Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003773.1 Hibiscus syriacus cultivar Beakdansim tig00008077_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: 61800
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1828 original size:23 final size:24
Alignment explanation
Indices: 1798--1851 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
1788 AATTACCACT
1798 CACGTTACG-TTTTTCTCTGGGCG
1 CACGTTACGTTTTTTCTCTGGGCG
*
1821 CACGTTACGTTTTTTTTCTGGGCG
1 CACGTTACGTTTTTTCTCTGGGCG
1845 CACGTTA
1 CACGTTA
1852 ACAGGACTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 9 0.31
24 20 0.69
ACGTcount: A:0.11, C:0.24, G:0.24, T:0.41
Consensus pattern (24 bp):
CACGTTACGTTTTTTCTCTGGGCG
Found at i:5400 original size:15 final size:15
Alignment explanation
Indices: 5382--5431 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
5372 TAAGAAGAAG
5382 AGGATATGGAAGTTA
1 AGGATATGGAAGTTA
* *
5397 AGGATAAGG-AG-AA
1 AGGATATGGAAGTTA
*
5410 GAGGATATGAAAGTTA
1 -AGGATATGGAAGTTA
5426 AGGATA
1 AGGATA
5432 GGATAAATGA
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
13 1 0.04
14 9 0.33
15 16 0.59
16 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.34, T:0.20
Consensus pattern (15 bp):
AGGATATGGAAGTTA
Found at i:5414 original size:29 final size:29
Alignment explanation
Indices: 5372--5431 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
5362 TTGAATTTCC
*
5372 TAAGAAGAAGAGGATATGGAAGTTAAGGA
1 TAAGAAGAAGAGGATATGAAAGTTAAGGA
*
5401 TAAGGAGAAGAGGATATGAAAGTTAAGGA
1 TAAGAAGAAGAGGATATGAAAGTTAAGGA
5430 TA
1 TA
5432 GGATAAATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.33, T:0.18
Consensus pattern (29 bp):
TAAGAAGAAGAGGATATGAAAGTTAAGGA
Found at i:6774 original size:32 final size:32
Alignment explanation
Indices: 6700--6774 Score: 107
Period size: 32 Copynumber: 2.3 Consensus size: 32
6690 AGAGTCGAGG
* *
6700 GTTACCTATGCCTTTCGAGACATATGGACAGT
1 GTTACCTATGTCTTTCGAGACATATGAACAGT
*
6732 GTTACCTATGTCTTTCGGGACATATGAACA-T
1 GTTACCTATGTCTTTCGAGACATATGAACAGT
6763 GATTACCTATGT
1 G-TTACCTATGT
6775 TCCAAGGAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
31 2 0.05
32 37 0.95
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (32 bp):
GTTACCTATGTCTTTCGAGACATATGAACAGT
Found at i:11306 original size:32 final size:32
Alignment explanation
Indices: 11232--11306 Score: 118
Period size: 31 Copynumber: 2.4 Consensus size: 32
11222 AAGAGTCGAG
11232 GGTTACCTATG-CCTTTCGAGACATATGGACA
1 GGTTACCTATGTCCTTTCGAGACATATGGACA
*
11263 TGTTACCTATGTCC-TTCGAGACATATGGACA
1 GGTTACCTATGTCCTTTCGAGACATATGGACA
11294 GGATTACCTATGT
1 GG-TTACCTATGT
11307 TCTAAGGAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
31 28 0.70
32 12 0.30
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.32
Consensus pattern (32 bp):
