Multiple sequence alignment - TraesCS3B01G365700

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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 TraesCS3B01G365700 chr3B 100.000 5256 0 0 1 5256 578393436 578388181 0.000000e+00 9707
1 TraesCS3B01G365700 chr3B 89.552 201 14 5 1039 1233 736491586 736491387 1.130000e-61 248
2 TraesCS3B01G365700 chr3B 79.208 404 46 20 4672 5043 606379561 606379164 4.070000e-61 246
3 TraesCS3B01G365700 chr3D 92.388 3455 164 44 1805 5209 441139878 441136473 0.000000e+00 4831
4 TraesCS3B01G365700 chr3D 92.403 2251 115 22 1 2222 441141917 441139694 0.000000e+00 3158
5 TraesCS3B01G365700 chr3A 90.779 2592 160 31 2043 4573 581266194 581263621 0.000000e+00 3389
6 TraesCS3B01G365700 chr3A 93.980 1960 90 14 89 2040 581267897 581265958 0.000000e+00 2940
7 TraesCS3B01G365700 chr3A 82.131 582 56 22 4506 5064 581263635 581263079 6.200000e-124 455
8 TraesCS3B01G365700 chr3A 87.097 310 26 6 7 305 581268475 581268169 6.520000e-89 339
9 TraesCS3B01G365700 chr6A 94.352 301 17 0 473 773 594368039 594368339 3.710000e-126 462
10 TraesCS3B01G365700 chr6A 86.721 369 31 6 27 382 594367681 594368044 1.370000e-105 394
11 TraesCS3B01G365700 chr6A 89.712 243 24 1 1076 1317 283735 283493 5.110000e-80 309
12 TraesCS3B01G365700 chr6A 80.101 397 46 16 4671 5036 592346296 592346690 1.120000e-66 265
13 TraesCS3B01G365700 chr1B 82.561 367 32 13 27 382 184230002 184230347 1.430000e-75 294
14 TraesCS3B01G365700 chr1B 96.154 130 5 0 474 603 184230343 184230472 4.120000e-51 213
15 TraesCS3B01G365700 chr2D 80.964 394 38 21 4671 5035 11777398 11777783 1.440000e-70 278
16 TraesCS3B01G365700 chr2D 79.795 391 50 18 4670 5035 430224878 430225264 1.880000e-64 257
17 TraesCS3B01G365700 chr2D 87.500 160 7 8 1039 1186 5934544 5934702 7.000000e-39 172
18 TraesCS3B01G365700 chr6B 86.885 244 29 3 1076 1317 3380346 3380104 2.410000e-68 270
19 TraesCS3B01G365700 chr6B 89.552 201 14 5 1039 1233 463400991 463400792 1.130000e-61 248
20 TraesCS3B01G365700 chr7A 79.040 396 52 18 4671 5036 649200235 649200629 5.260000e-60 243
21 TraesCS3B01G365700 chr1D 79.012 405 43 24 4671 5045 234066533 234066141 6.800000e-59 239
22 TraesCS3B01G365700 chr5D 80.588 340 37 19 4670 4991 424170016 424170344 8.800000e-58 235
23 TraesCS3B01G365700 chr2B 81.395 301 41 9 4668 4956 67894074 67894371 1.140000e-56 231
24 TraesCS3B01G365700 chr2B 88.060 201 17 5 1039 1233 622910362 622910163 1.140000e-56 231
25 TraesCS3B01G365700 chr2B 87.065 201 19 6 1039 1233 690781998 690781799 2.460000e-53 220
26 TraesCS3B01G365700 chrUn 91.096 146 12 1 1295 1440 51455576 51455720 4.150000e-46 196
27 TraesCS3B01G365700 chr5A 88.889 144 15 1 1297 1440 28620246 28620104 5.410000e-40 176


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 TraesCS3B01G365700 chr3B 578388181 578393436 5255 True 9707.00 9707 100.00000 1 5256 1 chr3B.!!$R1 5255
