Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003993.1 Hibiscus syriacus cultivar Beakdansim tig00008695_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: 54564
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:3001 original size:17 final size:17
Alignment explanation
Indices: 2979--3011 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2969 AAAGAGAACT
2979 CAAAGAATC-CATTAAAA
1 CAAAGAA-CGCATTAAAA
2996 CAAAGAACGCATTAAA
1 CAAAGAACGCATTAAA
3012 TATGGAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.07
17 14 0.93
ACGTcount: A:0.58, C:0.18, G:0.09, T:0.15
Consensus pattern (17 bp):
CAAAGAACGCATTAAAA
Found at i:11444 original size:7 final size:7
Alignment explanation
Indices: 11432--11462 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
11422 CGACCGACCC
11432 GACCGTT
1 GACCGTT
11439 GACCGTT
1 GACCGTT
11446 GACCG-T
1 GACCGTT
11452 GACCGTT
1 GACCGTT
11459 GACC
1 GACC
11463 TCCTTTTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.16, C:0.32, G:0.29, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:11456 original size:13 final size:14
Alignment explanation
Indices: 11432--11462 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
11422 CGACCGACCC
11432 GACCGTTGACCGTT
1 GACCGTTGACCGTT
11446 GACCG-TGACCGTT
1 GACCGTTGACCGTT
11459 GACC
1 GACC
11463 TCCTTTTGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.16, C:0.32, G:0.29, T:0.23
Consensus pattern (14 bp):
GACCGTTGACCGTT
Found at i:13616 original size:5 final size:5
Alignment explanation
Indices: 13606--13635 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
13596 TTTGACCGGT
13606 CCGAC CCGA- CCGAC CCGAC CCGAC CCGAC C
1 CCGAC CCGAC CCGAC CCGAC CCGAC CCGAC C
13636 GTTGACCGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.20, C:0.60, G:0.20, T:0.00
Consensus pattern (5 bp):
CCGAC
Found at i:13618 original size:9 final size:9
Alignment explanation
Indices: 13606--13636 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
13596 TTTGACCGGT
13606 CCGACCCGA
1 CCGACCCGA
13615 CCGACCCGA
1 CCGACCCGA
13624 CCCGACCCGA
1 -CCGACCCGA
13634 CCG
1 CCG
13637 TTGACCGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.58, G:0.23, T:0.00
Consensus pattern (9 bp):
CCGACCCGA
Found at i:13623 original size:14 final size:15
Alignment explanation
Indices: 13606--13635 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
13596 TTTGACCGGT
13606 CCGACCCGA-CCGAC
1 CCGACCCGACCCGAC
13620 CCGACCCGACCCGAC
1 CCGACCCGACCCGAC
13635 C
1 C
13636 GTTGACCGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.20, C:0.60, G:0.20, T:0.00
Consensus pattern (15 bp):
CCGACCCGACCCGAC
Found at i:25297 original size:45 final size:45
Alignment explanation
Indices: 25233--25322 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
25223 GAAAGAAACG
25233 GTGGATTAAATTGTAAAATTTCAAAGTTGGCAGACCATTTTAAGA
1 GTGGATTAAATTGTAAAATTTCAAAGTTGGCAGACCATTTTAAGA
* *
25278 GTGGATTAAATTGTAAAATTTCAAAGTTGGTAGACTATTTTAAGA
1 GTGGATTAAATTGTAAAATTTCAAAGTTGGCAGACCATTTTAAGA
25323 AGTGCAGGAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.36
Consensus pattern (45 bp):
GTGGATTAAATTGTAAAATTTCAAAGTTGGCAGACCATTTTAAGA
Found at i:28483 original size:48 final size:48
Alignment explanation
Indices: 28430--28538 Score: 114
