Multiple sequence alignment - TraesCS2D01G470900

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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 TraesCS2D01G470900 chr2D 100.000 2531 0 0 1 2531 575215892 575218422 0.000000e+00 4674.0
1 TraesCS2D01G470900 chr2D 97.481 516 12 1 2017 2531 635698436 635698951 0.000000e+00 880.0
2 TraesCS2D01G470900 chr2D 71.780 528 128 15 992 1507 574570543 574571061 2.040000e-26 130.0
3 TraesCS2D01G470900 chr2D 71.591 528 129 15 992 1507 574599168 574599686 9.510000e-25 124.0
4 TraesCS2D01G470900 chr2B 92.761 1257 69 11 291 1543 691189174 691190412 0.000000e+00 1797.0
5 TraesCS2D01G470900 chr2B 88.594 1280 96 21 293 1543 691413116 691414374 0.000000e+00 1509.0
6 TraesCS2D01G470900 chr2B 85.438 1085 151 5 461 1543 691402068 691403147 0.000000e+00 1122.0
7 TraesCS2D01G470900 chr2B 84.991 1086 154 7 461 1543 691186962 691188041 0.000000e+00 1094.0
8 TraesCS2D01G470900 chr2B 90.411 219 20 1 1545 1762 691414417 691414635 1.150000e-73 287.0
9 TraesCS2D01G470900 chr2B 87.615 218 25 1 1545 1762 691190455 691190670 4.180000e-63 252.0
10 TraesCS2D01G470900 chr2B 90.217 184 14 2 1765 1944 691190702 691190885 1.170000e-58 237.0
11 TraesCS2D01G470900 chr2B 91.765 170 11 2 1765 1932 691414667 691414835 1.510000e-57 233.0
12 TraesCS2D01G470900 chr2B 74.502 502 121 5 1007 1506 691051625 691052121 7.090000e-51 211.0
13 TraesCS2D01G470900 chr2A 93.822 777 48 0 763 1539 713461404 713462180 0.000000e+00 1170.0
14 TraesCS2D01G470900 chr2A 94.595 481 16 5 288 767 713455780 713456251 0.000000e+00 736.0
15 TraesCS2D01G470900 chr2A 86.454 502 37 13 1545 2016 713493306 713493806 2.890000e-144 521.0
16 TraesCS2D01G470900 chr2A 87.535 353 44 0 1191 1543 713453496 713453848 2.340000e-110 409.0
17 TraesCS2D01G470900 chrUn 100.000 545 0 0 1987 2531 371729398 371729942 0.000000e+00 1007.0
18 TraesCS2D01G470900 chrUn 81.928 83 13 2 1441 1522 476800727 476800646 4.520000e-08 69.4
19 TraesCS2D01G470900 chr5D 97.683 518 11 1 2015 2531 464467123 464467640 0.000000e+00 889.0
20 TraesCS2D01G470900 chr6D 97.481 516 11 2 2017 2531 20742215 20741701 0.000000e+00 880.0
21 TraesCS2D01G470900 chr6D 97.481 516 12 1 2017 2531 100796285 100796800 0.000000e+00 880.0
22 TraesCS2D01G470900 chr1D 97.481 516 12 1 2017 2531 67034934 67035449 0.000000e+00 880.0
23 TraesCS2D01G470900 chr7D 97.292 517 13 1 2016 2531 54488353 54487837 0.000000e+00 876.0
24 TraesCS2D01G470900 chr4D 97.110 519 14 1 2014 2531 413992948 413993466 0.000000e+00 874.0
25 TraesCS2D01G470900 chr3D 97.287 516 13 1 2017 2531 100744342 100744857 0.000000e+00 874.0


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 TraesCS2D01G470900 chr2D 575215892 575218422 2530 False 4674.000000 4674 100.000000 1 2531 1 chr2D.!!$F3 2530
1 TraesCS2D01G470900 chr2D 635698436 635698951 515 False 880.000000 880 97.481000 2017 2531 1 chr2D.!!$F4 514
2 TraesCS2D01G470900 chr2B 691402068 691403147 1079 False 1122.000000 1122 85.438000 461 1543 1 chr2B.!!$F2 1082
3 TraesCS2D01G470900 chr2B 691186962 691190885 3923 False 845.000000 1797 88.896000 291 1944 4 chr2B.!!$F3 1653
4 TraesCS2D01G470900 chr2B 691413116 691414835 1719 False 676.333333 1509 90.256667 293 1932 3 chr2B.!!$F4 1639
