Multiple sequence alignment - TraesCS4A01G126800

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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 TraesCS4A01G126800 chr4A 100.000 5485 0 0 1 5485 163830290 163824806 0.000000e+00 10129.0
1 TraesCS4A01G126800 chr4A 75.253 198 36 12 5278 5472 491011938 491011751 1.270000e-11 82.4
2 TraesCS4A01G126800 chr4D 93.041 3492 158 37 1367 4819 312792569 312796014 0.000000e+00 5024.0
3 TraesCS4A01G126800 chr4D 89.029 875 45 23 1 856 312791093 312791935 0.000000e+00 1037.0
4 TraesCS4A01G126800 chr4D 92.873 449 27 3 894 1338 312791934 312792381 0.000000e+00 647.0
5 TraesCS4A01G126800 chr4D 82.238 563 50 28 4950 5485 312796153 312796692 1.810000e-119 440.0
6 TraesCS4A01G126800 chr4D 94.318 88 1 2 4865 4952 312796022 312796105 1.240000e-26 132.0
7 TraesCS4A01G126800 chr4B 95.142 2388 100 10 1340 3720 389464402 389466780 0.000000e+00 3753.0
8 TraesCS4A01G126800 chr4B 93.081 1402 61 18 3719 5097 389466942 389468330 0.000000e+00 2019.0
9 TraesCS4A01G126800 chr4B 88.401 1345 94 39 1 1324 389463022 389464325 0.000000e+00 1563.0
10 TraesCS4A01G126800 chr4B 88.889 54 2 3 5432 5485 554834760 554834809 4.590000e-06 63.9
11 TraesCS4A01G126800 chr1B 78.039 255 42 9 5228 5471 463145899 463145648 1.230000e-31 148.0
12 TraesCS4A01G126800 chr1A 79.200 125 18 8 5274 5395 302925148 302925267 4.550000e-11 80.5
13 TraesCS4A01G126800 chr2B 94.000 50 0 2 5436 5485 329487285 329487239 7.620000e-09 73.1
14 TraesCS4A01G126800 chr2B 97.368 38 1 0 5448 5485 92791182 92791145 1.280000e-06 65.8
15 TraesCS4A01G126800 chr7D 100.000 38 0 0 5448 5485 102504544 102504581 2.740000e-08 71.3
16 TraesCS4A01G126800 chr1D 97.368 38 1 0 5448 5485 269988385 269988422 1.280000e-06 65.8
17 TraesCS4A01G126800 chr3A 81.609 87 6 8 5399 5484 91196061 91195984 4.590000e-06 63.9
18 TraesCS4A01G126800 chr7B 88.235 51 5 1 5436 5485 191684060 191684110 5.930000e-05 60.2


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 TraesCS4A01G126800 chr4A 163824806 163830290 5484 True 10129 10129 100.0000 1 5485 1 chr4A.!!$R1 5484
1 TraesCS4A01G126800 chr4D 312791093 312796692 5599 False 1456 5024 90.2998 1 5485 5 chr4D.!!$F1 5484
2 TraesCS4A01G126800 chr4B 389463022 389468330 5308 False 2445 3753 92.2080 1 5097 3 chr4B.!!$F2 5096

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
852 902 0.034186 TGGTAAAGGCTGCCTCATGG 60.034 55.0 23.61 0.0 30.89 3.66 F
1460 1676 0.179032 TCACTGGATGTTGCCGTGTT 60.179 50.0 0.00 0.0 35.46 3.32 F
2641 2871 0.108520 CCAACTGGCCACATCATTGC 60.109 55.0 0.00 0.0 0.00 3.56 F
3420 3652 1.021968 AGCCACCTGTTTTTGACGAC 58.978 50.0 0.00 0.0 0.00 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2298 2525 1.462670 GCGTGCTTCCTCTTCTTTCAG 59.537 52.381 0.00 0.0 0.00 3.02 R
2892 3122 1.334160 AAGGTAAAAACCCGGCAAGG 58.666 50.000 0.00 0.0 40.63 3.61 R
3856 4251 0.109132 CTTTTGGAGGGCATTGCGAC 60.109 55.000 1.91 0.0 0.00 5.19 R
