Multiple sequence alignment - TraesCS3B01G573700

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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 TraesCS3B01G573700 chr3B 100.000 4899 0 0 1 4899 804236819 804241717 0.000000e+00 9047.0
1 TraesCS3B01G573700 chr3B 85.912 3102 371 53 838 3897 804129992 804133069 0.000000e+00 3247.0
2 TraesCS3B01G573700 chr3B 86.357 2001 250 17 1892 3880 804228291 804230280 0.000000e+00 2161.0
3 TraesCS3B01G573700 chr3B 85.322 2037 266 25 1862 3876 804170646 804172671 0.000000e+00 2074.0
4 TraesCS3B01G573700 chr3B 86.495 970 115 7 866 1821 804167822 804168789 0.000000e+00 1051.0
5 TraesCS3B01G573700 chr3A 93.449 3984 225 22 560 4526 727469076 727473040 0.000000e+00 5879.0
6 TraesCS3B01G573700 chr3A 87.089 2494 280 30 912 3383 727397545 727400018 0.000000e+00 2784.0
7 TraesCS3B01G573700 chr3A 81.301 123 14 2 434 554 727468582 727468697 1.880000e-14 91.6
8 TraesCS3B01G573700 chr3D 94.561 3659 160 18 784 4422 597486582 597490221 0.000000e+00 5618.0
9 TraesCS3B01G573700 chr3D 85.765 1953 246 24 1935 3876 597295750 597297681 0.000000e+00 2037.0
10 TraesCS3B01G573700 chr3D 84.757 2060 273 26 1862 3897 597480264 597482306 0.000000e+00 2026.0
11 TraesCS3B01G573700 chr3D 85.816 1262 166 12 1902 3157 597409428 597410682 0.000000e+00 1327.0
12 TraesCS3B01G573700 chr3D 88.646 916 85 10 912 1821 597477568 597478470 0.000000e+00 1098.0
13 TraesCS3B01G573700 chr3D 86.961 905 113 5 904 1805 597407601 597408503 0.000000e+00 1013.0
14 TraesCS3B01G573700 chr3D 88.612 281 20 4 4613 4885 597490562 597490838 1.020000e-86 331.0
15 TraesCS3B01G573700 chr3D 83.523 352 22 15 8 332 597485905 597486247 3.710000e-76 296.0
16 TraesCS3B01G573700 chr3D 91.781 146 12 0 4420 4565 597490421 597490566 2.310000e-48 204.0
17 TraesCS3B01G573700 chr2A 93.926 3622 190 16 560 4167 605130188 605126583 0.000000e+00 5443.0
18 TraesCS3B01G573700 chr2A 86.515 2944 349 32 970 3886 605398590 605401512 0.000000e+00 3193.0
19 TraesCS3B01G573700 chr2A 81.103 979 154 21 2932 3897 605186530 605185570 0.000000e+00 754.0
20 TraesCS3B01G573700 chr2A 85.554 713 70 14 4187 4885 605125116 605124423 0.000000e+00 715.0
21 TraesCS3B01G573700 chr2A 81.656 785 120 16 3216 3995 605355066 605354301 8.950000e-177 630.0


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 TraesCS3B01G573700 chr3B 804236819 804241717 4898 False 9047.0 9047 100.000000 1 4899 1 chr3B.!!$F3 4898
1 TraesCS3B01G573700 chr3B 804129992 804133069 3077 False 3247.0 3247 85.912000 838 3897 1 chr3B.!!$F1 3059
2 TraesCS3B01G573700 chr3B 804228291 804230280 1989 False 2161.0 2161 86.357000 1892 3880 1 chr3B.!!$F2 1988
3 TraesCS3B01G573700 chr3B 804167822 804172671 4849 False 1562.5 2074 85.908500 866 3876 2 chr3B.!!$F4 3010
4 TraesCS3B01G573700 chr3A 727468582 727473040 4458 False 2985.3 5879 87.375000 434 4526 2 chr3A.!!$F2 4092
5 TraesCS3B01G573700 chr3A 727397545 727400018 2473 False 2784.0 2784 87.089000 912 3383 1 chr3A.!!$F1 2471
6 TraesCS3B01G573700 chr3D 597295750 597297681 1931 False 2037.0 2037 85.765000 1935 3876 1 chr3D.!!$F1 1941
7 TraesCS3B01G573700 chr3D 597477568 597490838 13270 False 1595.5 5618 88.646667 8 4885 6 chr3D.!!$F3 4877
8 TraesCS3B01G573700 chr3D 597407601 597410682 3081 False 1170.0 1327 86.388500 904 3157 2 chr3D.!!$F2 2253
9 TraesCS3B01G573700 chr2A 605398590 605401512 2922 False 3193.0 3193 86.515000 970 3886 1 chr2A.!!$F1 2916
10 TraesCS3B01G573700 chr2A 605124423 605130188 5765 True 3079.0 5443 89.740000 560 4885 2 chr2A.!!$R3 4325
11 TraesCS3B01G573700 chr2A 605185570 605186530 960 True 754.0 754 81.103000 2932 3897 1 chr2A.!!$R1 965
12 TraesCS3B01G573700 chr2A 605354301 605355066 765 True 630.0 630 81.656000 3216 3995 1 chr2A.!!$R2 779

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
419 8777 0.034670 AAGTCTGCATCCTTCCAGCC 60.035 55.000 0.00 0.00 0.00 4.85 F
823 9565 0.321564 TGGTCCTCCTTGTCAATGCG 60.322 55.000 0.00 0.00 34.23 4.73 F
830 9572 1.266718 TCCTTGTCAATGCGCTGAAAC 59.733 47.619 9.73 2.61 0.00 2.78 F
1092 9863 1.743252 GGAGGAGTTCGCCAAGCTG 60.743 63.158 0.00 0.00 35.24 4.24 F
2835 14285 2.226200 TGTCACAAGTGCGATCATTTGG 59.774 45.455 5.71 0.00 42.20 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1629 10400 4.669206 AAATGCACCACACTGAAATTCA 57.331 36.364 0.00 0.0 0.00 2.57 R
2490 13940 5.316987 GGCTTACCAACTCATGCCTATATT 58.683 41.667 0.00 0.0 37.58 1.28 R
2865 14315 6.429692 TCGAAGATACTTGAATTCTGCCAAAA 59.570 34.615 7.05 0.0 0.00 2.44 R
3095 14549 2.708216 TGCAGAGACAACAAACAGGA 57.292 45.000 0.00 0.0 0.00 3.86 R
4369 17312 0.107703 CCTTGGCGTGCCTCATCTTA 60.108 55.000 12.84 0.0 36.94 2.10 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 8367 1.427368 AGATCTCGGGCTGGATCTAGT 59.573 52.381 19.49 3.56 44.45 2.57
91 8423 2.602676 CGGGTGGATCTGGGTGGTT 61.603 63.158 0.00 0.00 0.00 3.67
