Multiple sequence alignment - TraesCS1A01G030800

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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 TraesCS1A01G030800 chr1A 100.000 3972 0 0 1 3972 14198862 14194891 0.000000e+00 7336.0
1 TraesCS1A01G030800 chr1A 96.483 3924 104 8 1 3922 208727824 208723933 0.000000e+00 6451.0
2 TraesCS1A01G030800 chr1A 98.039 51 1 0 3922 3972 208723638 208723588 5.470000e-14 89.8
3 TraesCS1A01G030800 chr3A 90.656 1220 98 8 1174 2392 724555064 724556268 0.000000e+00 1607.0
4 TraesCS1A01G030800 chr3A 89.811 1109 88 5 2 1106 724553979 724555066 0.000000e+00 1399.0
5 TraesCS1A01G030800 chr4A 81.227 1630 240 40 108 1714 78286401 78284815 0.000000e+00 1254.0
6 TraesCS1A01G030800 chr3B 86.876 861 102 9 3 856 705356081 705355225 0.000000e+00 953.0
7 TraesCS1A01G030800 chr3B 84.615 286 39 4 3 285 93903636 93903919 3.020000e-71 279.0
8 TraesCS1A01G030800 chr3B 84.561 285 36 7 291 575 93904928 93905204 3.910000e-70 276.0
9 TraesCS1A01G030800 chr3B 84.793 217 31 2 250 465 84452806 84452591 2.400000e-52 217.0
10 TraesCS1A01G030800 chr2B 88.961 154 17 0 2599 2752 794585195 794585042 1.460000e-44 191.0


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 TraesCS1A01G030800 chr1A 14194891 14198862 3971 True 7336.0 7336 100.0000 1 3972 1 chr1A.!!$R1 3971
1 TraesCS1A01G030800 chr1A 208723588 208727824 4236 True 3270.4 6451 97.2610 1 3972 2 chr1A.!!$R2 3971
2 TraesCS1A01G030800 chr3A 724553979 724556268 2289 False 1503.0 1607 90.2335 2 2392 2 chr3A.!!$F1 2390
3 TraesCS1A01G030800 chr4A 78284815 78286401 1586 True 1254.0 1254 81.2270 108 1714 1 chr4A.!!$R1 1606
4 TraesCS1A01G030800 chr3B 705355225 705356081 856 True 953.0 953 86.8760 3 856 1 chr3B.!!$R2 853
5 TraesCS1A01G030800 chr3B 93903636 93905204 1568 False 277.5 279 84.5880 3 575 2 chr3B.!!$F1 572

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
767 1799 0.438830 GACCTTGTGCGCGAAACTAG 59.561 55.000 12.1 13.32 0.00 2.57 F
1850 2907 0.394192 TCCACTGGAGAAGCACACAG 59.606 55.000 0.0 0.00 37.01 3.66 F
2716 3773 1.202417 AGTCACCATGAGTTATCCGCG 60.202 52.381 0.0 0.00 0.00 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2749 3806 1.357991 GCGCCTTCTCTCTTGCTGTC 61.358 60.0 0.0 0.0 0.0 3.51 R
2812 3869 0.609131 ATTTGTGTCCTTCGCCCCTG 60.609 55.0 0.0 0.0 0.0 4.45 R
