Multiple sequence alignment - TraesCS4B01G385500

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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 TraesCS4B01G385500 chr4B 100.000 2597 0 0 1 2597 664394362 664391766 0.000000e+00 4796.0
1 TraesCS4B01G385500 chr4B 91.304 69 6 0 1100 1168 664381768 664381700 7.650000e-16 95.3
2 TraesCS4B01G385500 chr4B 91.176 68 5 1 369 436 652990399 652990333 9.900000e-15 91.6
3 TraesCS4B01G385500 chr4B 85.185 81 11 1 76 155 665225679 665225599 5.960000e-12 82.4
4 TraesCS4B01G385500 chr4D 93.847 1349 74 1 545 1893 506746251 506747590 0.000000e+00 2023.0
5 TraesCS4B01G385500 chr4D 91.006 467 36 3 1893 2358 506748142 506748603 2.190000e-175 625.0
6 TraesCS4B01G385500 chr4D 86.828 577 45 13 1 549 506735074 506735647 1.320000e-172 616.0
7 TraesCS4B01G385500 chr4D 86.869 99 12 1 50 148 506773573 506773670 2.730000e-20 110.0
8 TraesCS4B01G385500 chr4D 88.095 84 10 0 60 143 506767840 506767923 1.640000e-17 100.0
9 TraesCS4B01G385500 chr4D 87.059 85 7 3 74 155 506781381 506781464 2.750000e-15 93.5
10 TraesCS4B01G385500 chr4D 87.059 85 7 3 74 155 506800757 506800840 2.750000e-15 93.5
11 TraesCS4B01G385500 chr5A 93.535 1222 79 0 610 1831 702996763 702997984 0.000000e+00 1820.0
12 TraesCS4B01G385500 chr5A 88.372 387 35 7 1885 2268 702998664 702999043 8.470000e-125 457.0
13 TraesCS4B01G385500 chr5A 87.000 100 9 4 1720 1818 703006180 703006276 2.730000e-20 110.0
14 TraesCS4B01G385500 chr5A 86.408 103 10 4 1720 1821 703148326 703148227 2.730000e-20 110.0
15 TraesCS4B01G385500 chr3B 95.184 1059 50 1 545 1602 800222483 800223541 0.000000e+00 1672.0
16 TraesCS4B01G385500 chr3B 91.314 898 77 1 1462 2358 800615441 800616338 0.000000e+00 1225.0
17 TraesCS4B01G385500 chr3B 89.936 467 42 2 1893 2358 800224080 800224542 4.780000e-167 597.0
18 TraesCS4B01G385500 chr3B 85.962 577 51 12 1 549 800218616 800219190 8.000000e-165 590.0
19 TraesCS4B01G385500 chr3B 90.155 193 18 1 1701 1893 800223589 800223780 1.540000e-62 250.0
20 TraesCS4B01G385500 chr3B 93.443 122 7 1 2353 2474 588418294 588418174 2.050000e-41 180.0
21 TraesCS4B01G385500 chr3B 94.845 97 4 1 2472 2568 800616337 800616432 1.610000e-32 150.0
22 TraesCS4B01G385500 chr3B 94.643 56 2 1 93 148 800676420 800676366 4.600000e-13 86.1
23 TraesCS4B01G385500 chr3D 89.655 174 18 0 194 367 582706123 582706296 3.360000e-54 222.0
24 TraesCS4B01G385500 chr3D 89.922 129 13 0 2353 2481 587436605 587436477 1.600000e-37 167.0
25 TraesCS4B01G385500 chr3D 100.000 29 0 0 1652 1680 54251019 54250991 1.000000e-03 54.7
26 TraesCS4B01G385500 chr3D 100.000 29 0 0 1652 1680 54255895 54255867 1.000000e-03 54.7
27 TraesCS4B01G385500 chr1D 87.931 174 21 0 194 367 404241589 404241762 3.390000e-49 206.0
28 TraesCS4B01G385500 chr1D 86.154 65 6 3 1985 2048 253017876 253017938 1.670000e-07 67.6
29 TraesCS4B01G385500 chr7B 87.283 173 21 1 194 366 469466960 469466789 2.040000e-46 196.0
30 TraesCS4B01G385500 chr7B 83.415 205 28 6 167 367 52367770 52367568 4.410000e-43 185.0
31 TraesCS4B01G385500 chr7B 89.552 134 11 3 2343 2475 141814426 141814557 1.600000e-37 167.0
32 TraesCS4B01G385500 chr4A 86.782 174 23 0 194 367 641453475 641453302 7.330000e-46 195.0
33 TraesCS4B01G385500 chr4A 91.176 68 4 2 372 439 691327269 691327204 9.900000e-15 91.6
