Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004295.1 Hibiscus syriacus cultivar Beakdansim tig00009426_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: 63566
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Found at i:3923 original size:15 final size:14
Alignment explanation
Indices: 3905--3944 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
3895 ATGCTTTGAG
3905 TGATGATGATGATT
1 TGATGATGATGATT
*
3919 ATGATGATGACGATT
1 -TGATGATGATGATT
3934 TGGATGATGAT
1 T-GATGATGAT
3945 TGTGATCTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 1 0.05
15 21 0.95
ACGTcount: A:0.30, C:0.03, G:0.30, T:0.38
Consensus pattern (14 bp):
TGATGATGATGATT
Found at i:4788 original size:18 final size:18
Alignment explanation
Indices: 4739--4788 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
4729 CATGCCACCA
*
4739 CCATACCCATACCCATAT
1 CCATACCCATACCCACAT
* * *
4757 CAATATCCATACCCGCAT
1 CCATACCCATACCCACAT
*
4775 CCATACCCACACCC
1 CCATACCCATACCC
4789 TCAACCCGAC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.32, C:0.48, G:0.02, T:0.18
Consensus pattern (18 bp):
CCATACCCATACCCACAT
Found at i:5193 original size:7 final size:7
Alignment explanation
Indices: 5181--5215 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
5171 TTTTTCTTTT
5181 CATGTTC
1 CATGTTC
5188 CATGTTC
1 CATGTTC
5195 CATGTTC
1 CATGTTC
5202 CATGTTC
1 CATGTTC
5209 CATGTTC
1 CATGTTC
5216 AACCAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.14, C:0.29, G:0.14, T:0.43
Consensus pattern (7 bp):
CATGTTC
Found at i:5571 original size:15 final size:15
Alignment explanation
Indices: 5538--5595 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
5528 TAACAAAGTT
5538 TTAAACTCGAGATTTG
1 TTAAACTCGAGA-TTG
*
5554 TTAAACCCGAGATTG
1 TTAAACTCGAGATTG
*
5569 TTAAACTCGAGATTA
1 TTAAACTCGAGATTG
5584 TTAAACTCGAGA
1 TTAAACTCGAGA
5596 CTTATTTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
15 28 0.72
16 11 0.28
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (15 bp):
TTAAACTCGAGATTG
Found at i:7831 original size:51 final size:51
Alignment explanation
Indices: 7755--7855 Score: 175
Period size: 51 Copynumber: 2.0 Consensus size: 51
7745 AAATACCCAT
*
7755 TTAGCACAACGTTCATAAGAACTCAAAACAATTTAAAAACAATTTTATATC
1 TTAGCACAACGTTCATAAGAACTCAAAACAATTTAAAAACAATTTAATATC
* *
7806 TTAGCACAAGGTTCATAAGAACTCAAAACAATTTGAAAACAATTTAATAT
1 TTAGCACAACGTTCATAAGAACTCAAAACAATTTAAAAACAATTTAATAT
7856 TTAAAGTTTG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.48, C:0.16, G:0.08, T:0.29
Consensus pattern (51 bp):
TTAGCACAACGTTCATAAGAACTCAAAACAATTTAAAAACAATTTAATATC
Found at i:8652 original size:60 final size:59
Alignment explanation
Indices: 8521--8646 Score: 148
Period size: 60 Copynumber: 2.1 Consensus size: 59
8511 ACACAAATGA
*
8521 TCCACCAACTATAGAGCGCTGCTTTATTAAGTCTCCCAATTATTAAAAGTTACAAAAGGG
1 TCCA-CAACTATAGAGCGCTGCTTTATTAAGTCTCCCAACTATTAAAAGTTACAAAAGGG
* * * * * *
8581 TTCCTCAACTATAGAGCGTTGTTTTGTTGAGTC-CCCTAACTATTAAAAGTTACAAAATGG
1 -TCCACAACTATAGAGCGCTGCTTTATTAAGTCTCCC-AACTATTAAAAGTTACAAAAGGG
8641 -CCACAA
1 TCCACAA
8647 GACTATTCAT
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
58 5 0.09
59 3 0.05
60 45 0.80
61 3 0.05
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.30
Consensus pattern (59 bp):
TCCACAACTATAGAGCGCTGCTTTATTAAGTCTCCCAACTATTAAAAGTTACAAAAGGG
Found at i:10424 original size:122 final size:122
Alignment explanation
Indices: 10264--10512 Score: 295
Period size: 122 Copynumber: 2.0 Consensus size: 122
10254 ATTTCAACGA
** * ** *
10264 CGTTTTTATAAAAACACCGCGATAGGGTATCACTTTAGCGGCGTTTTTATACAAACGCCGCAATA
1 CGTTTTTATAAAAACACCGCGATAAAGTAGCACTTTAGCGGCGTTTCGATACAAACACCGCAATA
* * * * * *
10329 GGTTCATCTATAGTGG-CGTTTTCAATAAACGTCGCA-ATGTGAGTAGTACTTTAGAGG
66 GGTTAATCCATAGTGGTAGTTTTCAACAAACGCCGCATATAT-AGT-GTACTTTAGAGG
* * * * *
10386 CGTTTTTATTAAAACGCCGCTATAAAGTAGCATTTTAGCGGCGTTTCGGTACAAACACCGCAATA
1 CGTTTTTATAAAAACACCGCGATAAAGTAGCACTTTAGCGGCGTTTCGATACAAACACCGCAATA
* *
10451 GGTTAATCCATAGTGGTATTTTTCAACAAACGCCGCATATATAGTGTACTTTAGTGG
66 GGTTAATCCATAGTGGTAGTTTTCAACAAACGCCGCATATATAGTGTACTTTAGAGG
10508 CGTTT
