Multiple sequence alignment - TraesCS4D01G108900

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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 TraesCS4D01G108900 chr4D 100.000 8826 0 0 1 8826 88134112 88125287 0.000000e+00 16299.0
1 TraesCS4D01G108900 chr4D 91.293 379 26 3 3902 4277 112874530 112874156 2.200000e-140 510.0
2 TraesCS4D01G108900 chr4D 93.805 226 12 2 3589 3813 88130108 88129884 1.100000e-88 339.0
3 TraesCS4D01G108900 chr4A 96.344 4021 127 12 4814 8826 500908284 500904276 0.000000e+00 6593.0
4 TraesCS4D01G108900 chr4A 95.482 1328 54 6 2284 3608 500910821 500909497 0.000000e+00 2115.0
5 TraesCS4D01G108900 chr4A 94.171 1321 67 9 861 2175 500912140 500910824 0.000000e+00 2004.0
6 TraesCS4D01G108900 chr4A 93.705 826 49 3 3902 4725 500909143 500908319 0.000000e+00 1234.0
7 TraesCS4D01G108900 chr4A 85.693 685 79 10 3589 4260 38669325 38668647 0.000000e+00 704.0
8 TraesCS4D01G108900 chr4A 92.932 382 21 3 426 804 500912838 500912460 1.300000e-152 551.0
9 TraesCS4D01G108900 chr4A 91.899 395 22 3 1 395 500958661 500958277 2.170000e-150 544.0
10 TraesCS4D01G108900 chr4A 91.392 395 27 1 1 395 500940386 500939999 1.300000e-147 534.0
11 TraesCS4D01G108900 chr4A 92.781 374 19 2 1 373 500954534 500954168 1.300000e-147 534.0
12 TraesCS4D01G108900 chr4A 86.503 326 33 9 3588 3903 522220162 522219838 1.820000e-91 348.0
13 TraesCS4D01G108900 chr4A 97.778 45 1 0 389 433 500913942 500913898 2.640000e-10 78.7
14 TraesCS4D01G108900 chr4B 97.173 3254 80 5 4839 8092 124749340 124746099 0.000000e+00 5489.0
15 TraesCS4D01G108900 chr4B 95.080 2988 113 20 622 3587 124753744 124750769 0.000000e+00 4673.0
16 TraesCS4D01G108900 chr4B 95.658 737 24 5 8097 8826 124745779 124745044 0.000000e+00 1177.0
17 TraesCS4D01G108900 chr4B 92.308 468 23 3 4281 4736 124750757 124750291 0.000000e+00 652.0
18 TraesCS4D01G108900 chr4B 96.497 314 10 1 1 314 124754274 124753962 1.310000e-142 518.0
19 TraesCS4D01G108900 chr4B 93.103 203 11 2 451 651 124753949 124753748 2.410000e-75 294.0
20 TraesCS4D01G108900 chr4B 98.182 110 2 0 4733 4842 124750136 124750027 9.040000e-45 193.0
21 TraesCS4D01G108900 chr3B 85.975 713 57 17 3601 4271 446705225 446705936 0.000000e+00 723.0
22 TraesCS4D01G108900 chr6A 91.601 381 24 4 3902 4279 315403054 315403429 3.650000e-143 520.0
23 TraesCS4D01G108900 chr6D 91.076 381 26 5 3902 4278 254969558 254969182 7.910000e-140 508.0
24 TraesCS4D01G108900 chr2A 91.444 374 25 3 3902 4272 408796366 408795997 2.840000e-139 507.0
25 TraesCS4D01G108900 chr3D 91.421 373 25 3 3902 4271 84931286 84931654 1.020000e-138 505.0
26 TraesCS4D01G108900 chr3D 83.279 305 31 10 3615 3903 505047011 505047311 6.800000e-66 263.0
27 TraesCS4D01G108900 chr1A 90.789 380 27 4 3902 4278 382779361 382778987 1.320000e-137 501.0
28 TraesCS4D01G108900 chr1A 85.583 326 36 5 3588 3903 174745154 174744830 1.840000e-86 331.0
29 TraesCS4D01G108900 chr7D 89.846 325 22 4 3589 3903 222244255 222244578 2.970000e-109 407.0
30 TraesCS4D01G108900 chr3A 89.231 325 24 5 3589 3903 298441318 298441641 6.420000e-106 396.0
31 TraesCS4D01G108900 chr3A 87.616 323 31 5 3589 3903 286731368 286731047 5.030000e-97 366.0
