Multiple sequence alignment - TraesCS2A01G301100

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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 TraesCS2A01G301100 chr2A 100.000 4943 0 0 1 4943 516391959 516396901 0.000000e+00 9129.0
1 TraesCS2A01G301100 chr2A 92.233 103 8 0 7 109 210748447 210748549 3.990000e-31 147.0
2 TraesCS2A01G301100 chr2D 94.293 4170 165 34 747 4899 382167966 382172079 0.000000e+00 6314.0
3 TraesCS2A01G301100 chr2D 86.595 649 71 9 121 760 382167142 382167783 0.000000e+00 702.0
4 TraesCS2A01G301100 chr2D 92.308 104 8 0 6 109 290348000 290348103 1.110000e-31 148.0
5 TraesCS2A01G301100 chr2D 91.589 107 8 1 4 109 296278020 296278126 3.990000e-31 147.0
6 TraesCS2A01G301100 chr2D 91.346 104 9 0 6 109 290238936 290239039 5.160000e-30 143.0
7 TraesCS2A01G301100 chr2B 95.269 3488 115 20 766 4232 453016545 453020003 0.000000e+00 5481.0
8 TraesCS2A01G301100 chr2B 86.161 672 77 10 123 786 453015287 453015950 0.000000e+00 712.0
9 TraesCS2A01G301100 chr2B 87.175 616 55 9 4279 4889 453020013 453020609 0.000000e+00 678.0
10 TraesCS2A01G301100 chr2B 97.872 47 1 0 4893 4939 58793923 58793969 1.140000e-11 82.4
11 TraesCS2A01G301100 chr7B 92.381 105 7 1 6 109 486668383 486668487 1.110000e-31 148.0
12 TraesCS2A01G301100 chr7A 92.308 104 8 0 6 109 44414020 44414123 1.110000e-31 148.0
13 TraesCS2A01G301100 chr7A 90.196 51 5 0 4889 4939 91932075 91932125 3.190000e-07 67.6
14 TraesCS2A01G301100 chr1D 92.308 104 8 0 6 109 310509619 310509722 1.110000e-31 148.0
15 TraesCS2A01G301100 chr3D 90.826 109 8 2 6 112 300768996 300769104 1.430000e-30 145.0
16 TraesCS2A01G301100 chr3D 100.000 36 0 0 4891 4926 253526406 253526441 3.190000e-07 67.6
17 TraesCS2A01G301100 chr3B 93.750 96 6 0 6 101 414286699 414286794 1.430000e-30 145.0
18 TraesCS2A01G301100 chr3B 96.078 51 2 0 4893 4943 791759958 791760008 3.170000e-12 84.2
19 TraesCS2A01G301100 chr4A 98.077 52 1 0 4892 4943 553535594 553535543 1.890000e-14 91.6
20 TraesCS2A01G301100 chr4A 92.683 41 3 0 4891 4931 716384674 716384714 5.340000e-05 60.2
21 TraesCS2A01G301100 chr3A 98.039 51 1 0 4892 4942 684746811 684746761 6.820000e-14 89.8
22 TraesCS2A01G301100 chr5A 98.000 50 1 0 4893 4942 33880419 33880468 2.450000e-13 87.9
23 TraesCS2A01G301100 chr5B 92.500 40 3 0 4892 4931 479812701 479812740 1.920000e-04 58.4


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 TraesCS2A01G301100 chr2A 516391959 516396901 4942 False 9129.000000 9129 100.000 1 4943 1 chr2A.!!$F2 4942
1 TraesCS2A01G301100 chr2D 382167142 382172079 4937 False 3508.000000 6314 90.444 121 4899 2 chr2D.!!$F4 4778
2 TraesCS2A01G301100 chr2B 453015287 453020609 5322 False 2290.333333 5481 89.535 123 4889 3 chr2B.!!$F2 4766

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
497 507 0.179234 TCACACCACGTTGTCCACAT 59.821 50.000 0.00 0.0 0.0 3.21 F
888 1708 1.095600 TCTCTCATCTGAACCGGTCG 58.904 55.000 8.04 0.0 0.0 4.79 F
1821 2643 0.948678 GCTCAAAACCAGTGGCGTAA 59.051 50.000 9.78 0.0 0.0 3.18 F
3455 4295 1.282157 GCCACCACTTCCAATCTAGGT 59.718 52.381 0.00 0.0 0.0 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1686 2508 0.397941 TGTTTCACAGCCCTCTCCAG 59.602 55.0 0.00 0.00 0.0 3.86 R
2469 3294 1.680338 ACAGAGGGCAAGTTGACAAC 58.320 50.0 11.70 10.47 0.0 3.32 R
3795 4635 0.471617 CCTTCAGCAGATCCCGGATT 59.528 55.0 0.73 0.00 0.0 3.01 R
4796 5642 0.876342 CTCCGAAATGCCCTACTCGC 60.876 60.0 0.00 0.00 0.0 5.03 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
25 26 8.394971 TGATGAATTTGTGTCTAGAATTGTGT 57.605 30.769 0.00 0.00 0.00 3.72
26 27 8.849168 TGATGAATTTGTGTCTAGAATTGTGTT 58.151 29.630 0.00 0.00 0.00 3.32
27 28 9.121517 GATGAATTTGTGTCTAGAATTGTGTTG 57.878 33.333 0.00 0.00 0.00 3.33
28 29 7.995289 TGAATTTGTGTCTAGAATTGTGTTGT 58.005 30.769 0.00 0.00 0.00 3.32
29 30 7.914871 TGAATTTGTGTCTAGAATTGTGTTGTG 59.085 33.333 0.00 0.00 0.00 3.33
30 31 6.993786 TTTGTGTCTAGAATTGTGTTGTGA 57.006 33.333 0.00 0.00 0.00 3.58
31 32 7.566760 TTTGTGTCTAGAATTGTGTTGTGAT 57.433 32.000 0.00 0.00 0.00 3.06
32 33 8.669946 TTTGTGTCTAGAATTGTGTTGTGATA 57.330 30.769 0.00 0.00 0.00 2.15
33 34 8.846943 TTGTGTCTAGAATTGTGTTGTGATAT 57.153 30.769 0.00 0.00 0.00 1.63
34 35 8.479313 TGTGTCTAGAATTGTGTTGTGATATC 57.521 34.615 0.00 0.00 0.00 1.63
