Multiple sequence alignment - TraesCS5A01G555600

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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 TraesCS5A01G555600 chr5A 100.000 2378 0 0 1 2378 706864155 706866532 0 4392
1 TraesCS5A01G555600 chrUn 95.348 2386 100 4 4 2378 245706822 245704437 0 3781
2 TraesCS5A01G555600 chrUn 95.306 2386 101 4 4 2378 291536194 291533809 0 3775
3 TraesCS5A01G555600 chrUn 95.144 2389 105 4 1 2378 67500251 67502639 0 3759
4 TraesCS5A01G555600 chrUn 95.019 2389 108 4 1 2378 229309470 229311858 0 3742
5 TraesCS5A01G555600 chrUn 94.803 2386 113 4 4 2378 199905498 199903113 0 3709
6 TraesCS5A01G555600 chrUn 94.761 2386 114 4 4 2378 199875578 199873193 0 3703
7 TraesCS5A01G555600 chr5D 95.096 2386 106 4 4 2378 18999678 18997293 0 3747
8 TraesCS5A01G555600 chr6B 94.935 2389 110 4 1 2378 111686032 111688420 0 3731
9 TraesCS5A01G555600 chr1B 94.845 2386 112 4 4 2378 544624390 544622005 0 3714


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 TraesCS5A01G555600 chr5A 706864155 706866532 2377 False 4392 4392 100.000 1 2378 1 chr5A.!!$F1 2377
1 TraesCS5A01G555600 chrUn 245704437 245706822 2385 True 3781 3781 95.348 4 2378 1 chrUn.!!$R3 2374
2 TraesCS5A01G555600 chrUn 291533809 291536194 2385 True 3775 3775 95.306 4 2378 1 chrUn.!!$R4 2374
3 TraesCS5A01G555600 chrUn 67500251 67502639 2388 False 3759 3759 95.144 1 2378 1 chrUn.!!$F1 2377
4 TraesCS5A01G555600 chrUn 229309470 229311858 2388 False 3742 3742 95.019 1 2378 1 chrUn.!!$F2 2377
5 TraesCS5A01G555600 chrUn 199903113 199905498 2385 True 3709 3709 94.803 4 2378 1 chrUn.!!$R2 2374
6 TraesCS5A01G555600 chrUn 199873193 199875578 2385 True 3703 3703 94.761 4 2378 1 chrUn.!!$R1 2374
7 TraesCS5A01G555600 chr5D 18997293 18999678 2385 True 3747 3747 95.096 4 2378 1 chr5D.!!$R1 2374
8 TraesCS5A01G555600 chr6B 111686032 111688420 2388 False 3731 3731 94.935 1 2378 1 chr6B.!!$F1 2377
9 TraesCS5A01G555600 chr1B 544622005 544624390 2385 True 3714 3714 94.845 4 2378 1 chr1B.!!$R1 2374

