Multiple sequence alignment - TraesCS4A01G069300

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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 TraesCS4A01G069300 chr4A 100.000 2321 0 0 1 2321 67425671 67423351 0.000000e+00 4287.0
1 TraesCS4A01G069300 chr3A 98.190 2321 41 1 1 2321 620784709 620782390 0.000000e+00 4052.0
2 TraesCS4A01G069300 chr3A 97.295 1331 33 2 991 2321 535554882 535553555 0.000000e+00 2255.0
3 TraesCS4A01G069300 chr3A 90.226 133 13 0 103 235 209768410 209768278 8.520000e-40 174.0
4 TraesCS4A01G069300 chr3A 87.333 150 12 5 27 175 445509646 445509789 5.130000e-37 165.0
5 TraesCS4A01G069300 chr5D 97.907 1672 32 2 650 2321 309718064 309716396 0.000000e+00 2891.0
6 TraesCS4A01G069300 chr5D 96.833 600 17 2 57 654 309718808 309718209 0.000000e+00 1002.0
7 TraesCS4A01G069300 chr5D 94.615 130 7 0 723 852 351014093 351013964 3.910000e-48 202.0
8 TraesCS4A01G069300 chr5D 100.000 53 0 0 650 702 351014506 351014454 5.280000e-17 99.0
9 TraesCS4A01G069300 chr2D 97.847 1672 35 1 650 2321 648400610 648398940 0.000000e+00 2887.0
10 TraesCS4A01G069300 chr2D 96.327 599 20 2 58 654 648401353 648400755 0.000000e+00 983.0
11 TraesCS4A01G069300 chr2D 93.064 173 10 2 383 554 528995304 528995475 3.830000e-63 252.0
12 TraesCS4A01G069300 chr2D 90.977 133 12 0 103 235 634528142 634528274 1.830000e-41 180.0
13 TraesCS4A01G069300 chr2D 94.545 110 6 0 723 832 295488722 295488613 1.100000e-38 171.0
14 TraesCS4A01G069300 chr2D 94.737 76 4 0 57 132 295488824 295488749 4.050000e-23 119.0
15 TraesCS4A01G069300 chr5A 96.062 1676 60 3 650 2321 104951021 104949348 0.000000e+00 2724.0
16 TraesCS4A01G069300 chr5A 96.844 1331 42 0 991 2321 37110510 37111840 0.000000e+00 2226.0
17 TraesCS4A01G069300 chr5A 95.167 600 27 2 57 654 104951765 104951166 0.000000e+00 946.0
18 TraesCS4A01G069300 chr5A 93.077 130 9 0 723 852 451487059 451486930 8.460000e-45 191.0
19 TraesCS4A01G069300 chr5A 100.000 53 0 0 650 702 451487744 451487692 5.280000e-17 99.0
20 TraesCS4A01G069300 chr1A 95.995 1473 53 3 850 2321 86564425 86562958 0.000000e+00 2388.0
21 TraesCS4A01G069300 chr7A 95.316 1473 68 1 850 2321 352831539 352830067 0.000000e+00 2337.0
22 TraesCS4A01G069300 chr7A 89.189 111 10 1 125 235 699860050 699860158 1.120000e-28 137.0
23 TraesCS4A01G069300 chr2B 96.920 1331 41 0 991 2321 87814122 87815452 0.000000e+00 2231.0
24 TraesCS4A01G069300 chr2B 90.244 123 12 0 456 578 627324733 627324855 6.640000e-36 161.0
25 TraesCS4A01G069300 chr2B 91.228 57 5 0 586 642 627325255 627325311 6.880000e-11 78.7
26 TraesCS4A01G069300 chr6A 94.022 1472 65 7 850 2321 291223494 291222046 0.000000e+00 2209.0
27 TraesCS4A01G069300 chr6A 96.850 254 7 1 57 310 225160644 225160392 7.670000e-115 424.0
28 TraesCS4A01G069300 chr2A 86.567 201 20 4 383 583 673420565 673420758 5.020000e-52 215.0
29 TraesCS4A01G069300 chr5B 93.846 130 8 0 723 852 411950565 411950436 1.820000e-46 196.0
30 TraesCS4A01G069300 chr5B 85.507 138 9 5 849 986 662034866 662034992 1.450000e-27 134.0
31 TraesCS4A01G069300 chr5B 94.545 55 1 1 650 702 411950980 411950926 1.480000e-12 84.2
32 TraesCS4A01G069300 chr3D 90.977 133 12 0 103 235 24455940 24455808 1.830000e-41 180.0
33 TraesCS4A01G069300 chr7D 91.011 89 3 1 57 145 60613919 60613836 5.240000e-22 115.0


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 TraesCS4A01G069300 chr4A 67423351 67425671 2320 True 4287.0 4287 100.0000 1 2321 1 chr4A.!!$R1 2320
1 TraesCS4A01G069300 chr3A 620782390 620784709 2319 True 4052.0 4052 98.1900 1 2321 1 chr3A.!!$R3 2320
2 TraesCS4A01G069300 chr3A 535553555 535554882 1327 True 2255.0 2255 97.2950 991 2321 1 chr3A.!!$R2 1330
3 TraesCS4A01G069300 chr5D 309716396 309718808 2412 True 1946.5 2891 97.3700 57 2321 2 chr5D.!!$R1 2264
4 TraesCS4A01G069300 chr2D 648398940 648401353 2413 True 1935.0 2887 97.0870 58 2321 2 chr2D.!!$R2 2263
5 TraesCS4A01G069300 chr5A 37110510 37111840 1330 False 2226.0 2226 96.8440 991 2321 1 chr5A.!!$F1 1330
6 TraesCS4A01G069300 chr5A 104949348 104951765 2417 True 1835.0 2724 95.6145 57 2321 2 chr5A.!!$R1 2264
7 TraesCS4A01G069300 chr1A 86562958 86564425 1467 True 2388.0 2388 95.9950 850 2321 1 chr1A.!!$R1 1471
8 TraesCS4A01G069300 chr7A 352830067 352831539 1472 True 2337.0 2337 95.3160 850 2321 1 chr7A.!!$R1 1471
9 TraesCS4A01G069300 chr2B 87814122 87815452 1330 False 2231.0 2231 96.9200 991 2321 1 chr2B.!!$F1 1330
10 TraesCS4A01G069300 chr6A 291222046 291223494 1448 True 2209.0 2209 94.0220 850 2321 1 chr6A.!!$R2 1471

