Multiple sequence alignment - TraesCS3A01G266100

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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 TraesCS3A01G266100 chr3A 100.000 5637 0 0 1 5637 490612343 490617979 0.000000e+00 10410.0
1 TraesCS3A01G266100 chr3A 94.366 142 8 0 2312 2453 490614484 490614625 9.510000e-53 219.0
2 TraesCS3A01G266100 chr3A 94.366 142 8 0 2142 2283 490614654 490614795 9.510000e-53 219.0
3 TraesCS3A01G266100 chr3A 95.789 95 4 0 2049 2143 601131332 601131426 2.720000e-33 154.0
4 TraesCS3A01G266100 chr3A 92.391 92 7 0 5485 5576 556845934 556845843 1.270000e-26 132.0
5 TraesCS3A01G266100 chr3A 88.000 100 8 3 2055 2150 635387505 635387604 1.280000e-21 115.0
6 TraesCS3A01G266100 chr3D 97.435 4951 101 9 1 4943 369402783 369407715 0.000000e+00 8416.0
7 TraesCS3A01G266100 chr3D 94.397 232 11 2 4951 5181 369409065 369409295 6.950000e-94 355.0
8 TraesCS3A01G266100 chr3D 88.142 253 1 6 5262 5489 369409312 369409560 2.000000e-69 274.0
9 TraesCS3A01G266100 chr3D 99.296 142 1 0 2312 2453 369404926 369405067 2.020000e-64 257.0
10 TraesCS3A01G266100 chr3D 94.366 142 8 0 2142 2283 369405096 369405237 9.510000e-53 219.0
11 TraesCS3A01G266100 chr3D 95.789 95 4 0 2049 2143 458883365 458883459 2.720000e-33 154.0
12 TraesCS3A01G266100 chr3D 95.652 69 2 1 5570 5637 369409558 369409626 5.970000e-20 110.0
13 TraesCS3A01G266100 chr3D 81.538 130 11 4 2032 2148 134505021 134505150 1.670000e-15 95.3
14 TraesCS3A01G266100 chr3D 85.714 91 9 3 2064 2150 496120321 496120411 6.010000e-15 93.5
15 TraesCS3A01G266100 chr3D 84.615 91 14 0 2056 2146 458883452 458883362 2.160000e-14 91.6
16 TraesCS3A01G266100 chr3B 96.925 2634 61 9 2312 4943 480340905 480343520 0.000000e+00 4397.0
17 TraesCS3A01G266100 chr3B 94.363 1703 67 6 584 2283 480339370 480341046 0.000000e+00 2586.0
18 TraesCS3A01G266100 chr3B 94.422 251 12 2 4951 5200 480343561 480343810 8.860000e-103 385.0
19 TraesCS3A01G266100 chr3B 88.889 117 8 3 5256 5369 480343807 480343921 7.620000e-29 139.0
20 TraesCS3A01G266100 chr3B 92.632 95 3 1 2049 2143 263261030 263260940 3.540000e-27 134.0
21 TraesCS3A01G266100 chr3B 95.312 64 2 1 5570 5632 480369492 480369555 3.590000e-17 100.0
22 TraesCS3A01G266100 chr3B 97.872 47 1 0 5210 5256 5596417 5596371 1.300000e-11 82.4
23 TraesCS3A01G266100 chr3B 96.000 50 2 0 5207 5256 5735013 5735062 1.300000e-11 82.4
24 TraesCS3A01G266100 chr3B 88.525 61 5 2 434 492 480332231 480332291 7.830000e-09 73.1
25 TraesCS3A01G266100 chr7A 85.849 106 14 1 5472 5577 94634878 94634982 1.660000e-20 111.0
26 TraesCS3A01G266100 chr7A 94.643 56 3 0 5201 5256 555465433 555465378 2.800000e-13 87.9
27 TraesCS3A01G266100 chr1D 87.037 108 1 5 2049 2143 335588794 335588901 5.970000e-20 110.0
28 TraesCS3A01G266100 chr1D 83.333 102 14 3 5479 5578 458575583 458575683 2.160000e-14 91.6
29 TraesCS3A01G266100 chr1D 91.667 60 5 0 5197 5256 10816141 10816200 3.620000e-12 84.2
30 TraesCS3A01G266100 chr2D 89.535 86 7 2 5488 5572 52018996 52018912 2.150000e-19 108.0
31 TraesCS3A01G266100 chr2D 97.872 47 1 0 5210 5256 590363621 590363575 1.300000e-11 82.4
32 TraesCS3A01G266100 chr5B 85.859 99 14 0 5486 5584 12859251 12859153 7.720000e-19 106.0
33 TraesCS3A01G266100 chr6A 86.667 90 12 0 5488 5577 250692228 250692317 3.590000e-17 100.0
34 TraesCS3A01G266100 chr6A 85.556 90 13 0 5488 5577 250609439 250609528 1.670000e-15 95.3
