Multiple sequence alignment - TraesCS3A01G150100

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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 TraesCS3A01G150100 chr3A 100.000 5915 0 0 1 5915 136533274 136527360 0.000000e+00 10924.0
1 TraesCS3A01G150100 chr3B 92.713 2086 83 27 762 2836 180884712 180882685 0.000000e+00 2946.0
2 TraesCS3A01G150100 chr3B 94.668 1069 48 6 3008 4070 180882294 180881229 0.000000e+00 1650.0
3 TraesCS3A01G150100 chr3B 94.188 757 28 9 4075 4824 180880993 180880246 0.000000e+00 1140.0
4 TraesCS3A01G150100 chr3B 92.391 552 27 8 4841 5380 754030053 754029505 0.000000e+00 773.0
5 TraesCS3A01G150100 chr3B 77.842 519 66 28 5418 5913 795063827 795063335 5.840000e-70 276.0
6 TraesCS3A01G150100 chr3B 77.649 519 67 30 5418 5913 65168498 65168006 2.720000e-68 270.0
7 TraesCS3A01G150100 chr3B 84.669 287 27 6 1 284 180885643 180885371 2.720000e-68 270.0
8 TraesCS3A01G150100 chr3D 91.882 2094 99 24 760 2833 126370811 126368769 0.000000e+00 2859.0
9 TraesCS3A01G150100 chr3D 94.143 1622 67 13 3234 4840 126366304 126364696 0.000000e+00 2444.0
10 TraesCS3A01G150100 chr3D 91.712 555 31 8 4837 5380 281597668 281598218 0.000000e+00 756.0
11 TraesCS3A01G150100 chr3D 94.855 311 15 1 2936 3245 126368474 126368164 8.910000e-133 484.0
12 TraesCS3A01G150100 chr3D 90.566 53 5 0 1 53 126384468 126384416 2.960000e-08 71.3
13 TraesCS3A01G150100 chr2A 95.212 543 20 4 4840 5380 72322537 72321999 0.000000e+00 854.0
14 TraesCS3A01G150100 chr2A 93.370 543 23 6 4840 5380 71888574 71889105 0.000000e+00 791.0
15 TraesCS3A01G150100 chr2A 92.913 508 11 5 5409 5915 22589584 22590067 0.000000e+00 715.0
16 TraesCS3A01G150100 chr2A 92.653 490 22 5 5427 5915 700237767 700237291 0.000000e+00 693.0
17 TraesCS3A01G150100 chr2A 92.128 470 20 8 5412 5880 772956025 772956478 0.000000e+00 647.0
18 TraesCS3A01G150100 chr2A 92.619 420 6 5 5497 5915 22627938 22628333 1.100000e-161 580.0
19 TraesCS3A01G150100 chr2A 88.400 250 13 7 5133 5380 515482048 515482283 2.700000e-73 287.0
20 TraesCS3A01G150100 chr2A 87.500 128 13 2 267 394 179289311 179289187 1.720000e-30 145.0
21 TraesCS3A01G150100 chr5A 96.055 507 15 3 5410 5915 383828588 383829090 0.000000e+00 821.0
22 TraesCS3A01G150100 chr5A 89.286 56 6 0 2364 2419 668269489 668269434 2.960000e-08 71.3
23 TraesCS3A01G150100 chr1A 94.716 511 15 5 5410 5915 97163671 97163168 0.000000e+00 784.0
24 TraesCS3A01G150100 chr2D 93.069 505 22 4 5412 5915 647524613 647524121 0.000000e+00 726.0
25 TraesCS3A01G150100 chr2D 89.655 551 41 9 4833 5380 166799404 166798867 0.000000e+00 688.0
26 TraesCS3A01G150100 chr2D 87.786 131 12 3 265 394 170619938 170620065 3.690000e-32 150.0
27 TraesCS3A01G150100 chr2D 81.319 91 17 0 2369 2459 28046887 28046797 2.290000e-09 75.0
28 TraesCS3A01G150100 chr7D 88.605 509 28 15 5410 5915 11127653 11127172 5.100000e-165 592.0
29 TraesCS3A01G150100 chr7D 90.426 94 9 0 4840 4933 136704336 136704243 2.240000e-24 124.0
30 TraesCS3A01G150100 chr4B 94.717 265 13 1 5652 5915 223386473 223386737 1.530000e-110 411.0
31 TraesCS3A01G150100 chr7A 94.839 155 8 0 5226 5380 227089512 227089666 5.920000e-60 243.0
32 TraesCS3A01G150100 chr2B 85.606 132 18 1 271 402 773748406 773748276 2.870000e-28 137.0
33 TraesCS3A01G150100 chr2B 100.000 28 0 0 2561 2588 200579612 200579639 1.100000e-02 52.8
34 TraesCS3A01G150100 chr6B 86.777 121 14 2 277 396 570743330 570743211 3.720000e-27 134.0
35 TraesCS3A01G150100 chr6B 86.777 121 14 2 277 396 650877515 650877634 3.720000e-27 134.0
36 TraesCS3A01G150100 chr1B 86.066 122 15 2 276 396 581833513 581833393 4.810000e-26 130.0
37 TraesCS3A01G150100 chr1B 86.111 108 13 1 5410 5517 66929736 66929631 1.350000e-21 115.0
38 TraesCS3A01G150100 chr1B 85.000 120 10 6 5410 5525 289306087 289305972 1.350000e-21 115.0
39 TraesCS3A01G150100 chr7B 86.555 119 13 3 277 394 89706052 89705936 1.730000e-25 128.0
40 TraesCS3A01G150100 chr5D 85.950 121 15 2 277 396 112793084 112793203 1.730000e-25 128.0
41 TraesCS3A01G150100 chr1D 85.950 121 16 1 277 397 222871280 222871161 1.730000e-25 128.0
42 TraesCS3A01G150100 chr5B 83.333 78 13 0 2366 2443 339930261 339930184 8.220000e-09 73.1


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 TraesCS3A01G150100 chr3A 136527360 136533274 5914 True 10924.0 10924 100.000000 1 5915 1 chr3A.!!$R1 5914
1 TraesCS3A01G150100 chr3B 180880246 180885643 5397 True 1501.5 2946 91.559500 1 4824 4 chr3B.!!$R4 4823
