Multiple sequence alignment - TraesCS4D01G135200

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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 TraesCS4D01G135200 chr4D 100.000 2877 0 0 1 2877 121969625 121972501 0.000000e+00 5313.0
1 TraesCS4D01G135200 chr4B 93.950 1124 39 11 2 1108 184863724 184864835 0.000000e+00 1672.0
2 TraesCS4D01G135200 chr4B 97.896 903 19 0 1111 2013 184864867 184865769 0.000000e+00 1563.0
3 TraesCS4D01G135200 chr4B 93.468 842 43 10 1993 2827 184878313 184879149 0.000000e+00 1240.0
4 TraesCS4D01G135200 chr4B 95.833 48 0 1 1991 2038 574003777 574003732 3.070000e-10 76.8
5 TraesCS4D01G135200 chr4B 95.652 46 0 2 1991 2036 226468090 226468047 3.980000e-09 73.1
6 TraesCS4D01G135200 chr4B 97.222 36 1 0 1504 1539 494692058 494692023 8.610000e-06 62.1
7 TraesCS4D01G135200 chr4A 93.683 1124 45 9 2 1108 449118915 449117801 0.000000e+00 1659.0
8 TraesCS4D01G135200 chr4A 97.056 917 21 4 1111 2027 449117769 449116859 0.000000e+00 1539.0
9 TraesCS4D01G135200 chr4A 88.043 92 10 1 2221 2312 449116661 449116571 1.090000e-19 108.0
10 TraesCS4D01G135200 chr2D 85.885 503 55 5 2349 2835 140245162 140244660 3.280000e-144 521.0
11 TraesCS4D01G135200 chr2D 83.130 575 69 20 2322 2875 626804226 626803659 1.540000e-137 499.0
12 TraesCS4D01G135200 chr7B 83.072 573 69 16 2322 2869 710459266 710458697 1.990000e-136 496.0
13 TraesCS4D01G135200 chr7B 78.365 208 33 11 1338 1539 590500936 590500735 1.080000e-24 124.0
14 TraesCS4D01G135200 chr3A 80.560 571 70 16 2325 2876 733869453 733870001 4.470000e-108 401.0
15 TraesCS4D01G135200 chr6B 84.825 257 31 5 2320 2572 331054067 331054319 4.760000e-63 252.0
16 TraesCS4D01G135200 chr3B 80.667 300 39 9 2508 2792 567281704 567281999 6.240000e-52 215.0
17 TraesCS4D01G135200 chr3B 87.912 91 9 2 2631 2720 421093816 421093905 3.920000e-19 106.0
18 TraesCS4D01G135200 chr5D 88.000 125 14 1 2423 2547 40783587 40783464 2.310000e-31 147.0
19 TraesCS4D01G135200 chr5D 72.781 338 55 29 1500 1811 520910292 520910618 2.380000e-11 80.5
20 TraesCS4D01G135200 chr5D 89.474 57 1 3 1992 2047 98721696 98721748 1.850000e-07 67.6
21 TraesCS4D01G135200 chr7D 77.404 208 35 11 1338 1539 547458011 547457810 2.340000e-21 113.0
22 TraesCS4D01G135200 chr7A 76.037 217 40 11 1329 1539 631365248 631365458 5.070000e-18 102.0
23 TraesCS4D01G135200 chr7A 92.157 51 2 2 1992 2041 711779142 711779093 1.430000e-08 71.3
24 TraesCS4D01G135200 chr3D 84.112 107 14 3 2629 2733 300145564 300145459 1.820000e-17 100.0
25 TraesCS4D01G135200 chr3D 93.617 47 1 2 1983 2027 508320441 508320487 5.140000e-08 69.4
26 TraesCS4D01G135200 chr5B 86.747 83 11 0 2496 2578 619292354 619292272 3.050000e-15 93.5
