Multiple sequence alignment - TraesCS5D01G475100

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 TraesCS5D01G475100 chr5D 100.000 2457 0 0 1 2457 514966759 514964303 0 4538
1 TraesCS5D01G475100 chr5D 96.291 1537 52 4 925 2457 514947898 514946363 0 2518
2 TraesCS5D01G475100 chr5D 95.695 1533 63 3 925 2457 514974308 514972779 0 2462
3 TraesCS5D01G475100 chr5D 94.980 1534 74 3 925 2457 514995740 514994209 0 2403
4 TraesCS5D01G475100 chr5D 94.837 1530 77 2 925 2452 515025097 515023568 0 2386
5 TraesCS5D01G475100 chr5D 96.344 930 30 3 1 926 514948081 514947152 0 1526
6 TraesCS5D01G475100 chr5D 94.181 928 51 3 1 926 515025280 515024354 0 1411
7 TraesCS5D01G475100 chr5D 93.966 928 53 2 1 926 514995923 514994997 0 1400
8 TraesCS5D01G475100 chr5D 93.427 928 57 3 1 926 514974491 514973566 0 1373
9 TraesCS5D01G475100 chr5A 91.835 1531 122 2 925 2453 643033852 643032323 0 2132
10 TraesCS5D01G475100 chr5A 91.367 1529 122 6 928 2453 643039347 643037826 0 2084
11 TraesCS5D01G475100 chr5A 90.933 1533 132 5 925 2454 643046966 643045438 0 2054
12 TraesCS5D01G475100 chr5A 90.856 1531 136 4 925 2453 643041947 643040419 0 2049
13 TraesCS5D01G475100 chr5A 90.105 1526 145 5 933 2454 643205467 643203944 0 1977
14 TraesCS5D01G475100 chr5A 91.603 917 71 4 10 924 643034023 643033111 0 1262
15 TraesCS5D01G475100 chr5A 90.879 921 78 4 6 924 643029029 643028113 0 1230
16 TraesCS5D01G475100 chr5B 92.052 931 66 3 1 924 647464237 647463308 0 1303
17 TraesCS5D01G475100 chr5B 91.123 935 71 4 1 924 647405032 647404099 0 1256
18 TraesCS5D01G475100 chr5B 90.635 929 79 5 1 924 647698304 647697379 0 1227


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 TraesCS5D01G475100 chr5D 514964303 514966759 2456 True 4538.000000 4538 100.0000 1 2457 1 chr5D.!!$R1 2456
1 TraesCS5D01G475100 chr5D 514946363 514948081 1718 True 2022.000000 2518 96.3175 1 2457 2 chr5D.!!$R2 2456
2 TraesCS5D01G475100 chr5D 514972779 514974491 1712 True 1917.500000 2462 94.5610 1 2457 2 chr5D.!!$R3 2456
3 TraesCS5D01G475100 chr5D 514994209 514995923 1714 True 1901.500000 2403 94.4730 1 2457 2 chr5D.!!$R4 2456
4 TraesCS5D01G475100 chr5D 515023568 515025280 1712 True 1898.500000 2386 94.5090 1 2452 2 chr5D.!!$R5 2451
5 TraesCS5D01G475100 chr5A 643203944 643205467 1523 True 1977.000000 1977 90.1050 933 2454 1 chr5A.!!$R1 1521
6 TraesCS5D01G475100 chr5A 643028113 643046966 18853 True 1801.833333 2132 91.2455 6 2454 6 chr5A.!!$R2 2448
7 TraesCS5D01G475100 chr5B 647463308 647464237 929 True 1303.000000 1303 92.0520 1 924 1 chr5B.!!$R2 923
8 TraesCS5D01G475100 chr5B 647404099 647405032 933 True 1256.000000 1256 91.1230 1 924 1 chr5B.!!$R1 923
9 TraesCS5D01G475100 chr5B 647697379 647698304 925 True 1227.000000 1227 90.6350 1 924 1 chr5B.!!$R3 923

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