2 TraesCS3A01G150100 chr3B 754029505 754030053 548 True 773.0 773 92.391000 4841 5380 1 chr3B.!!$R2 539
3 TraesCS3A01G150100 chr3D 126364696 126370811 6115 True 1929.0 2859 93.626667 760 4840 3 chr3D.!!$R2 4080
4 TraesCS3A01G150100 chr3D 281597668 281598218 550 False 756.0 756 91.712000 4837 5380 1 chr3D.!!$F1 543
5 TraesCS3A01G150100 chr2A 72321999 72322537 538 True 854.0 854 95.212000 4840 5380 1 chr2A.!!$R1 540
6 TraesCS3A01G150100 chr2A 71888574 71889105 531 False 791.0 791 93.370000 4840 5380 1 chr2A.!!$F3 540
7 TraesCS3A01G150100 chr5A 383828588 383829090 502 False 821.0 821 96.055000 5410 5915 1 chr5A.!!$F1 505
8 TraesCS3A01G150100 chr1A 97163168 97163671 503 True 784.0 784 94.716000 5410 5915 1 chr1A.!!$R1 505
9 TraesCS3A01G150100 chr2D 166798867 166799404 537 True 688.0 688 89.655000 4833 5380 1 chr2D.!!$R2 547

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
71 72 1.180456 TGCCAAACATGCTGTGAGGG 61.180 55.000 0.00 0.0 0.0 4.30 F
984 1248 2.108952 ACAGCCCTTTGTTCTCTTCCAT 59.891 45.455 0.00 0.0 0.0 3.41 F
1614 1886 0.339859 ATCAGCTGGTCAGGAGGGTA 59.660 55.000 15.13 0.0 0.0 3.69 F
2845 3120 0.109723 CCTTTTTCGGGTGGGTGAGA 59.890 55.000 0.00 0.0 0.0 3.27 F
3308 5675 0.389426 GTTCAAGGAGAGCGGCGTTA 60.389 55.000 9.37 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1095 1367 0.695347 CTGCCTCCCAACCTTCTTCT 59.305 55.0 0.00 0.0 0.00 2.85 R
2362 2635 1.162181 GGCCTAATAAACCCGGACGC 61.162 60.0 0.73 0.0 0.00 5.19 R
3308 5675 0.035056 CTCCGGCCTTGAAGGACATT 60.035 55.0 18.75 0.0 46.60 2.71 R
3989 6359 0.618458 CAGTAGGTTGGCCTGGCTAA 59.382 55.0 19.68 16.8 46.47 3.09 R
4960 7573 0.629058 GGTTTCCTCCCCCTATTGCA 59.371 55.0 0.00 0.0 0.00 4.08 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
36 37 9.479549 TCTATTTTCCAAAGCCTAAATCTCATT 57.520 29.630 0.00 0.00 0.00 2.57
39 40 4.536765 TCCAAAGCCTAAATCTCATTCCC 58.463 43.478 0.00 0.00 0.00 3.97
40 41 4.230502 TCCAAAGCCTAAATCTCATTCCCT 59.769 41.667 0.00 0.00 0.00 4.20
41 42 4.340381 CCAAAGCCTAAATCTCATTCCCTG 59.660 45.833 0.00 0.00 0.00 4.45
43 44 4.870021 AGCCTAAATCTCATTCCCTGTT 57.130 40.909 0.00 0.00 0.00 3.16
61 62 1.615392 GTTTCTCAGGCTGCCAAACAT 59.385 47.619 22.65 0.00 0.00 2.71
63 64 1.214589 CTCAGGCTGCCAAACATGC 59.785 57.895 22.65 0.00 0.00 4.06
66 67 1.532316 AGGCTGCCAAACATGCTGT 60.532 52.632 22.65 0.00 0.00 4.40
67 68 1.373748 GGCTGCCAAACATGCTGTG 60.374 57.895 15.17 0.00 0.00 3.66
71 72 1.180456 TGCCAAACATGCTGTGAGGG 61.180 55.000 0.00 0.00 0.00 4.30
78 79 2.880443 ACATGCTGTGAGGGAATGTTT 58.120 42.857 0.00 0.00 29.32 2.83
80 81 3.256631 ACATGCTGTGAGGGAATGTTTTC 59.743 43.478 0.00 0.00 29.32 2.29
171 174 9.850198 TTTCTTTCTTGATTTTCCAATTTCCAT 57.150 25.926 0.00 0.00 0.00 3.41
177 180 9.624373 TCTTGATTTTCCAATTTCCATTTTTGA 57.376 25.926 0.00 0.00 0.00 2.69
180 183 7.447853 TGATTTTCCAATTTCCATTTTTGAGGG 59.552 33.333 0.00 0.00 0.00 4.30
181 184 4.906747 TCCAATTTCCATTTTTGAGGGG 57.093 40.909 0.00 0.00 0.00 4.79
182 185 3.586618 TCCAATTTCCATTTTTGAGGGGG 59.413 43.478 0.00 0.00 0.00 5.40
183 186 3.330405 CCAATTTCCATTTTTGAGGGGGT 59.670 43.478 0.00 0.00 0.00 4.95
184 187 4.202556 CCAATTTCCATTTTTGAGGGGGTT 60.203 41.667 0.00 0.00 0.00 4.11
185 188 5.384336 CAATTTCCATTTTTGAGGGGGTTT 58.616 37.500 0.00 0.00 0.00 3.27
186 189 4.698201 TTTCCATTTTTGAGGGGGTTTC 57.302 40.909 0.00 0.00 0.00 2.78
187 190 3.628832 TCCATTTTTGAGGGGGTTTCT 57.371 42.857 0.00 0.00 0.00 2.52
188 191 3.506398 TCCATTTTTGAGGGGGTTTCTC 58.494 45.455 0.00 0.00 0.00 2.87
189 192 3.142028 TCCATTTTTGAGGGGGTTTCTCT 59.858 43.478 0.00 0.00 32.78 3.10
190 193 3.903714 CCATTTTTGAGGGGGTTTCTCTT 59.096 43.478 0.00 0.00 32.78 2.85
191 194 4.347876 CCATTTTTGAGGGGGTTTCTCTTT 59.652 41.667 0.00 0.00 32.78 2.52
284 287 7.416213 CGATTTCTATTACCTGCATCCCAAAAA 60.416 37.037 0.00 0.00 0.00 1.94
286 289 6.959639 TCTATTACCTGCATCCCAAAAATC 57.040 37.500 0.00 0.00 0.00 2.17
289 292 3.967332 ACCTGCATCCCAAAAATCTTG 57.033 42.857 0.00 0.00 0.00 3.02
290 293 2.568509 ACCTGCATCCCAAAAATCTTGG 59.431 45.455 0.00 0.00 39.25 3.61
295 298 4.081531 TGCATCCCAAAAATCTTGGCTTAG 60.082 41.667 0.00 0.00 38.23 2.18
296 299 4.160252 GCATCCCAAAAATCTTGGCTTAGA 59.840 41.667 0.00 0.00 38.23 2.10
297 300 5.163374 GCATCCCAAAAATCTTGGCTTAGAT 60.163 40.000 0.00 0.00 38.23 1.98
298 301 6.631088 GCATCCCAAAAATCTTGGCTTAGATT 60.631 38.462 8.87 8.87 44.62 2.40
311 314 9.823647 TCTTGGCTTAGATTTTTCTAGATACAG 57.176 33.333 0.00 0.00 0.00 2.74
312 315 9.823647 CTTGGCTTAGATTTTTCTAGATACAGA 57.176 33.333 0.00 0.00 0.00 3.41
