Multiple sequence alignment - TraesCS2B01G314500

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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 TraesCS2B01G314500 chr2B 100.000 3296 0 0 1 3296 449517004 449513709 0.000000e+00 6087.0
1 TraesCS2B01G314500 chr2B 85.227 88 11 2 3153 3239 218292568 218292482 4.530000e-14 89.8
2 TraesCS2B01G314500 chr2D 94.768 2714 79 22 1 2662 378364704 378362002 0.000000e+00 4167.0
3 TraesCS2B01G314500 chr2D 91.917 433 28 6 2831 3258 378360600 378360170 1.690000e-167 599.0
4 TraesCS2B01G314500 chr2D 91.579 190 5 6 144 322 378365424 378365235 5.460000e-63 252.0
5 TraesCS2B01G314500 chr2D 92.683 164 11 1 2652 2814 378360747 378360584 5.500000e-58 235.0
6 TraesCS2B01G314500 chr2D 93.233 133 8 1 15 146 378365866 378365734 9.330000e-46 195.0
7 TraesCS2B01G314500 chr2D 85.915 71 8 2 3156 3225 523135046 523134977 1.270000e-09 75.0
8 TraesCS2B01G314500 chr2D 95.556 45 2 0 3252 3296 378360140 378360096 4.560000e-09 73.1
9 TraesCS2B01G314500 chr2A 94.656 2657 80 18 136 2765 513095486 513092865 0.000000e+00 4063.0
10 TraesCS2B01G314500 chr2A 89.421 397 38 3 2849 3242 513092852 513092457 6.350000e-137 497.0
11 TraesCS2B01G314500 chr2A 96.250 80 3 0 58 137 513095692 513095613 7.420000e-27 132.0
12 TraesCS2B01G314500 chr1A 87.903 124 14 1 3132 3255 71056941 71057063 9.530000e-31 145.0
13 TraesCS2B01G314500 chr6A 89.535 86 9 0 3157 3242 176992617 176992702 3.480000e-20 110.0
14 TraesCS2B01G314500 chr3B 85.556 90 9 3 3153 3239 56343406 56343318 1.260000e-14 91.6
15 TraesCS2B01G314500 chr3D 84.270 89 11 3 3153 3239 33382665 33382578 2.110000e-12 84.2
16 TraesCS2B01G314500 chr6B 95.238 42 2 0 3252 3293 652524005 652524046 2.120000e-07 67.6
17 TraesCS2B01G314500 chr1D 84.286 70 9 2 3153 3221 474988455 474988387 2.120000e-07 67.6


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 TraesCS2B01G314500 chr2B 449513709 449517004 3295 True 6087.000000 6087 100.000000 1 3296 1 chr2B.!!$R2 3295
1 TraesCS2B01G314500 chr2D 378360096 378365866 5770 True 920.183333 4167 93.289333 1 3296 6 chr2D.!!$R2 3295
2 TraesCS2B01G314500 chr2A 513092457 513095692 3235 True 1564.000000 4063 93.442333 58 3242 3 chr2A.!!$R1 3184

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
652 1952 0.605319 TTGTTCATCGCCACACCTCC 60.605 55.0 0.0 0.0 0.00 4.30 F
994 2297 0.804544 CACGGTGCGATACGACCAAT 60.805 55.0 0.0 0.0 31.22 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1800 3103 0.534412 CCTGGAGTGCGATCTTGACT 59.466 55.0 0.0 0.0 0.00 3.41 R
2816 5437 1.133363 TGGTCAGGAAACCCTTTCGA 58.867 50.0 0.0 0.0 40.57 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
51 1213 8.340618 TCAACTGCTGAAGCTTAATAGAAATT 57.659 30.769 0.00 0.00 42.66 1.82
