Multiple sequence alignment - TraesCS2B01G609000

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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 TraesCS2B01G609000 chr2B 100.000 2487 0 0 576 3062 789296119 789293633 0.000000e+00 4593
1 TraesCS2B01G609000 chr2B 97.871 2489 42 5 576 3062 571963685 571961206 0.000000e+00 4292
2 TraesCS2B01G609000 chr2B 97.429 2489 48 9 576 3062 571851376 571848902 0.000000e+00 4228
3 TraesCS2B01G609000 chr2B 96.390 2493 71 11 576 3062 789358003 789355524 0.000000e+00 4087
4 TraesCS2B01G609000 chr2B 96.208 2505 61 5 576 3062 571994331 571991843 0.000000e+00 4069
5 TraesCS2B01G609000 chr2B 96.232 2495 70 14 576 3062 789406307 789403829 0.000000e+00 4065
6 TraesCS2B01G609000 chr2B 95.947 2492 81 7 576 3062 789375101 789372625 0.000000e+00 4024
7 TraesCS2B01G609000 chr2B 95.385 2492 75 10 576 3062 571833342 571830886 0.000000e+00 3928
8 TraesCS2B01G609000 chr2B 95.854 2388 68 10 682 3062 789326514 789324151 0.000000e+00 3832
9 TraesCS2B01G609000 chr2B 96.204 2134 64 9 576 2697 571877250 571875122 0.000000e+00 3476
10 TraesCS2B01G609000 chr2B 95.773 2011 55 12 576 2582 789424688 789422704 0.000000e+00 3216
11 TraesCS2B01G609000 chr2B 100.000 279 0 0 1 279 789296694 789296416 1.630000e-142 516
12 TraesCS2B01G609000 chr2B 98.208 279 5 0 1 279 571994682 571994404 3.550000e-134 488
13 TraesCS2B01G609000 chr2B 98.208 279 4 1 1 279 789375440 789375163 1.280000e-133 486
14 TraesCS2B01G609000 chr2B 97.849 279 6 0 1 279 571964036 571963758 1.650000e-132 483
15 TraesCS2B01G609000 chr2B 97.491 279 6 1 1 279 571877590 571877313 2.760000e-130 475
16 TraesCS2B01G609000 chr2B 97.491 279 6 1 1 279 789358342 789358065 2.760000e-130 475
17 TraesCS2B01G609000 chr2B 97.491 279 5 2 1 279 789406655 789406379 2.760000e-130 475
18 TraesCS2B01G609000 chr2B 96.797 281 7 2 1 279 571851728 571851448 4.620000e-128 468
19 TraesCS2B01G609000 chr2B 97.101 276 7 1 4 279 789326787 789326513 5.980000e-127 464
20 TraesCS2B01G609000 chr2B 96.774 279 4 3 1 279 571910060 571909787 7.740000e-126 460
21 TraesCS2B01G609000 chr2A 92.591 2011 132 11 1058 3062 773380317 773378318 0.000000e+00 2872


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 TraesCS2B01G609000 chr2B 789293633 789296694 3061 True 2554.5 4593 100.0000 1 3062 2 chr2B.!!$R8 3061
1 TraesCS2B01G609000 chr2B 571830886 571833342 2456 True 3928.0 3928 95.3850 576 3062 1 chr2B.!!$R1 2486
2 TraesCS2B01G609000 chr2B 789422704 789424688 1984 True 3216.0 3216 95.7730 576 2582 1 chr2B.!!$R3 2006
3 TraesCS2B01G609000 chr2B 571961206 571964036 2830 True 2387.5 4292 97.8600 1 3062 2 chr2B.!!$R6 3061
4 TraesCS2B01G609000 chr2B 571848902 571851728 2826 True 2348.0 4228 97.1130 1 3062 2 chr2B.!!$R4 3061
5 TraesCS2B01G609000 chr2B 789355524 789358342 2818 True 2281.0 4087 96.9405 1 3062 2 chr2B.!!$R10 3061
6 TraesCS2B01G609000 chr2B 571991843 571994682 2839 True 2278.5 4069 97.2080 1 3062 2 chr2B.!!$R7 3061
7 TraesCS2B01G609000 chr2B 789403829 789406655 2826 True 2270.0 4065 96.8615 1 3062 2 chr2B.!!$R12 3061
8 TraesCS2B01G609000 chr2B 789372625 789375440 2815 True 2255.0 4024 97.0775 1 3062 2 chr2B.!!$R11 3061
9 TraesCS2B01G609000 chr2B 789324151 789326787 2636 True 2148.0 3832 96.4775 4 3062 2 chr2B.!!$R9 3058
10 TraesCS2B01G609000 chr2B 571875122 571877590 2468 True 1975.5 3476 96.8475 1 2697 2 chr2B.!!$R5 2696
11 TraesCS2B01G609000 chr2A 773378318 773380317 1999 True 2872.0 2872 92.5910 1058 3062 1 chr2A.!!$R1 2004

