Multiple sequence alignment - TraesCS7D01G202800

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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 TraesCS7D01G202800 chr7D 100.000 3797 0 0 1 3797 161290247 161286451 0.000000e+00 7012.0
1 TraesCS7D01G202800 chr7A 96.070 3028 102 7 775 3797 162529326 162526311 0.000000e+00 4916.0
2 TraesCS7D01G202800 chr7A 76.391 665 151 4 103 766 682989123 682988464 1.680000e-93 353.0
3 TraesCS7D01G202800 chr7A 95.349 43 2 0 1 43 162529362 162529320 6.810000e-08 69.4
4 TraesCS7D01G202800 chr7B 94.491 2142 94 11 775 2907 123437811 123435685 0.000000e+00 3280.0
5 TraesCS7D01G202800 chr7B 97.674 43 1 0 1 43 123437847 123437805 1.460000e-09 75.0
6 TraesCS7D01G202800 chr5D 98.455 712 11 0 56 767 302345835 302345124 0.000000e+00 1254.0
7 TraesCS7D01G202800 chr5D 78.881 715 143 7 55 766 543877274 543877983 9.540000e-131 477.0
8 TraesCS7D01G202800 chr4D 97.436 702 18 0 66 767 359738437 359739138 0.000000e+00 1197.0
9 TraesCS7D01G202800 chr6A 84.292 713 107 5 56 767 539700297 539699589 0.000000e+00 691.0
10 TraesCS7D01G202800 chr6D 98.365 367 6 0 56 422 450849040 450848674 0.000000e+00 645.0
11 TraesCS7D01G202800 chr2B 89.355 310 33 0 54 363 237626105 237625796 1.280000e-104 390.0
12 TraesCS7D01G202800 chr3B 89.305 187 19 1 73 259 250567733 250567918 2.280000e-57 233.0
13 TraesCS7D01G202800 chr2D 77.686 363 75 5 56 415 650590341 650590700 2.300000e-52 217.0


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 TraesCS7D01G202800 chr7D 161286451 161290247 3796 True 7012.0 7012 100.0000 1 3797 1 chr7D.!!$R1 3796
1 TraesCS7D01G202800 chr7A 162526311 162529362 3051 True 2492.7 4916 95.7095 1 3797 2 chr7A.!!$R2 3796
2 TraesCS7D01G202800 chr7A 682988464 682989123 659 True 353.0 353 76.3910 103 766 1 chr7A.!!$R1 663
3 TraesCS7D01G202800 chr7B 123435685 123437847 2162 True 1677.5 3280 96.0825 1 2907 2 chr7B.!!$R1 2906
4 TraesCS7D01G202800 chr5D 302345124 302345835 711 True 1254.0 1254 98.4550 56 767 1 chr5D.!!$R1 711
5 TraesCS7D01G202800 chr5D 543877274 543877983 709 False 477.0 477 78.8810 55 766 1 chr5D.!!$F1 711
6 TraesCS7D01G202800 chr4D 359738437 359739138 701 False 1197.0 1197 97.4360 66 767 1 chr4D.!!$F1 701
7 TraesCS7D01G202800 chr6A 539699589 539700297 708 True 691.0 691 84.2920 56 767 1 chr6A.!!$R1 711

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
376 377 1.202976 AGGTCATCTGCAAAAGCCAGT 60.203 47.619 0.0 0.0 0.00 4.00 F
1611 1621 0.314302 CTGGTTCAGACTCGGACGTT 59.686 55.000 0.0 0.0 32.44 3.99 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1650 1660 0.178992 CCCTCCCACTCTTGCACAAA 60.179 55.0 0.0 0.0 0.00 2.83 R
3035 3045 0.101759 GCGCTCATGGATGCAAACAT 59.898 50.0 0.0 0.0 39.98 2.71 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