5 TraesCS2D01G470900 chr2A 713461404 713462180 776 False 1170.000000 1170 93.822000 763 1539 1 chr2A.!!$F1 776
6 TraesCS2D01G470900 chr2A 713453496 713456251 2755 False 572.500000 736 91.065000 288 1543 2 chr2A.!!$F3 1255
7 TraesCS2D01G470900 chr2A 713493306 713493806 500 False 521.000000 521 86.454000 1545 2016 1 chr2A.!!$F2 471
8 TraesCS2D01G470900 chrUn 371729398 371729942 544 False 1007.000000 1007 100.000000 1987 2531 1 chrUn.!!$F1 544
9 TraesCS2D01G470900 chr5D 464467123 464467640 517 False 889.000000 889 97.683000 2015 2531 1 chr5D.!!$F1 516
10 TraesCS2D01G470900 chr6D 20741701 20742215 514 True 880.000000 880 97.481000 2017 2531 1 chr6D.!!$R1 514
11 TraesCS2D01G470900 chr6D 100796285 100796800 515 False 880.000000 880 97.481000 2017 2531 1 chr6D.!!$F1 514
12 TraesCS2D01G470900 chr1D 67034934 67035449 515 False 880.000000 880 97.481000 2017 2531 1 chr1D.!!$F1 514
13 TraesCS2D01G470900 chr7D 54487837 54488353 516 True 876.000000 876 97.292000 2016 2531 1 chr7D.!!$R1 515
14 TraesCS2D01G470900 chr4D 413992948 413993466 518 False 874.000000 874 97.110000 2014 2531 1 chr4D.!!$F1 517
15 TraesCS2D01G470900 chr3D 100744342 100744857 515 False 874.000000 874 97.287000 2017 2531 1 chr3D.!!$F1 514

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
192 193 0.036671 GTGTGTTTAGCTAGCCCGGT 60.037 55.0 12.13 0.0 0.0 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1715 3755 0.512952 GAACGAGCGAGCAACACAAT 59.487 50.0 0.0 0.0 0.0 2.71 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
31 32 4.992511 TTAACGCGGCGCCACCTT 62.993 61.111 28.98 15.50 35.61 3.50
38 39 3.056328 GGCGCCACCTTCCTTCAC 61.056 66.667 24.80 0.00 34.51 3.18
39 40 2.032681 GCGCCACCTTCCTTCACT 59.967 61.111 0.00 0.00 0.00 3.41
40 41 1.600916 GCGCCACCTTCCTTCACTT 60.601 57.895 0.00 0.00 0.00 3.16
41 42 1.172812 GCGCCACCTTCCTTCACTTT 61.173 55.000 0.00 0.00 0.00 2.66
43 44 1.681264 CGCCACCTTCCTTCACTTTTT 59.319 47.619 0.00 0.00 0.00 1.94
44 45 2.882137 CGCCACCTTCCTTCACTTTTTA 59.118 45.455 0.00 0.00 0.00 1.52
45 46 3.304458 CGCCACCTTCCTTCACTTTTTAC 60.304 47.826 0.00 0.00 0.00 2.01
47 48 4.211920 CCACCTTCCTTCACTTTTTACCA 58.788 43.478 0.00 0.00 0.00 3.25
49 50 5.221244 CCACCTTCCTTCACTTTTTACCAAG 60.221 44.000 0.00 0.00 0.00 3.61
50 51 5.359860 CACCTTCCTTCACTTTTTACCAAGT 59.640 40.000 0.00 0.00 37.49 3.16
52 53 6.439375 ACCTTCCTTCACTTTTTACCAAGTTT 59.561 34.615 0.00 0.00 34.60 2.66
53 54 7.038587 ACCTTCCTTCACTTTTTACCAAGTTTT 60.039 33.333 0.00 0.00 34.60 2.43
95 96 5.356882 TTTTCTATTGACTTTGGACGCTG 57.643 39.130 0.00 0.00 0.00 5.18
96 97 3.953712 TCTATTGACTTTGGACGCTGA 57.046 42.857 0.00 0.00 0.00 4.26
97 98 3.585862 TCTATTGACTTTGGACGCTGAC 58.414 45.455 0.00 0.00 0.00 3.51
99 100 1.495584 TTGACTTTGGACGCTGACGC 61.496 55.000 0.00 0.00 45.53 5.19
100 101 1.664965 GACTTTGGACGCTGACGCT 60.665 57.895 0.00 0.00 45.53 5.07
101 102 0.388134 GACTTTGGACGCTGACGCTA 60.388 55.000 0.00 0.00 45.53 4.26
102 103 0.388649 ACTTTGGACGCTGACGCTAG 60.389 55.000 0.00 0.00 45.53 3.42
103 104 1.687494 CTTTGGACGCTGACGCTAGC 61.687 60.000 4.06 4.06 45.53 3.42
104 105 2.428960 TTTGGACGCTGACGCTAGCA 62.429 55.000 16.45 0.00 45.53 3.49
105 106 2.126071 GGACGCTGACGCTAGCAA 60.126 61.111 16.45 0.00 45.53 3.91
