Multiple sequence alignment - TraesCS2D01G271500

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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 TraesCS2D01G271500 chr2D 100.000 3791 0 0 1 3791 335122770 335118980 0.000000e+00 7001.0
1 TraesCS2D01G271500 chr2D 100.000 2257 0 0 4039 6295 335118732 335116476 0.000000e+00 4169.0
2 TraesCS2D01G271500 chr2D 83.415 205 28 4 2306 2507 83811821 83811620 1.080000e-42 185.0
3 TraesCS2D01G271500 chr2D 100.000 31 0 0 5483 5513 373745560 373745530 2.450000e-04 58.4
4 TraesCS2D01G271500 chr2A 94.118 3842 147 25 3 3782 445716734 445712910 0.000000e+00 5770.0
5 TraesCS2D01G271500 chr2A 96.928 1465 36 4 4039 5502 445712742 445711286 0.000000e+00 2447.0
6 TraesCS2D01G271500 chr2A 89.029 793 66 12 5516 6295 445710735 445709951 0.000000e+00 963.0
7 TraesCS2D01G271500 chr2A 88.372 129 9 5 1725 1849 144653698 144653824 3.930000e-32 150.0
8 TraesCS2D01G271500 chr2B 96.407 1475 35 6 714 2172 403092308 403090836 0.000000e+00 2414.0
9 TraesCS2D01G271500 chr2B 91.078 1670 98 26 2165 3791 403088254 403086593 0.000000e+00 2211.0
10 TraesCS2D01G271500 chr2B 97.049 881 19 2 4039 4919 403086460 403085587 0.000000e+00 1476.0
11 TraesCS2D01G271500 chr2B 95.810 716 24 4 3 714 403097733 403097020 0.000000e+00 1151.0
12 TraesCS2D01G271500 chr2B 96.774 527 11 4 4918 5443 403085427 403084906 0.000000e+00 874.0
13 TraesCS2D01G271500 chr2B 79.333 150 25 6 5480 5627 399936808 399936953 4.020000e-17 100.0
14 TraesCS2D01G271500 chr4D 88.402 1026 91 14 4283 5300 459390310 459389305 0.000000e+00 1210.0
15 TraesCS2D01G271500 chr4D 82.558 774 68 36 969 1726 459423138 459422416 2.490000e-173 619.0
16 TraesCS2D01G271500 chr4D 83.495 309 44 6 5482 5785 8262141 8262447 1.340000e-71 281.0
17 TraesCS2D01G271500 chr4D 75.483 518 96 18 2048 2550 335182720 335182219 2.280000e-54 224.0
18 TraesCS2D01G271500 chr4D 76.000 350 69 4 2191 2526 498561395 498561047 3.900000e-37 167.0
19 TraesCS2D01G271500 chr4B 86.469 776 62 23 969 1726 574176486 574175736 0.000000e+00 811.0
20 TraesCS2D01G271500 chr4B 85.751 772 64 19 4541 5300 574175074 574174337 0.000000e+00 774.0
21 TraesCS2D01G271500 chr4B 91.844 282 22 1 4249 4529 574175411 574175130 5.920000e-105 392.0
22 TraesCS2D01G271500 chr4B 80.000 135 21 5 5655 5787 20690559 20690689 1.870000e-15 95.3
23 TraesCS2D01G271500 chr4A 84.925 670 58 21 4248 4907 9398326 9398962 6.880000e-179 638.0
24 TraesCS2D01G271500 chr4A 90.508 453 38 3 4865 5317 9398957 9399404 1.510000e-165 593.0
25 TraesCS2D01G271500 chr4A 95.283 212 10 0 969 1180 9397335 9397546 2.810000e-88 337.0
26 TraesCS2D01G271500 chr4A 87.879 132 13 2 1725 1853 60654159 60654290 1.090000e-32 152.0
27 TraesCS2D01G271500 chr4A 88.372 129 8 5 1723 1845 29077400 29077527 1.410000e-31 148.0
28 TraesCS2D01G271500 chr4A 84.416 77 11 1 3469 3544 338716259 338716335 2.430000e-09 75.0
29 TraesCS2D01G271500 chr7D 76.975 886 137 34 2045 2886 146986888 146986026 1.610000e-120 444.0
30 TraesCS2D01G271500 chr7D 77.521 476 88 9 2045 2505 154594886 154595357 1.040000e-67 268.0
31 TraesCS2D01G271500 chr7D 77.667 300 53 7 2043 2341 154922422 154922136 3.020000e-38 171.0
