Multiple sequence alignment - TraesCS7A01G397600

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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 TraesCS7A01G397600 chr7A 100.000 3214 0 0 1 3214 576403208 576406421 0.000000e+00 5936
1 TraesCS7A01G397600 chr7A 97.303 3114 65 4 106 3214 658706742 658703643 0.000000e+00 5267
2 TraesCS7A01G397600 chr7A 96.364 110 3 1 1 110 658707574 658707466 2.550000e-41 180
3 TraesCS7A01G397600 chr4A 97.379 2594 60 4 625 3214 628881991 628884580 0.000000e+00 4407
4 TraesCS7A01G397600 chr4A 93.706 143 9 0 399 541 715634096 715633954 6.980000e-52 215
5 TraesCS7A01G397600 chr4A 98.438 64 0 1 547 609 715621686 715621623 9.430000e-21 111
6 TraesCS7A01G397600 chr1A 96.839 2594 57 5 625 3214 13813934 13811362 0.000000e+00 4313
7 TraesCS7A01G397600 chr1A 96.572 2596 61 7 625 3214 34337446 34340019 0.000000e+00 4276
8 TraesCS7A01G397600 chr1A 96.078 2601 76 6 619 3214 566074881 566072302 0.000000e+00 4215
9 TraesCS7A01G397600 chr5A 96.647 2595 74 4 624 3214 697625372 697627957 0.000000e+00 4298
10 TraesCS7A01G397600 chr5A 95.644 2594 66 25 625 3214 546845988 546848538 0.000000e+00 4120
11 TraesCS7A01G397600 chr5A 95.605 2116 84 6 624 2734 640389062 640386951 0.000000e+00 3384
12 TraesCS7A01G397600 chr2A 96.453 2594 67 5 625 3214 752883172 752880600 0.000000e+00 4257
13 TraesCS7A01G397600 chr5D 94.489 2595 83 29 625 3214 356119496 356116957 0.000000e+00 3945
14 TraesCS7A01G397600 chr4D 94.194 2618 81 29 624 3214 392724847 392722274 0.000000e+00 3927
15 TraesCS7A01G397600 chr7D 94.039 2617 78 31 625 3214 538836051 538838616 0.000000e+00 3897
16 TraesCS7A01G397600 chr7D 92.704 2618 84 30 624 3214 426837237 426834700 0.000000e+00 3677
17 TraesCS7A01G397600 chr7D 94.236 399 16 3 233 624 569232265 569231867 1.280000e-168 603
18 TraesCS7A01G397600 chr7D 94.118 136 8 0 1 136 569233676 569233541 1.170000e-49 207
19 TraesCS7A01G397600 chr7D 91.209 91 8 0 149 239 569233556 569233466 1.210000e-24 124
20 TraesCS7A01G397600 chr3D 93.662 2619 77 34 624 3214 52842441 52844998 0.000000e+00 3834


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 TraesCS7A01G397600 chr7A 576403208 576406421 3213 False 5936.000000 5936 100.000000 1 3214 1 chr7A.!!$F1 3213
1 TraesCS7A01G397600 chr7A 658703643 658707574 3931 True 2723.500000 5267 96.833500 1 3214 2 chr7A.!!$R1 3213
2 TraesCS7A01G397600 chr4A 628881991 628884580 2589 False 4407.000000 4407 97.379000 625 3214 1 chr4A.!!$F1 2589
3 TraesCS7A01G397600 chr1A 13811362 13813934 2572 True 4313.000000 4313 96.839000 625 3214 1 chr1A.!!$R1 2589
4 TraesCS7A01G397600 chr1A 34337446 34340019 2573 False 4276.000000 4276 96.572000 625 3214 1 chr1A.!!$F1 2589
5 TraesCS7A01G397600 chr1A 566072302 566074881 2579 True 4215.000000 4215 96.078000 619 3214 1 chr1A.!!$R2 2595
6 TraesCS7A01G397600 chr5A 697625372 697627957 2585 False 4298.000000 4298 96.647000 624 3214 1 chr5A.!!$F2 2590
7 TraesCS7A01G397600 chr5A 546845988 546848538 2550 False 4120.000000 4120 95.644000 625 3214 1 chr5A.!!$F1 2589
8 TraesCS7A01G397600 chr5A 640386951 640389062 2111 True 3384.000000 3384 95.605000 624 2734 1 chr5A.!!$R1 2110
9 TraesCS7A01G397600 chr2A 752880600 752883172 2572 True 4257.000000 4257 96.453000 625 3214 1 chr2A.!!$R1 2589
10 TraesCS7A01G397600 chr5D 356116957 356119496 2539 True 3945.000000 3945 94.489000 625 3214 1 chr5D.!!$R1 2589
11 TraesCS7A01G397600 chr4D 392722274 392724847 2573 True 3927.000000 3927 94.194000 624 3214 1 chr4D.!!$R1 2590
12 TraesCS7A01G397600 chr7D 538836051 538838616 2565 False 3897.000000 3897 94.039000 625 3214 1 chr7D.!!$F1 2589
13 TraesCS7A01G397600 chr7D 426834700 426837237 2537 True 3677.000000 3677 92.704000 624 3214 1 chr7D.!!$R1 2590
14 TraesCS7A01G397600 chr7D 569231867 569233676 1809 True 311.333333 603 93.187667 1 624 3 chr7D.!!$R2 623
15 TraesCS7A01G397600 chr3D 52842441 52844998 2557 False 3834.000000 3834 93.662000 624 3214 1 chr3D.!!$F1 2590

