Multiple sequence alignment - TraesCS2B01G454900

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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 TraesCS2B01G454900 chr2B 100.000 2639 0 0 1 2639 649709239 649706601 0.000000e+00 4874.0
1 TraesCS2B01G454900 chr2B 94.672 1783 80 9 1 1770 649751237 649749457 0.000000e+00 2752.0
2 TraesCS2B01G454900 chr2B 94.566 1693 80 7 1 1682 649715078 649713387 0.000000e+00 2606.0
3 TraesCS2B01G454900 chr2B 93.242 1539 85 11 248 1770 649756880 649755345 0.000000e+00 2248.0
4 TraesCS2B01G454900 chr2B 85.133 1130 127 22 653 1768 649947456 649946354 0.000000e+00 1118.0
5 TraesCS2B01G454900 chr2B 92.000 250 19 1 1 249 649762186 649761937 1.500000e-92 350.0
6 TraesCS2B01G454900 chr2A 90.316 1838 110 28 1 1776 686802950 686801119 0.000000e+00 2346.0
7 TraesCS2B01G454900 chr2A 87.710 1131 104 22 653 1769 686812727 686811618 0.000000e+00 1286.0
8 TraesCS2B01G454900 chr2A 86.507 1171 115 21 628 1769 686808027 686806871 0.000000e+00 1247.0
9 TraesCS2B01G454900 chr2A 91.180 839 48 12 1822 2639 237997548 237998381 0.000000e+00 1116.0
10 TraesCS2B01G454900 chr2A 80.313 767 121 22 884 1632 771339862 771340616 1.070000e-153 553.0
11 TraesCS2B01G454900 chr2D 91.186 1577 93 23 100 1653 544465770 544464217 0.000000e+00 2100.0
12 TraesCS2B01G454900 chr2D 91.921 916 71 2 838 1750 544327179 544326264 0.000000e+00 1279.0
13 TraesCS2B01G454900 chr2D 86.045 1168 116 26 626 1769 544566816 544565672 0.000000e+00 1210.0
14 TraesCS2B01G454900 chr2D 90.813 566 31 13 576 1137 544496819 544496271 0.000000e+00 737.0
15 TraesCS2B01G454900 chr2D 86.724 467 47 8 355 810 544327635 544327173 3.030000e-139 505.0
16 TraesCS2B01G454900 chr2D 90.370 135 11 2 4 136 544465905 544465771 2.700000e-40 176.0
17 TraesCS2B01G454900 chr2D 100.000 32 0 0 297 328 60764796 60764765 2.840000e-05 60.2
18 TraesCS2B01G454900 chr3B 95.048 828 20 10 1821 2627 721052763 721051936 0.000000e+00 1282.0
19 TraesCS2B01G454900 chr6B 85.848 749 87 13 1820 2562 688988541 688987806 0.000000e+00 778.0
20 TraesCS2B01G454900 chr6B 91.489 47 3 1 297 342 1204507 1204553 2.190000e-06 63.9
21 TraesCS2B01G454900 chr4B 100.000 32 0 0 303 334 105148720 105148751 2.840000e-05 60.2


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 TraesCS2B01G454900 chr2B 649706601 649709239 2638 True 4874.000000 4874 100.000000 1 2639 1 chr2B.!!$R1 2638
1 TraesCS2B01G454900 chr2B 649749457 649751237 1780 True 2752.000000 2752 94.672000 1 1770 1 chr2B.!!$R3 1769
2 TraesCS2B01G454900 chr2B 649713387 649715078 1691 True 2606.000000 2606 94.566000 1 1682 1 chr2B.!!$R2 1681
