Multiple sequence alignment - TraesCS6B01G171700

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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 TraesCS6B01G171700 chr6B 100.000 4259 0 0 1 4259 184151626 184147368 0.000000e+00 7866.0
1 TraesCS6B01G171700 chr6B 81.606 386 44 16 372 740 565196546 565196921 1.160000e-75 294.0
2 TraesCS6B01G171700 chr6B 83.835 266 20 11 2500 2742 73888609 73888344 9.210000e-57 231.0
3 TraesCS6B01G171700 chr6B 81.271 299 30 11 2470 2742 172275986 172275688 7.170000e-53 219.0
4 TraesCS6B01G171700 chr6D 93.317 1212 51 6 458 1660 99796159 99794969 0.000000e+00 1762.0
5 TraesCS6B01G171700 chr6D 92.818 905 40 6 1659 2563 99794903 99794024 0.000000e+00 1288.0
6 TraesCS6B01G171700 chr6D 93.289 745 31 5 3533 4259 99792913 99792170 0.000000e+00 1081.0
7 TraesCS6B01G171700 chr6D 88.889 720 39 8 926 1642 100356070 100355389 0.000000e+00 848.0
8 TraesCS6B01G171700 chr6D 96.520 431 14 1 1 430 99796584 99796154 0.000000e+00 712.0
9 TraesCS6B01G171700 chr6D 91.853 491 35 5 1870 2358 100352536 100352049 0.000000e+00 680.0
10 TraesCS6B01G171700 chr6D 86.473 621 27 6 2630 3213 99794012 99793412 2.800000e-176 628.0
11 TraesCS6B01G171700 chr6D 82.030 473 39 12 2636 3070 100350317 100349853 1.130000e-95 361.0
12 TraesCS6B01G171700 chr6D 92.237 219 16 1 3211 3428 99793332 99793114 4.140000e-80 309.0
13 TraesCS6B01G171700 chr6D 82.558 344 29 10 3700 4020 100349070 100348735 1.510000e-69 274.0
14 TraesCS6B01G171700 chr6D 88.333 60 6 1 2300 2359 99794339 99794281 2.120000e-08 71.3
15 TraesCS6B01G171700 chr6A 88.183 1244 79 31 2247 3428 119754957 119753720 0.000000e+00 1421.0
16 TraesCS6B01G171700 chr6A 93.099 739 33 9 926 1660 119758679 119757955 0.000000e+00 1066.0
17 TraesCS6B01G171700 chr6A 91.375 742 43 4 3533 4259 119753471 119752736 0.000000e+00 996.0
18 TraesCS6B01G171700 chr6A 96.352 466 16 1 1834 2299 119757491 119757027 0.000000e+00 765.0
19 TraesCS6B01G171700 chr6A 79.377 514 72 18 372 857 70226497 70225990 8.830000e-87 331.0
20 TraesCS6B01G171700 chr6A 96.316 190 7 0 1659 1848 119757889 119757700 3.200000e-81 313.0
21 TraesCS6B01G171700 chr6A 77.621 496 77 27 372 845 520391012 520391495 1.950000e-68 270.0
22 TraesCS6B01G171700 chr7B 82.979 376 54 5 372 740 205632275 205631903 8.830000e-87 331.0
23 TraesCS6B01G171700 chr7B 81.979 283 27 10 2481 2739 642774260 642774542 7.170000e-53 219.0
24 TraesCS6B01G171700 chr7B 84.483 116 9 5 254 368 356102178 356102071 5.820000e-19 106.0
25 TraesCS6B01G171700 chr7B 80.645 124 14 4 247 368 470417972 470418087 2.110000e-13 87.9
26 TraesCS6B01G171700 chr2D 84.733 262 32 5 484 740 506519415 506519157 5.460000e-64 255.0
27 TraesCS6B01G171700 chr5B 85.950 242 29 2 374 613 491819895 491820133 1.970000e-63 254.0
28 TraesCS6B01G171700 chr5B 83.761 117 14 5 254 368 678400327 678400440 5.820000e-19 106.0
29 TraesCS6B01G171700 chr5B 80.833 120 14 3 251 368 554793960 554794072 7.590000e-13 86.1
30 TraesCS6B01G171700 chr2B 85.124 242 31 2 374 613 632384307 632384069 4.250000e-60 243.0
31 TraesCS6B01G171700 chr2B 84.711 242 32 2 374 613 98400435 98400673 1.980000e-58 237.0
32 TraesCS6B01G171700 chr2B 82.332 283 26 10 2481 2739 66034811 66035093 1.540000e-54 224.0
33 TraesCS6B01G171700 chr4A 86.916 214 18 4 2481 2684 714216444 714216231 9.210000e-57 231.0
