Multiple sequence alignment - TraesCS3B01G587600

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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 TraesCS3B01G587600 chr3B 100.000 5813 0 0 1 5813 813960139 813965951 0.000000e+00 10735.0
1 TraesCS3B01G587600 chr3B 83.745 2750 418 21 997 3739 813947866 813950593 0.000000e+00 2575.0
2 TraesCS3B01G587600 chr3B 83.253 2693 421 23 975 3650 815050829 815048150 0.000000e+00 2447.0
3 TraesCS3B01G587600 chr3B 83.495 1757 265 16 1799 3547 814172549 814170810 0.000000e+00 1615.0
4 TraesCS3B01G587600 chr3B 81.590 956 163 10 2596 3549 814162367 814161423 0.000000e+00 778.0
5 TraesCS3B01G587600 chr3B 82.588 850 139 8 908 1752 814173474 814172629 0.000000e+00 741.0
6 TraesCS3B01G587600 chr3B 78.631 1081 188 27 4027 5086 815048017 815046959 0.000000e+00 676.0
7 TraesCS3B01G587600 chr3B 81.089 661 102 13 4015 4662 814170795 814170145 1.870000e-139 507.0
8 TraesCS3B01G587600 chr3B 79.940 668 110 16 4011 4666 813950646 813951301 2.450000e-128 470.0
9 TraesCS3B01G587600 chr3B 78.808 151 27 3 1 148 814903041 814902893 4.790000e-16 97.1
10 TraesCS3B01G587600 chr3B 76.159 151 24 5 1 148 814662585 814662444 1.050000e-07 69.4
11 TraesCS3B01G587600 chrUn 95.920 5073 159 14 770 5808 46226294 46231352 0.000000e+00 8178.0
12 TraesCS3B01G587600 chrUn 83.285 2746 432 19 1001 3739 46218706 46221431 0.000000e+00 2503.0
13 TraesCS3B01G587600 chrUn 93.140 379 13 3 395 773 46225853 46226218 1.420000e-150 544.0
14 TraesCS3B01G587600 chrUn 79.910 667 112 14 4011 4666 46221484 46222139 2.450000e-128 470.0
15 TraesCS3B01G587600 chrUn 92.949 156 6 4 1 152 46225505 46225659 7.580000e-54 222.0
16 TraesCS3B01G587600 chrUn 93.023 43 2 1 5067 5108 46230725 46230767 1.750000e-05 62.1
17 TraesCS3B01G587600 chrUn 92.308 39 3 0 189 227 46225736 46225774 8.140000e-04 56.5
18 TraesCS3B01G587600 chr3A 95.295 5058 198 28 774 5813 737214382 737219417 0.000000e+00 7986.0
19 TraesCS3B01G587600 chr3A 83.285 2746 433 18 1001 3739 737207187 737209913 0.000000e+00 2505.0
20 TraesCS3B01G587600 chr3A 83.767 2150 311 30 1819 3961 737290006 737292124 0.000000e+00 2002.0
21 TraesCS3B01G587600 chr3A 85.652 913 122 8 846 1752 737289063 737289972 0.000000e+00 952.0
22 TraesCS3B01G587600 chr3A 81.747 641 110 7 4014 4651 737292147 737292783 3.990000e-146 529.0
23 TraesCS3B01G587600 chr3A 93.075 361 20 4 282 639 737213866 737214224 1.860000e-144 523.0
24 TraesCS3B01G587600 chr3A 80.689 668 105 17 4011 4666 737209966 737210621 1.120000e-136 497.0
25 TraesCS3B01G587600 chr3A 96.000 100 3 1 674 773 737214224 737214322 1.680000e-35 161.0
26 TraesCS3B01G587600 chr3A 79.897 194 11 10 1 193 737213576 737213742 3.680000e-22 117.0
27 TraesCS3B01G587600 chr3A 97.436 39 1 0 189 227 737213797 737213835 3.760000e-07 67.6
28 TraesCS3B01G587600 chr3A 93.023 43 2 1 5067 5108 737218805 737218847 1.750000e-05 62.1
29 TraesCS3B01G587600 chr1B 74.119 2612 551 90 990 3573 7256972 7254458 0.000000e+00 963.0
30 TraesCS3B01G587600 chr1A 74.010 2601 537 98 996 3555 6341258 6338756 0.000000e+00 929.0
31 TraesCS3B01G587600 chr7B 73.871 731 167 20 3909 4627 714619823 714619105 2.670000e-68 270.0
32 TraesCS3B01G587600 chr3D 79.718 355 66 4 4047 4396 612267567 612267920 9.670000e-63 252.0
33 TraesCS3B01G587600 chr3D 78.756 193 29 9 1 189 606485084 606484900 1.020000e-22 119.0
34 TraesCS3B01G587600 chr3D 91.045 67 5 1 81 147 606486409 606486344 8.020000e-14 89.8


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 TraesCS3B01G587600 chr3B 813960139 813965951 5812 False 10735.000000 10735 100.000000 1 5813 1 chr3B.!!$F1 5812
1 TraesCS3B01G587600 chr3B 815046959 815050829 3870 True 1561.500000 2447 80.942000 975 5086 2 chr3B.!!$R5 4111
2 TraesCS3B01G587600 chr3B 813947866 813951301 3435 False 1522.500000 2575 81.842500 997 4666 2 chr3B.!!$F2 3669
3 TraesCS3B01G587600 chr3B 814170145 814173474 3329 True 954.333333 1615 82.390667 908 4662 3 chr3B.!!$R4 3754
4 TraesCS3B01G587600 chr3B 814161423 814162367 944 True 778.000000 778 81.590000 2596 3549 1 chr3B.!!$R1 953
5 TraesCS3B01G587600 chrUn 46218706 46231352 12646 False 1719.371429 8178 90.076429 1 5808 7 chrUn.!!$F1 5807
6 TraesCS3B01G587600 chr3A 737207187 737219417 12230 False 1489.837500 7986 89.837500 1 5813 8 chr3A.!!$F1 5812
7 TraesCS3B01G587600 chr3A 737289063 737292783 3720 False 1161.000000 2002 83.722000 846 4651 3 chr3A.!!$F2 3805
