Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008914.1 Hibiscus syriacus cultivar Beakdansim tig00112217_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: 1601432
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 8
Found at i:1577825 original size:31 final size:29
Alignment explanation
Indices: 1577737--1577841 Score: 93
Period size: 31 Copynumber: 3.4 Consensus size: 29
1577727 GGGCTTGAGA
* *
1577737 GCCTACACAAGAAAGTTACTCGGGACCACGGG
1 GCCTACCCAAGAAAGATA-TCGGG-CCAC-GG
* * *
1577769 GCCTACCTAAGAAATATCTCGGGGCCACAGG
1 GCCTACCCAAGAAAGATATC-GGGCCAC-GG
*
1577800 GCCTACCCAAGAAAGATATCAGGGCCTCGG
1 GCCTACCCAAGAAAGATATC-GGGCCACGG
1577830 AGCCTACCCAAG
1 -GCCTACCCAAG
1577842 GGTCGCCTTA
Statistics
Matches: 60, Mismatches: 11, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
30 2 0.03
31 42 0.70
32 16 0.27
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.13
Consensus pattern (29 bp):
GCCTACCCAAGAAAGATATCGGGCCACGG
Found at i:1580083 original size:22 final size:22
Alignment explanation
Indices: 1580013--1580085 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
1580003 TTCGGTCAAA
* * *
1580013 GTCAAAGTCAATGGTCAGACCG
1 GTCAAAGTCAACGGTCAAACTG
* *
1580035 GTCAAAGTCAACAGTCTAA-TCG
1 GTCAAAGTCAACGGTCAAACT-G
* *
1580057 ATCAAAGTTAACGGTCAAACTG
1 GTCAAAGTCAACGGTCAAACTG
1580079 GTCAAAG
1 GTCAAAG
1580086 ATTCAGGTCA
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
22 38 0.97
23 1 0.03
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.21
Consensus pattern (22 bp):
GTCAAAGTCAACGGTCAAACTG
Found at i:1583553 original size:12 final size:12
Alignment explanation
Indices: 1583536--1583569 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1583526 CGTCAGCCCC
1583536 GTCATGCCCAGA
1 GTCATGCCCAGA
*
1583548 GTCATGCTCAGA
1 GTCATGCCCAGA
1583560 GTCATGCCCA
1 GTCATGCCCA
1583570 TGTCTCTAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.21
Consensus pattern (12 bp):
GTCATGCCCAGA
Found at i:1584316 original size:17 final size:17
Alignment explanation
Indices: 1584277--1584318 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
1584267 TTTTTTTTGT
*
1584277 TGTTGTTTCGTTTTCCA
1 TGTTTTTTCGTTTTCCA
*
1584294 TGTTTTTTCTTTTTCC-
1 TGTTTTTTCGTTTTCCA
1584310 T-TTTTTTCG
1 TGTTTTTTCG
1584319 AACAACATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 7 0.32
16 1 0.05
17 14 0.64
ACGTcount: A:0.02, C:0.17, G:0.12, T:0.69
Consensus pattern (17 bp):
TGTTTTTTCGTTTTCCA
Found at i:1584361 original size:29 final size:31
Alignment explanation
Indices: 1584292--1584350 Score: 86
Period size: 29 Copynumber: 1.9 Consensus size: 31
1584282 TTTCGTTTTC
*
1584292 CATGTTTTTTCTTTTTCCTTTTTTTCGAACAA
1 CATGTTTTTTCTTCTT-CTTTTTTTCGAACAA
1584324 CAT-TTTTTTCTTCTT-TTTTTTTCGAAC
1 CATGTTTTTTCTTCTTCTTTTTTTCGAAC
1584351 TGCTGTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 12 0.46
31 11 0.42
32 3 0.12
ACGTcount: A:0.14, C:0.19, G:0.05, T:0.63