56 1218 7.693952 TGCTGAAGCTTAATAGAAATTAACCG 58.306 34.615 0.00 0.00 42.66 4.44
182 1472 1.592669 CCATGGTCGGTCTCGCATC 60.593 63.158 2.57 0.00 36.13 3.91
350 1641 0.973496 AGAGGCCGGGAGAAGAAGAC 60.973 60.000 2.18 0.00 0.00 3.01
372 1663 3.797256 CGGAACAGTCGAATAGGTGAATC 59.203 47.826 0.00 0.00 0.00 2.52
652 1952 0.605319 TTGTTCATCGCCACACCTCC 60.605 55.000 0.00 0.00 0.00 4.30
715 2015 4.800993 CCTGCGTTTCAGATAAGACTACTG 59.199 45.833 0.00 0.00 45.72 2.74
716 2016 5.393135 CCTGCGTTTCAGATAAGACTACTGA 60.393 44.000 0.00 0.00 45.72 3.41
869 2169 2.202295 CTTCAGAAGCTACCTCGCTC 57.798 55.000 0.00 0.00 39.86 5.03
882 2182 4.180946 CGCTCGGACGACCAGAGG 62.181 72.222 20.11 11.12 37.33 3.69
897 2198 2.158986 CCAGAGGCATCCTGTCTACTTG 60.159 54.545 0.00 0.00 28.93 3.16
898 2199 1.484240 AGAGGCATCCTGTCTACTTGC 59.516 52.381 0.00 0.00 28.93 4.01
899 2200 1.484240 GAGGCATCCTGTCTACTTGCT 59.516 52.381 0.00 0.00 28.93 3.91
900 2201 2.695666 GAGGCATCCTGTCTACTTGCTA 59.304 50.000 0.00 0.00 28.93 3.49
907 2208 4.856509 TCCTGTCTACTTGCTAGCTAGAA 58.143 43.478 29.13 11.88 0.00 2.10
994 2297 0.804544 CACGGTGCGATACGACCAAT 60.805 55.000 0.00 0.00 31.22 3.16
1355 2658 4.329545 GCTGGTGGCGTCCCTGAA 62.330 66.667 5.77 0.00 0.00 3.02
1510 2813 2.037641 CAGGAGGATCATATGTTCGGCA 59.962 50.000 1.90 0.00 36.25 5.69
1513 2816 1.072331 AGGATCATATGTTCGGCACCC 59.928 52.381 1.90 0.00 0.00 4.61
1566 2869 5.451520 GGAGGACGTAGCTTTAAGCATTCTA 60.452 44.000 19.63 0.00 45.56 2.10
1572 2875 9.193133 GACGTAGCTTTAAGCATTCTATATTCA 57.807 33.333 19.63 0.00 45.56 2.57
1671 2974 1.605058 GGCGACCAAGCTACCTCTCA 61.605 60.000 0.00 0.00 37.29 3.27
1800 3103 1.603455 CAAGCTTTCCGGGAAGGCA 60.603 57.895 35.74 12.29 45.12 4.75
2037 3340 4.547367 GCGGTTATGGCGAGGGCT 62.547 66.667 0.00 0.00 39.81 5.19
2305 3608 6.143206 TCCTACCCTTCTTGATATCACATGA 58.857 40.000 4.48 1.66 0.00 3.07
2373 3696 2.338577 TTTGGCCATTTTTGGGTGTG 57.661 45.000 6.09 0.00 0.00 3.82
2434 3757 1.625818 GCTCTCTGAAACTGGGGAGAA 59.374 52.381 0.00 0.00 34.93 2.87
2498 3821 0.903942 AACATTTGGCGGGCATGATT 59.096 45.000 11.54 0.00 0.00 2.57
2500 3823 0.460722 CATTTGGCGGGCATGATTCA 59.539 50.000 4.64 0.00 0.00 2.57
2506 3829 1.536709 GGCGGGCATGATTCATTGTTC 60.537 52.381 0.00 0.00 0.00 3.18
2511 3834 4.498009 CGGGCATGATTCATTGTTCTTACC 60.498 45.833 0.00 0.00 0.00 2.85
2529 3852 8.986847 GTTCTTACCTAGGTTTTCTTTAGTGAC 58.013 37.037 22.11 6.63 0.00 3.67
2686 5302 7.584485 GCTTTCTTAATTCTTTTCGATCGGATC 59.416 37.037 16.41 7.95 0.00 3.36
2710 5330 3.000684 AGGTACTAGACGCATGTGAGA 57.999 47.619 14.43 0.00 36.02 3.27
2756 5376 8.306038 CAACAATGTTTCCCTGATCAAAATCTA 58.694 33.333 0.00 0.00 32.75 1.98
2757 5377 8.421249 ACAATGTTTCCCTGATCAAAATCTAA 57.579 30.769 0.00 0.00 32.75 2.10