32 TraesCS2D01G271500 chr7D 87.786 131 12 2 1721 1848 534359220 534359349 3.930000e-32 150.0
33 TraesCS2D01G271500 chr5D 76.583 521 90 17 2433 2931 217922415 217922925 2.250000e-64 257.0
34 TraesCS2D01G271500 chr5D 82.703 185 30 2 2043 2226 390414774 390414591 5.050000e-36 163.0
35 TraesCS2D01G271500 chr5D 88.406 138 10 5 1709 1843 105020942 105021076 1.820000e-35 161.0
36 TraesCS2D01G271500 chr5D 73.994 323 49 14 3286 3575 529272644 529272964 1.440000e-16 99.0
37 TraesCS2D01G271500 chr3B 77.880 434 69 16 2094 2523 639145409 639145819 1.750000e-60 244.0
38 TraesCS2D01G271500 chr3B 81.140 228 43 0 2299 2526 14332656 14332429 3.880000e-42 183.0
39 TraesCS2D01G271500 chr3B 77.122 271 47 10 2037 2300 370411839 370412101 6.580000e-30 143.0
40 TraesCS2D01G271500 chr3B 74.026 231 47 8 3197 3414 564312797 564313027 1.450000e-11 82.4
41 TraesCS2D01G271500 chr6D 73.988 692 125 32 2043 2698 381908896 381909568 4.910000e-56 230.0
42 TraesCS2D01G271500 chr6D 81.481 216 39 1 2293 2507 383489205 383489420 6.490000e-40 176.0
43 TraesCS2D01G271500 chr6D 100.000 30 0 0 5484 5513 422193271 422193300 8.820000e-04 56.5
44 TraesCS2D01G271500 chr6D 100.000 28 0 0 5486 5513 405670332 405670305 1.100000e-02 52.8
45 TraesCS2D01G271500 chr6A 75.840 476 88 17 2047 2505 524300136 524300601 3.820000e-52 217.0
46 TraesCS2D01G271500 chr6A 75.625 320 72 5 2087 2404 411149302 411149617 3.040000e-33 154.0
47 TraesCS2D01G271500 chr6A 72.011 711 121 49 2330 3014 523427364 523428022 8.510000e-29 139.0
48 TraesCS2D01G271500 chr6A 93.023 43 3 0 3482 3524 538093827 538093869 5.270000e-06 63.9
49 TraesCS2D01G271500 chr3D 82.447 188 31 2 2043 2229 943266 943452 5.050000e-36 163.0
50 TraesCS2D01G271500 chr3D 73.196 388 70 18 3285 3647 156975479 156975857 6.670000e-20 110.0
51 TraesCS2D01G271500 chr3D 76.970 165 21 11 2566 2729 590522203 590522055 1.880000e-10 78.7
52 TraesCS2D01G271500 chr7A 86.765 136 13 4 1725 1856 627236815 627236949 5.090000e-31 147.0
53 TraesCS2D01G271500 chr7A 89.362 47 2 3 3512 3556 545607482 545607527 8.820000e-04 56.5
54 TraesCS2D01G271500 chr1A 86.331 139 14 4 1723 1856 498176960 498176822 5.090000e-31 147.0
55 TraesCS2D01G271500 chr1D 80.822 146 20 8 3279 3417 490126407 490126551 2.400000e-19 108.0
56 TraesCS2D01G271500 chr1D 73.203 306 62 14 3446 3739 204803648 204803351 6.720000e-15 93.5
57 TraesCS2D01G271500 chr5B 80.741 135 20 5 5655 5787 572161976 572162106 4.020000e-17 100.0
58 TraesCS2D01G271500 chr5B 94.286 35 1 1 5479 5513 36548200 36548233 1.100000e-02 52.8
59 TraesCS2D01G271500 chr5A 82.143 112 14 5 3289 3394 570477742 570477631 2.420000e-14 91.6
60 TraesCS2D01G271500 chr6B 78.322 143 24 6 3278 3414 570900664 570900805 1.120000e-12 86.1
61 TraesCS2D01G271500 chr6B 83.562 73 6 5 2940 3012 144037603 144037537 5.270000e-06 63.9
62 TraesCS2D01G271500 chr7B 81.053 95 16 2 3452 3544 499258176 499258082 2.430000e-09 75.0
63 TraesCS2D01G271500 chr1B 100.000 30 0 0 5484 5513 678056047 678056018 8.820000e-04 56.5


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 TraesCS2D01G271500 chr2D 335116476 335122770 6294 True 5585.000000 7001 100.000000 1 6295 2 chr2D.!!$R3 6294
