Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004776.1 Hibiscus syriacus cultivar Beakdansim tig00010772_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: 51462
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:14428 original size:39 final size:39
Alignment explanation
Indices: 14374--14450 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
14364 CATCACTCTT
14374 TAAATCTTAGTTGATTGATTCGAATGCCAAAGATCCCTA
1 TAAATCTTAGTTGATTGATTCGAATGCCAAAGATCCCTA
* * *
14413 TAAATCTTAGTTGATTGATTTGAATGTCAGAGATCCCT
1 TAAATCTTAGTTGATTGATTCGAATGCCAAAGATCCCT
14451 CTTTTGATAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (39 bp):
TAAATCTTAGTTGATTGATTCGAATGCCAAAGATCCCTA
Found at i:14948 original size:20 final size:20
Alignment explanation
Indices: 14923--14963 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
14913 GTAAAACCGT
14923 AAGATTGATTAGCTGTCAAC
1 AAGATTGATTAGCTGTCAAC
14943 AAGATTGATTAGCTGTCAAC
1 AAGATTGATTAGCTGTCAAC
14963 A
1 A
14964 GTCAACATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.29
Consensus pattern (20 bp):
AAGATTGATTAGCTGTCAAC
Found at i:15662 original size:31 final size:31
Alignment explanation
Indices: 15607--15693 Score: 129
Period size: 31 Copynumber: 2.8 Consensus size: 31
15597 TAGAAGTTAC
15607 AAAATGGTCATTAAACTTTATCAAACTATTAT
1 AAAATGGTCATTAAAC-TTATCAAACTATTAT
*
15639 AAAATGGTCATTAAACTTATCAAACTGTTAT
1 AAAATGGTCATTAAACTTATCAAACTATTAT
* * *
15670 TAGATGGTCCTTAAACTTATCAAA
1 AAAATGGTCATTAAACTTATCAAA
15694 ATTTGTCACT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
31 35 0.69
32 16 0.31
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (31 bp):
AAAATGGTCATTAAACTTATCAAACTATTAT
Found at i:17895 original size:17 final size:18
Alignment explanation
Indices: 17863--17896 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17853 GTTGCACTTA
*
17863 TATTTTTTTGAAAAAATT
1 TATTCTTTTGAAAAAATT
17881 TATTCTTTT-AAAAAAT
1 TATTCTTTTGAAAAAAT
17897 ATTTTTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (18 bp):
TATTCTTTTGAAAAAATT
Found at i:25223 original size:2 final size:2
Alignment explanation
Indices: 25216--25279 Score: 110
Period size: 2 Copynumber: 32.0 Consensus size: 2
25206 AGTTAAGCTT
* *
25216 TA TA TA TA TA CA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25258 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
25280 AGAGATTAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:36213 original size:28 final size:29
Alignment explanation
Indices: 36174--36240 Score: 100
Period size: 28 Copynumber: 2.3 Consensus size: 29
36164 AATAGTGAAA
* *
36174 TTTTAATAATTTGATCTTTGAACTTTAT-
1 TTTTAATTATTTGATCTTCGAACTTTATG
*
36202 TTTTAATTATTTGATCTTCGAACTTTGTG
1 TTTTAATTATTTGATCTTCGAACTTTATG
36231 TTTTAATTAT
1 TTTTAATTAT
36241 ACAAACCGTC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
28 25 0.71
29 10 0.29
ACGTcount: A:0.25, C:0.07, G:0.09, T:0.58
Consensus pattern (29 bp):
TTTTAATTATTTGATCTTCGAACTTTATG
