Multiple sequence alignment - TraesCS3D01G226800

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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 TraesCS3D01G226800 chr3D 100.000 3503 0 0 1 3503 308560645 308557143 0.000000e+00 6469
1 TraesCS3D01G226800 chr4D 96.355 3512 106 10 1 3503 123348129 123351627 0.000000e+00 5757
2 TraesCS3D01G226800 chr4D 96.014 3512 120 12 1 3503 134977428 134980928 0.000000e+00 5692
3 TraesCS3D01G226800 chr4D 94.842 3509 154 15 1 3503 240996763 240993276 0.000000e+00 5452
4 TraesCS3D01G226800 chr4D 94.208 915 36 9 2595 3503 123561662 123562565 0.000000e+00 1380
5 TraesCS3D01G226800 chr4D 92.754 897 43 11 2600 3494 450897577 450896701 0.000000e+00 1277
6 TraesCS3D01G226800 chr5D 96.294 3508 109 9 3 3503 301052409 301055902 0.000000e+00 5738
7 TraesCS3D01G226800 chr6D 95.501 3512 120 20 1 3503 370020527 370024009 0.000000e+00 5576
8 TraesCS3D01G226800 chr7B 96.893 3315 86 6 1 3310 742950731 742947429 0.000000e+00 5535
9 TraesCS3D01G226800 chr2A 96.891 3313 85 7 1 3307 755478555 755481855 0.000000e+00 5531
10 TraesCS3D01G226800 chr7A 96.742 3315 91 6 1 3310 60170760 60167458 0.000000e+00 5507
11 TraesCS3D01G226800 chr5A 96.649 3312 93 7 1 3307 420183710 420187008 0.000000e+00 5485
12 TraesCS3D01G226800 chr6A 96.359 3323 103 7 1 3317 155855306 155858616 0.000000e+00 5450
13 TraesCS3D01G226800 chr6A 95.973 2980 111 8 345 3318 338514981 338517957 0.000000e+00 4830
14 TraesCS3D01G226800 chr1D 96.338 3250 103 5 1 3247 185745754 185742518 0.000000e+00 5328
15 TraesCS3D01G226800 chr1D 95.541 2893 98 9 616 3503 269428127 269425261 0.000000e+00 4599
16 TraesCS3D01G226800 chr6B 93.069 202 13 1 3303 3503 606986076 606986277 9.510000e-76 294


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 TraesCS3D01G226800 chr3D 308557143 308560645 3502 True 6469 6469 100.000 1 3503 1 chr3D.!!$R1 3502
1 TraesCS3D01G226800 chr4D 123348129 123351627 3498 False 5757 5757 96.355 1 3503 1 chr4D.!!$F1 3502
2 TraesCS3D01G226800 chr4D 134977428 134980928 3500 False 5692 5692 96.014 1 3503 1 chr4D.!!$F3 3502
3 TraesCS3D01G226800 chr4D 240993276 240996763 3487 True 5452 5452 94.842 1 3503 1 chr4D.!!$R1 3502
4 TraesCS3D01G226800 chr4D 123561662 123562565 903 False 1380 1380 94.208 2595 3503 1 chr4D.!!$F2 908
5 TraesCS3D01G226800 chr4D 450896701 450897577 876 True 1277 1277 92.754 2600 3494 1 chr4D.!!$R2 894
6 TraesCS3D01G226800 chr5D 301052409 301055902 3493 False 5738 5738 96.294 3 3503 1 chr5D.!!$F1 3500
7 TraesCS3D01G226800 chr6D 370020527 370024009 3482 False 5576 5576 95.501 1 3503 1 chr6D.!!$F1 3502
8 TraesCS3D01G226800 chr7B 742947429 742950731 3302 True 5535 5535 96.893 1 3310 1 chr7B.!!$R1 3309
9 TraesCS3D01G226800 chr2A 755478555 755481855 3300 False 5531 5531 96.891 1 3307 1 chr2A.!!$F1 3306