35 36 8.314021 TGTGTCTAGAATTGTGTTGTGATATCT 58.686 33.333 3.98 0.00 0.00 1.98
36 37 9.155975 GTGTCTAGAATTGTGTTGTGATATCTT 57.844 33.333 3.98 0.00 0.00 2.40
37 38 9.371136 TGTCTAGAATTGTGTTGTGATATCTTC 57.629 33.333 3.98 0.00 0.00 2.87
38 39 8.821894 GTCTAGAATTGTGTTGTGATATCTTCC 58.178 37.037 3.98 0.00 0.00 3.46
39 40 7.987458 TCTAGAATTGTGTTGTGATATCTTCCC 59.013 37.037 3.98 0.00 0.00 3.97
40 41 5.586243 AGAATTGTGTTGTGATATCTTCCCG 59.414 40.000 3.98 0.00 0.00 5.14
41 42 3.973206 TGTGTTGTGATATCTTCCCGT 57.027 42.857 3.98 0.00 0.00 5.28
42 43 5.408880 TTGTGTTGTGATATCTTCCCGTA 57.591 39.130 3.98 0.00 0.00 4.02
43 44 5.408880 TGTGTTGTGATATCTTCCCGTAA 57.591 39.130 3.98 0.00 0.00 3.18
44 45 5.416083 TGTGTTGTGATATCTTCCCGTAAG 58.584 41.667 3.98 0.00 36.45 2.34
45 46 4.270325 GTGTTGTGATATCTTCCCGTAAGC 59.730 45.833 3.98 0.00 34.97 3.09
46 47 3.746045 TGTGATATCTTCCCGTAAGCC 57.254 47.619 3.98 0.00 34.97 4.35
47 48 3.305720 TGTGATATCTTCCCGTAAGCCT 58.694 45.455 3.98 0.00 34.97 4.58
48 49 3.321111 TGTGATATCTTCCCGTAAGCCTC 59.679 47.826 3.98 0.00 34.97 4.70
49 50 3.574826 GTGATATCTTCCCGTAAGCCTCT 59.425 47.826 3.98 0.00 34.97 3.69
50 51 3.574396 TGATATCTTCCCGTAAGCCTCTG 59.426 47.826 3.98 0.00 34.97 3.35
51 52 2.160721 ATCTTCCCGTAAGCCTCTGA 57.839 50.000 0.00 0.00 34.97 3.27
52 53 2.160721 TCTTCCCGTAAGCCTCTGAT 57.839 50.000 0.00 0.00 34.97 2.90
53 54 2.032620 TCTTCCCGTAAGCCTCTGATC 58.967 52.381 0.00 0.00 34.97 2.92
54 55 2.035632 CTTCCCGTAAGCCTCTGATCT 58.964 52.381 0.00 0.00 0.00 2.75
55 56 2.160721 TCCCGTAAGCCTCTGATCTT 57.839 50.000 0.00 0.00 0.00 2.40
56 57 1.757118 TCCCGTAAGCCTCTGATCTTG 59.243 52.381 0.00 0.00 0.00 3.02
57 58 1.757118 CCCGTAAGCCTCTGATCTTGA 59.243 52.381 0.00 0.00 0.00 3.02
58 59 2.366916 CCCGTAAGCCTCTGATCTTGAT 59.633 50.000 0.00 0.00 0.00 2.57
59 60 3.553922 CCCGTAAGCCTCTGATCTTGATC 60.554 52.174 3.82 3.82 0.00 2.92
60 61 3.068732 CCGTAAGCCTCTGATCTTGATCA 59.931 47.826 12.10 12.10 0.00 2.92
61 62 4.262377 CCGTAAGCCTCTGATCTTGATCAT 60.262 45.833 12.94 1.50 0.00 2.45
62 63 4.685165 CGTAAGCCTCTGATCTTGATCATG 59.315 45.833 12.94 0.00 0.00 3.07
63 64 3.128852 AGCCTCTGATCTTGATCATGC 57.871 47.619 12.94 14.58 0.00 4.06
64 65 2.438392 AGCCTCTGATCTTGATCATGCA 59.562 45.455 20.98 0.00 0.00 3.96
65 66 3.073209 AGCCTCTGATCTTGATCATGCAT 59.927 43.478 20.98 0.00 0.00 3.96
66 67 4.286291 AGCCTCTGATCTTGATCATGCATA 59.714 41.667 20.98 0.00 0.00 3.14
67 68 5.045505 AGCCTCTGATCTTGATCATGCATAT 60.046 40.000 20.98 0.00 0.00 1.78
68 69 5.648526 GCCTCTGATCTTGATCATGCATATT 59.351 40.000 12.94 0.00 0.00 1.28
69 70 6.151312 GCCTCTGATCTTGATCATGCATATTT 59.849 38.462 12.94 0.00 0.00 1.40
70 71 7.336176 GCCTCTGATCTTGATCATGCATATTTA 59.664 37.037 12.94 0.00 0.00 1.40
71 72 8.666573 CCTCTGATCTTGATCATGCATATTTAC 58.333 37.037 12.94 0.00 0.00 2.01
72 73 8.248117 TCTGATCTTGATCATGCATATTTACG 57.752 34.615 12.94 0.00 0.00 3.18
73 74 7.874528 TCTGATCTTGATCATGCATATTTACGT 59.125 33.333 12.94 0.00 0.00 3.57
74 75 7.799784 TGATCTTGATCATGCATATTTACGTG 58.200 34.615 9.02 0.00 0.00 4.49
75 76 7.442062 TGATCTTGATCATGCATATTTACGTGT 59.558 33.333 9.02 0.00 0.00 4.49
76 77 8.831715 ATCTTGATCATGCATATTTACGTGTA 57.168 30.769 0.00 0.00 0.00 2.90
77 78 8.831715 TCTTGATCATGCATATTTACGTGTAT 57.168 30.769 0.00 0.00 0.00 2.29
78 79 8.711457 TCTTGATCATGCATATTTACGTGTATG 58.289 33.333 0.00 5.73 39.03 2.39
79 80 8.600449 TTGATCATGCATATTTACGTGTATGA 57.400 30.769 16.65 11.40 46.39 2.15
84 85 9.705290 TCATGCATATTTACGTGTATGATTAGT 57.295 29.630 16.65 0.00 40.77 2.24
85 86 9.745323 CATGCATATTTACGTGTATGATTAGTG 57.255 33.333 16.65 7.19 39.74 2.74
86 87 7.792925 TGCATATTTACGTGTATGATTAGTGC 58.207 34.615 16.65 7.45 31.48 4.40
87 88 7.439655 TGCATATTTACGTGTATGATTAGTGCA 59.560 33.333 16.65 9.35 31.48 4.57
88 89 7.740346 GCATATTTACGTGTATGATTAGTGCAC 59.260 37.037 9.40 9.40 31.48 4.57
96 97 7.464830 GTGTATGATTAGTGCACGATTAAGT 57.535 36.000 12.01 0.00 0.00 2.24
97 98 7.556433 GTGTATGATTAGTGCACGATTAAGTC 58.444 38.462 12.01 5.01 0.00 3.01
108 109 3.159353 CGATTAAGTCGGGACATCACA 57.841 47.619 1.17 0.00 46.47 3.58
109 110 3.717707 CGATTAAGTCGGGACATCACAT 58.282 45.455 1.17 0.00 46.47 3.21
110 111 3.490896 CGATTAAGTCGGGACATCACATG 59.509 47.826 1.17 0.00 46.47 3.21
