Multiple sequence alignment - TraesCS7D01G376900

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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 TraesCS7D01G376900 chr7D 100.000 4481 0 0 1 4481 488543780 488548260 0.000000e+00 8275.0
1 TraesCS7D01G376900 chr7D 85.757 674 85 8 3811 4477 521553912 521554581 0.000000e+00 702.0
2 TraesCS7D01G376900 chr7D 84.808 678 88 10 3809 4477 113787411 113786740 0.000000e+00 667.0
3 TraesCS7D01G376900 chr7A 97.790 1403 28 3 2410 3810 555938516 555939917 0.000000e+00 2416.0
4 TraesCS7D01G376900 chr7A 92.583 1591 68 16 810 2361 555936938 555938517 0.000000e+00 2239.0
5 TraesCS7D01G376900 chr7A 83.732 627 92 6 3857 4477 601462161 601462783 6.460000e-163 584.0
6 TraesCS7D01G376900 chr7A 89.326 356 21 1 29 384 555931040 555931378 8.900000e-117 431.0
7 TraesCS7D01G376900 chr7A 84.701 451 22 11 387 807 555932931 555933364 1.500000e-109 407.0
8 TraesCS7D01G376900 chr7B 86.775 1293 114 41 1911 3162 516791932 516793208 0.000000e+00 1387.0
9 TraesCS7D01G376900 chr7B 91.156 848 52 13 1075 1904 516790922 516791764 0.000000e+00 1129.0
10 TraesCS7D01G376900 chr7B 89.031 547 46 13 3167 3709 516793712 516794248 0.000000e+00 665.0
11 TraesCS7D01G376900 chr7B 84.047 677 95 8 3809 4477 555211813 555212484 1.360000e-179 640.0
12 TraesCS7D01G376900 chr7B 88.418 354 32 3 29 381 516785536 516785881 6.930000e-113 418.0
13 TraesCS7D01G376900 chr7B 84.463 354 51 3 4127 4477 721403413 721403765 3.320000e-91 346.0
14 TraesCS7D01G376900 chr7B 93.617 47 1 2 1 45 95008663 95008617 8.040000e-08 69.4
15 TraesCS7D01G376900 chr1B 86.467 569 66 6 3916 4480 423923941 423924502 8.240000e-172 614.0
16 TraesCS7D01G376900 chr6B 81.422 689 103 19 3809 4477 77871918 77872601 1.420000e-149 540.0
17 TraesCS7D01G376900 chr6B 91.905 210 14 1 3809 4015 548130016 548130225 1.580000e-74 291.0
18 TraesCS7D01G376900 chr6B 95.455 44 1 1 3767 3810 149729796 149729754 8.040000e-08 69.4
19 TraesCS7D01G376900 chr1A 90.404 396 36 2 3809 4204 400964648 400965041 1.850000e-143 520.0
20 TraesCS7D01G376900 chr2B 80.640 687 110 17 3809 4477 695700333 695699652 1.110000e-140 510.0
21 TraesCS7D01G376900 chr2B 88.889 54 2 4 1 51 627059179 627059231 3.740000e-06 63.9
22 TraesCS7D01G376900 chr4B 79.681 689 114 21 3809 4477 98853611 98852929 1.460000e-129 473.0
23 TraesCS7D01G376900 chr4B 79.941 339 61 7 29 364 43765302 43764968 4.480000e-60 243.0
24 TraesCS7D01G376900 chr4B 91.667 48 3 1 1 47 59675144 59675097 1.040000e-06 65.8
25 TraesCS7D01G376900 chr4B 88.679 53 5 1 1 53 544625505 544625556 3.740000e-06 63.9
26 TraesCS7D01G376900 chr3A 78.348 351 65 10 33 377 425282378 425282723 2.710000e-52 217.0
27 TraesCS7D01G376900 chr3A 83.333 66 7 4 1 63 601998635 601998699 1.740000e-04 58.4
28 TraesCS7D01G376900 chr5D 78.171 339 65 7 31 364 40726719 40727053 1.630000e-49 207.0
29 TraesCS7D01G376900 chr5D 78.035 346 63 10 31 370 340762390 340762052 5.880000e-49 206.0
30 TraesCS7D01G376900 chr5A 77.810 347 65 10 31 371 28760424 28760764 2.110000e-48 204.0
31 TraesCS7D01G376900 chr4A 77.876 339 67 7 31 364 3866486 3866821 2.110000e-48 204.0
