Multiple sequence alignment - TraesCS4D01G129700

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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 TraesCS4D01G129700 chr4D 100.000 3533 0 0 1 3533 115126424 115122892 0.000000e+00 6525
1 TraesCS4D01G129700 chr4D 93.057 821 49 3 7 826 504103081 504102268 0.000000e+00 1194
2 TraesCS4D01G129700 chr4D 94.063 539 31 1 2995 3533 472131767 472132304 0.000000e+00 817
3 TraesCS4D01G129700 chr4D 89.277 429 23 7 2567 2994 447980694 447980288 1.880000e-142 516
4 TraesCS4D01G129700 chr4A 94.518 2189 90 14 822 2991 462201427 462203604 0.000000e+00 3350
5 TraesCS4D01G129700 chr4A 88.167 431 26 8 2567 2994 611200498 611200090 1.140000e-134 490
6 TraesCS4D01G129700 chr4B 95.366 1079 42 6 1917 2991 175563662 175562588 0.000000e+00 1709
7 TraesCS4D01G129700 chr4B 95.005 1081 47 7 842 1918 175564852 175563775 0.000000e+00 1690
8 TraesCS4D01G129700 chr1D 96.506 830 27 2 1 830 118577815 118578642 0.000000e+00 1371
9 TraesCS4D01G129700 chr1D 96.145 830 29 2 1 830 458803365 458802539 0.000000e+00 1352
10 TraesCS4D01G129700 chr1D 93.889 540 31 2 2995 3533 171332324 171331786 0.000000e+00 813
11 TraesCS4D01G129700 chr5D 96.386 830 30 0 1 830 520905820 520906649 0.000000e+00 1367
12 TraesCS4D01G129700 chr5D 93.530 541 34 1 2994 3533 500322730 500322190 0.000000e+00 804
13 TraesCS4D01G129700 chr5D 93.519 540 32 3 2995 3533 266689258 266688721 0.000000e+00 800
14 TraesCS4D01G129700 chr2D 96.163 834 31 1 1 833 240223439 240224272 0.000000e+00 1362
15 TraesCS4D01G129700 chr3A 95.427 831 37 1 1 830 513532689 513533519 0.000000e+00 1323
16 TraesCS4D01G129700 chr3A 94.337 830 42 4 1 830 206092832 206092008 0.000000e+00 1267
17 TraesCS4D01G129700 chr1A 95.066 831 37 3 1 830 127295466 127294639 0.000000e+00 1304
18 TraesCS4D01G129700 chr1A 93.530 541 33 2 2994 3533 563166529 563165990 0.000000e+00 804
19 TraesCS4D01G129700 chr1A 92.883 548 37 2 2986 3533 260954343 260954888 0.000000e+00 795
20 TraesCS4D01G129700 chr5A 91.236 833 69 4 1 830 111560240 111559409 0.000000e+00 1131
21 TraesCS4D01G129700 chr5A 93.878 539 32 1 2995 3533 662224622 662225159 0.000000e+00 811
22 TraesCS4D01G129700 chr1B 95.176 539 21 2 2995 3533 348100579 348101112 0.000000e+00 846
23 TraesCS4D01G129700 chr7D 93.738 543 33 1 2992 3533 417992297 417992839 0.000000e+00 813
24 TraesCS4D01G129700 chr3D 87.354 514 42 7 2481 2994 554393038 554392548 5.120000e-158 568
25 TraesCS4D01G129700 chr2B 88.967 426 24 7 2567 2991 654361609 654362012 4.070000e-139 505
26 TraesCS4D01G129700 chr7B 88.578 429 26 8 2567 2994 686930325 686929919 1.890000e-137 499
27 TraesCS4D01G129700 chr7B 90.432 324 24 5 2481 2803 109180449 109180132 1.520000e-113 420
28 TraesCS4D01G129700 chr7B 92.810 153 11 0 2839 2991 109171475 109171627 4.590000e-54 222
