Multiple sequence alignment - TraesCS2D01G526400

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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 TraesCS2D01G526400 chr2D 100.000 2546 0 0 1 2546 614811751 614809206 0.000000e+00 4702
1 TraesCS2D01G526400 chr2D 91.444 1835 122 17 579 2397 12544114 12542299 0.000000e+00 2486
2 TraesCS2D01G526400 chr2D 91.376 1832 126 20 577 2397 590929813 590928003 0.000000e+00 2479
3 TraesCS2D01G526400 chr2D 91.549 284 14 4 311 584 614804456 614804173 1.430000e-102 383
4 TraesCS2D01G526400 chr2D 91.304 184 13 1 87 267 614819363 614819180 5.440000e-62 248
5 TraesCS2D01G526400 chr7B 91.433 1821 144 12 587 2397 27463287 27465105 0.000000e+00 2488
6 TraesCS2D01G526400 chr7B 91.350 1815 134 10 588 2397 685254374 685252578 0.000000e+00 2460
7 TraesCS2D01G526400 chr5D 91.708 1821 110 30 591 2397 257136361 257138154 0.000000e+00 2488
8 TraesCS2D01G526400 chr3A 92.290 1751 108 18 584 2328 47284896 47286625 0.000000e+00 2460
9 TraesCS2D01G526400 chr1B 90.939 1821 142 14 587 2396 577793171 577791363 0.000000e+00 2427
10 TraesCS2D01G526400 chr5B 90.819 1819 143 14 586 2397 548479693 548477892 0.000000e+00 2412
11 TraesCS2D01G526400 chr6D 90.970 1794 117 14 611 2397 14242658 14244413 0.000000e+00 2374
12 TraesCS2D01G526400 chr4B 90.110 1820 134 21 587 2397 94513638 94515420 0.000000e+00 2322
13 TraesCS2D01G526400 chr1A 89.837 1840 135 23 572 2397 2863299 2861498 0.000000e+00 2314
14 TraesCS2D01G526400 chr3D 90.536 1511 114 17 894 2397 80249123 80250611 0.000000e+00 1971
15 TraesCS2D01G526400 chrUn 93.356 1189 68 10 1215 2397 110637311 110638494 0.000000e+00 1748
16 TraesCS2D01G526400 chr2B 94.118 578 24 6 12 584 749147879 749147307 0.000000e+00 870
17 TraesCS2D01G526400 chr2B 82.500 560 54 17 59 584 749138972 749138423 3.860000e-123 451
18 TraesCS2D01G526400 chr2B 87.081 209 20 3 59 267 749181343 749181142 1.970000e-56 230
19 TraesCS2D01G526400 chr2A 92.453 583 30 10 12 586 745096962 745096386 0.000000e+00 821
20 TraesCS2D01G526400 chr2A 79.826 575 56 29 59 584 745092685 745092122 5.180000e-97 364
21 TraesCS2D01G526400 chr2A 87.544 281 20 10 311 584 745091348 745091076 6.840000e-81 311
22 TraesCS2D01G526400 chr2A 89.671 213 18 3 59 267 745112008 745111796 4.180000e-68 268
23 TraesCS2D01G526400 chr2A 93.750 96 2 2 214 309 745091476 745091385 9.500000e-30 141


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 TraesCS2D01G526400 chr2D 614809206 614811751 2545 True 4702.00 4702 100.00000 1 2546 1 chr2D.!!$R4 2545
1 TraesCS2D01G526400 chr2D 12542299 12544114 1815 True 2486.00 2486 91.44400 579 2397 1 chr2D.!!$R1 1818
