Multiple sequence alignment - TraesCS4D01G227000

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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 TraesCS4D01G227000 chr4D 100.000 2831 0 0 1 2831 386201008 386203838 0.000000e+00 5228.0
1 TraesCS4D01G227000 chr4D 97.678 689 16 0 1 689 267162391 267161703 0.000000e+00 1184.0
2 TraesCS4D01G227000 chr4D 85.606 264 37 1 2280 2542 389570751 389570488 2.780000e-70 276.0
3 TraesCS4D01G227000 chr4A 88.789 1998 192 12 841 2831 654800344 654802316 0.000000e+00 2420.0
4 TraesCS4D01G227000 chr4A 90.141 142 9 2 689 826 67332520 67332660 2.240000e-41 180.0
5 TraesCS4D01G227000 chr2B 87.171 1255 129 20 838 2068 646976914 646978160 0.000000e+00 1397.0
6 TraesCS4D01G227000 chr2B 91.782 937 69 5 841 1775 786050426 786051356 0.000000e+00 1297.0
7 TraesCS4D01G227000 chr2B 90.103 970 85 7 1866 2831 786051640 786052602 0.000000e+00 1249.0
8 TraesCS4D01G227000 chr2B 77.155 232 53 0 1521 1752 767657768 767657999 4.920000e-28 135.0
9 TraesCS4D01G227000 chr6A 86.964 1143 133 11 857 1993 475900547 475901679 0.000000e+00 1271.0
10 TraesCS4D01G227000 chr1D 97.533 689 17 0 1 689 328176453 328177141 0.000000e+00 1179.0
11 TraesCS4D01G227000 chr1D 97.388 689 18 0 1 689 328160734 328161422 0.000000e+00 1173.0
12 TraesCS4D01G227000 chr6D 97.388 689 18 0 1 689 336112091 336112779 0.000000e+00 1173.0
13 TraesCS4D01G227000 chr6D 97.242 689 19 0 1 689 444839477 444840165 0.000000e+00 1168.0
14 TraesCS4D01G227000 chr6D 95.856 724 25 5 1 721 99537684 99538405 0.000000e+00 1166.0
15 TraesCS4D01G227000 chr3D 97.395 691 15 3 1 689 45220026 45220715 0.000000e+00 1173.0
16 TraesCS4D01G227000 chr3D 79.041 563 111 7 2273 2831 272496146 272496705 2.060000e-101 379.0
17 TraesCS4D01G227000 chr5D 97.388 689 17 1 1 689 274441611 274442298 0.000000e+00 1171.0
18 TraesCS4D01G227000 chr5D 97.242 689 18 1 1 689 68605519 68606206 0.000000e+00 1166.0
19 TraesCS4D01G227000 chr5D 76.280 586 130 7 2247 2829 12590022 12589443 1.270000e-78 303.0
20 TraesCS4D01G227000 chr7A 85.974 1098 137 11 903 1995 634456385 634457470 0.000000e+00 1158.0
21 TraesCS4D01G227000 chr3A 78.750 560 116 3 2274 2831 328600624 328601182 3.440000e-99 372.0
22 TraesCS4D01G227000 chr3A 74.190 895 210 17 986 1872 645628234 645629115 1.250000e-93 353.0
23 TraesCS4D01G227000 chr3A 74.000 900 215 15 986 1878 476153811 476152924 5.800000e-92 348.0
24 TraesCS4D01G227000 chr2A 78.495 558 115 4 2277 2831 752085013 752084458 7.460000e-96 361.0
25 TraesCS4D01G227000 chr1B 74.906 801 187 10 1076 1872 558922118 558922908 1.250000e-93 353.0
26 TraesCS4D01G227000 chr1B 73.975 561 131 14 2277 2829 646989626 646990179 2.210000e-51 213.0
27 TraesCS4D01G227000 chr4B 78.198 555 108 11 2277 2824 193492706 193492158 2.700000e-90 342.0
28 TraesCS4D01G227000 chr5B 77.297 555 112 12 2277 2824 531712414 531712961 5.890000e-82 315.0
29 TraesCS4D01G227000 chr7B 73.345 559 134 13 2279 2829 556342648 556342097 2.880000e-45 193.0
30 TraesCS4D01G227000 chr5A 69.658 468 133 8 2277 2739 549222821 549223284 5.060000e-08 69.4


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 TraesCS4D01G227000 chr4D 386201008 386203838 2830 False 5228 5228 100.0000 1 2831 1 chr4D.!!$F1 2830
1 TraesCS4D01G227000 chr4D 267161703 267162391 688 True 1184 1184 97.6780 1 689 1 chr4D.!!$R1 688
