Multiple sequence alignment - TraesCS5D01G214400

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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 TraesCS5D01G214400 chr5D 100.000 3173 0 0 1 3173 324113617 324110445 0.000000e+00 5860
1 TraesCS5D01G214400 chr5D 89.760 2334 228 8 847 3173 365335355 365337684 0.000000e+00 2976
2 TraesCS5D01G214400 chr2D 92.628 2333 166 4 842 3173 586951017 586953344 0.000000e+00 3350
3 TraesCS5D01G214400 chr2D 82.759 725 109 14 1 721 601991466 601992178 1.610000e-177 632
4 TraesCS5D01G214400 chr7A 92.210 2054 151 5 1127 3173 126212000 126214051 0.000000e+00 2898
5 TraesCS5D01G214400 chr7A 89.431 1722 179 3 845 2565 138625619 138623900 0.000000e+00 2169
6 TraesCS5D01G214400 chr7A 83.564 724 107 11 3 721 143351819 143351103 0.000000e+00 667
7 TraesCS5D01G214400 chr3D 89.066 2323 235 7 853 3173 32305453 32307758 0.000000e+00 2865
8 TraesCS5D01G214400 chr3D 83.233 2332 385 6 845 3171 141200262 141197932 0.000000e+00 2135
9 TraesCS5D01G214400 chr3D 88.466 1604 172 12 846 2443 63107209 63105613 0.000000e+00 1925
10 TraesCS5D01G214400 chr3D 90.164 1159 101 5 1036 2194 9552117 9553262 0.000000e+00 1496
11 TraesCS5D01G214400 chr3B 84.113 2329 362 8 843 3169 125580146 125582468 0.000000e+00 2244
12 TraesCS5D01G214400 chr3B 85.597 729 83 18 1 721 199549508 199550222 0.000000e+00 745
13 TraesCS5D01G214400 chr3B 85.322 729 85 19 1 721 199593838 199594552 0.000000e+00 734
14 TraesCS5D01G214400 chr3B 83.175 737 109 14 1 730 157905509 157906237 0.000000e+00 660
15 TraesCS5D01G214400 chr3A 80.017 2342 427 35 847 3168 697071661 697069341 0.000000e+00 1694
16 TraesCS5D01G214400 chr6B 88.440 1410 149 5 1768 3173 616931028 616929629 0.000000e+00 1688
17 TraesCS5D01G214400 chr6B 88.338 969 98 7 1482 2449 36023096 36022142 0.000000e+00 1149
18 TraesCS5D01G214400 chr7B 87.058 1329 159 7 843 2171 553087302 553085987 0.000000e+00 1489
19 TraesCS5D01G214400 chr7D 90.686 977 90 1 2195 3171 615566167 615565192 0.000000e+00 1299
20 TraesCS5D01G214400 chr4D 86.264 728 83 15 1 721 319338039 319337322 0.000000e+00 774
21 TraesCS5D01G214400 chr6D 84.341 728 99 11 2 721 102489556 102490276 0.000000e+00 699
22 TraesCS5D01G214400 chr2B 83.654 728 105 13 1 721 582812513 582813233 0.000000e+00 673
23 TraesCS5D01G214400 chr5A 83.424 736 100 20 1 729 318101296 318100576 0.000000e+00 664


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 TraesCS5D01G214400 chr5D 324110445 324113617 3172 True 5860 5860 100.000 1 3173 1 chr5D.!!$R1 3172
1 TraesCS5D01G214400 chr5D 365335355 365337684 2329 False 2976 2976 89.760 847 3173 1 chr5D.!!$F1 2326
2 TraesCS5D01G214400 chr2D 586951017 586953344 2327 False 3350 3350 92.628 842 3173 1 chr2D.!!$F1 2331
3 TraesCS5D01G214400 chr2D 601991466 601992178 712 False 632 632 82.759 1 721 1 chr2D.!!$F2 720
4 TraesCS5D01G214400 chr7A 126212000 126214051 2051 False 2898 2898 92.210 1127 3173 1 chr7A.!!$F1 2046
5 TraesCS5D01G214400 chr7A 138623900 138625619 1719 True 2169 2169 89.431 845 2565 1 chr7A.!!$R1 1720
6 TraesCS5D01G214400 chr7A 143351103 143351819 716 True 667 667 83.564 3 721 1 chr7A.!!$R2 718
7 TraesCS5D01G214400 chr3D 32305453 32307758 2305 False 2865 2865 89.066 853 3173 1 chr3D.!!$F2 2320
8 TraesCS5D01G214400 chr3D 141197932 141200262 2330 True 2135 2135 83.233 845 3171 1 chr3D.!!$R2 2326
9 TraesCS5D01G214400 chr3D 63105613 63107209 1596 True 1925 1925 88.466 846 2443 1 chr3D.!!$R1 1597
10 TraesCS5D01G214400 chr3D 9552117 9553262 1145 False 1496 1496 90.164 1036 2194 1 chr3D.!!$F1 1158
