Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000211.1 Hibiscus syriacus cultivar Beakdansim tig00000374_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: 48275
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:2038 original size:17 final size:17
Alignment explanation
Indices: 2007--2048 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1997 GAGAGAAAAG
2007 TAAAA-AAAGGAAATAAA
1 TAAAAGAAAGGAAAT-AA
2024 TAAAAGAAAGG-AATAA
1 TAAAAGAAAGGAAATAA
2040 TCAAAAGAA
1 T-AAAAGAA
2049 TATTTTCCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 3 0.13
17 15 0.65
18 5 0.22
ACGTcount: A:0.71, C:0.02, G:0.14, T:0.12
Consensus pattern (17 bp):
TAAAAGAAAGGAAATAA
Found at i:3956 original size:17 final size:17
Alignment explanation
Indices: 3936--3969 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3926 TCGCATCACA
3936 CATTAGCTCAAATGGTG
1 CATTAGCTCAAATGGTG
3953 CATTAGCTCAAATGGTG
1 CATTAGCTCAAATGGTG
3970 ATGTCCAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (17 bp):
CATTAGCTCAAATGGTG
Found at i:6221 original size:64 final size:63
Alignment explanation
Indices: 6124--6264 Score: 167
Period size: 64 Copynumber: 2.2 Consensus size: 63
6114 CACATTGAAT
* * *
6124 GTGCATCGATGCACTCTTTAAAGAAGAAACATCGAATGCAATTGGTGCATCGATGCATAAGGA
1 GTGCATCGATGCACCCCTTAAAGAAGAAACATCGAAGGCAATTGGTGCATCGATGCATAAGGA
* * * * * * *
6187 GTGCATCGATGCATCCCCTTAAA-ATGAAAACATCGAAGGTAATTTGTGTATCTATGCATGAGTA
1 GTGCATCGATGCA-CCCCTTAAAGAAG-AAACATCGAAGGCAATTGGTGCATCGATGCATAAGGA
6251 GTGCATCGATGCAC
1 GTGCATCGATGCAC
6265 ATGTTAAAGA
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
63 16 0.24
64 50 0.76
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (63 bp):
GTGCATCGATGCACCCCTTAAAGAAGAAACATCGAAGGCAATTGGTGCATCGATGCATAAGGA
Found at i:7591 original size:18 final size:18
Alignment explanation
Indices: 7548--7674 Score: 209
Period size: 18 Copynumber: 6.9 Consensus size: 18
7538 AGGGATTATC
*
7548 AGTGGTCCTTCGGGACAAAC
1 AGTGGTCCTTCGGGAC--AT
*
7568 AGTGGTCCTTCGAGACAT
1 AGTGGTCCTTCGGGACAT
7586 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
7604 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
7622 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
7640 AGTGGTCCTTCAGGACAT
1 AGTGGTCCTTCGGGACAT
7658 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
7675 AATATTCAGT
Statistics
Matches: 102, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
18 87 0.85
20 15 0.15
ACGTcount: A:0.20, C:0.23, G:0.31, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:13363 original size:37 final size:37
Alignment explanation
Indices: 13252--13364 Score: 90
Period size: 37 Copynumber: 3.0 Consensus size: 37
13242 TTCCATTTAC
* * **
13252 AAAATAGGAAACTAAATCCAACGATTTATTTCCTTTT
1 AAAATAGGAAAATAAATCTAACGATTTATTTATTTTT
* *
13289 AAAACCA-GAAAACTAAATTCT-ATGA-TTA-TTACTTTTTT
1 AAAA-TAGGAAAA-TAAA-TCTAACGATTTATTTA--TTTTT
*
13327 TAAATAGGAAAATAAATCTAACGATTTATTTATTTTT
1 AAAATAGGAAAATAAATCTAACGATTTATTTATTTTT
13364 A
1 A
13365 CATATCAGAA
Statistics
Matches: 57, Mismatches: 10, Indels: 18
0.67 0.12 0.21
Matches are distributed among these distances:
36 5 0.09
37 24 0.42
38 23 0.40
39 5 0.09
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (37 bp):
AAAATAGGAAAATAAATCTAACGATTTATTTATTTTT
Found at i:13363 original size:38 final size:38
Alignment explanation
Indices: 13252--13363 Score: 90
Period size: 38 Copynumber: 3.0 Consensus size: 38
13242 TTCCATTTAC
* * **
13252 AAAATAGGAAACTAAATCCAACGATTTATTT-CCTTTT
1 AAAATAGGAAAATAAATCTAACGATTTATTTATTTTTT
* *
13289 AAAACCA-GAAAACTAAATTCT-ATGA-TTA-TTACTTTTTT
1 AAAA-TAGGAAAA-TAAA-TCTAACGATTTATTTA-TTTTTT
*
13327 TAAATAGGAAAATAAATCTAACGATTTATTTATTTTT
1 AAAATAGGAAAATAAATCTAACGATTTATTTATTTTT
13364 ACATATCAGA
Statistics
Matches: 57, Mismatches: 9, Indels: 17
0.69 0.11 0.20
Matches are distributed among these distances:
36 5 0.09
37 19 0.33
38 28 0.49
39 5 0.09
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (38 bp):
AAAATAGGAAAATAAATCTAACGATTTATTTATTTTTT
Found at i:16395 original size:31 final size:30
Alignment explanation
