Multiple sequence alignment - TraesCS5A01G047400

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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 TraesCS5A01G047400 chr5A 100.000 2978 0 0 1 2978 42697367 42694390 0.000000e+00 5500.0
1 TraesCS5A01G047400 chr5A 99.563 1373 6 0 818 2190 43253788 43252416 0.000000e+00 2503.0
2 TraesCS5A01G047400 chr5A 92.593 648 40 8 1 647 43404830 43404190 0.000000e+00 924.0
3 TraesCS5A01G047400 chr5B 94.638 1380 44 20 828 2190 57494821 57493455 0.000000e+00 2111.0
4 TraesCS5A01G047400 chr5B 90.946 497 37 7 1 496 669601986 669601497 0.000000e+00 662.0
5 TraesCS5A01G047400 chr5B 84.739 249 16 6 543 781 57495064 57494828 2.310000e-56 230.0
6 TraesCS5A01G047400 chr5D 94.568 1307 48 7 684 1980 54784570 54785863 0.000000e+00 1999.0
7 TraesCS5A01G047400 chr5D 85.830 494 61 7 1 494 439738354 439738838 1.580000e-142 516.0
8 TraesCS5A01G047400 chr5D 84.008 494 71 6 1 494 440066252 440066737 4.490000e-128 468.0
9 TraesCS5A01G047400 chr5D 86.707 331 24 8 1635 1964 54720508 54720197 1.700000e-92 350.0
10 TraesCS5A01G047400 chr5D 93.855 179 9 2 2014 2190 54710072 54709894 4.890000e-68 268.0
11 TraesCS5A01G047400 chr7A 97.345 791 19 2 2190 2978 8737055 8737845 0.000000e+00 1343.0
12 TraesCS5A01G047400 chr7A 96.456 790 25 3 2190 2978 48229034 48228247 0.000000e+00 1301.0
13 TraesCS5A01G047400 chr7A 84.486 477 51 12 2189 2662 728286084 728285628 1.630000e-122 449.0
14 TraesCS5A01G047400 chr7A 98.182 55 1 0 2189 2243 287518862 287518916 2.440000e-16 97.1
15 TraesCS5A01G047400 chr4B 96.619 769 21 5 2215 2978 469520106 469519338 0.000000e+00 1271.0
16 TraesCS5A01G047400 chr4B 94.545 55 3 0 2189 2243 401122778 401122832 5.290000e-13 86.1
17 TraesCS5A01G047400 chr4A 97.207 752 16 5 2230 2978 584140147 584140896 0.000000e+00 1267.0
18 TraesCS5A01G047400 chr4A 96.941 752 20 3 2230 2978 24611620 24612371 0.000000e+00 1258.0
19 TraesCS5A01G047400 chr4A 87.008 508 57 8 1 507 133845793 133846292 5.570000e-157 564.0
20 TraesCS5A01G047400 chr4A 86.895 496 54 8 1 496 98782131 98782615 2.020000e-151 545.0
21 TraesCS5A01G047400 chr2A 97.067 750 20 2 2231 2978 193461775 193461026 0.000000e+00 1262.0
22 TraesCS5A01G047400 chr2A 96.941 752 21 2 2229 2978 650661147 650661898 0.000000e+00 1260.0
23 TraesCS5A01G047400 chr2A 96.933 750 20 3 2232 2978 193460302 193459553 0.000000e+00 1254.0
24 TraesCS5A01G047400 chr2A 94.643 56 3 0 2188 2243 193460370 193460315 1.470000e-13 87.9
25 TraesCS5A01G047400 chr3A 97.059 748 20 2 2232 2978 688923003 688922257 0.000000e+00 1258.0
26 TraesCS5A01G047400 chr3A 85.484 496 64 7 1 495 131297184 131297672 7.360000e-141 510.0
