Multiple sequence alignment - TraesCS3A01G407300

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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 TraesCS3A01G407300 chr3A 100.000 2669 0 0 1 2669 652026746 652024078 0.000000 4929.0
1 TraesCS3A01G407300 chr3B 92.455 2717 117 45 1 2669 680424204 680426880 0.000000 3801.0
2 TraesCS3A01G407300 chr3D 91.795 2730 120 52 1 2669 516879722 516877036 0.000000 3705.0
3 TraesCS3A01G407300 chr6D 95.122 41 1 1 2491 2530 132775281 132775241 0.000002 63.9


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 TraesCS3A01G407300 chr3A 652024078 652026746 2668 True 4929 4929 100.000 1 2669 1 chr3A.!!$R1 2668
1 TraesCS3A01G407300 chr3B 680424204 680426880 2676 False 3801 3801 92.455 1 2669 1 chr3B.!!$F1 2668
2 TraesCS3A01G407300 chr3D 516877036 516879722 2686 True 3705 3705 91.795 1 2669 1 chr3D.!!$R1 2668

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
595 606 0.450983 CGAGGAACCGGTAGAGTGTC 59.549 60.0 8.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2219 2307 0.1791 GTTGCTCATCGGCTCTGCTA 60.179 55.0 0.0 0.0 0.0 3.49 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
67 68 9.458374 AATGTTTCTGTTAAACTTGATAAACCG 57.542 29.630 0.00 0.00 0.00 4.44
68 69 7.987649 TGTTTCTGTTAAACTTGATAAACCGT 58.012 30.769 0.00 0.00 0.00 4.83
111 113 7.279536 AGTTAGTGACAATGCTCACAGATATTG 59.720 37.037 14.80 0.00 42.74 1.90
280 284 2.029649 CCCTTCTTCTGGTTTGCACATG 60.030 50.000 0.00 0.00 0.00 3.21
481 492 4.713814 ACTTGAGATGCTCAGTGATCCTTA 59.286 41.667 0.00 0.00 41.75 2.69
492 503 2.107204 AGTGATCCTTATGGCCATGGTC 59.893 50.000 29.04 17.42 0.00 4.02
593 604 1.171308 TTCGAGGAACCGGTAGAGTG 58.829 55.000 8.00 0.00 0.00 3.51
595 606 0.450983 CGAGGAACCGGTAGAGTGTC 59.549 60.000 8.00 0.00 0.00 3.67
596 607 1.542492 GAGGAACCGGTAGAGTGTCA 58.458 55.000 8.00 0.00 0.00 3.58
683 699 5.882557 GGTATAGTATTGGGGATGCATCTTG 59.117 44.000 25.28 0.00 0.00 3.02
713 729 7.096023 CGGCTATCATCTGTAACTGTTGTATTC 60.096 40.741 2.69 0.00 0.00 1.75
770 786 7.601705 AAAAATCATTCCCTCTTTCACTTCA 57.398 32.000 0.00 0.00 0.00 3.02
780 796 5.767168 CCCTCTTTCACTTCAGTTGAATCTT 59.233 40.000 0.00 0.00 33.01 2.40
786 802 2.808543 ACTTCAGTTGAATCTTCGCACC 59.191 45.455 0.00 0.00 33.01 5.01
825 843 6.488344 TGGTGATGTTCTTTGCTTGTGTAATA 59.512 34.615 0.00 0.00 0.00 0.98
976 994 5.241506 GTCTCATCAAACCCAACAATCTCAA 59.758 40.000 0.00 0.00 0.00 3.02
1587 1607 1.153939 CTTCGTCGTCAGCCTCCTG 60.154 63.158 0.00 0.00 40.54 3.86