5184 5667 0.248565 GGTAACCGGGTCCTGAGAAC 59.751 60.000 6.32 0.0 0.00 3.01 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
39 40 0.616111 TCCCTCTTCCTCCTCTGCAC 60.616 60.000 0.00 0.00 0.00 4.57
57 58 2.270986 CCCACAGCAACAGCTTCCC 61.271 63.158 0.00 0.00 36.19 3.97
83 85 2.997315 TCAGACCCACCCTCGCTG 60.997 66.667 0.00 0.00 0.00 5.18
137 148 0.179161 GCTTTCTGCTAGCTCGTCGA 60.179 55.000 17.23 0.00 38.95 4.20
152 163 1.347320 GTCGAGTTGAAGGTAAGCCG 58.653 55.000 0.00 0.00 40.50 5.52
153 164 0.389426 TCGAGTTGAAGGTAAGCCGC 60.389 55.000 0.00 0.00 40.50 6.53
154 165 0.669318 CGAGTTGAAGGTAAGCCGCA 60.669 55.000 0.00 0.00 40.50 5.69
155 166 1.519408 GAGTTGAAGGTAAGCCGCAA 58.481 50.000 0.00 0.00 40.50 4.85
156 167 1.464997 GAGTTGAAGGTAAGCCGCAAG 59.535 52.381 0.00 0.00 40.50 4.01
157 168 0.109735 GTTGAAGGTAAGCCGCAAGC 60.110 55.000 0.00 0.00 44.25 4.01
158 169 1.241315 TTGAAGGTAAGCCGCAAGCC 61.241 55.000 0.00 0.00 45.47 4.35
175 186 3.845259 CGCAAGCGCCTACCCCTA 61.845 66.667 2.29 0.00 33.11 3.53
227 238 5.666185 GCGAATTTTGCATTTCTTGTGCTAC 60.666 40.000 3.65 0.00 42.92 3.58
246 257 1.021202 CTCGAGGAGGTACAGCTCTG 58.979 60.000 3.91 0.00 0.00 3.35
252 263 1.686052 GGAGGTACAGCTCTGATCTGG 59.314 57.143 12.61 0.00 35.94 3.86
254 265 3.027412 GAGGTACAGCTCTGATCTGGAA 58.973 50.000 12.61 0.00 35.94 3.53
257 268 4.832266 AGGTACAGCTCTGATCTGGAATAG 59.168 45.833 12.61 0.00 35.94 1.73
262 273 4.036518 AGCTCTGATCTGGAATAGGTGTT 58.963 43.478 0.00 0.00 0.00 3.32
263 274 4.125703 GCTCTGATCTGGAATAGGTGTTG 58.874 47.826 0.00 0.00 0.00 3.33
269 280 7.565029 TCTGATCTGGAATAGGTGTTGAGATTA 59.435 37.037 0.00 0.00 0.00 1.75
270 281 8.267620 TGATCTGGAATAGGTGTTGAGATTAT 57.732 34.615 0.00 0.00 0.00 1.28
271 282 8.152898 TGATCTGGAATAGGTGTTGAGATTATG 58.847 37.037 0.00 0.00 0.00 1.90
272 283 6.291377 TCTGGAATAGGTGTTGAGATTATGC 58.709 40.000 0.00 0.00 0.00 3.14
323 334 2.165030 CTCATTGGTTTCATGCCCTGTC 59.835 50.000 0.00 0.00 0.00 3.51
356 392 5.542779 ACTACGACTCATTTCTCTTTGCTT 58.457 37.500 0.00 0.00 0.00 3.91
382 418 6.478673 TGTTCATTTGAGTAGTACACACACTG 59.521 38.462 2.52 0.93 0.00 3.66
383 419 6.156748 TCATTTGAGTAGTACACACACTGT 57.843 37.500 2.52 0.00 36.82 3.55
387 423 8.822855 CATTTGAGTAGTACACACACTGTTTTA 58.177 33.333 2.52 0.00 33.91 1.52
396 432 3.498397 CACACACTGTTTTAAGCGAGGAT 59.502 43.478 0.00 0.00 0.00 3.24
397 433 4.024048 CACACACTGTTTTAAGCGAGGATT 60.024 41.667 0.00 0.00 0.00 3.01
398 434 4.213482 ACACACTGTTTTAAGCGAGGATTC 59.787 41.667 0.00 0.00 0.00 2.52
399 435 4.452455 CACACTGTTTTAAGCGAGGATTCT 59.548 41.667 0.00 0.00 0.00 2.40
400 436 4.691216 ACACTGTTTTAAGCGAGGATTCTC 59.309 41.667 0.00 0.00 36.69 2.87
405 441 7.492994 ACTGTTTTAAGCGAGGATTCTCTTATC 59.507 37.037 0.00 0.00 37.86 1.75
440 476 2.457366 AGCAGCAGTAACCAGTACAC 57.543 50.000 0.00 0.00 34.88 2.90
460 496 4.516698 ACACATCTGTAAACTGCTTTCTGG 59.483 41.667 0.00 0.00 0.00 3.86
476 512 5.406477 GCTTTCTGGAAATGTTTTGTCATCC 59.594 40.000 0.00 0.00 0.00 3.51