2 TraesCS4D01G227000 chr4A 654800344 654802316 1972 False 2420 2420 88.7890 841 2831 1 chr4A.!!$F2 1990
3 TraesCS4D01G227000 chr2B 646976914 646978160 1246 False 1397 1397 87.1710 838 2068 1 chr2B.!!$F1 1230
4 TraesCS4D01G227000 chr2B 786050426 786052602 2176 False 1273 1297 90.9425 841 2831 2 chr2B.!!$F3 1990
5 TraesCS4D01G227000 chr6A 475900547 475901679 1132 False 1271 1271 86.9640 857 1993 1 chr6A.!!$F1 1136
6 TraesCS4D01G227000 chr1D 328176453 328177141 688 False 1179 1179 97.5330 1 689 1 chr1D.!!$F2 688
7 TraesCS4D01G227000 chr1D 328160734 328161422 688 False 1173 1173 97.3880 1 689 1 chr1D.!!$F1 688
8 TraesCS4D01G227000 chr6D 336112091 336112779 688 False 1173 1173 97.3880 1 689 1 chr6D.!!$F2 688
9 TraesCS4D01G227000 chr6D 444839477 444840165 688 False 1168 1168 97.2420 1 689 1 chr6D.!!$F3 688
10 TraesCS4D01G227000 chr6D 99537684 99538405 721 False 1166 1166 95.8560 1 721 1 chr6D.!!$F1 720
11 TraesCS4D01G227000 chr3D 45220026 45220715 689 False 1173 1173 97.3950 1 689 1 chr3D.!!$F1 688
12 TraesCS4D01G227000 chr3D 272496146 272496705 559 False 379 379 79.0410 2273 2831 1 chr3D.!!$F2 558
13 TraesCS4D01G227000 chr5D 274441611 274442298 687 False 1171 1171 97.3880 1 689 1 chr5D.!!$F2 688
14 TraesCS4D01G227000 chr5D 68605519 68606206 687 False 1166 1166 97.2420 1 689 1 chr5D.!!$F1 688
15 TraesCS4D01G227000 chr5D 12589443 12590022 579 True 303 303 76.2800 2247 2829 1 chr5D.!!$R1 582
16 TraesCS4D01G227000 chr7A 634456385 634457470 1085 False 1158 1158 85.9740 903 1995 1 chr7A.!!$F1 1092
17 TraesCS4D01G227000 chr3A 328600624 328601182 558 False 372 372 78.7500 2274 2831 1 chr3A.!!$F1 557
18 TraesCS4D01G227000 chr3A 645628234 645629115 881 False 353 353 74.1900 986 1872 1 chr3A.!!$F2 886
19 TraesCS4D01G227000 chr3A 476152924 476153811 887 True 348 348 74.0000 986 1878 1 chr3A.!!$R1 892
20 TraesCS4D01G227000 chr2A 752084458 752085013 555 True 361 361 78.4950 2277 2831 1 chr2A.!!$R1 554
21 TraesCS4D01G227000 chr1B 558922118 558922908 790 False 353 353 74.9060 1076 1872 1 chr1B.!!$F1 796
22 TraesCS4D01G227000 chr1B 646989626 646990179 553 False 213 213 73.9750 2277 2829 1 chr1B.!!$F2 552
23 TraesCS4D01G227000 chr4B 193492158 193492706 548 True 342 342 78.1980 2277 2824 1 chr4B.!!$R1 547
24 TraesCS4D01G227000 chr5B 531712414 531712961 547 False 315 315 77.2970 2277 2824 1 chr5B.!!$F1 547

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
726 729 0.033306 TGCAGCAAGATTATGGGCCA 60.033 50.0 9.61 9.61 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2194 2418 0.107312 CCCCTTCACTCTCAGCCATG 60.107 60.0 0.0 0.0 0.0 3.66 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
51 53 1.002868 GAGCAGCCCGGCATGATAT 60.003 57.895 13.15 0.00 35.83 1.63
262 264 4.339814 AGAAGAACTTCGTCTCTGTCACTT 59.660 41.667 8.59 0.00 43.97 3.16
415 417 5.412904 GGTGTTTCCTATGACTCAAGAAAGG 59.587 44.000 3.65 0.00 0.00 3.11
516 518 7.436376 CCAATTTCTTCACTTTCAAAGTCTTCC 59.564 37.037 0.00 0.00 40.46 3.46
522 525 7.713507 TCTTCACTTTCAAAGTCTTCCGAAATA 59.286 33.333 0.00 0.00 40.46 1.40
568 571 5.566469 TCATTTTTAGGGGTCGACTTTCAT 58.434 37.500 16.46 6.05 0.00 2.57
693 696 5.786401 CACTAGATGCACTTACAACCTTC 57.214 43.478 0.00 0.00 0.00 3.46
694 697 4.631813 CACTAGATGCACTTACAACCTTCC 59.368 45.833 0.00 0.00 0.00 3.46
