Multiple sequence alignment - TraesCS1B01G114200

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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 TraesCS1B01G114200 chr1B 100.000 2216 0 0 1 2216 133124192 133126407 0.000000e+00 4093.0
1 TraesCS1B01G114200 chr1B 89.961 508 50 1 1553 2059 426498272 426498779 0.000000e+00 654.0
2 TraesCS1B01G114200 chr5D 93.071 1472 78 14 765 2216 289496822 289498289 0.000000e+00 2132.0
3 TraesCS1B01G114200 chr5D 92.210 1104 61 9 281 1372 289355633 289356723 0.000000e+00 1539.0
4 TraesCS1B01G114200 chr5D 89.589 682 59 8 1544 2216 289356809 289357487 0.000000e+00 856.0
5 TraesCS1B01G114200 chr5D 89.051 137 6 2 2 137 289355365 289355493 6.330000e-36 161.0
6 TraesCS1B01G114200 chr5D 90.722 97 4 2 188 279 289355491 289355587 8.310000e-25 124.0
7 TraesCS1B01G114200 chr5D 97.619 42 1 0 270 311 29906417 29906376 3.050000e-09 73.1
8 TraesCS1B01G114200 chr2B 93.705 1382 76 8 844 2216 127790642 127792021 0.000000e+00 2060.0
9 TraesCS1B01G114200 chr2B 93.474 1088 61 9 730 1812 135512235 135511153 0.000000e+00 1607.0
10 TraesCS1B01G114200 chr2B 96.451 479 16 1 1739 2216 135510810 135510332 0.000000e+00 789.0
11 TraesCS1B01G114200 chr2B 88.535 157 13 4 326 482 135512476 135512325 3.760000e-43 185.0
12 TraesCS1B01G114200 chr2B 90.909 55 5 0 53 107 135512533 135512479 8.490000e-10 75.0
13 TraesCS1B01G114200 chr7A 89.661 1654 111 32 584 2216 627234269 627235883 0.000000e+00 2052.0
14 TraesCS1B01G114200 chr7A 91.626 609 41 5 695 1293 628386315 628386923 0.000000e+00 833.0
15 TraesCS1B01G114200 chr7A 88.276 580 54 11 765 1335 627045820 627046394 0.000000e+00 682.0
16 TraesCS1B01G114200 chr7A 89.824 511 48 4 1553 2059 627046518 627047028 0.000000e+00 652.0
17 TraesCS1B01G114200 chr7A 89.583 144 8 5 513 656 628386177 628386313 2.260000e-40 176.0
18 TraesCS1B01G114200 chr7A 96.970 99 2 1 326 424 627234131 627234228 4.900000e-37 165.0
19 TraesCS1B01G114200 chr7A 82.550 149 16 6 516 654 580504667 580504815 2.990000e-24 122.0
20 TraesCS1B01G114200 chr7A 98.214 56 1 0 1 56 628385965 628386020 5.040000e-17 99.0
21 TraesCS1B01G114200 chr7A 85.897 78 2 1 110 178 628386022 628386099 8.490000e-10 75.0
22 TraesCS1B01G114200 chr7A 100.000 33 0 0 55 87 627232616 627232648 6.610000e-06 62.1
23 TraesCS1B01G114200 chr7B 95.009 1062 45 3 281 1337 588878495 588879553 0.000000e+00 1661.0
24 TraesCS1B01G114200 chr7B 96.391 665 20 3 1553 2216 588879674 588880335 0.000000e+00 1092.0
25 TraesCS1B01G114200 chr7B 83.057 844 102 24 516 1337 537825744 537826568 0.000000e+00 728.0
26 TraesCS1B01G114200 chr7B 92.132 394 4 2 20 413 589919855 589919489 4.190000e-147 531.0
27 TraesCS1B01G114200 chr7B 96.835 158 4 1 1 157 588878299 588878456 1.690000e-66 263.0
