Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000283.1 Hibiscus syriacus cultivar Beakdansim tig00000524_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: 69728
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1782 original size:19 final size:18
Alignment explanation
Indices: 1755--1793 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
1745 ATCTCTATTA
*
1755 TAAATATAATATTATAAAT
1 TAAAAATAATATT-TAAAT
1774 TAAAAATAATATTTAAAT
1 TAAAAATAATATTTAAAT
1792 TA
1 TA
1794 TATTTACATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TAAAAATAATATTTAAAT
Found at i:1997 original size:2 final size:2
Alignment explanation
Indices: 1986--2030 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
1976 TTAAGGATAG
*
1986 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2027 TA TA
1 TA TA
2031 ATTTTTAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:7775 original size:24 final size:24
Alignment explanation
Indices: 7723--7775 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
7713 AACAATTAAG
**
7723 GATAAAATCCTAAAACATTCAAAT
1 GATAAAATCCTAAAACAAACAAAT
* * *
7747 AATAAAATCCTAAAATAAACAAGT
1 GATAAAATCCTAAAACAAACAAAT
7771 GATAA
1 GATAA
7776 TTCCAAAAAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.58, C:0.13, G:0.06, T:0.23
Consensus pattern (24 bp):
GATAAAATCCTAAAACAAACAAAT
Found at i:9236 original size:21 final size:21
Alignment explanation
Indices: 9212--9260 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
9202 TAACAATTAT
*
9212 ATGTGATGAATTATTATGTTG
1 ATGTGATGAATTATTATATTG
9233 ATGTGATGAATTATTATATTG
1 ATGTGATGAATTATTATATTG
*
9254 ATATGAT
1 ATGTGAT
9261 ATTTCATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (21 bp):
ATGTGATGAATTATTATATTG
Found at i:9289 original size:2 final size:2
Alignment explanation
Indices: 9282--9310 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9272 TTGACGTGAC
9282 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 T
9311 GAATAATGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24938 original size:21 final size:21
Alignment explanation
Indices: 24914--24984 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 21
24904 CTGAGGTCAT
*
24914 AGTATCAATAGTACTATATAA
1 AGTATCAATACTACTATATAA
* * *
24935 AGTATTATCAATACTCCTTTAATTA
1 AG---TATCAATACTACTAT-ATAA
24960 AGTATCAATACTACTATATAA
1 AGTATCAATACTACTATATAA
24981 AGTA
1 AGTA
24985 GTATCGATAC
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
21 9 0.23
22 13 0.33
24 12 0.31
25 5 0.13
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.37
Consensus pattern (21 bp):
AGTATCAATACTACTATATAA
Found at i:24944 original size:24 final size:24
Alignment explanation
Indices: 24913--24995 Score: 91
Period size: 24 Copynumber: 3.5 Consensus size: 24
24903 ACTGAGGTCA
*
24913 TAGTATCAATAGTACTATATAAAG
1 TAGTATCAATACTACTATATAAAG
* * *
24937 TATTATCAATACTCCT-T-T-AAT
1 TAGTATCAATACTACTATATAAAG
24958 TAAGTATCAATACTACTATATAAAG
1 T-AGTATCAATACTACTATATAAAG
*
24983 TAGTATCGATACT
1 TAGTATCAATACT
24996 CCTTTAATTA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
21 3 0.06
22 14 0.30
23 2 0.04
24 25 0.53
25 3 0.06
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.37
