Multiple sequence alignment - TraesCS1A01G421200

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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 TraesCS1A01G421200 chr1A 100.000 3410 0 0 1 3410 577540109 577536700 0.000000e+00 6298
1 TraesCS1A01G421200 chr1A 79.905 1264 205 30 1091 2336 577720158 577718926 0.000000e+00 881
2 TraesCS1A01G421200 chr1A 78.935 1277 219 31 1082 2336 578544819 578546067 0.000000e+00 822
3 TraesCS1A01G421200 chr1D 91.812 1600 76 16 808 2367 481011143 481012727 0.000000e+00 2178
4 TraesCS1A01G421200 chr1D 79.589 1264 209 31 1091 2336 481326778 481325546 0.000000e+00 859
5 TraesCS1A01G421200 chr1D 78.836 1271 225 27 1082 2336 481718064 481719306 0.000000e+00 817
6 TraesCS1A01G421200 chr1B 91.682 1587 90 11 808 2367 669219075 669220646 0.000000e+00 2161
7 TraesCS1A01G421200 chr1B 79.796 1272 207 32 1084 2336 669703388 669702148 0.000000e+00 880
8 TraesCS1A01G421200 chr1B 90.997 622 34 9 835 1444 669331859 669331248 0.000000e+00 819
9 TraesCS1A01G421200 chr3A 98.145 1024 17 2 2367 3390 61527398 61528419 0.000000e+00 1784
10 TraesCS1A01G421200 chr3A 89.698 728 69 5 1 723 65351912 65351186 0.000000e+00 924
11 TraesCS1A01G421200 chr6B 92.241 1031 66 8 2368 3390 232737406 232736382 0.000000e+00 1448
12 TraesCS1A01G421200 chr5B 91.732 1028 65 11 2368 3390 380325096 380326108 0.000000e+00 1410
13 TraesCS1A01G421200 chr3B 90.732 1025 80 8 2370 3390 828519060 828520073 0.000000e+00 1352
14 TraesCS1A01G421200 chr3B 81.065 338 35 18 3077 3390 747740831 747740499 3.400000e-60 243
15 TraesCS1A01G421200 chr3B 93.103 87 4 2 2375 2460 747738794 747738879 3.570000e-25 126
16 TraesCS1A01G421200 chr2A 90.114 789 61 13 2368 3152 676224971 676224196 0.000000e+00 1009
17 TraesCS1A01G421200 chr2A 79.321 1267 209 33 1084 2328 30869087 30870322 0.000000e+00 839
18 TraesCS1A01G421200 chr2A 89.712 243 20 4 3151 3390 676185202 676184962 4.280000e-79 305
19 TraesCS1A01G421200 chr5D 92.566 686 48 3 1 684 251910861 251910177 0.000000e+00 981
20 TraesCS1A01G421200 chr5D 90.587 733 63 6 1 730 410492835 410492106 0.000000e+00 966
21 TraesCS1A01G421200 chr5D 89.651 744 66 8 1 735 403559044 403558303 0.000000e+00 937
22 TraesCS1A01G421200 chr5D 89.917 724 68 5 1 721 52238487 52239208 0.000000e+00 928
23 TraesCS1A01G421200 chr7D 92.548 671 45 5 1 668 264480268 264480936 0.000000e+00 957
24 TraesCS1A01G421200 chr7D 89.889 722 70 3 1 721 426818914 426818195 0.000000e+00 926
25 TraesCS1A01G421200 chr4B 87.383 856 67 16 2538 3390 587772294 587771477 0.000000e+00 944
26 TraesCS1A01G421200 chr3D 89.931 725 70 3 1 723 252338591 252337868 0.000000e+00 931
27 TraesCS1A01G421200 chrUn 89.821 727 66 5 1 723 5440297 5441019 0.000000e+00 926
28 TraesCS1A01G421200 chr2D 79.685 1270 207 31 1087 2335 27970728 27969489 0.000000e+00 869
29 TraesCS1A01G421200 chr7A 90.941 574 47 2 2367 2940 125887483 125888051 0.000000e+00 767
30 TraesCS1A01G421200 chr6D 90.203 541 50 1 1036 1576 205268052 205267515 0.000000e+00 702
31 TraesCS1A01G421200 chr5A 85.235 149 19 3 2719 2865 14195053 14195200 2.120000e-32 150


