Multiple sequence alignment - TraesCS4B01G275900

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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 TraesCS4B01G275900 chr4B 100.000 2585 0 0 1 2585 554240559 554243143 0 4774
1 TraesCS4B01G275900 chr1D 95.130 1889 80 7 699 2585 278102178 278100300 0 2968
2 TraesCS4B01G275900 chr4D 93.839 1899 97 12 696 2585 481887311 481889198 0 2841
3 TraesCS4B01G275900 chr4D 93.674 1897 102 11 699 2585 502108530 502106642 0 2822
4 TraesCS4B01G275900 chr2D 93.717 1894 110 6 696 2582 498273605 498275496 0 2830
5 TraesCS4B01G275900 chr2D 93.661 1893 107 6 696 2585 350066297 350068179 0 2819
6 TraesCS4B01G275900 chr2D 96.686 694 22 1 1 693 39458009 39458702 0 1153
7 TraesCS4B01G275900 chr6D 93.661 1893 103 9 699 2585 325418586 325416705 0 2815
8 TraesCS4B01G275900 chr3D 93.535 1887 109 9 699 2585 1283628 1281755 0 2796
9 TraesCS4B01G275900 chr7A 92.778 1897 116 9 699 2585 661593737 661591852 0 2724
10 TraesCS4B01G275900 chr3B 92.620 1897 121 11 696 2583 168094514 168096400 0 2710
11 TraesCS4B01G275900 chr3B 96.686 694 22 1 1 693 603553088 603553781 0 1153
12 TraesCS4B01G275900 chr3B 96.552 696 23 1 1 695 496876490 496875795 0 1151
13 TraesCS4B01G275900 chr7B 97.262 694 18 1 1 693 416357848 416358541 0 1175
14 TraesCS4B01G275900 chr7B 96.974 694 20 1 1 693 588353024 588353717 0 1164
15 TraesCS4B01G275900 chr5B 96.686 694 22 1 1 693 362835820 362835127 0 1153
16 TraesCS4B01G275900 chr5B 95.915 710 24 3 1 709 70701683 70700978 0 1146
17 TraesCS4B01G275900 chr2B 96.686 694 21 2 1 693 531747676 531748368 0 1153
18 TraesCS4B01G275900 chr1B 96.552 696 22 2 1 695 139386920 139386226 0 1151


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 TraesCS4B01G275900 chr4B 554240559 554243143 2584 False 4774 4774 100.000 1 2585 1 chr4B.!!$F1 2584
1 TraesCS4B01G275900 chr1D 278100300 278102178 1878 True 2968 2968 95.130 699 2585 1 chr1D.!!$R1 1886
2 TraesCS4B01G275900 chr4D 481887311 481889198 1887 False 2841 2841 93.839 696 2585 1 chr4D.!!$F1 1889
3 TraesCS4B01G275900 chr4D 502106642 502108530 1888 True 2822 2822 93.674 699 2585 1 chr4D.!!$R1 1886
4 TraesCS4B01G275900 chr2D 498273605 498275496 1891 False 2830 2830 93.717 696 2582 1 chr2D.!!$F3 1886
5 TraesCS4B01G275900 chr2D 350066297 350068179 1882 False 2819 2819 93.661 696 2585 1 chr2D.!!$F2 1889
6 TraesCS4B01G275900 chr2D 39458009 39458702 693 False 1153 1153 96.686 1 693 1 chr2D.!!$F1 692
7 TraesCS4B01G275900 chr6D 325416705 325418586 1881 True 2815 2815 93.661 699 2585 1 chr6D.!!$R1 1886
8 TraesCS4B01G275900 chr3D 1281755 1283628 1873 True 2796 2796 93.535 699 2585 1 chr3D.!!$R1 1886
