Multiple sequence alignment - TraesCS4A01G264600

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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 TraesCS4A01G264600 chr4A 100.000 3443 0 0 1 3443 576932965 576929523 0.000000e+00 6359
1 TraesCS4A01G264600 chr4A 82.178 1442 247 9 997 2433 486126018 486124582 0.000000e+00 1230
2 TraesCS4A01G264600 chr4D 95.231 2726 103 13 1 2713 26479006 26481717 0.000000e+00 4289
3 TraesCS4A01G264600 chr4D 81.989 1438 251 7 997 2430 94592339 94593772 0.000000e+00 1214
4 TraesCS4A01G264600 chr4D 81.168 1455 257 13 995 2441 50070787 50072232 0.000000e+00 1153
5 TraesCS4A01G264600 chr4D 81.349 504 27 33 2956 3428 26485326 26485793 7.070000e-92 348
6 TraesCS4A01G264600 chr4B 97.413 1933 39 6 913 2840 39014764 39016690 0.000000e+00 3282
7 TraesCS4A01G264600 chr4B 94.438 899 43 4 1 898 39013888 39014780 0.000000e+00 1376
8 TraesCS4A01G264600 chr4B 81.919 1438 252 7 997 2430 133853136 133854569 0.000000e+00 1208
9 TraesCS4A01G264600 chr4B 84.427 655 26 32 2832 3431 39017037 39017670 2.980000e-160 575
10 TraesCS4A01G264600 chr5B 90.782 1508 130 7 946 2446 577227179 577228684 0.000000e+00 2006
11 TraesCS4A01G264600 chr5D 90.749 1481 133 3 975 2452 469501768 469503247 0.000000e+00 1973
12 TraesCS4A01G264600 chr5A 90.186 1508 139 7 946 2446 590539984 590541489 0.000000e+00 1956
13 TraesCS4A01G264600 chr5A 86.439 789 60 21 248 1030 500583535 500582788 0.000000e+00 821
14 TraesCS4A01G264600 chr2A 87.571 877 64 23 162 1030 732301628 732300789 0.000000e+00 974
15 TraesCS4A01G264600 chr2A 86.675 788 59 20 248 1030 777177838 777178584 0.000000e+00 832
16 TraesCS4A01G264600 chr2A 85.696 790 65 21 248 1030 39913232 39913980 0.000000e+00 789
17 TraesCS4A01G264600 chr2B 86.384 874 76 20 164 1030 506804263 506803426 0.000000e+00 915
18 TraesCS4A01G264600 chr2B 79.787 470 33 26 2989 3430 799734188 799733753 5.620000e-73 285
19 TraesCS4A01G264600 chr7B 86.312 789 61 21 248 1030 595213605 595212858 0.000000e+00 815
20 TraesCS4A01G264600 chr3A 85.932 789 64 21 248 1030 603855941 603855194 0.000000e+00 798
21 TraesCS4A01G264600 chr1A 85.696 790 65 22 248 1030 10728229 10727481 0.000000e+00 789


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 TraesCS4A01G264600 chr4A 576929523 576932965 3442 True 6359.000000 6359 100.000000 1 3443 1 chr4A.!!$R2 3442