34 TraesCS4B01G385500 chr4A 80.000 100 16 3 1951 2048 146553863 146553766 1.290000e-08 71.3
35 TraesCS4B01G385500 chr1B 86.857 175 21 2 194 367 449127189 449127016 7.330000e-46 195.0
36 TraesCS4B01G385500 chr1B 86.782 174 23 0 194 367 521228923 521228750 7.330000e-46 195.0
37 TraesCS4B01G385500 chr1B 92.308 65 5 0 369 433 69573318 69573382 2.750000e-15 93.5
38 TraesCS4B01G385500 chr2B 92.248 129 8 2 2348 2474 101411067 101411195 5.710000e-42 182.0
39 TraesCS4B01G385500 chr2B 88.971 136 13 2 2340 2473 113275140 113275275 1.600000e-37 167.0
40 TraesCS4B01G385500 chr2B 93.651 63 3 1 372 434 436266148 436266087 2.750000e-15 93.5
41 TraesCS4B01G385500 chr2B 90.278 72 6 1 369 440 790011140 790011070 2.750000e-15 93.5
42 TraesCS4B01G385500 chr2D 94.118 119 6 1 2357 2474 69221126 69221008 2.050000e-41 180.0
43 TraesCS4B01G385500 chr5B 92.623 122 9 0 2353 2474 577244734 577244855 2.660000e-40 176.0
44 TraesCS4B01G385500 chr5B 87.075 147 17 2 195 340 406066488 406066633 5.750000e-37 165.0
45 TraesCS4B01G385500 chr5B 100.000 29 0 0 1652 1680 357998680 357998652 1.000000e-03 54.7
46 TraesCS4B01G385500 chr7D 93.277 119 6 2 2357 2474 240833898 240833781 9.550000e-40 174.0
47 TraesCS4B01G385500 chr7D 92.562 121 9 0 2357 2477 578069954 578069834 9.550000e-40 174.0
48 TraesCS4B01G385500 chr7D 91.304 69 6 0 372 440 9831126 9831058 7.650000e-16 95.3
49 TraesCS4B01G385500 chr5D 92.424 66 4 1 369 434 537372154 537372218 2.750000e-15 93.5
50 TraesCS4B01G385500 chr7A 78.676 136 18 10 1912 2041 644276408 644276278 2.140000e-11 80.5
51 TraesCS4B01G385500 chr1A 86.154 65 7 2 1985 2048 324567180 324567243 4.640000e-08 69.4
52 TraesCS4B01G385500 chr1A 93.333 45 2 1 2004 2048 496463773 496463730 6.000000e-07 65.8


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 TraesCS4B01G385500 chr4B 664391766 664394362 2596 True 4796.00 4796 100.00000 1 2597 1 chr4B.!!$R3 2596
1 TraesCS4B01G385500 chr4D 506746251 506748603 2352 False 1324.00 2023 92.42650 545 2358 2 chr4D.!!$F6 1813
2 TraesCS4B01G385500 chr4D 506735074 506735647 573 False 616.00 616 86.82800 1 549 1 chr4D.!!$F1 548
3 TraesCS4B01G385500 chr5A 702996763 702999043 2280 False 1138.50 1820 90.95350 610 2268 2 chr5A.!!$F2 1658
4 TraesCS4B01G385500 chr3B 800218616 800224542 5926 False 777.25 1672 90.30925 1 2358 4 chr3B.!!$F1 2357
5 TraesCS4B01G385500 chr3B 800615441 800616432 991 False 687.50 1225 93.07950 1462 2568 2 chr3B.!!$F2 1106

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
318 319 0.894184 GATAGAGGGGCGATGACGGA 60.894 60.000 0.0 0.0 40.15 4.69 F
1343 4669 1.071699 CTTCTTGTTCACGGAGGGGAA 59.928 52.381 0.0 0.0 0.00 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1550 4876 1.675641 GAATCAACCGGTGGCAGCT 60.676 57.895 8.52 0.0 0.00 4.24 R
2450 6945 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.0 44.66 2.12 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
39 40 1.963515 ACTCGCTTTCAATTTTGCCCT 59.036 42.857 0.00 0.00 0.00 5.19
67 68 1.804151 CGATTTTCGACCAAAGGCAGA 59.196 47.619 0.00 0.00 43.74 4.26
72 73 1.004560 CGACCAAAGGCAGAGCTCA 60.005 57.895 17.77 0.00 0.00 4.26
190 191 6.593770 GGTCTTCAAGTTTGTTTTTGGAACAT 59.406 34.615 0.00 0.00 39.30 2.71