1 TraesCS3B01G365700 chr3D 441136473 441141917 5444 True 3994.50 4831 92.39550 1 5209 2 chr3D.!!$R1 5208
2 TraesCS3B01G365700 chr3A 581263079 581268475 5396 True 1780.75 3389 88.49675 7 5064 4 chr3A.!!$R1 5057
3 TraesCS3B01G365700 chr6A 594367681 594368339 658 False 428.00 462 90.53650 27 773 2 chr6A.!!$F2 746

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
948 1457 0.179000 GACGGCTCAAGATGGGTCAT 59.821 55.000 0.00 0.00 0.00 3.06 F
1823 2343 1.459592 CGCCCACGAAGTAAGTCTTTG 59.540 52.381 0.00 0.00 41.61 2.77 F
2470 3239 1.406180 TGCATGTGCTGGCATAACATC 59.594 47.619 11.12 8.02 42.66 3.06 F
3266 4038 0.379669 GCATGCATCGTTTCAGAGGG 59.620 55.000 14.21 0.00 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2134 2894 2.092429 ACACTGGTGACTGATTGGTTGT 60.092 45.455 7.78 0.0 0.0 3.32 R
3162 3934 2.096417 GTGCACGCAACAGTTAACTAGG 60.096 50.000 8.04 0.0 0.0 3.02 R
4106 4880 0.730265 GTTCAGCACAAACCGACACA 59.270 50.000 0.00 0.0 0.0 3.72 R
5227 6121 0.184692 TGCTGGTGTGAACAATCCCA 59.815 50.000 0.00 0.0 0.0 4.37 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
48 49 8.702438 CAACAAGATTATTTTGTAAGGTGCAAG 58.298 33.333 1.53 0.00 37.77 4.01
109 121 1.069765 CGCACTTCCACCAGTGACT 59.930 57.895 5.01 0.00 46.29 3.41
203 215 3.778954 AATATGAACTAGGCAGGCCTC 57.221 47.619 17.57 3.05 44.43 4.70
205 217 0.543749 ATGAACTAGGCAGGCCTCAC 59.456 55.000 17.57 0.00 44.43 3.51
227 239 4.214971 ACTTCTGCAATTGATGACACAGTC 59.785 41.667 10.34 0.00 0.00 3.51
229 241 5.151297 TCTGCAATTGATGACACAGTCTA 57.849 39.130 10.34 0.00 33.15 2.59
232 244 6.314648 TCTGCAATTGATGACACAGTCTAATC 59.685 38.462 10.34 0.00 33.15 1.75
235 247 7.278646 TGCAATTGATGACACAGTCTAATCTAC 59.721 37.037 10.34 0.00 33.15 2.59
236 248 7.254590 GCAATTGATGACACAGTCTAATCTACC 60.255 40.741 10.34 0.00 33.15 3.18
237 249 6.850752 TTGATGACACAGTCTAATCTACCA 57.149 37.500 0.00 0.00 33.15 3.25
304 810 3.119137 TGCAGCGAGCTAACAATAGAGAA 60.119 43.478 0.00 0.00 45.94 2.87
307 813 4.266502 CAGCGAGCTAACAATAGAGAACAC 59.733 45.833 0.00 0.00 0.00 3.32
401 907 2.827190 TCGAGTAGCCATCCGCGT 60.827 61.111 4.92 0.00 44.76 6.01
703 1209 4.856801 CCTCGGGTTCGCCATGGG 62.857 72.222 15.13 3.69 39.65 4.00
783 1292 4.208686 ATCGGCGGCGGAGACTTC 62.209 66.667 31.73 0.00 0.00 3.01
883 1392 8.657387 AGAAGATATCCGAAGATATTTCCTCA 57.343 34.615 0.00 0.00 44.21 3.86
891 1400 5.050490 CGAAGATATTTCCTCACATTCGGT 58.950 41.667 0.00 0.00 35.80 4.69
938 1447 3.039588 GCGAAACGGACGGCTCAA 61.040 61.111 0.00 0.00 0.00 3.02
947 1456 1.596934 GACGGCTCAAGATGGGTCA 59.403 57.895 0.00 0.00 0.00 4.02
948 1457 0.179000 GACGGCTCAAGATGGGTCAT 59.821 55.000 0.00 0.00 0.00 3.06
962 1471 2.698797 TGGGTCATCTTCCTATCGTTCC 59.301 50.000 0.00 0.00 0.00 3.62
978 1487 2.159226 CGTTCCACGCTTATCCTCTTCT 60.159 50.000 0.00 0.00 33.65 2.85
984 1493 4.508662 CACGCTTATCCTCTTCTTCCTTT 58.491 43.478 0.00 0.00 0.00 3.11
1002 1522 1.460839 TTCCTCCCCCTTCCTCCAGA 61.461 60.000 0.00 0.00 0.00 3.86