695 698 2.699954 AGATGCACTTACAACCTTCCG 58.300 47.619 0.00 0.00 0.00 4.30
696 699 2.301870 AGATGCACTTACAACCTTCCGA 59.698 45.455 0.00 0.00 0.00 4.55
697 700 2.163818 TGCACTTACAACCTTCCGAG 57.836 50.000 0.00 0.00 0.00 4.63
698 701 1.414919 TGCACTTACAACCTTCCGAGT 59.585 47.619 0.00 0.00 0.00 4.18
699 702 2.629137 TGCACTTACAACCTTCCGAGTA 59.371 45.455 0.00 0.00 0.00 2.59
700 703 3.069872 TGCACTTACAACCTTCCGAGTAA 59.930 43.478 0.00 0.00 0.00 2.24
701 704 4.060205 GCACTTACAACCTTCCGAGTAAA 58.940 43.478 0.00 0.00 0.00 2.01
702 705 4.694037 GCACTTACAACCTTCCGAGTAAAT 59.306 41.667 0.00 0.00 0.00 1.40
703 706 5.870978 GCACTTACAACCTTCCGAGTAAATA 59.129 40.000 0.00 0.00 0.00 1.40
704 707 6.035758 GCACTTACAACCTTCCGAGTAAATAG 59.964 42.308 0.00 0.00 0.00 1.73
705 708 6.035758 CACTTACAACCTTCCGAGTAAATAGC 59.964 42.308 0.00 0.00 0.00 2.97
706 709 4.820894 ACAACCTTCCGAGTAAATAGCT 57.179 40.909 0.00 0.00 0.00 3.32
707 710 5.161943 ACAACCTTCCGAGTAAATAGCTT 57.838 39.130 0.00 0.00 0.00 3.74
708 711 4.935808 ACAACCTTCCGAGTAAATAGCTTG 59.064 41.667 0.00 0.00 0.00 4.01
709 712 3.532542 ACCTTCCGAGTAAATAGCTTGC 58.467 45.455 0.00 0.00 0.00 4.01
710 713 3.055385 ACCTTCCGAGTAAATAGCTTGCA 60.055 43.478 0.00 0.00 0.00 4.08
711 714 3.557595 CCTTCCGAGTAAATAGCTTGCAG 59.442 47.826 0.00 0.00 0.00 4.41
712 715 2.550978 TCCGAGTAAATAGCTTGCAGC 58.449 47.619 0.00 0.47 42.84 5.25
713 716 2.093711 TCCGAGTAAATAGCTTGCAGCA 60.094 45.455 10.16 0.00 45.56 4.41
714 717 2.677836 CCGAGTAAATAGCTTGCAGCAA 59.322 45.455 7.81 7.81 45.56 3.91
715 718 3.242543 CCGAGTAAATAGCTTGCAGCAAG 60.243 47.826 28.15 28.15 45.56 4.01
716 719 3.618594 CGAGTAAATAGCTTGCAGCAAGA 59.381 43.478 34.93 18.07 45.56 3.02
717 720 4.272018 CGAGTAAATAGCTTGCAGCAAGAT 59.728 41.667 34.93 31.46 45.56 2.40
718 721 5.220739 CGAGTAAATAGCTTGCAGCAAGATT 60.221 40.000 34.93 23.56 45.56 2.40
719 722 6.018751 CGAGTAAATAGCTTGCAGCAAGATTA 60.019 38.462 34.93 25.08 45.56 1.75
720 723 7.307632 CGAGTAAATAGCTTGCAGCAAGATTAT 60.308 37.037 34.93 25.96 45.56 1.28
721 724 7.646314 AGTAAATAGCTTGCAGCAAGATTATG 58.354 34.615 34.93 12.02 45.56 1.90
722 725 5.449107 AATAGCTTGCAGCAAGATTATGG 57.551 39.130 34.93 11.29 45.56 2.74
723 726 2.029623 AGCTTGCAGCAAGATTATGGG 58.970 47.619 34.93 10.57 45.56 4.00
724 727 1.537562 GCTTGCAGCAAGATTATGGGC 60.538 52.381 34.93 16.47 43.42 5.36
725 728 1.068127 CTTGCAGCAAGATTATGGGCC 59.932 52.381 28.50 0.00 43.42 5.80
726 729 0.033306 TGCAGCAAGATTATGGGCCA 60.033 50.000 9.61 9.61 0.00 5.36
727 730 1.335145 GCAGCAAGATTATGGGCCAT 58.665 50.000 24.69 24.69 0.00 4.40
728 731 1.690352 GCAGCAAGATTATGGGCCATT 59.310 47.619 26.58 7.53 0.00 3.16
729 732 2.103601 GCAGCAAGATTATGGGCCATTT 59.896 45.455 26.58 13.05 0.00 2.32
730 733 3.432608 GCAGCAAGATTATGGGCCATTTT 60.433 43.478 26.58 12.64 0.00 1.82
731 734 4.773013 CAGCAAGATTATGGGCCATTTTT 58.227 39.130 26.58 9.85 0.00 1.94
752 755 5.356882 TTTTGTCGAGCAAGGAGTTATTG 57.643 39.130 0.00 0.00 38.47 1.90
753 756 2.972625 TGTCGAGCAAGGAGTTATTGG 58.027 47.619 0.00 0.00 0.00 3.16
754 757 2.280628 GTCGAGCAAGGAGTTATTGGG 58.719 52.381 0.00 0.00 0.00 4.12
755 758 1.017387 CGAGCAAGGAGTTATTGGGC 58.983 55.000 0.00 0.00 0.00 5.36
756 759 1.407437 CGAGCAAGGAGTTATTGGGCT 60.407 52.381 0.00 0.00 0.00 5.19
757 760 2.728007 GAGCAAGGAGTTATTGGGCTT 58.272 47.619 0.00 0.00 0.00 4.35
