Multiple sequence alignment - TraesCS1B01G391000

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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 TraesCS1B01G391000 chr1B 100.000 5000 0 0 1 5000 624086125 624091124 0.000000e+00 9234.0
1 TraesCS1B01G391000 chr1B 82.307 1023 123 28 1287 2296 624502538 624503515 0.000000e+00 833.0
2 TraesCS1B01G391000 chr1B 80.503 954 123 35 3465 4388 624505180 624506100 0.000000e+00 673.0
3 TraesCS1B01G391000 chr1B 79.272 714 135 9 60 770 20810278 20810981 2.090000e-133 486.0
4 TraesCS1B01G391000 chr1B 73.532 971 172 51 1360 2296 624498959 624499878 1.760000e-74 291.0
5 TraesCS1B01G391000 chr1B 87.500 128 14 2 4676 4802 624506466 624506592 4.030000e-31 147.0
6 TraesCS1B01G391000 chr1A 96.678 4124 113 10 888 5000 548530842 548534952 0.000000e+00 6835.0
7 TraesCS1B01G391000 chr1A 100.000 69 0 0 771 839 548530208 548530276 1.460000e-25 128.0
8 TraesCS1B01G391000 chr1A 95.082 61 2 1 1 61 548530165 548530224 1.480000e-15 95.3
9 TraesCS1B01G391000 chr1D 96.827 2206 49 12 2812 5000 453825046 453827247 0.000000e+00 3666.0
10 TraesCS1B01G391000 chr1D 94.030 1541 52 14 771 2281 453821502 453823032 0.000000e+00 2300.0
11 TraesCS1B01G391000 chr1D 92.275 712 47 4 60 770 482340013 482340717 0.000000e+00 1003.0
12 TraesCS1B01G391000 chr1D 92.146 713 44 6 60 770 463320029 463319327 0.000000e+00 996.0
13 TraesCS1B01G391000 chr1D 96.838 506 8 2 2310 2815 453823366 453823863 0.000000e+00 839.0
14 TraesCS1B01G391000 chr1D 82.307 1023 123 27 1287 2296 453965505 453966482 0.000000e+00 833.0
15 TraesCS1B01G391000 chr1D 81.322 953 116 36 3465 4388 453968133 453969052 0.000000e+00 717.0
16 TraesCS1B01G391000 chr1D 73.368 965 176 50 1363 2296 453961916 453962830 2.950000e-72 283.0
17 TraesCS1B01G391000 chr1D 80.212 283 35 10 964 1227 453961539 453961819 5.110000e-45 193.0
18 TraesCS1B01G391000 chr1D 87.500 128 14 2 4676 4802 453969262 453969388 4.030000e-31 147.0
19 TraesCS1B01G391000 chr7D 92.717 714 42 6 59 770 510716244 510715539 0.000000e+00 1022.0
20 TraesCS1B01G391000 chr3B 88.219 713 75 4 59 770 199553103 199553807 0.000000e+00 843.0
21 TraesCS1B01G391000 chr3B 87.785 614 66 4 159 770 199608875 199609481 0.000000e+00 710.0
22 TraesCS1B01G391000 chr3B 92.308 104 8 0 59 162 199597442 199597545 1.120000e-31 148.0
23 TraesCS1B01G391000 chr3B 82.759 87 13 2 1668 1753 42475033 42474948 5.370000e-10 76.8
24 TraesCS1B01G391000 chr3B 79.348 92 18 1 58 148 41514193 41514284 4.180000e-06 63.9
25 TraesCS1B01G391000 chr6B 88.655 476 47 3 295 770 645419914 645420382 1.560000e-159 573.0
26 TraesCS1B01G391000 chr6B 92.704 233 16 1 62 293 645406820 645407052 8.020000e-88 335.0
27 TraesCS1B01G391000 chr6B 88.710 62 7 0 62 123 132153426 132153487 5.370000e-10 76.8
