Multiple sequence alignment - TraesCS1A01G159700

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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 TraesCS1A01G159700 chr1A 100.000 2819 0 0 1 2819 286914760 286917578 0.000000e+00 5206.0
1 TraesCS1A01G159700 chr1D 95.564 1375 56 2 899 2268 221444054 221445428 0.000000e+00 2196.0
2 TraesCS1A01G159700 chr1D 90.566 477 15 7 2366 2819 221445436 221445905 3.110000e-169 604.0
3 TraesCS1A01G159700 chr1B 95.973 1341 43 6 978 2312 317917645 317916310 0.000000e+00 2167.0
4 TraesCS1A01G159700 chr1B 81.299 770 117 16 3 753 438062541 438061780 1.450000e-167 599.0
5 TraesCS1A01G159700 chr1B 95.026 382 13 5 2374 2751 317916307 317915928 1.870000e-166 595.0
6 TraesCS1A01G159700 chr1B 74.892 697 151 23 149 828 313401583 313400894 2.120000e-76 296.0
7 TraesCS1A01G159700 chr1B 91.919 99 5 2 899 995 317917758 317917661 4.900000e-28 135.0
8 TraesCS1A01G159700 chr1B 81.208 149 23 5 675 821 633125256 633125401 6.380000e-22 115.0
9 TraesCS1A01G159700 chr1B 93.878 49 1 2 2304 2350 80041314 80041266 3.900000e-09 73.1
10 TraesCS1A01G159700 chr1B 85.714 70 5 5 2642 2711 155711529 155711593 5.040000e-08 69.4
11 TraesCS1A01G159700 chr6B 82.332 849 115 23 3 827 49894760 49895597 0.000000e+00 704.0
12 TraesCS1A01G159700 chr6B 82.927 164 20 5 672 827 214872122 214872285 1.050000e-29 141.0
13 TraesCS1A01G159700 chr6B 89.474 76 7 1 2345 2420 552501479 552501405 8.310000e-16 95.3
14 TraesCS1A01G159700 chr6B 85.507 69 6 4 2643 2711 213627746 213627682 5.040000e-08 69.4
15 TraesCS1A01G159700 chr6B 83.117 77 8 5 2635 2711 559472631 559472702 6.520000e-07 65.8
16 TraesCS1A01G159700 chr6D 82.097 849 120 23 3 827 27225315 27226155 0.000000e+00 697.0
17 TraesCS1A01G159700 chr6D 84.987 393 52 5 3 389 27212090 27212481 2.630000e-105 392.0
18 TraesCS1A01G159700 chr6D 74.265 816 159 43 42 827 451812042 451812836 2.120000e-76 296.0
19 TraesCS1A01G159700 chr6D 74.262 711 151 26 142 830 20464419 20465119 1.290000e-68 270.0
20 TraesCS1A01G159700 chr5B 79.953 848 142 18 3 827 138703417 138704259 1.450000e-167 599.0
21 TraesCS1A01G159700 chr5B 78.080 698 125 25 149 827 631828920 631828232 1.560000e-112 416.0
22 TraesCS1A01G159700 chr5B 95.556 45 1 1 2307 2350 391397268 391397312 1.400000e-08 71.3
23 TraesCS1A01G159700 chr5A 80.586 819 123 24 42 827 543922565 543921750 1.450000e-167 599.0
24 TraesCS1A01G159700 chr3D 79.232 703 120 14 153 833 360637202 360636504 1.530000e-127 466.0
25 TraesCS1A01G159700 chr3D 93.939 66 4 0 2350 2415 5400361 5400426 1.790000e-17 100.0
26 TraesCS1A01G159700 chr3D 91.667 72 6 0 2347 2418 341659385 341659456 1.790000e-17 100.0
27 TraesCS1A01G159700 chr3D 85.714 70 6 4 2642 2711 246618579 246618514 1.400000e-08 71.3
28 TraesCS1A01G159700 chr4D 75.931 806 160 27 40 822 319272255 319271461 1.580000e-102 383.0
29 TraesCS1A01G159700 chr4D 73.721 430 95 16 403 821 351752703 351752281 4.860000e-33 152.0
30 TraesCS1A01G159700 chr4D 92.308 52 3 1 2307 2357 62770236 62770185 3.900000e-09 73.1
31 TraesCS1A01G159700 chr5D 73.691 802 176 31 42 821 292022354 292021566 2.140000e-71 279.0
32 TraesCS1A01G159700 chr5D 73.061 709 140 31 161 827 543428587 543429286 1.320000e-48 204.0
33 TraesCS1A01G159700 chr5D 75.245 408 79 19 435 828 564487076 564486677 1.040000e-39 174.0
