Multiple sequence alignment - TraesCS6A01G317200

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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 TraesCS6A01G317200 chr6A 100.000 2738 0 0 1 2738 553461879 553459142 0.000000e+00 5057
1 TraesCS6A01G317200 chr6A 94.428 2782 105 25 1 2738 553396673 553393898 0.000000e+00 4233
2 TraesCS6A01G317200 chr6A 94.365 2786 101 28 1 2738 553434927 553432150 0.000000e+00 4224
3 TraesCS6A01G317200 chr6A 93.948 1702 66 17 263 1930 568279977 568278279 0.000000e+00 2538
4 TraesCS6A01G317200 chr6A 92.997 1228 78 5 555 1781 553559526 553558306 0.000000e+00 1784
5 TraesCS6A01G317200 chr6A 92.276 1230 86 6 555 1783 568294984 568293763 0.000000e+00 1736
6 TraesCS6A01G317200 chr6A 91.863 1229 91 6 555 1782 553388091 553386871 0.000000e+00 1707
7 TraesCS6A01G317200 chr6A 91.863 1229 91 6 555 1782 568271422 568270202 0.000000e+00 1707
8 TraesCS6A01G317200 chr6A 91.782 1229 92 6 555 1782 553426318 553425098 0.000000e+00 1701
9 TraesCS6A01G317200 chr6A 91.477 1232 92 9 555 1782 553453332 553452110 0.000000e+00 1681
10 TraesCS6A01G317200 chr6A 91.975 972 61 7 1782 2738 553558270 553557301 0.000000e+00 1347
11 TraesCS6A01G317200 chr6A 94.588 850 43 1 1 850 553525834 553524988 0.000000e+00 1312
12 TraesCS6A01G317200 chr6A 94.430 754 20 5 1994 2738 568277983 568277243 0.000000e+00 1140
13 TraesCS6A01G317200 chr6A 93.846 715 31 9 2034 2738 568307721 568307010 0.000000e+00 1064
14 TraesCS6A01G317200 chr6A 93.131 626 33 5 2122 2738 553473626 553473002 0.000000e+00 909
15 TraesCS6A01G317200 chr6A 94.737 266 13 1 1 265 568292059 568291794 1.960000e-111 412
16 TraesCS6A01G317200 chr6A 95.980 199 8 0 1 199 425794838 425795036 9.460000e-85 324
17 TraesCS6A01G317200 chr6A 95.980 199 8 0 1 199 525820384 525820582 9.460000e-85 324
18 TraesCS6A01G317200 chr6A 95.980 199 8 0 1 199 537332170 537332368 9.460000e-85 324
19 TraesCS6A01G317200 chr6A 93.989 183 11 0 1782 1964 568308180 568307998 7.470000e-71 278
20 TraesCS6A01G317200 chr6A 86.634 202 24 3 1945 2145 553424799 553424600 1.280000e-53 220
21 TraesCS6A01G317200 chr6A 83.824 204 26 5 1945 2145 553386573 553386374 1.290000e-43 187
22 TraesCS6A01G317200 chr6A 93.966 116 7 0 1782 1897 553473996 553473881 2.800000e-40 176
23 TraesCS6A01G317200 chr6B 92.321 586 40 4 234 817 639145370 639144788 0.000000e+00 828
24 TraesCS6A01G317200 chr2D 84.691 614 68 16 2144 2738 390062869 390063475 8.440000e-165 590
25 TraesCS6A01G317200 chr2D 81.729 613 73 21 2143 2726 323218041 323218643 2.470000e-130 475
26 TraesCS6A01G317200 chr2D 75.244 307 38 18 2143 2431 214019348 214019062 8.010000e-21 111
27 TraesCS6A01G317200 chr3D 86.654 532 55 13 2205 2727 373796208 373795684 2.360000e-160 575
28 TraesCS6A01G317200 chr3D 89.326 178 11 1 2142 2311 84323193 84323370 1.650000e-52 217
29 TraesCS6A01G317200 chr3B 86.004 543 60 13 2205 2738 341675987 341675452 3.960000e-158 568
30 TraesCS6A01G317200 chr5D 95.980 199 8 0 1 199 216309409 216309211 9.460000e-85 324
31 TraesCS6A01G317200 chr3A 95.980 199 8 0 1 199 473251396 473251198 9.460000e-85 324
32 TraesCS6A01G317200 chr4D 76.173 277 45 14 2143 2403 179811103 179810832 2.860000e-25 126


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 TraesCS6A01G317200 chr6A 553459142 553461879 2737 True 5057.0 5057 100.0000 1 2738 1 chr6A.!!$R4 2737