28 TraesCS1B01G391000 chr6A 77.116 319 70 2 1981 2296 556101195 556100877 1.110000e-41 182.0
29 TraesCS1B01G391000 chr6A 82.424 165 21 6 1072 1232 556094335 556094175 2.430000e-28 137.0
30 TraesCS1B01G391000 chr6D 76.803 319 71 2 1981 2296 411497825 411497507 5.140000e-40 176.0
31 TraesCS1B01G391000 chr3D 76.875 320 69 5 1981 2296 24102832 24102514 5.140000e-40 176.0
32 TraesCS1B01G391000 chr3D 82.609 161 20 6 1072 1228 24095204 24095048 8.730000e-28 135.0
33 TraesCS1B01G391000 chr3D 82.796 93 14 2 1662 1753 24872827 24872736 1.150000e-11 82.4
34 TraesCS1B01G391000 chr3A 76.176 319 69 7 1981 2294 33585068 33584752 1.440000e-35 161.0
35 TraesCS1B01G391000 chr3A 71.958 378 91 13 1925 2293 33885609 33885238 4.120000e-16 97.1
36 TraesCS1B01G391000 chr2D 82.353 187 29 3 1045 1229 26931381 26931565 5.180000e-35 159.0
37 TraesCS1B01G391000 chr2D 85.333 75 10 1 1352 1425 26931645 26931719 5.370000e-10 76.8
38 TraesCS1B01G391000 chr2B 82.703 185 24 6 1049 1229 42177663 42177843 1.860000e-34 158.0
39 TraesCS1B01G391000 chr2B 82.530 166 25 3 1067 1230 42176381 42176544 5.220000e-30 143.0
40 TraesCS1B01G391000 chr2A 82.036 167 24 4 1067 1230 29149311 29149474 2.430000e-28 137.0


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 TraesCS1B01G391000 chr1B 624086125 624091124 4999 False 9234.000000 9234 100.000000 1 5000 1 chr1B.!!$F2 4999
1 TraesCS1B01G391000 chr1B 20810278 20810981 703 False 486.000000 486 79.272000 60 770 1 chr1B.!!$F1 710
2 TraesCS1B01G391000 chr1B 624498959 624506592 7633 False 486.000000 833 80.960500 1287 4802 4 chr1B.!!$F3 3515
3 TraesCS1B01G391000 chr1A 548530165 548534952 4787 False 2352.766667 6835 97.253333 1 5000 3 chr1A.!!$F1 4999
4 TraesCS1B01G391000 chr1D 453821502 453827247 5745 False 2268.333333 3666 95.898333 771 5000 3 chr1D.!!$F2 4229
5 TraesCS1B01G391000 chr1D 482340013 482340717 704 False 1003.000000 1003 92.275000 60 770 1 chr1D.!!$F1 710
6 TraesCS1B01G391000 chr1D 463319327 463320029 702 True 996.000000 996 92.146000 60 770 1 chr1D.!!$R1 710
7 TraesCS1B01G391000 chr1D 453961539 453969388 7849 False 434.600000 833 80.941800 964 4802 5 chr1D.!!$F3 3838
8 TraesCS1B01G391000 chr7D 510715539 510716244 705 True 1022.000000 1022 92.717000 59 770 1 chr7D.!!$R1 711
9 TraesCS1B01G391000 chr3B 199553103 199553807 704 False 843.000000 843 88.219000 59 770 1 chr3B.!!$F2 711
10 TraesCS1B01G391000 chr3B 199608875 199609481 606 False 710.000000 710 87.785000 159 770 1 chr3B.!!$F4 611

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
497 500 0.105039 CAATAGTCCCTGCCGAGTCC 59.895 60.000 0.00 0.0 0.00 3.85 F
856 870 0.179056 CTGGGTCTGGACACAACGTT 60.179 55.000 7.12 0.0 45.20 3.99 F
861 875 0.179094 TCTGGACACAACGTTCGCTT 60.179 50.000 0.00 0.0 0.00 4.68 F
