Multiple sequence alignment - TraesCS7A01G289300

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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 TraesCS7A01G289300 chr7A 100.000 2162 0 0 1 2162 352182362 352180201 0 3993
1 TraesCS7A01G289300 chr2D 93.597 2202 98 8 1 2162 272794442 272792244 0 3245
2 TraesCS7A01G289300 chr2D 93.521 1281 62 8 902 2162 272564345 272565624 0 1886
3 TraesCS7A01G289300 chr3B 93.063 2220 95 13 1 2162 201526475 201528693 0 3192
4 TraesCS7A01G289300 chr3B 93.652 961 41 7 1221 2162 101911885 101912844 0 1419
5 TraesCS7A01G289300 chr3D 93.066 2221 90 17 1 2162 589280091 589277876 0 3190
6 TraesCS7A01G289300 chr1A 93.021 2221 94 15 1 2162 554511699 554513917 0 3186
7 TraesCS7A01G289300 chr5D 92.931 2221 96 13 1 2162 503217669 503219887 0 3175
8 TraesCS7A01G289300 chr5D 92.841 2221 98 15 1 2162 503278775 503276557 0 3164
9 TraesCS7A01G289300 chr5D 93.487 1213 58 8 970 2162 446174242 446175453 0 1783
10 TraesCS7A01G289300 chr6D 92.886 2221 97 15 1 2162 168254377 168256595 0 3169
11 TraesCS7A01G289300 chr6D 91.436 794 28 9 1 755 168250989 168251781 0 1053
12 TraesCS7A01G289300 chr6D 93.123 538 16 2 1 517 168252313 168251776 0 769
13 TraesCS7A01G289300 chr3A 92.841 2221 96 17 1 2162 672910556 672908340 0 3162
14 TraesCS7A01G289300 chrUn 92.793 2220 100 18 1 2162 216519151 216516934 0 3158
15 TraesCS7A01G289300 chrUn 92.871 2062 85 20 1 2003 93410180 93408122 0 2937
16 TraesCS7A01G289300 chrUn 92.445 2012 91 15 210 2162 346596834 346594825 0 2817
17 TraesCS7A01G289300 chrUn 92.413 1529 74 18 281 1769 389444786 389446312 0 2143
18 TraesCS7A01G289300 chrUn 95.131 1068 49 3 972 2038 444245952 444244887 0 1681
19 TraesCS7A01G289300 chrUn 93.309 538 15 2 1 517 216521215 216521752 0 774
20 TraesCS7A01G289300 chr1D 92.169 2222 111 29 1 2162 254398659 254396441 0 3081
21 TraesCS7A01G289300 chr4A 92.261 995 35 10 1 955 73813057 73812065 0 1373


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 TraesCS7A01G289300 chr7A 352180201 352182362 2161 True 3993 3993 100.000 1 2162 1 chr7A.!!$R1 2161
1 TraesCS7A01G289300 chr2D 272792244 272794442 2198 True 3245 3245 93.597 1 2162 1 chr2D.!!$R1 2161
2 TraesCS7A01G289300 chr2D 272564345 272565624 1279 False 1886 1886 93.521 902 2162 1 chr2D.!!$F1 1260
3 TraesCS7A01G289300 chr3B 201526475 201528693 2218 False 3192 3192 93.063 1 2162 1 chr3B.!!$F2 2161
4 TraesCS7A01G289300 chr3B 101911885 101912844 959 False 1419 1419 93.652 1221 2162 1 chr3B.!!$F1 941
5 TraesCS7A01G289300 chr3D 589277876 589280091 2215 True 3190 3190 93.066 1 2162 1 chr3D.!!$R1 2161
6 TraesCS7A01G289300 chr1A 554511699 554513917 2218 False 3186 3186 93.021 1 2162 1 chr1A.!!$F1 2161
7 TraesCS7A01G289300 chr5D 503217669 503219887 2218 False 3175 3175 92.931 1 2162 1 chr5D.!!$F2 2161
8 TraesCS7A01G289300 chr5D 503276557 503278775 2218 True 3164 3164 92.841 1 2162 1 chr5D.!!$R1 2161
