Multiple sequence alignment - TraesCS5A01G538300

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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 TraesCS5A01G538300 chr5A 100.000 3296 0 0 1 3296 696328867 696325572 0.000000e+00 6087
1 TraesCS5A01G538300 chr5A 96.515 3300 109 4 3 3296 670476767 670473468 0.000000e+00 5452
2 TraesCS5A01G538300 chr1A 95.912 3302 125 8 3 3296 449450050 449453349 0.000000e+00 5341
3 TraesCS5A01G538300 chr1A 95.703 3305 129 7 3 3296 374207763 374211065 0.000000e+00 5304
4 TraesCS5A01G538300 chr2D 95.068 3305 147 11 3 3296 197523403 197520104 0.000000e+00 5186
5 TraesCS5A01G538300 chr3A 94.549 3302 144 12 3 3296 1716803 1713530 0.000000e+00 5068
6 TraesCS5A01G538300 chr3A 89.130 1610 137 19 1676 3254 218169215 218167613 0.000000e+00 1969
7 TraesCS5A01G538300 chr3A 95.161 62 3 0 1620 1681 218173133 218173072 7.530000e-17 99
8 TraesCS5A01G538300 chr3D 91.677 2487 178 13 737 3202 303482138 303479660 0.000000e+00 3419
9 TraesCS5A01G538300 chr5D 92.451 1987 125 14 392 2374 51806380 51804415 0.000000e+00 2815
10 TraesCS5A01G538300 chr5D 88.390 913 77 14 2369 3254 51750724 51749814 0.000000e+00 1072
11 TraesCS5A01G538300 chr7A 95.870 1598 61 5 3 1598 206573459 206575053 0.000000e+00 2580
12 TraesCS5A01G538300 chr5B 95.679 1597 64 4 3 1598 701464827 701466419 0.000000e+00 2562
13 TraesCS5A01G538300 chr1B 95.003 1601 73 5 3 1598 23815843 23817441 0.000000e+00 2507
14 TraesCS5A01G538300 chr1B 95.209 1127 49 5 3 1127 388030453 388031576 0.000000e+00 1777
15 TraesCS5A01G538300 chr2B 94.388 1568 79 6 1736 3296 142888768 142890333 0.000000e+00 2399
16 TraesCS5A01G538300 chr2B 88.622 1582 118 29 1723 3251 634220834 634222406 0.000000e+00 1868
17 TraesCS5A01G538300 chr2A 87.070 1075 99 19 1625 2672 648155997 648157058 0.000000e+00 1179


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 TraesCS5A01G538300 chr5A 696325572 696328867 3295 True 6087 6087 100.0000 1 3296 1 chr5A.!!$R2 3295
1 TraesCS5A01G538300 chr5A 670473468 670476767 3299 True 5452 5452 96.5150 3 3296 1 chr5A.!!$R1 3293
2 TraesCS5A01G538300 chr1A 449450050 449453349 3299 False 5341 5341 95.9120 3 3296 1 chr1A.!!$F2 3293
3 TraesCS5A01G538300 chr1A 374207763 374211065 3302 False 5304 5304 95.7030 3 3296 1 chr1A.!!$F1 3293
4 TraesCS5A01G538300 chr2D 197520104 197523403 3299 True 5186 5186 95.0680 3 3296 1 chr2D.!!$R1 3293
5 TraesCS5A01G538300 chr3A 1713530 1716803 3273 True 5068 5068 94.5490 3 3296 1 chr3A.!!$R1 3293
6 TraesCS5A01G538300 chr3A 218167613 218173133 5520 True 1034 1969 92.1455 1620 3254 2 chr3A.!!$R2 1634
7 TraesCS5A01G538300 chr3D 303479660 303482138 2478 True 3419 3419 91.6770 737 3202 1 chr3D.!!$R1 2465
8 TraesCS5A01G538300 chr5D 51804415 51806380 1965 True 2815 2815 92.4510 392 2374 1 chr5D.!!$R2 1982
