Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002761.1 Hibiscus syriacus cultivar Beakdansim tig00005691_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: 83453
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:15093 original size:18 final size:17
Alignment explanation
Indices: 15070--15108 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
15060 GACCGGTCAC
15070 GACCCGACCCGACCCGTT
1 GACCCGACCCGA-CCGTT
*
15088 GACCCGACCCGATCGTT
1 GACCCGACCCGACCGTT
15105 GACC
1 GACC
15109 GTTGACCGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.13
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:20609 original size:24 final size:24
Alignment explanation
Indices: 20580--20644 Score: 73
Period size: 23 Copynumber: 2.8 Consensus size: 24
20570 AGTTTATTTT
*
20580 AAAACATATAAATATATAGCTTT-G
1 AAAACATATAAATATATAG-TTTAA
20604 AAAACATAT-AATATAGT-GTTTAA
1 AAAACATATAAATATA-TAGTTTAA
*
20627 AAAATATATAAATATATA
1 AAAACATATAAATATATA
20645 TAATTTATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
22 3 0.09
23 16 0.46
24 16 0.46
ACGTcount: A:0.55, C:0.05, G:0.06, T:0.34
Consensus pattern (24 bp):
AAAACATATAAATATATAGTTTAA
Found at i:26921 original size:21 final size:21
Alignment explanation
Indices: 26896--26937 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
26886 GACTATTTTT
*
26896 TTTTTTTTTCACACTTTTTTCG
1 TTTTGTTTTC-CACTTTTTTCG
*
26918 TTTTGTTTTCCATTTTTTTC
1 TTTTGTTTTCCACTTTTTTC
26938 ATGTCTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.07, C:0.17, G:0.05, T:0.71
Consensus pattern (21 bp):
TTTTGTTTTCCACTTTTTTCG
Found at i:26946 original size:13 final size:13
Alignment explanation
Indices: 26930--26962 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
26920 TTGTTTTCCA
26930 TTTTTTTCATGTC
1 TTTTTTTCATGTC
*
26943 TTTTTTT-TTGTC
1 TTTTTTTCATGTC
26955 TTTTTTTC
1 TTTTTTTC
26963 GAACTACTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.03, C:0.12, G:0.06, T:0.79
Consensus pattern (13 bp):
TTTTTTTCATGTC
Found at i:37278 original size:25 final size:25
Alignment explanation
Indices: 37239--37286 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
37229 ACCGATTTGA
*
37239 CCGGTCTGACCCGACCCGACCCGAC
1 CCGGTCTAACCCGACCCGACCCGAC
*
37264 CCGGTCTAACTCGACCCGACCCG
1 CCGGTCTAACCCGACCCGACCCG
37287 GTCTGAATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.17, C:0.50, G:0.23, T:0.10
Consensus pattern (25 bp):
CCGGTCTAACCCGACCCGACCCGAC
Found at i:37300 original size:19 final size:20
Alignment explanation
Indices: 37255--37304 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
37245 TGACCCGACC
37255 CGACCCGACCCGGTCTAACT
1 CGACCCGACCCGGTCTAACT
37275 CGACCCGACCCGGTCTGAA-T
1 CGACCCGACCCGGTCT-AACT
37295 -GACCCGACCC
1 CGACCCGACCC
37305 AACTACTCGA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 10 0.34