548 587 2.945080 ATGTCTATGTGGCCTCCATG 57.055 50.000 16.04 8.23 35.28 3.66
614 656 0.109781 CCGCAGGCACATGTGTTTAC 60.110 55.000 26.01 14.25 46.14 2.01
693 737 8.958119 TGTCTTTGCCACCTTTTATATACTAG 57.042 34.615 0.00 0.00 0.00 2.57
694 738 8.545472 TGTCTTTGCCACCTTTTATATACTAGT 58.455 33.333 0.00 0.00 0.00 2.57
724 769 1.407618 GTGGGTTGAGTGTTTTGGACC 59.592 52.381 0.00 0.00 0.00 4.46
768 816 6.558771 TTGATGATCAGGTGTTGTTTAGTG 57.441 37.500 0.09 0.00 0.00 2.74
852 902 0.034186 TGGTAAAGGCTGCCTCATGG 60.034 55.000 23.61 0.00 30.89 3.66
858 908 1.614317 AAGGCTGCCTCATGGTACAAC 60.614 52.381 23.61 0.00 35.24 3.32
892 942 9.653287 AAGAAGATGTTTTACGTCATCTGAATA 57.347 29.630 15.77 0.00 46.47 1.75
893 943 9.653287 AGAAGATGTTTTACGTCATCTGAATAA 57.347 29.630 15.77 0.00 46.47 1.40
905 955 9.342308 ACGTCATCTGAATAACCAAATTCATAT 57.658 29.630 0.14 0.00 43.16 1.78
939 989 4.022068 GTGTCCAAAGCCTGATTTCATTGA 60.022 41.667 0.00 0.00 0.00 2.57
950 1000 2.168326 TTTCATTGAGCGACTGCAGA 57.832 45.000 23.35 0.00 46.23 4.26
952 1002 2.391616 TCATTGAGCGACTGCAGATT 57.608 45.000 23.35 0.00 46.23 2.40
994 1044 3.102052 TGACAGTAACCTTCGGTTGTC 57.898 47.619 8.47 8.56 46.35 3.18
1008 1058 1.859080 GGTTGTCGGAAGATGTATCGC 59.141 52.381 0.00 0.00 45.19 4.58
1125 1175 3.414549 TTCGCAAAGAACACTGAAACC 57.585 42.857 0.00 0.00 33.14 3.27
1223 1274 6.484288 TCACACAATTCCCTCATATGACTTT 58.516 36.000 0.00 0.00 0.00 2.66
1224 1275 6.375174 TCACACAATTCCCTCATATGACTTTG 59.625 38.462 0.00 4.46 0.00 2.77
1225 1276 6.151648 CACACAATTCCCTCATATGACTTTGT 59.848 38.462 0.00 5.03 0.00 2.83
1328 1382 9.685276 AAAGTTCAGTCAACCATATCATATCAA 57.315 29.630 0.00 0.00 35.28 2.57
1338 1392 9.888878 CAACCATATCATATCAACTTTCATGAC 57.111 33.333 0.00 0.00 30.64 3.06
1460 1676 0.179032 TCACTGGATGTTGCCGTGTT 60.179 50.000 0.00 0.00 35.46 3.32
1496 1712 7.497249 GCATAGGAAGATGTGACTTCAGTTAAT 59.503 37.037 0.00 0.00 45.39 1.40
1546 1767 2.158957 ACATAGCGGTCTTACCCACATG 60.159 50.000 0.00 0.00 33.75 3.21
1557 1778 3.502164 CCCACATGGTGATCTTCCC 57.498 57.895 0.00 0.00 35.23 3.97
1615 1837 5.886960 AGTATCTTGTGCAGTTTCCAATC 57.113 39.130 0.00 0.00 0.00 2.67
1659 1881 3.296322 TGAACACGAAATTCAATGCCC 57.704 42.857 0.00 0.00 33.16 5.36
1660 1882 2.890311 TGAACACGAAATTCAATGCCCT 59.110 40.909 0.00 0.00 33.16 5.19
1670 1892 1.067295 TCAATGCCCTCAGTTCCTGT 58.933 50.000 0.00 0.00 32.61 4.00
1718 1940 2.958355 ACTTTTGGGTGTCCATGTCTTG 59.042 45.455 0.00 0.00 43.63 3.02
1783 2007 5.047235 AGTTCGAAGTTCTAGCCATACAGTT 60.047 40.000 0.00 0.00 0.00 3.16
1816 2040 6.270231 AGGGACTTCTGTTAGCTAGAAAAGAA 59.730 38.462 11.76 7.61 34.07 2.52
1817 2041 6.935208 GGGACTTCTGTTAGCTAGAAAAGAAA 59.065 38.462 3.91 0.00 34.07 2.52
1818 2042 7.444487 GGGACTTCTGTTAGCTAGAAAAGAAAA 59.556 37.037 3.91 0.00 34.07 2.29
2180 2407 7.509141 TGATACCATTGTAAGTGCCAATATG 57.491 36.000 0.00 0.00 31.52 1.78
2191 2418 5.057843 AGTGCCAATATGTCATCCATCTT 57.942 39.130 0.00 0.00 34.86 2.40