34 TraesCS1A01G159700 chr2D 74.290 704 152 25 143 827 249398110 249398803 1.290000e-68 270.0
35 TraesCS1A01G159700 chr2D 97.619 42 0 1 2304 2344 555158698 555158739 1.400000e-08 71.3
36 TraesCS1A01G159700 chrUn 74.043 705 152 27 143 827 94204129 94204822 2.790000e-65 259.0
37 TraesCS1A01G159700 chr3B 72.771 830 164 48 42 831 21237833 21238640 1.020000e-54 224.0
38 TraesCS1A01G159700 chr3B 91.228 57 4 1 2654 2710 6132746 6132801 3.010000e-10 76.8
39 TraesCS1A01G159700 chr7B 74.130 460 94 23 386 830 671707874 671708323 1.740000e-37 167.0
40 TraesCS1A01G159700 chr7B 80.000 225 43 2 3 225 380504100 380504324 6.250000e-37 165.0
41 TraesCS1A01G159700 chr7B 83.226 155 19 6 682 829 539202299 539202453 4.900000e-28 135.0
42 TraesCS1A01G159700 chr7B 100.000 40 0 0 2311 2350 638514088 638514049 1.080000e-09 75.0
43 TraesCS1A01G159700 chr6A 84.677 124 10 3 2295 2417 158047907 158047792 6.380000e-22 115.0
44 TraesCS1A01G159700 chr4B 95.714 70 2 1 2345 2414 92663299 92663231 8.250000e-21 111.0
45 TraesCS1A01G159700 chr4B 87.143 70 4 5 2643 2711 587032479 587032544 1.080000e-09 75.0
46 TraesCS1A01G159700 chr4B 95.652 46 1 1 2307 2351 92663314 92663269 3.900000e-09 73.1
47 TraesCS1A01G159700 chr7A 93.056 72 4 1 2345 2416 84745805 84745735 1.380000e-18 104.0
48 TraesCS1A01G159700 chr7A 100.000 40 0 0 2311 2350 667157819 667157780 1.080000e-09 75.0
49 TraesCS1A01G159700 chr7A 85.507 69 6 4 2642 2710 81927424 81927360 5.040000e-08 69.4
50 TraesCS1A01G159700 chr3A 91.667 72 6 0 2347 2418 511553350 511553421 1.790000e-17 100.0
51 TraesCS1A01G159700 chr3A 95.833 48 1 1 2304 2350 511553421 511553374 3.010000e-10 76.8
52 TraesCS1A01G159700 chr7D 91.549 71 5 1 2346 2416 571261926 571261995 2.310000e-16 97.1


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 TraesCS1A01G159700 chr1A 286914760 286917578 2818 False 5206.000000 5206 100.000 1 2819 1 chr1A.!!$F1 2818
1 TraesCS1A01G159700 chr1D 221444054 221445905 1851 False 1400.000000 2196 93.065 899 2819 2 chr1D.!!$F1 1920
2 TraesCS1A01G159700 chr1B 317915928 317917758 1830 True 965.666667 2167 94.306 899 2751 3 chr1B.!!$R4 1852
3 TraesCS1A01G159700 chr1B 438061780 438062541 761 True 599.000000 599 81.299 3 753 1 chr1B.!!$R3 750
4 TraesCS1A01G159700 chr1B 313400894 313401583 689 True 296.000000 296 74.892 149 828 1 chr1B.!!$R2 679
5 TraesCS1A01G159700 chr6B 49894760 49895597 837 False 704.000000 704 82.332 3 827 1 chr6B.!!$F1 824
6 TraesCS1A01G159700 chr6D 27225315 27226155 840 False 697.000000 697 82.097 3 827 1 chr6D.!!$F3 824
7 TraesCS1A01G159700 chr6D 451812042 451812836 794 False 296.000000 296 74.265 42 827 1 chr6D.!!$F4 785
8 TraesCS1A01G159700 chr6D 20464419 20465119 700 False 270.000000 270 74.262 142 830 1 chr6D.!!$F1 688
9 TraesCS1A01G159700 chr5B 138703417 138704259 842 False 599.000000 599 79.953 3 827 1 chr5B.!!$F1 824
10 TraesCS1A01G159700 chr5B 631828232 631828920 688 True 416.000000 416 78.080 149 827 1 chr5B.!!$R1 678
11 TraesCS1A01G159700 chr5A 543921750 543922565 815 True 599.000000 599 80.586 42 827 1 chr5A.!!$R1 785
12 TraesCS1A01G159700 chr3D 360636504 360637202 698 True 466.000000 466 79.232 153 833 1 chr3D.!!$R2 680
13 TraesCS1A01G159700 chr4D 319271461 319272255 794 True 383.000000 383 75.931 40 822 1 chr4D.!!$R2 782
