Multiple sequence alignment - TraesCS2A01G046600

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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 TraesCS2A01G046600 chr2A 100.000 5797 0 0 1 5797 18180905 18175109 0.000000e+00 10706.0
1 TraesCS2A01G046600 chr2A 99.160 3572 9 7 953 4518 18084586 18081030 0.000000e+00 6410.0
2 TraesCS2A01G046600 chr2A 95.876 1382 37 9 3671 5051 18078785 18077423 0.000000e+00 2218.0
3 TraesCS2A01G046600 chr2A 97.258 693 18 1 5104 5795 551826115 551825423 0.000000e+00 1173.0
4 TraesCS2A01G046600 chr2A 77.876 678 64 40 42 680 18085642 18085012 5.560000e-90 342.0
5 TraesCS2A01G046600 chr2A 91.837 49 3 1 4808 4855 745396870 745396822 3.750000e-07 67.6
6 TraesCS2A01G046600 chrUn 90.138 2535 153 35 2379 4868 24318575 24316093 0.000000e+00 3206.0
7 TraesCS2A01G046600 chrUn 90.110 2538 154 35 2376 4868 24351924 24354409 0.000000e+00 3206.0
8 TraesCS2A01G046600 chrUn 93.885 2077 108 13 263 2327 288302935 288300866 0.000000e+00 3114.0
9 TraesCS2A01G046600 chrUn 93.885 2077 108 13 263 2327 293847752 293845683 0.000000e+00 3114.0
10 TraesCS2A01G046600 chrUn 90.644 2362 143 21 6 2338 24321037 24318725 0.000000e+00 3066.0
11 TraesCS2A01G046600 chrUn 90.644 2362 143 21 6 2338 24349465 24351777 0.000000e+00 3066.0
12 TraesCS2A01G046600 chrUn 88.862 2478 145 45 2695 5103 288300553 288298138 0.000000e+00 2926.0
13 TraesCS2A01G046600 chrUn 88.862 2478 145 45 2695 5103 293845370 293842955 0.000000e+00 2926.0
14 TraesCS2A01G046600 chrUn 97.143 210 6 0 4894 5103 24316108 24315899 7.140000e-94 355.0
15 TraesCS2A01G046600 chrUn 97.143 210 6 0 4894 5103 24354394 24354603 7.140000e-94 355.0
16 TraesCS2A01G046600 chrUn 90.769 195 17 1 2381 2574 288300746 288300552 5.760000e-65 259.0
17 TraesCS2A01G046600 chrUn 90.769 195 17 1 2381 2574 293845563 293845369 5.760000e-65 259.0
18 TraesCS2A01G046600 chrUn 89.565 115 4 4 62 174 288303052 288302944 7.830000e-29 139.0
19 TraesCS2A01G046600 chrUn 86.250 80 2 5 569 644 467114406 467114332 1.730000e-10 78.7
20 TraesCS2A01G046600 chr2B 89.879 1729 105 28 2381 4082 28427162 28425477 0.000000e+00 2159.0
21 TraesCS2A01G046600 chr2B 91.134 1049 45 13 4081 5103 28425394 28424368 0.000000e+00 1378.0
22 TraesCS2A01G046600 chr2B 89.918 972 56 18 4164 5103 28472596 28471635 0.000000e+00 1214.0
23 TraesCS2A01G046600 chr2B 85.574 1123 99 31 1237 2336 28428516 28427434 0.000000e+00 1118.0
24 TraesCS2A01G046600 chr2B 90.967 631 49 5 1712 2338 28480823 28480197 0.000000e+00 843.0