11 TraesCS5D01G214400 chr3B 125580146 125582468 2322 False 2244 2244 84.113 843 3169 1 chr3B.!!$F1 2326
12 TraesCS5D01G214400 chr3B 199549508 199550222 714 False 745 745 85.597 1 721 1 chr3B.!!$F3 720
13 TraesCS5D01G214400 chr3B 199593838 199594552 714 False 734 734 85.322 1 721 1 chr3B.!!$F4 720
14 TraesCS5D01G214400 chr3B 157905509 157906237 728 False 660 660 83.175 1 730 1 chr3B.!!$F2 729
15 TraesCS5D01G214400 chr3A 697069341 697071661 2320 True 1694 1694 80.017 847 3168 1 chr3A.!!$R1 2321
16 TraesCS5D01G214400 chr6B 616929629 616931028 1399 True 1688 1688 88.440 1768 3173 1 chr6B.!!$R2 1405
17 TraesCS5D01G214400 chr6B 36022142 36023096 954 True 1149 1149 88.338 1482 2449 1 chr6B.!!$R1 967
18 TraesCS5D01G214400 chr7B 553085987 553087302 1315 True 1489 1489 87.058 843 2171 1 chr7B.!!$R1 1328
19 TraesCS5D01G214400 chr7D 615565192 615566167 975 True 1299 1299 90.686 2195 3171 1 chr7D.!!$R1 976
20 TraesCS5D01G214400 chr4D 319337322 319338039 717 True 774 774 86.264 1 721 1 chr4D.!!$R1 720
21 TraesCS5D01G214400 chr6D 102489556 102490276 720 False 699 699 84.341 2 721 1 chr6D.!!$F1 719
22 TraesCS5D01G214400 chr2B 582812513 582813233 720 False 673 673 83.654 1 721 1 chr2B.!!$F1 720
23 TraesCS5D01G214400 chr5A 318100576 318101296 720 True 664 664 83.424 1 729 1 chr5A.!!$R1 728

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
825 848 0.111442 CGCGTCAACACCGTTACAAG 60.111 55.0 0.0 0.0 0.0 3.16 F
1164 1192 0.098905 CGATTCAAGAGAGCGTCCGA 59.901 55.0 0.0 0.0 0.0 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1820 1851 0.251608 ACGGGTTTTGGCCTGCTTAT 60.252 50.000 3.32 0.0 38.45 1.73 R
2750 2817 1.305802 ACACACGCCCTATCCAGGA 60.306 57.895 0.00 0.0 45.91 3.86 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
60 62 0.811616 GCAGCACGATCCGAGGAAAT 60.812 55.000 0.00 0.00 0.00 2.17
162 164 3.694058 CTCCCTCATTGCCGCTGCT 62.694 63.158 0.70 0.00 38.71 4.24
431 439 2.697761 CGAGGTCGTCGTCCATGGT 61.698 63.158 12.58 0.00 44.20 3.55
436 445 1.977009 TCGTCGTCCATGGTGAGCT 60.977 57.895 12.58 0.00 0.00 4.09
439 448 2.046988 CGTCCATGGTGAGCTGCA 60.047 61.111 12.58 0.00 0.00 4.41
519 538 4.335647 CGACTGGCAAGCAGGGGT 62.336 66.667 0.00 0.00 0.00 4.95
532 551 4.692475 GGGGTGTAGTTGGCGCGT 62.692 66.667 8.43 0.00 0.00 6.01
680 702 4.712873 CGCCGCGACCAAACGAAC 62.713 66.667 8.23 0.00 35.09 3.95
681 703 4.712873 GCCGCGACCAAACGAACG 62.713 66.667 8.23 0.00 35.09 3.95
703 726 1.669760 GTGCGGACGAAATGGGTCA 60.670 57.895 0.00 0.00 36.12 4.02
704 727 1.024579 GTGCGGACGAAATGGGTCAT 61.025 55.000 0.00 0.00 36.12 3.06
721 744 0.592637 CATTGCGTTGGAGTTGCTCA 59.407 50.000 0.00 0.00 31.08 4.26
723 746 0.592637 TTGCGTTGGAGTTGCTCATG 59.407 50.000 0.00 0.00 31.08 3.07
725 748 0.445436 GCGTTGGAGTTGCTCATGAG 59.555 55.000 18.84 18.84 31.08 2.90
726 749 1.941209 GCGTTGGAGTTGCTCATGAGA 60.941 52.381 27.04 8.75 31.08 3.27
727 750 1.728971 CGTTGGAGTTGCTCATGAGAC 59.271 52.381 27.04 16.01 31.08 3.36
728 751 2.771089 GTTGGAGTTGCTCATGAGACA 58.229 47.619 27.04 19.42 31.08 3.41
730 753 2.771089 TGGAGTTGCTCATGAGACAAC 58.229 47.619 32.93 32.93 41.40 3.32
731 754 1.728971 GGAGTTGCTCATGAGACAACG 59.271 52.381 33.00 12.87 43.50 4.10
732 755 2.610479 GGAGTTGCTCATGAGACAACGA 60.610 50.000 33.00 16.12 43.50 3.85
733 756 3.059884 GAGTTGCTCATGAGACAACGAA 58.940 45.455 33.00 15.76 43.50 3.85
734 757 3.668447 AGTTGCTCATGAGACAACGAAT 58.332 40.909 33.00 23.49 43.50 3.34
735 758 3.434641 AGTTGCTCATGAGACAACGAATG 59.565 43.478 33.00 10.61 43.50 2.67
736 759 1.733912 TGCTCATGAGACAACGAATGC 59.266 47.619 27.04 8.07 0.00 3.56
