Multiple sequence alignment - TraesCS4A01G197500

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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 TraesCS4A01G197500 chr4A 100.000 4589 0 0 1 4589 481088393 481092981 0.000000e+00 8475
1 TraesCS4A01G197500 chr4A 88.588 2848 263 26 897 3724 90394584 90391779 0.000000e+00 3402
2 TraesCS4A01G197500 chr3B 99.085 4589 41 1 1 4589 768505294 768509881 0.000000e+00 8240
3 TraesCS4A01G197500 chr1A 98.562 4589 61 2 1 4589 146608815 146613398 0.000000e+00 8104
4 TraesCS4A01G197500 chr1A 98.890 3873 32 2 717 4589 482818549 482822410 0.000000e+00 6903
5 TraesCS4A01G197500 chr1A 84.863 2735 350 45 990 3694 555296116 555298816 0.000000e+00 2699
6 TraesCS4A01G197500 chr1A 97.922 722 15 0 1 722 482816841 482817562 0.000000e+00 1251
7 TraesCS4A01G197500 chr5D 97.348 4601 79 15 1 4589 550419957 550415388 0.000000e+00 7781
8 TraesCS4A01G197500 chr7D 97.110 4602 86 17 1 4589 4416617 4421184 0.000000e+00 7718
9 TraesCS4A01G197500 chr5A 97.833 4245 70 12 189 4432 612386600 612382377 0.000000e+00 7310
10 TraesCS4A01G197500 chrUn 98.880 2767 28 2 1825 4589 62686915 62689680 0.000000e+00 4935
11 TraesCS4A01G197500 chrUn 98.856 1835 20 1 1 1834 62671811 62673645 0.000000e+00 3271
12 TraesCS4A01G197500 chr3D 89.198 2944 251 40 897 3797 41716731 41719650 0.000000e+00 3613
13 TraesCS4A01G197500 chr7A 89.119 2849 268 26 897 3724 727630581 727627754 0.000000e+00 3506
14 TraesCS4A01G197500 chr1D 88.594 2937 263 42 897 3797 69859692 69862592 0.000000e+00 3502
15 TraesCS4A01G197500 chr1D 96.313 1329 24 10 3261 4589 334045201 334043898 0.000000e+00 2159
16 TraesCS4A01G197500 chr1D 95.856 917 28 2 1 907 334046136 334045220 0.000000e+00 1474
17 TraesCS4A01G197500 chr6B 91.934 1091 40 16 3514 4589 279329654 279328597 0.000000e+00 1483
18 TraesCS4A01G197500 chr6B 94.761 878 34 3 1 868 279330534 279329659 0.000000e+00 1356
19 TraesCS4A01G197500 chr4D 80.519 154 22 5 4330 4476 40412377 40412225 1.350000e-20 111


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 TraesCS4A01G197500 chr4A 481088393 481092981 4588 False 8475.0 8475 100.0000 1 4589 1 chr4A.!!$F1 4588
1 TraesCS4A01G197500 chr4A 90391779 90394584 2805 True 3402.0 3402 88.5880 897 3724 1 chr4A.!!$R1 2827
2 TraesCS4A01G197500 chr3B 768505294 768509881 4587 False 8240.0 8240 99.0850 1 4589 1 chr3B.!!$F1 4588
3 TraesCS4A01G197500 chr1A 146608815 146613398 4583 False 8104.0 8104 98.5620 1 4589 1 chr1A.!!$F1 4588
4 TraesCS4A01G197500 chr1A 482816841 482822410 5569 False 4077.0 6903 98.4060 1 4589 2 chr1A.!!$F3 4588
5 TraesCS4A01G197500 chr1A 555296116 555298816 2700 False 2699.0 2699 84.8630 990 3694 1 chr1A.!!$F2 2704
6 TraesCS4A01G197500 chr5D 550415388 550419957 4569 True 7781.0 7781 97.3480 1 4589 1 chr5D.!!$R1 4588
7 TraesCS4A01G197500 chr7D 4416617 4421184 4567 False 7718.0 7718 97.1100 1 4589 1 chr7D.!!$F1 4588
8 TraesCS4A01G197500 chr5A 612382377 612386600 4223 True 7310.0 7310 97.8330 189 4432 1 chr5A.!!$R1 4243
9 TraesCS4A01G197500 chrUn 62686915 62689680 2765 False 4935.0 4935 98.8800 1825 4589 1 chrUn.!!$F2 2764
10 TraesCS4A01G197500 chrUn 62671811 62673645 1834 False 3271.0 3271 98.8560 1 1834 1 chrUn.!!$F1 1833
11 TraesCS4A01G197500 chr3D 41716731 41719650 2919 False 3613.0 3613 89.1980 897 3797 1 chr3D.!!$F1 2900
12 TraesCS4A01G197500 chr7A 727627754 727630581 2827 True 3506.0 3506 89.1190 897 3724 1 chr7A.!!$R1 2827
13 TraesCS4A01G197500 chr1D 69859692 69862592 2900 False 3502.0 3502 88.5940 897 3797 1 chr1D.!!$F1 2900
14 TraesCS4A01G197500 chr1D 334043898 334046136 2238 True 1816.5 2159 96.0845 1 4589 2 chr1D.!!$R1 4588
15 TraesCS4A01G197500 chr6B 279328597 279330534 1937 True 1419.5 1483 93.3475 1 4589 2 chr6B.!!$R1 4588