542 7979 0.039035 ACAACCCGGGTATGCACAAT 59.961 50.0 30.52 5.19 0.0 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1973 14180 0.176219 TGTGAAGGTCGACCGTGTTT 59.824 50.0 28.16 17.02 42.08 2.83 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
108 7542 9.685276 TTAAGGCAAGATCTTCATTATTTGAGA 57.315 29.630 4.57 0.00 35.27 3.27
183 7617 0.179215 CGAACGCAAGCCATCACTTC 60.179 55.000 0.00 0.00 45.62 3.01
248 7685 7.498900 TCAGAATAAACAAGAAGTCAAGAGCAA 59.501 33.333 0.00 0.00 0.00 3.91
254 7691 3.498774 AGAAGTCAAGAGCAACACCAT 57.501 42.857 0.00 0.00 0.00 3.55
256 7693 2.191128 AGTCAAGAGCAACACCATCC 57.809 50.000 0.00 0.00 0.00 3.51
344 7781 1.379044 GTCCATGGCAAGGAGTGGG 60.379 63.158 12.49 0.00 35.42 4.61
368 7805 0.850100 TGGTGACAACAAGGGATGGT 59.150 50.000 0.00 0.00 37.44 3.55
415 7852 2.045926 AAGCACATCCAGTCCGGC 60.046 61.111 0.00 0.00 33.14 6.13
419 7856 2.994995 ACATCCAGTCCGGCGACA 60.995 61.111 9.30 0.00 41.87 4.35
421 7858 1.153369 CATCCAGTCCGGCGACATT 60.153 57.895 9.30 0.00 41.87 2.71
445 7882 7.303182 TCTTGGTGAGAACTCTAAAGATCAA 57.697 36.000 0.00 0.00 0.00 2.57
462 7899 6.323203 AGATCAAGTGATTGGTTGTTCTTG 57.677 37.500 0.00 0.00 31.55 3.02
530 7967 1.263217 GCAGTGTTCAAGTACAACCCG 59.737 52.381 0.00 0.00 0.00 5.28
531 7968 1.871039 CAGTGTTCAAGTACAACCCGG 59.129 52.381 0.00 0.00 0.00 5.73
532 7969 1.202722 AGTGTTCAAGTACAACCCGGG 60.203 52.381 22.25 22.25 0.00 5.73
542 7979 0.039035 ACAACCCGGGTATGCACAAT 59.961 50.000 30.52 5.19 0.00 2.71
561 7998 1.302832 GTGGTGCAGGTGGGAGAAG 60.303 63.158 0.00 0.00 0.00 2.85
633 8070 1.681166 GCAATGACCACATCCAGCTCT 60.681 52.381 0.00 0.00 35.50 4.09
637 8074 1.229625 ACCACATCCAGCTCTCCCA 60.230 57.895 0.00 0.00 0.00 4.37
639 8076 1.153489 CACATCCAGCTCTCCCACG 60.153 63.158 0.00 0.00 0.00 4.94
670 8107 2.709213 GTTCTTCATCTGCAGCCTTCT 58.291 47.619 9.47 0.00 0.00 2.85
722 8159 4.679197 GCTGTCACTGCTTAATAGATCTCG 59.321 45.833 0.00 0.00 0.00 4.04
723 8160 5.734786 GCTGTCACTGCTTAATAGATCTCGT 60.735 44.000 0.00 0.00 0.00 4.18
738 8175 1.135112 TCTCGTGCATATGCGTGTCTT 60.135 47.619 22.21 0.00 45.83 3.01
743 8180 3.001228 CGTGCATATGCGTGTCTTTGTAT 59.999 43.478 22.21 0.00 45.83 2.29
780 8217 3.941483 CCAAGTCTTTATGGTGTGCTAGG 59.059 47.826 0.00 0.00 31.84 3.02
781 8218 4.565652 CCAAGTCTTTATGGTGTGCTAGGT 60.566 45.833 0.00 0.00 31.84 3.08
782 8219 4.473477 AGTCTTTATGGTGTGCTAGGTC 57.527 45.455 0.00 0.00 0.00 3.85
788 8225 2.696989 TGGTGTGCTAGGTCATGATG 57.303 50.000 0.00 0.00 0.00 3.07
794 8231 4.036027 GTGTGCTAGGTCATGATGAATTGG 59.964 45.833 0.00 0.00 0.00 3.16
799 8236 6.183361 TGCTAGGTCATGATGAATTGGTGATA 60.183 38.462 0.00 0.00 0.00 2.15
828 8265 6.382869 AATAAATTGATCCTAGTGCAGTGC 57.617 37.500 8.58 8.58 0.00 4.40
829 8266 3.354948 AATTGATCCTAGTGCAGTGCA 57.645 42.857 15.37 15.37 35.60 4.57
885 8322 6.703607 CCAACATCTATTTGGACTAGCTACTG 59.296 42.308 0.00 0.00 45.69 2.74
