Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000408.1 Hibiscus syriacus cultivar Beakdansim tig00000753_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: 55734
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1940 original size:37 final size:37
Alignment explanation
Indices: 1888--1964 Score: 127
Period size: 37 Copynumber: 2.1 Consensus size: 37
1878 GCATTATAGA
* *
1888 GATAAACACTCCGAAAGCAACAATTACTTAGCTGATT
1 GATAAACACTCCGAAAGCAACAACTACTTAGCCGATT
*
1925 GATAAACACTGCGAAAGCAACAACTACTTAGCCGATT
1 GATAAACACTCCGAAAGCAACAACTACTTAGCCGATT
1962 GAT
1 GAT
1965 CCTTTAATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (37 bp):
GATAAACACTCCGAAAGCAACAACTACTTAGCCGATT
Found at i:3320 original size:37 final size:37
Alignment explanation
Indices: 3269--3377 Score: 200
Period size: 37 Copynumber: 2.9 Consensus size: 37
3259 AAATAGTTTC
*
3269 AAATATGTACGCATATGATTTGAATCATGGAATAATT
1 AAATATGTATGCATATGATTTGAATCATGGAATAATT
3306 AAATATGTATGCATATGATTTGAATCATGGAATAATT
1 AAATATGTATGCATATGATTTGAATCATGGAATAATT
*
3343 AAATATGTATGCATATGATTTGAATCTTGGAATAA
1 AAATATGTATGCATATGATTTGAATCATGGAATAA
3378 GGATGAAAAA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 70 1.00
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.37
Consensus pattern (37 bp):
AAATATGTATGCATATGATTTGAATCATGGAATAATT
Found at i:7278 original size:32 final size:30
Alignment explanation
Indices: 7222--7280 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
7212 TATCAAGATA
*
7222 ATTTTTTATTGAAAAACATATTTTAAATAG
1 ATTTTTTATTGAAAAAAATATTTTAAATAG
7252 ATTTTTTATGTTGAAATAAAAT-TTTTAAA
1 ATTTTTTA--TTGAAA-AAAATATTTTAAA
7281 ATAAAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 8 0.32
32 13 0.52
33 4 0.16
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (30 bp):
ATTTTTTATTGAAAAAAATATTTTAAATAG
Found at i:30978 original size:16 final size:17
Alignment explanation
Indices: 30942--30979 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
30932 CGGCATTTTA
30942 GTACCCGAAAATTCTGG
1 GTACCCGAAAATTCTGG
* *
30959 GTACCCGATATTTC-GG
1 GTACCCGAAAATTCTGG
30975 GTACC
1 GTACC
30980 TAAAAGTACG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (17 bp):
GTACCCGAAAATTCTGG
Found at i:36364 original size:2 final size:2
Alignment explanation
Indices: 36357--36400 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
36347 TTTGTTTGAC
36357 AT AT AT AT AT AT 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 AT AT AT AT AT AT
36399 AT
1 AT
36401 TATTTTTCTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50280 original size:39 final size:39
Alignment explanation
Indices: 50233--50395 Score: 184
Period size: 39 Copynumber: 4.2 Consensus size: 39
50223 AAGGCACCTA
*
50233 CCAAGCCACCAACTTATGCTCCTCCGCCCAAAGCACCAC
1 CCAAGCCACCAACTTATCCTCCTCCGCCCAAAGCACCAC
* * *
50272 CCAAGCCACCAACTTATCCTCCTCC-ACCAAAGGTACCAA
1 CCAAGCCACCAACTTATCCTCCTCCGCCCAAA-GCACCAC
* * * * * *
50311 CCAAGCCACCGACTTATGCACCTCCGCCCAAGGTACTAC
1 CCAAGCCACCAACTTATCCTCCTCCGCCCAAAGCACCAC
* * *
50350 CCAAGCCACCAACTTATCCTCCTCCACCCAAGGCAACAC
1 CCAAGCCACCAACTTATCCTCCTCCGCCCAAAGCACCAC
*
50389 CTAAGCC
1 CCAAGCC
50396 GCTGTCACCT
Statistics
Matches: 103, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
38 5 0.05
39 94 0.91
40 4 0.04
ACGTcount: A:0.29, C:0.46, G:0.10, T:0.14
Consensus pattern (39 bp):
CCAAGCCACCAACTTATCCTCCTCCGCCCAAAGCACCAC
Found at i:50395 original size:78 final size:78
Alignment explanation
Indices: 50221--50384 Score: 256
Period size: 78 Copynumber: 2.1 Consensus size: 78
50211 CCAACACCAT
* *
50221 CCAAGGCACCTACCAAGCCACCAACTTATGCTCCTCCGCCCAAAGCACCACCCAAGCCACCAACT
1 CCAAGGCACCAACCAAGCCACCAACTTATGCACCTCCGCCCAAAGCACCACCCAAGCCACCAACT
50286 TATCCTCCTCCAC
66 TATCCTCCTCCAC
* * * * * *
50299 CAAAGGTACCAACCAAGCCACCGACTTATGCACCTCCGCCCAAGGTACTACCCAAGCCACCAACT
1 CCAAGGCACCAACCAAGCCACCAACTTATGCACCTCCGCCCAAAGCACCACCCAAGCCACCAACT
50364 TATCCTCCTCCAC
66 TATCCTCCTCCAC
50377 CCAAGGCA
1 CCAAGGCA
50385 ACACCTAAGC
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
78 76 1.00
ACGTcount: A:0.29, C:0.46, G:0.11, T:0.14
Consensus pattern (78 bp):
CCAAGGCACCAACCAAGCCACCAACTTATGCACCTCCGCCCAAAGCACCACCCAAGCCACCAACT
TATCCTCCTCCAC
Found at i:51913 original size:47 final size:47
Alignment explanation
Indices: 51844--51945 Score: 195
Period size: 47 Copynumber: 2.2 Consensus size: 47
51834 AGATCATTTT
51844 ATAAATTTTAATAATCGAAAAGTTCAACAATACAACGTCTTATAATC
1 ATAAATTTTAATAATCGAAAAGTTCAACAATACAACGTCTTATAATC
*
51891 ATAAATTTTAATAATCGAAAAGTTCAACAATGCAACGTCTTATAATC
1 ATAAATTTTAATAATCGAAAAGTTCAACAATACAACGTCTTATAATC
51938 ATAAATTT
1 ATAAATTT
51946 AATTATAAAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 54 1.00
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.33
Consensus pattern (47 bp):
ATAAATTTTAATAATCGAAAAGTTCAACAATACAACGTCTTATAATC
Done.