Multiple sequence alignment - TraesCS2D01G007200

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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 TraesCS2D01G007200 chr2D 100.000 5921 0 0 1 5921 3972944 3967024 0.000000e+00 10935.0
1 TraesCS2D01G007200 chr2D 98.584 5932 68 12 1 5921 4030543 4024617 0.000000e+00 10475.0
2 TraesCS2D01G007200 chr2D 94.162 394 19 3 5284 5673 341646948 341646555 1.100000e-166 597.0
3 TraesCS2D01G007200 chr2B 94.899 1882 83 10 3405 5279 6957662 6955787 0.000000e+00 2931.0
4 TraesCS2D01G007200 chr2B 94.796 1883 86 10 3405 5281 454693265 454691389 0.000000e+00 2924.0
5 TraesCS2D01G007200 chr2B 93.949 1884 101 10 3405 5281 454719232 454717355 0.000000e+00 2835.0
6 TraesCS2D01G007200 chr2B 94.826 1778 80 9 3405 5175 6871036 6869264 0.000000e+00 2763.0
7 TraesCS2D01G007200 chr2B 89.545 2200 139 27 1 2146 6959819 6957657 0.000000e+00 2704.0
8 TraesCS2D01G007200 chr2B 94.489 1742 85 9 3405 5139 7001540 7003277 0.000000e+00 2675.0
9 TraesCS2D01G007200 chr2B 90.040 1978 122 25 1 1940 6873235 6871295 0.000000e+00 2492.0
10 TraesCS2D01G007200 chr2B 93.299 1358 80 8 3405 4755 7087573 7088926 0.000000e+00 1993.0
11 TraesCS2D01G007200 chr2B 92.336 1357 80 15 3405 4755 7161822 7163160 0.000000e+00 1908.0
12 TraesCS2D01G007200 chr2B 90.299 1237 90 16 935 2146 454694491 454693260 0.000000e+00 1592.0
13 TraesCS2D01G007200 chr2B 89.754 1259 98 13 913 2146 7086326 7087578 0.000000e+00 1581.0
14 TraesCS2D01G007200 chr2B 89.674 1259 99 13 913 2146 7048515 7049767 0.000000e+00 1576.0
15 TraesCS2D01G007200 chr2B 89.357 1259 103 13 913 2146 454720479 454719227 0.000000e+00 1554.0
16 TraesCS2D01G007200 chr2B 89.277 1259 104 13 913 2146 7160575 7161827 0.000000e+00 1548.0
17 TraesCS2D01G007200 chr2B 92.169 830 29 9 88 895 454695306 454694491 0.000000e+00 1140.0
18 TraesCS2D01G007200 chr2B 94.280 507 26 2 4784 5289 6998579 6998075 0.000000e+00 773.0
19 TraesCS2D01G007200 chr2B 86.817 622 52 14 1543 2146 7000936 7001545 0.000000e+00 667.0
20 TraesCS2D01G007200 chr2B 96.098 410 14 2 32 440 454788487 454788079 0.000000e+00 667.0
21 TraesCS2D01G007200 chr2B 95.433 416 17 2 26 440 7044487 7044901 0.000000e+00 662.0
22 TraesCS2D01G007200 chr2B 95.433 416 17 2 26 440 7157544 7157958 0.000000e+00 662.0
23 TraesCS2D01G007200 chr2B 79.772 613 121 3 4623 5233 7579152 7579763 5.450000e-120 442.0
24 TraesCS2D01G007200 chr2B 95.019 261 12 1 5661 5921 6998041 6997782 5.520000e-110 409.0
25 TraesCS2D01G007200 chr2B 94.253 261 14 1 5661 5921 7003753 7004012 1.200000e-106 398.0
26 TraesCS2D01G007200 chr2B 94.253 261 14 1 5661 5921 454691343 454691084 1.200000e-106 398.0
27 TraesCS2D01G007200 chr2B 93.103 261 17 1 5661 5921 454717309 454717050 1.200000e-101 381.0
28 TraesCS2D01G007200 chr2B 92.337 261 19 1 5661 5921 6955707 6955448 2.610000e-98 370.0
