Multiple sequence alignment - TraesCS2D01G319400

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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 TraesCS2D01G319400 chr2D 100.000 2366 0 0 1 2366 410241208 410238843 0.000000e+00 4370
1 TraesCS2D01G319400 chr2D 87.402 1778 191 23 1 1769 601992085 601990332 0.000000e+00 2012
2 TraesCS2D01G319400 chr2D 90.507 611 39 12 1766 2361 633894940 633895546 0.000000e+00 789
3 TraesCS2D01G319400 chr3D 90.087 2421 178 26 1 2366 562217401 562219814 0.000000e+00 3085
4 TraesCS2D01G319400 chr3D 90.056 1770 165 6 1 1769 586295518 586293759 0.000000e+00 2283
5 TraesCS2D01G319400 chr3D 89.814 1777 160 15 1 1766 121209339 121211105 0.000000e+00 2259
6 TraesCS2D01G319400 chr3D 90.422 616 43 9 1766 2366 586293728 586293114 0.000000e+00 797
7 TraesCS2D01G319400 chr3D 87.540 626 38 14 1766 2365 126394201 126394812 0.000000e+00 688
8 TraesCS2D01G319400 chr3D 87.500 544 41 15 1766 2283 467276363 467275821 9.360000e-169 603
9 TraesCS2D01G319400 chr6D 91.130 1770 144 10 1 1766 146941226 146942986 0.000000e+00 2386
10 TraesCS2D01G319400 chr6D 89.119 1783 160 22 1 1769 20360804 20359042 0.000000e+00 2187
11 TraesCS2D01G319400 chr6D 92.045 616 32 10 1766 2366 146943020 146943633 0.000000e+00 850
12 TraesCS2D01G319400 chr6D 87.769 605 61 9 1766 2366 456651027 456650432 0.000000e+00 695
13 TraesCS2D01G319400 chr6D 86.443 627 44 16 1766 2366 177796517 177797128 0.000000e+00 649
14 TraesCS2D01G319400 chr1D 88.652 1780 187 14 1 1769 415632880 415631105 0.000000e+00 2154
15 TraesCS2D01G319400 chr5A 85.774 1926 227 24 26 1911 440669687 440671605 0.000000e+00 1995
16 TraesCS2D01G319400 chr5D 86.356 1781 213 26 1 1769 476695813 476694051 0.000000e+00 1916
17 TraesCS2D01G319400 chr5D 89.474 475 28 7 1766 2218 237268365 237267891 4.380000e-162 580
18 TraesCS2D01G319400 chr7D 84.910 835 87 16 1568 2366 538893371 538894202 0.000000e+00 808
19 TraesCS2D01G319400 chr7D 90.065 614 44 6 1766 2364 620118690 620118079 0.000000e+00 780
20 TraesCS2D01G319400 chr7D 86.286 525 53 12 1773 2283 75313383 75312864 9.560000e-154 553
21 TraesCS2D01G319400 chr2B 90.228 614 43 10 1767 2366 61598462 61599072 0.000000e+00 785
22 TraesCS2D01G319400 chr3B 90.097 616 42 8 1766 2366 573996685 573996074 0.000000e+00 782
23 TraesCS2D01G319400 chr6B 86.799 606 60 12 1766 2366 694451581 694450991 0.000000e+00 658


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 TraesCS2D01G319400 chr2D 410238843 410241208 2365 True 4370 4370 100.0000 1 2366 1 chr2D.!!$R1 2365
1 TraesCS2D01G319400 chr2D 601990332 601992085 1753 True 2012 2012 87.4020 1 1769 1 chr2D.!!$R2 1768