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 TraesCS1A01G421200 chr1A 577536700 577540109 3409 True 6298 6298 100.000 1 3410 1 chr1A.!!$R1 3409
1 TraesCS1A01G421200 chr1A 577718926 577720158 1232 True 881 881 79.905 1091 2336 1 chr1A.!!$R2 1245
2 TraesCS1A01G421200 chr1A 578544819 578546067 1248 False 822 822 78.935 1082 2336 1 chr1A.!!$F1 1254
3 TraesCS1A01G421200 chr1D 481011143 481012727 1584 False 2178 2178 91.812 808 2367 1 chr1D.!!$F1 1559
4 TraesCS1A01G421200 chr1D 481325546 481326778 1232 True 859 859 79.589 1091 2336 1 chr1D.!!$R1 1245
5 TraesCS1A01G421200 chr1D 481718064 481719306 1242 False 817 817 78.836 1082 2336 1 chr1D.!!$F2 1254
6 TraesCS1A01G421200 chr1B 669219075 669220646 1571 False 2161 2161 91.682 808 2367 1 chr1B.!!$F1 1559
7 TraesCS1A01G421200 chr1B 669702148 669703388 1240 True 880 880 79.796 1084 2336 1 chr1B.!!$R2 1252
8 TraesCS1A01G421200 chr1B 669331248 669331859 611 True 819 819 90.997 835 1444 1 chr1B.!!$R1 609
9 TraesCS1A01G421200 chr3A 61527398 61528419 1021 False 1784 1784 98.145 2367 3390 1 chr3A.!!$F1 1023
10 TraesCS1A01G421200 chr3A 65351186 65351912 726 True 924 924 89.698 1 723 1 chr3A.!!$R1 722
11 TraesCS1A01G421200 chr6B 232736382 232737406 1024 True 1448 1448 92.241 2368 3390 1 chr6B.!!$R1 1022
12 TraesCS1A01G421200 chr5B 380325096 380326108 1012 False 1410 1410 91.732 2368 3390 1 chr5B.!!$F1 1022
13 TraesCS1A01G421200 chr3B 828519060 828520073 1013 False 1352 1352 90.732 2370 3390 1 chr3B.!!$F2 1020
14 TraesCS1A01G421200 chr2A 676224196 676224971 775 True 1009 1009 90.114 2368 3152 1 chr2A.!!$R2 784
15 TraesCS1A01G421200 chr2A 30869087 30870322 1235 False 839 839 79.321 1084 2328 1 chr2A.!!$F1 1244
16 TraesCS1A01G421200 chr5D 251910177 251910861 684 True 981 981 92.566 1 684 1 chr5D.!!$R1 683
17 TraesCS1A01G421200 chr5D 410492106 410492835 729 True 966 966 90.587 1 730 1 chr5D.!!$R3 729
18 TraesCS1A01G421200 chr5D 403558303 403559044 741 True 937 937 89.651 1 735 1 chr5D.!!$R2 734
19 TraesCS1A01G421200 chr5D 52238487 52239208 721 False 928 928 89.917 1 721 1 chr5D.!!$F1 720
20 TraesCS1A01G421200 chr7D 264480268 264480936 668 False 957 957 92.548 1 668 1 chr7D.!!$F1 667
21 TraesCS1A01G421200 chr7D 426818195 426818914 719 True 926 926 89.889 1 721 1 chr7D.!!$R1 720
22 TraesCS1A01G421200 chr4B 587771477 587772294 817 True 944 944 87.383 2538 3390 1 chr4B.!!$R1 852
23 TraesCS1A01G421200 chr3D 252337868 252338591 723 True 931 931 89.931 1 723 1 chr3D.!!$R1 722
24 TraesCS1A01G421200 chrUn 5440297 5441019 722 False 926 926 89.821 1 723 1 chrUn.!!$F1 722
25 TraesCS1A01G421200 chr2D 27969489 27970728 1239 True 869 869 79.685 1087 2335 1 chr2D.!!$R1 1248
26 TraesCS1A01G421200 chr7A 125887483 125888051 568 False 767 767 90.941 2367 2940 1 chr7A.!!$F1 573
27 TraesCS1A01G421200 chr6D 205267515 205268052 537 True 702 702 90.203 1036 1576 1 chr6D.!!$R1 540

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
731 740 0.105408 AGTTGGCCTTACGTTCGTGT 59.895 50.0 3.32 0.0 0.0 4.49 F
734 743 0.179078 TGGCCTTACGTTCGTGTTGT 60.179 50.0 3.32 0.0 0.0 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2344 2415 1.134075 CGGTCTCGAGTACACGGTG 59.866 63.158 13.13 6.58 39.00 4.94 R
