Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008364.1 Hibiscus syriacus cultivar Beakdansim tig00111105_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: 5892847
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 27 of 27
Found at i:5844016 original size:6 final size:6
Alignment explanation
Indices: 5844005--5844035 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
5843995 TCGTCTCGTC
5844005 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
5844036 AATACGTGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:5844158 original size:21 final size:21
Alignment explanation
Indices: 5844132--5844203 Score: 85
Period size: 21 Copynumber: 3.4 Consensus size: 21
5844122 ATTTTGGACT
5844132 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* *
5844153 ATCGCAACGCGAACTTGGACT--
1 ATCGCAA--CGAATTTGGAATAA
*
5844174 ATCGCAATGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
5844195 ATCGCAACG
1 ATCGCAACG
5844204 CGAACTTCGA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
19 9 0.22
21 22 0.54
23 10 0.24
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:5844186 original size:42 final size:42
Alignment explanation
Indices: 5844125--5844224 Score: 173
Period size: 42 Copynumber: 2.4 Consensus size: 42
5844115 CGTTGCGATT
5844125 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
*
5844167 TTGGACTATCGCAATGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* *
5844209 TTCGACTATCACAACG
1 TTGGACTATCGCAACG
5844225 CGAACTTCGA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (42 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
Found at i:5844225 original size:63 final size:61
Alignment explanation
Indices: 5844157--5844289 Score: 194
Period size: 61 Copynumber: 2.1 Consensus size: 61
5844147 GAATAAATCG
* * * *
5844157 CAACGCGAACTTGGACTATCGCAATGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCA
1 CAACGCGAACTTCGACTACCGCAACGAATTT-GAA-AAATCGCAACGCGAACTTAGACTATCA
*
5844220 CAACGCGAACTTCGACTACCGCAACGAATTTGAAAAATCGCAACGCGAACTTAGACTATCG
1 CAACGCGAACTTCGACTACCGCAACGAATTTGAAAAATCGCAACGCGAACTTAGACTATCA
*
5844281 CAATGCGAA
1 CAACGCGAA
5844290 TATATAAATC
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
61 33 0.52
62 3 0.05
63 28 0.44
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.20
Consensus pattern (61 bp):
CAACGCGAACTTCGACTACCGCAACGAATTTGAAAAATCGCAACGCGAACTTAGACTATCA
Found at i:5844280 original size:21 final size:21
Alignment explanation
Indices: 5844153--5844289 Score: 104
Period size: 21 Copynumber: 6.6 Consensus size: 21
5844143 TTTGGAATAA
*
5844153 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
* * * *
5844174 ATCGCAA--TGAATTTGGAAT
1 ATCGCAACGCGAACTTCGACT
5844193 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTCGACT
*
5844216 ATCACAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* * **
5844237 ACCGCAA--CGAA-TTTGAAAA
1 ATCGCAACGCGAACTTCG-ACT
*
5844256 ATCGCAACGCGAACTTAGACT
1 ATCGCAACGCGAACTTCGACT
*
5844277 ATCGCAATGCGAA
1 ATCGCAACGCGAA
5844290 TATATAAATC
Statistics
Matches: 90, Mismatches: 18, Indels: 16
0.73 0.15 0.13
Matches are distributed among these distances:
18 3 0.03
19 20 0.22
21 56 0.62
22 3 0.03
23 8 0.09
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:5844331 original size:21 final size:21
Alignment explanation
Indices: 5844298--5844343 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
5844288 AATATATAAA
*
5844298 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGAGATAGTCCAAGT
* *
5844319 TCGCGTTGAGATAGTCGAAGT
1 TCGCATTGAGATAGTCCAAGT
5844340 TCGC
1 TCGC
5844344 TTTGCGAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (21 bp):
TCGCATTGAGATAGTCCAAGT
Found at i:5844573 original size:7 final size:7
Alignment explanation
Indices: 5844563--5844630 Score: 64
Period size: 7 Copynumber: 9.7 Consensus size: 7
5844553 GTAATAAATG
5844563 CTAAACC
1 CTAAACC
*
5844570 CTAAAAC
1 CTAAACC
5844577 CTAAACC
1 CTAAACC
*
5844584 ATAAACC
1 CTAAACC
* * *
5844591 ATGAATC
1 CTAAACC
5844598 CTAAACC
1 CTAAACC
* *
5844605 ATAAACT
1 CTAAACC
*
5844612 ATAAACC
1 CTAAACC
5844619 CTAAACC
1 CTAAACC
5844626 CTAAA
1 CTAAA
5844631 TCCAATTATA
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
7 49 1.00
ACGTcount: A:0.50, C:0.31, G:0.01, T:0.18
Consensus pattern (7 bp):
CTAAACC
Found at i:5844588 original size:21 final size:21
Alignment explanation
Indices: 5844564--5844630 Score: 80
Period size: 21 Copynumber: 3.2 Consensus size: 21
5844554 TAATAAATGC
*
5844564 TAAACCCTAAAACCTAAACCA
1 TAAACCATAAAACCTAAACCA
* *