32 TraesCS4D01G108900 chr3A 87.066 317 30 5 3589 3895 111237699 111238014 1.820000e-91 348.0
33 TraesCS4D01G108900 chr2B 87.850 321 32 5 3589 3903 608656441 608656760 3.890000e-98 370.0
34 TraesCS4D01G108900 chr5A 85.846 325 35 9 3589 3903 468528611 468528934 1.420000e-87 335.0
35 TraesCS4D01G108900 chr5D 87.342 158 8 8 3757 3903 210799681 210799525 4.240000e-38 171.0


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 TraesCS4D01G108900 chr4D 88125287 88134112 8825 True 16299.000000 16299 100.000000 1 8826 1 chr4D.!!$R1 8825
1 TraesCS4D01G108900 chr4A 500904276 500913942 9666 True 2095.950000 6593 95.068667 389 8826 6 chr4A.!!$R4 8437
2 TraesCS4D01G108900 chr4A 38668647 38669325 678 True 704.000000 704 85.693000 3589 4260 1 chr4A.!!$R1 671
3 TraesCS4D01G108900 chr4A 500954168 500958661 4493 True 539.000000 544 92.340000 1 395 2 chr4A.!!$R5 394
4 TraesCS4D01G108900 chr4B 124745044 124754274 9230 True 1856.571429 5489 95.428714 1 8826 7 chr4B.!!$R1 8825
5 TraesCS4D01G108900 chr3B 446705225 446705936 711 False 723.000000 723 85.975000 3601 4271 1 chr3B.!!$F1 670

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
489 2126 1.218704 AGGGGTAGGCTTGGTCGTATA 59.781 52.381 0.00 0.00 0.00 1.47 F
1683 3622 0.387239 GTTGGTGGCAACTCGAATGC 60.387 55.000 13.06 13.06 43.08 3.56 F
1781 3720 0.911053 TGGCCAGCAGATGTCATACA 59.089 50.000 0.00 0.00 0.00 2.29 F
3143 5188 0.106708 ATGTGTCTGTGTTCGCAGGT 59.893 50.000 12.44 0.00 37.12 4.00 F
4276 7149 0.542805 TCCGGGGCATTACACTAACC 59.457 55.000 0.00 0.00 0.00 2.85 F
5005 8739 0.596577 GCGAGGAACCTTTTGAACCC 59.403 55.000 0.00 0.00 0.00 4.11 F
5038 8772 0.671472 TGCAGATTGGTCACTCAGCG 60.671 55.000 0.00 0.00 0.00 5.18 F
5046 8780 1.007336 GGTCACTCAGCGTACGTTGG 61.007 60.000 28.18 21.15 0.00 3.77 F
5881 9615 1.826385 AAATCCTCAAACTCCCAGCG 58.174 50.000 0.00 0.00 0.00 5.18 F
6267 10001 3.120041 GACGGCTTCTATTTCAGAGCTC 58.880 50.000 5.27 5.27 33.83 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2073 4016 0.532573 GAGGAGATCGAGGCACACAA 59.467 55.000 0.00 0.0 0.00 3.33 R
2918 4963 1.000896 GCCAAGCTAAGGCCCAAGA 60.001 57.895 17.14 0.0 46.50 3.02 R
3707 6515 1.128200 CCAATCGGTCACCCATCCTA 58.872 55.000 0.00 0.0 0.00 2.94 R
5046 8780 0.698818 ATCTGGTCCAAGTGGGGAAC 59.301 55.000 0.00 0.0 45.29 3.62 R
6155 9889 1.547372 CCAACCCATCTTTTGCTCCTG 59.453 52.381 0.00 0.0 0.00 3.86 R
6267 10001 1.745087 AGCATTTGCACCATAGAACGG 59.255 47.619 5.20 0.0 45.16 4.44 R
6585 10319 2.222729 CGATGTAGGAAAGTTTTCGCCG 60.223 50.000 0.00 0.0 38.06 6.46 R
6956 10690 4.476479 ACCCTTCTCCAAGAGCTTGATTAT 59.524 41.667 11.61 0.0 42.93 1.28 R
7566 11869 1.070786 GGTTGGTTGCGGTCTCTGA 59.929 57.895 0.00 0.0 0.00 3.27 R
8250 12872 2.290641 AGTTTTGTCACGATGCCTTGAC 59.709 45.455 0.00 0.0 40.67 3.18 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
159 160 4.571580 CGAGAGACTACTACGGAGACAAAT 59.428 45.833 0.00 0.00 0.00 2.32
247 248 6.310467 TCACAACACGACTTTATCATTAGAGC 59.690 38.462 0.00 0.00 0.00 4.09
314 315 2.287644 TGCGCATGTGTATTGTAGCATC 59.712 45.455 5.66 0.00 0.00 3.91
316 317 3.242706 GCGCATGTGTATTGTAGCATCAA 60.243 43.478 0.30 0.00 0.00 2.57
332 333 8.040727 TGTAGCATCAACATAGTAGACATGTTT 58.959 33.333 0.00 0.00 42.52 2.83
