Multiple sequence alignment - TraesCS2A01G462200

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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 TraesCS2A01G462200 chr2A 100.000 2899 0 0 1 2899 707795451 707798349 0.000000e+00 5354.0
1 TraesCS2A01G462200 chr2A 89.221 603 65 0 969 1571 707957877 707958479 0.000000e+00 754.0
2 TraesCS2A01G462200 chr2A 93.056 432 28 1 1836 2267 707958479 707958908 5.270000e-177 630.0
3 TraesCS2A01G462200 chr2A 88.889 54 5 1 2439 2491 707797919 707797972 6.710000e-07 65.8
4 TraesCS2A01G462200 chr2D 95.837 1297 50 3 971 2267 568308819 568310111 0.000000e+00 2093.0
5 TraesCS2A01G462200 chr2D 90.846 1300 112 5 969 2267 568464555 568465848 0.000000e+00 1735.0
6 TraesCS2A01G462200 chr2D 90.472 1186 100 7 1087 2267 568357759 568358936 0.000000e+00 1552.0
7 TraesCS2A01G462200 chr2D 88.547 358 22 6 1910 2267 568423406 568423744 1.610000e-112 416.0
8 TraesCS2A01G462200 chr2D 93.561 264 17 0 2004 2267 568445054 568445317 7.530000e-106 394.0
9 TraesCS2A01G462200 chr2D 80.616 552 64 30 2315 2852 27984432 27984954 1.260000e-103 387.0
10 TraesCS2A01G462200 chr2D 83.969 262 36 5 536 793 32777608 32777867 2.230000e-61 246.0
11 TraesCS2A01G462200 chr2B 95.528 1297 53 2 971 2267 680862747 680864038 0.000000e+00 2069.0
12 TraesCS2A01G462200 chr2B 82.367 414 48 15 134 526 36492822 36493231 1.290000e-88 337.0
13 TraesCS2A01G462200 chr2B 85.771 253 32 4 536 786 180427046 180427296 6.160000e-67 265.0
14 TraesCS2A01G462200 chr2B 83.333 222 26 2 2268 2478 4760499 4760720 8.200000e-46 195.0
15 TraesCS2A01G462200 chr2B 91.667 108 7 2 419 526 36493276 36493381 6.470000e-32 148.0
16 TraesCS2A01G462200 chr2B 100.000 32 0 0 1 32 36492794 36492825 3.120000e-05 60.2
17 TraesCS2A01G462200 chr2B 100.000 32 0 0 1 32 180426032 180426001 3.120000e-05 60.2
18 TraesCS2A01G462200 chr7A 80.851 1316 223 24 969 2267 705547291 705545988 0.000000e+00 1007.0
19 TraesCS2A01G462200 chr7A 96.727 550 12 4 1 544 190019041 190018492 0.000000e+00 911.0
20 TraesCS2A01G462200 chr7A 96.822 472 9 4 1 467 681922249 681922719 0.000000e+00 784.0
21 TraesCS2A01G462200 chr7A 97.257 401 9 1 395 793 190018494 190018094 0.000000e+00 678.0
22 TraesCS2A01G462200 chr7A 94.949 297 15 0 496 792 681922712 681923008 1.570000e-127 466.0
23 TraesCS2A01G462200 chr7A 78.056 638 76 37 2267 2899 40852662 40853240 7.690000e-91 344.0
24 TraesCS2A01G462200 chr7A 80.778 463 54 15 2268 2726 58336703 58337134 2.150000e-86 329.0
25 TraesCS2A01G462200 chr7B 77.040 1311 249 34 969 2267 730309861 730308591 0.000000e+00 706.0
26 TraesCS2A01G462200 chr7B 76.471 1190 240 28 1096 2267 704824984 704823817 6.870000e-171 610.0
27 TraesCS2A01G462200 chr7B 83.630 562 84 5 1712 2267 704826537 704825978 3.310000e-144 521.0
28 TraesCS2A01G462200 chr7B 94.545 110 6 0 28 137 683101575 683101466 1.380000e-38 171.0
29 TraesCS2A01G462200 chr1A 85.977 599 41 20 2268 2845 566191910 566192486 4.130000e-168 601.0
30 TraesCS2A01G462200 chr1A 85.606 396 35 3 2471 2845 566164675 566165069 2.090000e-106 396.0
31 TraesCS2A01G462200 chr1A 92.019 213 16 1 2268 2480 566164503 566164714 6.070000e-77 298.0
32 TraesCS2A01G462200 chr1A 90.000 220 13 4 2274 2484 482257318 482257099 2.850000e-70 276.0
