Multiple sequence alignment - TraesCS4B01G111600

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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 TraesCS4B01G111600 chr4B 100.000 2757 0 0 1 2757 125065625 125062869 0.000000e+00 5092.0
1 TraesCS4B01G111600 chr4B 95.432 2583 81 10 1 2554 491010176 491007602 0.000000e+00 4082.0
2 TraesCS4B01G111600 chr4B 94.872 312 15 1 1 312 222354516 222354206 1.150000e-133 486.0
3 TraesCS4B01G111600 chr4B 92.788 208 14 1 2550 2757 491007509 491007303 1.600000e-77 300.0
4 TraesCS4B01G111600 chr4B 96.689 151 5 0 2607 2757 404623509 404623359 4.560000e-63 252.0
5 TraesCS4B01G111600 chr1B 97.256 2770 62 3 1 2757 377096095 377098863 0.000000e+00 4682.0
6 TraesCS4B01G111600 chr1B 90.018 551 25 2 2030 2554 359604519 359605065 0.000000e+00 686.0
7 TraesCS4B01G111600 chr1B 93.750 208 12 1 2550 2757 359605158 359605364 7.410000e-81 311.0
8 TraesCS4B01G111600 chr6B 96.752 2771 76 3 1 2757 596914142 596916912 0.000000e+00 4606.0
9 TraesCS4B01G111600 chr6B 94.581 2030 62 10 1 2008 252385143 252383140 0.000000e+00 3096.0
10 TraesCS4B01G111600 chr6B 95.214 397 15 1 2155 2551 252383150 252382758 2.330000e-175 625.0
11 TraesCS4B01G111600 chr6B 95.513 312 13 1 1 312 193814532 193814222 5.300000e-137 497.0
12 TraesCS4B01G111600 chr6B 92.718 206 14 1 2550 2755 252382635 252382431 2.080000e-76 296.0
13 TraesCS4B01G111600 chr6B 96.104 154 6 0 2604 2757 476035803 476035956 4.560000e-63 252.0
14 TraesCS4B01G111600 chr2B 94.289 2574 92 13 1 2554 371934197 371936735 0.000000e+00 3888.0
15 TraesCS4B01G111600 chr2B 92.788 208 14 1 2550 2757 371936828 371937034 1.600000e-77 300.0
16 TraesCS4B01G111600 chr3B 94.518 2189 67 16 390 2554 829048935 829051094 0.000000e+00 3328.0
17 TraesCS4B01G111600 chr3B 94.924 394 17 2 1 392 829047234 829047626 5.050000e-172 614.0
18 TraesCS4B01G111600 chr6D 95.349 817 34 4 1229 2043 362255867 362255053 0.000000e+00 1295.0
19 TraesCS4B01G111600 chr6D 90.861 941 38 14 312 1228 362256813 362255897 0.000000e+00 1218.0
20 TraesCS4B01G111600 chr6D 94.118 187 9 1 2080 2266 362255053 362254869 1.620000e-72 283.0
21 TraesCS4B01G111600 chr6D 82.254 355 27 12 312 658 7272908 7273234 9.730000e-70 274.0
22 TraesCS4B01G111600 chr6D 94.624 93 5 0 2462 2554 362254880 362254788 7.960000e-31 145.0
23 TraesCS4B01G111600 chr6D 96.491 57 1 1 2550 2606 362254695 362254640 2.920000e-15 93.5
24 TraesCS4B01G111600 chr5D 92.193 538 33 9 697 1228 531266711 531266177 0.000000e+00 752.0
25 TraesCS4B01G111600 chr5D 95.238 168 7 1 1228 1394 531266145 531265978 5.850000e-67 265.0
26 TraesCS4B01G111600 chr5D 91.935 186 12 2 474 658 8263445 8263628 9.800000e-65 257.0
27 TraesCS4B01G111600 chr4A 95.513 312 13 1 1 312 116141562 116141252 5.300000e-137 497.0
28 TraesCS4B01G111600 chr7B 93.857 293 14 1 2030 2322 353971328 353971616 3.260000e-119 438.0
29 TraesCS4B01G111600 chr7B 93.852 244 15 0 2311 2554 353971632 353971875 4.340000e-98 368.0
30 TraesCS4B01G111600 chr7B 93.269 208 13 1 2550 2757 353971968 353972174 3.450000e-79 305.0
31 TraesCS4B01G111600 chr1D 75.529 331 74 6 1420 1746 400386853 400386526 3.680000e-34 156.0
32 TraesCS4B01G111600 chr1A 78.571 210 37 6 1529 1734 551598662 551598867 6.200000e-27 132.0