3 TraesCS2B01G454900 chr2B 649755345 649756880 1535 True 2248.000000 2248 93.242000 248 1770 1 chr2B.!!$R4 1522
4 TraesCS2B01G454900 chr2B 649946354 649947456 1102 True 1118.000000 1118 85.133000 653 1768 1 chr2B.!!$R6 1115
5 TraesCS2B01G454900 chr2A 686801119 686812727 11608 True 1626.333333 2346 88.177667 1 1776 3 chr2A.!!$R1 1775
6 TraesCS2B01G454900 chr2A 237997548 237998381 833 False 1116.000000 1116 91.180000 1822 2639 1 chr2A.!!$F1 817
7 TraesCS2B01G454900 chr2A 771339862 771340616 754 False 553.000000 553 80.313000 884 1632 1 chr2A.!!$F2 748
8 TraesCS2B01G454900 chr2D 544565672 544566816 1144 True 1210.000000 1210 86.045000 626 1769 1 chr2D.!!$R3 1143
9 TraesCS2B01G454900 chr2D 544464217 544465905 1688 True 1138.000000 2100 90.778000 4 1653 2 chr2D.!!$R5 1649
10 TraesCS2B01G454900 chr2D 544326264 544327635 1371 True 892.000000 1279 89.322500 355 1750 2 chr2D.!!$R4 1395
11 TraesCS2B01G454900 chr2D 544496271 544496819 548 True 737.000000 737 90.813000 576 1137 1 chr2D.!!$R2 561
12 TraesCS2B01G454900 chr3B 721051936 721052763 827 True 1282.000000 1282 95.048000 1821 2627 1 chr3B.!!$R1 806
13 TraesCS2B01G454900 chr6B 688987806 688988541 735 True 778.000000 778 85.848000 1820 2562 1 chr6B.!!$R1 742

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
56 9834 3.426159 CCGAGTTTCGTCAATGAATTGGG 60.426 47.826 3.31 0.0 38.4 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1723 11666 0.390735 GTAGGCACAAGTACGGTGGG 60.391 60.0 18.32 9.53 36.76 4.61 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
56 9834 3.426159 CCGAGTTTCGTCAATGAATTGGG 60.426 47.826 3.31 0.00 38.40 4.12
1305 11222 2.507102 CAGCGCGACGTGGAGATT 60.507 61.111 12.10 0.00 0.00 2.40
1425 11342 4.873129 GCGCTAGTGCCGCTGCTA 62.873 66.667 17.70 0.00 38.71 3.49
1474 11391 4.077184 GGGTCGCCGTGGTGATCA 62.077 66.667 14.26 0.00 37.48 2.92
1481 11398 1.218047 CCGTGGTGATCATCGTGGT 59.782 57.895 0.00 0.00 0.00 4.16
1488 11405 2.416296 GGTGATCATCGTGGTGACGTTA 60.416 50.000 0.00 0.00 46.20 3.18
1635 11554 1.153647 CCAGCGGCGTATGACAGAA 60.154 57.895 9.37 0.00 0.00 3.02
1722 11665 8.697846 TTCTCGGAATAAAATACACAGTACTG 57.302 34.615 21.44 21.44 0.00 2.74
1723 11666 6.755141 TCTCGGAATAAAATACACAGTACTGC 59.245 38.462 22.90 1.63 0.00 4.40
1737 11680 0.319083 TACTGCCCACCGTACTTGTG 59.681 55.000 5.64 5.64 0.00 3.33
1757 11703 3.675467 GCCTACGGCTGACTTATTTTG 57.325 47.619 0.00 0.00 46.69 2.44
1779 11725 8.815565 TTTGGTCCTTGCAATTTATATACTCA 57.184 30.769 0.00 0.00 0.00 3.41
1780 11726 8.815565 TTGGTCCTTGCAATTTATATACTCAA 57.184 30.769 0.00 0.00 0.00 3.02
1781 11727 8.815565 TGGTCCTTGCAATTTATATACTCAAA 57.184 30.769 0.00 0.00 0.00 2.69
