Multiple sequence alignment - TraesCS4A01G345100

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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 TraesCS4A01G345100 chr4A 100.000 3469 0 0 1 3469 624745674 624749142 0.000000e+00 6407.0
1 TraesCS4A01G345100 chr4A 88.961 770 79 4 1625 2390 624733529 624734296 0.000000e+00 946.0
2 TraesCS4A01G345100 chr4A 85.607 535 38 21 818 1328 624732905 624733424 3.070000e-145 525.0
3 TraesCS4A01G345100 chr5D 95.192 2059 80 7 776 2820 544816425 544818478 0.000000e+00 3236.0
4 TraesCS4A01G345100 chr5D 90.323 806 71 5 1589 2390 544799322 544800124 0.000000e+00 1050.0
5 TraesCS4A01G345100 chr5D 90.208 480 22 9 534 1007 544809853 544810313 1.380000e-168 603.0
6 TraesCS4A01G345100 chr5D 86.879 503 30 11 2981 3469 544824061 544824541 6.590000e-147 531.0
7 TraesCS4A01G345100 chr5D 84.317 542 44 18 818 1328 544798729 544799260 3.110000e-135 492.0
8 TraesCS4A01G345100 chr5D 93.130 262 17 1 24 284 544807621 544807882 1.950000e-102 383.0
9 TraesCS4A01G345100 chr5D 96.023 176 6 1 370 545 544809195 544809369 5.670000e-73 285.0
10 TraesCS4A01G345100 chr5D 91.626 203 14 3 545 747 544816156 544816355 9.480000e-71 278.0
11 TraesCS4A01G345100 chr5D 80.836 287 48 5 3160 3445 6822179 6822459 5.830000e-53 219.0
12 TraesCS4A01G345100 chr5D 92.593 108 2 1 2812 2919 544823957 544824058 2.160000e-32 150.0
13 TraesCS4A01G345100 chr5D 89.062 64 7 0 284 347 423870704 423870641 2.870000e-11 80.5
14 TraesCS4A01G345100 chr1A 97.811 1782 25 4 938 2709 569356262 569354485 0.000000e+00 3062.0
15 TraesCS4A01G345100 chr1A 88.918 767 79 4 1628 2390 569377068 569376304 0.000000e+00 941.0
16 TraesCS4A01G345100 chr1A 95.437 504 14 5 352 852 569356759 569356262 0.000000e+00 795.0
17 TraesCS4A01G345100 chr1A 86.168 535 36 22 818 1328 569377696 569377176 8.470000e-151 544.0
18 TraesCS4A01G345100 chr1A 91.864 295 11 5 1 284 569357024 569356732 1.940000e-107 399.0
19 TraesCS4A01G345100 chr5B 91.918 2091 130 21 539 2611 687325334 687327403 0.000000e+00 2889.0
20 TraesCS4A01G345100 chr5B 86.385 1939 145 48 773 2672 687259217 687261075 0.000000e+00 2008.0
21 TraesCS4A01G345100 chr5B 88.848 807 82 6 1588 2390 687212960 687213762 0.000000e+00 985.0
22 TraesCS4A01G345100 chr5B 90.080 746 65 7 1588 2328 687223956 687224697 0.000000e+00 959.0
23 TraesCS4A01G345100 chr5B 89.633 627 40 11 877 1487 687342057 687342674 0.000000e+00 774.0
24 TraesCS4A01G345100 chr5B 95.070 426 18 3 352 776 687324692 687325115 0.000000e+00 667.0
25 TraesCS4A01G345100 chr5B 91.784 426 22 7 352 776 687258724 687259137 6.450000e-162 580.0
26 TraesCS4A01G345100 chr5B 91.315 426 24 7 352 776 687339714 687340127 1.400000e-158 569.0
27 TraesCS4A01G345100 chr5B 84.043 564 43 27 817 1349 687223369 687223916 1.860000e-137 499.0
28 TraesCS4A01G345100 chr5B 90.847 295 15 3 1 284 687324426 687324719 5.430000e-103 385.0
29 TraesCS4A01G345100 chr5B 88.475 295 23 3 1 284 687339447 687339741 2.560000e-91 346.0
30 TraesCS4A01G345100 chr5B 88.112 143 14 2 143 284 687258611 687258751 2.140000e-37 167.0
31 TraesCS4A01G345100 chr4D 78.788 957 124 44 472 1394 441255171 441256082 1.400000e-158 569.0
32 TraesCS4A01G345100 chr7A 91.176 68 4 2 282 347 5659163 5659096 1.330000e-14 91.6
33 TraesCS4A01G345100 chr7A 90.323 62 6 0 287 348 706897142 706897203 7.980000e-12 82.4
34 TraesCS4A01G345100 chr5A 94.737 57 3 0 284 340 602973452 602973396 4.770000e-14 89.8
