Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005529.1 Hibiscus syriacus cultivar Beakdansim tig00012775_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: 52397
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:2832 original size:22 final size:22
Alignment explanation
Indices: 2779--2821 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2769 CGATTCCCCT
*
2779 AGGGGAATTGGTTCCCCTTCAA
1 AGGGGAATCGGTTCCCCTTCAA
2801 AGGGGAATCGGTTCCCCTTCA
1 AGGGGAATCGGTTCCCCTTCA
2822 GGGAGGTATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.26, G:0.28, T:0.26
Consensus pattern (22 bp):
AGGGGAATCGGTTCCCCTTCAA
Found at i:12804 original size:27 final size:27
Alignment explanation
Indices: 12753--12804 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
12743 TGTTGATGTT
*
12753 ATATATGAATGAATGTGATTAATATCA
1 ATATATGAATGAATGTGATGAATATCA
* *
12780 ATATTTGAATGAATGTGATGGATAT
1 ATATATGAATGAATGTGATGAATAT
12805 TTTTTGATGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.40, C:0.02, G:0.19, T:0.38
Consensus pattern (27 bp):
ATATATGAATGAATGTGATGAATATCA
Found at i:12854 original size:23 final size:23
Alignment explanation
Indices: 12828--12871 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
12818 ATTTGAATGA
*
12828 ATGTGATTAATATCAATATTTCT
1 ATGTGAATAATATCAATATTTCT
*
12851 ATGTGAATGATATCAATATTT
1 ATGTGAATAATATCAATATTT
12872 TATTTAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.45
Consensus pattern (23 bp):
ATGTGAATAATATCAATATTTCT
Found at i:14475 original size:101 final size:101
Alignment explanation
Indices: 14293--14522 Score: 225
Period size: 101 Copynumber: 2.2 Consensus size: 101
14283 AAAAACTGTT
* * * *
14293 AAATCAAAATAAATAGTCTAATTAATTTATATTTACAATAAAAACAAAAAATAAACAATAAAATT
1 AAAT-AAAATAAATAGTCTAA-TACTTAATA-TTAC--TCAATA-AAAAAATAAACAATAAAATT
** * * *
14358 TAAATTAAACTTACCAAACCACTCAAATACGATTTAATCTGTA
60 TAAATTAAACACACCAAACCACTCAAATACAACTTAATAT-TA
*
14401 AAATAAAA-ACAATTAGTCTAATACTTAATATTACTCAATAAAAAAATAAA-AA-ATAATTT-AA
1 AAATAAAATA-AA-TAGTCTAATACTTAATATTACTCAATAAAAAAATAAACAATAAAATTTAAA
* * *
14462 TCTAAACACACCAAACTACTTAAATACAACTTAATATTT
64 T-TAAACACACCAAACCACTCAAATACAACTTAATATTA
14501 AAATAAAATAAATAGTCTAATA
1 AAATAAAATAAATAGTCTAATA
14523 ATTATAATTT
Statistics
Matches: 105, Mismatches: 13, Indels: 17
0.78 0.10 0.13
Matches are distributed among these distances:
99 10 0.10
100 14 0.13
101 35 0.33
102 2 0.02
103 10 0.10
104 4 0.04
106 5 0.05
107 13 0.12
108 12 0.11
ACGTcount: A:0.56, C:0.13, G:0.02, T:0.30
Consensus pattern (101 bp):
AAATAAAATAAATAGTCTAATACTTAATATTACTCAATAAAAAAATAAACAATAAAATTTAAATT
AAACACACCAAACCACTCAAATACAACTTAATATTA
Found at i:18538 original size:29 final size:29
Alignment explanation
Indices: 18505--18586 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
18495 AAATTAAATT
**
18505 GATGTCATTGCTTACATTTTTTAAGTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
18534 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
18563 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
18587 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:19884 original size:15 final size:15
Alignment explanation
Indices: 19864--19893 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
19854 ACGAGGTTGG
19864 AATTCCAACAACAAC
1 AATTCCAACAACAAC
19879 AATTCCAACAACAAC
1 AATTCCAACAACAAC
19894 TATGAGAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.33, G:0.00, T:0.13
Consensus pattern (15 bp):
AATTCCAACAACAAC
Found at i:26092 original size:18 final size:18
Alignment explanation
Indices: 26069--26107 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
26059 AGTGATTAAA
26069 TTAGGATTAATTTGAAGG
1 TTAGGATTAATTTGAAGG
26087 TTAGGATTAATTTGAAGG
1 TTAGGATTAATTTGAAGG
26105 TTA
1 TTA
26108 AGTAATTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.26, T:0.41
Consensus pattern (18 bp):
TTAGGATTAATTTGAAGG
Found at i:29841 original size:6 final size:6
