Multiple sequence alignment - TraesCS2D01G486600

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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 TraesCS2D01G486600 chr2D 100.000 3723 0 0 1 3723 586901951 586905673 0.000000e+00 6876
1 TraesCS2D01G486600 chr2B 95.069 3103 122 15 1 3084 708383994 708387084 0.000000e+00 4854
2 TraesCS2D01G486600 chr2B 92.000 675 53 1 3049 3723 708387085 708387758 0.000000e+00 946
3 TraesCS2D01G486600 chr2A 96.169 1514 42 6 773 2281 721652700 721654202 0.000000e+00 2460
4 TraesCS2D01G486600 chr2A 95.699 837 29 6 2255 3084 721654267 721655103 0.000000e+00 1339
5 TraesCS2D01G486600 chr2A 94.318 792 32 9 1 784 721650846 721651632 0.000000e+00 1201
6 TraesCS2D01G486600 chr2A 92.000 675 50 2 3049 3723 721655104 721655774 0.000000e+00 944
7 TraesCS2D01G486600 chr5B 78.231 588 96 22 2959 3534 635798141 635797574 7.650000e-92 348
8 TraesCS2D01G486600 chr4A 78.268 589 94 23 2959 3534 632589194 632588627 7.650000e-92 348
9 TraesCS2D01G486600 chr4A 74.966 743 148 27 2968 3689 615111823 615111098 1.300000e-79 307
10 TraesCS2D01G486600 chr6D 77.911 584 105 18 2959 3532 32611358 32610789 3.560000e-90 342
11 TraesCS2D01G486600 chr4D 76.772 663 122 22 2959 3601 113415572 113416222 3.560000e-90 342
12 TraesCS2D01G486600 chr1B 78.960 423 76 12 2959 3369 25112501 25112080 3.660000e-70 276
13 TraesCS2D01G486600 chr1B 74.955 551 114 21 2959 3489 685083555 685084101 8.040000e-57 231
14 TraesCS2D01G486600 chr7D 81.624 234 32 8 2959 3183 131660686 131660917 2.280000e-42 183
15 TraesCS2D01G486600 chr3B 79.752 242 41 7 2959 3194 85328646 85328407 6.390000e-38 169


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 TraesCS2D01G486600 chr2D 586901951 586905673 3722 False 6876 6876 100.0000 1 3723 1 chr2D.!!$F1 3722
1 TraesCS2D01G486600 chr2B 708383994 708387758 3764 False 2900 4854 93.5345 1 3723 2 chr2B.!!$F1 3722
2 TraesCS2D01G486600 chr2A 721650846 721655774 4928 False 1486 2460 94.5465 1 3723 4 chr2A.!!$F1 3722
3 TraesCS2D01G486600 chr5B 635797574 635798141 567 True 348 348 78.2310 2959 3534 1 chr5B.!!$R1 575
4 TraesCS2D01G486600 chr4A 632588627 632589194 567 True 348 348 78.2680 2959 3534 1 chr4A.!!$R2 575
5 TraesCS2D01G486600 chr4A 615111098 615111823 725 True 307 307 74.9660 2968 3689 1 chr4A.!!$R1 721
6 TraesCS2D01G486600 chr6D 32610789 32611358 569 True 342 342 77.9110 2959 3532 1 chr6D.!!$R1 573