32 TraesCS7D01G376900 chr6A 77.644 331 70 3 38 365 586731041 586731370 9.830000e-47 198.0
33 TraesCS7D01G376900 chr6A 97.222 36 1 0 574 609 55020433 55020398 1.350000e-05 62.1
34 TraesCS7D01G376900 chr6A 88.462 52 4 2 1 52 467561835 467561786 1.350000e-05 62.1
35 TraesCS7D01G376900 chr3D 87.313 134 12 2 378 511 105707729 105707601 1.000000e-31 148.0
36 TraesCS7D01G376900 chr3D 87.500 112 8 3 378 489 7968950 7968845 1.690000e-24 124.0
37 TraesCS7D01G376900 chr3D 87.273 55 4 3 1 54 277686484 277686536 4.840000e-05 60.2
38 TraesCS7D01G376900 chr3D 85.000 60 6 3 1 59 343797149 343797206 1.740000e-04 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 TraesCS7D01G376900 chr7D 488543780 488548260 4480 False 8275.000000 8275 100.000000 1 4481 1 chr7D.!!$F1 4480
1 TraesCS7D01G376900 chr7D 521553912 521554581 669 False 702.000000 702 85.757000 3811 4477 1 chr7D.!!$F2 666
2 TraesCS7D01G376900 chr7D 113786740 113787411 671 True 667.000000 667 84.808000 3809 4477 1 chr7D.!!$R1 668
3 TraesCS7D01G376900 chr7A 555931040 555939917 8877 False 1373.250000 2416 91.100000 29 3810 4 chr7A.!!$F2 3781
4 TraesCS7D01G376900 chr7A 601462161 601462783 622 False 584.000000 584 83.732000 3857 4477 1 chr7A.!!$F1 620
5 TraesCS7D01G376900 chr7B 516790922 516794248 3326 False 1060.333333 1387 88.987333 1075 3709 3 chr7B.!!$F4 2634
6 TraesCS7D01G376900 chr7B 555211813 555212484 671 False 640.000000 640 84.047000 3809 4477 1 chr7B.!!$F2 668
7 TraesCS7D01G376900 chr1B 423923941 423924502 561 False 614.000000 614 86.467000 3916 4480 1 chr1B.!!$F1 564
8 TraesCS7D01G376900 chr6B 77871918 77872601 683 False 540.000000 540 81.422000 3809 4477 1 chr6B.!!$F1 668
9 TraesCS7D01G376900 chr2B 695699652 695700333 681 True 510.000000 510 80.640000 3809 4477 1 chr2B.!!$R1 668
10 TraesCS7D01G376900 chr4B 98852929 98853611 682 True 473.000000 473 79.681000 3809 4477 1 chr4B.!!$R3 668

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
295 296 0.037447 GACTGAAGGGCAAGCTCCTT 59.963 55.0 12.60 12.60 46.37 3.36 F
494 2045 0.180642 AGCCATGGAGCAGACTGATG 59.819 55.0 18.40 0.64 34.23 3.07 F
698 2278 0.248054 GTGAACGTGCAACCAGTGTG 60.248 55.0 0.00 0.00 0.00 3.82 F
1533 6685 0.251386 AGAGAGAGAGGACGTTGGCA 60.251 55.0 0.00 0.00 0.00 4.92 F
1595 6747 0.554792 ATCAAGGAGGCCATCTTGGG 59.445 55.0 27.03 11.59 40.35 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1632 6784 0.693430 ATGCCCTCTCTGCATCCAGA 60.693 55.000 0.00 0.0 46.04 3.86 R
2373 7745 0.604780 GGAAAGCTGCTGTGCTGAGA 60.605 55.000 1.35 0.0 43.24 3.27 R
2374 7746 1.584380 GGGAAAGCTGCTGTGCTGAG 61.584 60.000 11.29 0.0 43.24 3.35 R
3443 9322 0.247974 CAGCGCTTCTGCATTGTAGC 60.248 55.000 7.50 0.0 39.64 3.58 R
3697 9578 8.537223 CACAATCAGTTTTCTTTTTGACATCAG 58.463 33.333 0.00 0.0 0.00 2.90 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 28 4.982241 CCTCTAGGGCATATTTCCTTCA 57.018 45.455 0.00 0.00 34.75 3.02
58 59 4.292186 TGGAACTCTTAGAAGCAAGCAT 57.708 40.909 0.00 0.00 0.00 3.79
60 61 4.256920 GGAACTCTTAGAAGCAAGCATGA 58.743 43.478 0.00 0.00 0.00 3.07
78 79 4.212847 GCATGATGTGTCTGTATGCTTAGG 59.787 45.833 0.00 0.00 40.58 2.69