34 TraesCS6B01G171700 chr4A 79.933 299 24 14 2479 2742 734875567 734875270 2.020000e-43 187.0
35 TraesCS6B01G171700 chr4A 76.531 294 39 16 525 791 741531727 741532017 2.670000e-27 134.0
36 TraesCS6B01G171700 chr4A 81.215 181 15 8 2581 2742 736113745 736113565 1.240000e-25 128.0
37 TraesCS6B01G171700 chr4B 82.197 264 23 10 2503 2742 42543351 42543088 5.580000e-49 206.0
38 TraesCS6B01G171700 chr4B 80.672 119 13 5 253 368 311054225 311054114 2.730000e-12 84.2
39 TraesCS6B01G171700 chr7D 75.054 465 81 24 372 816 454095307 454094858 2.620000e-42 183.0
40 TraesCS6B01G171700 chr5D 89.565 115 11 1 254 368 543048357 543048244 1.230000e-30 145.0
41 TraesCS6B01G171700 chr5D 82.609 138 20 4 606 740 242616567 242616703 7.480000e-23 119.0
42 TraesCS6B01G171700 chr2A 84.874 119 16 2 251 368 656357586 656357469 7.480000e-23 119.0
43 TraesCS6B01G171700 chr3B 85.000 120 13 5 247 364 9227186 9227302 2.690000e-22 117.0
44 TraesCS6B01G171700 chr1D 84.706 85 10 3 657 740 467236783 467236865 9.820000e-12 82.4
45 TraesCS6B01G171700 chr1D 83.146 89 8 5 626 712 204795651 204795568 1.640000e-09 75.0
46 TraesCS6B01G171700 chr3A 88.462 52 5 1 886 936 460863311 460863362 1.280000e-05 62.1
47 TraesCS6B01G171700 chr3D 96.875 32 1 0 899 930 520728038 520728007 2.000000e-03 54.7


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 TraesCS6B01G171700 chr6B 184147368 184151626 4258 True 7866.00 7866 100.000000 1 4259 1 chr6B.!!$R3 4258
1 TraesCS6B01G171700 chr6D 99792170 99796584 4414 True 835.90 1762 91.855286 1 4259 7 chr6D.!!$R1 4258
2 TraesCS6B01G171700 chr6D 100348735 100356070 7335 True 540.75 848 86.332500 926 4020 4 chr6D.!!$R2 3094
3 TraesCS6B01G171700 chr6A 119752736 119758679 5943 True 912.20 1421 93.065000 926 4259 5 chr6A.!!$R2 3333
4 TraesCS6B01G171700 chr6A 70225990 70226497 507 True 331.00 331 79.377000 372 857 1 chr6A.!!$R1 485

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
879 939 0.250295 CACATCGGTTGGACACAGGT 60.250 55.0 0.00 0.0 0.00 4.00 F
981 1041 1.239347 GGCCCATCTTTATTCGGCTC 58.761 55.0 0.00 0.0 39.64 4.70 F
2230 7316 0.764890 TGCCTCTGTACTGTTTGGCT 59.235 50.0 22.68 0.0 40.82 4.75 F
2724 9356 0.689055 TCAATGGACACTGCTCTGCT 59.311 50.0 0.00 0.0 0.00 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1904 4845 0.251341 ATGGTGCCCAAACTCAGACC 60.251 55.000 0.0 0.0 36.95 3.85 R
2634 9266 1.756538 CAAACTCACCAAGCAAGGGTT 59.243 47.619 0.0 0.0 36.19 4.11 R
3081 9754 0.679505 AGGCTCACAGCTAACGAACA 59.320 50.000 0.0 0.0 41.99 3.18 R
3641 10834 1.357991 GAAGAGGCTTCTGCTCGCAC 61.358 60.000 0.0 0.0 39.59 5.34 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
23 24 5.641709 GCTTCTCTTATTTGCTAACCAACC 58.358 41.667 0.00 0.00 31.97 3.77
153 154 5.645056 TGATGCCCATCTAACCATAAGAA 57.355 39.130 9.44 0.00 38.60 2.52
160 161 5.455326 CCCATCTAACCATAAGAACCAGGAG 60.455 48.000 0.00 0.00 0.00 3.69
216 217 1.521681 GCAGTGTATCAGCCCGACC 60.522 63.158 0.00 0.00 0.00 4.79
231 232 1.483004 CCGACCAAAAAGGGGTGTTTT 59.517 47.619 0.00 0.00 43.89 2.43
251 252 2.112190 TCGATACACCTGGCAACCATA 58.888 47.619 0.00 0.00 30.82 2.74
252 253 2.502130 TCGATACACCTGGCAACCATAA 59.498 45.455 0.00 0.00 30.82 1.90
259 260 2.491693 ACCTGGCAACCATAATGAAACG 59.508 45.455 0.00 0.00 30.82 3.60
269 270 6.968131 ACCATAATGAAACGATCGATATGG 57.032 37.500 24.34 24.72 45.67 2.74
301 303 0.722676 AGGAGGTGGGGTGAATAGGA 59.277 55.000 0.00 0.00 0.00 2.94
