Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006585.1 Hibiscus syriacus cultivar Beakdansim tig00016142_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: 61714
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:2784 original size:29 final size:29
Alignment explanation
Indices: 2749--2823 Score: 114
Period size: 29 Copynumber: 2.6 Consensus size: 29
2739 AAACTAAATT
* *
2749 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
* *
2778 GCTGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
2807 GATGTCATTGCTTACAT
1 GATGTCATTGCTTACAT
2824 TAATTTAGTT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:4857 original size:29 final size:29
Alignment explanation
Indices: 4823--4929 Score: 189
Period size: 29 Copynumber: 3.7 Consensus size: 29
4813 TGTTTGTTTA
**
4823 TATTTTATAATAATTTATAAATTGTTTTG
1 TATTTTATTTTAATTTATAAATTGTTTTG
4852 TATTTTATTTTAATTTATAAATTGTTTTG
1 TATTTTATTTTAATTTATAAATTGTTTTG
4881 TATTTTATTTTAATTTATAAATTGTTTTG
1 TATTTTATTTTAATTTATAAATTGTTTTG
4910 TATTTTATTTTAATTT-TAAA
1 TATTTTATTTTAATTTATAAA
4930 AAAAATTGTA
Statistics
Matches: 76, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
28 4 0.05
29 72 0.95
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.64
Consensus pattern (29 bp):
TATTTTATTTTAATTTATAAATTGTTTTG
Found at i:4968 original size:57 final size:58
Alignment explanation
Indices: 4833--5026 Score: 194
Period size: 57 Copynumber: 3.3 Consensus size: 58
4823 TATTTTATAA
***** * *
4833 TAATTTATAAATTGTTTTGTATTTTATTTTAATTTATAAATTGTTTTGTATTTTATTT
1 TAATTTATAAATTGTTTTGTATTTTATTTTAATTTATAAAAAAAATTGTATTTAATTG
4891 TAATTTATAAATTGTTTTGTATTTTATTTTAATTT-TAAAAAAAATTGTATTTAATTG
1 TAATTTATAAATTGTTTTGTATTTTATTTTAATTTATAAAAAAAATTGTATTTAATTG
* ** * * * * *
4948 TAATTTATAAATAGCATTGTACTTTATTGTGATTTATAAAAAAATTATGTACTTT-ATTA
1 TAATTTATAAATTGTTTTGTATTTTATTTTAATTTATAAAAAAAAT-TGTA-TTTAATTG
* * *
5007 TGATTTATTAATAGTTTTGT
1 TAATTTATAAATTGTTTTGT
5027 TCTTTATGAT
Statistics
Matches: 114, Mismatches: 19, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
57 44 0.39
58 44 0.39
59 23 0.20
60 3 0.03
ACGTcount: A:0.34, C:0.02, G:0.08, T:0.57
Consensus pattern (58 bp):
TAATTTATAAATTGTTTTGTATTTTATTTTAATTTATAAAAAAAATTGTATTTAATTG
Found at i:6896 original size:7 final size:7
Alignment explanation
Indices: 6884--6924 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
6874 TCATTTCAAA
6884 AAAGAAG
1 AAAGAAG
6891 AAAGAAG
1 AAAGAAG
6898 AAAGAAG
1 AAAGAAG
6905 AAAGAAG
1 AAAGAAG
6912 AAAGAAG
1 AAAGAAG
6919 AAAGAA
1 AAAGAA
6925 ATCTCTCATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (7 bp):
AAAGAAG
Found at i:9669 original size:4 final size:4
Alignment explanation
Indices: 9660--9686 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
9650 TCTCATTTAA
9660 AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAA
9687 TCTCTCATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:18265 original size:18 final size:19
Alignment explanation
Indices: 18224--18265 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
18214 TATATGAGTT
**
18224 ATATGTTATTGTATGTGTG
1 ATATGTTATTGTATGAATG
18243 ATATGTT-TTGTATGAATG
1 ATATGTTATTGTATGAATG
*
18261 GTATG
1 ATATG
