Multiple sequence alignment - TraesCS7B01G256100

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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 TraesCS7B01G256100 chr7B 100.000 2891 0 0 1 2891 474641958 474644848 0.000000e+00 5339.0
1 TraesCS7B01G256100 chr7D 95.015 2909 85 24 1 2891 452152880 452155746 0.000000e+00 4514.0
2 TraesCS7B01G256100 chr7A 89.388 1357 83 28 484 1793 545474693 545473351 0.000000e+00 1652.0
3 TraesCS7B01G256100 chr7A 91.585 713 31 14 1823 2516 545473354 545472652 0.000000e+00 957.0
4 TraesCS7B01G256100 chr5D 88.889 117 12 1 1 117 66973937 66974052 3.000000e-30 143.0
5 TraesCS7B01G256100 chr5D 88.235 119 14 0 2 120 307096250 307096132 3.000000e-30 143.0
6 TraesCS7B01G256100 chr4A 87.500 120 14 1 1 120 720375963 720376081 1.400000e-28 137.0
7 TraesCS7B01G256100 chr4A 86.325 117 14 2 10 125 62950359 62950244 3.020000e-25 126.0
8 TraesCS7B01G256100 chr4A 80.172 116 18 4 2778 2888 3140707 3140592 6.640000e-12 82.4
9 TraesCS7B01G256100 chr3D 87.097 124 11 5 8 130 554152900 554153019 5.020000e-28 135.0
10 TraesCS7B01G256100 chr3A 88.496 113 12 1 7 119 686172659 686172548 5.020000e-28 135.0
11 TraesCS7B01G256100 chr2A 87.931 116 13 1 3 117 92474113 92473998 5.020000e-28 135.0
12 TraesCS7B01G256100 chr5A 86.441 118 14 1 1 118 607546765 607546650 8.410000e-26 128.0
13 TraesCS7B01G256100 chr2D 85.185 108 12 4 2651 2756 645286767 645286872 1.100000e-19 108.0
14 TraesCS7B01G256100 chr6A 85.556 90 11 2 2688 2776 603605386 603605474 3.070000e-15 93.5
15 TraesCS7B01G256100 chr6B 79.839 124 25 0 2653 2776 503606576 503606453 1.100000e-14 91.6


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 TraesCS7B01G256100 chr7B 474641958 474644848 2890 False 5339.0 5339 100.0000 1 2891 1 chr7B.!!$F1 2890
1 TraesCS7B01G256100 chr7D 452152880 452155746 2866 False 4514.0 4514 95.0150 1 2891 1 chr7D.!!$F1 2890
2 TraesCS7B01G256100 chr7A 545472652 545474693 2041 True 1304.5 1652 90.4865 484 2516 2 chr7A.!!$R1 2032

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
643 659 0.455633 CCTGCTGCAATGCGAGAAAC 60.456 55.0 3.02 0.0 35.36 2.78 F
1873 1935 0.662619 TTTGTTTGACGCAGCTCCAG 59.337 50.0 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
1885 1947 0.392998 ACCGTGCCTGGTGATCATTC 60.393 55.0 0.0 0.0 41.85 2.67 R
2856 2932 2.649742 AATGGAGAGGGAAGTGGAGA 57.350 50.0 0.0 0.0 0.00 3.71 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
117 119 5.351405 AGTAAAAAGGACCAGAGGGAGTAT 58.649 41.667 0.00 0.00 38.05 2.12
