Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002491.1 Hibiscus syriacus cultivar Beakdansim tig00005079_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: 62093
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:4032 original size:13 final size:13
Alignment explanation
Indices: 4016--4042 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4006 GAATATTGAT
4016 AATGAGCTATGAG
1 AATGAGCTATGAG
4029 AATGAGCTATGAG
1 AATGAGCTATGAG
4042 A
1 A
4043 TTATGTGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.30, T:0.22
Consensus pattern (13 bp):
AATGAGCTATGAG
Found at i:4482 original size:23 final size:24
Alignment explanation
Indices: 4448--4504 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
4438 AAATCTTATA
* *
4448 TGGCACTACGGTGC-ATTTCTACG
1 TGGCACTTCGGTGCAAATTCTACG
4471 TGGCACTTCGGTGCAAATTCTACG
1 TGGCACTTCGGTGCAAATTCTACG
4495 TGGCACTTCG
1 TGGCACTTCG
4505 ATACAATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 13 0.42
24 18 0.58
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.30
Consensus pattern (24 bp):
TGGCACTTCGGTGCAAATTCTACG
Found at i:4518 original size:24 final size:24
Alignment explanation
Indices: 4462--4518 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
4452 ACTACGGTGC
* *
4462 ATTTCTACGTGGCACTTCGGTGCA
1 ATTTCTACGTGGCACTTCGATACA
*
4486 AATTCTACGTGGCACTTCGATACA
1 ATTTCTACGTGGCACTTCGATACA
*
4510 ATTTATACG
1 ATTTCTACG
4519 AGCTATGGTG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (24 bp):
ATTTCTACGTGGCACTTCGATACA
Found at i:5276 original size:21 final size:21
Alignment explanation
Indices: 5252--5295 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
5242 AGCTGAAGTT
* *
5252 ACTATAGTAGTGCATCGGTAC
1 ACTATAGCAGTGCATCGATAC
5273 ACTATAGCAGTGCATCGATAC
1 ACTATAGCAGTGCATCGATAC
5294 AC
1 AC
5296 AATTTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (21 bp):
ACTATAGCAGTGCATCGATAC
Found at i:5343 original size:21 final size:21
Alignment explanation
Indices: 5317--5357 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
5307 GATGTTTTTA
*
5317 TGCATCGGTATACTGTAGCAG
1 TGCATCGGTACACTGTAGCAG
5338 TGCATCGGTACACTGTAGCA
1 TGCATCGGTACACTGTAGCA
5358 CTATTCATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (21 bp):
TGCATCGGTACACTGTAGCAG
Found at i:5792 original size:21 final size:22
Alignment explanation
Indices: 5759--5799 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
5749 TTAAAAATTA
5759 TAAAAGAAGTACCGATACTCAT
1 TAAAAGAAGTACCGATACTCAT
5781 TAAAAG-AGTACCGATACTC
1 TAAAAGAAGTACCGATACTC
5800 CTTGTCCTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.44, C:0.20, G:0.15, T:0.22
Consensus pattern (22 bp):
TAAAAGAAGTACCGATACTCAT
Found at i:7088 original size:26 final size:26
Alignment explanation
Indices: 7059--7112 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
7049 ACTGAAGTAC
* *
7059 TAATACACATAAGGTTGTGCCCATCA
1 TAATACACATAAGGTCGTGCCCACCA
*
7085 TAATAGACATAAGGTCGTGCCCACCA
1 TAATACACATAAGGTCGTGCCCACCA
7111 TA
1 TA
7113 CACATTAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (26 bp):
TAATACACATAAGGTCGTGCCCACCA
Found at i:8282 original size:25 final size:25
Alignment explanation
Indices: 8242--8298 Score: 87
Period size: 25 Copynumber: 2.2 Consensus size: 25
8232 TAACTTCAAA
*
8242 CCACCAAATTTCAACTTGTTCTTCAT
1 CCACC-AATTTCAACTTATTCTTCAT
*
8268 CCACCAATTTTAACTTATTCTTCAT
1 CCACCAATTTCAACTTATTCTTCAT
8293 CCACCA
1 CCACCA
8299 TATTCATGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 24 0.83
26 5 0.17
ACGTcount: A:0.28, C:0.33, G:0.02, T:0.37
Consensus pattern (25 bp):
CCACCAATTTCAACTTATTCTTCAT
Found at i:11753 original size:13 final size:13
Alignment explanation
Indices: 11735--11770 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
11725 TCCTAATGGG
11735 CAATTTTTGAAAA
1 CAATTTTTGAAAA
11748 CAA-TTTTGAAAA
1 CAATTTTTGAAAA
*
11760 CAATGTTTGAA
1 CAATTTTTGAA
11771 CAATTATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 12 0.57