1 TraesCS6A01G317200 chr6A 553393898 553396673 2775 True 4233.0 4233 94.4280 1 2738 1 chr6A.!!$R1 2737
2 TraesCS6A01G317200 chr6A 553432150 553434927 2777 True 4224.0 4224 94.3650 1 2738 1 chr6A.!!$R2 2737
3 TraesCS6A01G317200 chr6A 568277243 568279977 2734 True 1839.0 2538 94.1890 263 2738 2 chr6A.!!$R11 2475
4 TraesCS6A01G317200 chr6A 568270202 568271422 1220 True 1707.0 1707 91.8630 555 1782 1 chr6A.!!$R6 1227
5 TraesCS6A01G317200 chr6A 553452110 553453332 1222 True 1681.0 1681 91.4770 555 1782 1 chr6A.!!$R3 1227
6 TraesCS6A01G317200 chr6A 553557301 553559526 2225 True 1565.5 1784 92.4860 555 2738 2 chr6A.!!$R10 2183
7 TraesCS6A01G317200 chr6A 553524988 553525834 846 True 1312.0 1312 94.5880 1 850 1 chr6A.!!$R5 849
8 TraesCS6A01G317200 chr6A 568291794 568294984 3190 True 1074.0 1736 93.5065 1 1783 2 chr6A.!!$R12 1782
9 TraesCS6A01G317200 chr6A 553424600 553426318 1718 True 960.5 1701 89.2080 555 2145 2 chr6A.!!$R8 1590
10 TraesCS6A01G317200 chr6A 553386374 553388091 1717 True 947.0 1707 87.8435 555 2145 2 chr6A.!!$R7 1590
11 TraesCS6A01G317200 chr6A 568307010 568308180 1170 True 671.0 1064 93.9175 1782 2738 2 chr6A.!!$R13 956
12 TraesCS6A01G317200 chr6A 553473002 553473996 994 True 542.5 909 93.5485 1782 2738 2 chr6A.!!$R9 956
13 TraesCS6A01G317200 chr6B 639144788 639145370 582 True 828.0 828 92.3210 234 817 1 chr6B.!!$R1 583
14 TraesCS6A01G317200 chr2D 390062869 390063475 606 False 590.0 590 84.6910 2144 2738 1 chr2D.!!$F2 594
15 TraesCS6A01G317200 chr2D 323218041 323218643 602 False 475.0 475 81.7290 2143 2726 1 chr2D.!!$F1 583
16 TraesCS6A01G317200 chr3D 373795684 373796208 524 True 575.0 575 86.6540 2205 2727 1 chr3D.!!$R1 522
17 TraesCS6A01G317200 chr3B 341675452 341675987 535 True 568.0 568 86.0040 2205 2738 1 chr3B.!!$R1 533

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
336 337 0.389391 CCCATCATAGACGCGGACTT 59.611 55.0 12.47 0.0 0.0 3.01 F
1291 1297 0.685097 ATGCGGAACTACACACAGGT 59.315 50.0 0.00 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1514 1522 1.076906 ACTAGCTCGGTCTGGTGGT 59.923 57.895 0.0 0.0 0.0 4.16 R
2709 3232 6.874288 TTGGTTTTTAAATTTGCATCTGGG 57.126 33.333 0.0 0.0 0.0 4.45 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
84 85 9.788889 AGCTAATGATGATGATCATGAAACTTA 57.211 29.630 14.30 0.00 46.79 2.24
107 108 9.449719 CTTATGATCAAGTTACTACCAAACCTT 57.550 33.333 0.00 0.00 0.00 3.50
155 156 3.559069 CCAGAGTGGTACGGTAATCCTA 58.441 50.000 0.00 0.00 31.35 2.94
198 199 4.322198 GGACCATGACAAACCTACGAACTA 60.322 45.833 0.00 0.00 0.00 2.24
332 333 2.092323 TCTATCCCATCATAGACGCGG 58.908 52.381 12.47 0.00 31.53 6.46
336 337 0.389391 CCCATCATAGACGCGGACTT 59.611 55.000 12.47 0.00 0.00 3.01
512 513 5.703978 TTCCATTGTTGTGTGGACATTAG 57.296 39.130 0.00 0.00 43.85 1.73
590 591 9.469807 CTCAACCTAATATGTTCTACTGCTAAG 57.530 37.037 0.00 0.00 0.00 2.18
1243 1249 6.734137 TCAACGAACAACATTAGCAGAAAAT 58.266 32.000 0.00 0.00 0.00 1.82
1291 1297 0.685097 ATGCGGAACTACACACAGGT 59.315 50.000 0.00 0.00 0.00 4.00
1299 1305 1.890489 ACTACACACAGGTCGTATGCA 59.110 47.619 0.00 0.00 0.00 3.96
1345 1351 3.326006 ACCACTGTCTTCTCATGTCATGT 59.674 43.478 12.54 0.00 0.00 3.21