3888 4946 0.253044 GGCTGTTGACATAGGAGGCA 59.747 55.0 0.0 0.0 0.0 4.75 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
80 85 3.909732 TGGGATTGACACTGGTCTTTTT 58.090 40.909 0.00 0.00 44.61 1.94
104 109 4.729227 TTCAACTACAGTCACAGACACA 57.271 40.909 0.00 0.00 34.60 3.72
227 232 4.017958 TGCCTTCTATGGGGTTGACATTTA 60.018 41.667 0.00 0.00 0.00 1.40
285 290 1.916506 TCATGGGAATGCGGTTTCAA 58.083 45.000 0.00 0.00 0.00 2.69
286 291 1.543802 TCATGGGAATGCGGTTTCAAC 59.456 47.619 0.00 0.00 0.00 3.18
307 1315 1.139095 CAGGTACGGGAAGAGTCGC 59.861 63.158 0.00 0.00 0.00 5.19
514 1546 3.661944 AGCGATGATTAGATTGCTGAGG 58.338 45.455 0.00 0.00 40.91 3.86
530 1562 1.487976 TGAGGACTGAAGATGATGGCC 59.512 52.381 0.00 0.00 0.00 5.36
549 1581 3.181473 GGCCGGTACATATGTGAGTACAA 60.181 47.826 18.81 0.00 41.74 2.41
652 1684 5.126222 CACAAGAGAGCTGGTATCTCAACTA 59.874 44.000 4.31 0.00 44.68 2.24
767 1799 0.438830 GACCTTGTGCGCGAAACTAG 59.561 55.000 12.10 13.32 0.00 2.57
864 1896 8.517056 TGAATTCACTTATACAGTTCGTGTAGA 58.483 33.333 3.38 0.00 45.06 2.59
865 1897 9.350357 GAATTCACTTATACAGTTCGTGTAGAA 57.650 33.333 0.00 0.00 45.06 2.10
870 1902 6.822667 TTATACAGTTCGTGTAGAAGGTGA 57.177 37.500 0.00 0.00 45.06 4.02
871 1903 3.644884 ACAGTTCGTGTAGAAGGTGAG 57.355 47.619 0.00 0.00 39.95 3.51
872 1904 3.220110 ACAGTTCGTGTAGAAGGTGAGA 58.780 45.455 0.00 0.00 39.95 3.27
873 1905 3.253677 ACAGTTCGTGTAGAAGGTGAGAG 59.746 47.826 0.00 0.00 39.95 3.20
874 1906 3.253677 CAGTTCGTGTAGAAGGTGAGAGT 59.746 47.826 0.00 0.00 39.95 3.24
875 1907 4.454847 CAGTTCGTGTAGAAGGTGAGAGTA 59.545 45.833 0.00 0.00 39.95 2.59
876 1908 4.696402 AGTTCGTGTAGAAGGTGAGAGTAG 59.304 45.833 0.00 0.00 39.95 2.57
877 1909 4.548451 TCGTGTAGAAGGTGAGAGTAGA 57.452 45.455 0.00 0.00 0.00 2.59
878 1910 4.505808 TCGTGTAGAAGGTGAGAGTAGAG 58.494 47.826 0.00 0.00 0.00 2.43
879 1911 4.020396 TCGTGTAGAAGGTGAGAGTAGAGT 60.020 45.833 0.00 0.00 0.00 3.24
880 1912 4.696402 CGTGTAGAAGGTGAGAGTAGAGTT 59.304 45.833 0.00 0.00 0.00 3.01
881 1913 5.873712 CGTGTAGAAGGTGAGAGTAGAGTTA 59.126 44.000 0.00 0.00 0.00 2.24
882 1914 6.036300 CGTGTAGAAGGTGAGAGTAGAGTTAG 59.964 46.154 0.00 0.00 0.00 2.34
883 1915 7.104939 GTGTAGAAGGTGAGAGTAGAGTTAGA 58.895 42.308 0.00 0.00 0.00 2.10
1029 2061 4.983053 TCGGACTATTTGTTGGGGTTAAA 58.017 39.130 0.00 0.00 0.00 1.52
