Multiple sequence alignment - TraesCS5B01G115200

Loading Multiple Alignment...

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 TraesCS5B01G115200 chr5B 100.000 4820 0 0 1 4820 191958268 191963087 0.000000e+00 8901.0
1 TraesCS5B01G115200 chr5B 95.122 41 2 0 4197 4237 687221579 687221539 1.120000e-06 65.8
2 TraesCS5B01G115200 chr5D 96.173 4703 85 24 1 4668 177169301 177173943 0.000000e+00 7600.0
3 TraesCS5B01G115200 chr5D 91.447 152 11 1 4668 4819 177174020 177174169 1.760000e-49 207.0
4 TraesCS5B01G115200 chr5A 97.382 4049 91 9 1 4040 180991688 180995730 0.000000e+00 6876.0
5 TraesCS5B01G115200 chr5A 91.138 756 45 12 4051 4805 180995767 180996501 0.000000e+00 1005.0
6 TraesCS5B01G115200 chr5A 91.111 45 4 0 4193 4237 462534672 462534628 1.450000e-05 62.1
7 TraesCS5B01G115200 chr2D 81.424 323 47 9 2810 3127 598634698 598634384 8.010000e-63 252.0
8 TraesCS5B01G115200 chr1A 97.619 42 1 0 4198 4239 427816466 427816425 6.690000e-09 73.1
9 TraesCS5B01G115200 chr7A 97.436 39 1 0 4201 4239 724263285 724263323 3.110000e-07 67.6
10 TraesCS5B01G115200 chr3B 97.436 39 1 0 4201 4239 172005805 172005843 3.110000e-07 67.6
11 TraesCS5B01G115200 chr3B 95.122 41 2 0 4197 4237 641704501 641704461 1.120000e-06 65.8
12 TraesCS5B01G115200 chr6A 95.122 41 2 0 4197 4237 33557367 33557407 1.120000e-06 65.8
13 TraesCS5B01G115200 chr1D 95.000 40 2 0 4198 4237 459859036 459859075 4.030000e-06 63.9
14 TraesCS5B01G115200 chr4A 80.556 72 12 2 4676 4746 606630411 606630341 2.000000e-03 54.7


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 TraesCS5B01G115200 chr5B 191958268 191963087 4819 False 8901.0 8901 100.00 1 4820 1 chr5B.!!$F1 4819
1 TraesCS5B01G115200 chr5D 177169301 177174169 4868 False 3903.5 7600 93.81 1 4819 2 chr5D.!!$F1 4818
2 TraesCS5B01G115200 chr5A 180991688 180996501 4813 False 3940.5 6876 94.26 1 4805 2 chr5A.!!$F1 4804

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
811 817 0.610232 ATCTTTGCAGGGTGGTCAGC 60.610 55.000 0.00 0.0 0.0 4.26 F
2055 2061 1.003580 GGTGAGTGCTCCCAGAATTCA 59.996 52.381 8.44 0.0 0.0 2.57 F
3339 3352 0.031178 GGCTGCCTCAACTTGTTGTG 59.969 55.000 12.43 10.2 0.0 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2676 2685 0.973632 ACCGAGCCAACATACAGTCA 59.026 50.000 0.0 0.0 0.0 3.41 R
3790 3803 1.078848 CAAACTCCAGCTCCTCGGG 60.079 63.158 0.0 0.0 0.0 5.14 R