2474 2547 7.918076 TGAGGGACTATTTTGTAAAGATGAGT 58.082 34.615 0.00 0.00 41.55 3.41 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
27 28 1.974957 TGAAGACAATCTCGAACCCCA 59.025 47.619 0.00 0.00 0.00 4.96
132 134 0.975135 TGGGGTATCGTTCGAAACCA 59.025 50.000 16.50 6.96 33.46 3.67
141 143 1.002900 CGTTCGAAACCATGCACTGTT 60.003 47.619 0.00 0.00 0.00 3.16
156 158 3.813443 CACTGTTATGGGATGAAGGGAG 58.187 50.000 0.00 0.00 0.00 4.30
163 165 1.561542 TGGGATGAAGGGAGAGCTTTC 59.438 52.381 0.00 0.00 0.00 2.62
188 190 2.816087 GGTGATGACTGCTTGTGTGATT 59.184 45.455 0.00 0.00 0.00 2.57
209 211 2.008752 TGCACAACATGATCGTCGAT 57.991 45.000 7.63 7.63 0.00 3.59
265 267 7.983484 AGGATTTGATTATCAAGGTGAAAATGC 59.017 33.333 7.72 2.94 37.70 3.56
450 456 7.359595 TCAAGACAATTTCGATTTGGTTGTAG 58.640 34.615 16.73 7.10 33.55 2.74
629 638 4.195334 GGCCACCGCATCCCAGAT 62.195 66.667 0.00 0.00 36.38 2.90
635 644 2.815945 CCGCATCCCAGATCAGGCT 61.816 63.158 0.00 0.00 0.00 4.58
637 646 1.834996 GCATCCCAGATCAGGCTCA 59.165 57.895 0.00 0.00 0.00 4.26
639 648 0.397187 CATCCCAGATCAGGCTCAGG 59.603 60.000 0.00 0.00 0.00 3.86
659 668 2.572290 GCACGACCTTATTGGCCTATT 58.428 47.619 4.63 0.00 40.22 1.73
674 683 3.194755 GGCCTATTCAAACGGACCAAATT 59.805 43.478 0.00 0.00 0.00 1.82
684 693 1.877443 CGGACCAAATTCGGACAAAGT 59.123 47.619 0.00 0.00 0.00 2.66
688 697 4.941873 GGACCAAATTCGGACAAAGTAGAT 59.058 41.667 0.00 0.00 0.00 1.98
692 701 5.643777 CCAAATTCGGACAAAGTAGATGTCT 59.356 40.000 6.62 0.00 45.13 3.41
697 706 5.055642 CGGACAAAGTAGATGTCTGTGTA 57.944 43.478 7.21 0.00 45.13 2.90
698 707 5.466819 CGGACAAAGTAGATGTCTGTGTAA 58.533 41.667 7.21 0.00 45.13 2.41
699 708 5.924254 CGGACAAAGTAGATGTCTGTGTAAA 59.076 40.000 7.21 0.00 45.13 2.01
711 720 2.017783 GTGTAAAGTCGCGCGGTGA 61.018 57.895 31.69 8.02 0.00 4.02
724 733 1.908066 GCGGTGAAGTTGGCCTTACG 61.908 60.000 3.32 0.00 32.03 3.18
725 734 0.601841 CGGTGAAGTTGGCCTTACGT 60.602 55.000 3.32 0.00 32.03 3.57
726 735 1.601166 GGTGAAGTTGGCCTTACGTT 58.399 50.000 3.32 0.00 32.03 3.99
727 736 1.534163 GGTGAAGTTGGCCTTACGTTC 59.466 52.381 3.32 8.59 32.03 3.95
728 737 1.193874 GTGAAGTTGGCCTTACGTTCG 59.806 52.381 3.32 0.00 32.03 3.95
729 738 1.202557 TGAAGTTGGCCTTACGTTCGT 60.203 47.619 3.32 2.91 32.03 3.85
730 739 1.193874 GAAGTTGGCCTTACGTTCGTG 59.806 52.381 3.32 0.00 32.03 4.35
731 740 0.105408 AGTTGGCCTTACGTTCGTGT 59.895 50.000 3.32 0.00 0.00 4.49
732 741 0.939419 GTTGGCCTTACGTTCGTGTT 59.061 50.000 3.32 0.00 0.00 3.32
733 742 0.938713 TTGGCCTTACGTTCGTGTTG 59.061 50.000 3.32 0.00 0.00 3.33
734 743 0.179078 TGGCCTTACGTTCGTGTTGT 60.179 50.000 3.32 0.00 0.00 3.32
735 744 0.233848 GGCCTTACGTTCGTGTTGTG 59.766 55.000 8.14 0.00 0.00 3.33
736 745 0.932399 GCCTTACGTTCGTGTTGTGT 59.068 50.000 8.14 0.00 0.00 3.72
737 746 1.071041 GCCTTACGTTCGTGTTGTGTC 60.071 52.381 8.14 0.00 0.00 3.67
738 747 1.523934 CCTTACGTTCGTGTTGTGTCC 59.476 52.381 8.14 0.00 0.00 4.02
739 748 2.195096 CTTACGTTCGTGTTGTGTCCA 58.805 47.619 8.14 0.00 0.00 4.02
740 749 2.512485 TACGTTCGTGTTGTGTCCAT 57.488 45.000 8.14 0.00 0.00 3.41