2 TraesCS2D01G319400 chr2D 633894940 633895546 606 False 789 789 90.5070 1766 2361 1 chr2D.!!$F1 595
3 TraesCS2D01G319400 chr3D 562217401 562219814 2413 False 3085 3085 90.0870 1 2366 1 chr3D.!!$F3 2365
4 TraesCS2D01G319400 chr3D 121209339 121211105 1766 False 2259 2259 89.8140 1 1766 1 chr3D.!!$F1 1765
5 TraesCS2D01G319400 chr3D 586293114 586295518 2404 True 1540 2283 90.2390 1 2366 2 chr3D.!!$R2 2365
6 TraesCS2D01G319400 chr3D 126394201 126394812 611 False 688 688 87.5400 1766 2365 1 chr3D.!!$F2 599
7 TraesCS2D01G319400 chr3D 467275821 467276363 542 True 603 603 87.5000 1766 2283 1 chr3D.!!$R1 517
8 TraesCS2D01G319400 chr6D 20359042 20360804 1762 True 2187 2187 89.1190 1 1769 1 chr6D.!!$R1 1768
9 TraesCS2D01G319400 chr6D 146941226 146943633 2407 False 1618 2386 91.5875 1 2366 2 chr6D.!!$F2 2365
10 TraesCS2D01G319400 chr6D 456650432 456651027 595 True 695 695 87.7690 1766 2366 1 chr6D.!!$R2 600
11 TraesCS2D01G319400 chr6D 177796517 177797128 611 False 649 649 86.4430 1766 2366 1 chr6D.!!$F1 600
12 TraesCS2D01G319400 chr1D 415631105 415632880 1775 True 2154 2154 88.6520 1 1769 1 chr1D.!!$R1 1768
13 TraesCS2D01G319400 chr5A 440669687 440671605 1918 False 1995 1995 85.7740 26 1911 1 chr5A.!!$F1 1885
14 TraesCS2D01G319400 chr5D 476694051 476695813 1762 True 1916 1916 86.3560 1 1769 1 chr5D.!!$R2 1768
15 TraesCS2D01G319400 chr7D 538893371 538894202 831 False 808 808 84.9100 1568 2366 1 chr7D.!!$F1 798
16 TraesCS2D01G319400 chr7D 620118079 620118690 611 True 780 780 90.0650 1766 2364 1 chr7D.!!$R2 598
17 TraesCS2D01G319400 chr7D 75312864 75313383 519 True 553 553 86.2860 1773 2283 1 chr7D.!!$R1 510
18 TraesCS2D01G319400 chr2B 61598462 61599072 610 False 785 785 90.2280 1767 2366 1 chr2B.!!$F1 599
19 TraesCS2D01G319400 chr3B 573996074 573996685 611 True 782 782 90.0970 1766 2366 1 chr3B.!!$R1 600
20 TraesCS2D01G319400 chr6B 694450991 694451581 590 True 658 658 86.7990 1766 2366 1 chr6B.!!$R1 600

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
23 24 0.87439 GCATCTGCTTTTCGTCCACA 59.126 50.0 0.0 0.0 38.21 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1597 1642 0.538287 AGAGGTTGAAGCACTTGCCC 60.538 55.0 0.0 0.0 43.38 5.36 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
23 24 0.874390 GCATCTGCTTTTCGTCCACA 59.126 50.000 0.00 0.00 38.21 4.17
27 28 0.877071 CTGCTTTTCGTCCACATGCT 59.123 50.000 0.00 0.00 0.00 3.79
66 67 1.603456 TTTGAGCCAGATTTGCGTCA 58.397 45.000 0.00 0.00 0.00 4.35
82 83 2.661537 CAGCGCGGACACAAGACA 60.662 61.111 8.83 0.00 0.00 3.41
83 84 2.661866 AGCGCGGACACAAGACAC 60.662 61.111 8.83 0.00 0.00 3.67