18266 AGTATGTGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (19 bp):
ATATGTTATTGTATGAATG
Found at i:18476 original size:31 final size:32
Alignment explanation
Indices: 18438--18572 Score: 170
Period size: 31 Copynumber: 4.3 Consensus size: 32
18428 GAGTCGAGGG
18438 TTACCTATGTCTTTCGAGG-CATATGGACAGA
1 TTACCTATGTCTTTCGAGGACATATGGACAGA
* *
18469 TTACCTATATCTTTTG-GGACATATGGACAGA
1 TTACCTATGTCTTTCGAGGACATATGGACAGA
* * *
18500 TTACCTATGTATTTTGA-GACATATGGATAGGA
1 TTACCTATGTCTTTCGAGGACATATGGACA-GA
* *
18532 TTACCTATGTCCTTC-AGGACATATGGACAGT
1 TTACCTATGTCTTTCGAGGACATATGGACAGA
18563 TTACCTATGT
1 TTACCTATGT
18573 TCTTAGGAAC
Statistics
Matches: 90, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
30 2 0.02
31 63 0.70
32 25 0.28
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (32 bp):
TTACCTATGTCTTTCGAGGACATATGGACAGA
Found at i:18539 original size:32 final size:31
Alignment explanation
Indices: 18438--18591 Score: 168
Period size: 31 Copynumber: 4.9 Consensus size: 31
18428 GAGTCGAGGG
* *
18438 TTACCTATGTCTTTCGAGGCATATGGACAGA
1 TTACCTATGTCTTTTGAGACATATGGACAGA
* *
18469 TTACCTATATCTTTTGGGACATATGGACAGA
1 TTACCTATGTCTTTTGAGACATATGGACAGA
* *
18500 TTACCTATGTATTTTGAGACATATGGATAGGA
1 TTACCTATGTCTTTTGAGACATATGGACA-GA
* * *
18532 TTACCTATGTC-CTTCAGGACATATGGACAGT
1 TTACCTATGTCTTTTGA-GACATATGGACAGA
**
18563 TTACCTATGTTCTTAGGA-ACATATGGACA
1 TTACCTATG-TCTTTTGAGACATATGGACA
18592 TGTCCTTCGA
Statistics
Matches: 102, Mismatches: 17, Indels: 8
0.80 0.13 0.06
Matches are distributed among these distances:
31 76 0.75
32 25 0.25
33 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (31 bp):
TTACCTATGTCTTTTGAGACATATGGACAGA
Found at i:18555 original size:63 final size:62
Alignment explanation
Indices: 18438--18572 Score: 180
Period size: 63 Copynumber: 2.2 Consensus size: 62
18428 GAGTCGAGGG
* * * **
18438 TTACCTATGTCTTTCGAGGCATATGGACAGATTACCTATATCTTTTGGGACATATGGACAGA
1 TTACCTATGTATTTCGAGACATATGGACAGATTACCTATATCCTTCAGGACATATGGACAGA
* * * *
18500 TTACCTATGTATTTTGAGACATATGGATAGGATTACCTATGTCCTTCAGGACATATGGACAGT
1 TTACCTATGTATTTCGAGACATATGGACA-GATTACCTATATCCTTCAGGACATATGGACAGA
18563 TTACCTATGT
1 TTACCTATGT
18573 TCTTAGGAAC
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
62 25 0.40
63 38 0.60
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (62 bp):
TTACCTATGTATTTCGAGACATATGGACAGATTACCTATATCCTTCAGGACATATGGACAGA
Found at i:18585 original size:63 final size:62
Alignment explanation
Indices: 18438--18591 Score: 177
Period size: 63 Copynumber: 2.5 Consensus size: 62
18428 GAGTCGAGGG
* * * * **
18438 TTACCTATGTCTTTCGAGGCATATGGACAGATTACCTATATCTTTTGGGACATATGGACAGA
1 TTACCTATGTATTTGGAGACATATGGACAGATTACCTATATCCTTCAGGACATATGGACAGA
* * * *
18500 TTACCTATGTATTTTGAGACATATGGATAGGATTACCTATGTCCTTCAGGACATATGGACAGT
1 TTACCTATGTATTTGGAGACATATGGACA-GATTACCTATATCCTTCAGGACATATGGACAGA
18563 TTACCTATGT-TCTTAGGA-ACATATGGACA
1 TTACCTATGTAT-TT-GGAGACATATGGACA
18592 TGTCCTTCGA
Statistics
Matches: 78, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
62 26 0.33
63 50 0.64
64 2 0.03
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (62 bp):
TTACCTATGTATTTGGAGACATATGGACAGATTACCTATATCCTTCAGGACATATGGACAGA
