Multiple sequence alignment - TraesCS3A01G219300

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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 TraesCS3A01G219300 chr3A 100.000 3479 0 0 1 3479 402137682 402134204 0.000000e+00 6425.0
1 TraesCS3A01G219300 chr3A 93.396 106 5 2 1611 1714 443203692 443203587 4.650000e-34 156.0
2 TraesCS3A01G219300 chr3D 94.891 1781 53 21 1712 3478 321872164 321873920 0.000000e+00 2750.0
3 TraesCS3A01G219300 chr3D 93.972 846 30 8 796 1631 321871332 321872166 0.000000e+00 1260.0
4 TraesCS3A01G219300 chr3D 96.662 719 19 2 10 728 404559692 404560405 0.000000e+00 1190.0
5 TraesCS3A01G219300 chr3D 89.583 144 15 0 3130 3273 508465557 508465700 2.130000e-42 183.0
6 TraesCS3A01G219300 chr3D 94.737 95 5 0 1620 1714 263991631 263991725 7.780000e-32 148.0
7 TraesCS3A01G219300 chr3D 93.137 102 6 1 1629 1730 347592745 347592645 7.780000e-32 148.0
8 TraesCS3A01G219300 chr3D 81.967 183 14 8 3271 3440 508466470 508466646 1.680000e-28 137.0
9 TraesCS3A01G219300 chr3D 81.188 101 5 2 2968 3068 606777996 606777910 6.230000e-08 69.4
10 TraesCS3A01G219300 chr3B 94.976 836 28 6 792 1627 397679313 397678492 0.000000e+00 1299.0
11 TraesCS3A01G219300 chr3B 93.634 864 29 13 2626 3479 397677486 397676639 0.000000e+00 1267.0
12 TraesCS3A01G219300 chr3B 87.764 899 71 14 1716 2584 397678486 397677597 0.000000e+00 1014.0
13 TraesCS3A01G219300 chr3B 89.788 519 38 5 217 725 466387545 466388058 0.000000e+00 651.0
14 TraesCS3A01G219300 chr3B 90.175 458 13 14 10 467 478042350 478042775 5.040000e-158 568.0
15 TraesCS3A01G219300 chr3B 88.060 268 9 7 461 728 478047933 478048177 2.630000e-76 296.0
16 TraesCS3A01G219300 chr1B 94.049 857 34 10 2626 3479 637912902 637912060 0.000000e+00 1284.0
17 TraesCS3A01G219300 chr1B 86.318 899 75 22 1716 2587 637913886 637913009 0.000000e+00 935.0
18 TraesCS3A01G219300 chr1B 91.992 512 35 4 217 728 666941686 666942191 0.000000e+00 713.0
19 TraesCS3A01G219300 chr1B 90.336 476 33 3 217 682 289305076 289305548 2.300000e-171 612.0
20 TraesCS3A01G219300 chr1B 93.204 103 6 1 1620 1722 633092466 633092365 2.160000e-32 150.0
21 TraesCS3A01G219300 chr1B 97.059 34 1 0 2968 3001 565340907 565340940 1.350000e-04 58.4
22 TraesCS3A01G219300 chr1D 94.661 768 29 5 860 1627 462968196 462967441 0.000000e+00 1181.0
23 TraesCS3A01G219300 chr1D 94.271 768 32 7 860 1627 462927762 462927007 0.000000e+00 1164.0
24 TraesCS3A01G219300 chr1D 94.141 768 33 8 860 1627 462890812 462890057 0.000000e+00 1158.0
25 TraesCS3A01G219300 chr1D 94.010 768 34 7 860 1627 462913885 462913130 0.000000e+00 1153.0
26 TraesCS3A01G219300 chr1D 93.880 768 35 8 860 1627 462898498 462897743 0.000000e+00 1147.0
27 TraesCS3A01G219300 chr1D 93.880 768 34 8 860 1627 462921112 462920358 0.000000e+00 1146.0
28 TraesCS3A01G219300 chr1D 87.208 899 69 19 1716 2587 462966492 462965613 0.000000e+00 981.0
29 TraesCS3A01G219300 chr1D 93.323 659 26 10 2824 3479 462947671 462947028 0.000000e+00 957.0
30 TraesCS3A01G219300 chr1D 92.079 404 22 6 1716 2113 462904471 462904072 8.430000e-156 560.0
31 TraesCS3A01G219300 chr1D 91.832 404 23 6 1716 2113 462909554 462909155 3.920000e-154 555.0
32 TraesCS3A01G219300 chr1D 91.832 404 23 6 1716 2113 462916782 462916383 3.920000e-154 555.0
