Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004422.1 Hibiscus syriacus cultivar Beakdansim tig00009697_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: 75668
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:696 original size:12 final size:12
Alignment explanation
Indices: 676--709 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
666 CAATTACAAT
676 AACTTCAATATCA
1 AACTTCAAT-TCA
689 AA-TTCAATTCA
1 AACTTCAATTCA
700 AACTTCAATT
1 AACTTCAATT
710 TCCTACATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 5 0.25
12 13 0.65
13 2 0.10
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (12 bp):
AACTTCAATTCA
Found at i:3688 original size:15 final size:15
Alignment explanation
Indices: 3670--3700 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3660 ATTTGACCAA
*
3670 ATAATATTTTAATGG
1 ATAATATTTCAATGG
3685 ATAATATTTCAATGG
1 ATAATATTTCAATGG
3700 A
1 A
3701 ATTTGGTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.03, G:0.13, T:0.42
Consensus pattern (15 bp):
ATAATATTTCAATGG
Found at i:6028 original size:41 final size:41
Alignment explanation
Indices: 5978--6059 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 41
5968 AAGTGAGTAC
5978 TTATCAGTTC-TGCTTTGGTACATACGTGTATCAATGTTCAG
1 TTATCAGTTCAT-CTTTGGTACATACGTGTATCAATGTTCAG
* **
6019 TTATTAGTTCATCTTTGGTACATTTGTGTATCAATGTTCAG
1 TTATCAGTTCATCTTTGGTACATACGTGTATCAATGTTCAG
6060 CGCTGTTGGT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 36 0.97
42 1 0.03
ACGTcount: A:0.22, C:0.15, G:0.18, T:0.45
Consensus pattern (41 bp):
TTATCAGTTCATCTTTGGTACATACGTGTATCAATGTTCAG
Found at i:31009 original size:22 final size:22
Alignment explanation
Indices: 30979--31047 Score: 129
Period size: 22 Copynumber: 3.1 Consensus size: 22
30969 ATAAGTCCTC
*
30979 TTGTCTAATTCGTTTTGAAGGG
1 TTGTATAATTCGTTTTGAAGGG
31001 TTGTATAATTCGTTTTGAAGGG
1 TTGTATAATTCGTTTTGAAGGG
31023 TTGTATAATTCGTTTTGAAGGG
1 TTGTATAATTCGTTTTGAAGGG
31045 TTG
1 TTG
31048 AAAGTGTTAG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.20, C:0.06, G:0.28, T:0.46
Consensus pattern (22 bp):
TTGTATAATTCGTTTTGAAGGG
Found at i:38570 original size:2 final size:2
Alignment explanation
Indices: 38557--38589 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
38547 CTAAATGCTT
*
38557 TA TA TT 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 TA TA T
38590 TAATAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:41180 original size:25 final size:25
Alignment explanation
Indices: 41146--41208 Score: 119
Period size: 24 Copynumber: 2.6 Consensus size: 25
41136 TTTAACGTTC
41146 AATGGTTTAGGGTTTTTTGGGTTAA
1 AATGGTTTAGGGTTTTTTGGGTTAA
41171 AATGGTTTAGGG-TTTTTGGGTTAA
1 AATGGTTTAGGGTTTTTTGGGTTAA
41195 AATGGTTTAGGGTT
1 AATGGTTTAGGGTT
41209 AGGGTTTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
24 24 0.65
25 13 0.35
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.46
Consensus pattern (25 bp):
AATGGTTTAGGGTTTTTTGGGTTAA
Found at i:41234 original size:26 final size:25
Alignment explanation
Indices: 41205--41259 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
41195 AATGGTTTAG
*
41205 GGTTAGGGTTTTTTTA-ATGTTAAAAT
1 GGTTAGGATTTTTTTAGA-G-TAAAAT
*
41231 GGTTATGATTTTTTTAGAGTAAAAT
1 GGTTAGGATTTTTTTAGAGTAAAAT
41256 GGTT
1 GGTT
41260 TTGAATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 10 0.38
26 15 0.58
27 1 0.04
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (25 bp):
GGTTAGGATTTTTTTAGAGTAAAAT