20 17 0.59
21 2 0.07
ACGTcount: A:0.20, C:0.46, G:0.22, T:0.12
Consensus pattern (20 bp):
CGACCCGACCCGGTCTAACT
Found at i:39630 original size:24 final size:24
Alignment explanation
Indices: 39614--39673 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
39604 TTCTATTATA
**
39614 ATACTTGACCTGGATTCTCATCGG
1 ATACTTGACCTGGATTCTCATATG
*
39638 ATACTTGACCTGGATTCTGATATG
1 ATACTTGACCTGGATTCTCATATG
39662 ATACTTGACCTG
1 ATACTTGACCTG
39674 AAATATGCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (24 bp):
ATACTTGACCTGGATTCTCATATG
Found at i:43090 original size:24 final size:24
Alignment explanation
Indices: 43058--43117 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
43048 TTTTGTTATA
*
43058 ATACTTGACCTGGATTCTGATCTG
1 ATACTTGACCTGGATTCTGATATG
*
43082 ATACTTGACTTGGATTCTGATATG
1 ATACTTGACCTGGATTCTGATATG
*
43106 ATAGTTGACCTG
1 ATACTTGACCTG
43118 AATTATGTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (24 bp):
ATACTTGACCTGGATTCTGATATG
Found at i:45808 original size:18 final size:18
Alignment explanation
Indices: 45785--45831 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
45775 CTTTAAGTTT
**
45785 ATATTTTTAAATTTTTAA
1 ATATTTTTAAATTAATAA
*
45803 ATATTTTTAAAATAATAA
1 ATATTTTTAAATTAATAA
45821 AT-TTTTTAAAT
1 ATATTTTTAAAT
45832 GATTTTTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATATTTTTAAATTAATAA
Found at i:45815 original size:11 final size:10
Alignment explanation
Indices: 45785--45841 Score: 52
Period size: 8 Copynumber: 6.1 Consensus size: 10
45775 CTTTAAGTTT
45785 ATATTTTT-A
1 ATATTTTTAA
45794 A-ATTTTTAA
1 ATATTTTTAA
45803 ATATTTTTAA
1 ATATTTTTAA
**
45813 A-A-TAATAA
1 ATATTTTTAA
45821 AT-TTTTTAA
1 ATATTTTTAA
45830 ATGATTTTTAA
1 AT-ATTTTTAA
45841 A
1 A
45842 ATAAAAGCTA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
8 11 0.29
9 10 0.26
10 9 0.24
11 8 0.21
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (10 bp):
ATATTTTTAA
Found at i:45837 original size:28 final size:26
Alignment explanation
Indices: 45792--45845 Score: 90
Period size: 28 Copynumber: 2.0 Consensus size: 26
45782 TTTATATTTT
45792 TAAATTTTTAAATATTTTTAAAATAA
1 TAAATTTTTAAATATTTTTAAAATAA
45818 TAAATTTTTTAAATGATTTTTAAAATAA
1 TAAA-TTTTTAAAT-ATTTTTAAAATAA
45846 AAGCTAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 4 0.15
27 9 0.35
28 13 0.50
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (26 bp):
TAAATTTTTAAATATTTTTAAAATAA
Found at i:47214 original size:158 final size:156
Alignment explanation
Indices: 46924--47220 Score: 337
Period size: 158 Copynumber: 1.9 Consensus size: 156
46914 ATATAGTAGT
* * * * *
46924 ACTTTAGCGGCGTTTTTATAAAAACGCCGCAATATGTCCATCTATAGTGGCGTTTTTCAATTAAC
1 ACTTTAGCGACATTTTTATAAAAACGCCGCAATAGGTCCACCTATAGTGGCGTTTTTCAATAAAC
* * * * * ** *
