Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004067.1 Hibiscus syriacus cultivar Beakdansim tig00008907_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: 55970
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.31
Found at i:1626 original size:31 final size:31
Alignment explanation
Indices: 1588--1657 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
1578 CTTTTAAAAC
*
1588 TTGCAATACAAT-CCTCCAACATTTAGTCCGT
1 TTGCAATACAATCCCT-CAACATTTAGTCCAT
*** *
1619 TTGCAATATGGTCCCTCAACATTTAGTCTAT
1 TTGCAATACAATCCCTCAACATTTAGTCCAT
1650 TTGCAATA
1 TTGCAATA
1658 TGGTCCATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
31 30 0.91
32 3 0.09
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (31 bp):
TTGCAATACAATCCCTCAACATTTAGTCCAT
Found at i:1658 original size:31 final size:31
Alignment explanation
Indices: 1604--1663 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
1594 TACAATCCTC
*
1604 CAACATTTAGTCCGTTTGCAATATGGTCCCT
1 CAACATTTAGTCCATTTGCAATATGGTCCCT
*
1635 CAACATTTAGTCTATTTGCAATATGGTCC
1 CAACATTTAGTCCATTTGCAATATGGTCC
1664 ATGATGTAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (31 bp):
CAACATTTAGTCCATTTGCAATATGGTCCCT
Found at i:3104 original size:31 final size:31
Alignment explanation
Indices: 3069--3135 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
3059 TTAAAACTTA
3069 CAATACAATCCCCCAATATTTAGTCCATTTG
1 CAATACAATCCCCCAATATTTAGTCCATTTG
*** * *
3100 CAATATGGTCCCTCAATATTTAGTCCGTTTG
1 CAATACAATCCCCCAATATTTAGTCCATTTG
3131 CAATA
1 CAATA
3136 TGGTCCCGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.34
Consensus pattern (31 bp):
CAATACAATCCCCCAATATTTAGTCCATTTG
Found at i:3136 original size:31 final size:31
Alignment explanation
Indices: 3077--3142 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
3067 TACAATACAA
3077 TCCCCCAATATTTAGTCCATTTGCAATATGG
1 TCCCCCAATATTTAGTCCATTTGCAATATGG
* *
3108 TCCCTCAATATTTAGTCCGTTTGCAATATGG
1 TCCCCCAATATTTAGTCCATTTGCAATATGG
3139 TCCC
1 TCCC
3143 GATGTAACTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.23, C:0.27, G:0.14, T:0.36
Consensus pattern (31 bp):
TCCCCCAATATTTAGTCCATTTGCAATATGG
Found at i:8603 original size:2 final size:2
Alignment explanation
Indices: 8598--8622 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8588 TATATATATA
8598 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
8623 TAGTTTTAAT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:11889 original size:23 final size:23
Alignment explanation
Indices: 11863--11910 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
11853 CACTACAATT
11863 CAATTCTACGCGGCACTTCAGTG
1 CAATTCTACGCGGCACTTCAGTG
* * *
11886 CAATTCTATGTGGCACTTCGGTG
1 CAATTCTACGCGGCACTTCAGTG
11909 CA
1 CA
11911 TTTATGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.29
Consensus pattern (23 bp):
CAATTCTACGCGGCACTTCAGTG
Found at i:12141 original size:3 final size:3
Alignment explanation
Indices: 12133--12182 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
12123 CATTTCATTG
12133 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
12180 TTA
1 TTA
12183 CCTCACTAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:18428 original size:23 final size:23
Alignment explanation
Indices: 18390--18457 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
18380 CATCTTATAT
* *
18390 GGCACTACGGTACAATTATACGC
1 GGCACTTCGGTGCAATTATACGC
* * * *
18413 GGCACTTTGGTGCAATTCTATGT
1 GGCACTTCGGTGCAATTATACGC
*
18436 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCAATTATACG
18458 AGTTGTGGTG
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTATACGC
