Multiple sequence alignment - TraesCS2B01G186000

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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 TraesCS2B01G186000 chr2B 100.000 2411 0 0 1 2411 161025470 161027880 0.000000e+00 4453.0
1 TraesCS2B01G186000 chr1B 80.627 1626 126 90 900 2411 610560679 610562229 0.000000e+00 1083.0
2 TraesCS2B01G186000 chr1B 80.670 1402 138 68 900 2209 608053938 608052578 0.000000e+00 965.0
3 TraesCS2B01G186000 chr1B 94.073 523 26 4 898 1416 608462996 608462475 0.000000e+00 789.0
4 TraesCS2B01G186000 chr1B 86.918 558 48 13 1067 1599 608355307 608354750 9.540000e-169 603.0
5 TraesCS2B01G186000 chr1B 88.802 384 23 14 2041 2411 608354406 608354030 1.020000e-123 453.0
6 TraesCS2B01G186000 chr1B 85.175 371 37 6 1 353 608465332 608464962 4.900000e-97 364.0
7 TraesCS2B01G186000 chr1B 84.179 335 28 9 2077 2411 607428398 607428089 3.900000e-78 302.0
8 TraesCS2B01G186000 chr1B 86.928 153 14 3 1889 2035 607428557 607428405 1.480000e-37 167.0
9 TraesCS2B01G186000 chr1B 86.517 89 11 1 2324 2411 608051897 608051809 1.970000e-16 97.1
10 TraesCS2B01G186000 chr1D 85.933 1045 75 39 903 1893 446437008 446438034 0.000000e+00 1050.0
11 TraesCS2B01G186000 chr1D 91.499 647 33 17 972 1596 355825269 355825915 0.000000e+00 870.0
12 TraesCS2B01G186000 chr1D 81.944 792 57 35 1692 2411 445384975 445384198 2.060000e-165 592.0
13 TraesCS2B01G186000 chr1D 83.445 447 62 8 46 484 445387899 445387457 2.890000e-109 405.0
14 TraesCS2B01G186000 chr1D 77.939 757 59 48 1688 2377 355826008 355826723 8.140000e-100 374.0
15 TraesCS2B01G186000 chr1D 87.147 319 22 7 2109 2411 446438255 446438570 6.380000e-91 344.0
16 TraesCS2B01G186000 chr1D 86.230 305 24 6 613 900 445387425 445387122 5.000000e-82 315.0
17 TraesCS2B01G186000 chr1D 86.164 159 9 9 1452 1599 445385204 445385048 2.480000e-35 159.0
18 TraesCS2B01G186000 chr1D 89.855 69 6 1 1931 1998 446438116 446438184 1.190000e-13 87.9
19 TraesCS2B01G186000 chr1A 83.222 1049 85 50 901 1893 456650910 456651923 0.000000e+00 878.0
20 TraesCS2B01G186000 chr1A 80.253 1185 132 63 902 2035 541463449 541462316 0.000000e+00 798.0
21 TraesCS2B01G186000 chr1A 92.734 523 30 4 903 1418 541381275 541381796 0.000000e+00 749.0
22 TraesCS2B01G186000 chr1A 92.871 519 29 4 903 1414 542170278 542170795 0.000000e+00 747.0
23 TraesCS2B01G186000 chr1A 84.501 471 46 12 60 512 541464319 541463858 7.910000e-120 440.0
24 TraesCS2B01G186000 chr1A 89.811 265 17 5 2154 2411 541462285 541462024 4.970000e-87 331.0
25 TraesCS2B01G186000 chr1A 84.932 292 27 12 1932 2210 541320301 541320588 1.830000e-71 279.0
26 TraesCS2B01G186000 chr1A 86.038 265 24 11 2038 2294 456651949 456652208 3.050000e-69 272.0
27 TraesCS2B01G186000 chr1A 87.895 190 17 2 2225 2408 541320679 541320868 4.040000e-53 219.0
28 TraesCS2B01G186000 chr1A 83.884 242 19 6 175 404 541380294 541380527 1.880000e-51 213.0
29 TraesCS2B01G186000 chr3D 86.885 732 70 19 900 1612 114883203 114882479 0.000000e+00 797.0
30 TraesCS2B01G186000 chr3D 86.992 123 14 2 1768 1889 214364365 214364244 1.160000e-28 137.0
31 TraesCS2B01G186000 chr3A 92.898 521 29 7 900 1416 111106296 111105780 0.000000e+00 750.0
32 TraesCS2B01G186000 chr3A 85.294 102 9 4 1514 1613 111105658 111105561 1.530000e-17 100.0
33 TraesCS2B01G186000 chr3B 87.202 672 49 25 972 1613 168140451 168139787 0.000000e+00 730.0
34 TraesCS2B01G186000 chr3B 94.366 71 4 0 520 590 211111392 211111462 2.530000e-20 110.0
35 TraesCS2B01G186000 chr3B 88.889 81 7 2 1514 1593 168146540 168146461 5.490000e-17 99.0
