Multiple sequence alignment - TraesCS5A01G141500

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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 TraesCS5A01G141500 chr5A 100.000 4033 0 0 1 4033 313907636 313903604 0.000000e+00 7448.0
1 TraesCS5A01G141500 chr5B 95.729 2669 76 13 2 2642 263547845 263545187 0.000000e+00 4263.0
2 TraesCS5A01G141500 chr5B 90.789 684 41 11 2695 3376 263545189 263544526 0.000000e+00 894.0
3 TraesCS5A01G141500 chr5B 90.274 329 24 6 3364 3690 263544507 263544185 1.340000e-114 424.0
4 TraesCS5A01G141500 chr5B 90.574 244 22 1 3685 3928 263544105 263543863 5.030000e-84 322.0
5 TraesCS5A01G141500 chr5B 82.759 87 4 2 3947 4033 263543868 263543793 2.600000e-07 67.6
6 TraesCS5A01G141500 chr5D 95.827 1917 57 6 2 1895 239939196 239941112 0.000000e+00 3075.0
7 TraesCS5A01G141500 chr5D 93.698 1444 64 17 1880 3311 239941130 239942558 0.000000e+00 2137.0
8 TraesCS5A01G141500 chr5D 93.833 681 17 8 3366 4030 239942692 239943363 0.000000e+00 1002.0
9 TraesCS5A01G141500 chr1A 85.393 89 6 1 115 196 281893486 281893574 7.180000e-13 86.1


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 TraesCS5A01G141500 chr5A 313903604 313907636 4032 True 7448.000000 7448 100.000000 1 4033 1 chr5A.!!$R1 4032
1 TraesCS5A01G141500 chr5B 263543793 263547845 4052 True 1194.120000 4263 90.025000 2 4033 5 chr5B.!!$R1 4031
2 TraesCS5A01G141500 chr5D 239939196 239943363 4167 False 2071.333333 3075 94.452667 2 4030 3 chr5D.!!$F1 4028

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
361 384 0.879839 GCGGCACACAAATTGGCTTT 60.880 50.000 0.0 0.0 37.39 3.51 F
1122 1145 1.215423 AGTGAGGTTGAAAGCCACCTT 59.785 47.619 9.0 0.0 32.05 3.50 F
2261 2326 0.837272 ACGGCAGCACTGGGTATATT 59.163 50.000 0.0 0.0 0.00 1.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1374 1397 0.888736 CCCCAAACGACATCTGTGCA 60.889 55.0 0.00 0.00 0.00 4.57 R
2636 2706 0.107703 ATGATACCACAGGTGCACCG 60.108 55.0 29.68 24.87 42.08 4.94 R
3695 3948 0.034574 TGGCCGGCACACTATTTCAT 60.035 50.0 30.85 0.00 0.00 2.57 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
94 101 6.894682 TGGGCCTTTCATTTTCTTTAACTTT 58.105 32.000 4.53 0.00 0.00 2.66
95 102 8.024145 TGGGCCTTTCATTTTCTTTAACTTTA 57.976 30.769 4.53 0.00 0.00 1.85
98 106 7.386848 GGCCTTTCATTTTCTTTAACTTTACCC 59.613 37.037 0.00 0.00 0.00 3.69