93 94 2.349886 GCTTAGGTCTCTTGATTGCACG 59.650 50.000 0.00 0.00 0.00 5.34
98 99 2.337583 GTCTCTTGATTGCACGCACTA 58.662 47.619 0.00 0.00 0.00 2.74
160 161 5.183904 GTCAGGACCATGTTAAAAAGCTCAT 59.816 40.000 0.00 0.00 0.00 2.90
163 164 4.096732 ACCATGTTAAAAAGCTCATCGC 57.903 40.909 0.00 0.00 39.57 4.58
191 192 6.317140 TCATTGAAGAAGTTGCATCATAGGAC 59.683 38.462 0.00 0.00 0.00 3.85
194 195 4.148128 AGAAGTTGCATCATAGGACCTG 57.852 45.455 3.53 0.00 0.00 4.00
206 207 0.706433 AGGACCTGTGGATTTGGCAT 59.294 50.000 0.00 0.00 0.00 4.40
207 208 0.819582 GGACCTGTGGATTTGGCATG 59.180 55.000 0.00 0.00 0.00 4.06
248 249 1.066645 TCTCACAGACATCAATGCGCT 60.067 47.619 9.73 0.00 0.00 5.92
250 251 0.522705 CACAGACATCAATGCGCTGC 60.523 55.000 9.73 0.00 37.15 5.25
251 252 1.297378 CAGACATCAATGCGCTGCG 60.297 57.895 19.17 19.17 30.44 5.18
265 266 1.993369 GCTGCGGCAACCTCCATTAC 61.993 60.000 14.08 0.00 38.54 1.89
274 275 3.370527 GCAACCTCCATTACTTGCTAGGA 60.371 47.826 0.00 0.00 36.81 2.94
295 296 0.037447 GACTGAAGGGCAAGCTCCTT 59.963 55.000 12.60 12.60 46.37 3.36
315 316 4.394920 CCTTTGTGCAACTATACCGTCAAT 59.605 41.667 0.00 0.00 38.04 2.57
316 317 4.937696 TTGTGCAACTATACCGTCAATG 57.062 40.909 0.00 0.00 38.04 2.82
317 318 3.266636 TGTGCAACTATACCGTCAATGG 58.733 45.455 0.00 0.00 38.04 3.16
318 319 2.612212 GTGCAACTATACCGTCAATGGG 59.388 50.000 0.00 0.00 0.00 4.00
319 320 1.602377 GCAACTATACCGTCAATGGGC 59.398 52.381 0.00 0.00 0.00 5.36
320 321 2.912771 CAACTATACCGTCAATGGGCA 58.087 47.619 0.00 0.00 0.00 5.36
321 322 3.476552 CAACTATACCGTCAATGGGCAT 58.523 45.455 0.00 0.00 0.00 4.40
322 323 3.126001 ACTATACCGTCAATGGGCATG 57.874 47.619 0.00 0.00 0.00 4.06
323 324 2.703536 ACTATACCGTCAATGGGCATGA 59.296 45.455 0.00 0.00 0.00 3.07
324 325 1.967319 ATACCGTCAATGGGCATGAC 58.033 50.000 0.00 0.00 42.94 3.06
325 326 0.908910 TACCGTCAATGGGCATGACT 59.091 50.000 0.00 1.74 43.93 3.41
326 327 0.908910 ACCGTCAATGGGCATGACTA 59.091 50.000 0.00 0.00 43.93 2.59
327 328 1.490490 ACCGTCAATGGGCATGACTAT 59.510 47.619 0.00 0.00 43.93 2.12
328 329 2.703536 ACCGTCAATGGGCATGACTATA 59.296 45.455 0.00 0.00 43.93 1.31
329 330 3.135712 ACCGTCAATGGGCATGACTATAA 59.864 43.478 0.00 0.00 43.93 0.98
330 331 3.498397 CCGTCAATGGGCATGACTATAAC 59.502 47.826 0.00 0.00 43.93 1.89
331 332 4.126437 CGTCAATGGGCATGACTATAACA 58.874 43.478 0.00 0.00 43.93 2.41
365 366 7.639062 ATCTGGTTGATGGTATCTATCCTTT 57.361 36.000 0.00 0.00 33.43 3.11
371 372 7.257053 GGTTGATGGTATCTATCCTTTATGGGT 60.257 40.741 0.00 0.00 36.20 4.51
489 2040 1.530771 ATGGAGCCATGGAGCAGAC 59.469 57.895 18.40 0.00 35.03 3.51
494 2045 0.180642 AGCCATGGAGCAGACTGATG 59.819 55.000 18.40 0.64 34.23 3.07
570 2123 5.347994 TAGGGACAAACACTTTGGGGACC 62.348 52.174 0.12 0.00 44.81 4.46
637 2217 1.080025 GTTGGAGACGCGCTTACCT 60.080 57.895 5.73 0.00 0.00 3.08
651 2231 4.209870 CGCTTACCTCGTTTATAGACTCG 58.790 47.826 0.00 0.00 0.00 4.18
672 2252 2.514458 CCCCTGTGGCTGTAATTTCT 57.486 50.000 0.00 0.00 0.00 2.52
681 2261 6.676950 TGTGGCTGTAATTTCTATGTTTGTG 58.323 36.000 0.00 0.00 0.00 3.33
684 2264 7.326063 GTGGCTGTAATTTCTATGTTTGTGAAC 59.674 37.037 0.00 0.00 36.29 3.18
694 2274 1.135546 TGTTTGTGAACGTGCAACCAG 60.136 47.619 0.00 0.00 38.65 4.00
