Multiple sequence alignment - TraesCS7A01G447500

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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 TraesCS7A01G447500 chr7A 100.000 3004 0 0 1 3004 642158749 642161752 0.000000e+00 5548.0
1 TraesCS7A01G447500 chr7D 87.482 1374 100 28 755 2090 556448218 556449557 0.000000e+00 1519.0
2 TraesCS7A01G447500 chr7B 88.082 1074 81 25 755 1803 603992234 603993285 0.000000e+00 1230.0
3 TraesCS7A01G447500 chr7B 92.118 850 65 2 2155 3004 184420018 184420865 0.000000e+00 1197.0
4 TraesCS7A01G447500 chr7B 93.303 433 29 0 1266 1698 603663751 603664183 9.080000e-180 640.0
5 TraesCS7A01G447500 chr7B 77.809 712 115 23 946 1638 603835261 603835948 1.680000e-107 399.0
6 TraesCS7A01G447500 chr7B 84.935 385 50 5 892 1268 603944114 603944498 1.690000e-102 383.0
7 TraesCS7A01G447500 chr7B 83.121 314 40 10 956 1268 603663491 603663792 1.060000e-69 274.0
8 TraesCS7A01G447500 chr7B 89.848 197 16 3 767 959 603624507 603624703 1.790000e-62 250.0
9 TraesCS7A01G447500 chr7B 95.588 68 3 0 2091 2158 184419918 184419985 3.170000e-20 110.0
10 TraesCS7A01G447500 chr7B 94.828 58 3 0 677 734 619359326 619359269 1.150000e-14 91.6
11 TraesCS7A01G447500 chr7B 93.182 44 3 0 1682 1725 603944941 603944984 6.950000e-07 65.8
12 TraesCS7A01G447500 chr4A 92.661 763 47 5 2158 2920 735283645 735282892 0.000000e+00 1090.0
13 TraesCS7A01G447500 chr4A 95.588 68 3 0 2091 2158 735283748 735283681 3.170000e-20 110.0
14 TraesCS7A01G447500 chr4A 91.429 70 6 0 672 741 705177649 705177718 2.460000e-16 97.1
15 TraesCS7A01G447500 chr3D 88.602 851 90 6 2155 3003 461567103 461567948 0.000000e+00 1027.0
16 TraesCS7A01G447500 chr3D 81.195 686 118 9 2 678 558086645 558085962 2.630000e-150 542.0
17 TraesCS7A01G447500 chr3D 92.424 66 4 1 670 734 403329819 403329754 3.190000e-15 93.5
18 TraesCS7A01G447500 chr3D 89.041 73 7 1 670 741 427151676 427151748 4.120000e-14 89.8
19 TraesCS7A01G447500 chr2D 87.603 847 103 2 2158 3004 144436391 144435547 0.000000e+00 981.0
20 TraesCS7A01G447500 chr2D 94.872 39 2 0 1763 1801 427150332 427150370 8.990000e-06 62.1
21 TraesCS7A01G447500 chr3A 87.339 853 101 5 2155 3004 701917220 701918068 0.000000e+00 970.0
22 TraesCS7A01G447500 chr3A 86.401 853 107 8 2156 3004 208740045 208740892 0.000000e+00 924.0
23 TraesCS7A01G447500 chr1D 86.572 849 111 3 2156 3004 30236141 30236986 0.000000e+00 933.0
24 TraesCS7A01G447500 chr1D 85.395 849 122 2 2156 3004 335399916 335399070 0.000000e+00 880.0
25 TraesCS7A01G447500 chr3B 85.242 847 118 7 2161 3004 801049584 801050426 0.000000e+00 865.0
26 TraesCS7A01G447500 chr3B 80.556 684 122 9 2 677 740867853 740867173 1.600000e-142 516.0
27 TraesCS7A01G447500 chr6B 83.510 661 94 9 19 671 556795988 556795335 1.190000e-168 603.0
28 TraesCS7A01G447500 chr6B 80.820 683 115 10 2 678 624135442 624136114 3.430000e-144 521.0
29 TraesCS7A01G447500 chr5A 81.159 690 115 10 2 678 7396047 7396734 9.470000e-150 540.0
30 TraesCS7A01G447500 chr5A 80.058 687 119 11 2 676 569185961 569186641 7.480000e-136 494.0
31 TraesCS7A01G447500 chr5B 80.994 684 116 9 3 678 693880565 693881242 5.700000e-147 531.0
32 TraesCS7A01G447500 chr5B 80.753 691 117 12 2 678 640886433 640885745 2.650000e-145 525.0
33 TraesCS7A01G447500 chr5B 80.000 685 107 24 2 665 250232547 250231872 2.090000e-131 479.0
34 TraesCS7A01G447500 chr2B 95.238 63 3 0 672 734 152793771 152793709 1.910000e-17 100.0
