Multiple sequence alignment - TraesCS1A01G142700

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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 TraesCS1A01G142700 chr1A 100.000 4976 0 0 1 4976 244504810 244499835 0.000000e+00 9190
1 TraesCS1A01G142700 chr1A 87.951 1884 162 24 487 2334 474154409 474156263 0.000000e+00 2161
2 TraesCS1A01G142700 chr1A 94.177 1288 73 1 3398 4685 529400617 529401902 0.000000e+00 1962
3 TraesCS1A01G142700 chr1A 92.908 141 5 4 4684 4820 529421536 529421675 3.040000e-47 200
4 TraesCS1A01G142700 chr3B 99.337 4221 25 2 603 4820 697167762 697163542 0.000000e+00 7637
5 TraesCS1A01G142700 chr3B 99.437 2487 13 1 2343 4828 736480904 736483390 0.000000e+00 4514
6 TraesCS1A01G142700 chr3B 87.762 1912 163 23 459 2334 71887104 71888980 0.000000e+00 2169
7 TraesCS1A01G142700 chr3B 94.881 586 25 4 1 582 762379603 762380187 0.000000e+00 911
8 TraesCS1A01G142700 chr3B 96.520 546 10 6 1 542 817251295 817250755 0.000000e+00 894
9 TraesCS1A01G142700 chr5A 94.513 3918 167 15 924 4835 381553268 381549393 0.000000e+00 6000
10 TraesCS1A01G142700 chr5A 92.028 1869 105 11 487 2334 568064747 568066592 0.000000e+00 2586
11 TraesCS1A01G142700 chr5A 89.744 351 34 2 572 920 381563783 381563433 9.830000e-122 448
12 TraesCS1A01G142700 chr5A 88.142 253 23 4 449 699 549322171 549321924 1.350000e-75 294
13 TraesCS1A01G142700 chr5A 90.476 147 7 6 4684 4827 439830850 439830708 2.370000e-43 187
14 TraesCS1A01G142700 chr7A 99.437 2485 14 0 2343 4827 56201834 56199350 0.000000e+00 4512
15 TraesCS1A01G142700 chr7A 95.893 2362 83 10 2331 4682 630037505 630039862 0.000000e+00 3812
16 TraesCS1A01G142700 chr7A 90.005 1861 133 21 487 2334 607420385 607422205 0.000000e+00 2357
17 TraesCS1A01G142700 chr7A 90.744 1599 113 19 2331 3901 464232704 464234295 0.000000e+00 2100
18 TraesCS1A01G142700 chr7A 97.529 526 9 3 1 522 45189890 45189365 0.000000e+00 896
19 TraesCS1A01G142700 chr6B 99.434 2475 14 0 2343 4817 159797093 159799567 0.000000e+00 4494
20 TraesCS1A01G142700 chr6B 90.619 1599 115 19 2331 3901 232748042 232749633 0.000000e+00 2089
21 TraesCS1A01G142700 chr1D 96.738 1870 58 2 2816 4685 251295251 251297117 0.000000e+00 3112
22 TraesCS1A01G142700 chr1D 92.029 138 6 1 4684 4816 251298530 251298667 6.580000e-44 189
23 TraesCS1A01G142700 chr1D 93.388 121 8 0 4855 4975 375629921 375629801 3.960000e-41 180
24 TraesCS1A01G142700 chr1D 92.562 121 9 0 4855 4975 237676624 237676504 1.840000e-39 174
25 TraesCS1A01G142700 chr1D 87.681 138 15 2 4839 4975 296116889 296116753 5.160000e-35 159
26 TraesCS1A01G142700 chr7B 88.245 1880 156 24 490 2334 32562684 32560835 0.000000e+00 2187
