Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003635.1 Hibiscus syriacus cultivar Beakdansim tig00007696_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: 43387
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:1742 original size:41 final size:41
Alignment explanation
Indices: 1685--1763 Score: 140
Period size: 41 Copynumber: 1.9 Consensus size: 41
1675 ATAATTTCGT
* *
1685 CTCCACACTTTTATAATATTTATATATATATATTAGTATTA
1 CTCCACACTTTTATAATATTCACATATATATATTAGTATTA
1726 CTCCACACTTTTATAATATTCACATATATATATTAGTA
1 CTCCACACTTTTATAATATTCACATATATATATTAGTA
1764 CTAATTTCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.37, C:0.15, G:0.03, T:0.46
Consensus pattern (41 bp):
CTCCACACTTTTATAATATTCACATATATATATTAGTATTA
Found at i:3343 original size:26 final size:27
Alignment explanation
Indices: 3291--3343 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
3281 TTTTTATTAC
* * * *
3291 TGTTATATATCTTTTTATTTTTCCCAT
1 TGTTATATATCTTATCATTATTACCAT
3318 TGTT-TATATCTTATCATTATTACCAT
1 TGTTATATATCTTATCATTATTACCAT
3344 CATATACATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.23, C:0.15, G:0.04, T:0.58
Consensus pattern (27 bp):
TGTTATATATCTTATCATTATTACCAT
Found at i:8839 original size:65 final size:65
Alignment explanation
Indices: 8758--8891 Score: 268
Period size: 65 Copynumber: 2.1 Consensus size: 65
8748 GCCATTCAAA
8758 GAAGATGTGCTAGTCGTCAATGAACCTATAAAGGAGGAAGAAGCTAAAGAGTTCCTCAAGATCTT
1 GAAGATGTGCTAGTCGTCAATGAACCTATAAAGGAGGAAGAAGCTAAAGAGTTCCTCAAGATCTT
8823 GAAGATGTGCTAGTCGTCAATGAACCTATAAAGGAGGAAGAAGCTAAAGAGTTCCTCAAGATCTT
1 GAAGATGTGCTAGTCGTCAATGAACCTATAAAGGAGGAAGAAGCTAAAGAGTTCCTCAAGATCTT
8888 GAAG
1 GAAG
8892 CACAGCGAGT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 69 1.00
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.22
Consensus pattern (65 bp):
GAAGATGTGCTAGTCGTCAATGAACCTATAAAGGAGGAAGAAGCTAAAGAGTTCCTCAAGATCTT
Found at i:13857 original size:45 final size:47
Alignment explanation
Indices: 13790--13878 Score: 128
Period size: 45 Copynumber: 1.9 Consensus size: 47
13780 AATACTTCGC
* * *
13790 TTAGGATGAAAACCCGAGAGGGCGTCCTAAGTT-AAAAA-AAAACGT
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAGAAAACGT
*
13835 TTAGGGTGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAGAAAA
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAGAAAA
13879 AGAGGAAAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
45 29 0.76
46 5 0.13
47 4 0.11
ACGTcount: A:0.44, C:0.16, G:0.25, T:0.16
Consensus pattern (47 bp):
TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAGAAAACGT
Found at i:14789 original size:105 final size:105
Alignment explanation
Indices: 14607--15309 Score: 1226
Period size: 105 Copynumber: 6.7 Consensus size: 105
14597 AGGTTTTACC
*
14607 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
14672 ACGAAAGGACCGCTGGTTGTCAACAAACGTTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
14712 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
14777 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
14817 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
14882 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
14922 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
14987 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
15027 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
15092 ACGAAAGGACCGCTGGTTGTCAACAAACATTTCTCAATAT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
15132 CAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * * * *
15197 ACGAAGGGACCGCTGGTTGTCAATAAATAACTTCCCAACTT
66 ACGAAGGGACCGCTGGTTGTCAACAAA-CATTTCTCAATTT
* * **** *
15238 CAGAGCCAATTTCAACTTCACAACGAGGGATATTGGACTCAAGACAGTATAAGTTCAACTTCGCG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
15303 ACGAAGG
66 ACGAAGG
15310 AGCTATATAC
Statistics
Matches: 574, Mismatches: 23, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
105 502 0.87
106 72 0.13
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:15740 original size:41 final size:38
Alignment explanation
Indices: 15683--15758 Score: 125
Period size: 41 Copynumber: 1.9 Consensus size: 38
15673 ATAATTTCGT
15683 CTCCACACTTTTATAATATTTACATATATATATTAGTATTA
1 CTCCACACTTTTATAATA-TT-CA-ATATATATTAGTATTA
15724 CTCCACACTTTTATAATATTCAATATATATTAGTA
1 CTCCACACTTTTATAATATTCAATATATATTAGTA
15759 CTAATTTCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
38 13 0.37
39 2 0.06
40 2 0.06
41 18 0.51
ACGTcount: A:0.37, C:0.16, G:0.03, T:0.45
Consensus pattern (38 bp):
CTCCACACTTTTATAATATTCAATATATATTAGTATTA
Found at i:17017 original size:8 final size:8
Alignment explanation
Indices: 16982--17019 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
16972 TTATGTCACT
16982 TATATGT-
1 TATATGTA
16989 TATAT-TA
1 TATATGTA
*
16996 TATATATA
1 TATATGTA
17004 TATATGTA
1 TATATGTA
17012 TATATGTA
1 TATATGTA
17020 CACATTTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
6 1 0.04
7 10 0.36
8 17 0.61
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (8 bp):
TATATGTA
Found at i:26742 original size:20 final size:20
Alignment explanation
Indices: 26713--26750 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
26703 TTTGGTTCAC
26713 GGAATATAAGATTACCAGTG
1 GGAATATAAGATTACCAGTG
*
26733 GGAATGTAAGATTACCAG
1 GGAATATAAGATTACCAG
26751 GGAATAGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.11, G:0.26, T:0.24
Consensus pattern (20 bp):
GGAATATAAGATTACCAGTG
Found at i:26755 original size:18 final size:19
Alignment explanation
Indices: 26713--26756 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
26703 TTTGGTTCAC
26713 GGAATATAAGATTACCAGTG
1 GGAATATAAGATTACCAG-G
*
26733 GGAATGTAAGATTACCA-G
1 GGAATATAAGATTACCAGG
26751 GGAATA
1 GGAATA
26757 GGATTACTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 6 0.27
20 16 0.73
ACGTcount: A:0.41, C:0.09, G:0.27, T:0.23
Consensus pattern (19 bp):
GGAATATAAGATTACCAGG
Found at i:26920 original size:38 final size:37
Alignment explanation
Indices: 26875--26971 Score: 97
Period size: 38 Copynumber: 2.5 Consensus size: 37
26865 TTATCCTTAT
* * *
26875 TATATATTTTTAT-AATATTATAAGTTAGAAAATATTTA
1 TATATATTTTTATAAAAATT-TAAATT-CAAAATATTTA
* *
26913 TATATATTTTCTTTAAAAATTTAAATTCATAATATTTA
1 TATATATTTT-TATAAAAATTTAAATTCAAAATATTTA
*
26951 TATATATTTTTTTACAAAATT
1 TATATATTTTTATA-AAAATT
26972 AAAAATATAA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
37 4 0.08
38 35 0.69
39 7 0.14
40 5 0.10
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (37 bp):
TATATATTTTTATAAAAATTTAAATTCAAAATATTTA
Done.