1007 1527 3.083997 CCCTTCCTCCAGACCCCG 61.084 72.222 0.00 0.00 0.00 5.73
1014 1534 2.606519 TCCAGACCCCGACCCAAG 60.607 66.667 0.00 0.00 0.00 3.61
1101 1621 4.024984 CCTCCCCCTCCACCTCCA 62.025 72.222 0.00 0.00 0.00 3.86
1348 1868 2.440569 GCTGTCGCTCAAGTCGCTC 61.441 63.158 0.00 0.00 0.00 5.03
1375 1895 4.465446 TCCTCCTGCCTCCCCTCG 62.465 72.222 0.00 0.00 0.00 4.63
1462 1982 4.533124 TATCCGCTCGCCCCCTCA 62.533 66.667 0.00 0.00 0.00 3.86
1789 2309 5.220043 CGACGATTTGGATAAGATGATACGC 60.220 44.000 0.00 0.00 0.00 4.42
1822 2342 1.607251 CCGCCCACGAAGTAAGTCTTT 60.607 52.381 0.00 0.00 41.61 2.52
1823 2343 1.459592 CGCCCACGAAGTAAGTCTTTG 59.540 52.381 0.00 0.00 41.61 2.77
1824 2344 1.804748 GCCCACGAAGTAAGTCTTTGG 59.195 52.381 0.00 0.00 41.61 3.28
1875 2395 9.425577 GAATTGTAGTAGAGGTATAATTCTGGC 57.574 37.037 0.00 0.00 36.13 4.85
1914 2434 1.466167 ACAATGCGAGCAATCAGTCAC 59.534 47.619 0.57 0.00 0.00 3.67
1944 2465 6.816136 TGTTCAGAGTGTAAGAGTGAAATCA 58.184 36.000 0.00 0.00 0.00 2.57
2025 2784 2.022195 ACGAAGATAGCTGCCTACGAA 58.978 47.619 0.00 0.00 0.00 3.85
2048 2807 2.675658 AACACCTAAATGTGCCCACT 57.324 45.000 0.00 0.00 39.93 4.00
2052 2811 3.073946 ACACCTAAATGTGCCCACTAAGT 59.926 43.478 0.00 0.00 39.93 2.24
2086 2845 8.511321 TGATTATTAACTGAAAATGTGCGACTT 58.489 29.630 0.00 0.00 0.00 3.01
2087 2846 9.341899 GATTATTAACTGAAAATGTGCGACTTT 57.658 29.630 0.00 0.00 0.00 2.66
2095 2854 6.499172 TGAAAATGTGCGACTTTGAATTGTA 58.501 32.000 0.00 0.00 0.00 2.41
2133 2893 5.311649 AGTCTGGGTCATGCATTAGGATAAT 59.688 40.000 0.00 0.00 0.00 1.28
2134 2894 6.501805 AGTCTGGGTCATGCATTAGGATAATA 59.498 38.462 0.00 0.00 0.00 0.98
2138 2898 6.714810 TGGGTCATGCATTAGGATAATACAAC 59.285 38.462 0.00 0.00 0.00 3.32
2143 2903 9.013229 TCATGCATTAGGATAATACAACCAATC 57.987 33.333 0.00 0.00 0.00 2.67
2169 2929 2.285083 CCAGTGTGTTCCGAGTGAAAA 58.715 47.619 0.00 0.00 33.94 2.29
2262 3022 7.991460 AGCTGGATACCTGTTTAATACCTAAAC 59.009 37.037 0.00 1.32 46.58 2.01
2273 3033 3.975168 ATACCTAAACGTCAGCCTGTT 57.025 42.857 0.00 0.00 0.00 3.16
2470 3239 1.406180 TGCATGTGCTGGCATAACATC 59.594 47.619 11.12 8.02 42.66 3.06
2569 3339 4.127171 GTGGCTTTCTCAGTGAAGTTGTA 58.873 43.478 0.00 0.00 35.89 2.41
2634 3404 5.610982 TGCCCCTACATAATCCTGTTAGATT 59.389 40.000 0.00 0.00 39.73 2.40
2714 3485 4.575236 GTCCCTTTTATGTGCTAGCTAACC 59.425 45.833 17.23 1.90 0.00 2.85
3162 3934 4.547532 TCTTCACTGTCGCTTCTTCTTAC 58.452 43.478 0.00 0.00 0.00 2.34
3181 3953 2.140717 ACCTAGTTAACTGTTGCGTGC 58.859 47.619 18.56 0.00 0.00 5.34
3266 4038 0.379669 GCATGCATCGTTTCAGAGGG 59.620 55.000 14.21 0.00 0.00 4.30
3403 4175 2.554344 GCCTCCAGGTATTTTGACACCA 60.554 50.000 0.00 0.00 37.28 4.17
3417 4189 5.607939 TTGACACCACTAGTCTTTTCTCA 57.392 39.130 0.00 0.00 36.94 3.27
3421 4195 7.152645 TGACACCACTAGTCTTTTCTCATTAC 58.847 38.462 0.00 0.00 36.94 1.89
3432 4206 7.039223 AGTCTTTTCTCATTACGGTCTTCCTTA 60.039 37.037 0.00 0.00 0.00 2.69