Found at i:41242 original size:25 final size:24
Alignment explanation
Indices: 41213--41269 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 24
41203 AGGGTTAGGG
41213 TTTTTTTAATGTTAAAATGGTTATGA
1 TTTTTTTAA-G-TAAAATGGTTATGA
*
41239 TTTTTTTAGAGTAAAATGGTTTTGA
1 TTTTTTTA-AGTAAAATGGTTATGA
*
41264 ATTTTT
1 TTTTTT
41270 AAATGGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 18 0.64
26 9 0.32
27 1 0.04
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (24 bp):
TTTTTTTAAGTAAAATGGTTATGA
Found at i:43339 original size:24 final size:24
Alignment explanation
Indices: 43311--43360 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
43301 TATGCCAAAA
* *
43311 CTTATACTCTGAAACTATCAAACT
1 CTTATACTCTAAAACTACCAAACT
* *
43335 CTTATTCTCTAAAACTCCCAAACT
1 CTTATACTCTAAAACTACCAAACT
43359 CT
1 CT
43361 CAAACTCTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.30, G:0.02, T:0.34
Consensus pattern (24 bp):
CTTATACTCTAAAACTACCAAACT
Found at i:56591 original size:36 final size:36
Alignment explanation
Indices: 56544--56697 Score: 229
Period size: 36 Copynumber: 4.3 Consensus size: 36
56534 AGTCAATCCT
56544 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
1 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
* *
56580 AAGCCTTCACCGGAGAATAGTGAAGCAATCAATCTG
1 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
56616 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCAT-
1 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATC-TG
* * * *
56652 AAGTCTTCACCAGAGAGTAGTGAAGCAAACCATCTT
1 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
*
56688 AAGTCTTCAC
1 AAGCCTTCAC
56698 TAAAAAGTAG
Statistics
Matches: 109, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
35 1 0.01
36 107 0.98
37 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.19
Consensus pattern (36 bp):
AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
Found at i:56707 original size:36 final size:36
Alignment explanation
Indices: 56543--56732 Score: 177
Period size: 36 Copynumber: 5.2 Consensus size: 36
56533 AAGTCAATCC
* *
56543 TAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCT
1 TAAGCCTTCACCGAAAAATAGTGAAGCAAACCATCT
* * * * *
56579 GAAGCCTTCACCGGAGAATAGTGAAGCAATCAATCT
1 TAAGCCTTCACCGAAAAATAGTGAAGCAAACCATCT
* * * *
56615 GAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCA
1 TAAGCCTTCACCGAAAAATAGTGAAGCAAACCATCT
* * *
56651 TAAGTCTTCACC-AGAGAGTAGTGAAGCAAACCATCT
1 TAAGCCTTCACCGA-AAAATAGTGAAGCAAACCATCT
* * * *
56687 TAAGTCTTCA-CTAAAAAGTAGTGAAGCATATCCATTT
1 TAAGCCTTCACCGAAAAA-TAGTGAAGCA-AACCATCT
56724 TAAGCCTTC
1 TAAGCCTTC
56733 TCAGAAGAGT
Statistics
Matches: 134, Mismatches: 16, Indels: 7
0.85 0.10 0.04
Matches are distributed among these distances:
35 3 0.02
36 117 0.87
37 14 0.10
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (36 bp):
TAAGCCTTCACCGAAAAATAGTGAAGCAAACCATCT
Found at i:56709 original size:72 final size:72
Alignment explanation
Indices: 56544--56732 Score: 202
Period size: 72 Copynumber: 2.6 Consensus size: 72
56534 AGTCAATCCT
* * * *
56544 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTGAAGCCTTCACCGGAGAATAGTGAAGCAAT
1 AAGCCTTCACCGAAAAATAGTGAAGCAAACCATCTGAAGCCTTCACCAGAGAATAGTGAAGCAAA
56609 CAATCTG
66 CAATCTG
* * * *
56616 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCAT-AAGTCTTCACCAGAGAGTAGTGAAGCAA
1 AAGCCTTCACCGAAAAATAGTGAAGCAAACCATC-TGAAGCCTTCACCAGAGAATAGTGAAGCAA
* *
56680 ACCATCTT
65 ACAATCTG
* * * * *