210 232 7.821595 TCATTGATGCTTCAAAATGATGTTC 57.178 32.000 17.82 0.00 44.70 3.18
224 246 9.360514 CAAAATGATGTTCGACATTTGAAAAAG 57.639 29.630 11.20 0.00 43.07 2.27
254 276 8.046107 TCATGTGTACATTCCATGAAGTATGAA 58.954 33.333 19.73 1.59 41.33 2.57
266 288 8.134895 TCCATGAAGTATGAACAACAGTTTTTC 58.865 33.333 5.37 5.37 39.21 2.29
267 289 8.137437 CCATGAAGTATGAACAACAGTTTTTCT 58.863 33.333 12.38 2.77 39.21 2.52
268 290 9.173939 CATGAAGTATGAACAACAGTTTTTCTC 57.826 33.333 12.38 3.48 39.21 2.87
269 291 7.703328 TGAAGTATGAACAACAGTTTTTCTCC 58.297 34.615 12.38 2.34 0.00 3.71
281 303 6.394809 ACAGTTTTTCTCCGAAAAACATGTT 58.605 32.000 30.53 4.92 46.78 2.71
292 314 5.290643 CCGAAAAACATGTTCATTTGTGTGT 59.709 36.000 12.39 0.00 0.00 3.72
361 384 0.879839 GCGGCACACAAATTGGCTTT 60.880 50.000 0.00 0.00 37.39 3.51
417 440 8.223769 CCATGATCTATGTACAAAGTTATTCGC 58.776 37.037 0.00 0.00 34.87 4.70
615 638 2.777692 TCCTTCTTCAAGTCAGTGGGTT 59.222 45.455 0.00 0.00 0.00 4.11
955 978 5.063944 AGCTTACTGTTTCATGCTATCAACG 59.936 40.000 0.00 0.00 0.00 4.10
1122 1145 1.215423 AGTGAGGTTGAAAGCCACCTT 59.785 47.619 9.00 0.00 32.05 3.50
1374 1397 5.053978 AGAAAAGGAGTTCAGGTTGTGAT 57.946 39.130 0.00 0.00 34.17 3.06
1582 1605 2.357034 AGTCGATTGCGCAACCGT 60.357 55.556 34.03 15.64 37.46 4.83
1811 1835 8.557029 ACAGGTTTATTTTTCTGACTCTTTACG 58.443 33.333 0.00 0.00 0.00 3.18
1980 2043 2.944129 AGCACAACTCCCAAAAGCTAA 58.056 42.857 0.00 0.00 0.00 3.09
1981 2044 3.295973 AGCACAACTCCCAAAAGCTAAA 58.704 40.909 0.00 0.00 0.00 1.85
2245 2310 6.373216 TGTTCTGGGTTTATCTTAATTCACGG 59.627 38.462 0.00 0.00 0.00 4.94
2261 2326 0.837272 ACGGCAGCACTGGGTATATT 59.163 50.000 0.00 0.00 0.00 1.28
2262 2327 1.211949 ACGGCAGCACTGGGTATATTT 59.788 47.619 0.00 0.00 0.00 1.40
2343 2412 1.971962 CAAACGAGCTCGAATGCAAAC 59.028 47.619 40.58 0.00 43.02 2.93
2463 2532 7.848128 TGTTTGGTGGAGGTTTGTTTAATTTA 58.152 30.769 0.00 0.00 0.00 1.40
2636 2706 7.464710 CGCTTTGGATGTACTTCTCAAATACTC 60.465 40.741 17.58 10.94 0.00 2.59
2692 2762 6.489022 TGCAAGAATAAGCATAGAAGCATGAT 59.511 34.615 0.00 0.00 35.51 2.45
2693 2763 6.802348 GCAAGAATAAGCATAGAAGCATGATG 59.198 38.462 0.00 0.00 36.85 3.07
2719 2789 8.391106 GTGCTGAAAGAAATATTCGTTGAGTAT 58.609 33.333 6.96 0.00 35.54 2.12
2759 2829 9.422196 CGAAAGAATTATATTTCCGTGTTCTTC 57.578 33.333 4.17 0.00 34.08 2.87
