Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004504.1 Hibiscus syriacus cultivar Beakdansim tig00009938_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: 55297
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:10476 original size:24 final size:24
Alignment explanation
Indices: 10444--10492 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
10434 TCTCTGACCT
10444 ATAAGTCTATTCACGGTTACTTGA
1 ATAAGTCTATTCACGGTTACTTGA
* *
10468 ATAAGTCTATTGATGGTTACTTGA
1 ATAAGTCTATTCACGGTTACTTGA
10492 A
1 A
10493 GATTTAATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (24 bp):
ATAAGTCTATTCACGGTTACTTGA
Found at i:25828 original size:102 final size:102
Alignment explanation
Indices: 25640--26096 Score: 363
Period size: 102 Copynumber: 4.5 Consensus size: 102
25630 ATAGATGAAC
* * *
25640 TAAACAATTAAGTATCACTAAATCTATTATAAT-A-ATGCAGGTGATAATCTTATTCACCGATGG
1 TAAACAATTACG-ATCACTAAATCTATTCTAATAACATGC--GTGATCATCTTATTCACCGATGG
* * * **
25703 TGCATTGAATAAC-ATACCA--CCATATCAGTATTTAACTCG
63 TGCA-T-AAAAACTATACCAGTCCATATCGGTATTTCACTAA
* * *
25742 TAAACAATTACGAGTCACTAAATCTTTTCTAATAACATGCGTGATCATCTTGTTCACCGATGGTT
1 TAAACAATTACGA-TCACTAAATCTATTCTAATAACATGCGTGATCATCTTATTCACCGATGGTG
*
25807 CAT-AAAACTATGCCAGTCCATATCGGTATTTCACTAA
65 CATAAAAACTATACCAGTCCATATCGGTATTTCACTAA
* * * * *
25844 TACACAATTACATATCACTAAATCTATTC---TAACA-----AATCATCTTATTCACTGAAGGTG
1 TAAACAATTAC-GATCACTAAATCTATTCTAATAACATGCGTGATCATCTTATTCACCGATGGTG
* * **
25901 CATAAAATAATATACC-GT-CGTATCGGTATTTCACTCG
65 CATAAAA-ACTATACCAGTCCATATCGGTATTTCACTAA
* * * * ** * *
25938 TAAACAATTCCGTATCACCAAATATATTCTAATAGCATGCGTGATCATCTCGTTCACAGATGGTT
1 TAAACAATTACG-ATCACTAAATCTATTCTAATAACATGCGTGATCATCTTATTCACCGATGGTG
** *
26003 CAT-AAAACTATGTCAGTCCATATCGGTATTTTACTAA
65 CATAAAAACTATACCAGTCCATATCGGTATTTCACTAA
* * * ** *
26040 TACACAATTACATATCACTAAATCTATTCTAACAACGCGAGTGATCATCTTATTCAC
1 TAAACAATTAC-GATCACTAAATCTATTCTAATAACATGCGTGATCATCTTATTCAC
26097 TGATAGTGAA
Statistics
Matches: 278, Mismatches: 56, Indels: 42
0.74 0.15 0.11
Matches are distributed among these distances:
94 60 0.22
95 5 0.02
96 6 0.02
97 4 0.01
99 9 0.03
100 10 0.04
101 7 0.03
102 171 0.62
103 2 0.01
104 4 0.01
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.33
Consensus pattern (102 bp):
TAAACAATTACGATCACTAAATCTATTCTAATAACATGCGTGATCATCTTATTCACCGATGGTGC
ATAAAAACTATACCAGTCCATATCGGTATTTCACTAA
Found at i:25985 original size:196 final size:196
Alignment explanation
Indices: 25686--26074 Score: 591
Period size: 196 Copynumber: 2.0 Consensus size: 196
25676 GCAGGTGATA
* **
25686 ATCTTATTCACCGATGGTGCATTGAATAACATACCACCATATCAGTATTTAACTCGTAAACAATT
1 ATCTTATTCACCGAAGGTGCATAAAATAACATACCACCATATCAGTATTTAACTCGTAAACAATT
* * * * *
25751 ACGAGTCACTAAATCTTTTCTAATAACATGCGTGATCATCTTGTTCACCGATGGTTCATAAAACT
66 ACGAGTCACCAAATATATTCTAATAACATGCGTGATCATCTCGTTCACAGATGGTTCATAAAACT
25816 ATGCCAGTCCATATCGGTATTTCACTAATACACAATTACATATCACTAAATCTATTCTAACAAAT
131 ATGCCAGTCCATATCGGTATTTCACTAATACACAATTACATATCACTAAATCTATTCTAACAAAT
25881 C
196 C
* * ** * * *
25882 ATCTTATTCACTGAAGGTGCATAAAATAATATACCGTCGTATCGGTATTTCACTCGTAAACAATT
1 ATCTTATTCACCGAAGGTGCATAAAATAACATACCACCATATCAGTATTTAACTCGTAAACAATT
* *
25947 CCGTA-TCACCAAATATATTCTAATAGCATGCGTGATCATCTCGTTCACAGATGGTTCATAAAAC
66 ACG-AGTCACCAAATATATTCTAATAACATGCGTGATCATCTCGTTCACAGATGGTTCATAAAAC
* *
26011 TATGTCAGTCCATATCGGTATTTTACTAATACACAATTACATATCACTAAATCTATTCTAACAA
130 TATGCCAGTCCATATCGGTATTTCACTAATACACAATTACATATCACTAAATCTATTCTAACAA
26075 CGCGAGTGAT
Statistics
Matches: 173, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
196 172 0.99
197 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.33
Consensus pattern (196 bp):
ATCTTATTCACCGAAGGTGCATAAAATAACATACCACCATATCAGTATTTAACTCGTAAACAATT
ACGAGTCACCAAATATATTCTAATAACATGCGTGATCATCTCGTTCACAGATGGTTCATAAAACT
ATGCCAGTCCATATCGGTATTTCACTAATACACAATTACATATCACTAAATCTATTCTAACAAAT
C
Found at i:39607 original size:18 final size:18
Alignment explanation
Indices: 39569--39643 Score: 100
Period size: 18 Copynumber: 4.2 Consensus size: 18
39559 AAAAAATAAC
39569 AAAGTATTTCTAATCATCAA
1 AAAGTATTTCTAATC--CAA
39589 AAAGTATTTCTAATCCAA
1 AAAGTATTTCTAATCCAA
39607 AAAGTA-TT-TAATCCAA
1 AAAGTATTTCTAATCCAA
* *
39623 AGAGTATTTTTAATCCAA
1 AAAGTATTTCTAATCCAA
39641 AAA
1 AAA
39644 ACACATTATA
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
16 13 0.25
17 4 0.08
18 19 0.37
20 15 0.29
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (18 bp):
AAAGTATTTCTAATCCAA
Found at i:41219 original size:17 final size:18
Alignment explanation
Indices: 41194--41246 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
41184 GTGGATGAGT
*
41194 CAACCGAAGGA-GATGAA
1 CAACCGAAGAAGGATGAA
*
41211 CAACTGAAGAAGGATGAA
1 CAACCGAAGAAGGATGAA
* * *
41229 CGACCAAAGGAGGATGAA
1 CAACCGAAGAAGGATGAA
41247 TCGATTACAG
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
17 9 0.31
18 20 0.69
ACGTcount: A:0.47, C:0.15, G:0.30, T:0.08
Consensus pattern (18 bp):
CAACCGAAGAAGGATGAA
Done.