10 TraesCS3D01G226800 chr7A 60167458 60170760 3302 True 5507 5507 96.742 1 3310 1 chr7A.!!$R1 3309
11 TraesCS3D01G226800 chr5A 420183710 420187008 3298 False 5485 5485 96.649 1 3307 1 chr5A.!!$F1 3306
12 TraesCS3D01G226800 chr6A 155855306 155858616 3310 False 5450 5450 96.359 1 3317 1 chr6A.!!$F1 3316
13 TraesCS3D01G226800 chr6A 338514981 338517957 2976 False 4830 4830 95.973 345 3318 1 chr6A.!!$F2 2973
14 TraesCS3D01G226800 chr1D 185742518 185745754 3236 True 5328 5328 96.338 1 3247 1 chr1D.!!$R1 3246
15 TraesCS3D01G226800 chr1D 269425261 269428127 2866 True 4599 4599 95.541 616 3503 1 chr1D.!!$R2 2887

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
521 523 1.535833 GTCTGGTCAGGAAGACTCGA 58.464 55.000 0.0 0.0 46.72 4.04 F
1375 1379 1.943340 GAAAAGGGGCTCTAAGCGATG 59.057 52.381 0.0 0.0 43.62 3.84 F
1724 1728 0.035630 GCAGCCACCACTTCAGATCT 60.036 55.000 0.0 0.0 0.00 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1703 1707 0.403271 ATCTGAAGTGGTGGCTGCTT 59.597 50.000 0.00 0.0 0.0 3.91 R
2350 2354 0.464036 TCACAGAAGCCGTTGACAGT 59.536 50.000 0.00 0.0 0.0 3.55 R
2906 2924 1.074951 GTACTTGGGCCTGCACCTT 59.925 57.895 4.53 0.0 0.0 3.50 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
74 76 1.551452 AAGTGCTCGCCTCTAGTTCT 58.449 50.000 0.00 0.00 0.00 3.01
132 134 8.849543 AAGTAGTGGGTTATTGGAAGTATAGA 57.150 34.615 0.00 0.00 0.00 1.98
335 337 4.498894 AGCCCTTACCCATAACACTTAC 57.501 45.455 0.00 0.00 0.00 2.34
521 523 1.535833 GTCTGGTCAGGAAGACTCGA 58.464 55.000 0.00 0.00 46.72 4.04
534 536 5.047021 AGGAAGACTCGAAATCATTCTCACA 60.047 40.000 0.00 0.00 33.17 3.58
626 629 3.336694 AGTGGAAACCTGGGGAAATACAT 59.663 43.478 0.00 0.00 0.00 2.29
740 743 3.094484 TGTTTGGGCCGATTCCTTAAT 57.906 42.857 0.00 0.00 0.00 1.40
743 746 3.593442 TTGGGCCGATTCCTTAATGAT 57.407 42.857 0.00 0.00 0.00 2.45
803 807 2.041301 TATGGGTACGCTGGCCCT 60.041 61.111 11.59 0.00 45.06 5.19
1300 1304 5.905331 ACTGGATCTATTGTGGATGTTCCTA 59.095 40.000 0.00 0.00 37.46 2.94
1375 1379 1.943340 GAAAAGGGGCTCTAAGCGATG 59.057 52.381 0.00 0.00 43.62 3.84
1429 1433 7.221450 CCCAGGGATTATTGAACGTAAATCTA 58.779 38.462 0.00 0.00 0.00 1.98
1434 1438 8.230486 GGGATTATTGAACGTAAATCTATGCAG 58.770 37.037 0.00 0.00 0.00 4.41
1545 1549 7.651027 AACTGGAAATTCTGCAATAGCTATT 57.349 32.000 13.37 13.37 42.74 1.73
1632 1636 3.062639 GTGTCTATGTTGCGATTGGACAG 59.937 47.826 6.37 0.00 33.78 3.51
1671 1675 6.640499 TGGCACAATTAGTTCAAATTCTTTCG 59.360 34.615 0.00 0.00 31.92 3.46
1714 1718 1.250328 CATTCTTGAAGCAGCCACCA 58.750 50.000 0.00 0.00 0.00 4.17
1724 1728 0.035630 GCAGCCACCACTTCAGATCT 60.036 55.000 0.00 0.00 0.00 2.75
1797 1801 2.183478 TCCGCGATAATGGAATGCAT 57.817 45.000 8.23 0.00 0.00 3.96
1911 1915 6.850752 TTTCCAGGGGATGTTTTCTATTTC 57.149 37.500 0.00 0.00 0.00 2.17