35 TraesCS4A01G345100 chr6A 97.959 49 1 0 283 331 2137910 2137862 6.170000e-13 86.1
36 TraesCS4A01G345100 chr6A 89.552 67 6 1 283 348 453866237 453866303 2.220000e-12 84.2
37 TraesCS4A01G345100 chr7D 89.231 65 7 0 284 348 326722108 326722044 7.980000e-12 82.4
38 TraesCS4A01G345100 chr7D 86.842 76 5 5 283 354 69778184 69778110 2.870000e-11 80.5
39 TraesCS4A01G345100 chr7D 86.842 76 5 5 283 354 69801902 69801828 2.870000e-11 80.5
40 TraesCS4A01G345100 chr2A 87.143 70 7 2 2850 2919 699420556 699420623 1.030000e-10 78.7


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 TraesCS4A01G345100 chr4A 624745674 624749142 3468 False 6407.000000 6407 100.000000 1 3469 1 chr4A.!!$F1 3468
1 TraesCS4A01G345100 chr4A 624732905 624734296 1391 False 735.500000 946 87.284000 818 2390 2 chr4A.!!$F2 1572
2 TraesCS4A01G345100 chr5D 544816156 544818478 2322 False 1757.000000 3236 93.409000 545 2820 2 chr5D.!!$F4 2275
3 TraesCS4A01G345100 chr5D 544798729 544800124 1395 False 771.000000 1050 87.320000 818 2390 2 chr5D.!!$F2 1572
4 TraesCS4A01G345100 chr5D 544807621 544810313 2692 False 423.666667 603 93.120333 24 1007 3 chr5D.!!$F3 983
5 TraesCS4A01G345100 chr5D 544823957 544824541 584 False 340.500000 531 89.736000 2812 3469 2 chr5D.!!$F5 657
6 TraesCS4A01G345100 chr1A 569354485 569357024 2539 True 1418.666667 3062 95.037333 1 2709 3 chr1A.!!$R1 2708
7 TraesCS4A01G345100 chr1A 569376304 569377696 1392 True 742.500000 941 87.543000 818 2390 2 chr1A.!!$R2 1572
8 TraesCS4A01G345100 chr5B 687324426 687327403 2977 False 1313.666667 2889 92.611667 1 2611 3 chr5B.!!$F4 2610
9 TraesCS4A01G345100 chr5B 687212960 687213762 802 False 985.000000 985 88.848000 1588 2390 1 chr5B.!!$F1 802
10 TraesCS4A01G345100 chr5B 687258611 687261075 2464 False 918.333333 2008 88.760333 143 2672 3 chr5B.!!$F3 2529
11 TraesCS4A01G345100 chr5B 687223369 687224697 1328 False 729.000000 959 87.061500 817 2328 2 chr5B.!!$F2 1511
12 TraesCS4A01G345100 chr5B 687339447 687342674 3227 False 563.000000 774 89.807667 1 1487 3 chr5B.!!$F5 1486
13 TraesCS4A01G345100 chr4D 441255171 441256082 911 False 569.000000 569 78.788000 472 1394 1 chr4D.!!$F1 922

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
316 330 0.038251 CAACAGGACTCTGCTGCGTA 60.038 55.0 0.0 0.0 44.59 4.42 F
1246 5361 0.249280 TTCTCGTGTTCTGCTTCGCA 60.249 50.0 0.0 0.0 36.92 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1931 6069 1.000019 CTGGTAGAGGACGGGGACA 60.000 63.158 0.00 0.00 0.00 4.02 R
3142 7327 0.243907 CGTAGGCGCTAGTGGCATAT 59.756 55.000 29.02 13.18 41.91 1.78 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 35 0.107800 ACTCGACCTCGCTAGCACTA 60.108 55.000 16.45 0.00 39.60 2.74
50 60 2.002586 GACCGATGACATGTTGACCAG 58.997 52.381 0.00 0.00 0.00 4.00
52 62 2.224523 ACCGATGACATGTTGACCAGTT 60.225 45.455 0.00 0.00 0.00 3.16
53 63 2.813754 CCGATGACATGTTGACCAGTTT 59.186 45.455 0.00 0.00 0.00 2.66
125 135 9.487790 TTCTAAAGAAGTTTGGGCAATTAAATG 57.512 29.630 0.00 0.00 0.00 2.32
149 159 8.195617 TGTTCTTTGTGGAATTGAAAAATGTC 57.804 30.769 0.00 0.00 0.00 3.06
163 176 7.834068 TGAAAAATGTCCACGAATTTGAAAA 57.166 28.000 0.00 0.00 0.00 2.29
274 288 3.041946 AGGGGTGATCAGTGTCCTTATC 58.958 50.000 0.00 0.00 0.00 1.75
275 289 2.771943 GGGGTGATCAGTGTCCTTATCA 59.228 50.000 0.00 0.00 30.63 2.15
276 290 3.392616 GGGGTGATCAGTGTCCTTATCAT 59.607 47.826 0.00 0.00 34.66 2.45
277 291 4.384056 GGGTGATCAGTGTCCTTATCATG 58.616 47.826 0.00 0.00 34.66 3.07
