Multiple sequence alignment - TraesCS6B01G409500

Loading Multiple Alignment...

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 TraesCS6B01G409500 chr6B 100.000 5830 0 0 1 5830 683644875 683639046 0.000000e+00 10767
1 TraesCS6B01G409500 chr6B 100.000 1562 0 0 6103 7664 683638773 683637212 0.000000e+00 2885
2 TraesCS6B01G409500 chr4A 98.950 5047 50 3 784 5830 215125733 215130776 0.000000e+00 9023
3 TraesCS6B01G409500 chr4A 98.976 1563 15 1 6103 7664 215130784 215132346 0.000000e+00 2796
4 TraesCS6B01G409500 chr5A 98.554 5047 69 3 784 5830 604816676 604811634 0.000000e+00 8913
5 TraesCS6B01G409500 chr5A 93.139 4256 221 40 1614 5830 555373235 555377458 0.000000e+00 6176
6 TraesCS6B01G409500 chr5A 98.784 1563 16 3 6103 7664 604811629 604810069 0.000000e+00 2778
7 TraesCS6B01G409500 chr5A 91.546 1585 89 23 6103 7660 555377463 555379029 0.000000e+00 2143
8 TraesCS6B01G409500 chr5A 84.781 1715 201 38 2072 3772 644504384 644506052 0.000000e+00 1666
9 TraesCS6B01G409500 chr5A 86.702 940 84 18 784 1689 555353910 555354842 0.000000e+00 1005
10 TraesCS6B01G409500 chr5A 85.812 874 79 22 784 1621 555358956 555359820 0.000000e+00 885
11 TraesCS6B01G409500 chr1D 94.194 3617 178 26 2071 5668 2860845 2864448 0.000000e+00 5487
12 TraesCS6B01G409500 chr1D 92.109 659 42 10 6103 6758 2873377 2874028 0.000000e+00 920
13 TraesCS6B01G409500 chr1D 86.168 882 77 19 784 1631 2859421 2860291 0.000000e+00 911
14 TraesCS6B01G409500 chr1D 91.607 560 29 9 1537 2086 2860155 2860706 0.000000e+00 758
15 TraesCS6B01G409500 chr1D 92.461 451 23 7 6754 7198 2880732 2881177 1.080000e-177 634
16 TraesCS6B01G409500 chr1D 89.916 476 30 11 7190 7664 2881228 2881686 1.420000e-166 597
17 TraesCS6B01G409500 chr1D 93.567 171 8 3 5661 5830 2873204 2873372 1.280000e-62 252
18 TraesCS6B01G409500 chr2D 92.033 3753 221 43 2113 5823 192299025 192295309 0.000000e+00 5203
19 TraesCS6B01G409500 chr2D 84.422 873 94 26 786 1631 192300450 192299593 0.000000e+00 821
20 TraesCS6B01G409500 chr2D 90.048 623 50 11 6105 6724 192295296 192294683 0.000000e+00 797
21 TraesCS6B01G409500 chr2D 91.335 427 25 10 6754 7173 192294692 192294271 2.400000e-159 573
22 TraesCS6B01G409500 chr2D 87.795 508 39 12 1537 2030 192299731 192299233 2.400000e-159 573
23 TraesCS6B01G409500 chr2D 86.667 480 38 17 7190 7664 192294120 192293662 6.860000e-140 508
24 TraesCS6B01G409500 chr3B 84.387 3798 455 84 2074 5823 523144943 523141236 0.000000e+00 3602
25 TraesCS6B01G409500 chr3B 76.453 2340 442 75 3386 5693 69639807 69637545 0.000000e+00 1168
26 TraesCS6B01G409500 chr3B 82.199 382 51 13 1006 1376 523145709 523145334 5.770000e-81 313
27 TraesCS6B01G409500 chr3B 78.378 222 35 10 7450 7664 523139914 523139699 1.740000e-26 132
28 TraesCS6B01G409500 chr3A 84.105 3800 461 82 2077 5830 516786864 516783162 0.000000e+00 3539
29 TraesCS6B01G409500 chr3A 77.356 1369 190 80 6103 7420 516783155 516781856 0.000000e+00 701
30 TraesCS6B01G409500 chr3A 78.829 222 34 10 7450 7664 516781871 516781656 3.730000e-28 137
