Multiple sequence alignment - TraesCS4A01G138700

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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 TraesCS4A01G138700 chr4A 100.000 2479 0 0 1 2479 205924349 205926827 0.000000e+00 4578
1 TraesCS4A01G138700 chr4A 94.257 2490 126 5 1 2479 205932275 205934758 0.000000e+00 3790
2 TraesCS4A01G138700 chr4A 86.499 1348 145 29 1 1328 197215291 197213961 0.000000e+00 1447
3 TraesCS4A01G138700 chr4A 93.717 764 33 5 1416 2166 197213988 197213227 0.000000e+00 1131
4 TraesCS4A01G138700 chr4A 88.133 750 70 17 1 739 1955345 1954604 0.000000e+00 874
5 TraesCS4A01G138700 chr4A 86.280 707 77 16 1 697 369774981 369774285 0.000000e+00 750
6 TraesCS4A01G138700 chr4A 84.259 756 93 21 1 747 371441722 371442460 0.000000e+00 713
7 TraesCS4A01G138700 chr6A 90.873 2509 189 20 1 2479 259362610 259360112 0.000000e+00 3328
8 TraesCS4A01G138700 chr6A 86.434 1349 137 33 1 1328 266018708 266020031 0.000000e+00 1435
9 TraesCS4A01G138700 chr6A 85.979 1348 146 32 1 1328 266026586 266027910 0.000000e+00 1402
10 TraesCS4A01G138700 chr6A 85.153 1273 141 34 1 1239 430709011 430707753 0.000000e+00 1260
11 TraesCS4A01G138700 chr6A 93.404 758 36 5 1413 2157 266027880 266028636 0.000000e+00 1110
12 TraesCS4A01G138700 chr6A 93.090 767 38 5 1413 2166 266020001 266020765 0.000000e+00 1109
13 TraesCS4A01G138700 chr6A 83.959 773 94 26 1 758 349927720 349926963 0.000000e+00 713
14 TraesCS4A01G138700 chr3A 86.869 1348 139 30 1 1328 347832937 347831608 0.000000e+00 1474
15 TraesCS4A01G138700 chr3A 92.458 769 41 6 1416 2169 347831635 347830869 0.000000e+00 1083
16 TraesCS4A01G138700 chr3A 84.893 748 94 18 1 739 623792295 623791558 0.000000e+00 737
17 TraesCS4A01G138700 chr3A 84.085 754 102 16 1 747 169709855 169710597 0.000000e+00 712
18 TraesCS4A01G138700 chr5A 86.043 1347 153 28 1 1328 176943792 176942462 0.000000e+00 1413
19 TraesCS4A01G138700 chr5A 92.699 767 41 5 1416 2169 176942489 176941725 0.000000e+00 1092
20 TraesCS4A01G138700 chr5A 90.928 474 38 5 2009 2479 219163085 219162614 1.250000e-177 632
21 TraesCS4A01G138700 chr7A 92.960 767 39 5 1413 2166 420702670 420703434 0.000000e+00 1103
22 TraesCS4A01G138700 chr7A 91.942 695 43 9 636 1328 420702017 420702700 0.000000e+00 961
23 TraesCS4A01G138700 chr7A 90.336 476 44 2 2005 2479 116728665 116729139 7.530000e-175 623
24 TraesCS4A01G138700 chr7A 90.361 415 35 3 1248 1657 324967678 324968092 7.800000e-150 540
25 TraesCS4A01G138700 chr7A 90.541 370 23 9 1623 1988 324976882 324977243 1.720000e-131 479
26 TraesCS4A01G138700 chr1A 87.228 689 72 15 1 682 129379144 129379823 0.000000e+00 771
27 TraesCS4A01G138700 chr1A 91.458 480 40 1 2001 2479 183678824 183678345 0.000000e+00 658
