Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003254.1 Hibiscus syriacus cultivar Beakdansim tig00006839_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: 29100
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:6196 original size:63 final size:63
Alignment explanation
Indices: 6118--6253 Score: 209
Period size: 63 Copynumber: 2.2 Consensus size: 63
6108 ATTCTAAGTA
** * * *
6118 GAGTGCATCGATGCATCCTCAATTAATTGAACATCGAATGTCGTTAGTGCATCGATGCATAAG
1 GAGTGCATCGATGCATCCTCAATTAAAGGAACATCGAATGCCCTCAGTGCATCGATGCATAAG
**
6181 GAGTGCATCGATGCATTTTCAATTAAAGGAACATCGAATGCCCTCAGTGCATCGATGCATAAG
1 GAGTGCATCGATGCATCCTCAATTAAAGGAACATCGAATGCCCTCAGTGCATCGATGCATAAG
6244 GAGTGCATCG
1 GAGTGCATCG
6254 GTGTACCTCC
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 66 1.00
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (63 bp):
GAGTGCATCGATGCATCCTCAATTAAAGGAACATCGAATGCCCTCAGTGCATCGATGCATAAG
Found at i:6277 original size:63 final size:63
Alignment explanation
Indices: 6118--6283 Score: 194
Period size: 63 Copynumber: 2.6 Consensus size: 63
6108 ATTCTAAGTA
* * * *
6118 GAGTGCATCGATGCATCCTCAATTAATTG-AACATCGAATGTCGTTAGTGCATCGATGCATAAG
1 GAGTGCATCGATGCATCCTCAATTAA-AGAAACATCGAATGCCCTCAGTGCATCGATGCATAAG
** *
6181 GAGTGCATCGATGCATTTTCAATTAAAGGAACATCGAATGCCCTCAGTGCATCGATGCATAAG
1 GAGTGCATCGATGCATCCTCAATTAAAGAAACATCGAATGCCCTCAGTGCATCGATGCATAAG
* * *
6244 GAGTGCATCGGTGTA-CCTC-CTTAAAAGAAAACATCGAATG
1 GAGTGCATCGATGCATCCTCAATT-AAAG-AAACATCGAATG
6284 TAATTTGTGT
Statistics
Matches: 88, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
61 2 0.02
62 7 0.08
63 79 0.90
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (63 bp):
GAGTGCATCGATGCATCCTCAATTAAAGAAACATCGAATGCCCTCAGTGCATCGATGCATAAG
Found at i:6335 original size:24 final size:23
Alignment explanation
Indices: 6308--6365 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 23
6298 ATGCACAGTT
6308 AGTGCATCGATGCACACACTGTAG
1 AGTGCATCGATGCA-ACACTGTAG
*
6332 AGTGCATCGAT---ATACTGTAG
1 AGTGCATCGATGCAACACTGTAG
6352 AGTGCATCGATGCA
1 AGTGCATCGATGCA
6366 TACCTTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 19 0.63
24 11 0.37
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (23 bp):
AGTGCATCGATGCAACACTGTAG
Found at i:6747 original size:30 final size:28
Alignment explanation
Indices: 6692--6754 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
6682 TTATGAGTTA
* *
6692 TGATAAAGGTATGGAAATGATGTCTATG
1 TGATAAAGGTATGAAAATGATGTCTACG
*
6720 TGATAAAGGTATGAAAATAATATGTCTACG
1 TGATAAAGGTATGAAAAT--GATGTCTACG
6750 TGATA
1 TGATA
6755 CAAATTATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 17 0.57
30 13 0.43
ACGTcount: A:0.40, C:0.05, G:0.24, T:0.32
Consensus pattern (28 bp):
TGATAAAGGTATGAAAATGATGTCTACG
Found at i:6990 original size:23 final size:23
Alignment explanation
Indices: 6963--7023 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