14 TraesCS1A01G159700 chr5D 292021566 292022354 788 True 279.000000 279 73.691 42 821 1 chr5D.!!$R1 779
15 TraesCS1A01G159700 chr5D 543428587 543429286 699 False 204.000000 204 73.061 161 827 1 chr5D.!!$F1 666
16 TraesCS1A01G159700 chr2D 249398110 249398803 693 False 270.000000 270 74.290 143 827 1 chr2D.!!$F1 684
17 TraesCS1A01G159700 chrUn 94204129 94204822 693 False 259.000000 259 74.043 143 827 1 chrUn.!!$F1 684
18 TraesCS1A01G159700 chr3B 21237833 21238640 807 False 224.000000 224 72.771 42 831 1 chr3B.!!$F2 789

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
373 383 0.034896 TTCCCAGACCTCTTCGTTGC 59.965 55.0 0.0 0.0 0.0 4.17 F
496 514 0.036388 TTCCTCTTCGACATGCCACC 60.036 55.0 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1660 1773 0.862701 CACACAAACAGCAGCACACG 60.863 55.000 0.0 0.0 0.0 4.49 R
1884 2002 1.003928 GATTACCAACGACCCCCAAGT 59.996 52.381 0.0 0.0 0.0 3.16 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
19 20 0.318107 TTCACGAACCGAACCTCGAC 60.318 55.000 0.00 0.00 43.74 4.20
22 23 0.888285 ACGAACCGAACCTCGACTCT 60.888 55.000 0.00 0.00 43.74 3.24
27 28 1.642037 CCGAACCTCGACTCTACGCA 61.642 60.000 0.00 0.00 43.74 5.24
38 39 0.802222 CTCTACGCATGACCGTGTGG 60.802 60.000 8.41 0.52 42.15 4.17
80 83 1.066858 GCAGATTCTCCACGAAGTCCA 60.067 52.381 0.00 0.00 41.61 4.02
112 118 4.115199 GTAGCCACCCTGCCCCAG 62.115 72.222 0.00 0.00 0.00 4.45
128 134 0.918983 CCAGCCCCTTTGAGGTGATA 59.081 55.000 0.00 0.00 31.93 2.15
156 162 4.680172 CGATCTGTCTGCCTTTGAAGATCT 60.680 45.833 8.39 0.00 38.46 2.75
192 198 2.729862 GGATCCGCGGACGAATCG 60.730 66.667 33.75 0.00 43.93 3.34
212 218 4.680237 TCCGGCGTTGAGGTGCTG 62.680 66.667 6.01 0.00 37.22 4.41
228 234 1.279558 TGCTGAAACGTAATGGCCCTA 59.720 47.619 0.00 0.00 0.00 3.53
315 325 2.517959 CCCAATTTCTCTGGAGTTGCA 58.482 47.619 0.00 0.00 35.85 4.08
319 329 2.275134 TTTCTCTGGAGTTGCATGCA 57.725 45.000 18.46 18.46 0.00 3.96
359 369 1.454847 GTGCCACACCAACTTCCCA 60.455 57.895 0.00 0.00 0.00 4.37
373 383 0.034896 TTCCCAGACCTCTTCGTTGC 59.965 55.000 0.00 0.00 0.00 4.17
375 385 0.671781 CCCAGACCTCTTCGTTGCAG 60.672 60.000 0.00 0.00 0.00 4.41
459 477 1.801765 GCTCTGGACGGTTCGGAATAC 60.802 57.143 0.00 0.00 0.00 1.89
472 490 2.953648 TCGGAATACGCTAGTCATCCAA 59.046 45.455 0.00 0.00 43.86 3.53
489 507 2.821378 TCCAACGTATTCCTCTTCGACA 59.179 45.455 0.00 0.00 0.00 4.35
496 514 0.036388 TTCCTCTTCGACATGCCACC 60.036 55.000 0.00 0.00 0.00 4.61
519 538 4.204573 CGACGCGGTTTTTCAAATTTTGTA 59.795 37.500 12.47 0.00 0.00 2.41
571 590 1.440893 CTCAGGATCAGGACGCCAG 59.559 63.158 0.00 0.00 0.00 4.85
580 599 1.672356 AGGACGCCAGCAACATCAC 60.672 57.895 0.00 0.00 0.00 3.06
619 638 2.357952 CGATGACTCTCCGATTGGTACA 59.642 50.000 0.00 0.00 36.30 2.90
691 748 6.934083 CACCTGCTTTTTATGTTTATTTGGGT 59.066 34.615 0.00 0.00 0.00 4.51
771 851 8.511321 GGTGTGTGATTTTATTGTGATACTTGA 58.489 33.333 0.00 0.00 0.00 3.02
833 913 7.244192 CGAAAGGCCTTTTCAGTAATTTAGAG 58.756 38.462 30.89 4.76 44.42 2.43
834 914 7.119262 CGAAAGGCCTTTTCAGTAATTTAGAGA 59.881 37.037 30.89 0.00 44.42 3.10
835 915 8.885693 AAAGGCCTTTTCAGTAATTTAGAGAT 57.114 30.769 25.47 0.00 0.00 2.75
836 916 9.975218 AAAGGCCTTTTCAGTAATTTAGAGATA 57.025 29.630 25.47 0.00 0.00 1.98
837 917 9.620259 AAGGCCTTTTCAGTAATTTAGAGATAG 57.380 33.333 13.78 0.00 0.00 2.08