35 TraesCS7A01G447500 chr2B 93.651 63 4 0 672 734 153163370 153163432 8.870000e-16 95.3
36 TraesCS7A01G447500 chr5D 95.161 62 3 0 673 734 294426034 294425973 6.850000e-17 99.0
37 TraesCS7A01G447500 chr5D 92.308 52 4 0 1761 1812 257739868 257739919 1.150000e-09 75.0
38 TraesCS7A01G447500 chr4B 90.141 71 5 2 665 734 653120499 653120568 1.150000e-14 91.6
39 TraesCS7A01G447500 chr1B 90.000 70 7 0 672 741 475286579 475286648 1.150000e-14 91.6
40 TraesCS7A01G447500 chr2A 91.525 59 5 0 1751 1809 78809220 78809162 6.900000e-12 82.4
41 TraesCS7A01G447500 chr2A 91.304 46 2 2 1763 1807 695005611 695005567 8.990000e-06 62.1
42 TraesCS7A01G447500 chr4D 100.000 28 0 0 1763 1790 280173799 280173826 5.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G447500 chr7A 642158749 642161752 3003 False 5548.0 5548 100.0000 1 3004 1 chr7A.!!$F1 3003
1 TraesCS7A01G447500 chr7D 556448218 556449557 1339 False 1519.0 1519 87.4820 755 2090 1 chr7D.!!$F1 1335
2 TraesCS7A01G447500 chr7B 603992234 603993285 1051 False 1230.0 1230 88.0820 755 1803 1 chr7B.!!$F3 1048
3 TraesCS7A01G447500 chr7B 184419918 184420865 947 False 653.5 1197 93.8530 2091 3004 2 chr7B.!!$F4 913
4 TraesCS7A01G447500 chr7B 603663491 603664183 692 False 457.0 640 88.2120 956 1698 2 chr7B.!!$F5 742
5 TraesCS7A01G447500 chr7B 603835261 603835948 687 False 399.0 399 77.8090 946 1638 1 chr7B.!!$F2 692
6 TraesCS7A01G447500 chr7B 603944114 603944984 870 False 224.4 383 89.0585 892 1725 2 chr7B.!!$F6 833
7 TraesCS7A01G447500 chr4A 735282892 735283748 856 True 600.0 1090 94.1245 2091 2920 2 chr4A.!!$R1 829
8 TraesCS7A01G447500 chr3D 461567103 461567948 845 False 1027.0 1027 88.6020 2155 3003 1 chr3D.!!$F2 848
9 TraesCS7A01G447500 chr3D 558085962 558086645 683 True 542.0 542 81.1950 2 678 1 chr3D.!!$R2 676
10 TraesCS7A01G447500 chr2D 144435547 144436391 844 True 981.0 981 87.6030 2158 3004 1 chr2D.!!$R1 846
11 TraesCS7A01G447500 chr3A 701917220 701918068 848 False 970.0 970 87.3390 2155 3004 1 chr3A.!!$F2 849
12 TraesCS7A01G447500 chr3A 208740045 208740892 847 False 924.0 924 86.4010 2156 3004 1 chr3A.!!$F1 848
13 TraesCS7A01G447500 chr1D 30236141 30236986 845 False 933.0 933 86.5720 2156 3004 1 chr1D.!!$F1 848
14 TraesCS7A01G447500 chr1D 335399070 335399916 846 True 880.0 880 85.3950 2156 3004 1 chr1D.!!$R1 848
15 TraesCS7A01G447500 chr3B 801049584 801050426 842 False 865.0 865 85.2420 2161 3004 1 chr3B.!!$F1 843
16 TraesCS7A01G447500 chr3B 740867173 740867853 680 True 516.0 516 80.5560 2 677 1 chr3B.!!$R1 675
17 TraesCS7A01G447500 chr6B 556795335 556795988 653 True 603.0 603 83.5100 19 671 1 chr6B.!!$R1 652
18 TraesCS7A01G447500 chr6B 624135442 624136114 672 False 521.0 521 80.8200 2 678 1 chr6B.!!$F1 676
19 TraesCS7A01G447500 chr5A 7396047 7396734 687 False 540.0 540 81.1590 2 678 1 chr5A.!!$F1 676
20 TraesCS7A01G447500 chr5A 569185961 569186641 680 False 494.0 494 80.0580 2 676 1 chr5A.!!$F2 674
21 TraesCS7A01G447500 chr5B 693880565 693881242 677 False 531.0 531 80.9940 3 678 1 chr5B.!!$F1 675
22 TraesCS7A01G447500 chr5B 640885745 640886433 688 True 525.0 525 80.7530 2 678 1 chr5B.!!$R2 676
23 TraesCS7A01G447500 chr5B 250231872 250232547 675 True 479.0 479 80.0000 2 665 1 chr5B.!!$R1 663

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
329 347 0.184451 ATGGCATTCGGAAGATGGCT 59.816 50.0 15.91 3.07 41.33 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2012 2261 0.391661 CAACATGGGAGGTCCTCGTG 60.392 60.0 12.91 13.08 36.2 4.35 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
