Multiple sequence alignment - TraesCS2A01G167700

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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 TraesCS2A01G167700 chr2A 100.000 4182 0 0 1 4182 120735920 120740101 0.000000e+00 7723.0
1 TraesCS2A01G167700 chr2A 97.521 2178 32 4 616 2792 120752432 120754588 0.000000e+00 3703.0
2 TraesCS2A01G167700 chr2A 98.124 2026 28 4 350 2368 120720568 120722590 0.000000e+00 3522.0
3 TraesCS2A01G167700 chr2A 99.286 1820 10 2 2364 4182 120724549 120726366 0.000000e+00 3286.0
4 TraesCS2A01G167700 chr2A 90.119 1174 76 16 1625 2772 90069166 90068007 0.000000e+00 1489.0
5 TraesCS2A01G167700 chr2A 98.337 842 12 2 3342 4182 120754588 120755428 0.000000e+00 1476.0
6 TraesCS2A01G167700 chr2A 88.469 980 84 13 1817 2771 90218617 90217642 0.000000e+00 1157.0
7 TraesCS2A01G167700 chr2A 96.785 622 16 4 1 618 120749916 120750537 0.000000e+00 1035.0
8 TraesCS2A01G167700 chr2A 98.095 525 10 0 3658 4182 151901168 151901692 0.000000e+00 915.0
9 TraesCS2A01G167700 chr2D 91.701 1928 89 23 1286 3182 118844798 118846685 0.000000e+00 2608.0
10 TraesCS2A01G167700 chr2D 90.129 1084 72 15 1714 2774 90322045 90320974 0.000000e+00 1376.0
11 TraesCS2A01G167700 chr2D 86.243 189 11 4 2935 3119 90312409 90312232 1.530000e-44 191.0
12 TraesCS2A01G167700 chr2D 84.677 124 15 4 3536 3657 335862084 335861963 2.040000e-23 121.0
13 TraesCS2A01G167700 chr2D 88.406 69 8 0 1625 1693 90322114 90322046 2.680000e-12 84.2
14 TraesCS2A01G167700 chr2B 90.741 1512 69 31 1490 2980 170937577 170939038 0.000000e+00 1951.0
15 TraesCS2A01G167700 chr2B 90.218 1145 72 21 1625 2745 143000910 142999782 0.000000e+00 1458.0
16 TraesCS2A01G167700 chr2B 89.517 973 77 7 1817 2766 143133239 143132269 0.000000e+00 1208.0
17 TraesCS2A01G167700 chr2B 92.542 295 19 3 3365 3658 170950393 170950685 1.800000e-113 420.0
18 TraesCS2A01G167700 chr2B 90.608 181 17 0 1318 1498 170936990 170937170 1.500000e-59 241.0
19 TraesCS2A01G167700 chr2B 86.082 194 15 1 2983 3176 170950168 170950349 9.170000e-47 198.0
20 TraesCS2A01G167700 chr2B 93.814 97 6 0 2569 2665 793503986 793504082 3.370000e-31 147.0
21 TraesCS2A01G167700 chr2B 84.034 119 17 2 3540 3658 413088691 413088807 3.420000e-21 113.0
22 TraesCS2A01G167700 chr2B 82.759 116 16 4 3547 3660 265966823 265966936 2.660000e-17 100.0
23 TraesCS2A01G167700 chr2B 80.734 109 19 2 3553 3660 356741976 356742083 2.680000e-12 84.2
24 TraesCS2A01G167700 chr1B 90.222 900 64 16 350 1233 590997252 590996361 0.000000e+00 1153.0
25 TraesCS2A01G167700 chr1B 86.364 110 15 0 3549 3658 217192936 217193045 2.040000e-23 121.0
26 TraesCS2A01G167700 chr4A 88.791 910 78 13 350 1237 594705388 594706295 0.000000e+00 1094.0
27 TraesCS2A01G167700 chr4A 98.476 525 7 1 3658 4182 554973883 554974406 0.000000e+00 924.0
28 TraesCS2A01G167700 chr3D 88.255 894 95 2 1896 2779 442397504 442398397 0.000000e+00 1061.0
29 TraesCS2A01G167700 chr3D 85.500 400 21 8 1625 2001 442397128 442397513 2.360000e-102 383.0
30 TraesCS2A01G167700 chr5A 89.618 838 56 17 350 1167 454707474 454706648 0.000000e+00 1037.0
31 TraesCS2A01G167700 chr5A 98.289 526 8 1 3658 4182 71766301 71766826 0.000000e+00 920.0