218 219 1.933181 CTTGATTGACGGCGATTGCTA 59.067 47.619 16.62 0.00 42.25 3.49
269 270 2.808543 GCAAGATGACTTTCCGACTGTT 59.191 45.455 0.00 0.00 33.70 3.16
296 297 3.214328 CAACAAGTTGTGCCTAACTCCT 58.786 45.455 9.79 0.00 39.86 3.69
318 319 0.894184 GATAGAGGGGCGATGACGGA 60.894 60.000 0.00 0.00 40.15 4.69
360 361 1.257539 GTGCTTGTAGTCGTCGCTAC 58.742 55.000 15.52 15.52 41.13 3.58
387 416 5.091431 GTCGCTAGTATTCGTTGTACTGTT 58.909 41.667 0.00 0.00 34.43 3.16
427 456 2.442413 TCGGAAATTCTCCCGCAAAAT 58.558 42.857 8.48 0.00 44.96 1.82
485 514 6.842282 CACAAACGTTTATATATACACGCACC 59.158 38.462 24.37 0.00 39.34 5.01
509 538 2.093106 ACTCACCTCTACGACCACATC 58.907 52.381 0.00 0.00 0.00 3.06
550 3875 3.567478 AAACACCTCTCAGAGCACTTT 57.433 42.857 0.00 0.00 0.00 2.66
582 3907 5.499139 TTCTTATTTTGGGATAAGCTGCG 57.501 39.130 0.00 0.00 38.76 5.18
607 3932 3.985019 TTTTACTCCTCGCACCCAATA 57.015 42.857 0.00 0.00 0.00 1.90
611 3936 1.207329 ACTCCTCGCACCCAATACTTC 59.793 52.381 0.00 0.00 0.00 3.01
643 3968 2.549926 TGTGCTCTACAATGCATACGG 58.450 47.619 0.00 0.00 41.45 4.02
659 3984 8.846943 ATGCATACGGTTCATTATGATAAGAA 57.153 30.769 0.00 0.00 0.00 2.52
703 4028 3.904136 ACTGTGTGCATGCTTAGTTTC 57.096 42.857 20.33 3.29 0.00 2.78
747 4072 4.092816 CGCACACGTTTCACTTTTAGTTT 58.907 39.130 0.00 0.00 33.53 2.66
822 4148 8.860088 AGTGATTTTTGTAAAAGCTACTTCCAT 58.140 29.630 0.00 0.00 0.00 3.41
892 4218 5.886960 AAAGAAGAGATGATGAAAACGGG 57.113 39.130 0.00 0.00 0.00 5.28
925 4251 8.414003 CCTATATATATCGCAGAAACCAGCTTA 58.586 37.037 0.00 0.00 43.58 3.09
966 4292 1.745232 ACAAACCAGCGTTGTCTCAA 58.255 45.000 0.00 0.00 30.72 3.02
1227 4553 3.671411 AACGAGCTGCGAGACGGT 61.671 61.111 11.64 6.46 44.57 4.83
1233 4559 3.518998 CTGCGAGACGGTCCGGAT 61.519 66.667 17.28 2.77 0.00 4.18
1254 4580 3.805307 CTCCGCTCGTCGCTCTGT 61.805 66.667 0.00 0.00 36.73 3.41
1337 4663 2.198406 CGTCAACTTCTTGTTCACGGA 58.802 47.619 0.00 0.00 46.75 4.69
1343 4669 1.071699 CTTCTTGTTCACGGAGGGGAA 59.928 52.381 0.00 0.00 0.00 3.97
1394 4720 1.134670 CCCCATTCTGGACTTCGAGAC 60.135 57.143 0.00 0.00 40.96 3.36
1404 4730 1.289066 CTTCGAGACCACCTGCGAA 59.711 57.895 0.00 0.00 40.03 4.70
1512 4838 5.163642 CGATAAGTACAGTGTCTACAGGCTT 60.164 44.000 0.00 0.00 0.00 4.35
1550 4876 3.680786 CTCGGACCGTCTGCCACA 61.681 66.667 14.79 0.00 0.00 4.17
1633 4959 3.753797 GCTAGCTGCTTGGTTTAAGTTCT 59.246 43.478 7.79 0.00 38.70 3.01
1666 4992 2.551270 CGCCAGAAACGTGCTGTC 59.449 61.111 15.10 4.26 0.00 3.51
1695 5021 1.064314 TGCGGCCCAGGTTAATATGTT 60.064 47.619 0.00 0.00 0.00 2.71
1747 5073 0.620556 ACACCTAGTGCTTGGGGATG 59.379 55.000 8.82 0.00 36.98 3.51
1879 5793 3.199677 CCCACCATAAAATGCATGCAAG 58.800 45.455 26.68 10.20 0.00 4.01
1966 6461 5.049886 CGTTTCACCACATATCCATCTCATG 60.050 44.000 0.00 0.00 0.00 3.07
1973 6468 3.326006 ACATATCCATCTCATGAACGGCT 59.674 43.478 0.00 0.00 0.00 5.52
2134 6629 4.397103 CAGCAACACACATGGTATCATCTT 59.603 41.667 0.00 0.00 0.00 2.40
2142 6637 9.023962 ACACACATGGTATCATCTTGTAAAATT 57.976 29.630 0.00 0.00 29.91 1.82
2208 6703 0.548031 TGGGATGCTGGGACATCTTC 59.452 55.000 4.67 0.00 44.81 2.87
2211 6706 1.476471 GGATGCTGGGACATCTTCCTG 60.476 57.143 4.67 0.00 42.92 3.86
2269 6764 6.094048 GGCATCAGTTAGCTCTTGTATTCAAA 59.906 38.462 0.00 0.00 32.87 2.69
2271 6766 7.065085 GCATCAGTTAGCTCTTGTATTCAAAGA 59.935 37.037 0.00 0.00 32.87 2.52
