Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000346.1 Hibiscus syriacus cultivar Beakdansim tig00000637_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: 80656
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Found at i:93 original size:19 final size:20
Alignment explanation
Indices: 55--93 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
45 CGATCTTTGT
**
55 TTTTATTTGTAATTATAATA
1 TTTTATTTGTAAAAATAATA
75 TTTTATTT-TAAAAATAATA
1 TTTTATTTGTAAAAATAATA
94 ACTATTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (20 bp):
TTTTATTTGTAAAAATAATA
Found at i:789 original size:16 final size:17
Alignment explanation
Indices: 759--795 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
749 ACGATATGTT
*
759 TTTTTAAAATAAATATA
1 TTTTCAAAATAAATATA
776 TTTTCAAAAT-AATATA
1 TTTTCAAAATAAATATA
792 TTTT
1 TTTT
796 AGTTATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTTCAAAATAAATATA
Found at i:1247 original size:47 final size:49
Alignment explanation
Indices: 1166--1278 Score: 176
Period size: 47 Copynumber: 2.3 Consensus size: 49
1156 CATACATGTT
*
1166 TCTTGTTTATCTATTTTAGTATGTATTTATTTTAAAATTGATTATTGGGATA
1 TCTTGTTT-TGTA-TTTAGTATG-ATTTATTTTAAAATTGATTATTGGGATA
1218 TCTTG-TTTGTATTTAGTATG-TTTATTTTAAAATTGATTATTGGGATA
1 TCTTGTTTTGTATTTAGTATGATTTATTTTAAAATTGATTATTGGGATA
1265 TCTTGTTTTGTATT
1 TCTTGTTTTGTATT
1279 CAATAATTTT
Statistics
Matches: 59, Mismatches: 1, Indels: 6
0.89 0.02 0.09
Matches are distributed among these distances:
47 32 0.54
48 8 0.14
49 9 0.15
50 3 0.05
51 2 0.03
52 5 0.08
ACGTcount: A:0.24, C:0.04, G:0.15, T:0.58
Consensus pattern (49 bp):
TCTTGTTTTGTATTTAGTATGATTTATTTTAAAATTGATTATTGGGATA
Found at i:1912 original size:30 final size:30
Alignment explanation
Indices: 1849--1948 Score: 175
Period size: 30 Copynumber: 3.4 Consensus size: 30
1839 TTCCATGGAT
*
1849 CACCTGGCGACCTTCATTGGTCGCCCA-AA
1 CACCCGGCGACCTTCATTGGTCGCCCAGAA
1878 CACCCGGCGACCTTCATTGGTCGCCCAGAA
1 CACCCGGCGACCTTCATTGGTCGCCCAGAA
*
1908 CACCCGGCGACCTTCATTGGTCGCCCAGAC
1 CACCCGGCGACCTTCATTGGTCGCCCAGAA
1938 CACCCGGCGAC
1 CACCCGGCGAC
1949 TTTATTCGAA
Statistics
Matches: 68, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
29 26 0.38
30 42 0.62
ACGTcount: A:0.19, C:0.42, G:0.23, T:0.16
Consensus pattern (30 bp):
CACCCGGCGACCTTCATTGGTCGCCCAGAA
Found at i:4763 original size:20 final size:20
Alignment explanation
Indices: 4738--4786 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
4728 AAGCTTAGGG
*
4738 TATCGATACTGCATGACCAA
1 TATCGATACTGCATGAACAA
* *
4758 TATCGATATTGCATGAACAG
1 TATCGATACTGCATGAACAA
4778 TATCGATAC
1 TATCGATAC
4787 CATAAGGCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (20 bp):
TATCGATACTGCATGAACAA
Found at i:5691 original size:21 final size:21
Alignment explanation
Indices: 5658--5697 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5648 TTCTACGTGG
*
5658 TCCTTCGGGACATATATGTAA
1 TCCTTCGGAACATATATGTAA
*
5679 TCCTTTGGAACATATATGT
1 TCCTTCGGAACATATATGT
5698 GGTACTTCGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (21 bp):
