Multiple sequence alignment - TraesCS5D01G483100

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 TraesCS5D01G483100 chr5D 100.000 2627 0 0 1 2627 520113284 520115910 0.000000e+00 4852.0
1 TraesCS5D01G483100 chr5D 79.649 285 29 10 417 700 384883865 384883609 7.470000e-41 178.0
2 TraesCS5D01G483100 chr5B 91.132 1714 94 23 1 1697 655120699 655122371 0.000000e+00 2270.0
3 TraesCS5D01G483100 chr5B 93.930 939 53 3 1693 2627 40792717 40793655 0.000000e+00 1415.0
4 TraesCS5D01G483100 chr5A 90.591 1743 103 26 1 1698 647167240 647168966 0.000000e+00 2254.0
5 TraesCS5D01G483100 chr5A 94.962 933 44 2 1698 2627 605581849 605580917 0.000000e+00 1459.0
6 TraesCS5D01G483100 chr5A 82.168 286 29 9 417 700 485866298 485866033 2.630000e-55 226.0
7 TraesCS5D01G483100 chr3D 97.222 936 25 1 1693 2627 5325571 5324636 0.000000e+00 1583.0
8 TraesCS5D01G483100 chr3D 77.689 502 74 21 996 1460 111899134 111899634 3.330000e-69 272.0
9 TraesCS5D01G483100 chr3D 87.556 225 27 1 1235 1458 111925398 111925622 2.590000e-65 259.0
10 TraesCS5D01G483100 chr1D 96.455 931 30 3 1698 2627 459875125 459874197 0.000000e+00 1533.0
11 TraesCS5D01G483100 chr2B 96.026 931 31 4 1699 2627 535713534 535712608 0.000000e+00 1509.0
12 TraesCS5D01G483100 chr1B 94.973 935 42 4 1696 2627 684270113 684271045 0.000000e+00 1461.0
13 TraesCS5D01G483100 chr1B 86.869 297 27 6 1 291 667891134 667891424 3.260000e-84 322.0
14 TraesCS5D01G483100 chr1B 85.561 187 25 2 493 678 512051313 512051498 7.420000e-46 195.0
15 TraesCS5D01G483100 chr4B 94.516 930 49 2 1699 2627 185803834 185804762 0.000000e+00 1434.0
16 TraesCS5D01G483100 chr2D 94.516 930 50 1 1699 2627 555143886 555144815 0.000000e+00 1434.0
17 TraesCS5D01G483100 chr2D 94.030 938 48 5 1697 2627 522626278 522625342 0.000000e+00 1415.0
18 TraesCS5D01G483100 chr7A 78.378 740 106 38 1 700 639270941 639270216 5.190000e-117 431.0
19 TraesCS5D01G483100 chr2A 88.591 298 24 4 1 293 293857410 293857118 1.160000e-93 353.0
20 TraesCS5D01G483100 chr2A 84.492 187 27 2 493 678 165103976 165104161 1.610000e-42 183.0
21 TraesCS5D01G483100 chr2A 84.810 158 18 6 473 628 379822341 379822188 1.260000e-33 154.0
22 TraesCS5D01G483100 chr7B 87.879 297 25 5 1 291 115473327 115473618 3.240000e-89 339.0
23 TraesCS5D01G483100 chrUn 87.542 297 26 8 1 291 224515653 224515362 1.510000e-87 333.0
24 TraesCS5D01G483100 chrUn 87.542 297 26 8 1 291 393127328 393127619 1.510000e-87 333.0
25 TraesCS5D01G483100 chrUn 87.542 297 26 8 1 291 397217414 397217123 1.510000e-87 333.0