1070 2102 7.927092 TGTTATATACGCTGGTTTACTTATGCA 59.073 33.333 0.00 0.00 0.00 3.96
1366 2423 3.607741 TCGGGACTTTGTACAACAAACA 58.392 40.909 8.07 0.00 42.55 2.83
1546 2603 2.435372 TTTGCAGGGAAGTTCTGTGT 57.565 45.000 2.25 0.00 34.89 3.72
1847 2904 1.421268 ACATTCCACTGGAGAAGCACA 59.579 47.619 0.00 0.00 31.21 4.57
1850 2907 0.394192 TCCACTGGAGAAGCACACAG 59.606 55.000 0.00 0.00 37.01 3.66
1923 2980 3.801698 CAGCTGGCTCATACACTGTATT 58.198 45.455 5.57 0.00 0.00 1.89
1924 2981 4.740634 GCAGCTGGCTCATACACTGTATTA 60.741 45.833 17.12 0.00 40.25 0.98
1925 2982 4.747108 CAGCTGGCTCATACACTGTATTAC 59.253 45.833 5.57 0.00 0.00 1.89
1927 2984 4.508124 GCTGGCTCATACACTGTATTACAC 59.492 45.833 0.00 0.00 0.00 2.90
1928 2985 5.682471 GCTGGCTCATACACTGTATTACACT 60.682 44.000 0.00 0.00 0.00 3.55
1929 2986 5.660460 TGGCTCATACACTGTATTACACTG 58.340 41.667 0.00 0.00 0.00 3.66
1930 2987 5.186992 TGGCTCATACACTGTATTACACTGT 59.813 40.000 11.99 11.99 39.68 3.55
1931 2988 6.378848 TGGCTCATACACTGTATTACACTGTA 59.621 38.462 14.63 14.63 37.22 2.74
1932 2989 7.069455 TGGCTCATACACTGTATTACACTGTAT 59.931 37.037 16.84 16.84 38.07 2.29
1933 2990 7.595502 GGCTCATACACTGTATTACACTGTATC 59.404 40.741 18.51 11.87 36.58 2.24
1934 2991 8.135529 GCTCATACACTGTATTACACTGTATCA 58.864 37.037 18.51 10.77 36.58 2.15
1993 3050 4.225208 GTGAATGCAGAGAAAAGAAGCAC 58.775 43.478 0.00 0.00 38.12 4.40
2066 3123 2.620115 CAGATGCCAATGCGGACTATTT 59.380 45.455 0.00 0.00 41.78 1.40
2307 3364 8.237267 CCATCTTAAACATTACCAGAAAGACAC 58.763 37.037 0.00 0.00 0.00 3.67
2309 3366 7.211573 TCTTAAACATTACCAGAAAGACACGA 58.788 34.615 0.00 0.00 0.00 4.35
2336 3393 7.655328 GTCCTATTGAATCTCCAACATACAGAG 59.345 40.741 0.00 0.00 0.00 3.35
2342 3399 6.438741 TGAATCTCCAACATACAGAGACTCTT 59.561 38.462 0.98 0.00 39.36 2.85
2497 3554 3.088532 TGTGTTGGACAAAGCTTCAAGT 58.911 40.909 0.00 0.00 0.00 3.16
2552 3609 4.008330 GGGAGATATGAGCATGAACATGG 58.992 47.826 15.15 0.00 39.16 3.66
2667 3724 4.138487 ACGAAGGTGAAAGTTCAGAGTT 57.862 40.909 0.00 0.00 37.98 3.01
2716 3773 1.202417 AGTCACCATGAGTTATCCGCG 60.202 52.381 0.00 0.00 0.00 6.46
2843 3900 3.132646 AGGACACAAATGCACAACATGTT 59.867 39.130 4.92 4.92 39.60 2.71
2861 3918 3.076621 TGTTCAATGAGAGGTGATGCAC 58.923 45.455 0.00 0.00 0.00 4.57
2923 3980 2.292794 TAGCAGGGCATCGACGGAAC 62.293 60.000 0.00 0.00 0.00 3.62
