Multiple sequence alignment - TraesCS5D01G493000

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 TraesCS5D01G493000 chr5D 100.000 3622 0 0 1 3622 525956286 525959907 0.000000e+00 6689
1 TraesCS5D01G493000 chr5B 96.138 3366 67 25 1 3337 660587853 660591184 0.000000e+00 5437
2 TraesCS5D01G493000 chr5B 92.361 288 7 5 3336 3622 660591347 660591620 2.620000e-106 396
3 TraesCS5D01G493000 chr5B 85.845 219 28 2 1622 1837 112194761 112194543 2.810000e-56 230
4 TraesCS5D01G493000 chr5A 90.943 3522 116 73 1 3424 652645918 652649334 0.000000e+00 4549
5 TraesCS5D01G493000 chr3D 89.952 209 19 2 1626 1833 610544049 610544256 5.960000e-68 268
6 TraesCS5D01G493000 chr3B 89.952 209 19 2 1626 1833 828111449 828111656 5.960000e-68 268
7 TraesCS5D01G493000 chr3B 87.081 209 24 3 1616 1823 675649880 675650086 2.170000e-57 233
8 TraesCS5D01G493000 chr3A 88.942 208 23 0 1626 1833 744879519 744879726 1.290000e-64 257
9 TraesCS5D01G493000 chr1A 90.052 191 16 1 1660 1847 18461727 18461537 1.000000e-60 244
10 TraesCS5D01G493000 chr1D 85.398 226 28 3 1626 1847 17169107 17168883 2.810000e-56 230


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 TraesCS5D01G493000 chr5D 525956286 525959907 3621 False 6689.0 6689 100.0000 1 3622 1 chr5D.!!$F1 3621
1 TraesCS5D01G493000 chr5B 660587853 660591620 3767 False 2916.5 5437 94.2495 1 3622 2 chr5B.!!$F1 3621
2 TraesCS5D01G493000 chr5A 652645918 652649334 3416 False 4549.0 4549 90.9430 1 3424 1 chr5A.!!$F1 3423

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
703 723 0.327964 CTTCCATCTTCCCCCTCCCT 60.328 60.0 0.0 0.0 0.0 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2673 2770 1.73172 ACCTTTTGCAGAGAGATCGC 58.268 50.0 1.09 0.0 0.0 4.58 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
167 181 2.618816 CCATACATGCACCTGAACACCT 60.619 50.000 0.00 0.00 0.00 4.00
202 216 5.183904 AGTGTTGCTCATTTTGATAACCTCC 59.816 40.000 0.00 0.00 0.00 4.30
203 217 5.048083 GTGTTGCTCATTTTGATAACCTCCA 60.048 40.000 0.00 0.00 0.00 3.86
204 218 5.183713 TGTTGCTCATTTTGATAACCTCCAG 59.816 40.000 0.00 0.00 0.00 3.86
205 219 5.178096 TGCTCATTTTGATAACCTCCAGA 57.822 39.130 0.00 0.00 0.00 3.86
206 220 5.188434 TGCTCATTTTGATAACCTCCAGAG 58.812 41.667 0.00 0.00 0.00 3.35
207 221 4.036144 GCTCATTTTGATAACCTCCAGAGC 59.964 45.833 0.00 0.00 38.09 4.09
457 475 1.134098 CCACACCCATACATCCACCTC 60.134 57.143 0.00 0.00 0.00 3.85