92 8424 1.303282 GGGTGGATCTGGGTGGTTC 59.697 63.158 0.00 0.00 0.00 3.62
93 8425 1.078426 GGTGGATCTGGGTGGTTCG 60.078 63.158 0.00 0.00 0.00 3.95
112 8446 1.006832 GTGCCGCACGAGATTACATT 58.993 50.000 7.96 0.00 0.00 2.71
120 8454 2.609459 CACGAGATTACATTGCCAGTCC 59.391 50.000 0.00 0.00 0.00 3.85
124 8458 3.879892 GAGATTACATTGCCAGTCCCTTC 59.120 47.826 0.00 0.00 0.00 3.46
126 8460 1.271856 TACATTGCCAGTCCCTTCGA 58.728 50.000 0.00 0.00 0.00 3.71
135 8469 2.683933 TCCCTTCGAGTCCCAGCC 60.684 66.667 0.00 0.00 0.00 4.85
136 8470 3.003173 CCCTTCGAGTCCCAGCCA 61.003 66.667 0.00 0.00 0.00 4.75
156 8490 1.006688 GTCGCCGCCCACAAATTTT 60.007 52.632 0.00 0.00 0.00 1.82
158 8492 0.241481 TCGCCGCCCACAAATTTTAC 59.759 50.000 0.00 0.00 0.00 2.01
159 8493 0.734597 CGCCGCCCACAAATTTTACC 60.735 55.000 0.00 0.00 0.00 2.85
160 8494 0.390603 GCCGCCCACAAATTTTACCC 60.391 55.000 0.00 0.00 0.00 3.69
162 8496 0.109039 CGCCCACAAATTTTACCCGG 60.109 55.000 0.00 0.00 0.00 5.73
173 8530 1.247419 TTTACCCGGCCTGTTGCATG 61.247 55.000 0.00 0.00 43.89 4.06
184 8541 0.787787 TGTTGCATGAGCGTTCGTAC 59.212 50.000 0.00 0.00 46.23 3.67
186 8543 1.067693 TTGCATGAGCGTTCGTACTG 58.932 50.000 0.00 0.00 46.23 2.74
209 8566 2.546584 GCCTTTCTGAAGTTTTGCCCAG 60.547 50.000 0.00 0.00 0.00 4.45
224 8582 2.308570 TGCCCAGGTGTTAAGATGTGAT 59.691 45.455 0.00 0.00 0.00 3.06
225 8583 2.684881 GCCCAGGTGTTAAGATGTGATG 59.315 50.000 0.00 0.00 0.00 3.07
226 8584 3.622206 GCCCAGGTGTTAAGATGTGATGA 60.622 47.826 0.00 0.00 0.00 2.92
227 8585 3.941483 CCCAGGTGTTAAGATGTGATGAC 59.059 47.826 0.00 0.00 0.00 3.06
228 8586 4.565444 CCCAGGTGTTAAGATGTGATGACA 60.565 45.833 0.00 0.00 36.22 3.58
231 8589 5.579904 CAGGTGTTAAGATGTGATGACAGAG 59.420 44.000 0.00 0.00 34.87 3.35
232 8590 4.872691 GGTGTTAAGATGTGATGACAGAGG 59.127 45.833 0.00 0.00 34.87 3.69
233 8591 4.872691 GTGTTAAGATGTGATGACAGAGGG 59.127 45.833 0.00 0.00 34.87 4.30
234 8592 4.080919 TGTTAAGATGTGATGACAGAGGGG 60.081 45.833 0.00 0.00 34.87 4.79
235 8593 1.504912 AGATGTGATGACAGAGGGGG 58.495 55.000 0.00 0.00 34.87 5.40
236 8594 1.008815 AGATGTGATGACAGAGGGGGA 59.991 52.381 0.00 0.00 34.87 4.81
237 8595 1.839994 GATGTGATGACAGAGGGGGAA 59.160 52.381 0.00 0.00 34.87 3.97
238 8596 1.741028 TGTGATGACAGAGGGGGAAA 58.259 50.000 0.00 0.00 0.00 3.13
239 8597 2.061848 TGTGATGACAGAGGGGGAAAA 58.938 47.619 0.00 0.00 0.00 2.29
240 8598 2.445145 TGTGATGACAGAGGGGGAAAAA 59.555 45.455 0.00 0.00 0.00 1.94
302 8660 5.221204 GGTCTAATCCCTTGGAAGTAGTACG 60.221 48.000 0.00 0.00 34.34 3.67
304 8662 5.826737 TCTAATCCCTTGGAAGTAGTACGAG 59.173 44.000 0.00 0.00 34.34 4.18
326 8684 8.608102 CGAGTTATTTCGTCTCATCCATATAG 57.392 38.462 0.00 0.00 35.91 1.31
327 8685 8.237949 CGAGTTATTTCGTCTCATCCATATAGT 58.762 37.037 0.00 0.00 35.91 2.12
328 8686 9.562583 GAGTTATTTCGTCTCATCCATATAGTC 57.437 37.037 0.00 0.00 0.00 2.59
329 8687 8.524487 AGTTATTTCGTCTCATCCATATAGTCC 58.476 37.037 0.00 0.00 0.00 3.85
330 8688 6.918067 ATTTCGTCTCATCCATATAGTCCA 57.082 37.500 0.00 0.00 0.00 4.02
331 8689 6.724893 TTTCGTCTCATCCATATAGTCCAA 57.275 37.500 0.00 0.00 0.00 3.53
332 8690 6.724893 TTCGTCTCATCCATATAGTCCAAA 57.275 37.500 0.00 0.00 0.00 3.28
333 8691 6.724893 TCGTCTCATCCATATAGTCCAAAA 57.275 37.500 0.00 0.00 0.00 2.44
334 8692 7.119709 TCGTCTCATCCATATAGTCCAAAAA 57.880 36.000 0.00 0.00 0.00 1.94
335 8693 7.735917 TCGTCTCATCCATATAGTCCAAAAAT 58.264 34.615 0.00 0.00 0.00 1.82
336 8694 8.866093 TCGTCTCATCCATATAGTCCAAAAATA 58.134 33.333 0.00 0.00 0.00 1.40
337 8695 9.144747 CGTCTCATCCATATAGTCCAAAAATAG 57.855 37.037 0.00 0.00 0.00 1.73
338 8696 8.940952 GTCTCATCCATATAGTCCAAAAATAGC 58.059 37.037 0.00 0.00 0.00 2.97
339 8697 8.659527 TCTCATCCATATAGTCCAAAAATAGCA 58.340 33.333 0.00 0.00 0.00 3.49
340 8698 8.853077 TCATCCATATAGTCCAAAAATAGCAG 57.147 34.615 0.00 0.00 0.00 4.24
341 8699 7.391554 TCATCCATATAGTCCAAAAATAGCAGC 59.608 37.037 0.00 0.00 0.00 5.25
342 8700 6.841601 TCCATATAGTCCAAAAATAGCAGCT 58.158 36.000 0.00 0.00 0.00 4.24
344 8702 7.878127 TCCATATAGTCCAAAAATAGCAGCTAC 59.122 37.037 3.59 0.00 0.00 3.58
353 8711 6.459298 CCAAAAATAGCAGCTACTCCAATCAG 60.459 42.308 3.59 0.00 0.00 2.90
362 8720 4.081420 AGCTACTCCAATCAGAACGAACAT 60.081 41.667 0.00 0.00 0.00 2.71
365 8723 4.899502 ACTCCAATCAGAACGAACATTCT 58.100 39.130 0.00 0.00 39.60 2.40
368 8726 7.782049 ACTCCAATCAGAACGAACATTCTATA 58.218 34.615 0.00 0.00 36.78 1.31
369 8727 7.923344 ACTCCAATCAGAACGAACATTCTATAG 59.077 37.037 0.00 0.00 36.78 1.31
371 8729 7.921214 TCCAATCAGAACGAACATTCTATAGTC 59.079 37.037 0.00 0.00 36.78 2.59
372 8730 7.923344 CCAATCAGAACGAACATTCTATAGTCT 59.077 37.037 0.00 0.00 36.78 3.24
374 8732 7.625828 TCAGAACGAACATTCTATAGTCTCA 57.374 36.000 0.00 0.00 36.78 3.27
375 8733 8.226819 TCAGAACGAACATTCTATAGTCTCAT 57.773 34.615 0.00 0.00 36.78 2.90
377 8735 8.131731 CAGAACGAACATTCTATAGTCTCATGA 58.868 37.037 0.00 0.00 36.78 3.07