32 TraesCS2A01G167700 chr6D 85.967 905 96 19 350 1235 32383371 32382479 0.000000e+00 939.0
33 TraesCS2A01G167700 chr6D 84.012 344 41 10 3185 3518 82667854 82668193 6.750000e-83 318.0
34 TraesCS2A01G167700 chr6D 85.593 118 15 2 3541 3657 71739081 71739197 5.680000e-24 122.0
35 TraesCS2A01G167700 chr6D 90.909 55 3 2 1486 1538 10517145 10517199 5.800000e-09 73.1
36 TraesCS2A01G167700 chr7D 85.636 912 97 24 350 1233 174122690 174123595 0.000000e+00 928.0
37 TraesCS2A01G167700 chr7D 83.333 360 39 11 3178 3518 511668468 511668825 3.140000e-81 313.0
38 TraesCS2A01G167700 chr7D 90.110 91 8 1 3571 3660 265954035 265954125 2.640000e-22 117.0
39 TraesCS2A01G167700 chr7D 84.404 109 16 1 3553 3660 349906846 349906954 5.720000e-19 106.0
40 TraesCS2A01G167700 chr5D 85.730 911 93 26 350 1235 510168014 510168912 0.000000e+00 928.0
41 TraesCS2A01G167700 chr1A 98.476 525 6 2 3658 4182 528708822 528708300 0.000000e+00 924.0
42 TraesCS2A01G167700 chr1A 98.286 525 8 1 3658 4182 163051548 163052071 0.000000e+00 918.0
43 TraesCS2A01G167700 chr1A 98.095 525 10 0 3658 4182 135049351 135049875 0.000000e+00 915.0
44 TraesCS2A01G167700 chr1A 97.734 353 5 3 1 350 150577578 150577930 4.620000e-169 604.0
45 TraesCS2A01G167700 chr1A 97.472 356 6 3 1 353 316004182 316003827 4.620000e-169 604.0
46 TraesCS2A01G167700 chr1A 97.450 353 6 3 1 350 140927599 140927951 2.150000e-167 599.0
47 TraesCS2A01G167700 chr1A 97.450 353 6 3 1 350 412390011 412390363 2.150000e-167 599.0
48 TraesCS2A01G167700 chr1A 97.191 356 7 3 1 353 510775698 510775343 2.150000e-167 599.0
49 TraesCS2A01G167700 chr1A 97.450 353 6 3 1 350 517262550 517262902 2.150000e-167 599.0
50 TraesCS2A01G167700 chr1A 83.333 324 36 8 3223 3530 529324077 529323756 2.460000e-72 283.0
51 TraesCS2A01G167700 chr6A 85.385 910 102 21 350 1240 607820586 607821483 0.000000e+00 915.0
52 TraesCS2A01G167700 chr6A 97.191 356 7 3 1 353 389364457 389364102 2.150000e-167 599.0
53 TraesCS2A01G167700 chr3A 98.095 525 10 0 3658 4182 624221221 624220697 0.000000e+00 915.0
54 TraesCS2A01G167700 chr3A 97.472 356 6 3 1 353 104051701 104051346 4.620000e-169 604.0
55 TraesCS2A01G167700 chr3A 86.799 303 29 5 3225 3518 607224658 607224358 1.120000e-85 327.0
56 TraesCS2A01G167700 chr3A 86.667 105 8 1 1625 1729 583702784 583702882 1.230000e-20 111.0
57 TraesCS2A01G167700 chr4D 85.799 338 35 9 3185 3518 477585972 477586300 3.090000e-91 346.0
58 TraesCS2A01G167700 chr4D 92.500 160 10 2 2477 2635 374604693 374604535 1.170000e-55 228.0
59 TraesCS2A01G167700 chr4D 79.832 119 17 6 3547 3660 198296362 198296246 3.470000e-11 80.5
60 TraesCS2A01G167700 chr3B 86.913 298 30 5 3227 3518 49874097 49873803 4.030000e-85 326.0
61 TraesCS2A01G167700 chr3B 85.981 107 15 0 3553 3659 165280601 165280707 9.500000e-22 115.0
62 TraesCS2A01G167700 chrUn 84.437 302 35 6 3225 3518 38423793 38423496 1.900000e-73 287.0
63 TraesCS2A01G167700 chr1D 84.643 280 33 5 3185 3455 313862223 313861945 1.920000e-68 270.0
64 TraesCS2A01G167700 chr7B 85.841 113 13 3 3548 3658 493838509 493838398 2.640000e-22 117.0
65 TraesCS2A01G167700 chr7B 85.455 110 16 0 3549 3658 437142748 437142639 9.500000e-22 115.0
