Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006106.1 Hibiscus syriacus cultivar Beakdansim tig00014471_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: 74729
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:5555 original size:12 final size:12
Alignment explanation
Indices: 5538--5562 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5528 ATCTATAATT
5538 TCTTGTAATTTC
1 TCTTGTAATTTC
5550 TCTTGTAATTTC
1 TCTTGTAATTTC
5562 T
1 T
5563 TATTTCTCGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.16, G:0.08, T:0.60
Consensus pattern (12 bp):
TCTTGTAATTTC
Found at i:9423 original size:16 final size:15
Alignment explanation
Indices: 9402--9431 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
9392 TAAAAAGATC
9402 ATAAATAAAGTAAAAA
1 ATAAATAAA-TAAAAA
9418 ATAAATAAATAAAA
1 ATAAATAAATAAAA
9432 CAAACAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (15 bp):
ATAAATAAATAAAAA
Found at i:11223 original size:84 final size:84
Alignment explanation
Indices: 11127--11314 Score: 218
Period size: 84 Copynumber: 2.2 Consensus size: 84
11117 TTCCTTGAGT
* * * * * * *
11127 TATGCTGTAAATGATGTGCCTTGGAGCT-ATGCGTAGTTGAACTCGAGGGTC-TTTGGTTGACAT
1 TATGCTGTAAATGATGTGCCTTAGAGCTGA-GCATAGTCGAACTCAAAGATCTTTTGG-TGACAG
* * *
11190 ATAGCCCTTTTCGACTTAAGC
64 ATAACCCTTCTAGACTTAAGC
*
11211 TATGCTGCAAATGATGTGCCTTAGAGCTGAGCATAGTCGAACTCAAAGATCTTTTGGTGACAGAT
1 TATGCTGTAAATGATGTGCCTTAGAGCTGAGCATAGTCGAACTCAAAGATCTTTTGGTGACAGAT
* * *
11276 AACCCTTCTAGCCTTGAGT
66 AACCCTTCTAGACTTAAGC
11295 TATGCTGTAAATGATGTGCC
1 TATGCTGTAAATGATGTGCC
11315 CTCGAAGCTG
Statistics
Matches: 87, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
84 81 0.93
85 6 0.07
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.32
Consensus pattern (84 bp):
TATGCTGTAAATGATGTGCCTTAGAGCTGAGCATAGTCGAACTCAAAGATCTTTTGGTGACAGAT
AACCCTTCTAGACTTAAGC
Found at i:11541 original size:102 final size:102
Alignment explanation
Indices: 11415--11655 Score: 270
Period size: 102 Copynumber: 2.4 Consensus size: 102
11405 AAAGATTGAA
* * * ** **
11415 GTTTCAAGGAAAAACTGTCTCAAGAGAGACAAAATTTTATTTC-AAGGGAACCTATCTCAAGAGA
1 GTTTCAA-GAGAAACTGTCTCAAGAGAGACAAAA-CTTAGTTCTAAAAGAAAATATCTCAAGAGA
*** * *
11479 GACAAAATTCATTTCAAGGGAAA-TTTTTCCAATGTTTAT
64 GACAAAATTCATTTCAAGGGAAACAGATTCAAATATTT-T
* * *
11518 GTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAAATGTCTCAAGGGAGA
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAAATATCTCAAGAGAGA
* **
11583 CGAAATTTGTTTCAAGGGAAACAGATTCAAATATTTT
66 CAAAATTCATTTCAAGGGAAACAGATTCAAATATTTT
*
11620 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
11656 GGAAAATATC
Statistics
Matches: 116, Mismatches: 20, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
101 6 0.05
102 94 0.81
103 16 0.14
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.27
Consensus pattern (102 bp):
GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAAATATCTCAAGAGAGA
CAAAATTCATTTCAAGGGAAACAGATTCAAATATTTT
Found at i:12906 original size:32 final size:33
Alignment explanation
Indices: 12866--12961 Score: 131
Period size: 32 Copynumber: 2.9 Consensus size: 33
12856 ATTCCCAAAG
*
12866 ATGCCCCAATATTCGATGTTGAATCTCAAAAAA
1 ATGCCCCAATATTTGATGTTGAATCTCAAAAAA
* *
12899 ATGCCCAAATATTTGATGTTAAATCTC-AAAAA
1 ATGCCCCAATATTTGATGTTGAATCTCAAAAAA
**
12931 ATGCCCCAGCATTTGATGTTGAATCTTCAAA
1 ATGCCCCAATATTTGATGTTGAATC-TCAAA
12962 GATGCCCTCA
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
32 26 0.48
33 26 0.48
34 2 0.04
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (33 bp):
ATGCCCCAATATTTGATGTTGAATCTCAAAAAA
Found at i:12968 original size:32 final size:32
Alignment explanation
Indices: 12866--12961 Score: 129
Period size: 33 Copynumber: 2.9 Consensus size: 32
12856 ATTCCCAAAG
*
12866 ATGCCCCAATATTCGATGTTGAATCTCAAAAAA
1 ATGCCCCAATATTTGATGTTGAATCTC-AAAAA
* *
12899 ATGCCCAAATATTTGATGTTAAATCTCAAAAA
1 ATGCCCCAATATTTGATGTTGAATCTCAAAAA
**
12931 ATGCCCCAGCATTTGATGTTGAATCTTCAAA
1 ATGCCCCAATATTTGATGTTGAATC-TCAAA
12962 GATGCCCTCA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
32 26 0.47
33 29 0.53
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (32 bp):
ATGCCCCAATATTTGATGTTGAATCTCAAAAA
Found at i:14006 original size:69 final size:69
Alignment explanation