Found at i:37307 original size:104 final size:104
Alignment explanation
Indices: 37042--37441 Score: 638
Period size: 105 Copynumber: 3.8 Consensus size: 104
37032 AAATCCACTG
* *
37042 CAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAACGAGAA
1 CAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCTAAAGGAGAA
*
37107 GGTTCGTAATGAGAAGAGCATGTTCCTTTCAAATCCACC
66 GGTTCGTAATGAGAAGAGCATGTTCCTTTCAAATTCACC
*
37146 ACAGAAGGAGGTGACCCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCTAAAGGAGA
1 -CAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCTAAAGGAGA
37211 AGGTTCGTAATGAGAAGAGCATGTTCCTTTCAAATTCACC
65 AGGTTCGTAATGAGAAGAGCATGTTCCTTTCAAATTCACC
* *
37251 CAGAAGGAGGTGAACCGACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAA
1 CAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCTAAAGGAGAA
* * *
37316 GGTTTGTAATGAGAAGAACTTGTTCCTTTCAAATTCACCC
66 GGTTCGTAATGAGAAGAGCATGTTCCTTTCAAATTCA-CC
* *
37356 CAGAAGGAGGTGAATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCAAAAAAGGAG
1 CAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCC--TAAAGGAG
*
37421 AAGAAGTTCATAATGAGAAGA
64 AAG--GTTCGTAATGAGAAGA
37442 ACTTGTTCAA
Statistics
Matches: 274, Mismatches: 16, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
104 96 0.35
105 154 0.56
107 10 0.04
109 14 0.05
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.21
Consensus pattern (104 bp):
CAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCTAAAGGAGAA
GGTTCGTAATGAGAAGAGCATGTTCCTTTCAAATTCACC
Found at i:37402 original size:209 final size:211
Alignment explanation
Indices: 37042--37441 Score: 669
Period size: 209 Copynumber: 1.9 Consensus size: 211
37032 AAATCCACTG
37042 CAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAACGAGAA
1 CAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAACGAGAA
* *
37107 GGTTCGTAATGAGAAGAGCATGTTCCTTTCAAATCCACCACAGAAGGAGGTGACCCAACATTTCC
66 GGTTCGTAATGAGAAGAACATGTTCCTTTCAAATCCACCACAGAAGGAGGTGAACCAACATTTCC
* *
37172 AGAAGAGTTCATAATGAGAAGAACTCATCC-TAAAGGAGAAG-GTTCGTAATGAGAAGAGCATGT
131 AGAAGAGTTCATAATGAGAAGAACTCATCCAAAAAGGAGAAGAGTTCATAATGAGAAGAGCATGT
37235 TCCTTTCAAATTCACC
196 TCCTTTCAAATTCACC
* *
37251 CAGAAGGAGGTGAACCGACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAA
1 CAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAACGAGAA
* * * * *
37316 GGTTTGTAATGAGAAGAACTTGTTCCTTTCAAATTCACCCCAGAAGGAGGTGAATCAACATTTCC
66 GGTTCGTAATGAGAAGAACATGTTCCTTTCAAATCCACCACAGAAGGAGGTGAACCAACATTTCC
37381 AGAAGAGTTCATAATGAGAAGAACTCATCCAAAAAAGGAGAAGAAGTTCATAATGAGAAGA
131 AGAAGAGTTCATAATGAGAAGAACTCATCC-AAAAAGGAGAAG-AGTTCATAATGAGAAGA
37442 ACTTGTTCAA
Statistics
Matches: 176, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
209 151 0.86
211 10 0.06
213 15 0.09
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.21
Consensus pattern (211 bp):
CAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAACGAGAA
GGTTCGTAATGAGAAGAACATGTTCCTTTCAAATCCACCACAGAAGGAGGTGAACCAACATTTCC
AGAAGAGTTCATAATGAGAAGAACTCATCCAAAAAGGAGAAGAGTTCATAATGAGAAGAGCATGT
TCCTTTCAAATTCACC
Found at i:37672 original size:136 final size:135
Alignment explanation
Indices: 37384--37865 Score: 517
Period size: 136 Copynumber: 3.5 Consensus size: 135
37374 CATTTCCAGA
* *
37384 AGAGTTCATAATGAGAAGAACTCATCC-AAAAAAGGAGAAGAAGTTCATAATGAGAAGAACTTGT
1 AGAGTTCATAATGAGAAGAACTCATCCGATAAAGGGAGAAGAAGTTCATAATGAGAAGAACTTGT
** *
37448 TCAACCT-TAGCTCGATTCATCGCATATGGAGTTGAATCAACAACACCTCACTTGAGGGATCAAC
66 TCAACCTATA-CTCGATTCATAACAT-T----TTGAATCAACAACACCTCGCTTGAGGGATCAAC
*
37512 ACTTTAAATGG
125 ACTTTCAATGG
*