758 761 2.424956 GAGCAAGGAGTTATTGGGCTTG 59.575 50.000 0.00 0.00 0.00 4.01
759 762 1.478105 GCAAGGAGTTATTGGGCTTGG 59.522 52.381 0.00 0.00 0.00 3.61
760 763 1.478105 CAAGGAGTTATTGGGCTTGGC 59.522 52.381 0.00 0.00 0.00 4.52
778 781 2.336341 CCAGTTGGGCGTTTTAGCA 58.664 52.632 0.00 0.00 39.27 3.49
779 782 0.039527 CCAGTTGGGCGTTTTAGCAC 60.040 55.000 0.00 0.00 41.82 4.40
780 783 0.039527 CAGTTGGGCGTTTTAGCACC 60.040 55.000 0.00 0.00 40.47 5.01
781 784 0.179001 AGTTGGGCGTTTTAGCACCT 60.179 50.000 0.00 0.00 40.47 4.00
782 785 1.072648 AGTTGGGCGTTTTAGCACCTA 59.927 47.619 0.00 0.00 40.47 3.08
783 786 2.089201 GTTGGGCGTTTTAGCACCTAT 58.911 47.619 0.00 0.00 40.47 2.57
784 787 2.490509 GTTGGGCGTTTTAGCACCTATT 59.509 45.455 0.00 0.00 40.47 1.73
785 788 3.630892 TGGGCGTTTTAGCACCTATTA 57.369 42.857 0.00 0.00 40.47 0.98
786 789 4.159244 TGGGCGTTTTAGCACCTATTAT 57.841 40.909 0.00 0.00 40.47 1.28
787 790 4.528920 TGGGCGTTTTAGCACCTATTATT 58.471 39.130 0.00 0.00 40.47 1.40
788 791 4.951094 TGGGCGTTTTAGCACCTATTATTT 59.049 37.500 0.00 0.00 40.47 1.40
789 792 5.419471 TGGGCGTTTTAGCACCTATTATTTT 59.581 36.000 0.00 0.00 40.47 1.82
790 793 5.975344 GGGCGTTTTAGCACCTATTATTTTC 59.025 40.000 0.00 0.00 39.27 2.29
791 794 5.975344 GGCGTTTTAGCACCTATTATTTTCC 59.025 40.000 0.00 0.00 39.27 3.13
792 795 6.404954 GGCGTTTTAGCACCTATTATTTTCCA 60.405 38.462 0.00 0.00 39.27 3.53
793 796 6.471198 GCGTTTTAGCACCTATTATTTTCCAC 59.529 38.462 0.00 0.00 37.05 4.02
794 797 6.685403 CGTTTTAGCACCTATTATTTTCCACG 59.315 38.462 0.00 0.00 0.00 4.94
795 798 7.413219 CGTTTTAGCACCTATTATTTTCCACGA 60.413 37.037 0.00 0.00 0.00 4.35
796 799 7.548196 TTTAGCACCTATTATTTTCCACGAG 57.452 36.000 0.00 0.00 0.00 4.18
797 800 3.877508 AGCACCTATTATTTTCCACGAGC 59.122 43.478 0.00 0.00 0.00 5.03
798 801 3.877508 GCACCTATTATTTTCCACGAGCT 59.122 43.478 0.00 0.00 0.00 4.09
799 802 4.024809 GCACCTATTATTTTCCACGAGCTC 60.025 45.833 2.73 2.73 0.00 4.09
800 803 5.360591 CACCTATTATTTTCCACGAGCTCT 58.639 41.667 12.85 0.00 0.00 4.09
801 804 5.463724 CACCTATTATTTTCCACGAGCTCTC 59.536 44.000 12.85 0.00 0.00 3.20
812 815 2.800516 GAGCTCTCGAGGTCCATCA 58.199 57.895 13.56 0.00 46.96 3.07
813 816 1.327303 GAGCTCTCGAGGTCCATCAT 58.673 55.000 13.56 0.00 46.96 2.45
814 817 1.000385 GAGCTCTCGAGGTCCATCATG 60.000 57.143 13.56 0.00 46.96 3.07
815 818 1.035923 GCTCTCGAGGTCCATCATGA 58.964 55.000 13.56 0.00 0.00 3.07
816 819 1.410517 GCTCTCGAGGTCCATCATGAA 59.589 52.381 13.56 0.00 0.00 2.57
817 820 2.036992 GCTCTCGAGGTCCATCATGAAT 59.963 50.000 13.56 0.00 0.00 2.57
818 821 3.494048 GCTCTCGAGGTCCATCATGAATT 60.494 47.826 13.56 0.00 0.00 2.17
819 822 4.701765 CTCTCGAGGTCCATCATGAATTT 58.298 43.478 13.56 0.00 0.00 1.82
820 823 4.445453 TCTCGAGGTCCATCATGAATTTG 58.555 43.478 13.56 0.00 0.00 2.32
821 824 4.080919 TCTCGAGGTCCATCATGAATTTGT 60.081 41.667 13.56 0.00 0.00 2.83
822 825 4.588899 TCGAGGTCCATCATGAATTTGTT 58.411 39.130 0.00 0.00 0.00 2.83
823 826 4.635765 TCGAGGTCCATCATGAATTTGTTC 59.364 41.667 0.00 0.00 0.00 3.18
824 827 4.201950 CGAGGTCCATCATGAATTTGTTCC 60.202 45.833 0.00 0.00 0.00 3.62
825 828 4.939255 AGGTCCATCATGAATTTGTTCCT 58.061 39.130 0.00 1.25 0.00 3.36
826 829 4.952335 AGGTCCATCATGAATTTGTTCCTC 59.048 41.667 0.00 0.00 0.00 3.71
827 830 4.098501 GGTCCATCATGAATTTGTTCCTCC 59.901 45.833 0.00 0.00 0.00 4.30
