Multiple sequence alignment - TraesCS1A01G244800

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1A01G244800 chr1A 100.000 2699 0 0 1 2699 432851119 432853817 0.000000e+00 4985.0
1 TraesCS1A01G244800 chr1A 92.683 41 3 0 2433 2473 432853509 432853549 2.900000e-05 60.2
2 TraesCS1A01G244800 chr1A 92.683 41 3 0 2391 2431 432853551 432853591 2.900000e-05 60.2
3 TraesCS1A01G244800 chr1D 92.214 2376 88 41 167 2472 335286287 335288635 0.000000e+00 3273.0
4 TraesCS1A01G244800 chr1B 91.275 2235 85 37 167 2348 451133433 451135610 0.000000e+00 2946.0
5 TraesCS1A01G244800 chr2D 89.167 240 26 0 1039 1278 595659326 595659087 1.570000e-77 300.0
6 TraesCS1A01G244800 chr2D 86.957 69 9 0 2521 2589 71775779 71775711 8.010000e-11 78.7
7 TraesCS1A01G244800 chr2A 88.333 240 28 0 1039 1278 729627367 729627128 3.400000e-74 289.0
8 TraesCS1A01G244800 chr2A 90.000 60 5 1 2531 2589 513090976 513090917 2.880000e-10 76.8
9 TraesCS1A01G244800 chr2A 89.091 55 6 0 2535 2589 779660777 779660831 4.820000e-08 69.4
10 TraesCS1A01G244800 chr2B 88.559 236 27 0 1040 1275 723962805 723963040 1.220000e-73 287.0
11 TraesCS1A01G244800 chr3A 96.364 55 2 0 2535 2589 589846373 589846427 1.030000e-14 91.6
12 TraesCS1A01G244800 chr3A 100.000 29 0 0 1 29 715388623 715388595 1.000000e-03 54.7
13 TraesCS1A01G244800 chr4B 92.727 55 4 0 2535 2589 471305295 471305349 2.230000e-11 80.5
14 TraesCS1A01G244800 chr7B 89.831 59 6 0 2531 2589 435823952 435823894 2.880000e-10 76.8
15 TraesCS1A01G244800 chr7D 92.500 40 3 0 2654 2693 522377371 522377410 1.040000e-04 58.4
16 TraesCS1A01G244800 chr4D 100.000 30 0 0 1 30 196535328 196535357 3.750000e-04 56.5
17 TraesCS1A01G244800 chr3D 94.595 37 0 2 2563 2597 483176035 483175999 3.750000e-04 56.5
18 TraesCS1A01G244800 chr3D 100.000 28 0 0 1 28 391043112 391043085 5.000000e-03 52.8
19 TraesCS1A01G244800 chr5D 96.970 33 0 1 2594 2625 428416589 428416557 1.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G244800 chr1A 432851119 432853817 2698 False 1701.8 4985 95.122 1 2699 3 chr1A.!!$F1 2698
1 TraesCS1A01G244800 chr1D 335286287 335288635 2348 False 3273.0 3273 92.214 167 2472 1 chr1D.!!$F1 2305
2 TraesCS1A01G244800 chr1B 451133433 451135610 2177 False 2946.0 2946 91.275 167 2348 1 chr1B.!!$F1 2181

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
93 94 0.167908 CGCCGCAAAAATGCTAGACA 59.832 50.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2082 2141 0.24928 GTGCCCGGTTGTTTGGAAAG 60.249 55.0 0.0 0.0 0.0 2.62 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 4.771114 TGATACTCCCCATTACAACCAG 57.229 45.455 0.00 0.00 0.00 4.00
24 25 3.118038 TGATACTCCCCATTACAACCAGC 60.118 47.826 0.00 0.00 0.00 4.85
25 26 1.072266 ACTCCCCATTACAACCAGCA 58.928 50.000 0.00 0.00 0.00 4.41
26 27 1.640670 ACTCCCCATTACAACCAGCAT 59.359 47.619 0.00 0.00 0.00 3.79
27 28 2.042979 ACTCCCCATTACAACCAGCATT 59.957 45.455 0.00 0.00 0.00 3.56
28 29 3.268334 ACTCCCCATTACAACCAGCATTA 59.732 43.478 0.00 0.00 0.00 1.90
29 30 4.079212 ACTCCCCATTACAACCAGCATTAT 60.079 41.667 0.00 0.00 0.00 1.28
30 31 4.214310 TCCCCATTACAACCAGCATTATG 58.786 43.478 0.00 0.00 0.00 1.90
31 32 4.079500 TCCCCATTACAACCAGCATTATGA 60.080 41.667 0.00 0.00 0.00 2.15
32 33 4.648762 CCCCATTACAACCAGCATTATGAA 59.351 41.667 0.00 0.00 0.00 2.57
33 34 5.451798 CCCCATTACAACCAGCATTATGAAC 60.452 44.000 0.00 0.00 0.00 3.18
34 35 5.451798 CCCATTACAACCAGCATTATGAACC 60.452 44.000 0.00 0.00 0.00 3.62
35 36 5.451798 CCATTACAACCAGCATTATGAACCC 60.452 44.000 0.00 0.00 0.00 4.11
36 37 3.168035 ACAACCAGCATTATGAACCCA 57.832 42.857 0.00 0.00 0.00 4.51
37 38 3.505386 ACAACCAGCATTATGAACCCAA 58.495 40.909 0.00 0.00 0.00 4.12
38 39 3.900601 ACAACCAGCATTATGAACCCAAA 59.099 39.130 0.00 0.00 0.00 3.28
39 40 4.346418 ACAACCAGCATTATGAACCCAAAA 59.654 37.500 0.00 0.00 0.00 2.44
40 41 5.012975 ACAACCAGCATTATGAACCCAAAAT 59.987 36.000 0.00 0.00 0.00 1.82
41 42 5.760484 ACCAGCATTATGAACCCAAAATT 57.240 34.783 0.00 0.00 0.00 1.82
42 43 5.490159 ACCAGCATTATGAACCCAAAATTG 58.510 37.500 0.00 0.00 0.00 2.32
43 44 4.333372 CCAGCATTATGAACCCAAAATTGC 59.667 41.667 0.00 0.00 0.00 3.56
44 45 4.333372 CAGCATTATGAACCCAAAATTGCC 59.667 41.667 0.00 0.00 0.00 4.52
45 46 3.627123 GCATTATGAACCCAAAATTGCCC 59.373 43.478 0.00 0.00 0.00 5.36
46 47 4.626046 GCATTATGAACCCAAAATTGCCCT 60.626 41.667 0.00 0.00 0.00 5.19
47 48 4.817318 TTATGAACCCAAAATTGCCCTC 57.183 40.909 0.00 0.00 0.00 4.30
48 49 2.094100 TGAACCCAAAATTGCCCTCA 57.906 45.000 0.00 0.00 0.00 3.86
49 50 2.402564 TGAACCCAAAATTGCCCTCAA 58.597 42.857 0.00 0.00 36.51 3.02
50 51 2.368221 TGAACCCAAAATTGCCCTCAAG 59.632 45.455 0.00 0.00 35.37 3.02
51 52 0.686789 ACCCAAAATTGCCCTCAAGC 59.313 50.000 0.00 0.00 35.37 4.01
52 53 0.686224 CCCAAAATTGCCCTCAAGCA 59.314 50.000 0.00 0.00 42.17 3.91