106 107 1.736645 GGACGCTGACGCTAGCAAA 60.737 57.895 16.45 0.00 45.53 3.68
107 108 1.416434 GACGCTGACGCTAGCAAAC 59.584 57.895 16.45 5.71 45.53 2.93
108 109 1.282248 GACGCTGACGCTAGCAAACA 61.282 55.000 16.45 10.10 45.53 2.83
109 110 0.878523 ACGCTGACGCTAGCAAACAA 60.879 50.000 16.45 0.00 45.53 2.83
110 111 0.234625 CGCTGACGCTAGCAAACAAA 59.765 50.000 16.45 0.00 43.87 2.83
111 112 1.333702 CGCTGACGCTAGCAAACAAAA 60.334 47.619 16.45 0.00 43.87 2.44
112 113 2.665519 CGCTGACGCTAGCAAACAAAAT 60.666 45.455 16.45 0.00 43.87 1.82
113 114 2.911102 GCTGACGCTAGCAAACAAAATC 59.089 45.455 16.45 0.00 43.17 2.17
114 115 3.492313 CTGACGCTAGCAAACAAAATCC 58.508 45.455 16.45 0.00 0.00 3.01
115 116 2.881513 TGACGCTAGCAAACAAAATCCA 59.118 40.909 16.45 0.00 0.00 3.41
116 117 3.316588 TGACGCTAGCAAACAAAATCCAA 59.683 39.130 16.45 0.00 0.00 3.53
117 118 3.900941 ACGCTAGCAAACAAAATCCAAG 58.099 40.909 16.45 0.00 0.00 3.61
119 120 4.202111 ACGCTAGCAAACAAAATCCAAGTT 60.202 37.500 16.45 0.00 0.00 2.66
120 121 4.744631 CGCTAGCAAACAAAATCCAAGTTT 59.255 37.500 16.45 0.00 36.00 2.66
121 122 5.234116 CGCTAGCAAACAAAATCCAAGTTTT 59.766 36.000 16.45 0.00 33.54 2.43
122 123 6.238076 CGCTAGCAAACAAAATCCAAGTTTTT 60.238 34.615 16.45 0.00 33.54 1.94
171 172 3.714963 AAAAACCCGGCGTACGCG 61.715 61.111 31.78 25.32 43.06 6.01
181 182 3.136605 CGTACGCGCGTGTGTTTA 58.863 55.556 42.78 21.62 40.00 2.01
183 184 1.225289 GTACGCGCGTGTGTTTAGC 60.225 57.895 42.78 18.61 40.00 3.09
185 186 0.109827 TACGCGCGTGTGTTTAGCTA 60.110 50.000 42.78 18.35 40.00 3.32
186 187 1.340465 CGCGCGTGTGTTTAGCTAG 59.660 57.895 24.19 0.00 0.00 3.42
187 188 1.058903 GCGCGTGTGTTTAGCTAGC 59.941 57.895 6.62 6.62 0.00 3.42
190 191 1.693083 GCGTGTGTTTAGCTAGCCCG 61.693 60.000 12.13 2.50 0.00 6.13
191 192 1.082117 CGTGTGTTTAGCTAGCCCGG 61.082 60.000 12.13 0.00 0.00 5.73
192 193 0.036671 GTGTGTTTAGCTAGCCCGGT 60.037 55.000 12.13 0.00 0.00 5.28
193 194 0.036765 TGTGTTTAGCTAGCCCGGTG 60.037 55.000 12.13 0.00 0.00 4.94
194 195 0.248289 GTGTTTAGCTAGCCCGGTGA 59.752 55.000 12.13 0.00 0.00 4.02
195 196 0.248289 TGTTTAGCTAGCCCGGTGAC 59.752 55.000 12.13 2.88 0.00 3.67
208 209 2.387309 GGTGACGTCTCATGCATGG 58.613 57.895 25.97 16.47 0.00 3.66
209 210 0.391661 GGTGACGTCTCATGCATGGT 60.392 55.000 25.97 15.76 0.00 3.55
210 211 1.442769 GTGACGTCTCATGCATGGTT 58.557 50.000 25.97 6.50 0.00 3.67
212 213 1.270785 TGACGTCTCATGCATGGTTGT 60.271 47.619 25.97 18.30 0.00 3.32
213 214 1.129251 GACGTCTCATGCATGGTTGTG 59.871 52.381 25.97 14.48 0.00 3.33
214 215 1.159285 CGTCTCATGCATGGTTGTGT 58.841 50.000 25.97 0.00 0.00 3.72
215 216 2.289382 ACGTCTCATGCATGGTTGTGTA 60.289 45.455 25.97 4.34 0.00 2.90
216 217 2.094258 CGTCTCATGCATGGTTGTGTAC 59.906 50.000 25.97 12.25 0.00 2.90
218 219 2.076100 CTCATGCATGGTTGTGTACGT 58.924 47.619 25.97 0.00 0.00 3.57
220 221 1.535028 CATGCATGGTTGTGTACGTGT 59.465 47.619 19.40 0.00 0.00 4.49
221 222 2.528041 TGCATGGTTGTGTACGTGTA 57.472 45.000 0.00 0.00 0.00 2.90
222 223 2.136728 TGCATGGTTGTGTACGTGTAC 58.863 47.619 0.00 3.21 36.63 2.90
223 224 1.125384 GCATGGTTGTGTACGTGTACG 59.875 52.381 0.00 2.43 46.33 3.67
233 234 4.896881 CGTGTACGTGCGAATTCG 57.103 55.556 23.34 23.34 37.19 3.34
234 235 1.339134 CGTGTACGTGCGAATTCGG 59.661 57.895 27.78 14.60 35.70 4.30