34 35 6.016360 TCGATTCTCTCTGGAGATTGAAGATC 60.016 42.308 0.48 0.00 46.51 2.75
36 37 3.888323 TCTCTCTGGAGATTGAAGATCGG 59.112 47.826 0.48 0.00 42.95 4.18
37 38 3.888323 CTCTCTGGAGATTGAAGATCGGA 59.112 47.826 0.48 0.00 41.86 4.55
38 39 4.281657 TCTCTGGAGATTGAAGATCGGAA 58.718 43.478 0.00 0.00 31.41 4.30
39 40 4.340666 TCTCTGGAGATTGAAGATCGGAAG 59.659 45.833 0.00 0.00 31.41 3.46
40 41 3.386078 TCTGGAGATTGAAGATCGGAAGG 59.614 47.826 0.00 0.00 0.00 3.46
41 42 3.374764 TGGAGATTGAAGATCGGAAGGA 58.625 45.455 0.00 0.00 0.00 3.36
42 43 3.774766 TGGAGATTGAAGATCGGAAGGAA 59.225 43.478 0.00 0.00 0.00 3.36
43 44 4.141846 TGGAGATTGAAGATCGGAAGGAAG 60.142 45.833 0.00 0.00 0.00 3.46
44 45 4.100189 GGAGATTGAAGATCGGAAGGAAGA 59.900 45.833 0.00 0.00 0.00 2.87
45 46 5.275067 AGATTGAAGATCGGAAGGAAGAG 57.725 43.478 0.00 0.00 0.00 2.85
46 47 4.959210 AGATTGAAGATCGGAAGGAAGAGA 59.041 41.667 0.00 0.00 0.00 3.10
47 48 5.423610 AGATTGAAGATCGGAAGGAAGAGAA 59.576 40.000 0.00 0.00 0.00 2.87
48 49 4.727507 TGAAGATCGGAAGGAAGAGAAG 57.272 45.455 0.00 0.00 0.00 2.85
49 50 3.449018 TGAAGATCGGAAGGAAGAGAAGG 59.551 47.826 0.00 0.00 0.00 3.46
50 51 3.390175 AGATCGGAAGGAAGAGAAGGA 57.610 47.619 0.00 0.00 0.00 3.36
51 52 3.714144 AGATCGGAAGGAAGAGAAGGAA 58.286 45.455 0.00 0.00 0.00 3.36
52 53 4.294347 AGATCGGAAGGAAGAGAAGGAAT 58.706 43.478 0.00 0.00 0.00 3.01
53 54 4.719273 AGATCGGAAGGAAGAGAAGGAATT 59.281 41.667 0.00 0.00 0.00 2.17
376 377 1.202976 AGGTCATCTGCAAAAGCCAGT 60.203 47.619 0.00 0.00 0.00 4.00
767 770 4.081697 TCGTGAAACTTGCATGATCTAGGA 60.082 41.667 6.60 4.57 31.75 2.94
768 771 4.631377 CGTGAAACTTGCATGATCTAGGAA 59.369 41.667 6.60 0.00 31.75 3.36
769 772 5.220548 CGTGAAACTTGCATGATCTAGGAAG 60.221 44.000 6.60 14.36 38.87 3.46
770 773 5.877012 GTGAAACTTGCATGATCTAGGAAGA 59.123 40.000 20.03 1.93 36.77 2.87
771 774 6.372659 GTGAAACTTGCATGATCTAGGAAGAA 59.627 38.462 20.03 5.82 36.77 2.52
772 775 6.596888 TGAAACTTGCATGATCTAGGAAGAAG 59.403 38.462 20.03 5.83 36.77 2.85
773 776 5.946942 ACTTGCATGATCTAGGAAGAAGA 57.053 39.130 20.03 0.00 36.77 2.87
791 794 4.471747 AGAAGAGAAGGAAATGAGGTACCC 59.528 45.833 8.74 0.32 0.00 3.69
831 834 2.354003 CCGGATTGCATGAAAGCCTTTT 60.354 45.455 18.60 0.00 33.29 2.27
877 887 2.092212 CCAGCCCATTCTGAGTAACCAT 60.092 50.000 0.00 0.00 36.19 3.55
878 888 3.209410 CAGCCCATTCTGAGTAACCATC 58.791 50.000 0.00 0.00 36.19 3.51
879 889 2.158900 AGCCCATTCTGAGTAACCATCG 60.159 50.000 0.00 0.00 0.00 3.84
880 890 2.213499 CCCATTCTGAGTAACCATCGC 58.787 52.381 0.00 0.00 0.00 4.58
881 891 2.213499 CCATTCTGAGTAACCATCGCC 58.787 52.381 0.00 0.00 0.00 5.54
882 892 2.419990 CCATTCTGAGTAACCATCGCCA 60.420 50.000 0.00 0.00 0.00 5.69
