Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008224.1 Hibiscus syriacus cultivar Beakdansim tig00110856_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: 49980
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:17616 original size:64 final size:64
Alignment explanation
Indices: 17515--17647 Score: 239
Period size: 64 Copynumber: 2.1 Consensus size: 64
17505 TGTATAGTGA
*
17515 GGGAATGAAAGATAGTGAGCCGGTGGACAATAAAAGAAACTGCAAAACTATAGGCAGAGCTATG
1 GGGAATGAAAGATAGTGAGCCGGTGGACAATAAAAGAAACTGCAAAACCATAGGCAGAGCTATG
**
17579 GGGAATGAAAGATAGTGAGGTGGTGGACAATAAAAGAAACTGCAAAACCATAGGCAGAGCTATG
1 GGGAATGAAAGATAGTGAGCCGGTGGACAATAAAAGAAACTGCAAAACCATAGGCAGAGCTATG
17643 GGGAA
1 GGGAA
17648 AACCCCAATG
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.42, C:0.11, G:0.32, T:0.15
Consensus pattern (64 bp):
GGGAATGAAAGATAGTGAGCCGGTGGACAATAAAAGAAACTGCAAAACCATAGGCAGAGCTATG
Found at i:22693 original size:15 final size:15
Alignment explanation
Indices: 22669--22708 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
22659 GTCCGTCCGT
*
22669 CTCGGCTCGGCTCGG
1 CTCGGGTCGGCTCGG
*
22684 CTCGGGTCGGGTCGG
1 CTCGGGTCGGCTCGG
*
22699 GTCGGGTCGG
1 CTCGGGTCGG
22709 GGTCGGGGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.00, C:0.30, G:0.50, T:0.20
Consensus pattern (15 bp):
CTCGGGTCGGCTCGG
Found at i:22891 original size:6 final size:6
Alignment explanation
Indices: 22687--22887 Score: 282
Period size: 6 Copynumber: 34.0 Consensus size: 6
22677 GGCTCGGCTC
22687 GGGTC- GGGTC- GGGTC- GGGTCG GGGTCG GGGTCG GGGTCG GGGTCG
1 GGGTCG GGGTCG GGGTCG GGGTCG GGGTCG GGGTCG GGGTCG GGGTCG
* *
22732 GGGTCG GGGTCG GGGTCG TGGTCG TGGTCG GGGTCG GGGTCG GGGTCG
1 GGGTCG GGGTCG GGGTCG GGGTCG GGGTCG GGGTCG GGGTCG GGGTCG
* * *
22780 GGGTCG GGGTCG TGGTCG GGGTCG TGGTCG GGGTCG GGGTCG TGGTCG
1 GGGTCG GGGTCG GGGTCG GGGTCG GGGTCG GGGTCG GGGTCG GGGTCG
* * * *
22828 GGGTCG GGGTCG TGGTCG TGGTCG TGGTCG GGGTCG GGGTCG TGGTCG
1 GGGTCG GGGTCG GGGTCG GGGTCG GGGTCG GGGTCG GGGTCG GGGTCG
* *
22876 TGGTCG TGGTCG
1 GGGTCG GGGTCG
22888 TGGTAATACT
Statistics
Matches: 184, Mismatches: 11, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
5 15 0.08
6 169 0.92
ACGTcount: A:0.00, C:0.17, G:0.61, T:0.22
Consensus pattern (6 bp):
GGGTCG
Found at i:23033 original size:22 final size:21
Alignment explanation
Indices: 22999--23062 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 21
22989 TAACAGCTGA
*
22999 ATTTAATATCAGGAGTTATTTG
1 ATTTAAT-TCAGGAGTTATATG
* *
23021 ATTTAATTCCAGGGGTTACATG
1 ATTTAATT-CAGGAGTTATATG
* *
23043 ATATAATTTCGGGAGTTATA
1 ATTTAA-TTCAGGAGTTATA
23063 ACAGCTGAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
21 1 0.03
22 30 0.91
23 2 0.06
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.41
Consensus pattern (21 bp):
ATTTAATTCAGGAGTTATATG
Found at i:28600 original size:5 final size:5
Alignment explanation
Indices: 28590--28628 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
28580 ATCCGTCCGT
* * *
28590 CTCGG CTCGG CACGG CACGG CACGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
