Multiple sequence alignment - TraesCS2B01G306900

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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 TraesCS2B01G306900 chr2B 100.000 2899 0 0 1 2899 439225799 439222901 0.000000e+00 5354
1 TraesCS2B01G306900 chr2D 90.999 2822 147 32 144 2899 369481731 369478951 0.000000e+00 3705
2 TraesCS2B01G306900 chr2D 94.558 147 7 1 1 147 369481910 369481765 2.910000e-55 226
3 TraesCS2B01G306900 chr2A 95.821 1627 50 8 1281 2899 500531043 500529427 0.000000e+00 2612
4 TraesCS2B01G306900 chr2A 89.132 1141 72 17 144 1255 500532153 500531036 0.000000e+00 1373
5 TraesCS2B01G306900 chr2A 94.118 136 7 1 12 147 500532321 500532187 3.790000e-49 206


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 TraesCS2B01G306900 chr2B 439222901 439225799 2898 True 5354.0 5354 100.000000 1 2899 1 chr2B.!!$R1 2898
1 TraesCS2B01G306900 chr2D 369478951 369481910 2959 True 1965.5 3705 92.778500 1 2899 2 chr2D.!!$R1 2898
2 TraesCS2B01G306900 chr2A 500529427 500532321 2894 True 1397.0 2612 93.023667 12 2899 3 chr2A.!!$R1 2887

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
946 1021 0.40375 TTTTGTGGTAGGGGAGGGGT 60.404 55.0 0.0 0.0 0.0 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2264 2358 1.359117 CGTGGACGATGTCGCCTAT 59.641 57.895 13.93 0.0 44.43 2.57 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
75 76 7.391833 GCCTTTCTCATGTTATAATAGGAAGGG 59.608 40.741 19.01 16.28 41.47 3.95
81 82 9.930693 CTCATGTTATAATAGGAAGGGAAGTAC 57.069 37.037 0.00 0.00 0.00 2.73
117 118 5.276461 TGTCAAGTGAGTAAAAGCTCTGA 57.724 39.130 0.00 0.00 36.51 3.27
130 131 8.254508 AGTAAAAGCTCTGAGATACCAAGTAAG 58.745 37.037 9.28 0.00 0.00 2.34
135 136 5.128008 GCTCTGAGATACCAAGTAAGAACCT 59.872 44.000 9.28 0.00 0.00 3.50
215 256 9.470399 AGATTTTAGCCATGCATATATCATGAA 57.530 29.630 18.81 10.20 42.84 2.57
241 282 7.966246 ATAACATCAGATGAGAATGAAGAGC 57.034 36.000 17.81 0.00 0.00 4.09
244 285 4.831674 TCAGATGAGAATGAAGAGCCAA 57.168 40.909 0.00 0.00 0.00 4.52
256 297 5.363562 TGAAGAGCCAATATGTGTGAGAT 57.636 39.130 0.00 0.00 0.00 2.75
266 307 8.840321 GCCAATATGTGTGAGATTACATTTACT 58.160 33.333 0.00 0.00 38.41 2.24
361 409 6.514063 AGAACTAACACCAACTCTTCACTAC 58.486 40.000 0.00 0.00 0.00 2.73
368 416 5.817816 ACACCAACTCTTCACTACTTTCTTG 59.182 40.000 0.00 0.00 0.00 3.02
402 450 2.650608 GCTTTAACAGCCGAACAGTTG 58.349 47.619 0.00 0.00 43.65 3.16
426 474 1.204146 GGATACCTGTTGGGAGCAGA 58.796 55.000 0.00 0.00 33.23 4.26
444 492 4.081420 AGCAGAAGAAAGTACCATGACGAT 60.081 41.667 0.00 0.00 0.00 3.73
518 567 5.319140 TCAACTTCGATATGAAAGACGGA 57.681 39.130 0.00 0.00 35.79 4.69