6953 TTATATGGCA
*
6963 CGGTGCAATTCTACGCGGCACTC
1 CGGTGCAATTATACGCGGCACTC
* * ** *
6986 CGGTGTAATTTTACATGGCACTT
1 CGGTGCAATTATACGCGGCACTC
7009 CGGTGCAATTATACG
1 CGGTGCAATTATACG
7024 AGCTGTGGTG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.30
Consensus pattern (23 bp):
CGGTGCAATTATACGCGGCACTC
Found at i:13579 original size:30 final size:30
Alignment explanation
Indices: 13545--13613 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
13535 TTATATGAGT
* *
13545 TATGTGATAAAGGTATGGAAATGATATGTC
1 TATGTGATAAAGGTATGAAAATAATATGTC
13575 TATGTGATAAAGGTATGAAAATAATATGTC
1 TATGTGATAAAGGTATGAAAATAATATGTC
*
13605 TACGTGATA
1 TATGTGATA
13614 CAAACTATGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.39, C:0.04, G:0.23, T:0.33
Consensus pattern (30 bp):
TATGTGATAAAGGTATGAAAATAATATGTC
Found at i:13854 original size:23 final size:23
Alignment explanation
Indices: 13823--13888 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 23
13813 ATTATTATGG
13823 CACTACGGTGCAATTCTACGCGA
1 CACTACGGTGCAATTCTACGCGA
* * * *
13846 CACTCCGGTGTAATTCTACGTGG
1 CACTACGGTGCAATTCTACGCGA
* *
13869 CACTTCGGTGCAATTATACG
1 CACTACGGTGCAATTCTACG
13889 AGTGTGGTGA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (23 bp):
CACTACGGTGCAATTCTACGCGA
Found at i:14703 original size:32 final size:33
Alignment explanation
Indices: 14662--14745 Score: 102
Period size: 32 Copynumber: 2.6 Consensus size: 33
14652 CAATCTAAGG
* *
14662 GAGTACCTTGGGGCCTTAGAGCCTA-TCCAAGA
1 GAGTACCTTGGGGCCTAAGAGCCTACTCAAAGA
** *
14694 GAGTACCTT-GAACCTAAAAGCCTACTCAAAGA
1 GAGTACCTTGGGGCCTAAGAGCCTACTCAAAGA
14726 -AGTACCTTGGGGCCTAAGAG
1 GAGTACCTTGGGGCCTAAGAG
14746 TATACCCAAG
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
31 19 0.45
32 23 0.55
ACGTcount: A:0.31, C:0.24, G:0.25, T:0.20
Consensus pattern (33 bp):
GAGTACCTTGGGGCCTAAGAGCCTACTCAAAGA
Found at i:16757 original size:16 final size:17
Alignment explanation
Indices: 16735--16769 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
16725 ATAAAATATG
*
16735 ACTTTTTGAAAAAGTTA
1 ACTTTTGGAAAAAGTTA
*
16752 ACTTTTGGTAAAAGTTA
1 ACTTTTGGAAAAAGTTA
16769 A
1 A
16770 TGTTGGTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.06, G:0.14, T:0.40
Consensus pattern (17 bp):
ACTTTTGGAAAAAGTTA
Found at i:16775 original size:16 final size:17
Alignment explanation
Indices: 16744--16787 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
16734 GACTTTTTGA
*
16744 AAAAGTTAACTTTTGGT
1 AAAAGTTAACTGTTGGT
16761 AAAAGTTAA-TGTTGGT
1 AAAAGTTAACTGTTGGT
* *
16777 CAAAGTCAACT
1 AAAAGTTAACT
16788 CTGATCAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (17 bp):
AAAAGTTAACTGTTGGT
Found at i:19387 original size:26 final size:26
Alignment explanation
Indices: 19355--19415 Score: 104
Period size: 26 Copynumber: 2.3 Consensus size: 26
19345 CCAAGGCTCT
