Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002480.1 Hibiscus syriacus cultivar Beakdansim tig00005065_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: 63331
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:999 original size:19 final size:22
Alignment explanation
Indices: 967--1006 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
957 AACATAAAAA
967 ATATAAAAATTATAT-ATAATT
1 ATATAAAAATTATATAATAATT
988 ATAT-AAAA-TATATAATAAT
1 ATATAAAAATTATATAATAAT
1007 ATTATATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.28
20 9 0.50
21 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
ATATAAAAATTATATAATAATT
Found at i:1001 original size:30 final size:33
Alignment explanation
Indices: 945--1016 Score: 105
Period size: 31 Copynumber: 2.3 Consensus size: 33
935 CGAAAATATT
945 TTATATATAATTAACATAAAAAATATAA-AA-A
1 TTATATATAATTAACATAAAAAATATAATAATA
* *
976 TTATATATAATT-ATATAAAATATATAATAATA
1 TTATATATAATTAACATAAAAAATATAATAATA
1008 TTATATATA
1 TTATATATA
1017 TATCGGGGCG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
30 13 0.35
31 14 0.38
32 10 0.27
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (33 bp):
TTATATATAATTAACATAAAAAATATAATAATA
Found at i:1019 original size:19 final size:17
Alignment explanation
Indices: 977--1018 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
967 ATATAAAAAT
*
977 TATATATAATTATATAA
1 TATATATAATAATATAA
* *
994 AATATATAATAATATTA
1 TATATATAATAATATAA
1011 TATATATA
1 TATATATA
1019 TCGGGGCGGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TATATATAATAATATAA
Found at i:10816 original size:39 final size:41
Alignment explanation
Indices: 10758--10855 Score: 119
Period size: 42 Copynumber: 2.4 Consensus size: 41
10748 TTAACGGAAT
* *
10758 TCTGAGTTGTCAATTAAAAA-A-TATAAAAAATTAGAGAAA
1 TCTGAGTTATCAATAAAAAATATTATAAAAAATTAGAGAAA
* * * *
10797 TCTGAGTTATTAATAAAAAAATATTATAAAAAATTGGATAAG
1 TCTGAGTTATCAAT-AAAAAATATTATAAAAAATTAGAGAAA
10839 TCTGAGTTATCAATAAA
1 TCTGAGTTATCAATAAA
10856 TTTTTTAACA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
39 12 0.24
40 5 0.10
41 4 0.08
42 28 0.57
ACGTcount: A:0.51, C:0.05, G:0.12, T:0.32
Consensus pattern (41 bp):
TCTGAGTTATCAATAAAAAATATTATAAAAAATTAGAGAAA
Found at i:14359 original size:15 final size:15
Alignment explanation
Indices: 14339--14373 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
14329 AGCAAGGCTC
*
14339 TTCGAGTGATGCTTG
1 TTCGAGTGAAGCTTG
*
14354 TTCGAGTGAAGTTTG
1 TTCGAGTGAAGCTTG
14369 TTCGA
1 TTCGA
14374 ATGGTGAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.17, C:0.11, G:0.31, T:0.40
Consensus pattern (15 bp):
TTCGAGTGAAGCTTG
Found at i:26100 original size:5 final size:5
Alignment explanation
Indices: 26090--26115 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
26080 TCTTTTTGTC
26090 AAGAA AAGAA AAGAA AAGAA AAGAA A
1 AAGAA AAGAA AAGAA AAGAA AAGAA A
26116 GCACCCCCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:34930 original size:15 final size:15
Alignment explanation
Indices: 34910--34957 Score: 87
Period size: 15 Copynumber: 3.2 Consensus size: 15
34900 ATATTTAACT
34910 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGTG
*
34925 GGGCGGACGGATGTG
1 GGGCGGGCGGATGTG
34940 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGTG
34955 GGG
1 GGG
34958 AAGGCGAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.08, C:0.12, G:0.67, T:0.12
Consensus pattern (15 bp):
GGGCGGGCGGATGTG
Found at i:34963 original size:15 final size:14
Alignment explanation
Indices: 34915--34963 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
34905 TAACTGGGCG
*
34915 GGCGGATGTGGGGC
1 GGCGGATGTGGGGA
