Multiple sequence alignment - TraesCS7B01G117400

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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 TraesCS7B01G117400 chr7B 100.000 2210 0 0 1 2210 137025819 137028028 0.000000e+00 4082
1 TraesCS7B01G117400 chr7D 94.518 1806 59 19 1 1769 170729598 170731400 0.000000e+00 2750
2 TraesCS7B01G117400 chr7D 83.784 407 41 15 1784 2175 170731383 170731779 1.610000e-96 363
3 TraesCS7B01G117400 chr7A 93.827 1701 68 19 1 1666 173637588 173639286 0.000000e+00 2525
4 TraesCS7B01G117400 chr7A 89.057 265 17 4 1937 2195 173639885 173640143 3.540000e-83 318
5 TraesCS7B01G117400 chr7A 89.286 168 7 7 1784 1950 173639319 173639476 1.340000e-47 200
6 TraesCS7B01G117400 chr7A 100.000 53 0 0 1717 1769 173639284 173639336 5.020000e-17 99
7 TraesCS7B01G117400 chr3D 79.371 286 45 14 982 1260 327575506 327575784 2.900000e-44 189
8 TraesCS7B01G117400 chr3A 79.298 285 47 12 982 1260 441570621 441570899 2.900000e-44 189
9 TraesCS7B01G117400 chr3B 78.596 285 49 12 982 1260 422157812 422157534 6.270000e-41 178
10 TraesCS7B01G117400 chr6B 78.333 240 37 11 1015 1248 213467273 213467043 8.230000e-30 141
11 TraesCS7B01G117400 chr6A 77.500 240 42 8 1015 1248 162310356 162310589 1.380000e-27 134


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 TraesCS7B01G117400 chr7B 137025819 137028028 2209 False 4082.0 4082 100.0000 1 2210 1 chr7B.!!$F1 2209
1 TraesCS7B01G117400 chr7D 170729598 170731779 2181 False 1556.5 2750 89.1510 1 2175 2 chr7D.!!$F1 2174
2 TraesCS7B01G117400 chr7A 173637588 173640143 2555 False 785.5 2525 93.0425 1 2195 4 chr7A.!!$F1 2194

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
864 875 0.251165 GGGGTACTCCAGCTGCAAAA 60.251 55.0 6.99 0.0 37.22 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1714 1771 0.170339 GCGCCACAGACAATTAACCC 59.83 55.0 0.0 0.0 0.0 4.11 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
62 63 3.675775 GCACACAGCTGAAACCAGAAAAA 60.676 43.478 23.35 0.00 41.15 1.94
63 64 3.859386 CACACAGCTGAAACCAGAAAAAC 59.141 43.478 23.35 0.00 33.56 2.43
482 493 2.434331 CCTTTGAAGCCCGGGTGA 59.566 61.111 24.63 0.00 0.00 4.02
488 499 2.283388 AAGCCCGGGTGACTCGTA 60.283 61.111 24.63 0.00 0.00 3.43
605 616 1.593296 GGCCGGACTCGTAGAACAGT 61.593 60.000 5.05 0.00 34.09 3.55
863 874 1.378762 GGGGTACTCCAGCTGCAAA 59.621 57.895 6.99 0.00 37.22 3.68
864 875 0.251165 GGGGTACTCCAGCTGCAAAA 60.251 55.000 6.99 0.00 37.22 2.44
865 876 0.881796 GGGTACTCCAGCTGCAAAAC 59.118 55.000 8.66 3.58 35.00 2.43
914 926 9.982651 CTCCCTCTCTAATAATCGAAAATGTAA 57.017 33.333 0.00 0.00 0.00 2.41
942 959 9.249457 TCATACATTTCGTAGATCAGTGATTTC 57.751 33.333 7.16 0.00 35.04 2.17
944 961 9.823647 ATACATTTCGTAGATCAGTGATTTCTT 57.176 29.630 7.16 0.00 35.04 2.52