58 59 4.301505 TGCCCTCAAGCAATCGTC 57.698 55.556 0.00 0.00 40.56 4.20
59 60 1.679311 TGCCCTCAAGCAATCGTCT 59.321 52.632 0.00 0.00 40.56 4.18
60 61 0.391661 TGCCCTCAAGCAATCGTCTC 60.392 55.000 0.00 0.00 40.56 3.36
61 62 1.092345 GCCCTCAAGCAATCGTCTCC 61.092 60.000 0.00 0.00 0.00 3.71
62 63 0.462759 CCCTCAAGCAATCGTCTCCC 60.463 60.000 0.00 0.00 0.00 4.30
63 64 0.539051 CCTCAAGCAATCGTCTCCCT 59.461 55.000 0.00 0.00 0.00 4.20
64 65 1.649664 CTCAAGCAATCGTCTCCCTG 58.350 55.000 0.00 0.00 0.00 4.45
65 66 0.391661 TCAAGCAATCGTCTCCCTGC 60.392 55.000 0.00 0.00 34.96 4.85
66 67 1.448540 AAGCAATCGTCTCCCTGCG 60.449 57.895 0.00 0.00 39.80 5.18
67 68 3.567797 GCAATCGTCTCCCTGCGC 61.568 66.667 0.00 0.00 0.00 6.09
68 69 2.892425 CAATCGTCTCCCTGCGCC 60.892 66.667 4.18 0.00 0.00 6.53
69 70 4.162690 AATCGTCTCCCTGCGCCC 62.163 66.667 4.18 0.00 0.00 6.13
73 74 4.767255 GTCTCCCTGCGCCCTGTG 62.767 72.222 4.18 0.00 0.00 3.66
84 85 4.277593 CCCTGTGCGCCGCAAAAA 62.278 61.111 15.84 1.05 41.47 1.94
85 86 2.049248 CCTGTGCGCCGCAAAAAT 60.049 55.556 15.84 0.00 41.47 1.82
86 87 2.374226 CCTGTGCGCCGCAAAAATG 61.374 57.895 15.84 0.00 41.47 2.32
87 88 3.002404 CTGTGCGCCGCAAAAATGC 62.002 57.895 15.84 0.00 41.47 3.56
88 89 2.734346 GTGCGCCGCAAAAATGCT 60.734 55.556 15.84 0.00 41.47 3.79
89 90 1.443533 GTGCGCCGCAAAAATGCTA 60.444 52.632 15.84 0.00 41.47 3.49
90 91 1.154054 TGCGCCGCAAAAATGCTAG 60.154 52.632 10.46 0.00 34.76 3.42
91 92 1.136565 GCGCCGCAAAAATGCTAGA 59.863 52.632 3.15 0.00 0.00 2.43
92 93 1.133946 GCGCCGCAAAAATGCTAGAC 61.134 55.000 3.15 0.00 0.00 2.59
93 94 0.167908 CGCCGCAAAAATGCTAGACA 59.832 50.000 0.00 0.00 0.00 3.41
94 95 1.617740 GCCGCAAAAATGCTAGACAC 58.382 50.000 0.00 0.00 0.00 3.67
95 96 1.068610 GCCGCAAAAATGCTAGACACA 60.069 47.619 0.00 0.00 0.00 3.72
96 97 2.415893 GCCGCAAAAATGCTAGACACAT 60.416 45.455 0.00 0.00 0.00 3.21
97 98 3.173599 CCGCAAAAATGCTAGACACATG 58.826 45.455 0.00 0.00 0.00 3.21
98 99 3.173599 CGCAAAAATGCTAGACACATGG 58.826 45.455 0.00 0.00 0.00 3.66
99 100 3.119884 CGCAAAAATGCTAGACACATGGA 60.120 43.478 0.00 0.00 0.00 3.41
100 101 4.168760 GCAAAAATGCTAGACACATGGAC 58.831 43.478 0.00 0.00 0.00 4.02
101 102 4.082571 GCAAAAATGCTAGACACATGGACT 60.083 41.667 0.00 0.00 0.00 3.85
102 103 5.396484 CAAAAATGCTAGACACATGGACTG 58.604 41.667 0.00 0.00 0.00 3.51
103 104 3.988976 AATGCTAGACACATGGACTGT 57.011 42.857 0.00 0.00 39.20 3.55
104 105 3.533606 ATGCTAGACACATGGACTGTC 57.466 47.619 6.80 6.80 38.70 3.51
105 106 1.550524 TGCTAGACACATGGACTGTCC 59.449 52.381 19.96 19.96 39.15 4.02
121 122 8.335532 TGGACTGTCCACTCAATAATTTTAAG 57.664 34.615 25.12 0.00 42.67 1.85
122 123 7.393234 TGGACTGTCCACTCAATAATTTTAAGG 59.607 37.037 25.12 0.00 42.67 2.69
123 124 7.610305 GGACTGTCCACTCAATAATTTTAAGGA 59.390 37.037 21.70 0.00 36.28 3.36
124 125 8.336801 ACTGTCCACTCAATAATTTTAAGGAC 57.663 34.615 0.00 0.00 42.44 3.85
125 126 8.164070 ACTGTCCACTCAATAATTTTAAGGACT 58.836 33.333 0.00 0.00 42.54 3.85
126 127 8.335532 TGTCCACTCAATAATTTTAAGGACTG 57.664 34.615 0.00 0.00 42.54 3.51
127 128 7.393234 TGTCCACTCAATAATTTTAAGGACTGG 59.607 37.037 0.00 0.00 42.54 4.00
128 129 6.377146 TCCACTCAATAATTTTAAGGACTGGC 59.623 38.462 0.00 0.00 0.00 4.85
129 130 6.378280 CCACTCAATAATTTTAAGGACTGGCT 59.622 38.462 0.00 0.00 0.00 4.75
130 131 7.253422 CACTCAATAATTTTAAGGACTGGCTG 58.747 38.462 0.00 0.00 0.00 4.85
131 132 7.121168 CACTCAATAATTTTAAGGACTGGCTGA 59.879 37.037 0.00 0.00 0.00 4.26
132 133 7.121315 ACTCAATAATTTTAAGGACTGGCTGAC 59.879 37.037 0.00 0.00 0.00 3.51
133 134 6.377146 TCAATAATTTTAAGGACTGGCTGACC 59.623 38.462 4.81 4.81 0.00 4.02
134 135 4.388577 AATTTTAAGGACTGGCTGACCT 57.611 40.909 9.42 9.42 42.42 3.85
135 136 5.514500 AATTTTAAGGACTGGCTGACCTA 57.486 39.130 14.90 1.25 39.83 3.08
136 137 5.717119 ATTTTAAGGACTGGCTGACCTAT 57.283 39.130 14.90 8.66 39.83 2.57
137 138 5.514500 TTTTAAGGACTGGCTGACCTATT 57.486 39.130 14.90 4.41 39.83 1.73
138 139 5.514500 TTTAAGGACTGGCTGACCTATTT 57.486 39.130 14.90 3.76 39.83 1.40
139 140 5.514500 TTAAGGACTGGCTGACCTATTTT 57.486 39.130 14.90 3.44 39.83 1.82
140 141 3.356529 AGGACTGGCTGACCTATTTTG 57.643 47.619 13.19 0.00 38.99 2.44
141 142 2.644798 AGGACTGGCTGACCTATTTTGT 59.355 45.455 13.19 0.00 38.99 2.83
142 143 3.074538 AGGACTGGCTGACCTATTTTGTT 59.925 43.478 13.19 0.00 38.99 2.83
143 144 3.826729 GGACTGGCTGACCTATTTTGTTT 59.173 43.478 5.69 0.00 36.63 2.83
144 145 4.280929 GGACTGGCTGACCTATTTTGTTTT 59.719 41.667 5.69 0.00 36.63 2.43
145 146 5.475564 GGACTGGCTGACCTATTTTGTTTTA 59.524 40.000 5.69 0.00 36.63 1.52
146 147 6.015772 GGACTGGCTGACCTATTTTGTTTTAA 60.016 38.462 5.69 0.00 36.63 1.52
147 148 7.309805 GGACTGGCTGACCTATTTTGTTTTAAT 60.310 37.037 5.69 0.00 36.63 1.40
148 149 7.962441 ACTGGCTGACCTATTTTGTTTTAATT 58.038 30.769 0.00 0.00 36.63 1.40
