Multiple sequence alignment - TraesCS7D01G359400

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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 TraesCS7D01G359400 chr7D 100.000 3443 0 0 1 3443 461778910 461775468 0.000000e+00 6359
1 TraesCS7D01G359400 chr7D 84.364 550 52 24 6 542 571724668 571725196 3.070000e-140 508
2 TraesCS7D01G359400 chr7D 84.831 356 25 12 6 335 399448958 399449310 7.120000e-87 331
3 TraesCS7D01G359400 chr7D 86.207 319 12 5 3157 3443 421324688 421325006 1.990000e-82 316
4 TraesCS7D01G359400 chr7B 93.628 2417 88 25 977 3346 484594565 484592168 0.000000e+00 3550
5 TraesCS7D01G359400 chr7B 97.790 181 4 0 3263 3443 484592169 484591989 2.580000e-81 313
6 TraesCS7D01G359400 chr7A 92.039 1972 127 18 975 2935 538359766 538361718 0.000000e+00 2745
7 TraesCS7D01G359400 chr7A 86.047 516 44 15 2939 3442 538361901 538362400 2.350000e-146 529
8 TraesCS7D01G359400 chr1A 87.214 829 66 25 5 809 111624321 111625133 0.000000e+00 907
9 TraesCS7D01G359400 chr2A 88.338 686 63 13 135 809 768684469 768685148 0.000000e+00 808
10 TraesCS7D01G359400 chr6D 88.580 683 48 22 141 809 423361259 423361925 0.000000e+00 802
11 TraesCS7D01G359400 chr6D 88.227 688 56 19 141 813 22137607 22136930 0.000000e+00 798
12 TraesCS7D01G359400 chr6D 88.710 310 11 5 3158 3443 318448742 318448433 1.180000e-94 357
13 TraesCS7D01G359400 chr6A 88.496 678 54 19 141 807 58388389 58387725 0.000000e+00 798
14 TraesCS7D01G359400 chr2D 88.287 683 58 15 142 809 160320042 160320717 0.000000e+00 798
15 TraesCS7D01G359400 chr2D 86.271 590 53 16 6 581 345277286 345276711 1.760000e-172 616
16 TraesCS7D01G359400 chr2D 80.880 591 59 27 6 581 449565758 449566309 1.910000e-112 416
17 TraesCS7D01G359400 chr2D 87.031 293 24 6 6 295 390727692 390727973 5.540000e-83 318
18 TraesCS7D01G359400 chr2D 94.949 198 7 2 3156 3350 445700271 445700074 1.200000e-79 307
19 TraesCS7D01G359400 chr2D 84.713 314 34 9 9 317 624215430 624215126 5.580000e-78 302
20 TraesCS7D01G359400 chr2D 89.437 142 9 2 3162 3297 445629676 445629535 1.270000e-39 174
21 TraesCS7D01G359400 chr3A 88.116 690 57 18 137 809 130833711 130834392 0.000000e+00 797
22 TraesCS7D01G359400 chr3A 87.901 686 54 21 136 807 493096526 493097196 0.000000e+00 780
23 TraesCS7D01G359400 chr6B 84.587 824 89 26 6 807 601122857 601123664 0.000000e+00 784
24 TraesCS7D01G359400 chr6B 87.121 264 28 5 1 259 34810882 34811144 9.340000e-76 294
25 TraesCS7D01G359400 chr5A 88.387 310 12 5 3158 3443 53455808 53455499 5.470000e-93 351
26 TraesCS7D01G359400 chr5A 87.742 310 14 5 3158 3443 53374756 53374447 1.180000e-89 340
27 TraesCS7D01G359400 chr4B 86.817 311 11 7 3158 3443 670350943 670351248 1.540000e-83 320
28 TraesCS7D01G359400 chr4B 85.017 287 16 7 3158 3421 251468822 251469104 2.040000e-67 267
29 TraesCS7D01G359400 chr3B 80.324 432 50 16 385 809 583837923 583838326 9.340000e-76 294


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 TraesCS7D01G359400 chr7D 461775468 461778910 3442 True 6359.0 6359 100.000 1 3443 1 chr7D.!!$R1 3442
1 TraesCS7D01G359400 chr7D 571724668 571725196 528 False 508.0 508 84.364 6 542 1 chr7D.!!$F3 536
