Multiple sequence alignment - TraesCS2A01G257400

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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 TraesCS2A01G257400 chr2A 100.000 3149 0 0 1 3149 394758672 394755524 0.000000e+00 5816.0
1 TraesCS2A01G257400 chr2A 99.048 3151 9 3 1 3149 406451518 406454649 0.000000e+00 5633.0
2 TraesCS2A01G257400 chr2A 84.518 394 41 6 1 376 95135323 95135714 3.840000e-99 372.0
3 TraesCS2A01G257400 chr5B 90.981 632 29 13 2546 3149 177195498 177194867 0.000000e+00 826.0
4 TraesCS2A01G257400 chr5B 91.092 348 18 5 2202 2547 177195863 177195527 2.860000e-125 459.0
5 TraesCS2A01G257400 chr5B 82.836 134 21 2 244 377 403192678 403192547 5.520000e-23 119.0
6 TraesCS2A01G257400 chr5A 90.981 632 29 11 2546 3149 263509779 263509148 0.000000e+00 826.0
7 TraesCS2A01G257400 chr5A 91.092 348 18 5 2202 2547 263510144 263509808 2.860000e-125 459.0
8 TraesCS2A01G257400 chr5D 90.823 632 30 11 2546 3149 154528095 154528726 0.000000e+00 821.0
9 TraesCS2A01G257400 chr5D 90.805 348 19 5 2202 2547 154527730 154528066 1.330000e-123 453.0
10 TraesCS2A01G257400 chrUn 100.000 384 0 0 2060 2443 480941788 480941405 0.000000e+00 710.0
11 TraesCS2A01G257400 chr1D 83.130 492 56 19 2258 2732 19115239 19114758 1.040000e-114 424.0
12 TraesCS2A01G257400 chr1B 83.721 387 39 7 4 373 478902998 478902619 8.360000e-91 344.0
13 TraesCS2A01G257400 chr1B 83.123 397 37 13 3 376 510203610 510203221 5.030000e-88 335.0
14 TraesCS2A01G257400 chr1B 95.775 142 6 0 1 142 642800167 642800026 2.440000e-56 230.0
15 TraesCS2A01G257400 chr1B 84.848 231 29 6 142 370 642799957 642799731 8.790000e-56 228.0
16 TraesCS2A01G257400 chr6B 81.748 389 37 10 8 377 36818241 36817868 8.540000e-76 294.0
17 TraesCS2A01G257400 chr4D 89.950 199 15 3 2733 2926 40121322 40121520 5.210000e-63 252.0
18 TraesCS2A01G257400 chr4D 87.054 224 17 1 2921 3144 40122740 40122951 3.140000e-60 243.0
19 TraesCS2A01G257400 chr3B 85.271 129 16 3 248 376 573475268 573475143 2.550000e-26 130.0
20 TraesCS2A01G257400 chr2D 87.379 103 11 2 272 374 602706716 602706616 1.980000e-22 117.0
21 TraesCS2A01G257400 chr1A 92.537 67 4 1 310 376 360985521 360985456 9.300000e-16 95.3
22 TraesCS2A01G257400 chr2B 96.226 53 2 0 326 378 233561228 233561280 1.560000e-13 87.9
23 TraesCS2A01G257400 chr2B 89.231 65 4 3 311 373 294189497 294189434 9.360000e-11 78.7
24 TraesCS2A01G257400 chr6D 90.476 63 5 1 327 389 393646629 393646568 7.240000e-12 82.4
25 TraesCS2A01G257400 chr4B 95.833 48 2 0 3102 3149 58568856 58568903 9.360000e-11 78.7
26 TraesCS2A01G257400 chr4B 93.750 48 3 0 3102 3149 58597213 58597260 4.360000e-09 73.1