66 TraesCS2A01G167700 chr6B 81.579 114 12 4 3553 3659 228453069 228453180 7.450000e-13 86.1


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 TraesCS2A01G167700 chr2A 120735920 120740101 4181 False 7723.000000 7723 100.000000 1 4182 1 chr2A.!!$F1 4181
1 TraesCS2A01G167700 chr2A 120720568 120726366 5798 False 3404.000000 3522 98.705000 350 4182 2 chr2A.!!$F3 3832
2 TraesCS2A01G167700 chr2A 120749916 120755428 5512 False 2071.333333 3703 97.547667 1 4182 3 chr2A.!!$F4 4181
3 TraesCS2A01G167700 chr2A 90068007 90069166 1159 True 1489.000000 1489 90.119000 1625 2772 1 chr2A.!!$R1 1147
4 TraesCS2A01G167700 chr2A 90217642 90218617 975 True 1157.000000 1157 88.469000 1817 2771 1 chr2A.!!$R2 954
5 TraesCS2A01G167700 chr2A 151901168 151901692 524 False 915.000000 915 98.095000 3658 4182 1 chr2A.!!$F2 524
6 TraesCS2A01G167700 chr2D 118844798 118846685 1887 False 2608.000000 2608 91.701000 1286 3182 1 chr2D.!!$F1 1896
7 TraesCS2A01G167700 chr2D 90320974 90322114 1140 True 730.100000 1376 89.267500 1625 2774 2 chr2D.!!$R3 1149
8 TraesCS2A01G167700 chr2B 142999782 143000910 1128 True 1458.000000 1458 90.218000 1625 2745 1 chr2B.!!$R1 1120
9 TraesCS2A01G167700 chr2B 143132269 143133239 970 True 1208.000000 1208 89.517000 1817 2766 1 chr2B.!!$R2 949
10 TraesCS2A01G167700 chr2B 170936990 170939038 2048 False 1096.000000 1951 90.674500 1318 2980 2 chr2B.!!$F5 1662
11 TraesCS2A01G167700 chr2B 170950168 170950685 517 False 309.000000 420 89.312000 2983 3658 2 chr2B.!!$F6 675
12 TraesCS2A01G167700 chr1B 590996361 590997252 891 True 1153.000000 1153 90.222000 350 1233 1 chr1B.!!$R1 883
13 TraesCS2A01G167700 chr4A 594705388 594706295 907 False 1094.000000 1094 88.791000 350 1237 1 chr4A.!!$F2 887
14 TraesCS2A01G167700 chr4A 554973883 554974406 523 False 924.000000 924 98.476000 3658 4182 1 chr4A.!!$F1 524
15 TraesCS2A01G167700 chr3D 442397128 442398397 1269 False 722.000000 1061 86.877500 1625 2779 2 chr3D.!!$F1 1154
16 TraesCS2A01G167700 chr5A 454706648 454707474 826 True 1037.000000 1037 89.618000 350 1167 1 chr5A.!!$R1 817
17 TraesCS2A01G167700 chr5A 71766301 71766826 525 False 920.000000 920 98.289000 3658 4182 1 chr5A.!!$F1 524
18 TraesCS2A01G167700 chr6D 32382479 32383371 892 True 939.000000 939 85.967000 350 1235 1 chr6D.!!$R1 885
19 TraesCS2A01G167700 chr7D 174122690 174123595 905 False 928.000000 928 85.636000 350 1233 1 chr7D.!!$F1 883
20 TraesCS2A01G167700 chr5D 510168014 510168912 898 False 928.000000 928 85.730000 350 1235 1 chr5D.!!$F1 885
21 TraesCS2A01G167700 chr1A 528708300 528708822 522 True 924.000000 924 98.476000 3658 4182 1 chr1A.!!$R3 524
22 TraesCS2A01G167700 chr1A 163051548 163052071 523 False 918.000000 918 98.286000 3658 4182 1 chr1A.!!$F4 524
23 TraesCS2A01G167700 chr1A 135049351 135049875 524 False 915.000000 915 98.095000 3658 4182 1 chr1A.!!$F1 524
24 TraesCS2A01G167700 chr6A 607820586 607821483 897 False 915.000000 915 85.385000 350 1240 1 chr6A.!!$F1 890
25 TraesCS2A01G167700 chr3A 624220697 624221221 524 True 915.000000 915 98.095000 3658 4182 1 chr3A.!!$R3 524

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
298 303 1.003118 AGTCTTGCAGGCGGACAATAA 59.997 47.619 15.68 0.0 32.98 1.40 F
