Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003508.1 Hibiscus syriacus cultivar Beakdansim tig00007415_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: 51289
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:122 original size:15 final size:15
Alignment explanation
Indices: 95--128 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
85 ATACATATAA
95 TTTATATTTTATGTT
1 TTTATATTTTATGTT
110 GTTTATA-TTTATGTT
1 -TTTATATTTTATGTT
125 TTTA
1 TTTA
129 AGTCAACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 8 0.44
16 6 0.33
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.71
Consensus pattern (15 bp):
TTTATATTTTATGTT
Found at i:476 original size:17 final size:18
Alignment explanation
Indices: 454--487 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
444 ATTAAAGTTA
454 TTTT-AATCAATTTAAAC
1 TTTTAAATCAATTTAAAC
*
471 TTTTAAATGAATTTAAA
1 TTTTAAATCAATTTAAA
488 TTTGAATTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (18 bp):
TTTTAAATCAATTTAAAC
Found at i:1361 original size:157 final size:160
Alignment explanation
Indices: 1049--1366 Score: 583
Period size: 158 Copynumber: 2.0 Consensus size: 160
1039 CAACAATCCA
1049 ATGCACAAGTTATTTATATAAAAAATTCAAATAATTGAGATCGATTAAATTAATTAATTTTAATG
1 ATGCACAAGTTATTTATATAAAAAATTCAAATAATTGAGATCGATTAAATTAATTAATTTTAATG
1114 ATTGATATTAATTAAAGCTTTTTAATAGAAATTGTTAATTTTAATAAAAAAACATTTAAAATTAT
66 ATTGATATTAATTAAAGCTTTTTAATAGAAATTGTTAATTTTAATAAAAAAACATTTAAAATTAT
1179 AATAGAGATTTATAATCATAATTGTAAACT
131 AATAGAGATTTATAATCATAATTGTAAACT
1209 ATGCATCAAGTTATTTATAT-AAAAATTCAAATAATTTGAGATCGATTAAATTAA-TAATTTTAA
1 ATGCA-CAAGTTATTTATATAAAAAATTCAAATAA-TTGAGATCGATTAAATTAATTAATTTTAA
1272 -GATTGATATTAATT-AAGCTTTTTAATAGAAATTGTTAATTTTAATAAAAAAACATTT-AAATT
64 TGATTGATATTAATTAAAGCTTTTTAATAGAAATTGTTAATTTTAATAAAAAAACATTTAAAATT
1334 ATAATAGAGATTTATAATCATAATTGTAAACT
129 ATAATAGAGATTTATAATCATAATTGTAAACT
1366 A
1 A
1367 AGTGACAACG
Statistics
Matches: 156, Mismatches: 0, Indels: 7
0.96 0.00 0.04
Matches are distributed among these distances:
157 38 0.24
158 43 0.28
159 14 0.09
160 28 0.18
161 33 0.21
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.40
Consensus pattern (160 bp):
ATGCACAAGTTATTTATATAAAAAATTCAAATAATTGAGATCGATTAAATTAATTAATTTTAATG
ATTGATATTAATTAAAGCTTTTTAATAGAAATTGTTAATTTTAATAAAAAAACATTTAAAATTAT
AATAGAGATTTATAATCATAATTGTAAACT
Found at i:7213 original size:18 final size:17
Alignment explanation
Indices: 7180--7213 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
7170 TGTTACCTTA
*
7180 TTTCAAGTATATTAATG
1 TTTCAAGTACATTAATG
7197 TTTCAAGTACCATTAAT
1 TTTCAAGTA-CATTAAT
7214 CTGCCATGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (17 bp):
TTTCAAGTACATTAATG
Found at i:14323 original size:12 final size:12
Alignment explanation
Indices: 14306--14330 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
14296 TTTAATGACT
14306 AAATGTAAATCA
1 AAATGTAAATCA
14318 AAATGTAAATCA
1 AAATGTAAATCA
14330 A
1 A
14331 CGACATATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.08, G:0.08, T:0.24
Consensus pattern (12 bp):
AAATGTAAATCA
Found at i:17012 original size:12 final size:12
Alignment explanation
Indices: 16995--17027 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