314 317 9.770097 TGGCTTAGATTTTTCTAGATACAGATG 57.230 33.333 0.00 0.00 0.00 2.90
315 318 9.771534 GGCTTAGATTTTTCTAGATACAGATGT 57.228 33.333 0.00 0.00 0.00 3.06
436 439 7.485418 TTTCTTCAATGCGTGAGTACTTTTA 57.515 32.000 0.00 0.00 37.61 1.52
437 440 7.667043 TTCTTCAATGCGTGAGTACTTTTAT 57.333 32.000 0.00 0.00 37.61 1.40
912 1170 2.391821 CGTGCTTAACGCTCGCAG 59.608 61.111 7.90 0.00 46.99 5.18
984 1248 2.108952 ACAGCCCTTTGTTCTCTTCCAT 59.891 45.455 0.00 0.00 0.00 3.41
1095 1367 1.676968 CAACGATGGTGAGGGTGGA 59.323 57.895 0.00 0.00 0.00 4.02
1096 1368 0.391661 CAACGATGGTGAGGGTGGAG 60.392 60.000 0.00 0.00 0.00 3.86
1097 1369 0.544357 AACGATGGTGAGGGTGGAGA 60.544 55.000 0.00 0.00 0.00 3.71
1104 1376 1.353091 GTGAGGGTGGAGAAGAAGGT 58.647 55.000 0.00 0.00 0.00 3.50
1113 1385 0.693049 GAGAAGAAGGTTGGGAGGCA 59.307 55.000 0.00 0.00 0.00 4.75
1347 1619 1.194772 GGTTCGTTTGCTTTCTCTCCG 59.805 52.381 0.00 0.00 0.00 4.63
1455 1727 4.757149 GCAAGTTCTGGTCAGTTTCTACAT 59.243 41.667 0.00 0.00 0.00 2.29
1614 1886 0.339859 ATCAGCTGGTCAGGAGGGTA 59.660 55.000 15.13 0.00 0.00 3.69
1711 1983 1.616374 TCCCTTTTTCGGGCAATGTTC 59.384 47.619 0.00 0.00 44.30 3.18
1854 2126 9.444600 ACTAAATTCAATAGCTTCTTTTACGGA 57.555 29.630 0.00 0.00 0.00 4.69
1903 2175 2.096248 ACTTGACGCAAAGTGGGAAAA 58.904 42.857 2.74 0.00 38.95 2.29
1906 2178 2.028130 TGACGCAAAGTGGGAAAACAT 58.972 42.857 0.00 0.00 34.12 2.71
1935 2207 1.195115 CGATCAGGAAGGAAGACCCA 58.805 55.000 0.00 0.00 37.41 4.51
2091 2363 5.220381 GTCTCGAAGTTTGACTGTGATACA 58.780 41.667 0.00 0.00 0.00 2.29
2189 2461 9.331282 AGTCTACTTATTGATTTGCAATCTACC 57.669 33.333 0.00 0.00 43.64 3.18
2190 2462 9.109393 GTCTACTTATTGATTTGCAATCTACCA 57.891 33.333 0.00 0.00 43.64 3.25
2201 2473 5.402997 TGCAATCTACCAAATTTGCATGA 57.597 34.783 12.92 9.62 46.76 3.07
2203 2475 5.638657 TGCAATCTACCAAATTTGCATGAAC 59.361 36.000 12.92 5.17 46.76 3.18
2204 2476 5.870978 GCAATCTACCAAATTTGCATGAACT 59.129 36.000 12.92 0.28 43.00 3.01
2205 2477 6.035327 GCAATCTACCAAATTTGCATGAACTC 59.965 38.462 12.92 0.00 43.00 3.01
2206 2478 7.318141 CAATCTACCAAATTTGCATGAACTCT 58.682 34.615 12.92 0.00 0.00 3.24
2208 2480 7.994425 TCTACCAAATTTGCATGAACTCTTA 57.006 32.000 12.92 0.00 0.00 2.10
2209 2481 8.579850 TCTACCAAATTTGCATGAACTCTTAT 57.420 30.769 12.92 0.00 0.00 1.73
2251 2524 7.038659 CCTATGTAGATTGCATAGACCTAAGC 58.961 42.308 13.51 0.00 45.10 3.09
2269 2542 0.811281 GCCCTACACATTCCAACAGC 59.189 55.000 0.00 0.00 0.00 4.40
2295 2568 5.392703 GCTATTGTAGGGCAGTTTTACAACC 60.393 44.000 0.00 0.00 39.34 3.77
2304 2577 6.042666 AGGGCAGTTTTACAACCAATGTATTT 59.957 34.615 0.00 0.00 43.84 1.40
2307 2580 7.116233 GGCAGTTTTACAACCAATGTATTTCAG 59.884 37.037 0.00 0.00 43.84 3.02
2326 2599 2.101582 CAGATGACTAGTACTGGTGCCC 59.898 54.545 17.50 3.11 0.00 5.36
2337 2610 0.392998 CTGGTGCCCTCACACATACC 60.393 60.000 0.00 0.00 44.87 2.73
2419 2692 5.070313 AGCCAAAGTTTGACCATACATTTGT 59.930 36.000 17.33 0.00 0.00 2.83
2590 2865 1.357079 ACCCTGACGGAGGTAGTAGTT 59.643 52.381 2.39 0.00 40.87 2.24
2605 2880 6.071278 AGGTAGTAGTTGTCAAGGTCTTCATC 60.071 42.308 0.00 0.00 0.00 2.92
2634 2909 7.879160 TGTTAGGGGTTGTTACTGTAGTTATTG 59.121 37.037 0.00 0.00 0.00 1.90
2661 2936 5.574082 TGACAATTTGTTCCACTGTTTACG 58.426 37.500 3.08 0.00 0.00 3.18
2663 2938 5.336744 ACAATTTGTTCCACTGTTTACGTG 58.663 37.500 0.00 0.00 0.00 4.49
2674 2949 6.874664 TCCACTGTTTACGTGAATGCTAATTA 59.125 34.615 0.00 0.00 34.35 1.40
2677 2952 8.837059 CACTGTTTACGTGAATGCTAATTAAAC 58.163 33.333 0.00 0.00 34.35 2.01
2703 2978 8.220434 CCATTAAATTTTTCTAGTTGCCAAACG 58.780 33.333 0.00 0.00 41.45 3.60
2710 2985 3.734463 TCTAGTTGCCAAACGTGATCAA 58.266 40.909 0.00 0.00 41.45 2.57
2712 2987 1.336755 AGTTGCCAAACGTGATCAACC 59.663 47.619 15.12 0.00 41.45 3.77
2719 2994 4.083003 GCCAAACGTGATCAACCTATTTCA 60.083 41.667 0.00 0.00 0.00 2.69
2743 3018 8.742777 TCAAGAAAATAATGAACCTTGGAGATG 58.257 33.333 0.00 0.00 33.75 2.90
2748 3023 8.599624 AAATAATGAACCTTGGAGATGTGATT 57.400 30.769 0.00 0.00 0.00 2.57
2771 3046 0.602638 TGTAACGCCACAGCTCCTTG 60.603 55.000 0.00 0.00 36.60 3.61
2808 3083 2.682856 ACAAGTCGCACAAAATCACACT 59.317 40.909 0.00 0.00 0.00 3.55
2812 3087 2.031560 GTCGCACAAAATCACACTGTCA 59.968 45.455 0.00 0.00 0.00 3.58
2823 3098 1.059098 ACACTGTCAGGCTGAATCCA 58.941 50.000 20.62 12.34 0.00 3.41
2836 3111 3.066760 GCTGAATCCATACCTTTTTCGGG 59.933 47.826 0.00 0.00 0.00 5.14
2837 3112 4.270008 CTGAATCCATACCTTTTTCGGGT 58.730 43.478 0.00 0.00 40.53 5.28
