Multiple sequence alignment - TraesCS2B01G357200

Loading Multiple Alignment...

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 TraesCS2B01G357200 chr2B 100.000 3622 0 0 1 3622 510396184 510392563 0.000000e+00 6689.0
1 TraesCS2B01G357200 chr2B 90.217 920 76 10 1 911 184911149 184912063 0.000000e+00 1188.0
2 TraesCS2B01G357200 chr2A 95.721 1776 58 8 963 2724 554833759 554835530 0.000000e+00 2843.0
3 TraesCS2B01G357200 chr2A 93.733 750 36 3 2878 3622 554835591 554836334 0.000000e+00 1114.0
4 TraesCS2B01G357200 chr2A 95.588 68 2 1 2235 2301 688579312 688579245 1.380000e-19 108.0
5 TraesCS2B01G357200 chr2D 95.540 1749 51 9 986 2724 431503643 431501912 0.000000e+00 2772.0
6 TraesCS2B01G357200 chr2D 92.396 434 23 2 3079 3508 431501681 431501254 8.600000e-171 610.0
7 TraesCS2B01G357200 chr2D 87.222 180 10 5 2854 3021 431501866 431501688 3.690000e-45 193.0
8 TraesCS2B01G357200 chr2D 93.407 91 5 1 2768 2858 513253213 513253124 2.270000e-27 134.0
9 TraesCS2B01G357200 chr7D 90.424 919 76 11 1 911 572313768 572314682 0.000000e+00 1199.0
10 TraesCS2B01G357200 chr7D 89.844 896 78 10 1 887 381004707 381003816 0.000000e+00 1138.0
11 TraesCS2B01G357200 chr3B 90.263 914 80 8 1 909 504648421 504647512 0.000000e+00 1186.0
12 TraesCS2B01G357200 chr6D 89.924 923 78 13 1 912 464696222 464697140 0.000000e+00 1175.0
13 TraesCS2B01G357200 chr6D 89.685 921 82 9 1 912 313020607 313021523 0.000000e+00 1162.0
14 TraesCS2B01G357200 chrUn 89.189 925 82 14 1 912 228914452 228913533 0.000000e+00 1138.0
15 TraesCS2B01G357200 chrUn 89.177 924 83 14 1 912 266698810 266697892 0.000000e+00 1136.0
16 TraesCS2B01G357200 chrUn 93.407 91 5 1 2768 2858 67634463 67634374 2.270000e-27 134.0
17 TraesCS2B01G357200 chr5D 88.575 919 92 10 2 911 547820736 547821650 0.000000e+00 1103.0
18 TraesCS2B01G357200 chr5D 93.407 91 5 1 2768 2858 347656206 347656117 2.270000e-27 134.0
19 TraesCS2B01G357200 chr5D 93.407 91 5 1 2772 2862 502881715 502881626 2.270000e-27 134.0
20 TraesCS2B01G357200 chr1A 94.382 89 4 1 2769 2857 85040820 85040733 6.310000e-28 135.0
21 TraesCS2B01G357200 chr3D 93.407 91 5 1 2768 2858 281954100 281954189 2.270000e-27 134.0
22 TraesCS2B01G357200 chr1D 93.407 91 5 1 2768 2858 135048031 135048120 2.270000e-27 134.0
23 TraesCS2B01G357200 chr1D 89.091 55 6 0 1126 1180 163767469 163767523 6.490000e-08 69.4
24 TraesCS2B01G357200 chr3A 91.667 96 7 1 2767 2862 181138137 181138043 8.160000e-27 132.0
25 TraesCS2B01G357200 chr3A 92.857 56 4 0 2419 2474 624835458 624835403 8.340000e-12 82.4
26 TraesCS2B01G357200 chr5B 89.109 101 9 2 2769 2868 696200974 696201073 1.370000e-24 124.0
27 TraesCS2B01G357200 chr4A 96.429 56 2 0 2419 2474 677971122 677971067 3.850000e-15 93.5


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 TraesCS2B01G357200 chr2B 510392563 510396184 3621 True 6689.000000 6689 100.000000 1 3622 1 chr2B.!!$R1 3621
1 TraesCS2B01G357200 chr2B 184911149 184912063 914 False 1188.000000 1188 90.217000 1 911 1 chr2B.!!$F1 910
2 TraesCS2B01G357200 chr2A 554833759 554836334 2575 False 1978.500000 2843 94.727000 963 3622 2 chr2A.!!$F1 2659