9 TraesCS4B01G275900 chr7A 661591852 661593737 1885 True 2724 2724 92.778 699 2585 1 chr7A.!!$R1 1886
10 TraesCS4B01G275900 chr3B 168094514 168096400 1886 False 2710 2710 92.620 696 2583 1 chr3B.!!$F1 1887
11 TraesCS4B01G275900 chr3B 603553088 603553781 693 False 1153 1153 96.686 1 693 1 chr3B.!!$F2 692
12 TraesCS4B01G275900 chr3B 496875795 496876490 695 True 1151 1151 96.552 1 695 1 chr3B.!!$R1 694
13 TraesCS4B01G275900 chr7B 416357848 416358541 693 False 1175 1175 97.262 1 693 1 chr7B.!!$F1 692
14 TraesCS4B01G275900 chr7B 588353024 588353717 693 False 1164 1164 96.974 1 693 1 chr7B.!!$F2 692
15 TraesCS4B01G275900 chr5B 362835127 362835820 693 True 1153 1153 96.686 1 693 1 chr5B.!!$R2 692
16 TraesCS4B01G275900 chr5B 70700978 70701683 705 True 1146 1146 95.915 1 709 1 chr5B.!!$R1 708
17 TraesCS4B01G275900 chr2B 531747676 531748368 692 False 1153 1153 96.686 1 693 1 chr2B.!!$F1 692
18 TraesCS4B01G275900 chr1B 139386226 139386920 694 True 1151 1151 96.552 1 695 1 chr1B.!!$R1 694

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
621 623 0.178992 TCTTTGGCTCCCCTTGTGTG 60.179 55.0 0.0 0.0 0.0 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1807 1824 0.393448 TTGTCGTCGGGGATGTTGAA 59.607 50.0 0.0 0.0 0.0 2.69 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
301 302 7.700656 CGTATGACTATATTCGGAATACATGCA 59.299 37.037 12.39 9.35 0.00 3.96
345 346 4.097418 AGCTAGTTCTGTGTCACCCTATT 58.903 43.478 0.00 0.00 0.00 1.73
450 452 5.927954 TCGCTTATTTACTTTTCCGTTGT 57.072 34.783 0.00 0.00 0.00 3.32
466 468 5.358090 TCCGTTGTTACTGTTACAATCACA 58.642 37.500 14.48 0.00 37.77 3.58
511 513 4.689071 TGCCACTGTTACCATTACTATCG 58.311 43.478 0.00 0.00 0.00 2.92
621 623 0.178992 TCTTTGGCTCCCCTTGTGTG 60.179 55.000 0.00 0.00 0.00 3.82
661 663 5.105432 GGTTGAATACTCTACCCTCGAAAGT 60.105 44.000 0.00 0.00 40.45 2.66
742 744 2.203728 TACTGCCTCACCACCGGT 60.204 61.111 0.00 0.00 35.62 5.28
766 768 2.216898 GGCTGCGATTTTAGATCTGCT 58.783 47.619 5.18 0.00 0.00 4.24
778 780 0.891373 GATCTGCTCTATAGGCGGCA 59.109 55.000 13.08 13.34 36.16 5.69
792 803 1.153289 CGGCAGCAGCATAAGAGGT 60.153 57.895 2.65 0.00 44.61 3.85
804 815 2.386064 TAAGAGGTGGCGGCGTTTGT 62.386 55.000 9.37 0.00 0.00 2.83
827 838 1.566298 GGATCTGGTGCTCCCCTTGT 61.566 60.000 1.59 0.00 0.00 3.16
867 878 1.153086 CCTAGTCTGTGCCATGGCC 60.153 63.158 33.44 23.83 41.09 5.36
957 969 2.395619 AGGCCGTTAAGCTAGGTGTAT 58.604 47.619 0.00 0.00 0.00 2.29
1005 1017 4.395625 TCGATGTCGACTAGGTTATGGAT 58.604 43.478 17.92 0.00 44.22 3.41
1077 1089 2.863401 CATGGGTCATGTTCATGCAG 57.137 50.000 7.80 0.00 37.12 4.41
