Multiple sequence alignment - TraesCS2D01G590000

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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 TraesCS2D01G590000 chr2D 100.000 2889 0 0 1 2889 646086236 646083348 0.000000e+00 5336.0
1 TraesCS2D01G590000 chr2D 90.955 1791 99 28 500 2241 646054186 646055962 0.000000e+00 2351.0
2 TraesCS2D01G590000 chr2D 86.408 103 6 1 27 129 646053494 646053588 3.940000e-19 106.0
3 TraesCS2D01G590000 chr2D 82.353 68 7 2 2621 2685 531322063 531322128 1.000000e-03 54.7
4 TraesCS2D01G590000 chr2A 94.791 1939 67 10 961 2889 773302601 773304515 0.000000e+00 2990.0
5 TraesCS2D01G590000 chr2A 90.255 1334 98 18 933 2241 773380373 773379047 0.000000e+00 1714.0
6 TraesCS2D01G590000 chr2A 91.318 956 47 12 1 952 773296108 773297031 0.000000e+00 1273.0
7 TraesCS2D01G590000 chr2B 88.568 1732 113 46 572 2241 789296070 789294362 0.000000e+00 2023.0
8 TraesCS2D01G590000 chr2B 87.659 1807 124 49 506 2241 571963713 571961935 0.000000e+00 2010.0
9 TraesCS2D01G590000 chr2B 87.639 1804 126 49 506 2241 571851404 571849630 0.000000e+00 2006.0
10 TraesCS2D01G590000 chr2B 87.472 1812 117 55 506 2241 789406335 789404558 0.000000e+00 1988.0
11 TraesCS2D01G590000 chr2B 87.431 1806 126 52 506 2241 571833370 571831596 0.000000e+00 1984.0
12 TraesCS2D01G590000 chr2B 87.403 1802 124 52 506 2241 789424716 789422952 0.000000e+00 1975.0
13 TraesCS2D01G590000 chr2B 86.988 1806 135 49 506 2241 789375129 789373354 0.000000e+00 1941.0
14 TraesCS2D01G590000 chr2B 86.751 1819 127 51 506 2241 571994359 571992572 0.000000e+00 1919.0
15 TraesCS2D01G590000 chr2B 88.593 1613 115 39 664 2241 789326458 789324880 0.000000e+00 1895.0
16 TraesCS2D01G590000 chr2B 83.046 696 40 38 506 1145 571877278 571876605 6.990000e-156 560.0
17 TraesCS2D01G590000 chr2B 84.211 114 10 1 29 142 571834048 571833943 1.420000e-18 104.0
18 TraesCS2D01G590000 chr2B 84.211 114 10 1 29 142 571877973 571877868 1.420000e-18 104.0
19 TraesCS2D01G590000 chr2B 84.211 114 10 1 29 142 789327173 789327068 1.420000e-18 104.0
20 TraesCS2D01G590000 chr2B 84.211 114 10 1 29 142 789375823 789375718 1.420000e-18 104.0
21 TraesCS2D01G590000 chr2B 89.157 83 9 0 60 142 789407015 789406933 1.420000e-18 104.0
22 TraesCS2D01G590000 chr2B 84.211 114 10 1 29 142 789425388 789425283 1.420000e-18 104.0
23 TraesCS2D01G590000 chr2B 88.095 84 10 0 59 142 789358703 789358620 1.830000e-17 100.0


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 TraesCS2D01G590000 chr2D 646083348 646086236 2888 True 5336.0 5336 100.0000 1 2889 1 chr2D.!!$R1 2888