8 TraesCS3B01G587600 chr1B 7254458 7256972 2514 True 963.000000 963 74.119000 990 3573 1 chr1B.!!$R1 2583
9 TraesCS3B01G587600 chr1A 6338756 6341258 2502 True 929.000000 929 74.010000 996 3555 1 chr1A.!!$R1 2559
10 TraesCS3B01G587600 chr7B 714619105 714619823 718 True 270.000000 270 73.871000 3909 4627 1 chr7B.!!$R1 718

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
364 7240 0.457443 GGGTGCTTGAGGCTTAATGC 59.543 55.000 0.00 0.00 42.39 3.56 F
397 7273 1.050204 AATTTTGGCTGCAGCTTGGA 58.950 45.000 35.82 20.72 41.70 3.53 F
1322 8287 0.804364 TACAGCAAGCTCGGCATTTG 59.196 50.000 12.27 5.13 0.00 2.32 F
1848 8846 1.340568 GGGCGTAGATACCTCCTTGTC 59.659 57.143 0.00 0.00 0.00 3.18 F
3049 10065 0.032952 TGGTGGTCTCCGAAAACTCG 59.967 55.000 0.00 0.00 0.00 4.18 F
3802 18259 0.179000 AGCACCGGTTGATGGAGATC 59.821 55.000 2.97 0.00 0.00 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1294 8259 0.393537 AGCTTGCTGTAGTGCCCATC 60.394 55.000 0.00 0.00 0.00 3.51 R
1779 8777 0.895530 GGCCCTTCTTAAAAGGTGCC 59.104 55.000 19.97 19.97 42.37 5.01 R
2599 9609 1.699083 TGGAAGCCACTCAATCTGACA 59.301 47.619 0.00 0.00 0.00 3.58 R
3807 18264 0.179156 GAAATGCTGACCGTGCCATG 60.179 55.000 0.00 0.00 0.00 3.66 R
4670 19151 0.096454 TACAGCTGACGACGATGACG 59.904 55.000 23.35 0.00 45.75 4.35 R
5361 19886 1.511850 TGATTCCTTCGTGTGTGCTG 58.488 50.000 0.00 0.00 0.00 4.41 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
59 6860 6.939163 AGGATCATGCCATAATTTGAGTCTAC 59.061 38.462 0.00 0.00 0.00 2.59
197 7041 9.248291 TCTTTAAAACATTGCATTGTTTCTCTC 57.752 29.630 29.72 0.00 46.33 3.20
198 7042 7.621832 TTAAAACATTGCATTGTTTCTCTCG 57.378 32.000 29.72 0.00 46.33 4.04
235 7108 7.121759 CCAATGTGTTCTCTGAATCCAGTTATT 59.878 37.037 0.00 0.00 41.16 1.40
236 7109 7.621428 ATGTGTTCTCTGAATCCAGTTATTG 57.379 36.000 0.00 0.00 41.16 1.90
284 7160 9.778741 TTGATTTCTTCTCTGTGTATTTACAGT 57.221 29.630 5.89 0.00 46.32 3.55
285 7161 9.778741 TGATTTCTTCTCTGTGTATTTACAGTT 57.221 29.630 5.89 0.00 46.32 3.16
288 7164 8.958119 TTCTTCTCTGTGTATTTACAGTTTGT 57.042 30.769 5.89 0.00 46.32 2.83
289 7165 8.589335 TCTTCTCTGTGTATTTACAGTTTGTC 57.411 34.615 5.89 0.00 46.32 3.18
290 7166 8.421784 TCTTCTCTGTGTATTTACAGTTTGTCT 58.578 33.333 5.89 0.00 46.32 3.41
291 7167 8.589335 TTCTCTGTGTATTTACAGTTTGTCTC 57.411 34.615 5.89 0.00 46.32 3.36
292 7168 7.952671 TCTCTGTGTATTTACAGTTTGTCTCT 58.047 34.615 5.89 0.00 46.32 3.10
293 7169 8.421784 TCTCTGTGTATTTACAGTTTGTCTCTT 58.578 33.333 5.89 0.00 46.32 2.85
294 7170 9.692749 CTCTGTGTATTTACAGTTTGTCTCTTA 57.307 33.333 5.89 0.00 46.32 2.10
306 7182 9.890629 ACAGTTTGTCTCTTATATGCTATTTCA 57.109 29.630 0.00 0.00 0.00 2.69
308 7184 9.331282 AGTTTGTCTCTTATATGCTATTTCACC 57.669 33.333 0.00 0.00 0.00 4.02
309 7185 7.946655 TTGTCTCTTATATGCTATTTCACCG 57.053 36.000 0.00 0.00 0.00 4.94
310 7186 6.455647 TGTCTCTTATATGCTATTTCACCGG 58.544 40.000 0.00 0.00 0.00 5.28
311 7187 6.041637 TGTCTCTTATATGCTATTTCACCGGT 59.958 38.462 0.00 0.00 0.00 5.28
312 7188 6.366332 GTCTCTTATATGCTATTTCACCGGTG 59.634 42.308 29.26 29.26 0.00 4.94
313 7189 6.041637 TCTCTTATATGCTATTTCACCGGTGT 59.958 38.462 32.74 17.56 0.00 4.16
314 7190 6.220930 TCTTATATGCTATTTCACCGGTGTC 58.779 40.000 32.74 16.17 0.00 3.67
315 7191 4.689612 ATATGCTATTTCACCGGTGTCT 57.310 40.909 32.74 20.30 0.00 3.41
316 7192 2.851263 TGCTATTTCACCGGTGTCTT 57.149 45.000 32.74 20.11 0.00 3.01
317 7193 3.134574 TGCTATTTCACCGGTGTCTTT 57.865 42.857 32.74 18.44 0.00 2.52
318 7194 3.071479 TGCTATTTCACCGGTGTCTTTC 58.929 45.455 32.74 18.57 0.00 2.62
319 7195 3.071479 GCTATTTCACCGGTGTCTTTCA 58.929 45.455 32.74 11.09 0.00 2.69
320 7196 3.500680 GCTATTTCACCGGTGTCTTTCAA 59.499 43.478 32.74 16.72 0.00 2.69
321 7197 4.156008 GCTATTTCACCGGTGTCTTTCAAT 59.844 41.667 32.74 21.52 0.00 2.57
322 7198 5.335661 GCTATTTCACCGGTGTCTTTCAATT 60.336 40.000 32.74 16.89 0.00 2.32
323 7199 6.128117 GCTATTTCACCGGTGTCTTTCAATTA 60.128 38.462 32.74 17.08 0.00 1.40
324 7200 6.642707 ATTTCACCGGTGTCTTTCAATTAA 57.357 33.333 32.74 13.74 0.00 1.40
325 7201 6.452494 TTTCACCGGTGTCTTTCAATTAAA 57.548 33.333 32.74 18.63 0.00 1.52
326 7202 6.642707 TTCACCGGTGTCTTTCAATTAAAT 57.357 33.333 32.74 0.00 0.00 1.40
327 7203 7.747155 TTCACCGGTGTCTTTCAATTAAATA 57.253 32.000 32.74 5.91 0.00 1.40
328 7204 7.372451 TCACCGGTGTCTTTCAATTAAATAG 57.628 36.000 32.74 1.79 0.00 1.73
329 7205 6.373216 TCACCGGTGTCTTTCAATTAAATAGG 59.627 38.462 32.74 1.43 0.00 2.57
330 7206 6.373216 CACCGGTGTCTTTCAATTAAATAGGA 59.627 38.462 26.95 0.00 0.00 2.94
