Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005673.1 Hibiscus syriacus cultivar Beakdansim tig00013267_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: 46596
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:5825 original size:22 final size:20
Alignment explanation
Indices: 5775--5834 Score: 66
Period size: 22 Copynumber: 2.9 Consensus size: 20
5765 ATTTGAAATC
*
5775 TGTCCTGAATGACCTGATGTA
1 TGTCCCGAATGACCT-ATGTA
*
5796 TGTACCGAATGACCTATGTATA
1 TGTCCCGAATGACCTATG--TA
*
5818 TGTCCCGAAGGACCTAT
1 TGTCCCGAATGACCTAT
5835 ATAACCCTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 3 0.09
21 13 0.39
22 17 0.52
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.30
Consensus pattern (20 bp):
TGTCCCGAATGACCTATGTA
Found at i:18766 original size:3 final size:3
Alignment explanation
Indices: 18758--18808 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
18748 GGACCCACAA
18758 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
18806 AAT
1 AAT
18809 CCACTTTCTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:19403 original size:19 final size:19
Alignment explanation
Indices: 19376--19426 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
19366 CTAACAACTC
19376 TAACAACCTCAACCACCAT
1 TAACAACCTCAACCACCAT
*
19395 TACCAACCTCAACCACCAT
1 TAACAACCTCAACCACCAT
*
19414 TAACAGCCTCAAC
1 TAACAACCTCAAC
19427 GGTCATATAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.39, C:0.43, G:0.02, T:0.16
Consensus pattern (19 bp):
TAACAACCTCAACCACCAT
Found at i:19789 original size:22 final size:21
Alignment explanation
Indices: 19760--19801 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
19750 TGATCAAATG
19760 ATATTATTTTAGT-ATTTTTAT
1 ATATTATTTT-GTGATTTTTAT
19781 ATATATATTTTGTGATTTTTA
1 ATAT-TATTTTGTGATTTTTA
19802 GGTAGAATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (21 bp):
ATATTATTTTGTGATTTTTAT
Found at i:23902 original size:21 final size:21
Alignment explanation
Indices: 23876--23920 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
23866 GATTTCTGGG
* *
23876 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
23897 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
23918 CAA
1 CAA
23921 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:25014 original size:32 final size:32
Alignment explanation
Indices: 24973--25038 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
24963 GAGTTGAGGG
24973 TTTACCTATGT-TCTACG-GAACATATGGACAGT
1 TTTACCTATGTCT-TACGAG-ACATATGGACAGT
*
25005 TTTACCTATGTCTTTCGAGACATATGGACAGT
1 TTTACCTATGTCTTACGAGACATATGGACAGT
25037 TT
1 TT
25039 ACCGAGGATC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
32 29 0.94
33 2 0.06
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (32 bp):
TTTACCTATGTCTTACGAGACATATGGACAGT
Found at i:25073 original size:30 final size:30
Alignment explanation
Indices: 25029--25212 Score: 298
Period size: 30 Copynumber: 6.1 Consensus size: 30
25019 TCGAGACATA
25029 TGGACAGTTTACCGAGGATCGTTATGACCTC
1 TGGACAG-TTACCGAGGATCGTTATGACCTC
*
25060 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCGTTATGACCTC
25090 TGGACAGTTACCGAGGATCGTTATGACCTC
1 TGGACAGTTACCGAGGATCGTTATGACCTC
25120 TGGACAGTTACCGAGGATCGTTATGACCTC
1 TGGACAGTTACCGAGGATCGTTATGACCTC
*
25150 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCGTTATGACCTC
* * * *
25180 TGGACATTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCGTTATGACCTC
25209 TGGA
1 TGGA
25213 TAGGTCCTTC
Statistics
Matches: 147, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
29 18 0.12
30 122 0.83
31 7 0.05
ACGTcount: A:0.22, C:0.23, G:0.26, T:0.29
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCGTTATGACCTC
Found at i:28512 original size:13 final size:14
Alignment explanation
Indices: 28488--28522 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
28478 TTAATTAATT
*
28488 TTCAATTGAATTAA
1 TTCAATTAAATTAA
28502 TT-AATTAAATTAA
1 TTCAATTAAATTAA
28515 TTCAATTA
1 TTCAATTA