4554 4599 1.214367 TCGTGCAAACTTCGGAACTC 58.786 50.000 0.0 0.0 0.0 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
346 348 1.454111 GAGCTCGTGGAGGCTCCTA 60.454 63.158 32.28 17.16 46.32 2.94
348 350 1.755008 GCTCGTGGAGGCTCCTACT 60.755 63.158 32.28 0.00 37.46 2.57
378 380 1.533033 TCGCAGGAGTTCCACCAGA 60.533 57.895 0.28 0.00 38.89 3.86
380 382 1.821061 CGCAGGAGTTCCACCAGAGT 61.821 60.000 0.28 0.00 38.89 3.24
487 489 4.028490 TGCCCCCGTTCTCGCAAT 62.028 61.111 0.00 0.00 35.54 3.56
561 563 8.171840 GCTGAAATGTGTGAGAGATAGTAAAAC 58.828 37.037 0.00 0.00 0.00 2.43
567 569 6.166982 GTGTGAGAGATAGTAAAACAGCCTT 58.833 40.000 0.00 0.00 0.00 4.35
571 573 7.387948 GTGAGAGATAGTAAAACAGCCTTTTGA 59.612 37.037 0.89 0.00 0.00 2.69
606 608 1.561542 TGCCCTCTTCTCCCAAGATTC 59.438 52.381 0.00 0.00 0.00 2.52
669 671 3.995199 TGTGACAGGAACACTTCTGATC 58.005 45.455 0.00 0.00 38.81 2.92
693 695 4.610680 GCATTTGTTGTACTTCGTGGACTC 60.611 45.833 0.00 0.00 0.00 3.36
694 696 4.395959 TTTGTTGTACTTCGTGGACTCT 57.604 40.909 0.00 0.00 0.00 3.24
695 697 4.395959 TTGTTGTACTTCGTGGACTCTT 57.604 40.909 0.00 0.00 0.00 2.85
696 698 3.713288 TGTTGTACTTCGTGGACTCTTG 58.287 45.455 0.00 0.00 0.00 3.02
811 817 0.610232 ATCTTTGCAGGGTGGTCAGC 60.610 55.000 0.00 0.00 0.00 4.26
1186 1192 3.243907 GGCGATTGATAGCAGGACTTACT 60.244 47.826 0.00 0.00 34.54 2.24
1238 1244 3.924686 GCAGATTCTTTGTTGAAGCATGG 59.075 43.478 0.00 0.00 35.10 3.66
1274 1280 2.621407 GGTCAGGGCCATCTCAAATTGA 60.621 50.000 6.18 0.00 0.00 2.57
1625 1631 5.131642 TCCATTCTGCATCTTCTACCTCAAT 59.868 40.000 0.00 0.00 0.00 2.57
1929 1935 2.477825 CATGTATCAACCAGCTCCTCG 58.522 52.381 0.00 0.00 0.00 4.63
1934 1940 2.600769 AACCAGCTCCTCGTCGGT 60.601 61.111 0.00 0.00 0.00 4.69
1997 2003 7.201857 GGAGATAAATCCAGGACCAGAAAAATG 60.202 40.741 0.00 0.00 39.34 2.32
2055 2061 1.003580 GGTGAGTGCTCCCAGAATTCA 59.996 52.381 8.44 0.00 0.00 2.57
2208 2214 1.985895 CAACAGGGACCCTTAGGACTT 59.014 52.381 11.56 0.00 36.73 3.01
2561 2567 7.050970 TGAGTACTTAGAACTTCACACATGT 57.949 36.000 0.00 0.00 0.00 3.21
2662 2671 5.958380 ACCTAGTGATTACAATCTCTGACCA 59.042 40.000 13.98 0.00 39.03 4.02
2675 2684 1.630369 TCTGACCAAGCTACCATTGCT 59.370 47.619 0.00 0.00 43.32 3.91
2727 2736 8.695456 ACAGTAGTTCTTGATGTTCCAAATTTT 58.305 29.630 0.00 0.00 0.00 1.82
2733 2742 6.819284 TCTTGATGTTCCAAATTTTCTGCTT 58.181 32.000 0.00 0.00 0.00 3.91
2734 2743 7.950512 TCTTGATGTTCCAAATTTTCTGCTTA 58.049 30.769 0.00 0.00 0.00 3.09