343 345 9.801873 GCTCTTTTAATCAAATTATGGTTAGCA 57.198 29.630 0.00 0.00 36.04 3.49
432 434 3.489391 TCGAGATCGAGGCTACCAA 57.511 52.632 0.00 0.00 44.22 3.67
433 435 1.758936 TCGAGATCGAGGCTACCAAA 58.241 50.000 0.00 0.00 44.22 3.28
434 436 1.676529 TCGAGATCGAGGCTACCAAAG 59.323 52.381 0.00 0.00 44.22 2.77
435 437 1.866063 CGAGATCGAGGCTACCAAAGC 60.866 57.143 0.00 0.00 46.18 3.51
443 445 3.339547 GCTACCAAAGCCAAGACCA 57.660 52.632 0.00 0.00 46.25 4.02
444 446 1.616159 GCTACCAAAGCCAAGACCAA 58.384 50.000 0.00 0.00 46.25 3.67
445 447 1.960689 GCTACCAAAGCCAAGACCAAA 59.039 47.619 0.00 0.00 46.25 3.28
446 448 2.364002 GCTACCAAAGCCAAGACCAAAA 59.636 45.455 0.00 0.00 46.25 2.44
447 449 2.979814 ACCAAAGCCAAGACCAAAAC 57.020 45.000 0.00 0.00 0.00 2.43
448 450 2.183679 ACCAAAGCCAAGACCAAAACA 58.816 42.857 0.00 0.00 0.00 2.83
449 451 2.569404 ACCAAAGCCAAGACCAAAACAA 59.431 40.909 0.00 0.00 0.00 2.83
450 452 3.008485 ACCAAAGCCAAGACCAAAACAAA 59.992 39.130 0.00 0.00 0.00 2.83
451 453 4.006319 CCAAAGCCAAGACCAAAACAAAA 58.994 39.130 0.00 0.00 0.00 2.44
452 454 4.094739 CCAAAGCCAAGACCAAAACAAAAG 59.905 41.667 0.00 0.00 0.00 2.27
453 455 4.817318 AAGCCAAGACCAAAACAAAAGA 57.183 36.364 0.00 0.00 0.00 2.52
454 456 4.817318 AGCCAAGACCAAAACAAAAGAA 57.183 36.364 0.00 0.00 0.00 2.52
455 457 4.758688 AGCCAAGACCAAAACAAAAGAAG 58.241 39.130 0.00 0.00 0.00 2.85
456 458 4.222810 AGCCAAGACCAAAACAAAAGAAGT 59.777 37.500 0.00 0.00 0.00 3.01
457 459 4.329801 GCCAAGACCAAAACAAAAGAAGTG 59.670 41.667 0.00 0.00 0.00 3.16
458 460 4.869861 CCAAGACCAAAACAAAAGAAGTGG 59.130 41.667 0.00 0.00 0.00 4.00
459 461 4.123497 AGACCAAAACAAAAGAAGTGGC 57.877 40.909 0.00 0.00 0.00 5.01
716 765 3.549423 GCGTCGGCATGAACTATGTAGTA 60.549 47.826 0.00 0.00 39.08 1.82
740 800 1.766494 TTGAAGCCTGGCATGTATGG 58.234 50.000 22.65 0.00 0.00 2.74
762 822 1.550524 AGTCGCCAGCATAAACTCTGA 59.449 47.619 0.00 0.00 32.26 3.27
793 853 0.599728 GACCGCTGGCATGATCTCTC 60.600 60.000 0.00 0.00 0.00 3.20
837 897 8.385898 AGTTCAAATTATTTTCTACGTGGACA 57.614 30.769 0.00 0.00 0.00 4.02
861 921 1.543065 TTAGGTCGGCCGGTTAAGCA 61.543 55.000 27.83 0.00 40.50 3.91
865 925 1.448893 TCGGCCGGTTAAGCACATC 60.449 57.895 27.83 0.00 0.00 3.06
879 939 0.250295 CACATCGGTTGGACACAGGT 60.250 55.000 0.00 0.00 0.00 4.00
884 944 2.527497 TCGGTTGGACACAGGTGTATA 58.473 47.619 4.84 0.00 45.05 1.47
887 947 2.997986 GGTTGGACACAGGTGTATAACG 59.002 50.000 17.60 0.00 45.05 3.18
892 952 1.542915 ACACAGGTGTATAACGAGCGT 59.457 47.619 2.68 0.00 42.90 5.07
893 953 2.029649 ACACAGGTGTATAACGAGCGTT 60.030 45.455 13.11 13.11 42.90 4.84
902 962 2.807631 TAACGAGCGTTCAGGCGACC 62.808 60.000 11.89 0.00 39.31 4.79
917 977 3.937079 AGGCGACCTAAACGGATAAAAAG 59.063 43.478 0.00 0.00 36.31 2.27
918 978 3.486375 GGCGACCTAAACGGATAAAAAGC 60.486 47.826 0.00 0.00 36.31 3.51
919 979 3.783223 GCGACCTAAACGGATAAAAAGCG 60.783 47.826 0.00 0.00 36.31 4.68
920 980 3.242188 CGACCTAAACGGATAAAAAGCGG 60.242 47.826 0.00 0.00 36.31 5.52
921 981 3.934579 GACCTAAACGGATAAAAAGCGGA 59.065 43.478 0.00 0.00 36.31 5.54
922 982 3.686241 ACCTAAACGGATAAAAAGCGGAC 59.314 43.478 0.00 0.00 36.31 4.79
923 983 3.685756 CCTAAACGGATAAAAAGCGGACA 59.314 43.478 0.00 0.00 33.16 4.02
924 984 4.154556 CCTAAACGGATAAAAAGCGGACAA 59.845 41.667 0.00 0.00 33.16 3.18
981 1041 1.239347 GGCCCATCTTTATTCGGCTC 58.761 55.000 0.00 0.00 39.64 4.70
