Multiple sequence alignment - TraesCS3D01G444300

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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 TraesCS3D01G444300 chr3D 100.000 1752 0 0 1 1752 553356735 553358486 0.000000e+00 3236.0
1 TraesCS3D01G444300 chr3D 89.585 989 81 6 744 1711 553405894 553406881 0.000000e+00 1236.0
2 TraesCS3D01G444300 chr3D 100.000 453 0 0 2205 2657 553358939 553359391 0.000000e+00 837.0
3 TraesCS3D01G444300 chr3D 93.303 433 20 5 462 888 553405658 553406087 4.830000e-177 630.0
4 TraesCS3D01G444300 chr3D 87.206 383 39 5 1373 1752 548999104 548998729 6.800000e-116 427.0
5 TraesCS3D01G444300 chr3D 82.418 273 34 9 139 409 549000187 548999927 2.660000e-55 226.0
6 TraesCS3D01G444300 chr3D 79.233 313 43 12 58 363 553405362 553405659 5.800000e-47 198.0
7 TraesCS3D01G444300 chr3D 95.789 95 4 0 2561 2655 100762235 100762141 1.270000e-33 154.0
8 TraesCS3D01G444300 chr3D 90.385 52 5 0 1701 1752 553406897 553406948 4.750000e-08 69.4
9 TraesCS3D01G444300 chr3A 91.677 1574 94 18 190 1752 689659472 689661019 0.000000e+00 2146.0
10 TraesCS3D01G444300 chr3A 90.661 1574 103 19 190 1752 689666124 689667664 0.000000e+00 2071.0
11 TraesCS3D01G444300 chr3A 92.899 1352 83 12 412 1752 689662507 689663856 0.000000e+00 1953.0
12 TraesCS3D01G444300 chr3A 91.125 1262 92 10 412 1666 689608304 689609552 0.000000e+00 1692.0
13 TraesCS3D01G444300 chr3A 91.053 1263 94 8 412 1666 689523395 689524646 0.000000e+00 1688.0
14 TraesCS3D01G444300 chr3A 90.729 1262 97 10 412 1666 689578526 689579774 0.000000e+00 1664.0
15 TraesCS3D01G444300 chr3A 93.272 758 37 6 190 944 689846322 689847068 0.000000e+00 1105.0
16 TraesCS3D01G444300 chr3A 92.622 759 39 7 190 944 689866637 689867382 0.000000e+00 1075.0
17 TraesCS3D01G444300 chr3A 87.093 922 101 8 844 1752 686281144 686280228 0.000000e+00 1027.0
18 TraesCS3D01G444300 chr3A 89.711 797 72 3 694 1480 689867182 689867978 0.000000e+00 1009.0
19 TraesCS3D01G444300 chr3A 89.210 797 76 3 694 1480 689846868 689847664 0.000000e+00 987.0
20 TraesCS3D01G444300 chr3A 89.447 199 21 0 1 199 689845713 689845911 4.390000e-63 252.0
21 TraesCS3D01G444300 chr3A 89.447 199 21 0 1 199 689866031 689866229 4.390000e-63 252.0
22 TraesCS3D01G444300 chr3A 87.065 201 21 4 1 199 689652833 689653030 3.440000e-54 222.0
23 TraesCS3D01G444300 chr3A 87.065 201 21 4 1 199 689658865 689659062 3.440000e-54 222.0
24 TraesCS3D01G444300 chr3A 87.065 201 21 4 1 199 689665517 689665714 3.440000e-54 222.0
25 TraesCS3D01G444300 chr3A 90.076 131 4 5 2266 2388 689579848 689579977 7.610000e-36 161.0
26 TraesCS3D01G444300 chr3A 90.076 131 4 2 2266 2388 689609626 689609755 7.610000e-36 161.0
27 TraesCS3D01G444300 chr3A 90.435 115 8 2 2445 2558 689609757 689609869 5.930000e-32 148.0
28 TraesCS3D01G444300 chr3A 88.172 93 10 1 316 408 686281566 686281475 2.800000e-20 110.0
29 TraesCS3D01G444300 chr3B 85.604 389 36 9 1373 1752 728294962 728294585 8.920000e-105 390.0
30 TraesCS3D01G444300 chr3B 83.212 274 31 7 139 409 728308202 728307941 1.230000e-58 237.0
31 TraesCS3D01G444300 chr2D 98.969 97 1 0 2561 2657 105236873 105236777 9.780000e-40 174.0
32 TraesCS3D01G444300 chr1B 97.959 98 1 1 2561 2657 23081010 23080913 4.550000e-38 169.0
33 TraesCS3D01G444300 chr1B 92.784 97 7 0 2561 2657 581242556 581242460 9.920000e-30 141.0
34 TraesCS3D01G444300 chr5A 95.098 102 3 2 2558 2657 505045267 505045166 2.740000e-35 159.0
35 TraesCS3D01G444300 chr6A 94.845 97 5 0 2561 2657 50237047 50237143 4.580000e-33 152.0
36 TraesCS3D01G444300 chr2A 94.845 97 5 0 2561 2657 21076458 21076362 4.580000e-33 152.0
37 TraesCS3D01G444300 chr4A 93.878 98 6 0 2560 2657 21953491 21953394 5.930000e-32 148.0
38 TraesCS3D01G444300 chr7A 93.814 97 6 0 2561 2657 618510256 618510160 2.130000e-31 147.0
39 TraesCS3D01G444300 chr1D 84.000 100 12 3 310 407 391454444 391454541 2.820000e-15 93.5


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 TraesCS3D01G444300 chr3D 553356735 553359391 2656 False 2036.500000 3236 100.000000 1 2657 2 chr3D.!!$F1 2656
1 TraesCS3D01G444300 chr3D 553405362 553406948 1586 False 533.350000 1236 88.126500 58 1752 4 chr3D.!!$F2 1694
2 TraesCS3D01G444300 chr3D 548998729 549000187 1458 True 326.500000 427 84.812000 139 1752 2 chr3D.!!$R2 1613
3 TraesCS3D01G444300 chr3A 689523395 689524646 1251 False 1688.000000 1688 91.053000 412 1666 1 chr3A.!!$F1 1254
4 TraesCS3D01G444300 chr3A 689658865 689667664 8799 False 1322.800000 2146 89.873400 1 1752 5 chr3A.!!$F5 1751