31 TraesCS6B01G409500 chr6D 89.930 2433 209 31 2077 4493 439520142 439522554 0.000000e+00 3103
32 TraesCS6B01G409500 chr6D 89.609 1357 98 26 4491 5823 439541502 439542839 0.000000e+00 1685
33 TraesCS6B01G409500 chr6D 87.409 1104 96 28 6104 7198 439542856 439543925 0.000000e+00 1229
34 TraesCS6B01G409500 chr6D 83.518 813 81 31 784 1569 439518761 439519547 0.000000e+00 710
35 TraesCS6B01G409500 chr3D 84.501 2768 342 57 3091 5823 397186097 397183382 0.000000e+00 2654
36 TraesCS6B01G409500 chr3D 86.089 1028 119 16 2077 3095 397198480 397197468 0.000000e+00 1085
37 TraesCS6B01G409500 chr3D 79.730 222 32 10 7450 7664 397182065 397181850 1.720000e-31 148
38 TraesCS6B01G409500 chr2A 84.274 2162 274 39 2198 4311 571477648 571475505 0.000000e+00 2049
39 TraesCS6B01G409500 chr1A 81.055 2407 339 67 2167 4548 5813114 5810800 0.000000e+00 1810
40 TraesCS6B01G409500 chr1A 83.621 1563 194 49 4229 5757 496060131 496061665 0.000000e+00 1411
41 TraesCS6B01G409500 chr7A 83.878 1346 163 36 2077 3398 301248776 301247461 0.000000e+00 1234
42 TraesCS6B01G409500 chr5D 91.832 808 39 10 1 783 127878761 127877956 0.000000e+00 1101
43 TraesCS6B01G409500 chr7D 78.582 705 94 38 6103 6796 271055659 271055001 5.530000e-111 412
44 TraesCS6B01G409500 chr4B 87.857 280 25 4 426 697 502972702 502972424 3.450000e-83 320


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 TraesCS6B01G409500 chr6B 683637212 683644875 7663 True 6826.000000 10767 100.000000 1 7664 2 chr6B.!!$R1 7663
1 TraesCS6B01G409500 chr4A 215125733 215132346 6613 False 5909.500000 9023 98.963000 784 7664 2 chr4A.!!$F1 6880
2 TraesCS6B01G409500 chr5A 604810069 604816676 6607 True 5845.500000 8913 98.669000 784 7664 2 chr5A.!!$R1 6880
3 TraesCS6B01G409500 chr5A 555373235 555379029 5794 False 4159.500000 6176 92.342500 1614 7660 2 chr5A.!!$F4 6046
4 TraesCS6B01G409500 chr5A 644504384 644506052 1668 False 1666.000000 1666 84.781000 2072 3772 1 chr5A.!!$F3 1700
5 TraesCS6B01G409500 chr5A 555353910 555354842 932 False 1005.000000 1005 86.702000 784 1689 1 chr5A.!!$F1 905
6 TraesCS6B01G409500 chr5A 555358956 555359820 864 False 885.000000 885 85.812000 784 1621 1 chr5A.!!$F2 837
7 TraesCS6B01G409500 chr1D 2859421 2864448 5027 False 2385.333333 5487 90.656333 784 5668 3 chr1D.!!$F1 4884
8 TraesCS6B01G409500 chr1D 2880732 2881686 954 False 615.500000 634 91.188500 6754 7664 2 chr1D.!!$F3 910
9 TraesCS6B01G409500 chr1D 2873204 2874028 824 False 586.000000 920 92.838000 5661 6758 2 chr1D.!!$F2 1097
10 TraesCS6B01G409500 chr2D 192293662 192300450 6788 True 1412.500000 5203 88.716667 786 7664 6 chr2D.!!$R1 6878
11 TraesCS6B01G409500 chr3B 523139699 523145709 6010 True 1349.000000 3602 81.654667 1006 7664 3 chr3B.!!$R2 6658
12 TraesCS6B01G409500 chr3B 69637545 69639807 2262 True 1168.000000 1168 76.453000 3386 5693 1 chr3B.!!$R1 2307
13 TraesCS6B01G409500 chr3A 516781656 516786864 5208 True 1459.000000 3539 80.096667 2077 7664 3 chr3A.!!$R1 5587
