Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003928.1 Hibiscus syriacus cultivar Beakdansim tig00008491_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: 87554
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:4058 original size:14 final size:14
Alignment explanation
Indices: 4039--4068 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
4029 CCGCGGGAGT
4039 TTGCTTAAAATTTG
1 TTGCTTAAAATTTG
4053 TTGCTTAAAATTTG
1 TTGCTTAAAATTTG
4067 TT
1 TT
4069 TGAGCATCGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.07, G:0.13, T:0.53
Consensus pattern (14 bp):
TTGCTTAAAATTTG
Found at i:11574 original size:21 final size:21
Alignment explanation
Indices: 11550--11592 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
11540 AAAAAGTAAA
11550 AAATAAAACTGC-AATTGAAGC
1 AAATAAAAC-GCAAATTGAAGC
**
11571 AAATATGACGCAAATTGAAGC
1 AAATAAAACGCAAATTGAAGC
11592 A
1 A
11593 GAAACGCTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.51, C:0.14, G:0.16, T:0.19
Consensus pattern (21 bp):
AAATAAAACGCAAATTGAAGC
Found at i:12545 original size:22 final size:22
Alignment explanation
Indices: 12519--12560 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
12509 GATAAATTTC
* *
12519 AAAATATTCTCATTAATTTTTA
1 AAAATATTCTAACTAATTTTTA
12541 AAAATATTCTAACTAATTTT
1 AAAATATTCTAACTAATTTT
12561 CTAAGTTCAA
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:0.43, C:0.10, G:0.00, T:0.48
Consensus pattern (22 bp):
AAAATATTCTAACTAATTTTTA
Found at i:25208 original size:69 final size:69
Alignment explanation
Indices: 25097--25240 Score: 279
Period size: 69 Copynumber: 2.1 Consensus size: 69
25087 AAGCAGGTAC
*
25097 TATCAGCCATCTGCATTGTGCAACAAGTAACACTTCTTCTATATGCTGAACTATCGATTTGACAC
1 TATCAGCCATCTGCATTGTGCAACAAGTAACACTTCTTCTATATGCTGAACTATCAATTTGACAC
25162 TTTT
66 TTTT
25166 TATCAGCCATCTGCATTGTGCAACAAGTAACACTTCTTCTATATGCTGAACTATCAATTTGACAC
1 TATCAGCCATCTGCATTGTGCAACAAGTAACACTTCTTCTATATGCTGAACTATCAATTTGACAC
25231 TTTT
66 TTTT
25235 TATCAG
1 TATCAG
25241 TCAGGCAATA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 74 1.00
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.36
Consensus pattern (69 bp):
TATCAGCCATCTGCATTGTGCAACAAGTAACACTTCTTCTATATGCTGAACTATCAATTTGACAC
TTTT
Found at i:27056 original size:21 final size:21
Alignment explanation
Indices: 27030--27089 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
27020 ATTTACCGTG
27030 ATTGCGGTCGTCGCGGGTGCT
1 ATTGCGGTCGTCGCGGGTGCT
**
27051 ATTGCGGTCGTCGCGGACGCT
1 ATTGCGGTCGTCGCGGGTGCT
* *
27072 ATTGCGGCCGTCACGGGT
1 ATTGCGGTCGTCGCGGGT
27090 AACTCGGACA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.08, C:0.27, G:0.40, T:0.25
Consensus pattern (21 bp):
ATTGCGGTCGTCGCGGGTGCT
Found at i:29027 original size:90 final size:90
Alignment explanation
Indices: 28919--29099 Score: 308
Period size: 90 Copynumber: 2.0 Consensus size: 90
28909 ATCTTAATCA
* *
28919 TCATGTTAACTTCTAGCTTAAACAACAACCACTTTTTAACGAAAAATGACGAATTTAAAACATAA
1 TCATGTTAACCTCTAGCTTAAACAACAACAACTTTTTAACGAAAAATGACGAATTTAAAACATAA
* *
28984 TGAGTTTGGTGACCATTTTTTAACT
66 TGAGTTTGGTAACCATTTTGTAACT
* *
29009 TCATGTTAACCTCTAGCTTAAACAACAACAACTTTTTAACGGAAAATGACGAGTTTAAAACATAA
1 TCATGTTAACCTCTAGCTTAAACAACAACAACTTTTTAACGAAAAATGACGAATTTAAAACATAA
29074 TGAGTTTGGTAACCATTTTGTAACT
66 TGAGTTTGGTAACCATTTTGTAACT
29099 T
1 T
29100 TTGATAGTCG