27 TraesCS5A01G047400 chr3B 91.566 498 35 6 1 497 201886230 201885739 0.000000e+00 680.0
28 TraesCS5A01G047400 chr3B 88.400 500 49 8 1 497 594566721 594567214 7.110000e-166 593.0
29 TraesCS5A01G047400 chr3D 90.946 497 39 4 1 497 548474109 548474599 0.000000e+00 664.0
30 TraesCS5A01G047400 chr3D 85.972 499 62 7 1 497 537593555 537593063 7.310000e-146 527.0
31 TraesCS5A01G047400 chr6A 89.738 497 42 8 1 495 28321777 28321288 7.010000e-176 627.0
32 TraesCS5A01G047400 chr6B 89.149 470 43 8 1 469 49275782 49275320 1.990000e-161 579.0
33 TraesCS5A01G047400 chr6B 84.677 496 65 10 9 500 471004799 471005287 4.460000e-133 484.0
34 TraesCS5A01G047400 chr7D 88.840 457 46 4 6 461 499905089 499904637 9.320000e-155 556.0
35 TraesCS5A01G047400 chr7D 84.188 468 68 4 1 468 47386607 47386146 1.630000e-122 449.0
36 TraesCS5A01G047400 chr1D 86.600 500 50 10 1 497 439713988 439714473 1.210000e-148 536.0
37 TraesCS5A01G047400 chr1D 85.336 491 65 5 1 491 376279873 376280356 4.430000e-138 501.0
38 TraesCS5A01G047400 chr1D 87.113 388 47 3 1 388 58511248 58511632 1.270000e-118 436.0
39 TraesCS5A01G047400 chr1D 90.625 64 4 2 2181 2243 460556476 460556538 1.900000e-12 84.2
40 TraesCS5A01G047400 chr2D 86.593 455 54 5 4 457 398645697 398645249 2.060000e-136 496.0
41 TraesCS5A01G047400 chr2D 78.995 438 78 11 1 433 521409406 521409834 1.350000e-73 287.0
42 TraesCS5A01G047400 chr2D 96.364 55 2 0 2189 2243 494064297 494064243 1.140000e-14 91.6
43 TraesCS5A01G047400 chr6D 83.582 469 45 14 2 470 157168953 157168517 7.680000e-111 411.0


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 TraesCS5A01G047400 chr5A 42694390 42697367 2977 True 5500.000000 5500 100.000000 1 2978 1 chr5A.!!$R1 2977
1 TraesCS5A01G047400 chr5A 43252416 43253788 1372 True 2503.000000 2503 99.563000 818 2190 1 chr5A.!!$R2 1372
2 TraesCS5A01G047400 chr5A 43404190 43404830 640 True 924.000000 924 92.593000 1 647 1 chr5A.!!$R3 646
3 TraesCS5A01G047400 chr5B 57493455 57495064 1609 True 1170.500000 2111 89.688500 543 2190 2 chr5B.!!$R2 1647
4 TraesCS5A01G047400 chr5D 54784570 54785863 1293 False 1999.000000 1999 94.568000 684 1980 1 chr5D.!!$F1 1296
5 TraesCS5A01G047400 chr7A 8737055 8737845 790 False 1343.000000 1343 97.345000 2190 2978 1 chr7A.!!$F1 788
6 TraesCS5A01G047400 chr7A 48228247 48229034 787 True 1301.000000 1301 96.456000 2190 2978 1 chr7A.!!$R1 788
7 TraesCS5A01G047400 chr4B 469519338 469520106 768 True 1271.000000 1271 96.619000 2215 2978 1 chr4B.!!$R1 763
8 TraesCS5A01G047400 chr4A 584140147 584140896 749 False 1267.000000 1267 97.207000 2230 2978 1 chr4A.!!$F4 748