2298 2525 3.886123 ACACAGTATACCAATGGAAGGC 58.114 45.455 6.16 0.00 0.00 4.35
2396 2623 9.167311 GTGTATCACAGAGATTTGAAGGTAAAT 57.833 33.333 0.00 0.00 38.19 1.40
2397 2624 9.739276 TGTATCACAGAGATTTGAAGGTAAATT 57.261 29.630 0.00 0.00 38.19 1.82
2479 2707 9.744468 GGTAAAGTGACAAAATGATGTTAAACT 57.256 29.630 0.00 0.00 32.57 2.66
2486 2714 8.763356 TGACAAAATGATGTTAAACTTGCATTC 58.237 29.630 0.00 0.00 32.57 2.67
2585 2813 6.641474 AGCAAGTGAAGGTATTCTTACTACC 58.359 40.000 0.00 0.00 39.18 3.18
2641 2871 0.108520 CCAACTGGCCACATCATTGC 60.109 55.000 0.00 0.00 0.00 3.56
2892 3122 4.885325 TGCGGGGTAATCCTTTTTATTCTC 59.115 41.667 0.00 0.00 35.33 2.87
2943 3173 7.397892 TGAAAACATCATCGCCCTTTATAAA 57.602 32.000 0.00 0.00 31.50 1.40
2982 3212 9.979578 ATACAGTTCAAAAGATGTAAAAATGCA 57.020 25.926 0.00 0.00 32.31 3.96
3015 3245 2.982488 AGAGGCTTCTTTTCTCAGGGAA 59.018 45.455 0.00 0.00 0.00 3.97
3096 3326 3.688185 TCTCAGAAGCTCAATTCACATGC 59.312 43.478 0.00 0.00 0.00 4.06
3127 3357 5.307196 TGGTTTTCTACTGGAGCTAAGAAGT 59.693 40.000 2.97 0.00 30.19 3.01
3132 3362 6.859112 TCTACTGGAGCTAAGAAGTTGATT 57.141 37.500 2.97 0.00 0.00 2.57
3142 3372 8.870075 AGCTAAGAAGTTGATTACCAGAATTT 57.130 30.769 0.00 0.00 0.00 1.82
3205 3435 9.474920 TTTTGAATATGGTTGTTGAAATCACTC 57.525 29.630 0.00 0.00 0.00 3.51
3207 3437 8.175925 TGAATATGGTTGTTGAAATCACTCAA 57.824 30.769 0.00 0.00 32.89 3.02
3249 3481 5.478679 AGTCAGACTTGTGAGCAGTACTATT 59.521 40.000 0.00 0.00 0.00 1.73
3271 3503 7.745620 ATTAAAGAAACACCAGTAGTCCTTG 57.254 36.000 0.00 0.00 0.00 3.61
3276 3508 5.765182 AGAAACACCAGTAGTCCTTGATTTG 59.235 40.000 0.00 0.00 0.00 2.32
3278 3510 5.304686 ACACCAGTAGTCCTTGATTTGAA 57.695 39.130 0.00 0.00 0.00 2.69
3286 3518 8.253810 CAGTAGTCCTTGATTTGAATCTCAGTA 58.746 37.037 5.42 0.00 36.39 2.74
3290 3522 6.314896 GTCCTTGATTTGAATCTCAGTACTGG 59.685 42.308 22.48 13.18 36.39 4.00
3294 3526 8.690203 TTGATTTGAATCTCAGTACTGGAAAA 57.310 30.769 22.48 14.67 36.39 2.29
3318 3550 8.753497 AAAAGTTATAGAATCCCAACTCATCC 57.247 34.615 0.00 0.00 31.06 3.51
3420 3652 1.021968 AGCCACCTGTTTTTGACGAC 58.978 50.000 0.00 0.00 0.00 4.34
3441 3673 5.571741 CGACAAGTATGAAACTAGCTTCGAA 59.428 40.000 0.00 0.00 37.50 3.71
3997 4394 8.076178 GCACACATCTTCTGTTACAACTAAATT 58.924 33.333 0.00 0.00 35.29 1.82
4024 4421 7.883229 TGTATACATGTTAGCACATATTCGG 57.117 36.000 2.30 0.00 42.14 4.30
4158 4555 3.302170 CACCACGCAAACAAACAAACTAC 59.698 43.478 0.00 0.00 0.00 2.73
4295 4699 7.013369 GGATACTCTGGAATTTCAAATGGTACC 59.987 40.741 4.43 4.43 0.00 3.34
4296 4700 5.640147 ACTCTGGAATTTCAAATGGTACCA 58.360 37.500 18.99 18.99 0.00 3.25
4358 4762 7.201266 CGAATTTAACTACTGTCAAAGCATTGC 60.201 37.037 0.00 0.00 36.45 3.56
4433 4838 0.324738 TCTCGACCCAGCTCAAGGAT 60.325 55.000 0.97 0.00 0.00 3.24
4709 5131 2.158740 GGTCCAGAGGGAGATTAAAGCC 60.159 54.545 0.00 0.00 46.12 4.35
4733 5155 0.796870 GCGAAAGGCCGTATTGTTGC 60.797 55.000 0.00 0.00 34.80 4.17
4812 5237 7.759465 TCACTCTACTTAGCATTGTACTGTAC 58.241 38.462 10.98 10.98 0.00 2.90