33 TraesCS2A01G462200 chr1A 86.592 179 24 0 2721 2899 575815631 575815809 6.340000e-47 198.0
34 TraesCS2A01G462200 chr6A 81.221 655 77 20 2268 2899 27375865 27376496 1.210000e-133 486.0
35 TraesCS2A01G462200 chr7D 76.641 899 184 21 970 1853 613767191 613766304 9.400000e-130 473.0
36 TraesCS2A01G462200 chr7D 85.337 416 52 5 1858 2267 613765888 613765476 3.450000e-114 422.0
37 TraesCS2A01G462200 chr7D 83.805 389 40 12 134 503 620262873 620263257 5.950000e-92 348.0
38 TraesCS2A01G462200 chr7D 83.590 390 40 13 134 503 217966884 217966499 7.690000e-91 344.0
39 TraesCS2A01G462200 chr7D 91.045 67 6 0 830 896 107478670 107478736 1.110000e-14 91.6
40 TraesCS2A01G462200 chr7D 100.000 32 0 0 1 32 217966912 217966881 3.120000e-05 60.2
41 TraesCS2A01G462200 chr7D 100.000 32 0 0 1 32 620262845 620262876 3.120000e-05 60.2
42 TraesCS2A01G462200 chr3A 79.040 625 77 36 2267 2889 691360917 691360345 2.110000e-101 379.0
43 TraesCS2A01G462200 chr3A 88.703 239 25 2 555 792 44583077 44582840 1.020000e-74 291.0
44 TraesCS2A01G462200 chr3A 84.739 249 34 4 548 792 63427301 63427053 2.230000e-61 246.0
45 TraesCS2A01G462200 chr3A 100.000 32 0 0 1 32 63433477 63433508 3.120000e-05 60.2
46 TraesCS2A01G462200 chr5D 84.019 413 42 14 134 527 114474259 114474666 2.730000e-100 375.0
47 TraesCS2A01G462200 chr5D 86.911 191 16 8 2267 2455 552376399 552376216 3.790000e-49 206.0
48 TraesCS2A01G462200 chr5D 95.495 111 5 0 30 140 365693410 365693300 8.250000e-41 178.0
49 TraesCS2A01G462200 chr5D 93.694 111 6 1 28 138 382294703 382294594 6.430000e-37 165.0
50 TraesCS2A01G462200 chr5D 100.000 32 0 0 1 32 114474231 114474262 3.120000e-05 60.2
51 TraesCS2A01G462200 chr1D 79.229 597 77 29 2315 2899 37567600 37567039 3.530000e-99 372.0
52 TraesCS2A01G462200 chr1B 78.213 638 90 24 2268 2899 553909734 553909140 2.120000e-96 363.0
53 TraesCS2A01G462200 chr1B 92.857 98 7 0 830 927 486819658 486819755 3.010000e-30 143.0
54 TraesCS2A01G462200 chr4D 83.173 416 38 15 2315 2726 502057832 502058219 4.600000e-93 351.0
55 TraesCS2A01G462200 chr6B 85.135 296 33 6 2269 2564 271833218 271833502 2.830000e-75 292.0
56 TraesCS2A01G462200 chr6B 88.194 144 17 0 2717 2860 271833902 271834045 3.840000e-39 172.0
57 TraesCS2A01G462200 chr6B 100.000 32 0 0 1 32 36218325 36218294 3.120000e-05 60.2
58 TraesCS2A01G462200 chr3B 85.769 260 33 4 536 793 545382286 545382029 3.680000e-69 272.0
59 TraesCS2A01G462200 chr3B 79.236 419 54 13 138 535 545382941 545383347 7.970000e-66 261.0
60 TraesCS2A01G462200 chr3B 84.942 259 35 4 536 792 525618659 525618915 2.870000e-65 259.0
61 TraesCS2A01G462200 chr3B 77.914 326 39 23 2255 2577 237244187 237243892 3.840000e-39 172.0
62 TraesCS2A01G462200 chr3B 85.321 109 13 3 430 538 525614556 525614451 3.050000e-20 110.0
63 TraesCS2A01G462200 chr3D 95.495 111 5 0 29 139 43996207 43996317 8.250000e-41 178.0
64 TraesCS2A01G462200 chr3D 93.636 110 7 0 28 137 536331030 536331139 6.430000e-37 165.0
65 TraesCS2A01G462200 chr3D 93.578 109 7 0 30 138 30363627 30363735 2.310000e-36 163.0
66 TraesCS2A01G462200 chr5A 93.694 111 7 0 30 140 467377559 467377449 1.790000e-37 167.0
67 TraesCS2A01G462200 chr5A 90.476 63 5 1 134 196 631972939 631972878 6.660000e-12 82.4
