Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007161.1 Hibiscus syriacus cultivar Beakdansim tig00018764_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: 63879
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:9366 original size:116 final size:118
Alignment explanation
Indices: 9170--9449 Score: 494
Period size: 116 Copynumber: 2.4 Consensus size: 118
9160 CTAATTATCA
9170 ATTATTGTATTAATTTTTATGTTAATATTAATGATA-TTATTTTTTTATGATAGGTGTTTTTGAT
1 ATTATTGTATTAATTTTTATGTTAATATTAATGATATTTA-TTTTTTATGATAGGTGTTTTTGAT
* *
9234 CACTCTAAACAGTTGAGTTTGAATTATAATAAAACTAATTATCATTATATTATT
65 CACTCTAAACAATTGAGTTTGAATTATAATAAAACTAATTATCATTATAATATT
**
9288 ATTATTGTATTAA-TTTTATGTTAACGTTAATGATATTTATTTTTTATGAT-GGTGTTTTTGATC
1 ATTATTGTATTAATTTTTATGTTAATATTAATGATATTTATTTTTTATGATAGGTGTTTTTGATC
9351 ACTCTAAACAATTGAGTTTGAATTATAATAAAACTAATTATCATTATAATATT
66 ACTCTAAACAATTGAGTTTGAATTATAATAAAACTAATTATCATTATAATATT
9404 ATTATTGTATTAATTTTTATGTTAATATTAATGATATTTATTTTTT
1 ATTATTGTATTAATTTTTATGTTAATATTAATGATATTTATTTTTT
9450 TAACGTGGAC
Statistics
Matches: 154, Mismatches: 6, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
116 77 0.50
117 61 0.40
118 16 0.10
ACGTcount: A:0.34, C:0.05, G:0.10, T:0.52
Consensus pattern (118 bp):
ATTATTGTATTAATTTTTATGTTAATATTAATGATATTTATTTTTTATGATAGGTGTTTTTGATC
ACTCTAAACAATTGAGTTTGAATTATAATAAAACTAATTATCATTATAATATT
Found at i:10890 original size:36 final size:37
Alignment explanation
Indices: 10819--10903 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 37
10809 ATCCCATTAT
*
10819 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
* *
10855 TATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
1 CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
10891 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
10904 TTGGTTACCA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
36 13 0.30
37 30 0.70
ACGTcount: A:0.42, C:0.20, G:0.05, T:0.33
Consensus pattern (37 bp):
CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
Found at i:20161 original size:6 final size:6
Alignment explanation
Indices: 20150--20180 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
20140 ACCACTCGCT
20150 CCCTTC CCCTTC CCCTTC CCCTTC CTCCTTC
1 CCCTTC CCCTTC CCCTTC CCCTTC C-CCTTC
20181 ACGTTCTCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.79
7 5 0.21
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (6 bp):
CCCTTC
Found at i:23564 original size:21 final size:19
Alignment explanation
Indices: 23535--23573 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
23525 AATTTTGGTA
*
23535 AATTTAATAAATATATTTAAC
1 AATTCAATAAA-AT-TTTAAC
23556 AATTCAATAAAATTTTAA
1 AATTCAATAAAATTTTAA
23574 GATTTATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 10 0.59
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
AATTCAATAAAATTTTAAC
Found at i:28497 original size:33 final size:38
Alignment explanation
Indices: 28460--28551 Score: 96
Period size: 39 Copynumber: 2.6 Consensus size: 38
28450 TATTAAATTA
28460 TATTG-ATAATT-T-TA-ATAATATA-ATATTATACTT
1 TATTGTATAATTATATATATAATATATATATTATACTT
28493 TATTGTTATAATTATATATTATAATATATATATTATAC-T
1 TATTG-TATAATTATATA-TATAATATATATATTATACTT
28532 TATT-T-T-ATTA-ATATATAATA
1 TATTGTATAATTATATATATAATA
28552 AATTATTTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 14
0.79 0.00 0.21