Consensus pattern (31 bp):
CATGTTTTTTCTTCTTCTTTTTTTCGAACAA
Found at i:1593274 original size:32 final size:30
Alignment explanation
Indices: 1593199--1593275 Score: 77
Period size: 32 Copynumber: 2.5 Consensus size: 30
1593189 GAGCATATTG
*
1593199 GGGCCT-GAGCCT-CCCAAGAAAGTTCTCG
1 GGGCCTAGAGCCTACCCAAGAAAGTTCTCA
* * *
1593227 GGGCCTTGGGACCTACCCAAGAAAAGTTCTTA
1 GGGCCTAGAG-CCTACCCAAG-AAAGTTCTCA
1593259 GGGCCTCAGAGCCTACC
1 GGGCCT-AGAGCCTACC
1593276 TAAGGGTCGC
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
28 6 0.15
29 2 0.05
30 3 0.08
31 6 0.15
32 20 0.51
33 2 0.05
ACGTcount: A:0.23, C:0.31, G:0.27, T:0.18
Consensus pattern (30 bp):
GGGCCTAGAGCCTACCCAAGAAAGTTCTCA
Found at i:1595456 original size:13 final size:13
Alignment explanation
Indices: 1595438--1595466 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1595428 TTTAACTTTT
1595438 CGGTCAAAGTCAA
1 CGGTCAAAGTCAA
1595451 CGGTCAAAGTCAA
1 CGGTCAAAGTCAA
1595464 CGG
1 CGG
1595467 GTTGACTCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.24, G:0.28, T:0.14
Consensus pattern (13 bp):
CGGTCAAAGTCAA
Found at i:1596805 original size:51 final size:51
Alignment explanation
Indices: 1596722--1597351 Score: 710
Period size: 51 Copynumber: 12.5 Consensus size: 51
1596712 TTATTTCACC
*
1596722 GGTGTAAGTCTATGTTATGTTTTCACTG-TGGAAGTAAGGGTTAATTTAACT
1 GGTGTAAGTCTATGTTATG-TTTCACTGCTGGAATTAAGGGTTAATTTAACT
* * * *
1596773 GGTGTAAGTCTATGTTATGTTTCACTGTTGGAATTAAGTGTT-ATTTCACC
1 GGTGTAAGTCTATGTTATGTTTCACTGCTGGAATTAAGGGTTAATTTAACT
* * * *
1596823 GATGTAAGTCTATGTTATGTTTCACTACTCGAATTAAGGGTTAATTTAATT
1 GGTGTAAGTCTATGTTATGTTTCACTGCTGGAATTAAGGGTTAATTTAACT
** * * ** *
1596874 AATGTAAGTTTTATGTTATGTTTTACCACTGGAATTAAGGGTTAATTTAACC
1 GGTGTAAG-TCTATGTTATGTTTCACTGCTGGAATTAAGGGTTAATTTAACT
* *
1596926 GGTGTAAGTATATGTTATGTTTCACTGCTGGAATTAAGGGTTAATTTGACT
1 GGTGTAAGTCTATGTTATGTTTCACTGCTGGAATTAAGGGTTAATTTAACT
* * *
1596977 GGTGTAAGTATATGTTATGTTCCACTGCTGGAATTAAGGGTTAATTTGACT
1 GGTGTAAGTCTATGTTATGTTTCACTGCTGGAATTAAGGGTTAATTTAACT
* * * *
1597028 GGTGTAA-T-TATGTTATGTTTCACTTCTGGATTTAAGGGCTAATTTGA-T
1 GGTGTAAGTCTATGTTATGTTTCACTGCTGGAATTAAGGGTTAATTTAACT
* * * * * *
1597076 CGATATAAGTCTATGTTATGTTTCACTGTTGGAATTAAGTGTT-ATTTCACC
1 -GGTGTAAGTCTATGTTATGTTTCACTGCTGGAATTAAGGGTTAATTTAACT
* * * * *
1597127 AGTATAAGTCTATGTTATGTTTCATTACTGGAATT-A-GGTT-ATTTAACC
1 GGTGTAAGTCTATGTTATGTTTCACTGCTGGAATTAAGGGTTAATTTAACT
** **
1597175 AAT-TAAGTCTATGTTA--TTTCACTGCTGGAATTAAGGGTTAATTT-GGT
1 GGTGTAAGTCTATGTTATGTTTCACTGCTGGAATTAAGGGTTAATTTAACT
*
1597222 CGGTGTAAGTCTATGTTATGTTTCACTGCTGGAATTAAGGGTTAATTTAACC
1 -GGTGTAAGTCTATGTTATGTTTCACTGCTGGAATTAAGGGTTAATTTAACT
* ** *
1597274 GGTGTAAGTCTATGTAATGTTTCACTTTTAGAATTAAGGGTTAATTTAACT
1 GGTGTAAGTCTATGTTATGTTTCACTGCTGGAATTAAGGGTTAATTTAACT
* *
1597325 AGTGTAAGTCTATGTTAAGTTTCACTG
1 GGTGTAAGTCTATGTTATGTTTCACTG
1597352 GTGTAAATAT
Statistics
Matches: 496, Mismatches: 68, Indels: 30
0.84 0.11 0.05
