Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001181.1 Hibiscus syriacus cultivar Beakdansim tig00002347_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: 85817
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:43953 original size:8 final size:8
Alignment explanation
Indices: 43944--43973 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
43934 AAAATAAGTG
*
43944 AAAATATG
1 AAAATATA
43952 AAAATATA
1 AAAATATA
43960 AAAATATA
1 AAAATATA
43968 AAAATA
1 AAAATA
43974 AATATGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (8 bp):
AAAATATA
Found at i:45945 original size:2 final size:2
Alignment explanation
Indices: 45938--45962 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
45928 ATGAATTTTC
45938 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
45963 GTGTGTGACT
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:47984 original size:30 final size:30
Alignment explanation
Indices: 47950--48022 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
47940 CCCGAATGAC
47950 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
47980 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
48010 CTGTCCATAGGTC
1 CTATCCAGAGGTC
48023 CCGAAGAACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:48077 original size:31 final size:30
Alignment explanation
Indices: 48005--48163 Score: 187
Period size: 31 Copynumber: 5.2 Consensus size: 30
47995 AAAGATCCTC
* * * *
48005 GGTAACTGTCCATAGGTCCCGAAGAACCTA
1 GGTAACTGTCCATATGTTCCGTAGAACATA
*
48035 GGTAACTGTCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATATGTTCCGTAGAACATA
*
48065 GGTATACTGTCCATATGTTCCTTAGAACATA
1 GGTA-ACTGTCCATATGTTCCGTAGAACATA
*
48096 GGTATACTGTCCATATG-TCTCG-AAAGACATA
1 GGTA-ACTGTCCATATGTTC-CGTAGA-ACATA
48127 GGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGT--AACTGTCCATATGTTCCGTAGAACATA
48159 GGTAA
1 GGTAA
48164 ACCTTCGACT
Statistics
Matches: 114, Mismatches: 8, Indels: 14
0.84 0.06 0.10
Matches are distributed among these distances:
30 35 0.31
31 52 0.46
32 22 0.19
33 5 0.04
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.29
Consensus pattern (30 bp):
GGTAACTGTCCATATGTTCCGTAGAACATA
Found at i:48155 original size:63 final size:61
Alignment explanation
Indices: 48008--48163 Score: 197
Period size: 63 Copynumber: 2.5 Consensus size: 61
47998 GATCCTCGGT
* * * * **
48008 AACTGTCCATAGGTCCCGAAGAACCTAGGTAACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTAACTGTCCATATGTTCCAAAGAACATAGGTA
* * *
48069 TACTGTCCATATGTTCCTTAGAACATAGGTATACTGTCCATATGTCTCGAAAG-ACATAGGTAA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA-ACTGTCCATATGT-TCCAAAGAACATAGGT-A
48132 AACTGTCCATATGTTCCGTAGAACATAGGTAA
1 AACTGTCCATATGTTCCGTAGAACATAGGTAA
48164 ACCTTCGACT
Statistics
Matches: 81, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
61 25 0.31
62 22 0.27
63 34 0.42
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.29
Consensus pattern (61 bp):
AACTGTCCATATGTTCCGTAGAACATAGGTAACTGTCCATATGTTCCAAAGAACATAGGTA
Found at i:49684 original size:21 final size:21
Alignment explanation
Indices: 49654--49698 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
49644 TTTTGTTTGT
* *
49654 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
49675 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
49696 TTG
1 TTG
49699 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:53161 original size:30 final size:30
Alignment explanation
Indices: 53127--53223 Score: 131
Period size: 30 Copynumber: 3.2 Consensus size: 30
53117 CCCGAATGAC
53127 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
53157 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* * *** * *
53187 CTGTCCATAGGTCCCGAAGAACCTAGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
53217 CTATCCA
1 CTATCCA
53224 TATGTTCCTT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 59 1.00
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.23
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:53258 original size:31 final size:30
Alignment explanation
Indices: 53182--53340 Score: 176
Period size: 31 Copynumber: 5.2 Consensus size: 30
53172 AAAGATCCTC
* * * *
53182 GGTAACTGTCCATAGGTCCCGAAGAACCTA
1 GGTAACTGTCCATATGTTCCGTAGAACATA
* *