29 TraesCS2D01G007200 chr2B 90.256 195 18 1 1952 2146 6871224 6871031 2.740000e-63 254.0
30 TraesCS2D01G007200 chr2B 92.179 179 13 1 5661 5839 6867353 6867176 9.850000e-63 252.0
31 TraesCS2D01G007200 chr2B 97.727 44 1 0 775 818 7048409 7048452 6.360000e-10 76.8
32 TraesCS2D01G007200 chr2B 97.727 44 1 0 775 818 7086220 7086263 6.360000e-10 76.8
33 TraesCS2D01G007200 chr2B 97.727 44 1 0 775 818 7160469 7160512 6.360000e-10 76.8
34 TraesCS2D01G007200 chrUn 93.419 1170 63 10 4128 5291 11589951 11588790 0.000000e+00 1722.0
35 TraesCS2D01G007200 chrUn 83.314 857 81 32 1 818 11580981 11581814 0.000000e+00 734.0
36 TraesCS2D01G007200 chrUn 83.314 857 81 32 1 818 440301375 440300542 0.000000e+00 734.0
37 TraesCS2D01G007200 chrUn 96.098 410 14 2 32 440 360049887 360049479 0.000000e+00 667.0
38 TraesCS2D01G007200 chrUn 95.854 410 15 2 32 440 268875214 268874806 0.000000e+00 662.0
39 TraesCS2D01G007200 chrUn 90.647 139 11 2 5661 5798 11588753 11588616 3.640000e-42 183.0
40 TraesCS2D01G007200 chrUn 91.057 123 11 0 5799 5921 398109863 398109985 3.670000e-37 167.0
41 TraesCS2D01G007200 chrUn 91.057 123 11 0 5799 5921 468075067 468075189 3.670000e-37 167.0
42 TraesCS2D01G007200 chrUn 97.727 44 1 0 775 818 385833006 385833049 6.360000e-10 76.8
43 TraesCS2D01G007200 chrUn 97.619 42 1 0 32 73 424078558 424078517 8.230000e-09 73.1
44 TraesCS2D01G007200 chr5B 95.090 387 18 1 5281 5666 101020310 101020696 5.070000e-170 608.0
45 TraesCS2D01G007200 chr1D 94.560 386 18 2 5284 5666 174199601 174199216 1.420000e-165 593.0
46 TraesCS2D01G007200 chr4D 94.545 385 18 3 5284 5666 441294481 441294098 5.110000e-165 592.0
47 TraesCS2D01G007200 chr4A 94.286 385 20 2 5281 5663 311248596 311248980 6.610000e-164 588.0
48 TraesCS2D01G007200 chr3D 94.271 384 20 2 5285 5666 545201577 545201960 2.380000e-163 586.0
49 TraesCS2D01G007200 chr7D 94.256 383 20 2 5285 5666 391324565 391324184 8.550000e-163 584.0
50 TraesCS2D01G007200 chr1A 93.557 388 23 2 5281 5666 291682916 291683303 1.430000e-160 577.0
51 TraesCS2D01G007200 chr2A 77.671 936 169 27 994 1912 551721513 551722425 8.730000e-148 534.0
52 TraesCS2D01G007200 chr2A 78.142 183 28 9 368 541 44108003 44108182 8.120000e-19 106.0
53 TraesCS2D01G007200 chr5D 73.171 328 58 25 255 562 288573677 288573994 2.270000e-14 91.6


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 TraesCS2D01G007200 chr2D 3967024 3972944 5920 True 10935.000000 10935 100.000000 1 5921 1 chr2D.!!$R1 5920
1 TraesCS2D01G007200 chr2D 4024617 4030543 5926 True 10475.000000 10475 98.584000 1 5921 1 chr2D.!!$R2 5920
2 TraesCS2D01G007200 chr2B 6955448 6959819 4371 True 2001.666667 2931 92.260333 1 5921 3 chr2B.!!$R3 5920
3 TraesCS2D01G007200 chr2B 454717050 454720479 3429 True 1590.000000 2835 92.136333 913 5921 3 chr2B.!!$R6 5008
