Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006864.1 Hibiscus syriacus cultivar Beakdansim tig00017461_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: 70410
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Found at i:4964 original size:18 final size:18
Alignment explanation
Indices: 4941--4991 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
4931 GCCCCTTCGA
*
4941 ACCCCCTGGACCATCTTT
1 ACCCCCAGGACCATCTTT
4959 ACCCCCAGGACCATCTTT
1 ACCCCCAGGACCATCTTT
4977 ACCCCCAGGACCATC
1 ACCCCCAGGACCATC
4992 ATTATCCTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.22, C:0.47, G:0.12, T:0.20
Consensus pattern (18 bp):
ACCCCCAGGACCATCTTT
Found at i:16365 original size:55 final size:56
Alignment explanation
Indices: 16209--16428 Score: 291
Period size: 56 Copynumber: 3.9 Consensus size: 56
16199 TATATAGTTT
* * * *
16209 TTTCCATAACTATTTTATACTGCTGTAAATAGAAAGATGCTAGCCATAATTTCCTC
1 TTTCCATAGCTATTTTATACTGCTGTAAATAGAGAGATACCAGCCATAATTTCCTC
* * *
16265 TTTCCATAGCTATTTTATACTGCTG-GAATGAAAGAGATACCAGCCATAATTTCGTC
1 TTTCCATAGCTATTTTATACTGCTGTAAAT-AGAGAGATACCAGCCATAATTTCCTC
* *
16321 TTTCCATAGCTA-TTTATACTTCTGTAAATAGAGAGCTACCAGCCATAATTTCCTC
1 TTTCCATAGCTATTTTATACTGCTGTAAATAGAGAGATACCAGCCATAATTTCCTC
* * * *
16376 TTTTCACAGCTATTTGATACTGCTGTAAATAGAGAGATACCAGTCATAGATTT
1 TTTCCATAGCTATTTTATACTGCTGTAAATAGAGAGATACCAGCCATA-ATTT
16429 AGCTAAAAAT
Statistics
Matches: 142, Mismatches: 18, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
55 47 0.33
56 91 0.64
57 4 0.03
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.36
Consensus pattern (56 bp):
TTTCCATAGCTATTTTATACTGCTGTAAATAGAGAGATACCAGCCATAATTTCCTC
Found at i:16396 original size:111 final size:113
Alignment explanation
Indices: 16209--16428 Score: 302
Period size: 111 Copynumber: 2.0 Consensus size: 113
16199 TATATAGTTT
* * *
16209 TTTCCATAACTATTTTATACTGCTGTAAATAGAAAGATGCTAGCCATAATTTCCTCTTTCCATAG
1 TTTCCATAACTATTTTATACTGCTGTAAATAGAAAGATACCAGCCATAATTTCCTCTTTCCACAG
* *
16274 CTATTTTATACTGCTG-GAATGAAAGAGATACCAGCCATA-ATTTCGTC
66 CTATTTGATACTGCTGTAAAT-AAAGAGATACCAGCCATAGATTTCGTC
* * * * *
16321 TTTCCATAGCTA-TTTATACTTCTGTAAATAGAGAGCTACCAGCCATAATTTCCTCTTTTCACAG
1 TTTCCATAACTATTTTATACTGCTGTAAATAGAAAGATACCAGCCATAATTTCCTCTTTCCACAG
* *
16385 CTATTTGATACTGCTGTAAATAGAGAGATACCAGTCATAGATTT
66 CTATTTGATACTGCTGTAAATAAAGAGATACCAGCCATAGATTT
16429 AGCTAAAAAT
Statistics
Matches: 94, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
111 76 0.81
112 18 0.19
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.36
Consensus pattern (113 bp):
TTTCCATAACTATTTTATACTGCTGTAAATAGAAAGATACCAGCCATAATTTCCTCTTTCCACAG
CTATTTGATACTGCTGTAAATAAAGAGATACCAGCCATAGATTTCGTC
Found at i:18969 original size:14 final size:14
Alignment explanation
Indices: 18952--18978 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
18942 GGAAAAATGG
18952 GAGAGAGAAAAGTA
1 GAGAGAGAAAAGTA
18966 GAGAGAGAAAAGT
1 GAGAGAGAAAAGT
18979 TAAAAGGGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.37, T:0.07
Consensus pattern (14 bp):
GAGAGAGAAAAGTA
Found at i:19178 original size:17 final size:19
Alignment explanation
Indices: 19156--19190 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
19146 GCTTTTGTTC
19156 AGTTTG-AGAGGG-AATCT
1 AGTTTGAAGAGGGCAATCT
19173 AGTTTGAAGAGGGCAATC
1 AGTTTGAAGAGGGCAATC
19191 GAGATGTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 6 0.38
19 4 0.25
ACGTcount: A:0.31, C:0.09, G:0.34, T:0.26
Consensus pattern (19 bp):
AGTTTGAAGAGGGCAATCT
Found at i:22521 original size:2 final size:2
Alignment explanation
Indices: 22514--22538 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
22504 GATATTTACC
22514 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 T
22539 TCTGATAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23726 original size:113 final size:113
Alignment explanation
Indices: 23551--24442 Score: 1289
Period size: 113 Copynumber: 7.9 Consensus size: 113
23541 AGAGTCATGC
*
23551 AAAGGTTGAATAAGTTCTTCTCATTATGAACTTCTTC-TCC-TCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
** *
23614 ATGAACTCGAACTGGCAATGCTGATCCATCGAATGATGAATTCAAGCA
66 ATGAACTCGTTCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCA
* * * *
23662 AAATGTTAAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGTGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
23727 ATGAACTC-TTCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCA
66 ATGAACTCGTTCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCA
*