2 TraesCS7D01G359400 chr7B 484591989 484594565 2576 True 1931.5 3550 95.709 977 3443 2 chr7B.!!$R1 2466
3 TraesCS7D01G359400 chr7A 538359766 538362400 2634 False 1637.0 2745 89.043 975 3442 2 chr7A.!!$F1 2467
4 TraesCS7D01G359400 chr1A 111624321 111625133 812 False 907.0 907 87.214 5 809 1 chr1A.!!$F1 804
5 TraesCS7D01G359400 chr2A 768684469 768685148 679 False 808.0 808 88.338 135 809 1 chr2A.!!$F1 674
6 TraesCS7D01G359400 chr6D 423361259 423361925 666 False 802.0 802 88.580 141 809 1 chr6D.!!$F1 668
7 TraesCS7D01G359400 chr6D 22136930 22137607 677 True 798.0 798 88.227 141 813 1 chr6D.!!$R1 672
8 TraesCS7D01G359400 chr6A 58387725 58388389 664 True 798.0 798 88.496 141 807 1 chr6A.!!$R1 666
9 TraesCS7D01G359400 chr2D 160320042 160320717 675 False 798.0 798 88.287 142 809 1 chr2D.!!$F1 667
10 TraesCS7D01G359400 chr2D 345276711 345277286 575 True 616.0 616 86.271 6 581 1 chr2D.!!$R1 575
11 TraesCS7D01G359400 chr2D 449565758 449566309 551 False 416.0 416 80.880 6 581 1 chr2D.!!$F3 575
12 TraesCS7D01G359400 chr3A 130833711 130834392 681 False 797.0 797 88.116 137 809 1 chr3A.!!$F1 672
13 TraesCS7D01G359400 chr3A 493096526 493097196 670 False 780.0 780 87.901 136 807 1 chr3A.!!$F2 671
14 TraesCS7D01G359400 chr6B 601122857 601123664 807 False 784.0 784 84.587 6 807 1 chr6B.!!$F2 801

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
884 952 0.108585 GAGTGGGCTGAACTTGTCCA 59.891 55.0 0.00 0.0 36.78 4.02 F
1483 1551 0.103026 TCTCGATTGTCGGAGCATGG 59.897 55.0 0.00 0.0 40.88 3.66 F
1809 1880 0.107456 ACACAGTGAGGGTTCTGCTG 59.893 55.0 7.81 0.0 35.37 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2095 2166 0.540923 CTCTCCTCCCCTGAAAGCAG 59.459 60.000 0.0 0.0 41.93 4.24 R
2313 2384 2.051879 TCGAGACGAAGCACAGAAAG 57.948 50.000 0.0 0.0 31.06 2.62 R
2869 2959 2.571653 TGGATTTCACGACAATCTCCCT 59.428 45.455 0.0 0.0 32.13 4.20 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
64 65 1.265923 CGCGTCGAGATCTTCAAAACG 60.266 52.381 0.00 4.48 0.00 3.60
74 75 6.485830 AGATCTTCAAAACGAGATCCCATA 57.514 37.500 9.14 0.00 38.24 2.74
93 94 7.113437 TCCCATATTGATAGGTTTTGACGAAA 58.887 34.615 0.00 0.00 0.00 3.46
229 237 1.849097 AAACCGTGACTCTCGTGAAC 58.151 50.000 0.24 0.00 0.00 3.18
584 626 2.202295 ACAACAACGCATTTTTCGCT 57.798 40.000 0.00 0.00 0.00 4.93
586 628 3.696898 ACAACAACGCATTTTTCGCTAA 58.303 36.364 0.00 0.00 0.00 3.09
587 629 4.106197 ACAACAACGCATTTTTCGCTAAA 58.894 34.783 0.00 0.00 0.00 1.85
588 630 4.563184 ACAACAACGCATTTTTCGCTAAAA 59.437 33.333 0.00 0.00 39.88 1.52
677 740 2.461903 GTTTAAAAGGCCGAAAACGCA 58.538 42.857 0.00 0.00 0.00 5.24
809 877 2.478894 GAGCGCTTGTTAACTAGTTGCA 59.521 45.455 25.27 13.48 0.00 4.08
813 881 3.421826 CGCTTGTTAACTAGTTGCACTCG 60.422 47.826 18.56 15.77 0.00 4.18
814 882 3.664537 GCTTGTTAACTAGTTGCACTCGC 60.665 47.826 18.56 15.00 39.24 5.03
828 896 4.442038 TCGCAGAGAGGGTCACAT 57.558 55.556 0.00 0.00 0.00 3.21
829 897 3.588742 TCGCAGAGAGGGTCACATA 57.411 52.632 0.00 0.00 0.00 2.29
830 898 1.393603 TCGCAGAGAGGGTCACATAG 58.606 55.000 0.00 0.00 0.00 2.23
