Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002318.1 Hibiscus syriacus cultivar Beakdansim tig00004721_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: 72210
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:1574 original size:8 final size:8
Alignment explanation
Indices: 1561--1596 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
1551 ACATATGGAT
1561 GAAGTTTA
1 GAAGTTTA
1569 GAAGTTTA
1 GAAGTTTA
1577 GAAGTTTA
1 GAAGTTTA
*
1585 GAAGTTAA
1 GAAGTTTA
1593 GAAG
1 GAAG
1597 GTACTAAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.42, C:0.00, G:0.28, T:0.31
Consensus pattern (8 bp):
GAAGTTTA
Found at i:5129 original size:44 final size:44
Alignment explanation
Indices: 5016--5188 Score: 258
Period size: 44 Copynumber: 4.0 Consensus size: 44
5006 TATTACCGAA
* *
5016 ATAAATGAAAATGCATAACGGTGCATTATTGGCTGAAATGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
*
5060 ATAAAT-AAAATGCATAATGGTGCATTATTGGCAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* * * *
5103 ATAAATGAAAATGTATAACGATGCATTATTGGCATAAAGGTTCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* *
5147 ATAAATGAAAATGCATAATGGTGCATTATTGGCCGAAAGGTG
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTG
5189 TCACTCTTGG
Statistics
Matches: 114, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
43 40 0.35
44 74 0.65
ACGTcount: A:0.39, C:0.12, G:0.23, T:0.27
Consensus pattern (44 bp):
ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
Found at i:7526 original size:23 final size:23
Alignment explanation
Indices: 7500--7556 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
7490 AGAGCTTTGC
*
7500 AGAGAGTTTTACCATGAGATTGG
1 AGAGAGTTTTACCATGAGACTGG
**
7523 AGAGAACTTTACCATGAGACTGG
1 AGAGAGTTTTACCATGAGACTGG
7546 AGAGAGCTTTT
1 AGAGAG-TTTT
7557 CCGTGGGAGG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 25 0.89
24 3 0.11
ACGTcount: A:0.32, C:0.12, G:0.28, T:0.28
Consensus pattern (23 bp):
AGAGAGTTTTACCATGAGACTGG
Found at i:13001 original size:21 final size:21
Alignment explanation
Indices: 12977--13016 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
12967 TAAATATCTT
12977 TTAATT-TGACATATTCAAAGA
1 TTAATTATGA-ATATTCAAAGA
*
12998 TTAATTATTAATATTCAAA
1 TTAATTATGAATATTCAAA
13017 TGAAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TTAATTATGAATATTCAAAGA
Found at i:20710 original size:30 final size:30
Alignment explanation
Indices: 20674--20734 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
20664 TATCAATTAA
20674 ACGGATGTAAAATTATCACATCAGATATAT
1 ACGGATGTAAAATTATCACATCAGATATAT
*
20704 ACGGATGTAAAATTATTACATCAGATATAT
1 ACGGATGTAAAATTATCACATCAGATATAT
20734 A
1 A
20735 TGTTGATCGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.31
Consensus pattern (30 bp):
ACGGATGTAAAATTATCACATCAGATATAT
Found at i:25462 original size:6 final size:6
Alignment explanation
Indices: 25453--25488 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
25443 TTGTCGAATT
25453 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
25489 CGTGAAACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:33729 original size:48 final size:48
Alignment explanation
Indices: 33675--33769 Score: 181
Period size: 48 Copynumber: 2.0 Consensus size: 48
33665 AGTAAACATC
*
33675 TCATATTAAAGTTAGTACTTGGAGTCTCCGAATTATAAAATTTTAGTA
1 TCATATTAAAGTTAGTACTTGGAGTCTCCAAATTATAAAATTTTAGTA
33723 TCATATTAAAGTTAGTACTTGGAGTCTCCAAATTATAAAATTTTAGT
1 TCATATTAAAGTTAGTACTTGGAGTCTCCAAATTATAAAATTTTAGT
33770 GATTAAAAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.40
Consensus pattern (48 bp):
TCATATTAAAGTTAGTACTTGGAGTCTCCAAATTATAAAATTTTAGTA
Found at i:37553 original size:13 final size:13
Alignment explanation
Indices: 37535--37564 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
37525 CTGTGATGCG
37535 CATTTATGACACA
1 CATTTATGACACA
*
37548 CATTTATGACGCA