331 7207 7.067008 CACCGGTGTCTTTCAATTAAATAGGAT 59.933 37.037 26.95 0.00 0.00 3.24
332 7208 7.614192 ACCGGTGTCTTTCAATTAAATAGGATT 59.386 33.333 6.12 0.00 0.00 3.01
333 7209 8.466798 CCGGTGTCTTTCAATTAAATAGGATTT 58.533 33.333 0.00 0.00 0.00 2.17
334 7210 9.855021 CGGTGTCTTTCAATTAAATAGGATTTT 57.145 29.630 0.00 0.00 0.00 1.82
347 7223 9.515226 TTAAATAGGATTTTCGGAATCTATGGG 57.485 33.333 10.74 0.00 0.00 4.00
348 7224 6.704056 ATAGGATTTTCGGAATCTATGGGT 57.296 37.500 10.74 0.00 0.00 4.51
349 7225 4.718961 AGGATTTTCGGAATCTATGGGTG 58.281 43.478 10.74 0.00 0.00 4.61
350 7226 3.253432 GGATTTTCGGAATCTATGGGTGC 59.747 47.826 10.74 0.00 0.00 5.01
351 7227 3.644966 TTTTCGGAATCTATGGGTGCT 57.355 42.857 0.00 0.00 0.00 4.40
352 7228 3.644966 TTTCGGAATCTATGGGTGCTT 57.355 42.857 0.00 0.00 0.00 3.91
353 7229 2.620251 TCGGAATCTATGGGTGCTTG 57.380 50.000 0.00 0.00 0.00 4.01
354 7230 2.115427 TCGGAATCTATGGGTGCTTGA 58.885 47.619 0.00 0.00 0.00 3.02
355 7231 2.103094 TCGGAATCTATGGGTGCTTGAG 59.897 50.000 0.00 0.00 0.00 3.02
356 7232 2.808202 CGGAATCTATGGGTGCTTGAGG 60.808 54.545 0.00 0.00 0.00 3.86
357 7233 2.225467 GAATCTATGGGTGCTTGAGGC 58.775 52.381 0.00 0.00 42.22 4.70
358 7234 1.516110 ATCTATGGGTGCTTGAGGCT 58.484 50.000 0.00 0.00 42.39 4.58
359 7235 1.289160 TCTATGGGTGCTTGAGGCTT 58.711 50.000 0.00 0.00 42.39 4.35
360 7236 2.477245 TCTATGGGTGCTTGAGGCTTA 58.523 47.619 0.00 0.00 42.39 3.09
361 7237 2.843730 TCTATGGGTGCTTGAGGCTTAA 59.156 45.455 0.00 0.00 42.39 1.85
362 7238 2.834638 ATGGGTGCTTGAGGCTTAAT 57.165 45.000 0.00 0.00 42.39 1.40
363 7239 1.838112 TGGGTGCTTGAGGCTTAATG 58.162 50.000 0.00 0.00 42.39 1.90
364 7240 0.457443 GGGTGCTTGAGGCTTAATGC 59.543 55.000 0.00 0.00 42.39 3.56
365 7241 1.467920 GGTGCTTGAGGCTTAATGCT 58.532 50.000 12.19 0.00 42.39 3.79
366 7242 1.821136 GGTGCTTGAGGCTTAATGCTT 59.179 47.619 12.19 0.00 42.39 3.91
367 7243 2.416431 GGTGCTTGAGGCTTAATGCTTG 60.416 50.000 12.19 0.00 42.39 4.01
368 7244 1.203052 TGCTTGAGGCTTAATGCTTGC 59.797 47.619 12.19 4.72 42.39 4.01
369 7245 1.203052 GCTTGAGGCTTAATGCTTGCA 59.797 47.619 0.00 0.00 42.39 4.08
370 7246 2.353011 GCTTGAGGCTTAATGCTTGCAA 60.353 45.455 0.00 0.00 42.39 4.08
371 7247 3.508762 CTTGAGGCTTAATGCTTGCAAG 58.491 45.455 22.44 22.44 42.39 4.01
372 7248 2.794103 TGAGGCTTAATGCTTGCAAGA 58.206 42.857 30.39 15.09 42.39 3.02
373 7249 2.751259 TGAGGCTTAATGCTTGCAAGAG 59.249 45.455 30.39 18.00 42.39 2.85
374 7250 2.751806 GAGGCTTAATGCTTGCAAGAGT 59.248 45.455 30.39 15.85 42.39 3.24
375 7251 3.941483 GAGGCTTAATGCTTGCAAGAGTA 59.059 43.478 30.39 15.04 42.39 2.59
376 7252 4.335416 AGGCTTAATGCTTGCAAGAGTAA 58.665 39.130 30.39 20.22 42.39 2.24
377 7253 4.156739 AGGCTTAATGCTTGCAAGAGTAAC 59.843 41.667 30.39 12.13 42.39 2.50
378 7254 4.082787 GGCTTAATGCTTGCAAGAGTAACA 60.083 41.667 30.39 17.48 42.39 2.41
379 7255 5.460646 GCTTAATGCTTGCAAGAGTAACAA 58.539 37.500 30.39 13.19 38.95 2.83
380 7256 6.095377 GCTTAATGCTTGCAAGAGTAACAAT 58.905 36.000 30.39 12.93 38.95 2.71
381 7257 6.587608 GCTTAATGCTTGCAAGAGTAACAATT 59.412 34.615 30.39 16.59 38.95 2.32
382 7258 7.116805 GCTTAATGCTTGCAAGAGTAACAATTT 59.883 33.333 30.39 11.74 38.95 1.82
383 7259 8.885494 TTAATGCTTGCAAGAGTAACAATTTT 57.115 26.923 30.39 11.11 0.00 1.82
384 7260 6.774354 ATGCTTGCAAGAGTAACAATTTTG 57.226 33.333 30.39 0.00 0.00 2.44
385 7261 5.049167 TGCTTGCAAGAGTAACAATTTTGG 58.951 37.500 30.39 0.00 0.00 3.28
386 7262 4.084380 GCTTGCAAGAGTAACAATTTTGGC 60.084 41.667 30.39 5.51 0.00 4.52
387 7263 4.935352 TGCAAGAGTAACAATTTTGGCT 57.065 36.364 0.00 0.00 0.00 4.75
388 7264 4.619973 TGCAAGAGTAACAATTTTGGCTG 58.380 39.130 0.00 0.00 0.00 4.85
389 7265 3.429881 GCAAGAGTAACAATTTTGGCTGC 59.570 43.478 0.00 0.00 0.00 5.25
390 7266 4.619973 CAAGAGTAACAATTTTGGCTGCA 58.380 39.130 0.50 0.00 0.00 4.41
391 7267 4.510038 AGAGTAACAATTTTGGCTGCAG 57.490 40.909 10.11 10.11 0.00 4.41
392 7268 2.989166 GAGTAACAATTTTGGCTGCAGC 59.011 45.455 30.88 30.88 41.14 5.25
393 7269 2.629617 AGTAACAATTTTGGCTGCAGCT 59.370 40.909 35.82 15.32 41.70 4.24
394 7270 2.625695 AACAATTTTGGCTGCAGCTT 57.374 40.000 35.82 20.46 41.70 3.74
395 7271 1.873698 ACAATTTTGGCTGCAGCTTG 58.126 45.000 35.82 30.75 41.70 4.01
396 7272 1.153353 CAATTTTGGCTGCAGCTTGG 58.847 50.000 35.82 15.86 41.70 3.61
397 7273 1.050204 AATTTTGGCTGCAGCTTGGA 58.950 45.000 35.82 20.72 41.70 3.53
401 7277 2.148446 TTGGCTGCAGCTTGGAATAT 57.852 45.000 35.82 0.00 41.70 1.28
