Multiple sequence alignment - TraesCS3A01G178100

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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 TraesCS3A01G178100 chr3A 100.000 3920 0 0 1 3920 202633326 202637245 0.000000e+00 7239
1 TraesCS3A01G178100 chr7A 97.048 3930 92 17 1 3920 84772619 84768704 0.000000e+00 6593
2 TraesCS3A01G178100 chr7A 94.430 3950 148 41 1 3920 107628386 107624479 0.000000e+00 6010
3 TraesCS3A01G178100 chr3D 94.520 3978 130 49 1 3920 591980276 591984223 0.000000e+00 6058
4 TraesCS3A01G178100 chr6A 94.107 2817 109 32 1133 3920 194779043 194776255 0.000000e+00 4229
5 TraesCS3A01G178100 chr6A 93.821 2816 113 35 1133 3920 194751187 194748405 0.000000e+00 4180
6 TraesCS3A01G178100 chr6A 93.746 2814 119 33 1133 3920 194728252 194725470 0.000000e+00 4169
7 TraesCS3A01G178100 chr6A 95.712 513 13 7 1 510 194779543 194779037 0.000000e+00 817
8 TraesCS3A01G178100 chr6A 95.517 513 15 6 1 510 194751688 194751181 0.000000e+00 813
9 TraesCS3A01G178100 chr6A 95.322 513 16 6 1 510 194728753 194728246 0.000000e+00 808
10 TraesCS3A01G178100 chr3B 89.510 2612 209 42 560 3138 757880010 757877431 0.000000e+00 3245
11 TraesCS3A01G178100 chr3B 87.071 758 57 19 3168 3920 757877438 757876717 0.000000e+00 819
12 TraesCS3A01G178100 chr3B 92.128 343 24 3 1 342 757880348 757880008 7.620000e-132 481
13 TraesCS3A01G178100 chr2D 95.037 1068 43 7 1 1066 558931004 558932063 0.000000e+00 1670
14 TraesCS3A01G178100 chr2D 83.887 602 71 20 449 1046 610723751 610724330 5.720000e-153 551
15 TraesCS3A01G178100 chr2D 83.527 601 67 22 449 1046 87590647 87591218 2.070000e-147 532
16 TraesCS3A01G178100 chr1D 96.303 595 16 4 1 594 49524594 49524005 0.000000e+00 972
17 TraesCS3A01G178100 chr1D 83.860 601 73 20 449 1046 481577668 481578247 5.720000e-153 551
18 TraesCS3A01G178100 chr7D 84.027 601 68 21 449 1046 223977816 223978391 1.590000e-153 553


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 TraesCS3A01G178100 chr3A 202633326 202637245 3919 False 7239.0 7239 100.000000 1 3920 1 chr3A.!!$F1 3919
1 TraesCS3A01G178100 chr7A 84768704 84772619 3915 True 6593.0 6593 97.048000 1 3920 1 chr7A.!!$R1 3919
2 TraesCS3A01G178100 chr7A 107624479 107628386 3907 True 6010.0 6010 94.430000 1 3920 1 chr7A.!!$R2 3919
3 TraesCS3A01G178100 chr3D 591980276 591984223 3947 False 6058.0 6058 94.520000 1 3920 1 chr3D.!!$F1 3919
4 TraesCS3A01G178100 chr6A 194776255 194779543 3288 True 2523.0 4229 94.909500 1 3920 2 chr6A.!!$R3 3919
5 TraesCS3A01G178100 chr6A 194748405 194751688 3283 True 2496.5 4180 94.669000 1 3920 2 chr6A.!!$R2 3919
6 TraesCS3A01G178100 chr6A 194725470 194728753 3283 True 2488.5 4169 94.534000 1 3920 2 chr6A.!!$R1 3919
7 TraesCS3A01G178100 chr3B 757876717 757880348 3631 True 1515.0 3245 89.569667 1 3920 3 chr3B.!!$R1 3919
8 TraesCS3A01G178100 chr2D 558931004 558932063 1059 False 1670.0 1670 95.037000 1 1066 1 chr2D.!!$F2 1065
9 TraesCS3A01G178100 chr2D 610723751 610724330 579 False 551.0 551 83.887000 449 1046 1 chr2D.!!$F3 597
10 TraesCS3A01G178100 chr2D 87590647 87591218 571 False 532.0 532 83.527000 449 1046 1 chr2D.!!$F1 597
11 TraesCS3A01G178100 chr1D 49524005 49524594 589 True 972.0 972 96.303000 1 594 1 chr1D.!!$R1 593
12 TraesCS3A01G178100 chr1D 481577668 481578247 579 False 551.0 551 83.860000 449 1046 1 chr1D.!!$F1 597
13 TraesCS3A01G178100 chr7D 223977816 223978391 575 False 553.0 553 84.027000 449 1046 1 chr7D.!!$F1 597