3012 3025 6.374578 GTTTTATGTTGCAGAAGTTCTCCTC 58.625 40.000 1.26 0.00 0.00 3.71
3121 3134 6.154203 TGCTATCAGATTTTGATCTCTCGT 57.846 37.500 0.00 0.00 43.03 4.18
3129 3142 6.591834 CAGATTTTGATCTCTCGTTAAGGTGT 59.408 38.462 0.00 0.00 0.00 4.16
3339 3352 0.031178 GGCTGCCTCAACTTGTTGTG 59.969 55.000 12.43 10.20 0.00 3.33
3790 3803 0.908198 ATGTCTGGACTTCAGGAGCC 59.092 55.000 2.38 0.00 43.53 4.70
3907 3920 1.271926 GGTTGGGGCTGTCTGTACATT 60.272 52.381 0.00 0.00 34.37 2.71
4040 4054 4.501229 GGCTCCAGTTGATCTAGTGATCTG 60.501 50.000 12.83 0.00 46.84 2.90
4041 4055 4.619973 CTCCAGTTGATCTAGTGATCTGC 58.380 47.826 12.83 1.52 46.84 4.26
4048 4062 7.392953 CAGTTGATCTAGTGATCTGCTCCTATA 59.607 40.741 6.15 0.00 46.84 1.31
4049 4063 7.393234 AGTTGATCTAGTGATCTGCTCCTATAC 59.607 40.741 7.42 0.00 46.84 1.47
4068 4108 1.271597 ACCAGATCCACTGTTTCTGCC 60.272 52.381 6.63 0.00 44.40 4.85
4098 4138 4.439860 AGAGGGTGATTACCTTTCCTCTT 58.560 43.478 6.62 0.00 46.66 2.85
4174 4214 5.290386 ACTTCTGTGAAAGGAACTCTTACG 58.710 41.667 0.00 0.00 38.49 3.18
4226 4266 2.225727 CCTCCGTTCACTTTTGTAAGGC 59.774 50.000 0.00 0.00 35.61 4.35
4227 4267 1.868498 TCCGTTCACTTTTGTAAGGCG 59.132 47.619 0.00 0.00 35.61 5.52
4228 4268 1.600485 CCGTTCACTTTTGTAAGGCGT 59.400 47.619 0.00 0.00 35.61 5.68
4229 4269 2.032426 CCGTTCACTTTTGTAAGGCGTT 59.968 45.455 0.00 0.00 35.61 4.84
4230 4270 3.487879 CCGTTCACTTTTGTAAGGCGTTT 60.488 43.478 0.00 0.00 35.61 3.60
4231 4271 4.099824 CGTTCACTTTTGTAAGGCGTTTT 58.900 39.130 0.00 0.00 35.61 2.43
4232 4272 5.264712 CGTTCACTTTTGTAAGGCGTTTTA 58.735 37.500 0.00 0.00 35.61 1.52
4233 4273 5.394322 CGTTCACTTTTGTAAGGCGTTTTAG 59.606 40.000 0.00 0.00 35.61 1.85
4234 4274 6.488817 GTTCACTTTTGTAAGGCGTTTTAGA 58.511 36.000 0.00 0.00 35.61 2.10
4235 4275 6.051646 TCACTTTTGTAAGGCGTTTTAGAC 57.948 37.500 0.00 0.00 35.61 2.59
4236 4276 5.585445 TCACTTTTGTAAGGCGTTTTAGACA 59.415 36.000 0.00 0.00 35.61 3.41
4237 4277 6.261381 TCACTTTTGTAAGGCGTTTTAGACAT 59.739 34.615 0.00 0.00 35.61 3.06
4238 4278 6.915843 CACTTTTGTAAGGCGTTTTAGACATT 59.084 34.615 0.00 0.00 35.61 2.71
4239 4279 6.915843 ACTTTTGTAAGGCGTTTTAGACATTG 59.084 34.615 0.00 0.00 35.61 2.82
4240 4280 6.621316 TTTGTAAGGCGTTTTAGACATTGA 57.379 33.333 0.00 0.00 0.00 2.57
4280 4324 7.535997 ACAAAAGTGAACAGAGTAGGTTTTTC 58.464 34.615 0.00 0.00 0.00 2.29
4402 4447 3.911868 TGCAATGTGTATTTTGTCTGGC 58.088 40.909 0.00 0.00 0.00 4.85