3 TraesCS2B01G357200 chr2D 431501254 431503643 2389 True 1191.666667 2772 91.719333 986 3508 3 chr2D.!!$R2 2522
4 TraesCS2B01G357200 chr7D 572313768 572314682 914 False 1199.000000 1199 90.424000 1 911 1 chr7D.!!$F1 910
5 TraesCS2B01G357200 chr7D 381003816 381004707 891 True 1138.000000 1138 89.844000 1 887 1 chr7D.!!$R1 886
6 TraesCS2B01G357200 chr3B 504647512 504648421 909 True 1186.000000 1186 90.263000 1 909 1 chr3B.!!$R1 908
7 TraesCS2B01G357200 chr6D 464696222 464697140 918 False 1175.000000 1175 89.924000 1 912 1 chr6D.!!$F2 911
8 TraesCS2B01G357200 chr6D 313020607 313021523 916 False 1162.000000 1162 89.685000 1 912 1 chr6D.!!$F1 911
9 TraesCS2B01G357200 chrUn 228913533 228914452 919 True 1138.000000 1138 89.189000 1 912 1 chrUn.!!$R2 911
10 TraesCS2B01G357200 chrUn 266697892 266698810 918 True 1136.000000 1136 89.177000 1 912 1 chrUn.!!$R3 911
11 TraesCS2B01G357200 chr5D 547820736 547821650 914 False 1103.000000 1103 88.575000 2 911 1 chr5D.!!$F1 909

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
802 828 0.037303 CCCACACACCAGCTCAATCT 59.963 55.0 0.0 0.0 0.00 2.40 F
943 969 0.179084 TGTATGGAGTAAGCAGCCGC 60.179 55.0 0.0 0.0 38.99 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1950 1988 0.871163 AAATGCTTGTGTGCGTGTGC 60.871 50.000 0.0 0.0 43.2 4.57 R
2766 2824 2.478292 TGGGATGGAGGGAGTACTTTC 58.522 52.381 0.0 0.0 0.0 2.62 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
22 25 0.966370 GTCCCTCTCACACGCCTACT 60.966 60.000 0.00 0.00 0.00 2.57
43 46 4.531732 ACTTGTGGGCAAAATGGATAACAT 59.468 37.500 0.00 0.00 43.07 2.71
69 72 1.752436 CGACCTCTCTCAGCCACCTAT 60.752 57.143 0.00 0.00 0.00 2.57
75 78 2.243478 TCTCTCAGCCACCTATCTCACT 59.757 50.000 0.00 0.00 0.00 3.41
80 83 1.007721 AGCCACCTATCTCACTGGTCT 59.992 52.381 0.00 0.00 30.72 3.85
109 116 3.208884 GACAGTCACCACGCGTCCT 62.209 63.158 9.86 0.00 0.00 3.85
113 120 3.220658 TCACCACGCGTCCTCACA 61.221 61.111 9.86 0.00 0.00 3.58
178 185 0.389296 TGCCATGTCGGACAACTACG 60.389 55.000 15.72 2.33 36.56 3.51
214 221 2.211250 AACTGCAGTTGCCATCTCAT 57.789 45.000 30.66 2.58 41.18 2.90
223 230 2.816087 GTTGCCATCTCATGTCAAGTGT 59.184 45.455 0.00 0.00 0.00 3.55
228 235 3.931468 CCATCTCATGTCAAGTGTCAGAC 59.069 47.826 0.00 0.00 35.37 3.51
288 296 5.527582 GTCTGGTTTACTATAGTTGCCATGG 59.472 44.000 11.40 7.63 0.00 3.66
311 319 3.322191 TGAAAACTTTAGGGGTTGCCT 57.678 42.857 0.00 0.00 0.00 4.75
380 388 6.875195 CAGTTGCCATGATTTGAAAACCTTAT 59.125 34.615 0.00 0.00 0.00 1.73
382 390 5.177326 TGCCATGATTTGAAAACCTTATGC 58.823 37.500 0.00 0.00 0.00 3.14
412 420 4.591924 ACCTACTAACACTAGGCAGTTGTT 59.408 41.667 7.49 4.77 35.04 2.83
470 481 5.430007 TGTTTCGGGTAAAAAGAGAGTTGA 58.570 37.500 0.00 0.00 0.00 3.18
619 643 1.479730 TGCAAAACACATGGCAACTGA 59.520 42.857 0.00 0.00 32.54 3.41
701 727 1.403679 CCCTTGTGCGTGAGTGAAAAA 59.596 47.619 0.00 0.00 0.00 1.94
758 784 0.179029 CCCTCCCGTGTGTTGAAACT 60.179 55.000 0.00 0.00 0.00 2.66
796 822 1.604593 GAATGCCCACACACCAGCT 60.605 57.895 0.00 0.00 0.00 4.24
802 828 0.037303 CCCACACACCAGCTCAATCT 59.963 55.000 0.00 0.00 0.00 2.40