1898 6131 1.619654 CATGACCCTTCCAGTTGCAA 58.380 50.000 0.00 0.0 0.00 4.08 F
1970 6203 1.909302 TCTTTCTTCGGGAGATTGGCT 59.091 47.619 0.00 0.0 39.57 4.75 F
3359 9335 0.320374 TGTGCGGTCTCCACCTTAAG 59.680 55.000 0.00 0.0 41.17 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2041 6274 0.316204 TTTTCTGTCTCGTCGTCCCC 59.684 55.000 0.0 0.0 0.00 4.81 R
2077 6310 2.225167 GGGTGGGGGTGTAGAAAATCAA 60.225 50.000 0.0 0.0 0.00 2.57 R
2456 6993 8.204836 GTCCATACTCCATACTTGATTACTTGT 58.795 37.037 0.0 0.0 0.00 3.16 R
2937 8907 3.081710 ACCATGTAAAGCCCTTGTACC 57.918 47.619 0.0 0.0 0.00 3.34 R
3606 9826 5.174035 GGAATGATCAAACGTAGAGATGACG 59.826 44.000 0.0 0.0 45.75 4.35 R
4369 10617 1.323412 AGCCAGGCTCTATGTACTCG 58.677 55.000 8.7 0.0 30.62 4.18 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
27 28 4.376146 TGTTTGCAGGAAAACAAATAGGC 58.624 39.130 3.08 0.00 44.79 3.93
148 149 2.801483 CCACATGGGTTGGTACATCAA 58.199 47.619 0.00 0.00 39.30 2.57
183 184 6.037172 GCATAACATGTTCTACTGGGTACAAG 59.963 42.308 15.85 0.00 0.00 3.16
189 190 2.901051 CTACTGGGTACAAGCGGCCG 62.901 65.000 24.05 24.05 0.00 6.13
346 349 6.530120 TGAAGTCCATAGCTTCAACTAACAA 58.470 36.000 5.41 0.00 46.21 2.83
347 350 6.426937 TGAAGTCCATAGCTTCAACTAACAAC 59.573 38.462 5.41 0.00 46.21 3.32
366 369 0.455295 CTGTGAGTCCGTCTCGAAGC 60.455 60.000 0.00 0.00 45.46 3.86
380 383 0.175302 CGAAGCTGACTCTCAGGCAT 59.825 55.000 1.55 0.00 44.43 4.40
483 486 2.123428 GCCCTGGCTGCCACAATAG 61.123 63.158 19.30 7.64 38.26 1.73
488 491 1.207488 TGGCTGCCACAATAGTCCCT 61.207 55.000 19.30 0.00 0.00 4.20
497 500 0.105039 CAATAGTCCCTGCCGAGTCC 59.895 60.000 0.00 0.00 0.00 3.85
499 502 1.950748 ATAGTCCCTGCCGAGTCCCT 61.951 60.000 0.00 0.00 0.00 4.20
500 503 2.569218 TAGTCCCTGCCGAGTCCCTC 62.569 65.000 0.00 0.00 0.00 4.30
579 582 2.434761 GCGTTGATTTTCAGCATCTCG 58.565 47.619 0.00 0.00 0.00 4.04
690 694 1.452108 GGCTATTTCTGCTGCCGGT 60.452 57.895 1.90 0.00 35.79 5.28
748 752 0.327924 CCACCAATGCCACCAGTAGA 59.672 55.000 0.00 0.00 0.00 2.59
752 756 4.269183 CACCAATGCCACCAGTAGATTAA 58.731 43.478 0.00 0.00 0.00 1.40
856 870 0.179056 CTGGGTCTGGACACAACGTT 60.179 55.000 7.12 0.00 45.20 3.99
859 873 1.563173 GTCTGGACACAACGTTCGC 59.437 57.895 0.00 0.00 0.00 4.70
861 875 0.179094 TCTGGACACAACGTTCGCTT 60.179 50.000 0.00 0.00 0.00 4.68
1110 1655 3.646976 TCGGCGCGTATCTCCGAG 61.647 66.667 18.75 0.00 46.12 4.63
1151 1696 2.360852 GTCCAGGACGAGGGACGA 60.361 66.667 3.05 0.00 43.67 4.20
1591 5811 3.050089 TGGAGTAAGAAGGTTGGGTTGA 58.950 45.455 0.00 0.00 0.00 3.18
1729 5956 3.021695 AGACCGTTCGATGAACATCCTA 58.978 45.455 10.01 0.00 42.05 2.94
1730 5957 3.114065 GACCGTTCGATGAACATCCTAC 58.886 50.000 10.01 6.56 42.05 3.18
1845 6078 2.359107 CGTGATGTGGCCTGCTGT 60.359 61.111 3.32 0.00 0.00 4.40
