Multiple sequence alignment - TraesCS4A01G216400

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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 TraesCS4A01G216400 chr4A 100.000 2872 0 0 1 2872 515458192 515455321 0.000000e+00 5304.0
1 TraesCS4A01G216400 chr6A 98.228 2878 45 4 1 2872 18533775 18536652 0.000000e+00 5027.0
2 TraesCS4A01G216400 chr6A 91.346 104 7 2 2245 2346 493557701 493557598 1.070000e-29 141.0
3 TraesCS4A01G216400 chr1A 81.507 1022 135 24 1182 2168 535728829 535729831 0.000000e+00 791.0
4 TraesCS4A01G216400 chr1A 92.015 263 19 2 1 261 32407391 32407653 4.520000e-98 368.0
5 TraesCS4A01G216400 chr7D 78.376 1059 186 27 1188 2216 74459827 74458782 0.000000e+00 647.0
6 TraesCS4A01G216400 chr7D 84.416 154 24 0 964 1117 609606887 609606734 4.960000e-33 152.0
7 TraesCS4A01G216400 chr7D 89.320 103 6 2 2245 2346 25322313 25322411 1.080000e-24 124.0
8 TraesCS4A01G216400 chr2D 77.693 1049 197 24 1188 2209 15445812 15446850 8.800000e-170 606.0
9 TraesCS4A01G216400 chr2D 85.065 154 23 0 961 1114 15445289 15445442 1.070000e-34 158.0
10 TraesCS4A01G216400 chr2D 89.720 107 7 3 2244 2346 18197546 18197440 1.800000e-27 134.0
11 TraesCS4A01G216400 chr2D 88.889 108 7 3 2244 2346 33554441 33554334 8.350000e-26 128.0
12 TraesCS4A01G216400 chr2B 78.310 982 170 31 1257 2210 797769336 797770302 6.850000e-166 593.0
13 TraesCS4A01G216400 chr2B 95.785 261 9 2 3 261 519703207 519703467 1.230000e-113 420.0
14 TraesCS4A01G216400 chr2B 85.806 155 21 1 961 1114 797768782 797768936 2.290000e-36 163.0
15 TraesCS4A01G216400 chr2B 85.161 155 22 1 961 1114 797808395 797808549 1.070000e-34 158.0
16 TraesCS4A01G216400 chr2A 80.073 823 122 24 1445 2231 46343181 46343997 8.930000e-160 573.0
17 TraesCS4A01G216400 chr5A 97.719 263 4 2 1 261 275123172 275123434 4.360000e-123 451.0
18 TraesCS4A01G216400 chr5A 97.719 263 4 2 1 261 330508139 330508401 4.360000e-123 451.0
19 TraesCS4A01G216400 chr5A 93.396 106 5 2 2242 2346 618190316 618190212 3.830000e-34 156.0
20 TraesCS4A01G216400 chr3A 97.719 263 1 3 1 261 698257793 698258052 5.640000e-122 448.0
21 TraesCS4A01G216400 chr3A 79.245 318 51 13 779 1091 743691691 743691998 1.040000e-49 207.0
22 TraesCS4A01G216400 chr3D 79.964 559 93 16 1629 2177 31049369 31049918 7.460000e-106 394.0
23 TraesCS4A01G216400 chr3D 78.752 593 104 18 1629 2210 31000115 31000696 7.510000e-101 377.0
24 TraesCS4A01G216400 chr3D 95.238 42 2 0 1629 1670 31023850 31023891 1.850000e-07 67.6
25 TraesCS4A01G216400 chr3B 90.588 255 22 1 3 255 492623462 492623208 1.270000e-88 337.0
26 TraesCS4A01G216400 chr7B 82.201 309 50 1 1178 1481 121783420 121783728 7.890000e-66 261.0
27 TraesCS4A01G216400 chr4D 90.385 104 7 2 2244 2346 192289400 192289501 1.800000e-27 134.0
28 TraesCS4A01G216400 chr6B 88.182 110 9 3 2241 2346 46138489 46138598 8.350000e-26 128.0
29 TraesCS4A01G216400 chr5D 86.087 115 11 4 2244 2353 500952736 500952622 5.030000e-23 119.0


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 TraesCS4A01G216400 chr4A 515455321 515458192 2871 True 5304 5304 100.000 1 2872 1 chr4A.!!$R1 2871
1 TraesCS4A01G216400 chr6A 18533775 18536652 2877 False 5027 5027 98.228 1 2872 1 chr6A.!!$F1 2871