1 TraesCS2D01G271500 chr2A 445709951 445716734 6783 True 3060.000000 5770 93.358333 3 6295 3 chr2A.!!$R1 6292
2 TraesCS2D01G271500 chr2B 403084906 403092308 7402 True 1743.750000 2414 95.327000 714 5443 4 chr2B.!!$R2 4729
3 TraesCS2D01G271500 chr2B 403097020 403097733 713 True 1151.000000 1151 95.810000 3 714 1 chr2B.!!$R1 711
4 TraesCS2D01G271500 chr4D 459389305 459390310 1005 True 1210.000000 1210 88.402000 4283 5300 1 chr4D.!!$R2 1017
5 TraesCS2D01G271500 chr4D 459422416 459423138 722 True 619.000000 619 82.558000 969 1726 1 chr4D.!!$R3 757
6 TraesCS2D01G271500 chr4D 335182219 335182720 501 True 224.000000 224 75.483000 2048 2550 1 chr4D.!!$R1 502
7 TraesCS2D01G271500 chr4B 574174337 574176486 2149 True 659.000000 811 88.021333 969 5300 3 chr4B.!!$R1 4331
8 TraesCS2D01G271500 chr4A 9397335 9399404 2069 False 522.666667 638 90.238667 969 5317 3 chr4A.!!$F4 4348
9 TraesCS2D01G271500 chr7D 146986026 146986888 862 True 444.000000 444 76.975000 2045 2886 1 chr7D.!!$R1 841
10 TraesCS2D01G271500 chr5D 217922415 217922925 510 False 257.000000 257 76.583000 2433 2931 1 chr5D.!!$F2 498
11 TraesCS2D01G271500 chr6D 381908896 381909568 672 False 230.000000 230 73.988000 2043 2698 1 chr6D.!!$F1 655

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
73 74 0.324943 AACGAGGGACATCTTGTGGG 59.675 55.000 0.00 0.0 32.11 4.61 F
659 670 1.433471 GATTAGTTGGCGGCTTGGC 59.567 57.895 11.43 0.0 45.12 4.52 F
2120 2199 0.248866 GGACGTGTTTTGCCACCAAG 60.249 55.000 0.00 0.0 31.52 3.61 F
3580 6379 0.541863 GTTGGAGGGATGACGGTGAT 59.458 55.000 0.00 0.0 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1192 1204 5.605564 AAGCAAAACCACACAAAGAAAAC 57.394 34.783 0.00 0.0 0.00 2.43 R
2507 5209 0.312729 TATGTGCATCGCCGACGTAT 59.687 50.000 0.00 0.0 41.18 3.06 R
3629 6428 0.178984 TGTACTGGACGACCACCTCA 60.179 55.000 1.37 0.0 41.77 3.86 R
5342 8550 1.279496 TGCTCACATCTTACAGGCCT 58.721 50.000 0.00 0.0 0.00 5.19 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
25 26 6.664816 ACAATTGCCATCTAAATCTTGAAGGA 59.335 34.615 5.05 0.00 0.00 3.36
27 28 5.178096 TGCCATCTAAATCTTGAAGGACA 57.822 39.130 0.00 0.00 0.00 4.02
28 29 5.188434 TGCCATCTAAATCTTGAAGGACAG 58.812 41.667 0.00 0.00 0.00 3.51
47 48 5.413969 ACAGCTTGTTAACGTTTTAGTCC 57.586 39.130 5.91 0.00 0.00 3.85
56 57 6.701400 TGTTAACGTTTTAGTCCCTCACTAAC 59.299 38.462 5.91 0.00 45.64 2.34
73 74 0.324943 AACGAGGGACATCTTGTGGG 59.675 55.000 0.00 0.00 32.11 4.61
301 305 3.525800 AACTCAGTGCCTTAACCCATT 57.474 42.857 0.00 0.00 0.00 3.16
317 321 8.588290 TTAACCCATTTACAAGCATAAGTCAT 57.412 30.769 0.00 0.00 0.00 3.06
329 333 1.481871 TAAGTCATCTCCCACCGGTC 58.518 55.000 2.59 0.00 0.00 4.79
342 346 5.860611 TCCCACCGGTCTAATATGTAAATG 58.139 41.667 2.59 0.00 0.00 2.32
367 371 4.630894 TTGGACATTGACACTTTGACAC 57.369 40.909 0.00 0.00 0.00 3.67
368 372 2.611751 TGGACATTGACACTTTGACACG 59.388 45.455 0.00 0.00 0.00 4.49
659 670 1.433471 GATTAGTTGGCGGCTTGGC 59.567 57.895 11.43 0.00 45.12 4.52
804 815 1.668101 GGCTCGATTCGGTGAGACCT 61.668 60.000 6.18 0.00 35.66 3.85
946 958 5.635280 CGTGACTCTGACTGTATTTGACAAT 59.365 40.000 0.00 0.00 37.70 2.71
947 959 6.183360 CGTGACTCTGACTGTATTTGACAATC 60.183 42.308 0.00 0.00 37.70 2.67
1192 1204 2.233186 TCTGTCTCCATCTTGCAGTCAG 59.767 50.000 0.00 0.00 0.00 3.51