111 112 2.979814 TAAGTCGGGACATCACATGG 57.020 50.000 0.00 0.00 33.60 3.66
112 113 0.253044 AAGTCGGGACATCACATGGG 59.747 55.000 0.00 0.00 33.60 4.00
113 114 1.153168 GTCGGGACATCACATGGGG 60.153 63.158 0.00 0.00 33.60 4.96
114 115 1.615124 TCGGGACATCACATGGGGT 60.615 57.895 0.00 0.00 33.60 4.95
115 116 0.325765 TCGGGACATCACATGGGGTA 60.326 55.000 0.00 0.00 33.60 3.69
116 117 0.544223 CGGGACATCACATGGGGTAA 59.456 55.000 0.00 0.00 33.60 2.85
117 118 1.142870 CGGGACATCACATGGGGTAAT 59.857 52.381 0.00 0.00 33.60 1.89
118 119 2.422803 CGGGACATCACATGGGGTAATT 60.423 50.000 0.00 0.00 33.60 1.40
119 120 3.642141 GGGACATCACATGGGGTAATTT 58.358 45.455 0.00 0.00 33.60 1.82
120 121 4.030216 GGGACATCACATGGGGTAATTTT 58.970 43.478 0.00 0.00 33.60 1.82
121 122 5.205056 GGGACATCACATGGGGTAATTTTA 58.795 41.667 0.00 0.00 33.60 1.52
122 123 5.838521 GGGACATCACATGGGGTAATTTTAT 59.161 40.000 0.00 0.00 33.60 1.40
123 124 6.015434 GGGACATCACATGGGGTAATTTTATC 60.015 42.308 0.00 0.00 33.60 1.75
124 125 6.015434 GGACATCACATGGGGTAATTTTATCC 60.015 42.308 0.00 0.00 32.98 2.59
152 153 2.837532 AAAATTCATTTGCGGCCACT 57.162 40.000 2.24 0.00 0.00 4.00
156 157 3.508744 ATTCATTTGCGGCCACTAAAG 57.491 42.857 2.24 0.00 0.00 1.85
165 166 1.066303 CGGCCACTAAAGTTGTTGCAA 59.934 47.619 2.24 0.00 0.00 4.08
177 178 7.432350 AAAGTTGTTGCAAAATTCACTTTGA 57.568 28.000 14.40 0.00 38.35 2.69
178 179 7.614124 AAGTTGTTGCAAAATTCACTTTGAT 57.386 28.000 0.00 0.00 38.35 2.57
179 180 8.715191 AAGTTGTTGCAAAATTCACTTTGATA 57.285 26.923 0.00 0.00 38.35 2.15
180 181 8.356533 AGTTGTTGCAAAATTCACTTTGATAG 57.643 30.769 0.00 0.00 38.35 2.08
181 182 7.981225 AGTTGTTGCAAAATTCACTTTGATAGT 59.019 29.630 0.00 0.00 38.35 2.12
195 196 6.476378 ACTTTGATAGTGTCCTTTGCAGTAT 58.524 36.000 0.00 0.00 35.19 2.12
235 238 0.364515 GTTTAAGTGGCTCGCGTACG 59.635 55.000 11.84 11.84 42.01 3.67
246 249 1.263484 CTCGCGTACGGTCACTCATAT 59.737 52.381 18.39 0.00 40.63 1.78
288 291 4.186159 GCTTAGCTGGAATACGGTTAACA 58.814 43.478 8.10 0.00 29.50 2.41
289 292 4.814771 GCTTAGCTGGAATACGGTTAACAT 59.185 41.667 8.10 0.00 29.50 2.71
299 302 3.202829 ACGGTTAACATGTCCAACTGT 57.797 42.857 22.75 22.75 37.04 3.55
312 318 0.603707 CAACTGTCACATGGGCGACT 60.604 55.000 11.84 0.00 33.18 4.18
339 345 6.071503 TGTGGATATGATGTGACATTTTGCAA 60.072 34.615 0.00 0.00 0.00 4.08
341 347 7.331440 GTGGATATGATGTGACATTTTGCAAAA 59.669 33.333 25.76 25.76 0.00 2.44
388 398 7.117812 TCAGATGGACGAGAGAAATAAAAACAC 59.882 37.037 0.00 0.00 0.00 3.32
412 422 3.307975 CCTCGGCCATGGATATTTGATCT 60.308 47.826 18.40 0.00 0.00 2.75
422 432 4.230657 GGATATTTGATCTCACGACCTCG 58.769 47.826 0.00 0.00 46.33 4.63
438 448 2.824041 CGCGGGCTTGGCTAATGT 60.824 61.111 0.00 0.00 0.00 2.71
462 472 1.076265 GTGGGGCCCAGGGTATTTC 60.076 63.158 29.66 7.81 32.34 2.17
463 473 1.230482 TGGGGCCCAGGGTATTTCT 60.230 57.895 24.76 0.00 0.00 2.52
468 478 2.292257 GGGCCCAGGGTATTTCTTTTCT 60.292 50.000 19.95 0.00 0.00 2.52
478 488 8.579863 CAGGGTATTTCTTTTCTCTCAAAATGT 58.420 33.333 0.00 0.00 0.00 2.71
482 492 9.950680 GTATTTCTTTTCTCTCAAAATGTCACA 57.049 29.630 0.00 0.00 0.00 3.58
492 502 3.105203 CAAAATGTCACACCACGTTGTC 58.895 45.455 0.00 0.00 0.00 3.18
497 507 0.179234 TCACACCACGTTGTCCACAT 59.821 50.000 0.00 0.00 0.00 3.21
502 512 3.069872 ACACCACGTTGTCCACATAGTTA 59.930 43.478 0.00 0.00 0.00 2.24
504 514 4.328983 CACCACGTTGTCCACATAGTTATC 59.671 45.833 0.00 0.00 0.00 1.75
507 517 3.119245 ACGTTGTCCACATAGTTATCGCT 60.119 43.478 0.00 0.00 0.00 4.93
541 551 2.353605 GGACCCGTCAACCGTATAACAA 60.354 50.000 0.00 0.00 33.66 2.83
579 589 7.981789 ACGAATATCAAACTGTATGTGAGTCAT 59.018 33.333 0.00 0.00 40.25 3.06
619 629 9.793252 GTGATCATATTTTAGATGTTGCAAAGT 57.207 29.630 0.00 0.00 0.00 2.66
624 634 9.210426 CATATTTTAGATGTTGCAAAGTACGAC 57.790 33.333 0.00 0.00 0.00 4.34
626 636 2.066262 AGATGTTGCAAAGTACGACCG 58.934 47.619 0.00 0.00 0.00 4.79
735 746 3.516586 TGGAGGAGTAGTTGACATGGAA 58.483 45.455 0.00 0.00 0.00 3.53
888 1708 1.095600 TCTCTCATCTGAACCGGTCG 58.904 55.000 8.04 0.00 0.00 4.79
1394 2214 2.253603 GGCACATGCTTTAGCTTTTCG 58.746 47.619 3.48 0.00 42.66 3.46
1481 2302 5.466058 TGCTTGTTTTGGTTTATGATGCTTG 59.534 36.000 0.00 0.00 0.00 4.01
1512 2333 5.822519 TGCTTTTCAGATGTTTCTAGTGTGT 59.177 36.000 0.00 0.00 0.00 3.72