378 8736 8.855110 AGAACGAACATTCTATAGTCTCATGAT 58.145 33.333 0.00 0.00 37.16 2.45
381 8739 9.900710 ACGAACATTCTATAGTCTCATGATTAC 57.099 33.333 0.00 0.00 0.00 1.89
382 8740 9.899226 CGAACATTCTATAGTCTCATGATTACA 57.101 33.333 0.00 0.00 0.00 2.41
395 8753 9.387123 GTCTCATGATTACAAAACTGAAAACTC 57.613 33.333 0.00 0.00 0.00 3.01
397 8755 9.173939 CTCATGATTACAAAACTGAAAACTCAC 57.826 33.333 0.00 0.00 0.00 3.51
398 8756 8.681806 TCATGATTACAAAACTGAAAACTCACA 58.318 29.630 0.00 0.00 0.00 3.58
399 8757 9.467258 CATGATTACAAAACTGAAAACTCACAT 57.533 29.630 0.00 0.00 0.00 3.21
404 8762 9.997482 TTACAAAACTGAAAACTCACATAAGTC 57.003 29.630 0.00 0.00 0.00 3.01
405 8763 8.281212 ACAAAACTGAAAACTCACATAAGTCT 57.719 30.769 0.00 0.00 0.00 3.24
406 8764 8.184192 ACAAAACTGAAAACTCACATAAGTCTG 58.816 33.333 0.00 0.00 0.00 3.51
409 8767 6.000219 ACTGAAAACTCACATAAGTCTGCAT 59.000 36.000 0.00 0.00 0.00 3.96
410 8768 6.148480 ACTGAAAACTCACATAAGTCTGCATC 59.852 38.462 0.00 0.00 0.00 3.91
412 8770 4.833478 AACTCACATAAGTCTGCATCCT 57.167 40.909 0.00 0.00 0.00 3.24
414 8772 4.764172 ACTCACATAAGTCTGCATCCTTC 58.236 43.478 1.61 0.00 0.00 3.46
417 8775 3.875727 CACATAAGTCTGCATCCTTCCAG 59.124 47.826 1.61 0.00 0.00 3.86
418 8776 2.698855 TAAGTCTGCATCCTTCCAGC 57.301 50.000 1.61 0.00 0.00 4.85
419 8777 0.034670 AAGTCTGCATCCTTCCAGCC 60.035 55.000 0.00 0.00 0.00 4.85
420 8778 1.452833 GTCTGCATCCTTCCAGCCC 60.453 63.158 0.00 0.00 0.00 5.19
421 8779 2.123982 CTGCATCCTTCCAGCCCC 60.124 66.667 0.00 0.00 0.00 5.80
422 8780 2.614969 TGCATCCTTCCAGCCCCT 60.615 61.111 0.00 0.00 0.00 4.79
424 8782 2.922234 CATCCTTCCAGCCCCTCC 59.078 66.667 0.00 0.00 0.00 4.30
426 8784 1.085605 ATCCTTCCAGCCCCTCCTT 59.914 57.895 0.00 0.00 0.00 3.36
427 8785 0.553612 ATCCTTCCAGCCCCTCCTTT 60.554 55.000 0.00 0.00 0.00 3.11
429 8787 0.323816 CCTTCCAGCCCCTCCTTTTC 60.324 60.000 0.00 0.00 0.00 2.29
430 8788 0.405585 CTTCCAGCCCCTCCTTTTCA 59.594 55.000 0.00 0.00 0.00 2.69
431 8789 0.856982 TTCCAGCCCCTCCTTTTCAA 59.143 50.000 0.00 0.00 0.00 2.69
432 8790 0.856982 TCCAGCCCCTCCTTTTCAAA 59.143 50.000 0.00 0.00 0.00 2.69
443 8801 5.721480 CCCTCCTTTTCAAATAATCCCTTGT 59.279 40.000 0.00 0.00 0.00 3.16
450 8808 8.582657 TTTTCAAATAATCCCTTGTCGGAATA 57.417 30.769 0.00 0.00 34.93 1.75
454 8812 1.492764 ATCCCTTGTCGGAATACGGT 58.507 50.000 0.00 0.00 44.45 4.83
491 8851 5.520376 ACAAAACAGTTTGATCCTCAAGG 57.480 39.130 0.00 0.00 45.99 3.61
495 8855 6.736794 CAAAACAGTTTGATCCTCAAGGGAAG 60.737 42.308 0.00 0.00 45.99 3.46
496 8856 9.556446 CAAAACAGTTTGATCCTCAAGGGAAGG 62.556 44.444 0.00 0.00 45.99 3.46
525 8885 5.319043 TCAACTTGTAAGGGAAATCCAGT 57.681 39.130 1.22 0.00 38.24 4.00
528 8888 3.326880 ACTTGTAAGGGAAATCCAGTCGT 59.673 43.478 1.22 0.00 38.24 4.34
532 8892 3.502123 AAGGGAAATCCAGTCGTTTCA 57.498 42.857 1.22 0.00 36.34 2.69
542 8902 5.545658 TCCAGTCGTTTCATAATCAAAGC 57.454 39.130 0.00 0.00 0.00 3.51
556 8916 2.811410 TCAAAGCATGATTCAAGGGCT 58.189 42.857 0.00 5.36 36.13 5.19
575 9308 4.303282 GGCTTGCCGATTTTGTTAAAAGA 58.697 39.130 0.00 0.00 33.22 2.52
576 9309 4.149922 GGCTTGCCGATTTTGTTAAAAGAC 59.850 41.667 0.00 0.00 33.22 3.01
577 9310 4.742659 GCTTGCCGATTTTGTTAAAAGACA 59.257 37.500 0.00 0.00 33.22 3.41
580 9313 5.897050 TGCCGATTTTGTTAAAAGACACTT 58.103 33.333 0.00 0.00 33.22 3.16
581 9314 5.746245 TGCCGATTTTGTTAAAAGACACTTG 59.254 36.000 0.00 0.00 33.22 3.16
582 9315 5.974751 GCCGATTTTGTTAAAAGACACTTGA 59.025 36.000 0.00 0.00 33.22 3.02
583 9316 6.075046 GCCGATTTTGTTAAAAGACACTTGAC 60.075 38.462 0.00 0.00 33.22 3.18
596 9329 2.572104 ACACTTGACCCTATCAGGTTCC 59.428 50.000 0.00 0.00 44.90 3.62
609 9342 0.613777 AGGTTCCCTTAACAGGCTCG 59.386 55.000 0.00 0.00 40.08 5.03
633 9366 1.062525 CTGCGTAATTGCTTCCGGC 59.937 57.895 0.00 0.00 42.22 6.13
654 9387 5.215252 GCTTCTGCCATATAGTCAAGGTA 57.785 43.478 0.00 0.00 0.00 3.08
657 9390 6.295575 GCTTCTGCCATATAGTCAAGGTATCT 60.296 42.308 0.00 0.00 0.00 1.98
661 9394 9.326489 TCTGCCATATAGTCAAGGTATCTTATT 57.674 33.333 0.00 0.00 0.00 1.40
687 9421 4.985409 AGAAAGCGTCTAAAACTCTGTCTG 59.015 41.667 0.00 0.00 36.20 3.51
729 9463 9.595823 AAGACTGCGTATACTGTAATATTTTGT 57.404 29.630 0.56 0.00 0.00 2.83
757 9491 3.820557 CTTCAGTTTCAAAGTCTGGGGA 58.179 45.455 0.00 0.00 0.00 4.81
762 9496 4.159506 CAGTTTCAAAGTCTGGGGAAAACA 59.840 41.667 0.00 0.00 31.73 2.83
770 9504 1.691434 TCTGGGGAAAACATGGCAAAC 59.309 47.619 0.00 0.00 0.00 2.93
773 9507 1.270785 GGGGAAAACATGGCAAACAGG 60.271 52.381 0.00 0.00 36.81 4.00
814 9549 4.946160 TCCAAAATACATGGTCCTCCTT 57.054 40.909 0.00 0.00 39.09 3.36
823 9565 0.321564 TGGTCCTCCTTGTCAATGCG 60.322 55.000 0.00 0.00 34.23 4.73
830 9572 1.266718 TCCTTGTCAATGCGCTGAAAC 59.733 47.619 9.73 2.61 0.00 2.78
900 9643 1.829523 GCCCCATTTGCTTCTTGGCA 61.830 55.000 0.00 0.00 40.74 4.92
1092 9863 1.743252 GGAGGAGTTCGCCAAGCTG 60.743 63.158 0.00 0.00 35.24 4.24
1354 10125 2.824546 GCCATCAGATCGCTGGGA 59.175 61.111 11.61 0.00 42.53 4.37
