Multiple sequence alignment - TraesCS4B01G183400

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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 TraesCS4B01G183400 chr4B 100.000 3841 0 0 1 3841 402857006 402853166 0 7094
1 TraesCS4B01G183400 chr6B 96.468 3850 123 8 1 3839 524369810 524365963 0 6344
2 TraesCS4B01G183400 chr5B 96.360 3846 126 11 1 3841 49320364 49316528 0 6314
3 TraesCS4B01G183400 chr3B 96.284 3848 128 14 1 3841 730268159 730271998 0 6300
4 TraesCS4B01G183400 chr3B 94.809 3853 175 18 1 3841 772608843 772612682 0 5984
5 TraesCS4B01G183400 chr3B 94.597 3850 176 17 1 3841 9315791 9319617 0 5928
6 TraesCS4B01G183400 chr3B 94.338 3850 198 17 1 3839 770030848 770034688 0 5884
7 TraesCS4B01G183400 chr2B 95.841 3847 147 12 1 3841 82074 85913 0 6205
8 TraesCS4B01G183400 chr7B 95.242 3846 168 14 1 3841 747732460 747728625 0 6074
9 TraesCS4B01G183400 chr7B 95.138 3846 173 13 1 3841 379738211 379742047 0 6054


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 TraesCS4B01G183400 chr4B 402853166 402857006 3840 True 7094 7094 100.000 1 3841 1 chr4B.!!$R1 3840
1 TraesCS4B01G183400 chr6B 524365963 524369810 3847 True 6344 6344 96.468 1 3839 1 chr6B.!!$R1 3838
2 TraesCS4B01G183400 chr5B 49316528 49320364 3836 True 6314 6314 96.360 1 3841 1 chr5B.!!$R1 3840
3 TraesCS4B01G183400 chr3B 730268159 730271998 3839 False 6300 6300 96.284 1 3841 1 chr3B.!!$F2 3840
4 TraesCS4B01G183400 chr3B 772608843 772612682 3839 False 5984 5984 94.809 1 3841 1 chr3B.!!$F4 3840
5 TraesCS4B01G183400 chr3B 9315791 9319617 3826 False 5928 5928 94.597 1 3841 1 chr3B.!!$F1 3840
6 TraesCS4B01G183400 chr3B 770030848 770034688 3840 False 5884 5884 94.338 1 3839 1 chr3B.!!$F3 3838
7 TraesCS4B01G183400 chr2B 82074 85913 3839 False 6205 6205 95.841 1 3841 1 chr2B.!!$F1 3840
8 TraesCS4B01G183400 chr7B 747728625 747732460 3835 True 6074 6074 95.242 1 3841 1 chr7B.!!$R1 3840
9 TraesCS4B01G183400 chr7B 379738211 379742047 3836 False 6054 6054 95.138 1 3841 1 chr7B.!!$F1 3840

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
991 1008 2.050144 GTGATGATCAGAAGGGGGCTA 58.950 52.381 0.09 0.0 0.0 3.93 F
1557 1577 1.965930 GTGTGGTGCAGGCGAATCA 60.966 57.895 0.00 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2535 2609 0.250770 GTCCACCCCTCAACCAACTC 60.251 60.000 0.0 0.0 0.0 3.01 R
3159 3242 1.068434 CAGAAACATGGGTTGGCGTTT 59.932 47.619 0.0 0.0 37.3 3.60 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
64 65 2.423577 GGTAGTCAATGCAGTTTCGGT 58.576 47.619 0.00 0.00 0.00 4.69
141 142 6.547141 CCACTTGGATTGTATAATCATGTGGT 59.453 38.462 24.90 12.13 43.97 4.16
188 189 3.286329 TGCCACAATGCAGATATGACT 57.714 42.857 0.00 0.00 36.04 3.41
259 262 2.889045 GTGCCAGATGCCATATCATGTT 59.111 45.455 0.00 0.00 40.16 2.71
316 320 5.630680 GTCAGTACAAATGTGGCATTTTCAG 59.369 40.000 4.55 0.00 0.00 3.02
