Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002609.1 Hibiscus syriacus cultivar Beakdansim tig00005274_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: 167397
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
File 2 of 2
Found at i:145784 original size:42 final size:43
Alignment explanation
Indices: 145691--145789 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
145681 ATTTATGTGT
* *
145691 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
145732 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
145774 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
145790 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:147552 original size:21 final size:23
Alignment explanation
Indices: 147527--147578 Score: 72
Period size: 21 Copynumber: 2.3 Consensus size: 23
147517 GATTATTGGT
*
147527 ATAATTTACATTT-TATTTT-AA
1 ATAATTTACATTTAAATTTTCAA
147548 ATAATTTACATTTAAATTTTCAA
1 ATAATTTACATTTAAATTTTCAA
*
147571 CTAATTTA
1 ATAATTTA
147579 TAATTATATG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 13 0.48
22 5 0.19
23 9 0.33
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (23 bp):
ATAATTTACATTTAAATTTTCAA
Found at i:147906 original size:26 final size:24
Alignment explanation
Indices: 147877--147927 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 24
147867 TACTGAATAG
147877 TAAATATAAT-TTTTAAGATTTAATTA
1 TAAA-ATAATATTTTAA-ATTT-ATTA
*
147903 TAAAATTATATTTTAAATTTATTA
1 TAAAATAATATTTTAAATTTATTA
147927 T
1 T
147928 GAATTGGGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 5 0.22
25 8 0.35
26 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
TAAAATAATATTTTAAATTTATTA
Found at i:154017 original size:2 final size:2
Alignment explanation
Indices: 154010--154049 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
154000 CGCCTTATTA
154010 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
154050 TGTAATTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:159155 original size:29 final size:29
Alignment explanation
Indices: 159122--159188 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
159112 TTTAATATTT
* * *
159122 ATTTTTAATTGATATAAACAAGAAAATAT
1 ATTTTTAAATAATATAAACAAGAAAATAA
* *
159151 TTTTTTAAATAATATAAACATGAAAATAA
1 ATTTTTAAATAATATAAACAAGAAAATAA
159180 ATTTTTAAA
1 ATTTTTAAA
159189 ATTCATGGAC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.40
Consensus pattern (29 bp):
ATTTTTAAATAATATAAACAAGAAAATAA
Found at i:159834 original size:20 final size:19
Alignment explanation
Indices: 159788--159835 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
159778 ATGACCAACA
*
159788 AAATCGCAACGCGATCTCT
1 AAATCGCAACGCGATCTCC
159807 AAATCGCAACGCGATCTCC
1 AAATCGCAACGCGATCTCC
159826 AATATCGCAA
1 AA-ATCGCAA
159836 ATCAGTTTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 20 0.74
20 7 0.26
ACGTcount: A:0.35, C:0.31, G:0.15, T:0.19
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCC
Found at i:159899 original size:21 final size:21
Alignment explanation
Indices: 159870--159926 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
159860 ATTTTGACTA
* *
159870 TCGCATTGCGATTTTCCAAAT
1 TCGCGTTGCGATTTTCAAAAT
159891 TCGCGTTGCGATTTTCAAAAT
1 TCGCGTTGCGATTTTCAAAAT
159912 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
159927 AGAAAATCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.40
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCAAAAT
Found at i:159936 original size:21 final size:20
Alignment explanation
Indices: 159869--159936 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 20
159859 GATTTTGACT
* *
159869 ATCGCATTGCGATTTTCCAAA
1 ATCGCGTTGCGATTTT-AAAA
*
159890 TTCGCGTTGCGATTTTCAAAA
1 ATCGCGTTGCGATTTT-AAAA
*
159911 TTCGCGTTGCGATTTTAGAAA
1 ATCGCGTTGCGATTTTA-AAA
159932 ATCGC
1 ATCGC
159937 AATGTGAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
20 1 0.02
21 41 0.98
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (20 bp):
ATCGCGTTGCGATTTTAAAA
Found at i:160148 original size:17 final size:17
Alignment explanation
Indices: 160126--160163 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
160116 CGACATCCGT
160126 TCCTATATCCAACAACA
1 TCCTATATCCAACAACA
*
160143 TCCTATATCCAACGACA
1 TCCTATATCCAACAACA
160160 TCCT
1 TCCT
160164 TCCCCATCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.34, C:0.37, G:0.03, T:0.26
Consensus pattern (17 bp):
TCCTATATCCAACAACA
Found at i:160844 original size:24 final size:24
Alignment explanation
Indices: 160817--160870 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
160807 GTATTCAAAA
160817 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
160841 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
160865 TTTGAT
1 TTTGAT
160871 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:161086 original size:14 final size:14
Alignment explanation
Indices: 161057--161093 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
161047 AGAAGAAAAA
161057 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
161072 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
161086 GAAGAAAA
1 GAAGAAAA
161094 TGCCACGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:163352 original size:20 final size:20
Alignment explanation
Indices: 163327--163443 Score: 162
Period size: 20 Copynumber: 5.8 Consensus size: 20
163317 TTACACATTC
*