737 760 1.063174 GCTCATGAGACAACGAATGCC 59.937 52.381 27.04 0.00 0.00 4.40
738 761 2.349590 CTCATGAGACAACGAATGCCA 58.650 47.619 18.34 0.00 0.00 4.92
739 762 2.941064 CTCATGAGACAACGAATGCCAT 59.059 45.455 18.34 0.00 0.00 4.40
740 763 2.679336 TCATGAGACAACGAATGCCATG 59.321 45.455 0.00 0.00 33.32 3.66
741 764 1.452110 TGAGACAACGAATGCCATGG 58.548 50.000 7.63 7.63 0.00 3.66
742 765 1.271325 TGAGACAACGAATGCCATGGT 60.271 47.619 14.67 0.00 0.00 3.55
743 766 1.131126 GAGACAACGAATGCCATGGTG 59.869 52.381 14.67 4.03 0.00 4.17
744 767 1.164411 GACAACGAATGCCATGGTGA 58.836 50.000 14.67 0.10 0.00 4.02
745 768 1.539388 GACAACGAATGCCATGGTGAA 59.461 47.619 14.67 0.00 0.00 3.18
746 769 2.164219 GACAACGAATGCCATGGTGAAT 59.836 45.455 14.67 2.10 0.00 2.57
747 770 2.562298 ACAACGAATGCCATGGTGAATT 59.438 40.909 14.67 11.07 0.00 2.17
748 771 2.924926 CAACGAATGCCATGGTGAATTG 59.075 45.455 14.67 7.33 0.00 2.32
749 772 2.445427 ACGAATGCCATGGTGAATTGA 58.555 42.857 14.67 0.00 0.00 2.57
750 773 2.424601 ACGAATGCCATGGTGAATTGAG 59.575 45.455 14.67 9.65 0.00 3.02
751 774 2.223641 CGAATGCCATGGTGAATTGAGG 60.224 50.000 14.67 0.48 0.00 3.86
752 775 1.117150 ATGCCATGGTGAATTGAGGC 58.883 50.000 14.67 0.00 42.32 4.70
753 776 2.582272 GCCATGGTGAATTGAGGCA 58.418 52.632 14.67 0.00 41.63 4.75
754 777 0.458669 GCCATGGTGAATTGAGGCAG 59.541 55.000 14.67 0.00 41.63 4.85
755 778 1.956636 GCCATGGTGAATTGAGGCAGA 60.957 52.381 14.67 0.00 41.63 4.26
756 779 2.449464 CCATGGTGAATTGAGGCAGAA 58.551 47.619 2.57 0.00 0.00 3.02
757 780 2.426024 CCATGGTGAATTGAGGCAGAAG 59.574 50.000 2.57 0.00 0.00 2.85
758 781 3.349927 CATGGTGAATTGAGGCAGAAGA 58.650 45.455 0.00 0.00 0.00 2.87
759 782 3.507162 TGGTGAATTGAGGCAGAAGAA 57.493 42.857 0.00 0.00 0.00 2.52
760 783 4.038271 TGGTGAATTGAGGCAGAAGAAT 57.962 40.909 0.00 0.00 0.00 2.40
761 784 4.012374 TGGTGAATTGAGGCAGAAGAATC 58.988 43.478 0.00 0.00 0.00 2.52
762 785 4.012374 GGTGAATTGAGGCAGAAGAATCA 58.988 43.478 0.00 0.00 0.00 2.57
763 786 4.142513 GGTGAATTGAGGCAGAAGAATCAC 60.143 45.833 0.00 0.00 0.00 3.06
764 787 3.686241 TGAATTGAGGCAGAAGAATCACG 59.314 43.478 0.00 0.00 0.00 4.35
765 788 2.099141 TTGAGGCAGAAGAATCACGG 57.901 50.000 0.00 0.00 0.00 4.94
766 789 0.976641 TGAGGCAGAAGAATCACGGT 59.023 50.000 0.00 0.00 0.00 4.83
767 790 1.347707 TGAGGCAGAAGAATCACGGTT 59.652 47.619 0.00 0.00 0.00 4.44
768 791 1.734465 GAGGCAGAAGAATCACGGTTG 59.266 52.381 0.00 0.00 0.00 3.77
769 792 1.347707 AGGCAGAAGAATCACGGTTGA 59.652 47.619 0.00 0.00 35.73 3.18
770 793 1.464997 GGCAGAAGAATCACGGTTGAC 59.535 52.381 0.00 0.00 33.38 3.18
785 808 3.926616 GGTTGACGATTCCTTTCTCTCA 58.073 45.455 0.00 0.00 0.00 3.27
786 809 4.315803 GGTTGACGATTCCTTTCTCTCAA 58.684 43.478 0.00 0.00 0.00 3.02
787 810 4.152580 GGTTGACGATTCCTTTCTCTCAAC 59.847 45.833 0.00 0.00 36.74 3.18
788 811 3.926616 TGACGATTCCTTTCTCTCAACC 58.073 45.455 0.00 0.00 0.00 3.77
789 812 3.578716 TGACGATTCCTTTCTCTCAACCT 59.421 43.478 0.00 0.00 0.00 3.50
790 813 4.177783 GACGATTCCTTTCTCTCAACCTC 58.822 47.826 0.00 0.00 0.00 3.85
791 814 3.578716 ACGATTCCTTTCTCTCAACCTCA 59.421 43.478 0.00 0.00 0.00 3.86
792 815 4.040461 ACGATTCCTTTCTCTCAACCTCAA 59.960 41.667 0.00 0.00 0.00 3.02
793 816 4.390297 CGATTCCTTTCTCTCAACCTCAAC 59.610 45.833 0.00 0.00 0.00 3.18
794 817 4.771114 TTCCTTTCTCTCAACCTCAACA 57.229 40.909 0.00 0.00 0.00 3.33
795 818 4.982241 TCCTTTCTCTCAACCTCAACAT 57.018 40.909 0.00 0.00 0.00 2.71
796 819 5.310409 TCCTTTCTCTCAACCTCAACATT 57.690 39.130 0.00 0.00 0.00 2.71
797 820 6.433847 TCCTTTCTCTCAACCTCAACATTA 57.566 37.500 0.00 0.00 0.00 1.90
