Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004381.1 Hibiscus syriacus cultivar Beakdansim tig00009607_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: 53845
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:3259 original size:21 final size:20
Alignment explanation
Indices: 3235--3284 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
3225 TATTTTGATT
*
3235 AGAAATTTTGAAATTTCTACA
1 AGAAATTTCGAAATTT-TACA
*
3256 AG-AATTTCGAAATTTTCCA
1 AGAAATTTCGAAATTTTACA
3275 AGATAATTTC
1 AGA-AATTTC
3285 CTAAAAAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 5 0.20
20 12 0.48
21 8 0.32
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (20 bp):
AGAAATTTCGAAATTTTACA
Found at i:26202 original size:21 final size:21
Alignment explanation
Indices: 26160--26202 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
26150 TTTCTGGGCT
* *
26160 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
26181 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
26202 A
1 A
26203 CGAATATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:26252 original size:22 final size:22
Alignment explanation
Indices: 26227--26268 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
26217 CAGAATGCTA
*
26227 GAGGGGAATCGATACCCCCAGG
1 GAGGGGAACCGATACCCCCAGG
*
26249 GAGGGGAACCGATTCCCCCA
1 GAGGGGAACCGATACCCCCA
26269 TAATGAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.31, G:0.33, T:0.10
Consensus pattern (22 bp):
GAGGGGAACCGATACCCCCAGG
Found at i:26974 original size:103 final size:103
Alignment explanation
Indices: 26750--26975 Score: 391
Period size: 103 Copynumber: 2.2 Consensus size: 103
26740 GTAGAGGGTT
*
26750 TATGTGGTCCTTTGGGATATATATGTATTCTTTGCAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTTGGGACATATATGTATTCTTTGCAACATGTGTGAGGTCTGGTGAGACACATAC
*
26815 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATAATTCTTAAGGAATGA
* * *
26853 TATATGGTCATTTGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTTGGGACATATATGTATTCTTTGCAACATGTGTGAGGTCTGGTGAGACACATAC
26918 TTGATCCTTGGTATATGTATATAATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATAATTCTTAAGGAATGA
26956 TATGTGGTCCTTAT-GGACAT
1 TATGTGGTCCTT-TGGGACAT
26976 TATTATATGG
Statistics
Matches: 115, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
103 114 0.99
104 1 0.01
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTTGGGACATATATGTATTCTTTGCAACATGTGTGAGGTCTGGTGAGACACATAC
TTGATCCTTGGTATATGTATATAATTCTTAAGGAATGA
Found at i:27017 original size:23 final size:23
Alignment explanation
Indices: 26984--27035 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
26974 ATTATTATAT
26984 GGCACTACGGTACAATTCTACGC
1 GGCACTACGGTACAATTCTACGC
* * *
27007 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTACAATTCTACGC
27030 GGCACT
1 GGCACT
27036 TAGGTGCAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.21, C:0.31, G:0.25, T:0.23
Consensus pattern (23 bp):
GGCACTACGGTACAATTCTACGC
Found at i:27041 original size:23 final size:23
Alignment explanation
Indices: 26983--27046 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
26973 CATTATTATA
*
26983 TGGCAC-TACGGTACAATTCTACG
1 TGGCACTTA-GGTGCAATTCTACG
* **
27006 CGGCACTCCGGTGCAATTCTACG
1 TGGCACTTAGGTGCAATTCTACG
27029 TGGCACTTAGGTGCAATT
1 TGGCACTTAGGTGCAATT
27047 ATATGAGCTG
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.27
Consensus pattern (23 bp):
TGGCACTTAGGTGCAATTCTACG
Found at i:33149 original size:21 final size:21
Alignment explanation
Indices: 33110--33149 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
33100 CTGGGCTAGT
* *
33110 GGAATCGGTACCCATTCAAGG
1 GGAATCGATACCCACTCAAGG
*
33131 GGAATCGATACCCCCTCAA
1 GGAATCGATACCCACTCAA
33150 CGAATATGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.30, G:0.23, T:0.17
Consensus pattern (21 bp):
GGAATCGATACCCACTCAAGG
Found at i:33201 original size:20 final size:20
Alignment explanation
Indices: 33176--33213 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
33166 GAATGCTAGA
*
33176 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
33196 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
33214 TAATGAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:33874 original size:103 final size:103
Alignment explanation
Indices: 33695--33912 Score: 418
Period size: 103 Copynumber: 2.1 Consensus size: 103
33685 GTAGAGGGTC
33695 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
33760 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
*
33798 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAATATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
33863 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
*
33901 TATATGGTCCTT
1 TATGTGGTCCTT
33913 ATGGACATTA
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 113 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
Found at i:33963 original size:23 final size:23
Alignment explanation
Indices: 33937--33991 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
33927 ATGGCATTAT
*
33937 GGTGCAATTCTACGCGGCACTCC
1 GGTGCAATTCTACGCGGCACTCA
* *
33960 GGTGCAATTCTACGTGGCACTTA
1 GGTGCAATTCTACGCGGCACTCA
33983 GGTGCAATT
1 GGTGCAATT
33992 ATATGAGCTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.20, C:0.25, G:0.27, T:0.27
Consensus pattern (23 bp):
GGTGCAATTCTACGCGGCACTCA
Found at i:34760 original size:22 final size:24
Alignment explanation
Indices: 34698--34746 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