1919 1923 5.660864 GGGATGTTTTCTATTTCCATTCCCA 59.339 40.000 0.00 0.00 0.00 4.37
2060 2064 7.675161 TCTCCATTACAGATGGACAAATCTA 57.325 36.000 3.70 0.00 42.81 1.98
2287 2291 1.807142 GAGGTGCAAGGCTTACAGAAC 59.193 52.381 0.00 0.00 0.00 3.01
2522 2527 8.421002 TCTTTAAAAGAAAGCACTTTGCCTTAT 58.579 29.630 0.00 0.00 38.26 1.73
2523 2528 7.945033 TTAAAAGAAAGCACTTTGCCTTATG 57.055 32.000 0.00 0.00 46.52 1.90
2602 2607 1.005450 GCCAACTGAACCCCAATAGGA 59.995 52.381 0.00 0.00 38.24 2.94
2730 2736 0.919289 CAGGATACCCCACCCAACCT 60.919 60.000 0.00 0.00 37.41 3.50
2754 2760 3.084304 GGTTGTGGACCCCCTACC 58.916 66.667 0.00 0.00 43.06 3.18
2755 2761 1.540617 GGTTGTGGACCCCCTACCT 60.541 63.158 5.11 0.00 43.06 3.08
2756 2762 0.252835 GGTTGTGGACCCCCTACCTA 60.253 60.000 5.11 0.00 43.06 3.08
2757 2763 1.627195 GGTTGTGGACCCCCTACCTAT 60.627 57.143 5.11 0.00 43.06 2.57
2758 2764 2.360638 GGTTGTGGACCCCCTACCTATA 60.361 54.545 5.11 0.00 43.06 1.31
2759 2765 2.702478 GTTGTGGACCCCCTACCTATAC 59.298 54.545 0.00 0.00 0.00 1.47
2760 2766 1.221265 TGTGGACCCCCTACCTATACC 59.779 57.143 0.00 0.00 0.00 2.73
2761 2767 1.506859 GTGGACCCCCTACCTATACCT 59.493 57.143 0.00 0.00 0.00 3.08
2762 2768 2.724117 GTGGACCCCCTACCTATACCTA 59.276 54.545 0.00 0.00 0.00 3.08
2895 2913 4.889409 AGTGGTCTGCATAACCCAATATTG 59.111 41.667 14.11 8.58 35.84 1.90
2971 2992 5.774498 AGAAAGAACAGCGAAGGAAAAAT 57.226 34.783 0.00 0.00 0.00 1.82
2982 3003 5.010012 AGCGAAGGAAAAATGTGACAAGAAT 59.990 36.000 0.00 0.00 0.00 2.40
3076 3099 0.324943 AAGCTGCTGTCGGTATTGGT 59.675 50.000 1.35 0.00 0.00 3.67
3086 3109 2.424956 GTCGGTATTGGTAACGTCCTCT 59.575 50.000 0.00 0.00 41.68 3.69
3087 3110 3.091545 TCGGTATTGGTAACGTCCTCTT 58.908 45.455 0.00 0.00 41.68 2.85
3127 3150 1.536709 GCACGAAATCCATCATTGGCC 60.537 52.381 0.00 0.00 43.29 5.36
3231 3254 1.003851 TCATTCGTTTTCCGATCGCC 58.996 50.000 10.32 0.00 46.75 5.54
3378 3404 0.404040 AAAAGGGGTGCTTCGGATCA 59.596 50.000 0.00 0.00 0.00 2.92
3497 3525 9.730705 TCTATCATCTGATTCTTGTTTTTCAGT 57.269 29.630 0.00 0.00 37.46 3.41
3498 3526 9.770503 CTATCATCTGATTCTTGTTTTTCAGTG 57.229 33.333 0.00 0.00 37.46 3.66
3499 3527 6.973843 TCATCTGATTCTTGTTTTTCAGTGG 58.026 36.000 0.00 0.00 37.46 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
132 134 7.004086 TCCTTGGTGACACTTGAGAAATAATT 58.996 34.615 5.39 0.0 42.67 1.40
208 210 6.555463 ATCTCATTTCCCATTGCTTTCATT 57.445 33.333 0.00 0.0 0.00 2.57
335 337 5.163478 CCTCTTTTGGATAGCCCATTTTGAG 60.163 44.000 0.00 0.0 46.10 3.02
420 422 8.644374 AGTACCTTTGCTAATAATCCAAAACA 57.356 30.769 0.00 0.0 0.00 2.83
460 462 9.969001 AAATAAATAGGTTTGTAAGTGCCTAGA 57.031 29.630 0.00 0.0 37.07 2.43
521 523 2.450476 GGGTGGCTGTGAGAATGATTT 58.550 47.619 0.00 0.0 0.00 2.17
605 608 3.163616 TGTATTTCCCCAGGTTTCCAC 57.836 47.619 0.00 0.0 0.00 4.02