*
34929 GGACGGATGTGGGGCG
1 GG-CGGATGTGGGG-A
34945 GGCGGATGTGGGGAA
1 GGCGGATGTGGGG-A
34960 GGCG
1 GGCG
34964 AATGCAGGGC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
14 2 0.07
15 26 0.87
16 2 0.07
ACGTcount: A:0.12, C:0.12, G:0.63, T:0.12
Consensus pattern (14 bp):
GGCGGATGTGGGGA
Found at i:34974 original size:30 final size:30
Alignment explanation
Indices: 34910--34976 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
34900 ATATTTAACT
* * **
34910 GGGCGGGCGGATGTGGGGCGGACGGATGTG
1 GGGCGGGCGGATGTGGGGAGGACGAATGCA
34940 GGGCGGGCGGATGTGGGGAAGG-CGAATGCA
1 GGGCGGGCGGATGTGGGG-AGGACGAATGCA
34970 GGGCGGG
1 GGGCGGG
34977 TAAGGTCTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 30 0.94
31 2 0.06
ACGTcount: A:0.13, C:0.13, G:0.63, T:0.10
Consensus pattern (30 bp):
GGGCGGGCGGATGTGGGGAGGACGAATGCA
Found at i:44092 original size:14 final size:14
Alignment explanation
Indices: 44073--44114 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
44063 AGTCATTTTA
*
44073 ATTTTAATTTTAGC
1 ATTTTATTTTTAGC
*
44087 ATTTTATTCTTTAAC
1 ATTTTATT-TTTAGC
44102 ATTTTATTTTTAG
1 ATTTTATTTTTAG
44115 ACAAAAAAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.26, C:0.07, G:0.05, T:0.62
Consensus pattern (14 bp):
ATTTTATTTTTAGC
Found at i:48788 original size:20 final size:20
Alignment explanation
Indices: 48746--48790 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
48736 GGCTTAAGAT
**
48746 TTTAATTTTAAATTTTATGA
1 TTTAATTTTAAATTTTAAAA
*
48766 TTTAATTTTATATTTTAAAA
1 TTTAATTTTAAATTTTAAAA
48786 TTTAA
1 TTTAA
48791 AATTAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TTTAATTTTAAATTTTAAAA
Found at i:48833 original size:17 final size:18
Alignment explanation
Indices: 48794--48835 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
48784 AATTTAAAAT
48794 TAAAATAAATTAATTGTA
1 TAAAATAAATTAATTGTA
*
48812 T-AAATAAATTTA-TGTA
1 TAAAATAAATTAATTGTA
48828 TAAAATAA
1 TAAAATAA
48836 TAATTTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 5 0.23
17 16 0.73
18 1 0.05
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (18 bp):
TAAAATAAATTAATTGTA
Found at i:50301 original size:8 final size:8
Alignment explanation
Indices: 50288--50313 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
50278 ACTTGATGTA
50288 ATTTGTTT
1 ATTTGTTT
50296 ATTTGTTT
1 ATTTGTTT
50304 ATTTGTTT
1 ATTTGTTT
50312 AT
1 AT
50314 ATATATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.12, T:0.73
Consensus pattern (8 bp):
ATTTGTTT
Found at i:58970 original size:11 final size:11
Alignment explanation
Indices: 58932--58970 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
58922 GGTGTATATT
58932 GAACACATAAAC
1 GAACAC-TAAAC
*
58944 GAACACTAATC
1 GAACACTAAAC
*
58955 AAACACTAAAC
1 GAACACTAAAC
58966 GAACA
1 GAACA
58971 TATAAACAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
11 17 0.74
12 6 0.26
ACGTcount: A:0.56, C:0.26, G:0.08, T:0.10
Consensus pattern (11 bp):
GAACACTAAAC
Found at i:58980 original size:23 final size:23
Alignment explanation
Indices: 58933--58982 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
58923 GTGTATATTG
* *
58933 AACACATAAACGAACACTAATCA
1 AACACATAAACGAACAATAAACA
58956 AACAC-TAAACGAACATATAAACA
1 AACACATAAACGAACA-ATAAACA
58979 AACA
1 AACA
58983 TGTTCGCGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.60, C:0.24, G:0.04, T:0.12
Consensus pattern (23 bp):
AACACATAAACGAACAATAAACA
Found at i:59149 original size:41 final size:40
Alignment explanation
Indices: 59102--59227 Score: 128
Period size: 41 Copynumber: 3.4 Consensus size: 40
59092 AAATAAATAA
*
59102 ACGAACACAAACACGATATTAAAAATTTAAATGAACACGAG