4407 4452 3.674997 TGTGTATTTTGTCTGGCTCCTC 58.325 45.455 0.00 0.00 0.00 3.71
4554 4599 6.868339 GGGTTGGACAACTGAAATCTTAAATG 59.132 38.462 14.14 0.00 40.94 2.32
4560 4605 8.023706 GGACAACTGAAATCTTAAATGAGTTCC 58.976 37.037 0.00 0.00 39.43 3.62
4606 4651 4.245660 GTCACATTTCGAGAAGATGTGGA 58.754 43.478 23.88 15.75 46.54 4.02
4681 4803 5.012251 TGCCTTGTACTACAATGTAAGGTGA 59.988 40.000 12.02 0.00 37.48 4.02
4721 4843 8.539770 CAGTATCTATAAGCACTGGGTATTTG 57.460 38.462 0.00 0.00 35.77 2.32
4757 4879 9.569122 GGTAGATGTTTAATTAGGCATCCTTTA 57.431 33.333 19.19 9.34 38.67 1.85
4778 4900 9.587772 CCTTTATATGGAGATAGATAAACACCG 57.412 37.037 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.167900 AGACGAATCGACCTAAAAGGGG 59.832 50.000 10.55 0.00 40.58 4.79
148 150 4.083862 GGAGTGGAGTGTCCCGCC 62.084 72.222 0.00 0.00 37.42 6.13
152 154 2.574399 GAGCGGAGTGGAGTGTCC 59.426 66.667 0.00 0.00 36.96 4.02
346 348 2.045926 GCGAGGCCACATTCCAGT 60.046 61.111 5.01 0.00 0.00 4.00
348 350 2.046023 CTGCGAGGCCACATTCCA 60.046 61.111 5.01 0.00 0.00 3.53
561 563 1.117150 CCCATCCCATCAAAAGGCTG 58.883 55.000 0.00 0.00 0.00 4.85
567 569 3.033184 GCAAGATTCCCATCCCATCAAA 58.967 45.455 0.00 0.00 0.00 2.69
571 573 0.189327 GGGCAAGATTCCCATCCCAT 59.811 55.000 0.00 0.00 43.37 4.00
669 671 2.222213 TCCACGAAGTACAACAAATGCG 59.778 45.455 0.00 0.00 41.61 4.73
1186 1192 2.978824 GGGGCTAAGTGCTCGACA 59.021 61.111 0.00 0.00 44.88 4.35
1238 1244 3.557264 CCCTGACCTAGGTGTCTTTTGAC 60.557 52.174 22.10 1.33 45.80 3.18
1261 1267 3.698040 CCAGGGACTTCAATTTGAGATGG 59.302 47.826 0.00 0.53 34.60 3.51
1274 1280 1.439543 GGAGCATATCCCAGGGACTT 58.560 55.000 11.70 0.00 43.01 3.01
1401 1407 1.139853 CTGTGGATAGTCCCTGCTTCC 59.860 57.143 0.00 0.00 35.03 3.46
1625 1631 7.206789 TGGATCCTGACCTTTTGTATATCAA 57.793 36.000 14.23 0.00 0.00 2.57
1929 1935 2.953466 TACTAATGCTGGACACCGAC 57.047 50.000 0.00 0.00 0.00 4.79
1934 1940 3.118038 GGTGGGATTACTAATGCTGGACA 60.118 47.826 0.85 0.00 0.00 4.02
1997 2003 3.443037 CATTCAGACGACCTCTCATCAC 58.557 50.000 0.00 0.00 0.00 3.06
2055 2061 5.104776 TCCATACTCACTAATGCTGCTCTTT 60.105 40.000 0.00 0.00 0.00 2.52
2208 2214 5.290493 TCTTCAGAAGCCTAAAGTTGTCA 57.710 39.130 5.15 0.00 0.00 3.58
2561 2567 3.259064 GCAGGCGTCTGTAATACTGAAA 58.741 45.455 19.84 0.00 42.78 2.69
2675 2684 1.346395 ACCGAGCCAACATACAGTCAA 59.654 47.619 0.00 0.00 0.00 3.18
