Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003091.1 Hibiscus syriacus cultivar Beakdansim tig00006450_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: 66195
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.33
Found at i:2230 original size:14 final size:14
Alignment explanation
Indices: 2198--2224 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2188 TTGTTTCACT
2198 GAAAACATTTTCCA
1 GAAAACATTTTCCA
2212 GAAAACATTTTCC
1 GAAAACATTTTCC
2225 GTAAAATGAA
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:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (14 bp):
GAAAACATTTTCCA
Found at i:2381 original size:22 final size:22
Alignment explanation
Indices: 2356--2397 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2346 TATAATATAA
2356 TAATAATATTATTATAAAAACT
1 TAATAATATTATTATAAAAACT
* *
2378 TAATATTATTATTTTAAAAA
1 TAATAATATTATTATAAAAA
2398 TATTAGAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
TAATAATATTATTATAAAAACT
Found at i:5539 original size:20 final size:21
Alignment explanation
Indices: 5506--5546 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
5496 ATAAATAACA
5506 TAAAAACTACAATTTAATATT
1 TAAAAACTACAATTTAATATT
*
5527 TAAAAACT-TAATTTAATATT
1 TAAAAACTACAATTTAATATT
5547 GTACTATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAAAACTACAATTTAATATT
Found at i:6808 original size:26 final size:26
Alignment explanation
Indices: 6772--6825 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
6762 ACAGAAGTGC
* *
6772 TAATAGACATAAGGTCATTCCCACTA
1 TAATACACATAAGGTCATGCCCACTA
*
6798 TAATACACATAAGGTCGTGCCCACTA
1 TAATACACATAAGGTCATGCCCACTA
6824 TA
1 TA
6826 TGCACTTAGT
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:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (26 bp):
TAATACACATAAGGTCATGCCCACTA
Found at i:13291 original size:26 final size:26
Alignment explanation
Indices: 13257--13306 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
13247 GTGCTAATAC
*
13257 ACACATAAGGTTGTGCCCACCATAAT
1 ACACATAAGGTCGTGCCCACCATAAT
*
13283 ACACATAAGGTCGTGCCTACCATA
1 ACACATAAGGTCGTGCCCACCATA
13307 TGCACTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.22
Consensus pattern (26 bp):
ACACATAAGGTCGTGCCCACCATAAT
Found at i:19146 original size:14 final size:14
Alignment explanation
Indices: 19129--19157 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
19119 CAACGGTCAA
19129 CGGTCGGGTCGGGT
1 CGGTCGGGTCGGGT
19143 CGGTCGGGTCGGGT
1 CGGTCGGGTCGGGT
19157 C
1 C
19158 AGACCGATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.24, G:0.55, T:0.21
Consensus pattern (14 bp):
CGGTCGGGTCGGGT
Found at i:19201 original size:19 final size:19
Alignment explanation
Indices: 19156--19207 Score: 79
Period size: 19 Copynumber: 2.7 Consensus size: 19
19146 TCGGGTCGGG
*
19156 TCAGACCGATCAAACTGGT
1 TCAGACCGGTCAAACTGGT
19175 TCAGACCGGTCAAACTGGT
1 TCAGACCGGTCAAACTGGT
19194 TC-GAACCGGTCAAA
1 TCAG-ACCGGTCAAA
19208 ACCGGTTCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 1 0.03
19 30 0.97
ACGTcount: A:0.31, C:0.27, G:0.23, T:0.19
Consensus pattern (19 bp):
TCAGACCGGTCAAACTGGT
Found at i:19214 original size:20 final size:20
Alignment explanation
Indices: 19160--19234 Score: 73
Period size: 19 Copynumber: 3.8 Consensus size: 20
19150 GTCGGGTCAG
* * *
19160 ACCGATCAAACTGGTT-CAG
1 ACCGGTCAAACCGGTTCCAA
* *
19179 ACCGGTCAAACTGGTT-CGA
1 ACCGGTCAAACCGGTTCCAA
19198 ACCGGTCAAAACCGGTTCCAA
1 ACCGGTC-AAACCGGTTCCAA
*
19219 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
19235 TTCCACCTTC
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
19 23 0.48
20 17 0.35
21 8 0.17
ACGTcount: A:0.29, C:0.28, G:0.23, T:0.20
Consensus pattern (20 bp):
ACCGGTCAAACCGGTTCCAA
Found at i:19231 original size:9 final size:10
Alignment explanation
Indices: 19165--19234 Score: 65