1307 1320 8.682297 ACTTAATAGGTAAGAAGGGAAAGTCT 57.318 34.615 0.28 0.00 41.70 3.24
2015 2093 3.484407 GACAATGAAGGATCTGATGGGG 58.516 50.000 0.00 0.00 0.00 4.96
2120 2199 0.248866 GGACGTGTTTTGCCACCAAG 60.249 55.000 0.00 0.00 31.52 3.61
2343 5041 0.856641 CAACGGCCGGTATTGATACG 59.143 55.000 31.76 3.85 34.11 3.06
2720 5464 1.692411 TCATCATCTCGTCCGGTGAT 58.308 50.000 0.00 0.00 0.00 3.06
2735 5479 1.080907 TGATGAGGAGGACCAGGCA 59.919 57.895 0.00 0.00 38.94 4.75
2823 5583 1.065926 TGGAGCTCATGACGAAGCATT 60.066 47.619 17.19 0.00 0.00 3.56
3040 5801 2.433145 CGCAGCGTCCATGTCAGT 60.433 61.111 6.65 0.00 0.00 3.41
3155 5916 2.550978 CGCGGATAGTTTGTCAAGGAT 58.449 47.619 0.00 0.00 0.00 3.24
3243 6004 2.512286 GGCACGCTATGAGCAGCA 60.512 61.111 12.93 0.00 42.58 4.41
3313 6087 1.684248 GCAACGACCTAGACCTCCCTA 60.684 57.143 0.00 0.00 0.00 3.53
3344 6118 4.129737 CGACCGCTCCGTCACCAT 62.130 66.667 0.00 0.00 32.74 3.55
3349 6123 4.492160 GCTCCGTCACCATCGCGA 62.492 66.667 13.09 13.09 0.00 5.87
3562 6361 3.849951 CCGGCGCCCTATCACAGT 61.850 66.667 23.46 0.00 0.00 3.55
3580 6379 0.541863 GTTGGAGGGATGACGGTGAT 59.458 55.000 0.00 0.00 0.00 3.06
4066 6865 8.106247 TGATTTCTTGTGGGTATAAACTTCAC 57.894 34.615 0.00 0.00 33.49 3.18
4069 6868 8.528044 TTTCTTGTGGGTATAAACTTCACTTT 57.472 30.769 0.00 0.00 33.79 2.66
4213 7021 6.039159 GCCTACGTAGGTTCTAGTTCTTACAT 59.961 42.308 35.78 0.00 45.42 2.29
4214 7022 7.227512 GCCTACGTAGGTTCTAGTTCTTACATA 59.772 40.741 35.78 0.00 45.42 2.29
4215 7023 8.772705 CCTACGTAGGTTCTAGTTCTTACATAG 58.227 40.741 30.04 1.01 38.69 2.23
4280 7088 1.630244 CTTCTGCTGCACTGTACCGC 61.630 60.000 0.00 0.00 0.00 5.68
4339 7147 6.680810 AGTGTGTGAATGTACCATGAATTTG 58.319 36.000 0.00 0.00 0.00 2.32
4471 7279 4.954202 AGTCATGCAGGTGATGATCAAATT 59.046 37.500 0.00 0.00 32.53 1.82
4535 7345 7.910304 ACGATACTTGAAGCAGATTATTTGAC 58.090 34.615 0.00 0.00 0.00 3.18
4772 7630 6.423905 CGAAATATGTCCATTACTAGGTGGTG 59.576 42.308 9.90 0.00 36.84 4.17
4845 7703 5.439721 TGCTGAATTGGCATTAGTCACTAT 58.560 37.500 0.00 0.00 34.56 2.12
4946 8013 4.870021 AGAGCAAGAGGGTTATGGAAAT 57.130 40.909 0.00 0.00 0.00 2.17
4949 8016 6.302269 AGAGCAAGAGGGTTATGGAAATATG 58.698 40.000 0.00 0.00 0.00 1.78
5191 8292 1.300620 CACAGACGTTGCGGGAGAA 60.301 57.895 0.00 0.00 0.00 2.87
5319 8527 2.807967 TGCGTGTTTTCTCTTCATGGAG 59.192 45.455 0.00 0.00 34.88 3.86
5342 8550 7.546667 GGAGCAATCATTTATTCAGCTTTGAAA 59.453 33.333 0.00 0.00 29.45 2.69
5453 8662 7.517614 TGTAAGATGCAATTTAAGAACACCA 57.482 32.000 0.00 0.00 0.00 4.17
5454 8663 7.946207 TGTAAGATGCAATTTAAGAACACCAA 58.054 30.769 0.00 0.00 0.00 3.67
5514 9043 9.226606 CCTTCATTTACTTATACAAGACCACAA 57.773 33.333 0.00 0.00 35.60 3.33
5528 9274 8.288689 ACAAGACCACAAACTTAAATTACAGT 57.711 30.769 0.00 0.00 0.00 3.55
5574 9320 5.803020 ACTTTGTCAGTCAACTTGTCTTC 57.197 39.130 0.00 0.00 35.61 2.87
5583 9329 6.535150 TCAGTCAACTTGTCTTCTGTTTACTG 59.465 38.462 11.05 11.05 42.48 2.74
5605 9351 6.155475 TGGGTTAATTAATAAGGCACATGC 57.845 37.500 0.31 0.00 41.14 4.06
5607 9353 6.326064 TGGGTTAATTAATAAGGCACATGCAT 59.674 34.615 6.15 0.00 44.36 3.96
5608 9354 6.646240 GGGTTAATTAATAAGGCACATGCATG 59.354 38.462 25.09 25.09 44.36 4.06