2925 3982 1.811266 CAGGGCATCGACGGAACAG 60.811 63.158 0.00 0.00 0.00 3.16
2942 3999 1.827789 AGTTGCGGCAAGAAGGCAA 60.828 52.632 16.97 0.00 43.73 4.52
3043 4100 5.630061 CAACATGTATCTGCGATGAAACAA 58.370 37.500 0.00 0.00 0.00 2.83
3226 4283 4.970662 TTAATGAGTTCCTCAATGCTGC 57.029 40.909 0.00 0.00 44.04 5.25
3228 4285 0.035317 TGAGTTCCTCAATGCTGCGT 59.965 50.000 0.00 0.00 37.57 5.24
3459 4516 6.573664 TGTTCATTCTTTTGTCATGTAGGG 57.426 37.500 0.00 0.00 0.00 3.53
3472 4529 4.336433 GTCATGTAGGGTGAAATGGACATG 59.664 45.833 6.49 6.49 43.46 3.21
3503 4560 1.275291 CGAGGCCAACTTGAAGGAGTA 59.725 52.381 5.01 0.00 31.73 2.59
3536 4593 5.163519 GGCCTGCAATTAATACAATCAGTGT 60.164 40.000 0.00 0.00 44.82 3.55
3547 4604 4.749245 ACAATCAGTGTCGGATTCAAAC 57.251 40.909 0.00 0.00 34.38 2.93
3645 4702 4.848757 GCACATAGCCTATACTTGCAAAC 58.151 43.478 0.00 0.00 37.23 2.93
3830 4888 1.400494 GTTCCACACGAGTTGTTGCTT 59.600 47.619 0.00 0.00 35.67 3.91
3888 4946 2.251409 ATGCAGCGAATAGTGCTCAT 57.749 45.000 0.00 0.00 41.72 2.90
3962 5315 3.288964 GAAGAAGGATACGGAGAGACCA 58.711 50.000 0.00 0.00 46.39 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 8.166706 CGTTACATACAAATTAGGAGAACACAC 58.833 37.037 0.00 0.00 0.00 3.82
80 85 5.935206 TGTGTCTGTGACTGTAGTTGAAAAA 59.065 36.000 0.00 0.00 33.15 1.94
104 109 2.358615 TTCGTCAGGCATTGCGCT 60.359 55.556 9.73 0.00 41.91 5.92
227 232 2.383442 TAGGCCTCTCCTAGCGAATT 57.617 50.000 9.68 0.00 45.41 2.17
285 290 2.100989 GACTCTTCCCGTACCTGATGT 58.899 52.381 0.00 0.00 0.00 3.06
286 291 1.065701 CGACTCTTCCCGTACCTGATG 59.934 57.143 0.00 0.00 0.00 3.07
307 1315 5.050837 GCTTTTAGCACCTTTGACATTTGTG 60.051 40.000 0.00 0.00 41.89 3.33
514 1546 0.179000 ACCGGCCATCATCTTCAGTC 59.821 55.000 0.00 0.00 0.00 3.51
530 1562 6.561614 AGACTTTGTACTCACATATGTACCG 58.438 40.000 8.32 2.52 38.48 4.02
652 1684 5.147330 TGAGGTTGACATTATTCTGACGT 57.853 39.130 0.00 0.00 0.00 4.34
767 1799 0.251354 TCATCTGCTTGGTCTCTGCC 59.749 55.000 0.00 0.00 0.00 4.85
864 1896 6.207810 CACTGTTCTAACTCTACTCTCACCTT 59.792 42.308 0.00 0.00 0.00 3.50
865 1897 5.708230 CACTGTTCTAACTCTACTCTCACCT 59.292 44.000 0.00 0.00 0.00 4.00
866 1898 5.706369 TCACTGTTCTAACTCTACTCTCACC 59.294 44.000 0.00 0.00 0.00 4.02
867 1899 6.651643 TCTCACTGTTCTAACTCTACTCTCAC 59.348 42.308 0.00 0.00 0.00 3.51
868 1900 6.770542 TCTCACTGTTCTAACTCTACTCTCA 58.229 40.000 0.00 0.00 0.00 3.27