172 174 2.927553 ATGCATCTGAAAAGTTCCGC 57.072 45.000 0.00 0.00 0.00 5.54
201 203 3.764885 ATCTGCGGATTTGTACTTTGC 57.235 42.857 0.90 0.00 0.00 3.68
206 208 3.188460 TGCGGATTTGTACTTTGCTCTTC 59.812 43.478 0.00 0.00 0.00 2.87
212 214 6.652900 GGATTTGTACTTTGCTCTTCTCTTCT 59.347 38.462 0.00 0.00 0.00 2.85
213 215 7.174080 GGATTTGTACTTTGCTCTTCTCTTCTT 59.826 37.037 0.00 0.00 0.00 2.52
214 216 7.484035 TTTGTACTTTGCTCTTCTCTTCTTC 57.516 36.000 0.00 0.00 0.00 2.87
215 217 6.412362 TGTACTTTGCTCTTCTCTTCTTCT 57.588 37.500 0.00 0.00 0.00 2.85
216 218 7.526142 TGTACTTTGCTCTTCTCTTCTTCTA 57.474 36.000 0.00 0.00 0.00 2.10
217 219 7.371936 TGTACTTTGCTCTTCTCTTCTTCTAC 58.628 38.462 0.00 0.00 0.00 2.59
218 220 6.664428 ACTTTGCTCTTCTCTTCTTCTACT 57.336 37.500 0.00 0.00 0.00 2.57
219 221 7.768807 ACTTTGCTCTTCTCTTCTTCTACTA 57.231 36.000 0.00 0.00 0.00 1.82
220 222 8.361169 ACTTTGCTCTTCTCTTCTTCTACTAT 57.639 34.615 0.00 0.00 0.00 2.12
285 288 7.095774 TGTGCAAAGAACTAGTAAACGAGAATC 60.096 37.037 0.00 0.00 0.00 2.52
319 322 7.556733 AAATGCATGTTCATTGAGTTTGTTT 57.443 28.000 0.00 0.00 36.83 2.83
323 326 6.476380 TGCATGTTCATTGAGTTTGTTTTCTC 59.524 34.615 0.00 0.00 0.00 2.87
330 333 7.939782 TCATTGAGTTTGTTTTCTCTGCATAA 58.060 30.769 0.00 0.00 0.00 1.90
406 409 7.314393 TCATTAACATGTGTGGATGATTTGTG 58.686 34.615 0.00 0.00 30.36 3.33
412 415 5.437289 TGTGTGGATGATTTGTGAACTTC 57.563 39.130 0.00 0.00 0.00 3.01
448 451 6.936900 GGCAAATGTTTATCTATGCTAGGAGA 59.063 38.462 0.00 0.00 34.37 3.71
454 457 1.081108 CTATGCTAGGAGACGGCGC 60.081 63.158 6.90 0.00 36.89 6.53
514 517 3.370840 TTCACTGGATTCCCTTCATGG 57.629 47.619 0.00 0.00 0.00 3.66
637 653 4.789075 GCACCCTGCTGCAATGCG 62.789 66.667 14.81 0.00 40.96 4.73
643 659 0.455633 CCTGCTGCAATGCGAGAAAC 60.456 55.000 3.02 0.00 35.36 2.78
656 673 0.890996 GAGAAACCTGCACCCACCAG 60.891 60.000 0.00 0.00 0.00 4.00
668 685 1.570501 ACCCACCAGGACATGCATTAT 59.429 47.619 0.00 0.00 39.89 1.28
799 819 4.954970 CAGGTGGGCAAGTGGCGT 62.955 66.667 0.00 0.00 46.16 5.68
850 870 1.003442 CCACCCATCCTCCTCCTCA 59.997 63.158 0.00 0.00 0.00 3.86
852 872 1.132721 CCACCCATCCTCCTCCTCATA 60.133 57.143 0.00 0.00 0.00 2.15
853 873 2.255406 CACCCATCCTCCTCCTCATAG 58.745 57.143 0.00 0.00 0.00 2.23
854 874 1.274712 CCCATCCTCCTCCTCATAGC 58.725 60.000 0.00 0.00 0.00 2.97
855 875 1.274712 CCATCCTCCTCCTCATAGCC 58.725 60.000 0.00 0.00 0.00 3.93
912 942 4.329545 ACCGCACAACCAGCCGAT 62.330 61.111 0.00 0.00 0.00 4.18
1158 1207 1.536907 TCCCTCCCCAAAGTACGCA 60.537 57.895 0.00 0.00 0.00 5.24
1266 1322 1.592669 CCTGGTCCGTGCGATGATC 60.593 63.158 0.00 0.00 0.00 2.92
