Multiple sequence alignment - TraesCS2A01G345000

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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 TraesCS2A01G345000 chr2A 100.000 2537 0 0 901 3437 582839797 582842333 0 4686
1 TraesCS2A01G345000 chr2A 99.416 1542 9 0 901 2442 583097524 583095983 0 2798
2 TraesCS2A01G345000 chr2A 99.157 1542 13 0 901 2442 583105110 583103569 0 2776
3 TraesCS2A01G345000 chr2A 97.082 1542 43 1 901 2442 583266215 583264676 0 2597
4 TraesCS2A01G345000 chr2A 95.580 1561 39 12 901 2442 583254453 583252904 0 2473
5 TraesCS2A01G345000 chr2A 96.711 1064 34 1 1380 2442 583111360 583110297 0 1770
6 TraesCS2A01G345000 chr2A 100.000 800 0 0 1 800 582838897 582839696 0 1478
7 TraesCS2A01G345000 chr2A 95.013 782 36 3 2487 3265 583095980 583095199 0 1225
8 TraesCS2A01G345000 chr2A 94.878 781 38 2 2487 3265 583103566 583102786 0 1219
9 TraesCS2A01G345000 chr2A 94.675 770 39 2 2487 3255 583110294 583109526 0 1194
10 TraesCS2A01G345000 chr2A 94.241 764 42 2 2503 3265 583264672 583263910 0 1166
11 TraesCS2A01G345000 chr2D 97.410 1467 38 0 976 2442 439693780 439695246 0 2499
12 TraesCS2A01G345000 chr2D 95.513 1560 42 4 901 2442 439681497 439683046 0 2468
13 TraesCS2A01G345000 chr2D 95.321 1560 39 5 901 2442 439935798 439934255 0 2446
14 TraesCS2A01G345000 chr2D 95.798 952 38 2 2487 3437 439695249 439696199 0 1535
15 TraesCS2A01G345000 chr2D 95.483 952 41 2 2487 3437 439683049 439683999 0 1519
16 TraesCS2A01G345000 chr2D 95.574 949 40 2 2490 3437 439934249 439933302 0 1519
17 TraesCS2A01G345000 chr2B 96.503 1001 25 3 901 1901 517751429 517752419 0 1646
18 TraesCS2A01G345000 chr2B 94.872 780 39 1 2487 3265 517754453 517755232 0 1218
19 TraesCS2A01G345000 chr2B 92.958 781 38 4 2487 3265 517746971 517747736 0 1122
20 TraesCS2A01G345000 chr2B 97.133 558 16 0 1885 2442 517753893 517754450 0 942
21 TraesCS2A01G345000 chrUn 99.036 830 8 0 1613 2442 444720735 444719906 0 1489
22 TraesCS2A01G345000 chrUn 100.000 800 0 0 1 800 310450783 310451582 0 1478
23 TraesCS2A01G345000 chrUn 93.636 550 33 2 2718 3265 315295688 315295139 0 821
24 TraesCS2A01G345000 chr1A 94.110 798 46 1 2 798 300996127 300995330 0 1212
25 TraesCS2A01G345000 chr1A 93.367 799 51 2 2 798 126870091 126869293 0 1181
26 TraesCS2A01G345000 chr5D 94.508 783 42 1 17 798 348738760 348739542 0 1206
27 TraesCS2A01G345000 chr5D 94.125 783 45 1 17 798 362800081 362799299 0 1190