611 660 9.391006 GGTTCTGGTGTGATAGTCAATAATAAA 57.609 33.333 0.00 0.00 0.00 1.40
649 698 7.979537 GTGTATATCCTTTGGAAATTTTGGGTC 59.020 37.037 0.00 0.00 34.34 4.46
686 735 3.357203 TGTTAAGTCAAAAGGTGCACCA 58.643 40.909 36.39 14.05 38.89 4.17
693 742 3.630312 GTCAAAAGGTGCACCAAGACTTA 59.370 43.478 36.39 13.36 38.89 2.24
694 743 4.278419 GTCAAAAGGTGCACCAAGACTTAT 59.722 41.667 36.39 11.61 38.89 1.73
790 856 1.028130 TCAGCTCTCATGACCTAGCG 58.972 55.000 12.09 8.74 39.94 4.26
791 857 0.743688 CAGCTCTCATGACCTAGCGT 59.256 55.000 12.09 2.15 39.94 5.07
792 858 0.743688 AGCTCTCATGACCTAGCGTG 59.256 55.000 12.09 0.00 39.94 5.34
797 863 4.068599 CTCTCATGACCTAGCGTGATCTA 58.931 47.826 0.00 0.00 33.65 1.98
826 892 8.599774 GTGAAGCTTTACTGATCTGAAGATAAC 58.400 37.037 13.77 0.00 34.37 1.89
835 901 7.628234 ACTGATCTGAAGATAACATGGAAACT 58.372 34.615 6.60 0.00 34.37 2.66
846 912 3.736094 ACATGGAAACTGGGAGAGGATA 58.264 45.455 0.00 0.00 0.00 2.59
857 923 7.084268 ACTGGGAGAGGATATATGAAAAAGG 57.916 40.000 0.00 0.00 0.00 3.11
861 927 6.306987 GGAGAGGATATATGAAAAAGGCCAA 58.693 40.000 5.01 0.00 0.00 4.52
862 928 6.777580 GGAGAGGATATATGAAAAAGGCCAAA 59.222 38.462 5.01 0.00 0.00 3.28
863 929 7.040132 GGAGAGGATATATGAAAAAGGCCAAAG 60.040 40.741 5.01 0.00 0.00 2.77
864 930 6.779539 AGAGGATATATGAAAAAGGCCAAAGG 59.220 38.462 5.01 0.00 0.00 3.11
887 954 3.244561 CCAGTCTAATGTGTTGGTCCTGT 60.245 47.826 0.00 0.00 0.00 4.00
921 996 0.521242 GCATTTGCTTAGCGACCACG 60.521 55.000 0.00 0.00 39.24 4.94
946 1021 0.403750 TTTTGTGGTAGGGGAGGGGT 60.404 55.000 0.00 0.00 0.00 4.95
947 1022 1.137594 TTTGTGGTAGGGGAGGGGTG 61.138 60.000 0.00 0.00 0.00 4.61
948 1023 2.691252 GTGGTAGGGGAGGGGTGG 60.691 72.222 0.00 0.00 0.00 4.61
949 1024 4.033251 TGGTAGGGGAGGGGTGGG 62.033 72.222 0.00 0.00 0.00 4.61
990 1065 4.973168 TCACACAAGCTACCAATCTTTCT 58.027 39.130 0.00 0.00 0.00 2.52
1034 1109 4.389374 GTTTCTGATCAACTTCCCTGTCA 58.611 43.478 0.00 0.00 0.00 3.58
1105 1180 0.892358 CTCTGCCAATGCACACCACT 60.892 55.000 0.00 0.00 44.23 4.00
1111 1186 2.417243 GCCAATGCACACCACTAATTCC 60.417 50.000 0.00 0.00 37.47 3.01
1112 1187 3.091545 CCAATGCACACCACTAATTCCT 58.908 45.455 0.00 0.00 0.00 3.36
1116 1191 2.371841 TGCACACCACTAATTCCTGAGT 59.628 45.455 0.00 0.00 0.00 3.41
1169 1254 4.112634 CAATTCTGGCGAGTCTCGATTAA 58.887 43.478 26.11 13.13 43.74 1.40
1170 1255 3.422417 TTCTGGCGAGTCTCGATTAAG 57.578 47.619 26.11 15.12 43.74 1.85
1218 1303 4.746535 ATGGGTATCGTCACAATACACA 57.253 40.909 0.00 0.00 44.69 3.72
1242 1330 2.708325 AGTGAAAGAGAGAAAGCCCTGT 59.292 45.455 0.00 0.00 0.00 4.00
1271 1359 0.249398 GCTTTCCCCGTAAGCAGAGA 59.751 55.000 0.00 0.00 45.64 3.10
1363 1451 2.134346 TCGGCAAGCATTTCTTTTTGC 58.866 42.857 0.00 0.00 43.81 3.68
