Multiple sequence alignment - TraesCS5A01G264700

Loading Multiple Alignment...

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 TraesCS5A01G264700 chr5A 100.000 2633 0 0 1 2633 476766859 476764227 0.000000e+00 4863.0
1 TraesCS5A01G264700 chr5A 94.286 35 1 1 1719 1752 688842382 688842348 5.000000e-03 52.8
2 TraesCS5A01G264700 chr5B 93.524 2687 115 26 1 2633 448313460 448310779 0.000000e+00 3943.0
3 TraesCS5A01G264700 chr5B 77.577 553 104 16 2075 2612 602485329 602485876 1.520000e-82 316.0
4 TraesCS5A01G264700 chr5B 91.111 45 3 1 2555 2598 534332669 534332625 2.830000e-05 60.2
5 TraesCS5A01G264700 chr5D 87.440 1879 168 32 157 1991 375525242 375523388 0.000000e+00 2100.0
6 TraesCS5A01G264700 chr5D 88.541 1405 126 7 522 1892 375584290 375582887 0.000000e+00 1670.0
7 TraesCS5A01G264700 chr5D 90.396 656 59 4 1890 2543 375582806 375582153 0.000000e+00 859.0
8 TraesCS5A01G264700 chr5D 89.645 647 63 4 1988 2633 375470068 375469425 0.000000e+00 821.0
9 TraesCS5A01G264700 chr5D 91.468 293 17 6 157 442 375584920 375584629 1.900000e-106 396.0
10 TraesCS5A01G264700 chr5D 89.209 139 15 0 1 139 375585110 375584972 9.690000e-40 174.0
11 TraesCS5A01G264700 chr3D 77.778 468 83 13 2075 2530 516895496 516895038 4.320000e-68 268.0
12 TraesCS5A01G264700 chr3D 77.859 411 79 10 2214 2618 108958194 108958598 7.280000e-61 244.0
13 TraesCS5A01G264700 chr3D 76.485 421 90 8 2216 2630 47498673 47498256 1.230000e-53 220.0
14 TraesCS5A01G264700 chr7A 93.711 159 10 0 1448 1606 211358020 211358178 3.390000e-59 239.0
15 TraesCS5A01G264700 chr1B 92.453 159 12 0 1448 1606 338985459 338985301 7.330000e-56 228.0
16 TraesCS5A01G264700 chr4D 75.906 469 83 25 2074 2528 300242320 300241868 2.050000e-51 213.0
17 TraesCS5A01G264700 chr4D 94.505 91 5 0 1512 1602 405805757 405805667 9.830000e-30 141.0
18 TraesCS5A01G264700 chr2A 74.007 554 126 13 2092 2633 572445162 572444615 2.660000e-50 209.0
19 TraesCS5A01G264700 chr6A 73.805 523 96 26 2122 2632 603300736 603301229 4.510000e-38 169.0
20 TraesCS5A01G264700 chr6A 72.707 447 88 26 432 853 235052664 235053101 4.600000e-23 119.0
21 TraesCS5A01G264700 chr4A 82.667 150 25 1 2484 2633 700505894 700506042 5.910000e-27 132.0
22 TraesCS5A01G264700 chr6D 72.809 445 88 22 435 853 181712514 181712077 1.280000e-23 121.0
23 TraesCS5A01G264700 chr3A 79.389 131 23 4 2201 2327 745061207 745061337 3.610000e-14 89.8
24 TraesCS5A01G264700 chr3A 78.626 131 24 4 2201 2327 744972750 744972880 1.680000e-12 84.2