14 TraesCS6B01G409500 chr6D 439518761 439522554 3793 False 1906.500000 3103 86.724000 784 4493 2 chr6D.!!$F1 3709
15 TraesCS6B01G409500 chr6D 439541502 439543925 2423 False 1457.000000 1685 88.509000 4491 7198 2 chr6D.!!$F2 2707
16 TraesCS6B01G409500 chr3D 397181850 397186097 4247 True 1401.000000 2654 82.115500 3091 7664 2 chr3D.!!$R2 4573
17 TraesCS6B01G409500 chr3D 397197468 397198480 1012 True 1085.000000 1085 86.089000 2077 3095 1 chr3D.!!$R1 1018
18 TraesCS6B01G409500 chr2A 571475505 571477648 2143 True 2049.000000 2049 84.274000 2198 4311 1 chr2A.!!$R1 2113
19 TraesCS6B01G409500 chr1A 5810800 5813114 2314 True 1810.000000 1810 81.055000 2167 4548 1 chr1A.!!$R1 2381
20 TraesCS6B01G409500 chr1A 496060131 496061665 1534 False 1411.000000 1411 83.621000 4229 5757 1 chr1A.!!$F1 1528
21 TraesCS6B01G409500 chr7A 301247461 301248776 1315 True 1234.000000 1234 83.878000 2077 3398 1 chr7A.!!$R1 1321
22 TraesCS6B01G409500 chr5D 127877956 127878761 805 True 1101.000000 1101 91.832000 1 783 1 chr5D.!!$R1 782
23 TraesCS6B01G409500 chr7D 271055001 271055659 658 True 412.000000 412 78.582000 6103 6796 1 chr7D.!!$R1 693

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
620 621 0.106217 ACAAAATAGGGGGATGCGGG 60.106 55.000 0.00 0.0 0.00 6.13 F
726 727 0.108424 CTCTGTTCCTTGAGCGGAGG 60.108 60.000 8.43 0.0 40.81 4.30 F
1001 1023 0.605319 CTCTCTCTAGCTCGGGCGAT 60.605 60.000 0.00 0.0 44.37 4.58 F
1377 1432 1.579429 GGGTTGGTGTGTTGATCGC 59.421 57.895 0.00 0.0 0.00 4.58 F
2626 3109 1.894466 CAACATCCCATCAGGCAACAA 59.106 47.619 0.00 0.0 41.41 2.83 F
3155 3659 2.327343 GCTGCCATCAACGAGCACA 61.327 57.895 0.00 0.0 32.06 4.57 F
3160 3664 2.816672 TGCCATCAACGAGCACAAATTA 59.183 40.909 0.00 0.0 0.00 1.40 F
4206 4775 3.192422 GTGTAATGGCAGCAATGTGGTTA 59.808 43.478 0.00 0.0 0.00 2.85 F
4713 5291 4.281688 AGATGGACCATTGAAAACACAAGG 59.718 41.667 8.78 0.0 33.22 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1829 1922 1.128692 CCGAAAAAGCAGAGTAAGGCG 59.871 52.381 0.00 0.00 34.54 5.52 R
2421 2870 2.338577 GGTGCAATACCTCAGCTCAT 57.661 50.000 0.00 0.00 46.51 2.90 R
2626 3109 4.336713 GTCTCTTGAAAAGCTCAACTGGTT 59.663 41.667 0.00 0.00 45.70 3.67 R
3160 3664 3.193782 AGCCCTTGGGAGAGAATAGTTT 58.806 45.455 10.36 0.00 0.00 2.66 R
3569 4085 0.099436 GTTTCGCAGCCATGTCATCC 59.901 55.000 0.00 0.00 0.00 3.51 R
4206 4775 1.692519 ACTAGTTCGTGTGCCCTTCTT 59.307 47.619 0.00 0.00 0.00 2.52 R
4246 4816 3.004002 TGCATTCTCAAAACACTCTGCAG 59.996 43.478 7.63 7.63 33.80 4.41 R
6206 6849 7.547370 AGTCTGTTTTGAAAGAAGATAGATCCG 59.453 37.037 0.00 0.00 0.00 4.18 R
7477 8368 9.030301 GTACTGAAAAATTATGTGCACTTTGTT 57.970 29.630 19.41 7.82 0.00 2.83 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
56 57 6.119536 GGGGAAAAACACTGGAAAAGAATTT 58.880 36.000 0.00 0.00 42.41 1.82
62 63 4.479158 ACACTGGAAAAGAATTTAGGGCA 58.521 39.130 0.00 0.00 37.28 5.36
81 82 0.976641 AGATCACCGTTGGAAGCAGA 59.023 50.000 0.00 0.00 0.00 4.26
82 83 1.556911 AGATCACCGTTGGAAGCAGAT 59.443 47.619 0.00 0.00 0.00 2.90
126 127 2.900671 GATGTTGCAGAGGGAGGGGC 62.901 65.000 0.00 0.00 0.00 5.80