GGTTACCTATGTCCTTTCGAGACATATGGACA
Found at i:25459 original size:7 final size:7
Alignment explanation
Indices: 25447--25505 Score: 100
Period size: 7 Copynumber: 8.4 Consensus size: 7
25437 AATAAAGTAA
*
25447 CTTCTCT
1 CTTCCCT
*
25454 CTTCTCT
1 CTTCCCT
25461 CTTCCCT
1 CTTCCCT
25468 CTTCCCT
1 CTTCCCT
25475 CTTCCCT
1 CTTCCCT
25482 CTTCCCT
1 CTTCCCT
25489 CTTCCCT
1 CTTCCCT
25496 CTTCCCT
1 CTTCCCT
25503 CTT
1 CTT
25506 TTTATTTCCA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
7 51 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (7 bp):
CTTCCCT
Found at i:45193 original size:29 final size:30
Alignment explanation
Indices: 45148--45224 Score: 79
Period size: 29 Copynumber: 2.6 Consensus size: 30
45138 TTTGTTATTT
* *
45148 CTATTTT-AGTCCCTTAAGCTTCTATTT-TT
1 CTATTTTGA-TCCTTTAAGCTTCTATTTGTA
**
45177 CTATTTTGGAT-CTTTAAATTTCTATTTGTA
1 CTATTTT-GATCCTTTAAGCTTCTATTTGTA
45207 CTATTTTGATCCTTTAAG
1 CTATTTTGATCCTTTAAG
45225 TTTTTGTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
29 23 0.59
30 15 0.38
31 1 0.03
ACGTcount: A:0.21, C:0.16, G:0.09, T:0.55
Consensus pattern (30 bp):
CTATTTTGATCCTTTAAGCTTCTATTTGTA
Found at i:45213 original size:30 final size:29
Alignment explanation
Indices: 45167--45223 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
45157 TCCCTTAAGC
*
45167 TTCTATTTTTCTATTTTGGAT-CTTTAAAT
1 TTCTATTTTACTATTTT-GATCCTTTAAAT
45196 TTCTATTTGTACTATTTTGATCCTTTAA
1 TTCTATTT-TACTATTTTGATCCTTTAA
45224 GTTTTTGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.21, C:0.12, G:0.07, T:0.60
Consensus pattern (29 bp):
TTCTATTTTACTATTTTGATCCTTTAAAT
Found at i:46209 original size:2 final size:2
Alignment explanation
Indices: 46204--46230 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
46194 AATAGTTATG
46204 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
46231 CAAATCAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:48945 original size:24 final size:24
Alignment explanation
Indices: 48908--48957 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
48898 AAAATGGTTG
* *
48908 CTCTACTAATGGGAGTAGTCAAAC
1 CTCTACTAACGGGAGTAGTAAAAC
*
48932 CTCTATTAACGGGAGTAGTAAAAC
1 CTCTACTAACGGGAGTAGTAAAAC
48956 CT
1 CT
48958 ATACCATGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (24 bp):
CTCTACTAACGGGAGTAGTAAAAC
Found at i:52737 original size:9 final size:9
Alignment explanation
Indices: 52723--52758 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
52713 AGTCTTCATA
*
52723 CTTCTCCTT
1 CTTCTCCTC
52732 CTTCTCCTC
1 CTTCTCCTC
52741 CTTCTCCTC
1 CTTCTCCTC
*
52750 CTCCTCCTC
1 CTTCTCCTC
52759 GATTTCCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (9 bp):
CTTCTCCTC
Found at i:54697 original size:22 final size:22
Alignment explanation
Indices: 54643--54700 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 22