336 337 7.854422 GCATCAACATAGTAGACATGTTTCATG 59.146 37.037 0.00 7.99 42.52 3.07
337 338 8.886719 CATCAACATAGTAGACATGTTTCATGT 58.113 33.333 14.01 14.01 42.52 3.21
338 339 8.846943 TCAACATAGTAGACATGTTTCATGTT 57.153 30.769 15.02 8.63 42.52 2.71
339 340 8.935844 TCAACATAGTAGACATGTTTCATGTTC 58.064 33.333 15.02 9.41 42.52 3.18
340 341 7.849804 ACATAGTAGACATGTTTCATGTTCC 57.150 36.000 15.02 5.44 32.72 3.62
341 342 7.394016 ACATAGTAGACATGTTTCATGTTCCA 58.606 34.615 15.02 3.35 32.72 3.53
342 343 8.049117 ACATAGTAGACATGTTTCATGTTCCAT 58.951 33.333 15.02 6.77 32.72 3.41
343 344 9.546428 CATAGTAGACATGTTTCATGTTCCATA 57.454 33.333 15.02 8.31 31.52 2.74
344 345 9.770097 ATAGTAGACATGTTTCATGTTCCATAG 57.230 33.333 15.02 0.00 31.52 2.23
345 346 5.824904 AGACATGTTTCATGTTCCATAGC 57.175 39.130 15.02 3.05 31.52 2.97
346 347 4.333649 AGACATGTTTCATGTTCCATAGCG 59.666 41.667 15.02 0.00 31.52 4.26
351 352 2.330440 TCATGTTCCATAGCGCACAT 57.670 45.000 11.47 6.56 0.00 3.21
362 363 4.749598 CCATAGCGCACATAATGTTCACTA 59.250 41.667 11.47 0.00 0.00 2.74
368 369 5.682869 CGCACATAATGTTCACTATCATGG 58.317 41.667 0.00 0.00 0.00 3.66
371 372 5.532032 CACATAATGTTCACTATCATGGCCA 59.468 40.000 8.56 8.56 0.00 5.36
377 378 5.939447 TGTTCACTATCATGGCCATCAATA 58.061 37.500 17.61 15.31 0.00 1.90
417 418 9.083422 TGATAGTCAAGAGCTATGCTAAGTTAT 57.917 33.333 0.00 0.00 39.88 1.89
468 2105 5.779922 TGATATCACCAATACCTCGCTAAC 58.220 41.667 0.00 0.00 0.00 2.34
469 2106 5.303333 TGATATCACCAATACCTCGCTAACA 59.697 40.000 0.00 0.00 0.00 2.41
489 2126 1.218704 AGGGGTAGGCTTGGTCGTATA 59.781 52.381 0.00 0.00 0.00 1.47
1042 2980 0.460987 GTCCTGCCAAGACTCCATCG 60.461 60.000 0.00 0.00 0.00 3.84
1113 3051 2.490328 TTGGCTTGCTCGTTTTCTTG 57.510 45.000 0.00 0.00 0.00 3.02
1236 3174 2.969443 ACATTTGAAGCTTCCGAACG 57.031 45.000 23.42 13.04 0.00 3.95
1303 3242 9.368921 GCTTTATTGTTAACTCAATTGCAAAAC 57.631 29.630 1.71 1.76 38.68 2.43
1323 3262 2.693074 ACAATTGAGAAAAACTGCCCGT 59.307 40.909 13.59 0.00 0.00 5.28
1344 3283 5.864474 CCGTTGATGATTCTACAGTATAGGC 59.136 44.000 0.00 0.00 0.00 3.93
1363 3302 1.002033 GCATAATCTTCCCAGCTTGCG 60.002 52.381 0.00 0.00 0.00 4.85
1395 3334 6.655078 ATTGATTCAGTTACTGGTGCTTTT 57.345 33.333 12.79 0.00 31.51 2.27
1417 3356 1.878088 CAGATTGGGGATGAGATTGCG 59.122 52.381 0.00 0.00 0.00 4.85
1556 3495 2.380084 TGATGCTGTAAGGTTCCGTC 57.620 50.000 0.00 0.00 0.00 4.79
1575 3514 3.663233 CGTCGCTCTCGCTTTCTATCTAG 60.663 52.174 0.00 0.00 35.26 2.43
1639 3578 5.771666 CCTATAATTTGATGGTCATGGTGCT 59.228 40.000 0.00 0.00 0.00 4.40
1658 3597 5.525378 GGTGCTGTGATTCTAGTTTCTATGG 59.475 44.000 0.00 0.00 0.00 2.74
1683 3622 0.387239 GTTGGTGGCAACTCGAATGC 60.387 55.000 13.06 13.06 43.08 3.56
1781 3720 0.911053 TGGCCAGCAGATGTCATACA 59.089 50.000 0.00 0.00 0.00 2.29
1788 3727 5.066375 GCCAGCAGATGTCATACAAATAACA 59.934 40.000 0.00 0.00 0.00 2.41
1792 3731 6.094048 AGCAGATGTCATACAAATAACACACC 59.906 38.462 0.00 0.00 0.00 4.16
1849 3788 2.027100 AGTTAGTAGGCAAGCCAGAACC 60.027 50.000 14.40 0.00 38.92 3.62
1903 3843 8.819845 TGATGTATTTCTATATGCATCTCACCT 58.180 33.333 0.19 0.00 43.68 4.00
1904 3844 9.311916 GATGTATTTCTATATGCATCTCACCTC 57.688 37.037 0.19 0.00 41.54 3.85