1544 10315 5.190528 TCAGTTGGCTAAAAGATGAGGAGAT 59.809 40.000 0.00 0.00 0.00 2.75
1547 10318 5.901413 TGGCTAAAAGATGAGGAGATGAT 57.099 39.130 0.00 0.00 0.00 2.45
1689 10462 5.488262 AGCCAAATATGCCAAAACTTCTT 57.512 34.783 0.00 0.00 0.00 2.52
1756 10529 7.272244 TGACTGTGAGTTAAATGTTCTTCTCA 58.728 34.615 0.00 0.00 0.00 3.27
1844 10619 8.354426 GTTTAGATGTCCCTCTGATAGTTAGAC 58.646 40.741 0.00 0.00 0.00 2.59
2237 13687 2.828520 TGTCCAGGTCAACTCAGAGATC 59.171 50.000 3.79 0.00 0.00 2.75
2490 13940 4.771114 TGTTTCTGGAGGACTCTGAAAA 57.229 40.909 16.22 6.23 35.60 2.29
2835 14285 2.226200 TGTCACAAGTGCGATCATTTGG 59.774 45.455 5.71 0.00 42.20 3.28
2865 14315 6.120507 GAGAGGCTCCATGAATATACCTTT 57.879 41.667 11.71 0.00 0.00 3.11
3095 14549 5.588845 TCCCAATGGATATTTTTCACCTGT 58.411 37.500 0.00 0.00 35.03 4.00
3097 14551 5.163416 CCCAATGGATATTTTTCACCTGTCC 60.163 44.000 0.00 0.00 0.00 4.02
3341 14798 1.204231 GTAACCTCGACTCCCTGAACC 59.796 57.143 0.00 0.00 0.00 3.62
3460 14926 0.698818 ACTGGATTGGGGAACTCCAC 59.301 55.000 0.00 0.00 40.76 4.02
3792 15276 2.725221 AGAATCTCTGTGGGGATTGC 57.275 50.000 0.00 0.00 33.05 3.56
3864 15349 2.288642 ATCAACATGCATCCCGGCCT 62.289 55.000 0.00 0.00 0.00 5.19
3935 15420 2.913578 TGGTCGTACCAGCCACGT 60.914 61.111 3.02 0.00 44.79 4.49
3963 15448 5.625197 GCAGCTGGTATGTTCAAATTTCCAT 60.625 40.000 17.12 0.00 0.00 3.41
4001 15486 4.742012 TCCAGTCTGTCTCTTAGTTTCCT 58.258 43.478 0.00 0.00 0.00 3.36
4007 15492 7.596995 CAGTCTGTCTCTTAGTTTCCTAACTTG 59.403 40.741 0.00 0.00 41.85 3.16
4045 15530 4.377021 CTCGCCATAATACTGCACCTTTA 58.623 43.478 0.00 0.00 0.00 1.85
4066 15551 9.313118 CCTTTATTTTTGTTGTAGCAAGACTTT 57.687 29.630 0.00 0.00 0.00 2.66
4084 15570 9.107177 CAAGACTTTGTAGATCTATGCAGATTT 57.893 33.333 5.57 0.00 41.78 2.17
4129 15616 3.973206 TTGAAAATCCGGAGCTCTACA 57.027 42.857 14.64 2.48 0.00 2.74
4132 15619 4.843728 TGAAAATCCGGAGCTCTACAAAT 58.156 39.130 14.64 0.00 0.00 2.32
4165 17101 7.177216 TCAACATTTGAGCAGTTATGATTTCCT 59.823 33.333 0.00 0.00 34.08 3.36
4176 17112 7.415206 GCAGTTATGATTTCCTTTATGAACGGT 60.415 37.037 0.00 0.00 0.00 4.83
4177 17113 8.458843 CAGTTATGATTTCCTTTATGAACGGTT 58.541 33.333 0.00 0.00 0.00 4.44
4194 17131 3.537793 GGTTGTTAAGCGAGTCTTTGG 57.462 47.619 0.00 0.00 36.25 3.28
4216 17154 0.452184 ATGTCTAGGTCGAGTGTGCG 59.548 55.000 0.00 0.00 0.00 5.34
4241 17179 8.075574 CGCAATAAAATTTGAGGTGCATATAGA 58.924 33.333 12.34 0.00 0.00 1.98
4260 17198 9.429359 CATATAGATTGAAGTAAAGTAGCCCTG 57.571 37.037 0.00 0.00 0.00 4.45
4285 17223 9.713713 TGTATGTTAGCACTGTTTGATTAACTA 57.286 29.630 0.00 0.00 37.64 2.24
4288 17226 7.221450 TGTTAGCACTGTTTGATTAACTAGGT 58.779 34.615 0.00 0.00 37.64 3.08
4296 17234 7.988599 ACTGTTTGATTAACTAGGTAACACACA 59.011 33.333 1.37 10.90 37.64 3.72
4297 17235 8.373048 TGTTTGATTAACTAGGTAACACACAG 57.627 34.615 1.37 0.00 37.64 3.66
4301 17239 8.370266 TGATTAACTAGGTAACACACAGGTAT 57.630 34.615 1.37 0.00 41.41 2.73
4315 17253 7.155328 ACACACAGGTATTTTAGAGAGTTCAG 58.845 38.462 0.00 0.00 0.00 3.02
4337 17277 5.236695 CAGCCATTCTCATAGACACTGATTG 59.763 44.000 0.00 0.00 0.00 2.67
4350 17293 0.745845 CTGATTGTCAGGGAAGGCGG 60.746 60.000 0.00 0.00 40.71 6.13
4358 17301 1.700739 TCAGGGAAGGCGGTTCTTTTA 59.299 47.619 0.00 0.00 35.25 1.52
4369 17312 4.278419 GGCGGTTCTTTTATATGGAGCAAT 59.722 41.667 0.00 0.00 0.00 3.56
4417 17360 5.630121 TGAGGTGTCTCCAACATTTATGTT 58.370 37.500 2.33 2.33 43.10 2.71
4443 17588 4.694760 TGTAGTGGATGGAGATGGATTG 57.305 45.455 0.00 0.00 0.00 2.67
4499 17644 4.199310 TCACTTTGCTTTGTTCTGCTAGT 58.801 39.130 0.00 0.00 0.00 2.57
4518 17663 6.128200 TGCTAGTTATCTCGACGAACTGTTTA 60.128 38.462 9.61 0.00 35.17 2.01
4519 17664 6.194325 GCTAGTTATCTCGACGAACTGTTTAC 59.806 42.308 9.61 0.00 35.17 2.01
4520 17665 6.005583 AGTTATCTCGACGAACTGTTTACA 57.994 37.500 0.00 0.00 32.25 2.41
4530 17675 5.172934 ACGAACTGTTTACACTTTGTCTCA 58.827 37.500 0.00 0.00 0.00 3.27
4568 17713 0.600057 GCTTTGCTTGGGTTCTCCTG 59.400 55.000 0.00 0.00 36.20 3.86
4571 17716 2.859165 TTGCTTGGGTTCTCCTGTAG 57.141 50.000 0.00 0.00 36.20 2.74
4573 17718 2.897350 TGCTTGGGTTCTCCTGTAGTA 58.103 47.619 0.00 0.00 36.20 1.82
4574 17719 2.832129 TGCTTGGGTTCTCCTGTAGTAG 59.168 50.000 0.00 0.00 36.20 2.57
4578 17723 2.225293 TGGGTTCTCCTGTAGTAGTGCT 60.225 50.000 0.00 0.00 36.20 4.40
4579 17724 2.832733 GGGTTCTCCTGTAGTAGTGCTT 59.167 50.000 0.00 0.00 0.00 3.91
4584 17729 5.330455 TCTCCTGTAGTAGTGCTTGATTG 57.670 43.478 0.00 0.00 0.00 2.67
4585 17730 4.160439 TCTCCTGTAGTAGTGCTTGATTGG 59.840 45.833 0.00 0.00 0.00 3.16
4586 17731 3.838317 TCCTGTAGTAGTGCTTGATTGGT 59.162 43.478 0.00 0.00 0.00 3.67
4587 17732 3.935203 CCTGTAGTAGTGCTTGATTGGTG 59.065 47.826 0.00 0.00 0.00 4.17
4588 17733 3.935203 CTGTAGTAGTGCTTGATTGGTGG 59.065 47.826 0.00 0.00 0.00 4.61
4589 17734 2.496899 AGTAGTGCTTGATTGGTGGG 57.503 50.000 0.00 0.00 0.00 4.61