7 TraesCS2D01G486600 chr4D 113415572 113416222 650 False 342 342 76.7720 2959 3601 1 chr4D.!!$F1 642
8 TraesCS2D01G486600 chr1B 685083555 685084101 546 False 231 231 74.9550 2959 3489 1 chr1B.!!$F1 530

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
339 348 0.907230 AAGGGTGAGAGGCCTCTGTC 60.907 60.000 39.86 28.09 40.61 3.51 F
342 351 0.980231 GGTGAGAGGCCTCTGTCCAT 60.980 60.000 39.86 15.55 40.61 3.41 F
538 548 2.356382 TCAACTTTGCAAGGGTACAACG 59.644 45.455 13.65 0.00 0.00 4.10 F
1106 2195 2.404215 CGGCCTTGTATTGGATAGTCG 58.596 52.381 0.00 0.00 0.00 4.18 F
2020 3115 6.309389 AGGGATCTCGTGGTAAGTATTTTT 57.691 37.500 0.00 0.00 0.00 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1953 3048 1.271325 TGCATTCGCCTTTCTTCTCCA 60.271 47.619 0.00 0.0 37.32 3.86 R
1954 3049 1.453155 TGCATTCGCCTTTCTTCTCC 58.547 50.000 0.00 0.0 37.32 3.71 R
2330 3517 3.304911 TTCCACAATTGACACCCTTCA 57.695 42.857 13.59 0.0 0.00 3.02 R
2691 3880 5.532779 TCCTTTGCATGTTGTGTTGTGTATA 59.467 36.000 0.00 0.0 0.00 1.47 R
3214 4476 0.035056 GACTGGTGTTCCCATCCTGG 60.035 60.000 0.00 0.0 44.15 4.45 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
34 35 7.241042 AGTTACCGCCATGTAGATGTAATAT 57.759 36.000 0.00 0.00 0.00 1.28
35 36 7.097192 AGTTACCGCCATGTAGATGTAATATG 58.903 38.462 0.00 0.00 0.00 1.78
42 43 8.758715 CGCCATGTAGATGTAATATGTATGATG 58.241 37.037 0.00 0.00 0.00 3.07
208 210 5.337330 CCCTCTTTCAGATACTTAACACGGT 60.337 44.000 0.00 0.00 0.00 4.83
214 216 9.367444 CTTTCAGATACTTAACACGGTCTTTAT 57.633 33.333 0.00 0.00 0.00 1.40
297 299 8.335532 TGTCCATCTACATTAACAAGAAAAGG 57.664 34.615 0.00 0.00 0.00 3.11
321 328 6.257630 GGAACAAAGTTGCAATCAAAGCTAAA 59.742 34.615 0.59 0.00 33.37 1.85
339 348 0.907230 AAGGGTGAGAGGCCTCTGTC 60.907 60.000 39.86 28.09 40.61 3.51
342 351 0.980231 GGTGAGAGGCCTCTGTCCAT 60.980 60.000 39.86 15.55 40.61 3.41
424 433 2.889678 TGCTGATACATGGCAAACAACA 59.110 40.909 0.00 0.00 32.79 3.33
440 449 4.992381 ACAACATGTACTCTTCTTTCGC 57.008 40.909 0.00 0.00 0.00 4.70
538 548 2.356382 TCAACTTTGCAAGGGTACAACG 59.644 45.455 13.65 0.00 0.00 4.10
983 2072 3.070018 CCTACTCAAACTGTGCCTCTTG 58.930 50.000 0.00 0.00 0.00 3.02
1083 2172 2.697229 TGGAGACACCATATGCTCAGAG 59.303 50.000 9.42 0.00 44.64 3.35
1106 2195 2.404215 CGGCCTTGTATTGGATAGTCG 58.596 52.381 0.00 0.00 0.00 4.18
1275 2364 7.820648 ACATATTTGATCACCACAACTCTTTC 58.179 34.615 0.00 0.00 0.00 2.62