149 150 7.872483 ACTGGCTGACCTATTTTGTTTTAATTG 59.128 33.333 0.00 0.00 36.63 2.32
150 151 7.158021 TGGCTGACCTATTTTGTTTTAATTGG 58.842 34.615 0.00 0.00 36.63 3.16
151 152 6.092122 GGCTGACCTATTTTGTTTTAATTGGC 59.908 38.462 0.00 0.00 33.09 4.52
152 153 6.092122 GCTGACCTATTTTGTTTTAATTGGCC 59.908 38.462 0.00 0.00 33.09 5.36
153 154 7.067496 TGACCTATTTTGTTTTAATTGGCCA 57.933 32.000 0.00 0.00 33.09 5.36
154 155 7.509546 TGACCTATTTTGTTTTAATTGGCCAA 58.490 30.769 23.00 23.00 33.09 4.52
155 156 7.993183 TGACCTATTTTGTTTTAATTGGCCAAA 59.007 29.630 24.71 3.41 33.09 3.28
156 157 8.389779 ACCTATTTTGTTTTAATTGGCCAAAG 57.610 30.769 24.71 10.10 33.09 2.77
157 158 7.996066 ACCTATTTTGTTTTAATTGGCCAAAGT 59.004 29.630 24.71 16.12 33.09 2.66
158 159 9.495572 CCTATTTTGTTTTAATTGGCCAAAGTA 57.504 29.630 24.71 15.01 0.00 2.24
162 163 7.555306 TTGTTTTAATTGGCCAAAGTAAACC 57.445 32.000 29.82 24.44 37.87 3.27
163 164 6.890293 TGTTTTAATTGGCCAAAGTAAACCT 58.110 32.000 29.82 12.29 37.87 3.50
164 165 6.987404 TGTTTTAATTGGCCAAAGTAAACCTC 59.013 34.615 29.82 22.89 37.87 3.85
165 166 6.987403 TTTAATTGGCCAAAGTAAACCTCT 57.013 33.333 24.71 0.00 34.34 3.69
171 172 2.935676 GCCAAAGTAAACCTCTCCTCCG 60.936 54.545 0.00 0.00 0.00 4.63
417 437 3.701530 CACGTGCGAGCGCTCAAA 61.702 61.111 34.69 20.50 42.51 2.69
528 555 1.823169 CTGCACAAAAGCCATGCCCT 61.823 55.000 0.00 0.00 38.63 5.19
554 588 1.746615 GCTCATGCCATGGTGTCGT 60.747 57.895 14.67 0.00 0.00 4.34
555 589 1.709147 GCTCATGCCATGGTGTCGTC 61.709 60.000 14.67 0.00 0.00 4.20
559 593 2.509336 GCCATGGTGTCGTCGGAG 60.509 66.667 14.67 0.00 0.00 4.63
573 607 1.760613 GTCGGAGGAGAGAGAGAGAGA 59.239 57.143 0.00 0.00 0.00 3.10
575 609 2.039418 CGGAGGAGAGAGAGAGAGAGA 58.961 57.143 0.00 0.00 0.00 3.10
576 610 2.036475 CGGAGGAGAGAGAGAGAGAGAG 59.964 59.091 0.00 0.00 0.00 3.20
577 611 3.309296 GGAGGAGAGAGAGAGAGAGAGA 58.691 54.545 0.00 0.00 0.00 3.10
580 614 2.546795 GGAGAGAGAGAGAGAGAGAGCG 60.547 59.091 0.00 0.00 0.00 5.03
582 616 0.530650 AGAGAGAGAGAGAGAGCGCG 60.531 60.000 0.00 0.00 0.00 6.86
583 617 0.810031 GAGAGAGAGAGAGAGCGCGT 60.810 60.000 8.43 0.00 0.00 6.01
584 618 1.089481 AGAGAGAGAGAGAGCGCGTG 61.089 60.000 8.43 0.00 0.00 5.34
585 619 2.277884 GAGAGAGAGAGCGCGTGC 60.278 66.667 14.39 14.39 43.24 5.34
586 620 3.045277 GAGAGAGAGAGCGCGTGCA 62.045 63.158 24.79 0.00 46.23 4.57
588 622 3.335306 GAGAGAGAGCGCGTGCACT 62.335 63.158 24.79 22.81 45.16 4.40
589 623 3.177920 GAGAGAGCGCGTGCACTG 61.178 66.667 25.44 9.73 42.39 3.66
627 661 2.061773 CTCGCGGATGGATAATCACAC 58.938 52.381 6.13 0.00 36.98 3.82
628 662 1.410882 TCGCGGATGGATAATCACACA 59.589 47.619 6.13 0.00 36.98 3.72
631 665 3.141398 GCGGATGGATAATCACACATGT 58.859 45.455 0.00 0.00 36.98 3.21
632 666 3.058708 GCGGATGGATAATCACACATGTG 60.059 47.826 24.25 24.25 46.91 3.21
633 667 3.058708 CGGATGGATAATCACACATGTGC 60.059 47.826 25.68 7.27 45.25 4.57
634 668 4.139786 GGATGGATAATCACACATGTGCT 58.860 43.478 25.68 10.24 45.25 4.40
635 669 5.308014 GGATGGATAATCACACATGTGCTA 58.692 41.667 25.68 14.15 45.25 3.49
637 671 4.707105 TGGATAATCACACATGTGCTAGG 58.293 43.478 25.68 12.70 45.25 3.02
638 672 3.499918 GGATAATCACACATGTGCTAGGC 59.500 47.826 25.68 9.12 45.25 3.93
639 673 2.495155 AATCACACATGTGCTAGGCA 57.505 45.000 25.68 3.75 45.25 4.75
986 1026 4.219725 TCCAACACACTCATCGTCAATCTA 59.780 41.667 0.00 0.00 0.00 1.98
987 1027 5.105351 TCCAACACACTCATCGTCAATCTAT 60.105 40.000 0.00 0.00 0.00 1.98
988 1028 5.233050 CCAACACACTCATCGTCAATCTATC 59.767 44.000 0.00 0.00 0.00 2.08
989 1029 5.843673 ACACACTCATCGTCAATCTATCT 57.156 39.130 0.00 0.00 0.00 1.98
990 1030 5.826586 ACACACTCATCGTCAATCTATCTC 58.173 41.667 0.00 0.00 0.00 2.75
1305 1345 2.513204 CCGTCCCAGATGCAGCAG 60.513 66.667 4.07 0.00 0.00 4.24
1306 1346 3.200593 CGTCCCAGATGCAGCAGC 61.201 66.667 4.07 1.15 42.57 5.25
1353 1393 1.380403 CCAATGGTAATTCGGCGCCA 61.380 55.000 28.98 8.41 35.28 5.69
1359 1399 2.661066 TAATTCGGCGCCAGGGACA 61.661 57.895 28.98 3.03 0.00 4.02
1434 1474 2.046892 ACGGACATGGACTGCAGC 60.047 61.111 15.27 6.61 0.00 5.25
1560 1600 2.935481 CAGGAGGTGCCCCTGGAA 60.935 66.667 14.24 0.00 45.66 3.53
1593 1633 1.457643 CGGAGGAGGGGTCAGCATA 60.458 63.158 0.00 0.00 0.00 3.14
1603 1643 1.428869 GGTCAGCATATGGGACCTCT 58.571 55.000 4.56 0.00 45.99 3.69
1604 1644 1.346068 GGTCAGCATATGGGACCTCTC 59.654 57.143 4.56 0.00 45.99 3.20
1623 1663 3.092511 ATCGCCCCTGACATGGCT 61.093 61.111 0.00 0.00 45.71 4.75
1702 1742 1.673665 CAACCCAGCTGCTGAGGTC 60.674 63.158 30.08 0.00 35.23 3.85
1746 1786 3.573110 AGTAAGGAGTGGCCGTGATATAC 59.427 47.826 0.00 0.00 43.43 1.47
1839 1879 7.829378 AGTACTAGTATTTGCTTTTTCTCCG 57.171 36.000 5.75 0.00 0.00 4.63
1884 1924 1.595311 ATATTGGTGGGCAGGTGAGA 58.405 50.000 0.00 0.00 0.00 3.27
1990 2039 4.318332 TGCTATTGCAGATATCCGGAAAG 58.682 43.478 9.01 0.00 45.31 2.62