2765 2835 7.681939 TTATATTTCCGTGTTCTTCTGCTTT 57.318 32.000 0.00 0.00 0.00 3.51
2772 2842 4.377841 CCGTGTTCTTCTGCTTTCAAGATC 60.378 45.833 0.00 0.00 0.00 2.75
2787 2858 3.683802 CAAGATCTGCCTCTTGGTTTCT 58.316 45.455 0.00 0.00 45.46 2.52
2799 2870 5.063944 CCTCTTGGTTTCTCACATGAATACG 59.936 44.000 0.00 0.00 0.00 3.06
2802 2873 6.878923 TCTTGGTTTCTCACATGAATACGAAT 59.121 34.615 0.00 0.00 0.00 3.34
2836 2907 7.165485 AGTACATTATACTTGGTGCAGTTTGA 58.835 34.615 0.00 0.00 0.00 2.69
2900 2971 7.928167 TGTGAGCCTGTATTTATCTAGTGATTG 59.072 37.037 0.00 0.00 34.32 2.67
2914 2985 3.771216 AGTGATTGCCATTCACCTCTTT 58.229 40.909 14.36 0.00 43.62 2.52
2938 3009 0.856641 ACGACAACGATGTTTCACCG 59.143 50.000 0.00 0.95 40.74 4.94
2998 3069 0.322546 CCCCCTCCAGAACCGAAAAG 60.323 60.000 0.00 0.00 0.00 2.27
3031 3102 3.066064 AGAACGAGATCGACCTCATTCTG 59.934 47.826 17.09 0.00 42.10 3.02
3070 3141 4.272018 CAGGCTTCTGGTAGATTTTGATCG 59.728 45.833 0.00 0.00 34.96 3.69
3096 3167 2.988010 TGCTTTCTCCTCGCATGTAT 57.012 45.000 0.00 0.00 0.00 2.29
3168 3239 4.947645 ACACCCAACAATCTTGTGAAATG 58.052 39.130 0.00 0.00 41.31 2.32
3192 3263 1.077716 CCGGCCCTTAGGTTTCAGG 60.078 63.158 0.00 0.00 34.57 3.86
3193 3264 1.683441 CGGCCCTTAGGTTTCAGGT 59.317 57.895 0.00 0.00 34.57 4.00
3301 3372 3.249080 TGTAAGTTTTCGCTGCTGTAACC 59.751 43.478 0.00 0.00 0.00 2.85
3302 3373 2.256117 AGTTTTCGCTGCTGTAACCT 57.744 45.000 0.00 0.00 0.00 3.50
3321 3392 2.485479 CCTCTGTAGCCGCATGGTAAAT 60.485 50.000 0.00 0.00 37.67 1.40
3359 3477 4.960938 TCTGCTTTCAGAGTCTTTTAGCA 58.039 39.130 15.34 15.34 43.95 3.49
3384 3534 7.118971 CAGGAAGAGAATGTTCACCTAAGAAAG 59.881 40.741 0.00 0.00 40.68 2.62
3415 3570 2.738743 GGTCATTCCCATGTTCCATGT 58.261 47.619 3.75 0.00 0.00 3.21
3416 3571 3.099141 GGTCATTCCCATGTTCCATGTT 58.901 45.455 3.75 0.00 0.00 2.71
3417 3572 3.131046 GGTCATTCCCATGTTCCATGTTC 59.869 47.826 3.75 0.00 0.00 3.18
3418 3573 3.131046 GTCATTCCCATGTTCCATGTTCC 59.869 47.826 3.75 0.00 0.00 3.62
3419 3574 2.988636 TTCCCATGTTCCATGTTCCA 57.011 45.000 3.75 0.00 0.00 3.53
3420 3575 3.471430 TTCCCATGTTCCATGTTCCAT 57.529 42.857 3.75 0.00 0.00 3.41
3505 3663 2.238395 GAGGAGGTGGAAGAAGAAGCAT 59.762 50.000 0.00 0.00 0.00 3.79
3594 3752 4.512914 GGTCCATGGCCAGCCTCC 62.513 72.222 13.05 7.84 36.94 4.30