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 TraesCS4B01G111600 chr4B 125062869 125065625 2756 True 5092.000000 5092 100.000000 1 2757 1 chr4B.!!$R1 2756
1 TraesCS4B01G111600 chr4B 491007303 491010176 2873 True 2191.000000 4082 94.110000 1 2757 2 chr4B.!!$R4 2756
2 TraesCS4B01G111600 chr1B 377096095 377098863 2768 False 4682.000000 4682 97.256000 1 2757 1 chr1B.!!$F1 2756
3 TraesCS4B01G111600 chr1B 359604519 359605364 845 False 498.500000 686 91.884000 2030 2757 2 chr1B.!!$F2 727
4 TraesCS4B01G111600 chr6B 596914142 596916912 2770 False 4606.000000 4606 96.752000 1 2757 1 chr6B.!!$F2 2756
5 TraesCS4B01G111600 chr6B 252382431 252385143 2712 True 1339.000000 3096 94.171000 1 2755 3 chr6B.!!$R2 2754
6 TraesCS4B01G111600 chr2B 371934197 371937034 2837 False 2094.000000 3888 93.538500 1 2757 2 chr2B.!!$F1 2756
7 TraesCS4B01G111600 chr3B 829047234 829051094 3860 False 1971.000000 3328 94.721000 1 2554 2 chr3B.!!$F1 2553
8 TraesCS4B01G111600 chr6D 362254640 362256813 2173 True 606.900000 1295 94.288600 312 2606 5 chr6D.!!$R1 2294
9 TraesCS4B01G111600 chr5D 531265978 531266711 733 True 508.500000 752 93.715500 697 1394 2 chr5D.!!$R1 697
10 TraesCS4B01G111600 chr7B 353971328 353972174 846 False 370.333333 438 93.659333 2030 2757 3 chr7B.!!$F1 727

