Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006678.1 Hibiscus syriacus cultivar Beakdansim tig00016563_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: 1086949
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
File 5 of 5
Found at i:1054023 original size:32 final size:32
Alignment explanation
Indices: 1053982--1054043 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
1053972 ATTATGCTTG
1053982 AAGAAAAAAAAAA-AAAAAAAAAAGAAAAAGAA
1 AAGAAAAAAAAAAGAAAAAAAAAA-AAAAAGAA
*
1054014 AAGAAAAAAAAAAGAAAAAAAGAAAAAAAG
1 AAGAAAAAAAAAAGAAAAAAAAAAAAAAAG
1054044 GGGTCAAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 19 0.68
33 9 0.32
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (32 bp):
AAGAAAAAAAAAAGAAAAAAAAAAAAAAAGAA
Found at i:1054042 original size:11 final size:11
Alignment explanation
Indices: 1053982--1054034 Score: 90
Period size: 11 Copynumber: 4.9 Consensus size: 11
1053972 ATTATGCTTG
1053982 AAGAAAAAAAA
1 AAGAAAAAAAA
1053993 AA-AAAAAAAA
1 AAGAAAAAAAA
*
1054003 AAGAAAAAGAA
1 AAGAAAAAAAA
1054014 AAGAAAAAAAA
1 AAGAAAAAAAA
1054025 AAGAAAAAAA
1 AAGAAAAAAA
1054035 GAAAAAAAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
10 10 0.26
11 29 0.74
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:1055101 original size:52 final size:52
Alignment explanation
Indices: 1054977--1055426 Score: 777
Period size: 52 Copynumber: 8.8 Consensus size: 52
1054967 TATGTGCTCA
* *
1054977 ATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGGTTAGA-AGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1055028 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1055080 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
* * *
1055132 ATAGCATCTTCTGGAAGTGTTATTTAAGTTATCTGATCTGGTTAGA-AGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1055183 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
1055235 ATAGCATCTTCTGGAAGTGTTATTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1055287 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1055339 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC----TGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
* * *
1055387 ATAGCATCTTCTTGAAGTTTTCTTTGAGTTATCTAATCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1055427 ATTAGACATA
Statistics
Matches: 382, Mismatches: 13, Indels: 9
0.95 0.03 0.02
Matches are distributed among these distances:
48 45 0.12
51 92 0.24
52 245 0.64
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (52 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
Found at i:1055261 original size:155 final size:155
Alignment explanation
Indices: 1054977--1055426 Score: 784
Period size: 155 Copynumber: 2.9 Consensus size: 155
1054967 TATGTGCTCA
1054977 ATAGCATCTTCTGGAAGTGTTCTTTGAA-TTATCTGATCTGGTTAGAAGAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTT-AAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTG
1055041 GAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTG
65 GAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTG
1055106 AGTTATCTGATCTGGTTGGACAGAAC
130 AGTTATCTGATCTGGTTGGACAGAAC
*
1055132 ATAGCATCTTCTGGAAGTGTTATTTAAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGG
1 ATAGCATCTTCTGGAAGTGTTCTTTAAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGG
*
1055197 AAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTATTTGA
66 AAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTGA
1055262 GTTATCTGATCTGGTTGGACAGAAC
131 GTTATCTGATCTGGTTGGACAGAAC
* *
1055287 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTAAGTTATCTGATCTGGTTAGA-AGAACATAGCATCTTCTG
* *
1055352 GAAGTGTTCTTTGAGTTATCTGATC----TGGACAGAACATAGCATCTTCTTGAAGTTTTCTTTG
65 GAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTG
*
1055413 AGTTATCTAATCTG
130 AGTTATCTGATCTG
1055427 ATTAGACATA
Statistics
Matches: 284, Mismatches: 9, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
152 46 0.16
154 2 0.01
155 193 0.68
156 43 0.15
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (155 bp):
ATAGCATCTTCTGGAAGTGTTCTTTAAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGG
AAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTGA
GTTATCTGATCTGGTTGGACAGAAC
Found at i:1055331 original size:207 final size:203
Alignment explanation
Indices: 1054977--1055432 Score: 786
Period size: 207 Copynumber: 2.2 Consensus size: 203
1054967 TATGTGCTCA
*
1054977 ATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGG
*
1055042 AAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTGA
66 AAGTGTTATTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTGA
1055107 GTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTATTTAAGTTATCTGATCTG
131 GTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTATTTAAGTTATCTGATCTG
1055172 GTTAGAAGAAC
196 G--A-AAGAAC
*
1055183 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAACATAGCATCTTCTG
1055248 GAAGTGTTATTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTG
65 GAAGTGTTATTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTG
* *
1055313 AGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
130 AGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTATTTAAGTTATCTGATCT
*
1055378 GGACAGAAC
195 GGAAAGAAC
* * * *
1055387 ATAGCATCTTCTTGAAGTTTTCTTTGAGTTATCTAATCTGATTAGA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA
1055433 CATAATCAAA
Statistics
Matches: 238, Mismatches: 11, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
204 46 0.19
205 1 0.00
206 44 0.18
207 147 0.62
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (203 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGG
AAGTGTTATTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTGA
GTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTATTTAAGTTATCTGATCTG
GAAAGAAC
Found at i:1056283 original size:119 final size:118
Alignment explanation
Indices: 1056061--1056392 Score: 539
Period size: 119 Copynumber: 2.8 Consensus size: 118
1056051 CAAAGATTCA
* *
1056061 AATTCATCACTTGATGGATCATCATTTCCAAAGAAAGAGTTCATAATGAGAAGAACTCGTCATCT
1 AATTCATCAATTGATGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCT
1056126 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
66 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
*
1056179 AATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATC
1 AATTCATC-AATTGATGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATC
*
1056244 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTG
65 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
* * * *
1056298 AATTCATCAGTTGATGGATCAACATTACCAG-GTAA-AGTTCATAATGAGAAGAA--C-TCATCT
1 AATTCATCAATTGATGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCT
*
1056358 GAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACT
66 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
1056393 CATCAAGAGC
Statistics
Matches: 203, Mismatches: 10, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
113 39 0.19
114 1 0.00
116 18 0.09
117 3 0.01
118 28 0.14
119 114 0.56
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (118 bp):
AATTCATCAATTGATGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCT
GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
Found at i:1056647 original size:3 final size:3
Alignment explanation
Indices: 1056639--1056769 Score: 235
Period size: 3 Copynumber: 43.7 Consensus size: 3
1056629 TTTTTATCCA
*
1056639 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
1056687 TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1056735 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1056770 ATTTATATTA
Statistics
Matches: 122, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 122 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1071905 original size:20 final size:20
Alignment explanation
Indices: 1071869--1071906 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1071859 ATCCTATTCT
**
1071869 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
1071889 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1071907 GTGAACCAAA
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:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Done.