226 227 1.860950 CCGTCATAGAACCATCGCTTG 59.139 52.381 0.00 0.00 0.00 4.01
239 240 3.637273 GCTTGTCCGGTCAGGGGT 61.637 66.667 12.40 0.00 41.52 4.95
354 355 3.866582 GGGAGGGGCATCGTGAGG 61.867 72.222 0.00 0.00 0.00 3.86
376 377 4.704833 GGGAGTGAGGCTTGCGCA 62.705 66.667 5.66 5.66 38.10 6.09
395 396 1.986632 ATGGCGGCATGGATGTGAGA 61.987 55.000 25.20 0.00 0.00 3.27
396 397 1.451927 GGCGGCATGGATGTGAGAA 60.452 57.895 3.07 0.00 0.00 2.87
400 401 0.548031 GGCATGGATGTGAGAAGGGA 59.452 55.000 0.00 0.00 0.00 4.20
474 475 2.126307 CCGTCAGGCTCACACTCG 60.126 66.667 0.00 0.00 0.00 4.18
493 494 3.541713 GGCGGCGGAGAAGAGGAT 61.542 66.667 9.78 0.00 0.00 3.24
575 576 4.415332 GCGACAGCGACGGAGGAA 62.415 66.667 0.00 0.00 40.82 3.36
576 577 2.202492 CGACAGCGACGGAGGAAG 60.202 66.667 0.00 0.00 40.82 3.46
577 578 2.687805 CGACAGCGACGGAGGAAGA 61.688 63.158 0.00 0.00 40.82 2.87
578 579 1.810532 GACAGCGACGGAGGAAGAT 59.189 57.895 0.00 0.00 0.00 2.40
579 580 0.526524 GACAGCGACGGAGGAAGATG 60.527 60.000 0.00 0.00 0.00 2.90
580 581 1.227089 CAGCGACGGAGGAAGATGG 60.227 63.158 0.00 0.00 0.00 3.51
581 582 2.107141 GCGACGGAGGAAGATGGG 59.893 66.667 0.00 0.00 0.00 4.00
582 583 2.107141 CGACGGAGGAAGATGGGC 59.893 66.667 0.00 0.00 0.00 5.36
583 584 2.107141 GACGGAGGAAGATGGGCG 59.893 66.667 0.00 0.00 0.00 6.13
584 585 3.447025 GACGGAGGAAGATGGGCGG 62.447 68.421 0.00 0.00 0.00 6.13
585 586 4.241555 CGGAGGAAGATGGGCGGG 62.242 72.222 0.00 0.00 0.00 6.13
586 587 3.878667 GGAGGAAGATGGGCGGGG 61.879 72.222 0.00 0.00 0.00 5.73
587 588 2.768344 GAGGAAGATGGGCGGGGA 60.768 66.667 0.00 0.00 0.00 4.81
588 589 2.770048 AGGAAGATGGGCGGGGAG 60.770 66.667 0.00 0.00 0.00 4.30
589 590 3.878667 GGAAGATGGGCGGGGAGG 61.879 72.222 0.00 0.00 0.00 4.30
590 591 4.570874 GAAGATGGGCGGGGAGGC 62.571 72.222 0.00 0.00 45.91 4.70
602 603 4.475135 GGAGGCGGGAGAGGCAAC 62.475 72.222 0.00 0.00 39.37 4.17
603 604 3.706373 GAGGCGGGAGAGGCAACA 61.706 66.667 0.00 0.00 39.37 3.33
604 605 3.249189 AGGCGGGAGAGGCAACAA 61.249 61.111 0.00 0.00 39.37 2.83
605 606 2.282180 GGCGGGAGAGGCAACAAA 60.282 61.111 0.00 0.00 41.41 2.83
606 607 1.901464 GGCGGGAGAGGCAACAAAA 60.901 57.895 0.00 0.00 41.41 2.44
607 608 1.250840 GGCGGGAGAGGCAACAAAAT 61.251 55.000 0.00 0.00 41.41 1.82
608 609 1.459450 GCGGGAGAGGCAACAAAATA 58.541 50.000 0.00 0.00 41.41 1.40
609 610 1.401905 GCGGGAGAGGCAACAAAATAG 59.598 52.381 0.00 0.00 41.41 1.73
610 611 2.017049 CGGGAGAGGCAACAAAATAGG 58.983 52.381 0.00 0.00 41.41 2.57
611 612 2.379005 GGGAGAGGCAACAAAATAGGG 58.621 52.381 0.00 0.00 41.41 3.53
612 613 2.379005 GGAGAGGCAACAAAATAGGGG 58.621 52.381 0.00 0.00 41.41 4.79
613 614 2.379005 GAGAGGCAACAAAATAGGGGG 58.621 52.381 0.00 0.00 41.41 5.40
614 615 2.000048 AGAGGCAACAAAATAGGGGGA 59.000 47.619 0.00 0.00 41.41 4.81
615 616 2.587307 AGAGGCAACAAAATAGGGGGAT 59.413 45.455 0.00 0.00 41.41 3.85
616 617 2.695147 GAGGCAACAAAATAGGGGGATG 59.305 50.000 0.00 0.00 41.41 3.51
617 618 1.138859 GGCAACAAAATAGGGGGATGC 59.861 52.381 0.00 0.00 0.00 3.91
