Multiple sequence alignment - TraesCS4D01G208000

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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 TraesCS4D01G208000 chr4D 100.000 3155 0 0 1 3155 358038706 358035552 0.000000e+00 5827
1 TraesCS4D01G208000 chr4D 87.419 2774 285 39 417 3155 292849225 292851969 0.000000e+00 3131
2 TraesCS4D01G208000 chr4D 87.050 2780 292 40 417 3155 191721734 191718982 0.000000e+00 3077
3 TraesCS4D01G208000 chr4D 85.719 2794 315 51 417 3148 292635160 292637931 0.000000e+00 2872
4 TraesCS4D01G208000 chr4D 90.541 148 13 1 3009 3155 275360085 275360232 8.930000e-46 195
5 TraesCS4D01G208000 chr3A 92.642 2786 143 35 417 3155 91713227 91710457 0.000000e+00 3952
6 TraesCS4D01G208000 chr3A 92.601 2784 147 35 417 3155 91717854 91715085 0.000000e+00 3945
7 TraesCS4D01G208000 chr2A 92.014 2780 158 37 420 3155 679108786 679106027 0.000000e+00 3845
8 TraesCS4D01G208000 chr6A 91.840 2782 170 31 417 3155 345454413 345457180 0.000000e+00 3827
9 TraesCS4D01G208000 chr6A 86.418 589 46 23 2596 3155 209105953 209106536 5.780000e-172 614
10 TraesCS4D01G208000 chr7B 91.527 2632 172 33 417 3008 360407947 360405327 0.000000e+00 3578
11 TraesCS4D01G208000 chr7B 88.977 2785 231 51 426 3155 456121822 456124585 0.000000e+00 3373
12 TraesCS4D01G208000 chr5B 91.086 2625 188 29 421 3008 333648123 333650738 0.000000e+00 3509
13 TraesCS4D01G208000 chr5B 90.906 2628 189 30 417 3008 373340185 373342798 0.000000e+00 3483
14 TraesCS4D01G208000 chr5B 90.753 2628 193 30 417 3008 373348284 373350897 0.000000e+00 3461
15 TraesCS4D01G208000 chr5B 92.398 513 36 3 1 510 311568874 311568362 0.000000e+00 728
16 TraesCS4D01G208000 chr2D 86.095 1237 119 34 1947 3155 279506704 279505493 0.000000e+00 1282
17 TraesCS4D01G208000 chr2D 90.580 690 46 9 2484 3155 279510470 279509782 0.000000e+00 896
18 TraesCS4D01G208000 chr2D 92.360 445 27 5 2716 3155 319349703 319350145 7.430000e-176 627
19 TraesCS4D01G208000 chr4A 93.555 512 31 2 1 510 487349708 487349197 0.000000e+00 761
20 TraesCS4D01G208000 chr6D 92.383 512 35 4 1 510 359776476 359776985 0.000000e+00 726
21 TraesCS4D01G208000 chr6D 86.715 685 44 22 2501 3155 307409841 307409174 0.000000e+00 717
22 TraesCS4D01G208000 chr2B 92.203 513 35 5 1 510 571079088 571078578 0.000000e+00 721
23 TraesCS4D01G208000 chr3B 92.023 514 37 4 1 510 413603824 413604337 0.000000e+00 719
24 TraesCS4D01G208000 chr3B 92.008 513 36 5 1 510 545295497 545294987 0.000000e+00 715
25 TraesCS4D01G208000 chr3B 91.945 509 39 2 1 507 413612370 413611862 0.000000e+00 712
26 TraesCS4D01G208000 chr3D 91.797 512 37 5 1 510 372376280 372376788 0.000000e+00 708
27 TraesCS4D01G208000 chr3D 91.216 148 12 1 3009 3155 251245045 251245192 1.920000e-47 200
28 TraesCS4D01G208000 chr6B 91.423 513 39 5 1 510 295369865 295370375 0.000000e+00 699
29 TraesCS4D01G208000 chr7D 90.541 148 13 1 3009 3155 290729170 290729023 8.930000e-46 195


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 TraesCS4D01G208000 chr4D 358035552 358038706 3154 True 5827.0 5827 100.0000 1 3155 1 chr4D.!!$R2 3154
1 TraesCS4D01G208000 chr4D 292849225 292851969 2744 False 3131.0 3131 87.4190 417 3155 1 chr4D.!!$F3 2738
2 TraesCS4D01G208000 chr4D 191718982 191721734 2752 True 3077.0 3077 87.0500 417 3155 1 chr4D.!!$R1 2738