492 7368 4.874396 GGTTAGCTGTCCCTGTTGTTATAC 59.126 45.833 0.00 0.00 0.00 1.47
555 7431 5.048224 CCAGCTGGAATAAATATTGCTGAGG 60.048 44.000 29.88 13.06 40.11 3.86
565 7441 2.417978 TTGCTGAGGTGTTGCAAGG 58.582 52.632 0.00 0.00 41.06 3.61
592 7468 7.001674 TGGGTAGTTGACTTGTGATAAATTGT 58.998 34.615 0.00 0.00 0.00 2.71
611 7487 3.554934 TGTGATTGGTTGAAGAAGTGCT 58.445 40.909 0.00 0.00 0.00 4.40
648 7524 8.138074 CGACTCATCTGAAGGAGTATTTCATTA 58.862 37.037 13.27 0.00 46.04 1.90
734 7610 8.958060 AAGTCAGAATAGCTGTCCCTATTATA 57.042 34.615 0.00 0.00 45.14 0.98
736 7612 8.174085 AGTCAGAATAGCTGTCCCTATTATACT 58.826 37.037 0.00 0.00 45.14 2.12
811 7765 8.354426 GGAAGTGTTTTATTAAGTACAGCCAAA 58.646 33.333 0.00 0.00 0.00 3.28
812 7766 9.908152 GAAGTGTTTTATTAAGTACAGCCAAAT 57.092 29.630 0.00 0.00 0.00 2.32
832 7786 4.839668 ATCGGAGAAGAAGGTAATCGAG 57.160 45.455 0.00 0.00 43.58 4.04
903 7861 7.823799 GTCTTCCATTTTTCTCAGAAGATCTCT 59.176 37.037 0.00 0.00 43.37 3.10
940 7901 1.276421 CACCACCGTTCTCTTCTCCAT 59.724 52.381 0.00 0.00 0.00 3.41
1294 8259 1.738099 CGTCGTGAGGCCAAGAAGG 60.738 63.158 5.01 0.00 41.84 3.46
1321 8286 1.089920 CTACAGCAAGCTCGGCATTT 58.910 50.000 12.27 0.00 0.00 2.32
1322 8287 0.804364 TACAGCAAGCTCGGCATTTG 59.196 50.000 12.27 5.13 0.00 2.32
1334 8299 4.025647 GCTCGGCATTTGTACAGTAAGATC 60.026 45.833 0.00 0.00 0.00 2.75
1391 8356 5.477984 ACAAAATGGAGAAGAAGCTATGCAA 59.522 36.000 0.00 0.00 0.00 4.08
1432 8397 1.699083 TCCTTGTGGCTGAGATGAACA 59.301 47.619 0.00 0.00 0.00 3.18
1609 8574 4.371624 AATCTCACAGTTGTTCCCATCA 57.628 40.909 0.00 0.00 0.00 3.07
1662 8627 4.970662 AGCGCAACTCATTTACAATGAT 57.029 36.364 11.47 0.00 0.00 2.45
1670 8635 6.690194 ACTCATTTACAATGATCCTGAAGC 57.310 37.500 0.00 0.00 0.00 3.86
1848 8846 1.340568 GGGCGTAGATACCTCCTTGTC 59.659 57.143 0.00 0.00 0.00 3.18
1868 8866 3.104512 TCTTGGATGATGTACGGAACCT 58.895 45.455 0.00 0.00 0.00 3.50
1955 8956 1.661112 GGCAACTACTCGTGATGAAGC 59.339 52.381 0.00 0.00 0.00 3.86
2238 9242 4.184629 CTGAGGAGTCTGGAATTTTACCG 58.815 47.826 0.00 0.00 0.00 4.02
2241 9245 4.770795 AGGAGTCTGGAATTTTACCGATG 58.229 43.478 0.00 0.00 0.00 3.84
2322 9326 4.261801 CTGTGTTTCCCAAGGATTACGAT 58.738 43.478 0.00 0.00 0.00 3.73
2599 9609 2.619074 GCTCTTGCACCTAAGGAACCAT 60.619 50.000 0.00 0.00 39.41 3.55
2695 9711 4.326826 TGAATCTGTGGCGAAAAGATCTT 58.673 39.130 0.88 0.88 30.35 2.40
2720 9736 7.872962 TGGCTATCCAGACACTTATGTGTGC 62.873 48.000 18.24 12.75 46.51 4.57
2934 9950 7.394359 AGCCTACAAACATTGAACATATCTTGT 59.606 33.333 0.00 0.00 41.53 3.16
3000 10016 1.413077 GCCCTCTGTCACCTATACACC 59.587 57.143 0.00 0.00 0.00 4.16
3049 10065 0.032952 TGGTGGTCTCCGAAAACTCG 59.967 55.000 0.00 0.00 0.00 4.18
3302 17758 2.019984 GAAACCTCATGATGGACTGCC 58.980 52.381 15.51 0.00 0.00 4.85
3584 18041 0.770008 GCAAAGTTAACAGCGTTGCG 59.230 50.000 8.61 0.00 40.25 4.85
3779 18236 4.682787 TGTTCTATCCTGACAGCATTACG 58.317 43.478 0.00 0.00 0.00 3.18
3802 18259 0.179000 AGCACCGGTTGATGGAGATC 59.821 55.000 2.97 0.00 0.00 2.75
3806 18263 3.393800 CACCGGTTGATGGAGATCATAC 58.606 50.000 2.97 0.00 38.43 2.39
3807 18264 2.368875 ACCGGTTGATGGAGATCATACC 59.631 50.000 0.00 0.00 38.43 2.73
3897 18354 2.799412 GCATGCAGTCGAAGGATCTAAG 59.201 50.000 14.21 0.00 0.00 2.18
3898 18355 2.586258 TGCAGTCGAAGGATCTAAGC 57.414 50.000 0.00 0.00 0.00 3.09
3972 18429 8.249638 TGTGAAAATATGACAACATTATGTGGG 58.750 33.333 4.61 0.53 37.87 4.61
4006 18463 2.035632 CTAGCCTTCAGGAGATCCGTT 58.964 52.381 0.00 0.00 42.08 4.44
4116 18573 3.568430 TGTGGGTAGCTAGACATATGACG 59.432 47.826 10.38 0.00 0.00 4.35
4137 18594 5.547465 ACGTCATTGACCAATCTGAAACTA 58.453 37.500 11.12 0.00 0.00 2.24
4152 18609 8.980481 ATCTGAAACTAAAGAACCTTGAAGAA 57.020 30.769 0.00 0.00 0.00 2.52
4178 18650 2.282462 AACCTTGAAGGCGGCTGG 60.282 61.111 14.21 12.33 39.63 4.85
4263 18735 4.418392 CAATTATGCACTTGAGTGGCTTC 58.582 43.478 12.65 0.00 45.72 3.86
4398 18873 6.086011 TCCTTGAGGAGTCTAGAGATTTCT 57.914 41.667 0.00 0.00 39.78 2.52
4492 18967 4.087892 TCCTGCCAAGCCTCGAGC 62.088 66.667 6.99 2.54 44.25 5.03
4509 18984 5.180367 TCGAGCATCTCAAGATAGTTCAG 57.820 43.478 0.00 0.00 32.63 3.02
4542 19017 2.094130 GGTAGAGGTCTTCAAACTCCCG 60.094 54.545 0.00 0.00 31.70 5.14
4576 19051 8.431222 TGAGGAAAATGGAAATTCTTGATTGTT 58.569 29.630 0.00 0.00 0.00 2.83
4627 19108 2.033757 AGCAGGAACAGGCAGCAG 59.966 61.111 0.00 0.00 33.33 4.24
4633 19114 2.749044 AACAGGCAGCAGCATCGG 60.749 61.111 2.65 0.00 44.61 4.18