695 2275 1.135517 GTTTGTGAACGTGCAACCAGT 60.136 47.619 0.00 0.00 0.00 4.00
696 2276 0.449786 TTGTGAACGTGCAACCAGTG 59.550 50.000 0.00 0.00 0.00 3.66
697 2277 0.675208 TGTGAACGTGCAACCAGTGT 60.675 50.000 0.00 0.00 0.00 3.55
698 2278 0.248054 GTGAACGTGCAACCAGTGTG 60.248 55.000 0.00 0.00 0.00 3.82
699 2279 0.391793 TGAACGTGCAACCAGTGTGA 60.392 50.000 0.00 0.00 0.00 3.58
700 2280 0.730265 GAACGTGCAACCAGTGTGAA 59.270 50.000 0.00 0.00 0.00 3.18
701 2281 1.131504 GAACGTGCAACCAGTGTGAAA 59.868 47.619 0.00 0.00 0.00 2.69
702 2282 0.450184 ACGTGCAACCAGTGTGAAAC 59.550 50.000 0.00 0.00 37.35 2.78
756 2336 9.853177 AAAGACAGGAGAGATAAAAAGAGAAAA 57.147 29.630 0.00 0.00 0.00 2.29
757 2337 9.500785 AAGACAGGAGAGATAAAAAGAGAAAAG 57.499 33.333 0.00 0.00 0.00 2.27
758 2338 8.100164 AGACAGGAGAGATAAAAAGAGAAAAGG 58.900 37.037 0.00 0.00 0.00 3.11
759 2339 7.750655 ACAGGAGAGATAAAAAGAGAAAAGGT 58.249 34.615 0.00 0.00 0.00 3.50
760 2340 8.881262 ACAGGAGAGATAAAAAGAGAAAAGGTA 58.119 33.333 0.00 0.00 0.00 3.08
773 2353 4.469657 AGAAAAGGTAGCACATTGGACAA 58.530 39.130 0.00 0.00 0.00 3.18
776 2356 2.783135 AGGTAGCACATTGGACAACAG 58.217 47.619 0.00 0.00 0.00 3.16
816 2403 1.351017 TGGACAGAGAACCATCAACCC 59.649 52.381 0.00 0.00 0.00 4.11
961 6113 2.223386 CCAAACACACACTAAACACCGG 60.223 50.000 0.00 0.00 0.00 5.28
977 6129 3.597728 GGCGCCGACCTCTCCTAG 61.598 72.222 12.58 0.00 0.00 3.02
1050 6202 2.072298 GTTCTCGTCATCTGCTTGCTT 58.928 47.619 0.00 0.00 0.00 3.91
1058 6210 2.486982 TCATCTGCTTGCTTTCTCTTGC 59.513 45.455 0.00 0.00 0.00 4.01
1066 6218 3.051081 TGCTTTCTCTTGCTCTCTTCC 57.949 47.619 0.00 0.00 0.00 3.46
1077 6229 1.338579 GCTCTCTTCCTCCACAGGTTG 60.339 57.143 0.00 0.00 41.28 3.77
1096 6248 1.165270 GGCCGCACTTGTTCTACATT 58.835 50.000 0.00 0.00 0.00 2.71
1140 6292 4.130118 GGGATCTCGTGTGCTGAATTAAT 58.870 43.478 0.00 0.00 0.00 1.40
1533 6685 0.251386 AGAGAGAGAGGACGTTGGCA 60.251 55.000 0.00 0.00 0.00 4.92
1560 6712 3.590824 CCGGATGGTTTGTCTGGC 58.409 61.111 0.00 0.00 35.47 4.85
1568 6720 3.006112 TGGTTTGTCTGGCAACTACAA 57.994 42.857 0.00 5.82 40.04 2.41
1595 6747 0.554792 ATCAAGGAGGCCATCTTGGG 59.445 55.000 27.03 11.59 40.35 4.12
1632 6784 3.776969 TCATAGAAGAGGCAGTTGTCCAT 59.223 43.478 0.00 0.00 0.00 3.41
1668 6820 3.432749 GGGCATCACTCTTCTATGCTGAA 60.433 47.826 6.49 0.00 44.29 3.02
1762 6937 4.536765 AGACATGTTGTTTTGTTCCTCCT 58.463 39.130 0.00 0.00 0.00 3.69
1769 6944 1.810755 GTTTTGTTCCTCCTAAGGCCG 59.189 52.381 0.00 0.00 43.02 6.13
2216 7554 7.173863 AGTAAAATCGACATAATAACAGGCG 57.826 36.000 0.00 0.00 0.00 5.52
2268 7625 7.734924 TCTATAGCCAAATCAACATGTGATC 57.265 36.000 0.00 0.00 46.80 2.92
2348 7720 2.606272 CTCTACGGCCGTATTTCCAAAC 59.394 50.000 36.37 0.00 0.00 2.93
2364 7736 2.031157 CCAAACGACCAACCTTCATCAC 60.031 50.000 0.00 0.00 0.00 3.06
2366 7738 2.859165 ACGACCAACCTTCATCACAT 57.141 45.000 0.00 0.00 0.00 3.21
2373 7745 3.508793 CCAACCTTCATCACATCTGCTTT 59.491 43.478 0.00 0.00 0.00 3.51
2374 7746 4.380233 CCAACCTTCATCACATCTGCTTTC 60.380 45.833 0.00 0.00 0.00 2.62
2392 7764 0.604780 TCTCAGCACAGCAGCTTTCC 60.605 55.000 0.00 0.00 43.70 3.13