33 TraesCS3A01G219300 chr1D 91.542 402 24 6 1718 2113 462907008 462906611 2.360000e-151 545.0
34 TraesCS3A01G219300 chr1D 93.301 209 11 1 2626 2834 462965506 462965301 4.360000e-79 305.0
35 TraesCS3A01G219300 chr1D 91.667 108 6 3 1609 1714 485967746 485967852 2.800000e-31 147.0
36 TraesCS3A01G219300 chr2D 94.394 767 33 3 861 1627 634645040 634645796 0.000000e+00 1170.0
37 TraesCS3A01G219300 chr2D 87.458 901 66 19 1716 2587 634646754 634647636 0.000000e+00 994.0
38 TraesCS3A01G219300 chr2D 93.416 562 15 10 2922 3479 634649448 634649991 0.000000e+00 813.0
39 TraesCS3A01G219300 chr2D 93.750 304 16 1 2631 2934 634647748 634648048 1.470000e-123 453.0
40 TraesCS3A01G219300 chr4A 94.298 719 36 2 10 728 208812767 208813480 0.000000e+00 1096.0
41 TraesCS3A01G219300 chr5A 89.430 719 23 10 10 728 29421353 29420688 0.000000e+00 857.0
42 TraesCS3A01G219300 chr2B 88.734 719 25 10 10 728 3510891 3510229 0.000000e+00 828.0
43 TraesCS3A01G219300 chr2B 89.916 476 34 4 217 682 410188602 410189073 4.970000e-168 601.0
44 TraesCS3A01G219300 chr4D 90.631 523 33 5 217 728 81332149 81331632 0.000000e+00 680.0
45 TraesCS3A01G219300 chr5B 94.952 416 17 3 12 425 439431282 439431695 0.000000e+00 649.0
46 TraesCS3A01G219300 chr5B 90.851 470 29 4 217 676 361488523 361488058 4.930000e-173 617.0
47 TraesCS3A01G219300 chr6B 94.762 420 14 4 12 425 64111159 64111576 0.000000e+00 647.0
48 TraesCS3A01G219300 chr7D 91.685 457 35 3 44 498 27557849 27557394 6.340000e-177 630.0
49 TraesCS3A01G219300 chr7D 96.512 344 10 1 6 349 18125221 18125562 5.040000e-158 568.0
50 TraesCS3A01G219300 chr7D 85.075 268 24 6 3184 3440 41303797 41303535 3.440000e-65 259.0
51 TraesCS3A01G219300 chr7D 86.758 219 14 4 2968 3186 41306360 41306157 2.700000e-56 230.0
52 TraesCS3A01G219300 chr7D 87.500 104 10 3 1622 1724 494609360 494609461 2.190000e-22 117.0
53 TraesCS3A01G219300 chr4B 90.126 476 33 4 217 682 145517465 145517936 1.070000e-169 606.0
54 TraesCS3A01G219300 chr4B 94.118 102 2 3 1628 1729 29271837 29271934 6.010000e-33 152.0
55 TraesCS3A01G219300 chr6A 85.677 384 38 7 3107 3479 508249112 508249489 4.210000e-104 388.0
56 TraesCS3A01G219300 chr6D 86.517 178 11 5 3312 3479 367749542 367749716 2.130000e-42 183.0
57 TraesCS3A01G219300 chr7A 94.845 97 5 0 1621 1717 80994174 80994078 6.010000e-33 152.0
58 TraesCS3A01G219300 chr1A 91.667 108 6 3 1616 1721 575557256 575557362 2.800000e-31 147.0
59 TraesCS3A01G219300 chr1A 91.667 108 6 3 1609 1714 583530832 583530938 2.800000e-31 147.0


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 TraesCS3A01G219300 chr3A 402134204 402137682 3478 True 6425.000000 6425 100.000000 1 3479 1 chr3A.!!$R1 3478
1 TraesCS3A01G219300 chr3D 321871332 321873920 2588 False 2005.000000 2750 94.431500 796 3478 2 chr3D.!!$F3 2682
2 TraesCS3A01G219300 chr3D 404559692 404560405 713 False 1190.000000 1190 96.662000 10 728 1 chr3D.!!$F2 718
3 TraesCS3A01G219300 chr3B 397676639 397679313 2674 True 1193.333333 1299 92.124667 792 3479 3 chr3B.!!$R1 2687
4 TraesCS3A01G219300 chr3B 466387545 466388058 513 False 651.000000 651 89.788000 217 725 1 chr3B.!!$F1 508
5 TraesCS3A01G219300 chr1B 637912060 637913886 1826 True 1109.500000 1284 90.183500 1716 3479 2 chr1B.!!$R2 1763
