Multiple sequence alignment - TraesCS1D01G048700

Loading Multiple Alignment...

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 TraesCS1D01G048700 chr1D 100.000 6107 0 0 1 6107 28499647 28505753 0.000000e+00 11278.0
1 TraesCS1D01G048700 chr1D 97.800 4772 53 12 882 5612 28485670 28490430 0.000000e+00 8183.0
2 TraesCS1D01G048700 chr1D 95.012 2045 78 15 3173 5201 28969508 28967472 0.000000e+00 3190.0
3 TraesCS1D01G048700 chr1D 89.465 1215 65 14 882 2045 28978839 28977637 0.000000e+00 1476.0
4 TraesCS1D01G048700 chr1D 95.323 898 26 7 1 882 1443432 1442535 0.000000e+00 1411.0
5 TraesCS1D01G048700 chr1D 94.050 437 21 2 2742 3178 28975874 28975443 0.000000e+00 658.0
6 TraesCS1D01G048700 chr1D 84.765 617 86 8 4524 5136 29479057 29479669 4.050000e-171 612.0
7 TraesCS1D01G048700 chr1D 88.796 357 22 9 2086 2434 28977628 28977282 7.320000e-114 422.0
8 TraesCS1D01G048700 chr1D 87.805 164 10 6 2432 2593 28977169 28977014 3.760000e-42 183.0
9 TraesCS1D01G048700 chr1A 94.511 3316 115 20 1936 5217 29608750 29612032 0.000000e+00 5053.0
10 TraesCS1D01G048700 chr1A 94.307 1089 22 6 882 1938 29607645 29608725 0.000000e+00 1631.0
11 TraesCS1D01G048700 chr1A 96.734 398 11 1 5215 5612 29612178 29612573 0.000000e+00 662.0
12 TraesCS1D01G048700 chr1A 74.587 787 149 43 1251 2021 50845316 50844565 1.290000e-76 298.0
13 TraesCS1D01G048700 chr1A 76.080 602 119 16 4475 5065 29995654 29996241 2.150000e-74 291.0
14 TraesCS1D01G048700 chr1A 74.964 699 126 41 1251 1929 29883621 29882952 6.030000e-70 276.0
15 TraesCS1D01G048700 chr1A 82.564 195 27 7 1245 1435 50841072 50840881 1.360000e-36 165.0
16 TraesCS1D01G048700 chr1A 72.308 650 134 33 1245 1881 29993766 29994382 1.760000e-35 161.0
17 TraesCS1D01G048700 chr1A 75.887 141 28 6 1298 1435 29875125 29874988 3.950000e-07 67.6
18 TraesCS1D01G048700 chr1B 95.145 2307 82 16 2046 4342 47161545 47163831 0.000000e+00 3613.0
19 TraesCS1D01G048700 chr1B 97.887 852 15 1 4369 5217 47163923 47164774 0.000000e+00 1471.0
20 TraesCS1D01G048700 chr1B 91.182 1100 41 12 882 1938 47160160 47161246 0.000000e+00 1443.0
21 TraesCS1D01G048700 chr1B 91.929 508 36 5 5605 6107 395802064 395802571 0.000000e+00 706.0
22 TraesCS1D01G048700 chr1B 93.035 402 24 1 5215 5612 47164920 47165321 8.820000e-163 584.0
23 TraesCS1D01G048700 chr1B 86.577 447 55 3 4348 4790 46914897 46914452 7.110000e-134 488.0
24 TraesCS1D01G048700 chr1B 95.798 119 4 1 1935 2053 47161270 47161387 2.250000e-44 191.0