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 TraesCS2A01G257400 chr2A 394755524 394758672 3148 True 5816.0 5816 100.0000 1 3149 1 chr2A.!!$R1 3148
1 TraesCS2A01G257400 chr2A 406451518 406454649 3131 False 5633.0 5633 99.0480 1 3149 1 chr2A.!!$F2 3148
2 TraesCS2A01G257400 chr5B 177194867 177195863 996 True 642.5 826 91.0365 2202 3149 2 chr5B.!!$R2 947
3 TraesCS2A01G257400 chr5A 263509148 263510144 996 True 642.5 826 91.0365 2202 3149 2 chr5A.!!$R1 947
4 TraesCS2A01G257400 chr5D 154527730 154528726 996 False 637.0 821 90.8140 2202 3149 2 chr5D.!!$F1 947
5 TraesCS2A01G257400 chr4D 40121322 40122951 1629 False 247.5 252 88.5020 2733 3144 2 chr4D.!!$F1 411

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
970 971 2.043252 AGCTGTGGACTAAGGGTACTCT 59.957 50.0 0.0 0.0 0.0 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2775 2840 3.134458 CAGACTCAAGTCCTTGGTTGTC 58.866 50.0 6.54 11.83 45.85 3.18 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
252 253 3.662759 AGACAACCAACAGGGAGAAAA 57.337 42.857 0.00 0.00 41.15 2.29
894 895 7.490000 ACTACATTTATTACAGAGACCTTCCG 58.510 38.462 0.00 0.00 0.00 4.30
970 971 2.043252 AGCTGTGGACTAAGGGTACTCT 59.957 50.000 0.00 0.00 0.00 3.24
1540 1543 3.319122 GCTTCCAGTCCAAAGTGAACAAT 59.681 43.478 0.00 0.00 0.00 2.71
1606 1609 4.262164 GGAAGAACATGCATCAAACTTGGT 60.262 41.667 0.00 0.00 0.00 3.67
1736 1739 4.255833 TGAATGCAACCTGGATTGTTTC 57.744 40.909 0.00 9.39 38.55 2.78
2057 2060 1.813753 TAAATCGAGTGCCCGCAGC 60.814 57.895 0.00 0.00 44.14 5.25
2443 2453 6.096141 TGTTATATTGGTATTGGTGTTGCTGG 59.904 38.462 0.00 0.00 0.00 4.85
2775 2840 2.745884 TGGGCGCAATCTTCCGTG 60.746 61.111 10.83 0.00 0.00 4.94
2829 2894 0.512952 AGCGCTGCGTTTTCTTGTAG 59.487 50.000 24.04 0.00 0.00 2.74
2830 2895 0.511221 GCGCTGCGTTTTCTTGTAGA 59.489 50.000 24.04 0.00 0.00 2.59
2831 2896 1.462541 GCGCTGCGTTTTCTTGTAGAG 60.463 52.381 24.04 0.00 0.00 2.43
2832 2897 2.058798 CGCTGCGTTTTCTTGTAGAGA 58.941 47.619 14.93 0.00 0.00 3.10
2833 2898 2.159960 CGCTGCGTTTTCTTGTAGAGAC 60.160 50.000 14.93 0.00 33.02 3.36
2834 2899 2.159960 GCTGCGTTTTCTTGTAGAGACG 60.160 50.000 9.08 9.08 38.09 4.18
2835 2900 3.050619 CTGCGTTTTCTTGTAGAGACGT 58.949 45.455 12.78 0.00 37.67 4.34
2836 2901 3.450578 TGCGTTTTCTTGTAGAGACGTT 58.549 40.909 12.78 0.00 37.67 3.99
2837 2902 3.488310 TGCGTTTTCTTGTAGAGACGTTC 59.512 43.478 12.78 0.00 37.67 3.95
2838 2903 3.488310 GCGTTTTCTTGTAGAGACGTTCA 59.512 43.478 12.78 0.00 37.67 3.18
2839 2904 4.605573 GCGTTTTCTTGTAGAGACGTTCAC 60.606 45.833 12.78 0.00 37.67 3.18