4668 19149 5.403766 GCGATCACCTGTATATTCAGAGTTG 59.596 44.000 10.68 5.39 37.61 3.16
4669 19150 6.507900 CGATCACCTGTATATTCAGAGTTGT 58.492 40.000 10.68 0.00 37.61 3.32
4670 19151 6.638873 CGATCACCTGTATATTCAGAGTTGTC 59.361 42.308 10.68 6.60 37.61 3.18
4698 19179 1.907739 GTCAGCTGTATCCAGGGCA 59.092 57.895 14.67 0.00 39.22 5.36
4724 19205 6.479884 AGCATTCTCTCTTTCCATGTTTAGT 58.520 36.000 0.00 0.00 0.00 2.24
4820 19301 5.643379 ATTACCATTTGTTAGTGCAGTGG 57.357 39.130 3.69 0.00 34.35 4.00
4860 19341 4.705482 TCGGGAGAGATGCCATCA 57.295 55.556 7.56 0.00 0.00 3.07
5231 19726 4.746115 TCACATTTCAGCAACAAATTCAGC 59.254 37.500 0.00 0.00 0.00 4.26
5286 19786 9.534565 TCAGTTGTTCTAACTAATAGATGCATC 57.465 33.333 19.37 19.37 40.32 3.91
5465 19990 7.122948 CACTCCTTGTACCTATACTCTCTGTTT 59.877 40.741 0.00 0.00 32.00 2.83
5483 20008 4.499183 TGTTTGTTCGGTGCATTCTTTTT 58.501 34.783 0.00 0.00 0.00 1.94
5673 20198 4.459337 GGCTTTCTGTTATGGTTTGCTACT 59.541 41.667 0.00 0.00 0.00 2.57
5674 20199 5.048013 GGCTTTCTGTTATGGTTTGCTACTT 60.048 40.000 0.00 0.00 0.00 2.24
5675 20200 5.858581 GCTTTCTGTTATGGTTTGCTACTTG 59.141 40.000 0.00 0.00 0.00 3.16
5701 20226 7.403312 TGTTTCAAGACTCCATTTTCTCAAA 57.597 32.000 0.00 0.00 0.00 2.69
5702 20227 8.010733 TGTTTCAAGACTCCATTTTCTCAAAT 57.989 30.769 0.00 0.00 32.36 2.32
5703 20228 7.922278 TGTTTCAAGACTCCATTTTCTCAAATG 59.078 33.333 1.37 1.37 46.29 2.32
5715 20248 3.959535 TCTCAAATGAAAATGTGGCCC 57.040 42.857 0.00 0.00 0.00 5.80
5724 20257 3.258872 TGAAAATGTGGCCCTCTTTGATG 59.741 43.478 0.00 0.00 0.00 3.07
5767 20300 3.840831 CTACCAAGCAGCAGCAGTA 57.159 52.632 3.17 1.34 45.49 2.74
5771 20304 0.524862 CCAAGCAGCAGCAGTAAAGG 59.475 55.000 3.17 0.00 45.49 3.11
5798 20331 4.400251 AGATTTGATTATATGCATGGGCCG 59.600 41.667 10.16 0.00 40.13 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.016957 TCCAGATTATTGGATGAGAAGTATGCT 59.983 37.037 0.00 0.00 42.24 3.79
32 6833 6.489361 AGACTCAAATTATGGCATGATCCTTC 59.511 38.462 10.98 1.42 0.00 3.46
67 6868 6.605995 TCTGTACTGTAAGCAGGAAATAGCTA 59.394 38.462 0.00 0.00 46.62 3.32
68 6869 5.422331 TCTGTACTGTAAGCAGGAAATAGCT 59.578 40.000 0.00 0.00 46.62 3.32
69 6870 5.661458 TCTGTACTGTAAGCAGGAAATAGC 58.339 41.667 5.83 0.00 46.62 2.97
70 6871 7.324178 AGTTCTGTACTGTAAGCAGGAAATAG 58.676 38.462 5.83 0.00 46.62 1.73
71 6872 7.241042 AGTTCTGTACTGTAAGCAGGAAATA 57.759 36.000 5.83 0.00 46.62 1.40
72 6873 6.115448 AGTTCTGTACTGTAAGCAGGAAAT 57.885 37.500 5.83 0.00 46.62 2.17
75 6876 5.537295 TGTTAGTTCTGTACTGTAAGCAGGA 59.463 40.000 5.83 0.00 46.62 3.86
76 6877 5.779922 TGTTAGTTCTGTACTGTAAGCAGG 58.220 41.667 5.83 0.00 46.62 4.85
78 6879 6.041182 TCCTTGTTAGTTCTGTACTGTAAGCA 59.959 38.462 0.00 0.00 37.60 3.91
79 6880 6.453092 TCCTTGTTAGTTCTGTACTGTAAGC 58.547 40.000 0.00 0.00 37.60 3.09
178 6981 4.836125 ACGAGAGAAACAATGCAATGTT 57.164 36.364 14.42 14.42 45.12 2.71
180 6983 3.916172 CCAACGAGAGAAACAATGCAATG 59.084 43.478 0.00 0.00 0.00 2.82
182 6985 2.948979 ACCAACGAGAGAAACAATGCAA 59.051 40.909 0.00 0.00 0.00 4.08
183 6986 2.290367 CACCAACGAGAGAAACAATGCA 59.710 45.455 0.00 0.00 0.00 3.96
184 6987 2.290641 ACACCAACGAGAGAAACAATGC 59.709 45.455 0.00 0.00 0.00 3.56
187 6990 1.668751 GCACACCAACGAGAGAAACAA 59.331 47.619 0.00 0.00 0.00 2.83
195 7039 4.454948 TTGGAGCACACCAACGAG 57.545 55.556 6.05 0.00 43.79 4.18
280 7156 9.890629 TGAAATAGCATATAAGAGACAAACTGT 57.109 29.630 0.00 0.00 0.00 3.55
282 7158 9.331282 GGTGAAATAGCATATAAGAGACAAACT 57.669 33.333 0.00 0.00 0.00 2.66
283 7159 8.276325 CGGTGAAATAGCATATAAGAGACAAAC 58.724 37.037 0.00 0.00 0.00 2.93
284 7160 7.441157 CCGGTGAAATAGCATATAAGAGACAAA 59.559 37.037 0.00 0.00 0.00 2.83
285 7161 6.929049 CCGGTGAAATAGCATATAAGAGACAA 59.071 38.462 0.00 0.00 0.00 3.18
286 7162 6.041637 ACCGGTGAAATAGCATATAAGAGACA 59.958 38.462 6.12 0.00 0.00 3.41
287 7163 6.366332 CACCGGTGAAATAGCATATAAGAGAC 59.634 42.308 31.31 0.00 0.00 3.36
288 7164 6.041637 ACACCGGTGAAATAGCATATAAGAGA 59.958 38.462 40.21 0.00 0.00 3.10
289 7165 6.223852 ACACCGGTGAAATAGCATATAAGAG 58.776 40.000 40.21 8.01 0.00 2.85
290 7166 6.041637 AGACACCGGTGAAATAGCATATAAGA 59.958 38.462 40.21 0.00 0.00 2.10
291 7167 6.223852 AGACACCGGTGAAATAGCATATAAG 58.776 40.000 40.21 8.81 0.00 1.73
292 7168 6.169557 AGACACCGGTGAAATAGCATATAA 57.830 37.500 40.21 0.00 0.00 0.98
293 7169 5.801531 AGACACCGGTGAAATAGCATATA 57.198 39.130 40.21 0.00 0.00 0.86
294 7170 4.689612 AGACACCGGTGAAATAGCATAT 57.310 40.909 40.21 14.46 0.00 1.78