1 ACGAACACAAACACGATATTAAAAATTTAAAT-AACACTAG
*
59143 ACGAACACAAACAC----TT-AAAA---AAATAA-A-TAA
1 ACGAACACAAACACGATATTAAAAATTTAAATAACACTAG
59173 ACGAACACAAACACGATATTAAAAATTTAAATAAACACTAG
1 ACGAACACAAACACGATATTAAAAATTTAAAT-AACACTAG
* *
59214 CCGAACACGAACAC
1 ACGAACACAAACAC
59228 TTTAAAAAAT
Statistics
Matches: 69, Mismatches: 5, Indels: 22
0.72 0.05 0.23
Matches are distributed among these distances:
30 15 0.22
31 1 0.01
32 2 0.03
33 4 0.06
34 2 0.03
35 4 0.06
36 4 0.06
37 2 0.03
38 4 0.06
39 2 0.03
40 1 0.01
41 28 0.41
ACGTcount: A:0.56, C:0.20, G:0.09, T:0.15
Consensus pattern (40 bp):
ACGAACACAAACACGATATTAAAAATTTAAATAACACTAG
Found at i:59189 original size:71 final size:71
Alignment explanation
Indices: 59024--59283 Score: 351
Period size: 71 Copynumber: 3.6 Consensus size: 71
59014 ACAACCTCAA
** * * * *
59024 AAATAAATAAACACAAACATGATATTAAAATTTTAAATGAACATGA-ACCGAACACGAACATTTT
1 AAATAAACGAACACAAACACGATATTAAAAATTTAAATGAACACGAGA-CGAACACGAACA-CTT
*
59088 TCAAAAAT
64 TAAAAAAT
* *
59096 AAATAAACGAACACAAACACGATATTAAAAATTTAAATGAACACGAGACGAACACAAACACTTAA
1 AAATAAACGAACACAAACACGATATTAAAAATTTAAATGAACACGAGACGAACACGAACACTTTA
59161 AAAAAT
66 AAAAAT
* * *
59167 AAATAAACGAACACAAACACGATATTAAAAATTTAAATAAACACTAGCCGAACACGAACACTTTA
1 AAATAAACGAACACAAACACGATATTAAAAATTTAAATGAACACGAGACGAACACGAACACTTTA
59232 AAAAAT
66 AAAAAT
* * * *
59238 AAATAAACGAACACGAATACGATATTAAAAATTTAAAGGAATACGA
1 AAATAAACGAACACAAACACGATATTAAAAATTTAAATGAACACGA
59284 ACATTATCTT
Statistics
Matches: 167, Mismatches: 20, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
71 114 0.68
72 52 0.31
73 1 0.01
ACGTcount: A:0.57, C:0.15, G:0.08, T:0.20
Consensus pattern (71 bp):
AAATAAACGAACACAAACACGATATTAAAAATTTAAATGAACACGAGACGAACACGAACACTTTA
AAAAAT
Found at i:62955 original size:250 final size:251
Alignment explanation
Indices: 62457--62959 Score: 915
Period size: 250 Copynumber: 2.0 Consensus size: 251
62447 AGGAAAAAGC
*
62457 TAAGCTCTCCAAGGTTTTTTTAAAGTAAACTTATCGCCCAACAGTTTTACGACCTCTTCAATTTG
1 TAAGCTCTCCAAGGTTTTTTTAAAGTAAACTCATCGCCCAACAGTTTTACGACCTCTTCAATTTG
62522 CGCATTTGAGTCTCATGTTACCACTATATCATCCACATAAACCAACATGTACAAATACTGCCCTC
66 CGCATTTGAGTCTCATGTTACCACTATATCATCCACATAAACCAACATGTACAAATACTGCCCTC
62587 TAACACAAACGAACAAATAAAGAAGTATATGCCTTAGACTCCTTAATCCTATTCGAATAAAGCAC
131 TAACACAAACGAACAAATAAAGAAGTATATGCCTTAGACTCCTTAATCCTATTCGAATAAAGCAC
62652 TGTTTTAACTTGACATGCCAACTCTGAGGCCCCTATCTCAGCCATACAGGCCTTTT
196 TGTTTTAACTTGACATGCCAACTCTGAGGCCCCTATCTCAGCCATACAGGCCTTTT
62708 TAAGCTCTCCAAGGTTTTTTTAAAGTAAACTCATCGCCCAACA-TTTTACGACCTCTTCAATTTG
1 TAAGCTCTCCAAGGTTTTTTTAAAGTAAACTCATCGCCCAACAGTTTTACGACCTCTTCAATTTG
* *
62772 TGCATTTGAGTCTCCTGTTACCACTATATCATCCACATAAACCAACATGTACAAATACTGCCCTC
66 CGCATTTGAGTCTCATGTTACCACTATATCATCCACATAAACCAACATGTACAAATACTGCCCTC
*
62837 TAACAC-AA-GAAC-AATAAAGAAGTATATGCCTTAGACTCCTTAAATCCTATTCGAATCAAGCA
131 TAACACAAACGAACAAATAAAGAAGTATATGCCTTAGACTCCTT-AATCCTATTCGAATAAAGCA
62899 CTGTTTTAACTTGACATGCCAACTCTGAGGCCCCTATCTCAAGCCATACAAGGCCTTTT
195 CTGTTTTAACTTGACATGCCAACTCTGAGGCCCCTATCTC-AGCCATAC-AGGCCTTTT
62958 TA
1 TA
62960 GTTTATATAC
Statistics
Matches: 245, Mismatches: 4, Indels: 7
0.96 0.02 0.03
Matches are distributed among these distances:
247 29 0.12
248 63 0.26
249 10 0.04
250 101 0.41
251 42 0.17
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.30
Consensus pattern (251 bp):
TAAGCTCTCCAAGGTTTTTTTAAAGTAAACTCATCGCCCAACAGTTTTACGACCTCTTCAATTTG
CGCATTTGAGTCTCATGTTACCACTATATCATCCACATAAACCAACATGTACAAATACTGCCCTC
TAACACAAACGAACAAATAAAGAAGTATATGCCTTAGACTCCTTAATCCTATTCGAATAAAGCAC
TGTTTTAACTTGACATGCCAACTCTGAGGCCCCTATCTCAGCCATACAGGCCTTTT
Done.