618 619 1.202405 GCAACAAAATAGGGGGATGCG 60.202 52.381 0.00 0.00 0.00 4.73
619 620 1.408702 CAACAAAATAGGGGGATGCGG 59.591 52.381 0.00 0.00 0.00 5.69
620 621 0.106217 ACAAAATAGGGGGATGCGGG 60.106 55.000 0.00 0.00 0.00 6.13
621 622 0.184933 CAAAATAGGGGGATGCGGGA 59.815 55.000 0.00 0.00 0.00 5.14
622 623 0.478507 AAAATAGGGGGATGCGGGAG 59.521 55.000 0.00 0.00 0.00 4.30
623 624 1.427072 AAATAGGGGGATGCGGGAGG 61.427 60.000 0.00 0.00 0.00 4.30
669 670 3.917760 GGCGACGGAGGATGGAGG 61.918 72.222 0.00 0.00 0.00 4.30
670 671 4.593864 GCGACGGAGGATGGAGGC 62.594 72.222 0.00 0.00 0.00 4.70
671 672 4.271816 CGACGGAGGATGGAGGCG 62.272 72.222 0.00 0.00 0.00 5.52
672 673 3.917760 GACGGAGGATGGAGGCGG 61.918 72.222 0.00 0.00 0.00 6.13
673 674 4.458829 ACGGAGGATGGAGGCGGA 62.459 66.667 0.00 0.00 0.00 5.54
674 675 2.919856 CGGAGGATGGAGGCGGAT 60.920 66.667 0.00 0.00 0.00 4.18
675 676 2.746359 GGAGGATGGAGGCGGATG 59.254 66.667 0.00 0.00 0.00 3.51
676 677 2.746359 GAGGATGGAGGCGGATGG 59.254 66.667 0.00 0.00 0.00 3.51
677 678 2.851102 AGGATGGAGGCGGATGGG 60.851 66.667 0.00 0.00 0.00 4.00
678 679 3.958860 GGATGGAGGCGGATGGGG 61.959 72.222 0.00 0.00 0.00 4.96
679 680 3.958860 GATGGAGGCGGATGGGGG 61.959 72.222 0.00 0.00 0.00 5.40
689 690 4.962836 GATGGGGGCGGATGGCAG 62.963 72.222 0.00 0.00 46.16 4.85
694 695 4.864334 GGGCGGATGGCAGTGGAG 62.864 72.222 0.00 0.00 46.16 3.86
695 696 4.864334 GGCGGATGGCAGTGGAGG 62.864 72.222 0.00 0.00 46.16 4.30
716 717 4.379243 CGGCCGTGCTCTGTTCCT 62.379 66.667 19.50 0.00 0.00 3.36
717 718 2.032681 GGCCGTGCTCTGTTCCTT 59.967 61.111 0.00 0.00 0.00 3.36
718 719 2.328099 GGCCGTGCTCTGTTCCTTG 61.328 63.158 0.00 0.00 0.00 3.61
719 720 1.301716 GCCGTGCTCTGTTCCTTGA 60.302 57.895 0.00 0.00 0.00 3.02
720 721 1.294659 GCCGTGCTCTGTTCCTTGAG 61.295 60.000 0.00 0.00 0.00 3.02
723 724 3.882025 GCTCTGTTCCTTGAGCGG 58.118 61.111 0.00 0.00 44.72 5.52
724 725 1.293498 GCTCTGTTCCTTGAGCGGA 59.707 57.895 0.00 0.00 44.72 5.54
725 726 0.739112 GCTCTGTTCCTTGAGCGGAG 60.739 60.000 11.17 11.17 45.07 4.63
726 727 0.108424 CTCTGTTCCTTGAGCGGAGG 60.108 60.000 8.43 0.00 40.81 4.30
727 728 0.832135 TCTGTTCCTTGAGCGGAGGT 60.832 55.000 3.52 0.00 46.54 3.85
728 729 0.671781 CTGTTCCTTGAGCGGAGGTG 60.672 60.000 3.52 0.00 39.88 4.00
729 730 2.035442 GTTCCTTGAGCGGAGGTGC 61.035 63.158 3.52 0.00 39.88 5.01
730 731 3.589654 TTCCTTGAGCGGAGGTGCG 62.590 63.158 3.52 0.00 39.88 5.34
1001 1023 0.605319 CTCTCTCTAGCTCGGGCGAT 60.605 60.000 0.00 0.00 44.37 4.58
1216 1239 2.611292 CGCTGCTTGATCTCCTTTTAGG 59.389 50.000 0.00 0.00 36.46 2.69
1377 1432 1.579429 GGGTTGGTGTGTTGATCGC 59.421 57.895 0.00 0.00 0.00 4.58
1829 1922 4.134563 TGTTTTTGAACCAGAGCTAGACC 58.865 43.478 0.00 0.00 0.00 3.85
2421 2870 5.582689 ATGAATATCGACACTGACACTCA 57.417 39.130 0.00 0.00 0.00 3.41
2626 3109 1.894466 CAACATCCCATCAGGCAACAA 59.106 47.619 0.00 0.00 41.41 2.83
2875 3358 4.518970 GGACAAGGTCACTGATTTTGCTTA 59.481 41.667 0.00 0.00 33.68 3.09
3155 3659 2.327343 GCTGCCATCAACGAGCACA 61.327 57.895 0.00 0.00 32.06 4.57