1659 1679 1.505353 GACCGACCTCGTGTACCTG 59.495 63.158 0.00 0.00 37.74 4.00
1662 1682 2.960170 GACCTCGTGTACCTGCGT 59.040 61.111 0.00 0.00 0.00 5.24
1679 1699 0.729140 CGTCGCTGAACATTTTGGCC 60.729 55.000 0.00 0.00 0.00 5.36
1680 1700 0.729140 GTCGCTGAACATTTTGGCCG 60.729 55.000 0.00 0.00 0.00 6.13
1681 1701 1.169661 TCGCTGAACATTTTGGCCGT 61.170 50.000 0.00 0.00 0.00 5.68
1682 1702 1.003262 CGCTGAACATTTTGGCCGTG 61.003 55.000 0.00 0.00 0.00 4.94
1683 1703 1.284297 GCTGAACATTTTGGCCGTGC 61.284 55.000 0.00 0.00 0.00 5.34
1722 1742 1.830279 CATGTGCAGTGGACCTGAAT 58.170 50.000 13.58 0.00 44.49 2.57
1725 1745 0.036732 GTGCAGTGGACCTGAATCCA 59.963 55.000 2.86 0.00 46.92 3.41
1731 1751 1.661463 TGGACCTGAATCCAGAAGCT 58.339 50.000 0.00 0.00 44.14 3.74
1741 1761 4.937193 CAGAAGCTGAGGCCTCTG 57.063 61.111 32.28 31.05 46.33 3.35
1742 1762 4.883465 AGAAGCTGAGGCCTCTGA 57.117 55.556 36.14 17.29 37.79 3.27
1792 1822 9.917129 TGCATATATGATTTGATTTGTTGGATC 57.083 29.630 17.10 0.00 0.00 3.36
1808 1840 7.333528 TGTTGGATCTGTATATTTGAAAGGC 57.666 36.000 0.00 0.00 0.00 4.35
1809 1841 7.118723 TGTTGGATCTGTATATTTGAAAGGCT 58.881 34.615 0.00 0.00 0.00 4.58
1835 1867 5.482006 ACACGATTGATGATTCTCTTGTGA 58.518 37.500 0.00 0.00 0.00 3.58
1838 1870 6.740002 CACGATTGATGATTCTCTTGTGAAAC 59.260 38.462 0.00 0.00 37.35 2.78
1840 1872 6.959871 CGATTGATGATTCTCTTGTGAAACTG 59.040 38.462 0.00 0.00 38.04 3.16
1842 1874 7.430992 TTGATGATTCTCTTGTGAAACTGAG 57.569 36.000 0.00 0.00 38.68 3.35
1844 1876 4.707105 TGATTCTCTTGTGAAACTGAGCA 58.293 39.130 0.00 0.00 37.78 4.26
1852 1901 6.728200 TCTTGTGAAACTGAGCAAAATGTAG 58.272 36.000 0.00 0.00 38.04 2.74
1855 1904 5.822519 TGTGAAACTGAGCAAAATGTAGACT 59.177 36.000 0.00 0.00 38.04 3.24
1875 1924 6.565234 AGACTTATGTACATCCTTTCTCGTG 58.435 40.000 12.68 0.00 0.00 4.35
1878 1927 3.232213 TGTACATCCTTTCTCGTGCTC 57.768 47.619 0.00 0.00 0.00 4.26
1881 1930 1.205893 ACATCCTTTCTCGTGCTCCTC 59.794 52.381 0.00 0.00 0.00 3.71
1903 1953 4.273480 TCAGTACAAAGCTGAAAACAGAGC 59.727 41.667 0.00 0.00 39.70 4.09
1920 1970 3.642901 GCGTAAGGCGAGAGATTGA 57.357 52.632 0.00 0.00 44.77 2.57
1927 1977 0.173708 GGCGAGAGATTGAACGAGGT 59.826 55.000 0.00 0.00 0.00 3.85
1938 1988 2.615262 GAACGAGGTAGCTGCCGGAG 62.615 65.000 15.76 12.73 0.00 4.63
2054 2104 3.057104 TCGGCTCGAAAGTTATTCACAGA 60.057 43.478 0.00 0.00 31.06 3.41
2141 2225 3.952628 GACTTTGGGGCGGAGGTCG 62.953 68.421 0.00 0.00 42.76 4.79
2192 2276 1.374758 GGACAGAACCTGCAGACGG 60.375 63.158 17.39 9.45 34.37 4.79