68 TraesCS2A01G462200 chrUn 86.577 149 20 0 646 794 335951323 335951175 6.430000e-37 165.0
69 TraesCS2A01G462200 chr5B 86.667 75 10 0 833 907 375619640 375619566 1.850000e-12 84.2


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 TraesCS2A01G462200 chr2A 707795451 707798349 2898 False 2709.9 5354 94.4445 1 2899 2 chr2A.!!$F1 2898
1 TraesCS2A01G462200 chr2A 707957877 707958908 1031 False 692.0 754 91.1385 969 2267 2 chr2A.!!$F2 1298
2 TraesCS2A01G462200 chr2D 568308819 568310111 1292 False 2093.0 2093 95.8370 971 2267 1 chr2D.!!$F3 1296
3 TraesCS2A01G462200 chr2D 568464555 568465848 1293 False 1735.0 1735 90.8460 969 2267 1 chr2D.!!$F7 1298
4 TraesCS2A01G462200 chr2D 568357759 568358936 1177 False 1552.0 1552 90.4720 1087 2267 1 chr2D.!!$F4 1180
5 TraesCS2A01G462200 chr2D 27984432 27984954 522 False 387.0 387 80.6160 2315 2852 1 chr2D.!!$F1 537
6 TraesCS2A01G462200 chr2B 680862747 680864038 1291 False 2069.0 2069 95.5280 971 2267 1 chr2B.!!$F3 1296
7 TraesCS2A01G462200 chr7A 705545988 705547291 1303 True 1007.0 1007 80.8510 969 2267 1 chr7A.!!$R1 1298
8 TraesCS2A01G462200 chr7A 190018094 190019041 947 True 794.5 911 96.9920 1 793 2 chr7A.!!$R2 792
9 TraesCS2A01G462200 chr7A 681922249 681923008 759 False 625.0 784 95.8855 1 792 2 chr7A.!!$F3 791
10 TraesCS2A01G462200 chr7A 40852662 40853240 578 False 344.0 344 78.0560 2267 2899 1 chr7A.!!$F1 632
11 TraesCS2A01G462200 chr7B 730308591 730309861 1270 True 706.0 706 77.0400 969 2267 1 chr7B.!!$R2 1298
12 TraesCS2A01G462200 chr7B 704823817 704826537 2720 True 565.5 610 80.0505 1096 2267 2 chr7B.!!$R3 1171
13 TraesCS2A01G462200 chr1A 566191910 566192486 576 False 601.0 601 85.9770 2268 2845 1 chr1A.!!$F1 577
14 TraesCS2A01G462200 chr1A 566164503 566165069 566 False 347.0 396 88.8125 2268 2845 2 chr1A.!!$F3 577
15 TraesCS2A01G462200 chr6A 27375865 27376496 631 False 486.0 486 81.2210 2268 2899 1 chr6A.!!$F1 631
16 TraesCS2A01G462200 chr7D 613765476 613767191 1715 True 447.5 473 80.9890 970 2267 2 chr7D.!!$R2 1297
17 TraesCS2A01G462200 chr3A 691360345 691360917 572 True 379.0 379 79.0400 2267 2889 1 chr3A.!!$R3 622
18 TraesCS2A01G462200 chr1D 37567039 37567600 561 True 372.0 372 79.2290 2315 2899 1 chr1D.!!$R1 584
19 TraesCS2A01G462200 chr1B 553909140 553909734 594 True 363.0 363 78.2130 2268 2899 1 chr1B.!!$R1 631
20 TraesCS2A01G462200 chr6B 271833218 271834045 827 False 232.0 292 86.6645 2269 2860 2 chr6B.!!$F1 591

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
822 980 0.095935 CACTTATGTGAGCACGCAGC 59.904 55.0 3.31 0.0 46.55 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2744 3908 0.035439 ACCATAGGTTTGAGGCGGTG 60.035 55.0 0.0 0.0 27.29 4.94 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
70 71 8.821147 TTTTATAAGACGTTTCAGACAGCTTA 57.179 30.769 0.00 0.00 0.00 3.09
295 298 0.679640 CAGCCCATTTAACCTCCGCA 60.680 55.000 0.00 0.00 0.00 5.69
439 445 1.591703 GTCTCAGGTGACATGCGGA 59.408 57.895 0.00 0.00 36.97 5.54
480 636 3.314080 TGACAAAATCTTCCCACGTCAAC 59.686 43.478 0.00 0.00 0.00 3.18
724 882 2.772568 TTTCGCACCACTTCAATGTG 57.227 45.000 0.00 0.00 37.66 3.21
730 888 1.032014 ACCACTTCAATGTGCACCAC 58.968 50.000 15.69 0.00 36.68 4.16
