Multiple sequence alignment - TraesCS2D01G248400

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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 TraesCS2D01G248400 chr2D 100.000 3073 0 0 1 3073 292291255 292288183 0.000000e+00 5675.0
1 TraesCS2D01G248400 chr2D 93.407 182 11 1 2893 3073 54573149 54573330 5.050000e-68 268.0
2 TraesCS2D01G248400 chr2D 92.473 186 13 1 2889 3073 54531426 54531611 6.530000e-67 265.0
3 TraesCS2D01G248400 chr2D 92.896 183 12 1 2892 3073 302409045 302409227 6.530000e-67 265.0
4 TraesCS2D01G248400 chr2D 79.355 155 26 6 2743 2894 74135675 74135826 1.510000e-18 104.0
5 TraesCS2D01G248400 chr2D 82.353 119 18 3 2745 2862 565153445 565153561 1.950000e-17 100.0
6 TraesCS2D01G248400 chr2A 96.188 2256 77 6 822 3073 365285901 365283651 0.000000e+00 3681.0
7 TraesCS2D01G248400 chr2B 98.579 1478 21 0 822 2299 368616032 368614555 0.000000e+00 2614.0
8 TraesCS2D01G248400 chr2B 91.537 579 43 6 2400 2977 368614524 368613951 0.000000e+00 793.0
9 TraesCS2D01G248400 chr3D 92.637 842 29 10 1 822 512911283 512910455 0.000000e+00 1181.0
10 TraesCS2D01G248400 chr3D 91.311 610 35 10 216 821 192144306 192144901 0.000000e+00 817.0
11 TraesCS2D01G248400 chr3D 88.342 549 38 19 1 531 192143950 192144490 1.200000e-178 636.0
12 TraesCS2D01G248400 chr3D 92.896 183 12 1 2892 3073 301588332 301588514 6.530000e-67 265.0
13 TraesCS2D01G248400 chr1D 92.840 824 32 12 1 822 111396868 111397666 0.000000e+00 1170.0
14 TraesCS2D01G248400 chr1D 93.478 184 9 3 2892 3073 170633340 170633522 1.400000e-68 270.0
15 TraesCS2D01G248400 chr1D 92.896 183 12 1 2892 3073 75178010 75177828 6.530000e-67 265.0
16 TraesCS2D01G248400 chr7D 93.532 603 30 8 224 822 244599507 244600104 0.000000e+00 889.0
17 TraesCS2D01G248400 chr7D 94.318 440 17 6 1 436 244599224 244599659 0.000000e+00 667.0
18 TraesCS2D01G248400 chr5D 92.799 611 32 11 217 821 215147281 215147885 0.000000e+00 874.0
19 TraesCS2D01G248400 chr5D 93.607 438 24 4 1 436 215146984 215147419 0.000000e+00 651.0
20 TraesCS2D01G248400 chr5D 83.051 118 16 4 2746 2861 30433100 30432985 1.510000e-18 104.0
21 TraesCS2D01G248400 chr6D 91.830 612 37 12 217 821 411931425 411930820 0.000000e+00 841.0
22 TraesCS2D01G248400 chr6D 91.326 611 31 14 215 821 69091729 69092321 0.000000e+00 815.0
23 TraesCS2D01G248400 chr6D 93.607 438 24 3 1 436 411931742 411931307 0.000000e+00 651.0
24 TraesCS2D01G248400 chr6D 92.500 440 24 7 1 436 93759035 93758601 3.370000e-174 621.0
25 TraesCS2D01G248400 chr6D 92.255 439 29 3 1 436 69091474 69091910 4.350000e-173 617.0
26 TraesCS2D01G248400 chr6D 96.996 233 7 0 589 821 93758415 93758183 2.870000e-105 392.0