798 821 6.837312 TCCTTTCTCTCAACCTCAACATTAA 58.163 36.000 0.00 0.00 0.00 1.40
799 822 7.461749 TCCTTTCTCTCAACCTCAACATTAAT 58.538 34.615 0.00 0.00 0.00 1.40
800 823 8.602424 TCCTTTCTCTCAACCTCAACATTAATA 58.398 33.333 0.00 0.00 0.00 0.98
801 824 9.401058 CCTTTCTCTCAACCTCAACATTAATAT 57.599 33.333 0.00 0.00 0.00 1.28
803 826 7.792374 TCTCTCAACCTCAACATTAATATGC 57.208 36.000 0.00 0.00 35.03 3.14
804 827 6.767902 TCTCTCAACCTCAACATTAATATGCC 59.232 38.462 0.00 0.00 35.03 4.40
805 828 6.422333 TCTCAACCTCAACATTAATATGCCA 58.578 36.000 0.00 0.00 35.03 4.92
806 829 6.318648 TCTCAACCTCAACATTAATATGCCAC 59.681 38.462 0.00 0.00 35.03 5.01
807 830 5.065859 TCAACCTCAACATTAATATGCCACG 59.934 40.000 0.00 0.00 35.03 4.94
808 831 3.315191 ACCTCAACATTAATATGCCACGC 59.685 43.478 0.00 0.00 35.03 5.34
809 832 3.544651 CTCAACATTAATATGCCACGCG 58.455 45.455 3.53 3.53 35.03 6.01
810 833 2.939756 TCAACATTAATATGCCACGCGT 59.060 40.909 5.58 5.58 35.03 6.01
811 834 3.001838 TCAACATTAATATGCCACGCGTC 59.998 43.478 9.86 0.00 35.03 5.19
812 835 2.556257 ACATTAATATGCCACGCGTCA 58.444 42.857 9.86 5.78 35.03 4.35
813 836 2.939756 ACATTAATATGCCACGCGTCAA 59.060 40.909 9.86 0.00 35.03 3.18
814 837 3.242608 ACATTAATATGCCACGCGTCAAC 60.243 43.478 9.86 1.47 35.03 3.18
815 838 2.011540 TAATATGCCACGCGTCAACA 57.988 45.000 9.86 8.51 0.00 3.33
816 839 0.446222 AATATGCCACGCGTCAACAC 59.554 50.000 9.86 0.00 0.00 3.32
817 840 1.366111 ATATGCCACGCGTCAACACC 61.366 55.000 9.86 0.00 0.00 4.16
820 843 3.266376 CCACGCGTCAACACCGTT 61.266 61.111 9.86 0.00 32.18 4.44
821 844 1.950130 CCACGCGTCAACACCGTTA 60.950 57.895 9.86 0.00 32.18 3.18
822 845 1.199859 CACGCGTCAACACCGTTAC 59.800 57.895 9.86 0.00 32.18 2.50
823 846 1.226916 ACGCGTCAACACCGTTACA 60.227 52.632 5.58 0.00 0.00 2.41
824 847 0.805322 ACGCGTCAACACCGTTACAA 60.805 50.000 5.58 0.00 0.00 2.41
825 848 0.111442 CGCGTCAACACCGTTACAAG 60.111 55.000 0.00 0.00 0.00 3.16
826 849 0.383860 GCGTCAACACCGTTACAAGC 60.384 55.000 0.00 0.00 0.00 4.01
827 850 0.931702 CGTCAACACCGTTACAAGCA 59.068 50.000 0.00 0.00 0.00 3.91
828 851 1.529438 CGTCAACACCGTTACAAGCAT 59.471 47.619 0.00 0.00 0.00 3.79
829 852 2.661709 CGTCAACACCGTTACAAGCATG 60.662 50.000 0.00 0.00 0.00 4.06
830 853 1.876799 TCAACACCGTTACAAGCATGG 59.123 47.619 0.00 0.00 0.00 3.66
831 854 1.606668 CAACACCGTTACAAGCATGGT 59.393 47.619 0.00 0.00 33.43 3.55
832 855 1.519408 ACACCGTTACAAGCATGGTC 58.481 50.000 0.00 0.00 30.47 4.02
833 856 1.202710 ACACCGTTACAAGCATGGTCA 60.203 47.619 0.00 0.00 30.47 4.02
834 857 1.196808 CACCGTTACAAGCATGGTCAC 59.803 52.381 0.00 0.00 30.47 3.67
835 858 1.071699 ACCGTTACAAGCATGGTCACT 59.928 47.619 0.00 0.00 0.00 3.41
836 859 2.151202 CCGTTACAAGCATGGTCACTT 58.849 47.619 0.00 0.00 0.00 3.16
837 860 2.159627 CCGTTACAAGCATGGTCACTTC 59.840 50.000 0.00 0.00 0.00 3.01
838 861 2.159841 CGTTACAAGCATGGTCACTTCG 60.160 50.000 0.00 0.00 0.00 3.79
839 862 3.064207 GTTACAAGCATGGTCACTTCGA 58.936 45.455 0.00 0.00 0.00 3.71
840 863 2.479566 ACAAGCATGGTCACTTCGAT 57.520 45.000 0.00 0.00 0.00 3.59
891 915 3.517296 TCTCTCCTCTTAGGCGATCAT 57.483 47.619 0.00 0.00 34.61 2.45
982 1009 2.111043 CCCCTGTTGTGTCTGCGT 59.889 61.111 0.00 0.00 0.00 5.24
995 1023 1.040646 TCTGCGTTGAGACAGGAACT 58.959 50.000 0.00 0.00 43.88 3.01
1029 1057 4.361971 TCCGACTCCCACTCCGCT 62.362 66.667 0.00 0.00 0.00 5.52
1155 1183 3.639094 AGGATGACCCTACGATTCAAGAG 59.361 47.826 0.00 0.00 45.48 2.85
1164 1192 0.098905 CGATTCAAGAGAGCGTCCGA 59.901 55.000 0.00 0.00 0.00 4.55
