Multiple sequence alignment - TraesCS2B01G483700

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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 TraesCS2B01G483700 chr2B 100.000 4038 0 0 1 4038 680793951 680789914 0.000000e+00 7457
1 TraesCS2B01G483700 chr4B 98.337 2827 44 3 1111 3935 120261487 120258662 0.000000e+00 4957
2 TraesCS2B01G483700 chr4B 96.755 2835 75 9 1111 3938 40493896 40496720 0.000000e+00 4710
3 TraesCS2B01G483700 chr4B 96.540 2832 91 6 1111 3939 222596123 222598950 0.000000e+00 4680
4 TraesCS2B01G483700 chr4B 97.578 1115 26 1 1 1115 120269302 120268189 0.000000e+00 1908
5 TraesCS2B01G483700 chr4B 97.130 1115 32 0 1 1115 222587138 222588252 0.000000e+00 1882
6 TraesCS2B01G483700 chr5B 97.278 2829 72 5 1111 3935 10417766 10414939 0.000000e+00 4793
7 TraesCS2B01G483700 chr3A 96.959 2828 72 7 1111 3935 91839470 91842286 0.000000e+00 4734
8 TraesCS2B01G483700 chr3A 97.399 1115 27 2 1 1115 91831634 91832746 0.000000e+00 1897
9 TraesCS2B01G483700 chr3A 98.058 103 2 0 3936 4038 533975515 533975617 3.210000e-41 180
10 TraesCS2B01G483700 chr6B 96.818 2828 83 6 1111 3935 706415535 706412712 0.000000e+00 4717
11 TraesCS2B01G483700 chr6B 97.220 1115 31 0 1 1115 706423305 706422191 0.000000e+00 1888
12 TraesCS2B01G483700 chr6B 97.220 1115 28 2 1 1115 122830889 122829778 0.000000e+00 1884
13 TraesCS2B01G483700 chr6B 96.867 1117 33 1 1 1115 706364460 706363344 0.000000e+00 1868
14 TraesCS2B01G483700 chr6B 97.087 103 3 0 3936 4038 93914699 93914801 1.490000e-39 174
15 TraesCS2B01G483700 chr4A 96.791 2805 80 6 1111 3912 531953606 531956403 0.000000e+00 4673
16 TraesCS2B01G483700 chr4A 97.399 1115 28 1 1 1115 531941484 531942597 0.000000e+00 1897
17 TraesCS2B01G483700 chr4A 99.029 103 1 0 3936 4038 558484738 558484840 6.890000e-43 185
18 TraesCS2B01G483700 chr2D 95.270 2833 121 7 1111 3935 340330800 340327973 0.000000e+00 4477
19 TraesCS2B01G483700 chr5A 93.084 2834 184 7 1111 3935 220265504 220268334 0.000000e+00 4137
20 TraesCS2B01G483700 chr7B 97.035 1113 32 1 3 1115 504092335 504091224 0.000000e+00 1871
21 TraesCS2B01G483700 chr1B 96.861 1115 35 0 1 1115 666894909 666893795 0.000000e+00 1866
22 TraesCS2B01G483700 chr7A 98.058 103 2 0 3936 4038 642898555 642898657 3.210000e-41 180
23 TraesCS2B01G483700 chr3B 98.058 103 2 0 3936 4038 26435875 26435977 3.210000e-41 180
24 TraesCS2B01G483700 chr1A 98.058 103 2 0 3936 4038 64850699 64850597 3.210000e-41 180
25 TraesCS2B01G483700 chr1A 97.087 103 3 0 3936 4038 39823335 39823437 1.490000e-39 174
26 TraesCS2B01G483700 chr1A 97.087 103 3 0 3936 4038 587852336 587852438 1.490000e-39 174
27 TraesCS2B01G483700 chr6A 97.087 103 3 0 3936 4038 40529811 40529913 1.490000e-39 174


