Multiple sequence alignment - TraesCS4A01G401900

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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 TraesCS4A01G401900 chr4A 100.000 2355 0 0 313 2667 675806955 675809309 0.000000e+00 4349
1 TraesCS4A01G401900 chr4A 91.677 2403 147 20 313 2666 573895426 573897824 0.000000e+00 3280
2 TraesCS4A01G401900 chr4A 100.000 220 0 0 3061 3280 675809703 675809922 1.100000e-109 407
3 TraesCS4A01G401900 chr4A 97.285 221 5 1 3061 3280 573898109 573898329 1.110000e-99 374
4 TraesCS4A01G401900 chr4A 100.000 70 0 0 1 70 675806643 675806712 2.660000e-26 130
5 TraesCS4A01G401900 chr2B 95.297 2360 96 10 313 2665 639234250 639236601 0.000000e+00 3729
6 TraesCS4A01G401900 chr2B 99.091 220 2 0 3061 3280 639236884 639237103 2.370000e-106 396
7 TraesCS4A01G401900 chr2B 97.143 70 2 0 1 70 451926810 451926879 5.750000e-23 119
8 TraesCS4A01G401900 chr2B 97.143 70 2 0 1 70 639234121 639234190 5.750000e-23 119
9 TraesCS4A01G401900 chr3B 95.297 2275 90 4 313 2586 454881725 454879467 0.000000e+00 3592
10 TraesCS4A01G401900 chr3B 89.930 1847 113 29 872 2666 166664851 166663026 0.000000e+00 2313
11 TraesCS4A01G401900 chr3B 81.552 2087 318 45 314 2374 636125739 636127784 0.000000e+00 1659
12 TraesCS4A01G401900 chr3B 98.182 220 4 0 3061 3280 454879056 454878837 5.130000e-103 385
13 TraesCS4A01G401900 chr1B 93.594 2357 123 11 314 2667 649199133 649201464 0.000000e+00 3491
14 TraesCS4A01G401900 chr1B 93.995 2065 97 8 313 2374 543036452 543034412 0.000000e+00 3101
15 TraesCS4A01G401900 chr1B 93.850 2065 100 9 313 2374 543031103 543029063 0.000000e+00 3085
16 TraesCS4A01G401900 chr1B 94.135 1347 52 8 1329 2667 633865076 633866403 0.000000e+00 2025
17 TraesCS4A01G401900 chr1B 98.636 220 3 0 3061 3280 633866880 633867099 1.100000e-104 390
18 TraesCS4A01G401900 chr1B 97.143 70 2 0 1 70 595614428 595614359 5.750000e-23 119
19 TraesCS4A01G401900 chr5A 91.608 2419 130 28 313 2666 672023910 672021500 0.000000e+00 3275
20 TraesCS4A01G401900 chr5D 91.806 2392 127 30 313 2666 69960446 69962806 0.000000e+00 3267
21 TraesCS4A01G401900 chr5D 93.898 2065 87 13 313 2374 458755196 458753168 0.000000e+00 3079
22 TraesCS4A01G401900 chr7D 91.769 2357 156 14 313 2666 40834543 40832222 0.000000e+00 3243
23 TraesCS4A01G401900 chr7A 91.659 2314 144 20 313 2588 696139666 696141968 0.000000e+00 3158
24 TraesCS4A01G401900 chr3D 93.753 2065 93 12 313 2374 128999590 129001621 0.000000e+00 3066
25 TraesCS4A01G401900 chr6D 94.314 299 16 1 2365 2662 460505045 460504747 1.070000e-124 457
26 TraesCS4A01G401900 chr6D 96.847 222 5 2 3061 3280 31849600 31849821 1.440000e-98 370
27 TraesCS4A01G401900 chr2A 93.667 300 15 3 2371 2666 748520153 748519854 2.320000e-121 446
28 TraesCS4A01G401900 chr1D 98.190 221 3 1 3061 3280 226837586 226837806 5.130000e-103 385
29 TraesCS4A01G401900 chr1D 97.297 222 4 2 3061 3280 87085544 87085323 3.090000e-100 375
30 TraesCS4A01G401900 chr1D 97.143 70 2 0 1 70 87088486 87088417 5.750000e-23 119
31 TraesCS4A01G401900 chr5B 97.297 222 4 2 3061 3280 681339221 681339442 3.090000e-100 375
32 TraesCS4A01G401900 chr4D 97.285 221 5 1 3061 3280 118423303 118423523 1.110000e-99 374
33 TraesCS4A01G401900 chr4D 97.143 70 2 0 1 70 49796696 49796627 5.750000e-23 119
34 TraesCS4A01G401900 chrUn 97.143 70 2 0 1 70 91418320 91418389 5.750000e-23 119
35 TraesCS4A01G401900 chr7B 97.143 70 2 0 1 70 664094217 664094286 5.750000e-23 119
36 TraesCS4A01G401900 chr6B 97.143 70 2 0 1 70 374326111 374326042 5.750000e-23 119
37 TraesCS4A01G401900 chr2D 97.143 70 2 0 1 70 394543161 394543230 5.750000e-23 119