1905 3845 8.193953 TGTATTTCTATATGCATCTCACCTCA 57.806 34.615 0.19 0.00 0.00 3.86
1950 3891 3.770589 TGGTTTTGCCATCACCGG 58.229 55.556 0.00 0.00 43.61 5.28
1974 3917 7.201644 CGGACATGTCAACTATTATTGCTTCTT 60.202 37.037 26.47 0.00 0.00 2.52
2073 4016 6.283544 TCAATGATGCCAATACATGTTTGT 57.716 33.333 2.30 0.00 39.98 2.83
2110 4053 4.101448 GGGCTCCTGCGGTCATGT 62.101 66.667 0.00 0.00 40.82 3.21
2125 4068 4.033243 CGGTCATGTGAATGATAGTGTGTG 59.967 45.833 0.00 0.00 32.61 3.82
2142 4085 2.746277 GGCGTACAGGGCACTTGG 60.746 66.667 0.00 0.00 0.00 3.61
2230 4173 8.575649 TGCACGTATCTAGAATTATCTATCCA 57.424 34.615 0.00 0.00 37.52 3.41
2305 4249 3.754976 TGTGGGTAGAGGGGGAAATAAT 58.245 45.455 0.00 0.00 0.00 1.28
2341 4285 2.079925 GCCTTCTGTCATCACCTGAAC 58.920 52.381 0.00 0.00 35.07 3.18
2383 4327 1.153329 TGCCGAAGTTGTGACGGTT 60.153 52.632 0.00 0.00 46.95 4.44
2413 4357 3.567478 AGTGAAAGTTGGACTTCTGCT 57.433 42.857 0.00 0.00 37.47 4.24
2538 4483 9.565090 TTTCTTATGATGGATAGGAAATGACAG 57.435 33.333 0.00 0.00 37.58 3.51
2550 4495 5.091552 AGGAAATGACAGTCCTAGTAACCA 58.908 41.667 8.42 0.00 42.68 3.67
2689 4635 7.360691 GGGTTTTGAAGAAAGAAGGTCGTATAC 60.361 40.741 0.00 0.00 0.00 1.47
2802 4846 2.580589 CCAAACTAACAAATGCGACCG 58.419 47.619 0.00 0.00 0.00 4.79
2918 4963 2.308570 TGTGGCTATCTGATTGTTGGGT 59.691 45.455 0.00 0.00 0.00 4.51
2956 5001 1.393487 ATTTGCTGCTGGTGTGCACA 61.393 50.000 17.42 17.42 38.12 4.57
2972 5017 2.009042 GCACATCAGACTGGCTGGTAC 61.009 57.143 11.28 0.00 44.98 3.34
2991 5036 1.476891 ACTCTGCCACGTCGATAACAT 59.523 47.619 0.00 0.00 0.00 2.71
2993 5038 2.267426 TCTGCCACGTCGATAACATTG 58.733 47.619 0.00 0.00 0.00 2.82
3038 5083 5.163652 GCACTTAACAAGGTTTTCTGTGTCT 60.164 40.000 0.00 0.00 0.00 3.41
3143 5188 0.106708 ATGTGTCTGTGTTCGCAGGT 59.893 50.000 12.44 0.00 37.12 4.00
3465 5518 4.943705 TGGCCTAGATGTTTCAATCTTCAC 59.056 41.667 3.32 0.00 37.98 3.18
3519 5572 3.059884 TGCATCTTTCTCGTGTCTTGAC 58.940 45.455 0.00 0.00 0.00 3.18
3587 5640 3.707102 GGCCTTAGAGTCAGTCACCTAAT 59.293 47.826 0.00 0.00 0.00 1.73
3598 5721 4.130118 CAGTCACCTAATTGTGATAGCCC 58.870 47.826 2.30 0.00 46.20 5.19
3748 6556 4.947147 TTGGTCCCAGGTGCGCAC 62.947 66.667 32.15 32.15 0.00 5.34
3758 6566 2.355837 GTGCGCACGAGTGAGGAA 60.356 61.111 26.77 0.00 32.21 3.36
3766 6574 1.939934 CACGAGTGAGGAAAAAGTGCA 59.060 47.619 0.00 0.00 0.00 4.57
3787 6595 4.757149 GCACAGGAAAGACTAGTGTTGATT 59.243 41.667 5.96 0.00 32.99 2.57
3805 6613 0.690762 TTTGTGGGGCCAGTCTAGAC 59.309 55.000 15.41 15.41 0.00 2.59
4024 6896 6.934645 GTGTATGTGATAGCCTGGCTTAATAA 59.065 38.462 28.55 8.78 40.44 1.40
4110 6982 1.873591 CCAAAGTTAAGCGTGCTCAGT 59.126 47.619 0.00 0.00 0.00 3.41
4182 7054 2.497138 CATGAGTGAGGACAAAGTGCA 58.503 47.619 0.00 0.00 0.00 4.57
4276 7149 0.542805 TCCGGGGCATTACACTAACC 59.457 55.000 0.00 0.00 0.00 2.85
4386 7259 6.302269 ACCATTCTGAGAAAAGAGTGTCAAT 58.698 36.000 0.00 0.00 33.33 2.57
4473 7347 1.448540 CCTCCGCATTCGCAGTTCT 60.449 57.895 0.00 0.00 38.40 3.01
4478 7352 0.713883 CGCATTCGCAGTTCTTACGT 59.286 50.000 0.00 0.00 38.40 3.57
4515 7389 1.266178 TGCCACGATTCCTCTCTTCA 58.734 50.000 0.00 0.00 0.00 3.02
