Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001828.1 Hibiscus syriacus cultivar Beakdansim tig00003696_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: 48392
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:21041 original size:21 final size:21
Alignment explanation
Indices: 21015--21069 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
21005 GATTTTGACT
21015 GGGAGTATCAATATTGCCATA
1 GGGAGTATCAATATTGCCATA
21036 GGGAGTATCAATATTGCCATA
1 GGGAGTATCAATATTGCCATA
21057 GGGAGTATCAATA
1 GGGAGTATCAATA
21070 CTTCCTGCAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.27
Consensus pattern (21 bp):
GGGAGTATCAATATTGCCATA
Found at i:30945 original size:184 final size:182
Alignment explanation
Indices: 30631--31016 Score: 612
Period size: 184 Copynumber: 2.1 Consensus size: 182
30621 ATTAAATTTT
* *
30631 AAATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACTCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGAGCTAAGCCCAAACCATTTAAAACTCAATTAATAA
* *
30696 TTTAAGATCTAATAACTTTTAAACCTAAGTCAATATTAATTAATTAAAAAACTTATATAAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAACTTATATAAAATTT
* *
30761 TTATTTTATAATTATATATTATTTAAATTAATTGTAAATGTTTTTTTAATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAA--CTTTTTTAATTAAA
* *
30815 AAATATTATATATATTATATATAACATATGAGCTAAGCCCAAACTATTTAAAACTCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGAGCTAAGCCCAAACCATTTAAAACTCAATTAATAA
* * *
30880 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATCTGAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAACTTATATAAAATTT
*
30945 TTATTTTATAATTATATATTATTTAGATTAATTATAAACTTTTTTAATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTAATTAAA
* * *
30997 AAACATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
31017 AATTAGAAAA
Statistics
Matches: 186, Mismatches: 16, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
181 8 0.04
182 21 0.11
184 157 0.84
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (182 bp):
AAATATTAAATATATTATATATAACATATGAGCTAAGCCCAAACCATTTAAAACTCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAACTTATATAAAATTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTAATTAAA
Found at i:30994 original size:20 final size:20
Alignment explanation
Indices: 30953--30995 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
30943 TTTTATTTTA
*
30953 TAATTATATATTATTTAGAT
1 TAATTATAAATTATTTAGAT
*
30973 TAATTATAAACTTTTTTA-AT
1 TAATTATAAA-TTATTTAGAT
30993 TAA
1 TAA
30996 AAAACATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
TAATTATAAATTATTTAGAT
Found at i:31905 original size:3 final size:3
Alignment explanation
Indices: 31897--31935 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
31887 ATTGTTTAAT
31897 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
31936 ATATATATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:32833 original size:39 final size:40
Alignment explanation
Indices: 32790--32882 Score: 102
Period size: 39 Copynumber: 2.3 Consensus size: 40
32780 AAGTGTTCTG
*
32790 TAGCGGCGTTTACAATCCAAATGCCAC-A-A-AATGATACTT
1 TAGCGGCGTTTACAA--CAAATGCCACAATATAATGATAATT
* *
32829 TAGCGGCGTTTTTTCAACAAATGCCACAATATAATGGTAATT
1 TAGCGGCG--TTTACAACAAATGCCACAATATAATGATAATT
32871 TAGCGGCGTTTA
1 TAGCGGCGTTTA
32883 TAGCTCAAAC
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
