Multiple sequence alignment - TraesCS3A01G284300

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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 TraesCS3A01G284300 chr3A 100.000 2835 0 0 1 2835 513294788 513297622 0.000000e+00 5236
1 TraesCS3A01G284300 chr3A 93.700 1746 82 15 1 1739 733887578 733885854 0.000000e+00 2590
2 TraesCS3A01G284300 chr5A 95.782 2845 108 8 1 2835 133817573 133820415 0.000000e+00 4578
3 TraesCS3A01G284300 chr5A 95.602 2251 78 4 43 2291 345672974 345670743 0.000000e+00 3589
4 TraesCS3A01G284300 chr5A 93.519 1651 81 17 122 1764 168400319 168398687 0.000000e+00 2433
5 TraesCS3A01G284300 chr4A 95.608 2823 90 20 43 2835 490340826 490343644 0.000000e+00 4495
6 TraesCS3A01G284300 chr4A 94.984 1874 69 16 965 2835 655500326 655502177 0.000000e+00 2916
7 TraesCS3A01G284300 chr4A 95.554 1822 73 5 1 1820 429487960 429489775 0.000000e+00 2909
8 TraesCS3A01G284300 chr1A 95.156 2539 94 12 325 2835 575419163 575421700 0.000000e+00 3980
9 TraesCS3A01G284300 chr1A 93.616 1676 86 16 122 1792 443853300 443854959 0.000000e+00 2483
10 TraesCS3A01G284300 chr1A 94.737 1330 66 3 965 2291 7948173 7949501 0.000000e+00 2065
11 TraesCS3A01G284300 chr1A 97.265 585 15 1 124 707 497975155 497975739 0.000000e+00 990
12 TraesCS3A01G284300 chr1A 97.674 516 11 1 1 515 580782939 580783454 0.000000e+00 885
13 TraesCS3A01G284300 chr7A 94.621 2175 87 9 122 2291 644066816 644064667 0.000000e+00 3341
14 TraesCS3A01G284300 chr7A 93.855 1660 78 15 111 1764 49623241 49621600 0.000000e+00 2479
15 TraesCS3A01G284300 chr7A 95.181 1328 63 1 965 2291 493516367 493517694 0.000000e+00 2097
16 TraesCS3A01G284300 chr6A 95.666 1823 73 4 1 1820 401364267 401366086 0.000000e+00 2924
17 TraesCS3A01G284300 chr3B 94.928 1873 68 16 965 2835 62771266 62769419 0.000000e+00 2907
18 TraesCS3A01G284300 chr6B 94.946 1860 70 14 978 2835 643312891 643314728 0.000000e+00 2892
19 TraesCS3A01G284300 chr6B 94.762 1871 74 16 965 2833 703919238 703921086 0.000000e+00 2891
20 TraesCS3A01G284300 chr7B 94.564 1858 75 15 978 2835 20597917 20596086 0.000000e+00 2848
21 TraesCS3A01G284300 chr5B 93.807 1873 71 13 965 2835 672339246 672337417 0.000000e+00 2774
22 TraesCS3A01G284300 chr2B 95.411 1264 49 6 1580 2835 242205939 242207201 0.000000e+00 2004
23 TraesCS3A01G284300 chr6D 97.228 505 14 0 319 823 297179389 297178885 0.000000e+00 856
24 TraesCS3A01G284300 chr4D 94.888 313 10 3 322 634 261239527 261239221 4.250000e-133 484
25 TraesCS3A01G284300 chr4D 92.157 153 11 1 171 322 480889845 480889693 6.150000e-52 215