742 900 1.535462 GTGCACCACGACTTTTAGCAT 59.465 47.619 5.22 0.00 32.75 3.79
794 952 5.382303 CACCACGAATGTAATTGACTCAAC 58.618 41.667 0.00 0.00 36.07 3.18
795 953 5.179368 CACCACGAATGTAATTGACTCAACT 59.821 40.000 0.00 0.00 36.07 3.16
796 954 5.763204 ACCACGAATGTAATTGACTCAACTT 59.237 36.000 0.00 0.00 36.07 2.66
797 955 6.073222 ACCACGAATGTAATTGACTCAACTTC 60.073 38.462 0.00 0.00 36.07 3.01
798 956 6.073276 CCACGAATGTAATTGACTCAACTTCA 60.073 38.462 0.00 0.00 36.07 3.02
799 957 7.351981 CACGAATGTAATTGACTCAACTTCAA 58.648 34.615 0.00 0.00 36.07 2.69
801 959 8.567948 ACGAATGTAATTGACTCAACTTCAAAT 58.432 29.630 0.00 0.00 36.07 2.32
806 964 9.337396 TGTAATTGACTCAACTTCAAATACACT 57.663 29.630 8.30 0.00 41.32 3.55
813 971 8.902540 ACTCAACTTCAAATACACTTATGTGA 57.097 30.769 15.13 0.41 46.55 3.58
814 972 8.993121 ACTCAACTTCAAATACACTTATGTGAG 58.007 33.333 15.13 3.35 46.55 3.51
815 973 7.806690 TCAACTTCAAATACACTTATGTGAGC 58.193 34.615 15.13 0.00 46.55 4.26
816 974 7.443879 TCAACTTCAAATACACTTATGTGAGCA 59.556 33.333 15.13 1.24 46.55 4.26
817 975 7.133891 ACTTCAAATACACTTATGTGAGCAC 57.866 36.000 15.13 0.00 46.55 4.40
818 976 5.778161 TCAAATACACTTATGTGAGCACG 57.222 39.130 15.13 1.87 46.55 5.34
819 977 4.092821 TCAAATACACTTATGTGAGCACGC 59.907 41.667 15.13 0.00 46.55 5.34
820 978 2.734276 TACACTTATGTGAGCACGCA 57.266 45.000 15.13 0.00 46.55 5.24
822 980 0.095935 CACTTATGTGAGCACGCAGC 59.904 55.000 3.31 0.00 46.55 5.25
823 981 2.532666 CACTTATGTGAGCACGCAGCA 61.533 52.381 3.31 0.00 46.55 4.41
824 982 4.607946 CACTTATGTGAGCACGCAGCAC 62.608 54.545 3.31 7.76 46.55 4.40
835 993 3.726517 GCAGCACGCACGGACAAT 61.727 61.111 0.00 0.00 41.79 2.71
836 994 2.174107 CAGCACGCACGGACAATG 59.826 61.111 0.00 0.00 0.00 2.82
837 995 2.280797 AGCACGCACGGACAATGT 60.281 55.556 0.00 0.00 0.00 2.71
838 996 1.891919 AGCACGCACGGACAATGTT 60.892 52.632 0.00 0.00 0.00 2.71
839 997 0.601576 AGCACGCACGGACAATGTTA 60.602 50.000 0.00 0.00 0.00 2.41
840 998 0.179225 GCACGCACGGACAATGTTAG 60.179 55.000 0.00 0.00 0.00 2.34
841 999 1.424403 CACGCACGGACAATGTTAGA 58.576 50.000 0.00 0.00 0.00 2.10
842 1000 1.126113 CACGCACGGACAATGTTAGAC 59.874 52.381 0.00 0.00 0.00 2.59
843 1001 0.719465 CGCACGGACAATGTTAGACC 59.281 55.000 0.00 0.00 0.00 3.85
845 1003 2.416296 CGCACGGACAATGTTAGACCTA 60.416 50.000 0.00 0.00 0.00 3.08
847 1005 3.176708 CACGGACAATGTTAGACCTACG 58.823 50.000 0.00 0.00 0.00 3.51
848 1006 2.821969 ACGGACAATGTTAGACCTACGT 59.178 45.455 0.00 0.00 0.00 3.57
851 1009 4.795278 CGGACAATGTTAGACCTACGTAAC 59.205 45.833 0.00 0.00 0.00 2.50
852 1010 5.619757 CGGACAATGTTAGACCTACGTAACA 60.620 44.000 2.09 2.09 41.98 2.41
853 1011 6.158598 GGACAATGTTAGACCTACGTAACAA 58.841 40.000 3.64 0.00 41.31 2.83
854 1012 6.309737 GGACAATGTTAGACCTACGTAACAAG 59.690 42.308 3.64 3.10 41.31 3.16
855 1013 6.752168 ACAATGTTAGACCTACGTAACAAGT 58.248 36.000 3.64 3.63 41.31 3.16
856 1014 6.643770 ACAATGTTAGACCTACGTAACAAGTG 59.356 38.462 3.64 7.47 41.31 3.16
857 1015 5.772825 TGTTAGACCTACGTAACAAGTGT 57.227 39.130 0.00 0.00 36.45 3.55
858 1016 6.147864 TGTTAGACCTACGTAACAAGTGTT 57.852 37.500 1.75 1.75 36.45 3.32
888 1046 2.713927 CGTAAATAGCAACGTGGAGC 57.286 50.000 0.00 0.00 34.48 4.70