Consensus pattern (24 bp):
TAGTATCAATACTACTATATAAAG
Found at i:24967 original size:46 final size:46
Alignment explanation
Indices: 24914--25016 Score: 179
Period size: 46 Copynumber: 2.2 Consensus size: 46
24904 CTGAGGTCAT
* *
24914 AGTATCAATAGTACTATATAAAGTATTATCAATACTCCTTTAATTA
1 AGTATCAATACTACTATATAAAGTAGTATCAATACTCCTTTAATTA
*
24960 AGTATCAATACTACTATATAAAGTAGTATCGATACTCCTTTAATTA
1 AGTATCAATACTACTATATAAAGTAGTATCAATACTCCTTTAATTA
25006 AGTATCAATAC
1 AGTATCAATAC
25017 CAAAAATGTC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 54 1.00
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.37
Consensus pattern (46 bp):
AGTATCAATACTACTATATAAAGTAGTATCAATACTCCTTTAATTA
Found at i:24968 original size:22 final size:22
Alignment explanation
Indices: 24940--25016 Score: 93
Period size: 22 Copynumber: 3.4 Consensus size: 22
24930 TATAAAGTAT
24940 TATCAATACTCCTTTAATTAAG
1 TATCAATACTCCTTTAATTAAG
* *
24962 TATCAATACTACTATATAAAGT-AG
1 TATCAATACTCCT-T-T-AATTAAG
*
24986 TATCGATACTCCTTTAATTAAG
1 TATCAATACTCCTTTAATTAAG
25008 TATCAATAC
1 TATCAATAC
25017 CAAAAATGTC
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
21 3 0.07
22 23 0.51
23 2 0.04
24 14 0.31
25 3 0.07
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.38
Consensus pattern (22 bp):
TATCAATACTCCTTTAATTAAG
Found at i:29740 original size:14 final size:15
Alignment explanation
Indices: 29718--29746 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
29708 TAAAAAAATG
29718 ATATAATTATATATT
1 ATATAATTATATATT
29733 ATAT-ATTATATATT
1 ATATAATTATATATT
29747 TTGAGATAAA
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATATAATTATATATT
Found at i:32378 original size:20 final size:20
Alignment explanation
Indices: 32341--32378 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
32331 GGTCGTTTCT
*
32341 AGCCGTTGGGGATGATTTAG
1 AGCCGTTGGAGATGATTTAG
*
32361 AGCCGTTGGAGATTATTT
1 AGCCGTTGGAGATGATTT
32379 TTCTATAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.11, G:0.34, T:0.34
Consensus pattern (20 bp):
AGCCGTTGGAGATGATTTAG
Found at i:32752 original size:83 final size:83
Alignment explanation
Indices: 32646--32809 Score: 310
Period size: 83 Copynumber: 2.0 Consensus size: 83
32636 GATACTTCTC
32646 TTACCTTTGGTATCAGTACCACGTGAACATTATCAGTACTGTTCATGCAATATCGATATTGTAAG
1 TTACCTTTGGTATCAGTACCACGTGAACATTATCAGTACTGTTCATGCAATATCGATATTGTAAG
32711 AATAGTATTGGTACTATA
66 AATAGTATTGGTACTATA
* *
32729 TTACCTTTGGTATCAGTACCACGTGAACATTGTCAGTATTGTTCATGCAATATCGATATTGTAAG
1 TTACCTTTGGTATCAGTACCACGTGAACATTATCAGTACTGTTCATGCAATATCGATATTGTAAG
32794 AATAGTATTGGTACTA
66 AATAGTATTGGTACTA
32810 CGTACCCAGA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 79 1.00
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (83 bp):
TTACCTTTGGTATCAGTACCACGTGAACATTATCAGTACTGTTCATGCAATATCGATATTGTAAG
AATAGTATTGGTACTATA
Found at i:36399 original size:58 final size:58
Alignment explanation
Indices: 36331--36461 Score: 217
Period size: 58 Copynumber: 2.3 Consensus size: 58
36321 AATCTTGCGT
* * * *
36331 TGATTTTAACTTTGTAAGGAAAATAAATCGTTGAATTTATTTCCTTGAGAATCTTAAA
1 TGATTATAACTTTGTAAGGAAAATAAATCATTGAATTTATTTCCTTGAAAATCTCAAA
*
36389 TGATTCTAACTTTGTAAGGAAAATAAATCATTGAATTTATTTCCTTGAAAATCTCAAA