1450 1506 3.737172 GCGCTCCACGGCATGTTT 61.737 61.111 0.00 0.00 43.93 2.83
1573 1629 1.137872 GACTGGATGCTCGTTGGAGAT 59.862 52.381 0.00 0.00 43.27 2.75
1601 1657 5.011023 CCCTGGAAGTAAGCAAATCAAACTT 59.989 40.000 0.00 0.00 33.26 2.66
1772 1828 8.303156 CCAATAGTCTAAGATCATGTCCTACAG 58.697 40.741 0.00 0.00 0.00 2.74
1784 1840 2.159240 TGTCCTACAGCTACAATCAGCG 60.159 50.000 0.00 0.00 46.52 5.18
1820 1876 1.064803 TGAACACGCACAAACACATCC 59.935 47.619 0.00 0.00 0.00 3.51
1844 1900 8.893727 TCCTATAAGTACCAAGTTACTAACGTC 58.106 37.037 0.00 0.00 36.23 4.34
1845 1901 8.897752 CCTATAAGTACCAAGTTACTAACGTCT 58.102 37.037 0.00 0.00 36.23 4.18
1846 1902 9.928236 CTATAAGTACCAAGTTACTAACGTCTC 57.072 37.037 0.00 0.00 36.23 3.36
1873 1935 0.662619 TTTGTTTGACGCAGCTCCAG 59.337 50.000 0.00 0.00 0.00 3.86
1876 1938 1.004560 TTTGACGCAGCTCCAGGAG 60.005 57.895 12.81 12.81 0.00 3.69
2028 2090 4.665833 TGTGCTGTACTTGTCAAGTAGT 57.334 40.909 22.95 3.42 44.16 2.73
2294 2365 3.691118 TCTTTCCATCAATGCTGCAGTAC 59.309 43.478 16.64 0.00 0.00 2.73
2557 2633 4.467438 CCCTCAACCTAAAATCTTGGCAAT 59.533 41.667 0.00 0.00 0.00 3.56
2608 2684 8.451687 TTCATGAAGAAAATTAGATTTGTGCG 57.548 30.769 3.38 0.00 32.05 5.34
2614 2690 4.600012 AAATTAGATTTGTGCGACTCCG 57.400 40.909 0.00 0.00 39.16 4.63
2665 2741 2.172851 AACCATTGCAAAGTGGCATG 57.827 45.000 17.27 3.20 44.48 4.06
2667 2743 0.322322 CCATTGCAAAGTGGCATGGT 59.678 50.000 1.71 0.00 44.48 3.55
2683 2759 0.823356 TGGTTTGCTGCCAAGAGGAC 60.823 55.000 0.00 0.00 36.89 3.85
2685 2761 1.228552 TTTGCTGCCAAGAGGACCC 60.229 57.895 0.00 0.00 36.89 4.46
2746 2822 7.288852 AGTTATCATCAGCAAGGTAGTACTCAT 59.711 37.037 0.00 0.00 0.00 2.90
2768 2844 3.799366 TGTTGTAGTTGTGTCCGTTGAT 58.201 40.909 0.00 0.00 0.00 2.57
2809 2885 0.457851 GTGTGCCAGCGAGTCTATCT 59.542 55.000 0.00 0.00 0.00 1.98
2827 2903 3.664551 TCTCGGATTAGAACTCCTCCA 57.335 47.619 0.00 0.00 0.00 3.86
2836 2912 7.255977 CGGATTAGAACTCCTCCATTAGATCAA 60.256 40.741 0.00 0.00 0.00 2.57
2856 2932 5.139727 TCAACCCTTGATGTTCAGAATGTT 58.860 37.500 0.00 0.00 33.71 2.71
2878 2954 1.916181 TCCACTTCCCTCTCCATTTCC 59.084 52.381 0.00 0.00 0.00 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 97 5.189145 TCATACTCCCTCTGGTCCTTTTTAC 59.811 44.000 0.00 0.00 0.00 2.01
102 104 3.375699 TCTTTCATACTCCCTCTGGTCC 58.624 50.000 0.00 0.00 0.00 4.46
181 183 3.347216 AGCAAAGTACAAATCCGCAGAT 58.653 40.909 0.00 0.00 0.00 2.90
182 184 2.742053 GAGCAAAGTACAAATCCGCAGA 59.258 45.455 0.00 0.00 0.00 4.26
183 185 2.744202 AGAGCAAAGTACAAATCCGCAG 59.256 45.455 0.00 0.00 0.00 5.18