16985 GCAACTTCAA
16995 TGGTGGCATGAT
1 TGGTGGCATGAT
17007 TGGTGGCATGAT
1 TGGTGGCATGAT
*
17019 TGGCGGCAT
1 TGGTGGCAT
17028 CTTATTCATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.12, G:0.42, T:0.30
Consensus pattern (12 bp):
TGGTGGCATGAT
Found at i:21655 original size:22 final size:22
Alignment explanation
Indices: 21602--21664 Score: 56
Period size: 22 Copynumber: 2.7 Consensus size: 22
21592 GGAAATGTTA
* *
21602 AACATTTTAAGTAGAACCCAAAATT
1 AACATTTCAAGTAGAA---AAAAAT
21627 AACATTTTC-AGTAGAAAAAAAT
1 AACA-TTTCAAGTAGAAAAAAAT
*
21649 AATATTTCAAGTAGAA
1 AACATTTCAAGTAGAA
21665 TTTTACCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
21 4 0.12
22 15 0.45
25 11 0.33
26 3 0.09
ACGTcount: A:0.51, C:0.11, G:0.10, T:0.29
Consensus pattern (22 bp):
AACATTTCAAGTAGAAAAAAAT
Found at i:29809 original size:2 final size:2
Alignment explanation
Indices: 29802--29841 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
29792 GAACCCATTG
29802 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
29842 CATTTGAGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39972 original size:15 final size:16
Alignment explanation
Indices: 39947--39987 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
39937 AAGGTTGTTC
*
39947 GAAAG-AAAAAGAGA-
1 GAAAGAAAAAAGACAT
*
39961 GAGAGAAAAAAGACAT
1 GAAAGAAAAAAGACAT
39977 GAAAGAAAAAA
1 GAAAGAAAAAA
39988 ATGGAAAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 4 0.18
15 8 0.36
16 10 0.45
ACGTcount: A:0.71, C:0.02, G:0.24, T:0.02
Consensus pattern (16 bp):
GAAAGAAAAAAGACAT
Found at i:48045 original size:120 final size:120
Alignment explanation
Indices: 47832--48075 Score: 479
Period size: 120 Copynumber: 2.0 Consensus size: 120
47822 ATGTAGTTTC
*
47832 TCCAACCCTGCCCAAAGAAAAATGGCTGTATATTATCTTTGCTTTTTTATTCCACAGAAACTCAG
1 TCCAACCCTGCCCAAAGAAAAATGGCTCTATATTATCTTTGCTTTTTTATTCCACAGAAACTCAG
47897 ACGCCAGTCTTTGCATTTTGGTGAAACCCTGTTTTTCCAGTGTTGTATGCCCATT
66 ACGCCAGTCTTTGCATTTTGGTGAAACCCTGTTTTTCCAGTGTTGTATGCCCATT
47952 TCCAACCCTGCCCAAAGAAAAATGGCTCTATATTATCTTTGCTTTTTTATTCCACAGAAACTCAG
1 TCCAACCCTGCCCAAAGAAAAATGGCTCTATATTATCTTTGCTTTTTTATTCCACAGAAACTCAG
48017 ACGCCAGTCTTTGCATTTTGGTGAAACCCTGTTTTTCCAGTGTTGTATGCCCATT
66 ACGCCAGTCTTTGCATTTTGGTGAAACCCTGTTTTTCCAGTGTTGTATGCCCATT
48072 TCCA
1 TCCA
48076 CCCATTAATT
Statistics
Matches: 123, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 123 1.00
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.36
Consensus pattern (120 bp):
TCCAACCCTGCCCAAAGAAAAATGGCTCTATATTATCTTTGCTTTTTTATTCCACAGAAACTCAG
ACGCCAGTCTTTGCATTTTGGTGAAACCCTGTTTTTCCAGTGTTGTATGCCCATT
Found at i:49014 original size:17 final size:18
Alignment explanation
Indices: 48957--49020 Score: 71
Period size: 19 Copynumber: 3.6 Consensus size: 18
48947 CCGTTTTGGT
48957 TTTTTCGGTTCGGTTCGGG
1 TTTTTCGGTTCGGTTC-GG
*
48976 TTTTT---TAACGGTTCGG
1 TTTTTCGGT-TCGGTTCGG
48992 ATTTTTCGGTTCGGTTCGG
1 -TTTTTCGGTTCGGTTCGG
49011 TTTTTCGGTT
1 TTTTTCGGTT
49021 TTTCAATGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
16 3 0.08
17 11 0.29
18 10 0.26
19 13 0.34
20 1 0.03
ACGTcount: A:0.05, C:0.14, G:0.30, T:0.52
Consensus pattern (18 bp):
TTTTTCGGTTCGGTTCGG
Done.