Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002014.1 Hibiscus syriacus cultivar Beakdansim tig00004114_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: 93993
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:11094 original size:20 final size:20
Alignment explanation
Indices: 11043--11096 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
11033 AATGTATAGA
* *
11043 AAAACAGAAATAACAATAGT
1 AAAACAAAAATAACAATAAT
*
11063 AATACCTTAAAAATAACAATAAT
1 AA-AAC--AAAAATAACAATAAT
11086 AAAACAAAAAT
1 AAAACAAAAAT
11097 TTACCGTCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
20 8 0.30
21 2 0.07
22 2 0.07
23 15 0.56
ACGTcount: A:0.67, C:0.11, G:0.04, T:0.19
Consensus pattern (20 bp):
AAAACAAAAATAACAATAAT
Found at i:21558 original size:51 final size:53
Alignment explanation
Indices: 21497--21649 Score: 174
Period size: 51 Copynumber: 3.0 Consensus size: 53
21487 GACAGTCTCA
*
21497 CCGAGGAAGAA-CCGATGAAG-ACAAAAAAGTCCAAACCCGGGAAAAAGAAGT
1 CCGAGAAAGAATCCGATGAAGTACAAAAAAGTCCAAACCCGGGAAAAAGAAGT
** * *
21548 CCGAGAAAGAATCC-ATG-AGTACGGAAAAGTACAAACCCAGGAAAAAGAAGT
1 CCGAGAAAGAATCCGATGAAGTACAAAAAAGTCCAAACCCGGGAAAAAGAAGT
* * * * *
21599 CCGAGAAAGAATCCG--CAAGTGCAAAAAGGTCCAAACCTGGGAAAAATAAGT
1 CCGAGAAAGAATCCGATGAAGTACAAAAAAGTCCAAACCCGGGAAAAAGAAGT
21650 AATCTAAGTA
Statistics
Matches: 84, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
50 2 0.02
51 80 0.95
52 2 0.02
ACGTcount: A:0.48, C:0.19, G:0.24, T:0.09
Consensus pattern (53 bp):
CCGAGAAAGAATCCGATGAAGTACAAAAAAGTCCAAACCCGGGAAAAAGAAGT
Found at i:24954 original size:19 final size:19
Alignment explanation
Indices: 24927--24970 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
24917 TGCACCCCAG
* *
24927 ATATCTCTTCGTAGCTGGT
1 ATATATCTTCGTAACTGGT
*
24946 ATATATCTTCTTAACTGGT
1 ATATATCTTCGTAACTGGT
24965 ATATAT
1 ATATAT
24971 AAAACAGTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.45
Consensus pattern (19 bp):
ATATATCTTCGTAACTGGT
Found at i:49874 original size:15 final size:15
Alignment explanation
Indices: 49854--49890 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
49844 ATATTTAGCT
49854 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
49869 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
49884 GGGCGGG
1 GGGCGGG
49891 TAATGTCTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.05, C:0.19, G:0.70, T:0.05
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:55394 original size:25 final size:25
Alignment explanation
Indices: 55346--55394 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
55336 AAATTTATAA
*
55346 AATTTTAGAGAAAATAAACTTAAAG
1 AATTTTAGAGAAAATAAACATAAAG
*
55371 AATTTTATAGAAACATAAA-ATAAA
1 AATTTTAGAGAAA-ATAAACATAAA
55395 TTACTTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.59, C:0.04, G:0.08, T:0.29
Consensus pattern (25 bp):
AATTTTAGAGAAAATAAACATAAAG
Found at i:72254 original size:34 final size:34
Alignment explanation
Indices: 72205--72277 Score: 119
Period size: 34 Copynumber: 2.1 Consensus size: 34
72195 GAAACCATTC
* * *
72205 CATTTTCAACTATCTCACTGCAGCAACTTTAAAT
1 CATTATCAACAATCTCACTGCAGCAACTTCAAAT
72239 CATTATCAACAATCTCACTGCAGCAACTTCAAAT
1 CATTATCAACAATCTCACTGCAGCAACTTCAAAT
72273 CATTA
1 CATTA
72278 GCATATCTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.36, C:0.27, G:0.05, T:0.32
Consensus pattern (34 bp):