25 TraesCS1D01G048700 chr1B 79.167 264 39 12 1251 1508 47392975 47392722 1.050000e-37 169.0
26 TraesCS1D01G048700 chr1B 85.075 134 18 2 1245 1377 47544325 47544457 1.070000e-27 135.0
27 TraesCS1D01G048700 chr1B 100.000 30 0 0 4237 4266 47163828 47163857 8.550000e-04 56.5
28 TraesCS1D01G048700 chr6B 95.206 897 27 7 1 881 126933177 126932281 0.000000e+00 1404.0
29 TraesCS1D01G048700 chr6B 84.091 264 29 7 631 881 35938541 35938804 6.120000e-60 243.0
30 TraesCS1D01G048700 chr2D 95.206 897 25 9 1 880 372180936 372181831 0.000000e+00 1402.0
31 TraesCS1D01G048700 chr2D 93.927 494 27 3 5613 6104 333515567 333515075 0.000000e+00 743.0
32 TraesCS1D01G048700 chr2D 92.339 496 35 2 5613 6107 634276613 634276120 0.000000e+00 702.0
33 TraesCS1D01G048700 chr3B 93.717 748 23 10 160 883 804563589 804564336 0.000000e+00 1099.0
34 TraesCS1D01G048700 chr2A 95.260 654 13 8 246 881 762972596 762973249 0.000000e+00 1020.0
35 TraesCS1D01G048700 chr7B 88.302 795 82 10 1 784 739639099 739639893 0.000000e+00 942.0
36 TraesCS1D01G048700 chr7B 93.407 91 5 1 793 882 45265595 45265685 3.840000e-27 134.0
37 TraesCS1D01G048700 chrUn 88.161 794 84 9 1 784 359601233 359602026 0.000000e+00 937.0
38 TraesCS1D01G048700 chrUn 87.909 794 86 9 1 784 159051949 159051156 0.000000e+00 926.0
39 TraesCS1D01G048700 chrUn 87.909 794 86 9 1 784 329602289 329603082 0.000000e+00 926.0
40 TraesCS1D01G048700 chrUn 93.159 497 32 2 5613 6107 10764714 10764218 0.000000e+00 728.0
41 TraesCS1D01G048700 chrUn 92.958 497 33 2 5613 6107 10749086 10748590 0.000000e+00 723.0
42 TraesCS1D01G048700 chrUn 86.682 443 52 6 1 436 391121870 391122312 9.200000e-133 484.0
43 TraesCS1D01G048700 chr7D 95.766 496 20 1 5613 6107 75957893 75958388 0.000000e+00 798.0
44 TraesCS1D01G048700 chr7D 92.169 498 34 4 5611 6107 97006944 97007437 0.000000e+00 699.0
45 TraesCS1D01G048700 chr7D 91.617 501 40 2 5608 6107 438546404 438545905 0.000000e+00 691.0
46 TraesCS1D01G048700 chr5D 92.659 504 34 3 5606 6107 168013448 168013950 0.000000e+00 723.0
47 TraesCS1D01G048700 chr5B 87.245 196 14 10 698 882 702378014 702377819 4.800000e-51 213.0
48 TraesCS1D01G048700 chr5B 86.986 146 7 4 750 883 415809551 415809406 2.950000e-33 154.0


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 TraesCS1D01G048700 chr1D 28499647 28505753 6106 False 11278.000000 11278 100.000000 1 6107 1 chr1D.!!$F2 6106
1 TraesCS1D01G048700 chr1D 28485670 28490430 4760 False 8183.000000 8183 97.800000 882 5612 1 chr1D.!!$F1 4730