27 TraesCS4D01G135200 chr5B 94.118 51 0 2 1991 2040 529543410 529543362 1.110000e-09 75.0
28 TraesCS4D01G135200 chr5B 72.603 219 48 9 1326 1538 656925914 656926126 8.610000e-06 62.1
29 TraesCS4D01G135200 chr1B 89.831 59 1 4 1983 2039 647588627 647588572 1.430000e-08 71.3
30 TraesCS4D01G135200 chr5A 94.872 39 2 0 1500 1538 649441752 649441790 8.610000e-06 62.1


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 TraesCS4D01G135200 chr4D 121969625 121972501 2876 False 5313.0 5313 100.000000 1 2877 1 chr4D.!!$F1 2876
1 TraesCS4D01G135200 chr4B 184863724 184865769 2045 False 1617.5 1672 95.923000 2 2013 2 chr4B.!!$F2 2011
2 TraesCS4D01G135200 chr4B 184878313 184879149 836 False 1240.0 1240 93.468000 1993 2827 1 chr4B.!!$F1 834
3 TraesCS4D01G135200 chr4A 449116571 449118915 2344 True 1102.0 1659 92.927333 2 2312 3 chr4A.!!$R1 2310
4 TraesCS4D01G135200 chr2D 140244660 140245162 502 True 521.0 521 85.885000 2349 2835 1 chr2D.!!$R1 486
5 TraesCS4D01G135200 chr2D 626803659 626804226 567 True 499.0 499 83.130000 2322 2875 1 chr2D.!!$R2 553
6 TraesCS4D01G135200 chr7B 710458697 710459266 569 True 496.0 496 83.072000 2322 2869 1 chr7B.!!$R2 547
7 TraesCS4D01G135200 chr3A 733869453 733870001 548 False 401.0 401 80.560000 2325 2876 1 chr3A.!!$F1 551

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
989 1014 0.319383 AGCTCAGAGCAAGACACACG 60.319 55.0 24.64 0.0 45.56 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2513 2617 0.106469 TCTCTAGACGCTGGGAGCAT 60.106 55.0 0.0 0.0 42.58 3.79 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
60 62 8.837788 TGTGCATCTATCATTATAAACCAGAG 57.162 34.615 0.00 0.00 0.00 3.35
68 70 6.147864 TCATTATAAACCAGAGCAATTGGC 57.852 37.500 7.72 0.00 45.30 4.52
112 114 5.351465 TCTTCAGAGTTCAGTTGTTGTGTTC 59.649 40.000 0.00 0.00 0.00 3.18
166 168 5.105997 GGAAAGACAAAAGGGACTCATCATG 60.106 44.000 0.00 0.00 38.49 3.07
184 186 0.729690 TGAGCGACAGTGAGATCGAG 59.270 55.000 5.86 0.00 40.86 4.04
186 188 1.131504 GAGCGACAGTGAGATCGAGTT 59.868 52.381 5.86 0.00 40.86 3.01
359 361 2.928396 AACTGGGGCTACCGCTGT 60.928 61.111 7.29 7.29 46.81 4.40
511 519 8.903820 CAAAGGAGAAGGAGAAAAGAAAAGTTA 58.096 33.333 0.00 0.00 0.00 2.24
533 541 2.507407 ATTTGCAGGGGAACGTACAT 57.493 45.000 0.00 0.00 0.00 2.29
616 624 1.137872 CAGGTAGCCCACTCACTGATC 59.862 57.143 0.00 0.00 33.72 2.92
854 873 3.664107 TGCAGGAACAAAGTAGCAGTAG 58.336 45.455 0.00 0.00 0.00 2.57
855 874 3.071023 TGCAGGAACAAAGTAGCAGTAGT 59.929 43.478 0.00 0.00 0.00 2.73
856 875 4.282449 TGCAGGAACAAAGTAGCAGTAGTA 59.718 41.667 0.00 0.00 0.00 1.82
962 987 2.352805 CACCCCTGCTCCACTTCC 59.647 66.667 0.00 0.00 0.00 3.46
989 1014 0.319383 AGCTCAGAGCAAGACACACG 60.319 55.000 24.64 0.00 45.56 4.49
