Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000863.1 Hibiscus syriacus cultivar Beakdansim tig00001669_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: 81143
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:1037 original size:17 final size:17
Alignment explanation
Indices: 1015--1054 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1005 ACCTTAAAAT
*
1015 TTTTAAA-ATTTTATATA
1 TTTTAAATATTTT-TAAA
1032 TTTTAAATATTTTTAAA
1 TTTTAAATATTTTTAAA
1049 TTTTAA
1 TTTTAA
1055 TTTAAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTTAAATATTTTTAAA
Found at i:2849 original size:71 final size:71
Alignment explanation
Indices: 2762--2893 Score: 203
Period size: 71 Copynumber: 1.9 Consensus size: 71
2752 ACTCTCATAT
* ** * *
2762 GACTTGATCTAAATTTAGGTAAACTGCATTTGACCCGAAATTGATC-CAATTTTTAGGTAAAGAT
1 GACTTGATCTAAATTTAGGTAAACTCCACCTGACCCGAAATT-AACACAATTTTTAAGTAAAGAT
2826 CTACACC
65 CTACACC
2833 GACTTGATCTAAATTTAGGTAAACTCCACCTGACCCGAAATTAACACAATTTTTAAGTAAA
1 GACTTGATCTAAATTTAGGTAAACTCCACCTGACCCGAAATTAACACAATTTTTAAGTAAA
2894 AATCCACATC
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
70 2 0.04
71 53 0.96
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (71 bp):
GACTTGATCTAAATTTAGGTAAACTCCACCTGACCCGAAATTAACACAATTTTTAAGTAAAGATC
TACACC
Found at i:3978 original size:14 final size:15
Alignment explanation
Indices: 3959--3987 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3949 CTTATAAAAA
3959 ATAAATTTAT-ATTT
1 ATAAATTTATGATTT
3973 ATAAATTTATGATTT
1 ATAAATTTATGATTT
3988 CTACCCATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
ATAAATTTATGATTT
Found at i:4446 original size:2 final size:2
Alignment explanation
Indices: 4439--4463 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4429 TCGAAATCAA
4439 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4464 ACTTAATACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17649 original size:31 final size:31
Alignment explanation
Indices: 17611--17669 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
17601 TGTTTATTAT
*
17611 TGATTAGATAAAAATCATTAGTTAAATATAC
1 TGATTAGATAAAAATCATCAGTTAAATATAC
* *
17642 TGATTAGATGAAAATCATCAGTTGAATA
1 TGATTAGATAAAAATCATCAGTTAAATA
17670 ATTATTAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.46, C:0.07, G:0.14, T:0.34
Consensus pattern (31 bp):
TGATTAGATAAAAATCATCAGTTAAATATAC
Found at i:19817 original size:20 final size:20
Alignment explanation
Indices: 19789--19895 Score: 110
Period size: 20 Copynumber: 5.4 Consensus size: 20
19779 AATATGTAAA
*
19789 TCGCAACACATAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
* * **
19809 TCACAACACAAAACTCTTAT
1 TCGCAACACAAAAGTCAAAT
*
19829 TCGCAAC-CGATAA-TCAAAT
1 TCGCAACAC-AAAAGTCAAAT
19848 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
* * *
19868 TCACAACGCGAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
19888 TCGCAACA
1 TCGCAACA
19896 TGAATAGTAA
Statistics
Matches: 69, Mismatches: 15, Indels: 6
0.77 0.17 0.07
Matches are distributed among these distances:
19 15 0.22
20 54 0.78
ACGTcount: A:0.45, C:0.27, G:0.09, T:0.19
Consensus pattern (20 bp):
TCGCAACACAAAAGTCAAAT
Found at i:19833 original size:40 final size:40
Alignment explanation
Indices: 19789--19895 Score: 130
Period size: 39 Copynumber: 2.7 Consensus size: 40
19779 AATATGTAAA
* **
19789 TCGCAACAC-ATAAGTCAAATTCACAACACAAAACTCTTAT
1 TCGCAAC-CGATAAGTCAAATTCGCAACACAAAACTCAAAT
*
19829 TCGCAACCGATAA-TCAAATTCGCAACACAAAAGTCAAAT
1 TCGCAACCGATAAGTCAAATTCGCAACACAAAACTCAAAT
*
19868 TCACAACGCGA-AAGTCAAATTCGCAACA
1 TCGCAAC-CGATAAGTCAAATTCGCAACA
19896 TGAATAGTAA
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
39 31 0.53
40 28 0.47
ACGTcount: A:0.45, C:0.27, G:0.09, T:0.19
Consensus pattern (40 bp):
TCGCAACCGATAAGTCAAATTCGCAACACAAAACTCAAAT