741 750 0.934496 ACGTTCGTGTTGTGTCCATG 59.066 50.000 0.00 0.00 0.00 3.66
742 751 1.213491 CGTTCGTGTTGTGTCCATGA 58.787 50.000 0.00 0.00 0.00 3.07
743 752 1.070843 CGTTCGTGTTGTGTCCATGAC 60.071 52.381 0.00 0.00 0.00 3.06
744 753 1.070843 GTTCGTGTTGTGTCCATGACG 60.071 52.381 0.00 0.00 34.95 4.35
745 754 0.386113 TCGTGTTGTGTCCATGACGA 59.614 50.000 0.00 0.00 34.95 4.20
746 755 1.000394 TCGTGTTGTGTCCATGACGAT 60.000 47.619 0.00 0.00 34.95 3.73
747 756 1.126662 CGTGTTGTGTCCATGACGATG 59.873 52.381 0.00 0.00 34.95 3.84
748 757 1.135972 GTGTTGTGTCCATGACGATGC 60.136 52.381 0.00 0.00 34.95 3.91
749 758 1.155889 GTTGTGTCCATGACGATGCA 58.844 50.000 0.00 0.00 34.95 3.96
750 759 1.535028 GTTGTGTCCATGACGATGCAA 59.465 47.619 0.00 0.00 34.95 4.08
751 760 1.889545 TGTGTCCATGACGATGCAAA 58.110 45.000 0.00 0.00 34.95 3.68
752 761 1.535028 TGTGTCCATGACGATGCAAAC 59.465 47.619 0.00 0.00 34.95 2.93
753 762 1.135689 GTGTCCATGACGATGCAAACC 60.136 52.381 0.00 0.00 34.95 3.27
754 763 0.451783 GTCCATGACGATGCAAACCC 59.548 55.000 0.00 0.00 0.00 4.11
755 764 1.024046 TCCATGACGATGCAAACCCG 61.024 55.000 0.00 0.00 0.00 5.28
756 765 1.429021 CATGACGATGCAAACCCGG 59.571 57.895 0.00 0.00 0.00 5.73
757 766 2.406616 ATGACGATGCAAACCCGGC 61.407 57.895 0.00 0.00 0.00 6.13
758 767 3.810896 GACGATGCAAACCCGGCC 61.811 66.667 0.00 0.00 0.00 6.13
759 768 4.344865 ACGATGCAAACCCGGCCT 62.345 61.111 0.00 0.00 0.00 5.19
760 769 3.814268 CGATGCAAACCCGGCCTG 61.814 66.667 0.00 0.00 0.00 4.85
761 770 2.676471 GATGCAAACCCGGCCTGT 60.676 61.111 0.00 0.00 0.00 4.00
762 771 2.676471 ATGCAAACCCGGCCTGTC 60.676 61.111 0.00 0.00 0.00 3.51
763 772 4.966787 TGCAAACCCGGCCTGTCC 62.967 66.667 0.00 0.00 0.00 4.02
764 773 4.966787 GCAAACCCGGCCTGTCCA 62.967 66.667 0.00 0.00 34.01 4.02
765 774 2.983592 CAAACCCGGCCTGTCCAC 60.984 66.667 0.00 0.00 34.01 4.02
766 775 3.494254 AAACCCGGCCTGTCCACA 61.494 61.111 0.00 0.00 34.01 4.17
767 776 3.785122 AAACCCGGCCTGTCCACAC 62.785 63.158 0.00 0.00 34.01 3.82
770 779 4.619227 CCGGCCTGTCCACACGTT 62.619 66.667 0.00 0.00 34.01 3.99
771 780 2.590575 CGGCCTGTCCACACGTTT 60.591 61.111 0.00 0.00 34.01 3.60
772 781 2.892334 CGGCCTGTCCACACGTTTG 61.892 63.158 0.00 0.00 34.01 2.93
773 782 2.551912 GGCCTGTCCACACGTTTGG 61.552 63.158 14.78 14.78 38.10 3.28
774 783 3.030652 CCTGTCCACACGTTTGGC 58.969 61.111 16.10 11.38 36.48 4.52
775 784 2.551912 CCTGTCCACACGTTTGGCC 61.552 63.158 16.10 5.21 36.48 5.36
776 785 2.892334 CTGTCCACACGTTTGGCCG 61.892 63.158 16.10 4.32 36.48 6.13
777 786 4.322385 GTCCACACGTTTGGCCGC 62.322 66.667 16.10 5.10 36.48 6.53
782 791 4.622456 CACGTTTGGCCGCGCTTT 62.622 61.111 5.56 0.00 0.00 3.51
783 792 3.894947 ACGTTTGGCCGCGCTTTT 61.895 55.556 5.56 0.00 0.00 2.27
784 793 3.394062 CGTTTGGCCGCGCTTTTG 61.394 61.111 5.56 0.00 0.00 2.44
785 794 2.279186 GTTTGGCCGCGCTTTTGT 60.279 55.556 5.56 0.00 0.00 2.83
786 795 2.026879 TTTGGCCGCGCTTTTGTC 59.973 55.556 5.56 0.00 0.00 3.18
787 796 3.492311 TTTGGCCGCGCTTTTGTCC 62.492 57.895 5.56 0.00 0.00 4.02
790 799 4.322385 GCCGCGCTTTTGTCCGTT 62.322 61.111 5.56 0.00 0.00 4.44
