Multiple sequence alignment - TraesCS3A01G538800

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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 TraesCS3A01G538800 chr3A 100.000 3129 0 0 1 3129 749878413 749875285 0.000000e+00 5779.0
1 TraesCS3A01G538800 chr3A 86.899 977 105 16 1596 2554 748340179 748341150 0.000000e+00 1074.0
2 TraesCS3A01G538800 chr3A 83.896 652 71 19 853 1485 748339346 748339982 2.940000e-165 592.0
3 TraesCS3A01G538800 chr3A 100.000 110 0 0 3311 3420 749875103 749874994 1.610000e-48 204.0
4 TraesCS3A01G538800 chrUn 93.183 1555 83 12 1596 3129 37114614 37113062 0.000000e+00 2263.0
5 TraesCS3A01G538800 chrUn 93.183 1555 83 12 1596 3129 247032662 247034214 0.000000e+00 2263.0
6 TraesCS3A01G538800 chrUn 93.183 1555 83 12 1596 3129 300943343 300941791 0.000000e+00 2263.0
7 TraesCS3A01G538800 chrUn 89.761 1631 105 22 1 1601 247030417 247032015 0.000000e+00 2030.0
8 TraesCS3A01G538800 chrUn 94.253 609 30 2 997 1601 37115868 37115261 0.000000e+00 926.0
9 TraesCS3A01G538800 chrUn 94.253 609 30 2 997 1601 300944597 300943990 0.000000e+00 926.0
10 TraesCS3A01G538800 chrUn 100.000 299 0 0 1 299 478732951 478733249 1.390000e-153 553.0
11 TraesCS3A01G538800 chr3B 97.910 1244 17 3 877 2115 825849247 825850486 0.000000e+00 2145.0
12 TraesCS3A01G538800 chr3B 98.653 965 11 1 2149 3111 825850484 825851448 0.000000e+00 1709.0
13 TraesCS3A01G538800 chr3B 97.545 896 4 3 1 879 825847460 825848354 0.000000e+00 1517.0
14 TraesCS3A01G538800 chr3B 87.295 976 103 15 1596 2555 28607217 28606247 0.000000e+00 1096.0
15 TraesCS3A01G538800 chr3B 82.817 646 83 18 853 1485 28608044 28607414 1.390000e-153 553.0
16 TraesCS3A01G538800 chr3B 80.584 582 100 11 101 672 788579880 788579302 1.460000e-118 436.0
17 TraesCS3A01G538800 chr3B 77.960 549 91 19 87 626 28623902 28623375 1.980000e-82 316.0
18 TraesCS3A01G538800 chr3B 100.000 104 0 0 3314 3417 825851694 825851797 3.480000e-45 193.0
19 TraesCS3A01G538800 chr3B 97.297 37 1 0 3384 3420 788569296 788569260 2.850000e-06 63.9
20 TraesCS3A01G538800 chr3D 88.786 972 89 13 1600 2554 615456767 615457735 0.000000e+00 1173.0
21 TraesCS3A01G538800 chr3D 88.667 900 66 14 70 943 615454262 615455151 0.000000e+00 1064.0
22 TraesCS3A01G538800 chr3D 89.016 610 60 3 997 1601 615455490 615456097 0.000000e+00 749.0
23 TraesCS3A01G538800 chr5A 76.082 485 92 17 2649 3129 589040522 589040986 7.380000e-57 231.0
24 TraesCS3A01G538800 chr5B 82.110 218 38 1 1600 1816 672627592 672627375 5.830000e-43 185.0
25 TraesCS3A01G538800 chr5B 75.510 294 58 11 1015 1304 672631321 672631038 7.700000e-27 132.0
26 TraesCS3A01G538800 chr5D 81.553 206 38 0 1611 1816 532616027 532615822 1.630000e-38 171.0
27 TraesCS3A01G538800 chr5D 87.097 62 7 1 2974 3034 560238667 560238606 6.120000e-08 69.4
28 TraesCS3A01G538800 chr4A 81.643 207 37 1 1611 1816 639199053 639199259 1.630000e-38 171.0
29 TraesCS3A01G538800 chr4A 80.000 200 34 3 1012 1211 639196012 639196205 3.560000e-30 143.0


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 TraesCS3A01G538800 chr3A 749874994 749878413 3419 True 2991.500000 5779 100.0000 1 3420 2 chr3A.!!$R1 3419
1 TraesCS3A01G538800 chr3A 748339346 748341150 1804 False 833.000000 1074 85.3975 853 2554 2 chr3A.!!$F1 1701
2 TraesCS3A01G538800 chrUn 247030417 247034214 3797 False 2146.500000 2263 91.4720 1 3129 2 chrUn.!!$F2 3128
3 TraesCS3A01G538800 chrUn 37113062 37115868 2806 True 1594.500000 2263 93.7180 997 3129 2 chrUn.!!$R1 2132
4 TraesCS3A01G538800 chrUn 300941791 300944597 2806 True 1594.500000 2263 93.7180 997 3129 2 chrUn.!!$R2 2132
5 TraesCS3A01G538800 chr3B 825847460 825851797 4337 False 1391.000000 2145 98.5270 1 3417 4 chr3B.!!$F1 3416
6 TraesCS3A01G538800 chr3B 28606247 28608044 1797 True 824.500000 1096 85.0560 853 2555 2 chr3B.!!$R4 1702
7 TraesCS3A01G538800 chr3B 788579302 788579880 578 True 436.000000 436 80.5840 101 672 1 chr3B.!!$R3 571
8 TraesCS3A01G538800 chr3B 28623375 28623902 527 True 316.000000 316 77.9600 87 626 1 chr3B.!!$R1 539
9 TraesCS3A01G538800 chr3D 615454262 615457735 3473 False 995.333333 1173 88.8230 70 2554 3 chr3D.!!$F1 2484