1586 2408 8.467402 AAACAATCGAGTAGTTTGTATCAGAG 57.533 34.615 10.62 0.00 40.70 3.35
1613 2435 3.325716 GTGTGTCTTGGAGTAGGGGTTTA 59.674 47.826 0.00 0.00 0.00 2.01
1635 2457 8.303876 GTTTAATTGTTGAGTGTGGATAATGGT 58.696 33.333 0.00 0.00 0.00 3.55
1639 2461 7.825331 TTGTTGAGTGTGGATAATGGTTAAA 57.175 32.000 0.00 0.00 0.00 1.52
1646 2468 6.148811 AGTGTGGATAATGGTTAAACTTGACG 59.851 38.462 0.00 0.00 0.00 4.35
1649 2471 4.945543 GGATAATGGTTAAACTTGACGGGT 59.054 41.667 0.00 0.00 0.00 5.28
1651 2473 3.495434 ATGGTTAAACTTGACGGGTGA 57.505 42.857 0.00 0.00 0.00 4.02
1660 2482 3.939066 ACTTGACGGGTGAAGAATTAGG 58.061 45.455 5.03 0.00 0.00 2.69
1666 2488 3.262405 ACGGGTGAAGAATTAGGCTTGTA 59.738 43.478 0.00 0.00 0.00 2.41
1675 2497 9.109393 TGAAGAATTAGGCTTGTAATGACATAC 57.891 33.333 0.00 0.00 34.86 2.39
1686 2508 9.450807 GCTTGTAATGACATACAATTGTTATCC 57.549 33.333 17.78 5.21 42.96 2.59
1740 2562 3.760684 CAGTTTGGGGGATCTTGAAGAAG 59.239 47.826 0.00 0.00 0.00 2.85
1748 2570 6.663523 TGGGGGATCTTGAAGAAGTTTATTTC 59.336 38.462 0.00 0.00 0.00 2.17
1774 2596 5.254115 AGGTAGACCAAACCTAGAAAATGC 58.746 41.667 0.66 0.00 45.69 3.56
1780 2602 3.305335 CCAAACCTAGAAAATGCTGCGTT 60.305 43.478 0.24 0.24 0.00 4.84
1782 2604 5.457140 CAAACCTAGAAAATGCTGCGTTTA 58.543 37.500 19.21 4.40 0.00 2.01
1784 2606 5.485662 ACCTAGAAAATGCTGCGTTTATC 57.514 39.130 19.21 16.94 0.00 1.75
1785 2607 4.335594 ACCTAGAAAATGCTGCGTTTATCC 59.664 41.667 19.21 11.80 0.00 2.59
1786 2608 4.576463 CCTAGAAAATGCTGCGTTTATCCT 59.424 41.667 19.21 17.16 0.00 3.24
1787 2609 4.361451 AGAAAATGCTGCGTTTATCCTG 57.639 40.909 19.21 0.00 0.00 3.86
1789 2611 4.218417 AGAAAATGCTGCGTTTATCCTGTT 59.782 37.500 19.21 2.92 0.00 3.16
1791 2613 5.637006 AAATGCTGCGTTTATCCTGTTTA 57.363 34.783 17.64 0.00 0.00 2.01
1821 2643 0.948678 GCTCAAAACCAGTGGCGTAA 59.051 50.000 9.78 0.00 0.00 3.18
1841 2663 7.264221 GCGTAATAGAGATTCATGGAGATGAT 58.736 38.462 0.00 0.00 38.43 2.45
1865 2689 9.406828 GATAGTATTTATCATGACAAGTGCGTA 57.593 33.333 0.00 0.00 0.00 4.42
1961 2786 3.641434 ATGCATCTTTGTGTAGCCTCT 57.359 42.857 0.00 0.00 0.00 3.69
1962 2787 3.423539 TGCATCTTTGTGTAGCCTCTT 57.576 42.857 0.00 0.00 0.00 2.85
2220 3045 5.014228 ACAAAGGGGCATCTAGAAGTTAAGT 59.986 40.000 0.00 0.00 0.00 2.24
2223 3048 3.200165 GGGGCATCTAGAAGTTAAGTGGT 59.800 47.826 0.00 0.00 0.00 4.16
2295 3120 7.013750 TGTTTGATTACTGAGCATTGGTGTTTA 59.986 33.333 0.00 0.00 0.00 2.01
2440 3265 5.823861 AGGTTTATTTGGTCATGGCTTTT 57.176 34.783 0.00 0.00 0.00 2.27
2448 3273 3.084039 TGGTCATGGCTTTTCAGCTAAG 58.916 45.455 0.00 0.00 46.44 2.18
2481 3306 5.630680 CCTTTGTGATATGTTGTCAACTTGC 59.369 40.000 16.45 7.94 0.00 4.01
2549 3378 2.993899 CAAGGAGTTGCAGTACTTACGG 59.006 50.000 0.00 0.00 0.00 4.02
2616 3449 3.827876 TGCCCAGATAAATACATGCATGG 59.172 43.478 29.41 10.05 0.00 3.66
2904 3744 4.367023 TCGGACGGTTGCTTCGGG 62.367 66.667 0.00 0.00 0.00 5.14
2905 3745 4.675029 CGGACGGTTGCTTCGGGT 62.675 66.667 0.00 0.00 0.00 5.28
3094 3934 9.524106 TGGTTAGTGTATTTGTCTTATATCACG 57.476 33.333 0.00 0.00 0.00 4.35
3398 4238 8.942338 TGTTACAACACCATAGTCTGAATATC 57.058 34.615 0.00 0.00 33.17 1.63
3455 4295 1.282157 GCCACCACTTCCAATCTAGGT 59.718 52.381 0.00 0.00 0.00 3.08
3613 4453 1.799258 GCACAGTGCACAAAGGGAGG 61.799 60.000 21.22 0.42 44.26 4.30
3780 4620 3.069158 GGCTAATTCATGCAGCAAAGGAT 59.931 43.478 0.00 0.00 37.02 3.24
3795 4635 2.768253 AGGATGCAGACGTCAATGAA 57.232 45.000 19.50 2.70 33.10 2.57
4085 4925 1.730064 TCAGTTTAGCGGCGTCAATTC 59.270 47.619 9.37 0.23 0.00 2.17
4156 4996 2.394545 TGTGTCGTCGTGAACTGTAG 57.605 50.000 0.00 0.00 0.00 2.74
4159 4999 1.065851 TGTCGTCGTGAACTGTAGCAA 59.934 47.619 0.00 0.00 0.00 3.91
4249 5090 3.627577 GCAGTTGAACTTCTCAAACTCCA 59.372 43.478 0.00 0.00 45.67 3.86
4387 5228 8.559536 TGTTGTCAGTTTTTCTATCTGTCAATC 58.440 33.333 0.00 0.00 38.57 2.67
4398 5239 8.684386 TTCTATCTGTCAATCTCTAAGTCGAT 57.316 34.615 0.00 0.00 0.00 3.59
4408 5249 6.701145 ATCTCTAAGTCGATGCTAAGAACA 57.299 37.500 0.00 0.00 0.00 3.18
4584 5426 4.154015 TGAAAGTTCATGTTGGCGATAGTG 59.846 41.667 0.00 0.00 32.45 2.74
4588 5430 4.943705 AGTTCATGTTGGCGATAGTGAAAT 59.056 37.500 0.00 0.00 39.35 2.17
4589 5431 5.415701 AGTTCATGTTGGCGATAGTGAAATT 59.584 36.000 0.00 0.00 39.35 1.82
