Multiple sequence alignment - TraesCS4B01G319500

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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 TraesCS4B01G319500 chr4B 100.000 2420 0 0 1 2420 610245482 610243063 0.000000e+00 4470
1 TraesCS4B01G319500 chr4B 79.910 1105 131 45 845 1902 610098354 610097294 0.000000e+00 726
2 TraesCS4B01G319500 chr4B 92.105 76 6 0 2050 2125 610092181 610092106 9.150000e-20 108
3 TraesCS4B01G319500 chr5A 92.950 1546 88 8 891 2420 661666550 661668090 0.000000e+00 2231
4 TraesCS4B01G319500 chr5A 92.583 782 37 14 1 762 661665370 661666150 0.000000e+00 1103
5 TraesCS4B01G319500 chr5A 80.205 293 48 4 1023 1314 662052980 662052697 6.780000e-51 211
6 TraesCS4B01G319500 chr5A 89.189 148 12 4 1082 1228 435475897 435476041 5.310000e-42 182
7 TraesCS4B01G319500 chr3D 84.549 466 53 13 161 608 534166390 534165926 6.140000e-121 444
8 TraesCS4B01G319500 chr7A 84.615 390 41 8 164 535 717277685 717277297 1.060000e-98 370
9 TraesCS4B01G319500 chr7A 93.750 128 6 2 34 159 717277890 717277763 8.830000e-45 191
10 TraesCS4B01G319500 chr5B 91.304 138 10 2 1082 1218 390524026 390524162 1.140000e-43 187
11 TraesCS4B01G319500 chr5B 90.580 138 11 2 1082 1218 390403161 390403297 5.310000e-42 182
12 TraesCS4B01G319500 chrUn 81.735 219 35 3 986 1203 171662448 171662234 6.880000e-41 178
13 TraesCS4B01G319500 chrUn 81.364 220 33 6 986 1201 60909868 60910083 3.200000e-39 172
14 TraesCS4B01G319500 chr5D 81.277 235 31 9 1082 1311 333979031 333979257 6.880000e-41 178
15 TraesCS4B01G319500 chr4A 83.158 190 27 5 1021 1208 684061174 684060988 4.140000e-38 169


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 TraesCS4B01G319500 chr4B 610243063 610245482 2419 True 4470.0 4470 100.0000 1 2420 1 chr4B.!!$R3 2419
1 TraesCS4B01G319500 chr4B 610097294 610098354 1060 True 726.0 726 79.9100 845 1902 1 chr4B.!!$R2 1057
2 TraesCS4B01G319500 chr5A 661665370 661668090 2720 False 1667.0 2231 92.7665 1 2420 2 chr5A.!!$F2 2419
3 TraesCS4B01G319500 chr7A 717277297 717277890 593 True 280.5 370 89.1825 34 535 2 chr7A.!!$R1 501


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
865 1259 0.033504 ACACGTGACTCCGCTGAATT 59.966 50.0 25.01 0.0 0.0 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1668 2101 0.041576 AAACTTCGCGCCTTTCGAAC 60.042 50.0 0.0 0.0 40.49 3.95 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 26 0.310854 GGAAAACGGCAGGTGTGAAG 59.689 55.000 0.00 0.00 0.00 3.02
68 70 6.026947 ACTCGTATTTCAGTTTCAGTAGCT 57.973 37.500 0.00 0.00 0.00 3.32
78 80 4.574013 CAGTTTCAGTAGCTGATCCATTCC 59.426 45.833 0.00 0.00 40.39 3.01
324 416 0.329596 GGATGAGCCAGAACCAACCT 59.670 55.000 0.00 0.00 36.34 3.50