36 TraesCS2B01G186000 chr6A 88.000 100 10 2 1514 1613 67141530 67141433 1.510000e-22 117.0
37 TraesCS2B01G186000 chr6D 85.507 69 10 0 517 585 56346037 56346105 3.320000e-09 73.1
38 TraesCS2B01G186000 chr4D 91.489 47 4 0 544 590 302003439 302003485 5.560000e-07 65.8
39 TraesCS2B01G186000 chr7B 93.023 43 3 0 548 590 60602395 60602437 2.000000e-06 63.9
40 TraesCS2B01G186000 chr5A 100.000 31 0 0 561 591 248531275 248531245 9.310000e-05 58.4


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 TraesCS2B01G186000 chr2B 161025470 161027880 2410 False 4453.000000 4453 100.00000 1 2411 1 chr2B.!!$F1 2410
1 TraesCS2B01G186000 chr1B 610560679 610562229 1550 False 1083.000000 1083 80.62700 900 2411 1 chr1B.!!$F1 1511
2 TraesCS2B01G186000 chr1B 608462475 608465332 2857 True 576.500000 789 89.62400 1 1416 2 chr1B.!!$R4 1415
3 TraesCS2B01G186000 chr1B 608051809 608053938 2129 True 531.050000 965 83.59350 900 2411 2 chr1B.!!$R2 1511
4 TraesCS2B01G186000 chr1B 608354030 608355307 1277 True 528.000000 603 87.86000 1067 2411 2 chr1B.!!$R3 1344
5 TraesCS2B01G186000 chr1D 355825269 355826723 1454 False 622.000000 870 84.71900 972 2377 2 chr1D.!!$F1 1405
6 TraesCS2B01G186000 chr1D 446437008 446438570 1562 False 493.966667 1050 87.64500 903 2411 3 chr1D.!!$F2 1508
7 TraesCS2B01G186000 chr1D 445384198 445387899 3701 True 367.750000 592 84.44575 46 2411 4 chr1D.!!$R1 2365
8 TraesCS2B01G186000 chr1A 542170278 542170795 517 False 747.000000 747 92.87100 903 1414 1 chr1A.!!$F1 511
9 TraesCS2B01G186000 chr1A 456650910 456652208 1298 False 575.000000 878 84.63000 901 2294 2 chr1A.!!$F2 1393
10 TraesCS2B01G186000 chr1A 541462024 541464319 2295 True 523.000000 798 84.85500 60 2411 3 chr1A.!!$R1 2351
11 TraesCS2B01G186000 chr1A 541380294 541381796 1502 False 481.000000 749 88.30900 175 1418 2 chr1A.!!$F4 1243
12 TraesCS2B01G186000 chr1A 541320301 541320868 567 False 249.000000 279 86.41350 1932 2408 2 chr1A.!!$F3 476
13 TraesCS2B01G186000 chr3D 114882479 114883203 724 True 797.000000 797 86.88500 900 1612 1 chr3D.!!$R1 712
14 TraesCS2B01G186000 chr3A 111105561 111106296 735 True 425.000000 750 89.09600 900 1613 2 chr3A.!!$R1 713
15 TraesCS2B01G186000 chr3B 168139787 168140451 664 True 730.000000 730 87.20200 972 1613 1 chr3B.!!$R1 641

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
942 2810 0.17691 CCCCTTCTTCTTCCTCGCTC 59.823 60.0 0.0 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2035 5453 0.31179 CACAAGAACAACTGCGGCAT 59.688 50.0 1.75 0.0 0.0 4.4 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
27 31 3.586892 GTTAGTTCCAGACTGGTAGCAC 58.413 50.000 21.06 13.11 39.48 4.40
40 44 4.275936 ACTGGTAGCACTTGATTTTGTGAC 59.724 41.667 0.00 0.00 36.38 3.67
43 47 4.037446 GGTAGCACTTGATTTTGTGACCAA 59.963 41.667 0.00 0.00 36.38 3.67
44 48 4.045636 AGCACTTGATTTTGTGACCAAC 57.954 40.909 0.00 0.00 36.38 3.77
65 69 8.206189 ACCAACTTGTTGATGATTTGAAATCTT 58.794 29.630 17.76 12.06 0.00 2.40
67 71 9.037737 CAACTTGTTGATGATTTGAAATCTTGT 57.962 29.630 17.76 5.33 0.00 3.16
68 72 9.603921 AACTTGTTGATGATTTGAAATCTTGTT 57.396 25.926 17.76 8.62 0.00 2.83
75 79 6.012658 TGATTTGAAATCTTGTTAGCGCTT 57.987 33.333 18.68 0.00 0.00 4.68
89 93 5.748630 TGTTAGCGCTTATGAGTGATTACAG 59.251 40.000 18.68 0.00 36.69 2.74
94 98 4.572389 CGCTTATGAGTGATTACAGGCTTT 59.428 41.667 0.00 0.00 35.36 3.51
95 99 5.503031 CGCTTATGAGTGATTACAGGCTTTG 60.503 44.000 0.00 0.00 35.36 2.77
132 138 2.223852 GCAGGGTTTTTGCCTCGTTAAA 60.224 45.455 0.00 0.00 35.54 1.52