883 893 2.380084 TTCTGAGTAACCATCGCCAC 57.620 50.000 0.00 0.00 0.00 5.01
884 894 1.557099 TCTGAGTAACCATCGCCACT 58.443 50.000 0.00 0.00 0.00 4.00
885 895 1.204704 TCTGAGTAACCATCGCCACTG 59.795 52.381 0.00 0.00 0.00 3.66
1380 1390 1.904032 CTTCCTCTGTGCCTCCCTC 59.096 63.158 0.00 0.00 0.00 4.30
1426 1436 4.336713 AGACTTCTGTTTTCAACAAGCTCC 59.663 41.667 0.00 0.00 41.61 4.70
1428 1438 5.437060 ACTTCTGTTTTCAACAAGCTCCTA 58.563 37.500 0.00 0.00 41.61 2.94
1611 1621 0.314302 CTGGTTCAGACTCGGACGTT 59.686 55.000 0.00 0.00 32.44 3.99
1629 1639 3.487202 CGCCCGGATGTTGTCACG 61.487 66.667 0.73 0.00 0.00 4.35
1638 1648 1.937223 GATGTTGTCACGGTGAACACA 59.063 47.619 20.08 20.08 32.62 3.72
1641 1651 1.326548 GTTGTCACGGTGAACACAGTC 59.673 52.381 13.23 0.00 37.63 3.51
1650 1660 0.173935 TGAACACAGTCGTGAACGGT 59.826 50.000 2.59 0.00 46.80 4.83
1738 1748 1.269448 GACATGCACCCGACACATTTT 59.731 47.619 0.00 0.00 0.00 1.82
1801 1811 2.347114 CCATGGCGTGTGAGGTGA 59.653 61.111 0.00 0.00 0.00 4.02
1984 1994 0.473755 TCTGGTTCAGGCTTTGCTCA 59.526 50.000 0.00 0.00 31.51 4.26
2036 2046 6.302269 AGTTGTTCCATGAGATGAAAGAAGT 58.698 36.000 0.00 0.00 0.00 3.01
2038 2048 8.105829 AGTTGTTCCATGAGATGAAAGAAGTAT 58.894 33.333 0.00 0.00 0.00 2.12
2075 2085 9.643693 AAAGAAAACCATGTATTTCATCATGAC 57.356 29.630 17.64 0.00 42.52 3.06
2127 2137 2.747460 GCTTGCTCCATGGCGTCA 60.747 61.111 6.96 0.00 34.52 4.35
2433 2443 3.764885 AAAATAGATGAGGCGTTGCAC 57.235 42.857 0.00 0.00 0.00 4.57
2628 2638 2.987149 ACTTCGCGATAAGAATATGCCG 59.013 45.455 10.88 0.00 0.00 5.69
2676 2686 1.194781 TGAGGGAAGAGAGGTGCACC 61.195 60.000 29.22 29.22 0.00 5.01
3035 3045 6.231211 GGTACTCATCAGTTCCTTTTTCTGA 58.769 40.000 0.00 0.00 41.43 3.27
3105 3115 1.342496 TCAGTTCTCAGCTGGTCAGTG 59.658 52.381 15.13 10.66 34.89 3.66
3144 3154 2.984471 CAGCAACACATTCTTGACATGC 59.016 45.455 0.00 0.00 0.00 4.06
3145 3155 1.980844 GCAACACATTCTTGACATGCG 59.019 47.619 0.00 0.00 0.00 4.73
3149 3159 1.063006 CATTCTTGACATGCGGCCG 59.937 57.895 24.05 24.05 0.00 6.13
3165 3175 2.213499 GGCCGTCTACATCAAATGAGG 58.787 52.381 0.00 0.00 0.00 3.86
3175 3185 7.930865 GTCTACATCAAATGAGGCTCTTATTCT 59.069 37.037 16.72 0.00 0.00 2.40
3265 3278 2.362397 TCGTATGATGGAAGAGAGGTGC 59.638 50.000 0.00 0.00 0.00 5.01
3310 3323 7.083062 TGATATTCTTATGGAATGGCTGACT 57.917 36.000 6.15 0.00 43.68 3.41
3499 3513 5.402398 GTGTAATTTGTGATGGAAAGAGCC 58.598 41.667 0.00 0.00 0.00 4.70
3501 3515 2.270352 TTTGTGATGGAAAGAGCCGT 57.730 45.000 0.00 0.00 0.00 5.68
3502 3516 1.522668 TTGTGATGGAAAGAGCCGTG 58.477 50.000 0.00 0.00 0.00 4.94
3507 3521 0.400213 ATGGAAAGAGCCGTGTTGGA 59.600 50.000 0.00 0.00 42.00 3.53
3518 3532 2.554893 GCCGTGTTGGATAGAAAACCAA 59.445 45.455 0.00 0.00 42.78 3.67