5 TraesCS3D01G444300 chr3A 689578526 689579977 1451 False 912.500000 1664 90.402500 412 2388 2 chr3A.!!$F3 1976
6 TraesCS3D01G444300 chr3A 689845713 689847664 1951 False 781.333333 1105 90.643000 1 1480 3 chr3A.!!$F6 1479
7 TraesCS3D01G444300 chr3A 689866031 689867978 1947 False 778.666667 1075 90.593333 1 1480 3 chr3A.!!$F7 1479
8 TraesCS3D01G444300 chr3A 689608304 689609869 1565 False 667.000000 1692 90.545333 412 2558 3 chr3A.!!$F4 2146
9 TraesCS3D01G444300 chr3A 686280228 686281566 1338 True 568.500000 1027 87.632500 316 1752 2 chr3A.!!$R1 1436

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
249 678 0.652592 GATCTGGGCGTTGAATGACG 59.347 55.0 0.0 0.0 45.4 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2240 9627 0.038526 CCGTTCGTTGGTCTAGCAGT 60.039 55.0 0.0 0.0 0.0 4.4 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
26 27 4.760047 GGCGTGCCGGTCAGACAT 62.760 66.667 1.90 0.00 0.00 3.06
45 46 4.191544 ACATGACATCTATCCGTGGTTTG 58.808 43.478 0.00 0.00 0.00 2.93
50 51 4.023980 ACATCTATCCGTGGTTTGAGAGA 58.976 43.478 0.00 0.00 33.76 3.10
52 53 5.129485 ACATCTATCCGTGGTTTGAGAGATT 59.871 40.000 0.00 0.00 37.43 2.40
55 56 1.616865 TCCGTGGTTTGAGAGATTCGT 59.383 47.619 0.00 0.00 0.00 3.85
70 71 7.094805 TGAGAGATTCGTTTGGGTCTATTTTTG 60.095 37.037 0.00 0.00 0.00 2.44
73 74 5.441709 TTCGTTTGGGTCTATTTTTGGTC 57.558 39.130 0.00 0.00 0.00 4.02
86 87 5.720371 ATTTTTGGTCACCGATCAATGAA 57.280 34.783 0.00 0.00 32.42 2.57
129 131 2.092049 TGAGACGAGTATAAGAGGCCCA 60.092 50.000 0.00 0.00 0.00 5.36
246 675 2.028420 TCAGATCTGGGCGTTGAATG 57.972 50.000 22.42 0.00 0.00 2.67
249 678 0.652592 GATCTGGGCGTTGAATGACG 59.347 55.000 0.00 0.00 45.40 4.35
263 692 1.225855 ATGACGAAGCGCTCAACAAA 58.774 45.000 12.06 0.00 0.00 2.83
265 694 2.409012 TGACGAAGCGCTCAACAAATA 58.591 42.857 12.06 0.00 0.00 1.40
266 695 3.000041 TGACGAAGCGCTCAACAAATAT 59.000 40.909 12.06 0.00 0.00 1.28
267 696 3.062099 TGACGAAGCGCTCAACAAATATC 59.938 43.478 12.06 0.00 0.00 1.63
268 697 3.262420 ACGAAGCGCTCAACAAATATCT 58.738 40.909 12.06 0.00 0.00 1.98
269 698 3.684788 ACGAAGCGCTCAACAAATATCTT 59.315 39.130 12.06 0.00 0.00 2.40
270 699 4.154195 ACGAAGCGCTCAACAAATATCTTT 59.846 37.500 12.06 0.00 0.00 2.52
271 700 5.088739 CGAAGCGCTCAACAAATATCTTTT 58.911 37.500 12.06 0.00 0.00 2.27
272 701 5.569059 CGAAGCGCTCAACAAATATCTTTTT 59.431 36.000 12.06 0.00 0.00 1.94
273 702 6.740905 CGAAGCGCTCAACAAATATCTTTTTA 59.259 34.615 12.06 0.00 0.00 1.52
274 703 7.270365 CGAAGCGCTCAACAAATATCTTTTTAA 59.730 33.333 12.06 0.00 0.00 1.52
275 704 7.796958 AGCGCTCAACAAATATCTTTTTAAC 57.203 32.000 2.64 0.00 0.00 2.01
304 735 4.672899 TGGGATTTCTTTTTCGGGATTCT 58.327 39.130 0.00 0.00 0.00 2.40
367 798 9.938670 GTCGATGCTATATTCGTTAGATCTTAT 57.061 33.333 0.00 0.00 36.74 1.73
528 1100 1.400371 CCACGACGAGTTCTCTCACAG 60.400 57.143 0.00 0.00 40.44 3.66
529 1102 1.531578 CACGACGAGTTCTCTCACAGA 59.468 52.381 0.00 0.00 40.44 3.41
720 1300 8.530311 ACACAAATGCTTGTATCCAATATTTGA 58.470 29.630 18.91 0.00 44.15 2.69
1109 4626 3.942829 TCTCATGGCCTTCTGTAAGTTG 58.057 45.455 3.32 0.00 33.76 3.16
1173 4691 3.454042 TCAATCGATGAAACAACTGCG 57.546 42.857 0.00 0.00 34.30 5.18
1189 4707 5.163754 ACAACTGCGACTATAATTTTCTGGC 60.164 40.000 0.00 0.00 0.00 4.85
1196 4714 4.261801 ACTATAATTTTCTGGCGCACACT 58.738 39.130 10.83 0.00 0.00 3.55
1282 4800 1.172812 GGAGCCCTTGCAAGAACGTT 61.173 55.000 28.05 12.08 41.13 3.99
1398 4916 4.434989 CGACGACAACTTCTTTCACAAACA 60.435 41.667 0.00 0.00 0.00 2.83
1623 8978 3.016736 CAAATGGTCTATTCTGCCCGTT 58.983 45.455 0.00 0.00 0.00 4.44
1669 9024 6.545298 AGAGAGGAATTAATCAATGCTTGACC 59.455 38.462 1.44 0.00 43.48 4.02
1747 9134 2.464865 GAGTATGTCGCTGTGATGGTC 58.535 52.381 0.00 0.00 0.00 4.02
2222 9609 3.743714 CACATCCAAGGACCCAACA 57.256 52.632 0.00 0.00 0.00 3.33
2223 9610 1.247567 CACATCCAAGGACCCAACAC 58.752 55.000 0.00 0.00 0.00 3.32
2224 9611 0.112412 ACATCCAAGGACCCAACACC 59.888 55.000 0.00 0.00 0.00 4.16
2225 9612 0.405585 CATCCAAGGACCCAACACCT 59.594 55.000 0.00 0.00 38.23 4.00
2226 9613 0.405585 ATCCAAGGACCCAACACCTG 59.594 55.000 0.00 0.00 36.56 4.00
2227 9614 0.991355 TCCAAGGACCCAACACCTGT 60.991 55.000 0.00 0.00 36.56 4.00
2228 9615 0.106217 CCAAGGACCCAACACCTGTT 60.106 55.000 0.00 0.00 39.12 3.16
2229 9616 1.687996 CCAAGGACCCAACACCTGTTT 60.688 52.381 0.00 0.00 35.83 2.83
2230 9617 2.107366 CAAGGACCCAACACCTGTTTT 58.893 47.619 0.00 0.00 35.83 2.43
2231 9618 2.067365 AGGACCCAACACCTGTTTTC 57.933 50.000 0.00 0.00 35.83 2.29
2232 9619 1.037493 GGACCCAACACCTGTTTTCC 58.963 55.000 0.00 0.00 35.83 3.13
2233 9620 1.037493 GACCCAACACCTGTTTTCCC 58.963 55.000 0.00 0.00 35.83 3.97