Found at i:45612 original size:14 final size:15
Alignment explanation
Indices: 45593--45628 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
45583 TATAATTTTC
45593 TTTT-AAATTTTTAT
1 TTTTAAAATTTTTAT
45607 TTTTAAAATTTTTA-
1 TTTTAAAATTTTTAT
45621 TTTTAAAA
1 TTTTAAAA
45629 AATTATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTTAAAATTTTTAT
Found at i:45617 original size:15 final size:14
Alignment explanation
Indices: 45588--45628 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
45578 AATTGTATAA
*
45588 TTTTCTTTT-AAAT
1 TTTTATTTTAAAAT
45601 TTTTATTTTTAAAAT
1 TTTTA-TTTTAAAAT
45616 TTTTATTTTAAAA
1 TTTTATTTTAAAA
45629 AATTATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 4 0.16
14 12 0.48
15 9 0.36
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTTATTTTAAAAT
Found at i:45629 original size:15 final size:15
Alignment explanation
Indices: 45597--45629 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
45587 ATTTTCTTTT
*
45597 AAATTTTTATTTTTA
1 AAATTTTTATTTTAA
45612 AAATTTTTATTTTAA
1 AAATTTTTATTTTAA
45627 AAA
1 AAA
45630 ATTATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
AAATTTTTATTTTAA
Found at i:48744 original size:171 final size:170
Alignment explanation
Indices: 48372--48862 Score: 556
Period size: 171 Copynumber: 2.8 Consensus size: 170
48362 ACACAAGATG
* * * * *
48372 AGACTTAA-CCAACCACATTGTAAAACTAAACATCTAATTTCATAGATTTTGCATGCAAAAACCA
1 AGACTCAACCCAA-CACATTATAAAACTAAACATCT-ATTTCAAAGTTTTTGCATGCAAAAACTA
* * *
48436 AACCTTATTCATAAGTAATTTTAACACGAAA-ATCGCACTTACAAGCATATGATGTCTTGCATAG
64 AACCTTATTCATAAGTAATTTTAACAC-AAAGACCGCACTTTCAAGCATATGATG-C---C-T-T
* * * * *
48500 CCATAGTTGTAACTTGCAATAATATATGTACGTTATACAGCTCAAGACT
122 CCTTAGTTGTAACTTGCAACAATATATGTACATTACACAGCCCAAGACT
* *
48549 AGACTCAACCCACCACATTATAAAACTAAACATCGTATTTCAAAGTTTTTGCATGCAAAAACTAC
1 AGACTCAACCCAACACATTATAAAACTAAACATC-TATTTCAAAGTTTTTGCATGCAAAAACTAA
* * * * *
48614 ACTTTATTCCTATGAAATTTCAACACAAAGACCGCACTTTCAAGCATATGATGCCTTCCTTAGTT
65 ACCTTATTCATAAGTAATTTTAACACAAAGACCGCACTTTCAAGCATATGATGCCTTCCTTAGTT
* *
48679 GTAACTTGCCACAATATATGTACATTACGCAGCCCAAGACT
130 GTAACTTGCAACAATATATGTACATTACACAGCCCAAGACT
* * * * *
48720 AGACTCAACCCAACTCATTATAAAACTAGACATCTTATCTCAAA-TATTTTGCAAGCAAAATCTA
1 AGACTCAACCCAACACATTATAAAACTAAACATC-TATTTCAAAGT-TTTTGCATGCAAAAACTA
** * * * *
48784 AACCTTATTCATAAGTAATTTTAATGCAAAGACCACACTTTCAAGCATGTGATGCATTGCTTAGT
64 AACCTTATTCATAAGTAATTTTAACACAAAGACCGCACTTTCAAGCATATGATGCCTTCCTTAGT
48849 TGTAACTTGCAACA
129 TGTAACTTGCAACA
48863 GTGACACAGC
Statistics
Matches: 268, Mismatches: 42, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
170 1 0.00
171 163 0.61
172 1 0.00
173 1 0.00
176 4 0.01
177 94 0.35
178 4 0.01
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.30
Consensus pattern (170 bp):
AGACTCAACCCAACACATTATAAAACTAAACATCTATTTCAAAGTTTTTGCATGCAAAAACTAAA
CCTTATTCATAAGTAATTTTAACACAAAGACCGCACTTTCAAGCATATGATGCCTTCCTTAGTTG
TAACTTGCAACAATATATGTACATTACACAGCCCAAGACT
Done.