Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004094.1 Hibiscus syriacus cultivar Beakdansim tig00008954_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: 53863
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:1824 original size:48 final size:48
Alignment explanation
Indices: 1748--1839 Score: 159
Period size: 48 Copynumber: 1.9 Consensus size: 48
1738 TGACTGTTGA
1748 ACACAGGGTTCTTTTGCGGGGTGGTCAACGGACCAATTAAGCTTTCCC
1 ACACAGGGTTCTTTTGCGGGGTGGTCAACGGACCAATTAAGCTTTCCC
*
1796 ACACAAGGGTTCTTTTGC-GTGTGGTCAACGGACCAATTAAGCTT
1 ACAC-AGGGTTCTTTTGCGGGGTGGTCAACGGACCAATTAAGCTT
1840 CCCCCACCCC
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
48 29 0.69
49 13 0.31
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (48 bp):
ACACAGGGTTCTTTTGCGGGGTGGTCAACGGACCAATTAAGCTTTCCC
Found at i:2778 original size:32 final size:32
Alignment explanation
Indices: 2742--2802 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
2732 TTGGATCGGG
* **
2742 TTAAATTCGGTTCGGGTTACTTTCAGTTCGAC
1 TTAAATTCGATTCGAATTACTTTCAGTTCGAC
*
2774 TTAAATTCGATTTGAATTACTTTCAGTTC
1 TTAAATTCGATTCGAATTACTTTCAGTTC
2803 AGGTTATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.23, C:0.16, G:0.16, T:0.44
Consensus pattern (32 bp):
TTAAATTCGATTCGAATTACTTTCAGTTCGAC
Found at i:4367 original size:23 final size:24
Alignment explanation
Indices: 4324--4370 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
4314 ATATGGCATG
*
4324 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
4348 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
4371 ACAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:4623 original size:31 final size:31
Alignment explanation
Indices: 4585--4740 Score: 242
Period size: 31 Copynumber: 5.0 Consensus size: 31
4575 AGGGTCGAGG
4585 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
4616 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
4647 GTTTACCTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
4678 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
4709 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
4740 G
1 G
4741 GTCCTTCGGG
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 114 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:6664 original size:47 final size:47
Alignment explanation
Indices: 6549--6665 Score: 137
Period size: 47 Copynumber: 2.4 Consensus size: 47
6539 CAAAAAAACA
* * *
6549 AAAACCCAAAAATCATAACTCCATTGAAAATCATAAACTCTACAAAATT
1 AAAACCC-AAAATCATAAC-CCATTAAAAATCATAAACTCCACAAAATC
* **
6598 AAAACCCAAATAT-ACAACCCATTAAAAATCATATCCTCCACAAAATC
1 AAAACCCAAA-ATCATAACCCATTAAAAATCATAAACTCCACAAAATC
*
6645 AAAACTCAAAATCATAACCCA
1 AAAACCCAAAATCATAACCCA
6666 CAAAATGATT
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
46 2 0.03
47 40 0.69
48 7 0.12
49 9 0.16
ACGTcount: A:0.53, C:0.26, G:0.01, T:0.20
Consensus pattern (47 bp):
AAAACCCAAAATCATAACCCATTAAAAATCATAAACTCCACAAAATC
Found at i:7278 original size:151 final size:150
Alignment explanation
Indices: 7005--7295 Score: 537
Period size: 151 Copynumber: 1.9 Consensus size: 150
6995 TCGAATAAGC
7005 CCTTTACATAGACCATGCCTTTTTCACTAAGCTTAGTTCTTTCCTCATTTGATCTACTGCTGATC
1 CCTTTACATAGACCATGCCTTTTTCACTAAGCTTAGTTCTTTCCTCATTTGATCTACTGCTGATC
*