46989 ACCGCAACATATTAGTACTTTAGAAGTGTTTTTATACAAATGTCGTAATAGGGTTCACCTATAGT
66 ACCGCAACATATAAGAACTTTAGAAGCGTTTCTATACAAACGTCGTAATAGACTTCAACTATAGT
47054 GGCATTTTTCAATAAACGCCGCAACA
131 GGCATTTTTCAATAAACGCCGCAACA
* * * *
47080 ACTTTAGCGACATTTTTATACAAATGTCGCAATAAGGTTCACCTATAGTGGCGTTTTTTCAATAA
1 ACTTTAGCGACATTTTTATAAAAACGCCGCAAT-AGGTCCACCTATAGTGGCG-TTTTTCAATAA
* ** * *
47145 ACACCGCAATATATAAGAACTTTAGCGGCGTTTCTATACAAACGTTGGTAA-AGACTT-ATACTT
64 ACACCGCAACATATAAGAACTTTAGAAGCGTTTCTATACAAACG-TCGTAATAGACTTCA-ACTA
*
47208 TTGTGGCATTTTT
127 TAGTGGCATTTTT
47221 ATACAAACGC
Statistics
Matches: 114, Mismatches: 23, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
156 28 0.25
157 17 0.15
158 64 0.56
159 5 0.04
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (156 bp):
ACTTTAGCGACATTTTTATAAAAACGCCGCAATAGGTCCACCTATAGTGGCGTTTTTCAATAAAC
ACCGCAACATATAAGAACTTTAGAAGCGTTTCTATACAAACGTCGTAATAGACTTCAACTATAGT
GGCATTTTTCAATAAACGCCGCAACA
Found at i:51190 original size:29 final size:29
Alignment explanation
Indices: 51148--51320 Score: 105
Period size: 29 Copynumber: 5.9 Consensus size: 29
51138 ACCGTTGACC
* * * *
51148 GGTGCTATTCTGGGAATTTATTC-AATTTT
1 GGTGCTATTTTGGGAATTAATTCGAA-ATG
51177 GGTGCTATTTTGGGAATTAATTCGAAATG
1 GGTGCTATTTTGGGAATTAATTCGAAATG
* * ** ** **
51206 GGTGCTATTTTGGTTATTTTTTTTAAAAAA
1 GGTGCTATTTTGG-GAATTAATTCGAAATG
* *** ** ** *
51236 TGTAAAATTCAGGGAATTAATTCGATTTT
1 GGTGCTATTTTGGGAATTAATTCGAAATG
* *
51265 GGTGCTATTATGGGAATTAATTCAAAATG
1 GGTGCTATTTTGGGAATTAATTCGAAATG
*
51294 GGTGCTATTTTGGTAATTAATTCGAAA
1 GGTGCTATTTTGGGAATTAATTCGAAA
51321 AGGGGTACTA
Statistics
Matches: 101, Mismatches: 41, Indels: 4
0.69 0.28 0.03
Matches are distributed among these distances:
29 84 0.83
30 17 0.17
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.43
Consensus pattern (29 bp):
GGTGCTATTTTGGGAATTAATTCGAAATG
Found at i:52291 original size:42 final size:42
Alignment explanation
Indices: 52242--52618 Score: 526
Period size: 42 Copynumber: 8.9 Consensus size: 42
52232 GAAGGAAGTA
*
52242 TTACCAGGTCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGT
1 TTACCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
* *
52284 TTCCCAGGTCCCTTTGTTGTGTGCGAA-GGTAAGCCTTACAGT
1 TTACCAGGTCCCTTTGCTGTGTGC-AAGGGTAAGCCTTACAGT
*
52326 TTACCAGGTCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGT
1 TTACCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
*
52368 TTACCAGGTCTCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
1 TTACCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
*
52410 TTATCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
1 TTACCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
* * *
52452 TTCCCATGTCCTTTTGCTGTGTGCGAA-GGTAAGCCTTACAGT
1 TTACCAGGTCCCTTTGCTGTGTGC-AAGGGTAAGCCTTACAGT
*
