Multiple sequence alignment - TraesCS5B01G286300

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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 TraesCS5B01G286300 chr5B 100.000 3789 0 0 1 3789 472067997 472071785 0.000000e+00 6998.0
1 TraesCS5B01G286300 chr5B 95.870 1380 55 1 1417 2794 471918565 471917186 0.000000e+00 2231.0
2 TraesCS5B01G286300 chr5B 97.867 375 8 0 995 1369 471919022 471918648 0.000000e+00 649.0
3 TraesCS5B01G286300 chr5A 93.874 2269 90 29 701 2927 494972275 494974536 0.000000e+00 3374.0
4 TraesCS5B01G286300 chr5A 92.475 1980 111 29 846 2794 494878580 494876608 0.000000e+00 2796.0
5 TraesCS5B01G286300 chr5A 88.411 604 43 25 43 630 81497695 81498287 0.000000e+00 702.0
6 TraesCS5B01G286300 chr5A 93.617 47 3 0 1 47 81497523 81497569 1.890000e-08 71.3
7 TraesCS5B01G286300 chr5D 92.531 2343 90 32 701 2971 391781796 391784125 0.000000e+00 3278.0
8 TraesCS5B01G286300 chr5D 91.990 824 46 6 2977 3789 42935859 42936673 0.000000e+00 1138.0
9 TraesCS5B01G286300 chr5D 97.647 255 6 0 2563 2817 391785078 391785332 4.490000e-119 438.0
10 TraesCS5B01G286300 chr5D 95.798 119 4 1 2807 2924 391786169 391786287 1.390000e-44 191.0
11 TraesCS5B01G286300 chr5D 95.082 61 3 0 2911 2971 391786302 391786362 3.120000e-16 97.1
12 TraesCS5B01G286300 chr3A 92.476 824 50 5 2977 3789 671356440 671357262 0.000000e+00 1168.0
13 TraesCS5B01G286300 chr1D 92.467 823 52 3 2977 3789 422174198 422175020 0.000000e+00 1168.0
14 TraesCS5B01G286300 chr1D 94.465 542 28 2 3248 3789 204268166 204268705 0.000000e+00 833.0
15 TraesCS5B01G286300 chr1D 89.388 245 25 1 2977 3221 204268018 204267775 1.320000e-79 307.0
16 TraesCS5B01G286300 chr7B 98.974 585 6 0 46 630 363244221 363244805 0.000000e+00 1048.0
17 TraesCS5B01G286300 chr7B 93.562 466 25 4 1553 2018 588068990 588068530 0.000000e+00 689.0
18 TraesCS5B01G286300 chr7B 90.909 484 38 2 2019 2496 588067202 588066719 0.000000e+00 645.0
19 TraesCS5B01G286300 chr7B 100.000 47 0 0 1 47 363244046 363244092 1.870000e-13 87.9
20 TraesCS5B01G286300 chr7B 95.745 47 2 0 1 47 714075590 714075544 4.060000e-10 76.8
21 TraesCS5B01G286300 chr7B 93.617 47 3 0 1 47 27295069 27295023 1.890000e-08 71.3
22 TraesCS5B01G286300 chr1B 98.974 585 6 0 46 630 40613614 40613030 0.000000e+00 1048.0
23 TraesCS5B01G286300 chr1B 100.000 47 0 0 1 47 40613789 40613743 1.870000e-13 87.9
24 TraesCS5B01G286300 chr3B 98.291 585 10 0 46 630 824001168 824000584 0.000000e+00 1026.0
25 TraesCS5B01G286300 chr4D 93.188 690 37 3 2977 3656 278225825 278225136 0.000000e+00 1005.0
26 TraesCS5B01G286300 chr4D 92.806 139 10 0 3651 3789 278216500 278216362 6.420000e-48 202.0
27 TraesCS5B01G286300 chr2D 95.246 568 27 0 3222 3789 546689479 546688912 0.000000e+00 900.0
28 TraesCS5B01G286300 chr2D 94.247 591 22 8 46 631 422195686 422195103 0.000000e+00 893.0
29 TraesCS5B01G286300 chr7A 91.356 590 36 11 48 630 47802731 47802150 0.000000e+00 793.0
30 TraesCS5B01G286300 chr7A 93.617 47 3 0 1 47 47802908 47802862 1.890000e-08 71.3
31 TraesCS5B01G286300 chrUn 92.377 551 32 7 46 591 36154701 36154156 0.000000e+00 776.0
32 TraesCS5B01G286300 chrUn 95.745 47 2 0 1 47 36154876 36154830 4.060000e-10 76.8
33 TraesCS5B01G286300 chr6A 89.655 580 40 18 46 616 3694100 3693532 0.000000e+00 721.0