982 1042 1.476833 GGCCCATCTTTATTCGGCTCA 60.477 52.381 0.00 0.00 39.64 4.26
983 1043 1.604278 GCCCATCTTTATTCGGCTCAC 59.396 52.381 0.00 0.00 36.65 3.51
984 1044 2.222027 CCCATCTTTATTCGGCTCACC 58.778 52.381 0.00 0.00 0.00 4.02
1116 1188 2.674754 GGCATCGACCTTTCCCCA 59.325 61.111 0.00 0.00 0.00 4.96
1118 1190 1.299976 GCATCGACCTTTCCCCAGT 59.700 57.895 0.00 0.00 0.00 4.00
1246 1318 1.828595 GTTTCCCCTCCTCTCTCTGTC 59.171 57.143 0.00 0.00 0.00 3.51
1296 1368 3.609214 GAATTGGTGGGTGCGTGCG 62.609 63.158 0.00 0.00 0.00 5.34
1297 1369 4.947147 ATTGGTGGGTGCGTGCGT 62.947 61.111 0.00 0.00 0.00 5.24
1541 1619 3.509967 TCTCTCTGTTGGAATTACGCTGA 59.490 43.478 0.00 0.00 0.00 4.26
1566 1644 6.939163 ACCTTCTGTCCATATATGAGAAATGC 59.061 38.462 14.54 0.00 0.00 3.56
1569 1647 4.640364 TGTCCATATATGAGAAATGCGCA 58.360 39.130 14.96 14.96 0.00 6.09
1715 1860 5.936187 AATGGCCATTGAATTGTGACATA 57.064 34.783 30.17 0.00 0.00 2.29
1758 1903 2.364632 TGTATCAAACCCGCATGGAAG 58.635 47.619 0.00 0.00 37.49 3.46
1776 1921 4.142403 TGGAAGCAAAAATCTTAGATGCCG 60.142 41.667 0.00 0.00 37.73 5.69
1891 4832 4.930696 TGGTCACACTCTACTCTTCCATA 58.069 43.478 0.00 0.00 0.00 2.74
1912 4853 7.050377 CCATATTTTCAGTACATGGTCTGAGT 58.950 38.462 17.17 12.17 40.91 3.41
1915 4856 6.618287 TTTTCAGTACATGGTCTGAGTTTG 57.382 37.500 17.17 0.00 40.91 2.93
2229 7315 1.826385 ATGCCTCTGTACTGTTTGGC 58.174 50.000 18.84 18.84 40.62 4.52
2230 7316 0.764890 TGCCTCTGTACTGTTTGGCT 59.235 50.000 22.68 0.00 40.82 4.75
2231 7317 1.142870 TGCCTCTGTACTGTTTGGCTT 59.857 47.619 22.68 0.00 40.82 4.35
2232 7318 1.807142 GCCTCTGTACTGTTTGGCTTC 59.193 52.381 18.59 1.29 37.58 3.86
2233 7319 2.427506 CCTCTGTACTGTTTGGCTTCC 58.572 52.381 0.00 0.00 0.00 3.46
2234 7320 2.224523 CCTCTGTACTGTTTGGCTTCCA 60.225 50.000 0.00 0.00 0.00 3.53
2235 7321 3.560025 CCTCTGTACTGTTTGGCTTCCAT 60.560 47.826 0.00 0.00 31.53 3.41
2236 7322 3.674997 TCTGTACTGTTTGGCTTCCATC 58.325 45.455 0.00 0.00 31.53 3.51
2237 7323 2.749621 CTGTACTGTTTGGCTTCCATCC 59.250 50.000 0.00 0.00 31.53 3.51
2238 7324 2.092323 GTACTGTTTGGCTTCCATCCC 58.908 52.381 0.00 0.00 31.53 3.85
2239 7325 0.779997 ACTGTTTGGCTTCCATCCCT 59.220 50.000 0.00 0.00 31.53 4.20
2240 7326 1.992557 ACTGTTTGGCTTCCATCCCTA 59.007 47.619 0.00 0.00 31.53 3.53
2241 7327 2.025887 ACTGTTTGGCTTCCATCCCTAG 60.026 50.000 0.00 0.00 31.53 3.02
2242 7328 2.239654 CTGTTTGGCTTCCATCCCTAGA 59.760 50.000 0.00 0.00 31.53 2.43
2243 7329 2.239654 TGTTTGGCTTCCATCCCTAGAG 59.760 50.000 0.00 0.00 31.53 2.43
2244 7330 2.239907 GTTTGGCTTCCATCCCTAGAGT 59.760 50.000 0.00 0.00 31.53 3.24
2245 7331 2.270434 TGGCTTCCATCCCTAGAGTT 57.730 50.000 0.00 0.00 0.00 3.01
2246 7332 2.562296 TGGCTTCCATCCCTAGAGTTT 58.438 47.619 0.00 0.00 0.00 2.66
2247 7333 2.919602 TGGCTTCCATCCCTAGAGTTTT 59.080 45.455 0.00 0.00 0.00 2.43
2248 7334 3.333680 TGGCTTCCATCCCTAGAGTTTTT 59.666 43.478 0.00 0.00 0.00 1.94
2249 7335 3.696548 GGCTTCCATCCCTAGAGTTTTTG 59.303 47.826 0.00 0.00 0.00 2.44
2250 7336 3.696548 GCTTCCATCCCTAGAGTTTTTGG 59.303 47.826 0.00 0.00 0.00 3.28
2264 7350 5.299279 AGAGTTTTTGGTACATGACTGTTGG 59.701 40.000 0.00 0.00 39.30 3.77
2265 7351 4.953579 AGTTTTTGGTACATGACTGTTGGT 59.046 37.500 0.00 0.00 39.30 3.67
2331 7418 2.231478 ACTGTCGACCATGTTAGTCAGG 59.769 50.000 14.12 0.00 33.70 3.86
2413 7500 8.458843 TGAATTAACTTCTACTAATTGCTTGGC 58.541 33.333 0.00 0.00 34.75 4.52