201 203 9.119418 TGTGATCATAGTAGAAGAAGAGAAGAG 57.881 37.037 0.00 0.00 0.00 2.85
206 208 7.432059 TGCATGTGATCATAGTAGAAGAAGAG 58.568 38.462 0.00 0.00 32.47 2.85
212 214 6.758416 GTGAACTGCATGTGATCATAGTAGAA 59.242 38.462 13.91 0.00 32.47 2.10
213 215 6.097412 AGTGAACTGCATGTGATCATAGTAGA 59.903 38.462 13.91 0.00 32.47 2.59
214 216 6.279123 AGTGAACTGCATGTGATCATAGTAG 58.721 40.000 0.00 3.74 32.47 2.57
215 217 6.225981 AGTGAACTGCATGTGATCATAGTA 57.774 37.500 0.00 0.00 32.47 1.82
216 218 5.095145 AGTGAACTGCATGTGATCATAGT 57.905 39.130 0.00 0.00 32.47 2.12
217 219 5.729732 GCAAGTGAACTGCATGTGATCATAG 60.730 44.000 0.00 0.00 32.47 2.23
218 220 4.095334 GCAAGTGAACTGCATGTGATCATA 59.905 41.667 0.00 0.00 32.47 2.15
219 221 3.119602 GCAAGTGAACTGCATGTGATCAT 60.120 43.478 0.00 0.00 34.21 2.45
220 222 2.227149 GCAAGTGAACTGCATGTGATCA 59.773 45.455 0.00 0.00 0.00 2.92
285 288 6.730960 ATGAACATGCATTTTTAGCTTTGG 57.269 33.333 0.00 0.00 0.00 3.28
319 322 3.701205 TCTTGTGGCTTATGCAGAGAA 57.299 42.857 2.72 0.00 41.91 2.87
323 326 5.565592 TTGTATTCTTGTGGCTTATGCAG 57.434 39.130 2.72 0.00 41.91 4.41
386 389 5.302568 AGTTCACAAATCATCCACACATGTT 59.697 36.000 0.00 0.00 0.00 2.71
406 409 2.091541 TGCCATCATTTCGGGAAGTTC 58.908 47.619 0.00 0.00 0.00 3.01
412 415 2.965572 ACATTTGCCATCATTTCGGG 57.034 45.000 0.00 0.00 0.00 5.14
454 457 0.179134 CTAGCAAACGAGTCCGGGAG 60.179 60.000 0.00 0.00 40.78 4.30
514 517 9.235537 GAAGAAAATACCTCATTCGAGTAGTAC 57.764 37.037 0.00 0.00 37.59 2.73
637 653 0.890996 CTGGTGGGTGCAGGTTTCTC 60.891 60.000 0.00 0.00 0.00 2.87
643 659 2.910737 ATGTCCTGGTGGGTGCAGG 61.911 63.158 0.00 0.00 37.45 4.85
656 673 7.786178 TCTTTGTGTAGTATAATGCATGTCC 57.214 36.000 0.00 0.00 0.00 4.02
737 757 9.586435 CTTCACTCTTTGTTTTCCATAGTTTTT 57.414 29.630 0.00 0.00 0.00 1.94
738 758 8.966868 TCTTCACTCTTTGTTTTCCATAGTTTT 58.033 29.630 0.00 0.00 0.00 2.43
739 759 8.519799 TCTTCACTCTTTGTTTTCCATAGTTT 57.480 30.769 0.00 0.00 0.00 2.66
740 760 8.519799 TTCTTCACTCTTTGTTTTCCATAGTT 57.480 30.769 0.00 0.00 0.00 2.24
741 761 8.406297 GTTTCTTCACTCTTTGTTTTCCATAGT 58.594 33.333 0.00 0.00 0.00 2.12
753 773 4.273318 ACTTGCCTGTTTCTTCACTCTTT 58.727 39.130 0.00 0.00 0.00 2.52
799 819 2.289444 GCGGATGCTGCCTATAAAGGTA 60.289 50.000 0.00 0.00 40.90 3.08
850 870 1.152440 CCGTGGGAGAGGAGGCTAT 60.152 63.158 0.00 0.00 0.00 2.97
854 874 3.775654 GTGCCGTGGGAGAGGAGG 61.776 72.222 0.00 0.00 0.00 4.30
855 875 2.997315 TGTGCCGTGGGAGAGGAG 60.997 66.667 0.00 0.00 0.00 3.69
912 942 1.715862 CGGTCGCTAGCTAGCTGTCA 61.716 60.000 36.02 18.73 46.85 3.58