2406 7778 3.808218 TTTCCCACCACAGCCAGCC 62.808 63.158 0.00 0.00 0.00 4.85
2558 7931 1.514873 GCAATTGCTAGGTGTGCGC 60.515 57.895 23.21 0.00 38.21 6.09
2650 8024 5.104900 CCAAGACATAGTGGCTACCTTACTT 60.105 44.000 0.00 0.00 31.94 2.24
2679 8053 6.237915 GGTTTCTTGAACTGATGCAACAAAAG 60.238 38.462 0.00 0.83 38.35 2.27
2746 8120 4.811555 TCGACATTCTTGAACACTTTGG 57.188 40.909 0.00 0.00 0.00 3.28
2863 8240 7.232330 TGAGTACTATCATGCTAATCTGCTCTT 59.768 37.037 0.00 0.00 0.00 2.85
2947 8326 1.064389 GCTATGGTTCTGGAAAGCCCT 60.064 52.381 0.00 0.00 35.38 5.19
3254 9132 6.561737 TTCATTTTATTTACGAGCACCACA 57.438 33.333 0.00 0.00 0.00 4.17
3362 9240 5.049405 GCCAGAGAGATTTCGTTTTTCTTCA 60.049 40.000 0.00 0.00 0.00 3.02
3443 9322 5.975344 CCATGAATTTTCTGACCATGATTCG 59.025 40.000 0.00 0.00 37.41 3.34
3697 9578 3.941483 CCATCTAACTGATTGTGTGTCCC 59.059 47.826 0.00 0.00 32.05 4.46
3710 9591 3.631686 TGTGTGTCCCTGATGTCAAAAAG 59.368 43.478 0.00 0.00 0.00 2.27
3746 9627 4.019591 GTGTCCCAGTTAAATACACCCTCT 60.020 45.833 0.00 0.00 35.52 3.69
3760 9641 3.028850 CACCCTCTGTCCGGAATTACTA 58.971 50.000 5.23 0.00 0.00 1.82
3933 9817 1.286354 GCCCGACATCGAAACGAACA 61.286 55.000 2.09 0.00 39.99 3.18
3941 9825 0.393448 TCGAAACGAACACCATGGGA 59.607 50.000 18.09 0.00 31.06 4.37
3968 9852 4.207891 ACCTGACAGCACCATAGTTTAG 57.792 45.455 0.00 0.00 0.00 1.85
3974 9858 2.604914 CAGCACCATAGTTTAGCAGACG 59.395 50.000 0.00 0.00 0.00 4.18
3999 9883 7.043590 CGCACCAAATACTACAGTCTATTACAC 60.044 40.741 0.00 0.00 0.00 2.90
4058 9948 1.620819 CCTGAGTCACCAGTAGCACTT 59.379 52.381 0.00 0.00 32.43 3.16
4077 9973 5.510671 CACTTTGCAGACGAAGTTGTATTT 58.489 37.500 0.00 0.00 46.51 1.40
4121 10017 1.426816 CGCAGCATCGCACATCTTCT 61.427 55.000 0.00 0.00 0.00 2.85
4149 10045 2.338620 CGTGCTCGACCTGACCAA 59.661 61.111 1.00 0.00 39.71 3.67
4183 10079 1.814793 GCAACTCCTTGACTCCTTCC 58.185 55.000 0.00 0.00 0.00 3.46
4232 10128 5.906073 ACAAAAAGGAACACATGGAGAAAG 58.094 37.500 0.00 0.00 0.00 2.62
4258 10154 3.569701 TCTCAAAGGGTGTTTTGATCTGC 59.430 43.478 2.09 0.00 43.80 4.26
4270 10166 8.490355 GGTGTTTTGATCTGCTTTTATTCAAAG 58.510 33.333 0.00 0.00 44.44 2.77
4329 10225 1.522355 CAGCGAGGCCCACAGTATG 60.522 63.158 0.00 0.00 46.00 2.39
4407 10307 1.140052 CGGGCACATATCAGTACCCAA 59.860 52.381 3.50 0.00 44.09 4.12
4420 10320 2.806503 TACCCAACGCCATCCCAACG 62.807 60.000 0.00 0.00 0.00 4.10
4466 10366 5.811613 ACAGGACATGTGAAAAACAAATGTG 59.188 36.000 1.15 0.50 43.61 3.21
4480 10380 8.868522 AAAACAAATGTGGAGATGATTCTAGA 57.131 30.769 0.00 0.00 30.30 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.982241 TGAAGGAAATATGCCCTAGAGG 57.018 45.455 0.00 0.00 39.47 3.69
7 8 7.269477 CTTTTGAAGGAAATATGCCCTAGAG 57.731 40.000 0.00 0.00 31.36 2.43
23 24 4.077822 AGAGTTCCATGAGCCTTTTGAAG 58.922 43.478 0.00 0.00 0.00 3.02
24 25 4.104383 AGAGTTCCATGAGCCTTTTGAA 57.896 40.909 0.00 0.00 0.00 2.69
25 26 3.795688 AGAGTTCCATGAGCCTTTTGA 57.204 42.857 0.00 0.00 0.00 2.69
26 27 5.248640 TCTAAGAGTTCCATGAGCCTTTTG 58.751 41.667 0.00 0.00 0.00 2.44
27 28 5.505181 TCTAAGAGTTCCATGAGCCTTTT 57.495 39.130 0.00 0.00 0.00 2.27
41 42 4.634883 CACATCATGCTTGCTTCTAAGAGT 59.365 41.667 0.00 0.00 0.00 3.24