28 TraesCS4A01G138700 chr1A 90.966 476 41 2 2005 2479 217151403 217151877 7.480000e-180 640
29 TraesCS4A01G138700 chr1A 90.776 477 41 3 2005 2479 217121568 217122043 3.480000e-178 634
30 TraesCS4A01G138700 chr1A 90.295 474 44 2 2006 2479 170709921 170710392 9.740000e-174 619
31 TraesCS4A01G138700 chr2A 84.217 773 97 25 1 760 321720011 321719251 0.000000e+00 728
32 TraesCS4A01G138700 chr2A 83.829 773 103 20 1 762 274023103 274023864 0.000000e+00 715
33 TraesCS4A01G138700 chr2A 91.176 476 40 2 2005 2479 69182996 69182522 0.000000e+00 645


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 TraesCS4A01G138700 chr4A 205924349 205926827 2478 False 4578.0 4578 100.0000 1 2479 1 chr4A.!!$F1 2478
1 TraesCS4A01G138700 chr4A 205932275 205934758 2483 False 3790.0 3790 94.2570 1 2479 1 chr4A.!!$F2 2478
2 TraesCS4A01G138700 chr4A 197213227 197215291 2064 True 1289.0 1447 90.1080 1 2166 2 chr4A.!!$R3 2165
3 TraesCS4A01G138700 chr4A 1954604 1955345 741 True 874.0 874 88.1330 1 739 1 chr4A.!!$R1 738
4 TraesCS4A01G138700 chr4A 369774285 369774981 696 True 750.0 750 86.2800 1 697 1 chr4A.!!$R2 696
5 TraesCS4A01G138700 chr4A 371441722 371442460 738 False 713.0 713 84.2590 1 747 1 chr4A.!!$F3 746
6 TraesCS4A01G138700 chr6A 259360112 259362610 2498 True 3328.0 3328 90.8730 1 2479 1 chr6A.!!$R1 2478
7 TraesCS4A01G138700 chr6A 266018708 266020765 2057 False 1272.0 1435 89.7620 1 2166 2 chr6A.!!$F1 2165
8 TraesCS4A01G138700 chr6A 430707753 430709011 1258 True 1260.0 1260 85.1530 1 1239 1 chr6A.!!$R3 1238
9 TraesCS4A01G138700 chr6A 266026586 266028636 2050 False 1256.0 1402 89.6915 1 2157 2 chr6A.!!$F2 2156
10 TraesCS4A01G138700 chr6A 349926963 349927720 757 True 713.0 713 83.9590 1 758 1 chr6A.!!$R2 757
11 TraesCS4A01G138700 chr3A 347830869 347832937 2068 True 1278.5 1474 89.6635 1 2169 2 chr3A.!!$R2 2168
12 TraesCS4A01G138700 chr3A 623791558 623792295 737 True 737.0 737 84.8930 1 739 1 chr3A.!!$R1 738
13 TraesCS4A01G138700 chr3A 169709855 169710597 742 False 712.0 712 84.0850 1 747 1 chr3A.!!$F1 746
14 TraesCS4A01G138700 chr5A 176941725 176943792 2067 True 1252.5 1413 89.3710 1 2169 2 chr5A.!!$R2 2168
15 TraesCS4A01G138700 chr7A 420702017 420703434 1417 False 1032.0 1103 92.4510 636 2166 2 chr7A.!!$F4 1530
16 TraesCS4A01G138700 chr1A 129379144 129379823 679 False 771.0 771 87.2280 1 682 1 chr1A.!!$F1 681
17 TraesCS4A01G138700 chr2A 321719251 321720011 760 True 728.0 728 84.2170 1 760 1 chr2A.!!$R2 759
18 TraesCS4A01G138700 chr2A 274023103 274023864 761 False 715.0 715 83.8290 1 762 1 chr2A.!!$F1 761

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