3446 4220 7.601508 ACGGTCTTCCTTACTAATGTTTACTTG 59.398 37.037 0.00 0.00 0.00 3.16
3506 4280 4.970662 TGCTTGTCTTTTCATATCTGCC 57.029 40.909 0.00 0.00 0.00 4.85
3670 4444 1.599542 GAGCGTCTGGAATATGTTGGC 59.400 52.381 0.00 0.00 0.00 4.52
3722 4496 3.149196 GACCTTTTTCAGCATCTGACCA 58.851 45.455 0.00 0.00 40.46 4.02
3749 4523 9.421806 CTCTCCATTTGATCAATAGTCATACTC 57.578 37.037 9.40 0.00 0.00 2.59
3762 4536 7.726033 ATAGTCATACTCAAGGTCTGAACTT 57.274 36.000 1.18 1.18 33.78 2.66
3792 4566 5.840693 TGATCAGGATCTAGTATTGGCAGAA 59.159 40.000 10.38 0.00 38.60 3.02
3819 4593 0.867329 TCATGAAGCATCTCGACGCG 60.867 55.000 3.53 3.53 0.00 6.01
3856 4630 2.169352 TCAGAGAAGCATAGGAGGTTGC 59.831 50.000 0.00 0.00 39.17 4.17
4065 4839 4.196193 TGATGTTCGAGGTGTTTGACTTT 58.804 39.130 0.00 0.00 0.00 2.66
4068 4842 3.621268 TGTTCGAGGTGTTTGACTTTGAG 59.379 43.478 0.00 0.00 0.00 3.02
4106 4880 3.768757 GCTGTATGAGGAGGATATGCTCT 59.231 47.826 21.84 9.55 46.10 4.09
4168 4943 1.723003 CGCTTGAAGGAAAAATGCAGC 59.277 47.619 0.00 0.00 0.00 5.25
4169 4944 2.758009 GCTTGAAGGAAAAATGCAGCA 58.242 42.857 0.00 0.00 0.00 4.41
4206 4981 1.148157 CGGATCAGATCGCGCTGTTT 61.148 55.000 5.56 3.39 37.20 2.83
4231 5006 4.697756 TGAGCCCAAAGCCGGACG 62.698 66.667 5.05 0.00 45.47 4.79
4402 5187 7.984050 TGTAAATTCCAATTTGAGCAGAAACAA 59.016 29.630 7.42 0.00 38.90 2.83
4413 5198 2.543641 GCAGAAACAAAAACAGCTGCT 58.456 42.857 15.27 0.00 43.81 4.24
4524 5330 9.634021 TGTCATATGGGTGCATAAGTTTATTTA 57.366 29.630 2.13 0.00 0.00 1.40
4556 5409 2.228103 ACAGTACAATCGAAGTCGCTCA 59.772 45.455 0.00 0.00 39.60 4.26
4802 5667 5.964958 AGTGTAACAAGCATGCTTAACAT 57.035 34.783 31.48 19.20 41.43 2.71
4809 5674 6.774354 ACAAGCATGCTTAACATTTTTCAG 57.226 33.333 31.48 16.92 36.64 3.02
4817 5682 4.982295 GCTTAACATTTTTCAGGCGAAACT 59.018 37.500 4.44 0.00 40.84 2.66
4819 5684 6.345803 GCTTAACATTTTTCAGGCGAAACTTC 60.346 38.462 4.44 0.00 40.84 3.01
4820 5685 4.647424 ACATTTTTCAGGCGAAACTTCA 57.353 36.364 4.44 0.00 40.84 3.02
4822 5687 5.600696 ACATTTTTCAGGCGAAACTTCATT 58.399 33.333 4.44 0.00 40.84 2.57
4823 5688 5.463061 ACATTTTTCAGGCGAAACTTCATTG 59.537 36.000 4.44 1.64 40.84 2.82
4825 5690 4.647424 TTTCAGGCGAAACTTCATTGTT 57.353 36.364 0.00 0.00 36.19 2.83
4827 5692 3.210227 TCAGGCGAAACTTCATTGTTGA 58.790 40.909 0.00 0.00 0.00 3.18
4828 5693 3.629855 TCAGGCGAAACTTCATTGTTGAA 59.370 39.130 0.00 0.00 39.54 2.69
4829 5694 4.097135 TCAGGCGAAACTTCATTGTTGAAA 59.903 37.500 0.00 0.00 41.22 2.69
4830 5695 4.803088 CAGGCGAAACTTCATTGTTGAAAA 59.197 37.500 0.00 0.00 41.22 2.29
4831 5696 5.290643 CAGGCGAAACTTCATTGTTGAAAAA 59.709 36.000 0.00 0.00 41.22 1.94
4867 5757 7.581476 AGTATAACATTTGTCGTTTGACTTGG 58.419 34.615 0.00 0.00 45.70 3.61
4941 5831 4.037923 AGGTAGCATTTTGGTGTGACAAAG 59.962 41.667 0.00 0.00 40.97 2.77
5015 5906 1.302033 GGCAGGACCATATGCTCCG 60.302 63.158 10.77 7.66 42.19 4.63
5061 5953 2.299013 TGTGGCGTCTCTACAGTTTGAT 59.701 45.455 0.00 0.00 32.12 2.57