1 TraesCS2D01G590000 chr2D 646053494 646055962 2468 False 1228.5 2351 88.6815 27 2241 2 chr2D.!!$F2 2214
2 TraesCS2D01G590000 chr2A 773302601 773304515 1914 False 2990.0 2990 94.7910 961 2889 1 chr2A.!!$F2 1928
3 TraesCS2D01G590000 chr2A 773379047 773380373 1326 True 1714.0 1714 90.2550 933 2241 1 chr2A.!!$R1 1308
4 TraesCS2D01G590000 chr2A 773296108 773297031 923 False 1273.0 1273 91.3180 1 952 1 chr2A.!!$F1 951
5 TraesCS2D01G590000 chr2B 789294362 789296070 1708 True 2023.0 2023 88.5680 572 2241 1 chr2B.!!$R4 1669
6 TraesCS2D01G590000 chr2B 571961935 571963713 1778 True 2010.0 2010 87.6590 506 2241 1 chr2B.!!$R2 1735
7 TraesCS2D01G590000 chr2B 571849630 571851404 1774 True 2006.0 2006 87.6390 506 2241 1 chr2B.!!$R1 1735
8 TraesCS2D01G590000 chr2B 571992572 571994359 1787 True 1919.0 1919 86.7510 506 2241 1 chr2B.!!$R3 1735
9 TraesCS2D01G590000 chr2B 789404558 789407015 2457 True 1046.0 1988 88.3145 60 2241 2 chr2B.!!$R10 2181
10 TraesCS2D01G590000 chr2B 571831596 571834048 2452 True 1044.0 1984 85.8210 29 2241 2 chr2B.!!$R6 2212
11 TraesCS2D01G590000 chr2B 789422952 789425388 2436 True 1039.5 1975 85.8070 29 2241 2 chr2B.!!$R11 2212
12 TraesCS2D01G590000 chr2B 789373354 789375823 2469 True 1022.5 1941 85.5995 29 2241 2 chr2B.!!$R9 2212
13 TraesCS2D01G590000 chr2B 789324880 789327173 2293 True 999.5 1895 86.4020 29 2241 2 chr2B.!!$R8 2212
14 TraesCS2D01G590000 chr2B 571876605 571877973 1368 True 332.0 560 83.6285 29 1145 2 chr2B.!!$R7 1116

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
742 1086 0.392461 GCCCCAATGAACTGCGACTA 60.392 55.0 0.0 0.0 0.0 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2311 2783 0.4546 CTTAGCCGGTTCTAGCGTCA 59.545 55.0 1.9 0.0 37.4 4.35 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
42 43 5.480642 TGTTTGTTGCATGGATATGGTTT 57.519 34.783 0.00 0.00 34.79 3.27
129 130 1.377725 ACAGCGCCCAATTGGAGAG 60.378 57.895 26.60 17.40 35.62 3.20
188 205 3.782889 GGGGTAACTCGTACGTATGTT 57.217 47.619 16.05 18.86 33.01 2.71
228 471 4.187694 ACGTACGTTGGGTTCTTTGTTTA 58.812 39.130 16.72 0.00 0.00 2.01
364 676 3.484683 ACATTTTCGCAATTACCGAACG 58.515 40.909 11.30 7.13 43.48 3.95
469 781 9.862585 ATGAAAAACGCAAGATTATTTTGAAAC 57.137 25.926 0.00 0.00 43.62 2.78
471 783 9.356929 GAAAAACGCAAGATTATTTTGAAACTG 57.643 29.630 0.00 0.00 43.62 3.16
476 788 7.867403 ACGCAAGATTATTTTGAAACTGACAAT 59.133 29.630 0.00 0.00 43.62 2.71