235 236 1.339235 CGTGTACGTGCGAATTCGGT 61.339 55.000 27.78 19.25 35.70 4.69
249 250 4.882447 GAATTCGGTTCGTATTCTGTGTG 58.118 43.478 10.77 0.00 39.38 3.82
250 251 3.374220 TTCGGTTCGTATTCTGTGTGT 57.626 42.857 0.00 0.00 0.00 3.72
251 252 4.502171 TTCGGTTCGTATTCTGTGTGTA 57.498 40.909 0.00 0.00 0.00 2.90
253 254 2.591148 CGGTTCGTATTCTGTGTGTACG 59.409 50.000 0.00 0.00 41.71 3.67
259 260 4.789629 TCGTATTCTGTGTGTACGAAATCG 59.210 41.667 0.48 0.48 44.78 3.34
260 261 4.789629 CGTATTCTGTGTGTACGAAATCGA 59.210 41.667 10.16 0.00 42.65 3.59
261 262 5.284424 CGTATTCTGTGTGTACGAAATCGAA 59.716 40.000 10.16 0.00 42.65 3.71
262 263 4.959631 TTCTGTGTGTACGAAATCGAAC 57.040 40.909 10.16 5.61 43.02 3.95
263 264 2.975193 TCTGTGTGTACGAAATCGAACG 59.025 45.455 10.16 8.11 43.02 3.95
266 267 2.472488 GTGTGTACGAAATCGAACGGTT 59.528 45.455 10.16 0.00 43.02 4.44
267 268 3.060339 GTGTGTACGAAATCGAACGGTTT 60.060 43.478 10.16 5.14 43.02 3.27
268 269 4.148000 GTGTGTACGAAATCGAACGGTTTA 59.852 41.667 10.16 0.00 43.02 2.01
270 271 4.616802 GTGTACGAAATCGAACGGTTTAGA 59.383 41.667 16.79 0.00 43.02 2.10
271 272 4.853196 TGTACGAAATCGAACGGTTTAGAG 59.147 41.667 16.79 9.42 43.02 2.43
272 273 2.665052 ACGAAATCGAACGGTTTAGAGC 59.335 45.455 16.79 1.04 43.02 4.09
273 274 2.284288 CGAAATCGAACGGTTTAGAGCG 60.284 50.000 5.45 3.00 46.39 5.03
278 279 3.509388 AACGGTTTAGAGCGGTCAG 57.491 52.632 18.15 3.33 44.57 3.51
279 280 0.037605 AACGGTTTAGAGCGGTCAGG 60.038 55.000 18.15 1.54 44.57 3.86
280 281 1.888018 CGGTTTAGAGCGGTCAGGA 59.112 57.895 18.15 0.00 42.72 3.86
281 282 0.460311 CGGTTTAGAGCGGTCAGGAT 59.540 55.000 18.15 0.00 42.72 3.24
282 283 1.536284 CGGTTTAGAGCGGTCAGGATC 60.536 57.143 18.15 0.94 42.72 3.36
283 284 1.202545 GGTTTAGAGCGGTCAGGATCC 60.203 57.143 18.15 2.48 0.00 3.36
284 285 1.757699 GTTTAGAGCGGTCAGGATCCT 59.242 52.381 18.15 9.02 0.00 3.24
285 286 1.693627 TTAGAGCGGTCAGGATCCTC 58.306 55.000 12.69 0.74 0.00 3.71
286 287 0.178987 TAGAGCGGTCAGGATCCTCC 60.179 60.000 12.69 10.58 36.58 4.30
287 288 2.835431 AGCGGTCAGGATCCTCCG 60.835 66.667 29.12 29.12 42.75 4.63
288 289 3.148279 GCGGTCAGGATCCTCCGT 61.148 66.667 31.63 4.67 42.75 4.69
289 290 1.826921 GCGGTCAGGATCCTCCGTA 60.827 63.158 31.63 10.31 42.75 4.02
290 291 1.179814 GCGGTCAGGATCCTCCGTAT 61.180 60.000 31.63 3.59 42.75 3.06
319 2242 1.227205 CATGGCAGAGCGGAGAGAC 60.227 63.158 0.00 0.00 0.00 3.36
326 2249 3.375922 GGCAGAGCGGAGAGACTATATAC 59.624 52.174 0.00 0.00 0.00 1.47
330 2253 6.636705 CAGAGCGGAGAGACTATATACTACT 58.363 44.000 0.00 0.00 0.00 2.57
331 2254 6.755141 CAGAGCGGAGAGACTATATACTACTC 59.245 46.154 0.00 0.00 0.00 2.59
337 2260 6.972328 GGAGAGACTATATACTACTCCGTACG 59.028 46.154 8.69 8.69 34.26 3.67
338 2261 7.148154 GGAGAGACTATATACTACTCCGTACGA 60.148 44.444 18.76 1.79 34.26 3.43
339 2262 7.535139 AGAGACTATATACTACTCCGTACGAC 58.465 42.308 18.76 0.00 0.00 4.34
340 2263 7.175816 AGAGACTATATACTACTCCGTACGACA 59.824 40.741 18.76 1.31 0.00 4.35
343 2266 1.640428 TACTACTCCGTACGACACCG 58.360 55.000 18.76 4.60 42.50 4.94
345 2268 2.315038 CTACTCCGTACGACACCGGC 62.315 65.000 18.76 0.00 43.87 6.13
391 2314 8.347771 TGTCAAGTTCTCCGTATACATATACAC 58.652 37.037 3.32 0.78 38.72 2.90