5103 5995 8.999431 AGCTTTATTTTATCTCGTTCACAGAAA 58.001 29.630 0.00 0.00 0.00 2.52
5121 6013 1.369625 AACGCTAATTCTTCTGGGCG 58.630 50.000 0.00 0.00 46.47 6.13
5138 6030 3.182182 GGGCGAGATGAAAAATTGCTTC 58.818 45.455 0.00 0.00 0.00 3.86
5139 6031 3.119352 GGGCGAGATGAAAAATTGCTTCT 60.119 43.478 0.00 0.00 0.00 2.85
5140 6032 4.488879 GGCGAGATGAAAAATTGCTTCTT 58.511 39.130 0.00 0.00 0.00 2.52
5141 6033 4.560427 GGCGAGATGAAAAATTGCTTCTTC 59.440 41.667 0.00 7.72 0.00 2.87
5142 6034 5.397326 GCGAGATGAAAAATTGCTTCTTCT 58.603 37.500 14.16 14.16 39.00 2.85
5220 6114 2.596904 AAAATGCTGATGCCATGCTC 57.403 45.000 0.00 0.00 38.71 4.26
5221 6115 0.750850 AAATGCTGATGCCATGCTCC 59.249 50.000 0.00 0.00 38.71 4.70
5222 6116 1.452953 AATGCTGATGCCATGCTCCG 61.453 55.000 0.00 0.00 38.71 4.63
5223 6117 3.962421 GCTGATGCCATGCTCCGC 61.962 66.667 0.00 0.00 0.00 5.54
5224 6118 2.515290 CTGATGCCATGCTCCGCA 60.515 61.111 0.00 0.00 44.86 5.69
5225 6119 2.045143 TGATGCCATGCTCCGCAA 60.045 55.556 0.00 0.00 43.62 4.85
5226 6120 1.659622 CTGATGCCATGCTCCGCAAA 61.660 55.000 0.00 0.00 43.62 3.68
5227 6121 1.038681 TGATGCCATGCTCCGCAAAT 61.039 50.000 0.00 0.00 43.62 2.32
5228 6122 0.596600 GATGCCATGCTCCGCAAATG 60.597 55.000 0.00 0.00 43.62 2.32
5229 6123 2.023414 ATGCCATGCTCCGCAAATGG 62.023 55.000 4.53 4.53 43.62 3.16
5230 6124 2.809706 CCATGCTCCGCAAATGGG 59.190 61.111 1.48 0.00 43.62 4.00
5231 6125 1.753848 CCATGCTCCGCAAATGGGA 60.754 57.895 0.00 0.00 43.62 4.37
5232 6126 1.111116 CCATGCTCCGCAAATGGGAT 61.111 55.000 0.00 0.00 43.62 3.85
5233 6127 0.748450 CATGCTCCGCAAATGGGATT 59.252 50.000 0.00 0.00 43.62 3.01
5234 6128 0.748450 ATGCTCCGCAAATGGGATTG 59.252 50.000 0.00 0.00 43.62 2.67
5235 6129 0.611618 TGCTCCGCAAATGGGATTGT 60.612 50.000 0.00 0.00 34.76 2.71
5236 6130 0.532115 GCTCCGCAAATGGGATTGTT 59.468 50.000 0.00 0.00 31.99 2.83
5237 6131 1.469767 GCTCCGCAAATGGGATTGTTC 60.470 52.381 0.00 0.00 31.99 3.18
5238 6132 1.818060 CTCCGCAAATGGGATTGTTCA 59.182 47.619 0.00 0.00 31.99 3.18
5239 6133 1.543802 TCCGCAAATGGGATTGTTCAC 59.456 47.619 0.00 0.00 32.80 3.18
5240 6134 1.271934 CCGCAAATGGGATTGTTCACA 59.728 47.619 0.00 0.00 40.27 3.58
5241 6135 2.327568 CGCAAATGGGATTGTTCACAC 58.672 47.619 0.00 0.00 38.34 3.82
5242 6136 2.687370 GCAAATGGGATTGTTCACACC 58.313 47.619 0.00 0.00 38.34 4.16
5243 6137 2.036992 GCAAATGGGATTGTTCACACCA 59.963 45.455 0.00 0.00 38.34 4.17
5244 6138 3.861886 GCAAATGGGATTGTTCACACCAG 60.862 47.826 0.00 0.00 38.34 4.00
5245 6139 1.549203 ATGGGATTGTTCACACCAGC 58.451 50.000 0.00 0.00 38.34 4.85
5246 6140 0.184692 TGGGATTGTTCACACCAGCA 59.815 50.000 0.00 0.00 27.50 4.41
5247 6141 1.327303 GGGATTGTTCACACCAGCAA 58.673 50.000 0.00 0.00 0.00 3.91
5248 6142 1.686052 GGGATTGTTCACACCAGCAAA 59.314 47.619 0.00 0.00 0.00 3.68
5249 6143 2.299867 GGGATTGTTCACACCAGCAAAT 59.700 45.455 0.00 0.00 0.00 2.32
5250 6144 3.319755 GGATTGTTCACACCAGCAAATG 58.680 45.455 0.00 0.00 0.00 2.32