Matches are distributed among these distances:
33 12 0.23
34 3 0.06
35 10 0.19
36 2 0.04
37 3 0.06
39 13 0.25
40 9 0.17
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (38 bp):
TATTGTATAATTATATATATAATATATATATTATACTT
Found at i:28563 original size:36 final size:40
Alignment explanation
Indices: 28474--28563 Score: 111
Period size: 39 Copynumber: 2.4 Consensus size: 40
28464 GATAATTTTA
*
28474 ATAATATA-ATATTATACTTTATTGTTATAATTATATATT
1 ATAATATATATATTATACTTTATTGTTATAATTATATAAT
28513 ATAATATATATATTATAC-TTATT-TTATTAA-TATATAAT
1 ATAATATATATATTATACTTTATTGTTA-TAATTATATAAT
*
28551 A-AAT-TATTTATTA
1 ATAATATATATATTA
28564 ATTTCATAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
36 8 0.17
37 3 0.06
38 11 0.23
39 16 0.34
40 9 0.19
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.53
Consensus pattern (40 bp):
ATAATATATATATTATACTTTATTGTTATAATTATATAAT
Found at i:28576 original size:22 final size:22
Alignment explanation
Indices: 28535--28585 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
28525 TTATACTTAT
*
28535 TTTATTAATATATAATAAATTA
1 TTTATTAATATATAATAAATAA
*
28557 TTTATTAATTTCATAA-AAATAA
1 TTTATTAATAT-ATAATAAATAA
28579 TATTATT
1 T-TTATT
28586 GAATGGTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTATTAATATATAATAAATAA
Found at i:28618 original size:22 final size:22
Alignment explanation
Indices: 28592--28636 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
28582 TATTGAATGG
*
28592 TTAAATATTTAATA-AATACTCT
1 TTAAA-ATATAATATAATACTCT
*
28614 TTAAAATATAATATAATATTCT
1 TTAAAATATAATATAATACTCT
28636 T
1 T
28637 ATTTAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (22 bp):
TTAAAATATAATATAATACTCT
Found at i:29465 original size:43 final size:42
Alignment explanation
Indices: 29418--29561 Score: 125
Period size: 43 Copynumber: 3.4 Consensus size: 42
29408 GGGCTTATTG
* *
29418 ATAAAAGTAAAATGTGATATTGATAAAATTAGAGGCT-TCAATT
1 ATAAAAGTAAAAAGTGATATTGA-AAAATTA-AGGATCTCAATT
* * *
29461 ATAAAGGTAAAAGGTGATATTTAAGAAATTAAGGATCTCAATT
1 ATAAAAGTAAAAAGTGATATTGAA-AAATTAAGGATCTCAATT
* **
29504 AT-AAAGATAAAAAGTGAGATTGAAAAAACGACAGG-TCTCAATT
1 ATAAAAG-TAAAAAGTGATATTG-AAAAATTA-AGGATCTCAATT
29547 AT-AAAGATAAAAAGT
1 ATAAAAG-TAAAAAGT
29562 AAGACTACAA
Statistics
Matches: 86, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
42 8 0.09
43 73 0.85
44 5 0.06
ACGTcount: A:0.50, C:0.06, G:0.17, T:0.27
Consensus pattern (42 bp):
ATAAAAGTAAAAAGTGATATTGAAAAATTAAGGATCTCAATT
Found at i:33220 original size:19 final size:20
Alignment explanation
Indices: 33188--33225 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
33178 TCCTCTCATC
33188 TCTTCTTCCTTCTT-TCTTA
1 TCTTCTTCCTTCTTCTCTTA
33207 TCTTCTTCAC-TCTTCTCTT
1 TCTTCTTC-CTTCTTCTCTT
33226 CTTTCAAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.05, C:0.34, G:0.00, T:0.61
Consensus pattern (20 bp):
TCTTCTTCCTTCTTCTCTTA
Found at i:33731 original size:21 final size:21
Alignment explanation
Indices: 33689--33731 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
33679 TTTTTGGGCT
* *
33689 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
33710 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
33731 A
1 A
33732 CGAATATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:34475 original size:23 final size:23
Alignment explanation
Indices: 34431--34475 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