1 CGTTT
10513 GTAACTAAAA
Statistics
Matches: 106, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
122 84 0.79
123 19 0.18
124 3 0.03
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (122 bp):
CGTTTTTATAAAAACACCGCGATAAAGTAGCACTTTAGCGGCGTTTCGATACAAACACCGCAATA
GGTTAATCCATAGTGGTAGTTTTCAACAAACGCCGCATATATAGTGTACTTTAGAGG
Found at i:14729 original size:43 final size:43
Alignment explanation
Indices: 14679--15050 Score: 225
Period size: 43 Copynumber: 8.6 Consensus size: 43
14669 ATGGTAATTA
* *
14679 GCGGCGTTTATATCCAAAAACGTCGCTATAGATTTGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATTTGACCTTTT
** * * * *
14722 GTAGCGTTTGTATCTAAAAACGCCGCTATATATCTAACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATTTGACCTTTT
* * * *
14765 GCGGCATTTTTTTCC-AAAACCCCGCTATAGATCTTGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGAT-TTGACCTTTT
* * ** * *
14808 GCGGCGTTTGTATCCAACAACACCATTATATATAT-ACCCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATTTGA-CCTTTT
* * * * * *
14851 GCGGCATTT-T-TGGCAAAAACGTCGCTAGAGAACTTGACATTTT
1 GCGGCGTTTGTAT-CCAAAAACGCCGCTATAG-ATTTGACCTTTT
* *
14894 GCGGCGTTTGTATCCAAAAATGCCGCTATAGATCTCGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGAT-TTGACCTTTT
** * * * * * ** *
14938 ATGTCATTTGT-TCTAAAAATGCCGCTATAAATCTCAATCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGAT-TTGACCTTTT
* * * * *
14981 GTGGAGTTTGT-TCCAAAAACGCTGCTATATATCTTGACTTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGAT-TTGACCTTTT
* * * *
15024 ACGGCGTTTTTATATCACAAACGCCGC
1 GCGGCGTTTGTAT-CCAAAAACGCCGC
15051 CAGCGGCGCT
Statistics
Matches: 244, Mismatches: 74, Indels: 20
0.72 0.22 0.06
Matches are distributed among these distances:
41 1 0.00
42 27 0.11
43 161 0.66
44 44 0.18
45 11 0.05
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.35
Consensus pattern (43 bp):
GCGGCGTTTGTATCCAAAAACGCCGCTATAGATTTGACCTTTT
Found at i:14838 original size:86 final size:86
Alignment explanation
Indices: 14693--14913 Score: 264
Period size: 86 Copynumber: 2.6 Consensus size: 86
14683 CGTTTATATC
** ** * * * *
14693 CAAAAACGTCGCTATAGAT-TTGACCTTTTGTAGCGTTTGTATCTAAAAACGCCGCTATATATCT
1 CAAAAACCCCGCTATAGATCTTGACCTTTTGCGGCGTTTGTATCCAAAAACACCACTATATATAT
**
14757 AACCTTTTGCGGCATTTTTTT
66 AACCTTTTGCGGCATTTTTGG
* * *
14778 CCAAAACCCCGCTATAGATCTTGACCTTTTGCGGCGTTTGTATCCAACAACACCATTATATATAT
1 CAAAAACCCCGCTATAGATCTTGACCTTTTGCGGCGTTTGTATCCAAAAACACCACTATATATAT
*
14843 ACCCTTTTGCGGCATTTTTGG
66 AACCTTTTGCGGCATTTTTGG
** * * *
14864 CAAAAACGTCGCTAGAGAACTTGACATTTTGCGGCGTTTGTATCCAAAAA
1 CAAAAACCCCGCTATAGATCTTGACCTTTTGCGGCGTTTGTATCCAAAAA
14914 TGCCGCTATA
Statistics
Matches: 114, Mismatches: 21, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
85 16 0.14
86 98 0.86
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (86 bp):
CAAAAACCCCGCTATAGATCTTGACCTTTTGCGGCGTTTGTATCCAAAAACACCACTATATATAT
AACCTTTTGCGGCATTTTTGG
Found at i:17876 original size:13 final size:13
Alignment explanation
Indices: 17858--17905 Score: 55
Period size: 12 Copynumber: 3.8 Consensus size: 13
17848 AAAATAAAAG
*
17858 ACTAATACTAATT
1 ACTAATAATAATT
17871 ACTAATAATAA-T
1 ACTAATAATAATT
*
17883 AATAATAATAA-T
1 ACTAATAATAATT
*
17895 AATAATAATAA
1 ACTAATAATAA
17906 ACAAGAAAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
12 23 0.70
13 10 0.30
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.33
Consensus pattern (13 bp):
ACTAATAATAATT
Found at i:17881 original size:3 final size:3
Alignment explanation
Indices: 17873--17905 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
17863 TACTAATTAC
17873 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
17906 ACAAGAAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:18119 original size:3 final size:3
Alignment explanation
Indices: 18111--18135 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
18101 ATTCAACGAT
18111 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
18136 AACCCAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:18392 original size:14 final size:14
Alignment explanation
Indices: 18360--18393 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