25 TraesCS5A01G264700 chr2D 91.667 60 5 0 538 597 11311585 11311526 1.680000e-12 84.2
26 TraesCS5A01G264700 chr4B 83.117 77 11 2 2559 2633 15407928 15407852 4.700000e-08 69.4


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 TraesCS5A01G264700 chr5A 476764227 476766859 2632 True 4863.00 4863 100.0000 1 2633 1 chr5A.!!$R1 2632
1 TraesCS5A01G264700 chr5B 448310779 448313460 2681 True 3943.00 3943 93.5240 1 2633 1 chr5B.!!$R1 2632
2 TraesCS5A01G264700 chr5B 602485329 602485876 547 False 316.00 316 77.5770 2075 2612 1 chr5B.!!$F1 537
3 TraesCS5A01G264700 chr5D 375523388 375525242 1854 True 2100.00 2100 87.4400 157 1991 1 chr5D.!!$R2 1834
4 TraesCS5A01G264700 chr5D 375469425 375470068 643 True 821.00 821 89.6450 1988 2633 1 chr5D.!!$R1 645
5 TraesCS5A01G264700 chr5D 375582153 375585110 2957 True 774.75 1670 89.9035 1 2543 4 chr5D.!!$R3 2542
6 TraesCS5A01G264700 chr2A 572444615 572445162 547 True 209.00 209 74.0070 2092 2633 1 chr2A.!!$R1 541

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
960 1292 0.673333 AAGATCGCACATCAACCGCA 60.673 50.0 0.0 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2454 2893 1.00358 GCCATCAGTTCAGAGGGTTGA 59.996 52.381 0.0 0.0 41.38 3.18 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
69 71 9.847706 TGTAAATACGAATGCAACAACAATTAT 57.152 25.926 0.00 0.00 0.00 1.28
253 289 7.554959 AAGTAGAGGGAAAACTTACATCAGA 57.445 36.000 0.00 0.00 31.84 3.27
333 377 3.973657 ACTCGACGACAAACACATTAGT 58.026 40.909 0.00 0.00 0.00 2.24
351 395 6.665680 ACATTAGTCAACTACTCACTCCAGAT 59.334 38.462 0.00 0.00 39.80 2.90
389 434 4.506271 GCACATAATCTCCATCATCCCTGT 60.506 45.833 0.00 0.00 0.00 4.00
443 488 5.821516 AAAACTCGTTGATGGTGTTACAA 57.178 34.783 0.00 0.00 0.00 2.41
467 512 2.435059 GGAGCCTCAAGACACCGC 60.435 66.667 0.00 0.00 0.00 5.68
496 541 1.539929 CCATCAAGCCGATCTGAGACC 60.540 57.143 0.00 0.00 29.21 3.85
603 907 1.761174 GAGGCCAGGTCACCAGAAA 59.239 57.895 5.01 0.00 0.00 2.52
800 1131 2.044353 AGGGCCTGAACATGGGTAAATT 59.956 45.455 4.50 0.00 0.00 1.82
928 1260 1.001633 ACGTGTCGTGCTTTCCCTAAT 59.998 47.619 0.00 0.00 39.18 1.73
947 1279 5.925397 CCTAATCAAGATCCAGACAAGATCG 59.075 44.000 0.00 0.00 44.02 3.69
960 1292 0.673333 AAGATCGCACATCAACCGCA 60.673 50.000 0.00 0.00 0.00 5.69
977 1309 3.861341 CAATCTCTTTGCTCCCCGA 57.139 52.632 0.00 0.00 0.00 5.14
1026 1358 7.315142 TGAACATCATAACAAATTCAGAAGGC 58.685 34.615 0.00 0.00 0.00 4.35
1099 1438 6.293626 CCTGGAATTCATTGTCGATTCATACC 60.294 42.308 7.93 0.00 0.00 2.73