1419 1507 3.049674 GCTTGCGTGCTGTGCCTA 61.050 61.111 0.00 0.00 0.00 3.93
1472 1565 3.881688 GGCTTGAGACCAGTCGTAGTATA 59.118 47.826 0.00 0.00 34.09 1.47
1473 1566 4.337555 GGCTTGAGACCAGTCGTAGTATAA 59.662 45.833 0.00 0.00 34.09 0.98
1474 1567 5.009811 GGCTTGAGACCAGTCGTAGTATAAT 59.990 44.000 0.00 0.00 34.09 1.28
1501 1594 0.535102 CCCTTCCTCTGCGTTTGTGT 60.535 55.000 0.00 0.00 0.00 3.72
1553 1646 1.569548 TGGAGGTAGGAGTAGTCCAGG 59.430 57.143 19.00 0.00 46.80 4.45
1627 1721 0.743688 AACAAGCGCAACATGGTGAA 59.256 45.000 16.85 0.00 0.00 3.18
1769 1863 2.660802 CCAACCGGCGTCTTACCT 59.339 61.111 6.01 0.00 0.00 3.08
1776 1870 1.515736 GGCGTCTTACCTTCGTCCG 60.516 63.158 0.00 0.00 0.00 4.79
1874 1968 4.515404 CCGTACTAGGCAGGCAAC 57.485 61.111 0.00 0.00 0.00 4.17
1875 1969 1.594833 CCGTACTAGGCAGGCAACA 59.405 57.895 0.00 0.00 41.41 3.33
1928 2022 2.040412 GGGGTTCTTCTGATGGTGAAGT 59.960 50.000 0.00 0.00 41.04 3.01
2051 2145 5.634859 CAGCTTTTGGAATGGATTGTGTTAC 59.365 40.000 0.00 0.00 0.00 2.50
2075 2169 6.486657 ACTGCATTTAAACTCTCTAAGCACAA 59.513 34.615 0.00 0.00 0.00 3.33
2147 2241 1.747355 CAACAACATGAGCATCCCTCC 59.253 52.381 0.00 0.00 39.98 4.30
2219 2313 4.094887 GCTTCCTTGATTTGCTCGATTGTA 59.905 41.667 0.00 0.00 0.00 2.41
2240 2334 1.040646 ACACTCCGAAGAAGCTGTCA 58.959 50.000 0.00 0.00 0.00 3.58
2467 2561 8.237267 CCTCAATACAACACCTGAAAGATAAAC 58.763 37.037 0.00 0.00 34.07 2.01
2470 2564 5.668558 ACAACACCTGAAAGATAAACGTC 57.331 39.130 0.00 0.00 34.07 4.34
2487 2581 9.562583 GATAAACGTCAGATTGGATATACTCTC 57.437 37.037 0.00 0.00 0.00 3.20
2669 2763 3.117888 GGGATCCCTGCAGAAGAACATAA 60.118 47.826 24.69 0.00 0.00 1.90
2725 2821 6.879458 TCAGACAATAAAAGGAAGAGTAAGCC 59.121 38.462 0.00 0.00 0.00 4.35
2727 2823 6.881602 AGACAATAAAAGGAAGAGTAAGCCAG 59.118 38.462 0.00 0.00 0.00 4.85
2850 2955 1.689273 AGGATAGCAAGCTCCCTAACG 59.311 52.381 12.43 0.00 30.79 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 7.939039 CCTTCCTATTATAACATGAGAAAGGCA 59.061 37.037 0.00 0.00 0.00 4.75
49 50 7.391833 CCCTTCCTATTATAACATGAGAAAGGC 59.608 40.741 0.00 0.00 0.00 4.35
117 118 8.147244 ACATGTTAGGTTCTTACTTGGTATCT 57.853 34.615 0.00 0.00 0.00 1.98
130 131 8.051901 ACAAGCCTATAAAACATGTTAGGTTC 57.948 34.615 20.99 9.64 34.84 3.62
215 256 8.838365 GCTCTTCATTCTCATCTGATGTTATTT 58.162 33.333 16.66 0.00 0.00 1.40
287 328 4.332828 AGGGTTGCAAAGATGGTAGTTAC 58.667 43.478 0.00 0.00 0.00 2.50
289 330 3.525800 AGGGTTGCAAAGATGGTAGTT 57.474 42.857 0.00 0.00 0.00 2.24
290 331 3.525800 AAGGGTTGCAAAGATGGTAGT 57.474 42.857 0.00 0.00 0.00 2.73
291 332 4.559153 CAAAAGGGTTGCAAAGATGGTAG 58.441 43.478 0.00 0.00 0.00 3.18