458 476 1.559219 CACACCCATACATCCACCTCA 59.441 52.381 0.00 0.00 0.00 3.86
657 677 5.411669 TCCTTTTTATTCCTCTCGCTTTCAC 59.588 40.000 0.00 0.00 0.00 3.18
703 723 0.327964 CTTCCATCTTCCCCCTCCCT 60.328 60.000 0.00 0.00 0.00 4.20
774 801 2.632028 GAGCAGAGAGATCTATTGGCCA 59.368 50.000 0.00 0.00 0.00 5.36
841 872 1.304381 GCCATCCACCCTTGCTTGA 60.304 57.895 0.00 0.00 0.00 3.02
842 873 1.318158 GCCATCCACCCTTGCTTGAG 61.318 60.000 0.00 0.00 0.00 3.02
881 914 2.290464 CTATATACCCCTCGCCTCTCG 58.710 57.143 0.00 0.00 40.15 4.04
925 958 2.483013 GCAAGGAGGAACAAACAAACCC 60.483 50.000 0.00 0.00 0.00 4.11
1226 1271 5.500234 TCCCCTTCTTGAATATTCACACTG 58.500 41.667 17.76 8.69 36.83 3.66
1256 1302 5.406477 GCTTTTTAGTTGCTATGCTTTGCTT 59.594 36.000 7.48 0.00 0.00 3.91
1361 1422 2.561885 CAGCAGCAGCAGCAACTC 59.438 61.111 12.92 0.00 45.49 3.01
1391 1452 1.959085 CCAGATGTTTGCAAGCGGT 59.041 52.632 8.84 0.00 0.00 5.68
1469 1542 2.333938 CAACAGCAGCAGCACCAC 59.666 61.111 3.17 0.00 45.49 4.16
1574 1647 4.586235 GCAGGTGGTGGTGGTGCT 62.586 66.667 0.00 0.00 0.00 4.40
1575 1648 2.595463 CAGGTGGTGGTGGTGCTG 60.595 66.667 0.00 0.00 0.00 4.41
1576 1649 3.889692 AGGTGGTGGTGGTGCTGG 61.890 66.667 0.00 0.00 0.00 4.85
1577 1650 4.204028 GGTGGTGGTGGTGCTGGT 62.204 66.667 0.00 0.00 0.00 4.00
1578 1651 2.906897 GTGGTGGTGGTGCTGGTG 60.907 66.667 0.00 0.00 0.00 4.17
1579 1652 4.892965 TGGTGGTGGTGCTGGTGC 62.893 66.667 0.00 0.00 40.20 5.01
1916 1989 0.386858 CGTCGTCGTCCACAACATCT 60.387 55.000 0.00 0.00 0.00 2.90
2269 2366 1.753847 GCAAATGGCTGGCCTATACCA 60.754 52.381 13.05 6.69 40.25 3.25
2632 2729 0.837691 ATCCTGTGACTGTGAGGCCA 60.838 55.000 5.01 0.00 0.00 5.36
2673 2770 1.529948 ATGCATGGCGGAATGGAGG 60.530 57.895 0.00 0.00 30.90 4.30
2735 2832 6.255215 TCCGAATTGAAGCTTAATTTTAGCG 58.745 36.000 0.00 6.20 43.37 4.26
2853 2951 3.389983 ACTCTCGAGTGAGTCCTAGCTAT 59.610 47.826 20.64 0.00 43.04 2.97
2964 3062 5.537300 TCTTGGATCTCCTTAATTCTCCG 57.463 43.478 0.00 0.00 36.82 4.63
2965 3063 4.962995 TCTTGGATCTCCTTAATTCTCCGT 59.037 41.667 0.00 0.00 36.82 4.69
3119 3221 4.336889 TCGAGTTGATGAGTTGGTTTCT 57.663 40.909 0.00 0.00 0.00 2.52
3120 3222 4.703897 TCGAGTTGATGAGTTGGTTTCTT 58.296 39.130 0.00 0.00 0.00 2.52
3121 3223 4.750098 TCGAGTTGATGAGTTGGTTTCTTC 59.250 41.667 0.00 0.00 0.00 2.87
3174 3276 4.679373 ATGACAGTATGAGTAGCTTGGG 57.321 45.455 0.00 0.00 39.69 4.12
3272 3374 1.603456 TGCTTGCAATTCCACTCGAA 58.397 45.000 0.00 0.00 34.14 3.71