58 59 4.711846 AGACCTAAGCATACAGACACATCA 59.288 41.667 0.00 0.00 0.00 3.07
60 61 4.959210 AGAGACCTAAGCATACAGACACAT 59.041 41.667 0.00 0.00 0.00 3.21
78 79 1.151668 AGTGCGTGCAATCAAGAGAC 58.848 50.000 0.00 0.00 0.00 3.36
93 94 4.876679 GGGTAGTTCTTCCATTTCTAGTGC 59.123 45.833 0.00 0.00 0.00 4.40
98 99 6.064717 GCATATGGGTAGTTCTTCCATTTCT 58.935 40.000 4.56 0.00 41.14 2.52
160 161 2.162208 GCAACTTCTTCAATGATGGCGA 59.838 45.455 0.00 0.00 0.00 5.54
163 164 5.319140 TGATGCAACTTCTTCAATGATGG 57.681 39.130 0.00 0.00 0.00 3.51
191 192 0.974010 AGGCATGCCAAATCCACAGG 60.974 55.000 37.18 0.00 38.92 4.00
194 195 1.188863 AGAAGGCATGCCAAATCCAC 58.811 50.000 37.18 18.72 38.92 4.02
206 207 2.342650 GGGCATGCGAAAGAAGGCA 61.343 57.895 12.44 0.00 44.29 4.75
207 208 2.275547 CTGGGCATGCGAAAGAAGGC 62.276 60.000 12.44 0.00 0.00 4.35
248 249 0.037590 AAGTAATGGAGGTTGCCGCA 59.962 50.000 0.00 0.00 0.00 5.69
250 251 0.451783 GCAAGTAATGGAGGTTGCCG 59.548 55.000 0.00 0.00 39.52 5.69
251 252 1.839424 AGCAAGTAATGGAGGTTGCC 58.161 50.000 2.41 0.00 45.23 4.52
255 256 4.101741 GTCATCCTAGCAAGTAATGGAGGT 59.898 45.833 0.00 0.00 31.49 3.85
265 266 2.744494 GCCCTTCAGTCATCCTAGCAAG 60.744 54.545 0.00 0.00 0.00 4.01
274 275 0.034670 GGAGCTTGCCCTTCAGTCAT 60.035 55.000 0.00 0.00 0.00 3.06
295 296 3.687212 CCATTGACGGTATAGTTGCACAA 59.313 43.478 0.00 0.00 0.00 3.33
315 316 3.392285 AGCTCATGTTATAGTCATGCCCA 59.608 43.478 12.29 0.39 41.40 5.36
316 317 4.013267 AGCTCATGTTATAGTCATGCCC 57.987 45.455 12.29 7.68 41.40 5.36
317 318 5.788450 AGTAGCTCATGTTATAGTCATGCC 58.212 41.667 12.29 7.91 41.40 4.40
318 319 8.465999 AGATAGTAGCTCATGTTATAGTCATGC 58.534 37.037 12.29 5.31 41.40 4.06
319 320 9.786105 CAGATAGTAGCTCATGTTATAGTCATG 57.214 37.037 11.38 11.38 42.53 3.07
320 321 8.965819 CCAGATAGTAGCTCATGTTATAGTCAT 58.034 37.037 0.00 0.00 0.00 3.06
321 322 7.945109 ACCAGATAGTAGCTCATGTTATAGTCA 59.055 37.037 0.00 0.00 0.00 3.41
322 323 8.343168 ACCAGATAGTAGCTCATGTTATAGTC 57.657 38.462 0.00 0.00 0.00 2.59
323 324 8.580720 CAACCAGATAGTAGCTCATGTTATAGT 58.419 37.037 0.00 0.00 0.00 2.12
324 325 8.797438 TCAACCAGATAGTAGCTCATGTTATAG 58.203 37.037 0.00 0.00 0.00 1.31
325 326 8.706322 TCAACCAGATAGTAGCTCATGTTATA 57.294 34.615 0.00 0.00 0.00 0.98
326 327 7.603180 TCAACCAGATAGTAGCTCATGTTAT 57.397 36.000 0.00 0.00 0.00 1.89
327 328 7.436933 CATCAACCAGATAGTAGCTCATGTTA 58.563 38.462 0.00 0.00 34.43 2.41
328 329 5.939764 TCAACCAGATAGTAGCTCATGTT 57.060 39.130 0.00 0.00 0.00 2.71
329 330 5.221601 CCATCAACCAGATAGTAGCTCATGT 60.222 44.000 0.00 0.00 34.43 3.21
330 331 5.221601 ACCATCAACCAGATAGTAGCTCATG 60.222 44.000 0.00 0.00 34.43 3.07
331 332 4.904251 ACCATCAACCAGATAGTAGCTCAT 59.096 41.667 0.00 0.00 34.43 2.90
365 366 1.324740 CCGAACGGAGGTCACCCATA 61.325 60.000 7.53 0.00 37.50 2.74
471 2022 0.987081 AGTCTGCTCCATGGCTCCAT 60.987 55.000 6.96 0.00 37.08 3.41
472 2023 1.614525 AGTCTGCTCCATGGCTCCA 60.615 57.895 6.96 2.69 0.00 3.86
557 2110 0.179029 CAACTCGGTCCCCAAAGTGT 60.179 55.000 0.00 0.00 0.00 3.55
559 2112 1.057851 TCCAACTCGGTCCCCAAAGT 61.058 55.000 0.00 0.00 35.57 2.66
560 2113 0.328258 ATCCAACTCGGTCCCCAAAG 59.672 55.000 0.00 0.00 35.57 2.77