2 TraesCS4A01G216400 chr1A 535728829 535729831 1002 False 791 791 81.507 1182 2168 1 chr1A.!!$F2 986
3 TraesCS4A01G216400 chr7D 74458782 74459827 1045 True 647 647 78.376 1188 2216 1 chr7D.!!$R1 1028
4 TraesCS4A01G216400 chr2D 15445289 15446850 1561 False 382 606 81.379 961 2209 2 chr2D.!!$F1 1248
5 TraesCS4A01G216400 chr2B 797768782 797770302 1520 False 378 593 82.058 961 2210 2 chr2B.!!$F3 1249
6 TraesCS4A01G216400 chr2A 46343181 46343997 816 False 573 573 80.073 1445 2231 1 chr2A.!!$F1 786
7 TraesCS4A01G216400 chr3D 31049369 31049918 549 False 394 394 79.964 1629 2177 1 chr3D.!!$F3 548
8 TraesCS4A01G216400 chr3D 31000115 31000696 581 False 377 377 78.752 1629 2210 1 chr3D.!!$F1 581

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
382 383 2.096466 CGTTTTACTGCTGAATGTCGCA 60.096 45.455 0.00 0.0 34.54 5.10 F
1376 1683 1.060553 GTCGACCATTGCATGTACACG 59.939 52.381 3.51 0.0 0.00 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1841 2176 0.392706 TGCACACTCGGACAGTCATT 59.607 50.000 2.17 0.0 30.26 2.57 R
2560 2922 1.133325 ACCTGGCACATTTTGGGTGTA 60.133 47.619 0.00 0.0 38.20 2.90 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
350 351 4.429854 AGCATTACTCTCTCATTTCCCC 57.570 45.455 0.00 0.00 0.00 4.81
382 383 2.096466 CGTTTTACTGCTGAATGTCGCA 60.096 45.455 0.00 0.00 34.54 5.10
427 428 4.947388 TCATATCATCCATGGTGCATGATG 59.053 41.667 26.50 17.59 43.81 3.07
588 589 9.853555 CTGAGCATATTTTGGTTTATTTACACA 57.146 29.630 0.00 0.00 35.82 3.72
611 612 7.009083 CACAAGACAAAAATCACGATGTTTTCA 59.991 33.333 0.00 0.00 0.00 2.69
613 614 8.379161 CAAGACAAAAATCACGATGTTTTCAAA 58.621 29.630 0.00 0.00 0.00 2.69
660 661 7.934855 AGAGGATGTTCCAAATGATATATGC 57.065 36.000 0.00 0.00 39.61 3.14
667 668 8.214721 TGTTCCAAATGATATATGCGTTTACA 57.785 30.769 0.00 0.00 0.00 2.41
800 801 6.914259 TCTCTCTCACCATATACTTATTGCG 58.086 40.000 0.00 0.00 0.00 4.85
838 839 3.201726 ACATGCACGCTCACATAAAAC 57.798 42.857 0.00 0.00 0.00 2.43
1173 1372 3.199442 TGGAGTTATGAGGACCAGGAA 57.801 47.619 0.00 0.00 0.00 3.36
1368 1675 1.446099 GAGCTCGTCGACCATTGCA 60.446 57.895 10.58 0.00 0.00 4.08
1376 1683 1.060553 GTCGACCATTGCATGTACACG 59.939 52.381 3.51 0.00 0.00 4.49
1936 2272 8.144478 ACTATGAATCGTTCTGTGCTATATTGT 58.856 33.333 0.00 0.00 0.00 2.71
2246 2607 6.417635 CACATGATTGGTTTCAACACTTGTAC 59.582 38.462 0.00 0.00 35.48 2.90
2253 2614 4.444449 GGTTTCAACACTTGTACTCCCTCT 60.444 45.833 0.00 0.00 0.00 3.69
2317 2678 8.622948 ACAAAAACCAAATTTGAACTAAACCA 57.377 26.923 19.86 0.00 39.56 3.67
2318 2679 9.237187 ACAAAAACCAAATTTGAACTAAACCAT 57.763 25.926 19.86 0.00 39.56 3.55
2319 2680 9.500864 CAAAAACCAAATTTGAACTAAACCATG 57.499 29.630 19.86 0.77 39.56 3.66
2320 2681 9.454859 AAAAACCAAATTTGAACTAAACCATGA 57.545 25.926 19.86 0.00 0.00 3.07
2321 2682 9.625747 AAAACCAAATTTGAACTAAACCATGAT 57.374 25.926 19.86 0.00 0.00 2.45
2457 2819 1.214367 CACGTACGCAGTTGAAACCT 58.786 50.000 16.72 0.00 37.78 3.50
2560 2922 0.892755 CAGGCACATGATTGCAAGGT 59.107 50.000 4.94 0.00 44.94 3.50
2600 2962 3.515901 GGTCCATAGTCCAAACTGAGACT 59.484 47.826 0.00 0.00 45.20 3.24