4602 5444 6.507456 CGATAGTGAAATTTTTCGAGGGTACG 60.507 42.308 0.00 0.00 40.01 3.67
4603 5445 4.634199 AGTGAAATTTTTCGAGGGTACGA 58.366 39.130 0.00 0.00 40.01 3.43
4633 5477 7.278424 ACGTGAACTAGAGAGAGTACAATCTAC 59.722 40.741 0.00 0.00 0.00 2.59
4649 5493 6.469410 ACAATCTACGGATGGTTCTTTGTTA 58.531 36.000 0.00 0.00 32.53 2.41
4651 5495 5.988310 TCTACGGATGGTTCTTTGTTAGA 57.012 39.130 0.00 0.00 0.00 2.10
4694 5540 8.624367 TTCGTTTCTATAGGGACAATTTCAAA 57.376 30.769 0.00 0.00 0.00 2.69
4754 5600 3.191371 GTCTAGGGCCACTTTGATTTGTG 59.809 47.826 6.18 0.00 0.00 3.33
4771 5617 6.432783 TGATTTGTGGGATTCTCAAAACGTAT 59.567 34.615 0.00 0.00 40.68 3.06
4777 5623 7.065324 TGTGGGATTCTCAAAACGTATGAATAC 59.935 37.037 5.59 4.63 0.00 1.89
4787 5633 5.718649 AACGTATGAATACAGTGTCATGC 57.281 39.130 0.00 0.01 36.00 4.06
4796 5642 0.594602 CAGTGTCATGCCCACTTGTG 59.405 55.000 13.29 3.05 41.10 3.33
4831 5677 2.386661 GGAGACCGAGCTTCATGAAA 57.613 50.000 9.88 0.00 0.00 2.69
4854 5703 9.159470 GAAAGCCTTAATTTCGAGAAAATATCG 57.841 33.333 2.17 0.00 36.54 2.92
4868 5717 8.831372 CGAGAAAATATCGAACTTTTCAGTTTG 58.169 33.333 25.28 13.04 43.79 2.93
4937 5786 8.905103 TTAAACAAGAACTTCTTTAAGCACAC 57.095 30.769 0.92 0.00 33.78 3.82
4938 5787 5.500645 ACAAGAACTTCTTTAAGCACACC 57.499 39.130 0.92 0.00 33.78 4.16
4939 5788 5.193679 ACAAGAACTTCTTTAAGCACACCT 58.806 37.500 0.92 0.00 33.78 4.00
4940 5789 5.297029 ACAAGAACTTCTTTAAGCACACCTC 59.703 40.000 0.92 0.00 33.78 3.85
4941 5790 5.036117 AGAACTTCTTTAAGCACACCTCA 57.964 39.130 0.00 0.00 36.05 3.86
4942 5791 5.625150 AGAACTTCTTTAAGCACACCTCAT 58.375 37.500 0.00 0.00 36.05 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.121517 CAACACAATTCTAGACACAAATTCATC 57.878 33.333 0.00 0.00 0.00 2.92
2 3 8.632679 ACAACACAATTCTAGACACAAATTCAT 58.367 29.630 0.00 0.00 0.00 2.57
3 4 7.914871 CACAACACAATTCTAGACACAAATTCA 59.085 33.333 0.00 0.00 0.00 2.57
4 5 8.128582 TCACAACACAATTCTAGACACAAATTC 58.871 33.333 0.00 0.00 0.00 2.17
6 7 7.566760 TCACAACACAATTCTAGACACAAAT 57.433 32.000 0.00 0.00 0.00 2.32
7 8 6.993786 TCACAACACAATTCTAGACACAAA 57.006 33.333 0.00 0.00 0.00 2.83
8 9 8.846943 ATATCACAACACAATTCTAGACACAA 57.153 30.769 0.00 0.00 0.00 3.33
9 10 8.314021 AGATATCACAACACAATTCTAGACACA 58.686 33.333 5.32 0.00 0.00 3.72
10 11 8.709386 AGATATCACAACACAATTCTAGACAC 57.291 34.615 5.32 0.00 0.00 3.67
11 12 9.371136 GAAGATATCACAACACAATTCTAGACA 57.629 33.333 5.32 0.00 0.00 3.41
12 13 8.821894 GGAAGATATCACAACACAATTCTAGAC 58.178 37.037 5.32 0.00 0.00 2.59
13 14 7.987458 GGGAAGATATCACAACACAATTCTAGA 59.013 37.037 5.32 0.00 0.00 2.43
14 15 7.042456 CGGGAAGATATCACAACACAATTCTAG 60.042 40.741 5.32 0.00 0.00 2.43
15 16 6.761242 CGGGAAGATATCACAACACAATTCTA 59.239 38.462 5.32 0.00 0.00 2.10
16 17 5.586243 CGGGAAGATATCACAACACAATTCT 59.414 40.000 5.32 0.00 0.00 2.40
17 18 5.354234 ACGGGAAGATATCACAACACAATTC 59.646 40.000 5.32 0.00 0.00 2.17
18 19 5.253330 ACGGGAAGATATCACAACACAATT 58.747 37.500 5.32 0.00 0.00 2.32
19 20 4.843728 ACGGGAAGATATCACAACACAAT 58.156 39.130 5.32 0.00 0.00 2.71
20 21 4.280436 ACGGGAAGATATCACAACACAA 57.720 40.909 5.32 0.00 0.00 3.33
21 22 3.973206 ACGGGAAGATATCACAACACA 57.027 42.857 5.32 0.00 0.00 3.72
22 23 4.270325 GCTTACGGGAAGATATCACAACAC 59.730 45.833 3.58 0.00 37.33 3.32
23 24 4.439057 GCTTACGGGAAGATATCACAACA 58.561 43.478 3.58 0.00 37.33 3.33
24 25 3.808174 GGCTTACGGGAAGATATCACAAC 59.192 47.826 3.58 0.00 37.33 3.32
25 26 3.709653 AGGCTTACGGGAAGATATCACAA 59.290 43.478 3.58 0.00 37.33 3.33
26 27 3.305720 AGGCTTACGGGAAGATATCACA 58.694 45.455 3.58 0.00 37.33 3.58
27 28 3.574826 AGAGGCTTACGGGAAGATATCAC 59.425 47.826 3.58 0.00 37.33 3.06
28 29 3.574396 CAGAGGCTTACGGGAAGATATCA 59.426 47.826 3.58 0.00 37.33 2.15
29 30 3.827302 TCAGAGGCTTACGGGAAGATATC 59.173 47.826 3.58 0.00 37.33 1.63
30 31 3.845860 TCAGAGGCTTACGGGAAGATAT 58.154 45.455 3.58 0.00 37.33 1.63
31 32 3.308035 TCAGAGGCTTACGGGAAGATA 57.692 47.619 3.58 0.00 37.33 1.98
32 33 2.160721 TCAGAGGCTTACGGGAAGAT 57.839 50.000 3.58 0.00 37.33 2.40
33 34 2.032620 GATCAGAGGCTTACGGGAAGA 58.967 52.381 3.58 0.00 37.33 2.87
34 35 2.035632 AGATCAGAGGCTTACGGGAAG 58.964 52.381 0.00 0.00 38.30 3.46
35 36 2.160721 AGATCAGAGGCTTACGGGAA 57.839 50.000 0.00 0.00 0.00 3.97
