Multiple sequence alignment - TraesCS4D01G276900

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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 TraesCS4D01G276900 chr4D 100.000 3395 0 0 1 3395 448612060 448615454 0.000000e+00 6270.0
1 TraesCS4D01G276900 chr4D 97.671 3091 53 10 1 3089 390756175 390753102 0.000000e+00 5291.0
2 TraesCS4D01G276900 chr4D 91.599 1607 120 11 933 2534 448502796 448504392 0.000000e+00 2206.0
3 TraesCS4D01G276900 chr4D 91.372 1611 122 10 933 2534 390860125 390858523 0.000000e+00 2189.0
4 TraesCS4D01G276900 chr4D 88.630 1328 127 14 1267 2581 448152812 448154128 0.000000e+00 1594.0
5 TraesCS4D01G276900 chr4D 96.845 729 12 5 1 729 390678115 390677398 0.000000e+00 1208.0
6 TraesCS4D01G276900 chr4D 89.286 728 66 11 1 721 390862195 390861473 0.000000e+00 902.0
7 TraesCS4D01G276900 chr4D 89.271 727 64 12 1 721 448500550 448501268 0.000000e+00 898.0
8 TraesCS4D01G276900 chr4D 90.406 542 50 1 1586 2125 448187776 448188317 0.000000e+00 712.0
9 TraesCS4D01G276900 chr4D 89.006 473 51 1 1 473 448467776 448468247 4.880000e-163 584.0
10 TraesCS4D01G276900 chr4D 98.750 320 3 1 3077 3395 390739164 390738845 4.920000e-158 568.0
11 TraesCS4D01G276900 chr4D 91.282 390 32 1 1527 1914 448621859 448622248 6.450000e-147 531.0
12 TraesCS4D01G276900 chr4D 90.840 393 34 1 1527 1917 390732398 390732006 3.000000e-145 525.0
13 TraesCS4D01G276900 chr4D 90.187 214 16 2 976 1189 448152595 448152803 1.200000e-69 274.0
14 TraesCS4D01G276900 chr4D 86.408 103 8 1 802 904 448148312 448148408 1.290000e-19 108.0
15 TraesCS4D01G276900 chr4A 91.088 2637 159 27 791 3395 19167417 19164825 0.000000e+00 3498.0
16 TraesCS4D01G276900 chr4A 89.676 339 33 2 1 339 19168446 19168110 6.730000e-117 431.0
17 TraesCS4D01G276900 chr4A 91.873 283 17 2 3119 3395 742888100 742888382 1.140000e-104 390.0
18 TraesCS4D01G276900 chr4A 87.984 258 22 4 2800 3053 742887767 742888019 2.560000e-76 296.0
19 TraesCS4D01G276900 chr4A 77.959 245 46 7 2549 2789 567044883 567044643 2.730000e-31 147.0
20 TraesCS4D01G276900 chr4A 79.839 124 14 8 860 976 19121931 19121812 2.810000e-11 80.5
21 TraesCS4D01G276900 chr4B 90.622 1834 155 7 880 2705 561021297 561023121 0.000000e+00 2418.0
22 TraesCS4D01G276900 chr4B 86.667 570 46 20 100 659 561018797 561019346 3.750000e-169 604.0
23 TraesCS4D01G276900 chr4B 95.833 72 3 0 1 72 561018725 561018796 2.140000e-22 117.0
24 TraesCS4D01G276900 chr6D 92.195 615 32 4 2788 3395 460672105 460671500 0.000000e+00 856.0
25 TraesCS4D01G276900 chr3B 92.358 615 20 11 2789 3395 53223657 53224252 0.000000e+00 850.0
26 TraesCS4D01G276900 chr3B 83.265 245 39 2 2546 2789 730227930 730228173 1.230000e-54 224.0
27 TraesCS4D01G276900 chr3B 82.731 249 39 4 2542 2789 194268588 194268343 5.700000e-53 219.0
28 TraesCS4D01G276900 chr3B 81.106 217 40 1 2546 2762 547112415 547112630 4.500000e-39 172.0
29 TraesCS4D01G276900 chr6A 90.105 475 29 11 2783 3250 506596793 506596330 4.850000e-168 601.0
30 TraesCS4D01G276900 chr6A 91.845 233 12 2 3170 3395 506596321 506596089 5.470000e-83 318.0
31 TraesCS4D01G276900 chr2D 91.243 354 19 5 3053 3395 615719674 615720026 3.970000e-129 472.0
32 TraesCS4D01G276900 chr2D 89.179 268 20 4 2786 3053 615719372 615719630 3.270000e-85 326.0
33 TraesCS4D01G276900 chr5D 90.952 210 6 8 3187 3395 210198153 210198350 1.550000e-68 270.0
34 TraesCS4D01G276900 chr5D 78.632 234 45 4 126 355 346874438 346874206 2.110000e-32 150.0
35 TraesCS4D01G276900 chr6B 85.714 245 32 3 2548 2790 675396235 675395992 4.350000e-64 255.0
36 TraesCS4D01G276900 chr5A 86.383 235 31 1 2556 2789 81453448 81453214 4.350000e-64 255.0
37 TraesCS4D01G276900 chr1A 85.950 242 30 4 2550 2789 560408067 560407828 4.350000e-64 255.0
38 TraesCS4D01G276900 chr2A 85.833 240 32 2 2548 2786 61503265 61503503 1.560000e-63 254.0
39 TraesCS4D01G276900 chr7A 85.774 239 32 2 2549 2786 57132245 57132482 5.620000e-63 252.0
40 TraesCS4D01G276900 chr3A 85.477 241 35 0 2549 2789 644611395 644611155 5.620000e-63 252.0
41 TraesCS4D01G276900 chr2B 80.816 245 47 0 2545 2789 717097699 717097455 3.460000e-45 193.0
42 TraesCS4D01G276900 chr3D 78.099 242 45 6 120 357 452655522 452655285 2.730000e-31 147.0
43 TraesCS4D01G276900 chr3D 77.600 125 23 5 2274 2397 560797225 560797345 1.690000e-08 71.3


