Multiple sequence alignment - TraesCS5A01G505900

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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 TraesCS5A01G505900 chr5A 100.000 3218 0 0 1 3218 671174109 671177326 0.000000e+00 5943.0
1 TraesCS5A01G505900 chr5A 90.668 793 50 10 2439 3218 671182550 671183331 0.000000e+00 1033.0
2 TraesCS5A01G505900 chr5A 97.872 47 1 0 2418 2464 671182494 671182540 7.400000e-12 82.4
3 TraesCS5A01G505900 chr4D 93.579 1573 66 13 873 2411 489726206 489727777 0.000000e+00 2313.0
4 TraesCS5A01G505900 chr4D 91.269 1489 112 8 873 2351 122267135 122265655 0.000000e+00 2013.0
5 TraesCS5A01G505900 chr4D 84.403 1449 208 11 874 2314 122270711 122269273 0.000000e+00 1408.0
6 TraesCS5A01G505900 chr4D 94.543 788 30 6 2439 3218 489727882 489728664 0.000000e+00 1205.0
7 TraesCS5A01G505900 chr4D 91.173 793 45 9 2439 3218 489733159 489733939 0.000000e+00 1053.0
8 TraesCS5A01G505900 chr4D 92.982 171 10 1 2798 2968 122257220 122257052 6.890000e-62 248.0
9 TraesCS5A01G505900 chr4D 83.774 265 26 9 2966 3218 122256891 122256632 5.370000e-58 235.0
10 TraesCS5A01G505900 chr4D 91.558 154 8 2 2631 2784 122257605 122257457 1.170000e-49 207.0
11 TraesCS5A01G505900 chr4D 97.872 47 1 0 2418 2464 489733103 489733149 7.400000e-12 82.4
12 TraesCS5A01G505900 chr4D 100.000 39 0 0 2411 2449 122265546 122265508 4.450000e-09 73.1
13 TraesCS5A01G505900 chr4A 91.498 1482 117 3 873 2345 448100326 448101807 0.000000e+00 2030.0
14 TraesCS5A01G505900 chr4A 96.347 876 25 5 1 872 257020721 257019849 0.000000e+00 1434.0
15 TraesCS5A01G505900 chr4A 84.091 1452 207 15 874 2314 448096563 448098001 0.000000e+00 1380.0
16 TraesCS5A01G505900 chr4A 97.517 725 9 5 155 872 278350579 278349857 0.000000e+00 1230.0
17 TraesCS5A01G505900 chr4A 90.275 874 80 4 1 872 321127338 321128208 0.000000e+00 1138.0
18 TraesCS5A01G505900 chr4A 84.211 266 27 7 2966 3218 448105934 448106197 8.920000e-61 244.0
19 TraesCS5A01G505900 chr4A 92.398 171 11 1 2798 2968 448105663 448105831 3.210000e-60 243.0
20 TraesCS5A01G505900 chr4A 100.000 39 0 0 2411 2449 448101935 448101973 4.450000e-09 73.1
21 TraesCS5A01G505900 chr4B 91.336 1489 118 5 873 2351 185873772 185872285 0.000000e+00 2025.0
22 TraesCS5A01G505900 chr4B 92.705 1220 46 14 1283 2464 628066579 628067793 0.000000e+00 1720.0
23 TraesCS5A01G505900 chr4B 84.338 1443 204 14 882 2314 185906625 185905195 0.000000e+00 1393.0
24 TraesCS5A01G505900 chr4B 92.135 534 26 9 2613 3139 628068092 628068616 0.000000e+00 739.0
25 TraesCS5A01G505900 chr4B 94.415 376 19 1 873 1248 628066209 628066582 7.740000e-161 577.0
26 TraesCS5A01G505900 chr4B 87.067 433 37 10 2798 3218 185867286 185866861 3.760000e-129 472.0
27 TraesCS5A01G505900 chr4B 97.826 230 3 2 1 229 249086343 249086571 2.330000e-106 396.0
28 TraesCS5A01G505900 chr4B 97.826 230 3 2 1 229 316657696 316657468 2.330000e-106 396.0