*
19355 TCTTTAATTCTAGGACTTTCCTAGCT
1 TCTTTAATTCTAGGACTTTCCTAGCC
*
19381 TTTTTAATTCTAGGACTTTCCTAGCC
1 TCTTTAATTCTAGGACTTTCCTAGCC
19407 TCTTTAATT
1 TCTTTAATT
19416 TGTTTTTCCC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.20, C:0.21, G:0.10, T:0.49
Consensus pattern (26 bp):
TCTTTAATTCTAGGACTTTCCTAGCC
Found at i:20292 original size:29 final size:29
Alignment explanation
Indices: 20250--20307 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
20240 ATAAACGACA
*
20250 TATTCTCTGCTTTATTTTTCATTATGATG
1 TATTCTCTGCTTTATTTTTCAATATGATG
*
20279 TATTCTCTGTTTTATTTTTCAATATGATG
1 TATTCTCTGCTTTATTTTTCAATATGATG
20308 AACTGAGAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.19, C:0.12, G:0.10, T:0.59
Consensus pattern (29 bp):
TATTCTCTGCTTTATTTTTCAATATGATG
Found at i:25458 original size:40 final size:38
Alignment explanation
Indices: 25378--25509 Score: 151
Period size: 38 Copynumber: 3.4 Consensus size: 38
25368 TACTCTAGAT
* * * * *
25378 ATTTCAAA-TATTCTATAATTTTAAAAAATTTCATTGAG
1 ATTTTAAATTATTATATAA-TTTAAAAAAATTAAATGAG
25416 ATTTTAAATTATTATATAATATTAAAAAAATTAAATGTAG
1 ATTTTAAATTATTATATAAT-TTAAAAAAATTAAATG-AG
* *
25456 ATTTTAAATTATTATATAATTT-TAAAAACTAAATGATG
1 ATTTTAAATTATTATATAATTTAAAAAAATTAAATGA-G
25494 ATTTTAAATTATTATA
1 ATTTTAAATTATTATA
25510 ATTTATTAAT
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
37 1 0.01
38 36 0.43
39 24 0.29
40 22 0.27
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (38 bp):
ATTTTAAATTATTATATAATTTAAAAAAATTAAATGAG
Found at i:25477 original size:18 final size:18
Alignment explanation
Indices: 25416--25481 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 18
25406 TTTCATTGAG
25416 ATTTTAAATTATTATATA
1 ATTTTAAATTATTATATA
* ** *
25434 ATATTAAAAAAATTAAATGTA
1 AT-TTTAAATTATT--ATATA
25455 GATTTTAAATTATTATATA
1 -ATTTTAAATTATTATATA
25474 ATTTTAAA
1 ATTTTAAA
25482 AACTAAATGA
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
18 10 0.28
19 12 0.33
21 12 0.33
22 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
ATTTTAAATTATTATATA
Found at i:26097 original size:2 final size:2
Alignment explanation
Indices: 26090--26161 Score: 137
Period size: 2 Copynumber: 36.5 Consensus size: 2
26080 TTTGTTTGCT
26090 TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
26131 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
26162 TTGAAAATGT
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 68 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:26330 original size:34 final size:34
Alignment explanation
Indices: 26212--26386 Score: 138
Period size: 34 Copynumber: 5.0 Consensus size: 34
26202 ATCAGTTTTC
* * **
26212 GAAAATAAGTATATTATATGATTTTTGAAATTTTT
1 GAAAATAA-TATATTATATAATTTTTAAAACATTT
** * * * *
26247 TTATAT-ATATAATATATAGTTTTAAAAACATGTTT
1 GAAAATAATATATTATATAATTTTTAAAACA--TTT
26282 GAAAATATTTATATATTATATAATTTTTAAAACATTT