1114 1453 2.028130 CATACCGAGAGCTTCACCTCT 58.972 52.381 0.00 0.00 44.57 3.69
1122 1461 0.252467 AGCTTCACCTCTGTAGCCCT 60.252 55.000 0.00 0.00 40.74 5.19
1140 1479 1.270412 CCTGCACATTGCCAAACACAT 60.270 47.619 0.00 0.00 44.23 3.21
1179 1518 2.121042 AACCCACCCACCTCCCAT 60.121 61.111 0.00 0.00 0.00 4.00
1248 1587 1.836802 GTGGAGGAAGAGGAGAGCAAT 59.163 52.381 0.00 0.00 0.00 3.56
1485 1824 1.877443 GCGGAAGGTCTTTTAAGTGCA 59.123 47.619 0.00 0.00 0.00 4.57
1672 2011 5.121611 TGTCTAATAACGACAAATGGTGCAG 59.878 40.000 0.00 0.00 38.36 4.41
1722 2061 7.445096 TCAGAGAAAATAAGAGTGACATTTGCA 59.555 33.333 0.00 0.00 0.00 4.08
1723 2062 8.077991 CAGAGAAAATAAGAGTGACATTTGCAA 58.922 33.333 0.00 0.00 0.00 4.08
1759 2101 1.366319 AGTGATCTGGGGAAAGTGCT 58.634 50.000 0.00 0.00 0.00 4.40
1760 2102 1.004044 AGTGATCTGGGGAAAGTGCTG 59.996 52.381 0.00 0.00 0.00 4.41
1998 2423 5.822519 GCATTCAGTGGTTATATCTTGGTCA 59.177 40.000 0.00 0.00 0.00 4.02
2015 2440 1.519455 CAGGTCTCGGTTGATCGGC 60.519 63.158 0.00 0.00 0.00 5.54
2045 2470 0.539986 AATGTAGGTGGCGTAGTGGG 59.460 55.000 0.00 0.00 0.00 4.61
2069 2494 1.133792 AGACTTTGTTGGGGTGGTGAG 60.134 52.381 0.00 0.00 0.00 3.51
2192 2625 1.076533 CACGTCCGTCTCATTTCCCG 61.077 60.000 0.00 0.00 0.00 5.14
2270 2707 6.724441 TGTTGGAATAAGGTCTTCTAGTCTCA 59.276 38.462 0.00 0.00 0.00 3.27
2329 2766 3.424703 CTGTGAGAATTTGTGTCCCCAT 58.575 45.455 0.00 0.00 0.00 4.00
2338 2775 7.353525 AGAATTTGTGTCCCCATATATGTTGA 58.646 34.615 11.73 4.87 0.00 3.18
2412 2850 2.572095 CTATTGGTGCGGCGAGTCCA 62.572 60.000 12.98 12.67 34.01 4.02
2439 2877 6.279513 TCTTCTTTCATGTTGTTTTGTGGT 57.720 33.333 0.00 0.00 0.00 4.16
2454 2893 3.134574 TGTGGTATGGTTCGCTTTCTT 57.865 42.857 0.00 0.00 0.00 2.52
2474 2914 1.003580 TCAACCCTCTGAACTGATGGC 59.996 52.381 0.00 0.00 0.00 4.40
2603 3043 0.249676 TGGTATTGCGAGGGCGTTTA 59.750 50.000 0.00 0.00 44.10 2.01
2613 3057 1.071814 GGGCGTTTACAGGTGTCCA 59.928 57.895 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 3.320826 ACTGCCGTAATTTTCTTTGCCTT 59.679 39.130 0.00 0.00 0.00 4.35
51 53 7.745022 ATCTTCATAATTGTTGTTGCATTCG 57.255 32.000 0.00 0.00 0.00 3.34
69 71 5.963092 TGGGCCATTTCCATTATATCTTCA 58.037 37.500 0.00 0.00 0.00 3.02
153 189 6.071728 CCTCCTGCTTTGTCACTATGATTTTT 60.072 38.462 0.00 0.00 0.00 1.94
333 377 3.954904 GGCTATCTGGAGTGAGTAGTTGA 59.045 47.826 0.00 0.00 0.00 3.18
351 395 0.617535 TGTGCAGGCTCTAAGGGCTA 60.618 55.000 0.00 0.00 40.17 3.93
389 434 1.102809 GGCCATTGTGCCGATGATCA 61.103 55.000 0.00 0.00 42.54 2.92
