Multiple sequence alignment - TraesCS3D01G339400

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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 TraesCS3D01G339400 chr3D 100.000 2870 0 0 490 3359 452419802 452416933 0.000000 5301.0
1 TraesCS3D01G339400 chr3D 100.000 30 0 0 1 30 452420291 452420262 0.000468 56.5
2 TraesCS3D01G339400 chr3A 94.248 2851 134 12 490 3324 594670256 594667420 0.000000 4329.0
3 TraesCS3D01G339400 chr3B 93.785 2880 138 26 490 3359 594413308 594410460 0.000000 4289.0
4 TraesCS3D01G339400 chr3B 100.000 30 0 0 1 30 594413405 594413376 0.000468 56.5


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 TraesCS3D01G339400 chr3D 452416933 452420291 3358 True 2678.75 5301 100.0000 1 3359 2 chr3D.!!$R1 3358
1 TraesCS3D01G339400 chr3A 594667420 594670256 2836 True 4329.00 4329 94.2480 490 3324 1 chr3A.!!$R1 2834
2 TraesCS3D01G339400 chr3B 594410460 594413405 2945 True 2172.75 4289 96.8925 1 3359 2 chr3B.!!$R1 3358

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
712 719 1.008538 GCCACTGAACAAAGGTGCG 60.009 57.895 0.0 0.0 0.0 5.34 F
1578 1593 0.447801 CTGAAATCGGTTGGCTTCGG 59.552 55.000 0.0 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1795 1810 0.984230 ACATGACTGTCGATTGGGGT 59.016 50.000 0.0 0.0 0.0 4.95 R
2406 2424 1.270678 ACTTTGGCCGACAGACTTACC 60.271 52.381 0.0 0.0 0.0 2.85 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
585 586 3.017581 AAGATTCTGCCGCCCCCT 61.018 61.111 0.00 0.00 0.00 4.79
605 606 2.360600 ACCTCACTCTCGCTCGCT 60.361 61.111 0.00 0.00 0.00 4.93
629 633 1.074752 CGTCTTCTTCTTCCTGCAGC 58.925 55.000 8.66 0.00 0.00 5.25
636 640 2.158623 TCTTCTTCCTGCAGCCTTTTCA 60.159 45.455 8.66 0.00 0.00 2.69
648 655 4.556302 GCAGCCTTTTCACTTCTTCTTCTG 60.556 45.833 0.00 0.00 0.00 3.02
710 717 1.654220 CGGCCACTGAACAAAGGTG 59.346 57.895 2.24 0.00 0.00 4.00
712 719 1.008538 GCCACTGAACAAAGGTGCG 60.009 57.895 0.00 0.00 0.00 5.34
725 732 4.255301 CAAAGGTGCGGTACTAATAACCA 58.745 43.478 0.00 0.00 36.78 3.67
726 733 4.765813 AAGGTGCGGTACTAATAACCAT 57.234 40.909 0.00 0.00 36.78 3.55
727 734 4.067972 AGGTGCGGTACTAATAACCATG 57.932 45.455 0.00 0.00 36.78 3.66
764 772 7.905604 ACATGATCGAGTTCTTGTTTTGATA 57.094 32.000 0.00 0.00 31.96 2.15
912 920 1.134367 TGTCGAAATCCGCGATCTTCT 59.866 47.619 8.23 0.00 40.19 2.85
917 925 4.022475 CGAAATCCGCGATCTTCTTTTTC 58.978 43.478 8.23 4.10 0.00 2.29
918 926 4.201724 CGAAATCCGCGATCTTCTTTTTCT 60.202 41.667 8.23 0.00 0.00 2.52
919 927 5.629079 AAATCCGCGATCTTCTTTTTCTT 57.371 34.783 8.23 0.00 0.00 2.52
967 982 2.061220 CCTGTCTCAACCAGGCTCA 58.939 57.895 0.00 0.00 42.81 4.26