2 TraesCS2D01G526400 chr2D 590928003 590929813 1810 True 2479.00 2479 91.37600 577 2397 1 chr2D.!!$R2 1820
3 TraesCS2D01G526400 chr7B 27463287 27465105 1818 False 2488.00 2488 91.43300 587 2397 1 chr7B.!!$F1 1810
4 TraesCS2D01G526400 chr7B 685252578 685254374 1796 True 2460.00 2460 91.35000 588 2397 1 chr7B.!!$R1 1809
5 TraesCS2D01G526400 chr5D 257136361 257138154 1793 False 2488.00 2488 91.70800 591 2397 1 chr5D.!!$F1 1806
6 TraesCS2D01G526400 chr3A 47284896 47286625 1729 False 2460.00 2460 92.29000 584 2328 1 chr3A.!!$F1 1744
7 TraesCS2D01G526400 chr1B 577791363 577793171 1808 True 2427.00 2427 90.93900 587 2396 1 chr1B.!!$R1 1809
8 TraesCS2D01G526400 chr5B 548477892 548479693 1801 True 2412.00 2412 90.81900 586 2397 1 chr5B.!!$R1 1811
9 TraesCS2D01G526400 chr6D 14242658 14244413 1755 False 2374.00 2374 90.97000 611 2397 1 chr6D.!!$F1 1786
10 TraesCS2D01G526400 chr4B 94513638 94515420 1782 False 2322.00 2322 90.11000 587 2397 1 chr4B.!!$F1 1810
11 TraesCS2D01G526400 chr1A 2861498 2863299 1801 True 2314.00 2314 89.83700 572 2397 1 chr1A.!!$R1 1825
12 TraesCS2D01G526400 chr3D 80249123 80250611 1488 False 1971.00 1971 90.53600 894 2397 1 chr3D.!!$F1 1503
13 TraesCS2D01G526400 chrUn 110637311 110638494 1183 False 1748.00 1748 93.35600 1215 2397 1 chrUn.!!$F1 1182
14 TraesCS2D01G526400 chr2B 749147307 749147879 572 True 870.00 870 94.11800 12 584 1 chr2B.!!$R2 572
15 TraesCS2D01G526400 chr2B 749138423 749138972 549 True 451.00 451 82.50000 59 584 1 chr2B.!!$R1 525
16 TraesCS2D01G526400 chr2A 745091076 745096962 5886 True 409.25 821 88.39325 12 586 4 chr2A.!!$R2 574

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
620 662 0.46546 TTGCCCTCAGTGGTGTTCAC 60.465 55.0 0.0 0.0 46.39 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1779 1895 0.89832 GCACTTGGCTCTCCACTCTA 59.102 55.0 0.0 0.0 43.33 2.43 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
110 111 1.935873 GCGCATGCAGATCTACAGAAA 59.064 47.619 19.57 0.00 42.15 2.52
119 120 5.582269 TGCAGATCTACAGAAACATAGCAAC 59.418 40.000 0.00 0.00 0.00 4.17
156 157 3.362040 TTCCGGACGGAGGAAGTTA 57.638 52.632 13.64 0.00 46.06 2.24
173 174 4.171878 AGTTATCGAGATCAGGTCCAGA 57.828 45.455 0.00 0.00 0.00 3.86
178 179 3.365472 TCGAGATCAGGTCCAGAAATCA 58.635 45.455 0.00 0.00 0.00 2.57
184 185 0.546747 AGGTCCAGAAATCACCCGGA 60.547 55.000 0.73 0.00 0.00 5.14
189 190 2.169769 TCCAGAAATCACCCGGATGTAC 59.830 50.000 0.73 0.00 36.02 2.90
212 213 4.767255 GGGTCAGGCGCTCAGGTG 62.767 72.222 7.64 0.00 0.00 4.00
240 241 5.991933 ACATGGATGGTATGTAGAGCTAG 57.008 43.478 0.00 0.00 37.02 3.42