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 TraesCS4D01G276900 chr4D 448612060 448615454 3394 False 6270.000000 6270 100.000000 1 3395 1 chr4D.!!$F4 3394
1 TraesCS4D01G276900 chr4D 390753102 390756175 3073 True 5291.000000 5291 97.671000 1 3089 1 chr4D.!!$R4 3088
2 TraesCS4D01G276900 chr4D 448500550 448504392 3842 False 1552.000000 2206 90.435000 1 2534 2 chr4D.!!$F7 2533
3 TraesCS4D01G276900 chr4D 390858523 390862195 3672 True 1545.500000 2189 90.329000 1 2534 2 chr4D.!!$R5 2533
4 TraesCS4D01G276900 chr4D 390677398 390678115 717 True 1208.000000 1208 96.845000 1 729 1 chr4D.!!$R1 728
5 TraesCS4D01G276900 chr4D 448152595 448154128 1533 False 934.000000 1594 89.408500 976 2581 2 chr4D.!!$F6 1605
6 TraesCS4D01G276900 chr4D 448187776 448188317 541 False 712.000000 712 90.406000 1586 2125 1 chr4D.!!$F2 539
7 TraesCS4D01G276900 chr4A 19164825 19168446 3621 True 1964.500000 3498 90.382000 1 3395 2 chr4A.!!$R3 3394
8 TraesCS4D01G276900 chr4A 742887767 742888382 615 False 343.000000 390 89.928500 2800 3395 2 chr4A.!!$F1 595
9 TraesCS4D01G276900 chr4B 561018725 561023121 4396 False 1046.333333 2418 91.040667 1 2705 3 chr4B.!!$F1 2704
10 TraesCS4D01G276900 chr6D 460671500 460672105 605 True 856.000000 856 92.195000 2788 3395 1 chr6D.!!$R1 607
11 TraesCS4D01G276900 chr3B 53223657 53224252 595 False 850.000000 850 92.358000 2789 3395 1 chr3B.!!$F1 606
12 TraesCS4D01G276900 chr6A 506596089 506596793 704 True 459.500000 601 90.975000 2783 3395 2 chr6A.!!$R1 612
13 TraesCS4D01G276900 chr2D 615719372 615720026 654 False 399.000000 472 90.211000 2786 3395 2 chr2D.!!$F1 609