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
944 959 1.250840 GGGGTTTGTGCAGTGGATCC 61.251 60.0 4.2 4.2 0.00 3.36 F
1232 1248 2.099141 TTCTTCTGCCCGACATCAAG 57.901 50.0 0.0 0.0 0.00 3.02 F
2728 2785 1.753903 TTCCTCAAAGGACCCCATGA 58.246 50.0 0.0 0.0 45.78 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2728 2785 1.237285 GCTGGAGCACACATTTCCGT 61.237 55.000 0.0 0.0 41.59 4.69 R
2748 2805 1.734465 CCTGGAGCGAAAGTTGATGTC 59.266 52.381 0.0 0.0 0.00 3.06 R
3644 3726 0.107459 GGAGACCTCTGATTGTGCCC 60.107 60.000 0.0 0.0 0.00 5.36 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
798 813 3.146066 AGATTGCGACCAAAGCTTACAA 58.854 40.909 0.00 0.00 34.05 2.41
914 929 4.093743 TCTGTTGGAGCTGGTTGACTATA 58.906 43.478 0.00 0.00 0.00 1.31
944 959 1.250840 GGGGTTTGTGCAGTGGATCC 61.251 60.000 4.20 4.20 0.00 3.36
1042 1058 3.320610 TTGTGTTGGGGATTCCTTCAA 57.679 42.857 2.01 5.43 36.20 2.69
1216 1232 4.771577 TGGTTGTGGCATTATCAACATTCT 59.228 37.500 17.17 0.00 41.87 2.40
1232 1248 2.099141 TTCTTCTGCCCGACATCAAG 57.901 50.000 0.00 0.00 0.00 3.02
1572 1592 7.867403 TCTGTTGCCTTGATTTTACTGATTTTC 59.133 33.333 0.00 0.00 0.00 2.29
1743 1764 4.501915 CCAAAAGCATGACATCCTTTGTGT 60.502 41.667 5.11 0.00 39.18 3.72
2230 2262 4.546829 ATTGAATGCAAGCCAACAATCT 57.453 36.364 0.00 0.00 37.45 2.40
2638 2695 5.323371 TGCTAATAGGCCACACATTTTTC 57.677 39.130 5.01 0.00 0.00 2.29
2728 2785 1.753903 TTCCTCAAAGGACCCCATGA 58.246 50.000 0.00 0.00 45.78 3.07
2748 2805 1.503542 GGAAATGTGTGCTCCAGCG 59.496 57.895 0.00 0.00 45.83 5.18
3217 3287 5.635417 GCTTATTGGAGAAGCAAAAGAGT 57.365 39.130 2.70 0.00 46.97 3.24
3219 3289 7.145932 GCTTATTGGAGAAGCAAAAGAGTAA 57.854 36.000 2.70 0.00 46.97 2.24
3222 3292 8.635765 TTATTGGAGAAGCAAAAGAGTAACAT 57.364 30.769 0.00 0.00 0.00 2.71
3286 3356 5.879223 ACAGAGCTCATTCAGTCCAAAATAG 59.121 40.000 17.77 0.00 0.00 1.73
3402 3472 4.097437 CAGTGGCATTCATAGACATGCTTT 59.903 41.667 4.26 0.00 44.50 3.51
3408 3478 5.528690 GCATTCATAGACATGCTTTCCACTA 59.471 40.000 0.00 0.00 42.25 2.74
3507 3582 4.465632 AAACACACTTGAAAAAGGACCC 57.534 40.909 0.00 0.00 0.00 4.46
3508 3583 3.094484 ACACACTTGAAAAAGGACCCA 57.906 42.857 0.00 0.00 0.00 4.51
3519 3594 2.658807 AAGGACCCACAGAGGAAAAC 57.341 50.000 0.00 0.00 41.22 2.43
3644 3726 7.700322 ACTGAAGCATAGACATTAATGTACG 57.300 36.000 20.83 10.57 41.95 3.67
3645 3727 6.701841 ACTGAAGCATAGACATTAATGTACGG 59.298 38.462 20.83 11.75 41.95 4.02
3744 3832 1.039856 TGAGGTTTTTGCAAGAGGCC 58.960 50.000 0.00 0.00 43.89 5.19
3780 3868 4.499183 CGACTTTCTAGACAAGGCAAGAT 58.501 43.478 16.07 0.42 0.00 2.40