34421 ATTATTATAT
*
34431 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
34454 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
34476 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:40053 original size:19 final size:20
Alignment explanation
Indices: 40021--40058 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
40011 TCCTCTCATC
40021 TCTTCTTCCTTCTT-TCTTA
1 TCTTCTTCCTTCTTCTCTTA
40040 TCTTCTTCAC-TCTTCTCTT
1 TCTTCTTC-CTTCTTCTCTT
40059 CTTCCAAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.05, C:0.34, G:0.00, T:0.61
Consensus pattern (20 bp):
TCTTCTTCCTTCTTCTCTTA
Found at i:40553 original size:21 final size:21
Alignment explanation
Indices: 40511--40553 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
40501 TTTTTGGGCT
* *
40511 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
40532 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
40553 A
1 A
40554 CGAATATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:51091 original size:64 final size:64
Alignment explanation
Indices: 51023--51202 Score: 175
Period size: 67 Copynumber: 2.8 Consensus size: 64
51013 TAAAATAAAG
** *
51023 ACATCGAATGCAATTCGTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAGTGA-A
1 ACATCGAATGCAATTCGTGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGCAATAAT-ACA
* * *
51087 ACATCGAATGCAA-TCGGTGCATTTTTGATGCATAAGGAGTGCATTGATGCATCCCAGCAATAAT
1 ACATCGAATGCAATTC-GTGCA---TCGATGCATAAGTAGTGCATCGATGCATCCCAGCAATAAT
*
51151 ACT
62 ACA
* ** ** * *
51154 ACATCGAATACCTTTTATGCACCGATGCATCAGTAGTGCATCGATGCAT
1 ACATCGAATGCAATTCGTGCATCGATGCATAAGTAGTGCATCGATGCAT
51203 ACCTTCATTA
Statistics
Matches: 93, Mismatches: 17, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
63 2 0.02
64 41 0.44
66 1 0.01
67 48 0.52
68 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (64 bp):
ACATCGAATGCAATTCGTGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGCAATAATACA
Found at i:51528 original size:12 final size:12
Alignment explanation
Indices: 51511--51547 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
51501 ATATACGTTC
51511 ATGTGATATGAT
1 ATGTGATATGAT
*
51523 ATGTGATATGAC
1 ATGTGATATGAT
51535 ATGTGATATGAT
1 ATGTGATATGAT
51547 A
1 A
51548 ACATGATATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.38
Consensus pattern (12 bp):
ATGTGATATGAT
Found at i:51596 original size:29 final size:29
Alignment explanation
Indices: 51561--51634 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
51551 TGATATGAAG
51561 TGACATGAGCTACATGATCACAAGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
51590 TGACATGAGCTACATGATCACAAGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
51619 TGACATGAG-TACATGA
1 TGACATGAGCTACATGA
51635 ACATATGAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 7 0.16
29 38 0.84
ACGTcount: A:0.43, C:0.16, G:0.22, T:0.19
Consensus pattern (29 bp):
TGACATGAGCTACATGATCACAAGAGAAA
Found at i:51736 original size:15 final size:15
Alignment explanation
Indices: 51718--51780 Score: 108
Period size: 15 Copynumber: 4.2 Consensus size: 15
51708 GAGGGTATAA
51718 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
*
51733 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
51748 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
*
51763 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
51778 TAG
1 TAG