838 918 8.214364 AGGCCTTTTCAGTAATTTAGAGATAGG 58.786 37.037 0.00 0.00 0.00 2.57
839 919 7.041030 GGCCTTTTCAGTAATTTAGAGATAGGC 60.041 40.741 0.00 0.00 0.00 3.93
840 920 7.717436 GCCTTTTCAGTAATTTAGAGATAGGCT 59.283 37.037 0.00 0.00 0.00 4.58
849 929 9.157104 GTAATTTAGAGATAGGCTAGAAATGGC 57.843 37.037 0.00 0.00 0.00 4.40
850 930 3.951775 AGAGATAGGCTAGAAATGGCG 57.048 47.619 0.00 0.00 35.01 5.69
851 931 3.235200 AGAGATAGGCTAGAAATGGCGT 58.765 45.455 0.00 0.00 35.01 5.68
852 932 4.408276 AGAGATAGGCTAGAAATGGCGTA 58.592 43.478 0.00 0.00 34.20 4.42
853 933 4.833380 AGAGATAGGCTAGAAATGGCGTAA 59.167 41.667 0.00 0.00 33.58 3.18
854 934 5.304614 AGAGATAGGCTAGAAATGGCGTAAA 59.695 40.000 0.00 0.00 33.58 2.01
855 935 5.925509 AGATAGGCTAGAAATGGCGTAAAA 58.074 37.500 0.00 0.00 33.58 1.52
856 936 6.534634 AGATAGGCTAGAAATGGCGTAAAAT 58.465 36.000 0.00 0.00 33.58 1.82
857 937 6.998673 AGATAGGCTAGAAATGGCGTAAAATT 59.001 34.615 0.00 0.00 33.58 1.82
858 938 8.154856 AGATAGGCTAGAAATGGCGTAAAATTA 58.845 33.333 0.00 0.00 33.58 1.40
859 939 8.685838 ATAGGCTAGAAATGGCGTAAAATTAA 57.314 30.769 0.00 0.00 33.58 1.40
860 940 7.582667 AGGCTAGAAATGGCGTAAAATTAAT 57.417 32.000 0.00 0.00 35.01 1.40
861 941 7.425606 AGGCTAGAAATGGCGTAAAATTAATG 58.574 34.615 0.00 0.00 35.01 1.90
862 942 7.284489 AGGCTAGAAATGGCGTAAAATTAATGA 59.716 33.333 0.00 0.00 35.01 2.57
863 943 7.918562 GGCTAGAAATGGCGTAAAATTAATGAA 59.081 33.333 0.00 0.00 0.00 2.57
864 944 9.463443 GCTAGAAATGGCGTAAAATTAATGAAT 57.537 29.630 0.00 0.00 0.00 2.57
866 946 8.871686 AGAAATGGCGTAAAATTAATGAATCC 57.128 30.769 0.00 0.00 0.00 3.01
867 947 7.647715 AGAAATGGCGTAAAATTAATGAATCCG 59.352 33.333 0.00 0.00 0.00 4.18
868 948 6.627395 ATGGCGTAAAATTAATGAATCCGA 57.373 33.333 0.00 0.00 0.00 4.55
869 949 6.438259 TGGCGTAAAATTAATGAATCCGAA 57.562 33.333 0.00 0.00 0.00 4.30
870 950 7.033530 TGGCGTAAAATTAATGAATCCGAAT 57.966 32.000 0.00 0.00 0.00 3.34
871 951 7.484975 TGGCGTAAAATTAATGAATCCGAATT 58.515 30.769 0.00 0.00 0.00 2.17
872 952 7.976734 TGGCGTAAAATTAATGAATCCGAATTT 59.023 29.630 0.00 0.00 33.92 1.82
873 953 8.813282 GGCGTAAAATTAATGAATCCGAATTTT 58.187 29.630 11.57 11.57 41.74 1.82
879 959 9.816354 AAATTAATGAATCCGAATTTTACTGGG 57.184 29.630 0.00 0.00 29.38 4.45
880 960 7.948034 TTAATGAATCCGAATTTTACTGGGT 57.052 32.000 0.00 0.00 0.00 4.51
881 961 6.850752 AATGAATCCGAATTTTACTGGGTT 57.149 33.333 0.00 0.00 0.00 4.11
882 962 7.948034 AATGAATCCGAATTTTACTGGGTTA 57.052 32.000 0.00 0.00 0.00 2.85
883 963 7.948034 ATGAATCCGAATTTTACTGGGTTAA 57.052 32.000 0.00 0.00 0.00 2.01
884 964 7.148355 TGAATCCGAATTTTACTGGGTTAAC 57.852 36.000 0.00 0.00 0.00 2.01
885 965 6.943718 TGAATCCGAATTTTACTGGGTTAACT 59.056 34.615 5.42 0.00 0.00 2.24
886 966 7.449086 TGAATCCGAATTTTACTGGGTTAACTT 59.551 33.333 5.42 0.00 0.00 2.66
887 967 8.866970 AATCCGAATTTTACTGGGTTAACTTA 57.133 30.769 5.42 0.00 0.00 2.24
888 968 7.671495 TCCGAATTTTACTGGGTTAACTTAC 57.329 36.000 5.42 0.00 0.00 2.34
889 969 7.222872 TCCGAATTTTACTGGGTTAACTTACA 58.777 34.615 5.42 2.15 0.00 2.41
890 970 7.388500 TCCGAATTTTACTGGGTTAACTTACAG 59.612 37.037 17.72 17.72 37.01 2.74
891 971 7.361457 CCGAATTTTACTGGGTTAACTTACAGG 60.361 40.741 21.00 9.80 35.34 4.00
892 972 6.829229 ATTTTACTGGGTTAACTTACAGGC 57.171 37.500 21.00 0.43 35.34 4.85
893 973 5.571791 TTTACTGGGTTAACTTACAGGCT 57.428 39.130 21.00 10.06 35.34 4.58