29 TraesCS4D01G129700 chr7A 88.578 429 26 7 2567 2994 284785629 284785223 1.890000e-137 499
30 TraesCS4D01G129700 chr5B 88.732 426 25 7 2567 2991 629972435 629972838 1.890000e-137 499
31 TraesCS4D01G129700 chr2A 88.578 429 26 7 2567 2994 711071724 711071318 1.890000e-137 499


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 TraesCS4D01G129700 chr4D 115122892 115126424 3532 True 6525.0 6525 100.0000 1 3533 1 chr4D.!!$R1 3532
1 TraesCS4D01G129700 chr4D 504102268 504103081 813 True 1194.0 1194 93.0570 7 826 1 chr4D.!!$R3 819
2 TraesCS4D01G129700 chr4D 472131767 472132304 537 False 817.0 817 94.0630 2995 3533 1 chr4D.!!$F1 538
3 TraesCS4D01G129700 chr4A 462201427 462203604 2177 False 3350.0 3350 94.5180 822 2991 1 chr4A.!!$F1 2169
4 TraesCS4D01G129700 chr4B 175562588 175564852 2264 True 1699.5 1709 95.1855 842 2991 2 chr4B.!!$R1 2149
5 TraesCS4D01G129700 chr1D 118577815 118578642 827 False 1371.0 1371 96.5060 1 830 1 chr1D.!!$F1 829
6 TraesCS4D01G129700 chr1D 458802539 458803365 826 True 1352.0 1352 96.1450 1 830 1 chr1D.!!$R2 829
7 TraesCS4D01G129700 chr1D 171331786 171332324 538 True 813.0 813 93.8890 2995 3533 1 chr1D.!!$R1 538
8 TraesCS4D01G129700 chr5D 520905820 520906649 829 False 1367.0 1367 96.3860 1 830 1 chr5D.!!$F1 829
9 TraesCS4D01G129700 chr5D 500322190 500322730 540 True 804.0 804 93.5300 2994 3533 1 chr5D.!!$R2 539
10 TraesCS4D01G129700 chr5D 266688721 266689258 537 True 800.0 800 93.5190 2995 3533 1 chr5D.!!$R1 538
11 TraesCS4D01G129700 chr2D 240223439 240224272 833 False 1362.0 1362 96.1630 1 833 1 chr2D.!!$F1 832
12 TraesCS4D01G129700 chr3A 513532689 513533519 830 False 1323.0 1323 95.4270 1 830 1 chr3A.!!$F1 829
13 TraesCS4D01G129700 chr3A 206092008 206092832 824 True 1267.0 1267 94.3370 1 830 1 chr3A.!!$R1 829
14 TraesCS4D01G129700 chr1A 127294639 127295466 827 True 1304.0 1304 95.0660 1 830 1 chr1A.!!$R1 829
15 TraesCS4D01G129700 chr1A 563165990 563166529 539 True 804.0 804 93.5300 2994 3533 1 chr1A.!!$R2 539
16 TraesCS4D01G129700 chr1A 260954343 260954888 545 False 795.0 795 92.8830 2986 3533 1 chr1A.!!$F1 547
17 TraesCS4D01G129700 chr5A 111559409 111560240 831 True 1131.0 1131 91.2360 1 830 1 chr5A.!!$R1 829
18 TraesCS4D01G129700 chr5A 662224622 662225159 537 False 811.0 811 93.8780 2995 3533 1 chr5A.!!$F1 538
19 TraesCS4D01G129700 chr1B 348100579 348101112 533 False 846.0 846 95.1760 2995 3533 1 chr1B.!!$F1 538
20 TraesCS4D01G129700 chr7D 417992297 417992839 542 False 813.0 813 93.7380 2992 3533 1 chr7D.!!$F1 541

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
896 903 0.379316 AACAGAAACGCAACCGAACC 59.621 50.0 0.00 0.0 38.29 3.62 F
1435 1451 0.530744 TCGCGCACTCTTTGGTAGAT 59.469 50.0 8.75 0.0 30.92 1.98 F
1939 2079 0.323302 TCAAATGCTACCCGTGCTCA 59.677 50.0 0.00 0.0 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1759 1783 0.317479 ACTAAGGTGACAGACGGCAC 59.683 55.000 0.0 0.0 0.00 5.01 R