278 292 3.812053 GGTGATCAGTGTCCTTATCATGC 59.188 47.826 0.00 0.00 34.66 4.06
279 293 4.444022 GGTGATCAGTGTCCTTATCATGCT 60.444 45.833 0.00 0.00 34.66 3.79
280 294 5.121811 GTGATCAGTGTCCTTATCATGCTT 58.878 41.667 0.00 0.00 34.66 3.91
281 295 5.236047 GTGATCAGTGTCCTTATCATGCTTC 59.764 44.000 0.00 0.00 34.66 3.86
282 296 5.129980 TGATCAGTGTCCTTATCATGCTTCT 59.870 40.000 0.00 0.00 28.62 2.85
283 297 5.426689 TCAGTGTCCTTATCATGCTTCTT 57.573 39.130 0.00 0.00 0.00 2.52
284 298 5.809001 TCAGTGTCCTTATCATGCTTCTTT 58.191 37.500 0.00 0.00 0.00 2.52
285 299 6.240894 TCAGTGTCCTTATCATGCTTCTTTT 58.759 36.000 0.00 0.00 0.00 2.27
286 300 6.716628 TCAGTGTCCTTATCATGCTTCTTTTT 59.283 34.615 0.00 0.00 0.00 1.94
308 322 5.382664 TTTTAGGGAAACAACAGGACTCT 57.617 39.130 0.00 0.00 0.00 3.24
309 323 2.938956 AGGGAAACAACAGGACTCTG 57.061 50.000 0.00 0.00 46.10 3.35
310 324 1.202818 AGGGAAACAACAGGACTCTGC 60.203 52.381 0.00 0.00 44.59 4.26
311 325 1.202818 GGGAAACAACAGGACTCTGCT 60.203 52.381 0.00 0.00 44.59 4.24
312 326 1.876156 GGAAACAACAGGACTCTGCTG 59.124 52.381 0.00 0.00 44.59 4.41
313 327 1.265365 GAAACAACAGGACTCTGCTGC 59.735 52.381 0.00 0.00 44.59 5.25
314 328 0.882042 AACAACAGGACTCTGCTGCG 60.882 55.000 0.00 0.00 44.59 5.18
315 329 1.301244 CAACAGGACTCTGCTGCGT 60.301 57.895 0.00 0.00 44.59 5.24
316 330 0.038251 CAACAGGACTCTGCTGCGTA 60.038 55.000 0.00 0.00 44.59 4.42
317 331 0.898320 AACAGGACTCTGCTGCGTAT 59.102 50.000 0.00 0.00 44.59 3.06
318 332 0.898320 ACAGGACTCTGCTGCGTATT 59.102 50.000 0.00 0.00 44.59 1.89
319 333 1.276421 ACAGGACTCTGCTGCGTATTT 59.724 47.619 0.00 0.00 44.59 1.40
320 334 2.289694 ACAGGACTCTGCTGCGTATTTT 60.290 45.455 0.00 0.00 44.59 1.82
321 335 2.744202 CAGGACTCTGCTGCGTATTTTT 59.256 45.455 0.00 0.00 33.86 1.94
322 336 3.932710 CAGGACTCTGCTGCGTATTTTTA 59.067 43.478 0.00 0.00 33.86 1.52
323 337 4.572389 CAGGACTCTGCTGCGTATTTTTAT 59.428 41.667 0.00 0.00 33.86 1.40
324 338 5.065218 CAGGACTCTGCTGCGTATTTTTATT 59.935 40.000 0.00 0.00 33.86 1.40
325 339 6.257849 CAGGACTCTGCTGCGTATTTTTATTA 59.742 38.462 0.00 0.00 33.86 0.98
326 340 6.821665 AGGACTCTGCTGCGTATTTTTATTAA 59.178 34.615 0.00 0.00 0.00 1.40
327 341 7.499232 AGGACTCTGCTGCGTATTTTTATTAAT 59.501 33.333 0.00 0.00 0.00 1.40
328 342 8.129211 GGACTCTGCTGCGTATTTTTATTAATT 58.871 33.333 0.00 0.00 0.00 1.40
329 343 9.503427 GACTCTGCTGCGTATTTTTATTAATTT 57.497 29.630 0.00 0.00 0.00 1.82
330 344 9.855021 ACTCTGCTGCGTATTTTTATTAATTTT 57.145 25.926 0.00 0.00 0.00 1.82
332 346 9.081997 TCTGCTGCGTATTTTTATTAATTTTGG 57.918 29.630 0.00 0.00 0.00 3.28
333 347 8.190888 TGCTGCGTATTTTTATTAATTTTGGG 57.809 30.769 0.00 0.00 0.00 4.12
334 348 8.035394 TGCTGCGTATTTTTATTAATTTTGGGA 58.965 29.630 0.00 0.00 0.00 4.37
335 349 8.874816 GCTGCGTATTTTTATTAATTTTGGGAA 58.125 29.630 0.00 0.00 0.00 3.97
353 367 8.959676 TTTGGGAAATAAGGTACAAATAAGGT 57.040 30.769 0.00 0.00 0.00 3.50
356 370 9.856162 TGGGAAATAAGGTACAAATAAGGTATC 57.144 33.333 0.00 0.00 0.00 2.24
357 371 9.856162 GGGAAATAAGGTACAAATAAGGTATCA 57.144 33.333 0.00 0.00 0.00 2.15
363 377 6.885922 AGGTACAAATAAGGTATCAGTGTCC 58.114 40.000 0.00 0.00 0.00 4.02
364 378 6.672657 AGGTACAAATAAGGTATCAGTGTCCT 59.327 38.462 0.00 0.00 0.00 3.85
365 379 7.182206 AGGTACAAATAAGGTATCAGTGTCCTT 59.818 37.037 16.38 16.38 43.02 3.36
366 380 8.480501 GGTACAAATAAGGTATCAGTGTCCTTA 58.519 37.037 18.55 18.55 44.45 2.69
521 1855 1.134670 GGTGGCTAGAGTGACATCCAC 60.135 57.143 0.00 0.00 46.03 4.02