92 93 2.510464 ACAAGACACACGTGCGCA 60.510 55.556 17.22 5.66 0.00 6.09
250 269 4.824515 CCTCCCTCGCCTCGTCCT 62.825 72.222 0.00 0.00 0.00 3.85
251 270 2.756283 CTCCCTCGCCTCGTCCTT 60.756 66.667 0.00 0.00 0.00 3.36
266 285 0.982852 TCCTTCATGATGACCGCCCT 60.983 55.000 10.07 0.00 0.00 5.19
362 381 4.388499 GCGGGCAAAGGGAGTCGA 62.388 66.667 0.00 0.00 0.00 4.20
414 433 4.310672 GAGCGACGAAGCGATCAT 57.689 55.556 0.00 0.00 45.17 2.45
454 485 2.746359 GTGCAGCAGGAGGTCACT 59.254 61.111 0.00 0.00 0.00 3.41
521 552 1.271707 GGTTAAACCCTAGCCAGCACA 60.272 52.381 0.00 0.00 30.04 4.57
535 566 2.546494 GCACAGCCTTGTCAACGCT 61.546 57.895 3.51 3.51 34.62 5.07
572 603 2.125552 CCAGCTCATCCGCGTTCA 60.126 61.111 4.92 0.00 34.40 3.18
595 627 1.297689 GATGGTGCTGCCTGACTCA 59.702 57.895 0.00 0.00 38.35 3.41
836 869 2.357637 CACAACCTGTTTGACGGAATGT 59.642 45.455 0.00 0.00 38.73 2.71
949 988 1.428869 AGAGACACAAAGCCAGGACT 58.571 50.000 0.00 0.00 0.00 3.85
955 994 1.377725 CAAAGCCAGGACTGCCGAT 60.378 57.895 0.00 0.00 39.96 4.18
975 1014 2.742372 GCATTCACGCCGTCCACT 60.742 61.111 0.00 0.00 0.00 4.00
1059 1098 1.214589 CGACCACGAGTTTCCGGAT 59.785 57.895 4.15 0.00 42.66 4.18
1119 1158 0.253327 GGGAGCCTTTGTTCGAGGAT 59.747 55.000 0.00 0.00 36.33 3.24
1392 1431 2.821969 GGTGATCCAACAAGAGTGCAAT 59.178 45.455 0.00 0.00 0.00 3.56
1427 1466 2.515979 TTGAGAGCGTCAAGGCCCA 61.516 57.895 0.00 0.00 40.45 5.36
1485 1530 0.106015 AGTGGCTGGCCTCTTTTGTT 60.106 50.000 13.05 0.00 36.64 2.83
1523 1568 4.458256 TGCATGTCCATTTCCATATCCT 57.542 40.909 0.00 0.00 0.00 3.24
1525 1570 4.585581 TGCATGTCCATTTCCATATCCTTG 59.414 41.667 0.00 0.00 0.00 3.61
1555 1600 7.254966 CCAATATGCTTGCATGCAATACATTTT 60.255 33.333 35.01 31.03 46.61 1.82
1585 1630 3.389925 CAAGCTTTGGAGGCATTCAAA 57.610 42.857 4.50 4.50 0.00 2.69
1597 1642 1.666888 GCATTCAAAGCCCAACACGAG 60.667 52.381 0.00 0.00 0.00 4.18
1618 1663 1.544314 GGCAAGTGCTTCAACCTCTCT 60.544 52.381 2.85 0.00 41.70 3.10
1734 1784 4.680237 CGAGAAGCCACACCCGCA 62.680 66.667 0.00 0.00 0.00 5.69
1876 1960 1.198713 GAGGAGGCTTGAGATGGACA 58.801 55.000 0.00 0.00 0.00 4.02
1922 2006 1.267574 ATGGAGGCGGAGAAGCAAGA 61.268 55.000 0.00 0.00 39.27 3.02
1979 2063 0.606673 AAGGCGAAAGAAGTGGCTCC 60.607 55.000 0.00 0.00 37.56 4.70
1980 2064 2.391389 GGCGAAAGAAGTGGCTCCG 61.391 63.158 0.00 0.00 0.00 4.63
1982 2066 2.730672 CGAAAGAAGTGGCTCCGCG 61.731 63.158 0.00 0.00 0.00 6.46
2008 2094 0.620410 TGACCGGGGTGGAGATCATT 60.620 55.000 6.32 0.00 42.00 2.57
2019 2105 4.505742 GGTGGAGATCATTAAGGTGGATCC 60.506 50.000 4.20 4.20 38.52 3.36