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
527 1257 0.105039 GGGGTCGAGTTGGATGCTAG 59.895 60.0 0.0 0.0 0.00 3.42 F
1047 2380 0.030773 CATCCGACACCGACGATGAT 59.969 55.0 0.0 0.0 36.93 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1551 3257 9.066892 TGCAGTAACAAAGAAATTCAGTTAGAT 57.933 29.630 0.0 0.0 0.0 1.98 R
2921 4801 1.448540 GTCGCACAGCCAGCTATGT 60.449 57.895 0.0 0.0 0.0 2.29 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
239 968 3.136443 CAGGGGATGCAAGTACAATCCTA 59.864 47.826 13.39 0.00 0.00 2.94
317 1046 4.651778 AGGATTGTTTTTCGGTCAGATCA 58.348 39.130 0.00 0.00 0.00 2.92
380 1110 1.800286 GCAGGCAGGCGAAATTTCATC 60.800 52.381 17.99 8.96 0.00 2.92
417 1147 1.836166 TCAATCTTCTGGAGAGCCCTG 59.164 52.381 0.00 0.00 37.93 4.45
450 1180 3.841078 CCTCCAAGGGTCCACCAT 58.159 61.111 0.00 0.00 43.89 3.55
485 1215 2.368548 TCGCACATAACAGCCATCCTAT 59.631 45.455 0.00 0.00 0.00 2.57
527 1257 0.105039 GGGGTCGAGTTGGATGCTAG 59.895 60.000 0.00 0.00 0.00 3.42
545 1275 2.484742 AGATGCTTGCTGTGTCATCA 57.515 45.000 0.00 0.00 38.15 3.07
556 1286 4.092771 CTGTGTCATCAGCAATTTGAGG 57.907 45.455 0.00 0.00 0.00 3.86
566 1297 1.797320 CAATTTGAGGATGGGGCCAT 58.203 50.000 4.39 0.00 39.69 4.40
771 1513 3.062042 CGTCCAGTTAGCCGTTTTAACT 58.938 45.455 0.00 0.00 40.91 2.24
1047 2380 0.030773 CATCCGACACCGACGATGAT 59.969 55.000 0.00 0.00 36.93 2.45
1062 2395 4.876125 ACGATGATGAGTACATGGATGAC 58.124 43.478 0.00 0.00 36.82 3.06
1092 2425 5.290158 CAGCATGCAAATGGAGTATTTTGTC 59.710 40.000 21.98 0.00 36.87 3.18
2629 4395 7.962964 TTACATAGATAGCACAATACTTGCC 57.037 36.000 0.00 0.00 41.18 4.52
2996 4876 5.900425 TGTTGTGTTTGCATTTGATGTAGT 58.100 33.333 0.00 0.00 0.00 2.73
3176 5056 0.905357 GCCTTCTTCCTCACTGCCTA 59.095 55.000 0.00 0.00 0.00 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 1.386485 CCCTGATCCCACCCTCCAT 60.386 63.158 0.00 0.00 0.00 3.41
220 949 3.883489 GGTTAGGATTGTACTTGCATCCC 59.117 47.826 9.17 0.00 32.00 3.85
317 1046 2.100916 CTGCACGTACACCCTATAAGCT 59.899 50.000 0.00 0.00 0.00 3.74
380 1110 6.573664 AGATTGATCTATCCTCTTGTCTCG 57.426 41.667 12.72 0.00 34.85 4.04
417 1147 1.546029 GGAGGGCACTGAATTTTCCAC 59.454 52.381 0.00 0.00 0.00 4.02
485 1215 6.317642 CCCAATTCGTACAATATTCCTGAACA 59.682 38.462 0.00 0.00 0.00 3.18
527 1257 2.826979 CTGATGACACAGCAAGCATC 57.173 50.000 0.00 0.00 38.05 3.91
545 1275 0.688749 GGCCCCATCCTCAAATTGCT 60.689 55.000 0.00 0.00 0.00 3.91
566 1297 0.311790 CCTTGCAGCGCAGAAAAAGA 59.688 50.000 11.47 0.00 40.61 2.52
771 1513 2.436417 GCCATCCTTGTCAGTTAAGCA 58.564 47.619 0.00 0.00 0.00 3.91
1047 2380 5.624509 GCTGTTGTAGTCATCCATGTACTCA 60.625 44.000 0.00 0.00 0.00 3.41
1062 2395 3.192001 ACTCCATTTGCATGCTGTTGTAG 59.808 43.478 20.33 11.49 0.00 2.74
1551 3257 9.066892 TGCAGTAACAAAGAAATTCAGTTAGAT 57.933 29.630 0.00 0.00 0.00 1.98
2629 4395 7.348201 GTCAGTGTCAGTAATCTTCAGTTTTG 58.652 38.462 0.00 0.00 0.00 2.44
2708 4550 4.974103 AGTTTCAGATTCAGTTTCGTCG 57.026 40.909 0.00 0.00 0.00 5.12
2921 4801 1.448540 GTCGCACAGCCAGCTATGT 60.449 57.895 0.00 0.00 0.00 2.29
2996 4876 1.725641 CTATGTCGCTCCAGCACAAA 58.274 50.000 0.00 0.00 42.21 2.83
3070 4950 2.103094 TCGACATTCTCCTATGGGCAAG 59.897 50.000 0.00 0.00 0.00 4.01
3176 5056 1.427809 TAGGCTGGTAGATGCAGCAT 58.572 50.000 7.91 7.91 43.19 3.79


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

AutoCloner maintained by Alex Coulton.