327 419 0.823356 TGAGCCAGAACCAACCTTGC 60.823 55.000 0.00 0.00 0.00 4.01
384 477 2.216898 GCCGGAGATGAGAAAATCCTG 58.783 52.381 5.05 0.00 0.00 3.86
447 540 3.472726 GGATCGGCACCGGGGTTA 61.473 66.667 5.12 0.00 40.25 2.85
518 618 4.018409 GGGACTTGCATTCCCCAC 57.982 61.111 19.36 0.00 46.57 4.61
519 619 1.076549 GGGACTTGCATTCCCCACA 59.923 57.895 19.36 0.00 46.57 4.17
755 858 3.492353 CTGGCCCCGACATCCCAT 61.492 66.667 0.00 0.00 0.00 4.00
761 864 1.478654 GCCCCGACATCCCATATGTTT 60.479 52.381 1.24 0.00 31.52 2.83
762 865 2.224670 GCCCCGACATCCCATATGTTTA 60.225 50.000 1.24 0.00 31.52 2.01
763 866 3.749310 GCCCCGACATCCCATATGTTTAA 60.749 47.826 1.24 0.00 31.52 1.52
764 867 4.072131 CCCCGACATCCCATATGTTTAAG 58.928 47.826 1.24 0.00 31.52 1.85
775 878 4.876107 CCATATGTTTAAGTGCTCTTCCGT 59.124 41.667 3.91 0.00 35.36 4.69
776 879 5.354234 CCATATGTTTAAGTGCTCTTCCGTT 59.646 40.000 3.91 0.00 35.36 4.44
777 880 4.749245 ATGTTTAAGTGCTCTTCCGTTG 57.251 40.909 3.91 0.00 35.36 4.10
778 881 2.289547 TGTTTAAGTGCTCTTCCGTTGC 59.710 45.455 3.91 0.00 35.36 4.17
779 882 1.519408 TTAAGTGCTCTTCCGTTGCC 58.481 50.000 3.91 0.00 35.36 4.52
780 883 0.394938 TAAGTGCTCTTCCGTTGCCA 59.605 50.000 3.91 0.00 35.36 4.92
781 884 1.166531 AAGTGCTCTTCCGTTGCCAC 61.167 55.000 0.00 0.00 0.00 5.01
782 885 1.891919 GTGCTCTTCCGTTGCCACA 60.892 57.895 0.00 0.00 0.00 4.17
783 886 1.597854 TGCTCTTCCGTTGCCACAG 60.598 57.895 0.00 0.00 0.00 3.66
784 887 2.328099 GCTCTTCCGTTGCCACAGG 61.328 63.158 0.00 0.00 0.00 4.00
818 921 0.969894 CAAATTAACGCCCAACCCCA 59.030 50.000 0.00 0.00 0.00 4.96
864 1258 0.667487 CACACGTGACTCCGCTGAAT 60.667 55.000 25.01 0.00 0.00 2.57
865 1259 0.033504 ACACGTGACTCCGCTGAATT 59.966 50.000 25.01 0.00 0.00 2.17
921 1323 6.183360 CCGTGTATTTAATCCTTTGCTTAGCA 60.183 38.462 1.39 1.39 36.47 3.49
953 1355 3.254470 TCTGGTCGACTCTCTACTCTG 57.746 52.381 16.46 0.33 0.00 3.35
954 1356 1.668751 CTGGTCGACTCTCTACTCTGC 59.331 57.143 16.46 0.00 0.00 4.26
955 1357 1.018910 GGTCGACTCTCTACTCTGCC 58.981 60.000 16.46 0.00 0.00 4.85
956 1358 1.018910 GTCGACTCTCTACTCTGCCC 58.981 60.000 8.70 0.00 0.00 5.36
1052 1462 0.771755 AACCTTGAACTCACCCTCCC 59.228 55.000 0.00 0.00 0.00 4.30
1099 1509 3.858989 GCTTCTTCCTCTGCGCGC 61.859 66.667 27.26 27.26 0.00 6.86
1238 1648 4.742201 CGGTGCGCCTACTGCAGT 62.742 66.667 25.12 25.12 44.21 4.40
1240 1650 3.121030 GTGCGCCTACTGCAGTGG 61.121 66.667 29.57 25.88 44.21 4.00
1258 1668 2.765807 AGGATGAGGGCCAGACGG 60.766 66.667 6.18 0.00 0.00 4.79
1317 1727 0.253327 ATGGAAAGGCGAGAAGGACC 59.747 55.000 0.00 0.00 0.00 4.46
1332 1742 2.915659 ACCGAGCCGTGGAAGTCA 60.916 61.111 0.00 0.00 0.00 3.41
1344 1763 2.281761 AAGTCAGCCGCTGTTGGG 60.282 61.111 19.77 0.00 32.61 4.12
1439 1867 3.131755 TGATCGATCTGCTCATGTGTTCT 59.868 43.478 25.02 0.00 0.00 3.01