4813 5238 7.610692 TCACTCTACTTAGCATTGTACTGTACT 59.389 37.037 17.98 1.18 0.00 2.73
4814 5239 8.890718 CACTCTACTTAGCATTGTACTGTACTA 58.109 37.037 17.98 11.58 0.00 1.82
4815 5240 9.111613 ACTCTACTTAGCATTGTACTGTACTAG 57.888 37.037 17.98 8.59 0.00 2.57
4816 5241 9.111613 CTCTACTTAGCATTGTACTGTACTAGT 57.888 37.037 17.98 0.00 43.56 2.57
4838 5263 1.751924 GTAGCTATAGCCGGGGAGATG 59.248 57.143 21.17 0.00 43.38 2.90
4841 5266 1.893210 GCTATAGCCGGGGAGATGTCT 60.893 57.143 14.13 0.00 34.31 3.41
4842 5267 2.096248 CTATAGCCGGGGAGATGTCTC 58.904 57.143 2.18 1.33 42.14 3.36
4843 5268 0.485099 ATAGCCGGGGAGATGTCTCT 59.515 55.000 2.18 0.00 42.48 3.10
4844 5269 0.468214 TAGCCGGGGAGATGTCTCTG 60.468 60.000 2.18 0.00 42.48 3.35
4845 5270 2.060980 GCCGGGGAGATGTCTCTGT 61.061 63.158 2.18 0.00 42.48 3.41
4846 5271 0.755698 GCCGGGGAGATGTCTCTGTA 60.756 60.000 2.18 0.00 42.48 2.74
4847 5272 1.323412 CCGGGGAGATGTCTCTGTAG 58.677 60.000 9.68 0.69 42.48 2.74
4849 5274 2.158652 CCGGGGAGATGTCTCTGTAGTA 60.159 54.545 9.68 0.00 42.48 1.82
4850 5275 2.879646 CGGGGAGATGTCTCTGTAGTAC 59.120 54.545 9.68 0.00 42.48 2.73
4855 5287 5.179742 GGGAGATGTCTCTGTAGTACGTATG 59.820 48.000 9.68 0.00 42.48 2.39
4863 5295 7.224949 TGTCTCTGTAGTACGTATGAGATTCTG 59.775 40.741 0.00 0.00 33.89 3.02
4912 5344 2.953605 GCGATGCTGCGTGTGTGAA 61.954 57.895 0.00 0.00 0.00 3.18
4913 5345 1.131218 CGATGCTGCGTGTGTGAAG 59.869 57.895 0.00 0.00 0.00 3.02
4914 5346 1.499056 GATGCTGCGTGTGTGAAGG 59.501 57.895 0.00 0.00 0.00 3.46
4915 5347 0.950555 GATGCTGCGTGTGTGAAGGA 60.951 55.000 0.00 0.00 0.00 3.36
4952 5384 3.056821 TGGAATCGTAACTGACCAGTGAG 60.057 47.826 3.13 0.00 41.58 3.51
4978 5460 0.391661 ACCGATGTGAGTGTGGATGC 60.392 55.000 0.00 0.00 0.00 3.91
5015 5497 4.315803 ACAGAAAAATGTAGTCGGACCAG 58.684 43.478 4.14 0.00 0.00 4.00
5016 5498 3.125316 CAGAAAAATGTAGTCGGACCAGC 59.875 47.826 4.14 0.00 0.00 4.85
5202 5685 0.971386 TGTTCTCAGGACCCGGTTAC 59.029 55.000 0.00 0.00 0.00 2.50
5203 5686 0.248565 GTTCTCAGGACCCGGTTACC 59.751 60.000 0.00 0.03 0.00 2.85
5243 5741 1.079336 GGGGATTCCTATACGGCGC 60.079 63.158 6.90 0.00 0.00 6.53
5248 5746 2.765250 ATTCCTATACGGCGCGCAGG 62.765 60.000 33.28 28.53 0.00 4.85
5314 5824 2.683572 GGCCGGCCCATTTTCCTT 60.684 61.111 36.64 0.00 0.00 3.36
5316 5826 1.218047 GCCGGCCCATTTTCCTTTC 59.782 57.895 18.11 0.00 0.00 2.62
5317 5827 1.510844 CCGGCCCATTTTCCTTTCG 59.489 57.895 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 1.268283 GGTGGGTCTGAGGAGGAAGG 61.268 65.000 0.00 0.00 0.00 3.46
121 132 1.135660 CAACTCGACGAGCTAGCAGAA 60.136 52.381 24.38 1.75 32.04 3.02
137 148 1.523758 CTTGCGGCTTACCTTCAACT 58.476 50.000 0.00 0.00 0.00 3.16
153 164 4.166011 GTAGGCGCTTGCGGCTTG 62.166 66.667 39.50 4.83 44.32 4.01
158 169 2.862674 TTTAGGGGTAGGCGCTTGCG 62.863 60.000 7.64 10.90 40.46 4.85
175 186 5.675538 GCACAGTAGGGAACAGATAGATTT 58.324 41.667 0.00 0.00 0.00 2.17
227 238 1.021202 CAGAGCTGTACCTCCTCGAG 58.979 60.000 5.13 5.13 32.17 4.04
