Multiple sequence alignment - TraesCS2A01G578400

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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 TraesCS2A01G578400 chr2A 100.000 2755 0 0 1 2755 771711924 771714678 0.000000e+00 5088
1 TraesCS2A01G578400 chr2A 96.313 895 31 2 1862 2755 65081079 65081972 0.000000e+00 1469
2 TraesCS2A01G578400 chr2A 82.493 1011 100 25 789 1753 771609290 771610269 0.000000e+00 815
3 TraesCS2A01G578400 chr2A 87.915 331 31 5 1003 1324 771547120 771547450 5.570000e-102 381
4 TraesCS2A01G578400 chr2A 81.439 264 36 5 13 274 771598113 771598365 1.290000e-48 204
5 TraesCS2A01G578400 chr2D 94.222 1869 79 7 13 1859 645946870 645948731 0.000000e+00 2826
6 TraesCS2A01G578400 chr2D 81.148 1045 125 26 752 1753 645893139 645894154 0.000000e+00 773
7 TraesCS2A01G578400 chr2D 90.377 239 14 6 467 701 645892895 645893128 3.450000e-79 305
8 TraesCS2A01G578400 chr2D 82.282 333 46 7 13 343 645880525 645880846 2.700000e-70 276
9 TraesCS2A01G578400 chr2D 86.192 239 33 0 1004 1242 645933388 645933626 2.720000e-65 259
10 TraesCS2A01G578400 chr2B 89.929 1837 144 17 13 1844 789603045 789601245 0.000000e+00 2329
11 TraesCS2A01G578400 chr2B 81.952 748 111 13 1013 1753 789670346 789669616 1.810000e-171 612
12 TraesCS2A01G578400 chr2B 86.441 236 32 0 1007 1242 789609674 789609439 2.720000e-65 259
13 TraesCS2A01G578400 chr2B 84.906 159 18 3 749 907 789620546 789620394 3.670000e-34 156
14 TraesCS2A01G578400 chr4A 96.771 898 27 2 1859 2755 597317301 597316405 0.000000e+00 1496
15 TraesCS2A01G578400 chr5D 96.659 898 29 1 1859 2755 450523553 450524450 0.000000e+00 1491
16 TraesCS2A01G578400 chr1A 96.548 898 30 1 1859 2755 504105560 504104663 0.000000e+00 1485
17 TraesCS2A01G578400 chr3B 95.916 906 33 4 1851 2755 533024548 533025450 0.000000e+00 1465
18 TraesCS2A01G578400 chr5A 95.898 902 33 3 1855 2755 35739322 35738424 0.000000e+00 1458
19 TraesCS2A01G578400 chr7D 95.880 898 35 2 1859 2755 634755017 634755913 0.000000e+00 1452
20 TraesCS2A01G578400 chr1D 95.880 898 36 1 1859 2755 435762364 435761467 0.000000e+00 1452
21 TraesCS2A01G578400 chr3A 94.708 926 45 3 1832 2755 730651923 730652846 0.000000e+00 1435


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 TraesCS2A01G578400 chr2A 771711924 771714678 2754 False 5088 5088 100.0000 1 2755 1 chr2A.!!$F5 2754
1 TraesCS2A01G578400 chr2A 65081079 65081972 893 False 1469 1469 96.3130 1862 2755 1 chr2A.!!$F1 893
2 TraesCS2A01G578400 chr2A 771609290 771610269 979 False 815 815 82.4930 789 1753 1 chr2A.!!$F4 964