1027 1054 2.583101 TCCTCTAAGCTCTTCCTCCTCA 59.417 50.000 0.00 0.00 0.00 3.86
1064 1091 4.944619 TCTCCATGGCAATCACTAGTAG 57.055 45.455 6.96 0.00 0.00 2.57
1093 1125 3.310227 GCATGCATCATCATCTAGCTAGC 59.690 47.826 16.35 6.62 0.00 3.42
1098 1130 5.104374 GCATCATCATCTAGCTAGCTCTTC 58.896 45.833 23.26 0.00 0.00 2.87
1108 1140 7.646548 TCTAGCTAGCTCTTCAACTTCAATA 57.353 36.000 23.26 0.00 0.00 1.90
1109 1141 8.243961 TCTAGCTAGCTCTTCAACTTCAATAT 57.756 34.615 23.26 0.00 0.00 1.28
1141 1202 6.040247 AGTATGTACACGGTGATGTAATGTG 58.960 40.000 16.29 0.00 36.83 3.21
1379 1440 4.475135 GGGGCTGCTCCTTCGACC 62.475 72.222 12.38 0.00 34.39 4.79
1762 1823 1.471676 CCCACTATGTTCTCGCACCTC 60.472 57.143 0.00 0.00 0.00 3.85
1978 2039 2.344592 ACAGTATGAGGGTGTTTGGGA 58.655 47.619 0.00 0.00 39.69 4.37
2022 2083 5.734855 AAATGAGACACGTATTACCATGC 57.265 39.130 0.00 0.00 0.00 4.06
2026 2087 4.998033 TGAGACACGTATTACCATGCAAAA 59.002 37.500 0.00 0.00 0.00 2.44
2027 2088 5.121611 TGAGACACGTATTACCATGCAAAAG 59.878 40.000 0.00 0.00 0.00 2.27
2028 2089 5.001232 AGACACGTATTACCATGCAAAAGT 58.999 37.500 0.00 0.00 0.00 2.66
2030 2091 6.651643 AGACACGTATTACCATGCAAAAGTAA 59.348 34.615 8.48 8.48 0.00 2.24
2032 2093 7.822658 ACACGTATTACCATGCAAAAGTAAAT 58.177 30.769 9.71 0.75 30.33 1.40
2074 2136 6.459066 CATATATCTCTTTTCTTCTGCCCGA 58.541 40.000 0.00 0.00 0.00 5.14
2150 2212 5.649782 AGTCCGAAACTAAACCGATAAGA 57.350 39.130 0.00 0.00 36.07 2.10
2154 2216 7.064253 AGTCCGAAACTAAACCGATAAGATTTG 59.936 37.037 0.00 0.00 36.07 2.32
2227 2322 4.764823 TCGGATAGTTCAAAGGCACAAATT 59.235 37.500 0.00 0.00 0.00 1.82
2240 2335 6.949578 AGGCACAAATTTTAAACATCATCG 57.050 33.333 0.00 0.00 0.00 3.84
2243 2338 5.119898 GCACAAATTTTAAACATCATCGGCA 59.880 36.000 0.00 0.00 0.00 5.69
2317 2412 4.620982 GGCAACCATTATGAATAGGCAAC 58.379 43.478 0.00 0.00 0.00 4.17
2320 2415 5.221501 GCAACCATTATGAATAGGCAACCAT 60.222 40.000 0.00 0.00 37.17 3.55
2346 2441 0.392461 AGATGCCCGTGCGTTGTATT 60.392 50.000 0.00 0.00 41.78 1.89
2353 2448 1.651987 CGTGCGTTGTATTGGGAGAT 58.348 50.000 0.00 0.00 0.00 2.75
2443 2543 1.304052 GCCCACCATGTTAGCCACA 60.304 57.895 0.00 0.00 40.71 4.17
2499 2603 6.311723 CGTGTTGTCCATGTAAAACTAATCC 58.688 40.000 0.00 0.00 0.00 3.01
2609 2723 6.488006 GCCCAAATTCTAGAGCAATCTTATGA 59.512 38.462 0.00 0.00 0.00 2.15
2738 2859 4.106197 CAGCAGTTTAGAGTACACCGATC 58.894 47.826 0.00 0.00 0.00 3.69
2870 3004 8.669946 ACAAGTTTGGTTTTCTTTTCTTTTCA 57.330 26.923 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 40 7.912056 TGCTCTGGTTTATAATGATAGATGC 57.088 36.000 0.00 0.00 0.00 3.91
60 62 1.474077 CAGTTCTACCAGGCCAATTGC 59.526 52.381 5.01 0.00 40.16 3.56
68 70 3.264450 AGACCCAATTCAGTTCTACCAGG 59.736 47.826 0.00 0.00 0.00 4.45