25 TraesCS2A01G046600 chr2B 92.522 575 26 8 3608 4169 28478263 28477693 0.000000e+00 808.0
26 TraesCS2A01G046600 chr2B 90.706 581 43 6 3039 3608 28479882 28479302 0.000000e+00 763.0
27 TraesCS2A01G046600 chr2B 84.557 395 27 15 1225 1603 28481270 28480894 1.540000e-95 361.0
28 TraesCS2A01G046600 chr2B 82.151 437 58 11 136 558 28429706 28429276 1.990000e-94 357.0
29 TraesCS2A01G046600 chr2B 87.889 289 14 9 622 895 84217687 84217969 2.610000e-83 320.0
30 TraesCS2A01G046600 chr2B 93.367 196 8 2 2379 2569 28480075 28479880 9.510000e-73 285.0
31 TraesCS2A01G046600 chr2B 84.227 317 25 14 263 572 84216012 84216310 9.510000e-73 285.0
32 TraesCS2A01G046600 chr2B 88.517 209 18 4 958 1160 28428736 28428528 1.250000e-61 248.0
33 TraesCS2A01G046600 chr2B 85.281 231 17 5 240 463 33563014 33563234 7.560000e-54 222.0
34 TraesCS2A01G046600 chr2B 91.964 112 2 1 20 131 28482229 28482125 3.620000e-32 150.0
35 TraesCS2A01G046600 chr2B 100.000 46 0 0 635 680 28429227 28429182 1.030000e-12 86.1
36 TraesCS2A01G046600 chr7A 97.126 696 18 2 5104 5797 151294345 151293650 0.000000e+00 1173.0
37 TraesCS2A01G046600 chr7A 97.110 692 20 0 5104 5795 649873931 649873240 0.000000e+00 1168.0
38 TraesCS2A01G046600 chr6A 97.122 695 20 0 5101 5795 261963903 261964597 0.000000e+00 1173.0
39 TraesCS2A01G046600 chr6A 96.978 695 21 0 5101 5795 261980153 261980847 0.000000e+00 1168.0
40 TraesCS2A01G046600 chr6A 84.716 229 18 5 242 463 332739840 332740058 4.550000e-51 213.0
41 TraesCS2A01G046600 chr3A 97.254 692 19 0 5104 5795 177825141 177825832 0.000000e+00 1173.0
42 TraesCS2A01G046600 chr1A 97.118 694 20 0 5102 5795 34306113 34306806 0.000000e+00 1171.0
43 TraesCS2A01G046600 chr5A 96.970 693 21 0 5103 5795 659771706 659771014 0.000000e+00 1164.0
44 TraesCS2A01G046600 chr3D 96.974 694 19 2 5104 5795 487382848 487383541 0.000000e+00 1164.0
45 TraesCS2A01G046600 chr3D 95.683 695 28 2 5103 5795 246031028 246030334 0.000000e+00 1116.0
46 TraesCS2A01G046600 chr3D 80.848 731 108 28 5073 5786 441757326 441758041 3.950000e-151 545.0
47 TraesCS2A01G046600 chr7B 82.957 399 35 13 257 644 82209268 82209644 4.330000e-86 329.0
48 TraesCS2A01G046600 chr7B 87.543 289 15 8 622 895 82209667 82209949 1.210000e-81 315.0
49 TraesCS2A01G046600 chr7B 87.543 289 15 9 622 895 627394037 627393755 1.210000e-81 315.0
50 TraesCS2A01G046600 chr7B 82.650 317 30 9 263 572 627395709 627395411 2.070000e-64 257.0
51 TraesCS2A01G046600 chr7B 85.887 248 18 6 249 489 62790933 62791170 1.250000e-61 248.0