2234 9621 0.397957 ACCCAACACCTGTTTTCCCC 60.398 55.000 0.00 0.00 35.83 4.81
2235 9622 0.105709 CCCAACACCTGTTTTCCCCT 60.106 55.000 0.00 0.00 35.83 4.79
2236 9623 1.146152 CCCAACACCTGTTTTCCCCTA 59.854 52.381 0.00 0.00 35.83 3.53
2237 9624 2.425102 CCCAACACCTGTTTTCCCCTAA 60.425 50.000 0.00 0.00 35.83 2.69
2238 9625 3.301274 CCAACACCTGTTTTCCCCTAAA 58.699 45.455 0.00 0.00 35.83 1.85
2239 9626 3.707102 CCAACACCTGTTTTCCCCTAAAA 59.293 43.478 0.00 0.00 35.83 1.52
2240 9627 4.162509 CCAACACCTGTTTTCCCCTAAAAA 59.837 41.667 0.00 0.00 38.76 1.94
2241 9628 5.113383 CAACACCTGTTTTCCCCTAAAAAC 58.887 41.667 5.51 5.51 45.25 2.43
2242 9629 4.616553 ACACCTGTTTTCCCCTAAAAACT 58.383 39.130 12.01 0.00 45.26 2.66
2243 9630 4.404394 ACACCTGTTTTCCCCTAAAAACTG 59.596 41.667 12.01 11.16 45.26 3.16
2244 9631 3.386726 ACCTGTTTTCCCCTAAAAACTGC 59.613 43.478 12.01 0.00 45.26 4.40
2245 9632 3.641436 CCTGTTTTCCCCTAAAAACTGCT 59.359 43.478 12.01 0.00 45.26 4.24
2246 9633 4.830600 CCTGTTTTCCCCTAAAAACTGCTA 59.169 41.667 12.01 0.00 45.26 3.49
2247 9634 5.048013 CCTGTTTTCCCCTAAAAACTGCTAG 60.048 44.000 12.01 0.00 45.26 3.42
2248 9635 5.697067 TGTTTTCCCCTAAAAACTGCTAGA 58.303 37.500 12.01 0.00 45.26 2.43
2249 9636 5.533528 TGTTTTCCCCTAAAAACTGCTAGAC 59.466 40.000 12.01 0.00 45.26 2.59
2250 9637 3.994931 TCCCCTAAAAACTGCTAGACC 57.005 47.619 0.00 0.00 0.00 3.85
2251 9638 3.253220 TCCCCTAAAAACTGCTAGACCA 58.747 45.455 0.00 0.00 0.00 4.02
2252 9639 3.653836 TCCCCTAAAAACTGCTAGACCAA 59.346 43.478 0.00 0.00 0.00 3.67
2253 9640 3.756963 CCCCTAAAAACTGCTAGACCAAC 59.243 47.826 0.00 0.00 0.00 3.77
2254 9641 3.435671 CCCTAAAAACTGCTAGACCAACG 59.564 47.826 0.00 0.00 0.00 4.10
2255 9642 4.312443 CCTAAAAACTGCTAGACCAACGA 58.688 43.478 0.00 0.00 0.00 3.85
2256 9643 4.753107 CCTAAAAACTGCTAGACCAACGAA 59.247 41.667 0.00 0.00 0.00 3.85
2257 9644 4.547406 AAAAACTGCTAGACCAACGAAC 57.453 40.909 0.00 0.00 0.00 3.95
2258 9645 1.779569 AACTGCTAGACCAACGAACG 58.220 50.000 0.00 0.00 0.00 3.95
2259 9646 0.038526 ACTGCTAGACCAACGAACGG 60.039 55.000 0.00 0.00 0.00 4.44
2260 9647 0.736325 CTGCTAGACCAACGAACGGG 60.736 60.000 0.00 0.00 0.00 5.28
2261 9648 2.098831 GCTAGACCAACGAACGGGC 61.099 63.158 0.00 0.00 0.00 6.13
2262 9649 1.590147 CTAGACCAACGAACGGGCT 59.410 57.895 3.48 3.48 46.54 5.19
2263 9650 0.813184 CTAGACCAACGAACGGGCTA 59.187 55.000 5.25 5.25 41.45 3.93
2264 9651 0.527565 TAGACCAACGAACGGGCTAC 59.472 55.000 1.65 0.00 41.45 3.58
2286 9673 7.039993 GCTACTTTCCTTTCCAATCAAAACCTA 60.040 37.037 0.00 0.00 0.00 3.08
2353 9748 3.646162 TGTAGCGTTATCCTTCATCCCAT 59.354 43.478 0.00 0.00 0.00 4.00
2381 9776 5.795441 CGCTCGGATAAAAGAAAAGGAAAAG 59.205 40.000 0.00 0.00 0.00 2.27
2383 9778 6.802348 GCTCGGATAAAAGAAAAGGAAAAGTC 59.198 38.462 0.00 0.00 0.00 3.01
2385 9780 8.228035 TCGGATAAAAGAAAAGGAAAAGTCAA 57.772 30.769 0.00 0.00 0.00 3.18
2386 9781 8.856103 TCGGATAAAAGAAAAGGAAAAGTCAAT 58.144 29.630 0.00 0.00 0.00 2.57
2387 9782 8.915654 CGGATAAAAGAAAAGGAAAAGTCAATG 58.084 33.333 0.00 0.00 0.00 2.82
2388 9783 9.981114 GGATAAAAGAAAAGGAAAAGTCAATGA 57.019 29.630 0.00 0.00 0.00 2.57
2392 9787 9.755804 AAAAGAAAAGGAAAAGTCAATGAGATC 57.244 29.630 0.00 0.00 0.00 2.75
2393 9788 7.459795 AGAAAAGGAAAAGTCAATGAGATCC 57.540 36.000 0.00 0.00 0.00 3.36
2394 9789 6.435591 AGAAAAGGAAAAGTCAATGAGATCCC 59.564 38.462 0.00 0.00 0.00 3.85
2395 9790 3.878778 AGGAAAAGTCAATGAGATCCCG 58.121 45.455 0.00 0.00 0.00 5.14
2396 9791 2.356069 GGAAAAGTCAATGAGATCCCGC 59.644 50.000 0.00 0.00 0.00 6.13
2397 9792 1.656652 AAAGTCAATGAGATCCCGCG 58.343 50.000 0.00 0.00 0.00 6.46
2398 9793 0.824109 AAGTCAATGAGATCCCGCGA 59.176 50.000 8.23 0.00 0.00 5.87
2399 9794 0.824109 AGTCAATGAGATCCCGCGAA 59.176 50.000 8.23 0.00 0.00 4.70
2400 9795 1.202463 AGTCAATGAGATCCCGCGAAG 60.202 52.381 8.23 0.00 0.00 3.79
2417 9812 4.201208 CGAAGCATGAACACATATCCAC 57.799 45.455 0.00 0.00 0.00 4.02
2418 9813 3.622612 CGAAGCATGAACACATATCCACA 59.377 43.478 0.00 0.00 0.00 4.17
2419 9814 4.494690 CGAAGCATGAACACATATCCACAC 60.495 45.833 0.00 0.00 0.00 3.82
2420 9815 3.954200 AGCATGAACACATATCCACACA 58.046 40.909 0.00 0.00 0.00 3.72
2421 9816 3.691118 AGCATGAACACATATCCACACAC 59.309 43.478 0.00 0.00 0.00 3.82
2422 9817 3.181497 GCATGAACACATATCCACACACC 60.181 47.826 0.00 0.00 0.00 4.16
2423 9818 3.066291 TGAACACATATCCACACACCC 57.934 47.619 0.00 0.00 0.00 4.61
2424 9819 2.290641 TGAACACATATCCACACACCCC 60.291 50.000 0.00 0.00 0.00 4.95
2425 9820 1.367346 ACACATATCCACACACCCCA 58.633 50.000 0.00 0.00 0.00 4.96