138 144 6.041182 AGGGTTTTTGCCTCGTTAAATTTACT 59.959 34.615 0.00 0.00 0.00 2.24
189 195 4.458989 CCAAGCAGCTTGTTAATTCACCTA 59.541 41.667 29.36 0.00 39.58 3.08
252 261 9.851686 TTGAACATCAAGAATTAGTATATGGCT 57.148 29.630 0.00 0.00 31.83 4.75
267 278 0.260230 TGGCTCTGTTTGGTTGGGAA 59.740 50.000 0.00 0.00 0.00 3.97
272 283 4.058124 GCTCTGTTTGGTTGGGAATTTTC 58.942 43.478 0.00 0.00 0.00 2.29
314 337 2.604174 CGACCACCCAAACGTGCTC 61.604 63.158 0.00 0.00 32.10 4.26
353 376 7.864379 TCGAAAATAACTCGAAGTAGTGACTTT 59.136 33.333 0.00 0.00 46.23 2.66
362 1820 5.977725 TCGAAGTAGTGACTTTCAGAAACAG 59.022 40.000 0.00 0.00 46.23 3.16
363 1821 5.749109 CGAAGTAGTGACTTTCAGAAACAGT 59.251 40.000 0.00 0.00 46.23 3.55
385 1843 0.314618 TAGTTCGGCGTGTGTGCTAA 59.685 50.000 6.85 0.00 34.52 3.09
473 2198 8.008279 CAGATCAGTGTTTATGATGAATTAGCG 58.992 37.037 0.00 0.00 37.52 4.26
519 2284 9.903682 CTTCAGGGCATTACAAATAATTCATAG 57.096 33.333 0.00 0.00 0.00 2.23
521 2286 9.812347 TCAGGGCATTACAAATAATTCATAGAT 57.188 29.630 0.00 0.00 0.00 1.98
522 2287 9.850628 CAGGGCATTACAAATAATTCATAGATG 57.149 33.333 0.00 0.00 0.00 2.90
523 2288 9.592196 AGGGCATTACAAATAATTCATAGATGT 57.408 29.630 0.00 0.00 0.00 3.06
553 2318 8.824159 AGCACTGAAATATGTCTACATACATC 57.176 34.615 4.98 7.30 41.15 3.06
554 2319 8.424133 AGCACTGAAATATGTCTACATACATCA 58.576 33.333 4.98 10.77 41.15 3.07
555 2320 9.045223 GCACTGAAATATGTCTACATACATCAA 57.955 33.333 15.17 5.71 41.15 2.57
563 2328 6.588348 TGTCTACATACATCAATTTCAGCG 57.412 37.500 0.00 0.00 0.00 5.18
564 2329 6.337356 TGTCTACATACATCAATTTCAGCGA 58.663 36.000 0.00 0.00 0.00 4.93
565 2330 6.255670 TGTCTACATACATCAATTTCAGCGAC 59.744 38.462 0.00 0.00 0.00 5.19
566 2331 6.255670 GTCTACATACATCAATTTCAGCGACA 59.744 38.462 0.00 0.00 0.00 4.35
567 2332 5.878332 ACATACATCAATTTCAGCGACAA 57.122 34.783 0.00 0.00 0.00 3.18
568 2333 5.631026 ACATACATCAATTTCAGCGACAAC 58.369 37.500 0.00 0.00 0.00 3.32
569 2334 5.412594 ACATACATCAATTTCAGCGACAACT 59.587 36.000 0.00 0.00 0.00 3.16
570 2335 6.593770 ACATACATCAATTTCAGCGACAACTA 59.406 34.615 0.00 0.00 0.00 2.24
571 2336 5.940192 ACATCAATTTCAGCGACAACTAA 57.060 34.783 0.00 0.00 0.00 2.24
572 2337 6.500684 ACATCAATTTCAGCGACAACTAAT 57.499 33.333 0.00 0.00 0.00 1.73
573 2338 7.609760 ACATCAATTTCAGCGACAACTAATA 57.390 32.000 0.00 0.00 0.00 0.98
574 2339 8.213518 ACATCAATTTCAGCGACAACTAATAT 57.786 30.769 0.00 0.00 0.00 1.28
575 2340 9.325198 ACATCAATTTCAGCGACAACTAATATA 57.675 29.630 0.00 0.00 0.00 0.86
576 2341 9.803130 CATCAATTTCAGCGACAACTAATATAG 57.197 33.333 0.00 0.00 0.00 1.31
577 2342 9.764363 ATCAATTTCAGCGACAACTAATATAGA 57.236 29.630 0.00 0.00 0.00 1.98
578 2343 9.594478 TCAATTTCAGCGACAACTAATATAGAA 57.406 29.630 0.00 0.00 0.00 2.10
579 2344 9.638300 CAATTTCAGCGACAACTAATATAGAAC 57.362 33.333 0.00 0.00 0.00 3.01
580 2345 7.445900 TTTCAGCGACAACTAATATAGAACG 57.554 36.000 0.00 0.00 0.00 3.95
581 2346 5.516996 TCAGCGACAACTAATATAGAACGG 58.483 41.667 0.00 0.00 0.00 4.44
582 2347 5.297527 TCAGCGACAACTAATATAGAACGGA 59.702 40.000 0.00 0.00 0.00 4.69
583 2348 5.625721 CAGCGACAACTAATATAGAACGGAG 59.374 44.000 0.00 0.00 0.00 4.63
584 2349 4.916249 GCGACAACTAATATAGAACGGAGG 59.084 45.833 0.00 0.00 0.00 4.30
585 2350 5.458891 CGACAACTAATATAGAACGGAGGG 58.541 45.833 0.00 0.00 0.00 4.30
586 2351 5.240183 CGACAACTAATATAGAACGGAGGGA 59.760 44.000 0.00 0.00 0.00 4.20
587 2352 6.568081 CGACAACTAATATAGAACGGAGGGAG 60.568 46.154 0.00 0.00 0.00 4.30
588 2353 6.134754 ACAACTAATATAGAACGGAGGGAGT 58.865 40.000 0.00 0.00 0.00 3.85