3 TraesCS4D01G208000 chr4D 292635160 292637931 2771 False 2872.0 2872 85.7190 417 3148 1 chr4D.!!$F2 2731
4 TraesCS4D01G208000 chr3A 91710457 91717854 7397 True 3948.5 3952 92.6215 417 3155 2 chr3A.!!$R1 2738
5 TraesCS4D01G208000 chr2A 679106027 679108786 2759 True 3845.0 3845 92.0140 420 3155 1 chr2A.!!$R1 2735
6 TraesCS4D01G208000 chr6A 345454413 345457180 2767 False 3827.0 3827 91.8400 417 3155 1 chr6A.!!$F2 2738
7 TraesCS4D01G208000 chr6A 209105953 209106536 583 False 614.0 614 86.4180 2596 3155 1 chr6A.!!$F1 559
8 TraesCS4D01G208000 chr7B 360405327 360407947 2620 True 3578.0 3578 91.5270 417 3008 1 chr7B.!!$R1 2591
9 TraesCS4D01G208000 chr7B 456121822 456124585 2763 False 3373.0 3373 88.9770 426 3155 1 chr7B.!!$F1 2729
10 TraesCS4D01G208000 chr5B 333648123 333650738 2615 False 3509.0 3509 91.0860 421 3008 1 chr5B.!!$F1 2587
11 TraesCS4D01G208000 chr5B 373340185 373342798 2613 False 3483.0 3483 90.9060 417 3008 1 chr5B.!!$F2 2591
12 TraesCS4D01G208000 chr5B 373348284 373350897 2613 False 3461.0 3461 90.7530 417 3008 1 chr5B.!!$F3 2591
13 TraesCS4D01G208000 chr5B 311568362 311568874 512 True 728.0 728 92.3980 1 510 1 chr5B.!!$R1 509
14 TraesCS4D01G208000 chr2D 279505493 279510470 4977 True 1089.0 1282 88.3375 1947 3155 2 chr2D.!!$R1 1208
15 TraesCS4D01G208000 chr4A 487349197 487349708 511 True 761.0 761 93.5550 1 510 1 chr4A.!!$R1 509
16 TraesCS4D01G208000 chr6D 359776476 359776985 509 False 726.0 726 92.3830 1 510 1 chr6D.!!$F1 509
17 TraesCS4D01G208000 chr6D 307409174 307409841 667 True 717.0 717 86.7150 2501 3155 1 chr6D.!!$R1 654
18 TraesCS4D01G208000 chr2B 571078578 571079088 510 True 721.0 721 92.2030 1 510 1 chr2B.!!$R1 509
19 TraesCS4D01G208000 chr3B 413603824 413604337 513 False 719.0 719 92.0230 1 510 1 chr3B.!!$F1 509
20 TraesCS4D01G208000 chr3B 545294987 545295497 510 True 715.0 715 92.0080 1 510 1 chr3B.!!$R2 509
21 TraesCS4D01G208000 chr3B 413611862 413612370 508 True 712.0 712 91.9450 1 507 1 chr3B.!!$R1 506
22 TraesCS4D01G208000 chr3D 372376280 372376788 508 False 708.0 708 91.7970 1 510 1 chr3D.!!$F2 509
23 TraesCS4D01G208000 chr6B 295369865 295370375 510 False 699.0 699 91.4230 1 510 1 chr6B.!!$F1 509

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
465 472 1.777941 AGTTTGGGGCGTAAAAACCA 58.222 45.000 0.0 0.0 34.96 3.67 F
1101 1122 1.881973 AGCAACAACTATGCACCACAG 59.118 47.619 0.0 0.0 46.22 3.66 F
1417 1459 0.535780 CCTTGAGCTGAGTGTTGCCA 60.536 55.000 0.0 0.0 0.00 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1373 1415 0.319125 GGAGATAGTACTGCCAGCGC 60.319 60.000 5.39 0.0 0.0 5.92 R
2004 3875 3.640029 GGATAATACCCTCCAAGTCGTCA 59.360 47.826 0.00 0.0 0.0 4.35 R
3014 9615 3.711704 AGCCTGATCCCGAGAATAAAAGA 59.288 43.478 0.00 0.0 0.0 2.52 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
218 220 3.721035 TGAGTTGTGTGTGATGTCTGAG 58.279 45.455 0.00 0.00 0.00 3.35
256 258 6.423905 TGCTAGTGTTACTTGTCTGTTTGATC 59.576 38.462 0.00 0.00 0.00 2.92
357 363 2.371841 TCCAGTGGCTACTTGTTGTCAT 59.628 45.455 3.51 0.00 34.07 3.06
367 373 3.959943 ACTTGTTGTCATTACGGTTTGC 58.040 40.909 0.00 0.00 0.00 3.68
465 472 1.777941 AGTTTGGGGCGTAAAAACCA 58.222 45.000 0.00 0.00 34.96 3.67
543 552 6.072397 CGATTCTGTGAGGTTATAGACTAGGG 60.072 46.154 0.00 0.00 0.00 3.53