TCCTTCGGAACATATATGTAA
Found at i:6938 original size:35 final size:36
Alignment explanation
Indices: 6880--6950 Score: 126
Period size: 35 Copynumber: 2.0 Consensus size: 36
6870 TATGTACAGG
*
6880 GGGAATAGATTCCCCCCTGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCTGGGGGGTATCGATTCCCC
6916 GGGAACAGATT-CCCCCTGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCTGGGGGGTATCGATTCCCC
6951 CCTAAATGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 24 0.71
36 10 0.29
ACGTcount: A:0.17, C:0.31, G:0.31, T:0.21
Consensus pattern (36 bp):
GGGAACAGATTCCCCCCTGGGGGGTATCGATTCCCC
Found at i:11765 original size:20 final size:20
Alignment explanation
Indices: 11728--11766 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
11718 AGATTGAGTG
* * *
11728 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
11748 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
11767 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:11948 original size:21 final size:21
Alignment explanation
Indices: 11922--11961 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
11912 CAGAACCCCA
*
11922 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
11943 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
11962 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:11990 original size:20 final size:21
Alignment explanation
Indices: 11944--12004 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
11934 TTCCCCTGTG
11944 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
11967 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
11987 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
12005 TGCACAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:23064 original size:35 final size:37
Alignment explanation
Indices: 22999--23070 Score: 130
Period size: 35 Copynumber: 2.0 Consensus size: 37
22989 TATGTGCAGG
22999 GGGAACAGATTCCCCCCTGGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCTGGGGGGGTATCGATTCCCC
23036 GGGAACAGATT-CCCCCT-GGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCTGGGGGGGTATCGATTCCCC
23071 TTAAATGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
35 18 0.51
36 6 0.17
37 11 0.31
ACGTcount: A:0.17, C:0.32, G:0.32, T:0.19
Consensus pattern (37 bp):
GGGAACAGATTCCCCCCTGGGGGGGTATCGATTCCCC
Found at i:53975 original size:161 final size:163
Alignment explanation
Indices: 53700--53999 Score: 516
Period size: 161 Copynumber: 1.8 Consensus size: 163
53690 TATATCCTTT
* *
53700 CTTTGGTTTCTTTGGTTATTATATGCTTTTGTTTGTTTTAAAGGCCTTGGTGAGTTGGTGTCAGC
1 CTTTGCTTTCTTTGGTTATCATATGC--TTGTTTGTTTTAAAGGCCTTGGTGAGTTGGTGTCAGC
53765 GTTGCTCCTTGGTTACTTGTTTGTGCCATGCTTTATGCGCTGTACATTATGGACATTCATGGTGC
64 GTTGCTCCTTGGTTACTTGTTTGTGCCATGCTTTATGCGCTGTACATTATGGACATTCATGGTGC
53830 ACTCTTTTTCCTCAAATTTCCTTCTCCTTAGAATG
129 ACTCTTTTTCCTCAAATTTCCTTCTCCTTAGAATG
*
53865 CTTTGCTTTCTTTGGTTATCATATGC-T-TTTGTTTTAAAGGCCTTGGTGAGTTGGTGTCAGTGT
1 CTTTGCTTTCTTTGGTTATCATATGCTTGTTTGTTTTAAAGGCCTTGGTGAGTTGGTGTCAGCGT
53928 TGCTCCTTGGTTACTTGTTTGTGTCC-TGCTTTATGCGCTGTACATTATGGACATTCATGGTGCA