3 TraesCS2A01G578400 chr2D 645946870 645948731 1861 False 2826 2826 94.2220 13 1859 1 chr2D.!!$F3 1846
4 TraesCS2A01G578400 chr2D 645892895 645894154 1259 False 539 773 85.7625 467 1753 2 chr2D.!!$F4 1286
5 TraesCS2A01G578400 chr2B 789601245 789603045 1800 True 2329 2329 89.9290 13 1844 1 chr2B.!!$R1 1831
6 TraesCS2A01G578400 chr2B 789669616 789670346 730 True 612 612 81.9520 1013 1753 1 chr2B.!!$R4 740
7 TraesCS2A01G578400 chr4A 597316405 597317301 896 True 1496 1496 96.7710 1859 2755 1 chr4A.!!$R1 896
8 TraesCS2A01G578400 chr5D 450523553 450524450 897 False 1491 1491 96.6590 1859 2755 1 chr5D.!!$F1 896
9 TraesCS2A01G578400 chr1A 504104663 504105560 897 True 1485 1485 96.5480 1859 2755 1 chr1A.!!$R1 896
10 TraesCS2A01G578400 chr3B 533024548 533025450 902 False 1465 1465 95.9160 1851 2755 1 chr3B.!!$F1 904
11 TraesCS2A01G578400 chr5A 35738424 35739322 898 True 1458 1458 95.8980 1855 2755 1 chr5A.!!$R1 900
12 TraesCS2A01G578400 chr7D 634755017 634755913 896 False 1452 1452 95.8800 1859 2755 1 chr7D.!!$F1 896
13 TraesCS2A01G578400 chr1D 435761467 435762364 897 True 1452 1452 95.8800 1859 2755 1 chr1D.!!$R1 896
14 TraesCS2A01G578400 chr3A 730651923 730652846 923 False 1435 1435 94.7080 1832 2755 1 chr3A.!!$F1 923

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
939 972 0.250467 GCTGCCTTGACCAGAGTTCA 60.25 55.0 0.0 0.0 32.03 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2028 2101 0.250252 TGGCTGCGATGTCTGTTTGA 60.25 50.0 0.0 0.0 0.0 2.69 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
97 98 2.481568 CGACATTGTATGGCTATGGCAG 59.518 50.000 2.58 0.00 42.43 4.85
171 172 2.515523 GAGCGGCCACAGATGCAT 60.516 61.111 2.24 0.00 0.00 3.96
172 173 2.044650 AGCGGCCACAGATGCATT 60.045 55.556 2.24 0.00 0.00 3.56
173 174 2.103538 GCGGCCACAGATGCATTG 59.896 61.111 2.24 3.98 0.00 2.82
174 175 2.409055 GCGGCCACAGATGCATTGA 61.409 57.895 2.24 0.00 0.00 2.57
179 180 1.479323 GCCACAGATGCATTGACCATT 59.521 47.619 0.00 0.00 0.00 3.16
237 238 4.380843 TGAAATACAGATGTGGGGTTGT 57.619 40.909 0.00 0.00 0.00 3.32
346 347 8.739972 AGAACTTTAAACAAGTTGTCATTGTCT 58.260 29.630 9.40 4.20 39.91 3.41
397 398 7.201626 CCAATCAAATTGCAACAGTCAAAGAAA 60.202 33.333 0.00 0.00 38.92 2.52
419 420 2.616458 GGGAGTGGGCTGTTGGGAT 61.616 63.158 0.00 0.00 0.00 3.85
423 424 0.548682 AGTGGGCTGTTGGGATCTCT 60.549 55.000 0.00 0.00 0.00 3.10
440 441 7.565029 TGGGATCTCTCAACATCTATCTTTACA 59.435 37.037 0.00 0.00 0.00 2.41
441 442 8.087750 GGGATCTCTCAACATCTATCTTTACAG 58.912 40.741 0.00 0.00 0.00 2.74