1179 1194 8.504005 CAAAACCTAAACTACATCTACAACTGG 58.496 37.037 0.00 0.00 0.00 4.00
1253 1268 1.205893 GCTTGTCGAGACCTTCAGGAT 59.794 52.381 0.00 0.00 38.94 3.24
1258 1273 1.285078 TCGAGACCTTCAGGATCAGGA 59.715 52.381 0.00 0.00 38.94 3.86
1259 1274 2.103373 CGAGACCTTCAGGATCAGGAA 58.897 52.381 0.00 1.47 38.94 3.36
1267 1282 4.440880 CTTCAGGATCAGGAAGCTGTTAG 58.559 47.826 11.27 0.98 34.69 2.34
1332 1347 2.830923 CCTCCATGTTGTTGGCCATAAA 59.169 45.455 6.09 0.29 36.66 1.40
1353 1368 2.711009 ACAGAGGTTCAGGGTCATTCAA 59.289 45.455 0.00 0.00 0.00 2.69
1402 1417 5.112686 CCATCTCTAGGTACTTCAAGCAAC 58.887 45.833 0.00 0.00 41.75 4.17
1541 1558 6.866480 ACAATATACACTTTTCATGGCTTGG 58.134 36.000 0.09 0.00 0.00 3.61
1690 1707 1.002544 GGAGGAAGCACTACACAAGCT 59.997 52.381 0.00 0.00 41.03 3.74
1744 1761 3.912496 AGTTCACATATGTGCTGGCTA 57.088 42.857 27.71 9.51 45.25 3.93
1846 1863 4.777896 ACAAGTTCTACCTTGGAGATGCTA 59.222 41.667 5.96 0.00 44.89 3.49
1909 1926 2.271800 CAAGGTACCATCTCAACGAGC 58.728 52.381 15.94 0.00 0.00 5.03
2145 2162 1.280421 GTGCCTGAGGAGGAAGATGTT 59.720 52.381 0.65 0.00 42.93 2.71
2228 2246 2.243736 AGAACAAAAGGTTGGAGTGGGA 59.756 45.455 0.00 0.00 40.63 4.37
2241 2259 1.194781 AGTGGGAAGAGGCGATGTGT 61.195 55.000 0.00 0.00 0.00 3.72
2247 2265 3.432326 GGGAAGAGGCGATGTGTCTTAAT 60.432 47.826 0.00 0.00 30.55 1.40
2291 2321 5.240013 AGATGGAAGAAGAACAAGAAGCT 57.760 39.130 0.00 0.00 0.00 3.74
2292 2322 6.365970 AGATGGAAGAAGAACAAGAAGCTA 57.634 37.500 0.00 0.00 0.00 3.32
2293 2323 6.169800 AGATGGAAGAAGAACAAGAAGCTAC 58.830 40.000 0.00 0.00 0.00 3.58
2336 2378 3.723325 AGCAGAAGAAGAGGAGAGGAAT 58.277 45.455 0.00 0.00 0.00 3.01
2361 2409 1.625315 AGATCTGGTAGCAGCAACACA 59.375 47.619 17.20 0.00 0.00 3.72
2362 2410 2.038952 AGATCTGGTAGCAGCAACACAA 59.961 45.455 17.20 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
301 302 7.285566 AGCTCCAGTTCATCAATGTAATGTAT 58.714 34.615 0.00 0.00 0.00 2.29
450 452 9.562583 GAAGTTTTGTTGTGATTGTAACAGTAA 57.437 29.630 0.00 0.00 37.98 2.24
466 468 9.529325 GGCAAAAGTAAAGATAGAAGTTTTGTT 57.471 29.630 13.23 0.00 41.94 2.83
550 552 5.418840 GTCAATTCAACCACACCTGGATAAT 59.581 40.000 0.00 0.00 40.55 1.28
661 663 0.981183 AGTGTAGGGGATCGCAACAA 59.019 50.000 15.70 2.27 0.00 2.83
723 725 1.982395 CCGGTGGTGAGGCAGTAGA 60.982 63.158 0.00 0.00 0.00 2.59
742 744 0.463654 ATCTAAAATCGCAGCCGCCA 60.464 50.000 0.00 0.00 33.11 5.69
766 768 1.475169 ATGCTGCTGCCGCCTATAGA 61.475 55.000 13.49 0.00 38.71 1.98
778 780 1.153289 CGCCACCTCTTATGCTGCT 60.153 57.895 0.00 0.00 0.00 4.24
781 783 2.190578 GCCGCCACCTCTTATGCT 59.809 61.111 0.00 0.00 0.00 3.79
785 793 1.669760 CAAACGCCGCCACCTCTTA 60.670 57.895 0.00 0.00 0.00 2.10
