Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001313.1 Hibiscus syriacus cultivar Beakdansim tig00002559_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: 75694
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:4528 original size:19 final size:19
Alignment explanation
Indices: 4484--4530 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
4474 TTGTGTTCTT
4484 TTTTTCTTTCGAACAGTCTC
1 TTTTT-TTTCGAACAGTCTC
*
4504 TCTTTTTTCGAACAG-CTGC
1 TTTTTTTTCGAACAGTCT-C
4523 TTTTTTTT
1 TTTTTTTT
4531 TCATTCAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 2 0.08
19 18 0.75
20 4 0.17
ACGTcount: A:0.13, C:0.21, G:0.11, T:0.55
Consensus pattern (19 bp):
TTTTTTTTCGAACAGTCTC
Found at i:5391 original size:16 final size:16
Alignment explanation
Indices: 5370--5401 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5360 TGCTTAATCG
*
5370 GAAAAAAATAATAAAA
1 GAAAAAAAAAATAAAA
5386 GAAAAAAAAAATAAAA
1 GAAAAAAAAAATAAAA
5402 ATAACGGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.06, T:0.09
Consensus pattern (16 bp):
GAAAAAAAAAATAAAA
Found at i:23499 original size:21 final size:21
Alignment explanation
Indices: 23461--23500 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
23451 AAACAGTTAG
*
23461 TAAAAAAAAAATAGAAATGAA
1 TAAAAAAAAAAGAGAAATGAA
23482 TAAAAATAAAAAGA-AAATG
1 TAAAAA-AAAAAGAGAAATG
23501 TCAAGAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.75, C:0.00, G:0.10, T:0.15
Consensus pattern (21 bp):
TAAAAAAAAAAGAGAAATGAA
Found at i:24608 original size:38 final size:40
Alignment explanation
Indices: 24539--24618 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 40
24529 AATATATATA
*
24539 TATATATATATACATCAAAGTATTAATAAAATA-AATAAGC
1 TATATATATATACAACAAAGTATTAATAAAATAGAA-AAGC
*
24579 TATATATATATACAACAAA-TATTTA-AAAATAGAAAAGC
1 TATATATATATACAACAAAGTATTAATAAAATAGAAAAGC
24617 TA
1 TA
24619 ACCTCTCACT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
38 12 0.32
39 7 0.19
40 18 0.49
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.31
Consensus pattern (40 bp):
TATATATATATACAACAAAGTATTAATAAAATAGAAAAGC
Found at i:25029 original size:2 final size:2
Alignment explanation
Indices: 25022--25087 Score: 125
Period size: 2 Copynumber: 33.5 Consensus size: 2
25012 TATTAAAGAA
25022 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
25064 AT AT AT AT AT AT A- AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
25088 AAATATAGTA
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 62 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25587 original size:35 final size:35
Alignment explanation
Indices: 25548--25619 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
25538 CTAAAAAACC
25548 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
25583 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
25618 CT
1 CT
25620 TCTTTTTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (35 bp):
CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
Found at i:26393 original size:23 final size:24
Alignment explanation
Indices: 26342--26394 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
26332 CATTTAAATG
* *
26342 ATAAACGAACACAAATGAACGAAC
1 ATAAACAAACACAAATAAACGAAC
*
26366 ATAAACAAACAC-AATAAACGGAC
1 ATAAACAAACACAAATAAACGAAC
*
26389 CTAAAC
1 ATAAAC
26395 GAACGTAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.58, C:0.23, G:0.09, T:0.09
Consensus pattern (24 bp):
ATAAACAAACACAAATAAACGAAC
Found at i:26624 original size:24 final size:24
Alignment explanation
Indices: 26597--26642 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
26587 AAATAAACAC
26597 ACATAAACAAACATAAACGAACGA
1 ACATAAACAAACATAAACGAACGA
** *
26621 ACATAAATGAACATAAATGAAC
1 ACATAAACAAACATAAACGAAC
26643 ATATTACCGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.61, C:0.17, G:0.09, T:0.13
Consensus pattern (24 bp):
ACATAAACAAACATAAACGAACGA
Found at i:30910 original size:29 final size:29
Alignment explanation
Indices: 30875--30956 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
30865 AAACTAAATT
*
30875 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
30904 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
30933 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
30957 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:35669 original size:29 final size:29
Alignment explanation
Indices: 35634--35715 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
35624 AAACTAAATT
*
35634 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
35663 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
35692 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
35716 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:42131 original size:20 final size:20
Alignment explanation
Indices: 42106--42152 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
42096 GAGCTATCTC
42106 TGTCGTTCTTACGTTTTTCA
1 TGTCGTTCTTACGTTTTTCA
42126 TGTCGTTCTTACGTTTTTCA
1 TGTCGTTCTTACGTTTTTCA
42146 TGTCGTT
1 TGTCGTT
42153 TATTGCTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.09, C:0.19, G:0.17, T:0.55
Consensus pattern (20 bp):
TGTCGTTCTTACGTTTTTCA
Found at i:55264 original size:29 final size:30
Alignment explanation
Indices: 55202--55267 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
55192 CGGTGGTTTG
*
55202 ATTGAATCAATTAAATAGTTGGATGGTCTA
1 ATTGATTCAATTAAATAGTTGGATGGTCTA
*
55232 ATTGATTCAATTGAA-AGTTTGG-TGGTC-A
1 ATTGATTCAATTAAATAG-TTGGATGGTCTA
55260 CATTGATT
1 -ATTGATT
55268 TTTTATCATA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 1 0.03
29 14 0.44
30 17 0.53
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.39
Consensus pattern (30 bp):
ATTGATTCAATTAAATAGTTGGATGGTCTA
Found at i:55884 original size:2 final size:2
Alignment explanation
Indices: 55877--55902 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
55867 TGTGTAATTG
55877 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
55903 GGTTATATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:69882 original size:2 final size:2
Alignment explanation
Indices: 69875--69920 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
69865 TAGACCAATC
69875 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
69917 AT AT
1 AT AT
69921 CAATGCATTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:70306 original size:20 final size:20
Alignment explanation
Indices: 70277--70317 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
70267 GTAAAAGTTC
*
70277 TGGTCAACGAAGGTTAACGG
1 TGGTCAACGAAGGTCAACGG
* *
70297 TGGTCTACGACGGTCAACGG
1 TGGTCAACGAAGGTCAACGG
70317 T
1 T
70318 TTTACACAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.20, G:0.34, T:0.22
Consensus pattern (20 bp):
TGGTCAACGAAGGTCAACGG
Found at i:73041 original size:25 final size:25
Alignment explanation
Indices: 73007--73055 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
72997 AGACTTTTTA
73007 TTATAATTAAATA-TTATTTAGTATTT
1 TTATAATTAAA-AGTTATTTA-TATTT
73033 TTAT-ATTAAAAGTTATTTATATT
1 TTATAATTAAAAGTTATTTATATT
73056 ATATATTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 5 0.23
25 13 0.59
26 4 0.18
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (25 bp):
TTATAATTAAAAGTTATTTATATTT
Done.