824 850 5.992829 TCTTACGTGATACCACAAACATGTT 59.007 36.000 4.92 4.92 43.34 2.71
887 913 1.580845 GCAAGATGCAACCGCTCACT 61.581 55.000 0.00 0.00 44.26 3.41
888 914 0.877071 CAAGATGCAACCGCTCACTT 59.123 50.000 0.00 0.00 39.64 3.16
891 917 1.001974 AGATGCAACCGCTCACTTGTA 59.998 47.619 0.00 0.00 39.64 2.41
912 938 6.123651 TGTATGGGCATTAGTATTTCCGTTT 58.876 36.000 0.00 0.00 0.00 3.60
913 939 4.974368 TGGGCATTAGTATTTCCGTTTG 57.026 40.909 0.00 0.00 0.00 2.93
914 940 4.590918 TGGGCATTAGTATTTCCGTTTGA 58.409 39.130 0.00 0.00 0.00 2.69
915 941 5.197451 TGGGCATTAGTATTTCCGTTTGAT 58.803 37.500 0.00 0.00 0.00 2.57
916 942 5.654650 TGGGCATTAGTATTTCCGTTTGATT 59.345 36.000 0.00 0.00 0.00 2.57
917 943 6.829298 TGGGCATTAGTATTTCCGTTTGATTA 59.171 34.615 0.00 0.00 0.00 1.75
918 944 7.504238 TGGGCATTAGTATTTCCGTTTGATTAT 59.496 33.333 0.00 0.00 0.00 1.28
919 945 8.021396 GGGCATTAGTATTTCCGTTTGATTATC 58.979 37.037 0.00 0.00 0.00 1.75
920 946 8.021396 GGCATTAGTATTTCCGTTTGATTATCC 58.979 37.037 0.00 0.00 0.00 2.59
921 947 7.744715 GCATTAGTATTTCCGTTTGATTATCCG 59.255 37.037 0.00 0.00 0.00 4.18
922 948 8.770828 CATTAGTATTTCCGTTTGATTATCCGT 58.229 33.333 0.00 0.00 0.00 4.69
923 949 9.985730 ATTAGTATTTCCGTTTGATTATCCGTA 57.014 29.630 0.00 0.00 0.00 4.02
924 950 9.985730 TTAGTATTTCCGTTTGATTATCCGTAT 57.014 29.630 0.00 0.00 0.00 3.06
925 951 8.306680 AGTATTTCCGTTTGATTATCCGTATG 57.693 34.615 0.00 0.00 0.00 2.39
926 952 7.929785 AGTATTTCCGTTTGATTATCCGTATGT 59.070 33.333 0.00 0.00 0.00 2.29
927 953 9.195411 GTATTTCCGTTTGATTATCCGTATGTA 57.805 33.333 0.00 0.00 0.00 2.29
928 954 8.842358 ATTTCCGTTTGATTATCCGTATGTAT 57.158 30.769 0.00 0.00 0.00 2.29
929 955 7.646446 TTCCGTTTGATTATCCGTATGTATG 57.354 36.000 0.00 0.00 0.00 2.39
930 956 6.160684 TCCGTTTGATTATCCGTATGTATGG 58.839 40.000 0.00 0.00 0.00 2.74
931 957 6.015265 TCCGTTTGATTATCCGTATGTATGGA 60.015 38.462 3.58 3.58 44.89 3.41
932 958 6.310467 CCGTTTGATTATCCGTATGTATGGAG 59.690 42.308 7.06 0.00 44.09 3.86
933 959 6.866770 CGTTTGATTATCCGTATGTATGGAGT 59.133 38.462 7.06 0.00 44.09 3.85
934 960 8.024865 CGTTTGATTATCCGTATGTATGGAGTA 58.975 37.037 7.06 0.00 44.09 2.59
935 961 9.701098 GTTTGATTATCCGTATGTATGGAGTAA 57.299 33.333 7.06 6.45 44.09 2.24
936 962 9.923143 TTTGATTATCCGTATGTATGGAGTAAG 57.077 33.333 7.06 0.00 44.09 2.34
937 963 7.544622 TGATTATCCGTATGTATGGAGTAAGC 58.455 38.462 7.06 8.50 44.09 3.09
938 964 6.904463 TTATCCGTATGTATGGAGTAAGCA 57.096 37.500 7.06 0.00 44.09 3.91
939 965 4.848562 TCCGTATGTATGGAGTAAGCAG 57.151 45.455 0.00 0.00 36.49 4.24
940 966 3.005472 TCCGTATGTATGGAGTAAGCAGC 59.995 47.826 0.00 0.00 36.49 5.25
941 967 3.318017 CGTATGTATGGAGTAAGCAGCC 58.682 50.000 0.00 0.00 0.00 4.85
942 968 2.533266 ATGTATGGAGTAAGCAGCCG 57.467 50.000 0.00 0.00 0.00 5.52
943 969 0.179084 TGTATGGAGTAAGCAGCCGC 60.179 55.000 0.00 0.00 38.99 6.53
953 979 2.787915 GCAGCCGCTTTAGACAGC 59.212 61.111 0.00 0.00 36.33 4.40
959 985 3.865830 GCTTTAGACAGCGGCGGC 61.866 66.667 9.78 8.43 40.37 6.53
960 986 3.195698 CTTTAGACAGCGGCGGCC 61.196 66.667 13.24 9.54 41.24 6.13