1158 1207 0.326713 GGGGAAGGTAGGAGAAGGCT 60.327 60.000 0.00 0.00 0.00 4.58
1254 1310 1.064134 TCAGTCGATCATCGCACGG 59.936 57.895 0.80 3.06 40.21 4.94
1410 1466 3.537874 GCAGGGCCTCGTATCCGT 61.538 66.667 0.95 0.00 35.01 4.69
1414 1470 3.227276 CGGAGCAGGGCCTCGTAT 61.227 66.667 0.95 0.00 32.57 3.06
1517 1573 2.769652 TAGGTGGGCACGTACTCGGT 62.770 60.000 0.00 0.00 41.85 4.69
1573 1629 1.440618 TTGCTTACTTCCAGGGGACA 58.559 50.000 0.00 0.00 0.00 4.02
1601 1657 3.701205 TCTGCAAGAACTATGGCAAGA 57.299 42.857 0.00 0.00 42.31 3.02
1745 1801 6.107901 AGGACATGATCTTAGACTATTGGC 57.892 41.667 0.00 0.00 0.00 4.52
1752 1808 5.782893 AGCTGTAGGACATGATCTTAGAC 57.217 43.478 0.00 0.00 0.00 2.59
1772 1828 1.996292 TGTCAGACGCTGATTGTAGC 58.004 50.000 11.73 0.00 42.73 3.58
1784 1840 5.377358 CGTGTTCATCTTCATTTGTCAGAC 58.623 41.667 0.00 0.00 0.00 3.51
1820 1876 9.928236 GAGACGTTAGTAACTTGGTACTTATAG 57.072 37.037 11.17 0.00 35.85 1.31
1844 1900 5.356882 TGCGTCAAACAAATTAAGAGGAG 57.643 39.130 0.00 0.00 0.00 3.69
1845 1901 4.320202 GCTGCGTCAAACAAATTAAGAGGA 60.320 41.667 0.00 0.00 0.00 3.71
1846 1902 3.914364 GCTGCGTCAAACAAATTAAGAGG 59.086 43.478 0.00 0.00 0.00 3.69
1873 1935 2.805099 GTGATCATTCGGAAGATGCTCC 59.195 50.000 0.00 0.00 41.60 4.70
1876 1938 2.547211 CTGGTGATCATTCGGAAGATGC 59.453 50.000 0.00 0.00 41.60 3.91
1885 1947 0.392998 ACCGTGCCTGGTGATCATTC 60.393 55.000 0.00 0.00 41.85 2.67
2028 2090 9.581099 GAAACATGGAAGAAACTAAGAACAAAA 57.419 29.630 0.00 0.00 0.00 2.44
2082 2145 2.126189 GGCCGTACGTGACCTGTC 60.126 66.667 15.21 0.00 0.00 3.51
2294 2365 3.284323 ACAAGACACAGCACGTACTAG 57.716 47.619 0.00 0.00 0.00 2.57
2604 2680 2.273370 TATGAACTTCGGAGTCGCAC 57.727 50.000 0.00 0.00 34.21 5.34
2608 2684 8.649973 ATCTACAAAATATGAACTTCGGAGTC 57.350 34.615 0.00 0.00 34.21 3.36
2665 2741 1.527433 GGTCCTCTTGGCAGCAAACC 61.527 60.000 0.00 0.00 0.00 3.27
2667 2743 1.228552 GGGTCCTCTTGGCAGCAAA 60.229 57.895 0.00 0.00 0.00 3.68
2683 2759 3.427503 GCGTTTGTGAAGACCATATTGGG 60.428 47.826 0.00 0.00 43.37 4.12
2685 2761 3.727673 CGGCGTTTGTGAAGACCATATTG 60.728 47.826 0.00 0.00 0.00 1.90
2746 2822 3.597255 TCAACGGACACAACTACAACAA 58.403 40.909 0.00 0.00 0.00 2.83
2809 2885 5.702266 TCTAATGGAGGAGTTCTAATCCGA 58.298 41.667 0.00 0.00 42.02 4.55
2813 2889 7.202139 GGGTTGATCTAATGGAGGAGTTCTAAT 60.202 40.741 0.00 0.00 0.00 1.73
2836 2912 4.990526 AGAACATTCTGAACATCAAGGGT 58.009 39.130 0.00 0.00 35.89 4.34
2856 2932 2.649742 AATGGAGAGGGAAGTGGAGA 57.350 50.000 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.