1867 6100 6.372981 TGTGATGATTTGATCAAGTTTGTCG 58.627 36.000 8.41 0.00 43.50 4.35
1898 6131 1.619654 CATGACCCTTCCAGTTGCAA 58.380 50.000 0.00 0.00 0.00 4.08
1902 6135 2.278330 CCCTTCCAGTTGCAAGCCC 61.278 63.158 0.00 0.00 0.00 5.19
1970 6203 1.909302 TCTTTCTTCGGGAGATTGGCT 59.091 47.619 0.00 0.00 39.57 4.75
1971 6204 2.093447 TCTTTCTTCGGGAGATTGGCTC 60.093 50.000 0.00 0.00 43.17 4.70
2041 6274 2.109126 GCTTTACTGCCGGAGCTGG 61.109 63.158 5.05 0.00 41.92 4.85
2077 6310 7.775561 AGACAGAAAAGTTACACCTGAAGAAAT 59.224 33.333 0.00 0.00 0.00 2.17
2579 7119 8.766000 TCGTGAGTACTTTGCTTCATTATAAA 57.234 30.769 0.00 0.00 0.00 1.40
2849 8819 6.650390 CCATTGAATCGAAAATTGAACCCTTT 59.350 34.615 0.00 0.00 0.00 3.11
2937 8907 5.236478 CAGGCGTAGATATAACCAACAAAGG 59.764 44.000 0.00 0.00 0.00 3.11
2945 8915 7.116736 AGATATAACCAACAAAGGGTACAAGG 58.883 38.462 0.00 0.00 37.77 3.61
2954 8924 4.086457 CAAAGGGTACAAGGGCTTTACAT 58.914 43.478 0.00 0.00 0.00 2.29
3359 9335 0.320374 TGTGCGGTCTCCACCTTAAG 59.680 55.000 0.00 0.00 41.17 1.85
3567 9784 3.989817 GGTCAATGCTTGGAACATGAAAC 59.010 43.478 0.00 0.00 39.30 2.78
3606 9826 1.181786 AGCTCACTAGTCTGTCCAGC 58.818 55.000 0.00 0.00 0.00 4.85
3625 9845 3.483922 CAGCGTCATCTCTACGTTTGATC 59.516 47.826 0.00 0.00 42.26 2.92
3913 10140 0.250295 TTCCTCTGTTGGTGAAGGCG 60.250 55.000 0.00 0.00 0.00 5.52
3974 10201 8.374327 TCACGGTATATACACGAGGATATATG 57.626 38.462 22.42 6.84 0.00 1.78
4069 10296 3.077359 AGATTTCAACTGGCTACTGTGC 58.923 45.455 0.00 0.00 0.00 4.57
4093 10320 0.247814 CGCGAAGTGATGCATCAACC 60.248 55.000 30.24 18.89 43.07 3.77
4110 10337 5.755409 TCAACCTCTACTAAAGCCATGAA 57.245 39.130 0.00 0.00 0.00 2.57
4151 10396 8.803235 CCACCCTTAAAGCTTTAAAGAAGTATT 58.197 33.333 27.06 7.75 32.73 1.89
4369 10617 2.587522 GAGGGACCAGGCCATAAAATC 58.412 52.381 5.01 0.00 0.00 2.17
4415 10726 3.879295 CGGTGCCAATCTATTCTGTGATT 59.121 43.478 0.00 0.00 33.69 2.57
4882 11286 6.007703 CCTCAAAAGGTATAACAAACCCTGA 58.992 40.000 0.00 0.00 37.77 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
137 138 3.750371 CACTGGGAGTTTGATGTACCAA 58.250 45.455 0.00 0.00 0.00 3.67
148 149 3.439857 ACATGTTATGCACTGGGAGTT 57.560 42.857 0.00 0.00 0.00 3.01
189 190 3.070018 AGCGCATGAGTTAGCCAATATC 58.930 45.455 11.47 0.00 0.00 1.63
346 349 0.875728 CTTCGAGACGGACTCACAGT 59.124 55.000 8.14 0.00 45.14 3.55
347 350 0.455295 GCTTCGAGACGGACTCACAG 60.455 60.000 8.14 3.97 45.14 3.66
366 369 0.464870 CTGGGATGCCTGAGAGTCAG 59.535 60.000 4.35 0.00 43.91 3.51
380 383 4.020617 CTTGCAGCCGACCTGGGA 62.021 66.667 0.00 0.00 42.03 4.37
593 596 0.038744 AGCCTGTCTGGACAAATGGG 59.961 55.000 4.94 4.06 41.33 4.00
672 676 1.452108 ACCGGCAGCAGAAATAGCC 60.452 57.895 0.00 0.00 43.61 3.93
690 694 2.766828 GAGGAAAGGGAAGCTAGTAGCA 59.233 50.000 23.77 0.00 45.56 3.49