1392 1398 7.975616 TGGTTTTCTTCTTTCTTTCACAATCTG 59.024 33.333 0.00 0.00 0.00 2.90
1500 1508 5.047943 ACAGATACTGACCTGTGTACAACTC 60.048 44.000 0.00 0.00 41.59 3.01
1514 1522 5.432645 TGTACAACTCTGGACAATTGTTCA 58.567 37.500 18.60 18.60 43.78 3.18
1688 1696 4.073293 ACTAGAAATATTGCGTGGAGGG 57.927 45.455 0.00 0.00 0.00 4.30
1855 1898 4.371624 AGATTGGAATTCTCACACCACA 57.628 40.909 5.23 0.00 31.87 4.17
1862 1905 4.082571 GGAATTCTCACACCACAATGGAAG 60.083 45.833 5.23 0.00 40.96 3.46
1894 1937 6.516718 AGATTATCCCTGATTGTAGTCGTTG 58.483 40.000 0.00 0.00 0.00 4.10
1974 2119 2.052690 ACGATCTCACTCACCCCCG 61.053 63.158 0.00 0.00 0.00 5.73
2060 2412 1.982223 CTTCTTTGTCTCTCGCAGTCG 59.018 52.381 0.00 0.00 0.00 4.18
2399 2908 2.459644 TGTTTAACGCCCTAGCTAGGA 58.540 47.619 36.80 16.96 46.63 2.94
2648 3169 5.601583 TGAAATCTACGGGCACATACTTA 57.398 39.130 0.00 0.00 0.00 2.24
2729 3252 5.555966 TCCCCCAGATGCAAATTTAAAAAC 58.444 37.500 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 7.669304 TGTAGGAATCATTGGAACTGATTTCAA 59.331 33.333 6.99 0.00 42.03 2.69
84 85 7.231467 ACAAGGTTTGGTAGTAACTTGATCAT 58.769 34.615 6.86 0.00 34.12 2.45
107 108 4.710375 GGATCTTACTCTGGTTGACCTACA 59.290 45.833 1.34 0.00 36.82 2.74
155 156 4.080863 GTCCAGTAACATGACCTCCAGAAT 60.081 45.833 0.00 0.00 0.00 2.40
198 199 8.732746 ACACGGCTAATAGTTATGAAAAATCT 57.267 30.769 0.00 0.00 0.00 2.40
217 218 9.859692 GTAATAGTTATGAAAATCTTACACGGC 57.140 33.333 0.00 0.00 28.45 5.68
336 337 7.033791 GTGTCGATTTCATTCCTACTACTGAA 58.966 38.462 0.00 0.00 0.00 3.02
489 490 5.185635 CCTAATGTCCACACAACAATGGAAT 59.814 40.000 0.00 0.00 46.53 3.01
496 497 1.423541 AGCCCTAATGTCCACACAACA 59.576 47.619 0.00 0.00 35.64 3.33
499 500 0.618458 GGAGCCCTAATGTCCACACA 59.382 55.000 0.00 0.00 36.78 3.72
590 591 6.363896 GCTAATAGGCTACTCGATTTCTTGAC 59.636 42.308 0.00 0.00 0.00 3.18
596 597 3.005472 TGCGCTAATAGGCTACTCGATTT 59.995 43.478 9.73 0.00 0.00 2.17
791 795 9.243105 ACTAAGTGTTGCCACATTATTCTTTAT 57.757 29.630 0.00 0.00 44.39 1.40
1212 1218 7.418408 TGCTAATGTTGTTCGTTGATTTTGTA 58.582 30.769 0.00 0.00 0.00 2.41
1213 1219 6.269315 TGCTAATGTTGTTCGTTGATTTTGT 58.731 32.000 0.00 0.00 0.00 2.83
1243 1249 5.046304 GCCATGGGAGATAGTTAGCTATTCA 60.046 44.000 15.13 0.00 37.99 2.57
1291 1297 2.430694 ACAAGAGCTACCATGCATACGA 59.569 45.455 0.00 0.00 34.99 3.43
1345 1351 1.784358 ACCTACATAACGCCCTGCTA 58.216 50.000 0.00 0.00 0.00 3.49
1392 1398 6.715344 TTGTGTATCCAAATACGAGTGAAC 57.285 37.500 0.00 0.00 40.63 3.18
1500 1508 2.294233 CTGGTGGTGAACAATTGTCCAG 59.706 50.000 20.89 20.89 35.90 3.86
1514 1522 1.076906 ACTAGCTCGGTCTGGTGGT 59.923 57.895 0.00 0.00 0.00 4.16
1542 1550 1.663695 ACACAGTTAGCTTTGCACGT 58.336 45.000 0.00 0.00 0.00 4.49
1688 1696 8.647226 GTTTCACACAAACAATATAAGCATTCC 58.353 33.333 0.00 0.00 0.00 3.01
1855 1898 6.276568 AGGGATAATCTATGGCTTCTTCCATT 59.723 38.462 0.21 0.00 44.04 3.16
1862 1905 6.479884 ACAATCAGGGATAATCTATGGCTTC 58.520 40.000 0.00 0.00 0.00 3.86
1894 1937 5.487845 ACCCTATATATGGCTTGTTCCCTAC 59.512 44.000 4.10 0.00 0.00 3.18
2060 2412 1.147153 GTAGCTGGGAGCATGGGTC 59.853 63.158 0.00 0.00 45.56 4.46
2202 2556 9.304335 TGGTATATCATTGATTTGATCTTGCAT 57.696 29.630 4.14 0.00 37.51 3.96
2709 3232 6.874288 TTGGTTTTTAAATTTGCATCTGGG 57.126 33.333 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.