894 974 6.684897 TTTACTGGGTTAACTTACAGGCTA 57.315 37.500 21.00 9.39 35.34 3.93
895 975 4.820894 ACTGGGTTAACTTACAGGCTAG 57.179 45.455 21.00 8.31 35.34 3.42
896 976 4.422984 ACTGGGTTAACTTACAGGCTAGA 58.577 43.478 21.00 0.00 35.34 2.43
897 977 4.466726 ACTGGGTTAACTTACAGGCTAGAG 59.533 45.833 21.00 0.00 35.34 2.43
912 994 1.339610 CTAGAGACGGAGGGAGCAATG 59.660 57.143 0.00 0.00 0.00 2.82
1096 1209 2.683933 ACCGTAGCCTCCCCAGTG 60.684 66.667 0.00 0.00 0.00 3.66
1276 1389 1.379044 GCATCCCCACCTCAACCAG 60.379 63.158 0.00 0.00 0.00 4.00
1321 1434 1.076777 CCCCGCCAACATCCAGATT 60.077 57.895 0.00 0.00 0.00 2.40
1660 1773 1.615392 GGCAAGTTCCATGATATGCCC 59.385 52.381 13.57 0.00 45.84 5.36
1712 1825 4.746535 TCCGTAAAATGCCTCTGTGATA 57.253 40.909 0.00 0.00 0.00 2.15
1884 2002 5.530543 TCTGTTGCTAATTGTTGATGTGACA 59.469 36.000 0.00 0.00 0.00 3.58
1892 2010 1.247567 GTTGATGTGACACTTGGGGG 58.752 55.000 7.20 0.00 0.00 5.40
1966 2084 1.082104 CTTGTTTCTCGCAACCGCC 60.082 57.895 0.00 0.00 33.11 6.13
2086 2209 8.641541 ACTTGTTTGGTCATATTCATCAGTTTT 58.358 29.630 0.00 0.00 0.00 2.43
2177 2300 7.865707 ACAATTTTATCTGGTGCTATCGATTC 58.134 34.615 1.71 0.00 0.00 2.52
2240 2363 2.906389 TGACAGGAAGGTCAGCTTGTAT 59.094 45.455 0.00 0.00 42.56 2.29
2309 2432 8.803397 AGTTTATCCCATTTTACTGTTCTACC 57.197 34.615 0.00 0.00 0.00 3.18
2312 2435 4.180723 TCCCATTTTACTGTTCTACCCCT 58.819 43.478 0.00 0.00 0.00 4.79
2313 2436 4.226620 TCCCATTTTACTGTTCTACCCCTC 59.773 45.833 0.00 0.00 0.00 4.30
2314 2437 4.524053 CCATTTTACTGTTCTACCCCTCC 58.476 47.826 0.00 0.00 0.00 4.30
2315 2438 3.967332 TTTTACTGTTCTACCCCTCCG 57.033 47.619 0.00 0.00 0.00 4.63
2316 2439 2.610438 TTACTGTTCTACCCCTCCGT 57.390 50.000 0.00 0.00 0.00 4.69
2317 2440 2.610438 TACTGTTCTACCCCTCCGTT 57.390 50.000 0.00 0.00 0.00 4.44
2318 2441 1.264295 ACTGTTCTACCCCTCCGTTC 58.736 55.000 0.00 0.00 0.00 3.95
2319 2442 0.535797 CTGTTCTACCCCTCCGTTCC 59.464 60.000 0.00 0.00 0.00 3.62
2320 2443 0.115745 TGTTCTACCCCTCCGTTCCT 59.884 55.000 0.00 0.00 0.00 3.36
2321 2444 1.358787 TGTTCTACCCCTCCGTTCCTA 59.641 52.381 0.00 0.00 0.00 2.94
2322 2445 2.225343 TGTTCTACCCCTCCGTTCCTAA 60.225 50.000 0.00 0.00 0.00 2.69
2323 2446 2.833943 GTTCTACCCCTCCGTTCCTAAA 59.166 50.000 0.00 0.00 0.00 1.85
2324 2447 3.409804 TCTACCCCTCCGTTCCTAAAT 57.590 47.619 0.00 0.00 0.00 1.40
2325 2448 4.541250 TCTACCCCTCCGTTCCTAAATA 57.459 45.455 0.00 0.00 0.00 1.40
2326 2449 5.083953 TCTACCCCTCCGTTCCTAAATAT 57.916 43.478 0.00 0.00 0.00 1.28
2327 2450 6.218195 TCTACCCCTCCGTTCCTAAATATA 57.782 41.667 0.00 0.00 0.00 0.86
2328 2451 6.808357 TCTACCCCTCCGTTCCTAAATATAT 58.192 40.000 0.00 0.00 0.00 0.86
2329 2452 5.757099 ACCCCTCCGTTCCTAAATATATG 57.243 43.478 0.00 0.00 0.00 1.78
2330 2453 5.408824 ACCCCTCCGTTCCTAAATATATGA 58.591 41.667 0.00 0.00 0.00 2.15
2331 2454 5.247792 ACCCCTCCGTTCCTAAATATATGAC 59.752 44.000 0.00 0.00 0.00 3.06
2332 2455 5.408356 CCCTCCGTTCCTAAATATATGACG 58.592 45.833 0.00 0.00 0.00 4.35
2333 2456 5.047519 CCCTCCGTTCCTAAATATATGACGT 60.048 44.000 0.00 0.00 0.00 4.34
2334 2457 6.453092 CCTCCGTTCCTAAATATATGACGTT 58.547 40.000 0.00 0.00 0.00 3.99
2335 2458 6.927381 CCTCCGTTCCTAAATATATGACGTTT 59.073 38.462 0.00 0.00 0.00 3.60
2336 2459 7.440255 CCTCCGTTCCTAAATATATGACGTTTT 59.560 37.037 0.00 0.00 0.00 2.43
