Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006521.1 Hibiscus syriacus cultivar Beakdansim tig00015893_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: 50805
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:7912 original size:842 final size:841
Alignment explanation
Indices: 6291--7975 Score: 3221
Period size: 842 Copynumber: 2.0 Consensus size: 841
6281 GAATTCCACT
6291 ATGATTCATATACATCAGGAAAGCGTTCAGGAATAACCTGAGTGATTTGAGCTAATAAAAGAAAA
1 ATGATTCATATACATCAGGAAAGCGTTCAGGAATAACCTGAGTGATTTGAGCTAATAAAAGAAAA
*
6356 ACGGAGATTCCAGACATTACAATTCATGTTGATCGATCGGTTTATCGTACTATTTGAACTGAACA
66 ACAGAGATTCCAGACATTACAATTCATGTTGATCGATCGGTTTATCGTACTATTTGAACTGAACA
* *
6421 ACTCTTAGAACTAATGCGTGTTGACCCGTCAATTTATTGCCTTTCCAAGTATTCACTCTTTAATA
131 ACTCTCAGAACTAATGCGTGTCGACCCGTCAATTTATTGCCTTTCCAAGTATTCACTCTTTAATA
*
6486 CTAACAATTCTTGTACATAAATCATTTTCGTAACCATTGCTGAATAGATCTTCCTATGGGCTTTA
196 CTAACAATTCTTGTACATAAATCATCTTCGTAACCATTGCTGAATAGATCTTCCTATGGGCTTTA
6551 TTTCATTTCCACGTTTCAACAATATAAAAAACAGACGTACTTAATTCATGGTTCATGACCCATAA
261 TTTCATTTCCACGTTTCAACAATATAAAAAACAGACGTACTTAATTCATGGTTCATGACCCATAA
*
6616 AGACAATTCATCATATATATTTATCAGTGTTTTCAAACTCATCCAATCACCTATTAAATCCTCAG
326 AGACAATTCATCATATATATTTATCAGTGTTTCCAAACTCATCCAATCACCTATTAAATCCTCAG
6681 TCATTGAGGTTACTTAGTTCATTTAGCACGCAAGTCTATCCCGGTTACTTCAGAGTTTTCCAGAT
391 TCATTGAGGTTACTTAGTTCATTTAGCACGCAAGTCTATCCCGGTTACTTCAGAGTTTTCCAGAT
* *
6746 TAATTCAGAAACTTCTGAGTTTCAGGTACATGTTGTACTTCCATTCATTTCACTTTCTTCATATA
456 TAATTCAGAAACTTCTAAGTTTCAGGTACATGTTGTACTTCCATTCATTTCACTTTCATCATATA
6811 CTTAAATCATTTTAGTATTCGTGATTGATTTATCTCACGAATATCCACTTCTTAATATCGAATGC
521 CTTAAATCATTTTAGTATTCGTGATTGATTTATCTCACGAATATCCACTTCTTAATATCGAATGC
6876 GCTCTAGCGTTGAGCTGAGCTGAGTACTTCCATAATTATTATCAATCCAAACTTGAGGAGACGAA
586 GCTCTAGCGTTGAGCTGAGCTGAGTACTTCCATAATTATTATCAATCCAAACTTGAGGAGACGAA
6941 CTAGCATTCAAGTGGTACCTATGCCATTCAAGTAATGATATATCACTATCATTGTTTGACCGGCT
651 CTAGCATTCAAGTGGTACCTATGCCATTCAAGTAATGATATATCACTATCATTGTTTGACCGGCT
7006 TAAATTGCGTTTCATAACATTAAAAAGAAGTACAACATTCATGTTTATTACAATTTCTTAATTAA
716 TAAATTGCGTTTCATAACATTAAAAAGAAGTACAACATTCATGTTTATTACAATTTCTTAATTAA
*
7071 TCCAAGACATTTACTTAGTATAGTCTATAAGGGCATTTTGGTGCTCAATGTTTTTCCATTC
781 TCCAAGACATTTACTTAGTATAGTCTATAAGGGCATTTTGGTGCTCAATGTTTTCCCATTC
*
7132 ATGATTCATATACATCAGGAAAGTGTTCAGGAATAACCTGAGTGATTTGAGCTAATAAAAGAAAA
1 ATGATTCATATACATCAGGAAAGCGTTCAGGAATAACCTGAGTGATTTGAGCTAATAAAAGAAAA
7197 ACAGAGATTCCAGACATTACAATTCATGTTGATCGATCGGTTTATCGTACTATTTGAACTGAACA
66 ACAGAGATTCCAGACATTACAATTCATGTTGATCGATCGGTTTATCGTACTATTTGAACTGAACA
7262 ACTCTCAGAACTAATGCGTGTCGACCCGTCAATTTATTGCCTTTCCAAGTATTCACTCTTTAATA
131 ACTCTCAGAACTAATGCGTGTCGACCCGTCAATTTATTGCCTTTCCAAGTATTCACTCTTTAATA
*
7327 CTAAC-ATTCTTGTACATAAATCATCTTCGTAACCATTGCTGAATAGATCTTCCTATGGTCTTTA