2 TraesCS1D01G048700 chr1D 28967472 28969508 2036 True 3190.000000 3190 95.012000 3173 5201 1 chr1D.!!$R2 2028
3 TraesCS1D01G048700 chr1D 1442535 1443432 897 True 1411.000000 1411 95.323000 1 882 1 chr1D.!!$R1 881
4 TraesCS1D01G048700 chr1D 28975443 28978839 3396 True 684.750000 1476 90.029000 882 3178 4 chr1D.!!$R3 2296
5 TraesCS1D01G048700 chr1D 29479057 29479669 612 False 612.000000 612 84.765000 4524 5136 1 chr1D.!!$F3 612
6 TraesCS1D01G048700 chr1A 29607645 29612573 4928 False 2448.666667 5053 95.184000 882 5612 3 chr1A.!!$F1 4730
7 TraesCS1D01G048700 chr1A 29882952 29883621 669 True 276.000000 276 74.964000 1251 1929 1 chr1A.!!$R2 678
8 TraesCS1D01G048700 chr1A 50840881 50845316 4435 True 231.500000 298 78.575500 1245 2021 2 chr1A.!!$R3 776
9 TraesCS1D01G048700 chr1A 29993766 29996241 2475 False 226.000000 291 74.194000 1245 5065 2 chr1A.!!$F2 3820
10 TraesCS1D01G048700 chr1B 47160160 47165321 5161 False 1226.416667 3613 95.507833 882 5612 6 chr1B.!!$F3 4730
11 TraesCS1D01G048700 chr1B 395802064 395802571 507 False 706.000000 706 91.929000 5605 6107 1 chr1B.!!$F2 502
12 TraesCS1D01G048700 chr6B 126932281 126933177 896 True 1404.000000 1404 95.206000 1 881 1 chr6B.!!$R1 880
13 TraesCS1D01G048700 chr2D 372180936 372181831 895 False 1402.000000 1402 95.206000 1 880 1 chr2D.!!$F1 879
14 TraesCS1D01G048700 chr3B 804563589 804564336 747 False 1099.000000 1099 93.717000 160 883 1 chr3B.!!$F1 723
15 TraesCS1D01G048700 chr2A 762972596 762973249 653 False 1020.000000 1020 95.260000 246 881 1 chr2A.!!$F1 635
16 TraesCS1D01G048700 chr7B 739639099 739639893 794 False 942.000000 942 88.302000 1 784 1 chr7B.!!$F2 783
17 TraesCS1D01G048700 chrUn 359601233 359602026 793 False 937.000000 937 88.161000 1 784 1 chrUn.!!$F2 783
18 TraesCS1D01G048700 chrUn 159051156 159051949 793 True 926.000000 926 87.909000 1 784 1 chrUn.!!$R3 783
19 TraesCS1D01G048700 chrUn 329602289 329603082 793 False 926.000000 926 87.909000 1 784 1 chrUn.!!$F1 783
20 TraesCS1D01G048700 chr5D 168013448 168013950 502 False 723.000000 723 92.659000 5606 6107 1 chr5D.!!$F1 501

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
926 961 0.611714 GGTCTAGGGTTTCTTGGCGA 59.388 55.000 0.0 0.0 0.0 5.54 F
975 1010 2.182030 GAGGCGGAAGTGGACTCG 59.818 66.667 0.0 0.0 0.0 4.18 F
1144 1185 2.278206 CGGTGGAGATGAGCGTCG 60.278 66.667 0.0 0.0 0.0 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2670 3303 2.690497 TGAACAGGTTTTCCAAATCGCA 59.310 40.909 0.0 0.0 43.73 5.10 R