1 TGATTATAACTTTGTAAGGAAAATAAATCATTGAATTTATTTCCTTGAAAATCTCAAA
36447 TGATTATAACTTTGT
1 TGATTATAACTTTGT
36462 CTATTTATTT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 68 1.00
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (58 bp):
TGATTATAACTTTGTAAGGAAAATAAATCATTGAATTTATTTCCTTGAAAATCTCAAA
Found at i:36560 original size:99 final size:97
Alignment explanation
Indices: 36364--36646 Score: 227
Period size: 99 Copynumber: 2.8 Consensus size: 97
36354 TAAATCGTTG
* * * * ** *
36364 AATTTATTTCCTTGAGAATCTTAAATGATTCTAACTTTGT-AAGGAAAATAAATCATTGAATTTA
1 AATTTATTTTCTTGAAAAT-TTAAA-GATTCT-ATTTTGTAAAAGAAAATAAATTGTTAAATTTA
* * * **
36428 TTTCCTTGAAAATCTCAAATGATTATAACTTTGTCT
63 TTTTCTTGAAAATCTCGAATAAAAATAACTTTGT-T
36464 -ATTTATTTTCTTGAAAATATTAAAGGATTCTATTTTGTAAAAGAAAATAAATTGTTAAATTTAT
1 AATTTATTTTCTTGAAAAT-TTAAA-GATTCTATTTTGTAAAAGAAAATAAATTGTTAAATTTAT
*
36528 TTTCTTGATAATCTCGAATAAAAAATAA-TTTGTT
64 TTTCTTGAAAATCTCGAAT-AAAAATAACTTTGTT
* ** * *
36562 GAATTTATTTTCTCAGGAACCTTTAATA-ATTATATCTTT-TAAAATG-AAATAAATTGTTACAT
1 -AATTTATTTTCT--TGAAAATTTAA-AGATTCTAT-TTTGTAAAA-GAAAATAAATTGTTAAAT
* *
36624 TTATTTTCTTGAGAATCTTGAAT
60 TTATTTTCTTGAAAATCTCGAAT
36647 GATTCTATTT
Statistics
Matches: 152, Mismatches: 22, Indels: 18
0.79 0.11 0.09
Matches are distributed among these distances:
98 7 0.05
99 69 0.45
100 63 0.41
101 8 0.05
102 5 0.03
ACGTcount: A:0.37, C:0.09, G:0.10, T:0.44
Consensus pattern (97 bp):
AATTTATTTTCTTGAAAATTTAAAGATTCTATTTTGTAAAAGAAAATAAATTGTTAAATTTATTT
TCTTGAAAATCTCGAATAAAAATAACTTTGTT
Found at i:36731 original size:37 final size:39
Alignment explanation
Indices: 36649--36786 Score: 117
Period size: 38 Copynumber: 3.6 Consensus size: 39
36639 TCTTGAATGA
* * *
36649 TTCTATTTTGAAAGAA-AAACAAATCGTTAAATTTATTT
1 TTCTATTTTGAAAAAAGAAATAAATCGTTAAATTTAGTT
*
36687 TTCTA-TTT-AAAAAAGAAATAAATCGTTACATTT-GTT
1 TTCTATTTTGAAAAAAGAAATAAATCGTTAAATTTAGTT
* * ** * *
36723 TTCATATTTTGTAAAAGGAAATAAATCACTAGATCTA--T
1 TTC-TATTTTGAAAAAAGAAATAAATCGTTAAATTTAGTT
*
36761 TTCTTATTTTGAAAAAGGAAATAAAT
1 TTC-TATTTTGAAAAAAGAAATAAAT
36787 TATTATATTT
Statistics
Matches: 83, Mismatches: 12, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
36 10 0.12
37 21 0.25
38 33 0.40
39 19 0.23
ACGTcount: A:0.43, C:0.08, G:0.09, T:0.40
Consensus pattern (39 bp):
TTCTATTTTGAAAAAAGAAATAAATCGTTAAATTTAGTT
Found at i:36829 original size:39 final size:39
Alignment explanation
Indices: 36696--36825 Score: 136
Period size: 39 Copynumber: 3.4 Consensus size: 39
36686 TTTCTATTTA
* * *
36696 AAAAAGAAATAAATCGTTACATTTGTTTTCATATTTTGT
1 AAAAGGAAATAAATCATTACATTTATTTTCATATTTTGT
* * * * *
36735 AAAAGGAAATAAATCACTAGATCTA-TTTCTTATTTTGA
1 AAAAGGAAATAAATCATTACATTTATTTTCATATTTTGT
* * * *
36773 AAAAGGAAATAAATTATTATATTTATTTTCATGTTTTTT
1 AAAAGGAAATAAATCATTACATTTATTTTCATATTTTGT
*
36812 AAAATGAAATAAAT
1 AAAAGGAAATAAAT
36826 TATTGAATTT
Statistics
Matches: 73, Mismatches: 17, Indels: 2
0.79 0.18 0.02
Matches are distributed among these distances:
38 32 0.44
39 41 0.56
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.42
Consensus pattern (39 bp):
AAAAGGAAATAAATCATTACATTTATTTTCATATTTTGT
Found at i:36908 original size:39 final size:38