485 797 8.710835 ATTTTGAAACTGACAATAAAAACCGT 57.289 26.923 0.00 0.00 0.00 4.83
546 860 8.463930 ACAAAATTTGGAAATCAGACAGACTA 57.536 30.769 10.71 0.00 34.12 2.59
548 862 8.786898 CAAAATTTGGAAATCAGACAGACTAGA 58.213 33.333 0.00 0.00 0.00 2.43
734 1078 3.049227 GCAATTCGCCCCAATGAAC 57.951 52.632 0.00 0.00 32.94 3.18
735 1079 0.532115 GCAATTCGCCCCAATGAACT 59.468 50.000 0.00 0.00 32.94 3.01
736 1080 1.736696 GCAATTCGCCCCAATGAACTG 60.737 52.381 0.00 0.00 32.94 3.16
737 1081 0.532115 AATTCGCCCCAATGAACTGC 59.468 50.000 0.00 0.00 0.00 4.40
738 1082 1.656818 ATTCGCCCCAATGAACTGCG 61.657 55.000 0.00 0.00 46.09 5.18
740 1084 2.877691 GCCCCAATGAACTGCGAC 59.122 61.111 0.00 0.00 0.00 5.19
741 1085 1.675641 GCCCCAATGAACTGCGACT 60.676 57.895 0.00 0.00 0.00 4.18
742 1086 0.392461 GCCCCAATGAACTGCGACTA 60.392 55.000 0.00 0.00 0.00 2.59
743 1087 1.369625 CCCCAATGAACTGCGACTAC 58.630 55.000 0.00 0.00 0.00 2.73
744 1088 0.999406 CCCAATGAACTGCGACTACG 59.001 55.000 0.00 0.00 42.93 3.51
749 1093 2.228138 TGAACTGCGACTACGGTTTT 57.772 45.000 0.00 0.00 40.15 2.43
953 1335 4.647853 CAGATCACACAATCAATTCCCCAT 59.352 41.667 0.00 0.00 0.00 4.00
1064 1496 1.511768 CCGTCGACTTCCCTTCCTC 59.488 63.158 14.70 0.00 0.00 3.71
1666 2134 7.504238 CCTAATCTATCTATCTAGTTCCGCCAT 59.496 40.741 0.00 0.00 0.00 4.40
1732 2201 2.618241 GTGACATGTGACAGAAAAGCCA 59.382 45.455 10.82 0.00 0.00 4.75
2299 2771 1.576421 GAAGGTCAAGTGCAAGCCG 59.424 57.895 0.00 0.00 0.00 5.52
2311 2783 0.243636 GCAAGCCGTAGCCAACAAAT 59.756 50.000 0.00 0.00 41.25 2.32
2370 2842 0.388006 TGTCACCGCACTACATGTCG 60.388 55.000 0.00 0.00 0.00 4.35
2447 2919 1.507141 GCCAGTGTCCTTTGTCACCG 61.507 60.000 0.00 0.00 35.45 4.94
2480 2952 0.252197 AGACCTCCATTGCCGGTAAC 59.748 55.000 7.28 0.00 0.00 2.50
2502 2974 4.263572 CGACCCCACTGCCCACAA 62.264 66.667 0.00 0.00 0.00 3.33
2560 3032 5.139727 TCATGTTTTCATCAAAGAGGTGGT 58.860 37.500 0.00 0.00 38.64 4.16
2608 3080 4.639078 TGTGTGGGAGATGATCTTTGAA 57.361 40.909 0.00 0.00 0.00 2.69
2776 3248 2.622436 AGTGAGAGATAAGTTTGCGCC 58.378 47.619 4.18 0.00 0.00 6.53
2828 3300 1.813859 CCCGTTCTAGATGCACCGA 59.186 57.895 0.00 0.00 0.00 4.69
2838 3310 2.382882 AGATGCACCGATCTCTCTTCA 58.617 47.619 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 6.982160 ACCATATCCATGCAACAAACATAT 57.018 33.333 0.00 0.00 0.00 1.78
42 43 9.695526 GTACAATACATATATACACCCAACGAA 57.304 33.333 0.00 0.00 0.00 3.85
195 212 5.723295 ACCCAACGTACGTATGAGTTATTT 58.277 37.500 23.12 0.00 0.00 1.40
469 781 9.672086 TCTTCAATTTACGGTTTTTATTGTCAG 57.328 29.630 0.00 0.00 0.00 3.51