2671 3304 3.049912 GTGAACAGGTTTTCCAAATCGC 58.950 45.455 0.0 0.0 43.73 4.58 R
5670 8200 4.673320 CGGTGACATGACGTAATCTGTGTA 60.673 45.833 0.0 0.0 30.24 2.90 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
179 185 5.003804 TGGAGCATTTACTCTTTCTTCCAC 58.996 41.667 0.00 0.00 36.87 4.02
384 394 0.698818 GAAACCCTGGGTGGATGAGT 59.301 55.000 21.38 0.00 35.34 3.41
444 454 3.454042 TTCGATGTTGATTCACTTGCG 57.546 42.857 0.00 0.00 0.00 4.85
658 669 2.526432 ACGAGGGCTACTCTTCTTCAA 58.474 47.619 0.00 0.00 44.33 2.69
763 775 5.836898 ACAATATGATGGCTCATGAATTGGT 59.163 36.000 14.01 1.83 42.19 3.67
781 800 9.959721 TGAATTGGTTAGAATAGCTAGTTTCTT 57.040 29.630 13.45 0.00 34.22 2.52
841 873 4.641094 TGATTGTAAACGACACAACCCTTT 59.359 37.500 0.00 0.00 38.63 3.11
926 961 0.611714 GGTCTAGGGTTTCTTGGCGA 59.388 55.000 0.00 0.00 0.00 5.54
975 1010 2.182030 GAGGCGGAAGTGGACTCG 59.818 66.667 0.00 0.00 0.00 4.18
1114 1155 3.804193 GCTCAAAGAAGGCGGCGG 61.804 66.667 9.78 0.00 0.00 6.13
1144 1185 2.278206 CGGTGGAGATGAGCGTCG 60.278 66.667 0.00 0.00 0.00 5.12
1156 1197 4.814294 GCGTCGGCGAGGTGGAAT 62.814 66.667 27.50 0.00 41.33 3.01
1157 1198 2.582498 CGTCGGCGAGGTGGAATC 60.582 66.667 20.45 0.53 41.33 2.52
1158 1199 2.893398 GTCGGCGAGGTGGAATCT 59.107 61.111 11.20 0.00 0.00 2.40
1602 1666 7.173907 CCATTGCTGCTTATTATTACTGCTAGT 59.826 37.037 0.00 0.00 0.00 2.57
2434 2782 9.831737 CAAAAATAGTATGGAGCATGTATAAGC 57.168 33.333 0.00 0.00 0.00 3.09
2670 3303 0.739462 CGTCCAGTGTGTGTGTGTGT 60.739 55.000 0.00 0.00 0.00 3.72
2671 3304 0.726827 GTCCAGTGTGTGTGTGTGTG 59.273 55.000 0.00 0.00 0.00 3.82
5670 8200 1.070786 CGCCCACACGCCCTATAAT 59.929 57.895 0.00 0.00 0.00 1.28
5678 8208 4.262463 CCACACGCCCTATAATACACAGAT 60.262 45.833 0.00 0.00 0.00 2.90
5683 8213 5.242393 ACGCCCTATAATACACAGATTACGT 59.758 40.000 0.00 0.00 0.00 3.57
5701 8231 1.298602 GTCATGTCACCGCATGCATA 58.701 50.000 19.57 0.00 44.20 3.14
5783 8345 7.636150 AATCAGATTGAAGATCCGTTTTCAT 57.364 32.000 0.00 0.00 33.68 2.57
5796 8358 7.561356 AGATCCGTTTTCATCATTAAATCCCTT 59.439 33.333 0.00 0.00 0.00 3.95
5844 8406 7.668525 TCTCATATCGATATATTACGGCGAT 57.331 36.000 16.62 10.13 43.24 4.58
5848 8410 9.524106 TCATATCGATATATTACGGCGATTTTT 57.476 29.630 16.62 0.00 41.35 1.94
5908 8472 5.756195 TGCCATGATATTTACACTGAAGC 57.244 39.130 0.00 0.00 0.00 3.86
5924 8488 4.708421 ACTGAAGCTGCCATGATATGTTTT 59.292 37.500 0.00 0.00 0.00 2.43
5929 8493 4.891756 AGCTGCCATGATATGTTTTAGCTT 59.108 37.500 0.00 0.00 35.65 3.74