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 TraesCS2B01G483700 chr2B 680789914 680793951 4037 True 7457 7457 100.000 1 4038 1 chr2B.!!$R1 4037
1 TraesCS2B01G483700 chr4B 120258662 120261487 2825 True 4957 4957 98.337 1111 3935 1 chr4B.!!$R1 2824
2 TraesCS2B01G483700 chr4B 40493896 40496720 2824 False 4710 4710 96.755 1111 3938 1 chr4B.!!$F1 2827
3 TraesCS2B01G483700 chr4B 222596123 222598950 2827 False 4680 4680 96.540 1111 3939 1 chr4B.!!$F3 2828
4 TraesCS2B01G483700 chr4B 120268189 120269302 1113 True 1908 1908 97.578 1 1115 1 chr4B.!!$R2 1114
5 TraesCS2B01G483700 chr4B 222587138 222588252 1114 False 1882 1882 97.130 1 1115 1 chr4B.!!$F2 1114
6 TraesCS2B01G483700 chr5B 10414939 10417766 2827 True 4793 4793 97.278 1111 3935 1 chr5B.!!$R1 2824
7 TraesCS2B01G483700 chr3A 91839470 91842286 2816 False 4734 4734 96.959 1111 3935 1 chr3A.!!$F2 2824
8 TraesCS2B01G483700 chr3A 91831634 91832746 1112 False 1897 1897 97.399 1 1115 1 chr3A.!!$F1 1114
9 TraesCS2B01G483700 chr6B 706412712 706415535 2823 True 4717 4717 96.818 1111 3935 1 chr6B.!!$R3 2824
10 TraesCS2B01G483700 chr6B 706422191 706423305 1114 True 1888 1888 97.220 1 1115 1 chr6B.!!$R4 1114
11 TraesCS2B01G483700 chr6B 122829778 122830889 1111 True 1884 1884 97.220 1 1115 1 chr6B.!!$R1 1114
12 TraesCS2B01G483700 chr6B 706363344 706364460 1116 True 1868 1868 96.867 1 1115 1 chr6B.!!$R2 1114
13 TraesCS2B01G483700 chr4A 531953606 531956403 2797 False 4673 4673 96.791 1111 3912 1 chr4A.!!$F2 2801
14 TraesCS2B01G483700 chr4A 531941484 531942597 1113 False 1897 1897 97.399 1 1115 1 chr4A.!!$F1 1114
15 TraesCS2B01G483700 chr2D 340327973 340330800 2827 True 4477 4477 95.270 1111 3935 1 chr2D.!!$R1 2824
16 TraesCS2B01G483700 chr5A 220265504 220268334 2830 False 4137 4137 93.084 1111 3935 1 chr5A.!!$F1 2824
17 TraesCS2B01G483700 chr7B 504091224 504092335 1111 True 1871 1871 97.035 3 1115 1 chr7B.!!$R1 1112
18 TraesCS2B01G483700 chr1B 666893795 666894909 1114 True 1866 1866 96.861 1 1115 1 chr1B.!!$R1 1114

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
724 733 2.952978 ACAACCGCATAAAGTTGGAACA 59.047 40.909 7.69 0.0 46.07 3.18 F
2541 2564 1.142748 GCATGAGCTAGCGAGGTGT 59.857 57.895 9.55 0.0 37.91 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2722 2745 0.040425 ACGCAACATTCCGCTTGTTC 60.040 50.000 0.00 0.0 35.18 3.18 R
3963 3998 2.105128 GAGGACGAGCGGGTCATG 59.895 66.667 8.06 0.0 38.70 3.07 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
171 172 8.428186 TGTTTCTTTGACAACGTATAAGAAGT 57.572 30.769 0.00 0.00 36.52 3.01
275 284 7.825270 TCGTGCCTTTAAATTATCCTTTGACTA 59.175 33.333 0.00 0.00 0.00 2.59
396 405 8.359642 CAATAAGTCAAATGAGAGAAAAACCCA 58.640 33.333 0.00 0.00 0.00 4.51
410 419 7.344612 AGAGAAAAACCCATTAACAAACTTCCT 59.655 33.333 0.00 0.00 0.00 3.36
