Multiple sequence alignment - TraesCS3D01G489100

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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 TraesCS3D01G489100 chr3D 100.000 2702 0 0 1 2702 583283142 583280441 0.000000e+00 4990.0
1 TraesCS3D01G489100 chr3D 96.839 2531 68 7 1 2524 583186264 583183739 0.000000e+00 4220.0
2 TraesCS3D01G489100 chr3D 92.063 2167 122 21 386 2515 583223355 583221202 0.000000e+00 3003.0
3 TraesCS3D01G489100 chr3D 97.749 622 13 1 1 621 583180272 583179651 0.000000e+00 1070.0
4 TraesCS3D01G489100 chr3D 95.522 268 10 2 140 405 583188904 583188637 6.910000e-116 427.0
5 TraesCS3D01G489100 chr3D 88.028 284 29 3 2200 2483 583188629 583188351 5.580000e-87 331.0
6 TraesCS3D01G489100 chr3D 94.972 179 9 0 2524 2702 583183680 583183502 5.700000e-72 281.0
7 TraesCS3D01G489100 chr3D 79.762 168 30 2 2537 2700 1891322 1891489 4.730000e-23 119.0
8 TraesCS3D01G489100 chr3D 77.301 163 35 2 2540 2701 6950454 6950615 7.960000e-16 95.3
9 TraesCS3D01G489100 chr3B 94.023 1924 73 13 1 1919 780300721 780298835 0.000000e+00 2878.0
10 TraesCS3D01G489100 chr3B 88.740 2167 149 38 369 2483 780339427 780337304 0.000000e+00 2562.0
11 TraesCS3D01G489100 chr3B 89.426 1967 122 41 563 2483 780314286 780312360 0.000000e+00 2401.0
12 TraesCS3D01G489100 chr3B 89.431 1968 121 34 563 2483 780324265 780322338 0.000000e+00 2401.0
13 TraesCS3D01G489100 chr3B 86.414 817 51 20 1690 2483 780317743 780316964 0.000000e+00 839.0
14 TraesCS3D01G489100 chr3B 86.414 817 51 20 1690 2483 780327722 780326943 0.000000e+00 839.0
15 TraesCS3D01G489100 chr3B 91.252 503 31 8 2018 2512 780298825 780298328 0.000000e+00 673.0
16 TraesCS3D01G489100 chr3B 95.411 414 17 2 2112 2524 780332516 780332104 0.000000e+00 658.0
17 TraesCS3D01G489100 chr3B 94.203 414 22 2 2112 2524 780308093 780307681 4.910000e-177 630.0
18 TraesCS3D01G489100 chr3B 89.256 242 22 4 563 801 780327999 780327759 1.570000e-77 300.0
19 TraesCS3D01G489100 chr3B 91.620 179 15 0 2524 2702 780332045 780331867 5.780000e-62 248.0
20 TraesCS3D01G489100 chr3B 83.260 227 25 9 302 521 780314516 780314296 2.120000e-46 196.0
21 TraesCS3D01G489100 chr3B 83.260 227 25 9 302 521 780328229 780328009 2.120000e-46 196.0
22 TraesCS3D01G489100 chrUn 90.465 1699 99 27 810 2483 352585812 352587472 0.000000e+00 2182.0
23 TraesCS3D01G489100 chr6A 88.889 1215 98 21 796 1992 34278094 34276899 0.000000e+00 1461.0
24 TraesCS3D01G489100 chr6A 88.797 1214 98 22 796 1992 34273292 34272100 0.000000e+00 1454.0
25 TraesCS3D01G489100 chr7B 82.278 158 23 2 2548 2700 438878408 438878565 6.070000e-27 132.0
26 TraesCS3D01G489100 chr7B 79.290 169 26 4 2538 2702 684099368 684099205 2.840000e-20 110.0
27 TraesCS3D01G489100 chr7B 95.238 42 2 0 385 426 244635311 244635352 1.740000e-07 67.6
28 TraesCS3D01G489100 chr3A 79.006 181 30 4 2526 2702 646297202 646297026 1.700000e-22 117.0
29 TraesCS3D01G489100 chr3A 93.333 60 0 4 2468 2524 461904032 461903974 4.790000e-13 86.1
30 TraesCS3D01G489100 chr7D 77.528 178 34 4 2526 2698 9204812 9204988 4.760000e-18 102.0
31 TraesCS3D01G489100 chr6D 98.000 50 0 1 2476 2524 7170688 7170737 4.790000e-13 86.1
32 TraesCS3D01G489100 chr5D 94.545 55 1 2 2472 2524 446510924 446510978 1.720000e-12 84.2
33 TraesCS3D01G489100 chr1D 89.062 64 5 2 2462 2524 62152123 62152185 8.020000e-11 78.7