831 899 0.387202 CGCAGAGAGGGTCACATAGG 59.613 60.000 0.00 0.00 0.00 2.57
832 900 1.781786 GCAGAGAGGGTCACATAGGA 58.218 55.000 0.00 0.00 0.00 2.94
833 901 2.111384 GCAGAGAGGGTCACATAGGAA 58.889 52.381 0.00 0.00 0.00 3.36
834 902 2.102252 GCAGAGAGGGTCACATAGGAAG 59.898 54.545 0.00 0.00 0.00 3.46
835 903 3.370104 CAGAGAGGGTCACATAGGAAGT 58.630 50.000 0.00 0.00 0.00 3.01
836 904 3.383185 CAGAGAGGGTCACATAGGAAGTC 59.617 52.174 0.00 0.00 0.00 3.01
837 905 2.696187 GAGAGGGTCACATAGGAAGTCC 59.304 54.545 0.00 0.00 0.00 3.85
838 906 1.763545 GAGGGTCACATAGGAAGTCCC 59.236 57.143 0.00 0.00 36.42 4.46
839 907 0.837940 GGGTCACATAGGAAGTCCCC 59.162 60.000 0.00 0.00 36.42 4.81
840 908 1.625508 GGGTCACATAGGAAGTCCCCT 60.626 57.143 0.00 0.00 40.29 4.79
841 909 1.763545 GGTCACATAGGAAGTCCCCTC 59.236 57.143 0.00 0.00 37.74 4.30
842 910 1.763545 GTCACATAGGAAGTCCCCTCC 59.236 57.143 0.00 0.00 37.74 4.30
843 911 1.132500 CACATAGGAAGTCCCCTCCC 58.868 60.000 0.00 0.00 37.74 4.30
844 912 0.722676 ACATAGGAAGTCCCCTCCCA 59.277 55.000 0.00 0.00 37.74 4.37
845 913 1.344496 ACATAGGAAGTCCCCTCCCAG 60.344 57.143 0.00 0.00 37.74 4.45
846 914 1.062121 CATAGGAAGTCCCCTCCCAGA 60.062 57.143 0.00 0.00 37.74 3.86
847 915 0.637195 TAGGAAGTCCCCTCCCAGAG 59.363 60.000 0.00 0.00 37.74 3.35
866 934 7.841282 CCAGAGGGAGTCATTTACTATTAGA 57.159 40.000 0.00 0.00 39.07 2.10
867 935 7.891561 CCAGAGGGAGTCATTTACTATTAGAG 58.108 42.308 0.00 0.00 39.07 2.43
868 936 7.507616 CCAGAGGGAGTCATTTACTATTAGAGT 59.492 40.741 0.00 0.00 39.07 3.24
869 937 8.356657 CAGAGGGAGTCATTTACTATTAGAGTG 58.643 40.741 0.00 0.00 39.07 3.51
870 938 7.507616 AGAGGGAGTCATTTACTATTAGAGTGG 59.492 40.741 0.00 0.00 39.07 4.00
871 939 6.555360 AGGGAGTCATTTACTATTAGAGTGGG 59.445 42.308 0.00 0.00 39.07 4.61
872 940 6.224584 GGAGTCATTTACTATTAGAGTGGGC 58.775 44.000 0.00 0.00 39.07 5.36
873 941 6.042208 GGAGTCATTTACTATTAGAGTGGGCT 59.958 42.308 0.00 0.00 39.07 5.19
874 942 6.821388 AGTCATTTACTATTAGAGTGGGCTG 58.179 40.000 0.00 0.00 39.39 4.85
875 943 6.611642 AGTCATTTACTATTAGAGTGGGCTGA 59.388 38.462 0.00 0.00 39.39 4.26
876 944 7.125811 AGTCATTTACTATTAGAGTGGGCTGAA 59.874 37.037 0.00 0.00 39.39 3.02
877 945 7.224949 GTCATTTACTATTAGAGTGGGCTGAAC 59.775 40.741 0.00 0.00 39.39 3.18
878 946 6.869206 TTTACTATTAGAGTGGGCTGAACT 57.131 37.500 0.00 0.00 39.39 3.01
879 947 6.869206 TTACTATTAGAGTGGGCTGAACTT 57.131 37.500 0.00 0.00 39.39 2.66
880 948 5.091261 ACTATTAGAGTGGGCTGAACTTG 57.909 43.478 0.00 0.00 36.87 3.16
881 949 4.532521 ACTATTAGAGTGGGCTGAACTTGT 59.467 41.667 0.00 0.00 36.87 3.16
882 950 3.402628 TTAGAGTGGGCTGAACTTGTC 57.597 47.619 0.00 0.00 0.00 3.18
883 951 0.398318 AGAGTGGGCTGAACTTGTCC 59.602 55.000 0.00 0.00 0.00 4.02
884 952 0.108585 GAGTGGGCTGAACTTGTCCA 59.891 55.000 0.00 0.00 36.78 4.02
885 953 0.109342 AGTGGGCTGAACTTGTCCAG 59.891 55.000 0.00 0.00 40.14 3.86
886 954 0.179018 GTGGGCTGAACTTGTCCAGT 60.179 55.000 0.00 0.00 40.14 4.00
887 955 1.071699 GTGGGCTGAACTTGTCCAGTA 59.928 52.381 0.00 0.00 40.14 2.74
888 956 1.347707 TGGGCTGAACTTGTCCAGTAG 59.652 52.381 0.00 0.00 33.83 2.57
889 957 1.339151 GGGCTGAACTTGTCCAGTAGG 60.339 57.143 0.00 0.00 32.94 3.18