23774 AAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
** * **
23839 ATGAACTTTTTCTGGAAAAGCTGATCCATC-AGATGATTG-ATTTGAGCA
66 ATGAACTCGTTCTGGAAATGCTGATCCATCGA-ATGA-TGAATTCAAGCA
*
23887 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
** *
23952 ATGAACTCGAACTGGAAATACTGAAT-CATCGAATGATGAATTCAAGCGA
66 ATGAACTCGTTCTGGAAATGCTG-ATCCATCGAATGATGAATTCAAGC-A
24001 AAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
** * *
24065 ATGAACTCGAACTGGTAATGTTGATCCATCGAATGATGAATTCAAGCA
66 ATGAACTCGTTCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCA
* * * *
24113 AAAGGTTGAACAAATTCTTCTCATTATGAATTTGTTCTTCCTTCTTCAGATGTGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
** *
24178 ATGAACTTTTTCTGGAAATGCTGATCCATCGAATAATGAATTCAAGCA
66 ATGAACTCGTTCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCA
*
24226 AAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
** * * **
24291 ATGAACTTTTTCTGGAAAAGCTGATCCATC-AGATGATGGATTTGAGCA
66 ATGAACTCGTTCTGGAAATGCTGATCCATCGA-ATGATGAATTCAAGCA
* *
24339 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
** *
24404 ATGAACTTTTTTCTGGAAAAGCTGATCCATC-ATATGATG
66 ATGAAC-TCGTTCTGGAAATGCTGATCCATCGA-ATGATG
24443 GATTTGAATC
Statistics
Matches: 712, Mismatches: 56, Indels: 23
0.90 0.07 0.03
Matches are distributed among these distances:
111 33 0.05
112 116 0.16
113 523 0.73
114 40 0.06
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (113 bp):
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTCGTTCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCA
Found at i:24150 original size:20 final size:20
Alignment explanation
Indices: 24127--24182 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 20
24117 GTTGAACAAA
*
24127 TTCTTCTCATTATGAATTTG
1 TTCTTCTCATTATGAATGTG
24147 TTCTTCCTTC-TTCA-G-ATGTG
1 TTCTT-C-TCATT-ATGAATGTG
24167 TTCTTCTCATTATGAA
1 TTCTTCTCATTATGAA
24183 CTTTTTCTGG
Statistics
Matches: 29, Mismatches: 1, Indels: 12
0.69 0.02 0.29
Matches are distributed among these distances:
18 3 0.10
19 4 0.14
20 15 0.52
21 4 0.14
22 3 0.10
ACGTcount: A:0.18, C:0.20, G:0.11, T:0.52
Consensus pattern (20 bp):
TTCTTCTCATTATGAATGTG
Found at i:33768 original size:15 final size:13
Alignment explanation
Indices: 33738--33775 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
33728 AACTATGACA
33738 AAAT-AAATAATG
1 AAATAAAATAATG
33750 AAATAAAATAATTG
1 AAATAAAATAA-TG
33764 CAAATAAAATAA
1 -AAATAAAATAA
33776 AACATATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.17
13 6 0.26
14 2 0.09
15 11 0.48
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (13 bp):
AAATAAAATAATG
Found at i:49894 original size:15 final size:15
Alignment explanation
Indices: 49874--49902 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
49864 TTCCGGATTT
49874 TCGGGTACCCGGAAA
1 TCGGGTACCCGGAAA
49889 TCGGGTACCCGGAA
1 TCGGGTACCCGGAA
49903 CATCCGGATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.28, G:0.34, T:0.14
Consensus pattern (15 bp):
TCGGGTACCCGGAAA
Found at i:50290 original size:24 final size:24
Alignment explanation
Indices: 50234--50283 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
50224 TTGTTTACTT
* * *
50234 TAATTTAATATATAATATTATTAA
1 TAATTAAATATATAATAATATAAA
50258 TAATTAAATATATAATAATAGTAAA
1 TAATTAAATATATAATAATA-TAAA
50283 T
1 T
50284 CATAAATCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
TAATTAAATATATAATAATATAAA
Found at i:52957 original size:17 final size:16
Alignment explanation
Indices: 52918--52973 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 16
52908 TACCCCAAAA
52918 ATTATAAA-AAATAAT
1 ATTATAAATAAATAAT
*
52933 ATTA-AAATAAATAGT
1 ATTATAAATAAATAAT
* *
52948 ATATATAAATTAATAAAA
1 AT-TATAAATAAAT-AAT
52966 ATTATAAA
1 ATTATAAA
52974 AATTATTCTG
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
14 3 0.09
15 12 0.36
16 2 0.06
17 13 0.39
18 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (16 bp):
ATTATAAATAAATAAT
Found at i:56963 original size:37 final size:36
Alignment explanation
Indices: 56904--57023 Score: 172
Period size: 35 Copynumber: 3.3 Consensus size: 36
56894 ATCCCATTAT
* *
56904 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAA
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
*
56939 CTATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 C-ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
*
56976 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAT
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