648 2480 1.715519 CAAGAAAATTGAACGGCTGCG 59.284 47.619 0.00 0.00 0.00 5.18
698 2533 1.909700 TAAGTTGGCCAGGCAGAAAG 58.090 50.000 15.19 0.00 0.00 2.62
864 3174 7.246674 TCAGTTAACCTATCATTTCGAATGC 57.753 36.000 0.00 0.00 0.00 3.56
947 5009 0.874390 GCGCAAGTCAATCTGTGGAA 59.126 50.000 0.30 0.00 41.68 3.53
1099 5190 3.330405 TCACAATCATTCCTCACCTCCAA 59.670 43.478 0.00 0.00 0.00 3.53
1100 5191 4.081406 CACAATCATTCCTCACCTCCAAA 58.919 43.478 0.00 0.00 0.00 3.28
1101 5192 4.708421 CACAATCATTCCTCACCTCCAAAT 59.292 41.667 0.00 0.00 0.00 2.32
1102 5193 5.186409 CACAATCATTCCTCACCTCCAAATT 59.814 40.000 0.00 0.00 0.00 1.82
1171 5286 1.516110 CCCAACCATCTGATCTCCCT 58.484 55.000 0.00 0.00 0.00 4.20
1174 5289 3.312890 CCAACCATCTGATCTCCCTAGT 58.687 50.000 0.00 0.00 0.00 2.57
1197 5312 0.622136 AAGATGTCAGCTGGGATGCA 59.378 50.000 15.13 6.13 34.99 3.96
1246 5361 0.249280 TTCTCGTGTTCTGCTTCGCA 60.249 50.000 0.00 0.00 36.92 5.10
1828 5966 2.903135 CCAATTTTTGCCCTCCCAACTA 59.097 45.455 0.00 0.00 0.00 2.24
2010 6148 3.462483 TGAACGGCTTCAACTACTTCA 57.538 42.857 0.00 0.00 33.20 3.02
2240 6378 1.410004 TGTTCGGACAGACCTTCACT 58.590 50.000 0.00 0.00 36.31 3.41
2660 6837 0.540830 CCCCCTCTATGTCTCCTCCG 60.541 65.000 0.00 0.00 0.00 4.63
2770 6951 9.418045 CCATGGTTAAGTTTAAGTTATGTTTGG 57.582 33.333 2.57 0.00 0.00 3.28
2842 7023 9.596308 AGGGTAAACAAATAAAATTGTACTCCT 57.404 29.630 0.00 0.00 42.49 3.69
2910 7091 5.807011 GCCAACAGACTTTAATTATGGCTTG 59.193 40.000 12.96 2.43 46.52 4.01
2960 7141 7.749377 TCATTTAACTAGAATTCCCTCCTCA 57.251 36.000 0.65 0.00 0.00 3.86
2961 7142 7.565680 TCATTTAACTAGAATTCCCTCCTCAC 58.434 38.462 0.65 0.00 0.00 3.51
2962 7143 5.952347 TTAACTAGAATTCCCTCCTCACC 57.048 43.478 0.65 0.00 0.00 4.02
2963 7144 3.786213 ACTAGAATTCCCTCCTCACCT 57.214 47.619 0.65 0.00 0.00 4.00
2964 7145 3.648739 ACTAGAATTCCCTCCTCACCTC 58.351 50.000 0.65 0.00 0.00 3.85
2965 7146 2.959421 AGAATTCCCTCCTCACCTCT 57.041 50.000 0.65 0.00 0.00 3.69
2966 7147 2.476199 AGAATTCCCTCCTCACCTCTG 58.524 52.381 0.65 0.00 0.00 3.35
2967 7148 0.915364 AATTCCCTCCTCACCTCTGC 59.085 55.000 0.00 0.00 0.00 4.26
2968 7149 0.252881 ATTCCCTCCTCACCTCTGCA 60.253 55.000 0.00 0.00 0.00 4.41
2969 7150 0.473694 TTCCCTCCTCACCTCTGCAA 60.474 55.000 0.00 0.00 0.00 4.08
2970 7151 0.906756 TCCCTCCTCACCTCTGCAAG 60.907 60.000 0.00 0.00 0.00 4.01
2971 7152 0.906756 CCCTCCTCACCTCTGCAAGA 60.907 60.000 0.00 0.00 43.69 3.02
2972 7153 1.202330 CCTCCTCACCTCTGCAAGAT 58.798 55.000 0.00 0.00 45.62 2.40
2973 7154 1.558756 CCTCCTCACCTCTGCAAGATT 59.441 52.381 0.00 0.00 45.62 2.40
2974 7155 2.026449 CCTCCTCACCTCTGCAAGATTT 60.026 50.000 0.00 0.00 45.62 2.17
2975 7156 3.008330 CTCCTCACCTCTGCAAGATTTG 58.992 50.000 0.00 0.00 45.62 2.32
2976 7157 2.639347 TCCTCACCTCTGCAAGATTTGA 59.361 45.455 0.00 0.00 45.62 2.69
2977 7158 3.265221 TCCTCACCTCTGCAAGATTTGAT 59.735 43.478 0.00 0.00 45.62 2.57
2978 7159 3.626670 CCTCACCTCTGCAAGATTTGATC 59.373 47.826 0.00 0.00 45.62 2.92
2979 7160 4.259356 CTCACCTCTGCAAGATTTGATCA 58.741 43.478 0.00 0.00 45.62 2.92
3091 7273 9.533831 AAAGAAAGAATGTATTGACATAACCCT 57.466 29.630 0.00 0.00 45.93 4.34
3097 7279 6.861065 ATGTATTGACATAACCCTAAAGCG 57.139 37.500 0.00 0.00 44.77 4.68
3106 7291 6.420638 ACATAACCCTAAAGCGAAGGTAATT 58.579 36.000 0.00 0.00 37.06 1.40
3142 7327 7.581213 AAGTGGACACAATGAAAGATAAACA 57.419 32.000 5.14 0.00 0.00 2.83
3143 7328 7.765695 AGTGGACACAATGAAAGATAAACAT 57.234 32.000 5.14 0.00 0.00 2.71