5251 6145 3.243839 GGATTGTTCACACCAGCAAATGT 60.244 43.478 0.00 0.00 0.00 2.71
5252 6146 3.883830 TTGTTCACACCAGCAAATGTT 57.116 38.095 0.00 0.00 0.00 2.71
5253 6147 3.435105 TGTTCACACCAGCAAATGTTC 57.565 42.857 0.00 0.00 0.00 3.18
5254 6148 2.757314 TGTTCACACCAGCAAATGTTCA 59.243 40.909 0.00 0.00 0.00 3.18
5255 6149 3.181488 TGTTCACACCAGCAAATGTTCAG 60.181 43.478 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.678101 GTTGCCTCAGTTGCAGTCTTT 59.322 47.619 0.00 0.00 40.35 2.52
14 15 7.054491 ACAAAATAATCTTGTTGCCTCAGTT 57.946 32.000 0.00 0.00 33.16 3.16
64 65 4.142859 TGAACACGTTGTTGTAACACCTTC 60.143 41.667 7.89 0.00 41.28 3.46
151 163 6.609212 AGATACTCCAACTCTTGCTCAATCTA 59.391 38.462 0.00 0.00 0.00 1.98
153 165 5.669477 AGATACTCCAACTCTTGCTCAATC 58.331 41.667 0.00 0.00 0.00 2.67
155 167 5.717178 AGTAGATACTCCAACTCTTGCTCAA 59.283 40.000 0.00 0.00 0.00 3.02
203 215 4.023450 ACTGTGTCATCAATTGCAGAAGTG 60.023 41.667 13.35 1.57 0.00 3.16
205 217 4.454847 AGACTGTGTCATCAATTGCAGAAG 59.545 41.667 13.35 5.85 34.60 2.85
227 239 5.426509 TGGCAGGGATGATATGGTAGATTAG 59.573 44.000 0.00 0.00 0.00 1.73
229 241 4.018960 GTGGCAGGGATGATATGGTAGATT 60.019 45.833 0.00 0.00 0.00 2.40
232 244 2.639347 TGTGGCAGGGATGATATGGTAG 59.361 50.000 0.00 0.00 0.00 3.18
235 247 2.893215 ATGTGGCAGGGATGATATGG 57.107 50.000 0.00 0.00 0.00 2.74
236 248 3.087031 GGAATGTGGCAGGGATGATATG 58.913 50.000 0.00 0.00 0.00 1.78
237 249 2.718062 TGGAATGTGGCAGGGATGATAT 59.282 45.455 0.00 0.00 0.00 1.63
304 810 5.734311 CGAATTCTACGTTTTCAGTTGTGT 58.266 37.500 3.52 0.00 0.00 3.72
307 813 3.833061 CGCGAATTCTACGTTTTCAGTTG 59.167 43.478 0.00 0.00 0.00 3.16
578 1084 1.743252 CCTCCACTTCCTGAAGCGC 60.743 63.158 0.00 0.00 41.99 5.92
783 1292 1.540267 TCCGTCTCGAGAGAAAAGGTG 59.460 52.381 17.22 0.00 41.32 4.00
902 1411 1.579698 CGTTGGATGGCTCAGATCTG 58.420 55.000 17.07 17.07 0.00 2.90
962 1471 3.810310 AGGAAGAAGAGGATAAGCGTG 57.190 47.619 0.00 0.00 0.00 5.34
978 1487 0.198696 AGGAAGGGGGAGGAAAGGAA 59.801 55.000 0.00 0.00 0.00 3.36
984 1493 1.866997 TCTGGAGGAAGGGGGAGGA 60.867 63.158 0.00 0.00 0.00 3.71
1007 1527 2.338620 GTTTTGCGGGCTTGGGTC 59.661 61.111 0.00 0.00 0.00 4.46
1348 1868 3.847602 CAGGAGGAGAGCAGCGGG 61.848 72.222 0.00 0.00 0.00 6.13
1496 2016 1.212229 GGAGGACGTCGAAGTGGAC 59.788 63.158 9.23 0.00 0.00 4.02
1497 2017 0.959372 GAGGAGGACGTCGAAGTGGA 60.959 60.000 9.23 0.00 0.00 4.02
1675 2195 4.344865 AACACCCGCTCCCGCATT 62.345 61.111 0.00 0.00 35.30 3.56
1789 2309 2.359975 GGCGGTTCCCTGTCCTTG 60.360 66.667 0.00 0.00 0.00 3.61
1822 2342 3.146066 GCACATTTCCAGTCAGTAACCA 58.854 45.455 0.00 0.00 0.00 3.67
1823 2343 2.488153 GGCACATTTCCAGTCAGTAACC 59.512 50.000 0.00 0.00 0.00 2.85
1824 2344 3.146066 TGGCACATTTCCAGTCAGTAAC 58.854 45.455 0.00 0.00 0.00 2.50
1875 2395 2.107031 TGTCCTAATGCATGATCCCAGG 59.893 50.000 0.00 0.77 0.00 4.45