925 1008 0.037326 TGAAGAAGAACGGCAGCGAT 60.037 50.0 0.0 0.0 0.0 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1727 1934 0.395311 CACCTCCTGCAGCCATGAAT 60.395 55.0 8.66 0.0 0.0 2.57 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
19 20 2.082366 GCACGATGCGCAAACAAGG 61.082 57.895 17.11 3.23 31.71 3.61
92 96 6.542370 GCAATCCTACAAATTAAGTGGAGCTA 59.458 38.462 0.00 0.00 0.00 3.32
97 101 9.609346 TCCTACAAATTAAGTGGAGCTAAATAC 57.391 33.333 0.00 0.00 0.00 1.89
117 122 1.536766 CGCAACGGGATGCATATTGAT 59.463 47.619 0.00 0.00 46.76 2.57
251 262 2.435372 TAAATGAGGCCGGAAGCAAT 57.565 45.000 5.05 0.00 46.50 3.56
258 270 0.316841 GGCCGGAAGCAATGAACAAA 59.683 50.000 5.05 0.00 46.50 2.83
425 441 7.647907 ACAACCGAGTTACTGTTATTTAGTG 57.352 36.000 0.00 0.00 0.00 2.74
462 478 9.125906 GCATTTTAGCATATTCATAGAGCAAAG 57.874 33.333 0.00 0.00 0.00 2.77
925 1008 0.037326 TGAAGAAGAACGGCAGCGAT 60.037 50.000 0.00 0.00 0.00 4.58
996 1079 3.407967 GGACCCAGCCGGATCCAA 61.408 66.667 13.41 0.00 33.98 3.53
1331 1527 3.509659 GCCACGGGCTTGGATAAC 58.490 61.111 9.54 0.00 46.69 1.89
1341 1537 2.433436 GCTTGGATAACCGGAGTTTGT 58.567 47.619 9.46 0.00 37.42 2.83
1370 1566 1.606350 GACGACGTTGACGAAGCAGG 61.606 60.000 10.51 0.00 43.02 4.85
1376 1572 2.144078 TTGACGAAGCAGGGGTCCA 61.144 57.895 0.00 0.00 0.00 4.02
1389 1585 0.323629 GGGTCCAACGAATCCAGACA 59.676 55.000 0.00 0.00 0.00 3.41
1396 1592 1.448540 CGAATCCAGACAGCGGCTT 60.449 57.895 0.00 0.00 0.00 4.35
1408 1604 3.604667 CGGCTTGCAACAAGGGCA 61.605 61.111 9.50 0.00 40.00 5.36
1423 1619 3.132801 GCAGCAGAGGAGGCAAGC 61.133 66.667 0.00 0.00 0.00 4.01
1586 1782 1.000993 ATGGAGTCGGGTGCTCTCT 59.999 57.895 0.00 0.00 33.73 3.10
1676 1883 3.681835 GTCGGTCCTGGTCGCAGT 61.682 66.667 7.18 0.00 0.00 4.40
1800 2007 3.559171 GCAGACTAGGGAGAGATCGAGAT 60.559 52.174 0.00 0.00 0.00 2.75
1936 2143 2.435693 GGGAGGAGTGGATGGGACG 61.436 68.421 0.00 0.00 0.00 4.79
2044 2253 2.081462 CGGGCGGTCAAGAAAAATAGT 58.919 47.619 0.00 0.00 0.00 2.12
2150 2359 0.901114 TCCGGGACAGATTTCGGACA 60.901 55.000 0.00 0.00 45.37 4.02
2189 2398 2.082231 CGGACTGACGAGAGAGGTTAA 58.918 52.381 0.00 0.00 35.47 2.01
2218 2427 1.139947 GCGGTGAGAGGTAGACTGC 59.860 63.158 0.00 0.00 34.97 4.40
2342 2552 5.014202 AGTTTAACGGTTGGGCTATCAAAT 58.986 37.500 3.07 0.00 0.00 2.32
2371 2581 4.064388 TGAATGCGATGAAACTTGACAGA 58.936 39.130 0.00 0.00 0.00 3.41
2420 2630 1.760029 ACGCCAACTTTCAACCCATTT 59.240 42.857 0.00 0.00 0.00 2.32
2424 2634 3.491792 GCCAACTTTCAACCCATTTCGAA 60.492 43.478 0.00 0.00 0.00 3.71
2436 2646 4.038162 ACCCATTTCGAAAACATTTTCCGA 59.962 37.500 15.66 8.76 42.66 4.55
2446 2656 6.959311 CGAAAACATTTTCCGACCACTTATAG 59.041 38.462 10.70 0.00 42.66 1.31