35 TraesCS3A01G266100 chr1B 84.946 93 14 0 5481 5573 651955960 651956052 1.670000e-15 95.3
36 TraesCS3A01G266100 chr5D 84.848 99 7 7 5481 5576 455323421 455323328 6.010000e-15 93.5
37 TraesCS3A01G266100 chrUn 97.872 47 1 0 5210 5256 110731968 110732014 1.300000e-11 82.4
38 TraesCS3A01G266100 chrUn 97.872 47 1 0 5210 5256 232649824 232649870 1.300000e-11 82.4
39 TraesCS3A01G266100 chr5A 96.000 50 2 0 5207 5256 666314291 666314340 1.300000e-11 82.4
40 TraesCS3A01G266100 chr2A 96.078 51 1 1 5210 5259 778801910 778801960 1.300000e-11 82.4


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 TraesCS3A01G266100 chr3A 490612343 490617979 5636 False 3616.000000 10410 96.244000 1 5637 3 chr3A.!!$F3 5636
1 TraesCS3A01G266100 chr3D 369402783 369409626 6843 False 1605.166667 8416 94.881333 1 5637 6 chr3D.!!$F4 5636
2 TraesCS3A01G266100 chr3B 480339370 480343921 4551 False 1876.750000 4397 93.649750 584 5369 4 chr3B.!!$F4 4785

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
547 554 0.549950 ACTGGGCCTGAGGAATCATG 59.450 55.000 18.12 0.0 0.00 3.07 F
1232 1240 0.749649 CACTCCTCTTCCTCCCATCG 59.250 60.000 0.00 0.0 0.00 3.84 F
1820 1828 1.336795 GCCTGCCATTAAAGCGTTTGT 60.337 47.619 0.00 0.0 0.00 2.83 F
2252 2261 1.268845 GGGTGCAAAAGTGTGTTACCG 60.269 52.381 0.00 0.0 32.15 4.02 F
3615 3624 1.134521 TGGCCTGCTGATAACCTTACG 60.135 52.381 3.32 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1382 1390 0.251916 TAACCATGGGAAGCCACTCG 59.748 55.000 18.09 0.0 0.00 4.18 R
2252 2261 1.070758 TGCTATGAGGGAGGAATTCGC 59.929 52.381 0.00 0.0 38.95 4.70 R
3295 3304 0.107703 GGAACGCACCATGAGATCCA 60.108 55.000 0.00 0.0 38.60 3.41 R
3900 3909 0.625849 AGCAACTATTGGGAGGGGTG 59.374 55.000 0.00 0.0 0.00 4.61 R
5605 6984 0.827368 AACATGGCGTTTTGGTTGGT 59.173 45.000 0.00 0.0 32.35 3.67 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
80 81 5.243981 CACTGTGGAGAAAGTTCTGATGAT 58.756 41.667 0.00 0.00 37.73 2.45
85 86 7.428020 TGTGGAGAAAGTTCTGATGATTTTTG 58.572 34.615 0.00 0.00 37.73 2.44
114 115 2.595536 CGAATGCAAAAGAAATCTGCGG 59.404 45.455 0.00 0.00 38.97 5.69
176 177 2.995547 CCTTTGGGGGTCTACCGG 59.004 66.667 0.00 0.00 41.60 5.28
209 210 1.363629 TGGTAGGGTTAGTGGCCTACT 59.636 52.381 3.32 8.73 43.56 2.57
210 211 2.586838 TGGTAGGGTTAGTGGCCTACTA 59.413 50.000 3.32 7.64 40.89 1.82
214 215 1.686115 GGGTTAGTGGCCTACTACCGA 60.686 57.143 3.32 0.00 41.48 4.69
229 230 1.260544 ACCGAGGTTAGTGGTGGTAC 58.739 55.000 0.00 0.00 33.91 3.34
230 231 1.203100 ACCGAGGTTAGTGGTGGTACT 60.203 52.381 0.00 0.00 33.91 2.73
256 258 1.078709 CCACATAGGCACAGTCAACG 58.921 55.000 0.00 0.00 0.00 4.10
280 282 3.066814 GACCAGCGTCTACCGGGT 61.067 66.667 6.32 4.46 35.99 5.28
302 304 3.268330 GGTAGCCTGTTAGCTTTACCAC 58.732 50.000 0.00 0.00 41.41 4.16
304 306 1.084289 GCCTGTTAGCTTTACCACCG 58.916 55.000 0.00 0.00 0.00 4.94
354 356 3.444388 AGACCGTGCAAAACTTTAAACCA 59.556 39.130 0.00 0.00 0.00 3.67
355 357 3.776340 ACCGTGCAAAACTTTAAACCAG 58.224 40.909 0.00 0.00 0.00 4.00
547 554 0.549950 ACTGGGCCTGAGGAATCATG 59.450 55.000 18.12 0.00 0.00 3.07
560 567 8.597167 CCTGAGGAATCATGTATAGTCCAAATA 58.403 37.037 0.00 0.00 0.00 1.40
751 759 3.702555 GCTATACGGCGCGCCTTG 61.703 66.667 43.60 32.52 0.00 3.61
859 867 4.366684 GCCCTTCCCCCACCACTG 62.367 72.222 0.00 0.00 0.00 3.66
1232 1240 0.749649 CACTCCTCTTCCTCCCATCG 59.250 60.000 0.00 0.00 0.00 3.84
