Multiple sequence alignment - TraesCS5A01G430200

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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 TraesCS5A01G430200 chr5A 100.000 2685 0 0 1 2685 614230676 614233360 0.000000e+00 4959
1 TraesCS5A01G430200 chr5A 97.839 694 14 1 1993 2685 603610470 603611163 0.000000e+00 1197
2 TraesCS5A01G430200 chr5A 98.108 687 12 1 1999 2685 691115021 691115706 0.000000e+00 1195
3 TraesCS5A01G430200 chr5A 97.550 694 17 0 1992 2685 6477057 6476364 0.000000e+00 1188
4 TraesCS5A01G430200 chr5A 97.547 693 17 0 1993 2685 220943680 220944372 0.000000e+00 1186
5 TraesCS5A01G430200 chr5A 81.910 398 39 18 737 1101 613957323 613957720 3.360000e-79 305
6 TraesCS5A01G430200 chr5A 88.966 145 12 1 608 748 613940721 613940865 2.750000e-40 176
7 TraesCS5A01G430200 chr5B 85.217 1637 129 51 433 1998 606636644 606638238 0.000000e+00 1578
8 TraesCS5A01G430200 chr5B 92.275 712 40 10 1291 1995 606813898 606814601 0.000000e+00 996
9 TraesCS5A01G430200 chr5B 91.618 513 25 4 778 1272 606813398 606813910 0.000000e+00 693
10 TraesCS5A01G430200 chr5B 87.736 212 26 0 968 1179 606834924 606835135 5.740000e-62 248
11 TraesCS5A01G430200 chr5B 84.483 232 32 3 952 1179 606843081 606843312 2.690000e-55 226
12 TraesCS5A01G430200 chr5B 79.918 244 49 0 1389 1632 605526476 605526233 2.120000e-41 180
13 TraesCS5A01G430200 chr2A 98.547 688 10 0 1998 2685 418797948 418798635 0.000000e+00 1216
14 TraesCS5A01G430200 chr2A 98.253 687 12 0 1999 2685 174239461 174238775 0.000000e+00 1203
15 TraesCS5A01G430200 chr2A 97.691 693 16 0 1993 2685 208584015 208584707 0.000000e+00 1192
16 TraesCS5A01G430200 chr7A 97.983 694 14 0 1992 2685 484527868 484528561 0.000000e+00 1205
17 TraesCS5A01G430200 chr3A 97.959 686 14 0 2000 2685 1721736 1722421 0.000000e+00 1190
18 TraesCS5A01G430200 chr5D 93.671 711 37 3 570 1272 491678511 491679221 0.000000e+00 1057
19 TraesCS5A01G430200 chr5D 93.390 711 44 1 1291 1998 491679209 491679919 0.000000e+00 1050
20 TraesCS5A01G430200 chr5D 90.701 613 22 9 3 584 491672195 491672803 0.000000e+00 784
21 TraesCS5A01G430200 chr5D 80.488 246 48 0 1387 1632 490973155 490972910 3.530000e-44 189


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 TraesCS5A01G430200 chr5A 614230676 614233360 2684 False 4959.0 4959 100.0000 1 2685 1 chr5A.!!$F5 2684
1 TraesCS5A01G430200 chr5A 603610470 603611163 693 False 1197.0 1197 97.8390 1993 2685 1 chr5A.!!$F2 692
2 TraesCS5A01G430200 chr5A 691115021 691115706 685 False 1195.0 1195 98.1080 1999 2685 1 chr5A.!!$F6 686
3 TraesCS5A01G430200 chr5A 6476364 6477057 693 True 1188.0 1188 97.5500 1992 2685 1 chr5A.!!$R1 693