2766 5386 8.971073 TCCCTGATCAAAATCTAAAGAATTTCC 58.029 33.333 0.00 0.00 40.09 3.13
2767 5387 8.200120 CCCTGATCAAAATCTAAAGAATTTCCC 58.800 37.037 0.00 0.00 40.09 3.97
2818 5439 8.620416 TGGATTGACCACTAATATTTTTGATCG 58.380 33.333 0.00 0.00 44.64 3.69
2819 5440 8.836413 GGATTGACCACTAATATTTTTGATCGA 58.164 33.333 0.00 0.00 38.79 3.59
2823 5444 8.673711 TGACCACTAATATTTTTGATCGAAAGG 58.326 33.333 8.14 6.42 0.00 3.11
2824 5445 7.996385 ACCACTAATATTTTTGATCGAAAGGG 58.004 34.615 8.14 0.00 0.00 3.95
2825 5446 7.614192 ACCACTAATATTTTTGATCGAAAGGGT 59.386 33.333 8.14 3.62 0.00 4.34
2826 5447 8.466798 CCACTAATATTTTTGATCGAAAGGGTT 58.533 33.333 8.14 7.18 0.00 4.11
2827 5448 9.855021 CACTAATATTTTTGATCGAAAGGGTTT 57.145 29.630 8.14 4.79 0.00 3.27
2829 5450 9.516314 CTAATATTTTTGATCGAAAGGGTTTCC 57.484 33.333 8.14 0.00 36.30 3.13
2831 5452 4.846779 TTTTGATCGAAAGGGTTTCCTG 57.153 40.909 3.86 0.00 44.07 3.86
2832 5453 3.780804 TTGATCGAAAGGGTTTCCTGA 57.219 42.857 0.00 0.00 44.07 3.86
2833 5454 3.053831 TGATCGAAAGGGTTTCCTGAC 57.946 47.619 0.00 0.00 44.07 3.51
2834 5455 2.290071 TGATCGAAAGGGTTTCCTGACC 60.290 50.000 0.00 0.00 44.07 4.02
2835 5456 1.133363 TCGAAAGGGTTTCCTGACCA 58.867 50.000 0.00 0.00 44.07 4.02
2836 5457 1.202722 TCGAAAGGGTTTCCTGACCAC 60.203 52.381 0.00 0.00 44.07 4.16
2837 5458 1.202770 CGAAAGGGTTTCCTGACCACT 60.203 52.381 0.00 0.00 44.07 4.00
2838 5459 2.038033 CGAAAGGGTTTCCTGACCACTA 59.962 50.000 0.00 0.00 44.07 2.74
2850 5471 9.850628 GTTTCCTGACCACTAATATTTTTAACC 57.149 33.333 0.00 0.00 0.00 2.85
3000 5622 7.951530 ATTTTACTTGAAGCATGTCCAAAAG 57.048 32.000 0.00 0.00 0.00 2.27
3009 5631 2.431782 GCATGTCCAAAAGGGCACATAT 59.568 45.455 0.00 0.00 36.21 1.78
3094 5720 9.267084 GAATAACTTTTTGCATAAACCCTTTGA 57.733 29.630 0.00 0.00 0.00 2.69
3097 5723 8.518430 AACTTTTTGCATAAACCCTTTGAATT 57.482 26.923 0.00 0.00 0.00 2.17
3123 5749 2.037641 GCCCCATTTGCATAGGGATTTC 59.962 50.000 17.58 3.42 45.80 2.17
3130 5756 6.925165 CCATTTGCATAGGGATTTCAACATAC 59.075 38.462 1.15 0.00 0.00 2.39
3151 5777 3.056393 ACGACCTGAATATCCAACGAACA 60.056 43.478 0.00 0.00 0.00 3.18
3180 5806 4.511617 TTTAAGCATGGCAAATCGAACA 57.488 36.364 0.00 0.00 0.00 3.18
3190 5816 5.536260 TGGCAAATCGAACATTTTTCATGA 58.464 33.333 0.00 0.00 0.00 3.07
3197 5823 9.866936 AAATCGAACATTTTTCATGACAAATTG 57.133 25.926 15.54 15.64 0.00 2.32
3242 5868 0.602060 TTGGCAAGCATCGCAAATCA 59.398 45.000 0.00 0.00 0.00 2.57
3247 5873 3.184541 GCAAGCATCGCAAATCAATCTT 58.815 40.909 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 1185 7.369803 TCTATTAAGCTTCAGCAGTTGAAAG 57.630 36.000 0.00 0.00 44.84 2.62
80 1242 5.057149 ACGATGCATGGAGTTAATACCTTC 58.943 41.667 16.26 0.00 0.00 3.46