26 TraesCS5D01G483100 chrUn 90.741 54 5 0 625 678 480490539 480490486 3.630000e-09 73.1
27 TraesCS5D01G483100 chr3B 88.077 260 26 1 1 255 197795761 197795502 1.180000e-78 303.0
28 TraesCS5D01G483100 chr3B 78.169 426 67 14 1060 1460 162521519 162521943 5.610000e-62 248.0
29 TraesCS5D01G483100 chr4D 85.382 301 33 4 1 296 468902217 468901923 4.250000e-78 302.0
30 TraesCS5D01G483100 chr1A 85.664 286 32 6 1 280 36181747 36181465 2.560000e-75 292.0
31 TraesCS5D01G483100 chr1A 83.860 285 35 9 417 694 36175555 36175275 7.210000e-66 261.0
32 TraesCS5D01G483100 chr3A 78.104 443 71 12 1043 1460 118588238 118587797 9.330000e-65 257.0


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 TraesCS5D01G483100 chr5D 520113284 520115910 2626 False 4852 4852 100.000 1 2627 1 chr5D.!!$F1 2626
1 TraesCS5D01G483100 chr5B 655120699 655122371 1672 False 2270 2270 91.132 1 1697 1 chr5B.!!$F2 1696
2 TraesCS5D01G483100 chr5B 40792717 40793655 938 False 1415 1415 93.930 1693 2627 1 chr5B.!!$F1 934
3 TraesCS5D01G483100 chr5A 647167240 647168966 1726 False 2254 2254 90.591 1 1698 1 chr5A.!!$F1 1697
4 TraesCS5D01G483100 chr5A 605580917 605581849 932 True 1459 1459 94.962 1698 2627 1 chr5A.!!$R2 929
5 TraesCS5D01G483100 chr3D 5324636 5325571 935 True 1583 1583 97.222 1693 2627 1 chr3D.!!$R1 934
6 TraesCS5D01G483100 chr3D 111899134 111899634 500 False 272 272 77.689 996 1460 1 chr3D.!!$F1 464
7 TraesCS5D01G483100 chr1D 459874197 459875125 928 True 1533 1533 96.455 1698 2627 1 chr1D.!!$R1 929
8 TraesCS5D01G483100 chr2B 535712608 535713534 926 True 1509 1509 96.026 1699 2627 1 chr2B.!!$R1 928
9 TraesCS5D01G483100 chr1B 684270113 684271045 932 False 1461 1461 94.973 1696 2627 1 chr1B.!!$F3 931
10 TraesCS5D01G483100 chr4B 185803834 185804762 928 False 1434 1434 94.516 1699 2627 1 chr4B.!!$F1 928
11 TraesCS5D01G483100 chr2D 555143886 555144815 929 False 1434 1434 94.516 1699 2627 1 chr2D.!!$F1 928
12 TraesCS5D01G483100 chr2D 522625342 522626278 936 True 1415 1415 94.030 1697 2627 1 chr2D.!!$R1 930
13 TraesCS5D01G483100 chr7A 639270216 639270941 725 True 431 431 78.378 1 700 1 chr7A.!!$R1 699

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
547 635 0.241213 GGCGAGGAAGAAAAAGGCAC 59.759 55.0 0.0 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1706 1861 1.144093 CCGGGGGTATGCCTTCATTTA 59.856 52.381 0.0 0.0 34.22 1.4 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
165 174 0.321653 AGTCCAACTGCCATCGGAAC 60.322 55.000 0.00 0.0 0.00 3.62