2548 9180 6.287359 TCCATCCCCCATATATTTGGTAGAT 58.713 40.000 10.82 9.14 34.77 1.98
2621 9253 7.563020 AGTCAATATGATCTATGCCCATACAG 58.437 38.462 0.00 0.00 0.00 2.74
2625 9257 5.830799 ATGATCTATGCCCATACAGTGAA 57.169 39.130 0.00 0.00 0.00 3.18
2634 9266 5.565509 TGCCCATACAGTGAATTAACTTGA 58.434 37.500 0.00 0.00 0.00 3.02
2684 9316 6.207810 TGTTAGTAATTCCGCATTCCAAGTTT 59.792 34.615 0.00 0.00 0.00 2.66
2720 9352 2.481952 GACTGTTCAATGGACACTGCTC 59.518 50.000 0.00 0.00 0.00 4.26
2724 9356 0.689055 TCAATGGACACTGCTCTGCT 59.311 50.000 0.00 0.00 0.00 4.24
2799 9457 6.299141 ACCTACATGATGTCTCTTTGTTTGT 58.701 36.000 0.00 0.00 0.00 2.83
2801 9459 5.348418 ACATGATGTCTCTTTGTTTGTCG 57.652 39.130 0.00 0.00 0.00 4.35
2804 9463 5.596268 TGATGTCTCTTTGTTTGTCGATG 57.404 39.130 0.00 0.00 0.00 3.84
2825 9484 6.570378 CGATGTTCCTTTCATTTTGTTAGCCT 60.570 38.462 0.00 0.00 0.00 4.58
2941 9604 0.982704 AGCCAGTGACTGCTGAAGAT 59.017 50.000 7.16 0.00 38.70 2.40
2959 9622 4.970860 AGATATGGCTAACATGTCAGCT 57.029 40.909 20.36 4.46 46.63 4.24
2960 9623 4.892433 AGATATGGCTAACATGTCAGCTC 58.108 43.478 20.36 10.09 46.63 4.09
3075 9748 4.475944 CGATGAACTTGGAATGTTGGAAC 58.524 43.478 0.00 0.00 34.00 3.62
3081 9754 6.549364 TGAACTTGGAATGTTGGAACTGTAAT 59.451 34.615 0.00 0.00 34.00 1.89
3083 9756 5.833131 ACTTGGAATGTTGGAACTGTAATGT 59.167 36.000 0.00 0.00 0.00 2.71
3094 9767 4.689345 GGAACTGTAATGTTCGTTAGCTGT 59.311 41.667 0.00 0.00 45.11 4.40
3135 9818 7.604164 CAGGTTAAGATTATCAGTCTGTGTTGT 59.396 37.037 0.00 0.00 0.00 3.32
3158 9845 5.007136 GTCAACCTGTTGTTCTCTTCTTGAG 59.993 44.000 9.65 0.00 41.28 3.02
3178 9891 0.322906 GAGGGGGCTCTTTCCTGTTG 60.323 60.000 0.00 0.00 0.00 3.33
3267 10063 9.499585 GTCTTGATATGATGTGAATTTGTCTTG 57.500 33.333 0.00 0.00 0.00 3.02
3287 10083 8.201464 TGTCTTGTACGATGTGGACATATTAAT 58.799 33.333 0.00 0.00 36.57 1.40
3293 10089 9.042008 GTACGATGTGGACATATTAATTTGTCT 57.958 33.333 27.38 14.92 41.55 3.41
3342 10138 2.869101 TAACTGCCAATGTGCTACCA 57.131 45.000 0.00 0.00 0.00 3.25
3349 10145 1.339438 CCAATGTGCTACCACTGCTCT 60.339 52.381 0.00 0.00 42.54 4.09
3357 10153 2.693069 CTACCACTGCTCTCAACCTTG 58.307 52.381 0.00 0.00 0.00 3.61
3527 10667 8.902540 AAAACAAGATATGATCGGTATTAGCA 57.097 30.769 0.00 0.00 0.00 3.49
3531 10671 6.214191 AGATATGATCGGTATTAGCACAGG 57.786 41.667 0.00 0.00 0.00 4.00
3565 10758 7.622893 AAAATAAACAACATTGGCAAACAGT 57.377 28.000 3.01 0.26 0.00 3.55
3568 10761 3.441496 ACAACATTGGCAAACAGTGAG 57.559 42.857 3.01 3.45 38.97 3.51
3682 10890 5.070001 TCCAGAAAGGATAACAAACCACTG 58.930 41.667 0.00 0.00 43.07 3.66
3697 10905 1.798813 CCACTGAACCGTGTTCTAAGC 59.201 52.381 14.95 0.00 33.07 3.09
3708 10916 1.135199 TGTTCTAAGCTCTAACCCGCG 60.135 52.381 0.00 0.00 0.00 6.46
3866 11075 1.494721 TCAAAGAAACCAGGTCCAGCT 59.505 47.619 0.00 0.00 0.00 4.24
4157 11390 4.153117 GCAGTTACCATCAAGAACAGACAG 59.847 45.833 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 6.594547 AGATATGCACATATAGCAAGCAGAAG 59.405 38.462 3.17 0.00 46.27 2.85
153 154 0.818296 GCACATACGAGTCTCCTGGT 59.182 55.000 0.00 0.00 33.81 4.00
160 161 4.388773 TGAGAATTGTTGCACATACGAGTC 59.611 41.667 0.00 0.00 0.00 3.36
216 217 4.979815 GTGTATCGAAAACACCCCTTTTTG 59.020 41.667 18.75 0.00 41.10 2.44
231 232 0.908910 ATGGTTGCCAGGTGTATCGA 59.091 50.000 0.00 0.00 36.75 3.59