6 TraesCS3A01G219300 chr1B 666941686 666942191 505 False 713.000000 713 91.992000 217 728 1 chr1B.!!$F3 511
7 TraesCS3A01G219300 chr1D 462927007 462927762 755 True 1164.000000 1164 94.271000 860 1627 1 chr1D.!!$R3 767
8 TraesCS3A01G219300 chr1D 462890057 462890812 755 True 1158.000000 1158 94.141000 860 1627 1 chr1D.!!$R1 767
9 TraesCS3A01G219300 chr1D 462897743 462898498 755 True 1147.000000 1147 93.880000 860 1627 1 chr1D.!!$R2 767
10 TraesCS3A01G219300 chr1D 462947028 462947671 643 True 957.000000 957 93.323000 2824 3479 1 chr1D.!!$R4 655
11 TraesCS3A01G219300 chr1D 462965301 462968196 2895 True 822.333333 1181 91.723333 860 2834 3 chr1D.!!$R6 1974
12 TraesCS3A01G219300 chr1D 462904072 462921112 17040 True 752.333333 1153 92.529167 860 2113 6 chr1D.!!$R5 1253
13 TraesCS3A01G219300 chr2D 634645040 634649991 4951 False 857.500000 1170 92.254500 861 3479 4 chr2D.!!$F1 2618
14 TraesCS3A01G219300 chr4A 208812767 208813480 713 False 1096.000000 1096 94.298000 10 728 1 chr4A.!!$F1 718
15 TraesCS3A01G219300 chr5A 29420688 29421353 665 True 857.000000 857 89.430000 10 728 1 chr5A.!!$R1 718
16 TraesCS3A01G219300 chr2B 3510229 3510891 662 True 828.000000 828 88.734000 10 728 1 chr2B.!!$R1 718
17 TraesCS3A01G219300 chr4D 81331632 81332149 517 True 680.000000 680 90.631000 217 728 1 chr4D.!!$R1 511
18 TraesCS3A01G219300 chr7D 41303535 41306360 2825 True 244.500000 259 85.916500 2968 3440 2 chr7D.!!$R2 472

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
130 131 0.249031 TCTGACTATGGATGCACGCG 60.249 55.0 3.53 3.53 0.00 6.01 F
1485 1511 0.029967 TGCTCGATCTCATGCTCGAC 59.970 55.0 9.76 8.32 38.86 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1848 15143 0.037326 AGCCATGTCGTCGTTGATGT 60.037 50.000 0.0 0.0 0.0 3.06 R
3164 19146 4.445452 ACAGATGGACATGCACAATTTC 57.555 40.909 0.0 0.0 0.0 2.17 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
40 41 5.770162 CCAGTTCAGTTTCCATTAGAAAGGT 59.230 40.000 0.00 0.00 45.11 3.50
41 42 6.940298 CCAGTTCAGTTTCCATTAGAAAGGTA 59.060 38.462 0.00 0.00 45.11 3.08
130 131 0.249031 TCTGACTATGGATGCACGCG 60.249 55.000 3.53 3.53 0.00 6.01
201 202 3.068873 CCGGATTAGAGAGAGGGAACAAG 59.931 52.174 0.00 0.00 0.00 3.16
259 260 4.759782 AGACCCTAATCAAACATCACGAG 58.240 43.478 0.00 0.00 0.00 4.18
327 328 7.627311 TCCAAAGGATGATCCATCAGTATATG 58.373 38.462 14.90 0.00 42.13 1.78
364 376 4.154195 ACGAATGATTACCAACTCAAGCAC 59.846 41.667 0.00 0.00 0.00 4.40
737 749 4.114997 CCGGCGCCATGTTGGTTC 62.115 66.667 28.98 0.00 40.46 3.62
738 750 4.459331 CGGCGCCATGTTGGTTCG 62.459 66.667 28.98 3.82 40.46 3.95
739 751 4.776647 GGCGCCATGTTGGTTCGC 62.777 66.667 24.80 9.23 44.56 4.70
740 752 3.737172 GCGCCATGTTGGTTCGCT 61.737 61.111 0.00 0.00 42.87 4.93
741 753 2.953821 CGCCATGTTGGTTCGCTT 59.046 55.556 0.00 0.00 40.46 4.68
742 754 1.154225 CGCCATGTTGGTTCGCTTC 60.154 57.895 0.00 0.00 40.46 3.86
743 755 1.212751 GCCATGTTGGTTCGCTTCC 59.787 57.895 0.00 0.00 40.46 3.46
744 756 1.883021 CCATGTTGGTTCGCTTCCC 59.117 57.895 0.00 0.00 31.35 3.97
745 757 0.609131 CCATGTTGGTTCGCTTCCCT 60.609 55.000 0.00 0.00 31.35 4.20
746 758 1.247567 CATGTTGGTTCGCTTCCCTT 58.752 50.000 0.00 0.00 0.00 3.95
747 759 1.613437 CATGTTGGTTCGCTTCCCTTT 59.387 47.619 0.00 0.00 0.00 3.11
