Multiple sequence alignment - TraesCS3B01G171700

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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 TraesCS3B01G171700 chr3B 100.000 2501 0 0 1 2501 172702409 172704909 0 4619
1 TraesCS3B01G171700 chr3D 92.492 2504 99 34 1 2486 120630684 120633116 0 3500
2 TraesCS3B01G171700 chr3A 91.558 2535 108 54 1 2501 127355683 127353221 0 3398


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 TraesCS3B01G171700 chr3B 172702409 172704909 2500 False 4619 4619 100.000 1 2501 1 chr3B.!!$F1 2500
1 TraesCS3B01G171700 chr3D 120630684 120633116 2432 False 3500 3500 92.492 1 2486 1 chr3D.!!$F1 2485
2 TraesCS3B01G171700 chr3A 127353221 127355683 2462 True 3398 3398 91.558 1 2501 1 chr3A.!!$R1 2500

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
614 632 0.110688 CGTACGCATATGCATGTGCC 60.111 55.0 33.97 22.57 44.92 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2180 2232 0.457851 CCTCATCTCGGAAACTCGCT 59.542 55.0 0.0 0.0 0.0 4.93 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
152 153 1.582168 GACGTACGTACTGCGAGCC 60.582 63.158 22.87 1.09 44.77 4.70
153 154 2.244436 GACGTACGTACTGCGAGCCA 62.244 60.000 22.87 0.00 44.77 4.75
161 162 4.426112 CTGCGAGCCAGTCTGCGA 62.426 66.667 2.94 0.00 36.79 5.10
162 163 4.426112 TGCGAGCCAGTCTGCGAG 62.426 66.667 2.94 0.00 36.02 5.03
352 367 3.043586 CGAGATTCCATGCTACGTACAC 58.956 50.000 0.00 0.00 0.00 2.90
419 434 1.303236 CCGTCTGCCCAACCATCAA 60.303 57.895 0.00 0.00 0.00 2.57
510 528 2.897271 TCCAACTGCAACCCACATAT 57.103 45.000 0.00 0.00 0.00 1.78
522 540 7.174413 TGCAACCCACATATAATATACATGCT 58.826 34.615 0.00 0.00 0.00 3.79
524 542 7.336679 GCAACCCACATATAATATACATGCTCA 59.663 37.037 0.00 0.00 0.00 4.26
525 543 8.668353 CAACCCACATATAATATACATGCTCAC 58.332 37.037 0.00 0.00 0.00 3.51
526 544 7.041721 ACCCACATATAATATACATGCTCACG 58.958 38.462 0.00 0.00 0.00 4.35
527 545 6.018751 CCCACATATAATATACATGCTCACGC 60.019 42.308 0.00 0.00 0.00 5.34
540 558 1.532078 TCACGCACCCTCCACAGTA 60.532 57.895 0.00 0.00 0.00 2.74
603 621 1.317431 TAGTGGCTGGACGTACGCAT 61.317 55.000 16.72 0.00 0.00 4.73
614 632 0.110688 CGTACGCATATGCATGTGCC 60.111 55.000 33.97 22.57 44.92 5.01
630 648 1.743394 GTGCCTGCGCTTTTTATAGGT 59.257 47.619 9.73 0.00 35.36 3.08
761 779 5.064071 GCTAATCTGGACACAGTAAGAAAGC 59.936 44.000 0.00 0.00 45.14 3.51
763 781 4.689612 TCTGGACACAGTAAGAAAGCTT 57.310 40.909 0.00 0.00 45.14 3.74
764 782 4.380531 TCTGGACACAGTAAGAAAGCTTG 58.619 43.478 0.00 0.00 45.14 4.01
765 783 2.878406 TGGACACAGTAAGAAAGCTTGC 59.122 45.455 0.00 0.00 37.04 4.01
766 784 2.878406 GGACACAGTAAGAAAGCTTGCA 59.122 45.455 7.33 0.00 38.95 4.08