961 987 3.665675 CTTTAGACAGCGGCGGCCT 62.666 63.158 18.34 5.71 41.24 5.19
979 1005 2.358125 CAATCCGCACCACCACGA 60.358 61.111 0.00 0.00 0.00 4.35
981 1007 2.879233 AATCCGCACCACCACGACT 61.879 57.895 0.00 0.00 0.00 4.18
983 1009 3.991051 CCGCACCACCACGACTCT 61.991 66.667 0.00 0.00 0.00 3.24
1039 1065 2.124819 AGCTCTTGGCATGCCTCG 60.125 61.111 35.53 25.37 44.79 4.63
1104 1142 1.294659 CGCCAAGCAAGAGACACTCC 61.295 60.000 0.00 0.00 0.00 3.85
1117 1155 4.316823 ACTCCGCCTCACCCTCCA 62.317 66.667 0.00 0.00 0.00 3.86
1560 1598 4.135153 GAGCTTCTCCTCGCCGCA 62.135 66.667 0.00 0.00 0.00 5.69
1696 1734 3.277211 GACTACGTGCCGTGGCTCA 62.277 63.158 12.84 0.00 41.87 4.26
1795 1833 3.390135 GTGATCGACAGTCACCTCAAAA 58.610 45.455 6.40 0.00 39.99 2.44
1857 1895 4.479993 GTGCTCCTCCGCCTGCAT 62.480 66.667 0.00 0.00 37.76 3.96
1950 1988 4.853196 CGTGCACCTCAATAAGAACAAATG 59.147 41.667 12.15 0.00 0.00 2.32
2027 2065 1.451387 GTTCATTGCCGGGACCGAT 60.451 57.895 13.13 0.00 42.83 4.18
2589 2627 2.094649 GTGTACAGGAAGAACCCTCTCG 60.095 54.545 0.00 0.00 40.05 4.04
2591 2629 2.599408 ACAGGAAGAACCCTCTCGTA 57.401 50.000 0.00 0.00 40.05 3.43
2642 2683 7.570161 CGTAGTACGATGTTGTGATCTATGTA 58.430 38.462 17.85 0.00 46.05 2.29
2712 2754 6.882610 TCAGTCAACATATCAGTTTTGCTT 57.117 33.333 0.00 0.00 0.00 3.91
2713 2755 6.902341 TCAGTCAACATATCAGTTTTGCTTC 58.098 36.000 0.00 0.00 0.00 3.86
2717 2759 8.078596 AGTCAACATATCAGTTTTGCTTCTTTC 58.921 33.333 0.00 0.00 0.00 2.62
2718 2760 7.059945 GTCAACATATCAGTTTTGCTTCTTTCG 59.940 37.037 0.00 0.00 0.00 3.46
2721 2763 7.648142 ACATATCAGTTTTGCTTCTTTCGAAA 58.352 30.769 10.71 10.71 0.00 3.46
2722 2764 8.299570 ACATATCAGTTTTGCTTCTTTCGAAAT 58.700 29.630 11.70 0.00 0.00 2.17
2723 2765 9.773328 CATATCAGTTTTGCTTCTTTCGAAATA 57.227 29.630 11.70 0.70 0.00 1.40
2724 2766 9.994432 ATATCAGTTTTGCTTCTTTCGAAATAG 57.006 29.630 11.70 12.59 0.00 1.73
2725 2767 7.259290 TCAGTTTTGCTTCTTTCGAAATAGT 57.741 32.000 11.70 0.00 0.00 2.12
2726 2768 7.703328 TCAGTTTTGCTTCTTTCGAAATAGTT 58.297 30.769 11.70 0.00 0.00 2.24
2727 2769 8.832521 TCAGTTTTGCTTCTTTCGAAATAGTTA 58.167 29.630 11.70 3.72 0.00 2.24
2728 2770 9.612620 CAGTTTTGCTTCTTTCGAAATAGTTAT 57.387 29.630 11.70 0.00 0.00 1.89
2766 2824 9.212641 CTAACATATCCATCTGACCTAAACATG 57.787 37.037 0.00 0.00 0.00 3.21
2774 2832 7.038302 TCCATCTGACCTAAACATGAAAGTACT 60.038 37.037 0.00 0.00 0.00 2.73
2775 2833 7.278868 CCATCTGACCTAAACATGAAAGTACTC 59.721 40.741 0.00 0.00 0.00 2.59
2776 2834 6.698380 TCTGACCTAAACATGAAAGTACTCC 58.302 40.000 0.00 0.00 0.00 3.85
2777 2835 5.801380 TGACCTAAACATGAAAGTACTCCC 58.199 41.667 0.00 0.00 0.00 4.30
2778 2836 5.546499 TGACCTAAACATGAAAGTACTCCCT 59.454 40.000 0.00 0.00 0.00 4.20
2779 2837 6.051179 ACCTAAACATGAAAGTACTCCCTC 57.949 41.667 0.00 0.00 0.00 4.30
2780 2838 5.045797 ACCTAAACATGAAAGTACTCCCTCC 60.046 44.000 0.00 0.00 0.00 4.30
2781 2839 4.993705 AAACATGAAAGTACTCCCTCCA 57.006 40.909 0.00 0.00 0.00 3.86
2782 2840 5.520748 AAACATGAAAGTACTCCCTCCAT 57.479 39.130 0.00 0.00 0.00 3.41
2783 2841 4.762289 ACATGAAAGTACTCCCTCCATC 57.238 45.455 0.00 0.00 0.00 3.51
2784 2842 3.456277 ACATGAAAGTACTCCCTCCATCC 59.544 47.826 0.00 0.00 0.00 3.51