748 760 1.028905 TGTTGGTTCGCTTCCCTTTG 58.971 50.000 0.00 0.00 0.00 2.77
749 761 0.318699 GTTGGTTCGCTTCCCTTTGC 60.319 55.000 0.00 0.00 0.00 3.68
750 762 0.753479 TTGGTTCGCTTCCCTTTGCA 60.753 50.000 0.00 0.00 0.00 4.08
751 763 0.539438 TGGTTCGCTTCCCTTTGCAT 60.539 50.000 0.00 0.00 0.00 3.96
752 764 0.603065 GGTTCGCTTCCCTTTGCATT 59.397 50.000 0.00 0.00 0.00 3.56
753 765 1.669795 GGTTCGCTTCCCTTTGCATTG 60.670 52.381 0.00 0.00 0.00 2.82
754 766 1.000274 GTTCGCTTCCCTTTGCATTGT 60.000 47.619 0.00 0.00 0.00 2.71
755 767 1.327303 TCGCTTCCCTTTGCATTGTT 58.673 45.000 0.00 0.00 0.00 2.83
756 768 1.000385 TCGCTTCCCTTTGCATTGTTG 60.000 47.619 0.00 0.00 0.00 3.33
757 769 1.799544 GCTTCCCTTTGCATTGTTGG 58.200 50.000 0.00 0.00 0.00 3.77
758 770 1.344114 GCTTCCCTTTGCATTGTTGGA 59.656 47.619 0.00 0.00 0.00 3.53
759 771 2.867647 GCTTCCCTTTGCATTGTTGGAC 60.868 50.000 0.00 0.00 0.00 4.02
760 772 2.380064 TCCCTTTGCATTGTTGGACT 57.620 45.000 0.00 0.00 0.00 3.85
761 773 1.962807 TCCCTTTGCATTGTTGGACTG 59.037 47.619 0.00 0.00 0.00 3.51
762 774 1.688197 CCCTTTGCATTGTTGGACTGT 59.312 47.619 0.00 0.00 0.00 3.55
763 775 2.102925 CCCTTTGCATTGTTGGACTGTT 59.897 45.455 0.00 0.00 0.00 3.16
764 776 3.125316 CCTTTGCATTGTTGGACTGTTG 58.875 45.455 0.00 0.00 0.00 3.33
765 777 3.181477 CCTTTGCATTGTTGGACTGTTGA 60.181 43.478 0.00 0.00 0.00 3.18
766 778 4.501915 CCTTTGCATTGTTGGACTGTTGAT 60.502 41.667 0.00 0.00 0.00 2.57
767 779 4.669206 TTGCATTGTTGGACTGTTGATT 57.331 36.364 0.00 0.00 0.00 2.57
768 780 4.669206 TGCATTGTTGGACTGTTGATTT 57.331 36.364 0.00 0.00 0.00 2.17
769 781 4.370049 TGCATTGTTGGACTGTTGATTTG 58.630 39.130 0.00 0.00 0.00 2.32
770 782 3.184986 GCATTGTTGGACTGTTGATTTGC 59.815 43.478 0.00 0.00 0.00 3.68
771 783 4.624015 CATTGTTGGACTGTTGATTTGCT 58.376 39.130 0.00 0.00 0.00 3.91
772 784 4.734398 TTGTTGGACTGTTGATTTGCTT 57.266 36.364 0.00 0.00 0.00 3.91
773 785 4.044336 TGTTGGACTGTTGATTTGCTTG 57.956 40.909 0.00 0.00 0.00 4.01
774 786 3.698539 TGTTGGACTGTTGATTTGCTTGA 59.301 39.130 0.00 0.00 0.00 3.02
775 787 4.159321 TGTTGGACTGTTGATTTGCTTGAA 59.841 37.500 0.00 0.00 0.00 2.69
776 788 4.305989 TGGACTGTTGATTTGCTTGAAC 57.694 40.909 0.00 0.00 0.00 3.18
777 789 3.243035 TGGACTGTTGATTTGCTTGAACG 60.243 43.478 0.00 0.00 0.00 3.95
778 790 3.300009 GACTGTTGATTTGCTTGAACGG 58.700 45.455 0.00 0.00 0.00 4.44
779 791 2.948979 ACTGTTGATTTGCTTGAACGGA 59.051 40.909 0.00 0.00 0.00 4.69
780 792 3.380004 ACTGTTGATTTGCTTGAACGGAA 59.620 39.130 0.00 0.00 0.00 4.30
781 793 3.963665 TGTTGATTTGCTTGAACGGAAG 58.036 40.909 0.00 0.00 0.00 3.46
782 794 3.243367 TGTTGATTTGCTTGAACGGAAGG 60.243 43.478 0.00 0.00 0.00 3.46
783 795 2.857483 TGATTTGCTTGAACGGAAGGA 58.143 42.857 0.00 0.00 0.00 3.36
784 796 3.218453 TGATTTGCTTGAACGGAAGGAA 58.782 40.909 0.00 0.00 32.07 3.36
785 797 3.634448 TGATTTGCTTGAACGGAAGGAAA 59.366 39.130 11.29 11.29 44.32 3.13
786 798 4.098654 TGATTTGCTTGAACGGAAGGAAAA 59.901 37.500 12.41 0.00 43.69 2.29
787 799 4.457834 TTTGCTTGAACGGAAGGAAAAA 57.542 36.364 7.86 0.00 39.47 1.94
809 821 1.002659 TGAACATAACAGGACCCACCG 59.997 52.381 0.00 0.00 44.74 4.94
812 824 2.676265 ATAACAGGACCCACCGCCC 61.676 63.158 0.00 0.00 44.74 6.13
828 840 1.961180 GCCCGCAGAGGAAGCTAGAA 61.961 60.000 0.00 0.00 45.00 2.10