52494 TTACTAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
1 TTACCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
* * * *
52536 TTCCCAAGTCCCTTTGCTGTGTGCAAGGATAAACCTTACAGT
1 TTACCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
* * * *
52578 TTTCCTAGG-CTCCTCTGCTTTGTGCACAGGTTAAGCCTTAC
1 TTACC-AGGTC-CCTTTGCTGTGTGCA-AGGGTAAGCCTTAC
52619 TGGTGTATAG
Statistics
Matches: 303, Mismatches: 25, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
41 4 0.01
42 268 0.88
43 19 0.06
44 12 0.04
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.34
Consensus pattern (42 bp):
TTACCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
Found at i:64446 original size:12 final size:12
Alignment explanation
Indices: 64400--64454 Score: 51
Period size: 12 Copynumber: 4.4 Consensus size: 12
64390 TAACTAATTT
64400 AATAATTTTT-A
1 AATAATTTTTAA
64411 AAT-ATTTTTAAA
1 AATAATTTTT-AA
*
64423 ATAGTAAATTTTTTA
1 A-A-T-AATTTTTAA
64438 AATAATTTTTAA
1 AATAATTTTTAA
64450 AATAA
1 AATAA
64455 AAGTTAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
10 6 0.17
11 3 0.08
12 15 0.42
13 2 0.06
14 2 0.06
15 2 0.06
16 6 0.17
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (12 bp):
AATAATTTTTAA
Found at i:65628 original size:82 final size:82
Alignment explanation
Indices: 65436--65887 Score: 313
Period size: 82 Copynumber: 5.5 Consensus size: 82
65426 TCCAAACGCC
* * * * * *
65436 ACAAAATAGTAACTTTAGTGGCGTTTCTT-TAAAAACGCCTCAATAGTATTCATCCATAGTGGCG
1 ACAAATTAGT-ACTTTAGCGGCGTTT-TTATATAAACGCCGCAATAG-GTTCATCTATAGTGGCG
* *
65500 TTTTTCTTGAA-AAACGCCACA
63 -TTTT-TTCAATAAACGCCGCA
* * *** *
65521 ACAGAGTAGTACTTTAGCATAGTTTTTATATAAACGCCGCAATAGGTCCATCTATAGTGGCGTTT
1 ACAAATTAGTACTTTAGCGGCGTTTTTATATAAACGCCGCAATAGGTTCATCTATAGTGGCGTTT
*
65586 TTTCAATAAACACCGCA
66 TTTCAATAAACGCCGCA
* * * * * * *
65603 ACAAATTAGTACTTTAGCGGTGTTTTTATATAAATGTCGTAATAGGGTTCACCTATAATGGTG-T
1 ACAAATTAGTACTTTAGCGGCGTTTTTATATAAACGCCGCAATA-GGTTCATCTATAGTGGCGTT
*
65667 TTTTCAATAAATGCCGCA
65 TTTTCAATAAACGCCGCA
* * * * * * * *
65685 ATAAATTAGAACTTTAGCGGCATTTTTACATAAATGCTG---TAGGGTTCACCTATAGTGGTGTT
1 ACAAATTAGTACTTTAGCGGCGTTTTTATATAAACGCCGCAATA-GGTTCATCTATAGTGGCGTT
****
65747 TTTTCAATAAACAATACA
65 TTTTCAATAAACGCCGCA
* * * ** * ** * * * *
65765 ACATATTAGAACTTTAGTGGTATTTTTATACAAACATCGTAATAGTATTTATCTATAGTGGCCTT
1 ACAAATTAGTACTTTAGCGGCGTTTTTATATAAACGCCGCAATAG-GTTCATCTATAGTGGCGTT
* *
65830 TTTTCAATAAGCGTCGCA
65 TTTTCAATAAACGCCGCA
* * * *
65848 ATATATTAGTACTTTAGCGGCGTTTATATACAAACGCCGC
1 ACAAATTAGTACTTTAGCGGCGTTTTTATATAAACGCCGC
65888 TAAAGACACA
Statistics
Matches: 289, Mismatches: 70, Indels: 18
0.77 0.19 0.05
Matches are distributed among these distances:
79 20 0.07
80 43 0.15
81 4 0.01
82 98 0.34
83 90 0.31
84 26 0.09
85 8 0.03
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (82 bp):