39 18 0.40
40 4 0.09
41 7 0.16
42 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Consensus pattern (40 bp):
TAGCGGCGTTTACAACAAATGCCACAATATAATGATAATT
Found at i:33563 original size:22 final size:22
Alignment explanation
Indices: 33532--33581 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
33522 GTGTTTTTCT
*
33532 GCTTTCGAATAGAAA-ACTAATA
1 GCTTTTGAATAGAAACA-TAATA
* *
33554 GCTTTTGAATTGGAACATAATA
1 GCTTTTGAATAGAAACATAATA
33576 GCTTTT
1 GCTTTT
33582 CAAAACGTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (22 bp):
GCTTTTGAATAGAAACATAATA
Found at i:34606 original size:40 final size:41
Alignment explanation
Indices: 34544--34734 Score: 102
Period size: 40 Copynumber: 4.6 Consensus size: 41
34534 GTTTATAGCG
* *
34544 GCGTTTTGGTATAAAAACGCCGCTAAA-TTCTATACTTTAGTA
1 GCGTTTT-GTATAAAAACGCCGCAAAAGGTC-ATACTTTAGTA
* * *
34586 GCGTTTT-TATAAAAATGCCGCAAAAGGTCGTACTTTAGTC
1 GCGTTTTGTATAAAAACGCCGCAAAAGGTCATACTTTAGTA
** * * * * * *
34626 GCGTTTTACATACAAACGTCGCTAATTA-CTCATACTCTAGTG
1 GCGTTTTGTATAAAAACGCCGC-AA-AAGGTCATACTTTAGTA
** * * * * *
34668 GCGTTTTAGTCCATAAACGCTGCAAAATAGTAATACTTTAGTG
1 GCGTTTT-GTATAAAAACGCCGCAAAA-GGTCATACTTTAGTA
* *
34711 GCG-TTTGTTTACAAACGCCGCAAA
1 GCGTTTTGTATAAAAACGCCGCAAA
34735 TGCCGTAAAA
Statistics
Matches: 113, Mismatches: 29, Indels: 15
0.72 0.18 0.10
Matches are distributed among these distances:
40 32 0.28
41 27 0.24
42 31 0.27
43 23 0.20
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Consensus pattern (41 bp):
GCGTTTTGTATAAAAACGCCGCAAAAGGTCATACTTTAGTA
Found at i:35022 original size:7 final size:7
Alignment explanation
Indices: 35007--35036 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
34997 CAGTTGTCTT
*
35007 CATCTAG
1 CATCCAG
35014 CATCCAG
1 CATCCAG
35021 CATCCAG
1 CATCCAG
35028 CATCCAG
1 CATCCAG
35035 CA
1 CA
35037 GTTGTCTGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.30, C:0.40, G:0.13, T:0.17
Consensus pattern (7 bp):
CATCCAG
Found at i:37340 original size:36 final size:36
Alignment explanation
Indices: 37239--37341 Score: 154
Period size: 36 Copynumber: 2.9 Consensus size: 36
37229 GGTGGAAAAA
*
37239 AGTTTACCTATAATAATTAACTACACCAAGGAGAAT
1 AGTTTACCTATAATAATTAACTACACCAATGAGAAT
* * *
37275 GGGTTACCTAGAATAATTAACTACACCAATGA-ATAT
1 AGTTTACCTATAATAATTAACTACACCAATGAGA-AT
37311 AGTTTACCTATAATAATTAACTACACCAATG
1 AGTTTACCTATAATAATTAACTACACCAATG
37342 CTGATATTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
35 1 0.02
36 58 0.98
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (36 bp):
AGTTTACCTATAATAATTAACTACACCAATGAGAAT
Found at i:39052 original size:88 final size:88
Alignment explanation
Indices: 38973--39181 Score: 294
Period size: 88 Copynumber: 2.4 Consensus size: 88
38963 TTTTTTTTTA
* * * * *
38973 TAAAAATGCCGTTATATACCA-ACTTTTAGCGGCGTTTATATCTTAAAAATACCGCTATATACTA
1 TAAAAATGCCGCTAAATACCAGACTTTTAGCGGCGTTTATATCATAAAAACACCGCTATATACCA
39037 GACCTATCACGACGTTTGTATCC
66 GACCTATCACGACGTTTGTATCC
* * * * *
39060 TAAAAACGCCGCTAAATACCAGACCTTTAGCGGCGTTTGTATCATAAAAACGCTGCTATATACCA
1 TAAAAATGCCGCTAAATACCAGACTTTTAGCGGCGTTTATATCATAAAAACACCGCTATATACCA
* *
39125 GACCTATCGCGGCGTTTGTATCC
66 GACCTATCACGACGTTTGTATCC
*
39148 TAAAAATGCCGCTAAATACCAGAATTTTAGCGGC
1 TAAAAATGCCGCTAAATACCAGACTTTTAGCGGC
39182 ATTTTCATAA
Statistics
Matches: 106, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