36 37 1.757118 CAAGATCAGAGGCTTACGGGA 59.243 52.381 0.00 0.00 0.00 5.14
37 38 1.757118 TCAAGATCAGAGGCTTACGGG 59.243 52.381 0.00 0.00 0.00 5.28
38 39 3.068732 TGATCAAGATCAGAGGCTTACGG 59.931 47.826 8.61 0.00 42.42 4.02
39 40 4.313277 TGATCAAGATCAGAGGCTTACG 57.687 45.455 8.61 0.00 42.42 3.18
50 51 7.800767 ACACGTAAATATGCATGATCAAGATC 58.199 34.615 10.16 3.12 38.29 2.75
51 52 7.734924 ACACGTAAATATGCATGATCAAGAT 57.265 32.000 10.16 0.00 0.00 2.40
52 53 8.711457 CATACACGTAAATATGCATGATCAAGA 58.289 33.333 10.16 0.00 0.00 3.02
53 54 8.711457 TCATACACGTAAATATGCATGATCAAG 58.289 33.333 10.16 0.00 0.00 3.02
54 55 8.600449 TCATACACGTAAATATGCATGATCAA 57.400 30.769 10.16 0.00 0.00 2.57
55 56 8.776376 ATCATACACGTAAATATGCATGATCA 57.224 30.769 10.16 0.00 28.30 2.92
58 59 9.705290 ACTAATCATACACGTAAATATGCATGA 57.295 29.630 10.16 0.00 0.00 3.07
59 60 9.745323 CACTAATCATACACGTAAATATGCATG 57.255 33.333 10.16 0.00 0.00 4.06
60 61 8.443160 GCACTAATCATACACGTAAATATGCAT 58.557 33.333 3.79 3.79 0.00 3.96
61 62 7.439655 TGCACTAATCATACACGTAAATATGCA 59.560 33.333 8.19 0.00 33.75 3.96
62 63 7.740346 GTGCACTAATCATACACGTAAATATGC 59.260 37.037 10.32 0.00 0.00 3.14
63 64 7.944649 CGTGCACTAATCATACACGTAAATATG 59.055 37.037 16.19 7.13 46.56 1.78
64 65 8.003508 CGTGCACTAATCATACACGTAAATAT 57.996 34.615 16.19 0.00 46.56 1.28
65 66 7.384358 CGTGCACTAATCATACACGTAAATA 57.616 36.000 16.19 0.00 46.56 1.40
66 67 6.268797 CGTGCACTAATCATACACGTAAAT 57.731 37.500 16.19 0.00 46.56 1.40
67 68 5.689927 CGTGCACTAATCATACACGTAAA 57.310 39.130 16.19 0.00 46.56 2.01
72 73 7.464830 ACTTAATCGTGCACTAATCATACAC 57.535 36.000 16.19 0.00 0.00 2.90
73 74 6.416750 CGACTTAATCGTGCACTAATCATACA 59.583 38.462 16.19 0.00 46.25 2.29
74 75 6.798214 CGACTTAATCGTGCACTAATCATAC 58.202 40.000 16.19 0.41 46.25 2.39
75 76 6.986424 CGACTTAATCGTGCACTAATCATA 57.014 37.500 16.19 0.00 46.25 2.15
76 77 5.890110 CGACTTAATCGTGCACTAATCAT 57.110 39.130 16.19 0.00 46.25 2.45
89 90 3.809832 CCATGTGATGTCCCGACTTAATC 59.190 47.826 0.00 0.00 0.00 1.75
90 91 3.433598 CCCATGTGATGTCCCGACTTAAT 60.434 47.826 0.00 0.00 0.00 1.40
91 92 2.093181 CCCATGTGATGTCCCGACTTAA 60.093 50.000 0.00 0.00 0.00 1.85
92 93 1.484653 CCCATGTGATGTCCCGACTTA 59.515 52.381 0.00 0.00 0.00 2.24
93 94 0.253044 CCCATGTGATGTCCCGACTT 59.747 55.000 0.00 0.00 0.00 3.01
94 95 1.626356 CCCCATGTGATGTCCCGACT 61.626 60.000 0.00 0.00 0.00 4.18
95 96 1.153168 CCCCATGTGATGTCCCGAC 60.153 63.158 0.00 0.00 0.00 4.79
96 97 0.325765 TACCCCATGTGATGTCCCGA 60.326 55.000 0.00 0.00 0.00 5.14
97 98 0.544223 TTACCCCATGTGATGTCCCG 59.456 55.000 0.00 0.00 0.00 5.14
98 99 3.312736 AATTACCCCATGTGATGTCCC 57.687 47.619 0.00 0.00 0.00 4.46
99 100 6.015434 GGATAAAATTACCCCATGTGATGTCC 60.015 42.308 0.00 0.00 0.00 4.02
100 101 6.015434 GGGATAAAATTACCCCATGTGATGTC 60.015 42.308 0.00 0.00 38.69 3.06
101 102 5.838521 GGGATAAAATTACCCCATGTGATGT 59.161 40.000 0.00 0.00 38.69 3.06
102 103 6.345096 GGGATAAAATTACCCCATGTGATG 57.655 41.667 0.00 0.00 38.69 3.07
111 112 7.727578 TTTTCTCTTGGGGATAAAATTACCC 57.272 36.000 0.00 0.00 43.64 3.69
118 119 9.723601 CAAATGAATTTTTCTCTTGGGGATAAA 57.276 29.630 0.00 0.00 0.00 1.40
119 120 7.823799 GCAAATGAATTTTTCTCTTGGGGATAA 59.176 33.333 0.00 0.00 0.00 1.75
120 121 7.330262 GCAAATGAATTTTTCTCTTGGGGATA 58.670 34.615 0.00 0.00 0.00 2.59
121 122 6.175471 GCAAATGAATTTTTCTCTTGGGGAT 58.825 36.000 0.00 0.00 0.00 3.85
122 123 5.550290 GCAAATGAATTTTTCTCTTGGGGA 58.450 37.500 0.00 0.00 0.00 4.81
123 124 4.389687 CGCAAATGAATTTTTCTCTTGGGG 59.610 41.667 9.19 0.00 34.46 4.96
124 125 4.389687 CCGCAAATGAATTTTTCTCTTGGG 59.610 41.667 9.70 9.70 36.08 4.12
125 126 4.143052 GCCGCAAATGAATTTTTCTCTTGG 60.143 41.667 0.00 0.00 0.00 3.61
152 153 8.539770 TCAAAGTGAATTTTGCAACAACTTTA 57.460 26.923 17.02 8.67 37.83 1.85
156 157 8.130307 ACTATCAAAGTGAATTTTGCAACAAC 57.870 30.769 0.00 0.00 36.93 3.32
177 178 5.435686 TTGGATACTGCAAAGGACACTAT 57.564 39.130 0.00 0.00 37.61 2.12
178 179 4.901197 TTGGATACTGCAAAGGACACTA 57.099 40.909 0.00 0.00 37.61 2.74
179 180 3.788227 TTGGATACTGCAAAGGACACT 57.212 42.857 0.00 0.00 37.61 3.55
180 181 4.846779 TTTTGGATACTGCAAAGGACAC 57.153 40.909 0.00 0.00 38.84 3.67
181 182 7.099266 CATATTTTGGATACTGCAAAGGACA 57.901 36.000 0.00 0.00 38.84 4.02