9 TraesCS5A01G538300 chr5D 51749814 51750724 910 True 1072 1072 88.3900 2369 3254 1 chr5D.!!$R1 885
10 TraesCS5A01G538300 chr7A 206573459 206575053 1594 False 2580 2580 95.8700 3 1598 1 chr7A.!!$F1 1595
11 TraesCS5A01G538300 chr5B 701464827 701466419 1592 False 2562 2562 95.6790 3 1598 1 chr5B.!!$F1 1595
12 TraesCS5A01G538300 chr1B 23815843 23817441 1598 False 2507 2507 95.0030 3 1598 1 chr1B.!!$F1 1595
13 TraesCS5A01G538300 chr1B 388030453 388031576 1123 False 1777 1777 95.2090 3 1127 1 chr1B.!!$F2 1124
14 TraesCS5A01G538300 chr2B 142888768 142890333 1565 False 2399 2399 94.3880 1736 3296 1 chr2B.!!$F1 1560
15 TraesCS5A01G538300 chr2B 634220834 634222406 1572 False 1868 1868 88.6220 1723 3251 1 chr2B.!!$F2 1528
16 TraesCS5A01G538300 chr2A 648155997 648157058 1061 False 1179 1179 87.0700 1625 2672 1 chr2A.!!$F1 1047

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
365 376 0.40404 TTCATGTGGGTGGGAAGGTC 59.596 55.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2363 6287 1.331756 GCTCCAGTCAATAATGCCACG 59.668 52.381 0.0 0.0 0.0 4.94 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
300 311 0.912006 AGGAAAGGAGCCCTCTCACC 60.912 60.000 0.00 0.00 41.13 4.02
324 335 5.448904 CGAATGTCATGGTTGCATGTGATTA 60.449 40.000 0.00 0.00 34.39 1.75
364 375 0.856982 TTTCATGTGGGTGGGAAGGT 59.143 50.000 0.00 0.00 0.00 3.50
365 376 0.404040 TTCATGTGGGTGGGAAGGTC 59.596 55.000 0.00 0.00 0.00 3.85
448 459 9.273016 GATGGAAAATTTTATCTCGTAGATGGA 57.727 33.333 2.75 0.00 35.37 3.41
505 516 2.569059 CGAGGAGTTCGGTATCACCTA 58.431 52.381 0.00 0.00 45.54 3.08
506 517 3.147629 CGAGGAGTTCGGTATCACCTAT 58.852 50.000 0.00 0.00 45.54 2.57
587 598 3.956199 CAACCATACCCATGCAATTCTCT 59.044 43.478 0.00 0.00 0.00 3.10
686 698 4.003648 GAGTCACAAATCAAGATTCCGGT 58.996 43.478 0.00 0.00 0.00 5.28
689 701 2.819608 CACAAATCAAGATTCCGGTGGT 59.180 45.455 0.00 0.00 0.00 4.16
793 805 8.177663 CACCAGAAACATATGTTGATGTTCTAC 58.822 37.037 21.46 5.66 46.84 2.59
865 877 2.225491 ACTCTTAGAGATCAGATCGCGC 59.775 50.000 16.95 0.00 34.06 6.86
947 960 9.470399 TTTTCTCACCTTTTCTTAGGTAAAGTT 57.530 29.630 0.00 0.00 46.80 2.66
998 1011 6.154363 CCCCATTGTTGGTTCAATAATGTAGT 59.846 38.462 20.44 0.00 45.12 2.73
1053 1066 5.412594 TGCATATGAGAAAGGTCTTGTTGAC 59.587 40.000 6.97 0.00 44.63 3.18
1111 1124 2.564062 CAAAATGGGTGGACTGCTGAAT 59.436 45.455 0.00 0.00 0.00 2.57
1167 1181 8.734386 CAGAAATTTCCACTAGCTAATTTCACT 58.266 33.333 22.74 8.51 43.95 3.41
1248 1262 2.357517 CGGAAACAGAGCGGCACT 60.358 61.111 1.45 0.00 0.00 4.40
1270 1284 2.549754 GGATGGGATGATACACTTTGCG 59.450 50.000 0.00 0.00 0.00 4.85
1301 1315 6.518493 TCGTTGAACCTGTAATATGGGATAC 58.482 40.000 0.00 0.00 0.00 2.24
1382 1396 7.894708 TCTTCAAGGCATTGTTTTATTGATCA 58.105 30.769 11.36 0.00 37.68 2.92