196 CTAACAATTCTTGTACATAAATCATCTTCGTAACCATTGCTGAATAGATCTTCCTATGGGCTTTA
*
7391 TTTCATTTCTACGTTTCAACAATATCAGAAAATACAGACGTACTTAATTCATGGTTCATGACCCA
261 TTTCATTTCCACGTTTCAACAATAT-A-AAAA-ACAGACGTACTTAATTCATGGTTCATGACCCA
7456 TAAAGACAATTCATCATATATATTTATCAGTGTTTCCAAACTCATCCAATCACCTATTAAATCCT
323 TAAAGACAATTCATCATATATATTTATCAGTGTTTCCAAACTCATCCAATCACCTATTAAATCCT
7521 CAGTCATTGAGGTTACTTAGTTCATTTAGCACGCAAGTCTATCCCGGTTACTTCAGAGTTTTCCA
388 CAGTCATTGAGGTTACTTAGTTCATTTAGCACGCAAGTCTATCCCGGTTACTTCAGAGTTTTCCA
*
7586 GATTAATTCAGACACTTCTAAGTTTCAGGTACATGTTGTACTTCCATTCATTTCACTTTCATCAT
453 GATTAATTCAGAAACTTCTAAGTTTCAGGTACATGTTGTACTTCCATTCATTTCACTTTCATCAT
7651 ATACTTAAATCATTTTAGTA-TCGTGATTGATTTATCTCACGAATATCCACTTCTTAATATCGAA
518 ATACTTAAATCATTTTAGTATTCGTGATTGATTTATCTCACGAATATCCACTTCTTAATATCGAA
7715 TGCGCTCTAGCGTTGAGCTGAGCTGAGTACTTCCATAATTATTATCAATCCAAACTTGAGGAGAC
583 TGCGCTCTAGCGTTGAGCTGAGCTGAGTACTTCCATAATTATTATCAATCCAAACTTGAGGAGAC
7780 GAACTAGCATTCAAGTGGTACCTATGCCATTCAAGTAATGATATATCACTATCATTGTTTGACCG
648 GAACTAGCATTCAAGTGGTACCTATGCCATTCAAGTAATGATATATCACTATCATTGTTTGACCG
7845 GCTTAAATTGCGTTTCATAACATTAAAAAGAAGTACAACATTCATGTTTATTACAATTTCTTAAT
713 GCTTAAATTGCGTTTCATAACATTAAAAAGAAGTACAACATTCATGTTTATTACAATTTCTTAAT
7910 TAATCCAAGACATTTACTTAGTATAGTCTATAAGGGCATTTTGGTGCTCAATGTTTTCCCATTC
778 TAATCCAAGACATTTACTTAGTATAGTCTATAAGGGCATTTTGGTGCTCAATGTTTTCCCATTC
7974 AT
1 AT
7976 TTCAAAGCTG
Statistics
Matches: 829, Mismatches: 12, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
840 81 0.10
841 197 0.24
842 308 0.37
843 243 0.29
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (841 bp):
ATGATTCATATACATCAGGAAAGCGTTCAGGAATAACCTGAGTGATTTGAGCTAATAAAAGAAAA
ACAGAGATTCCAGACATTACAATTCATGTTGATCGATCGGTTTATCGTACTATTTGAACTGAACA
ACTCTCAGAACTAATGCGTGTCGACCCGTCAATTTATTGCCTTTCCAAGTATTCACTCTTTAATA
CTAACAATTCTTGTACATAAATCATCTTCGTAACCATTGCTGAATAGATCTTCCTATGGGCTTTA
TTTCATTTCCACGTTTCAACAATATAAAAAACAGACGTACTTAATTCATGGTTCATGACCCATAA
AGACAATTCATCATATATATTTATCAGTGTTTCCAAACTCATCCAATCACCTATTAAATCCTCAG
TCATTGAGGTTACTTAGTTCATTTAGCACGCAAGTCTATCCCGGTTACTTCAGAGTTTTCCAGAT
TAATTCAGAAACTTCTAAGTTTCAGGTACATGTTGTACTTCCATTCATTTCACTTTCATCATATA
CTTAAATCATTTTAGTATTCGTGATTGATTTATCTCACGAATATCCACTTCTTAATATCGAATGC
GCTCTAGCGTTGAGCTGAGCTGAGTACTTCCATAATTATTATCAATCCAAACTTGAGGAGACGAA
CTAGCATTCAAGTGGTACCTATGCCATTCAAGTAATGATATATCACTATCATTGTTTGACCGGCT
TAAATTGCGTTTCATAACATTAAAAAGAAGTACAACATTCATGTTTATTACAATTTCTTAATTAA
TCCAAGACATTTACTTAGTATAGTCTATAAGGGCATTTTGGTGCTCAATGTTTTCCCATTC
Found at i:9703 original size:21 final size:20
Alignment explanation
Indices: 9665--9703 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
9655 CGATAATTAA
*
9665 AAAAAAACCCAATCAAGAAG
1 AAAAAAACCCAAACAAGAAG
*
9685 AAAAACACCCAAACGAAGA
1 AAAAAAACCCAAAC-AAGA
9704 TCGAAGCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.64, C:0.23, G:0.10, T:0.03