13 9 0.43
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.36
Consensus pattern (13 bp):
CAATTTTTGAAAA
Found at i:13650 original size:17 final size:17
Alignment explanation
Indices: 13628--13668 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
13618 ATATAGTGTC
13628 AACCTTCCCTTTTGAAA
1 AACCTTCCCTTTTGAAA
**
13645 AACCTTTTTCTTTTGAAA
1 AACC-TTCCCTTTTGAAA
13663 AACCTT
1 AACCTT
13669 TTTCTTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.29, C:0.24, G:0.05, T:0.41
Consensus pattern (17 bp):
AACCTTCCCTTTTGAAA
Found at i:13682 original size:18 final size:18
Alignment explanation
Indices: 13636--13681 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
13626 TCAACCTTCC
13636 CTTTTGAAAAACCTTTTT
1 CTTTTGAAAAACCTTTTT
13654 CTTTTGAAAAACCTTTTT
1 CTTTTGAAAAACCTTTTT
13672 CTTTT-AAAAA
1 CTTTTGAAAAA
13682 ATTTGACAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 5 0.18
18 23 0.82
ACGTcount: A:0.33, C:0.15, G:0.04, T:0.48
Consensus pattern (18 bp):
CTTTTGAAAAACCTTTTT
Found at i:18202 original size:64 final size:65
Alignment explanation
Indices: 18133--18279 Score: 210
Period size: 64 Copynumber: 2.3 Consensus size: 65
18123 TACACTTGGG
* *
18133 GTGTATCAGTACACTAATTGCATTCGATGTTTTAATAAAGCCA-GAGTGTATCGATGCATAGGAT
1 GTGTATCAGTACACAAAATGCATTCGATGTTTTAATAAAGCCAGGAGTGTATCGATGCATAGGAT
** *
18197 GTGTATTGGTACACAAAATGCATTCGATGTTTTAATAAAGCCAGGAGTGTATCGATGCAT-GGTT
1 GTGTATCAGTACACAAAATGCATTCGATGTTTTAATAAAGCCAGGAGTGTATCGATGCATAGGAT
*
18261 GTGCATC-GATACACAAAAT
1 GTGTATCAG-TACACAAAAT
18280 AGCTTCAATG
Statistics
Matches: 74, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
63 1 0.01
64 57 0.77
65 16 0.22
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.31
Consensus pattern (65 bp):
GTGTATCAGTACACAAAATGCATTCGATGTTTTAATAAAGCCAGGAGTGTATCGATGCATAGGAT
Found at i:22446 original size:19 final size:19
Alignment explanation
Indices: 22422--22465 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
22412 CTTTCCGACA
*
22422 GAAACATAAATAAGAGAGG
1 GAAACAGAAATAAGAGAGG
22441 GAAACAGAAATAAGAGAGG
1 GAAACAGAAATAAGAGAGG
22460 GAAACA
1 GAAACA
22466 ATTTAGATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.59, C:0.07, G:0.27, T:0.07
Consensus pattern (19 bp):
GAAACAGAAATAAGAGAGG
Found at i:22669 original size:2 final size:2
Alignment explanation
Indices: 22664--22708 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
22654 TTAGTATATC
*
22664 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG GG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
22706 AG A
1 AG A
22709 AACAATTTAG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:37188 original size:17 final size:17
Alignment explanation
Indices: 37166--37200 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
37156 AGGCTAATGT
37166 GGTAGCTGACGCACTTA
1 GGTAGCTGACGCACTTA
37183 GGTAGCTGACGCACTTA
1 GGTAGCTGACGCACTTA
37200 G
1 G
37201 CCCAAAAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.31, T:0.23
Consensus pattern (17 bp):
GGTAGCTGACGCACTTA
Found at i:41465 original size:18 final size:17
Alignment explanation
Indices: 41442--41475 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
41432 CAGTCTGTTT
41442 TATTTTAATGATTTTATA
1 TATTTTAAT-ATTTTATA
*
41460 TATTTTGATATTTTAT
1 TATTTTAATATTTTAT
41476 TTAATTATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
TATTTTAATATTTTATA
Found at i:48103 original size:21 final size:21
Alignment explanation
Indices: 48076--48122 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
48066 AGGGTTTCAT
48076 ATTCGGGATAATACAGTGGTC
1 ATTCGGGATAATACAGTGGTC
*
48097 CTTCGGGATAATACAGTGGTC
1 ATTCGGGATAATACAGTGGTC
48118 ATTCG
1 ATTCG
48123 AGACAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (21 bp):
ATTCGGGATAATACAGTGGTC
Found at i:50643 original size:2 final size:2
Alignment explanation
Indices: 50636--50678 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