34 TraesCS5B01G286300 chr6A 95.745 47 2 0 1 47 3694275 3694229 4.060000e-10 76.8
35 TraesCS5B01G286300 chr4A 88.576 604 42 25 43 630 586705308 586705900 0.000000e+00 708.0
36 TraesCS5B01G286300 chr4A 95.745 47 2 0 1 47 586705136 586705182 4.060000e-10 76.8
37 TraesCS5B01G286300 chr2B 94.667 75 3 1 3715 3789 561230706 561230633 8.600000e-22 115.0


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 TraesCS5B01G286300 chr5B 472067997 472071785 3788 False 6998.000 6998 100.0000 1 3789 1 chr5B.!!$F1 3788
1 TraesCS5B01G286300 chr5B 471917186 471919022 1836 True 1440.000 2231 96.8685 995 2794 2 chr5B.!!$R1 1799
2 TraesCS5B01G286300 chr5A 494972275 494974536 2261 False 3374.000 3374 93.8740 701 2927 1 chr5A.!!$F1 2226
3 TraesCS5B01G286300 chr5A 494876608 494878580 1972 True 2796.000 2796 92.4750 846 2794 1 chr5A.!!$R1 1948
4 TraesCS5B01G286300 chr5A 81497523 81498287 764 False 386.650 702 91.0140 1 630 2 chr5A.!!$F2 629
5 TraesCS5B01G286300 chr5D 42935859 42936673 814 False 1138.000 1138 91.9900 2977 3789 1 chr5D.!!$F1 812
6 TraesCS5B01G286300 chr5D 391781796 391786362 4566 False 1001.025 3278 95.2645 701 2971 4 chr5D.!!$F2 2270
7 TraesCS5B01G286300 chr3A 671356440 671357262 822 False 1168.000 1168 92.4760 2977 3789 1 chr3A.!!$F1 812
8 TraesCS5B01G286300 chr1D 422174198 422175020 822 False 1168.000 1168 92.4670 2977 3789 1 chr1D.!!$F2 812
9 TraesCS5B01G286300 chr1D 204268166 204268705 539 False 833.000 833 94.4650 3248 3789 1 chr1D.!!$F1 541
10 TraesCS5B01G286300 chr7B 588066719 588068990 2271 True 667.000 689 92.2355 1553 2496 2 chr7B.!!$R3 943
11 TraesCS5B01G286300 chr7B 363244046 363244805 759 False 567.950 1048 99.4870 1 630 2 chr7B.!!$F1 629
12 TraesCS5B01G286300 chr1B 40613030 40613789 759 True 567.950 1048 99.4870 1 630 2 chr1B.!!$R1 629
13 TraesCS5B01G286300 chr3B 824000584 824001168 584 True 1026.000 1026 98.2910 46 630 1 chr3B.!!$R1 584
14 TraesCS5B01G286300 chr4D 278225136 278225825 689 True 1005.000 1005 93.1880 2977 3656 1 chr4D.!!$R2 679
15 TraesCS5B01G286300 chr2D 546688912 546689479 567 True 900.000 900 95.2460 3222 3789 1 chr2D.!!$R2 567
16 TraesCS5B01G286300 chr2D 422195103 422195686 583 True 893.000 893 94.2470 46 631 1 chr2D.!!$R1 585
17 TraesCS5B01G286300 chr7A 47802150 47802908 758 True 432.150 793 92.4865 1 630 2 chr7A.!!$R1 629
18 TraesCS5B01G286300 chrUn 36154156 36154876 720 True 426.400 776 94.0610 1 591 2 chrUn.!!$R1 590
19 TraesCS5B01G286300 chr6A 3693532 3694275 743 True 398.900 721 92.7000 1 616 2 chr6A.!!$R1 615
20 TraesCS5B01G286300 chr4A 586705136 586705900 764 False 392.400 708 92.1605 1 630 2 chr4A.!!$F1 629

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
909 1064 0.465097 CATCCACACCAGGCCTGATC 60.465 60.0 34.91 0.0 0.00 2.92 F
1373 1559 0.238289 GTCGTCGACAGGGTACGAAA 59.762 55.0 20.28 0.0 46.08 3.46 F
2515 4121 0.249911 GTCACGACTTCTGGGTGCTT 60.250 55.0 0.00 0.0 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1955 2228 0.037232 GACGCAGCCCAGTAGTTTCT 60.037 55.0 0.00 0.0 0.00 2.52 R
2680 4286 0.038599 TGCCCATGAACACATGAGCT 59.961 50.0 15.19 0.0 43.06 4.09 R
3649 7513 0.981943 AAACCTCTCTAACACCCCGG 59.018 55.0 0.00 0.0 0.00 5.73 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