767 785 3.058639 GGACACAGTAAGAAAGCTTGCAG 60.059 47.826 7.33 0.00 38.95 4.41
768 786 2.880890 ACACAGTAAGAAAGCTTGCAGG 59.119 45.455 7.33 0.00 38.95 4.85
769 787 2.880890 CACAGTAAGAAAGCTTGCAGGT 59.119 45.455 7.33 0.00 38.95 4.00
770 788 4.065088 CACAGTAAGAAAGCTTGCAGGTA 58.935 43.478 7.33 0.00 38.95 3.08
771 789 4.065789 ACAGTAAGAAAGCTTGCAGGTAC 58.934 43.478 7.33 6.07 38.95 3.34
772 790 4.065088 CAGTAAGAAAGCTTGCAGGTACA 58.935 43.478 7.33 0.00 38.95 2.90
773 791 4.515191 CAGTAAGAAAGCTTGCAGGTACAA 59.485 41.667 7.33 0.00 38.95 2.41
879 897 0.259647 ATATGGAGCCAAGCCAAGCA 59.740 50.000 0.00 0.00 39.21 3.91
946 964 5.348997 GCACTGAAAACCTTAGTACTGCTAG 59.651 44.000 5.39 0.12 0.00 3.42
947 965 5.348997 CACTGAAAACCTTAGTACTGCTAGC 59.651 44.000 8.10 8.10 0.00 3.42
948 966 5.246429 ACTGAAAACCTTAGTACTGCTAGCT 59.754 40.000 17.23 0.00 0.00 3.32
949 967 6.436532 ACTGAAAACCTTAGTACTGCTAGCTA 59.563 38.462 17.23 0.00 0.00 3.32
985 1003 1.001815 GCTCGAGGAAGAGAGAATCCG 60.002 57.143 15.58 0.00 40.57 4.18
988 1006 2.092861 TCGAGGAAGAGAGAATCCGACT 60.093 50.000 0.00 0.00 40.78 4.18
989 1007 2.032799 CGAGGAAGAGAGAATCCGACTG 59.967 54.545 0.00 0.00 40.78 3.51
990 1008 3.283751 GAGGAAGAGAGAATCCGACTGA 58.716 50.000 0.00 0.00 40.78 3.41
991 1009 3.287222 AGGAAGAGAGAATCCGACTGAG 58.713 50.000 0.00 0.00 40.78 3.35
992 1010 3.020984 GGAAGAGAGAATCCGACTGAGT 58.979 50.000 0.00 0.00 33.66 3.41
1089 1107 1.199558 GCCGATCGGTCTGTATACCTC 59.800 57.143 33.33 9.96 37.39 3.85
1181 1204 2.203788 AGGACGAAGCAGGGGTCA 60.204 61.111 0.00 0.00 32.39 4.02
1253 1276 1.762460 CCTCCAGCCCGACACCTAT 60.762 63.158 0.00 0.00 0.00 2.57
1289 1312 1.520787 GGCCATCGTCGACGGATTT 60.521 57.895 35.05 16.48 40.29 2.17
1426 1461 6.818142 TGGCATATATGATCGGTTGAACTATG 59.182 38.462 17.10 0.00 0.00 2.23
1496 1531 1.625818 GGAGAAGAACCAGGAGCTTGA 59.374 52.381 0.00 0.00 0.00 3.02
1589 1626 5.190677 TGGAAGCTTGGTTTAGTATAAGCC 58.809 41.667 2.10 0.00 44.90 4.35
1618 1655 4.184629 GGAGAACGTTGATCAGTTGCTAT 58.815 43.478 5.00 0.00 0.00 2.97
1718 1755 5.814764 AATGTCAAGATCAAGCTTAGCTG 57.185 39.130 7.77 2.27 39.62 4.24
1724 1761 3.911868 AGATCAAGCTTAGCTGCTATCG 58.088 45.455 7.77 6.20 43.24 2.92
1814 1855 6.641169 AGTTCATCATCGATCTTACTAGCA 57.359 37.500 0.00 0.00 0.00 3.49
1820 1861 4.278669 TCATCGATCTTACTAGCAAGGGTC 59.721 45.833 2.83 1.86 0.00 4.46
1821 1862 3.899726 TCGATCTTACTAGCAAGGGTCT 58.100 45.455 2.83 0.00 0.00 3.85
1822 1863 5.045012 TCGATCTTACTAGCAAGGGTCTA 57.955 43.478 2.83 0.00 0.00 2.59
1885 1926 7.867403 CCCTGCAATGTAATGGTGATTATAAAC 59.133 37.037 0.00 0.00 0.00 2.01
1960 2001 4.057406 AGCTCATGCATGTACTCTCTTC 57.943 45.455 25.43 6.25 42.74 2.87
1990 2031 1.166989 CATGCATGGCAGTGTGTGTA 58.833 50.000 19.40 0.00 43.65 2.90