2426 9821 1.922447 ACACATATCCACACACCCCAT 59.078 47.619 0.00 0.00 0.00 4.00
2427 9822 2.092429 ACACATATCCACACACCCCATC 60.092 50.000 0.00 0.00 0.00 3.51
2428 9823 2.173356 CACATATCCACACACCCCATCT 59.827 50.000 0.00 0.00 0.00 2.90
2429 9824 2.439507 ACATATCCACACACCCCATCTC 59.560 50.000 0.00 0.00 0.00 2.75
2430 9825 1.507140 TATCCACACACCCCATCTCC 58.493 55.000 0.00 0.00 0.00 3.71
2431 9826 1.281925 ATCCACACACCCCATCTCCC 61.282 60.000 0.00 0.00 0.00 4.30
2432 9827 2.677228 CACACACCCCATCTCCCC 59.323 66.667 0.00 0.00 0.00 4.81
2433 9828 2.209809 ACACACCCCATCTCCCCA 59.790 61.111 0.00 0.00 0.00 4.96
2434 9829 1.465188 ACACACCCCATCTCCCCAA 60.465 57.895 0.00 0.00 0.00 4.12
2435 9830 1.000896 CACACCCCATCTCCCCAAC 60.001 63.158 0.00 0.00 0.00 3.77
2436 9831 2.238701 ACACCCCATCTCCCCAACC 61.239 63.158 0.00 0.00 0.00 3.77
2437 9832 2.212761 ACCCCATCTCCCCAACCA 59.787 61.111 0.00 0.00 0.00 3.67
2438 9833 1.230616 ACCCCATCTCCCCAACCAT 60.231 57.895 0.00 0.00 0.00 3.55
2439 9834 1.231068 CCCCATCTCCCCAACCATG 59.769 63.158 0.00 0.00 0.00 3.66
2440 9835 1.583784 CCCCATCTCCCCAACCATGT 61.584 60.000 0.00 0.00 0.00 3.21
2441 9836 0.106519 CCCATCTCCCCAACCATGTC 60.107 60.000 0.00 0.00 0.00 3.06
2442 9837 0.464373 CCATCTCCCCAACCATGTCG 60.464 60.000 0.00 0.00 0.00 4.35
2443 9838 1.097547 CATCTCCCCAACCATGTCGC 61.098 60.000 0.00 0.00 0.00 5.19
2490 9885 0.165944 CGAGAAAATTTGCCGACGCT 59.834 50.000 0.00 0.00 35.36 5.07
2493 9888 0.387239 GAAAATTTGCCGACGCTGCT 60.387 50.000 0.00 0.00 35.36 4.24
2512 9907 1.118965 TCCACTCCTCGTTTGCCTCA 61.119 55.000 0.00 0.00 0.00 3.86
2518 9913 1.026718 CCTCGTTTGCCTCATGGTCC 61.027 60.000 0.00 0.00 35.27 4.46
2523 9918 1.139498 TTTGCCTCATGGTCCTGGGA 61.139 55.000 0.00 0.00 35.27 4.37
2524 9919 1.565390 TTGCCTCATGGTCCTGGGAG 61.565 60.000 0.00 0.00 35.27 4.30
2540 9935 4.227134 AGCACGGCCGCTAGGATG 62.227 66.667 28.58 16.46 41.55 3.51
2550 9945 2.285868 CTAGGATGGGGGACGGGT 59.714 66.667 0.00 0.00 0.00 5.28
2551 9946 2.041301 TAGGATGGGGGACGGGTG 60.041 66.667 0.00 0.00 0.00 4.61
2564 9959 3.702048 GGGTGGGAGCGTGCACTA 61.702 66.667 16.19 0.00 0.00 2.74
2565 9960 2.434359 GGTGGGAGCGTGCACTAC 60.434 66.667 16.19 6.97 0.00 2.73
2566 9961 2.342279 GTGGGAGCGTGCACTACA 59.658 61.111 16.19 3.59 0.00 2.74
2567 9962 1.301401 GTGGGAGCGTGCACTACAA 60.301 57.895 16.19 0.00 0.00 2.41
2568 9963 1.005037 TGGGAGCGTGCACTACAAG 60.005 57.895 16.19 0.00 0.00 3.16
2569 9964 1.292223 GGGAGCGTGCACTACAAGA 59.708 57.895 16.19 0.00 0.00 3.02
2570 9965 0.320421 GGGAGCGTGCACTACAAGAA 60.320 55.000 16.19 0.00 0.00 2.52
2571 9966 1.508632 GGAGCGTGCACTACAAGAAA 58.491 50.000 16.19 0.00 0.00 2.52
2572 9967 1.194772 GGAGCGTGCACTACAAGAAAC 59.805 52.381 16.19 0.00 0.00 2.78
2573 9968 1.194772 GAGCGTGCACTACAAGAAACC 59.805 52.381 16.19 0.00 0.00 3.27
2574 9969 1.202651 AGCGTGCACTACAAGAAACCT 60.203 47.619 16.19 0.00 0.00 3.50
2575 9970 1.069906 GCGTGCACTACAAGAAACCTG 60.070 52.381 16.19 0.00 0.00 4.00
2576 9971 2.210116 CGTGCACTACAAGAAACCTGT 58.790 47.619 16.19 0.00 0.00 4.00
2577 9972 2.612212 CGTGCACTACAAGAAACCTGTT 59.388 45.455 16.19 0.00 0.00 3.16
2578 9973 3.805422 CGTGCACTACAAGAAACCTGTTA 59.195 43.478 16.19 0.00 0.00 2.41
2579 9974 4.271533 CGTGCACTACAAGAAACCTGTTAA 59.728 41.667 16.19 0.00 0.00 2.01
2580 9975 5.049680 CGTGCACTACAAGAAACCTGTTAAT 60.050 40.000 16.19 0.00 0.00 1.40
2581 9976 6.371389 GTGCACTACAAGAAACCTGTTAATC 58.629 40.000 10.32 0.00 0.00 1.75
2582 9977 5.472137 TGCACTACAAGAAACCTGTTAATCC 59.528 40.000 0.00 0.00 0.00 3.01
2583 9978 5.472137 GCACTACAAGAAACCTGTTAATCCA 59.528 40.000 0.00 0.00 0.00 3.41
2584 9979 6.151144 GCACTACAAGAAACCTGTTAATCCAT 59.849 38.462 0.00 0.00 0.00 3.41
2585 9980 7.530010 CACTACAAGAAACCTGTTAATCCATG 58.470 38.462 0.00 0.00 0.00 3.66
2586 9981 7.390440 CACTACAAGAAACCTGTTAATCCATGA 59.610 37.037 0.00 0.00 0.00 3.07
2587 9982 6.575162 ACAAGAAACCTGTTAATCCATGAC 57.425 37.500 0.00 0.00 0.00 3.06
2588 9983 5.181245 ACAAGAAACCTGTTAATCCATGACG 59.819 40.000 0.00 0.00 0.00 4.35
2589 9984 4.261801 AGAAACCTGTTAATCCATGACGG 58.738 43.478 0.00 0.00 0.00 4.79
2599 9994 2.401583 TCCATGACGGATTTCTGGTG 57.598 50.000 0.00 0.00 39.64 4.17
2600 9995 1.905894 TCCATGACGGATTTCTGGTGA 59.094 47.619 0.00 0.00 39.64 4.02
2601 9996 2.009774 CCATGACGGATTTCTGGTGAC 58.990 52.381 0.00 0.00 36.56 3.67
2602 9997 2.615240 CCATGACGGATTTCTGGTGACA 60.615 50.000 0.00 0.00 36.56 3.58
2603 9998 3.273434 CATGACGGATTTCTGGTGACAT 58.727 45.455 0.00 0.00 41.51 3.06
2604 9999 3.417069 TGACGGATTTCTGGTGACATT 57.583 42.857 0.00 0.00 41.51 2.71
2605 10000 3.750371 TGACGGATTTCTGGTGACATTT 58.250 40.909 0.00 0.00 41.51 2.32