450 581 6.964086 AGATTAAGGGAGGGTGTTAGAGTTTA 59.036 38.462 0.00 0.00 0.00 2.01
630 780 4.515432 GAACGCTTTCGCCAATCTAATAC 58.485 43.478 0.00 0.00 39.84 1.89
631 781 3.793559 ACGCTTTCGCCAATCTAATACT 58.206 40.909 0.00 0.00 39.84 2.12
632 782 3.555956 ACGCTTTCGCCAATCTAATACTG 59.444 43.478 0.00 0.00 39.84 2.74
633 783 3.604772 CGCTTTCGCCAATCTAATACTGC 60.605 47.826 0.00 0.00 0.00 4.40
634 784 3.561725 GCTTTCGCCAATCTAATACTGCT 59.438 43.478 0.00 0.00 0.00 4.24
635 785 4.553547 GCTTTCGCCAATCTAATACTGCTG 60.554 45.833 0.00 0.00 0.00 4.41
636 786 4.400529 TTCGCCAATCTAATACTGCTGA 57.599 40.909 0.00 0.00 0.00 4.26
637 787 4.607293 TCGCCAATCTAATACTGCTGAT 57.393 40.909 0.00 0.00 0.00 2.90
638 788 4.960938 TCGCCAATCTAATACTGCTGATT 58.039 39.130 0.00 0.00 0.00 2.57
639 789 6.096673 TCGCCAATCTAATACTGCTGATTA 57.903 37.500 0.00 0.00 0.00 1.75
640 790 6.521162 TCGCCAATCTAATACTGCTGATTAA 58.479 36.000 0.00 0.00 0.00 1.40
641 791 7.161404 TCGCCAATCTAATACTGCTGATTAAT 58.839 34.615 0.00 0.00 0.00 1.40
642 792 7.661437 TCGCCAATCTAATACTGCTGATTAATT 59.339 33.333 0.00 0.00 0.00 1.40
643 793 7.959651 CGCCAATCTAATACTGCTGATTAATTC 59.040 37.037 0.00 0.00 0.00 2.17
644 794 9.007901 GCCAATCTAATACTGCTGATTAATTCT 57.992 33.333 0.00 0.00 0.00 2.40
672 822 8.000780 AGTCAATTAGCAAGGTTTAATCATCC 57.999 34.615 0.00 0.00 0.00 3.51
673 823 7.068716 AGTCAATTAGCAAGGTTTAATCATCCC 59.931 37.037 0.00 0.00 0.00 3.85
674 824 6.323739 TCAATTAGCAAGGTTTAATCATCCCC 59.676 38.462 0.00 0.00 0.00 4.81
675 825 3.756082 AGCAAGGTTTAATCATCCCCA 57.244 42.857 0.00 0.00 0.00 4.96
676 826 3.635591 AGCAAGGTTTAATCATCCCCAG 58.364 45.455 0.00 0.00 0.00 4.45
677 827 3.011708 AGCAAGGTTTAATCATCCCCAGT 59.988 43.478 0.00 0.00 0.00 4.00
678 828 3.381590 GCAAGGTTTAATCATCCCCAGTC 59.618 47.826 0.00 0.00 0.00 3.51
679 829 3.560636 AGGTTTAATCATCCCCAGTCG 57.439 47.619 0.00 0.00 0.00 4.18
680 830 2.844348 AGGTTTAATCATCCCCAGTCGT 59.156 45.455 0.00 0.00 0.00 4.34
681 831 3.118371 AGGTTTAATCATCCCCAGTCGTC 60.118 47.826 0.00 0.00 0.00 4.20
682 832 3.118371 GGTTTAATCATCCCCAGTCGTCT 60.118 47.826 0.00 0.00 0.00 4.18
683 833 4.120589 GTTTAATCATCCCCAGTCGTCTC 58.879 47.826 0.00 0.00 0.00 3.36
684 834 2.166907 AATCATCCCCAGTCGTCTCT 57.833 50.000 0.00 0.00 0.00 3.10
685 835 2.166907 ATCATCCCCAGTCGTCTCTT 57.833 50.000 0.00 0.00 0.00 2.85
686 836 1.938585 TCATCCCCAGTCGTCTCTTT 58.061 50.000 0.00 0.00 0.00 2.52
687 837 2.257207 TCATCCCCAGTCGTCTCTTTT 58.743 47.619 0.00 0.00 0.00 2.27
688 838 2.637872 TCATCCCCAGTCGTCTCTTTTT 59.362 45.455 0.00 0.00 0.00 1.94
689 839 2.543777 TCCCCAGTCGTCTCTTTTTG 57.456 50.000 0.00 0.00 0.00 2.44
690 840 1.766496 TCCCCAGTCGTCTCTTTTTGT 59.234 47.619 0.00 0.00 0.00 2.83
691 841 2.171870 TCCCCAGTCGTCTCTTTTTGTT 59.828 45.455 0.00 0.00 0.00 2.83
692 842 2.290641 CCCCAGTCGTCTCTTTTTGTTG 59.709 50.000 0.00 0.00 0.00 3.33
693 843 2.287009 CCCAGTCGTCTCTTTTTGTTGC 60.287 50.000 0.00 0.00 0.00 4.17
694 844 2.599848 CCAGTCGTCTCTTTTTGTTGCG 60.600 50.000 0.00 0.00 0.00 4.85
695 845 2.284150 CAGTCGTCTCTTTTTGTTGCGA 59.716 45.455 0.00 0.00 0.00 5.10
696 846 2.540101 AGTCGTCTCTTTTTGTTGCGAG 59.460 45.455 0.00 0.00 0.00 5.03
697 847 2.284417 GTCGTCTCTTTTTGTTGCGAGT 59.716 45.455 0.00 0.00 0.00 4.18
698 848 3.488310 GTCGTCTCTTTTTGTTGCGAGTA 59.512 43.478 0.00 0.00 0.00 2.59