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 TraesCS3D01G489100 chr3D 583280441 583283142 2701 True 4990.000000 4990 100.000000 1 2702 1 chr3D.!!$R2 2701
1 TraesCS3D01G489100 chr3D 583221202 583223355 2153 True 3003.000000 3003 92.063000 386 2515 1 chr3D.!!$R1 2129
2 TraesCS3D01G489100 chr3D 583179651 583188904 9253 True 1265.800000 4220 94.622000 1 2702 5 chr3D.!!$R3 2701
3 TraesCS3D01G489100 chr3B 780337304 780339427 2123 True 2562.000000 2562 88.740000 369 2483 1 chr3B.!!$R2 2114
4 TraesCS3D01G489100 chr3B 780298328 780300721 2393 True 1775.500000 2878 92.637500 1 2512 2 chr3B.!!$R3 2511
5 TraesCS3D01G489100 chr3B 780312360 780317743 5383 True 1145.333333 2401 86.366667 302 2483 3 chr3B.!!$R4 2181
6 TraesCS3D01G489100 chr3B 780322338 780332516 10178 True 773.666667 2401 89.232000 302 2702 6 chr3B.!!$R5 2400
7 TraesCS3D01G489100 chrUn 352585812 352587472 1660 False 2182.000000 2182 90.465000 810 2483 1 chrUn.!!$F1 1673
8 TraesCS3D01G489100 chr6A 34272100 34278094 5994 True 1457.500000 1461 88.843000 796 1992 2 chr6A.!!$R1 1196

