Multiple sequence alignment - TraesCS1A01G034400

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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 TraesCS1A01G034400 chr1A 100.000 3453 0 0 1 3453 17143193 17139741 0.000000e+00 6377
1 TraesCS1A01G034400 chr1A 96.082 3471 90 17 1 3453 333971062 333967620 0.000000e+00 5614
2 TraesCS1A01G034400 chr7A 97.226 3461 87 4 1 3453 700893794 700890335 0.000000e+00 5851
3 TraesCS1A01G034400 chr7A 91.738 2336 133 14 514 2804 610018016 610020336 0.000000e+00 3190
4 TraesCS1A01G034400 chr7A 93.034 646 45 0 2798 3443 610030750 610031395 0.000000e+00 944
5 TraesCS1A01G034400 chr7A 94.269 506 26 3 18 522 610017451 610017954 0.000000e+00 771
6 TraesCS1A01G034400 chr4A 97.221 3455 83 6 1 3453 483400265 483396822 0.000000e+00 5836
7 TraesCS1A01G034400 chr2D 93.702 2969 139 14 519 3443 373401314 373404278 0.000000e+00 4403
8 TraesCS1A01G034400 chr2D 90.627 2806 173 25 519 3249 557109176 557106386 0.000000e+00 3642
9 TraesCS1A01G034400 chr2D 91.607 417 30 4 111 522 557109658 557109242 3.870000e-159 571
10 TraesCS1A01G034400 chr2D 92.746 193 14 0 3251 3443 557106118 557105926 2.620000e-71 279
11 TraesCS1A01G034400 chr1D 91.800 2805 148 24 519 3249 406710168 406707372 0.000000e+00 3831
12 TraesCS1A01G034400 chr1D 93.012 415 26 2 111 522 406710647 406710233 1.370000e-168 603
13 TraesCS1A01G034400 chr5D 90.951 2807 164 26 519 3249 448510427 448507635 0.000000e+00 3694
14 TraesCS1A01G034400 chr5D 92.566 417 26 4 111 522 448510908 448510492 8.250000e-166 593
15 TraesCS1A01G034400 chr5D 91.710 193 16 0 3251 3443 448507366 448507174 5.680000e-68 268
16 TraesCS1A01G034400 chr4B 89.733 2805 211 26 519 3249 141024700 141027501 0.000000e+00 3513
17 TraesCS1A01G034400 chr4B 92.208 154 12 0 369 522 141024481 141024634 5.800000e-53 219
18 TraesCS1A01G034400 chrUn 91.899 2370 152 12 917 3249 31815550 31817916 0.000000e+00 3277
19 TraesCS1A01G034400 chr3D 94.359 2145 91 13 519 2643 387329214 387327080 0.000000e+00 3264
20 TraesCS1A01G034400 chr3D 94.757 801 42 0 2643 3443 387327041 387326241 0.000000e+00 1247
21 TraesCS1A01G034400 chr3D 91.827 416 28 5 111 521 534045256 534045670 2.990000e-160 575
22 TraesCS1A01G034400 chr3D 87.302 252 18 5 519 756 534045737 534045988 3.390000e-70 276
23 TraesCS1A01G034400 chr4D 84.364 582 63 18 649 1208 485608928 485609503 2.340000e-151 545
24 TraesCS1A01G034400 chr7D 91.667 168 14 0 3251 3418 592074582 592074749 2.070000e-57 233
25 TraesCS1A01G034400 chr2A 84.375 160 21 3 139 298 207120538 207120383 1.660000e-33 154