54633 GCAACGCGAT
* *
54643 TTTGAAAAATGTGTTGCGATAG
1 TTTGAAAAATGTGTTGTGAGAG
54665 -TT--AAAATGTGTTGTGAGAG
1 TTTGAAAAATGTGTTGTGAGAG
*
54684 TTTGAAAAACGTGTTGT
1 TTTGAAAAATGTGTTGT
54701 TGCGATAGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 15 0.50
20 2 0.07
21 2 0.07
22 11 0.37
ACGTcount: A:0.31, C:0.03, G:0.28, T:0.38
Consensus pattern (22 bp):
TTTGAAAAATGTGTTGTGAGAG
Found at i:54714 original size:22 final size:22
Alignment explanation
Indices: 54654--54714 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 22
54644 TTGAAAAATG
* *
54654 TGTTGCGATAGTTAAAATGTGT
1 TGTTGCGATAGTGAAAACGTGT
* *
54676 TG-TGAGAGT-TTGAAAAACGTGT
1 TGTTGCGA-TAGTG-AAAACGTGT
54698 TGTTGCGATAGTGAAAA
1 TGTTGCGATAGTGAAAA
54715 ATCCAAAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
21 5 0.17
22 18 0.62
23 6 0.21
ACGTcount: A:0.31, C:0.05, G:0.30, T:0.34
Consensus pattern (22 bp):
TGTTGCGATAGTGAAAACGTGT
Found at i:55135 original size:21 final size:21
Alignment explanation
Indices: 55111--55422 Score: 116
Period size: 21 Copynumber: 15.2 Consensus size: 21
55101 CGTTGCGATT
55111 TTGGAAAATCGCAACGCGAAC
1 TTGGAAAATCGCAACGCGAAC
** *
55132 TTGGACTATCGCAA--CGAAT
1 TTGGAAAATCGCAACGCGAAC
*
55151 TTGAAAAATCGCAACGCGAAC
1 TTGGAAAATCGCAACGCGAAC
* * *
55172 TT-GAACTATCGCAA--CAAAT
1 TTGGAA-AATCGCAACGCGAAC
* *
55191 TTGAAAAATCGCAACACGAAC
1 TTGGAAAATCGCAACGCGAAC
* *
55212 TTCGACTAACTATCGCAA--CGAAT
1 TTGGA--AA--ATCGCAACGCGAAC
* *
55235 TTGAAAAATCGCAACGTGAAC
1 TTGGAAAATCGCAACGCGAAC
* *
55256 TT--AAACTATCACAA--CGAAT
1 TTGGAAA--ATCGCAACGCGAAC
* *
55275 TTGGAAAATCACAACGTGAAC
1 TTGGAAAATCGCAACGCGAAC
* ** *
55296 TTAGACTATCGCAA--CGAAT
1 TTGGAAAATCGCAACGCGAAC
* *
55315 TTGAAAAATCGCAACACGAAC
1 TTGGAAAATCGCAACGCGAAC
* *
55336 TT-CAACTATCGCAACGCGAAC
1 TTGGAA-AATCGCAACGCGAAC
* ** * **
55357 TTCGACTATCGCAATGTAAAC
1 TTGGAAAATCGCAACGCGAAC
** *
55378 TTGGACTATCGCAA--CGAAT
1 TTGGAAAATCGCAACGCGAAC
* *
55397 TTGAAAAATCGCAACGTGAAC
1 TTGGAAAATCGCAACGCGAAC
55418 TTGGA
1 TTGGA
55423 CTATCACAAC
Statistics
Matches: 211, Mismatches: 56, Indels: 48
0.67 0.18 0.15
Matches are distributed among these distances:
19 75 0.36
20 6 0.03
21 113 0.54
22 1 0.00
23 9 0.04
25 7 0.03
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.21
Consensus pattern (21 bp):
TTGGAAAATCGCAACGCGAAC
Found at i:55168 original size:40 final size:40
Alignment explanation
Indices: 55110--55463 Score: 399
Period size: 40 Copynumber: 8.7 Consensus size: 40
55100 TCGTTGCGAT
* *
55110 TTTGGAAAATCGCAACGCGAACTTGGACTATCGCAACGAA
1 TTTGAAAAATCGCAACGCGAACTTGAACTATCGCAACGAA
*
55150 TTTGAAAAATCGCAACGCGAACTTGAACTATCGCAACAAA
1 TTTGAAAAATCGCAACGCGAACTTGAACTATCGCAACGAA
*
55190 TTTGAAAAATCGCAACACGAACTTCGACTAACTATCGCAACGAA
1 TTTGAAAAATCGCAACGCGAACTT-G---AACTATCGCAACGAA
* * *