4627 7502 4.056740 CTGGTAGCATTGCATCTACTCTG 58.943 47.826 11.91 9.60 36.37 3.35
4634 7509 3.900966 TTGCATCTACTCTGTCTGCAT 57.099 42.857 0.00 0.00 41.95 3.96
4687 7573 6.389906 CATGTTCCCTGTTCCAAAACTTATC 58.610 40.000 0.00 0.00 36.30 1.75
4807 7851 1.866015 TCGGTTGAGGTCCTCATGAT 58.134 50.000 22.45 0.00 40.39 2.45
4913 8647 8.956533 ATTTACAGTTAGTTTTGCCAAAATGT 57.043 26.923 5.81 8.37 32.22 2.71
4925 8659 3.132646 TGCCAAAATGTATGCCCATCTTC 59.867 43.478 0.00 0.00 0.00 2.87
5005 8739 0.596577 GCGAGGAACCTTTTGAACCC 59.403 55.000 0.00 0.00 0.00 4.11
5006 8740 1.975660 CGAGGAACCTTTTGAACCCA 58.024 50.000 0.00 0.00 0.00 4.51
5038 8772 0.671472 TGCAGATTGGTCACTCAGCG 60.671 55.000 0.00 0.00 0.00 5.18
5046 8780 1.007336 GGTCACTCAGCGTACGTTGG 61.007 60.000 28.18 21.15 0.00 3.77
5393 9127 8.607459 CGGAAGGTATAATTGCTGAATCATATC 58.393 37.037 0.00 0.00 0.00 1.63
5817 9551 5.993055 TCATTTCTTGATAGGATGCTGTCA 58.007 37.500 9.63 9.63 0.00 3.58
5881 9615 1.826385 AAATCCTCAAACTCCCAGCG 58.174 50.000 0.00 0.00 0.00 5.18
5947 9681 3.306294 GGTCCCTTTTGAATCAGCCTTTG 60.306 47.826 0.00 0.00 0.00 2.77
6155 9889 6.633634 CGCTACTTAGAAGCATTACTAGACAC 59.366 42.308 0.00 0.00 40.08 3.67
6191 9925 6.739331 TGGGTTGGTGTTGATTAAGAAATT 57.261 33.333 0.00 0.00 0.00 1.82
6267 10001 3.120041 GACGGCTTCTATTTCAGAGCTC 58.880 50.000 5.27 5.27 33.83 4.09
6325 10059 3.326880 GTCCTTGGTAAGAAACAGAGGGA 59.673 47.826 0.00 0.00 34.24 4.20
6585 10319 3.502211 CGATTGTTGGGTATATCTTGGCC 59.498 47.826 0.00 0.00 0.00 5.36
6956 10690 5.939764 AGCTTGTCCAGTATGAGATTACA 57.060 39.130 0.00 0.00 39.69 2.41
7083 11386 3.517296 TTTGACATACCTGGCCTTGAA 57.483 42.857 3.32 0.00 0.00 2.69
7196 11499 9.762933 ACTTGCTGTGACATTTGTTTAAATTAT 57.237 25.926 0.00 0.00 34.34 1.28
7295 11598 6.550108 GGAGGTATCAATACTCTTGAGGTACA 59.450 42.308 2.55 0.00 33.81 2.90
7412 11715 6.471233 TTGAATCTCGATCTGGAACTACAT 57.529 37.500 0.00 0.00 0.00 2.29
7468 11771 5.562506 TTGGAACTGTCTAGATCAGTACG 57.437 43.478 20.91 4.13 44.03 3.67
7521 11824 7.388776 TCTTGTCTCCACAACATCAGATTTTAG 59.611 37.037 0.00 0.00 37.61 1.85
7566 11869 4.277174 ACGTCAGATCGCAGATCTCTAATT 59.723 41.667 15.23 0.00 45.12 1.40
7643 11946 6.678547 AGCATATAACCCAAATCCCTGTTTA 58.321 36.000 0.00 0.00 0.00 2.01
7971 12274 8.731605 TTGTTAAGTCACAATGTTGTAAACTCA 58.268 29.630 11.29 5.56 38.56 3.41
8092 12395 7.404671 TTCATATAGTGTCAGCAGTACAAGA 57.595 36.000 0.00 0.00 33.76 3.02
8250 12872 5.543507 ATTGCCTACCTCTACAATCTCTG 57.456 43.478 0.00 0.00 0.00 3.35
8321 12943 3.553508 CCTGAAACTTCCAAATGCACCAG 60.554 47.826 0.00 0.00 0.00 4.00
8379 13001 3.694566 GGTTCTCTTGTTGTTGGACACTT 59.305 43.478 0.00 0.00 0.00 3.16
8382 13004 4.584874 TCTCTTGTTGTTGGACACTTTGA 58.415 39.130 0.00 0.00 0.00 2.69
8568 13192 2.620886 GCACCCTACAGTCTCTGTCCTA 60.621 54.545 5.66 0.00 41.21 2.94
8784 13408 0.595825 GCTGTCCAGTTTGTTGCTGC 60.596 55.000 0.00 0.00 32.93 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
159 160 2.224769 CCTAGCCAACCCAAGTTTGAGA 60.225 50.000 0.00 0.00 32.45 3.27
272 273 4.299155 CAGTGCATAGTCTATGTTACCCG 58.701 47.826 18.92 10.18 38.43 5.28
304 305 8.206867 ACATGTCTACTATGTTGATGCTACAAT 58.793 33.333 0.00 0.00 35.32 2.71