9 TraesCS7A01G289300 chr5D 446174242 446175453 1211 False 1783 1783 93.487 970 2162 1 chr5D.!!$F1 1192
10 TraesCS7A01G289300 chr6D 168250989 168256595 5606 False 2111 3169 92.161 1 2162 2 chr6D.!!$F1 2161
11 TraesCS7A01G289300 chr6D 168251776 168252313 537 True 769 769 93.123 1 517 1 chr6D.!!$R1 516
12 TraesCS7A01G289300 chr3A 672908340 672910556 2216 True 3162 3162 92.841 1 2162 1 chr3A.!!$R1 2161
13 TraesCS7A01G289300 chrUn 216516934 216519151 2217 True 3158 3158 92.793 1 2162 1 chrUn.!!$R2 2161
14 TraesCS7A01G289300 chrUn 93408122 93410180 2058 True 2937 2937 92.871 1 2003 1 chrUn.!!$R1 2002
15 TraesCS7A01G289300 chrUn 346594825 346596834 2009 True 2817 2817 92.445 210 2162 1 chrUn.!!$R3 1952
16 TraesCS7A01G289300 chrUn 389444786 389446312 1526 False 2143 2143 92.413 281 1769 1 chrUn.!!$F2 1488
17 TraesCS7A01G289300 chrUn 444244887 444245952 1065 True 1681 1681 95.131 972 2038 1 chrUn.!!$R4 1066
18 TraesCS7A01G289300 chrUn 216521215 216521752 537 False 774 774 93.309 1 517 1 chrUn.!!$F1 516
19 TraesCS7A01G289300 chr1D 254396441 254398659 2218 True 3081 3081 92.169 1 2162 1 chr1D.!!$R1 2161
20 TraesCS7A01G289300 chr4A 73812065 73813057 992 True 1373 1373 92.261 1 955 1 chr4A.!!$R1 954

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
987 4417 0.761802 GCTTATGACCTCCCCCTCTG 59.238 60.0 0.0 0.0 0.0 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1962 5415 6.942532 TCCTTGTTATCAATGCCAACTATC 57.057 37.5 0.0 0.0 32.82 2.08 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
89 90 1.165270 CCCTTCCACGTGTGATTTCC 58.835 55.000 15.65 0.00 0.00 3.13
357 3766 6.261826 GGCTTATGTTCTTCATGTAGCATTCT 59.738 38.462 13.97 0.00 42.20 2.40
383 3794 9.762933 TGATCGAATGACTATGAAATTATGTCA 57.237 29.630 0.00 0.00 41.07 3.58
564 3992 5.586643 TGCGTGCTTCAAACAATACCATATA 59.413 36.000 0.00 0.00 0.00 0.86
612 4040 8.429641 TGAGGAACTACTAAACTCAATCACTTT 58.570 33.333 0.00 0.00 41.55 2.66
613 4041 8.608844 AGGAACTACTAAACTCAATCACTTTG 57.391 34.615 0.00 0.00 36.02 2.77
614 4042 7.173390 AGGAACTACTAAACTCAATCACTTTGC 59.827 37.037 0.00 0.00 36.02 3.68
616 4044 5.989777 ACTACTAAACTCAATCACTTTGCGT 59.010 36.000 0.00 0.00 34.79 5.24
617 4045 7.149973 ACTACTAAACTCAATCACTTTGCGTA 58.850 34.615 0.00 0.00 32.18 4.42
627 4055 6.649141 TCAATCACTTTGCGTAGTTACTCAAT 59.351 34.615 0.00 0.00 35.16 2.57
635 4063 6.956299 TGCGTAGTTACTCAATAGTTTTCC 57.044 37.500 0.00 0.00 37.15 3.13
758 4186 4.638865 AGTTGAAACCACACTCAAAGGTAC 59.361 41.667 0.00 0.00 33.52 3.34
759 4187 4.223556 TGAAACCACACTCAAAGGTACA 57.776 40.909 0.00 0.00 34.63 2.90
760 4188 4.590918 TGAAACCACACTCAAAGGTACAA 58.409 39.130 0.00 0.00 34.63 2.41
905 4335 7.771361 TGCATTTCAATTAGGGTCGTATTCTAA 59.229 33.333 0.00 0.00 0.00 2.10
911 4341 9.151177 TCAATTAGGGTCGTATTCTAAGGTTAT 57.849 33.333 0.00 0.00 0.00 1.89
987 4417 0.761802 GCTTATGACCTCCCCCTCTG 59.238 60.000 0.00 0.00 0.00 3.35