3528 3542 4.396478 GGATAGAAAACCAACTCCTGAAGC 59.604 45.833 0.00 0.00 0.00 3.86
3547 3561 5.310594 TGAAGCCTGGCTGACCTAATATAAT 59.689 40.000 24.16 0.31 39.62 1.28
3550 3564 4.265073 CCTGGCTGACCTAATATAATGGC 58.735 47.826 0.00 0.00 36.63 4.40
3572 3586 2.019984 GCCCCTGTGATCAGAATTGTC 58.980 52.381 0.00 0.00 43.76 3.18
3605 3619 2.616960 TCATAAACAGCCAGCAGTACG 58.383 47.619 0.00 0.00 0.00 3.67
3672 3686 5.247862 ACATATGTGATTTGTGACAGCTGA 58.752 37.500 23.35 0.00 0.00 4.26
3683 3697 4.265893 TGTGACAGCTGACCAAGTTTTTA 58.734 39.130 23.35 0.00 0.00 1.52
3688 3702 3.983344 CAGCTGACCAAGTTTTTATGTGC 59.017 43.478 8.42 0.00 0.00 4.57
3709 3724 0.606401 AATCAGGGCACTGTTGGTCG 60.606 55.000 17.28 0.00 45.14 4.79
3720 3735 3.781307 TTGGTCGGGGGCTCATCG 61.781 66.667 0.00 0.00 0.00 3.84
3756 3771 0.969917 TTTGCCGGCACCTGCATTAT 60.970 50.000 32.95 0.00 44.36 1.28
3767 3782 5.300286 GGCACCTGCATTATAACTGAAGAAT 59.700 40.000 0.00 0.00 44.36 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 4.479786 AGAATTCCTTCTCTTCCTTCCG 57.520 45.455 0.65 0.00 37.09 4.30
376 377 1.560004 CTTTCGCGTGCAGAGAAGCA 61.560 55.000 5.77 0.00 39.71 3.91
443 444 1.611491 CAATGGCGTGTACTTGGGTTT 59.389 47.619 0.00 0.00 0.00 3.27
767 770 6.056090 GGTACCTCATTTCCTTCTCTTCTT 57.944 41.667 4.06 0.00 0.00 2.52
768 771 5.685520 GGTACCTCATTTCCTTCTCTTCT 57.314 43.478 4.06 0.00 0.00 2.85
791 794 0.179103 GCCCAAAATGGATCAAGCCG 60.179 55.000 0.00 0.00 40.96 5.52
831 834 6.423182 ACTGTTGGGCTATTTAGATAAAGCA 58.577 36.000 0.00 0.00 0.00 3.91
834 837 6.964464 TGGACTGTTGGGCTATTTAGATAAA 58.036 36.000 0.00 0.00 0.00 1.40
1239 1249 3.591835 GAGAGGAGGAGCGCGAGG 61.592 72.222 12.10 0.00 0.00 4.63
1240 1250 3.591835 GGAGAGGAGGAGCGCGAG 61.592 72.222 12.10 0.00 0.00 5.03
1297 1307 1.551329 GGATAAGAGGGCGGAGAGGAT 60.551 57.143 0.00 0.00 0.00 3.24
1611 1621 2.047655 GTGACAACATCCGGGCGA 60.048 61.111 0.00 0.00 0.00 5.54
1629 1639 0.575390 CGTTCACGACTGTGTTCACC 59.425 55.000 0.00 0.00 46.49 4.02
1638 1648 0.741574 TGCACAAACCGTTCACGACT 60.742 50.000 0.00 0.00 43.02 4.18
1641 1651 0.375454 TCTTGCACAAACCGTTCACG 59.625 50.000 0.00 0.00 39.44 4.35
1650 1660 0.178992 CCCTCCCACTCTTGCACAAA 60.179 55.000 0.00 0.00 0.00 2.83
1738 1748 0.394938 TCGGCCAAGCAGTTGTAAGA 59.605 50.000 2.24 0.00 30.95 2.10
1801 1811 0.649992 TCCCTCTCCATCCTCCCAAT 59.350 55.000 0.00 0.00 0.00 3.16
1950 1960 0.969149 CCAGAGTGCTGTAGGTCACA 59.031 55.000 0.00 0.00 40.63 3.58
1984 1994 3.056607 GCCACATCCACATTTTTAGTGCT 60.057 43.478 0.00 0.00 35.69 4.40
2030 2040 2.969821 TGGTGGTTGCCATACTTCTT 57.030 45.000 0.00 0.00 35.28 2.52
2036 2046 3.070302 GGTTTTCTTTGGTGGTTGCCATA 59.930 43.478 0.00 0.00 38.48 2.74
2038 2048 1.208293 GGTTTTCTTTGGTGGTTGCCA 59.792 47.619 0.00 0.00 36.62 4.92