699 849 4.026310 GTCGTCTCTTTTTGTTGCGAGTAA 60.026 41.667 0.00 0.00 0.00 2.24
894 1049 3.004315 ACGAAAACACACCAACATCATCC 59.996 43.478 0.00 0.00 0.00 3.51
899 1054 1.541147 CACACCAACATCATCCACACC 59.459 52.381 0.00 0.00 0.00 4.16
900 1055 1.144708 ACACCAACATCATCCACACCA 59.855 47.619 0.00 0.00 0.00 4.17
901 1056 1.814394 CACCAACATCATCCACACCAG 59.186 52.381 0.00 0.00 0.00 4.00
903 1058 0.813184 CAACATCATCCACACCAGGC 59.187 55.000 0.00 0.00 0.00 4.85
905 1060 1.210204 ACATCATCCACACCAGGCCT 61.210 55.000 0.00 0.00 0.00 5.19
906 1061 0.750546 CATCATCCACACCAGGCCTG 60.751 60.000 26.87 26.87 0.00 4.85
908 1063 0.915872 TCATCCACACCAGGCCTGAT 60.916 55.000 34.91 16.40 0.00 2.90
909 1064 0.465097 CATCCACACCAGGCCTGATC 60.465 60.000 34.91 0.00 0.00 2.92
910 1065 1.639635 ATCCACACCAGGCCTGATCC 61.640 60.000 34.91 0.00 0.00 3.36
911 1066 2.605607 CCACACCAGGCCTGATCCA 61.606 63.158 34.91 0.00 0.00 3.41
913 1068 1.847506 ACACCAGGCCTGATCCACA 60.848 57.895 34.91 0.00 0.00 4.17
914 1069 1.377725 CACCAGGCCTGATCCACAC 60.378 63.158 34.91 0.00 0.00 3.82
917 1072 1.376086 CAGGCCTGATCCACACACA 59.624 57.895 29.88 0.00 0.00 3.72
1207 1393 1.833606 ACGTTGGGTGACACCATCA 59.166 52.632 25.75 12.85 41.02 3.07
1369 1555 0.449388 ATTCGTCGTCGACAGGGTAC 59.551 55.000 24.13 4.33 46.03 3.34
1371 1557 2.382746 CGTCGTCGACAGGGTACGA 61.383 63.158 24.13 2.42 42.83 3.43
1372 1558 1.868997 GTCGTCGACAGGGTACGAA 59.131 57.895 20.28 0.00 46.08 3.85
1373 1559 0.238289 GTCGTCGACAGGGTACGAAA 59.762 55.000 20.28 0.00 46.08 3.46
1374 1560 0.950836 TCGTCGACAGGGTACGAAAA 59.049 50.000 17.16 0.00 42.18 2.29
1375 1561 1.336440 TCGTCGACAGGGTACGAAAAA 59.664 47.619 17.16 0.00 42.18 1.94
1376 1562 1.453148 CGTCGACAGGGTACGAAAAAC 59.547 52.381 17.16 0.00 40.12 2.43
1377 1563 2.747436 GTCGACAGGGTACGAAAAACT 58.253 47.619 11.55 0.00 40.12 2.66
1378 1564 3.609175 CGTCGACAGGGTACGAAAAACTA 60.609 47.826 17.16 0.00 40.12 2.24
1379 1565 3.670523 GTCGACAGGGTACGAAAAACTAC 59.329 47.826 11.55 0.00 40.12 2.73
1380 1566 3.317711 TCGACAGGGTACGAAAAACTACA 59.682 43.478 0.00 0.00 35.62 2.74
1381 1567 4.022068 TCGACAGGGTACGAAAAACTACAT 60.022 41.667 0.00 0.00 35.62 2.29
1382 1568 4.687483 CGACAGGGTACGAAAAACTACATT 59.313 41.667 0.00 0.00 0.00 2.71
1383 1569 5.863397 CGACAGGGTACGAAAAACTACATTA 59.137 40.000 0.00 0.00 0.00 1.90
1384 1570 6.183360 CGACAGGGTACGAAAAACTACATTAC 60.183 42.308 0.00 0.00 0.00 1.89
1385 1571 6.523840 ACAGGGTACGAAAAACTACATTACA 58.476 36.000 0.00 0.00 0.00 2.41
1386 1572 7.163441 ACAGGGTACGAAAAACTACATTACAT 58.837 34.615 0.00 0.00 0.00 2.29
1387 1573 8.313292 ACAGGGTACGAAAAACTACATTACATA 58.687 33.333 0.00 0.00 0.00 2.29
1388 1574 9.321562 CAGGGTACGAAAAACTACATTACATAT 57.678 33.333 0.00 0.00 0.00 1.78
1389 1575 9.321562 AGGGTACGAAAAACTACATTACATATG 57.678 33.333 0.00 0.00 0.00 1.78
1390 1576 9.316730 GGGTACGAAAAACTACATTACATATGA 57.683 33.333 10.38 0.00 0.00 2.15
1423 1611 9.918630 ACTCTCTTCATTCCAAAATTAAATGTG 57.081 29.630 0.00 0.00 33.22 3.21
1810 2083 2.036414 AGCCTCACCTCGCTCTCA 59.964 61.111 0.00 0.00 0.00 3.27
1828 2101 4.884247 TCTCATCGCTCTACTTCGAGATA 58.116 43.478 0.00 0.00 38.17 1.98
2461 4067 2.490903 GCAGAACTCCAACATGCTCAAT 59.509 45.455 0.00 0.00 34.10 2.57
2515 4121 0.249911 GTCACGACTTCTGGGTGCTT 60.250 55.000 0.00 0.00 0.00 3.91