57011 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
57024 TTGGTTACCA
Statistics
Matches: 77, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
35 35 0.45
36 8 0.10
37 34 0.44
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.33
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
Found at i:56979 original size:21 final size:20
Alignment explanation
Indices: 56952--57015 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
56942 TTTTTCAAAG
56952 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
*
56972 AAACCATTT-TCAAA----G-
1 AAA-CATTTACCAAACTTTGA
56987 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
57007 AAATCATTT
1 AAA-CATTT
57016 TTTCAAAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 7 0.21
16 1 0.03
19 1 0.03
20 10 0.29
21 10 0.29
ACGTcount: A:0.45, C:0.19, G:0.05, T:0.31
Consensus pattern (20 bp):
AAACATTTACCAAACTTTGA
Found at i:58085 original size:21 final size:21
Alignment explanation
Indices: 58059--58108 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
58049 TATAATCTCT
*
58059 TGCATGTCTGAGCCTGCAACG
1 TGCATGTCTGAGCCTACAACG
58080 TGCATGTCTGAGCCTACAACG
1 TGCATGTCTGAGCCTACAACG
*
58101 AGCATGTC
1 TGCATGTC
58109 ATCAACGTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.22, C:0.28, G:0.26, T:0.24
Consensus pattern (21 bp):
TGCATGTCTGAGCCTACAACG
Found at i:61605 original size:37 final size:36
Alignment explanation
Indices: 61546--61665 Score: 172
Period size: 35 Copynumber: 3.3 Consensus size: 36
61536 ATCCCATTAT
* *
61546 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAA
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
*
61581 CTATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 C-ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
*
61618 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAT
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
61653 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
61666 TTGGTTACCA
Statistics
Matches: 77, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
35 35 0.45
36 8 0.10
37 34 0.44
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.33
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
Found at i:61621 original size:21 final size:20
Alignment explanation
Indices: 61594--61657 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
61584 TTTTTCAAAG
61594 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
*
61614 AAACCATTT-TCAAA----G-
1 AAA-CATTTACCAAACTTTGA
61629 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
61649 AAATCATTT
1 AAA-CATTT
61658 TTTCAAAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 7 0.21
16 1 0.03
19 1 0.03
20 10 0.29
21 10 0.29
ACGTcount: A:0.45, C:0.19, G:0.05, T:0.31
Consensus pattern (20 bp):
AAACATTTACCAAACTTTGA
Found at i:62727 original size:21 final size:21
Alignment explanation
Indices: 62701--62750 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
62691 TATAATCTCT
*
62701 TGCATGTCTGAGCCTGCAACG
1 TGCATGTCTGAGCCTACAACG
62722 TGCATGTCTGAGCCTACAACG
1 TGCATGTCTGAGCCTACAACG
*
62743 AGCATGTC
1 TGCATGTC
62751 ATCAACGTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.22, C:0.28, G:0.26, T:0.24
Consensus pattern (21 bp):
TGCATGTCTGAGCCTACAACG
Found at i:66242 original size:37 final size:36
Alignment explanation
Indices: 66183--66301 Score: 163
Period size: 37 Copynumber: 3.3 Consensus size: 36
66173 ATCCCATTAT
* *
66183 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAA
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
*
66218 CTATTTTTCAAAGAAACATTTACCAAACTTTG-AAAC
1 C-ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
*
66254 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAT
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
66289 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
66302 TTGGTTACCA
Statistics
Matches: 75, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
34 28 0.37
35 7 0.09
36 11 0.15
37 29 0.39
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.33
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
Found at i:67360 original size:21 final size:21
Alignment explanation
Indices: 67334--67383 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
67324 TATAATCTCT
*
67334 TGCATGTCTGAGCCTGCAACG
1 TGCATGTCTGAGCCTACAACG
67355 TGCATGTCTGAGCCTACAACG
1 TGCATGTCTGAGCCTACAACG
*
67376 AGCATGTC
1 TGCATGTC
67384 ATCAACGTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.22, C:0.28, G:0.26, T:0.24
Consensus pattern (21 bp):
TGCATGTCTGAGCCTACAACG
Done.