886 8323 7.268586 CAACATCTATTTGGACTAGCTACTGT 58.731 38.462 0.00 0.00 0.00 3.55
887 8324 7.425224 ACATCTATTTGGACTAGCTACTGTT 57.575 36.000 0.00 0.00 0.00 3.16
918 8355 8.147244 ACAAGTAGACATAAGTTCCTACCATT 57.853 34.615 0.00 0.00 33.78 3.16
927 13123 3.297736 AGTTCCTACCATTCTACCGAGG 58.702 50.000 0.00 0.00 0.00 4.63
930 13126 4.194678 TCCTACCATTCTACCGAGGAAT 57.805 45.455 0.00 0.00 34.21 3.01
939 13135 2.171237 TCTACCGAGGAATCGACCACTA 59.829 50.000 0.00 0.00 34.64 2.74
945 13141 3.797256 CGAGGAATCGACCACTATTTCAC 59.203 47.826 0.00 0.00 34.64 3.18
1328 13524 1.977854 ACTACAACTCATGCAGGGTCA 59.022 47.619 0.00 0.00 0.00 4.02
1658 13865 8.977267 ATACGAGTAGACATAAGTTTCTACCT 57.023 34.615 8.85 0.00 43.62 3.08
1711 13918 6.430451 GGCAAACAATTATGAAGGTCTATCG 58.570 40.000 0.00 0.00 0.00 2.92
1726 13933 6.763355 AGGTCTATCGCAGTCATATGAATTT 58.237 36.000 7.07 0.00 0.00 1.82
1883 14090 2.174764 CTGACTTCGTCGATTACACCG 58.825 52.381 0.00 0.00 34.95 4.94
1894 14101 3.508793 TCGATTACACCGGAGAAGTCTTT 59.491 43.478 9.46 0.00 0.00 2.52
1906 14113 3.649986 GTCTTTGTGCACGCGCCT 61.650 61.111 13.13 0.00 37.32 5.52
1951 14158 5.589192 CCCTAGTCGTCGAGTCAATTTAAT 58.411 41.667 5.70 0.00 0.00 1.40
1973 14180 2.471815 ACTAGATCCACCAATCCGGA 57.528 50.000 6.61 6.61 38.63 5.14
2065 14272 3.053842 ACTGCTCCACTCCATGATTTCAT 60.054 43.478 0.00 0.00 36.96 2.57
2126 14333 3.471680 GATTGGAGCTGGAGTAACATCC 58.528 50.000 0.00 0.00 40.03 3.51
2431 14640 8.547967 AGAAAAGTAAGAGATTTACGCAATCA 57.452 30.769 9.86 0.00 43.63 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 5.762179 ATCCTCCAACTTGTACAATCTGA 57.238 39.130 9.13 3.28 0.00 3.27
8 9 5.711976 CCAAATCCTCCAACTTGTACAATCT 59.288 40.000 9.13 0.00 0.00 2.40
9 10 5.476945 ACCAAATCCTCCAACTTGTACAATC 59.523 40.000 9.13 0.00 0.00 2.67
16 4856 3.420893 TGCTACCAAATCCTCCAACTTG 58.579 45.455 0.00 0.00 0.00 3.16
183 7617 4.759782 AGTGAAATAGTGGTCGATTCCTG 58.240 43.478 0.00 0.00 0.00 3.86
224 7661 7.283127 TGTTGCTCTTGACTTCTTGTTTATTCT 59.717 33.333 0.00 0.00 0.00 2.40
226 7663 7.196331 GTGTTGCTCTTGACTTCTTGTTTATT 58.804 34.615 0.00 0.00 0.00 1.40
228 7665 5.065988 GGTGTTGCTCTTGACTTCTTGTTTA 59.934 40.000 0.00 0.00 0.00 2.01
229 7666 4.142381 GGTGTTGCTCTTGACTTCTTGTTT 60.142 41.667 0.00 0.00 0.00 2.83
230 7667 3.378427 GGTGTTGCTCTTGACTTCTTGTT 59.622 43.478 0.00 0.00 0.00 2.83
256 7693 3.069946 ATGGTTGCCCGTGCCATG 61.070 61.111 0.00 0.00 41.05 3.66
294 7731 1.785041 GCAGCAAACGACCAGAAGCA 61.785 55.000 0.00 0.00 0.00 3.91
323 7760 0.107508 CACTCCTTGCCATGGACGAT 60.108 55.000 18.40 0.00 0.00 3.73
387 7824 0.035630 GATGTGCTTGCCACTCTCCT 60.036 55.000 0.00 0.00 44.92 3.69
392 7829 0.607489 GACTGGATGTGCTTGCCACT 60.607 55.000 0.00 0.00 44.92 4.00
415 7852 3.919216 AGAGTTCTCACCAAGAATGTCG 58.081 45.455 2.64 0.00 45.57 4.35