4590 17735 0.811281 GTAGTGCTTGATTGGTGGGC 59.189 55.000 0.00 0.00 0.00 5.36
4591 17736 0.403655 TAGTGCTTGATTGGTGGGCA 59.596 50.000 0.00 0.00 0.00 5.36
4592 17737 0.896940 AGTGCTTGATTGGTGGGCAG 60.897 55.000 0.00 0.00 33.47 4.85
4593 17738 1.607178 TGCTTGATTGGTGGGCAGG 60.607 57.895 0.00 0.00 0.00 4.85
4594 17739 1.304381 GCTTGATTGGTGGGCAGGA 60.304 57.895 0.00 0.00 0.00 3.86
4595 17740 1.318158 GCTTGATTGGTGGGCAGGAG 61.318 60.000 0.00 0.00 0.00 3.69
4596 17741 0.329261 CTTGATTGGTGGGCAGGAGA 59.671 55.000 0.00 0.00 0.00 3.71
4597 17742 0.776810 TTGATTGGTGGGCAGGAGAA 59.223 50.000 0.00 0.00 0.00 2.87
4598 17743 0.329261 TGATTGGTGGGCAGGAGAAG 59.671 55.000 0.00 0.00 0.00 2.85
4599 17744 1.000396 ATTGGTGGGCAGGAGAAGC 60.000 57.895 0.00 0.00 0.00 3.86
4650 17795 7.661127 TGTATATGTGTACGTTTGCTTCTTT 57.339 32.000 0.00 0.00 0.00 2.52
4675 17820 7.518161 TCATCAAACGTATTCAACTGAACATC 58.482 34.615 0.00 0.00 36.80 3.06
4680 17825 9.825972 CAAACGTATTCAACTGAACATCTATTT 57.174 29.630 0.00 0.00 36.80 1.40
4701 17846 9.334693 CTATTTCTTGTACTGTTTGCATTTCTC 57.665 33.333 0.00 0.00 0.00 2.87
4706 17851 8.031864 TCTTGTACTGTTTGCATTTCTCAAAAA 58.968 29.630 0.00 0.00 35.49 1.94
4735 17882 9.970395 CAGTTTATATGTTGTATTTCATGGCAT 57.030 29.630 0.00 0.00 0.00 4.40
4742 17889 6.339730 TGTTGTATTTCATGGCATTGATTCC 58.660 36.000 0.00 0.00 0.00 3.01
4781 17930 8.708378 TGTTGGATCACTGATTGTTCTATCTAT 58.292 33.333 0.00 0.00 0.00 1.98
4786 17935 9.770097 GATCACTGATTGTTCTATCTATGGAAA 57.230 33.333 0.00 0.00 0.00 3.13
4807 17956 9.781834 TGGAAAGCATACTAAATAATTTCAACG 57.218 29.630 0.00 0.00 0.00 4.10
4813 17962 9.016623 GCATACTAAATAATTTCAACGGTTTCC 57.983 33.333 0.00 0.00 0.00 3.13
4818 17967 6.779115 AATAATTTCAACGGTTTCCTTTGC 57.221 33.333 0.00 0.00 33.55 3.68
4820 17969 3.810310 TTTCAACGGTTTCCTTTGCAT 57.190 38.095 0.00 0.00 33.55 3.96
4829 17978 4.578516 CGGTTTCCTTTGCATATGGACATA 59.421 41.667 4.56 0.00 30.25 2.29
4830 17979 5.241506 CGGTTTCCTTTGCATATGGACATAT 59.758 40.000 4.56 0.00 34.50 1.78
4840 17989 4.334759 GCATATGGACATATGGATGCTGTC 59.665 45.833 25.43 9.33 46.62 3.51
4874 18030 2.359900 CATGTTTCCTACAGGGAGCAC 58.640 52.381 0.00 0.00 46.01 4.40
4885 18041 1.143620 GGGAGCACTAGCAGAGCAG 59.856 63.158 7.91 0.00 45.49 4.24
4886 18042 1.326213 GGGAGCACTAGCAGAGCAGA 61.326 60.000 7.91 0.00 45.49 4.26
4887 18043 0.102844 GGAGCACTAGCAGAGCAGAG 59.897 60.000 7.91 0.00 45.49 3.35
4888 18044 0.528249 GAGCACTAGCAGAGCAGAGC 60.528 60.000 7.91 0.00 45.49 4.09
4889 18045 1.217511 GCACTAGCAGAGCAGAGCA 59.782 57.895 0.00 0.00 41.58 4.26
4890 18046 0.179078 GCACTAGCAGAGCAGAGCAT 60.179 55.000 0.00 0.00 41.58 3.79
4891 18047 1.573026 CACTAGCAGAGCAGAGCATG 58.427 55.000 0.00 0.00 0.00 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 5.725362 CCCGAGATCTAAAATCATACTCCC 58.275 45.833 0.00 0.00 0.00 4.30
3 4 5.046950 AGCCCGAGATCTAAAATCATACTCC 60.047 44.000 0.00 0.00 0.00 3.85
4 5 5.866633 CAGCCCGAGATCTAAAATCATACTC 59.133 44.000 0.00 0.00 0.00 2.59
6 7 4.932200 CCAGCCCGAGATCTAAAATCATAC 59.068 45.833 0.00 0.00 0.00 2.39
7 8 4.838423 TCCAGCCCGAGATCTAAAATCATA 59.162 41.667 0.00 0.00 0.00 2.15
11 12 3.906846 AGATCCAGCCCGAGATCTAAAAT 59.093 43.478 0.00 0.00 45.76 1.82
93 8425 1.006832 AATGTAATCTCGTGCGGCAC 58.993 50.000 22.78 22.78 0.00 5.01
99 8431 2.609459 GGACTGGCAATGTAATCTCGTG 59.391 50.000 0.00 0.00 0.00 4.35
104 8436 2.614057 CGAAGGGACTGGCAATGTAATC 59.386 50.000 0.00 0.00 40.86 1.75
112 8446 2.283529 GGACTCGAAGGGACTGGCA 61.284 63.158 0.00 0.00 40.86 4.92
120 8454 1.153289 CATGGCTGGGACTCGAAGG 60.153 63.158 0.00 0.00 0.00 3.46
124 8458 2.202797 CGACATGGCTGGGACTCG 60.203 66.667 0.00 0.00 0.00 4.18
126 8460 4.101448 GGCGACATGGCTGGGACT 62.101 66.667 0.00 0.00 40.72 3.85
135 8469 2.211619 AATTTGTGGGCGGCGACATG 62.212 55.000 26.39 0.00 0.00 3.21
136 8470 1.531739 AAATTTGTGGGCGGCGACAT 61.532 50.000 26.39 10.94 0.00 3.06
149 8483 2.682836 CAACAGGCCGGGTAAAATTTG 58.317 47.619 8.08 0.00 0.00 2.32
156 8490 2.045438 CATGCAACAGGCCGGGTA 60.045 61.111 8.08 0.00 43.89 3.69
158 8492 3.136123 CTCATGCAACAGGCCGGG 61.136 66.667 8.08 1.20 43.89 5.73
159 8493 3.818787 GCTCATGCAACAGGCCGG 61.819 66.667 0.00 0.00 43.89 6.13
160 8494 4.170062 CGCTCATGCAACAGGCCG 62.170 66.667 0.00 0.00 43.89 6.13
162 8496 1.154150 GAACGCTCATGCAACAGGC 60.154 57.895 0.00 0.00 45.13 4.85
184 8541 2.388121 CAAAACTTCAGAAAGGCGCAG 58.612 47.619 10.83 0.00 36.78 5.18
186 8543 1.131771 GCAAAACTTCAGAAAGGCGC 58.868 50.000 0.00 0.00 36.78 6.53
209 8566 4.872691 CCTCTGTCATCACATCTTAACACC 59.127 45.833 0.00 0.00 0.00 4.16
237 8595 5.137551 ACCAATGTACAGTAGCTGGTTTTT 58.862 37.500 0.33 0.00 33.37 1.94
238 8596 4.725490 ACCAATGTACAGTAGCTGGTTTT 58.275 39.130 0.33 0.00 33.37 2.43
239 8597 4.367039 ACCAATGTACAGTAGCTGGTTT 57.633 40.909 0.33 0.00 33.37 3.27
240 8598 4.081087 CCTACCAATGTACAGTAGCTGGTT 60.081 45.833 16.68 0.00 38.17 3.67
