Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001506.1 Hibiscus syriacus cultivar Beakdansim tig00002950_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: 74634
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:8675 original size:27 final size:27
Alignment explanation
Indices: 8645--8698 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
8635 CAAATATGAC
8645 CTAAATGCAACTAATATGCTATGGCAA
1 CTAAATGCAACTAATATGCTATGGCAA
*
8672 CTAAATGCAACTAATATGTTATGGCAA
1 CTAAATGCAACTAATATGCTATGGCAA
8699 TGACTTTTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.28
Consensus pattern (27 bp):
CTAAATGCAACTAATATGCTATGGCAA
Found at i:12761 original size:24 final size:24
Alignment explanation
Indices: 12734--12791 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
12724 AACTTCTTTT
12734 GCAGCTTCAGCCGCTGCCATGTAC
1 GCAGCTTCAGCCGCTGCCATGTAC
12758 GCAGCTTCAGCCGCTGCCATGTAC
1 GCAGCTTCAGCCGCTGCCATGTAC
*
12782 TCAGCTTCAG
1 GCAGCTTCAG
12792 TTGTAGATAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.17, C:0.36, G:0.24, T:0.22
Consensus pattern (24 bp):
GCAGCTTCAGCCGCTGCCATGTAC
Found at i:19039 original size:23 final size:25
Alignment explanation
Indices: 18999--19053 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 25
18989 CGGTTATTTT
* *
18999 AACCGGTTTTTTTACC-GGATAAAA
1 AACCGGTTTTTATACCGGGAAAAAA
19023 AACCGGTTTTTAT-CCGGGAAAAAA
1 AACCGGTTTTTATACCGGGAAAAAA
19047 AACCGGT
1 AACCGGT
19054 CTGGGTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 2 0.07
24 26 0.93
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (25 bp):
AACCGGTTTTTATACCGGGAAAAAA
Found at i:21357 original size:21 final size:21
Alignment explanation
Indices: 21333--21374 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
21323 AGTTTATTTT
21333 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
21354 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
21375 AACTTGAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:21422 original size:33 final size:33
Alignment explanation
Indices: 21369--21467 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
21359 TTTGTTTCAA
21369 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
21401 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
21434 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
21467 T
1 T
21468 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:22626 original size:15 final size:15
Alignment explanation
Indices: 22574--22629 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
22564 TTTAATAATA
*
22574 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
22589 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
* *
22604 TAAAAAAACTGGTTTTT
1 T--TAAAACCGGTTTTT
22621 TTAAAACCG
1 TTAAAACCG
22630 AAACCGGTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
15 20 0.62
17 12 0.38
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:22719 original size:15 final size:17
Alignment explanation
Indices: 22693--22724 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
22683 TTCTATGGGA
22693 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
22709 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
22725 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:23685 original size:43 final size:43
Alignment explanation
Indices: 23635--23736 Score: 204
Period size: 43 Copynumber: 2.4 Consensus size: 43
23625 CACAGGGATA
23635 AAAGATATATCTGCTGTATATGTCGAACACAAAGGGATGGCGG
1 AAAGATATATCTGCTGTATATGTCGAACACAAAGGGATGGCGG
23678 AAAGATATATCTGCTGTATATGTCGAACACAAAGGGATGGCGG
1 AAAGATATATCTGCTGTATATGTCGAACACAAAGGGATGGCGG
23721 AAAGATATATCTGCTG
1 AAAGATATATCTGCTG
23737 CATTGTACGA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.35, C:0.14, G:0.26, T:0.25