1 TraesCS4A01G264600 chr4A 486124582 486126018 1436 True 1230.000000 1230 82.178000 997 2433 1 chr4A.!!$R1 1436
2 TraesCS4A01G264600 chr4D 26479006 26485793 6787 False 2318.500000 4289 88.290000 1 3428 2 chr4D.!!$F3 3427
3 TraesCS4A01G264600 chr4D 94592339 94593772 1433 False 1214.000000 1214 81.989000 997 2430 1 chr4D.!!$F2 1433
4 TraesCS4A01G264600 chr4D 50070787 50072232 1445 False 1153.000000 1153 81.168000 995 2441 1 chr4D.!!$F1 1446
5 TraesCS4A01G264600 chr4B 39013888 39017670 3782 False 1744.333333 3282 92.092667 1 3431 3 chr4B.!!$F2 3430
6 TraesCS4A01G264600 chr4B 133853136 133854569 1433 False 1208.000000 1208 81.919000 997 2430 1 chr4B.!!$F1 1433
7 TraesCS4A01G264600 chr5B 577227179 577228684 1505 False 2006.000000 2006 90.782000 946 2446 1 chr5B.!!$F1 1500
8 TraesCS4A01G264600 chr5D 469501768 469503247 1479 False 1973.000000 1973 90.749000 975 2452 1 chr5D.!!$F1 1477
9 TraesCS4A01G264600 chr5A 590539984 590541489 1505 False 1956.000000 1956 90.186000 946 2446 1 chr5A.!!$F1 1500
10 TraesCS4A01G264600 chr5A 500582788 500583535 747 True 821.000000 821 86.439000 248 1030 1 chr5A.!!$R1 782
11 TraesCS4A01G264600 chr2A 732300789 732301628 839 True 974.000000 974 87.571000 162 1030 1 chr2A.!!$R1 868
12 TraesCS4A01G264600 chr2A 777177838 777178584 746 False 832.000000 832 86.675000 248 1030 1 chr2A.!!$F2 782
13 TraesCS4A01G264600 chr2A 39913232 39913980 748 False 789.000000 789 85.696000 248 1030 1 chr2A.!!$F1 782
14 TraesCS4A01G264600 chr2B 506803426 506804263 837 True 915.000000 915 86.384000 164 1030 1 chr2B.!!$R1 866
15 TraesCS4A01G264600 chr7B 595212858 595213605 747 True 815.000000 815 86.312000 248 1030 1 chr7B.!!$R1 782
16 TraesCS4A01G264600 chr3A 603855194 603855941 747 True 798.000000 798 85.932000 248 1030 1 chr3A.!!$R1 782
17 TraesCS4A01G264600 chr1A 10727481 10728229 748 True 789.000000 789 85.696000 248 1030 1 chr1A.!!$R1 782

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
255 265 0.670546 TTGTAGGCACGCAGCTTCTC 60.671 55.000 0.27 0.0 44.79 2.87 F
837 850 1.407618 GTGTCAACCCTTTTCCACACC 59.592 52.381 0.00 0.0 0.00 4.16 F
1185 1214 1.891919 GGTTGTCAAGGCGTGCAGA 60.892 57.895 0.00 0.0 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1683 1712 0.815213 CGGACATGGCATTCACGGAT 60.815 55.000 0.00 0.0 0.0 4.18 R
2433 2462 2.771943 TGTGGAGAGGAATTAGGCGATT 59.228 45.455 0.00 0.0 0.0 3.34 R
