Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002971.1 Hibiscus syriacus cultivar Beakdansim tig00006146_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: 54638
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:1518 original size:5 final size:5
Alignment explanation
Indices: 1509--1561 Score: 52
Period size: 5 Copynumber: 10.6 Consensus size: 5
1499 AATCCTACTT
* * * * * *
1509 GGAGG AGAGG GGAGG GGAGG GGAGG GGAAG GGAAG GGAAG GGAAG GGAAG
1 GGAGG GGAGG GGAGG GGAGG GGAGG GGAGG GGAGG GGAGG GGAGG GGAGG
1559 GGA
1 GGA
1562 AAATTCTAGG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 45 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (5 bp):
GGAGG
Found at i:1562 original size:5 final size:5
Alignment explanation
Indices: 1518--1562 Score: 63
Period size: 5 Copynumber: 9.0 Consensus size: 5
1508 TGGAGGAGAG
* * *
1518 GGGAG GGGAG GGGAG GGGAA GGGAA GGGAA GGGAA GGGAA GGGAA
1 GGGAA GGGAA GGGAA GGGAA GGGAA GGGAA GGGAA GGGAA GGGAA
1563 AATTCTAGGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (5 bp):
GGGAA
Found at i:8504 original size:2 final size:2
Alignment explanation
Indices: 8497--8525 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
8487 GATGACAAAA
8497 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
8526 CTTTCTACAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:22998 original size:71 final size:75
Alignment explanation
Indices: 22872--23019 Score: 200
Period size: 71 Copynumber: 2.0 Consensus size: 75
22862 TTTTAAGTTT
* * *
22872 AATAATTAAAAAAGTATTTTTAAACATATTTTTTTAATTTTAAATACTCGAAAATAT-GATAATT
1 AATAATTAAAAAAG-ATATTTAAACATATTTTTTTAATTTAAAAAACTCGAAAATATAG-TAATT
22936 TAGTGGG-TCCC
64 TAGTGGGATCCC
22947 AATAATTAAAAAA-A-ATTTAAACATCA-TTTTTT-ATTTAAAAAACTCGAAAATATAGTAATTT
1 AATAATTAAAAAAGATATTTAAACAT-ATTTTTTTAATTTAAAAAACTCGAAAATATAGTAATTT
23008 AGTGGGATCCC
65 AGTGGGATCCC
23019 A
1 A
23020 TTTTAATGAT
Statistics
Matches: 67, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
71 31 0.46
72 21 0.31
73 2 0.03
75 13 0.19
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.38
Consensus pattern (75 bp):
AATAATTAAAAAAGATATTTAAACATATTTTTTTAATTTAAAAAACTCGAAAATATAGTAATTTA
GTGGGATCCC
Found at i:24693 original size:14 final size:15
Alignment explanation
Indices: 24661--24695 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
24651 TATTTTTACA
24661 TAAATCAAAATAATAT
1 TAAATCAAAAT-ATAT
24677 TAAATCAAAAT-TAT
1 TAAATCAAAATATAT
24691 TAAAT
1 TAAAT
24696 ATTTAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.42
16 11 0.58
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (15 bp):
TAAATCAAAATATAT
Found at i:28232 original size:23 final size:22
Alignment explanation
Indices: 28197--28240 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
28187 TTATTATAAT
28197 CTTTTTATCCATTATTTTTTCTA
1 CTTTTTATCCATT-TTTTTTCTA
* *
28220 CTTTTTCTTCATTTTTTTTCT
1 CTTTTTATCCATTTTTTTTCT
28241 TGCTTCATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.11, C:0.18, G:0.00, T:0.70
Consensus pattern (22 bp):
CTTTTTATCCATTTTTTTTCTA
Found at i:32028 original size:14 final size:14
Alignment explanation
Indices: 32009--32051 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
31999 CGTTCGGTAA
32009 TCCGTTCGTTTATG
1 TCCGTTCGTTTATG
*
32023 TCCGTTCGTTTATA
1 TCCGTTCGTTTATG
* *
32037 TTCGTTCATTTATG
1 TCCGTTCGTTTATG
32051 T
1 T
32052 ACGTGTATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.12, C:0.19, G:0.16, T:0.53
Consensus pattern (14 bp):
TCCGTTCGTTTATG
Found at i:32294 original size:23 final size:23
Alignment explanation
Indices: 32268--32328 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
32258 TGTTGTTTAC
* *
32268 GTTCATTTATGTTTATTTATTGT
1 GTTCATTTATGTTCATCTATTGT
* *
32291 GTTCGTTTATGTACATCTATTGT
1 GTTCATTTATGTTCATCTATTGT
32314 GTTCATTTATGTTCA
1 GTTCATTTATGTTCA
32329 CTTATGTTCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.18, C:0.10, G:0.15, T:0.57
Consensus pattern (23 bp):
GTTCATTTATGTTCATCTATTGT
Found at i:32328 original size:10 final size:10
Alignment explanation
Indices: 32263--32342 Score: 52
Period size: 10 Copynumber: 7.4 Consensus size: 10
32253 ATCGTTGTTG
*
32263 TTTACGTTCA
1 TTTATGTTCA
*
32273 TTTATGTTTA
1 TTTATGTTCA
*
32283 TTTATTGTGTTCG