3160 3664 2.816672 TGCCATCAACGAGCACAAATTA 59.183 40.909 0.00 0.00 0.00 1.40
3820 4383 4.335315 TGCTTCCATACCGATGACAATTTC 59.665 41.667 0.00 0.00 34.73 2.17
3911 4474 3.764237 TCGGAGTTAAAAGGTGCTCTT 57.236 42.857 0.00 0.00 37.28 2.85
4206 4775 3.192422 GTGTAATGGCAGCAATGTGGTTA 59.808 43.478 0.00 0.00 0.00 2.85
4713 5291 4.281688 AGATGGACCATTGAAAACACAAGG 59.718 41.667 8.78 0.00 33.22 3.61
4916 5494 5.089970 TGTCATGAAGAGGTACAAGATGG 57.910 43.478 0.00 0.00 0.00 3.51
6206 6849 1.656095 CGAAGAGTCGGATTTCACAGC 59.344 52.381 0.00 0.00 43.81 4.40
6443 7093 7.948034 AAATTTTGATGGCCAAATGATGAAT 57.052 28.000 10.96 1.25 43.59 2.57
6624 7281 5.948742 TTTTCCATCCTTTGAACAAGGTT 57.051 34.783 0.59 0.00 38.55 3.50
7477 8368 7.630082 AGCAGTAATATGAACCAAAACCTCTA 58.370 34.615 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 0.616395 TCCAACGGTGATCTGCCCTA 60.616 55.000 0.00 0.00 0.00 3.53
62 63 0.976641 TCTGCTTCCAACGGTGATCT 59.023 50.000 0.00 0.00 0.00 2.75
81 82 2.044650 AATGCGCAGGTGAGCCAT 60.045 55.556 18.32 0.00 40.22 4.40
82 83 3.057548 CAATGCGCAGGTGAGCCA 61.058 61.111 18.32 0.00 40.22 4.75
226 227 4.016706 CACCACCCCTGACCGGAC 62.017 72.222 9.46 1.07 33.16 4.79
239 240 2.445085 ACGACCAGGTCACCACCA 60.445 61.111 20.13 0.00 46.68 4.17
302 303 0.250684 TCTGCAACATCGCCTTTCCA 60.251 50.000 0.00 0.00 0.00 3.53
354 355 1.301293 CAAGCCTCACTCCCTTCCC 59.699 63.158 0.00 0.00 0.00 3.97
376 377 1.527611 CTCACATCCATGCCGCCAT 60.528 57.895 0.00 0.00 0.00 4.40
384 385 2.776536 CCTCTTCCCTTCTCACATCCAT 59.223 50.000 0.00 0.00 0.00 3.41
395 396 2.689034 CTCCCCGCCTCTTCCCTT 60.689 66.667 0.00 0.00 0.00 3.95
396 397 4.806339 CCTCCCCGCCTCTTCCCT 62.806 72.222 0.00 0.00 0.00 4.20
421 422 3.556306 CACGTCCCCCACACACCT 61.556 66.667 0.00 0.00 0.00 4.00
440 441 2.501610 GCTACCCCTCGCTTCCTG 59.498 66.667 0.00 0.00 0.00 3.86
482 483 0.387565 GTCAGCCGATCCTCTTCTCC 59.612 60.000 0.00 0.00 0.00 3.71
558 559 4.415332 TTCCTCCGTCGCTGTCGC 62.415 66.667 0.00 0.00 35.26 5.19
559 560 1.994507 ATCTTCCTCCGTCGCTGTCG 61.995 60.000 0.00 0.00 0.00 4.35
560 561 0.526524 CATCTTCCTCCGTCGCTGTC 60.527 60.000 0.00 0.00 0.00 3.51
561 562 1.513158 CATCTTCCTCCGTCGCTGT 59.487 57.895 0.00 0.00 0.00 4.40
562 563 1.227089 CCATCTTCCTCCGTCGCTG 60.227 63.158 0.00 0.00 0.00 5.18
563 564 2.427245 CCCATCTTCCTCCGTCGCT 61.427 63.158 0.00 0.00 0.00 4.93
564 565 2.107141 CCCATCTTCCTCCGTCGC 59.893 66.667 0.00 0.00 0.00 5.19
565 566 2.107141 GCCCATCTTCCTCCGTCG 59.893 66.667 0.00 0.00 0.00 5.12
566 567 2.107141 CGCCCATCTTCCTCCGTC 59.893 66.667 0.00 0.00 0.00 4.79
567 568 3.470888 CCGCCCATCTTCCTCCGT 61.471 66.667 0.00 0.00 0.00 4.69
568 569 4.241555 CCCGCCCATCTTCCTCCG 62.242 72.222 0.00 0.00 0.00 4.63
569 570 3.878667 CCCCGCCCATCTTCCTCC 61.879 72.222 0.00 0.00 0.00 4.30
570 571 2.768344 TCCCCGCCCATCTTCCTC 60.768 66.667 0.00 0.00 0.00 3.71
571 572 2.770048 CTCCCCGCCCATCTTCCT 60.770 66.667 0.00 0.00 0.00 3.36
572 573 3.878667 CCTCCCCGCCCATCTTCC 61.879 72.222 0.00 0.00 0.00 3.46