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
732 752 1.070758 CATGATTCCGACCCTCCGAAT 59.929 52.381 0.0 0.0 0.0 3.34 F
1807 3754 1.339727 CCCCAACTACTACAAGTGCCC 60.340 57.143 0.0 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2000 3956 0.889994 TGGCTAAAGCAATGGCACAG 59.110 50.000 4.07 0.0 43.38 3.66 R
2612 4579 2.338620 CCTCGGTCGTTCTGCACA 59.661 61.111 0.00 0.0 0.00 4.57 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
732 752 1.070758 CATGATTCCGACCCTCCGAAT 59.929 52.381 0.00 0.0 0.00 3.34
875 912 3.202829 ACATGAAAACAGTACCACGGT 57.797 42.857 0.00 0.0 0.00 4.83
904 1835 6.612306 GGCTGGTAAGTTCTGTCTTTAAATG 58.388 40.000 0.00 0.0 0.00 2.32
1807 3754 1.339727 CCCCAACTACTACAAGTGCCC 60.340 57.143 0.00 0.0 0.00 5.36
2080 4036 4.778143 ACATCACCGCTTCCGCCC 62.778 66.667 0.00 0.0 0.00 6.13
2143 4099 2.172505 TGAAAAGACTGGCTTCACTGGA 59.827 45.455 0.00 0.0 35.24 3.86
2160 4116 4.100035 CACTGGAGCCATCAACTACTATCA 59.900 45.833 0.00 0.0 0.00 2.15
2612 4579 1.144057 GCACGATCGAGGGGTCATT 59.856 57.895 24.34 0.0 0.00 2.57
2653 4626 0.804989 GTGCCAGTGTCATGCCTTAC 59.195 55.000 0.00 0.0 0.00 2.34
2726 4700 5.509498 TCACAAAGAATTGGATCCTTAGGG 58.491 41.667 14.23 0.0 41.01 3.53
3099 5081 0.035458 GTGTCTCCACCCTTCCACTG 59.965 60.000 0.00 0.0 35.44 3.66
3117 5099 1.937899 CTGTTCGACTGTTCGGGTTTT 59.062 47.619 0.00 0.0 45.90 2.43
3417 5442 0.105246 TGCAAGGGGTTGTTTGGGAT 60.105 50.000 0.00 0.0 0.00 3.85
3418 5443 0.321346 GCAAGGGGTTGTTTGGGATG 59.679 55.000 0.00 0.0 0.00 3.51
3419 5444 0.975887 CAAGGGGTTGTTTGGGATGG 59.024 55.000 0.00 0.0 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
732 752 0.904865 CCACACTAGTCCTGCTCCCA 60.905 60.000 0.00 0.00 0.00 4.37
904 1835 2.360475 GAGCCTGTGGGAGTTGCC 60.360 66.667 0.00 0.00 33.58 4.52
1189 2443 1.602237 CACCATAGCCACGGAGGTT 59.398 57.895 0.00 0.00 40.61 3.50
1226 2480 2.544726 GCTGTGTAAGAGGCCACAC 58.455 57.895 15.39 15.39 44.26 3.82
1975 3931 2.437180 CTCATCAGGCGCTTGGCA 60.437 61.111 20.24 0.84 46.16 4.92
2000 3956 0.889994 TGGCTAAAGCAATGGCACAG 59.110 50.000 4.07 0.00 43.38 3.66
2080 4036 3.385384 TCTGCCTCGGTGAGCCAG 61.385 66.667 0.00 0.00 36.61 4.85
2143 4099 5.683876 AGTTGTGATAGTAGTTGATGGCT 57.316 39.130 0.00 0.00 0.00 4.75
2160 4116 3.006940 TCGCAGTTCTTGTCAAAGTTGT 58.993 40.909 0.00 0.00 34.78 3.32
2612 4579 2.338620 CCTCGGTCGTTCTGCACA 59.661 61.111 0.00 0.00 0.00 4.57
2653 4626 7.389053 AGCTTAGTGTGGAAGAAAAATCTGTAG 59.611 37.037 0.00 0.00 0.00 2.74
2741 4715 3.363970 GGAGTTTGTGTACACATGAAGCG 60.364 47.826 28.35 0.00 41.52 4.68
3310 5292 5.067674 GTCATTCTTATGCCACTTTGCCATA 59.932 40.000 0.00 0.00 0.00 2.74
3311 5293 4.025360 TCATTCTTATGCCACTTTGCCAT 58.975 39.130 0.00 0.00 0.00 4.40
3312 5294 3.193267 GTCATTCTTATGCCACTTTGCCA 59.807 43.478 0.00 0.00 0.00 4.92


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

AutoCloner maintained by Alex Coulton.