2001 2042 3.315191 GCAGTGTGTGTATGACTTTTGGT 59.685 43.478 0.00 0.00 0.00 3.67
2111 2154 6.618287 TGTGAAAACTACAAGACAAGGATG 57.382 37.500 0.00 0.00 0.00 3.51
2112 2155 6.353323 TGTGAAAACTACAAGACAAGGATGA 58.647 36.000 0.00 0.00 0.00 2.92
2113 2156 6.483307 TGTGAAAACTACAAGACAAGGATGAG 59.517 38.462 0.00 0.00 0.00 2.90
2114 2157 5.997746 TGAAAACTACAAGACAAGGATGAGG 59.002 40.000 0.00 0.00 0.00 3.86
2277 2333 3.660111 GTGGTTCTGTGCGTGCCC 61.660 66.667 0.00 0.00 0.00 5.36
2433 2489 1.228367 CCTGACAAAGCTGCCACCT 60.228 57.895 0.00 0.00 0.00 4.00
2461 2517 0.974010 ACTGTAGGATCCCCGCGAAA 60.974 55.000 8.23 0.00 37.58 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
135 136 2.249557 CTGGCTCGCAGTACGTACGT 62.250 60.000 25.98 25.98 44.19 3.57
163 164 4.383861 TGTGAGCAGAGCGGGCAG 62.384 66.667 0.00 0.00 0.00 4.85
216 230 3.197790 ATGCATGTCGTCGCAGCC 61.198 61.111 0.00 0.00 42.37 4.85
272 287 0.902048 CTGCACCTGGGACTCAGAGA 60.902 60.000 3.10 0.00 46.18 3.10
419 434 7.172190 CGTGAGCAATATCCAATAGAATGTCTT 59.828 37.037 0.00 0.00 0.00 3.01
522 540 1.532078 TACTGTGGAGGGTGCGTGA 60.532 57.895 0.00 0.00 0.00 4.35
524 542 2.580601 GGTACTGTGGAGGGTGCGT 61.581 63.158 0.00 0.00 0.00 5.24
525 543 2.264794 GGTACTGTGGAGGGTGCG 59.735 66.667 0.00 0.00 0.00 5.34
526 544 3.807368 AGGTACTGTGGAGGGTGC 58.193 61.111 0.00 0.00 37.18 5.01
603 621 1.314534 AAAGCGCAGGCACATGCATA 61.315 50.000 11.47 0.00 46.87 3.14
614 632 5.277538 GGAATCTCACCTATAAAAAGCGCAG 60.278 44.000 11.47 0.00 0.00 5.18
630 648 3.394274 TGAACTTGGTCAAGGGAATCTCA 59.606 43.478 14.29 5.24 42.53 3.27
761 779 2.393271 AGCTAGCTTGTACCTGCAAG 57.607 50.000 12.68 1.84 46.21 4.01
763 781 1.137086 GCTAGCTAGCTTGTACCTGCA 59.863 52.381 33.71 0.00 45.62 4.41
764 782 1.859383 GCTAGCTAGCTTGTACCTGC 58.141 55.000 33.71 11.86 45.62 4.85
775 793 4.089105 CGGGAGGGAGCTAGCTAG 57.911 66.667 19.38 16.84 0.00 3.42
867 885 2.356673 GTGCTTGCTTGGCTTGGC 60.357 61.111 0.00 0.00 0.00 4.52
895 913 9.249053 GGGTAATGACTAATGATATGAGAGAGA 57.751 37.037 0.00 0.00 0.00 3.10
896 914 8.187480 CGGGTAATGACTAATGATATGAGAGAG 58.813 40.741 0.00 0.00 0.00 3.20
897 915 7.363007 GCGGGTAATGACTAATGATATGAGAGA 60.363 40.741 0.00 0.00 0.00 3.10
898 916 6.754209 GCGGGTAATGACTAATGATATGAGAG 59.246 42.308 0.00 0.00 0.00 3.20
899 917 6.210584 TGCGGGTAATGACTAATGATATGAGA 59.789 38.462 0.00 0.00 0.00 3.27
985 1003 1.975363 GCCATTGCTCGCACTCAGTC 61.975 60.000 0.00 0.00 33.53 3.51
988 1006 3.120385 CGCCATTGCTCGCACTCA 61.120 61.111 0.00 0.00 34.43 3.41
989 1007 2.301902 CTTCGCCATTGCTCGCACTC 62.302 60.000 0.00 0.00 34.43 3.51
990 1008 2.358615 TTCGCCATTGCTCGCACT 60.359 55.556 0.00 0.00 34.43 4.40
991 1009 2.099062 CTTCGCCATTGCTCGCAC 59.901 61.111 0.00 0.00 34.43 5.34