1253 1281 4.652131 TGCATGGAACCCGGCGTT 62.652 61.111 6.01 7.90 37.41 4.84
1276 1304 0.458889 CGTGAGATTTCGGCCGGTTA 60.459 55.000 27.83 11.47 0.00 2.85
1424 1453 4.223032 TGAGGAGGTGGAGTTCTTTCATAC 59.777 45.833 0.00 0.00 0.00 2.39
1426 1455 4.846940 AGGAGGTGGAGTTCTTTCATACTT 59.153 41.667 0.00 0.00 0.00 2.24
1586 1616 3.060272 GTGAAACATGATATCCGACAGCG 60.060 47.826 0.00 0.00 36.32 5.18
1812 1843 2.240162 GACCCACTAAGGCGACAGGG 62.240 65.000 0.00 0.00 42.07 4.45
1820 1851 1.568504 AAGGCGACAGGGAATGAGTA 58.431 50.000 0.00 0.00 0.00 2.59
1859 1890 5.720371 CGTAAGGATGGAAGATCTGATCT 57.280 43.478 14.31 14.31 42.61 2.75
1885 1916 3.649502 ACATGCACCATATGATCCTGAGA 59.350 43.478 3.65 0.00 0.00 3.27
2215 2282 2.281276 GGAACCGCCGGACAGTTT 60.281 61.111 11.71 0.00 0.00 2.66
2228 2295 2.758423 GGACAGTTTGTGAGGTTTTGGT 59.242 45.455 0.00 0.00 0.00 3.67
2363 2430 3.074369 TGATGGAAGGAGCGGCGA 61.074 61.111 12.98 0.00 0.00 5.54
2492 2559 2.084546 GACCTTTGTTTATGGCGAGCT 58.915 47.619 0.00 0.00 0.00 4.09
2575 2642 1.382240 CCTTGGGTGGTATGTGGCA 59.618 57.895 0.00 0.00 0.00 4.92
2596 2663 4.070716 CAACTTCAATGAAGCTCTCTGGT 58.929 43.478 21.69 0.00 42.79 4.00
2618 2685 1.202510 GCACGAGCATCTCTCAAGGAT 60.203 52.381 0.00 0.00 41.98 3.24
2695 2762 1.197812 GCGGGACCTAGGGTTTTCTA 58.802 55.000 14.81 0.00 35.25 2.10
2750 2817 1.470098 GAATCGCAATGTTCAGGTGCT 59.530 47.619 8.76 0.00 36.10 4.40
2768 2835 1.305802 TCCTGGATAGGGCGTGTGT 60.306 57.895 0.00 0.00 44.70 3.72
2825 2892 2.552373 GGGTTGTGCACTTAGCTACCTT 60.552 50.000 19.41 0.00 45.94 3.50
2926 2993 1.690219 GATCATGTGGGAGCGGGACT 61.690 60.000 0.00 0.00 0.00 3.85
2941 3008 1.376037 GACTTCAAGCTCCCCACGG 60.376 63.158 0.00 0.00 0.00 4.94
2947 3014 2.670148 AAGCTCCCCACGGTCATCC 61.670 63.158 0.00 0.00 0.00 3.51
3061 3128 4.871933 AAAGCTACCTTTGGGAATGTTG 57.128 40.909 0.00 0.00 39.72 3.33
3088 3155 5.916661 AGAGATAGAAAGTTTGCGAGGTA 57.083 39.130 0.00 0.00 0.00 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 50 3.065655 CTCATCTGCATTTCCTCGGATC 58.934 50.000 0.00 0.00 0.00 3.36
119 121 4.142004 CGCTGATGTACCTAGGGTTAAACT 60.142 45.833 14.81 0.00 37.09 2.66
292 295 2.354259 CAAGCCGAAGAAGAAGCTGAT 58.646 47.619 0.00 0.00 35.30 2.90
409 417 1.030488 ATGGACGACGACCTCGATGT 61.030 55.000 16.98 0.00 46.14 3.06
450 459 4.643387 AACCTTCTTGCCCGCGCT 62.643 61.111 5.56 0.00 35.36 5.92
452 463 2.255252 CAAACCTTCTTGCCCGCG 59.745 61.111 0.00 0.00 0.00 6.46
458 469 3.295973 TCCACTTTCCCAAACCTTCTTG 58.704 45.455 0.00 0.00 0.00 3.02
459 470 3.566351 CTCCACTTTCCCAAACCTTCTT 58.434 45.455 0.00 0.00 0.00 2.52
462 473 1.133167 CCCTCCACTTTCCCAAACCTT 60.133 52.381 0.00 0.00 0.00 3.50
463 474 0.482887 CCCTCCACTTTCCCAAACCT 59.517 55.000 0.00 0.00 0.00 3.50
464 475 0.481128 TCCCTCCACTTTCCCAAACC 59.519 55.000 0.00 0.00 0.00 3.27
465 476 2.375014 TTCCCTCCACTTTCCCAAAC 57.625 50.000 0.00 0.00 0.00 2.93
510 522 1.074951 GCCAACTACACCCCTGCTT 59.925 57.895 0.00 0.00 0.00 3.91
511 523 2.757077 GCCAACTACACCCCTGCT 59.243 61.111 0.00 0.00 0.00 4.24
519 538 2.731721 CGACACGCGCCAACTACA 60.732 61.111 5.73 0.00 0.00 2.74
703 726 1.200716 CATGAGCAACTCCAACGCAAT 59.799 47.619 0.00 0.00 0.00 3.56
704 727 0.592637 CATGAGCAACTCCAACGCAA 59.407 50.000 0.00 0.00 0.00 4.85
721 744 2.019249 CCATGGCATTCGTTGTCTCAT 58.981 47.619 0.00 0.00 0.00 2.90
723 746 1.131126 CACCATGGCATTCGTTGTCTC 59.869 52.381 13.04 0.00 0.00 3.36
725 748 1.164411 TCACCATGGCATTCGTTGTC 58.836 50.000 13.04 0.00 0.00 3.18
726 749 1.614996 TTCACCATGGCATTCGTTGT 58.385 45.000 13.04 0.00 0.00 3.32
727 750 2.924926 CAATTCACCATGGCATTCGTTG 59.075 45.455 13.04 6.24 0.00 4.10
