Multiple sequence alignment - TraesCS4B01G033000

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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 TraesCS4B01G033000 chr4B 100.000 3936 0 0 1 3936 24666964 24663029 0.000000e+00 7269.0
1 TraesCS4B01G033000 chr4A 91.929 2354 124 23 693 3021 586726535 586728847 0.000000e+00 3234.0
2 TraesCS4B01G033000 chr4A 90.788 1346 80 22 693 2016 456473364 456474687 0.000000e+00 1759.0
3 TraesCS4B01G033000 chr4A 94.907 1021 47 4 2005 3021 456474706 456475725 0.000000e+00 1592.0
4 TraesCS4B01G033000 chr4A 98.077 676 13 0 1 676 617923297 617923972 0.000000e+00 1177.0
5 TraesCS4B01G033000 chr4A 97.788 678 13 1 1 678 564650985 564650310 0.000000e+00 1168.0
6 TraesCS4B01G033000 chr4A 86.516 927 99 16 3021 3927 456476220 456477140 0.000000e+00 996.0
7 TraesCS4B01G033000 chr4A 86.393 926 99 17 3021 3927 586729321 586730238 0.000000e+00 987.0
8 TraesCS4B01G033000 chr4D 91.576 2386 128 22 673 3021 14560129 14562478 0.000000e+00 3225.0
9 TraesCS4B01G033000 chr4D 89.223 2431 134 49 676 3021 14832350 14829963 0.000000e+00 2920.0
10 TraesCS4B01G033000 chr4D 87.408 953 85 22 1012 1944 14523127 14524064 0.000000e+00 1062.0
11 TraesCS4B01G033000 chr4D 85.987 942 81 14 3022 3936 14563175 14564092 0.000000e+00 961.0
12 TraesCS4B01G033000 chr4D 87.819 353 16 9 673 1023 14522160 14522487 4.770000e-104 388.0
13 TraesCS4B01G033000 chr4D 94.891 137 6 1 2033 2169 14525436 14525571 3.080000e-51 213.0
14 TraesCS4B01G033000 chr3B 92.774 1370 60 13 676 2016 452746420 452747779 0.000000e+00 1945.0
15 TraesCS4B01G033000 chr3B 95.163 889 43 0 2033 2921 452754393 452755281 0.000000e+00 1404.0
16 TraesCS4B01G033000 chr3B 98.966 677 7 0 1 677 602779467 602780143 0.000000e+00 1212.0
17 TraesCS4B01G033000 chr3B 83.204 905 106 28 3022 3885 505039157 505038258 0.000000e+00 787.0
18 TraesCS4B01G033000 chr3B 100.000 34 0 0 2008 2041 452747786 452747819 3.280000e-06 63.9
19 TraesCS4B01G033000 chr7A 98.253 687 11 1 1 687 679805260 679804575 0.000000e+00 1201.0
20 TraesCS4B01G033000 chr7A 98.523 677 9 1 1 677 27641924 27642599 0.000000e+00 1194.0
21 TraesCS4B01G033000 chr7A 98.227 677 11 1 1 677 688842184 688841509 0.000000e+00 1182.0
22 TraesCS4B01G033000 chr7A 78.014 141 25 6 2403 2540 94915871 94916008 2.520000e-12 84.2
23 TraesCS4B01G033000 chr2B 98.523 677 10 0 1 677 91840567 91841243 0.000000e+00 1195.0
24 TraesCS4B01G033000 chr2B 97.640 678 14 2 1 677 450261189 450261865 0.000000e+00 1162.0