295 7171 4.481368 AAGACACCGGTGAAATAGCATA 57.519 40.909 40.21 0.00 0.00 3.14
296 7172 3.350219 AAGACACCGGTGAAATAGCAT 57.650 42.857 40.21 16.10 0.00 3.79
297 7173 2.851263 AAGACACCGGTGAAATAGCA 57.149 45.000 40.21 0.00 0.00 3.49
298 7174 3.071479 TGAAAGACACCGGTGAAATAGC 58.929 45.455 40.21 22.70 0.00 2.97
299 7175 5.880054 ATTGAAAGACACCGGTGAAATAG 57.120 39.130 40.21 14.10 0.00 1.73
300 7176 7.747155 TTAATTGAAAGACACCGGTGAAATA 57.253 32.000 40.21 17.08 0.00 1.40
301 7177 6.642707 TTAATTGAAAGACACCGGTGAAAT 57.357 33.333 40.21 19.44 0.00 2.17
302 7178 6.452494 TTTAATTGAAAGACACCGGTGAAA 57.548 33.333 40.21 21.86 0.00 2.69
303 7179 6.642707 ATTTAATTGAAAGACACCGGTGAA 57.357 33.333 40.21 22.90 0.00 3.18
304 7180 6.373216 CCTATTTAATTGAAAGACACCGGTGA 59.627 38.462 40.21 17.19 0.00 4.02
305 7181 6.373216 TCCTATTTAATTGAAAGACACCGGTG 59.627 38.462 32.83 32.83 0.00 4.94
306 7182 6.478129 TCCTATTTAATTGAAAGACACCGGT 58.522 36.000 0.00 0.00 0.00 5.28
307 7183 6.995511 TCCTATTTAATTGAAAGACACCGG 57.004 37.500 0.00 0.00 0.00 5.28
308 7184 9.855021 AAAATCCTATTTAATTGAAAGACACCG 57.145 29.630 0.00 0.00 0.00 4.94
321 7197 9.515226 CCCATAGATTCCGAAAATCCTATTTAA 57.485 33.333 6.82 0.00 0.00 1.52
322 7198 8.665906 ACCCATAGATTCCGAAAATCCTATTTA 58.334 33.333 6.82 0.00 0.00 1.40
323 7199 7.448469 CACCCATAGATTCCGAAAATCCTATTT 59.552 37.037 6.82 0.00 0.00 1.40
324 7200 6.942576 CACCCATAGATTCCGAAAATCCTATT 59.057 38.462 6.82 0.00 0.00 1.73
325 7201 6.476378 CACCCATAGATTCCGAAAATCCTAT 58.524 40.000 6.82 0.00 0.00 2.57
326 7202 5.744887 GCACCCATAGATTCCGAAAATCCTA 60.745 44.000 6.82 0.00 0.00 2.94
327 7203 4.718961 CACCCATAGATTCCGAAAATCCT 58.281 43.478 6.82 0.00 0.00 3.24
328 7204 3.253432 GCACCCATAGATTCCGAAAATCC 59.747 47.826 6.82 0.00 0.00 3.01
329 7205 4.137543 AGCACCCATAGATTCCGAAAATC 58.862 43.478 3.16 3.16 0.00 2.17
330 7206 4.170468 AGCACCCATAGATTCCGAAAAT 57.830 40.909 0.00 0.00 0.00 1.82
331 7207 3.644966 AGCACCCATAGATTCCGAAAA 57.355 42.857 0.00 0.00 0.00 2.29
332 7208 3.054728 TCAAGCACCCATAGATTCCGAAA 60.055 43.478 0.00 0.00 0.00 3.46
333 7209 2.503765 TCAAGCACCCATAGATTCCGAA 59.496 45.455 0.00 0.00 0.00 4.30
334 7210 2.103094 CTCAAGCACCCATAGATTCCGA 59.897 50.000 0.00 0.00 0.00 4.55
335 7211 2.487934 CTCAAGCACCCATAGATTCCG 58.512 52.381 0.00 0.00 0.00 4.30
336 7212 2.856222 CCTCAAGCACCCATAGATTCC 58.144 52.381 0.00 0.00 0.00 3.01
337 7213 2.225467 GCCTCAAGCACCCATAGATTC 58.775 52.381 0.00 0.00 42.97 2.52
338 7214 2.355010 GCCTCAAGCACCCATAGATT 57.645 50.000 0.00 0.00 42.97 2.40
356 7232 5.046910 TGTTACTCTTGCAAGCATTAAGC 57.953 39.130 21.99 11.99 46.19 3.09
357 7233 8.524870 AAATTGTTACTCTTGCAAGCATTAAG 57.475 30.769 21.99 15.22 0.00 1.85
358 7234 8.763356 CAAAATTGTTACTCTTGCAAGCATTAA 58.237 29.630 21.99 14.30 0.00 1.40
359 7235 7.384660 CCAAAATTGTTACTCTTGCAAGCATTA 59.615 33.333 21.99 9.21 0.00 1.90
360 7236 6.203338 CCAAAATTGTTACTCTTGCAAGCATT 59.797 34.615 21.99 10.20 0.00 3.56
361 7237 5.697633 CCAAAATTGTTACTCTTGCAAGCAT 59.302 36.000 21.99 13.85 0.00 3.79
362 7238 5.049167 CCAAAATTGTTACTCTTGCAAGCA 58.951 37.500 21.99 10.46 0.00 3.91
363 7239 4.084380 GCCAAAATTGTTACTCTTGCAAGC 60.084 41.667 21.99 7.80 0.00 4.01
364 7240 5.176223 CAGCCAAAATTGTTACTCTTGCAAG 59.824 40.000 20.81 20.81 0.00 4.01
365 7241 5.049167 CAGCCAAAATTGTTACTCTTGCAA 58.951 37.500 0.00 0.00 0.00 4.08
366 7242 4.619973 CAGCCAAAATTGTTACTCTTGCA 58.380 39.130 0.00 0.00 0.00 4.08
367 7243 3.429881 GCAGCCAAAATTGTTACTCTTGC 59.570 43.478 0.00 0.00 0.00 4.01
368 7244 4.619973 TGCAGCCAAAATTGTTACTCTTG 58.380 39.130 0.00 0.00 0.00 3.02
369 7245 4.797275 GCTGCAGCCAAAATTGTTACTCTT 60.797 41.667 28.76 0.00 34.31 2.85
370 7246 3.305608 GCTGCAGCCAAAATTGTTACTCT 60.306 43.478 28.76 0.00 34.31 3.24
371 7247 2.989166 GCTGCAGCCAAAATTGTTACTC 59.011 45.455 28.76 0.00 34.31 2.59
372 7248 2.629617 AGCTGCAGCCAAAATTGTTACT 59.370 40.909 34.39 8.85 43.38 2.24
373 7249 3.030668 AGCTGCAGCCAAAATTGTTAC 57.969 42.857 34.39 2.87 43.38 2.50
374 7250 3.391965 CAAGCTGCAGCCAAAATTGTTA 58.608 40.909 34.39 0.00 43.38 2.41
375 7251 2.215196 CAAGCTGCAGCCAAAATTGTT 58.785 42.857 34.39 16.94 43.38 2.83
376 7252 1.541670 CCAAGCTGCAGCCAAAATTGT 60.542 47.619 34.39 11.28 43.38 2.71
377 7253 1.153353 CCAAGCTGCAGCCAAAATTG 58.847 50.000 34.39 28.14 43.38 2.32
378 7254 1.050204 TCCAAGCTGCAGCCAAAATT 58.950 45.000 34.39 19.22 43.38 1.82
379 7255 1.050204 TTCCAAGCTGCAGCCAAAAT 58.950 45.000 34.39 13.75 43.38 1.82