27 TraesCS1A01G142700 chr7B 87.454 1889 164 31 487 2334 161929119 161930975 0.000000e+00 2108
28 TraesCS1A01G142700 chr2B 88.004 1884 160 25 487 2334 53932 55785 0.000000e+00 2167
29 TraesCS1A01G142700 chr2A 84.599 2292 222 57 110 2334 719357710 719355483 0.000000e+00 2156
30 TraesCS1A01G142700 chr2A 93.644 236 15 0 2099 2334 424506828 424506593 2.200000e-93 353
31 TraesCS1A01G142700 chr3A 87.879 1881 161 23 490 2334 704401605 704399756 0.000000e+00 2148
32 TraesCS1A01G142700 chr3A 97.519 524 11 1 1 522 668571435 668571958 0.000000e+00 894
33 TraesCS1A01G142700 chr1B 87.507 1881 166 27 490 2334 112365415 112363568 0.000000e+00 2108
34 TraesCS1A01G142700 chr1B 87.434 1886 167 26 487 2334 569422367 569424220 0.000000e+00 2106
35 TraesCS1A01G142700 chr1B 95.993 549 16 5 1 546 120641018 120640473 0.000000e+00 887
36 TraesCS1A01G142700 chr1B 95.307 554 19 5 1 550 662243559 662244109 0.000000e+00 872
37 TraesCS1A01G142700 chr1B 84.545 220 21 7 490 699 39295534 39295318 6.530000e-49 206
38 TraesCS1A01G142700 chr4D 96.190 1286 49 0 2331 3616 471711485 471710200 0.000000e+00 2104
39 TraesCS1A01G142700 chr4D 89.262 149 10 2 4684 4826 471702466 471702318 1.100000e-41 182
40 TraesCS1A01G142700 chr2D 93.170 1347 83 8 3340 4684 267287978 267289317 0.000000e+00 1969
41 TraesCS1A01G142700 chr2D 95.000 120 6 0 4856 4975 272945193 272945074 6.580000e-44 189
42 TraesCS1A01G142700 chr6A 94.407 590 29 3 1 587 600008877 600009465 0.000000e+00 904
43 TraesCS1A01G142700 chr6A 89.706 136 11 2 4838 4973 542842024 542841892 2.380000e-38 171
44 TraesCS1A01G142700 chr6A 84.431 167 12 6 544 699 233344478 233344641 8.630000e-33 152
45 TraesCS1A01G142700 chr4B 94.585 591 21 8 1 583 429690710 429690123 0.000000e+00 904
46 TraesCS1A01G142700 chr4B 92.029 138 6 4 4684 4819 1766362 1766496 6.580000e-44 189
47 TraesCS1A01G142700 chr5B 93.960 596 26 7 1 587 26448648 26449242 0.000000e+00 893
48 TraesCS1A01G142700 chr6D 89.326 178 7 1 4810 4975 98592012 98592189 3.900000e-51 213
49 TraesCS1A01G142700 chr6D 87.429 175 8 2 4813 4975 98479105 98479277 6.580000e-44 189
50 TraesCS1A01G142700 chr6D 89.437 142 12 3 4810 4951 224780885 224781023 5.120000e-40 176
51 TraesCS1A01G142700 chr4A 92.562 121 9 0 4855 4975 341595567 341595447 1.840000e-39 174
52 TraesCS1A01G142700 chr4A 92.000 125 6 4 4706 4827 64816918 64817041 6.620000e-39 172


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 TraesCS1A01G142700 chr1A 244499835 244504810 4975 True 9190.0 9190 100.0000 1 4976 1 chr1A.!!$R1 4975
1 TraesCS1A01G142700 chr1A 474154409 474156263 1854 False 2161.0 2161 87.9510 487 2334 1 chr1A.!!$F1 1847