25 TraesCS4B01G033000 chr3A 98.227 677 12 0 1 677 710254899 710255575 0.000000e+00 1184.0
26 TraesCS4B01G033000 chr1A 88.073 218 21 4 3022 3235 74327856 74328072 1.820000e-63 254.0
27 TraesCS4B01G033000 chr6D 83.133 166 27 1 2375 2540 429945116 429944952 2.450000e-32 150.0
28 TraesCS4B01G033000 chr2D 79.630 162 25 7 2415 2572 584898264 584898421 4.160000e-20 110.0
29 TraesCS4B01G033000 chr7D 79.137 139 25 4 2403 2539 92763516 92763652 4.190000e-15 93.5


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 TraesCS4B01G033000 chr4B 24663029 24666964 3935 True 7269.000000 7269 100.000000 1 3936 1 chr4B.!!$R1 3935
1 TraesCS4B01G033000 chr4A 586726535 586730238 3703 False 2110.500000 3234 89.161000 693 3927 2 chr4A.!!$F3 3234
2 TraesCS4B01G033000 chr4A 456473364 456477140 3776 False 1449.000000 1759 90.737000 693 3927 3 chr4A.!!$F2 3234
3 TraesCS4B01G033000 chr4A 617923297 617923972 675 False 1177.000000 1177 98.077000 1 676 1 chr4A.!!$F1 675
4 TraesCS4B01G033000 chr4A 564650310 564650985 675 True 1168.000000 1168 97.788000 1 678 1 chr4A.!!$R1 677
5 TraesCS4B01G033000 chr4D 14829963 14832350 2387 True 2920.000000 2920 89.223000 676 3021 1 chr4D.!!$R1 2345
6 TraesCS4B01G033000 chr4D 14560129 14564092 3963 False 2093.000000 3225 88.781500 673 3936 2 chr4D.!!$F2 3263
7 TraesCS4B01G033000 chr4D 14522160 14525571 3411 False 554.333333 1062 90.039333 673 2169 3 chr4D.!!$F1 1496
8 TraesCS4B01G033000 chr3B 452754393 452755281 888 False 1404.000000 1404 95.163000 2033 2921 1 chr3B.!!$F1 888
9 TraesCS4B01G033000 chr3B 602779467 602780143 676 False 1212.000000 1212 98.966000 1 677 1 chr3B.!!$F2 676
10 TraesCS4B01G033000 chr3B 452746420 452747819 1399 False 1004.450000 1945 96.387000 676 2041 2 chr3B.!!$F3 1365
11 TraesCS4B01G033000 chr3B 505038258 505039157 899 True 787.000000 787 83.204000 3022 3885 1 chr3B.!!$R1 863
12 TraesCS4B01G033000 chr7A 679804575 679805260 685 True 1201.000000 1201 98.253000 1 687 1 chr7A.!!$R1 686
13 TraesCS4B01G033000 chr7A 27641924 27642599 675 False 1194.000000 1194 98.523000 1 677 1 chr7A.!!$F1 676
14 TraesCS4B01G033000 chr7A 688841509 688842184 675 True 1182.000000 1182 98.227000 1 677 1 chr7A.!!$R2 676
15 TraesCS4B01G033000 chr2B 91840567 91841243 676 False 1195.000000 1195 98.523000 1 677 1 chr2B.!!$F1 676
16 TraesCS4B01G033000 chr2B 450261189 450261865 676 False 1162.000000 1162 97.640000 1 677 1 chr2B.!!$F2 676
17 TraesCS4B01G033000 chr3A 710254899 710255575 676 False 1184.000000 1184 98.227000 1 677 1 chr3A.!!$F1 676