2521 4127 1.304713 CTTCTGGGTGCTTGGCCAT 60.305 57.895 6.09 0.00 0.00 4.40
2524 4130 3.892104 CTGGGTGCTTGGCCATGGT 62.892 63.158 19.47 0.00 0.00 3.55
2683 4289 4.758692 CACTGTCACGTGGAAGCT 57.241 55.556 17.00 2.30 0.00 3.74
2933 6786 2.930682 GCTAAGGTCATCGGTTTGTCTC 59.069 50.000 0.00 0.00 0.00 3.36
2934 6787 3.616560 GCTAAGGTCATCGGTTTGTCTCA 60.617 47.826 0.00 0.00 0.00 3.27
2942 6795 5.411669 GTCATCGGTTTGTCTCATTAAGGTT 59.588 40.000 0.00 0.00 0.00 3.50
2971 6824 5.929992 GGGCATCAACAAATCATATTCATGG 59.070 40.000 0.00 0.00 32.61 3.66
2972 6825 5.929992 GGCATCAACAAATCATATTCATGGG 59.070 40.000 0.00 0.00 32.61 4.00
2973 6826 5.929992 GCATCAACAAATCATATTCATGGGG 59.070 40.000 0.00 0.00 32.61 4.96
2974 6827 6.463331 GCATCAACAAATCATATTCATGGGGT 60.463 38.462 0.00 0.00 32.61 4.95
2975 6828 6.713762 TCAACAAATCATATTCATGGGGTC 57.286 37.500 0.00 0.00 32.61 4.46
3024 6877 6.877322 GGTCCTTAGCGCTAAATATTATCCAA 59.123 38.462 28.44 6.02 0.00 3.53
3028 6881 8.946085 CCTTAGCGCTAAATATTATCCAAATGA 58.054 33.333 28.44 2.50 0.00 2.57
3053 6906 3.799281 TTGTTGAAAGCTGGTCCAAAG 57.201 42.857 0.00 0.00 0.00 2.77
3054 6907 2.031120 TGTTGAAAGCTGGTCCAAAGG 58.969 47.619 0.00 0.00 0.00 3.11
3056 6909 2.893489 GTTGAAAGCTGGTCCAAAGGAT 59.107 45.455 0.00 0.00 32.73 3.24
3079 6932 3.537580 GGTCGTCCTATACATGGCAAAA 58.462 45.455 0.00 0.00 0.00 2.44
3081 6934 4.024048 GGTCGTCCTATACATGGCAAAATG 60.024 45.833 0.00 0.00 0.00 2.32
3099 6952 1.079127 GTCGTGGCAGGCATACAGT 60.079 57.895 0.00 0.00 0.00 3.55
3111 6964 3.071479 GGCATACAGTCGTTCCAAAGAA 58.929 45.455 0.00 0.00 0.00 2.52
3137 6990 2.471815 TATGGAGAGTTGGATCCGGT 57.528 50.000 7.39 0.00 38.52 5.28
3138 6991 0.833287 ATGGAGAGTTGGATCCGGTG 59.167 55.000 7.39 0.00 38.52 4.94
3189 7042 0.036388 ACCAACTAGTGCATCACGGG 60.036 55.000 0.00 0.00 39.64 5.28
3224 7087 4.846367 CCAAGGGGGATGAATATACTGAGA 59.154 45.833 0.00 0.00 40.01 3.27
3244 7107 6.528321 TGAGAATCTCATTGATCCATACACC 58.472 40.000 9.18 0.00 35.39 4.16
3282 7145 4.214332 GGAGCTTCTTCGTGATTGTTTCTT 59.786 41.667 0.00 0.00 0.00 2.52
3325 7189 8.077836 GGATACTACAAATTCCTCTTCATTCG 57.922 38.462 0.00 0.00 0.00 3.34
3362 7226 6.024552 ACTTTGTCGCATGGAATTTTACAT 57.975 33.333 0.00 0.00 29.87 2.29
3454 7318 1.623542 GGCCGGACAGACAGGGTAAT 61.624 60.000 5.05 0.00 34.46 1.89
3493 7357 4.853924 TTGGAAAGAAGCATGGAAACTC 57.146 40.909 0.00 0.00 0.00 3.01
3502 7366 3.565307 AGCATGGAAACTCAAAGTTCCA 58.435 40.909 7.53 7.53 37.47 3.53
3613 7477 0.748005 AATGCCCACGGTGCACTATC 60.748 55.000 17.98 0.00 42.38 2.08
3647 7511 5.128919 ACATTCATCATACTCTCTTTGGGC 58.871 41.667 0.00 0.00 0.00 5.36
3648 7512 3.459232 TCATCATACTCTCTTTGGGCG 57.541 47.619 0.00 0.00 0.00 6.13
3649 7513 1.869767 CATCATACTCTCTTTGGGCGC 59.130 52.381 0.00 0.00 0.00 6.53
3650 7514 0.178068 TCATACTCTCTTTGGGCGCC 59.822 55.000 21.18 21.18 0.00 6.53
3651 7515 1.144057 ATACTCTCTTTGGGCGCCG 59.856 57.895 22.54 6.52 0.00 6.46
3652 7516 2.311688 ATACTCTCTTTGGGCGCCGG 62.312 60.000 22.54 10.64 0.00 6.13
3669 7541 1.066358 CCGGGGTGTTAGAGAGGTTTC 60.066 57.143 0.00 0.00 0.00 2.78
3694 7566 2.746904 TCATTTAGGCATGTTGGACACG 59.253 45.455 0.00 0.00 0.00 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 175 3.356529 AGCACTCCAGGAAATAAGGTG 57.643 47.619 0.00 0.00 0.00 4.00