182 1472 1.464608 CTTGGTACACTGCATGTTCGG 59.535 52.381 7.02 0.00 43.19 4.30
328 1619 2.756283 CTTCTCCCGGCCTCTCGT 60.756 66.667 0.00 0.00 0.00 4.18
350 1641 2.933495 TCACCTATTCGACTGTTCCG 57.067 50.000 0.00 0.00 0.00 4.30
397 1692 6.526674 CGGCTTCGCTAATTTCTTTGTTTTAT 59.473 34.615 0.00 0.00 0.00 1.40
398 1693 5.854338 CGGCTTCGCTAATTTCTTTGTTTTA 59.146 36.000 0.00 0.00 0.00 1.52
670 1970 0.320771 GGCTGCTTTCAGTCGGAAGA 60.321 55.000 0.00 0.00 42.29 2.87
671 1971 2.166270 GGCTGCTTTCAGTCGGAAG 58.834 57.895 0.00 0.00 42.29 3.46
715 2015 1.068333 ACACGACCATGCAATTTGCTC 60.068 47.619 21.19 10.05 45.31 4.26
716 2016 0.961019 ACACGACCATGCAATTTGCT 59.039 45.000 21.19 1.71 45.31 3.91
869 2169 2.105128 GATGCCTCTGGTCGTCCG 59.895 66.667 0.00 0.00 36.30 4.79
882 2182 2.102252 AGCTAGCAAGTAGACAGGATGC 59.898 50.000 18.83 0.00 42.53 3.91
907 2208 3.199508 ACATGCATGAAGCTAGGAGAAGT 59.800 43.478 32.75 2.07 45.94 3.01
994 2297 3.060614 GCAGCCCCTCCATTGCCTA 62.061 63.158 0.00 0.00 0.00 3.93
1355 2658 3.893763 CGATGTCCGCGAGCTCCT 61.894 66.667 8.23 0.00 0.00 3.69
1467 2770 2.656002 GATTCTAAAGGCTTGGGGGTC 58.344 52.381 0.00 0.00 0.00 4.46
1500 2803 1.600107 GACCAGGGTGCCGAACATA 59.400 57.895 0.00 0.00 0.00 2.29
1513 2816 2.742372 CTTTGGCGACCCGACCAG 60.742 66.667 0.00 0.00 35.40 4.00
1656 2959 1.185618 TGCGTGAGAGGTAGCTTGGT 61.186 55.000 0.00 0.00 0.00 3.67
1782 3085 1.589716 CTGCCTTCCCGGAAAGCTTG 61.590 60.000 19.36 10.08 31.11 4.01
1800 3103 0.534412 CCTGGAGTGCGATCTTGACT 59.466 55.000 0.00 0.00 0.00 3.41
2269 3572 3.567478 AGGGTAGGATGCATTCAGTTC 57.433 47.619 7.96 0.00 0.00 3.01
2305 3608 6.203723 GCATGATAAGGCGAAGAAGATACTTT 59.796 38.462 0.00 0.00 0.00 2.66
2373 3696 8.447833 TCGGTTGTAACAATCAATACAATCTTC 58.552 33.333 7.18 0.00 42.21 2.87
2434 3757 8.659925 TTGAACATACTCATTTTTGCAAATGT 57.340 26.923 13.65 8.77 46.61 2.71
2498 3821 8.990163 AAAGAAAACCTAGGTAAGAACAATGA 57.010 30.769 16.67 0.00 0.00 2.57
2506 3829 7.447594 TGGTCACTAAAGAAAACCTAGGTAAG 58.552 38.462 16.67 6.87 0.00 2.34
2511 3834 5.940470 AGCATGGTCACTAAAGAAAACCTAG 59.060 40.000 0.00 0.00 0.00 3.02
2600 3923 4.273480 GGCGTCAACTATGCATTACAAGAT 59.727 41.667 3.54 0.00 42.33 2.40
2686 5302 5.008712 TCTCACATGCGTCTAGTACCTTATG 59.991 44.000 0.00 0.00 0.00 1.90
2710 5330 4.935352 TGCAGATTTTAAAGTGTGCCTT 57.065 36.364 23.93 0.00 33.79 4.35
2766 5386 3.225104 CACATTGTGATATGGAAGGGGG 58.775 50.000 11.45 0.00 35.23 5.40
2767 5387 3.225104 CCACATTGTGATATGGAAGGGG 58.775 50.000 18.33 0.00 35.23 4.79
2806 5427 7.396055 TCAGGAAACCCTTTCGATCAAAAATAT 59.604 33.333 0.00 0.00 40.57 1.28
2807 5428 6.717540 TCAGGAAACCCTTTCGATCAAAAATA 59.282 34.615 0.00 0.00 40.57 1.40
2808 5429 5.538433 TCAGGAAACCCTTTCGATCAAAAAT 59.462 36.000 0.00 0.00 40.57 1.82
