Multiple sequence alignment - TraesCS7A01G118600

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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 TraesCS7A01G118600 chr7A 100.000 3030 0 0 1 3030 76483149 76480120 0.000000e+00 5596
1 TraesCS7A01G118600 chr7A 98.353 2611 38 1 420 3030 76426420 76423815 0.000000e+00 4578
2 TraesCS7A01G118600 chr7A 98.238 2611 41 1 420 3030 76399724 76397119 0.000000e+00 4562
3 TraesCS7A01G118600 chr7A 82.256 2012 276 45 420 2399 76292361 76290399 0.000000e+00 1663
4 TraesCS7A01G118600 chr7A 80.921 1672 259 47 974 2614 76356113 76354471 0.000000e+00 1266
5 TraesCS7A01G118600 chr7A 89.198 648 53 6 2385 3024 76367178 76366540 0.000000e+00 793
6 TraesCS7A01G118600 chr7A 93.593 437 15 8 1 425 76400231 76399796 9.160000e-180 640
7 TraesCS7A01G118600 chr7A 93.364 437 16 8 1 425 76426927 76426492 4.260000e-178 634
8 TraesCS7A01G118600 chr7B 93.030 2640 147 16 420 3030 12381931 12379300 0.000000e+00 3821
9 TraesCS7A01G118600 chr7B 82.033 1436 223 25 984 2398 12364511 12363090 0.000000e+00 1190
10 TraesCS7A01G118600 chr7B 90.293 443 21 8 1 425 12382451 12382013 7.340000e-156 560
11 TraesCS7A01G118600 chr7B 77.686 242 35 11 1 234 12206806 12206576 2.450000e-26 130
12 TraesCS7A01G118600 chr7B 89.583 96 9 1 1 96 12241936 12241842 1.480000e-23 121
13 TraesCS7A01G118600 chr7D 93.501 1831 98 6 1219 3030 69811214 69809386 0.000000e+00 2702
14 TraesCS7A01G118600 chr7D 82.960 2007 269 45 420 2399 69710707 69708747 0.000000e+00 1744
15 TraesCS7A01G118600 chr7D 80.630 1714 259 54 967 2641 69782321 69780642 0.000000e+00 1258
16 TraesCS7A01G118600 chr7D 80.583 1715 258 56 967 2641 69806016 69804337 0.000000e+00 1253
17 TraesCS7A01G118600 chr7D 86.352 806 72 20 438 1217 69812092 69811299 0.000000e+00 845
18 TraesCS7A01G118600 chr7D 83.149 451 47 14 1 425 69812640 69812193 4.740000e-103 385
19 TraesCS7A01G118600 chr7D 76.451 293 44 16 1 281 69777511 69777232 5.270000e-28 135
20 TraesCS7A01G118600 chr7D 76.451 293 44 16 1 281 69801229 69800950 5.270000e-28 135
21 TraesCS7A01G118600 chr7D 90.110 91 8 1 3 93 69783065 69782976 1.910000e-22 117
22 TraesCS7A01G118600 chrUn 97.615 1216 24 1 420 1635 386058985 386057775 0.000000e+00 2080
23 TraesCS7A01G118600 chrUn 93.038 316 10 5 122 425 386059372 386059057 4.610000e-123 451
24 TraesCS7A01G118600 chr6A 80.346 1618 249 48 965 2546 106736887 106738471 0.000000e+00 1162


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 TraesCS7A01G118600 chr7A 76480120 76483149 3029 True 5596.000000 5596 100.0000 1 3030 1 chr7A.!!$R4 3029
1 TraesCS7A01G118600 chr7A 76423815 76426927 3112 True 2606.000000 4578 95.8585 1 3030 2 chr7A.!!$R6 3029
2 TraesCS7A01G118600 chr7A 76397119 76400231 3112 True 2601.000000 4562 95.9155 1 3030 2 chr7A.!!$R5 3029
3 TraesCS7A01G118600 chr7A 76290399 76292361 1962 True 1663.000000 1663 82.2560 420 2399 1 chr7A.!!$R1 1979
4 TraesCS7A01G118600 chr7A 76354471 76356113 1642 True 1266.000000 1266 80.9210 974 2614 1 chr7A.!!$R2 1640
5 TraesCS7A01G118600 chr7A 76366540 76367178 638 True 793.000000 793 89.1980 2385 3024 1 chr7A.!!$R3 639
6 TraesCS7A01G118600 chr7B 12379300 12382451 3151 True 2190.500000 3821 91.6615 1 3030 2 chr7B.!!$R4 3029
7 TraesCS7A01G118600 chr7B 12363090 12364511 1421 True 1190.000000 1190 82.0330 984 2398 1 chr7B.!!$R3 1414
8 TraesCS7A01G118600 chr7D 69708747 69710707 1960 True 1744.000000 1744 82.9600 420 2399 1 chr7D.!!$R1 1979
9 TraesCS7A01G118600 chr7D 69800950 69812640 11690 True 1064.000000 2702 84.0072 1 3030 5 chr7D.!!$R3 3029
10 TraesCS7A01G118600 chr7D 69777232 69783065 5833 True 503.333333 1258 82.3970 1 2641 3 chr7D.!!$R2 2640
11 TraesCS7A01G118600 chrUn 386057775 386059372 1597 True 1265.500000 2080 95.3265 122 1635 2 chrUn.!!$R1 1513
12 TraesCS7A01G118600 chr6A 106736887 106738471 1584 False 1162.000000 1162 80.3460 965 2546 1 chr6A.!!$F1 1581