7070 ATTTCCTTGAACAACAACCTCGGACATGGTCCCGTCGTCGGCAACCAGCATATTCACTTTGATCT
66 ATCTCCTTGAACAACAACCTCGGACATGGTCCCGTCGTCGGCAACCAGCATATTCACTTTGATCT
7135 GCTCCTTCCTGGATCATCTT
131 GCTCCTTCCTGGATCATCTT
*
7155 CCTTTACATAGACCATGCCTTTTTCACTAAGCTTAGTTCTTTTCTCATTTGATCTACTTGCTGAT
1 CCTTTACATAGACCATGCCTTTTTCACTAAGCTTAGTTCTTTCCTCATTTGATCTAC-TGCTGAT
* *
7220 CATCTCCTTGAACAATAACCTCGGACATGGTCCCGTCGTCGGCAACCAGCATCTTCACTTTGATC
65 CATCTCCTTGAACAACAACCTCGGACATGGTCCCGTCGTCGGCAACCAGCATATTCACTTTGATC
7285 TGCTCCTTCCT
130 TGCTCCTTCCT
7296 TGATGCCTTC
Statistics
Matches: 136, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
150 56 0.41
151 80 0.59
ACGTcount: A:0.20, C:0.30, G:0.14, T:0.36
Consensus pattern (150 bp):
CCTTTACATAGACCATGCCTTTTTCACTAAGCTTAGTTCTTTCCTCATTTGATCTACTGCTGATC
ATCTCCTTGAACAACAACCTCGGACATGGTCCCGTCGTCGGCAACCAGCATATTCACTTTGATCT
GCTCCTTCCTGGATCATCTT
Found at i:14351 original size:21 final size:22
Alignment explanation
Indices: 14327--14374 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
14317 AGAGCAAGTT
14327 GGAGAAGAG-GAAGAAG-AGAGA
1 GGAGAAGAGAGAAGAAGAAGA-A
*
14348 GGAG-AGGGAGAAGAAGAAGAA
1 GGAGAAGAGAGAAGAAGAAGAA
14369 GGAGAA
1 GGAGAA
14375 CATATTGAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 3 0.13
21 16 0.70
22 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (22 bp):
GGAGAAGAGAGAAGAAGAAGAA
Found at i:18488 original size:15 final size:15
Alignment explanation
Indices: 18469--18524 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
18459 TAACCGGTTT
18469 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
18484 TGGTTTTTTAAAAAAAC
1 CGG--TTTTAAAAAAAC
*
18501 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
18516 CGATTTTAA
1 CGGTTTTAA
18525 TATTCCAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 20 0.59
17 14 0.41
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:18494 original size:17 final size:17
Alignment explanation
Indices: 18472--18522 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
18462 CCGGTTTCGG
*
18472 TTTTAAAAAAACTGGTT
1 TTTTAAAAAAACCGGTT
18489 TTTTAAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
18504 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
18521 TT
1 TT
18523 AATATTCCAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 13 0.45
17 16 0.55
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:18718 original size:21 final size:21
Alignment explanation
Indices: 18694--18746 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
18684 ACACTTAGGG
18694 AACCGATTCCCTATGAGAGGA
1 AACCGATTCCCTATGAGAGGA
*
18715 AACCGATTCCCTATGAGAGGG
1 AACCGATTCCCTATGAGAGGA
*
18736 TACCGATTCCC
1 AACCGATTCCC
18747 CCACGCTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (21 bp):
AACCGATTCCCTATGAGAGGA
Found at i:22998 original size:32 final size:32
Alignment explanation
Indices: 22957--23021 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
22947 AAACTTGAAC
* *
22957 AACAAGATTAAAGAGGATGGCATTAGCTATTA
1 AACAAGATTAAAGAAGATGACATTAGCTATTA
22989 AACAAGATTAAAGAAGATGACATTAGCTATTA
1 AACAAGATTAAAGAAGATGACATTAGCTATTA
23021 A
1 A
23022 GACTTCTTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.48, C:0.09, G:0.18, T:0.25
Consensus pattern (32 bp):
AACAAGATTAAAGAAGATGACATTAGCTATTA
Found at i:29917 original size:23 final size:23