2303 6798 8.671921 GCAGTCTTTCTCTTTGATCATTCATAA 58.328 33.333 0.00 0.00 0.00 1.90
2363 6858 9.372369 GGCTAGATTCAATATAAATTACTCGCT 57.628 33.333 0.00 0.00 0.00 4.93
2366 6861 8.467402 AGATTCAATATAAATTACTCGCTCCG 57.533 34.615 0.00 0.00 0.00 4.63
2367 6862 8.088981 AGATTCAATATAAATTACTCGCTCCGT 58.911 33.333 0.00 0.00 0.00 4.69
2368 6863 7.633361 TTCAATATAAATTACTCGCTCCGTC 57.367 36.000 0.00 0.00 0.00 4.79
2369 6864 6.154445 TCAATATAAATTACTCGCTCCGTCC 58.846 40.000 0.00 0.00 0.00 4.79
2370 6865 2.480224 TAAATTACTCGCTCCGTCCG 57.520 50.000 0.00 0.00 0.00 4.79
2371 6866 0.179119 AAATTACTCGCTCCGTCCGG 60.179 55.000 0.00 0.00 0.00 5.14
2372 6867 1.033746 AATTACTCGCTCCGTCCGGA 61.034 55.000 0.00 0.00 42.90 5.14
2373 6868 1.033746 ATTACTCGCTCCGTCCGGAA 61.034 55.000 5.23 0.00 44.66 4.30
2374 6869 1.243342 TTACTCGCTCCGTCCGGAAA 61.243 55.000 5.23 0.00 44.66 3.13
2375 6870 1.033746 TACTCGCTCCGTCCGGAAAT 61.034 55.000 5.23 0.00 44.66 2.17
2376 6871 1.033746 ACTCGCTCCGTCCGGAAATA 61.034 55.000 5.23 0.00 44.66 1.40
2377 6872 0.594284 CTCGCTCCGTCCGGAAATAC 60.594 60.000 5.23 0.00 44.66 1.89
2378 6873 1.033746 TCGCTCCGTCCGGAAATACT 61.034 55.000 5.23 0.00 44.66 2.12
2379 6874 0.179119 CGCTCCGTCCGGAAATACTT 60.179 55.000 5.23 0.00 44.66 2.24
2380 6875 1.287425 GCTCCGTCCGGAAATACTTG 58.713 55.000 5.23 0.00 44.66 3.16
2381 6876 1.405121 GCTCCGTCCGGAAATACTTGT 60.405 52.381 5.23 0.00 44.66 3.16
2382 6877 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
2383 6878 2.165845 CTCCGTCCGGAAATACTTGTCT 59.834 50.000 5.23 0.00 44.66 3.41
2384 6879 2.165030 TCCGTCCGGAAATACTTGTCTC 59.835 50.000 5.23 0.00 42.05 3.36
2385 6880 2.182825 CGTCCGGAAATACTTGTCTCG 58.817 52.381 5.23 0.00 0.00 4.04
2386 6881 2.537401 GTCCGGAAATACTTGTCTCGG 58.463 52.381 5.23 0.00 37.61 4.63
2387 6882 1.479323 TCCGGAAATACTTGTCTCGGG 59.521 52.381 0.00 0.00 36.99 5.14
2388 6883 1.479323 CCGGAAATACTTGTCTCGGGA 59.521 52.381 0.00 0.00 31.69 5.14
2389 6884 2.102588 CCGGAAATACTTGTCTCGGGAT 59.897 50.000 0.00 0.00 31.69 3.85
2390 6885 3.431766 CCGGAAATACTTGTCTCGGGATT 60.432 47.826 0.00 0.00 31.69 3.01
2391 6886 3.555956 CGGAAATACTTGTCTCGGGATTG 59.444 47.826 0.00 0.00 0.00 2.67
2392 6887 3.877508 GGAAATACTTGTCTCGGGATTGG 59.122 47.826 0.00 0.00 0.00 3.16
2393 6888 4.383770 GGAAATACTTGTCTCGGGATTGGA 60.384 45.833 0.00 0.00 0.00 3.53
2394 6889 5.368989 GAAATACTTGTCTCGGGATTGGAT 58.631 41.667 0.00 0.00 0.00 3.41
2395 6890 2.698855 ACTTGTCTCGGGATTGGATG 57.301 50.000 0.00 0.00 0.00 3.51
2396 6891 1.909302 ACTTGTCTCGGGATTGGATGT 59.091 47.619 0.00 0.00 0.00 3.06
2397 6892 3.104512 ACTTGTCTCGGGATTGGATGTA 58.895 45.455 0.00 0.00 0.00 2.29
2398 6893 3.711704 ACTTGTCTCGGGATTGGATGTAT 59.288 43.478 0.00 0.00 0.00 2.29
2399 6894 4.202264 ACTTGTCTCGGGATTGGATGTATC 60.202 45.833 0.00 0.00 0.00 2.24
2400 6895 3.576861 TGTCTCGGGATTGGATGTATCT 58.423 45.455 0.00 0.00 0.00 1.98
2401 6896 4.736473 TGTCTCGGGATTGGATGTATCTA 58.264 43.478 0.00 0.00 0.00 1.98
2402 6897 4.767409 TGTCTCGGGATTGGATGTATCTAG 59.233 45.833 0.00 0.00 0.00 2.43
2403 6898 5.010933 GTCTCGGGATTGGATGTATCTAGA 58.989 45.833 0.00 0.00 0.00 2.43
2404 6899 5.654650 GTCTCGGGATTGGATGTATCTAGAT 59.345 44.000 10.73 10.73 0.00 1.98