995 4425 2.935481 TCCCCCTCTGTGCCTTGG 60.935 66.667 0.00 0.00 0.00 3.61
1104 4534 1.005867 TACGGTTCCCTTGCGTGTC 60.006 57.895 0.00 0.00 0.00 3.67
1110 4540 4.003788 CCCTTGCGTGTCCTCGGT 62.004 66.667 0.00 0.00 0.00 4.69
1138 4568 8.012957 AGGTGTTTTGTATAAATGTTTCACCA 57.987 30.769 16.92 0.00 42.43 4.17
1252 4684 2.770447 TGTATGGCCCAGAATAGGTCA 58.230 47.619 0.00 0.00 44.69 4.02
1285 4717 0.539986 TTTCCAGGTAGTCGATGGCC 59.460 55.000 0.00 0.00 33.92 5.36
1324 4756 6.661805 ACCTTAACACCAAAGAAGAGTTTGAA 59.338 34.615 0.00 0.00 39.40 2.69
1380 4813 9.793245 CCGATTCGACATTAAAAGTATATTGAC 57.207 33.333 7.83 0.00 0.00 3.18
1395 4828 9.474313 AAGTATATTGACTCTTGCCCAATAAAA 57.526 29.630 0.00 0.00 36.65 1.52
1403 4836 5.474876 ACTCTTGCCCAATAAAAGAAGACTG 59.525 40.000 0.00 0.00 29.93 3.51
1437 4890 6.560253 AATACTGCGTATTTGATTCCATCC 57.440 37.500 7.75 0.00 35.50 3.51
1446 4899 7.323420 CGTATTTGATTCCATCCTATGCTCTA 58.677 38.462 0.00 0.00 0.00 2.43
1454 4907 4.968719 TCCATCCTATGCTCTAAGTTCCAA 59.031 41.667 0.00 0.00 0.00 3.53
1476 4929 9.841880 TCCAATATCGATAAGAATTCTAGTTCG 57.158 33.333 20.22 20.22 33.36 3.95
1565 5018 1.967066 CATGGATAGAGAGCCGGTTCT 59.033 52.381 22.00 22.00 31.83 3.01
1567 5020 2.865079 TGGATAGAGAGCCGGTTCTAG 58.135 52.381 21.86 0.00 31.83 2.43
1576 5029 4.198530 AGAGCCGGTTCTAGTAGACTTAC 58.801 47.826 20.45 0.00 0.00 2.34
1587 5040 6.421485 TCTAGTAGACTTACGGAATGTTCCT 58.579 40.000 9.90 0.70 45.33 3.36
1597 5050 1.535462 GGAATGTTCCTGTTCGTGTGG 59.465 52.381 4.53 0.00 44.11 4.17
1601 5054 1.691976 TGTTCCTGTTCGTGTGGATCT 59.308 47.619 0.00 0.00 0.00 2.75
1691 5144 5.739070 GCTTAACAGGGATCATCGTACATCA 60.739 44.000 0.00 0.00 0.00 3.07
1774 5227 6.639671 CGAGATGGAAAATATTCGGAGATC 57.360 41.667 0.00 0.00 36.36 2.75
1949 5402 2.280628 GATTGAACGACCAGGATCCAC 58.719 52.381 15.82 1.40 0.00 4.02
1962 5415 7.546250 ACCAGGATCCACTTACTTATGATAG 57.454 40.000 15.82 0.00 0.00 2.08
1963 5416 7.306013 ACCAGGATCCACTTACTTATGATAGA 58.694 38.462 15.82 0.00 0.00 1.98
2094 5547 2.921754 CTCGTGTGGGACTAATCGTTTC 59.078 50.000 0.00 0.00 0.00 2.78
2131 5584 0.382873 AAAAACCTGTTCGTTCCGCC 59.617 50.000 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.749063 CAAAAGAGGGTAAATCGGCCC 59.251 52.381 0.00 0.00 45.16 5.80
120 121 9.267084 GAGAAAAGAAGAATCTACTTCAACTGT 57.733 33.333 0.00 0.00 45.83 3.55
193 195 8.630054 AGATCGTCATATACTTCTAGAAAGCT 57.370 34.615 6.63 0.00 0.00 3.74
204 206 7.768582 CCATCTGTCTAGAGATCGTCATATACT 59.231 40.741 0.00 0.00 36.14 2.12
357 3766 9.762933 TGACATAATTTCATAGTCATTCGATCA 57.237 29.630 0.00 0.00 34.59 2.92
390 3801 6.959954 TCTCCTATGCTACCCATAATATGTGT 59.040 38.462 0.00 0.00 36.04 3.72
406 3817 4.323868 GGGAAATAGGGATGTCTCCTATGC 60.324 50.000 3.71 0.69 44.38 3.14
408 3819 4.439860 GGGGAAATAGGGATGTCTCCTAT 58.560 47.826 0.00 0.00 46.39 2.57
564 3992 9.956640 CCTCATAGAAAATTATTGGCTCTAGAT 57.043 33.333 0.00 0.00 0.00 1.98