Period size: 48 Copynumber: 2.3 Consensus size: 48
28420 ATATTTTATC
* *
28430 TGATTTCCGACT-TGAATTATGTTCTGATA-CATTACCTGAATTCTGTTA
1 TGATTTCCGA-TATGAATTATGTTATGATATC-TGACCTGAATTCTGTTA
* * * * *
28478 TGATTTCTGATATGGATTCTGTTATGATATCTGATCTGAATTCTGTTT
1 TGATTTCCGATATGAATTATGTTATGATATCTGACCTGAATTCTGTTA
*
28526 TGATTTCTGATAT
1 TGATTTCCGATAT
28539 CTCTGTTTAC
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
47 1 0.02
48 50 0.96
49 1 0.02
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.48
Consensus pattern (48 bp):
TGATTTCCGATATGAATTATGTTATGATATCTGACCTGAATTCTGTTA
Found at i:28485 original size:12 final size:12
Alignment explanation
Indices: 28470--28534 Score: 60
Period size: 12 Copynumber: 5.4 Consensus size: 12
28460 ATTACCTGAA
28470 TTCTGTTATGAT
1 TTCTGTTATGAT
*
28482 TTCTGATATGGA-
1 TTCTGTTAT-GAT
28494 TTCTGTTATGAT
1 TTCTGTTATGAT
* * * *
28506 ATCTGATCTGAA
1 TTCTGTTATGAT
*
28518 TTCTGTTTTGAT
1 TTCTGTTATGAT
28530 TTCTG
1 TTCTG
28535 ATATCTCTGT
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
11 2 0.05
12 37 0.90
13 2 0.05
ACGTcount: A:0.18, C:0.11, G:0.18, T:0.52
Consensus pattern (12 bp):
TTCTGTTATGAT
Found at i:28496 original size:24 final size:24
Alignment explanation
Indices: 28466--28538 Score: 110
Period size: 24 Copynumber: 3.0 Consensus size: 24
28456 ATACATTACC
28466 TGAATTCTGTTATGATTTCTGATA
1 TGAATTCTGTTATGATTTCTGATA
* * *
28490 TGGATTCTGTTATGATATCTGATC
1 TGAATTCTGTTATGATTTCTGATA
*
28514 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTATGATTTCTGATA
28538 T
1 T
28539 CTCTGTTTAC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.22, C:0.10, G:0.18, T:0.51
Consensus pattern (24 bp):
TGAATTCTGTTATGATTTCTGATA
Found at i:29980 original size:45 final size:45
Alignment explanation
Indices: 29916--30006 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
29906 AAAGAAATAT
29916 AGTGGATTAAATTGTAAAATTTCAAAGTTGGCAGACCATTTTAAG
1 AGTGGATTAAATTGTAAAATTTCAAAGTTGGCAGACCATTTTAAG
*
29961 AGTGGATTAAATTGTAAAATTTCAAAGTTGGTAGACCATTTTAAG
1 AGTGGATTAAATTGTAAAATTTCAAAGTTGGCAGACCATTTTAAG
30006 A
1 A
30007 AGTGCAGGAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.38, C:0.08, G:0.20, T:0.34
Consensus pattern (45 bp):
AGTGGATTAAATTGTAAAATTTCAAAGTTGGCAGACCATTTTAAG
Found at i:30644 original size:9 final size:9
Alignment explanation
Indices: 30602--30658 Score: 60
Period size: 9 Copynumber: 6.0 Consensus size: 9
30592 ATGGTCCAAA
30602 TGACCGGTT
1 TGACCGGTT
*
30611 TGATCGGTCT
1 TGACCGGT-T
* *
30621 TAGAGCAGATT
1 T-GA-CCGGTT
30632 TGACCGGTT
1 TGACCGGTT
30641 TGACCGGTT
1 TGACCGGTT
30650 TGACCGGTT
1 TGACCGGTT
30659 ACAACCCCAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 29 0.74
10 4 0.10
11 4 0.10
12 2 0.05
ACGTcount: A:0.16, C:0.19, G:0.32, T:0.33
Consensus pattern (9 bp):
TGACCGGTT
Found at i:30707 original size:12 final size:13
Alignment explanation
Indices: 30685--30713 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
30675 CCGTTAACCC
30685 GACCGGACCCGTT
1 GACCGGACCCGTT
30698 GACC-GACCCGTT
1 GACCGGACCCGTT
30710 GACC
1 GACC
30714 TGTCTATCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.17, C:0.41, G:0.28, T:0.14
Consensus pattern (13 bp):
GACCGGACCCGTT
Found at i:33207 original size:48 final size:48