4 TraesCS5A01G430200 chr5A 220943680 220944372 692 False 1186.0 1186 97.5470 1993 2685 1 chr5A.!!$F1 692
5 TraesCS5A01G430200 chr5B 606636644 606638238 1594 False 1578.0 1578 85.2170 433 1998 1 chr5B.!!$F1 1565
6 TraesCS5A01G430200 chr5B 606813398 606814601 1203 False 844.5 996 91.9465 778 1995 2 chr5B.!!$F4 1217
7 TraesCS5A01G430200 chr2A 418797948 418798635 687 False 1216.0 1216 98.5470 1998 2685 1 chr2A.!!$F2 687
8 TraesCS5A01G430200 chr2A 174238775 174239461 686 True 1203.0 1203 98.2530 1999 2685 1 chr2A.!!$R1 686
9 TraesCS5A01G430200 chr2A 208584015 208584707 692 False 1192.0 1192 97.6910 1993 2685 1 chr2A.!!$F1 692
10 TraesCS5A01G430200 chr7A 484527868 484528561 693 False 1205.0 1205 97.9830 1992 2685 1 chr7A.!!$F1 693
11 TraesCS5A01G430200 chr3A 1721736 1722421 685 False 1190.0 1190 97.9590 2000 2685 1 chr3A.!!$F1 685
12 TraesCS5A01G430200 chr5D 491678511 491679919 1408 False 1053.5 1057 93.5305 570 1998 2 chr5D.!!$F2 1428
13 TraesCS5A01G430200 chr5D 491672195 491672803 608 False 784.0 784 90.7010 3 584 1 chr5D.!!$F1 581

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
693 732 1.864029 GCATGCACGTCTCGTATGCTA 60.864 52.381 14.21 2.84 43.8 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1949 2061 1.291132 GGAGTAGCTCGCAAACCATC 58.709 55.0 0.0 0.0 0.0 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
236 247 3.007473 ACCAAAGAAAACCGGTGAAGA 57.993 42.857 8.52 0.00 0.00 2.87
238 249 3.211045 CCAAAGAAAACCGGTGAAGAGA 58.789 45.455 8.52 0.00 0.00 3.10
256 267 8.076781 GTGAAGAGATAAAACCCAAAGAGAAAC 58.923 37.037 0.00 0.00 0.00 2.78
258 269 6.610830 AGAGATAAAACCCAAAGAGAAACCA 58.389 36.000 0.00 0.00 0.00 3.67
261 272 7.726216 AGATAAAACCCAAAGAGAAACCAAAG 58.274 34.615 0.00 0.00 0.00 2.77
266 289 6.560003 ACCCAAAGAGAAACCAAAGAAAAT 57.440 33.333 0.00 0.00 0.00 1.82
277 300 5.845391 ACCAAAGAAAATGAACGGAAAGA 57.155 34.783 0.00 0.00 0.00 2.52
349 381 7.450074 TGGACAAATATTGGCTGGTATAGTAG 58.550 38.462 0.00 0.00 39.20 2.57
375 407 3.008049 AGTGCGTAGGAAATTCTTCAGGT 59.992 43.478 0.00 0.00 32.75 4.00
394 426 2.435805 GGTAGGACATGCTTCCATCTGA 59.564 50.000 5.24 0.00 38.25 3.27
584 619 5.843019 AGACACTGAAAGAGGGGAAAATA 57.157 39.130 0.00 0.00 37.43 1.40
609 644 2.654912 GACCGACGACCAGCAAACG 61.655 63.158 0.00 0.00 0.00 3.60
693 732 1.864029 GCATGCACGTCTCGTATGCTA 60.864 52.381 14.21 2.84 43.80 3.49
858 930 3.200825 TCTTGACCATTTCTCCTCCCATC 59.799 47.826 0.00 0.00 0.00 3.51
964 1051 7.937942 ACAGAGTACAGTTCAGTAAGTAGAAGA 59.062 37.037 0.00 0.00 0.00 2.87
991 1090 3.904136 AGTTTCAATTTCAGTGCTCGG 57.096 42.857 0.00 0.00 0.00 4.63
1128 1227 0.974383 CCCTCGGGTTTGACTACACT 59.026 55.000 0.00 0.00 0.00 3.55