5844585 TAAACCATGAATCCTAAACCA
1 TAAACCATAAAACCTAAACCA
* * *
5844606 TAAACTATAAACCCTAAACCC
1 TAAACCATAAAACCTAAACCA
5844627 TAAA
1 TAAA
5844631 TCCAATTATA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.51, C:0.30, G:0.01, T:0.18
Consensus pattern (21 bp):
TAAACCATAAAACCTAAACCA
Found at i:5846786 original size:11 final size:11
Alignment explanation
Indices: 5846770--5846858 Score: 106
Period size: 11 Copynumber: 7.8 Consensus size: 11
5846760 ATTAAAACCC
5846770 ATCGAGCTTGA
1 ATCGAGCTTGA
**
5846781 ATCGAGCTCAAA
1 ATCGAGCT-TGA
*
5846793 ATCAAGCTTGA
1 ATCGAGCTTGA
5846804 ATCGAGCTTGA
1 ATCGAGCTTGA
*
5846815 ATCGAGCTTAAA
1 ATCGAGCTT-GA
5846827 ATCGAGCTTGA
1 ATCGAGCTTGA
*
5846838 ATCGAGCTTAAA
1 ATCGAGCTT-GA
5846850 ATCGAGCTT
1 ATCGAGCTT
5846859 CAGTCGAGTT
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
11 38 0.58
12 28 0.42
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (11 bp):
ATCGAGCTTGA
Found at i:5846813 original size:34 final size:34
Alignment explanation
Indices: 5846770--5846857 Score: 140
Period size: 34 Copynumber: 2.6 Consensus size: 34
5846760 ATTAAAACCC
5846770 ATCGAGCTTGAATCGAGCTCAAAATCAAGCTTGA
1 ATCGAGCTTGAATCGAGCTCAAAATCAAGCTTGA
* *
5846804 ATCGAGCTTGAATCGAGCTTAAAATCGAGCTTGA
1 ATCGAGCTTGAATCGAGCTCAAAATCAAGCTTGA
*
5846838 ATCGAGCTTAAAATCGAGCT
1 ATCGAGCTT-GAATCGAGCT
5846858 TCAGTCGAGT
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
34 41 0.82
35 9 0.18
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (34 bp):
ATCGAGCTTGAATCGAGCTCAAAATCAAGCTTGA
Found at i:5846866 original size:23 final size:23
Alignment explanation
Indices: 5846803--5846858 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
5846793 ATCAAGCTTG
5846803 AATCGAGCTTGAATCGAGCTTAA
1 AATCGAGCTTGAATCGAGCTTAA
5846826 AATCGAGCTTGAATCGAGCTTAA
1 AATCGAGCTTGAATCGAGCTTAA
5846849 AATCGAGCTT
1 AATCGAGCTT
5846859 CAGTCGAGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (23 bp):
AATCGAGCTTGAATCGAGCTTAA
Found at i:5866925 original size:20 final size:20
Alignment explanation
Indices: 5866900--5866983 Score: 69
Period size: 20 Copynumber: 4.0 Consensus size: 20
5866890 TTTTGGTGCA
*
5866900 GAGGGAATCGATCCCCCCCT
1 GAGGGAACCGATCCCCCCCT
**
5866920 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGA-TCCCCCCCT
* *
5866941 GAAGGGGAACCGATTCCCCCCA
1 G-A-GGGAACCGATCCCCCCCT
* * *
5866963 CAGGGAATCGATACCCCCCT
1 GAGGGAACCGATCCCCCCCT
5866983 G
1 G
5866984 GGGTTCTGTT
Statistics
Matches: 49, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
20 25 0.51
21 9 0.18
22 6 0.12
23 9 0.18
ACGTcount: A:0.23, C:0.37, G:0.25, T:0.15
Consensus pattern (20 bp):
GAGGGAACCGATCCCCCCCT
Found at i:5884532 original size:7 final size:7
Alignment explanation
Indices: 5884520--5884565 Score: 92
Period size: 7 Copynumber: 6.6 Consensus size: 7
5884510 AGAGATGAGG
5884520 GGAAGAA
1 GGAAGAA
5884527 GGAAGAA
1 GGAAGAA
5884534 GGAAGAA
1 GGAAGAA
5884541 GGAAGAA
1 GGAAGAA
5884548 GGAAGAA
1 GGAAGAA
5884555 GGAAGAA
1 GGAAGAA
5884562 GGAA
1 GGAA
5884566 AAATGAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (7 bp):
GGAAGAA
Found at i:5889765 original size:3 final size:3
Alignment explanation
Indices: 5889759--5889807 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
5889749 TTTTTTTTAA
**
5889759 TAT TAT TAT TAT TAT CGT TA- TAT TAT TAT TAT TACT T-T TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
5889803 TAT TA
1 TAT TA
5889808 ATTTACAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 4 0.10
3 33 0.85
4 2 0.05
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:5889783 original size:20 final size:18
Alignment explanation
Indices: 5889758--5889807 Score: 73
Period size: 20 Copynumber: 2.7 Consensus size: 18
5889748 TTTTTTTTTA
5889758 ATATTATTATTATTATCGTT
1 ATATTATTATTATTA-C-TT
5889778 ATATTATTATTATTACTT
1 ATATTATTATTATTACTT
*
5889796 TTATTATTATTA
1 ATATTATTATTA
5889808 ATTTACAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 13 0.45
19 1 0.03
20 15 0.52
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (18 bp):
ATATTATTATTATTACTT
Found at i:5890961 original size:19 final size:19
Alignment explanation
Indices: 5890915--5890961 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
5890905 CATTAATTTG
*
5890915 TATATTATGTTTGCTGATAT
1 TATATT-TGGTTGCTGATAT
5890935 TATAATTTGGTTG-TGATATT
1 TAT-ATTTGGTTGCTGATA-T
5890955 TATATTT
1 TATATTT
5890962 ATTTCGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 9 0.38
20 12 0.50
21 3 0.12
ACGTcount: A:0.26, C:0.02, G:0.15, T:0.57
Consensus pattern (19 bp):
TATATTTGGTTGCTGATAT
Done.