4 TraesCS2D01G007200 chr2B 454691084 454695306 4222 True 1513.500000 2924 92.879250 88 5921 4 chr2B.!!$R5 5833
5 TraesCS2D01G007200 chr2B 6867176 6873235 6059 True 1440.250000 2763 91.825250 1 5839 4 chr2B.!!$R2 5838
6 TraesCS2D01G007200 chr2B 7000936 7004012 3076 False 1246.666667 2675 91.853000 1543 5921 3 chr2B.!!$F2 4378
7 TraesCS2D01G007200 chr2B 7086220 7088926 2706 False 1216.933333 1993 93.593333 775 4755 3 chr2B.!!$F4 3980
8 TraesCS2D01G007200 chr2B 7157544 7163160 5616 False 1048.700000 1908 93.693250 26 4755 4 chr2B.!!$F5 4729
9 TraesCS2D01G007200 chr2B 7044487 7049767 5280 False 771.600000 1576 94.278000 26 2146 3 chr2B.!!$F3 2120
10 TraesCS2D01G007200 chr2B 6997782 6998579 797 True 591.000000 773 94.649500 4784 5921 2 chr2B.!!$R4 1137
11 TraesCS2D01G007200 chr2B 7579152 7579763 611 False 442.000000 442 79.772000 4623 5233 1 chr2B.!!$F1 610
12 TraesCS2D01G007200 chrUn 11588616 11589951 1335 True 952.500000 1722 92.033000 4128 5798 2 chrUn.!!$R5 1670
13 TraesCS2D01G007200 chrUn 11580981 11581814 833 False 734.000000 734 83.314000 1 818 1 chrUn.!!$F1 817
14 TraesCS2D01G007200 chrUn 440300542 440301375 833 True 734.000000 734 83.314000 1 818 1 chrUn.!!$R4 817
15 TraesCS2D01G007200 chr2A 551721513 551722425 912 False 534.000000 534 77.671000 994 1912 1 chr2A.!!$F2 918

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
459 498 0.317160 ACGGACATCTCGCACTCAAA 59.683 50.000 0.00 0.0 0.00 2.69 F
1134 4472 1.001746 CCATGGACTCTCCCGATCATG 59.998 57.143 5.56 0.0 35.03 3.07 F
2423 5826 0.471401 AGGTATTCTAGCCCGTCCCC 60.471 60.000 0.00 0.0 0.00 4.81 F
2424 5827 1.478526 GGTATTCTAGCCCGTCCCCC 61.479 65.000 0.00 0.0 0.00 5.40 F
2970 6377 1.851304 TCCAGGCCATTTGCTAAAGG 58.149 50.000 5.01 0.0 40.92 3.11 F
4161 7572 1.942657 GAGGAAATCATGCGCTGCTAA 59.057 47.619 9.73 0.0 0.00 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1395 4736 1.630369 AGCTCCACAATGCAGACCTTA 59.370 47.619 0.00 0.00 0.00 2.69 R
3128 6535 1.533625 TGCAAAGTGTGGGACTATGC 58.466 50.000 0.00 0.00 33.09 3.14 R
3327 6734 3.803778 CGGCAGAGCAAAAACTCAAAAAT 59.196 39.130 0.00 0.00 39.26 1.82 R
3389 6796 5.619220 AGGTCATTTCTGAGATATCCAAGC 58.381 41.667 0.00 0.00 30.18 4.01 R
4215 7626 6.095440 GCATCTCTATAGTGGCAAAAGGAAAA 59.905 38.462 0.00 0.00 0.00 2.29 R
5273 10691 2.109774 TGGATTTTCCCCATGCATGAC 58.890 47.619 28.31 8.07 35.03 3.06 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
459 498 0.317160 ACGGACATCTCGCACTCAAA 59.683 50.000 0.00 0.00 0.00 2.69
807 4117 2.406596 TTTGTACTAACCCCATCGCC 57.593 50.000 0.00 0.00 0.00 5.54
1134 4472 1.001746 CCATGGACTCTCCCGATCATG 59.998 57.143 5.56 0.00 35.03 3.07
2423 5826 0.471401 AGGTATTCTAGCCCGTCCCC 60.471 60.000 0.00 0.00 0.00 4.81
2424 5827 1.478526 GGTATTCTAGCCCGTCCCCC 61.479 65.000 0.00 0.00 0.00 5.40