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 TraesCS1A01G034400 chr1A 17139741 17143193 3452 True 6377.000000 6377 100.000000 1 3453 1 chr1A.!!$R1 3452
1 TraesCS1A01G034400 chr1A 333967620 333971062 3442 True 5614.000000 5614 96.082000 1 3453 1 chr1A.!!$R2 3452
2 TraesCS1A01G034400 chr7A 700890335 700893794 3459 True 5851.000000 5851 97.226000 1 3453 1 chr7A.!!$R1 3452
3 TraesCS1A01G034400 chr7A 610017451 610020336 2885 False 1980.500000 3190 93.003500 18 2804 2 chr7A.!!$F2 2786
4 TraesCS1A01G034400 chr7A 610030750 610031395 645 False 944.000000 944 93.034000 2798 3443 1 chr7A.!!$F1 645
5 TraesCS1A01G034400 chr4A 483396822 483400265 3443 True 5836.000000 5836 97.221000 1 3453 1 chr4A.!!$R1 3452
6 TraesCS1A01G034400 chr2D 373401314 373404278 2964 False 4403.000000 4403 93.702000 519 3443 1 chr2D.!!$F1 2924
7 TraesCS1A01G034400 chr2D 557105926 557109658 3732 True 1497.333333 3642 91.660000 111 3443 3 chr2D.!!$R1 3332
8 TraesCS1A01G034400 chr1D 406707372 406710647 3275 True 2217.000000 3831 92.406000 111 3249 2 chr1D.!!$R1 3138
9 TraesCS1A01G034400 chr5D 448507174 448510908 3734 True 1518.333333 3694 91.742333 111 3443 3 chr5D.!!$R1 3332
10 TraesCS1A01G034400 chr4B 141024481 141027501 3020 False 1866.000000 3513 90.970500 369 3249 2 chr4B.!!$F1 2880
11 TraesCS1A01G034400 chrUn 31815550 31817916 2366 False 3277.000000 3277 91.899000 917 3249 1 chrUn.!!$F1 2332
12 TraesCS1A01G034400 chr3D 387326241 387329214 2973 True 2255.500000 3264 94.558000 519 3443 2 chr3D.!!$R1 2924
13 TraesCS1A01G034400 chr3D 534045256 534045988 732 False 425.500000 575 89.564500 111 756 2 chr3D.!!$F1 645
14 TraesCS1A01G034400 chr4D 485608928 485609503 575 False 545.000000 545 84.364000 649 1208 1 chr4D.!!$F1 559