Alignment explanation
Indices: 29830--29861 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
29820 AAAAATTACT
29830 AAAATA AAAATA AAAATA AAAAT- AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAA
29862 GAATGATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:29845 original size:12 final size:11
Alignment explanation
Indices: 29806--29861 Score: 60
Period size: 11 Copynumber: 4.8 Consensus size: 11
29796 TGTCAATAGC
*
29806 AAAATATAAAT
1 AAAATAAAAAT
29817 AAAA-AAAATTACT
1 AAAATAAAA--A-T
29830 AAAATAAAAAT
1 AAAATAAAAAT
29841 AAAAATAAAAAT
1 -AAAATAAAAAT
29853 AAAATAAAA
1 AAAATAAAA
29862 GAATGATTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
10 3 0.08
11 14 0.36
12 13 0.33
13 5 0.13
14 4 0.10
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.20
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:31044 original size:17 final size:18
Alignment explanation
Indices: 31030--31065 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
31020 CCAAAAAAAG
31030 AAAATAA-ATAAAAAATA
1 AAAATAATATAAAAAATA
*
31047 AAAATAATATAATAAATA
1 AAAATAATATAAAAAATA
31065 A
1 A
31066 TATATAACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (18 bp):
AAAATAATATAAAAAATA
Found at i:31110 original size:26 final size:27
Alignment explanation
Indices: 31081--31157 Score: 102
Period size: 27 Copynumber: 2.9 Consensus size: 27
31071 AACACTATAC
*
31081 TATATAATATATATTTTTAAAAAAAT-
1 TATATAATATATATTTTTCAAAAAATA
* *
31107 TATATATTATATATATTTTCAAAAACTA
1 TATATAATATATAT-TTTTCAAAAAATA
*
31135 TATATTATATATATTTTTCAAAA
1 TATATAATATATATTTTTCAAAA
31158 TATTTTCAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
26 13 0.30
27 19 0.43
28 12 0.27
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (27 bp):
TATATAATATATATTTTTCAAAAAATA
Found at i:31121 original size:28 final size:27
Alignment explanation
Indices: 31081--31157 Score: 102
Period size: 26 Copynumber: 2.9 Consensus size: 27
31071 AACACTATAC
* *
31081 TATATAATATATATTTTTAAAAAAATTA
1 TATATTATATATATTTTT-AAAAAACTA
*
31109 TATATTATATATA-TTTTCAAAAACTA
1 TATATTATATATATTTTTAAAAAACTA
*
31135 TATATTATATATATTTTTCAAAA
1 TATATTATATATATTTTTAAAAA
31158 TATTTTCAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
26 20 0.44
27 13 0.29
28 12 0.27
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (27 bp):
TATATTATATATATTTTTAAAAAACTA
Found at i:31164 original size:38 final size:39
Alignment explanation
Indices: 31119--31214 Score: 167
Period size: 38 Copynumber: 2.5 Consensus size: 39
31109 TATATTATAT
31119 ATATTTTCAAAAACTATATATTATATATAT-TTTTCAAA
1 ATATTTTCAAAAACTATATATTATATATATATTTTCAAA
*
31157 ATATTTTCAAAAATTATATATTATATATATATTTTCAAA
1 ATATTTTCAAAAACTATATATTATATATATATTTTCAAA
*
31196 ATGTTTTCAAAAACTATAT
1 ATATTTTCAAAAACTATAT
31215 GTTTTCAAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
38 29 0.54
39 25 0.46
ACGTcount: A:0.45, C:0.07, G:0.01, T:0.47
Consensus pattern (39 bp):
ATATTTTCAAAAACTATATATTATATATATATTTTCAAA
Found at i:31213 original size:28 final size:27
Alignment explanation
Indices: 31182--31244 Score: 99
Period size: 28 Copynumber: 2.3 Consensus size: 27
31172 ATATATTATA
*
31182 TATATATTTTCAAAATGTTTTCAAAAAC
1 TATATATTTTCAAAATATTTTC-AAAAC
*
31210 TATATGTTTTCAAAATATTTTCAAAAC
1 TATATATTTTCAAAATATTTTCAAAAC
31237 TATATATT
1 TATATATT
31245 ATATATGTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
27 12 0.38
28 20 0.62
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.46
Consensus pattern (27 bp):
TATATATTTTCAAAATATTTTCAAAAC
Found at i:31228 original size:39 final size:38
Alignment explanation
Indices: 31119--31235 Score: 155
Period size: 39 Copynumber: 3.0 Consensus size: 38
31109 TATATTATAT
31119 ATATTTTCAAAAACTATATATTAT-ATATATTTTTCAAA
1 ATATTTTCAAAAACTATATATTATAATATA-TTTTCAAA
*
31157 ATATTTTCAAAAATTATATATTATATATATATTTTCAAA
1 ATATTTTCAAAAACTATATATTATA-ATATATTTTCAAA
* * * *
31196 ATGTTTTCAAAAACTATATGTTTTCAAAATATTTTCAAA