2838 3113 4.013728 TGAATCCATACCTTTTTCGGGTG 58.986 43.478 0.00 0.00 37.65 4.61
2839 3114 2.500392 TCCATACCTTTTTCGGGTGG 57.500 50.000 0.00 0.00 37.65 4.61
2840 3115 1.004979 TCCATACCTTTTTCGGGTGGG 59.995 52.381 0.00 0.00 37.65 4.61
2841 3116 1.272258 CCATACCTTTTTCGGGTGGGT 60.272 52.381 0.00 0.00 37.65 4.51
2842 3117 1.816224 CATACCTTTTTCGGGTGGGTG 59.184 52.381 0.00 0.00 37.65 4.61
2843 3118 1.138568 TACCTTTTTCGGGTGGGTGA 58.861 50.000 0.00 0.00 37.65 4.02
2844 3119 0.179001 ACCTTTTTCGGGTGGGTGAG 60.179 55.000 0.00 0.00 35.51 3.51
2845 3120 0.109723 CCTTTTTCGGGTGGGTGAGA 59.890 55.000 0.00 0.00 0.00 3.27
2846 3121 1.523758 CTTTTTCGGGTGGGTGAGAG 58.476 55.000 0.00 0.00 0.00 3.20
2847 3122 0.109723 TTTTTCGGGTGGGTGAGAGG 59.890 55.000 0.00 0.00 0.00 3.69
2848 3123 1.774894 TTTTCGGGTGGGTGAGAGGG 61.775 60.000 0.00 0.00 0.00 4.30
2849 3124 4.715130 TCGGGTGGGTGAGAGGGG 62.715 72.222 0.00 0.00 0.00 4.79
2851 3126 3.330720 GGGTGGGTGAGAGGGGTG 61.331 72.222 0.00 0.00 0.00 4.61
2852 3127 3.330720 GGTGGGTGAGAGGGGTGG 61.331 72.222 0.00 0.00 0.00 4.61
2853 3128 2.529389 GTGGGTGAGAGGGGTGGT 60.529 66.667 0.00 0.00 0.00 4.16
2854 3129 2.529136 TGGGTGAGAGGGGTGGTG 60.529 66.667 0.00 0.00 0.00 4.17
2855 3130 3.330720 GGGTGAGAGGGGTGGTGG 61.331 72.222 0.00 0.00 0.00 4.61
2856 3131 3.330720 GGTGAGAGGGGTGGTGGG 61.331 72.222 0.00 0.00 0.00 4.61
2857 3132 3.330720 GTGAGAGGGGTGGTGGGG 61.331 72.222 0.00 0.00 0.00 4.96
2858 3133 4.675303 TGAGAGGGGTGGTGGGGG 62.675 72.222 0.00 0.00 0.00 5.40
2859 3134 4.677151 GAGAGGGGTGGTGGGGGT 62.677 72.222 0.00 0.00 0.00 4.95
2879 3154 1.377612 GGGGGTGTTAGGTGTGTCC 59.622 63.158 0.00 0.00 0.00 4.02
2881 3156 0.769247 GGGGTGTTAGGTGTGTCCTT 59.231 55.000 0.00 0.00 45.67 3.36
2882 3157 1.271217 GGGGTGTTAGGTGTGTCCTTC 60.271 57.143 0.00 0.00 45.67 3.46
2883 3158 1.697982 GGGTGTTAGGTGTGTCCTTCT 59.302 52.381 0.00 0.00 45.67 2.85
2884 3159 2.105993 GGGTGTTAGGTGTGTCCTTCTT 59.894 50.000 0.00 0.00 45.67 2.52
2885 3160 3.325716 GGGTGTTAGGTGTGTCCTTCTTA 59.674 47.826 0.00 0.00 45.67 2.10
2886 3161 4.019591 GGGTGTTAGGTGTGTCCTTCTTAT 60.020 45.833 0.00 0.00 45.67 1.73
2887 3162 5.514310 GGGTGTTAGGTGTGTCCTTCTTATT 60.514 44.000 0.00 0.00 45.67 1.40
2888 3163 6.296030 GGGTGTTAGGTGTGTCCTTCTTATTA 60.296 42.308 0.00 0.00 45.67 0.98
2889 3164 6.592994 GGTGTTAGGTGTGTCCTTCTTATTAC 59.407 42.308 0.00 0.00 45.67 1.89
2890 3165 6.309737 GTGTTAGGTGTGTCCTTCTTATTACG 59.690 42.308 0.00 0.00 45.67 3.18
2891 3166 6.209192 TGTTAGGTGTGTCCTTCTTATTACGA 59.791 38.462 0.00 0.00 45.67 3.43
2892 3167 5.934402 AGGTGTGTCCTTCTTATTACGAT 57.066 39.130 0.00 0.00 45.67 3.73
2893 3168 6.295719 AGGTGTGTCCTTCTTATTACGATT 57.704 37.500 0.00 0.00 45.67 3.34
2894 3169 6.708285 AGGTGTGTCCTTCTTATTACGATTT 58.292 36.000 0.00 0.00 45.67 2.17
2895 3170 6.817140 AGGTGTGTCCTTCTTATTACGATTTC 59.183 38.462 0.00 0.00 45.67 2.17
2896 3171 6.036844 GGTGTGTCCTTCTTATTACGATTTCC 59.963 42.308 0.00 0.00 0.00 3.13
2897 3172 6.592607 GTGTGTCCTTCTTATTACGATTTCCA 59.407 38.462 0.00 0.00 0.00 3.53
2898 3173 7.280205 GTGTGTCCTTCTTATTACGATTTCCAT 59.720 37.037 0.00 0.00 0.00 3.41
2899 3174 7.494625 TGTGTCCTTCTTATTACGATTTCCATC 59.505 37.037 0.00 0.00 0.00 3.51
2900 3175 7.494625 GTGTCCTTCTTATTACGATTTCCATCA 59.505 37.037 0.00 0.00 0.00 3.07
2901 3176 8.044309 TGTCCTTCTTATTACGATTTCCATCAA 58.956 33.333 0.00 0.00 0.00 2.57
2902 3177 9.057089 GTCCTTCTTATTACGATTTCCATCAAT 57.943 33.333 0.00 0.00 0.00 2.57
2910 3185 8.964476 ATTACGATTTCCATCAATACTCAAGT 57.036 30.769 0.00 0.00 0.00 3.16
2911 3186 8.786826 TTACGATTTCCATCAATACTCAAGTT 57.213 30.769 0.00 0.00 0.00 2.66
2912 3187 7.687941 ACGATTTCCATCAATACTCAAGTTT 57.312 32.000 0.00 0.00 0.00 2.66
2913 3188 7.752695 ACGATTTCCATCAATACTCAAGTTTC 58.247 34.615 0.00 0.00 0.00 2.78
2914 3189 7.390440 ACGATTTCCATCAATACTCAAGTTTCA 59.610 33.333 0.00 0.00 0.00 2.69
2915 3190 7.907045 CGATTTCCATCAATACTCAAGTTTCAG 59.093 37.037 0.00 0.00 0.00 3.02
2916 3191 8.868522 ATTTCCATCAATACTCAAGTTTCAGA 57.131 30.769 0.00 0.00 0.00 3.27
2917 3192 8.868522 TTTCCATCAATACTCAAGTTTCAGAT 57.131 30.769 0.00 0.00 0.00 2.90
2918 3193 7.854557 TCCATCAATACTCAAGTTTCAGATG 57.145 36.000 0.00 0.00 0.00 2.90
2919 3194 7.397221 TCCATCAATACTCAAGTTTCAGATGT 58.603 34.615 0.00 0.00 31.04 3.06
2920 3195 7.550551 TCCATCAATACTCAAGTTTCAGATGTC 59.449 37.037 0.00 0.00 31.04 3.06
2921 3196 7.551974 CCATCAATACTCAAGTTTCAGATGTCT 59.448 37.037 0.00 0.00 31.04 3.41
2922 3197 7.895975 TCAATACTCAAGTTTCAGATGTCTG 57.104 36.000 3.61 3.61 45.08 3.51