1307 1315 6.308371 TCTTCTTTTTCACCGTGGTTATTC 57.692 37.500 0.00 0.00 0.00 1.75
1360 1368 3.311596 GCGATCGGTACCTTAGCAAAATT 59.688 43.478 18.30 0.00 0.00 1.82
1361 1369 4.508861 GCGATCGGTACCTTAGCAAAATTA 59.491 41.667 18.30 0.00 0.00 1.40
1373 1381 8.293699 CCTTAGCAAAATTAAGGGTTGAGTAT 57.706 34.615 3.63 0.00 42.20 2.12
1437 1445 1.963515 GGCAAACCATCCATATCCACC 59.036 52.381 0.00 0.00 35.26 4.61
1820 1828 1.336795 GCCTGCCATTAAAGCGTTTGT 60.337 47.619 0.00 0.00 0.00 2.83
1936 1944 8.615878 AGAGTAATGCTTGTAAACATACACAA 57.384 30.769 0.00 0.00 33.76 3.33
1993 2001 7.669427 TGAAGTTAAAGACATGCCAATTTCAT 58.331 30.769 0.00 0.00 0.00 2.57
2028 2037 3.368013 CGCAAGTGAAGGGTGTCATACTA 60.368 47.826 0.00 0.00 0.00 1.82
2149 2158 2.177734 GGACGGAGGGAGTAGTTCTTT 58.822 52.381 0.00 0.00 0.00 2.52
2158 2167 3.323979 GGGAGTAGTTCTTTCCTGTGTCA 59.676 47.826 0.00 0.00 0.00 3.58
2191 2200 7.010606 TGTACAGTTTTATTACAAATGTCGCG 58.989 34.615 0.00 0.00 0.00 5.87
2209 2218 2.011548 GCGGGGAAATGCCAAAATTCC 61.012 52.381 0.00 0.00 41.53 3.01
2239 2248 3.896888 ACAAATGAAAGATCTGGGTGCAA 59.103 39.130 0.00 0.00 0.00 4.08
2252 2261 1.268845 GGGTGCAAAAGTGTGTTACCG 60.269 52.381 0.00 0.00 32.15 4.02
2290 2299 1.652124 GCAAGCATTTTCAGCGACATG 59.348 47.619 0.00 0.00 37.01 3.21
2608 2617 5.783360 TGGTTACTCCTTACAATCCTCAGAA 59.217 40.000 0.00 0.00 37.07 3.02
2852 2861 2.034053 GGATTTCAAACGTGCTGGAACA 59.966 45.455 0.00 0.00 0.00 3.18
3131 3140 5.663106 TCCTGACTGGAAGCTTGATATTACT 59.337 40.000 2.10 0.00 42.94 2.24
3295 3304 2.753029 GCTCTTGGAGTGCCCACT 59.247 61.111 0.00 0.00 46.62 4.00
3438 3447 3.173953 TCTTACCGGGTTACTTCAGGA 57.826 47.619 4.31 0.00 0.00 3.86
3615 3624 1.134521 TGGCCTGCTGATAACCTTACG 60.135 52.381 3.32 0.00 0.00 3.18
3775 3784 6.627287 GCTTTTTGTTCAGGTTACTTGAAGGT 60.627 38.462 10.16 0.00 0.00 3.50
3793 3802 1.862827 GGTGTGGTACGTTCTGTGAAC 59.137 52.381 0.00 0.77 0.00 3.18
3900 3909 0.877213 CCTTTTGCACTGCTTGTGGC 60.877 55.000 1.98 5.62 46.27 5.01
3997 4006 2.926778 AGGGCAGTGCTGATAATCTC 57.073 50.000 16.11 0.00 0.00 2.75
3999 4008 1.544314 GGGCAGTGCTGATAATCTCCC 60.544 57.143 16.11 0.00 0.00 4.30
4008 4017 2.700897 CTGATAATCTCCCAACCGAGGT 59.299 50.000 0.00 0.00 0.00 3.85
4093 4102 8.284945 TGATTGTTTCACTACTACCGTACTAT 57.715 34.615 0.00 0.00 0.00 2.12
4412 4421 5.709631 TGTGCTTCAAATATACTTCTTGCCA 59.290 36.000 0.00 0.00 0.00 4.92
4534 4543 1.220749 GGAATGGAGTAGCGCCACA 59.779 57.895 9.06 0.00 35.91 4.17
4659 4668 6.928520 AGATTGTTTGATCTGGGAATGTTTC 58.071 36.000 0.00 0.00 35.13 2.78
4869 4880 1.167851 CTGGATTGTTGTGGACGCAT 58.832 50.000 0.00 0.00 0.00 4.73
4870 4881 1.131126 CTGGATTGTTGTGGACGCATC 59.869 52.381 0.00 0.00 0.00 3.91
4871 4882 1.164411 GGATTGTTGTGGACGCATCA 58.836 50.000 0.00 0.00 0.00 3.07
4872 4883 1.135689 GGATTGTTGTGGACGCATCAC 60.136 52.381 0.00 0.00 35.82 3.06
4873 4884 1.535028 GATTGTTGTGGACGCATCACA 59.465 47.619 2.57 2.57 42.57 3.58
4876 4887 3.395210 TTGTGGACGCATCACAACT 57.605 47.368 12.66 0.00 46.29 3.16
4943 4954 0.527565 CAGTGGGCTGTGCAAATACC 59.472 55.000 0.00 0.00 37.92 2.73
4946 4957 1.550072 GTGGGCTGTGCAAATACCAAT 59.450 47.619 1.50 0.00 0.00 3.16
4947 4958 1.549620 TGGGCTGTGCAAATACCAATG 59.450 47.619 0.00 0.00 0.00 2.82
4949 4960 1.205417 GGCTGTGCAAATACCAATGCT 59.795 47.619 0.00 0.00 42.97 3.79
5127 6481 5.698832 TCGAAATGATAACCTGCAAAACTG 58.301 37.500 0.00 0.00 0.00 3.16