CATTATCAACAATCTCACTGCAGCAACTTCAAAT
Found at i:77148 original size:24 final size:24
Alignment explanation
Indices: 77020--77131 Score: 154
Period size: 24 Copynumber: 4.7 Consensus size: 24
77010 ATTTGAATTA
77020 TGATCTGATACTTGACATGGATTC
1 TGATCTGATACTTGACATGGATTC
77044 TGATCTGATA-TCTGACATGGATTC
1 TGATCTGATACT-TGACATGGATTC
* *
77068 TGATCTAATACTTGACTTGGATTC
1 TGATCTGATACTTGACATGGATTC
* * *
77092 TGATCTGTTACTTGACCTGGATTT
1 TGATCTGATACTTGACATGGATTC
*
77116 TGATATGATACTTGAC
1 TGATCTGATACTTGAC
77132 GTGAATTATG
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.01
24 76 0.97
25 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (24 bp):
TGATCTGATACTTGACATGGATTC
Found at i:77264 original size:35 final size:35
Alignment explanation
Indices: 77218--77284 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
77208 AAATGCATGG
* *
77218 AGGTTCCTCGGCTGTGTGCTTATGGCCTTACTTAC
1 AGGTTCCTCGGCTGTGTGCTCAGGGCCTTACTTAC
77253 AGGTTCCTCGGCTGTGTGCTCAGGGCCTTACT
1 AGGTTCCTCGGCTGTGTGCTCAGGGCCTTACT
77285 GGACGTGACG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.10, C:0.27, G:0.28, T:0.34
Consensus pattern (35 bp):
AGGTTCCTCGGCTGTGTGCTCAGGGCCTTACTTAC
Found at i:81874 original size:24 final size:24
Alignment explanation
Indices: 81746--81857 Score: 145
Period size: 24 Copynumber: 4.7 Consensus size: 24
81736 ATTTGAATTA
81746 TGATCTGATACTTGACATGGATTC
1 TGATCTGATACTTGACATGGATTC
81770 TGATCTGATA-TCTGACATGGATTC
1 TGATCTGATACT-TGACATGGATTC
** *
81794 TGATCTTTTACTTGACTTGGATTC
1 TGATCTGATACTTGACATGGATTC
* * *
81818 TGATCTGTTACTTGACCTGGATTT
1 TGATCTGATACTTGACATGGATTC
*
81842 TGATATGATACTTGAC
1 TGATCTGATACTTGAC
81858 GTGAATTATG
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.01
24 76 0.97
25 1 0.01
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.42
Consensus pattern (24 bp):
TGATCTGATACTTGACATGGATTC
Found at i:84945 original size:28 final size:27
Alignment explanation
Indices: 84895--84967 Score: 69
Period size: 27 Copynumber: 2.6 Consensus size: 27
84885 TGGGGAAAGG
84895 ATTTTCAATAAAAAAAATTAATTATTAATT
1 ATTTT-AATAAAAAAAA-TAATTATT-ATT
*
84925 ATTTTAATAAAAAAACA-AATTGTTATT
1 ATTTTAATAAAAAAA-ATAATTATTATT
*
84952 -TTAGTAATAAAAAAAA
1 ATT-TTAATAAAAAAAA
84968 ATCATGCCTC
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
26 3 0.08
27 14 0.36
28 6 0.15
29 10 0.26
30 6 0.15
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (27 bp):
ATTTTAATAAAAAAAATAATTATTATT
Found at i:84952 original size:24 final size:25
Alignment explanation
Indices: 84923--84969 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
84913 TAATTATTAA
*
84923 TTATTTTAATAA-AAAAACAAATTG
1 TTATTTTAATAATAAAAAAAAATTG
*
84947 TTATTTTAGTAATAAAAAAAAAT
1 TTATTTTAATAATAAAAAAAAAT
84970 CATGCCTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.38
Consensus pattern (25 bp):
TTATTTTAATAATAAAAAAAAATTG
Found at i:86188 original size:29 final size:30
Alignment explanation
Indices: 86156--86213 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
86146 AAATATGGTT
86156 TGAAACAAA-TAAAAGTCTAAGTACTAAAA
1 TGAAACAAACTAAAAGTCTAAGTACTAAAA
* * *
86185 TGAAACAAACTGATAGTTTAAGTACTAAA
1 TGAAACAAACTAAAAGTCTAAGTACTAAA
86214 CATCTTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.53, C:0.10, G:0.12, T:0.24
Consensus pattern (30 bp):
TGAAACAAACTAAAAGTCTAAGTACTAAAA
Done.