52 TraesCS2A01G046600 chr7B 84.810 79 4 5 569 644 627394130 627394057 8.060000e-09 73.1
53 TraesCS2A01G046600 chr4B 88.235 289 13 9 622 895 650567700 650567982 5.600000e-85 326.0
54 TraesCS2A01G046600 chr5B 87.889 289 14 9 622 895 698088196 698088478 2.610000e-83 320.0
55 TraesCS2A01G046600 chr5B 83.596 317 27 9 263 572 698079042 698079340 2.060000e-69 274.0
56 TraesCS2A01G046600 chr2D 86.122 245 18 4 240 477 462618040 462618275 3.470000e-62 250.0
57 TraesCS2A01G046600 chr1B 82.075 318 30 10 263 572 31300535 31300833 4.490000e-61 246.0
58 TraesCS2A01G046600 chr1B 85.714 77 4 4 571 644 31302117 31302189 2.240000e-09 75.0
59 TraesCS2A01G046600 chr5D 86.857 175 11 2 240 414 507902839 507902677 9.920000e-43 185.0
60 TraesCS2A01G046600 chr7D 95.455 44 2 0 4804 4847 605179141 605179184 2.900000e-08 71.3


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 TraesCS2A01G046600 chr2A 18175109 18180905 5796 True 10706.000000 10706 100.000000 1 5797 1 chr2A.!!$R1 5796
1 TraesCS2A01G046600 chr2A 18077423 18085642 8219 True 2990.000000 6410 90.970667 42 5051 3 chr2A.!!$R4 5009
2 TraesCS2A01G046600 chr2A 551825423 551826115 692 True 1173.000000 1173 97.258000 5104 5795 1 chr2A.!!$R2 691
3 TraesCS2A01G046600 chrUn 24315899 24321037 5138 True 2209.000000 3206 92.641667 6 5103 3 chrUn.!!$R2 5097
4 TraesCS2A01G046600 chrUn 24349465 24354603 5138 False 2209.000000 3206 92.632333 6 5103 3 chrUn.!!$F1 5097
5 TraesCS2A01G046600 chrUn 293842955 293847752 4797 True 2099.666667 3114 91.172000 263 5103 3 chrUn.!!$R4 4840
6 TraesCS2A01G046600 chrUn 288298138 288303052 4914 True 1609.500000 3114 90.770250 62 5103 4 chrUn.!!$R3 5041
7 TraesCS2A01G046600 chr2B 28471635 28472596 961 True 1214.000000 1214 89.918000 4164 5103 1 chr2B.!!$R1 939
8 TraesCS2A01G046600 chr2B 28424368 28429706 5338 True 891.016667 2159 89.542500 136 5103 6 chr2B.!!$R2 4967
9 TraesCS2A01G046600 chr2B 28477693 28482229 4536 True 535.000000 843 90.680500 20 4169 6 chr2B.!!$R3 4149
10 TraesCS2A01G046600 chr2B 84216012 84217969 1957 False 302.500000 320 86.058000 263 895 2 chr2B.!!$F2 632
11 TraesCS2A01G046600 chr7A 151293650 151294345 695 True 1173.000000 1173 97.126000 5104 5797 1 chr7A.!!$R1 693
12 TraesCS2A01G046600 chr7A 649873240 649873931 691 True 1168.000000 1168 97.110000 5104 5795 1 chr7A.!!$R2 691
13 TraesCS2A01G046600 chr6A 261963903 261964597 694 False 1173.000000 1173 97.122000 5101 5795 1 chr6A.!!$F1 694
14 TraesCS2A01G046600 chr6A 261980153 261980847 694 False 1168.000000 1168 96.978000 5101 5795 1 chr6A.!!$F2 694