992 1010 3.803082 GCTTCGCCATTGCTCGCA 61.803 61.111 0.00 0.00 34.43 5.10
1089 1107 5.459768 TGCAAGCCATTATATTTATGTGCG 58.540 37.500 0.00 0.00 29.84 5.34
1289 1312 2.748647 TCGGTGATCTCGACGGCA 60.749 61.111 7.46 0.00 0.00 5.69
1426 1461 2.233654 CGCTCGCCTGCATCAGTAC 61.234 63.158 0.00 0.00 0.00 2.73
1496 1531 2.173519 CTGGATGTTTGGCTGGTCAAT 58.826 47.619 0.00 0.00 0.00 2.57
1581 1618 3.206964 GTTCTCCAGCCTTGGCTTATAC 58.793 50.000 11.99 2.91 44.63 1.47
1589 1626 1.734465 GATCAACGTTCTCCAGCCTTG 59.266 52.381 0.00 0.00 0.00 3.61
1595 1632 2.143122 GCAACTGATCAACGTTCTCCA 58.857 47.619 0.00 0.00 0.00 3.86
1600 1637 6.163476 TGACTAATAGCAACTGATCAACGTT 58.837 36.000 0.00 0.00 0.00 3.99
1618 1655 2.671596 GCCGCAAAAGCAATTGACTAA 58.328 42.857 10.34 0.00 31.84 2.24
1705 1742 3.742433 ACGATAGCAGCTAAGCTTGAT 57.258 42.857 9.86 0.00 43.70 2.57
1796 1833 4.835615 ACCCTTGCTAGTAAGATCGATGAT 59.164 41.667 20.79 0.00 0.00 2.45
1814 1855 6.492087 GCTCTGAATATCAGTAGTAGACCCTT 59.508 42.308 7.21 0.00 44.58 3.95
1820 1861 8.165239 AGTCTTGCTCTGAATATCAGTAGTAG 57.835 38.462 7.21 0.00 44.58 2.57
1821 1862 8.526667 AAGTCTTGCTCTGAATATCAGTAGTA 57.473 34.615 7.21 1.67 44.58 1.82
1822 1863 7.416964 AAGTCTTGCTCTGAATATCAGTAGT 57.583 36.000 7.21 0.00 44.58 2.73
1839 1880 6.211515 CAGGGTTCAAATCTTCAAAGTCTTG 58.788 40.000 0.00 0.00 0.00 3.02
1841 1882 4.279420 GCAGGGTTCAAATCTTCAAAGTCT 59.721 41.667 0.00 0.00 0.00 3.24
1853 1894 3.900601 ACCATTACATTGCAGGGTTCAAA 59.099 39.130 0.00 0.00 0.00 2.69
1960 2001 1.507630 CATGCATGTTGGACACCGG 59.492 57.895 18.91 0.00 0.00 5.28
2106 2149 2.637165 ACAAAACCTCCTCCTCATCCT 58.363 47.619 0.00 0.00 0.00 3.24
2107 2150 3.084786 CAACAAAACCTCCTCCTCATCC 58.915 50.000 0.00 0.00 0.00 3.51
2108 2151 4.021102 TCAACAAAACCTCCTCCTCATC 57.979 45.455 0.00 0.00 0.00 2.92
2109 2152 4.043310 TCATCAACAAAACCTCCTCCTCAT 59.957 41.667 0.00 0.00 0.00 2.90
2110 2153 3.394274 TCATCAACAAAACCTCCTCCTCA 59.606 43.478 0.00 0.00 0.00 3.86
2111 2154 4.006319 CTCATCAACAAAACCTCCTCCTC 58.994 47.826 0.00 0.00 0.00 3.71
2112 2155 3.395941 ACTCATCAACAAAACCTCCTCCT 59.604 43.478 0.00 0.00 0.00 3.69
2113 2156 3.503748 CACTCATCAACAAAACCTCCTCC 59.496 47.826 0.00 0.00 0.00 4.30
2114 2157 3.503748 CCACTCATCAACAAAACCTCCTC 59.496 47.826 0.00 0.00 0.00 3.71
2176 2228 1.134367 CATCTCGGAAACTCGCTGGTA 59.866 52.381 0.00 0.00 0.00 3.25
2179 2231 1.554392 CTCATCTCGGAAACTCGCTG 58.446 55.000 0.00 0.00 0.00 5.18
2180 2232 0.457851 CCTCATCTCGGAAACTCGCT 59.542 55.000 0.00 0.00 0.00 4.93
2277 2333 1.269174 ACTGCATCGATCATCTCTCCG 59.731 52.381 0.00 0.00 0.00 4.63
2433 2489 2.238847 GATCCTACAGTGCACCGCCA 62.239 60.000 14.63 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.