Multiple sequence alignment - TraesCS2B01G142700

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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 TraesCS2B01G142700 chr2B 100.000 2510 0 0 1 2510 109780804 109783313 0.000000e+00 4636.0
1 TraesCS2B01G142700 chr2B 97.648 2509 55 4 3 2510 109153250 109155755 0.000000e+00 4303.0
2 TraesCS2B01G142700 chr2B 96.366 798 23 4 3 796 109073897 109074692 0.000000e+00 1308.0
3 TraesCS2B01G142700 chr2B 89.738 497 29 7 2 491 8178755 8178274 1.280000e-172 616.0
4 TraesCS2B01G142700 chr2B 89.278 485 29 8 14 491 8014649 8014181 1.000000e-163 586.0
5 TraesCS2B01G142700 chr2B 85.072 489 48 8 2 488 55693262 55692797 2.260000e-130 475.0
6 TraesCS2B01G142700 chr2B 84.431 501 50 13 2 498 44307390 44306914 3.780000e-128 468.0
7 TraesCS2B01G142700 chr2B 76.768 495 78 25 3 491 552324489 552324952 2.490000e-60 243.0
8 TraesCS2B01G142700 chr4A 89.202 1704 142 21 813 2510 501476845 501475178 0.000000e+00 2089.0
9 TraesCS2B01G142700 chr6D 77.550 1657 338 29 813 2453 423001242 423002880 0.000000e+00 968.0
10 TraesCS2B01G142700 chr6D 92.500 40 3 0 1139 1178 433532672 433532633 9.700000e-05 58.4
11 TraesCS2B01G142700 chr3B 77.095 1659 348 30 813 2453 50391855 50393499 0.000000e+00 929.0
12 TraesCS2B01G142700 chr3B 84.456 386 53 6 2 381 782665900 782665516 8.480000e-100 374.0
13 TraesCS2B01G142700 chr3B 92.188 64 5 0 417 480 782665513 782665450 9.560000e-15 91.6
14 TraesCS2B01G142700 chr6A 76.439 1702 358 37 814 2492 103764361 103766042 0.000000e+00 881.0
15 TraesCS2B01G142700 chr6A 81.980 394 67 4 2119 2510 720115 719724 5.180000e-87 331.0
16 TraesCS2B01G142700 chr6A 71.901 242 64 4 1184 1423 553143406 553143167 1.610000e-07 67.6
17 TraesCS2B01G142700 chr7B 89.357 498 35 5 2 496 653874993 653874511 5.940000e-171 610.0
18 TraesCS2B01G142700 chr4B 89.400 500 31 6 2 494 613083418 613082934 5.940000e-171 610.0
19 TraesCS2B01G142700 chr2D 97.705 305 7 0 492 796 72622092 72622396 2.210000e-145 525.0
20 TraesCS2B01G142700 chr2D 96.721 305 9 1 492 796 72351826 72352129 8.010000e-140 507.0
21 TraesCS2B01G142700 chr2D 92.683 41 3 0 1139 1179 101362233 101362193 2.700000e-05 60.2
22 TraesCS2B01G142700 chr5B 92.055 365 21 3 2 358 598433402 598433038 8.010000e-140 507.0
23 TraesCS2B01G142700 chr5B 74.903 514 126 3 1022 1534 647978856 647978345 5.400000e-57 231.0
24 TraesCS2B01G142700 chr2A 93.791 306 17 2 492 796 71071743 71072047 2.280000e-125 459.0
25 TraesCS2B01G142700 chr2A 86.971 307 29 4 492 797 71107872 71108168 4.000000e-88 335.0
26 TraesCS2B01G142700 chr2A 84.667 300 36 5 492 791 71109687 71109976 8.780000e-75 291.0
27 TraesCS2B01G142700 chr6B 76.431 751 159 15 957 1699 250341201 250341941 8.420000e-105 390.0
28 TraesCS2B01G142700 chr1A 82.639 432 55 15 66 493 27369218 27368803 5.100000e-97 364.0
29 TraesCS2B01G142700 chr1A 83.038 395 62 5 2109 2501 520838028 520838419 1.100000e-93 353.0
30 TraesCS2B01G142700 chr1A 79.487 507 93 10 2011 2510 372294121 372293619 1.430000e-92 350.0
31 TraesCS2B01G142700 chr5D 79.915 473 91 3 2040 2510 379016607 379016137 6.650000e-91 344.0
32 TraesCS2B01G142700 chr3A 78.647 473 96 4 2040 2510 7377022 7376553 2.420000e-80 309.0
33 TraesCS2B01G142700 chr3A 93.750 64 4 0 428 491 1579705 1579642 2.060000e-16 97.1
34 TraesCS2B01G142700 chr1B 80.418 383 73 2 2129 2510 570849597 570849216 8.780000e-75 291.0
35 TraesCS2B01G142700 chr5A 72.657 779 200 13 1036 1809 529811444 529812214 1.930000e-61 246.0
36 TraesCS2B01G142700 chr7D 87.500 72 8 1 427 498 84400981 84401051 5.750000e-12 82.4