2405 6900 5.654209 TCTCGGGATTGGATGTATCTAGATG 59.346 44.000 15.79 0.00 0.00 2.90
2406 6901 5.333581 TCGGGATTGGATGTATCTAGATGT 58.666 41.667 15.79 1.25 0.00 3.06
2407 6902 6.490492 TCGGGATTGGATGTATCTAGATGTA 58.510 40.000 15.79 4.44 0.00 2.29
2408 6903 7.126061 TCGGGATTGGATGTATCTAGATGTAT 58.874 38.462 15.79 9.11 0.00 2.29
2409 6904 7.619698 TCGGGATTGGATGTATCTAGATGTATT 59.380 37.037 15.79 0.00 0.00 1.89
2410 6905 8.260818 CGGGATTGGATGTATCTAGATGTATTT 58.739 37.037 15.79 0.00 0.00 1.40
2411 6906 9.965902 GGGATTGGATGTATCTAGATGTATTTT 57.034 33.333 15.79 0.00 0.00 1.82
2462 6957 4.996062 TTTTCGACAAGTATTTCCGGAC 57.004 40.909 1.83 0.00 0.00 4.79
2463 6958 2.267188 TCGACAAGTATTTCCGGACG 57.733 50.000 1.83 0.27 0.00 4.79
2464 6959 1.135315 TCGACAAGTATTTCCGGACGG 60.135 52.381 1.83 3.96 0.00 4.79
2465 6960 1.135315 CGACAAGTATTTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
2466 6961 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
2467 6962 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
2468 6963 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
2469 6964 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
2470 6965 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
2471 6966 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
2472 6967 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
2473 6968 0.032813 TTTCCGGACGGAGGGAGTAT 60.033 55.000 13.64 0.00 46.06 2.12
2474 6969 0.032813 TTCCGGACGGAGGGAGTATT 60.033 55.000 13.64 0.00 46.06 1.89
2475 6970 0.846015 TCCGGACGGAGGGAGTATTA 59.154 55.000 9.76 0.00 39.76 0.98
2476 6971 1.426598 TCCGGACGGAGGGAGTATTAT 59.573 52.381 9.76 0.00 39.76 1.28
2477 6972 1.817447 CCGGACGGAGGGAGTATTATC 59.183 57.143 4.40 0.00 37.50 1.75
2478 6973 1.817447 CGGACGGAGGGAGTATTATCC 59.183 57.143 0.00 0.00 38.76 2.59
2479 6974 2.816712 CGGACGGAGGGAGTATTATCCA 60.817 54.545 0.00 0.00 41.52 3.41
2480 6975 3.442076 GGACGGAGGGAGTATTATCCAT 58.558 50.000 0.00 0.00 41.52 3.41
2481 6976 3.195825 GGACGGAGGGAGTATTATCCATG 59.804 52.174 0.00 0.00 41.52 3.66
2489 6984 5.046014 AGGGAGTATTATCCATGCTAAGCTG 60.046 44.000 0.00 0.00 41.52 4.24
2536 7031 7.670979 TCCATCAAATCAGATACCCCAAATATG 59.329 37.037 0.00 0.00 0.00 1.78
2561 7056 2.726691 GACGTCCGAATGTGCCACG 61.727 63.158 3.51 0.00 36.54 4.94
2574 7069 3.813596 CCACGGGCAGCAGATAAC 58.186 61.111 0.00 0.00 0.00 1.89
2575 7070 2.173669 CCACGGGCAGCAGATAACG 61.174 63.158 0.00 0.00 0.00 3.18
2576 7071 2.173669 CACGGGCAGCAGATAACGG 61.174 63.158 0.00 0.00 0.00 4.44
2577 7072 2.588877 CGGGCAGCAGATAACGGG 60.589 66.667 0.00 0.00 0.00 5.28
2578 7073 2.902343 GGGCAGCAGATAACGGGC 60.902 66.667 0.00 0.00 0.00 6.13
2579 7074 2.124736 GGCAGCAGATAACGGGCA 60.125 61.111 0.00 0.00 0.00 5.36
2580 7075 2.182842 GGCAGCAGATAACGGGCAG 61.183 63.158 0.00 0.00 0.00 4.85
2581 7076 2.828128 GCAGCAGATAACGGGCAGC 61.828 63.158 0.00 0.00 33.03 5.25
2582 7077 2.182842 CAGCAGATAACGGGCAGCC 61.183 63.158 1.26 1.26 0.00 4.85
2583 7078 2.124736 GCAGATAACGGGCAGCCA 60.125 61.111 15.19 0.00 0.00 4.75
2584 7079 1.526917 GCAGATAACGGGCAGCCAT 60.527 57.895 15.19 0.00 0.00 4.40
2585 7080 1.510480 GCAGATAACGGGCAGCCATC 61.510 60.000 15.19 7.61 0.00 3.51
2586 7081 0.886490 CAGATAACGGGCAGCCATCC 60.886 60.000 15.19 0.00 0.00 3.51
2587 7082 1.148273 GATAACGGGCAGCCATCCA 59.852 57.895 15.19 0.00 0.00 3.41