2442 2585 1.272147 GGAAAGCCAACCTCAGATGGT 60.272 52.381 0.0 0.0 43.11 3.55 R
2816 2959 2.217393 CGCGATGTCTGATTAAGCACTC 59.783 50.000 0.0 0.0 0.00 3.51 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
29 30 2.954318 GCACCTCCACATGCATATCTTT 59.046 45.455 0.00 0.00 41.65 2.52
71 72 3.708631 CTCTTCCCTCTTATCCTCTGCAA 59.291 47.826 0.00 0.00 0.00 4.08
285 287 0.690762 GGCACCTGTAGAAGACCCAA 59.309 55.000 0.00 0.00 0.00 4.12
320 322 3.126514 TCCGTGTTCGACAGATAGAACTC 59.873 47.826 9.30 5.40 44.95 3.01
716 723 2.112815 GTGGCATACGGGGAACAGC 61.113 63.158 0.00 0.00 0.00 4.40
771 778 7.491048 GGTGACCGTATTAACCGTATTTCTAAA 59.509 37.037 0.00 0.00 0.00 1.85
858 865 4.441792 CTTTTCCCAAACAAAAGACCTGG 58.558 43.478 0.00 0.00 41.52 4.45
896 903 0.379316 AACAGAAACGCAACCGAACC 59.621 50.000 0.00 0.00 38.29 3.62
1147 1163 4.806339 CTCTCCCCCGCTTCCCCT 62.806 72.222 0.00 0.00 0.00 4.79
1162 1178 2.678934 CCTCCGTCGGGGTCAGAA 60.679 66.667 10.99 0.00 37.00 3.02
1177 1193 2.036387 TCAGAACCGGTCACTTCTTCA 58.964 47.619 8.04 0.00 0.00 3.02
1179 1195 3.071023 TCAGAACCGGTCACTTCTTCAAT 59.929 43.478 8.04 0.00 0.00 2.57
1181 1197 1.523758 ACCGGTCACTTCTTCAATGC 58.476 50.000 0.00 0.00 0.00 3.56
1184 1200 2.416747 CGGTCACTTCTTCAATGCTCA 58.583 47.619 0.00 0.00 0.00 4.26
1254 1270 3.712907 GTAGCCGCCTTCCCCACA 61.713 66.667 0.00 0.00 0.00 4.17
1400 1416 8.131100 ACTAATCGCATTTTGGAATTATCTGTG 58.869 33.333 0.00 0.00 0.00 3.66
1435 1451 0.530744 TCGCGCACTCTTTGGTAGAT 59.469 50.000 8.75 0.00 30.92 1.98
1512 1528 1.923204 CGTGCTCTCGGAAGATTCTTG 59.077 52.381 3.03 0.00 40.84 3.02
1635 1658 0.811281 GTGGATGTTGGTGCCTAAGC 59.189 55.000 0.00 0.00 40.48 3.09
1713 1737 4.623886 GCTACTGAATCATGGGTGACTGAA 60.624 45.833 0.00 0.00 37.14 3.02
1757 1781 2.167693 TGGGGCATAACACTAGTTCGAG 59.832 50.000 0.00 0.00 39.15 4.04
1758 1782 2.202566 GGGCATAACACTAGTTCGAGC 58.797 52.381 0.00 0.00 39.15 5.03
1759 1783 1.852895 GGCATAACACTAGTTCGAGCG 59.147 52.381 0.00 0.00 39.15 5.03
1760 1784 2.527100 GCATAACACTAGTTCGAGCGT 58.473 47.619 0.00 0.00 39.15 5.07
1762 1786 1.973138 TAACACTAGTTCGAGCGTGC 58.027 50.000 7.10 0.00 39.15 5.34
1763 1787 0.666577 AACACTAGTTCGAGCGTGCC 60.667 55.000 7.10 0.00 30.46 5.01
1771 1795 4.700365 CGAGCGTGCCGTCTGTCA 62.700 66.667 0.00 0.00 0.00 3.58
1790 1814 7.280652 GTCTGTCACCTTAGTTCTACTACTAGG 59.719 44.444 0.00 0.00 32.54 3.02
1848 1873 2.198827 ATGTCATTTTGGCGTCTGGA 57.801 45.000 0.00 0.00 0.00 3.86
1870 1895 2.610727 GGGCGTGCCTCTATGTTCTATC 60.611 54.545 11.25 0.00 36.10 2.08
1909 1934 6.590656 AATATGAAAGATGGGGGAACTGTA 57.409 37.500 0.00 0.00 0.00 2.74
1910 1935 6.786843 ATATGAAAGATGGGGGAACTGTAT 57.213 37.500 0.00 0.00 0.00 2.29
1911 1936 7.888514 ATATGAAAGATGGGGGAACTGTATA 57.111 36.000 0.00 0.00 0.00 1.47
1939 2079 0.323302 TCAAATGCTACCCGTGCTCA 59.677 50.000 0.00 0.00 0.00 4.26