375 380 7.663081 ACTGACTTTTGTGATATCTGAACACAT 59.337 33.333 3.98 3.08 42.65 3.21
927 944 5.858581 GCAGAAGAAGAAACGTATTTGCAAT 59.141 36.000 0.00 0.00 0.00 3.56
991 1008 2.050144 GTGATGATCAGAAGGGGGCTA 58.950 52.381 0.09 0.00 0.00 3.93
994 1011 2.270434 TGATCAGAAGGGGGCTACTT 57.730 50.000 0.00 0.00 0.00 2.24
1146 1163 3.247648 CGTTGAACGAGGATTCTGTGTTT 59.752 43.478 13.13 0.00 46.05 2.83
1267 1284 2.202946 TGCCGAACACGTCTGCAA 60.203 55.556 0.00 0.00 42.75 4.08
1340 1357 5.658634 TGAAGCTACTCATGTACCTCATCTT 59.341 40.000 0.00 0.00 34.09 2.40
1557 1577 1.965930 GTGTGGTGCAGGCGAATCA 60.966 57.895 0.00 0.00 0.00 2.57
1619 1639 3.242220 CGACTTTCTCCATGATGCTTTCG 60.242 47.826 0.00 0.00 0.00 3.46
1770 1792 3.966979 ACTGCCATAATGACAATGTGGA 58.033 40.909 10.28 0.00 31.59 4.02
1776 1798 5.104374 CCATAATGACAATGTGGAAACTGC 58.896 41.667 0.01 0.00 31.59 4.40
1777 1799 3.665745 AATGACAATGTGGAAACTGCC 57.334 42.857 0.00 0.00 0.00 4.85
1778 1800 2.064434 TGACAATGTGGAAACTGCCA 57.936 45.000 0.00 0.00 35.02 4.92
1779 1801 2.596346 TGACAATGTGGAAACTGCCAT 58.404 42.857 0.00 0.00 40.68 4.40
1780 1802 3.760738 TGACAATGTGGAAACTGCCATA 58.239 40.909 0.00 0.00 40.68 2.74
1781 1803 4.148079 TGACAATGTGGAAACTGCCATAA 58.852 39.130 0.00 0.00 40.68 1.90
1782 1804 4.771577 TGACAATGTGGAAACTGCCATAAT 59.228 37.500 0.00 0.00 40.68 1.28
1783 1805 5.075858 ACAATGTGGAAACTGCCATAATG 57.924 39.130 0.00 0.00 40.68 1.90
1784 1806 4.771577 ACAATGTGGAAACTGCCATAATGA 59.228 37.500 0.00 0.00 40.68 2.57
1785 1807 4.989279 ATGTGGAAACTGCCATAATGAC 57.011 40.909 0.00 0.00 40.68 3.06
1786 1808 3.760738 TGTGGAAACTGCCATAATGACA 58.239 40.909 0.00 0.00 40.68 3.58
1787 1809 4.148079 TGTGGAAACTGCCATAATGACAA 58.852 39.130 0.00 0.00 40.68 3.18
1788 1810 4.771577 TGTGGAAACTGCCATAATGACAAT 59.228 37.500 0.00 0.00 40.68 2.71
1789 1811 5.104374 GTGGAAACTGCCATAATGACAATG 58.896 41.667 0.00 0.00 40.68 2.82
1790 1812 4.771577 TGGAAACTGCCATAATGACAATGT 59.228 37.500 0.00 0.00 31.66 2.71
1791 1813 5.104374 GGAAACTGCCATAATGACAATGTG 58.896 41.667 0.00 0.00 0.00 3.21
1792 1814 4.724074 AACTGCCATAATGACAATGTGG 57.276 40.909 2.01 2.01 0.00 4.17
1797 1819 4.724074 CCATAATGACAATGTGGCAACT 57.276 40.909 0.00 0.00 39.86 3.16
1798 1820 4.426416 CCATAATGACAATGTGGCAACTG 58.574 43.478 0.00 0.00 39.86 3.16
2495 2569 2.475666 GGCACCAGTTGAGCATCTC 58.524 57.895 0.00 0.00 34.92 2.75
2676 2750 0.178992 CAACAGTTCCCAAGAGCCCA 60.179 55.000 0.00 0.00 0.00 5.36
3159 3242 0.863144 GTTACGAAGAAACAGGCGCA 59.137 50.000 10.83 0.00 0.00 6.09
3397 3481 5.278169 GCTTGTCACATGTTCTTCTGTCATT 60.278 40.000 0.00 0.00 0.00 2.57
3445 3529 8.768019 GTTTTTCCAAATGATTTCTTCCTTCAG 58.232 33.333 0.00 0.00 0.00 3.02
3728 3817 7.260558 ACTACTAGCTTTTCCACTTGTTTTC 57.739 36.000 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