589 2354 7.293073 ACAACTAATATAGAACGGAGGGAGTA 58.707 38.462 0.00 0.00 0.00 2.59
590 2355 7.230309 ACAACTAATATAGAACGGAGGGAGTAC 59.770 40.741 0.00 0.00 0.00 2.73
591 2356 5.936956 ACTAATATAGAACGGAGGGAGTACG 59.063 44.000 0.00 0.00 0.00 3.67
592 2357 2.725221 ATAGAACGGAGGGAGTACGT 57.275 50.000 0.00 0.00 43.43 3.57
593 2358 3.845781 ATAGAACGGAGGGAGTACGTA 57.154 47.619 0.00 0.00 40.31 3.57
594 2359 1.743996 AGAACGGAGGGAGTACGTAC 58.256 55.000 18.10 18.10 40.31 3.67
642 2419 4.570772 TCACCGAAACTCTTCTTGTCAAAG 59.429 41.667 0.00 0.00 34.45 2.77
667 2446 6.619801 AAAGCACTACTTTCGTCAATTCTT 57.380 33.333 0.00 0.00 45.78 2.52
750 2560 4.040461 TCCTCAGAGTCCATTTTCGTTTCT 59.960 41.667 0.00 0.00 0.00 2.52
794 2604 3.136443 TGACTTGTCTCCAACCAATCAGT 59.864 43.478 2.35 0.00 0.00 3.41
806 2626 3.529341 AATCAGTGCGCGTCCCACA 62.529 57.895 15.98 0.00 35.69 4.17
816 2636 3.083997 GTCCCACAGATCGCCCCT 61.084 66.667 0.00 0.00 0.00 4.79
840 2661 3.112205 GCAGATCCCAGCCGTCCAT 62.112 63.158 0.00 0.00 0.00 3.41
859 2680 2.860293 CACGACACATCCAACGCC 59.140 61.111 0.00 0.00 0.00 5.68
936 2804 0.553333 CCCATCCCCCTTCTTCTTCC 59.447 60.000 0.00 0.00 0.00 3.46
937 2805 1.601248 CCATCCCCCTTCTTCTTCCT 58.399 55.000 0.00 0.00 0.00 3.36
939 2807 1.139853 CATCCCCCTTCTTCTTCCTCG 59.860 57.143 0.00 0.00 0.00 4.63
941 2809 1.268283 CCCCCTTCTTCTTCCTCGCT 61.268 60.000 0.00 0.00 0.00 4.93
942 2810 0.176910 CCCCTTCTTCTTCCTCGCTC 59.823 60.000 0.00 0.00 0.00 5.03
944 2812 0.898320 CCTTCTTCTTCCTCGCTCCA 59.102 55.000 0.00 0.00 0.00 3.86
945 2813 1.134848 CCTTCTTCTTCCTCGCTCCAG 60.135 57.143 0.00 0.00 0.00 3.86
979 2860 3.535962 GCGCTCCTCCCTCCTCAG 61.536 72.222 0.00 0.00 0.00 3.35
1314 3201 1.321074 CCTACCTCGTCGGGCTCTTT 61.321 60.000 0.00 0.00 36.97 2.52
1443 4690 1.138266 GCTTGGCGTGTTAGATCCCTA 59.862 52.381 0.00 0.00 0.00 3.53
1444 4691 2.419574 GCTTGGCGTGTTAGATCCCTAA 60.420 50.000 0.00 0.00 32.76 2.69
1462 4716 4.003648 CCTAATAGGCATCGGTGGAAATC 58.996 47.826 0.00 0.00 0.00 2.17
1490 4754 5.696724 GTGCTACTAGTGTTTCAGAATGTGT 59.303 40.000 5.39 0.00 37.40 3.72
1506 4806 4.882671 ATGTGTCTGTGTTGTTCTTGTC 57.117 40.909 0.00 0.00 0.00 3.18
1507 4807 3.669536 TGTGTCTGTGTTGTTCTTGTCA 58.330 40.909 0.00 0.00 0.00 3.58
1512 4812 4.094887 GTCTGTGTTGTTCTTGTCATGTGT 59.905 41.667 0.00 0.00 0.00 3.72
1576 4888 3.243367 TGAAAATGTTGGCTTCCTGTTCG 60.243 43.478 0.00 0.00 0.00 3.95
1599 4911 1.532523 TCATCTGCGTTTGAATGCCA 58.467 45.000 5.55 0.00 40.18 4.92
1600 4912 1.885233 TCATCTGCGTTTGAATGCCAA 59.115 42.857 5.55 0.00 40.18 4.52
1604 4933 3.058450 TCTGCGTTTGAATGCCAAATTG 58.942 40.909 5.55 0.00 45.48 2.32
1623 4952 1.001520 TGTCGCCTGTTTTAGCTAGCA 59.998 47.619 18.83 0.00 0.00 3.49
1626 4955 1.268234 CGCCTGTTTTAGCTAGCATGC 60.268 52.381 18.83 10.51 0.00 4.06
1632 4961 6.459066 CCTGTTTTAGCTAGCATGCTCTATA 58.541 40.000 26.57 12.53 42.97 1.31
1635 4964 8.908786 TGTTTTAGCTAGCATGCTCTATATTT 57.091 30.769 26.57 6.73 42.97 1.40
1638 4967 9.784531 TTTTAGCTAGCATGCTCTATATTTCTT 57.215 29.630 26.57 0.00 42.97 2.52
1645 4977 8.930846 AGCATGCTCTATATTTCTTAATTGGT 57.069 30.769 16.30 0.00 0.00 3.67
1662 4994 9.357652 CTTAATTGGTCTTGAATTAACATGTGG 57.642 33.333 0.00 0.00 33.64 4.17
1670 5002 3.761218 TGAATTAACATGTGGCCGTCAAT 59.239 39.130 0.00 0.00 0.00 2.57
1685 5017 5.379827 GCCGTCAATTTTTGTACTGAGTAC 58.620 41.667 15.57 15.57 39.24 2.73
1691 5023 7.441458 GTCAATTTTTGTACTGAGTACTCTGGT 59.559 37.037 27.33 23.39 39.49 4.00
1711 5043 0.898320 TAGCTGCCTCTGAACCTGAC 59.102 55.000 0.00 0.00 0.00 3.51
