Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000151.1 Hibiscus syriacus cultivar Beakdansim tig00000268_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: 51304
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:8394 original size:21 final size:21
Alignment explanation
Indices: 8365--8404 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
8355 TGAGAATTGT
8365 TTTTAAAATAT-AAAAATGATA
1 TTTTAAAAT-TGAAAAATGATA
*
8386 TTTTGAAATTGAAAAATGA
1 TTTTAAAATTGAAAAATGA
8405 AAATAATCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.38
Consensus pattern (21 bp):
TTTTAAAATTGAAAAATGATA
Found at i:12245 original size:23 final size:22
Alignment explanation
Indices: 12219--12276 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 22
12209 TGTGCATAGA
12219 GTATCGATACCCCCTT-TGAATG
1 GTATCGATACCCCCTTCT-AATG
* *
12241 TGTATTGATA--CCCTTCTTATG
1 -GTATCGATACCCCCTTCTAATG
12262 GTATCGATACCCCCT
1 GTATCGATACCCCCT
12277 GTCGGGTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
20 8 0.28
21 8 0.28
22 5 0.17
23 8 0.28
ACGTcount: A:0.21, C:0.28, G:0.16, T:0.36
Consensus pattern (22 bp):
GTATCGATACCCCCTTCTAATG
Found at i:20086 original size:21 final size:21
Alignment explanation
Indices: 20057--20107 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
20047 AATTTATTGA
*
20057 GTATTGATACTCTTATTTAGG
1 GTATAGATACTCTTATTTAGG
*
20078 GTATAGATATTCTTATTTAGG
1 GTATAGATACTCTTATTTAGG
*
20099 GTATCGATA
1 GTATAGATA
20108 ATTTCTTGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.27, C:0.08, G:0.20, T:0.45
Consensus pattern (21 bp):
GTATAGATACTCTTATTTAGG
Found at i:26337 original size:43 final size:43
Alignment explanation
Indices: 26288--26702 Score: 627
Period size: 43 Copynumber: 9.7 Consensus size: 43
26278 AAAAATGCCA
* *
26288 CAAAAGGTCGAGATATATAGCGGCATTTTTGGAACAAACGCCG
1 CAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCG
* *
26331 CAAAAGGTCGAGATCTATAGCGGCATTTTTAGAACAAACGCCG
1 CAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCG
*
26374 TAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCG
1 CAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCG
* * *
26417 CTAAAGGTCGAGATTTATAACGGCGTTTTTGGAACAAACGCCG
1 CAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCG
* *
26460 CAAAAGGTCGAGATCTATAGTGGCGTTTTTGGAACAAACGTCG
1 CAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCG
* * *
26503 CAAAAGGTCGAGATTTATAGCGGCATTTTTGGAACAAATGCCG
1 CAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCG
26546 CAAAAGGTC-AGATCTATAGCGGCGTTTTTGGAACAAACGCCG
1 CAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCG
* * * **
26588 CAAAAGGTTGAGATTTATAGCGGCGTTTTTTGAACAAATACCG
1 CAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCG
26631 CAAAAGGTC-AGATCTATAGCGGCGTTTTTGGAACAAACGCCG
1 CAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCG
* * *
26673 TAAAAGGTCGAGATTTATAGCGGCGCTTTT
1 CAAAAGGTCGAGATCTATAGCGGCGTTTTT
26703 CTATACAAAC
Statistics
Matches: 335, Mismatches: 35, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
42 75 0.22
43 260 0.78
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.25
Consensus pattern (43 bp):
CAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCG
Found at i:26861 original size:21 final size:21
Alignment explanation
Indices: 26837--26897 Score: 113
Period size: 21 Copynumber: 2.9 Consensus size: 21
26827 TAATTAAAAC
26837 ACAAACTTGAAATCCATAACA
1 ACAAACTTGAAATCCATAACA
26858 ACAAACTTGAAATCCATAACA
1 ACAAACTTGAAATCCATAACA
*
26879 AGAAACTTGAAATCCATAA
1 ACAAACTTGAAATCCATAA
26898 TAATAAATCA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.52, C:0.21, G:0.07, T:0.20
Consensus pattern (21 bp):
ACAAACTTGAAATCCATAACA
Found at i:28916 original size:42 final size:42
Alignment explanation
Indices: 28807--28924 Score: 125