380 7256 1.050204 ATTCCAAGCTGCAGCCAAAA 58.950 45.000 34.39 22.65 43.38 2.44
381 7257 1.921982 TATTCCAAGCTGCAGCCAAA 58.078 45.000 34.39 22.31 43.38 3.28
382 7258 1.752498 CATATTCCAAGCTGCAGCCAA 59.248 47.619 34.39 21.50 43.38 4.52
383 7259 1.341285 ACATATTCCAAGCTGCAGCCA 60.341 47.619 34.39 13.95 43.38 4.75
384 7260 1.396653 ACATATTCCAAGCTGCAGCC 58.603 50.000 34.39 17.05 43.38 4.85
385 7261 3.119388 TGAAACATATTCCAAGCTGCAGC 60.119 43.478 31.53 31.53 42.49 5.25
386 7262 4.707030 TGAAACATATTCCAAGCTGCAG 57.293 40.909 10.11 10.11 0.00 4.41
387 7263 5.412640 CAATGAAACATATTCCAAGCTGCA 58.587 37.500 1.02 0.00 0.00 4.41
388 7264 4.807304 CCAATGAAACATATTCCAAGCTGC 59.193 41.667 0.00 0.00 0.00 5.25
389 7265 4.807304 GCCAATGAAACATATTCCAAGCTG 59.193 41.667 0.00 0.00 0.00 4.24
390 7266 4.713321 AGCCAATGAAACATATTCCAAGCT 59.287 37.500 0.00 0.00 0.00 3.74
391 7267 4.807304 CAGCCAATGAAACATATTCCAAGC 59.193 41.667 0.00 0.00 0.00 4.01
392 7268 4.807304 GCAGCCAATGAAACATATTCCAAG 59.193 41.667 0.00 0.00 0.00 3.61
393 7269 4.222366 TGCAGCCAATGAAACATATTCCAA 59.778 37.500 0.00 0.00 0.00 3.53
394 7270 3.768215 TGCAGCCAATGAAACATATTCCA 59.232 39.130 0.00 0.00 0.00 3.53
395 7271 4.114794 GTGCAGCCAATGAAACATATTCC 58.885 43.478 0.00 0.00 0.00 3.01
396 7272 4.746729 TGTGCAGCCAATGAAACATATTC 58.253 39.130 0.00 0.00 0.00 1.75
397 7273 4.804868 TGTGCAGCCAATGAAACATATT 57.195 36.364 0.00 0.00 0.00 1.28
401 7277 3.510753 ACATATGTGCAGCCAATGAAACA 59.489 39.130 7.78 0.00 33.24 2.83
456 7332 3.118038 ACAGCTAACCAAACCTTCTGACA 60.118 43.478 0.00 0.00 0.00 3.58
492 7368 3.651803 TTGTTAATTTCTGGGTTGGCG 57.348 42.857 0.00 0.00 0.00 5.69
530 7406 4.279169 TCAGCAATATTTATTCCAGCTGGC 59.721 41.667 28.91 11.37 45.76 4.85
532 7408 5.533903 ACCTCAGCAATATTTATTCCAGCTG 59.466 40.000 6.78 6.78 46.76 4.24
533 7409 5.533903 CACCTCAGCAATATTTATTCCAGCT 59.466 40.000 0.00 0.00 0.00 4.24
534 7410 5.300286 ACACCTCAGCAATATTTATTCCAGC 59.700 40.000 0.00 0.00 0.00 4.85
535 7411 6.949352 ACACCTCAGCAATATTTATTCCAG 57.051 37.500 0.00 0.00 0.00 3.86
536 7412 6.405731 GCAACACCTCAGCAATATTTATTCCA 60.406 38.462 0.00 0.00 0.00 3.53
537 7413 5.979517 GCAACACCTCAGCAATATTTATTCC 59.020 40.000 0.00 0.00 0.00 3.01
538 7414 6.563422 TGCAACACCTCAGCAATATTTATTC 58.437 36.000 0.00 0.00 34.97 1.75
539 7415 6.528537 TGCAACACCTCAGCAATATTTATT 57.471 33.333 0.00 0.00 34.97 1.40
540 7416 6.406177 CCTTGCAACACCTCAGCAATATTTAT 60.406 38.462 0.00 0.00 45.94 1.40
541 7417 5.105797 CCTTGCAACACCTCAGCAATATTTA 60.106 40.000 0.00 0.00 45.94 1.40
542 7418 4.322198 CCTTGCAACACCTCAGCAATATTT 60.322 41.667 0.00 0.00 45.94 1.40
543 7419 3.194116 CCTTGCAACACCTCAGCAATATT 59.806 43.478 0.00 0.00 45.94 1.28
544 7420 2.756760 CCTTGCAACACCTCAGCAATAT 59.243 45.455 0.00 0.00 45.94 1.28
555 7431 1.687563 ACTACCCAACCTTGCAACAC 58.312 50.000 0.00 0.00 0.00 3.32
565 7441 6.870971 TTTATCACAAGTCAACTACCCAAC 57.129 37.500 0.00 0.00 0.00 3.77
592 7468 3.819368 TCAGCACTTCTTCAACCAATCA 58.181 40.909 0.00 0.00 0.00 2.57
611 7487 3.445096 TCAGATGAGTCGAGCTTTGATCA 59.555 43.478 0.00 0.00 0.00 2.92
669 7545 5.067805 GGGGCATCTTTATTTCTTACCACAG 59.932 44.000 0.00 0.00 0.00 3.66
757 7633 0.815734 GTAGTAGCTCAGCACCGGAA 59.184 55.000 9.46 0.00 0.00 4.30
811 7765 3.570550 CCTCGATTACCTTCTTCTCCGAT 59.429 47.826 0.00 0.00 0.00 4.18
812 7766 2.950309 CCTCGATTACCTTCTTCTCCGA 59.050 50.000 0.00 0.00 0.00 4.55
832 7786 2.615747 GGAGAAGTAGTGGTTGCTTCCC 60.616 54.545 0.00 0.00 46.21 3.97
903 7861 1.086067 GTGCGAGCAAGCTAGATGCA 61.086 55.000 19.28 4.97 46.22 3.96
906 7864 0.460987 GTGGTGCGAGCAAGCTAGAT 60.461 55.000 6.36 0.00 38.13 1.98
940 7901 0.842030 ATCCCAGTTGCAGTCCAGGA 60.842 55.000 0.00 0.00 0.00 3.86
1245 8210 8.662141 GCCTCGTACTTGAACTCATTAAAAATA 58.338 33.333 0.00 0.00 0.00 1.40
1248 8213 5.119588 CGCCTCGTACTTGAACTCATTAAAA 59.880 40.000 0.00 0.00 0.00 1.52
1252 8217 2.607187 CGCCTCGTACTTGAACTCATT 58.393 47.619 0.00 0.00 0.00 2.57
1294 8259 0.393537 AGCTTGCTGTAGTGCCCATC 60.394 55.000 0.00 0.00 0.00 3.51
1321 8286 3.093814 TGGCGAAGGATCTTACTGTACA 58.906 45.455 0.00 0.00 0.00 2.90
1322 8287 3.445857 GTGGCGAAGGATCTTACTGTAC 58.554 50.000 0.00 0.00 0.00 2.90
1334 8299 2.983592 GGTTGTGGGTGGCGAAGG 60.984 66.667 0.00 0.00 0.00 3.46
1391 8356 1.829222 CCTCAATGGCCTGCAAGATTT 59.171 47.619 3.32 0.00 34.07 2.17
1432 8397 6.434028 TGCTGCTGATATTTAAAGTCAAAGGT 59.566 34.615 0.00 0.00 0.00 3.50
1670 8635 3.114693 GCAACTCGAAATGCTTCTGAG 57.885 47.619 13.30 0.00 39.46 3.35