28523 TGTTCTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (14 bp):
TTCAATTAAATTAA
Found at i:30659 original size:15 final size:15
Alignment explanation
Indices: 30641--30697 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
30631 GTAACCGGTT
30641 TCGGTTTTAAAAAAA
1 TCGGTTTTAAAAAAA
*
30656 TCGGTTTTTTTAAAAAA
1 TCGG--TTTTAAAAAAA
*
30673 TCGGTTATAAAAAAA
1 TCGGTTTTAAAAAAA
* *
30688 CCGATTTTAA
1 TCGGTTTTAA
30698 TATTCCAGAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 20 0.59
17 14 0.41
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (15 bp):
TCGGTTTTAAAAAAA
Found at i:30670 original size:17 final size:17
Alignment explanation
Indices: 30645--30678 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
30635 CCGGTTTCGG
30645 TTTTAAAAAAATCGGTT
1 TTTTAAAAAAATCGGTT
*
30662 TTTTTAAAAAATCGGTT
1 TTTTAAAAAAATCGGTT
30679 ATAAAAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (17 bp):
TTTTAAAAAAATCGGTT
Found at i:30890 original size:21 final size:21
Alignment explanation
Indices: 30866--30920 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
30856 ACACTTAGGG
30866 AACCGATTCCCTCTGAGAGGA
1 AACCGATTCCCTCTGAGAGGA
* *
30887 AACCGATTCCCTATGAGAGGG
1 AACCGATTCCCTCTGAGAGGA
*
30908 TACCGATTCCCTC
1 AACCGATTCCCTC
30921 ACGCTCGAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.25, C:0.31, G:0.22, T:0.22
Consensus pattern (21 bp):
AACCGATTCCCTCTGAGAGGA
Found at i:31135 original size:13 final size:13
Alignment explanation
Indices: 31114--31143 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
31104 AAGTTCGATA
31114 AATTCAAATACTT
1 AATTCAAATACTT
*
31127 AATTGAAATACTT
1 AATTCAAATACTT
31140 AATT
1 AATT
31144 AACTCAACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (13 bp):
AATTCAAATACTT
Found at i:31250 original size:32 final size:33
Alignment explanation
Indices: 31154--31252 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
31144 AACTCAACAT
* * * *
31154 AATTGAAATATTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
31187 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
31220 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
31252 A
1 A
31253 TTGAAACAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 12 0.19
33 50 0.81
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.33
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:31271 original size:21 final size:21
Alignment explanation
Indices: 31247--31286 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
31237 ACTTCAAGTT
31247 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
31268 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
31287 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:33612 original size:11 final size:12
Alignment explanation
Indices: 33591--33636 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
33581 TCCGGATAAA
33591 AACCGGTTTTTT
1 AACCGGTTTTTT
33603 AACCGGTTTTTTT
1 AACCGG-TTTTTT
33616 CAAACCGGTTTTTT
1 --AACCGGTTTTTT
*
33630 ATCCGGT
1 AACCGGT
33637 AAAAAAACCG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 12 0.40
13 6 0.20
14 6 0.20
15 6 0.20
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:33621 original size:15 final size:14
Alignment explanation
Indices: 33590--33629 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
33580 TTCCGGATAA
33590 AAACCGG-TTTTTT
1 AAACCGGTTTTTTT
33603 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
33616 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
33630 ATCCGGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
15 12 0.50
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:37025 original size:13 final size:13
Alignment explanation
Indices: 37007--37031 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36997 CATCGTTGAA
37007 CAGTCTTCATATG
1 CAGTCTTCATATG
37020 CAGTCTTCATAT
1 CAGTCTTCATAT
37032 CCGCGAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.40
Consensus pattern (13 bp):
CAGTCTTCATATG
Done.