3163 7348 2.026301 GCCACTAGCGCCTACGAG 59.974 66.667 2.29 0.00 43.93 4.18
3164 7349 2.722487 CCACTAGCGCCTACGAGG 59.278 66.667 2.29 0.00 43.93 4.63
3171 7356 2.408022 CGCCTACGAGGACGAAGG 59.592 66.667 5.24 0.00 43.93 3.46
3176 7361 1.015868 CTACGAGGACGAAGGAGGAC 58.984 60.000 0.00 0.00 42.66 3.85
3178 7363 1.242665 ACGAGGACGAAGGAGGACAC 61.243 60.000 0.00 0.00 42.66 3.67
3181 7366 0.900647 AGGACGAAGGAGGACACCAG 60.901 60.000 0.00 0.00 0.00 4.00
3242 7430 2.573340 CCCTTTGGATGCGTTGCC 59.427 61.111 0.00 0.00 0.00 4.52
3266 7454 1.683917 CGGAGGGTAGAAGACATGGAG 59.316 57.143 0.00 0.00 0.00 3.86
3267 7455 2.753247 GGAGGGTAGAAGACATGGAGT 58.247 52.381 0.00 0.00 0.00 3.85
3277 7465 2.815211 CATGGAGTGCGGTGGTCG 60.815 66.667 0.00 0.00 42.76 4.79
3307 7495 2.620251 TTACATGCCGATGAAGGAGG 57.380 50.000 0.00 0.00 33.36 4.30
3308 7496 1.788229 TACATGCCGATGAAGGAGGA 58.212 50.000 0.00 0.00 33.36 3.71
3309 7497 0.179000 ACATGCCGATGAAGGAGGAC 59.821 55.000 0.00 0.00 33.36 3.85
3310 7498 0.178767 CATGCCGATGAAGGAGGACA 59.821 55.000 0.00 0.00 0.00 4.02
3311 7499 1.135094 ATGCCGATGAAGGAGGACAT 58.865 50.000 0.00 0.00 0.00 3.06
3312 7500 0.178767 TGCCGATGAAGGAGGACATG 59.821 55.000 0.00 0.00 0.00 3.21
3313 7501 0.533755 GCCGATGAAGGAGGACATGG 60.534 60.000 0.00 0.00 0.00 3.66
3314 7502 0.833287 CCGATGAAGGAGGACATGGT 59.167 55.000 0.00 0.00 0.00 3.55
3315 7503 1.473965 CCGATGAAGGAGGACATGGTG 60.474 57.143 0.00 0.00 0.00 4.17
3316 7504 1.473965 CGATGAAGGAGGACATGGTGG 60.474 57.143 0.00 0.00 0.00 4.61
3317 7505 0.257039 ATGAAGGAGGACATGGTGGC 59.743 55.000 0.00 0.00 0.00 5.01
3318 7506 1.450312 GAAGGAGGACATGGTGGCG 60.450 63.158 0.00 0.00 0.00 5.69
3319 7507 2.876368 GAAGGAGGACATGGTGGCGG 62.876 65.000 0.00 0.00 0.00 6.13
3345 7533 0.110328 CGATAGTAGTGTAGCGGCCG 60.110 60.000 24.05 24.05 0.00 6.13
3360 7548 2.117156 GCCGAGGTAGGTGTCGCTA 61.117 63.158 0.00 0.00 34.78 4.26
3431 7621 2.809601 GAGCGTGACGGCGTTGAT 60.810 61.111 16.19 6.11 38.18 2.57
3445 7635 0.796312 GTTGATCGTTCGGCATGTGT 59.204 50.000 0.00 0.00 0.00 3.72
3449 7644 3.266636 TGATCGTTCGGCATGTGTTATT 58.733 40.909 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.674651 TGCTAGCGAGGTCGAGTGT 60.675 57.895 10.77 0.00 43.02 3.55
25 35 0.895530 AACATGTCATCGGTCGACCT 59.104 50.000 30.92 12.01 32.15 3.85
50 60 7.702348 GGTTTAGCAATCAATGGTCTATGAAAC 59.298 37.037 0.00 0.00 40.93 2.78
52 62 7.118723 AGGTTTAGCAATCAATGGTCTATGAA 58.881 34.615 0.00 0.00 40.93 2.57
53 63 6.662755 AGGTTTAGCAATCAATGGTCTATGA 58.337 36.000 0.00 0.00 40.93 2.15
125 135 7.279758 TGGACATTTTTCAATTCCACAAAGAAC 59.720 33.333 0.00 0.00 30.67 3.01
208 222 4.526970 CAAGGCATAGAATTACACCCAGT 58.473 43.478 0.00 0.00 0.00 4.00
212 226 4.270008 ACACCAAGGCATAGAATTACACC 58.730 43.478 0.00 0.00 0.00 4.16
285 299 5.592688 CAGAGTCCTGTTGTTTCCCTAAAAA 59.407 40.000 0.00 0.00 35.70 1.94
286 300 5.130350 CAGAGTCCTGTTGTTTCCCTAAAA 58.870 41.667 0.00 0.00 35.70 1.52
287 301 4.714632 CAGAGTCCTGTTGTTTCCCTAAA 58.285 43.478 0.00 0.00 35.70 1.85
288 302 3.496160 GCAGAGTCCTGTTGTTTCCCTAA 60.496 47.826 0.00 0.00 42.35 2.69
289 303 2.038557 GCAGAGTCCTGTTGTTTCCCTA 59.961 50.000 0.00 0.00 42.35 3.53
290 304 1.202818 GCAGAGTCCTGTTGTTTCCCT 60.203 52.381 0.00 0.00 42.35 4.20
291 305 1.202818 AGCAGAGTCCTGTTGTTTCCC 60.203 52.381 0.00 0.00 42.35 3.97
292 306 1.876156 CAGCAGAGTCCTGTTGTTTCC 59.124 52.381 0.00 0.00 43.77 3.13
298 312 0.898320 ATACGCAGCAGAGTCCTGTT 59.102 50.000 0.00 0.00 42.35 3.16