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
449 451 0.75085 GTGGGATCTAGGTTAGCGCA 59.249 55.0 11.47 0.0 0.0 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2202 2214 0.179029 CCCTGACCAAAACAGACCGT 60.179 55.0 0.0 0.0 37.54 4.83 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
125 127 1.247567 GCTTACCCATGTGCAAGTGT 58.752 50.000 0.00 0.00 0.00 3.55
155 157 1.900486 GGAACCTTTCTCCTCTTCGGA 59.100 52.381 0.00 0.00 40.30 4.55
211 213 2.942796 AAGATCTGCACCGACGGCA 61.943 57.895 15.39 6.18 39.32 5.69
279 281 1.410850 CCTACTCATCGGGGCATGGT 61.411 60.000 0.00 0.00 0.00 3.55
341 343 1.949525 CATCCATTTTCGGGGCTAGTG 59.050 52.381 0.00 0.00 0.00 2.74
349 351 2.432300 CGGGGCTAGTGGATTCGGT 61.432 63.158 0.00 0.00 0.00 4.69
383 385 2.301870 ACACACTCCTTAGCGGATTTCA 59.698 45.455 0.00 0.00 42.12 2.69
429 431 3.683340 GTCTTAATCGACCAACACCCTTC 59.317 47.826 0.00 0.00 0.00 3.46
449 451 0.750850 GTGGGATCTAGGTTAGCGCA 59.249 55.000 11.47 0.00 0.00 6.09
486 488 2.674754 GGCTTCCGGTTCATCCCA 59.325 61.111 0.00 0.00 0.00 4.37
683 685 3.198635 CAGCTATCCTGAGGGAAACTTCA 59.801 47.826 0.00 0.00 45.78 3.02
684 686 4.043596 AGCTATCCTGAGGGAAACTTCAT 58.956 43.478 0.00 0.00 46.26 2.57
741 743 2.339769 GCCCCTATACCCAAGTCAGAT 58.660 52.381 0.00 0.00 0.00 2.90
753 755 3.438087 CCAAGTCAGATGAACGATTTGCT 59.562 43.478 0.00 0.00 30.04 3.91
786 788 1.216710 CGAGCCTCCACCAGAGTTC 59.783 63.158 0.00 0.00 41.47 3.01
835 837 0.838554 TCACCATCTTTCGGGTCCCA 60.839 55.000 9.12 0.00 34.45 4.37
874 876 3.323691 TCGAACCCTTCACAGAAGATCAA 59.676 43.478 8.26 0.00 0.00 2.57
970 972 1.006220 ACTCGCACGCATGTCAGAA 60.006 52.632 0.00 0.00 0.00 3.02
993 995 2.285083 CTTGGTCCGTGTTTCAAGACA 58.715 47.619 0.00 0.00 38.96 3.41
1052 1054 2.342279 CGAGGGACACGCCTTTCA 59.658 61.111 0.00 0.00 34.76 2.69
1117 1119 3.984732 GGCCCCCAGTCTTTGGCT 61.985 66.667 0.00 0.00 46.32 4.75
1148 1150 1.529796 GACAACAGTCCACACCCCA 59.470 57.895 0.00 0.00 0.00 4.96
1257 1259 4.054671 AGCACTCTTTGACTCTCTTTTCG 58.945 43.478 0.00 0.00 0.00 3.46
1281 1283 3.328050 AGTCCTTTTCATCTTTCCCTCGT 59.672 43.478 0.00 0.00 0.00 4.18
1326 1328 2.438021 TCGCCTGTATTTAGCCTTGGAT 59.562 45.455 0.00 0.00 0.00 3.41
1341 1343 1.760875 GGATGGAGTCTACCGCCCA 60.761 63.158 0.00 0.00 0.00 5.36
1475 1477 2.052690 CCGGTCCGTCACTGAGGAT 61.053 63.158 11.06 0.00 38.97 3.24
1529 1531 1.078214 CCGATTCTCAAGCTGGGCA 60.078 57.895 0.00 0.00 0.00 5.36
1555 1557 1.226491 GCTCGCTCGCCGTTACTAA 60.226 57.895 0.00 0.00 38.35 2.24
1638 1646 1.264749 CCTGGGGTCATGGTCGAAGA 61.265 60.000 0.00 0.00 0.00 2.87
1648 1656 3.173240 GTCGAAGAGACGTGCGCC 61.173 66.667 4.18 0.00 40.43 6.53
1663 1671 2.281484 GCCTCGTTTGCTGGGTCA 60.281 61.111 0.00 0.00 0.00 4.02
1666 1674 1.247567 CCTCGTTTGCTGGGTCATTT 58.752 50.000 0.00 0.00 0.00 2.32
1676 1684 1.753073 CTGGGTCATTTTGAGGCCATC 59.247 52.381 5.01 0.00 0.00 3.51
1707 1715 4.077188 GTCGGCTGCACTGCGTTC 62.077 66.667 0.50 0.00 0.00 3.95
1715 1723 1.197492 CTGCACTGCGTTCATAAAGCA 59.803 47.619 0.00 0.61 39.25 3.91
1812 1820 2.507944 GACCAGATGCCGCATCCT 59.492 61.111 26.36 13.20 41.36 3.24
2039 2048 1.522668 CTTTGCAACACGAGGGATGA 58.477 50.000 0.00 0.00 0.00 2.92
2159 2168 1.899437 GAGGTGGTCGAGGCATTGGA 61.899 60.000 0.00 0.00 0.00 3.53
2190 2202 1.152984 AATGCCGCCGATGGATTGA 60.153 52.632 0.00 0.00 0.00 2.57
2202 2214 0.952984 TGGATTGAATGACGCGTGCA 60.953 50.000 20.70 15.51 0.00 4.57