2 TraesCS1A01G142700 chr1A 529400617 529401902 1285 False 1962.0 1962 94.1770 3398 4685 1 chr1A.!!$F2 1287
3 TraesCS1A01G142700 chr3B 697163542 697167762 4220 True 7637.0 7637 99.3370 603 4820 1 chr3B.!!$R1 4217
4 TraesCS1A01G142700 chr3B 736480904 736483390 2486 False 4514.0 4514 99.4370 2343 4828 1 chr3B.!!$F2 2485
5 TraesCS1A01G142700 chr3B 71887104 71888980 1876 False 2169.0 2169 87.7620 459 2334 1 chr3B.!!$F1 1875
6 TraesCS1A01G142700 chr3B 762379603 762380187 584 False 911.0 911 94.8810 1 582 1 chr3B.!!$F3 581
7 TraesCS1A01G142700 chr3B 817250755 817251295 540 True 894.0 894 96.5200 1 542 1 chr3B.!!$R2 541
8 TraesCS1A01G142700 chr5A 381549393 381553268 3875 True 6000.0 6000 94.5130 924 4835 1 chr5A.!!$R1 3911
9 TraesCS1A01G142700 chr5A 568064747 568066592 1845 False 2586.0 2586 92.0280 487 2334 1 chr5A.!!$F1 1847
10 TraesCS1A01G142700 chr7A 56199350 56201834 2484 True 4512.0 4512 99.4370 2343 4827 1 chr7A.!!$R2 2484
11 TraesCS1A01G142700 chr7A 630037505 630039862 2357 False 3812.0 3812 95.8930 2331 4682 1 chr7A.!!$F3 2351
12 TraesCS1A01G142700 chr7A 607420385 607422205 1820 False 2357.0 2357 90.0050 487 2334 1 chr7A.!!$F2 1847
13 TraesCS1A01G142700 chr7A 464232704 464234295 1591 False 2100.0 2100 90.7440 2331 3901 1 chr7A.!!$F1 1570
14 TraesCS1A01G142700 chr7A 45189365 45189890 525 True 896.0 896 97.5290 1 522 1 chr7A.!!$R1 521
15 TraesCS1A01G142700 chr6B 159797093 159799567 2474 False 4494.0 4494 99.4340 2343 4817 1 chr6B.!!$F1 2474
16 TraesCS1A01G142700 chr6B 232748042 232749633 1591 False 2089.0 2089 90.6190 2331 3901 1 chr6B.!!$F2 1570
17 TraesCS1A01G142700 chr1D 251295251 251298667 3416 False 1650.5 3112 94.3835 2816 4816 2 chr1D.!!$F1 2000
18 TraesCS1A01G142700 chr7B 32560835 32562684 1849 True 2187.0 2187 88.2450 490 2334 1 chr7B.!!$R1 1844
19 TraesCS1A01G142700 chr7B 161929119 161930975 1856 False 2108.0 2108 87.4540 487 2334 1 chr7B.!!$F1 1847
20 TraesCS1A01G142700 chr2B 53932 55785 1853 False 2167.0 2167 88.0040 487 2334 1 chr2B.!!$F1 1847
21 TraesCS1A01G142700 chr2A 719355483 719357710 2227 True 2156.0 2156 84.5990 110 2334 1 chr2A.!!$R2 2224
22 TraesCS1A01G142700 chr3A 704399756 704401605 1849 True 2148.0 2148 87.8790 490 2334 1 chr3A.!!$R1 1844
23 TraesCS1A01G142700 chr3A 668571435 668571958 523 False 894.0 894 97.5190 1 522 1 chr3A.!!$F1 521
24 TraesCS1A01G142700 chr1B 112363568 112365415 1847 True 2108.0 2108 87.5070 490 2334 1 chr1B.!!$R2 1844
25 TraesCS1A01G142700 chr1B 569422367 569424220 1853 False 2106.0 2106 87.4340 487 2334 1 chr1B.!!$F1 1847
26 TraesCS1A01G142700 chr1B 120640473 120641018 545 True 887.0 887 95.9930 1 546 1 chr1B.!!$R3 545
27 TraesCS1A01G142700 chr1B 662243559 662244109 550 False 872.0 872 95.3070 1 550 1 chr1B.!!$F2 549
