Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007126.1 Hibiscus syriacus cultivar Beakdansim tig00018617_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: 141974
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
File 2 of 2
Found at i:131195 original size:113 final size:118
Alignment explanation
Indices: 131021--131229 Score: 302
Period size: 113 Copynumber: 1.8 Consensus size: 118
131011 ATCGAGTGAT
* *
131021 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTAT
1 AGGTCGAACAAGCTCTTATCATTATGAACTTCTTCTCCCTCTGTAGGATGAGTTCTTCTCATTAT
*
131086 GAACTCTCCATTGAAAATGCTGATCCACCTCTTTTTGTGATGGAACCAAACCA
66 GAACTCTCCACTGAAAATGCTGATCCACCTCTTTTTGTGATGGAACCAAACCA
* * *
131139 AGGTTGAACAAGTTCTTATTATTATGAACTT-TT-T-CCT-T-TAGGATGAGTTCTTCTCATTAT
1 AGGTCGAACAAGCTCTTATCATTATGAACTTCTTCTCCCTCTGTAGGATGAGTTCTTCTCATTAT
* * *
131199 GAACTCTTCACTGGAAATGTTGATCCACCTC
66 GAACTCTCCACTGAAAATGCTGATCCACCTC
131230 CTTCTGCGGT
Statistics
Matches: 82, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
113 48 0.59
114 1 0.01
115 3 0.04
116 1 0.01
117 2 0.02
118 27 0.33
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (118 bp):
AGGTCGAACAAGCTCTTATCATTATGAACTTCTTCTCCCTCTGTAGGATGAGTTCTTCTCATTAT
GAACTCTCCACTGAAAATGCTGATCCACCTCTTTTTGTGATGGAACCAAACCA
Found at i:132097 original size:10 final size:10
Alignment explanation
Indices: 132077--132115 Score: 60
Period size: 10 Copynumber: 3.7 Consensus size: 10
132067 TCCTTCTTCA
132077 TTTTTTCTTTC
1 TTTTTT-TTTC
132088 TTTTTTTTTC
1 TTTTTTTTTC
132098 TTTTTTTTTC
1 TTTTTTTTTC
132108 TTCTTTTT
1 TT-TTTTT
132116 ATTTTTTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 16 0.59
11 11 0.41
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:132105 original size:23 final size:26
Alignment explanation
Indices: 132077--132136 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
132067 TCCTTCTTCA
*
132077 TTTTTTCTT-TCTTT-TTTTTTCTTT
1 TTTTTTCTTCTCTTTATTTTTTCATT
*
132101 TTTTTTCTTCTTTTTATTTTTTCATT
1 TTTTTTCTTCTCTTTATTTTTTCATT
132127 TTTTTTCTTC
1 TTTTTTCTTC
132137 AAGCATAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 9 0.28
25 4 0.12
26 19 0.59
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.83
Consensus pattern (26 bp):
TTTTTTCTTCTCTTTATTTTTTCATT
Found at i:132121 original size:20 final size:19
Alignment explanation
Indices: 132076--132132 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
132066 CTCCTTCTTC
132076 ATTTTTTCTTTCTTTTTTT
1 ATTTTTTCTTTCTTTTTTT
* *
132095 TTCTTTTTTTTTCTTCTTTTT
1 AT-TTTTTCTTTCTT-TTTTT
132116 ATTTTTTCATTT-TTTTT
1 ATTTTTTC-TTTCTTTTT
132133 CTTCAAGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
19 4 0.13
20 18 0.58
21 9 0.29
ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84
Consensus pattern (19 bp):
ATTTTTTCTTTCTTTTTTT
Found at i:132137 original size:13 final size:13
Alignment explanation
Indices: 132070--132137 Score: 65
Period size: 13 Copynumber: 5.5 Consensus size: 13
132060 CGAACCCTCC
132070 TTCTTCATTTTTT
1 TTCTTCATTTTTT
*
132083 CT-TTC--TTTTT
1 TTCTTCATTTTTT
*
132093 TT-TTCTTTTTTT
1 TTCTTCATTTTTT
132105 TTCTTC-TTTTTAT
1 TTCTTCATTTTT-T
*
132118 TTTTTCATTTTTT
1 TTCTTCATTTTTT
132131 TTCTTCA
1 TTCTTCA
132138 AGCATAGTAC
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
10 9 0.20
12 15 0.33
13 17 0.37
14 5 0.11
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (13 bp):
TTCTTCATTTTTT
Done.