1996 2045 2.141517 CAGATATCCGGAAAGCAGCAG 58.858 52.381 9.01 0.00 0.00 4.24
2011 2062 4.087182 AGCAGCAGGTAAGTAGTGACTTA 58.913 43.478 0.00 0.00 44.36 2.24
2021 2072 4.258457 AGTAGTGACTTAGGGCATCTCT 57.742 45.455 0.00 0.00 28.61 3.10
2028 2087 4.160439 TGACTTAGGGCATCTCTAACACAG 59.840 45.833 0.00 0.00 0.00 3.66
2066 2125 2.961531 TGGAATTTCCGTCCCTCAAA 57.038 45.000 10.79 0.00 40.17 2.69
2098 2157 0.309612 CGACTTTCCAAACAACCGGG 59.690 55.000 6.32 0.00 0.00 5.73
2221 2280 2.351276 CCCTCACTTTGGACCCCG 59.649 66.667 0.00 0.00 0.00 5.73
2239 2298 4.704833 GCAAGCAGGAGCCACCGA 62.705 66.667 0.00 0.00 44.74 4.69
2240 2299 2.743928 CAAGCAGGAGCCACCGAC 60.744 66.667 0.00 0.00 44.74 4.79
2241 2300 2.925170 AAGCAGGAGCCACCGACT 60.925 61.111 0.00 0.00 44.74 4.18
2242 2301 3.245668 AAGCAGGAGCCACCGACTG 62.246 63.158 0.00 0.00 44.74 3.51
2273 2332 1.518325 CCTTGTTGACATGGTGCGTA 58.482 50.000 0.00 0.00 36.67 4.42
2424 2516 8.534333 ACGTGATTGTATATACATTCCATGTC 57.466 34.615 24.65 12.83 43.67 3.06
2426 2518 7.201435 CGTGATTGTATATACATTCCATGTCCG 60.201 40.741 24.65 16.42 43.67 4.79
2474 2566 9.825109 TGTATATACATTCGATGTTCAAAAGGA 57.175 29.630 11.62 0.00 41.63 3.36
2477 2569 7.687941 ATACATTCGATGTTCAAAAGGAAGT 57.312 32.000 5.94 0.00 41.63 3.01
2478 2570 6.391227 ACATTCGATGTTCAAAAGGAAGTT 57.609 33.333 0.00 0.00 41.63 2.66
2479 2571 6.805713 ACATTCGATGTTCAAAAGGAAGTTT 58.194 32.000 0.00 0.00 41.63 2.66
2480 2572 7.264947 ACATTCGATGTTCAAAAGGAAGTTTT 58.735 30.769 0.00 0.00 41.63 2.43
2481 2573 7.763985 ACATTCGATGTTCAAAAGGAAGTTTTT 59.236 29.630 0.00 0.00 41.63 1.94
2482 2574 7.749539 TTCGATGTTCAAAAGGAAGTTTTTC 57.250 32.000 0.00 0.00 36.11 2.29
2483 2575 7.095695 TCGATGTTCAAAAGGAAGTTTTTCT 57.904 32.000 0.00 0.00 36.11 2.52
2484 2576 7.543756 TCGATGTTCAAAAGGAAGTTTTTCTT 58.456 30.769 0.00 0.00 36.11 2.52
2485 2577 8.032451 TCGATGTTCAAAAGGAAGTTTTTCTTT 58.968 29.630 0.00 0.00 36.11 2.52
2486 2578 9.296400 CGATGTTCAAAAGGAAGTTTTTCTTTA 57.704 29.630 0.00 0.00 36.11 1.85
2602 2694 9.998381 AAACGCTTTTATAATTTTAAACGCTTC 57.002 25.926 19.84 1.99 35.39 3.86
2603 2695 8.959734 ACGCTTTTATAATTTTAAACGCTTCT 57.040 26.923 19.84 6.87 35.39 2.85
2622 2714 9.915629 ACGCTTCTATATTAATTTACAGAGGAG 57.084 33.333 0.00 0.00 0.00 3.69
2623 2715 9.915629 CGCTTCTATATTAATTTACAGAGGAGT 57.084 33.333 0.00 0.00 0.00 3.85
2635 2727 9.574516 AATTTACAGAGGAGTATGTGAGTTTTT 57.425 29.630 0.00 0.00 28.80 1.94
2653 2745 3.347958 TTTTTCACACACTTCATCGGC 57.652 42.857 0.00 0.00 0.00 5.54
2654 2746 1.234821 TTTCACACACTTCATCGGCC 58.765 50.000 0.00 0.00 0.00 6.13
2655 2747 0.396435 TTCACACACTTCATCGGCCT 59.604 50.000 0.00 0.00 0.00 5.19
2656 2748 0.037326 TCACACACTTCATCGGCCTC 60.037 55.000 0.00 0.00 0.00 4.70
2657 2749 0.036952 CACACACTTCATCGGCCTCT 60.037 55.000 0.00 0.00 0.00 3.69
2658 2750 0.687354 ACACACTTCATCGGCCTCTT 59.313 50.000 0.00 0.00 0.00 2.85
2659 2751 1.899814 ACACACTTCATCGGCCTCTTA 59.100 47.619 0.00 0.00 0.00 2.10
2660 2752 2.093973 ACACACTTCATCGGCCTCTTAG 60.094 50.000 0.00 0.00 0.00 2.18
2661 2753 2.166459 CACACTTCATCGGCCTCTTAGA 59.834 50.000 0.00 0.00 0.00 2.10
2662 2754 2.166664 ACACTTCATCGGCCTCTTAGAC 59.833 50.000 0.00 0.00 0.00 2.59
2663 2755 2.428890 CACTTCATCGGCCTCTTAGACT 59.571 50.000 0.00 0.00 0.00 3.24
2664 2756 3.632604 CACTTCATCGGCCTCTTAGACTA 59.367 47.826 0.00 0.00 0.00 2.59
2665 2757 3.886505 ACTTCATCGGCCTCTTAGACTAG 59.113 47.826 0.00 0.00 0.00 2.57
2666 2758 2.231529 TCATCGGCCTCTTAGACTAGC 58.768 52.381 0.00 0.00 0.00 3.42
2667 2759 1.271102 CATCGGCCTCTTAGACTAGCC 59.729 57.143 0.00 3.78 40.33 3.93
2668 2760 0.257905 TCGGCCTCTTAGACTAGCCA 59.742 55.000 0.00 0.07 44.06 4.75
2669 2761 1.133450 TCGGCCTCTTAGACTAGCCAT 60.133 52.381 0.00 0.00 44.06 4.40
2670 2762 2.107726 TCGGCCTCTTAGACTAGCCATA 59.892 50.000 0.00 0.00 44.06 2.74
2671 2763 2.490115 CGGCCTCTTAGACTAGCCATAG 59.510 54.545 0.00 0.00 44.06 2.23
2672 2764 3.502356 GGCCTCTTAGACTAGCCATAGT 58.498 50.000 0.00 0.00 45.16 2.12
2673 2765 4.664392 GGCCTCTTAGACTAGCCATAGTA 58.336 47.826 0.00 0.00 42.46 1.82
2674 2766 4.703093 GGCCTCTTAGACTAGCCATAGTAG 59.297 50.000 0.00 0.00 42.46 2.57
2675 2767 4.703093 GCCTCTTAGACTAGCCATAGTAGG 59.297 50.000 0.00 0.00 42.46 3.18
2676 2768 5.515184 GCCTCTTAGACTAGCCATAGTAGGA 60.515 48.000 5.69 0.00 42.46 2.94
2677 2769 6.177610 CCTCTTAGACTAGCCATAGTAGGAG 58.822 48.000 0.00 0.00 42.46 3.69
2678 2770 6.240060 CCTCTTAGACTAGCCATAGTAGGAGT 60.240 46.154 0.00 0.00 42.46 3.85
2679 2771 7.038160 CCTCTTAGACTAGCCATAGTAGGAGTA 60.038 44.444 0.00 0.00 42.46 2.59
2680 2772 8.272659 TCTTAGACTAGCCATAGTAGGAGTAA 57.727 38.462 0.00 0.00 42.46 2.24
2681 2773 8.721479 TCTTAGACTAGCCATAGTAGGAGTAAA 58.279 37.037 0.00 0.00 42.46 2.01
2682 2774 9.523168 CTTAGACTAGCCATAGTAGGAGTAAAT 57.477 37.037 0.00 0.00 42.46 1.40