41 43 2.609459 GTGTGGATCGTCTTAGGCATTG 59.391 50.000 0.00 0.00 0.00 2.82
60 62 1.272258 TGGTAGCTTAGGGTTTTGGGC 60.272 52.381 0.00 0.00 0.00 5.36
62 64 2.240414 GGTAGCTTAGGGTTTTGGGCTA 59.760 50.000 0.00 0.00 0.00 3.93
65 67 3.365472 AGCTTAGGGTTTTGGGCTATTG 58.635 45.455 0.00 0.00 0.00 1.90
78 80 2.037251 GGGCTATTGATCGTCTTGGCTA 59.963 50.000 0.00 0.00 0.00 3.93
111 116 1.403679 TGGCGCCGGATAAAAATTCTG 59.596 47.619 23.90 0.00 0.00 3.02
117 122 4.213270 CGCCGGATAAAAATTCTGCAGATA 59.787 41.667 19.04 6.86 0.00 1.98
124 129 8.897752 GGATAAAAATTCTGCAGATACTTCACT 58.102 33.333 19.04 0.00 0.00 3.41
160 171 1.623311 GTGGGGGTTGGATTTGGAAAG 59.377 52.381 0.00 0.00 0.00 2.62
185 200 4.348168 AGTCTGTTCAAGTAAGGATGGTGT 59.652 41.667 0.00 0.00 0.00 4.16
210 228 1.074775 GGCATCCTTGTGGTGGACA 59.925 57.895 0.00 0.00 36.30 4.02
299 317 0.254178 AGGAGCGGATGCAGATTGTT 59.746 50.000 0.00 0.00 46.23 2.83
304 322 1.063174 GCGGATGCAGATTGTTGTCTC 59.937 52.381 0.00 0.00 42.15 3.36
328 346 1.035139 AATGGCATTCGGAAGATGGC 58.965 50.000 6.96 10.07 41.60 4.40
329 347 0.184451 ATGGCATTCGGAAGATGGCT 59.816 50.000 15.91 3.07 41.33 4.75
362 380 1.203052 GGTTCGTGGTTCGTGATAGGA 59.797 52.381 0.00 0.00 40.80 2.94
402 421 0.892358 ACGTCTTAGTCGTGCAGGGA 60.892 55.000 6.56 0.00 40.07 4.20
411 430 1.452651 CGTGCAGGGATGCCAGATT 60.453 57.895 5.86 0.00 0.00 2.40
443 463 1.362717 CGTGTCCGGAGTGTTGTCT 59.637 57.895 3.06 0.00 0.00 3.41
458 478 3.057734 GTTGTCTCGGTCTGATTCGTTT 58.942 45.455 3.96 0.00 0.00 3.60
466 486 2.676342 GGTCTGATTCGTTTAACGGCAT 59.324 45.455 17.59 9.89 42.81 4.40
473 493 1.609555 TCGTTTAACGGCATTGGCTTT 59.390 42.857 17.59 7.87 42.81 3.51
513 533 2.618045 CCTTGGAGGTCCGCAAAACTAT 60.618 50.000 0.00 0.00 39.43 2.12
524 544 4.921515 TCCGCAAAACTATATATCAGCGAC 59.078 41.667 0.00 0.00 46.01 5.19
550 572 1.515954 CGTTGAGCTCGGGTATGGT 59.484 57.895 9.64 0.00 0.00 3.55
552 574 0.535335 GTTGAGCTCGGGTATGGTGA 59.465 55.000 9.64 0.00 0.00 4.02
555 577 0.753262 GAGCTCGGGTATGGTGATGT 59.247 55.000 0.00 0.00 0.00 3.06
565 589 4.443739 GGGTATGGTGATGTTCCGTCATTA 60.444 45.833 0.00 0.00 31.77 1.90
604 629 1.192146 GGTGGTGCCAGAGACAGGTA 61.192 60.000 0.00 0.00 37.17 3.08
618 643 3.729698 GGTAACGGGCGTTGGTGC 61.730 66.667 0.00 0.00 38.92 5.01
642 674 1.202475 GCTCAGAGGATTCTTCGGTCC 60.202 57.143 0.00 0.00 34.64 4.46
667 700 7.595130 CCTGTTTGTATTTTTACTTCTTGGCTC 59.405 37.037 0.00 0.00 0.00 4.70
678 711 2.325583 TCTTGGCTCGTGTTTCTGTT 57.674 45.000 0.00 0.00 0.00 3.16
680 713 3.013921 TCTTGGCTCGTGTTTCTGTTTT 58.986 40.909 0.00 0.00 0.00 2.43
681 714 2.842208 TGGCTCGTGTTTCTGTTTTG 57.158 45.000 0.00 0.00 0.00 2.44
682 715 1.202245 TGGCTCGTGTTTCTGTTTTGC 60.202 47.619 0.00 0.00 0.00 3.68
683 716 1.477105 GCTCGTGTTTCTGTTTTGCC 58.523 50.000 0.00 0.00 0.00 4.52
684 717 1.202245 GCTCGTGTTTCTGTTTTGCCA 60.202 47.619 0.00 0.00 0.00 4.92
685 718 2.719798 CTCGTGTTTCTGTTTTGCCAG 58.280 47.619 0.00 0.00 0.00 4.85
686 719 1.403679 TCGTGTTTCTGTTTTGCCAGG 59.596 47.619 0.00 0.00 33.14 4.45
687 720 1.134175 CGTGTTTCTGTTTTGCCAGGT 59.866 47.619 0.00 0.00 33.14 4.00
688 721 2.794631 CGTGTTTCTGTTTTGCCAGGTC 60.795 50.000 0.00 0.00 33.14 3.85
689 722 2.165437 GTGTTTCTGTTTTGCCAGGTCA 59.835 45.455 0.00 0.00 33.14 4.02
690 723 2.426738 TGTTTCTGTTTTGCCAGGTCAG 59.573 45.455 0.00 0.00 33.14 3.51
691 724 2.427095 GTTTCTGTTTTGCCAGGTCAGT 59.573 45.455 0.00 0.00 33.14 3.41