27 TraesCS2D01G248400 chr6D 90.566 53 5 0 2451 2503 150779623 150779571 1.530000e-08 71.3
28 TraesCS2D01G248400 chr5A 87.520 633 33 22 224 822 475781474 475780854 0.000000e+00 689.0
29 TraesCS2D01G248400 chr5B 82.459 610 78 18 221 821 122942789 122943378 9.830000e-140 507.0
30 TraesCS2D01G248400 chr5B 80.000 150 24 6 2745 2891 391158689 391158835 4.190000e-19 106.0
31 TraesCS2D01G248400 chr5B 87.234 94 11 1 2747 2839 422938121 422938214 4.190000e-19 106.0
32 TraesCS2D01G248400 chr6A 92.896 183 12 1 2892 3073 388206586 388206768 6.530000e-67 265.0
33 TraesCS2D01G248400 chr3B 91.803 183 14 1 2892 3073 257322605 257322787 1.410000e-63 254.0
34 TraesCS2D01G248400 chr1B 85.405 185 19 7 2892 3073 221249025 221248846 5.230000e-43 185.0
35 TraesCS2D01G248400 chr3A 80.597 201 24 15 2880 3073 404263447 404263639 1.150000e-29 141.0
36 TraesCS2D01G248400 chr3A 78.000 150 27 5 2745 2891 552303225 552303371 4.220000e-14 89.8
37 TraesCS2D01G248400 chr7A 82.308 130 21 2 2745 2873 688152939 688153067 9.010000e-21 111.0
38 TraesCS2D01G248400 chr6B 91.525 59 5 0 2451 2509 274992502 274992560 7.060000e-12 82.4
39 TraesCS2D01G248400 chr6B 88.462 52 5 1 2501 2551 83143142 83143091 9.200000e-06 62.1


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 TraesCS2D01G248400 chr2D 292288183 292291255 3072 True 5675.0 5675 100.0000 1 3073 1 chr2D.!!$R1 3072
1 TraesCS2D01G248400 chr2A 365283651 365285901 2250 True 3681.0 3681 96.1880 822 3073 1 chr2A.!!$R1 2251
2 TraesCS2D01G248400 chr2B 368613951 368616032 2081 True 1703.5 2614 95.0580 822 2977 2 chr2B.!!$R1 2155
3 TraesCS2D01G248400 chr3D 512910455 512911283 828 True 1181.0 1181 92.6370 1 822 1 chr3D.!!$R1 821
4 TraesCS2D01G248400 chr3D 192143950 192144901 951 False 726.5 817 89.8265 1 821 2 chr3D.!!$F2 820
5 TraesCS2D01G248400 chr1D 111396868 111397666 798 False 1170.0 1170 92.8400 1 822 1 chr1D.!!$F1 821
6 TraesCS2D01G248400 chr7D 244599224 244600104 880 False 778.0 889 93.9250 1 822 2 chr7D.!!$F1 821
7 TraesCS2D01G248400 chr5D 215146984 215147885 901 False 762.5 874 93.2030 1 821 2 chr5D.!!$F1 820
8 TraesCS2D01G248400 chr6D 411930820 411931742 922 True 746.0 841 92.7185 1 821 2 chr6D.!!$R3 820
9 TraesCS2D01G248400 chr6D 69091474 69092321 847 False 716.0 815 91.7905 1 821 2 chr6D.!!$F1 820
10 TraesCS2D01G248400 chr6D 93758183 93759035 852 True 506.5 621 94.7480 1 821 2 chr6D.!!$R2 820
11 TraesCS2D01G248400 chr5A 475780854 475781474 620 True 689.0 689 87.5200 224 822 1 chr5A.!!$R1 598
12 TraesCS2D01G248400 chr5B 122942789 122943378 589 False 507.0 507 82.4590 221 821 1 chr5B.!!$F1 600

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