828 831 4.952335 GTCCATCATGAATTTGTTCCTCCT 59.048 41.667 0.00 0.00 0.00 3.69
829 832 6.122277 GTCCATCATGAATTTGTTCCTCCTA 58.878 40.000 0.00 0.00 0.00 2.94
830 833 6.038714 GTCCATCATGAATTTGTTCCTCCTAC 59.961 42.308 0.00 0.00 0.00 3.18
831 834 5.008019 CCATCATGAATTTGTTCCTCCTACG 59.992 44.000 0.00 0.00 0.00 3.51
832 835 3.938963 TCATGAATTTGTTCCTCCTACGC 59.061 43.478 0.00 0.00 0.00 4.42
833 836 2.706890 TGAATTTGTTCCTCCTACGCC 58.293 47.619 0.00 0.00 0.00 5.68
834 837 1.664151 GAATTTGTTCCTCCTACGCCG 59.336 52.381 0.00 0.00 0.00 6.46
835 838 0.611714 ATTTGTTCCTCCTACGCCGT 59.388 50.000 0.00 0.00 0.00 5.68
836 839 0.393820 TTTGTTCCTCCTACGCCGTT 59.606 50.000 0.00 0.00 0.00 4.44
837 840 0.393820 TTGTTCCTCCTACGCCGTTT 59.606 50.000 0.00 0.00 0.00 3.60
838 841 0.037975 TGTTCCTCCTACGCCGTTTC 60.038 55.000 0.00 0.00 0.00 2.78
839 842 1.074872 GTTCCTCCTACGCCGTTTCG 61.075 60.000 0.00 0.00 0.00 3.46
900 906 3.064931 GCTAGCCGCCGTAATTTATCTT 58.935 45.455 2.29 0.00 0.00 2.40
907 913 4.988540 CCGCCGTAATTTATCTTCTGATCA 59.011 41.667 0.00 0.00 34.32 2.92
1130 1142 2.781431 GAATTGCCGGACTTGGGGGT 62.781 60.000 5.05 0.00 0.00 4.95
1189 1201 9.930158 ATACACCAAAATCTTTTAGCCCTAATA 57.070 29.630 0.00 0.00 0.00 0.98
1190 1202 8.658840 ACACCAAAATCTTTTAGCCCTAATAA 57.341 30.769 0.00 0.00 0.00 1.40
1191 1203 9.267071 ACACCAAAATCTTTTAGCCCTAATAAT 57.733 29.630 0.00 0.00 0.00 1.28
1426 1438 1.942657 CGGTCTGGGCTCAAATACATG 59.057 52.381 0.00 0.00 0.00 3.21
1433 1445 3.266772 TGGGCTCAAATACATGTTCTCCT 59.733 43.478 2.30 0.00 0.00 3.69
1446 1458 6.735556 ACATGTTCTCCTGGATAATTTCCTT 58.264 36.000 0.00 0.00 45.68 3.36
1526 1538 0.537371 AAACTCCCGGCAGGTTTCTG 60.537 55.000 0.00 0.00 43.64 3.02
1621 1644 3.702045 AGGAGAAGAAAGGGTGAGATACG 59.298 47.826 0.00 0.00 0.00 3.06
1631 1654 3.193691 AGGGTGAGATACGAAGTGAAGTG 59.806 47.826 0.00 0.00 45.73 3.16
1953 2170 1.474320 CGGGAGTTCAGGTTGTGACAA 60.474 52.381 0.00 0.00 33.71 3.18
2017 2241 2.095059 CAGCAAAGAATAAGCGTGCCTT 60.095 45.455 0.00 0.00 35.80 4.35
2039 2263 0.895100 TGGAACATCTGCCAAGCACC 60.895 55.000 0.00 0.00 33.79 5.01
2071 2295 1.676006 ACAAGTTGTGGGCGAGAAAAG 59.324 47.619 7.96 0.00 0.00 2.27
2073 2297 2.554032 CAAGTTGTGGGCGAGAAAAGAT 59.446 45.455 0.00 0.00 0.00 2.40
2085 2309 5.277538 GGCGAGAAAAGATATGATCACAACC 60.278 44.000 0.00 0.00 0.00 3.77
2087 2311 5.050769 CGAGAAAAGATATGATCACAACCCG 60.051 44.000 0.00 0.00 0.00 5.28
2154 2378 3.072476 CCCTCCGGTATATGTTTCACCAT 59.928 47.826 0.00 0.00 32.32 3.55
2160 2384 4.574421 CGGTATATGTTTCACCATGCAAGA 59.426 41.667 0.00 0.00 32.32 3.02
2188 2412 5.071788 TCAAGAGACCAAAGAACACTGGTAT 59.928 40.000 0.00 0.00 46.12 2.73
2189 2413 4.899502 AGAGACCAAAGAACACTGGTATG 58.100 43.478 0.00 0.00 46.12 2.39
2190 2414 4.593206 AGAGACCAAAGAACACTGGTATGA 59.407 41.667 0.00 0.00 46.12 2.15
2191 2415 4.642429 AGACCAAAGAACACTGGTATGAC 58.358 43.478 0.00 0.00 46.12 3.06
2192 2416 4.102524 AGACCAAAGAACACTGGTATGACA 59.897 41.667 0.00 0.00 46.12 3.58
2194 2418 4.578928 ACCAAAGAACACTGGTATGACAAC 59.421 41.667 0.00 0.00 44.28 3.32
2195 2419 4.578516 CCAAAGAACACTGGTATGACAACA 59.421 41.667 0.00 0.00 0.00 3.33
2196 2420 5.241506 CCAAAGAACACTGGTATGACAACAT 59.758 40.000 0.00 0.00 40.16 2.71
2197 2421 5.947228 AAGAACACTGGTATGACAACATG 57.053 39.130 0.00 0.00 37.87 3.21
2198 2422 4.326826 AGAACACTGGTATGACAACATGG 58.673 43.478 0.00 0.00 37.87 3.66