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 TraesCS4A01G401900 chr4A 675806643 675809922 3279 False 1628.666667 4349 100.0000 1 3280 3 chr4A.!!$F2 3279
1 TraesCS4A01G401900 chr4A 573895426 573898329 2903 False 1827.000000 3280 94.4810 313 3280 2 chr4A.!!$F1 2967
2 TraesCS4A01G401900 chr2B 639234121 639237103 2982 False 1414.666667 3729 97.1770 1 3280 3 chr2B.!!$F2 3279
3 TraesCS4A01G401900 chr3B 166663026 166664851 1825 True 2313.000000 2313 89.9300 872 2666 1 chr3B.!!$R1 1794
4 TraesCS4A01G401900 chr3B 454878837 454881725 2888 True 1988.500000 3592 96.7395 313 3280 2 chr3B.!!$R2 2967
5 TraesCS4A01G401900 chr3B 636125739 636127784 2045 False 1659.000000 1659 81.5520 314 2374 1 chr3B.!!$F1 2060
6 TraesCS4A01G401900 chr1B 649199133 649201464 2331 False 3491.000000 3491 93.5940 314 2667 1 chr1B.!!$F1 2353
7 TraesCS4A01G401900 chr1B 543029063 543036452 7389 True 3093.000000 3101 93.9225 313 2374 2 chr1B.!!$R2 2061
8 TraesCS4A01G401900 chr1B 633865076 633867099 2023 False 1207.500000 2025 96.3855 1329 3280 2 chr1B.!!$F2 1951
9 TraesCS4A01G401900 chr5A 672021500 672023910 2410 True 3275.000000 3275 91.6080 313 2666 1 chr5A.!!$R1 2353
10 TraesCS4A01G401900 chr5D 69960446 69962806 2360 False 3267.000000 3267 91.8060 313 2666 1 chr5D.!!$F1 2353
11 TraesCS4A01G401900 chr5D 458753168 458755196 2028 True 3079.000000 3079 93.8980 313 2374 1 chr5D.!!$R1 2061
12 TraesCS4A01G401900 chr7D 40832222 40834543 2321 True 3243.000000 3243 91.7690 313 2666 1 chr7D.!!$R1 2353
13 TraesCS4A01G401900 chr7A 696139666 696141968 2302 False 3158.000000 3158 91.6590 313 2588 1 chr7A.!!$F1 2275
14 TraesCS4A01G401900 chr3D 128999590 129001621 2031 False 3066.000000 3066 93.7530 313 2374 1 chr3D.!!$F1 2061
15 TraesCS4A01G401900 chr1D 87085323 87088486 3163 True 247.000000 375 97.2200 1 3280 2 chr1D.!!$R1 3279