5188 6542 8.244113 AGCAACATTGATTCTGCATATCATATG 58.756 33.333 18.94 18.94 37.26 1.78
5190 6544 9.556030 CAACATTGATTCTGCATATCATATGAC 57.444 33.333 22.74 0.93 32.43 3.06
5210 6564 5.927030 TGACTGAAATTTATTGTCTCGCAC 58.073 37.500 14.54 0.00 0.00 5.34
5211 6565 5.700832 TGACTGAAATTTATTGTCTCGCACT 59.299 36.000 14.54 0.00 0.00 4.40
5212 6566 6.128553 TGACTGAAATTTATTGTCTCGCACTC 60.129 38.462 14.54 0.00 0.00 3.51
5213 6567 5.122396 ACTGAAATTTATTGTCTCGCACTCC 59.878 40.000 0.00 0.00 0.00 3.85
5214 6568 4.394920 TGAAATTTATTGTCTCGCACTCCC 59.605 41.667 0.00 0.00 0.00 4.30
5215 6569 3.914426 ATTTATTGTCTCGCACTCCCT 57.086 42.857 0.00 0.00 0.00 4.20
5216 6570 2.961526 TTATTGTCTCGCACTCCCTC 57.038 50.000 0.00 0.00 0.00 4.30
5217 6571 2.145397 TATTGTCTCGCACTCCCTCT 57.855 50.000 0.00 0.00 0.00 3.69
5218 6572 0.534412 ATTGTCTCGCACTCCCTCTG 59.466 55.000 0.00 0.00 0.00 3.35
5219 6573 0.827925 TTGTCTCGCACTCCCTCTGT 60.828 55.000 0.00 0.00 0.00 3.41
5220 6574 0.037734 TGTCTCGCACTCCCTCTGTA 59.962 55.000 0.00 0.00 0.00 2.74
5221 6575 1.174783 GTCTCGCACTCCCTCTGTAA 58.825 55.000 0.00 0.00 0.00 2.41
5222 6576 1.544691 GTCTCGCACTCCCTCTGTAAA 59.455 52.381 0.00 0.00 0.00 2.01
5223 6577 1.544691 TCTCGCACTCCCTCTGTAAAC 59.455 52.381 0.00 0.00 0.00 2.01
5224 6578 1.546476 CTCGCACTCCCTCTGTAAACT 59.454 52.381 0.00 0.00 0.00 2.66
5225 6579 2.753452 CTCGCACTCCCTCTGTAAACTA 59.247 50.000 0.00 0.00 0.00 2.24
5226 6580 2.753452 TCGCACTCCCTCTGTAAACTAG 59.247 50.000 0.00 0.00 0.00 2.57
5227 6581 2.492484 CGCACTCCCTCTGTAAACTAGT 59.508 50.000 0.00 0.00 0.00 2.57
5228 6582 3.693085 CGCACTCCCTCTGTAAACTAGTA 59.307 47.826 0.00 0.00 0.00 1.82
5229 6583 4.338682 CGCACTCCCTCTGTAAACTAGTAT 59.661 45.833 0.00 0.00 0.00 2.12
5230 6584 5.530171 CGCACTCCCTCTGTAAACTAGTATA 59.470 44.000 0.00 0.00 0.00 1.47
5231 6585 6.039047 CGCACTCCCTCTGTAAACTAGTATAA 59.961 42.308 0.00 0.00 0.00 0.98
5232 6586 7.427214 GCACTCCCTCTGTAAACTAGTATAAG 58.573 42.308 0.00 0.00 0.00 1.73
5233 6587 7.284944 GCACTCCCTCTGTAAACTAGTATAAGA 59.715 40.741 0.00 0.00 0.00 2.10
5234 6588 8.842280 CACTCCCTCTGTAAACTAGTATAAGAG 58.158 40.741 13.80 13.80 0.00 2.85
5235 6589 7.503230 ACTCCCTCTGTAAACTAGTATAAGAGC 59.497 40.741 14.73 0.00 0.00 4.09
5236 6590 6.485984 TCCCTCTGTAAACTAGTATAAGAGCG 59.514 42.308 14.73 9.57 0.00 5.03
5237 6591 6.262720 CCCTCTGTAAACTAGTATAAGAGCGT 59.737 42.308 14.73 0.00 0.00 5.07
5238 6592 7.201803 CCCTCTGTAAACTAGTATAAGAGCGTT 60.202 40.741 14.73 0.00 0.00 4.84
5239 6593 8.189460 CCTCTGTAAACTAGTATAAGAGCGTTT 58.811 37.037 14.73 0.00 0.00 3.60
5415 6772 1.307097 TGTGGCCATTTTTGCTTTGC 58.693 45.000 9.72 0.00 0.00 3.68
5438 6817 5.561145 GCACAATGCTGAAATGATGCAAAAA 60.561 36.000 0.00 0.00 40.96 1.94
5497 6876 7.817910 TTTAGAAAATAAGGTACTCCCTCCA 57.182 36.000 0.00 0.00 45.47 3.86
5498 6877 8.401955 TTTAGAAAATAAGGTACTCCCTCCAT 57.598 34.615 0.00 0.00 45.47 3.41
5499 6878 6.502074 AGAAAATAAGGTACTCCCTCCATC 57.498 41.667 0.00 0.00 45.47 3.51
5500 6879 5.369993 AGAAAATAAGGTACTCCCTCCATCC 59.630 44.000 0.00 0.00 45.47 3.51
5501 6880 2.789323 TAAGGTACTCCCTCCATCCC 57.211 55.000 0.00 0.00 45.47 3.85
5502 6881 0.722676 AAGGTACTCCCTCCATCCCA 59.277 55.000 0.00 0.00 45.47 4.37
5503 6882 0.952659 AGGTACTCCCTCCATCCCAT 59.047 55.000 0.00 0.00 40.71 4.00
5504 6883 2.161624 AGGTACTCCCTCCATCCCATA 58.838 52.381 0.00 0.00 40.71 2.74
5505 6884 2.527057 AGGTACTCCCTCCATCCCATAA 59.473 50.000 0.00 0.00 40.71 1.90