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
775 952 2.498167 GGCCTCATCTTCGCACAATAT 58.502 47.619 0.0 0.0 0.0 1.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2254 2566 4.019321 AGAAAGGTTCCGGAGATTTGATCA 60.019 41.667 3.34 0.0 0.0 2.92 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
90 91 4.280929 GGAACAAAGAAAAGCTGGTGGTAT 59.719 41.667 0.00 0.00 0.00 2.73
260 288 8.739039 CAGGTGAAAATGTTATTGGATAAGACA 58.261 33.333 0.00 0.00 0.00 3.41
319 351 4.263860 TGAATGTGGAGGATTGGTCAATCA 60.264 41.667 20.88 4.94 46.77 2.57
450 584 3.057596 GTGATCAATTTCAAACGCAGGGA 60.058 43.478 0.00 0.00 0.00 4.20
454 588 3.052036 CAATTTCAAACGCAGGGACAAG 58.948 45.455 0.00 0.00 0.00 3.16
477 611 8.777413 CAAGCTCTAAATTACAATGCAGCTATA 58.223 33.333 0.00 0.00 34.89 1.31
727 904 8.515414 GTTAATACTCCCTTATGCCATCAATTC 58.485 37.037 0.00 0.00 0.00 2.17
728 905 4.524802 ACTCCCTTATGCCATCAATTCA 57.475 40.909 0.00 0.00 0.00 2.57
729 906 4.870636 ACTCCCTTATGCCATCAATTCAA 58.129 39.130 0.00 0.00 0.00 2.69
730 907 5.461327 ACTCCCTTATGCCATCAATTCAAT 58.539 37.500 0.00 0.00 0.00 2.57
731 908 5.901276 ACTCCCTTATGCCATCAATTCAATT 59.099 36.000 0.00 0.00 0.00 2.32
775 952 2.498167 GGCCTCATCTTCGCACAATAT 58.502 47.619 0.00 0.00 0.00 1.28
1087 1275 1.673168 CAGAGGTCCAAGCCTATTGC 58.327 55.000 0.00 0.00 39.34 3.56
1277 1563 2.285083 GTCAACATATTGGCAGCGGTA 58.715 47.619 0.00 0.00 40.37 4.02
1849 2147 2.885266 GTCCGTAGAGCCATCTGTGATA 59.115 50.000 0.00 0.00 36.96 2.15
2254 2566 7.419711 TGAAATAGACTAAGGGAGAACGAAT 57.580 36.000 0.00 0.00 0.00 3.34
2798 3126 2.445145 TCCAAAGGTTGTCTCCCATCAA 59.555 45.455 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 91 7.057894 ACAAAGGAGTGAAATAGTTTGGTACA 58.942 34.615 0.00 0.00 30.75 2.90
228 241 8.017418 TCCAATAACATTTTCACCTGTTTTCT 57.983 30.769 0.00 0.00 36.92 2.52
260 288 5.759059 TGAACTATTTCAGGATTGGAGCAT 58.241 37.500 0.00 0.00 36.79 3.79
450 584 5.416952 AGCTGCATTGTAATTTAGAGCTTGT 59.583 36.000 1.02 0.00 31.53 3.16
477 611 2.014068 GCCTGAGAGCCGCTGTTATTT 61.014 52.381 0.00 0.00 0.00 1.40
727 904 5.118664 CGCACCGGACTCAATAGTATAATTG 59.881 44.000 9.46 0.00 35.56 2.32
728 905 5.010314 TCGCACCGGACTCAATAGTATAATT 59.990 40.000 9.46 0.00 35.56 1.40
729 906 4.521639 TCGCACCGGACTCAATAGTATAAT 59.478 41.667 9.46 0.00 35.56 1.28
730 907 3.884693 TCGCACCGGACTCAATAGTATAA 59.115 43.478 9.46 0.00 35.56 0.98
731 908 3.479489 TCGCACCGGACTCAATAGTATA 58.521 45.455 9.46 0.00 35.56 1.47
775 952 2.422597 CTGTCAAGATTGTTGGCGGTA 58.577 47.619 0.00 0.00 0.00 4.02
1087 1275 1.134280 CACCTTCAGTATGCCAGGGAG 60.134 57.143 0.00 0.00 39.76 4.30
1142 1338 6.265577 AGATAGCAAACAAACAGTGACAAAC 58.734 36.000 0.00 0.00 0.00 2.93
1277 1563 3.621892 GAACACGTAGGAGCCGCGT 62.622 63.158 4.92 6.41 39.59 6.01
1849 2147 6.969993 TTACTAGTGCTTTGGGTGAAATTT 57.030 33.333 5.39 0.00 0.00 1.82
1995 2293 5.764686 TCTGCAACAAAGTCTTGTATCACAT 59.235 36.000 0.00 0.00 45.25 3.21
2215 2520 8.127150 AGTCTATTTCATGTCGATATGATCCA 57.873 34.615 23.25 12.29 36.97 3.41
2254 2566 4.019321 AGAAAGGTTCCGGAGATTTGATCA 60.019 41.667 3.34 0.00 0.00 2.92
2324 2640 4.160252 GGCCCAGCTAAGAAAATTTGATCA 59.840 41.667 0.00 0.00 0.00 2.92
2798 3126 9.942131 CAAGAGAAATTGATAGCCGGAAGGAGT 62.942 44.444 5.05 0.00 42.99 3.85


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

AutoCloner maintained by Alex Coulton.