28 TraesCS1A01G142700 chr4D 471710200 471711485 1285 True 2104.0 2104 96.1900 2331 3616 1 chr4D.!!$R2 1285
29 TraesCS1A01G142700 chr2D 267287978 267289317 1339 False 1969.0 1969 93.1700 3340 4684 1 chr2D.!!$F1 1344
30 TraesCS1A01G142700 chr6A 600008877 600009465 588 False 904.0 904 94.4070 1 587 1 chr6A.!!$F2 586
31 TraesCS1A01G142700 chr4B 429690123 429690710 587 True 904.0 904 94.5850 1 583 1 chr4B.!!$R1 582
32 TraesCS1A01G142700 chr5B 26448648 26449242 594 False 893.0 893 93.9600 1 587 1 chr5B.!!$F1 586

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
393 400 8.610896 GTTCATGATTTCGAGAAATTGAGAGAT 58.389 33.333 11.77 0.00 40.77 2.75 F
1008 1101 1.578215 AAGCCAGGCTCATGGACCAT 61.578 55.000 16.53 0.00 43.57 3.55 F
2216 2336 0.099968 CGGCCTCTTGCATGAACATG 59.900 55.000 0.00 10.04 43.89 3.21 F
2217 2337 1.466856 GGCCTCTTGCATGAACATGA 58.533 50.000 17.40 1.83 43.89 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2152 2272 3.624777 CTTTGAATCACCCTGGTAGCAT 58.375 45.455 0.00 0.0 0.00 3.79 R
2966 3096 2.827755 TGTGACAGGGCCACTAATAGA 58.172 47.619 6.18 0.0 35.66 1.98 R
3486 3616 1.135257 CAGAGTGAAGCGACGGAGAAT 60.135 52.381 0.00 0.0 0.00 2.40 R
4348 4516 5.874261 TCATCGAAGAACACATTTGATGCTA 59.126 36.000 9.93 0.0 43.68 3.49 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
393 400 8.610896 GTTCATGATTTCGAGAAATTGAGAGAT 58.389 33.333 11.77 0.00 40.77 2.75
1008 1101 1.578215 AAGCCAGGCTCATGGACCAT 61.578 55.000 16.53 0.00 43.57 3.55
1221 1314 2.199652 CCAGCTGGCGGGTGAAAAA 61.200 57.895 26.22 0.00 45.36 1.94
2152 2272 2.249844 GGAACGACAGAGGGTTTGAA 57.750 50.000 0.00 0.00 0.00 2.69
2212 2332 1.177895 TTTGCGGCCTCTTGCATGAA 61.178 50.000 0.00 0.00 43.89 2.57
2213 2333 1.865788 TTGCGGCCTCTTGCATGAAC 61.866 55.000 0.00 0.00 43.89 3.18
2214 2334 2.334946 GCGGCCTCTTGCATGAACA 61.335 57.895 0.00 0.00 43.89 3.18
2215 2335 1.660560 GCGGCCTCTTGCATGAACAT 61.661 55.000 0.00 0.00 43.89 2.71
2216 2336 0.099968 CGGCCTCTTGCATGAACATG 59.900 55.000 0.00 10.04 43.89 3.21
2217 2337 1.466856 GGCCTCTTGCATGAACATGA 58.533 50.000 17.40 1.83 43.89 3.07
2218 2338 2.029623 GGCCTCTTGCATGAACATGAT 58.970 47.619 17.40 0.00 43.89 2.45
2219 2339 2.429610 GGCCTCTTGCATGAACATGATT 59.570 45.455 17.40 0.00 43.89 2.57
2966 3096 3.016736 CTGTTGCATTACTCCCCGATTT 58.983 45.455 0.00 0.00 0.00 2.17
3224 3354 5.759763 AGAAAACAAAATCAAGGACCAATGC 59.240 36.000 0.00 0.00 0.00 3.56
3297 3427 7.944554 TGGAACATATTCTTTTTCTCTCCTTGT 59.055 33.333 0.00 0.00 34.98 3.16
3486 3616 2.239400 CAGCATGACCTACCCTATCGA 58.761 52.381 0.00 0.00 39.69 3.59
4053 4221 6.894735 TCATTACCCCCAGTATTTTAGTCA 57.105 37.500 0.00 0.00 0.00 3.41