3683 3851 6.993786 TCGAAATGTGCATCTTTGGTATTA 57.006 33.333 0.00 0.00 0.00 0.98
3911 4167 4.755123 AGTTTCCTGGATTCGTAAGTGTTG 59.245 41.667 0.00 0.00 39.48 3.33
3922 4178 2.147958 GTAAGTGTTGGGCATCGAACA 58.852 47.619 0.00 0.00 38.87 3.18
3923 4179 1.238439 AAGTGTTGGGCATCGAACAG 58.762 50.000 0.00 0.00 41.14 3.16
3924 4180 0.396435 AGTGTTGGGCATCGAACAGA 59.604 50.000 0.00 0.00 41.14 3.41
3925 4181 0.517316 GTGTTGGGCATCGAACAGAC 59.483 55.000 0.00 0.00 41.14 3.51
3926 4182 0.396435 TGTTGGGCATCGAACAGACT 59.604 50.000 0.00 0.00 36.83 3.24
3927 4183 1.202758 TGTTGGGCATCGAACAGACTT 60.203 47.619 0.00 0.00 36.83 3.01
3928 4184 1.880027 GTTGGGCATCGAACAGACTTT 59.120 47.619 0.00 0.00 32.80 2.66
3929 4185 2.270352 TGGGCATCGAACAGACTTTT 57.730 45.000 0.00 0.00 0.00 2.27
3930 4186 2.582052 TGGGCATCGAACAGACTTTTT 58.418 42.857 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 75 7.790782 AGTTAAAGAAAATGAAAGGCCCATA 57.209 32.000 0.00 0.00 0.00 2.74
74 81 7.876068 GGGGGTAAAGTTAAAGAAAATGAAAGG 59.124 37.037 0.00 0.00 0.00 3.11
98 106 2.734755 TTGGCAGATTATCACCAGGG 57.265 50.000 6.99 0.00 32.79 4.45
105 113 6.543831 ACTGGACTAACATTTGGCAGATTATC 59.456 38.462 0.00 0.00 0.00 1.75
113 121 4.575885 TGAGTACTGGACTAACATTTGGC 58.424 43.478 0.00 0.00 39.06 4.52
210 232 6.692681 ACACATGAGTTCTTTTTCAAATGTCG 59.307 34.615 0.00 0.00 0.00 4.35
254 276 5.774630 TGTTTTTCGGAGAAAAACTGTTGT 58.225 33.333 32.49 0.00 45.43 3.32
266 288 5.748152 ACACAAATGAACATGTTTTTCGGAG 59.252 36.000 13.36 4.44 0.00 4.63
267 289 5.518128 CACACAAATGAACATGTTTTTCGGA 59.482 36.000 13.36 0.00 0.00 4.55
268 290 5.290643 ACACACAAATGAACATGTTTTTCGG 59.709 36.000 13.36 7.00 0.00 4.30
269 291 6.329838 ACACACAAATGAACATGTTTTTCG 57.670 33.333 13.36 6.39 0.00 3.46
361 384 2.583024 TGGACATGCAAATGGTCAGA 57.417 45.000 11.57 0.00 33.26 3.27
417 440 4.084171 CCATTCTTCATATACTGTGCTGCG 60.084 45.833 0.00 0.00 0.00 5.18
955 978 6.765036 ACCAATGACACTATTGATGATCAGTC 59.235 38.462 0.09 0.00 39.79 3.51
1122 1145 0.970640 TACTAAGAAGTGGCGCACCA 59.029 50.000 10.83 0.00 46.51 4.17
1374 1397 0.888736 CCCCAAACGACATCTGTGCA 60.889 55.000 0.00 0.00 0.00 4.57
1582 1605 1.879380 CGAAGGGATTGCAACACTCAA 59.121 47.619 0.00 0.00 0.00 3.02
1811 1835 9.593134 ACAAGTTCTATAGTCATGACTTGAATC 57.407 33.333 32.14 22.44 42.54 2.52
1900 1957 6.014669 GGATCCTACATGAGAGCTAATTCACT 60.015 42.308 3.84 0.00 0.00 3.41