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
317 318 1.204146 ATAATGTCTCCCACGCCTGT 58.796 50.0 0.0 0.0 0.0 4.00 F
1642 4944 0.905357 CCACCATCTTCCTCTCCGTT 59.095 55.0 0.0 0.0 0.0 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1824 5127 1.302431 CAGGTCGGGCATTCACACA 60.302 57.895 0.0 0.0 0.0 3.72 R
2618 5937 2.440817 ATAGGGGTAGGGTGTGCGC 61.441 63.158 0.0 0.0 0.0 6.09 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
317 318 1.204146 ATAATGTCTCCCACGCCTGT 58.796 50.000 0.00 0.00 0.00 4.00
674 841 2.188161 GGTTGGGTCGAAAACGGCA 61.188 57.895 0.00 0.00 0.00 5.69
987 4273 4.471548 ACGAGCTATATAGGTTGTGGACT 58.528 43.478 26.84 8.29 44.37 3.85
1642 4944 0.905357 CCACCATCTTCCTCTCCGTT 59.095 55.000 0.00 0.00 0.00 4.44
1783 5086 2.159114 GCTTTGCTCACACCAAAAAGGA 60.159 45.455 0.00 0.00 41.22 3.36
1847 5150 1.450312 GAATGCCCGACCTGGACAG 60.450 63.158 0.00 0.00 42.00 3.51
2618 5937 6.499172 ACACTCATCTCTATGAATACACACG 58.501 40.000 0.00 0.00 41.57 4.49
2649 5969 2.759355 ACCCCTATGAACATCTCCGAA 58.241 47.619 0.00 0.00 0.00 4.30
2661 5981 0.608308 TCTCCGAAAGACTGAGCCGA 60.608 55.000 0.00 0.00 31.43 5.54
2712 6033 2.177531 GCGCCTTGTAGTCGACGA 59.822 61.111 10.46 0.94 0.00 4.20
2713 6034 1.868251 GCGCCTTGTAGTCGACGAG 60.868 63.158 10.46 7.07 39.10 4.18
3044 6375 0.398696 TTCCTGCCTTTAAGCCACGA 59.601 50.000 0.00 0.00 0.00 4.35
3266 6746 2.260743 GGGAAAGCTTGCAGCAGC 59.739 61.111 6.80 1.95 45.56 5.25
3276 6756 2.022195 CTTGCAGCAGCTTATGGACAT 58.978 47.619 1.76 0.00 42.74 3.06
3325 6813 3.616721 AAGCCTGAGTCCACGCGT 61.617 61.111 5.58 5.58 31.07 6.01
3378 6867 2.354259 CCTCCTTCTAGCTTTGTGCAG 58.646 52.381 0.00 0.00 45.94 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
317 318 0.034756 CGCATCATTGGACGGGGATA 59.965 55.000 0.00 0.00 0.00 2.59
421 423 2.090967 CGCATCAATTTGTTTGCCTTCG 59.909 45.455 16.07 4.52 35.16 3.79
674 841 6.423604 CCAAGGAAATTCAAGTAAACGCAAAT 59.576 34.615 0.00 0.00 0.00 2.32
987 4273 8.521170 TCTCTTTATAAAATCTCTCTCGGTCA 57.479 34.615 0.00 0.00 0.00 4.02
1116 4402 3.225940 TCATGCACGACTAGATGGAGAT 58.774 45.455 0.00 0.00 0.00 2.75
1117 4403 2.654863 TCATGCACGACTAGATGGAGA 58.345 47.619 0.00 0.00 0.00 3.71
1295 4597 3.425713 CTTGCTGCCGACGCACAT 61.426 61.111 0.00 0.00 41.12 3.21
1471 4773 6.403866 ACAAATTTGTAGTTGAAGCCATCA 57.596 33.333 22.10 0.00 40.16 3.07
1642 4944 2.121963 AAGGTGCCCCTGTCCTCA 60.122 61.111 0.00 0.00 41.56 3.86
1783 5086 3.079131 ATTGCACACGGCGATGTAT 57.921 47.368 16.62 6.84 45.17 2.29
1824 5127 1.302431 CAGGTCGGGCATTCACACA 60.302 57.895 0.00 0.00 0.00 3.72
1847 5150 1.823169 TACACCCTGTCCTTGACGGC 61.823 60.000 0.00 0.00 37.59 5.68
2428 5744 2.093973 CCTACCTGACGCTCATTGAGTT 60.094 50.000 14.90 2.83 31.39 3.01
2618 5937 2.440817 ATAGGGGTAGGGTGTGCGC 61.441 63.158 0.00 0.00 0.00 6.09
2633 5953 5.895928 TCAGTCTTTCGGAGATGTTCATAG 58.104 41.667 0.00 0.00 36.61 2.23
2649 5969 3.894427 AGATGATATGTCGGCTCAGTCTT 59.106 43.478 0.00 0.00 0.00 3.01
2712 6033 3.718815 GTTCAGTGGAAGAAGACGTTCT 58.281 45.455 0.00 0.00 45.56 3.01
2713 6034 2.471743 CGTTCAGTGGAAGAAGACGTTC 59.528 50.000 0.00 0.00 32.62 3.95
3044 6375 3.201487 TGATCTCTCCTTTGCATGATGGT 59.799 43.478 0.00 0.00 0.00 3.55
3266 6746 4.987408 TGGCATTTGTCATGTCCATAAG 57.013 40.909 0.00 0.00 0.00 1.73
3276 6756 6.182627 ACTAGATTGAAGATGGCATTTGTCA 58.817 36.000 0.00 2.98 0.00 3.58
3331 6819 3.923864 ACGACACGGAGCTGCCAA 61.924 61.111 0.00 0.00 35.94 4.52


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

AutoCloner maintained by Alex Coulton.