251 252 6.049149 AGTCAACCATATCGATCGTTTCATT 58.951 36.000 15.94 1.47 0.00 2.57
252 253 5.601662 AGTCAACCATATCGATCGTTTCAT 58.398 37.500 15.94 3.51 0.00 2.57
259 260 5.010933 TCCCTCTAGTCAACCATATCGATC 58.989 45.833 0.00 0.00 0.00 3.69
269 270 2.104170 CACCTCCTCCCTCTAGTCAAC 58.896 57.143 0.00 0.00 0.00 3.18
335 337 5.047660 AGACAACTTGTTTTGTTGCTAACCA 60.048 36.000 6.53 0.00 46.03 3.67
343 345 7.230510 TGGCATATCTAGACAACTTGTTTTGTT 59.769 33.333 0.00 0.00 39.88 2.83
428 430 2.183679 TGTTTTGGTCTTGGCTTTGGT 58.816 42.857 0.00 0.00 0.00 3.67
429 431 2.977772 TGTTTTGGTCTTGGCTTTGG 57.022 45.000 0.00 0.00 0.00 3.28
430 432 4.934602 TCTTTTGTTTTGGTCTTGGCTTTG 59.065 37.500 0.00 0.00 0.00 2.77
431 433 5.159273 TCTTTTGTTTTGGTCTTGGCTTT 57.841 34.783 0.00 0.00 0.00 3.51
432 434 4.817318 TCTTTTGTTTTGGTCTTGGCTT 57.183 36.364 0.00 0.00 0.00 4.35
433 435 4.222810 ACTTCTTTTGTTTTGGTCTTGGCT 59.777 37.500 0.00 0.00 0.00 4.75
434 436 4.329801 CACTTCTTTTGTTTTGGTCTTGGC 59.670 41.667 0.00 0.00 0.00 4.52
435 437 4.869861 CCACTTCTTTTGTTTTGGTCTTGG 59.130 41.667 0.00 0.00 0.00 3.61
436 438 4.329801 GCCACTTCTTTTGTTTTGGTCTTG 59.670 41.667 0.00 0.00 0.00 3.02
437 439 4.020662 TGCCACTTCTTTTGTTTTGGTCTT 60.021 37.500 0.00 0.00 0.00 3.01
438 440 3.513515 TGCCACTTCTTTTGTTTTGGTCT 59.486 39.130 0.00 0.00 0.00 3.85
439 441 3.616821 GTGCCACTTCTTTTGTTTTGGTC 59.383 43.478 0.00 0.00 0.00 4.02
440 442 3.260632 AGTGCCACTTCTTTTGTTTTGGT 59.739 39.130 0.00 0.00 0.00 3.67
441 443 3.860641 AGTGCCACTTCTTTTGTTTTGG 58.139 40.909 0.00 0.00 0.00 3.28
442 444 3.547468 CGAGTGCCACTTCTTTTGTTTTG 59.453 43.478 0.00 0.00 0.00 2.44
443 445 3.769536 CGAGTGCCACTTCTTTTGTTTT 58.230 40.909 0.00 0.00 0.00 2.43
444 446 2.479560 GCGAGTGCCACTTCTTTTGTTT 60.480 45.455 0.00 0.00 33.98 2.83
445 447 1.065551 GCGAGTGCCACTTCTTTTGTT 59.934 47.619 0.00 0.00 33.98 2.83
446 448 0.663153 GCGAGTGCCACTTCTTTTGT 59.337 50.000 0.00 0.00 33.98 2.83
447 449 0.947244 AGCGAGTGCCACTTCTTTTG 59.053 50.000 0.00 0.00 44.31 2.44
448 450 1.334869 CAAGCGAGTGCCACTTCTTTT 59.665 47.619 0.00 0.00 44.31 2.27
449 451 0.947244 CAAGCGAGTGCCACTTCTTT 59.053 50.000 0.00 0.00 44.31 2.52
450 452 1.510480 GCAAGCGAGTGCCACTTCTT 61.510 55.000 0.00 3.15 44.31 2.52
451 453 1.963338 GCAAGCGAGTGCCACTTCT 60.963 57.895 0.00 0.00 44.31 2.85
452 454 1.580845 ATGCAAGCGAGTGCCACTTC 61.581 55.000 0.00 0.00 44.26 3.01
453 455 1.601759 ATGCAAGCGAGTGCCACTT 60.602 52.632 0.00 0.00 44.26 3.16
454 456 2.033141 ATGCAAGCGAGTGCCACT 59.967 55.556 0.00 0.00 44.26 4.00
455 457 2.133742 AACATGCAAGCGAGTGCCAC 62.134 55.000 8.11 0.00 44.26 5.01
456 458 1.898094 AACATGCAAGCGAGTGCCA 60.898 52.632 8.11 0.00 44.26 4.92
457 459 1.443194 CAACATGCAAGCGAGTGCC 60.443 57.895 8.11 0.00 44.26 5.01
458 460 0.040157 TTCAACATGCAAGCGAGTGC 60.040 50.000 0.00 3.96 45.15 4.40
459 461 1.400629 CCTTCAACATGCAAGCGAGTG 60.401 52.381 0.00 0.00 0.00 3.51
520 554 0.602905 CGAACCAAGGCCTCTTCGTT 60.603 55.000 22.90 15.65 37.10 3.85
727 776 1.162181 CGACTGCCATACATGCCAGG 61.162 60.000 5.31 0.00 0.00 4.45
742 802 1.550524 TCAGAGTTTATGCTGGCGACT 59.449 47.619 0.00 0.00 33.05 4.18
762 822 3.204827 GCGGTCATTGCCATCGCT 61.205 61.111 0.00 0.00 42.62 4.93
793 853 1.463444 CTTAGAAAAAGGTCCGTGGCG 59.537 52.381 0.00 0.00 0.00 5.69
832 892 1.065709 GGCCGACCTAATTCTTGTCCA 60.066 52.381 0.00 0.00 0.00 4.02
836 896 0.107848 ACCGGCCGACCTAATTCTTG 60.108 55.000 30.73 7.48 0.00 3.02