26 TraesCS3A01G284300 chr4D 85.393 178 10 7 1 176 480890046 480889883 1.350000e-38 171
27 TraesCS3A01G284300 chr4B 93.548 155 7 3 171 322 608980300 608980146 7.900000e-56 228


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 TraesCS3A01G284300 chr3A 513294788 513297622 2834 False 5236 5236 100.000 1 2835 1 chr3A.!!$F1 2834
1 TraesCS3A01G284300 chr3A 733885854 733887578 1724 True 2590 2590 93.700 1 1739 1 chr3A.!!$R1 1738
2 TraesCS3A01G284300 chr5A 133817573 133820415 2842 False 4578 4578 95.782 1 2835 1 chr5A.!!$F1 2834
3 TraesCS3A01G284300 chr5A 345670743 345672974 2231 True 3589 3589 95.602 43 2291 1 chr5A.!!$R2 2248
4 TraesCS3A01G284300 chr5A 168398687 168400319 1632 True 2433 2433 93.519 122 1764 1 chr5A.!!$R1 1642
5 TraesCS3A01G284300 chr4A 490340826 490343644 2818 False 4495 4495 95.608 43 2835 1 chr4A.!!$F2 2792
6 TraesCS3A01G284300 chr4A 655500326 655502177 1851 False 2916 2916 94.984 965 2835 1 chr4A.!!$F3 1870
7 TraesCS3A01G284300 chr4A 429487960 429489775 1815 False 2909 2909 95.554 1 1820 1 chr4A.!!$F1 1819
8 TraesCS3A01G284300 chr1A 575419163 575421700 2537 False 3980 3980 95.156 325 2835 1 chr1A.!!$F4 2510
9 TraesCS3A01G284300 chr1A 443853300 443854959 1659 False 2483 2483 93.616 122 1792 1 chr1A.!!$F2 1670
10 TraesCS3A01G284300 chr1A 7948173 7949501 1328 False 2065 2065 94.737 965 2291 1 chr1A.!!$F1 1326
11 TraesCS3A01G284300 chr1A 497975155 497975739 584 False 990 990 97.265 124 707 1 chr1A.!!$F3 583
12 TraesCS3A01G284300 chr1A 580782939 580783454 515 False 885 885 97.674 1 515 1 chr1A.!!$F5 514
13 TraesCS3A01G284300 chr7A 644064667 644066816 2149 True 3341 3341 94.621 122 2291 1 chr7A.!!$R2 2169
14 TraesCS3A01G284300 chr7A 49621600 49623241 1641 True 2479 2479 93.855 111 1764 1 chr7A.!!$R1 1653
15 TraesCS3A01G284300 chr7A 493516367 493517694 1327 False 2097 2097 95.181 965 2291 1 chr7A.!!$F1 1326
16 TraesCS3A01G284300 chr6A 401364267 401366086 1819 False 2924 2924 95.666 1 1820 1 chr6A.!!$F1 1819
17 TraesCS3A01G284300 chr3B 62769419 62771266 1847 True 2907 2907 94.928 965 2835 1 chr3B.!!$R1 1870
18 TraesCS3A01G284300 chr6B 643312891 643314728 1837 False 2892 2892 94.946 978 2835 1 chr6B.!!$F1 1857
19 TraesCS3A01G284300 chr6B 703919238 703921086 1848 False 2891 2891 94.762 965 2833 1 chr6B.!!$F2 1868
20 TraesCS3A01G284300 chr7B 20596086 20597917 1831 True 2848 2848 94.564 978 2835 1 chr7B.!!$R1 1857
21 TraesCS3A01G284300 chr5B 672337417 672339246 1829 True 2774 2774 93.807 965 2835 1 chr5B.!!$R1 1870
22 TraesCS3A01G284300 chr2B 242205939 242207201 1262 False 2004 2004 95.411 1580 2835 1 chr2B.!!$F1 1255