Indices: 13893--14025 Score: 223
Period size: 69 Copynumber: 1.9 Consensus size: 69
13883 TCTCTCTCTT
* *
13893 GATGCTCTATGATCTTCGAGTGGAGTGATTCAGTGATTCAGAAATGATTGTGCTTGATCAATCTT
1 GATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAGAAATGATTATGCTTGATCAATCTT
13958 ATTA
66 ATTA
*
13962 GATGCTCTATGATCTTCGAGTGAAGT-AGTTCAGTGATTCGGAAATGATTATGCTTGATCAATCT
1 GATGCTCTATGATCTTCGAGTGAAGTGA-TTCAGTGATTCAGAAATGATTATGCTTGATCAATCT
14026 CATAGTTTGA
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
68 1 0.02
69 59 0.98
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (69 bp):
GATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAGAAATGATTATGCTTGATCAATCTT
ATTA
Found at i:23821 original size:50 final size:50
Alignment explanation
Indices: 23746--23845 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
23736 ATCACTCTAG
23746 ATGGTGAAAAATGAACATCATTACCACTAAAATAGAAATGCATCTAACGT
1 ATGGTGAAAAATGAACATCATTACCACTAAAATAGAAATGCATCTAACGT
23796 ATGGTGAAAAATGAACATCATTACCACTAAAATAGAAATGCATCTAACGT
1 ATGGTGAAAAATGAACATCATTACCACTAAAATAGAAATGCATCTAACGT
23846 TGGCAGCACG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.46, C:0.16, G:0.14, T:0.24
Consensus pattern (50 bp):
ATGGTGAAAAATGAACATCATTACCACTAAAATAGAAATGCATCTAACGT
Found at i:27964 original size:36 final size:36
Alignment explanation
Indices: 27922--27997 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
27912 TTATAGCTAA
*
27922 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
27958 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
27994 AAAA
1 AAAA
27998 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:48011 original size:61 final size:61
Alignment explanation
Indices: 47916--48037 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
47906 ATCTGATGAA
47916 ACTGTCACCTTTATTCCTACTACATATATAATTTCTTTGTCATTATATCGAACATCTTGTC
1 ACTGTCACCTTTATTCCTACTACATATATAATTTCTTTGTCATTATATCGAACATCTTGTC
47977 ACTGTCACCTTTATTCCTACTACATATATAATTTCTTTGTCATTATATCGAACATCTTGTC
1 ACTGTCACCTTTATTCCTACTACATATATAATTTCTTTGTCATTATATCGAACATCTTGTC
48038 TTGGGATTAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.26, C:0.23, G:0.07, T:0.44
Consensus pattern (61 bp):
ACTGTCACCTTTATTCCTACTACATATATAATTTCTTTGTCATTATATCGAACATCTTGTC
Found at i:51245 original size:12 final size:12
Alignment explanation
Indices: 51228--51253 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
51218 CCTCGAAGAC
51228 CTCTCTTACCAT
1 CTCTCTTACCAT
51240 CTCTCTTACCAT
1 CTCTCTTACCAT
51252 CT
1 CT
51254 AATCCCCAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.42, G:0.00, T:0.42
Consensus pattern (12 bp):
CTCTCTTACCAT
Found at i:54492 original size:31 final size:31
Alignment explanation
Indices: 54452--54512 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
54442 CATTTATTGG
54452 ACTTAGATTTTAATCCTCAATGCAGTTTTAT
1 ACTTAGATTTTAATCCTCAATGCAGTTTTAT
*
54483 ACTTTGATTTTAATCCTCAATGCAGTTTTA
1 ACTTAGATTTTAATCCTCAATGCAGTTTTA
54513 CACATTCCTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.46
Consensus pattern (31 bp):
ACTTAGATTTTAATCCTCAATGCAGTTTTAT
Found at i:67468 original size:34 final size:34
Alignment explanation
Indices: 67425--67489 Score: 130
Period size: 34 Copynumber: 1.9 Consensus size: 34
67415 TGAAAAGGAG
67425 AATGAAATATTTAATAAACCAGCACAATAATGCA
1 AATGAAATATTTAATAAACCAGCACAATAATGCA
67459 AATGAAATATTTAATAAACCAGCACAATAAT
1 AATGAAATATTTAATAAACCAGCACAATAAT
67490 CCCCATTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.54, C:0.14, G:0.08, T:0.25
Consensus pattern (34 bp):
AATGAAATATTTAATAAACCAGCACAATAATGCA
Found at i:69540 original size:43 final size:43
Alignment explanation
Indices: 69473--69597 Score: 142
Period size: 43 Copynumber: 2.9 Consensus size: 43
69463 ATATAAGATT
* * *
69473 CAAATGATTCAGCTCAGTTATAAAGTTCACACTATTAACCTAA
1 CAAAGGATTCAGCTCAATTCTAAAGTTCACACTATTAACCTAA
* * * *
69516 CAAAGGATTCGGCTCACTTCTAAAGTTCACACTATTAAGCTAG
1 CAAAGGATTCAGCTCAATTCTAAAGTTCACACTATTAACCTAA
* * * * *
69559 CAATGAATTCATCTCAATACTAAAGTTCACATTATTAAC
1 CAAAGGATTCAGCTCAATTCTAAAGTTCACACTATTAAC
69598 AAAATAGAAC
Statistics
Matches: 68, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 68 1.00
ACGTcount: A:0.38, C:0.22, G:0.10, T:0.30
Consensus pattern (43 bp):
CAAAGGATTCAGCTCAATTCTAAAGTTCACACTATTAACCTAA
Done.