348 353 2.290641 TGGTCTTATGAACATGGCGGTT 60.291 45.455 0.00 0.0 34.53 4.44 F
1487 3436 1.413118 AGCCCTTGTTGGTTTTCCTG 58.587 50.000 0.00 0.0 41.38 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1487 3436 4.357279 AGGGGAGGCTTGCTGCAC 62.357 66.667 0.0 0.0 45.15 4.57 R
2820 7323 1.812571 CTGGAGTGGTACATTGTTGCC 59.187 52.381 0.0 0.0 44.52 4.52 R
3281 7796 2.517650 TTTTTGCCACGCCTTTTAGG 57.482 45.000 0.0 0.0 38.80 2.69 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
23 24 5.684704 TGGGTTATGAAAGCTTAGATCCAG 58.315 41.667 0.00 0.00 33.51 3.86
47 48 9.589461 CAGATTAGGACTAATAGGGAGAGTAAA 57.411 37.037 4.66 0.00 36.02 2.01
50 51 6.734502 AGGACTAATAGGGAGAGTAAAAGC 57.265 41.667 0.00 0.00 0.00 3.51
51 52 5.302313 AGGACTAATAGGGAGAGTAAAAGCG 59.698 44.000 0.00 0.00 0.00 4.68
52 53 5.301298 GGACTAATAGGGAGAGTAAAAGCGA 59.699 44.000 0.00 0.00 0.00 4.93
53 54 6.015265 GGACTAATAGGGAGAGTAAAAGCGAT 60.015 42.308 0.00 0.00 0.00 4.58
145 148 1.791555 GCAATGGCGTCAGACGATTTG 60.792 52.381 27.29 22.86 46.05 2.32
153 158 3.799035 CGTCAGACGATTTGGTTTTCTG 58.201 45.455 18.63 0.00 46.05 3.02
246 251 4.946157 AGCAATAAGTCTAAGTGCAGCATT 59.054 37.500 0.00 0.00 37.68 3.56
264 269 4.758165 AGCATTTGAGAATTTTGGCTTTGG 59.242 37.500 0.00 0.00 0.00 3.28
298 303 1.003118 AGTCTTGCAGGCGGACAATAA 59.997 47.619 15.68 0.00 32.98 1.40
348 353 2.290641 TGGTCTTATGAACATGGCGGTT 60.291 45.455 0.00 0.00 34.53 4.44
415 427 7.032598 AGGGAAGTTTCCTGATAAGAAATGA 57.967 36.000 0.32 0.00 46.72 2.57
1487 3436 1.413118 AGCCCTTGTTGGTTTTCCTG 58.587 50.000 0.00 0.00 41.38 3.86
1649 4016 3.126858 GCATCATTCGTAGCCAGTTTCAA 59.873 43.478 0.00 0.00 0.00 2.69
3281 7796 7.617935 GCAAAAGTTCATCACGAAATCACATTC 60.618 37.037 0.00 0.00 34.69 2.67
4005 8524 6.183360 CCAGTAACTCGTTGAAGACAATGATC 60.183 42.308 0.00 0.00 46.51 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 2.457366 ACTTCGTTCCTGAATCGCTT 57.543 45.000 0.00 0.00 0.00 4.68
49 50 2.602878 TGTACTTCGTTCCTGAATCGC 58.397 47.619 0.00 0.00 0.00 4.58
50 51 5.579718 ACTATGTACTTCGTTCCTGAATCG 58.420 41.667 0.00 0.00 0.00 3.34
51 52 8.404000 TCTTACTATGTACTTCGTTCCTGAATC 58.596 37.037 0.00 0.00 0.00 2.52
52 53 8.189460 GTCTTACTATGTACTTCGTTCCTGAAT 58.811 37.037 0.00 0.00 0.00 2.57
53 54 7.362401 GGTCTTACTATGTACTTCGTTCCTGAA 60.362 40.741 0.00 0.00 0.00 3.02
145 148 2.278332 AAGGTCTCCAGCAGAAAACC 57.722 50.000 0.00 0.00 30.72 3.27
153 158 1.377856 GCAGGGAAAGGTCTCCAGC 60.378 63.158 0.00 0.00 37.20 4.85
246 251 3.993920 GCTCCAAAGCCAAAATTCTCAA 58.006 40.909 0.00 0.00 43.10 3.02
264 269 2.079925 CAAGACTGTTTGCTAGGGCTC 58.920 52.381 0.00 0.00 39.59 4.70
313 318 6.042777 TCATAAGACCAAGAACTATTCTGCG 58.957 40.000 0.00 0.00 40.59 5.18
801 2735 5.386958 AGTGTAATGTAAGAGCGAAGTCA 57.613 39.130 0.00 0.00 0.00 3.41
890 2824 5.235850 TGTTGGGTGAGTGTAATGTACAT 57.764 39.130 1.41 1.41 41.34 2.29
1487 3436 4.357279 AGGGGAGGCTTGCTGCAC 62.357 66.667 0.00 0.00 45.15 4.57
2820 7323 1.812571 CTGGAGTGGTACATTGTTGCC 59.187 52.381 0.00 0.00 44.52 4.52
3281 7796 2.517650 TTTTTGCCACGCCTTTTAGG 57.482 45.000 0.00 0.00 38.80 2.69


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

AutoCloner maintained by Alex Coulton.