1712 5044 1.376553 GCTGCCTCTGAACCTGACC 60.377 63.158 0.00 0.00 0.00 4.02
1713 5045 1.835927 GCTGCCTCTGAACCTGACCT 61.836 60.000 0.00 0.00 0.00 3.85
1714 5046 0.036577 CTGCCTCTGAACCTGACCTG 60.037 60.000 0.00 0.00 0.00 4.00
1715 5047 0.471780 TGCCTCTGAACCTGACCTGA 60.472 55.000 0.00 0.00 0.00 3.86
1716 5048 0.248843 GCCTCTGAACCTGACCTGAG 59.751 60.000 0.00 0.00 0.00 3.35
1735 5068 1.550524 AGCGAACTGGCAGTTGAGATA 59.449 47.619 35.57 0.00 38.80 1.98
1808 5168 0.792640 CGGTGTGTCTGATGTTCAGC 59.207 55.000 0.00 0.00 43.95 4.26
1812 5172 0.441533 GTGTCTGATGTTCAGCGCAG 59.558 55.000 11.47 0.00 43.95 5.18
1877 5237 1.066143 ACCCTGCAAGTCTATGAACCG 60.066 52.381 0.00 0.00 0.00 4.44
1927 5317 5.186021 TCTTCAGATCTTACAGGTTCAGGAC 59.814 44.000 0.00 0.00 0.00 3.85
1947 5362 1.545582 CCGGCCTGCAATATTATTGGG 59.454 52.381 16.22 11.39 0.00 4.12
1969 5385 3.088532 TGCATCACCCACAATTCCTAAC 58.911 45.455 0.00 0.00 0.00 2.34
1981 5399 2.754946 TTCCTAACTAACGCACCAGG 57.245 50.000 0.00 0.00 0.00 4.45
1998 5416 2.964389 GGCATCGAGGAAGCGCTC 60.964 66.667 12.06 4.06 0.00 5.03
1999 5417 2.105930 GCATCGAGGAAGCGCTCT 59.894 61.111 12.06 3.70 0.00 4.09
2017 5435 5.295950 CGCTCTCCACTATTGATCAGAATT 58.704 41.667 0.00 0.00 0.00 2.17
2024 5442 7.058525 TCCACTATTGATCAGAATTTCATGCT 58.941 34.615 0.00 0.00 0.00 3.79
2032 5450 5.762825 TCAGAATTTCATGCTATTCCTGC 57.237 39.130 12.99 0.00 32.43 4.85
2035 5453 7.056006 TCAGAATTTCATGCTATTCCTGCTTA 58.944 34.615 12.99 0.00 32.43 3.09
2049 5490 0.521291 TGCTTATGCCGCAGTTGTTC 59.479 50.000 0.00 0.00 38.71 3.18
2052 5496 2.855180 CTTATGCCGCAGTTGTTCTTG 58.145 47.619 0.00 0.00 0.00 3.02
2084 5528 4.240881 TGGATCGGCCATTGCTTC 57.759 55.556 2.24 0.00 43.33 3.86
2085 5529 1.609239 TGGATCGGCCATTGCTTCT 59.391 52.632 2.24 0.00 43.33 2.85
2094 5554 1.878734 GCCATTGCTTCTGGATAGAGC 59.121 52.381 4.26 0.00 35.70 4.09
2199 5665 9.496873 TTTAGCTACTGTGTTCTTAATTGCTTA 57.503 29.630 0.00 0.00 0.00 3.09
2222 5771 9.937175 CTTAGATTTTGTAGTAGCTTAAATGGC 57.063 33.333 0.00 0.00 0.00 4.40
2257 5819 7.165318 GTCAAAATTCGAAATAACTATTCCGGC 59.835 37.037 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 21 4.275936 GTCACAAAATCAAGTGCTACCAGT 59.724 41.667 0.00 0.00 35.76 4.00
20 24 3.568007 TGGTCACAAAATCAAGTGCTACC 59.432 43.478 0.00 0.00 34.78 3.18
21 25 4.829064 TGGTCACAAAATCAAGTGCTAC 57.171 40.909 0.00 0.00 35.76 3.58
27 31 6.098679 TCAACAAGTTGGTCACAAAATCAAG 58.901 36.000 12.54 0.00 40.78 3.02
40 44 8.492748 CAAGATTTCAAATCATCAACAAGTTGG 58.507 33.333 12.74 0.00 40.78 3.77
65 69 5.656480 TGTAATCACTCATAAGCGCTAACA 58.344 37.500 12.05 0.00 0.00 2.41
67 71 5.289595 CCTGTAATCACTCATAAGCGCTAA 58.710 41.667 12.05 0.00 0.00 3.09
68 72 4.796290 GCCTGTAATCACTCATAAGCGCTA 60.796 45.833 12.05 0.00 0.00 4.26
75 79 5.580691 CGTTCAAAGCCTGTAATCACTCATA 59.419 40.000 0.00 0.00 0.00 2.15
89 93 4.558860 GCTTGATTATGTTCGTTCAAAGCC 59.441 41.667 0.00 0.00 0.00 4.35
94 98 3.689161 CCCTGCTTGATTATGTTCGTTCA 59.311 43.478 0.00 0.00 0.00 3.18
95 99 3.689649 ACCCTGCTTGATTATGTTCGTTC 59.310 43.478 0.00 0.00 0.00 3.95
132 138 6.204882 GCTTGTGACCACTAAACTCAGTAAAT 59.795 38.462 1.62 0.00 0.00 1.40
138 144 3.838244 AGCTTGTGACCACTAAACTCA 57.162 42.857 1.62 0.00 0.00 3.41
252 261 4.681074 GGAAAATTCCCAACCAAACAGA 57.319 40.909 0.43 0.00 41.62 3.41
353 376 3.365666 CGCCGAACTACTACTGTTTCTGA 60.366 47.826 0.00 0.00 0.00 3.27
362 1820 1.334054 CACACACGCCGAACTACTAC 58.666 55.000 0.00 0.00 0.00 2.73
363 1821 0.387622 GCACACACGCCGAACTACTA 60.388 55.000 0.00 0.00 0.00 1.82
385 1843 8.037166 AGAATTTCTTTTCAGTTTTGACTGCTT 58.963 29.630 1.78 0.00 37.63 3.91