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 TraesCS2B01G142700 chr2B 109780804 109783313 2509 False 4636 4636 100.000 1 2510 1 chr2B.!!$F3 2509
1 TraesCS2B01G142700 chr2B 109153250 109155755 2505 False 4303 4303 97.648 3 2510 1 chr2B.!!$F2 2507
2 TraesCS2B01G142700 chr2B 109073897 109074692 795 False 1308 1308 96.366 3 796 1 chr2B.!!$F1 793
3 TraesCS2B01G142700 chr4A 501475178 501476845 1667 True 2089 2089 89.202 813 2510 1 chr4A.!!$R1 1697
4 TraesCS2B01G142700 chr6D 423001242 423002880 1638 False 968 968 77.550 813 2453 1 chr6D.!!$F1 1640
5 TraesCS2B01G142700 chr3B 50391855 50393499 1644 False 929 929 77.095 813 2453 1 chr3B.!!$F1 1640
6 TraesCS2B01G142700 chr6A 103764361 103766042 1681 False 881 881 76.439 814 2492 1 chr6A.!!$F1 1678
7 TraesCS2B01G142700 chr5B 647978345 647978856 511 True 231 231 74.903 1022 1534 1 chr5B.!!$R2 512
8 TraesCS2B01G142700 chr2A 71107872 71109976 2104 False 313 335 85.819 492 797 2 chr2A.!!$F2 305
9 TraesCS2B01G142700 chr6B 250341201 250341941 740 False 390 390 76.431 957 1699 1 chr6B.!!$F1 742
10 TraesCS2B01G142700 chr1A 372293619 372294121 502 True 350 350 79.487 2011 2510 1 chr1A.!!$R2 499
11 TraesCS2B01G142700 chr5A 529811444 529812214 770 False 246 246 72.657 1036 1809 1 chr5A.!!$F1 773