4819 6407 5.051816 GCACGGGCATTTGTACTAGTATAA 58.948 41.667 3.77 6.94 40.72 0.98
4852 6440 9.445786 AAAACATCCTCGCATAATTAATTTACG 57.554 29.630 5.91 8.21 0.00 3.18
4853 6441 6.599437 ACATCCTCGCATAATTAATTTACGC 58.401 36.000 5.91 6.12 0.00 4.42
4854 6442 6.203915 ACATCCTCGCATAATTAATTTACGCA 59.796 34.615 5.91 0.00 0.00 5.24
4855 6443 6.606234 TCCTCGCATAATTAATTTACGCAA 57.394 33.333 5.91 0.00 0.00 4.85
4856 6444 7.017498 TCCTCGCATAATTAATTTACGCAAA 57.983 32.000 5.91 0.00 0.00 3.68
4857 6445 7.129622 TCCTCGCATAATTAATTTACGCAAAG 58.870 34.615 5.91 7.13 0.00 2.77
4858 6446 7.011576 TCCTCGCATAATTAATTTACGCAAAGA 59.988 33.333 5.91 1.73 0.00 2.52
4859 6447 7.321271 CCTCGCATAATTAATTTACGCAAAGAG 59.679 37.037 5.91 8.58 0.00 2.85
4860 6448 7.911343 TCGCATAATTAATTTACGCAAAGAGA 58.089 30.769 5.91 0.00 0.00 3.10
4861 6449 8.556194 TCGCATAATTAATTTACGCAAAGAGAT 58.444 29.630 5.91 0.00 0.00 2.75
4862 6450 8.621487 CGCATAATTAATTTACGCAAAGAGATG 58.379 33.333 5.91 0.97 0.00 2.90
4863 6451 9.450807 GCATAATTAATTTACGCAAAGAGATGT 57.549 29.630 5.91 0.00 0.00 3.06
4865 6453 9.950680 ATAATTAATTTACGCAAAGAGATGTGG 57.049 29.630 5.91 0.00 35.13 4.17
4866 6454 3.764885 ATTTACGCAAAGAGATGTGGC 57.235 42.857 0.00 0.00 35.13 5.01
4867 6455 1.448985 TTACGCAAAGAGATGTGGCC 58.551 50.000 0.00 0.00 35.13 5.36
4868 6456 0.613260 TACGCAAAGAGATGTGGCCT 59.387 50.000 3.32 0.00 35.13 5.19
4869 6457 0.957395 ACGCAAAGAGATGTGGCCTG 60.957 55.000 3.32 0.00 35.13 4.85
4870 6458 1.651240 CGCAAAGAGATGTGGCCTGG 61.651 60.000 3.32 0.00 0.00 4.45
4871 6459 1.941999 GCAAAGAGATGTGGCCTGGC 61.942 60.000 11.05 11.05 0.00 4.85
4872 6460 1.377725 AAAGAGATGTGGCCTGGCG 60.378 57.895 13.40 0.00 0.00 5.69
4873 6461 2.129555 AAAGAGATGTGGCCTGGCGT 62.130 55.000 13.40 0.00 0.00 5.68
4874 6462 2.512515 GAGATGTGGCCTGGCGTC 60.513 66.667 13.40 8.63 0.00 5.19
4875 6463 4.457496 AGATGTGGCCTGGCGTCG 62.457 66.667 13.40 0.00 0.00 5.12
4876 6464 4.451150 GATGTGGCCTGGCGTCGA 62.451 66.667 13.40 0.00 0.00 4.20
4877 6465 3.950794 GATGTGGCCTGGCGTCGAA 62.951 63.158 13.40 0.00 0.00 3.71
4878 6466 3.958147 ATGTGGCCTGGCGTCGAAG 62.958 63.158 13.40 0.00 0.00 3.79
4887 6475 2.395690 GCGTCGAAGCCAATGTCG 59.604 61.111 12.67 0.00 38.62 4.35
4888 6476 2.092291 GCGTCGAAGCCAATGTCGA 61.092 57.895 12.67 0.00 43.61 4.20
4889 6477 1.421410 GCGTCGAAGCCAATGTCGAT 61.421 55.000 12.67 0.00 46.91 3.59
4890 6478 0.298707 CGTCGAAGCCAATGTCGATG 59.701 55.000 0.00 0.07 46.91 3.84
4891 6479 0.026803 GTCGAAGCCAATGTCGATGC 59.973 55.000 0.00 0.00 46.91 3.91
4892 6480 1.011904 CGAAGCCAATGTCGATGCG 60.012 57.895 0.00 0.00 39.64 4.73
4893 6481 1.353103 GAAGCCAATGTCGATGCGG 59.647 57.895 0.00 0.00 0.00 5.69