443 488 2.612115 CTTGAGGCTCCCCTGGGT 60.612 66.667 12.86 0.00 43.12 4.51
496 541 0.836400 ACCCTATAGCATCGTGGGGG 60.836 60.000 0.00 0.00 42.00 5.40
501 546 1.633774 CTGGGACCCTATAGCATCGT 58.366 55.000 13.00 0.00 0.00 3.73
505 564 1.461461 GGCCTGGGACCCTATAGCA 60.461 63.158 13.00 0.00 0.00 3.49
800 1131 4.144297 CTCAAAGGGGAAACATGAGACAA 58.856 43.478 0.00 0.00 39.85 3.18
882 1214 3.728373 CACCACCCCCTACCTGGC 61.728 72.222 0.00 0.00 0.00 4.85
928 1260 2.497273 TGCGATCTTGTCTGGATCTTGA 59.503 45.455 0.00 0.00 37.88 3.02
947 1279 1.089920 AGAGATTGCGGTTGATGTGC 58.910 50.000 0.00 0.00 0.00 4.57
960 1292 3.309296 TCTATCGGGGAGCAAAGAGATT 58.691 45.455 0.00 0.00 0.00 2.40
977 1309 4.223953 TGTCCCTAAAGGCGAAGATCTAT 58.776 43.478 0.00 0.00 34.51 1.98
1026 1358 4.084013 GGATTGTAGGTGTTGACAACTTCG 60.084 45.833 18.73 0.00 42.10 3.79
1084 1423 3.319405 AGCTCTCGGTATGAATCGACAAT 59.681 43.478 0.00 0.00 0.00 2.71
1099 1438 1.202245 GCTACAGAGGTGAAGCTCTCG 60.202 57.143 9.03 7.90 35.34 4.04
1114 1453 4.001248 GCAATGTGCAGGGCTACA 57.999 55.556 0.00 0.00 44.26 2.74
1218 1557 2.435069 CTCTTCCTCCACATCATGCTCT 59.565 50.000 0.00 0.00 0.00 4.09
1327 1666 1.932156 TTGGTGTTGTCCCTGCCACT 61.932 55.000 0.00 0.00 0.00 4.00
1485 1824 2.335316 TTTCTGTGCGGGTACAACTT 57.665 45.000 0.00 0.00 0.00 2.66
1759 2101 2.019249 GGCTCATGCTTGATGCTAACA 58.981 47.619 17.27 0.00 43.37 2.41
1760 2102 2.019249 TGGCTCATGCTTGATGCTAAC 58.981 47.619 17.27 7.41 43.37 2.34
1998 2423 1.668101 GAGCCGATCAACCGAGACCT 61.668 60.000 0.00 0.00 0.00 3.85
2015 2440 3.193479 GCCACCTACATTTTGAAAGGGAG 59.807 47.826 0.00 0.00 31.47 4.30
2045 2470 2.041216 ACCACCCCAACAAAGTCTATCC 59.959 50.000 0.00 0.00 0.00 2.59
2069 2494 2.508663 GACGGCTAGGGTTGCGAC 60.509 66.667 0.00 0.00 0.00 5.19
2270 2707 3.555795 CGGATCAAATGTCATCGAGGGAT 60.556 47.826 0.00 0.00 0.00 3.85
2329 2766 9.565090 CCAAGATCTGAAGGAAATCAACATATA 57.435 33.333 0.00 0.00 0.00 0.86
2338 2775 4.313020 ACTGCCAAGATCTGAAGGAAAT 57.687 40.909 12.05 0.00 0.00 2.17
2412 2850 7.278424 CCACAAAACAACATGAAAGAAGATGTT 59.722 33.333 0.00 0.00 42.29 2.71
2439 2877 3.078837 GGGTTGAAGAAAGCGAACCATA 58.921 45.455 0.00 0.00 39.79 2.74
2454 2893 1.003580 GCCATCAGTTCAGAGGGTTGA 59.996 52.381 0.00 0.00 41.38 3.18
2474 2914 1.577328 AACAAGCTTGCGGTCCATCG 61.577 55.000 26.27 0.00 0.00 3.84
2603 3043 4.724279 AGTAAAGGAAATGGACACCTGT 57.276 40.909 0.00 0.00 34.03 4.00


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

AutoCloner maintained by Alex Coulton.