890 958 1.443802 GCTGAACTTGTCCAGTAGGC 58.556 55.000 0.00 0.00 32.94 3.93
891 959 1.946283 GCTGAACTTGTCCAGTAGGCC 60.946 57.143 0.00 0.00 32.94 5.19
892 960 0.690762 TGAACTTGTCCAGTAGGCCC 59.309 55.000 0.00 0.00 32.94 5.80
893 961 0.690762 GAACTTGTCCAGTAGGCCCA 59.309 55.000 0.00 0.00 32.94 5.36
894 962 1.073284 GAACTTGTCCAGTAGGCCCAA 59.927 52.381 0.00 0.00 32.94 4.12
895 963 0.400594 ACTTGTCCAGTAGGCCCAAC 59.599 55.000 0.00 0.00 31.97 3.77
896 964 0.693049 CTTGTCCAGTAGGCCCAACT 59.307 55.000 0.00 0.00 33.74 3.16
897 965 0.400213 TTGTCCAGTAGGCCCAACTG 59.600 55.000 23.13 23.13 43.26 3.16
907 975 2.668632 CCCAACTGGCGCCTCTAA 59.331 61.111 29.70 5.90 0.00 2.10
908 976 1.002624 CCCAACTGGCGCCTCTAAA 60.003 57.895 29.70 5.44 0.00 1.85
909 977 0.394352 CCCAACTGGCGCCTCTAAAT 60.394 55.000 29.70 4.89 0.00 1.40
910 978 1.134220 CCCAACTGGCGCCTCTAAATA 60.134 52.381 29.70 3.67 0.00 1.40
911 979 2.639065 CCAACTGGCGCCTCTAAATAA 58.361 47.619 29.70 2.78 0.00 1.40
912 980 3.013921 CCAACTGGCGCCTCTAAATAAA 58.986 45.455 29.70 1.91 0.00 1.40
913 981 3.442273 CCAACTGGCGCCTCTAAATAAAA 59.558 43.478 29.70 1.03 0.00 1.52
914 982 4.082463 CCAACTGGCGCCTCTAAATAAAAA 60.082 41.667 29.70 0.41 0.00 1.94
929 997 1.515487 AAAAATCGCGGGAATGGCC 59.485 52.632 6.13 0.00 0.00 5.36
930 998 2.278182 AAAAATCGCGGGAATGGCCG 62.278 55.000 6.13 0.00 37.63 6.13
938 1006 4.189580 GGAATGGCCGGGCTGCTA 62.190 66.667 29.87 9.19 0.00 3.49
939 1007 2.902343 GAATGGCCGGGCTGCTAC 60.902 66.667 29.87 11.95 0.00 3.58
940 1008 4.506255 AATGGCCGGGCTGCTACC 62.506 66.667 29.87 7.37 0.00 3.18
943 1011 4.506255 GGCCGGGCTGCTACCAAT 62.506 66.667 22.87 0.00 0.00 3.16
944 1012 2.440247 GCCGGGCTGCTACCAATT 60.440 61.111 12.87 0.00 0.00 2.32
945 1013 2.052104 GCCGGGCTGCTACCAATTT 61.052 57.895 12.87 0.00 0.00 1.82
946 1014 1.809207 CCGGGCTGCTACCAATTTG 59.191 57.895 0.00 0.00 0.00 2.32
947 1015 1.139520 CGGGCTGCTACCAATTTGC 59.860 57.895 0.00 0.00 0.00 3.68
948 1016 1.594194 CGGGCTGCTACCAATTTGCA 61.594 55.000 0.00 0.00 35.30 4.08
949 1017 0.607620 GGGCTGCTACCAATTTGCAA 59.392 50.000 0.00 0.00 36.22 4.08
950 1018 1.404583 GGGCTGCTACCAATTTGCAAG 60.405 52.381 0.00 0.00 36.22 4.01
951 1019 1.545582 GGCTGCTACCAATTTGCAAGA 59.454 47.619 0.00 0.00 36.22 3.02
952 1020 2.029110 GGCTGCTACCAATTTGCAAGAA 60.029 45.455 0.00 0.00 36.22 2.52
953 1021 3.554752 GGCTGCTACCAATTTGCAAGAAA 60.555 43.478 0.00 0.00 36.22 2.52
954 1022 4.248058 GCTGCTACCAATTTGCAAGAAAT 58.752 39.130 0.00 0.00 36.22 2.17
955 1023 4.692155 GCTGCTACCAATTTGCAAGAAATT 59.308 37.500 0.00 0.00 36.22 1.82
956 1024 5.179929 GCTGCTACCAATTTGCAAGAAATTT 59.820 36.000 0.00 0.00 36.22 1.82
957 1025 6.293571 GCTGCTACCAATTTGCAAGAAATTTT 60.294 34.615 0.00 0.00 36.22 1.82
958 1026 7.188468 TGCTACCAATTTGCAAGAAATTTTC 57.812 32.000 0.00 0.66 33.48 2.29
959 1027 6.765036 TGCTACCAATTTGCAAGAAATTTTCA 59.235 30.769 11.53 0.00 33.48 2.69
960 1028 7.281774 TGCTACCAATTTGCAAGAAATTTTCAA 59.718 29.630 11.53 0.00 33.48 2.69
961 1029 8.127954 GCTACCAATTTGCAAGAAATTTTCAAA 58.872 29.630 11.53 4.44 0.00 2.69
964 1032 9.356433 ACCAATTTGCAAGAAATTTTCAAAAAG 57.644 25.926 11.53 2.13 31.55 2.27