612 4040 5.574055 CGGAAAACTATTGAGTAACTACGCA 59.426 40.000 0.00 0.00 33.58 5.24
613 4041 5.574443 ACGGAAAACTATTGAGTAACTACGC 59.426 40.000 0.00 0.00 33.58 4.42
614 4042 7.326789 TCAACGGAAAACTATTGAGTAACTACG 59.673 37.037 0.00 0.00 33.58 3.51
616 4044 7.816031 CCTCAACGGAAAACTATTGAGTAACTA 59.184 37.037 10.89 0.00 44.28 2.24
617 4045 6.649557 CCTCAACGGAAAACTATTGAGTAACT 59.350 38.462 10.89 0.00 44.28 2.24
627 4055 4.161001 GGGATAGACCTCAACGGAAAACTA 59.839 45.833 0.00 0.00 38.98 2.24
635 4063 2.548904 CTCTACGGGATAGACCTCAACG 59.451 54.545 0.00 0.00 34.80 4.10
739 4167 4.396790 TGTTGTACCTTTGAGTGTGGTTTC 59.603 41.667 0.00 0.00 35.48 2.78
745 4173 4.583073 GGGAAATGTTGTACCTTTGAGTGT 59.417 41.667 0.00 0.00 0.00 3.55
829 4259 8.926710 GGATGGTGAGAACAGATATATTTTACG 58.073 37.037 0.00 0.00 0.00 3.18
843 4273 2.505819 ACACTATGGGGATGGTGAGAAC 59.494 50.000 5.65 0.00 36.65 3.01
887 4317 9.151177 TCATAACCTTAGAATACGACCCTAATT 57.849 33.333 0.00 0.00 0.00 1.40
905 4335 8.964533 AGACATATCTGGTAGAATCATAACCT 57.035 34.615 0.00 0.00 32.29 3.50
987 4417 2.031870 GGAATCATTACCCCAAGGCAC 58.968 52.381 0.00 0.00 36.11 5.01
1040 4470 6.710295 TCCACGAAATAATTTGATCCATCGAT 59.290 34.615 0.00 0.00 33.61 3.59
1043 4473 7.596248 CCAATCCACGAAATAATTTGATCCATC 59.404 37.037 0.00 0.00 0.00 3.51
1104 4534 8.770828 CATTTATACAAAACACCTATACCGAGG 58.229 37.037 0.00 0.00 42.89 4.63
1181 4613 5.527582 CCTTCAACCGGGTTATTCTATCTTG 59.472 44.000 12.95 0.00 0.00 3.02
1182 4614 5.397559 CCCTTCAACCGGGTTATTCTATCTT 60.398 44.000 12.95 0.00 36.91 2.40
1183 4615 4.102681 CCCTTCAACCGGGTTATTCTATCT 59.897 45.833 12.95 0.00 36.91 1.98
1184 4616 4.386711 CCCTTCAACCGGGTTATTCTATC 58.613 47.826 12.95 0.00 36.91 2.08
1285 4717 4.154195 GTGTTAAGGTGGTAGCTGTGAATG 59.846 45.833 0.00 0.00 0.00 2.67
1347 4779 7.916552 ACTTTTAATGTCGAATCGGGATTTAG 58.083 34.615 1.76 3.57 0.00 1.85
1349 4781 6.753107 ACTTTTAATGTCGAATCGGGATTT 57.247 33.333 1.76 0.00 0.00 2.17
1380 4813 5.474876 ACAGTCTTCTTTTATTGGGCAAGAG 59.525 40.000 0.00 0.00 0.00 2.85
1385 4818 7.169813 CAGAAAAACAGTCTTCTTTTATTGGGC 59.830 37.037 0.00 0.00 29.29 5.36
1395 4828 8.560374 GCAGTATTTACAGAAAAACAGTCTTCT 58.440 33.333 0.00 0.00 31.99 2.85
1518 4971 9.848710 GAATCTCATCCATCATCCATACATAAT 57.151 33.333 0.00 0.00 0.00 1.28
1587 5040 3.959293 TCCTACTAGATCCACACGAACA 58.041 45.455 0.00 0.00 0.00 3.18
1597 5050 4.202223 TGCGGGTTCAATTCCTACTAGATC 60.202 45.833 0.00 0.00 0.00 2.75
1601 5054 3.985019 TTGCGGGTTCAATTCCTACTA 57.015 42.857 0.00 0.00 0.00 1.82
1644 5097 4.046286 TCCATGGCTGAATGGTTAAAGT 57.954 40.909 6.96 0.00 46.24 2.66
1774 5227 5.152623 TCCAGAGAGGTGTTTTCATAGTG 57.847 43.478 0.00 0.00 39.02 2.74
1962 5415 6.942532 TCCTTGTTATCAATGCCAACTATC 57.057 37.500 0.00 0.00 32.82 2.08
1963 5416 7.293073 AGATCCTTGTTATCAATGCCAACTAT 58.707 34.615 0.00 0.00 32.82 2.12


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

AutoCloner maintained by Alex Coulton.