56688 AAGTCTTCA-CTAAAAAGTAGTGAAGCATATCCATTTTAAGCCTTC
1 AAGCCTTCACCGAAAAA-TAGTGAAGCA-AACCATCTGAAGCCTTC
56733 TCAGAAGAGT
Statistics
Matches: 100, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
71 4 0.04
72 83 0.83
73 13 0.13
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.22
Consensus pattern (72 bp):
AAGCCTTCACCGAAAAATAGTGAAGCAAACCATCTGAAGCCTTCACCAGAGAATAGTGAAGCAAA
CAATCTG
Found at i:57188 original size:51 final size:51
Alignment explanation
Indices: 57112--57465 Score: 435
Period size: 51 Copynumber: 6.8 Consensus size: 51
57102 TGAAAATATG
* *
57112 CGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCAG-TTGAAGATGTT
1 CGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCC-GTTTGAAGATGTT
* *
57163 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG--TGAAGAGATGTT
1 CGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTG-A-AGATGTT
* * *
57214 CGAGTTCCATACTCCCTAAAGAAAGAGGGAGCAAACCCATTTGAAGATGTT
1 CGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAAGATGTT
* *
57265 CGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
1 CGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAAGATGTT
* * *
57316 CGAGTTCTATACTCCTTAAAGAAGGAAGGAGCGAACCCGTTTGAAGAGATGTT
1 CGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTG-A-AGATGTT
* * *
57369 CGAGTTCTATACTCCCTAGAGAAAGGGGGAGCGAACCCGTTTGAAGAATATGT
1 CGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAAG-ATGT-T
* * * * *
57422 CTGAGTTCCATACTCCCTAGAGAAATAGGGAGTGAACCCATTTG
1 C-GAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTG
57466 TTGAAGATTG
Statistics
Matches: 270, Mismatches: 24, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
49 2 0.01
50 2 0.01
51 174 0.64
52 6 0.02
53 49 0.18
54 37 0.14
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.23
Consensus pattern (51 bp):
CGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAAGATGTT
Found at i:57612 original size:55 final size:53
Alignment explanation
Indices: 57465--57614 Score: 228
Period size: 53 Copynumber: 2.8 Consensus size: 53
57455 GAACCCATTT
* *
57465 GTTGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATC
1 GTTGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGAGAAGACACGATA
* *
57518 GTTGAAGATTGTGGGTCTTATACTCTCTGAAGATATAGGGGGAAGACACGATA
1 GTTGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGAGAAGACACGATA
* *
57571 GTTGAAGATTGTTCGAGTCTTATACTCTCTGGAGAAATAGGGAG
1 GTTGAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGAG
57615 CGAACCTGTT
Statistics
Matches: 87, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
53 60 0.69
54 1 0.01
55 26 0.30
ACGTcount: A:0.29, C:0.13, G:0.29, T:0.29
Consensus pattern (53 bp):
GTTGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGAGAAGACACGATA
Found at i:57635 original size:55 final size:54
Alignment explanation
Indices: 57442--57617 Score: 218
Period size: 53 Copynumber: 3.3 Consensus size: 54
57432 TACTCCCTAG
* *
57442 AGAAATAGGGAGTGA-AC-CCATTTGTTGAAGATTGTGGGTCTTATACTCTCTGA
1 AGAAATAGGGAGCGAGACACGA-TTGTTGAAGATTGTGGGTCTTATACTCTCTGA
*
57495 AGAAATAGGGAGC-AGACACGATCGTTGAAGATTGTGGGTCTTATACTCTCTGA
1 AGAAATAGGGAGCGAGACACGATTGTTGAAGATTGTGGGTCTTATACTCTCTGA
* * * *
57548 AGATATAGGG-G-GAAGACACGATAGTTGAAGATTGTTCGAGTCTTATACTCTCTGG
1 AGAAATAGGGAGCG-AGACACGATTGTTGAAGATTG-T-GGGTCTTATACTCTCTGA
57603 AGAAATAGGGAGCGA
1 AGAAATAGGGAGCGA
57618 ACCTGTTTTT
Statistics
Matches: 107, Mismatches: 8, Indels: 13
0.84 0.06 0.10
Matches are distributed among these distances:
