Multiple sequence alignment - TraesCS7B01G165800

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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 TraesCS7B01G165800 chr7B 100.000 3839 0 0 1 3839 228800033 228803871 0.000000e+00 7090.0
1 TraesCS7B01G165800 chr7B 92.857 182 12 1 1956 2136 186866518 186866699 2.940000e-66 263.0
2 TraesCS7B01G165800 chr2D 95.115 1740 48 13 2121 3839 29095953 29094230 0.000000e+00 2708.0
3 TraesCS7B01G165800 chr2D 93.813 986 46 4 1 986 29097332 29096362 0.000000e+00 1469.0
4 TraesCS7B01G165800 chr2D 96.747 830 25 2 1032 1861 606090954 606090127 0.000000e+00 1382.0
5 TraesCS7B01G165800 chr2D 95.685 788 23 3 3052 3839 606090007 606089231 0.000000e+00 1256.0
6 TraesCS7B01G165800 chr2D 94.567 681 25 2 362 1035 606091668 606090993 0.000000e+00 1042.0
7 TraesCS7B01G165800 chr2D 95.341 279 13 0 1 279 606091981 606091703 9.790000e-121 444.0
8 TraesCS7B01G165800 chr2D 93.889 180 11 0 1949 2128 620615636 620615815 4.890000e-69 272.0
9 TraesCS7B01G165800 chr2D 93.750 176 10 1 1959 2133 100746584 100746759 2.940000e-66 263.0
10 TraesCS7B01G165800 chr7A 94.282 1714 57 12 2121 3809 658272231 658273928 0.000000e+00 2584.0
11 TraesCS7B01G165800 chr7A 94.059 1717 62 11 2121 3812 576792803 576791102 0.000000e+00 2569.0
12 TraesCS7B01G165800 chr7A 91.189 454 35 3 1032 1482 41464429 41463978 2.540000e-171 612.0
13 TraesCS7B01G165800 chr7A 91.353 451 34 3 1032 1479 617598849 617599297 2.540000e-171 612.0
14 TraesCS7B01G165800 chr2A 93.298 1716 58 12 2121 3809 764883083 764884768 0.000000e+00 2479.0
15 TraesCS7B01G165800 chr2A 91.131 451 35 3 1032 1479 756524816 756525264 1.180000e-169 606.0
16 TraesCS7B01G165800 chr2A 96.951 164 5 0 1959 2122 683721488 683721325 3.780000e-70 276.0
17 TraesCS7B01G165800 chr2A 90.576 191 16 2 1947 2135 505099607 505099797 6.370000e-63 252.0
18 TraesCS7B01G165800 chr5D 94.371 1581 55 18 2264 3839 27284055 27285606 0.000000e+00 2396.0
19 TraesCS7B01G165800 chr5D 96.069 1399 39 5 2441 3839 431987936 431989318 0.000000e+00 2265.0
20 TraesCS7B01G165800 chr5D 91.383 1265 77 15 2121 3363 127939521 127938267 0.000000e+00 1703.0
21 TraesCS7B01G165800 chr5D 97.627 927 21 1 1034 1960 27281231 27282156 0.000000e+00 1589.0
22 TraesCS7B01G165800 chr5D 94.401 1018 35 6 18 1035 27280195 27281190 0.000000e+00 1544.0
23 TraesCS7B01G165800 chr5D 95.386 932 38 5 1032 1960 431973453 431974382 0.000000e+00 1478.0
24 TraesCS7B01G165800 chr5D 93.702 651 31 2 3 653 431972707 431973347 0.000000e+00 966.0
25 TraesCS7B01G165800 chr5D 92.698 493 33 1 1471 1960 127940012 127939520 0.000000e+00 708.0
26 TraesCS7B01G165800 chr5D 90.462 346 12 2 2121 2445 431974381 431974726 1.640000e-118 436.0
27 TraesCS7B01G165800 chr5D 85.465 172 3 3 2121 2270 27282155 27282326 3.970000e-35 159.0
28 TraesCS7B01G165800 chr7D 91.587 1260 77 12 2121 3359 530740460 530739209 0.000000e+00 1712.0
29 TraesCS7B01G165800 chr7D 91.118 1261 81 17 2121 3359 340174113 340175364 0.000000e+00 1679.0
30 TraesCS7B01G165800 chr7D 92.495 493 34 1 1471 1960 340173622 340174114 0.000000e+00 702.0
31 TraesCS7B01G165800 chr6D 91.515 1261 76 14 2121 3359 450188857 450187606 0.000000e+00 1707.0
32 TraesCS7B01G165800 chr6D 96.663 929 29 2 1032 1960 440673816 440674742 0.000000e+00 1543.0
33 TraesCS7B01G165800 chr6D 94.670 788 25 3 3052 3839 440675606 440676376 0.000000e+00 1206.0