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
910 13889 0.442699 GTATAAATAGGCGGCAGCGC 59.557 55.0 13.08 0.0 46.35 5.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2675 15761 0.598158 GTGCGTCAGACCGGTTTGTA 60.598 55.0 23.2 8.81 0.0 2.41 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
146 2787 4.749245 CAAGACGTAATCCAAACTTGCT 57.251 40.909 0.00 0.00 0.00 3.91
196 2838 9.281371 CCATATAATGATTCTCAACACACAGAT 57.719 33.333 0.00 0.00 0.00 2.90
288 2932 5.348986 TCACCTAAGTAAAGATGACGATGC 58.651 41.667 0.00 0.00 0.00 3.91
316 4728 8.173775 CGAGAATCAGTTAGTACGACTAAAAGA 58.826 37.037 8.43 9.39 37.48 2.52
730 5154 4.080072 TGGCTGGAACATGATAATGTGGTA 60.080 41.667 0.00 0.00 38.20 3.25
910 13889 0.442699 GTATAAATAGGCGGCAGCGC 59.557 55.000 13.08 0.00 46.35 5.92
1051 14031 1.133407 CTTCTAGGCCTCACGTCAGTC 59.867 57.143 9.68 0.00 0.00 3.51
1085 14065 0.461693 CAAGAGCTCCACTGCCTAGC 60.462 60.000 10.93 0.00 36.48 3.42
1161 14141 1.003116 CTTGCAAGCATCTACGATGGC 60.003 52.381 14.65 2.25 0.00 4.40
1188 14168 6.122277 TGAAGAGATTATTTGCCTACCAAGG 58.878 40.000 0.00 0.00 46.76 3.61
1322 14302 2.573009 TCATCATCCAAGAGCTCCAACA 59.427 45.455 10.93 0.00 0.00 3.33
1416 14396 4.559502 GCCAGGAAACATTTCAAGAAGTCC 60.560 45.833 6.68 0.00 38.92 3.85
1714 14694 6.372937 TCTTAGCTCATAGATACTCCACATCG 59.627 42.308 0.00 0.00 0.00 3.84
2002 15012 5.904362 AACAGCAAGATGATTTTAGACCC 57.096 39.130 0.00 0.00 0.00 4.46
2012 15022 3.763360 TGATTTTAGACCCACATGCAAGG 59.237 43.478 0.00 0.00 0.00 3.61
2013 15023 2.969821 TTTAGACCCACATGCAAGGT 57.030 45.000 1.72 1.72 36.31 3.50
2014 15024 2.969821 TTAGACCCACATGCAAGGTT 57.030 45.000 0.00 0.00 32.81 3.50
2138 15155 1.180456 TAGGACACGCCAGGTCGAAA 61.180 55.000 9.87 0.00 40.02 3.46
2395 15417 3.071874 TGGTATGCTGGTTTCTTCTGG 57.928 47.619 0.00 0.00 0.00 3.86
2401 15423 4.842531 TGCTGGTTTCTTCTGGATGATA 57.157 40.909 0.00 0.00 0.00 2.15
2402 15424 5.178096 TGCTGGTTTCTTCTGGATGATAA 57.822 39.130 0.00 0.00 0.00 1.75
2409 15432 8.632679 TGGTTTCTTCTGGATGATAATATTTGC 58.367 33.333 0.00 0.00 0.00 3.68
2526 15612 1.530771 GCCTCTGCATCTGGGATGT 59.469 57.895 8.93 0.00 37.47 3.06
2532 15618 2.093288 TCTGCATCTGGGATGTCTGAAC 60.093 50.000 8.93 0.00 0.00 3.18
2555 15641 1.176527 CCATCCTGGCGACATTTGTT 58.823 50.000 0.00 0.00 41.51 2.83
2618 15704 1.683917 CCGAATACCCAGACCTCTCAG 59.316 57.143 0.00 0.00 0.00 3.35
2655 15741 3.876300 CCGAAGGCCTGAACGAAG 58.124 61.111 22.74 8.36 46.14 3.79
2669 15755 2.961526 ACGAAGCCACATACTAGGTG 57.038 50.000 0.00 0.00 36.03 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
146 2787 2.685897 AGGAACAAAACTTTGCGCACTA 59.314 40.909 11.12 0.00 41.79 2.74
282 2926 0.537188 AACTGATTCTCGGGCATCGT 59.463 50.000 0.00 0.00 40.32 3.73
288 2932 3.626670 AGTCGTACTAACTGATTCTCGGG 59.373 47.826 0.00 0.00 0.00 5.14
665 5088 4.766404 AAAAAGATGCGGTTTAGTCTGG 57.234 40.909 0.00 0.00 0.00 3.86
730 5154 4.164796 TGCCTAATGTCCATGAGATGAGTT 59.835 41.667 0.00 0.00 0.00 3.01
910 13889 6.961359 TCTTGTTTGATGTATCTACCGTTG 57.039 37.500 0.00 0.00 0.00 4.10
1051 14031 0.241213 TCTTGCTCGACTTCGGTCTG 59.759 55.000 0.00 0.00 42.42 3.51
1161 14141 6.122277 TGGTAGGCAAATAATCTCTTCAAGG 58.878 40.000 0.00 0.00 0.00 3.61
1188 14168 0.962855 GGGAGGAGCAAGCTTGGTTC 60.963 60.000 30.17 28.23 39.30 3.62
1322 14302 5.428131 ACATCATCTCCTTTTCTTAGAGCCT 59.572 40.000 0.00 0.00 0.00 4.58
1416 14396 0.734942 CAAATGCAGGCTTCTTGGCG 60.735 55.000 0.00 0.00 46.88 5.69
1714 14694 1.474143 GCCAATCACAGGGAGTAGAGC 60.474 57.143 0.00 0.00 0.00 4.09
2057 15067 4.698583 AATCAAGAATCTTGTGCAGCTC 57.301 40.909 20.91 0.00 0.00 4.09
2376 15398 3.350219 TCCAGAAGAAACCAGCATACC 57.650 47.619 0.00 0.00 0.00 2.73
2401 15423 8.945195 TCATCTCCCATGAAATAGCAAATATT 57.055 30.769 0.00 0.00 35.51 1.28
2402 15424 9.543231 AATCATCTCCCATGAAATAGCAAATAT 57.457 29.630 0.00 0.00 0.00 1.28
2409 15432 9.696572 ATCCAATAATCATCTCCCATGAAATAG 57.303 33.333 0.00 0.00 0.00 1.73
2526 15612 2.989639 CAGGATGGCGGGTTCAGA 59.010 61.111 0.00 0.00 0.00 3.27
2551 15637 5.076182 TCAATTGGATAGGAGTTGCAACAA 58.924 37.500 30.11 14.01 0.00 2.83
2555 15641 5.114764 TCATCAATTGGATAGGAGTTGCA 57.885 39.130 5.42 0.00 33.95 4.08
2618 15704 4.155280 TCGGTTTTAGATGTTAGGCTTTGC 59.845 41.667 0.00 0.00 0.00 3.68
2669 15755 0.604511 CAGACCGGTTTGTACCCCAC 60.605 60.000 16.79 0.00 41.75 4.61
2675 15761 0.598158 GTGCGTCAGACCGGTTTGTA 60.598 55.000 23.20 8.81 0.00 2.41
2676 15762 1.885850 GTGCGTCAGACCGGTTTGT 60.886 57.895 23.20 1.98 0.00 2.83


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

AutoCloner maintained by Alex Coulton.