Found at i:26559 original size:51 final size:51
Alignment explanation
Indices: 26483--26588 Score: 176
Period size: 51 Copynumber: 2.1 Consensus size: 51
26473 AAACCAAAGG
* * *
26483 AGTAAAACCAACCTTTCTTGCCCCCTTGTCTTTGCCACCTGCAACACATAA
1 AGTAAAACCAACCCTTCTTGCCCCCTCGTCTTTACCACCTGCAACACATAA
*
26534 AGTAAAACCAACCCTTCTTGCCCCCTCGTCTTTACCACCTGCAACACTTAA
1 AGTAAAACCAACCCTTCTTGCCCCCTCGTCTTTACCACCTGCAACACATAA
26585 AGTA
1 AGTA
26589 TTCAATGAGT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.28, C:0.36, G:0.09, T:0.26
Consensus pattern (51 bp):
AGTAAAACCAACCCTTCTTGCCCCCTCGTCTTTACCACCTGCAACACATAA
Found at i:28974 original size:25 final size:25
Alignment explanation
Indices: 28946--28995 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
28936 GACATTAATC
28946 ATGTTTGTAGTTCAATCTATTAAAA
1 ATGTTTGTAGTTCAATCTATTAAAA
28971 ATGTTTGTAGTTCAATCTATTAAAA
1 ATGTTTGTAGTTCAATCTATTAAAA
28996 TATAAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.44
Consensus pattern (25 bp):
ATGTTTGTAGTTCAATCTATTAAAA
Found at i:35955 original size:60 final size:60
Alignment explanation
Indices: 35878--36067 Score: 197
Period size: 60 Copynumber: 3.2 Consensus size: 60
35868 TATTTGGTTG
* * *
35878 AATTTGGGGATGAGATTGGAA-GATCTAAAACTTTAGGGACCAATTTAGAATGAGATTCAT
1 AATTTGAGGATGAGATTGGAATG-TCTAAAACTTTAAGGACTAATTTAGAATGAGATTCAT
* * * *
35938 AATTTGAGGATGCGATTGGAATG-CTCAAAAGC-TTAAGGACTAATATGGAATGAAATTCAT
1 AATTTGAGGATGAGATTGGAATGTCT-AAAA-CTTTAAGGACTAATTTAGAATGAGATTCAT
* ** * * * *
35998 AGTTTGAGGATGAGATTAAAATGTTTAAAAGTTTAAGGACTAATTTAAAATGAGAATCAT
1 AATTTGAGGATGAGATTGGAATGTCTAAAACTTTAAGGACTAATTTAGAATGAGATTCAT
*
36058 AGTTTGAGGA
1 AATTTGAGGA
36068 CATATGATAC
Statistics
Matches: 107, Mismatches: 18, Indels: 10
0.79 0.13 0.07
Matches are distributed among these distances:
59 2 0.02
60 102 0.95
61 3 0.03
ACGTcount: A:0.39, C:0.07, G:0.24, T:0.31
Consensus pattern (60 bp):
AATTTGAGGATGAGATTGGAATGTCTAAAACTTTAAGGACTAATTTAGAATGAGATTCAT
Found at i:37263 original size:34 final size:35
Alignment explanation
Indices: 37219--37292 Score: 114
Period size: 34 Copynumber: 2.1 Consensus size: 35
37209 AAAATACTTC
*
37219 AATTTAGGGTTTAGAATGTAATTGAATTATTTT-G
1 AATTTAGGGTTTAGAATGTAATTGAAGTATTTTGG
* *
37253 AATTTGGGGTTTAGAATGTAATTGAAGTGTTTTGG
1 AATTTAGGGTTTAGAATGTAATTGAAGTATTTTGG
37288 AATTT
1 AATTT
37293 TGAACATGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
34 30 0.83
35 6 0.17
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.46
Consensus pattern (35 bp):
AATTTAGGGTTTAGAATGTAATTGAAGTATTTTGG
Found at i:49191 original size:21 final size:21
Alignment explanation
Indices: 49167--49209 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
49157 TTTTGATAAA
49167 AAAATTGAAAGTTTAGGTACT
1 AAAATTGAAAGTTTAGGTACT
* *
49188 AAAATTGATAGTTTGGGTACT
1 AAAATTGAAAGTTTAGGTACT
49209 A
1 A
49210 GATACATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.35
Consensus pattern (21 bp):
AAAATTGAAAGTTTAGGTACT
Found at i:52147 original size:65 final size:63
Alignment explanation
Indices: 52078--52237 Score: 187
Period size: 65 Copynumber: 2.5 Consensus size: 63
52068 AATTAAATTG
* * *