34 TraesCS7B01G165800 chr6D 95.007 681 21 2 362 1035 440673103 440673777 0.000000e+00 1057.0
35 TraesCS7B01G165800 chr6D 92.566 686 34 5 1 684 137153227 137152557 0.000000e+00 968.0
36 TraesCS7B01G165800 chr6D 93.467 597 17 8 2121 2695 440674741 440675337 0.000000e+00 867.0
37 TraesCS7B01G165800 chr6D 92.975 484 31 1 1480 1960 450189339 450188856 0.000000e+00 702.0
38 TraesCS7B01G165800 chr6D 93.458 321 10 3 1 318 440672787 440673099 2.090000e-127 466.0
39 TraesCS7B01G165800 chr6D 90.358 363 15 3 675 1035 137148258 137147914 3.500000e-125 459.0
40 TraesCS7B01G165800 chr6D 96.364 165 6 0 1959 2123 235137341 235137177 4.890000e-69 272.0
41 TraesCS7B01G165800 chr6D 96.875 32 1 0 3445 3476 13478547 13478578 2.000000e-03 54.7
42 TraesCS7B01G165800 chr1D 91.515 1261 76 14 2121 3359 415597041 415598292 0.000000e+00 1707.0
43 TraesCS7B01G165800 chr1D 92.495 493 34 1 1471 1960 415596550 415597042 0.000000e+00 702.0
44 TraesCS7B01G165800 chr2B 97.419 930 23 1 1032 1960 134341802 134342731 0.000000e+00 1583.0
45 TraesCS7B01G165800 chr2B 94.231 1040 38 12 1 1035 134340741 134341763 0.000000e+00 1568.0
46 TraesCS7B01G165800 chr2B 93.874 1012 32 11 2121 3109 134342730 134343734 0.000000e+00 1498.0
47 TraesCS7B01G165800 chr4D 93.864 1043 42 7 1 1035 85853385 85852357 0.000000e+00 1552.0
48 TraesCS7B01G165800 chr4D 96.663 929 25 1 1032 1960 85852318 85851396 0.000000e+00 1539.0
49 TraesCS7B01G165800 chr4D 98.758 161 2 0 3679 3839 85849885 85849725 1.750000e-73 287.0
50 TraesCS7B01G165800 chr4D 94.737 171 9 0 1959 2129 122586285 122586115 2.270000e-67 267.0
51 TraesCS7B01G165800 chr4A 90.545 973 52 9 75 1035 658380915 658381859 0.000000e+00 1251.0
52 TraesCS7B01G165800 chr4A 96.414 725 20 1 1032 1756 658381898 658382616 0.000000e+00 1190.0
53 TraesCS7B01G165800 chr6A 95.766 685 26 1 1032 1713 163167725 163167041 0.000000e+00 1101.0
54 TraesCS7B01G165800 chr6A 92.393 539 30 3 1 539 163168730 163168203 0.000000e+00 758.0
55 TraesCS7B01G165800 chr6A 94.595 444 18 1 592 1035 163168201 163167764 0.000000e+00 682.0
56 TraesCS7B01G165800 chr6A 92.441 463 14 2 2121 2562 163163293 163162831 3.230000e-180 641.0
57 TraesCS7B01G165800 chr3B 94.436 647 23 2 2830 3476 60387593 60388226 0.000000e+00 983.0
58 TraesCS7B01G165800 chr3B 92.251 542 28 3 2906 3447 775657913 775657386 0.000000e+00 756.0
59 TraesCS7B01G165800 chr3B 94.937 316 14 1 3496 3809 60389384 60389699 9.580000e-136 494.0
60 TraesCS7B01G165800 chr1B 91.074 717 41 5 2121 2815 289693747 289694462 0.000000e+00 948.0
61 TraesCS7B01G165800 chr3D 91.892 481 22 5 188 666 614099918 614099453 0.000000e+00 656.0
62 TraesCS7B01G165800 chr3D 95.317 363 15 2 675 1035 614089797 614089435 3.330000e-160 575.0
63 TraesCS7B01G165800 chr6B 95.906 171 7 0 1959 2129 400633558 400633728 1.050000e-70 278.0
64 TraesCS7B01G165800 chr6B 95.294 170 6 2 1956 2123 226362648 226362479 6.320000e-68 268.0


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 TraesCS7B01G165800 chr7B 228800033 228803871 3838 False 7090.000000 7090 100.000000 1 3839 1 chr7B.!!$F2 3838
1 TraesCS7B01G165800 chr2D 29094230 29097332 3102 True 2088.500000 2708 94.464000 1 3839 2 chr2D.!!$R1 3838
2 TraesCS7B01G165800 chr2D 606089231 606091981 2750 True 1031.000000 1382 95.585000 1 3839 4 chr2D.!!$R2 3838