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
316 321 0.109597 GGCTTCAATGCAACTGGTCG 60.110 55.0 0.0 0.0 34.04 4.79 F
1204 1347 0.391661 CATCCCAGTCACTCCCAACG 60.392 60.0 0.0 0.0 0.00 4.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2157 2305 0.738762 CCAGAGTCCATGCTGTCACG 60.739 60.000 0.0 0.0 0.0 4.35 R
2923 3116 4.163427 AGAGAGGAAGATCAAGGACAACA 58.837 43.478 0.0 0.0 0.0 3.33 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
286 291 7.173218 GTGGACTCAGTAATCAAAATTGAGTGA 59.827 37.037 9.87 4.02 46.04 3.41
316 321 0.109597 GGCTTCAATGCAACTGGTCG 60.110 55.000 0.00 0.00 34.04 4.79
489 496 2.151369 CCATACCTATGGCCGGGTT 58.849 57.895 17.86 5.92 45.92 4.11
760 855 4.079730 GGGAAAGGGAGGCATATATTAGGG 60.080 50.000 0.00 0.00 0.00 3.53
932 1071 1.755380 GCTACGGGTCCTGACATAACT 59.245 52.381 4.16 0.00 0.00 2.24
1204 1347 0.391661 CATCCCAGTCACTCCCAACG 60.392 60.000 0.00 0.00 0.00 4.10
1399 1543 8.313113 TCGTTTGTTTGAGTTTACGTTTATTG 57.687 30.769 0.00 0.00 0.00 1.90
1711 1858 4.175516 CCAATGCGCTCATTAACAATGTT 58.824 39.130 9.73 3.43 40.74 2.71
1773 1920 6.489022 ACCCCTACAATTGTAAGTTTTCTCAC 59.511 38.462 18.55 0.00 0.00 3.51
1827 1974 5.412286 GGCGTTTACCTTTGTCTACCAAATA 59.588 40.000 0.00 0.00 42.02 1.40
1851 1998 3.976654 AGTATATTCTCCCACTGGCACAT 59.023 43.478 0.00 0.00 38.20 3.21
2397 2551 3.184628 TGATGGTCAGGGAGAATGAAGT 58.815 45.455 0.00 0.00 0.00 3.01
2398 2552 3.198635 TGATGGTCAGGGAGAATGAAGTC 59.801 47.826 0.00 0.00 0.00 3.01
2821 3014 7.229106 TCCATACACGCACTGTTATACTATACA 59.771 37.037 0.00 0.00 33.91 2.29
3004 3198 7.466725 GCGCTGATTATATTTTGTGTGTTCCTA 60.467 37.037 0.00 0.00 0.00 2.94
3108 3303 4.450082 AGATATGTTACTGTGCACGTCA 57.550 40.909 13.13 8.68 0.00 4.35
3275 3751 4.877378 TTCTCGCCTAAAACTACTTCCA 57.123 40.909 0.00 0.00 0.00 3.53
3279 3755 3.006940 CGCCTAAAACTACTTCCATGCA 58.993 45.455 0.00 0.00 0.00 3.96
3348 3824 1.153958 GCCTTAGCAGCGCTTTTGG 60.154 57.895 7.50 7.27 40.44 3.28
3420 3896 1.303155 GCCTTGAGCTTGCAGGTCT 60.303 57.895 13.80 5.04 42.83 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
286 291 3.575256 TGCATTGAAGCCTTCTCACAATT 59.425 39.130 5.96 0.00 31.71 2.32
316 321 6.924111 TCCACTTGGAATTTTTGATAGCTTC 58.076 36.000 0.00 0.00 42.18 3.86
489 496 0.474854 TGGGCAAAGGTAGGGACAGA 60.475 55.000 0.00 0.00 0.00 3.41
912 1050 1.755380 AGTTATGTCAGGACCCGTAGC 59.245 52.381 0.00 0.00 0.00 3.58
932 1071 1.008815 AGGAGGGATCAGTGGATGACA 59.991 52.381 0.00 0.00 41.91 3.58
1204 1347 7.602517 AGTAGCTTATCACTTGTTCAACATC 57.397 36.000 0.00 0.00 0.00 3.06
1526 1672 1.522668 TTGAAGCACAACGGATGGAG 58.477 50.000 0.00 0.00 33.18 3.86
1597 1743 4.623932 ATGTGTCTTTCCAACAGAGCTA 57.376 40.909 0.00 0.00 0.00 3.32
1711 1858 3.360867 TCTTGGAAAAGGTTCAAGCACA 58.639 40.909 0.00 0.00 35.25 4.57
1791 1938 7.496263 ACAAAGGTAAACGCCAAACAAAATAAT 59.504 29.630 0.00 0.00 0.00 1.28
1827 1974 3.134804 GTGCCAGTGGGAGAATATACTGT 59.865 47.826 12.15 0.00 39.02 3.55
1851 1998 2.097036 AGACCGTATGACGAATCCACA 58.903 47.619 0.00 0.00 46.05 4.17
2157 2305 0.738762 CCAGAGTCCATGCTGTCACG 60.739 60.000 0.00 0.00 0.00 4.35
2397 2551 6.962182 ACTTGATCTGGAATGTTATCCTTGA 58.038 36.000 0.00 0.00 40.35 3.02
2398 2552 7.636150 AACTTGATCTGGAATGTTATCCTTG 57.364 36.000 0.00 0.00 40.35 3.61
2821 3014 6.875195 TGATTATTACCGACGAAGAAAACCTT 59.125 34.615 0.00 0.00 37.93 3.50
2923 3116 4.163427 AGAGAGGAAGATCAAGGACAACA 58.837 43.478 0.00 0.00 0.00 3.33
3082 3277 6.493116 ACGTGCACAGTAACATATCTACTAC 58.507 40.000 18.64 0.00 0.00 2.73
3108 3303 9.853555 TTTGTTGTATCGCAATAGAAAATTCAT 57.146 25.926 0.00 0.00 39.55 2.57
3152 3356 5.312895 TGTTCAATACTTCCTGCTTTGCTA 58.687 37.500 0.00 0.00 0.00 3.49
3257 3728 3.267483 GCATGGAAGTAGTTTTAGGCGA 58.733 45.455 0.00 0.00 0.00 5.54
3279 3755 0.886563 GCTTTGAGCTTGCCAGACAT 59.113 50.000 0.00 0.00 38.45 3.06
3345 3821 4.957759 GACTTAATCTTTAAGGCGCCAA 57.042 40.909 31.54 12.95 0.00 4.52
3420 3896 4.889832 TTGTTTTTAAGGCGTCCGTAAA 57.110 36.364 10.97 10.97 36.12 2.01


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

AutoCloner maintained by Alex Coulton.