804 815 3.785859 GGAGCACCAGATCCGCCA 61.786 66.667 0.00 0.00 41.08 5.69
827 838 2.203280 CCAGACGGTGGCCAACAA 60.203 61.111 23.36 0.00 40.39 2.83
929 941 2.181975 AGCTTAACGGCCTAACCACTA 58.818 47.619 0.00 0.00 39.03 2.74
957 969 4.014569 TCGTTCAGTGGGAAATCAATCA 57.985 40.909 0.00 0.00 37.23 2.57
1005 1017 0.829990 TTATCAGCCTCATCCGTGCA 59.170 50.000 0.00 0.00 0.00 4.57
1077 1089 1.081108 ACGACGAACAGCTCTCTGC 60.081 57.895 0.00 0.00 44.10 4.26
1158 1173 8.258007 TCATTCCAGTTGTAGATGTAGTTTAGG 58.742 37.037 0.00 0.00 0.00 2.69
1161 1176 7.450074 TGTCATTCCAGTTGTAGATGTAGTTT 58.550 34.615 0.00 0.00 0.00 2.66
1179 1194 2.200067 CACAGAGCCTCGATGTCATTC 58.800 52.381 0.00 0.00 0.00 2.67
1253 1268 4.711846 TGCTATCTTCTAACAGCTTCCTGA 59.288 41.667 0.00 0.00 41.77 3.86
1258 1273 6.314896 GTGTTGATGCTATCTTCTAACAGCTT 59.685 38.462 0.00 0.00 35.05 3.74
1259 1274 5.814705 GTGTTGATGCTATCTTCTAACAGCT 59.185 40.000 0.00 0.00 35.05 4.24
1267 1282 4.256920 ACACTGGTGTTGATGCTATCTTC 58.743 43.478 0.01 0.00 41.83 2.87
1332 1347 2.338809 TGAATGACCCTGAACCTCTGT 58.661 47.619 0.00 0.00 0.00 3.41
1353 1368 3.753272 CCATTGATCTCCTGAACGTGTTT 59.247 43.478 0.00 0.00 0.00 2.83
1411 1426 3.467483 TCTCCTCTAAGCTCCCCAATAGA 59.533 47.826 0.00 0.00 0.00 1.98
1561 1578 1.802960 CAAGCCTGTGTTAGTGCTCAG 59.197 52.381 0.00 0.00 33.55 3.35
1690 1707 3.882288 TCAACAACAGCAAGCACATTCTA 59.118 39.130 0.00 0.00 0.00 2.10
1807 1824 0.393448 TTGTCGTCGGGGATGTTGAA 59.607 50.000 0.00 0.00 0.00 2.69
1846 1863 2.280389 CGGCCGACATGCATAGCT 60.280 61.111 24.07 0.00 0.00 3.32
1883 1900 4.755123 CGTTGAGATGGTACCTTGTTTTCT 59.245 41.667 14.36 5.71 0.00 2.52
2096 2113 0.551131 AAAGCCCCACTGGAGGATCT 60.551 55.000 0.00 0.00 35.39 2.75
2145 2162 2.930887 GCTAACAACATCGTCAGGCTCA 60.931 50.000 0.00 0.00 0.00 4.26
2200 2217 4.349365 TCCAACCTTTTGTTCTTCCAAGT 58.651 39.130 0.00 0.00 34.00 3.16
2228 2246 5.221342 CCTCTATTAAGACACATCGCCTCTT 60.221 44.000 0.00 0.00 0.00 2.85
2241 2259 4.610333 TCCTGCACTGACCTCTATTAAGA 58.390 43.478 0.00 0.00 0.00 2.10
2247 2265 3.173151 TCAAATCCTGCACTGACCTCTA 58.827 45.455 0.00 0.00 0.00 2.43
2291 2321 1.404717 GCTTCTGCTACTGCTGCTGTA 60.405 52.381 16.83 16.83 40.48 2.74
2292 2322 0.673022 GCTTCTGCTACTGCTGCTGT 60.673 55.000 16.37 16.37 40.48 4.40
2293 2323 0.672711 TGCTTCTGCTACTGCTGCTG 60.673 55.000 4.89 4.89 40.48 4.41
2336 2378 3.032265 TGCTGCTACCAGATCTTCCTA 57.968 47.619 0.00 0.00 41.77 2.94
2361 2409 9.660544 ATTGGCTAAATAAGGGATAGTTCATTT 57.339 29.630 0.00 0.00 0.00 2.32
2362 2410 9.082313 CATTGGCTAAATAAGGGATAGTTCATT 57.918 33.333 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.