692 725 3.569194 TTCTGTTTTGCCAGGTCAGTA 57.431 42.857 0.00 0.00 33.14 2.74
693 726 3.788227 TCTGTTTTGCCAGGTCAGTAT 57.212 42.857 0.00 0.00 33.14 2.12
694 727 3.411446 TCTGTTTTGCCAGGTCAGTATG 58.589 45.455 0.00 0.00 33.14 2.39
695 728 3.149196 CTGTTTTGCCAGGTCAGTATGT 58.851 45.455 0.00 0.00 37.40 2.29
696 729 4.041075 TCTGTTTTGCCAGGTCAGTATGTA 59.959 41.667 0.00 0.00 33.18 2.29
697 730 4.069304 TGTTTTGCCAGGTCAGTATGTAC 58.931 43.478 0.00 0.00 37.40 2.90
698 731 2.665649 TTGCCAGGTCAGTATGTACG 57.334 50.000 0.00 0.00 37.40 3.67
699 732 1.552578 TGCCAGGTCAGTATGTACGT 58.447 50.000 0.00 0.00 37.40 3.57
700 733 1.203758 TGCCAGGTCAGTATGTACGTG 59.796 52.381 0.00 0.00 37.40 4.49
701 734 1.470979 GCCAGGTCAGTATGTACGTGG 60.471 57.143 0.00 9.27 45.81 4.94
702 735 1.470979 CCAGGTCAGTATGTACGTGGC 60.471 57.143 0.00 0.00 41.46 5.01
703 736 1.476891 CAGGTCAGTATGTACGTGGCT 59.523 52.381 0.00 0.00 37.40 4.75
704 737 2.094182 CAGGTCAGTATGTACGTGGCTT 60.094 50.000 0.00 0.00 37.40 4.35
705 738 2.094182 AGGTCAGTATGTACGTGGCTTG 60.094 50.000 0.00 0.00 37.40 4.01
706 739 2.353406 GGTCAGTATGTACGTGGCTTGT 60.353 50.000 0.00 0.00 37.40 3.16
707 740 3.119388 GGTCAGTATGTACGTGGCTTGTA 60.119 47.826 0.00 0.00 37.40 2.41
708 741 3.855950 GTCAGTATGTACGTGGCTTGTAC 59.144 47.826 0.00 11.33 41.97 2.90
709 742 3.760151 TCAGTATGTACGTGGCTTGTACT 59.240 43.478 16.75 0.00 42.09 2.73
710 743 4.943093 TCAGTATGTACGTGGCTTGTACTA 59.057 41.667 16.75 7.49 42.09 1.82
711 744 5.591472 TCAGTATGTACGTGGCTTGTACTAT 59.409 40.000 16.75 12.18 42.09 2.12
712 745 5.685954 CAGTATGTACGTGGCTTGTACTATG 59.314 44.000 16.75 9.09 42.09 2.23
713 746 4.994907 ATGTACGTGGCTTGTACTATGA 57.005 40.909 16.75 2.28 42.09 2.15
714 747 4.994907 TGTACGTGGCTTGTACTATGAT 57.005 40.909 16.75 0.00 42.09 2.45
715 748 5.333299 TGTACGTGGCTTGTACTATGATT 57.667 39.130 16.75 0.00 42.09 2.57
716 749 5.345702 TGTACGTGGCTTGTACTATGATTC 58.654 41.667 16.75 0.00 42.09 2.52
717 750 4.737855 ACGTGGCTTGTACTATGATTCT 57.262 40.909 0.00 0.00 0.00 2.40
718 751 5.086104 ACGTGGCTTGTACTATGATTCTT 57.914 39.130 0.00 0.00 0.00 2.52
719 752 6.216801 ACGTGGCTTGTACTATGATTCTTA 57.783 37.500 0.00 0.00 0.00 2.10
720 753 6.817184 ACGTGGCTTGTACTATGATTCTTAT 58.183 36.000 0.00 0.00 0.00 1.73
721 754 6.701841 ACGTGGCTTGTACTATGATTCTTATG 59.298 38.462 0.00 0.00 0.00 1.90
722 755 6.923508 CGTGGCTTGTACTATGATTCTTATGA 59.076 38.462 0.00 0.00 0.00 2.15
723 756 7.600375 CGTGGCTTGTACTATGATTCTTATGAT 59.400 37.037 0.00 0.00 0.00 2.45
724 757 9.929180 GTGGCTTGTACTATGATTCTTATGATA 57.071 33.333 0.00 0.00 0.00 2.15
815 856 5.834204 ACACTAATCTACTCCCCACTATGAC 59.166 44.000 0.00 0.00 0.00 3.06
858 899 0.709467 CATTGCGCAAATGTCAACCG 59.291 50.000 28.81 3.42 40.78 4.44
863 904 1.334239 GCGCAAATGTCAACCGTGTAA 60.334 47.619 0.30 0.00 0.00 2.41
900 941 5.649395 ACATGCATGCATTGAGTAGTTTACT 59.351 36.000 30.32 2.29 36.73 2.24
907 948 7.539712 TGCATTGAGTAGTTTACTTAGATGC 57.460 36.000 16.67 16.67 42.43 3.91
909 950 6.292381 GCATTGAGTAGTTTACTTAGATGCCG 60.292 42.308 14.60 0.00 39.71 5.69
962 1009 3.391296 CCTAGAGCTGGGTGCCTATAAAA 59.609 47.826 0.00 0.00 44.23 1.52
985 1033 2.370445 ACCTCGGCTCCTTCCATGG 61.370 63.158 4.97 4.97 0.00 3.66
1022 1070 3.718815 ACAGTTCTCTCGTGTTTCTTCC 58.281 45.455 0.00 0.00 0.00 3.46
1039 1087 0.978146 TCCCTGGCTAGCTCAAGGTC 60.978 60.000 22.08 4.83 0.00 3.85
1041 1089 1.689575 CCCTGGCTAGCTCAAGGTCTA 60.690 57.143 22.08 0.00 0.00 2.59