271 273 6.312672 ACTTTTTCCAAAAATCGGTGAACTTG 59.687 34.615 0.00 0.0 37.27 3.16 F
573 1035 6.851222 TTTGTGAACAAAGCAACAGAAAAA 57.149 29.167 4.52 0.0 40.55 1.94 F
1262 1753 0.399949 TCTATTCCCGTCCATGGCCT 60.400 55.000 6.96 0.0 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1249 1740 0.034477 AGTAAAAGGCCATGGACGGG 60.034 55.000 18.4 0.0 0.00 5.28 R
1934 2425 2.032528 TCCGGCTTGCTCTTGGTG 59.967 61.111 0.0 0.0 0.00 4.17 R
2863 3357 1.338973 TCCTCTTAGTGACGCACGTTT 59.661 47.619 0.0 0.0 39.64 3.60 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
102 103 8.717821 CCTCATGTTGTAGAATCGTTCTTTTTA 58.282 33.333 5.74 0.00 41.14 1.52
271 273 6.312672 ACTTTTTCCAAAAATCGGTGAACTTG 59.687 34.615 0.00 0.00 37.27 3.16
573 1035 6.851222 TTTGTGAACAAAGCAACAGAAAAA 57.149 29.167 4.52 0.00 40.55 1.94
1249 1740 7.329717 CCGTAAGCTGACTAATCCATTCTATTC 59.670 40.741 0.00 0.00 0.00 1.75
1262 1753 0.399949 TCTATTCCCGTCCATGGCCT 60.400 55.000 6.96 0.00 0.00 5.19
1271 1762 1.065418 CGTCCATGGCCTTTTACTCCT 60.065 52.381 6.96 0.00 0.00 3.69
1272 1763 2.369394 GTCCATGGCCTTTTACTCCTG 58.631 52.381 6.96 0.00 0.00 3.86
2237 2731 4.003648 CTGTTATTGTTTCTTCCTCGCCT 58.996 43.478 0.00 0.00 0.00 5.52
2276 2770 4.696402 CCCCCATGAATGTTCACAAAATTG 59.304 41.667 0.00 0.00 40.49 2.32
2278 2772 5.409214 CCCCATGAATGTTCACAAAATTGTC 59.591 40.000 0.00 0.00 39.91 3.18
2282 2776 7.306925 CCATGAATGTTCACAAAATTGTCTGTG 60.307 37.037 0.00 8.56 43.53 3.66
2324 2818 7.365497 ACCTTCCTTTTGATTTGAATTGTCT 57.635 32.000 0.00 0.00 0.00 3.41
2396 2890 1.811965 TGATAAGTGCCACATGTGTGC 59.188 47.619 23.79 23.98 44.34 4.57
2415 2909 4.397730 TGTGCTACAAACACATGACAACTT 59.602 37.500 0.00 0.00 42.88 2.66
2476 2970 5.138125 ACAACTTTAATGGTCAAGCATGG 57.862 39.130 0.00 0.00 0.00 3.66
2483 2977 0.961019 TGGTCAAGCATGGCAACTTC 59.039 50.000 0.00 0.00 30.82 3.01
2584 3078 7.349711 CCACACGTATGGTACTTATTATTTGC 58.650 38.462 4.19 0.00 34.77 3.68
2689 3183 1.082690 GCACTTCACTTGAGCTAGCC 58.917 55.000 12.13 3.49 0.00 3.93
2788 3282 5.529289 TGGTTAGGAGGACAGTGATATCTT 58.471 41.667 3.98 0.00 0.00 2.40
2792 3286 8.652290 GGTTAGGAGGACAGTGATATCTTTAAT 58.348 37.037 3.98 0.00 0.00 1.40
2799 3293 8.328758 AGGACAGTGATATCTTTAATCCAACAA 58.671 33.333 3.98 0.00 0.00 2.83
2833 3327 3.674997 AGACTTACATTGGTGTTCGCAT 58.325 40.909 0.00 0.00 39.77 4.73
2863 3357 1.291109 TTTATTCCAGGCCTTCCGGA 58.709 50.000 0.00 3.77 37.47 5.14
2900 3394 3.640029 AGAGGAAACGTTCTGTTGTAGGA 59.360 43.478 0.00 0.00 40.84 2.94
2937 3431 2.158667 GGTCTTTTCACACTTGGAGGGA 60.159 50.000 0.00 0.00 0.00 4.20
2941 3435 5.020132 TCTTTTCACACTTGGAGGGAAAAA 58.980 37.500 5.07 0.00 37.11 1.94
3002 3497 3.069443 ACAAAACCCAATCACACATCCAC 59.931 43.478 0.00 0.00 0.00 4.02