791 800 2.330041 CCGCGCTTTTGTCCGTTT 59.670 55.556 5.56 0.00 0.00 3.60
792 801 1.298788 CCGCGCTTTTGTCCGTTTT 60.299 52.632 5.56 0.00 0.00 2.43
793 802 0.868177 CCGCGCTTTTGTCCGTTTTT 60.868 50.000 5.56 0.00 0.00 1.94
794 803 1.597445 CCGCGCTTTTGTCCGTTTTTA 60.597 47.619 5.56 0.00 0.00 1.52
795 804 2.110226 CGCGCTTTTGTCCGTTTTTAA 58.890 42.857 5.56 0.00 0.00 1.52
796 805 2.722116 CGCGCTTTTGTCCGTTTTTAAT 59.278 40.909 5.56 0.00 0.00 1.40
797 806 3.180782 CGCGCTTTTGTCCGTTTTTAATT 59.819 39.130 5.56 0.00 0.00 1.40
798 807 4.659676 CGCGCTTTTGTCCGTTTTTAATTC 60.660 41.667 5.56 0.00 0.00 2.17
799 808 4.659676 GCGCTTTTGTCCGTTTTTAATTCG 60.660 41.667 0.00 0.00 0.00 3.34
800 809 4.438471 CGCTTTTGTCCGTTTTTAATTCGT 59.562 37.500 0.00 0.00 0.00 3.85
801 810 5.385615 CGCTTTTGTCCGTTTTTAATTCGTC 60.386 40.000 0.00 0.00 0.00 4.20
802 811 5.456173 GCTTTTGTCCGTTTTTAATTCGTCA 59.544 36.000 0.00 0.00 0.00 4.35
803 812 6.344702 GCTTTTGTCCGTTTTTAATTCGTCAG 60.345 38.462 0.00 0.00 0.00 3.51
804 813 5.987777 TTGTCCGTTTTTAATTCGTCAGA 57.012 34.783 0.00 0.00 0.00 3.27
805 814 6.548441 TTGTCCGTTTTTAATTCGTCAGAT 57.452 33.333 0.00 0.00 0.00 2.90
806 815 5.922546 TGTCCGTTTTTAATTCGTCAGATG 58.077 37.500 0.00 0.00 0.00 2.90
871 881 1.597663 ACTTTGAGTTGTCGCTTTCCG 59.402 47.619 0.00 0.00 38.61 4.30
942 990 0.396811 ATTACTACGATGCCCTGCCC 59.603 55.000 0.00 0.00 0.00 5.36
947 995 0.540133 TACGATGCCCTGCCCGTATA 60.540 55.000 0.00 0.00 37.77 1.47
1009 1062 2.507944 GCCGAGCCATGGAGTCAT 59.492 61.111 18.40 0.00 0.00 3.06
1015 1068 1.153086 GCCATGGAGTCATCGCCTT 60.153 57.895 18.40 0.00 32.47 4.35
1029 1082 3.730761 CCTTGTGCGGTGCAGCTC 61.731 66.667 14.92 6.64 40.08 4.09
1030 1083 3.730761 CTTGTGCGGTGCAGCTCC 61.731 66.667 14.92 3.13 40.08 4.70
1031 1084 4.560743 TTGTGCGGTGCAGCTCCA 62.561 61.111 14.92 8.14 40.08 3.86
1032 1085 4.994471 TGTGCGGTGCAGCTCCAG 62.994 66.667 14.92 7.50 40.08 3.86
1102 1155 1.668151 GCGTTTCCAAGAGAGGCGT 60.668 57.895 0.00 0.00 0.00 5.68
1331 1393 3.518003 GCTCTCGCGTAACCCCTA 58.482 61.111 5.77 0.00 0.00 3.53
1533 1595 3.827898 GCCGGTGAGAGCTACGCT 61.828 66.667 1.90 0.00 43.88 5.07
1583 1645 4.111016 CCTCGCTGCGTACACGGA 62.111 66.667 22.48 0.00 40.23 4.69
1901 1963 2.049433 CGAGTTCGTGAACCGGCT 60.049 61.111 0.00 0.00 42.06 5.52
2336 2407 2.906897 AGTGTTTGGTGGCGGCAG 60.907 61.111 13.91 0.00 0.00 4.85
2474 2547 2.532250 TCTAGTGAGGGATCTGTGCA 57.468 50.000 0.00 0.00 0.00 4.57
2819 2897 2.237392 GCCAATCTCCAGGTACAGTTCT 59.763 50.000 0.00 0.00 0.00 3.01
2971 3049 4.974645 ACAAACTGAACTCCCTGTATCA 57.025 40.909 0.00 0.00 0.00 2.15
3022 3102 1.340405 CCCCTCCCAGATTTGTCACAG 60.340 57.143 0.00 0.00 0.00 3.66
3146 3233 0.250234 TGGCTTATTCAGACGCTGCT 59.750 50.000 0.00 0.00 29.50 4.24
3246 3334 7.201444 CGTTGGAAGTTCAGTGTAGATATGTTC 60.201 40.741 5.01 0.00 0.00 3.18
3332 3421 6.785963 TGAGGGTTAATTATAGTCCGATCCTT 59.214 38.462 0.00 0.00 0.00 3.36
3377 3466 6.150140 AGTTCAGAATAGCCACAACAGATTTC 59.850 38.462 0.00 0.00 0.00 2.17
3390 3479 6.361481 CACAACAGATTTCAAATAGCACACTG 59.639 38.462 0.00 0.00 0.00 3.66
3391 3480 6.039717 ACAACAGATTTCAAATAGCACACTGT 59.960 34.615 0.00 0.00 37.62 3.55