55234 TTTGAAAAATCGCAACGTGAACTTAAACTATCACAACGAA
1 TTTGAAAAATCGCAACGCGAACTTGAACTATCGCAACGAA
* * *
55274 TTTGGAAAATCACAACGTGAACTT-AGACTATCGCAACGAA
1 TTTGAAAAATCGCAACGCGAACTTGA-ACTATCGCAACGAA
* *
55314 TTTGAAAAATCGCAACACGAACTTCAACTATCGCAACGCGAA
1 TTTGAAAAATCGCAACGCGAACTTGAACTATCGCAA--CGAA
* ** * ** *
55356 CTTCG-ACTATCGCAATGTAAACTTGGACTATCGCAACGAA
1 -TTTGAAAAATCGCAACGCGAACTTGAACTATCGCAACGAA
* * *
55396 TTTGAAAAATCGCAACGTGAACTTGGACTATCACAACGAA
1 TTTGAAAAATCGCAACGCGAACTTGAACTATCGCAACGAA
*
55436 TTT-AAAAATCGCAACACGAACTTCGAAC
1 TTTGAAAAATCGCAACGCGAACTT-GAAC
55464 GTGAACTTGG
Statistics
Matches: 269, Mismatches: 34, Indels: 22
0.83 0.10 0.07
Matches are distributed among these distances:
39 22 0.08
40 179 0.67
41 2 0.01
42 27 0.10
43 3 0.01
44 36 0.13
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.21
Consensus pattern (40 bp):
TTTGAAAAATCGCAACGCGAACTTGAACTATCGCAACGAA
Found at i:55277 original size:124 final size:124
Alignment explanation
Indices: 55114--55461 Score: 476
Period size: 124 Copynumber: 2.8 Consensus size: 124
55104 TGCGATTTTG
* *
55114 GAAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGAAAAATCGCAACGCGAACTTGAACT
1 GAAAATCGCAACGTGAACTTGGACTATCGCAACGAATTTGAAAAATCGCAACGTGAACTTGAACT
*
55179 ATCGCAACAAATTTGAAAAATCGCAACACGAACTTCGACTAACTATCGCAA-CGAA-TTT
66 ATCGCAACGAATTTGAAAAATCGCAACACGAACTTCGAC-AACTATCGCAACCGAACTTT
** * * *
55237 GAAAAATCGCAACGTGAACTTAAACTATCACAACGAATTTGGAAAATCACAACGTGAACTT-AGA
1 G-AAAATCGCAACGTGAACTTGGACTATCGCAACGAATTTGAAAAATCGCAACGTGAACTTGA-A
*
55301 CTATCGCAACGAATTTGAAAAATCGCAACACGAACTT---CAACTATCGCAACGCGAACTTC
64 CTATCGCAACGAATTTGAAAAATCGCAACACGAACTTCGACAACTATCGCAAC-CGAACTTT
** * * *
55360 GACTATCGCAATGTAAACTTGGACTATCGCAACGAATTTGAAAAATCGCAACGTGAACTTGGACT
1 GAAAATCGCAACGTGAACTTGGACTATCGCAACGAATTTGAAAAATCGCAACGTGAACTTGAACT
*
55425 ATCACAACGAATTT-AAAAATCGCAACACGAACTTCGA
66 ATCGCAACGAATTTGAAAAATCGCAACACGAACTTCGA
55462 ACGTGAACTT
Statistics
Matches: 196, Mismatches: 20, Indels: 17
0.84 0.09 0.07
Matches are distributed among these distances:
120 11 0.06
121 21 0.11
122 70 0.36
123 5 0.03
124 89 0.45
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.21
Consensus pattern (124 bp):
GAAAATCGCAACGTGAACTTGGACTATCGCAACGAATTTGAAAAATCGCAACGTGAACTTGAACT
ATCGCAACGAATTTGAAAAATCGCAACACGAACTTCGACAACTATCGCAACCGAACTTT
Found at i:55334 original size:61 final size:59
Alignment explanation
Indices: 55145--55552 Score: 284
Period size: 61 Copynumber: 6.8 Consensus size: 59
55135 GACTATCGCA
* * * *
55145 ACGAATTTGAAAAATCGCAACGCGAACTTGAACTATCGCAACAAATTTGAAAAATCGCAAC
1 ACGAACTT-AAAAATCGCAACGTGAACTTGGACTATCGCAACGAATTT-AAAAATCGCAAC
* * * ** * * *
55206 ACGAACTTCGACTAACTATCGCAAC--GAATTTGAAAAATCGCAACGTGAACTTAAACTATCAC-
1 ACGAACTT--A--AA-AATCGCAACGTGAACTTGGACTATCGCAAC--GAATTTAAA-AATCGCA
55268 A-