87 18 0.17
88 88 0.83
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (88 bp):
TAAAAATGCCGCTAAATACCAGACTTTTAGCGGCGTTTATATCATAAAAACACCGCTATATACCA
GACCTATCACGACGTTTGTATCC
Found at i:39181 original size:44 final size:44
Alignment explanation
Indices: 38973--39181 Score: 224
Period size: 44 Copynumber: 4.8 Consensus size: 44
38963 TTTTTTTTTA
* * *
38973 TAAAAATGCCGTTATATACCA-ACTTTTAGCGGCGTTTATATCT
1 TAAAAATGCCGCTATATACCAGACTTTTAGCGGCGTTTGTATCC
* * * * *
39016 TAAAAATACCGCTATATACTAGACCTATCA-CGACGTTTGTATCC
1 TAAAAATGCCGCTATATACCAGA-CTTTTAGCGGCGTTTGTATCC
* * * *
39060 TAAAAACGCCGCTAAATACCAGACCTTTAGCGGCGTTTGTATCA
1 TAAAAATGCCGCTATATACCAGACTTTTAGCGGCGTTTGTATCC
* * * * *
39104 TAAAAACGCTGCTATATACCAGACCTATCGCGGCGTTTGTATCC
1 TAAAAATGCCGCTATATACCAGACTTTTAGCGGCGTTTGTATCC
* *
39148 TAAAAATGCCGCTAAATACCAGAATTTTAGCGGC
1 TAAAAATGCCGCTATATACCAGACTTTTAGCGGC
39182 ATTTTCATAA
Statistics
Matches: 134, Mismatches: 29, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
43 21 0.16
44 109 0.81
45 4 0.03
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (44 bp):
TAAAAATGCCGCTATATACCAGACTTTTAGCGGCGTTTGTATCC
Found at i:39231 original size:88 final size:88
Alignment explanation
Indices: 39031--39207 Score: 223
Period size: 88 Copynumber: 2.0 Consensus size: 88
39021 ATACCGCTAT
* * * *
39031 ATACTAGACCTATCACGACGTTTGTATCCTAAAAACGCCGCTAAATACCAGACCTTTAGCGGCGT
1 ATACCAGACCTATCGCGACGTTTGTATCCTAAAAACGCCGCTAAATACCAGAACTTTAGCGGCAT
* * ** *
39096 TTGTATCATAAAAACGCTGCTAT
66 TTGTATCAAAAAAAAGCCACTAA
* * *
39119 ATACCAGACCTATCGCGGCGTTTGTATCCTAAAAATGCCGCTAAATACCAGAATTTTAGCGGCAT
1 ATACCAGACCTATCGCGACGTTTGTATCCTAAAAACGCCGCTAAATACCAGAACTTTAGCGGCAT
39184 TT-TCAT-AAAAAAAAGCCACTAA
66 TTGT-ATCAAAAAAAAGCCACTAA
39206 AT
1 AT
39208 CTCAACACTT
Statistics
Matches: 76, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
87 14 0.18
88 62 0.82
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (88 bp):
ATACCAGACCTATCGCGACGTTTGTATCCTAAAAACGCCGCTAAATACCAGAACTTTAGCGGCAT
TTGTATCAAAAAAAAGCCACTAA
Found at i:39272 original size:42 final size:42
Alignment explanation
Indices: 39199--39316 Score: 137
Period size: 42 Copynumber: 2.8 Consensus size: 42
39189 TAAAAAAAAG
* * * * *
39199 CCACTAAATCTCAACACTTATTGCGACGTTTGTGATAAAAACA
1 CCACTAAATATCAATACCTATTGCG-CGTTTGTAAGAAAAACA
* *
39242 CCGCTAAATATCAATACCTATTGCGCGTTTGTAAGACAAACA
1 CCACTAAATATCAATACCTATTGCGCGTTTGTAAGAAAAACA
* *
39284 CCACTAAATATCAGTACGTATTGCGGCGTTTGT
1 CCACTAAATATCAATACCTATTGC-GCGTTTGT
39317 TTAACAAACG
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
42 35 0.55
43 29 0.45
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (42 bp):
CCACTAAATATCAATACCTATTGCGCGTTTGTAAGAAAAACA
Found at i:39341 original size:27 final size:28
Alignment explanation
Indices: 39303--39356 Score: 83
Period size: 27 Copynumber: 1.9 Consensus size: 28
39293 ATCAGTACGT
39303 ATTGCGGCGTTTGT-TTAACAAACGCGG
1 ATTGCGGCGTTTGTATTAACAAACGCGG
*
39330 ATTGCGGCGTTTTTCATTAACAAACGC
1 ATTGCGGCGTTTGT-ATTAACAAACGC
39357 CGCGAACTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 13 0.54
29 11 0.46
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.31
Consensus pattern (28 bp):
ATTGCGGCGTTTGTATTAACAAACGCGG
Found at i:41723 original size:18 final size:19
Alignment explanation