2606 10001 4.141287 TGACGGATTTCTGGTGACATTTT 58.859 39.130 0.00 0.00 41.51 1.82
2607 10002 4.215399 TGACGGATTTCTGGTGACATTTTC 59.785 41.667 0.00 0.00 41.51 2.29
2608 10003 4.141287 ACGGATTTCTGGTGACATTTTCA 58.859 39.130 0.00 0.00 41.51 2.69
2609 10004 4.216257 ACGGATTTCTGGTGACATTTTCAG 59.784 41.667 0.00 0.00 41.51 3.02
2610 10005 4.455533 CGGATTTCTGGTGACATTTTCAGA 59.544 41.667 0.00 0.00 41.51 3.27
2611 10006 5.048782 CGGATTTCTGGTGACATTTTCAGAA 60.049 40.000 0.00 0.00 42.34 3.02
2614 10009 6.773976 TTTCTGGTGACATTTTCAGAAACT 57.226 33.333 11.72 0.00 45.49 2.66
2615 10010 5.756195 TCTGGTGACATTTTCAGAAACTG 57.244 39.130 10.86 10.86 41.51 3.16
2616 10011 5.192927 TCTGGTGACATTTTCAGAAACTGT 58.807 37.500 16.58 16.58 41.51 3.55
2617 10012 5.296780 TCTGGTGACATTTTCAGAAACTGTC 59.703 40.000 27.68 27.68 41.51 3.51
2618 10013 4.946772 TGGTGACATTTTCAGAAACTGTCA 59.053 37.500 30.89 30.89 38.91 3.58
2619 10014 5.593909 TGGTGACATTTTCAGAAACTGTCAT 59.406 36.000 34.17 11.68 40.74 3.06
2620 10015 5.916883 GGTGACATTTTCAGAAACTGTCATG 59.083 40.000 34.17 20.84 40.74 3.07
2621 10016 5.916883 GTGACATTTTCAGAAACTGTCATGG 59.083 40.000 34.17 7.94 40.74 3.66
2622 10017 5.827267 TGACATTTTCAGAAACTGTCATGGA 59.173 36.000 30.89 17.22 37.79 3.41
2623 10018 6.491062 TGACATTTTCAGAAACTGTCATGGAT 59.509 34.615 30.89 7.27 37.79 3.41
2624 10019 6.684686 ACATTTTCAGAAACTGTCATGGATG 58.315 36.000 12.04 5.30 32.61 3.51
2625 10020 6.491062 ACATTTTCAGAAACTGTCATGGATGA 59.509 34.615 12.04 0.00 32.61 2.92
2636 10031 3.627395 TCATGGATGACCTGGTACAAC 57.373 47.619 0.00 0.00 38.70 3.32
2637 10032 2.238646 TCATGGATGACCTGGTACAACC 59.761 50.000 0.00 8.75 38.70 3.77
2638 10033 0.988832 TGGATGACCTGGTACAACCC 59.011 55.000 16.85 13.73 38.70 4.11
2639 10034 0.255033 GGATGACCTGGTACAACCCC 59.745 60.000 0.00 0.63 38.70 4.95
2640 10035 0.107848 GATGACCTGGTACAACCCCG 60.108 60.000 0.00 0.00 38.70 5.73
2641 10036 2.046604 GACCTGGTACAACCCCGC 60.047 66.667 0.00 0.00 38.70 6.13
2642 10037 2.850130 ACCTGGTACAACCCCGCA 60.850 61.111 0.00 0.00 38.70 5.69
2643 10038 2.400269 GACCTGGTACAACCCCGCAA 62.400 60.000 0.00 0.00 38.70 4.85
2644 10039 1.674322 CCTGGTACAACCCCGCAAG 60.674 63.158 0.00 0.00 38.70 4.01
2645 10040 2.281900 TGGTACAACCCCGCAAGC 60.282 61.111 0.00 0.00 37.50 4.01
2646 10041 3.060000 GGTACAACCCCGCAAGCC 61.060 66.667 0.00 0.00 30.04 4.35
2647 10042 3.060000 GTACAACCCCGCAAGCCC 61.060 66.667 0.00 0.00 0.00 5.19
2648 10043 4.708386 TACAACCCCGCAAGCCCG 62.708 66.667 0.00 0.00 0.00 6.13
2654 10049 3.508840 CCCGCAAGCCCGCTAAAG 61.509 66.667 0.00 0.00 0.00 1.85
2655 10050 4.179579 CCGCAAGCCCGCTAAAGC 62.180 66.667 0.00 0.00 37.78 3.51
2656 10051 4.179579 CGCAAGCCCGCTAAAGCC 62.180 66.667 0.00 0.00 37.91 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 4.405680 TCTCAAACCACGGATAGATGTCAT 59.594 41.667 0.00 0.00 0.00 3.06
26 27 3.767131 TCTCAAACCACGGATAGATGTCA 59.233 43.478 0.00 0.00 0.00 3.58
32 33 4.045104 CGAATCTCTCAAACCACGGATAG 58.955 47.826 0.00 0.00 0.00 2.08
38 39 3.058224 CCCAAACGAATCTCTCAAACCAC 60.058 47.826 0.00 0.00 0.00 4.16
39 40 3.146066 CCCAAACGAATCTCTCAAACCA 58.854 45.455 0.00 0.00 0.00 3.67
45 46 6.986904 AAAATAGACCCAAACGAATCTCTC 57.013 37.500 0.00 0.00 0.00 3.20
50 51 5.536916 TGACCAAAAATAGACCCAAACGAAT 59.463 36.000 0.00 0.00 0.00 3.34
52 53 4.276431 GTGACCAAAAATAGACCCAAACGA 59.724 41.667 0.00 0.00 0.00 3.85
55 56 3.570550 CGGTGACCAAAAATAGACCCAAA 59.429 43.478 1.11 0.00 0.00 3.28
70 71 1.006832 CCGTTCATTGATCGGTGACC 58.993 55.000 22.42 0.00 39.29 4.02
73 74 0.645355 CGTCCGTTCATTGATCGGTG 59.355 55.000 26.98 19.62 43.08 4.94
104 105 4.142227 GGCCTCTTATACTCGTCTCAAACA 60.142 45.833 0.00 0.00 0.00 2.83
129 131 7.017551 TGGTCATTTGGCTTGGTATCTATATCT 59.982 37.037 0.00 0.00 0.00 1.98
189 197 8.627403 ACCTAATAATGCAACATCTTCATTCAG 58.373 33.333 0.00 0.00 33.13 3.02
246 675 3.307242 AGATATTTGTTGAGCGCTTCGTC 59.693 43.478 13.26 0.00 0.00 4.20
249 678 6.934561 AAAAAGATATTTGTTGAGCGCTTC 57.065 33.333 13.26 5.55 0.00 3.86
304 735 5.991861 AGTCCTTAGTCGAGTGAGATTCTA 58.008 41.667 13.31 0.00 0.00 2.10
367 798 8.954950 AACAAAATTTTACATGAATCACCACA 57.045 26.923 2.44 0.00 0.00 4.17
572 1145 3.004734 GTGGCAGTGTAAGAGCAAAACAT 59.995 43.478 0.00 0.00 0.00 2.71
1151 4668 4.154015 TCGCAGTTGTTTCATCGATTGATT 59.846 37.500 0.00 0.00 33.34 2.57
1173 4691 4.332819 AGTGTGCGCCAGAAAATTATAGTC 59.667 41.667 4.18 0.00 0.00 2.59
1189 4707 5.102313 TGTGACATAGAATTAGAGTGTGCG 58.898 41.667 0.00 0.00 0.00 5.34
1196 4714 6.051074 CACCTGCATGTGACATAGAATTAGA 58.949 40.000 16.24 0.00 38.55 2.10