28 TraesCS2A01G345000 chr4D 93.992 799 45 3 1 798 71869795 71868999 0 1206
29 TraesCS2A01G345000 chr4A 93.617 799 50 1 1 798 527137607 527136809 0 1192
30 TraesCS2A01G345000 chr3D 94.133 784 42 4 17 798 314553599 314552818 0 1190
31 TraesCS2A01G345000 chr7D 93.375 800 51 2 1 798 275406552 275405753 0 1182


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 TraesCS2A01G345000 chr2A 582838897 582842333 3436 False 3082.0 4686 100.0000 1 3437 2 chr2A.!!$F1 3436
1 TraesCS2A01G345000 chr2A 583252904 583254453 1549 True 2473.0 2473 95.5800 901 2442 1 chr2A.!!$R1 1541
2 TraesCS2A01G345000 chr2A 583095199 583097524 2325 True 2011.5 2798 97.2145 901 3265 2 chr2A.!!$R2 2364
3 TraesCS2A01G345000 chr2A 583102786 583105110 2324 True 1997.5 2776 97.0175 901 3265 2 chr2A.!!$R3 2364
4 TraesCS2A01G345000 chr2A 583263910 583266215 2305 True 1881.5 2597 95.6615 901 3265 2 chr2A.!!$R5 2364
5 TraesCS2A01G345000 chr2A 583109526 583111360 1834 True 1482.0 1770 95.6930 1380 3255 2 chr2A.!!$R4 1875
6 TraesCS2A01G345000 chr2D 439693780 439696199 2419 False 2017.0 2499 96.6040 976 3437 2 chr2D.!!$F2 2461
7 TraesCS2A01G345000 chr2D 439681497 439683999 2502 False 1993.5 2468 95.4980 901 3437 2 chr2D.!!$F1 2536
8 TraesCS2A01G345000 chr2D 439933302 439935798 2496 True 1982.5 2446 95.4475 901 3437 2 chr2D.!!$R1 2536
9 TraesCS2A01G345000 chr2B 517746971 517755232 8261 False 1232.0 1646 95.3665 901 3265 4 chr2B.!!$F1 2364
10 TraesCS2A01G345000 chrUn 444719906 444720735 829 True 1489.0 1489 99.0360 1613 2442 1 chrUn.!!$R2 829
11 TraesCS2A01G345000 chrUn 310450783 310451582 799 False 1478.0 1478 100.0000 1 800 1 chrUn.!!$F1 799
12 TraesCS2A01G345000 chrUn 315295139 315295688 549 True 821.0 821 93.6360 2718 3265 1 chrUn.!!$R1 547
13 TraesCS2A01G345000 chr1A 300995330 300996127 797 True 1212.0 1212 94.1100 2 798 1 chr1A.!!$R2 796
14 TraesCS2A01G345000 chr1A 126869293 126870091 798 True 1181.0 1181 93.3670 2 798 1 chr1A.!!$R1 796
15 TraesCS2A01G345000 chr5D 348738760 348739542 782 False 1206.0 1206 94.5080 17 798 1 chr5D.!!$F1 781
16 TraesCS2A01G345000 chr5D 362799299 362800081 782 True 1190.0 1190 94.1250 17 798 1 chr5D.!!$R1 781
17 TraesCS2A01G345000 chr4D 71868999 71869795 796 True 1206.0 1206 93.9920 1 798 1 chr4D.!!$R1 797
18 TraesCS2A01G345000 chr4A 527136809 527137607 798 True 1192.0 1192 93.6170 1 798 1 chr4A.!!$R1 797
19 TraesCS2A01G345000 chr3D 314552818 314553599 781 True 1190.0 1190 94.1330 17 798 1 chr3D.!!$R1 781