419 7856 7.911651 TGATCTTTAGAGTTCTCACCAAGAAT 58.088 34.615 2.64 0.00 45.57 2.40
421 7858 6.918067 TGATCTTTAGAGTTCTCACCAAGA 57.082 37.500 2.64 6.68 0.00 3.02
472 7909 8.484641 ACACAAGAATACATATCAGAACACAG 57.515 34.615 0.00 0.00 0.00 3.66
542 7979 2.055689 CTTCTCCCACCTGCACCACA 62.056 60.000 0.00 0.00 0.00 4.17
561 7998 1.002366 CTGCATGAGTTGTAGTCGCC 58.998 55.000 0.00 0.00 33.73 5.54
633 8070 4.697756 CGCTTTGCCTCCGTGGGA 62.698 66.667 0.00 0.00 36.00 4.37
637 8074 1.227853 AAGAACGCTTTGCCTCCGT 60.228 52.632 0.00 0.00 36.68 4.69
639 8076 1.131315 GATGAAGAACGCTTTGCCTCC 59.869 52.381 0.00 0.00 33.61 4.30
670 8107 2.113774 CTTGCTGGCAGTGACCCA 59.886 61.111 17.16 1.66 0.00 4.51
698 8135 5.595885 GAGATCTATTAAGCAGTGACAGCA 58.404 41.667 2.10 0.00 0.00 4.41
722 8159 2.900122 ACAAAGACACGCATATGCAC 57.100 45.000 26.52 14.18 42.21 4.57
723 8160 5.559427 AAATACAAAGACACGCATATGCA 57.441 34.783 26.52 4.04 42.21 3.96
780 8217 8.442632 TTCTTCTATCACCAATTCATCATGAC 57.557 34.615 0.00 0.00 0.00 3.06
781 8218 9.636789 ATTTCTTCTATCACCAATTCATCATGA 57.363 29.630 0.00 0.00 0.00 3.07
799 8236 9.118300 CTGCACTAGGATCAATTTATTTCTTCT 57.882 33.333 0.00 0.00 0.00 2.85
828 8265 6.280643 AGATTCCATGAAAACATGATGCATG 58.719 36.000 2.46 13.92 46.18 4.06
829 8266 6.479972 AGATTCCATGAAAACATGATGCAT 57.520 33.333 0.00 0.00 34.66 3.96
850 8287 8.956426 GTCCAAATAGATGTTGGTTTATCAAGA 58.044 33.333 3.28 0.00 44.96 3.02
895 8332 8.611051 AGAATGGTAGGAACTTATGTCTACTT 57.389 34.615 0.00 0.00 41.75 2.24
910 8347 3.057456 CGATTCCTCGGTAGAATGGTAGG 60.057 52.174 1.08 0.00 41.27 3.18
918 8355 1.064906 AGTGGTCGATTCCTCGGTAGA 60.065 52.381 0.00 0.00 45.10 2.59
927 13123 7.365840 AGAAAAGTGAAATAGTGGTCGATTC 57.634 36.000 0.00 0.00 0.00 2.52
930 13126 8.311836 AGAATAGAAAAGTGAAATAGTGGTCGA 58.688 33.333 0.00 0.00 0.00 4.20
945 13141 7.602517 ACCGAAGATCACAAGAATAGAAAAG 57.397 36.000 0.00 0.00 0.00 2.27
1066 13262 0.107508 CACTCCTTGCCATGGACGAT 60.108 55.000 18.40 0.00 0.00 3.73
1382 13578 3.695060 CAGATGAAGAATGCTTTGCCTCT 59.305 43.478 0.00 0.00 33.61 3.69
1658 13865 8.851541 AATGTTTAAAGTATGGTCGGTAGAAA 57.148 30.769 0.00 0.00 0.00 2.52
1711 13918 6.690194 AAGACTCCAAATTCATATGACTGC 57.310 37.500 4.48 0.00 0.00 4.40
1868 14075 1.452110 TCTCCGGTGTAATCGACGAA 58.548 50.000 0.00 0.00 0.00 3.85
1883 14090 0.235926 GCGTGCACAAAGACTTCTCC 59.764 55.000 18.64 0.00 0.00 3.71
1894 14101 2.612567 CCTTAAAGGCGCGTGCACA 61.613 57.895 24.18 0.76 45.35 4.57
1906 14113 3.102204 CTCCGGGGAACTAGTCCTTAAA 58.898 50.000 0.00 0.00 46.92 1.52
1951 14158 4.291792 TCCGGATTGGTGGATCTAGTTTA 58.708 43.478 0.00 0.00 39.52 2.01
1973 14180 0.176219 TGTGAAGGTCGACCGTGTTT 59.824 50.000 28.16 17.02 42.08 2.83
2126 14333 5.240891 TCTCTGCTCCAGTAAAATGAACTG 58.759 41.667 0.00 0.00 43.26 3.16


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

AutoCloner maintained by Alex Coulton.