288 291 1.887956 GCCCATGTGACAGTTGGACAT 60.888 52.381 6.79 0.00 31.94 3.06
289 292 0.537143 GCCCATGTGACAGTTGGACA 60.537 55.000 6.79 0.00 31.94 4.02
312 318 6.625520 GCAAAATGTCACATCATATCCACACA 60.626 38.462 0.00 0.00 0.00 3.72
341 347 5.376625 TGACAGATAGCTCAAGGTGTTTTT 58.623 37.500 0.00 0.00 0.00 1.94
353 363 2.884012 CTCGTCCATCTGACAGATAGCT 59.116 50.000 17.54 0.00 44.71 3.32
356 366 4.423625 TCTCTCGTCCATCTGACAGATA 57.576 45.455 17.54 0.53 44.71 1.98
388 398 0.405585 AAATATCCATGGCCGAGGGG 59.594 55.000 6.96 4.57 0.00 4.79
422 432 2.800736 CACATTAGCCAAGCCCGC 59.199 61.111 0.00 0.00 0.00 6.13
434 444 4.702274 GGCCCCACCCTGCACATT 62.702 66.667 0.00 0.00 0.00 2.71
454 464 8.576442 TGACATTTTGAGAGAAAAGAAATACCC 58.424 33.333 0.00 0.00 0.00 3.69
458 468 7.922811 GGTGTGACATTTTGAGAGAAAAGAAAT 59.077 33.333 0.00 0.00 0.00 2.17
462 472 5.973565 GTGGTGTGACATTTTGAGAGAAAAG 59.026 40.000 0.00 0.00 0.00 2.27
463 473 5.448496 CGTGGTGTGACATTTTGAGAGAAAA 60.448 40.000 0.00 0.00 0.00 2.29
468 478 2.912771 ACGTGGTGTGACATTTTGAGA 58.087 42.857 0.00 0.00 0.00 3.27
478 488 0.179234 ATGTGGACAACGTGGTGTGA 59.821 50.000 0.00 0.00 0.00 3.58
482 492 2.922740 AACTATGTGGACAACGTGGT 57.077 45.000 0.00 0.00 40.93 4.16
560 570 7.094805 GGCTTAAATGACTCACATACAGTTTGA 60.095 37.037 0.00 0.00 38.38 2.69
579 589 3.410631 TGATCACCGAAGTGGCTTAAA 57.589 42.857 0.00 0.00 44.64 1.52
597 607 9.157104 TCGTACTTTGCAACATCTAAAATATGA 57.843 29.630 0.00 0.00 0.00 2.15
605 615 3.247442 CGGTCGTACTTTGCAACATCTA 58.753 45.455 0.00 0.00 0.00 1.98
606 616 2.066262 CGGTCGTACTTTGCAACATCT 58.934 47.619 0.00 0.00 0.00 2.90
608 618 0.515564 GCGGTCGTACTTTGCAACAT 59.484 50.000 0.00 0.00 0.00 2.71
610 620 1.154727 CGCGGTCGTACTTTGCAAC 60.155 57.895 0.00 0.00 0.00 4.17
710 721 4.163078 CCATGTCAACTACTCCTCCATCTT 59.837 45.833 0.00 0.00 0.00 2.40
750 761 8.126700 GGTTTCTTTGTCGTCAATTCTTCTAAA 58.873 33.333 0.00 0.00 33.32 1.85
764 971 2.150397 ACTCCTCGGTTTCTTTGTCG 57.850 50.000 0.00 0.00 0.00 4.35
888 1708 3.576004 CAGTCTTGCAGAGCAGCC 58.424 61.111 0.00 0.00 40.61 4.85
1197 2017 0.179073 CATCCCAGTGGCGGTAGAAG 60.179 60.000 2.61 0.00 0.00 2.85
1394 2214 0.517316 AATTCGCGACCAAACAGCTC 59.483 50.000 9.15 0.00 0.00 4.09
1512 2333 1.634960 TACCATCCTGACACGAACCA 58.365 50.000 0.00 0.00 0.00 3.67
1586 2408 0.601558 TACTCCAAGACACACGCCTC 59.398 55.000 0.00 0.00 0.00 4.70
1613 2435 6.916360 AACCATTATCCACACTCAACAATT 57.084 33.333 0.00 0.00 0.00 2.32
1635 2457 6.428771 CCTAATTCTTCACCCGTCAAGTTTAA 59.571 38.462 0.00 0.00 0.00 1.52
1639 2461 3.868754 GCCTAATTCTTCACCCGTCAAGT 60.869 47.826 0.00 0.00 0.00 3.16
1646 2468 5.885912 TCATTACAAGCCTAATTCTTCACCC 59.114 40.000 0.00 0.00 0.00 4.61
1649 2471 9.109393 GTATGTCATTACAAGCCTAATTCTTCA 57.891 33.333 0.00 0.00 39.58 3.02
1651 2473 9.461312 TTGTATGTCATTACAAGCCTAATTCTT 57.539 29.630 0.00 0.00 39.58 2.52
1660 2482 9.450807 GGATAACAATTGTATGTCATTACAAGC 57.549 33.333 12.39 0.00 43.30 4.01
1666 2488 8.274322 TCTCCAGGATAACAATTGTATGTCATT 58.726 33.333 12.39 0.00 31.81 2.57
1675 2497 3.117738 AGCCCTCTCCAGGATAACAATTG 60.118 47.826 3.24 3.24 43.65 2.32
1686 2508 0.397941 TGTTTCACAGCCCTCTCCAG 59.602 55.000 0.00 0.00 0.00 3.86
1740 2562 6.875726 AGGTTTGGTCTACCTACGAAATAAAC 59.124 38.462 0.02 0.64 44.11 2.01
1748 2570 5.649782 TTTCTAGGTTTGGTCTACCTACG 57.350 43.478 0.02 0.00 44.11 3.51
1774 2596 9.825972 CCATAATAATAAACAGGATAAACGCAG 57.174 33.333 0.00 0.00 0.00 5.18
1782 2604 8.995027 TTGAGCACCATAATAATAAACAGGAT 57.005 30.769 0.00 0.00 0.00 3.24
1784 2606 9.301153 GTTTTGAGCACCATAATAATAAACAGG 57.699 33.333 0.00 0.00 0.00 4.00
1785 2607 9.301153 GGTTTTGAGCACCATAATAATAAACAG 57.699 33.333 0.00 0.00 34.04 3.16
1786 2608 8.807118 TGGTTTTGAGCACCATAATAATAAACA 58.193 29.630 0.00 0.00 39.53 2.83
1787 2609 9.301153 CTGGTTTTGAGCACCATAATAATAAAC 57.699 33.333 0.00 0.00 43.60 2.01
1789 2611 8.465999 CACTGGTTTTGAGCACCATAATAATAA 58.534 33.333 0.00 0.00 43.60 1.40
1791 2613 6.127366 CCACTGGTTTTGAGCACCATAATAAT 60.127 38.462 0.00 0.00 43.60 1.28
1841 2663 9.589111 TTTACGCACTTGTCATGATAAATACTA 57.411 29.630 6.35 0.00 0.00 1.82
1865 2689 7.272037 ACAATTAATCGACAAGGTTCACTTT 57.728 32.000 0.00 0.00 37.29 2.66