2962 3429 8.491152 GTCGAATACACAATATCCAATTCTCTG 58.509 37.037 0.00 0.00 0.00 3.35
2967 3434 6.715280 ACACAATATCCAATTCTCTGTCACT 58.285 36.000 0.00 0.00 0.00 3.41
2981 3448 3.570975 TCTGTCACTTGCTGCATCATTTT 59.429 39.130 1.84 0.00 0.00 1.82
3032 3526 9.472361 TTTGTAACTTAAGAGATGAGTGTGTAC 57.528 33.333 10.09 0.00 0.00 2.90
3308 5675 0.389426 GTTCAAGGAGAGCGGCGTTA 60.389 55.000 9.37 0.00 0.00 3.18
3338 5705 2.430367 GCCGGAGACAAACAGGGT 59.570 61.111 5.05 0.00 0.00 4.34
3371 5738 8.612619 CGTTATGTGAGGCAGTCTAAATTATTT 58.387 33.333 0.00 0.00 0.00 1.40
3393 5760 4.572985 TCAGAAAGCAGGAACAAATGTG 57.427 40.909 0.00 0.00 0.00 3.21
3623 5990 3.881089 TGAAGGAGCATAATGTCAGCATG 59.119 43.478 0.00 0.00 35.15 4.06
3687 6054 6.369890 TGTTGCAGCACAAAGAAAAATTAACA 59.630 30.769 0.00 0.00 40.82 2.41
3688 6055 6.343226 TGCAGCACAAAGAAAAATTAACAC 57.657 33.333 0.00 0.00 0.00 3.32
3777 6147 9.220767 ACATGAGATAGTTTCTTTTTCCTGTAC 57.779 33.333 0.00 0.00 33.74 2.90
3793 6163 4.034858 TCCTGTACGTGCTCTCTTTATACG 59.965 45.833 4.97 0.00 40.30 3.06
3818 6188 7.226720 CGTAGGGAGAAGTAATATGCAATTTGT 59.773 37.037 0.00 0.00 0.00 2.83
3847 6217 6.176183 AGTTCAGTTATATGCAAAGCTCTGT 58.824 36.000 0.00 0.00 0.00 3.41
3854 6224 7.810282 AGTTATATGCAAAGCTCTGTATAGTCG 59.190 37.037 4.15 0.00 29.06 4.18
3877 6247 6.657541 TCGTAAGTTTGAGATTTTATGGGCTT 59.342 34.615 0.00 0.00 39.48 4.35
3887 6257 6.365520 AGATTTTATGGGCTTATTCTTCCGT 58.634 36.000 0.00 0.00 0.00 4.69
3912 6282 6.539173 TGTCAACCAACCTGAAATATAGTGT 58.461 36.000 0.00 0.00 0.00 3.55
3929 6299 8.972262 ATATAGTGTAAGTCTTGCACATATCG 57.028 34.615 28.47 0.00 46.85 2.92
3943 6313 4.601019 CACATATCGGAACATTCAAAGCC 58.399 43.478 0.00 0.00 0.00 4.35
3983 6353 2.324541 TCCAACCCAAGTTCCCAAATG 58.675 47.619 0.00 0.00 32.45 2.32
3988 6358 4.193240 ACCCAAGTTCCCAAATGTAACT 57.807 40.909 0.00 0.00 35.01 2.24
3989 6359 4.552674 ACCCAAGTTCCCAAATGTAACTT 58.447 39.130 0.00 0.00 36.33 2.66
4041 6414 0.984230 TTTTGCACCAAACCCAACCA 59.016 45.000 0.00 0.00 32.79 3.67
4052 6425 0.251341 ACCCAACCAGTCTGAATGGC 60.251 55.000 22.91 0.00 41.87 4.40
4104 6708 4.497473 TTTGGTTTGATCATCCGTTGAC 57.503 40.909 0.00 0.00 37.11 3.18
4140 6744 3.290710 AGTTCCATGTGCAGTCAGTTTT 58.709 40.909 0.00 0.00 0.00 2.43
4147 6751 6.070824 TCCATGTGCAGTCAGTTTTAGAGATA 60.071 38.462 0.00 0.00 0.00 1.98
4175 6779 6.604171 TGGATATGCATTATTTCTCACTGGT 58.396 36.000 3.54 0.00 0.00 4.00
4184 6788 9.455847 GCATTATTTCTCACTGGTATTCATTTC 57.544 33.333 0.00 0.00 0.00 2.17
4233 6837 5.645067 TGTACTTACTAGTCAGCGTGTACAT 59.355 40.000 0.00 0.00 35.58 2.29
4254 6858 9.601217 GTACATCACTGTCCTAATCTTGTTTAT 57.399 33.333 0.00 0.00 36.79 1.40
4263 6867 9.290988 TGTCCTAATCTTGTTTATGCTGTAAAA 57.709 29.630 0.00 0.00 0.00 1.52
4296 6902 8.938801 TTCCATGGTAAAATCATGCATATAGT 57.061 30.769 12.58 0.00 40.29 2.12
4297 6903 8.938801 TCCATGGTAAAATCATGCATATAGTT 57.061 30.769 12.58 0.00 40.29 2.24
4405 7016 0.955905 GGGCAACGGAAGCAACTTTA 59.044 50.000 0.00 0.00 37.60 1.85
4408 7019 3.554129 GGGCAACGGAAGCAACTTTATTT 60.554 43.478 0.00 0.00 37.60 1.40
4562 7175 2.859165 ACCTCGAAGCAGAATTGGAA 57.141 45.000 0.00 0.00 0.00 3.53
4757 7370 4.667573 TGGTATGTTTTGGCCTATCAACA 58.332 39.130 3.32 5.54 33.78 3.33
5281 7902 6.308015 TCTACCACCAAGCAAATGTACTAT 57.692 37.500 0.00 0.00 0.00 2.12
5303 7942 2.728922 GTATACAAAGACTCGGCTCCG 58.271 52.381 1.14 1.14 41.35 4.63
5397 8036 9.733556 ATTCATTATCTCTATCTGTACGTCTCT 57.266 33.333 0.00 0.00 0.00 3.10
5399 8038 9.642327 TCATTATCTCTATCTGTACGTCTCTAC 57.358 37.037 0.00 0.00 0.00 2.59
5477 8121 3.666797 CGACGTTTTTGCATAAAAGTCCC 59.333 43.478 28.49 15.37 40.84 4.46
5498 8142 6.257849 GTCCCTTTGTTTTTCAGAATTCAACC 59.742 38.462 8.44 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 1.000938 GTTTGGCAGCCTGAGAAACAG 60.001 52.381 14.15 0.00 45.36 3.16
40 41 1.032014 GTTTGGCAGCCTGAGAAACA 58.968 50.000 14.15 0.00 0.00 2.83
41 42 1.032014 TGTTTGGCAGCCTGAGAAAC 58.968 50.000 14.15 14.82 0.00 2.78
43 44 1.250328 CATGTTTGGCAGCCTGAGAA 58.750 50.000 14.15 0.00 0.00 2.87
61 62 2.238521 GGAAAACATTCCCTCACAGCA 58.761 47.619 0.00 0.00 35.06 4.41
63 64 2.484264 GACGGAAAACATTCCCTCACAG 59.516 50.000 2.19 0.00 37.84 3.66
66 67 3.146066 CAAGACGGAAAACATTCCCTCA 58.854 45.455 2.19 0.00 37.84 3.86
67 68 3.146847 ACAAGACGGAAAACATTCCCTC 58.853 45.455 2.19 1.07 37.84 4.30
71 72 9.887406 TTAATTAAGACAAGACGGAAAACATTC 57.113 29.630 0.00 0.00 0.00 2.67
78 79 8.092068 TGAGTGATTAATTAAGACAAGACGGAA 58.908 33.333 3.94 0.00 0.00 4.30