869 1901 6.877322 ACTCTCACTGTTCTAACTCTACTCTC 59.123 42.308 0.00 0.00 0.00 3.20
870 1902 6.775708 ACTCTCACTGTTCTAACTCTACTCT 58.224 40.000 0.00 0.00 0.00 3.24
871 1903 8.036575 TCTACTCTCACTGTTCTAACTCTACTC 58.963 40.741 0.00 0.00 0.00 2.59
872 1904 7.909518 TCTACTCTCACTGTTCTAACTCTACT 58.090 38.462 0.00 0.00 0.00 2.57
873 1905 7.820872 ACTCTACTCTCACTGTTCTAACTCTAC 59.179 40.741 0.00 0.00 0.00 2.59
874 1906 7.909518 ACTCTACTCTCACTGTTCTAACTCTA 58.090 38.462 0.00 0.00 0.00 2.43
875 1907 6.775708 ACTCTACTCTCACTGTTCTAACTCT 58.224 40.000 0.00 0.00 0.00 3.24
876 1908 7.443259 AACTCTACTCTCACTGTTCTAACTC 57.557 40.000 0.00 0.00 0.00 3.01
877 1909 8.377034 TCTAACTCTACTCTCACTGTTCTAACT 58.623 37.037 0.00 0.00 0.00 2.24
878 1910 8.550710 TCTAACTCTACTCTCACTGTTCTAAC 57.449 38.462 0.00 0.00 0.00 2.34
879 1911 9.001542 GTTCTAACTCTACTCTCACTGTTCTAA 57.998 37.037 0.00 0.00 0.00 2.10
880 1912 8.155510 TGTTCTAACTCTACTCTCACTGTTCTA 58.844 37.037 0.00 0.00 0.00 2.10
881 1913 6.999272 TGTTCTAACTCTACTCTCACTGTTCT 59.001 38.462 0.00 0.00 0.00 3.01
882 1914 7.040961 AGTGTTCTAACTCTACTCTCACTGTTC 60.041 40.741 0.00 0.00 33.37 3.18
883 1915 6.773685 AGTGTTCTAACTCTACTCTCACTGTT 59.226 38.462 0.00 0.00 33.37 3.16
959 1991 8.692710 TCCTGTAGGTAGTATCAAATGTAACAG 58.307 37.037 0.00 0.00 36.34 3.16
1029 2061 7.012044 GCGTATATAACACTCTGGAAATGGTTT 59.988 37.037 0.00 0.00 0.00 3.27
1060 2092 9.755804 CTCTACTTTCTCATCATGCATAAGTAA 57.244 33.333 13.98 7.29 0.00 2.24
1070 2102 8.757877 AGTTAAAGCTCTCTACTTTCTCATCAT 58.242 33.333 0.00 0.00 38.31 2.45
1366 2423 4.505742 GGAACTCAACCCTGAATTCACTCT 60.506 45.833 3.38 0.00 39.13 3.24
1546 2603 1.205655 GCTGTGTGCTAGTCATCCTGA 59.794 52.381 0.00 0.00 38.95 3.86
1701 2758 8.429641 AGAGATGAGTACTGAAACTTTTACCAA 58.570 33.333 0.00 0.00 0.00 3.67
1847 2904 4.189231 GTCCTCGTGTATATTTTGCCTGT 58.811 43.478 0.00 0.00 0.00 4.00
1850 2907 5.065988 ACATTGTCCTCGTGTATATTTTGCC 59.934 40.000 0.00 0.00 0.00 4.52
1923 2980 6.117488 TCGGTGTTATCTCTGATACAGTGTA 58.883 40.000 5.24 5.24 32.61 2.90
1924 2981 4.948004 TCGGTGTTATCTCTGATACAGTGT 59.052 41.667 0.00 0.00 32.61 3.55
1925 2982 5.500645 TCGGTGTTATCTCTGATACAGTG 57.499 43.478 0.00 0.00 32.61 3.66
1927 2984 6.378710 TCTTCGGTGTTATCTCTGATACAG 57.621 41.667 0.00 0.00 0.00 2.74