892 906 4.422840 CATAGACTCTGTCTCTGCACTTG 58.577 47.826 3.30 0.00 42.40 3.16
894 908 3.491342 AGACTCTGTCTCTGCACTTGTA 58.509 45.455 0.00 0.00 38.71 2.41
906 920 5.588240 TCTGCACTTGTATTGTATAGGACG 58.412 41.667 0.00 0.00 0.00 4.79
908 922 5.106442 TGCACTTGTATTGTATAGGACGTG 58.894 41.667 0.00 0.00 0.00 4.49
965 979 0.399091 CAGATCTGCCTCCTACCCCA 60.399 60.000 10.38 0.00 0.00 4.96
970 984 0.471617 CTGCCTCCTACCCCATCTTG 59.528 60.000 0.00 0.00 0.00 3.02
1101 1120 0.733729 CTCCTACGGTCTTCCTCACG 59.266 60.000 0.00 0.00 0.00 4.35
1233 1252 2.413351 GGATGAGCGCGCAGAGTA 59.587 61.111 35.10 14.43 0.00 2.59
1399 1424 2.248487 GAGTGCTTCAAGGTACGTACG 58.752 52.381 18.98 15.01 0.00 3.67
1400 1425 1.610522 AGTGCTTCAAGGTACGTACGT 59.389 47.619 25.98 25.98 0.00 3.57
1401 1426 2.813754 AGTGCTTCAAGGTACGTACGTA 59.186 45.455 23.60 23.60 0.00 3.57
1429 1454 2.103263 ACTCACGTCTCCTCTGCTTTTT 59.897 45.455 0.00 0.00 0.00 1.94
1485 1511 0.029967 TGCTCGATCTCATGCTCGAC 59.970 55.000 9.76 8.32 38.86 4.20
1493 1519 3.869272 CATGCTCGACTTGCGGCC 61.869 66.667 0.00 0.00 41.33 6.13
1578 1604 1.005394 TTCGGAGTGAAAGGCGGTC 60.005 57.895 0.00 0.00 32.37 4.79
1640 10328 7.185318 TCATTTATTTTGTACTCCCTCCGTA 57.815 36.000 0.00 0.00 0.00 4.02
1641 10329 7.622713 TCATTTATTTTGTACTCCCTCCGTAA 58.377 34.615 0.00 0.00 0.00 3.18
1642 10330 8.102047 TCATTTATTTTGTACTCCCTCCGTAAA 58.898 33.333 0.00 0.00 0.00 2.01
1643 10331 7.671495 TTTATTTTGTACTCCCTCCGTAAAC 57.329 36.000 0.00 0.00 0.00 2.01
1644 10332 4.961438 TTTTGTACTCCCTCCGTAAACT 57.039 40.909 0.00 0.00 0.00 2.66
1649 10337 7.902920 TTGTACTCCCTCCGTAAACTAATAT 57.097 36.000 0.00 0.00 0.00 1.28
1651 10339 8.995027 TGTACTCCCTCCGTAAACTAATATAA 57.005 34.615 0.00 0.00 0.00 0.98
1653 10341 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
1654 10342 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
1656 10344 8.174733 TCCCTCCGTAAACTAATATAAGAGTG 57.825 38.462 0.00 0.00 0.00 3.51
1658 10346 8.419442 CCCTCCGTAAACTAATATAAGAGTGTT 58.581 37.037 0.00 0.00 0.00 3.32
1659 10347 9.813446 CCTCCGTAAACTAATATAAGAGTGTTT 57.187 33.333 0.00 0.00 0.00 2.83
1741 15033 6.812312 GCATTATACTTTATGCTCAGTCGTC 58.188 40.000 0.00 0.00 42.91 4.20
1780 15075 1.450312 AGCGGCTCAACCACATAGC 60.450 57.895 0.00 0.00 39.03 2.97
1830 15125 0.248866 GGTGAAACACTTGCCCGTTG 60.249 55.000 0.00 0.00 39.98 4.10
1848 15143 0.035915 TGGAATGGATCGTCCGCAAA 60.036 50.000 4.74 0.00 40.17 3.68
1888 15183 2.042464 TCTCAGTCCACAGAAGCAAGT 58.958 47.619 0.00 0.00 0.00 3.16
1889 15184 3.230976 TCTCAGTCCACAGAAGCAAGTA 58.769 45.455 0.00 0.00 0.00 2.24
1890 15185 3.834813 TCTCAGTCCACAGAAGCAAGTAT 59.165 43.478 0.00 0.00 0.00 2.12
1893 15188 3.931468 CAGTCCACAGAAGCAAGTATCAG 59.069 47.826 0.00 0.00 0.00 2.90
1951 15248 2.401583 TGGATGTTGATCTTGGTCCG 57.598 50.000 0.00 0.00 0.00 4.79
1964 15261 2.485122 GTCCGCCAAATCAAGCCG 59.515 61.111 0.00 0.00 0.00 5.52
1997 15294 8.103948 AGTTCTATTTTCAACATCCTTGTCAG 57.896 34.615 0.00 0.00 34.06 3.51
2035 15332 2.261835 GCTACTGCTATGCCGAATCGG 61.262 57.143 18.67 18.67 42.44 4.18
2116 15420 2.101415 GGAGCAATAAAGATGGGCCAAC 59.899 50.000 11.89 8.41 0.00 3.77
2212 15914 6.845302 TCATGAACAGTTTGATGTGATAAGC 58.155 36.000 0.00 0.00 32.52 3.09
2291 15993 3.455990 TGCAAGTGACAGTTTACCGTA 57.544 42.857 0.00 0.00 0.00 4.02