80 81 7.545965 AGTGAGTGATTAATTAAGACAAGACGG 59.454 37.037 3.94 0.00 0.00 4.79
161 164 3.330405 ACCCCCTCAAAAATGGAAATTGG 59.670 43.478 0.00 0.00 0.00 3.16
169 172 5.551305 AAAGAGAAACCCCCTCAAAAATG 57.449 39.130 0.00 0.00 33.25 2.32
171 174 5.277250 AGAAAAGAGAAACCCCCTCAAAAA 58.723 37.500 0.00 0.00 33.25 1.94
177 180 3.467483 AGGAAAGAAAAGAGAAACCCCCT 59.533 43.478 0.00 0.00 0.00 4.79
258 261 4.641396 TGGGATGCAGGTAATAGAAATCG 58.359 43.478 0.00 0.00 0.00 3.34
259 262 6.959639 TTTGGGATGCAGGTAATAGAAATC 57.040 37.500 0.00 0.00 0.00 2.17
273 276 3.339253 AAGCCAAGATTTTTGGGATGC 57.661 42.857 7.97 0.00 39.90 3.91
286 289 9.823647 TCTGTATCTAGAAAAATCTAAGCCAAG 57.176 33.333 0.00 0.00 0.00 3.61
289 292 9.771534 ACATCTGTATCTAGAAAAATCTAAGCC 57.228 33.333 0.00 0.00 0.00 4.35
308 311 8.922676 CACGTTTTAGTGTTTAGATACATCTGT 58.077 33.333 1.88 0.00 36.26 3.41
323 326 8.697846 TGGATTTATCTAGACACGTTTTAGTG 57.302 34.615 0.00 0.00 46.83 2.74
370 373 4.067944 ACTCCCTCTGTCCTGAATTACT 57.932 45.455 0.00 0.00 0.00 2.24
378 381 7.698163 ATTAATGAAATACTCCCTCTGTCCT 57.302 36.000 0.00 0.00 0.00 3.85
822 1080 9.685276 ACCATACATTGTTTCTTGATTATCTGA 57.315 29.630 0.00 0.00 0.00 3.27
827 1085 6.127479 GCCCACCATACATTGTTTCTTGATTA 60.127 38.462 0.00 0.00 0.00 1.75
830 1088 3.509575 GCCCACCATACATTGTTTCTTGA 59.490 43.478 0.00 0.00 0.00 3.02
840 1098 2.124320 GTGCGGCCCACCATACAT 60.124 61.111 12.03 0.00 38.55 2.29
912 1170 1.212616 CTGTGCTATACGCTGCTTCC 58.787 55.000 0.00 0.00 40.11 3.46
984 1248 2.616842 GGGAACGAACTGCAAAAGAGAA 59.383 45.455 0.00 0.00 0.00 2.87
1086 1358 1.699634 CAACCTTCTTCTCCACCCTCA 59.300 52.381 0.00 0.00 0.00 3.86
1092 1364 1.362224 CCTCCCAACCTTCTTCTCCA 58.638 55.000 0.00 0.00 0.00 3.86
1095 1367 0.695347 CTGCCTCCCAACCTTCTTCT 59.305 55.000 0.00 0.00 0.00 2.85
1096 1368 0.962855 GCTGCCTCCCAACCTTCTTC 60.963 60.000 0.00 0.00 0.00 2.87
1097 1369 1.075659 GCTGCCTCCCAACCTTCTT 59.924 57.895 0.00 0.00 0.00 2.52
1347 1619 2.202756 GTCGCCGTCATGGTCTCC 60.203 66.667 0.00 0.00 41.21 3.71
1711 1983 9.371136 TCAAATCAGCATACTAACACTCTTAAG 57.629 33.333 0.00 0.00 0.00 1.85
1854 2126 2.507944 GCATGAGCATCCTCCCGT 59.492 61.111 0.00 0.00 41.58 5.28
1878 2150 2.286772 CCCACTTTGCGTCAAGTAACAC 60.287 50.000 1.60 0.00 0.00 3.32
1894 2166 3.763897 GCAAGATACCATGTTTTCCCACT 59.236 43.478 0.00 0.00 0.00 4.00
2091 2363 7.224297 TCTCTTCTTGCCAAACTAAGTGTAAT 58.776 34.615 0.00 0.00 0.00 1.89
2182 2454 7.472334 AGAGTTCATGCAAATTTGGTAGATT 57.528 32.000 19.47 0.00 0.00 2.40
2189 2461 7.878477 ACACATAAGAGTTCATGCAAATTTG 57.122 32.000 14.03 14.03 0.00 2.32
2190 2462 7.927629 ACAACACATAAGAGTTCATGCAAATTT 59.072 29.630 0.00 0.00 0.00 1.82
2201 2473 6.827727 AGTTCTACCACAACACATAAGAGTT 58.172 36.000 0.00 0.00 0.00 3.01
2203 2475 5.869888 GGAGTTCTACCACAACACATAAGAG 59.130 44.000 0.00 0.00 0.00 2.85
2204 2476 5.542635 AGGAGTTCTACCACAACACATAAGA 59.457 40.000 0.00 0.00 0.00 2.10
2205 2477 5.794894 AGGAGTTCTACCACAACACATAAG 58.205 41.667 0.00 0.00 0.00 1.73
2206 2478 5.818678 AGGAGTTCTACCACAACACATAA 57.181 39.130 0.00 0.00 0.00 1.90
2208 2480 5.248477 ACATAGGAGTTCTACCACAACACAT 59.752 40.000 0.00 0.00 0.00 3.21
2209 2481 4.591498 ACATAGGAGTTCTACCACAACACA 59.409 41.667 0.00 0.00 0.00 3.72
2251 2524 2.086869 CAGCTGTTGGAATGTGTAGGG 58.913 52.381 5.25 0.00 0.00 3.53
2295 2568 9.254133 CCAGTACTAGTCATCTGAAATACATTG 57.746 37.037 18.16 0.00 0.00 2.82
2304 2577 3.024547 GGCACCAGTACTAGTCATCTGA 58.975 50.000 18.16 0.00 0.00 3.27
2359 2632 1.814211 CTAATAAACCCGGACGCGCG 61.814 60.000 30.96 30.96 0.00 6.86
2360 2633 1.493134 CCTAATAAACCCGGACGCGC 61.493 60.000 5.73 0.00 0.00 6.86
2361 2634 1.493134 GCCTAATAAACCCGGACGCG 61.493 60.000 0.73 3.53 0.00 6.01
2362 2635 1.162181 GGCCTAATAAACCCGGACGC 61.162 60.000 0.73 0.00 0.00 5.19
2461 2734 5.293324 TGTCGGATTCGTATTCAAATGAAGG 59.707 40.000 1.98 0.00 36.20 3.46
2541 2814 3.196901 GGCCCCTTGTATTTTGGGTTAAG 59.803 47.826 0.00 0.00 40.36 1.85
2562 2835 3.470645 CCTCCGTCAGGGTTTATTAGG 57.529 52.381 0.00 0.00 38.91 2.69
2574 2849 3.144657 TGACAACTACTACCTCCGTCA 57.855 47.619 0.00 0.00 0.00 4.35
2590 2865 5.939883 CCTAACAATGATGAAGACCTTGACA 59.060 40.000 0.00 0.00 0.00 3.58
2605 2880 6.235664 ACTACAGTAACAACCCCTAACAATG 58.764 40.000 0.00 0.00 0.00 2.82
2634 2909 5.186996 ACAGTGGAACAAATTGTCATCAC 57.813 39.130 14.18 14.18 44.16 3.06
2653 2928 8.018520 TGGTTTAATTAGCATTCACGTAAACAG 58.981 33.333 0.00 0.00 0.00 3.16
2674 2949 9.620259 TTGGCAACTAGAAAAATTTAATGGTTT 57.380 25.926 0.00 0.00 37.61 3.27