392 2315 8.347771 GTCAAGTTCTCCGTATACATATACACA 58.652 37.037 3.32 0.00 38.72 3.72
394 2317 9.181805 CAAGTTCTCCGTATACATATACACAAG 57.818 37.037 3.32 3.95 38.72 3.16
395 2318 8.687292 AGTTCTCCGTATACATATACACAAGA 57.313 34.615 3.32 5.75 38.72 3.02
396 2319 8.566260 AGTTCTCCGTATACATATACACAAGAC 58.434 37.037 3.32 3.19 38.72 3.01
397 2320 7.444629 TCTCCGTATACATATACACAAGACC 57.555 40.000 3.32 0.00 38.72 3.85
426 2349 1.226888 GTCGTGACCTACCCATCGC 60.227 63.158 0.00 0.00 0.00 4.58
427 2350 2.278596 CGTGACCTACCCATCGCG 60.279 66.667 0.00 0.00 41.81 5.87
428 2351 2.585247 GTGACCTACCCATCGCGC 60.585 66.667 0.00 0.00 0.00 6.86
443 2366 2.911143 CGCCCTGCACTCCCTTAT 59.089 61.111 0.00 0.00 0.00 1.73
641 2587 1.470805 CGGCTACACATGGACGATCAA 60.471 52.381 0.00 0.00 0.00 2.57
717 2664 0.539207 TGTATTGCACCAGCCAAGCA 60.539 50.000 0.00 0.00 41.13 3.91
730 2677 1.021202 CCAAGCAAACAACGTGAGGA 58.979 50.000 0.00 0.00 0.00 3.71
741 2688 2.569134 GTGAGGACGCGCTTCTCT 59.431 61.111 14.02 9.03 0.00 3.10
834 2781 0.889186 CACCACACTACAGTTGGGGC 60.889 60.000 12.28 0.00 33.49 5.80
1101 3049 2.750166 TGCACGTTCTCTGGTTTTCAAA 59.250 40.909 0.00 0.00 0.00 2.69
1236 3189 2.099921 AGATGACGATGAAGACGAAGGG 59.900 50.000 0.00 0.00 34.70 3.95
1335 3288 2.541120 GCTGCATGAGGGCATCGAC 61.541 63.158 0.00 0.00 43.97 4.20
1470 3423 2.159282 GGCAACTGATGGATTCAAGCAG 60.159 50.000 4.74 4.74 36.26 4.24
1478 3431 1.550524 TGGATTCAAGCAGCTCGTAGT 59.449 47.619 0.00 0.00 0.00 2.73
1481 3434 3.552294 GGATTCAAGCAGCTCGTAGTTAC 59.448 47.826 0.00 0.00 0.00 2.50
1512 3465 6.499106 TTGCTCATGGAGGATATACTGAAA 57.501 37.500 0.00 0.00 28.56 2.69
1570 3564 9.606631 GACCATGTTAGATTTTAGTCATCTTCT 57.393 33.333 0.00 0.00 32.94 2.85
1604 3642 8.516234 ACACTTTTTACGTTGCCATGATAATTA 58.484 29.630 0.00 0.00 0.00 1.40
1707 3747 8.063200 TCGAGAAAAAGATAGGATTGTAGTCA 57.937 34.615 0.00 0.00 0.00 3.41
1715 3755 7.862274 AGATAGGATTGTAGTCATGGATGAA 57.138 36.000 0.00 0.00 38.75 2.57
1719 3759 6.666678 AGGATTGTAGTCATGGATGAATTGT 58.333 36.000 0.00 0.00 38.75 2.71
1728 3768 1.199789 TGGATGAATTGTGTTGCTCGC 59.800 47.619 0.00 0.00 0.00 5.03
1745 3785 1.476891 TCGCTCGTTCTATCTTTGCCT 59.523 47.619 0.00 0.00 0.00 4.75
1811 3881 2.176045 TCCACTGATGAACTAAGCCGA 58.824 47.619 0.00 0.00 0.00 5.54
1815 3885 3.093057 ACTGATGAACTAAGCCGACTCT 58.907 45.455 0.00 0.00 0.00 3.24
1925 5105 2.223611 AGATTAGCGACACGGACTATCG 59.776 50.000 0.00 0.00 38.87 2.92
1975 5178 2.424234 CCCCTCCTGACAGGAAAAACAA 60.424 50.000 24.34 1.12 45.28 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 4.992511 AAGGTGGCGCCGCGTTAA 62.993 61.111 38.26 12.21 43.70 2.01
20 21 4.697756 TGAAGGAAGGTGGCGCCG 62.698 66.667 23.90 0.00 43.70 6.46
25 26 4.211920 TGGTAAAAAGTGAAGGAAGGTGG 58.788 43.478 0.00 0.00 0.00 4.61
26 27 5.359860 ACTTGGTAAAAAGTGAAGGAAGGTG 59.640 40.000 0.00 0.00 38.95 4.00
27 28 5.516044 ACTTGGTAAAAAGTGAAGGAAGGT 58.484 37.500 0.00 0.00 38.95 3.50
28 29 6.465439 AACTTGGTAAAAAGTGAAGGAAGG 57.535 37.500 0.00 0.00 40.28 3.46
73 74 5.049680 GTCAGCGTCCAAAGTCAATAGAAAA 60.050 40.000 0.00 0.00 0.00 2.29
74 75 4.451096 GTCAGCGTCCAAAGTCAATAGAAA 59.549 41.667 0.00 0.00 0.00 2.52
75 76 3.994392 GTCAGCGTCCAAAGTCAATAGAA 59.006 43.478 0.00 0.00 0.00 2.10
78 79 2.333926 CGTCAGCGTCCAAAGTCAATA 58.666 47.619 0.00 0.00 0.00 1.90