626 629 7.943413 TTCAAAATCGAATGAATTGAGCAAA 57.057 28.000 7.36 0.0 36.20 3.68
740 743 1.269102 GGCGCTTTCGACTAGCTATCA 60.269 52.381 7.64 0.0 41.47 2.15
743 746 1.317431 TGGGCGCTTTCGACTAGCTA 61.317 55.000 7.64 0.0 44.85 3.32
803 807 1.543065 TTGCTTACCGCCCCTCGTAA 61.543 55.000 0.00 0.0 38.05 3.18
999 1003 2.092538 AGCTCTGGGTGAGAATTCCATG 60.093 50.000 0.65 0.0 45.39 3.66
1225 1229 4.081087 AGCGGTATCACTACCAAAGACAAT 60.081 41.667 2.96 0.0 46.80 2.71
1300 1304 0.034477 CCTAACATGGCCTTTCCCGT 60.034 55.000 3.32 0.0 0.00 5.28
1333 1337 3.716872 CCATCAATAGGTACTCCCAAGGT 59.283 47.826 0.00 0.0 41.75 3.50
1429 1433 0.609662 GTTTGCATGGGTTCCTGCAT 59.390 50.000 6.60 0.0 46.87 3.96
1434 1438 1.187567 AGCCTGTTTGCATGGGTTCC 61.188 55.000 0.00 0.0 0.00 3.62
1632 1636 1.954146 TGCCACAGTCGAGCGTTTC 60.954 57.895 0.00 0.0 0.00 2.78
1703 1707 0.403271 ATCTGAAGTGGTGGCTGCTT 59.597 50.000 0.00 0.0 0.00 3.91
1714 1718 2.093553 GCAGAGGAGCAAGATCTGAAGT 60.094 50.000 0.00 0.0 42.48 3.01
1865 1869 4.033776 CATGGCCTGGTGGTCGGT 62.034 66.667 3.32 0.0 41.88 4.69
1880 1884 1.063417 CATCCCCTGGAAAAGCCTCAT 60.063 52.381 0.00 0.0 34.34 2.90
1890 1894 4.293634 TGGAAATAGAAAACATCCCCTGGA 59.706 41.667 0.00 0.0 35.55 3.86
2060 2064 6.623767 GCGATAAAAGAGCTCTGTTTCCAAAT 60.624 38.462 24.05 11.2 0.00 2.32
2287 2291 3.257873 TCATATTGTGGTTGTTTGGGCAG 59.742 43.478 0.00 0.0 0.00 4.85
2350 2354 0.464036 TCACAGAAGCCGTTGACAGT 59.536 50.000 0.00 0.0 0.00 3.55
2452 2456 5.427036 TCGTTAGTTAAGCCACCTTTTTG 57.573 39.130 0.00 0.0 32.47 2.44
2545 2550 2.307768 CTACATCTGCGAGTAAGGGGA 58.692 52.381 0.00 0.0 0.00 4.81
2742 2748 1.945786 AGGTATAGGTAGGGGGTCCA 58.054 55.000 0.00 0.0 34.83 4.02
2743 2749 4.078922 GGTATAGGTATAGGTAGGGGGTCC 60.079 54.167 0.00 0.0 0.00 4.46
2745 2751 4.807492 AGGTATAGGTATAGGTAGGGGGT 58.193 47.826 0.00 0.0 0.00 4.95
2746 2752 7.019053 GGTATAGGTATAGGTATAGGTAGGGGG 59.981 48.148 0.00 0.0 0.00 5.40
2758 2764 9.530341 TCATCAGGTATAGGTATAGGTATAGGT 57.470 37.037 0.00 0.0 0.00 3.08
2895 2913 3.430790 GGCCTGCACCTTCATAATTTTCC 60.431 47.826 0.00 0.0 0.00 3.13
2906 2924 1.074951 GTACTTGGGCCTGCACCTT 59.925 57.895 4.53 0.0 0.00 3.50
2971 2992 6.200286 GTCGAGAAAACACTATTCTTGTCACA 59.800 38.462 0.00 0.0 38.76 3.58
3076 3099 7.979444 ATGAATCAAAGAAAAGAGGACGTTA 57.021 32.000 0.00 0.0 0.00 3.18
3086 3109 4.038522 TGCCACGGAATGAATCAAAGAAAA 59.961 37.500 0.00 0.0 0.00 2.29
3087 3110 3.571828 TGCCACGGAATGAATCAAAGAAA 59.428 39.130 0.00 0.0 0.00 2.52
3378 3404 4.470602 CCCTTTCAAAAGTGGTTACTCCT 58.529 43.478 2.09 0.0 35.69 3.69
3427 3455 6.041296 GGATTTCCTTTTCATGCCATATGTCT 59.959 38.462 1.24 0.0 0.00 3.41
3439 3467 5.799827 ACCGAAATTGGATTTCCTTTTCA 57.200 34.783 17.77 0.0 44.40 2.69


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

AutoCloner maintained by Alex Coulton.