2676 2685 0.973632 ACCGAGCCAACATACAGTCA 59.026 50.000 0.00 0.00 0.00 3.41
2677 2686 2.094762 AACCGAGCCAACATACAGTC 57.905 50.000 0.00 0.00 0.00 3.51
2790 2799 4.858850 AGAATGGCATGATGTGTTTAGGA 58.141 39.130 0.00 0.00 0.00 2.94
3012 3025 1.570813 TGTGAAGATATTCCAGCGCG 58.429 50.000 0.00 0.00 0.00 6.86
3121 3134 2.419667 GGCGCTAACAGAACACCTTAA 58.580 47.619 7.64 0.00 0.00 1.85
3339 3352 1.811679 GCGTGCTTCTGTAGGCTCC 60.812 63.158 0.00 0.00 36.88 4.70
3676 3689 1.207089 TCGTATCAAGGCCCAGTTCAG 59.793 52.381 0.00 0.00 0.00 3.02
3790 3803 1.078848 CAAACTCCAGCTCCTCGGG 60.079 63.158 0.00 0.00 0.00 5.14
3907 3920 5.582269 GCAACTGAGCATACAAGAATCTACA 59.418 40.000 0.00 0.00 0.00 2.74
4040 4054 3.951775 CAGTGGATCTGGTATAGGAGC 57.048 52.381 0.00 0.00 40.23 4.70
4041 4055 5.600484 AGAAACAGTGGATCTGGTATAGGAG 59.400 44.000 0.00 0.00 44.18 3.69
4068 4108 2.369394 GTAATCACCCTCTTGCCCTTG 58.631 52.381 0.00 0.00 0.00 3.61
4120 4160 4.065088 TGTAGGTGAAACATCAGTGCTTC 58.935 43.478 0.00 0.00 39.98 3.86
4233 4273 5.407387 TGTAAGGCGTTTTAGACTCAATGTC 59.593 40.000 0.00 0.00 45.67 3.06
4234 4274 5.302360 TGTAAGGCGTTTTAGACTCAATGT 58.698 37.500 0.00 0.00 0.00 2.71
4235 4275 5.856126 TGTAAGGCGTTTTAGACTCAATG 57.144 39.130 0.00 0.00 0.00 2.82
4236 4276 6.870971 TTTGTAAGGCGTTTTAGACTCAAT 57.129 33.333 0.00 0.00 0.00 2.57
4237 4277 6.316890 ACTTTTGTAAGGCGTTTTAGACTCAA 59.683 34.615 0.00 0.00 35.61 3.02
4238 4278 5.818857 ACTTTTGTAAGGCGTTTTAGACTCA 59.181 36.000 0.00 0.00 35.61 3.41
4239 4279 6.018507 TCACTTTTGTAAGGCGTTTTAGACTC 60.019 38.462 0.00 0.00 35.61 3.36
4240 4280 5.818857 TCACTTTTGTAAGGCGTTTTAGACT 59.181 36.000 0.00 0.00 35.61 3.24
4280 4324 7.615757 ACCAAGAAACCCTATTTCATTCTTAGG 59.384 37.037 2.51 0.00 38.04 2.69
4292 4336 4.650972 TTACTGCACCAAGAAACCCTAT 57.349 40.909 0.00 0.00 0.00 2.57
4407 4452 3.275848 TGGACAATAGGATCCTAGGGG 57.724 52.381 25.35 18.48 35.86 4.79
4455 4500 6.419710 CGCACAAGCATATGAATGATTTGATT 59.580 34.615 6.97 0.00 39.66 2.57
4554 4599 1.214367 TCGTGCAAACTTCGGAACTC 58.786 50.000 0.00 0.00 0.00 3.01
4560 4605 4.202959 GCATCATAAATCGTGCAAACTTCG 59.797 41.667 0.00 0.00 37.52 3.79
4702 4824 7.391148 ACAAACAAATACCCAGTGCTTATAG 57.609 36.000 0.00 0.00 0.00 1.31
4757 4879 8.367660 ACATCGGTGTTTATCTATCTCCATAT 57.632 34.615 0.00 0.00 34.01 1.78


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

AutoCloner maintained by Alex Coulton.