Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008005.1 Hibiscus syriacus cultivar Beakdansim tig00110467_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: 1778185
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 7 of 7
Found at i:1767028 original size:77 final size:77
Alignment explanation
Indices: 1766900--1767058 Score: 248
Period size: 77 Copynumber: 2.1 Consensus size: 77
1766890 AATACTATCA
* * *
1766900 CAACGTGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGCGA
1 CAACGAGATTTTCAAATTCCCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGAGA
1766965 TTTACAAATTCG
66 TTTACAAATTCG
* * *
1766977 CAACGAGATTTTCAAATTCACCAATGCTAATTACCGATATAGGT-AATAGTACTATCGCAACGAT
1 CAACGAGATTTTCAAATTC-CCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGAG
1767041 ATTTACAAATTCG
65 ATTTACAAATTCG
1767054 CAACG
1 CAACG
1767059 CTAATTATCG
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
77 53 0.71
78 22 0.29
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.28
Consensus pattern (77 bp):
CAACGAGATTTTCAAATTCCCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGAGA
TTTACAAATTCG
Found at i:1767035 original size:57 final size:57
Alignment explanation
Indices: 1766974--1767103 Score: 165
Period size: 57 Copynumber: 2.3 Consensus size: 57
1766964 ATTTACAAAT
* * * *
1766974 TCGCAACGAGATTTTCAAATTCACCAATGCTAATTACCGATATAGGT-AATAGTACTA
1 TCGCAACGAGATTTACAAATTC-CCAACGCTAATTACCGATATAAGTAAACAGTACTA
* * *
1767031 TCGCAACGATATTTACAAATTCGCAACGCTAATTATCGATATAAGTAAACAGTACTA
1 TCGCAACGAGATTTACAAATTCCCAACGCTAATTACCGATATAAGTAAACAGTACTA
1767088 TCGCAACGCA-ATTTAC
1 TCGCAACG-AGATTTAC
1767104 CGATATAGGT
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
56 20 0.31
57 43 0.67
58 1 0.02
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (57 bp):
TCGCAACGAGATTTACAAATTCCCAACGCTAATTACCGATATAAGTAAACAGTACTA
Found at i:1767092 original size:37 final size:37
Alignment explanation
Indices: 1767051--1767138 Score: 106
Period size: 37 Copynumber: 2.4 Consensus size: 37
1767041 ATTTACAAAT
*
1767051 TCGCAACGCTAA-TTATCGATATAAGTAAACAGTACTA
1 TCGCAACGC-AATTTACCGATATAAGTAAACAGTACTA
* * **
1767088 TCGCAACGCAATTTACCGATATAGGTAACCAGTGTTA
1 TCGCAACGCAATTTACCGATATAAGTAAACAGTACTA
*
1767125 TCGCAACGCGATTT
1 TCGCAACGCAATTT
1767139 TCAAATTCGC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
36 2 0.05
37 42 0.95
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (37 bp):
TCGCAACGCAATTTACCGATATAAGTAAACAGTACTA
Found at i:1767150 original size:20 final size:20
Alignment explanation
Indices: 1767125--1767193 Score: 111
Period size: 20 Copynumber: 3.4 Consensus size: 20
1767115 ACCAGTGTTA
1767125 TCGCAACGCGATTTTCAAAT
1 TCGCAACGCGATTTTCAAAT
* *
1767145 TCGCAACGAGATTTTCAAAAA
1 TCGCAACGCGATTTTC-AAAT
1767166 TCGCAACGCGATTTTCAAAT
1 TCGCAACGCGATTTTCAAAT
1767186 TCGCAACG
1 TCGCAACG
1767194 GTAATTACTG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
20 26 0.59
21 18 0.41
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTTTCAAAT
Found at i:1767253 original size:19 final size:19
Alignment explanation
Indices: 1767229--1767311 Score: 71
Period size: 20 Copynumber: 4.3 Consensus size: 19
1767219 ACTATCGCAA
1767229 TGCGATTTTGGAAATGTGT
1 TGCGATTTTGGAAATGTGT
** *
1767248 TGCGA-TTTACAAAT-TCGCG
1 TGCGATTTTGGAAATGT-G-T
1767267 TGCGATTTTGGAAACTGTGT
1 TGCGATTTTGGAAA-TGTGT
* *
1767287 TACAATTTTGGAACATGTGT
1 TGCGATTTTGGAA-ATGTGT
1767307 TGCGA
1 TGCGA
1767312 AATTAGAGTT
Statistics
Matches: 48, Mismatches: 10, Indels: 11
0.70 0.14 0.16
Matches are distributed among these distances:
17 1 0.02
18 8 0.17
19 10 0.21
20 25 0.52
21 3 0.06
22 1 0.02
ACGTcount: A:0.24, C:0.12, G:0.27, T:0.37
Consensus pattern (19 bp):
TGCGATTTTGGAAATGTGT
Found at i:1768459 original size:24 final size:24
Alignment explanation
Indices: 1768409--1768469 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
1768399 AAAGCCTTGT
* *
1768409 ATTTATTTATAATCAACGATATTTA
1 ATTTATTTA-AATCAACCATATCTA
1768434 ATTTATTTTAAATC-ACCATATCTA
1 ATTTA-TTTAAATCAACCATATCTA
1768458 ATTTATTTAAAT
1 ATTTATTTAAAT
1768470 ATGAACATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 7 0.21
24 13 0.39
25 9 0.27
26 4 0.12
ACGTcount: A:0.39, C:0.10, G:0.02, T:0.49
Consensus pattern (24 bp):
ATTTATTTAAATCAACCATATCTA
Found at i:1774920 original size:22 final size:22
Alignment explanation
Indices: 1774892--1774941 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
1774882 CGAAGGAAGC
1774892 AGTAAATAAGGGGATTCAATCT
1 AGTAAATAAGGGGATTCAATCT
1774914 AGTAAATAAGGGGATTCAATCT
1 AGTAAATAAGGGGATTCAATCT
1774936 AGTAAA
1 AGTAAA
1774942 ATAATAGTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.44, C:0.08, G:0.22, T:0.26
Consensus pattern (22 bp):
AGTAAATAAGGGGATTCAATCT
Done.