23 TraesCS3A01G284300 chr6D 297178885 297179389 504 True 856 856 97.228 319 823 1 chr6D.!!$R1 504

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
104 105 2.031012 CAGCCCAACTGTCGAGCA 59.969 61.111 0.00 0.0 41.86 4.26 F
237 239 2.499693 TGTGGTTCTCTTCACAGTGACA 59.500 45.455 1.52 0.0 38.75 3.58 F
1592 1641 2.036414 ACGAGGAGCAGAGCAGGA 59.964 61.111 0.00 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1135 1145 0.323178 CCTCTGCAGCAAGGGTCAAT 60.323 55.000 9.47 0.0 0.00 2.57 R
1771 1994 0.327924 CCACCACCATAGCAAGGTCA 59.672 55.000 0.00 0.0 37.23 4.02 R
2587 2955 1.001378 GAGCCGTGCAAATCTGTTGTT 60.001 47.619 0.00 0.0 0.00 2.83 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
104 105 2.031012 CAGCCCAACTGTCGAGCA 59.969 61.111 0.00 0.00 41.86 4.26
137 138 7.331026 CACATTCAGAGGGATTTTGTAGACTA 58.669 38.462 0.00 0.00 0.00 2.59
138 139 7.989741 CACATTCAGAGGGATTTTGTAGACTAT 59.010 37.037 0.00 0.00 0.00 2.12
237 239 2.499693 TGTGGTTCTCTTCACAGTGACA 59.500 45.455 1.52 0.00 38.75 3.58
585 590 9.793245 CGACTATAAAGTTGTTCAGTTTTGTAG 57.207 33.333 10.24 10.24 35.56 2.74
1124 1134 3.012518 GTCTAGTGCTTGATTGCCACAT 58.987 45.455 0.00 0.00 0.00 3.21
1135 1145 4.148079 TGATTGCCACATTTAACCACTGA 58.852 39.130 0.00 0.00 0.00 3.41
1144 1154 5.243730 CACATTTAACCACTGATTGACCCTT 59.756 40.000 0.00 0.00 0.00 3.95
1316 1326 3.430862 GAGCATTTCGCCCGTGCA 61.431 61.111 4.90 0.00 44.04 4.57
1589 1638 2.673341 ACGACGAGGAGCAGAGCA 60.673 61.111 0.00 0.00 0.00 4.26
1592 1641 2.036414 ACGAGGAGCAGAGCAGGA 59.964 61.111 0.00 0.00 0.00 3.86
1758 1981 4.175489 CGACGACCTCGCGATGGT 62.175 66.667 24.15 24.15 44.43 3.55
1759 1982 2.579787 GACGACCTCGCGATGGTG 60.580 66.667 27.44 21.47 44.43 4.17
1760 1983 4.129737 ACGACCTCGCGATGGTGG 62.130 66.667 27.44 26.68 44.43 4.61
1761 1984 4.129737 CGACCTCGCGATGGTGGT 62.130 66.667 27.44 22.72 38.03 4.16
1762 1985 2.509336 GACCTCGCGATGGTGGTG 60.509 66.667 27.44 8.42 38.03 4.17
1763 1986 4.082523 ACCTCGCGATGGTGGTGG 62.083 66.667 23.55 16.07 36.30 4.61
1764 1987 4.082523 CCTCGCGATGGTGGTGGT 62.083 66.667 10.36 0.00 0.00 4.16
1765 1988 2.815211 CTCGCGATGGTGGTGGTG 60.815 66.667 10.36 0.00 0.00 4.17
1766 1989 4.386951 TCGCGATGGTGGTGGTGG 62.387 66.667 3.71 0.00 0.00 4.61
1767 1990 4.386951 CGCGATGGTGGTGGTGGA 62.387 66.667 0.00 0.00 0.00 4.02
1768 1991 2.746277 GCGATGGTGGTGGTGGAC 60.746 66.667 0.00 0.00 0.00 4.02
1769 1992 2.434185 CGATGGTGGTGGTGGACG 60.434 66.667 0.00 0.00 0.00 4.79
1770 1993 2.938086 CGATGGTGGTGGTGGACGA 61.938 63.158 0.00 0.00 0.00 4.20