1782 11728 8.902806 TGGTCCTTGCAATTTATATACTCAAAG 58.097 33.333 0.00 0.00 0.00 2.77
1783 11729 8.903820 GGTCCTTGCAATTTATATACTCAAAGT 58.096 33.333 0.00 0.00 0.00 2.66
1784 11730 9.937175 GTCCTTGCAATTTATATACTCAAAGTC 57.063 33.333 0.00 0.00 0.00 3.01
1785 11731 9.905713 TCCTTGCAATTTATATACTCAAAGTCT 57.094 29.630 0.00 0.00 0.00 3.24
1786 11732 9.941664 CCTTGCAATTTATATACTCAAAGTCTG 57.058 33.333 0.00 0.00 0.00 3.51
1790 11736 9.657121 GCAATTTATATACTCAAAGTCTGAAGC 57.343 33.333 0.00 0.00 32.17 3.86
1791 11737 9.855361 CAATTTATATACTCAAAGTCTGAAGCG 57.145 33.333 0.00 0.00 32.17 4.68
1792 11738 9.601217 AATTTATATACTCAAAGTCTGAAGCGT 57.399 29.630 0.00 0.00 32.17 5.07
1793 11739 8.997621 TTTATATACTCAAAGTCTGAAGCGTT 57.002 30.769 0.00 0.00 32.17 4.84
1794 11740 8.997621 TTATATACTCAAAGTCTGAAGCGTTT 57.002 30.769 0.00 0.00 32.17 3.60
1795 11741 3.951979 ACTCAAAGTCTGAAGCGTTTG 57.048 42.857 0.00 0.00 32.17 2.93
1796 11742 2.032178 ACTCAAAGTCTGAAGCGTTTGC 59.968 45.455 0.00 0.00 43.24 3.68
1797 11743 2.013400 TCAAAGTCTGAAGCGTTTGCA 58.987 42.857 0.00 0.00 46.23 4.08
1798 11744 2.618241 TCAAAGTCTGAAGCGTTTGCAT 59.382 40.909 0.00 0.00 46.23 3.96
1799 11745 3.066621 TCAAAGTCTGAAGCGTTTGCATT 59.933 39.130 0.00 0.00 46.23 3.56
1800 11746 3.715628 AAGTCTGAAGCGTTTGCATTT 57.284 38.095 0.00 0.00 46.23 2.32
1801 11747 3.004024 AGTCTGAAGCGTTTGCATTTG 57.996 42.857 0.00 0.00 46.23 2.32
1802 11748 2.358898 AGTCTGAAGCGTTTGCATTTGT 59.641 40.909 0.00 0.00 46.23 2.83
1803 11749 3.115554 GTCTGAAGCGTTTGCATTTGTT 58.884 40.909 0.00 0.00 46.23 2.83
1804 11750 3.180387 GTCTGAAGCGTTTGCATTTGTTC 59.820 43.478 0.00 0.00 46.23 3.18
1805 11751 3.066621 TCTGAAGCGTTTGCATTTGTTCT 59.933 39.130 0.00 0.00 46.23 3.01
1806 11752 3.371168 TGAAGCGTTTGCATTTGTTCTC 58.629 40.909 0.00 0.00 46.23 2.87
1807 11753 2.036556 AGCGTTTGCATTTGTTCTCG 57.963 45.000 0.00 0.00 46.23 4.04
1808 11754 1.052287 GCGTTTGCATTTGTTCTCGG 58.948 50.000 0.00 0.00 42.15 4.63
1809 11755 1.334599 GCGTTTGCATTTGTTCTCGGA 60.335 47.619 0.00 0.00 42.15 4.55
1810 11756 2.574322 CGTTTGCATTTGTTCTCGGAG 58.426 47.619 0.00 0.00 0.00 4.63
1811 11757 2.032030 CGTTTGCATTTGTTCTCGGAGT 60.032 45.455 4.69 0.00 0.00 3.85
1812 11758 3.185594 CGTTTGCATTTGTTCTCGGAGTA 59.814 43.478 4.69 0.00 0.00 2.59
1813 11759 4.142902 CGTTTGCATTTGTTCTCGGAGTAT 60.143 41.667 4.69 0.00 0.00 2.12
1814 11760 5.062934 CGTTTGCATTTGTTCTCGGAGTATA 59.937 40.000 4.69 0.00 0.00 1.47
1815 11761 6.238103 CGTTTGCATTTGTTCTCGGAGTATAT 60.238 38.462 4.69 0.00 0.00 0.86
1816 11762 7.042992 CGTTTGCATTTGTTCTCGGAGTATATA 60.043 37.037 4.69 0.00 0.00 0.86
1817 11763 7.709269 TTGCATTTGTTCTCGGAGTATATAC 57.291 36.000 4.60 4.60 0.00 1.47