573 574 4.570874 GCCTCCCCGCCCATCTTC 62.571 72.222 0.00 0.00 0.00 2.87
585 586 4.475135 GTTGCCTCTCCCGCCTCC 62.475 72.222 0.00 0.00 0.00 4.30
586 587 2.748058 TTTGTTGCCTCTCCCGCCTC 62.748 60.000 0.00 0.00 0.00 4.70
587 588 2.351924 TTTTGTTGCCTCTCCCGCCT 62.352 55.000 0.00 0.00 0.00 5.52
588 589 1.250840 ATTTTGTTGCCTCTCCCGCC 61.251 55.000 0.00 0.00 0.00 6.13
589 590 1.401905 CTATTTTGTTGCCTCTCCCGC 59.598 52.381 0.00 0.00 0.00 6.13
590 591 2.017049 CCTATTTTGTTGCCTCTCCCG 58.983 52.381 0.00 0.00 0.00 5.14
591 592 2.379005 CCCTATTTTGTTGCCTCTCCC 58.621 52.381 0.00 0.00 0.00 4.30
592 593 2.379005 CCCCTATTTTGTTGCCTCTCC 58.621 52.381 0.00 0.00 0.00 3.71
593 594 2.025321 TCCCCCTATTTTGTTGCCTCTC 60.025 50.000 0.00 0.00 0.00 3.20
594 595 2.000048 TCCCCCTATTTTGTTGCCTCT 59.000 47.619 0.00 0.00 0.00 3.69
595 596 2.525105 TCCCCCTATTTTGTTGCCTC 57.475 50.000 0.00 0.00 0.00 4.70
596 597 2.750814 CATCCCCCTATTTTGTTGCCT 58.249 47.619 0.00 0.00 0.00 4.75
597 598 1.138859 GCATCCCCCTATTTTGTTGCC 59.861 52.381 0.00 0.00 0.00 4.52
598 599 1.202405 CGCATCCCCCTATTTTGTTGC 60.202 52.381 0.00 0.00 0.00 4.17
599 600 1.408702 CCGCATCCCCCTATTTTGTTG 59.591 52.381 0.00 0.00 0.00 3.33
600 601 1.687996 CCCGCATCCCCCTATTTTGTT 60.688 52.381 0.00 0.00 0.00 2.83
601 602 0.106217 CCCGCATCCCCCTATTTTGT 60.106 55.000 0.00 0.00 0.00 2.83
602 603 0.184933 TCCCGCATCCCCCTATTTTG 59.815 55.000 0.00 0.00 0.00 2.44
603 604 0.478507 CTCCCGCATCCCCCTATTTT 59.521 55.000 0.00 0.00 0.00 1.82
604 605 1.427072 CCTCCCGCATCCCCCTATTT 61.427 60.000 0.00 0.00 0.00 1.40
605 606 1.847968 CCTCCCGCATCCCCCTATT 60.848 63.158 0.00 0.00 0.00 1.73
606 607 2.203998 CCTCCCGCATCCCCCTAT 60.204 66.667 0.00 0.00 0.00 2.57
627 628 4.463879 CCACTGCTCCCGCCTCTG 62.464 72.222 0.00 0.00 34.43 3.35
628 629 4.704103 TCCACTGCTCCCGCCTCT 62.704 66.667 0.00 0.00 34.43 3.69
629 630 4.154347 CTCCACTGCTCCCGCCTC 62.154 72.222 0.00 0.00 34.43 4.70
651 652 4.271816 CTCCATCCTCCGTCGCCG 62.272 72.222 0.00 0.00 0.00 6.46
652 653 3.917760 CCTCCATCCTCCGTCGCC 61.918 72.222 0.00 0.00 0.00 5.54
653 654 4.593864 GCCTCCATCCTCCGTCGC 62.594 72.222 0.00 0.00 0.00 5.19
654 655 4.271816 CGCCTCCATCCTCCGTCG 62.272 72.222 0.00 0.00 0.00 5.12
655 656 3.917760 CCGCCTCCATCCTCCGTC 61.918 72.222 0.00 0.00 0.00 4.79
656 657 3.758133 ATCCGCCTCCATCCTCCGT 62.758 63.158 0.00 0.00 0.00 4.69
657 658 2.919856 ATCCGCCTCCATCCTCCG 60.920 66.667 0.00 0.00 0.00 4.63
658 659 2.746359 CATCCGCCTCCATCCTCC 59.254 66.667 0.00 0.00 0.00 4.30
659 660 2.746359 CCATCCGCCTCCATCCTC 59.254 66.667 0.00 0.00 0.00 3.71
660 661 2.851102 CCCATCCGCCTCCATCCT 60.851 66.667 0.00 0.00 0.00 3.24
661 662 3.958860 CCCCATCCGCCTCCATCC 61.959 72.222 0.00 0.00 0.00 3.51
662 663 3.958860 CCCCCATCCGCCTCCATC 61.959 72.222 0.00 0.00 0.00 3.51
672 673 4.962836 CTGCCATCCGCCCCCATC 62.963 72.222 0.00 0.00 36.24 3.51
677 678 4.864334 CTCCACTGCCATCCGCCC 62.864 72.222 0.00 0.00 36.24 6.13
678 679 4.864334 CCTCCACTGCCATCCGCC 62.864 72.222 0.00 0.00 36.24 6.13
699 700 3.883744 AAGGAACAGAGCACGGCCG 62.884 63.158 26.86 26.86 0.00 6.13