2785 2843 2.478292 TGAAAGTACTCCCTCCATCCC 58.522 52.381 0.00 0.00 0.00 3.85
2786 2844 2.225779 TGAAAGTACTCCCTCCATCCCA 60.226 50.000 0.00 0.00 0.00 4.37
2787 2845 2.897823 AAGTACTCCCTCCATCCCAT 57.102 50.000 0.00 0.00 0.00 4.00
2788 2846 4.232091 GAAAGTACTCCCTCCATCCCATA 58.768 47.826 0.00 0.00 0.00 2.74
2789 2847 4.295905 AAGTACTCCCTCCATCCCATAA 57.704 45.455 0.00 0.00 0.00 1.90
2790 2848 4.510303 AGTACTCCCTCCATCCCATAAT 57.490 45.455 0.00 0.00 0.00 1.28
2791 2849 5.633473 AGTACTCCCTCCATCCCATAATA 57.367 43.478 0.00 0.00 0.00 0.98
2792 2850 6.185677 AGTACTCCCTCCATCCCATAATAT 57.814 41.667 0.00 0.00 0.00 1.28
2793 2851 7.312162 AGTACTCCCTCCATCCCATAATATA 57.688 40.000 0.00 0.00 0.00 0.86
2794 2852 7.729350 AGTACTCCCTCCATCCCATAATATAA 58.271 38.462 0.00 0.00 0.00 0.98
2795 2853 8.191110 AGTACTCCCTCCATCCCATAATATAAA 58.809 37.037 0.00 0.00 0.00 1.40
2796 2854 7.516450 ACTCCCTCCATCCCATAATATAAAG 57.484 40.000 0.00 0.00 0.00 1.85
2797 2855 7.263901 ACTCCCTCCATCCCATAATATAAAGA 58.736 38.462 0.00 0.00 0.00 2.52
2798 2856 7.744068 ACTCCCTCCATCCCATAATATAAAGAA 59.256 37.037 0.00 0.00 0.00 2.52
2799 2857 7.928873 TCCCTCCATCCCATAATATAAAGAAC 58.071 38.462 0.00 0.00 0.00 3.01
2800 2858 6.823689 CCCTCCATCCCATAATATAAAGAACG 59.176 42.308 0.00 0.00 0.00 3.95
2801 2859 7.394816 CCTCCATCCCATAATATAAAGAACGT 58.605 38.462 0.00 0.00 0.00 3.99
2802 2860 7.883311 CCTCCATCCCATAATATAAAGAACGTT 59.117 37.037 0.00 0.00 0.00 3.99
2803 2861 9.284968 CTCCATCCCATAATATAAAGAACGTTT 57.715 33.333 0.46 0.00 0.00 3.60
2804 2862 9.635404 TCCATCCCATAATATAAAGAACGTTTT 57.365 29.630 0.46 0.00 0.00 2.43
2821 2879 9.485206 AGAACGTTTTTGATATTAGTGTAGTGT 57.515 29.630 0.46 0.00 0.00 3.55
2851 2909 9.893305 AAACGTTCTTATATTTTGAAACAGAGG 57.107 29.630 0.00 0.00 0.00 3.69
2852 2910 8.040716 ACGTTCTTATATTTTGAAACAGAGGG 57.959 34.615 0.00 0.00 0.00 4.30
2853 2911 7.881232 ACGTTCTTATATTTTGAAACAGAGGGA 59.119 33.333 0.00 0.00 0.00 4.20
2854 2912 8.391106 CGTTCTTATATTTTGAAACAGAGGGAG 58.609 37.037 0.00 0.00 0.00 4.30
2855 2913 9.232473 GTTCTTATATTTTGAAACAGAGGGAGT 57.768 33.333 0.00 0.00 0.00 3.85
2857 2915 9.886132 TCTTATATTTTGAAACAGAGGGAGTAC 57.114 33.333 0.00 0.00 0.00 2.73
2858 2916 9.667107 CTTATATTTTGAAACAGAGGGAGTACA 57.333 33.333 0.00 0.00 0.00 2.90
2891 2957 8.051901 ACGATAACATATTGATCGGACATCTA 57.948 34.615 12.73 0.00 45.22 1.98
2971 3049 4.697352 AGTAACTTTGCGAGATTGAGCATT 59.303 37.500 0.00 0.00 43.42 3.56
3038 3116 1.104630 ACTCTAGCACGTCTTAGGGC 58.895 55.000 3.25 0.00 41.77 5.19
3047 3125 0.179045 CGTCTTAGGGCCCTGATTGG 60.179 60.000 35.81 14.92 0.00 3.16
3059 3138 3.283751 CCCTGATTGGCGTAATAAACCA 58.716 45.455 0.00 0.00 0.00 3.67
3098 3177 1.033746 TCGTCCTAGTAGGGTTGCCG 61.034 60.000 16.44 10.61 35.59 5.69
3124 3203 1.135199 GGAAGCGTCTATGACCGACAA 60.135 52.381 0.00 0.00 0.00 3.18
3128 3207 2.094182 AGCGTCTATGACCGACAATGTT 60.094 45.455 0.00 0.00 0.00 2.71
3147 3226 2.126071 ACCTTGATGTCGTCGGCG 60.126 61.111 1.15 1.15 39.92 6.46
3169 3248 5.521735 GCGTGTTGATGATGAAGAGAAGTAT 59.478 40.000 0.00 0.00 0.00 2.12