473 2198 5.068987 TGAAGCCCTGGAACATTATTTATGC 59.931 40.000 0.00 0.00 38.20 3.14
484 2209 2.361737 GCCCTGAAGCCCTGGAAC 60.362 66.667 0.00 0.00 36.07 3.62
486 2211 0.918799 TAATGCCCTGAAGCCCTGGA 60.919 55.000 0.00 0.00 36.07 3.86
527 2292 9.914131 GATGTATGTAGACATATTTCAGTGCTA 57.086 33.333 5.69 0.00 40.18 3.49
528 2293 8.424133 TGATGTATGTAGACATATTTCAGTGCT 58.576 33.333 5.69 0.00 40.18 4.40
529 2294 8.593492 TGATGTATGTAGACATATTTCAGTGC 57.407 34.615 5.69 0.00 40.18 4.40
537 2302 8.929746 CGCTGAAATTGATGTATGTAGACATAT 58.070 33.333 5.69 0.00 40.18 1.78
538 2303 8.141268 TCGCTGAAATTGATGTATGTAGACATA 58.859 33.333 0.00 0.00 40.18 2.29
539 2304 6.986231 TCGCTGAAATTGATGTATGTAGACAT 59.014 34.615 0.08 0.08 42.82 3.06
540 2305 6.255670 GTCGCTGAAATTGATGTATGTAGACA 59.744 38.462 0.00 0.00 0.00 3.41
541 2306 6.255670 TGTCGCTGAAATTGATGTATGTAGAC 59.744 38.462 0.00 0.00 0.00 2.59
542 2307 6.337356 TGTCGCTGAAATTGATGTATGTAGA 58.663 36.000 0.00 0.00 0.00 2.59
543 2308 6.588348 TGTCGCTGAAATTGATGTATGTAG 57.412 37.500 0.00 0.00 0.00 2.74
544 2309 6.593770 AGTTGTCGCTGAAATTGATGTATGTA 59.406 34.615 0.00 0.00 0.00 2.29
545 2310 5.412594 AGTTGTCGCTGAAATTGATGTATGT 59.587 36.000 0.00 0.00 0.00 2.29
546 2311 5.872635 AGTTGTCGCTGAAATTGATGTATG 58.127 37.500 0.00 0.00 0.00 2.39
547 2312 7.609760 TTAGTTGTCGCTGAAATTGATGTAT 57.390 32.000 0.00 0.00 0.00 2.29
548 2313 7.609760 ATTAGTTGTCGCTGAAATTGATGTA 57.390 32.000 0.00 0.00 0.00 2.29
549 2314 5.940192 TTAGTTGTCGCTGAAATTGATGT 57.060 34.783 0.00 0.00 0.00 3.06
550 2315 9.803130 CTATATTAGTTGTCGCTGAAATTGATG 57.197 33.333 0.00 0.00 0.00 3.07
551 2316 9.764363 TCTATATTAGTTGTCGCTGAAATTGAT 57.236 29.630 0.00 0.00 0.00 2.57
552 2317 9.594478 TTCTATATTAGTTGTCGCTGAAATTGA 57.406 29.630 0.00 0.00 0.00 2.57
553 2318 9.638300 GTTCTATATTAGTTGTCGCTGAAATTG 57.362 33.333 0.00 0.00 0.00 2.32
554 2319 8.540492 CGTTCTATATTAGTTGTCGCTGAAATT 58.460 33.333 0.00 0.00 0.00 1.82
555 2320 7.169308 CCGTTCTATATTAGTTGTCGCTGAAAT 59.831 37.037 0.00 0.00 0.00 2.17
556 2321 6.474427 CCGTTCTATATTAGTTGTCGCTGAAA 59.526 38.462 0.00 0.00 0.00 2.69
557 2322 5.975344 CCGTTCTATATTAGTTGTCGCTGAA 59.025 40.000 0.00 0.00 0.00 3.02
558 2323 5.297527 TCCGTTCTATATTAGTTGTCGCTGA 59.702 40.000 0.00 0.00 0.00 4.26
559 2324 5.516996 TCCGTTCTATATTAGTTGTCGCTG 58.483 41.667 0.00 0.00 0.00 5.18
560 2325 5.278364 CCTCCGTTCTATATTAGTTGTCGCT 60.278 44.000 0.00 0.00 0.00 4.93
561 2326 4.916249 CCTCCGTTCTATATTAGTTGTCGC 59.084 45.833 0.00 0.00 0.00 5.19
562 2327 5.240183 TCCCTCCGTTCTATATTAGTTGTCG 59.760 44.000 0.00 0.00 0.00 4.35
563 2328 6.264970 ACTCCCTCCGTTCTATATTAGTTGTC 59.735 42.308 0.00 0.00 0.00 3.18
564 2329 6.134754 ACTCCCTCCGTTCTATATTAGTTGT 58.865 40.000 0.00 0.00 0.00 3.32
565 2330 6.651975 ACTCCCTCCGTTCTATATTAGTTG 57.348 41.667 0.00 0.00 0.00 3.16
566 2331 6.429385 CGTACTCCCTCCGTTCTATATTAGTT 59.571 42.308 0.00 0.00 0.00 2.24
567 2332 5.936956 CGTACTCCCTCCGTTCTATATTAGT 59.063 44.000 0.00 0.00 0.00 2.24
568 2333 5.936956 ACGTACTCCCTCCGTTCTATATTAG 59.063 44.000 0.00 0.00 0.00 1.73
569 2334 5.869579 ACGTACTCCCTCCGTTCTATATTA 58.130 41.667 0.00 0.00 0.00 0.98
570 2335 4.723309 ACGTACTCCCTCCGTTCTATATT 58.277 43.478 0.00 0.00 0.00 1.28
571 2336 4.363991 ACGTACTCCCTCCGTTCTATAT 57.636 45.455 0.00 0.00 0.00 0.86
572 2337 3.845781 ACGTACTCCCTCCGTTCTATA 57.154 47.619 0.00 0.00 0.00 1.31
573 2338 2.725221 ACGTACTCCCTCCGTTCTAT 57.275 50.000 0.00 0.00 0.00 1.98
574 2339 2.738643 CGTACGTACTCCCTCCGTTCTA 60.739 54.545 22.55 0.00 36.12 2.10