1968 2110 2.488952 GAAGCAGGGCTGAGTAATAGC 58.511 52.381 0.00 0.00 39.62 2.97
1988 2130 2.727777 CTGATGCATTCTGAATTGCCG 58.272 47.619 0.00 2.86 0.00 5.69
2163 2305 0.899717 ATTTCCACGTGGCCTGCATT 60.900 50.000 30.25 6.93 34.44 3.56
2286 2428 3.330701 TGATAGTAATTCCCCCATGCTCC 59.669 47.826 0.00 0.00 0.00 4.70
2328 2471 2.964310 ATGCCGCTGCCTGTTCTCT 61.964 57.895 0.00 0.00 36.33 3.10
2417 2560 5.311649 AGATTCAGGTAGTATGCCATCCATT 59.688 40.000 0.00 0.00 46.86 3.16
2442 2585 2.083774 GATCAGGGAAACAATGCGACA 58.916 47.619 0.00 0.00 0.00 4.35
2459 2602 0.773644 ACACCATCTGAGGTTGGCTT 59.226 50.000 2.81 0.00 40.77 4.35
2486 2629 4.102524 TGGTGAGAATAACAACCAGACAGT 59.897 41.667 0.00 0.00 0.00 3.55
2512 2655 3.006112 TGAACATAGAGAGTCCTCGCT 57.994 47.619 5.86 5.86 44.08 4.93
2545 2688 3.813443 CTGCCATGATGTAAAGCCTAGT 58.187 45.455 0.00 0.00 0.00 2.57
2552 2695 7.275920 CCATGATGTAAAGCCTAGTTAGAAGT 58.724 38.462 0.00 0.00 0.00 3.01
2554 2697 8.821894 CATGATGTAAAGCCTAGTTAGAAGTTC 58.178 37.037 0.00 0.00 0.00 3.01
2570 2713 8.467598 GTTAGAAGTTCCTTGAAGTTCCTTTTT 58.532 33.333 16.75 5.14 46.92 1.94
2781 2924 2.416547 CAGGTATGCACAGTTTCTTCCG 59.583 50.000 0.00 0.00 0.00 4.30
2816 2959 1.281867 TGCATCTACTTGGAACTGGGG 59.718 52.381 0.00 0.00 0.00 4.96
2837 2980 2.196749 AGTGCTTAATCAGACATCGCG 58.803 47.619 0.00 0.00 0.00 5.87
2859 3002 3.614616 GCAGTGTATGTCTAGTGAAGCAC 59.385 47.826 0.00 0.00 34.10 4.40
2873 3016 3.505680 GTGAAGCACCATGTGTCCATTTA 59.494 43.478 0.00 0.00 35.75 1.40
2934 3077 5.415701 GTCACCAGGATAACATGTGAATGTT 59.584 40.000 0.00 8.92 45.64 2.71
2976 3119 3.000925 GCTGATAATACCCGTCAACGTTG 59.999 47.826 22.35 22.35 37.74 4.10
3068 3211 2.621998 CCCGTATAGTCAGTGGGTACAG 59.378 54.545 0.00 0.00 35.05 2.74
3250 3395 4.011023 TCTCAGCTCAGTAACAGGTAGAC 58.989 47.826 0.00 0.00 0.00 2.59
3424 3571 3.309121 GCTATACCCGTACCCTACCCATA 60.309 52.174 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 2.320781 AGCCGTAGATGCATTAGGAGT 58.679 47.619 0.00 0.00 0.00 3.85
285 287 2.600769 ACGGAGAAGCACGAGGGT 60.601 61.111 0.00 0.00 0.00 4.34
771 778 3.000727 GCGCTCACTTTGGTTACTGTAT 58.999 45.455 0.00 0.00 0.00 2.29
778 785 1.230324 GAAGAGCGCTCACTTTGGTT 58.770 50.000 36.87 21.43 0.00 3.67
1147 1163 2.993264 GGTTCTGACCCCGACGGA 60.993 66.667 17.49 0.00 40.25 4.69
1162 1178 1.072331 AGCATTGAAGAAGTGACCGGT 59.928 47.619 6.92 6.92 0.00 5.28
1172 1188 2.688507 GGTCGAACTGAGCATTGAAGA 58.311 47.619 0.00 0.00 44.60 2.87
1177 1193 1.741770 GGCGGTCGAACTGAGCATT 60.742 57.895 0.00 0.00 45.52 3.56
1179 1195 3.573772 CTGGCGGTCGAACTGAGCA 62.574 63.158 0.00 0.00 45.52 4.26
1181 1197 2.125912 CCTGGCGGTCGAACTGAG 60.126 66.667 0.00 0.00 0.00 3.35
1184 1200 3.692406 GTCCCTGGCGGTCGAACT 61.692 66.667 0.00 0.00 0.00 3.01
1306 1322 1.695114 CCGAGGGGCACATACATGGA 61.695 60.000 0.00 0.00 0.00 3.41