728 751 2.824936 TCAATTCACCATGGCATTCGTT 59.175 40.909 13.04 0.00 0.00 3.85
730 753 2.223641 CCTCAATTCACCATGGCATTCG 60.224 50.000 13.04 3.86 0.00 3.34
731 754 2.482490 GCCTCAATTCACCATGGCATTC 60.482 50.000 13.04 0.00 40.04 2.67
732 755 1.483415 GCCTCAATTCACCATGGCATT 59.517 47.619 13.04 5.06 40.04 3.56
733 756 1.117150 GCCTCAATTCACCATGGCAT 58.883 50.000 13.04 0.00 40.04 4.40
734 757 0.251698 TGCCTCAATTCACCATGGCA 60.252 50.000 13.04 0.00 46.59 4.92
735 758 0.458669 CTGCCTCAATTCACCATGGC 59.541 55.000 13.04 0.00 40.62 4.40
736 759 2.133281 TCTGCCTCAATTCACCATGG 57.867 50.000 11.19 11.19 0.00 3.66
737 760 3.349927 TCTTCTGCCTCAATTCACCATG 58.650 45.455 0.00 0.00 0.00 3.66
738 761 3.726557 TCTTCTGCCTCAATTCACCAT 57.273 42.857 0.00 0.00 0.00 3.55
739 762 3.507162 TTCTTCTGCCTCAATTCACCA 57.493 42.857 0.00 0.00 0.00 4.17
740 763 4.012374 TGATTCTTCTGCCTCAATTCACC 58.988 43.478 0.00 0.00 0.00 4.02
741 764 4.436584 CGTGATTCTTCTGCCTCAATTCAC 60.437 45.833 0.00 0.00 0.00 3.18
742 765 3.686241 CGTGATTCTTCTGCCTCAATTCA 59.314 43.478 0.00 0.00 0.00 2.57
743 766 3.064545 CCGTGATTCTTCTGCCTCAATTC 59.935 47.826 0.00 0.00 0.00 2.17
744 767 3.012518 CCGTGATTCTTCTGCCTCAATT 58.987 45.455 0.00 0.00 0.00 2.32
745 768 2.026822 ACCGTGATTCTTCTGCCTCAAT 60.027 45.455 0.00 0.00 0.00 2.57
746 769 1.347707 ACCGTGATTCTTCTGCCTCAA 59.652 47.619 0.00 0.00 0.00 3.02
747 770 0.976641 ACCGTGATTCTTCTGCCTCA 59.023 50.000 0.00 0.00 0.00 3.86
748 771 1.734465 CAACCGTGATTCTTCTGCCTC 59.266 52.381 0.00 0.00 0.00 4.70
749 772 1.347707 TCAACCGTGATTCTTCTGCCT 59.652 47.619 0.00 0.00 0.00 4.75
750 773 1.464997 GTCAACCGTGATTCTTCTGCC 59.535 52.381 0.00 0.00 35.80 4.85
751 774 1.126846 CGTCAACCGTGATTCTTCTGC 59.873 52.381 0.00 0.00 35.80 4.26
752 775 2.672714 TCGTCAACCGTGATTCTTCTG 58.327 47.619 0.00 0.00 35.80 3.02
753 776 3.594603 ATCGTCAACCGTGATTCTTCT 57.405 42.857 0.00 0.00 35.80 2.85
754 777 3.062234 GGAATCGTCAACCGTGATTCTTC 59.938 47.826 12.33 0.00 44.60 2.87
755 778 3.000727 GGAATCGTCAACCGTGATTCTT 58.999 45.455 12.33 0.00 44.60 2.52
756 779 2.233922 AGGAATCGTCAACCGTGATTCT 59.766 45.455 12.33 0.00 44.60 2.40
757 780 2.618053 AGGAATCGTCAACCGTGATTC 58.382 47.619 5.78 5.78 44.52 2.52
758 781 2.762535 AGGAATCGTCAACCGTGATT 57.237 45.000 0.00 0.00 35.80 2.57
759 782 2.762535 AAGGAATCGTCAACCGTGAT 57.237 45.000 0.00 0.00 35.80 3.06
760 783 2.036733 AGAAAGGAATCGTCAACCGTGA 59.963 45.455 0.00 0.00 37.94 4.35
761 784 2.412089 GAGAAAGGAATCGTCAACCGTG 59.588 50.000 0.00 0.00 37.94 4.94
762 785 2.299297 AGAGAAAGGAATCGTCAACCGT 59.701 45.455 0.00 0.00 37.94 4.83
763 786 2.924290 GAGAGAAAGGAATCGTCAACCG 59.076 50.000 0.00 0.00 38.13 4.44
764 787 3.926616 TGAGAGAAAGGAATCGTCAACC 58.073 45.455 0.00 0.00 0.00 3.77
765 788 4.152580 GGTTGAGAGAAAGGAATCGTCAAC 59.847 45.833 12.99 12.99 41.96 3.18
766 789 4.040461 AGGTTGAGAGAAAGGAATCGTCAA 59.960 41.667 0.00 0.00 0.00 3.18
767 790 3.578716 AGGTTGAGAGAAAGGAATCGTCA 59.421 43.478 0.00 0.00 0.00 4.35
768 791 4.177783 GAGGTTGAGAGAAAGGAATCGTC 58.822 47.826 0.00 0.00 0.00 4.20
769 792 3.578716 TGAGGTTGAGAGAAAGGAATCGT 59.421 43.478 0.00 0.00 0.00 3.73
770 793 4.193826 TGAGGTTGAGAGAAAGGAATCG 57.806 45.455 0.00 0.00 0.00 3.34
771 794 5.308825 TGTTGAGGTTGAGAGAAAGGAATC 58.691 41.667 0.00 0.00 0.00 2.52
772 795 5.310409 TGTTGAGGTTGAGAGAAAGGAAT 57.690 39.130 0.00 0.00 0.00 3.01
773 796 4.771114 TGTTGAGGTTGAGAGAAAGGAA 57.229 40.909 0.00 0.00 0.00 3.36
774 797 4.982241 ATGTTGAGGTTGAGAGAAAGGA 57.018 40.909 0.00 0.00 0.00 3.36
775 798 7.693969 ATTAATGTTGAGGTTGAGAGAAAGG 57.306 36.000 0.00 0.00 0.00 3.11
