Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005510.1 Hibiscus syriacus cultivar Beakdansim tig00012722_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: 41041
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Found at i:10701 original size:13 final size:13
Alignment explanation
Indices: 10664--10693 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
10654 TGGGAAATTG
*
10664 TTTTATTTTTTAA
1 TTTTATTTTTCAA
10677 TTTTATTTTTCAA
1 TTTTATTTTTCAA
10690 TTTT
1 TTTT
10694 TTTGTTCACG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTATTTTTCAA
Found at i:16163 original size:32 final size:31
Alignment explanation
Indices: 16126--16185 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
16116 GCCCATTTTA
* *
16126 ATTCAATTCTATT-TATTCAGATTTTATATTAT
1 ATTCAAATC-ATTATATTC-GAATTTATATTAT
16158 ATTCAAATCATTATATTCGAATTTATAT
1 ATTCAAATCATTATATTCGAATTTATAT
16186 CAAATTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 12 0.48
32 13 0.52
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.52
Consensus pattern (31 bp):
ATTCAAATCATTATATTCGAATTTATATTAT
Found at i:25575 original size:20 final size:20
Alignment explanation
Indices: 25550--25590 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
25540 TTTTAATTTC
25550 TTTTACATCTTAATTATTGA
1 TTTTACATCTTAATTATTGA
25570 TTTTACATCTTAATTATTGA
1 TTTTACATCTTAATTATTGA
25590 T
1 T
25591 AAAGATGGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.10, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTTACATCTTAATTATTGA
Found at i:38217 original size:2 final size:2
Alignment explanation
Indices: 38210--38257 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
38200 TTTTTAATGA
38210 AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38251 AT AT AT A
1 AT AT AT A
38258 ATTTGTGTTC
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38540 original size:81 final size:80
Alignment explanation
Indices: 38381--38541 Score: 191
Period size: 81 Copynumber: 2.0 Consensus size: 80
38371 ATGTTCTCTC
* * * *
38381 AATATTCGAGAACATGTTTTTTTAAAGTATGTGAGCATCTTTATTTAACGTTTGTTTAATGTTCA
1 AATATTCGAGAACATGTTTTTTTAAAGTATGTAAACATCTTTATTTAACGTTCGTTTAATATTCA
**
38446 ATATCATGCTCATTT
66 ATAAAATGCTCATTT
* * *
38461 AATATTC-ACGAATATGTTTTATTTAAAGTATGTAAACATGTTTATTTATCGTTCGTTTAATATT
1 AATATTCGA-GAACATGTTTT-TTTAAAGTATGTAAACATCTTTATTTAACGTTCGTTTAATATT
*
38525 CACA-AAAATGTTCATTT
64 CA-ATAAAATGCTCATTT
38542 GACGTATGTC
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
79 1 0.01
80 17 0.25
81 49 0.72
82 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.46
Consensus pattern (80 bp):
AATATTCGAGAACATGTTTTTTTAAAGTATGTAAACATCTTTATTTAACGTTCGTTTAATATTCA
ATAAAATGCTCATTT
Found at i:38565 original size:57 final size:58
Alignment explanation
Indices: 38458--38578 Score: 163
Period size: 57 Copynumber: 2.1 Consensus size: 58
38448 ATCATGCTCA
* * * * *
38458 TTTAATATTCACGAATATGTTTTATTTAAAGTATGTAAACATGTTTATTTATCGTTCG
1 TTTAATATTCACAAAAATGTTTCATTTAAAGTATGTAAACATGTTAATTTAACGTTCG
* * *
38516 TTTAATATTCACAAAAATG-TTCATTTGACGTATGTCAACATGTTAATTTAACGTTCG
1 TTTAATATTCACAAAAATGTTTCATTTAAAGTATGTAAACATGTTAATTTAACGTTCG
38573 TTTAAT
1 TTTAAT
38579 GTTCGATAAC
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
57 38 0.69
58 17 0.31
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (58 bp):
TTTAATATTCACAAAAATGTTTCATTTAAAGTATGTAAACATGTTAATTTAACGTTCG
Found at i:38888 original size:2 final size:2
Alignment explanation
Indices: 38881--38907 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
38871 CTGGGCATTA
38881 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
38908 ACTCCATAAA
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:39408 original size:28 final size:26
Alignment explanation
Indices: 39357--39408 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
39347 CATGAGTTGA
*
39357 TTTTTAAAAAATAAATTATTTAAATT
1 TTTTTAAAAAATAAATTAGTTAAATT
*
39383 TTTTTAAAACAATAAAATTGGTTAAA
1 TTTTTAAAA-AAT-AAATTAGTTAAA
39409 CTATACAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 9 0.41
27 3 0.14
28 10 0.45
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (26 bp):
TTTTTAAAAAATAAATTAGTTAAATT
Done.