: 4919--4973 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
4909 TGGTTCCAAC
*
4919 CCGACCCGACCCGTTTACCCGA
1 CCGACCCGACCCGTTGACCCGA
4941 CCGA-CCGACCC-TTGACCCGA
1 CCGACCCGACCCGTTGACCCGA
*
4961 CTTGACCCGACCC
1 C-CGACCCGACCC
4974 ATCCGCCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 9 0.31
21 9 0.31
22 11 0.38
ACGTcount: A:0.18, C:0.51, G:0.18, T:0.13
Consensus pattern (22 bp):
CCGACCCGACCCGTTGACCCGA
Found at i:9507 original size:5 final size:5
Alignment explanation
Indices: 9493--9554 Score: 63
Period size: 5 Copynumber: 12.0 Consensus size: 5
9483 ATCGGTTCCA
* * *
9493 ACCCA ACCCG ACCCG TTACCCG ACCCG ACCCTT ACCCA ACCCG ACCCG
1 ACCCG ACCCG ACCCG --ACCCG ACCCG ACCC-G ACCCG ACCCG ACCCG
9541 ACCCG ACCCG -CCCG
1 ACCCG ACCCG ACCCG
9555 TTGATCCGGC
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
4 4 0.08
5 37 0.74
6 4 0.08
7 5 0.10
ACGTcount: A:0.21, C:0.58, G:0.15, T:0.06
Consensus pattern (5 bp):
ACCCG
Found at i:9529 original size:16 final size:16
Alignment explanation
Indices: 9493--9539 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
9483 ATCGGTTCCA
9493 ACCCAACCCGACCCGTT
1 ACCCAACCCGACCC-TT
*
9510 ACCCGACCCGACCCTT
1 ACCCAACCCGACCCTT
9526 ACCCAACCCGACCC
1 ACCCAACCCGACCC
9540 GACCCGACCC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
16 15 0.54
17 13 0.46
ACGTcount: A:0.23, C:0.57, G:0.11, T:0.09
Consensus pattern (16 bp):
ACCCAACCCGACCCTT
Found at i:15627 original size:17 final size:17
Alignment explanation
Indices: 15604--15649 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
15594 GACAAAACAT
*
15604 AATACTATTTTGGTACC
1 AATACTATTTTAGTACC
* *
15621 GATACTATTTCAGTACC
1 AATACTATTTTAGTACC
15638 AATACTACTTTT
1 AATACTA-TTTT
15650 CATATCAGTA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
17 20 0.87
18 3 0.13
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (17 bp):
AATACTATTTTAGTACC
Found at i:17201 original size:20 final size:21
Alignment explanation
Indices: 17165--17203 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
17155 TGATGGTTAA
17165 GGAAGAAGAAAAGAAAGAAAT
1 GGAAGAAGAAAAGAAAGAAAT
17186 GGAA-AAGAAGAA-AAAGAA
1 GGAAGAAGAA-AAGAAAGAA
17204 TGGTGTTGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.03
Consensus pattern (21 bp):
GGAAGAAGAAAAGAAAGAAAT
Found at i:20342 original size:18 final size:18
Alignment explanation
Indices: 20316--20350 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20306 TCGAAATGAA
*
20316 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
20334 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
20351 CCGGATATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:21515 original size:24 final size:24
Alignment explanation
Indices: 21488--21575 Score: 113
Period size: 24 Copynumber: 3.7 Consensus size: 24
21478 TTATATTATA
* *
21488 ATACCTGACCTGGATTCTGATCGG
1 ATACTTGACCTGGATTCTGATCCG
* *
21512 ATACTTGACCTGGATTCTTATCCA
1 ATACTTGACCTGGATTCTGATCCG
* **
21536 ATACTTGACCTGGATTTTGATTTG
1 ATACTTGACCTGGATTCTGATCCG
21560 ATACTTGACCTGGATT
1 ATACTTGACCTGGATT
21576 ATATTTTGAT
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (24 bp):
ATACTTGACCTGGATTCTGATCCG
Found at i:26581 original size:19 final size:20
Alignment explanation
Indices: 26536--26581 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
26526 TCTTTGGTAC
*
26536 AATATATTTTTAGACATACT
1 AATATATTTTTAGAAATACT
26556 AAT-TATTTTTA-AAATA-T
1 AATATATTTTTAGAAATACT
26573 ATATATATT
1 A-ATATATT
26582 AAGCCCATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 2 0.09
18 6 0.26
19 12 0.52
20 3 0.13
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.50
Consensus pattern (20 bp):
AATATATTTTTAGAAATACT
Found at i:41019 original size:27 final size:27
Alignment explanation
Indices: 40981--41049 Score: 129
Period size: 27 Copynumber: 2.6 Consensus size: 27
40971 ATATCCTGTC
*
40981 GCTCATGGTTGGCAATGTTAACAACGT
1 GCTCCTGGTTGGCAATGTTAACAACGT
41008 GCTCCTGGTTGGCAATGTTAACAACGT
1 GCTCCTGGTTGGCAATGTTAACAACGT
41035 GCTCCTGGTTGGCAA
1 GCTCCTGGTTGGCAA
41050 CCTACTTCTG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.29
Consensus pattern (27 bp):
GCTCCTGGTTGGCAATGTTAACAACGT
Found at i:43966 original size:26 final size:26
Alignment explanation
Indices: 43929--43993 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
43919 AAATGAATTT
* *
43929 AAAGAAAATTAAAAGGAATATGGTTAA
1 AAAG-AAATTAAAAGGAATAAGATTAA
*
43956 AAAGAAATT-AAAGGATTAAGATTAA
1 AAAGAAATTAAAAGGAATAAGATTAA
* *
43981 GAAGAACTTAAAA
1 AAAGAAATTAAAA
43994 TGGTCATTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
25 20 0.62
26 8 0.25
27 4 0.12
ACGTcount: A:0.60, C:0.02, G:0.17, T:0.22
Consensus pattern (26 bp):
AAAGAAATTAAAAGGAATAAGATTAA
Found at i:45087 original size:20 final size:20
Alignment explanation
Indices: 45042--45080 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
45032 AAAACTAAAG
*
45042 AATTAAAAATCTAAGGTTTA
1 AATTAAAAATCTAAGGCTTA
*
45062 AATTAAAAGTCTAAGGCTT
1 AATTAAAAATCTAAGGCTT
45081 GATTTAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (20 bp):
AATTAAAAATCTAAGGCTTA
Done.