1818 11764 6.220930 TGCATTTGTTCTCGGAGTATATACC 58.779 40.000 9.32 1.51 0.00 2.73
1819 11765 6.041637 TGCATTTGTTCTCGGAGTATATACCT 59.958 38.462 9.32 0.00 0.00 3.08
1841 11787 0.801067 CTAGATAATACCCCGCGCGC 60.801 60.000 27.36 23.91 0.00 6.86
1870 11816 8.537049 TGCGGTAATTTATAGCATTACGTAAT 57.463 30.769 15.07 15.07 37.80 1.89
2038 11987 4.943705 AGCAAGAAACAAAGAGACTTCACA 59.056 37.500 0.00 0.00 0.00 3.58
2276 12226 5.451798 GGTTTTGTTTGATCCTCTCAGCAAA 60.452 40.000 0.00 0.00 38.07 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 9834 5.515797 ACCTTTTCTTCTGTACTTTTGCC 57.484 39.130 0.00 0.00 0.00 4.52
105 9883 0.447801 CGCTTGTTTGGAAGGGATCG 59.552 55.000 0.00 0.00 37.96 3.69
287 10105 7.280428 TGTCGTAGTTTTGAACTATGGTTGAAA 59.720 33.333 16.03 0.00 46.31 2.69
308 10129 5.121768 CCCTTCGATTCAAAATAAGTGTCGT 59.878 40.000 0.00 0.00 0.00 4.34
1383 11300 2.512515 GAGAAAGCCAGCGCGGAT 60.513 61.111 20.06 12.32 41.18 4.18
1635 11554 2.785868 GCGATGAAGGCCTTGTCAT 58.214 52.632 26.25 21.52 37.19 3.06
1722 11665 2.175035 TAGGCACAAGTACGGTGGGC 62.175 60.000 16.05 16.05 45.03 5.36
1723 11666 0.390735 GTAGGCACAAGTACGGTGGG 60.391 60.000 18.32 9.53 36.76 4.61
1757 11703 8.903820 ACTTTGAGTATATAAATTGCAAGGACC 58.096 33.333 4.94 0.00 0.00 4.46
1776 11722 2.032054 TGCAAACGCTTCAGACTTTGAG 59.968 45.455 0.00 0.00 37.07 3.02
1777 11723 2.013400 TGCAAACGCTTCAGACTTTGA 58.987 42.857 0.00 0.00 0.00 2.69
1778 11724 2.473530 TGCAAACGCTTCAGACTTTG 57.526 45.000 0.00 0.00 0.00 2.77
1779 11725 3.715628 AATGCAAACGCTTCAGACTTT 57.284 38.095 0.00 0.00 0.00 2.66
1780 11726 3.181487 ACAAATGCAAACGCTTCAGACTT 60.181 39.130 0.00 0.00 0.00 3.01
1781 11727 2.358898 ACAAATGCAAACGCTTCAGACT 59.641 40.909 0.00 0.00 0.00 3.24
1782 11728 2.731217 ACAAATGCAAACGCTTCAGAC 58.269 42.857 0.00 0.00 0.00 3.51
1783 11729 3.066621 AGAACAAATGCAAACGCTTCAGA 59.933 39.130 0.00 0.00 0.00 3.27
1784 11730 3.374745 AGAACAAATGCAAACGCTTCAG 58.625 40.909 0.00 0.00 0.00 3.02
1785 11731 3.371168 GAGAACAAATGCAAACGCTTCA 58.629 40.909 0.00 0.00 0.00 3.02
1786 11732 2.401720 CGAGAACAAATGCAAACGCTTC 59.598 45.455 0.00 0.00 0.00 3.86
1787 11733 2.384382 CGAGAACAAATGCAAACGCTT 58.616 42.857 0.00 0.00 0.00 4.68
1788 11734 1.334960 CCGAGAACAAATGCAAACGCT 60.335 47.619 0.00 0.00 0.00 5.07
1789 11735 1.052287 CCGAGAACAAATGCAAACGC 58.948 50.000 0.00 0.00 0.00 4.84
1790 11736 2.032030 ACTCCGAGAACAAATGCAAACG 60.032 45.455 1.33 0.00 0.00 3.60
1791 11737 3.626028 ACTCCGAGAACAAATGCAAAC 57.374 42.857 1.33 0.00 0.00 2.93
1792 11738 7.225931 GGTATATACTCCGAGAACAAATGCAAA 59.774 37.037 12.54 0.00 0.00 3.68
1793 11739 6.704493 GGTATATACTCCGAGAACAAATGCAA 59.296 38.462 12.54 0.00 0.00 4.08