29 TraesCS5A01G505900 chr4B 76.461 599 125 6 1294 1887 653515614 653515027 8.670000e-81 311.0
30 TraesCS5A01G505900 chr4B 96.023 176 7 0 2439 2614 628067803 628067978 1.460000e-73 287.0
31 TraesCS5A01G505900 chr4B 89.677 155 10 3 2631 2784 185867671 185867522 3.280000e-45 193.0
32 TraesCS5A01G505900 chr2A 98.053 873 15 1 1 873 98133734 98134604 0.000000e+00 1517.0
33 TraesCS5A01G505900 chr1A 97.592 872 18 2 1 872 29790948 29790080 0.000000e+00 1491.0
34 TraesCS5A01G505900 chr7B 95.102 245 11 1 1 244 577561357 577561601 5.040000e-103 385.0
35 TraesCS5A01G505900 chr2B 95.102 245 11 1 1 244 440820210 440819966 5.040000e-103 385.0
36 TraesCS5A01G505900 chr6A 91.273 275 23 1 1 275 596553774 596554047 1.090000e-99 374.0
37 TraesCS5A01G505900 chr2D 90.283 247 15 7 637 876 159860745 159860989 6.700000e-82 315.0
38 TraesCS5A01G505900 chr2D 90.083 242 13 8 637 873 85604996 85604761 1.450000e-78 303.0
39 TraesCS5A01G505900 chr2D 90.041 241 14 6 637 872 196351363 196351128 1.450000e-78 303.0
40 TraesCS5A01G505900 chr7D 90.083 242 13 7 637 873 554146040 554145805 1.450000e-78 303.0


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 TraesCS5A01G505900 chr5A 671174109 671177326 3217 False 5943.00 5943 100.000000 1 3218 1 chr5A.!!$F1 3217
1 TraesCS5A01G505900 chr5A 671182494 671183331 837 False 557.70 1033 94.270000 2418 3218 2 chr5A.!!$F2 800
2 TraesCS5A01G505900 chr4D 489726206 489728664 2458 False 1759.00 2313 94.061000 873 3218 2 chr4D.!!$F1 2345
3 TraesCS5A01G505900 chr4D 122265508 122270711 5203 True 1164.70 2013 91.890667 873 2449 3 chr4D.!!$R2 1576
4 TraesCS5A01G505900 chr4D 489733103 489733939 836 False 567.70 1053 94.522500 2418 3218 2 chr4D.!!$F2 800
5 TraesCS5A01G505900 chr4D 122256632 122257605 973 True 230.00 248 89.438000 2631 3218 3 chr4D.!!$R1 587
6 TraesCS5A01G505900 chr4A 257019849 257020721 872 True 1434.00 1434 96.347000 1 872 1 chr4A.!!$R1 871
7 TraesCS5A01G505900 chr4A 278349857 278350579 722 True 1230.00 1230 97.517000 155 872 1 chr4A.!!$R2 717
8 TraesCS5A01G505900 chr4A 321127338 321128208 870 False 1138.00 1138 90.275000 1 872 1 chr4A.!!$F1 871
9 TraesCS5A01G505900 chr4A 448096563 448106197 9634 False 794.02 2030 90.439600 873 3218 5 chr4A.!!$F2 2345
10 TraesCS5A01G505900 chr4B 185872285 185873772 1487 True 2025.00 2025 91.336000 873 2351 1 chr4B.!!$R1 1478
11 TraesCS5A01G505900 chr4B 185905195 185906625 1430 True 1393.00 1393 84.338000 882 2314 1 chr4B.!!$R2 1432
12 TraesCS5A01G505900 chr4B 628066209 628068616 2407 False 830.75 1720 93.819500 873 3139 4 chr4B.!!$F2 2266
13 TraesCS5A01G505900 chr4B 185866861 185867671 810 True 332.50 472 88.372000 2631 3218 2 chr4B.!!$R5 587
14 TraesCS5A01G505900 chr4B 653515027 653515614 587 True 311.00 311 76.461000 1294 1887 1 chr4B.!!$R4 593