1376 2465 7.283127 GGCTGACAGGTGAATTCATATTCTTAA 59.717 37.037 12.12 0.00 40.68 1.85
1377 2466 8.844244 GCTGACAGGTGAATTCATATTCTTAAT 58.156 33.333 12.12 0.00 40.68 1.40
1610 2700 9.066892 AGATAATTCAAACAAGAAGTGTAGCAA 57.933 29.630 0.00 0.00 40.60 3.91
1697 2787 8.928733 CAAGCAACAAATTTATACATGAAAGCT 58.071 29.630 0.00 0.00 0.00 3.74
1806 2896 7.494952 AGGCTCGAACTATAAAAGGTATGAAAC 59.505 37.037 0.00 0.00 0.00 2.78
1942 3037 7.582435 TTCTCGAGCAAAAGATTTACTAGTG 57.418 36.000 7.81 0.00 0.00 2.74
1953 3048 8.807948 AAAGATTTACTAGTGCACCATATTGT 57.192 30.769 14.63 4.68 0.00 2.71
1954 3049 7.792374 AGATTTACTAGTGCACCATATTGTG 57.208 36.000 14.63 2.56 39.29 3.33
2020 3115 6.309389 AGGGATCTCGTGGTAAGTATTTTT 57.691 37.500 0.00 0.00 0.00 1.94
2252 3347 8.941995 AGTGCAGAGACTTGATATAAGGTATA 57.058 34.615 0.00 0.00 0.00 1.47
2691 3880 3.939740 TGCTCCATGGCTCTTAGAAAT 57.060 42.857 6.96 0.00 0.00 2.17
2756 3945 7.933396 TCCAACATGATGTCAAATATCACATC 58.067 34.615 0.00 12.42 46.26 3.06
2954 4145 8.347035 GTCTCACCACTAAAGAGTAGACATATC 58.653 40.741 0.00 0.00 37.45 1.63
3067 4273 3.667960 CGCCAACAACTAGCAAAGTCATC 60.668 47.826 0.00 0.00 37.50 2.92
3210 4472 8.465999 AGACAACAAGATTATTGAACAACAACA 58.534 29.630 0.00 0.00 41.52 3.33
3214 4476 9.683069 AACAAGATTATTGAACAACAACATCTC 57.317 29.630 0.00 0.00 39.20 2.75
3220 4482 4.371624 TGAACAACAACATCTCCAGGAT 57.628 40.909 0.00 0.00 34.51 3.24
3303 4567 5.006896 TCACCCTGAAGAGTTAGTCCTAA 57.993 43.478 0.00 0.00 0.00 2.69
3356 4620 0.165079 CGTAAAGAACGCGGCATTGT 59.835 50.000 12.47 0.00 46.10 2.71
3422 4691 2.933287 AGGCCGGGTCCATGACAA 60.933 61.111 2.18 0.00 33.68 3.18
3432 4701 2.238521 GTCCATGACAACACCACCATT 58.761 47.619 0.00 0.00 32.09 3.16
3506 4776 1.153647 GATGTGTGACCATCGCCGA 60.154 57.895 0.00 0.00 32.58 5.54
3702 4981 2.676163 GAACACCACCAAGCCGTCCT 62.676 60.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 82 8.091449 AGACCTGACTAAGTGAAATAGAAACAG 58.909 37.037 0.00 0.00 0.00 3.16
92 94 9.930693 AACTTTCTTATTAGACCTGACTAAGTG 57.069 33.333 0.00 0.00 36.11 3.16
127 129 6.613233 ACACACGTTTGAGTTGTATTTTGAA 58.387 32.000 9.03 0.00 0.00 2.69
155 157 9.502091 GTACAAGCCCTCAATAATCAACATATA 57.498 33.333 0.00 0.00 0.00 0.86
214 216 8.090831 GTCATCTATTATGTCTTCATGTAGCCA 58.909 37.037 0.00 0.00 35.70 4.75
291 293 6.660887 TTGATTGCAACTTTGTTCCTTTTC 57.339 33.333 0.00 0.00 0.00 2.29
296 298 4.122046 AGCTTTGATTGCAACTTTGTTCC 58.878 39.130 0.00 0.00 32.79 3.62