2653 3015 4.320910 TGTTGCCCAAACACACGA 57.679 50.000 0.00 0.00 43.96 4.35
2733 3095 7.009999 GCATGATGTCTATATCATCGGAAGTTC 59.990 40.741 0.00 0.00 43.93 3.01
2788 3150 1.802365 ACGAAAACTATGCAACCGGTC 59.198 47.619 8.04 0.00 0.00 4.79
2803 3165 1.600164 CCGGTCGTTCGTAACTTGACA 60.600 52.381 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
350 351 4.034048 CAGCAGTAAAACGCCTAATACCAG 59.966 45.833 0.00 0.00 0.00 4.00
382 383 2.203070 GGGATGCGTTGCCGATCT 60.203 61.111 0.00 0.00 35.63 2.75
427 428 1.932511 TGTTACACCGAAACACGTTCC 59.067 47.619 0.00 0.00 40.78 3.62
505 506 3.196254 AGCCATGCCCTTTTTGTATCAAG 59.804 43.478 0.00 0.00 0.00 3.02
547 548 1.336887 GCTCAGGTTAAGCTGACGTGA 60.337 52.381 28.81 18.89 38.96 4.35
588 589 8.472683 TTTGAAAACATCGTGATTTTTGTCTT 57.527 26.923 0.00 0.00 0.00 3.01
613 614 3.005261 TGTTATGCACAGGCGAATGTTTT 59.995 39.130 0.00 0.00 45.35 2.43
622 623 2.113860 TCCTCTTGTTATGCACAGGC 57.886 50.000 0.00 0.00 36.48 4.85
660 661 8.286800 TCTGAAACTTATGTTTGGATGTAAACG 58.713 33.333 11.15 0.00 45.36 3.60
667 668 6.351286 GGGCATTCTGAAACTTATGTTTGGAT 60.351 38.462 11.15 0.00 45.36 3.41
800 801 5.696270 TGCATGTTCCAGATTATCGTGTATC 59.304 40.000 0.00 0.00 0.00 2.24
838 839 2.979006 CGTGTAATAGCGCTCAACAG 57.021 50.000 16.34 7.37 0.00 3.16
916 917 5.508567 TGTCCAGAATCTTTGCCATGAATA 58.491 37.500 0.00 0.00 0.00 1.75
1173 1372 2.524559 GCCAGCCATCCCCATGAT 59.475 61.111 0.00 0.00 30.57 2.45
1376 1683 9.220767 GAATATTCAAACTGATGTATACCCCTC 57.779 37.037 10.68 0.00 0.00 4.30
1714 2042 6.159299 TGCCATCTTTTGATTTCTTGAACA 57.841 33.333 0.00 0.00 36.97 3.18
1814 2145 3.118454 CCAGCGCGTTCGTGGAAT 61.118 61.111 8.43 0.00 38.36 3.01
1841 2176 0.392706 TGCACACTCGGACAGTCATT 59.607 50.000 2.17 0.00 30.26 2.57
1936 2272 2.455291 GCGCAGATGCACGATCACA 61.455 57.895 0.30 0.00 42.21 3.58
1976 2333 5.428253 GGCTACAAGTTACAGATTCATGGA 58.572 41.667 0.00 0.00 0.00 3.41
2246 2607 4.184629 CGAGTAATTTGGAACAGAGGGAG 58.815 47.826 0.00 0.00 42.39 4.30
2253 2614 3.061322 CCACGACGAGTAATTTGGAACA 58.939 45.455 0.00 0.00 0.00 3.18
2294 2655 9.454859 TCATGGTTTAGTTCAAATTTGGTTTTT 57.545 25.926 17.90 3.20 0.00 1.94
2315 2676 4.881273 TCCGTTCCAAATTACTCATCATGG 59.119 41.667 0.00 0.00 0.00 3.66
2317 2678 5.126067 CCTCCGTTCCAAATTACTCATCAT 58.874 41.667 0.00 0.00 0.00 2.45
2318 2679 4.513442 CCTCCGTTCCAAATTACTCATCA 58.487 43.478 0.00 0.00 0.00 3.07
2319 2680 3.877508 CCCTCCGTTCCAAATTACTCATC 59.122 47.826 0.00 0.00 0.00 2.92
2320 2681 3.521937 TCCCTCCGTTCCAAATTACTCAT 59.478 43.478 0.00 0.00 0.00 2.90
2321 2682 2.907696 TCCCTCCGTTCCAAATTACTCA 59.092 45.455 0.00 0.00 0.00 3.41
2440 2802 1.719780 GAGAGGTTTCAACTGCGTACG 59.280 52.381 11.84 11.84 0.00 3.67
2560 2922 1.133325 ACCTGGCACATTTTGGGTGTA 60.133 47.619 0.00 0.00 38.20 2.90
2653 3015 4.760047 GACCCACACGCCGCTCAT 62.760 66.667 0.00 0.00 0.00 2.90
2715 3077 6.038936 TGTGAACGAACTTCCGATGATATAGA 59.961 38.462 0.00 0.00 0.00 1.98
2733 3095 2.450160 GTTGAAGCTGGTTTGTGAACG 58.550 47.619 0.00 0.00 36.61 3.95
2788 3150 4.266976 GGTATGGATGTCAAGTTACGAACG 59.733 45.833 0.00 0.00 36.23 3.95
2803 3165 7.174946 CCGAAATATAAGTTGCTTGGTATGGAT 59.825 37.037 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.