3428 3708 8.807948 TTCCCTAGAAATTCAGTTTATCCTTG 57.192 34.615 0.00 0.00 0.00 3.61
3448 3728 7.090173 TCCTTGTAAAATTTAGTCTTGCATGC 58.910 34.615 11.82 11.82 0.00 4.06
3450 3730 7.546667 CCTTGTAAAATTTAGTCTTGCATGCAT 59.453 33.333 23.37 9.20 0.00 3.96
3451 3731 8.464770 TTGTAAAATTTAGTCTTGCATGCATC 57.535 30.769 23.37 14.81 0.00 3.91
3452 3732 6.746822 TGTAAAATTTAGTCTTGCATGCATCG 59.253 34.615 23.37 15.80 0.00 3.84
3453 3733 3.976793 ATTTAGTCTTGCATGCATCGG 57.023 42.857 23.37 14.66 0.00 4.18
3481 3761 5.934625 ACTTGTCTAGGTTGCTAATTGTGAG 59.065 40.000 0.00 0.00 0.00 3.51
3482 3762 5.483685 TGTCTAGGTTGCTAATTGTGAGT 57.516 39.130 0.00 0.00 0.00 3.41
3483 3763 5.865085 TGTCTAGGTTGCTAATTGTGAGTT 58.135 37.500 0.00 0.00 0.00 3.01
3484 3764 6.296026 TGTCTAGGTTGCTAATTGTGAGTTT 58.704 36.000 0.00 0.00 0.00 2.66
3485 3765 6.204688 TGTCTAGGTTGCTAATTGTGAGTTTG 59.795 38.462 0.00 0.00 0.00 2.93
3486 3766 6.204882 GTCTAGGTTGCTAATTGTGAGTTTGT 59.795 38.462 0.00 0.00 0.00 2.83
3487 3767 5.186996 AGGTTGCTAATTGTGAGTTTGTG 57.813 39.130 0.00 0.00 0.00 3.33
3488 3768 4.887071 AGGTTGCTAATTGTGAGTTTGTGA 59.113 37.500 0.00 0.00 0.00 3.58
3495 3775 2.418368 TGTGAGTTTGTGACCAAGCT 57.582 45.000 0.00 0.00 43.79 3.74
3501 3781 3.935828 GAGTTTGTGACCAAGCTATCCTC 59.064 47.826 0.00 0.00 41.54 3.71
3516 3796 4.283212 GCTATCCTCTGCTAACCATCTTCT 59.717 45.833 0.00 0.00 0.00 2.85
3610 3891 5.284660 CGCTGAATACAAGAAGATTGCAAAC 59.715 40.000 1.71 0.00 0.00 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
167 181 0.395586 AGCAACACTTGTGCCTTGGA 60.396 50.000 0.10 0.00 0.00 3.53
207 221 3.657038 ATTGGAGCTGGCTGGCTGG 62.657 63.158 9.95 0.85 43.20 4.85
457 475 1.269206 GCAAGGGAATGTGTGTGTGTG 60.269 52.381 0.00 0.00 0.00 3.82
458 476 1.032014 GCAAGGGAATGTGTGTGTGT 58.968 50.000 0.00 0.00 0.00 3.72
730 757 1.072806 TCTGCACACAAGAATGGAGCT 59.927 47.619 0.00 0.00 34.52 4.09
731 758 1.467734 CTCTGCACACAAGAATGGAGC 59.532 52.381 0.00 0.00 34.52 4.70
774 801 1.376466 CACCACCCACTAGCAGCTT 59.624 57.895 0.00 0.00 0.00 3.74
898 931 3.632145 TGTTTGTTCCTCCTTGCTTCTTC 59.368 43.478 0.00 0.00 0.00 2.87
925 958 1.959282 AGTGGCTGCTTCTTCCTTTTG 59.041 47.619 0.00 0.00 0.00 2.44
979 1012 1.351683 GGTGGTGGTGGTGTGGTATAA 59.648 52.381 0.00 0.00 0.00 0.98
1226 1271 2.749280 AGCAACTAAAAAGCCATGGC 57.251 45.000 30.12 30.12 42.33 4.40
1256 1302 8.465999 AGAAACTAATCACAATCACACAAAACA 58.534 29.630 0.00 0.00 0.00 2.83