1055 1104 0.531200 GGTCTACTTCCCGTGTCCAG 59.469 60.000 0.00 0.00 0.00 3.86
1069 1118 3.830192 CCAGGGCGCAATGGCTTC 61.830 66.667 16.09 0.00 44.11 3.86
1070 1119 3.063704 CAGGGCGCAATGGCTTCA 61.064 61.111 10.83 0.00 44.11 3.02
1071 1120 2.283101 AGGGCGCAATGGCTTCAA 60.283 55.556 10.83 0.00 44.11 2.69
1080 1132 1.274167 CAATGGCTTCAACAGGTGCAT 59.726 47.619 0.00 0.00 0.00 3.96
1092 1144 1.078848 GGTGCATCCGCTCTCACTT 60.079 57.895 0.00 0.00 39.64 3.16
1109 1161 1.507141 CTTTGAAGCTGGCCGTCGTT 61.507 55.000 0.00 0.00 0.00 3.85
1232 1329 1.376683 CATACCACCACCACCACCG 60.377 63.158 0.00 0.00 0.00 4.94
1233 1330 2.598787 ATACCACCACCACCACCGG 61.599 63.158 0.00 0.00 0.00 5.28
1256 1353 4.974721 GCACCACCCCCACCACTG 62.975 72.222 0.00 0.00 0.00 3.66
1257 1354 4.284550 CACCACCCCCACCACTGG 62.285 72.222 0.00 0.00 37.29 4.00
1258 1355 4.525028 ACCACCCCCACCACTGGA 62.525 66.667 0.71 0.00 40.55 3.86
1259 1356 3.650950 CCACCCCCACCACTGGAG 61.651 72.222 0.71 0.00 40.55 3.86
1260 1357 3.650950 CACCCCCACCACTGGAGG 61.651 72.222 0.71 2.88 41.48 4.30
1264 1361 3.402681 CCCACCACTGGAGGCGAT 61.403 66.667 6.02 0.00 40.55 4.58
1479 1618 2.138320 CAGTGATCAAGAAGTGCACGT 58.862 47.619 12.01 8.44 34.82 4.49
1531 1676 0.166814 GAAGCCGACAAGTCATGCAC 59.833 55.000 12.38 4.68 31.71 4.57
1538 1683 0.036952 ACAAGTCATGCACCTCCGAG 60.037 55.000 0.00 0.00 0.00 4.63
1562 1707 3.801698 CTCCTACAATACATGCAGCTGT 58.198 45.455 16.64 0.00 0.00 4.40
1726 1939 3.800506 ACTGTGTCTGCTTGTTTACGTAC 59.199 43.478 0.00 0.00 0.00 3.67
1751 1964 2.306805 TGCATGTATCCATGGGAGGATC 59.693 50.000 13.02 0.00 45.16 3.36
1753 1966 3.621709 GCATGTATCCATGGGAGGATCTG 60.622 52.174 13.02 2.84 45.16 2.90
1756 1969 2.729383 ATCCATGGGAGGATCTGCTA 57.271 50.000 13.02 0.00 45.16 3.49
1757 1970 2.729383 TCCATGGGAGGATCTGCTAT 57.271 50.000 13.02 0.00 33.73 2.97
1766 2004 2.894126 GAGGATCTGCTATTTCCTCCGA 59.106 50.000 6.90 0.00 46.54 4.55
1769 2007 3.368948 GGATCTGCTATTTCCTCCGATCC 60.369 52.174 0.00 0.00 38.81 3.36
1781 2019 6.494666 TTCCTCCGATCCATATTACTTGTT 57.505 37.500 0.00 0.00 0.00 2.83
1785 2023 8.148351 TCCTCCGATCCATATTACTTGTTTTAG 58.852 37.037 0.00 0.00 0.00 1.85
1801 2039 9.686683 ACTTGTTTTAGATTTGCCTAGATACAT 57.313 29.630 0.00 0.00 0.00 2.29
1979 2228 7.864108 TGTGTTTACTTATGATGAATCTGGG 57.136 36.000 0.00 0.00 0.00 4.45
1985 2234 5.240891 ACTTATGATGAATCTGGGCATACG 58.759 41.667 0.00 0.00 0.00 3.06
2006 2255 2.032377 GTGCGAATCGGACAAACAGAAA 60.032 45.455 21.81 0.00 46.80 2.52
2007 2256 2.614520 TGCGAATCGGACAAACAGAAAA 59.385 40.909 4.35 0.00 0.00 2.29
2012 2261 4.830826 ATCGGACAAACAGAAAAGGAAC 57.169 40.909 0.00 0.00 0.00 3.62
2019 2268 3.553828 AACAGAAAAGGAACACGAGGA 57.446 42.857 0.00 0.00 0.00 3.71
2036 2285 0.107459 GGACCTCCCATGTTGCTCTC 60.107 60.000 0.00 0.00 34.14 3.20
2040 2289 2.825836 CCCATGTTGCTCTCCCGC 60.826 66.667 0.00 0.00 0.00 6.13
2049 2298 4.335584 CTCTCCCGCGAGCGATCC 62.336 72.222 19.72 0.00 42.83 3.36
2165 2450 3.334583 TGCAAAGCCACTACTAGGAAG 57.665 47.619 0.00 0.00 0.00 3.46
2377 2663 2.774234 AGAGGTCCAGAGAGAGAGAGAG 59.226 54.545 0.00 0.00 0.00 3.20
2378 2664 2.771943 GAGGTCCAGAGAGAGAGAGAGA 59.228 54.545 0.00 0.00 0.00 3.10
2476 2762 0.104672 TGGAAACTCCCTCAGGTCCA 60.105 55.000 0.00 0.00 37.85 4.02
2731 3017 7.776618 TCTGTTCTACCAGAAGTATTGAGAA 57.223 36.000 0.00 0.00 38.49 2.87
2932 3221 1.474330 CCAATAGGTTTGGCCCTGTC 58.526 55.000 0.00 0.00 38.26 3.51