Alignment explanation
Indices: 29891--29935 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
29881 AATTGAGCAT
*
29891 AACTGAAAAAATCATAATTTAAA
1 AACTGAAAAAATCATAAATTAAA
**
29914 AACTTTAAAAATCATAAATTAA
1 AACTGAAAAAATCATAAATTAA
29936 TATAAAACCC
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:0.60, C:0.09, G:0.02, T:0.29
Consensus pattern (23 bp):
AACTGAAAAAATCATAAATTAAA
Found at i:30162 original size:6 final size:6
Alignment explanation
Indices: 30144--30179 Score: 54
Period size: 6 Copynumber: 5.7 Consensus size: 6
30134 ATCATTTAAA
30144 TAAAAT CTAAAAT TAAAAT TGAAAAT TAAAAT TAAA
1 TAAAAT -TAAAAT TAAAAT T-AAAAT TAAAAT TAAA
30180 TTCTCCATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 16 0.57
7 12 0.43
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (6 bp):
TAAAAT
Found at i:30162 original size:13 final size:12
Alignment explanation
Indices: 30144--30179 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 12
30134 ATCATTTAAA
30144 TAAAATCTAAAAT
1 TAAAAT-TAAAAT
30157 TAAAATTGAAAAT
1 TAAAATT-AAAAT
30170 TAAAATTAAA
1 TAAAATTAAA
30180 TTCTCCATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 18 0.82
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (12 bp):
TAAAATTAAAAT
Found at i:34383 original size:200 final size:199
Alignment explanation
Indices: 33940--34700 Score: 731
Period size: 200 Copynumber: 3.8 Consensus size: 199
33930 TTTTGTTTCA
* * * * * * * *
33940 AACCATTTTTAATG-CAATTTTA-CCCACTTATAATGTCTCGTATGTGCCGATATTAACCTCAAT
1 AACCATTTTCAATGTGATTTTTACCCCTCTTACAATATCTCGTATGTG-TGATATTAGCCTCAAT
* * **
34003 TGAAAGATAAGTTCTAATACTACGCCTCTAATCTTATAAATTACG-AAAATTTTCATCTTAACTT
65 TGAAAGATAAGTTCCAATACTACGCCTCTAATCTTATAAATTATGAAAAATTTTCAGATTAACTT
* ** * * * * *
34067 T-TGAAAATACCCTTCGGGCATGGC-TATCAAGTCATTTTAGCTTATTCTTCACGCATAAAACCA
130 TCCGAAAATACCC-TCGAACAT-GCTTATCAAGCCATTTTAGCTCA-TCTTCATGTACAAAACCA
* *
34130 AGTTTTAT
192 AGCTTTAG
* * *
34138 AACAATTTTCAATGTGATTTTTACCCCGTC-TACAATGTCTCGTATGTGCTTATATTAGCCTCAA
1 AACCATTTTCAATGTGATTTTTACCCC-TCTTACAATATCTCGTATGTG-TGATATTAGCCTCAA
* *
34202 TTGAAAGATAAGTTCCAATACTACGCTTCTAATCTTATAAATTATGAAAAATATT-AGATTAACT
64 TTGAAAGATAAGTTCCAATACTACGCCTCTAATCTTATAAATTATGAAAAATTTTCAGATTAACT
* * * * *
34266 TTCCAAAAATAACCCTCAAATATGCTTATTAAGCCATTTTAGCATCAGCTTCATGTACAAAACCA
129 TTCCGAAAAT-ACCCTCGAACATGCTTATCAAGCCATTTTAGC-TCATCTTCATGTACAAAACCA
*
34331 AGCTTTGG
192 AGCTTTAG
* * *
34339 AACCATTTTCAACGTGATTTTTGCCCCTCTTACAATAT-TCGTATGTTTCGATATTAGCCTCAAT
1 AACCATTTTCAATGTGATTTTTACCCCTCTTACAATATCTCGTATGTGT-GATATTAGCCTCAAT
* * * *
34403 TTAAAGAAAAGTTCCAATACTACACCTCTAATCTTATAAATTA-CAAAAATTTTCAGATTAA-TT
65 TGAAAGATAAGTTCCAATACTACGCCTCTAATCTTATAAATTATGAAAAATTTTCAGATTAACTT
* * ** *
34466 TCCCGACAATACCTATCGAACATG-TATATCAAGCCATTTTAATTTCTTCTTCATGTACAAAACC
130 T-CCGAAAATACC-CTCGAACATGCT-TATCAAGCCATTTT-AGCTCATCTTCATGTACAAAACC
34530 AAGCTTTAG
191 AAGCTTTAG
* ** * * *
34539 AAACATTTTCAATGCT-ATTTTTACCCGACTTACAATATCTTGTATATGTCGATATT-GATCTCA
1 AACCATTTTCAATG-TGATTTTTACCCCTCTTACAATATCTCGTATGTGT-GATATTAG-CCTCA
* ** * * * * *
34602 ATTTAAAGATAAACTCCAATACTACGCCACTAATCTCATAAATTATGAAAAA-TTTCATATCAAT
63 ATTGAAAGATAAGTTCCAATACTACGCCTCTAATCTTATAAATTATGAAAAATTTTCAGATTAAC
* *
