Multiple sequence alignment - TraesCS1B01G160100

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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 TraesCS1B01G160100 chr1B 100.000 5024 0 0 1 5024 275356118 275361141 0.000000e+00 9278.0
1 TraesCS1B01G160100 chr1B 98.547 5025 54 9 1 5024 275456123 275461129 0.000000e+00 8857.0
2 TraesCS1B01G160100 chr1B 98.086 3658 46 7 905 4557 275551979 275555617 0.000000e+00 6346.0
3 TraesCS1B01G160100 chr1B 97.135 2862 60 9 2170 5024 275671865 275674711 0.000000e+00 4811.0
4 TraesCS1B01G160100 chr1B 96.128 1033 34 1 1 1033 275550884 275551910 0.000000e+00 1681.0
5 TraesCS1B01G160100 chr1B 98.635 879 12 0 1092 1970 275670422 275671300 0.000000e+00 1557.0
6 TraesCS1B01G160100 chr1B 96.282 511 17 2 4515 5024 275555617 275556126 0.000000e+00 837.0
7 TraesCS1B01G160100 chr1B 98.565 209 3 0 1964 2172 275671864 275671656 2.210000e-98 370.0
8 TraesCS1B01G160100 chr1A 96.418 3071 68 14 1114 4163 246130450 246127401 0.000000e+00 5024.0
9 TraesCS1B01G160100 chr1A 92.494 866 52 5 4161 5024 246127332 246126478 0.000000e+00 1227.0
10 TraesCS1B01G160100 chr1A 89.655 290 13 7 567 839 246131294 246131005 2.220000e-93 353.0
11 TraesCS1B01G160100 chr1A 84.462 251 27 8 301 544 472439356 472439601 2.340000e-58 237.0
12 TraesCS1B01G160100 chr1A 83.459 266 19 14 848 1096 246130691 246130434 1.820000e-54 224.0
13 TraesCS1B01G160100 chr2A 83.104 1598 203 34 2250 3799 610176624 610178202 0.000000e+00 1393.0
14 TraesCS1B01G160100 chr2A 83.825 1323 161 28 2524 3799 607512930 607514246 0.000000e+00 1208.0
15 TraesCS1B01G160100 chr2A 82.297 1045 168 9 2734 3775 138527481 138526451 0.000000e+00 889.0
16 TraesCS1B01G160100 chr2A 82.712 885 93 27 1127 1998 610175346 610176183 0.000000e+00 732.0
17 TraesCS1B01G160100 chr2A 84.948 485 35 17 73 543 24441786 24441326 1.650000e-124 457.0
18 TraesCS1B01G160100 chr2A 84.559 272 34 7 1151 1416 607511721 607511990 3.860000e-66 263.0
19 TraesCS1B01G160100 chr2A 81.343 134 25 0 2563 2696 138527691 138527558 5.320000e-20 110.0
20 TraesCS1B01G160100 chr2B 82.875 1600 204 36 2250 3799 545152384 545153963 0.000000e+00 1373.0
21 TraesCS1B01G160100 chr2B 80.103 1357 202 41 2563 3870 186403262 186404599 0.000000e+00 948.0
22 TraesCS1B01G160100 chr2B 84.842 884 96 21 1127 1998 545151110 545151967 0.000000e+00 856.0
23 TraesCS1B01G160100 chr2B 81.497 708 126 3 1196 1902 186402048 186402751 1.210000e-160 577.0
24 TraesCS1B01G160100 chr2B 85.141 249 28 7 301 543 541912033 541911788 3.880000e-61 246.0
25 TraesCS1B01G160100 chr2D 85.752 765 96 7 3034 3793 462240875 462241631 0.000000e+00 797.0
26 TraesCS1B01G160100 chr2D 86.640 494 26 14 64 545 115107931 115107466 1.250000e-140 510.0
27 TraesCS1B01G160100 chr2D 82.182 550 61 17 2516 3029 462240236 462240784 5.970000e-119 438.0
28 TraesCS1B01G160100 chr2D 88.087 277 28 5 1143 1416 462228830 462229104 1.740000e-84 324.0
29 TraesCS1B01G160100 chr2D 84.211 190 19 6 1816 1998 462229108 462229293 1.860000e-39 174.0
30 TraesCS1B01G160100 chr2D 81.203 133 25 0 2563 2695 131642938 131642806 1.910000e-19 108.0
31 TraesCS1B01G160100 chr1D 90.224 491 31 8 61 543 389353336 389353817 4.270000e-175 625.0
32 TraesCS1B01G160100 chrUn 89.091 495 36 9 64 544 108466030 108465540 2.590000e-167 599.0
33 TraesCS1B01G160100 chr5A 87.602 492 38 8 61 538 701632800 701633282 2.640000e-152 549.0
34 TraesCS1B01G160100 chr7B 87.872 470 35 9 64 513 214928676 214928209 2.660000e-147 532.0
35 TraesCS1B01G160100 chr5D 87.755 294 20 8 266 544 343509285 343508993 3.750000e-86 329.0
36 TraesCS1B01G160100 chr3B 84.800 250 26 8 301 543 30696478 30696722 1.810000e-59 241.0
37 TraesCS1B01G160100 chr7A 89.189 74 4 4 4329 4402 562324660 562324591 6.930000e-14 89.8
38 TraesCS1B01G160100 chr5B 95.745 47 1 1 4114 4159 658146430 658146476 1.940000e-09 75.0