2941 3230 4.083565 GGTTTGGCCCTGTCTGTAATTTA 58.916 43.478 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 2.877360 TAAGACGATCCACACGCGCC 62.877 60.000 5.73 0.00 0.00 6.53
16 17 1.472276 CTAAGACGATCCACACGCGC 61.472 60.000 5.73 0.00 0.00 6.86
31 33 3.136626 ACCCTAAGCTACCAATGCCTAAG 59.863 47.826 0.00 0.00 0.00 2.18
41 43 1.005569 AGCCCAAAACCCTAAGCTACC 59.994 52.381 0.00 0.00 0.00 3.18
60 62 3.681897 GCCATAGCCAAGACGATCAATAG 59.318 47.826 0.00 0.00 0.00 1.73
62 64 2.498167 GCCATAGCCAAGACGATCAAT 58.502 47.619 0.00 0.00 0.00 2.57
65 67 0.032130 TCGCCATAGCCAAGACGATC 59.968 55.000 0.00 0.00 34.57 3.69
78 80 2.592574 CGCCATCACCATCGCCAT 60.593 61.111 0.00 0.00 0.00 4.40
99 104 9.713740 CAGTGAAGTATCTGCAGAATTTTTATC 57.286 33.333 22.50 12.81 0.00 1.75
111 116 3.129871 GCCTCATCAGTGAAGTATCTGC 58.870 50.000 0.00 0.00 33.05 4.26
117 122 2.106566 AGATCGCCTCATCAGTGAAGT 58.893 47.619 0.00 0.00 33.05 3.01
124 129 1.227060 CACGCAGATCGCCTCATCA 60.227 57.895 4.37 0.00 43.23 3.07
142 153 0.613260 GCTTTCCAAATCCAACCCCC 59.387 55.000 0.00 0.00 0.00 5.40
160 171 3.686726 CCATCCTTACTTGAACAGACTGC 59.313 47.826 1.25 0.00 0.00 4.40
230 248 1.154836 GAGCAAACGTCGTCGCAAG 60.155 57.895 18.56 1.44 41.18 4.01
317 335 0.103026 CACGATCAGCCATCTTCCGA 59.897 55.000 0.00 0.00 0.00 4.55
318 336 0.179100 ACACGATCAGCCATCTTCCG 60.179 55.000 0.00 0.00 0.00 4.30
328 346 1.280982 CGAACCCATCACACGATCAG 58.719 55.000 0.00 0.00 0.00 2.90
329 347 0.606096 ACGAACCCATCACACGATCA 59.394 50.000 0.00 0.00 0.00 2.92
362 380 1.838077 CGGAGGAGGAAACCATACCTT 59.162 52.381 0.00 0.00 36.57 3.50
398 417 1.302907 ACTCCAAATCTGGCATCCCT 58.697 50.000 0.00 0.00 43.17 4.20
402 421 2.232941 CAGCAAACTCCAAATCTGGCAT 59.767 45.455 0.00 0.00 43.17 4.40
411 430 1.295792 GACACGTCAGCAAACTCCAA 58.704 50.000 0.00 0.00 0.00 3.53
421 440 0.939577 CAACACTCCGGACACGTCAG 60.940 60.000 0.00 0.00 38.78 3.51
443 463 2.598589 CCGTTAAACGAATCAGACCGA 58.401 47.619 0.00 0.00 46.05 4.69
458 478 2.500392 AGGTAAAGCCAATGCCGTTA 57.500 45.000 0.00 0.00 40.61 3.18
466 486 3.422796 TCGCCAATAAAGGTAAAGCCAA 58.577 40.909 0.00 0.00 40.61 4.52
513 533 1.873863 CGGCTCCGTCGCTGATATA 59.126 57.895 0.00 0.00 38.57 0.86
535 555 0.752658 CATCACCATACCCGAGCTCA 59.247 55.000 15.40 0.00 0.00 4.26
550 572 5.356751 CCAAAGGAATAATGACGGAACATCA 59.643 40.000 0.00 0.00 32.53 3.07
552 574 5.125417 CACCAAAGGAATAATGACGGAACAT 59.875 40.000 0.00 0.00 0.00 2.71
555 577 4.698304 GTCACCAAAGGAATAATGACGGAA 59.302 41.667 0.00 0.00 0.00 4.30
565 589 2.958355 CCACAACAGTCACCAAAGGAAT 59.042 45.455 0.00 0.00 0.00 3.01
618 643 2.548875 CGAAGAATCCTCTGAGCTTGG 58.451 52.381 0.00 0.00 30.03 3.61
642 674 7.323656 CGAGCCAAGAAGTAAAAATACAAACAG 59.676 37.037 0.00 0.00 0.00 3.16
667 700 1.134175 ACCTGGCAAAACAGAAACACG 59.866 47.619 0.00 0.00 40.97 4.49
678 711 2.300723 ACGTACATACTGACCTGGCAAA 59.699 45.455 0.00 0.00 0.00 3.68
680 713 1.203758 CACGTACATACTGACCTGGCA 59.796 52.381 0.00 0.00 0.00 4.92
681 714 1.470979 CCACGTACATACTGACCTGGC 60.471 57.143 0.00 0.00 0.00 4.85
682 715 1.470979 GCCACGTACATACTGACCTGG 60.471 57.143 0.00 0.00 0.00 4.45
683 716 1.476891 AGCCACGTACATACTGACCTG 59.523 52.381 0.00 0.00 0.00 4.00
684 717 1.848652 AGCCACGTACATACTGACCT 58.151 50.000 0.00 0.00 0.00 3.85
685 718 2.268298 CAAGCCACGTACATACTGACC 58.732 52.381 0.00 0.00 0.00 4.02
686 719 2.955614 ACAAGCCACGTACATACTGAC 58.044 47.619 0.00 0.00 0.00 3.51
687 720 3.760151 AGTACAAGCCACGTACATACTGA 59.240 43.478 9.73 0.00 41.40 3.41
688 721 4.106029 AGTACAAGCCACGTACATACTG 57.894 45.455 9.73 0.00 41.40 2.74