837 897 0.616891 AACCGGCCGACCTAATTCTT 59.383 50.000 30.73 0.00 0.00 2.52
861 921 0.250295 CACCTGTGTCCAACCGATGT 60.250 55.000 0.00 0.00 0.00 3.06
865 925 2.997986 GTTATACACCTGTGTCCAACCG 59.002 50.000 6.14 0.00 43.74 4.44
879 939 1.796253 CGCCTGAACGCTCGTTATACA 60.796 52.381 7.70 1.74 38.60 2.29
884 944 2.733593 GTCGCCTGAACGCTCGTT 60.734 61.111 7.43 7.43 41.54 3.85
887 947 0.389426 TTTAGGTCGCCTGAACGCTC 60.389 55.000 8.44 0.00 36.72 5.03
892 952 0.899720 ATCCGTTTAGGTCGCCTGAA 59.100 50.000 8.44 4.18 41.99 3.02
893 953 1.766494 TATCCGTTTAGGTCGCCTGA 58.234 50.000 8.44 0.00 41.99 3.86
902 962 4.932268 TGTCCGCTTTTTATCCGTTTAG 57.068 40.909 0.00 0.00 0.00 1.85
918 978 2.252260 CAAGCCTGCGTTTGTCCG 59.748 61.111 0.00 0.00 0.00 4.79
919 979 2.050077 GCAAGCCTGCGTTTGTCC 60.050 61.111 0.00 0.00 39.20 4.02
1246 1318 2.162608 CAGACAGAAGGTAGACAGACGG 59.837 54.545 0.00 0.00 0.00 4.79
1515 1591 5.185249 AGCGTAATTCCAACAGAGAGAAGTA 59.815 40.000 0.00 0.00 0.00 2.24
1541 1619 6.939163 GCATTTCTCATATATGGACAGAAGGT 59.061 38.462 12.78 5.27 0.00 3.50
1758 1903 5.915196 GGAATACGGCATCTAAGATTTTTGC 59.085 40.000 0.00 0.00 0.00 3.68
1776 1921 7.547227 ACAATTTTACATTCTGCCAGGAATAC 58.453 34.615 0.00 0.00 34.59 1.89
1828 1973 7.284919 TCGCTATAGTCCAGAAATACATTGA 57.715 36.000 0.84 0.00 0.00 2.57
1891 4832 6.207417 CCAAACTCAGACCATGTACTGAAAAT 59.793 38.462 16.14 6.26 41.58 1.82
1903 4844 1.150536 GGTGCCCAAACTCAGACCA 59.849 57.895 0.00 0.00 0.00 4.02
1904 4845 0.251341 ATGGTGCCCAAACTCAGACC 60.251 55.000 0.00 0.00 36.95 3.85
1912 4853 2.380064 ACAAGAAGATGGTGCCCAAA 57.620 45.000 0.00 0.00 36.95 3.28
1915 4856 3.004752 ACATACAAGAAGATGGTGCCC 57.995 47.619 0.00 0.00 0.00 5.36
2229 7315 4.923415 ACCAAAAACTCTAGGGATGGAAG 58.077 43.478 13.03 0.00 0.00 3.46
2230 7316 5.311121 TGTACCAAAAACTCTAGGGATGGAA 59.689 40.000 13.03 0.21 0.00 3.53
2231 7317 4.847512 TGTACCAAAAACTCTAGGGATGGA 59.152 41.667 13.03 0.00 0.00 3.41
2232 7318 5.174037 TGTACCAAAAACTCTAGGGATGG 57.826 43.478 0.00 1.71 0.00 3.51
2233 7319 6.316390 GTCATGTACCAAAAACTCTAGGGATG 59.684 42.308 0.00 0.00 0.00 3.51
2234 7320 6.215636 AGTCATGTACCAAAAACTCTAGGGAT 59.784 38.462 0.00 0.00 0.00 3.85
2235 7321 5.546499 AGTCATGTACCAAAAACTCTAGGGA 59.454 40.000 0.00 0.00 0.00 4.20
2236 7322 5.643777 CAGTCATGTACCAAAAACTCTAGGG 59.356 44.000 0.00 0.00 0.00 3.53
2237 7323 6.231211 ACAGTCATGTACCAAAAACTCTAGG 58.769 40.000 0.00 0.00 38.09 3.02
2238 7324 7.307989 CCAACAGTCATGTACCAAAAACTCTAG 60.308 40.741 0.00 0.00 39.29 2.43
2239 7325 6.485313 CCAACAGTCATGTACCAAAAACTCTA 59.515 38.462 0.00 0.00 39.29 2.43
2240 7326 5.299279 CCAACAGTCATGTACCAAAAACTCT 59.701 40.000 0.00 0.00 39.29 3.24
2241 7327 5.067283 ACCAACAGTCATGTACCAAAAACTC 59.933 40.000 0.00 0.00 39.29 3.01
2242 7328 4.953579 ACCAACAGTCATGTACCAAAAACT 59.046 37.500 0.00 0.00 39.29 2.66
2243 7329 5.257082 ACCAACAGTCATGTACCAAAAAC 57.743 39.130 0.00 0.00 39.29 2.43
2244 7330 5.508200 GACCAACAGTCATGTACCAAAAA 57.492 39.130 0.00 0.00 45.55 1.94
2264 7350 4.820894 ACCTTACCCTGACTAACATGAC 57.179 45.455 0.00 0.00 0.00 3.06
2265 7351 5.335261 TGTACCTTACCCTGACTAACATGA 58.665 41.667 0.00 0.00 0.00 3.07
2331 7418 9.634163 CCAAAATTTTGTCTTATGTACCTTACC 57.366 33.333 25.25 0.00 36.45 2.85
2413 7500 8.020819 ACACAATGGTTAACATAATCAAACTCG 58.979 33.333 8.10 0.00 39.40 4.18