28 TraesCS1B01G114200 chr7B 89.781 137 7 1 8 144 498300111 498300240 3.780000e-38 169.0
29 TraesCS1B01G114200 chr7B 100.000 28 0 0 386 413 589934849 589934822 4.000000e-03 52.8
30 TraesCS1B01G114200 chr6A 90.248 564 49 3 772 1335 107263822 107263265 0.000000e+00 732.0
31 TraesCS1B01G114200 chr6A 94.118 68 4 0 1 68 107264322 107264255 1.080000e-18 104.0
32 TraesCS1B01G114200 chr6A 100.000 32 0 0 392 423 107264106 107264075 2.380000e-05 60.2
33 TraesCS1B01G114200 chr7D 84.783 184 19 5 520 694 509579870 509580053 2.260000e-40 176.0
34 TraesCS1B01G114200 chr7D 100.000 32 0 0 449 480 509599005 509599036 2.380000e-05 60.2
35 TraesCS1B01G114200 chr7D 96.875 32 0 1 603 633 545254753 545254722 4.000000e-03 52.8


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 TraesCS1B01G114200 chr1B 133124192 133126407 2215 False 4093.000000 4093 100.000000 1 2216 1 chr1B.!!$F1 2215
1 TraesCS1B01G114200 chr1B 426498272 426498779 507 False 654.000000 654 89.961000 1553 2059 1 chr1B.!!$F2 506
2 TraesCS1B01G114200 chr5D 289496822 289498289 1467 False 2132.000000 2132 93.071000 765 2216 1 chr5D.!!$F1 1451
3 TraesCS1B01G114200 chr5D 289355365 289357487 2122 False 670.000000 1539 90.393000 2 2216 4 chr5D.!!$F2 2214
4 TraesCS1B01G114200 chr2B 127790642 127792021 1379 False 2060.000000 2060 93.705000 844 2216 1 chr2B.!!$F1 1372
5 TraesCS1B01G114200 chr2B 135510332 135512533 2201 True 664.000000 1607 92.342250 53 2216 4 chr2B.!!$R1 2163
6 TraesCS1B01G114200 chr7A 627232616 627235883 3267 False 759.700000 2052 95.543667 55 2216 3 chr7A.!!$F3 2161
7 TraesCS1B01G114200 chr7A 627045820 627047028 1208 False 667.000000 682 89.050000 765 2059 2 chr7A.!!$F2 1294
8 TraesCS1B01G114200 chr7A 628385965 628386923 958 False 295.750000 833 91.330000 1 1293 4 chr7A.!!$F4 1292
9 TraesCS1B01G114200 chr7B 588878299 588880335 2036 False 1005.333333 1661 96.078333 1 2216 3 chr7B.!!$F3 2215
10 TraesCS1B01G114200 chr7B 537825744 537826568 824 False 728.000000 728 83.057000 516 1337 1 chr7B.!!$F2 821
11 TraesCS1B01G114200 chr6A 107263265 107264322 1057 True 298.733333 732 94.788667 1 1335 3 chr6A.!!$R1 1334

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
171 1584 3.347958 TTTTGGCACGAATGTCTGAAC 57.652 42.857 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1312 2897 0.111832 CAGGCCTGGCATATGTGGAT 59.888 55.0 26.14 0.0 0.0 3.41 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
171 1584 3.347958 TTTTGGCACGAATGTCTGAAC 57.652 42.857 0.00 0.00 0.00 3.18
182 1595 3.744719 TCTGAACCCGAGTCGGCG 61.745 66.667 26.60 20.44 46.86 6.46
203 1616 3.496130 CGCAGGCATAACTAATTCCTCAG 59.504 47.826 0.00 0.00 0.00 3.35
700 2180 3.670055 GCAAACAATTGTTCTCATGTCCG 59.330 43.478 23.47 5.96 38.85 4.79