Consensus pattern (20 bp):
AAAAAAACCCAAACAAGAAG
Found at i:24479 original size:55 final size:55
Alignment explanation
Indices: 24413--24889 Score: 463
Period size: 55 Copynumber: 8.8 Consensus size: 55
24403 GTGAAGCAAA
* *
24413 TGAAGATTGTTCGAGTCTTATACTCTCTGAACAAATAGAGAGCAGACACGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* * * * * * *
24468 TGAAGATTGTTCAAGTCTCATACTCTCTTAAGCAATAGGGAGCAGACATGAATAT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* * *
24523 TGAAAATTGTTCGAGTCTAATACTCTCTGAAGAAATAGGGAGCAGACACGAATGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* * * * *
24578 TGAAAATTATTTGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* * * * *
24633 TGAAGGTTGTTCAAGTCATATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* * * * * *
24688 TGAAGGTTGTTCAAGTCATATACTCTCTGAAAAAATAGGGAGCGGACACGTTTGAT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG-T
* * * *
24744 TGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATGGGGAGCGGACAC-ATTTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA-TTGT
* * * * ** *
24795 TGAAGA-T-TT--AGTCCTATACTCTCTGAAGGAATAGAGAACAGACTTG-TTTT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* * *
24845 ATGAAGATTGTTTGAGTTTTATACTCCCTGAAGCAAA-AGGGAGCA
1 -TGAAGATTGTTCGAGTCTTATACTCTCTGAAG-AAATAGGGAGCA
24890 AACCCAGTGG
Statistics
Matches: 361, Mismatches: 51, Indels: 20
0.84 0.12 0.05
Matches are distributed among these distances:
50 3 0.01
51 43 0.12
52 38 0.11
53 4 0.01
55 265 0.73
56 8 0.02
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (55 bp):
TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
Found at i:30735 original size:30 final size:29
Alignment explanation
Indices: 30650--30747 Score: 97
Period size: 30 Copynumber: 3.3 Consensus size: 29
30640 GAGAATTCAT
* * *
30650 TTCCCTTCTTAATACTGCATGGGACTTCG
1 TTCCCATCCTAATACTACATGGGACTTCG
* * *
30679 TTCCCCATCCTGATTCTACATAGGACTTCG
1 TT-CCCATCCTAATACTACATGGGACTTCG
**
30709 TTCCCAGTCCTAATACTTTATGGGACTTCG
1 TTCCCA-TCCTAATACTACATGGGACTTCG
30739 TTCCTCATC
1 TTCC-CATC
30748 TTGTTTTTTC
Statistics
Matches: 55, Mismatches: 11, Indels: 5
0.77 0.15 0.07
Matches are distributed among these distances:
29 6 0.11
30 47 0.85
31 2 0.04
ACGTcount: A:0.18, C:0.31, G:0.14, T:0.37
Consensus pattern (29 bp):
TTCCCATCCTAATACTACATGGGACTTCG
Found at i:41750 original size:19 final size:19
Alignment explanation
Indices: 41726--41778 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
41716 GAATGCATTT
*
41726 CATGCATCGATGCACGTAC
1 CATGCACCGATGCACGTAC
41745 CATGCACCGATGCACGTAC
1 CATGCACCGATGCACGTAC
41764 CATGCACCGATGCAC
1 CATGCACCGATGCAC
41779 TGAGGATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.26, C:0.36, G:0.21, T:0.17
Consensus pattern (19 bp):
CATGCACCGATGCACGTAC