548 862 8.457261 ACGAGAAAAAGAATATGTACGTAGTCT 58.543 33.333 17.23 17.23 43.93 3.24
734 1078 1.193874 GTTGGAAAACCGTAGTCGCAG 59.806 52.381 0.00 0.00 35.54 5.18
735 1079 1.219646 GTTGGAAAACCGTAGTCGCA 58.780 50.000 0.00 0.00 35.54 5.10
736 1080 1.193874 CTGTTGGAAAACCGTAGTCGC 59.806 52.381 0.00 0.00 35.54 5.19
737 1081 2.746269 TCTGTTGGAAAACCGTAGTCG 58.254 47.619 0.00 0.00 0.00 4.18
738 1082 6.980051 ATATTCTGTTGGAAAACCGTAGTC 57.020 37.500 0.00 0.00 37.49 2.59
739 1083 6.713450 ACAATATTCTGTTGGAAAACCGTAGT 59.287 34.615 0.00 0.00 37.49 2.73
740 1084 7.141100 ACAATATTCTGTTGGAAAACCGTAG 57.859 36.000 0.00 0.00 37.49 3.51
741 1085 7.148606 CGTACAATATTCTGTTGGAAAACCGTA 60.149 37.037 0.00 0.00 37.49 4.02
742 1086 6.347888 CGTACAATATTCTGTTGGAAAACCGT 60.348 38.462 0.00 0.00 37.49 4.83
743 1087 6.019152 CGTACAATATTCTGTTGGAAAACCG 58.981 40.000 0.00 0.00 37.49 4.44
744 1088 6.905578 ACGTACAATATTCTGTTGGAAAACC 58.094 36.000 0.00 0.00 37.49 3.27
986 1370 2.409055 CCCATCGTCGTCCGTGGTA 61.409 63.158 13.10 0.00 36.57 3.25
1064 1496 2.414481 CACTGTTTTCTCTGGCGATCAG 59.586 50.000 0.00 0.00 44.68 2.90
1594 2062 1.330655 CCACCACCAGCCGTCTAGAT 61.331 60.000 0.00 0.00 0.00 1.98
1732 2201 3.074412 CCTACTCTTGAAACGGCACATT 58.926 45.455 0.00 0.00 0.00 2.71
2095 2567 9.868277 GAATGGTTATTTCACATGAAACCATAA 57.132 29.630 21.51 10.56 45.34 1.90
2299 2771 3.259064 TCTAGCGTCATTTGTTGGCTAC 58.741 45.455 0.00 0.00 35.28 3.58
2311 2783 0.454600 CTTAGCCGGTTCTAGCGTCA 59.545 55.000 1.90 0.00 37.40 4.35
2370 2842 2.700773 GGAGGCAATGAACGTGGCC 61.701 63.158 0.00 0.00 46.77 5.36
2447 2919 3.054655 TGGAGGTCTTACTATGGCCAAAC 60.055 47.826 10.96 0.00 0.00 2.93
2480 2952 2.722201 GGGCAGTGGGGTCGTAGAG 61.722 68.421 0.00 0.00 36.95 2.43
2502 2974 4.942761 AGATGCAATTTGACAAACACCT 57.057 36.364 1.94 0.00 0.00 4.00
2560 3032 7.170277 TGAAGAGTTTCATGATCCATTTGAGA 58.830 34.615 0.00 0.00 38.37 3.27
2608 3080 5.055265 TCTTCCTCCTCTGACGATAATCT 57.945 43.478 0.00 0.00 0.00 2.40
2617 3089 4.876580 TCATCATCTTCTTCCTCCTCTGA 58.123 43.478 0.00 0.00 0.00 3.27
2619 3091 6.462768 CGAATTCATCATCTTCTTCCTCCTCT 60.463 42.308 6.22 0.00 0.00 3.69
2694 3166 3.226346 TCGACCAATCTAAGAACCACG 57.774 47.619 0.00 0.00 0.00 4.94
2776 3248 8.964476 ATATTAAAGGGGATATACTGCATTCG 57.036 34.615 0.00 0.00 0.00 3.34
2828 3300 2.224281 TGCAACGGTGTTGAAGAGAGAT 60.224 45.455 13.48 0.00 0.00 2.75
2838 3310 2.675348 CCACAATTTTTGCAACGGTGTT 59.325 40.909 0.66 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.