2199 2423 2.436417 ACACTGGTATGACAACATGGC 58.564 47.619 0.00 0.00 37.87 4.40
2204 2428 2.571202 TGGTATGACAACATGGCTGAGA 59.429 45.455 0.00 0.00 37.87 3.27
2206 2430 3.369892 GGTATGACAACATGGCTGAGAGT 60.370 47.826 0.00 0.00 37.87 3.24
2264 2488 1.476488 AGTGAAGCAACACCAACCAAC 59.524 47.619 9.14 0.00 41.12 3.77
2302 2526 2.681778 CTCCGAGGAGTGCCACCT 60.682 66.667 10.88 0.00 40.80 4.00
2555 2780 7.094634 CCCAATAAATATTGAGATTCTCGGTGG 60.095 40.741 13.42 5.62 44.40 4.61
2757 2983 1.605710 CCGGATGAACATGAAGGCATC 59.394 52.381 0.00 6.52 37.11 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 53 7.724951 TCATATCATTGAAGGGCATTTATGTCA 59.275 33.333 7.49 0.00 33.08 3.58
123 125 2.841215 ACTCAAATTTCCGACCGTTGA 58.159 42.857 0.00 0.00 0.00 3.18
156 158 1.771255 AGTGAGGAACATGATAGCCCC 59.229 52.381 0.00 0.00 0.00 5.80
312 314 5.557866 ACTCAAAATCCTACACCTACCAAC 58.442 41.667 0.00 0.00 0.00 3.77
415 417 8.865978 ACTTTTGTTTTCGTAGTTTCATTTTCC 58.134 29.630 0.00 0.00 0.00 3.13
516 518 6.448053 TTCGACTGAAGACTTTGTATTTCG 57.552 37.500 0.00 0.00 0.00 3.46
689 692 3.531538 TGCAAGCTATTTACTCGGAAGG 58.468 45.455 0.00 0.00 0.00 3.46
690 693 4.785669 CTGCAAGCTATTTACTCGGAAG 57.214 45.455 0.00 0.00 0.00 3.46
705 708 1.068127 GGCCCATAATCTTGCTGCAAG 59.932 52.381 31.26 31.26 42.25 4.01
706 709 1.113788 GGCCCATAATCTTGCTGCAA 58.886 50.000 15.16 15.16 0.00 4.08
707 710 0.033306 TGGCCCATAATCTTGCTGCA 60.033 50.000 0.00 0.00 0.00 4.41
708 711 1.335145 ATGGCCCATAATCTTGCTGC 58.665 50.000 0.00 0.00 0.00 5.25
709 712 4.411256 AAAATGGCCCATAATCTTGCTG 57.589 40.909 0.00 0.00 0.00 4.41
729 732 5.278266 CCAATAACTCCTTGCTCGACAAAAA 60.278 40.000 2.82 0.00 37.96 1.94
730 733 4.215399 CCAATAACTCCTTGCTCGACAAAA 59.785 41.667 2.82 0.00 37.96 2.44
731 734 3.751175 CCAATAACTCCTTGCTCGACAAA 59.249 43.478 2.82 0.00 37.96 2.83
732 735 3.334691 CCAATAACTCCTTGCTCGACAA 58.665 45.455 0.00 0.00 36.62 3.18
733 736 2.354704 CCCAATAACTCCTTGCTCGACA 60.355 50.000 0.00 0.00 0.00 4.35
734 737 2.280628 CCCAATAACTCCTTGCTCGAC 58.719 52.381 0.00 0.00 0.00 4.20
735 738 1.406887 GCCCAATAACTCCTTGCTCGA 60.407 52.381 0.00 0.00 0.00 4.04
736 739 1.017387 GCCCAATAACTCCTTGCTCG 58.983 55.000 0.00 0.00 0.00 5.03
737 740 2.424956 CAAGCCCAATAACTCCTTGCTC 59.575 50.000 0.00 0.00 0.00 4.26
738 741 2.450476 CAAGCCCAATAACTCCTTGCT 58.550 47.619 0.00 0.00 0.00 3.91
739 742 1.478105 CCAAGCCCAATAACTCCTTGC 59.522 52.381 0.00 0.00 33.40 4.01
740 743 1.478105 GCCAAGCCCAATAACTCCTTG 59.522 52.381 0.00 0.00 34.26 3.61
741 744 1.619704 GGCCAAGCCCAATAACTCCTT 60.620 52.381 0.00 0.00 44.06 3.36
742 745 0.033109 GGCCAAGCCCAATAACTCCT 60.033 55.000 0.00 0.00 44.06 3.69
743 746 2.504920 GGCCAAGCCCAATAACTCC 58.495 57.895 0.00 0.00 44.06 3.85
760 763 0.039527 GTGCTAAAACGCCCAACTGG 60.040 55.000 0.00 0.00 37.09 4.00
761 764 0.039527 GGTGCTAAAACGCCCAACTG 60.040 55.000 0.00 0.00 33.92 3.16
762 765 0.179001 AGGTGCTAAAACGCCCAACT 60.179 50.000 0.00 0.00 41.36 3.16
763 766 1.525941 TAGGTGCTAAAACGCCCAAC 58.474 50.000 0.00 0.00 41.36 3.77
764 767 2.500392 ATAGGTGCTAAAACGCCCAA 57.500 45.000 0.00 0.00 41.36 4.12
765 768 2.500392 AATAGGTGCTAAAACGCCCA 57.500 45.000 0.00 0.00 41.36 5.36
766 769 5.509716 AAATAATAGGTGCTAAAACGCCC 57.490 39.130 0.00 0.00 41.36 6.13
767 770 5.975344 GGAAAATAATAGGTGCTAAAACGCC 59.025 40.000 0.00 0.00 40.71 5.68