Alignment explanation
Indices: 36865--36976 Score: 118
Period size: 38 Copynumber: 2.9 Consensus size: 38
36855 ATTATTCTGG
* *
36865 TTTGTAAAAGGAAATAAATCATTATATTTATTTTTCTAA
1 TTTGTAAAAGGAAATAAATTATTA-ATTTATTTTCCTAA
* * * **
36904 TTTGTAAAATGAAATAAATTGTTGGATTTA-TTTCCTGT
1 TTTGTAAAAGGAAATAAATTATT-AATTTATTTTCCTAA
*
36942 TTTGTATAAGGAAATAAATTATTGAATTTATTTTC
1 TTTGTAAAAGGAAATAAATTATT-AATTTATTTTC
36977 TTAACAATTT
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
38 31 0.52
39 29 0.48
ACGTcount: A:0.37, C:0.04, G:0.12, T:0.47
Consensus pattern (38 bp):
TTTGTAAAAGGAAATAAATTATTAATTTATTTTCCTAA
Found at i:36997 original size:135 final size:135
Alignment explanation
Indices: 36730--37018 Score: 330
Period size: 135 Copynumber: 2.1 Consensus size: 135
36720 GTTTTCATAT
* *
36730 TTTGTAAAAGGAAATAAATCACTAGATCTATTTCTTATTTTGAAAAAGGAAATAAATTATTATAT
1 TTTGTAAAAGGAAATAAATCACTAGATCTATTTCTTAATTTGAAAAAGGAAATAAATTATTAGAT
* * * * *
36795 TTATTTTCATGTTTTTTAAAATGAAATAAATTATTGAATTTAATTTACTGAGAATCTCACATTAT
66 TTATTTTCATGTTTTGTAAAAGGAAATAAATTATTGAATTTAATTTACTAACAATCTCACATGAT
36860 TCTGG
131 TCTGG
* * * * * * * *
36865 TTTGTAAAAGGAAATAAATCATTATATTTATTTTTCTAATTTGTAAAATGAAATAAATTGTTGGA
1 TTTGTAAAAGGAAATAAATCACTAGATCTATTTCT-TAATTTGAAAAAGGAAATAAATTATTAGA
* * * * * *
36930 TTTA-TTTCCTGTTTTGTATAAGGAAATAAATTATTGAATTT-ATTTTCTTAACAATTTTATATG
65 TTTATTTTCATGTTTTGTAAAAGGAAATAAATTATTGAATTTAATTTAC-TAACAATCTCACATG
36993 ATTCTGG
129 ATTCTGG
* *
37000 GTTGTAAAAGAAAAATAAA
1 TTTGTAAAAG-GAAATAAA
37019 CCGTTGAATT
Statistics
Matches: 128, Mismatches: 23, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
134 5 0.04
135 89 0.70
136 34 0.27
ACGTcount: A:0.39, C:0.06, G:0.11, T:0.44
Consensus pattern (135 bp):
TTTGTAAAAGGAAATAAATCACTAGATCTATTTCTTAATTTGAAAAAGGAAATAAATTATTAGAT
TTATTTTCATGTTTTGTAAAAGGAAATAAATTATTGAATTTAATTTACTAACAATCTCACATGAT
TCTGG
Found at i:40007 original size:44 final size:44
Alignment explanation
Indices: 39958--40042 Score: 143
Period size: 44 Copynumber: 1.9 Consensus size: 44
39948 TTTTCTTCTA
* *
39958 TTCTTTTAATTTCTAATAACTCTGTTTTTATAACATGTTTTTTC
1 TTCTTTTAATTTCTAATAACTATGTCTTTATAACATGTTTTTTC
*
40002 TTCTTTTAATTTCTAATGACTATGTCTTTATAACATGTTTT
1 TTCTTTTAATTTCTAATAACTATGTCTTTATAACATGTTTT
40043 CTTTTGCTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.24, C:0.13, G:0.06, T:0.58
Consensus pattern (44 bp):
TTCTTTTAATTTCTAATAACTATGTCTTTATAACATGTTTTTTC
Found at i:45739 original size:2 final size:2
Alignment explanation
Indices: 45732--45770 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
45722 CCTAAATTAA
45732 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT A
45771 AATTGATTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:51521 original size:15 final size:15
Alignment explanation
Indices: 51498--51541 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
51488 ATAAAACTTA
*
51498 ATTAATAATAATAAT
1 ATTATTAATAATAAT
51513 ATTATTAATAAT--T
1 ATTATTAATAATAAT
51526 ATTATT-ATAATAAT
1 ATTATTAATAATAAT
51540 AT
1 AT
51542 AAAAGGGGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 5 0.19
13 7 0.27
14 3 0.12
15 11 0.42
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATTAATAATAAT
Done.