20 TraesCS2A01G345000 chr7D 275405753 275406552 799 True 1182.0 1182 93.3750 1 798 1 chr7D.!!$R1 797

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
2181 7274 4.348486 TCAGCTTCACTCTCAAGGTAGAT 58.652 43.478 0.0 0.0 30.39 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3008 8103 0.537371 AAAAGTGGTTGAGAGCGGGG 60.537 55.0 0.0 0.0 0.0 5.73 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
2181 7274 4.348486 TCAGCTTCACTCTCAAGGTAGAT 58.652 43.478 0.00 0.0 30.39 1.98
2271 7364 4.510038 AACGCTTTTCATCAGCAGATTT 57.490 36.364 0.00 0.0 37.07 2.17
2338 7431 3.613494 TTCATTTTATCGACACGGGGA 57.387 42.857 0.00 0.0 0.00 4.81
2400 7493 6.078456 TGGAGGGACATTGAATACTTTGAT 57.922 37.500 0.00 0.0 0.00 2.57
2442 7535 6.073314 TCCCGAGCTAGTGGTTTAATACTAT 58.927 40.000 0.00 0.0 0.00 2.12
2444 7537 7.070322 TCCCGAGCTAGTGGTTTAATACTATTT 59.930 37.037 0.00 0.0 0.00 1.40
2445 7538 7.170998 CCCGAGCTAGTGGTTTAATACTATTTG 59.829 40.741 0.00 0.0 0.00 2.32
2446 7539 7.709613 CCGAGCTAGTGGTTTAATACTATTTGT 59.290 37.037 0.00 0.0 0.00 2.83
2447 7540 9.095065 CGAGCTAGTGGTTTAATACTATTTGTT 57.905 33.333 0.00 0.0 0.00 2.83
2461 7554 6.780706 ACTATTTGTTACTTTGAGTCCACG 57.219 37.500 0.00 0.0 0.00 4.94
2462 7555 5.699458 ACTATTTGTTACTTTGAGTCCACGG 59.301 40.000 0.00 0.0 0.00 4.94
2463 7556 2.536761 TGTTACTTTGAGTCCACGGG 57.463 50.000 0.00 0.0 0.00 5.28
2464 7557 1.071071 TGTTACTTTGAGTCCACGGGG 59.929 52.381 0.00 0.0 0.00 5.73
2465 7558 0.688487 TTACTTTGAGTCCACGGGGG 59.312 55.000 2.42 0.0 38.37 5.40
2466 7559 0.178926 TACTTTGAGTCCACGGGGGA 60.179 55.000 2.42 0.0 45.89 4.81
2474 7567 3.402833 TCCACGGGGGAGAAATACA 57.597 52.632 2.42 0.0 42.15 2.29
2475 7568 1.659022 TCCACGGGGGAGAAATACAA 58.341 50.000 2.42 0.0 42.15 2.41
2476 7569 1.279846 TCCACGGGGGAGAAATACAAC 59.720 52.381 2.42 0.0 42.15 3.32
2477 7570 1.003812 CCACGGGGGAGAAATACAACA 59.996 52.381 0.00 0.0 40.01 3.33
2478 7571 2.356741 CCACGGGGGAGAAATACAACAT 60.357 50.000 0.00 0.0 40.01 2.71
2479 7572 2.682856 CACGGGGGAGAAATACAACATG 59.317 50.000 0.00 0.0 0.00 3.21
2480 7573 2.574369 ACGGGGGAGAAATACAACATGA 59.426 45.455 0.00 0.0 0.00 3.07
2481 7574 2.943033 CGGGGGAGAAATACAACATGAC 59.057 50.000 0.00 0.0 0.00 3.06
2482 7575 2.943033 GGGGGAGAAATACAACATGACG 59.057 50.000 0.00 0.0 0.00 4.35
2483 7576 3.606687 GGGGAGAAATACAACATGACGT 58.393 45.455 0.00 0.0 0.00 4.34
2484 7577 3.374058 GGGGAGAAATACAACATGACGTG 59.626 47.826 0.00 0.0 0.00 4.49