1692 8657 4.578871 TGTCAGAGACACAAACCCATATG 58.421 43.478 0.00 0.00 37.67 1.78
1779 8777 0.895530 GGCCCTTCTTAAAAGGTGCC 59.104 55.000 19.97 19.97 42.37 5.01
1848 8846 3.543680 AGGTTCCGTACATCATCCAAG 57.456 47.619 0.00 0.00 0.00 3.61
1868 8866 5.105310 AGCTTTTTCCACTTATCGCTCTCTA 60.105 40.000 0.00 0.00 0.00 2.43
1955 8956 5.106317 ACTGTACCCATTATTTTTGCGACTG 60.106 40.000 0.00 0.00 0.00 3.51
2238 9242 2.306341 TGTAGCTGAGCTTGAGCATC 57.694 50.000 14.14 11.65 45.16 3.91
2241 9245 2.351111 GTCATTGTAGCTGAGCTTGAGC 59.649 50.000 14.14 10.04 40.44 4.26
2322 9326 4.250464 GGATCAGTTTGTCCACGTCAATA 58.750 43.478 0.00 0.00 34.57 1.90
2599 9609 1.699083 TGGAAGCCACTCAATCTGACA 59.301 47.619 0.00 0.00 0.00 3.58
2695 9711 4.769688 CACATAAGTGTCTGGATAGCCAA 58.230 43.478 0.00 0.00 41.44 4.52
2720 9736 6.480320 CCGAACTCCCATTTCTAGATAACAAG 59.520 42.308 0.00 0.00 0.00 3.16
2728 9744 2.678336 GCAACCGAACTCCCATTTCTAG 59.322 50.000 0.00 0.00 0.00 2.43
3000 10016 2.226437 CCTCAACTTCGGACAACAATGG 59.774 50.000 0.00 0.00 0.00 3.16
3584 18041 0.465460 TCCAAGCAGTGTTGTGTCCC 60.465 55.000 0.00 0.00 0.00 4.46
3779 18236 2.046285 CCATCAACCGGTGCTTCCC 61.046 63.158 8.52 0.00 0.00 3.97
3802 18259 1.439353 GCTGACCGTGCCATGGTATG 61.439 60.000 14.67 14.69 37.69 2.39
3806 18263 1.597797 AAATGCTGACCGTGCCATGG 61.598 55.000 7.63 7.63 0.00 3.66
3807 18264 0.179156 GAAATGCTGACCGTGCCATG 60.179 55.000 0.00 0.00 0.00 3.66
3897 18354 5.997385 TGAGGAAACATTAACTTTTCTCGC 58.003 37.500 9.64 4.75 33.10 5.03
3898 18355 6.073003 AGCTGAGGAAACATTAACTTTTCTCG 60.073 38.462 9.64 6.99 33.10 4.04
3972 18429 2.501610 CTAGGGAAGGTCCGCTGC 59.498 66.667 0.00 0.00 37.43 5.25
4006 18463 3.064820 GTCAGCTTTGGACAAAACTCGAA 59.935 43.478 0.00 0.00 35.36 3.71
4116 18573 8.099364 TCTTTAGTTTCAGATTGGTCAATGAC 57.901 34.615 4.51 4.51 0.00 3.06
4137 18594 4.712122 TTGCGTTTCTTCAAGGTTCTTT 57.288 36.364 0.00 0.00 0.00 2.52
4152 18609 1.000274 GCCTTCAAGGTTGATTGCGTT 60.000 47.619 5.03 0.00 37.80 4.84
4178 18650 5.761234 TCCACCACTTGTGTCAAACTATTAC 59.239 40.000 0.00 0.00 43.85 1.89
4223 18695 7.544622 CATAATTGCCATAGGGAAATCATCTG 58.455 38.462 0.00 0.00 42.00 2.90
4263 18735 1.000955 AGCTCAGTTACACCCGACTTG 59.999 52.381 0.00 0.00 0.00 3.16
4398 18873 1.680735 CCAACCAGTTGCTTGCAGTAA 59.319 47.619 4.96 0.00 39.16 2.24
4492 18967 7.412781 GCTTTCACACTGAACTATCTTGAGATG 60.413 40.741 3.79 0.00 35.89 2.90
4509 18984 3.003480 GACCTCTACCATGCTTTCACAC 58.997 50.000 0.00 0.00 0.00 3.82
4542 19017 1.063717 TCCATTTTCCTCAGGGATGCC 60.064 52.381 0.00 0.00 41.87 4.40
4576 19051 5.211973 ACTGAATATGGACCTGAGCTTAGA 58.788 41.667 7.16 0.00 0.00 2.10
4627 19108 1.502163 CGCCCTTGAAGATCCGATGC 61.502 60.000 0.00 0.00 0.00 3.91
4633 19114 1.139853 AGGTGATCGCCCTTGAAGATC 59.860 52.381 21.82 0.00 40.68 2.75
4668 19149 1.128724 CAGCTGACGACGATGACGAC 61.129 60.000 8.42 0.00 42.66 4.34
4669 19150 1.134694 CAGCTGACGACGATGACGA 59.865 57.895 8.42 0.00 42.66 4.20
4670 19151 0.096454 TACAGCTGACGACGATGACG 59.904 55.000 23.35 0.00 45.75 4.35
4724 19205 6.972490 TGACACCCCCGTATGTATATAGATA 58.028 40.000 0.00 0.00 0.00 1.98
4816 19297 2.030027 TCCACTGATCTCAACCCACT 57.970 50.000 0.00 0.00 0.00 4.00
4820 19301 4.478206 TGAGATTCCACTGATCTCAACC 57.522 45.455 12.86 0.00 45.26 3.77
4860 19341 4.697352 CCGATCTTGAGTTTCTCCAACAAT 59.303 41.667 0.00 0.00 37.93 2.71
5231 19726 6.884295 AGCTCAAGCAGTAGTATATCTAGAGG 59.116 42.308 4.59 0.00 45.16 3.69
5286 19786 7.651027 AAATCAAGACCCTCCTCATTTAATG 57.349 36.000 0.00 0.00 0.00 1.90
5361 19886 1.511850 TGATTCCTTCGTGTGTGCTG 58.488 50.000 0.00 0.00 0.00 4.41
5465 19990 3.380004 ACTGAAAAAGAATGCACCGAACA 59.620 39.130 0.00 0.00 0.00 3.18
5483 20008 4.960938 ACTAGCATCAAAGTTGACACTGA 58.039 39.130 0.00 0.00 40.49 3.41
5673 20198 7.093988 TGAGAAAATGGAGTCTTGAAACAACAA 60.094 33.333 0.00 0.00 0.00 2.83
5674 20199 6.376864 TGAGAAAATGGAGTCTTGAAACAACA 59.623 34.615 0.00 0.00 0.00 3.33
5675 20200 6.795399 TGAGAAAATGGAGTCTTGAAACAAC 58.205 36.000 0.00 0.00 0.00 3.32
5701 20226 3.509442 TCAAAGAGGGCCACATTTTCAT 58.491 40.909 6.18 0.00 0.00 2.57
5702 20227 2.956132 TCAAAGAGGGCCACATTTTCA 58.044 42.857 6.18 0.00 0.00 2.69
5703 20228 3.368739 CCATCAAAGAGGGCCACATTTTC 60.369 47.826 6.18 0.00 0.00 2.29
5771 20304 7.256286 GCCCATGCATATAATCAAATCTCTTC 58.744 38.462 0.00 0.00 37.47 2.87
5792 20325 1.588674 CAAAATATAGCGACGGCCCA 58.411 50.000 0.00 0.00 41.24 5.36


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

AutoCloner maintained by Alex Coulton.