Multiple sequence alignment - TraesCS7A01G052200

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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 TraesCS7A01G052200 chr7A 100.000 2359 0 0 1 2359 25224713 25222355 0.000000e+00 4357
1 TraesCS7A01G052200 chr7A 92.929 2079 128 10 1 2065 116468467 116466394 0.000000e+00 3007
2 TraesCS7A01G052200 chr5A 96.698 2362 74 4 1 2359 539825676 539823316 0.000000e+00 3927
3 TraesCS7A01G052200 chr5A 96.530 2363 76 6 1 2359 374024447 374022087 0.000000e+00 3904
4 TraesCS7A01G052200 chr5A 93.750 80 3 1 305 382 630722938 630723017 4.120000e-23 119
5 TraesCS7A01G052200 chr6A 95.093 2364 109 7 1 2359 471275619 471273258 0.000000e+00 3716
6 TraesCS7A01G052200 chr3A 96.134 2095 74 6 1 2090 496386020 496388112 0.000000e+00 3413
7 TraesCS7A01G052200 chr3D 93.575 2070 120 10 2 2065 578589352 578591414 0.000000e+00 3073
8 TraesCS7A01G052200 chr4D 92.334 2074 129 15 1 2065 168888698 168890750 0.000000e+00 2922
9 TraesCS7A01G052200 chr2D 95.655 1703 67 6 661 2359 92462904 92464603 0.000000e+00 2728
10 TraesCS7A01G052200 chr2D 91.813 171 14 0 62 232 92462666 92462836 3.030000e-59 239
11 TraesCS7A01G052200 chr2D 95.522 67 3 0 567 633 92462839 92462905 8.920000e-20 108
12 TraesCS7A01G052200 chr5B 95.557 1238 53 2 1124 2359 617730963 617729726 0.000000e+00 1980
13 TraesCS7A01G052200 chr1B 96.846 539 15 2 1822 2359 563481025 563480488 0.000000e+00 900
14 TraesCS7A01G052200 chrUn 96.660 539 17 1 1822 2359 280615524 280614986 0.000000e+00 894
15 TraesCS7A01G052200 chrUn 96.481 540 15 3 1822 2359 1841802 1842339 0.000000e+00 889
16 TraesCS7A01G052200 chr2B 94.004 567 31 2 585 1150 724448988 724448424 0.000000e+00 856
17 TraesCS7A01G052200 chr5D 92.714 398 27 1 1 396 61858922 61859319 7.310000e-160 573
18 TraesCS7A01G052200 chr4B 91.597 119 10 0 1 119 603004335 603004453 5.220000e-37 165
19 TraesCS7A01G052200 chr4B 92.632 95 7 0 346 440 642751932 642751838 1.140000e-28 137


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 TraesCS7A01G052200 chr7A 25222355 25224713 2358 True 4357 4357 100.000 1 2359 1 chr7A.!!$R1 2358
1 TraesCS7A01G052200 chr7A 116466394 116468467 2073 True 3007 3007 92.929 1 2065 1 chr7A.!!$R2 2064
2 TraesCS7A01G052200 chr5A 539823316 539825676 2360 True 3927 3927 96.698 1 2359 1 chr5A.!!$R2 2358
3 TraesCS7A01G052200 chr5A 374022087 374024447 2360 True 3904 3904 96.530 1 2359 1 chr5A.!!$R1 2358
4 TraesCS7A01G052200 chr6A 471273258 471275619 2361 True 3716 3716 95.093 1 2359 1 chr6A.!!$R1 2358
5 TraesCS7A01G052200 chr3A 496386020 496388112 2092 False 3413 3413 96.134 1 2090 1 chr3A.!!$F1 2089
6 TraesCS7A01G052200 chr3D 578589352 578591414 2062 False 3073 3073 93.575 2 2065 1 chr3D.!!$F1 2063
7 TraesCS7A01G052200 chr4D 168888698 168890750 2052 False 2922 2922 92.334 1 2065 1 chr4D.!!$F1 2064
8 TraesCS7A01G052200 chr2D 92462666 92464603 1937 False 1025 2728 94.330 62 2359 3 chr2D.!!$F1 2297
9 TraesCS7A01G052200 chr5B 617729726 617730963 1237 True 1980 1980 95.557 1124 2359 1 chr5B.!!$R1 1235
10 TraesCS7A01G052200 chr1B 563480488 563481025 537 True 900 900 96.846 1822 2359 1 chr1B.!!$R1 537
11 TraesCS7A01G052200 chrUn 280614986 280615524 538 True 894 894 96.660 1822 2359 1 chrUn.!!$R1 537
12 TraesCS7A01G052200 chrUn 1841802 1842339 537 False 889 889 96.481 1822 2359 1 chrUn.!!$F1 537
13 TraesCS7A01G052200 chr2B 724448424 724448988 564 True 856 856 94.004 585 1150 1 chr2B.!!$R1 565