34666 TTTCCGAAAATCCCCTCGAACATGCCTATCAAGCC
128 TTTCCGAAAATACCCTCGAACATGCTTATCAAGCC
34701 TATAACGCCC
Statistics
Matches: 466, Mismatches: 76, Indels: 40
0.80 0.13 0.07
Matches are distributed among these distances:
198 12 0.03
199 22 0.05
200 259 0.56
201 159 0.34
202 14 0.03
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.35
Consensus pattern (199 bp):
AACCATTTTCAATGTGATTTTTACCCCTCTTACAATATCTCGTATGTGTGATATTAGCCTCAATT
GAAAGATAAGTTCCAATACTACGCCTCTAATCTTATAAATTATGAAAAATTTTCAGATTAACTTT
CCGAAAATACCCTCGAACATGCTTATCAAGCCATTTTAGCTCATCTTCATGTACAAAACCAAGCT
TTAG
Found at i:43298 original size:2 final size:2
Alignment explanation
Indices: 43293--43321 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
43283 AAAATTTATT
43293 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 T
43322 TTCTAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:43364 original size:18 final size:19
Alignment explanation
Indices: 43328--43367 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
43318 ATATTTCTAA
*
43328 AAATAAAACATAAATTTTG
1 AAATAAAACATAAACTTTG
*
43347 AAATAAACCAT-AACTTTG
1 AAATAAAACATAAACTTTG
43365 AAA
1 AAA
43368 ACATTTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.57, C:0.10, G:0.05, T:0.28
Consensus pattern (19 bp):
AAATAAAACATAAACTTTG
Found at i:48116 original size:14 final size:15
Alignment explanation
Indices: 48089--48120 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
48079 GTGCTTATAC
48089 GAAAATGCTCGATGT
1 GAAAATGCTCGATGT
48104 GAAAATGCT-GATGT
1 GAAAATGCTCGATGT
48118 GAA
1 GAA
48121 CAAGACACTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.38, C:0.09, G:0.28, T:0.25
Consensus pattern (15 bp):
GAAAATGCTCGATGT
Found at i:51862 original size:97 final size:97
Alignment explanation
Indices: 51734--51923 Score: 353
Period size: 97 Copynumber: 2.0 Consensus size: 97
51724 AAACTAGCAA
*
51734 CTTAATATCACATGAGGATCATATAAGTAAATATTAAATTTAACCAAGAAACTCGAACAAAGATA
1 CTTAATATCACATGAGGATCATATAAGTAAATATTAAATCTAACCAAGAAACTCGAACAAAGATA
51799 AATACAATCAGATCTGATCACATCGATAGACT
66 AATACAATCAGATCTGATCACATCGATAGACT
51831 CTTAATATCACATGAGGATCATATAAGTAAATATTAAATCTAACCAAGAAACTCGAACAAAGATA
1 CTTAATATCACATGAGGATCATATAAGTAAATATTAAATCTAACCAAGAAACTCGAACAAAGATA
* *
51896 TATACAATCAGATTTGATCACATCGATA
66 AATACAATCAGATCTGATCACATCGATA
51924 AACGAAGCAT
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
97 90 1.00
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.26
Consensus pattern (97 bp):
CTTAATATCACATGAGGATCATATAAGTAAATATTAAATCTAACCAAGAAACTCGAACAAAGATA
AATACAATCAGATCTGATCACATCGATAGACT
Found at i:52822 original size:2 final size:2
Alignment explanation
Indices: 52815--52861 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
52805 AATTATAATT
52815 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
52856 TA TA TA
1 TA TA TA
52862 ATAAAAATTG
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:53515 original size:2 final size:2
Alignment explanation
Indices: 53502--53561 Score: 102
Period size: 2 Copynumber: 30.0 Consensus size: 2
53492 TTCACGTACC
*
53502 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
53544 AT AT AT AA AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
53562 CATGTCATGC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.