4894 6482 2.051804 GAAGCCAATGTCGATGCGGG 62.052 60.000 0.00 0.00 0.00 6.13
4895 6483 3.585990 GCCAATGTCGATGCGGGG 61.586 66.667 0.00 0.00 0.00 5.73
4896 6484 3.585990 CCAATGTCGATGCGGGGC 61.586 66.667 0.00 0.00 0.00 5.80
4897 6485 3.940640 CAATGTCGATGCGGGGCG 61.941 66.667 0.00 0.00 0.00 6.13
4898 6486 4.467084 AATGTCGATGCGGGGCGT 62.467 61.111 0.00 0.00 0.00 5.68
4899 6487 4.891727 ATGTCGATGCGGGGCGTC 62.892 66.667 0.00 0.00 40.75 5.19
4921 6509 2.523015 GCATGACAAAGCCTGAATTCG 58.477 47.619 0.00 0.00 0.00 3.34
4922 6510 2.523015 CATGACAAAGCCTGAATTCGC 58.477 47.619 0.04 0.00 0.00 4.70
4923 6511 1.603456 TGACAAAGCCTGAATTCGCA 58.397 45.000 7.88 0.00 0.00 5.10
4924 6512 1.536766 TGACAAAGCCTGAATTCGCAG 59.463 47.619 7.88 0.00 35.66 5.18
4939 6527 4.410400 CAGGGCGGTCCAAGTCCC 62.410 72.222 0.00 0.00 38.24 4.46
4942 6530 3.961414 GGCGGTCCAAGTCCCCAA 61.961 66.667 0.00 0.00 0.00 4.12
4943 6531 2.355115 GCGGTCCAAGTCCCCAAT 59.645 61.111 0.00 0.00 0.00 3.16
4944 6532 2.046285 GCGGTCCAAGTCCCCAATG 61.046 63.158 0.00 0.00 0.00 2.82
4945 6533 2.046285 CGGTCCAAGTCCCCAATGC 61.046 63.158 0.00 0.00 0.00 3.56
4946 6534 2.046285 GGTCCAAGTCCCCAATGCG 61.046 63.158 0.00 0.00 0.00 4.73
4947 6535 2.046285 GTCCAAGTCCCCAATGCGG 61.046 63.158 0.00 0.00 0.00 5.69
4948 6536 3.451894 CCAAGTCCCCAATGCGGC 61.452 66.667 0.00 0.00 0.00 6.53
4949 6537 3.814268 CAAGTCCCCAATGCGGCG 61.814 66.667 0.51 0.51 0.00 6.46
4950 6538 4.344865 AAGTCCCCAATGCGGCGT 62.345 61.111 9.37 0.00 0.00 5.68
4951 6539 3.860930 AAGTCCCCAATGCGGCGTT 62.861 57.895 9.37 0.61 0.00 4.84
4952 6540 3.810896 GTCCCCAATGCGGCGTTC 61.811 66.667 9.37 0.00 0.00 3.95
4963 6551 2.431260 GGCGTTCGCCGAACTGTA 60.431 61.111 25.54 0.00 41.76 2.74
4964 6552 2.442188 GGCGTTCGCCGAACTGTAG 61.442 63.158 25.54 12.48 41.76 2.74
4965 6553 1.443194 GCGTTCGCCGAACTGTAGA 60.443 57.895 25.54 0.00 40.05 2.59
4966 6554 1.671880 GCGTTCGCCGAACTGTAGAC 61.672 60.000 25.54 6.37 40.05 2.59
4967 6555 1.393597 CGTTCGCCGAACTGTAGACG 61.394 60.000 25.54 9.48 40.05 4.18
4969 6557 2.202570 CGCCGAACTGTAGACGGG 60.203 66.667 17.64 8.24 45.66 5.28
4970 6558 2.693762 CGCCGAACTGTAGACGGGA 61.694 63.158 17.64 0.00 45.66 5.14
4971 6559 1.588082 GCCGAACTGTAGACGGGAA 59.412 57.895 17.64 0.00 45.66 3.97
4972 6560 0.037975 GCCGAACTGTAGACGGGAAA 60.038 55.000 17.64 0.00 45.66 3.13
4973 6561 1.706443 CCGAACTGTAGACGGGAAAC 58.294 55.000 11.32 0.00 42.48 2.78
4974 6562 1.271656 CCGAACTGTAGACGGGAAACT 59.728 52.381 11.32 0.00 42.48 2.66
4975 6563 2.593257 CGAACTGTAGACGGGAAACTC 58.407 52.381 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
179 184 3.062042 GCAATTTTCCTGAACTGGCAAG 58.938 45.455 0.00 0.00 0.00 4.01