Period size: 10 Copynumber: 7.1 Consensus size: 10
19155 GTCAGACCGA
*
19165 TCAAACTGGT
1 TCAAACCGGT
*
19175 TCAGACCGG-
1 TCAAACCGGT
*
19184 TCAAACTGGT
1 TCAAACCGGT
*
19194 TCGAACCGG-
1 TCAAACCGGT
19203 TCAAAACCGGT
1 TC-AAACCGGT
19214 TCCAAACCGGT
1 T-CAAACCGGT
19225 T-AAACCGGT
1 TCAAACCGGT
19234 T
1 T
19235 TTCCACCTTC
Statistics
Matches: 49, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
9 18 0.37
10 20 0.41
11 10 0.20
12 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.21
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:26375 original size:19 final size:19
Alignment explanation
Indices: 26353--26391 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
26343 TCGGGTCGGG
26353 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
**
26372 TCAGTTCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
26391 T
1 T
26392 TGAACCGATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.28, G:0.26, T:0.23
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:28072 original size:12 final size:12
Alignment explanation
Indices: 28055--28079 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28045 GTTCTTAAGA
28055 GAAGATAATGAG
1 GAAGATAATGAG
28067 GAAGATAATGAG
1 GAAGATAATGAG
28079 G
1 G
28080 GTAACGGTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.36, T:0.16
Consensus pattern (12 bp):
GAAGATAATGAG
Found at i:37553 original size:47 final size:47
Alignment explanation
Indices: 37496--37749 Score: 427
Period size: 47 Copynumber: 5.4 Consensus size: 47
37486 AATACATCAT
*
37496 TTTCAAGCATTTTCAATTATGGCATCCGTTCATGCCTTAATGCATCC
1 TTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATGCATCC
* * * *
37543 TTTCATGCATTTTCAATTATGACATCCGTACATGCCTTTATGTATCC
1 TTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATGCATCC
* *
37590 TTTCATGCATTTTCAATTATGGTATCCGTTCATGCCTTAATGCATCA
1 TTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATGCATCC
*
37637 TTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATGCATCT
1 TTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATGCATCC
*
37684 TTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTTATGCATCC
1 TTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATGCATCC
37731 TTTCATGCATTTTCAATTA
1 TTTCATGCATTTTCAATTA
37750 AGAAATTGAT
Statistics
Matches: 192, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 192 1.00
ACGTcount: A:0.22, C:0.23, G:0.12, T:0.43
Consensus pattern (47 bp):
TTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATGCATCC
Found at i:37621 original size:27 final size:26
Alignment explanation
Indices: 37497--37749 Score: 107
Period size: 20 Copynumber: 10.7 Consensus size: 26
37487 ATACATCATT
*
37497 TTCAAGCATTTTCAATTATGGCATCCG
1 TTCATGCATTTTCAATTAT-GCATCCG
* *
37524 TTCATGC--CTT--A--ATGCATCCT
1 TTCATGCATTTTCAATTATGCATCCG
37544 TTCATGCATTTTCAATTATGACATCCG
1 TTCATGCATTTTCAATTATG-CATCCG
* * * *
37571 TACATGC-----C-TTTATGTATCCT
1 TTCATGCATTTTCAATTATGCATCCG
*
37591 TTCATGCATTTTCAATTATGGTATCCG
1 TTCATGCATTTTCAATTAT-GCATCCG
* **
37618 TTCATGC--CTT--A--ATGCATCAT
1 TTCATGCATTTTCAATTATGCATCCG
37638 TTCATGCATTTTCAATTATGGCATCCG
1 TTCATGCATTTTCAATTAT-GCATCCG
* **
37665 TTCATGC--CTT--A--ATGCATCTT
1 TTCATGCATTTTCAATTATGCATCCG
37685 TTCATGCATTTTCAATTATGGCATCCG
1 TTCATGCATTTTCAATTAT-GCATCCG
* *
37712 TTCATGC-----C-TTTATGCATCCT
1 TTCATGCATTTTCAATTATGCATCCG
37732 TTCATGCATTTTCAATTA
1 TTCATGCATTTTCAATTA
37750 AGAAATTGAT
Statistics
Matches: 164, Mismatches: 28, Indels: 69
0.63 0.11 0.26
Matches are distributed among these distances:
20 59 0.36
21 15 0.09
22 8 0.05
23 3 0.02
24 3 0.02
25 8 0.05
26 14 0.09
27 54 0.33
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.42
Consensus pattern (26 bp):
TTCATGCATTTTCAATTATGCATCCG
Found at i:39824 original size:30 final size:31
Alignment explanation
Indices: 39788--39935 Score: 140