1914 2434 5.636965 CACTCTTACACTCTGAACAGAATGG 59.363 44.000 15.71 6.79 43.62 3.16
2001 2522 3.003482 CGTAGGCAGCTATCTTCGTTACT 59.997 47.826 0.00 0.00 0.00 2.24
2025 2784 5.083821 AGTGGGCACATTTAGGTGTTAAAT 58.916 37.500 0.00 0.00 41.55 1.40
2095 2854 5.488919 TGACCCAGACTGGAATTTAATCTCT 59.511 40.000 23.77 0.00 40.96 3.10
2108 2867 2.171237 TCCTAATGCATGACCCAGACTG 59.829 50.000 0.00 0.00 0.00 3.51
2133 2893 3.135712 ACACTGGTGACTGATTGGTTGTA 59.864 43.478 7.78 0.00 0.00 2.41
2134 2894 2.092429 ACACTGGTGACTGATTGGTTGT 60.092 45.455 7.78 0.00 0.00 3.32
2226 2986 7.534723 AACAGGTATCCAGCTATCGTAATTA 57.465 36.000 0.00 0.00 0.00 1.40
2262 3022 2.386661 ATCTAACCAACAGGCTGACG 57.613 50.000 23.66 11.18 0.00 4.35
2496 3265 4.636206 GGACTAAAGAGTGGCCACAAATAG 59.364 45.833 36.39 29.22 35.45 1.73
2502 3272 2.561478 TTGGACTAAAGAGTGGCCAC 57.439 50.000 29.22 29.22 35.45 5.01
2539 3309 4.046462 CACTGAGAAAGCCACAAAACATG 58.954 43.478 0.00 0.00 0.00 3.21
2545 3315 3.281727 ACTTCACTGAGAAAGCCACAA 57.718 42.857 0.00 0.00 35.40 3.33
2569 3339 5.109903 GCTGTAGAACATCTAACAACGGAT 58.890 41.667 0.00 0.00 29.58 4.18
2714 3485 2.476241 GCAAAGAAAATTTCCACGGCAG 59.524 45.455 1.57 0.00 0.00 4.85
2822 3593 9.431887 CCAGTTAACAGTACAAATAGCTCTAAA 57.568 33.333 8.61 0.00 0.00 1.85
3162 3934 2.096417 GTGCACGCAACAGTTAACTAGG 60.096 50.000 8.04 0.00 0.00 3.02
3266 4038 9.750125 GGTCTATTATCAAAATCCCAAATGTTC 57.250 33.333 0.00 0.00 0.00 3.18
3403 4175 6.837471 AGACCGTAATGAGAAAAGACTAGT 57.163 37.500 0.00 0.00 0.00 2.57
3417 4189 9.591792 GTAAACATTAGTAAGGAAGACCGTAAT 57.408 33.333 0.75 0.00 41.83 1.89
3421 4195 7.601508 ACAAGTAAACATTAGTAAGGAAGACCG 59.398 37.037 0.75 0.00 41.83 4.79
3432 4206 7.801716 TGCAGAGAAACAAGTAAACATTAGT 57.198 32.000 0.00 0.00 0.00 2.24
3499 4273 3.300388 CTGGACAACTAGGAGGCAGATA 58.700 50.000 0.00 0.00 0.00 1.98
3670 4444 5.531096 AGGCAACAAACCTGAATCTTCTGG 61.531 45.833 12.71 12.71 44.82 3.86
3722 4496 8.932610 AGTATGACTATTGATCAAATGGAGAGT 58.067 33.333 13.09 8.84 31.45 3.24
3749 4523 6.409704 TGATCATAAGGAAGTTCAGACCTTG 58.590 40.000 5.01 0.00 42.85 3.61
3832 4606 3.030291 ACCTCCTATGCTTCTCTGACAG 58.970 50.000 0.00 0.00 0.00 3.51
3856 4630 2.223340 GCCCGCAATACTTGTTCATCAG 60.223 50.000 0.00 0.00 0.00 2.90
4065 4839 2.454832 CTTTCGGCTGGACCTGCTCA 62.455 60.000 21.23 6.95 35.61 4.26
4068 4842 3.435186 GCTTTCGGCTGGACCTGC 61.435 66.667 14.68 14.68 38.06 4.85
4106 4880 0.730265 GTTCAGCACAAACCGACACA 59.270 50.000 0.00 0.00 0.00 3.72
4168 4943 2.096069 CCGCGCTAGGATTTTGATGATG 60.096 50.000 5.56 0.00 0.00 3.07
4169 4944 2.146342 CCGCGCTAGGATTTTGATGAT 58.854 47.619 5.56 0.00 0.00 2.45
4206 4981 1.003355 CTTTGGGCTCAGGCTTCGA 60.003 57.895 0.00 0.00 38.73 3.71
4231 5006 3.221964 CAGTGCTTGCTTTAATCCACC 57.778 47.619 0.00 0.00 0.00 4.61
4427 5212 9.615295 GTTTCTCACGGATAACTCTATATCTTC 57.385 37.037 0.00 0.00 33.63 2.87
4428 5213 9.132923 TGTTTCTCACGGATAACTCTATATCTT 57.867 33.333 0.00 0.00 33.63 2.40