9 TraesCS5A01G047400 chr4A 24611620 24612371 751 False 1258.000000 1258 96.941000 2230 2978 1 chr4A.!!$F1 748
10 TraesCS5A01G047400 chr2A 650661147 650661898 751 False 1260.000000 1260 96.941000 2229 2978 1 chr2A.!!$F1 749
11 TraesCS5A01G047400 chr2A 193459553 193461775 2222 True 867.966667 1262 96.214333 2188 2978 3 chr2A.!!$R1 790
12 TraesCS5A01G047400 chr3A 688922257 688923003 746 True 1258.000000 1258 97.059000 2232 2978 1 chr3A.!!$R1 746

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
735 736 0.731514 TCATCCGTTGTTCGCTCGAC 60.732 55.0 0.0 0.0 38.35 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2329 2386 0.178955 TTGAGGTGGGACGAGGTACA 60.179 55.0 0.0 0.0 0.0 2.9 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
116 117 9.607285 ACATATGAAATGTGAAACGTCTAAAAC 57.393 29.630 10.38 0.00 42.39 2.43
176 177 3.795688 AAAGTTCTTGATGCCAGGAGA 57.204 42.857 0.00 0.00 29.78 3.71
177 178 2.777832 AGTTCTTGATGCCAGGAGAC 57.222 50.000 0.00 0.00 29.78 3.36
186 187 5.645056 TGATGCCAGGAGACCAAATATAA 57.355 39.130 0.00 0.00 0.00 0.98
299 300 4.045590 AGGTAGAGTGGGAGGAGAAACTTA 59.954 45.833 0.00 0.00 0.00 2.24
304 305 3.910627 AGTGGGAGGAGAAACTTACATGT 59.089 43.478 2.69 2.69 0.00 3.21
309 310 5.176592 GGAGGAGAAACTTACATGTGTACC 58.823 45.833 9.11 1.90 0.00 3.34
329 330 2.140717 CGTCCCTGACAAAAGGTGTAC 58.859 52.381 0.00 0.00 41.96 2.90
359 360 3.382227 TCCATTATGCTGCCACTGATTTG 59.618 43.478 0.00 0.00 0.00 2.32
362 363 0.806868 ATGCTGCCACTGATTTGACG 59.193 50.000 0.00 0.00 0.00 4.35
400 401 7.676947 ACAAGAAATATACCGGTGCTATACAT 58.323 34.615 19.93 2.69 0.00 2.29
401 402 8.809066 ACAAGAAATATACCGGTGCTATACATA 58.191 33.333 19.93 5.29 0.00 2.29
402 403 9.817809 CAAGAAATATACCGGTGCTATACATAT 57.182 33.333 19.93 7.68 0.00 1.78
432 433 8.340443 GGTGGGTTATACATTTTTACGAATCTC 58.660 37.037 0.00 0.00 0.00 2.75
433 434 8.060090 GTGGGTTATACATTTTTACGAATCTCG 58.940 37.037 0.00 0.00 46.93 4.04
503 504 5.270083 TCAAAAATGACTTTGCGTGTACAG 58.730 37.500 0.00 0.00 36.44 2.74
607 608 9.678941 GGAACTTTGACTAACCAAGAATAAAAG 57.321 33.333 0.00 0.00 0.00 2.27
651 652 9.444600 TGTTCCTTTTCATTGTAGGTTATACTC 57.555 33.333 0.00 0.00 0.00 2.59
652 653 9.668497 GTTCCTTTTCATTGTAGGTTATACTCT 57.332 33.333 0.00 0.00 0.00 3.24
715 716 2.149578 CAGCTTGAGACAGTTTGGAGG 58.850 52.381 0.00 0.00 0.00 4.30
735 736 0.731514 TCATCCGTTGTTCGCTCGAC 60.732 55.000 0.00 0.00 38.35 4.20
2348 2405 0.178955 TGTACCTCGTCCCACCTCAA 60.179 55.000 0.00 0.00 0.00 3.02
2613 2670 8.147244 TCTTTCTTACCTTAGCCAAATCTACT 57.853 34.615 0.00 0.00 0.00 2.57
2827 2890 5.414454 CCCTCACTTCATCGGTTTATTTTCA 59.586 40.000 0.00 0.00 0.00 2.69