1771 1994 1.602237 GATGGTGGTGGTGGACGAT 59.398 57.895 0.00 0.00 0.00 3.73
1772 1995 0.744414 GATGGTGGTGGTGGACGATG 60.744 60.000 0.00 0.00 0.00 3.84
1773 1996 1.198094 ATGGTGGTGGTGGACGATGA 61.198 55.000 0.00 0.00 0.00 2.92
1774 1997 1.375523 GGTGGTGGTGGACGATGAC 60.376 63.158 0.00 0.00 0.00 3.06
1843 2201 1.233019 CAATCCCATAGCTTGGCGAG 58.767 55.000 8.85 0.00 44.97 5.03
1933 2297 3.772025 TGATGAAGGAGAAGAAGGAGGAC 59.228 47.826 0.00 0.00 0.00 3.85
1996 2360 8.213518 AGCTTGTTAGTGTAATATGAACATGG 57.786 34.615 0.00 0.00 30.61 3.66
2038 2402 5.409214 GGTTTAATTTTGTGCATGCTCATGT 59.591 36.000 22.01 9.27 40.80 3.21
2117 2483 8.042515 CAGTTTGGTAATTGATGGGAATTGAAT 58.957 33.333 0.00 0.00 0.00 2.57
2191 2558 9.850628 GCATGCTCATGTATGAAACAATATAAT 57.149 29.630 11.37 0.00 42.70 1.28
2244 2611 3.066190 CCTAGCCACGGACGACCA 61.066 66.667 4.48 0.00 35.59 4.02
2461 2829 1.583054 GTAGCTACTCCCGGCAATTG 58.417 55.000 16.88 0.00 0.00 2.32
2528 2896 1.690219 CGGGTCCTCCATAGCTTGCT 61.690 60.000 0.00 0.00 34.36 3.91
2548 2916 8.699749 GCTTGCTCGTTATTTTCACTAAAAATT 58.300 29.630 1.51 0.00 43.51 1.82
2587 2955 4.883585 GGTAGGCATTTCATCACAGAATCA 59.116 41.667 0.00 0.00 0.00 2.57
2644 3012 1.798725 GTCGCCGTGACGAAATCGA 60.799 57.895 6.54 7.02 44.93 3.59
2655 3023 1.941975 ACGAAATCGACCGGTTTTTGT 59.058 42.857 9.42 12.92 43.02 2.83
2761 3132 7.457024 AAAATACTAAACTTGCAATACCGGT 57.543 32.000 13.98 13.98 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 105 2.649312 TCCCTCTGAATGTGGTCCAATT 59.351 45.455 0.00 0.00 0.00 2.32
137 138 7.826747 AGGGACCTAAATCTAAATGCCTAAAT 58.173 34.615 0.00 0.00 0.00 1.40
138 139 7.220890 AGGGACCTAAATCTAAATGCCTAAA 57.779 36.000 0.00 0.00 0.00 1.85
434 439 9.813826 ATTTGCTTTGCTAGGGTTTATATAGAT 57.186 29.630 0.00 0.00 0.00 1.98
435 440 9.640952 AATTTGCTTTGCTAGGGTTTATATAGA 57.359 29.630 0.00 0.00 0.00 1.98
585 590 4.081087 ACACACCTACCCAATACAGTCATC 60.081 45.833 0.00 0.00 0.00 2.92
1124 1134 3.572255 GCAAGGGTCAATCAGTGGTTAAA 59.428 43.478 0.00 0.00 0.00 1.52
1135 1145 0.323178 CCTCTGCAGCAAGGGTCAAT 60.323 55.000 9.47 0.00 0.00 2.57
1333 1343 2.249139 AGCGGAAGACAAGGAAGTACT 58.751 47.619 0.00 0.00 0.00 2.73
1589 1638 1.140589 CGCTCTGCTCGTCATTCCT 59.859 57.895 0.00 0.00 0.00 3.36
1592 1641 2.185350 CCCGCTCTGCTCGTCATT 59.815 61.111 0.00 0.00 0.00 2.57
1748 1944 2.815211 CACCACCACCATCGCGAG 60.815 66.667 16.66 4.02 0.00 5.03
1749 1945 4.386951 CCACCACCACCATCGCGA 62.387 66.667 13.09 13.09 0.00 5.87
1750 1946 4.386951 TCCACCACCACCATCGCG 62.387 66.667 0.00 0.00 0.00 5.87
1751 1947 2.746277 GTCCACCACCACCATCGC 60.746 66.667 0.00 0.00 0.00 4.58