2588 7083 1.152963 ATAACGGGCAGCCATCCAC 60.153 57.895 15.19 0.00 0.00 4.02
2589 7084 2.624674 ATAACGGGCAGCCATCCACC 62.625 60.000 15.19 0.00 0.00 4.61
2591 7086 3.479203 CGGGCAGCCATCCACCTA 61.479 66.667 15.19 0.00 0.00 3.08
2592 7087 2.822637 CGGGCAGCCATCCACCTAT 61.823 63.158 15.19 0.00 0.00 2.57
2593 7088 1.480212 CGGGCAGCCATCCACCTATA 61.480 60.000 15.19 0.00 0.00 1.31
2594 7089 0.995024 GGGCAGCCATCCACCTATAT 59.005 55.000 15.19 0.00 0.00 0.86
2595 7090 1.340405 GGGCAGCCATCCACCTATATG 60.340 57.143 15.19 0.00 0.00 1.78
2596 7091 1.630369 GGCAGCCATCCACCTATATGA 59.370 52.381 6.55 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 4.657502 TCGAAAATCGCACCGACA 57.342 50.000 0.00 0.00 40.21 4.35
72 73 3.612247 ATCGGTTGGCTGCTCGCTT 62.612 57.895 0.00 0.00 39.13 4.68
152 153 5.580998 ACTTGAAGACCCAGTAGACTATCA 58.419 41.667 0.00 0.00 0.00 2.15
190 191 7.351981 CAATCGCCGTCAATCAAGAATAATTA 58.648 34.615 0.00 0.00 0.00 1.40
204 205 1.570813 CAGAATAGCAATCGCCGTCA 58.429 50.000 0.00 0.00 39.83 4.35
218 219 0.981183 TAGGACCAACGCACCAGAAT 59.019 50.000 0.00 0.00 0.00 2.40
269 270 6.350906 AGTTAGGCACAACTTGTTGTAGTAA 58.649 36.000 17.26 12.30 35.16 2.24
290 291 1.403687 GCCCCTCTATCGCAGGAGTT 61.404 60.000 0.00 0.00 31.91 3.01
296 297 1.530655 TCATCGCCCCTCTATCGCA 60.531 57.895 0.00 0.00 0.00 5.10
360 361 1.844357 CAACGAATACTAGCGACCACG 59.156 52.381 0.00 0.00 42.93 4.94
367 368 8.798748 ATCATAACAGTACAACGAATACTAGC 57.201 34.615 0.00 0.00 31.53 3.42
409 438 6.394809 TCTTTTATTTTGCGGGAGAATTTCC 58.605 36.000 0.00 0.00 46.00 3.13
416 445 5.983118 ACAAACTTCTTTTATTTTGCGGGAG 59.017 36.000 0.00 0.00 33.13 4.30
427 456 8.888579 TGTGTTCCAAAAACAAACTTCTTTTA 57.111 26.923 0.00 0.00 31.20 1.52
485 514 2.419324 GTGGTCGTAGAGGTGAGTGTAG 59.581 54.545 0.00 0.00 36.95 2.74
509 538 0.750850 CAGGGATAGGGTGTACGTGG 59.249 60.000 0.00 0.00 0.00 4.94
550 3875 3.326297 CCCAAAATAAGAAAGGTTGGCCA 59.674 43.478 0.00 0.00 37.91 5.36
582 3907 2.418976 GGGTGCGAGGAGTAAAAACATC 59.581 50.000 0.00 0.00 0.00 3.06
607 3932 4.018960 AGAGCACATGGTCCAAATAGAAGT 60.019 41.667 7.44 0.00 43.11 3.01
611 3936 4.769688 TGTAGAGCACATGGTCCAAATAG 58.230 43.478 7.44 0.00 43.11 1.73
659 3984 5.496556 TCGAACCAAATCCTGTGTGATAAT 58.503 37.500 0.00 0.00 0.00 1.28
747 4072 2.747989 CCTGTCGCACACTCTAGAGTTA 59.252 50.000 23.01 3.84 40.20 2.24
822 4148 3.120130 ACGACGCAAAAGTGAAAACTTCA 60.120 39.130 0.00 0.00 37.33 3.02
885 4211 1.587066 TATAGGCTCCACCCCGTTTT 58.413 50.000 0.00 0.00 40.58 2.43
892 4218 4.827835 TCTGCGATATATATAGGCTCCACC 59.172 45.833 15.45 0.00 39.61 4.61
966 4292 6.523840 TGGTAGTATGAACGTACTGGTTTTT 58.476 36.000 14.56 0.00 36.39 1.94
1079 4405 4.676586 CCCAAACGTTGTCGCCGC 62.677 66.667 0.00 0.00 41.18 6.53
1185 4511 4.612412 ACGCCGAACTGCCCGAAA 62.612 61.111 0.00 0.00 0.00 3.46
1428 4754 2.558821 CGCGCCATCCGAAAAACA 59.441 55.556 0.00 0.00 40.02 2.83
1512 4838 3.326006 AGCTGACTTGAATGAAGAGGTCA 59.674 43.478 0.00 0.00 41.67 4.02
1550 4876 1.675641 GAATCAACCGGTGGCAGCT 60.676 57.895 8.52 0.00 0.00 4.24
1593 4919 6.540189 CAGCTAGCACAACCTTAGTATTTCAT 59.460 38.462 18.83 0.00 0.00 2.57
1633 4959 3.320826 TCTGGCGCTACAGATAATAAGCA 59.679 43.478 11.71 0.00 42.26 3.91
1695 5021 1.818060 TCGATTTTACTCCGACGGGAA 59.182 47.619 15.25 3.31 43.27 3.97