Period size: 42 Copynumber: 2.8 Consensus size: 42
28797 GTTAATGGGT
* * * **
28807 AAACGCCAATGAAGTACTAGGTTTTAGCGGCG--TTTGTCTA
1 AAACGCCACTAAAGTATTAGGTTTTAGCGGCGTTTTTGAATA
* *
28847 AAATCGTCACTAAAGTATGA-GTATTTAGCGGCGTTTTTGAATA
1 AAA-CGCCACTAAAGTATTAGGT-TTTAGCGGCGTTTTTGAATA
*
28890 AAACGCCACTAAAGTATTAGGTTTTAGCGGTGTTT
1 AAACGCCACTAAAGTATTAGGTTTTAGCGGCGTTT
28925 ATTTACAAAC
Statistics
Matches: 63, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
40 5 0.08
41 21 0.33
42 26 0.41
43 11 0.17
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (42 bp):
AAACGCCACTAAAGTATTAGGTTTTAGCGGCGTTTTTGAATA
Found at i:29047 original size:41 final size:41
Alignment explanation
Indices: 28958--29101 Score: 132
Period size: 41 Copynumber: 3.5 Consensus size: 41
28948 TACCCTATTG
* **
28958 CGGCGTTTGTTTAAAAACGCCACTAAAGAACGATTCTATGG
1 CGGCGTTTGTTTAAAAACGCCACTAAAGTACGATTCTATAA
* * *
28999 CGGCGTTTGTTTACAAACGCCACTAAAGTAC-TTATCTTTAA
1 CGGCGTTTGTTTAAAAACGCCACTAAAGTACGAT-TCTATAA
* ** *
29040 CGTCGTTTGTCGAATAAACGCCACTAAAGTACGAGTT-T-TAG
1 CGGCGTTTGTTTAA-AAACGCCACTAAAGTACGA-TTCTATAA
* *
29081 CGGCATTTGTTGAAAAACGCC
1 CGGCGTTTGTTTAAAAACGCC
29102 GTTAATGTTA
Statistics
Matches: 84, Mismatches: 15, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
40 8 0.10
41 56 0.67
42 18 0.21
43 1 0.01
44 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (41 bp):
CGGCGTTTGTTTAAAAACGCCACTAAAGTACGATTCTATAA
Found at i:29084 original size:82 final size:83
Alignment explanation
Indices: 28806--29101 Score: 241
Period size: 82 Copynumber: 3.6 Consensus size: 83
28796 GGTTAATGGG
* * * * * * * *
28806 TAAACGCCAATGAAGTACTAGGTTTTAGCGGCGTTTGTCTA-AAATCGTCACTAAAGTATGAGTA
1 TAAACGCCACTAAAGTACGAGGTTTTAGCGGCGTTTGTTTACAAA-CGCCACTAAAGTATTACTC
28870 TTTAGCGGCGTTT-TTGAA
65 TTTAGCGGCGTTTGTTGAA
** * * * * * *
28888 TAAAACGCCACTAAAGTATTAGGTTTTAGCGGTGTTTATTTACAAACGCAACGATA-TATGTACC
1 T-AAACGCCACTAAAGTACGAGGTTTTAGCGGCGTTTGTTTACAAACGCCACTAAAGTAT-TACT
*
28952 CTATT-GCGGCGTTTGTTTAA
64 CT-TTAGCGGCGTTTGTTGAA
* *
28972 -AAACGCCACTAAAGAACGA--TTCTATGGCGGCGTTTGTTTACAAACGCCACTAAAGTACTTA-
1 TAAACGCCACTAAAGTACGAGGTT-T-TAGCGGCGTTTGTTTACAAACGCCACTAAAGTA-TTAC
* * *
29033 TCTTTAACGTCGTTTGTCGAA
63 TCTTTAGCGGCGTTTGTTGAA
* * *
29054 TAAACGCCACTAAAGTACGA-GTTTTAGCGGCATTTGTTGAAAAACGCC
1 TAAACGCCACTAAAGTACGAGGTTTTAGCGGCGTTTGTTTACAAACGCC
29102 GTTAATGTTA
Statistics
Matches: 168, Mismatches: 34, Indels: 24
0.74 0.15 0.11
Matches are distributed among these distances:
80 2 0.01
81 3 0.02
82 77 0.46
83 74 0.44
84 12 0.07
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.31
Consensus pattern (83 bp):
TAAACGCCACTAAAGTACGAGGTTTTAGCGGCGTTTGTTTACAAACGCCACTAAAGTATTACTCT
TTAGCGGCGTTTGTTGAA
Found at i:41498 original size:14 final size:14
Alignment explanation
Indices: 41479--41505 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41469 ATAAAAAAAT
41479 TAATAAATTTATTA
1 TAATAAATTTATTA
41493 TAATAAATTTATT
1 TAATAAATTTATT
41506 TATCAATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TAATAAATTTATTA
Found at i:49362 original size:43 final size:45
Alignment explanation
Indices: 49250--49369 Score: 146
Period size: 43 Copynumber: 2.8 Consensus size: 45
49240 ATAAAATCTC
49250 TTACCATTT-A-TCC-TAAGCTCGTAAGC-TATTTTACCAAAATA
1 TTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
49291 TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
1 TTACCATTT-AATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
*
49337 CTTGCCA-TT-ATT-CATAAGCTCGTAAGCTTATTT
1 -TTACCATTTAATTCCATAAGCTCGTAAGCTTATTT
49370 GCATCTTACC
Statistics
Matches: 70, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
41 9 0.13
43 22 0.31
44 6 0.09
45 13 0.19
46 15 0.21
47 5 0.07
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (45 bp):
TTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Done.