2623 16980 8.450578 TGTTATTATCTTCCAAATAGCCACAG 57.549 34.615 0.00 0.00 0.00 3.66
2624 16981 7.502226 TGTTATTATCTTCCAAATAGCCACAGG 59.498 37.037 0.00 0.00 0.00 4.00
2629 17048 4.534500 TCTTCCAAATAGCCACAGGTTAGA 59.466 41.667 0.00 0.00 0.00 2.10
2643 17062 7.387948 GCCACAGGTTAGAACATATATGGTTAG 59.612 40.741 16.96 0.30 0.00 2.34
2737 17156 3.495001 GTGAAAAGTCTACACTGGACTGC 59.505 47.826 0.00 0.00 42.39 4.40
2740 17159 4.522722 AAAGTCTACACTGGACTGCTAC 57.477 45.455 0.00 0.00 42.39 3.58
2779 17198 8.523658 ACACAAGCATATATTAGAAGCTATCGA 58.476 33.333 0.00 0.00 34.66 3.59
2797 17216 6.700081 GCTATCGACATAAATTACTGGTGTGA 59.300 38.462 0.00 0.00 0.00 3.58
2814 17233 6.041511 TGGTGTGATCAATCAAAACAAACAG 58.958 36.000 0.00 0.00 38.72 3.16
2837 17256 7.490000 CAGTATAACTGGGGTACAACTCTTAG 58.510 42.308 0.00 0.00 42.35 2.18
2878 17301 7.819415 TGTAACATGAAATTCAGTAGTGAGGAG 59.181 37.037 0.00 0.00 32.98 3.69
3014 18848 2.106511 AGGCACAAGCTTCTCCACTTAA 59.893 45.455 0.00 0.00 41.70 1.85
3164 19146 8.689061 TCAGAAGAAAAATAATGATCATGTGGG 58.311 33.333 9.46 0.00 0.00 4.61
3300 21646 1.376424 CGCCTGCAGGAACACAGAT 60.376 57.895 37.21 0.00 37.01 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 5.183904 CCTTTCTAATGGAAACTGAACTGGG 59.816 44.000 0.00 0.00 38.81 4.45
26 27 7.929785 CGCTTACCTTATACCTTTCTAATGGAA 59.070 37.037 1.92 0.00 0.00 3.53
40 41 3.028850 AGGTCTGCACGCTTACCTTATA 58.971 45.455 9.29 0.00 39.32 0.98
41 42 1.831736 AGGTCTGCACGCTTACCTTAT 59.168 47.619 9.29 0.00 39.32 1.73
130 131 1.523938 GGCTACGTGATTCTGGCCC 60.524 63.158 0.00 0.00 34.19 5.80
201 202 6.088883 CGTACCAAAACCATGCTTGTATTTTC 59.911 38.462 8.15 0.52 0.00 2.29
259 260 6.500684 TTCTGAATTCCAAACAGTATGCTC 57.499 37.500 2.27 0.00 42.53 4.26
327 328 3.815809 TCATTCGTGGGTGATTTATCCC 58.184 45.455 0.00 0.00 43.67 3.85
342 344 4.437390 GGTGCTTGAGTTGGTAATCATTCG 60.437 45.833 0.00 0.00 0.00 3.34
645 657 4.020378 CGGTTTGTTCCGGTGGCG 62.020 66.667 0.00 0.00 45.88 5.69
728 740 1.613437 CAAAGGGAAGCGAACCAACAT 59.387 47.619 0.00 0.00 0.00 2.71
729 741 1.028905 CAAAGGGAAGCGAACCAACA 58.971 50.000 0.00 0.00 0.00 3.33
730 742 0.318699 GCAAAGGGAAGCGAACCAAC 60.319 55.000 0.00 0.00 0.00 3.77
731 743 0.753479 TGCAAAGGGAAGCGAACCAA 60.753 50.000 0.00 0.00 0.00 3.67
732 744 0.539438 ATGCAAAGGGAAGCGAACCA 60.539 50.000 0.00 0.00 0.00 3.67
733 745 0.603065 AATGCAAAGGGAAGCGAACC 59.397 50.000 0.00 0.00 0.00 3.62
734 746 1.000274 ACAATGCAAAGGGAAGCGAAC 60.000 47.619 0.00 0.00 0.00 3.95
735 747 1.327303 ACAATGCAAAGGGAAGCGAA 58.673 45.000 0.00 0.00 0.00 4.70
736 748 1.000385 CAACAATGCAAAGGGAAGCGA 60.000 47.619 0.00 0.00 0.00 4.93
737 749 1.421382 CAACAATGCAAAGGGAAGCG 58.579 50.000 0.00 0.00 0.00 4.68
738 750 1.344114 TCCAACAATGCAAAGGGAAGC 59.656 47.619 0.00 0.00 0.00 3.86
739 751 2.629617 AGTCCAACAATGCAAAGGGAAG 59.370 45.455 0.00 0.00 0.00 3.46
740 752 2.364970 CAGTCCAACAATGCAAAGGGAA 59.635 45.455 0.00 0.00 0.00 3.97
741 753 1.962807 CAGTCCAACAATGCAAAGGGA 59.037 47.619 0.00 0.00 0.00 4.20
742 754 1.688197 ACAGTCCAACAATGCAAAGGG 59.312 47.619 0.00 0.00 0.00 3.95
743 755 3.125316 CAACAGTCCAACAATGCAAAGG 58.875 45.455 0.00 0.00 0.00 3.11
744 756 4.044336 TCAACAGTCCAACAATGCAAAG 57.956 40.909 0.00 0.00 0.00 2.77