1395 1411 2.443952 ATCGATCCCCGCCACAGA 60.444 61.111 0.00 0.00 38.37 3.41
1400 1416 2.182030 GATCGATCGATCCCCGCC 59.818 66.667 36.97 18.96 43.71 6.13
1435 1451 0.546122 CCCCCAATCACCGATCTGAA 59.454 55.000 0.00 0.00 0.00 3.02
1480 1496 0.108585 AGAGCACGCCAAGAGGAAAA 59.891 50.000 0.00 0.00 36.89 2.29
1484 1500 2.507992 CGAGAGCACGCCAAGAGG 60.508 66.667 0.00 0.00 38.23 3.69
1512 1528 6.824305 ATATATACTTGTTCCTTGGCATGC 57.176 37.500 9.90 9.90 0.00 4.06
1635 1658 3.192633 GGTACTAAAGTGGCATGGTTTGG 59.807 47.826 0.00 0.00 0.00 3.28
1699 1723 1.142667 TGCAAGTTCAGTCACCCATGA 59.857 47.619 0.00 0.00 0.00 3.07
1713 1737 8.632679 CCCATTATATTCAGTAACAATGCAAGT 58.367 33.333 0.00 0.00 0.00 3.16
1759 1783 0.317479 ACTAAGGTGACAGACGGCAC 59.683 55.000 0.00 0.00 0.00 5.01
1760 1784 1.000506 GAACTAAGGTGACAGACGGCA 59.999 52.381 0.00 0.00 0.00 5.69
1762 1786 3.757493 AGTAGAACTAAGGTGACAGACGG 59.243 47.826 0.00 0.00 0.00 4.79
1763 1787 5.642919 AGTAGTAGAACTAAGGTGACAGACG 59.357 44.000 0.00 0.00 31.62 4.18
1771 1795 7.697946 AGAACACCTAGTAGTAGAACTAAGGT 58.302 38.462 6.14 5.12 35.58 3.50
1870 1895 4.379652 TCATATTCGTGTGATGTCCCATG 58.620 43.478 0.00 0.00 0.00 3.66
1909 1934 5.763204 CGGGTAGCATTTGACCTATTTGTAT 59.237 40.000 0.00 0.00 35.91 2.29
1910 1935 5.120399 CGGGTAGCATTTGACCTATTTGTA 58.880 41.667 0.00 0.00 35.91 2.41
1911 1936 3.945285 CGGGTAGCATTTGACCTATTTGT 59.055 43.478 0.00 0.00 35.91 2.83
1939 2079 0.998145 AGCCCTGCTTCCTTCTCATT 59.002 50.000 0.00 0.00 33.89 2.57
1968 2110 2.098607 ACGGCAATTCAGAATGCATCAG 59.901 45.455 0.00 0.00 44.32 2.90
2286 2428 1.550524 TCGGATCTTGACACTTCAGGG 59.449 52.381 0.00 0.00 31.71 4.45
2417 2560 2.621407 GCATTGTTTCCCTGATCCTCCA 60.621 50.000 0.00 0.00 0.00 3.86
2442 2585 1.272147 GGAAAGCCAACCTCAGATGGT 60.272 52.381 0.00 0.00 43.11 3.55
2459 2602 4.349636 TCTGGTTGTTATTCTCACCAGGAA 59.650 41.667 15.49 0.00 43.43 3.36
2486 2629 6.333416 CGAGGACTCTCTATGTTCAATTTCA 58.667 40.000 0.00 0.00 37.86 2.69
2682 2825 3.630312 TGTGGCGCTTTAAGAAGAAAACT 59.370 39.130 7.64 0.00 34.71 2.66
2816 2959 2.217393 CGCGATGTCTGATTAAGCACTC 59.783 50.000 0.00 0.00 0.00 3.51
2837 2980 3.614616 GTGCTTCACTAGACATACACTGC 59.385 47.826 0.00 0.00 0.00 4.40
2859 3002 9.492973 AAAAGAAAAGAATAAATGGACACATGG 57.507 29.630 0.00 0.00 37.40 3.66
2908 3051 4.842531 TCACATGTTATCCTGGTGACAT 57.157 40.909 0.00 0.30 41.51 3.06
2910 3053 4.943705 ACATTCACATGTTATCCTGGTGAC 59.056 41.667 0.00 0.00 41.16 3.67
2934 3077 3.053693 AGCCTACTGTTTGATGGCCATTA 60.054 43.478 21.84 14.01 44.19 1.90
2976 3119 7.389053 CCATCCTTAAGCAGATGTAATTCTACC 59.611 40.741 16.05 0.00 38.57 3.18
3068 3211 3.007290 GGGTACGGGTATGGGTAGAATTC 59.993 52.174 0.00 0.00 0.00 2.17
3238 3383 6.032717 GGTCATTTACTCGTCTACCTGTTAC 58.967 44.000 0.00 0.00 0.00 2.50
3424 3571 2.773661 CCCATACCCTACCCGTTAAGTT 59.226 50.000 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.