Multiple sequence alignment - TraesCS5A01G074000

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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 TraesCS5A01G074000 chr5A 100.000 4811 0 0 1 4811 86667525 86662715 0.000000e+00 8885.0
1 TraesCS5A01G074000 chr5B 95.749 3976 123 20 77 4023 98668888 98664930 0.000000e+00 6364.0
2 TraesCS5A01G074000 chr5B 97.550 653 15 1 4159 4811 98664517 98663866 0.000000e+00 1116.0
3 TraesCS5A01G074000 chr5B 95.918 49 1 1 34 81 98674207 98674159 1.440000e-10 78.7
4 TraesCS5A01G074000 chr5D 97.583 3393 65 8 1430 4811 93068554 93065168 0.000000e+00 5795.0
5 TraesCS5A01G074000 chr5D 94.600 1463 47 7 1 1435 93070534 93069076 0.000000e+00 2235.0
6 TraesCS5A01G074000 chr5D 90.000 70 3 4 1407 1474 508283909 508283842 2.390000e-13 87.9
7 TraesCS5A01G074000 chr4D 93.333 75 4 1 1407 1481 113153527 113153600 5.090000e-20 110.0
8 TraesCS5A01G074000 chr3A 91.429 70 4 2 1407 1476 290447795 290447728 1.430000e-15 95.3
9 TraesCS5A01G074000 chr3D 93.651 63 3 1 1414 1476 54732419 54732358 5.130000e-15 93.5
10 TraesCS5A01G074000 chr3B 91.429 70 3 3 1407 1475 42146542 42146609 5.130000e-15 93.5
11 TraesCS5A01G074000 chr2B 92.188 64 5 0 1407 1470 296018016 296018079 1.840000e-14 91.6
12 TraesCS5A01G074000 chr1D 89.855 69 5 2 1407 1474 160717059 160717126 2.390000e-13 87.9
13 TraesCS5A01G074000 chr4A 97.500 40 1 0 532 571 45538926 45538887 8.640000e-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 TraesCS5A01G074000 chr5A 86662715 86667525 4810 True 8885 8885 100.0000 1 4811 1 chr5A.!!$R1 4810
1 TraesCS5A01G074000 chr5B 98663866 98668888 5022 True 3740 6364 96.6495 77 4811 2 chr5B.!!$R2 4734
2 TraesCS5A01G074000 chr5D 93065168 93070534 5366 True 4015 5795 96.0915 1 4811 2 chr5D.!!$R2 4810

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
772 810 0.716108 GGCGTTTCATCAGTGACGAG 59.284 55.0 5.57 0.0 33.11 4.18 F
1227 1265 1.879575 TGGTAGGTCCTGAATCCCAG 58.120 55.0 0.00 0.0 42.55 4.45 F
2468 3034 1.886886 TACGGAAAAGACCTGGTTGC 58.113 50.0 0.00 0.0 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2199 2765 1.479757 GCACCTCCCCAAACACCTTTA 60.480 52.381 0.0 0.0 0.0 1.85 R
2561 3127 1.536073 CCCAGAGACGTCAAGGAGCA 61.536 60.000 19.5 0.0 0.0 4.26 R
4105 4741 0.105760 ATGCTGGTTGGTGGGTTGAA 60.106 50.000 0.0 0.0 0.0 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
163 178 1.073768 GAAGCACCGCTCGACTCTTC 61.074 60.000 0.00 0.00 38.25 2.87
279 315 4.037923 TCAAGCATTCTTTTTCCTGTGACC 59.962 41.667 0.00 0.00 0.00 4.02