ACAAATTAGTACTTTAGCGGCGTTTTTATATAAACGCCGCAATAGGTTCATCTATAGTGGCGTTT
TTTCAATAAACGCCGCA
Found at i:65750 original size:162 final size:162
Alignment explanation
Indices: 65572--65868 Score: 380
Period size: 162 Copynumber: 1.8 Consensus size: 162
65562 ATAGGTCCAT
* * * * *
65572 CTATAGTGGCGTTTTTTCAATAAACACCGCAACAAATTAGTACTTTAGCGGTGTTTTTATATAAA
1 CTATAGTGGCGTTTTTTCAATAAACAACACAACAAATTAGAACTTTAGCGGTATTTTTATACAAA
** * *
65637 TGTCGTAATAGGGTTCACCTATAATGG-TGTTTTTCAATAAATGCCGCAATAAATTAGAACTTTA
66 CATCGTAATAGGATTCACCTATAATGGCT-TTTTTCAATAAACGCCGCAATAAATTAGAACTTTA
65701 GCGGCATTTTTACATAAATGCTGTAGGGTTCAC
130 GCGGCATTTTTACATAAATGCTGTAGGGTTCAC
* * * *
65734 CTATAGTGGTGTTTTTTCAATAAACAATACAACATATTAGAACTTTAGTGGTATTTTTATACAAA
1 CTATAGTGGCGTTTTTTCAATAAACAACACAACAAATTAGAACTTTAGCGGTATTTTTATACAAA
* * * * * * * *
65799 CATCGTAATAGTATTTATCTATAGTGGCCTTTTTTCAATAAGCGTCGCAATATATTAGTACTTTA
66 CATCGTAATAGGATTCACCTATAATGG-CTTTTTTCAATAAACGCCGCAATAAATTAGAACTTTA
65864 GCGGC
130 GCGGC
65869 GTTTATATAC
Statistics
Matches: 112, Mismatches: 21, Indels: 3
0.82 0.15 0.02
Matches are distributed among these distances:
162 76 0.68
163 35 0.31
164 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.37
Consensus pattern (162 bp):
CTATAGTGGCGTTTTTTCAATAAACAACACAACAAATTAGAACTTTAGCGGTATTTTTATACAAA
CATCGTAATAGGATTCACCTATAATGGCTTTTTTCAATAAACGCCGCAATAAATTAGAACTTTAG
CGGCATTTTTACATAAATGCTGTAGGGTTCAC
Found at i:77892 original size:259 final size:259
Alignment explanation
Indices: 77460--77995 Score: 934
Period size: 259 Copynumber: 2.1 Consensus size: 259
77450 GAATGATTCC
77460 ATATGTAACGACAAATATCGATATAAGACAACGACACACACATAACTATCATAGAGATTGGGAAA
1 ATATGTAACGACAAATATCGATATAAGACAACGACACACACATAACTATCATAGAGATTGGGAAA
77525 TGATCAACACATTCAGAGTCTCTTTTATAAATACAATGGTTTCAACATTATTGTGATACATGTGT
66 TGATCAACACATTCAGAGTCTCTTTTATAAATACAATGGTTTCAACATTATTGTGATACATGTGT
* *
77590 TAAATTTAAGGAAATTTTAAAAAGTATTTGGCTCGATCATATATAAAATTTCAGTTATTGATAAT
131 TAAATTTAAGGAAAATTTAAAAAGTATTTGGCTCGATCATATATAAAATTTCAGTTATTAATAAT
77655 ATAACTAACAACAAATATTATTTTAT-ATAACAAC-AATACATATAACCACATCTGATGATACA
196 ATAACTAACAACAAATATTATTTTATAATAACAACAAATACATATAACCACATCTGATGATACA
77717 ATATGTAACGACAAATATCGATATAAGACAACGACAAACACACATAACTATCATAGAGATTGGGA
1 ATATGTAACGACAAATATCGATATAAGACAACGAC--ACACACATAACTATCATAGAGATTGGGA
*
77782 AATGATCAACACATTCAGAGTCTGTTTTAT-AATACAATGGTTTTCAACATTATTGTGATACATG
64 AATGATCAACACATTCAGAGTCTCTTTTATAAATACAATGG-TTTCAACATTATTGTGATACATG
* *
77846 TGTTAAATTTATGGAAAATTTATAAAGTATTTGGCTCGATCATATATAAAATTTCAGTTATTAAT
128 TGTTAAATTTAAGGAAAATTTAAAAAGTATTTGGCTCGATCATATATAAAATTTCAGTTATTAAT
* * * *
77911 AATATAATTAACGACAAATATTATTTTATAATAACAACAAATACATATAACCATATCTGATGATG
193 AATATAACTAACAACAAATATTATTTTATAATAACAACAAATACATATAACCACATCTGATGATA
77976 CA
258 CA
*
77978 ATATGTAACGAAAAATAT