166 175 1.002624 TCCAACTGCCATCGGAACC 60.003 57.895 0.00 0.0 0.00 3.62
167 176 1.002134 CCAACTGCCATCGGAACCT 60.002 57.895 0.00 0.0 0.00 3.50
176 185 2.351244 ATCGGAACCTGCTCGCTCA 61.351 57.895 0.00 0.0 0.00 4.26
310 369 4.856607 GGCGCCTCTCGTCCTTCG 62.857 72.222 22.15 0.0 41.07 3.79
481 569 6.858478 TGCGTTCAATTTGTCGAAATCAAATA 59.142 30.769 11.53 0.0 42.31 1.40
547 635 0.241213 GGCGAGGAAGAAAAAGGCAC 59.759 55.000 0.00 0.0 0.00 5.01
551 641 0.539669 AGGAAGAAAAAGGCACGGGG 60.540 55.000 0.00 0.0 0.00 5.73
568 658 5.212194 CACGGGGAAAAATATAAGCGAATG 58.788 41.667 0.00 0.0 0.00 2.67
569 659 4.226761 CGGGGAAAAATATAAGCGAATGC 58.773 43.478 0.00 0.0 43.24 3.56
605 695 2.131776 AGTTTGTGGGGTTTGTTCGA 57.868 45.000 0.00 0.0 0.00 3.71
609 699 1.524393 GTGGGGTTTGTTCGACCGT 60.524 57.895 0.00 0.0 38.08 4.83
645 735 5.040635 CCCTTAAAATATGTTTTGCGCGAT 58.959 37.500 12.10 0.0 38.01 4.58
649 739 3.338818 AATATGTTTTGCGCGATCTGG 57.661 42.857 12.10 0.0 0.00 3.86
700 791 3.827302 GGGTCCGCTAGAGATGATCTTAA 59.173 47.826 0.00 0.0 39.64 1.85
702 793 5.465935 GGTCCGCTAGAGATGATCTTAAAG 58.534 45.833 0.00 0.0 39.64 1.85
769 860 0.869730 GCCTTTTAGTCAAACCGCGA 59.130 50.000 8.23 0.0 0.00 5.87
817 908 3.189080 TGATCGTCTCAGTGGCAATTTTG 59.811 43.478 0.00 0.0 0.00 2.44
883 974 0.386476 TACGTGACACTGACACCACC 59.614 55.000 0.00 0.0 35.17 4.61
920 1011 1.065854 TCTTGCCCAAGCTAAGCTCTC 60.066 52.381 3.18 0.0 38.25 3.20
921 1012 0.987294 TTGCCCAAGCTAAGCTCTCT 59.013 50.000 4.43 0.0 38.25 3.10
922 1013 0.539051 TGCCCAAGCTAAGCTCTCTC 59.461 55.000 4.43 0.0 38.25 3.20
943 1034 3.396560 CAGATAAATCCATCTGCTCGCA 58.603 45.455 0.51 0.0 43.95 5.10
948 1042 0.538584 ATCCATCTGCTCGCACTTGA 59.461 50.000 0.00 0.0 0.00 3.02
949 1043 0.390340 TCCATCTGCTCGCACTTGAC 60.390 55.000 0.00 0.0 0.00 3.18
957 1051 1.634702 CTCGCACTTGACTTCCTAGC 58.365 55.000 0.00 0.0 0.00 3.42
959 1053 1.687494 CGCACTTGACTTCCTAGCGC 61.687 60.000 0.00 0.0 37.20 5.92
987 1084 7.770366 TGATTTGTAGTACCAGACAGAGTTA 57.230 36.000 0.00 0.0 0.00 2.24
992 1089 5.583854 TGTAGTACCAGACAGAGTTATCGAC 59.416 44.000 0.00 0.0 0.00 4.20
994 1091 1.743958 ACCAGACAGAGTTATCGACCG 59.256 52.381 0.00 0.0 0.00 4.79
1104 1213 0.600255 CGCTCACCGTCTCTTTGGTT 60.600 55.000 0.00 0.0 35.96 3.67
1228 1355 1.449423 CGGTCCGTTGGCATGATCA 60.449 57.895 2.08 0.0 0.00 2.92
1648 1800 8.671028 GCTAGAAGTAATCAGATAGTAGCCTAC 58.329 40.741 0.00 0.0 0.00 3.18