314 315 8.177663 GGAACATGAAACATGTCTACTATGTTG 58.822 37.037 21.22 6.68 45.28 3.33
316 317 7.394016 TGGAACATGAAACATGTCTACTATGT 58.606 34.615 15.96 3.77 40.30 2.29
336 337 4.035091 TGAACATTATGTGCGCTATGGAAC 59.965 41.667 9.73 0.00 0.00 3.62
337 338 4.035091 GTGAACATTATGTGCGCTATGGAA 59.965 41.667 9.73 0.00 33.66 3.53
338 339 3.559655 GTGAACATTATGTGCGCTATGGA 59.440 43.478 9.73 0.00 33.66 3.41
339 340 3.561310 AGTGAACATTATGTGCGCTATGG 59.439 43.478 17.01 0.97 44.52 2.74
340 341 4.801147 AGTGAACATTATGTGCGCTATG 57.199 40.909 17.01 7.17 44.52 2.23
344 345 4.794248 TGATAGTGAACATTATGTGCGC 57.206 40.909 8.75 8.75 36.67 6.09
345 346 5.682869 CCATGATAGTGAACATTATGTGCG 58.317 41.667 0.00 0.00 0.00 5.34
346 347 5.455392 GCCATGATAGTGAACATTATGTGC 58.545 41.667 0.00 0.00 0.00 4.57
351 352 5.939447 TGATGGCCATGATAGTGAACATTA 58.061 37.500 26.56 0.00 0.00 1.90
417 418 2.543777 AGCTCTTCAAAGTAACCGCA 57.456 45.000 0.00 0.00 0.00 5.69
468 2105 0.974010 TACGACCAAGCCTACCCCTG 60.974 60.000 0.00 0.00 0.00 4.45
469 2106 0.031414 ATACGACCAAGCCTACCCCT 60.031 55.000 0.00 0.00 0.00 4.79
489 2126 6.464222 TCGTCAAGGTTTCATAAACTCTCAT 58.536 36.000 2.84 0.00 41.14 2.90
539 2176 7.978982 AGTTGAGGAAATTTCAGATGATAACG 58.021 34.615 19.49 0.00 0.00 3.18
762 2436 1.227380 GGCTGCTACACGGGAGATG 60.227 63.158 0.00 0.00 0.00 2.90
812 2486 3.582164 GAGGAGAGATGGATACCACCTT 58.418 50.000 0.00 0.00 35.80 3.50
1042 2980 1.084370 CGAAGTGATTCGACCTGGCC 61.084 60.000 4.44 0.00 46.52 5.36
1236 3174 7.201617 CCACTCGTTTTAAGATGGATTACTTCC 60.202 40.741 0.00 0.00 45.69 3.46
1303 3242 3.369546 ACGGGCAGTTTTTCTCAATTG 57.630 42.857 0.00 0.00 0.00 2.32
1311 3250 3.573967 AGAATCATCAACGGGCAGTTTTT 59.426 39.130 0.00 0.00 42.02 1.94
1363 3302 9.331282 ACCAGTAACTGAATCAATTTCTATAGC 57.669 33.333 0.00 0.00 35.23 2.97
1395 3334 2.940158 CAATCTCATCCCCAATCTGCA 58.060 47.619 0.00 0.00 0.00 4.41
1575 3514 8.703604 TGTAGATTTCAGTAGTTGCTTGATAC 57.296 34.615 0.00 0.00 0.00 2.24
1639 3578 5.487488 ACCACCCATAGAAACTAGAATCACA 59.513 40.000 0.00 0.00 0.00 3.58
1683 3622 8.554528 CAGTAATGCTACAGGACATTCATTAAG 58.445 37.037 0.00 0.00 37.63 1.85
1849 3788 5.627499 AAAACCAGTGTGCATACATGTAG 57.373 39.130 16.44 5.01 39.39 2.74
1903 3843 7.460214 AAACTCATGTTAGGGGGTTATATGA 57.540 36.000 0.00 0.00 34.96 2.15
1904 3844 9.231297 CATAAACTCATGTTAGGGGGTTATATG 57.769 37.037 0.00 0.00 34.96 1.78
1905 3845 8.390921 CCATAAACTCATGTTAGGGGGTTATAT 58.609 37.037 0.00 0.00 34.96 0.86
1945 3886 5.504010 GCAATAATAGTTGACATGTCCGGTG 60.504 44.000 22.85 8.88 0.00 4.94
1946 3887 4.574828 GCAATAATAGTTGACATGTCCGGT 59.425 41.667 22.85 9.48 0.00 5.28
1948 3889 5.991328 AGCAATAATAGTTGACATGTCCG 57.009 39.130 22.85 0.51 0.00 4.79
1949 3890 7.559590 AGAAGCAATAATAGTTGACATGTCC 57.440 36.000 22.85 8.64 0.00 4.02
1950 3891 9.846248 AAAAGAAGCAATAATAGTTGACATGTC 57.154 29.630 19.27 19.27 0.00 3.06
1974 3917 4.043310 AGAAAGGGTGAGATGGATGTCAAA 59.957 41.667 0.00 0.00 31.46 2.69
2073 4016 0.532573 GAGGAGATCGAGGCACACAA 59.467 55.000 0.00 0.00 0.00 3.33
2110 4053 2.760634 ACGCCACACACTATCATTCA 57.239 45.000 0.00 0.00 0.00 2.57
2125 4068 2.746277 CCAAGTGCCCTGTACGCC 60.746 66.667 0.00 0.00 0.00 5.68
2243 4186 5.679127 GCTTCTACGGCTGTTATACTTGAGT 60.679 44.000 1.99 0.00 0.00 3.41