Matches are distributed among these distances:
45 14 0.03
46 1 0.00
47 17 0.03
48 18 0.04
49 54 0.11
50 88 0.18
51 261 0.53
52 43 0.09
ACGTcount: A:0.27, C:0.10, G:0.21, T:0.42
Consensus pattern (51 bp):
GGTGTAAGTCTATGTTATGTTTCACTGCTGGAATTAAGGGTTAATTTAACT
Found at i:1596977 original size:25 final size:25
Alignment explanation
Indices: 1596949--1597037 Score: 74
Period size: 25 Copynumber: 3.5 Consensus size: 25
1596939 GTTATGTTTC
1596949 ACTGCTGGAATTAAGGGTTAATTTG
1 ACTGCTGGAATTAAGGGTTAATTTG
* * * * *
1596974 ACTGGTGTAAGTATA-TGTT-ATGTTCC
1 ACTGCTGGAATTA-AGGGTTAAT-TT-G
1597000 ACTGCTGGAATTAAGGGTTAATTTG
1 ACTGCTGGAATTAAGGGTTAATTTG
* *
1597025 ACTGGTGTAATTA
1 ACTGCTGGAATTA
1597038 TGTTATGTTT
Statistics
Matches: 47, Mismatches: 12, Indels: 10
0.68 0.17 0.14
Matches are distributed among these distances:
24 2 0.04
25 27 0.57
26 16 0.34
27 2 0.04
ACGTcount: A:0.27, C:0.09, G:0.26, T:0.38
Consensus pattern (25 bp):
ACTGCTGGAATTAAGGGTTAATTTG
Found at i:1597003 original size:26 final size:25
Alignment explanation
Indices: 1596926--1597003 Score: 61
Period size: 25 Copynumber: 3.0 Consensus size: 25
1596916 TAATTTAACC
1596926 GGTGTAAGTATATGTTATGTTTCACT
1 GGTGTAAGTATATGTTATG-TTCACT
* * * * *
1596952 GCTGGAATTA-AGGGTTAAT-TTGACT
1 GGTGTAAGTATA-TGTT-ATGTTCACT
1596977 GGTGTAAGTATATGTTATGTTCCACT
1 GGTGTAAGTATATGTTATGTT-CACT
1597003 G
1 G
1597004 CTGGAATTAA
Statistics
Matches: 37, Mismatches: 10, Indels: 10
0.65 0.18 0.18
Matches are distributed among these distances:
24 2 0.05
25 18 0.49
26 15 0.41
27 2 0.05
ACGTcount: A:0.24, C:0.09, G:0.26, T:0.41
Consensus pattern (25 bp):
GGTGTAAGTATATGTTATGTTCACT
Found at i:1597019 original size:26 final size:25
Alignment explanation
Indices: 1596939--1597019 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 25
1596929 GTAAGTATAT
1596939 GTTATGTTTCACTGCTGGAATTAAGG
1 GTTATG-TTCACTGCTGGAATTAAGG
* * * * *
1596965 GTTAAT-TTGACTGGTGTAAGTATA-T
1 GTT-ATGTTCACTGCTGGAATTA-AGG
1596990 GTTATGTTCCACTGCTGGAATTAAGG
1 GTTATGTT-CACTGCTGGAATTAAGG
1597016 GTTA
1 GTTA
1597020 ATTTGACTGG
Statistics
Matches: 40, Mismatches: 10, Indels: 10
0.67 0.17 0.17
Matches are distributed among these distances:
24 2 0.05
25 18 0.45
26 18 0.45
27 2 0.05
ACGTcount: A:0.25, C:0.10, G:0.26, T:0.40
Consensus pattern (25 bp):
GTTATGTTCACTGCTGGAATTAAGG
Found at i:1597310 original size:297 final size:305
Alignment explanation
Indices: 1596723--1597350 Score: 855
Period size: 297 Copynumber: 2.1 Consensus size: 305
1596713 TATTTCACCG
* * ** * * * *
1596723 GTGTAAGTCTATGTTATGTTTTCAC-TGTGGAAGTAAGGGTTAATTT-AACTGGTGTAAGTCTAT
1 GTGTAAGTCTATGTTAAG-TTTCACTTCTGGATTTAAGGGCTAATTTGATC-GATATAAGTCTAT
*
1596786 GTTATGTTTCACTGTTGGAATTAAGTGTTATTTCACCGATGTAAGTCTATGTTATGTTTCACTAC
64 GTTATGTTTCACTGTTGGAATTAAGTGTTATTTCACCGATATAAGTCTATGTTATGTTTCACTAC
** * *
1596851 TCGAATTAAGGGTTAATTTAATTAATGTAAGTTTTATGTTATGTTTTACCACTGGAATTAAGGGT