889 1047 1.996898 CGTAAATAGCAACGTGGAGCA 59.003 47.619 10.03 0.00 34.48 4.26
890 1048 2.607635 CGTAAATAGCAACGTGGAGCAT 59.392 45.455 10.03 0.58 34.48 3.79
891 1049 3.063452 CGTAAATAGCAACGTGGAGCATT 59.937 43.478 10.03 5.60 34.48 3.56
892 1050 4.269123 CGTAAATAGCAACGTGGAGCATTA 59.731 41.667 10.03 4.49 34.48 1.90
894 1052 5.835113 AAATAGCAACGTGGAGCATTATT 57.165 34.783 10.03 4.38 0.00 1.40
895 1053 6.935741 AAATAGCAACGTGGAGCATTATTA 57.064 33.333 10.03 0.00 0.00 0.98
896 1054 6.545504 AATAGCAACGTGGAGCATTATTAG 57.454 37.500 10.03 0.00 0.00 1.73
898 1056 3.623060 AGCAACGTGGAGCATTATTAGTG 59.377 43.478 10.03 0.00 0.00 2.74
899 1057 3.242739 GCAACGTGGAGCATTATTAGTGG 60.243 47.826 0.00 0.00 0.00 4.00
900 1058 4.188462 CAACGTGGAGCATTATTAGTGGA 58.812 43.478 0.00 0.00 0.00 4.02
902 1060 5.036117 ACGTGGAGCATTATTAGTGGATT 57.964 39.130 0.00 0.00 0.00 3.01
903 1061 6.169557 ACGTGGAGCATTATTAGTGGATTA 57.830 37.500 0.00 0.00 0.00 1.75
904 1062 6.769512 ACGTGGAGCATTATTAGTGGATTAT 58.230 36.000 0.00 0.00 0.00 1.28
905 1063 7.224297 ACGTGGAGCATTATTAGTGGATTATT 58.776 34.615 0.00 0.00 0.00 1.40
906 1064 8.372459 ACGTGGAGCATTATTAGTGGATTATTA 58.628 33.333 0.00 0.00 0.00 0.98
908 1066 9.167311 GTGGAGCATTATTAGTGGATTATTAGG 57.833 37.037 0.00 0.00 0.00 2.69
909 1067 8.890472 TGGAGCATTATTAGTGGATTATTAGGT 58.110 33.333 0.00 0.00 0.00 3.08
910 1068 9.167311 GGAGCATTATTAGTGGATTATTAGGTG 57.833 37.037 0.00 0.00 0.00 4.00
911 1069 9.726438 GAGCATTATTAGTGGATTATTAGGTGT 57.274 33.333 0.00 0.00 0.00 4.16
912 1070 9.507329 AGCATTATTAGTGGATTATTAGGTGTG 57.493 33.333 0.00 0.00 0.00 3.82
913 1071 9.502091 GCATTATTAGTGGATTATTAGGTGTGA 57.498 33.333 0.00 0.00 0.00 3.58
916 1074 6.494666 TTAGTGGATTATTAGGTGTGAGGG 57.505 41.667 0.00 0.00 0.00 4.30
918 1076 2.441750 TGGATTATTAGGTGTGAGGGGC 59.558 50.000 0.00 0.00 0.00 5.80
919 1077 2.224793 GGATTATTAGGTGTGAGGGGCC 60.225 54.545 0.00 0.00 0.00 5.80
920 1078 1.218844 TTATTAGGTGTGAGGGGCCC 58.781 55.000 17.12 17.12 0.00 5.80
921 1079 0.696485 TATTAGGTGTGAGGGGCCCC 60.696 60.000 35.90 35.90 0.00 5.80
922 1080 2.798760 ATTAGGTGTGAGGGGCCCCA 62.799 60.000 42.48 21.63 38.92 4.96
933 1091 2.863275 GGCCCCACCCCCTAAAAA 59.137 61.111 0.00 0.00 0.00 1.94
934 1092 1.394557 GGCCCCACCCCCTAAAAAT 59.605 57.895 0.00 0.00 0.00 1.82
935 1093 0.980754 GGCCCCACCCCCTAAAAATG 60.981 60.000 0.00 0.00 0.00 2.32
937 1095 3.315544 CCCACCCCCTAAAAATGGG 57.684 57.895 0.00 0.00 44.02 4.00
961 1119 2.744377 GGGGGCGAGAAGATAGGC 59.256 66.667 0.00 0.00 0.00 3.93
962 1120 2.140792 GGGGGCGAGAAGATAGGCA 61.141 63.158 0.00 0.00 0.00 4.75
966 1124 1.134371 GGGCGAGAAGATAGGCAAGTT 60.134 52.381 0.00 0.00 0.00 2.66
967 1125 2.102588 GGGCGAGAAGATAGGCAAGTTA 59.897 50.000 0.00 0.00 0.00 2.24
1007 1165 4.760047 GCGCGAGGTCATGGTGGT 62.760 66.667 12.10 0.00 0.00 4.16
1014 1172 2.819595 GTCATGGTGGTGCGCGAT 60.820 61.111 12.10 0.00 0.00 4.58
1029 1187 3.713936 CGATGTAGACTTCGCCACA 57.286 52.632 5.20 0.00 36.87 4.17
1068 1228 2.131709 CCGCCTGTCTATCCCCGAA 61.132 63.158 0.00 0.00 0.00 4.30
1452 1915 0.454600 GTCAGATGAAGCGGTACCGA 59.545 55.000 37.62 17.49 42.83 4.69
1896 2790 0.673644 GAACTACATGCGCCTGGTGT 60.674 55.000 17.19 12.79 0.00 4.16
1897 2791 0.955428 AACTACATGCGCCTGGTGTG 60.955 55.000 17.19 2.70 0.00 3.82