3 TraesCS7B01G165800 chr7A 658272231 658273928 1697 False 2584.000000 2584 94.282000 2121 3809 1 chr7A.!!$F2 1688
4 TraesCS7B01G165800 chr7A 576791102 576792803 1701 True 2569.000000 2569 94.059000 2121 3812 1 chr7A.!!$R2 1691
5 TraesCS7B01G165800 chr2A 764883083 764884768 1685 False 2479.000000 2479 93.298000 2121 3809 1 chr2A.!!$F3 1688
6 TraesCS7B01G165800 chr5D 431987936 431989318 1382 False 2265.000000 2265 96.069000 2441 3839 1 chr5D.!!$F1 1398
7 TraesCS7B01G165800 chr5D 27280195 27285606 5411 False 1422.000000 2396 92.966000 18 3839 4 chr5D.!!$F2 3821
8 TraesCS7B01G165800 chr5D 127938267 127940012 1745 True 1205.500000 1703 92.040500 1471 3363 2 chr5D.!!$R1 1892
9 TraesCS7B01G165800 chr5D 431972707 431974726 2019 False 960.000000 1478 93.183333 3 2445 3 chr5D.!!$F3 2442
10 TraesCS7B01G165800 chr7D 530739209 530740460 1251 True 1712.000000 1712 91.587000 2121 3359 1 chr7D.!!$R1 1238
11 TraesCS7B01G165800 chr7D 340173622 340175364 1742 False 1190.500000 1679 91.806500 1471 3359 2 chr7D.!!$F1 1888
12 TraesCS7B01G165800 chr6D 450187606 450189339 1733 True 1204.500000 1707 92.245000 1480 3359 2 chr6D.!!$R4 1879
13 TraesCS7B01G165800 chr6D 440672787 440676376 3589 False 1027.800000 1543 94.653000 1 3839 5 chr6D.!!$F2 3838
14 TraesCS7B01G165800 chr6D 137152557 137153227 670 True 968.000000 968 92.566000 1 684 1 chr6D.!!$R2 683
15 TraesCS7B01G165800 chr1D 415596550 415598292 1742 False 1204.500000 1707 92.005000 1471 3359 2 chr1D.!!$F1 1888
16 TraesCS7B01G165800 chr2B 134340741 134343734 2993 False 1549.666667 1583 95.174667 1 3109 3 chr2B.!!$F1 3108
17 TraesCS7B01G165800 chr4D 85849725 85853385 3660 True 1126.000000 1552 96.428333 1 3839 3 chr4D.!!$R2 3838
18 TraesCS7B01G165800 chr4A 658380915 658382616 1701 False 1220.500000 1251 93.479500 75 1756 2 chr4A.!!$F1 1681
19 TraesCS7B01G165800 chr6A 163162831 163168730 5899 True 795.500000 1101 93.798750 1 2562 4 chr6A.!!$R1 2561
20 TraesCS7B01G165800 chr3B 775657386 775657913 527 True 756.000000 756 92.251000 2906 3447 1 chr3B.!!$R1 541
21 TraesCS7B01G165800 chr3B 60387593 60389699 2106 False 738.500000 983 94.686500 2830 3809 2 chr3B.!!$F1 979
22 TraesCS7B01G165800 chr1B 289693747 289694462 715 False 948.000000 948 91.074000 2121 2815 1 chr1B.!!$F1 694

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
681 718 0.753111 CTTAATGGAGCAGGTGGGCC 60.753 60.000 0.0 0.0 0.0 5.80 F
1650 1755 1.204704 CGATGGAGCAGTTGTAGGACA 59.795 52.381 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2059 5672 0.249868 ATGGCGACCACATACGGATG 60.250 55.000 5.94 5.94 35.80 3.51 R
3325 8759 2.157738 GGATGATTATGGCTGAGGCAC 58.842 52.381 12.06 0.00 41.84 5.01 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
191 209 2.003548 GTCCCAGGGGCTCAAGGAT 61.004 63.158 1.32 0.00 34.68 3.24
274 292 1.404851 GCCGTTCAGAGGAAGAGGAAG 60.405 57.143 0.00 0.00 35.26 3.46
275 293 2.171840 CCGTTCAGAGGAAGAGGAAGA 58.828 52.381 0.00 0.00 35.26 2.87
276 294 2.165437 CCGTTCAGAGGAAGAGGAAGAG 59.835 54.545 0.00 0.00 35.26 2.85
277 295 2.416701 CGTTCAGAGGAAGAGGAAGAGC 60.417 54.545 0.00 0.00 32.62 4.09
278 296 2.564947 GTTCAGAGGAAGAGGAAGAGCA 59.435 50.000 0.00 0.00 32.62 4.26
279 297 2.455557 TCAGAGGAAGAGGAAGAGCAG 58.544 52.381 0.00 0.00 0.00 4.24
280 298 2.178580 CAGAGGAAGAGGAAGAGCAGT 58.821 52.381 0.00 0.00 0.00 4.40