1445 1873 4.276058 TCTGCTCATGTGTTCTTGATCA 57.724 40.909 0.00 0.00 0.00 2.92
1456 1884 0.036388 TCTTGATCACGGCCCAGTTC 60.036 55.000 0.00 0.00 0.00 3.01
1485 1914 2.289382 TGATTTGCTAGTTGACCTCGCA 60.289 45.455 0.00 0.00 39.86 5.10
1593 2026 3.000041 TCTGCGTGTGTTGGATTCATAC 59.000 45.455 0.00 0.00 0.00 2.39
1660 2093 7.283807 ACCAGAAAGAACGTTTGGTAATTTACT 59.716 33.333 17.80 0.00 40.21 2.24
1663 2096 9.726232 AGAAAGAACGTTTGGTAATTTACTTTC 57.274 29.630 17.28 17.28 39.40 2.62
1668 2101 8.496872 AACGTTTGGTAATTTACTTTCATTCG 57.503 30.769 0.00 6.74 0.00 3.34
1680 2113 0.165079 TTCATTCGTTCGAAAGGCGC 59.835 50.000 11.22 0.00 40.61 6.53
1916 2368 2.455032 CACGAGATCGAGTGTTGATCC 58.545 52.381 9.58 0.00 42.57 3.36
1942 2394 3.368843 GGAGAAGCTAGCATCTTGTGTGA 60.369 47.826 22.42 0.00 0.00 3.58
1943 2395 3.594134 AGAAGCTAGCATCTTGTGTGAC 58.406 45.455 16.53 0.00 0.00 3.67
1954 2406 2.880268 TCTTGTGTGACTGATTTGGCTG 59.120 45.455 0.00 0.00 0.00 4.85
1956 2408 0.242017 GTGTGACTGATTTGGCTGGC 59.758 55.000 0.00 0.00 0.00 4.85
1966 2418 1.778017 TTTGGCTGGCAGGAGCACTA 61.778 55.000 17.64 0.00 44.61 2.74
2021 2473 5.630680 CCTCTGAAATTTCCACATTTGAACG 59.369 40.000 15.48 0.00 0.00 3.95
2022 2474 6.384258 TCTGAAATTTCCACATTTGAACGA 57.616 33.333 15.48 0.00 0.00 3.85
2025 2477 7.925483 TCTGAAATTTCCACATTTGAACGAAAT 59.075 29.630 15.48 0.00 35.27 2.17
2129 2582 6.398918 AGAGATTATGGTTAGTGTGTGTCAC 58.601 40.000 0.00 0.00 46.46 3.67
2131 2584 6.711277 AGATTATGGTTAGTGTGTGTCACAT 58.289 36.000 9.31 0.00 46.32 3.21
2132 2585 6.595326 AGATTATGGTTAGTGTGTGTCACATG 59.405 38.462 9.31 0.00 46.32 3.21
2172 2625 3.140814 GGTGGCCCTCGCAAATCC 61.141 66.667 0.00 0.00 36.38 3.01
2191 2644 6.737720 AATCCAAGTGCATCATCTCTAGTA 57.262 37.500 0.00 0.00 0.00 1.82
2192 2645 5.781210 TCCAAGTGCATCATCTCTAGTAG 57.219 43.478 0.00 0.00 0.00 2.57
2206 2659 4.820716 TCTCTAGTAGGTTGAGTATTCGCC 59.179 45.833 0.00 0.00 0.00 5.54
2219 2672 2.368655 ATTCGCCAGACATTTTTGCC 57.631 45.000 0.00 0.00 0.00 4.52
2221 2674 0.881118 TCGCCAGACATTTTTGCCTC 59.119 50.000 0.00 0.00 0.00 4.70
2236 2689 3.627395 TGCCTCCTAATTACACCACTG 57.373 47.619 0.00 0.00 0.00 3.66
2238 2691 3.585289 TGCCTCCTAATTACACCACTGAA 59.415 43.478 0.00 0.00 0.00 3.02
2239 2692 3.939592 GCCTCCTAATTACACCACTGAAC 59.060 47.826 0.00 0.00 0.00 3.18
2252 2705 3.003275 ACCACTGAACGCAAAATACACAG 59.997 43.478 0.00 0.00 0.00 3.66
2278 2731 9.646427 GTATTTGTGCCTTGGACATTTATTTTA 57.354 29.630 0.00 0.00 33.22 1.52
2340 2793 1.948104 TGAACAAACTGACAGGGTCG 58.052 50.000 7.51 0.00 34.95 4.79
2373 2826 5.607477 TCTCTCAGTAAACAACAATTCGGT 58.393 37.500 0.00 0.00 0.00 4.69
2379 2832 4.641094 AGTAAACAACAATTCGGTGTGGAA 59.359 37.500 0.28 0.00 0.00 3.53