748 752 7.812191 TCTTTAGAAACGCATGCACATTTTAAT 59.188 29.630 19.57 7.75 0.00 1.40
752 756 5.119931 TCTTTAGAAACGCATGCACATTT 57.880 34.783 19.57 14.35 0.00 2.32
856 870 0.250295 CAAGAAGGGACACCAAGCGA 60.250 55.000 0.00 0.00 40.13 4.93
859 873 2.427506 GCTACAAGAAGGGACACCAAG 58.572 52.381 0.00 0.00 40.13 3.61
861 875 0.320374 CGCTACAAGAAGGGACACCA 59.680 55.000 0.00 0.00 40.13 4.17
893 1418 4.344474 CGCGACGGCTCCCTATCC 62.344 72.222 0.00 0.00 36.88 2.59
1110 1655 2.331451 GTGGTTGCGTTGTGGAGC 59.669 61.111 0.00 0.00 0.00 4.70
1288 1833 2.801162 CTCCGCACAGACGACGTG 60.801 66.667 4.58 0.00 37.43 4.49
1476 5684 1.878522 CACGACATAGTGCTCGCCC 60.879 63.158 0.00 0.00 35.17 6.13
1591 5811 8.335484 TCTCTCATTAGACTCTGATATAGCCAT 58.665 37.037 0.00 0.00 0.00 4.40
1729 5956 3.378339 GAAACGGGATGTATTCGATCGT 58.622 45.455 15.94 0.00 0.00 3.73
1730 5957 2.729882 GGAAACGGGATGTATTCGATCG 59.270 50.000 9.36 9.36 0.00 3.69
1845 6078 6.602179 GTCGACAAACTTGATCAAATCATCA 58.398 36.000 11.55 0.00 39.39 3.07
1867 6100 4.501058 GGAAGGGTCATGGTATTCTACGTC 60.501 50.000 0.00 0.00 0.00 4.34
1950 6183 1.909302 AGCCAATCTCCCGAAGAAAGA 59.091 47.619 0.00 0.00 37.61 2.52
1998 6231 6.094603 CAGAATAACTTTGGTCAAGGGAGATG 59.905 42.308 0.00 0.00 36.72 2.90
2041 6274 0.316204 TTTTCTGTCTCGTCGTCCCC 59.684 55.000 0.00 0.00 0.00 4.81
2077 6310 2.225167 GGGTGGGGGTGTAGAAAATCAA 60.225 50.000 0.00 0.00 0.00 2.57
2456 6993 8.204836 GTCCATACTCCATACTTGATTACTTGT 58.795 37.037 0.00 0.00 0.00 3.16
2849 8819 8.602424 TCAGGAAGGAAACTGTATAATTTCTGA 58.398 33.333 3.81 3.81 42.68 3.27
2937 8907 3.081710 ACCATGTAAAGCCCTTGTACC 57.918 47.619 0.00 0.00 0.00 3.34
2945 8915 8.075593 CAAAATATGCATTACCATGTAAAGCC 57.924 34.615 3.54 0.00 32.28 4.35
3359 9335 6.475402 CCACCAAAGTTACAGATCACAAAAAC 59.525 38.462 0.00 0.00 0.00 2.43
3567 9784 6.019881 TGAGCTACAATCGATGTAAATTGACG 60.020 38.462 0.00 0.00 43.75 4.35
3606 9826 5.174035 GGAATGATCAAACGTAGAGATGACG 59.826 44.000 0.00 0.00 45.75 4.35
3625 9845 8.524487 ACTAGAACAGAACTTACTACTGGAATG 58.476 37.037 0.00 0.00 36.17 2.67
3974 10201 6.956299 AATTCAACATAGAATTGCACAAGC 57.044 33.333 1.50 0.00 44.26 4.01
3986 10213 7.798596 ATAGAGCCAAGTCAATTCAACATAG 57.201 36.000 0.00 0.00 0.00 2.23
4069 10296 1.985447 ATGCATCACTTCGCGGCTTG 61.985 55.000 6.13 0.17 0.00 4.01
4093 10320 8.553459 TTTTTCTCTTCATGGCTTTAGTAGAG 57.447 34.615 0.00 0.00 0.00 2.43
4110 10337 8.950007 TTTAAGGGTGGTATTGATTTTTCTCT 57.050 30.769 0.00 0.00 0.00 3.10
4369 10617 1.323412 AGCCAGGCTCTATGTACTCG 58.677 55.000 8.70 0.00 30.62 4.18
4415 10726 4.704833 GCCTGCCTTCTCACCGCA 62.705 66.667 0.00 0.00 0.00 5.69
4882 11286 6.660521 TCTCAATATTGGCTTCAGTTGATTGT 59.339 34.615 15.36 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.