466 502 6.924060 AGATTCGATACTGTTTAGGTGTATGC 59.076 38.462 0.00 0.00 0.00 3.14
485 521 1.358152 CTGGGAAGGGAGTTGGTGTA 58.642 55.000 0.00 0.00 0.00 2.90
487 523 1.359168 GGGAAGGGAGTTGGTGTAGT 58.641 55.000 0.00 0.00 0.00 2.73
606 642 2.453521 TGAGCGGAACAGGTAGTACAT 58.546 47.619 2.06 0.00 0.00 2.29
645 681 5.779771 TCTTCAGTATCTTTGGGGCAATTTT 59.220 36.000 0.00 0.00 0.00 1.82
772 810 0.716108 GGCGTTTCATCAGTGACGAG 59.284 55.000 5.57 0.00 33.11 4.18
882 920 4.753233 CTGTCACTTTCAGCTATGCTAGT 58.247 43.478 0.00 0.00 36.40 2.57
1227 1265 1.879575 TGGTAGGTCCTGAATCCCAG 58.120 55.000 0.00 0.00 42.55 4.45
1237 1275 5.011227 GGTCCTGAATCCCAGTAATACTCTC 59.989 48.000 0.00 0.00 41.33 3.20
1618 2183 6.913132 GTCTTCACTTAGCAAGTTTTTCCTTC 59.087 38.462 0.00 0.00 40.46 3.46
1672 2238 6.978343 TTACCGTCTTTTCATAATGGTCTG 57.022 37.500 0.00 0.00 0.00 3.51
1685 2251 7.410174 TCATAATGGTCTGGTTTATGGTCTTT 58.590 34.615 0.00 0.00 35.18 2.52
1689 2255 6.381498 TGGTCTGGTTTATGGTCTTTATGA 57.619 37.500 0.00 0.00 0.00 2.15
2024 2590 1.933853 AGACTTCTGAACGTGCAACAC 59.066 47.619 0.00 0.00 35.74 3.32
2066 2632 7.971368 ATTAGTGCATTAAAAATACACCCCT 57.029 32.000 5.71 0.00 31.58 4.79
2393 2959 8.747666 GCGCTATATAAGTAACTATGCTCATTC 58.252 37.037 0.00 0.00 0.00 2.67
2468 3034 1.886886 TACGGAAAAGACCTGGTTGC 58.113 50.000 0.00 0.00 0.00 4.17
3177 3743 4.822896 TGCCAGAAACATACTTTACCGTTT 59.177 37.500 0.00 0.00 34.41 3.60
3271 3837 4.081586 GGAGTTCTTTCCATAGACTTCGGT 60.082 45.833 0.00 0.00 37.20 4.69
3615 4181 0.829990 GGCTGGAGAAGAGGGAAGAG 59.170 60.000 0.00 0.00 0.00 2.85
3627 4193 1.149288 AGGGAAGAGTACCACCTGACA 59.851 52.381 0.00 0.00 0.00 3.58
3631 4197 1.261480 AGAGTACCACCTGACAGCTG 58.739 55.000 13.48 13.48 0.00 4.24
3744 4310 2.301346 CAAGTTTCTGCCAGTTCACCT 58.699 47.619 0.00 0.00 0.00 4.00
3801 4367 3.267812 TCTTCCCAGATTTTGAGGCTGAT 59.732 43.478 0.00 0.00 0.00 2.90
3969 4535 9.598517 AACAAATTCACAATAAAGAAAAGCTCA 57.401 25.926 0.00 0.00 0.00 4.26
4033 4669 9.939802 GAGGTTGTCTCCTACTTTATAAGAAAA 57.060 33.333 0.00 0.00 38.02 2.29
4105 4741 8.960591 ACAGAAATTATTATAAACTGCTGCTGT 58.039 29.630 6.33 6.33 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 0.458543 CAGCGGTATGACGACAAGCT 60.459 55.000 0.00 0.00 35.47 3.74
14 15 0.458543 AGCAGCGGTATGACGACAAG 60.459 55.000 0.00 0.00 35.47 3.16
71 73 6.617371 TCCTCTTTATATCTCCCTTTGAAGCT 59.383 38.462 0.00 0.00 0.00 3.74
163 178 2.671177 CCGTTTGTCAGAGGCTGCG 61.671 63.158 0.00 0.00 0.00 5.18
293 329 4.496336 AGCCAAGGGATGCTCCGC 62.496 66.667 0.00 0.00 37.43 5.54
466 502 1.279271 CTACACCAACTCCCTTCCCAG 59.721 57.143 0.00 0.00 0.00 4.45