1 ATATGTAACGACAAATAT
77996 TGTTATAAAA
Statistics
Matches: 264, Mismatches: 10, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
257 35 0.13
258 10 0.04
259 168 0.64
260 8 0.03
261 43 0.16
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (259 bp):
ATATGTAACGACAAATATCGATATAAGACAACGACACACACATAACTATCATAGAGATTGGGAAA
TGATCAACACATTCAGAGTCTCTTTTATAAATACAATGGTTTCAACATTATTGTGATACATGTGT
TAAATTTAAGGAAAATTTAAAAAGTATTTGGCTCGATCATATATAAAATTTCAGTTATTAATAAT
ATAACTAACAACAAATATTATTTTATAATAACAACAAATACATATAACCACATCTGATGATACA
Found at i:82564 original size:24 final size:24
Alignment explanation
Indices: 82520--82565 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
82510 ATTTAGAGTT
*
82520 TTTTAAAATTAATCATCTTTTTAA
1 TTTTAAAATAAATCATCTTTTTAA
*
82544 TTTTAATAATAAAT-ATTTTTTT
1 TTTTAA-AATAAATCATCTTTTT
82566 TTATTTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 13 0.68
25 6 0.32
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (24 bp):
TTTTAAAATAAATCATCTTTTTAA
Found at i:82840 original size:241 final size:241
Alignment explanation
Indices: 82412--82886 Score: 807
Period size: 241 Copynumber: 2.0 Consensus size: 241
82402 TCGATATTCT
82412 TTTTTAATTTACATAAGTAACAAGTCATAATTTAAATAAAAATTTGAACTCGAATAAGTGTGTAA
1 TTTTTAATTTACATAAGTAACAAGTCATAATTTAAATAAAAATTTGAACTCGAATAAGTGTGTAA
82477 TAGTTTTATCATTTTTATAGTAATTATGTTATAATTTAGAGTTTTTTAAAATTAATCATCTTTTT
66 TAGTTTTATCATTTTTATAGTAATTATGTTATAATTTAGAGTTTTTTAAAATTAATCATCTTTTT
82542 AATTTTAATAATAAATATTTTTTTTTATTTTCAAACAATTTTAAAATGTCAAAAAATAAAATACT
131 AATTTTAATAATAAATA-TTTTTTTTATTTTCAAACAATTTTAAAATGTCAAAAAATAAAATACT
82607 TTAATATTATTTAAATTTACTATTTTGTATAATTTTGAAATAATAAAC
195 TTAATATTATTTAAATTTACTATTTTGTAT-ATTTTGAAATAATAAAC
* * *
82655 TTTTTAATTTGCATAAGTAACGAGTCATAATTTAAA-AAGAA-TTGAACTCGAATAAGTGTGTAA
1 TTTTTAATTTACATAAGTAACAAGTCATAATTTAAATAAAAATTTGAACTCGAATAAGTGTGTAA
*
82718 TAGTTTTATGATTTTTATAGTAATTATGTTATAATTTAGAG-TTTTTAAAATTAATCATCTTTTA
66 TAGTTTTATCATTTTTATAGTAATTATGTTATAATTTAGAGTTTTTTAAAATTAATCATCTTTT-
82782 TAATTTTAATAATATTAATA-TTTTTTTATTTTCAAACAATTTTAAAATGTTC-AAAAATAAAAT
130 TAATTTTAATAATA--AATATTTTTTTTATTTTCAAACAATTTTAAAATG-TCAAAAAATAAAAT
* *
82845 ATTTTAATATTCTTTAAATTTACTATTTTGTATATTTTGAAA
192 ACTTTAATATTATTTAAATTTACTATTTTGTATATTTTGAAA
82887 ATATTATTAT
Statistics
Matches: 222, Mismatches: 6, Indels: 11
0.93 0.03 0.05
Matches are distributed among these distances:
240 31 0.14
241 147 0.66
242 6 0.03
243 38 0.17
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.47
Consensus pattern (241 bp):
TTTTTAATTTACATAAGTAACAAGTCATAATTTAAATAAAAATTTGAACTCGAATAAGTGTGTAA
TAGTTTTATCATTTTTATAGTAATTATGTTATAATTTAGAGTTTTTTAAAATTAATCATCTTTTT
AATTTTAATAATAAATATTTTTTTTATTTTCAAACAATTTTAAAATGTCAAAAAATAAAATACTT
TAATATTATTTAAATTTACTATTTTGTATATTTTGAAATAATAAAC
Done.