2683 2775 9.878737 TTAGACTAGCCATAGTAGGAGTAAATT 57.121 33.333 0.00 0.00 42.46 1.82
2684 2776 8.411991 AGACTAGCCATAGTAGGAGTAAATTC 57.588 38.462 0.00 0.00 42.46 2.17
2685 2777 8.005388 AGACTAGCCATAGTAGGAGTAAATTCA 58.995 37.037 0.00 0.00 42.46 2.57
2686 2778 8.184304 ACTAGCCATAGTAGGAGTAAATTCAG 57.816 38.462 0.00 0.00 40.57 3.02
2687 2779 5.859495 AGCCATAGTAGGAGTAAATTCAGC 58.141 41.667 0.00 0.00 0.00 4.26
2688 2780 5.366768 AGCCATAGTAGGAGTAAATTCAGCA 59.633 40.000 0.00 0.00 0.00 4.41
2689 2781 5.698545 GCCATAGTAGGAGTAAATTCAGCAG 59.301 44.000 0.00 0.00 0.00 4.24
2690 2782 6.686632 GCCATAGTAGGAGTAAATTCAGCAGT 60.687 42.308 0.00 0.00 0.00 4.40
2691 2783 7.471539 GCCATAGTAGGAGTAAATTCAGCAGTA 60.472 40.741 0.00 0.00 0.00 2.74
2692 2784 8.421784 CCATAGTAGGAGTAAATTCAGCAGTAA 58.578 37.037 0.00 0.00 0.00 2.24
2693 2785 9.817809 CATAGTAGGAGTAAATTCAGCAGTAAA 57.182 33.333 0.00 0.00 0.00 2.01
2696 2788 9.384764 AGTAGGAGTAAATTCAGCAGTAAATTC 57.615 33.333 0.00 0.00 0.00 2.17
2697 2789 7.308782 AGGAGTAAATTCAGCAGTAAATTCG 57.691 36.000 0.00 0.00 0.00 3.34
2698 2790 7.103641 AGGAGTAAATTCAGCAGTAAATTCGA 58.896 34.615 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.221843 GCTGGTTGTAATGGGGAGTATCATA 60.222 44.000 0.00 0.00 36.25 2.15
1 2 4.446311 GCTGGTTGTAATGGGGAGTATCAT 60.446 45.833 0.00 0.00 36.25 2.45
2 3 3.118038 GCTGGTTGTAATGGGGAGTATCA 60.118 47.826 0.00 0.00 36.25 2.15
3 4 3.118038 TGCTGGTTGTAATGGGGAGTATC 60.118 47.826 0.00 0.00 0.00 2.24
4 5 2.849943 TGCTGGTTGTAATGGGGAGTAT 59.150 45.455 0.00 0.00 0.00 2.12
5 6 2.270858 TGCTGGTTGTAATGGGGAGTA 58.729 47.619 0.00 0.00 0.00 2.59
6 7 1.072266 TGCTGGTTGTAATGGGGAGT 58.928 50.000 0.00 0.00 0.00 3.85
7 8 2.442236 ATGCTGGTTGTAATGGGGAG 57.558 50.000 0.00 0.00 0.00 4.30
8 9 2.917713 AATGCTGGTTGTAATGGGGA 57.082 45.000 0.00 0.00 0.00 4.81
9 10 4.214310 TCATAATGCTGGTTGTAATGGGG 58.786 43.478 0.00 0.00 0.00 4.96
10 11 5.451798 GGTTCATAATGCTGGTTGTAATGGG 60.452 44.000 0.00 0.00 0.00 4.00
11 12 5.451798 GGGTTCATAATGCTGGTTGTAATGG 60.452 44.000 0.00 0.00 0.00 3.16
12 13 5.126869 TGGGTTCATAATGCTGGTTGTAATG 59.873 40.000 0.00 0.00 0.00 1.90
13 14 5.268387 TGGGTTCATAATGCTGGTTGTAAT 58.732 37.500 0.00 0.00 0.00 1.89
14 15 4.667573 TGGGTTCATAATGCTGGTTGTAA 58.332 39.130 0.00 0.00 0.00 2.41
15 16 4.308526 TGGGTTCATAATGCTGGTTGTA 57.691 40.909 0.00 0.00 0.00 2.41
16 17 3.168035 TGGGTTCATAATGCTGGTTGT 57.832 42.857 0.00 0.00 0.00 3.32
17 18 4.533919 TTTGGGTTCATAATGCTGGTTG 57.466 40.909 0.00 0.00 0.00 3.77
18 19 5.760484 ATTTTGGGTTCATAATGCTGGTT 57.240 34.783 0.00 0.00 0.00 3.67
19 20 5.490159 CAATTTTGGGTTCATAATGCTGGT 58.510 37.500 0.00 0.00 0.00 4.00
20 21 4.333372 GCAATTTTGGGTTCATAATGCTGG 59.667 41.667 0.00 0.00 0.00 4.85
21 22 4.333372 GGCAATTTTGGGTTCATAATGCTG 59.667 41.667 0.00 0.00 0.00 4.41
22 23 4.516323 GGCAATTTTGGGTTCATAATGCT 58.484 39.130 0.00 0.00 0.00 3.79
23 24 3.627123 GGGCAATTTTGGGTTCATAATGC 59.373 43.478 0.00 0.00 0.00 3.56
24 25 5.101648 AGGGCAATTTTGGGTTCATAATG 57.898 39.130 0.00 0.00 0.00 1.90
25 26 4.782156 TGAGGGCAATTTTGGGTTCATAAT 59.218 37.500 0.00 0.00 0.00 1.28
26 27 4.163427 TGAGGGCAATTTTGGGTTCATAA 58.837 39.130 0.00 0.00 0.00 1.90
27 28 3.784178 TGAGGGCAATTTTGGGTTCATA 58.216 40.909 0.00 0.00 0.00 2.15
28 29 2.618794 TGAGGGCAATTTTGGGTTCAT 58.381 42.857 0.00 0.00 0.00 2.57
29 30 2.094100 TGAGGGCAATTTTGGGTTCA 57.906 45.000 0.00 0.00 0.00 3.18
30 31 2.871637 GCTTGAGGGCAATTTTGGGTTC 60.872 50.000 0.00 0.00 32.68 3.62
31 32 1.072173 GCTTGAGGGCAATTTTGGGTT 59.928 47.619 0.00 0.00 32.68 4.11
32 33 0.686789 GCTTGAGGGCAATTTTGGGT 59.313 50.000 0.00 0.00 32.68 4.51
33 34 0.686224 TGCTTGAGGGCAATTTTGGG 59.314 50.000 0.00 0.00 39.43 4.12
34 35 2.547299 TTGCTTGAGGGCAATTTTGG 57.453 45.000 0.00 0.00 45.64 3.28
41 42 0.391661 GAGACGATTGCTTGAGGGCA 60.392 55.000 0.00 0.00 40.74 5.36
42 43 1.092345 GGAGACGATTGCTTGAGGGC 61.092 60.000 0.00 0.00 0.00 5.19
43 44 0.462759 GGGAGACGATTGCTTGAGGG 60.463 60.000 0.00 0.00 0.00 4.30
44 45 0.539051 AGGGAGACGATTGCTTGAGG 59.461 55.000 0.00 0.00 0.00 3.86
45 46 1.649664 CAGGGAGACGATTGCTTGAG 58.350 55.000 0.00 0.00 0.00 3.02
46 47 0.391661 GCAGGGAGACGATTGCTTGA 60.392 55.000 0.00 0.00 33.88 3.02
47 48 1.699656 CGCAGGGAGACGATTGCTTG 61.700 60.000 0.00 0.00 34.50 4.01
48 49 1.448540 CGCAGGGAGACGATTGCTT 60.449 57.895 0.00 0.00 34.50 3.91
49 50 2.185350 CGCAGGGAGACGATTGCT 59.815 61.111 0.00 0.00 34.50 3.91
50 51 3.567797 GCGCAGGGAGACGATTGC 61.568 66.667 0.30 0.00 0.00 3.56
51 52 2.892425 GGCGCAGGGAGACGATTG 60.892 66.667 10.83 0.00 0.00 2.67
52 53 4.162690 GGGCGCAGGGAGACGATT 62.163 66.667 10.83 0.00 0.00 3.34
56 57 4.767255 CACAGGGCGCAGGGAGAC 62.767 72.222 10.83 0.00 0.00 3.36
67 68 3.572196 ATTTTTGCGGCGCACAGGG 62.572 57.895 36.57 0.00 38.71 4.45