37523 AGAGTTCATAATGAGAAGAACTCATCCGATAAAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGT
1 AGAGTTCATAATGAGAAGAACTCATCCGATAAAGGGAGAAGAAGTTCATAATGAGAAGAACTTGT
* * * *** * * *
37588 TCGACCTATCACTTGATTCATTACATTTTGAATCAGTGACGCCTTGCTTGAGGGAAT-GACA-TT
66 TCAACCTAT-ACTCGATTCATAACATTTTGAATCAACAACACCTCGCTTGAGGG-ATCAACACTT
*
37651 TCATATAG
129 TCA-ATGG
* * * *
37659 AGAGTTCATAATGAGAAGAACTCATCTGACAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGT
1 AGAGTTCATAATGAGAAGAACTCATCCGATAAAGGGAGAAGAAGTTCATAATGAGAAGAACTTGT
* * * * * * * *
37724 TCGACCTATTGCTCGATTCACAACACTTCGAATCAACAATACCTCGCTTGAAGGATCAACATTTT
66 TCAACCTA-TACTCGATTCATAACATTTTGAATCAACAACACCTCGCTTGAGGGATCAACACTTT
*
37789 CAGTGG
130 CAATGG
* * * *
37795 ATAGTTCATAATGAGAAGAACTTATCCGAT-GAGAGGA-AAGAAGTTCGTAATGAGAAGAACTTG
1 AGAGTTCATAATGAGAAGAACTCATCCGATAAAG-GGAGAAGAAGTTCATAATGAGAAGAACTTG
37858 TTCAACCT
65 TTCAACCT
37866 TAACTTGTTT
Statistics
Matches: 292, Mismatches: 42, Indels: 22
0.82 0.12 0.06
Matches are distributed among these distances:
135 40 0.14
136 162 0.55
137 8 0.03
139 27 0.09
140 41 0.14
141 13 0.04
142 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (135 bp):
AGAGTTCATAATGAGAAGAACTCATCCGATAAAGGGAGAAGAAGTTCATAATGAGAAGAACTTGT
TCAACCTATACTCGATTCATAACATTTTGAATCAACAACACCTCGCTTGAGGGATCAACACTTTC
AATGG
Found at i:39493 original size:24 final size:25
Alignment explanation
Indices: 39443--39496 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
39433 GTTTTATGTT
* * * *
39443 TTATATATTTATTTTGTTTGTATTA
1 TTATATATTTACTTTGTATATAATA
39468 TTATATA-TTACTTTGTATATAATA
1 TTATATATTTACTTTGTATATAATA
39492 TTATA
1 TTATA
39497 GCATGATAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (25 bp):
TTATATATTTACTTTGTATATAATA
Found at i:53026 original size:29 final size:29
Alignment explanation
Indices: 52984--53042 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
52974 AATGCAGATA
52984 TCTCAGACTTTCATAGTTGTATGGAAGAC
1 TCTCAGACTTTCATAGTTGTATGGAAGAC
53013 TCTCAGACTTTCATAGTTGTATGGAAGAC
1 TCTCAGACTTTCATAGTTGTATGGAAGAC
53042 T
1 T
53043 TAGAAGTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (29 bp):
TCTCAGACTTTCATAGTTGTATGGAAGAC
Found at i:54864 original size:29 final size:29
Alignment explanation
Indices: 54818--54898 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
54808 TTCCATATGT
54818 TCATGTA-CTCATGCCATTTCTCTTGTGA
1 TCATGTAGCTCATGCCATTTCTCTTGTGA
*
54846 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGCCATTTCTCTTGTGA
*
54875 TCATGTAGCTCATGGCATGTTCTC
1 TCATGTAGCTCATGCCAT-TTCTC
54899 ATATCACATA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
28 7 0.14
29 37 0.76
30 5 0.10
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.42
Consensus pattern (29 bp):
TCATGTAGCTCATGCCATTTCTCTTGTGA
Found at i:55332 original size:62 final size:62
Alignment explanation
Indices: 55266--55413 Score: 151
Period size: 62 Copynumber: 2.4 Consensus size: 62
55256 TAATGAAGGC
**
55266 ATGCATCGATGCACTACTTGTGCATCGTGCATA-AAAATGCATTCGATGTTT-T-TATTAATGGA
1 ATGCATCGATGCACTACTTGTGCATC--G-ATACAAAATGCATTCGATGTTTATATATTAAAAGA
* * * * *
55328 ATGCATCGATGCA-TGCCTTATGCATCGATACTAATTGCATTCGATGTTTATATTTTAAAAGA
1 ATGCATCGATGCACT-ACTTGTGCATCGATACAAAATGCATTCGATGTTTATATATTAAAAGA
* *
55390 GTGCATCGATGCACTACCTGTGCA
1 ATGCATCGATGCACTACTTGTGCA
55414 CACCTTCAAA
Statistics
Matches: 70, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
59 3 0.04
60 17 0.24
61 2 0.03
62 47 0.67
63 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.34
Consensus pattern (62 bp):
ATGCATCGATGCACTACTTGTGCATCGATACAAAATGCATTCGATGTTTATATATTAAAAGA
Done.