Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007653.1 Hibiscus syriacus cultivar Beakdansim tig00024946_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: 91259
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Found at i:9121 original size:15 final size:15
Alignment explanation
Indices: 9101--9139 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
9091 ATGAAGTACT
9101 ACCTTTCCCGATGCA
1 ACCTTTCCCGATGCA
* * *
9116 ACCTTTCCTGGTGCT
1 ACCTTTCCCGATGCA
9131 ACCTTTCCC
1 ACCTTTCCC
9140 TAGAATGAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.13, C:0.41, G:0.13, T:0.33
Consensus pattern (15 bp):
ACCTTTCCCGATGCA
Found at i:10018 original size:31 final size:31
Alignment explanation
Indices: 9983--10044 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
9973 CTCCTGTTAT
*
9983 TTACTCGGGCTGAGCAGCACTTACTGAATCA
1 TTACTCGGACTGAGCAGCACTTACTGAATCA
10014 TTACTCGGACTGAGCAGCACTTACTGAATCA
1 TTACTCGGACTGAGCAGCACTTACTGAATCA
10045 GAGCAGTTGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (31 bp):
TTACTCGGACTGAGCAGCACTTACTGAATCA
Found at i:21070 original size:21 final size:21
Alignment explanation
Indices: 21046--21085 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
21036 TAGACGGGCG
21046 TCAAGAAC-TACATCAGCGGGA
1 TCAAGAACGT-CATCAGCGGGA
*
21067 TCAATAACGTCATCAGCGG
1 TCAAGAACGTCATCAGCGG
21086 ATCCGTAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.35, C:0.25, G:0.23, T:0.17
Consensus pattern (21 bp):
TCAAGAACGTCATCAGCGGGA
Found at i:28663 original size:2 final size:2
Alignment explanation
Indices: 28658--28688 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
28648 TAAAAAAGAA
28658 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28689 TACCTTACCG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:49610 original size:15 final size:15
Alignment explanation
Indices: 49590--49628 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
49580 ATGAAGTACT
49590 ACCTTTCCCGATGCA
1 ACCTTTCCCGATGCA
* * *
49605 ACCTTTCCTGGTGCT
1 ACCTTTCCCGATGCA
49620 ACCTTTCCC
1 ACCTTTCCC
49629 TAGAATGAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.13, C:0.41, G:0.13, T:0.33
Consensus pattern (15 bp):
ACCTTTCCCGATGCA
Found at i:50507 original size:31 final size:31
Alignment explanation
Indices: 50472--50533 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
50462 CTCCTGTTAT
*
50472 TTACTCGGGCTGAGCAGCACTTACTGAATCA
1 TTACTCGGACTGAGCAGCACTTACTGAATCA
50503 TTACTCGGACTGAGCAGCACTTACTGAATCA
1 TTACTCGGACTGAGCAGCACTTACTGAATCA
50534 GAGCAGTTGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (31 bp):
TTACTCGGACTGAGCAGCACTTACTGAATCA
Found at i:61677 original size:21 final size:21
Alignment explanation
Indices: 61653--61692 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
61643 TAGACGGGCG
61653 TCAAGAAC-TACATCAGCGGGA
1 TCAAGAACGT-CATCAGCGGGA
*
61674 TCAATAACGTCATCAGCGG
1 TCAAGAACGTCATCAGCGG
61693 ATCCGTAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.35, C:0.25, G:0.23, T:0.17
Consensus pattern (21 bp):
TCAAGAACGTCATCAGCGGGA
Found at i:69265 original size:2 final size:2
Alignment explanation
Indices: 69260--69286 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
69250 TAAAAAAGAA
69260 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
69287 CCTTACCGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:90193 original size:15 final size:15
Alignment explanation
Indices: 90173--90211 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
90163 ATGAAGTACT
90173 ACCTTTCCCGATGCA
1 ACCTTTCCCGATGCA
* * *
90188 ACCTTTCCTGGTGCT
1 ACCTTTCCCGATGCA
90203 ACCTTTCCC
1 ACCTTTCCC
90212 TAGAATGAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.13, C:0.41, G:0.13, T:0.33
Consensus pattern (15 bp):
ACCTTTCCCGATGCA
Found at i:91087 original size:31 final size:31
Alignment explanation
Indices: 91052--91113 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
91042 CCTCCTGTTT
*
91052 TTACTCGGGCTGAGCAGCACTTACTGAATCA
1 TTACTCGGACTGAGCAGCACTTACTGAATCA
91083 TTACTCGGACTGAGCAGCACTTACTGAATCA
1 TTACTCGGACTGAGCAGCACTTACTGAATCA
91114 GAGCAGTTGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (31 bp):
TTACTCGGACTGAGCAGCACTTACTGAATCA
Done.