393 400 4.048504 CGTTGCATCACCGAGATACAATA 58.951 43.478 6.71 0.00 40.97 1.90
514 546 1.192757 CAAAATTGGCGACGACGTACA 59.807 47.619 9.33 5.97 41.98 2.90
570 609 8.073467 ACATTTTCTCACTTTAAAAAGGACCA 57.927 30.769 7.34 0.00 40.31 4.02
1973 2089 8.382030 TGTCATATATATGCCACTTCAGTTTG 57.618 34.615 16.59 0.00 33.76 2.93
2151 2271 3.737559 TTGAATCACCCTGGTAGCATT 57.262 42.857 0.00 0.00 0.00 3.56
2152 2272 3.624777 CTTTGAATCACCCTGGTAGCAT 58.375 45.455 0.00 0.00 0.00 3.79
2219 2339 9.671279 CATGTCATGGAATATAAGCTACCATTA 57.329 33.333 4.78 0.00 38.99 1.90
2966 3096 2.827755 TGTGACAGGGCCACTAATAGA 58.172 47.619 6.18 0.00 35.66 1.98
3297 3427 7.880713 TGCAATACTGTACTCCATTAACTCAAA 59.119 33.333 0.00 0.00 0.00 2.69
3486 3616 1.135257 CAGAGTGAAGCGACGGAGAAT 60.135 52.381 0.00 0.00 0.00 2.40
4348 4516 5.874261 TCATCGAAGAACACATTTGATGCTA 59.126 36.000 9.93 0.00 43.68 3.49
4839 6427 9.950680 CCACATCTCTTTGCGTAAATTAATTAT 57.049 29.630 0.01 0.00 0.00 1.28
4840 6428 7.913297 GCCACATCTCTTTGCGTAAATTAATTA 59.087 33.333 0.01 0.00 0.00 1.40
4841 6429 6.751888 GCCACATCTCTTTGCGTAAATTAATT 59.248 34.615 0.00 0.00 0.00 1.40
4842 6430 6.265577 GCCACATCTCTTTGCGTAAATTAAT 58.734 36.000 0.00 0.00 0.00 1.40
4843 6431 5.392595 GGCCACATCTCTTTGCGTAAATTAA 60.393 40.000 0.00 0.00 0.00 1.40
4844 6432 4.095782 GGCCACATCTCTTTGCGTAAATTA 59.904 41.667 0.00 0.00 0.00 1.40
4845 6433 3.119495 GGCCACATCTCTTTGCGTAAATT 60.119 43.478 0.00 0.00 0.00 1.82
4846 6434 2.423538 GGCCACATCTCTTTGCGTAAAT 59.576 45.455 0.00 0.00 0.00 1.40
4847 6435 1.810151 GGCCACATCTCTTTGCGTAAA 59.190 47.619 0.00 0.00 0.00 2.01
4848 6436 1.003118 AGGCCACATCTCTTTGCGTAA 59.997 47.619 5.01 0.00 0.00 3.18
4849 6437 0.613260 AGGCCACATCTCTTTGCGTA 59.387 50.000 5.01 0.00 0.00 4.42
4850 6438 0.957395 CAGGCCACATCTCTTTGCGT 60.957 55.000 5.01 0.00 0.00 5.24
4851 6439 1.651240 CCAGGCCACATCTCTTTGCG 61.651 60.000 5.01 0.00 0.00 4.85
4852 6440 1.941999 GCCAGGCCACATCTCTTTGC 61.942 60.000 5.01 0.00 0.00 3.68
4853 6441 1.651240 CGCCAGGCCACATCTCTTTG 61.651 60.000 5.01 0.00 0.00 2.77
4854 6442 1.377725 CGCCAGGCCACATCTCTTT 60.378 57.895 5.01 0.00 0.00 2.52
4855 6443 2.270205 CGCCAGGCCACATCTCTT 59.730 61.111 5.01 0.00 0.00 2.85
4856 6444 3.005539 ACGCCAGGCCACATCTCT 61.006 61.111 5.01 0.00 0.00 3.10
4857 6445 2.512515 GACGCCAGGCCACATCTC 60.513 66.667 5.01 0.00 0.00 2.75
4858 6446 4.457496 CGACGCCAGGCCACATCT 62.457 66.667 5.01 0.00 0.00 2.90
4859 6447 3.950794 TTCGACGCCAGGCCACATC 62.951 63.158 5.01 0.00 0.00 3.06
4860 6448 3.958147 CTTCGACGCCAGGCCACAT 62.958 63.158 5.01 0.00 0.00 3.21
4861 6449 4.680237 CTTCGACGCCAGGCCACA 62.680 66.667 5.01 0.00 0.00 4.17
4870 6458 1.421410 ATCGACATTGGCTTCGACGC 61.421 55.000 5.12 5.12 46.41 5.19