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 85 1.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.34
Consensus pattern (90 bp):
TCATGTTAACCTCTAGCTTAAACAACAACAACTTTTTAACGAAAAATGACGAATTTAAAACATAA
TGAGTTTGGTAACCATTTTGTAACT
Found at i:29138 original size:30 final size:32
Alignment explanation
Indices: 29099--29159 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 32
29089 TTTTGTAACT
*
29099 TTTGATAGTCGAAGGACTTAA-AAAACAATAC
1 TTTGATAGTCAAAGGACTTAATAAAACAATAC
*
29130 TTTG-TAGTCAAAGGAGTTAATAAAACAATA
1 TTTGATAGTCAAAGGACTTAATAAAACAATA
29160 TCTTATGGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 14 0.52
31 13 0.48
ACGTcount: A:0.46, C:0.10, G:0.16, T:0.28
Consensus pattern (32 bp):
TTTGATAGTCAAAGGACTTAATAAAACAATAC
Found at i:35627 original size:16 final size:16
Alignment explanation
Indices: 35606--35638 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
35596 AATTTTCTTT
35606 CCTATAGAGAGTGACA
1 CCTATAGAGAGTGACA
35622 CCTATAGAGAGTGACA
1 CCTATAGAGAGTGACA
35638 C
1 C
35639 GTGACACCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.18
Consensus pattern (16 bp):
CCTATAGAGAGTGACA
Found at i:40140 original size:42 final size:42
Alignment explanation
Indices: 40093--40183 Score: 164
Period size: 42 Copynumber: 2.2 Consensus size: 42
40083 ATAAACCATG
*
40093 AACCCTGTACTATAGCCTCATAACTTCTAAACCATAACCCTA
1 AACCCTATACTATAGCCTCATAACTTCTAAACCATAACCCTA
40135 AACCCTATACTATAGCCTCATAACTTCTAAACCATAACCCTA
1 AACCCTATACTATAGCCTCATAACTTCTAAACCATAACCCTA
*
40177 AATCCTA
1 AACCCTA
40184 ACTTAAAACT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.37, C:0.33, G:0.03, T:0.26
Consensus pattern (42 bp):
AACCCTATACTATAGCCTCATAACTTCTAAACCATAACCCTA
Found at i:48320 original size:381 final size:381
Alignment explanation
Indices: 47617--48382 Score: 1523
Period size: 381 Copynumber: 2.0 Consensus size: 381
47607 CTGATAGACA
47617 CAAGATCCTTCTCTACAACGGAAAAAGAAACAAATTGTAGGAATTTCACTCCTGAAATGAATTCA
1 CAAGATCCTTCTCTACAACGGAAAAAGAAACAAATTGTAGGAATTTCACTCCTGAAATGAATTCA
47682 TGGAGCAGACTGCAGCAGAGGTTTGCAAAGCAGCCCGAGTCAAGTTATCCAATACAGTGAGGATT
66 TGGAGCAGACTGCAGCAGAGGTTTGCAAAGCAGCCCGAGTCAAGTTATCCAATACAGTGAGGATT
47747 CAAGAGAGTCACTTATATTTATATGCTCCGTAAGGGAAATATAAATGCAGTGAGCTTCTCAATCT
131 CAAGAGAGTCACTTATATTTATATGCTCCGTAAGGGAAATATAAATGCAGTGAGCTTCTCAATCT
47812 GCATTTATATGCATTTATAGGACTGGATCAGATCATCTAAAGATATAAATGCAGTCAACGGTTCA
196 GCATTTATATGCATTTATAGGACTGGATCAGATCATCTAAAGATATAAATGCAGTCAACGGTTCA
47877 AACAATTTTGAATTATCAAAAGAGTTATATTTGTAACTTGATCAGTGATCATAGAGAAAGCTGTA
261 AACAATTTTGAATTATCAAAAGAGTTATATTTGTAACTTGATCAGTGATCATAGAGAAAGCTGTA
47942 AGCACATTACTTGTAAACACCAGCGATAATAAATTCCGTGTACATATGTAAACCAT
326 AGCACATTACTTGTAAACACCAGCGATAATAAATTCCGTGTACATATGTAAACCAT
47998 CAAGATCCTTCTCTACAACGGAAAAAGAAACAAATTGTAGGAATTTCACTCCTGAAATGAATTCA
1 CAAGATCCTTCTCTACAACGGAAAAAGAAACAAATTGTAGGAATTTCACTCCTGAAATGAATTCA
48063 TGGAGCAGACTGCAGCAGAGGTTTGCAAAGCAGCCCGAGTCAAGTTATCCAATACAGTGAGGATT
66 TGGAGCAGACTGCAGCAGAGGTTTGCAAAGCAGCCCGAGTCAAGTTATCCAATACAGTGAGGATT
48128 CAAGAGAGTCACTTATATTTATATGCTCCGTAAGGGAAATATAAATGCAGTGAGCTTCTCAATCT
131 CAAGAGAGTCACTTATATTTATATGCTCCGTAAGGGAAATATAAATGCAGTGAGCTTCTCAATCT
48193 GCATTTATATGCATTTATAGGACTGGATCAGATCATCTAAAGATATAAATGCAGTCAACGGTTCA
196 GCATTTATATGCATTTATAGGACTGGATCAGATCATCTAAAGATATAAATGCAGTCAACGGTTCA
48258 AACAATTTTGAATTATCAAAAGAGTTATATTTGTAACTTGATCAGTGATCATAGAGAAAGCTGTA
261 AACAATTTTGAATTATCAAAAGAGTTATATTTGTAACTTGATCAGTGATCATAGAGAAAGCTGTA