68 69 2.049248 ATTTTTGCGGCGCACAGG 60.049 55.556 36.57 0.00 38.71 4.00
69 70 3.002404 GCATTTTTGCGGCGCACAG 62.002 57.895 36.57 21.98 38.71 3.66
70 71 2.134968 TAGCATTTTTGCGGCGCACA 62.135 50.000 36.57 27.24 38.71 4.57
71 72 1.405469 CTAGCATTTTTGCGGCGCAC 61.405 55.000 36.57 21.90 38.71 5.34
72 73 1.154054 CTAGCATTTTTGCGGCGCA 60.154 52.632 33.07 33.07 40.27 6.09
73 74 1.133946 GTCTAGCATTTTTGCGGCGC 61.134 55.000 27.44 27.44 40.27 6.53
74 75 0.167908 TGTCTAGCATTTTTGCGGCG 59.832 50.000 0.51 0.51 40.27 6.46
75 76 1.068610 TGTGTCTAGCATTTTTGCGGC 60.069 47.619 0.00 0.00 40.27 6.53
76 77 2.987413 TGTGTCTAGCATTTTTGCGG 57.013 45.000 0.00 0.00 40.27 5.69
77 78 3.119884 TCCATGTGTCTAGCATTTTTGCG 60.120 43.478 0.00 0.00 40.27 4.85
78 79 4.082571 AGTCCATGTGTCTAGCATTTTTGC 60.083 41.667 0.00 0.00 0.00 3.68
79 80 5.048504 ACAGTCCATGTGTCTAGCATTTTTG 60.049 40.000 0.00 0.00 41.91 2.44
80 81 5.072741 ACAGTCCATGTGTCTAGCATTTTT 58.927 37.500 0.00 0.00 41.91 1.94
81 82 4.655963 ACAGTCCATGTGTCTAGCATTTT 58.344 39.130 0.00 0.00 41.91 1.82
82 83 4.256920 GACAGTCCATGTGTCTAGCATTT 58.743 43.478 7.50 0.00 44.17 2.32
83 84 3.369892 GGACAGTCCATGTGTCTAGCATT 60.370 47.826 15.43 0.00 44.17 3.56
84 85 2.169352 GGACAGTCCATGTGTCTAGCAT 59.831 50.000 15.43 0.00 44.17 3.79
85 86 1.550524 GGACAGTCCATGTGTCTAGCA 59.449 52.381 15.43 0.00 44.17 3.49
86 87 1.550524 TGGACAGTCCATGTGTCTAGC 59.449 52.381 19.21 0.60 42.67 3.42
96 97 7.393234 CCTTAAAATTATTGAGTGGACAGTCCA 59.607 37.037 19.21 19.21 45.98 4.02
97 98 7.610305 TCCTTAAAATTATTGAGTGGACAGTCC 59.390 37.037 13.35 13.35 36.96 3.85
98 99 8.451748 GTCCTTAAAATTATTGAGTGGACAGTC 58.548 37.037 0.00 0.21 40.56 3.51
99 100 8.164070 AGTCCTTAAAATTATTGAGTGGACAGT 58.836 33.333 16.48 0.00 42.54 3.55
100 101 8.454106 CAGTCCTTAAAATTATTGAGTGGACAG 58.546 37.037 16.48 9.24 42.54 3.51
101 102 7.393234 CCAGTCCTTAAAATTATTGAGTGGACA 59.607 37.037 16.48 0.00 43.06 4.02
102 103 7.628580 GCCAGTCCTTAAAATTATTGAGTGGAC 60.629 40.741 19.99 13.01 43.06 4.02
103 104 6.377146 GCCAGTCCTTAAAATTATTGAGTGGA 59.623 38.462 19.99 3.99 43.06 4.02
104 105 6.378280 AGCCAGTCCTTAAAATTATTGAGTGG 59.622 38.462 15.36 15.36 43.19 4.00
105 106 7.121168 TCAGCCAGTCCTTAAAATTATTGAGTG 59.879 37.037 0.00 0.00 0.00 3.51
106 107 7.121315 GTCAGCCAGTCCTTAAAATTATTGAGT 59.879 37.037 0.00 0.00 0.00 3.41
107 108 7.415653 GGTCAGCCAGTCCTTAAAATTATTGAG 60.416 40.741 0.00 0.00 34.09 3.02
108 109 6.377146 GGTCAGCCAGTCCTTAAAATTATTGA 59.623 38.462 0.00 0.00 34.09 2.57
109 110 6.378280 AGGTCAGCCAGTCCTTAAAATTATTG 59.622 38.462 0.00 0.00 31.23 1.90
110 111 6.494059 AGGTCAGCCAGTCCTTAAAATTATT 58.506 36.000 0.00 0.00 31.23 1.40
111 112 6.079712 AGGTCAGCCAGTCCTTAAAATTAT 57.920 37.500 0.00 0.00 31.23 1.28
112 113 5.514500 AGGTCAGCCAGTCCTTAAAATTA 57.486 39.130 0.00 0.00 31.23 1.40
113 114 4.388577 AGGTCAGCCAGTCCTTAAAATT 57.611 40.909 0.00 0.00 31.23 1.82
114 115 5.717119 ATAGGTCAGCCAGTCCTTAAAAT 57.283 39.130 0.00 0.00 37.04 1.82
115 116 5.514500 AATAGGTCAGCCAGTCCTTAAAA 57.486 39.130 0.00 0.00 37.04 1.52
116 117 5.514500 AAATAGGTCAGCCAGTCCTTAAA 57.486 39.130 0.00 0.00 37.04 1.52
117 118 5.222048 ACAAAATAGGTCAGCCAGTCCTTAA 60.222 40.000 0.00 0.00 37.04 1.85
118 119 4.288626 ACAAAATAGGTCAGCCAGTCCTTA 59.711 41.667 0.00 0.00 37.04 2.69
119 120 3.074538 ACAAAATAGGTCAGCCAGTCCTT 59.925 43.478 0.00 0.00 37.04 3.36
120 121 2.644798 ACAAAATAGGTCAGCCAGTCCT 59.355 45.455 0.00 0.00 39.25 3.85
121 122 3.073274 ACAAAATAGGTCAGCCAGTCC 57.927 47.619 0.00 0.00 37.19 3.85
122 123 5.453567 AAAACAAAATAGGTCAGCCAGTC 57.546 39.130 0.00 0.00 37.19 3.51
123 124 6.969993 TTAAAACAAAATAGGTCAGCCAGT 57.030 33.333 0.00 0.00 37.19 4.00
124 125 7.331687 CCAATTAAAACAAAATAGGTCAGCCAG 59.668 37.037 0.00 0.00 37.19 4.85
125 126 7.158021 CCAATTAAAACAAAATAGGTCAGCCA 58.842 34.615 0.00 0.00 37.19 4.75
126 127 6.092122 GCCAATTAAAACAAAATAGGTCAGCC 59.908 38.462 0.00 0.00 0.00 4.85
127 128 6.092122 GGCCAATTAAAACAAAATAGGTCAGC 59.908 38.462 0.00 0.00 0.00 4.26
128 129 7.158021 TGGCCAATTAAAACAAAATAGGTCAG 58.842 34.615 0.61 0.00 0.00 3.51
129 130 7.067496 TGGCCAATTAAAACAAAATAGGTCA 57.933 32.000 0.61 0.00 0.00 4.02
130 131 7.971183 TTGGCCAATTAAAACAAAATAGGTC 57.029 32.000 16.05 0.00 0.00 3.85
131 132 7.996066 ACTTTGGCCAATTAAAACAAAATAGGT 59.004 29.630 21.26 0.00 31.52 3.08
132 133 8.389779 ACTTTGGCCAATTAAAACAAAATAGG 57.610 30.769 21.26 0.00 31.52 2.57
136 137 8.459635 GGTTTACTTTGGCCAATTAAAACAAAA 58.540 29.630 30.73 17.98 31.52 2.44
137 138 7.829706 AGGTTTACTTTGGCCAATTAAAACAAA 59.170 29.630 31.00 18.68 0.00 2.83
138 139 7.339482 AGGTTTACTTTGGCCAATTAAAACAA 58.661 30.769 31.00 13.89 0.00 2.83
139 140 6.890293 AGGTTTACTTTGGCCAATTAAAACA 58.110 32.000 31.00 14.48 0.00 2.83
140 141 7.214381 AGAGGTTTACTTTGGCCAATTAAAAC 58.786 34.615 26.55 26.55 0.00 2.43