514 523 3.081061 TGTTCCTCCAATCCATCAAACG 58.919 45.455 0.00 0.00 0.00 3.60
724 733 2.952978 ACAACCGCATAAAGTTGGAACA 59.047 40.909 7.69 0.00 46.07 3.18
801 810 6.636454 AGTTCCTCATAAACTGGTTCCATA 57.364 37.500 0.00 0.00 35.68 2.74
849 858 8.803397 GGTAACCTGGAATAATCAAAGTAAGT 57.197 34.615 0.00 0.00 0.00 2.24
1076 1085 1.466856 GATGCTCCATCCTTTGTGCA 58.533 50.000 0.00 0.00 35.07 4.57
1135 1144 6.837312 TCTTGATTCCTGAAGTGTTTTCCTA 58.163 36.000 0.00 0.00 0.00 2.94
1158 1167 5.497464 TGTCTCTTTTGTCATATGGGTGA 57.503 39.130 2.13 0.00 0.00 4.02
1167 1176 4.525996 TGTCATATGGGTGATGTTTCTGG 58.474 43.478 2.13 0.00 0.00 3.86
1209 1218 3.315191 CCTGAAAAGAAACGACCACACAT 59.685 43.478 0.00 0.00 0.00 3.21
1216 1225 6.817765 AAGAAACGACCACACATATCAAAT 57.182 33.333 0.00 0.00 0.00 2.32
1539 1548 2.097825 TCCTAAGCAAGTCTACGGTCC 58.902 52.381 0.00 0.00 0.00 4.46
1975 1984 4.758688 TCGTCTATGCAACATGACATTCT 58.241 39.130 0.00 0.00 0.00 2.40
2297 2313 4.646040 TGAGGGAAACGAGGAATATTACGA 59.354 41.667 13.41 0.00 0.00 3.43
2366 2388 1.676006 CACACCGCTCAAAAAGAAGGT 59.324 47.619 0.00 0.00 37.84 3.50
2541 2564 1.142748 GCATGAGCTAGCGAGGTGT 59.857 57.895 9.55 0.00 37.91 4.16
2812 2835 4.006319 AGTTAGGTGCTGAATTTGCTCTC 58.994 43.478 6.07 0.00 0.00 3.20
2860 2883 5.911178 TGATAATGAGGAGTTGGTAAGGGAT 59.089 40.000 0.00 0.00 0.00 3.85
2950 2973 8.141909 GCTTTTGTAAGTTACAATCTTCCCTTT 58.858 33.333 25.14 0.00 46.89 3.11
3047 3071 3.370840 AGGATGGTTGATTTGCAGCTA 57.629 42.857 0.00 0.00 0.00 3.32
3312 3340 5.574055 TCGTACGAATTTCTGTATGTGTTCC 59.426 40.000 17.11 0.00 0.00 3.62
3939 3974 0.321671 TGTGCTCTTGTAGTGCCTCC 59.678 55.000 0.00 0.00 34.08 4.30
3940 3975 0.610687 GTGCTCTTGTAGTGCCTCCT 59.389 55.000 0.00 0.00 34.08 3.69
3941 3976 0.610174 TGCTCTTGTAGTGCCTCCTG 59.390 55.000 0.00 0.00 34.08 3.86
3942 3977 0.107945 GCTCTTGTAGTGCCTCCTGG 60.108 60.000 0.00 0.00 0.00 4.45
3943 3978 1.270907 CTCTTGTAGTGCCTCCTGGT 58.729 55.000 0.00 0.00 35.27 4.00
3944 3979 0.976641 TCTTGTAGTGCCTCCTGGTG 59.023 55.000 0.00 0.00 35.27 4.17
3945 3980 0.036010 CTTGTAGTGCCTCCTGGTGG 60.036 60.000 10.46 10.46 35.27 4.61
3971 4006 4.838152 CCACTCCGCCATGACCCG 62.838 72.222 0.00 0.00 0.00 5.28
3974 4009 4.899239 CTCCGCCATGACCCGCTC 62.899 72.222 0.00 0.00 0.00 5.03
3979 4014 3.461773 CCATGACCCGCTCGTCCT 61.462 66.667 0.00 0.00 31.35 3.85
3980 4015 2.105128 CATGACCCGCTCGTCCTC 59.895 66.667 0.00 0.00 31.35 3.71
3981 4016 3.148279 ATGACCCGCTCGTCCTCC 61.148 66.667 0.00 0.00 31.35 4.30
3982 4017 3.663815 ATGACCCGCTCGTCCTCCT 62.664 63.158 0.00 0.00 31.35 3.69
3983 4018 3.827898 GACCCGCTCGTCCTCCTG 61.828 72.222 0.00 0.00 0.00 3.86
3992 4027 3.827898 GTCCTCCTGGGCGACGAG 61.828 72.222 0.00 0.00 35.68 4.18
4032 4067 4.373116 TGCTCCGCACGGTCTTCC 62.373 66.667 9.23 0.00 31.71 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