163327 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
163347 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
163367 ATTTGACTATCACAACACGA
1 ATTTGACTATCGCAACGCGA
*
163387 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* * * *
163407 ATTTGATTATCACAATGGGA
1 ATTTGACTATCGCAACGCGA
163427 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
163444 AGAAAATCGC
Statistics
Matches: 84, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 84 1.00
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:163545 original size:20 final size:20
Alignment explanation
Indices: 163482--163559 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
163472 GCAACGCGAA
*
163482 TTGACTTTCGCGTTGCGATT
1 TTGACTTTCGCATTGCGATT
*
163502 TTGGCTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
163522 TTGACTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
* * *
163542 TTGAGTTTAGCGTTGCGA
1 TTGACTTTCGCATTGCGA
163560 AAATGTACAT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.13, C:0.18, G:0.26, T:0.44
Consensus pattern (20 bp):
TTGACTTTCGCATTGCGATT
Found at i:163698 original size:14 final size:14
Alignment explanation
Indices: 163679--163715 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
163669 CATCAATTAA
163679 ACAAATCAACTTTT
1 ACAAATCAACTTTT
163693 ACAAATCAACTTTT
1 ACAAATCAACTTTT
163707 ACAAATCAA
1 ACAAATCAA
163716 TTAAACAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:165123 original size:21 final size:21
Alignment explanation
Indices: 165097--165167 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 21
165087 TGTGAATCGG
165097 CCTCTTGAATGGTGGGAGGGA
1 CCTCTTGAATGGTGGGAGGGA
* * ** *
165118 CCTCTTCAATGATGACAGGGG
1 CCTCTTGAATGGTGGGAGGGA
165139 CCTCTTGAATGGTGGGAGGGGA
1 CCTCTTGAATGGTGGGA-GGGA
165161 -CTCTTGA
1 CCTCTTGA
165168 GGGATGATAG
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
21 36 0.92
22 3 0.08
ACGTcount: A:0.20, C:0.18, G:0.37, T:0.25
Consensus pattern (21 bp):
CCTCTTGAATGGTGGGAGGGA
Found at i:165154 original size:42 final size:42
Alignment explanation
Indices: 165095--165220 Score: 148
Period size: 42 Copynumber: 3.0 Consensus size: 42
165085 CGTGTGAATC
*
165095 GGCCTCTTGAATGGTGGGAGGGACCTCTTCAATGATGACAGG
1 GGCCTCTTGAATGGTGGGAGGGACCTCTTGAATGATGACAGG
** *
165137 GGCCTCTTGAATGGTGGGAGGGGA-CTCTTGAGGGATGATAGG
1 GGCCTCTTGAATGGTGGGA-GGGACCTCTTGAATGATGACAGG
* * * *
165179 GGCCTCTTGAACGATAGGAGAGG-CCTCTTGAATGATAACAGG
1 GGCCTCTTGAATGGTGGGAG-GGACCTCTTGAATGATGACAGG
165221 TGAGTCAAGC
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 1 0.01
42 65 0.93
43 4 0.06
ACGTcount: A:0.23, C:0.17, G:0.37, T:0.23
Consensus pattern (42 bp):
GGCCTCTTGAATGGTGGGAGGGACCTCTTGAATGATGACAGG
Found at i:165710 original size:20 final size:20
Alignment explanation
Indices: 165685--165728 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
165675 AATAGTTTCT
165685 GAAACTTAAAATCGCAACAC
1 GAAACTTAAAATCGCAACAC
*
165705 GAAACTTAAAATCGCAACGC
1 GAAACTTAAAATCGCAACAC
165725 GAAA
1 GAAA
165729 ATAACTATCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.50, C:0.23, G:0.14, T:0.14
Consensus pattern (20 bp):
GAAACTTAAAATCGCAACAC
Found at i:165738 original size:20 final size:20
Alignment explanation
Indices: 165715--165782 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
165705 GAAACTTAAA
*
165715 ATCGCAACGCGAAAATAACT
1 ATCGCAACGCGAAAATGACT
*
165735 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
165755 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
165775 ATCGCAAC
1 ATCGCAAC
165783 AAGATAATCG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:165892 original size:33 final size:34
Alignment explanation
Indices: 165831--165906 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 34
165821 ACTAAATTCG
* *
165831 CGTTGCGATTTTCATTTTTGCATTGCGATTTTCA
1 CGTTGCGATTTTCATTTTCGCATTGCGATTATCA
* *
165865 CGTTGCGATTTTTA-TTTCGCATTGCGATTATCC
1 CGTTGCGATTTTCATTTTCGCATTGCGATTATCA
165898 CGTTGCGAT
1 CGTTGCGAT
165907 AGTCAAATTC
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
33 25 0.66
34 13 0.34
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.46
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTATCA
Found at i:165923 original size:20 final size:20
Alignment explanation
Indices: 165898--165966 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
165888 GCGATTATCC
*
165898 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAATTTCG
165918 CGTTGCGATAGTC-ATTTCCG
1 CGTTGCGATAGTCAATTT-CG
* *
165938 CGTTGTGATAGTCATTTTCG
1 CGTTGCGATAGTCAATTTCG
165958 CGTTGCGAT
1 CGTTGCGAT
165967 TTTAAGTTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.07
20 37 0.86
21 3 0.07
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTTCG
Found at i:165924 original size:34 final size:37
Alignment explanation
Indices: 165880--165967 Score: 92
Period size: 40 Copynumber: 2.4 Consensus size: 37
165870 CGATTTTTAT
*
165880 TTCGCATTGCGATT-A-TCC-CGTTGCGATAGTCAAA
1 TTCGCGTTGCGATTCATTCCGCGTTGCGATAGTCAAA
* **
165914 TTCGCGTTGCGATAGTCATTTCCGCGTTGTGATAGTCATT
1 TTCGCGTTGCGAT--TCA-TTCCGCGTTGCGATAGTCAAA
165954 TTCGCGTTGCGATT
1 TTCGCGTTGCGATT
165968 TTAAGTTTCG
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
34 12 0.27
36 1 0.02
37 1 0.02
38 1 0.02
39 3 0.07
40 26 0.59
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.38
Consensus pattern (37 bp):
TTCGCGTTGCGATTCATTCCGCGTTGCGATAGTCAAA
Done.