5609 9355 7.432869 GGTTAATTAATAAGGCACATGCATGA 58.567 34.615 32.75 9.93 44.36 3.07
5610 9356 7.925483 GGTTAATTAATAAGGCACATGCATGAA 59.075 33.333 32.75 13.39 44.36 2.57
5611 9357 8.971321 GTTAATTAATAAGGCACATGCATGAAG 58.029 33.333 32.75 23.31 44.36 3.02
5612 9358 6.720112 ATTAATAAGGCACATGCATGAAGT 57.280 33.333 32.75 14.50 44.36 3.01
5622 9369 6.183360 GGCACATGCATGAAGTAAAAATTGAG 60.183 38.462 32.75 0.84 44.36 3.02
5627 9374 7.230849 TGCATGAAGTAAAAATTGAGTGGAT 57.769 32.000 0.00 0.00 0.00 3.41
5628 9375 7.092079 TGCATGAAGTAAAAATTGAGTGGATG 58.908 34.615 0.00 0.00 0.00 3.51
5629 9376 7.092716 GCATGAAGTAAAAATTGAGTGGATGT 58.907 34.615 0.00 0.00 0.00 3.06
5668 9415 9.950496 AGTTGAGACTATTATTGTCATTCACTT 57.050 29.630 9.21 0.00 36.94 3.16
5677 9424 5.654603 ATTGTCATTCACTTCATGCATGT 57.345 34.783 25.43 4.41 33.98 3.21
5681 9428 4.155462 GTCATTCACTTCATGCATGTGAGT 59.845 41.667 25.43 24.28 39.63 3.41
5690 9437 6.936900 ACTTCATGCATGTGAGTAGTTAAACT 59.063 34.615 26.03 8.12 0.00 2.66
5727 9474 6.855763 ATGAGGCAAGGTCATCAATTTTTA 57.144 33.333 0.00 0.00 30.20 1.52
5729 9476 5.047377 TGAGGCAAGGTCATCAATTTTTACC 60.047 40.000 0.00 0.00 0.00 2.85
5739 9486 8.364894 GGTCATCAATTTTTACCTTGGTTACTT 58.635 33.333 0.00 0.00 0.00 2.24
5759 9506 5.186198 ACTTTTGGTAGCCTTGTATAGCTG 58.814 41.667 0.00 0.00 40.28 4.24
5766 9513 4.644103 AGCCTTGTATAGCTGCAAAATG 57.356 40.909 1.02 0.00 38.11 2.32
5781 9528 6.237915 GCTGCAAAATGTATTTTCATAGTGGC 60.238 38.462 0.00 0.87 37.86 5.01
5790 9537 4.846779 TTTTCATAGTGGCCTTGTTGTC 57.153 40.909 3.32 0.00 0.00 3.18
5795 9542 2.550830 AGTGGCCTTGTTGTCTACAG 57.449 50.000 3.32 0.00 38.19 2.74
5807 9554 7.042658 CCTTGTTGTCTACAGAAACTGAAGTAC 60.043 40.741 5.76 0.00 38.19 2.73
5812 9559 9.565090 TTGTCTACAGAAACTGAAGTACTAGTA 57.435 33.333 0.00 0.00 35.18 1.82
5813 9560 9.217278 TGTCTACAGAAACTGAAGTACTAGTAG 57.783 37.037 1.87 0.00 35.18 2.57
5814 9561 9.218440 GTCTACAGAAACTGAAGTACTAGTAGT 57.782 37.037 8.14 8.14 35.18 2.73
5815 9562 9.790344 TCTACAGAAACTGAAGTACTAGTAGTT 57.210 33.333 20.57 20.57 35.18 2.24
5833 9580 6.174049 AGTAGTTTAGATGCTTTGAAGGGTC 58.826 40.000 0.00 0.00 0.00 4.46
5858 9605 3.569194 TGTACTCCCTCTGTGCAAAAA 57.431 42.857 0.00 0.00 0.00 1.94
5878 9625 2.851195 ACAGAAACGAAGCAAGACCAT 58.149 42.857 0.00 0.00 0.00 3.55
5883 9630 1.800805 ACGAAGCAAGACCATGACAG 58.199 50.000 0.00 0.00 0.00 3.51
5894 9641 5.255397 AGACCATGACAGTTATTTTGGGA 57.745 39.130 0.00 0.00 0.00 4.37
5898 9645 6.758254 ACCATGACAGTTATTTTGGGAAAAG 58.242 36.000 0.00 0.00 33.22 2.27
5899 9646 6.165577 CCATGACAGTTATTTTGGGAAAAGG 58.834 40.000 0.00 0.00 33.22 3.11
5900 9647 6.239572 CCATGACAGTTATTTTGGGAAAAGGT 60.240 38.462 0.00 0.00 33.22 3.50
5901 9648 6.155475 TGACAGTTATTTTGGGAAAAGGTG 57.845 37.500 0.00 0.00 33.22 4.00
5949 9697 9.886132 TTTAGGACTGAGGAAGTATATCAAAAC 57.114 33.333 0.00 0.00 40.07 2.43
5953 9701 7.775561 GGACTGAGGAAGTATATCAAAACCATT 59.224 37.037 0.00 0.00 40.07 3.16
5957 9705 7.556275 TGAGGAAGTATATCAAAACCATTGGAC 59.444 37.037 10.37 0.00 0.00 4.02
5966 9714 9.793259 ATATCAAAACCATTGGACGAATATACT 57.207 29.630 10.37 0.00 0.00 2.12
5987 9735 4.629634 ACTGCGTTTTCATCGATACAATGA 59.370 37.500 0.00 0.00 0.00 2.57