1398 4916 4.578928 ACATGCACGTCTTTTTCTTAGGTT 59.421 37.500 0.00 0.00 0.00 3.50
1435 8761 0.694196 GTGGTGGTGGGGCTTTACTA 59.306 55.000 0.00 0.00 0.00 1.82
1590 8945 2.363306 ACCATTTGCTCACTGGTCAA 57.637 45.000 0.00 0.00 38.99 3.18
1623 8978 8.560355 TCTCTTATTGAAATCATTTTCCACGA 57.440 30.769 0.00 0.00 40.49 4.35
1669 9024 6.267070 TGCAATCAATTATGCATGTGTACAG 58.733 36.000 10.16 0.00 46.87 2.74
2204 9591 1.247567 GTGTTGGGTCCTTGGATGTG 58.752 55.000 0.00 0.00 0.00 3.21
2205 9592 0.112412 GGTGTTGGGTCCTTGGATGT 59.888 55.000 0.00 0.00 0.00 3.06
2206 9593 0.405585 AGGTGTTGGGTCCTTGGATG 59.594 55.000 0.00 0.00 0.00 3.51
2207 9594 0.405585 CAGGTGTTGGGTCCTTGGAT 59.594 55.000 0.00 0.00 30.91 3.41
2208 9595 0.991355 ACAGGTGTTGGGTCCTTGGA 60.991 55.000 0.00 0.00 30.91 3.53
2209 9596 0.106217 AACAGGTGTTGGGTCCTTGG 60.106 55.000 0.00 0.00 36.80 3.61
2210 9597 1.775385 AAACAGGTGTTGGGTCCTTG 58.225 50.000 0.00 0.00 38.44 3.61
2211 9598 2.384828 GAAAACAGGTGTTGGGTCCTT 58.615 47.619 0.00 0.00 38.44 3.36
2212 9599 1.411074 GGAAAACAGGTGTTGGGTCCT 60.411 52.381 10.92 0.00 38.44 3.85
2213 9600 1.037493 GGAAAACAGGTGTTGGGTCC 58.963 55.000 0.00 1.07 38.44 4.46
2214 9601 1.037493 GGGAAAACAGGTGTTGGGTC 58.963 55.000 0.00 0.00 38.44 4.46
2215 9602 0.397957 GGGGAAAACAGGTGTTGGGT 60.398 55.000 0.00 0.00 38.44 4.51
2216 9603 0.105709 AGGGGAAAACAGGTGTTGGG 60.106 55.000 0.00 0.00 38.44 4.12
2217 9604 2.668144 TAGGGGAAAACAGGTGTTGG 57.332 50.000 0.00 0.00 38.44 3.77
2218 9605 5.105106 AGTTTTTAGGGGAAAACAGGTGTTG 60.105 40.000 13.64 0.00 46.72 3.33
2219 9606 5.027460 AGTTTTTAGGGGAAAACAGGTGTT 58.973 37.500 13.64 0.00 46.72 3.32
2220 9607 4.404394 CAGTTTTTAGGGGAAAACAGGTGT 59.596 41.667 13.64 0.00 46.72 4.16
2221 9608 4.739436 GCAGTTTTTAGGGGAAAACAGGTG 60.739 45.833 13.64 6.38 46.72 4.00
2222 9609 3.386726 GCAGTTTTTAGGGGAAAACAGGT 59.613 43.478 13.64 0.00 46.72 4.00
2223 9610 3.641436 AGCAGTTTTTAGGGGAAAACAGG 59.359 43.478 13.64 7.78 46.72 4.00
2224 9611 4.937201 AGCAGTTTTTAGGGGAAAACAG 57.063 40.909 13.64 8.14 46.72 3.16
2225 9612 5.533528 GTCTAGCAGTTTTTAGGGGAAAACA 59.466 40.000 13.64 0.00 46.72 2.83
2226 9613 5.048224 GGTCTAGCAGTTTTTAGGGGAAAAC 60.048 44.000 5.36 5.36 45.40 2.43
2227 9614 5.074804 GGTCTAGCAGTTTTTAGGGGAAAA 58.925 41.667 0.00 0.00 35.16 2.29
2228 9615 4.105057 TGGTCTAGCAGTTTTTAGGGGAAA 59.895 41.667 0.00 0.00 0.00 3.13
2229 9616 3.653836 TGGTCTAGCAGTTTTTAGGGGAA 59.346 43.478 0.00 0.00 0.00 3.97
2230 9617 3.253220 TGGTCTAGCAGTTTTTAGGGGA 58.747 45.455 0.00 0.00 0.00 4.81
2231 9618 3.713826 TGGTCTAGCAGTTTTTAGGGG 57.286 47.619 0.00 0.00 0.00 4.79
2232 9619 3.435671 CGTTGGTCTAGCAGTTTTTAGGG 59.564 47.826 0.00 0.00 0.00 3.53
2233 9620 4.312443 TCGTTGGTCTAGCAGTTTTTAGG 58.688 43.478 0.00 0.00 0.00 2.69
2234 9621 5.611844 CGTTCGTTGGTCTAGCAGTTTTTAG 60.612 44.000 0.00 0.00 0.00 1.85
2235 9622 4.209703 CGTTCGTTGGTCTAGCAGTTTTTA 59.790 41.667 0.00 0.00 0.00 1.52
2236 9623 3.001939 CGTTCGTTGGTCTAGCAGTTTTT 59.998 43.478 0.00 0.00 0.00 1.94
2237 9624 2.542595 CGTTCGTTGGTCTAGCAGTTTT 59.457 45.455 0.00 0.00 0.00 2.43
2238 9625 2.132762 CGTTCGTTGGTCTAGCAGTTT 58.867 47.619 0.00 0.00 0.00 2.66
2239 9626 1.604693 CCGTTCGTTGGTCTAGCAGTT 60.605 52.381 0.00 0.00 0.00 3.16
2240 9627 0.038526 CCGTTCGTTGGTCTAGCAGT 60.039 55.000 0.00 0.00 0.00 4.40
2241 9628 0.736325 CCCGTTCGTTGGTCTAGCAG 60.736 60.000 0.00 0.00 0.00 4.24
2242 9629 1.290955 CCCGTTCGTTGGTCTAGCA 59.709 57.895 0.00 0.00 0.00 3.49
2243 9630 2.098831 GCCCGTTCGTTGGTCTAGC 61.099 63.158 0.00 0.00 0.00 3.42
2244 9631 0.813184 TAGCCCGTTCGTTGGTCTAG 59.187 55.000 0.00 0.00 0.00 2.43
2245 9632 0.527565 GTAGCCCGTTCGTTGGTCTA 59.472 55.000 0.00 0.00 0.00 2.59
2246 9633 1.183676 AGTAGCCCGTTCGTTGGTCT 61.184 55.000 0.00 0.00 0.00 3.85
2247 9634 0.320160 AAGTAGCCCGTTCGTTGGTC 60.320 55.000 0.00 0.00 0.00 4.02
2248 9635 0.107268 AAAGTAGCCCGTTCGTTGGT 59.893 50.000 0.00 0.00 0.00 3.67
2249 9636 0.794473 GAAAGTAGCCCGTTCGTTGG 59.206 55.000 0.00 0.00 0.00 3.77
2250 9637 0.794473 GGAAAGTAGCCCGTTCGTTG 59.206 55.000 0.00 0.00 32.96 4.10
2251 9638 0.683412 AGGAAAGTAGCCCGTTCGTT 59.317 50.000 0.00 0.00 32.96 3.85
2252 9639 0.683412 AAGGAAAGTAGCCCGTTCGT 59.317 50.000 0.00 0.00 32.96 3.85
2253 9640 1.730612 GAAAGGAAAGTAGCCCGTTCG 59.269 52.381 0.00 0.00 32.87 3.95
2254 9641 2.082231 GGAAAGGAAAGTAGCCCGTTC 58.918 52.381 0.00 0.00 39.25 3.95
2255 9642 1.422402 TGGAAAGGAAAGTAGCCCGTT 59.578 47.619 0.00 0.00 0.00 4.44
2256 9643 1.061546 TGGAAAGGAAAGTAGCCCGT 58.938 50.000 0.00 0.00 0.00 5.28
2257 9644 2.194201 TTGGAAAGGAAAGTAGCCCG 57.806 50.000 0.00 0.00 0.00 6.13
