Multiple sequence alignment - TraesCS1D01G336000

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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 TraesCS1D01G336000 chr1D 100.000 2174 0 0 1 2174 426179964 426182137 0.000000e+00 4015
1 TraesCS1D01G336000 chr1B 93.673 2181 110 15 1 2172 575866627 575868788 0.000000e+00 3238
2 TraesCS1D01G336000 chr1A 88.694 911 70 13 1282 2174 521323403 521324298 0.000000e+00 1081
3 TraesCS1D01G336000 chr1A 89.110 652 43 11 1 639 521322157 521322793 0.000000e+00 785
4 TraesCS1D01G336000 chr1A 88.030 401 38 5 856 1250 521322941 521323337 1.180000e-127 466


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 TraesCS1D01G336000 chr1D 426179964 426182137 2173 False 4015.000000 4015 100.000000 1 2174 1 chr1D.!!$F1 2173
1 TraesCS1D01G336000 chr1B 575866627 575868788 2161 False 3238.000000 3238 93.673000 1 2172 1 chr1B.!!$F1 2171
2 TraesCS1D01G336000 chr1A 521322157 521324298 2141 False 777.333333 1081 88.611333 1 2174 3 chr1A.!!$F1 2173

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
368 380 0.318614 GTTGTTGTGGTGGGCAATCG 60.319 55.0 0.0 0.0 0.0 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1694 1784 1.112113 GGTCAAGGATCGACAGCCTA 58.888 55.0 3.98 0.0 34.97 3.93 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
153 163 2.613691 GCTTTCCACGGTAAATCTCGA 58.386 47.619 0.00 0.00 0.00 4.04
368 380 0.318614 GTTGTTGTGGTGGGCAATCG 60.319 55.000 0.00 0.00 0.00 3.34
441 453 0.846693 GCTAATGGGTCCATCAGGGT 59.153 55.000 2.62 0.00 35.31 4.34
449 461 1.906574 GGTCCATCAGGGTGTAGACAA 59.093 52.381 0.00 0.00 38.11 3.18
658 679 5.293814 CAGGTCAGCAATGTGATCTCTAAAG 59.706 44.000 0.00 0.00 35.61 1.85
659 680 5.046014 AGGTCAGCAATGTGATCTCTAAAGT 60.046 40.000 0.00 0.00 31.95 2.66
660 681 5.293079 GGTCAGCAATGTGATCTCTAAAGTC 59.707 44.000 0.00 0.00 0.00 3.01
661 682 6.105333 GTCAGCAATGTGATCTCTAAAGTCT 58.895 40.000 0.00 0.00 0.00 3.24
662 683 7.261325 GTCAGCAATGTGATCTCTAAAGTCTA 58.739 38.462 0.00 0.00 0.00 2.59
663 684 7.434897 GTCAGCAATGTGATCTCTAAAGTCTAG 59.565 40.741 0.00 0.00 0.00 2.43
664 685 7.340487 TCAGCAATGTGATCTCTAAAGTCTAGA 59.660 37.037 0.00 0.00 0.00 2.43
712 733 8.873215 AATCCAAAACTGTAGTAGATGTATCG 57.127 34.615 0.00 0.00 0.00 2.92
722 743 3.573110 AGTAGATGTATCGGGTAACAGGC 59.427 47.826 0.00 0.00 39.74 4.85
723 744 1.692519 AGATGTATCGGGTAACAGGCC 59.307 52.381 0.00 0.00 39.74 5.19
734 755 2.757868 GGTAACAGGCCATATGTGCAAA 59.242 45.455 5.01 0.00 0.00 3.68
748 769 2.560542 TGTGCAAACCCATATGACCAAC 59.439 45.455 3.65 0.00 0.00 3.77
750 771 1.469079 GCAAACCCATATGACCAACGC 60.469 52.381 3.65 0.00 0.00 4.84
756 777 1.651987 CATATGACCAACGCGAACCT 58.348 50.000 15.93 0.00 0.00 3.50
757 778 1.327460 CATATGACCAACGCGAACCTG 59.673 52.381 15.93 4.05 0.00 4.00
804 829 5.833667 ACTTATATTCTCCGGATGTGTCTCA 59.166 40.000 3.57 0.00 0.00 3.27
805 830 6.323996 ACTTATATTCTCCGGATGTGTCTCAA 59.676 38.462 3.57 0.00 0.00 3.02