80 81 1.495584 GCGTCAGCGTCCAAAGTCAA 61.496 55.000 0.00 0.00 40.81 3.18
81 82 1.954146 GCGTCAGCGTCCAAAGTCA 60.954 57.895 0.00 0.00 40.81 3.41
82 83 2.853914 GCGTCAGCGTCCAAAGTC 59.146 61.111 0.00 0.00 40.81 3.01
94 95 2.881513 TGGATTTTGTTTGCTAGCGTCA 59.118 40.909 10.77 6.23 0.00 4.35
95 96 3.552604 TGGATTTTGTTTGCTAGCGTC 57.447 42.857 10.77 3.50 0.00 5.19
96 97 3.317993 ACTTGGATTTTGTTTGCTAGCGT 59.682 39.130 10.77 0.00 0.00 5.07
97 98 3.900941 ACTTGGATTTTGTTTGCTAGCG 58.099 40.909 10.77 0.00 0.00 4.26
98 99 6.603237 AAAACTTGGATTTTGTTTGCTAGC 57.397 33.333 8.10 8.10 34.63 3.42
165 166 1.225289 GCTAAACACACGCGCGTAC 60.225 57.895 37.24 13.29 0.00 3.67
166 167 0.109827 TAGCTAAACACACGCGCGTA 60.110 50.000 37.24 18.45 0.00 4.42
167 168 1.342082 CTAGCTAAACACACGCGCGT 61.342 55.000 32.73 32.73 0.00 6.01
168 169 1.340465 CTAGCTAAACACACGCGCG 59.660 57.895 30.96 30.96 0.00 6.86
169 170 1.058903 GCTAGCTAAACACACGCGC 59.941 57.895 5.73 0.00 0.00 6.86
171 172 1.693083 CGGGCTAGCTAAACACACGC 61.693 60.000 15.72 0.00 0.00 5.34
172 173 1.082117 CCGGGCTAGCTAAACACACG 61.082 60.000 15.72 6.65 0.00 4.49
174 175 0.036765 CACCGGGCTAGCTAAACACA 60.037 55.000 15.72 0.00 0.00 3.72
175 176 0.248289 TCACCGGGCTAGCTAAACAC 59.752 55.000 15.72 0.00 0.00 3.32
176 177 0.248289 GTCACCGGGCTAGCTAAACA 59.752 55.000 15.72 0.00 0.00 2.83
177 178 0.804933 CGTCACCGGGCTAGCTAAAC 60.805 60.000 15.72 0.00 0.00 2.01
179 180 1.660560 GACGTCACCGGGCTAGCTAA 61.661 60.000 15.72 0.00 38.78 3.09
180 181 2.044650 ACGTCACCGGGCTAGCTA 60.045 61.111 15.72 0.00 38.78 3.32
181 182 3.450115 GACGTCACCGGGCTAGCT 61.450 66.667 15.72 0.00 38.78 3.32
183 184 1.384989 ATGAGACGTCACCGGGCTAG 61.385 60.000 19.50 0.00 38.78 3.42
185 186 2.680352 ATGAGACGTCACCGGGCT 60.680 61.111 19.50 0.00 38.78 5.19
186 187 2.509336 CATGAGACGTCACCGGGC 60.509 66.667 19.50 0.19 38.78 6.13
187 188 2.509336 GCATGAGACGTCACCGGG 60.509 66.667 19.50 4.90 38.78 5.73
190 191 0.391661 ACCATGCATGAGACGTCACC 60.392 55.000 28.31 9.65 34.75 4.02
191 192 1.129251 CAACCATGCATGAGACGTCAC 59.871 52.381 28.31 12.69 34.75 3.67
192 193 1.270785 ACAACCATGCATGAGACGTCA 60.271 47.619 28.31 0.00 37.02 4.35
193 194 1.129251 CACAACCATGCATGAGACGTC 59.871 52.381 28.31 7.70 0.00 4.34
194 195 1.159285 CACAACCATGCATGAGACGT 58.841 50.000 28.31 14.06 0.00 4.34
195 196 1.159285 ACACAACCATGCATGAGACG 58.841 50.000 28.31 13.38 0.00 4.18
197 198 2.289382 ACGTACACAACCATGCATGAGA 60.289 45.455 28.31 1.94 0.00 3.27
198 199 2.076100 ACGTACACAACCATGCATGAG 58.924 47.619 28.31 19.16 0.00 2.90
199 200 1.803555 CACGTACACAACCATGCATGA 59.196 47.619 28.31 2.78 0.00 3.07
200 201 1.535028 ACACGTACACAACCATGCATG 59.465 47.619 20.19 20.19 0.00 4.06
201 202 1.890876 ACACGTACACAACCATGCAT 58.109 45.000 0.00 0.00 0.00 3.96
202 203 2.136728 GTACACGTACACAACCATGCA 58.863 47.619 2.45 0.00 36.15 3.96
213 214 4.134025 CCGAATTCGCACGTACACGTAC 62.134 54.545 22.36 0.70 44.03 3.67
214 215 2.050725 CCGAATTCGCACGTACACGTA 61.051 52.381 22.36 0.00 44.03 3.57
215 216 1.339235 CCGAATTCGCACGTACACGT 61.339 55.000 22.36 0.68 44.60 4.49
216 217 1.339134 CCGAATTCGCACGTACACG 59.661 57.895 22.36 0.00 40.91 4.49
218 219 1.062258 GAACCGAATTCGCACGTACA 58.938 50.000 22.36 0.00 38.18 2.90