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
160 161 1.656587 TAGGACTGCACACCTCCATT 58.343 50.000 9.81 0.00 37.68 3.16 F
206 207 2.837591 TCCGGTCTTCAATCAGGATTCA 59.162 45.455 0.00 0.00 0.00 2.57 F
1957 2970 1.000827 GAGATGGATGATGAGACGCGT 60.001 52.381 13.85 13.85 0.00 6.01 F
2315 3348 6.355144 GGTTATTCAAAACAACTCGTAACACG 59.645 38.462 0.00 0.00 44.19 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1176 2184 4.817517 TCTCTACCCTTGAATCGTTGAAC 58.182 43.478 0.00 0.0 0.00 3.18 R
2315 3348 8.604890 GTTTTCTGAGCACCAGTTAATATAGAC 58.395 37.037 6.11 0.0 43.38 2.59 R
2878 3916 3.438781 TGCCATTACATTTTGAGACGGAC 59.561 43.478 0.00 0.0 0.00 4.79 R
4188 5262 1.886777 GGCGATTCAGAGGAGCAGC 60.887 63.158 0.00 0.0 0.00 5.25 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
36 37 6.265422 GCCTATATAACAGGATTTTGTTGGCT 59.735 38.462 7.73 0.00 39.82 4.75
160 161 1.656587 TAGGACTGCACACCTCCATT 58.343 50.000 9.81 0.00 37.68 3.16
206 207 2.837591 TCCGGTCTTCAATCAGGATTCA 59.162 45.455 0.00 0.00 0.00 2.57
350 351 5.047906 ACCCTATTTTCCATACAACCCCTA 58.952 41.667 0.00 0.00 0.00 3.53
543 553 9.442047 AGTAGTTAGTTTTTCATGAGAAGGATG 57.558 33.333 0.00 0.00 34.71 3.51
1176 2184 4.240888 CATGGCGTGATATCTTAGGACAG 58.759 47.826 0.00 0.00 0.00 3.51
1957 2970 1.000827 GAGATGGATGATGAGACGCGT 60.001 52.381 13.85 13.85 0.00 6.01
2315 3348 6.355144 GGTTATTCAAAACAACTCGTAACACG 59.645 38.462 0.00 0.00 44.19 4.49
2878 3916 7.227156 ACTCCTTATAGAAATAGGCATGGTTG 58.773 38.462 0.00 0.00 0.00 3.77
3095 4134 4.005650 CTGTGCTATGAAACCTCATGTGT 58.994 43.478 0.00 0.00 42.48 3.72
3128 4168 8.806429 TTTTATCTTGTTGATTCAGGCTATGA 57.194 30.769 0.00 0.00 36.65 2.15
3797 4871 8.728088 AATGAAGCAACAAATAAACTACTTCG 57.272 30.769 0.00 0.00 36.04 3.79
4253 5327 3.737972 CGCTGTTACTCATGGTCATGCTA 60.738 47.826 6.10 0.00 38.65 3.49
4360 5434 2.281139 GCCGGCATTCTAGGGAGC 60.281 66.667 24.80 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 3.555324 TGGAGAACGCACCCTGCA 61.555 61.111 0.00 0.00 45.36 4.41
95 96 3.576078 AAGGCGATGTATTCCATCCAA 57.424 42.857 0.00 0.00 46.10 3.53
160 161 7.370905 AGATGATGATGATAACAAGAGGTCA 57.629 36.000 0.00 0.00 0.00 4.02
206 207 1.212935 GTGTAGGATGGGTGAAGCCAT 59.787 52.381 13.71 13.71 39.65 4.40
824 1827 9.274206 GTCTAGGAGTGAACTAATCTTTTGTTT 57.726 33.333 0.00 0.00 0.00 2.83
1176 2184 4.817517 TCTCTACCCTTGAATCGTTGAAC 58.182 43.478 0.00 0.00 0.00 3.18
2315 3348 8.604890 GTTTTCTGAGCACCAGTTAATATAGAC 58.395 37.037 6.11 0.00 43.38 2.59
2878 3916 3.438781 TGCCATTACATTTTGAGACGGAC 59.561 43.478 0.00 0.00 0.00 4.79
3095 4134 9.859427 CTGAATCAACAAGATAAAATTTGCCTA 57.141 29.630 0.00 0.00 35.39 3.93
3128 4168 7.694093 TGGGGCAATAAATTTTGGAGTATTTT 58.306 30.769 0.00 0.00 0.00 1.82
3451 4491 5.179368 CACGAACTTGTTGATCACCATAGTT 59.821 40.000 15.44 15.44 0.00 2.24
3797 4871 6.084326 ACATAAGAACACACCCATTTGAAC 57.916 37.500 0.00 0.00 0.00 3.18
4188 5262 1.886777 GGCGATTCAGAGGAGCAGC 60.887 63.158 0.00 0.00 0.00 5.25
4360 5434 2.872557 CTCAACGCACATGCCTGG 59.127 61.111 0.00 0.00 37.91 4.45


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

AutoCloner maintained by Alex Coulton.