Period size: 31 Copynumber: 4.8 Consensus size: 31
39778 AATGTGACTC
*
39788 TTGGGTAGGCTCTGCGGCCC-GAGATCATTA
1 TTGGGTAGGCCCTGCGGCCCTGAGATCATTA
* *
39818 TTGGGTAGGCCCTGCGGCCCTGGGAT-TTTA
1 TTGGGTAGGCCCTGCGGCCCTGAGATCATTA
* * * * *
39848 CTTGGGTAAGCCCCGTGGCCCTGAGACCATTC
1 -TTGGGTAGGCCCTGCGGCCCTGAGATCATTA
* * *
39880 TTGGGTAGGCCCTACGGCCCTAAGAT-ATTTC
1 TTGGGTAGGCCCTGCGGCCCTGAGATCA-TTA
* *
39911 TTGGGTAGGCCCCGTGGCCCTGAGA
1 TTGGGTAGGCCCTGCGGCCCTGAGA
39936 ACTTTCTTGA
Statistics
Matches: 94, Mismatches: 20, Indels: 7
0.78 0.17 0.06
Matches are distributed among these distances:
30 23 0.24
31 69 0.73
32 2 0.02
ACGTcount: A:0.15, C:0.27, G:0.32, T:0.26
Consensus pattern (31 bp):
TTGGGTAGGCCCTGCGGCCCTGAGATCATTA
Found at i:39892 original size:62 final size:62
Alignment explanation
Indices: 39803--39944 Score: 189
Period size: 62 Copynumber: 2.3 Consensus size: 62
39793 TAGGCTCTGC
* * * **
39803 GGCCC-GAGATCATTATTGGGTAGGCCCTGCGGCCCTGGGAT-TTTACTTGGGTAAGCCCCGT
1 GGCCCTGAGAACATTCTTGGGTAGGCCCTACGGCCCTAAGATATTT-CTTGGGTAAGCCCCGT
* *
39864 GGCCCTGAGACCATTCTTGGGTAGGCCCTACGGCCCTAAGATATTTCTTGGGTAGGCCCCGT
1 GGCCCTGAGAACATTCTTGGGTAGGCCCTACGGCCCTAAGATATTTCTTGGGTAAGCCCCGT
*
39926 GGCCCTGAGAACTTTCTTG
1 GGCCCTGAGAACATTCTTG
39945 AATAGGCTCT
Statistics
Matches: 71, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
61 5 0.07
62 63 0.89
63 3 0.04
ACGTcount: A:0.15, C:0.27, G:0.30, T:0.27
Consensus pattern (62 bp):
GGCCCTGAGAACATTCTTGGGTAGGCCCTACGGCCCTAAGATATTTCTTGGGTAAGCCCCGT
Found at i:39961 original size:62 final size:62
Alignment explanation
Indices: 39848--39967 Score: 161
Period size: 62 Copynumber: 1.9 Consensus size: 62
39838 TGGGATTTTA
* ** *
39848 CTTGGGTAAGCCCCGTGGCCCTGAGACCATTCTTGGGTAGGCCCTACGGCCCTAAGATATTT
1 CTTGGGTAAGCCCCGTGGCCCTGAGAACATTCTTGAATAGGCCCTACGGCCCCAAGATATTT
* * *
39910 CTTGGGTAGGCCCCGTGGCCCTGAGAACTTTCTTGAATAGGCTCTGA-GGCCCCAAGAT
1 CTTGGGTAAGCCCCGTGGCCCTGAGAACATTCTTGAATAGGCCCT-ACGGCCCCAAGAT
39968 GCTCTTTTAG
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
62 49 0.98
63 1 0.02
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.25
Consensus pattern (62 bp):
CTTGGGTAAGCCCCGTGGCCCTGAGAACATTCTTGAATAGGCCCTACGGCCCCAAGATATTT
Found at i:50664 original size:4 final size:4
Alignment explanation
Indices: 50657--50725 Score: 90
Period size: 4 Copynumber: 18.0 Consensus size: 4
50647 GTGTGTGTTT
* *
50657 ATAC ATAC ATAC ATAC ATAC AT-- ATAG ACAC ATAC AT-C ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
50702 ATAC ATAC ATAC ATAC ATAT ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC
50726 CAACTAGAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
2 2 0.04
3 3 0.05
4 52 0.91
ACGTcount: A:0.49, C:0.23, G:0.01, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:56630 original size:58 final size:59
Alignment explanation
Indices: 56557--56667 Score: 161
Period size: 59 Copynumber: 1.9 Consensus size: 59
56547 AATCCTCCGA
** *
56557 CTATAGGATGTTACTTTATTGA-TTCATCAATTATTAAAAGTTATAAAATGGTACCCGG
1 CTATAGGATACTACTTTATTGAGTTCATCAACTATTAAAAGTTATAAAATGGTACCCGG
* * *
56615 CTATAGGATACTACTTTATTGAGTTCCTCGACTATTAAAATTTATAAAATGGT
1 CTATAGGATACTACTTTATTGAGTTCATCAACTATTAAAAGTTATAAAATGGT
56668 CACCTAACTA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
58 20 0.43
59 26 0.57
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (59 bp):
CTATAGGATACTACTTTATTGAGTTCATCAACTATTAAAAGTTATAAAATGGTACCCGG
Found at i:62839 original size:21 final size:21
Alignment explanation
Indices: 62809--62856 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
62799 TAATTTTCAA
62809 ACATTATTGCACCTAATTTTG
1 ACATTATTGCACCTAATTTTG
*
62830 ACATTGTTGCACCTAATTTTG
1 ACATTATTGCACCTAATTTTG
62851 ACATTA
1 ACATTA
62857 CAATATTAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.42
Consensus pattern (21 bp):
ACATTATTGCACCTAATTTTG
Done.