15 TraesCS2A01G046600 chr3A 177825141 177825832 691 False 1173.000000 1173 97.254000 5104 5795 1 chr3A.!!$F1 691
16 TraesCS2A01G046600 chr1A 34306113 34306806 693 False 1171.000000 1171 97.118000 5102 5795 1 chr1A.!!$F1 693
17 TraesCS2A01G046600 chr5A 659771014 659771706 692 True 1164.000000 1164 96.970000 5103 5795 1 chr5A.!!$R1 692
18 TraesCS2A01G046600 chr3D 487382848 487383541 693 False 1164.000000 1164 96.974000 5104 5795 1 chr3D.!!$F2 691
19 TraesCS2A01G046600 chr3D 246030334 246031028 694 True 1116.000000 1116 95.683000 5103 5795 1 chr3D.!!$R1 692
20 TraesCS2A01G046600 chr3D 441757326 441758041 715 False 545.000000 545 80.848000 5073 5786 1 chr3D.!!$F1 713
21 TraesCS2A01G046600 chr7B 82209268 82209949 681 False 322.000000 329 85.250000 257 895 2 chr7B.!!$F2 638
22 TraesCS2A01G046600 chr7B 627393755 627395709 1954 True 215.033333 315 85.001000 263 895 3 chr7B.!!$R1 632

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
42 43 0.393077 ACTGACTAGCGGTTGTGCTT 59.607 50.0 6.40 0.0 44.46 3.91 F
483 527 0.463295 TACTCCTCTGGTACGCCTCG 60.463 60.0 0.00 0.0 35.27 4.63 F
530 588 0.738975 CCATGCTCTGATTGCCACTG 59.261 55.0 0.00 0.0 0.00 3.66 F
631 2029 1.896220 TGTGCCCAAGTCTGTTCATC 58.104 50.0 0.00 0.0 0.00 2.92 F
4518 11246 0.031716 TCCTGCTGTGGAGCTCCTAT 60.032 55.0 32.28 0.0 46.39 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1248 2889 2.400467 AGGACAGTTGTCTACCCAGT 57.600 50.000 11.67 0.00 44.20 4.00 R
3668 7167 9.642343 TTCATGTCATGGATAGTTAGTAGTACT 57.358 33.333 12.90 8.14 0.00 2.73 R
4518 11246 7.987750 TTCTGTGCTACAAATGTATTTACCA 57.012 32.000 0.00 0.00 0.00 3.25 R
4573 11301 4.687901 TCAACAGAACTTCTGGTCATCA 57.312 40.909 20.58 0.00 41.32 3.07 R
5569 12337 3.981071 ATGACAAATCCCAGTCTCGAA 57.019 42.857 0.00 0.00 35.81 3.71 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
42 43 0.393077 ACTGACTAGCGGTTGTGCTT 59.607 50.000 6.40 0.0 44.46 3.91
43 44 0.792640 CTGACTAGCGGTTGTGCTTG 59.207 55.000 6.40 0.0 44.46 4.01
46 47 2.080286 ACTAGCGGTTGTGCTTGTAG 57.920 50.000 0.00 0.0 46.49 2.74
47 48 1.337823 ACTAGCGGTTGTGCTTGTAGG 60.338 52.381 0.00 0.0 46.49 3.18
60 61 3.181479 TGCTTGTAGGTTGTAGCGATAGG 60.181 47.826 0.00 0.0 36.43 2.57
483 527 0.463295 TACTCCTCTGGTACGCCTCG 60.463 60.000 0.00 0.0 35.27 4.63
490 545 2.256461 GGTACGCCTCGTGTTCGT 59.744 61.111 1.77 7.1 41.39 3.85
491 546 2.084681 GGTACGCCTCGTGTTCGTG 61.085 63.158 10.78 0.0 41.39 4.35
492 547 2.429571 TACGCCTCGTGTTCGTGC 60.430 61.111 10.78 0.0 41.39 5.34