994 1009 3.278592 GAAGGTTCGCGGTCGGAGT 62.279 63.158 6.13 0.00 36.13 3.85
1061 1076 2.654877 GACGGCGAGGAAGGTGAA 59.345 61.111 16.62 0.00 0.00 3.18
1068 1083 1.551452 CGAGGAAGGTGAAGAGGACT 58.449 55.000 0.00 0.00 0.00 3.85
1320 1335 2.634777 CTCCTCGACGCGATCTCC 59.365 66.667 15.93 0.00 34.61 3.71
1326 1341 2.543802 CGACGCGATCTCCTGCCTA 61.544 63.158 15.93 0.00 0.00 3.93
1356 1371 4.880696 GCCTATGTCAATCTTCAGAAAGCT 59.119 41.667 0.00 0.00 32.18 3.74
1479 1494 1.673808 AATGGAGCGACCCGAGGTAC 61.674 60.000 0.00 0.00 35.25 3.34
1578 1593 0.447801 CTGAAATCGGTTGGCTTCGG 59.552 55.000 0.00 0.00 0.00 4.30
1623 1638 3.339141 GAAGAACATGGAACTGGAGGAC 58.661 50.000 0.00 0.00 0.00 3.85
1692 1707 1.222567 AGGGGGTGTCAACTGAAGTT 58.777 50.000 0.00 0.00 39.12 2.66
1743 1758 4.250464 AGTGCATCCATGATTTTGCAAAG 58.750 39.130 12.41 0.00 45.74 2.77
1791 1806 1.067582 GTGGAACCTCGGCCTATCG 59.932 63.158 0.00 0.00 0.00 2.92
1795 1810 0.458669 GAACCTCGGCCTATCGACAA 59.541 55.000 0.00 0.00 35.18 3.18
1796 1811 0.175073 AACCTCGGCCTATCGACAAC 59.825 55.000 0.00 0.00 35.18 3.32
1797 1812 1.067582 CCTCGGCCTATCGACAACC 59.932 63.158 0.00 0.00 35.18 3.77
1798 1813 1.067582 CTCGGCCTATCGACAACCC 59.932 63.158 0.00 0.00 35.18 4.11
1812 1827 1.351017 ACAACCCCAATCGACAGTCAT 59.649 47.619 0.41 0.00 0.00 3.06
1833 1848 2.225467 GTTGCATATGAGAGAAGGGCC 58.775 52.381 6.97 0.00 0.00 5.80
1944 1959 6.126825 ACTGTATCATGAGCTTCAAAGATCCT 60.127 38.462 0.09 0.00 40.59 3.24
1950 1965 6.662234 TCATGAGCTTCAAAGATCCTTTTGAT 59.338 34.615 10.06 0.00 44.12 2.57
1983 1998 4.956700 ACTGATCCAGATTCTAGTTTCGGA 59.043 41.667 0.45 1.16 35.18 4.55
2070 2085 3.504906 ACTTGGATCACAGAGCATTTGTG 59.495 43.478 8.45 8.45 45.61 3.33
2079 2094 0.674895 GAGCATTTGTGGAGAGCGGT 60.675 55.000 0.00 0.00 0.00 5.68
2130 2145 5.841957 AATTTGTGAGGATGGCAAGATAC 57.158 39.130 0.00 0.00 0.00 2.24
2156 2171 0.667487 GCACTACTCGCAGTTGCTCA 60.667 55.000 2.29 0.00 39.32 4.26
2171 2186 4.012374 GTTGCTCATTCTCTGAATCCCAA 58.988 43.478 0.00 0.00 32.14 4.12
2199 2214 6.446318 TGAAATGTTTTATGTCAAGAGTGGC 58.554 36.000 0.00 0.00 0.00 5.01
2202 2217 3.496884 TGTTTTATGTCAAGAGTGGCGTC 59.503 43.478 0.00 0.00 29.33 5.19
2244 2259 3.055094 TGGAAAGTACTCCAGCCAAGATC 60.055 47.826 0.00 0.00 40.71 2.75
2329 2347 4.454678 TGTCATCAGATGCAGGGTTTATC 58.545 43.478 5.41 0.00 0.00 1.75
2332 2350 3.565764 TCAGATGCAGGGTTTATCTGG 57.434 47.619 10.48 0.00 44.88 3.86
2396 2414 5.533903 CAGCCATTAGGTAAGCAGAATCAAT 59.466 40.000 0.00 0.00 37.19 2.57
2400 2418 7.445402 GCCATTAGGTAAGCAGAATCAATTAGA 59.555 37.037 0.00 0.00 37.19 2.10
2406 2424 9.941325 AGGTAAGCAGAATCAATTAGATCTATG 57.059 33.333 2.58 0.00 35.39 2.23