66 TGCTCCTTGGTTACTTGTTTGTG-CCATGCTTTATGCGCTGTACATTATGGACATTCATGGTGCA
*
53992 TTCTTTTT
130 CTCTTTTT
54000 TCTTTAAGTA
Statistics
Matches: 130, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
161 103 0.79
162 3 0.02
165 24 0.18
ACGTcount: A:0.14, C:0.17, G:0.22, T:0.47
Consensus pattern (163 bp):
CTTTGCTTTCTTTGGTTATCATATGCTTGTTTGTTTTAAAGGCCTTGGTGAGTTGGTGTCAGCGT
TGCTCCTTGGTTACTTGTTTGTGCCATGCTTTATGCGCTGTACATTATGGACATTCATGGTGCAC
TCTTTTTCCTCAAATTTCCTTCTCCTTAGAATG
Found at i:55331 original size:17 final size:16
Alignment explanation
Indices: 55309--55357 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
55299 AAAATTATAA
55309 AAAAATTAAAAAATAT
1 AAAAATTAAAAAATAT
*
55325 CATAAA-TAAAAATATTAT
1 -AAAAATTAAAAA-A-TAT
55343 AAAAATTAAAAAATA
1 AAAAATTAAAAAATA
55358 AAGAATAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
16 8 0.30
17 10 0.37
18 9 0.33
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAAATTAAAAAATAT
Found at i:55354 original size:18 final size:18
Alignment explanation
Indices: 55296--55354 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
55286 ATGAAAATCT
*
55296 TTAAAAAT-TATAAAAAAA
1 TTAAAAATAT-TATAAAAA
*
55314 TTAAAAA-A-TATCATAAA
1 TTAAAAATATTAT-AAAAA
55331 -TAAAAATATTATAAAAA
1 TTAAAAATATTATAAAAA
55348 TTAAAAA
1 TTAAAAA
55355 ATAAAGAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
16 8 0.24
17 9 0.27
18 16 0.48
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (18 bp):
TTAAAAATATTATAAAAA
Found at i:55380 original size:26 final size:25
Alignment explanation
Indices: 55317--55397 Score: 67
Period size: 26 Copynumber: 3.1 Consensus size: 25
55307 AAAAAAATTA
* *
55317 AAAAATATCATAAATAAAAATATTAT
1 AAAAAT-TCAAAAATAAAAATACTAT
*
55343 AAAAATTAAAAAATAAAGAATAACTAT
1 AAAAATTCAAAAATAAA-AAT-ACTAT
*
55370 -AAAATTCAAAATATCATAAA-ACTAT
1 AAAAATTCAAAA-AT-AAAAATACTAT
55395 AAA
1 AAA
55398 TAATAAATTA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
25 14 0.31
26 21 0.47
27 8 0.18
28 2 0.04
ACGTcount: A:0.67, C:0.06, G:0.01, T:0.26
Consensus pattern (25 bp):
AAAAATTCAAAAATAAAAATACTAT
Found at i:55383 original size:44 final size:44
Alignment explanation
Indices: 55333--55432 Score: 114
Period size: 45 Copynumber: 2.3 Consensus size: 44
55323 ATCATAAATA
* *
55333 AAAATATTATAAAAAT-TAAAAAATAAAGAATAACTATAAAATTC
1 AAAATATTATAAAAATATAAAAAATAAAGAATAAATATAAAA-AC
* * * **
55377 AAAATATCATAAAACTATAAATAATAAATTATAAATATAAAAAC
1 AAAATATTATAAAAATATAAAAAATAAAGAATAAATATAAAAAC
55421 AAAAT-TTATAAA
1 AAAATATTATAAA
55433 TATTTATAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
43 6 0.13
44 20 0.43
45 21 0.45
ACGTcount: A:0.66, C:0.05, G:0.01, T:0.28
Consensus pattern (44 bp):
AAAATATTATAAAAATATAAAAAATAAAGAATAAATATAAAAAC
Found at i:65039 original size:3 final size:3
Alignment explanation
Indices: 64991--65020 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
64981 CAATTTGGTT
*
64991 GAA GAA GAA GAA TAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
65021 CGGGTTGGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.03
Consensus pattern (3 bp):
GAA
Done.