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
94 95 5.220491 GCGAACATTTCTTTCTGGTAGCTAG 60.220 44.0 0.00 0.0 29.37 3.42 F
1391 1455 0.035439 CGGCCATTACAACTCCAGGT 60.035 55.0 2.24 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1833 1907 1.337823 ACGCGCACCTACTCTTGAAAT 60.338 47.619 5.73 0.0 0.0 2.17 R
2517 2595 1.800805 ACGACAAGAGAACATGCCAG 58.199 50.000 0.00 0.0 0.0 4.85 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
94 95 5.220491 GCGAACATTTCTTTCTGGTAGCTAG 60.220 44.000 0.00 0.00 29.37 3.42
274 277 7.470289 TTGTGAACATAATTTTGAAAACGGG 57.530 32.000 2.69 0.00 0.00 5.28
610 613 8.038492 AGACTCTCGACTACGTACTTATTTTT 57.962 34.615 0.00 0.00 40.69 1.94
1041 1051 3.181418 ACACAATCAATTCCCCACCTCTT 60.181 43.478 0.00 0.00 0.00 2.85
1207 1255 4.961438 TTATACTTCCATACGTTCCCCC 57.039 45.455 0.00 0.00 0.00 5.40
1391 1455 0.035439 CGGCCATTACAACTCCAGGT 60.035 55.000 2.24 0.00 0.00 4.00
1833 1907 0.537143 ACAGAAAAGCCGATGTGCCA 60.537 50.000 0.00 0.00 0.00 4.92
1883 1957 4.262377 CGGATAGATTTCAGATCCTGCACT 60.262 45.833 8.86 0.00 37.57 4.40
1987 2061 4.747108 CCTTTCATGCTTAGATAGACACGG 59.253 45.833 0.00 0.00 0.00 4.94
2270 2347 1.913762 CTTCTCCTCACCCACCGGT 60.914 63.158 0.00 0.00 46.31 5.28
2517 2595 1.159285 GGCCTGCCTTTTTGCATTTC 58.841 50.000 0.00 0.00 41.16 2.17
2569 2647 2.849294 AGCTTCTCCAGTGTTCTTCC 57.151 50.000 0.00 0.00 0.00 3.46
2618 2696 5.940470 GGTGATTTCTCTTGGAAAGCTTCTA 59.060 40.000 0.00 0.00 46.71 2.10
2641 2719 6.882656 TAGAATTCTCTCACAAGCATTAGCT 58.117 36.000 12.24 0.00 42.51 3.32
2759 2837 2.564947 GGTCATCCATAGCTAGGACCAG 59.435 54.545 12.12 7.24 43.27 4.00
2840 2918 3.503363 TGCCAGATCAAGTGCTTTGTAAG 59.497 43.478 0.00 0.00 38.01 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
115 116 5.537188 CTTTCAAAAATTGTTCCCGGATCA 58.463 37.500 0.73 0.00 0.00 2.92
795 799 1.912763 GGCAAAGTCCATTGGGGCA 60.913 57.895 2.09 0.00 43.06 5.36
858 868 4.083537 CGTATTTTGCTGCCTACAAAGACA 60.084 41.667 0.00 0.00 38.20 3.41
1041 1051 7.804129 CGTCCGTGGTTATCTTTTTATTTTTCA 59.196 33.333 0.00 0.00 0.00 2.69
1205 1253 2.370189 GAGAGAGAGAGAGAGAGAGGGG 59.630 59.091 0.00 0.00 0.00 4.79
1206 1254 3.312890 AGAGAGAGAGAGAGAGAGAGGG 58.687 54.545 0.00 0.00 0.00 4.30
1207 1255 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.00 0.00 3.69
1208 1256 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1209 1257 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1210 1258 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1211 1259 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
1212 1260 4.892345 TGAGAGAGAGAGAGAGAGAGAGAG 59.108 50.000 0.00 0.00 0.00 3.20
1213 1261 4.871822 TGAGAGAGAGAGAGAGAGAGAGA 58.128 47.826 0.00 0.00 0.00 3.10
1391 1455 7.794041 ACATGACATAAAATACTTACCGGGTA 58.206 34.615 6.32 1.88 0.00 3.69
1682 1751 3.506096 CGTCTAGACCGGCGCTCA 61.506 66.667 17.23 0.00 0.00 4.26
1833 1907 1.337823 ACGCGCACCTACTCTTGAAAT 60.338 47.619 5.73 0.00 0.00 2.17
1883 1957 2.558359 TGAACTCTTCAGCATCACTCGA 59.442 45.455 0.00 0.00 34.08 4.04
1987 2061 7.415229 ACAAAACAGTGCTTAGCTAAGTTTAC 58.585 34.615 29.42 24.34 35.75 2.01
2270 2347 3.061563 CGGCTTAAATGTCGATTTCGTCA 59.938 43.478 2.63 2.63 41.07 4.35
2504 2582 3.404899 ACATGCCAGAAATGCAAAAAGG 58.595 40.909 0.00 0.00 42.92 3.11
2517 2595 1.800805 ACGACAAGAGAACATGCCAG 58.199 50.000 0.00 0.00 0.00 4.85
2569 2647 6.148480 CCTGGAAAGTCTTCAAAGTATGACTG 59.852 42.308 0.00 0.00 39.39 3.51
2641 2719 3.431415 TGAGTAAACTGGCAGAGAGCTA 58.569 45.455 23.66 1.78 44.79 3.32
2742 2820 3.619900 TGTCTGGTCCTAGCTATGGAT 57.380 47.619 13.05 0.00 35.87 3.41
2759 2837 6.642131 CAGCAAGCTAAGAAGAGAGATATGTC 59.358 42.308 0.00 0.00 0.00 3.06
2840 2918 3.603532 TGATGATTCAAGAGTGTCCTGC 58.396 45.455 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.