53212 GGTAACTATCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATATGTTCCGTAGAACATA
*
53242 GGTATACTGTCCATATGTTCCTTAGAACATA
1 GGTA-ACTGTCCATATGTTCCGTAGAACATA
***
53273 GGTATACTGTCCATATGTCTCAAAAG-ACATA
1 GGTA-ACTGTCCATATGT-TCCGTAGAACATA
53304 GGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGT--AACTGTCCATATGTTCCGTAGAACATA
53336 GGTAA
1 GGTAA
53341 ACCCTCGACT
Statistics
Matches: 111, Mismatches: 13, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
30 30 0.27
31 55 0.50
32 25 0.23
33 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (30 bp):
GGTAACTGTCCATATGTTCCGTAGAACATA
Found at i:53331 original size:63 final size:61
Alignment explanation
Indices: 53185--53340 Score: 188
Period size: 63 Copynumber: 2.5 Consensus size: 61
53175 GATCCTCGGT
* * * * ***
53185 AACTGTCCATAGGTCCCGAAGAACCTAGGTAACTATCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTAACTATCCATATGTTCAAAAGAACATAGGTA
* * *
53246 TACTGTCCATATGTTCCTTAGAACATAGGTATACTGTCCATATGTCTCAAAAG-ACATAGGTAA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA-ACTATCCATATGT-TCAAAAGAACATAGGT-A
53309 AACTGTCCATATGTTCCGTAGAACATAGGTAA
1 AACTGTCCATATGTTCCGTAGAACATAGGTAA
53341 ACCCTCGACT
Statistics
Matches: 80, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
61 25 0.31
62 21 0.26
63 34 0.43
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (61 bp):
AACTGTCCATATGTTCCGTAGAACATAGGTAACTATCCATATGTTCAAAAGAACATAGGTA
Found at i:54880 original size:21 final size:21
Alignment explanation
Indices: 54850--54894 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
54840 TTTTGTTTGT
* *
54850 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
54871 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
54892 TTG
1 TTG
54895 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:56327 original size:2 final size:2
Alignment explanation
Indices: 56320--56370 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
56310 AAAGTAGCCA
56320 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
56362 AT AT AT AT A
1 AT AT AT AT A
56371 ATTTATATGG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:64364 original size:13 final size:13
Alignment explanation
Indices: 64346--64374 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
64336 AACATATATA
64346 ATTATAAAAAATT
1 ATTATAAAAAATT
64359 ATTATAAAAAATT
1 ATTATAAAAAATT
64372 ATT
1 ATT
64375 TTACAACGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
ATTATAAAAAATT
Found at i:67773 original size:60 final size:60
Alignment explanation
Indices: 67654--67820 Score: 176
Period size: 60 Copynumber: 2.8 Consensus size: 60
67644 TATTTGGATG
* * * * *
67654 AATTTGGGGATGAAATTAGATTATTCAAAAGTTTGAGGAT-TAATTTATAAAGAGGGTCAT
1 AATTTAGGGATGAAATTAGAATATTCAAAAGTTT-AAGATCTAATTTATAAACAGAGTCAT
* * *
67714 AATTTAGGGATGAAATTAGAATGTTTAAAAGTTTAAGATCTAATTTATAATCAGAGTCAT
1 AATTTAGGGATGAAATTAGAATATTCAAAAGTTTAAGATCTAATTTATAAACAGAGTCAT
* * ** * *
67774 AGTTTTA-AGATGAAATTTTAATATTCAAAAATTTAAGAACTAATTTA
1 A-ATTTAGGGATGAAATTAGAATATTCAAAAGTTTAAGATCTAATTTA
67821 AATGAGGGTT
Statistics
Matches: 89, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
59 4 0.04
60 81 0.91
61 4 0.04
ACGTcount: A:0.42, C:0.04, G:0.17, T:0.37
Consensus pattern (60 bp):
AATTTAGGGATGAAATTAGAATATTCAAAAGTTTAAGATCTAATTTATAAACAGAGTCAT
Found at i:75299 original size:21 final size:21
Alignment explanation
Indices: 75273--75312 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
75263 AAAAATTAAT
*
75273 TAAAATATTATTATTTTTAGC
1 TAAAATATTAATATTTTTAGC
*
75294 TAAAATATTAATGTTTTTA
1 TAAAATATTAATATTTTTA
75313 TCATTTCATG
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:0.40, C:0.03, G:0.05, T:0.53
Consensus pattern (21 bp):
TAAAATATTAATATTTTTAGC
Found at i:83529 original size:19 final size:19
Alignment explanation
Indices: 83505--83557 Score: 74
Period size: 18 Copynumber: 2.8 Consensus size: 19
83495 TATTGGGTTT
83505 TATCGGTTTGTTATTTTTC
1 TATCGGTTTGTTATTTTTC
83524 TATCGG-TT-TTATTTTTTC
1 TATCGGTTTGTTA-TTTTTC
83542 TATCGGTTTTGTTATT
1 TATCGG-TTTGTTATT
83558 GTTGGGCACT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 3 0.10
18 14 0.47
19 6 0.20
20 4 0.13
21 3 0.10
ACGTcount: A:0.11, C:0.09, G:0.15, T:0.64
Consensus pattern (19 bp):
TATCGGTTTGTTATTTTTC
Done.