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
375 377 0.108585 TGCGAAACTGAAGCTTCCCT 59.891 50.000 23.42 5.58 0.0 4.20 F
399 1714 2.300152 ACTTCGGAGCAGTCAATTGAGA 59.700 45.455 8.80 0.00 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1686 3105 0.326238 TTCCCTCCTTATCGGCCTGT 60.326 55.000 0.00 0.0 0.00 4.00 R
2263 3694 1.478510 GATTCAGGCTCGGAGAAGACA 59.521 52.381 9.69 0.0 34.09 3.41 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
59 60 5.282055 TGAGCTTACAACCTCTGGATATG 57.718 43.478 0.00 0.00 0.00 1.78
60 61 4.962362 TGAGCTTACAACCTCTGGATATGA 59.038 41.667 0.00 0.00 0.00 2.15
299 301 1.074405 TGGATCAAGCAGCCAAGACTT 59.926 47.619 0.00 0.00 0.00 3.01
375 377 0.108585 TGCGAAACTGAAGCTTCCCT 59.891 50.000 23.42 5.58 0.00 4.20
399 1714 2.300152 ACTTCGGAGCAGTCAATTGAGA 59.700 45.455 8.80 0.00 0.00 3.27
575 1901 8.574251 AATTGTAGCAATATTAGTGTTGGTCA 57.426 30.769 2.79 0.40 38.06 4.02
687 2026 5.690409 GGATTCGTCGTGCTATTTCTGATTA 59.310 40.000 0.00 0.00 0.00 1.75
688 2027 6.200286 GGATTCGTCGTGCTATTTCTGATTAA 59.800 38.462 0.00 0.00 0.00 1.40
689 2028 6.954616 TTCGTCGTGCTATTTCTGATTAAA 57.045 33.333 0.00 0.00 0.00 1.52
690 2029 6.954616 TCGTCGTGCTATTTCTGATTAAAA 57.045 33.333 0.00 0.00 0.00 1.52
691 2030 7.354025 TCGTCGTGCTATTTCTGATTAAAAA 57.646 32.000 0.00 0.00 0.00 1.94
692 2031 7.970384 TCGTCGTGCTATTTCTGATTAAAAAT 58.030 30.769 0.00 0.00 0.00 1.82
694 2033 9.358123 CGTCGTGCTATTTCTGATTAAAAATAG 57.642 33.333 10.89 10.89 43.54 1.73
1130 2487 2.337583 CGAAGCTCGGAACAATCTTCA 58.662 47.619 0.00 0.00 36.00 3.02
1139 2496 6.183360 GCTCGGAACAATCTTCAATACATTGA 60.183 38.462 0.45 0.45 44.42 2.57
1408 2827 5.355071 GCAGTCTGAACCATTCATTGTATCA 59.645 40.000 3.32 0.00 39.30 2.15
1600 3019 2.629617 AGCTTGTGTGGCAAAATAAGCT 59.370 40.909 21.89 21.89 44.12 3.74
1686 3105 6.784473 AGGATCCTCACTTCACATATCATGTA 59.216 38.462 9.02 0.00 42.70 2.29
1720 3140 1.134788 AGGGAAGGATAAACGCACTCG 60.135 52.381 0.00 0.00 42.43 4.18
1997 3419 9.056005 GTGAGCATTATGTAGATGGAATTGTAA 57.944 33.333 0.00 0.00 0.00 2.41
2135 3560 9.909644 GTAGTTTTGAGTTGTAGTCAGATTCTA 57.090 33.333 0.00 0.00 0.00 2.10
2263 3694 1.250840 GGGCAAAAATGGCTCCGTCT 61.251 55.000 2.35 0.00 34.52 4.18
2410 3868 0.109412 GGAAGGTGTCGAGGTGTACG 60.109 60.000 0.00 0.00 0.00 3.67
2632 4214 8.629158 TGTTATATTCTGCTTTTGTCAGTTTGT 58.371 29.630 0.00 0.00 33.48 2.83
2655 4237 8.568676 TGTTGGTTCATATTAATTTCCTCGAA 57.431 30.769 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 7.642186 AGCTCATGATACTCCTACTATCTCAT 58.358 38.462 0.00 0.00 0.00 2.90
299 301 2.646175 GCTGCCCGACCACACTCTA 61.646 63.158 0.00 0.00 0.00 2.43
375 377 2.807967 CAATTGACTGCTCCGAAGTTCA 59.192 45.455 0.00 0.00 0.00 3.18
399 1714 1.822990 ACATACCGTCGTGTCCATCTT 59.177 47.619 0.00 0.00 0.00 2.40
575 1901 5.067805 GGACTGAACTTCACAATTTTCCACT 59.932 40.000 0.00 0.00 0.00 4.00
1130 2487 7.792374 AATCGTATGCTTCACTCAATGTATT 57.208 32.000 0.00 0.00 0.00 1.89
1139 2496 8.177663 CAGATTGTAAAAATCGTATGCTTCACT 58.822 33.333 0.00 0.00 0.00 3.41
1408 2827 0.379316 TATCGTCTGCGCATACGTGT 59.621 50.000 36.48 29.27 42.83 4.49
1458 2877 3.349927 TCTTCATCAAATCCCTGCTGTG 58.650 45.455 0.00 0.00 0.00 3.66
1686 3105 0.326238 TTCCCTCCTTATCGGCCTGT 60.326 55.000 0.00 0.00 0.00 4.00
1720 3140 1.532794 TGTCCCCATTTGCCCACAC 60.533 57.895 0.00 0.00 0.00 3.82
1997 3419 6.569226 GCTCAAAACAGTGCTACTTGATTCAT 60.569 38.462 0.00 0.00 0.00 2.57
2263 3694 1.478510 GATTCAGGCTCGGAGAAGACA 59.521 52.381 9.69 0.00 34.09 3.41
2410 3868 3.533606 TGCAGCTACCAATCTTCTCTC 57.466 47.619 0.00 0.00 0.00 3.20
2529 3987 4.116961 CAAAAGTTACGGTGTCAGTCAGA 58.883 43.478 0.00 0.00 0.00 3.27
2632 4214 8.801882 AGTTCGAGGAAATTAATATGAACCAA 57.198 30.769 8.36 0.00 36.12 3.67


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

AutoCloner maintained by Alex Coulton.