3392 3481 6.246420 ACAGATTTCAAATAGCACACTGTC 57.754 37.500 0.00 0.00 31.87 3.51
3393 3482 5.106948 ACAGATTTCAAATAGCACACTGTCG 60.107 40.000 0.00 0.00 31.87 4.35
3394 3483 4.393062 AGATTTCAAATAGCACACTGTCGG 59.607 41.667 0.00 0.00 0.00 4.79
3395 3484 3.394674 TTCAAATAGCACACTGTCGGA 57.605 42.857 0.00 0.00 0.00 4.55
3396 3485 2.959516 TCAAATAGCACACTGTCGGAG 58.040 47.619 0.00 0.00 0.00 4.63
3397 3486 2.299013 TCAAATAGCACACTGTCGGAGT 59.701 45.455 0.00 0.00 34.02 3.85
3398 3487 3.508402 TCAAATAGCACACTGTCGGAGTA 59.492 43.478 0.00 0.00 31.73 2.59
3399 3488 4.021807 TCAAATAGCACACTGTCGGAGTAA 60.022 41.667 0.00 0.00 31.73 2.24
3400 3489 4.530710 AATAGCACACTGTCGGAGTAAA 57.469 40.909 0.00 0.00 31.73 2.01
3401 3490 4.737855 ATAGCACACTGTCGGAGTAAAT 57.262 40.909 0.00 0.00 31.73 1.40
3402 3491 2.688507 AGCACACTGTCGGAGTAAATG 58.311 47.619 0.00 0.00 31.73 2.32
3403 3492 2.299013 AGCACACTGTCGGAGTAAATGA 59.701 45.455 0.00 0.00 31.73 2.57
3404 3493 2.412089 GCACACTGTCGGAGTAAATGAC 59.588 50.000 0.00 0.00 31.73 3.06
3405 3494 2.993899 CACACTGTCGGAGTAAATGACC 59.006 50.000 0.00 0.00 31.73 4.02
3406 3495 2.631062 ACACTGTCGGAGTAAATGACCA 59.369 45.455 0.00 0.00 31.73 4.02
3407 3496 2.993899 CACTGTCGGAGTAAATGACCAC 59.006 50.000 0.00 0.00 31.73 4.16
3408 3497 2.259618 CTGTCGGAGTAAATGACCACG 58.740 52.381 0.00 0.00 0.00 4.94
3409 3498 1.067425 TGTCGGAGTAAATGACCACGG 60.067 52.381 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 6.206438 GGCAAATCTCTTTCTCTTCTCACTTT 59.794 38.462 0.00 0.00 0.00 2.66
132 134 3.559069 CCTTCATCCCATAACAGTGCAT 58.441 45.455 0.00 0.00 0.00 3.96
141 143 2.803285 AGCTCTCCCTTCATCCCATA 57.197 50.000 0.00 0.00 0.00 2.74
156 158 1.205893 AGTCATCACCTCCGAAAGCTC 59.794 52.381 0.00 0.00 0.00 4.09
163 165 0.036952 ACAAGCAGTCATCACCTCCG 60.037 55.000 0.00 0.00 0.00 4.63
188 190 3.157932 TCGACGATCATGTTGTGCATA 57.842 42.857 0.00 0.00 35.74 3.14
209 211 1.212751 CCTGTCATCACGCTCGTCA 59.787 57.895 0.00 0.00 0.00 4.35
265 267 2.360852 CTTGGTGCAGGGGCTCAG 60.361 66.667 0.00 0.00 41.91 3.35
553 560 0.958822 GTCCGTCAGGGCAAAAATGT 59.041 50.000 0.00 0.00 43.06 2.71
629 638 3.695606 GGTCGTGCCTGAGCCTGA 61.696 66.667 0.00 0.00 38.69 3.86
648 657 3.054287 TGGTCCGTTTGAATAGGCCAATA 60.054 43.478 5.01 0.00 31.62 1.90
653 662 4.421058 GAATTTGGTCCGTTTGAATAGGC 58.579 43.478 0.00 0.00 0.00 3.93
659 668 1.874872 GTCCGAATTTGGTCCGTTTGA 59.125 47.619 11.68 0.00 0.00 2.69
674 683 3.572682 ACACAGACATCTACTTTGTCCGA 59.427 43.478 0.46 0.00 43.62 4.55
684 693 3.754955 CGCGACTTTACACAGACATCTA 58.245 45.455 0.00 0.00 0.00 1.98
688 697 1.272784 CGCGCGACTTTACACAGACA 61.273 55.000 28.94 0.00 0.00 3.41
692 701 2.027897 ACCGCGCGACTTTACACA 59.972 55.556 34.63 0.00 0.00 3.72
695 704 1.280206 ACTTCACCGCGCGACTTTAC 61.280 55.000 34.63 0.00 0.00 2.01
697 706 1.885850 AACTTCACCGCGCGACTTT 60.886 52.632 34.63 12.14 0.00 2.66
698 707 2.279918 AACTTCACCGCGCGACTT 60.280 55.556 34.63 12.58 0.00 3.01
699 708 3.036084 CAACTTCACCGCGCGACT 61.036 61.111 34.63 13.47 0.00 4.18
711 720 1.223187 CACGAACGTAAGGCCAACTT 58.777 50.000 5.01 0.00 46.39 2.66