3062 6521 0.389817 CTCGATCGACAACAGGCCAA 60.390 55.000 15.15 0.0 0.0 4.52 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
255 265 0.670546 TTGTAGGCACGCAGCTTCTC 60.671 55.000 0.27 0.00 44.79 2.87
350 360 6.407187 CCCTGATCCATGCATCAATTTTTACA 60.407 38.462 0.03 0.00 32.24 2.41
372 382 7.028926 ACATAGTTTGTAGTCTGGTATCTCG 57.971 40.000 0.00 0.00 36.57 4.04
383 393 3.319122 TCTGGTATCTCGTCCATCATGTG 59.681 47.826 0.00 0.00 33.01 3.21
438 448 9.823098 CTTTCTCATGTTTTCTGAAGATACTTG 57.177 33.333 0.00 0.85 0.00 3.16
441 451 7.445096 TCTCATGTTTTCTGAAGATACTTGCAA 59.555 33.333 0.00 0.00 0.00 4.08
488 499 5.131642 AGGATCCATTGACTTTGCTGATCTA 59.868 40.000 15.82 0.00 0.00 1.98
514 526 4.586841 CCTGGTTTGATTTGGTAACCTGAA 59.413 41.667 0.00 0.00 40.98 3.02
517 529 5.835819 TGGTTTGATTTGGTAACCTGAATCA 59.164 36.000 8.64 8.64 41.47 2.57
554 566 7.827236 TGTCATGAATTTATTCTACTTTCCCGT 59.173 33.333 0.00 0.00 37.67 5.28
577 589 9.649024 CCGTTTTTAGTTTAGAATTACGTTTCA 57.351 29.630 0.00 0.00 0.00 2.69
652 665 3.055819 TCAGTCTGCCATTCTCCTTACAC 60.056 47.826 0.00 0.00 0.00 2.90
710 723 8.009409 GCAACAAAAGGCACATAGTTTATTTTC 58.991 33.333 0.00 0.00 0.00 2.29
795 808 2.871096 TGGGGCGTCTTTGTTAGAAT 57.129 45.000 0.00 0.00 33.81 2.40
837 850 1.407618 GTGTCAACCCTTTTCCACACC 59.592 52.381 0.00 0.00 0.00 4.16
852 865 4.361783 TCCACACCAGGATCTGAATCTTA 58.638 43.478 0.00 0.00 32.44 2.10
855 868 5.762218 CCACACCAGGATCTGAATCTTAATC 59.238 44.000 0.00 0.00 32.44 1.75
900 913 8.589701 TGTCTTAACTATGTCTGATCTAACCA 57.410 34.615 0.00 0.00 0.00 3.67
1185 1214 1.891919 GGTTGTCAAGGCGTGCAGA 60.892 57.895 0.00 0.00 0.00 4.26
2433 2462 2.046023 CTCAAGGACATGCCCGCA 60.046 61.111 0.00 0.00 37.37 5.69
2541 2572 4.982295 GGTTGTGTTGGTATCTTTGCTTTC 59.018 41.667 0.00 0.00 0.00 2.62
2599 2630 1.909700 TGTTCCTCAATCCTTGTGCC 58.090 50.000 0.00 0.00 0.00 5.01
2722 2754 6.964908 TCAATGTATTTTTCGTTGAGAGCAA 58.035 32.000 0.00 0.00 36.37 3.91
2727 2759 6.910433 TGTATTTTTCGTTGAGAGCAAACTTC 59.090 34.615 0.00 0.00 35.42 3.01
2801 4216 3.567164 CACCTTGAGCTGTTTGACATCTT 59.433 43.478 0.00 0.00 0.00 2.40
2803 4218 5.239306 CACCTTGAGCTGTTTGACATCTTTA 59.761 40.000 0.00 0.00 0.00 1.85
2835 4250 8.645487 GGTTGTTTCTTTGTATTCTACTACGAG 58.355 37.037 0.00 0.00 0.00 4.18
2840 4255 6.484540 TCTTTGTATTCTACTACGAGCGAAG 58.515 40.000 0.00 0.00 0.00 3.79
2843 4258 6.615264 TGTATTCTACTACGAGCGAAGAAT 57.385 37.500 0.00 7.96 39.54 2.40