129 TCGAATTAAGGGTTAATTTAACCAATGTAAGTTCTATGTTA-GTTTCACCACTGGAATTAAGGGT
* *
1596916 TAATTTAACCGGTGTAAGTATATGTTATGTTTCACTGCTGGAATTAAGGGTTAATTTGACTGGTG
193 TAATTTAACCGGTGTAAGTATATGTTATGTTTCACTGCTGGAATTAAGGGTTAATTTAACCGGTG
* * * *
1596981 TAAGTATATGTTATGTTCCACTGCTGGAATTAAGGGTTAATTTGACTG
258 TAAGTATATGTAATGTTCCACTGCTAGAATTAAGGGTTAATTTAACTA
*
1597029 GTGTAA-T-TATGTTATGTTTCACTTCTGGATTTAAGGGCTAATTTGATCGATATAAGTCTATGT
1 GTGTAAGTCTATGTTAAGTTTCACTTCTGGATTTAAGGGCTAATTTGATCGATATAAGTCTATGT
*
1597092 TATGTTTCACTGTTGGAATTAAGTGTTATTTCACC-AGTATAAGTCTATGTTATGTTTCATTACT
66 TATGTTTCACTGTTGGAATTAAGTGTTATTTCACCGA-TATAAGTCTATGTTATGTTTCACTACT
* **
1597156 GGAATT-A-GGTT-ATTTAACCAAT-TAAG-TCTATGTTA-TTTCACTGCTGGAATTAAGGGTTA
130 CGAATTAAGGGTTAATTTAACCAATGTAAGTTCTATGTTAGTTTCACCACTGGAATTAAGGGTTA
*** *
1597215 ATTTGGTCGGTGTAAGTCTATGTTATGTTTCACTGCTGGAATTAAGGGTTAATTTAACCGGTGTA
195 ATTTAACCGGTGTAAGTATATGTTATGTTTCACTGCTGGAATTAAGGGTTAATTTAACCGGTGTA
* * **
1597280 AGTCTATGTAATGTTTCACTTTTAGAATTAAGGGTTAATTTAACTA
260 AGTATATGTAATGTTCCACTGCTAGAATTAAGGGTTAATTTAACTA
1597326 GTGTAAGTCTATGTTAAGTTTCACT
1 GTGTAAGTCTATGTTAAGTTTCACT
1597351 GGTGTAAATA
Statistics
Matches: 286, Mismatches: 31, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
297 124 0.43
298 1 0.00
299 23 0.08
300 4 0.01
301 9 0.03
302 4 0.01
303 8 0.03
304 104 0.36
305 3 0.01
306 6 0.02
ACGTcount: A:0.27, C:0.10, G:0.21, T:0.42
Consensus pattern (305 bp):
GTGTAAGTCTATGTTAAGTTTCACTTCTGGATTTAAGGGCTAATTTGATCGATATAAGTCTATGT
TATGTTTCACTGTTGGAATTAAGTGTTATTTCACCGATATAAGTCTATGTTATGTTTCACTACTC
GAATTAAGGGTTAATTTAACCAATGTAAGTTCTATGTTAGTTTCACCACTGGAATTAAGGGTTAA
TTTAACCGGTGTAAGTATATGTTATGTTTCACTGCTGGAATTAAGGGTTAATTTAACCGGTGTAA
GTATATGTAATGTTCCACTGCTAGAATTAAGGGTTAATTTAACTA
Found at i:1597765 original size:69 final size:69
Alignment explanation
Indices: 1597555--1597827 Score: 309
Period size: 68 Copynumber: 4.0 Consensus size: 69
1597545 TACTTATTTC
* * * ** *
1597555 GAGTGACTCGCACGAGAGCACCTAATCATACTTTTTTCGGGTGACTCATATGGGAGCCC-GAAGG
1 GAGTGACTCGCACGGGAGCACCTAATCATACTTATTTCAGGTGACTCGCACGGGAGCCCAGAAGG
1597619 ATTA
66 ATTA
* * * * * ** *
1597623 GAGTGACCCGTACAGGAGCACCTAATCATACTTATTT-GGGTGACTTGCACATGAGCCCTGAAGG
1 GAGTGACTCGCACGGGAGCACCTAATCATACTTATTTCAGGTGACTCGCACGGGAGCCCAGAAGG
1597687 ATTA
66 ATTA
* * * *
1597691 GAGTGACTCGCACGGGAGCACTTAATCATACTAATTTCAGGTGGCTCGCATGGGAGCCTC-GAAG
1 GAGTGACTCGCACGGGAGCACCTAATCATACTTATTTCAGGTGACTCGCACGGGAGCC-CAGAAG
1597755 GATTA
65 GATTA
* * * *
1597760 GAGTGACTCGTACGGGTGCACCTAATCATACATTGTTTCAAGTGACTCGCACGGGAGCCCAGAAG
1 GAGTGACTCGCACGGGAGCACCTAATCATAC-TTATTTCAGGTGACTCGCACGGGAGCCCAGAAG
1597825 GAT
65 GAT
1597828 CTAAATACAT
Statistics
Matches: 170, Mismatches: 30, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
67 15 0.09
68 73 0.43
69 52 0.31
70 30 0.18
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (69 bp):
GAGTGACTCGCACGGGAGCACCTAATCATACTTATTTCAGGTGACTCGCACGGGAGCCCAGAAGG
ATTA
Done.