1 CATTTATGACACA
37561 CATT
1 CATT
37565 GTGCGTCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (13 bp):
CATTTATGACACA
Found at i:37626 original size:85 final size:85
Alignment explanation
Indices: 37536--37693 Score: 219
Period size: 85 Copynumber: 1.9 Consensus size: 85
37526 TGTGATGCGC
* * * *
37536 ATTTATGACACACATTTATGACGCACATTGTGCGTCATTGAAACCCCCGTCA-TAAATGAAGATG
1 ATTTATGACACACATTTATGACGCACATTGCGCGTCATTGAAACACACGTCATTAAA-AAAGATG
37600 ACACACATTTGTGTGTCATAA
65 ACACACATTTGTGTGTCATAA
** * * *
37621 ATTTATGACACACATTTATGACTTACATTGCGTGTCATTGAAGCACATGTCATTAAAAAAGATGA
1 ATTTATGACACACATTTATGACGCACATTGCGCGTCATTGAAACACACGTCATTAAAAAAGATGA
37686 CACACATT
66 CACACATT
37694 CATGTGTCGT
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
85 59 0.94
86 4 0.06
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (85 bp):
ATTTATGACACACATTTATGACGCACATTGCGCGTCATTGAAACACACGTCATTAAAAAAGATGA
CACACATTTGTGTGTCATAA
Found at i:45912 original size:29 final size:29
Alignment explanation
Indices: 45877--45958 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
45867 AAACTAAATT
* *
45877 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
45906 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
45935 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
45959 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:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:50682 original size:29 final size:29
Alignment explanation
Indices: 50647--50728 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
50637 AAACTAAATT
* *
50647 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
50676 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
50705 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
50729 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:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:54630 original size:5 final size:5
Alignment explanation
Indices: 54622--54708 Score: 56
Period size: 5 Copynumber: 16.8 Consensus size: 5
54612 ACATAAATAC
* *
54622 TATAA TATAAA TATAA T-TAA TATAA TA-ATA TATAT TAT-T TATAA TATAA
1 TATAA TAT-AA TATAA TATAA TATAA TATA-A TATAA TATAA TATAA TATAA
*
54671 -ATAC TCCATAA TATTAA TATATA TAATAA TATAA TATA
1 TATAA T--ATAA TA-TAA TATA-A T-ATAA TATAA TATA
54709 TACTATATTA
Statistics
Matches: 67, Mismatches: 4, Indels: 22
0.72 0.04 0.24
Matches are distributed among these distances:
4 12 0.18
5 33 0.49
6 15 0.22
7 7 0.10
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (5 bp):
TATAA
Found at i:54698 original size:55 final size:54
Alignment explanation
Indices: 54614--54720 Score: 139
Period size: 55 Copynumber: 2.0 Consensus size: 54
54604 AATAAAATAC
*
54614 ATAAATACTATAATATAAATATAATTAAT-ATAATAATATATATTAT-TTATAAT
1 ATAAATACTATAATATAAATATAATTAATAAT-ATAATATATACTATATTATAAT
*
54667 ATAAATACTCCATAATATTAATAT-ATATAATAATATAATATATACTATATTATA
1 ATAAATACT--ATAATATAAATATAAT-TAATAATATAATATATACTATATTATA
54721 TAACTAATAT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
53 9 0.19
54 2 0.04
55 29 0.62
56 7 0.15
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (54 bp):
ATAAATACTATAATATAAATATAATTAATAATATAATATATACTATATTATAAT
Found at i:54715 original size:7 final size:7
Alignment explanation
Indices: 54617--54733 Score: 60
Period size: 7 Copynumber: 15.1 Consensus size: 7
54607 AAAATACATA
54617 AATACTAT
1 AATA-TAT
54625 AATATA-
1 AATATAT
54631 AATATAATT
1 AATAT-A-T
54640 AATATAAT
1 AATAT-AT
54648 AATATAT
1 AATATAT
*
54655 ATTATTTAT
1 A--ATATAT
54664 AATATA-
1 AATATAT
54670 AATACTCCAT
1 AATA-T--AT
54680 AATAT-T
1 AATATAT
54686 AATATATAT
1 -A-ATATAT
54695 AATAATAT
1 AAT-ATAT
54703 AATATAT
1 AATATAT
*
54710 ACTATAT
1 AATATAT
*
54717 TATATAACT
1 AATAT-A-T
54726 AATATAT
1 AATATAT
54733 A
1 A
54734 TTATGTCTAT
Statistics
Matches: 88, Mismatches: 6, Indels: 31
0.70 0.05 0.25