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
977 1034 1.068127 AGCAAGCAAGCAACCAAGAAG 59.932 47.619 3.19 0.0 36.85 2.85 F
1374 2082 0.252558 TACCCTTCTCCACCCAGTCC 60.253 60.000 0.00 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2641 4721 1.334243 CTACCGTCCTCGTCTTCCATC 59.666 57.143 0.0 0.0 35.01 3.51 R
3074 5899 1.135527 TCAAGGTGAGACACGTCGTTT 59.864 47.619 0.0 0.0 34.83 3.60 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
207 208 7.819900 GCTATATGGGTTTGACTCTACAATAGG 59.180 40.741 0.00 0.00 0.00 2.57
590 591 9.057089 CAGTTAGAGACTTTGGAATTTTGTACT 57.943 33.333 0.00 0.00 36.10 2.73
764 766 2.161855 TGGCATAAATCCGATCCATGC 58.838 47.619 14.56 14.56 40.96 4.06
765 767 2.161855 GGCATAAATCCGATCCATGCA 58.838 47.619 20.49 0.00 42.94 3.96
800 804 1.818060 TGTCAATACATGGCCTTGTGC 59.182 47.619 29.43 16.04 40.16 4.57
853 859 5.363580 AGTTATTGGAATTAATGGTGCCAGG 59.636 40.000 0.00 0.00 0.00 4.45
873 880 3.589288 AGGACAGAGCAATAAACCTCCTT 59.411 43.478 0.00 0.00 0.00 3.36
882 889 6.389906 AGCAATAAACCTCCTTCATTTTTCG 58.610 36.000 0.00 0.00 0.00 3.46
904 919 3.563808 GCCATATGCATGTTAACCTTCGA 59.436 43.478 10.16 0.00 40.77 3.71
973 1030 2.867251 GCATTAGCAAGCAAGCAACCAA 60.867 45.455 3.19 0.00 41.58 3.67
974 1031 2.798976 TTAGCAAGCAAGCAACCAAG 57.201 45.000 3.19 0.00 36.85 3.61
975 1032 1.979855 TAGCAAGCAAGCAACCAAGA 58.020 45.000 3.19 0.00 36.85 3.02
977 1034 1.068127 AGCAAGCAAGCAACCAAGAAG 59.932 47.619 3.19 0.00 36.85 2.85
978 1035 1.494824 CAAGCAAGCAACCAAGAAGC 58.505 50.000 0.00 0.00 0.00 3.86
980 1037 1.113788 AGCAAGCAACCAAGAAGCAA 58.886 45.000 0.00 0.00 0.00 3.91
1018 1726 0.681887 CATGGCCAATGTCCTGCTCA 60.682 55.000 10.96 0.00 0.00 4.26
1374 2082 0.252558 TACCCTTCTCCACCCAGTCC 60.253 60.000 0.00 0.00 0.00 3.85
1620 2328 2.663602 CTCGTTCGATGAGTTGGAGTTG 59.336 50.000 6.95 0.00 0.00 3.16
1641 2355 9.406113 GAGTTGGAGGTAGTAAGATCTAACTTA 57.594 37.037 0.00 0.00 41.67 2.24
1754 2483 4.830826 ACTTTCGATTTGTGAGGTTTCC 57.169 40.909 0.00 0.00 0.00 3.13
1840 2569 1.134220 AGAAAGAAACTGCACGTGGGA 60.134 47.619 18.88 0.00 0.00 4.37
2155 4226 1.449601 CTTCACCTACGGCGCCAAT 60.450 57.895 28.98 16.86 0.00 3.16
2356 4427 3.536917 CTCCCGCGCCACATCCTA 61.537 66.667 0.00 0.00 0.00 2.94
2470 4547 3.535629 CTGCGGCTGGAACTCCACA 62.536 63.158 0.00 0.00 42.01 4.17
2659 4739 0.611062 TGATGGAAGACGAGGACGGT 60.611 55.000 0.00 0.00 44.46 4.83
2938 5018 2.269241 GCCGGGGAGAAGTGAAGG 59.731 66.667 2.18 0.00 0.00 3.46
2949 5029 4.321675 GGAGAAGTGAAGGAAGTCTCACTC 60.322 50.000 5.27 0.00 41.90 3.51