969 986 9.995003 TTGCAATAATTAGTGGACTGAAATTTT 57.005 25.926 14.26 0.00 0.00 1.82
978 995 6.725246 AGTGGACTGAAATTTTAAACTGACG 58.275 36.000 0.00 0.00 0.00 4.35
979 996 5.912955 GTGGACTGAAATTTTAAACTGACGG 59.087 40.000 0.00 0.00 0.00 4.79
1137 1178 1.745489 CCAGCGCCACCTAAGGAAC 60.745 63.158 2.29 0.00 0.00 3.62
1269 1310 0.039618 AAATGTCGCATCCCTTGGGT 59.960 50.000 5.51 0.00 39.25 4.51
1402 1443 0.458260 GAGGAAGAGGACGAAGAGGC 59.542 60.000 0.00 0.00 0.00 4.70
1475 1516 3.036429 GCTGGTTCGGGGATCTGCT 62.036 63.158 0.00 0.00 0.00 4.24
1477 1518 0.462759 CTGGTTCGGGGATCTGCTTC 60.463 60.000 0.00 0.00 0.00 3.86
1714 1771 0.301687 GCAATGTACATGGCGACGAG 59.698 55.000 19.25 0.00 0.00 4.18
1762 1819 2.681152 GGTACGTCAGCTTTGGTTTG 57.319 50.000 0.00 0.00 0.00 2.93
1763 1820 2.215196 GGTACGTCAGCTTTGGTTTGA 58.785 47.619 0.00 0.00 0.00 2.69
1764 1821 2.812011 GGTACGTCAGCTTTGGTTTGAT 59.188 45.455 0.00 0.00 0.00 2.57
1765 1822 3.364964 GGTACGTCAGCTTTGGTTTGATG 60.365 47.826 0.00 0.00 34.74 3.07
1766 1823 1.608590 ACGTCAGCTTTGGTTTGATGG 59.391 47.619 0.00 0.00 33.26 3.51
1767 1824 1.068333 CGTCAGCTTTGGTTTGATGGG 60.068 52.381 0.00 0.00 0.00 4.00
1768 1825 2.238521 GTCAGCTTTGGTTTGATGGGA 58.761 47.619 0.00 0.00 0.00 4.37
1769 1826 2.029918 GTCAGCTTTGGTTTGATGGGAC 60.030 50.000 0.00 0.00 0.00 4.46
1770 1827 1.273327 CAGCTTTGGTTTGATGGGACC 59.727 52.381 0.00 0.00 36.45 4.46
1771 1828 0.608130 GCTTTGGTTTGATGGGACCC 59.392 55.000 2.45 2.45 34.99 4.46
1772 1829 1.827245 GCTTTGGTTTGATGGGACCCT 60.827 52.381 13.00 0.00 34.99 4.34
1773 1830 2.171003 CTTTGGTTTGATGGGACCCTC 58.829 52.381 13.00 7.52 34.99 4.30
1774 1831 1.153539 TTGGTTTGATGGGACCCTCA 58.846 50.000 13.00 10.16 34.99 3.86
1775 1832 1.153539 TGGTTTGATGGGACCCTCAA 58.846 50.000 13.00 15.43 34.99 3.02
1776 1833 1.501170 TGGTTTGATGGGACCCTCAAA 59.499 47.619 23.49 23.49 38.64 2.69
1777 1834 2.091055 TGGTTTGATGGGACCCTCAAAA 60.091 45.455 26.52 16.02 41.57 2.44
1778 1835 2.969262 GGTTTGATGGGACCCTCAAAAA 59.031 45.455 26.52 14.67 41.57 1.94
1802 1859 4.769345 AAAGCTTTGGTTTGATGGGAAA 57.231 36.364 11.80 0.00 31.83 3.13
1805 1862 2.289631 GCTTTGGTTTGATGGGAAAGGG 60.290 50.000 0.00 0.00 0.00 3.95
1807 1864 0.544120 TGGTTTGATGGGAAAGGGCC 60.544 55.000 0.00 0.00 0.00 5.80
1811 1868 4.440829 GATGGGAAAGGGCCGGCA 62.441 66.667 30.85 4.70 0.00 5.69
1850 1912 1.334599 CGCCTGCGCTTTACTTTGAAA 60.335 47.619 9.73 0.00 0.00 2.69
1914 1999 0.927537 TTTGTCGAGCGGATAATGCG 59.072 50.000 0.00 0.00 37.44 4.73
1924 2009 1.308998 GGATAATGCGGTCACTTGGG 58.691 55.000 0.00 0.00 0.00 4.12
1925 2010 0.663153 GATAATGCGGTCACTTGGGC 59.337 55.000 0.00 0.00 0.00 5.36
1926 2011 0.034574 ATAATGCGGTCACTTGGGCA 60.035 50.000 0.00 0.00 40.06 5.36