5506 6885 3.146833 AGGTACTCCCTCCATCCCATAAT 59.853 47.826 0.00 0.00 40.71 1.28
5507 6886 4.363217 AGGTACTCCCTCCATCCCATAATA 59.637 45.833 0.00 0.00 40.71 0.98
5508 6887 5.018962 AGGTACTCCCTCCATCCCATAATAT 59.981 44.000 0.00 0.00 40.71 1.28
5509 6888 6.223994 AGGTACTCCCTCCATCCCATAATATA 59.776 42.308 0.00 0.00 40.71 0.86
5510 6889 6.906901 GGTACTCCCTCCATCCCATAATATAA 59.093 42.308 0.00 0.00 0.00 0.98
5511 6890 7.071321 GGTACTCCCTCCATCCCATAATATAAG 59.929 44.444 0.00 0.00 0.00 1.73
5512 6891 6.826727 ACTCCCTCCATCCCATAATATAAGA 58.173 40.000 0.00 0.00 0.00 2.10
5513 6892 7.263901 ACTCCCTCCATCCCATAATATAAGAA 58.736 38.462 0.00 0.00 0.00 2.52
5514 6893 7.182930 ACTCCCTCCATCCCATAATATAAGAAC 59.817 40.741 0.00 0.00 0.00 3.01
5515 6894 7.028760 TCCCTCCATCCCATAATATAAGAACA 58.971 38.462 0.00 0.00 0.00 3.18
5516 6895 7.688534 TCCCTCCATCCCATAATATAAGAACAT 59.311 37.037 0.00 0.00 0.00 2.71
5517 6896 8.339247 CCCTCCATCCCATAATATAAGAACATT 58.661 37.037 0.00 0.00 0.00 2.71
5518 6897 9.759473 CCTCCATCCCATAATATAAGAACATTT 57.241 33.333 0.00 0.00 0.00 2.32
5545 6924 8.867112 TCAATCTATATTAGCTCGAAAAACGT 57.133 30.769 0.00 0.00 43.13 3.99
5546 6925 9.309516 TCAATCTATATTAGCTCGAAAAACGTT 57.690 29.630 0.00 0.00 43.13 3.99
5547 6926 9.569212 CAATCTATATTAGCTCGAAAAACGTTC 57.431 33.333 0.00 0.00 43.13 3.95
5548 6927 9.530633 AATCTATATTAGCTCGAAAAACGTTCT 57.469 29.630 0.00 0.00 43.13 3.01
5549 6928 8.922058 TCTATATTAGCTCGAAAAACGTTCTT 57.078 30.769 0.00 0.00 43.13 2.52
5552 6931 6.774354 ATTAGCTCGAAAAACGTTCTTACA 57.226 33.333 0.00 0.00 43.13 2.41
5553 6932 6.774354 TTAGCTCGAAAAACGTTCTTACAT 57.226 33.333 0.00 0.00 43.13 2.29
5554 6933 5.668558 AGCTCGAAAAACGTTCTTACATT 57.331 34.783 0.00 0.00 43.13 2.71
5555 6934 6.774354 AGCTCGAAAAACGTTCTTACATTA 57.226 33.333 0.00 0.00 43.13 1.90
5556 6935 7.360575 AGCTCGAAAAACGTTCTTACATTAT 57.639 32.000 0.00 0.00 43.13 1.28
5557 6936 7.234384 AGCTCGAAAAACGTTCTTACATTATG 58.766 34.615 0.00 0.00 43.13 1.90
5558 6937 7.117236 AGCTCGAAAAACGTTCTTACATTATGA 59.883 33.333 0.00 0.00 43.13 2.15
5559 6938 7.422746 GCTCGAAAAACGTTCTTACATTATGAG 59.577 37.037 0.00 3.64 43.13 2.90
5560 6939 8.523523 TCGAAAAACGTTCTTACATTATGAGA 57.476 30.769 0.00 0.00 43.13 3.27
5561 6940 8.430063 TCGAAAAACGTTCTTACATTATGAGAC 58.570 33.333 0.00 0.00 43.13 3.36
5562 6941 8.218441 CGAAAAACGTTCTTACATTATGAGACA 58.782 33.333 0.00 0.00 37.22 3.41
5563 6942 9.872757 GAAAAACGTTCTTACATTATGAGACAA 57.127 29.630 0.00 0.00 0.00 3.18
5565 6944 9.878599 AAAACGTTCTTACATTATGAGACAAAG 57.121 29.630 0.00 0.00 0.00 2.77
5566 6945 7.596749 ACGTTCTTACATTATGAGACAAAGG 57.403 36.000 0.00 0.00 0.00 3.11
5567 6946 6.594159 ACGTTCTTACATTATGAGACAAAGGG 59.406 38.462 0.00 0.00 0.00 3.95
5568 6947 6.816640 CGTTCTTACATTATGAGACAAAGGGA 59.183 38.462 0.00 0.00 0.00 4.20
5605 6984 2.936919 TCAAGCTTCAAAGGCTGAGA 57.063 45.000 0.00 0.00 40.19 3.27
5626 7006 1.202463 CCAACCAAAACGCCATGTTCA 60.202 47.619 0.00 0.00 40.84 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 2.494918 CCCTGTCGTCATCGTCCC 59.505 66.667 0.00 0.00 38.33 4.46
15 16 2.494918 CCCCTGTCGTCATCGTCC 59.505 66.667 0.00 0.00 38.33 4.79
25 26 2.677848 GGGCTTCTTCCCCCTGTC 59.322 66.667 0.00 0.00 40.51 3.51
80 81 3.639716 TGCATTCGACATCTGCAAAAA 57.360 38.095 8.26 0.00 42.53 1.94
85 86 3.476295 TCTTTTGCATTCGACATCTGC 57.524 42.857 0.00 0.00 36.45 4.26
176 177 0.320247 CCTACCATCTGATCCTGCGC 60.320 60.000 0.00 0.00 0.00 6.09