Indices: 16360--16433 Score: 111
Period size: 26 Copynumber: 2.6 Consensus size: 30
16350 GTTTCACCCG
16360 ACCCGACCCGACCCGAATATATAACTTAGA
1 ACCCGACCCGACCCGAATATATAACTTAGA
16390 A----ACCCGACCCGAATATATAACTTAGAA
1 ACCCGACCCGACCCGAATATATAACTTAG-A
16417 ACCCGACCCGACCCGAA
1 ACCCGACCCGACCCGAA
16434 ATAAAAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
26 24 0.62
27 2 0.05
30 1 0.03
31 12 0.31
ACGTcount: A:0.38, C:0.35, G:0.14, T:0.14
Consensus pattern (30 bp):
ACCCGACCCGACCCGAATATATAACTTAGA
Found at i:16401 original size:26 final size:26
Alignment explanation
Indices: 16365--16427 Score: 126
Period size: 26 Copynumber: 2.4 Consensus size: 26
16355 ACCCGACCCG
16365 ACCCGACCCGAATATATAACTTAGAA
1 ACCCGACCCGAATATATAACTTAGAA
16391 ACCCGACCCGAATATATAACTTAGAA
1 ACCCGACCCGAATATATAACTTAGAA
16417 ACCCGACCCGA
1 ACCCGACCCGA
16428 CCCGAAATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.40, C:0.32, G:0.13, T:0.16
Consensus pattern (26 bp):
ACCCGACCCGAATATATAACTTAGAA
Found at i:17522 original size:15 final size:16
Alignment explanation
Indices: 17498--17531 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
17488 CTAATTTATA
17498 TATAAATTTT-AATTT
1 TATAAATTTTAAATTT
*
17513 TATAACTTTTAAATTT
1 TATAAATTTTAAATTT
17529 TAT
1 TAT
17532 TTTTATAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (16 bp):
TATAAATTTTAAATTT
Found at i:17754 original size:21 final size:20
Alignment explanation
Indices: 17730--17775 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 20
17720 AATAATATAT
17730 TTTTTATTTTT-AGTAATTTAA
1 TTTTTATTTTTGA-T-ATTTAA
17751 TTTTTATTTTTGATATTTAA
1 TTTTTATTTTTGATATTTAA
17771 TTTTT
1 TTTTT
17776 GAGCAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.46
21 12 0.50
22 1 0.04
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (20 bp):
TTTTTATTTTTGATATTTAA
Found at i:17760 original size:20 final size:21
Alignment explanation
Indices: 17730--17775 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 21
17720 AATAATATAT
17730 TTTTTATTTTTAG-TAATTTAA
1 TTTTTATTTTTAGAT-ATTTAA
17751 TTTTTATTTTT-GATATTTAA
1 TTTTTATTTTTAGATATTTAA
17771 TTTTT
1 TTTTT
17776 GAGCAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (21 bp):
TTTTTATTTTTAGATATTTAA
Found at i:21744 original size:29 final size:29
Alignment explanation
Indices: 21686--21747 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
21676 GGGATTAGAA
* * * *
21686 TAAAGGTTTTCAAAGTTTTAGATTTTTTT
1 TAAAGATTTTCAAAGTCTTAGAGTTCTTT
21715 TAAAGATTTTCAAAAGTCTT-GAGTTCTTT
1 TAAAGATTTTC-AAAGTCTTAGAGTTCTTT
21744 TAAA
1 TAAA
21748 AATAAAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 21 0.75
30 7 0.25
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.48
Consensus pattern (29 bp):
TAAAGATTTTCAAAGTCTTAGAGTTCTTT
Found at i:22208 original size:12 final size:11
Alignment explanation
Indices: 22189--22218 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
22179 GCATTATTAT
22189 ATAAAAAAAAA
1 ATAAAAAAAAA
*
22200 CTAAAAAAAAA
1 ATAAAAAAAAA
22211 ATAAAAAA
1 ATAAAAAA
22219 TTGGACAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.10
Consensus pattern (11 bp):
ATAAAAAAAAA
Found at i:26091 original size:6 final size:6
Alignment explanation
Indices: 26080--26146 Score: 107
Period size: 6 Copynumber: 11.2 Consensus size: 6
26070 GACACGTATT
* * *
26080 ACCACG ACCACG ACCACG ACCACG ACCACG ACCTCG ACCTCG ACCTCG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
26128 ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG A
26147 GCCGAGCCGA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 59 1.00
ACGTcount: A:0.30, C:0.49, G:0.16, T:0.04
Consensus pattern (6 bp):
ACCACG
Found at i:26154 original size:5 final size:5
Alignment explanation
Indices: 26144--26192 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
26134 ACCACGACCA
* * * *
26144 CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC CGTGC CGAGC CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
26193 ACGGACGGAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.16, C:0.37, G:0.41, T:0.06