2337 2460 8.133754 TCCGTTCCTAAATATATGACGTTTTG 57.866 34.615 0.00 0.00 0.00 2.44
2338 2461 7.225145 TCCGTTCCTAAATATATGACGTTTTGG 59.775 37.037 0.00 0.00 0.00 3.28
2339 2462 7.011669 CCGTTCCTAAATATATGACGTTTTGGT 59.988 37.037 0.00 0.00 32.19 3.67
2340 2463 9.033481 CGTTCCTAAATATATGACGTTTTGGTA 57.967 33.333 0.00 0.00 32.19 3.25
2613 2754 1.812571 GTCCATGTCGGTTTCAGCAAT 59.187 47.619 0.00 0.00 35.57 3.56
2629 2770 7.945033 TTCAGCAATGTTCCTTCAAAATTAC 57.055 32.000 0.00 0.00 0.00 1.89
2768 2918 4.783227 ACCATAGCTCCTACTCCTGAAAAA 59.217 41.667 0.00 0.00 0.00 1.94
2780 2930 6.248569 ACTCCTGAAAAAGAAACTACTCCA 57.751 37.500 0.00 0.00 0.00 3.86
2789 2939 2.957006 AGAAACTACTCCACACAGTCGT 59.043 45.455 0.00 0.00 0.00 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.318107 GTCGAGGTTCGGTTCGTGAA 60.318 55.000 0.00 0.00 40.88 3.18
1 2 1.168407 AGTCGAGGTTCGGTTCGTGA 61.168 55.000 0.00 0.00 40.88 4.35
11 12 1.132643 GTCATGCGTAGAGTCGAGGTT 59.867 52.381 0.00 0.00 0.00 3.50
19 20 0.802222 CCACACGGTCATGCGTAGAG 60.802 60.000 0.00 0.00 0.00 2.43
22 23 2.433491 GCCACACGGTCATGCGTA 60.433 61.111 0.00 0.00 33.28 4.42
27 28 4.722700 GCCAGGCCACACGGTCAT 62.723 66.667 5.01 0.00 40.51 3.06
80 83 1.007734 CTACGATGGCGCGGTACAT 60.008 57.895 8.83 0.00 42.48 2.29
111 117 1.496429 CCATATCACCTCAAAGGGGCT 59.504 52.381 0.00 0.00 39.16 5.19
112 118 1.479389 CCCATATCACCTCAAAGGGGC 60.479 57.143 0.00 0.00 39.16 5.80
128 134 1.630126 AAGGCAGACAGATCGCCCAT 61.630 55.000 5.09 0.00 42.20 4.00
156 162 3.765381 TCCATTGCCACAAGAAGATTCA 58.235 40.909 0.00 0.00 0.00 2.57
212 218 2.934553 GTCACTAGGGCCATTACGTTTC 59.065 50.000 6.18 0.00 0.00 2.78
228 234 1.979693 GAGGGCAGAGACCGTCACT 60.980 63.158 0.40 0.00 42.83 3.41
315 325 0.107508 CCACCGAACATCTCCTGCAT 60.108 55.000 0.00 0.00 0.00 3.96
319 329 1.194781 ACTGCCACCGAACATCTCCT 61.195 55.000 0.00 0.00 0.00 3.69
359 369 1.412710 TGAACTGCAACGAAGAGGTCT 59.587 47.619 0.00 0.00 0.00 3.85
373 383 1.153289 CGAGGGGATGCCTGAACTG 60.153 63.158 2.19 0.00 0.00 3.16
375 385 1.153349 GTCGAGGGGATGCCTGAAC 60.153 63.158 2.19 0.00 0.00 3.18
426 440 4.400961 AGAGCGTCCAGGCAAGGC 62.401 66.667 0.00 0.00 34.64 4.35
459 477 3.050619 GGAATACGTTGGATGACTAGCG 58.949 50.000 0.00 0.00 37.26 4.26
472 490 2.481449 GGCATGTCGAAGAGGAATACGT 60.481 50.000 0.00 0.00 36.95 3.57
496 514 3.000575 ACAAAATTTGAAAAACCGCGTCG 60.001 39.130 13.19 0.00 0.00 5.12
506 525 7.548780 AGCTGCAAGAAACTACAAAATTTGAAA 59.451 29.630 13.19 0.00 34.07 2.69
519 538 0.031178 CGCCAAAGCTGCAAGAAACT 59.969 50.000 1.02 0.00 34.07 2.66
571 590 2.953466 ATCAGCAATGGTGATGTTGC 57.047 45.000 24.84 6.69 46.87 4.17
580 599 2.890109 GCGCGGAGATCAGCAATGG 61.890 63.158 8.83 0.00 36.87 3.16
691 748 0.106769 TGAGGGCACAGCTCAACAAA 60.107 50.000 0.00 0.00 0.00 2.83
753 812 7.902920 AGGCCATCAAGTATCACAATAAAAT 57.097 32.000 5.01 0.00 0.00 1.82
771 851 0.763986 AGCAAACCACCAAAGGCCAT 60.764 50.000 5.01 0.00 0.00 4.40
833 913 6.803154 ATTTTACGCCATTTCTAGCCTATC 57.197 37.500 0.00 0.00 0.00 2.08
834 914 8.685838 TTAATTTTACGCCATTTCTAGCCTAT 57.314 30.769 0.00 0.00 0.00 2.57
835 915 8.564574 CATTAATTTTACGCCATTTCTAGCCTA 58.435 33.333 0.00 0.00 0.00 3.93
836 916 7.284489 TCATTAATTTTACGCCATTTCTAGCCT 59.716 33.333 0.00 0.00 0.00 4.58
837 917 7.422399 TCATTAATTTTACGCCATTTCTAGCC 58.578 34.615 0.00 0.00 0.00 3.93