2075 2085 1.080569 GCTTGTGCCAATCCCAACG 60.081 57.895 0.00 0.00 0.00 4.10
2118 2128 1.856802 TCTTCATCGATGACGCCATG 58.143 50.000 27.28 12.92 36.36 3.66
2127 2137 0.835941 AGCCTGCCTTCTTCATCGAT 59.164 50.000 0.00 0.00 0.00 3.59
2433 2443 6.000219 AGATTCATCCATAGACCGGAAAATG 59.000 40.000 9.46 8.10 35.77 2.32
2628 2638 2.568623 TCAGTTCAAAGGCCTTCTCC 57.431 50.000 20.79 7.37 0.00 3.71
2676 2686 3.370840 TCAATGGTCAAGGAATCAGGG 57.629 47.619 0.00 0.00 0.00 4.45
2806 2816 4.357918 AGACTACTTCATTGTGCCAACT 57.642 40.909 0.00 0.00 0.00 3.16
2821 2831 6.094048 TGCCTGCATAATTTGAGAAAGACTAC 59.906 38.462 0.00 0.00 0.00 2.73
2841 2851 2.671396 GCTGAAGCAAAATTCATGCCTG 59.329 45.455 11.39 4.59 44.91 4.85
3035 3045 0.101759 GCGCTCATGGATGCAAACAT 59.898 50.000 0.00 0.00 39.98 2.71
3090 3100 2.291865 ACTATCCACTGACCAGCTGAGA 60.292 50.000 17.39 0.31 0.00 3.27
3105 3115 3.132289 TGCTGCCTGTTACACTACTATCC 59.868 47.826 0.00 0.00 0.00 2.59
3144 3154 1.860950 CTCATTTGATGTAGACGGCCG 59.139 52.381 26.86 26.86 0.00 6.13
3145 3155 2.213499 CCTCATTTGATGTAGACGGCC 58.787 52.381 0.00 0.00 0.00 6.13
3149 3159 7.930865 AGAATAAGAGCCTCATTTGATGTAGAC 59.069 37.037 0.00 0.00 0.00 2.59
3193 3203 7.753132 GGCATATTCTATACGAAGTCTCTTCAG 59.247 40.741 9.61 5.46 43.93 3.02
3265 3278 0.249120 TGGCCACGTAATCTGGAGTG 59.751 55.000 0.00 0.00 0.00 3.51
3310 3323 5.532032 TCATCTTTCTGTTTCAGCAATGACA 59.468 36.000 0.00 0.00 0.00 3.58
3472 3486 7.214467 TCTTTCCATCACAAATTACACCTTC 57.786 36.000 0.00 0.00 0.00 3.46
3507 3521 4.043435 AGGCTTCAGGAGTTGGTTTTCTAT 59.957 41.667 0.00 0.00 0.00 1.98
3518 3532 1.537397 TCAGCCAGGCTTCAGGAGT 60.537 57.895 12.86 0.00 36.40 3.85
3528 3542 4.018960 AGCCATTATATTAGGTCAGCCAGG 60.019 45.833 0.00 0.00 37.19 4.45
3547 3561 2.934932 TGATCACAGGGGCAGCCA 60.935 61.111 15.19 0.00 0.00 4.75
3550 3564 2.022195 CAATTCTGATCACAGGGGCAG 58.978 52.381 0.00 0.00 43.60 4.85
3590 3604 0.105964 TGAACGTACTGCTGGCTGTT 59.894 50.000 10.10 0.00 0.00 3.16
3605 3619 7.934120 AGAATTCAGTATGGCCTATAACTGAAC 59.066 37.037 28.70 21.66 39.43 3.18
3672 3686 6.071391 CCCTGATTAGCACATAAAAACTTGGT 60.071 38.462 0.00 0.00 0.00 3.67
3688 3702 2.359900 GACCAACAGTGCCCTGATTAG 58.640 52.381 2.19 0.00 41.50 1.73
3709 3724 2.211468 AAAGGAACCGATGAGCCCCC 62.211 60.000 0.00 0.00 0.00 5.40
3720 3735 2.034685 GCAAACACCAGAGAAAGGAACC 59.965 50.000 0.00 0.00 0.00 3.62
3752 3767 8.607459 CGACTTTCTGCATTCTTCAGTTATAAT 58.393 33.333 0.00 0.00 33.48 1.28
3756 3771 5.538118 TCGACTTTCTGCATTCTTCAGTTA 58.462 37.500 0.00 0.00 33.48 2.24
3767 3782 3.125146 GTGCAATGTATCGACTTTCTGCA 59.875 43.478 8.71 8.71 0.00 4.41
3772 3787 7.139896 TGTAAATGTGCAATGTATCGACTTT 57.860 32.000 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.