806 831 3.981071 ATTCTCCGGATGTGTCTCAAA 57.019 42.857 3.57 0.00 0.00 2.69
807 832 3.981071 TTCTCCGGATGTGTCTCAAAT 57.019 42.857 3.57 0.00 0.00 2.32
809 834 3.861840 TCTCCGGATGTGTCTCAAATTC 58.138 45.455 3.57 0.00 0.00 2.17
810 835 3.515502 TCTCCGGATGTGTCTCAAATTCT 59.484 43.478 3.57 0.00 0.00 2.40
811 836 3.861840 TCCGGATGTGTCTCAAATTCTC 58.138 45.455 0.00 0.00 0.00 2.87
836 868 5.565592 TCTTAACATTGTATGGCTTGCTG 57.434 39.130 0.00 0.00 33.60 4.41
837 869 2.660189 AACATTGTATGGCTTGCTGC 57.340 45.000 0.00 0.00 41.94 5.25
873 905 8.242729 TGCTAGATGTATGAGATTTCTCTTGA 57.757 34.615 8.91 0.00 43.25 3.02
956 991 3.485394 TCTAATGTTCTGTTTGCCTGCA 58.515 40.909 0.00 0.00 0.00 4.41
975 1010 4.768583 TGCAGCATTTTCAGTTTCCTTTT 58.231 34.783 0.00 0.00 0.00 2.27
976 1011 4.571580 TGCAGCATTTTCAGTTTCCTTTTG 59.428 37.500 0.00 0.00 0.00 2.44
978 1013 4.812626 CAGCATTTTCAGTTTCCTTTTGCT 59.187 37.500 0.00 0.00 38.36 3.91
979 1014 4.812626 AGCATTTTCAGTTTCCTTTTGCTG 59.187 37.500 0.00 0.00 36.62 4.41
980 1015 4.553351 GCATTTTCAGTTTCCTTTTGCTGC 60.553 41.667 0.00 0.00 0.00 5.25
1122 1157 4.888917 AGAAGCTTGAGTTCAGGAAGTAC 58.111 43.478 2.10 0.00 0.00 2.73
1236 1274 5.569413 ACTGTTCATTTTCGTTGAAGACAC 58.431 37.500 0.00 0.00 33.95 3.67
1253 1293 5.024785 AGACACTGCTACCTTTATTAGCC 57.975 43.478 0.00 0.00 41.20 3.93
1329 1407 5.070770 TGCCTGCCTGTTTATTTGTATTG 57.929 39.130 0.00 0.00 0.00 1.90
1435 1515 3.951037 TCTGAAACTTAAAGCAGCCACAA 59.049 39.130 0.00 0.00 0.00 3.33
1542 1623 5.699458 CCTAAAATATTTATGCCGTCTCCGT 59.301 40.000 0.01 0.00 0.00 4.69
1658 1748 9.406113 TGTGGATGACATCATATATCAACAAAA 57.594 29.630 17.08 0.00 36.57 2.44
1744 1834 5.762218 AGAATTAGCATTGGCAAGTAGCTAG 59.238 40.000 22.38 0.00 44.61 3.42
1803 1893 1.618343 TCCTCAGACGCATGAAACTGA 59.382 47.619 0.00 6.45 37.71 3.41
1804 1894 1.728971 CCTCAGACGCATGAAACTGAC 59.271 52.381 0.00 0.00 35.85 3.51
1845 1935 1.708993 TTGCTTCACCCCAGCTCTGT 61.709 55.000 0.00 0.00 38.19 3.41
2021 2111 0.323629 TAAGCTCCGTTGGGGAACAG 59.676 55.000 0.00 0.00 46.61 3.16
2026 2116 2.526046 CCGTTGGGGAACAGGTCCT 61.526 63.158 3.92 0.00 46.92 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 89 4.322801 GGACGGGAATGAAGAAGAAGAAGA 60.323 45.833 0.00 0.00 0.00 2.87
153 163 3.864789 ATTATTCAACGGATCCTGCCT 57.135 42.857 10.75 0.00 0.00 4.75
269 279 1.743394 GAAATTTCGGTTCCAGGCGAT 59.257 47.619 1.68 0.00 0.00 4.58
368 380 1.539929 CGATCAATCTGCTCCCAGGAC 60.540 57.143 0.00 0.00 39.61 3.85
441 453 8.630054 ATGGTAAATAAGCAGTTTTGTCTACA 57.370 30.769 0.00 0.00 39.39 2.74
449 461 9.908152 GTAAACTCAATGGTAAATAAGCAGTTT 57.092 29.630 0.00 0.00 39.39 2.66
541 554 5.426689 AGTCTTAGATTGGTCATTCAGCA 57.573 39.130 0.00 0.00 0.00 4.41
658 679 5.434352 TGTACATATCGCCTTGTCTAGAC 57.566 43.478 16.32 16.32 0.00 2.59
659 680 7.166167 TCTATGTACATATCGCCTTGTCTAGA 58.834 38.462 15.81 4.26 0.00 2.43
660 681 7.379098 TCTATGTACATATCGCCTTGTCTAG 57.621 40.000 15.81 1.92 0.00 2.43
661 682 7.754851 TTCTATGTACATATCGCCTTGTCTA 57.245 36.000 15.81 0.00 0.00 2.59