575 2340 1.743996 GTACGTACTCCCTCCGTTCT 58.256 55.000 18.47 0.00 36.12 3.01
576 2341 0.375106 CGTACGTACTCCCTCCGTTC 59.625 60.000 22.55 0.00 36.12 3.95
577 2342 0.321653 ACGTACGTACTCCCTCCGTT 60.322 55.000 21.41 0.00 36.12 4.44
578 2343 0.535335 TACGTACGTACTCCCTCCGT 59.465 55.000 23.60 15.61 38.53 4.69
579 2344 1.212616 CTACGTACGTACTCCCTCCG 58.787 60.000 23.60 10.64 0.00 4.63
580 2345 2.317530 ACTACGTACGTACTCCCTCC 57.682 55.000 23.60 0.00 0.00 4.30
581 2346 4.048241 ACTACTACGTACGTACTCCCTC 57.952 50.000 23.60 0.00 0.00 4.30
582 2347 4.888239 TCTACTACTACGTACGTACTCCCT 59.112 45.833 23.60 8.26 0.00 4.20
583 2348 5.184340 TCTACTACTACGTACGTACTCCC 57.816 47.826 23.60 0.00 0.00 4.30
584 2349 6.034591 TGTTCTACTACTACGTACGTACTCC 58.965 44.000 23.60 5.59 0.00 3.85
585 2350 7.507672 TTGTTCTACTACTACGTACGTACTC 57.492 40.000 23.60 7.32 0.00 2.59
586 2351 7.884816 TTTGTTCTACTACTACGTACGTACT 57.115 36.000 23.60 16.88 0.00 2.73
587 2352 8.169268 ACATTTGTTCTACTACTACGTACGTAC 58.831 37.037 23.60 15.90 0.00 3.67
588 2353 8.251750 ACATTTGTTCTACTACTACGTACGTA 57.748 34.615 25.41 25.41 0.00 3.57
589 2354 7.133891 ACATTTGTTCTACTACTACGTACGT 57.866 36.000 25.98 25.98 0.00 3.57
590 2355 7.371875 GCTACATTTGTTCTACTACTACGTACG 59.628 40.741 15.01 15.01 0.00 3.67
591 2356 8.177663 TGCTACATTTGTTCTACTACTACGTAC 58.822 37.037 0.00 0.00 0.00 3.67
592 2357 8.267620 TGCTACATTTGTTCTACTACTACGTA 57.732 34.615 0.00 0.00 0.00 3.57
593 2358 7.149569 TGCTACATTTGTTCTACTACTACGT 57.850 36.000 0.00 0.00 0.00 3.57
594 2359 8.630278 ATTGCTACATTTGTTCTACTACTACG 57.370 34.615 0.00 0.00 0.00 3.51
604 2369 4.678509 TCGGTGATTGCTACATTTGTTC 57.321 40.909 0.00 0.00 0.00 3.18
667 2446 1.028905 CGAAAACCTCAGCCCAAACA 58.971 50.000 0.00 0.00 0.00 2.83
706 2516 0.110192 GCGCGGCTATATTTTGCTCC 60.110 55.000 8.83 0.00 0.00 4.70
750 2560 0.173481 CGGATCGTGGAGAAGCAGAA 59.827 55.000 0.00 0.00 0.00 3.02
777 2587 1.877680 CGCACTGATTGGTTGGAGACA 60.878 52.381 0.00 0.00 39.83 3.41
794 2604 4.794439 CGATCTGTGGGACGCGCA 62.794 66.667 5.73 5.58 45.01 6.09
816 2636 2.184322 GCTGGGATCTGCGTTCGA 59.816 61.111 0.00 0.00 0.00 3.71
822 2643 3.112205 ATGGACGGCTGGGATCTGC 62.112 63.158 0.00 0.00 37.15 4.26
840 2661 2.603247 GCGTTGGATGTGTCGTGCA 61.603 57.895 0.00 0.00 0.00 4.57
936 2804 0.955919 GTTTGGGGAACTGGAGCGAG 60.956 60.000 0.00 0.00 35.31 5.03
937 2805 1.072505 GTTTGGGGAACTGGAGCGA 59.927 57.895 0.00 0.00 35.31 4.93
939 2807 0.609406 GAGGTTTGGGGAACTGGAGC 60.609 60.000 0.00 0.00 38.35 4.70
941 2809 1.432023 GGGAGGTTTGGGGAACTGGA 61.432 60.000 0.00 0.00 38.35 3.86
942 2810 1.076727 GGGAGGTTTGGGGAACTGG 59.923 63.158 0.00 0.00 38.35 4.00
944 2812 2.081585 GCTGGGAGGTTTGGGGAACT 62.082 60.000 0.00 0.00 38.35 3.01
945 2813 1.606601 GCTGGGAGGTTTGGGGAAC 60.607 63.158 0.00 0.00 37.53 3.62
1230 3117 0.109226 GGAGGTCGGTCTTGAAGTCG 60.109 60.000 0.00 0.00 0.00 4.18
1425 4634 4.039973 CCTATTAGGGATCTAACACGCCAA 59.960 45.833 1.37 0.00 38.19 4.52
1427 4636 3.616802 GCCTATTAGGGATCTAACACGCC 60.617 52.174 11.72 0.00 38.19 5.68
1429 4638 4.866508 TGCCTATTAGGGATCTAACACG 57.133 45.455 11.72 0.00 38.19 4.49
1443 4690 3.117888 ACAGATTTCCACCGATGCCTATT 60.118 43.478 0.00 0.00 0.00 1.73
1444 4691 2.439507 ACAGATTTCCACCGATGCCTAT 59.560 45.455 0.00 0.00 0.00 2.57
1462 4716 4.871513 TCTGAAACACTAGTAGCACACAG 58.128 43.478 0.00 1.74 0.00 3.66
1490 4754 4.260985 ACACATGACAAGAACAACACAGA 58.739 39.130 0.00 0.00 0.00 3.41
1498 4785 7.201591 CCATCAGATTAGACACATGACAAGAAC 60.202 40.741 0.00 0.00 0.00 3.01