768 771 6.471198 GTGGAAAATAATAGGTGCTAAAACGC 59.529 38.462 0.00 0.00 0.00 4.84
769 772 6.685403 CGTGGAAAATAATAGGTGCTAAAACG 59.315 38.462 0.00 0.00 0.00 3.60
770 773 7.754625 TCGTGGAAAATAATAGGTGCTAAAAC 58.245 34.615 0.00 0.00 0.00 2.43
771 774 7.414762 GCTCGTGGAAAATAATAGGTGCTAAAA 60.415 37.037 0.00 0.00 0.00 1.52
772 775 6.037830 GCTCGTGGAAAATAATAGGTGCTAAA 59.962 38.462 0.00 0.00 0.00 1.85
773 776 5.526111 GCTCGTGGAAAATAATAGGTGCTAA 59.474 40.000 0.00 0.00 0.00 3.09
774 777 5.054477 GCTCGTGGAAAATAATAGGTGCTA 58.946 41.667 0.00 0.00 0.00 3.49
775 778 3.877508 GCTCGTGGAAAATAATAGGTGCT 59.122 43.478 0.00 0.00 0.00 4.40
776 779 3.877508 AGCTCGTGGAAAATAATAGGTGC 59.122 43.478 0.00 0.00 0.00 5.01
777 780 5.360591 AGAGCTCGTGGAAAATAATAGGTG 58.639 41.667 8.37 0.00 0.00 4.00
778 781 5.602628 GAGAGCTCGTGGAAAATAATAGGT 58.397 41.667 8.37 0.00 0.00 3.08
779 782 4.681942 CGAGAGCTCGTGGAAAATAATAGG 59.318 45.833 8.37 0.00 46.99 2.57
780 783 5.814314 CGAGAGCTCGTGGAAAATAATAG 57.186 43.478 8.37 0.00 46.99 1.73
794 797 1.000385 CATGATGGACCTCGAGAGCTC 60.000 57.143 15.71 5.27 0.00 4.09
795 798 1.039068 CATGATGGACCTCGAGAGCT 58.961 55.000 15.71 0.00 0.00 4.09
796 799 1.035923 TCATGATGGACCTCGAGAGC 58.964 55.000 15.71 4.88 0.00 4.09
797 800 4.333913 AATTCATGATGGACCTCGAGAG 57.666 45.455 15.71 6.69 0.00 3.20
798 801 4.080919 ACAAATTCATGATGGACCTCGAGA 60.081 41.667 15.71 0.00 0.00 4.04
799 802 4.194640 ACAAATTCATGATGGACCTCGAG 58.805 43.478 5.13 5.13 0.00 4.04
800 803 4.220693 ACAAATTCATGATGGACCTCGA 57.779 40.909 0.00 0.00 0.00 4.04
801 804 4.201950 GGAACAAATTCATGATGGACCTCG 60.202 45.833 0.00 0.00 36.46 4.63
802 805 4.952335 AGGAACAAATTCATGATGGACCTC 59.048 41.667 0.00 0.00 36.46 3.85
803 806 4.939255 AGGAACAAATTCATGATGGACCT 58.061 39.130 0.00 3.04 36.46 3.85
804 807 4.098501 GGAGGAACAAATTCATGATGGACC 59.901 45.833 0.00 0.72 36.46 4.46
805 808 4.952335 AGGAGGAACAAATTCATGATGGAC 59.048 41.667 0.00 0.00 36.46 4.02
806 809 5.197224 AGGAGGAACAAATTCATGATGGA 57.803 39.130 0.00 0.00 36.46 3.41
807 810 5.008019 CGTAGGAGGAACAAATTCATGATGG 59.992 44.000 0.00 0.00 36.46 3.51
808 811 5.504665 GCGTAGGAGGAACAAATTCATGATG 60.505 44.000 0.00 0.00 36.46 3.07
809 812 4.576463 GCGTAGGAGGAACAAATTCATGAT 59.424 41.667 0.00 0.00 36.46 2.45
810 813 3.938963 GCGTAGGAGGAACAAATTCATGA 59.061 43.478 0.00 0.00 36.46 3.07
811 814 3.065371 GGCGTAGGAGGAACAAATTCATG 59.935 47.826 0.00 0.00 36.46 3.07
812 815 3.279434 GGCGTAGGAGGAACAAATTCAT 58.721 45.455 0.00 0.00 36.46 2.57
813 816 2.706890 GGCGTAGGAGGAACAAATTCA 58.293 47.619 0.00 0.00 36.46 2.57
814 817 1.664151 CGGCGTAGGAGGAACAAATTC 59.336 52.381 0.00 0.00 0.00 2.17
815 818 1.002773 ACGGCGTAGGAGGAACAAATT 59.997 47.619 12.58 0.00 0.00 1.82
816 819 0.611714 ACGGCGTAGGAGGAACAAAT 59.388 50.000 12.58 0.00 0.00 2.32
817 820 0.393820 AACGGCGTAGGAGGAACAAA 59.606 50.000 15.20 0.00 0.00 2.83
818 821 0.393820 AAACGGCGTAGGAGGAACAA 59.606 50.000 15.20 0.00 0.00 2.83
819 822 0.037975 GAAACGGCGTAGGAGGAACA 60.038 55.000 15.20 0.00 0.00 3.18
820 823 1.074872 CGAAACGGCGTAGGAGGAAC 61.075 60.000 15.20 0.00 0.00 3.62
821 824 1.213537 CGAAACGGCGTAGGAGGAA 59.786 57.895 15.20 0.00 0.00 3.36
822 825 2.879907 CGAAACGGCGTAGGAGGA 59.120 61.111 15.20 0.00 0.00 3.71
823 826 2.884207 GCGAAACGGCGTAGGAGG 60.884 66.667 15.20 2.31 0.00 4.30