2485 7578 3.374058 GGGAGAAATACAACATGACGTGG 59.626 47.826 0.00 0.0 0.00 4.94
2635 7728 9.031537 CCCCCTTTGTTTTAAAAGACACTATAT 57.968 33.333 0.00 0.0 39.12 0.86
2674 7767 5.054477 GGGTACACTATGCAATGTCGTAAT 58.946 41.667 5.02 0.0 0.00 1.89
2733 7826 6.821665 ACATATGAGGTTACGCAAAGTTGTAT 59.178 34.615 10.38 0.0 0.00 2.29
2746 7839 6.043411 GCAAAGTTGTATCCTAGACTACCAG 58.957 44.000 0.00 0.0 0.00 4.00
2882 7977 5.579511 GGCAGAATCATTGTTGGAAAATGAG 59.420 40.000 5.24 0.0 44.81 2.90
2917 8012 2.277373 CGTACGCTCTCTCGTGCC 60.277 66.667 0.52 0.0 43.21 5.01
2960 8055 2.565645 CCGCGTGCCTATAGGAGCT 61.566 63.158 23.61 0.0 37.39 4.09
3008 8103 1.300233 CCGCACCTTATCTCCTCGC 60.300 63.158 0.00 0.0 0.00 5.03
3011 8106 1.749033 CACCTTATCTCCTCGCCCC 59.251 63.158 0.00 0.0 0.00 5.80
3082 8178 3.787001 GGGCCACGAAGAGGAGGG 61.787 72.222 4.39 0.0 42.26 4.30
3207 8304 4.287781 TGCCGCCGTCGAAGAACA 62.288 61.111 0.00 0.0 39.69 3.18
3255 8352 3.837213 GAGGCCGCCTCCCTCCTAT 62.837 68.421 26.79 0.0 44.36 2.57
3298 8395 3.201494 CGTGAGGAGGACGCTCAT 58.799 61.111 0.00 0.0 0.00 2.90
3355 8452 3.483869 AAGGCCGCCTCCATCCTC 61.484 66.667 13.72 0.0 30.89 3.71
3421 8518 4.147449 CGGAGATGCTGCCACCGA 62.147 66.667 14.96 0.0 45.31 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2148 7241 7.241628 TGAGAGTGAAGCTGATATTATAGGGA 58.758 38.462 0.00 0.00 0.00 4.20
2338 7431 8.686334 AGTTTGTGACTTCATGTTGTATTTCTT 58.314 29.630 0.00 0.00 33.92 2.52
2400 7493 5.852763 TCGGGAGAAAAGATCCACATGGAA 61.853 45.833 4.35 0.00 41.76 3.53
2442 7535 3.207778 CCCGTGGACTCAAAGTAACAAA 58.792 45.455 0.00 0.00 0.00 2.83
2444 7537 1.071071 CCCCGTGGACTCAAAGTAACA 59.929 52.381 0.00 0.00 0.00 2.41
2445 7538 1.609841 CCCCCGTGGACTCAAAGTAAC 60.610 57.143 0.00 0.00 35.39 2.50
2446 7539 0.688487 CCCCCGTGGACTCAAAGTAA 59.312 55.000 0.00 0.00 35.39 2.24
2447 7540 0.178926 TCCCCCGTGGACTCAAAGTA 60.179 55.000 0.00 0.00 38.61 2.24
2448 7541 1.460689 TCCCCCGTGGACTCAAAGT 60.461 57.895 0.00 0.00 38.61 2.66
2449 7542 1.192146 TCTCCCCCGTGGACTCAAAG 61.192 60.000 0.00 0.00 38.61 2.77
2450 7543 0.765135 TTCTCCCCCGTGGACTCAAA 60.765 55.000 0.00 0.00 38.61 2.69
2451 7544 0.765135 TTTCTCCCCCGTGGACTCAA 60.765 55.000 0.00 0.00 38.61 3.02
2452 7545 0.546747 ATTTCTCCCCCGTGGACTCA 60.547 55.000 0.00 0.00 38.61 3.41
2453 7546 1.138464 GTATTTCTCCCCCGTGGACTC 59.862 57.143 0.00 0.00 38.61 3.36
2454 7547 1.201424 GTATTTCTCCCCCGTGGACT 58.799 55.000 0.00 0.00 38.61 3.85