1962 2859 3.777925 GCGCGAGTGCATGAACGT 61.778 61.111 12.10 0.00 42.97 3.99
2023 2920 4.680237 CTCGTCAACGCCTGGGCA 62.680 66.667 12.34 0.00 42.06 5.36
2219 3122 0.727398 GCTGCTGTACCATTTCGACC 59.273 55.000 0.00 0.00 0.00 4.79
2288 3191 7.130917 GGAGTGTTAGACTGTATATACACGTG 58.869 42.308 15.48 15.48 40.44 4.49
2330 3233 7.839907 ACTGTAACGTTGTATTGTATCCCTTA 58.160 34.615 11.99 0.00 0.00 2.69
2436 3344 0.808847 GGGTTACGATGTCTTCCGCC 60.809 60.000 0.00 0.00 0.00 6.13
2437 3351 0.108520 GGTTACGATGTCTTCCGCCA 60.109 55.000 0.00 0.00 0.00 5.69
2579 3517 4.115199 GGCCTTCGGTGCCTCCAT 62.115 66.667 0.00 0.00 45.70 3.41
2590 3528 2.818132 CCTCCATCTCGCCAGACC 59.182 66.667 0.00 0.00 0.00 3.85
2739 3903 4.760047 CCCCTGCCGTCGTCTTGG 62.760 72.222 0.00 0.00 0.00 3.61
2874 4140 1.756408 TTCAAACCTACCCGGCGTCA 61.756 55.000 6.01 0.00 35.61 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
295 298 3.961477 TGTATTTTAATCGCAGCGCAT 57.039 38.095 10.87 3.40 0.00 4.73
439 445 3.515901 GTCACCTCTATGAGAAGTGGGTT 59.484 47.826 5.60 0.00 34.98 4.11
641 799 2.276116 GGAGTCGGTGCTGACCAGA 61.276 63.158 7.47 0.00 43.33 3.86
724 882 1.804151 TGATGCTAAAAGTCGTGGTGC 59.196 47.619 0.00 0.00 0.00 5.01
730 888 5.698832 TGGTCATTTTGATGCTAAAAGTCG 58.301 37.500 0.00 0.00 33.49 4.18
742 900 6.627395 ACTTGACGTAAATGGTCATTTTGA 57.373 33.333 13.24 0.00 43.37 2.69
794 952 6.243551 CGTGCTCACATAAGTGTATTTGAAG 58.756 40.000 0.00 0.00 46.01 3.02
795 953 5.390461 GCGTGCTCACATAAGTGTATTTGAA 60.390 40.000 0.00 0.00 46.01 2.69
796 954 4.092821 GCGTGCTCACATAAGTGTATTTGA 59.907 41.667 0.00 0.00 46.01 2.69
797 955 4.142924 TGCGTGCTCACATAAGTGTATTTG 60.143 41.667 0.00 0.00 46.01 2.32
798 956 4.000325 TGCGTGCTCACATAAGTGTATTT 59.000 39.130 0.00 0.00 46.01 1.40
799 957 3.595173 TGCGTGCTCACATAAGTGTATT 58.405 40.909 0.00 0.00 46.01 1.89
801 959 2.606108 CTGCGTGCTCACATAAGTGTA 58.394 47.619 0.00 0.00 46.01 2.90
802 960 1.432514 CTGCGTGCTCACATAAGTGT 58.567 50.000 0.00 0.00 46.01 3.55
803 961 2.532666 TGCTGCGTGCTCACATAAGTG 61.533 52.381 0.00 0.00 42.53 3.16
804 962 0.320683 TGCTGCGTGCTCACATAAGT 60.321 50.000 0.00 0.00 43.37 2.24
805 963 0.095935 GTGCTGCGTGCTCACATAAG 59.904 55.000 11.10 0.00 43.37 1.73
806 964 1.625759 CGTGCTGCGTGCTCACATAA 61.626 55.000 14.56 0.00 43.37 1.90
807 965 2.094066 CGTGCTGCGTGCTCACATA 61.094 57.895 14.56 0.00 43.37 2.29
808 966 3.417224 CGTGCTGCGTGCTCACAT 61.417 61.111 14.56 0.00 43.37 3.21
818 976 3.726517 ATTGTCCGTGCGTGCTGC 61.727 61.111 0.00 0.00 46.70 5.25
819 977 2.116736 AACATTGTCCGTGCGTGCTG 62.117 55.000 0.00 0.00 0.00 4.41
820 978 0.601576 TAACATTGTCCGTGCGTGCT 60.602 50.000 0.00 0.00 0.00 4.40
822 980 1.126113 GTCTAACATTGTCCGTGCGTG 59.874 52.381 0.00 0.00 0.00 5.34
823 981 1.425412 GTCTAACATTGTCCGTGCGT 58.575 50.000 0.00 0.00 0.00 5.24
824 982 0.719465 GGTCTAACATTGTCCGTGCG 59.281 55.000 0.00 0.00 0.00 5.34
825 983 2.094762 AGGTCTAACATTGTCCGTGC 57.905 50.000 0.00 0.00 0.00 5.34
826 984 3.176708 CGTAGGTCTAACATTGTCCGTG 58.823 50.000 0.00 0.00 0.00 4.94
827 985 2.821969 ACGTAGGTCTAACATTGTCCGT 59.178 45.455 0.00 0.00 0.00 4.69
828 986 3.498927 ACGTAGGTCTAACATTGTCCG 57.501 47.619 0.00 0.00 0.00 4.79
829 987 5.713025 TGTTACGTAGGTCTAACATTGTCC 58.287 41.667 0.00 0.00 29.72 4.02