309 319 1.734117 GCCTCAAAATGGTGTGCGC 60.734 57.895 0.00 0.00 0.00 6.09
457 492 6.293626 CGATCAAGTGTTTGTTTTCTCTCCAT 60.294 38.462 0.00 0.00 35.73 3.41
580 622 1.331756 CTGTGGCGTGGCTATCATTTC 59.668 52.381 0.00 0.00 0.00 2.17
620 662 0.465460 TTGCCCTCAGTGGTGTTCAC 60.465 55.000 0.00 0.00 46.39 3.18
634 676 2.080693 TGTTCACGTGCTCAGTTTTGT 58.919 42.857 11.67 0.00 0.00 2.83
669 711 0.881796 GTGCTCAGTTTTGCCCCTAC 59.118 55.000 0.00 0.00 0.00 3.18
684 726 1.429825 CTACTCTGTCCGCACCGAG 59.570 63.158 0.00 0.00 39.24 4.63
753 795 0.840722 CCTTACAGGTGGGACCAGGT 60.841 60.000 0.00 0.00 41.95 4.00
796 839 3.707700 CGTTGCACGCGTGGCTTA 61.708 61.111 37.47 19.24 33.65 3.09
1114 1176 0.530744 TGATCGGAGGGTTTCTCACG 59.469 55.000 0.00 0.00 44.19 4.35
1266 1332 2.567985 TGTTTCTTCCTTTGGGTCGAC 58.432 47.619 7.13 7.13 0.00 4.20
1545 1617 8.828688 TGTTGAAATTGTATGAAAATGCATGA 57.171 26.923 0.00 0.00 0.00 3.07
1546 1618 9.269453 TGTTGAAATTGTATGAAAATGCATGAA 57.731 25.926 0.00 0.00 0.00 2.57
1553 1625 9.754382 ATTGTATGAAAATGCATGAATTAGACC 57.246 29.630 0.00 0.00 0.00 3.85
1554 1626 7.715657 TGTATGAAAATGCATGAATTAGACCC 58.284 34.615 0.00 0.00 0.00 4.46
1710 1823 8.026026 GGAGAAGAAATGAGAAATTCAGAAACC 58.974 37.037 0.00 0.00 39.68 3.27
1779 1895 2.519013 GTCTCTCTGTGGGCCAAATTT 58.481 47.619 8.40 0.00 0.00 1.82
1784 1900 3.330701 TCTCTGTGGGCCAAATTTAGAGT 59.669 43.478 8.40 0.00 33.68 3.24
1807 1923 2.190578 GCCAAGTGCCGGCTAGAT 59.809 61.111 29.70 8.48 46.56 1.98
1840 1956 2.040939 TGCATCCAATTAGGCCCATTG 58.959 47.619 15.61 15.61 37.29 2.82
1869 1987 3.198068 GGCAAATGAGATCTCTTGCGTA 58.802 45.455 29.05 10.96 39.91 4.42
2092 5586 6.321435 GGAAAATATGCCTTAGCTTTGGTAGT 59.679 38.462 0.00 0.00 40.80 2.73
2212 5888 1.123928 AAAATTGGTGCGGTTGGGAA 58.876 45.000 0.00 0.00 0.00 3.97
2245 5921 0.171007 CACATGGGTTCGTGGCATTC 59.829 55.000 0.00 0.00 34.31 2.67
2263 5939 0.606096 TCAAGGCTGCGCTAGTAACA 59.394 50.000 9.73 0.00 0.00 2.41
2331 6007 6.204301 GCTATACATAGTGAGACCGTGACTTA 59.796 42.308 0.00 0.00 32.96 2.24
2397 6321 3.680937 CGCGTGATAGTGGTTTTCCTTTA 59.319 43.478 0.00 0.00 41.38 1.85
2398 6322 4.152759 CGCGTGATAGTGGTTTTCCTTTAA 59.847 41.667 0.00 0.00 41.38 1.52
2399 6323 5.628134 GCGTGATAGTGGTTTTCCTTTAAG 58.372 41.667 0.00 0.00 41.38 1.85
2400 6324 5.391629 GCGTGATAGTGGTTTTCCTTTAAGG 60.392 44.000 4.29 4.29 41.38 2.69
2402 6326 6.206048 CGTGATAGTGGTTTTCCTTTAAGGTT 59.794 38.462 11.13 0.00 41.38 3.50
2404 6328 8.418662 GTGATAGTGGTTTTCCTTTAAGGTTTT 58.581 33.333 11.13 0.00 41.38 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.181489 CCGTTGTCATAGGTAGGAGTGTC 60.181 52.174 0.00 0.00 0.00 3.67