18350 AAGAAGTAAT
*
18360 CCCTGCAAATAAAT
1 CCCTGCAAATAAAA
*
18374 TCCTGCAAATAAAA
1 CCCTGCAAATAAAA
18388 CCCTGC
1 CCCTGC
18394 GAAAAATAGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.32, G:0.09, T:0.21
Consensus pattern (14 bp):
CCCTGCAAATAAAA
Found at i:21524 original size:21 final size:21
Alignment explanation
Indices: 21500--21543 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
21490 TTTCTTAAGG
21500 TGTCAAATTGGAAGAAAGTGT
1 TGTCAAATTGGAAGAAAGTGT
21521 TGTCAAATTGGAAGAAAGTGT
1 TGTCAAATTGGAAGAAAGTGT
21542 TG
1 TG
21544 CACTTTGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.05, G:0.30, T:0.30
Consensus pattern (21 bp):
TGTCAAATTGGAAGAAAGTGT
Found at i:23118 original size:2 final size:2
Alignment explanation
Indices: 23111--23145 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
23101 AGCGTGGCCT
23111 TA TA 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 TA TA T
23146 TCGTAAATAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:26836 original size:18 final size:19
Alignment explanation
Indices: 26808--26844 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
26798 CCATCTAATT
26808 ATTATTTTAATTTTATTTA
1 ATTATTTTAATTTTATTTA
*
26827 ATTA-TTTAATTTTTTTTA
1 ATTATTTTAATTTTATTTA
26845 TATAAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
ATTATTTTAATTTTATTTA
Found at i:28497 original size:2 final size:2
Alignment explanation
Indices: 28490--28579 Score: 180
Period size: 2 Copynumber: 45.0 Consensus size: 2
28480 TATTCCAATA
28490 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
28532 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
28574 AT AT AT
1 AT AT AT
28580 CATCAATTAT
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 88 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35222 original size:2 final size:2
Alignment explanation
Indices: 35215--35247 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
35205 GACACTAAAT
35215 TA 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 TA T
35248 GCATATTAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:43007 original size:16 final size:16
Alignment explanation
Indices: 42983--43017 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
42973 AGAATTATAT
*
42983 TTAAAAAAATCGAAAAC
1 TTAAAAAAA-CCAAAAC
43000 TTAAAAAAACCAAAAC
1 TTAAAAAAACCAAAAC
43016 TT
1 TT
43018 TGAAAACTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.63, C:0.14, G:0.03, T:0.20
Consensus pattern (16 bp):
TTAAAAAAACCAAAAC
Found at i:45206 original size:18 final size:19
Alignment explanation
Indices: 45183--45226 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
45173 AACATTCTCA
45183 GTAATCCT-ATTCTCACTG
1 GTAATCCTAATTCTCACTG
* *
45201 GTAATCTTACATTCTTACTG
1 GTAATCCTA-ATTCTCACTG
45221 GTAATC
1 GTAATC
45227 TTACATTCCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
20 15 0.68
ACGTcount: A:0.25, C:0.23, G:0.11, T:0.41
Consensus pattern (19 bp):
GTAATCCTAATTCTCACTG
Found at i:45220 original size:20 final size:20
Alignment explanation
Indices: 45191--45234 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
45181 CAGTAATCCT
45191 ATTCTCACTGGTAATCTTAC
1 ATTCTCACTGGTAATCTTAC
*
45211 ATTCTTACTGGTAATCTTAC
1 ATTCTCACTGGTAATCTTAC
45231 ATTC
1 ATTC
45235 CGTGAATCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.25, C:0.23, G:0.09, T:0.43
Consensus pattern (20 bp):
ATTCTCACTGGTAATCTTAC
Found at i:54922 original size:2 final size:2
Alignment explanation
Indices: 54915--54940 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
54905 TTTAAGAAGA
54915 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
54941 GCATTAACAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58246 original size:21 final size:21
Alignment explanation
Indices: 58222--58266 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
58212 CCGTAGCCAT
*
58222 CACCTCCACCGCCC-CCTCCAC
1 CACCACCACC-CCCACCTCCAC
*
58243 CACCACCACCCCCACTTCCAC
1 CACCACCACCCCCACCTCCAC
58264 CAC
1 CAC
58267 AACAACCTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.20, C:0.69, G:0.02, T:0.09
Consensus pattern (21 bp):
CACCACCACCCCCACCTCCAC
Done.