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
258 263 0.31179 CAACAAAGGCATGCTGTCGT 59.688 50.0 18.92 7.57 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1834 2377 0.106719 AAGGGTTGGACTGTGTGGTG 60.107 55.0 0.0 0.0 0.0 4.17 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
258 263 0.311790 CAACAAAGGCATGCTGTCGT 59.688 50.000 18.92 7.57 0.00 4.34
273 278 1.964933 TGTCGTAGTGGTTGTGGATGA 59.035 47.619 0.00 0.00 0.00 2.92
341 346 8.423349 TGCCATCCTATTTTCCTATTTTTCATG 58.577 33.333 0.00 0.00 0.00 3.07
965 975 2.567615 GGGTTCGTGCTAGGGATCATAT 59.432 50.000 0.00 0.00 0.00 1.78
1219 1233 0.919710 GAGGGTAGCCTGGGATTTGT 59.080 55.000 20.52 0.00 0.00 2.83
1507 1522 5.762045 CAGAACCGAAATCACATGACTTTT 58.238 37.500 0.00 0.00 0.00 2.27
1518 1533 6.377327 TCACATGACTTTTGAAGGAAACTC 57.623 37.500 0.00 0.00 42.68 3.01
1737 2280 2.174639 TGGTTTTCAAAGAGCTCAGGGA 59.825 45.455 17.77 6.81 0.00 4.20
1834 2377 1.004918 CAGAGGTGGTGGTCGTTCC 60.005 63.158 0.00 0.00 0.00 3.62
1914 2460 1.827399 AACGTCGCAATGGAGGAGGT 61.827 55.000 0.00 0.00 0.00 3.85
1946 2492 0.978146 GAAGAGGGGAGCAGCAGGTA 60.978 60.000 0.00 0.00 0.00 3.08
2175 2829 1.432270 GGTCGCACCTAGAGCAATGC 61.432 60.000 0.00 0.00 34.73 3.56
2253 2907 1.599542 GCGATCTAGCGAGGCAATTTT 59.400 47.619 0.00 0.00 0.00 1.82
2363 3238 2.889045 TGCAGTTAGTAGTTCTGGTCGT 59.111 45.455 0.00 0.00 0.00 4.34
2468 3524 2.040145 TGATGAGATGGTGGACTTGCAA 59.960 45.455 0.00 0.00 0.00 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 103 7.942341 TCCTTTTCCTGCTATGTTTCTTCTTTA 59.058 33.333 0.00 0.00 0.00 1.85
258 263 6.539173 ACTTTAACATCATCCACAACCACTA 58.461 36.000 0.00 0.00 0.00 2.74
273 278 6.238814 CCCACGACCACTTAAAACTTTAACAT 60.239 38.462 0.00 0.00 0.00 2.71
341 346 0.674269 CCCATTTGTTGTGGCATGCC 60.674 55.000 30.54 30.54 35.35 4.40
424 429 7.775561 AGGGTAATATGGACTTTTCACAATCTC 59.224 37.037 0.00 0.00 0.00 2.75
802 807 3.442076 ACGAGAGGGGAAAAGTATCAGT 58.558 45.455 0.00 0.00 0.00 3.41
965 975 1.546589 ATTACTTGGTCCGTGGGCGA 61.547 55.000 0.00 0.00 41.33 5.54
1219 1233 3.360867 GTCTGATCTTCACCTCCTGAGA 58.639 50.000 0.00 0.00 0.00 3.27
1518 1533 0.455633 CCTTACTCGAACACGGACGG 60.456 60.000 0.00 0.00 0.00 4.79
1737 2280 1.076438 AGGCCCTCTAAACCAGCTTT 58.924 50.000 0.00 0.00 0.00 3.51
1834 2377 0.106719 AAGGGTTGGACTGTGTGGTG 60.107 55.000 0.00 0.00 0.00 4.17
1914 2460 5.367060 GCTCCCCTCTTCCTATTTTTCTCTA 59.633 44.000 0.00 0.00 0.00 2.43
1946 2492 0.555769 TTGGGCTTTGGGACTTCAGT 59.444 50.000 0.00 0.00 0.00 3.41
2162 2816 3.070159 ACATCATACGCATTGCTCTAGGT 59.930 43.478 7.12 0.00 0.00 3.08
2175 2829 3.060761 CGACAGTTCCAACACATCATACG 59.939 47.826 0.00 0.00 0.00 3.06
2253 2907 7.136885 TCTACAATACAAAAGATAGAGGGGGA 58.863 38.462 0.00 0.00 0.00 4.81
2363 3238 3.850173 AGAAAATTCCTAGGCCACCACTA 59.150 43.478 5.01 0.00 0.00 2.74
2468 3524 5.235516 CCATACACAAAGGTTACTCGAACT 58.764 41.667 0.00 0.00 38.21 3.01


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

AutoCloner maintained by Alex Coulton.