51781 GAGTCCTACG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.14, C:0.22, G:0.33, T:0.30
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:51754 original size:30 final size:30
Alignment explanation
Indices: 51718--51780 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
51708 GAGGGTATAA
51718 TAGTCCTTCGGGACGTAGTCCTTCGGGATG
1 TAGTCCTTCGGGACGTAGTCCTTCGGGATG
51748 TAGTCCTTCGGGACGTAGTCCTTCGGGATG
1 TAGTCCTTCGGGACGTAGTCCTTCGGGATG
51778 TAG
1 TAG
51781 GAGTCCTACG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.14, C:0.22, G:0.33, T:0.30
Consensus pattern (30 bp):
TAGTCCTTCGGGACGTAGTCCTTCGGGATG
Found at i:52234 original size:17 final size:18
Alignment explanation
Indices: 52207--52243 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
52197 AAGTATGTAC
52207 TTGGTTATGT-ATAGAGTG
1 TTGGTTATGTAATA-AGTG
52225 TTGG-TATGTAATAAGTG
1 TTGGTTATGTAATAAGTG
52242 TT
1 TT
52244 AATTACGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.46
Consensus pattern (18 bp):
TTGGTTATGTAATAAGTG
Found at i:52835 original size:38 final size:38
Alignment explanation
Indices: 52788--52872 Score: 116
Period size: 38 Copynumber: 2.2 Consensus size: 38
52778 AGACCGAATA
* *
52788 ACCTATCATCCTAAAGGATGTCATCTGTGTCCCGAAGG
1 ACCTATCATCCCAAAGGATGTAATCTGTGTCCCGAAGG
* * * *
52826 ACCTGTCATCCCGAATGATGTAATCTGTGTCCCGTAGG
1 ACCTATCATCCCAAAGGATGTAATCTGTGTCCCGAAGG
52864 ACCTATCAT
1 ACCTATCAT
52873 ATGTCTTATA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (38 bp):
ACCTATCATCCCAAAGGATGTAATCTGTGTCCCGAAGG
Found at i:53087 original size:46 final size:44
Alignment explanation
Indices: 53020--53112 Score: 132
Period size: 46 Copynumber: 2.1 Consensus size: 44
53010 TATGTGTAAC
*
53020 CATGTATCACATATTAAATATTCATATGTCATTTCATATCATATCA
1 CATGTATCACATATTAAATATTCATATATCATTTCATAT-A-ATCA
* **
53066 CATGTATCACGTATTGCATATTCATATATCATTTCATATAATCA
1 CATGTATCACATATTAAATATTCATATATCATTTCATATAATCA
53110 CAT
1 CAT
53113 AGCTTATCTC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 7 0.16
45 1 0.02
46 35 0.81
ACGTcount: A:0.35, C:0.18, G:0.05, T:0.41
Consensus pattern (44 bp):
CATGTATCACATATTAAATATTCATATATCATTTCATATAATCA
Found at i:55420 original size:3 final size:3
Alignment explanation
Indices: 55405--55438 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
55395 TGCCACATAT
* *
55405 TAA TAA AAA TAA TAA TAA TAA TAA TAA CAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
55439 TGTGCGTGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:61971 original size:29 final size:30
Alignment explanation
Indices: 61938--61998 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
61928 TATGTCTTTT
* *
61938 TTTCAGTTTAGTGCCTATTGTTT-TTTTCG
1 TTTCAGTTTAGTGCCTATCGTTTCATTTCG
*
61967 TTTCAGTTTGGTGCCTATCGTTTCATTTCG
1 TTTCAGTTTAGTGCCTATCGTTTCATTTCG
61997 TT
1 TT
61999 ACTCAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 21 0.75
30 7 0.25
ACGTcount: A:0.10, C:0.16, G:0.18, T:0.56
Consensus pattern (30 bp):
TTTCAGTTTAGTGCCTATCGTTTCATTTCG
Found at i:63325 original size:16 final size:15
Alignment explanation
Indices: 63294--63328 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
63284 TTTAATATAA
*
63294 TTATTAATATTTAAT
1 TTATTAATAATTAAT
63309 TTATTAACTAATTAAT
1 TTATTAA-TAATTAAT
63325 TTAT
1 TTAT
63329 ATAAAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATTAATAATTAAT
Done.