838 918 8.850454 TTCATTAATTTTACGCCATTTCTAGC 57.150 30.769 0.00 0.00 0.00 3.42
840 920 9.959749 GGATTCATTAATTTTACGCCATTTCTA 57.040 29.630 0.00 0.00 0.00 2.10
841 921 7.647715 CGGATTCATTAATTTTACGCCATTTCT 59.352 33.333 0.00 0.00 0.00 2.52
842 922 7.646130 TCGGATTCATTAATTTTACGCCATTTC 59.354 33.333 0.00 0.00 0.00 2.17
843 923 7.484975 TCGGATTCATTAATTTTACGCCATTT 58.515 30.769 0.00 0.00 0.00 2.32
844 924 7.033530 TCGGATTCATTAATTTTACGCCATT 57.966 32.000 0.00 0.00 0.00 3.16
845 925 6.627395 TCGGATTCATTAATTTTACGCCAT 57.373 33.333 0.00 0.00 0.00 4.40
846 926 6.438259 TTCGGATTCATTAATTTTACGCCA 57.562 33.333 0.00 0.00 0.00 5.69
847 927 7.924103 AATTCGGATTCATTAATTTTACGCC 57.076 32.000 0.00 0.00 0.00 5.68
853 933 9.816354 CCCAGTAAAATTCGGATTCATTAATTT 57.184 29.630 0.00 0.00 34.00 1.82
854 934 8.977412 ACCCAGTAAAATTCGGATTCATTAATT 58.023 29.630 0.00 0.00 0.00 1.40
855 935 8.533569 ACCCAGTAAAATTCGGATTCATTAAT 57.466 30.769 0.00 0.00 0.00 1.40
856 936 7.948034 ACCCAGTAAAATTCGGATTCATTAA 57.052 32.000 0.00 0.00 0.00 1.40
857 937 7.948034 AACCCAGTAAAATTCGGATTCATTA 57.052 32.000 0.00 0.00 0.00 1.90
858 938 6.850752 AACCCAGTAAAATTCGGATTCATT 57.149 33.333 0.00 0.00 0.00 2.57
859 939 7.614192 AGTTAACCCAGTAAAATTCGGATTCAT 59.386 33.333 0.88 0.00 0.00 2.57
860 940 6.943718 AGTTAACCCAGTAAAATTCGGATTCA 59.056 34.615 0.88 0.00 0.00 2.57
861 941 7.387119 AGTTAACCCAGTAAAATTCGGATTC 57.613 36.000 0.88 0.00 0.00 2.52
862 942 7.770366 AAGTTAACCCAGTAAAATTCGGATT 57.230 32.000 0.88 0.00 0.00 3.01
863 943 7.884354 TGTAAGTTAACCCAGTAAAATTCGGAT 59.116 33.333 0.88 0.00 0.00 4.18
864 944 7.222872 TGTAAGTTAACCCAGTAAAATTCGGA 58.777 34.615 0.88 0.00 0.00 4.55
865 945 7.361457 CCTGTAAGTTAACCCAGTAAAATTCGG 60.361 40.741 0.88 0.00 0.00 4.30
866 946 7.524065 CCTGTAAGTTAACCCAGTAAAATTCG 58.476 38.462 0.88 0.00 0.00 3.34
867 947 7.176165 AGCCTGTAAGTTAACCCAGTAAAATTC 59.824 37.037 0.88 0.00 0.00 2.17
868 948 7.008332 AGCCTGTAAGTTAACCCAGTAAAATT 58.992 34.615 0.88 0.00 0.00 1.82
869 949 6.549242 AGCCTGTAAGTTAACCCAGTAAAAT 58.451 36.000 0.88 0.00 0.00 1.82
870 950 5.944135 AGCCTGTAAGTTAACCCAGTAAAA 58.056 37.500 0.88 0.00 0.00 1.52
871 951 5.571791 AGCCTGTAAGTTAACCCAGTAAA 57.428 39.130 0.88 0.00 0.00 2.01
872 952 6.018469 TCTAGCCTGTAAGTTAACCCAGTAA 58.982 40.000 0.88 0.00 0.00 2.24
873 953 5.582953 TCTAGCCTGTAAGTTAACCCAGTA 58.417 41.667 0.88 0.00 0.00 2.74
874 954 4.422984 TCTAGCCTGTAAGTTAACCCAGT 58.577 43.478 0.88 0.00 0.00 4.00
875 955 4.710375 TCTCTAGCCTGTAAGTTAACCCAG 59.290 45.833 0.88 6.30 0.00 4.45
876 956 4.465305 GTCTCTAGCCTGTAAGTTAACCCA 59.535 45.833 0.88 0.00 0.00 4.51
877 957 4.439837 CGTCTCTAGCCTGTAAGTTAACCC 60.440 50.000 0.88 0.00 0.00 4.11
878 958 4.439837 CCGTCTCTAGCCTGTAAGTTAACC 60.440 50.000 0.88 0.00 0.00 2.85
879 959 4.397417 TCCGTCTCTAGCCTGTAAGTTAAC 59.603 45.833 0.00 0.00 0.00 2.01
880 960 4.592942 TCCGTCTCTAGCCTGTAAGTTAA 58.407 43.478 0.00 0.00 0.00 2.01
881 961 4.197750 CTCCGTCTCTAGCCTGTAAGTTA 58.802 47.826 0.00 0.00 0.00 2.24
882 962 3.018149 CTCCGTCTCTAGCCTGTAAGTT 58.982 50.000 0.00 0.00 0.00 2.66
883 963 2.645802 CTCCGTCTCTAGCCTGTAAGT 58.354 52.381 0.00 0.00 0.00 2.24
884 964 1.950909 CCTCCGTCTCTAGCCTGTAAG 59.049 57.143 0.00 0.00 0.00 2.34
885 965 1.409802 CCCTCCGTCTCTAGCCTGTAA 60.410 57.143 0.00 0.00 0.00 2.41