209 210 2.041620 AGTACCACCACTAACCTCGGTA 59.958 50.000 0.00 0.00 0.00 4.02
210 211 1.203100 AGTACCACCACTAACCTCGGT 60.203 52.381 0.00 0.00 0.00 4.69
214 215 3.271153 AAGGAGTACCACCACTAACCT 57.729 47.619 8.98 0.00 38.94 3.50
266 268 2.048023 TACCACCCGGTAGACGCTG 61.048 63.158 0.00 0.00 46.71 5.18
280 282 2.907696 TGGTAAAGCTAACAGGCTACCA 59.092 45.455 6.93 6.93 44.09 3.25
302 304 0.821517 TCTACCACCATACACAGCGG 59.178 55.000 0.00 0.00 0.00 5.52
304 306 4.730949 TTAGTCTACCACCATACACAGC 57.269 45.455 0.00 0.00 0.00 4.40
354 356 9.236006 ACATTGAGTTTAGCATAAAATGACTCT 57.764 29.630 0.00 0.00 33.80 3.24
355 357 9.846248 AACATTGAGTTTAGCATAAAATGACTC 57.154 29.630 0.00 0.00 37.03 3.36
432 434 8.672815 CCCAAAATCACTGTTTTTATTTTGTGT 58.327 29.630 14.67 0.00 43.14 3.72
441 443 5.125257 CCAAAAGCCCAAAATCACTGTTTTT 59.875 36.000 0.00 0.00 0.00 1.94
547 554 9.660180 GGAATCTCTTGGATATTTGGACTATAC 57.340 37.037 0.00 0.00 33.71 1.47
560 567 3.201708 CAGGACCTTGGAATCTCTTGGAT 59.798 47.826 0.00 0.00 35.97 3.41
751 759 0.602060 AACGAGGAAGGTTCTCCGAC 59.398 55.000 0.00 0.00 40.75 4.79
1232 1240 3.503748 AGAGGTATGTGTTCTTTGCAAGC 59.496 43.478 0.00 0.00 0.00 4.01
1307 1315 8.746052 TACAAATTTATTGTACAGGGGATCTG 57.254 34.615 0.00 0.00 40.13 2.90
1360 1368 6.554784 TCGGGTATATCATACTCAACCCTTA 58.445 40.000 6.76 0.00 43.67 2.69
1361 1369 5.399991 TCGGGTATATCATACTCAACCCTT 58.600 41.667 6.76 0.00 43.67 3.95
1366 1374 4.219944 GCCACTCGGGTATATCATACTCAA 59.780 45.833 0.00 0.00 39.65 3.02
1373 1381 1.968493 GGAAGCCACTCGGGTATATCA 59.032 52.381 0.00 0.00 44.22 2.15
1382 1390 0.251916 TAACCATGGGAAGCCACTCG 59.748 55.000 18.09 0.00 0.00 4.18
1437 1445 4.675565 ACGATAAGATGAATACTTGACGCG 59.324 41.667 3.53 3.53 34.06 6.01
1820 1828 8.756486 AATAACCATCACAGATTTCATCATGA 57.244 30.769 0.00 0.00 33.16 3.07
1993 2001 5.989168 CCTTCACTTGCGTTATATCACCATA 59.011 40.000 0.00 0.00 0.00 2.74
2028 2037 9.654663 GGTTGTACTATTTACTCTTGACAATCT 57.345 33.333 0.00 0.00 0.00 2.40
2149 2158 5.221641 ACTGTACATTAAAGCTGACACAGGA 60.222 40.000 0.00 0.00 35.97 3.86
2189 2198 1.368641 GAATTTTGGCATTTCCCCGC 58.631 50.000 0.00 0.00 0.00 6.13
2191 2200 3.774766 ACTAGGAATTTTGGCATTTCCCC 59.225 43.478 16.36 4.70 39.83 4.81
2209 2218 6.320171 CCAGATCTTTCATTTGTTGCACTAG 58.680 40.000 0.00 0.00 0.00 2.57
2239 2248 2.224784 GGAATTCGCGGTAACACACTTT 59.775 45.455 6.13 0.00 0.00 2.66
2252 2261 1.070758 TGCTATGAGGGAGGAATTCGC 59.929 52.381 0.00 0.00 38.95 4.70
2290 2299 4.708726 ATGAATTAAAGCAGACACAGGC 57.291 40.909 0.00 0.00 0.00 4.85
2608 2617 8.462016 GTGATAATACTTCATTTGCCTGAACTT 58.538 33.333 0.00 0.00 31.98 2.66
2852 2861 2.953284 ATATGAGAGCAGCAGCCATT 57.047 45.000 0.00 0.00 43.56 3.16
3131 3140 1.770658 CCCTCCACATAATCAGAGGCA 59.229 52.381 0.00 0.00 43.86 4.75
3295 3304 0.107703 GGAACGCACCATGAGATCCA 60.108 55.000 0.00 0.00 38.60 3.41
3438 3447 8.757789 CGTTTGAAATATTTCATAGCAATGCAT 58.242 29.630 27.11 0.00 45.65 3.96
3615 3624 6.884280 ATTGAACAGGCCTATTATAACAGC 57.116 37.500 3.98 0.00 0.00 4.40
3775 3784 2.963548 TGTTCACAGAACGTACCACA 57.036 45.000 5.53 0.00 0.00 4.17
3793 3802 2.964740 TGGAACTTCTCGAGCAGATTG 58.035 47.619 19.24 2.34 0.00 2.67
3900 3909 0.625849 AGCAACTATTGGGAGGGGTG 59.374 55.000 0.00 0.00 0.00 4.61
3953 3962 5.879237 TGTTTTACTGGCATCGATTGATTC 58.121 37.500 0.00 0.00 30.49 2.52
3999 4008 7.394959 CATTTCCATGATCCAACCTCGGTTG 62.395 48.000 19.44 19.44 42.51 3.77