1794 11740 6.041637 AGGTATATACTCCGAGAACAAATGCA 59.958 38.462 12.54 0.00 0.00 3.96
1795 11741 6.456501 AGGTATATACTCCGAGAACAAATGC 58.543 40.000 12.54 0.00 0.00 3.56
1796 11742 9.408069 GTTAGGTATATACTCCGAGAACAAATG 57.592 37.037 12.54 0.00 0.00 2.32
1797 11743 9.364653 AGTTAGGTATATACTCCGAGAACAAAT 57.635 33.333 12.54 0.00 0.00 2.32
1798 11744 8.757982 AGTTAGGTATATACTCCGAGAACAAA 57.242 34.615 12.54 0.00 0.00 2.83
1799 11745 9.499479 CTAGTTAGGTATATACTCCGAGAACAA 57.501 37.037 12.54 0.00 0.00 2.83
1800 11746 8.874156 TCTAGTTAGGTATATACTCCGAGAACA 58.126 37.037 12.54 0.00 0.00 3.18
1801 11747 9.889128 ATCTAGTTAGGTATATACTCCGAGAAC 57.111 37.037 12.54 7.93 0.00 3.01
1811 11757 9.799106 GCGGGGTATTATCTAGTTAGGTATATA 57.201 37.037 0.00 0.00 0.00 0.86
1812 11758 7.446625 CGCGGGGTATTATCTAGTTAGGTATAT 59.553 40.741 0.00 0.00 0.00 0.86
1813 11759 6.767902 CGCGGGGTATTATCTAGTTAGGTATA 59.232 42.308 0.00 0.00 0.00 1.47
1814 11760 5.591877 CGCGGGGTATTATCTAGTTAGGTAT 59.408 44.000 0.00 0.00 0.00 2.73
1815 11761 4.943705 CGCGGGGTATTATCTAGTTAGGTA 59.056 45.833 0.00 0.00 0.00 3.08
1816 11762 3.760684 CGCGGGGTATTATCTAGTTAGGT 59.239 47.826 0.00 0.00 0.00 3.08
1817 11763 3.428589 GCGCGGGGTATTATCTAGTTAGG 60.429 52.174 8.83 0.00 0.00 2.69
1818 11764 3.730061 CGCGCGGGGTATTATCTAGTTAG 60.730 52.174 24.84 0.00 0.00 2.34
1819 11765 2.162208 CGCGCGGGGTATTATCTAGTTA 59.838 50.000 24.84 0.00 0.00 2.24
1841 11787 5.362556 AATGCTATAAATTACCGCAGCAG 57.637 39.130 0.00 0.00 41.83 4.24
1870 11816 5.865085 TCTTTTGCTCCAGAAAGCTTACTA 58.135 37.500 0.00 0.00 42.94 1.82
1877 11824 9.298774 GATTTCATTATCTTTTGCTCCAGAAAG 57.701 33.333 0.00 0.00 34.87 2.62
2038 11987 6.738453 GCACCACAAAAGGATGTCAAATTAGT 60.738 38.462 0.00 0.00 0.00 2.24
2141 12090 5.419788 TCATAGTCAGAAGCAATGCCATTTT 59.580 36.000 0.00 0.00 0.00 1.82
2415 12368 8.181487 TCACTTGATAAATGTAAGCGTCTAAC 57.819 34.615 0.00 0.00 0.00 2.34
2563 12516 2.320681 AAGGGTGCAGAGTGTAGGTA 57.679 50.000 0.00 0.00 0.00 3.08
2564 12517 2.320681 TAAGGGTGCAGAGTGTAGGT 57.679 50.000 0.00 0.00 0.00 3.08
2565 12518 3.914426 AATAAGGGTGCAGAGTGTAGG 57.086 47.619 0.00 0.00 0.00 3.18
2566 12519 4.579869 ACAAATAAGGGTGCAGAGTGTAG 58.420 43.478 0.00 0.00 0.00 2.74
2567 12520 4.041075 TGACAAATAAGGGTGCAGAGTGTA 59.959 41.667 0.00 0.00 0.00 2.90
2570 12523 3.788227 TGACAAATAAGGGTGCAGAGT 57.212 42.857 0.00 0.00 0.00 3.24
2571 12524 4.095483 GTGATGACAAATAAGGGTGCAGAG 59.905 45.833 0.00 0.00 0.00 3.35
2572 12525 4.009675 GTGATGACAAATAAGGGTGCAGA 58.990 43.478 0.00 0.00 0.00 4.26
2574 12527 3.760738 TGTGATGACAAATAAGGGTGCA 58.239 40.909 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.