2455 7548 0.906775 TGTATTTCTCCCCCGTGGAC 59.093 55.000 0.00 0.00 38.61 4.02
2456 7549 1.279846 GTTGTATTTCTCCCCCGTGGA 59.720 52.381 0.00 0.00 42.41 4.02
2457 7550 1.003812 TGTTGTATTTCTCCCCCGTGG 59.996 52.381 0.00 0.00 0.00 4.94
2458 7551 2.483014 TGTTGTATTTCTCCCCCGTG 57.517 50.000 0.00 0.00 0.00 4.94
2459 7552 2.574369 TCATGTTGTATTTCTCCCCCGT 59.426 45.455 0.00 0.00 0.00 5.28
2460 7553 2.943033 GTCATGTTGTATTTCTCCCCCG 59.057 50.000 0.00 0.00 0.00 5.73
2461 7554 2.943033 CGTCATGTTGTATTTCTCCCCC 59.057 50.000 0.00 0.00 0.00 5.40
2462 7555 3.374058 CACGTCATGTTGTATTTCTCCCC 59.626 47.826 0.00 0.00 0.00 4.81
2463 7556 3.374058 CCACGTCATGTTGTATTTCTCCC 59.626 47.826 0.00 0.00 0.00 4.30
2464 7557 4.250464 TCCACGTCATGTTGTATTTCTCC 58.750 43.478 0.00 0.00 0.00 3.71
2465 7558 5.812642 AGATCCACGTCATGTTGTATTTCTC 59.187 40.000 0.00 0.00 0.00 2.87
2466 7559 5.582269 CAGATCCACGTCATGTTGTATTTCT 59.418 40.000 0.00 0.00 0.00 2.52
2467 7560 5.351465 ACAGATCCACGTCATGTTGTATTTC 59.649 40.000 0.00 0.00 0.00 2.17
2468 7561 5.245531 ACAGATCCACGTCATGTTGTATTT 58.754 37.500 0.00 0.00 0.00 1.40
2469 7562 4.832248 ACAGATCCACGTCATGTTGTATT 58.168 39.130 0.00 0.00 0.00 1.89
2470 7563 4.471904 ACAGATCCACGTCATGTTGTAT 57.528 40.909 0.00 0.00 0.00 2.29
2471 7564 3.953712 ACAGATCCACGTCATGTTGTA 57.046 42.857 0.00 0.00 0.00 2.41
2472 7565 2.839486 ACAGATCCACGTCATGTTGT 57.161 45.000 0.00 0.00 0.00 3.32
2473 7566 4.488126 AAAACAGATCCACGTCATGTTG 57.512 40.909 0.00 0.00 34.50 3.33
2647 7740 2.026636 ACATTGCATAGTGTACCCCGTT 60.027 45.455 0.00 0.00 0.00 4.44
2648 7741 1.557832 ACATTGCATAGTGTACCCCGT 59.442 47.619 0.00 0.00 0.00 5.28
2674 7767 6.266323 TCAACTTTGCATAACGTTGCTTTTA 58.734 32.000 11.99 0.00 42.50 1.52
2746 7839 7.657336 TCTTTTATTGTTTTGATGTGGAGACC 58.343 34.615 0.00 0.00 0.00 3.85
2798 7892 1.088306 TCGTTCTCGCTCTCTCTTCC 58.912 55.000 0.00 0.00 36.96 3.46
2853 7948 3.266772 TCCAACAATGATTCTGCCTAGGT 59.733 43.478 11.31 0.00 0.00 3.08
2882 7977 3.482783 GTGCGGCGCTTCTCTGTC 61.483 66.667 33.26 8.95 0.00 3.51
3008 8103 0.537371 AAAAGTGGTTGAGAGCGGGG 60.537 55.000 0.00 0.00 0.00 5.73
3138 8234 2.419198 GGATCCGATGCGTGCTCT 59.581 61.111 0.00 0.00 0.00 4.09
3207 8304 3.461773 CCCGATGTGCTCTCCCGT 61.462 66.667 0.00 0.00 0.00 5.28
3417 8514 4.595538 TTGCCTGCGTTCGTCGGT 62.596 61.111 0.00 0.00 40.26 4.69


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

AutoCloner maintained by Alex Coulton.