338 386 6.514063 AGTAGTGAAGAGTTGGTGTTAGTTC 58.486 40.000 0.00 0.00 0.00 3.01
361 409 1.820519 TGGCAAGGCATAGCAAGAAAG 59.179 47.619 0.00 0.00 0.00 2.62
368 416 1.392589 TAAAGCTGGCAAGGCATAGC 58.607 50.000 1.37 8.15 39.41 2.97
393 441 4.115516 CAGGTATCCTCATCAACTGTTCG 58.884 47.826 0.00 0.00 0.00 3.95
400 448 3.455910 CTCCCAACAGGTATCCTCATCAA 59.544 47.826 0.00 0.00 36.75 2.57
402 450 2.224402 GCTCCCAACAGGTATCCTCATC 60.224 54.545 0.00 0.00 36.75 2.92
426 474 4.929808 GTCACATCGTCATGGTACTTTCTT 59.070 41.667 0.00 0.00 33.82 2.52
444 492 6.053632 AGGATGATAACAATGACAGTCACA 57.946 37.500 5.05 0.00 0.00 3.58
518 567 2.094286 CACAGCCTCTTCTTGAGATCGT 60.094 50.000 0.00 0.00 45.39 3.73
549 598 4.927978 TGTCCTAACACCCACAAAATTG 57.072 40.909 0.00 0.00 0.00 2.32
649 698 8.251750 TGACTTAACAAAAGATATCTGTTCGG 57.748 34.615 5.86 0.00 35.09 4.30
686 735 5.880332 TGCAGAATTAAGCGGAATAAGTCTT 59.120 36.000 0.00 0.00 36.02 3.01
693 742 1.064060 GCGTGCAGAATTAAGCGGAAT 59.936 47.619 0.00 0.00 0.00 3.01
694 743 0.446222 GCGTGCAGAATTAAGCGGAA 59.554 50.000 0.00 0.00 0.00 4.30
790 856 6.341316 TCAGTAAAGCTTCACCATAGATCAC 58.659 40.000 0.00 0.00 0.00 3.06
791 857 6.544928 TCAGTAAAGCTTCACCATAGATCA 57.455 37.500 0.00 0.00 0.00 2.92
792 858 7.384660 CAGATCAGTAAAGCTTCACCATAGATC 59.615 40.741 0.00 6.69 0.00 2.75
797 863 5.426689 TCAGATCAGTAAAGCTTCACCAT 57.573 39.130 0.00 0.00 0.00 3.55
826 892 4.989875 ATATCCTCTCCCAGTTTCCATG 57.010 45.455 0.00 0.00 0.00 3.66
835 901 5.222130 GGCCTTTTTCATATATCCTCTCCCA 60.222 44.000 0.00 0.00 0.00 4.37
861 927 2.108250 ACCAACACATTAGACTGGCCTT 59.892 45.455 3.32 0.00 0.00 4.35
862 928 1.705186 ACCAACACATTAGACTGGCCT 59.295 47.619 3.32 0.00 0.00 5.19
863 929 2.084546 GACCAACACATTAGACTGGCC 58.915 52.381 0.00 0.00 0.00 5.36
864 930 2.084546 GGACCAACACATTAGACTGGC 58.915 52.381 0.00 0.00 0.00 4.85
865 931 3.244561 ACAGGACCAACACATTAGACTGG 60.245 47.826 0.00 0.00 0.00 4.00
866 932 4.008074 ACAGGACCAACACATTAGACTG 57.992 45.455 0.00 0.00 0.00 3.51
873 939 3.297134 AACTCAACAGGACCAACACAT 57.703 42.857 0.00 0.00 0.00 3.21
921 996 1.422402 TCCCCTACCACAAAACACCTC 59.578 52.381 0.00 0.00 0.00 3.85
929 1004 1.540367 CACCCCTCCCCTACCACAA 60.540 63.158 0.00 0.00 0.00 3.33
946 1021 1.281867 GTGACCAGGATTCATCACCCA 59.718 52.381 0.00 0.00 36.31 4.51
947 1022 1.281867 TGTGACCAGGATTCATCACCC 59.718 52.381 0.00 0.00 40.63 4.61
948 1023 2.787473 TGTGACCAGGATTCATCACC 57.213 50.000 0.00 0.00 40.63 4.02
949 1024 3.877559 TGATGTGACCAGGATTCATCAC 58.122 45.455 15.69 9.57 39.53 3.06
990 1065 9.391006 GAAACCACAATAAATACTGGAGATGTA 57.609 33.333 0.00 0.00 0.00 2.29
1006 1081 4.524328 GGGAAGTTGATCAGAAACCACAAT 59.476 41.667 0.00 0.00 0.00 2.71