1201 1300 3.620488 TCATTCCAAGTCTTATGGCACC 58.380 45.455 0.00 0.00 37.88 5.01
1203 1302 3.517296 TTCCAAGTCTTATGGCACCAA 57.483 42.857 0.00 0.00 37.88 3.67
1380 1491 8.757982 AGCTAATTGACTAATTCATCCACATT 57.242 30.769 0.00 0.00 37.64 2.71
1407 1518 8.752766 CTGATTGCAGTCTTCAATTACAAAAT 57.247 30.769 10.82 0.00 37.37 1.82
1599 1710 2.513204 CACCATCCTCGCAGCAGG 60.513 66.667 4.87 4.87 34.40 4.85
1615 1726 4.443266 GGCGCGTCTTCTCCTGCT 62.443 66.667 8.43 0.00 0.00 4.24
1644 1755 3.958147 CTCCGTGGGCTGCATCGTT 62.958 63.158 0.50 0.00 0.00 3.85
1683 1794 1.444212 CCAAGCGGCCATTCGTTTG 60.444 57.895 2.24 2.96 46.03 2.93
1760 1871 3.320826 TGTCAATGTGAGAAACCGAGAGA 59.679 43.478 0.00 0.00 0.00 3.10
1786 1897 4.400884 TGAGTTGTGCATGGTTTTGTAGTT 59.599 37.500 0.00 0.00 0.00 2.24
1884 1996 6.148315 GCCCTTGAAATTTCTTCATTCAAAGG 59.852 38.462 18.64 17.63 43.09 3.11
1942 2054 1.005289 AGAGAGGGGATGGTGCCAT 59.995 57.895 2.95 2.95 39.69 4.40
1976 2088 1.226323 CGAGCTACTCCACGTTCGG 60.226 63.158 0.00 0.00 31.55 4.30
2053 2165 1.890876 TAAAGCCACATGACAGCGTT 58.109 45.000 0.00 6.27 32.94 4.84
2501 2613 7.966117 GCTTTGGCTAGGGTTCGAATATCGA 62.966 48.000 0.00 0.00 40.36 3.59
2645 2757 4.431131 CCGAGCCAGGCCCATTGT 62.431 66.667 8.22 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 6.533367 TGGTTTTCTTTTTAACACATGTCTGC 59.467 34.615 0.00 0.00 0.00 4.26
214 225 3.379057 TCTTCACCGGTTTTCTTTGGTTC 59.621 43.478 2.97 0.00 30.72 3.62
236 247 7.563556 TCTTTGGTTTCTCTTTGGGTTTTATCT 59.436 33.333 0.00 0.00 0.00 1.98
238 249 7.669089 TCTTTGGTTTCTCTTTGGGTTTTAT 57.331 32.000 0.00 0.00 0.00 1.40
256 267 7.491048 TCTTTTCTTTCCGTTCATTTTCTTTGG 59.509 33.333 0.00 0.00 0.00 3.28
258 269 8.996024 TTCTTTTCTTTCCGTTCATTTTCTTT 57.004 26.923 0.00 0.00 0.00 2.52
261 272 9.849607 GATTTTCTTTTCTTTCCGTTCATTTTC 57.150 29.630 0.00 0.00 0.00 2.29
266 289 5.977129 GCTGATTTTCTTTTCTTTCCGTTCA 59.023 36.000 0.00 0.00 0.00 3.18
277 300 3.555518 GCTCGTTCGCTGATTTTCTTTT 58.444 40.909 0.00 0.00 0.00 2.27
306 338 1.965930 ATTTGTCGCTTGCTCGCCA 60.966 52.632 0.00 0.00 0.00 5.69
313 345 5.289193 CCAATATTTGTCCATTTGTCGCTTG 59.711 40.000 0.00 0.00 0.00 4.01
349 381 4.927425 TGAAGAATTTCCTACGCACTACAC 59.073 41.667 0.00 0.00 32.09 2.90
375 407 2.435805 GGTCAGATGGAAGCATGTCCTA 59.564 50.000 4.17 0.00 38.62 2.94
394 426 1.837439 TGGGAGCATCTCGTTTATGGT 59.163 47.619 0.00 0.00 39.79 3.55
584 619 0.249741 CTGGTCGTCGGTCCAAAGTT 60.250 55.000 10.29 0.00 33.06 2.66
693 732 3.872603 TCCACCTGTGCGCTTGGT 61.873 61.111 9.73 11.39 33.87 3.67
858 930 2.054687 TTCACGTACGCTTGTAGTGG 57.945 50.000 16.72 0.00 32.65 4.00
964 1051 7.009540 CGAGCACTGAAATTGAAACTTCTTTTT 59.990 33.333 0.00 0.00 0.00 1.94