Found at i:41821 original size:65 final size:64
Alignment explanation
Indices: 41746--41888 Score: 182
Period size: 65 Copynumber: 2.2 Consensus size: 64
41736 TGCACGTACC
* * * *
41746 ATGCACCGATGCACGTA-CCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCATT
1 ATGCATCGATGCAC-CAGCCATGCACCGATGCACTCAGGATATTT-TG-AAACATCGAATGCACT
41809 TG
63 TG
* * *
41811 ATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTG
1 ATGCATCGATGCACCAGCCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCACTTG
41875 ATGCATCGATGCAC
1 ATGCATCGATGCAC
41889 TGAGTGCATC
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
64 32 0.46
65 34 0.49
66 3 0.04
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (64 bp):
ATGCATCGATGCACCAGCCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCACTTG
Found at i:41888 original size:17 final size:18
Alignment explanation
Indices: 41860--41906 Score: 71
Period size: 17 Copynumber: 2.7 Consensus size: 18
41850 TATTTTGAAA
41860 CATCGAATGCACTTGA-TG
1 CATCG-ATGCACTTGAGTG
41878 CATCGATGCAC-TGAGTG
1 CATCGATGCACTTGAGTG
41895 CATCGATGCACT
1 CATCGATGCACT
41907 AAGGATCCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 3 0.11
17 19 0.70
18 5 0.19
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (18 bp):
CATCGATGCACTTGAGTG
Found at i:49175 original size:21 final size:21
Alignment explanation
Indices: 49133--49176 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
49123 ACTCCGGGAG
* *
49133 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
49154 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
49175 CT
1 CT
49177 CCTCCTCCTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:49177 original size:3 final size:3
Alignment explanation
Indices: 49169--49196 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
49159 TCCTCTCGTG
49169 CTC CTC CTC CTC CTC CTC CTC CTC CTC C
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC C
49197 GACTTCTGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (3 bp):
CTC
Found at i:50373 original size:64 final size:65
Alignment explanation
Indices: 50273--50429 Score: 189
Period size: 65 Copynumber: 2.4 Consensus size: 65
50263 TTAAATTGAT
*
50273 CATCGAATGCATTTCATGCATCGATGCA-CATACCATGCACCGATGCACT-GAGGAT-TTTATGA
1 CATCGAATGCATTTGATGCATCGATGCACCATACCATGCACCGATGCACTCGA-GATATTT-TG-
50335 AAA
63 AAA
* * * *
50338 CATCGAATGCATTTGATGCATCGA-GCACCA-GCCATGCATCGATGCACTCTAGCTATTTTGAAA
1 CATCGAATGCATTTGATGCATCGATGCACCATACCATGCACCGATGCACTCGAGATATTTTGAAA
* *
50401 CATTGAATGCACTTGATGCATCGATGCAC
1 CATCGAATGCATTTGATGCATCGATGCAC
50430 TAAGGATCCA
Statistics
Matches: 81, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
63 25 0.31
64 27 0.33
65 29 0.36
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (65 bp):
CATCGAATGCATTTGATGCATCGATGCACCATACCATGCACCGATGCACTCGAGATATTTTGAAA
Done.