1 ATATTTTCAAAAACTATATATTAT-AATATATTTTCAAA
31235 A
1 A
31236 CTATATATTA
Statistics
Matches: 70, Mismatches: 6, Indels: 5
0.86 0.07 0.06
Matches are distributed among these distances:
38 23 0.33
39 41 0.59
40 6 0.09
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (38 bp):
ATATTTTCAAAAACTATATATTATAATATATTTTCAAA
Found at i:31263 original size:66 final size:66
Alignment explanation
Indices: 31143--31282 Score: 180
Period size: 66 Copynumber: 2.1 Consensus size: 66
31133 TATATATTAT
* * *
31143 ATATATTTTTCAAAATATTTTCAAAAATTATATATTATATATATATTTTCAAAATGTTTT-CAAA
1 ATATATTTTTCAAAATATTTTCAAAAACTATATATTATATATATATTATCAAAATATTTTCCAAA
31207 A
66 A
*
31208 ACTATATGTTTTCAAAATATTTTC-AAAACTATATA-T-TATATATGTTATCAAAAAATATTTTC
1 A-TATAT-TTTTCAAAATATTTTCAAAAACTATATATTATATATATATTATC--AAAATATTTTC
31270 CAAAA
62 CAAAA
31275 ATATATTT
1 ATATATTT
31283 ATTATATATA
Statistics
Matches: 66, Mismatches: 4, Indels: 10
0.82 0.05 0.12
Matches are distributed among these distances:
64 11 0.17
65 4 0.06
66 29 0.44
67 22 0.33
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (66 bp):
ATATATTTTTCAAAATATTTTCAAAAACTATATATTATATATATATTATCAAAATATTTTCCAAA
A
Found at i:32801 original size:43 final size:43
Alignment explanation
Indices: 32754--32838 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
32744 GGACCTATAT
*
32754 TTTTTTCAATTTAAGG-CCTCCTTTCGGGTTTTCACCCTAAACG
1 TTTTTTCAACTTAAGGTCC-CCTTTCGGGTTTTCACCCTAAACG
* * * *
32797 TTTTTTTAACTTGAGGTGCCCTTTCGGGTTTTCACCTTAAAC
1 TTTTTTCAACTTAAGGTCCCCTTTCGGGTTTTCACCCTAAAC
32839 AAAATATTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
43 35 0.97
44 1 0.03
ACGTcount: A:0.18, C:0.24, G:0.15, T:0.44
Consensus pattern (43 bp):
TTTTTTCAACTTAAGGTCCCCTTTCGGGTTTTCACCCTAAACG
Found at i:40628 original size:14 final size:14
Alignment explanation
Indices: 40609--40643 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
40599 ACCTTATAAA
*
40609 TCTTCCTTCGTCAG
1 TCTTCCTGCGTCAG
40623 TCTTCCTGCGTCAG
1 TCTTCCTGCGTCAG
40637 TCTTCCT
1 TCTTCCT
40644 ACAATGGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.06, C:0.37, G:0.14, T:0.43
Consensus pattern (14 bp):
TCTTCCTGCGTCAG
Found at i:43637 original size:16 final size:16
Alignment explanation
Indices: 43616--43668 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 16
43606 ATTTTGGACC
43616 AAAAAAGAAAATAAAT
1 AAAAAAGAAAATAAAT
43632 AAAAAAGAAAATGAAAAT
1 AAAAAAGAAAAT--AAAT
*
43650 AAATAAAGTATAATAAAT
1 AAA-AAAG-AAAATAAAT
43668 A
1 A
43669 TATATATATA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
16 12 0.38
18 12 0.38
19 4 0.12
20 4 0.12
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (16 bp):
AAAAAAGAAAATAAAT
Found at i:43673 original size:2 final size:2
Alignment explanation
Indices: 43666--43705 Score: 64
Period size: 2 Copynumber: 20.0 Consensus size: 2
43656 AGTATAATAA
43666 AT AT AT AT AT AT ACT AT A- AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
43706 TTTAAAAAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 33 0.92
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:43683 original size:22 final size:21
Alignment explanation
Indices: 43658--43704 Score: 76
Period size: 22 Copynumber: 2.2 Consensus size: 21
43648 ATAAATAAAG
43658 TATAATAAATATATATATATA
1 TATAATAAATATATATATATA
*
43679 CTATAATATATATATATATATA
1 -TATAATAAATATATATATATA
43701 TATA
1 TATA
43705 TTTTAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
TATAATAAATATATATATATA
Found at i:45349 original size:33 final size:33
Alignment explanation
Indices: 45312--45381 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
45302 CCAGATGAAC
45312 TCAAAGCTATGATTGATAGATTTTCCGTGATTG
1 TCAAAGCTATGATTGATAGATTTTCCGTGATTG
45345 TCAAAGCTATGATTGATAGATTTTCCGTGATTG
1 TCAAAGCTATGATTGATAGATTTTCCGTGATTG
45378 TCAA
1 TCAA
45382 CGGTCTCAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.39
Consensus pattern (33 bp):
TCAAAGCTATGATTGATAGATTTTCCGTGATTG
Done.