Alignment explanation
Indices: 33152--33262 Score: 145
Period size: 48 Copynumber: 2.3 Consensus size: 48
33142 AAATATTTTA
*
33152 TCTGATTTCTGACT-TGAATTCTATTATGATA-CATTACCTGAATTCTGT
1 TCTGATTTCTGA-TATGAATTCTATTATGATATC-TGACCTGAATTCTGT
* * *
33200 TCTGATTTCTGATATGGATTCTGTTATGATATCTGATCTGAATTCTGT
1 TCTGATTTCTGATATGAATTCTATTATGATATCTGACCTGAATTCTGT
*
33248 TTTGATTTCTGATAT
1 TCTGATTTCTGATAT
33263 CTCTGTTTAC
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
47 1 0.02
48 54 0.96
49 1 0.02
ACGTcount: A:0.23, C:0.14, G:0.15, T:0.49
Consensus pattern (48 bp):
TCTGATTTCTGATATGAATTCTATTATGATATCTGACCTGAATTCTGT
Found at i:33209 original size:12 final size:12
Alignment explanation
Indices: 33189--33258 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
33179 GATACATTAC
*
33189 CTGAATTCTGTT
1 CTGATTTCTGTT
*
33201 CTGATTTCTGAT
1 CTGATTTCTGTT
*
33213 ATGGA-TTCTGTT
1 CT-GATTTCTGTT
* * *
33225 ATGATATCTGAT
1 CTGATTTCTGTT
*
33237 CTGAATTCTGTT
1 CTGATTTCTGTT
*
33249 TTGATTTCTG
1 CTGATTTCTG
33259 ATATCTCTGT
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
11 2 0.05
12 40 0.91
13 2 0.05
ACGTcount: A:0.19, C:0.13, G:0.19, T:0.50
Consensus pattern (12 bp):
CTGATTTCTGTT
Found at i:33220 original size:24 final size:24
Alignment explanation
Indices: 33190--33262 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 24
33180 ATACATTACC
*
33190 TGAATTCTGTTCTGATTTCTGATA
1 TGAATTCTGTTATGATTTCTGATA
* * *
33214 TGGATTCTGTTATGATATCTGATC
1 TGAATTCTGTTATGATTTCTGATA
*
33238 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTATGATTTCTGATA
33262 T
1 T
33263 CTCTGTTTAC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.21, C:0.11, G:0.18, T:0.51
Consensus pattern (24 bp):
TGAATTCTGTTATGATTTCTGATA
Found at i:34826 original size:26 final size:26
Alignment explanation
Indices: 34797--34860 Score: 119
Period size: 26 Copynumber: 2.5 Consensus size: 26
34787 TTTTTATTAT
*
34797 TTCGGGTCGGGTTTTTAAGTCATATA
1 TTCGGGTCGAGTTTTTAAGTCATATA
34823 TTCGGGTCGAGTTTTTAAGTCATATA
1 TTCGGGTCGAGTTTTTAAGTCATATA
34849 TTCGGGTCGAGT
1 TTCGGGTCGAGT
34861 CGAATCTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.19, C:0.12, G:0.28, T:0.41
Consensus pattern (26 bp):
TTCGGGTCGAGTTTTTAAGTCATATA
Found at i:35207 original size:60 final size:59
Alignment explanation
Indices: 35142--35314 Score: 161
Period size: 60 Copynumber: 2.9 Consensus size: 59
35132 ATATGTCCCA
* * * **
35142 AAACTATAATCCTTATTTTAAATTAGTATTTAAAATTTTGAATATTCTAATTTCCCCCTT
1 AAACTATGA-CCTTATTTTAAATTAGTACTTAAAATTTTGAACATTCTAATTTAACCCTT
* * * * *
35202 AAACTATGACTCTCATTCTAAATTAGTCCTTAAACTTTTGAACATTCTAATTTAATCCTT
1 AAACTATGAC-CTTATTTTAAATTAGTACTTAAAATTTTGAACATTCTAATTTAACCCTT
* * * *
35262 AAACTATGACCCTCT-TTTTAAATTGGT-CTCCAAACTTTTGAACATTCCAATTT
1 AAACTATGA-CCT-TATTTTAAATTAGTACT-TAAAATTTTGAACATTCTAATTT
35315 CATCCCCCAA
Statistics
Matches: 94, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
59 3 0.03
60 90 0.96
61 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.43
Consensus pattern (59 bp):
AAACTATGACCTTATTTTAAATTAGTACTTAAAATTTTGAACATTCTAATTTAACCCTT
Found at i:35233 original size:31 final size:30
Alignment explanation
Indices: 35198--35272 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 30