965 1033 9.570488 CCAATTTGCAAGAAATTTTCAAAAAGA 57.430 25.926 11.53 0.00 31.55 2.52
1284 1352 2.509561 GCCTCTCGCGTCCTTTCC 60.510 66.667 5.77 0.00 0.00 3.13
1473 1541 1.078848 GTGGCTGCCTCTCGATTGT 60.079 57.895 21.03 0.00 0.00 2.71
1483 1551 0.103026 TCTCGATTGTCGGAGCATGG 59.897 55.000 0.00 0.00 40.88 3.66
1526 1594 2.814805 CAGGATGGTTTGGATGGAGT 57.185 50.000 0.00 0.00 0.00 3.85
1527 1595 3.091633 CAGGATGGTTTGGATGGAGTT 57.908 47.619 0.00 0.00 0.00 3.01
1528 1596 3.019564 CAGGATGGTTTGGATGGAGTTC 58.980 50.000 0.00 0.00 0.00 3.01
1529 1597 2.017049 GGATGGTTTGGATGGAGTTCG 58.983 52.381 0.00 0.00 0.00 3.95
1530 1598 2.017049 GATGGTTTGGATGGAGTTCGG 58.983 52.381 0.00 0.00 0.00 4.30
1537 1605 0.178301 GGATGGAGTTCGGGGAGTTC 59.822 60.000 0.00 0.00 0.00 3.01
1566 1634 2.045536 CTGGGGCTGGAGCAAGAC 60.046 66.667 0.20 0.00 44.36 3.01
1589 1660 2.158900 AGTATTCGTTCATGCAGGAGGG 60.159 50.000 0.00 0.00 0.00 4.30
1778 1849 1.584724 AGCTTAGTACAGCCATGGGT 58.415 50.000 11.62 11.62 41.12 4.51
1809 1880 0.107456 ACACAGTGAGGGTTCTGCTG 59.893 55.000 7.81 0.00 35.37 4.41
1905 1976 5.949952 ACCAAAGTTACTTGACCTTCAAAGT 59.050 36.000 0.00 0.00 35.73 2.66
1920 1991 0.886563 AAAGTGCAGCTTCATCTGGC 59.113 50.000 0.00 0.00 36.17 4.85
1953 2024 2.159531 TGCATTAGATGTCTGCAAACGC 60.160 45.455 0.00 0.00 42.53 4.84
2262 2333 3.181471 CCATCGAGAAGCTAGTGTCCATT 60.181 47.826 0.00 0.00 0.00 3.16
2313 2384 4.546570 AGTCGCTTAAATTTGGCAACTTC 58.453 39.130 0.00 0.00 37.61 3.01
2355 2426 5.824904 AGTGTTGGCATGAATGTAAGATC 57.175 39.130 0.00 0.00 0.00 2.75
2393 2464 0.321021 AGAGCTGCTGAGACAACCAG 59.679 55.000 7.01 0.00 34.88 4.00
2518 2589 6.533723 TCAGATTAACCAAGTATGTAACTGCG 59.466 38.462 0.00 0.00 38.88 5.18
2764 2844 4.449068 CAGCTTGTGTAGTACCAGAAACAG 59.551 45.833 0.00 0.00 0.00 3.16
2870 2960 5.752892 ATGACTCAAATGCAGCAAGATAG 57.247 39.130 0.00 0.00 0.00 2.08
2902 2993 3.012518 GTGAAATCCAGGATGTCCAGTG 58.987 50.000 16.22 0.00 38.89 3.66
2907 2998 2.187958 TCCAGGATGTCCAGTGTAAGG 58.812 52.381 1.30 0.00 38.89 2.69
2912 3003 5.104527 CCAGGATGTCCAGTGTAAGGAAATA 60.105 44.000 1.30 0.00 33.17 1.40
2982 3274 5.766174 TCAATTTCAGTTGTACCTACCCAAC 59.234 40.000 0.00 0.00 40.94 3.77
3134 3427 3.732212 TGTCATAGGCACACAGATATGC 58.268 45.455 0.00 0.00 41.29 3.14
3250 3553 1.418334 AATGAGTCGAGGATGGGAGG 58.582 55.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.062587 GGTTCGAGATTTGGACGCATG 59.937 52.381 0.00 0.00 0.00 4.06
64 65 7.118390 CGTCAAAACCTATCAATATGGGATCTC 59.882 40.741 0.00 0.00 37.20 2.75
114 119 0.666374 CTCCCGGTTCGCTTTTTGTT 59.334 50.000 0.00 0.00 0.00 2.83
609 661 2.000447 CGGTCTTCCTTAGCTTTTCGG 59.000 52.381 0.00 0.00 0.00 4.30
694 759 3.568443 GCCCCCTCCGGATTTTATTTTA 58.432 45.455 3.57 0.00 0.00 1.52
742 808 3.684990 ACTTGGCGCGCTCTCAGA 61.685 61.111 32.29 10.20 0.00 3.27
809 877 0.613292 ATGTGACCCTCTCTGCGAGT 60.613 55.000 5.66 0.00 38.11 4.18
813 881 1.781786 TCCTATGTGACCCTCTCTGC 58.218 55.000 0.00 0.00 0.00 4.26
814 882 3.370104 ACTTCCTATGTGACCCTCTCTG 58.630 50.000 0.00 0.00 0.00 3.35
815 883 3.628769 GGACTTCCTATGTGACCCTCTCT 60.629 52.174 0.00 0.00 0.00 3.10