991 1090 1.808945 CTTGGAAGCCATGGATATCGC 59.191 52.381 18.40 0.00 31.53 4.58
1110 1209 1.939838 GCAGTGTAGTCAAACCCGAGG 60.940 57.143 0.00 0.00 0.00 4.63
1128 1227 2.922503 TTGCTCTCGGACCAGGCA 60.923 61.111 0.00 0.00 0.00 4.75
1275 1381 7.639113 TGCGGATTAGTTCCTTTTCAATAAT 57.361 32.000 0.00 0.00 42.99 1.28
1276 1382 7.639113 ATGCGGATTAGTTCCTTTTCAATAA 57.361 32.000 0.00 0.00 42.99 1.40
1278 1384 6.530019 AATGCGGATTAGTTCCTTTTCAAT 57.470 33.333 0.00 0.00 42.99 2.57
1280 1386 5.975693 AAATGCGGATTAGTTCCTTTTCA 57.024 34.783 1.39 0.00 42.99 2.69
1281 1387 6.127842 TGGTAAATGCGGATTAGTTCCTTTTC 60.128 38.462 1.39 0.00 42.99 2.29
1287 1393 5.527582 ACTGATGGTAAATGCGGATTAGTTC 59.472 40.000 1.39 0.00 0.00 3.01
1288 1394 5.437060 ACTGATGGTAAATGCGGATTAGTT 58.563 37.500 1.39 0.00 0.00 2.24
1289 1395 5.036117 ACTGATGGTAAATGCGGATTAGT 57.964 39.130 1.39 0.00 0.00 2.24
1290 1396 5.760253 AGAACTGATGGTAAATGCGGATTAG 59.240 40.000 1.39 0.00 0.00 1.73
1291 1397 5.680619 AGAACTGATGGTAAATGCGGATTA 58.319 37.500 1.39 0.00 0.00 1.75
1292 1398 4.526970 AGAACTGATGGTAAATGCGGATT 58.473 39.130 0.00 0.00 0.00 3.01
1293 1399 4.156455 AGAACTGATGGTAAATGCGGAT 57.844 40.909 0.00 0.00 0.00 4.18
1294 1400 3.627395 AGAACTGATGGTAAATGCGGA 57.373 42.857 0.00 0.00 0.00 5.54
1295 1401 5.123186 TGTTAAGAACTGATGGTAAATGCGG 59.877 40.000 0.00 0.00 0.00 5.69
1296 1402 6.176975 TGTTAAGAACTGATGGTAAATGCG 57.823 37.500 0.00 0.00 0.00 4.73
1420 1531 1.836391 CCCACTCACTTCCACCACA 59.164 57.895 0.00 0.00 0.00 4.17
1599 1710 2.883253 GAGCAGGAGAAGACGCGC 60.883 66.667 5.73 0.00 0.00 6.86
1644 1755 1.657751 CGCAGGATGAGGAGTCGACA 61.658 60.000 19.50 0.00 39.69 4.35
1683 1794 6.070656 TGAAATCATATCACCCCTTGGAATC 58.929 40.000 0.00 0.00 34.81 2.52
1760 1871 3.195396 ACAAAACCATGCACAACTCAACT 59.805 39.130 0.00 0.00 0.00 3.16
1907 2019 4.568804 CCTCTCTCAGTTCTCTCACCCTAA 60.569 50.000 0.00 0.00 0.00 2.69
1908 2020 3.053991 CCTCTCTCAGTTCTCTCACCCTA 60.054 52.174 0.00 0.00 0.00 3.53
1912 2024 2.099405 CCCCTCTCTCAGTTCTCTCAC 58.901 57.143 0.00 0.00 0.00 3.51
1942 2054 1.452110 CTCGCAAACCATCACCATGA 58.548 50.000 0.00 0.00 30.57 3.07
1949 2061 1.291132 GGAGTAGCTCGCAAACCATC 58.709 55.000 0.00 0.00 0.00 3.51
2053 2165 3.893200 TCTCTTTCCTGTTTGGTCTCGTA 59.107 43.478 0.00 0.00 37.07 3.43
2350 2462 1.680338 AGCCTGCTGACGTTCTTTTT 58.320 45.000 0.00 0.00 0.00 1.94
2501 2613 2.133858 TGGAACCCCTCCTCTTTCTT 57.866 50.000 0.00 0.00 45.64 2.52
2528 2640 1.998315 CTGTGTCAGATCTTGGCTTCG 59.002 52.381 0.00 0.00 32.44 3.79
2645 2757 3.057315 GCTGCTGACCAGATTAAAAAGCA 60.057 43.478 0.47 0.00 44.64 3.91


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

AutoCloner maintained by Alex Coulton.