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 TraesCS1B01G160100 chr1B 275356118 275361141 5023 False 9278.000000 9278 100.0000 1 5024 1 chr1B.!!$F1 5023
1 TraesCS1B01G160100 chr1B 275456123 275461129 5006 False 8857.000000 8857 98.5470 1 5024 1 chr1B.!!$F2 5023
2 TraesCS1B01G160100 chr1B 275670422 275674711 4289 False 3184.000000 4811 97.8850 1092 5024 2 chr1B.!!$F4 3932
3 TraesCS1B01G160100 chr1B 275550884 275556126 5242 False 2954.666667 6346 96.8320 1 5024 3 chr1B.!!$F3 5023
4 TraesCS1B01G160100 chr1A 246126478 246131294 4816 True 1707.000000 5024 90.5065 567 5024 4 chr1A.!!$R1 4457
5 TraesCS1B01G160100 chr2A 610175346 610178202 2856 False 1062.500000 1393 82.9080 1127 3799 2 chr2A.!!$F2 2672
6 TraesCS1B01G160100 chr2A 607511721 607514246 2525 False 735.500000 1208 84.1920 1151 3799 2 chr2A.!!$F1 2648
7 TraesCS1B01G160100 chr2A 138526451 138527691 1240 True 499.500000 889 81.8200 2563 3775 2 chr2A.!!$R2 1212
8 TraesCS1B01G160100 chr2B 545151110 545153963 2853 False 1114.500000 1373 83.8585 1127 3799 2 chr2B.!!$F2 2672
9 TraesCS1B01G160100 chr2B 186402048 186404599 2551 False 762.500000 948 80.8000 1196 3870 2 chr2B.!!$F1 2674
10 TraesCS1B01G160100 chr2D 462240236 462241631 1395 False 617.500000 797 83.9670 2516 3793 2 chr2D.!!$F2 1277

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
260 261 0.759436 GGAGCGATAGGAAGGGGTCA 60.759 60.000 0.00 0.0 0.00 4.02 F
487 489 1.065199 CAAGGCTGCTGAGGTGGATAA 60.065 52.381 0.00 0.0 0.00 1.75 F
1340 1858 1.825474 GAAGATCACGTCCCTGAGGAA 59.175 52.381 0.00 0.0 46.38 3.36 F
2805 4256 1.142185 CGCAGTGAGTCCTATGCACG 61.142 60.000 10.71 0.0 38.60 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1340 1858 2.874010 CTTCTGGCACGCGATCTCGT 62.874 60.000 15.93 4.61 44.35 4.18 R
2805 4256 1.154301 CCGGCGTGCAATGTGTAAC 60.154 57.895 6.01 0.00 37.35 2.50 R
3024 4476 9.142014 TGGAAAACAGAGAGAAATTTGGAATAA 57.858 29.630 0.00 0.00 0.00 1.40 R
4537 6210 2.997303 ACGTTTGTTTTTGCCCAAACTC 59.003 40.909 11.93 0.00 45.12 3.01 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
128 129 2.600769 AGTTGGAGGTCGAGCGGT 60.601 61.111 9.28 0.0 0.00 5.68
248 249 3.532155 GGCGAGAGGTGGAGCGAT 61.532 66.667 0.00 0.0 0.00 4.58
260 261 0.759436 GGAGCGATAGGAAGGGGTCA 60.759 60.000 0.00 0.0 0.00 4.02
349 350 6.734918 TGGGCTCCCTTTATCCATTATTAT 57.265 37.500 6.50 0.0 36.94 1.28
360 361 9.635520 CTTTATCCATTATTATACCGACTCGTT 57.364 33.333 0.00 0.0 0.00 3.85
487 489 1.065199 CAAGGCTGCTGAGGTGGATAA 60.065 52.381 0.00 0.0 0.00 1.75
922 1246 4.729227 AACGGAGAGGCAAAAAGAAAAA 57.271 36.364 0.00 0.0 0.00 1.94
1340 1858 1.825474 GAAGATCACGTCCCTGAGGAA 59.175 52.381 0.00 0.0 46.38 3.36
2805 4256 1.142185 CGCAGTGAGTCCTATGCACG 61.142 60.000 10.71 0.0 38.60 5.34
5014 6689 3.438087 CACTTACGGAAACTCTCCTACGA 59.562 47.826 0.00 0.0 42.85 3.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 3.755628 CCTCTTCGTTCGGCCCGA 61.756 66.667 0.00 0.00 0.00 5.14
103 104 0.679505 CGACCTCCAACTCCAACTCA 59.320 55.000 0.00 0.00 0.00 3.41
211 212 4.824515 CGAGCCTCCTCCCGGTCT 62.825 72.222 0.00 0.00 34.49 3.85
248 249 1.084084 CCCCCTTGACCCCTTCCTA 59.916 63.158 0.00 0.00 0.00 2.94
360 361 2.111384 GAAGAGGCCTCCATGTAGACA 58.889 52.381 29.54 0.00 0.00 3.41
446 447 6.375455 CCTTGCTACCTCATCAATTACTGTTT 59.625 38.462 0.00 0.00 0.00 2.83
487 489 4.080695 TCCTATTTCTCTTGACATGCAGCT 60.081 41.667 0.00 0.00 0.00 4.24
1340 1858 2.874010 CTTCTGGCACGCGATCTCGT 62.874 60.000 15.93 4.61 44.35 4.18
2805 4256 1.154301 CCGGCGTGCAATGTGTAAC 60.154 57.895 6.01 0.00 37.35 2.50
3024 4476 9.142014 TGGAAAACAGAGAGAAATTTGGAATAA 57.858 29.630 0.00 0.00 0.00 1.40
4537 6210 2.997303 ACGTTTGTTTTTGCCCAAACTC 59.003 40.909 11.93 0.00 45.12 3.01


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

AutoCloner maintained by Alex Coulton.