227 228 4.387862 ACACACAGAATACGAACCGAATTC 59.612 41.667 0.00 0.00 0.00 2.17
228 229 4.312443 ACACACAGAATACGAACCGAATT 58.688 39.130 0.00 0.00 0.00 2.17
229 230 3.921677 ACACACAGAATACGAACCGAAT 58.078 40.909 0.00 0.00 0.00 3.34
230 231 3.374220 ACACACAGAATACGAACCGAA 57.626 42.857 0.00 0.00 0.00 4.30
232 233 2.591148 CGTACACACAGAATACGAACCG 59.409 50.000 0.00 0.00 43.37 4.44
233 234 3.825308 TCGTACACACAGAATACGAACC 58.175 45.455 3.43 0.00 45.52 3.62
238 239 6.456026 GTTCGATTTCGTACACACAGAATAC 58.544 40.000 5.07 0.00 39.06 1.89
240 241 4.089493 CGTTCGATTTCGTACACACAGAAT 59.911 41.667 9.78 0.00 39.16 2.40
241 242 3.422876 CGTTCGATTTCGTACACACAGAA 59.577 43.478 9.78 0.00 39.16 3.02
243 244 2.090041 CCGTTCGATTTCGTACACACAG 59.910 50.000 9.78 0.00 39.16 3.66
244 245 2.052891 CCGTTCGATTTCGTACACACA 58.947 47.619 9.78 0.00 39.16 3.72
245 246 2.053627 ACCGTTCGATTTCGTACACAC 58.946 47.619 9.78 0.00 39.16 3.82
246 247 2.420628 ACCGTTCGATTTCGTACACA 57.579 45.000 9.78 0.00 39.16 3.72
247 248 3.776043 AAACCGTTCGATTTCGTACAC 57.224 42.857 9.78 1.51 39.16 2.90
248 249 4.793071 TCTAAACCGTTCGATTTCGTACA 58.207 39.130 9.78 0.00 39.16 2.90
249 250 4.259174 GCTCTAAACCGTTCGATTTCGTAC 60.259 45.833 0.00 0.00 40.80 3.67
250 251 3.853671 GCTCTAAACCGTTCGATTTCGTA 59.146 43.478 0.00 0.00 40.80 3.43
251 252 2.665052 GCTCTAAACCGTTCGATTTCGT 59.335 45.455 0.00 0.00 40.80 3.85
253 254 2.028883 CCGCTCTAAACCGTTCGATTTC 59.971 50.000 0.00 0.00 0.00 2.17
255 256 1.067354 ACCGCTCTAAACCGTTCGATT 60.067 47.619 0.00 0.00 0.00 3.34
256 257 0.529378 ACCGCTCTAAACCGTTCGAT 59.471 50.000 0.00 0.00 0.00 3.59
257 258 0.109597 GACCGCTCTAAACCGTTCGA 60.110 55.000 0.00 0.00 0.00 3.71
258 259 0.387622 TGACCGCTCTAAACCGTTCG 60.388 55.000 0.00 0.00 0.00 3.95
259 260 1.347320 CTGACCGCTCTAAACCGTTC 58.653 55.000 0.00 0.00 0.00 3.95
260 261 0.037605 CCTGACCGCTCTAAACCGTT 60.038 55.000 0.00 0.00 0.00 4.44
261 262 0.896940 TCCTGACCGCTCTAAACCGT 60.897 55.000 0.00 0.00 0.00 4.83
262 263 0.460311 ATCCTGACCGCTCTAAACCG 59.540 55.000 0.00 0.00 0.00 4.44
263 264 1.202545 GGATCCTGACCGCTCTAAACC 60.203 57.143 3.84 0.00 0.00 3.27
266 267 1.693627 GAGGATCCTGACCGCTCTAA 58.306 55.000 22.02 0.00 0.00 2.10
267 268 3.423344 GAGGATCCTGACCGCTCTA 57.577 57.895 22.02 0.00 0.00 2.43
268 269 4.268720 GAGGATCCTGACCGCTCT 57.731 61.111 22.02 0.00 0.00 4.09
279 280 6.158023 TGTAAGGAGAAAATACGGAGGATC 57.842 41.667 0.00 0.00 0.00 3.36
280 281 6.464465 CCATGTAAGGAGAAAATACGGAGGAT 60.464 42.308 0.00 0.00 0.00 3.24
281 282 5.163343 CCATGTAAGGAGAAAATACGGAGGA 60.163 44.000 0.00 0.00 0.00 3.71
282 283 5.057149 CCATGTAAGGAGAAAATACGGAGG 58.943 45.833 0.00 0.00 0.00 4.30
283 284 4.511826 GCCATGTAAGGAGAAAATACGGAG 59.488 45.833 0.00 0.00 0.00 4.63
284 285 4.080807 TGCCATGTAAGGAGAAAATACGGA 60.081 41.667 0.00 0.00 0.00 4.69
285 286 4.196193 TGCCATGTAAGGAGAAAATACGG 58.804 43.478 0.00 0.00 0.00 4.02
286 287 5.116180 TCTGCCATGTAAGGAGAAAATACG 58.884 41.667 0.00 0.00 0.00 3.06
287 288 5.008118 GCTCTGCCATGTAAGGAGAAAATAC 59.992 44.000 0.00 0.00 0.00 1.89
288 289 5.126067 GCTCTGCCATGTAAGGAGAAAATA 58.874 41.667 0.00 0.00 0.00 1.40
289 290 3.950395 GCTCTGCCATGTAAGGAGAAAAT 59.050 43.478 0.00 0.00 0.00 1.82
290 291 3.347216 GCTCTGCCATGTAAGGAGAAAA 58.653 45.455 0.00 0.00 0.00 2.29