58 AC
* * * *
55269 ACGAATTTGGAAAATCACAACGTGAACTTAGACTATCGCAACGAATTTGAAAAATCGCAAC
1 ACGAACTT-AAAAATCGCAACGTGAACTTGGACTATCGCAACGAATTT-AAAAATCGCAAC
** * * * ** **
55330 ACGAACTTCAACTATCGCAACGCGAACTTCGACTATCGCAATGTAAACTTGGACTATCGC-A-
1 ACGAACTT-AAAAATCGCAACGTGAACTTGGACTATCGCAACG--AA-TTTAAAAATCGCAAC
* *
55391 ACGAATTTGAAAAATCGCAACGTGAACTTGGACTATCACAACGAATTTAAAAATCGCAAC
1 ACGAACTT-AAAAATCGCAACGTGAACTTGGACTATCGCAACGAATTTAAAAATCGCAAC
*
55451 ACGAAC-T-----TCG-AACGTGAACTTGGACTATCGCAACGAATTTAGAAAATCACAAC
1 ACGAACTTAAAAATCGCAACGTGAACTTGGACTATCGCAACGAATTTA-AAAATCGCAAC
**
55504 ACGAACTTCAACTATCGCAACGTGAACTTGGACTATCGCAACGAATTTA
1 ACGAACTT-AAAAATCGCAACGTGAACTTGGACTATCGCAACGAATTTA
55553 GACTAACGTA
Statistics
Matches: 272, Mismatches: 49, Indels: 52
0.73 0.13 0.14
Matches are distributed among these distances:
52 30 0.11
53 19 0.07
54 1 0.00
58 8 0.03
59 20 0.07
60 14 0.05
61 121 0.44
62 4 0.01
63 31 0.11
64 8 0.03
65 16 0.06
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.22
Consensus pattern (59 bp):
ACGAACTTAAAAATCGCAACGTGAACTTGGACTATCGCAACGAATTTAAAAATCGCAAC
Found at i:55409 original size:19 final size:19
Alignment explanation
Indices: 55385--55450 Score: 62
Period size: 21 Copynumber: 3.4 Consensus size: 19
55375 AACTTGGACT
55385 ATCGCAACGAATTTGAAAA
1 ATCGCAACGAATTTGAAAA
* * **
55404 ATCGCAACGTGAACTTGGACT
1 ATCGCAAC--GAATTTGAAAA
*
55425 ATCACAACGAATTT-AAAA
1 ATCGCAACGAATTTGAAAA
55443 ATCGCAAC
1 ATCGCAAC
55451 ACGAACTTCG
Statistics
Matches: 35, Mismatches: 10, Indels: 5
0.70 0.20 0.10
Matches are distributed among these distances:
18 8 0.23
19 13 0.37
21 14 0.40
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.21
Consensus pattern (19 bp):
ATCGCAACGAATTTGAAAA
Found at i:55546 original size:21 final size:21
Alignment explanation
Indices: 55461--55546 Score: 77
Period size: 21 Copynumber: 4.2 Consensus size: 21
55451 ACGAACTTCG
55461 AACGTGAACTTGGACTATCGC
1 AACGTGAACTTGGACTATCGC
* * ** *
55482 AAC--GAATTTAGAAAATCAC
1 AACGTGAACTTGGACTATCGC
** **
55501 AACACGAACTTCAACTATCGC
1 AACGTGAACTTGGACTATCGC
55522 AACGTGAACTTGGACTATCGC
1 AACGTGAACTTGGACTATCGC
55543 AACG
1 AACG
55547 AATTTAGACT
Statistics
Matches: 48, Mismatches: 15, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
19 14 0.29
21 34 0.71
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.21
Consensus pattern (21 bp):
AACGTGAACTTGGACTATCGC
Found at i:61444 original size:18 final size:18
Alignment explanation
Indices: 61423--61457 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
61413 TAATTTACTC
61423 TATTTTAATAAATTCAAT
1 TATTTTAATAAATTCAAT
* *
61441 TATTTTATTCAATTCAA
1 TATTTTAATAAATTCAA
61458 CGTTGAATTT
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:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTTTAATAAATTCAAT
Done.