4008 4017 3.710724 TGAAGCCATTTCCATGATCCAA 58.289 40.909 0.00 0.00 34.77 3.53
4093 4102 4.771114 ACCATCGGGAATTTGACTGATA 57.229 40.909 0.00 0.00 38.05 2.15
4534 4543 8.932610 AGATGGACAAGAAACAGATACAGATAT 58.067 33.333 0.00 0.00 0.00 1.63
4659 4668 8.031864 ACATCTGTTACACTGTTCTAGATCTTG 58.968 37.037 0.00 0.00 0.00 3.02
4840 4851 3.758023 CACAACAATCCAGCATCCTTACA 59.242 43.478 0.00 0.00 0.00 2.41
4869 4880 4.404394 TCTGGACTACTTGTGAAGTTGTGA 59.596 41.667 8.05 0.00 45.20 3.58
4870 4881 4.693283 TCTGGACTACTTGTGAAGTTGTG 58.307 43.478 8.05 0.00 45.20 3.33
4872 4883 5.201713 TCTCTGGACTACTTGTGAAGTTG 57.798 43.478 0.00 0.00 42.81 3.16
4873 4884 7.179338 ACATATCTCTGGACTACTTGTGAAGTT 59.821 37.037 0.00 0.00 42.81 2.66
4874 4885 6.665680 ACATATCTCTGGACTACTTGTGAAGT 59.334 38.462 0.00 0.00 45.40 3.01
4875 4886 6.977502 CACATATCTCTGGACTACTTGTGAAG 59.022 42.308 0.00 0.00 35.20 3.02
4876 4887 6.628175 GCACATATCTCTGGACTACTTGTGAA 60.628 42.308 0.00 0.00 35.20 3.18
4943 4954 3.438087 CAGGTAGTTCAGGAACAGCATTG 59.562 47.826 14.06 3.05 43.47 2.82
4946 4957 1.347707 CCAGGTAGTTCAGGAACAGCA 59.652 52.381 14.06 0.00 43.47 4.41
4947 4958 1.348036 ACCAGGTAGTTCAGGAACAGC 59.652 52.381 14.06 9.43 43.47 4.40
4949 4960 2.632996 CAGACCAGGTAGTTCAGGAACA 59.367 50.000 14.06 0.00 43.47 3.18
5083 6437 5.468746 TCGAAAGTTTTCCTACACCAATGAG 59.531 40.000 0.00 0.00 33.68 2.90
5169 6523 9.563748 TTTCAGTCATATGATATGCAGAATCAA 57.436 29.630 16.05 8.22 36.95 2.57
5188 6542 6.170675 AGTGCGAGACAATAAATTTCAGTC 57.829 37.500 0.00 1.80 0.00 3.51
5190 6544 5.447818 GGGAGTGCGAGACAATAAATTTCAG 60.448 44.000 0.00 0.00 0.00 3.02
5207 6561 5.855740 ATACTAGTTTACAGAGGGAGTGC 57.144 43.478 0.00 0.00 0.00 4.40
5210 6564 7.308109 CGCTCTTATACTAGTTTACAGAGGGAG 60.308 44.444 24.21 9.71 40.49 4.30
5211 6565 6.485984 CGCTCTTATACTAGTTTACAGAGGGA 59.514 42.308 24.21 2.16 40.49 4.20
5212 6566 6.262720 ACGCTCTTATACTAGTTTACAGAGGG 59.737 42.308 25.26 25.26 42.53 4.30
5213 6567 7.261829 ACGCTCTTATACTAGTTTACAGAGG 57.738 40.000 20.49 16.22 0.00 3.69
5248 6602 9.423061 GTGCCAAAGAATGATGTAAACTATTTT 57.577 29.630 0.00 0.00 0.00 1.82
5249 6603 8.034804 GGTGCCAAAGAATGATGTAAACTATTT 58.965 33.333 0.00 0.00 0.00 1.40
5250 6604 7.178274 TGGTGCCAAAGAATGATGTAAACTATT 59.822 33.333 0.00 0.00 0.00 1.73
5251 6605 6.663093 TGGTGCCAAAGAATGATGTAAACTAT 59.337 34.615 0.00 0.00 0.00 2.12
5252 6606 6.007076 TGGTGCCAAAGAATGATGTAAACTA 58.993 36.000 0.00 0.00 0.00 2.24
5253 6607 4.832266 TGGTGCCAAAGAATGATGTAAACT 59.168 37.500 0.00 0.00 0.00 2.66
5254 6608 5.132897 TGGTGCCAAAGAATGATGTAAAC 57.867 39.130 0.00 0.00 0.00 2.01
5255 6609 5.510520 GGTTGGTGCCAAAGAATGATGTAAA 60.511 40.000 5.09 0.00 37.70 2.01
5256 6610 4.021544 GGTTGGTGCCAAAGAATGATGTAA 60.022 41.667 5.09 0.00 37.70 2.41
5257 6611 3.509575 GGTTGGTGCCAAAGAATGATGTA 59.490 43.478 5.09 0.00 37.70 2.29
5258 6612 2.299867 GGTTGGTGCCAAAGAATGATGT 59.700 45.455 5.09 0.00 37.70 3.06
5259 6613 2.299582 TGGTTGGTGCCAAAGAATGATG 59.700 45.455 5.09 0.00 37.70 3.07
5260 6614 2.607499 TGGTTGGTGCCAAAGAATGAT 58.393 42.857 5.09 0.00 37.70 2.45
5261 6615 2.079170 TGGTTGGTGCCAAAGAATGA 57.921 45.000 5.09 0.00 37.70 2.57
5262 6616 2.906691 TTGGTTGGTGCCAAAGAATG 57.093 45.000 5.09 0.00 44.67 2.67
5389 6746 2.616001 GCAAAAATGGCCACATGTCCAT 60.616 45.455 8.16 12.24 44.46 3.41
5390 6747 1.270732 GCAAAAATGGCCACATGTCCA 60.271 47.619 8.16 8.60 37.40 4.02