2621 9253 5.453567 AGCAAGGGTTCAAGTTAATTCAC 57.546 39.130 0.00 0.00 0.00 3.18
2625 9257 4.039124 CACCAAGCAAGGGTTCAAGTTAAT 59.961 41.667 0.00 0.00 36.19 1.40
2634 9266 1.756538 CAAACTCACCAAGCAAGGGTT 59.243 47.619 0.00 0.00 36.19 4.11
2684 9316 5.857268 TGAACAGTCATGAAGAGAATGTGA 58.143 37.500 0.00 0.00 42.69 3.58
2799 9457 6.378582 GCTAACAAAATGAAAGGAACATCGA 58.621 36.000 0.00 0.00 0.00 3.59
2801 9459 6.587608 CAGGCTAACAAAATGAAAGGAACATC 59.412 38.462 0.00 0.00 0.00 3.06
2804 9463 5.842907 ACAGGCTAACAAAATGAAAGGAAC 58.157 37.500 0.00 0.00 0.00 3.62
2825 9484 6.441284 ACCACTACATGTTACCATACCTAACA 59.559 38.462 2.30 0.00 38.23 2.41
2941 9604 2.224042 CCGAGCTGACATGTTAGCCATA 60.224 50.000 32.14 0.47 42.42 2.74
2959 9622 2.037121 TCAACTGTTCTGATTCTGCCGA 59.963 45.455 0.00 0.00 0.00 5.54
2960 9623 2.158449 GTCAACTGTTCTGATTCTGCCG 59.842 50.000 0.00 0.00 0.00 5.69
3075 9748 4.201628 GCTCACAGCTAACGAACATTACAG 60.202 45.833 0.00 0.00 38.45 2.74
3081 9754 0.679505 AGGCTCACAGCTAACGAACA 59.320 50.000 0.00 0.00 41.99 3.18
3083 9756 0.679505 ACAGGCTCACAGCTAACGAA 59.320 50.000 0.00 0.00 41.99 3.85
3135 9818 5.097742 TCAAGAAGAGAACAACAGGTTGA 57.902 39.130 18.28 0.00 42.93 3.18
3158 9845 1.501654 AACAGGAAAGAGCCCCCTCC 61.502 60.000 0.00 0.00 38.96 4.30
3178 9891 4.153117 CCTGACAAATGAACTGCTCAGTAC 59.847 45.833 2.62 0.00 41.58 2.73
3229 10025 8.366401 ACATCATATCAAGACATGAGGACTTAG 58.634 37.037 9.63 0.00 42.53 2.18
3235 10031 7.981102 ATTCACATCATATCAAGACATGAGG 57.019 36.000 0.00 1.86 42.53 3.86
3267 10063 9.042008 AGACAAATTAATATGTCCACATCGTAC 57.958 33.333 4.70 0.00 45.55 3.67
3342 10138 1.722034 TCTCCAAGGTTGAGAGCAGT 58.278 50.000 0.00 0.00 0.00 4.40
3349 10145 0.843309 TGGCACTTCTCCAAGGTTGA 59.157 50.000 0.00 0.00 33.37 3.18
3357 10153 6.759497 AATAACTAAATGTGGCACTTCTCC 57.241 37.500 19.83 0.00 0.00 3.71
3428 10252 4.515191 GTCATGTTAAAGTCTTGCACAGGA 59.485 41.667 7.38 7.38 0.00 3.86
3429 10253 4.516698 AGTCATGTTAAAGTCTTGCACAGG 59.483 41.667 0.00 3.67 0.00 4.00
3430 10254 5.679734 AGTCATGTTAAAGTCTTGCACAG 57.320 39.130 0.00 0.00 0.00 3.66
3471 10311 8.844865 TGCCAGGATAGTACAATCATATCTAT 57.155 34.615 0.00 0.00 0.00 1.98
3553 10746 3.554934 TCTGAACTCACTGTTTGCCAAT 58.445 40.909 0.00 0.00 39.30 3.16
3565 10758 5.223449 AGAAATAACCGGTTCTGAACTCA 57.777 39.130 26.16 3.39 32.84 3.41
3568 10761 5.934935 TCAAGAAATAACCGGTTCTGAAC 57.065 39.130 26.16 12.05 34.33 3.18
3638 10831 2.047844 GGCTTCTGCTCGCACTCA 60.048 61.111 0.00 0.00 39.59 3.41
3639 10832 1.809209 GAGGCTTCTGCTCGCACTC 60.809 63.158 0.00 0.00 39.59 3.51
3641 10834 1.357991 GAAGAGGCTTCTGCTCGCAC 61.358 60.000 0.00 0.00 39.59 5.34
3682 10890 3.925299 GGTTAGAGCTTAGAACACGGTTC 59.075 47.826 8.26 8.26 0.00 3.62
3697 10905 2.894240 TTTAGCGCCGCGGGTTAGAG 62.894 60.000 29.38 2.50 0.00 2.43
3735 10943 3.798878 CACATATTGAGCTGTACCACTCG 59.201 47.826 0.00 0.00 35.61 4.18
3738 10946 3.873910 ACCACATATTGAGCTGTACCAC 58.126 45.455 0.00 0.00 0.00 4.16
3866 11075 2.287308 CGGCCACGAACTGAAATCAAAA 60.287 45.455 2.24 0.00 44.60 2.44
3896 11105 2.562738 TGATGACATGGTCGCTATAGGG 59.437 50.000 10.48 10.48 34.95 3.53
3902 11111 3.057969 TCTTTTGATGACATGGTCGCT 57.942 42.857 0.00 0.00 34.95 4.93
4041 11274 5.655394 TCACCAGATGGCTCTATAGGTATT 58.345 41.667 0.00 0.00 39.32 1.89
4157 11390 5.125100 TGTTGCATGTGAAAGAGAATTCC 57.875 39.130 0.65 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.