Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006154.1 Hibiscus syriacus cultivar Beakdansim tig00014623_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: 160070
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:139140 original size:8 final size:8
Alignment explanation
Indices: 139119--139159 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
139109 TAATCTTTTA
*
139119 TTATTGTT
1 TTATTATT
139127 TT-TTATT
1 TTATTATT
139134 ATT-TTATT
1 -TTATTATT
139142 TTATTATT
1 TTATTATT
139150 TTATTATT
1 TTATTATT
139158 TT
1 TT
139160 CTTTTTCCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
7 6 0.20
8 24 0.80
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (8 bp):
TTATTATT
Found at i:139140 original size:21 final size:21
Alignment explanation
Indices: 139114--139164 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
139104 TTAACTAATC
*
139114 TTTTATTATTGTT-TTTTATTA
1 TTTTATT-TTATTATTTTATTA
139135 TTTTATTTTATTATTTTATTA
1 TTTTATTTTATTATTTTATTA
*
139156 TTTTCTTTT
1 TTTTATTTT
139165 TCCTTCTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (21 bp):
TTTTATTTTATTATTTTATTA
Found at i:139143 original size:26 final size:27
Alignment explanation
Indices: 139069--139149 Score: 76
Period size: 26 Copynumber: 3.0 Consensus size: 27
139059 TTTACTACAT
*
139069 TTTTTTATTATTTTTATTCTTATTTATTTG
1 TTTTTTATTACTTTTATT-TTA-TTA-TTG
* ** *
139099 TTTTTT-TAACTAATCTTTTATTATTG
1 TTTTTTATTACTTTTATTTTATTATTG
139125 TTTTTTATTA-TTTTATTTTATTATT
1 TTTTTTATTACTTTTATTTTATTATT
139150 TTATTATTTT
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
26 21 0.51
27 5 0.12
28 3 0.07
29 6 0.15
30 6 0.15
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.74
Consensus pattern (27 bp):
TTTTTTATTACTTTTATTTTATTATTG
Found at i:139327 original size:12 final size:13
Alignment explanation
Indices: 139305--139333 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
139295 GAATCGAGTT
139305 TTTTAAATTTTAA
1 TTTTAAATTTTAA
139318 TTTT-AATTTTAA
1 TTTTAAATTTTAA
139330 TTTT
1 TTTT
139334 CGCAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:147632 original size:26 final size:28
Alignment explanation
Indices: 147593--147648 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 28
147583 GATGATGATA
147593 ATAAATATTTTATA-ATTT-AAAAAATT
1 ATAAATATTTTATATATTTGAAAAAATT
*
147619 ATAAAT-TTTATATATTTTTGAAAAAATT
1 ATAAATATTT-TATATATTTGAAAAAATT
147647 AT
1 AT
147649 TGACTTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 3 0.12
26 10 0.38
27 3 0.12
28 10 0.38
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (28 bp):
ATAAATATTTTATATATTTGAAAAAATT
Found at i:148231 original size:17 final size:17
Alignment explanation
Indices: 148204--148244 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
148194 TAGCTTTACA
148204 TTATATTTTTATTGAATT
1 TTAT-TTTTTATTGAATT
*
148222 TTATTTTTTATTGCATT
1 TTATTTTTTATTGAATT
148239 TTATTT
1 TTATTT
148245 ATTTTTGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (17 bp):
TTATTTTTTATTGAATT
Found at i:152910 original size:3 final size:3
Alignment explanation
Indices: 152904--152937 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
152894 ACCATCATCA
* *
152904 TCG TCG TCG TCG TCG TCG TTG TCG TCG TCA TCG T
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG T
152938 GAGCAGCTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.03, C:0.29, G:0.29, T:0.38
Consensus pattern (3 bp):
TCG
Found at i:154993 original size:23 final size:23
Alignment explanation
Indices: 154961--155006 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
154951 TAAATAATTT
154961 AAATAGTTAAATAAAATAATAATA
1 AAATAGTTAAATAAAATAA-AATA
*
154985 AAATA-TTAAATATAATAAAATA
1 AAATAGTTAAATAAAATAAAATA
155007 TACCTTAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 4 0.19
23 12 0.57
24 5 0.24
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (23 bp):
AAATAGTTAAATAAAATAAAATA
Found at i:155001 original size:17 final size:18
Alignment explanation
Indices: 154974--155007 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
154964 TAGTTAAATA
154974 AAATAATAATAAAATATT
1 AAATAATAATAAAATATT
154992 AAAT-ATAATAAAATAT
1 AAATAATAATAAAATAT
155008 ACCTTAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AAATAATAATAAAATATT
Found at i:155036 original size:19 final size:19
Alignment explanation
Indices: 155012--155050 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
155002 AAATATACCT
155012 TAAAGA-TATATAAGAGAAA
1 TAAAGAGTAT-TAAGAGAAA
*
155031 TAAAGAGTATTGAGAGAAA
1 TAAAGAGTATTAAGAGAAA
155050 T
1 T
155051 TGAGAGGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.56, C:0.00, G:0.21, T:0.23
Consensus pattern (19 bp):
TAAAGAGTATTAAGAGAAA
Found at i:156037 original size:14 final size:14
Alignment explanation
Indices: 156018--156045 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
156008 TAATTTTAAA
156018 TAAAATTTAATATT
1 TAAAATTTAATATT
156032 TAAAATTTAATATT
1 TAAAATTTAATATT
156046 AGTATAAGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAAAATTTAATATT
Found at i:158177 original size:24 final size:23
Alignment explanation
Indices: 158119--158177 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 23
158109 TTACAAGGAT
* * *
158119 ATGTGATATGTGAAAGTGAATCAT
1 ATGT-ATATGTGAAAATGAAGCAC
158143 ATGT-TATGTGAAAATGAGAGCAC
1 ATGTATATGTGAAAATGA-AGCAC
158166 ATGTATATGTGA
1 ATGTATATGTGA
158178 TTATGAATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 12 0.40
23 7 0.23
24 11 0.37
ACGTcount: A:0.37, C:0.05, G:0.25, T:0.32
Consensus pattern (23 bp):
ATGTATATGTGAAAATGAAGCAC
Found at i:159953 original size:25 final size:24
Alignment explanation
Indices: 159902--159959 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 24
159892 TAAATTTATT
159902 TTAAGAAATTATTAAAAATACCTTA
1 TTAA-AAATTATTAAAAATACCTTA
159927 TTAGAAAATTATTTAAGAAATA-C-TA
1 TTA-AAAATTA-TTAA-AAATACCTTA
159952 TTAAAAAT
1 TTAAAAAT
159960 AACTTATAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
24 5 0.17
25 14 0.47
26 6 0.20
27 5 0.17
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.36
Consensus pattern (24 bp):
TTAAAAATTATTAAAAATACCTTA
Done.