816 884 2.696187 GGACTTCCTATGTGACCCTCTC 59.304 54.545 0.00 0.00 0.00 3.20
817 885 2.627217 GGGACTTCCTATGTGACCCTCT 60.627 54.545 0.00 0.00 35.95 3.69
818 886 1.763545 GGGACTTCCTATGTGACCCTC 59.236 57.143 0.00 0.00 35.95 4.30
819 887 1.625508 GGGGACTTCCTATGTGACCCT 60.626 57.143 0.00 0.00 36.47 4.34
820 888 0.837940 GGGGACTTCCTATGTGACCC 59.162 60.000 0.00 0.00 35.95 4.46
821 889 1.763545 GAGGGGACTTCCTATGTGACC 59.236 57.143 0.00 0.00 44.43 4.02
822 890 1.763545 GGAGGGGACTTCCTATGTGAC 59.236 57.143 0.00 0.00 44.43 3.67
823 891 2.176247 GGAGGGGACTTCCTATGTGA 57.824 55.000 0.00 0.00 44.43 3.58
831 899 4.058434 CCTCTGGGAGGGGACTTC 57.942 66.667 5.73 0.00 45.43 3.01
841 909 5.896073 AATAGTAAATGACTCCCTCTGGG 57.104 43.478 0.00 0.00 46.11 4.45
842 910 7.507616 ACTCTAATAGTAAATGACTCCCTCTGG 59.492 40.741 0.00 0.00 39.81 3.86
843 911 8.356657 CACTCTAATAGTAAATGACTCCCTCTG 58.643 40.741 0.00 0.00 39.81 3.35
844 912 7.507616 CCACTCTAATAGTAAATGACTCCCTCT 59.492 40.741 0.00 0.00 39.81 3.69
845 913 7.256012 CCCACTCTAATAGTAAATGACTCCCTC 60.256 44.444 0.00 0.00 39.81 4.30
846 914 6.555360 CCCACTCTAATAGTAAATGACTCCCT 59.445 42.308 0.00 0.00 39.81 4.20
847 915 6.741801 GCCCACTCTAATAGTAAATGACTCCC 60.742 46.154 0.00 0.00 39.81 4.30
848 916 6.042208 AGCCCACTCTAATAGTAAATGACTCC 59.958 42.308 0.00 0.00 39.81 3.85
849 917 6.926272 CAGCCCACTCTAATAGTAAATGACTC 59.074 42.308 0.00 0.00 39.81 3.36
850 918 6.611642 TCAGCCCACTCTAATAGTAAATGACT 59.388 38.462 0.00 0.00 42.69 3.41
851 919 6.817184 TCAGCCCACTCTAATAGTAAATGAC 58.183 40.000 0.00 0.00 35.76 3.06
852 920 7.125811 AGTTCAGCCCACTCTAATAGTAAATGA 59.874 37.037 0.00 0.00 35.76 2.57
853 921 7.275920 AGTTCAGCCCACTCTAATAGTAAATG 58.724 38.462 0.00 0.00 35.76 2.32
854 922 7.439108 AGTTCAGCCCACTCTAATAGTAAAT 57.561 36.000 0.00 0.00 35.76 1.40
855 923 6.869206 AGTTCAGCCCACTCTAATAGTAAA 57.131 37.500 0.00 0.00 35.76 2.01
856 924 6.212791 ACAAGTTCAGCCCACTCTAATAGTAA 59.787 38.462 0.00 0.00 35.76 2.24
857 925 5.720041 ACAAGTTCAGCCCACTCTAATAGTA 59.280 40.000 0.00 0.00 35.76 1.82
858 926 4.532521 ACAAGTTCAGCCCACTCTAATAGT 59.467 41.667 0.00 0.00 39.81 2.12
859 927 5.091261 ACAAGTTCAGCCCACTCTAATAG 57.909 43.478 0.00 0.00 0.00 1.73
860 928 4.081087 GGACAAGTTCAGCCCACTCTAATA 60.081 45.833 0.00 0.00 0.00 0.98
861 929 3.307762 GGACAAGTTCAGCCCACTCTAAT 60.308 47.826 0.00 0.00 0.00 1.73
862 930 2.038557 GGACAAGTTCAGCCCACTCTAA 59.961 50.000 0.00 0.00 0.00 2.10
863 931 1.623811 GGACAAGTTCAGCCCACTCTA 59.376 52.381 0.00 0.00 0.00 2.43
864 932 0.398318 GGACAAGTTCAGCCCACTCT 59.602 55.000 0.00 0.00 0.00 3.24
865 933 0.108585 TGGACAAGTTCAGCCCACTC 59.891 55.000 0.00 0.00 0.00 3.51
866 934 0.109342 CTGGACAAGTTCAGCCCACT 59.891 55.000 0.00 0.00 0.00 4.00
867 935 0.179018 ACTGGACAAGTTCAGCCCAC 60.179 55.000 8.41 0.00 34.57 4.61
868 936 1.347707 CTACTGGACAAGTTCAGCCCA 59.652 52.381 8.41 0.00 40.56 5.36
869 937 1.339151 CCTACTGGACAAGTTCAGCCC 60.339 57.143 8.41 0.00 40.56 5.19
870 938 1.946283 GCCTACTGGACAAGTTCAGCC 60.946 57.143 8.41 0.00 40.56 4.85
871 939 1.443802 GCCTACTGGACAAGTTCAGC 58.556 55.000 8.41 0.00 40.56 4.26
872 940 1.339151 GGGCCTACTGGACAAGTTCAG 60.339 57.143 0.84 6.96 45.45 3.02
