Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004809.1 Hibiscus syriacus cultivar Beakdansim tig00010830_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: 51882
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:872 original size:11 final size:11
Alignment explanation
Indices: 849--886 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
839 ATCCTTCGAG
849 TATAAAA-AAT
1 TATAAAATAAT
859 TATAAAATAAT
1 TATAAAATAAT
870 TATAAAATTAA-
1 TATAAAA-TAAT
881 TATAAA
1 TATAAA
887 GGCTTAATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 7 0.27
11 16 0.62
12 3 0.12
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
TATAAAATAAT
Found at i:5180 original size:29 final size:30
Alignment explanation
Indices: 5147--5208 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
5137 TCATCCATCC
*
5147 ATATAATA-TTTCATCATCTTCTACATTTA
1 ATATAATATTTTCATCATCTTCCACATTTA
*
5176 ATATAATATTTTCATCATTTTCCACATTTA
1 ATATAATATTTTCATCATCTTCCACATTTA
5206 ATA
1 ATA
5209 ATTTTTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 8 0.27
30 22 0.73
ACGTcount: A:0.35, C:0.16, G:0.00, T:0.48
Consensus pattern (30 bp):
ATATAATATTTTCATCATCTTCCACATTTA
Found at i:16054 original size:17 final size:16
Alignment explanation
Indices: 16028--16061 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
16018 TTTCACTAAT
*
16028 AGAGGAAATATTACAA
1 AGAGGAAATAATACAA
16044 AGAGAGAAATAATACAA
1 AGAG-GAAATAATACAA
16061 A
1 A
16062 TAGCCTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.62, C:0.06, G:0.18, T:0.15
Consensus pattern (16 bp):
AGAGGAAATAATACAA
Found at i:20662 original size:17 final size:16
Alignment explanation
Indices: 20636--20669 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
20626 TTTCACTAAT
*
20636 AGAGGAAATATTACAA
1 AGAGGAAATAATACAA
20652 AGAGAGAAATAATACAA
1 AGAG-GAAATAATACAA
20669 A
1 A
20670 TAGCCTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.62, C:0.06, G:0.18, T:0.15
Consensus pattern (16 bp):
AGAGGAAATAATACAA
Found at i:23958 original size:91 final size:91
Alignment explanation
Indices: 23803--23986 Score: 359
Period size: 91 Copynumber: 2.0 Consensus size: 91
23793 CTGAAATGAC
23803 TAGATGAACCTGACTCAGAAATAGTCCAGGTTCACTGTATCATTATTCAGCTGTTATAACTCCCG
1 TAGATGAACCTGACTCAGAAATAGTCCAGGTTCACTGTATCATTATTCAGCTGTTATAACTCCCG
23868 AAATTATATCATGTAACCCCTGGAAT
66 AAATTATATCATGTAACCCCTGGAAT
*
23894 TAGATGAACCTGACTCAGAAATAGTCCAGGTTCATTGTATCATTATTCAGCTGTTATAACTCCCG
1 TAGATGAACCTGACTCAGAAATAGTCCAGGTTCACTGTATCATTATTCAGCTGTTATAACTCCCG
23959 AAATTATATCATGTAACCCCTGGAAT
66 AAATTATATCATGTAACCCCTGGAAT
23985 TA
1 TA
23987 AATCAAATAA
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 92 1.00
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (91 bp):
TAGATGAACCTGACTCAGAAATAGTCCAGGTTCACTGTATCATTATTCAGCTGTTATAACTCCCG
AAATTATATCATGTAACCCCTGGAAT
Found at i:24248 original size:6 final size:6
Alignment explanation
Indices: 24237--24303 Score: 134
Period size: 6 Copynumber: 11.2 Consensus size: 6
24227 GACACGTATT
24237 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
24285 ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG A
24304 AGCCGAGCCG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 61 1.00
ACGTcount: A:0.34, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:24314 original size:5 final size:5
Alignment explanation
Indices: 24304--24385 Score: 101
Period size: 5 Copynumber: 16.4 Consensus size: 5
24294 ACGACCACGA
*
24304 AGCCG AGCCG AGCCG AGCCG AGCCG AGCCG AGCCG AGCCG AGCCG TGCCG
1 AGCCG AGCCG AGCCG AGCCG AGCCG AGCCG AGCCG AGCCG AGCCG AGCCG
* * * * * *
24354 AGACG AGACG AGACG AGACG AGACG AGACG AG
1 AGCCG AGCCG AGCCG AGCCG AGCCG AGCCG AG
24386 ACGGACGGAC
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 74 1.00
ACGTcount: A:0.27, C:0.32, G:0.40, T:0.01
Consensus pattern (5 bp):
AGCCG
Found at i:24386 original size:5 final size:5
Alignment explanation
Indices: 24352--24396 Score: 76
Period size: 5 Copynumber: 9.4 Consensus size: 5
24342 CGAGCCGTGC
24352 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG-GA CG-GA CG
1 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG
24397 GCGGCGGCGG
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
4 8 0.20
5 32 0.80
ACGTcount: A:0.36, C:0.22, G:0.42, T:0.00
Consensus pattern (5 bp):
CGAGA
Found at i:25955 original size:38 final size:36
Alignment explanation
Indices: 25912--25987 Score: 89
Period size: 38 Copynumber: 2.1 Consensus size: 36
25902 TTACGAGAAT
* *
25912 ATGTGGAACATGTTAAATACGTTATCAATAAATTATTA
1 ATGTGGAACACGTTAAATACATTATCAAT--ATTATTA
** *
25950 ATGTGGAGGACGTTAACTACATTATCAATATTATTA
1 ATGTGGAACACGTTAAATACATTATCAATATTATTA
25986 AT
1 AT
25988 AAAGTATTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
36 9 0.27
38 24 0.73
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.37
Consensus pattern (36 bp):
ATGTGGAACACGTTAAATACATTATCAATATTATTA
Found at i:27174 original size:18 final size:19
Alignment explanation
Indices: 27139--27175 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
27129 CACAGAATGT
27139 AAGATTACCAGTGAGAATAA
1 AAGATTACCAG-GAGAATAA
27159 AAGATTACCA-GAGAATA
1 AAGATTACCAGGAGAATA
27176 TGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.51, C:0.11, G:0.19, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGAGAATAA
Found at i:39801 original size:15 final size:16
Alignment explanation
Indices: 39778--39819 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
39768 AAAAAAAAAT
39778 AAATATAAAATAAT-AA
1 AAAT-TAAAATAATAAA
* *
39794 AAATTAAATTACTAAA
1 AAATTAAAATAATAAA
39810 AAATTAAAAT
1 AAATTAAAAT
39820 GTTTATATGC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATTAAAATAATAAA
Found at i:41110 original size:41 final size:41
Alignment explanation
Indices: 41044--41124 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
41034 AATTTATAAT
*
41044 TAAACTATAATAATAAATATGTCATTAATATTCTTTTAAAAA
1 TAAACTATAATAATAAATATATCATTAATATT-TTTTAAAAA
* * *
41086 TAAACTAT-ATATTAAATTTATCATTGATATTTTTTAAAA
1 TAAACTATAATAATAAATATATCATTAATATTTTTTAAAA
41125 TAAGGACACC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 8 0.23
41 19 0.54
42 8 0.23
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.44
Consensus pattern (41 bp):
TAAACTATAATAATAAATATATCATTAATATTTTTTAAAAA
Found at i:48072 original size:2 final size:2
Alignment explanation
Indices: 48065--48097 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
48055 GCTTTTAAAC
48065 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
48098 GGTTATGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.