2809 5430 4.890581 TCAGGAAACCCTTTCGATCAAAAA 59.109 37.500 0.00 0.00 40.57 1.94
2810 5431 4.277423 GTCAGGAAACCCTTTCGATCAAAA 59.723 41.667 0.00 0.00 40.57 2.44
2811 5432 3.818773 GTCAGGAAACCCTTTCGATCAAA 59.181 43.478 0.00 0.00 40.57 2.69
2812 5433 3.408634 GTCAGGAAACCCTTTCGATCAA 58.591 45.455 0.00 0.00 40.57 2.57
2813 5434 2.290071 GGTCAGGAAACCCTTTCGATCA 60.290 50.000 0.00 0.00 40.57 2.92
2814 5435 2.290071 TGGTCAGGAAACCCTTTCGATC 60.290 50.000 0.00 0.00 40.57 3.69
2815 5436 1.702957 TGGTCAGGAAACCCTTTCGAT 59.297 47.619 0.00 0.00 40.57 3.59
2816 5437 1.133363 TGGTCAGGAAACCCTTTCGA 58.867 50.000 0.00 0.00 40.57 3.71
2817 5438 1.202770 AGTGGTCAGGAAACCCTTTCG 60.203 52.381 0.00 0.00 40.57 3.46
2818 5439 2.658807 AGTGGTCAGGAAACCCTTTC 57.341 50.000 0.00 0.00 38.65 2.62
2819 5440 4.741928 ATTAGTGGTCAGGAAACCCTTT 57.258 40.909 0.00 0.00 38.65 3.11
2820 5441 6.402981 AATATTAGTGGTCAGGAAACCCTT 57.597 37.500 0.00 0.00 38.65 3.95
2821 5442 6.402981 AAATATTAGTGGTCAGGAAACCCT 57.597 37.500 0.00 0.00 38.65 4.34
2822 5443 7.476540 AAAAATATTAGTGGTCAGGAAACCC 57.523 36.000 0.00 0.00 38.65 4.11
2823 5444 9.850628 GTTAAAAATATTAGTGGTCAGGAAACC 57.149 33.333 0.00 0.00 39.94 3.27
2824 5445 9.850628 GGTTAAAAATATTAGTGGTCAGGAAAC 57.149 33.333 0.00 0.00 0.00 2.78
2825 5446 9.589461 TGGTTAAAAATATTAGTGGTCAGGAAA 57.411 29.630 0.00 0.00 0.00 3.13
2826 5447 9.016438 GTGGTTAAAAATATTAGTGGTCAGGAA 57.984 33.333 0.00 0.00 0.00 3.36
2827 5448 8.164733 TGTGGTTAAAAATATTAGTGGTCAGGA 58.835 33.333 0.00 0.00 0.00 3.86
2828 5449 8.343168 TGTGGTTAAAAATATTAGTGGTCAGG 57.657 34.615 0.00 0.00 0.00 3.86
3009 5631 9.219603 CAATCTAATCGCCTCCATATTAGAAAA 57.780 33.333 7.79 0.00 42.45 2.29
3115 5741 3.517901 TCAGGTCGTATGTTGAAATCCCT 59.482 43.478 0.00 0.00 0.00 4.20
3123 5749 5.051039 CGTTGGATATTCAGGTCGTATGTTG 60.051 44.000 0.00 0.00 0.00 3.33
3130 5756 3.517602 TGTTCGTTGGATATTCAGGTCG 58.482 45.455 0.00 0.00 0.00 4.79
3151 5777 6.477688 CGATTTGCCATGCTTAAAAATCTGAT 59.522 34.615 0.00 0.00 35.87 2.90
3163 5789 3.598019 AAATGTTCGATTTGCCATGCT 57.402 38.095 0.00 0.00 0.00 3.79
3180 5806 7.911205 CAGCAAACACAATTTGTCATGAAAAAT 59.089 29.630 16.73 16.73 37.51 1.82
3190 5816 2.765699 ACCCTCAGCAAACACAATTTGT 59.234 40.909 0.00 0.00 41.74 2.83
3197 5823 1.391157 TTGCCACCCTCAGCAAACAC 61.391 55.000 0.00 0.00 45.51 3.32
3228 5854 9.585099 TTTAAATAAGATTGATTTGCGATGCTT 57.415 25.926 0.00 0.00 0.00 3.91
3247 5873 6.039616 GGCGCAAGGATGACAAATTTAAATA 58.960 36.000 10.83 0.00 38.28 1.40
3264 5927 1.660104 GGCAATTTATGTTGGCGCAAG 59.340 47.619 10.83 0.00 43.36 4.01
3266 5929 3.432517 GGCAATTTATGTTGGCGCA 57.567 47.368 10.83 0.00 43.36 6.09


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

AutoCloner maintained by Alex Coulton.