873 941 0.690762 GGGCCTACTGGACAAGTTCA 59.309 55.000 0.84 0.00 45.45 3.18
874 942 0.690762 TGGGCCTACTGGACAAGTTC 59.309 55.000 4.53 0.00 45.45 3.01
875 943 1.145571 TTGGGCCTACTGGACAAGTT 58.854 50.000 4.53 0.00 45.45 2.66
876 944 0.400594 GTTGGGCCTACTGGACAAGT 59.599 55.000 11.03 0.00 45.45 3.16
877 945 0.693049 AGTTGGGCCTACTGGACAAG 59.307 55.000 19.95 0.00 45.45 3.16
878 946 0.400213 CAGTTGGGCCTACTGGACAA 59.600 55.000 32.22 7.32 45.45 3.18
879 947 2.066340 CAGTTGGGCCTACTGGACA 58.934 57.895 32.22 1.51 45.45 4.02
890 958 0.394352 ATTTAGAGGCGCCAGTTGGG 60.394 55.000 31.54 0.00 40.85 4.12
891 959 2.325583 TATTTAGAGGCGCCAGTTGG 57.674 50.000 31.54 0.00 38.53 3.77
892 960 4.695217 TTTTATTTAGAGGCGCCAGTTG 57.305 40.909 31.54 0.00 0.00 3.16
911 979 1.515487 GGCCATTCCCGCGATTTTT 59.485 52.632 8.23 0.00 0.00 1.94
912 980 2.770589 CGGCCATTCCCGCGATTTT 61.771 57.895 8.23 0.00 42.03 1.82
913 981 3.209097 CGGCCATTCCCGCGATTT 61.209 61.111 8.23 0.00 42.03 2.17
921 989 4.189580 TAGCAGCCCGGCCATTCC 62.190 66.667 5.55 0.00 0.00 3.01
922 990 2.902343 GTAGCAGCCCGGCCATTC 60.902 66.667 5.55 0.00 0.00 2.67
923 991 4.506255 GGTAGCAGCCCGGCCATT 62.506 66.667 5.55 0.00 0.00 3.16
926 994 4.506255 ATTGGTAGCAGCCCGGCC 62.506 66.667 5.55 0.00 0.00 6.13
927 995 2.052104 AAATTGGTAGCAGCCCGGC 61.052 57.895 0.00 0.00 0.00 6.13
928 996 1.809207 CAAATTGGTAGCAGCCCGG 59.191 57.895 0.00 0.00 0.00 5.73
929 997 1.139520 GCAAATTGGTAGCAGCCCG 59.860 57.895 0.00 0.00 0.00 6.13
930 998 0.607620 TTGCAAATTGGTAGCAGCCC 59.392 50.000 0.00 0.00 39.72 5.19
931 999 1.545582 TCTTGCAAATTGGTAGCAGCC 59.454 47.619 0.00 0.00 39.72 4.85
932 1000 3.302365 TTCTTGCAAATTGGTAGCAGC 57.698 42.857 0.00 0.00 39.72 5.25
933 1001 6.790285 AAATTTCTTGCAAATTGGTAGCAG 57.210 33.333 0.00 0.00 39.72 4.24
934 1002 6.765036 TGAAAATTTCTTGCAAATTGGTAGCA 59.235 30.769 7.29 0.00 36.32 3.49
935 1003 7.188468 TGAAAATTTCTTGCAAATTGGTAGC 57.812 32.000 7.29 0.00 30.94 3.58
938 1006 9.356433 CTTTTTGAAAATTTCTTGCAAATTGGT 57.644 25.926 7.29 0.00 30.94 3.67
939 1007 9.570488 TCTTTTTGAAAATTTCTTGCAAATTGG 57.430 25.926 7.29 0.00 30.94 3.16
959 1027 9.755804 TGCAAATTGGTTTTTCTTTTTCTTTTT 57.244 22.222 0.00 0.00 0.00 1.94
960 1028 9.755804 TTGCAAATTGGTTTTTCTTTTTCTTTT 57.244 22.222 0.00 0.00 0.00 2.27
961 1029 9.409312 CTTGCAAATTGGTTTTTCTTTTTCTTT 57.591 25.926 0.00 0.00 0.00 2.52
962 1030 8.791675 TCTTGCAAATTGGTTTTTCTTTTTCTT 58.208 25.926 0.00 0.00 0.00 2.52
963 1031 8.334263 TCTTGCAAATTGGTTTTTCTTTTTCT 57.666 26.923 0.00 0.00 0.00 2.52
964 1032 8.450180 TCTCTTGCAAATTGGTTTTTCTTTTTC 58.550 29.630 0.00 0.00 0.00 2.29
965 1033 8.236586 GTCTCTTGCAAATTGGTTTTTCTTTTT 58.763 29.630 0.00 0.00 0.00 1.94
966 1034 7.148255 GGTCTCTTGCAAATTGGTTTTTCTTTT 60.148 33.333 0.00 0.00 0.00 2.27
967 1035 6.316140 GGTCTCTTGCAAATTGGTTTTTCTTT 59.684 34.615 0.00 0.00 0.00 2.52
968 1036 5.817296 GGTCTCTTGCAAATTGGTTTTTCTT 59.183 36.000 0.00 0.00 0.00 2.52
969 1037 5.104982 TGGTCTCTTGCAAATTGGTTTTTCT 60.105 36.000 0.00 0.00 0.00 2.52
970 1038 5.006649 GTGGTCTCTTGCAAATTGGTTTTTC 59.993 40.000 0.00 0.00 0.00 2.29