2117 2182 6.441088 AAATCCAGAACAGAAGTAGTCCTT 57.559 37.500 0.00 0.00 35.59 3.36
2210 2275 7.918076 AGATAAACCCAGAACAGAAGTAATCA 58.082 34.615 0.00 0.00 0.00 2.57
2245 2310 4.399303 ACAAAGAAATATACCCAGTGCTGC 59.601 41.667 0.00 0.00 0.00 5.25
2343 2412 3.161067 TCTCCTCTTCCAGACAAGACAG 58.839 50.000 0.00 0.00 0.00 3.51
2636 2706 0.107703 ATGATACCACAGGTGCACCG 60.108 55.000 29.68 24.87 42.08 4.94
2692 2762 6.204688 ACTCAACGAATATTTCTTTCAGCACA 59.795 34.615 0.00 0.00 0.00 4.57
2693 2763 6.603095 ACTCAACGAATATTTCTTTCAGCAC 58.397 36.000 0.00 0.00 0.00 4.40
2727 2797 6.540914 ACGGAAATATAATTCTTTCGGCAGAA 59.459 34.615 0.00 0.00 36.00 3.02
2728 2798 6.018262 CACGGAAATATAATTCTTTCGGCAGA 60.018 38.462 0.71 0.00 36.00 4.26
2759 2829 2.988570 AGAGGCAGATCTTGAAAGCAG 58.011 47.619 0.00 0.00 0.00 4.24
2760 2830 3.430042 AAGAGGCAGATCTTGAAAGCA 57.570 42.857 0.00 0.00 38.12 3.91
2772 2842 2.260844 TGTGAGAAACCAAGAGGCAG 57.739 50.000 0.00 0.00 39.06 4.85
2787 2858 7.386573 ACTTGTGTGTTATTCGTATTCATGTGA 59.613 33.333 0.00 0.00 0.00 3.58
2826 2897 1.748493 TGGTTCTTGGTCAAACTGCAC 59.252 47.619 0.00 0.00 0.00 4.57
2900 2971 3.938963 TCGTCAATAAAGAGGTGAATGGC 59.061 43.478 0.00 0.00 0.00 4.40
2914 2985 4.150980 GGTGAAACATCGTTGTCGTCAATA 59.849 41.667 12.16 0.00 39.98 1.90
2938 3009 0.455633 CAACTCCTGCAAGCGAATGC 60.456 55.000 5.97 5.97 46.58 3.56
2998 3069 0.456221 TCTCGTTCTCCGAAGATGCC 59.544 55.000 0.00 0.00 46.75 4.40
3031 3102 4.457834 AGCCTGTACTCTACACACAATC 57.542 45.455 0.00 0.00 34.46 2.67
3070 3141 1.135831 GCGAGGAGAAAGCAAAAGAGC 60.136 52.381 0.00 0.00 0.00 4.09
3096 3167 3.402110 CAAACTGCACACACTCCATAGA 58.598 45.455 0.00 0.00 0.00 1.98
3192 3263 6.654793 TTGCAACAACCAGATTTACAAAAC 57.345 33.333 0.00 0.00 0.00 2.43
3193 3264 7.856145 ATTTGCAACAACCAGATTTACAAAA 57.144 28.000 0.00 0.00 0.00 2.44
3301 3372 2.309528 TTTACCATGCGGCTACAGAG 57.690 50.000 0.00 0.00 34.57 3.35
3302 3373 3.202906 GAATTTACCATGCGGCTACAGA 58.797 45.455 0.00 0.00 34.57 3.41
3321 3392 4.574674 AGCAGATACAGGGTTCATTGAA 57.425 40.909 0.00 0.00 0.00 2.69
3355 3473 3.840666 AGGTGAACATTCTCTTCCTGCTA 59.159 43.478 0.00 0.00 0.00 3.49
3356 3474 2.641815 AGGTGAACATTCTCTTCCTGCT 59.358 45.455 0.00 0.00 0.00 4.24
3358 3476 6.042638 TCTTAGGTGAACATTCTCTTCCTG 57.957 41.667 0.00 0.00 0.00 3.86