1385 1399 7.092079 TCAAGGCATTGTTTTATTGATCACAG 58.908 34.615 11.36 0.00 37.68 3.66
1618 1632 0.037975 TTTACGTCGGACCCTGCTTC 60.038 55.000 1.91 0.00 0.00 3.86
1699 5575 5.010708 ACTTTATTTCTGGAATGGGTGGT 57.989 39.130 0.00 0.00 0.00 4.16
1705 5582 4.563140 TTCTGGAATGGGTGGTAGTAAC 57.437 45.455 0.00 0.00 0.00 2.50
1805 5713 3.627577 GTGTTGCTTCAGGAGACTTGAAA 59.372 43.478 0.00 0.00 40.21 2.69
1819 5727 9.525826 AGGAGACTTGAAATTTGTATCAATTCT 57.474 29.630 9.13 9.13 43.79 2.40
1848 5756 1.372582 TCTCACAAGCGATGCCATTC 58.627 50.000 0.00 0.00 0.00 2.67
1879 5787 6.359804 TGGATTCCTCTACCAATGATTTGAG 58.640 40.000 3.95 0.00 34.60 3.02
1918 5826 5.595542 CCAATGTTGATGATGGTATGTCCTT 59.404 40.000 0.00 0.00 37.07 3.36
1988 5896 5.423610 AGCTACAACATCTACCAACTCTGAT 59.576 40.000 0.00 0.00 0.00 2.90
2004 5913 2.373169 TCTGATCAAAAGGGAGCACTGT 59.627 45.455 0.00 0.00 0.00 3.55
2037 5946 1.656652 GAAGCAAAGCCAGATCGCTA 58.343 50.000 0.00 0.00 38.44 4.26
2102 6013 4.095610 CAAAACTGGTTGACGAGTTGAAC 58.904 43.478 11.45 0.00 42.72 3.18
2113 6026 2.616842 ACGAGTTGAACGAAAAAGCCAT 59.383 40.909 0.00 0.00 34.70 4.40
2144 6057 6.303054 TGTTCTCAATTGGAAACTGTATGGA 58.697 36.000 18.44 1.79 0.00 3.41
2331 6254 4.272748 GTGTAACCAGTTCACCTTCTTGTC 59.727 45.833 0.00 0.00 0.00 3.18
2443 6367 6.449635 AGATAAGCAAAGACAAAACACACA 57.550 33.333 0.00 0.00 0.00 3.72
2474 6398 8.157476 TCTTTTAAAACTGACTAGAAGAGCCAT 58.843 33.333 0.00 0.00 0.00 4.40
2507 6431 7.226523 GGAGAAATGTTAATGCCTTTTGTTTGT 59.773 33.333 0.00 0.00 0.00 2.83
2573 6523 0.551377 TGGCCTCCTCCCATTGGTTA 60.551 55.000 3.32 0.00 0.00 2.85
2636 6586 2.679349 GCCCTGTTCATCTGGAGACTTC 60.679 54.545 0.00 0.00 37.33 3.01
2655 6605 8.293699 AGACTTCTTCAAGTAAACAAATTGGT 57.706 30.769 0.00 0.00 43.37 3.67
2736 6688 5.630896 GCACATTGCACAAATCATATGTC 57.369 39.130 1.90 0.00 44.26 3.06
2920 6896 0.825425 TTTGCGGCCCATCTTGTTCA 60.825 50.000 0.00 0.00 0.00 3.18
2929 6905 4.706962 GGCCCATCTTGTTCAAAAGTATCT 59.293 41.667 0.00 0.00 0.00 1.98
3062 7044 1.206072 GCCAATGCTCGATCATCGC 59.794 57.895 0.80 4.08 40.21 4.58
3112 7094 9.334947 CTTGATGAAGTGATGGATAAGTTGTAT 57.665 33.333 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 6.630203 TTGGGCTAGAGTTGGAATAAAGTA 57.370 37.500 0.00 0.00 0.00 2.24
6 7 5.975988 ATCTTTGGGCTAGAGTTGGAATA 57.024 39.130 0.00 0.00 0.00 1.75
448 459 2.017049 GAAGGCGTGTTTGCATATCCT 58.983 47.619 0.00 0.00 36.28 3.24
505 516 1.680338 GCCGCCTCCTAAATTCACAT 58.320 50.000 0.00 0.00 0.00 3.21
506 517 0.742990 CGCCGCCTCCTAAATTCACA 60.743 55.000 0.00 0.00 0.00 3.58
554 565 2.081462 GGTATGGTTGAACAACTCCCG 58.919 52.381 15.60 0.00 40.94 5.14
587 598 1.610624 GCTCCTTTCGATGTGGTTCCA 60.611 52.381 0.00 0.00 0.00 3.53
686 698 5.995446 TGTTATGGAATACAGCACATACCA 58.005 37.500 0.00 0.00 0.00 3.25
689 701 8.922931 AATGATGTTATGGAATACAGCACATA 57.077 30.769 0.00 0.00 36.38 2.29