824 827 2.884207 GGCGAAACGGCGTAGGAG 60.884 66.667 15.20 6.66 43.33 3.69
890 895 6.283694 ACAGCGCTGATCAGAAGATAAATTA 58.716 36.000 42.03 0.00 33.72 1.40
900 906 0.737804 GAGAGACAGCGCTGATCAGA 59.262 55.000 42.03 0.00 0.00 3.27
1035 1047 2.145397 ACTCATCCGCAGTCTCCTTA 57.855 50.000 0.00 0.00 0.00 2.69
1189 1201 1.134401 CATGTCCCCGTACAGAGCATT 60.134 52.381 0.00 0.00 31.70 3.56
1190 1202 0.465705 CATGTCCCCGTACAGAGCAT 59.534 55.000 0.00 0.00 31.70 3.79
1191 1203 1.897423 CATGTCCCCGTACAGAGCA 59.103 57.895 0.00 0.00 31.70 4.26
1446 1458 1.410004 CCCTGACTGCCCGTTCTATA 58.590 55.000 0.00 0.00 0.00 1.31
1526 1538 4.078516 CCCGGACGAACTCCCCAC 62.079 72.222 0.73 0.00 35.21 4.61
1621 1644 3.810386 GGGAGTTTCTCACACTTCACTTC 59.190 47.826 0.00 0.00 33.47 3.01
1631 1654 5.774498 ACAAAAGATTGGGAGTTTCTCAC 57.226 39.130 0.00 0.00 41.01 3.51
1747 1770 1.202976 AGGCCTGAAGCTCACATTGTT 60.203 47.619 3.11 0.00 43.05 2.83
1827 1851 0.906066 GTTCCCTCCCTCTTCCTCAC 59.094 60.000 0.00 0.00 0.00 3.51
1828 1852 0.252742 GGTTCCCTCCCTCTTCCTCA 60.253 60.000 0.00 0.00 0.00 3.86
1953 2170 0.842030 TCACCACTGGGCTTCTCCAT 60.842 55.000 0.00 0.00 37.90 3.41
1996 2220 1.470098 AGGCACGCTTATTCTTTGCTG 59.530 47.619 0.00 0.00 33.55 4.41
2017 2241 0.961019 GCTTGGCAGATGTTCCACAA 59.039 50.000 0.00 0.00 30.97 3.33
2033 2257 2.050144 TGTTTCTCCTCTGAGGTGCTT 58.950 47.619 22.50 0.00 39.23 3.91
2039 2263 3.812053 CCACAACTTGTTTCTCCTCTGAG 59.188 47.826 0.00 0.00 40.17 3.35
2071 2295 1.271379 CCCCCGGGTTGTGATCATATC 60.271 57.143 21.85 0.00 0.00 1.63
2073 2297 1.990160 GCCCCCGGGTTGTGATCATA 61.990 60.000 21.85 0.00 37.65 2.15
2087 2311 4.910585 CGCACTATGACCGCCCCC 62.911 72.222 0.00 0.00 0.00 5.40
2154 2378 3.490439 TGGTCTCTTGATGTTCTTGCA 57.510 42.857 0.00 0.00 0.00 4.08
2160 2384 5.297776 CAGTGTTCTTTGGTCTCTTGATGTT 59.702 40.000 0.00 0.00 0.00 2.71
2186 2410 3.515104 TCACTCTCAGCCATGTTGTCATA 59.485 43.478 0.00 0.00 32.47 2.15
2188 2412 1.693606 TCACTCTCAGCCATGTTGTCA 59.306 47.619 0.00 0.00 0.00 3.58
2189 2413 2.462456 TCACTCTCAGCCATGTTGTC 57.538 50.000 0.00 0.00 0.00 3.18
2190 2414 2.551721 CCTTCACTCTCAGCCATGTTGT 60.552 50.000 0.00 0.00 0.00 3.32
2191 2415 2.082231 CCTTCACTCTCAGCCATGTTG 58.918 52.381 0.00 0.00 0.00 3.33
2192 2416 1.004044 CCCTTCACTCTCAGCCATGTT 59.996 52.381 0.00 0.00 0.00 2.71
2194 2418 0.107312 CCCCTTCACTCTCAGCCATG 60.107 60.000 0.00 0.00 0.00 3.66
2195 2419 1.277580 CCCCCTTCACTCTCAGCCAT 61.278 60.000 0.00 0.00 0.00 4.40
2196 2420 1.920325 CCCCCTTCACTCTCAGCCA 60.920 63.158 0.00 0.00 0.00 4.75
2197 2421 1.613630 TCCCCCTTCACTCTCAGCC 60.614 63.158 0.00 0.00 0.00 4.85
2198 2422 0.907230 ACTCCCCCTTCACTCTCAGC 60.907 60.000 0.00 0.00 0.00 4.26
2199 2423 1.190643 GACTCCCCCTTCACTCTCAG 58.809 60.000 0.00 0.00 0.00 3.35
2264 2488 2.882366 GCCCGCCGATAAAGCTTCG 61.882 63.158 0.00 0.00 36.38 3.79
2302 2526 2.738643 GCTTAGAATACTCACTGCGCCA 60.739 50.000 4.18 0.00 0.00 5.69
2309 2533 5.725362 ACAGTTCCAGCTTAGAATACTCAC 58.275 41.667 0.00 0.00 0.00 3.51
2458 2683 6.263168 ACAGCATAGCCATTATCAAAACCTAC 59.737 38.462 0.00 0.00 0.00 3.18
2555 2780 4.394300 AGCAGTCAATGTGATAAACTGAGC 59.606 41.667 5.07 0.00 39.72 4.26
2757 2983 1.736586 AGCATTACTCCGCTCTCCG 59.263 57.895 0.00 0.00 31.16 4.63


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

AutoCloner maintained by Alex Coulton.