Indices: 41680--41725 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
41670 TTCTAGTAAT
*
41680 TTTAAAAAATTTATTTAAA
1 TTTAAAAAAATTATTTAAA
* *
41699 ATT-AAAAAATTA-TTATA
1 TTTAAAAAAATTATTTAAA
41716 TTTAAAAAAA
1 TTTAAAAAAA
41726 CTCAAATATT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
17 6 0.27
18 14 0.64
19 2 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TTTAAAAAAATTATTTAAA
Found at i:42433 original size:35 final size:35
Alignment explanation
Indices: 42393--42464 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
42383 TATTATCTTA
42393 TTAAAAGTAATGGATATGTAATTTTTTTTTCATTT
1 TTAAAAGTAATGGATATGTAATTTTTTTTTCATTT
*
42428 TTAAAAGTAATGGATATGTATTTTTTTTTTCATTT
1 TTAAAAGTAATGGATATGTAATTTTTTTTTCATTT
42463 TT
1 TT
42465 CATTTTTTCT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.57
Consensus pattern (35 bp):
TTAAAAGTAATGGATATGTAATTTTTTTTTCATTT
Found at i:45569 original size:65 final size:65
Alignment explanation
Indices: 45465--45602 Score: 231
Period size: 65 Copynumber: 2.1 Consensus size: 65
45455 AATTCCTGCA
* * *
45465 CCTGCACCACGACCAAGCTTTAATCCTATCCCTCATGCATGCATTGCATCCATAGCTGGGAGATT
1 CCTGCATCACGACCAAGCTTTAACCCTATCCCTCATGCATGCATTACATCCATAGCTGGGAGATT
* *
45530 CCTGCATCGCGACCAAGCTTTAACCCTATCCCTCATGCATGCGTTACATCCATAGCTGGGAGATT
1 CCTGCATCACGACCAAGCTTTAACCCTATCCCTCATGCATGCATTACATCCATAGCTGGGAGATT
45595 CCTGCATC
1 CCTGCATC
45603 CGTAGCTGCA
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 68 1.00
ACGTcount: A:0.23, C:0.33, G:0.17, T:0.26
Consensus pattern (65 bp):
CCTGCATCACGACCAAGCTTTAACCCTATCCCTCATGCATGCATTACATCCATAGCTGGGAGATT
Found at i:46016 original size:21 final size:22
Alignment explanation
Indices: 45984--46028 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
45974 AATCTAGTTA
45984 ATTAGTTTTGTTAGTATAAATT
1 ATTAGTTTTGTTAGTATAAATT
* *
46006 ATTAG-TTTGTTAGTTTAAGTT
1 ATTAGTTTTGTTAGTATAAATT
46027 AT
1 AT
46029 ATTATATTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.56
Consensus pattern (22 bp):
ATTAGTTTTGTTAGTATAAATT
Found at i:46044 original size:27 final size:28
Alignment explanation
Indices: 46005--46066 Score: 99
Period size: 27 Copynumber: 2.2 Consensus size: 28
45995 TAGTATAAAT
46005 TATTAGTTTGTTAGTTTAAGTTATATTA
1 TATTAGTTTGTTAGTTTAAGTTATATTA
46033 TATT-GTTTGTTAGTTTAAGTTATATATTA
1 TATTAGTTTGTTAGTTTAAG-T-TATATTA
46062 TATTA
1 TATTA
46067 TATAAAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
27 15 0.48
28 5 0.16
29 11 0.35
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (28 bp):
TATTAGTTTGTTAGTTTAAGTTATATTA
Found at i:46601 original size:21 final size:22
Alignment explanation
Indices: 46559--46601 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
46549 AATTGTGTTT
**
46559 AAAAATATTTAGTGTTGTTTTA
1 AAAAATATTTAGTGTTAATTTA
*
46581 AAAAATATTTTGT-TTAATTTA
1 AAAAATATTTAGTGTTAATTTA
46602 TATTGTATGT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (22 bp):
AAAAATATTTAGTGTTAATTTA
Found at i:46773 original size:20 final size:20
Alignment explanation
Indices: 46737--46780 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
46727 AATCATGATT
* *
46737 ATTAGTATAATTACTAAATG
1 ATTAGTATAAATACTAAATC
46757 ATTAGTATCAAAT-CTAAATC
1 ATTAGTAT-AAATACTAAATC
46777 ATTA
1 ATTA
46781 AATTTATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.39
Consensus pattern (20 bp):
ATTAGTATAAATACTAAATC
Done.