Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000968.1 Hibiscus syriacus cultivar Beakdansim tig00001933_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: 83714
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:5101 original size:19 final size:18
Alignment explanation
Indices: 5062--5102 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
5052 GATAAATAGG
* *
5062 TATCGATACTCCTCAATA
1 TATCGATACTCCTAAAGA
5080 TATCGATACATCCTAAAGA
1 TATCGATAC-TCCTAAAGA
5099 TATC
1 TATC
5103 CTTCAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.37, C:0.24, G:0.07, T:0.32
Consensus pattern (18 bp):
TATCGATACTCCTAAAGA
Found at i:6610 original size:40 final size:40
Alignment explanation
Indices: 6550--6716 Score: 105
Period size: 40 Copynumber: 4.2 Consensus size: 40
6540 GTGGTGTATA
* *
6550 TATATAAAAACTA-CATTAAAGTAGAGTATTTAGTGGCGTT
1 TATATAAAAAC-ACCACTAAAGTAGAGTATTTAGCGGCGTT
* * *
6590 TATATAAAAACGCCACTAAAGTACGAGTCTTTGGCGGCGTT
1 TATATAAAAACACCACTAAAGTA-GAGTATTTAGCGGCGTT
* * * ** *
6631 TGTGCTTAAAACACCACTAAAGTATTGTATTTAACGGC---
1 TAT-ATAAAAACACCACTAAAGTAGAGTATTTAGCGGCGTT
** * *
6669 -ATAT-AAAATGCTACTAAAGTACGAGTATTTACCGGCGTT
1 TATATAAAAACACCACTAAAGTA-GAGTATTTAGCGGCGTT
*
6708 TGT-TAAAAA
1 TATATAAAAA
6717 AGCGTCGCCA
Statistics
Matches: 95, Mismatches: 23, Indels: 18
0.70 0.17 0.13
Matches are distributed among these distances:
35 14 0.15
36 12 0.13
37 1 0.01
39 1 0.01
40 25 0.26
41 25 0.26
42 17 0.18
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (40 bp):
TATATAAAAACACCACTAAAGTAGAGTATTTAGCGGCGTT
Found at i:8034 original size:31 final size:33
Alignment explanation
Indices: 7999--8069 Score: 110
Period size: 34 Copynumber: 2.2 Consensus size: 33
7989 TCCTTACACT
*
7999 ATTTTAGATTTAC-AAAAAA-TCCATAATTAGA
1 ATTTTAGATTTACAAAAAAAGTCCATAATTAAA
8030 ATTTTAGATTTACAAAAAAAAGTCCATAATTAAA
1 ATTTTAGATTTAC-AAAAAAAGTCCATAATTAAA
8064 ATTTTA
1 ATTTTA
8070 TATGAAGTTC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
31 13 0.36
33 6 0.17
34 17 0.47
ACGTcount: A:0.49, C:0.08, G:0.06, T:0.37
Consensus pattern (33 bp):
ATTTTAGATTTACAAAAAAAGTCCATAATTAAA
Found at i:9331 original size:39 final size:40
Alignment explanation
Indices: 9288--9371 Score: 91
Period size: 39 Copynumber: 2.1 Consensus size: 40
9278 AGCTAAATAT
* * * *
9288 GAAGACT-CTACAATTGCATGGCGTCTTTAGGCAAATGAA
1 GAAGACTCCTACAACTGCATGACATCTTCAGGCAAATGAA
* * *
9327 GAAGA-TCCTACGACTGCATGATATGTTCAGGCAAATGAA
1 GAAGACTCCTACAACTGCATGACATCTTCAGGCAAATGAA
9366 GAAGAC
1 GAAGAC
9372 CCAGGAGTGC
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
38 1 0.03
39 35 0.97
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.23
Consensus pattern (40 bp):
GAAGACTCCTACAACTGCATGACATCTTCAGGCAAATGAA
Found at i:9857 original size:19 final size:19
Alignment explanation
Indices: 9833--9874 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
9823 CAATCCATAT
9833 AATGTATGGCACATGGTAA
1 AATGTATGGCACATGGTAA
9852 AATGTATGGCACATGGTAA
1 AATGTATGGCACATGGTAA
9871 AATG
1 AATG
9875 CATGTCTAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.26
Consensus pattern (19 bp):
AATGTATGGCACATGGTAA
Found at i:12628 original size:42 final size:42
Alignment explanation
Indices: 12507--12631 Score: 205
Period size: 42 Copynumber: 3.0 Consensus size: 42
12497 CAATCGAATC
** *
12507 ATTAGGTGAATCATTGGAATTTCCAATATTATTATTAAAAGT
1 ATTAGGTGAATCATTGGAATTTCCAATAGGATTATTAGAAGT
*
12549 ATTAGGTGAATCATTGAAATTTCCAATAGGATTATTAGAAGT
1 ATTAGGTGAATCATTGGAATTTCCAATAGGATTATTAGAAGT
*
12591 ATTAGGTGAATCATTGGAATTTCCAATCGGATTATTAGAAG
1 ATTAGGTGAATCATTGGAATTTCCAATAGGATTATTAGAAG
12632 GTTTAACCGG
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 77 1.00
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (42 bp):
ATTAGGTGAATCATTGGAATTTCCAATAGGATTATTAGAAGT
Found at i:12785 original size:27 final size:28
Alignment explanation
Indices: 12755--12812 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 28
12745 ACATATTTAA
*
12755 AAGTAATCAATAAAA-AAATATAGTAGC
1 AAGTAAACAATAAAACAAATATAGTAGC
*
12782 AAGTAAACAATAAAACAAATATATTAGC