2398 2851 4.586421 TGGAATTGTGAGCACACCAATAAA 59.414 37.500 11.92 0.00 45.40 1.40
2408 2861 3.247411 GCACACCAATAAAACAAACCTGC 59.753 43.478 0.00 0.00 0.00 4.85
2413 2866 6.259829 ACACCAATAAAACAAACCTGCATTTC 59.740 34.615 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 3.034030 GTGCACTTCACACCTGCC 58.966 61.111 10.32 0.00 44.98 4.85
25 26 5.961843 CGAGTTATTGAAATGATCTGTGCAC 59.038 40.000 10.75 10.75 0.00 4.57
68 70 8.328758 AGAACTATTTGTTACTGGAATGGATCA 58.671 33.333 0.00 0.00 39.30 2.92
280 372 3.309410 CCTTGATTTCTCCCTGGTCCATT 60.309 47.826 0.00 0.00 0.00 3.16
324 416 1.300542 TCGCCATCGATATGCGCAA 60.301 52.632 27.31 14.67 40.21 4.85
495 595 1.885871 GAATGCAAGTCCCACAGGC 59.114 57.895 0.00 0.00 0.00 4.85
551 654 2.100631 CGGGTCAATCTCCACGCAC 61.101 63.158 0.00 0.00 0.00 5.34
744 847 4.024048 GCACTTAAACATATGGGATGTCGG 60.024 45.833 7.80 0.00 0.00 4.79
754 857 5.163754 GCAACGGAAGAGCACTTAAACATAT 60.164 40.000 0.00 0.00 36.39 1.78
755 858 4.153475 GCAACGGAAGAGCACTTAAACATA 59.847 41.667 0.00 0.00 36.39 2.29
761 864 0.394938 TGGCAACGGAAGAGCACTTA 59.605 50.000 0.00 0.00 42.51 2.24
762 865 1.148273 TGGCAACGGAAGAGCACTT 59.852 52.632 0.00 0.00 42.51 3.16
763 866 1.598130 GTGGCAACGGAAGAGCACT 60.598 57.895 0.00 0.00 42.51 4.40
764 867 1.845809 CTGTGGCAACGGAAGAGCAC 61.846 60.000 0.00 0.00 42.51 4.40
784 887 1.595093 ATTTGCTAACGGCTGTGGGC 61.595 55.000 14.01 14.01 42.39 5.36
785 888 0.887933 AATTTGCTAACGGCTGTGGG 59.112 50.000 0.00 0.00 42.39 4.61
786 889 3.498082 GTTAATTTGCTAACGGCTGTGG 58.502 45.455 0.00 0.00 42.39 4.17
787 890 3.160545 CGTTAATTTGCTAACGGCTGTG 58.839 45.455 0.00 0.00 46.58 3.66
788 891 3.465122 CGTTAATTTGCTAACGGCTGT 57.535 42.857 7.81 0.00 46.58 4.40
794 897 3.247442 GGTTGGGCGTTAATTTGCTAAC 58.753 45.455 0.00 0.00 0.00 2.34
795 898 2.231721 GGGTTGGGCGTTAATTTGCTAA 59.768 45.455 0.00 0.00 0.00 3.09
796 899 1.819903 GGGTTGGGCGTTAATTTGCTA 59.180 47.619 0.00 0.00 0.00 3.49
797 900 0.606096 GGGTTGGGCGTTAATTTGCT 59.394 50.000 0.00 0.00 0.00 3.91
798 901 0.390603 GGGGTTGGGCGTTAATTTGC 60.391 55.000 0.00 0.00 0.00 3.68
864 1258 1.400142 CAGAGAACGGTTGTTGCACAA 59.600 47.619 0.00 0.00 38.78 3.33
865 1259 1.013596 CAGAGAACGGTTGTTGCACA 58.986 50.000 0.00 0.00 38.78 4.57
921 1323 5.419471 AGAGTCGACCAGAACTTATTAGCTT 59.581 40.000 13.01 0.00 0.00 3.74
953 1355 1.224870 GGCTGAAAGGTAGAGGGGC 59.775 63.158 0.00 0.00 0.00 5.80
954 1356 0.833949 GAGGCTGAAAGGTAGAGGGG 59.166 60.000 0.00 0.00 0.00 4.79
955 1357 1.573108 TGAGGCTGAAAGGTAGAGGG 58.427 55.000 0.00 0.00 0.00 4.30
956 1358 3.323403 CCTATGAGGCTGAAAGGTAGAGG 59.677 52.174 0.00 0.00 0.00 3.69
1099 1509 1.342082 CGGAACTTACGGTCGCAGTG 61.342 60.000 0.00 0.00 0.00 3.66