777 800 8.677300 GCATATTAATGTTGAGGTTGAGAGAAA 58.323 33.333 0.00 0.00 35.38 2.52
778 801 7.283127 GGCATATTAATGTTGAGGTTGAGAGAA 59.717 37.037 0.00 0.00 35.38 2.87
779 802 6.767902 GGCATATTAATGTTGAGGTTGAGAGA 59.232 38.462 0.00 0.00 35.38 3.10
780 803 6.543465 TGGCATATTAATGTTGAGGTTGAGAG 59.457 38.462 0.00 0.00 35.38 3.20
781 804 6.318648 GTGGCATATTAATGTTGAGGTTGAGA 59.681 38.462 0.00 0.00 35.38 3.27
782 805 6.498304 GTGGCATATTAATGTTGAGGTTGAG 58.502 40.000 0.00 0.00 35.38 3.02
783 806 5.065859 CGTGGCATATTAATGTTGAGGTTGA 59.934 40.000 0.00 0.00 35.38 3.18
784 807 5.273170 CGTGGCATATTAATGTTGAGGTTG 58.727 41.667 0.00 0.00 35.38 3.77
785 808 4.202010 GCGTGGCATATTAATGTTGAGGTT 60.202 41.667 0.00 0.00 35.38 3.50
786 809 3.315191 GCGTGGCATATTAATGTTGAGGT 59.685 43.478 0.00 0.00 35.38 3.85
787 810 3.606846 CGCGTGGCATATTAATGTTGAGG 60.607 47.826 0.00 0.00 35.38 3.86
788 811 3.002246 ACGCGTGGCATATTAATGTTGAG 59.998 43.478 12.93 0.00 35.38 3.02
789 812 2.939756 ACGCGTGGCATATTAATGTTGA 59.060 40.909 12.93 0.00 35.38 3.18
790 813 3.242576 TGACGCGTGGCATATTAATGTTG 60.243 43.478 20.70 0.00 35.38 3.33
791 814 2.939756 TGACGCGTGGCATATTAATGTT 59.060 40.909 20.70 0.00 35.38 2.71
792 815 2.556257 TGACGCGTGGCATATTAATGT 58.444 42.857 20.70 0.00 35.38 2.71
793 816 3.242576 TGTTGACGCGTGGCATATTAATG 60.243 43.478 20.70 0.00 36.09 1.90
794 817 2.939756 TGTTGACGCGTGGCATATTAAT 59.060 40.909 20.70 0.00 0.00 1.40
795 818 2.094575 GTGTTGACGCGTGGCATATTAA 59.905 45.455 20.70 0.00 0.00 1.40
796 819 1.661617 GTGTTGACGCGTGGCATATTA 59.338 47.619 20.70 0.00 0.00 0.98
797 820 0.446222 GTGTTGACGCGTGGCATATT 59.554 50.000 20.70 0.00 0.00 1.28
798 821 1.366111 GGTGTTGACGCGTGGCATAT 61.366 55.000 20.70 0.00 0.00 1.78
799 822 2.030401 GGTGTTGACGCGTGGCATA 61.030 57.895 20.70 0.00 0.00 3.14
800 823 3.353836 GGTGTTGACGCGTGGCAT 61.354 61.111 20.70 0.00 0.00 4.40
803 826 1.950130 TAACGGTGTTGACGCGTGG 60.950 57.895 20.70 0.00 31.84 4.94
804 827 1.199859 GTAACGGTGTTGACGCGTG 59.800 57.895 20.70 1.77 31.84 5.34
805 828 0.805322 TTGTAACGGTGTTGACGCGT 60.805 50.000 13.85 13.85 32.50 6.01
806 829 0.111442 CTTGTAACGGTGTTGACGCG 60.111 55.000 3.53 3.53 34.00 6.01
807 830 0.383860 GCTTGTAACGGTGTTGACGC 60.384 55.000 0.00 0.00 34.00 5.19
808 831 0.931702 TGCTTGTAACGGTGTTGACG 59.068 50.000 0.00 0.00 37.36 4.35
809 832 2.350388 CCATGCTTGTAACGGTGTTGAC 60.350 50.000 0.00 0.00 0.00 3.18
810 833 1.876799 CCATGCTTGTAACGGTGTTGA 59.123 47.619 0.00 0.00 0.00 3.18
811 834 1.606668 ACCATGCTTGTAACGGTGTTG 59.393 47.619 0.00 0.00 0.00 3.33
812 835 1.877443 GACCATGCTTGTAACGGTGTT 59.123 47.619 0.00 0.00 0.00 3.32
813 836 1.202710 TGACCATGCTTGTAACGGTGT 60.203 47.619 0.00 0.00 0.00 4.16
814 837 1.196808 GTGACCATGCTTGTAACGGTG 59.803 52.381 0.00 0.00 0.00 4.94
815 838 1.071699 AGTGACCATGCTTGTAACGGT 59.928 47.619 0.00 0.00 0.00 4.83
816 839 1.808411 AGTGACCATGCTTGTAACGG 58.192 50.000 0.00 0.00 0.00 4.44
817 840 2.159841 CGAAGTGACCATGCTTGTAACG 60.160 50.000 0.00 0.00 0.00 3.18
818 841 3.064207 TCGAAGTGACCATGCTTGTAAC 58.936 45.455 0.00 0.00 0.00 2.50
819 842 3.394674 TCGAAGTGACCATGCTTGTAA 57.605 42.857 0.00 0.00 0.00 2.41
820 843 3.610040 ATCGAAGTGACCATGCTTGTA 57.390 42.857 0.00 0.00 0.00 2.41
821 844 2.479566 ATCGAAGTGACCATGCTTGT 57.520 45.000 0.00 0.00 0.00 3.16
822 845 3.935203 AGTTATCGAAGTGACCATGCTTG 59.065 43.478 0.00 0.00 0.00 4.01
823 846 4.207891 AGTTATCGAAGTGACCATGCTT 57.792 40.909 0.00 0.00 0.00 3.91
824 847 3.895232 AGTTATCGAAGTGACCATGCT 57.105 42.857 0.00 0.00 0.00 3.79