28629 TGGTCGTGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.08, C:0.41, G:0.38, T:0.13
Consensus pattern (5 bp):
CTCGG
Found at i:28637 original size:6 final size:6
Alignment explanation
Indices: 28626--28704 Score: 140
Period size: 6 Copynumber: 13.2 Consensus size: 6
28616 TCGGCTCGGC
* *
28626 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
28674 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
28705 AATACGTGTC
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 71 1.00
ACGTcount: A:0.03, C:0.16, G:0.49, T:0.32
Consensus pattern (6 bp):
TCGTGG
Found at i:29004 original size:22 final size:22
Alignment explanation
Indices: 28979--29033 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
28969 TCAGGAGTTA
* *
28979 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
29001 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
29023 CGGGAGTTATA
1 CAGGAGTTATA
29034 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:35834 original size:35 final size:35
Alignment explanation
Indices: 35785--35918 Score: 92
Period size: 35 Copynumber: 3.6 Consensus size: 35
35775 TTAAAAGTTA
*
35785 TAAAAGTTTGATATTATTTTTAACTTCTAAATTTT
1 TAAAAGTTTAATATTATTTTTAACTTCTAAATTTT
* * *
35820 TAAAAATTTAATATT-TTTAAAATTAAAATTTGTTAAAATTTT
1 TAAAAGTTTAATATTATTT----TT--AACTT-CT-AAATTTT
* *
35862 CTAAAAGTTTGATATTATTTTTAACTTCGAAA-TTT
1 -TAAAAGTTTAATATTATTTTTAACTTCTAAATTTT
* *
35897 TAAAATTTTTAATATTTTTTTT
1 TAAAA-GTTTAATATTATTTTT
35919 TTGATTTTAT
Statistics
Matches: 76, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
34 8 0.11
35 29 0.38
36 3 0.04
38 6 0.08
40 6 0.08
41 1 0.01
42 7 0.09
43 13 0.17
44 3 0.04
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (35 bp):
TAAAAGTTTAATATTATTTTTAACTTCTAAATTTT
Found at i:35855 original size:16 final size:15
Alignment explanation
Indices: 35813--35859 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 15
35803 TTTAACTTCT
35813 AAATTTTTAAAAATTTA
1 AAATTTTT-AAAA-TTA
*
35830 ATATTTTTAAAATTA
1 AAATTTTTAAAATTA
35845 AAATTTGTTAAAATT
1 AAATTT-TTAAAATT
35860 TTCTAAAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 8 0.30
16 12 0.44
17 7 0.26
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (15 bp):
AAATTTTTAAAATTA
Found at i:35867 original size:78 final size:78
Alignment explanation
Indices: 35767--35915 Score: 230
Period size: 78 Copynumber: 1.9 Consensus size: 78
35757 AAAGAATTTC
*
35767 AAATTTGTTTAAAAGTTATAAAAGTTTGATATTATTTTTAACTTCTAAATTTTTAAAA-ATTTAA
1 AAATTTGTTTAAAAGTTATAAAAGTTTGATATTATTTTTAACTTCGAAA-TTTTAAAATATTTAA
35831 TATTTTTAAAATTA
65 TATTTTTAAAATTA
* * *
35845 AAATTTG-TTAAAATTTTCTAAAAGTTTGATATTATTTTTAACTTCGAAATTTTAAAATTTTTAA
1 AAATTTGTTTAAAA-GTTATAAAAGTTTGATATTATTTTTAACTTCGAAATTTTAAAATATTTAA
35909 TATTTTT
65 TATTTTT
35916 TTTTTGATTT
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
77 14 0.22
78 51 0.78
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (78 bp):
AAATTTGTTTAAAAGTTATAAAAGTTTGATATTATTTTTAACTTCGAAATTTTAAAATATTTAAT
ATTTTTAAAATTA
Done.