1927 2012 0.250945 TAATGCGGTCACTTGGGCAA 60.251 50.000 0.00 0.00 39.09 4.52
1983 2491 2.709125 CTTCACCGTGGCCGTGAGAA 62.709 60.000 11.18 5.60 0.00 2.87
1996 2504 2.576406 CGTGAGAACACTCGAGAACTC 58.424 52.381 21.68 19.28 43.99 3.01
2003 2511 3.802948 ACACTCGAGAACTCAAGTGTT 57.197 42.857 21.68 7.23 37.21 3.32
2130 2643 2.434884 CCGTCTTCGCACAGGCAT 60.435 61.111 0.00 0.00 41.24 4.40
2175 2692 2.200067 CGGTGATGATCTGTCTGAAGC 58.800 52.381 0.00 0.00 0.00 3.86
2176 2693 2.200067 GGTGATGATCTGTCTGAAGCG 58.800 52.381 0.00 0.00 0.00 4.68
2177 2694 2.200067 GTGATGATCTGTCTGAAGCGG 58.800 52.381 0.00 0.00 0.00 5.52
2180 2697 1.256812 TGATCTGTCTGAAGCGGTGA 58.743 50.000 0.00 0.00 0.00 4.02
2196 2713 4.891727 GACACCGGCGGCATCGAT 62.892 66.667 28.71 1.09 39.00 3.59
2197 2714 4.891727 ACACCGGCGGCATCGATC 62.892 66.667 28.71 0.00 39.00 3.69
2207 2724 3.417224 CATCGATCGGCCCGCATG 61.417 66.667 16.41 6.55 0.00 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.490115 TGTTACGGAAATTCCATGTGGC 59.510 45.455 13.04 1.80 35.91 5.01
62 63 2.202518 CCGTAATGTCGTCGGCGT 60.203 61.111 10.18 0.00 37.90 5.68
63 64 2.202518 ACCGTAATGTCGTCGGCG 60.203 61.111 1.15 1.15 46.92 6.46
303 314 3.760035 GGAGGAGTTCGCGCAGGA 61.760 66.667 8.75 0.00 0.00 3.86
467 478 1.072505 GAGTCACCCGGGCTTCAAA 59.927 57.895 24.08 0.00 0.00 2.69
482 493 4.430765 CTGCGGGCGGTTACGAGT 62.431 66.667 0.00 0.00 44.60 4.18
630 641 1.438562 GACTACCTCGTCCTCTCGGC 61.439 65.000 0.00 0.00 0.00 5.54
677 688 3.574445 CTCGACGAGCCGGACGAT 61.574 66.667 23.84 11.01 38.43 3.73
734 745 1.006102 CGTCAAGGCGAACCAGTCT 60.006 57.895 0.00 0.00 39.06 3.24
886 898 8.705594 ACATTTTCGATTATTAGAGAGGGAGAA 58.294 33.333 0.00 0.00 0.00 2.87
914 926 9.770097 AATCACTGATCTACGAAATGTATGATT 57.230 29.630 0.00 0.00 33.56 2.57
920 932 7.413438 GCAAGAAATCACTGATCTACGAAATGT 60.413 37.037 0.00 0.00 0.00 2.71
925 937 5.072040 TGCAAGAAATCACTGATCTACGA 57.928 39.130 0.00 0.00 0.00 3.43
926 938 5.784750 TTGCAAGAAATCACTGATCTACG 57.215 39.130 0.00 0.00 0.00 3.51
937 954 8.677300 TCAGTCCACTAATTATTGCAAGAAATC 58.323 33.333 11.02 0.00 0.00 2.17
942 959 9.643693 AAATTTCAGTCCACTAATTATTGCAAG 57.356 29.630 4.94 0.00 0.00 4.01
953 970 7.041644 CCGTCAGTTTAAAATTTCAGTCCACTA 60.042 37.037 0.00 0.00 0.00 2.74
969 986 3.387374 TGTCCAAGGTAACCGTCAGTTTA 59.613 43.478 0.00 0.00 40.05 2.01
970 987 2.171027 TGTCCAAGGTAACCGTCAGTTT 59.829 45.455 0.00 0.00 40.05 2.66
972 989 1.416243 TGTCCAAGGTAACCGTCAGT 58.584 50.000 0.00 0.00 37.17 3.41
973 990 2.036733 TCTTGTCCAAGGTAACCGTCAG 59.963 50.000 7.16 0.00 38.88 3.51
974 991 2.036733 CTCTTGTCCAAGGTAACCGTCA 59.963 50.000 7.16 0.00 38.88 4.35
975 992 2.612221 CCTCTTGTCCAAGGTAACCGTC 60.612 54.545 7.16 0.00 38.88 4.79