Found at i:19912 original size:21 final size:21
Alignment explanation
Indices: 19871--19957 Score: 106
Period size: 21 Copynumber: 4.2 Consensus size: 21
19861 GTCAAATTCA
* * *
19871 CAACGCGAA-AGTCAAATTCG
1 CAACGTGAATAGTAAAAATCG
*
19891 CAACATGAATAGTAAAAATCG
1 CAACGTGAATAGTAAAAATCG
19912 CAACGTGAATAGTAAAAATCG
1 CAACGTGAATAGTAAAAATCG
* *
19933 TAACGTGAATAGT-AAAATTG
1 CAACGTGAATAGTAAAAATCG
19953 CAACG
1 CAACG
19958 AATCTATATG
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 17 0.29
21 41 0.71
ACGTcount: A:0.46, C:0.16, G:0.18, T:0.20
Consensus pattern (21 bp):
CAACGTGAATAGTAAAAATCG
Found at i:20346 original size:21 final size:21
Alignment explanation
Indices: 20317--20391 Score: 89
Period size: 21 Copynumber: 3.6 Consensus size: 21
20307 GATTTTCTAA
* *
20317 ATTCGCGTTGCGATTTTTACT
1 ATTCACGTTACGATTTTTACT
*
20338 ATTTACGTTACGA-TTTTACT
1 ATTCACGTTACGATTTTTACT
* *
20358 ATTCATGTTATGATTTTTACT
1 ATTCACGTTACGATTTTTACT
*
20379 ATTCATGTTACGA
1 ATTCACGTTACGA
20392 AATTGAAAAC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
20 17 0.37
21 29 0.63
ACGTcount: A:0.23, C:0.15, G:0.13, T:0.49
Consensus pattern (21 bp):
ATTCACGTTACGATTTTTACT
Found at i:20356 original size:20 final size:21
Alignment explanation
Indices: 20327--20391 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
20317 ATTCGCGTTG
* *
20327 CGATTTTTACTATTTACGTTA
1 CGATTTTTACTATTCATGTTA
20348 CGA-TTTTACTATTCATGTTA
1 CGATTTTTACTATTCATGTTA
*
20368 TGATTTTTACTATTCATGTTA
1 CGATTTTTACTATTCATGTTA
20389 CGA
1 CGA
20392 AATTGAAAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 17 0.44
21 22 0.56
ACGTcount: A:0.25, C:0.14, G:0.11, T:0.51
Consensus pattern (21 bp):
CGATTTTTACTATTCATGTTA
Found at i:25093 original size:60 final size:59
Alignment explanation
Indices: 24970--25094 Score: 146
Period size: 60 Copynumber: 2.1 Consensus size: 59
24960 GGATGAGGAC
* * **
24970 CATAGTTTGAGGATGAAATTGGAATTTTCAAAAATTTAAGGACTAGTTTAAATTGAGTAT
1 CATAGTTTGAGGATGAAATTAGAATTTTCAAAAATTTAAGGACCAGTTTAAATAAAG-AT
* *
25030 CATAGTTTGAGGATGAAATTATAATATTT-AAAAATTTAAGGACCATTTTAGAATAAA-AGT
1 CATAGTTTGAGGATGAAATTAGAAT-TTTCAAAAATTTAAGGACCAGTTTA-AATAAAGA-T
25090 CATAG
1 CATAG
25095 ATTAGGGGCA
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
59 1 0.02
60 48 0.86
61 7 0.12
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.35
Consensus pattern (59 bp):
CATAGTTTGAGGATGAAATTAGAATTTTCAAAAATTTAAGGACCAGTTTAAATAAAGAT
Found at i:27822 original size:32 final size:32
Alignment explanation
Indices: 27786--27852 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
27776 AAAATATTGT
27786 AATTATTTGTTTAATTTACAATTATACTAGTA
1 AATTATTTGTTTAATTTACAATTATACTAGTA
*
27818 AATTATTTGTTTAATTTACAATTTTACTAGTA
1 AATTATTTGTTTAATTTACAATTATACTAGTA
27850 AAT
1 AAT
27853 GAGATGGAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (32 bp):
AATTATTTGTTTAATTTACAATTATACTAGTA
Found at i:28646 original size:3 final size:3
Alignment explanation
Indices: 28638--28666 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
28628 AGCCAAAAAC
28638 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
28667 GGCTTAACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:36144 original size:25 final size:25
Alignment explanation
Indices: 36094--36145 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
36084 CTAATGGGCA
*
36094 AAGTTTTAAAAACAATTTGAAAAAC
1 AAGTTTTAAAAACAATATGAAAAAC
* *
36119 AAGTTTTGAAAATCAATAT-AATAAC
1 AAGTTTT-AAAAACAATATGAAAAAC
36144 AA
1 AA
36146 CATAATTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.29
Consensus pattern (25 bp):
AAGTTTTAAAAACAATATGAAAAAC
Found at i:36643 original size:22 final size:23
Alignment explanation
Indices: 36596--36656 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