700 701 2.032681 AAGGAACAGAGCACGGCC 59.967 61.111 0.00 0.00 0.00 6.13
701 702 1.294659 CTCAAGGAACAGAGCACGGC 61.295 60.000 0.00 0.00 0.00 5.68
702 703 2.832931 CTCAAGGAACAGAGCACGG 58.167 57.895 0.00 0.00 0.00 4.94
707 708 0.108424 CCTCCGCTCAAGGAACAGAG 60.108 60.000 0.00 0.00 40.25 3.35
708 709 0.832135 ACCTCCGCTCAAGGAACAGA 60.832 55.000 3.21 0.00 40.25 3.41
709 710 0.671781 CACCTCCGCTCAAGGAACAG 60.672 60.000 3.21 0.00 40.25 3.16
710 711 1.371183 CACCTCCGCTCAAGGAACA 59.629 57.895 3.21 0.00 40.25 3.18
711 712 2.035442 GCACCTCCGCTCAAGGAAC 61.035 63.158 3.21 0.00 40.25 3.62
712 713 2.347490 GCACCTCCGCTCAAGGAA 59.653 61.111 3.21 0.00 40.25 3.36
713 714 4.069232 CGCACCTCCGCTCAAGGA 62.069 66.667 3.21 0.00 37.35 3.36
758 759 2.940890 ATAACCTCCGGCCATGCACG 62.941 60.000 2.24 0.85 0.00 5.34
759 760 0.751643 AATAACCTCCGGCCATGCAC 60.752 55.000 2.24 0.00 0.00 4.57
760 761 0.033601 AAATAACCTCCGGCCATGCA 60.034 50.000 2.24 0.00 0.00 3.96
761 762 1.111277 AAAATAACCTCCGGCCATGC 58.889 50.000 2.24 0.00 0.00 4.06
778 779 5.289917 GCTGTTTTAGAGCGTTTTCCAAAAA 59.710 36.000 0.00 0.00 0.00 1.94
779 780 4.801516 GCTGTTTTAGAGCGTTTTCCAAAA 59.198 37.500 0.00 0.00 0.00 2.44
780 781 4.356289 GCTGTTTTAGAGCGTTTTCCAAA 58.644 39.130 0.00 0.00 0.00 3.28
781 782 3.243267 GGCTGTTTTAGAGCGTTTTCCAA 60.243 43.478 0.00 0.00 37.32 3.53
782 783 2.292292 GGCTGTTTTAGAGCGTTTTCCA 59.708 45.455 0.00 0.00 37.32 3.53
1181 1203 1.883021 CAGCGCGGGGAGAAAATTT 59.117 52.632 8.83 0.00 0.00 1.82
1216 1239 4.215399 TGGGATTAATCGCGAAATGAATCC 59.785 41.667 28.64 28.64 42.06 3.01
1377 1432 5.104527 TCCAAACCCTATCTACAACATGGAG 60.105 44.000 0.00 0.00 0.00 3.86
1829 1922 1.128692 CCGAAAAAGCAGAGTAAGGCG 59.871 52.381 0.00 0.00 34.54 5.52
2421 2870 2.338577 GGTGCAATACCTCAGCTCAT 57.661 50.000 0.00 0.00 46.51 2.90
2626 3109 4.336713 GTCTCTTGAAAAGCTCAACTGGTT 59.663 41.667 0.00 0.00 45.70 3.67
2875 3358 5.565439 GCAACACTTAAAACATGCTCATCCT 60.565 40.000 0.00 0.00 0.00 3.24
3155 3659 6.607600 GCCCTTGGGAGAGAATAGTTTAATTT 59.392 38.462 10.36 0.00 0.00 1.82
3160 3664 3.193782 AGCCCTTGGGAGAGAATAGTTT 58.806 45.455 10.36 0.00 0.00 2.66
3569 4085 0.099436 GTTTCGCAGCCATGTCATCC 59.901 55.000 0.00 0.00 0.00 3.51
3820 4383 8.492673 TGGTAGCTGACAAAATGTATAGAAAG 57.507 34.615 0.00 0.00 0.00 2.62
3911 4474 2.622942 CAACACTTGCCCAAAAGAGCTA 59.377 45.455 0.00 0.00 0.00 3.32
4168 4737 5.106038 CCATTACACTCATGAGCATTGTTGT 60.106 40.000 22.83 18.83 0.00 3.32
4206 4775 1.692519 ACTAGTTCGTGTGCCCTTCTT 59.307 47.619 0.00 0.00 0.00 2.52
4246 4816 3.004002 TGCATTCTCAAAACACTCTGCAG 59.996 43.478 7.63 7.63 33.80 4.41
4713 5291 4.177783 GCTAACTAGAACAACTGGCTCTC 58.822 47.826 0.00 0.00 0.00 3.20
4916 5494 5.628797 ATTTCCCCTCTCTTCATCTTCTC 57.371 43.478 0.00 0.00 0.00 2.87
6206 6849 7.547370 AGTCTGTTTTGAAAGAAGATAGATCCG 59.453 37.037 0.00 0.00 0.00 4.18
7477 8368 9.030301 GTACTGAAAAATTATGTGCACTTTGTT 57.970 29.630 19.41 7.82 0.00 2.83


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

AutoCloner maintained by Alex Coulton.