2219 2307 1.390123 CACGCGACAACGATGAGAAAT 59.610 47.619 15.93 0.00 42.66 2.17
2263 2351 1.144936 GAGTGGCGAGAGAATGGGG 59.855 63.158 0.00 0.00 0.00 4.96
2480 2569 0.040958 GGAAATGCATCATCGTCGGC 60.041 55.000 0.00 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 5.100751 ACTCTATACGATAAAACCGACGG 57.899 43.478 13.61 13.61 0.00 4.79
67 68 8.338259 TCACTAACTCTATACGATAAAACCGAC 58.662 37.037 0.00 0.00 0.00 4.79
68 69 8.338259 GTCACTAACTCTATACGATAAAACCGA 58.662 37.037 0.00 0.00 0.00 4.69
76 78 7.013369 TGAGCATTGTCACTAACTCTATACGAT 59.987 37.037 0.00 0.00 0.00 3.73
111 113 7.648510 CCTGCAAGCAAGTAGTATTAGTAGTAC 59.351 40.741 2.75 2.75 37.11 2.73
123 127 1.446907 CCAGTCCTGCAAGCAAGTAG 58.553 55.000 0.00 0.00 0.00 2.57
481 492 1.829533 GAATGCGGACCATGGCCAT 60.830 57.895 14.09 14.09 33.49 4.40
492 503 4.818546 ACTGGATAGAATGAAAGAATGCGG 59.181 41.667 0.00 0.00 0.00 5.69
628 639 7.307101 CGGTTCCTCAAAAACAAAAATACATGG 60.307 37.037 0.00 0.00 0.00 3.66
683 699 4.037684 ACAGTTACAGATGATAGCCGGTAC 59.962 45.833 1.90 0.00 0.00 3.34
713 729 9.852091 CTTCAGATTCTTTCCCTATTTTCAAAG 57.148 33.333 0.00 0.00 0.00 2.77
750 766 5.511386 ACTGAAGTGAAAGAGGGAATGAT 57.489 39.130 0.00 0.00 0.00 2.45
770 786 4.520492 AGAAAATGGTGCGAAGATTCAACT 59.480 37.500 0.00 0.00 0.00 3.16
780 796 2.513753 ACCAATGAGAAAATGGTGCGA 58.486 42.857 0.00 0.00 45.47 5.10
786 802 5.395682 ACATCACCACCAATGAGAAAATG 57.604 39.130 0.00 0.00 0.00 2.32
825 843 0.598065 GAGGCAAACGGAACATTGCT 59.402 50.000 9.95 0.00 45.95 3.91
832 850 3.353836 GCAGCGAGGCAAACGGAA 61.354 61.111 0.00 0.00 0.00 4.30
996 1016 0.172803 CTTCTTGCTCAGCCATTGCC 59.827 55.000 0.00 0.00 38.69 4.52
997 1017 0.172803 CCTTCTTGCTCAGCCATTGC 59.827 55.000 0.00 0.00 37.95 3.56
1587 1607 2.178912 TGGAAGGGAACATGACGAAC 57.821 50.000 0.00 0.00 0.00 3.95
1659 1679 1.337110 GCCAAAATGTTCAGCGACGC 61.337 55.000 13.03 13.03 0.00 5.19
1662 1682 1.169661 ACGGCCAAAATGTTCAGCGA 61.170 50.000 2.24 0.00 0.00 4.93
1690 1710 3.663176 ACATGCACAGCACGGCAC 61.663 61.111 0.00 0.00 43.04 5.01
1691 1711 3.662153 CACATGCACAGCACGGCA 61.662 61.111 0.00 0.00 43.04 5.69
1702 1722 3.271014 CAGGTCCACTGCACATGC 58.729 61.111 0.00 0.00 40.97 4.06
1722 1742 3.719121 GAGGCCTCAGCTTCTGGA 58.281 61.111 28.43 0.00 41.71 3.86
1730 1750 1.336440 CGATACAGTCAGAGGCCTCAG 59.664 57.143 33.90 26.54 0.00 3.35
1731 1751 1.393603 CGATACAGTCAGAGGCCTCA 58.606 55.000 33.90 12.52 0.00 3.86
1741 1761 0.455633 ACACGCGTTCCGATACAGTC 60.456 55.000 10.22 0.00 41.02 3.51