*
48323 AGCACATTACTTGTAAACACCAGTGATAATAAATTCCGTGTACATATGTAAACCAT
326 AGCACATTACTTGTAAACACCAGCGATAATAAATTCCGTGTACATATGTAAACCAT
48379 CAAG
1 CAAG
48383 CCTTAAATCA
Statistics
Matches: 384, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
381 384 1.00
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (381 bp):
CAAGATCCTTCTCTACAACGGAAAAAGAAACAAATTGTAGGAATTTCACTCCTGAAATGAATTCA
TGGAGCAGACTGCAGCAGAGGTTTGCAAAGCAGCCCGAGTCAAGTTATCCAATACAGTGAGGATT
CAAGAGAGTCACTTATATTTATATGCTCCGTAAGGGAAATATAAATGCAGTGAGCTTCTCAATCT
GCATTTATATGCATTTATAGGACTGGATCAGATCATCTAAAGATATAAATGCAGTCAACGGTTCA
AACAATTTTGAATTATCAAAAGAGTTATATTTGTAACTTGATCAGTGATCATAGAGAAAGCTGTA
AGCACATTACTTGTAAACACCAGCGATAATAAATTCCGTGTACATATGTAAACCAT
Found at i:50295 original size:21 final size:21
Alignment explanation
Indices: 50264--50319 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
50254 CTAAATTGGT
* *
50264 AACTCCCATGTTAGTATCGTG
1 AACTGCCATGTTAGCATCGTG
*
50285 CACTGCCATGTTAGCATCGTG
1 AACTGCCATGTTAGCATCGTG
*
50306 AACTGCCACGTTAG
1 AACTGCCATGTTAG
50320 GACTGTAATG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (21 bp):
AACTGCCATGTTAGCATCGTG
Found at i:50783 original size:27 final size:27
Alignment explanation
Indices: 50748--50800 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
50738 TTTCTATCGA
*
50748 TTTTATTATTATTAGGTGTTTTACCGG
1 TTTTATTATTATTAGGTATTTTACCGG
* *
50775 TTTTGTTATTATTTGGTATTTTACCG
1 TTTTATTATTATTAGGTATTTTACCG
50801 AAAATATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.17, C:0.08, G:0.17, T:0.58
Consensus pattern (27 bp):
TTTTATTATTATTAGGTATTTTACCGG
Found at i:53597 original size:21 final size:21
Alignment explanation
Indices: 53573--53617 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
53563 TAATTTTTAA
53573 AAAATCAAATCAAAT-TAAATT
1 AAAATC-AATCAAATATAAATT
**
53594 AAAATCCTTCAAATATAAATT
1 AAAATCAATCAAATATAAATT
53615 AAA
1 AAA
53618 TTACCATCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.29
Consensus pattern (21 bp):
AAAATCAATCAAATATAAATT
Found at i:58963 original size:2 final size:2
Alignment explanation
Indices: 58958--58990 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
58948 TATATAAATT
58958 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
58991 ACAAGGTTGT
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:63279 original size:21 final size:21
Alignment explanation
Indices: 63232--63286 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
63222 GGTGGTGGAG
* *
63232 GTGAATGTGGTGGCGGGGGTG
1 GTGAATGTGGTGGAGGGGGTA
* *
63253 GAGAATGTGGTGGAGGTGGTA
1 GTGAATGTGGTGGAGGGGGTA
*
63274 GTGAATGTTGTGG
1 GTGAATGTGGTGG
63287 CAGCGGTGGG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.16, C:0.02, G:0.55, T:0.27
Consensus pattern (21 bp):
GTGAATGTGGTGGAGGGGGTA
Found at i:66827 original size:36 final size:36
Alignment explanation
Indices: 66786--66908 Score: 200
Period size: 34 Copynumber: 3.5 Consensus size: 36
66776 ATTATATATA
*
66786 TATATATATATAATATTTTTTATTTTTTATATTAAT
1 TATATATATATAATATTTTTTATATTTTATATTAAT
66822 TATATATATATAATATTTTTTATATTTTATATTAA-
1 TATATATATATAATATTTTTTATATTTTATATTAAT
*
66857 T-TATATATATAATATTTTATATATTTTATATTAAT
1 TATATATATATAATATTTTTTATATTTTATATTAAT
66892 TATATATA-A-AATATTTT
1 TATATATATATAATATTTT
66909 CAGGTTCGGG
Statistics
Matches: 83, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
34 40 0.48