3225 3304 7.231115 TCAATGACATGGGTCCAATATGTAATG 59.769 37.037 0.00 6.08 43.65 1.90
3297 3380 3.316029 CCTCGAAAAGCATATGGAATGCA 59.684 43.478 12.12 0.00 46.77 3.96
3430 3513 8.822805 AGGGAGTATGAAACAGTAATACAAAGA 58.177 33.333 0.00 0.00 30.67 2.52
3432 3515 9.654663 GGAGTATGAAACAGTAATACAAAGACT 57.345 33.333 0.00 0.00 30.67 3.24
3552 3635 7.487484 TGATAGAACAGATGCTCAAGTCTAAG 58.513 38.462 0.00 0.00 0.00 2.18
3579 3662 3.921677 AGCAAATGCACTTGAGAATTGG 58.078 40.909 12.91 0.00 45.16 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 25 5.083533 GATGTTATCCATTTTGCCCACAA 57.916 39.130 0.00 0.00 32.56 3.33
43 46 1.244697 GCTGAGAGAGGTCGTGTGGA 61.245 60.000 0.00 0.00 0.00 4.02
69 72 2.954611 CGTGCGAGACCAGTGAGA 59.045 61.111 0.00 0.00 0.00 3.27
109 116 1.608055 CAGACCATGGCAACTTGTGA 58.392 50.000 13.04 0.00 40.00 3.58
178 185 0.319813 GTTGAGCAACCATGGCAACC 60.320 55.000 13.04 0.00 35.36 3.77
214 221 0.392706 ATGGCGTCTGACACTTGACA 59.607 50.000 8.73 0.00 34.45 3.58
223 230 1.606668 GTTGTCCAAAATGGCGTCTGA 59.393 47.619 0.00 0.00 37.47 3.27
228 235 0.031857 TGCAGTTGTCCAAAATGGCG 59.968 50.000 0.00 0.00 37.47 5.69
288 296 4.124238 GGCAACCCCTAAAGTTTTCAAAC 58.876 43.478 0.00 0.00 39.17 2.93
311 319 4.413760 ACAACTGCCTAGTGTTAGTAGGA 58.586 43.478 12.73 0.00 42.66 2.94
382 390 2.450609 AGTGTTAGTAGGTGGCAACG 57.549 50.000 0.00 0.00 42.51 4.10
412 420 2.295070 TGTCTCTTTGTAGCGCTACACA 59.705 45.455 41.78 35.18 44.81 3.72
581 603 3.453424 TGCAGTATACATGGCAACTACG 58.547 45.455 12.61 0.00 32.54 3.51
619 643 1.151450 CTCCCACACCCAAAGCTGT 59.849 57.895 0.00 0.00 0.00 4.40
711 737 2.224018 TGTGGGCGTTTAGTAGTTCGTT 60.224 45.455 0.00 0.00 0.00 3.85
712 738 1.340889 TGTGGGCGTTTAGTAGTTCGT 59.659 47.619 0.00 0.00 0.00 3.85
719 745 1.595929 CGGTGTGTGGGCGTTTAGT 60.596 57.895 0.00 0.00 0.00 2.24
758 784 3.968568 CCGGTCGTCCACACGTCA 61.969 66.667 0.00 0.00 46.76 4.35
796 822 6.224584 TGTTTGTGGTATCACGTAAGATTGA 58.775 36.000 0.81 0.00 46.42 2.57
802 828 7.656542 TCTTAACATGTTTGTGGTATCACGTAA 59.343 33.333 17.78 0.00 46.42 3.18
824 850 3.303461 CGTTTGTGGTTGCACGAATCTTA 60.303 43.478 0.00 0.00 34.49 2.10
870 896 0.877071 CAAGTGAGCGGTTGCATCTT 59.123 50.000 0.00 0.00 46.23 2.40
879 905 0.464373 ATGCCCATACAAGTGAGCGG 60.464 55.000 0.00 0.00 0.00 5.52
887 913 5.686753 ACGGAAATACTAATGCCCATACAA 58.313 37.500 0.00 0.00 0.00 2.41
888 914 5.298989 ACGGAAATACTAATGCCCATACA 57.701 39.130 0.00 0.00 0.00 2.29
891 917 5.197451 TCAAACGGAAATACTAATGCCCAT 58.803 37.500 0.00 0.00 0.00 4.00
912 938 7.177744 TGCTTACTCCATACATACGGATAATCA 59.822 37.037 0.00 0.00 0.00 2.57
913 939 7.544622 TGCTTACTCCATACATACGGATAATC 58.455 38.462 0.00 0.00 0.00 1.75
914 940 7.476540 TGCTTACTCCATACATACGGATAAT 57.523 36.000 0.00 0.00 0.00 1.28
915 941 6.571731 GCTGCTTACTCCATACATACGGATAA 60.572 42.308 0.00 0.00 0.00 1.75
916 942 5.105877 GCTGCTTACTCCATACATACGGATA 60.106 44.000 0.00 0.00 0.00 2.59
917 943 4.322049 GCTGCTTACTCCATACATACGGAT 60.322 45.833 0.00 0.00 0.00 4.18
918 944 3.005472 GCTGCTTACTCCATACATACGGA 59.995 47.826 0.00 0.00 0.00 4.69
919 945 3.318017 GCTGCTTACTCCATACATACGG 58.682 50.000 0.00 0.00 0.00 4.02