591 741 3.563223 CGTTCCTACTCCCTCATAAGGA 58.437 50.000 0.00 0.00 46.67 3.36
597 747 1.549170 GAAAGCGTTCCTACTCCCTCA 59.451 52.381 0.30 0.00 0.00 3.86
646 796 8.470002 GGATGATTAAACCTTGCTAATTGACTT 58.530 33.333 0.00 0.00 0.00 3.01
647 797 7.068716 GGGATGATTAAACCTTGCTAATTGACT 59.931 37.037 0.00 0.00 0.00 3.41
648 798 7.203218 GGGATGATTAAACCTTGCTAATTGAC 58.797 38.462 0.00 0.00 0.00 3.18
649 799 6.323739 GGGGATGATTAAACCTTGCTAATTGA 59.676 38.462 0.00 0.00 0.00 2.57
650 800 6.098124 TGGGGATGATTAAACCTTGCTAATTG 59.902 38.462 0.00 0.00 0.00 2.32
651 801 6.201591 TGGGGATGATTAAACCTTGCTAATT 58.798 36.000 0.00 0.00 0.00 1.40
652 802 5.776358 TGGGGATGATTAAACCTTGCTAAT 58.224 37.500 0.00 0.00 0.00 1.73
653 803 5.199982 TGGGGATGATTAAACCTTGCTAA 57.800 39.130 0.00 0.00 0.00 3.09
654 804 4.229582 ACTGGGGATGATTAAACCTTGCTA 59.770 41.667 0.00 0.00 0.00 3.49
655 805 3.011708 ACTGGGGATGATTAAACCTTGCT 59.988 43.478 0.00 0.00 0.00 3.91
656 806 3.365472 ACTGGGGATGATTAAACCTTGC 58.635 45.455 0.00 0.00 0.00 4.01
657 807 3.627577 CGACTGGGGATGATTAAACCTTG 59.372 47.826 0.00 0.00 0.00 3.61
658 808 3.265995 ACGACTGGGGATGATTAAACCTT 59.734 43.478 0.00 0.00 0.00 3.50
659 809 2.844348 ACGACTGGGGATGATTAAACCT 59.156 45.455 0.00 0.00 0.00 3.50
660 810 3.118371 AGACGACTGGGGATGATTAAACC 60.118 47.826 0.00 0.00 0.00 3.27
661 811 4.120589 GAGACGACTGGGGATGATTAAAC 58.879 47.826 0.00 0.00 0.00 2.01
662 812 4.030913 AGAGACGACTGGGGATGATTAAA 58.969 43.478 0.00 0.00 0.00 1.52
663 813 3.643237 AGAGACGACTGGGGATGATTAA 58.357 45.455 0.00 0.00 0.00 1.40
664 814 3.314307 AGAGACGACTGGGGATGATTA 57.686 47.619 0.00 0.00 0.00 1.75
665 815 2.166907 AGAGACGACTGGGGATGATT 57.833 50.000 0.00 0.00 0.00 2.57
666 816 2.166907 AAGAGACGACTGGGGATGAT 57.833 50.000 0.00 0.00 0.00 2.45
667 817 1.938585 AAAGAGACGACTGGGGATGA 58.061 50.000 0.00 0.00 0.00 2.92
668 818 2.744202 CAAAAAGAGACGACTGGGGATG 59.256 50.000 0.00 0.00 0.00 3.51
669 819 2.372172 ACAAAAAGAGACGACTGGGGAT 59.628 45.455 0.00 0.00 0.00 3.85
670 820 1.766496 ACAAAAAGAGACGACTGGGGA 59.234 47.619 0.00 0.00 0.00 4.81
671 821 2.256117 ACAAAAAGAGACGACTGGGG 57.744 50.000 0.00 0.00 0.00 4.96
672 822 2.287009 GCAACAAAAAGAGACGACTGGG 60.287 50.000 0.00 0.00 0.00 4.45
673 823 2.599848 CGCAACAAAAAGAGACGACTGG 60.600 50.000 0.00 0.00 0.00 4.00
674 824 2.284150 TCGCAACAAAAAGAGACGACTG 59.716 45.455 0.00 0.00 0.00 3.51
675 825 2.540101 CTCGCAACAAAAAGAGACGACT 59.460 45.455 0.00 0.00 32.84 4.18
676 826 2.284417 ACTCGCAACAAAAAGAGACGAC 59.716 45.455 0.00 0.00 34.98 4.34
677 827 2.546778 ACTCGCAACAAAAAGAGACGA 58.453 42.857 0.00 0.00 34.98 4.20
678 828 4.201576 GTTACTCGCAACAAAAAGAGACG 58.798 43.478 0.00 0.00 34.98 4.18
679 829 5.151632 TGTTACTCGCAACAAAAAGAGAC 57.848 39.130 0.00 0.00 35.53 3.36
680 830 4.873827 ACTGTTACTCGCAACAAAAAGAGA 59.126 37.500 0.00 0.00 37.93 3.10
681 831 5.156804 ACTGTTACTCGCAACAAAAAGAG 57.843 39.130 0.00 0.00 37.93 2.85
682 832 4.260051 CGACTGTTACTCGCAACAAAAAGA 60.260 41.667 0.00 0.00 37.93 2.52
683 833 3.960002 CGACTGTTACTCGCAACAAAAAG 59.040 43.478 0.00 0.00 37.93 2.27
684 834 3.371591 ACGACTGTTACTCGCAACAAAAA 59.628 39.130 0.00 0.00 37.93 1.94
685 835 2.931325 ACGACTGTTACTCGCAACAAAA 59.069 40.909 0.00 0.00 37.93 2.44