141 142 7.368198 AGAGGTTTACTTTGGCCAATTAAAA 57.632 32.000 24.26 18.90 0.00 1.52
142 143 6.014925 GGAGAGGTTTACTTTGGCCAATTAAA 60.015 38.462 21.26 21.09 0.00 1.52
143 144 5.479027 GGAGAGGTTTACTTTGGCCAATTAA 59.521 40.000 21.26 16.55 0.00 1.40
144 145 5.014202 GGAGAGGTTTACTTTGGCCAATTA 58.986 41.667 21.26 11.13 0.00 1.40
145 146 3.832490 GGAGAGGTTTACTTTGGCCAATT 59.168 43.478 21.26 12.24 0.00 2.32
146 147 3.076032 AGGAGAGGTTTACTTTGGCCAAT 59.924 43.478 21.26 8.08 0.00 3.16
147 148 2.445525 AGGAGAGGTTTACTTTGGCCAA 59.554 45.455 16.05 16.05 0.00 4.52
148 149 2.039879 GAGGAGAGGTTTACTTTGGCCA 59.960 50.000 0.00 0.00 0.00 5.36
149 150 2.618302 GGAGGAGAGGTTTACTTTGGCC 60.618 54.545 0.00 0.00 0.00 5.36
150 151 2.712709 GGAGGAGAGGTTTACTTTGGC 58.287 52.381 0.00 0.00 0.00 4.52
151 152 2.565834 TCGGAGGAGAGGTTTACTTTGG 59.434 50.000 0.00 0.00 0.00 3.28
152 153 3.851098 CTCGGAGGAGAGGTTTACTTTG 58.149 50.000 0.00 0.00 43.27 2.77
162 163 2.520741 GGGAGCCTCGGAGGAGAG 60.521 72.222 27.95 1.19 43.27 3.20
163 164 3.347590 TGGGAGCCTCGGAGGAGA 61.348 66.667 27.95 2.69 43.27 3.71
164 165 3.151022 GTGGGAGCCTCGGAGGAG 61.151 72.222 27.95 2.36 37.67 3.69
165 166 3.539593 TTGTGGGAGCCTCGGAGGA 62.540 63.158 27.95 2.99 37.67 3.71
171 172 0.961753 CAGGTTTTTGTGGGAGCCTC 59.038 55.000 0.00 0.00 0.00 4.70
374 394 3.550992 GCGTGTATCCGTGCGTGG 61.551 66.667 0.00 0.00 0.00 4.94
417 437 1.668101 CGGCGGAAGAGCTCTAGGTT 61.668 60.000 18.59 0.00 37.29 3.50
432 452 2.658593 GACCATCGGACATCGGCG 60.659 66.667 0.00 0.00 39.77 6.46
528 555 1.684450 CCATGGCATGAGCAAGCAATA 59.316 47.619 28.43 0.00 44.61 1.90
554 588 2.039418 CTCTCTCTCTCTCTCCTCCGA 58.961 57.143 0.00 0.00 0.00 4.55
555 589 2.036475 CTCTCTCTCTCTCTCTCCTCCG 59.964 59.091 0.00 0.00 0.00 4.63
559 593 2.546795 CGCTCTCTCTCTCTCTCTCTCC 60.547 59.091 0.00 0.00 0.00 3.71
585 619 3.575400 TGCGTGTGTGCAGCAGTG 61.575 61.111 0.00 0.00 40.62 3.66
591 625 3.807631 GAGGGTCTGCGTGTGTGCA 62.808 63.158 0.00 0.00 43.95 4.57
592 626 3.044305 GAGGGTCTGCGTGTGTGC 61.044 66.667 0.00 0.00 0.00 4.57
631 665 3.769739 TCTTTTTCTCAGTGCCTAGCA 57.230 42.857 0.00 0.00 35.60 3.49
632 666 4.275936 TGTTTCTTTTTCTCAGTGCCTAGC 59.724 41.667 0.00 0.00 0.00 3.42
633 667 6.376978 CATGTTTCTTTTTCTCAGTGCCTAG 58.623 40.000 0.00 0.00 0.00 3.02
634 668 5.241506 CCATGTTTCTTTTTCTCAGTGCCTA 59.758 40.000 0.00 0.00 0.00 3.93
635 669 4.038402 CCATGTTTCTTTTTCTCAGTGCCT 59.962 41.667 0.00 0.00 0.00 4.75
637 671 5.009010 TCTCCATGTTTCTTTTTCTCAGTGC 59.991 40.000 0.00 0.00 0.00 4.40
638 672 6.624352 TCTCCATGTTTCTTTTTCTCAGTG 57.376 37.500 0.00 0.00 0.00 3.66
639 673 7.056635 TCTTCTCCATGTTTCTTTTTCTCAGT 58.943 34.615 0.00 0.00 0.00 3.41
986 1026 4.263112 CCTGCTCCATTGATGAGATGAGAT 60.263 45.833 0.00 0.00 0.00 2.75
987 1027 3.071167 CCTGCTCCATTGATGAGATGAGA 59.929 47.826 0.00 0.00 0.00 3.27
988 1028 3.071167 TCCTGCTCCATTGATGAGATGAG 59.929 47.826 0.00 0.00 0.00 2.90
989 1029 3.043418 TCCTGCTCCATTGATGAGATGA 58.957 45.455 0.00 0.00 0.00 2.92
990 1030 3.403968 CTCCTGCTCCATTGATGAGATG 58.596 50.000 0.00 0.00 0.00 2.90
1305 1345 2.045536 CCTTGAGCTGGAGGGTGC 60.046 66.667 0.00 0.00 0.00 5.01
1306 1346 2.045536 GCCTTGAGCTGGAGGGTG 60.046 66.667 12.61 0.00 38.99 4.61
1307 1347 2.530151 TGCCTTGAGCTGGAGGGT 60.530 61.111 12.61 0.00 44.23 4.34
1338 1378 2.124901 CCTGGCGCCGAATTACCA 60.125 61.111 23.90 0.00 0.00 3.25
1353 1393 4.008933 GAGCAGCACGGTGTCCCT 62.009 66.667 10.24 3.34 0.00 4.20
1359 1399 3.241530 TTGGAGGAGCAGCACGGT 61.242 61.111 0.00 0.00 0.00 4.83
1593 1633 2.143419 GGCGATGGAGAGGTCCCAT 61.143 63.158 0.00 0.00 46.40 4.00
1603 1643 2.745308 CCATGTCAGGGGCGATGGA 61.745 63.158 0.00 0.00 38.10 3.41
1604 1644 2.203252 CCATGTCAGGGGCGATGG 60.203 66.667 0.00 0.00 0.00 3.51
1839 1879 2.906153 CTAGTATGCTACTGCGACGAC 58.094 52.381 0.00 0.00 43.34 4.34
1884 1924 7.169813 CGATTATATCATACACACACTTGCACT 59.830 37.037 0.00 0.00 0.00 4.40
1985 2034 3.003480 CACTACTTACCTGCTGCTTTCC 58.997 50.000 0.00 0.00 0.00 3.13
1986 2035 3.680458 GTCACTACTTACCTGCTGCTTTC 59.320 47.826 0.00 0.00 0.00 2.62
1990 2039 3.320673 AAGTCACTACTTACCTGCTGC 57.679 47.619 0.00 0.00 44.26 5.25
1996 2045 4.650131 AGATGCCCTAAGTCACTACTTACC 59.350 45.833 0.00 0.00 44.26 2.85
2011 2062 3.378512 TGATCTGTGTTAGAGATGCCCT 58.621 45.455 0.00 0.00 39.20 5.19
2021 2072 3.771479 AGTCAGCCAGATGATCTGTGTTA 59.229 43.478 20.06 1.74 42.80 2.41
2028 2087 2.550423 CCATGGAGTCAGCCAGATGATC 60.550 54.545 5.56 0.00 42.15 2.92
2039 2098 2.355716 GGACGGAAATTCCATGGAGTCA 60.356 50.000 23.50 9.10 35.91 3.41
2066 2125 2.418334 GGAAAGTCGAAGTCCGCCTTAT 60.418 50.000 0.00 0.00 35.20 1.73
2082 2141 0.249280 GTGCCCGGTTGTTTGGAAAG 60.249 55.000 0.00 0.00 0.00 2.62
2098 2157 5.751243 ATATCAATAAAAGGTCGGTGTGC 57.249 39.130 0.00 0.00 0.00 4.57
2134 2193 7.444183 TCGAGGATCTTCTTTTGTGTACAATTT 59.556 33.333 0.00 0.00 35.55 1.82