745 757 4.669206 ATCAACAGTCCAACAATGCAAA 57.331 36.364 0.00 0.00 0.00 3.68
746 758 4.669206 AATCAACAGTCCAACAATGCAA 57.331 36.364 0.00 0.00 0.00 4.08
747 759 4.370049 CAAATCAACAGTCCAACAATGCA 58.630 39.130 0.00 0.00 0.00 3.96
748 760 3.184986 GCAAATCAACAGTCCAACAATGC 59.815 43.478 0.00 0.00 0.00 3.56
749 761 4.624015 AGCAAATCAACAGTCCAACAATG 58.376 39.130 0.00 0.00 0.00 2.82
750 762 4.942761 AGCAAATCAACAGTCCAACAAT 57.057 36.364 0.00 0.00 0.00 2.71
751 763 4.159321 TCAAGCAAATCAACAGTCCAACAA 59.841 37.500 0.00 0.00 0.00 2.83
752 764 3.698539 TCAAGCAAATCAACAGTCCAACA 59.301 39.130 0.00 0.00 0.00 3.33
753 765 4.305989 TCAAGCAAATCAACAGTCCAAC 57.694 40.909 0.00 0.00 0.00 3.77
754 766 4.681744 GTTCAAGCAAATCAACAGTCCAA 58.318 39.130 0.00 0.00 0.00 3.53
755 767 3.243035 CGTTCAAGCAAATCAACAGTCCA 60.243 43.478 0.00 0.00 0.00 4.02
756 768 3.300009 CGTTCAAGCAAATCAACAGTCC 58.700 45.455 0.00 0.00 0.00 3.85
757 769 3.003275 TCCGTTCAAGCAAATCAACAGTC 59.997 43.478 0.00 0.00 0.00 3.51
758 770 2.948979 TCCGTTCAAGCAAATCAACAGT 59.051 40.909 0.00 0.00 0.00 3.55
759 771 3.624326 TCCGTTCAAGCAAATCAACAG 57.376 42.857 0.00 0.00 0.00 3.16
760 772 3.243367 CCTTCCGTTCAAGCAAATCAACA 60.243 43.478 0.00 0.00 0.00 3.33
761 773 3.004315 TCCTTCCGTTCAAGCAAATCAAC 59.996 43.478 0.00 0.00 0.00 3.18
762 774 3.218453 TCCTTCCGTTCAAGCAAATCAA 58.782 40.909 0.00 0.00 0.00 2.57
763 775 2.857483 TCCTTCCGTTCAAGCAAATCA 58.143 42.857 0.00 0.00 0.00 2.57
764 776 3.915437 TTCCTTCCGTTCAAGCAAATC 57.085 42.857 0.00 0.00 0.00 2.17
765 777 4.664150 TTTTCCTTCCGTTCAAGCAAAT 57.336 36.364 0.00 0.00 0.00 2.32
766 778 4.457834 TTTTTCCTTCCGTTCAAGCAAA 57.542 36.364 0.00 0.00 0.00 3.68
784 796 5.011635 GGTGGGTCCTGTTATGTTCATTTTT 59.988 40.000 0.00 0.00 0.00 1.94
785 797 4.526650 GGTGGGTCCTGTTATGTTCATTTT 59.473 41.667 0.00 0.00 0.00 1.82
786 798 4.086457 GGTGGGTCCTGTTATGTTCATTT 58.914 43.478 0.00 0.00 0.00 2.32
787 799 3.697166 GGTGGGTCCTGTTATGTTCATT 58.303 45.455 0.00 0.00 0.00 2.57
788 800 2.355716 CGGTGGGTCCTGTTATGTTCAT 60.356 50.000 0.00 0.00 0.00 2.57
789 801 1.002659 CGGTGGGTCCTGTTATGTTCA 59.997 52.381 0.00 0.00 0.00 3.18
790 802 1.734163 CGGTGGGTCCTGTTATGTTC 58.266 55.000 0.00 0.00 0.00 3.18
809 821 1.961180 TTCTAGCTTCCTCTGCGGGC 61.961 60.000 0.00 0.00 35.28 6.13
812 824 1.686052 AGGATTCTAGCTTCCTCTGCG 59.314 52.381 0.00 0.00 37.89 5.18
873 885 2.315176 ACAAGTGCAGAGACAGAGTCT 58.685 47.619 0.00 0.00 46.42 3.24
889 901 7.591006 ACAAACACGTCCTATACAATACAAG 57.409 36.000 0.00 0.00 0.00 3.16
892 906 6.815142 AGGAACAAACACGTCCTATACAATAC 59.185 38.462 0.00 0.00 0.00 1.89
894 908 5.801380 AGGAACAAACACGTCCTATACAAT 58.199 37.500 0.00 0.00 0.00 2.71
906 920 2.405172 GAGTCTCCGAGGAACAAACAC 58.595 52.381 0.00 0.00 0.00 3.32
908 922 2.081725 GGAGTCTCCGAGGAACAAAC 57.918 55.000 2.28 0.00 0.00 2.93
928 942 1.723542 CTGTTCGAGTCTGATGCACAC 59.276 52.381 0.00 0.00 0.00 3.82
929 943 1.613437 TCTGTTCGAGTCTGATGCACA 59.387 47.619 0.00 0.00 0.00 4.57
965 979 0.419459 AGGGTCAGAGGGGACAAGAT 59.581 55.000 0.00 0.00 39.59 2.40
970 984 0.906066 GAAGAAGGGTCAGAGGGGAC 59.094 60.000 0.00 0.00 37.06 4.46
1101 1120 3.255725 CATGCATGTGAATGTGGTTTCC 58.744 45.455 18.91 0.00 0.00 3.13
1108 1127 1.182667 AGCTGCATGCATGTGAATGT 58.817 45.000 26.79 5.66 45.94 2.71