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 4.275689 TCATTAAACCGGACATGCATCATC 59.724 41.667 9.46 0.00 0.00 2.92
66 70 5.125417 GCTCCACTTAATTTGTAGGATTGCA 59.875 40.000 0.00 0.00 0.00 4.08
92 96 1.388547 ATGCATCCCGTTGCGTATTT 58.611 45.000 0.00 0.00 45.77 1.40
97 101 0.943673 TCAATATGCATCCCGTTGCG 59.056 50.000 0.19 0.00 45.77 4.85
117 122 2.631160 AACTCGAATGTGGTGTTCCA 57.369 45.000 0.00 0.00 42.05 3.53
251 262 5.279556 GGGGATTTACCGGAATTTTTGTTCA 60.280 40.000 9.46 0.00 40.11 3.18
258 270 4.526650 GCATATGGGGATTTACCGGAATTT 59.473 41.667 9.46 0.00 40.11 1.82
878 961 0.169230 CAGCAGTAACTCGCTCGTCT 59.831 55.000 0.00 0.00 35.96 4.18
890 973 2.296190 TCTTCAGAAACGAGCAGCAGTA 59.704 45.455 0.00 0.00 0.00 2.74
925 1008 1.647346 CATCGCCGCTGTTTTACCTA 58.353 50.000 0.00 0.00 0.00 3.08
996 1079 1.687612 CCCAACCCTCTGCATCACT 59.312 57.895 0.00 0.00 0.00 3.41
1188 1271 2.363795 CCTCCGTCCCCTGCTACA 60.364 66.667 0.00 0.00 0.00 2.74
1263 1346 4.680237 CGCGCCAACCTCCTGTCA 62.680 66.667 0.00 0.00 0.00 3.58
1334 1530 1.659335 TCACGTCGCCGACAAACTC 60.659 57.895 18.40 0.00 37.88 3.01
1357 1553 1.671379 GGACCCCTGCTTCGTCAAC 60.671 63.158 0.00 0.00 0.00 3.18
1362 1558 2.725203 TTCGTTGGACCCCTGCTTCG 62.725 60.000 0.00 0.00 0.00 3.79
1370 1566 0.323629 TGTCTGGATTCGTTGGACCC 59.676 55.000 0.00 0.00 0.00 4.46
1376 1572 1.741770 GCCGCTGTCTGGATTCGTT 60.742 57.895 0.00 0.00 0.00 3.85
1389 1585 3.297620 CCCTTGTTGCAAGCCGCT 61.298 61.111 0.00 0.00 43.06 5.52
1396 1592 1.900016 CTCTGCTGCCCTTGTTGCA 60.900 57.895 0.00 0.00 37.17 4.08
1408 1604 4.093291 CCGCTTGCCTCCTCTGCT 62.093 66.667 0.00 0.00 0.00 4.24
1586 1782 3.254166 GTCTCTGTACCAGGTACGAACAA 59.746 47.826 22.53 5.98 41.41 2.83
1676 1883 0.960364 GGCAACCGAAGCTCCATCAA 60.960 55.000 0.00 0.00 0.00 2.57
1727 1934 0.395311 CACCTCCTGCAGCCATGAAT 60.395 55.000 8.66 0.00 0.00 2.57
1800 2007 1.373435 CAAACCGTAGCCCTCCACA 59.627 57.895 0.00 0.00 0.00 4.17
1856 2063 2.746277 GTTTGTCCCATCGCCGCT 60.746 61.111 0.00 0.00 0.00 5.52
1936 2143 0.622446 TCAACCCCTAACCCTAGGCC 60.622 60.000 2.05 0.00 43.25 5.19
2044 2253 4.627284 TTTGTTAATTGGACTCCCTCGA 57.373 40.909 0.00 0.00 0.00 4.04
2101 2310 0.596600 ACAGTCGTTACCGCTGTGTG 60.597 55.000 8.46 0.00 44.15 3.82
2189 2398 4.715130 TCACCGCCAGGCCCTACT 62.715 66.667 5.63 0.00 42.76 2.57
2218 2427 1.007964 CAGCTCGAGACCGCCTATG 60.008 63.158 18.75 0.00 35.37 2.23
2342 2552 4.318332 AGTTTCATCGCATTCAGAGTTCA 58.682 39.130 0.00 0.00 0.00 3.18
2371 2581 9.447157 GGTCTTATTATAGTGTAGATAGACCGT 57.553 37.037 0.00 0.00 32.92 4.83
2420 2630 3.207778 AGTGGTCGGAAAATGTTTTCGA 58.792 40.909 10.98 0.00 45.68 3.71
2424 2634 7.989416 TTCTATAAGTGGTCGGAAAATGTTT 57.011 32.000 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.