1 AAGTAAACAATAAAACAAATATAGTAGC
12810 AAG
1 AAG
12813 GAAAGATACA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
27 14 0.50
28 14 0.50
ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21
Consensus pattern (28 bp):
AAGTAAACAATAAAACAAATATAGTAGC
Found at i:13176 original size:28 final size:28
Alignment explanation
Indices: 13144--13198 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
13134 ATACTAAGTT
13144 TGCCGACTAAACATG-AAAGAAATGAGTG
1 TGCCGACTAAACATGCAAA-AAATGAGTG
13172 TGCCGACTAAACATGCAAAAAATGAGT
1 TGCCGACTAAACATGCAAAAAATGAGT
13199 AAGTTGAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 23 0.88
29 3 0.12
ACGTcount: A:0.44, C:0.16, G:0.22, T:0.18
Consensus pattern (28 bp):
TGCCGACTAAACATGCAAAAAATGAGTG
Found at i:22315 original size:23 final size:21
Alignment explanation
Indices: 22278--22321 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 21
22268 TATAATTAAT
22278 AAAATTTAAATAAATAAAATA
1 AAAATTTAAATAAATAAAATA
22299 AAAATATTAAAATAAATAAAATA
1 AAAAT-TT-AAATAAATAAAATA
22322 TCAAATAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 5 0.24
22 2 0.10
23 14 0.67
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (21 bp):
AAAATTTAAATAAATAAAATA
Found at i:39635 original size:20 final size:22
Alignment explanation
Indices: 39590--39647 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
39580 GCATGGGTAG
39590 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
39614 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
39634 TGTATCGATGCACT
1 TGCATCGATGCACT
39648 TCAAAGGGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:40347 original size:24 final size:24
Alignment explanation
Indices: 40317--40372 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
40307 TAGAAGTTCG
*
40317 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAACTCA
40341 ATTGAAGCCTAAAATTTGAACTCA
1 ATTGAAGCCTAAAATTTGAACTCA
40365 ATTGAAGC
1 ATTGAAGC
40373 GAAAGAATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTTGAACTCA
Found at i:40907 original size:10 final size:11
Alignment explanation
Indices: 40870--40911 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
40860 ATATAAAATC
40870 CGGTTCAACCG
1 CGGTTCAACCG
40881 CGGTTCAACCG
1 CGGTTCAACCG
*
40892 CGGTTGAACC-
1 CGGTTCAACCG
*
40902 CGGTTGAACC
1 CGGTTCAACC
40912 AGTGAACCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
10 10 0.33
11 20 0.67
ACGTcount: A:0.19, C:0.33, G:0.29, T:0.19
Consensus pattern (11 bp):
CGGTTCAACCG
Found at i:42256 original size:23 final size:23
Alignment explanation
Indices: 42230--42293 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
42220 GGACATTATA
*
42230 TGGCACTACGGTGCATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
*
42253 TGGCACTTCAGTGCATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
*
42276 CGGCACTTCGGTGCATTT
1 TGGCACTTCGGTGCATTT
42294 ACATGAGCTG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.16, C:0.27, G:0.25, T:0.33
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:53540 original size:15 final size:16
Alignment explanation
Indices: 53497--53540 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
53487 AACTTCTTAC
53497 TCATTTAATATTTGAA
1 TCATTTAATATTTGAA
* *
53513 TCATTCAGTATTT-AA
1 TCATTTAATATTTGAA
*
53528 TCATTTAAAATTT
1 TCATTTAATATTT
53541 TTATCTTCTA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.50
Consensus pattern (16 bp):
TCATTTAATATTTGAA
Found at i:69842 original size:14 final size:14
Alignment explanation
Indices: 69823--69852 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
69813 TATAATTATC
*
69823 AATAATGTATTTTT
1 AATAATGTAATTTT
69837 AATAATGTAATTTT
1 AATAATGTAATTTT
69851 AA
1 AA
69853 AAAATCTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
AATAATGTAATTTT
Found at i:70455 original size:2 final size:2
Alignment explanation
Indices: 70448--70478 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
70438 TACCAATTCC
70448 TA 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 TA T
70479 CTAACTCATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:74102 original size:30 final size:30