241 8599 3.451178 CCTACCAATGTACAGTAGCTGGT 59.549 47.826 12.92 14.61 40.26 4.00
242 8600 3.704566 TCCTACCAATGTACAGTAGCTGG 59.295 47.826 12.92 10.62 35.51 4.85
243 8601 5.303078 AGATCCTACCAATGTACAGTAGCTG 59.697 44.000 12.92 4.01 37.52 4.24
302 8660 9.562583 GACTATATGGATGAGACGAAATAACTC 57.437 37.037 0.00 0.00 0.00 3.01
304 8662 8.304596 TGGACTATATGGATGAGACGAAATAAC 58.695 37.037 0.00 0.00 0.00 1.89
324 8682 5.188948 TGGAGTAGCTGCTATTTTTGGACTA 59.811 40.000 13.20 0.00 0.00 2.59
325 8683 4.019321 TGGAGTAGCTGCTATTTTTGGACT 60.019 41.667 13.20 4.86 0.00 3.85
326 8684 4.261801 TGGAGTAGCTGCTATTTTTGGAC 58.738 43.478 13.20 0.00 0.00 4.02
327 8685 4.568072 TGGAGTAGCTGCTATTTTTGGA 57.432 40.909 13.20 0.00 0.00 3.53
328 8686 5.357878 TGATTGGAGTAGCTGCTATTTTTGG 59.642 40.000 13.20 0.00 0.00 3.28
329 8687 6.317140 TCTGATTGGAGTAGCTGCTATTTTTG 59.683 38.462 13.20 0.00 0.00 2.44
330 8688 6.418101 TCTGATTGGAGTAGCTGCTATTTTT 58.582 36.000 13.20 0.00 0.00 1.94
331 8689 5.994250 TCTGATTGGAGTAGCTGCTATTTT 58.006 37.500 13.20 1.93 0.00 1.82
332 8690 5.620738 TCTGATTGGAGTAGCTGCTATTT 57.379 39.130 13.20 4.53 0.00 1.40
333 8691 5.363939 GTTCTGATTGGAGTAGCTGCTATT 58.636 41.667 13.20 8.69 0.00 1.73
334 8692 4.500545 CGTTCTGATTGGAGTAGCTGCTAT 60.501 45.833 13.20 0.00 0.00 2.97
335 8693 3.181486 CGTTCTGATTGGAGTAGCTGCTA 60.181 47.826 3.57 5.02 0.00 3.49
336 8694 2.417924 CGTTCTGATTGGAGTAGCTGCT 60.418 50.000 3.08 3.08 0.00 4.24
337 8695 1.929836 CGTTCTGATTGGAGTAGCTGC 59.070 52.381 0.00 0.00 0.00 5.25
338 8696 3.510388 TCGTTCTGATTGGAGTAGCTG 57.490 47.619 0.00 0.00 0.00 4.24
339 8697 3.258372 TGTTCGTTCTGATTGGAGTAGCT 59.742 43.478 0.00 0.00 0.00 3.32
340 8698 3.585862 TGTTCGTTCTGATTGGAGTAGC 58.414 45.455 0.00 0.00 0.00 3.58
341 8699 6.102663 AGAATGTTCGTTCTGATTGGAGTAG 58.897 40.000 6.49 0.00 37.08 2.57
342 8700 6.037786 AGAATGTTCGTTCTGATTGGAGTA 57.962 37.500 6.49 0.00 37.08 2.59
344 8702 7.923344 ACTATAGAATGTTCGTTCTGATTGGAG 59.077 37.037 6.78 7.32 38.79 3.86
353 8711 9.469807 AATCATGAGACTATAGAATGTTCGTTC 57.530 33.333 6.78 0.00 0.00 3.95
368 8726 9.125026 AGTTTTCAGTTTTGTAATCATGAGACT 57.875 29.630 0.09 0.00 0.00 3.24
369 8727 9.387123 GAGTTTTCAGTTTTGTAATCATGAGAC 57.613 33.333 0.09 2.44 0.00 3.36
371 8729 9.173939 GTGAGTTTTCAGTTTTGTAATCATGAG 57.826 33.333 0.09 0.00 32.98 2.90
372 8730 8.681806 TGTGAGTTTTCAGTTTTGTAATCATGA 58.318 29.630 0.00 0.00 32.98 3.07
378 8736 9.997482 GACTTATGTGAGTTTTCAGTTTTGTAA 57.003 29.630 0.00 0.00 32.98 2.41
381 8739 7.166473 GCAGACTTATGTGAGTTTTCAGTTTTG 59.834 37.037 0.00 0.00 32.98 2.44
382 8740 7.148086 TGCAGACTTATGTGAGTTTTCAGTTTT 60.148 33.333 0.00 0.00 32.98 2.43
385 8743 5.368145 TGCAGACTTATGTGAGTTTTCAGT 58.632 37.500 0.00 0.00 32.98 3.41
386 8744 5.929697 TGCAGACTTATGTGAGTTTTCAG 57.070 39.130 0.00 0.00 32.98 3.02
387 8745 5.412594 GGATGCAGACTTATGTGAGTTTTCA 59.587 40.000 0.00 0.00 0.00 2.69
388 8746 5.645497 AGGATGCAGACTTATGTGAGTTTTC 59.355 40.000 0.00 0.00 0.00 2.29
390 8748 5.171339 AGGATGCAGACTTATGTGAGTTT 57.829 39.130 0.00 0.00 0.00 2.66
392 8750 4.383552 GGAAGGATGCAGACTTATGTGAGT 60.384 45.833 5.74 0.00 0.00 3.41
393 8751 4.125703 GGAAGGATGCAGACTTATGTGAG 58.874 47.826 5.74 0.00 0.00 3.51
395 8753 3.877559 TGGAAGGATGCAGACTTATGTG 58.122 45.455 5.74 0.00 0.00 3.21
402 8760 4.232310 GGCTGGAAGGATGCAGAC 57.768 61.111 1.28 0.00 46.47 3.51
404 8762 2.123982 GGGGCTGGAAGGATGCAG 60.124 66.667 0.00 0.00 46.85 4.41
405 8763 2.614969 AGGGGCTGGAAGGATGCA 60.615 61.111 0.00 0.00 0.00 3.96
406 8764 2.194326 GAGGGGCTGGAAGGATGC 59.806 66.667 0.00 0.00 0.00 3.91
409 8767 0.776080 AAAAGGAGGGGCTGGAAGGA 60.776 55.000 0.00 0.00 0.00 3.36
410 8768 0.323816 GAAAAGGAGGGGCTGGAAGG 60.324 60.000 0.00 0.00 0.00 3.46
412 8770 0.856982 TTGAAAAGGAGGGGCTGGAA 59.143 50.000 0.00 0.00 0.00 3.53
414 8772 1.942776 ATTTGAAAAGGAGGGGCTGG 58.057 50.000 0.00 0.00 0.00 4.85
417 8775 3.388024 GGGATTATTTGAAAAGGAGGGGC 59.612 47.826 0.00 0.00 0.00 5.80
418 8776 4.883759 AGGGATTATTTGAAAAGGAGGGG 58.116 43.478 0.00 0.00 0.00 4.79
419 8777 5.721480 ACAAGGGATTATTTGAAAAGGAGGG 59.279 40.000 0.00 0.00 0.00 4.30
420 8778 6.404734 CGACAAGGGATTATTTGAAAAGGAGG 60.405 42.308 0.00 0.00 0.00 4.30
421 8779 6.404734 CCGACAAGGGATTATTTGAAAAGGAG 60.405 42.308 0.00 0.00 35.97 3.69
422 8780 5.417580 CCGACAAGGGATTATTTGAAAAGGA 59.582 40.000 0.00 0.00 35.97 3.36
424 8782 6.509418 TCCGACAAGGGATTATTTGAAAAG 57.491 37.500 0.00 0.00 41.52 2.27
426 8784 7.201661 CGTATTCCGACAAGGGATTATTTGAAA 60.202 37.037 0.00 0.00 39.53 2.69
427 8785 6.259167 CGTATTCCGACAAGGGATTATTTGAA 59.741 38.462 0.00 0.00 39.53 2.69
429 8787 5.049680 CCGTATTCCGACAAGGGATTATTTG 60.050 44.000 0.00 0.00 39.53 2.32
430 8788 5.061179 CCGTATTCCGACAAGGGATTATTT 58.939 41.667 0.00 0.00 39.53 1.40
431 8789 4.102054 ACCGTATTCCGACAAGGGATTATT 59.898 41.667 0.00 0.00 39.53 1.40