1739 5065 2.075355 AACTTCGCCACCATCCCCAA 62.075 55.000 0.00 0.00 0.00 4.12
1747 5073 2.554893 TCCATTAACAAACTTCGCCACC 59.445 45.455 0.00 0.00 0.00 4.61
1843 5757 3.403322 TGGTGGGCCCTTAAAGAGATAT 58.597 45.455 25.70 0.00 0.00 1.63
1943 6437 6.057533 TCATGAGATGGATATGTGGTGAAAC 58.942 40.000 0.00 0.00 0.00 2.78
1945 6439 5.892524 TCATGAGATGGATATGTGGTGAA 57.107 39.130 0.00 0.00 0.00 3.18
1966 6461 2.030946 GCATATGTTCAGTGAGCCGTTC 59.969 50.000 4.29 0.00 0.00 3.95
1973 6468 3.929955 TCCCATGCATATGTTCAGTGA 57.070 42.857 0.00 0.00 32.21 3.41
2037 6532 9.620660 AACACGAATATTTGGAATAGTCAAAAC 57.379 29.630 7.61 0.00 37.60 2.43
2096 6591 3.441222 TGTTGCTGTAGGAATCATTGCAG 59.559 43.478 0.00 0.00 0.00 4.41
2208 6703 5.238868 CAGGATGATATTGTTTCTCAGCAGG 59.761 44.000 0.00 0.00 39.69 4.85
2211 6706 5.371526 TCCAGGATGATATTGTTTCTCAGC 58.628 41.667 0.00 0.00 39.69 4.26
2269 6764 5.247110 TCAAAGAGAAAGACTGCCTGTATCT 59.753 40.000 0.00 0.00 0.00 1.98
2271 6766 5.489792 TCAAAGAGAAAGACTGCCTGTAT 57.510 39.130 0.00 0.00 0.00 2.29
2303 6798 2.445682 CTGGACACTAGGTCTAGCCT 57.554 55.000 10.10 10.10 46.27 4.58
2358 6853 0.594284 GTATTTCCGGACGGAGCGAG 60.594 60.000 13.64 0.00 46.06 5.03
2360 6855 0.179119 AAGTATTTCCGGACGGAGCG 60.179 55.000 13.64 0.00 46.06 5.03
2361 6856 1.287425 CAAGTATTTCCGGACGGAGC 58.713 55.000 13.64 6.15 46.06 4.70
2363 6858 2.165030 GAGACAAGTATTTCCGGACGGA 59.835 50.000 1.83 9.76 43.52 4.69
2364 6859 2.537401 GAGACAAGTATTTCCGGACGG 58.463 52.381 1.83 3.96 0.00 4.79
2365 6860 2.182825 CGAGACAAGTATTTCCGGACG 58.817 52.381 1.83 0.00 0.00 4.79
2366 6861 2.537401 CCGAGACAAGTATTTCCGGAC 58.463 52.381 1.83 0.00 37.87 4.79
2367 6862 1.479323 CCCGAGACAAGTATTTCCGGA 59.521 52.381 0.00 0.00 37.87 5.14
2368 6863 1.479323 TCCCGAGACAAGTATTTCCGG 59.521 52.381 0.00 0.00 35.68 5.14
2369 6864 2.953466 TCCCGAGACAAGTATTTCCG 57.047 50.000 0.00 0.00 0.00 4.30
2370 6865 3.877508 CCAATCCCGAGACAAGTATTTCC 59.122 47.826 0.00 0.00 0.00 3.13
2371 6866 4.766375 TCCAATCCCGAGACAAGTATTTC 58.234 43.478 0.00 0.00 0.00 2.17
2372 6867 4.837093 TCCAATCCCGAGACAAGTATTT 57.163 40.909 0.00 0.00 0.00 1.40
2373 6868 4.164221 ACATCCAATCCCGAGACAAGTATT 59.836 41.667 0.00 0.00 0.00 1.89
2374 6869 3.711704 ACATCCAATCCCGAGACAAGTAT 59.288 43.478 0.00 0.00 0.00 2.12
2375 6870 3.104512 ACATCCAATCCCGAGACAAGTA 58.895 45.455 0.00 0.00 0.00 2.24
2376 6871 1.909302 ACATCCAATCCCGAGACAAGT 59.091 47.619 0.00 0.00 0.00 3.16
2377 6872 2.698855 ACATCCAATCCCGAGACAAG 57.301 50.000 0.00 0.00 0.00 3.16
2378 6873 3.967326 AGATACATCCAATCCCGAGACAA 59.033 43.478 0.00 0.00 0.00 3.18
2379 6874 3.576861 AGATACATCCAATCCCGAGACA 58.423 45.455 0.00 0.00 0.00 3.41
2380 6875 5.010933 TCTAGATACATCCAATCCCGAGAC 58.989 45.833 0.00 0.00 0.00 3.36
2381 6876 5.256806 TCTAGATACATCCAATCCCGAGA 57.743 43.478 0.00 0.00 0.00 4.04
2382 6877 5.420421 ACATCTAGATACATCCAATCCCGAG 59.580 44.000 4.54 0.00 0.00 4.63
2383 6878 5.333581 ACATCTAGATACATCCAATCCCGA 58.666 41.667 4.54 0.00 0.00 5.14
2384 6879 5.667539 ACATCTAGATACATCCAATCCCG 57.332 43.478 4.54 0.00 0.00 5.14
2385 6880 9.965902 AAAATACATCTAGATACATCCAATCCC 57.034 33.333 4.54 0.00 0.00 3.85
2440 6935 4.084433 CGTCCGGAAATACTTGTCGAAAAA 60.084 41.667 5.23 0.00 0.00 1.94