580 616 3.751698 ACTACCTGTTCCGCTCAAAATTC 59.248 43.478 0.00 0.00 0.00 2.17
584 620 2.629137 TGTACTACCTGTTCCGCTCAAA 59.371 45.455 0.00 0.00 0.00 2.69
741 779 5.698832 TGATGAAACGCCATTTTAACTCAG 58.301 37.500 0.00 0.00 0.00 3.35
772 810 8.425577 TCAGCTTAGCTTTATTCATGTAAGAC 57.574 34.615 3.00 0.00 36.40 3.01
879 917 4.362677 AGGTCCAAATTCCTGCTCTACTA 58.637 43.478 0.00 0.00 32.29 1.82
881 919 3.636153 AGGTCCAAATTCCTGCTCTAC 57.364 47.619 0.00 0.00 32.29 2.59
882 920 4.567747 GGAAAGGTCCAAATTCCTGCTCTA 60.568 45.833 11.82 0.00 44.26 2.43
1276 1314 4.518970 TGGAAATTCGGAGAAAGACCAAAG 59.481 41.667 0.00 0.00 45.90 2.77
1368 1406 8.127327 GGGAGTTGTAACTGAAAAGTAGAAAAC 58.873 37.037 1.35 0.00 39.88 2.43
1618 2183 7.484035 AAGTGAAGAAACTAGCTACACAAAG 57.516 36.000 10.06 0.00 0.00 2.77
1666 2232 6.177610 GTCATAAAGACCATAAACCAGACCA 58.822 40.000 0.00 0.00 41.56 4.02
1685 2251 3.711704 GGGGAAGAAGATGAGGTGTCATA 59.288 47.826 0.00 0.00 43.92 2.15
1689 2255 1.912043 CAGGGGAAGAAGATGAGGTGT 59.088 52.381 0.00 0.00 0.00 4.16
2016 2582 7.940850 ACTTTATCCCATAATATGTGTTGCAC 58.059 34.615 0.00 0.00 34.56 4.57
2061 2627 8.727100 AGATTTTAAAAGAAAGATGAAGGGGT 57.273 30.769 6.79 0.00 0.00 4.95
2199 2765 1.479757 GCACCTCCCCAAACACCTTTA 60.480 52.381 0.00 0.00 0.00 1.85
2238 2804 8.980481 AAACAGTATATTCCATAAACTCCTGG 57.020 34.615 0.00 0.00 0.00 4.45
2393 2959 5.661056 TCCACTCAGTTCATTACCTAGTG 57.339 43.478 0.00 0.00 38.67 2.74
2468 3034 6.233430 ACTGATTGACGATCTTTTGAAGTG 57.767 37.500 4.31 0.00 35.69 3.16
2561 3127 1.536073 CCCAGAGACGTCAAGGAGCA 61.536 60.000 19.50 0.00 0.00 4.26
2867 3433 4.361253 CGGCTGCCGCTGTTATAT 57.639 55.556 29.58 0.00 41.17 0.86
3177 3743 8.737168 AAGTTTAGTAATCTGAAGCATATGCA 57.263 30.769 28.62 8.81 45.16 3.96
3307 3873 2.351455 GCCACTCTTACCTTCTGCTTC 58.649 52.381 0.00 0.00 0.00 3.86
3498 4064 4.451150 CCTTGCGCTAGGCCGACA 62.451 66.667 24.62 0.00 42.61 4.35
3615 4181 1.618837 TCTTCAGCTGTCAGGTGGTAC 59.381 52.381 27.27 0.00 43.47 3.34
3627 4193 2.657237 CGGTTCCCGTCTTCAGCT 59.343 61.111 0.00 0.00 42.73 4.24
3744 4310 1.081442 CAGCGGCGCGACATAGATA 60.081 57.895 27.59 0.00 0.00 1.98
3768 4334 2.506438 GGGAAGACGACGAAGGCG 60.506 66.667 0.00 0.00 44.79 5.52
3801 4367 7.801280 AACTACAGTTCATCGCTAGCAAGCA 62.801 44.000 16.45 0.00 40.61 3.91
3900 4466 3.243839 GGGCAGAACACATCAACACAAAT 60.244 43.478 0.00 0.00 0.00 2.32
4087 4723 6.094881 GGGTTGAACAGCAGCAGTTTATAATA 59.905 38.462 4.46 0.00 0.00 0.98
4105 4741 0.105760 ATGCTGGTTGGTGGGTTGAA 60.106 50.000 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.