2473 2491 2.183679 CCTAGGAGTTGAGGAGCACTT 58.816 52.381 1.05 0.00 34.46 3.16
2474 2492 2.093764 CCTAGGAGTTGAGGAGCACTTG 60.094 54.545 1.05 0.00 34.46 3.16
2510 2528 9.623000 AATACCCCATAATGTTAACTTGTAGTC 57.377 33.333 7.22 0.00 0.00 2.59
2690 2714 5.126067 CACATTACTGTCCTAATCCCTTGG 58.874 45.833 0.00 0.00 31.62 3.61
2919 2943 2.027561 CCAACCTTCCTCCACGTATTCA 60.028 50.000 0.00 0.00 0.00 2.57
2980 3004 7.916977 TCAGCATTCAGTAACATGATTTATTGC 59.083 33.333 0.00 0.00 0.00 3.56
3004 3028 3.181440 TGTTGTTTGCTCAGAGGAAGGAT 60.181 43.478 4.36 0.00 0.00 3.24
3085 3114 9.832445 TTAATCCTAACAGTTTATTCTGCCTAG 57.168 33.333 0.00 0.00 38.84 3.02
3086 3115 5.671493 TCCTAACAGTTTATTCTGCCTAGC 58.329 41.667 0.00 0.00 38.84 3.42
3087 3116 5.188948 TCCTAACAGTTTATTCTGCCTAGCA 59.811 40.000 0.00 0.00 38.84 3.49
3088 3117 6.058183 CCTAACAGTTTATTCTGCCTAGCAT 58.942 40.000 0.00 0.00 38.13 3.79
3178 3207 0.983378 ACTGAGGGTATGGACAGGGC 60.983 60.000 0.00 0.00 35.08 5.19
3301 3331 6.646240 GCATAAGGAAAACTTGCAGATTTCAA 59.354 34.615 17.31 7.37 38.33 2.69
3354 3385 2.235155 TGGCGGTTCAGTGTATGTATGT 59.765 45.455 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
585 586 2.041115 CGAGCGAGAGTGAGGTGGA 61.041 63.158 0.00 0.00 0.00 4.02
605 606 0.681733 AGGAAGAAGAAGACGCAGCA 59.318 50.000 0.00 0.00 0.00 4.41
629 633 3.058639 CGGCAGAAGAAGAAGTGAAAAGG 60.059 47.826 0.00 0.00 0.00 3.11
636 640 0.038159 CGGACGGCAGAAGAAGAAGT 60.038 55.000 0.00 0.00 0.00 3.01
648 655 4.072088 CGTTCTTGCACGGACGGC 62.072 66.667 15.89 0.00 36.47 5.68
710 717 4.056050 CAGTCCATGGTTATTAGTACCGC 58.944 47.826 12.58 0.00 38.55 5.68
712 719 4.814771 GCACAGTCCATGGTTATTAGTACC 59.185 45.833 12.58 0.00 36.17 3.34
725 732 3.701205 TCATGTAACAGCACAGTCCAT 57.299 42.857 0.00 0.00 0.00 3.41
726 733 3.599343 GATCATGTAACAGCACAGTCCA 58.401 45.455 0.00 0.00 0.00 4.02
727 734 2.604914 CGATCATGTAACAGCACAGTCC 59.395 50.000 0.00 0.00 0.00 3.85
764 772 2.681848 CGATTGCAAAGCAGAGGAGAAT 59.318 45.455 1.71 0.00 40.61 2.40
912 920 6.314896 ACATGCACGAATTCCAAAAAGAAAAA 59.685 30.769 0.00 0.00 0.00 1.94
917 925 5.006552 ACAAACATGCACGAATTCCAAAAAG 59.993 36.000 0.00 0.00 0.00 2.27
918 926 4.872691 ACAAACATGCACGAATTCCAAAAA 59.127 33.333 0.00 0.00 0.00 1.94
919 927 4.437239 ACAAACATGCACGAATTCCAAAA 58.563 34.783 0.00 0.00 0.00 2.44
965 980 1.478510 GCGAACCTTCTCTCCTCATGA 59.521 52.381 0.00 0.00 0.00 3.07
966 981 1.800655 CGCGAACCTTCTCTCCTCATG 60.801 57.143 0.00 0.00 0.00 3.07
967 982 0.457851 CGCGAACCTTCTCTCCTCAT 59.542 55.000 0.00 0.00 0.00 2.90
994 1009 3.390521 AAGGCGAGACATGGCGGA 61.391 61.111 0.00 0.00 36.92 5.54
1326 1341 4.263905 TGAAGATTGACATAGGCCACCTTT 60.264 41.667 5.01 0.00 34.61 3.11