3798 3886 6.404293 GGCAAGATAAAAATACTTCTTCGCCA 60.404 38.462 14.45 0.00 39.49 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
469 475 9.903682 GCAACACAAATCATTCATTAGCTATAT 57.096 29.630 0.00 0.0 0.00 0.86
470 476 8.352201 GGCAACACAAATCATTCATTAGCTATA 58.648 33.333 0.00 0.0 0.00 1.31
721 735 4.655963 TCCTTGCTCTCTGCTACAAAAAT 58.344 39.130 0.00 0.0 43.37 1.82
728 743 2.169352 GGTCAATCCTTGCTCTCTGCTA 59.831 50.000 0.00 0.0 43.37 3.49
798 813 0.179056 GTATGGCATGCTACACCGGT 60.179 55.000 18.92 0.0 0.00 5.28
944 959 3.798337 GCTTTTGTGTCAACATTGTCAGG 59.202 43.478 0.00 0.0 35.83 3.86
1042 1058 8.934023 TCTTTAGTGTTTATGATTGTTTCCCT 57.066 30.769 0.00 0.0 0.00 4.20
1216 1232 0.955428 GTGCTTGATGTCGGGCAGAA 60.955 55.000 0.00 0.0 35.29 3.02
1232 1248 2.880963 TTTGGTGCTTGGTTTAGTGC 57.119 45.000 0.00 0.0 0.00 4.40
1304 1320 2.925724 ACTCCCAATCGTGAACAAACA 58.074 42.857 0.00 0.0 0.00 2.83
1548 1568 6.640499 CGAAAATCAGTAAAATCAAGGCAACA 59.360 34.615 0.00 0.0 41.41 3.33
1572 1592 4.644103 AAGATGGGATTTGAATTGAGCG 57.356 40.909 0.00 0.0 0.00 5.03
2131 2163 1.675552 TGATGCGGATCGTGTCTAGA 58.324 50.000 12.54 0.0 0.00 2.43
2230 2262 3.958147 TGACAGTGTCTCCTGAGTTGTTA 59.042 43.478 23.29 0.0 36.30 2.41
2638 2695 5.344884 TGGTTAGACGCAAAAAGAAAAAGG 58.655 37.500 0.00 0.0 0.00 3.11
2728 2785 1.237285 GCTGGAGCACACATTTCCGT 61.237 55.000 0.00 0.0 41.59 4.69
2748 2805 1.734465 CCTGGAGCGAAAGTTGATGTC 59.266 52.381 0.00 0.0 0.00 3.06
3127 3197 3.181429 TGGGCTTCATCCTTTTCTTCACT 60.181 43.478 0.00 0.0 0.00 3.41
3219 3289 7.118390 GCACTCTCTACTACATTTTGAACATGT 59.882 37.037 2.30 2.3 38.45 3.21
3222 3292 5.932303 GGCACTCTCTACTACATTTTGAACA 59.068 40.000 0.00 0.0 0.00 3.18
3236 3306 1.077169 TGTCCTCCTTGGCACTCTCTA 59.923 52.381 0.00 0.0 35.26 2.43
3286 3356 4.564769 TGTTTGCTTTGATTCCGTGAAAAC 59.435 37.500 0.00 0.0 0.00 2.43
3402 3472 9.219603 CAAAAAGATTGACAACTAGATAGTGGA 57.780 33.333 0.00 0.0 36.50 4.02
3408 3478 9.566432 AGAAGACAAAAAGATTGACAACTAGAT 57.434 29.630 0.00 0.0 0.00 1.98
3507 3582 3.826729 CCCCCTAAAAGTTTTCCTCTGTG 59.173 47.826 3.60 0.0 0.00 3.66
3508 3583 3.754172 GCCCCCTAAAAGTTTTCCTCTGT 60.754 47.826 3.60 0.0 0.00 3.41
3644 3726 0.107459 GGAGACCTCTGATTGTGCCC 60.107 60.000 0.00 0.0 0.00 5.36
3645 3727 0.908198 AGGAGACCTCTGATTGTGCC 59.092 55.000 0.00 0.0 0.00 5.01
3780 3868 8.342634 GCTATCATTGGCGAAGAAGTATTTTTA 58.657 33.333 0.00 0.0 0.00 1.52
3798 3886 2.785269 TGAATGAGGGGGTGCTATCATT 59.215 45.455 0.00 0.0 43.26 2.57
3825 3913 3.066342 CCACATTCATCCACATCTTCAGC 59.934 47.826 0.00 0.0 0.00 4.26


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

AutoCloner maintained by Alex Coulton.