1238 1648 1.690633 GTCTGGCCCTCATCCTCCA 60.691 63.158 0.00 0.00 0.00 3.86
1240 1650 2.801631 CCGTCTGGCCCTCATCCTC 61.802 68.421 0.00 0.00 0.00 3.71
1258 1668 4.937431 GCCTCTGCCGCCATACCC 62.937 72.222 0.00 0.00 0.00 3.69
1289 1699 2.115291 GCCTTTCCATCCGCAGACC 61.115 63.158 0.00 0.00 0.00 3.85
1317 1727 2.811317 GCTGACTTCCACGGCTCG 60.811 66.667 0.00 0.00 36.79 5.03
1389 1817 1.078759 GAGCCAAGTCCACATCGTCG 61.079 60.000 0.00 0.00 0.00 5.12
1439 1867 1.002624 GGAACTGGGCCGTGATCAA 60.003 57.895 0.00 0.00 0.00 2.57
1456 1884 0.625849 ACTAGCAAATCAGGGTGGGG 59.374 55.000 0.00 0.00 0.00 4.96
1660 2093 1.399215 GCGCCTTTCGAACGAATGAAA 60.399 47.619 19.19 0.00 41.67 2.69
1663 2096 1.577616 CGCGCCTTTCGAACGAATG 60.578 57.895 10.44 12.03 41.67 2.67
1668 2101 0.041576 AAACTTCGCGCCTTTCGAAC 60.042 50.000 0.00 0.00 40.49 3.95
1703 2136 7.856145 AGCAAAGATAGAACAATAGAACTGG 57.144 36.000 0.00 0.00 0.00 4.00
1784 2223 9.561069 GTAACACAATAGACATTAATCAGGGAT 57.439 33.333 0.00 0.00 0.00 3.85
1916 2368 3.640967 ACAAGATGCTAGCTTCTCCTAGG 59.359 47.826 27.76 18.31 36.23 3.02
1942 2394 0.323178 CTCCTGCCAGCCAAATCAGT 60.323 55.000 0.00 0.00 0.00 3.41
1943 2395 1.664321 GCTCCTGCCAGCCAAATCAG 61.664 60.000 0.00 0.00 32.76 2.90
1954 2406 0.955919 GGTGTTGTAGTGCTCCTGCC 60.956 60.000 0.00 0.00 38.71 4.85
1956 2408 0.396435 TGGGTGTTGTAGTGCTCCTG 59.604 55.000 0.00 0.00 0.00 3.86
1966 2418 3.305720 TGTCTCTCTAAGTGGGTGTTGT 58.694 45.455 0.00 0.00 0.00 3.32
2045 2497 9.926158 ATGTGCATGTTTTACATTCATTTTCTA 57.074 25.926 0.00 0.00 36.53 2.10
2172 2625 5.528043 ACCTACTAGAGATGATGCACTTG 57.472 43.478 0.00 0.00 0.00 3.16
2191 2644 1.899814 TGTCTGGCGAATACTCAACCT 59.100 47.619 0.00 0.00 0.00 3.50
2192 2645 2.380084 TGTCTGGCGAATACTCAACC 57.620 50.000 0.00 0.00 0.00 3.77
2206 2659 7.029563 GTGTAATTAGGAGGCAAAAATGTCTG 58.970 38.462 0.00 0.00 0.00 3.51
2219 2672 3.617263 GCGTTCAGTGGTGTAATTAGGAG 59.383 47.826 0.00 0.00 0.00 3.69
2221 2674 3.331150 TGCGTTCAGTGGTGTAATTAGG 58.669 45.455 0.00 0.00 0.00 2.69
2252 2705 8.546597 AAAATAAATGTCCAAGGCACAAATAC 57.453 30.769 0.00 0.00 0.00 1.89
2313 2766 7.458397 ACCCTGTCAGTTTGTTCATAGATAAA 58.542 34.615 0.00 0.00 0.00 1.40
2316 2769 5.491982 GACCCTGTCAGTTTGTTCATAGAT 58.508 41.667 0.00 0.00 32.09 1.98
2321 2774 1.483004 TCGACCCTGTCAGTTTGTTCA 59.517 47.619 0.00 0.00 32.09 3.18
2326 2779 3.771577 AAGAATCGACCCTGTCAGTTT 57.228 42.857 0.00 0.00 32.09 2.66
2373 2826 1.317613 GGTGTGCTCACAATTCCACA 58.682 50.000 19.67 0.00 45.45 4.17
2379 2832 5.528043 TGTTTTATTGGTGTGCTCACAAT 57.472 34.783 19.67 17.27 45.45 2.71
2382 2835 4.506288 GGTTTGTTTTATTGGTGTGCTCAC 59.494 41.667 10.44 10.44 43.19 3.51



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

AutoCloner maintained by Alex Coulton.