2345 2508 6.352565 CCCATCTCCTCTTGATTAAGTTGTCT 60.353 42.308 0.00 0.0 35.38 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 62 1.546998 GGTTCGGTGGGGATGTTTTCT 60.547 52.381 0.00 0.00 0.00 2.52
310 369 1.300697 ACGAGCACCGGACTGAAAC 60.301 57.895 9.46 0.00 43.93 2.78
481 569 6.473758 AGATGCTCTGAACATGCATACATAT 58.526 36.000 0.00 0.00 45.90 1.78
525 613 1.305930 CCTTTTTCTTCCTCGCCCCG 61.306 60.000 0.00 0.00 0.00 5.73
540 628 4.142026 GCTTATATTTTTCCCCGTGCCTTT 60.142 41.667 0.00 0.00 0.00 3.11
547 635 4.226761 GCATTCGCTTATATTTTTCCCCG 58.773 43.478 0.00 0.00 34.30 5.73
568 658 6.195798 CACAAACTTAAACTGTAAAACCGAGC 59.804 38.462 0.00 0.00 0.00 5.03
569 659 6.689669 CCACAAACTTAAACTGTAAAACCGAG 59.310 38.462 0.00 0.00 0.00 4.63
605 695 2.105766 AGGGTCGATTTAAGCTACGGT 58.894 47.619 0.00 0.00 0.00 4.83
609 699 9.841295 ACATATTTTAAGGGTCGATTTAAGCTA 57.159 29.630 0.00 0.00 0.00 3.32
639 729 2.276680 GCGTTTTCCAGATCGCGC 60.277 61.111 0.00 0.00 39.35 6.86
769 860 7.461182 TGTTCCTTTGGATTAATTTGATCGT 57.539 32.000 0.00 0.00 0.00 3.73
817 908 3.359002 ACACGGGGTGACGAGTAC 58.641 61.111 2.29 0.00 35.97 2.73
939 1030 0.109272 CGCTAGGAAGTCAAGTGCGA 60.109 55.000 0.00 0.00 43.81 5.10
941 1032 0.670546 TGCGCTAGGAAGTCAAGTGC 60.671 55.000 9.73 10.06 44.89 4.40
942 1033 1.071605 GTGCGCTAGGAAGTCAAGTG 58.928 55.000 9.73 0.00 0.00 3.16
943 1034 0.969894 AGTGCGCTAGGAAGTCAAGT 59.030 50.000 9.73 0.00 0.00 3.16
948 1042 2.744202 CAAATCAAGTGCGCTAGGAAGT 59.256 45.455 9.73 0.00 0.00 3.01
949 1043 2.744202 ACAAATCAAGTGCGCTAGGAAG 59.256 45.455 9.73 0.00 0.00 3.46
957 1051 4.091509 GTCTGGTACTACAAATCAAGTGCG 59.908 45.833 0.00 0.00 0.00 5.34
959 1053 6.455647 TCTGTCTGGTACTACAAATCAAGTG 58.544 40.000 0.00 0.00 0.00 3.16
987 1084 2.186903 GACATGGCACCGGTCGAT 59.813 61.111 2.59 0.00 0.00 3.59
992 1089 3.266686 TTCCCTGACATGGCACCGG 62.267 63.158 0.00 0.00 0.00 5.28
994 1091 1.678970 GGTTCCCTGACATGGCACC 60.679 63.158 0.00 3.03 0.00 5.01
1104 1213 1.025041 CGACGGTGATCATCAGGAGA 58.975 55.000 6.80 0.00 0.00 3.71
1562 1701 4.379243 ACGGAGAGCCACCTTGCG 62.379 66.667 0.00 0.00 36.02 4.85
1705 1860 2.423660 CCGGGGGTATGCCTTCATTTAA 60.424 50.000 0.00 0.00 34.22 1.52
1706 1861 1.144093 CCGGGGGTATGCCTTCATTTA 59.856 52.381 0.00 0.00 34.22 1.40
2384 2547 4.893608 AGGTTCCTTTGCGCATTAAATTT 58.106 34.783 12.75 0.00 0.00 1.82
2385 2548 4.535526 AGGTTCCTTTGCGCATTAAATT 57.464 36.364 12.75 0.00 0.00 1.82
2536 2700 5.989477 TGGTTCGGAGATTGATAGATGTTT 58.011 37.500 0.00 0.00 35.04 2.83


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

AutoCloner maintained by Alex Coulton.