Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006082.1 Hibiscus syriacus cultivar Beakdansim tig00014408_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: 54239
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:4530 original size:19 final size:19
Alignment explanation
Indices: 4506--4543 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
4496 TTCAGTTGTC
4506 CTCCTAATCGCATATTTGA
1 CTCCTAATCGCATATTTGA
4525 CTCCTAATCGCATATTTGA
1 CTCCTAATCGCATATTTGA
4544 TTTGATAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.37
Consensus pattern (19 bp):
CTCCTAATCGCATATTTGA
Found at i:7307 original size:2 final size:2
Alignment explanation
Indices: 7300--7329 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
7290 GATATAAGAA
7300 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7330 CAAATATCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10577 original size:60 final size:60
Alignment explanation
Indices: 10451--10630 Score: 174
Period size: 60 Copynumber: 3.0 Consensus size: 60
10441 ATGAAATTAA
* ** * * * * *
10451 GGATGAAATTGGAAA-ATTCAAAAGTTTGGGGACCAA--TATAATGAGAGTCATAGTTTAT
1 GGATGAAATT-GAAATATTTAAAAGTTTAAGGATCAATTTAAAATGAAAGTCATAATTTAG
* *
10509 GGATGAAATTGAAAT-TTTCAAAAGTTTAAGGAAT-AATTTAGAATGAAAGTCATAATTTGG
1 GGATGAAATTGAAATATTT-AAAAGTTTAAGG-ATCAATTTAAAATGAAAGTCATAATTTAG
* * *
10569 GGATGAAATTGGAATATTTAAAAGTTTAAGGATCAATTTAAAATGAGAGT-ATATTTTAG
1 GGATGAAATTGAAATATTTAAAAGTTTAAGGATCAATTTAAAATGAAAGTCATAATTTAG
10628 GGA
1 GGA
10631 CATATGATGC
Statistics
Matches: 101, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
57 6 0.06
58 22 0.22
59 13 0.13
60 57 0.56
61 3 0.03
ACGTcount: A:0.42, C:0.04, G:0.22, T:0.32
Consensus pattern (60 bp):
GGATGAAATTGAAATATTTAAAAGTTTAAGGATCAATTTAAAATGAAAGTCATAATTTAG
Found at i:16147 original size:23 final size:23
Alignment explanation
Indices: 16121--16176 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
16111 CACGTCACTA
*
16121 CTGATTGGATCTTCTAGAAGCTG
1 CTGATTGGACCTTCTAGAAGCTG
* *
16144 CTGACTAGG-CCTTCTAGAAGTTG
1 CTGA-TTGGACCTTCTAGAAGCTG
*
16167 TTGATTGGAC
1 CTGATTGGAC
16177 GCCACATTAG
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
22 3 0.12
23 20 0.77
24 3 0.12
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.34
Consensus pattern (23 bp):
CTGATTGGACCTTCTAGAAGCTG
Found at i:30299 original size:68 final size:68
Alignment explanation
Indices: 30189--30322 Score: 182
Period size: 68 Copynumber: 2.0 Consensus size: 68
30179 AAAAGAAGAA
* * * *
30189 AAAAGAAAACAGAACAAAAAAGTAAAGTTCCATAGTGCATCACTTGAA-CAT-AGAAGCATTAAT
1 AAAAGAAAACAAAACAAAAAAGTAAAGCTCCAAAGTGAATCACTT-AACCATCA-AAGCATTAAT
30252 AGGGT
64 AGGGT
**
30257 AAAAGAAAACAAAACACGAAAGTAAAGCTCCAAAGTGAATCACTTAACCATCAAAGCATTAATAG
1 AAAAGAAAACAAAACAAAAAAGTAAAGCTCCAAAGTGAATCACTTAACCATCAAAGCATTAATAG
30322 G
66 G
30323 CCTTTCCAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
67 2 0.03
68 55 0.95
69 1 0.02
ACGTcount: A:0.51, C:0.16, G:0.16, T:0.17
Consensus pattern (68 bp):
AAAAGAAAACAAAACAAAAAAGTAAAGCTCCAAAGTGAATCACTTAACCATCAAAGCATTAATAG
GGT
Found at i:40889 original size:59 final size:60
Alignment explanation
Indices: 40821--40951 Score: 131
Period size: 59 Copynumber: 2.2 Consensus size: 60
40811 AAGGGTAAAG
* *
40821 TACACAAATGGTCC-CCAACTATAGAGTACTATTTTATTAAGTCTCTCAACTATTAAAAAC
1 TACA-AAATGGTCCTCCAACTATAGAATACTAATTTATTAAGTCTCTCAACTATTAAAAAC
* ** * * * ** **
40881 TATAAAAT-GTCCTCTTACTATAGAATATTAATTTGTTATGTCTCTGGACTATTAAAAGT
1 TACAAAATGGTCCTCCAACTATAGAATACTAATTTATTAAGTCTCTCAACTATTAAAAAC
40940 TACAAAATGGTC
1 TACAAAATGGTC
40952 ACATGACTAT
Statistics
Matches: 56, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
58 4 0.07
59 46 0.82
60 6 0.11
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.36
Consensus pattern (60 bp):
TACAAAATGGTCCTCCAACTATAGAATACTAATTTATTAAGTCTCTCAACTATTAAAAAC
Found at i:51523 original size:60 final size:59
Alignment explanation
Indices: 51438--51574 Score: 166
Period size: 60 Copynumber: 2.3 Consensus size: 59
51428 TAAAGTACAC
* **
51438 AAATGATCCCCAACTATAAAATATTATTTTATTAAGTCTCTTGACTAGTAAAAATTATA
1 AAATGATCCCCAACTATAAAATATTATTTTATTAAGTCCCTCAACTAGTAAAAATTATA
* * * * * *
51497 AAATGATCCTCCAACTATAGAGTATTATTTTGTTGAGTCCCTCAACTATTAAAAGTTATA
1 AAATGATCC-CCAACTATAAAATATTATTTTATTAAGTCCCTCAACTAGTAAAAATTATA
*
51557 AAATGGTCACCCAACTAT
1 AAATGATC-CCCAACTAT
51575 TCATTATATT
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
59 9 0.14
60 56 0.85
61 1 0.02
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (59 bp):
AAATGATCCCCAACTATAAAATATTATTTTATTAAGTCCCTCAACTAGTAAAAATTATA
Found at i:51727 original size:38 final size:38
Alignment explanation
Indices: 51671--51745 Score: 114
Period size: 38 Copynumber: 2.0 Consensus size: 38
51661 CGACACGATC
* *
51671 CGAAAAATATACATCTTTCTCCTGACCCGAGCCCGACT
1 CGAAAAATATACACCTTTCACCTGACCCGAGCCCGACT
* *
51709 CGAAAAATATACGCCTTTCACCTGACTCGAGCCCGAC
1 CGAAAAATATACACCTTTCACCTGACCCGAGCCCGAC
51746 CCGCCTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.29, C:0.35, G:0.15, T:0.21
Consensus pattern (38 bp):
CGAAAAATATACACCTTTCACCTGACCCGAGCCCGACT
Done.