2840 2905 4.738740 CGTTTTCTTGTAGAGACGTTCACT 59.261 41.667 0.00 0.00 33.71 3.41
2841 2906 5.911280 CGTTTTCTTGTAGAGACGTTCACTA 59.089 40.000 0.00 0.00 33.71 2.74
2842 2907 6.086502 CGTTTTCTTGTAGAGACGTTCACTAG 59.913 42.308 0.00 0.00 33.71 2.57
2843 2908 6.630444 TTTCTTGTAGAGACGTTCACTAGT 57.370 37.500 0.00 0.00 33.02 2.57
2844 2909 7.734924 TTTCTTGTAGAGACGTTCACTAGTA 57.265 36.000 0.00 0.00 33.02 1.82
2845 2910 6.964741 TCTTGTAGAGACGTTCACTAGTAG 57.035 41.667 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
252 253 1.358152 TCTTTCATTCCTCCACCGGT 58.642 50.000 0.00 0.00 0.00 5.28
894 895 8.988064 TCGATTCCTTCAATAGATATACTTGC 57.012 34.615 0.00 0.00 0.00 4.01
970 971 4.425772 TGGACCTATCTTCTCTGGTTTCA 58.574 43.478 0.00 0.00 32.30 2.69
1606 1609 5.880901 AGCTTCAAAGTCTTTATCCTCCAA 58.119 37.500 0.00 0.00 0.00 3.53
1736 1739 4.756642 TCAAATTCTCAAGCCTACACACAG 59.243 41.667 0.00 0.00 0.00 3.66
2443 2453 4.003648 AGTAGCAACCACTGAAGTAATGC 58.996 43.478 6.30 6.30 33.22 3.56
2775 2840 3.134458 CAGACTCAAGTCCTTGGTTGTC 58.866 50.000 6.54 11.83 45.85 3.18
2829 2894 7.117236 CAGATATCTCCTACTAGTGAACGTCTC 59.883 44.444 5.39 0.00 0.00 3.36
2830 2895 6.932400 CAGATATCTCCTACTAGTGAACGTCT 59.068 42.308 5.39 0.00 0.00 4.18
2831 2896 6.930164 TCAGATATCTCCTACTAGTGAACGTC 59.070 42.308 5.39 0.00 0.00 4.34
2832 2897 6.828788 TCAGATATCTCCTACTAGTGAACGT 58.171 40.000 5.39 0.00 0.00 3.99
2833 2898 7.915293 ATCAGATATCTCCTACTAGTGAACG 57.085 40.000 5.39 0.00 0.00 3.95
2834 2899 9.169592 GGTATCAGATATCTCCTACTAGTGAAC 57.830 40.741 5.39 0.00 0.00 3.18
2835 2900 8.891501 TGGTATCAGATATCTCCTACTAGTGAA 58.108 37.037 5.39 0.00 0.00 3.18
2836 2901 8.450780 TGGTATCAGATATCTCCTACTAGTGA 57.549 38.462 5.39 0.00 0.00 3.41
2837 2902 9.693739 ATTGGTATCAGATATCTCCTACTAGTG 57.306 37.037 5.39 0.00 0.00 2.74
2838 2903 9.693739 CATTGGTATCAGATATCTCCTACTAGT 57.306 37.037 1.03 0.00 0.00 2.57
2839 2904 9.913310 TCATTGGTATCAGATATCTCCTACTAG 57.087 37.037 1.03 0.00 0.00 2.57
2841 2906 9.781425 ATTCATTGGTATCAGATATCTCCTACT 57.219 33.333 1.03 0.00 0.00 2.57
2842 2907 9.814899 CATTCATTGGTATCAGATATCTCCTAC 57.185 37.037 1.03 7.37 0.00 3.18
2843 2908 9.774071 TCATTCATTGGTATCAGATATCTCCTA 57.226 33.333 1.03 0.00 0.00 2.94
2844 2909 8.676397 TCATTCATTGGTATCAGATATCTCCT 57.324 34.615 1.03 0.00 0.00 3.69
2845 2910 9.381033 CTTCATTCATTGGTATCAGATATCTCC 57.619 37.037 1.03 1.58 0.00 3.71


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

AutoCloner maintained by Alex Coulton.