2312 2324 3.771577 AAGGTTCAATGGACTTCTCGT 57.228 42.857 0.00 0.00 0.00 4.18
2319 2331 1.244816 ATGGACTTCTCGTGACGTCA 58.755 50.000 15.76 15.76 41.50 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.358247 GATGTGGCGGTTGACGGT 60.358 61.111 0.00 0.00 44.51 4.83
26 28 4.166246 GGGAATCGGGTTAAGATTTCCT 57.834 45.455 8.58 0.00 45.83 3.36
71 73 1.752833 GGTAACCCCGGCAGATAGG 59.247 63.158 0.00 0.00 0.00 2.57
98 100 0.469917 ACATGGGTAAGCCGATCCTG 59.530 55.000 0.00 0.00 30.32 3.86
133 135 2.354203 CCGAAGAGGAGAAAGGTTCCAG 60.354 54.545 0.00 0.00 45.00 3.86
341 343 3.329929 AACAACTCACCTACCGAATCC 57.670 47.619 0.00 0.00 0.00 3.01
383 385 3.625745 GACGGTGGTCATGGAAGTT 57.374 52.632 0.00 0.00 42.91 2.66
402 404 4.454504 GGTGTTGGTCGATTAAGACAACAT 59.545 41.667 11.08 0.00 42.62 2.71
405 407 3.071892 AGGGTGTTGGTCGATTAAGACAA 59.928 43.478 11.90 0.00 42.62 3.18
429 431 0.318784 GCGCTAACCTAGATCCCACG 60.319 60.000 0.00 0.00 0.00 4.94
435 437 2.418746 CCAACTGTGCGCTAACCTAGAT 60.419 50.000 9.73 0.00 0.00 1.98
486 488 1.676014 GGTAAGCAGAACTGGCGATGT 60.676 52.381 3.99 0.00 36.08 3.06
683 685 4.140663 ACCATCTAGTAGCTGGTTCCCTAT 60.141 45.833 18.12 0.00 41.58 2.57
684 686 3.206866 ACCATCTAGTAGCTGGTTCCCTA 59.793 47.826 18.12 0.00 41.58 3.53
753 755 0.027716 GCTCGAAGCGATACTGACGA 59.972 55.000 0.00 0.00 36.83 4.20
806 808 4.442893 CCGAAAGATGGTGAACTATGCCTA 60.443 45.833 0.00 0.00 0.00 3.93
835 837 1.598130 GAGTTGGAGCACGCCTGTT 60.598 57.895 0.00 0.00 0.00 3.16
970 972 2.105821 TCTTGAAACACGGACCAAGGAT 59.894 45.455 0.00 0.00 37.27 3.24
1227 1229 6.545298 AGAGAGTCAAAGAGTGCTTGAAATTT 59.455 34.615 0.00 0.00 33.79 1.82
1257 1259 4.393371 CGAGGGAAAGATGAAAAGGACTTC 59.607 45.833 0.00 0.00 0.00 3.01
1281 1283 1.820519 ACCGATAGCGAACAAGTACCA 59.179 47.619 0.00 0.00 40.82 3.25
1326 1328 0.988832 AAATTGGGCGGTAGACTCCA 59.011 50.000 0.00 0.00 0.00 3.86
1475 1477 2.166459 CGAATTGTAGTCTGGAGAGGCA 59.834 50.000 0.00 0.00 0.00 4.75
1538 1540 0.591741 CCTTAGTAACGGCGAGCGAG 60.592 60.000 16.62 3.34 0.00 5.03
1628 1636 1.154016 CGCACGTCTCTTCGACCAT 60.154 57.895 0.00 0.00 39.56 3.55
1629 1637 2.254350 CGCACGTCTCTTCGACCA 59.746 61.111 0.00 0.00 39.56 4.02
1638 1646 3.036084 CAAACGAGGCGCACGTCT 61.036 61.111 26.20 14.44 43.16 4.18
1648 1656 2.293122 TCAAAATGACCCAGCAAACGAG 59.707 45.455 0.00 0.00 0.00 4.18
1688 1696 4.687215 ACGCAGTGCAGCCGACAT 62.687 61.111 16.83 0.00 42.51 3.06
1689 1697 4.908687 AACGCAGTGCAGCCGACA 62.909 61.111 16.83 0.00 45.00 4.35
1707 1715 0.451783 GTGGGCGTCCTTGCTTTATG 59.548 55.000 7.97 0.00 34.52 1.90
1743 1751 4.697756 GGCTGCCAGTGTACCGCA 62.698 66.667 15.17 0.00 0.00 5.69
1834 1843 1.063488 GTCACGCCAAAACACGCTT 59.937 52.632 0.00 0.00 0.00 4.68
2039 2048 0.179034 GGCATGGCTAGCTTGCTAGT 60.179 55.000 29.29 8.11 36.62 2.57
2073 2082 1.566018 CGAAGGCGTCAAGGAACACC 61.566 60.000 0.55 0.00 0.00 4.16
2127 2136 2.947785 ACCTCCCCTCCTCGGAGT 60.948 66.667 11.76 0.00 44.75 3.85
2159 2168 2.809601 GCATTGTCCGTCGCTCGT 60.810 61.111 0.00 0.00 37.94 4.18
2173 2182 0.538057 ATTCAATCCATCGGCGGCAT 60.538 50.000 10.53 0.00 0.00 4.40
2183 2195 0.952984 TGCACGCGTCATTCAATCCA 60.953 50.000 9.86 0.00 0.00 3.41
2190 2202 3.411351 GACCGTGCACGCGTCATT 61.411 61.111 35.23 18.52 38.50 2.57
2202 2214 0.179029 CCCTGACCAAAACAGACCGT 60.179 55.000 0.00 0.00 37.54 4.83


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

AutoCloner maintained by Alex Coulton.