3 4 2.481449 GCCGTTGTCATAGGTAGGAGTG 60.481 54.545 0.00 0.00 0.00 3.51
5 6 1.754803 TGCCGTTGTCATAGGTAGGAG 59.245 52.381 0.00 0.00 0.00 3.69
7 8 2.872245 CAATGCCGTTGTCATAGGTAGG 59.128 50.000 0.00 0.00 33.01 3.18
8 9 2.287915 GCAATGCCGTTGTCATAGGTAG 59.712 50.000 0.00 0.00 40.07 3.18
10 11 1.094785 GCAATGCCGTTGTCATAGGT 58.905 50.000 0.00 0.00 40.07 3.08
110 111 2.742053 CGTAGTTGCCAAGTTGCTATGT 59.258 45.455 0.00 0.00 0.00 2.29
119 120 0.321653 AAGCCTCCGTAGTTGCCAAG 60.322 55.000 0.00 0.00 0.00 3.61
156 157 3.963374 TGATTTCTGGACCTGATCTCGAT 59.037 43.478 1.39 0.00 0.00 3.59
173 174 2.710096 CTGGTACATCCGGGTGATTT 57.290 50.000 24.73 0.51 38.20 2.17
206 207 5.191727 ACCATCCATGTTAATTCACCTGA 57.808 39.130 0.00 0.00 0.00 3.86
212 213 7.880195 AGCTCTACATACCATCCATGTTAATTC 59.120 37.037 0.00 0.00 37.74 2.17
240 241 1.282265 GCCGTACGTAGAGGCTAGC 59.718 63.158 26.14 6.04 46.83 3.42
309 319 9.086336 AGAACATTGTAACAAACTGAAACATTG 57.914 29.630 0.00 0.00 0.00 2.82
482 521 6.095377 GTCTTTCCTTTCACCATGCATTTAG 58.905 40.000 0.00 0.00 0.00 1.85
568 610 5.450818 AACCCTTACAGAAATGATAGCCA 57.549 39.130 0.00 0.00 0.00 4.75
580 622 7.417456 GGGCAAAAGGATAATTAACCCTTACAG 60.417 40.741 17.67 13.08 39.21 2.74
620 662 1.528586 CTGAGGACAAAACTGAGCACG 59.471 52.381 0.00 0.00 0.00 5.34
634 676 1.014044 GCACGATTCGCAACTGAGGA 61.014 55.000 5.86 0.00 0.00 3.71
669 711 2.179517 GACTCGGTGCGGACAGAG 59.820 66.667 29.69 29.69 46.53 3.35
753 795 2.875485 GTCTACGCGTCTCTGCCA 59.125 61.111 18.63 0.00 0.00 4.92
796 839 0.251787 GGCTCTTTGTTGGGTCCCAT 60.252 55.000 12.68 0.00 31.53 4.00
1114 1176 2.277084 ACGATTATGGTTCTTCGGTGC 58.723 47.619 0.00 0.00 35.98 5.01
1266 1332 0.603707 TCAAAGTCTTGGCCAGAGCG 60.604 55.000 5.11 0.00 41.24 5.03
1478 1550 4.432712 CATACCTACAAATGCCCAAAAGC 58.567 43.478 0.00 0.00 0.00 3.51
1539 1611 3.949586 TCATGGGGTCTAATTCATGCA 57.050 42.857 0.00 0.00 37.49 3.96
1710 1823 5.066634 AGAGAGCTGCATTTCATTGATCAAG 59.933 40.000 14.54 6.44 0.00 3.02
1761 1877 3.944015 CTCTAAATTTGGCCCACAGAGAG 59.056 47.826 0.00 1.57 31.72 3.20
1779 1895 0.898320 GCACTTGGCTCTCCACTCTA 59.102 55.000 0.00 0.00 43.33 2.43
1784 1900 4.020617 CCGGCACTTGGCTCTCCA 62.021 66.667 0.90 0.00 44.01 3.86
1807 1923 2.475155 TGGATGCAATTGGCCCATTAA 58.525 42.857 7.72 0.00 43.89 1.40
2212 5888 2.426522 CCATGTGGTCTTGTGTTCGAT 58.573 47.619 0.00 0.00 0.00 3.59
2236 5912 2.180017 GCAGCCTTGAATGCCACG 59.820 61.111 0.00 0.00 36.41 4.94
2263 5939 1.488393 GTCTTTCCATCTGCCCTAGCT 59.512 52.381 0.00 0.00 40.80 3.32
2331 6007 8.835439 CAAACATGCATTTTTAAACCCTAAACT 58.165 29.630 10.36 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.