Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000710.1 Hibiscus syriacus cultivar Beakdansim tig00001379_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: 58736
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:89 original size:13 final size:15
Alignment explanation
Indices: 50--87 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
40 AGGATTTATT
50 TTATTTTTTTAAGAA
1 TTATTTTTTTAAGAA
65 TTATTTTTTTAAGAA
1 TTATTTTTTTAAGAA
80 -TATTTTTT
1 TTATTTTTT
88 AATTTGAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 8 0.35
15 15 0.65
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (15 bp):
TTATTTTTTTAAGAA
Found at i:1246 original size:21 final size:19
Alignment explanation
Indices: 1208--1253 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
1198 AATTAATCCT
1208 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
1228 ACTAATATTAAAGAGCTAAGA
1 ACTAATATT-AA-AGCTAAGA
1249 A-TAAT
1 ACTAAT
1254 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.17
20 11 0.46
21 9 0.38
ACGTcount: A:0.52, C:0.09, G:0.13, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:11447 original size:21 final size:19
Alignment explanation
Indices: 11409--11454 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
11399 AATTAATCCT
11409 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
11429 ACTAATATTAAAGAGCTAAGA
1 ACTAATATT-AA-AGCTAAGA
11450 A-TAAT
1 ACTAAT
11455 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.17
20 11 0.46
21 9 0.38
ACGTcount: A:0.52, C:0.09, G:0.13, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:17906 original size:21 final size:19
Alignment explanation
Indices: 17876--17921 Score: 74
Period size: 21 Copynumber: 2.3 Consensus size: 19
17866 CTTTTGATTA
17876 ATTTTCATTTTCATTTTTT
1 ATTTTCATTTTCATTTTTT
17895 AGTTTTCAATTTTCATTTTTT
1 A-TTTTC-ATTTTCATTTTTT
17916 ATTTTC
1 ATTTTC
17922 GTTCCTCGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 10 0.40
21 14 0.56
ACGTcount: A:0.17, C:0.11, G:0.02, T:0.70
Consensus pattern (19 bp):
ATTTTCATTTTCATTTTTT
Found at i:18244 original size:39 final size:39
Alignment explanation
Indices: 18190--18274 Score: 170
Period size: 39 Copynumber: 2.2 Consensus size: 39
18180 AGTGCAACCC
18190 AAATCCCAAATTTATCCTCTTGCCGCCTAACACCCCTCA
1 AAATCCCAAATTTATCCTCTTGCCGCCTAACACCCCTCA
18229 AAATCCCAAATTTATCCTCTTGCCGCCTAACACCCCTCA
1 AAATCCCAAATTTATCCTCTTGCCGCCTAACACCCCTCA
18268 AAATCCC
1 AAATCCC
18275 CCCTAAATTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.29, C:0.41, G:0.05, T:0.25
Consensus pattern (39 bp):
AAATCCCAAATTTATCCTCTTGCCGCCTAACACCCCTCA
Found at i:20155 original size:48 final size:48
Alignment explanation
Indices: 20084--20190 Score: 214
Period size: 48 Copynumber: 2.2 Consensus size: 48
20074 CAAAGTATTG
20084 ATTTTGTTGATGTGATTGAGTCTGCAATTGATGAATTTATTGAAACTA
1 ATTTTGTTGATGTGATTGAGTCTGCAATTGATGAATTTATTGAAACTA
20132 ATTTTGTTGATGTGATTGAGTCTGCAATTGATGAATTTATTGAAACTA
1 ATTTTGTTGATGTGATTGAGTCTGCAATTGATGAATTTATTGAAACTA
20180 ATTTTGTTGAT
1 ATTTTGTTGAT
20191 AAATTTTGTA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 59 1.00
ACGTcount: A:0.28, C:0.06, G:0.21, T:0.46
Consensus pattern (48 bp):
ATTTTGTTGATGTGATTGAGTCTGCAATTGATGAATTTATTGAAACTA
Found at i:20173 original size:24 final size:24
Alignment explanation
Indices: 20098--20174 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
20088 TGTTGATGTG
20098 ATTGAGTCTGCAATTGATGAATTT
1 ATTGAGTCTGCAATTGATGAATTT
** * *
20122 ATTGAAACT--AATTTTGTTG-ATGTG
1 ATTGAGTCTGCAA--TTGATGAAT-TT
20146 ATTGAGTCTGCAATTGATGAATTT
1 ATTGAGTCTGCAATTGATGAATTT
20170 ATTGA
1 ATTGA
20175 AACTAATTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 12
0.66 0.14 0.20
Matches are distributed among these distances:
22 2 0.05
23 2 0.05
24 31 0.79
25 2 0.05
26 2 0.05
ACGTcount: A:0.30, C:0.06, G:0.21, T:0.43
Consensus pattern (24 bp):
ATTGAGTCTGCAATTGATGAATTT
Found at i:40532 original size:16 final size:16
Alignment explanation
Indices: 40511--40546 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
40501 GAATCTAAAA
40511 TGAATATAATATGATC
1 TGAATATAATATGATC
40527 TGAATATAATATGATC
1 TGAATATAATATGATC
40543 TGAA
1 TGAA
40547 AGCCCATTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.36
Consensus pattern (16 bp):
TGAATATAATATGATC
Found at i:51825 original size:19 final size:21
Alignment explanation
Indices: 51787--51835 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
51777 TTTAAAAGCT
51787 ATATATTTTTACTCGTAAATGA
1 ATAT-TTTTTACTCGTAAATGA
*
51809 ATATTTTTTA-TCG-AAATTA
1 ATATTTTTTACTCGTAAATGA
*
51828 ATGTTTTT
1 ATATTTTT
51836 ATGGGAAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 12 0.48
20 3 0.12
21 6 0.24
22 4 0.16
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.53
Consensus pattern (21 bp):
ATATTTTTTACTCGTAAATGA
Found at i:53769 original size:13 final size:14
Alignment explanation
Indices: 53751--53786 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
53741 AGTCAACATT
53751 GTATGATTT-TAAA
1 GTATGATTTCTAAA
*
53764 GTATGATTTCTAAC
1 GTATGATTTCTAAA
53778 GTATGATTT
1 GTATGATTT
53787 AATTTTGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.47
Consensus pattern (14 bp):
GTATGATTTCTAAA
Found at i:58466 original size:56 final size:56
Alignment explanation
Indices: 58353--58458 Score: 133
Period size: 56 Copynumber: 1.9 Consensus size: 56
58343 AGGGTATTAT
* * *
58353 TTTGTTGAGTCCCTTGACAATTAAAAGTTACAAAATAATTATATGATTATAGGATG
1 TTTGTTGAGTCCCCTAACAATTAAAAGTTACAAAATAATTATATGACTATAGGATG
* * * *
58409 TTTGTTGAGTCCTCCTAACTATTAAAA-TTATAAAATAGTTATTTGACTAT
1 TTTGTTGAGTCC-CCTAACAATTAAAAGTTACAAAATAATTATATGACTAT
58459 TATATGTTCA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
56 31 0.74
57 11 0.26
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (56 bp):
TTTGTTGAGTCCCCTAACAATTAAAAGTTACAAAATAATTATATGACTATAGGATG
Done.