453 458 6.539173 TCTATCTTTACAGTTTTTCCTGCCA 58.461 36.000 0.00 0.00 35.83 4.92
460 465 4.406456 ACAGTTTTTCCTGCCACATATCA 58.594 39.130 0.00 0.00 35.83 2.15
498 503 0.948678 TGCGTTTGCTACTTGGAACC 59.051 50.000 0.00 0.00 43.34 3.62
598 614 1.064952 GGGCATATACAACAACACCGC 59.935 52.381 0.00 0.00 0.00 5.68
708 724 3.236816 CTGCCTTCTTGCATAAACAACG 58.763 45.455 0.00 0.00 41.16 4.10
769 785 1.970917 GACCGATGCGTGCCAAAGAG 61.971 60.000 0.00 0.00 0.00 2.85
939 972 0.250467 GCTGCCTTGACCAGAGTTCA 60.250 55.000 0.00 0.00 32.03 3.18
941 974 2.787994 CTGCCTTGACCAGAGTTCAAT 58.212 47.619 0.00 0.00 32.03 2.57
998 1041 0.620556 GGACAGGGCATGGAGAAAGA 59.379 55.000 3.46 0.00 0.00 2.52
1370 1431 9.990360 TTTAATTTTCTGTTGGAGTAAATTCCC 57.010 29.630 0.00 0.00 39.55 3.97
1407 1479 6.018751 CGTGTTCATTTATCCGTGATCATCTT 60.019 38.462 0.00 0.00 0.00 2.40
1529 1601 2.747686 GAGGTGCTCGGGGACAAA 59.252 61.111 9.87 0.00 35.41 2.83
1565 1637 3.206150 CGATGAATTCGGGTTCTTGGAT 58.794 45.455 0.04 0.00 44.28 3.41
1689 1761 1.840635 GCAGGGAAAGGGAGAGTGTAT 59.159 52.381 0.00 0.00 0.00 2.29
1709 1781 1.956629 GCGAGGTTCTTCCCGATGGA 61.957 60.000 0.00 0.00 39.54 3.41
1757 1829 3.059188 AGTTTTACGGCATTGAGTGAACG 60.059 43.478 0.00 0.00 36.31 3.95
1803 1875 7.610305 TGTACTCCCTCTGTTCCAAAATAATTC 59.390 37.037 0.00 0.00 0.00 2.17
1827 1899 7.974504 TCAAGTTGTAGGATTTTCCTTAGTCT 58.025 34.615 2.11 0.00 46.91 3.24
1934 2007 7.855904 CGGCCACTTTATTAATTATTCTCACAC 59.144 37.037 2.24 0.00 0.00 3.82
2020 2093 2.134287 GGGGCGCAGATAGTCTGGA 61.134 63.158 10.83 0.00 44.43 3.86
2028 2101 4.158764 GCGCAGATAGTCTGGACCTAATAT 59.841 45.833 0.30 0.00 44.43 1.28
2107 2180 3.716195 CGGGCATGGGTCTCACCA 61.716 66.667 0.00 0.00 46.24 4.17
2303 2377 1.805254 GCACCATGCTGCCAAGTAG 59.195 57.895 1.22 0.00 40.96 2.57
2586 2662 3.344137 AACCGCCGCCATCAGGAAT 62.344 57.895 0.00 0.00 36.89 3.01
2595 2671 2.037144 GCCATCAGGAATGCCAAGAAT 58.963 47.619 0.00 0.00 36.89 2.40
2597 2673 3.028850 CCATCAGGAATGCCAAGAATGT 58.971 45.455 0.00 0.00 36.89 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.037737 GCAAGTTCGTAGGTATAACATCAAATA 57.962 33.333 0.00 0.00 0.00 1.40
11 12 7.551262 TGCAAGTTCGTAGGTATAACATCAAAT 59.449 33.333 0.00 0.00 0.00 2.32
65 66 7.871853 AGCCATACAATGTCGGTAATTTTATC 58.128 34.615 0.00 0.00 0.00 1.75
110 111 2.412089 GTGTCGTGCTGGAAGAATACAC 59.588 50.000 0.00 0.00 34.07 2.90
165 166 4.841443 TCATAGCAATGGTCAATGCATC 57.159 40.909 12.72 0.00 44.95 3.91
168 169 5.002464 AGTTTCATAGCAATGGTCAATGC 57.998 39.130 3.02 3.02 42.87 3.56
169 170 7.087409 TGTAGTTTCATAGCAATGGTCAATG 57.913 36.000 0.00 0.00 33.61 2.82