246 257 7.118971 GCATAATCTCAACACCTATTCCAGATC 59.881 40.741 0.00 0.00 0.00 2.75
252 263 6.376978 GCATGCATAATCTCAACACCTATTC 58.623 40.000 14.21 0.00 0.00 1.75
254 265 4.453478 CGCATGCATAATCTCAACACCTAT 59.547 41.667 19.57 0.00 0.00 2.57
257 268 2.855953 GCGCATGCATAATCTCAACACC 60.856 50.000 19.57 0.00 42.15 4.16
323 334 9.959775 GAGAAATGAGTCGTAGTAAAATCTTTG 57.040 33.333 0.00 0.00 0.00 2.77
356 392 7.011016 CAGTGTGTGTACTACTCAAATGAACAA 59.989 37.037 0.00 0.00 34.84 2.83
382 418 8.970293 GTAGATAAGAGAATCCTCGCTTAAAAC 58.030 37.037 3.05 0.07 44.10 2.43
383 419 8.142551 GGTAGATAAGAGAATCCTCGCTTAAAA 58.857 37.037 3.05 0.00 44.10 1.52
387 423 5.390387 AGGTAGATAAGAGAATCCTCGCTT 58.610 41.667 0.00 0.00 43.28 4.68
396 432 8.674925 TTTTGGGAGTAAGGTAGATAAGAGAA 57.325 34.615 0.00 0.00 0.00 2.87
397 433 7.147707 GCTTTTGGGAGTAAGGTAGATAAGAGA 60.148 40.741 0.00 0.00 0.00 3.10
398 434 6.987404 GCTTTTGGGAGTAAGGTAGATAAGAG 59.013 42.308 0.00 0.00 0.00 2.85
399 435 6.442564 TGCTTTTGGGAGTAAGGTAGATAAGA 59.557 38.462 0.00 0.00 0.00 2.10
400 436 6.650120 TGCTTTTGGGAGTAAGGTAGATAAG 58.350 40.000 0.00 0.00 0.00 1.73
405 441 3.010420 GCTGCTTTTGGGAGTAAGGTAG 58.990 50.000 0.00 0.00 35.71 3.18
440 476 5.947228 TTCCAGAAAGCAGTTTACAGATG 57.053 39.130 0.00 0.00 0.00 2.90
460 496 6.612306 GTCACCTAGGATGACAAAACATTTC 58.388 40.000 26.50 7.24 44.87 2.17
476 512 1.064906 TCCTACCCGACAGTCACCTAG 60.065 57.143 0.41 0.00 0.00 3.02
614 656 3.255888 CCATGAGATGCATCATCCCAAAG 59.744 47.826 27.81 14.87 41.36 2.77
655 697 6.314784 GTGGCAAAGACATATCTACAACAAC 58.685 40.000 0.00 0.00 33.57 3.32
657 699 4.941263 GGTGGCAAAGACATATCTACAACA 59.059 41.667 0.00 0.00 33.57 3.33
658 700 5.186198 AGGTGGCAAAGACATATCTACAAC 58.814 41.667 0.00 0.00 33.57 3.32
689 733 6.126854 ACTCAACCCACTTTGACTTTACTAGT 60.127 38.462 0.00 0.00 40.71 2.57
690 734 6.202954 CACTCAACCCACTTTGACTTTACTAG 59.797 42.308 0.00 0.00 32.02 2.57
691 735 6.053005 CACTCAACCCACTTTGACTTTACTA 58.947 40.000 0.00 0.00 32.02 1.82
692 736 4.881850 CACTCAACCCACTTTGACTTTACT 59.118 41.667 0.00 0.00 32.02 2.24
693 737 4.638865 ACACTCAACCCACTTTGACTTTAC 59.361 41.667 0.00 0.00 32.02 2.01
694 738 4.850680 ACACTCAACCCACTTTGACTTTA 58.149 39.130 0.00 0.00 32.02 1.85
724 769 9.037737 CATCAAAAATATAAAATGACCAGCCTG 57.962 33.333 0.00 0.00 0.00 4.85
744 789 6.545666 ACACTAAACAACACCTGATCATCAAA 59.454 34.615 0.00 0.00 0.00 2.69
745 790 6.061441 ACACTAAACAACACCTGATCATCAA 58.939 36.000 0.00 0.00 0.00 2.57
801 849 7.202001 CCCAAAAAGGATAAAAGGAAGAACAGT 60.202 37.037 0.00 0.00 41.22 3.55
852 902 8.856490 AAACATCTTCTTGTTTCATGTTGTAC 57.144 30.769 0.00 0.00 44.39 2.90
858 908 7.855409 TGACGTAAAACATCTTCTTGTTTCATG 59.145 33.333 3.32 0.00 46.33 3.07
892 942 8.084073 CACTGTGAACTTGATATGAATTTGGTT 58.916 33.333 0.32 0.00 0.00 3.67
893 943 7.231317 ACACTGTGAACTTGATATGAATTTGGT 59.769 33.333 15.86 0.00 0.00 3.67
905 955 2.682856 GCTTTGGACACTGTGAACTTGA 59.317 45.455 15.86 0.00 0.00 3.02