1599 4911 4.379499 GCTAGCTAAAACAGGCGACAATTT 60.379 41.667 7.70 0.00 0.00 1.82
1600 4912 3.127030 GCTAGCTAAAACAGGCGACAATT 59.873 43.478 7.70 0.00 0.00 2.32
1604 4933 1.722011 TGCTAGCTAAAACAGGCGAC 58.278 50.000 17.23 0.00 0.00 5.19
1638 4967 7.319646 GCCACATGTTAATTCAAGACCAATTA 58.680 34.615 0.00 0.00 0.00 1.40
1639 4968 6.165577 GCCACATGTTAATTCAAGACCAATT 58.834 36.000 0.00 0.00 0.00 2.32
1640 4969 5.337491 GGCCACATGTTAATTCAAGACCAAT 60.337 40.000 0.00 0.00 0.00 3.16
1641 4970 4.021544 GGCCACATGTTAATTCAAGACCAA 60.022 41.667 0.00 0.00 0.00 3.67
1644 4976 3.190535 ACGGCCACATGTTAATTCAAGAC 59.809 43.478 2.24 0.00 0.00 3.01
1645 4977 3.417101 ACGGCCACATGTTAATTCAAGA 58.583 40.909 2.24 0.00 0.00 3.02
1655 4987 2.102252 ACAAAAATTGACGGCCACATGT 59.898 40.909 2.24 0.00 0.00 3.21
1660 4992 3.215151 TCAGTACAAAAATTGACGGCCA 58.785 40.909 2.24 0.00 0.00 5.36
1662 4994 4.483476 ACTCAGTACAAAAATTGACGGC 57.517 40.909 0.00 0.00 0.00 5.68
1670 5002 6.927381 GCTAACCAGAGTACTCAGTACAAAAA 59.073 38.462 24.44 0.72 41.03 1.94
1685 5017 1.189752 TCAGAGGCAGCTAACCAGAG 58.810 55.000 7.65 0.00 0.00 3.35
1691 5023 1.276421 GTCAGGTTCAGAGGCAGCTAA 59.724 52.381 0.00 0.00 0.00 3.09
1711 5043 1.302033 AACTGCCAGTTCGCTCAGG 60.302 57.895 3.74 0.00 31.77 3.86
1712 5044 0.601046 TCAACTGCCAGTTCGCTCAG 60.601 55.000 7.22 0.00 36.03 3.35
1713 5045 0.601046 CTCAACTGCCAGTTCGCTCA 60.601 55.000 7.22 0.00 36.03 4.26
1714 5046 0.319900 TCTCAACTGCCAGTTCGCTC 60.320 55.000 7.22 0.00 36.03 5.03
1715 5047 0.322975 ATCTCAACTGCCAGTTCGCT 59.677 50.000 7.22 0.00 36.03 4.93
1716 5048 1.929836 CTATCTCAACTGCCAGTTCGC 59.070 52.381 7.22 0.00 36.03 4.70
1735 5068 3.502211 CGGACAAGCAATTTTCAGGTACT 59.498 43.478 0.00 0.00 43.88 2.73
1812 5172 6.705863 AGGGATGCTTTTCAACAGAATATC 57.294 37.500 0.00 0.00 0.00 1.63
1877 5237 4.451435 GGACACCAACTAAGTTTAGAGCAC 59.549 45.833 5.93 0.00 34.84 4.40
1927 5317 1.545582 CCCAATAATATTGCAGGCCGG 59.454 52.381 7.45 0.00 0.00 6.13
1928 5318 2.030007 CACCCAATAATATTGCAGGCCG 60.030 50.000 7.45 0.00 0.00 6.13
1947 5362 1.549203 AGGAATTGTGGGTGATGCAC 58.451 50.000 0.00 0.00 0.00 4.57
1969 5385 2.173669 CGATGCCCTGGTGCGTTAG 61.174 63.158 3.84 0.00 0.00 2.34
1981 5399 2.964389 GAGCGCTTCCTCGATGCC 60.964 66.667 13.26 0.00 30.42 4.40
1998 5416 7.228906 AGCATGAAATTCTGATCAATAGTGGAG 59.771 37.037 0.00 0.00 0.00 3.86
1999 5417 7.058525 AGCATGAAATTCTGATCAATAGTGGA 58.941 34.615 0.00 0.00 0.00 4.02
2017 5435 3.822735 GGCATAAGCAGGAATAGCATGAA 59.177 43.478 0.00 0.00 44.61 2.57
2032 5450 2.226437 ACAAGAACAACTGCGGCATAAG 59.774 45.455 1.75 0.00 0.00 1.73
2035 5453 0.311790 CACAAGAACAACTGCGGCAT 59.688 50.000 1.75 0.00 0.00 4.40
2094 5554 7.864108 TGAATGTAACCTATGTTTCAGGATG 57.136 36.000 0.00 0.00 35.58 3.51
2101 5561 6.779860 ACACTCCTGAATGTAACCTATGTTT 58.220 36.000 0.00 0.00 35.87 2.83
2107 5567 6.497259 TCTCTTTACACTCCTGAATGTAACCT 59.503 38.462 1.05 0.00 40.19 3.50
2199 5665 7.611855 ACTGCCATTTAAGCTACTACAAAATCT 59.388 33.333 0.00 0.00 0.00 2.40
2210 5676 5.160607 ACACAGTACTGCCATTTAAGCTA 57.839 39.130 22.90 0.00 0.00 3.32
2211 5677 4.003648 GACACAGTACTGCCATTTAAGCT 58.996 43.478 22.90 0.00 0.00 3.74
2212 5678 3.751175 TGACACAGTACTGCCATTTAAGC 59.249 43.478 22.90 3.23 0.00 3.09
2222 5771 9.103048 GTTATTTCGAATTTTGACACAGTACTG 57.897 33.333 21.44 21.44 0.00 2.74
2257 5819 1.672356 CAGGTTCCGAGGCAACCAG 60.672 63.158 18.70 11.29 45.20 4.00
2357 6401 2.297701 GCAGGGTTGAGACACTTTCAA 58.702 47.619 0.00 0.00 37.45 2.69


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

AutoCloner maintained by Alex Coulton.