886 966 0.183014 CCCTCCGTCTCTAGCCTGTA 59.817 60.000 0.00 0.00 0.00 2.74
887 967 1.076632 CCCTCCGTCTCTAGCCTGT 60.077 63.158 0.00 0.00 0.00 4.00
888 968 0.821711 CTCCCTCCGTCTCTAGCCTG 60.822 65.000 0.00 0.00 0.00 4.85
889 969 1.534697 CTCCCTCCGTCTCTAGCCT 59.465 63.158 0.00 0.00 0.00 4.58
890 970 2.197605 GCTCCCTCCGTCTCTAGCC 61.198 68.421 0.00 0.00 0.00 3.93
891 971 1.038130 TTGCTCCCTCCGTCTCTAGC 61.038 60.000 0.00 0.00 0.00 3.42
892 972 1.339610 CATTGCTCCCTCCGTCTCTAG 59.660 57.143 0.00 0.00 0.00 2.43
893 973 1.342076 ACATTGCTCCCTCCGTCTCTA 60.342 52.381 0.00 0.00 0.00 2.43
894 974 0.616111 ACATTGCTCCCTCCGTCTCT 60.616 55.000 0.00 0.00 0.00 3.10
895 975 1.112113 TACATTGCTCCCTCCGTCTC 58.888 55.000 0.00 0.00 0.00 3.36
896 976 0.824759 GTACATTGCTCCCTCCGTCT 59.175 55.000 0.00 0.00 0.00 4.18
897 977 0.179081 GGTACATTGCTCCCTCCGTC 60.179 60.000 0.00 0.00 0.00 4.79
912 994 4.019231 AGGGTCCAAGAAGAGAAATGGTAC 60.019 45.833 0.00 0.00 34.50 3.34
1077 1190 3.470888 CTGGGGAGGCTACGGTGG 61.471 72.222 0.00 0.00 0.00 4.61
1199 1312 1.144057 GGATGCGGAAGACGGTGAT 59.856 57.895 0.00 0.00 44.51 3.06
1276 1389 2.824880 TAGGTGGTGGTGGTGGTGC 61.825 63.158 0.00 0.00 0.00 5.01
1384 1497 2.579201 AGGATGTCCTTGACGCGG 59.421 61.111 12.47 0.00 46.09 6.46
1660 1773 0.862701 CACACAAACAGCAGCACACG 60.863 55.000 0.00 0.00 0.00 4.49
1712 1825 2.429610 CACTACTACGGCCCAACTACAT 59.570 50.000 0.00 0.00 0.00 2.29
1851 1969 5.846203 ACAATTAGCAACAGAGCAAACATT 58.154 33.333 0.00 0.00 36.85 2.71
1884 2002 1.003928 GATTACCAACGACCCCCAAGT 59.996 52.381 0.00 0.00 0.00 3.16
1892 2010 7.838771 ACCTAATAAACAGATTACCAACGAC 57.161 36.000 0.00 0.00 0.00 4.34
1966 2084 3.891366 AGACCTCCAAAGTTTCAACCATG 59.109 43.478 0.00 0.00 0.00 3.66
2086 2209 6.445786 ACTTGGGGTAAGTCAATGAATAGGTA 59.554 38.462 0.00 0.00 46.55 3.08
2149 2272 5.333339 CGATAGCACCAGATAAAATTGTCCG 60.333 44.000 0.00 0.00 0.00 4.79
2240 2363 7.676004 TCAAGAACATCTACCACTTGTCAATA 58.324 34.615 0.00 0.00 38.94 1.90
2309 2432 5.047519 ACGTCATATATTTAGGAACGGAGGG 60.048 44.000 0.00 0.00 0.00 4.30
2312 2435 7.225145 CCAAAACGTCATATATTTAGGAACGGA 59.775 37.037 0.00 0.00 0.00 4.69
2313 2436 7.011669 ACCAAAACGTCATATATTTAGGAACGG 59.988 37.037 0.00 0.00 0.00 4.44
2314 2437 7.912383 ACCAAAACGTCATATATTTAGGAACG 58.088 34.615 0.00 0.00 0.00 3.95
2387 2510 6.079336 TCCCTCCGTTCCTAAATATATGACA 58.921 40.000 0.00 0.00 0.00 3.58
2568 2709 5.710567 GCATTCCCCTTACCCAAGATATAAC 59.289 44.000 0.00 0.00 33.20 1.89
2613 2754 9.300681 AGATGAGATTGTAATTTTGAAGGAACA 57.699 29.630 0.00 0.00 0.00 3.18
2647 2788 4.330894 CGCATTTTGCATACTCTCTCTCAA 59.669 41.667 0.00 0.00 45.36 3.02
2648 2789 3.867493 CGCATTTTGCATACTCTCTCTCA 59.133 43.478 0.00 0.00 45.36 3.27
2755 2905 7.385478 GTGGAGTAGTTTCTTTTTCAGGAGTAG 59.615 40.741 0.00 0.00 0.00 2.57
2756 2906 7.147620 TGTGGAGTAGTTTCTTTTTCAGGAGTA 60.148 37.037 0.00 0.00 0.00 2.59
2757 2907 6.056236 GTGGAGTAGTTTCTTTTTCAGGAGT 58.944 40.000 0.00 0.00 0.00 3.85
2758 2908 6.017852 GTGTGGAGTAGTTTCTTTTTCAGGAG 60.018 42.308 0.00 0.00 0.00 3.69
2768 2918 2.957006 ACGACTGTGTGGAGTAGTTTCT 59.043 45.455 0.00 0.00 28.42 2.52
2780 2930 6.276832 ACTAATGGTATACAACGACTGTGT 57.723 37.500 5.01 1.91 39.20 3.72
2789 2939 3.455177 TGCCCGGAACTAATGGTATACAA 59.545 43.478 0.73 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.