939 989 0.035317 TTGGACAATCTGCAGTCGCT 59.965 50.000 14.67 0.00 39.64 4.93
950 1000 4.590222 ACCTTCAAAATGCTCTTGGACAAT 59.410 37.500 0.00 0.00 0.00 2.71
952 1002 3.565307 ACCTTCAAAATGCTCTTGGACA 58.435 40.909 0.00 0.00 0.00 4.02
994 1044 0.874175 TTGGCGCGATACATCTTCCG 60.874 55.000 12.10 0.00 0.00 4.30
1008 1058 1.303799 ACAATGCAGCTCTCTTGGCG 61.304 55.000 0.00 0.00 34.52 5.69
1328 1382 3.748083 ACTGTGCATCTGTCATGAAAGT 58.252 40.909 12.74 0.00 0.00 2.66
1435 1651 2.648059 GGCAACATCCAGTGAAGCTAT 58.352 47.619 0.00 0.00 33.70 2.97
1443 1659 1.808411 CTAACACGGCAACATCCAGT 58.192 50.000 0.00 0.00 0.00 4.00
1460 1676 2.407562 TCTTCCTATGCCACCATGCTA 58.592 47.619 0.00 0.00 32.85 3.49
1468 1684 3.519107 TGAAGTCACATCTTCCTATGCCA 59.481 43.478 4.39 0.00 41.96 4.92
1557 1778 8.037382 ACTGAGTTTGTGATATGACTTCAATG 57.963 34.615 0.00 0.00 0.00 2.82
1615 1837 3.607422 TTGCACAAAGTTCAGACATCG 57.393 42.857 0.00 0.00 0.00 3.84
1670 1892 3.134623 CAGGGGACACATATGCTGAAGTA 59.865 47.826 1.58 0.00 0.00 2.24
1718 1940 9.384764 AGTAGTGAAGGCAATTAAATAGAACTC 57.615 33.333 0.00 0.00 0.00 3.01
2180 2407 4.110482 GCAATTGCAGAAAGATGGATGAC 58.890 43.478 25.36 0.00 41.59 3.06
2191 2418 2.309613 ACAACCTCAGCAATTGCAGAA 58.690 42.857 30.89 15.00 45.16 3.02
2298 2525 1.462670 GCGTGCTTCCTCTTCTTTCAG 59.537 52.381 0.00 0.00 0.00 3.02
2398 2625 4.658063 ACACATGACCCGGAAGATAAAAA 58.342 39.130 0.73 0.00 0.00 1.94
2399 2626 4.295141 ACACATGACCCGGAAGATAAAA 57.705 40.909 0.73 0.00 0.00 1.52
2486 2714 5.458452 TCAAGCAACAAATTTTCTAACTGCG 59.542 36.000 0.00 0.00 33.83 5.18
2753 2983 7.512130 ACACATGATCTTAAGATGATAAGCCA 58.488 34.615 22.61 12.19 34.37 4.75
2892 3122 1.334160 AAGGTAAAAACCCGGCAAGG 58.666 50.000 0.00 0.00 40.63 3.61
2992 3222 3.515901 TCCCTGAGAAAAGAAGCCTCTAC 59.484 47.826 0.00 0.00 0.00 2.59
2993 3223 3.791320 TCCCTGAGAAAAGAAGCCTCTA 58.209 45.455 0.00 0.00 0.00 2.43
3046 3276 8.848474 TGTTATTCCAGAAGAGAGTAAAAAGG 57.152 34.615 0.00 0.00 0.00 3.11
3047 3277 9.712305 TCTGTTATTCCAGAAGAGAGTAAAAAG 57.288 33.333 0.00 0.00 38.49 2.27
3057 3287 7.724490 TTCTGAGATCTGTTATTCCAGAAGA 57.276 36.000 13.78 0.00 44.21 2.87
3096 3326 2.642807 TCCAGTAGAAAACCAAGAGGGG 59.357 50.000 0.00 0.00 42.91 4.79
3127 3357 5.650283 AGGGTCCAAAATTCTGGTAATCAA 58.350 37.500 0.00 0.00 37.74 2.57
3132 3362 5.494706 AGGATTAGGGTCCAAAATTCTGGTA 59.505 40.000 0.00 0.00 40.90 3.25
3142 3372 1.992557 AGTTGCAGGATTAGGGTCCAA 59.007 47.619 0.00 0.00 40.90 3.53
3222 3452 3.491342 ACTGCTCACAAGTCTGACTCTA 58.509 45.455 11.31 0.00 0.00 2.43
3249 3481 6.488769 TCAAGGACTACTGGTGTTTCTTTA 57.511 37.500 0.00 0.00 0.00 1.85
3294 3526 6.992715 CGGATGAGTTGGGATTCTATAACTTT 59.007 38.462 0.00 0.00 33.83 2.66
3318 3550 4.862018 ACATTCAACAACAAAAACAGGACG 59.138 37.500 0.00 0.00 0.00 4.79
3420 3652 7.276658 ACATCTTCGAAGCTAGTTTCATACTTG 59.723 37.037 20.56 11.74 38.33 3.16
3441 3673 4.135306 CTCCAAATGCAGCATAGACATCT 58.865 43.478 8.75 0.00 0.00 2.90