2932 2995 7.582435 TCAATCACGAACAATCTCTAAAGAC 57.418 36.000 0.00 0.00 33.32 3.01
2933 2996 6.308041 TCAATCACGAACAATCTCTAAAGACG 59.692 38.462 0.00 0.00 33.32 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
116 117 8.417780 TTTGGTCACATTTCAAACACATTTAG 57.582 30.769 0.00 0.00 0.00 1.85
277 278 2.822697 AGTTTCTCCTCCCACTCTACC 58.177 52.381 0.00 0.00 0.00 3.18
299 300 0.606604 GTCAGGGACGGTACACATGT 59.393 55.000 0.00 0.00 0.00 3.21
304 305 1.071071 CCTTTTGTCAGGGACGGTACA 59.929 52.381 0.00 0.00 34.95 2.90
309 310 2.140717 GTACACCTTTTGTCAGGGACG 58.859 52.381 0.00 0.00 39.91 4.79
329 330 2.360165 GGCAGCATAATGGACTCCAAAG 59.640 50.000 0.66 0.00 36.95 2.77
383 384 8.689061 CACCTAAATATGTATAGCACCGGTATA 58.311 37.037 6.87 3.53 0.00 1.47
384 385 7.364408 CCACCTAAATATGTATAGCACCGGTAT 60.364 40.741 6.87 0.00 0.00 2.73
385 386 6.071221 CCACCTAAATATGTATAGCACCGGTA 60.071 42.308 6.87 0.00 0.00 4.02
387 388 5.175859 CCACCTAAATATGTATAGCACCGG 58.824 45.833 0.00 0.00 0.00 5.28
401 402 9.683870 TCGTAAAAATGTATAACCCACCTAAAT 57.316 29.630 0.00 0.00 0.00 1.40
402 403 9.512588 TTCGTAAAAATGTATAACCCACCTAAA 57.487 29.630 0.00 0.00 0.00 1.85
426 427 3.748568 GCCATCCACTTATTCCGAGATTC 59.251 47.826 0.00 0.00 0.00 2.52
432 433 0.474184 AGGGCCATCCACTTATTCCG 59.526 55.000 6.18 0.00 38.24 4.30
433 434 2.979678 TCTAGGGCCATCCACTTATTCC 59.020 50.000 6.18 0.00 38.24 3.01
437 438 3.637821 AGATCTAGGGCCATCCACTTA 57.362 47.619 6.18 0.00 38.24 2.24
503 504 6.818142 CCTCAACCCAATTTCCAAACATATTC 59.182 38.462 0.00 0.00 0.00 1.75
625 626 9.444600 GAGTATAACCTACAATGAAAAGGAACA 57.555 33.333 7.75 0.00 34.34 3.18
715 716 0.731514 TCGAGCGAACAACGGATGAC 60.732 55.000 0.00 0.00 42.83 3.06
742 743 2.416372 GATACAACAGCATCGCCGCG 62.416 60.000 6.39 6.39 36.85 6.46
743 744 1.276844 GATACAACAGCATCGCCGC 59.723 57.895 0.00 0.00 0.00 6.53
744 745 1.559814 CGATACAACAGCATCGCCG 59.440 57.895 0.00 0.00 37.79 6.46
1477 1496 4.766088 GCCGTCGACCGCTACGTT 62.766 66.667 19.66 0.00 37.40 3.99
2256 2310 5.474532 GTCCCTGGTTAACCTACGAAATTTT 59.525 40.000 24.78 0.00 36.82 1.82
2329 2386 0.178955 TTGAGGTGGGACGAGGTACA 60.179 55.000 0.00 0.00 0.00 2.90
2348 2405 1.670083 GGTTCGTGGCGGCTTAGTT 60.670 57.895 11.43 0.00 0.00 2.24
2526 2583 4.192317 AGAGATCCGTTGATTTGGCTAAC 58.808 43.478 0.00 0.00 0.00 2.34
2613 2670 9.740239 GCAAATTGCATTAATGAGAGAGATTTA 57.260 29.630 19.73 0.00 44.26 1.40
2827 2890 0.104304 GTTGTGTGAGAGGGTGACGT 59.896 55.000 0.00 0.00 0.00 4.34
2882 2945 8.712285 TTCTACATTACTAAATAACTTGCGCT 57.288 30.769 9.73 0.00 0.00 5.92


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

AutoCloner maintained by Alex Coulton.