281 299 3.010696 TCAGAGGAAGAGGAAGAGCAGTA 59.989 47.826 0.00 0.00 0.00 2.74
295 313 1.945354 GCAGTAGAGCACCCTACGCA 61.945 60.000 15.30 0.00 42.77 5.24
360 378 4.011517 GGCCCCGTGAAGGTCGAA 62.012 66.667 0.00 0.00 38.74 3.71
447 465 2.104928 CGGATCACGCTGCTGCTA 59.895 61.111 14.03 0.00 36.97 3.49
681 718 0.753111 CTTAATGGAGCAGGTGGGCC 60.753 60.000 0.00 0.00 0.00 5.80
710 747 7.504238 TCCCTTTTGTCTAAGATTTTGCAAGTA 59.496 33.333 0.00 0.00 0.00 2.24
770 809 3.076621 TCTGCAGTTGCTGATTCGATTT 58.923 40.909 14.67 0.00 42.71 2.17
771 810 3.503363 TCTGCAGTTGCTGATTCGATTTT 59.497 39.130 14.67 0.00 42.71 1.82
772 811 4.022935 TCTGCAGTTGCTGATTCGATTTTT 60.023 37.500 14.67 0.00 42.71 1.94
826 869 1.378514 GGGCCGGAGCTTCAATGAA 60.379 57.895 5.05 0.00 39.73 2.57
1260 1359 3.134458 CTGAACCTCACTGTTGGAGTTC 58.866 50.000 3.91 0.00 36.47 3.01
1432 1534 8.730948 AGTAATACTAGTCTGGTATCCCAAGTA 58.269 37.037 9.12 0.00 41.27 2.24
1560 1665 4.923415 CCCTTCTGGTTTAGGAAAGTGAT 58.077 43.478 0.00 0.00 33.13 3.06
1650 1755 1.204704 CGATGGAGCAGTTGTAGGACA 59.795 52.381 0.00 0.00 0.00 4.02
1654 1759 2.371841 TGGAGCAGTTGTAGGACATTGT 59.628 45.455 0.00 0.00 0.00 2.71
1794 5404 7.450014 TGACCATCCAGCTTTAAATTTTAGTGA 59.550 33.333 0.00 0.00 0.00 3.41
1832 5442 7.435068 TGCAATTGAACTCTTCTTAAGGTAC 57.565 36.000 10.34 0.00 0.00 3.34
1892 5502 2.192664 TCCTTGGTCTTTTGCGCATA 57.807 45.000 12.75 2.60 0.00 3.14
1912 5522 7.358683 GCGCATATAAAATGCCAGAGAAAATTC 60.359 37.037 0.30 0.00 41.71 2.17
1958 5571 4.653801 ACAAAGCTAAGGTGTTTCCCATTT 59.346 37.500 0.00 0.00 36.75 2.32
1959 5572 5.836358 ACAAAGCTAAGGTGTTTCCCATTTA 59.164 36.000 0.00 0.00 36.75 1.40
1960 5573 5.977489 AAGCTAAGGTGTTTCCCATTTAC 57.023 39.130 0.00 0.00 36.75 2.01
1961 5574 5.256806 AGCTAAGGTGTTTCCCATTTACT 57.743 39.130 0.00 0.00 36.75 2.24
1962 5575 5.254115 AGCTAAGGTGTTTCCCATTTACTC 58.746 41.667 0.00 0.00 36.75 2.59
1963 5576 4.398358 GCTAAGGTGTTTCCCATTTACTCC 59.602 45.833 0.00 0.00 36.75 3.85
1964 5577 3.451402 AGGTGTTTCCCATTTACTCCC 57.549 47.619 0.00 0.00 36.75 4.30
1965 5578 2.993863 AGGTGTTTCCCATTTACTCCCT 59.006 45.455 0.00 0.00 36.75 4.20
1966 5579 3.401342 AGGTGTTTCCCATTTACTCCCTT 59.599 43.478 0.00 0.00 36.75 3.95
1967 5580 3.762288 GGTGTTTCCCATTTACTCCCTTC 59.238 47.826 0.00 0.00 0.00 3.46
1968 5581 3.439129 GTGTTTCCCATTTACTCCCTTCG 59.561 47.826 0.00 0.00 0.00 3.79
1969 5582 3.073356 TGTTTCCCATTTACTCCCTTCGT 59.927 43.478 0.00 0.00 0.00 3.85
1970 5583 4.077108 GTTTCCCATTTACTCCCTTCGTT 58.923 43.478 0.00 0.00 0.00 3.85
1971 5584 3.622166 TCCCATTTACTCCCTTCGTTC 57.378 47.619 0.00 0.00 0.00 3.95
1972 5585 2.237893 TCCCATTTACTCCCTTCGTTCC 59.762 50.000 0.00 0.00 0.00 3.62
1973 5586 2.238898 CCCATTTACTCCCTTCGTTCCT 59.761 50.000 0.00 0.00 0.00 3.36
1974 5587 3.453353 CCCATTTACTCCCTTCGTTCCTA 59.547 47.826 0.00 0.00 0.00 2.94
1975 5588 4.080751 CCCATTTACTCCCTTCGTTCCTAA 60.081 45.833 0.00 0.00 0.00 2.69
1976 5589 5.493809 CCATTTACTCCCTTCGTTCCTAAA 58.506 41.667 0.00 0.00 0.00 1.85
1977 5590 6.120220 CCATTTACTCCCTTCGTTCCTAAAT 58.880 40.000 0.00 0.00 0.00 1.40
1978 5591 7.277396 CCATTTACTCCCTTCGTTCCTAAATA 58.723 38.462 0.00 0.00 0.00 1.40
1979 5592 7.937394 CCATTTACTCCCTTCGTTCCTAAATAT 59.063 37.037 0.00 0.00 0.00 1.28
1980 5593 9.338622 CATTTACTCCCTTCGTTCCTAAATATT 57.661 33.333 0.00 0.00 0.00 1.28
1981 5594 9.916360 ATTTACTCCCTTCGTTCCTAAATATTT 57.084 29.630 5.89 5.89 0.00 1.40