724 733 1.070843 CGTCATGGACACAACACGAAC 60.071 52.381 0.00 0.00 37.71 3.95
725 734 1.202428 TCGTCATGGACACAACACGAA 60.202 47.619 0.00 0.00 39.98 3.85
726 735 0.386113 TCGTCATGGACACAACACGA 59.614 50.000 0.00 0.00 40.37 4.35
727 736 1.126662 CATCGTCATGGACACAACACG 59.873 52.381 0.00 0.00 37.17 4.49
728 737 1.135972 GCATCGTCATGGACACAACAC 60.136 52.381 0.00 0.00 32.09 3.32
729 738 1.155889 GCATCGTCATGGACACAACA 58.844 50.000 0.00 0.00 32.09 3.33
730 739 1.155889 TGCATCGTCATGGACACAAC 58.844 50.000 0.00 0.00 32.09 3.32
731 740 1.889545 TTGCATCGTCATGGACACAA 58.110 45.000 0.00 0.00 28.35 3.33
732 741 1.535028 GTTTGCATCGTCATGGACACA 59.465 47.619 0.00 0.00 32.69 3.72
733 742 1.135689 GGTTTGCATCGTCATGGACAC 60.136 52.381 0.00 0.00 31.87 3.67
734 743 1.164411 GGTTTGCATCGTCATGGACA 58.836 50.000 0.00 0.00 28.35 4.02
735 744 0.451783 GGGTTTGCATCGTCATGGAC 59.548 55.000 0.00 0.00 28.35 4.02
736 745 1.024046 CGGGTTTGCATCGTCATGGA 61.024 55.000 0.00 0.00 0.00 3.41
737 746 1.429021 CGGGTTTGCATCGTCATGG 59.571 57.895 0.00 0.00 0.00 3.66
738 747 1.429021 CCGGGTTTGCATCGTCATG 59.571 57.895 0.00 0.00 0.00 3.07
739 748 2.406616 GCCGGGTTTGCATCGTCAT 61.407 57.895 2.18 0.00 0.00 3.06
740 749 3.053291 GCCGGGTTTGCATCGTCA 61.053 61.111 2.18 0.00 0.00 4.35
741 750 3.810896 GGCCGGGTTTGCATCGTC 61.811 66.667 2.18 0.00 0.00 4.20
742 751 4.344865 AGGCCGGGTTTGCATCGT 62.345 61.111 2.18 0.00 0.00 3.73
743 752 3.814268 CAGGCCGGGTTTGCATCG 61.814 66.667 2.18 0.00 0.00 3.84
744 753 2.676471 ACAGGCCGGGTTTGCATC 60.676 61.111 8.08 0.00 0.00 3.91
745 754 2.676471 GACAGGCCGGGTTTGCAT 60.676 61.111 8.08 0.00 0.00 3.96
746 755 4.966787 GGACAGGCCGGGTTTGCA 62.967 66.667 8.08 0.00 0.00 4.08
747 756 4.966787 TGGACAGGCCGGGTTTGC 62.967 66.667 8.08 0.00 40.66 3.68
748 757 2.983592 GTGGACAGGCCGGGTTTG 60.984 66.667 8.08 0.00 40.66 2.93
749 758 3.494254 TGTGGACAGGCCGGGTTT 61.494 61.111 8.08 0.00 40.66 3.27
750 759 4.265056 GTGTGGACAGGCCGGGTT 62.265 66.667 8.08 0.00 40.66 4.11
753 762 4.619227 AACGTGTGGACAGGCCGG 62.619 66.667 0.00 0.00 40.66 6.13
754 763 2.590575 AAACGTGTGGACAGGCCG 60.591 61.111 0.00 0.00 40.66 6.13
755 764 2.551912 CCAAACGTGTGGACAGGCC 61.552 63.158 20.95 0.00 41.65 5.19
756 765 3.030652 CCAAACGTGTGGACAGGC 58.969 61.111 20.95 0.00 41.65 4.85
757 766 3.030652 GCCAAACGTGTGGACAGG 58.969 61.111 29.47 1.16 41.65 4.00
760 769 4.322385 GCGGCCAAACGTGTGGAC 62.322 66.667 29.47 25.79 44.10 4.02
765 774 4.622456 AAAGCGCGGCCAAACGTG 62.622 61.111 8.83 0.00 46.30 4.49
766 775 3.894947 AAAAGCGCGGCCAAACGT 61.895 55.556 8.83 0.00 35.98 3.99
767 776 3.394062 CAAAAGCGCGGCCAAACG 61.394 61.111 8.83 4.19 0.00 3.60
768 777 2.279186 ACAAAAGCGCGGCCAAAC 60.279 55.556 8.83 0.00 0.00 2.93
769 778 2.026879 GACAAAAGCGCGGCCAAA 59.973 55.556 8.83 0.00 0.00 3.28
770 779 3.972276 GGACAAAAGCGCGGCCAA 61.972 61.111 8.83 0.00 0.00 4.52
773 782 3.817274 AAACGGACAAAAGCGCGGC 62.817 57.895 8.83 0.00 0.00 6.53
774 783 0.868177 AAAAACGGACAAAAGCGCGG 60.868 50.000 8.83 0.00 0.00 6.46
775 784 1.744374 TAAAAACGGACAAAAGCGCG 58.256 45.000 0.00 0.00 0.00 6.86
776 785 4.659676 CGAATTAAAAACGGACAAAAGCGC 60.660 41.667 0.00 0.00 0.00 5.92