1 TTTA---TGTTCA
*
32296 TTTATGTACA
1 TTTATGTTCA
*
32306 TCTATTGTGTTCA
1 --T-TTATGTTCA
32319 TTTATGTTCA
1 TTTATGTTCA
*
32329 CTTATGTTCA
1 TTTATGTTCA
32339 TTTA
1 TTTA
32343 CATCTGTTCG
Statistics
Matches: 53, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
10 36 0.68
11 1 0.02
12 1 0.02
13 15 0.28
ACGTcount: A:0.19, C:0.11, G:0.12, T:0.57
Consensus pattern (10 bp):
TTTATGTTCA
Found at i:39044 original size:16 final size:16
Alignment explanation
Indices: 39023--39055 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
39013 TAATATTAAG
39023 ATTACTTGATGAGTTT
1 ATTACTTGATGAGTTT
39039 ATTACTTGATGAGTTT
1 ATTACTTGATGAGTTT
39055 A
1 A
39056 CTATATCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.27, C:0.06, G:0.18, T:0.48
Consensus pattern (16 bp):
ATTACTTGATGAGTTT
Found at i:39217 original size:14 final size:13
Alignment explanation
Indices: 39200--39254 Score: 62
Period size: 13 Copynumber: 4.3 Consensus size: 13
39190 AAATAAATTT
39200 TAAATTAAAATATA
1 TAAATTAAAATA-A
*
39214 TAAA-TAACATAA
1 TAAATTAAAATAA
39226 TTAAATTAAAATAA
1 -TAAATTAAAATAA
39240 T-AATT-AAATAA
1 TAAATTAAAATAA
39251 TAAA
1 TAAA
39255 AATTAAATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
11 7 0.19
12 7 0.19
13 11 0.31
14 11 0.31
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (13 bp):
TAAATTAAAATAA
Found at i:39231 original size:27 final size:25
Alignment explanation
Indices: 39190--39261 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 25
39180 GTATTTTTTA
*
39190 AAATAAAT-TTTAAATTAAAATATAT
1 AAATAAATAATTAAATTAAAATA-AT
39215 AAATAACATAATTAAATTAAAATAAT
1 AAATAA-ATAATTAAATTAAAATAAT
* *
39241 AATTAAATAATAAAAATTAAA
1 AAATAAATAAT-TAAATTAAA
39262 TGTATAACTT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
25 11 0.27
26 17 0.41
27 13 0.32
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (25 bp):
AAATAAATAATTAAATTAAAATAAT
Found at i:39839 original size:30 final size:29
Alignment explanation
Indices: 39799--39876 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 29
39789 TAGAAAATAA
* * *
39799 TTTATGTAAAATAGATTATCTGAAAATTGT
1 TTTATGTAAAATAAATTACCT-AAAACTGT
* *
39829 TTTACGTAAAACAAATTACCTAAAACTGT
1 TTTATGTAAAATAAATTACCTAAAACTGT
*
39858 TTTATGTAAAATGAATTAC
1 TTTATGTAAAATAAATTAC
39877 ATATTCCAGG
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 23 0.57
30 17 0.43
ACGTcount: A:0.42, C:0.09, G:0.10, T:0.38
Consensus pattern (29 bp):
TTTATGTAAAATAAATTACCTAAAACTGT
Found at i:42626 original size:80 final size:78
Alignment explanation
Indices: 42529--42685 Score: 217
Period size: 78 Copynumber: 2.0 Consensus size: 78
42519 AAAAAACAAT
* *
42529 ATTTTAGGTTGCACCCAATATTAACATTTCC-AGTAGAAAAAAATAATGTTTTAGCTAGCGCTTT
1 ATTTTAGGTAGCACCCAATATTAACATTTCCGA-TAG--AAAAATAATGTTTTAGCTAACGCTTT
*
42593 ATCGAAAATGTTAAAC
63 ACCGAAAATGTTAAAC
* * *
42609 ATTTTAGGTAGCGCCCAATATTAACATTTCCGATAGAAAAATAATGTTTTAGGTAACGTTTTACC
1 ATTTTAGGTAGCACCCAATATTAACATTTCCGATAGAAAAATAATGTTTTAGCTAACGCTTTACC
*
42674 GGAAATGTTAAA
66 GAAAATGTTAAA
42686 AAAAATATTA
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
78 36 0.52
80 32 0.46
81 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (78 bp):
ATTTTAGGTAGCACCCAATATTAACATTTCCGATAGAAAAATAATGTTTTAGCTAACGCTTTACC
GAAAATGTTAAAC
Found at i:50618 original size:21 final size:21
Alignment explanation
Indices: 50548--50622 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
50538 GTTTCCAGAT
* *
50548 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
* * *
50569 TCGCAA--CAAATTTGGAATAAA
1 TCGCAATGCGAACTTGGACT--A
*
50590 TCACAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
50611 TCGCAATGCGAA
1 TCGCAATGCGAA
50623 TATGTAAATC
Statistics
Matches: 41, Mismatches: 9, Indels: 8
0.71 0.16 0.14
Matches are distributed among these distances:
19 8 0.20
21 24 0.59
23 9 0.22
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:50635 original size:20 final size:20
Alignment explanation
Indices: 50610--50661 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
50600 AACTTGGACT
50610 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
50630 ATCGCAATACGAATATGTAA
1 ATCGCAATGCGAATATGTAA
50650 ATCGCAATGCGA
1 ATCGCAATGCGA
50662 TAGTCGAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Done.