662 683 6.650427 TTCTATGTACATATCGCCTTGTCT 57.350 37.500 15.81 0.00 0.00 3.41
663 684 7.709269 TTTTCTATGTACATATCGCCTTGTC 57.291 36.000 15.81 0.00 0.00 3.18
664 685 8.677148 ATTTTTCTATGTACATATCGCCTTGT 57.323 30.769 15.81 0.00 0.00 3.16
712 733 1.318576 GCACATATGGCCTGTTACCC 58.681 55.000 3.32 0.00 0.00 3.69
734 755 0.250793 TTCGCGTTGGTCATATGGGT 59.749 50.000 5.77 0.00 0.00 4.51
748 769 0.941542 TCTCCAAAAACAGGTTCGCG 59.058 50.000 0.00 0.00 0.00 5.87
750 771 5.831997 AGAAATTCTCCAAAAACAGGTTCG 58.168 37.500 0.00 0.00 0.00 3.95
784 809 5.614324 TTTGAGACACATCCGGAGAATAT 57.386 39.130 11.34 0.00 0.00 1.28
804 829 9.807649 GCCATACAATGTTAAGATTGAGAATTT 57.192 29.630 26.90 9.88 36.89 1.82
805 830 9.193806 AGCCATACAATGTTAAGATTGAGAATT 57.806 29.630 26.90 10.50 36.89 2.17
806 831 8.757982 AGCCATACAATGTTAAGATTGAGAAT 57.242 30.769 26.90 15.72 36.89 2.40
807 832 8.461222 CAAGCCATACAATGTTAAGATTGAGAA 58.539 33.333 26.90 14.44 36.89 2.87
809 834 6.694411 GCAAGCCATACAATGTTAAGATTGAG 59.306 38.462 26.90 16.84 36.89 3.02
810 835 6.377996 AGCAAGCCATACAATGTTAAGATTGA 59.622 34.615 26.90 13.75 36.89 2.57
811 836 6.474427 CAGCAAGCCATACAATGTTAAGATTG 59.526 38.462 20.52 20.52 38.97 2.67
836 868 8.370493 TCATACATCTAGCAAAAGAATACTGC 57.630 34.615 0.00 0.00 36.29 4.40
837 869 9.755804 TCTCATACATCTAGCAAAAGAATACTG 57.244 33.333 0.00 0.00 0.00 2.74
873 905 3.956848 GGAGCAAAAGGAGGATAGCAAAT 59.043 43.478 0.00 0.00 0.00 2.32
956 991 4.812626 CAGCAAAAGGAAACTGAAAATGCT 59.187 37.500 0.00 0.00 42.68 3.79
975 1010 0.392461 GGGTATGAACTTCCGCAGCA 60.392 55.000 0.00 0.00 0.00 4.41
976 1011 0.392461 TGGGTATGAACTTCCGCAGC 60.392 55.000 0.00 0.00 0.00 5.25
978 1013 0.981183 AGTGGGTATGAACTTCCGCA 59.019 50.000 0.00 0.00 32.64 5.69
979 1014 2.429610 TCTAGTGGGTATGAACTTCCGC 59.570 50.000 0.00 0.00 0.00 5.54
980 1015 4.501571 CCATCTAGTGGGTATGAACTTCCG 60.502 50.000 4.04 0.00 44.79 4.30
1023 1058 5.466728 TGCTGAAACGAGCCTGATAAATATC 59.533 40.000 0.00 0.00 38.28 1.63
1236 1274 4.816925 GGAACAGGCTAATAAAGGTAGCAG 59.183 45.833 5.85 0.82 44.82 4.24
1329 1407 6.963805 GCAGCTCATTTCAGTGATAAACTTAC 59.036 38.462 0.00 0.00 36.83 2.34
1337 1415 2.163815 GCTTGCAGCTCATTTCAGTGAT 59.836 45.455 0.00 0.00 38.45 3.06
1339 1417 1.402456 GGCTTGCAGCTCATTTCAGTG 60.402 52.381 7.85 0.00 41.99 3.66
1362 1440 6.151144 ACAACACTAGATGGGCATTACTTTTC 59.849 38.462 0.00 0.00 0.00 2.29
1370 1448 3.200605 TCATCACAACACTAGATGGGCAT 59.799 43.478 0.00 0.00 39.59 4.40
1435 1515 3.491766 TCAGACCCTCTACCCTTCATT 57.508 47.619 0.00 0.00 0.00 2.57
1620 1701 5.437289 TGTCATCCACACAAAAGAACATC 57.563 39.130 0.00 0.00 0.00 3.06
1694 1784 1.112113 GGTCAAGGATCGACAGCCTA 58.888 55.000 3.98 0.00 34.97 3.93
1744 1834 6.174049 ACCTGACCTTTTAGAATTAGACAGC 58.826 40.000 0.00 0.00 0.00 4.40
1845 1935 2.042464 CCTAGCTCCAGGATGTGCTTA 58.958 52.381 6.99 0.00 40.22 3.09
2026 2116 2.732016 CGTCGTGTTCCTGGACCA 59.268 61.111 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.