50626 ACTGAAAAGA
50636 AT AT AT AT AT AT -T AT AT A- AT AT -T 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
50675 AT AT
1 AT AT
50679 GGATAATTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.08
2 35 0.92
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:54150 original size:21 final size:21
Alignment explanation
Indices: 54124--54180 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
54114 GGGTTTCATA
*
54124 GGTCCTTCAGGATAATACAGT
1 GGTCCTTCAGGACAATACAGT
*
54145 GGTCCTTCGGGACAATACAGT
1 GGTCCTTCAGGACAATACAGT
* *
54166 GGTCATTCGGGACAA
1 GGTCCTTCAGGACAA
54181 ATTTCATATG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (21 bp):
GGTCCTTCAGGACAATACAGT
Found at i:57598 original size:27 final size:28
Alignment explanation
Indices: 57567--57619 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
57557 ATTAGCATAT
57567 AAACTCGAAT-AACTCAATAAA-TTTCTC
1 AAACTCGAATCAACTCAA-AAAGTTTCTC
*
57594 AAACTCGACTCAACTCAAAAAGTTTC
1 AAACTCGAATCAACTCAAAAAGTTTC
57620 AAGTTAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.43, C:0.25, G:0.06, T:0.26
Consensus pattern (28 bp):
AAACTCGAATCAACTCAAAAAGTTTCTC
Found at i:58780 original size:20 final size:19
Alignment explanation
Indices: 58734--58781 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
58724 ATGACCAACA
* * *
58734 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCAATCTCC
58753 AAATCGCAACGCAATCTCC
1 AAATCGCAACGCAATCTCC
58772 AATATCGCAA
1 AA-ATCGCAA
58782 ATCAGTTTCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.38, C:0.29, G:0.12, T:0.21
Consensus pattern (19 bp):
AAATCGCAACGCAATCTCC
Found at i:58905 original size:21 final size:21
Alignment explanation
Indices: 58876--58931 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
58866 CGAATATGTA
*
58876 AATCACAACACGATAATACAT
1 AATCGCAACACGATAATACAT
*
58897 AATCGCAACGCGATAATACAT
1 AATCGCAACACGATAATACAT
*
58918 AATCGCAACTCGAT
1 AATCGCAACACGAT
58932 TCTGACTATC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.45, C:0.25, G:0.11, T:0.20
Consensus pattern (21 bp):
AATCGCAACACGATAATACAT
Found at i:58944 original size:20 final size:20
Alignment explanation
Indices: 58919--58986 Score: 102
Period size: 20 Copynumber: 3.4 Consensus size: 20
58909 ATAATACATA
58919 ATCGCAACTCGATTCTGACT
1 ATCGCAACTCGATTCTGACT
*
58939 ATCGCAACGCGATTCTGACT
1 ATCGCAACTCGATTCTGACT
58959 ATCGCAACGT-GATTCTGACT
1 ATCGCAAC-TCGATTCTGACT
*
58979 GTCGCAAC
1 ATCGCAAC
58987 ACTGAATTTC
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.26
Consensus pattern (20 bp):
ATCGCAACTCGATTCTGACT
Found at i:59826 original size:24 final size:23
Alignment explanation
Indices: 59798--59851 Score: 90
Period size: 24 Copynumber: 2.3 Consensus size: 23
59788 AGTATTCGAA
59798 ATTTGATCTTGGTCAATACCCGG
1 ATTTGATCTTGGTCAATACCCGG
*
59821 ACTTTGATCTTGGTCAATACTCGG
1 A-TTTGATCTTGGTCAATACCCGG
59845 ATTTGAT
1 ATTTGAT
59852 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 7 0.24
24 22 0.76
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (23 bp):
ATTTGATCTTGGTCAATACCCGG
Found at i:60054 original size:12 final size:13
Alignment explanation
Indices: 60039--60071 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
60029 AAAAGAATAA
60039 GAAGAAA-TCCCC
1 GAAGAAAGTCCCC
60051 GAAGAAAAGTCCCC
1 GAAG-AAAGTCCCC
60065 GAAGAAA
1 GAAGAAA
60072 ATGCCACGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.21
13 6 0.32
14 9 0.47
ACGTcount: A:0.48, C:0.24, G:0.21, T:0.06
Consensus pattern (13 bp):
GAAGAAAGTCCCC
Found at i:60065 original size:14 final size:14
Alignment explanation
Indices: 60046--60072 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
60036 TAAGAAGAAA
60046 TCCCCGAAGAAAAG
1 TCCCCGAAGAAAAG
60060 TCCCCGAAGAAAA
1 TCCCCGAAGAAAA
60073 TGCCACGGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.30, G:0.19, T:0.07
Consensus pattern (14 bp):
TCCCCGAAGAAAAG
Done.