432 8790 3.644738 ACCGTATTCCGACAAGGGATTAT 59.355 43.478 0.00 0.00 39.53 1.28
454 8812 0.895530 TTTGTTGGTTGGCGGTCAAA 59.104 45.000 0.00 0.00 37.08 2.69
461 8821 3.330267 TCAAACTGTTTTGTTGGTTGGC 58.670 40.909 2.41 0.00 42.51 4.52
497 8857 7.288852 TGGATTTCCCTTACAAGTTGATTTCAA 59.711 33.333 10.54 0.00 35.38 2.69
498 8858 6.780031 TGGATTTCCCTTACAAGTTGATTTCA 59.220 34.615 10.54 0.00 35.38 2.69
499 8859 7.039714 ACTGGATTTCCCTTACAAGTTGATTTC 60.040 37.037 10.54 0.00 35.38 2.17
500 8860 6.782494 ACTGGATTTCCCTTACAAGTTGATTT 59.218 34.615 10.54 0.00 35.38 2.17
501 8861 6.314917 ACTGGATTTCCCTTACAAGTTGATT 58.685 36.000 10.54 0.00 35.38 2.57
514 8874 5.588648 TGATTATGAAACGACTGGATTTCCC 59.411 40.000 0.00 0.00 34.52 3.97
516 8876 7.218963 GCTTTGATTATGAAACGACTGGATTTC 59.781 37.037 0.00 0.00 35.73 2.17
542 8902 0.101759 CGGCAAGCCCTTGAATCATG 59.898 55.000 11.96 0.00 42.93 3.07
554 8914 4.742659 TGTCTTTTAACAAAATCGGCAAGC 59.257 37.500 0.00 0.00 0.00 4.01
556 8916 5.897050 AGTGTCTTTTAACAAAATCGGCAA 58.103 33.333 0.00 0.00 0.00 4.52
609 9342 1.937546 AAGCAATTACGCAGCCAGGC 61.938 55.000 1.84 1.84 0.00 4.85
633 9366 7.238486 AGATACCTTGACTATATGGCAGAAG 57.762 40.000 0.00 0.00 33.66 2.85
654 9387 9.220767 AGTTTTAGACGCTTTCTTCAATAAGAT 57.779 29.630 0.00 0.00 41.36 2.40
657 9390 8.495949 CAGAGTTTTAGACGCTTTCTTCAATAA 58.504 33.333 0.00 0.00 36.14 1.40
661 9394 5.357257 ACAGAGTTTTAGACGCTTTCTTCA 58.643 37.500 0.00 0.00 36.14 3.02
669 9403 3.903360 AGACAGACAGAGTTTTAGACGC 58.097 45.455 0.00 0.00 0.00 5.19
687 9421 3.675698 CAGTCTTTACAAGAGGCGAAGAC 59.324 47.826 6.46 6.46 43.94 3.01
736 9470 3.820557 TCCCCAGACTTTGAAACTGAAG 58.179 45.455 0.00 0.00 34.07 3.02
744 9478 3.230134 CCATGTTTTCCCCAGACTTTGA 58.770 45.455 0.00 0.00 0.00 2.69
757 9491 4.571919 CATCATCCTGTTTGCCATGTTTT 58.428 39.130 0.00 0.00 0.00 2.43
770 9504 2.553904 GGTTGGATAGGGCATCATCCTG 60.554 54.545 11.17 0.00 41.21 3.86
773 9507 2.957402 TGGTTGGATAGGGCATCATC 57.043 50.000 0.00 0.00 35.11 2.92
814 9549 1.163420 ACGGTTTCAGCGCATTGACA 61.163 50.000 11.47 0.00 43.79 3.58
830 9572 5.432885 ACAACAGGTTTTATTTCTGACGG 57.567 39.130 0.00 0.00 33.19 4.79
877 9619 1.067354 CAAGAAGCAAATGGGGCAGAC 60.067 52.381 0.00 0.00 0.00 3.51
984 9746 0.911045 TCATCTCTGGCTGGGCAAGA 60.911 55.000 0.00 5.22 36.10 3.02
1092 9863 2.027653 CACCTCCTTCCTCAGGTTCTTC 60.028 54.545 0.00 0.00 41.41 2.87
1179 9950 4.036971 CAGCTAGCGGTCTGTTTATCTAGT 59.963 45.833 9.55 0.00 0.00 2.57
1182 9953 2.101582 CCAGCTAGCGGTCTGTTTATCT 59.898 50.000 13.96 0.00 0.00 1.98
1354 10125 5.003096 AGTTTCTTGATGTCCCCAATCTT 57.997 39.130 0.00 0.00 0.00 2.40
1464 10235 9.323985 ACAAGTTTAGATGATTCTTCATAGAGC 57.676 33.333 2.77 0.00 42.73 4.09
1547 10318 8.862325 ACCAATAACTGATACAATCTTCAACA 57.138 30.769 0.00 0.00 0.00 3.33
1629 10400 4.669206 AAATGCACCACACTGAAATTCA 57.331 36.364 0.00 0.00 0.00 2.57
1828 10603 7.899648 TTAAGGAAGTCTAACTATCAGAGGG 57.100 40.000 0.00 0.00 0.00 4.30
1863 12463 9.613428 ATTGATTCTCGTATGGAAGAACATAAA 57.387 29.630 0.00 0.00 35.29 1.40
2237 13687 7.226325 ACACTTCTTGAGAATCTCAACTGAAAG 59.774 37.037 20.61 20.12 44.27 2.62
2490 13940 5.316987 GGCTTACCAACTCATGCCTATATT 58.683 41.667 0.00 0.00 37.58 1.28
2865 14315 6.429692 TCGAAGATACTTGAATTCTGCCAAAA 59.570 34.615 7.05 0.00 0.00 2.44
3095 14549 2.708216 TGCAGAGACAACAAACAGGA 57.292 45.000 0.00 0.00 0.00 3.86
3097 14551 7.648908 TGAAAAATATGCAGAGACAACAAACAG 59.351 33.333 0.00 0.00 0.00 3.16
3341 14798 7.995488 AGGTATCCAAGAATCAGGTGAAAATAG 59.005 37.037 0.00 0.00 0.00 1.73
3792 15276 4.169508 CTGTTCAGATTCAGTACCACTCG 58.830 47.826 0.00 0.00 0.00 4.18
3864 15349 6.345298 TGGATATCGACTTTAATGTGAGCAA 58.655 36.000 0.00 0.00 0.00 3.91
3920 15405 2.126189 GGACGTGGCTGGTACGAC 60.126 66.667 0.00 0.00 43.82 4.34
3921 15406 2.598099 TGGACGTGGCTGGTACGA 60.598 61.111 0.00 0.00 43.82 3.43
3923 15408 2.434359 GCTGGACGTGGCTGGTAC 60.434 66.667 0.00 0.00 0.00 3.34
3924 15409 2.920384 TGCTGGACGTGGCTGGTA 60.920 61.111 0.00 0.00 0.00 3.25
3927 15412 4.694233 AGCTGCTGGACGTGGCTG 62.694 66.667 0.00 0.00 31.68 4.85
3928 15413 4.694233 CAGCTGCTGGACGTGGCT 62.694 66.667 21.71 0.00 0.00 4.75
3963 15448 2.043664 ACTGGAGTCAGGAGATTGGAGA 59.956 50.000 0.00 0.00 44.99 3.71
4001 15486 4.612088 GCTACAGCCCAAACTGCAAGTTA 61.612 47.826 2.60 0.00 46.43 2.24
4007 15492 1.639298 CGAGCTACAGCCCAAACTGC 61.639 60.000 0.00 0.00 41.60 4.40
4045 15530 8.682710 TCTACAAAGTCTTGCTACAACAAAAAT 58.317 29.630 0.00 0.00 35.84 1.82
4095 15581 8.690884 TCCGGATTTTCAATTTAATGAAGCATA 58.309 29.630 0.00 0.00 40.21 3.14
4110 15597 3.973206 TTGTAGAGCTCCGGATTTTCA 57.027 42.857 10.93 0.00 0.00 2.69
4151 15639 7.985476 ACCGTTCATAAAGGAAATCATAACTG 58.015 34.615 0.00 0.00 0.00 3.16
4165 17101 4.751098 ACTCGCTTAACAACCGTTCATAAA 59.249 37.500 0.00 0.00 36.52 1.40
4176 17112 5.298276 ACATTTCCAAAGACTCGCTTAACAA 59.702 36.000 0.00 0.00 35.24 2.83