1752 1948 2.238847 ATCGTCCACCACCACCATCG 62.239 60.000 0.00 0.00 0.00 3.84
1753 1949 0.744414 CATCGTCCACCACCACCATC 60.744 60.000 0.00 0.00 0.00 3.51
1754 1950 1.198094 TCATCGTCCACCACCACCAT 61.198 55.000 0.00 0.00 0.00 3.55
1755 1951 1.839296 TCATCGTCCACCACCACCA 60.839 57.895 0.00 0.00 0.00 4.17
1756 1952 1.375523 GTCATCGTCCACCACCACC 60.376 63.158 0.00 0.00 0.00 4.61
1757 1980 1.375523 GGTCATCGTCCACCACCAC 60.376 63.158 0.00 0.00 32.33 4.16
1758 1981 1.125093 AAGGTCATCGTCCACCACCA 61.125 55.000 2.95 0.00 34.80 4.17
1759 1982 0.673644 CAAGGTCATCGTCCACCACC 60.674 60.000 2.95 0.00 34.80 4.61
1760 1983 1.298859 GCAAGGTCATCGTCCACCAC 61.299 60.000 2.95 0.00 34.80 4.16
1761 1984 1.003839 GCAAGGTCATCGTCCACCA 60.004 57.895 2.95 0.00 34.80 4.17
1762 1985 0.535335 TAGCAAGGTCATCGTCCACC 59.465 55.000 0.00 0.00 0.00 4.61
1763 1986 2.205074 CATAGCAAGGTCATCGTCCAC 58.795 52.381 0.00 0.00 0.00 4.02
1764 1987 1.138859 CCATAGCAAGGTCATCGTCCA 59.861 52.381 0.00 0.00 0.00 4.02
1765 1988 1.139058 ACCATAGCAAGGTCATCGTCC 59.861 52.381 0.00 0.00 32.90 4.79
1766 1989 2.205074 CACCATAGCAAGGTCATCGTC 58.795 52.381 0.00 0.00 37.23 4.20
1767 1990 1.134401 CCACCATAGCAAGGTCATCGT 60.134 52.381 0.00 0.00 37.23 3.73
1768 1991 1.134401 ACCACCATAGCAAGGTCATCG 60.134 52.381 0.00 0.00 37.23 3.84
1769 1992 2.292267 CACCACCATAGCAAGGTCATC 58.708 52.381 0.00 0.00 37.23 2.92
1770 1993 1.064463 CCACCACCATAGCAAGGTCAT 60.064 52.381 0.00 0.00 37.23 3.06
1771 1994 0.327924 CCACCACCATAGCAAGGTCA 59.672 55.000 0.00 0.00 37.23 4.02
1772 1995 1.032114 GCCACCACCATAGCAAGGTC 61.032 60.000 0.00 0.00 37.23 3.85
1773 1996 1.000896 GCCACCACCATAGCAAGGT 60.001 57.895 0.00 0.00 40.85 3.50
1774 1997 2.114670 CGCCACCACCATAGCAAGG 61.115 63.158 0.00 0.00 0.00 3.61
1843 2201 0.819582 CCACAATTGGCATGGTCCTC 59.180 55.000 10.83 0.00 35.56 3.71
1933 2297 6.348050 GCTGAACACCTTCTTAACATCTTCAG 60.348 42.308 0.00 0.00 36.65 3.02
1996 2360 9.855021 AATTAAACCTGACATACTTAACATTGC 57.145 29.630 0.00 0.00 0.00 3.56
2244 2611 1.153706 CGGCGGATTTAGTCACGGT 60.154 57.895 0.00 0.00 0.00 4.83
2309 2677 3.367992 AACGCATGTCTTTTGCATTCA 57.632 38.095 0.00 0.00 40.14 2.57
2335 2703 1.519455 CCTCCTTGTAGCCGCTTCG 60.519 63.158 0.00 0.00 0.00 3.79
2548 2916 4.202419 TGCCTACCTGTGAAGCTAAAAAGA 60.202 41.667 0.00 0.00 0.00 2.52
2587 2955 1.001378 GAGCCGTGCAAATCTGTTGTT 60.001 47.619 0.00 0.00 0.00 2.83
2761 3132 8.879342 TTTGAGAACACTTTTTCAAGAAAACA 57.121 26.923 7.44 0.00 39.70 2.83


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

AutoCloner maintained by Alex Coulton.