493 548 3.902162 TACGCCTCGTGTTCGTGCC 62.902 63.158 10.78 0.0 41.39 5.01
530 588 0.738975 CCATGCTCTGATTGCCACTG 59.261 55.000 0.00 0.0 0.00 3.66
631 2029 1.896220 TGTGCCCAAGTCTGTTCATC 58.104 50.000 0.00 0.0 0.00 2.92
830 2272 4.100963 ACCACCTGATTATGCGAATCTACA 59.899 41.667 11.26 0.0 0.00 2.74
931 2531 8.347771 GTGAGTTATCCTTTTCTTTTAAACGGT 58.652 33.333 0.00 0.0 0.00 4.83
1248 2889 4.203226 TGTGTGACAGTGCTTCCATTTAA 58.797 39.130 0.00 0.0 0.00 1.52
1249 2890 4.036262 TGTGTGACAGTGCTTCCATTTAAC 59.964 41.667 0.00 0.0 0.00 2.01
1251 2892 4.275689 TGTGACAGTGCTTCCATTTAACTG 59.724 41.667 0.00 0.0 43.07 3.16
3667 7166 2.627699 CCATGTGTTACTTTTGGGCACT 59.372 45.455 0.00 0.0 0.00 4.40
3668 7167 3.823873 CCATGTGTTACTTTTGGGCACTA 59.176 43.478 0.00 0.0 0.00 2.74
3669 7168 4.082787 CCATGTGTTACTTTTGGGCACTAG 60.083 45.833 0.00 0.0 0.00 2.57
4518 11246 0.031716 TCCTGCTGTGGAGCTCCTAT 60.032 55.000 32.28 0.0 46.39 2.57
4538 11266 8.671384 TCCTATGGTAAATACATTTGTAGCAC 57.329 34.615 0.00 0.0 33.52 4.40
4573 11301 6.671779 ACCTTCTGATCAAGAGAATAGTTCCT 59.328 38.462 0.00 0.0 35.91 3.36
4575 11303 7.147759 CCTTCTGATCAAGAGAATAGTTCCTGA 60.148 40.741 0.00 0.0 35.91 3.86
4588 11317 4.278975 AGTTCCTGATGACCAGAAGTTC 57.721 45.455 0.00 0.0 45.78 3.01
4625 11354 5.934625 TGTTTTGTTTTGCTTGTACACCATT 59.065 32.000 0.00 0.0 0.00 3.16
4801 11530 6.293244 GGAATTAACCGAGCTGCGTAAATTAT 60.293 38.462 0.00 0.0 38.67 1.28
4829 11558 7.690256 ACTTCCTCTGTTCCATAATTACTGTT 58.310 34.615 0.00 0.0 0.00 3.16
4885 11638 8.504815 CATGGTTTCAATTCAAATTATGCAACA 58.495 29.630 0.00 0.0 0.00 3.33
5017 11770 8.504005 ACGATTGACAAATAACCTACAAAGAAG 58.496 33.333 0.00 0.0 0.00 2.85
5070 11830 9.125026 CTCTACTTGTATCCCAATAAATTTGCT 57.875 33.333 0.00 0.0 31.20 3.91
5123 11883 5.388654 CCTTGTTGGAAATATGCCCTAGAT 58.611 41.667 0.00 0.0 38.35 1.98
5260 12022 4.447908 CCATGTCCCTAGTAAGCCTCTAGA 60.448 50.000 8.41 0.0 37.62 2.43
5264 12026 5.075205 TGTCCCTAGTAAGCCTCTAGATGAT 59.925 44.000 0.00 0.0 37.62 2.45
5455 12222 8.868522 TCATTTCTTTAGACCATGAGATTGTT 57.131 30.769 0.00 0.0 0.00 2.83
5569 12337 0.387565 GTTTGTTGGGTTGGCACGAT 59.612 50.000 0.00 0.0 0.00 3.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.299297 GCTAGTCAGTACCCGCCAATAT 59.701 50.000 0.00 0.00 0.00 1.28
14 15 1.895238 GCTAGTCAGTACCCGCCAA 59.105 57.895 0.00 0.00 0.00 4.52
18 19 0.179145 CAACCGCTAGTCAGTACCCG 60.179 60.000 0.00 0.00 0.00 5.28
41 42 4.280174 GGATCCTATCGCTACAACCTACAA 59.720 45.833 3.84 0.00 0.00 2.41
42 43 3.825014 GGATCCTATCGCTACAACCTACA 59.175 47.826 3.84 0.00 0.00 2.74