Consensus pattern (5 bp):
CGAGC
Found at i:32057 original size:6 final size:6
Alignment explanation
Indices: 32046--32098 Score: 74
Period size: 6 Copynumber: 9.2 Consensus size: 6
32036 GACACGTATT
* *
32046 ACCACG ACCACG ACCACG A-C-CG ACCTCG ACCTCG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
32092 ACCACG A
1 ACCACG A
32099 GCCGAGCCGA
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
4 3 0.07
5 2 0.05
6 39 0.89
ACGTcount: A:0.30, C:0.49, G:0.17, T:0.04
Consensus pattern (6 bp):
ACCACG
Found at i:32106 original size:5 final size:5
Alignment explanation
Indices: 32096--32144 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
32086 ACCACGACCA
* * * *
32096 CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC CGTGC CGAGC CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
32145 ACGGACGGAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.16, C:0.37, G:0.41, T:0.06
Consensus pattern (5 bp):
CGAGC
Found at i:39566 original size:2 final size:2
Alignment explanation
Indices: 39559--39584 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39549 TCGAGTTTCG
39559 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
39585 TGAGTTATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40814 original size:65 final size:64
Alignment explanation
Indices: 40745--40930 Score: 200
Period size: 65 Copynumber: 2.9 Consensus size: 64
40735 AATTAAATTG
* * * *
40745 AACATCGAATGCATTTCATGCATAGATGCACATACCATGCACCGATGCACTGAGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACATACAATGCACCGATGCACTAAGGATATTT-TG-
40809 A
64 A
* * ** *
40810 AACATCGAATGCATTTGATGCATCGATGCACCA-ACAATACATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCA-CATACAATGCACCGATGCACTAAGGATATTTTGA
* *
40874 AACATCGAATGCACTTGATGCATCGATGCAC-T-CTTAGTGCACCGATGCACTAAGGAT
1 AACATCGAATGCATTTGATGCATCGATGCACATAC--AATGCACCGATGCACTAAGGAT
40931 CCAACGGTCA
Statistics
Matches: 101, Mismatches: 15, Indels: 11
0.80 0.12 0.09
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 46 0.46
65 48 0.48
66 5 0.05
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCGATGCACATACAATGCACCGATGCACTAAGGATATTTTGA
Found at i:40897 original size:64 final size:66
Alignment explanation
Indices: 40745--40904 Score: 202
Period size: 65 Copynumber: 2.5 Consensus size: 66
40735 AATTAAATTG
* * * * *
40745 AACATCGAATGCATTTCATGCATAGATGCA-CATACCATGCACCGATGCACTGAGGATTTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACCATACAATACACCGATGCACTCAGGATTTTATGA
40809 A
66 A
* * *
40810 AACATCGAATGCATTTGATGCATCGATGCACCA-ACAATACATCGATGCACTCTGGCTATTT-TG
1 AACATCGAATGCATTTGATGCATCGATGCACCATACAATACACCGATGCACTCAGGAT-TTTATG
40873 -A
65 AA
*
40874 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
40905 TCTTAGTGCA
Statistics
Matches: 84, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 31 0.37
65 48 0.57
66 5 0.06
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (66 bp):
AACATCGAATGCATTTGATGCATCGATGCACCATACAATACACCGATGCACTCAGGATTTTATGA
A
Found at i:40904 original size:17 final size:19
Alignment explanation
Indices: 40876--40924 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
40866 TATTTTGAAA
40876 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
40894 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
40913 CACCGATGCACT
1 CATCGATGCACT
40925 AAGGATCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:46710 original size:24 final size:24
Alignment explanation
Indices: 46678--46758 Score: 75
Period size: 24 Copynumber: 3.5 Consensus size: 24
46668 AAACTTAACA
46678 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCATCCCTTTGAAT
* *
46702 GTGCATCGATTCAT-CATGTTG-A-
1 GTGCATCGATGCATCCCT-TTGAAT
*
46724 -TGCACCGATGCA-CGCC-TTGAAT
1 GTGCATCGATGCATC-CCTTTGAAT
46746 GTGCATCGATGCA
1 GTGCATCGATGCA
46759 CCTGGTCATG
Statistics
Matches: 45, Mismatches: 6, Indels: 13
0.70 0.09 0.20
Matches are distributed among these distances:
20 3 0.07
21 11 0.24
22 1 0.02
23 14 0.31
24 16 0.36
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.30
Consensus pattern (24 bp):
GTGCATCGATGCATCCCTTTGAAT
Done.