297 299 6.826893 TTAGCTTTGATTGCAACTTTGTTC 57.173 33.333 0.00 0.00 32.79 3.18
321 328 1.305718 GACAGAGGCCTCTCACCCT 60.306 63.158 33.06 12.37 42.34 4.34
424 433 7.907214 AATTTAGTGCGAAAGAAGAGTACAT 57.093 32.000 0.00 0.00 0.00 2.29
440 449 8.669243 GTTGAGAGGGACTGAATAAATTTAGTG 58.331 37.037 2.34 0.00 41.55 2.74
538 548 2.226674 GGCACTTCAGCTTAACTTCCAC 59.773 50.000 0.00 0.00 34.17 4.02
983 2072 7.226720 ACGATTCCATTAGAATGTGTGGTTATC 59.773 37.037 0.00 0.00 45.52 1.75
1083 2172 1.873591 CTATCCAATACAAGGCCGCAC 59.126 52.381 0.00 0.00 0.00 5.34
1106 2195 7.646922 GCCAATCATCTTTCTCATCAATGTAAC 59.353 37.037 0.00 0.00 0.00 2.50
1275 2364 1.792949 GACTTCTGTATATTGCCGCGG 59.207 52.381 24.05 24.05 0.00 6.46
1610 2700 6.628919 ATGCGGTTAGTTCACTTAGTTTTT 57.371 33.333 0.00 0.00 0.00 1.94
1630 2720 3.118905 TGCCCAACCTAAAAACAATGC 57.881 42.857 0.00 0.00 0.00 3.56
1953 3048 1.271325 TGCATTCGCCTTTCTTCTCCA 60.271 47.619 0.00 0.00 37.32 3.86
1954 3049 1.453155 TGCATTCGCCTTTCTTCTCC 58.547 50.000 0.00 0.00 37.32 3.71
2330 3517 3.304911 TTCCACAATTGACACCCTTCA 57.695 42.857 13.59 0.00 0.00 3.02
2368 3556 7.933577 TGCAAAATGTAAACATGTTTATTGGGA 59.066 29.630 28.69 17.38 37.37 4.37
2542 3731 6.486248 TCGCATGCAAAGAATCTATACAAAC 58.514 36.000 19.57 0.00 0.00 2.93
2691 3880 5.532779 TCCTTTGCATGTTGTGTTGTGTATA 59.467 36.000 0.00 0.00 0.00 1.47
2954 4145 5.803461 TCGTGTTTGTATCCTCTTGATAACG 59.197 40.000 0.00 0.00 37.69 3.18
3067 4273 8.235226 TCTCGTCTACACATAACTTTGTCTTAG 58.765 37.037 0.00 0.00 0.00 2.18
3144 4406 4.696877 TGATTGGTGCGGATATGATCATTC 59.303 41.667 14.65 10.82 0.00 2.67
3210 4472 1.216990 GGTGTTCCCATCCTGGAGAT 58.783 55.000 1.52 0.00 40.96 2.75
3214 4476 0.035056 GACTGGTGTTCCCATCCTGG 60.035 60.000 0.00 0.00 44.15 4.45
3220 4482 1.134220 GTCACTTGACTGGTGTTCCCA 60.134 52.381 1.92 0.00 41.65 4.37
3228 4490 0.320683 TGATGGCGTCACTTGACTGG 60.321 55.000 5.03 0.00 42.66 4.00
3303 4567 4.156008 GTCGAAGGTTTTGCTTGGATATGT 59.844 41.667 0.00 0.00 0.00 2.29
3356 4620 5.251932 TCTGACCCAAATTGGTTATACCTGA 59.748 40.000 11.52 0.91 39.24 3.86
3407 4674 2.033448 TGTTGTCATGGACCCGGC 59.967 61.111 0.00 0.00 0.00 6.13
3422 4691 2.806745 CGAGTGACTTCAATGGTGGTGT 60.807 50.000 0.00 0.00 0.00 4.16
3506 4776 1.108776 GCATGAGGATGGTTGTGCAT 58.891 50.000 0.00 0.00 33.09 3.96
3625 4904 2.818432 ACTGTACTGTAACGACCTCCTG 59.182 50.000 3.21 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.