2191 2323 1.617850 CCCTTTTTGTGTGCTGGCATA 59.382 47.619 0.00 0.00 0.00 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.470098 GCATGTGGACGAAAAGCAGAT 59.530 47.619 0.00 0.00 0.00 2.90
9 10 0.592637 CAGCATGTGGACGAAAAGCA 59.407 50.000 0.00 0.00 0.00 3.91
23 24 2.597340 CCGGGAATGGGTCAGCAT 59.403 61.111 0.00 0.00 0.00 3.79
66 67 2.661866 GTGTCTTGTGTCCGCGCT 60.662 61.111 5.56 0.00 0.00 5.92
92 93 3.453679 GGAGGAGAAGGCGAGCGT 61.454 66.667 0.00 0.00 0.00 5.07
250 269 0.465705 GAGAGGGCGGTCATCATGAA 59.534 55.000 0.00 0.00 0.00 2.57
251 270 1.402896 GGAGAGGGCGGTCATCATGA 61.403 60.000 0.00 0.00 0.00 3.07
266 285 2.672996 GCTTGCCTTTGCCGGAGA 60.673 61.111 5.05 0.00 36.33 3.71
351 370 0.889306 CCTCTTCGTCGACTCCCTTT 59.111 55.000 14.70 0.00 0.00 3.11
362 381 3.391382 CCGGCCCTTCCTCTTCGT 61.391 66.667 0.00 0.00 0.00 3.85
396 415 0.867329 CATGATCGCTTCGTCGCTCA 60.867 55.000 0.00 4.30 38.65 4.26
400 419 2.920964 CGCCATGATCGCTTCGTCG 61.921 63.158 0.00 0.00 0.00 5.12
557 588 1.153745 GAGTGAACGCGGATGAGCT 60.154 57.895 12.47 0.00 34.40 4.09
572 603 3.005539 AGGCAGCACCATCCGAGT 61.006 61.111 0.00 0.00 43.14 4.18
632 664 4.509737 GGCCTGCGGGTAGACGTC 62.510 72.222 14.55 7.70 35.98 4.34
713 746 2.264794 GTTGAGGTCGATGGGCGT 59.735 61.111 0.00 0.00 41.80 5.68
816 849 2.616842 GACATTCCGTCAAACAGGTTGT 59.383 45.455 0.00 0.00 44.69 3.32
914 953 1.380785 TCTTCGGGGTCGTAGCCAT 60.381 57.895 5.64 0.00 37.54 4.40
975 1014 3.091545 GGCCACCTGATCTTGATCAAAA 58.908 45.455 9.88 0.00 0.00 2.44
1059 1098 0.895530 CTTCCTCTTGCCCGTAGTCA 59.104 55.000 0.00 0.00 0.00 3.41
1119 1158 2.669569 GCTTGGTTGGCGAGCTCA 60.670 61.111 15.40 0.00 33.72 4.26
1353 1392 3.772572 TCACCCTCCATCACTTCGAAATA 59.227 43.478 0.00 0.00 0.00 1.40
1392 1431 4.776349 TCTCAAGAGTGGCACAAAACTTA 58.224 39.130 21.41 2.75 44.16 2.24
1485 1530 4.082300 ACATGCAAGCATAAACGGAATGAA 60.082 37.500 7.29 0.00 34.91 2.57
1525 1570 1.595794 GCATGCAAGCATATTGGCAAC 59.404 47.619 14.21 0.00 40.02 4.17
1597 1642 0.538287 AGAGGTTGAAGCACTTGCCC 60.538 55.000 0.00 0.00 43.38 5.36
1618 1663 3.805066 TTGATGACCCTCCAACAATGA 57.195 42.857 0.00 0.00 0.00 2.57
1734 1784 0.977395 CTTGGAGTTCGTCTTCCCCT 59.023 55.000 0.00 0.00 0.00 4.79
1851 1935 1.734655 TCTCAAGCCTCCTCCTTTGT 58.265 50.000 0.00 0.00 0.00 2.83
1876 1960 2.434428 CATCTTGGCTTGCTTCTCTGT 58.566 47.619 0.00 0.00 0.00 3.41
1922 2006 2.295909 GCCTCGATCTCTAGCATCTTGT 59.704 50.000 0.00 0.00 0.00 3.16
1982 2066 2.516930 CACCCCGGTCATCATGCC 60.517 66.667 0.00 0.00 0.00 4.40
2019 2105 2.892334 CTTGGCGACACGGTGTTGG 61.892 63.158 25.66 16.96 42.67 3.77
2226 2360 7.944729 ATGTCAGCTTTAGAAAATACCACAT 57.055 32.000 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.