Multiple sequence alignment - TraesCS4A01G211900

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 TraesCS4A01G211900 chr4A 100.000 2421 0 0 1 2421 507109270 507106850 0.000000e+00 4471
1 TraesCS4A01G211900 chr5D 96.795 1685 54 0 737 2421 545193814 545195498 0.000000e+00 2813
2 TraesCS4A01G211900 chr5D 97.301 741 16 2 1 740 545192042 545192779 0.000000e+00 1254
3 TraesCS4A01G211900 chr6D 96.499 1685 59 0 737 2421 348140 346456 0.000000e+00 2785
4 TraesCS4A01G211900 chr6D 97.571 741 17 1 1 740 349913 349173 0.000000e+00 1267
5 TraesCS4A01G211900 chr4D 96.439 1685 60 0 737 2421 400125829 400127513 0.000000e+00 2780
6 TraesCS4A01G211900 chr4D 97.571 741 17 1 1 740 400124055 400124795 0.000000e+00 1267
7 TraesCS4A01G211900 chr3A 96.142 1685 64 1 737 2421 40978391 40976708 0.000000e+00 2750
8 TraesCS4A01G211900 chr3A 96.045 885 35 0 737 1621 500030156 500031040 0.000000e+00 1441
9 TraesCS4A01G211900 chr3A 95.528 805 35 1 1617 2421 500038670 500039473 0.000000e+00 1286
10 TraesCS4A01G211900 chr3A 97.301 741 19 1 1 740 40980165 40979425 0.000000e+00 1256
11 TraesCS4A01G211900 chr3A 97.301 741 19 1 1 740 500028382 500029122 0.000000e+00 1256
12 TraesCS4A01G211900 chr1A 95.730 1686 59 3 737 2421 45392719 45394392 0.000000e+00 2702
13 TraesCS4A01G211900 chr1A 96.896 741 22 1 1 740 45390944 45391684 0.000000e+00 1240
14 TraesCS4A01G211900 chrUn 96.455 1636 58 0 737 2372 43101618 43099983 0.000000e+00 2700
15 TraesCS4A01G211900 chrUn 97.119 590 16 1 151 740 43103235 43102647 0.000000e+00 994
16 TraesCS4A01G211900 chr1D 96.721 61 1 1 1 60 54558040 54558100 1.530000e-17 100


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 TraesCS4A01G211900 chr4A 507106850 507109270 2420 True 4471.0 4471 100.0000 1 2421 1 chr4A.!!$R1 2420
1 TraesCS4A01G211900 chr5D 545192042 545195498 3456 False 2033.5 2813 97.0480 1 2421 2 chr5D.!!$F1 2420
2 TraesCS4A01G211900 chr6D 346456 349913 3457 True 2026.0 2785 97.0350 1 2421 2 chr6D.!!$R1 2420
3 TraesCS4A01G211900 chr4D 400124055 400127513 3458 False 2023.5 2780 97.0050 1 2421 2 chr4D.!!$F1 2420
4 TraesCS4A01G211900 chr3A 40976708 40980165 3457 True 2003.0 2750 96.7215 1 2421 2 chr3A.!!$R1 2420
5 TraesCS4A01G211900 chr3A 500028382 500031040 2658 False 1348.5 1441 96.6730 1 1621 2 chr3A.!!$F2 1620
6 TraesCS4A01G211900 chr3A 500038670 500039473 803 False 1286.0 1286 95.5280 1617 2421 1 chr3A.!!$F1 804
7 TraesCS4A01G211900 chr1A 45390944 45394392 3448 False 1971.0 2702 96.3130 1 2421 2 chr1A.!!$F1 2420
8 TraesCS4A01G211900 chrUn 43099983 43103235 3252 True 1847.0 2700 96.7870 151 2372 2 chrUn.!!$R1 2221