1034 1109 1.980772 GCTCTTGGGGCAATGCAGT 60.981 57.895 7.79 0.00 0.00 4.40
1155 1240 2.605097 GGGTAGCTTAATCGAGACTCGC 60.605 54.545 20.11 4.85 40.21 5.03
1169 1254 3.904339 TCTCTTCTTGTGAAAGGGTAGCT 59.096 43.478 0.00 0.00 0.00 3.32
1170 1255 3.997681 GTCTCTTCTTGTGAAAGGGTAGC 59.002 47.826 0.00 0.00 0.00 3.58
1218 1303 3.650461 AGGGCTTTCTCTCTTTCACTCTT 59.350 43.478 0.00 0.00 0.00 2.85
1242 1330 5.472137 GCTTACGGGGAAAGCAATAATCATA 59.528 40.000 3.07 0.00 46.85 2.15
1332 1420 1.982073 GCTTGCCGAAAGACGATGGG 61.982 60.000 0.00 0.00 45.77 4.00
1472 1565 2.690936 GCAGAGGAAGGGGGCAATTATT 60.691 50.000 0.00 0.00 0.00 1.40
1473 1566 1.133356 GCAGAGGAAGGGGGCAATTAT 60.133 52.381 0.00 0.00 0.00 1.28
1474 1567 0.258774 GCAGAGGAAGGGGGCAATTA 59.741 55.000 0.00 0.00 0.00 1.40
1501 1594 0.605319 GGCTGGATCACCAACACGAA 60.605 55.000 0.00 0.00 46.32 3.85
1553 1646 2.930040 CGCTCTCTATCTCTCTCCGATC 59.070 54.545 0.00 0.00 0.00 3.69
1627 1721 1.360852 TCTTCTTCCTCTGCTCCCTCT 59.639 52.381 0.00 0.00 0.00 3.69
1707 1801 3.615811 TCCCAGGCTGTCCTCCCT 61.616 66.667 14.43 0.00 41.93 4.20
1793 1887 3.827898 CCCTCCGACGAGCCTGAC 61.828 72.222 0.00 0.00 34.49 3.51
1869 1963 2.744202 CTCACACATAACCTCTGTTGCC 59.256 50.000 0.00 0.00 35.87 4.52
1870 1964 2.744202 CCTCACACATAACCTCTGTTGC 59.256 50.000 0.00 0.00 35.87 4.17
1872 1966 4.706842 AACCTCACACATAACCTCTGTT 57.293 40.909 0.00 0.00 38.52 3.16
1873 1967 5.818678 TTAACCTCACACATAACCTCTGT 57.181 39.130 0.00 0.00 0.00 3.41
1874 1968 6.464222 TCTTTAACCTCACACATAACCTCTG 58.536 40.000 0.00 0.00 0.00 3.35
1875 1969 6.681729 TCTTTAACCTCACACATAACCTCT 57.318 37.500 0.00 0.00 0.00 3.69
1928 2022 3.119708 GCACAAAAATGGGTTGCAACAAA 60.120 39.130 29.55 17.72 0.00 2.83
2051 2145 6.486253 TGTGCTTAGAGAGTTTAAATGCAG 57.514 37.500 0.00 0.00 0.00 4.41
2075 2169 2.554032 GCCAAACTCAGTACTGCAATGT 59.446 45.455 18.45 10.71 0.00 2.71
2195 2289 2.479566 TCGAGCAAATCAAGGAAGCT 57.520 45.000 0.00 0.00 38.43 3.74
2219 2313 2.158957 TGACAGCTTCTTCGGAGTGTTT 60.159 45.455 0.00 0.00 0.00 2.83
2240 2334 2.743938 GTGATCAACGCCGTCATAGAT 58.256 47.619 0.00 0.00 0.00 1.98
2264 2358 1.359117 CGTGGACGATGTCGCCTAT 59.641 57.895 13.93 0.00 44.43 2.57
2467 2561 9.347934 GTTTATGAGAGTATATCCAATCTGACG 57.652 37.037 0.00 0.00 0.00 4.35
2470 2564 9.987272 TGTGTTTATGAGAGTATATCCAATCTG 57.013 33.333 0.00 0.00 0.00 2.90
2509 2603 5.009610 CCTCAGGTTAGATCTCTGCTACTTC 59.990 48.000 0.00 0.00 0.00 3.01
2725 2821 1.538047 ATTGTGTTGCCTAGCACCTG 58.462 50.000 0.00 0.00 38.71 4.00
2727 2823 4.881850 AGTTATATTGTGTTGCCTAGCACC 59.118 41.667 0.00 0.00 38.71 5.01


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

AutoCloner maintained by Alex Coulton.