825 848 4.201822 GGAAAGTTATCGAAGTGACCATGC 60.202 45.833 0.00 0.00 0.00 4.06
826 849 4.332819 GGGAAAGTTATCGAAGTGACCATG 59.667 45.833 0.00 0.00 0.00 3.66
827 850 4.514401 GGGAAAGTTATCGAAGTGACCAT 58.486 43.478 0.00 0.00 0.00 3.55
828 851 3.307199 GGGGAAAGTTATCGAAGTGACCA 60.307 47.826 0.00 0.00 0.00 4.02
829 852 3.055312 AGGGGAAAGTTATCGAAGTGACC 60.055 47.826 0.00 0.00 0.00 4.02
830 853 4.203654 AGGGGAAAGTTATCGAAGTGAC 57.796 45.455 0.00 0.00 0.00 3.67
831 854 4.142315 CGTAGGGGAAAGTTATCGAAGTGA 60.142 45.833 0.00 0.00 0.00 3.41
832 855 4.110482 CGTAGGGGAAAGTTATCGAAGTG 58.890 47.826 0.00 0.00 0.00 3.16
833 856 3.429960 GCGTAGGGGAAAGTTATCGAAGT 60.430 47.826 0.00 0.00 0.00 3.01
834 857 3.121544 GCGTAGGGGAAAGTTATCGAAG 58.878 50.000 0.00 0.00 0.00 3.79
835 858 2.159057 GGCGTAGGGGAAAGTTATCGAA 60.159 50.000 0.00 0.00 0.00 3.71
836 859 1.410153 GGCGTAGGGGAAAGTTATCGA 59.590 52.381 0.00 0.00 0.00 3.59
837 860 1.411612 AGGCGTAGGGGAAAGTTATCG 59.588 52.381 0.00 0.00 0.00 2.92
838 861 2.169978 ACAGGCGTAGGGGAAAGTTATC 59.830 50.000 0.00 0.00 0.00 1.75
839 862 2.169978 GACAGGCGTAGGGGAAAGTTAT 59.830 50.000 0.00 0.00 0.00 1.89
840 863 1.551883 GACAGGCGTAGGGGAAAGTTA 59.448 52.381 0.00 0.00 0.00 2.24
891 915 0.174389 GCAAGACTCAGAGGCGATCA 59.826 55.000 1.53 0.00 0.00 2.92
982 1009 2.038952 CCATCACCAGTTCCTGTCTCAA 59.961 50.000 0.00 0.00 0.00 3.02
995 1023 1.323271 GGAGAGAGTCGCCATCACCA 61.323 60.000 0.00 0.00 36.28 4.17
1144 1172 0.179161 CGGACGCTCTCTTGAATCGT 60.179 55.000 0.00 0.00 35.33 3.73
1155 1183 3.567797 GCAAGCCATCGGACGCTC 61.568 66.667 2.22 0.00 33.09 5.03
1253 1281 1.011968 CGGCCGAAATCTCACGTTCA 61.012 55.000 24.07 0.00 0.00 3.18
1276 1304 1.084289 GCGACAAAACGATTAGGGCT 58.916 50.000 0.00 0.00 35.09 5.19
1424 1453 3.924686 GTGAATCTGCAGCCAAATTGAAG 59.075 43.478 9.47 0.00 0.00 3.02
1426 1455 2.892215 TGTGAATCTGCAGCCAAATTGA 59.108 40.909 9.47 0.00 0.00 2.57
1586 1616 2.150397 ACTGACGTACTTTGTGAGGC 57.850 50.000 0.00 0.00 0.00 4.70
1812 1843 5.450550 GGTTTTGGCCTGCTTATACTCATTC 60.451 44.000 3.32 0.00 0.00 2.67
1820 1851 0.251608 ACGGGTTTTGGCCTGCTTAT 60.252 50.000 3.32 0.00 38.45 1.73
1859 1890 3.138839 AGGATCATATGGTGCATGTTCCA 59.861 43.478 10.37 12.03 41.64 3.53
1885 1916 2.029828 GGCTCGAAGTCGTATCCATGAT 60.030 50.000 0.00 0.00 40.80 2.45
2119 2150 3.684788 GCCGCCGATATCTCATTATTGTT 59.315 43.478 0.34 0.00 0.00 2.83
2228 2295 3.563479 GGGGTTATTGGCTTTTGAGAGGA 60.563 47.826 0.00 0.00 0.00 3.71
2363 2430 1.558756 CCTCCCAGAACAGAGCAAGAT 59.441 52.381 0.00 0.00 0.00 2.40
2492 2559 1.724623 GCTGACGATTTTCTACACGCA 59.275 47.619 0.00 0.00 0.00 5.24
2575 2642 4.363991 ACCAGAGAGCTTCATTGAAGTT 57.636 40.909 23.66 19.50 41.27 2.66
2618 2685 1.687563 TTGTGTCTCTGACCGAGTCA 58.312 50.000 6.57 6.57 40.50 3.41
2678 2745 1.489649 GGCTAGAAAACCCTAGGTCCC 59.510 57.143 8.29 0.00 37.27 4.46
2695 2762 2.263895 TTGTATGTGTAGGGGAGGCT 57.736 50.000 0.00 0.00 0.00 4.58
2750 2817 1.305802 ACACACGCCCTATCCAGGA 60.306 57.895 0.00 0.00 45.91 3.86
2768 2835 4.776322 CCCGCAACGCCTCATCCA 62.776 66.667 0.00 0.00 0.00 3.41
2825 2892 3.695606 GGCTGTGGTCCGAGCAGA 61.696 66.667 13.33 0.00 36.90 4.26
2926 2993 1.488705 ATGACCGTGGGGAGCTTGAA 61.489 55.000 0.00 0.00 36.97 2.69
2941 3008 2.914289 CCAGGCCTCAGGGATGAC 59.086 66.667 0.00 0.00 33.58 3.06
2947 3014 4.479993 CTTCGCCCAGGCCTCAGG 62.480 72.222 0.00 8.41 37.98 3.86
3061 3128 6.401581 CCTCGCAAACTTTCTATCTCTTTCAC 60.402 42.308 0.00 0.00 0.00 3.18
3129 3196 3.855255 TGATTCATCTTTGCCCGGATA 57.145 42.857 0.73 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.