2258 9645 3.697166 TGATTGGAAAGGAAAGTAGCCC 58.303 45.455 0.00 0.00 0.00 5.19
2259 9646 5.722021 TTTGATTGGAAAGGAAAGTAGCC 57.278 39.130 0.00 0.00 0.00 3.93
2260 9647 5.926542 GGTTTTGATTGGAAAGGAAAGTAGC 59.073 40.000 0.00 0.00 0.00 3.58
2261 9648 7.290110 AGGTTTTGATTGGAAAGGAAAGTAG 57.710 36.000 0.00 0.00 0.00 2.57
2262 9649 7.231925 GGTAGGTTTTGATTGGAAAGGAAAGTA 59.768 37.037 0.00 0.00 0.00 2.24
2263 9650 6.041637 GGTAGGTTTTGATTGGAAAGGAAAGT 59.958 38.462 0.00 0.00 0.00 2.66
2264 9651 6.041523 TGGTAGGTTTTGATTGGAAAGGAAAG 59.958 38.462 0.00 0.00 0.00 2.62
2329 9716 4.246458 GGGATGAAGGATAACGCTACATC 58.754 47.826 0.00 0.00 34.06 3.06
2353 9748 3.322211 TTTCTTTTATCCGAGCGTGGA 57.678 42.857 2.29 2.29 43.58 4.02
2381 9776 1.212616 CTTCGCGGGATCTCATTGAC 58.787 55.000 6.13 0.00 0.00 3.18
2383 9778 0.811219 TGCTTCGCGGGATCTCATTG 60.811 55.000 6.13 0.00 0.00 2.82
2385 9780 0.602106 CATGCTTCGCGGGATCTCAT 60.602 55.000 6.13 4.53 0.00 2.90
2386 9781 1.227350 CATGCTTCGCGGGATCTCA 60.227 57.895 6.13 2.17 0.00 3.27
2387 9782 0.530650 TTCATGCTTCGCGGGATCTC 60.531 55.000 6.13 0.00 0.00 2.75
2388 9783 0.811616 GTTCATGCTTCGCGGGATCT 60.812 55.000 6.13 0.00 0.00 2.75
2389 9784 1.089481 TGTTCATGCTTCGCGGGATC 61.089 55.000 6.13 0.00 0.00 3.36
2390 9785 1.078497 TGTTCATGCTTCGCGGGAT 60.078 52.632 6.13 0.00 0.00 3.85
2391 9786 2.032634 GTGTTCATGCTTCGCGGGA 61.033 57.895 6.13 0.00 0.00 5.14
2392 9787 1.647545 ATGTGTTCATGCTTCGCGGG 61.648 55.000 6.13 0.11 32.51 6.13
2393 9788 1.006086 TATGTGTTCATGCTTCGCGG 58.994 50.000 6.13 0.00 35.70 6.46
2394 9789 2.348872 GGATATGTGTTCATGCTTCGCG 60.349 50.000 0.00 0.00 35.70 5.87
2395 9790 2.613595 TGGATATGTGTTCATGCTTCGC 59.386 45.455 0.00 0.00 35.70 4.70
2396 9791 3.622612 TGTGGATATGTGTTCATGCTTCG 59.377 43.478 0.00 0.00 35.70 3.79
2397 9792 4.395854 TGTGTGGATATGTGTTCATGCTTC 59.604 41.667 0.00 0.00 35.70 3.86
2398 9793 4.156556 GTGTGTGGATATGTGTTCATGCTT 59.843 41.667 0.00 0.00 35.70 3.91
2399 9794 3.691118 GTGTGTGGATATGTGTTCATGCT 59.309 43.478 0.00 0.00 35.70 3.79
2400 9795 3.181497 GGTGTGTGGATATGTGTTCATGC 60.181 47.826 0.00 0.00 35.70 4.06
2401 9796 3.378112 GGGTGTGTGGATATGTGTTCATG 59.622 47.826 0.00 0.00 35.70 3.07
2402 9797 3.620488 GGGTGTGTGGATATGTGTTCAT 58.380 45.455 0.00 0.00 38.00 2.57
2403 9798 2.290641 GGGGTGTGTGGATATGTGTTCA 60.291 50.000 0.00 0.00 0.00 3.18
2404 9799 2.290641 TGGGGTGTGTGGATATGTGTTC 60.291 50.000 0.00 0.00 0.00 3.18
2405 9800 1.707989 TGGGGTGTGTGGATATGTGTT 59.292 47.619 0.00 0.00 0.00 3.32
2406 9801 1.367346 TGGGGTGTGTGGATATGTGT 58.633 50.000 0.00 0.00 0.00 3.72
2407 9802 2.173356 AGATGGGGTGTGTGGATATGTG 59.827 50.000 0.00 0.00 0.00 3.21
2408 9803 2.439507 GAGATGGGGTGTGTGGATATGT 59.560 50.000 0.00 0.00 0.00 2.29
2409 9804 2.224621 GGAGATGGGGTGTGTGGATATG 60.225 54.545 0.00 0.00 0.00 1.78
2410 9805 2.057922 GGAGATGGGGTGTGTGGATAT 58.942 52.381 0.00 0.00 0.00 1.63
2411 9806 1.507140 GGAGATGGGGTGTGTGGATA 58.493 55.000 0.00 0.00 0.00 2.59
2412 9807 1.281925 GGGAGATGGGGTGTGTGGAT 61.282 60.000 0.00 0.00 0.00 3.41
2413 9808 1.923395 GGGAGATGGGGTGTGTGGA 60.923 63.158 0.00 0.00 0.00 4.02
2414 9809 2.677228 GGGAGATGGGGTGTGTGG 59.323 66.667 0.00 0.00 0.00 4.17
2415 9810 1.788518 TTGGGGAGATGGGGTGTGTG 61.789 60.000 0.00 0.00 0.00 3.82
2416 9811 1.465188 TTGGGGAGATGGGGTGTGT 60.465 57.895 0.00 0.00 0.00 3.72
2417 9812 1.000896 GTTGGGGAGATGGGGTGTG 60.001 63.158 0.00 0.00 0.00 3.82
2418 9813 2.238701 GGTTGGGGAGATGGGGTGT 61.239 63.158 0.00 0.00 0.00 4.16
2419 9814 1.583784 ATGGTTGGGGAGATGGGGTG 61.584 60.000 0.00 0.00 0.00 4.61
2420 9815 1.230616 ATGGTTGGGGAGATGGGGT 60.231 57.895 0.00 0.00 0.00 4.95
2421 9816 1.231068 CATGGTTGGGGAGATGGGG 59.769 63.158 0.00 0.00 0.00 4.96
2422 9817 0.106519 GACATGGTTGGGGAGATGGG 60.107 60.000 0.00 0.00 0.00 4.00
2423 9818 0.464373 CGACATGGTTGGGGAGATGG 60.464 60.000 0.00 0.00 0.00 3.51
2424 9819 1.097547 GCGACATGGTTGGGGAGATG 61.098 60.000 0.00 0.00 0.00 2.90
2425 9820 1.224592 GCGACATGGTTGGGGAGAT 59.775 57.895 0.00 0.00 0.00 2.75
2426 9821 2.668632 GCGACATGGTTGGGGAGA 59.331 61.111 0.00 0.00 0.00 3.71
2427 9822 2.438434 GGCGACATGGTTGGGGAG 60.438 66.667 0.00 0.00 0.00 4.30
2428 9823 4.041762 GGGCGACATGGTTGGGGA 62.042 66.667 0.00 0.00 0.00 4.81
2429 9824 4.358841 TGGGCGACATGGTTGGGG 62.359 66.667 0.00 0.00 0.00 4.96
2430 9825 3.061848 GTGGGCGACATGGTTGGG 61.062 66.667 0.00 0.00 0.00 4.12
2431 9826 3.430862 CGTGGGCGACATGGTTGG 61.431 66.667 0.00 0.00 41.33 3.77
2432 9827 2.358125 TCGTGGGCGACATGGTTG 60.358 61.111 0.00 0.00 42.81 3.77