2305 4249 3.960102 AGAAGGCACCACATTTCTTTCAA 59.040 39.130 0.00 0.00 0.00 2.69
2383 4327 7.062749 AGTCCAACTTTCACTATGAACTACA 57.937 36.000 0.00 0.00 35.89 2.74
2538 4483 2.990066 AGCATGCTGGTTACTAGGAC 57.010 50.000 21.98 0.00 0.00 3.85
2550 4495 2.301346 GCATACCAAGGTTAGCATGCT 58.699 47.619 25.99 25.99 35.01 3.79
2571 4516 3.898123 ACCTCACAGTACTCATGACACTT 59.102 43.478 0.00 0.00 0.00 3.16
2613 4558 6.375736 TCTTATTCTAGCATCCCGTATCTCTG 59.624 42.308 0.00 0.00 0.00 3.35
2622 4567 4.566426 ATGCCTCTTATTCTAGCATCCC 57.434 45.455 0.00 0.00 39.95 3.85
2689 4635 5.008019 AGTGCAGCCATTATTATCAAGAACG 59.992 40.000 0.00 0.00 0.00 3.95
2802 4846 2.126467 GAGAGCTGCACTGATCGATTC 58.874 52.381 3.82 0.00 0.00 2.52
2918 4963 1.000896 GCCAAGCTAAGGCCCAAGA 60.001 57.895 17.14 0.00 46.50 3.02
2956 5001 2.106566 CAGAGTACCAGCCAGTCTGAT 58.893 52.381 0.00 0.00 45.72 2.90
2972 5017 2.209838 ATGTTATCGACGTGGCAGAG 57.790 50.000 0.00 0.00 0.00 3.35
2991 5036 8.777413 GTGCATATAAGAATACTGCATCTTCAA 58.223 33.333 3.60 0.00 43.89 2.69
2993 5038 8.545229 AGTGCATATAAGAATACTGCATCTTC 57.455 34.615 3.60 0.00 43.89 2.87
3017 5062 8.674607 AGTAAAGACACAGAAAACCTTGTTAAG 58.325 33.333 0.00 0.00 0.00 1.85
3071 5116 4.082679 AGACAGACCATTTCTCGAGTACAC 60.083 45.833 13.13 0.00 28.96 2.90
3128 5173 1.279840 GCAACCTGCGAACACAGAC 59.720 57.895 0.00 0.00 40.25 3.51
3143 5188 5.350633 CAAAACTTGAATTCCACTCAGCAA 58.649 37.500 2.27 0.00 0.00 3.91
3285 5330 2.443416 GGGTTAAGCACCTCGGAAATT 58.557 47.619 7.03 0.00 46.38 1.82
3587 5640 3.244422 CCTATTAAGCCGGGCTATCACAA 60.244 47.826 24.16 11.63 38.25 3.33
3598 5721 5.923733 AGTCTATCATCCCTATTAAGCCG 57.076 43.478 0.00 0.00 0.00 5.52
3707 6515 1.128200 CCAATCGGTCACCCATCCTA 58.872 55.000 0.00 0.00 0.00 2.94
3748 6556 1.939934 TGTGCACTTTTTCCTCACTCG 59.060 47.619 19.41 0.00 0.00 4.18
3758 6566 4.576463 CACTAGTCTTTCCTGTGCACTTTT 59.424 41.667 19.41 0.00 0.00 2.27
3766 6574 6.260936 CACAAATCAACACTAGTCTTTCCTGT 59.739 38.462 0.00 0.00 0.00 4.00
3787 6595 1.198759 GGTCTAGACTGGCCCCACAA 61.199 60.000 21.88 0.00 0.00 3.33
4050 6922 3.686016 TCCCAGAAAAGAAGGAATTCCG 58.314 45.455 18.82 1.19 42.08 4.30
4110 6982 2.833338 CCCATCCTGAAATTGCTCCAAA 59.167 45.455 0.00 0.00 0.00 3.28
4182 7054 5.305644 ACAGATCAACACTAGTCTTTCCTGT 59.694 40.000 0.00 0.13 0.00 4.00
4265 7138 8.983702 TGTAAAAACTCCTTGGTTAGTGTAAT 57.016 30.769 0.00 0.00 0.00 1.89
4276 7149 6.423182 TCATCCCCTATGTAAAAACTCCTTG 58.577 40.000 0.00 0.00 36.89 3.61
4473 7347 3.992943 ATCATTCCCTGTTCCACGTAA 57.007 42.857 0.00 0.00 0.00 3.18
4478 7352 3.053019 TGGCATTATCATTCCCTGTTCCA 60.053 43.478 0.00 0.00 0.00 3.53
4627 7502 5.368256 AACAGAGATCAAACAATGCAGAC 57.632 39.130 0.00 0.00 0.00 3.51
4634 7509 6.459573 GCCACTAACAAACAGAGATCAAACAA 60.460 38.462 0.00 0.00 0.00 2.83
4687 7573 6.230472 TCATGGTGACCTTATGATAAATCCG 58.770 40.000 2.11 0.00 0.00 4.18
4834 7878 9.091220 GTTCTTACTGATACCCTCATATAAGGT 57.909 37.037 0.00 0.00 35.30 3.50
4891 8625 7.596995 GCATACATTTTGGCAAAACTAACTGTA 59.403 33.333 25.89 25.89 32.37 2.74
4913 8647 5.912149 AGTGAATAAGGAAGATGGGCATA 57.088 39.130 0.00 0.00 0.00 3.14
5005 8739 6.342906 ACCAATCTGCAATAAATTCACCATG 58.657 36.000 0.00 0.00 0.00 3.66