2844 4259 7.024340 TGTATTCTACTACGAGCGAAGAATT 57.976 36.000 14.33 0.00 37.85 2.17
2845 4260 8.146479 TGTATTCTACTACGAGCGAAGAATTA 57.854 34.615 14.33 6.94 37.85 1.40
2920 6370 2.753966 GCACGGTGCATTCTCGCAT 61.754 57.895 27.10 0.00 45.26 4.73
2957 6410 6.399639 AAAAGGCCGATAAAAGAAGAAACA 57.600 33.333 0.00 0.00 0.00 2.83
2958 6411 6.590234 AAAGGCCGATAAAAGAAGAAACAT 57.410 33.333 0.00 0.00 0.00 2.71
2959 6412 5.819825 AGGCCGATAAAAGAAGAAACATC 57.180 39.130 0.00 0.00 0.00 3.06
2960 6413 4.332819 AGGCCGATAAAAGAAGAAACATCG 59.667 41.667 0.00 0.00 36.07 3.84
2961 6414 4.331717 GGCCGATAAAAGAAGAAACATCGA 59.668 41.667 3.54 0.00 37.95 3.59
2962 6415 5.256352 GCCGATAAAAGAAGAAACATCGAC 58.744 41.667 3.54 0.00 37.95 4.20
3005 6464 2.799916 GCGTGTGTCGAGACGTCC 60.800 66.667 13.01 2.76 40.86 4.79
3046 6505 1.456705 GGCACCGGGATCTCTCTCT 60.457 63.158 6.32 0.00 0.00 3.10
3051 6510 2.882137 CACCGGGATCTCTCTCTACTTC 59.118 54.545 6.32 0.00 0.00 3.01
3052 6511 2.510382 ACCGGGATCTCTCTCTACTTCA 59.490 50.000 6.32 0.00 0.00 3.02
3053 6512 3.053544 ACCGGGATCTCTCTCTACTTCAA 60.054 47.826 6.32 0.00 0.00 2.69
3055 6514 4.204012 CGGGATCTCTCTCTACTTCAACT 58.796 47.826 0.00 0.00 0.00 3.16
3056 6515 4.642885 CGGGATCTCTCTCTACTTCAACTT 59.357 45.833 0.00 0.00 0.00 2.66
3057 6516 5.449862 CGGGATCTCTCTCTACTTCAACTTG 60.450 48.000 0.00 0.00 0.00 3.16
3058 6517 5.163457 GGGATCTCTCTCTACTTCAACTTGG 60.163 48.000 0.00 0.00 0.00 3.61
3059 6518 4.792521 TCTCTCTCTACTTCAACTTGGC 57.207 45.455 0.00 0.00 0.00 4.52
3060 6519 4.411927 TCTCTCTCTACTTCAACTTGGCT 58.588 43.478 0.00 0.00 0.00 4.75
3061 6520 4.219507 TCTCTCTCTACTTCAACTTGGCTG 59.780 45.833 0.00 0.00 0.00 4.85
3062 6521 3.898123 TCTCTCTACTTCAACTTGGCTGT 59.102 43.478 0.00 0.00 0.00 4.40
3063 6522 4.345257 TCTCTCTACTTCAACTTGGCTGTT 59.655 41.667 0.00 0.00 0.00 3.16
3064 6523 4.380531 TCTCTACTTCAACTTGGCTGTTG 58.619 43.478 14.57 14.57 46.09 3.33
3065 6524 3.476552 TCTACTTCAACTTGGCTGTTGG 58.523 45.455 18.46 9.80 45.15 3.77
3066 6525 0.746659 ACTTCAACTTGGCTGTTGGC 59.253 50.000 18.46 0.00 45.15 4.52
3165 6629 1.140052 TGGTTTCGTTTCAGAGCCTCA 59.860 47.619 0.00 0.00 0.00 3.86
3242 6717 1.860078 CTTGTCAGTTTCCGACGGC 59.140 57.895 9.66 0.00 36.11 5.68
3357 6850 3.056328 GCCAACAAGTCTCCGGGC 61.056 66.667 0.00 0.00 0.00 6.13
3375 6868 4.657824 CGGCGTCCTTGTCCGTGT 62.658 66.667 0.00 0.00 38.47 4.49