Alignment explanation
Indices: 74081--74170 Score: 171
Period size: 30 Copynumber: 3.0 Consensus size: 30
74071 CTATGGACAA
74081 TTACCGAGGATCTTTATGACCTCTGGATAG
1 TTACCGAGGATCTTTATGACCTCTGGATAG
*
74111 TTACCGAGGATCTTTATGACCTCTAGATAG
1 TTACCGAGGATCTTTATGACCTCTGGATAG
74141 TTACCGAGGATCTTTATGACCTCTGGATAG
1 TTACCGAGGATCTTTATGACCTCTGGATAG
74171 GTCCTTCGGA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 58 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (30 bp):
TTACCGAGGATCTTTATGACCTCTGGATAG
Found at i:77276 original size:22 final size:22
Alignment explanation
Indices: 77248--77347 Score: 182
Period size: 22 Copynumber: 4.5 Consensus size: 22
77238 GGACTATTAT
77248 GTCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
77270 GTCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
77292 GTCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
*
77314 GTCCCGAAGGACCACTAGATAC
1 GTCCCGAAGGACCACTGGATAC
*
77336 TTCCCGAAGGAC
1 GTCCCGAAGGAC
77348 TAATATACCC
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 76 1.00
ACGTcount: A:0.28, C:0.32, G:0.26, T:0.14
Consensus pattern (22 bp):
GTCCCGAAGGACCACTGGATAC
Found at i:78796 original size:64 final size:64
Alignment explanation
Indices: 78687--78849 Score: 163
Period size: 64 Copynumber: 2.5 Consensus size: 64
78677 TCCCTTGACG
* * *
78687 GGTGCATCGATGCACTACC-CATGCATCGGTGCATAAATCCTATTCGATGTT-TGTATTTTAAGC
1 GGTGCATCGATGCACT-CCTTATGCATCGATGCATAAATCCTATTCGATGTTATGTAATTTAA--
78750 A-
63 AT
** * *
78751 GGTGCATCGATGCACTCCTTATGCATCGATGCATCCATGGC-ATTCGATGTTCATTTAATTTAAA
1 GGTGCATCGATGCACTCCTTATGCATCGATGCATAAAT-CCTATTCGATGTT-ATGTAATTTAAA
78815 T
64 T
* *
78816 GAGTGCATCAATGAACTCCTTATGCATCGATGCA
1 G-GTGCATCGATGCACTCCTTATGCATCGATGCA
78850 CCTTCAATAA
Statistics
Matches: 84, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
63 2 0.02
64 42 0.50
65 2 0.02
66 38 0.45
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.33
Consensus pattern (64 bp):
GGTGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTATGTAATTTAAAT
Found at i:80994 original size:64 final size:63
Alignment explanation
Indices: 80923--81099 Score: 153
Period size: 65 Copynumber: 2.7 Consensus size: 63
80913 TTGGACCCTT
*
80923 AGTGCATCGGTGCA-CTAAGAGTGCATCAATGCATCAAGTGCATTCGATG-TTTCA-AAATAGCC
1 AGTGCATCGGTGCAGCT--G-GTGCATCAATGCATCAAATGCATTCGATGTTTTCATAAA-AGCC
*
80985 AG
62 AC
* * * * *
80987 AGTGCATCGATGAATGGCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTC
1 AGTGCATCGGTGCA--GCTGGTGCATCAATGCATCAAATGCATTCGATGTTTTCATAAAAGCCAC
* * * * *
81052 AGTGCATCGGTGCATGGTATGTGCATCGATACATGAAATGCATTCGAT
1 AGTGCATCGGTGCA-GCT-GGTGCATCAATGCATCAAATGCATTCGAT
81100 ATTCAATTTA
Statistics
Matches: 93, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
64 41 0.44
65 47 0.51
66 3 0.03
67 2 0.02
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (63 bp):
AGTGCATCGGTGCAGCTGGTGCATCAATGCATCAAATGCATTCGATGTTTTCATAAAAGCCAC
Found at i:81079 original size:65 final size:64
Alignment explanation
Indices: 80943--81099 Score: 183
Period size: 65 Copynumber: 2.4 Consensus size: 64
80933 TGCACTAAGA
* * *
80943 GTGCATCAATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGAATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGAATGGCTG
* * * *
81007 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-T
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAGCCACAGTGCATCGATGAATGGCT
*
81070 AT
64 -G
* *
81072 GTGCATCGATACATGAAATGCATTCGAT
1 GTGCATCGATGCATCAAATGCATTCGAT
81100 ATTCAATTTA
Statistics
Matches: 80, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
64 28 0.35
65 49 0.61
66 3 0.04
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGAATGGCTG
Found at i:81603 original size:2 final size:2
Alignment explanation
Indices: 81596--81642 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
81586 AACCAATTGA
81596 AT AT AT 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
81638 AT AT A
1 AT AT A
81643 GCTTAAGCTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.