Matches are distributed among these distances:
6 10 0.11
7 29 0.33
8 24 0.27
9 21 0.24
10 4 0.05
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (7 bp):
AATATAT
Found at i:60174 original size:15 final size:15
Alignment explanation
Indices: 60154--60187 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
60144 CTGGATTTTT
*
60154 TTTTTAATTTTTTAA
1 TTTTTAACTTTTTAA
*
60169 TTTTTAACTTTTTCA
1 TTTTTAACTTTTTAA
60184 TTTT
1 TTTT
60188 CTTTTTCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTAACTTTTTAA
Found at i:61944 original size:2 final size:2
Alignment explanation
Indices: 61937--61987 Score: 70
Period size: 2 Copynumber: 26.0 Consensus size: 2
61927 ACTTATTTTA
*
61937 AT AT AT AT ACT AT AT -T TT AT A- AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
61978 AT AT AT AT AT
1 AT AT AT AT AT
61988 TCAAAACTAC
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
1 2 0.04
2 41 0.91
3 2 0.04
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:62013 original size:73 final size:73
Alignment explanation
Indices: 61897--62037 Score: 173
Period size: 73 Copynumber: 1.9 Consensus size: 73
61887 AAATGAAATA
* * *
61897 ATATACATATATATATATTAAACATATAATACTTATTTTAATATA-TATACTATATTTTATAATA
1 ATATACATATATATATATTAAACATACAATACTTATTTAAATATACTATA-TATATTATATAATA
61961 TATATATAT
65 TATATATAT
* *
61970 ATATATATATATATATATTCAAA-ACTACAATA-TGTA-TTAAATATACTATATATGTTATATAA
1 ATATACATATATATATATT-AAACA-TACAATACT-TATTTAAATATACTATATATATTATATAA
62032 TATATA
63 TATATA
62038 ACTTATAATA
Statistics
Matches: 59, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
73 44 0.75
74 15 0.25
ACGTcount: A:0.48, C:0.06, G:0.01, T:0.45
Consensus pattern (73 bp):
ATATACATATATATATATTAAACATACAATACTTATTTAAATATACTATATATATTATATAATAT
ATATATAT
Found at i:62469 original size:142 final size:142
Alignment explanation
Indices: 62284--62545 Score: 346
Period size: 142 Copynumber: 1.8 Consensus size: 142
62274 TATTTATTAT
* * * * * *
62284 GGTAGGTTAGATCAAAATAGATTTACTCCACTGCTCTTTAGGGTAGGTCAAATCTTGAGAAAATA
1 GGTAGGTCAGATCAAAATAGATTTACTCCAATACTCTTGAGGGTAGGTC-AATCTAGAGAAAAGA
* * * * ****
62349 AAAAGTATTTGCAGCACTGCTTTTTA-GGTAGGTCAAATTTGGATAAAAGAAAGGTGATTTACTT
65 AAAAGTATCTACACCACTACTCAACATGGTAGGTCAAATTTGGATAAAAGAAAGGTGATTTACTT
62413 CGTTACTCTTCAG
130 CGTTACTCTTCAG
* * *
62426 GGTAGGTCAGATCTAAATAGATTTGCTCCAATACTCTTGAGGGTAGGTCATTCTAGAGAAAAGAA
1 GGTAGGTCAGATCAAAATAGATTTACTCCAATACTCTTGAGGGTAGGTCAATCTAGAGAAAAGAA
*
62491 AAAGTATCTACTCCACTACTCAACATGGTAGGTCAAATTTGGATAAAAGAAAGGT
66 AAAGTATCTACACCACTACTCAACATGGTAGGTCAAATTTGGATAAAAGAAAGGT
62546 CATCTGCTCC
Statistics
Matches: 101, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
141 29 0.29
142 72 0.71
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.30
Consensus pattern (142 bp):
GGTAGGTCAGATCAAAATAGATTTACTCCAATACTCTTGAGGGTAGGTCAATCTAGAGAAAAGAA
AAAGTATCTACACCACTACTCAACATGGTAGGTCAAATTTGGATAAAAGAAAGGTGATTTACTTC
GTTACTCTTCAG
Found at i:69471 original size:88 final size:87
Alignment explanation
Indices: 69325--69495 Score: 290
Period size: 88 Copynumber: 2.0 Consensus size: 87
69315 ACTAACACAC
*
69325 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATAAATCTATAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGATTTTATTATTTCAAATTAATAAATCTATAT
*
69390 TTAATTAATTAGAATTTAATAAT
66 TTAATTAATT-GAAATTAATAAT
*
69413 CCTTTTATATCCAAGTTACCCTAATCATA-TAGGATTTTATTATTTCAAATTAATTAAATCTATA
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGATTTTATTATTTCAAATTAA-TAAATCTATA
69477 TTTAATTAATTGAAATTAA
65 TTTAATTAATTGAAATTAA
69496 ATATTTGGGA
Statistics
Matches: 79, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
87 30 0.38
88 49 0.62
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (87 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAGGATTTTATTATTTCAAATTAATAAATCTATAT
TTAATTAATTGAAATTAATAAT
Done.