3056 3551 5.913137 ACATGAACAGTCAAAGGAAACAA 57.087 34.783 0.00 0.00 37.30 2.83
3060 3555 4.402155 TGAACAGTCAAAGGAAACAAGCAT 59.598 37.500 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
528 987 4.687901 TCTCAAGAACACATGGAACTGA 57.312 40.909 0.00 0.00 0.00 3.41
532 991 5.827267 TCACAAATCTCAAGAACACATGGAA 59.173 36.000 0.00 0.00 0.00 3.53
1249 1740 0.034477 AGTAAAAGGCCATGGACGGG 60.034 55.000 18.40 0.00 0.00 5.28
1262 1753 2.038557 GCTGGACTGGACAGGAGTAAAA 59.961 50.000 4.14 0.00 36.48 1.52
1271 1762 1.285078 TCTAGCTAGCTGGACTGGACA 59.715 52.381 25.33 3.00 0.00 4.02
1272 1763 1.953686 CTCTAGCTAGCTGGACTGGAC 59.046 57.143 25.33 0.00 30.42 4.02
1934 2425 2.032528 TCCGGCTTGCTCTTGGTG 59.967 61.111 0.00 0.00 0.00 4.17
2237 2731 6.031386 TCATGGGGGATCAATATCATGAGTA 58.969 40.000 0.09 0.00 36.91 2.59
2276 2770 2.822764 ACGAAGAAAGTGTCCACAGAC 58.177 47.619 0.00 0.00 43.83 3.51
2278 2772 4.616181 AAAACGAAGAAAGTGTCCACAG 57.384 40.909 0.00 0.00 0.00 3.66
2282 2776 5.277683 GGAAGGTAAAACGAAGAAAGTGTCC 60.278 44.000 0.00 0.00 0.00 4.02
2371 2865 3.444742 CACATGTGGCACTTATCATGGTT 59.555 43.478 18.51 0.00 41.01 3.67
2374 2868 3.732774 GCACACATGTGGCACTTATCATG 60.733 47.826 28.64 15.37 45.72 3.07
2385 2879 2.998772 GTGTTTGTAGCACACATGTGG 58.001 47.619 28.64 18.29 45.72 4.17
2396 2890 5.651172 TCGAAGTTGTCATGTGTTTGTAG 57.349 39.130 0.00 0.00 0.00 2.74
2409 2903 4.347813 CCGTGAAAAACATTCGAAGTTGT 58.652 39.130 3.35 0.65 0.00 3.32
2415 2909 3.422417 TTTGCCGTGAAAAACATTCGA 57.578 38.095 0.00 0.00 0.00 3.71
2476 2970 3.643159 ACCATCCGAAAAAGAAGTTGC 57.357 42.857 0.00 0.00 0.00 4.17
2505 2999 9.877178 TTAAAACTAAAGTTGCCATCTGAAAAA 57.123 25.926 0.00 0.00 38.44 1.94
2506 3000 9.877178 TTTAAAACTAAAGTTGCCATCTGAAAA 57.123 25.926 0.00 0.00 38.44 2.29
2600 3094 9.920946 TCAATGGCTCTTTACCTTTATTTCTAT 57.079 29.630 0.00 0.00 0.00 1.98
2640 3134 2.799562 GCTCTCAAAATTAATGGCCCGC 60.800 50.000 0.00 0.00 0.00 6.13
2641 3135 2.426738 TGCTCTCAAAATTAATGGCCCG 59.573 45.455 0.00 0.00 0.00 6.13
2689 3183 2.155155 GTGCCGTCGTCTAACAAAAGAG 59.845 50.000 0.00 0.00 0.00 2.85
2792 3286 7.696992 AGTCTAAAACTTGAACTTTGTTGGA 57.303 32.000 0.00 0.00 33.03 3.53
2863 3357 1.338973 TCCTCTTAGTGACGCACGTTT 59.661 47.619 0.00 0.00 39.64 3.60
2878 3372 3.640029 TCCTACAACAGAACGTTTCCTCT 59.360 43.478 0.46 0.00 34.86 3.69
2917 3411 3.208747 TCCCTCCAAGTGTGAAAAGAC 57.791 47.619 0.00 0.00 0.00 3.01
2941 3435 3.222603 GTGTTCTTGGTGTTCATCCCTT 58.777 45.455 0.00 0.00 0.00 3.95
3002 3497 7.115520 CGTGGATCTATGTGTTTGCTATTCTAG 59.884 40.741 0.00 0.00 0.00 2.43
3043 3538 5.453567 ACCTAATGCTTGTTTCCTTTGAC 57.546 39.130 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.