1982 5595 8.726870 TTACTCCCTTCGTTCCTAAATATTTG 57.273 34.615 11.05 1.40 0.00 2.32
1983 5596 6.718294 ACTCCCTTCGTTCCTAAATATTTGT 58.282 36.000 11.05 0.00 0.00 2.83
1984 5597 6.822170 ACTCCCTTCGTTCCTAAATATTTGTC 59.178 38.462 11.05 0.00 0.00 3.18
1985 5598 6.954232 TCCCTTCGTTCCTAAATATTTGTCT 58.046 36.000 11.05 0.00 0.00 3.41
1986 5599 7.399634 TCCCTTCGTTCCTAAATATTTGTCTT 58.600 34.615 11.05 0.00 0.00 3.01
1987 5600 7.886446 TCCCTTCGTTCCTAAATATTTGTCTTT 59.114 33.333 11.05 0.00 0.00 2.52
1988 5601 8.182227 CCCTTCGTTCCTAAATATTTGTCTTTC 58.818 37.037 11.05 0.00 0.00 2.62
1989 5602 8.947115 CCTTCGTTCCTAAATATTTGTCTTTCT 58.053 33.333 11.05 0.00 0.00 2.52
2007 5620 9.996554 TGTCTTTCTAGATATTTCAACAAGTGA 57.003 29.630 0.00 0.00 31.86 3.41
2016 5629 9.302345 AGATATTTCAACAAGTGACTACATACG 57.698 33.333 0.00 0.00 35.39 3.06
2017 5630 6.721571 ATTTCAACAAGTGACTACATACGG 57.278 37.500 0.00 0.00 35.39 4.02
2018 5631 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
2019 5632 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
2020 5633 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
2021 5634 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
2022 5635 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
2023 5636 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
2024 5637 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
2025 5638 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
2026 5639 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
2027 5640 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
2028 5641 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
2029 5642 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
2030 5643 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
2031 5644 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
2032 5645 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
2033 5646 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
2034 5647 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
2035 5648 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
2036 5649 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
2037 5650 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
2038 5651 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
2039 5652 5.122239 CGGAGCAAAATGAGTGAATCTACAA 59.878 40.000 0.00 0.00 0.00 2.41
2040 5653 6.183360 CGGAGCAAAATGAGTGAATCTACAAT 60.183 38.462 0.00 0.00 0.00 2.71
2041 5654 7.192232 GGAGCAAAATGAGTGAATCTACAATC 58.808 38.462 0.00 0.00 35.78 2.67
2042 5655 7.066766 GGAGCAAAATGAGTGAATCTACAATCT 59.933 37.037 0.00 0.00 36.14 2.40
2043 5656 9.102757 GAGCAAAATGAGTGAATCTACAATCTA 57.897 33.333 0.00 0.00 36.14 1.98
2044 5657 9.453572 AGCAAAATGAGTGAATCTACAATCTAA 57.546 29.630 0.00 0.00 36.14 2.10
2075 5688 2.058798 CATACATCCGTATGTGGTCGC 58.941 52.381 3.56 0.00 46.70 5.19
2076 5689 0.386476 TACATCCGTATGTGGTCGCC 59.614 55.000 3.56 0.00 45.99 5.54
2077 5690 1.142965 CATCCGTATGTGGTCGCCA 59.857 57.895 0.00 0.00 0.00 5.69
2078 5691 0.249868 CATCCGTATGTGGTCGCCAT 60.250 55.000 1.90 0.00 35.28 4.40
2079 5692 0.468226 ATCCGTATGTGGTCGCCATT 59.532 50.000 1.90 0.00 35.28 3.16
2080 5693 0.250793 TCCGTATGTGGTCGCCATTT 59.749 50.000 1.90 0.00 35.28 2.32
2081 5694 0.376852 CCGTATGTGGTCGCCATTTG 59.623 55.000 1.90 0.00 35.28 2.32
2082 5695 1.364721 CGTATGTGGTCGCCATTTGA 58.635 50.000 1.90 0.00 35.28 2.69