4177 17113 4.819630 ACATTTCCAAAGACTCGCTTAACA 59.180 37.500 0.00 0.00 35.24 2.41
4185 17122 4.865365 CGACCTAGACATTTCCAAAGACTC 59.135 45.833 0.00 0.00 0.00 3.36
4194 17131 2.924290 GCACACTCGACCTAGACATTTC 59.076 50.000 0.00 0.00 0.00 2.17
4216 17154 9.918630 ATCTATATGCACCTCAAATTTTATTGC 57.081 29.630 0.00 0.00 0.00 3.56
4241 17179 6.958767 ACATACAGGGCTACTTTACTTCAAT 58.041 36.000 0.00 0.00 0.00 2.57
4285 17223 7.234988 ACTCTCTAAAATACCTGTGTGTTACCT 59.765 37.037 0.00 0.00 0.00 3.08
4288 17226 8.644216 TGAACTCTCTAAAATACCTGTGTGTTA 58.356 33.333 0.00 0.00 0.00 2.41
4296 17234 6.567602 ATGGCTGAACTCTCTAAAATACCT 57.432 37.500 0.00 0.00 0.00 3.08
4297 17235 7.051000 AGAATGGCTGAACTCTCTAAAATACC 58.949 38.462 0.00 0.00 0.00 2.73
4301 17239 6.114187 TGAGAATGGCTGAACTCTCTAAAA 57.886 37.500 0.00 0.00 36.18 1.52
4315 17253 5.121811 ACAATCAGTGTCTATGAGAATGGC 58.878 41.667 0.00 0.00 34.38 4.40
4337 17277 0.250770 AAAGAACCGCCTTCCCTGAC 60.251 55.000 0.00 0.00 0.00 3.51
4347 17287 4.893424 TTGCTCCATATAAAAGAACCGC 57.107 40.909 0.00 0.00 0.00 5.68
4358 17301 5.251764 GTGCCTCATCTTATTGCTCCATAT 58.748 41.667 0.00 0.00 0.00 1.78
4369 17312 0.107703 CCTTGGCGTGCCTCATCTTA 60.108 55.000 12.84 0.00 36.94 2.10
4417 17360 5.215845 TCCATCTCCATCCACTACAATACA 58.784 41.667 0.00 0.00 0.00 2.29
4443 17588 0.449388 CGACAGGGAGAAAATGCAGC 59.551 55.000 0.00 0.00 0.00 5.25
4469 17614 2.744202 ACAAAGCAAAGTGATAGCTCGG 59.256 45.455 0.00 0.00 37.70 4.63
4499 17644 6.005583 AGTGTAAACAGTTCGTCGAGATAA 57.994 37.500 0.00 0.00 0.00 1.75
4518 17663 6.566564 CGTGCATAATCTTTGAGACAAAGTGT 60.567 38.462 19.09 12.72 0.00 3.55
4519 17664 5.791974 CGTGCATAATCTTTGAGACAAAGTG 59.208 40.000 19.09 13.08 0.00 3.16
4520 17665 5.700832 TCGTGCATAATCTTTGAGACAAAGT 59.299 36.000 19.09 7.88 0.00 2.66
4530 17675 5.734855 AAGCGTAATCGTGCATAATCTTT 57.265 34.783 0.00 0.00 39.49 2.52
4568 17713 3.270877 CCCACCAATCAAGCACTACTAC 58.729 50.000 0.00 0.00 0.00 2.73
4571 17716 0.811281 GCCCACCAATCAAGCACTAC 59.189 55.000 0.00 0.00 0.00 2.73
4573 17718 0.896940 CTGCCCACCAATCAAGCACT 60.897 55.000 0.00 0.00 0.00 4.40
4574 17719 1.588082 CTGCCCACCAATCAAGCAC 59.412 57.895 0.00 0.00 0.00 4.40
4578 17723 0.776810 TTCTCCTGCCCACCAATCAA 59.223 50.000 0.00 0.00 0.00 2.57
4579 17724 0.329261 CTTCTCCTGCCCACCAATCA 59.671 55.000 0.00 0.00 0.00 2.57
4589 17734 1.148048 GATCCCTGGCTTCTCCTGC 59.852 63.158 0.00 0.00 35.26 4.85
4590 17735 1.138568 ATGATCCCTGGCTTCTCCTG 58.861 55.000 0.00 0.00 35.26 3.86
4591 17736 2.803285 TATGATCCCTGGCTTCTCCT 57.197 50.000 0.00 0.00 35.26 3.69
4592 17737 2.641815 ACATATGATCCCTGGCTTCTCC 59.358 50.000 10.38 0.00 0.00 3.71
4593 17738 4.041444 AGAACATATGATCCCTGGCTTCTC 59.959 45.833 10.38 0.00 0.00 2.87
4594 17739 3.979347 AGAACATATGATCCCTGGCTTCT 59.021 43.478 10.38 1.77 0.00 2.85
4595 17740 4.363991 AGAACATATGATCCCTGGCTTC 57.636 45.455 10.38 0.00 0.00 3.86
4596 17741 4.079558 ACAAGAACATATGATCCCTGGCTT 60.080 41.667 10.38 0.00 0.00 4.35
4597 17742 3.461085 ACAAGAACATATGATCCCTGGCT 59.539 43.478 10.38 0.00 0.00 4.75
4598 17743 3.825328 ACAAGAACATATGATCCCTGGC 58.175 45.455 10.38 0.00 0.00 4.85
4599 17744 7.503566 ACAATAACAAGAACATATGATCCCTGG 59.496 37.037 10.38 1.07 0.00 4.45
4600 17745 8.455903 ACAATAACAAGAACATATGATCCCTG 57.544 34.615 10.38 9.97 0.00 4.45
4601 17746 8.906867 CAACAATAACAAGAACATATGATCCCT 58.093 33.333 10.38 0.00 0.00 4.20
4602 17747 8.686334 ACAACAATAACAAGAACATATGATCCC 58.314 33.333 10.38 0.00 0.00 3.85
4630 17775 6.425417 TGATGAAAGAAGCAAACGTACACATA 59.575 34.615 0.00 0.00 0.00 2.29
4631 17776 5.238432 TGATGAAAGAAGCAAACGTACACAT 59.762 36.000 0.00 0.00 0.00 3.21
4650 17795 6.852858 TGTTCAGTTGAATACGTTTGATGA 57.147 33.333 0.00 0.00 36.33 2.92
4675 17820 9.334693 GAGAAATGCAAACAGTACAAGAAATAG 57.665 33.333 0.00 0.00 0.00 1.73
4680 17825 6.691754 TTGAGAAATGCAAACAGTACAAGA 57.308 33.333 0.00 0.00 0.00 3.02
4708 17853 9.183368 TGCCATGAAATACAACATATAAACTGA 57.817 29.630 0.00 0.00 0.00 3.41
4729 17876 5.818678 AATTGCATAGGAATCAATGCCAT 57.181 34.783 14.48 8.34 46.34 4.40
4735 17882 5.895636 ACACGAAATTGCATAGGAATCAA 57.104 34.783 0.00 0.00 0.00 2.57
4742 17889 5.030295 GTGATCCAACACGAAATTGCATAG 58.970 41.667 0.00 0.00 0.00 2.23
4751 17898 3.738982 ACAATCAGTGATCCAACACGAA 58.261 40.909 5.98 0.00 44.35 3.85
4781 17930 9.781834 CGTTGAAATTATTTAGTATGCTTTCCA 57.218 29.630 0.00 0.00 0.00 3.53
4786 17935 9.783256 GAAACCGTTGAAATTATTTAGTATGCT 57.217 29.630 0.00 0.00 0.00 3.79
4807 17956 6.449698 CATATGTCCATATGCAAAGGAAACC 58.550 40.000 12.87 0.00 42.66 3.27
4813 17962 5.417894 AGCATCCATATGTCCATATGCAAAG 59.582 40.000 17.90 10.40 45.72 2.77
4818 17967 5.742063 AGACAGCATCCATATGTCCATATG 58.258 41.667 16.82 16.82 46.31 1.78
4820 17969 6.153510 GTCTAGACAGCATCCATATGTCCATA 59.846 42.308 18.20 0.00 43.47 2.74
4840 17989 2.001812 AACATGCGTGCTCTGTCTAG 57.998 50.000 5.64 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.