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
376 378 1.067565 CGCGAGACCTATATGCCATGT 60.068 52.381 0.0 0.0 0.0 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1535 2578 0.179018 ACTCGCCTTTTGCTTCTGGT 60.179 50.0 0.0 0.0 38.05 4.0 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
45 46 9.147732 AGAAAGAGATTTGAATACCCAAAAAGT 57.852 29.630 0.00 0.00 39.20 2.66
247 249 7.803131 TGGCTATATCGATGTAGATACTACCT 58.197 38.462 27.53 0.00 36.10 3.08
376 378 1.067565 CGCGAGACCTATATGCCATGT 60.068 52.381 0.00 0.00 0.00 3.21
380 382 4.825422 CGAGACCTATATGCCATGTCATT 58.175 43.478 0.00 0.00 0.00 2.57
458 460 3.003394 TGGAGATACAAATGTGCCAGG 57.997 47.619 0.00 0.00 0.00 4.45
496 498 3.118956 CGAAAGTTGGTCTAGATCTGGCT 60.119 47.826 5.18 0.00 0.00 4.75
565 567 2.630098 GTTGATCCCGGAGATGATGAGA 59.370 50.000 0.73 0.00 34.42 3.27
657 659 3.958704 ACTCGACGAATCTGATGATGAC 58.041 45.455 0.00 0.00 32.44 3.06
724 726 3.766591 GAGAGAAACAGATCTGTCCCTGA 59.233 47.826 28.01 0.00 44.13 3.86
752 1795 9.338622 GCTTGGTGTTATATAGGTACAATTTCT 57.661 33.333 0.00 0.00 0.00 2.52
808 1851 6.541641 TGCATGGCAATTTAAAAACAGAGTTT 59.458 30.769 0.00 0.00 34.76 2.66
838 1881 7.617225 TCTGGGATTTTAATCGACAGAAAGTA 58.383 34.615 18.20 4.36 42.15 2.24
839 1882 8.098286 TCTGGGATTTTAATCGACAGAAAGTAA 58.902 33.333 18.20 3.89 42.15 2.24
870 1913 2.529389 AAGGGGCGAGGTGTCCTT 60.529 61.111 0.00 0.00 44.07 3.36
922 1965 2.037641 GCCAATGGTTCCTCAAAGCTTT 59.962 45.455 5.69 5.69 36.31 3.51
1057 2100 4.842531 TGGTCTGCCATTGATTCTTCTA 57.157 40.909 0.00 0.00 40.46 2.10
1309 2352 0.731417 CTGATGCTCAAAGAAGGGCG 59.269 55.000 0.00 0.00 0.00 6.13
1535 2578 5.461032 AGCCACAAAAATACGGAAAATCA 57.539 34.783 0.00 0.00 0.00 2.57
1582 2625 2.735134 GCTGGTTCAAAATCGTACTCGT 59.265 45.455 0.00 0.00 38.33 4.18
1639 2682 1.153353 AATGCACCTTTGTACGGTCG 58.847 50.000 0.00 0.00 30.82 4.79
1726 2769 6.489022 GGAACCAACTATTCTACAACTTTGGT 59.511 38.462 0.00 0.00 45.60 3.67
1928 2971 4.080299 GCCAGATTAGGGAGAAAGAAGGAA 60.080 45.833 0.00 0.00 0.00 3.36
1963 3006 6.534793 GTCCAATTTCAAGTGAAGAGCAAAAA 59.465 34.615 0.00 0.00 35.21 1.94
2018 3061 4.773674 TGGAAATGACATCATTGAAGCCTT 59.226 37.500 7.86 0.00 45.06 4.35
2123 3166 3.195825 CCTCGAGGTTCATGACTTAAGGT 59.804 47.826 24.04 0.00 0.00 3.50
2207 3250 3.829026 GGAAAAACAGCTTGAGGAGGAAT 59.171 43.478 0.00 0.00 0.00 3.01
2322 3365 2.128035 GCAGATATTGGGAACTCGACG 58.872 52.381 0.00 0.00 0.00 5.12
2326 3369 1.784358 TATTGGGAACTCGACGGGAT 58.216 50.000 0.00 0.00 0.00 3.85
2329 3372 0.686441 TGGGAACTCGACGGGATGAT 60.686 55.000 0.00 0.00 0.00 2.45
2415 3458 5.255687 TCTTGTGAGTTATCCATGCAATGT 58.744 37.500 0.00 0.00 44.81 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 1.567175 ACCCCTAACAACAACACCACT 59.433 47.619 0.00 0.00 0.00 4.00
44 45 1.679153 CACCCCTAACAACAACACCAC 59.321 52.381 0.00 0.00 0.00 4.16