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
430 431 0.885196 GACTGCTCCGAGAACTCTGT 59.115 55.000 0.0 0.0 0.0 3.41 F
1127 1136 1.001887 AACACACACCACCAACCGT 60.002 52.632 0.0 0.0 0.0 4.83 F
1550 1560 0.252375 AGGCGGGTTTAGGGAGTACA 60.252 55.000 0.0 0.0 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1550 1560 1.905215 CACTCTGTTCATGAGGGGTCT 59.095 52.381 0.0 0.0 35.98 3.85 R
2032 2110 2.897326 TCCTCACCATGTTCTTCTTCGA 59.103 45.455 0.0 0.0 0.00 3.71 R
2601 2841 3.485463 TTTTGGTCACAGAAGATCGGT 57.515 42.857 0.0 0.0 0.00 4.69 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
430 431 0.885196 GACTGCTCCGAGAACTCTGT 59.115 55.000 0.00 0.0 0.00 3.41
581 588 9.624697 TTGCTTTACATTTTGACATCTTATCAC 57.375 29.630 0.00 0.0 0.00 3.06
634 642 1.587933 GGAGAGCGGAAGTCACGTCT 61.588 60.000 0.00 0.0 0.00 4.18
707 715 2.203788 TGGGCCGTCCAGAGAAGT 60.204 61.111 0.00 0.0 41.46 3.01
875 884 4.163458 TCACGCCTTTCCAGGTATAAGAAT 59.837 41.667 0.00 0.0 43.18 2.40
939 948 5.129634 TCACTTGAGCCTAACATTGTTTGA 58.870 37.500 7.45 0.0 0.00 2.69
973 982 2.626266 TGGCGGTCGTATAGTGATGATT 59.374 45.455 0.00 0.0 0.00 2.57
1123 1132 4.423231 TGCAACACACACCACCAA 57.577 50.000 0.00 0.0 0.00 3.67
1127 1136 1.001887 AACACACACCACCAACCGT 60.002 52.632 0.00 0.0 0.00 4.83
1550 1560 0.252375 AGGCGGGTTTAGGGAGTACA 60.252 55.000 0.00 0.0 0.00 2.90
1811 1856 7.816031 TCGAGAAGTTAACATATTCTTCCGTTT 59.184 33.333 8.61 0.0 37.56 3.60
2032 2110 2.262915 CGCAGAAGAAGAGGGCGT 59.737 61.111 0.00 0.0 42.51 5.68
2223 2373 2.250939 CGCAAGAAGACAACGGCCA 61.251 57.895 2.24 0.0 43.02 5.36
2423 2655 7.396418 TGTGGTGTGTGCATCATATATCATAT 58.604 34.615 0.00 0.0 38.12 1.78
3163 4720 4.096382 CCCCCAATTAGTTTGAGTCAATCG 59.904 45.833 6.36 0.0 37.53 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
430 431 5.010933 GGAAGTCGAGATACATCCATAGGA 58.989 45.833 0.00 0.0 37.24 2.94
545 549 7.860373 GTCAAAATGTAAAGCAACACACATCTA 59.140 33.333 0.00 0.0 31.40 1.98
549 555 5.714047 TGTCAAAATGTAAAGCAACACACA 58.286 33.333 0.00 0.0 30.75 3.72
581 588 3.820467 TCAAGCTACAAACCATGTTCAGG 59.180 43.478 0.00 0.0 43.63 3.86
615 622 1.153997 GACGTGACTTCCGCTCTCC 60.154 63.158 0.00 0.0 0.00 3.71
634 642 3.118075 CCCATACACATCCACACATACCA 60.118 47.826 0.00 0.0 0.00 3.25
792 801 0.248907 CGATTCGCCCGTGTAGACAT 60.249 55.000 0.00 0.0 0.00 3.06
875 884 7.759489 ATGGTAAGCTCAAGTGAAAATGTAA 57.241 32.000 0.00 0.0 0.00 2.41
939 948 3.385755 ACGACCGCCAAGTAACCTATAAT 59.614 43.478 0.00 0.0 0.00 1.28
973 982 0.832135 AGCTCGAACCCCAACTCTCA 60.832 55.000 0.00 0.0 0.00 3.27
1310 1319 2.223537 TCATGCACGTATCTCGCATT 57.776 45.000 7.51 0.0 43.67 3.56
1550 1560 1.905215 CACTCTGTTCATGAGGGGTCT 59.095 52.381 0.00 0.0 35.98 3.85
1811 1856 5.681337 TGTTGACGTATTTCTGCAATGAA 57.319 34.783 0.00 0.0 0.00 2.57
2032 2110 2.897326 TCCTCACCATGTTCTTCTTCGA 59.103 45.455 0.00 0.0 0.00 3.71
2223 2373 3.132289 TCGTTATCCTTGGATCGCTTCTT 59.868 43.478 5.30 0.0 0.00 2.52
2601 2841 3.485463 TTTTGGTCACAGAAGATCGGT 57.515 42.857 0.00 0.0 0.00 4.69
3163 4720 6.341316 TCATATGGCTATAAGAAAGCGGATC 58.659 40.000 2.13 0.0 41.03 3.36


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

AutoCloner maintained by Alex Coulton.