689 722 5.591472 TCATAGTACAAGCCACGTACATACT 59.409 40.000 9.73 0.00 41.40 2.12
690 723 5.824429 TCATAGTACAAGCCACGTACATAC 58.176 41.667 9.73 0.00 41.40 2.39
691 724 6.644248 ATCATAGTACAAGCCACGTACATA 57.356 37.500 9.73 2.10 41.40 2.29
692 725 4.994907 TCATAGTACAAGCCACGTACAT 57.005 40.909 9.73 1.12 41.40 2.29
693 726 4.994907 ATCATAGTACAAGCCACGTACA 57.005 40.909 9.73 0.00 41.40 2.90
694 727 5.589192 AGAATCATAGTACAAGCCACGTAC 58.411 41.667 0.00 0.00 39.64 3.67
695 728 5.847111 AGAATCATAGTACAAGCCACGTA 57.153 39.130 0.00 0.00 0.00 3.57
696 729 4.737855 AGAATCATAGTACAAGCCACGT 57.262 40.909 0.00 0.00 0.00 4.49
697 730 6.923508 TCATAAGAATCATAGTACAAGCCACG 59.076 38.462 0.00 0.00 0.00 4.94
698 731 8.839310 ATCATAAGAATCATAGTACAAGCCAC 57.161 34.615 0.00 0.00 0.00 5.01
743 776 9.719279 AATACGTGTCTTATTTTTGTCGAAAAA 57.281 25.926 0.00 0.00 43.51 1.94
745 778 9.796062 GTAATACGTGTCTTATTTTTGTCGAAA 57.204 29.630 0.00 0.00 0.00 3.46
746 779 8.434661 GGTAATACGTGTCTTATTTTTGTCGAA 58.565 33.333 0.00 0.00 0.00 3.71
747 780 7.598118 TGGTAATACGTGTCTTATTTTTGTCGA 59.402 33.333 0.00 0.00 0.00 4.20
748 781 7.731720 TGGTAATACGTGTCTTATTTTTGTCG 58.268 34.615 0.00 0.00 0.00 4.35
749 782 9.485591 CATGGTAATACGTGTCTTATTTTTGTC 57.514 33.333 0.00 0.00 0.00 3.18
750 783 9.221933 TCATGGTAATACGTGTCTTATTTTTGT 57.778 29.630 0.00 0.00 0.00 2.83
783 816 5.246203 GGGGAGTAGATTAGTGTCATGCATA 59.754 44.000 0.00 0.00 0.00 3.14
785 818 3.388024 GGGGAGTAGATTAGTGTCATGCA 59.612 47.826 0.00 0.00 0.00 3.96
786 819 3.388024 TGGGGAGTAGATTAGTGTCATGC 59.612 47.826 0.00 0.00 0.00 4.06
789 830 4.332683 AGTGGGGAGTAGATTAGTGTCA 57.667 45.455 0.00 0.00 0.00 3.58
792 833 6.071984 AGTCATAGTGGGGAGTAGATTAGTG 58.928 44.000 0.00 0.00 0.00 2.74
798 839 3.181431 GGCTAGTCATAGTGGGGAGTAGA 60.181 52.174 7.50 0.00 38.68 2.59
799 840 3.158676 GGCTAGTCATAGTGGGGAGTAG 58.841 54.545 0.00 0.00 39.15 2.57
804 845 1.887198 CTACGGCTAGTCATAGTGGGG 59.113 57.143 0.00 0.00 0.00 4.96
815 856 2.361119 TGCATGTTACTCCTACGGCTAG 59.639 50.000 0.00 0.00 0.00 3.42
848 889 3.610585 CGCCATTTTACACGGTTGACATT 60.611 43.478 0.00 0.00 0.00 2.71
858 899 5.025826 GCATGTTACTACGCCATTTTACAC 58.974 41.667 0.00 0.00 0.00 2.90
863 904 3.489059 GCATGCATGTTACTACGCCATTT 60.489 43.478 26.79 0.00 0.00 2.32
907 948 3.059884 ACTGAAATATGCGTAGATGCGG 58.940 45.455 0.00 0.00 37.81 5.69
909 950 5.406477 TCATCACTGAAATATGCGTAGATGC 59.594 40.000 0.00 0.00 32.58 3.91
962 1009 1.078143 GAAGGAGCCGAGGTGCATT 60.078 57.895 0.00 0.00 0.00 3.56
968 1015 2.066393 TCCATGGAAGGAGCCGAGG 61.066 63.158 13.46 0.00 32.77 4.63
985 1033 6.149807 AGAGAACTGTAACTACTGCTGTACTC 59.850 42.308 0.00 2.45 0.00 2.59
992 1040 4.159857 CACGAGAGAACTGTAACTACTGC 58.840 47.826 0.00 0.00 0.00 4.40
1022 1070 1.410882 GTAGACCTTGAGCTAGCCAGG 59.589 57.143 19.24 19.24 0.00 4.45
1039 1087 1.898154 CCCTGGACACGGGAAGTAG 59.102 63.158 0.00 0.00 46.80 2.57
1041 1089 3.637273 GCCCTGGACACGGGAAGT 61.637 66.667 0.00 0.00 46.80 3.01
1055 1104 2.125952 GTTGAAGCCATTGCGCCC 60.126 61.111 4.18 0.00 44.33 6.13
1069 1118 1.364626 GAGAGCGGATGCACCTGTTG 61.365 60.000 0.00 0.00 46.23 3.33
1070 1119 1.078848 GAGAGCGGATGCACCTGTT 60.079 57.895 0.00 0.00 46.23 3.16
1071 1120 2.285773 TGAGAGCGGATGCACCTGT 61.286 57.895 0.00 0.00 46.23 4.00
1080 1132 0.681733 AGCTTCAAAGTGAGAGCGGA 59.318 50.000 0.00 0.00 36.41 5.54
1092 1144 2.110213 AACGACGGCCAGCTTCAA 59.890 55.556 2.24 0.00 0.00 2.69