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
898 1055 0.460811 CTGCTCGCACCTTGCATCTA 60.461 55.0 0.0 0.0 45.36 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1806 1966 0.890542 ATGTGCGCACAACACCTGAT 60.891 50.0 43.14 23.95 45.41 2.9 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
44 45 1.096386 CGTCCCCTCCTCGTCTACAG 61.096 65.000 0.00 0.00 0.00 2.74
51 52 2.093973 CCTCCTCGTCTACAGCAACAAT 60.094 50.000 0.00 0.00 0.00 2.71
488 489 7.730332 TGCTTCTCAGTTTAGATCCCATATCTA 59.270 37.037 0.00 0.00 0.00 1.98
547 548 9.775854 CAATATGTAGAAGTGATGGAATTCTCT 57.224 33.333 5.23 1.06 35.09 3.10
554 555 3.387374 AGTGATGGAATTCTCTCGCTCAT 59.613 43.478 14.25 4.93 0.00 2.90
578 579 4.449743 GCGAGTACAGTGTCCAATGTTTTA 59.550 41.667 5.65 0.00 40.38 1.52
812 968 9.438291 CAATTTAATCGTTAGATGGTAAAGCTG 57.562 33.333 0.00 0.00 37.14 4.24
884 1041 8.720562 GCTACTAGTACTAGTATTAACCTGCTC 58.279 40.741 32.85 11.77 44.76 4.26
898 1055 0.460811 CTGCTCGCACCTTGCATCTA 60.461 55.000 0.00 0.00 45.36 1.98
1010 1167 8.267894 ACTAGTAATTTGAGGCATGTCTACATT 58.732 33.333 0.00 1.51 33.61 2.71
1214 1371 1.395635 CATATTGCAGAGGCTTGCCA 58.604 50.000 14.54 8.08 43.43 4.92
1680 1840 7.390718 AGGAAGAAATAGTTCGTTGCTTAACAT 59.609 33.333 0.00 0.00 38.90 2.71
1806 1966 5.076182 TCCTTGAAGGTCAACATTTGCATA 58.924 37.500 11.60 0.00 36.53 3.14
2168 2328 6.658831 TGAAGAGCTTACTTTGATTGTTTCG 58.341 36.000 0.00 0.00 0.00 3.46
2265 2425 1.446907 GCAGACCTCTGATGTGTTGG 58.553 55.000 6.49 0.00 46.59 3.77
2273 2433 4.202609 ACCTCTGATGTGTTGGAGGAATTT 60.203 41.667 13.78 0.00 45.79 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 5.868687 TGAAGTGGTTCGTGCATTGTTGC 62.869 47.826 0.00 0.00 41.45 4.17
51 52 2.425312 ACAAATTGAAGTGGTTCGTGCA 59.575 40.909 0.00 0.00 35.17 4.57
488 489 9.553064 GTGTCAAATAGAAGGATGATTCAGTAT 57.447 33.333 0.00 0.00 0.00 2.12
554 555 1.343142 ACATTGGACACTGTACTCGCA 59.657 47.619 0.00 0.00 0.00 5.10
578 579 7.996098 TTCTCAAAAAGAATATCGGGAAACT 57.004 32.000 0.00 0.00 39.12 2.66
750 902 9.593134 CAGTCTTGCTAATATTTCTTACTGAGT 57.407 33.333 0.00 0.00 34.05 3.41
898 1055 2.112928 TGCGTGGCCTGTGAATGT 59.887 55.556 3.32 0.00 0.00 2.71
1010 1167 0.331954 AGCACTCTCCGAACCCTCTA 59.668 55.000 0.00 0.00 0.00 2.43
1128 1285 7.073457 TCCATAGTATTTGCACATAGCCTTA 57.927 36.000 0.00 0.00 44.83 2.69
1214 1371 2.100252 CTGCAAGCATCCGGAATTGATT 59.900 45.455 23.93 15.26 0.00 2.57
1263 1421 3.951680 ACAAACAGACCTTCGGATGTTTT 59.048 39.130 13.98 7.30 40.83 2.43
1649 1809 6.758886 AGCAACGAACTATTTCTTCCTCTATG 59.241 38.462 0.00 0.00 0.00 2.23
1680 1840 3.678965 TTTGCCTCTTATGCCCCATTA 57.321 42.857 0.00 0.00 0.00 1.90
1779 1939 2.957402 TGTTGACCTTCAAGGAGCAT 57.043 45.000 11.59 0.00 37.00 3.79
1806 1966 0.890542 ATGTGCGCACAACACCTGAT 60.891 50.000 43.14 23.95 45.41 2.90
2265 2425 1.098050 ATCACTGCCGCAAATTCCTC 58.902 50.000 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.