141 142 9.283768 ACAGACATTGTGTTCACATTCTATTTA 57.716 29.630 6.47 0.00 38.99 1.40
188 189 1.069427 GCAGCCAATTTGCCACACA 59.931 52.632 0.00 0.00 35.54 3.72
275 278 3.809832 ACTGACTGTAACATGACAACAGC 59.190 43.478 19.57 14.80 43.53 4.40
316 320 4.388790 GAAAAATTGCGTCCGTAGTACAC 58.611 43.478 0.38 0.00 0.00 2.90
392 397 9.775854 AATGAAACCACATTTGAATTGATAACA 57.224 25.926 0.00 0.00 37.20 2.41
707 721 1.340248 CGGTTACGCTATGGTGGATCT 59.660 52.381 0.00 0.00 0.00 2.75
922 939 1.583556 TCTTGGGAGGCTCTATTGCA 58.416 50.000 15.23 0.00 34.04 4.08
927 944 1.183549 GTCGTTCTTGGGAGGCTCTA 58.816 55.000 15.23 0.88 0.00 2.43
972 989 2.050144 GTAGCCCCCTTCTGATCATCA 58.950 52.381 0.00 0.00 0.00 3.07
991 1008 0.622136 TGCATGCCCATCTCAGAAGT 59.378 50.000 16.68 0.00 0.00 3.01
994 1011 0.179702 GACTGCATGCCCATCTCAGA 59.820 55.000 16.68 0.00 0.00 3.27
1043 1060 1.806623 GCCAGTCGCATACAGGGTTAG 60.807 57.143 0.64 0.00 35.33 2.34
1044 1061 0.177141 GCCAGTCGCATACAGGGTTA 59.823 55.000 0.64 0.00 35.33 2.85
1225 1242 0.547075 TCCGACCCAGGAAACAAACA 59.453 50.000 0.00 0.00 37.36 2.83
1340 1357 0.872881 GGTCGGCGCGAAAATAGCTA 60.873 55.000 12.10 0.00 37.72 3.32
1377 1394 4.192429 CAGGATGGGGAAACATTTGTTC 57.808 45.455 0.00 0.00 37.25 3.18
1557 1577 7.147846 ACCAGTTCATGTTCTTCACATTTTTCT 60.148 33.333 0.00 0.00 44.40 2.52
1619 1639 5.629079 CCCTTCTGGTACATCTTGTTTTC 57.371 43.478 0.00 0.00 38.20 2.29
1770 1792 5.075858 CCACATTGTCATTATGGCAGTTT 57.924 39.130 0.00 0.00 31.48 2.66
1776 1798 4.426416 CAGTTGCCACATTGTCATTATGG 58.574 43.478 0.00 0.00 0.00 2.74
1777 1799 3.861113 GCAGTTGCCACATTGTCATTATG 59.139 43.478 0.00 0.00 34.31 1.90
1778 1800 4.114058 GCAGTTGCCACATTGTCATTAT 57.886 40.909 0.00 0.00 34.31 1.28
1779 1801 3.574284 GCAGTTGCCACATTGTCATTA 57.426 42.857 0.00 0.00 34.31 1.90
1780 1802 2.443887 GCAGTTGCCACATTGTCATT 57.556 45.000 0.00 0.00 34.31 2.57
1792 1814 5.224888 CCATATTGTCATTATGGCAGTTGC 58.775 41.667 16.95 0.00 39.63 4.17
2003 2076 6.038985 CAGATCAAGACAGTCGACATACATT 58.961 40.000 19.50 2.81 0.00 2.71
2495 2569 0.458889 CGGATGCAAACTGCCCAATG 60.459 55.000 0.00 0.00 44.23 2.82
2535 2609 0.250770 GTCCACCCCTCAACCAACTC 60.251 60.000 0.00 0.00 0.00 3.01
2676 2750 5.728637 TCTACATCATCTTGTGTGTCACT 57.271 39.130 4.27 0.00 35.11 3.41
3104 3187 2.186903 CGGCTCCCTGCACGTAAT 59.813 61.111 0.00 0.00 45.15 1.89
3159 3242 1.068434 CAGAAACATGGGTTGGCGTTT 59.932 47.619 0.00 0.00 37.30 3.60
3365 3449 4.398988 AGAACATGTGACAAGCTGAAACAA 59.601 37.500 0.00 0.00 0.00 2.83
3452 3539 6.611642 AGACCAATAGGAGTTGTCATAAGCTA 59.388 38.462 0.00 0.00 38.69 3.32
3455 3542 9.099454 GTAAAGACCAATAGGAGTTGTCATAAG 57.901 37.037 0.00 0.00 38.69 1.73
3702 3791 7.640597 AAACAAGTGGAAAAGCTAGTAGTTT 57.359 32.000 0.00 0.00 0.00 2.66
3709 3798 6.767524 TTGAGAAAACAAGTGGAAAAGCTA 57.232 33.333 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.