920 946 3.318017 GGCTGCTTACTCCATACATACG 58.682 50.000 0.00 0.00 0.00 3.06
921 947 3.318017 CGGCTGCTTACTCCATACATAC 58.682 50.000 0.00 0.00 0.00 2.39
922 948 2.288825 GCGGCTGCTTACTCCATACATA 60.289 50.000 11.21 0.00 38.39 2.29
923 949 1.541233 GCGGCTGCTTACTCCATACAT 60.541 52.381 11.21 0.00 38.39 2.29
924 950 0.179084 GCGGCTGCTTACTCCATACA 60.179 55.000 11.21 0.00 38.39 2.29
925 951 2.606275 GCGGCTGCTTACTCCATAC 58.394 57.895 11.21 0.00 38.39 2.39
936 962 2.787915 GCTGTCTAAAGCGGCTGC 59.212 61.111 10.33 10.33 43.24 5.25
942 968 3.865830 GCCGCCGCTGTCTAAAGC 61.866 66.667 0.00 0.00 39.94 3.51
943 969 3.195698 GGCCGCCGCTGTCTAAAG 61.196 66.667 0.00 0.00 34.44 1.85
944 970 3.659089 GAGGCCGCCGCTGTCTAAA 62.659 63.158 5.80 0.00 34.44 1.85
945 971 4.143333 GAGGCCGCCGCTGTCTAA 62.143 66.667 5.80 0.00 34.44 2.10
957 983 3.134127 GTGGTGCGGATTGAGGCC 61.134 66.667 0.00 0.00 0.00 5.19
958 984 3.134127 GGTGGTGCGGATTGAGGC 61.134 66.667 0.00 0.00 0.00 4.70
959 985 2.040544 GTGGTGGTGCGGATTGAGG 61.041 63.158 0.00 0.00 0.00 3.86
960 986 2.390599 CGTGGTGGTGCGGATTGAG 61.391 63.158 0.00 0.00 0.00 3.02
961 987 2.358125 CGTGGTGGTGCGGATTGA 60.358 61.111 0.00 0.00 0.00 2.57
979 1005 0.657840 GCAAACTGTTGTCGCAGAGT 59.342 50.000 0.00 0.00 39.62 3.24
981 1007 0.746204 TGGCAAACTGTTGTCGCAGA 60.746 50.000 10.69 0.00 42.60 4.26
983 1009 0.030504 CATGGCAAACTGTTGTCGCA 59.969 50.000 10.69 1.26 42.60 5.10
1089 1115 1.004440 GGCGGAGTGTCTCTTGCTT 60.004 57.895 11.65 0.00 34.28 3.91
1100 1126 3.625632 ATGGAGGGTGAGGCGGAGT 62.626 63.158 0.00 0.00 0.00 3.85
1104 1142 3.866582 GGGATGGAGGGTGAGGCG 61.867 72.222 0.00 0.00 0.00 5.52
1170 1208 4.680537 AGGGAGTCGTGCGGGAGT 62.681 66.667 0.00 0.00 0.00 3.85
1416 1454 2.604686 AGGAGCTCGGACAGGCAA 60.605 61.111 7.83 0.00 0.00 4.52
1560 1598 1.334059 CGTCGCACAATCTTGTTGCTT 60.334 47.619 12.37 0.00 39.91 3.91
1936 1974 4.551056 GCGTGTGCATTTGTTCTTATTG 57.449 40.909 0.00 0.00 42.15 1.90
1950 1988 0.871163 AAATGCTTGTGTGCGTGTGC 60.871 50.000 0.00 0.00 43.20 4.57
1995 2033 4.262164 GGCAATGAACATGTCCTTCAAAGT 60.262 41.667 0.00 0.00 31.48 2.66
2150 2188 3.751018 TAGCTGAGCCCCGGGAGA 61.751 66.667 26.32 0.58 0.00 3.71
2689 2730 6.712095 AGAAGCAAAACTGATATGTTGACTGA 59.288 34.615 0.00 0.00 0.00 3.41
2730 2772 9.421399 TCAGATGGATATGTTAGTTGACTTAGA 57.579 33.333 0.00 0.00 0.00 2.10
2731 2773 9.469807 GTCAGATGGATATGTTAGTTGACTTAG 57.530 37.037 0.00 0.00 32.04 2.18
2732 2774 8.421784 GGTCAGATGGATATGTTAGTTGACTTA 58.578 37.037 0.00 0.00 34.43 2.24
2733 2775 7.126421 AGGTCAGATGGATATGTTAGTTGACTT 59.874 37.037 0.00 0.00 34.43 3.01
2734 2776 6.613271 AGGTCAGATGGATATGTTAGTTGACT 59.387 38.462 0.00 0.00 34.43 3.41
2735 2777 6.821388 AGGTCAGATGGATATGTTAGTTGAC 58.179 40.000 0.00 0.00 33.51 3.18
2736 2778 8.547481 TTAGGTCAGATGGATATGTTAGTTGA 57.453 34.615 0.00 0.00 0.00 3.18
2737 2779 9.046296 GTTTAGGTCAGATGGATATGTTAGTTG 57.954 37.037 0.00 0.00 0.00 3.16
2738 2780 8.768397 TGTTTAGGTCAGATGGATATGTTAGTT 58.232 33.333 0.00 0.00 0.00 2.24
2746 2788 7.861629 ACTTTCATGTTTAGGTCAGATGGATA 58.138 34.615 0.00 0.00 0.00 2.59