6032 8930 7.058023 ACTAAAATTGCCATGATACATGCAT 57.942 32.000 0.00 0.00 33.08 3.96
6059 8957 7.999450 AAAATTGCCATGGTTCATACAAAAT 57.001 28.000 14.67 0.00 0.00 1.82
6064 8962 9.985730 ATTGCCATGGTTCATACAAAATAATAG 57.014 29.630 14.67 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
129 135 1.500474 CTCTCCTGCCCTATCAACCA 58.500 55.000 0.00 0.00 0.00 3.67
384 394 1.909459 TTGCATAGCCGAGCCTTGGA 61.909 55.000 0.80 0.00 0.00 3.53
444 454 1.348036 AGTACTGCTCCAACTGAACCC 59.652 52.381 0.00 0.00 0.00 4.11
747 759 6.208204 GCTATTCTAACCAATTCATGAGCCAT 59.792 38.462 0.00 0.00 0.00 4.40
763 775 6.672657 ACCAGGGAAGAAACTAGCTATTCTAA 59.327 38.462 9.49 0.00 34.90 2.10
841 873 8.689061 CATCATCCTCCTTTATTCAATTGTCAA 58.311 33.333 5.13 0.00 0.00 3.18
926 961 2.821366 CCATCGCCGCTCTGCTTT 60.821 61.111 0.00 0.00 0.00 3.51
1144 1185 1.672881 CAAATCAGATTCCACCTCGCC 59.327 52.381 0.00 0.00 0.00 5.54
1154 1195 1.207089 TCGTCCTCGCCAAATCAGATT 59.793 47.619 0.00 0.00 36.96 2.40
1155 1196 0.824109 TCGTCCTCGCCAAATCAGAT 59.176 50.000 0.00 0.00 36.96 2.90
1156 1197 0.173481 CTCGTCCTCGCCAAATCAGA 59.827 55.000 0.00 0.00 36.96 3.27
1157 1198 0.807667 CCTCGTCCTCGCCAAATCAG 60.808 60.000 0.00 0.00 36.96 2.90
1158 1199 1.218047 CCTCGTCCTCGCCAAATCA 59.782 57.895 0.00 0.00 36.96 2.57
1602 1666 7.451501 TGTCAATCAATCAAGATGCTTACAA 57.548 32.000 0.00 0.00 0.00 2.41
2323 2667 9.122954 ACATGGTGGTATTAATATCCTTATCCA 57.877 33.333 3.27 10.87 0.00 3.41
2403 2747 6.377996 ACATGCTCCATACTATTTTTGCTTCA 59.622 34.615 0.00 0.00 0.00 3.02
2408 2752 9.831737 GCTTATACATGCTCCATACTATTTTTG 57.168 33.333 0.00 0.00 0.00 2.44
2434 2782 5.523552 TGCATACTCCTGAAAATGTGATACG 59.476 40.000 0.00 0.00 0.00 3.06
2670 3303 2.690497 TGAACAGGTTTTCCAAATCGCA 59.310 40.909 0.00 0.00 43.73 5.10
2671 3304 3.049912 GTGAACAGGTTTTCCAAATCGC 58.950 45.455 0.00 0.00 43.73 4.58
5670 8200 4.673320 CGGTGACATGACGTAATCTGTGTA 60.673 45.833 0.00 0.00 30.24 2.90
5678 8208 3.824621 ATGCGGTGACATGACGTAA 57.175 47.368 0.00 0.00 0.00 3.18
5783 8345 3.118920 TCTCGTCGCAAGGGATTTAATGA 60.119 43.478 0.00 0.00 38.47 2.57
5848 8410 5.104259 ACATGGCAACTTTTAACCCAAAA 57.896 34.783 0.00 0.00 34.89 2.44
5852 8414 5.914898 ATAGACATGGCAACTTTTAACCC 57.085 39.130 0.00 0.00 37.61 4.11
6032 8930 8.908786 TTTGTATGAACCATGGCAATTTTAAA 57.091 26.923 13.04 3.97 0.00 1.52
6064 8962 8.655970 GCAATTCCAGTATTTTAACCATGAAAC 58.344 33.333 0.00 0.00 0.00 2.78


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

AutoCloner maintained by Alex Coulton.