3639 3871 5.048782 CCTCGAACAAATTGTCCAGATTCAA 60.049 40.000 0.00 0.00 0.00 2.69
3856 4251 0.109132 CTTTTGGAGGGCATTGCGAC 60.109 55.000 1.91 0.00 0.00 5.19
3895 4290 1.905354 AAGTGGCCTTGCAGCTTCC 60.905 57.895 3.32 0.00 0.00 3.46
4012 4409 1.065491 TGCCAACTCCGAATATGTGCT 60.065 47.619 0.00 0.00 0.00 4.40
4020 4417 1.885887 CAATTTCCTGCCAACTCCGAA 59.114 47.619 0.00 0.00 0.00 4.30
4024 4421 4.762251 ACTAGTTCAATTTCCTGCCAACTC 59.238 41.667 0.00 0.00 0.00 3.01
4158 4555 7.447238 TGGGTAATCCTTCTTTAGTGTTCAAAG 59.553 37.037 0.00 0.00 36.20 2.77
4358 4762 6.124088 ACTCTTGTTACTTGCTTGTGAAAG 57.876 37.500 0.00 0.00 34.96 2.62
4433 4838 1.225376 CGCCGCACTTCCAAACTACA 61.225 55.000 0.00 0.00 0.00 2.74
4488 4893 5.594317 AGGGACTATGTACATGGAAAATTGC 59.406 40.000 24.30 7.81 36.02 3.56
4635 5054 2.173126 AGATAGGCTCTTCCACAGCT 57.827 50.000 0.00 0.00 37.05 4.24
4812 5237 3.199508 TCCCCGGCTATAGCTACTACTAG 59.800 52.174 23.53 5.89 41.70 2.57
4813 5238 3.184628 TCCCCGGCTATAGCTACTACTA 58.815 50.000 23.53 2.18 41.70 1.82
4814 5239 1.991070 TCCCCGGCTATAGCTACTACT 59.009 52.381 23.53 0.00 41.70 2.57
4815 5240 2.026449 TCTCCCCGGCTATAGCTACTAC 60.026 54.545 23.53 6.29 41.70 2.73
4816 5241 2.272698 TCTCCCCGGCTATAGCTACTA 58.727 52.381 23.53 6.02 41.70 1.82
4817 5242 1.073931 TCTCCCCGGCTATAGCTACT 58.926 55.000 23.53 0.00 41.70 2.57
4838 5263 7.438757 TCAGAATCTCATACGTACTACAGAGAC 59.561 40.741 0.00 0.00 35.24 3.36
4841 5266 8.678593 ATTCAGAATCTCATACGTACTACAGA 57.321 34.615 0.00 0.00 0.00 3.41
4912 5344 1.563410 CCATGAGCTTCCTTCCTTCCT 59.437 52.381 0.00 0.00 0.00 3.36
4913 5345 1.561542 TCCATGAGCTTCCTTCCTTCC 59.438 52.381 0.00 0.00 0.00 3.46
4914 5346 3.356529 TTCCATGAGCTTCCTTCCTTC 57.643 47.619 0.00 0.00 0.00 3.46
4915 5347 3.683847 CGATTCCATGAGCTTCCTTCCTT 60.684 47.826 0.00 0.00 0.00 3.36
4952 5384 3.120199 CCACACTCACATCGGTTTCATTC 60.120 47.826 0.00 0.00 0.00 2.67
4978 5460 4.589216 TTTCTGTTGGCAATTTGGAGAG 57.411 40.909 1.92 0.00 0.00 3.20
4991 5473 4.513692 TGGTCCGACTACATTTTTCTGTTG 59.486 41.667 0.00 0.00 0.00 3.33
5032 5514 0.733909 GCTTTCATCTTTGCCCGCAC 60.734 55.000 0.00 0.00 0.00 5.34
5036 5518 0.533951 CCAGGCTTTCATCTTTGCCC 59.466 55.000 0.00 0.00 45.94 5.36
5070 5552 4.181010 ATGGCAGAATCGGCGCCT 62.181 61.111 26.68 5.36 46.39 5.52
5080 5562 1.620739 GCAGAGGGAGACATGGCAGA 61.621 60.000 0.00 0.00 0.00 4.26
5135 5618 2.228822 TCAAAGCTGAGAAAAATCCGGC 59.771 45.455 0.00 0.00 0.00 6.13
5174 5657 3.257561 CTGAGAACATCGGCGCCG 61.258 66.667 42.13 42.13 41.35 6.46
5184 5667 0.248565 GGTAACCGGGTCCTGAGAAC 59.751 60.000 6.32 0.00 0.00 3.01
5209 5692 4.410400 CCTCCGGTCAAGGCCACC 62.410 72.222 5.01 2.33 0.00 4.61
5210 5693 4.410400 CCCTCCGGTCAAGGCCAC 62.410 72.222 5.01 0.00 32.15 5.01
5233 5731 2.729862 GACCTGCGCGCCGTATAG 60.730 66.667 30.77 18.69 0.00 1.31
5297 5800 2.238847 GAAAGGAAAATGGGCCGGCC 62.239 60.000 38.57 38.57 0.00 6.13


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

AutoCloner maintained by Alex Coulton.