299 313 0.898320 AATACGCAGCAGAGTCCTGT 59.102 50.000 0.00 0.00 42.35 4.00
300 314 2.015736 AAATACGCAGCAGAGTCCTG 57.984 50.000 0.00 0.00 43.22 3.86
301 315 2.770164 AAAATACGCAGCAGAGTCCT 57.230 45.000 0.00 0.00 0.00 3.85
302 316 5.485662 AATAAAAATACGCAGCAGAGTCC 57.514 39.130 0.00 0.00 0.00 3.85
303 317 9.503427 AAATTAATAAAAATACGCAGCAGAGTC 57.497 29.630 0.00 0.00 0.00 3.36
304 318 9.855021 AAAATTAATAAAAATACGCAGCAGAGT 57.145 25.926 0.00 0.00 0.00 3.24
306 320 9.081997 CCAAAATTAATAAAAATACGCAGCAGA 57.918 29.630 0.00 0.00 0.00 4.26
307 321 8.327429 CCCAAAATTAATAAAAATACGCAGCAG 58.673 33.333 0.00 0.00 0.00 4.24
308 322 8.035394 TCCCAAAATTAATAAAAATACGCAGCA 58.965 29.630 0.00 0.00 0.00 4.41
309 323 8.413899 TCCCAAAATTAATAAAAATACGCAGC 57.586 30.769 0.00 0.00 0.00 5.25
327 341 9.382307 ACCTTATTTGTACCTTATTTCCCAAAA 57.618 29.630 0.00 0.00 0.00 2.44
328 342 8.959676 ACCTTATTTGTACCTTATTTCCCAAA 57.040 30.769 0.00 0.00 0.00 3.28
330 344 9.856162 GATACCTTATTTGTACCTTATTTCCCA 57.144 33.333 0.00 0.00 0.00 4.37
331 345 9.856162 TGATACCTTATTTGTACCTTATTTCCC 57.144 33.333 0.00 0.00 0.00 3.97
337 351 8.480501 GGACACTGATACCTTATTTGTACCTTA 58.519 37.037 0.00 0.00 0.00 2.69
338 352 7.182206 AGGACACTGATACCTTATTTGTACCTT 59.818 37.037 0.00 0.00 0.00 3.50
339 353 6.672657 AGGACACTGATACCTTATTTGTACCT 59.327 38.462 0.00 0.00 0.00 3.08
340 354 6.885922 AGGACACTGATACCTTATTTGTACC 58.114 40.000 0.00 0.00 0.00 3.34
348 362 6.554982 AGCATGATAAGGACACTGATACCTTA 59.445 38.462 0.00 0.00 45.96 2.69
349 363 5.367937 AGCATGATAAGGACACTGATACCTT 59.632 40.000 0.00 0.00 44.67 3.50
350 364 4.904251 AGCATGATAAGGACACTGATACCT 59.096 41.667 0.00 0.00 35.36 3.08
351 365 5.220710 AGCATGATAAGGACACTGATACC 57.779 43.478 0.00 0.00 0.00 2.73
352 366 6.520272 AGAAGCATGATAAGGACACTGATAC 58.480 40.000 0.00 0.00 0.00 2.24
353 367 6.737720 AGAAGCATGATAAGGACACTGATA 57.262 37.500 0.00 0.00 0.00 2.15
354 368 5.627182 AGAAGCATGATAAGGACACTGAT 57.373 39.130 0.00 0.00 0.00 2.90
355 369 5.181009 CAAGAAGCATGATAAGGACACTGA 58.819 41.667 0.00 0.00 0.00 3.41
356 370 4.940046 ACAAGAAGCATGATAAGGACACTG 59.060 41.667 0.00 0.00 0.00 3.66
357 371 4.940046 CACAAGAAGCATGATAAGGACACT 59.060 41.667 0.00 0.00 0.00 3.55
358 372 4.437930 GCACAAGAAGCATGATAAGGACAC 60.438 45.833 0.00 0.00 0.00 3.67
359 373 3.691118 GCACAAGAAGCATGATAAGGACA 59.309 43.478 0.00 0.00 0.00 4.02
360 374 3.944015 AGCACAAGAAGCATGATAAGGAC 59.056 43.478 0.00 0.00 0.00 3.85
361 375 3.943381 CAGCACAAGAAGCATGATAAGGA 59.057 43.478 0.00 0.00 0.00 3.36
362 376 3.693085 ACAGCACAAGAAGCATGATAAGG 59.307 43.478 0.00 0.00 0.00 2.69
363 377 4.959596 ACAGCACAAGAAGCATGATAAG 57.040 40.909 0.00 0.00 0.00 1.73
364 378 6.825213 AGATTACAGCACAAGAAGCATGATAA 59.175 34.615 0.00 0.00 0.00 1.75
365 379 6.259387 CAGATTACAGCACAAGAAGCATGATA 59.741 38.462 0.00 0.00 0.00 2.15
366 380 5.066117 CAGATTACAGCACAAGAAGCATGAT 59.934 40.000 0.00 0.00 0.00 2.45
367 381 4.393990 CAGATTACAGCACAAGAAGCATGA 59.606 41.667 0.00 0.00 0.00 3.07
408 1742 6.136541 CCTCTTTGGTAGTTGAATTATGCC 57.863 41.667 0.00 0.00 0.00 4.40
648 2480 3.499918 GGCACCACAGAAGATGCATATAC 59.500 47.826 0.00 0.00 39.92 1.47
698 2533 5.523552 GGTGCAAGTTTATGATATTTTGGCC 59.476 40.000 0.00 0.00 0.00 5.36
813 3123 4.218417 ACCGATTTGACATTCTTCCAAAGG 59.782 41.667 0.00 0.00 33.91 3.11
1099 5190 1.208535 TGGCGATCGAGTGGGTTAATT 59.791 47.619 21.57 0.00 0.00 1.40
1100 5191 0.828022 TGGCGATCGAGTGGGTTAAT 59.172 50.000 21.57 0.00 0.00 1.40