2766 2824 2.478292 TGGGATGGAGGGAGTACTTTC 58.522 52.381 0.00 0.00 0.00 2.62
2774 2832 7.311046 CGTTCTTTATATTATGGGATGGAGGGA 60.311 40.741 0.00 0.00 0.00 4.20
2775 2833 6.823689 CGTTCTTTATATTATGGGATGGAGGG 59.176 42.308 0.00 0.00 0.00 4.30
2776 2834 7.394816 ACGTTCTTTATATTATGGGATGGAGG 58.605 38.462 0.00 0.00 0.00 4.30
2777 2835 8.848474 AACGTTCTTTATATTATGGGATGGAG 57.152 34.615 0.00 0.00 0.00 3.86
2778 2836 9.635404 AAAACGTTCTTTATATTATGGGATGGA 57.365 29.630 0.00 0.00 0.00 3.41
2795 2853 9.485206 ACACTACACTAATATCAAAAACGTTCT 57.515 29.630 0.00 0.00 0.00 3.01
2825 2883 9.893305 CCTCTGTTTCAAAATATAAGAACGTTT 57.107 29.630 0.46 0.00 0.00 3.60
2826 2884 8.512138 CCCTCTGTTTCAAAATATAAGAACGTT 58.488 33.333 0.00 0.00 0.00 3.99
2827 2885 7.881232 TCCCTCTGTTTCAAAATATAAGAACGT 59.119 33.333 0.00 0.00 0.00 3.99
2828 2886 8.263940 TCCCTCTGTTTCAAAATATAAGAACG 57.736 34.615 0.00 0.00 0.00 3.95
2829 2887 9.232473 ACTCCCTCTGTTTCAAAATATAAGAAC 57.768 33.333 0.00 0.00 0.00 3.01
2831 2889 9.886132 GTACTCCCTCTGTTTCAAAATATAAGA 57.114 33.333 0.00 0.00 0.00 2.10
2832 2890 9.667107 TGTACTCCCTCTGTTTCAAAATATAAG 57.333 33.333 0.00 0.00 0.00 1.73
2835 2893 8.934023 TTTGTACTCCCTCTGTTTCAAAATAT 57.066 30.769 0.00 0.00 0.00 1.28
2836 2894 8.754991 TTTTGTACTCCCTCTGTTTCAAAATA 57.245 30.769 0.00 0.00 31.93 1.40
2837 2895 7.654022 TTTTGTACTCCCTCTGTTTCAAAAT 57.346 32.000 0.00 0.00 31.93 1.82
2838 2896 7.469537 TTTTTGTACTCCCTCTGTTTCAAAA 57.530 32.000 0.00 0.00 33.31 2.44
2863 2921 7.780008 TGTCCGATCAATATGTTATCGTTTT 57.220 32.000 11.44 0.00 40.60 2.43
2891 2957 9.698309 CTTATAAATATCTCTGTCGACATTGGT 57.302 33.333 20.40 13.29 0.00 3.67
2971 3049 3.305403 GCATAGAGACAACATAGCCGCTA 60.305 47.826 1.73 1.73 0.00 4.26
2979 3057 2.932614 GACGCTTGCATAGAGACAACAT 59.067 45.455 6.63 0.00 0.00 2.71
3038 3116 3.283751 TGGTTTATTACGCCAATCAGGG 58.716 45.455 0.00 0.00 38.09 4.45
3047 3125 6.141685 CGGCTAAAATCATTGGTTTATTACGC 59.858 38.462 0.00 0.00 0.00 4.42
3048 3126 7.411274 TCGGCTAAAATCATTGGTTTATTACG 58.589 34.615 0.00 0.19 0.00 3.18
3059 3138 4.981794 CGACCTTTTCGGCTAAAATCATT 58.018 39.130 0.00 0.00 44.60 2.57
3088 3167 1.756408 TTCCAACGTCGGCAACCCTA 61.756 55.000 0.00 0.00 0.00 3.53
3124 3203 2.337583 CGACGACATCAAGGTCAACAT 58.662 47.619 0.00 0.00 37.66 2.71
3128 3207 1.080093 GCCGACGACATCAAGGTCA 60.080 57.895 0.00 0.00 37.66 4.02
3147 3226 9.593134 ACTTATACTTCTCTTCATCATCAACAC 57.407 33.333 0.00 0.00 0.00 3.32
3225 3304 7.173218 TCGCCATATCTCAACCTTCATAATTTC 59.827 37.037 0.00 0.00 0.00 2.17
3272 3355 4.415881 TTCCATATGCTTTTCGAGGCTA 57.584 40.909 0.00 1.03 0.00 3.93
3383 3466 8.996651 TCCCTTATTCTTCTATTTCCATTTCC 57.003 34.615 0.00 0.00 0.00 3.13
3384 3467 9.634021 ACTCCCTTATTCTTCTATTTCCATTTC 57.366 33.333 0.00 0.00 0.00 2.17
3388 3471 9.447279 TCATACTCCCTTATTCTTCTATTTCCA 57.553 33.333 0.00 0.00 0.00 3.53
3540 3623 5.424121 TTGCTTGTTTCTTAGACTTGAGC 57.576 39.130 0.00 0.00 0.00 4.26
3552 3635 4.362279 TCTCAAGTGCATTTGCTTGTTTC 58.638 39.130 16.52 0.00 41.83 2.78
3579 3662 5.710984 TGCTTAGCTTTGTACTCTGTCTAC 58.289 41.667 5.60 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.