2703 6106 7.598759 TCCTATGTTACTATTCCTGGTCTTC 57.401 40.000 0.00 0.00 0.00 2.87
2956 6363 2.898729 AGCATCACGATACTTCCAGG 57.101 50.000 0.00 0.00 0.00 4.45
2969 6376 2.827921 ACTTCCAGGCCATTTGCTAAAG 59.172 45.455 5.01 1.63 40.92 1.85
2970 6377 1.851304 TCCAGGCCATTTGCTAAAGG 58.149 50.000 5.01 0.00 40.92 3.11
3128 6535 7.550196 AGTGGGCTATTTGAAGCAAATTTAATG 59.450 33.333 10.26 0.22 40.60 1.90
3210 6617 8.497745 AGGAGATCATATCACAAATTGTAACCT 58.502 33.333 0.00 0.00 0.00 3.50
3427 6834 8.298854 CAGAAATGACCTCATAAACATGTGAAA 58.701 33.333 0.00 0.00 35.10 2.69
3681 7092 5.509501 CGCCATGTTATTTGCCTATCCATTT 60.510 40.000 0.00 0.00 0.00 2.32
3877 7288 9.705103 TGATGGAGATCTTTTTATTCTTGGAAT 57.295 29.630 0.00 0.00 0.00 3.01
4161 7572 1.942657 GAGGAAATCATGCGCTGCTAA 59.057 47.619 9.73 0.00 0.00 3.09
4215 7626 9.423061 CCTATGTTGCTTTATTAAGTTTGCTTT 57.577 29.630 0.00 0.00 36.22 3.51
4716 8134 3.193903 TCGTCCGTCATCCTGAAACAATA 59.806 43.478 0.00 0.00 0.00 1.90
4723 8141 7.827236 TCCGTCATCCTGAAACAATATTTAAGT 59.173 33.333 0.00 0.00 0.00 2.24
5331 10749 3.634397 AGTTACCCCACATGTCTCATG 57.366 47.619 0.00 7.99 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 14 2.561373 GTTTGGGCCGCTTTCTCG 59.439 61.111 0.00 0.00 0.00 4.04
271 298 0.250124 ACGGGCATCACGAACTCAAA 60.250 50.000 0.00 0.00 34.93 2.69
807 4117 5.444122 GTTTTCTCTTGTCAATTGGTCTCG 58.556 41.667 5.42 0.00 0.00 4.04
887 4214 2.030893 TGCATGTTCTTTTTCTGGCGAG 60.031 45.455 0.00 0.00 0.00 5.03
948 4277 6.379417 AGTGGTAGTGGTACTGATAACTTACC 59.621 42.308 0.00 0.00 36.55 2.85
1134 4472 1.673808 CTACGTGGTGGAGGCTACCC 61.674 65.000 0.00 0.82 37.40 3.69
1395 4736 1.630369 AGCTCCACAATGCAGACCTTA 59.370 47.619 0.00 0.00 0.00 2.69
1426 4767 3.807538 CATGCGCCTGACCTGCAC 61.808 66.667 6.88 0.00 42.11 4.57
1862 5203 4.202567 TGCTCTTTGTGGTTAGAGGGAATT 60.203 41.667 0.00 0.00 38.63 2.17
2703 6106 9.003658 ACAAAATAGGTACAAATGAACTCTGAG 57.996 33.333 2.45 2.45 0.00 3.35
3002 6409 8.903820 AGTTTGCTAATTTGTTCTTCAAGTAGT 58.096 29.630 0.00 0.00 37.35 2.73
3128 6535 1.533625 TGCAAAGTGTGGGACTATGC 58.466 50.000 0.00 0.00 33.09 3.14
3327 6734 3.803778 CGGCAGAGCAAAAACTCAAAAAT 59.196 39.130 0.00 0.00 39.26 1.82
3389 6796 5.619220 AGGTCATTTCTGAGATATCCAAGC 58.381 41.667 0.00 0.00 30.18 4.01
3681 7092 6.260700 ACCCTTATATTGCTACACCATGAA 57.739 37.500 0.00 0.00 0.00 2.57
4215 7626 6.095440 GCATCTCTATAGTGGCAAAAGGAAAA 59.905 38.462 0.00 0.00 0.00 2.29
4507 7923 9.733556 TGTATGTGGTATTTTGAAGTGAACTAT 57.266 29.630 0.00 0.00 0.00 2.12
5273 10691 2.109774 TGGATTTTCCCCATGCATGAC 58.890 47.619 28.31 8.07 35.03 3.06
5565 11003 3.630769 TCAAATCGGAGAGTATGTACGCT 59.369 43.478 0.00 0.00 43.63 5.07
5566 11004 3.961182 TCAAATCGGAGAGTATGTACGC 58.039 45.455 0.00 0.00 43.63 4.42


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

AutoCloner maintained by Alex Coulton.