112 114 4.191544 TGAAGAAGCGAGGATTATGGTTG 58.808 43.478 0.00 0.00 0.00 3.77
166 168 0.730265 ACTCGATCTCACTGTCGCTC 59.270 55.000 0.00 0.00 37.74 5.03
184 186 3.733337 TCAGAAAGGCAGACTCTTCAAC 58.267 45.455 0.00 0.00 0.00 3.18
186 188 4.630644 AATCAGAAAGGCAGACTCTTCA 57.369 40.909 0.00 0.00 0.00 3.02
359 361 9.496873 TTTGGATAACTAACGAAAAGAATGAGA 57.503 29.630 0.00 0.00 0.00 3.27
389 391 0.036388 TTGGCTACCTACTGTGCTGC 60.036 55.000 0.00 0.00 0.00 5.25
511 519 2.303600 TGTACGTTCCCCTGCAAATACT 59.696 45.455 0.00 0.00 0.00 2.12
616 624 5.053145 CAGGCTAGCTGGTAGATTAACTTG 58.947 45.833 15.72 2.74 0.00 3.16
692 706 7.556635 TCTGAACTGAAACTATGCTAGCTACTA 59.443 37.037 17.23 4.32 0.00 1.82
734 753 4.516323 TGCATTCAAGCTGCATTCTACTA 58.484 39.130 1.02 0.00 44.30 1.82
735 754 3.349927 TGCATTCAAGCTGCATTCTACT 58.650 40.909 1.02 0.00 44.30 2.57
736 755 3.770263 TGCATTCAAGCTGCATTCTAC 57.230 42.857 1.02 0.00 44.30 2.59
854 873 8.597662 TGACAGTTGAACCACTTAATAAGTAC 57.402 34.615 5.23 0.00 40.46 2.73
855 874 9.616156 TTTGACAGTTGAACCACTTAATAAGTA 57.384 29.630 5.23 0.00 40.46 2.24
856 875 8.514330 TTTGACAGTTGAACCACTTAATAAGT 57.486 30.769 0.00 0.00 44.06 2.24
962 987 1.725706 CTTGCTCTGAGCTCGAACTTG 59.274 52.381 28.04 7.55 42.97 3.16
1027 1054 2.709397 TGGAGATGATGGCACTGATGAT 59.291 45.455 0.00 0.00 0.00 2.45
1064 1091 3.744942 AGATGATGATGCATGCTTACGAC 59.255 43.478 20.33 6.81 0.00 4.34
1093 1125 9.107177 ACTCTGCATTATATTGAAGTTGAAGAG 57.893 33.333 4.54 4.54 0.00 2.85
1108 1140 5.068591 TCACCGTGTACATACTCTGCATTAT 59.931 40.000 0.00 0.00 0.00 1.28
1109 1141 4.399934 TCACCGTGTACATACTCTGCATTA 59.600 41.667 0.00 0.00 0.00 1.90
2040 2101 9.927081 AAGAAAAGAGATATATGGTGTTTGGAT 57.073 29.630 0.00 0.00 0.00 3.41
2057 2118 1.929836 CGATCGGGCAGAAGAAAAGAG 59.070 52.381 7.38 0.00 0.00 2.85
2064 2125 0.807667 CCAGTTCGATCGGGCAGAAG 60.808 60.000 16.41 0.00 0.00 2.85
2074 2136 1.227380 GCGCTCCATCCAGTTCGAT 60.227 57.895 0.00 0.00 0.00 3.59
2150 2212 4.442375 TGTTGTTCGTTTGTGGACAAAT 57.558 36.364 8.14 0.00 46.12 2.32
2154 2216 2.170770 CGTTGTTGTTCGTTTGTGGAC 58.829 47.619 0.00 0.00 0.00 4.02
2243 2338 4.814294 GGACGCCGACGCCATCTT 62.814 66.667 0.00 0.00 45.53 2.40
2443 2543 9.273016 CAACAACGAGGGTGAGAAATAATATAT 57.727 33.333 0.00 0.00 0.00 0.86
2513 2617 0.106469 TCTCTAGACGCTGGGAGCAT 60.106 55.000 0.00 0.00 42.58 3.79
2515 2619 1.898902 TATCTCTAGACGCTGGGAGC 58.101 55.000 0.00 0.00 38.02 4.70
2791 2915 7.610580 AAATGGGAGACAAAAAGAAATGGTA 57.389 32.000 0.00 0.00 0.00 3.25
2792 2916 6.499106 AAATGGGAGACAAAAAGAAATGGT 57.501 33.333 0.00 0.00 0.00 3.55
2845 2979 8.669946 TGAAAAGAAAAGAAAACCAAACTTGT 57.330 26.923 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.