686 836 2.536803 GACGACTGTTACTCGCAACAAA 59.463 45.455 0.00 0.00 37.93 2.83
687 837 2.121786 GACGACTGTTACTCGCAACAA 58.878 47.619 0.00 0.00 37.93 2.83
688 838 1.335810 AGACGACTGTTACTCGCAACA 59.664 47.619 0.00 0.00 36.94 3.33
689 839 1.977412 GAGACGACTGTTACTCGCAAC 59.023 52.381 0.00 0.00 34.34 4.17
690 840 1.399343 CGAGACGACTGTTACTCGCAA 60.399 52.381 14.95 0.00 43.71 4.85
691 841 0.165295 CGAGACGACTGTTACTCGCA 59.835 55.000 14.95 0.00 43.71 5.10
692 842 2.913887 CGAGACGACTGTTACTCGC 58.086 57.895 14.95 0.00 43.71 5.03
694 844 3.124976 AGCTAACGAGACGACTGTTACTC 59.875 47.826 0.00 0.00 0.00 2.59
695 845 3.072944 AGCTAACGAGACGACTGTTACT 58.927 45.455 0.00 1.00 0.00 2.24
696 846 3.468304 AGCTAACGAGACGACTGTTAC 57.532 47.619 0.00 0.00 0.00 2.50
697 847 4.248859 AGTAGCTAACGAGACGACTGTTA 58.751 43.478 0.00 1.51 0.00 2.41
698 848 3.072944 AGTAGCTAACGAGACGACTGTT 58.927 45.455 0.00 0.34 0.00 3.16
699 849 2.697654 AGTAGCTAACGAGACGACTGT 58.302 47.619 0.00 0.00 0.00 3.55
743 896 2.434331 CGGTCATGGTGGGTGGTT 59.566 61.111 0.00 0.00 0.00 3.67
744 897 2.852075 ACGGTCATGGTGGGTGGT 60.852 61.111 0.00 0.00 0.00 4.16
894 1049 1.377725 GTGGATCAGGCCTGGTGTG 60.378 63.158 32.23 7.87 0.00 3.82
899 1054 0.250858 TTGTGTGTGGATCAGGCCTG 60.251 55.000 27.87 27.87 0.00 4.85
900 1055 0.037303 CTTGTGTGTGGATCAGGCCT 59.963 55.000 0.00 0.00 0.00 5.19
901 1056 1.589716 GCTTGTGTGTGGATCAGGCC 61.590 60.000 0.00 0.00 0.00 5.19
903 1058 1.300971 CCGCTTGTGTGTGGATCAGG 61.301 60.000 0.00 0.00 39.82 3.86
905 1060 0.179032 AACCGCTTGTGTGTGGATCA 60.179 50.000 0.00 0.00 39.82 2.92
906 1061 1.732259 CTAACCGCTTGTGTGTGGATC 59.268 52.381 0.85 0.00 39.82 3.36
908 1063 0.882927 GCTAACCGCTTGTGTGTGGA 60.883 55.000 0.85 0.00 39.82 4.02
909 1064 1.574428 GCTAACCGCTTGTGTGTGG 59.426 57.895 0.00 0.00 42.85 4.17
1192 1378 0.690192 ACGATGATGGTGTCACCCAA 59.310 50.000 19.57 1.65 40.28 4.12
1388 1574 9.958180 TTTTGGAATGAAGAGAGTATATTGTCA 57.042 29.630 0.00 0.00 0.00 3.58
1409 1597 8.663911 ACACAGACAAAACACATTTAATTTTGG 58.336 29.630 13.15 2.28 44.12 3.28
1417 1605 6.128580 GCTGAAAACACAGACAAAACACATTT 60.129 34.615 0.00 0.00 39.94 2.32
1418 1606 5.348451 GCTGAAAACACAGACAAAACACATT 59.652 36.000 0.00 0.00 39.94 2.71
1428 1616 0.312102 GCCAGGCTGAAAACACAGAC 59.688 55.000 17.94 0.00 45.37 3.51
1430 1618 0.031178 GTGCCAGGCTGAAAACACAG 59.969 55.000 17.94 0.00 40.43 3.66
1492 1765 0.740868 CCACGATCATGCCGTTGAGT 60.741 55.000 9.69 0.00 38.29 3.41
1810 2083 4.250464 CCTCTATCTCGAAGTAGAGCGAT 58.750 47.826 20.46 6.53 41.55 4.58
1828 2101 1.351080 CCATCATGGAGTGGCCCTCT 61.351 60.000 17.51 8.90 40.96 3.69
1840 2113 1.524621 GGCCTCCACGACCATCATG 60.525 63.158 0.00 0.00 0.00 3.07
1885 2158 0.985490 AGATGAAGAGGCCCCTCACC 60.985 60.000 16.19 7.83 44.99 4.02
1955 2228 0.037232 GACGCAGCCCAGTAGTTTCT 60.037 55.000 0.00 0.00 0.00 2.52
2185 3785 1.484444 GGGTGTTGAGGAGGAGCAGT 61.484 60.000 0.00 0.00 0.00 4.40
2515 4121 1.072266 ACTTACCTTCACCATGGCCA 58.928 50.000 13.04 8.56 0.00 5.36
2521 4127 2.781174 AGGGTTGAACTTACCTTCACCA 59.219 45.455 0.00 0.00 35.92 4.17
2524 4130 2.488347 GGCAGGGTTGAACTTACCTTCA 60.488 50.000 0.00 0.00 35.92 3.02
2581 4187 1.131126 GGCACCGTGTTCTTCATGATG 59.869 52.381 0.00 0.00 35.23 3.07
2680 4286 0.038599 TGCCCATGAACACATGAGCT 59.961 50.000 15.19 0.00 43.06 4.09