171 172 8.383175 ACAATGACAAGTATTTTCTTCCTCCTA 58.617 33.333 0.00 0.00 0.00 2.94
206 215 2.323599 TCAGGCCAGATCTACATCCTG 58.676 52.381 18.36 18.36 41.69 3.86
216 225 3.053095 AGGACATGAAAATCAGGCCAGAT 60.053 43.478 5.01 4.73 30.14 2.90
275 284 4.219919 GACACTTCTAGGAATAGAGGGCT 58.780 47.826 0.00 0.00 0.00 5.19
514 523 5.344066 TGAGTTTCGCTATGAATCTGACTC 58.656 41.667 0.00 0.00 39.53 3.36
849 858 3.133721 GCATGAAAGCCTCCTCTCTTCTA 59.866 47.826 0.00 0.00 0.00 2.10
1029 1038 7.225538 CGTCATATAGTTGATTCAGAGGCTTTT 59.774 37.037 0.00 0.00 0.00 2.27
1030 1039 6.703607 CGTCATATAGTTGATTCAGAGGCTTT 59.296 38.462 0.00 0.00 0.00 3.51
1045 1054 1.886542 TGGAGCATCGCGTCATATAGT 59.113 47.619 5.77 0.00 34.37 2.12
1076 1085 4.471904 TTAAGATGGCATGACGAAGAGT 57.528 40.909 3.81 0.00 0.00 3.24
1135 1144 6.065976 TCACCCATATGACAAAAGAGACAT 57.934 37.500 3.65 0.00 0.00 3.06
1158 1167 4.098914 TGCCTCTACAAACCAGAAACAT 57.901 40.909 0.00 0.00 0.00 2.71
1167 1176 2.680339 GGATCAGCTTGCCTCTACAAAC 59.320 50.000 0.00 0.00 0.00 2.93
1216 1225 8.445275 TCTTCTTGTGAGTTGCTAAATAAACA 57.555 30.769 0.00 0.00 0.00 2.83
1539 1548 1.064505 TCTTTAGATACCGTGGCGTCG 59.935 52.381 0.00 0.00 0.00 5.12
1917 1926 3.118261 GGTCCATTGCACTGGATTCTCTA 60.118 47.826 26.57 1.74 46.67 2.43
1975 1984 8.492748 GCGAACGTGATAAATTATTATCCTCAA 58.507 33.333 0.00 0.00 44.52 3.02
2188 2204 4.799564 ACTTCAAAACTCAAAAGGCACA 57.200 36.364 0.00 0.00 0.00 4.57
2366 2388 6.837312 TCTTTACCTTGATGGAAGAAGAACA 58.163 36.000 0.00 0.00 39.71 3.18
2490 2513 5.728351 TTATCGTTTACTTGCATACAGCC 57.272 39.130 0.00 0.00 44.83 4.85
2541 2564 1.906574 ACGAAGTCTAATGCCCAAGGA 59.093 47.619 0.00 0.00 29.74 3.36
2722 2745 0.040425 ACGCAACATTCCGCTTGTTC 60.040 50.000 0.00 0.00 35.18 3.18
2812 2835 0.248336 TAGGTTCGTCTATGCGCACG 60.248 55.000 14.90 12.80 37.36 5.34
2860 2883 5.291178 CCAATTGTCTTGCAATCAGAAACA 58.709 37.500 0.00 0.00 46.29 2.83
3156 3181 4.034975 TGTCGCATTTGCATCAATTCGATA 59.965 37.500 8.67 4.35 42.21 2.92
3954 3989 4.838152 CGGGTCATGGCGGAGTGG 62.838 72.222 0.00 0.00 0.00 4.00
3957 3992 4.899239 GAGCGGGTCATGGCGGAG 62.899 72.222 1.64 0.00 0.00 4.63
3962 3997 3.432051 GAGGACGAGCGGGTCATGG 62.432 68.421 8.06 0.00 38.70 3.66
3963 3998 2.105128 GAGGACGAGCGGGTCATG 59.895 66.667 8.06 0.00 38.70 3.07
3964 3999 3.148279 GGAGGACGAGCGGGTCAT 61.148 66.667 8.06 4.96 38.70 3.06
3965 4000 4.361971 AGGAGGACGAGCGGGTCA 62.362 66.667 8.06 0.00 38.70 4.02
3966 4001 3.827898 CAGGAGGACGAGCGGGTC 61.828 72.222 0.00 0.00 36.18 4.46
3972 4007 3.827898 GTCGCCCAGGAGGACGAG 61.828 72.222 0.00 0.00 42.31 4.18
3975 4010 3.827898 CTCGTCGCCCAGGAGGAC 61.828 72.222 0.00 0.00 38.24 3.85


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

AutoCloner maintained by Alex Coulton.