35 3 0.04
36 40 0.48
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (36 bp):
TATATATATATAATATTTTTTATATTTTATATTAAT
Found at i:69297 original size:36 final size:35
Alignment explanation
Indices: 69252--69319 Score: 91
Period size: 36 Copynumber: 1.9 Consensus size: 35
69242 TACTATATTA
*
69252 TAATCCCCATTTTACGCATTATATTATTATTTTTAT
1 TAATCCCCATTTTACGCATTAAATTATT-TTTTTAT
* * *
69288 TAATTCCCATTTTACTCGTTAAATTATTTTTT
1 TAATCCCCATTTTACGCATTAAATTATTTTTT
69320 ATAAATTTAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 4 0.14
36 24 0.86
ACGTcount: A:0.26, C:0.16, G:0.03, T:0.54
Consensus pattern (35 bp):
TAATCCCCATTTTACGCATTAAATTATTTTTTTAT
Found at i:72916 original size:16 final size:16
Alignment explanation
Indices: 72895--72943 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 16
72885 TAACTTTTTA
72895 TTTAAATATAATATTT
1 TTTAAATATAATATTT
*
72911 TTTAAAAATATATAAATTT
1 TTT--AAATATA-ATATTT
72930 TTTAAATTATAATA
1 TTTAAA-TATAATA
72944 ACGACACGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
16 3 0.11
17 5 0.19
18 11 0.41
19 8 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTTAAATATAATATTT
Found at i:72944 original size:19 final size:18
Alignment explanation
Indices: 72895--72944 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
72885 TAACTTTTTA
72895 TTTAAATATAAT--ATTT
1 TTTAAATATAATAAATTT
*
72911 TTTAAAAATATATAAATTT
1 TTTAAATATA-ATAAATTT
72930 TTTAAATTATAATAA
1 TTTAAA-TATAATAA
72945 CGACACGTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
16 9 0.32
17 2 0.07
19 14 0.50
20 3 0.11
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTAAATATAATAAATTT
Found at i:73431 original size:12 final size:12
Alignment explanation
Indices: 73414--73438 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
73404 ATATTTCTGA
73414 TAAAATATTATT
1 TAAAATATTATT
73426 TAAAATATTATT
1 TAAAATATTATT
73438 T
1 T
73439 TTTAATCAAA
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:0.00, T:0.52
Consensus pattern (12 bp):
TAAAATATTATT
Found at i:77465 original size:17 final size:17
Alignment explanation
Indices: 77439--77475 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
77429 CCCTTAAAAT
77439 TTTTAAATTTTTATATA
1 TTTTAAATTTTTATATA
* *
77456 TTTTAGATTTTTTTATA
1 TTTTAAATTTTTATATA
77473 TTT
1 TTT
77476 CTATTGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (17 bp):
TTTTAAATTTTTATATA
Found at i:77466 original size:108 final size:106
Alignment explanation
Indices: 77244--77457 Score: 403
Period size: 108 Copynumber: 2.0 Consensus size: 106
77234 GTCGAAACCC
77244 TAAAATTTTAATTTCACAAAATTCTCATTGCTTACTTGTTTATTGTGAGTAGGGATGAATCTAGC
1 TAAAATTTTAATTTCACAAAATTCTCATTGCTTACTTGTTTATTGTGAGTAGGGATGAATCTAGC
77309 TGGGGAGGACATCCCTTAAAATTTTTAAATTTTTTATATAT
66 TGGGGAGGACATCCCTTAAAATTTTTAAATTTTTTATATAT
77350 TAAAATTTTAATTTCACAAAATTCTCATTTGCTTACTTTGTTTATTGTGAGTAGGGATGAATCTA
1 TAAAATTTTAATTTCACAAAATTCTCA-TTGCTTAC-TTGTTTATTGTGAGTAGGGATGAATCTA
77415 GCTGGGGAGGACATCCCTTAAAATTTTTAAA-TTTTTATATAT
64 GCTGGGGAGGACATCCCTTAAAATTTTTAAATTTTTTATATAT
77457 T
1 T
77458 TTAGATTTTT
Statistics
Matches: 106, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
106 27 0.25
107 20 0.19
108 59 0.56
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.43
Consensus pattern (106 bp):
TAAAATTTTAATTTCACAAAATTCTCATTGCTTACTTGTTTATTGTGAGTAGGGATGAATCTAGC
TGGGGAGGACATCCCTTAAAATTTTTAAATTTTTTATATAT
Done.