5990 9738 6.550843 TGCGTTTTCATCGATACAATGAAAT 58.449 32.000 10.91 0.00 46.75 2.17
6098 9846 6.436843 CCTATTTTAGGGCACTAAACTGTG 57.563 41.667 20.74 12.19 46.01 3.66
6140 9891 8.435430 GCAACATCTCAAAGTAATTTTTAAGGC 58.565 33.333 0.00 0.00 0.00 4.35
6144 9895 7.589958 TCTCAAAGTAATTTTTAAGGCACCA 57.410 32.000 0.00 0.00 0.00 4.17
6145 9896 8.012957 TCTCAAAGTAATTTTTAAGGCACCAA 57.987 30.769 0.00 0.00 0.00 3.67
6227 9979 2.939460 AAAATAGGCATTCGCACCAC 57.061 45.000 0.00 0.00 41.24 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.664816 TCCTTCAAGATTTAGATGGCAATTGT 59.335 34.615 7.40 0.00 0.00 2.71
1 2 6.976925 GTCCTTCAAGATTTAGATGGCAATTG 59.023 38.462 0.00 0.00 0.00 2.32
25 26 4.274214 GGGACTAAAACGTTAACAAGCTGT 59.726 41.667 0.00 0.00 0.00 4.40
27 28 4.711399 AGGGACTAAAACGTTAACAAGCT 58.289 39.130 0.00 0.00 36.02 3.74
28 29 4.512571 TGAGGGACTAAAACGTTAACAAGC 59.487 41.667 0.00 0.00 41.55 4.01
56 57 0.324943 AACCCACAAGATGTCCCTCG 59.675 55.000 0.00 0.00 0.00 4.63
73 74 7.012704 TGCTCTTTCATCCAATTAGCATCTAAC 59.987 37.037 0.00 0.00 33.84 2.34
82 83 4.705991 TGCACATGCTCTTTCATCCAATTA 59.294 37.500 5.31 0.00 42.66 1.40
209 213 7.872113 AACCAAGCAAAAATGTTTATTCCAA 57.128 28.000 0.00 0.00 0.00 3.53
301 305 5.428253 GTGGGAGATGACTTATGCTTGTAA 58.572 41.667 0.00 0.00 0.00 2.41
317 321 3.323774 ACATATTAGACCGGTGGGAGA 57.676 47.619 14.63 0.00 36.97 3.71
342 346 5.866633 TGTCAAAGTGTCAATGTCCAAAAAC 59.133 36.000 0.00 0.00 0.00 2.43
569 573 7.125792 ACGGATACTACCTCTGATTCAAAAT 57.874 36.000 0.00 0.00 0.00 1.82
804 815 6.899089 TCATCAAAATAGATTCCTGCCACTA 58.101 36.000 0.00 0.00 0.00 2.74
838 849 3.998913 TCCCACTTGATCAATAGCACA 57.001 42.857 8.96 0.00 0.00 4.57
1192 1204 5.605564 AAGCAAAACCACACAAAGAAAAC 57.394 34.783 0.00 0.00 0.00 2.43
1307 1320 6.403527 CCTGACGAGATTGCAAAACATTATCA 60.404 38.462 1.71 1.31 0.00 2.15
1818 1893 8.095452 ACCTCTGATCCATATTACTTGTCTTT 57.905 34.615 0.00 0.00 0.00 2.52
2015 2093 6.679327 ATAAGCGAGTTACTTTCCCATTTC 57.321 37.500 0.00 0.00 0.00 2.17
2094 2172 1.512156 GCAAAACACGTCCGGACCAT 61.512 55.000 28.52 14.60 0.00 3.55
2120 2199 4.603946 GACCGATACAGGCCCGCC 62.604 72.222 0.00 0.00 33.69 6.13
2343 5041 2.158959 CGTCCGATCACGTTGCTCC 61.159 63.158 0.00 0.00 37.88 4.70
2507 5209 0.312729 TATGTGCATCGCCGACGTAT 59.687 50.000 0.00 0.00 41.18 3.06
2720 5464 2.607750 GGTGCCTGGTCCTCCTCA 60.608 66.667 0.00 0.00 34.23 3.86
2823 5583 0.461548 CGAGCCCATCTAACAGAGCA 59.538 55.000 0.00 0.00 0.00 4.26
2868 5628 1.299976 GATGGCGGTTCCTCCTTGT 59.700 57.895 0.00 0.00 35.26 3.16
2975 5736 4.193334 TCCGATCTGGACGCAGCG 62.193 66.667 14.82 14.82 43.74 5.18
3048 5809 3.708220 GACGCTGGCTCCTCCTTCG 62.708 68.421 0.00 0.00 36.71 3.79
3074 5835 2.032071 GGCCTAGCGGTTGTGTGT 59.968 61.111 0.00 0.00 0.00 3.72
3095 5856 2.159296 CGACACAGACCCGTCAATATGA 60.159 50.000 0.00 0.00 32.24 2.15
3141 5902 3.338249 GCAGCTCATCCTTGACAAACTA 58.662 45.455 0.00 0.00 0.00 2.24
3282 6050 1.375523 GTCGTTGCGGACCCATTCT 60.376 57.895 0.00 0.00 0.00 2.40
3283 6051 3.174788 GTCGTTGCGGACCCATTC 58.825 61.111 0.00 0.00 0.00 2.67
3302 6076 1.229359 CAGGCGGTAGGGAGGTCTA 59.771 63.158 0.00 0.00 0.00 2.59
3479 6278 2.960688 GCCGCTCCACTTCCTCCTT 61.961 63.158 0.00 0.00 0.00 3.36