1961 2786 8.616942 TGATTGAAATAAAACTTGACAGACGAA 58.383 29.630 0.00 0.00 0.00 3.85
1962 2787 8.148807 TGATTGAAATAAAACTTGACAGACGA 57.851 30.769 0.00 0.00 0.00 4.20
2220 3045 5.624281 GCAATGCTTATGCCTTTCTTAACCA 60.624 40.000 0.00 0.00 37.85 3.67
2223 3048 5.920193 AGCAATGCTTATGCCTTTCTTAA 57.080 34.783 0.00 0.00 44.91 1.85
2440 3265 4.065088 CAAAGGCAGTTACACTTAGCTGA 58.935 43.478 0.00 0.00 38.49 4.26
2448 3273 5.880054 ACATATCACAAAGGCAGTTACAC 57.120 39.130 0.00 0.00 0.00 2.90
2469 3294 1.680338 ACAGAGGGCAAGTTGACAAC 58.320 50.000 11.70 10.47 0.00 3.32
2481 3306 5.065218 CGAACCATGATCTTTTTACAGAGGG 59.935 44.000 0.00 0.00 0.00 4.30
2583 3416 4.860802 TTATCTGGGCAAGGAAATGAGA 57.139 40.909 0.00 0.00 0.00 3.27
2661 3501 6.336842 AGCAGCAGATCTGTTAAAACAATT 57.663 33.333 23.38 0.00 44.66 2.32
2904 3744 3.512033 TGTACCAACAAAAGTTGCCAC 57.488 42.857 2.95 3.91 33.30 5.01
3341 4181 7.043565 AGTAAAATGAATTACGTACCGTCCAT 58.956 34.615 0.00 0.00 41.54 3.41
3380 4220 3.910627 GGGGGATATTCAGACTATGGTGT 59.089 47.826 0.00 0.00 0.00 4.16
3398 4238 0.673644 CAGTTTCAGTACAGCGGGGG 60.674 60.000 0.00 0.00 0.00 5.40
3492 4332 8.510243 AGTTAAGATGTCATCAATTACATGCA 57.490 30.769 15.20 0.00 36.48 3.96
3613 4453 2.924926 TGTAATGATGCCGTTCACGTAC 59.075 45.455 0.00 0.00 37.74 3.67
3688 4528 2.762887 CTCTAGCAGACCAGATGAACCA 59.237 50.000 0.00 0.00 0.00 3.67
3780 4620 1.731709 CGGATTTCATTGACGTCTGCA 59.268 47.619 17.92 0.81 0.00 4.41
3795 4635 0.471617 CCTTCAGCAGATCCCGGATT 59.528 55.000 0.73 0.00 0.00 3.01
3843 4683 2.166270 GGCTCTCTGTGAAAAGCCG 58.834 57.895 0.00 0.00 44.37 5.52
4122 4962 3.565482 ACGACACAAGCTCAAAACATGAT 59.435 39.130 0.00 0.00 37.44 2.45
4159 4999 2.641815 AGAGGAAAGAACACAGCAGGAT 59.358 45.455 0.00 0.00 0.00 3.24
4168 5008 0.756294 TCGGTGCAGAGGAAAGAACA 59.244 50.000 0.00 0.00 0.00 3.18
4387 5228 7.763172 AATTGTTCTTAGCATCGACTTAGAG 57.237 36.000 0.00 0.00 0.00 2.43
4469 5310 9.454585 CATAACGCAAATCTCAATGTTCATATT 57.545 29.630 0.00 0.00 0.00 1.28
4487 5328 5.079689 TCTCTACCAACATTCATAACGCA 57.920 39.130 0.00 0.00 0.00 5.24
4488 5329 6.417191 TTTCTCTACCAACATTCATAACGC 57.583 37.500 0.00 0.00 0.00 4.84
4562 5403 4.391830 TCACTATCGCCAACATGAACTTTC 59.608 41.667 0.00 0.00 0.00 2.62
4584 5426 6.291479 CGTATCTCGTACCCTCGAAAAATTTC 60.291 42.308 0.00 0.00 39.34 2.17
4588 5430 4.019919 CGTATCTCGTACCCTCGAAAAA 57.980 45.455 0.00 0.00 39.34 1.94
4589 5431 3.680642 CGTATCTCGTACCCTCGAAAA 57.319 47.619 0.00 0.00 39.34 2.29
4602 5444 6.979817 TGTACTCTCTCTAGTTCACGTATCTC 59.020 42.308 0.00 0.00 0.00 2.75
4603 5445 6.876155 TGTACTCTCTCTAGTTCACGTATCT 58.124 40.000 0.00 0.00 0.00 1.98
4633 5477 6.872020 TCTTTAGTCTAACAAAGAACCATCCG 59.128 38.462 0.00 0.00 37.72 4.18
4660 5506 7.832187 TGTCCCTATAGAAACGAAAAATGGATT 59.168 33.333 0.00 0.00 0.00 3.01
4727 5573 4.919774 TCAAAGTGGCCCTAGACATTAA 57.080 40.909 0.00 0.00 0.00 1.40
4754 5600 7.280205 ACTGTATTCATACGTTTTGAGAATCCC 59.720 37.037 0.00 0.00 36.06 3.85
4771 5617 2.305635 AGTGGGCATGACACTGTATTCA 59.694 45.455 18.93 0.00 46.67 2.57
4787 5633 1.079127 CCCTACTCGCACAAGTGGG 60.079 63.158 10.63 10.63 45.03 4.61
4796 5642 0.876342 CTCCGAAATGCCCTACTCGC 60.876 60.000 0.00 0.00 0.00 5.03
4824 5670 7.447374 TTTCTCGAAATTAAGGCTTTCATGA 57.553 32.000 4.45 0.00 33.20 3.07
4829 5675 8.889717 TCGATATTTTCTCGAAATTAAGGCTTT 58.110 29.630 4.45 0.00 41.79 3.51
4911 5760 9.516314 GTGTGCTTAAAGAAGTTCTTGTTTAAT 57.484 29.630 18.70 4.81 36.71 1.40
4912 5761 7.971722 GGTGTGCTTAAAGAAGTTCTTGTTTAA 59.028 33.333 18.70 19.16 36.71 1.52
4913 5762 7.338449 AGGTGTGCTTAAAGAAGTTCTTGTTTA 59.662 33.333 18.70 5.25 36.71 2.01
4914 5763 6.152831 AGGTGTGCTTAAAGAAGTTCTTGTTT 59.847 34.615 18.70 6.23 36.71 2.83
4915 5764 5.652452 AGGTGTGCTTAAAGAAGTTCTTGTT 59.348 36.000 18.70 6.95 36.71 2.83
4916 5765 5.193679 AGGTGTGCTTAAAGAAGTTCTTGT 58.806 37.500 18.70 11.18 36.71 3.16
4917 5766 5.296780 TGAGGTGTGCTTAAAGAAGTTCTTG 59.703 40.000 18.70 7.86 36.71 3.02
4918 5767 5.437060 TGAGGTGTGCTTAAAGAAGTTCTT 58.563 37.500 12.50 12.50 38.59 2.52
4919 5768 5.036117 TGAGGTGTGCTTAAAGAAGTTCT 57.964 39.130 0.00 0.00 34.90 3.01
4920 5769 5.948992 ATGAGGTGTGCTTAAAGAAGTTC 57.051 39.130 0.00 0.00 34.90 3.01


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

AutoCloner maintained by Alex Coulton.