15 TraesCS5A01G505900 chr2A 98133734 98134604 870 False 1517.00 1517 98.053000 1 873 1 chr2A.!!$F1 872
16 TraesCS5A01G505900 chr1A 29790080 29790948 868 True 1491.00 1491 97.592000 1 872 1 chr1A.!!$R1 871

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
320 332 0.706433 AGGAATCAGTGGTGGCCAAT 59.294 50.000 7.24 0.0 34.18 3.16 F
1172 4070 1.198713 CAGCAGTACTCCTCACCCAT 58.801 55.000 0.00 0.0 0.00 4.00 F
1222 4120 1.228894 TTCGCTGAGGGTCTGGAGT 60.229 57.895 0.00 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1569 4482 0.107703 CACCAAGCTCTCGGGCAATA 60.108 55.000 0.00 0.0 34.17 1.90 R
2122 5042 0.620556 AGCCATTGGTGATCCTCGTT 59.379 50.000 4.26 0.0 34.23 3.85 R
2566 5849 1.209019 AGGGACATCATGTGCTCTGTC 59.791 52.381 9.41 0.0 38.83 3.51 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
25 26 1.227943 GGCGGCCTGATTAGCATCA 60.228 57.895 12.87 0.0 37.05 3.07
320 332 0.706433 AGGAATCAGTGGTGGCCAAT 59.294 50.000 7.24 0.0 34.18 3.16
443 455 4.115199 GGACCGGGCAGCTGGATT 62.115 66.667 17.12 0.0 0.00 3.01
522 534 1.767681 GGATCAGGACTTCAGGCAGAT 59.232 52.381 0.00 0.0 0.00 2.90
902 3800 2.863809 ACCGAAAGAGAAAAGTGGCAT 58.136 42.857 0.00 0.0 0.00 4.40
917 3815 2.109126 GCATCGGCCACAAGGACTC 61.109 63.158 2.24 0.0 42.67 3.36
1172 4070 1.198713 CAGCAGTACTCCTCACCCAT 58.801 55.000 0.00 0.0 0.00 4.00
1215 4113 1.258445 CCTACTGGTTCGCTGAGGGT 61.258 60.000 0.00 0.0 0.00 4.34
1222 4120 1.228894 TTCGCTGAGGGTCTGGAGT 60.229 57.895 0.00 0.0 0.00 3.85
1266 4164 2.487265 CCAGGTGTATGGGATGCTTACC 60.487 54.545 0.00 0.0 36.64 2.85
1569 4482 1.399714 TCGGTAATCGGCTGACTGAT 58.600 50.000 0.00 0.0 44.11 2.90
1692 4612 3.138304 TGCTGTGAATGACCTGTACAAC 58.862 45.455 0.00 0.0 0.00 3.32
1725 4645 2.368655 TGGATGAGTGTGTCGTCATG 57.631 50.000 0.00 0.0 42.39 3.07
2233 5173 8.316214 CCCACTGTTAACTGTAGTATTTTCCTA 58.684 37.037 16.61 0.0 0.00 2.94
2256 5196 7.928167 CCTACAGTTGAACATAAGCAGATATGA 59.072 37.037 10.12 0.0 36.87 2.15
2317 5266 4.583907 TCAACCTGAAAGATGCATTTGACA 59.416 37.500 0.00 0.0 34.07 3.58
2319 5268 3.890756 ACCTGAAAGATGCATTTGACACA 59.109 39.130 0.00 0.0 34.07 3.72
2328 5277 5.889853 AGATGCATTTGACACATCCAATACT 59.110 36.000 0.00 0.0 40.87 2.12
2333 5282 7.557358 TGCATTTGACACATCCAATACTTATCT 59.443 33.333 0.00 0.0 0.00 1.98
2345 5294 7.568349 TCCAATACTTATCTGACAGCTTGAAT 58.432 34.615 0.00 0.0 0.00 2.57
2353 5320 5.287170 TCTGACAGCTTGAATCATTTTCG 57.713 39.130 0.00 0.0 0.00 3.46
2379 5346 5.525378 AGCTCTTTTCTTGTACTCAACTGTG 59.475 40.000 0.00 0.0 0.00 3.66
2573 5856 5.362556 TCATTGCTTACTTTTGACAGAGC 57.637 39.130 0.00 0.0 0.00 4.09
2599 5882 8.960591 CACATGATGTCCCTTTTATAAAGAAGT 58.039 33.333 0.00 0.0 0.00 3.01
2616 8393 5.122512 AGAAGTGTCGTCCCGATATATTG 57.877 43.478 0.00 0.0 38.42 1.90
2732 8872 9.912634 TCAAACATCTTAAATTTTGCTCTTAGG 57.087 29.630 0.00 0.0 0.00 2.69