3556 6355 0.608130 CGTCATCCCTCCAACTGTGA 59.392 55.000 0.00 0.00 0.00 3.58
3562 6361 0.541392 CATCACCGTCATCCCTCCAA 59.459 55.000 0.00 0.00 0.00 3.53
3621 6420 0.389426 ACGACCACCTCATTACACGC 60.389 55.000 0.00 0.00 0.00 5.34
3628 6427 1.183549 GTACTGGACGACCACCTCAT 58.816 55.000 1.37 0.00 41.77 2.90
3629 6428 0.178984 TGTACTGGACGACCACCTCA 60.179 55.000 1.37 0.00 41.77 3.86
3711 6510 6.422701 ACACGACGAAATTCATTCAAGTTCTA 59.577 34.615 0.00 0.00 37.01 2.10
4066 6865 5.418310 AACAAAGTGGTGACGTATCAAAG 57.582 39.130 0.00 0.00 36.31 2.77
4069 6868 5.603596 ACTTAACAAAGTGGTGACGTATCA 58.396 37.500 0.00 0.00 0.00 2.15
4168 6976 1.413812 CCTTCTGCCTTGCCAACTTTT 59.586 47.619 0.00 0.00 0.00 2.27
4169 6977 1.043022 CCTTCTGCCTTGCCAACTTT 58.957 50.000 0.00 0.00 0.00 2.66
4170 6978 1.466851 GCCTTCTGCCTTGCCAACTT 61.467 55.000 0.00 0.00 0.00 2.66
4171 6979 1.905354 GCCTTCTGCCTTGCCAACT 60.905 57.895 0.00 0.00 0.00 3.16
4535 7345 1.949525 CATAGGCCAAAGGATTCACCG 59.050 52.381 5.01 0.00 44.74 4.94
4772 7630 3.315470 TCACAGGATAGTGCACGATAGTC 59.685 47.826 12.75 6.90 42.27 2.59
4845 7703 5.183530 ACAAGTCCTGATTCCATGATCAA 57.816 39.130 0.00 0.00 35.74 2.57
4946 8013 4.268359 TGCAACACCAACAGCATATCATA 58.732 39.130 0.00 0.00 31.05 2.15
4949 8016 3.788333 ATGCAACACCAACAGCATATC 57.212 42.857 0.00 0.00 45.09 1.63
5191 8292 1.824329 AGATCCATCGCCTCGACGT 60.824 57.895 0.00 0.00 39.18 4.34
5319 8527 7.675637 GCCTTTCAAAGCTGAATAAATGATTGC 60.676 37.037 0.00 0.00 41.22 3.56
5342 8550 1.279496 TGCTCACATCTTACAGGCCT 58.721 50.000 0.00 0.00 0.00 5.19
5453 8662 9.020731 ACTTTGGATCCGTAATAACTTCATTTT 57.979 29.630 7.39 0.00 0.00 1.82
5454 8663 8.458843 CACTTTGGATCCGTAATAACTTCATTT 58.541 33.333 7.39 0.00 0.00 2.32
5548 9294 3.877508 ACAAGTTGACTGACAAAGTAGGC 59.122 43.478 10.54 0.00 40.07 3.93
5549 9295 5.360591 AGACAAGTTGACTGACAAAGTAGG 58.639 41.667 10.54 0.00 40.07 3.18
5552 9298 5.352569 CAGAAGACAAGTTGACTGACAAAGT 59.647 40.000 10.54 0.00 43.85 2.66
5553 9299 5.352569 ACAGAAGACAAGTTGACTGACAAAG 59.647 40.000 10.54 4.71 40.36 2.77
5559 9305 6.238211 CCAGTAAACAGAAGACAAGTTGACTG 60.238 42.308 10.54 12.82 46.90 3.51
5574 9320 8.962679 TGCCTTATTAATTAACCCAGTAAACAG 58.037 33.333 0.00 0.00 0.00 3.16
5583 9329 6.155475 TGCATGTGCCTTATTAATTAACCC 57.845 37.500 0.00 0.00 41.18 4.11
5596 9342 4.870123 TTTTTACTTCATGCATGTGCCT 57.130 36.364 25.43 9.80 41.18 4.75
5607 9353 8.792633 CCTTACATCCACTCAATTTTTACTTCA 58.207 33.333 0.00 0.00 0.00 3.02
5608 9354 8.244113 CCCTTACATCCACTCAATTTTTACTTC 58.756 37.037 0.00 0.00 0.00 3.01
5609 9355 7.947890 TCCCTTACATCCACTCAATTTTTACTT 59.052 33.333 0.00 0.00 0.00 2.24
5610 9356 7.466804 TCCCTTACATCCACTCAATTTTTACT 58.533 34.615 0.00 0.00 0.00 2.24
5611 9357 7.610305 TCTCCCTTACATCCACTCAATTTTTAC 59.390 37.037 0.00 0.00 0.00 2.01
5612 9358 7.695055 TCTCCCTTACATCCACTCAATTTTTA 58.305 34.615 0.00 0.00 0.00 1.52
5622 9369 5.678955 ACTACTTTCTCCCTTACATCCAC 57.321 43.478 0.00 0.00 0.00 4.02
5627 9374 6.075984 AGTCTCAACTACTTTCTCCCTTACA 58.924 40.000 0.00 0.00 32.59 2.41
5628 9375 6.593268 AGTCTCAACTACTTTCTCCCTTAC 57.407 41.667 0.00 0.00 32.59 2.34
5629 9376 8.896722 AATAGTCTCAACTACTTTCTCCCTTA 57.103 34.615 0.00 0.00 40.74 2.69