170 171 7.701539 TTGTAGTTTCATAGCAATGGTCAAT 57.298 32.000 0.00 0.00 33.61 2.57
171 172 7.392953 TCATTGTAGTTTCATAGCAATGGTCAA 59.607 33.333 13.34 0.00 43.63 3.18
172 173 6.883756 TCATTGTAGTTTCATAGCAATGGTCA 59.116 34.615 13.34 0.00 43.63 4.02
173 174 7.320443 TCATTGTAGTTTCATAGCAATGGTC 57.680 36.000 13.34 0.00 43.63 4.02
174 175 7.886629 ATCATTGTAGTTTCATAGCAATGGT 57.113 32.000 13.34 5.80 43.63 3.55
179 180 8.210265 TGGTCATATCATTGTAGTTTCATAGCA 58.790 33.333 0.00 0.00 0.00 3.49
281 282 7.081857 ACCCCCTTCGTATAAAAATATAGCA 57.918 36.000 0.00 0.00 0.00 3.49
377 378 4.566360 CGGTTTCTTTGACTGTTGCAATTT 59.434 37.500 0.59 0.00 0.00 1.82
423 424 9.793259 AGGAAAAACTGTAAAGATAGATGTTGA 57.207 29.630 0.00 0.00 0.00 3.18
440 441 4.702131 GTCTGATATGTGGCAGGAAAAACT 59.298 41.667 0.00 0.00 33.05 2.66
441 442 4.458989 TGTCTGATATGTGGCAGGAAAAAC 59.541 41.667 0.00 0.00 33.05 2.43
453 458 6.593770 TGCGTAGTTGAATTTGTCTGATATGT 59.406 34.615 0.00 0.00 0.00 2.29
460 465 3.424829 CGCATGCGTAGTTGAATTTGTCT 60.425 43.478 31.33 0.00 34.35 3.41
708 724 4.412207 GTTCTGTGTTTGTTCACTTGGAC 58.588 43.478 0.00 0.00 38.90 4.02
796 812 4.757149 AGAAAAGTAAAACATCGCTCAGCT 59.243 37.500 0.00 0.00 0.00 4.24
939 972 3.409804 AATGGAGCCTTGGATTGGATT 57.590 42.857 0.00 0.00 0.00 3.01
941 974 2.312741 AGAAATGGAGCCTTGGATTGGA 59.687 45.455 0.00 0.00 0.00 3.53
998 1041 1.293498 GTCACCTCGCTGTCCATGT 59.707 57.895 0.00 0.00 0.00 3.21
1529 1601 2.715046 TCATCGCCAGAAAAGAAGCAT 58.285 42.857 0.00 0.00 0.00 3.79
1565 1637 4.014569 TGAAAATGGGATGAAGACGACA 57.985 40.909 0.00 0.00 0.00 4.35
1646 1718 1.227089 CTTCTCCCATCGCGTGAGG 60.227 63.158 5.77 3.76 0.00 3.86
1689 1761 1.218047 CATCGGGAAGAACCTCGCA 59.782 57.895 0.00 0.00 38.98 5.10
1709 1781 5.217978 TGTGTAATTCGTACTGGACCTTT 57.782 39.130 0.00 0.00 33.46 3.11
1757 1829 3.308866 ACATTCGATTCGACCGAAATTCC 59.691 43.478 20.80 0.00 46.97 3.01
1934 2007 7.647907 ACTGTTGTATTACTTTGTAAGGTCG 57.352 36.000 0.00 0.00 0.00 4.79
2020 2093 5.670485 TGCGATGTCTGTTTGATATTAGGT 58.330 37.500 0.00 0.00 0.00 3.08
2028 2101 0.250252 TGGCTGCGATGTCTGTTTGA 60.250 50.000 0.00 0.00 0.00 2.69
2303 2377 2.037136 AAGCTGTGTCGGCTGATGC 61.037 57.895 0.00 1.55 46.32 3.91
2586 2662 1.961378 CTGCAGCACATTCTTGGCA 59.039 52.632 0.00 0.00 0.00 4.92
2595 2671 3.876236 TGGGACAGCTGCAGCACA 61.876 61.111 38.24 24.54 45.16 4.57
2641 2717 1.601419 CCGGCTCCGTCACCTTCTTA 61.601 60.000 7.59 0.00 37.81 2.10


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

AutoCloner maintained by Alex Coulton.