2083 5696 1.735018 CGTATGTGGTCGCCATTTGAA 59.265 47.619 1.90 0.00 35.28 2.69
2084 5697 2.160615 CGTATGTGGTCGCCATTTGAAA 59.839 45.455 1.90 0.00 35.28 2.69
2085 5698 3.181501 CGTATGTGGTCGCCATTTGAAAT 60.182 43.478 1.90 0.00 35.28 2.17
2086 5699 2.721274 TGTGGTCGCCATTTGAAATG 57.279 45.000 10.84 10.84 35.28 2.32
2087 5700 1.959985 TGTGGTCGCCATTTGAAATGT 59.040 42.857 15.93 0.00 35.28 2.71
2088 5701 2.030363 TGTGGTCGCCATTTGAAATGTC 60.030 45.455 15.93 3.00 35.28 3.06
2089 5702 2.228822 GTGGTCGCCATTTGAAATGTCT 59.771 45.455 15.93 0.00 35.28 3.41
2090 5703 3.438781 GTGGTCGCCATTTGAAATGTCTA 59.561 43.478 15.93 0.00 35.28 2.59
2091 5704 3.689161 TGGTCGCCATTTGAAATGTCTAG 59.311 43.478 15.93 2.82 0.00 2.43
2092 5705 3.938963 GGTCGCCATTTGAAATGTCTAGA 59.061 43.478 15.93 7.28 0.00 2.43
2093 5706 4.394920 GGTCGCCATTTGAAATGTCTAGAA 59.605 41.667 15.93 0.00 0.00 2.10
2094 5707 5.106317 GGTCGCCATTTGAAATGTCTAGAAA 60.106 40.000 15.93 0.00 0.00 2.52
2095 5708 6.024049 GTCGCCATTTGAAATGTCTAGAAAG 58.976 40.000 15.93 0.50 0.00 2.62
2096 5709 5.937540 TCGCCATTTGAAATGTCTAGAAAGA 59.062 36.000 15.93 2.21 0.00 2.52
2118 5731 9.768215 AAAGACAAATATTTAGGAATTGAGGGA 57.232 29.630 0.00 0.00 0.00 4.20
2119 5732 8.986929 AGACAAATATTTAGGAATTGAGGGAG 57.013 34.615 0.00 0.00 0.00 4.30
2202 5837 3.592059 CAATTCCAAAGTTCCATGCCTG 58.408 45.455 0.00 0.00 0.00 4.85
2207 5842 2.426024 CCAAAGTTCCATGCCTGATCTG 59.574 50.000 0.00 0.00 0.00 2.90
2271 7644 6.894682 TGAGCACCCACAAGTAATATATTCA 58.105 36.000 0.00 0.00 0.00 2.57
2476 7851 0.825010 CTGAAGCTGGTGGCAAGGTT 60.825 55.000 3.44 3.44 44.79 3.50
2504 7879 1.007118 TCAGAGATGTCACAGGGGCTA 59.993 52.381 0.00 0.00 0.00 3.93
2530 7906 3.446161 AGAACTCCAATGGCATTGACATG 59.554 43.478 35.39 23.70 42.83 3.21
2954 8336 3.021269 AGCTGCATTTGTTGACACATG 57.979 42.857 1.02 6.02 37.17 3.21
3325 8759 2.473868 CGTTGCTACAAGTGCATTACCG 60.474 50.000 0.00 0.00 40.34 4.02
3424 8858 3.811722 TGTCAATGAGCAAGTTTAGCG 57.188 42.857 0.00 0.00 37.01 4.26
3548 10130 4.843728 TCACTTTCTGGAATGGTATGGTC 58.156 43.478 2.25 0.00 0.00 4.02
3834 10456 4.745620 GTCTGCTCCATCCGTTTATAAGAC 59.254 45.833 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
186 204 0.817654 TGCATCAGACGTCGATCCTT 59.182 50.000 16.44 0.00 0.00 3.36
191 209 2.181777 GGCTGCATCAGACGTCGA 59.818 61.111 10.46 11.04 32.44 4.20
259 277 2.225242 ACTGCTCTTCCTCTTCCTCTGA 60.225 50.000 0.00 0.00 0.00 3.27
274 292 0.382515 CGTAGGGTGCTCTACTGCTC 59.617 60.000 7.54 0.00 37.92 4.26
275 293 1.668101 GCGTAGGGTGCTCTACTGCT 61.668 60.000 14.23 0.00 37.92 4.24
276 294 1.227002 GCGTAGGGTGCTCTACTGC 60.227 63.158 7.54 8.43 37.92 4.40
277 295 0.101399 CTGCGTAGGGTGCTCTACTG 59.899 60.000 7.54 3.11 37.92 2.74
278 296 1.038130 CCTGCGTAGGGTGCTCTACT 61.038 60.000 12.40 1.43 40.63 2.57
279 297 1.437986 CCTGCGTAGGGTGCTCTAC 59.562 63.158 12.40 0.00 40.63 2.59
280 298 0.613853 AACCTGCGTAGGGTGCTCTA 60.614 55.000 24.20 0.00 44.33 2.43
281 299 1.889530 GAACCTGCGTAGGGTGCTCT 61.890 60.000 24.20 0.00 46.63 4.09
447 465 2.762459 TCCGGCCTGGATTACGCT 60.762 61.111 11.66 0.00 43.74 5.07
588 623 4.990543 TGTGCTTCGTCAGATACTTTTG 57.009 40.909 0.00 0.00 0.00 2.44
618 655 4.359434 TTTAGTTACATGGCCACTGTGA 57.641 40.909 23.16 16.01 0.00 3.58
681 718 6.152379 GCAAAATCTTAGACAAAAGGGAGTG 58.848 40.000 0.00 0.00 0.00 3.51