777 786 4.438471 ACGAATTAAAAACGGACAAAAGCG 59.562 37.500 0.00 0.00 0.00 4.68
778 787 5.456173 TGACGAATTAAAAACGGACAAAAGC 59.544 36.000 0.00 0.00 0.00 3.51
779 788 6.908284 TCTGACGAATTAAAAACGGACAAAAG 59.092 34.615 0.00 0.00 0.00 2.27
780 789 6.783162 TCTGACGAATTAAAAACGGACAAAA 58.217 32.000 0.00 0.00 0.00 2.44
781 790 6.360844 TCTGACGAATTAAAAACGGACAAA 57.639 33.333 0.00 0.00 0.00 2.83
782 791 5.987777 TCTGACGAATTAAAAACGGACAA 57.012 34.783 0.00 0.00 0.00 3.18
783 792 5.467399 ACATCTGACGAATTAAAAACGGACA 59.533 36.000 0.00 0.00 0.00 4.02
784 793 5.923665 ACATCTGACGAATTAAAAACGGAC 58.076 37.500 0.00 0.00 0.00 4.79
785 794 6.425721 AGAACATCTGACGAATTAAAAACGGA 59.574 34.615 0.00 0.00 0.00 4.69
786 795 6.599437 AGAACATCTGACGAATTAAAAACGG 58.401 36.000 0.00 0.00 0.00 4.44
787 796 7.287950 TGAGAACATCTGACGAATTAAAAACG 58.712 34.615 0.00 0.00 0.00 3.60
788 797 9.267096 GATGAGAACATCTGACGAATTAAAAAC 57.733 33.333 0.00 0.00 46.47 2.43
803 812 6.946649 CAGCCATTTCCAGGATGAGAACATC 61.947 48.000 0.00 0.00 45.12 3.06
804 813 3.053095 AGCCATTTCCAGGATGAGAACAT 60.053 43.478 0.00 0.00 39.69 2.71
805 814 2.309755 AGCCATTTCCAGGATGAGAACA 59.690 45.455 0.00 0.00 39.69 3.18
806 815 2.686915 CAGCCATTTCCAGGATGAGAAC 59.313 50.000 0.00 0.00 45.12 3.01
871 881 3.440173 ACATGGTCATTGACACGAAATCC 59.560 43.478 18.09 0.00 33.68 3.01
942 990 3.619483 CGGGAGTGAGAGAGCTATATACG 59.381 52.174 0.00 0.00 0.00 3.06
947 995 0.825840 GGCGGGAGTGAGAGAGCTAT 60.826 60.000 0.00 0.00 0.00 2.97
993 1046 1.300465 CGATGACTCCATGGCTCGG 60.300 63.158 6.96 0.00 32.09 4.63
1015 1068 4.994471 CTGGAGCTGCACCGCACA 62.994 66.667 2.72 0.00 33.79 4.57
1032 1085 1.633852 CGAGAAGAACCAGCAGCAGC 61.634 60.000 0.00 0.00 42.56 5.25
1033 1086 1.018226 CCGAGAAGAACCAGCAGCAG 61.018 60.000 0.00 0.00 0.00 4.24
1034 1087 1.004560 CCGAGAAGAACCAGCAGCA 60.005 57.895 0.00 0.00 0.00 4.41
1500 1562 4.083862 GCGAGGAAGAAGGGGCGT 62.084 66.667 0.00 0.00 0.00 5.68
1572 1634 4.735132 GGCAGCTCCGTGTACGCA 62.735 66.667 7.29 0.00 38.18 5.24
2037 2099 4.457496 AGCACACGCATCCCCTCG 62.457 66.667 0.00 0.00 42.27 4.63
2038 2100 2.821366 CAGCACACGCATCCCCTC 60.821 66.667 0.00 0.00 42.27 4.30
2041 2103 3.807538 CAGCAGCACACGCATCCC 61.808 66.667 0.00 0.00 42.27 3.85
2049 2111 2.207229 ACCCTCGTACAGCAGCACA 61.207 57.895 0.00 0.00 0.00 4.57
2184 2246 4.435970 TACCCGGCGAGCTCCTCA 62.436 66.667 9.30 0.00 0.00 3.86
2344 2415 1.134075 CGGTCTCGAGTACACGGTG 59.866 63.158 13.13 6.58 39.00 4.94
2474 2547 7.918076 TGAGGGACTATTTTGTAAAGATGAGT 58.082 34.615 0.00 0.00 41.55 3.41
2819 2897 1.595929 GTTGTCCTCGGCGTTTGGA 60.596 57.895 6.85 10.75 0.00 3.53
2971 3049 6.759272 TGTTGAGTTAAGCTACTGAGACATT 58.241 36.000 0.00 0.00 0.00 2.71
3022 3102 2.172293 AGGGTCATCTGGCTGATTCTTC 59.828 50.000 3.90 0.00 32.05 2.87
3146 3233 8.775527 TGAAAAGAATTGTAGTATGCAACGTTA 58.224 29.630 0.00 0.00 45.30 3.18
3332 3421 4.903054 ACTTCACTGCTCTCAATGATTGA 58.097 39.130 7.73 7.73 38.17 2.57
3377 3466 2.688507 ACTCCGACAGTGTGCTATTTG 58.311 47.619 0.00 0.00 32.26 2.32
3390 3479 1.636988 CCGTGGTCATTTACTCCGAC 58.363 55.000 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.