2768 8909 4.584518 CACAGGGTGCCACTGCCA 62.585 66.667 4.55 0.0 39.55 4.92
2787 8936 2.868583 CCACATGCTAAATGTCTCTCCG 59.131 50.000 0.00 0.0 0.00 4.63
2877 9250 8.300286 TGCGTTTTCATCTTACAAATCCATTTA 58.700 29.630 0.00 0.0 0.00 1.40
3046 9590 2.418976 CAGTGCTACTGCTACTACACGA 59.581 50.000 0.00 0.0 39.62 4.35
3165 9731 5.251764 AGATGGACATGGTCTTTCTCAAAG 58.748 41.667 0.00 0.0 39.88 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 3.103080 ACTCCATCGGTTCTTCCTACT 57.897 47.619 0.00 0.0 0.00 2.57
320 332 2.034878 CCCGATTGAGACTCCTGATCA 58.965 52.381 0.00 0.0 0.00 2.92
460 472 4.096003 CCCGCCCGTGATCCAGTT 62.096 66.667 0.00 0.0 0.00 3.16
522 534 3.993584 AACGCCCGTGGTCGCTAA 61.994 61.111 0.00 0.0 35.54 3.09
902 3800 2.599281 TCGAGTCCTTGTGGCCGA 60.599 61.111 0.00 0.0 0.00 5.54
908 3806 1.964891 TCGTCGCTCGAGTCCTTGT 60.965 57.895 15.13 0.0 44.01 3.16
917 3815 4.180946 CCTCCACCTCGTCGCTCG 62.181 72.222 0.00 0.0 41.41 5.03
1172 4070 2.260154 CGCTGTGTGCCATCACCAA 61.260 57.895 0.00 0.0 42.46 3.67
1215 4113 2.276116 GGTGAGCCGTGACTCCAGA 61.276 63.158 0.00 0.0 35.72 3.86
1266 4164 2.583593 GCAGAGGTAGCCTTCGCG 60.584 66.667 0.00 0.0 41.18 5.87
1569 4482 0.107703 CACCAAGCTCTCGGGCAATA 60.108 55.000 0.00 0.0 34.17 1.90
1692 4612 5.121811 CACTCATCCATTAAGGTCCTGAAG 58.878 45.833 0.00 0.0 39.02 3.02
1734 4654 1.969589 GACAACATCGCGGGGGTTT 60.970 57.895 6.13 0.0 0.00 3.27
1931 4851 1.152839 ACAACCCACCCAAAGACGG 60.153 57.895 0.00 0.0 0.00 4.79
1968 4888 3.001406 ACCCGGTCCTTTCCCTCG 61.001 66.667 0.00 0.0 0.00 4.63
2122 5042 0.620556 AGCCATTGGTGATCCTCGTT 59.379 50.000 4.26 0.0 34.23 3.85
2262 5205 5.544650 ACCACACCACAAACAGTATAGTAC 58.455 41.667 0.00 0.0 0.00 2.73
2317 5266 6.491714 AGCTGTCAGATAAGTATTGGATGT 57.508 37.500 3.32 0.0 0.00 3.06
2319 5268 7.129457 TCAAGCTGTCAGATAAGTATTGGAT 57.871 36.000 3.32 0.0 0.00 3.41
2328 5277 7.119699 ACGAAAATGATTCAAGCTGTCAGATAA 59.880 33.333 3.32 0.0 0.00 1.75
2333 5282 5.390885 GCTACGAAAATGATTCAAGCTGTCA 60.391 40.000 0.00 0.0 0.00 3.58
2345 5294 6.861065 ACAAGAAAAGAGCTACGAAAATGA 57.139 33.333 0.00 0.0 0.00 2.57
2353 5320 6.702282 ACAGTTGAGTACAAGAAAAGAGCTAC 59.298 38.462 0.00 0.0 36.64 3.58
2566 5849 1.209019 AGGGACATCATGTGCTCTGTC 59.791 52.381 9.41 0.0 38.83 3.51
2573 5856 8.960591 ACTTCTTTATAAAAGGGACATCATGTG 58.039 33.333 0.00 0.0 0.00 3.21
2616 8393 4.631813 ACGCAGAAAATGTATCAGAAGGAC 59.368 41.667 0.00 0.0 0.00 3.85
2723 8863 4.400529 TTCATATTCGTGCCTAAGAGCA 57.599 40.909 0.00 0.0 41.46 4.26
2732 8872 3.001838 TGTGGCGTTATTCATATTCGTGC 59.998 43.478 0.00 0.0 0.00 5.34
2768 8909 2.501723 ACCGGAGAGACATTTAGCATGT 59.498 45.455 9.46 0.0 34.52 3.21
2787 8936 2.137523 CTTTGAACAATGCAGGCAACC 58.862 47.619 0.00 0.0 37.17 3.77
3046 9590 1.486310 TGTCAGGCTGTTGTGAGTTCT 59.514 47.619 15.27 0.0 0.00 3.01


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

AutoCloner maintained by Alex Coulton.