563 2116 1.229368 TCATCCAACTCGGTCCCCA 60.229 57.895 0.00 0.00 35.57 4.96
570 2123 1.519455 GAGCCGGTCATCCAACTCG 60.519 63.158 1.90 0.00 0.00 4.18
637 2217 1.035139 GGGGCCGAGTCTATAAACGA 58.965 55.000 0.00 0.00 0.00 3.85
672 2252 2.683362 TGGTTGCACGTTCACAAACATA 59.317 40.909 8.88 0.00 38.52 2.29
681 2261 0.730265 TTCACACTGGTTGCACGTTC 59.270 50.000 0.00 0.00 0.00 3.95
684 2264 0.732571 AGTTTCACACTGGTTGCACG 59.267 50.000 0.00 0.00 32.83 5.34
694 2274 7.492352 ACCTACTTTATTCACAGTTTCACAC 57.508 36.000 0.00 0.00 0.00 3.82
695 2275 8.514330 AAACCTACTTTATTCACAGTTTCACA 57.486 30.769 0.00 0.00 0.00 3.58
697 2277 9.841295 ACTAAACCTACTTTATTCACAGTTTCA 57.159 29.630 0.00 0.00 0.00 2.69
699 2279 9.623000 ACACTAAACCTACTTTATTCACAGTTT 57.377 29.630 0.00 0.00 0.00 2.66
731 2311 9.500785 CTTTTCTCTTTTTATCTCTCCTGTCTT 57.499 33.333 0.00 0.00 0.00 3.01
735 2315 9.377312 CTACCTTTTCTCTTTTTATCTCTCCTG 57.623 37.037 0.00 0.00 0.00 3.86
749 2329 4.202461 TGTCCAATGTGCTACCTTTTCTCT 60.202 41.667 0.00 0.00 0.00 3.10
750 2330 4.072131 TGTCCAATGTGCTACCTTTTCTC 58.928 43.478 0.00 0.00 0.00 2.87
751 2331 4.098914 TGTCCAATGTGCTACCTTTTCT 57.901 40.909 0.00 0.00 0.00 2.52
752 2332 4.037446 TGTTGTCCAATGTGCTACCTTTTC 59.963 41.667 0.00 0.00 0.00 2.29
756 2336 2.783135 CTGTTGTCCAATGTGCTACCT 58.217 47.619 0.00 0.00 0.00 3.08
757 2337 1.200020 GCTGTTGTCCAATGTGCTACC 59.800 52.381 0.00 0.00 0.00 3.18
758 2338 1.879380 TGCTGTTGTCCAATGTGCTAC 59.121 47.619 0.00 0.00 0.00 3.58
759 2339 2.268762 TGCTGTTGTCCAATGTGCTA 57.731 45.000 0.00 0.00 0.00 3.49
760 2340 1.624336 ATGCTGTTGTCCAATGTGCT 58.376 45.000 0.00 0.00 0.00 4.40
773 2353 9.558396 TCCAATTTTATTTTCTCAAAATGCTGT 57.442 25.926 4.76 0.00 41.01 4.40
776 2356 9.815936 CTGTCCAATTTTATTTTCTCAAAATGC 57.184 29.630 4.76 0.00 41.01 3.56
816 2403 4.235360 CTGCTGCTTCTCCTCAATTTTTG 58.765 43.478 0.00 0.00 0.00 2.44
895 6047 3.133721 CAGTAGATTGAAGAGGGTCAGGG 59.866 52.174 0.00 0.00 0.00 4.45
901 6053 4.826274 TGGAACAGTAGATTGAAGAGGG 57.174 45.455 0.00 0.00 0.00 4.30
961 6113 3.597728 CCTAGGAGAGGTCGGCGC 61.598 72.222 1.05 0.00 40.98 6.53
977 6129 0.739813 CGGTGAGATGGGACGAAACC 60.740 60.000 0.00 0.00 0.00 3.27
981 6133 1.753078 CTCCGGTGAGATGGGACGA 60.753 63.158 0.00 0.00 41.42 4.20
982 6134 1.753078 TCTCCGGTGAGATGGGACG 60.753 63.158 0.00 0.00 42.73 4.79
1029 6181 0.368227 GCAAGCAGATGACGAGAACG 59.632 55.000 0.00 0.00 45.75 3.95
1050 6202 2.564947 GTGGAGGAAGAGAGCAAGAGAA 59.435 50.000 0.00 0.00 0.00 2.87
1058 6210 2.758736 CAACCTGTGGAGGAAGAGAG 57.241 55.000 0.00 0.00 42.93 3.20
1077 6229 1.165270 AATGTAGAACAAGTGCGGCC 58.835 50.000 0.00 0.00 0.00 6.13
1096 6248 4.530946 CCCAAAGGTTCACTAGAGGAGTAA 59.469 45.833 0.00 0.00 35.64 2.24
1140 6292 2.679092 CCATCCCCTCTGCAGCAA 59.321 61.111 9.47 0.00 0.00 3.91
1434 6586 8.367911 TCAGACTCAGATTACACAAAACTACAT 58.632 33.333 0.00 0.00 0.00 2.29
1533 6685 2.428171 CAAACCATCCGGCTTGATCATT 59.572 45.455 0.00 0.00 40.27 2.57
1595 6747 8.040132 CCTCTTCTATGATATCAAATCCAGACC 58.960 40.741 9.99 0.00 0.00 3.85
1632 6784 0.693430 ATGCCCTCTCTGCATCCAGA 60.693 55.000 0.00 0.00 46.04 3.86