1101 5192 0.108520 GTGGCGATCGAGTGGGTTAA 60.109 55.000 21.57 0.00 0.00 2.01
1102 5193 1.252215 TGTGGCGATCGAGTGGGTTA 61.252 55.000 21.57 0.00 0.00 2.85
1171 5286 4.093743 TCCCAGCTGACATCTTTGTACTA 58.906 43.478 17.39 0.00 35.79 1.82
1174 5289 3.877559 CATCCCAGCTGACATCTTTGTA 58.122 45.455 17.39 0.00 35.79 2.41
1703 5841 1.459450 ACAAGCCGTTGTTGAACAGT 58.541 45.000 0.00 0.00 45.00 3.55
1729 5867 1.067565 ACGTGATGAGGTAGCACTGTG 60.068 52.381 2.76 2.76 43.39 3.66
1828 5966 4.704103 TGTCGCTGGGGAGAGCCT 62.704 66.667 0.00 0.00 35.36 4.58
1931 6069 1.000019 CTGGTAGAGGACGGGGACA 60.000 63.158 0.00 0.00 0.00 4.02
2240 6378 1.185618 AGTCGAACTGCTGCCAGGTA 61.186 55.000 0.00 0.00 39.67 3.08
2660 6837 7.324178 CACTCCTAGTATATATTGTTCCAGGC 58.676 42.308 0.00 0.00 0.00 4.85
2770 6951 7.510549 TCCTAAATTGTTTGCATAGATAGGC 57.489 36.000 0.00 0.00 0.00 3.93
2808 6989 9.869757 AATTTTATTTGTTTACCCTATCTGCAC 57.130 29.630 0.00 0.00 0.00 4.57
2838 7019 8.738645 ATGTTTTGCTTCCTAAACTATAGGAG 57.261 34.615 4.43 0.00 43.85 3.69
2839 7020 9.528489 AAATGTTTTGCTTCCTAAACTATAGGA 57.472 29.630 4.43 0.07 41.64 2.94
2884 7065 5.102313 GCCATAATTAAAGTCTGTTGGCAC 58.898 41.667 14.64 0.00 45.93 5.01
2934 7115 8.781951 TGAGGAGGGAATTCTAGTTAAATGAAT 58.218 33.333 5.23 0.00 32.52 2.57
2935 7116 8.047310 GTGAGGAGGGAATTCTAGTTAAATGAA 58.953 37.037 5.23 0.00 0.00 2.57
2936 7117 7.365652 GGTGAGGAGGGAATTCTAGTTAAATGA 60.366 40.741 5.23 0.00 0.00 2.57
2937 7118 6.768381 GGTGAGGAGGGAATTCTAGTTAAATG 59.232 42.308 5.23 0.00 0.00 2.32
2938 7119 6.678857 AGGTGAGGAGGGAATTCTAGTTAAAT 59.321 38.462 5.23 0.00 0.00 1.40
2939 7120 6.030082 AGGTGAGGAGGGAATTCTAGTTAAA 58.970 40.000 5.23 0.00 0.00 1.52
2940 7121 5.600749 AGGTGAGGAGGGAATTCTAGTTAA 58.399 41.667 5.23 0.00 0.00 2.01
2941 7122 5.043281 AGAGGTGAGGAGGGAATTCTAGTTA 60.043 44.000 5.23 0.00 0.00 2.24
2942 7123 4.034410 GAGGTGAGGAGGGAATTCTAGTT 58.966 47.826 5.23 0.00 0.00 2.24
2943 7124 3.273618 AGAGGTGAGGAGGGAATTCTAGT 59.726 47.826 5.23 0.00 0.00 2.57
2944 7125 3.640967 CAGAGGTGAGGAGGGAATTCTAG 59.359 52.174 5.23 0.00 0.00 2.43
2945 7126 3.647636 CAGAGGTGAGGAGGGAATTCTA 58.352 50.000 5.23 0.00 0.00 2.10
2946 7127 2.476199 CAGAGGTGAGGAGGGAATTCT 58.524 52.381 5.23 0.00 0.00 2.40
2947 7128 1.134250 GCAGAGGTGAGGAGGGAATTC 60.134 57.143 0.00 0.00 0.00 2.17
2948 7129 0.915364 GCAGAGGTGAGGAGGGAATT 59.085 55.000 0.00 0.00 0.00 2.17
2949 7130 0.252881 TGCAGAGGTGAGGAGGGAAT 60.253 55.000 0.00 0.00 0.00 3.01
2950 7131 0.473694 TTGCAGAGGTGAGGAGGGAA 60.474 55.000 0.00 0.00 0.00 3.97
2951 7132 0.906756 CTTGCAGAGGTGAGGAGGGA 60.907 60.000 0.00 0.00 0.00 4.20
2952 7133 0.906756 TCTTGCAGAGGTGAGGAGGG 60.907 60.000 0.00 0.00 0.00 4.30
2953 7134 1.202330 ATCTTGCAGAGGTGAGGAGG 58.798 55.000 0.00 0.00 0.00 4.30
2954 7135 3.008330 CAAATCTTGCAGAGGTGAGGAG 58.992 50.000 0.00 0.00 0.00 3.69
2955 7136 2.639347 TCAAATCTTGCAGAGGTGAGGA 59.361 45.455 0.00 0.00 0.00 3.71
2956 7137 3.063510 TCAAATCTTGCAGAGGTGAGG 57.936 47.619 0.00 0.00 0.00 3.86
2957 7138 4.259356 TGATCAAATCTTGCAGAGGTGAG 58.741 43.478 0.00 0.00 28.46 3.51
2958 7139 4.290711 TGATCAAATCTTGCAGAGGTGA 57.709 40.909 0.00 0.00 0.00 4.02
2959 7140 4.698780 TCTTGATCAAATCTTGCAGAGGTG 59.301 41.667 9.88 0.00 0.00 4.00
2960 7141 4.914983 TCTTGATCAAATCTTGCAGAGGT 58.085 39.130 9.88 0.00 0.00 3.85
2961 7142 5.357314 ACATCTTGATCAAATCTTGCAGAGG 59.643 40.000 9.88 4.86 0.00 3.69
2962 7143 6.316640 AGACATCTTGATCAAATCTTGCAGAG 59.683 38.462 9.88 0.00 0.00 3.35