3000 5089 0.370273 CTGCATTACTTCGTCGTGGC 59.630 55.000 0.00 0.00 0.00 5.01
3059 5882 8.290959 GAGCAAACTGCATTTGATGGACCATA 62.291 42.308 19.34 0.00 46.79 2.74
3060 5883 5.999205 AAACTGCATTTGATGGACCATAA 57.001 34.783 7.05 0.00 0.00 1.90
3074 5899 7.675619 TGATGGACCATAAGAGCTAGATTGATA 59.324 37.037 7.05 0.00 0.00 2.15
3077 5902 8.150945 TGGACCATAAGAGCTAGATTGATAAAC 58.849 37.037 0.00 0.00 0.00 2.01
3080 5905 7.868415 ACCATAAGAGCTAGATTGATAAACGAC 59.132 37.037 0.00 0.00 0.00 4.34
3088 5913 5.055642 AGATTGATAAACGACGTGTCTCA 57.944 39.130 0.00 0.93 0.00 3.27
3095 5920 0.959553 ACGACGTGTCTCACCTTGAT 59.040 50.000 0.00 0.00 0.00 2.57
3101 5926 2.164422 CGTGTCTCACCTTGATCTAGCA 59.836 50.000 0.00 0.00 0.00 3.49
3105 5930 6.520272 GTGTCTCACCTTGATCTAGCATAAT 58.480 40.000 0.00 0.00 0.00 1.28
3117 5942 8.158169 TGATCTAGCATAATGATGTTTTCCAC 57.842 34.615 0.00 0.00 35.30 4.02
3125 5950 5.612725 AATGATGTTTTCCACAACCAGTT 57.387 34.783 0.00 0.00 39.50 3.16
3217 6043 5.671493 CTTACAGAAACGAACCCATAGGAT 58.329 41.667 0.00 0.00 36.73 3.24
3237 6063 7.765695 AGGATGTTGTGTCAATATTTTGAGT 57.234 32.000 0.00 0.00 42.41 3.41
3241 6067 7.800155 TGTTGTGTCAATATTTTGAGTCTCA 57.200 32.000 0.00 0.00 42.41 3.27
3326 6152 5.907079 TCTACGGATCCCCTAATAAAACCTT 59.093 40.000 6.06 0.00 0.00 3.50
3329 6155 7.157947 ACGGATCCCCTAATAAAACCTTTAT 57.842 36.000 6.06 0.00 0.00 1.40
3353 6179 4.823790 AAGCGACGGTTTATTTTGTTCT 57.176 36.364 6.44 0.00 0.00 3.01
3690 6522 9.165014 CACAAGCATTTTTCAAAAATCATGAAG 57.835 29.630 5.04 0.00 38.01 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 118 0.958822 AAAAGCAATGTGGACCGTCC 59.041 50.000 10.96 10.96 36.96 4.79
207 208 4.120589 GACTCCAACCCGAATATGTCTTC 58.879 47.826 0.00 0.00 0.00 2.87
764 766 8.267620 TGTATTGACAAGAGTTTATCCATGTG 57.732 34.615 0.00 0.00 30.76 3.21
765 767 8.896744 CATGTATTGACAAGAGTTTATCCATGT 58.103 33.333 0.00 0.00 39.59 3.21
853 859 4.579869 TGAAGGAGGTTTATTGCTCTGTC 58.420 43.478 0.00 0.00 0.00 3.51
882 889 3.563808 TCGAAGGTTAACATGCATATGGC 59.436 43.478 8.10 0.00 45.13 4.40
904 919 9.823647 GATCAGATCACCCGATTATATAACATT 57.176 33.333 5.44 0.00 29.66 2.71
973 1030 1.683385 GGTTGCTTCTTGGTTGCTTCT 59.317 47.619 0.00 0.00 0.00 2.85
974 1031 1.408702 TGGTTGCTTCTTGGTTGCTTC 59.591 47.619 0.00 0.00 0.00 3.86
975 1032 1.484038 TGGTTGCTTCTTGGTTGCTT 58.516 45.000 0.00 0.00 0.00 3.91
977 1034 1.069049 ACATGGTTGCTTCTTGGTTGC 59.931 47.619 0.00 0.00 0.00 4.17
978 1035 2.288395 GGACATGGTTGCTTCTTGGTTG 60.288 50.000 0.00 0.00 0.00 3.77
980 1037 1.133513 TGGACATGGTTGCTTCTTGGT 60.134 47.619 0.00 0.00 0.00 3.67