830 988 6.865205 ACTTGTTACGTAGGTCTAACATTGTC 59.135 38.462 5.09 0.00 33.82 3.18
831 989 6.643770 CACTTGTTACGTAGGTCTAACATTGT 59.356 38.462 5.09 5.26 33.82 2.71
832 990 6.643770 ACACTTGTTACGTAGGTCTAACATTG 59.356 38.462 5.09 7.72 33.82 2.82
833 991 6.752168 ACACTTGTTACGTAGGTCTAACATT 58.248 36.000 5.09 0.00 33.82 2.71
834 992 6.336842 ACACTTGTTACGTAGGTCTAACAT 57.663 37.500 5.09 0.00 33.82 2.71
835 993 5.772825 ACACTTGTTACGTAGGTCTAACA 57.227 39.130 0.00 0.00 32.26 2.41
848 1006 5.313749 CGTAAAGCACGTAACACTTGTTA 57.686 39.130 0.00 0.00 45.82 2.41
871 1029 6.935741 AATAATGCTCCACGTTGCTATTTA 57.064 33.333 6.53 3.62 0.00 1.40
872 1030 5.835113 AATAATGCTCCACGTTGCTATTT 57.165 34.783 6.53 1.96 0.00 1.40
874 1032 5.466728 CACTAATAATGCTCCACGTTGCTAT 59.533 40.000 6.53 0.00 0.00 2.97
875 1033 4.808895 CACTAATAATGCTCCACGTTGCTA 59.191 41.667 6.53 0.00 0.00 3.49
876 1034 3.623060 CACTAATAATGCTCCACGTTGCT 59.377 43.478 6.53 0.00 0.00 3.91
877 1035 3.242739 CCACTAATAATGCTCCACGTTGC 60.243 47.826 0.00 0.00 0.00 4.17
878 1036 4.188462 TCCACTAATAATGCTCCACGTTG 58.812 43.478 0.00 0.00 0.00 4.10
880 1038 4.689612 ATCCACTAATAATGCTCCACGT 57.310 40.909 0.00 0.00 0.00 4.49
881 1039 7.672983 AATAATCCACTAATAATGCTCCACG 57.327 36.000 0.00 0.00 0.00 4.94
882 1040 9.167311 CCTAATAATCCACTAATAATGCTCCAC 57.833 37.037 0.00 0.00 0.00 4.02
883 1041 8.890472 ACCTAATAATCCACTAATAATGCTCCA 58.110 33.333 0.00 0.00 0.00 3.86
884 1042 9.167311 CACCTAATAATCCACTAATAATGCTCC 57.833 37.037 0.00 0.00 0.00 4.70
885 1043 9.726438 ACACCTAATAATCCACTAATAATGCTC 57.274 33.333 0.00 0.00 0.00 4.26
886 1044 9.507329 CACACCTAATAATCCACTAATAATGCT 57.493 33.333 0.00 0.00 0.00 3.79
890 1048 8.656806 CCCTCACACCTAATAATCCACTAATAA 58.343 37.037 0.00 0.00 0.00 1.40
891 1049 7.236847 CCCCTCACACCTAATAATCCACTAATA 59.763 40.741 0.00 0.00 0.00 0.98
892 1050 6.044404 CCCCTCACACCTAATAATCCACTAAT 59.956 42.308 0.00 0.00 0.00 1.73
894 1052 4.905456 CCCCTCACACCTAATAATCCACTA 59.095 45.833 0.00 0.00 0.00 2.74
895 1053 3.716872 CCCCTCACACCTAATAATCCACT 59.283 47.826 0.00 0.00 0.00 4.00
896 1054 3.747708 GCCCCTCACACCTAATAATCCAC 60.748 52.174 0.00 0.00 0.00 4.02
898 1056 2.224793 GGCCCCTCACACCTAATAATCC 60.225 54.545 0.00 0.00 0.00 3.01
899 1057 2.224793 GGGCCCCTCACACCTAATAATC 60.225 54.545 12.23 0.00 0.00 1.75
900 1058 1.780919 GGGCCCCTCACACCTAATAAT 59.219 52.381 12.23 0.00 0.00 1.28
902 1060 0.696485 GGGGCCCCTCACACCTAATA 60.696 60.000 35.49 0.00 0.00 0.98
903 1061 2.006991 GGGGCCCCTCACACCTAAT 61.007 63.158 35.49 0.00 0.00 1.73
904 1062 2.612746 GGGGCCCCTCACACCTAA 60.613 66.667 35.49 0.00 0.00 2.69
905 1063 3.948360 TGGGGCCCCTCACACCTA 61.948 66.667 40.66 16.48 36.94 3.08
916 1074 0.980754 CATTTTTAGGGGGTGGGGCC 60.981 60.000 0.00 0.00 0.00 5.80
918 1076 0.326143 CCCATTTTTAGGGGGTGGGG 60.326 60.000 0.75 0.00 44.62 4.96
919 1077 3.315544 CCCATTTTTAGGGGGTGGG 57.684 57.895 0.00 0.00 42.90 4.61
944 1102 1.696097 TTGCCTATCTTCTCGCCCCC 61.696 60.000 0.00 0.00 0.00 5.40
945 1103 0.250081 CTTGCCTATCTTCTCGCCCC 60.250 60.000 0.00 0.00 0.00 5.80
947 1105 2.317530 AACTTGCCTATCTTCTCGCC 57.682 50.000 0.00 0.00 0.00 5.54
948 1106 3.670991 CGATAACTTGCCTATCTTCTCGC 59.329 47.826 0.00 0.00 0.00 5.03