333 2256 2.774799 ATACGGGCCGGTGTCGTAC 61.775 63.158 31.78 0.00 41.23 3.67
334 2257 2.440065 ATACGGGCCGGTGTCGTA 60.440 61.111 31.78 18.52 42.34 3.43
335 2258 4.137872 CATACGGGCCGGTGTCGT 62.138 66.667 31.78 16.91 40.40 4.34
353 2276 6.430451 GGAGAACTTGACATTATTATTGCCG 58.570 40.000 0.00 0.00 0.00 5.69
365 2288 8.347771 GTGTATATGTATACGGAGAACTTGACA 58.652 37.037 0.00 0.00 41.04 3.58
383 2306 3.780902 TGAGCGTGGTCTTGTGTATATG 58.219 45.455 0.39 0.00 0.00 1.78
387 2310 3.257375 ACTTATGAGCGTGGTCTTGTGTA 59.743 43.478 0.39 0.00 0.00 2.90
391 2314 1.920574 CGACTTATGAGCGTGGTCTTG 59.079 52.381 0.39 0.00 0.00 3.02
392 2315 1.544691 ACGACTTATGAGCGTGGTCTT 59.455 47.619 6.26 0.00 35.42 3.01
394 2317 1.135489 TCACGACTTATGAGCGTGGTC 60.135 52.381 23.55 0.00 45.17 4.02
395 2318 0.885879 TCACGACTTATGAGCGTGGT 59.114 50.000 23.55 0.00 45.17 4.16
396 2319 1.269166 GTCACGACTTATGAGCGTGG 58.731 55.000 23.55 12.32 45.17 4.94
397 2320 1.135373 AGGTCACGACTTATGAGCGTG 60.135 52.381 20.41 20.41 46.74 5.34
426 2349 1.097547 CAATAAGGGAGTGCAGGGCG 61.098 60.000 0.00 0.00 0.00 6.13
427 2350 2.799176 CAATAAGGGAGTGCAGGGC 58.201 57.895 0.00 0.00 0.00 5.19
589 2535 0.787183 GTGCTCGAGCTGACAAACTC 59.213 55.000 35.27 12.17 42.66 3.01
730 2677 2.022129 CGTCCAAAGAGAAGCGCGT 61.022 57.895 8.43 0.00 0.00 6.01
741 2688 2.649531 ATTTCTCCACCACGTCCAAA 57.350 45.000 0.00 0.00 0.00 3.28
834 2781 6.207614 TCGATTTCTGGACATATCTCTGGTAG 59.792 42.308 0.00 0.00 0.00 3.18
975 2923 1.684386 CGAGGCTCTCCATCAGGCTT 61.684 60.000 13.50 0.00 46.34 4.35
982 2930 1.047596 ATGTGCTCGAGGCTCTCCAT 61.048 55.000 15.58 4.44 42.39 3.41
983 2931 1.683707 ATGTGCTCGAGGCTCTCCA 60.684 57.895 15.58 3.80 42.39 3.86
1101 3049 1.768684 TTGGTCCAAAGAGCTCCGCT 61.769 55.000 10.93 0.00 43.88 5.52
1119 3067 3.160269 CCCTGTCTTGCTTTCCTTCATT 58.840 45.455 0.00 0.00 0.00 2.57
1296 3249 5.048921 CAGCTTGTCTTCACACATGATCTTT 60.049 40.000 0.00 0.00 33.85 2.52
1470 3423 3.123116 GCAAAGGACAAGTAACTACGAGC 59.877 47.826 0.00 0.00 0.00 5.03
1478 3431 4.326826 CTCCATGAGCAAAGGACAAGTAA 58.673 43.478 0.00 0.00 0.00 2.24
1481 3434 2.089980 CCTCCATGAGCAAAGGACAAG 58.910 52.381 0.00 0.00 0.00 3.16
1570 3564 5.575995 GGCAACGTAAAAAGTGTGGTAAAAA 59.424 36.000 0.00 0.00 0.00 1.94
1616 3655 9.601217 AAATGTGAAATCGAGTAGCTTATAAGT 57.399 29.630 13.91 3.98 0.00 2.24
1707 3747 2.159338 GCGAGCAACACAATTCATCCAT 60.159 45.455 0.00 0.00 0.00 3.41
1715 3755 0.512952 GAACGAGCGAGCAACACAAT 59.487 50.000 0.00 0.00 0.00 2.71
1719 3759 1.472878 AGATAGAACGAGCGAGCAACA 59.527 47.619 0.00 0.00 0.00 3.33
1728 3768 1.590238 CGCAGGCAAAGATAGAACGAG 59.410 52.381 0.00 0.00 0.00 4.18
1811 3881 5.009811 GGATCGCTACACATTTACCTAGAGT 59.990 44.000 0.00 0.00 0.00 3.24
1815 3885 4.038763 CAGGGATCGCTACACATTTACCTA 59.961 45.833 12.54 0.00 0.00 3.08
1894 4820 4.553815 CGTGTCGCTAATCTACCATTATCG 59.446 45.833 0.00 0.00 0.00 2.92
1925 5105 2.683362 GCACTTTGATGCCTTACCCTAC 59.317 50.000 0.00 0.00 39.86 3.18
1958 5142 3.287222 CCAGTTGTTTTTCCTGTCAGGA 58.713 45.455 18.15 18.15 44.10 3.86
1975 5178 4.783227 ACTCTACATTATTGTCCCACCAGT 59.217 41.667 0.00 0.00 37.28 4.00


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

AutoCloner maintained by Alex Coulton.