45 46 1.564818 TCACCCCTAACAACAACACCA 59.435 47.619 0.00 0.00 0.00 4.17
376 378 5.257082 TCGTCATCATTTCCTACGAATGA 57.743 39.130 2.43 2.43 44.81 2.57
380 382 3.634910 TCCATCGTCATCATTTCCTACGA 59.365 43.478 0.00 0.00 45.44 3.43
458 460 0.387929 TTCGACATCCCCGTCTATGC 59.612 55.000 0.00 0.00 33.54 3.14
496 498 1.227823 CACCACTCGCACCTTCCAA 60.228 57.895 0.00 0.00 0.00 3.53
565 567 7.960262 TCACAGCTATCACTATCAGATTCAAT 58.040 34.615 0.00 0.00 0.00 2.57
724 726 9.640952 AAATTGTACCTATATAACACCAAGCAT 57.359 29.630 0.00 0.00 0.00 3.79
752 1795 4.253685 GAGCCAAGTCAACAGTAATGCTA 58.746 43.478 0.00 0.00 0.00 3.49
808 1851 7.165485 TCTGTCGATTAAAATCCCAGAAAAGA 58.835 34.615 13.33 4.34 37.16 2.52
838 1881 2.899900 GCCCCTTCTTCTTTTGACCATT 59.100 45.455 0.00 0.00 0.00 3.16
839 1882 2.529632 GCCCCTTCTTCTTTTGACCAT 58.470 47.619 0.00 0.00 0.00 3.55
870 1913 3.008594 TCTTGGCGACCTTGATTCCTTTA 59.991 43.478 0.00 0.00 0.00 1.85
1057 2100 4.264253 TCAGCAACGATTGAATCCTTCAT 58.736 39.130 0.00 0.00 39.84 2.57
1105 2148 4.826183 GGAGAGGCTATGAAAAATGCTGAT 59.174 41.667 0.00 0.00 0.00 2.90
1147 2190 4.888326 AGGAATGATGATAGGAGTCTGC 57.112 45.455 0.00 0.00 0.00 4.26
1157 2200 7.286316 CCACTTAGCCTAAAAAGGAATGATGAT 59.714 37.037 0.00 0.00 0.00 2.45
1309 2352 5.055144 GGAGTTACATCCTCGGGTTTATTC 58.945 45.833 0.00 0.00 36.35 1.75
1369 2412 8.803235 ACAGAAGTAACCTGGAATTTTAAATCC 58.197 33.333 0.00 1.47 36.03 3.01
1427 2470 5.812642 CACCTAAGAGGCATGTTGTAACTAG 59.187 44.000 0.00 0.00 39.63 2.57
1471 2514 9.407380 ACAATATAATGAGAGGCATGTTGTAAA 57.593 29.630 0.00 0.00 37.28 2.01
1517 2560 6.642707 TCTGGTGATTTTCCGTATTTTTGT 57.357 33.333 0.00 0.00 0.00 2.83
1518 2561 6.089417 GCTTCTGGTGATTTTCCGTATTTTTG 59.911 38.462 0.00 0.00 0.00 2.44
1535 2578 0.179018 ACTCGCCTTTTGCTTCTGGT 60.179 50.000 0.00 0.00 38.05 4.00
1554 2597 7.497595 AGTACGATTTTGAACCAGCTATATGA 58.502 34.615 0.00 0.00 0.00 2.15
1582 2625 9.642343 TTTGAGTACCTTCTCATAGCTAATCTA 57.358 33.333 0.00 0.00 42.84 1.98
1726 2769 6.709018 TCCATTTCGTGTATGAGTGATCTA 57.291 37.500 0.00 0.00 0.00 1.98
2001 3044 2.821378 CCACAAGGCTTCAATGATGTCA 59.179 45.455 0.00 0.00 0.00 3.58
2002 3045 3.498927 CCACAAGGCTTCAATGATGTC 57.501 47.619 0.00 0.00 0.00 3.06
2018 3061 1.829456 CCATGTATCCTCGGCCACA 59.171 57.895 2.24 0.00 0.00 4.17
2123 3166 3.529533 CCTGTTGTTCAACAATTTGCCA 58.470 40.909 17.14 0.00 40.59 4.92
2207 3250 1.197812 TCTCTCTGCCTTGCTATGCA 58.802 50.000 0.00 0.00 36.47 3.96
2326 3369 6.459985 GCATTTGTATTACCTGATGTGCATCA 60.460 38.462 13.43 13.43 44.83 3.07
2329 3372 4.949238 AGCATTTGTATTACCTGATGTGCA 59.051 37.500 0.00 0.00 0.00 4.57
2387 3430 8.523915 TTGCATGGATAACTCACAAGATTTAT 57.476 30.769 0.00 0.00 33.73 1.40


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

AutoCloner maintained by Alex Coulton.