36586 GATTCCCTCC
*
36596 AGGGGGAATCAGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
36619 AGGGGGAATCGGTTCCCCTTC-A
1 AGGGGGAATCGGTTCCCCTTCAA
* *
36641 AGGGGGTATCGATTCC
1 AGGGGGAATCGGTTCC
36657 TCCTGTCCTA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 15 0.43
23 20 0.57
ACGTcount: A:0.21, C:0.25, G:0.31, T:0.23
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCCTTCAA
Found at i:53823 original size:143 final size:143
Alignment explanation
Indices: 53653--53924 Score: 501
Period size: 143 Copynumber: 1.9 Consensus size: 143
53643 GAAAAAAAAA
53653 TTTAATCAATGCATTCAAATTCATTTGACTGTATATTTTTTCAAGATTTTTTTATAAATAAAGTC
1 TTTAATCAATGCATTCAAATTCATTTGACTGTATATTTTTTCAAGATTTTTTTATAAATAAAGTC
* *
53718 ACAAATTTTATAGTATTAAGAAGTTCAAAAATTT-TGTTTTAAAATGTACCAAAATTGTATTATT
66 ACAAATTTTATAGAATTAAGAAG-TCAAAAATTTGTGTTTTAAAATGTACCAAAAATGTATTATT
53782 TTCAAAAGAAAATT
130 TTCAAAAGAAAATT
53796 TTTAATCAATGCATTCAAATTCATTTGACTGTATATTTTTTCAAGATTTTTTTATAAATAAAGTC
1 TTTAATCAATGCATTCAAATTCATTTGACTGTATATTTTTTCAAGATTTTTTTATAAATAAAGTC
*
53861 ACAAATTTTATAGAATTAAGAAGTCCAAAATTTGTGTTTTAAAATGTACCAAAAATGTATTATT
66 ACAAATTTTATAGAATTAAGAAGTCAAAAATTTGTGTTTTAAAATGTACCAAAAATGTATTATT
53925 CTAATAAAAA
Statistics
Matches: 125, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
142 9 0.07
143 116 0.93
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (143 bp):
TTTAATCAATGCATTCAAATTCATTTGACTGTATATTTTTTCAAGATTTTTTTATAAATAAAGTC
ACAAATTTTATAGAATTAAGAAGTCAAAAATTTGTGTTTTAAAATGTACCAAAAATGTATTATTT
TCAAAAGAAAATT
Found at i:56180 original size:4 final size:4
Alignment explanation
Indices: 56171--56213 Score: 86
Period size: 4 Copynumber: 10.8 Consensus size: 4
56161 GTTAAGGTAT
56171 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
56214 TATGTTATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:62165 original size:22 final size:22
Alignment explanation
Indices: 62114--62175 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 22
62104 ATATATTAAG
62114 CAAAA-TA-TAAT-AATTT-TA
1 CAAAACTATTAATAAATTTATA
62132 CAAAACTATTAATAAATTTATA
1 CAAAACTATTAATAAATTTATA
62154 -AAAATCTATTAATCATAATTTA
1 CAAAA-CTATTAAT-A-AATTTA
62176 AATTATATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
18 5 0.14
19 2 0.05
20 4 0.11
21 9 0.24
22 10 0.27
23 1 0.03
24 6 0.16
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (22 bp):
CAAAACTATTAATAAATTTATA
Found at i:69237 original size:41 final size:41
Alignment explanation
Indices: 69180--69257 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
69170 TGAAAACTGT
69180 ATGTTTCATTTATTTTAATTGACATGTATGAGAGTACCTTC
1 ATGTTTCATTTATTTTAATTGACATGTATGAGAGTACCTTC
*
69221 ATGTTTCATTTATTTTAATTGACGTGTATGAGAGTAC
1 ATGTTTCATTTATTTTAATTGACATGTATGAGAGTAC
69258 TTTTAACCAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.46
Consensus pattern (41 bp):
ATGTTTCATTTATTTTAATTGACATGTATGAGAGTACCTTC
Found at i:78875 original size:16 final size:16
Alignment explanation
Indices: 78835--78876 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
78825 AACAAAAATT
78835 TAAATAT-AATATAAA
1 TAAATATCAATATAAA
* *
78850 TAGATATCAATATATA
1 TAAATATCAATATAAA
*
78866 TAAATGTCAAT
1 TAAATATCAAT
78877 CTGAGTTGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.36
Consensus pattern (16 bp):
TAAATATCAATATAAA
Found at i:79909 original size:15 final size:15
Alignment explanation
Indices: 79886--79937 Score: 77
Period size: 15 Copynumber: 3.5 Consensus size: 15
79876 TGAGACATTA
*
79886 CCCGCCCCGCATCTG
1 CCCGCCCCGCATCCG
*
79901 CCTGCCCCGCATCCG
1 CCCGCCCCGCATCCG
*
79916 CCCGCCCCACATCCG
1 CCCGCCCCGCATCCG
79931 CCCGCCC
1 CCCGCCC
79938 AGCTAAATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.08, C:0.65, G:0.17, T:0.10
Consensus pattern (15 bp):
CCCGCCCCGCATCCG
Done.