5391 6748 1.002315 AGCAAAAATGGCCACATGTCC 59.998 47.619 8.16 0.00 37.40 4.02
5415 6772 5.599359 TTTTGCATCATTTCAGCATTGTG 57.401 34.783 0.00 0.00 38.19 3.33
5438 6817 1.111277 GGCAGGTGTTTGAAAGTGGT 58.889 50.000 0.00 0.00 0.00 4.16
5486 6865 7.844779 TCTTATATTATGGGATGGAGGGAGTAC 59.155 40.741 0.00 0.00 0.00 2.73
5487 6866 7.961940 TCTTATATTATGGGATGGAGGGAGTA 58.038 38.462 0.00 0.00 0.00 2.59
5488 6867 6.826727 TCTTATATTATGGGATGGAGGGAGT 58.173 40.000 0.00 0.00 0.00 3.85
5489 6868 7.182749 TGTTCTTATATTATGGGATGGAGGGAG 59.817 40.741 0.00 0.00 0.00 4.30
5490 6869 7.028760 TGTTCTTATATTATGGGATGGAGGGA 58.971 38.462 0.00 0.00 0.00 4.20
5491 6870 7.270832 TGTTCTTATATTATGGGATGGAGGG 57.729 40.000 0.00 0.00 0.00 4.30
5492 6871 9.759473 AAATGTTCTTATATTATGGGATGGAGG 57.241 33.333 0.00 0.00 0.00 4.30
5519 6898 9.309516 ACGTTTTTCGAGCTAATATAGATTGAA 57.690 29.630 2.08 2.08 41.45 2.69
5520 6899 8.867112 ACGTTTTTCGAGCTAATATAGATTGA 57.133 30.769 0.00 0.00 42.86 2.57
5521 6900 9.569212 GAACGTTTTTCGAGCTAATATAGATTG 57.431 33.333 0.46 0.00 42.86 2.67
5522 6901 9.530633 AGAACGTTTTTCGAGCTAATATAGATT 57.469 29.630 0.46 0.00 42.86 2.40
5523 6902 9.530633 AAGAACGTTTTTCGAGCTAATATAGAT 57.469 29.630 0.46 0.00 42.86 1.98
5524 6903 8.922058 AAGAACGTTTTTCGAGCTAATATAGA 57.078 30.769 0.46 0.00 42.86 1.98
5526 6905 9.571810 TGTAAGAACGTTTTTCGAGCTAATATA 57.428 29.630 7.42 0.00 42.86 0.86
5527 6906 8.470040 TGTAAGAACGTTTTTCGAGCTAATAT 57.530 30.769 7.42 0.00 42.86 1.28
5528 6907 7.872163 TGTAAGAACGTTTTTCGAGCTAATA 57.128 32.000 7.42 0.00 42.86 0.98
5529 6908 6.774354 TGTAAGAACGTTTTTCGAGCTAAT 57.226 33.333 7.42 0.00 42.86 1.73
5530 6909 6.774354 ATGTAAGAACGTTTTTCGAGCTAA 57.226 33.333 7.42 0.00 42.86 3.09
5531 6910 6.774354 AATGTAAGAACGTTTTTCGAGCTA 57.226 33.333 7.42 0.00 42.86 3.32
5532 6911 5.668558 AATGTAAGAACGTTTTTCGAGCT 57.331 34.783 7.42 0.00 42.86 4.09
5533 6912 7.231607 TCATAATGTAAGAACGTTTTTCGAGC 58.768 34.615 7.42 0.00 42.86 5.03
5534 6913 8.644619 TCTCATAATGTAAGAACGTTTTTCGAG 58.355 33.333 7.42 4.29 42.86 4.04
5535 6914 8.430063 GTCTCATAATGTAAGAACGTTTTTCGA 58.570 33.333 7.42 0.00 42.86 3.71
5536 6915 8.218441 TGTCTCATAATGTAAGAACGTTTTTCG 58.782 33.333 7.42 0.00 46.00 3.46
5537 6916 9.872757 TTGTCTCATAATGTAAGAACGTTTTTC 57.127 29.630 7.42 1.35 36.28 2.29
5539 6918 9.878599 CTTTGTCTCATAATGTAAGAACGTTTT 57.121 29.630 0.46 0.00 36.28 2.43
5540 6919 8.504005 CCTTTGTCTCATAATGTAAGAACGTTT 58.496 33.333 0.46 0.00 36.28 3.60
5541 6920 7.119262 CCCTTTGTCTCATAATGTAAGAACGTT 59.881 37.037 0.00 0.00 38.41 3.99
5542 6921 6.594159 CCCTTTGTCTCATAATGTAAGAACGT 59.406 38.462 0.00 0.00 0.00 3.99
5543 6922 6.816640 TCCCTTTGTCTCATAATGTAAGAACG 59.183 38.462 0.00 0.00 0.00 3.95
5544 6923 7.824779 ACTCCCTTTGTCTCATAATGTAAGAAC 59.175 37.037 0.00 0.00 0.00 3.01
5545 6924 7.918076 ACTCCCTTTGTCTCATAATGTAAGAA 58.082 34.615 0.00 0.00 0.00 2.52
5546 6925 7.496346 ACTCCCTTTGTCTCATAATGTAAGA 57.504 36.000 0.00 0.00 0.00 2.10
5556 6935 9.613428 CATTTGTATTATACTCCCTTTGTCTCA 57.387 33.333 3.92 0.00 0.00 3.27
5557 6936 9.832445 TCATTTGTATTATACTCCCTTTGTCTC 57.168 33.333 3.92 0.00 0.00 3.36
5565 6944 9.899226 GCTTGAAATCATTTGTATTATACTCCC 57.101 33.333 3.92 0.00 0.00 4.30
5605 6984 0.827368 AACATGGCGTTTTGGTTGGT 59.173 45.000 0.00 0.00 32.35 3.67


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

AutoCloner maintained by Alex Coulton.