785 828 7.416664 GCCCTTATCAATCTAACAAAGCATTGA 60.417 37.037 8.96 1.45 38.94 2.57
826 869 6.109359 GGCTGTGTGTTGAATAGTAGATTCT 58.891 40.000 0.00 0.00 0.00 2.40
1219 1318 9.522804 GGTTCAGATCTACTTCAGTACATAAAG 57.477 37.037 0.00 0.00 0.00 1.85
1260 1359 9.746711 CTTTTACTTAACATCGACTCAAAGATG 57.253 33.333 4.15 4.15 46.95 2.90
1560 1665 8.665643 TCCGTCTAAACAATTTCTGAAAACTA 57.334 30.769 6.95 0.00 0.00 2.24
1794 5404 9.798994 GAGTTCAATTGCAATATCTTGAGATTT 57.201 29.630 13.39 1.02 36.05 2.17
1875 5485 6.508404 GCATTTTATATGCGCAAAAGACCAAG 60.508 38.462 17.11 1.68 35.17 3.61
1912 5522 7.147312 TGTGTGAAAATTAAAGAGATTGGCAG 58.853 34.615 0.00 0.00 0.00 4.85
1958 5571 7.854337 ACAAATATTTAGGAACGAAGGGAGTA 58.146 34.615 0.00 0.00 0.00 2.59
1959 5572 6.718294 ACAAATATTTAGGAACGAAGGGAGT 58.282 36.000 0.00 0.00 0.00 3.85
1960 5573 7.048512 AGACAAATATTTAGGAACGAAGGGAG 58.951 38.462 0.00 0.00 0.00 4.30
1961 5574 6.954232 AGACAAATATTTAGGAACGAAGGGA 58.046 36.000 0.00 0.00 0.00 4.20
1962 5575 7.625828 AAGACAAATATTTAGGAACGAAGGG 57.374 36.000 0.00 0.00 0.00 3.95
1963 5576 8.947115 AGAAAGACAAATATTTAGGAACGAAGG 58.053 33.333 0.00 0.00 0.00 3.46
1981 5594 9.996554 TCACTTGTTGAAATATCTAGAAAGACA 57.003 29.630 0.00 0.00 33.57 3.41
1990 5603 9.302345 CGTATGTAGTCACTTGTTGAAATATCT 57.698 33.333 0.00 0.00 35.39 1.98
1991 5604 8.540492 CCGTATGTAGTCACTTGTTGAAATATC 58.460 37.037 0.00 0.00 35.39 1.63
1992 5605 8.255206 TCCGTATGTAGTCACTTGTTGAAATAT 58.745 33.333 0.00 0.00 35.39 1.28
1993 5606 7.604549 TCCGTATGTAGTCACTTGTTGAAATA 58.395 34.615 0.00 0.00 35.39 1.40
1994 5607 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
1995 5608 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
1996 5609 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
1997 5610 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
1998 5611 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
1999 5612 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
2000 5613 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
2001 5614 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
2002 5615 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
2003 5616 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
2004 5617 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
2005 5618 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
2006 5619 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
2007 5620 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
2008 5621 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
2009 5622 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
2010 5623 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
2011 5624 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
2012 5625 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
2013 5626 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
2014 5627 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
2015 5628 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
2016 5629 6.500684 TTGTAGATTCACTCATTTTGCTCC 57.499 37.500 0.00 0.00 0.00 4.70
2017 5630 7.983307 AGATTGTAGATTCACTCATTTTGCTC 58.017 34.615 0.00 0.00 0.00 4.26
2018 5631 7.934855 AGATTGTAGATTCACTCATTTTGCT 57.065 32.000 0.00 0.00 0.00 3.91
2056 5669 1.000506 GGCGACCACATACGGATGTAT 59.999 52.381 14.23 4.48 44.82 2.29
2057 5670 0.386476 GGCGACCACATACGGATGTA 59.614 55.000 14.23 0.00 44.82 2.29