2683 4289 1.476477 CCATGCCCATGAACACATGA 58.524 50.000 9.73 0.00 41.93 3.07
2933 6786 3.750371 TGATGCCCCGATAACCTTAATG 58.250 45.455 0.00 0.00 0.00 1.90
2934 6787 4.142038 GTTGATGCCCCGATAACCTTAAT 58.858 43.478 0.00 0.00 0.00 1.40
2942 6795 3.289407 TGATTTGTTGATGCCCCGATA 57.711 42.857 0.00 0.00 0.00 2.92
2972 6825 1.599797 CAAGGTGTCCGGGTTGACC 60.600 63.158 0.00 2.56 34.25 4.02
2973 6826 1.147600 ACAAGGTGTCCGGGTTGAC 59.852 57.895 0.00 0.00 35.77 3.18
2974 6827 1.147376 CACAAGGTGTCCGGGTTGA 59.853 57.895 0.00 0.00 0.00 3.18
2975 6828 1.153046 ACACAAGGTGTCCGGGTTG 60.153 57.895 0.00 0.66 43.92 3.77
2985 6838 1.056700 AGGACCTGAGCACACAAGGT 61.057 55.000 0.00 0.00 35.30 3.50
2987 6840 2.693069 CTAAGGACCTGAGCACACAAG 58.307 52.381 0.00 0.00 0.00 3.16
3024 6877 6.260714 GGACCAGCTTTCAACAAATTTTCATT 59.739 34.615 0.00 0.00 0.00 2.57
3028 6881 5.096443 TGGACCAGCTTTCAACAAATTTT 57.904 34.783 0.00 0.00 0.00 1.82
3036 6889 2.746279 TCCTTTGGACCAGCTTTCAA 57.254 45.000 0.00 0.00 0.00 2.69
3053 6906 2.233922 CCATGTATAGGACGACCCATCC 59.766 54.545 0.00 0.00 37.41 3.51
3054 6907 2.353803 GCCATGTATAGGACGACCCATC 60.354 54.545 0.00 0.00 37.41 3.51
3056 6909 1.045407 GCCATGTATAGGACGACCCA 58.955 55.000 0.00 0.00 37.41 4.51
3079 6932 0.462581 CTGTATGCCTGCCACGACAT 60.463 55.000 0.00 0.00 0.00 3.06
3081 6934 1.079127 ACTGTATGCCTGCCACGAC 60.079 57.895 0.00 0.00 0.00 4.34
3099 6952 7.069455 TCTCCATATACATCTTCTTTGGAACGA 59.931 37.037 0.00 0.00 31.81 3.85
3111 6964 5.420421 CGGATCCAACTCTCCATATACATCT 59.580 44.000 13.41 0.00 0.00 2.90
3189 7042 1.064685 CCCCCTTGGTGTGATTACCTC 60.065 57.143 0.00 0.00 41.43 3.85
3224 7087 4.645535 CCGGTGTATGGATCAATGAGATT 58.354 43.478 0.00 0.00 37.00 2.40
3244 7107 3.083349 TCCTCATCCCACCTGCCG 61.083 66.667 0.00 0.00 0.00 5.69
3282 7145 2.203408 TTTGCACATCCACCGGCA 60.203 55.556 0.00 0.00 0.00 5.69
3325 7189 1.940613 ACAAAGTCTTCGGTGAACTGC 59.059 47.619 0.00 0.00 0.00 4.40
3454 7318 9.973661 TCTTTCCAAACTCCATTTATCTGAATA 57.026 29.630 0.00 0.00 0.00 1.75
3493 7357 6.033966 GTGTTTGACTTTACCTGGAACTTTG 58.966 40.000 0.00 0.00 0.00 2.77
3502 7366 5.299279 CCATGTGAAGTGTTTGACTTTACCT 59.701 40.000 0.00 0.00 46.07 3.08
3613 7477 7.493971 AGAGTATGATGAATGTTTTCTTCTCCG 59.506 37.037 0.00 0.00 37.09 4.63
3647 7511 2.494918 CTCTCTAACACCCCGGCG 59.505 66.667 0.00 0.00 0.00 6.46
3648 7512 1.551019 AACCTCTCTAACACCCCGGC 61.551 60.000 0.00 0.00 0.00 6.13
3649 7513 0.981943 AAACCTCTCTAACACCCCGG 59.018 55.000 0.00 0.00 0.00 5.73
3650 7514 1.403780 CGAAACCTCTCTAACACCCCG 60.404 57.143 0.00 0.00 0.00 5.73
3651 7515 1.066358 CCGAAACCTCTCTAACACCCC 60.066 57.143 0.00 0.00 0.00 4.95
3652 7516 1.675116 GCCGAAACCTCTCTAACACCC 60.675 57.143 0.00 0.00 0.00 4.61
3653 7517 1.275573 AGCCGAAACCTCTCTAACACC 59.724 52.381 0.00 0.00 0.00 4.16
3654 7518 2.029290 TGAGCCGAAACCTCTCTAACAC 60.029 50.000 0.00 0.00 0.00 3.32
3669 7541 1.066002 CCAACATGCCTAAATGAGCCG 59.934 52.381 0.00 0.00 0.00 5.52
3694 7566 7.556844 TGTCTTCAGATATAGTTTTCTGGACC 58.443 38.462 2.09 0.00 39.84 4.46
3704 7576 5.144100 CCCAGACCTGTCTTCAGATATAGT 58.856 45.833 0.00 0.00 43.76 2.12
3770 7642 1.686110 CAGCTACCGGGAGTCCCTT 60.686 63.158 26.04 14.91 42.67 3.95


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

AutoCloner maintained by Alex Coulton.