2677 2952 8.220434 CGTTTGGCAACTAGAAAAATTTAATGG 58.780 33.333 0.00 0.00 37.61 3.16
2719 2994 8.526147 CACATCTCCAAGGTTCATTATTTTCTT 58.474 33.333 0.00 0.00 0.00 2.52
2731 3006 3.703001 ACGAATCACATCTCCAAGGTT 57.297 42.857 0.00 0.00 0.00 3.50
2771 3046 3.105283 ACTTGTGGGGTAGACATCCTAC 58.895 50.000 0.00 0.00 45.48 3.18
2808 3083 2.481441 AGGTATGGATTCAGCCTGACA 58.519 47.619 0.00 0.00 33.12 3.58
2812 3087 3.947834 CGAAAAAGGTATGGATTCAGCCT 59.052 43.478 0.00 0.00 34.93 4.58
2823 3098 1.706305 TCACCCACCCGAAAAAGGTAT 59.294 47.619 0.00 0.00 35.24 2.73
2836 3111 2.529389 ACCACCCCTCTCACCCAC 60.529 66.667 0.00 0.00 0.00 4.61
2837 3112 2.529136 CACCACCCCTCTCACCCA 60.529 66.667 0.00 0.00 0.00 4.51
2838 3113 3.330720 CCACCACCCCTCTCACCC 61.331 72.222 0.00 0.00 0.00 4.61
2839 3114 3.330720 CCCACCACCCCTCTCACC 61.331 72.222 0.00 0.00 0.00 4.02
2840 3115 3.330720 CCCCACCACCCCTCTCAC 61.331 72.222 0.00 0.00 0.00 3.51
2841 3116 4.675303 CCCCCACCACCCCTCTCA 62.675 72.222 0.00 0.00 0.00 3.27
2842 3117 4.677151 ACCCCCACCACCCCTCTC 62.677 72.222 0.00 0.00 0.00 3.20
2861 3136 1.377612 GGACACACCTAACACCCCC 59.622 63.158 0.00 0.00 35.41 5.40
2871 3146 6.036844 GGAAATCGTAATAAGAAGGACACACC 59.963 42.308 0.00 0.00 39.35 4.16
2872 3147 6.592607 TGGAAATCGTAATAAGAAGGACACAC 59.407 38.462 0.00 0.00 0.00 3.82
2873 3148 6.703319 TGGAAATCGTAATAAGAAGGACACA 58.297 36.000 0.00 0.00 0.00 3.72
2874 3149 7.494625 TGATGGAAATCGTAATAAGAAGGACAC 59.505 37.037 0.00 0.00 0.00 3.67
2875 3150 7.561251 TGATGGAAATCGTAATAAGAAGGACA 58.439 34.615 0.00 0.00 0.00 4.02
2876 3151 8.433421 TTGATGGAAATCGTAATAAGAAGGAC 57.567 34.615 0.00 0.00 0.00 3.85
2885 3160 8.964476 ACTTGAGTATTGATGGAAATCGTAAT 57.036 30.769 0.00 0.00 0.00 1.89
2886 3161 8.786826 AACTTGAGTATTGATGGAAATCGTAA 57.213 30.769 0.00 0.00 0.00 3.18
2887 3162 8.786826 AAACTTGAGTATTGATGGAAATCGTA 57.213 30.769 0.00 0.00 0.00 3.43
2888 3163 7.390440 TGAAACTTGAGTATTGATGGAAATCGT 59.610 33.333 0.00 0.00 0.00 3.73
2889 3164 7.751732 TGAAACTTGAGTATTGATGGAAATCG 58.248 34.615 0.00 0.00 0.00 3.34
2890 3165 8.950210 TCTGAAACTTGAGTATTGATGGAAATC 58.050 33.333 0.00 0.00 0.00 2.17
2891 3166 8.868522 TCTGAAACTTGAGTATTGATGGAAAT 57.131 30.769 0.00 0.00 0.00 2.17
2892 3167 8.733458 CATCTGAAACTTGAGTATTGATGGAAA 58.267 33.333 0.00 0.00 0.00 3.13
2893 3168 7.884877 ACATCTGAAACTTGAGTATTGATGGAA 59.115 33.333 0.00 0.00 34.77 3.53
2894 3169 7.397221 ACATCTGAAACTTGAGTATTGATGGA 58.603 34.615 0.00 0.00 34.77 3.41
2895 3170 7.551974 AGACATCTGAAACTTGAGTATTGATGG 59.448 37.037 0.00 0.00 34.77 3.51
2896 3171 8.388853 CAGACATCTGAAACTTGAGTATTGATG 58.611 37.037 2.51 0.00 46.59 3.07
2897 3172 8.489990 CAGACATCTGAAACTTGAGTATTGAT 57.510 34.615 2.51 0.00 46.59 2.57
2898 3173 7.895975 CAGACATCTGAAACTTGAGTATTGA 57.104 36.000 2.51 0.00 46.59 2.57
2913 3188 7.199541 ACAAAAAGACAGAATCAGACATCTG 57.800 36.000 11.80 11.80 46.69 2.90
2914 3189 6.146837 CGACAAAAAGACAGAATCAGACATCT 59.853 38.462 0.00 0.00 0.00 2.90
2915 3190 6.146184 TCGACAAAAAGACAGAATCAGACATC 59.854 38.462 0.00 0.00 0.00 3.06
2916 3191 5.991606 TCGACAAAAAGACAGAATCAGACAT 59.008 36.000 0.00 0.00 0.00 3.06
2917 3192 5.356426 TCGACAAAAAGACAGAATCAGACA 58.644 37.500 0.00 0.00 0.00 3.41
2918 3193 5.907197 TCGACAAAAAGACAGAATCAGAC 57.093 39.130 0.00 0.00 0.00 3.51
2919 3194 7.655732 TGTATTCGACAAAAAGACAGAATCAGA 59.344 33.333 0.00 0.00 34.15 3.27
2920 3195 7.742089 GTGTATTCGACAAAAAGACAGAATCAG 59.258 37.037 0.00 0.00 40.66 2.90
2921 3196 7.225734 TGTGTATTCGACAAAAAGACAGAATCA 59.774 33.333 0.00 0.00 40.66 2.57
2922 3197 7.572759 TGTGTATTCGACAAAAAGACAGAATC 58.427 34.615 0.00 0.00 40.66 2.52
2923 3198 7.490962 TGTGTATTCGACAAAAAGACAGAAT 57.509 32.000 0.00 0.00 40.66 2.40
2924 3199 6.912203 TGTGTATTCGACAAAAAGACAGAA 57.088 33.333 0.00 0.00 40.66 3.02
2925 3200 6.912203 TTGTGTATTCGACAAAAAGACAGA 57.088 33.333 0.00 0.00 40.66 3.41
2926 3201 9.478019 GATATTGTGTATTCGACAAAAAGACAG 57.522 33.333 0.00 0.00 38.80 3.51
2927 3202 8.447833 GGATATTGTGTATTCGACAAAAAGACA 58.552 33.333 0.00 0.00 38.80 3.41
2928 3203 8.447833 TGGATATTGTGTATTCGACAAAAAGAC 58.552 33.333 0.00 0.00 38.80 3.01
2929 3204 8.554835 TGGATATTGTGTATTCGACAAAAAGA 57.445 30.769 0.00 0.00 38.80 2.52
2930 3205 9.787532 ATTGGATATTGTGTATTCGACAAAAAG 57.212 29.630 0.00 0.00 38.80 2.27
2932 3207 9.781834 GAATTGGATATTGTGTATTCGACAAAA 57.218 29.630 0.00 0.00 40.66 2.44
2933 3208 9.173021 AGAATTGGATATTGTGTATTCGACAAA 57.827 29.630 0.00 0.00 40.66 2.83