976 993 1.346722 CCTCTTGTCCAAGGTAACCGT 59.653 52.381 7.16 0.00 38.88 4.83
977 994 1.944430 GCCTCTTGTCCAAGGTAACCG 60.944 57.143 7.16 0.00 38.88 4.44
978 995 1.073284 TGCCTCTTGTCCAAGGTAACC 59.927 52.381 7.16 0.00 38.88 2.85
979 996 2.152016 GTGCCTCTTGTCCAAGGTAAC 58.848 52.381 7.16 0.00 38.88 2.50
1312 1353 1.874345 GCCTCAGTTTCCTCGTCGGA 61.874 60.000 0.00 0.00 41.06 4.55
1455 1496 2.363795 AGATCCCCGAACCAGCGA 60.364 61.111 0.00 0.00 0.00 4.93
1475 1516 1.737838 CTTCTGGCCATTGTAGCGAA 58.262 50.000 5.51 3.17 0.00 4.70
1477 1518 1.723870 GCTTCTGGCCATTGTAGCG 59.276 57.895 5.51 0.00 34.27 4.26
1714 1771 0.170339 GCGCCACAGACAATTAACCC 59.830 55.000 0.00 0.00 0.00 4.11
1779 1836 4.769345 TCCCATCAAACCAAAGCTTTTT 57.231 36.364 9.53 0.00 0.00 1.94
1780 1837 4.769345 TTCCCATCAAACCAAAGCTTTT 57.231 36.364 9.53 0.00 0.00 2.27
1781 1838 4.444733 CCTTTCCCATCAAACCAAAGCTTT 60.445 41.667 5.69 5.69 0.00 3.51
1782 1839 3.071457 CCTTTCCCATCAAACCAAAGCTT 59.929 43.478 0.00 0.00 0.00 3.74
1783 1840 2.634453 CCTTTCCCATCAAACCAAAGCT 59.366 45.455 0.00 0.00 0.00 3.74
1784 1841 2.289631 CCCTTTCCCATCAAACCAAAGC 60.290 50.000 0.00 0.00 0.00 3.51
1785 1842 2.289631 GCCCTTTCCCATCAAACCAAAG 60.290 50.000 0.00 0.00 0.00 2.77
1786 1843 1.696884 GCCCTTTCCCATCAAACCAAA 59.303 47.619 0.00 0.00 0.00 3.28
1787 1844 1.347062 GCCCTTTCCCATCAAACCAA 58.653 50.000 0.00 0.00 0.00 3.67
1788 1845 0.544120 GGCCCTTTCCCATCAAACCA 60.544 55.000 0.00 0.00 0.00 3.67
1789 1846 1.604147 CGGCCCTTTCCCATCAAACC 61.604 60.000 0.00 0.00 0.00 3.27
1790 1847 1.604147 CCGGCCCTTTCCCATCAAAC 61.604 60.000 0.00 0.00 0.00 2.93
1830 1892 0.237235 TTCAAAGTAAAGCGCAGGCG 59.763 50.000 11.47 9.68 46.35 5.52
1843 1905 0.450482 CCAGTACGCGCGTTTCAAAG 60.450 55.000 42.10 22.89 0.00 2.77
1880 1942 2.479837 GACAAAGTGTCACGTGATGGA 58.520 47.619 23.12 6.15 46.22 3.41
1914 1999 1.363807 GTTGCTTGCCCAAGTGACC 59.636 57.895 9.53 0.00 40.45 4.02
1924 2009 1.897398 GCATTGCTGCTGTTGCTTGC 61.897 55.000 0.16 0.00 45.32 4.01
1925 2010 2.150424 GCATTGCTGCTGTTGCTTG 58.850 52.632 0.16 0.00 45.32 4.01
1926 2011 4.667420 GCATTGCTGCTGTTGCTT 57.333 50.000 0.16 0.00 45.32 3.91
1996 2504 1.001378 GCCCTTGTGCTACAACACTTG 60.001 52.381 0.00 0.00 41.30 3.16
2003 2511 2.662596 CTCCGCCCTTGTGCTACA 59.337 61.111 0.00 0.00 0.00 2.74
2034 2547 0.250467 GCGGCACCTCATCATACCAT 60.250 55.000 0.00 0.00 0.00 3.55
2035 2548 1.146041 GCGGCACCTCATCATACCA 59.854 57.895 0.00 0.00 0.00 3.25
2123 2636 2.437281 CTGGGTCTCTCATTATGCCTGT 59.563 50.000 0.00 0.00 0.00 4.00
2130 2643 0.824109 CGGTGCTGGGTCTCTCATTA 59.176 55.000 0.00 0.00 0.00 1.90
2180 2697 4.891727 GATCGATGCCGCCGGTGT 62.892 66.667 15.14 0.00 35.37 4.16


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

AutoCloner maintained by Alex Coulton.