1147 1855 4.719369 GGACTCGACGCGCACCTT 62.719 66.667 5.73 0.00 0.00 3.50
1352 2060 0.613853 CTGGGTGGAGAAGGGTACGA 60.614 60.000 0.00 0.00 0.00 3.43
1436 2144 3.530910 CTGACCCCCGCGTTGTCTT 62.531 63.158 17.14 0.00 0.00 3.01
1754 2483 4.583489 TCGACTTAGTATGGGGCTAGAAAG 59.417 45.833 0.00 0.00 0.00 2.62
2155 4226 4.043100 TCCTCCGGGTCGAGCAGA 62.043 66.667 17.59 11.37 0.00 4.26
2293 4364 2.353610 CCACAGGAATGGCTTGCCC 61.354 63.158 9.35 0.00 31.52 5.36
2351 4422 2.023318 CCGTCGCTTCGTCTAGGAT 58.977 57.895 0.00 0.00 0.00 3.24
2356 4427 4.755614 GACGCCGTCGCTTCGTCT 62.756 66.667 18.79 0.00 46.21 4.18
2641 4721 1.334243 CTACCGTCCTCGTCTTCCATC 59.666 57.143 0.00 0.00 35.01 3.51
2882 4962 3.888093 CGAACTCGTCCAGGTTCTT 57.112 52.632 0.00 0.00 39.47 2.52
2938 5018 4.619973 CATGCCAGATAGAGTGAGACTTC 58.380 47.826 0.00 0.00 0.00 3.01
2949 5029 2.424557 GAGACCATGCATGCCAGATAG 58.575 52.381 21.69 8.18 0.00 2.08
3059 5882 5.744345 CACGTCGTTTATCAATCTAGCTCTT 59.256 40.000 0.00 0.00 0.00 2.85
3060 5883 5.163642 ACACGTCGTTTATCAATCTAGCTCT 60.164 40.000 0.00 0.00 0.00 4.09
3074 5899 1.135527 TCAAGGTGAGACACGTCGTTT 59.864 47.619 0.00 0.00 34.83 3.60
3077 5902 1.200252 AGATCAAGGTGAGACACGTCG 59.800 52.381 0.00 0.00 34.83 5.12
3080 5905 2.164422 TGCTAGATCAAGGTGAGACACG 59.836 50.000 0.00 0.00 34.83 4.49
3088 5913 8.757982 AAAACATCATTATGCTAGATCAAGGT 57.242 30.769 0.00 0.00 36.50 3.50
3095 5920 7.148086 GGTTGTGGAAAACATCATTATGCTAGA 60.148 37.037 0.00 0.00 38.99 2.43
3101 5926 6.916360 ACTGGTTGTGGAAAACATCATTAT 57.084 33.333 0.00 0.00 38.99 1.28
3105 5930 6.723298 ATTAACTGGTTGTGGAAAACATCA 57.277 33.333 0.00 0.00 38.99 3.07
3217 6043 7.800155 TGAGACTCAAAATATTGACACAACA 57.200 32.000 1.64 0.00 40.59 3.33
3237 6063 4.703093 AGAAAAAGGTTTCCGTGTTTGAGA 59.297 37.500 0.00 0.00 43.65 3.27
3241 6067 5.394443 GGGTTAGAAAAAGGTTTCCGTGTTT 60.394 40.000 0.00 0.00 43.65 2.83
3300 6126 5.541484 GGTTTTATTAGGGGATCCGTAGAGA 59.459 44.000 5.45 0.00 38.33 3.10
3307 6133 9.871175 TTACATAAAGGTTTTATTAGGGGATCC 57.129 33.333 1.92 1.92 0.00 3.36
3326 6152 7.131498 ACAAAATAAACCGTCGCTTACATAA 57.869 32.000 0.00 0.00 0.00 1.90
3329 6155 5.236911 AGAACAAAATAAACCGTCGCTTACA 59.763 36.000 0.00 0.00 0.00 2.41
3471 6298 8.349245 TCGTGAAATAAACAATGTCTGTGAAAT 58.651 29.630 0.00 0.00 38.67 2.17
3472 6299 7.698628 TCGTGAAATAAACAATGTCTGTGAAA 58.301 30.769 0.00 0.00 38.67 2.69
3647 6478 9.926158 AATGCTTGTGTATTCAAAACATATTCA 57.074 25.926 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.