1 GAAAATA---ATATATTATATAATTTTTAAAACATTT
** *
26319 GAAAATAATATAACATATAGTTTTTAAAACATTT
1 GAAAATAATATATTATATAATTTTTAAAACATTT
* *
26353 TAAAA-ATATATATTATATAATTTTTAAAATATTT
1 GAAAATA-ATATATTATATAATTTTTAAAACATTT
26387 TGGAAATATA
Statistics
Matches: 109, Mismatches: 24, Indels: 15
0.74 0.16 0.10
Matches are distributed among these distances:
33 17 0.16
34 52 0.48
35 9 0.08
37 10 0.09
39 21 0.19
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (34 bp):
GAAAATAATATATTATATAATTTTTAAAACATTT
Found at i:26373 original size:68 final size:72
Alignment explanation
Indices: 26253--26386 Score: 204
Period size: 68 Copynumber: 1.9 Consensus size: 72
26243 TTTTTTATAT
*
26253 ATATAATATATAGTTTTAAAAACATGTTTGAAAATATTTATATATTATATAATTTTTAAAACATT
1 ATATAACATATAGTTTTAAAAACATGTTTGAAAATA-TTATATATTATATAATTTTTAAAACATT
26318 TGAAAATA
65 TGAAAATA
* *
26326 ATATAACATATAGTTTTTAAAACAT-TTT-AAAA-A-TATATATTATATAATTTTTAAAATATTT
1 ATATAACATATAGTTTTAAAAACATGTTTGAAAATATTATATATTATATAATTTTTAAAACATTT
26387 TGGAAATATA
Statistics
Matches: 58, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
68 27 0.47
70 1 0.02
71 4 0.07
72 3 0.05
73 23 0.40
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.46
Consensus pattern (72 bp):
ATATAACATATAGTTTTAAAAACATGTTTGAAAATATTATATATTATATAATTTTTAAAACATTT
GAAAATA
Found at i:26387 original size:34 final size:34
Alignment explanation
Indices: 26142--26396 Score: 131
Period size: 34 Copynumber: 7.1 Consensus size: 34
26132 ATATATATAT
* *
26142 ATATATATATATATATATATTTGAAAAT-GTTTAGAAA
1 ATATATAT-TATATA-AT-TTTTAAAATATTTTA-AAA
* ** *
26179 A-ATATAGTATATAATTTCCATAAATCAGTTTTCGAAA
1 ATATATATTATATAATTTTTA-AAAT-A-TTTT-AAAA
* * ** *
26216 ATAAGTATATTATATGATTTTTGAAAT-TTTTTTAT
1 AT-A-TATATTATATAATTTTTAAAATATTTTAAAA
* * * *
26251 ATATATAATATATAGTTTTAAAAACATGTTTGAAAA
1 ATATATATTATATAATTTTTAAAATAT-TTT-AAAA
* *
26287 TATTTATATATTATATAATTTTTAAAACA-TTTGAAA
1 -A--TATATATTATATAATTTTTAAAATATTTTAAAA
** * *
26323 ATAATATAACATATAGTTTTTAAAACATTTTAAAA
1 AT-ATATATTATATAATTTTTAAAATATTTTAAAA
**
26358 ATATATATTATATAATTTTTAAAATATTTTGGAA
1 ATATATATTATATAATTTTTAAAATATTTTAAAA
26392 ATATA
1 ATATA
26397 ATACAATTTT
Statistics
Matches: 166, Mismatches: 36, Indels: 35
0.70 0.15 0.15
Matches are distributed among these distances:
33 20 0.12
34 60 0.36
35 21 0.13
36 13 0.08
37 12 0.07
39 27 0.16
40 13 0.08
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (34 bp):
ATATATATTATATAATTTTTAAAATATTTTAAAA
Found at i:27873 original size:13 final size:13
Alignment explanation
Indices: 27855--27883 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
27845 CGAACCGAAT
27855 TTTTAAATTTTAA
1 TTTTAAATTTTAA
27868 TTTTAAATTTTAA
1 TTTTAAATTTTAA
27881 TTT
1 TTT
27884 CGCAACTAAG
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:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TTTTAAATTTTAA
Done.