5668 9415 8.257306 TCATAGTTTAACTACTCACATGCATGA 58.743 33.333 32.75 11.95 32.84 3.07
5690 9437 6.183361 ACCTTGCCTCATATTAGCAACTCATA 60.183 38.462 0.00 0.00 41.35 2.15
5727 9474 3.139584 AGGCTACCAAAAGTAACCAAGGT 59.860 43.478 0.00 0.00 39.34 3.50
5729 9476 4.583073 ACAAGGCTACCAAAAGTAACCAAG 59.417 41.667 0.00 0.00 39.34 3.61
5731 9478 4.173290 ACAAGGCTACCAAAAGTAACCA 57.827 40.909 0.00 0.00 39.34 3.67
5739 9486 3.054728 TGCAGCTATACAAGGCTACCAAA 60.055 43.478 0.00 0.00 37.00 3.28
5759 9506 6.340522 AGGCCACTATGAAAATACATTTTGC 58.659 36.000 5.01 1.04 39.86 3.68
5766 9513 6.151144 AGACAACAAGGCCACTATGAAAATAC 59.849 38.462 5.01 0.00 0.00 1.89
5781 9528 5.817816 ACTTCAGTTTCTGTAGACAACAAGG 59.182 40.000 9.63 0.00 37.74 3.61
5807 9554 7.331791 ACCCTTCAAAGCATCTAAACTACTAG 58.668 38.462 0.00 0.00 0.00 2.57
5812 9559 4.003648 CGACCCTTCAAAGCATCTAAACT 58.996 43.478 0.00 0.00 0.00 2.66
5813 9560 3.751698 ACGACCCTTCAAAGCATCTAAAC 59.248 43.478 0.00 0.00 0.00 2.01
5814 9561 4.015872 ACGACCCTTCAAAGCATCTAAA 57.984 40.909 0.00 0.00 0.00 1.85
5815 9562 3.695830 ACGACCCTTCAAAGCATCTAA 57.304 42.857 0.00 0.00 0.00 2.10
5816 9563 3.695830 AACGACCCTTCAAAGCATCTA 57.304 42.857 0.00 0.00 0.00 1.98
5817 9564 2.568623 AACGACCCTTCAAAGCATCT 57.431 45.000 0.00 0.00 0.00 2.90
5818 9565 3.689649 ACATAACGACCCTTCAAAGCATC 59.310 43.478 0.00 0.00 0.00 3.91
5821 9568 4.251268 AGTACATAACGACCCTTCAAAGC 58.749 43.478 0.00 0.00 0.00 3.51
5833 9580 2.165641 TGCACAGAGGGAGTACATAACG 59.834 50.000 0.00 0.00 0.00 3.18
5858 9605 2.325583 TGGTCTTGCTTCGTTTCTGT 57.674 45.000 0.00 0.00 0.00 3.41
5865 9612 1.800805 ACTGTCATGGTCTTGCTTCG 58.199 50.000 0.00 0.00 0.00 3.79
5878 9625 5.894393 TCACCTTTTCCCAAAATAACTGTCA 59.106 36.000 0.00 0.00 0.00 3.58
5883 9630 9.549078 TTGTTATTCACCTTTTCCCAAAATAAC 57.451 29.630 0.00 0.00 38.04 1.89
5894 9641 8.650143 AGTATCATGGTTGTTATTCACCTTTT 57.350 30.769 0.00 0.00 0.00 2.27
5926 9674 6.443849 TGGTTTTGATATACTTCCTCAGTCCT 59.556 38.462 0.00 0.00 36.88 3.85
5928 9676 8.616076 CAATGGTTTTGATATACTTCCTCAGTC 58.384 37.037 0.00 0.00 36.88 3.51
5940 9688 9.793259 AGTATATTCGTCCAATGGTTTTGATAT 57.207 29.630 0.00 1.97 0.00 1.63
5949 9697 3.390135 ACGCAGTATATTCGTCCAATGG 58.610 45.455 0.00 0.00 41.94 3.16
5953 9701 4.496360 TGAAAACGCAGTATATTCGTCCA 58.504 39.130 0.00 0.00 45.00 4.02
5957 9705 5.555190 TCGATGAAAACGCAGTATATTCG 57.445 39.130 0.00 0.00 45.00 3.34
5966 9714 5.538067 TTCATTGTATCGATGAAAACGCA 57.462 34.783 8.54 0.00 40.15 5.24
5990 9738 8.043710 AGTGACAACCAACAAAATAATTTCCAA 58.956 29.630 0.00 0.00 0.00 3.53
6043 9791 6.007076 TGGAGATGGTTTAACTACAAATGCA 58.993 36.000 0.00 0.00 0.00 3.96
6052 9800 5.104067 GGGACCTATTGGAGATGGTTTAACT 60.104 44.000 0.00 0.00 37.04 2.24
6058 9806 2.897823 AGGGACCTATTGGAGATGGT 57.102 50.000 0.00 0.00 37.04 3.55
6059 9807 5.850046 AAATAGGGACCTATTGGAGATGG 57.150 43.478 21.02 0.00 45.37 3.51
6153 9904 3.711863 AGGGCATTTATTGGAGAAGCAA 58.288 40.909 0.00 0.00 0.00 3.91
6157 9908 8.477419 CCTATTTTAGGGCATTTATTGGAGAA 57.523 34.615 0.00 0.00 42.42 2.87
6189 9940 2.584835 TAGGGCAACTGTTTGAGCAT 57.415 45.000 4.12 0.00 34.24 3.79


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

AutoCloner maintained by Alex Coulton.