2059 5672 0.249868 ATGGCGACCACATACGGATG 60.250 55.000 5.94 5.94 35.80 3.51
2060 5673 0.468226 AATGGCGACCACATACGGAT 59.532 50.000 0.50 0.00 35.80 4.18
2061 5674 0.250793 AAATGGCGACCACATACGGA 59.749 50.000 0.50 0.00 35.80 4.69
2062 5675 0.376852 CAAATGGCGACCACATACGG 59.623 55.000 0.50 0.00 35.80 4.02
2063 5676 1.364721 TCAAATGGCGACCACATACG 58.635 50.000 0.50 0.00 35.80 3.06
2064 5677 3.840890 TTTCAAATGGCGACCACATAC 57.159 42.857 0.50 0.00 35.80 2.39
2065 5678 3.761218 ACATTTCAAATGGCGACCACATA 59.239 39.130 14.70 0.00 35.80 2.29
2066 5679 2.562298 ACATTTCAAATGGCGACCACAT 59.438 40.909 14.70 0.00 35.80 3.21
2067 5680 1.959985 ACATTTCAAATGGCGACCACA 59.040 42.857 14.70 0.00 35.80 4.17
2068 5681 2.228822 AGACATTTCAAATGGCGACCAC 59.771 45.455 14.70 0.00 35.80 4.16
2069 5682 2.513753 AGACATTTCAAATGGCGACCA 58.486 42.857 14.70 1.01 38.19 4.02
2070 5683 3.938963 TCTAGACATTTCAAATGGCGACC 59.061 43.478 14.70 0.00 30.86 4.79
2071 5684 5.545658 TTCTAGACATTTCAAATGGCGAC 57.454 39.130 14.70 3.48 30.86 5.19
2072 5685 5.937540 TCTTTCTAGACATTTCAAATGGCGA 59.062 36.000 14.70 6.83 30.86 5.54
2073 5686 6.182039 TCTTTCTAGACATTTCAAATGGCG 57.818 37.500 14.70 0.00 30.86 5.69
2092 5705 9.768215 TCCCTCAATTCCTAAATATTTGTCTTT 57.232 29.630 11.05 0.00 0.00 2.52
2093 5706 9.413734 CTCCCTCAATTCCTAAATATTTGTCTT 57.586 33.333 11.05 0.00 0.00 3.01
2094 5707 8.560903 ACTCCCTCAATTCCTAAATATTTGTCT 58.439 33.333 11.05 0.00 0.00 3.41
2095 5708 8.753497 ACTCCCTCAATTCCTAAATATTTGTC 57.247 34.615 11.05 0.00 0.00 3.18
2106 5719 9.676129 TCTCTAAATTATACTCCCTCAATTCCT 57.324 33.333 0.00 0.00 0.00 3.36
2107 5720 9.713713 GTCTCTAAATTATACTCCCTCAATTCC 57.286 37.037 0.00 0.00 0.00 3.01
2111 5724 8.204836 GCTTGTCTCTAAATTATACTCCCTCAA 58.795 37.037 0.00 0.00 0.00 3.02
2112 5725 7.344612 TGCTTGTCTCTAAATTATACTCCCTCA 59.655 37.037 0.00 0.00 0.00 3.86
2113 5726 7.727181 TGCTTGTCTCTAAATTATACTCCCTC 58.273 38.462 0.00 0.00 0.00 4.30
2114 5727 7.676683 TGCTTGTCTCTAAATTATACTCCCT 57.323 36.000 0.00 0.00 0.00 4.20
2115 5728 8.371699 AGATGCTTGTCTCTAAATTATACTCCC 58.628 37.037 0.00 0.00 0.00 4.30
2116 5729 9.771534 AAGATGCTTGTCTCTAAATTATACTCC 57.228 33.333 0.00 0.00 0.00 3.85
2202 5837 4.192000 CACGTGAGGTGGCAGATC 57.808 61.111 10.90 0.00 43.16 2.75
2271 7644 5.327732 AGGCATGCTTGTATATATTTGGCT 58.672 37.500 18.92 0.00 34.39 4.75
2504 7879 4.159135 GTCAATGCCATTGGAGTTCTTGAT 59.841 41.667 16.96 0.00 40.61 2.57
2954 8336 4.224433 CTGTCAGTCAATGTGTGAAATGC 58.776 43.478 0.00 0.00 38.23 3.56
2955 8337 5.428496 ACTGTCAGTCAATGTGTGAAATG 57.572 39.130 0.00 0.00 38.23 2.32
2956 8338 6.524734 TCTACTGTCAGTCAATGTGTGAAAT 58.475 36.000 9.26 0.00 38.23 2.17
2957 8339 5.912892 TCTACTGTCAGTCAATGTGTGAAA 58.087 37.500 9.26 0.00 38.23 2.69
3325 8759 2.157738 GGATGATTATGGCTGAGGCAC 58.842 52.381 12.06 0.00 41.84 5.01
3424 8858 8.425577 ACTAGATCAGCAATGTACAAACATAC 57.574 34.615 0.00 0.00 45.79 2.39
3480 8914 8.361139 GCTGTGATCCTCTAGCTAGTTTTAATA 58.639 37.037 20.10 0.00 33.53 0.98
3481 8915 7.147655 TGCTGTGATCCTCTAGCTAGTTTTAAT 60.148 37.037 20.10 8.27 37.10 1.40
3482 8916 6.154534 TGCTGTGATCCTCTAGCTAGTTTTAA 59.845 38.462 20.10 0.00 37.10 1.52
3652 10235 5.833082 AGTAGTACACAAGACTTGACACAG 58.167 41.667 21.95 8.16 0.00 3.66


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

AutoCloner maintained by Alex Coulton.