1928 2985 6.769134 TTCTTCGGTGTTATCTCTGATACA 57.231 37.500 0.00 0.00 0.00 2.29
1929 2986 8.543774 CAATTTCTTCGGTGTTATCTCTGATAC 58.456 37.037 0.00 0.00 0.00 2.24
1930 2987 8.258007 ACAATTTCTTCGGTGTTATCTCTGATA 58.742 33.333 0.00 0.00 0.00 2.15
1931 2988 7.106239 ACAATTTCTTCGGTGTTATCTCTGAT 58.894 34.615 0.00 0.00 0.00 2.90
1932 2989 6.464222 ACAATTTCTTCGGTGTTATCTCTGA 58.536 36.000 0.00 0.00 0.00 3.27
1933 2990 6.727824 ACAATTTCTTCGGTGTTATCTCTG 57.272 37.500 0.00 0.00 0.00 3.35
1934 2991 7.383687 TGTACAATTTCTTCGGTGTTATCTCT 58.616 34.615 0.00 0.00 0.00 3.10
2066 3123 2.158682 GCATACCATACCCATGTGGTCA 60.159 50.000 8.88 0.00 46.83 4.02
2146 3203 7.071196 TGTCAATCTACCTTAGCAATCATAGGT 59.929 37.037 0.00 0.00 43.23 3.08
2186 3243 5.595542 CCAATACCATCATCACCAGACAATT 59.404 40.000 0.00 0.00 0.00 2.32
2193 3250 4.794311 ACATCCAATACCATCATCACCA 57.206 40.909 0.00 0.00 0.00 4.17
2307 3364 5.011090 TGTTGGAGATTCAATAGGACTCG 57.989 43.478 0.00 0.00 30.92 4.18
2309 3366 7.345653 TCTGTATGTTGGAGATTCAATAGGACT 59.654 37.037 0.00 0.00 0.00 3.85
2336 3393 3.424962 GCGGCATTGTACAAAGAAGAGTC 60.425 47.826 13.23 0.00 0.00 3.36
2342 3399 1.890876 AGTGCGGCATTGTACAAAGA 58.109 45.000 13.23 0.00 0.00 2.52
2667 3724 7.107639 TCAGGTGAGAATACATCGTTCATTA 57.892 36.000 0.00 0.00 0.00 1.90
2749 3806 1.357991 GCGCCTTCTCTCTTGCTGTC 61.358 60.000 0.00 0.00 0.00 3.51
2812 3869 0.609131 ATTTGTGTCCTTCGCCCCTG 60.609 55.000 0.00 0.00 0.00 4.45
2923 3980 2.074230 TTGCCTTCTTGCCGCAACTG 62.074 55.000 0.38 0.00 37.58 3.16
2925 3982 1.010419 CATTGCCTTCTTGCCGCAAC 61.010 55.000 0.38 0.00 44.63 4.17
2942 3999 6.429692 TCCATAACAATCTTGTCGTTGAACAT 59.570 34.615 0.00 0.00 41.31 2.71
3221 4278 6.154534 AGGTGGATAATAATATCTACGCAGCA 59.845 38.462 7.88 0.00 45.83 4.41
3225 4282 7.817962 ACACAAGGTGGATAATAATATCTACGC 59.182 37.037 7.88 2.82 45.83 4.42
3431 4488 9.546909 CTACATGACAAAAGAATGAACATGTAC 57.453 33.333 17.89 0.00 42.85 2.90
3459 4516 3.379372 CCCATCAGTCATGTCCATTTCAC 59.621 47.826 0.00 0.00 0.00 3.18
3574 4631 2.743871 GAACAAAGACGACCGCACGC 62.744 60.000 0.00 0.00 36.70 5.34
3581 4638 9.894783 TGCTTCTATATATAGAACAAAGACGAC 57.105 33.333 25.02 13.16 42.66 4.34
3796 4853 2.037251 TGTGGAACTAGTTCTGTGGAGC 59.963 50.000 29.66 15.03 39.45 4.70
3888 4946 0.253044 GGCTGTTGACATAGGAGGCA 59.747 55.000 0.00 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.