4871 6459 0.298707 CATCGACATTGGCTTCGACG 59.701 55.000 0.60 0.00 46.41 5.12
4872 6460 0.026803 GCATCGACATTGGCTTCGAC 59.973 55.000 0.60 0.00 46.41 4.20
4874 6462 1.011904 CGCATCGACATTGGCTTCG 60.012 57.895 0.00 0.00 36.55 3.79
4875 6463 1.353103 CCGCATCGACATTGGCTTC 59.647 57.895 0.00 0.00 0.00 3.86
4876 6464 2.114670 CCCGCATCGACATTGGCTT 61.115 57.895 0.00 0.00 0.00 4.35
4877 6465 2.514592 CCCGCATCGACATTGGCT 60.515 61.111 0.00 0.00 0.00 4.75
4878 6466 3.585990 CCCCGCATCGACATTGGC 61.586 66.667 0.00 0.00 0.00 4.52
4879 6467 3.585990 GCCCCGCATCGACATTGG 61.586 66.667 0.00 0.00 0.00 3.16
4880 6468 3.940640 CGCCCCGCATCGACATTG 61.941 66.667 0.00 0.00 0.00 2.82
4881 6469 4.467084 ACGCCCCGCATCGACATT 62.467 61.111 0.00 0.00 0.00 2.71
4882 6470 4.891727 GACGCCCCGCATCGACAT 62.892 66.667 0.00 0.00 0.00 3.06
4901 6489 2.523015 CGAATTCAGGCTTTGTCATGC 58.477 47.619 6.22 0.00 0.00 4.06
4902 6490 2.095110 TGCGAATTCAGGCTTTGTCATG 60.095 45.455 6.22 0.00 0.00 3.07
4903 6491 2.161855 TGCGAATTCAGGCTTTGTCAT 58.838 42.857 6.22 0.00 0.00 3.06
4904 6492 1.536766 CTGCGAATTCAGGCTTTGTCA 59.463 47.619 6.22 0.00 0.00 3.58
4905 6493 1.135575 CCTGCGAATTCAGGCTTTGTC 60.136 52.381 6.22 0.00 46.11 3.18
4906 6494 0.883833 CCTGCGAATTCAGGCTTTGT 59.116 50.000 6.22 0.00 46.11 2.83
4907 6495 3.708195 CCTGCGAATTCAGGCTTTG 57.292 52.632 6.22 0.00 46.11 2.77
4922 6510 4.410400 GGGACTTGGACCGCCCTG 62.410 72.222 0.00 0.00 37.59 4.45
4925 6513 3.282374 ATTGGGGACTTGGACCGCC 62.282 63.158 0.00 0.00 39.18 6.13
4926 6514 2.046285 CATTGGGGACTTGGACCGC 61.046 63.158 0.00 0.00 40.13 5.68
4927 6515 2.046285 GCATTGGGGACTTGGACCG 61.046 63.158 0.00 0.00 0.00 4.79
4928 6516 2.046285 CGCATTGGGGACTTGGACC 61.046 63.158 0.00 0.00 0.00 4.46
4929 6517 2.046285 CCGCATTGGGGACTTGGAC 61.046 63.158 14.33 0.00 37.91 4.02
4930 6518 2.354729 CCGCATTGGGGACTTGGA 59.645 61.111 14.33 0.00 37.91 3.53
4931 6519 3.451894 GCCGCATTGGGGACTTGG 61.452 66.667 22.88 0.00 37.91 3.61
4947 6535 1.443194 TCTACAGTTCGGCGAACGC 60.443 57.895 37.63 21.92 45.96 4.84
4948 6536 1.393597 CGTCTACAGTTCGGCGAACG 61.394 60.000 37.63 32.89 45.96 3.95
4949 6537 1.069378 CCGTCTACAGTTCGGCGAAC 61.069 60.000 37.86 37.86 42.25 3.95
4950 6538 1.210931 CCGTCTACAGTTCGGCGAA 59.789 57.895 19.83 19.83 37.90 4.70
4951 6539 2.693762 CCCGTCTACAGTTCGGCGA 61.694 63.158 4.99 4.99 42.48 5.54
4952 6540 2.202570 CCCGTCTACAGTTCGGCG 60.203 66.667 0.00 0.00 42.48 6.46
4953 6541 0.037975 TTTCCCGTCTACAGTTCGGC 60.038 55.000 0.00 0.00 42.48 5.54
4954 6542 1.271656 AGTTTCCCGTCTACAGTTCGG 59.728 52.381 0.00 0.00 43.30 4.30
4955 6543 2.593257 GAGTTTCCCGTCTACAGTTCG 58.407 52.381 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.