1233 1252 2.237143 TCGGGCTTCTTCTTCATGATGT 59.763 45.455 8.33 0.00 0.00 3.06
1258 1277 1.745087 GCGATGATCTTGGGCTTGAAA 59.255 47.619 0.00 0.00 0.00 2.69
1429 1454 4.260170 AGTCATGCAAGGCAAAACAAAAA 58.740 34.783 0.00 0.00 43.62 1.94
1430 1455 3.871485 AGTCATGCAAGGCAAAACAAAA 58.129 36.364 0.00 0.00 43.62 2.44
1485 1511 4.735132 TTCGAGACGGGCCGCAAG 62.735 66.667 28.71 15.32 0.00 4.01
1493 1519 1.464429 CGTGCTTCGATTCGAGACGG 61.464 60.000 20.55 10.67 42.86 4.79
1494 1520 1.464429 CCGTGCTTCGATTCGAGACG 61.464 60.000 21.01 21.01 42.86 4.18
1578 1604 1.810853 TGTGGCGATCGATGCACTG 60.811 57.895 21.57 0.00 0.00 3.66
1660 10348 9.250624 GCGTTTAGATCACTAAAATAGTCATCT 57.749 33.333 8.62 8.62 46.42 2.90
1661 10349 9.250624 AGCGTTTAGATCACTAAAATAGTCATC 57.749 33.333 0.00 0.00 45.97 2.92
1662 10350 9.250624 GAGCGTTTAGATCACTAAAATAGTCAT 57.749 33.333 0.00 0.00 45.97 3.06
1663 10351 8.467598 AGAGCGTTTAGATCACTAAAATAGTCA 58.532 33.333 0.00 0.00 45.97 3.41
1664 10352 8.859517 AGAGCGTTTAGATCACTAAAATAGTC 57.140 34.615 0.00 0.00 45.97 2.59
1684 10465 7.883217 TCCCTCAGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
1685 10466 8.862085 ACTCCCTCAGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 31.37 4.09
1696 10477 3.693578 GCTACGTACTCCCTCAGTAAACT 59.306 47.826 0.00 0.00 39.44 2.66
1697 10478 3.441572 TGCTACGTACTCCCTCAGTAAAC 59.558 47.826 0.00 0.00 39.44 2.01
1698 10479 3.689347 TGCTACGTACTCCCTCAGTAAA 58.311 45.455 0.00 0.00 39.44 2.01
1699 10480 3.354948 TGCTACGTACTCCCTCAGTAA 57.645 47.619 0.00 0.00 39.44 2.24
1700 10481 3.572632 ATGCTACGTACTCCCTCAGTA 57.427 47.619 0.00 0.00 36.43 2.74
1703 10484 5.628130 AGTATAATGCTACGTACTCCCTCA 58.372 41.667 0.00 0.00 0.00 3.86
1704 10485 6.572167 AAGTATAATGCTACGTACTCCCTC 57.428 41.667 0.00 0.00 0.00 4.30
1741 15033 4.112634 CTGGCAATTGATCATGCAAGAAG 58.887 43.478 17.50 8.37 44.75 2.85
1772 15067 0.817654 TCAGGACTGTCGCTATGTGG 59.182 55.000 1.07 0.00 0.00 4.17
1780 15075 2.232452 AGATGTTCCTTCAGGACTGTCG 59.768 50.000 1.07 0.00 45.39 4.35
1830 15125 0.377203 GTTTGCGGACGATCCATTCC 59.623 55.000 0.00 0.00 35.91 3.01
1848 15143 0.037326 AGCCATGTCGTCGTTGATGT 60.037 50.000 0.00 0.00 0.00 3.06
1951 15248 2.573340 CCCACGGCTTGATTTGGC 59.427 61.111 0.00 0.00 0.00 4.52
1964 15261 4.825085 TGTTGAAAATAGAACTCACCCCAC 59.175 41.667 0.00 0.00 0.00 4.61
1997 15294 1.415659 AGCACAGGAGTAGATGGCATC 59.584 52.381 19.78 19.78 0.00 3.91
2116 15420 4.142859 CGATTGGGATTTTTGTTGGCAATG 60.143 41.667 1.92 0.00 34.18 2.82
2212 15914 7.530010 CAGGTGTAAATACATCACAAAGAAGG 58.470 38.462 6.61 0.00 39.75 3.46
2643 17062 7.112779 TCTCAGGGAAAAGATTTGGAAGATAC 58.887 38.462 0.00 0.00 0.00 2.24
2740 17159 9.973450 ATATATGCTTGTGTTCTACTACTTCTG 57.027 33.333 0.00 0.00 0.00 3.02
2769 17188 7.438459 ACACCAGTAATTTATGTCGATAGCTTC 59.562 37.037 0.00 0.00 0.00 3.86
2779 17198 8.806429 TGATTGATCACACCAGTAATTTATGT 57.194 30.769 0.00 0.00 0.00 2.29
2797 17216 9.912634 CCAGTTATACTGTTTGTTTTGATTGAT 57.087 29.630 6.13 0.00 44.50 2.57
2814 17233 7.415592 ACTAAGAGTTGTACCCCAGTTATAC 57.584 40.000 0.00 0.00 0.00 1.47
2878 17301 5.163992 CGACCGGCATGTGTTGATATATAAC 60.164 44.000 0.00 0.00 0.00 1.89
3164 19146 4.445452 ACAGATGGACATGCACAATTTC 57.555 40.909 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.