52078 AACATCAAATGCATTTCATGCATCGATGCACATACCATGCACCGATGCACTGAGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACA-ACCATGCACCGATGCACTCAGGATATTT-TG-
52142 A
63 A
* * * * *
52143 AACATCGAATGAATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCA-CAACCATGCACCGATGCACTCAGGATATTTTGA
* *
52207 AACATCGAATACACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
52238 TCTTAGTGCA
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
63 1 0.01
64 28 0.34
65 48 0.59
66 5 0.06
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACAACCATGCACCGATGCACTCAGGATATTTTGA
Found at i:52253 original size:64 final size:63
Alignment explanation
Indices: 52095--52257 Score: 154
Period size: 64 Copynumber: 2.5 Consensus size: 63
52085 AATGCATTTC
* * * *
52095 ATGCATCGATGCACATACCATGCACCGATGCACTGAGGATTTTATGAAAACATCGAATGAATTTG
1 ATGCATCGATGCAC-CAGC-TGCACCGATGCACTCAGGATTTTATGAAAACATCGAATGAACTTG
* * *
52160 ATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTT-TG-AAACATCGAAT-ACACT
1 ATGCATCGATGCACCAG-C-TGCACCGATGCACTCAGGAT-TTTATGAAAACATCGAATGA-ACT
52222 TG
62 TG
52224 ATGCATCGATGCACTCTTAG-TGCACCGATGCACT
1 ATGCATCGATGCAC-C--AGCTGCACCGATGCACT
52258 AAGGGTCCAA
Statistics
Matches: 84, Mismatches: 8, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
63 1 0.01
64 43 0.51
65 35 0.42
66 3 0.04
67 2 0.02
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (63 bp):
ATGCATCGATGCACCAGCTGCACCGATGCACTCAGGATTTTATGAAAACATCGAATGAACTTG
Found at i:58029 original size:22 final size:21
Alignment explanation
Indices: 57987--58041 Score: 51
Period size: 22 Copynumber: 2.6 Consensus size: 21
57977 CACTTAACAG
*
57987 TGCATCGATGCATCCCTTTGAA
1 TGCATCGATGCATCCATTTG-A
*
58009 TGCATCGATTCAT-CATGTTGA
1 TGCATCGATGCATCCAT-TTGA
58030 TGCA-CTGATGCA
1 TGCATC-GATGCA
58042 CGCCTTGAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 1 0.04
21 12 0.43
22 15 0.54
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33
Consensus pattern (21 bp):
TGCATCGATGCATCCATTTGA
Found at i:59586 original size:21 final size:21
Alignment explanation
Indices: 59544--59587 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
59534 ACTCCGTGAG
* *
59544 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
59565 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
59586 CT
1 CT
59588 CCTCCAGCTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:60736 original size:64 final size:59
Alignment explanation
Indices: 60651--60804 Score: 175
Period size: 64 Copynumber: 2.5 Consensus size: 59
60641 AATTAAATTG
* * *
60651 ACATCGAATGCATTTCATGCATCGATGCACATACCATGCACCGATGCACTGAGGATTTTATGAAA
1 ACATCGAATGCACTTGATGCATCGATGCACA-ACCATGCACCGATGCACT--CGA-TTT-TG-AA
* * * *
60716 ACATCGAATGCA-TTGATGCATCAATGCACCAGCCATGCATCGATGCACTCTATTTTGAA
1 ACATCGAATGCACTTGATGCATCGATGCA-CAACCATGCACCGATGCACTCGATTTTGAA
60775 ACATCGAATGCACTTGATGCATCGATGCAC
1 ACATCGAATGCACTTGATGCATCGATGCAC
60805 TCTTAGTCCA
Statistics
Matches: 80, Mismatches: 7, Indels: 10
0.82 0.07 0.10
Matches are distributed among these distances:
59 15 0.19
60 17 0.21
61 3 0.04
62 1 0.01
64 30 0.38
65 14 0.17
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (59 bp):
ACATCGAATGCACTTGATGCATCGATGCACAACCATGCACCGATGCACTCGATTTTGAA
Done.