3376 6869 2.652530 GGCGTCCTTGTCCGTGTA 59.347 61.111 0.00 0.00 0.00 2.90
3431 6924 2.807895 CCGTTAGACGTGTGCCGG 60.808 66.667 9.79 9.79 40.58 6.13
3432 6925 2.256158 CGTTAGACGTGTGCCGGA 59.744 61.111 5.05 0.00 42.24 5.14
3433 6926 2.084681 CGTTAGACGTGTGCCGGAC 61.085 63.158 5.05 0.46 42.24 4.79
3434 6927 1.007038 GTTAGACGTGTGCCGGACA 60.007 57.895 5.05 3.75 42.24 4.02
3435 6928 0.389426 GTTAGACGTGTGCCGGACAT 60.389 55.000 5.05 0.00 42.24 3.06
3436 6929 0.389296 TTAGACGTGTGCCGGACATG 60.389 55.000 5.05 14.73 45.83 3.21
3439 6932 4.513519 CGTGTGCCGGACATGTAT 57.486 55.556 5.05 0.00 36.89 2.29
3440 6933 2.005995 CGTGTGCCGGACATGTATG 58.994 57.895 5.05 0.00 36.89 2.39
3441 6934 0.459411 CGTGTGCCGGACATGTATGA 60.459 55.000 5.05 0.00 36.89 2.15
3442 6935 1.006832 GTGTGCCGGACATGTATGAC 58.993 55.000 5.05 0.00 36.78 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
255 265 1.719600 CCGCAGAGAAGAAACAGAGG 58.280 55.000 0.00 0.00 0.00 3.69
350 360 6.262720 GGACGAGATACCAGACTACAAACTAT 59.737 42.308 0.00 0.00 0.00 2.12
372 382 3.525537 CCACACTACTCACATGATGGAC 58.474 50.000 0.00 0.00 0.00 4.02
438 448 5.411053 AGCAAACTCTAAGATCTGAAGTTGC 59.589 40.000 14.81 15.77 0.00 4.17
441 451 7.179338 TCCTAAGCAAACTCTAAGATCTGAAGT 59.821 37.037 0.00 0.00 0.00 3.01
488 499 4.141018 AGGTTACCAAATCAAACCAGGACT 60.141 41.667 3.51 0.00 44.21 3.85
549 561 7.961325 ACGTAATTCTAAACTAAAAACGGGA 57.039 32.000 0.00 0.00 32.47 5.14
550 562 9.106286 GAAACGTAATTCTAAACTAAAAACGGG 57.894 33.333 0.00 0.00 32.47 5.28
577 589 5.299279 CGGCCATAGGAACAATCAGTAAAAT 59.701 40.000 2.24 0.00 0.00 1.82
619 632 3.785486 TGGCAGACTGAAGAATATCACG 58.215 45.455 6.65 0.00 0.00 4.35
710 723 3.319122 AGCTAACTTGAGGTGGCAAAAAG 59.681 43.478 7.15 0.00 32.59 2.27
795 808 3.664107 GACAGACACATACAAAGCCAGA 58.336 45.455 0.00 0.00 0.00 3.86
837 850 7.986320 ACAGAAGTGATTAAGATTCAGATCCTG 59.014 37.037 0.00 0.00 32.44 3.86
1185 1214 1.627834 CTGAAGAAGAGGTTCCTGCCT 59.372 52.381 0.00 0.00 42.53 4.75
1683 1712 0.815213 CGGACATGGCATTCACGGAT 60.815 55.000 0.00 0.00 0.00 4.18
2433 2462 2.771943 TGTGGAGAGGAATTAGGCGATT 59.228 45.455 0.00 0.00 0.00 3.34
2461 2490 4.803088 CGCAAAAGTTTGTTGAATTCCTGA 59.197 37.500 2.27 0.00 40.24 3.86
2463 2492 4.119136 CCGCAAAAGTTTGTTGAATTCCT 58.881 39.130 2.27 0.00 40.24 3.36
2541 2572 3.047796 GCAGTGCAAGAATGAACAACTG 58.952 45.455 11.09 0.00 37.59 3.16