2441 6936 3.429543 CGTCCGGAAATACTTGTCGAAAA 59.570 43.478 5.23 0.00 0.00 2.29
2442 6937 2.988493 CGTCCGGAAATACTTGTCGAAA 59.012 45.455 5.23 0.00 0.00 3.46
2443 6938 2.598589 CGTCCGGAAATACTTGTCGAA 58.401 47.619 5.23 0.00 0.00 3.71
2444 6939 1.135315 CCGTCCGGAAATACTTGTCGA 60.135 52.381 5.23 0.00 37.50 4.20
2445 6940 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
2446 6941 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
2447 6942 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
2448 6943 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
2449 6944 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
2450 6945 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
2451 6946 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
2452 6947 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
2453 6948 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
2454 6949 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
2455 6950 0.032813 AATACTCCCTCCGTCCGGAA 60.033 55.000 5.23 0.00 44.66 4.30
2456 6951 0.846015 TAATACTCCCTCCGTCCGGA 59.154 55.000 0.00 0.00 42.90 5.14
2457 6952 1.817447 GATAATACTCCCTCCGTCCGG 59.183 57.143 0.00 0.00 0.00 5.14
2458 6953 1.817447 GGATAATACTCCCTCCGTCCG 59.183 57.143 0.00 0.00 0.00 4.79
2459 6954 2.885616 TGGATAATACTCCCTCCGTCC 58.114 52.381 0.00 0.00 34.12 4.79
2460 6955 3.368531 GCATGGATAATACTCCCTCCGTC 60.369 52.174 0.00 0.00 34.12 4.79
2461 6956 2.567615 GCATGGATAATACTCCCTCCGT 59.432 50.000 0.00 0.00 34.12 4.69
2462 6957 2.834549 AGCATGGATAATACTCCCTCCG 59.165 50.000 0.00 0.00 34.12 4.63
2463 6958 5.627968 GCTTAGCATGGATAATACTCCCTCC 60.628 48.000 0.00 0.00 34.12 4.30
2464 6959 5.188751 AGCTTAGCATGGATAATACTCCCTC 59.811 44.000 7.07 0.00 34.12 4.30
2465 6960 5.046014 CAGCTTAGCATGGATAATACTCCCT 60.046 44.000 7.07 0.00 34.12 4.20
2466 6961 5.181748 CAGCTTAGCATGGATAATACTCCC 58.818 45.833 7.07 0.00 34.12 4.30
2467 6962 4.633565 GCAGCTTAGCATGGATAATACTCC 59.366 45.833 7.07 0.00 35.74 3.85
2468 6963 5.240891 TGCAGCTTAGCATGGATAATACTC 58.759 41.667 7.07 0.00 40.11 2.59
2469 6964 5.233083 TGCAGCTTAGCATGGATAATACT 57.767 39.130 7.07 0.00 40.11 2.12
2470 6965 5.936054 CTTGCAGCTTAGCATGGATAATAC 58.064 41.667 7.07 0.00 45.19 1.89
2478 6973 1.317431 TGCCCTTGCAGCTTAGCATG 61.317 55.000 7.07 3.16 44.23 4.06
2479 6974 1.000521 TGCCCTTGCAGCTTAGCAT 60.001 52.632 7.07 0.00 44.23 3.79
2480 6975 2.435663 TGCCCTTGCAGCTTAGCA 59.564 55.556 7.07 0.00 44.23 3.49
2489 6984 2.568090 CGTTGGACATGCCCTTGC 59.432 61.111 0.00 0.00 34.97 4.01
2561 7056 2.902343 GCCCGTTATCTGCTGCCC 60.902 66.667 0.00 0.00 0.00 5.36
2568 7063 1.344953 TGGATGGCTGCCCGTTATCT 61.345 55.000 17.53 0.00 0.00 1.98
2569 7064 1.148273 TGGATGGCTGCCCGTTATC 59.852 57.895 17.53 11.99 0.00 1.75
2570 7065 1.152963 GTGGATGGCTGCCCGTTAT 60.153 57.895 17.53 2.00 0.00 1.89
2571 7066 2.270850 GTGGATGGCTGCCCGTTA 59.729 61.111 17.53 0.00 0.00 3.18
2572 7067 4.740822 GGTGGATGGCTGCCCGTT 62.741 66.667 17.53 0.20 0.00 4.44
2574 7069 1.480212 TATAGGTGGATGGCTGCCCG 61.480 60.000 17.53 0.00 0.00 6.13
2575 7070 0.995024 ATATAGGTGGATGGCTGCCC 59.005 55.000 17.53 0.58 0.00 5.36
2576 7071 1.630369 TCATATAGGTGGATGGCTGCC 59.370 52.381 12.87 12.87 0.00 4.85


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

AutoCloner maintained by Alex Coulton.