3359 3477 6.688073 TTCTTAGGTGAACATTCTCTTCCT 57.312 37.500 0.00 0.00 0.00 3.36
3384 3534 0.744771 GGAATGACCGCAAGAGGGAC 60.745 60.000 0.00 0.00 43.02 4.46
3415 3570 3.700539 CACAATGGTAGATGGCAATGGAA 59.299 43.478 0.00 0.00 0.00 3.53
3416 3571 3.289836 CACAATGGTAGATGGCAATGGA 58.710 45.455 0.00 0.00 0.00 3.41
3417 3572 2.363038 CCACAATGGTAGATGGCAATGG 59.637 50.000 0.00 0.00 31.35 3.16
3418 3573 3.720949 CCACAATGGTAGATGGCAATG 57.279 47.619 0.00 0.00 31.35 2.82
3505 3663 0.251165 GGCCAAGTTAACTGCCCAGA 60.251 55.000 21.09 0.00 37.94 3.86
3594 3752 1.554160 AGCTTGGACTCTCACATGGAG 59.446 52.381 0.00 1.04 45.49 3.86
3683 3851 8.028938 GGCACACTATTTCATTGTGTTATTTCT 58.971 33.333 1.81 0.00 44.64 2.52
3695 3948 0.034574 TGGCCGGCACACTATTTCAT 60.035 50.000 30.85 0.00 0.00 2.57
3696 3949 0.250945 TTGGCCGGCACACTATTTCA 60.251 50.000 30.85 10.76 0.00 2.69
3730 3986 6.065374 ACATGATCCGAATCAGAGTAGTACT 58.935 40.000 1.37 1.37 44.90 2.73
3930 4186 3.878160 ACGCCTCCAGTTTTTGAAAAA 57.122 38.095 0.00 0.00 0.00 1.94
3931 4187 3.878160 AACGCCTCCAGTTTTTGAAAA 57.122 38.095 0.00 0.00 0.00 2.29
3932 4188 3.316868 CCTAACGCCTCCAGTTTTTGAAA 59.683 43.478 0.00 0.00 33.42 2.69
3933 4189 2.882137 CCTAACGCCTCCAGTTTTTGAA 59.118 45.455 0.00 0.00 33.42 2.69
3934 4190 2.500229 CCTAACGCCTCCAGTTTTTGA 58.500 47.619 0.00 0.00 33.42 2.69
3935 4191 1.539827 CCCTAACGCCTCCAGTTTTTG 59.460 52.381 0.00 0.00 33.42 2.44
3936 4192 1.905637 CCCTAACGCCTCCAGTTTTT 58.094 50.000 0.00 0.00 33.42 1.94
3937 4193 0.608308 GCCCTAACGCCTCCAGTTTT 60.608 55.000 0.00 0.00 33.42 2.43
3938 4194 1.002502 GCCCTAACGCCTCCAGTTT 60.003 57.895 0.00 0.00 33.42 2.66
3939 4195 1.489560 AAGCCCTAACGCCTCCAGTT 61.490 55.000 0.00 0.00 35.75 3.16
3940 4196 1.918800 AAGCCCTAACGCCTCCAGT 60.919 57.895 0.00 0.00 0.00 4.00
3941 4197 1.450312 CAAGCCCTAACGCCTCCAG 60.450 63.158 0.00 0.00 0.00 3.86
3942 4198 1.271840 ATCAAGCCCTAACGCCTCCA 61.272 55.000 0.00 0.00 0.00 3.86
3943 4199 0.756903 TATCAAGCCCTAACGCCTCC 59.243 55.000 0.00 0.00 0.00 4.30
3944 4200 2.614829 TTATCAAGCCCTAACGCCTC 57.385 50.000 0.00 0.00 0.00 4.70
3945 4201 2.224548 GGATTATCAAGCCCTAACGCCT 60.225 50.000 0.00 0.00 0.00 5.52
3949 4229 7.606456 TCGATTAATGGATTATCAAGCCCTAAC 59.394 37.037 0.00 0.00 35.65 2.34


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

AutoCloner maintained by Alex Coulton.