Consensus pattern (43 bp):
AAAGATATATCTGCTGTATATGTCGAACACAAAGGGATGGCGG
Found at i:29897 original size:27 final size:27
Alignment explanation
Indices: 29857--29910 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
29847 CGAAACAAAT
* *
29857 GAAATTTTAAGTACTAAAACAAAACAA
1 GAAATCTTAAGTACAAAAACAAAACAA
* *
29884 GAAATCTTAGGTACAAAAAGAAAACAA
1 GAAATCTTAAGTACAAAAACAAAACAA
29911 AACTGATAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.59, C:0.11, G:0.11, T:0.19
Consensus pattern (27 bp):
GAAATCTTAAGTACAAAAACAAAACAA
Found at i:55537 original size:24 final size:24
Alignment explanation
Indices: 55509--55556 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
55499 CTTCTCCACC
55509 GAACAGTCCACGTTTCTACCAGCT
1 GAACAGTCCACGTTTCTACCAGCT
55533 GAACAGTCCACGTTTCTACCAGCT
1 GAACAGTCCACGTTTCTACCAGCT
55557 CCCTCAAGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (24 bp):
GAACAGTCCACGTTTCTACCAGCT
Found at i:67446 original size:18 final size:19
Alignment explanation
Indices: 67408--67446 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
67398 TAAATTTAAT
*
67408 AAAATAAAATATAGGTCTA
1 AAAATAAAATATAGATCTA
*
67427 AAAATAAAAT-TAGATTTA
1 AAAATAAAATATAGATCTA
67445 AA
1 AA
67447 GTAAAAATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.62, C:0.03, G:0.08, T:0.28
Consensus pattern (19 bp):
AAAATAAAATATAGATCTA
Found at i:68417 original size:17 final size:17
Alignment explanation
Indices: 68395--68428 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
68385 GGGTGTAACG
68395 ATTAATTCGATCACCAA
1 ATTAATTCGATCACCAA
68412 ATTAATTCGATCACCAA
1 ATTAATTCGATCACCAA
68429 CCGAACCGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.24, G:0.06, T:0.29
Consensus pattern (17 bp):
ATTAATTCGATCACCAA
Found at i:72595 original size:232 final size:232
Alignment explanation
Indices: 72186--72711 Score: 657
Period size: 233 Copynumber: 2.2 Consensus size: 232
72176 GGAAATTCCC
* * * * *
72186 TTTTTACTTTTTAAAAACTTCAATTTTCAGATTTAAATGAGAAACTTTTCTTATTTTTTTGGAAA
1 TTTTTACTTTTCAAAAATTTTAATTTTCAGATTTAAATGAGAAACTTTTCTCA--TTTTTCG--A
*
72251 AAAAACATGTGAAACTCATGCCCGAAGATCTTATGGATGGCCCGAAAGACTTACCATCTTGCTCG
62 AAAAACATATGAAACTCATGCCCGAAGATCTTATGGATGGCCCGAAAGACTTACCATCTTGCTCG
** * * * *
72316 AAAGGCTTATAGATAACCCAAAAGATTTATGCATCATGCTTGAAAGACTTACTGATGG-CCGAAT
127 AAAAACTTACAGATAACCCAAAAGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAG
* * * **
72380 GACTTACCAATTTTGGGAATATTTTATTAGGTAAGAAACTT
192 GACTTACCAATTTTGGAAATAGTTTACTAAATAAGAAACTT
* * *
72421 TTTTTACTTTTCAAAAATTTTAATTTTCAGATTTAAGTGAGAAACTTTTCTCATTTTTCG-AGAG
1 TTTTTACTTTTCAAAAATTTTAATTTTCAGATTTAAATGAGAAACTTTTCTCATTTTTCGAAAAA
* * * *
72485 ACATATGATAACATCCT-CCCAGAAGGTCTTATGGATTGCCCGAATA-ACTTATCATCTTGCTCG
66 ACATATGA-AAC-TCATGCCC-GAAGATCTTATGGATGGCCCGAA-AGACTTACCATCTTGCTCG
* * * *
72548 AAAAACTTACATATGACCCAAATGATTTAAGCTTCATGCTCGAAAGACTTACTGATGGCCCGAAG
127 AAAAACTTACAGATAACCCAAAAGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAG
*
72613 GACTTACTAATTTTGGAAATAGTTTACTAAATAAGAAACTT
192 GACTTACCAATTTTGGAAATAGTTTACTAAATAAGAAACTT
* *
72654 TTATTACTTTTCAAAAATTTTAATATTT-AGATTTAAATGAGAAATTTTTCTCATTTTT
1 TTTTTACTTTTCAAAAATTTTAAT-TTTCAGATTTAAATGAGAAACTTTTCTCATTTTT
72712 AACCTATAAA
Statistics
Matches: 253, Mismatches: 32, Indels: 14
0.85 0.11 0.05
Matches are distributed among these distances:
230 9 0.04
231 6 0.02
232 89 0.35
233 98 0.39
234 3 0.01
235 48 0.19
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.37
Consensus pattern (232 bp):
TTTTTACTTTTCAAAAATTTTAATTTTCAGATTTAAATGAGAAACTTTTCTCATTTTTCGAAAAA
ACATATGAAACTCATGCCCGAAGATCTTATGGATGGCCCGAAAGACTTACCATCTTGCTCGAAAA
ACTTACAGATAACCCAAAAGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACT
TACCAATTTTGGAAATAGTTTACTAAATAAGAAACTT
Done.