2490 9885 1.301716 GCAAACGAGGAGTGGAGCA 60.302 57.895 0.00 0.00 0.00 4.26
2493 9888 1.118965 TGAGGCAAACGAGGAGTGGA 61.119 55.000 0.00 0.00 0.00 4.02
2512 9907 3.402681 CCGTGCTCCCAGGACCAT 61.403 66.667 0.00 0.00 32.47 3.55
2534 9929 2.041301 CACCCGTCCCCCATCCTA 60.041 66.667 0.00 0.00 0.00 2.94
2550 9945 1.005037 CTTGTAGTGCACGCTCCCA 60.005 57.895 12.01 2.07 0.00 4.37
2551 9946 0.320421 TTCTTGTAGTGCACGCTCCC 60.320 55.000 12.01 0.00 0.00 4.30
2554 9949 1.202651 AGGTTTCTTGTAGTGCACGCT 60.203 47.619 12.01 0.00 0.00 5.07
2555 9950 1.069906 CAGGTTTCTTGTAGTGCACGC 60.070 52.381 12.01 9.34 0.00 5.34
2556 9951 2.210116 ACAGGTTTCTTGTAGTGCACG 58.790 47.619 12.01 0.00 0.00 5.34
2557 9952 5.744666 TTAACAGGTTTCTTGTAGTGCAC 57.255 39.130 9.40 9.40 0.00 4.57
2558 9953 5.472137 GGATTAACAGGTTTCTTGTAGTGCA 59.528 40.000 0.00 0.00 0.00 4.57
2559 9954 5.472137 TGGATTAACAGGTTTCTTGTAGTGC 59.528 40.000 0.00 0.00 0.00 4.40
2560 9955 7.390440 TCATGGATTAACAGGTTTCTTGTAGTG 59.610 37.037 0.00 0.00 0.00 2.74
2561 9956 7.390718 GTCATGGATTAACAGGTTTCTTGTAGT 59.609 37.037 0.00 0.00 0.00 2.73
2562 9957 7.413000 CGTCATGGATTAACAGGTTTCTTGTAG 60.413 40.741 0.00 0.00 0.00 2.74
2563 9958 6.370442 CGTCATGGATTAACAGGTTTCTTGTA 59.630 38.462 0.00 0.00 0.00 2.41
2564 9959 5.181245 CGTCATGGATTAACAGGTTTCTTGT 59.819 40.000 0.00 0.00 0.00 3.16
2565 9960 5.391950 CCGTCATGGATTAACAGGTTTCTTG 60.392 44.000 0.00 0.00 42.00 3.02
2566 9961 4.700213 CCGTCATGGATTAACAGGTTTCTT 59.300 41.667 0.00 0.00 42.00 2.52
2567 9962 4.019681 TCCGTCATGGATTAACAGGTTTCT 60.020 41.667 0.00 0.00 43.74 2.52
2568 9963 4.258543 TCCGTCATGGATTAACAGGTTTC 58.741 43.478 0.00 0.00 43.74 2.78
2569 9964 4.295141 TCCGTCATGGATTAACAGGTTT 57.705 40.909 0.00 0.00 43.74 3.27
2570 9965 3.992943 TCCGTCATGGATTAACAGGTT 57.007 42.857 0.00 0.00 43.74 3.50
2581 9976 2.009774 GTCACCAGAAATCCGTCATGG 58.990 52.381 0.00 0.00 40.09 3.66
2582 9977 2.698803 TGTCACCAGAAATCCGTCATG 58.301 47.619 0.00 0.00 0.00 3.07
2583 9978 3.634397 ATGTCACCAGAAATCCGTCAT 57.366 42.857 0.00 0.00 0.00 3.06
2584 9979 3.417069 AATGTCACCAGAAATCCGTCA 57.583 42.857 0.00 0.00 0.00 4.35
2585 9980 4.215399 TGAAAATGTCACCAGAAATCCGTC 59.785 41.667 0.00 0.00 0.00 4.79
2586 9981 4.141287 TGAAAATGTCACCAGAAATCCGT 58.859 39.130 0.00 0.00 0.00 4.69
2587 9982 4.455533 TCTGAAAATGTCACCAGAAATCCG 59.544 41.667 0.00 0.00 33.26 4.18
2588 9983 5.964958 TCTGAAAATGTCACCAGAAATCC 57.035 39.130 0.00 0.00 33.26 3.01
2590 9985 7.147846 ACAGTTTCTGAAAATGTCACCAGAAAT 60.148 33.333 25.27 4.28 45.43 2.17
2591 9986 6.152661 ACAGTTTCTGAAAATGTCACCAGAAA 59.847 34.615 25.27 11.05 45.43 2.52
2592 9987 5.652014 ACAGTTTCTGAAAATGTCACCAGAA 59.348 36.000 25.27 0.00 45.43 3.02
2593 9988 5.192927 ACAGTTTCTGAAAATGTCACCAGA 58.807 37.500 25.27 0.00 45.43 3.86
2594 9989 5.505173 ACAGTTTCTGAAAATGTCACCAG 57.495 39.130 25.27 5.56 45.43 4.00
2601 9996 6.916440 TCATCCATGACAGTTTCTGAAAATG 58.084 36.000 24.09 24.09 41.82 2.32
2615 10010 3.931374 GGTTGTACCAGGTCATCCATGAC 60.931 52.174 10.74 10.74 45.86 3.06
2616 10011 2.238646 GGTTGTACCAGGTCATCCATGA 59.761 50.000 0.00 0.00 38.42 3.07
2617 10012 2.643551 GGTTGTACCAGGTCATCCATG 58.356 52.381 0.00 0.00 38.42 3.66
2618 10013 1.564348 GGGTTGTACCAGGTCATCCAT 59.436 52.381 0.00 0.00 41.02 3.41
2619 10014 0.988832 GGGTTGTACCAGGTCATCCA 59.011 55.000 0.00 0.00 41.02 3.41
2620 10015 0.255033 GGGGTTGTACCAGGTCATCC 59.745 60.000 0.00 3.14 41.02 3.51
2621 10016 0.107848 CGGGGTTGTACCAGGTCATC 60.108 60.000 0.00 0.00 41.02 2.92
2622 10017 1.988015 CGGGGTTGTACCAGGTCAT 59.012 57.895 0.00 0.00 41.02 3.06
2623 10018 2.886134 GCGGGGTTGTACCAGGTCA 61.886 63.158 0.00 0.00 41.02 4.02
2624 10019 2.046604 GCGGGGTTGTACCAGGTC 60.047 66.667 0.00 0.00 41.02 3.85
2625 10020 2.406002 CTTGCGGGGTTGTACCAGGT 62.406 60.000 0.00 0.00 41.02 4.00
2626 10021 1.674322 CTTGCGGGGTTGTACCAGG 60.674 63.158 0.00 0.00 41.02 4.45
2627 10022 2.332654 GCTTGCGGGGTTGTACCAG 61.333 63.158 0.00 0.00 41.02 4.00
2628 10023 2.281900 GCTTGCGGGGTTGTACCA 60.282 61.111 0.00 0.00 41.02 3.25
2629 10024 3.060000 GGCTTGCGGGGTTGTACC 61.060 66.667 0.00 0.00 37.60 3.34
2630 10025 3.060000 GGGCTTGCGGGGTTGTAC 61.060 66.667 0.00 0.00 0.00 2.90
2631 10026 4.708386 CGGGCTTGCGGGGTTGTA 62.708 66.667 0.00 0.00 0.00 2.41
2637 10032 3.508840 CTTTAGCGGGCTTGCGGG 61.509 66.667 0.00 0.00 40.67 6.13
2638 10033 4.179579 GCTTTAGCGGGCTTGCGG 62.180 66.667 0.00 0.00 40.67 5.69
2639 10034 4.179579 GGCTTTAGCGGGCTTGCG 62.180 66.667 0.00 0.00 43.26 4.85


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

AutoCloner maintained by Alex Coulton.