971 1039 4.875536 GTGGTCTCTTGCAAATTGGTTTTT 59.124 37.500 0.00 0.00 0.00 1.94
972 1040 4.162131 AGTGGTCTCTTGCAAATTGGTTTT 59.838 37.500 0.00 0.00 0.00 2.43
973 1041 3.706086 AGTGGTCTCTTGCAAATTGGTTT 59.294 39.130 0.00 0.00 0.00 3.27
1120 1188 2.038975 CACCGGGGAGAGGAGGAA 59.961 66.667 6.32 0.00 0.00 3.36
1410 1478 1.026718 CCTCTGCTTTAAGCCACGGG 61.027 60.000 14.80 7.58 41.51 5.28
1508 1576 2.356125 CGAACTCCATCCAAACCATCCT 60.356 50.000 0.00 0.00 0.00 3.24
1518 1586 0.178301 GAACTCCCCGAACTCCATCC 59.822 60.000 0.00 0.00 0.00 3.51
1522 1590 1.824224 AACCGAACTCCCCGAACTCC 61.824 60.000 0.00 0.00 0.00 3.85
1523 1591 0.669625 CAACCGAACTCCCCGAACTC 60.670 60.000 0.00 0.00 0.00 3.01
1524 1592 1.370064 CAACCGAACTCCCCGAACT 59.630 57.895 0.00 0.00 0.00 3.01
1525 1593 1.670083 CCAACCGAACTCCCCGAAC 60.670 63.158 0.00 0.00 0.00 3.95
1526 1594 1.823169 CTCCAACCGAACTCCCCGAA 61.823 60.000 0.00 0.00 0.00 4.30
1527 1595 2.203669 TCCAACCGAACTCCCCGA 60.204 61.111 0.00 0.00 0.00 5.14
1528 1596 2.264794 CTCCAACCGAACTCCCCG 59.735 66.667 0.00 0.00 0.00 5.73
1529 1597 1.192803 AGACTCCAACCGAACTCCCC 61.193 60.000 0.00 0.00 0.00 4.81
1530 1598 0.246910 GAGACTCCAACCGAACTCCC 59.753 60.000 0.00 0.00 0.00 4.30
1537 1605 2.982130 CCCCAGAGACTCCAACCG 59.018 66.667 0.00 0.00 0.00 4.44
1589 1660 2.435059 GAGAAGGAGCACGCCCAC 60.435 66.667 0.00 0.00 0.00 4.61
1778 1849 3.131755 CCTCACTGTGTCATCATCAGCTA 59.868 47.826 7.79 0.00 33.12 3.32
1809 1880 5.235516 TCTTCCTCGAGTACCAAATTTGAC 58.764 41.667 19.86 10.53 0.00 3.18
1905 1976 0.679002 GAAGGCCAGATGAAGCTGCA 60.679 55.000 5.01 0.00 34.56 4.41
1920 1991 4.639310 ACATCTAATGCAGCAGAAAGAAGG 59.361 41.667 0.00 3.63 0.00 3.46
1953 2024 4.655647 AGTGCAGCAGCTGGGTGG 62.656 66.667 24.13 0.00 45.14 4.61
1989 2060 5.004448 AGGCCTTGTTTTCTAAGAACTAGC 58.996 41.667 0.00 0.00 31.45 3.42
2064 2135 2.568090 GCGGTGACATGCAAAGGG 59.432 61.111 0.00 0.00 0.00 3.95
2095 2166 0.540923 CTCTCCTCCCCTGAAAGCAG 59.459 60.000 0.00 0.00 41.93 4.24
2262 2333 9.023962 GGGAACTTTATTGCCATATCATCAATA 57.976 33.333 0.00 0.00 33.13 1.90
2286 2357 2.993220 GCCAAATTTAAGCGACTTTGGG 59.007 45.455 13.15 1.84 44.98 4.12
2313 2384 2.051879 TCGAGACGAAGCACAGAAAG 57.948 50.000 0.00 0.00 31.06 2.62
2355 2426 4.319177 CTCTCTCAAGTAAAACCCTGTGG 58.681 47.826 0.00 0.00 37.80 4.17
2393 2464 8.125448 CCAATATAGCTTTAGTCAAGAAAGTGC 58.875 37.037 0.00 0.00 36.47 4.40
2544 2615 5.977129 CGAACTACAAAAGCTGTCCATTTTT 59.023 36.000 0.00 0.00 39.64 1.94
2545 2616 5.298276 TCGAACTACAAAAGCTGTCCATTTT 59.702 36.000 0.00 0.00 39.64 1.82
2711 2791 7.469537 TTCAAAAGTCAAAGACAACCCTTAA 57.530 32.000 0.00 0.00 34.60 1.85
2764 2844 3.960002 GCGTATATGCATCGTTGTTCAAC 59.040 43.478 12.17 5.70 34.15 3.18
2869 2959 2.571653 TGGATTTCACGACAATCTCCCT 59.428 45.455 0.00 0.00 32.13 4.20
2870 2960 2.939103 CTGGATTTCACGACAATCTCCC 59.061 50.000 0.00 0.00 32.13 4.30
2982 3274 8.724229 CATACATATCACATGAAACCTATGGTG 58.276 37.037 0.00 0.00 35.34 4.17
3250 3553 6.801862 GGAAACATGTATGCACTAGAAAACAC 59.198 38.462 0.00 0.00 0.00 3.32
3383 3768 9.174166 GACAAAATTTATCCCAGAGCTTACTAA 57.826 33.333 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.