35188 CTAATTTCCC
*
35198 CCTTAAACTATGACTCTCATTCTAAATTAGT
1 CCTTAAACTATGAC-CTCATTCTAAATTAAT
* * *
35229 CCTTAAACTTTTGA--ACATTCTAATTTAAT
1 CCTTAAAC-TATGACCTCATTCTAAATTAAT
35258 CCTTAAACTATGACC
1 CCTTAAACTATGACC
35273 CTCTTTTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
28 4 0.11
29 20 0.56
31 8 0.22
32 4 0.11
ACGTcount: A:0.33, C:0.23, G:0.05, T:0.39
Consensus pattern (30 bp):
CCTTAAACTATGACCTCATTCTAAATTAAT
Found at i:43409 original size:51 final size:51
Alignment explanation
Indices: 43350--43528 Score: 295
Period size: 51 Copynumber: 3.5 Consensus size: 51
43340 GTATATGTAA
*
43350 ATATAGACATGCAGGTTCATACGCATATATCATACATGTAATCTATTGGAT
1 ATATAGACATGCAGGTTCATACGCATACATCATACATGTAATCTATTGGAT
* *
43401 ATATAGACATGTAGGTTCATACGCATACATCATAAATGTAATCTATTGGAT
1 ATATAGACATGCAGGTTCATACGCATACATCATACATGTAATCTATTGGAT
* * *
43452 ATTTAGACAGGCAGGTTCATACGCATACATCATACGTGTAATCTATTGGAT
1 ATATAGACATGCAGGTTCATACGCATACATCATACATGTAATCTATTGGAT
*
43503 ATATAGACATGCAGGTTCATATGCAT
1 ATATAGACATGCAGGTTCATACGCAT
43529 CATGAAAATT
Statistics
Matches: 117, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 117 1.00
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (51 bp):
ATATAGACATGCAGGTTCATACGCATACATCATACATGTAATCTATTGGAT
Found at i:45545 original size:13 final size:13
Alignment explanation
Indices: 45527--45551 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45517 TTCTATTTGA
45527 AAAAAAATTAATT
1 AAAAAAATTAATT
45540 AAAAAAATTAAT
1 AAAAAAATTAAT
45552 AATTTATTCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAAAAATTAATT
Found at i:46462 original size:7 final size:7
Alignment explanation
Indices: 46444--46536 Score: 55
Period size: 7 Copynumber: 13.4 Consensus size: 7
46434 CACATGTTAT
46444 CCTAAA-
1 CCTAAAC
46450 CCTAAAC
1 CCTAAAC
46457 CCTAAAC
1 CCTAAAC
46464 CCTAAAC
1 CCTAAAC
* *
46471 TCTAATC
1 CCTAAAC
*
46478 TCTAAA-
1 CCTAAAC
*
46484 TCTCAAAC
1 CCT-AAAC
46492 CCTAAAC
1 CCTAAAC
* * *
46499 CATGAAT
1 CCTAAAC
*
46506 ACTAAAC
1 CCTAAAC
**
46513 CCTAAGT
1 CCTAAAC
*
46520 CCTAAAA
1 CCTAAAC
*
46527 CCTAAGC
1 CCTAAAC
46534 CCT
1 CCT
46537 TAATATAATT
Statistics
Matches: 66, Mismatches: 18, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
6 9 0.14
7 55 0.83
8 2 0.03
ACGTcount: A:0.41, C:0.34, G:0.03, T:0.22
Consensus pattern (7 bp):
CCTAAAC
Found at i:46797 original size:14 final size:14
Alignment explanation
Indices: 46769--46813 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
46759 GTTAGATTAC
*
46769 ACCCTAAACTCTAA
1 ACCCTAAACTATAA
* *
46783 ACTCTAAATTATAA
1 ACCCTAAACTATAA
46797 ACCCTAAACTATAA
1 ACCCTAAACTATAA
46811 ACC
1 ACC
46814 ATAAGCCCTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (14 bp):
ACCCTAAACTATAA
Found at i:46803 original size:21 final size:21
Alignment explanation
Indices: 46773--46834 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
46763 GATTACACCC
* * **
46773 TAAACTCTAAACTCTAAATTA
1 TAAACCCTAAACTATAAACCA
46794 TAAACCCTAAACTATAAACCA
1 TAAACCCTAAACTATAAACCA
*
46815 TAAGCCCTAAACCT-TAAACC
1 TAAACCCTAAA-CTATAAACC
46835 CTTAATCTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 33 0.94
22 2 0.06
ACGTcount: A:0.47, C:0.27, G:0.02, T:0.24
Consensus pattern (21 bp):
TAAACCCTAAACTATAAACCA
Done.