1356 1371 2.038659 TCAGGATCATACGGCACATGA 58.961 47.619 0.00 1.00 0.00 3.07
1479 1494 8.801299 TGAATTCTAGAGCTTATATGAGACAGG 58.199 37.037 7.05 0.00 0.00 4.00
1623 1638 3.187058 CCGTTCCGGCCAATCTTG 58.813 61.111 2.24 0.00 41.17 3.02
1635 1650 1.272781 CTTCTCTGCACGATCCGTTC 58.727 55.000 0.00 0.00 38.32 3.95
1743 1758 6.002062 ACTTTCGTCCAATCAAAGATGAAC 57.998 37.500 0.00 0.00 39.49 3.18
1773 1788 1.067582 CGATAGGCCGAGGTTCCAC 59.932 63.158 0.00 0.00 0.00 4.02
1791 1806 1.270625 TGACTGTCGATTGGGGTTGTC 60.271 52.381 2.98 0.00 0.00 3.18
1795 1810 0.984230 ACATGACTGTCGATTGGGGT 59.016 50.000 0.00 0.00 0.00 4.95
1796 1811 1.739466 CAACATGACTGTCGATTGGGG 59.261 52.381 0.00 0.00 33.36 4.96
1797 1812 1.131126 GCAACATGACTGTCGATTGGG 59.869 52.381 15.71 7.31 33.36 4.12
1798 1813 1.805943 TGCAACATGACTGTCGATTGG 59.194 47.619 15.71 3.46 33.36 3.16
1812 1827 2.421952 GGCCCTTCTCTCATATGCAACA 60.422 50.000 0.00 0.00 0.00 3.33
1833 1848 3.369147 CCTCAACAGCATACTTCTTGTCG 59.631 47.826 0.00 0.00 0.00 4.35
1944 1959 4.880120 GGATCAGTCATGAGAGCATCAAAA 59.120 41.667 0.00 0.00 42.53 2.44
1950 1965 2.743553 TCTGGATCAGTCATGAGAGCA 58.256 47.619 0.00 0.00 39.29 4.26
2070 2085 1.899437 TTGGATGACCACCGCTCTCC 61.899 60.000 0.00 0.00 46.80 3.71
2079 2094 1.561769 ATGGCGTCCTTGGATGACCA 61.562 55.000 19.54 19.54 45.34 4.02
2130 2145 1.079197 TGCGAGTAGTGCCCATGTG 60.079 57.895 0.00 0.00 0.00 3.21
2156 2171 4.581309 TCAGCTTTGGGATTCAGAGAAT 57.419 40.909 0.00 0.00 29.82 2.40
2171 2186 7.864379 CACTCTTGACATAAAACATTTCAGCTT 59.136 33.333 0.00 0.00 0.00 3.74
2199 2214 1.145803 GTTCCTTCCGAAACTGGACG 58.854 55.000 0.00 0.00 37.89 4.79
2202 2217 1.961793 TGTGTTCCTTCCGAAACTGG 58.038 50.000 0.00 0.00 30.39 4.00
2244 2259 5.782047 ACACTGAACTTCTCTTCTCTGATG 58.218 41.667 0.00 0.00 0.00 3.07
2396 2414 5.241064 GCCGACAGACTTACCATAGATCTAA 59.759 44.000 6.52 0.00 0.00 2.10
2400 2418 2.628657 GGCCGACAGACTTACCATAGAT 59.371 50.000 0.00 0.00 0.00 1.98
2402 2420 1.754803 TGGCCGACAGACTTACCATAG 59.245 52.381 0.00 0.00 0.00 2.23
2406 2424 1.270678 ACTTTGGCCGACAGACTTACC 60.271 52.381 0.00 0.00 0.00 2.85
2473 2491 8.911018 ACATTATGGGGTATTATCTACTAGCA 57.089 34.615 0.00 0.00 0.00 3.49
2539 2557 6.566079 TGGAGAAATAGATGAACCACTGAT 57.434 37.500 0.00 0.00 0.00 2.90
2628 2646 6.990798 TGTGAAATGGTTTTTGATGAGCATA 58.009 32.000 0.00 0.00 33.94 3.14
2919 2943 5.587043 TGTTTCTGAAAATACAGTTGACGGT 59.413 36.000 4.09 0.00 38.79 4.83
2980 3004 3.057736 CCTTCCTCTGAGCAAACAACATG 60.058 47.826 0.00 0.00 0.00 3.21
3019 3043 9.952030 TGTATAAGAATATTTTGTCTCACACCA 57.048 29.630 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.