949 1107 3.670991 GCGATAACTTGCCTATCTTCTCG 59.329 47.826 0.00 0.00 0.00 4.04
960 1118 0.876342 CGGAGGAGGCGATAACTTGC 60.876 60.000 0.00 0.00 0.00 4.01
961 1119 0.876342 GCGGAGGAGGCGATAACTTG 60.876 60.000 0.00 0.00 0.00 3.16
962 1120 1.327690 TGCGGAGGAGGCGATAACTT 61.328 55.000 0.00 0.00 0.00 2.66
966 1124 2.194212 GTCTGCGGAGGAGGCGATA 61.194 63.158 3.37 0.00 43.12 2.92
967 1125 3.532155 GTCTGCGGAGGAGGCGAT 61.532 66.667 3.37 0.00 43.12 4.58
1007 1165 4.377471 CGAAGTCTACATCGCGCA 57.623 55.556 8.75 0.00 30.38 6.09
1014 1172 1.372499 GCGTGTGGCGAAGTCTACA 60.372 57.895 0.00 0.00 44.77 2.74
1068 1228 2.066999 GGCGATCCCCTCTGTTCCT 61.067 63.158 0.00 0.00 0.00 3.36
1130 1589 1.285950 CTGAACAGCTCGACGGTGA 59.714 57.895 17.10 0.00 43.75 4.02
1240 1699 1.301716 GCTTGCTGAGGTTCACCGA 60.302 57.895 0.00 0.00 42.08 4.69
1307 1766 1.460689 TCCCGGTCCTTGAACCTGT 60.461 57.895 0.00 0.00 37.15 4.00
1434 1893 0.738975 CTCGGTACCGCTTCATCTGA 59.261 55.000 29.64 7.92 39.59 3.27
1680 2156 4.211164 ACGATACATTACATGCATGAACGG 59.789 41.667 32.75 19.73 0.00 4.44
1838 2321 3.521937 CCTCTATTACCTTGGGTTGTCCA 59.478 47.826 0.00 0.00 45.43 4.02
1948 2842 1.417592 GCAGACGTTCATGCACTCG 59.582 57.895 14.23 0.00 42.11 4.18
2155 3058 1.375396 CAAGCCGAACGACATCCCA 60.375 57.895 0.00 0.00 0.00 4.37
2288 3191 4.939052 ACAGTACATGTATACAGAGGCC 57.061 45.455 9.18 0.00 41.60 5.19
2371 3274 2.951475 TTTGGGGACTGCACGACACC 62.951 60.000 0.00 0.00 0.00 4.16
2411 3315 4.202080 CGGAAGACATCGTAACCCAATCTA 60.202 45.833 0.00 0.00 0.00 1.98
2417 3321 0.808847 GGCGGAAGACATCGTAACCC 60.809 60.000 0.00 0.00 40.66 4.11
2523 3461 0.951040 CAAGGAACGGTGAGGCAGTC 60.951 60.000 0.00 0.00 0.00 3.51
2577 3515 2.765807 AGGGGGTCTGGCGAGATG 60.766 66.667 0.38 0.00 0.00 2.90
2579 3517 3.317436 ATCAGGGGGTCTGGCGAGA 62.317 63.158 0.00 0.00 43.53 4.04
2590 3528 2.203640 TCCCGATCCGATCAGGGG 60.204 66.667 25.47 19.93 40.88 4.79
2741 3905 2.869503 ATAGGTTTGAGGCGGTGGCG 62.870 60.000 0.00 0.00 41.24 5.69
2742 3906 1.077716 ATAGGTTTGAGGCGGTGGC 60.078 57.895 0.00 0.00 38.90 5.01
2743 3907 0.748005 CCATAGGTTTGAGGCGGTGG 60.748 60.000 0.00 0.00 0.00 4.61
2744 3908 0.035439 ACCATAGGTTTGAGGCGGTG 60.035 55.000 0.00 0.00 27.29 4.94
2745 3909 0.035439 CACCATAGGTTTGAGGCGGT 60.035 55.000 0.00 0.00 31.02 5.68
2746 3910 1.376609 GCACCATAGGTTTGAGGCGG 61.377 60.000 0.00 0.00 31.02 6.13
2747 3911 1.705337 CGCACCATAGGTTTGAGGCG 61.705 60.000 3.95 3.95 31.02 5.52
2748 3912 1.993369 GCGCACCATAGGTTTGAGGC 61.993 60.000 0.30 0.00 31.02 4.70
2749 3913 1.376609 GGCGCACCATAGGTTTGAGG 61.377 60.000 10.83 0.00 31.02 3.86
2750 3914 1.705337 CGGCGCACCATAGGTTTGAG 61.705 60.000 10.83 0.00 31.02 3.02
2751 3915 1.743623 CGGCGCACCATAGGTTTGA 60.744 57.895 10.83 0.00 31.02 2.69
2752 3916 2.791256 CGGCGCACCATAGGTTTG 59.209 61.111 10.83 0.00 31.02 2.93
2772 3936 3.870955 CCATAGGGCTGCTACGGA 58.129 61.111 0.00 0.00 0.00 4.69
2801 4013 1.226859 GCGCCGTAGTAGTGATGCA 60.227 57.895 0.00 0.00 0.00 3.96
2855 4067 1.004679 GACGCCGGGTAGGTTTGAA 60.005 57.895 2.18 0.00 43.70 2.69
2860 4072 3.152400 GGATGACGCCGGGTAGGT 61.152 66.667 2.18 0.00 43.70 3.08
2874 4140 4.047125 CCTTGCGGGTGTGGGGAT 62.047 66.667 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.