2963 7144 6.093633 CAGACATCTTGATCAAATCTTGCAGA 59.906 38.462 9.88 0.62 0.00 4.26
2964 7145 6.127980 ACAGACATCTTGATCAAATCTTGCAG 60.128 38.462 9.88 0.00 0.00 4.41
2965 7146 5.708697 ACAGACATCTTGATCAAATCTTGCA 59.291 36.000 9.88 0.00 0.00 4.08
2966 7147 6.192234 ACAGACATCTTGATCAAATCTTGC 57.808 37.500 9.88 0.00 0.00 4.01
2967 7148 7.063898 ACGTACAGACATCTTGATCAAATCTTG 59.936 37.037 9.88 7.22 0.00 3.02
2968 7149 7.099764 ACGTACAGACATCTTGATCAAATCTT 58.900 34.615 9.88 0.00 0.00 2.40
2969 7150 6.634805 ACGTACAGACATCTTGATCAAATCT 58.365 36.000 9.88 7.37 0.00 2.40
2970 7151 6.893958 ACGTACAGACATCTTGATCAAATC 57.106 37.500 9.88 5.25 0.00 2.17
2971 7152 7.148407 GGAAACGTACAGACATCTTGATCAAAT 60.148 37.037 9.88 3.72 0.00 2.32
2972 7153 6.147164 GGAAACGTACAGACATCTTGATCAAA 59.853 38.462 9.88 1.39 0.00 2.69
2973 7154 5.637810 GGAAACGTACAGACATCTTGATCAA 59.362 40.000 8.12 8.12 0.00 2.57
2974 7155 5.168569 GGAAACGTACAGACATCTTGATCA 58.831 41.667 0.00 0.00 0.00 2.92
2975 7156 5.062308 GTGGAAACGTACAGACATCTTGATC 59.938 44.000 0.00 0.00 0.00 2.92
2976 7157 4.929808 GTGGAAACGTACAGACATCTTGAT 59.070 41.667 0.00 0.00 0.00 2.57
2977 7158 4.202172 TGTGGAAACGTACAGACATCTTGA 60.202 41.667 0.00 0.00 0.00 3.02
2978 7159 4.055360 TGTGGAAACGTACAGACATCTTG 58.945 43.478 0.00 0.00 0.00 3.02
2979 7160 4.330944 TGTGGAAACGTACAGACATCTT 57.669 40.909 0.00 0.00 0.00 2.40
3081 7263 3.870274 ACCTTCGCTTTAGGGTTATGTC 58.130 45.455 0.00 0.00 37.09 3.06
3128 7313 8.571336 GCTAGTGGCATATGTTTATCTTTCATT 58.429 33.333 4.29 0.00 41.35 2.57
3142 7327 0.243907 CGTAGGCGCTAGTGGCATAT 59.756 55.000 29.02 13.18 41.91 1.78
3143 7328 0.820482 TCGTAGGCGCTAGTGGCATA 60.820 55.000 29.02 16.27 41.91 3.14
3163 7348 1.592223 CTGGTGTCCTCCTTCGTCC 59.408 63.158 0.00 0.00 0.00 4.79
3164 7349 0.898789 TCCTGGTGTCCTCCTTCGTC 60.899 60.000 0.00 0.00 0.00 4.20
3171 7356 2.262915 CGCACTCCTGGTGTCCTC 59.737 66.667 0.00 0.00 46.86 3.71
3178 7363 1.153289 AGCTATTGCGCACTCCTGG 60.153 57.895 11.12 0.00 45.42 4.45
3181 7366 2.711924 GCAGCTATTGCGCACTCC 59.288 61.111 11.12 0.00 44.09 3.85
3220 7408 3.864686 CGCATCCAAAGGGCGTCG 61.865 66.667 0.00 0.00 45.27 5.12
3242 7430 2.441532 TCTTCTACCCTCCGGCGG 60.442 66.667 22.51 22.51 0.00 6.13
3257 7445 2.172483 GACCACCGCACTCCATGTCT 62.172 60.000 0.00 0.00 0.00 3.41
3266 7454 4.595538 TCACCACGACCACCGCAC 62.596 66.667 0.00 0.00 43.32 5.34
3267 7455 4.293648 CTCACCACGACCACCGCA 62.294 66.667 0.00 0.00 43.32 5.69
3277 7465 1.670811 CGGCATGTAAATCCTCACCAC 59.329 52.381 0.00 0.00 0.00 4.16
3318 7506 3.974757 ACTACTATCGCCGCGGCC 61.975 66.667 42.07 25.29 37.98 6.13
3319 7507 2.121564 TACACTACTATCGCCGCGGC 62.122 60.000 39.82 39.82 37.85 6.53
3320 7508 0.110328 CTACACTACTATCGCCGCGG 60.110 60.000 24.05 24.05 0.00 6.46
3321 7509 0.725118 GCTACACTACTATCGCCGCG 60.725 60.000 6.39 6.39 0.00 6.46
3322 7510 0.725118 CGCTACACTACTATCGCCGC 60.725 60.000 0.00 0.00 0.00 6.53
3323 7511 0.110328 CCGCTACACTACTATCGCCG 60.110 60.000 0.00 0.00 0.00 6.46
3324 7512 0.386985 GCCGCTACACTACTATCGCC 60.387 60.000 0.00 0.00 0.00 5.54
3325 7513 0.386985 GGCCGCTACACTACTATCGC 60.387 60.000 0.00 0.00 0.00 4.58
3345 7533 3.004524 CCTATGTTAGCGACACCTACCTC 59.995 52.174 0.00 0.00 42.04 3.85
3360 7548 2.319136 TCGTATTTGGCGCCTATGTT 57.681 45.000 29.70 10.66 0.00 2.71
3421 7611 2.807895 CCGAACGATCAACGCCGT 60.808 61.111 0.00 0.00 46.94 5.68
3431 7621 2.413796 GACAATAACACATGCCGAACGA 59.586 45.455 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.