1239 1336 4.974721 CAGTGGTGGGGGTGGTGC 62.975 72.222 0.00 0.00 0.00 5.01
1240 1337 4.284550 CCAGTGGTGGGGGTGGTG 62.285 72.222 0.00 0.00 40.67 4.17
1241 1338 4.525028 TCCAGTGGTGGGGGTGGT 62.525 66.667 9.54 0.00 45.11 4.16
1242 1339 3.650950 CTCCAGTGGTGGGGGTGG 61.651 72.222 9.54 0.00 41.33 4.61
1247 1344 2.063979 TATCGCCTCCAGTGGTGGG 61.064 63.158 27.55 21.53 45.11 4.61
1248 1345 1.144057 GTATCGCCTCCAGTGGTGG 59.856 63.158 23.58 23.58 46.63 4.61
1249 1346 1.144057 GGTATCGCCTCCAGTGGTG 59.856 63.158 9.54 6.66 38.85 4.17
1250 1347 1.305802 TGGTATCGCCTCCAGTGGT 60.306 57.895 9.54 0.00 38.35 4.16
1251 1348 1.144057 GTGGTATCGCCTCCAGTGG 59.856 63.158 1.40 1.40 38.35 4.00
1252 1349 4.835927 GTGGTATCGCCTCCAGTG 57.164 61.111 0.00 0.00 38.35 3.66
1256 1353 2.416260 GTCGGTGGTATCGCCTCC 59.584 66.667 3.62 0.00 45.21 4.30
1257 1354 2.025727 CGTCGGTGGTATCGCCTC 59.974 66.667 3.62 0.00 41.26 4.70
1258 1355 4.203076 GCGTCGGTGGTATCGCCT 62.203 66.667 3.62 0.00 42.33 5.52
1259 1356 4.501714 TGCGTCGGTGGTATCGCC 62.502 66.667 0.00 0.00 46.57 5.54
1261 1358 2.278596 CCTGCGTCGGTGGTATCG 60.279 66.667 0.00 0.00 0.00 2.92
1262 1359 2.585247 GCCTGCGTCGGTGGTATC 60.585 66.667 0.00 0.00 0.00 2.24
1263 1360 4.508128 CGCCTGCGTCGGTGGTAT 62.508 66.667 2.83 0.00 34.35 2.73
1531 1676 1.115467 ATTGTAGGAGCACTCGGAGG 58.885 55.000 10.23 0.00 0.00 4.30
1538 1683 2.289002 GCTGCATGTATTGTAGGAGCAC 59.711 50.000 0.00 0.00 38.40 4.40
1562 1707 4.649310 TCACGGCTGTACGCGCAA 62.649 61.111 5.73 0.00 40.44 4.85
1675 1884 6.460261 CCATAGAGTACATGTATAGCCGGATG 60.460 46.154 5.05 0.22 0.00 3.51
1751 1964 3.692257 ATGGATCGGAGGAAATAGCAG 57.308 47.619 0.00 0.00 0.00 4.24
1753 1966 6.879400 AGTAATATGGATCGGAGGAAATAGC 58.121 40.000 0.00 0.00 0.00 2.97
1756 1969 7.079451 ACAAGTAATATGGATCGGAGGAAAT 57.921 36.000 0.00 0.00 0.00 2.17
1757 1970 6.494666 ACAAGTAATATGGATCGGAGGAAA 57.505 37.500 0.00 0.00 0.00 3.13
1985 2234 1.144969 TCTGTTTGTCCGATTCGCAC 58.855 50.000 0.00 0.00 0.00 5.34
2002 2251 2.037381 GAGGTCCTCGTGTTCCTTTTCT 59.963 50.000 2.28 0.00 0.00 2.52
2006 2255 1.192803 GGGAGGTCCTCGTGTTCCTT 61.193 60.000 12.91 0.00 35.95 3.36
2007 2256 1.609794 GGGAGGTCCTCGTGTTCCT 60.610 63.158 12.91 0.00 35.95 3.36
2012 2261 0.391661 CAACATGGGAGGTCCTCGTG 60.392 60.000 12.91 13.08 36.20 4.35
2019 2268 1.566298 GGGAGAGCAACATGGGAGGT 61.566 60.000 0.00 0.00 0.00 3.85
2036 2285 3.544167 CTACTGGATCGCTCGCGGG 62.544 68.421 6.13 2.60 40.25 6.13
2040 2289 2.541999 GGTTTCTCTACTGGATCGCTCG 60.542 54.545 0.00 0.00 0.00 5.03
2049 2298 2.418334 GGCGGGTAAGGTTTCTCTACTG 60.418 54.545 0.00 0.00 0.00 2.74
2052 2301 0.819582 CGGCGGGTAAGGTTTCTCTA 59.180 55.000 0.00 0.00 0.00 2.43
2099 2348 4.591321 AACTTCATCAAAGCCAGGGATA 57.409 40.909 0.00 0.00 38.67 2.59
2302 2587 3.273434 TCATTCAGCTCACCTGCAATAC 58.727 45.455 0.00 0.00 41.50 1.89
2377 2663 7.175293 CCAGTGTTATACTCACCCTCTAGTATC 59.825 44.444 0.00 0.00 39.19 2.24
2378 2664 7.005296 CCAGTGTTATACTCACCCTCTAGTAT 58.995 42.308 0.00 0.00 40.92 2.12
2456 2742 1.064825 GGACCTGAGGGAGTTTCCAA 58.935 55.000 2.38 0.00 38.64 3.53
2476 2762 0.192566 TACCTTGGGTGTCCTCCACT 59.807 55.000 0.00 0.00 43.94 4.00
2602 2888 9.428097 GGACTTTCAAGCAAATTAAAATGATCT 57.572 29.630 0.00 0.00 0.00 2.75
2941 3230 5.045286 AGCAGTCTGATTGGGAGAAATTAGT 60.045 40.000 3.32 0.00 0.00 2.24
2956 3245 2.224621 CCCTTTCAGGAAAGCAGTCTGA 60.225 50.000 14.76 0.00 44.76 3.27


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

AutoCloner maintained by Alex Coulton.