43 44 3.119919 CGGATCCTATCGCTACAACCTAC 60.120 52.174 10.75 0.00 0.00 3.18
44 45 3.079578 CGGATCCTATCGCTACAACCTA 58.920 50.000 10.75 0.00 0.00 3.08
45 46 1.887198 CGGATCCTATCGCTACAACCT 59.113 52.381 10.75 0.00 0.00 3.50
46 47 1.612463 ACGGATCCTATCGCTACAACC 59.388 52.381 10.75 0.00 0.00 3.77
47 48 2.553172 AGACGGATCCTATCGCTACAAC 59.447 50.000 10.75 0.00 0.00 3.32
60 61 1.320344 GGGGCCCAAAAAGACGGATC 61.320 60.000 26.86 0.00 0.00 3.36
180 183 0.900647 ACTAGCAGGTGAGGTCGCTT 60.901 55.000 0.00 0.00 35.93 4.68
510 565 0.330604 AGTGGCAATCAGAGCATGGT 59.669 50.000 0.00 0.00 0.00 3.55
530 588 1.376037 AGCTAGTTGGGCGCAGTTC 60.376 57.895 10.83 0.00 34.52 3.01
631 2029 3.074412 CCACCACAGTAAGCAACTAAGG 58.926 50.000 7.27 7.27 35.76 2.69
830 2272 2.766313 TCTGAACAACTTGCGCTATGT 58.234 42.857 9.73 5.51 0.00 2.29
967 2588 4.623886 CGGGGTTCTCTTCTGAAATGATCA 60.624 45.833 0.00 0.00 36.38 2.92
1248 2889 2.400467 AGGACAGTTGTCTACCCAGT 57.600 50.000 11.67 0.00 44.20 4.00
1249 2890 3.193691 CAGTAGGACAGTTGTCTACCCAG 59.806 52.174 11.67 3.61 44.20 4.45
1251 2892 3.163467 ACAGTAGGACAGTTGTCTACCC 58.837 50.000 11.67 0.00 44.20 3.69
3668 7167 9.642343 TTCATGTCATGGATAGTTAGTAGTACT 57.358 33.333 12.90 8.14 0.00 2.73
4518 11246 7.987750 TTCTGTGCTACAAATGTATTTACCA 57.012 32.000 0.00 0.00 0.00 3.25
4561 11289 5.860941 TCTGGTCATCAGGAACTATTCTC 57.139 43.478 0.00 0.00 43.53 2.87
4573 11301 4.687901 TCAACAGAACTTCTGGTCATCA 57.312 40.909 20.58 0.00 41.32 3.07
4575 11303 4.978099 ACATCAACAGAACTTCTGGTCAT 58.022 39.130 20.58 5.59 41.32 3.06
4588 11317 7.590689 AGCAAAACAAAACAAAAACATCAACAG 59.409 29.630 0.00 0.00 0.00 3.16
4625 11354 7.931578 AAATGTACCTGAAATTAATCCGTCA 57.068 32.000 0.00 0.00 0.00 4.35
4860 11589 8.618702 TGTTGCATAATTTGAATTGAAACCAT 57.381 26.923 0.00 0.00 0.00 3.55
4867 11596 6.632909 TCCCTCTGTTGCATAATTTGAATTG 58.367 36.000 0.00 0.00 0.00 2.32
4885 11638 1.207791 CCAAGCCATGTACTCCCTCT 58.792 55.000 0.00 0.00 0.00 3.69
5030 11783 2.915869 AGTAGAGATCAAACCACCCCA 58.084 47.619 0.00 0.00 0.00 4.96
5070 11830 0.826715 AGCCTTATCAAGCTCGCTCA 59.173 50.000 0.00 0.00 32.71 4.26
5260 12022 7.548427 CCATCTATTGATCAACGAGCTAATCAT 59.452 37.037 11.07 0.00 0.00 2.45
5264 12026 6.161855 ACCATCTATTGATCAACGAGCTAA 57.838 37.500 11.07 0.00 0.00 3.09
5437 12204 6.655003 GGAGTTGAACAATCTCATGGTCTAAA 59.345 38.462 0.00 0.00 37.90 1.85
5569 12337 3.981071 ATGACAAATCCCAGTCTCGAA 57.019 42.857 0.00 0.00 35.81 3.71


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

AutoCloner maintained by Alex Coulton.