1668 6820 3.118629 TGAAGAAGCTTCTATCGGCATGT 60.119 43.478 28.67 10.26 36.28 3.21
1762 6937 1.075698 TCAAATTTCCCCACGGCCTTA 59.924 47.619 0.00 0.00 0.00 2.69
1769 6944 4.875536 GTGGCATTAATCAAATTTCCCCAC 59.124 41.667 0.00 0.00 33.20 4.61
1907 7084 9.717994 ACATATATCAATCATCTGATCTCCTCT 57.282 33.333 0.00 0.00 37.27 3.69
1990 7328 7.591057 TGAACAATTGTCTTTTCTAAATCGCTG 59.409 33.333 12.39 0.00 0.00 5.18
2268 7625 4.750098 GGGTACTCGGATGATTGTATGTTG 59.250 45.833 0.00 0.00 0.00 3.33
2348 7720 2.674852 CAGATGTGATGAAGGTTGGTCG 59.325 50.000 0.00 0.00 0.00 4.79
2373 7745 0.604780 GGAAAGCTGCTGTGCTGAGA 60.605 55.000 1.35 0.00 43.24 3.27
2374 7746 1.584380 GGGAAAGCTGCTGTGCTGAG 61.584 60.000 11.29 0.00 43.24 3.35
2383 7755 2.924105 GCTGTGGTGGGAAAGCTGC 61.924 63.158 0.00 0.00 32.82 5.25
2384 7756 2.270986 GGCTGTGGTGGGAAAGCTG 61.271 63.158 0.00 0.00 35.93 4.24
2406 7778 2.031012 TGTCAGAAGCGGCTGTGG 59.969 61.111 1.81 0.00 37.20 4.17
2409 7781 2.320587 GGTGTGTCAGAAGCGGCTG 61.321 63.158 1.81 2.85 37.24 4.85
2650 8024 4.724399 TGCATCAGTTCAAGAAACCCTAA 58.276 39.130 0.00 0.00 38.76 2.69
2679 8053 5.242838 TCACAACATTGTCTCCAATTTACCC 59.757 40.000 0.00 0.00 39.28 3.69
2746 8120 4.283403 TTGGGCAGCGCAAAGTGC 62.283 61.111 21.81 10.98 40.69 4.40
2863 8240 2.302733 TGTCAGAGGCTGCTTTGTATGA 59.697 45.455 0.00 0.00 0.00 2.15
2947 8326 2.182496 CCAGCGTGAAATGGCATCA 58.818 52.632 0.00 0.00 0.00 3.07
3236 9114 5.302360 AGAAGTGTGGTGCTCGTAAATAAA 58.698 37.500 0.00 0.00 0.00 1.40
3254 9132 5.982356 TGCTCTAATGCTGTAATGAGAAGT 58.018 37.500 0.00 0.00 0.00 3.01
3362 9240 4.141620 ACGCCAACCAGATTTATCATCTCT 60.142 41.667 0.00 0.00 0.00 3.10
3417 9296 5.648178 TCATGGTCAGAAAATTCATGGTG 57.352 39.130 0.00 0.00 36.72 4.17
3443 9322 0.247974 CAGCGCTTCTGCATTGTAGC 60.248 55.000 7.50 0.00 39.64 3.58
3697 9578 8.537223 CACAATCAGTTTTCTTTTTGACATCAG 58.463 33.333 0.00 0.00 0.00 2.90
3710 9591 3.632145 ACTGGGACACACAATCAGTTTTC 59.368 43.478 0.00 0.00 35.44 2.29
3746 9627 2.093890 TGCGACTAGTAATTCCGGACA 58.906 47.619 1.83 0.00 0.00 4.02
3760 9641 6.531948 GTCTAGTTACATTCATTTCTGCGACT 59.468 38.462 0.00 0.00 0.00 4.18
3853 9734 1.612442 TCTTTCCCTCCCCCTGTCG 60.612 63.158 0.00 0.00 0.00 4.35
3933 9817 0.768622 TCAGGTTTTCGTCCCATGGT 59.231 50.000 11.73 0.00 0.00 3.55
3941 9825 0.107410 TGGTGCTGTCAGGTTTTCGT 60.107 50.000 1.14 0.00 0.00 3.85
3968 9852 2.343101 TGTAGTATTTGGTGCGTCTGC 58.657 47.619 0.00 0.00 43.20 4.26
3974 9858 7.224167 GGTGTAATAGACTGTAGTATTTGGTGC 59.776 40.741 1.48 0.00 0.00 5.01
4018 9904 1.811558 GCTCTGGGATGCTGCGATTTA 60.812 52.381 0.00 0.00 0.00 1.40
4058 9948 5.743026 TGAAAATACAACTTCGTCTGCAA 57.257 34.783 0.00 0.00 0.00 4.08
4077 9973 2.576191 AGACCAATCGAAGGGGAATGAA 59.424 45.455 11.44 0.00 0.00 2.57
4121 10017 0.103390 TCGAGCACGGTGAGTTTGAA 59.897 50.000 13.29 0.00 40.21 2.69
4232 10128 4.320608 TCAAAACACCCTTTGAGATTGC 57.679 40.909 0.00 0.00 39.74 3.56
4258 10154 6.371825 AGAACCGAGCTACCTTTGAATAAAAG 59.628 38.462 0.00 0.00 44.27 2.27
4407 10307 2.824041 GATGCGTTGGGATGGCGT 60.824 61.111 0.00 0.00 0.00 5.68
4420 10320 1.202076 GCTAGAGTTGTTTGGCGATGC 60.202 52.381 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.