34688 GAAAGGACAT
34698 AAGAAAGAATATGAAATATATAAC
1 AAGAAAGAATATGAAATATATAAC
34722 AAGAAAGAATATGAAATATATAAC
1 AAGAAAGAATATGAAATATATAAC
34746 A
1 A
34747 TATGAATATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.63, C:0.04, G:0.12, T:0.20
Consensus pattern (24 bp):
AAGAAAGAATATGAAATATATAAC
Found at i:34867 original size:2 final size:2
Alignment explanation
Indices: 34860--34909 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
34850 AGTATACGTG
*
34860 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
34901 AT TT AT AT A
1 AT AT AT AT A
34910 AGTTATTGGA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:35001 original size:4 final size:4
Alignment explanation
Indices: 34992--35024 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
34982 AAATGATGAC
34992 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
35025 ATGGTTATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:35311 original size:30 final size:30
Alignment explanation
Indices: 35277--35529 Score: 452
Period size: 30 Copynumber: 8.4 Consensus size: 30
35267 GGTTCCTCGG
* *
35277 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
35307 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
35337 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
* *
35367 GACATCTAGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
35397 GACCTCTGGATAGTTACTGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
35427 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
35457 GACCTCTGGATAGTTACTGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
35487 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
35517 GACCTCTGGATAG
1 GACCTCTGGATAG
35530 GTCCTTCAGA
Statistics
Matches: 213, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 213 1.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:39067 original size:64 final size:62
Alignment explanation
Indices: 38937--39072 Score: 159
Period size: 64 Copynumber: 2.1 Consensus size: 62
38927 TTCAGTGTGT
* * * *
38937 ATCGATGCACAGGAAGTGCATCGATGCACCTATTAAAATGGAAACATCGAATGCAATTGGTGC
1 ATCGATGCAAAGGAAGTGCATCGATGCACCCATTAAAATGAAAACATCGAATG-AATTGGTAC
* *
39000 ATCGATGCATAAGG-AGTGCATCGATGCATCCCCTTAAAATGAAAACATCGAA-GATGATTTGTA
1 ATCGATGCA-AAGGAAGTGCATCGATGCA-CCCATTAAAATGAAAACATCGAATGA--ATTGGTA
39063 C
62 C
39064 ATCGATGCA
1 ATCGATGCA
39073 CGTGTACTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
62 1 0.02
63 24 0.38
64 38 0.60
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (62 bp):
ATCGATGCAAAGGAAGTGCATCGATGCACCCATTAAAATGAAAACATCGAATGAATTGGTAC
Found at i:40176 original size:31 final size:31
Alignment explanation
Indices: 40138--40210 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
40128 GTCAAAGAAC
**
40138 TACCTATG-TCTTTCGAGACATATGGATAGTA
1 TACCTATGTTCTAACGA-ACATATGGATAGTA
* *
40169 TACCTATGTTCTAAGGAACATATGGATAGTT
1 TACCTATGTTCTAACGAACATATGGATAGTA
*
40200 TACCTAGGTTC
1 TACCTATGTTC
40211 CTCGGGACCT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
31 31 0.86
32 5 0.14
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (31 bp):
TACCTATGTTCTAACGAACATATGGATAGTA
Found at i:40250 original size:30 final size:30
Alignment explanation
Indices: 40216--40498 Score: 494
Period size: 30 Copynumber: 9.4 Consensus size: 30
40206 GGTTCCTCGG
*
40216 GACCTATGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
40246 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
40276 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
* *
40306 GACCTGTGGATAGTTACCGATGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
* *
40336 AACCTGTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
40366 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
**
40396 GACCTCTGGATAGTTATTGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
40426 GACCTCTGGATAGTTACCGAGGATCTTAAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
40456 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
40486 GACCTCTGGATAG
1 GACCTCTGGATAG
40499 GTCCTTCGGA
Statistics
Matches: 240, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 240 1.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:48016 original size:14 final size:14
Alignment explanation
Indices: 47997--48032 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
47987 GTGCAATGTA
47997 GCTGATGTGTATAG
1 GCTGATGTGTATAG
48011 GCTGATGTGTATAG
1 GCTGATGTGTATAG
48025 GCTGATGT
1 GCTGATGT
48033 ATGTAGGCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.19, C:0.08, G:0.36, T:0.36
Consensus pattern (14 bp):
GCTGATGTGTATAG
Found at i:48039 original size:14 final size:14
Alignment explanation
Indices: 47997--48040 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
47987 GTGCAATGTA
*
47997 GCTGATGTGTATAG
1 GCTGATGTATATAG
*
48011 GCTGATGTGTATAG
1 GCTGATGTATATAG
*
48025 GCTGATGTATGTAG
1 GCTGATGTATATAG
48039 GC
1 GC
48041 AGTTGCAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.20, C:0.09, G:0.36, T:0.34
Consensus pattern (14 bp):
GCTGATGTATATAG
Found at i:52971 original size:13 final size:13
Alignment explanation
Indices: 52951--52985 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
52941 GGAATGTAGT
52951 TGATGTGTAAAGC
1 TGATGTGTAAAGC
*
52964 TTATGTGTAAAGC
1 TGATGTGTAAAGC
52977 TGATGTGTA
1 TGATGTGTA
52986 TAAGATGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.29, C:0.06, G:0.29, T:0.37
Consensus pattern (13 bp):
TGATGTGTAAAGC
Done.