1579 1652 4.767255 GACCTCCGCCAGCACCAG 62.767 72.222 0.00 0.00 0.00 4.00
1916 1989 4.308458 CCAGCCGTGGTCGTGGAA 62.308 66.667 0.00 0.00 39.30 3.53
2269 2366 2.050351 CGTCAGTGGCGTCGAACT 60.050 61.111 9.46 0.00 0.00 3.01
2673 2770 1.731720 ACCTTTTGCAGAGAGATCGC 58.268 50.000 1.09 0.00 0.00 4.58
2735 2832 2.730626 CGATCGATCGGAAGCCATC 58.269 57.895 34.54 8.62 45.93 3.51
2853 2951 5.247792 AGAACAGCATGCATGGAGATAGATA 59.752 40.000 27.34 0.00 42.53 1.98
2964 3062 8.382130 CCAATTAACATGCATTACAATGACAAC 58.618 33.333 0.00 0.00 38.70 3.32
2965 3063 8.093307 ACCAATTAACATGCATTACAATGACAA 58.907 29.630 0.00 0.00 38.70 3.18
3120 3222 9.929180 GGTATGAAGATTGCACTAATATACTGA 57.071 33.333 0.00 0.00 0.00 3.41
3121 3223 9.155975 GGGTATGAAGATTGCACTAATATACTG 57.844 37.037 0.00 0.00 0.00 2.74
3130 3232 3.053395 ACATGGGGTATGAAGATTGCACT 60.053 43.478 0.00 0.00 39.21 4.40
3174 3276 5.695851 AGTGAGTGGAAACATTGAACATC 57.304 39.130 0.00 0.00 46.14 3.06
3272 3374 9.872684 AATGAAATGGACCTCATGATATAAACT 57.127 29.630 0.00 0.00 35.99 2.66
3372 3652 3.065786 TGCAAATTAGATGCTAGCAGTGC 59.934 43.478 23.89 20.16 44.14 4.40
3428 3708 6.197096 CCGATGCATGCAAGACTAAATTTTAC 59.803 38.462 26.68 0.00 0.00 2.01
3447 3727 2.271800 CCTAGACAAGTGAACCGATGC 58.728 52.381 0.00 0.00 0.00 3.91
3448 3728 3.594603 ACCTAGACAAGTGAACCGATG 57.405 47.619 0.00 0.00 0.00 3.84
3450 3730 2.547218 GCAACCTAGACAAGTGAACCGA 60.547 50.000 0.00 0.00 0.00 4.69
3451 3731 1.798813 GCAACCTAGACAAGTGAACCG 59.201 52.381 0.00 0.00 0.00 4.44
3452 3732 3.127425 AGCAACCTAGACAAGTGAACC 57.873 47.619 0.00 0.00 0.00 3.62
3453 3733 6.204882 ACAATTAGCAACCTAGACAAGTGAAC 59.795 38.462 0.00 0.00 0.00 3.18
3481 3761 3.686726 CAGAGGATAGCTTGGTCACAAAC 59.313 47.826 0.00 0.00 35.89 2.93
3482 3762 3.869912 GCAGAGGATAGCTTGGTCACAAA 60.870 47.826 0.00 0.00 35.89 2.83
3483 3763 2.355108 GCAGAGGATAGCTTGGTCACAA 60.355 50.000 0.00 0.00 34.87 3.33
3484 3764 1.208052 GCAGAGGATAGCTTGGTCACA 59.792 52.381 0.00 0.00 0.00 3.58
3485 3765 1.484240 AGCAGAGGATAGCTTGGTCAC 59.516 52.381 0.00 0.00 38.01 3.67
3486 3766 1.871418 AGCAGAGGATAGCTTGGTCA 58.129 50.000 0.00 0.00 38.01 4.02
3487 3767 3.493524 GGTTAGCAGAGGATAGCTTGGTC 60.494 52.174 0.00 0.00 42.05 4.02
3488 3768 2.436173 GGTTAGCAGAGGATAGCTTGGT 59.564 50.000 0.00 0.00 42.05 3.67
3495 3775 5.070981 CCAAGAAGATGGTTAGCAGAGGATA 59.929 44.000 0.00 0.00 35.65 2.59


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

AutoCloner maintained by Alex Coulton.