2599 2630 8.574196 AACATTCTTTTACAATCCTCAAAACG 57.426 30.769 0.00 0.00 0.00 3.60
2722 2754 7.516198 AATGATGAGTTAAAGCACTGAAGTT 57.484 32.000 0.00 0.00 0.00 2.66
2752 2785 5.505181 AGATTAGCTGTCCCAAGAAAAGA 57.495 39.130 0.00 0.00 0.00 2.52
2915 6365 2.470983 TTTCTGTGGATGTCATGCGA 57.529 45.000 0.00 0.00 0.00 5.10
2941 6394 7.278211 TCTGTCGATGTTTCTTCTTTTATCG 57.722 36.000 0.00 0.00 38.86 2.92
2950 6403 5.765182 ACTCCATTTTCTGTCGATGTTTCTT 59.235 36.000 0.00 0.00 0.00 2.52
2952 6405 5.385617 CACTCCATTTTCTGTCGATGTTTC 58.614 41.667 0.00 0.00 0.00 2.78
2955 6408 3.244561 ACCACTCCATTTTCTGTCGATGT 60.245 43.478 0.00 0.00 0.00 3.06
2956 6409 3.338249 ACCACTCCATTTTCTGTCGATG 58.662 45.455 0.00 0.00 0.00 3.84
2957 6410 3.703001 ACCACTCCATTTTCTGTCGAT 57.297 42.857 0.00 0.00 0.00 3.59
2958 6411 3.399330 GAACCACTCCATTTTCTGTCGA 58.601 45.455 0.00 0.00 0.00 4.20
2959 6412 2.484264 GGAACCACTCCATTTTCTGTCG 59.516 50.000 0.00 0.00 44.67 4.35
3058 6517 1.237285 ATCGACAACAGGCCAACAGC 61.237 55.000 5.01 0.00 42.60 4.40
3059 6518 0.798776 GATCGACAACAGGCCAACAG 59.201 55.000 5.01 0.00 0.00 3.16
3060 6519 0.948623 CGATCGACAACAGGCCAACA 60.949 55.000 10.26 0.00 0.00 3.33
3061 6520 0.669318 TCGATCGACAACAGGCCAAC 60.669 55.000 15.15 0.00 0.00 3.77
3062 6521 0.389817 CTCGATCGACAACAGGCCAA 60.390 55.000 15.15 0.00 0.00 4.52
3063 6522 1.215382 CTCGATCGACAACAGGCCA 59.785 57.895 15.15 0.00 0.00 5.36
3064 6523 2.167861 GCTCGATCGACAACAGGCC 61.168 63.158 15.15 0.00 0.00 5.19
3065 6524 2.167861 GGCTCGATCGACAACAGGC 61.168 63.158 15.15 14.69 0.00 4.85
3066 6525 0.803768 CAGGCTCGATCGACAACAGG 60.804 60.000 15.15 4.44 0.00 4.00
3117 6576 2.680352 GAGAGGGAGACGTGGGCA 60.680 66.667 0.00 0.00 0.00 5.36
3165 6629 2.681778 CTGGCCTCGTGTCTCCCT 60.682 66.667 3.32 0.00 0.00 4.20
3242 6717 0.790814 GGAAAACTCTCCACGCTTCG 59.209 55.000 0.00 0.00 35.36 3.79
3331 6824 1.518903 GACTTGTTGGCAGCTCCACC 61.519 60.000 2.28 0.00 46.55 4.61
3336 6829 1.302033 CGGAGACTTGTTGGCAGCT 60.302 57.895 2.28 0.00 0.00 4.24
3372 6865 1.101331 CTCCGGGGTCTACACTACAC 58.899 60.000 0.00 0.00 0.00 2.90
3373 6866 0.994247 TCTCCGGGGTCTACACTACA 59.006 55.000 0.00 0.00 0.00 2.74
3374 6867 1.677942 CTCTCCGGGGTCTACACTAC 58.322 60.000 0.00 0.00 0.00 2.73
3375 6868 0.549950 CCTCTCCGGGGTCTACACTA 59.450 60.000 0.00 0.00 0.00 2.74
3376 6869 1.306970 CCTCTCCGGGGTCTACACT 59.693 63.158 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.