5006 8740 6.154877 TGACCAATCTGCAATAAATTCACCAT 59.845 34.615 0.00 0.00 0.00 3.55
5046 8780 0.698818 ATCTGGTCCAAGTGGGGAAC 59.301 55.000 0.00 0.00 45.29 3.62
5155 8889 7.453393 AGGTGAAATCTCTTTCTGTGTATGAA 58.547 34.615 0.41 0.00 41.18 2.57
5156 8890 7.009179 AGGTGAAATCTCTTTCTGTGTATGA 57.991 36.000 0.41 0.00 41.18 2.15
5311 9045 5.997746 AGAGAAAATCATCGGAAAGTGACAA 59.002 36.000 0.00 0.00 0.00 3.18
5393 9127 2.455674 TCCTCACGGTGATTTGACAG 57.544 50.000 11.86 0.00 0.00 3.51
5793 9527 7.390996 GATGACAGCATCCTATCAAGAAATGAT 59.609 37.037 0.00 0.00 45.87 2.45
5881 9615 2.409948 ACAGTAGCTTGGGAATGCTC 57.590 50.000 0.00 0.00 40.35 4.26
5947 9681 3.412386 TGCTCTTAGTTTCTTCCTTGCC 58.588 45.455 0.00 0.00 0.00 4.52
6155 9889 1.547372 CCAACCCATCTTTTGCTCCTG 59.453 52.381 0.00 0.00 0.00 3.86
6191 9925 2.239654 AGCTGTAAAGCCTCCATAAGCA 59.760 45.455 0.00 0.00 34.90 3.91
6267 10001 1.745087 AGCATTTGCACCATAGAACGG 59.255 47.619 5.20 0.00 45.16 4.44
6585 10319 2.222729 CGATGTAGGAAAGTTTTCGCCG 60.223 50.000 0.00 0.00 38.06 6.46
6956 10690 4.476479 ACCCTTCTCCAAGAGCTTGATTAT 59.524 41.667 11.61 0.00 42.93 1.28
7056 11359 3.270877 GCCAGGTATGTCAAATCTCGTT 58.729 45.455 0.00 0.00 0.00 3.85
7083 11386 3.825014 GGCCAACAGCTGATGAATGATAT 59.175 43.478 24.19 0.00 43.05 1.63
7158 11461 6.264832 TGTCACAGCAAGTAAGAAAACAATG 58.735 36.000 0.00 0.00 0.00 2.82
7196 11499 3.088532 AGGCAAAACAACTGTGAGTTCA 58.911 40.909 0.24 0.00 36.03 3.18
7386 11689 7.426410 TGTAGTTCCAGATCGAGATTCAATAC 58.574 38.462 0.00 0.00 0.00 1.89
7387 11690 7.582667 TGTAGTTCCAGATCGAGATTCAATA 57.417 36.000 0.00 0.00 0.00 1.90
7388 11691 6.471233 TGTAGTTCCAGATCGAGATTCAAT 57.529 37.500 0.00 0.00 0.00 2.57
7412 11715 9.995003 AATTAAAATCTTGTTGTGCATCCTTAA 57.005 25.926 0.00 0.00 0.00 1.85
7468 11771 8.722394 GGTTCTACTGGATATTAATAAAGCAGC 58.278 37.037 0.00 0.00 0.00 5.25
7499 11802 7.173218 TGAACTAAAATCTGATGTTGTGGAGAC 59.827 37.037 3.27 0.00 0.00 3.36
7566 11869 1.070786 GGTTGGTTGCGGTCTCTGA 59.929 57.895 0.00 0.00 0.00 3.27
7643 11946 6.992715 AGACAACACTGCTTTCTAACACTAAT 59.007 34.615 0.00 0.00 0.00 1.73
7971 12274 6.613699 TGAGCAATGAGGGTGGAAATTATAT 58.386 36.000 0.00 0.00 0.00 0.86
8076 12379 6.598753 TTAGTTTTCTTGTACTGCTGACAC 57.401 37.500 0.00 0.00 0.00 3.67
8085 12388 7.378728 GCCATTGTCTGTTTAGTTTTCTTGTAC 59.621 37.037 0.00 0.00 0.00 2.90
8092 12395 5.606348 TTGGCCATTGTCTGTTTAGTTTT 57.394 34.783 6.09 0.00 0.00 2.43
8250 12872 2.290641 AGTTTTGTCACGATGCCTTGAC 59.709 45.455 0.00 0.00 40.67 3.18
8321 12943 1.322538 ATGGAAATGAAGCCGTGGCC 61.323 55.000 7.39 0.00 43.17 5.36
8379 13001 4.533707 ACACCAAGATTCTCCAGAGATCAA 59.466 41.667 0.00 0.00 37.29 2.57
8382 13004 4.081198 GTGACACCAAGATTCTCCAGAGAT 60.081 45.833 0.00 0.00 37.29 2.75
8519 13143 3.056328 GCCCCTCACGCCAAACTC 61.056 66.667 0.00 0.00 0.00 3.01
8520 13144 3.570212 AGCCCCTCACGCCAAACT 61.570 61.111 0.00 0.00 0.00 2.66
8568 13192 1.302511 CAACGGTAGCCTGCCTGTT 60.303 57.895 0.00 0.49 0.00 3.16
8657 13281 6.749118 GGACACAAAACATTGATTATCTCAGC 59.251 38.462 0.00 0.00 34.68 4.26
8784 13408 1.377994 GCATAGCCCCAGATCCAGG 59.622 63.158 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.