52 2 0.02
53 74 0.69
54 3 0.03
55 25 0.23
56 2 0.02
57 1 0.01
ACGTcount: A:0.31, C:0.13, G:0.29, T:0.27
Consensus pattern (54 bp):
AGAAATAGGGAGCGAGACACGATTGTTGAAGATTGTGGGTCTTATACTCTCTGA
Found at i:65619 original size:29 final size:28
Alignment explanation
Indices: 65536--65612 Score: 109
Period size: 28 Copynumber: 2.7 Consensus size: 28
65526 TAATTTTGAT
*
65536 ATAACCCTAAACTATTTTAAAATAAAAAC
1 ATAACCCTAAACCA-TTTAAAATAAAAAC
* *
65565 TTAACCCTAAATCATTTAAAATAAAAAC
1 ATAACCCTAAACCATTTAAAATAAAAAC
65593 ATAACCCTAAACCACTTTAA
1 ATAACCCTAAACCA-TTTAA
65613 CCAAAAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
28 26 0.62
29 16 0.38
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.27
Consensus pattern (28 bp):
ATAACCCTAAACCATTTAAAATAAAAAC
Found at i:66552 original size:20 final size:20
Alignment explanation
Indices: 66527--66565 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
66517 TCCGGGTTTG
66527 AGTATCAATAATGGATGAAT
1 AGTATCAATAATGGATGAAT
* *
66547 AGTATCGATATTGGATGAA
1 AGTATCAATAATGGATGAA
66566 ATTAGACGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.05, G:0.23, T:0.31
Consensus pattern (20 bp):
AGTATCAATAATGGATGAAT
Found at i:66619 original size:21 final size:21
Alignment explanation
Indices: 66594--66636 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
66584 ATTTCCAATT
*
66594 GGGAGTATTGATGTTGTTGGG
1 GGGAGTATTGATGCTGTTGGG
66615 GGGAGTATTGATGCTGTTGGG
1 GGGAGTATTGATGCTGTTGGG
66636 G
1 G
66637 AGAGCAATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.02, G:0.49, T:0.35
Consensus pattern (21 bp):
GGGAGTATTGATGCTGTTGGG
Found at i:66647 original size:21 final size:21
Alignment explanation
Indices: 66602--66647 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
66592 TTGGGAGTAT
* * * *
66602 TGATGTTGTTGGGGGGAGTAT
1 TGATGCTGTTGGGGAGAGCAA
66623 TGATGCTGTTGGGGAGAGCAA
1 TGATGCTGTTGGGGAGAGCAA
66644 TGAT
1 TGAT
66648 ATTGTCCCTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.04, G:0.43, T:0.33
Consensus pattern (21 bp):
TGATGCTGTTGGGGAGAGCAA
Found at i:68972 original size:21 final size:21
Alignment explanation
Indices: 68944--68998 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
68934 TGGGAAAGGT
68944 AGTATCAATACTCATTAATGA
1 AGTATCAATACTCATTAATGA
* * *
68965 ATTATCAATAATCATTCATGA
1 AGTATCAATACTCATTAATGA
*
68986 AGTATTAATACTC
1 AGTATCAATACTC
68999 CTAGTAGGGG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.36
Consensus pattern (21 bp):
AGTATCAATACTCATTAATGA
Found at i:72156 original size:23 final size:24
Alignment explanation
Indices: 72126--72173 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
72116 ATAATTGTCA
*
72126 TTGTGACACAT-TTTTCTCTGCTC
1 TTGTGACACATATTTTCTCTACTC
*
72149 TTGTGACACGTATTTTCTCTACTC
1 TTGTGACACATATTTTCTCTACTC
72173 T
1 T
72174 AGTGGCACGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.15, C:0.25, G:0.12, T:0.48
Consensus pattern (24 bp):
TTGTGACACATATTTTCTCTACTC
Found at i:72173 original size:24 final size:23
Alignment explanation
Indices: 72126--72182 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
72116 ATAATTGTCA
* *
72126 TTGTGACACATTTTTCTCTGCTC
1 TTGTGACACGTTTTTCTCTACTC
72149 TTGTGACACGTATTTTCTCTACTC
1 TTGTGACACGT-TTTTCTCTACTC
* *
72173 TAGTGGCACG
1 TTGTGACACG
72183 ATCCTTCTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 10 0.34
24 19 0.66
ACGTcount: A:0.16, C:0.25, G:0.18, T:0.42
Consensus pattern (23 bp):
TTGTGACACGTTTTTCTCTACTC
Done.