1742 1762 0.731514 CACACGCGTTCCGATACAGT 60.732 55.000 10.22 0.00 41.02 3.55
1757 1786 6.962686 TCAAATCATATATGCAAGCTCACAC 58.037 36.000 7.92 0.00 0.00 3.82
1792 1822 7.970384 TCGTGTAAAGCCTTTCAAATATACAG 58.030 34.615 0.00 0.00 0.00 2.74
1798 1830 6.325919 TCAATCGTGTAAAGCCTTTCAAAT 57.674 33.333 0.00 0.00 0.00 2.32
1808 1840 7.901889 CACAAGAGAATCATCAATCGTGTAAAG 59.098 37.037 0.00 0.00 37.82 1.85
1809 1841 7.602265 TCACAAGAGAATCATCAATCGTGTAAA 59.398 33.333 0.00 0.00 37.82 2.01
1835 1867 8.396272 ACATAAGTCTACATTTTGCTCAGTTT 57.604 30.769 0.00 0.00 0.00 2.66
1838 1870 8.479313 TGTACATAAGTCTACATTTTGCTCAG 57.521 34.615 0.00 0.00 0.00 3.35
1840 1872 8.552034 GGATGTACATAAGTCTACATTTTGCTC 58.448 37.037 8.71 0.00 33.78 4.26
1842 1874 8.438676 AGGATGTACATAAGTCTACATTTTGC 57.561 34.615 8.71 0.00 33.78 3.68
1852 1901 5.232414 GCACGAGAAAGGATGTACATAAGTC 59.768 44.000 8.71 4.44 0.00 3.01
1855 1904 5.339008 AGCACGAGAAAGGATGTACATAA 57.661 39.130 8.71 0.00 0.00 1.90
1869 1918 1.905637 TTGTACTGAGGAGCACGAGA 58.094 50.000 0.00 0.00 0.00 4.04
1870 1919 2.600731 CTTTGTACTGAGGAGCACGAG 58.399 52.381 0.00 0.00 0.00 4.18
1875 1924 2.751166 TCAGCTTTGTACTGAGGAGC 57.249 50.000 0.00 0.00 39.21 4.70
1878 1927 4.816385 TCTGTTTTCAGCTTTGTACTGAGG 59.184 41.667 0.00 0.00 44.55 3.86
1881 1930 4.531332 GCTCTGTTTTCAGCTTTGTACTG 58.469 43.478 0.00 0.00 46.59 2.74
1903 1953 1.846782 CGTTCAATCTCTCGCCTTACG 59.153 52.381 0.00 0.00 45.62 3.18
1918 1968 2.571757 CGGCAGCTACCTCGTTCA 59.428 61.111 0.42 0.00 0.00 3.18
1919 1969 2.202756 CCGGCAGCTACCTCGTTC 60.203 66.667 0.42 0.00 0.00 3.95
1920 1970 2.678934 TCCGGCAGCTACCTCGTT 60.679 61.111 0.42 0.00 0.00 3.85
1938 1988 1.529309 GAGGAATGAGGAGCCACCC 59.471 63.158 0.00 0.00 40.05 4.61
2054 2104 7.453393 TGAACTCTCACTGAATTTACCAGAAT 58.547 34.615 0.00 0.00 35.69 2.40
2117 2201 2.672996 CGCCCCAAAGTCAGGGTG 60.673 66.667 0.00 0.00 46.88 4.61
2141 2225 3.743017 TTCCTGGCCATGCTCCCC 61.743 66.667 5.51 0.00 0.00 4.81
2192 2276 1.434379 CGTTGTCGCGTGTTCGTTC 60.434 57.895 5.77 0.00 39.49 3.95
2219 2307 0.179100 GTTGCTCATCGGCTCTGCTA 60.179 55.000 0.00 0.00 0.00 3.49
2263 2351 0.683504 TCTACGAGGCCAAGGTCTCC 60.684 60.000 14.68 0.00 43.36 3.71
2410 2498 1.139853 CTTAGCTTAGCTGACTGGGGG 59.860 57.143 17.97 0.00 40.10 5.40
2414 2502 3.446799 CTCTGCTTAGCTTAGCTGACTG 58.553 50.000 24.72 15.33 42.05 3.51
2480 2569 4.135153 CCCGGTCCGTCAGCAGAG 62.135 72.222 11.06 0.00 0.00 3.35


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

AutoCloner maintained by Alex Coulton.