2139 2198 6.157211 TCTTCGAGGATCTTCTTTTGTGTAC 58.843 40.000 3.09 0.00 0.00 2.90
2147 2206 5.491323 AGGTTTTCTTCGAGGATCTTCTT 57.509 39.130 0.00 0.00 0.00 2.52
2149 2208 7.668525 TTTTAGGTTTTCTTCGAGGATCTTC 57.331 36.000 0.00 0.00 0.00 2.87
2194 2253 2.308866 CCAAAGTGAGGGGTGGAGTATT 59.691 50.000 0.00 0.00 32.54 1.89
2235 2294 1.289066 CACATGTCGGTCAGTCGGT 59.711 57.895 0.00 0.00 0.00 4.69
2236 2295 2.094659 GCACATGTCGGTCAGTCGG 61.095 63.158 0.00 0.00 0.00 4.79
2237 2296 2.094659 GGCACATGTCGGTCAGTCG 61.095 63.158 0.00 0.00 0.00 4.18
2238 2297 0.320771 AAGGCACATGTCGGTCAGTC 60.321 55.000 0.00 0.00 0.00 3.51
2239 2298 0.603707 CAAGGCACATGTCGGTCAGT 60.604 55.000 0.00 0.00 0.00 3.41
2240 2299 0.603707 ACAAGGCACATGTCGGTCAG 60.604 55.000 0.00 0.00 33.94 3.51
2241 2300 0.179032 AACAAGGCACATGTCGGTCA 60.179 50.000 0.00 0.00 40.34 4.02
2242 2301 0.238289 CAACAAGGCACATGTCGGTC 59.762 55.000 0.00 0.00 40.34 4.79
2424 2516 7.808381 ACAATCACGTATATAGATCACTTTCGG 59.192 37.037 0.00 0.00 0.00 4.30
2453 2545 7.687941 ACTTCCTTTTGAACATCGAATGTAT 57.312 32.000 0.00 0.00 44.07 2.29
2457 2549 8.197439 AGAAAAACTTCCTTTTGAACATCGAAT 58.803 29.630 0.00 0.00 32.05 3.34
2460 2552 7.755582 AAGAAAAACTTCCTTTTGAACATCG 57.244 32.000 0.00 0.00 32.91 3.84
2596 2688 9.915629 CTCCTCTGTAAATTAATATAGAAGCGT 57.084 33.333 0.00 0.00 0.00 5.07
2597 2689 9.915629 ACTCCTCTGTAAATTAATATAGAAGCG 57.084 33.333 0.00 0.00 0.00 4.68
2609 2701 9.574516 AAAAACTCACATACTCCTCTGTAAATT 57.425 29.630 0.00 0.00 0.00 1.82
2633 2725 2.034053 GGCCGATGAAGTGTGTGAAAAA 59.966 45.455 0.00 0.00 0.00 1.94
2634 2726 1.606668 GGCCGATGAAGTGTGTGAAAA 59.393 47.619 0.00 0.00 0.00 2.29
2635 2727 1.202758 AGGCCGATGAAGTGTGTGAAA 60.203 47.619 0.00 0.00 0.00 2.69
2636 2728 0.396435 AGGCCGATGAAGTGTGTGAA 59.604 50.000 0.00 0.00 0.00 3.18
2637 2729 0.037326 GAGGCCGATGAAGTGTGTGA 60.037 55.000 0.00 0.00 0.00 3.58
2638 2730 0.036952 AGAGGCCGATGAAGTGTGTG 60.037 55.000 0.00 0.00 0.00 3.82
2639 2731 0.687354 AAGAGGCCGATGAAGTGTGT 59.313 50.000 0.00 0.00 0.00 3.72
2640 2732 2.166459 TCTAAGAGGCCGATGAAGTGTG 59.834 50.000 0.00 0.00 0.00 3.82
2641 2733 2.166664 GTCTAAGAGGCCGATGAAGTGT 59.833 50.000 0.00 0.00 0.00 3.55
2642 2734 2.428890 AGTCTAAGAGGCCGATGAAGTG 59.571 50.000 0.00 0.00 0.00 3.16
2643 2735 2.741145 AGTCTAAGAGGCCGATGAAGT 58.259 47.619 0.00 0.00 0.00 3.01
2644 2736 3.305064 GCTAGTCTAAGAGGCCGATGAAG 60.305 52.174 0.00 0.00 0.00 3.02
2645 2737 2.623889 GCTAGTCTAAGAGGCCGATGAA 59.376 50.000 0.00 0.00 0.00 2.57
2646 2738 2.231529 GCTAGTCTAAGAGGCCGATGA 58.768 52.381 0.00 0.00 0.00 2.92
2647 2739 1.271102 GGCTAGTCTAAGAGGCCGATG 59.729 57.143 0.00 0.00 33.30 3.84
2648 2740 1.133450 TGGCTAGTCTAAGAGGCCGAT 60.133 52.381 0.00 0.00 45.06 4.18
2649 2741 0.257905 TGGCTAGTCTAAGAGGCCGA 59.742 55.000 0.00 0.00 45.06 5.54
2650 2742 1.333177 ATGGCTAGTCTAAGAGGCCG 58.667 55.000 0.00 0.00 45.06 6.13
2651 2743 3.502356 ACTATGGCTAGTCTAAGAGGCC 58.498 50.000 0.00 0.00 42.73 5.19
2652 2744 4.703093 CCTACTATGGCTAGTCTAAGAGGC 59.297 50.000 0.00 0.00 39.04 4.70
2653 2745 6.129414 TCCTACTATGGCTAGTCTAAGAGG 57.871 45.833 0.00 3.05 39.04 3.69
2654 2746 6.775708 ACTCCTACTATGGCTAGTCTAAGAG 58.224 44.000 0.00 0.00 39.04 2.85
2655 2747 6.766997 ACTCCTACTATGGCTAGTCTAAGA 57.233 41.667 0.00 0.00 39.04 2.10
2656 2748 8.921353 TTTACTCCTACTATGGCTAGTCTAAG 57.079 38.462 0.00 0.00 39.04 2.18
2657 2749 9.878737 AATTTACTCCTACTATGGCTAGTCTAA 57.121 33.333 0.00 0.00 39.04 2.10
2658 2750 9.517868 GAATTTACTCCTACTATGGCTAGTCTA 57.482 37.037 0.00 0.00 39.04 2.59
2659 2751 8.005388 TGAATTTACTCCTACTATGGCTAGTCT 58.995 37.037 0.00 0.00 39.04 3.24
2660 2752 8.179509 TGAATTTACTCCTACTATGGCTAGTC 57.820 38.462 0.00 0.00 39.04 2.59
2661 2753 7.256012 GCTGAATTTACTCCTACTATGGCTAGT 60.256 40.741 0.00 2.91 41.19 2.57
2662 2754 7.093992 GCTGAATTTACTCCTACTATGGCTAG 58.906 42.308 0.00 0.00 0.00 3.42
2663 2755 6.553476 TGCTGAATTTACTCCTACTATGGCTA 59.447 38.462 0.00 0.00 0.00 3.93
2664 2756 5.366768 TGCTGAATTTACTCCTACTATGGCT 59.633 40.000 0.00 0.00 0.00 4.75
2665 2757 5.611374 TGCTGAATTTACTCCTACTATGGC 58.389 41.667 0.00 0.00 0.00 4.40
2666 2758 6.821388 ACTGCTGAATTTACTCCTACTATGG 58.179 40.000 0.00 0.00 0.00 2.74
2667 2759 9.817809 TTTACTGCTGAATTTACTCCTACTATG 57.182 33.333 0.00 0.00 0.00 2.23
2670 2762 9.384764 GAATTTACTGCTGAATTTACTCCTACT 57.615 33.333 0.00 0.00 0.00 2.57
2671 2763 8.328864 CGAATTTACTGCTGAATTTACTCCTAC 58.671 37.037 0.00 0.00 0.00 3.18
2672 2764 8.255206 TCGAATTTACTGCTGAATTTACTCCTA 58.745 33.333 0.00 0.00 0.00 2.94
2673 2765 7.103641 TCGAATTTACTGCTGAATTTACTCCT 58.896 34.615 0.00 0.00 0.00 3.69
2674 2766 7.303634 TCGAATTTACTGCTGAATTTACTCC 57.696 36.000 0.00 0.00 0.00 3.85


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.