1082 2665 1.238439 GATTGGCCCATGTATGTCGG 58.762 55.000 0.00 0.00 0.00 4.79
1083 2666 0.823356 ATTGGCCCATGTATGTCGGC 60.823 55.000 0.00 0.15 40.85 5.54
1150 2733 1.549203 AGGCACCATTGGTAAGCTTG 58.451 50.000 9.86 0.00 32.11 4.01
1173 2756 2.670509 GCTTTCAGAGTTCAGCATTGCC 60.671 50.000 4.70 0.00 32.17 4.52
1193 2778 1.825090 GCAACATCTGTCATGGTGGA 58.175 50.000 1.96 0.00 37.22 4.02
1197 2782 1.091771 CATCTGTCATGGTGGACCGC 61.092 60.000 0.00 0.00 39.43 5.68
1282 2867 3.376636 TCATATCCGTCCCCTAACAACA 58.623 45.455 0.00 0.00 0.00 3.33
1312 2897 1.619654 CTCATGCAACCTTTGGTCCA 58.380 50.000 0.00 0.00 33.12 4.02
1432 3052 5.957842 TGCTTTTACACACCCTATTTGAG 57.042 39.130 0.00 0.00 0.00 3.02
1660 3288 0.248458 AAACGCCAAAGCTGAACACG 60.248 50.000 0.00 0.00 36.60 4.49
1701 3329 4.859326 ACTCCTCGAGATGCATACTCTGC 61.859 52.174 15.71 0.00 41.17 4.26
1738 3368 7.201461 CCACTGAAAAGTGAAACAAAAGATGTG 60.201 37.037 7.43 0.00 40.87 3.21
1744 3374 7.396540 AAGTGAAACAAAAGATGTGAAGACT 57.603 32.000 0.00 0.00 42.99 3.24
1745 3375 6.789262 AGTGAAACAAAAGATGTGAAGACTG 58.211 36.000 0.00 0.00 42.99 3.51
1826 3878 1.137086 CTGATACCTGGTTCCCACGAG 59.863 57.143 3.84 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
182 1595 4.708177 TCTGAGGAATTAGTTATGCCTGC 58.292 43.478 0.00 0.00 42.99 4.85
188 1601 8.814038 ATTGTGCTTTCTGAGGAATTAGTTAT 57.186 30.769 0.00 0.00 0.00 1.89
189 1602 7.882791 TGATTGTGCTTTCTGAGGAATTAGTTA 59.117 33.333 0.00 0.00 0.00 2.24
203 1616 5.595952 AGGAGGGATTTATGATTGTGCTTTC 59.404 40.000 0.00 0.00 0.00 2.62
266 1684 9.189156 ACAAGCAGGCATTTTAGATTTCTTATA 57.811 29.630 0.00 0.00 0.00 0.98
700 2180 7.916552 ACAGTTATTCGCATGTCCTTTTATAC 58.083 34.615 0.00 0.00 0.00 1.47
797 2337 5.850557 TTCCATGGGCTACATTGTAATTG 57.149 39.130 13.02 0.00 37.84 2.32
1173 2756 0.448990 CCACCATGACAGATGTTGCG 59.551 55.000 0.00 0.00 0.00 4.85
1193 2778 1.519719 GAAGATCCAGCAGAGCGGT 59.480 57.895 0.00 0.00 35.47 5.68
1197 2782 1.202557 GCTCAGGAAGATCCAGCAGAG 60.203 57.143 0.00 2.32 39.61 3.35
1282 2867 2.089980 GTTGCATGAGCTTGTGGATCT 58.910 47.619 0.00 0.00 42.74 2.75
1312 2897 0.111832 CAGGCCTGGCATATGTGGAT 59.888 55.000 26.14 0.00 0.00 3.41
1660 3288 4.144534 AGTTTACTCGACGAAGACAGAC 57.855 45.455 0.00 0.00 0.00 3.51
1701 3329 5.036737 CACTTTTCAGTGGTTACAAAGCTG 58.963 41.667 0.00 0.00 46.10 4.24
1738 3368 6.096141 TCAGATGTCCTAATCTCACAGTCTTC 59.904 42.308 0.00 0.00 34.60 2.87
1744 3374 6.768483 TGTTTTCAGATGTCCTAATCTCACA 58.232 36.000 0.00 0.00 34.60 3.58
1745 3375 7.672983 TTGTTTTCAGATGTCCTAATCTCAC 57.327 36.000 0.00 0.00 34.60 3.51
1826 3878 1.448013 GAAGGGCACACGAGTAGGC 60.448 63.158 0.00 0.00 0.00 3.93
2147 4209 5.932303 GGCTACAACAGATCTAGTTTTCACA 59.068 40.000 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.