1101 1122 1.881973 AGCAACAACTATGCACCACAG 59.118 47.619 0.00 0.00 46.22 3.66
1114 1135 3.510753 TGCACCACAGCAATTGTATTCAT 59.489 39.130 7.40 0.00 42.46 2.57
1292 1334 3.808618 GCCGAAGATGATCCAATTAGGCT 60.809 47.826 13.93 0.00 39.48 4.58
1373 1415 8.040132 AGTAAGGAAGATTGAGAAGAACATCAG 58.960 37.037 0.00 0.00 0.00 2.90
1417 1459 0.535780 CCTTGAGCTGAGTGTTGCCA 60.536 55.000 0.00 0.00 0.00 4.92
1476 1518 3.036819 ACATCCAGCTGAGCAAGATAGA 58.963 45.455 17.39 0.00 0.00 1.98
1643 1694 7.285172 TGTGATTGAAGATGAAGAACCAGAAAA 59.715 33.333 0.00 0.00 0.00 2.29
1737 1788 7.254727 CCTTATGAGATCTTTGCTGCTACTTTC 60.255 40.741 0.00 0.00 0.00 2.62
1758 1809 5.940192 TCCATTGCGTTATACCATCAATC 57.060 39.130 0.00 0.00 0.00 2.67
1767 1818 6.128795 GCGTTATACCATCAATCAAGCTAGAC 60.129 42.308 0.00 0.00 0.00 2.59
2007 3878 9.760660 GCTTATGTAATTGGATATTCGATTGAC 57.239 33.333 6.73 2.84 0.00 3.18
2037 3908 4.635699 GGGTATTATCCCTACCACTTGG 57.364 50.000 0.00 0.00 43.85 3.61
2469 8995 4.438148 TCTACATATTGCGTGCTTTGCTA 58.562 39.130 0.00 0.00 0.00 3.49
2524 9050 9.331282 GCTCAAATCCATAGTACACTAGAAAAT 57.669 33.333 0.00 0.00 0.00 1.82
2593 9119 3.054875 TCAGATGCTGAGTTTGTGCCTAT 60.055 43.478 0.00 0.00 35.39 2.57
2703 9232 9.897744 GATGAGTGATGATTCTTGTTTTTGTTA 57.102 29.630 0.00 0.00 0.00 2.41
2892 9457 2.990284 TGGTATGTTCCTTTGGGGAGAA 59.010 45.455 0.00 0.00 46.01 2.87
3014 9615 9.097257 CAAATTCAATAAGTGGTTCACAACTTT 57.903 29.630 5.03 0.00 36.74 2.66
3033 9642 7.119846 ACAACTTTCTTTTATTCTCGGGATCAG 59.880 37.037 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 90 2.957402 TGAGGATTCAGCAAAGGTGT 57.043 45.000 0.00 0.00 32.43 4.16
164 166 1.670406 GTGACAGCAGCTCACAGGG 60.670 63.158 9.40 0.00 38.36 4.45
218 220 1.945394 CACTAGCACATGGAAGATGGC 59.055 52.381 0.00 0.00 0.00 4.40
357 363 4.130857 TGAACAGATGAAGCAAACCGTAA 58.869 39.130 0.00 0.00 0.00 3.18
465 472 9.086336 CCAAAATGATCATTTGTAAAATAGCGT 57.914 29.630 29.52 10.37 40.57 5.07
523 532 6.793505 AAACCCTAGTCTATAACCTCACAG 57.206 41.667 0.00 0.00 0.00 3.66
543 552 5.411361 AGCACAAAGGGAAAAACAAGAAAAC 59.589 36.000 0.00 0.00 0.00 2.43
1101 1122 7.976135 ATGAGTAGGAGATGAATACAATTGC 57.024 36.000 5.05 0.00 0.00 3.56
1114 1135 6.069331 GGTGTTGAGGTATATGAGTAGGAGA 58.931 44.000 0.00 0.00 0.00 3.71
1292 1334 7.619698 TCTTCTTCATTTCCTCTAGTATCACCA 59.380 37.037 0.00 0.00 0.00 4.17
1373 1415 0.319125 GGAGATAGTACTGCCAGCGC 60.319 60.000 5.39 0.00 0.00 5.92
1417 1459 5.398353 CCTCACATGTATCAAGGGGAATCTT 60.398 44.000 0.00 0.00 0.00 2.40
1476 1518 4.041075 GGTCTTTCTTCCTCTGGACTCTTT 59.959 45.833 0.00 0.00 0.00 2.52
1643 1694 1.949525 GTATGACGATGGGCAAATGCT 59.050 47.619 5.25 0.00 41.70 3.79
1737 1788 5.687770 TGATTGATGGTATAACGCAATGG 57.312 39.130 11.93 0.00 30.06 3.16
1767 1818 8.991026 TCATGTCCAAGCAAATAATTTTTCAAG 58.009 29.630 0.00 0.00 0.00 3.02
2004 3875 3.640029 GGATAATACCCTCCAAGTCGTCA 59.360 47.826 0.00 0.00 0.00 4.35
2007 3878 3.679824 GGGATAATACCCTCCAAGTCG 57.320 52.381 0.00 0.00 45.90 4.18
2037 3908 7.489574 AGAACTCTCAACAAAAGAGACAATC 57.510 36.000 7.12 1.16 42.39 2.67
3014 9615 3.711704 AGCCTGATCCCGAGAATAAAAGA 59.288 43.478 0.00 0.00 0.00 2.52
3033 9642 4.321304 GCCAAAAGTTTCCTAAAGAGAGCC 60.321 45.833 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.