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
282 284 2.203139 CTCACACCACGCCAACCA 60.203 61.111 0.00 0.0 0.00 3.67 F
1017 1033 1.751544 GATGCACCATGCTGCTCCA 60.752 57.895 13.92 0.0 45.31 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1133 1149 0.238817 GATCAGCGCCGACTAGTAGG 59.761 60.000 17.1 17.1 0.0 3.18 R
2265 2422 2.643551 ACAGGGTCAACAACAGTTCAG 58.356 47.619 0.0 0.0 0.0 3.02 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
74 75 7.023197 GTAGTTCACCTACAATTTTGTGTGT 57.977 36.000 6.21 0.84 44.65 3.72
98 100 2.899976 TCACACTGAGAGTTCGCAAAA 58.100 42.857 0.00 0.00 0.00 2.44
124 126 6.432581 AGTTTTTATCTCCCCAAATAGGTCC 58.567 40.000 0.00 0.00 34.66 4.46
150 152 3.359033 AGTGTGTGCTGATTGCCATTAT 58.641 40.909 0.00 0.00 42.00 1.28
282 284 2.203139 CTCACACCACGCCAACCA 60.203 61.111 0.00 0.00 0.00 3.67
437 442 4.454847 AGTGCATCTGATGAAACAAGAGTG 59.545 41.667 21.30 0.00 0.00 3.51
623 630 3.450457 TGCCCAATCTGTTGTTCAAGTTT 59.550 39.130 0.00 0.00 33.36 2.66
1017 1033 1.751544 GATGCACCATGCTGCTCCA 60.752 57.895 13.92 0.00 45.31 3.86
1133 1149 1.416401 TGACAAGGTCAGGTTCAGGTC 59.584 52.381 0.00 0.00 37.67 3.85
1150 1166 1.094073 GTCCTACTAGTCGGCGCTGA 61.094 60.000 16.69 16.69 0.00 4.26
1292 1308 1.613630 AGGGGACTGCAAGGACGAT 60.614 57.895 0.00 0.00 41.13 3.73
1307 1323 0.968901 ACGATGAGGGCGTCAAGGTA 60.969 55.000 14.47 0.00 39.19 3.08
1567 1590 5.198965 GACATCCACAAGGTAGTACTCCTA 58.801 45.833 12.50 0.58 34.56 2.94
1797 1821 7.586349 AGTATGATTCCAAGGAAACATATGGT 58.414 34.615 25.11 15.20 45.09 3.55
2162 2319 6.647334 TTCTACAGATGTTGCCAAATGAAA 57.353 33.333 0.00 0.00 0.00 2.69
2265 2422 7.209475 TGAAATCCTGGTTCATTTTCAAAGAC 58.791 34.615 0.00 0.00 34.39 3.01
2266 2423 6.983906 AATCCTGGTTCATTTTCAAAGACT 57.016 33.333 0.00 0.00 0.00 3.24
2270 2427 5.979517 CCTGGTTCATTTTCAAAGACTGAAC 59.020 40.000 11.22 11.22 43.90 3.18
2295 2452 4.974645 TGTTGACCCTGTTCTTCTATGT 57.025 40.909 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 1.869754 GCGAACTCTCAGTGTGAGCAA 60.870 52.381 19.62 0.0 43.95 3.91
98 100 7.285340 ACCTATTTGGGGAGATAAAAACTCT 57.715 36.000 0.00 0.0 41.11 3.24
124 126 1.068748 GCAATCAGCACACACTTCTGG 60.069 52.381 0.00 0.0 44.79 3.86
150 152 2.288666 GCCATCGACAAATTCAGCCTA 58.711 47.619 0.00 0.0 0.00 3.93
209 211 8.697507 ACCTTCAATTCACTATTTCAGTTCTT 57.302 30.769 0.00 0.0 34.26 2.52
282 284 3.403038 GCCACTATGTTGTGAAGTCACT 58.597 45.455 12.43 0.0 46.55 3.41
431 436 1.072965 CAGGGCCACTTCTTCACTCTT 59.927 52.381 6.18 0.0 0.00 2.85
437 442 1.039856 TTTTGCAGGGCCACTTCTTC 58.960 50.000 6.18 0.0 0.00 2.87
486 493 9.474313 AGCCCTAAATCATTTCACTTTGTAATA 57.526 29.630 0.00 0.0 0.00 0.98
492 499 7.544804 AAGAAGCCCTAAATCATTTCACTTT 57.455 32.000 0.00 0.0 0.00 2.66
623 630 8.150945 GTCTGAATCTAATATTCAACTAGCCCA 58.849 37.037 0.00 0.0 37.55 5.36
1017 1033 2.273449 CTCAGCCGGCCTTCCAAT 59.727 61.111 26.15 0.0 0.00 3.16
1113 1129 1.416401 GACCTGAACCTGACCTTGTCA 59.584 52.381 0.00 0.0 40.50 3.58
1133 1149 0.238817 GATCAGCGCCGACTAGTAGG 59.761 60.000 17.10 17.1 0.00 3.18
1292 1308 0.830444 AGTGTACCTTGACGCCCTCA 60.830 55.000 0.00 0.0 0.00 3.86
1307 1323 2.260869 GGCACCAACGATGCAGTGT 61.261 57.895 0.00 0.0 45.27 3.55
1567 1590 2.123033 GGGCACTTGGGGTTTGGT 60.123 61.111 0.00 0.0 0.00 3.67
1797 1821 8.028354 CCAATGTGAACAGTTTCAGCATTATTA 58.972 33.333 11.44 0.0 42.60 0.98
2162 2319 4.221703 CCTAAGGAGAGACATGTTGACACT 59.778 45.833 0.00 0.0 0.00 3.55
2265 2422 2.643551 ACAGGGTCAACAACAGTTCAG 58.356 47.619 0.00 0.0 0.00 3.02
2266 2423 2.799126 ACAGGGTCAACAACAGTTCA 57.201 45.000 0.00 0.0 0.00 3.18
2270 2427 3.545703 AGAAGAACAGGGTCAACAACAG 58.454 45.455 0.00 0.0 0.00 3.16
2295 2452 9.869844 CAAAATGCGACATTTTTACCATTTAAA 57.130 25.926 20.50 0.0 33.31 1.52


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

AutoCloner maintained by Alex Coulton.