793 805 3.012518 GTTGGTTGACATCATCTCCCTG 58.987 50.000 0.00 0.00 0.00 4.45
865 877 5.163530 TGTTATAATCAGCCCACATTTGCAG 60.164 40.000 0.00 0.00 0.00 4.41
1014 1027 1.105167 ATGCATGGTCCCAAGATGCG 61.105 55.000 0.00 0.00 40.79 4.73
1053 1066 5.104374 GGATTGTTGTGGTCAAGCATTATG 58.896 41.667 0.00 0.00 33.61 1.90
1111 1124 9.391006 GAATGTATTTGTAATTCTAGTCCACCA 57.609 33.333 0.00 0.00 0.00 4.17
1167 1181 5.630121 TCCTTCTCTTGGATTTGTTGCTTA 58.370 37.500 0.00 0.00 0.00 3.09
1248 1262 3.554934 GCAAAGTGTATCATCCCATCCA 58.445 45.455 0.00 0.00 0.00 3.41
1270 1284 7.307396 CCATATTACAGGTTCAACGATGATCAC 60.307 40.741 0.00 0.00 34.96 3.06
1301 1315 7.913674 AGAAAAGAGCTAACCTTGATAAGTG 57.086 36.000 0.00 0.00 0.00 3.16
1382 1396 2.627221 TGCAACAACATTGTATGGCTGT 59.373 40.909 13.61 0.00 41.31 4.40
1385 1399 4.244066 TGAATGCAACAACATTGTATGGC 58.756 39.130 0.00 3.75 41.31 4.40
1602 1616 2.915659 TGAAGCAGGGTCCGACGT 60.916 61.111 0.00 0.00 0.00 4.34
1604 1618 1.374758 CACTGAAGCAGGGTCCGAC 60.375 63.158 0.00 0.00 35.51 4.79
1682 5558 5.014755 TGTTACTACCACCCATTCCAGAAAT 59.985 40.000 0.00 0.00 0.00 2.17
1805 5713 6.839124 TCCACTTGCAGAATTGATACAAAT 57.161 33.333 0.00 0.00 0.00 2.32
1819 5727 1.527034 GCTTGTGAGATCCACTTGCA 58.473 50.000 13.32 0.00 45.86 4.08
1848 5756 4.133526 TGGTAGAGGAATCCATAGGAGG 57.866 50.000 0.61 0.00 34.05 4.30
1879 5787 2.628657 ACATTGGTAGAGGAGATACGGC 59.371 50.000 0.00 0.00 0.00 5.68
1918 5826 2.237143 CCTTGCCCTTGTAGATCAGACA 59.763 50.000 0.00 0.00 0.00 3.41
1988 5896 1.490490 ACAGACAGTGCTCCCTTTTGA 59.510 47.619 0.00 0.00 0.00 2.69
2004 5913 4.202050 GCTTTGCTTCCTCTTTTTCACAGA 60.202 41.667 0.00 0.00 0.00 3.41
2102 6013 5.883661 AGAACATGTCATATGGCTTTTTCG 58.116 37.500 9.09 0.00 0.00 3.46
2113 6026 7.448161 ACAGTTTCCAATTGAGAACATGTCATA 59.552 33.333 19.34 0.54 0.00 2.15
2144 6057 2.092968 TCTTCCATTGGTTCTAGCGCAT 60.093 45.455 11.47 0.00 0.00 4.73
2254 6174 4.340617 TCCTTCAACCAATAAAGCCGAAT 58.659 39.130 0.00 0.00 0.00 3.34
2363 6287 1.331756 GCTCCAGTCAATAATGCCACG 59.668 52.381 0.00 0.00 0.00 4.94
2493 6417 9.389755 ACATAAAAACTAACAAACAAAAGGCAT 57.610 25.926 0.00 0.00 0.00 4.40
2573 6523 4.040755 AGTTATGAGGCAATAGGAGGTGT 58.959 43.478 0.00 0.00 0.00 4.16
2655 6605 3.788227 ATCACAAGGCTGTCCAGTAAA 57.212 42.857 0.00 0.00 31.64 2.01
2719 6671 4.457257 TCAACCGACATATGATTTGTGCAA 59.543 37.500 10.38 0.00 0.00 4.08
2736 6688 7.772332 AGCAAACTAGAAATAGTATCAACCG 57.228 36.000 0.00 0.00 0.00 4.44
2829 6783 3.483808 TGTACCACAACTTGATGCTGA 57.516 42.857 0.00 0.00 0.00 4.26
2920 6896 4.002906 TGTCCAACGCAGAGATACTTTT 57.997 40.909 0.00 0.00 0.00 2.27
2929 6905 1.228094 TTGCCATGTCCAACGCAGA 60.228 52.632 0.00 0.00 31.86 4.26
3062 7044 6.423302 AGCTTAAGATATCAGTCTGCATTTCG 59.577 38.462 6.67 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.