Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005261.1 Hibiscus syriacus cultivar Beakdansim tig00011899_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: 49177
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:6879 original size:30 final size:30
Alignment explanation
Indices: 6852--6912 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
6842 TTTCAGAAGA
*
6852 AGCTAACAAAACAGAGACAACCCCAGAAAC
1 AGCTAACAAAACAGAGACAACCACAGAAAC
* *
6882 AGCTAACGAAACAGAGGCAACCACAGAAAC
1 AGCTAACAAAACAGAGACAACCACAGAAAC
6912 A
1 A
6913 TCGAAGCTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.52, C:0.28, G:0.16, T:0.03
Consensus pattern (30 bp):
AGCTAACAAAACAGAGACAACCACAGAAAC
Found at i:13156 original size:21 final size:21
Alignment explanation
Indices: 13066--13163 Score: 81
Period size: 21 Copynumber: 4.7 Consensus size: 21
13056 AATCCATCGA
**
13066 GAAAAATGATCGATCCCTTCC
1 GAAAAATGATCGATCCCTTTG
*
13087 GAAAAATGATTGATCCCTTTG
1 GAAAAATGATCGATCCCTTTG
* * * * ****
13108 GTATAACGGTCGAAATATTT-
1 GAAAAATGATCGATCCCTTTG
13128 GAAAAATGATCGATCCCTTTG
1 GAAAAATGATCGATCCCTTTG
*
13149 GTAAAATGATCGATC
1 GAAAAATGATCGATC
13164 TGTTATGCCT
Statistics
Matches: 55, Mismatches: 21, Indels: 2
0.71 0.27 0.03
Matches are distributed among these distances:
20 12 0.22
21 43 0.78
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (21 bp):
GAAAAATGATCGATCCCTTTG
Found at i:13947 original size:21 final size:21
Alignment explanation
Indices: 13905--13947 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
13895 TTTATGGGCT
*
13905 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
13926 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
13947 A
1 A
13948 ACGAATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:14000 original size:20 final size:20
Alignment explanation
Indices: 13975--14012 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
13965 TAACGCTAGA
*
13975 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
13995 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
14013 TAATAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:14669 original size:103 final size:103
Alignment explanation
Indices: 14485--14703 Score: 357
Period size: 103 Copynumber: 2.1 Consensus size: 103
14475 GTAGAGGGTC
* * * * * *
14485 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAATATGTGTGAGGTCTAGTGAGACACCTAC
1 TATGTGGTCCTTAGGAACATATATGTATTCTTTAGAACATGTGTGAGGTCTAGTGAGACACATAC
*
14550 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
14588 TATGTGGTCCTTAGGAACATATATGTATTCTTTAGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTAGGAACATATATGTATTCTTTAGAACATGTGTGAGGTCTAGTGAGACACATAC
*
14653 TTGATCCTTGGCATATGTATGTGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
14691 TATGTGGTCCTTA
1 TATGTGGTCCTTA
14704 TGGACATTAT
Statistics
Matches: 107, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTAGGAACATATATGTATTCTTTAGAACATGTGTGAGGTCTAGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:14770 original size:23 final size:23
Alignment explanation
Indices: 14721--14781 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 23
14711 TATTATATGG
* *
14721 CACTACGGTGCAATTCTACGCGG
1 CACTACGGTGCAATTCTAAGCGC
* * *
14744 CACTCCGGTGCAATTTTAAGTGC
1 CACTACGGTGCAATTCTAAGCGC
**
14767 CACTTGGGTGCAATT
1 CACTACGGTGCAATT
14782 ATACGAGCTG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.21, C:0.26, G:0.25, T:0.28
Consensus pattern (23 bp):
CACTACGGTGCAATTCTAAGCGC
Found at i:33347 original size:21 final size:21
Alignment explanation
Indices: 33321--33360 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
33311 GTCCATCGTT
33321 GGCTTGTATCGCAACGCTGCC
1 GGCTTGTATCGCAACGCTGCC
*
33342 GGCTTGTATCGTAACGCTG
1 GGCTTGTATCGCAACGCTG
33361 ATCATACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.28, G:0.30, T:0.28
Consensus pattern (21 bp):
GGCTTGTATCGCAACGCTGCC
Found at i:43736 original size:15 final size:13
Alignment explanation
Indices: 43708--43732 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43698 CATAGATTAA
43708 TAAAAAAATTATT
1 TAAAAAAATTATT
43721 TAAAAAAATTAT
1 TAAAAAAATTAT
43733 ATTTTAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TAAAAAAATTATT
Found at i:44105 original size:18 final size:16
Alignment explanation
Indices: 44068--44114 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
44058 TCACATTCAA
*
44068 ATTTTATTTAAAAATT
1 ATTTTATTTAAAAAAT
*
44084 ATTTTA---AAATAAT
1 ATTTTATTTAAAAAAT
44097 ATTTTATTTAAAAAAT
1 ATTTTATTTAAAAAAT
44113 AT
1 AT
44115 ATATGTGACA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
13 11 0.44
16 14 0.56
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTTTATTTAAAAAAT
Found at i:45396 original size:16 final size:16
Alignment explanation
Indices: 45364--45404 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
45354 GTTTACTTTA
*
45364 GAATGATT-AAGTGCT
1 GAATGATTCAAATGCT
45379 GAATGATTCAAATGCT
1 GAATGATTCAAATGCT
45395 GAATGATTCA
1 GAATGATTCA
45405 GAGACTATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.32
Consensus pattern (16 bp):
GAATGATTCAAATGCT
Done.