2934 3209 8.731275 AGAATTGGATATTGTGTATTCGACAA 57.269 30.769 0.00 0.00 40.66 3.18
2983 3450 9.681692 CAAAAGCATAACATAAGCAGCAATATA 57.318 29.630 0.00 0.00 0.00 0.86
2984 3451 8.199449 ACAAAAGCATAACATAAGCAGCAATAT 58.801 29.630 0.00 0.00 0.00 1.28
3001 3492 8.725148 CACTCATCTCTTAAGTTACAAAAGCAT 58.275 33.333 1.63 0.00 0.00 3.79
3032 3526 7.960738 CAGTAATAAAAACACCATACTGGAACG 59.039 37.037 0.00 0.00 40.96 3.95
3108 3602 8.264347 TGCTGAATTATCAACAATACCTGTAGA 58.736 33.333 0.00 0.00 37.23 2.59
3114 3608 9.669353 CACTAATGCTGAATTATCAACAATACC 57.331 33.333 0.00 0.00 35.43 2.73
3238 3734 9.859427 CAAATTCTAGCATTACCATTCAAGAAA 57.141 29.630 0.00 0.00 0.00 2.52
3282 5649 4.189231 GCCGCTCTCCTTGAACTATAAAA 58.811 43.478 0.00 0.00 0.00 1.52
3308 5675 0.035056 CTCCGGCCTTGAAGGACATT 60.035 55.000 18.75 0.00 46.60 2.71
3338 5705 2.483877 CTGCCTCACATAACGAAAAGCA 59.516 45.455 0.00 0.00 0.00 3.91
3371 5738 4.737352 GCACATTTGTTCCTGCTTTCTGAA 60.737 41.667 0.00 0.00 0.00 3.02
3393 5760 5.086104 TCAACCCTCTCTAATAGTTGTGC 57.914 43.478 0.00 0.00 39.05 4.57
3464 5831 7.907389 TGGACATCTGTCTCTTGTAAAACTAT 58.093 34.615 9.98 0.00 44.20 2.12
3467 5834 6.861065 TTGGACATCTGTCTCTTGTAAAAC 57.139 37.500 9.98 0.00 44.20 2.43
3596 5963 4.529897 TGACATTATGCTCCTTCATTGCT 58.470 39.130 0.00 0.00 0.00 3.91
3623 5990 5.899631 TTAGGTGGGTATTAATGTCCTCC 57.100 43.478 16.08 16.08 34.22 4.30
3653 6020 0.953727 GTGCTGCAACAAGGTCATCA 59.046 50.000 2.77 0.00 0.00 3.07
3687 6054 4.102681 AGTTGACAACTTACCTAAGGCAGT 59.897 41.667 15.23 0.00 39.04 4.40
3688 6055 4.642429 AGTTGACAACTTACCTAAGGCAG 58.358 43.478 15.23 0.00 39.04 4.85
3765 6132 3.654414 AGAGAGCACGTACAGGAAAAAG 58.346 45.455 0.00 0.00 0.00 2.27
3777 6147 3.562973 TCCCTACGTATAAAGAGAGCACG 59.437 47.826 0.00 0.00 38.52 5.34
3793 6163 8.451908 ACAAATTGCATATTACTTCTCCCTAC 57.548 34.615 0.00 0.00 0.00 3.18
3818 6188 5.586243 GCTTTGCATATAACTGAACTCCTGA 59.414 40.000 0.00 0.00 0.00 3.86
3870 6240 3.279434 GACAACGGAAGAATAAGCCCAT 58.721 45.455 0.00 0.00 0.00 4.00
3887 6257 7.001674 ACACTATATTTCAGGTTGGTTGACAA 58.998 34.615 0.00 0.00 36.54 3.18
3912 6282 5.079689 TGTTCCGATATGTGCAAGACTTA 57.920 39.130 0.00 0.00 0.00 2.24
3929 6299 1.001974 GGGTTGGGCTTTGAATGTTCC 59.998 52.381 0.00 0.00 0.00 3.62
3943 6313 2.584835 TCAGATTTGGACTGGGTTGG 57.415 50.000 0.00 0.00 36.22 3.77
3983 6353 1.816835 GGTTGGCCTGGCTAAAGTTAC 59.183 52.381 19.55 7.15 29.49 2.50
3988 6358 1.004277 CAGTAGGTTGGCCTGGCTAAA 59.996 52.381 19.55 10.92 46.47 1.85
3989 6359 0.618458 CAGTAGGTTGGCCTGGCTAA 59.382 55.000 19.68 16.80 46.47 3.09
4041 6414 4.851639 AGGTTTCATAGCCATTCAGACT 57.148 40.909 0.00 0.00 0.00 3.24
4073 6677 7.254727 CGGATGATCAAACCAAAACACAAAATT 60.255 33.333 18.14 0.00 0.00 1.82
4104 6708 5.122239 ACATGGAACTCAAATATGTGTCGTG 59.878 40.000 0.00 0.00 32.36 4.35
4147 6751 9.976511 CAGTGAGAAATAATGCATATCCATTTT 57.023 29.630 0.00 0.00 36.80 1.82
4172 6776 6.587206 TCATTTGCACAGAAATGAATACCA 57.413 33.333 8.71 0.00 45.21 3.25
4184 6788 6.849502 ACTAAGAACATGATCATTTGCACAG 58.150 36.000 5.16 2.61 0.00 3.66
4233 6837 6.595326 CAGCATAAACAAGATTAGGACAGTGA 59.405 38.462 0.00 0.00 0.00 3.41
4405 7016 7.278875 TGGCTTGTCACAAATTAAGGAAAAAT 58.721 30.769 0.00 0.00 0.00 1.82
4408 7019 5.860941 TGGCTTGTCACAAATTAAGGAAA 57.139 34.783 0.00 0.00 0.00 3.13
4427 7040 8.322091 ACTACCTACATATAAAGATCCATTGGC 58.678 37.037 0.00 0.00 0.00 4.52
4640 7253 2.926200 CAGGTTATTGCTCAGTGACTCG 59.074 50.000 0.00 0.00 0.00 4.18
4960 7573 0.629058 GGTTTCCTCCCCCTATTGCA 59.371 55.000 0.00 0.00 0.00 4.08
4981 7594 0.759959 TCTGGTTGCTTCGGTGGTAA 59.240 50.000 0.00 0.00 0.00 2.85
5137 7754 4.318332 TCTGCATGTTTGGAACTACTGAG 58.682 43.478 0.00 0.00 0.00 3.35
5191 7810 9.902196 TGATTAATGCTACAAGATGCAATAATG 57.098 29.630 11.41 0.00 42.05 1.90
5257 7878 4.980573 AGTACATTTGCTTGGTGGTAGAA 58.019 39.130 0.00 0.00 0.00 2.10
5281 7902 2.357009 GGAGCCGAGTCTTTGTATACGA 59.643 50.000 0.00 0.00 0.00 3.43
5303 7942 8.989653 ACTTAGTTATGCTTGAAGAGAGTAAC 57.010 34.615 0.00 0.00 31.91 2.50
5408 8047 7.464358 TCGTTGGTTTATTAGTACGTAGAGAC 58.536 38.462 0.00 0.00 0.00 3.36
5477 8121 5.276820 GCGGGTTGAATTCTGAAAAACAAAG 60.277 40.000 7.05 0.00 0.00 2.77
5551 8195 8.799367 GGTTGAATATACCAAAGTACAGGTTTT 58.201 33.333 9.52 3.33 39.31 2.43
5557 8201 4.877251 GCGGGTTGAATATACCAAAGTACA 59.123 41.667 0.00 0.00 37.40 2.90
5558 8202 4.025480 CGCGGGTTGAATATACCAAAGTAC 60.025 45.833 0.00 0.00 37.40 2.73


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

AutoCloner maintained by Alex Coulton.