4429 5214 8.693120 TGTTTCTCACGGATAACTCTATATCT 57.307 34.615 0.00 0.00 33.63 1.98
4432 5217 7.014326 AGCATGTTTCTCACGGATAACTCTATA 59.986 37.037 0.00 0.00 0.00 1.31
4556 5409 5.415701 CACAAGATAAACTTATGCACCCAGT 59.584 40.000 0.00 0.00 37.03 4.00
4678 5531 1.531602 GCACCCCAGAGCCAAAACT 60.532 57.895 0.00 0.00 0.00 2.66
4791 5656 4.484236 TCGCCTGAAAAATGTTAAGCATG 58.516 39.130 0.00 0.00 37.96 4.06
4792 5657 4.782019 TCGCCTGAAAAATGTTAAGCAT 57.218 36.364 0.00 0.00 40.03 3.79
4802 5667 5.004922 ACAATGAAGTTTCGCCTGAAAAA 57.995 34.783 0.00 0.00 45.22 1.94
4809 5674 5.710613 TTTTTCAACAATGAAGTTTCGCC 57.289 34.783 0.00 0.00 45.82 5.54
4913 5803 5.183140 GTCACACCAAAATGCTACCTACAAT 59.817 40.000 0.00 0.00 0.00 2.71
4917 5807 4.359434 TGTCACACCAAAATGCTACCTA 57.641 40.909 0.00 0.00 0.00 3.08
4988 5879 1.546228 TGGTCCTGCCCACCATTTT 59.454 52.632 0.00 0.00 39.11 1.82
4989 5880 3.270944 TGGTCCTGCCCACCATTT 58.729 55.556 0.00 0.00 39.11 2.32
5015 5906 3.016736 TGGAAATCCAATTCGGCTCTTC 58.983 45.455 0.00 0.00 44.35 2.87
5061 5953 1.717032 AGCTGAGTTGTGGTCCAGTA 58.283 50.000 0.00 0.00 0.00 2.74
5065 5957 5.453567 AAAATAAAGCTGAGTTGTGGTCC 57.546 39.130 0.00 0.00 0.00 4.46
5068 5960 7.148407 ACGAGATAAAATAAAGCTGAGTTGTGG 60.148 37.037 0.00 0.00 0.00 4.17
5103 5995 0.535335 TCGCCCAGAAGAATTAGCGT 59.465 50.000 0.00 0.00 43.73 5.07
5108 6000 3.634397 TTCATCTCGCCCAGAAGAATT 57.366 42.857 0.00 0.00 34.56 2.17
5109 6001 3.634397 TTTCATCTCGCCCAGAAGAAT 57.366 42.857 0.26 0.00 38.37 2.40
5218 6112 1.818060 TGAACAATCCCATTTGCGGAG 59.182 47.619 0.00 0.00 31.41 4.63
5219 6113 1.543802 GTGAACAATCCCATTTGCGGA 59.456 47.619 0.00 0.00 0.00 5.54
5220 6114 1.271934 TGTGAACAATCCCATTTGCGG 59.728 47.619 0.00 0.00 0.00 5.69
5221 6115 2.327568 GTGTGAACAATCCCATTTGCG 58.672 47.619 0.00 0.00 0.00 4.85
5222 6116 2.036992 TGGTGTGAACAATCCCATTTGC 59.963 45.455 0.00 0.00 0.00 3.68
5223 6117 3.861886 GCTGGTGTGAACAATCCCATTTG 60.862 47.826 0.00 0.00 0.00 2.32
5224 6118 2.299867 GCTGGTGTGAACAATCCCATTT 59.700 45.455 0.00 0.00 0.00 2.32
5225 6119 1.895131 GCTGGTGTGAACAATCCCATT 59.105 47.619 0.00 0.00 0.00 3.16
5226 6120 1.203038 TGCTGGTGTGAACAATCCCAT 60.203 47.619 0.00 0.00 0.00 4.00
5227 6121 0.184692 TGCTGGTGTGAACAATCCCA 59.815 50.000 0.00 0.00 0.00 4.37
5228 6122 1.327303 TTGCTGGTGTGAACAATCCC 58.673 50.000 0.00 0.00 0.00 3.85
5229 6123 3.243839 ACATTTGCTGGTGTGAACAATCC 60.244 43.478 0.00 0.00 0.00 3.01
5230 6124 3.981211 ACATTTGCTGGTGTGAACAATC 58.019 40.909 0.00 0.00 0.00 2.67
5231 6125 4.141981 TGAACATTTGCTGGTGTGAACAAT 60.142 37.500 0.00 0.00 0.00 2.71
5232 6126 3.194329 TGAACATTTGCTGGTGTGAACAA 59.806 39.130 0.00 0.00 0.00 2.83
5233 6127 2.757314 TGAACATTTGCTGGTGTGAACA 59.243 40.909 0.00 0.00 0.00 3.18
5234 6128 3.374745 CTGAACATTTGCTGGTGTGAAC 58.625 45.455 0.00 0.00 0.00 3.18
5235 6129 3.713858 CTGAACATTTGCTGGTGTGAA 57.286 42.857 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.