Multiple sequence alignment - TraesCS7D01G015200

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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 TraesCS7D01G015200 chr7D 100.000 3454 0 0 1 3454 6581269 6584722 0.000000e+00 6379.0
1 TraesCS7D01G015200 chr7D 81.742 1561 208 44 845 2343 6490878 6492423 0.000000e+00 1232.0
2 TraesCS7D01G015200 chr7D 87.916 571 55 12 898 1458 6465183 6464617 0.000000e+00 660.0
3 TraesCS7D01G015200 chr7D 83.013 677 62 19 2418 3054 6492523 6493186 6.470000e-157 564.0
4 TraesCS7D01G015200 chr7A 95.282 2840 90 16 640 3454 7633839 7636659 0.000000e+00 4462.0
5 TraesCS7D01G015200 chr7A 88.317 2080 198 15 1178 3219 7669550 7671622 0.000000e+00 2453.0
6 TraesCS7D01G015200 chr7A 81.419 1550 210 43 845 2343 7628688 7630210 0.000000e+00 1195.0
7 TraesCS7D01G015200 chr7A 91.873 566 36 6 1 564 7667722 7668279 0.000000e+00 782.0
8 TraesCS7D01G015200 chr7A 83.146 712 73 17 2418 3092 7630310 7631011 1.060000e-169 606.0
9 TraesCS7D01G015200 chr7A 77.931 580 75 20 568 1132 7668930 7669471 2.590000e-81 313.0
10 TraesCS7D01G015200 chr4A 85.837 2683 272 57 776 3382 733640546 733637896 0.000000e+00 2750.0
11 TraesCS7D01G015200 chr4A 84.092 1471 203 18 898 2343 733741277 733742741 0.000000e+00 1391.0
12 TraesCS7D01G015200 chr4A 82.413 1558 213 36 845 2348 733672323 733670773 0.000000e+00 1303.0
13 TraesCS7D01G015200 chr4A 90.909 561 42 4 6 564 733662519 733661966 0.000000e+00 745.0
14 TraesCS7D01G015200 chr4A 92.901 493 34 1 1 492 415469621 415470113 0.000000e+00 715.0
15 TraesCS7D01G015200 chr4A 83.251 806 90 26 843 1613 733759891 733760686 0.000000e+00 699.0
16 TraesCS7D01G015200 chr4A 79.841 754 130 16 1610 2343 733761469 733762220 6.560000e-147 531.0
17 TraesCS7D01G015200 chr4A 85.653 467 54 8 2498 2958 733762368 733762827 2.410000e-131 479.0
18 TraesCS7D01G015200 chr4A 86.735 196 14 9 2418 2606 733670678 733670488 1.260000e-49 207.0
19 TraesCS7D01G015200 chr4A 93.701 127 5 2 2967 3092 733670144 733670020 1.640000e-43 187.0
20 TraesCS7D01G015200 chr4A 88.136 59 3 3 3400 3454 733670712 733670654 2.220000e-07 67.6
21 TraesCS7D01G015200 chr4A 85.294 68 6 3 3391 3454 733762283 733762350 2.220000e-07 67.6
22 TraesCS7D01G015200 chr4A 97.297 37 1 0 3418 3454 733638892 733638856 2.880000e-06 63.9
23 TraesCS7D01G015200 chr3B 91.906 556 36 6 10 564 225452759 225453306 0.000000e+00 769.0
24 TraesCS7D01G015200 chr3B 89.286 560 52 3 6 564 689984294 689984846 0.000000e+00 695.0
25 TraesCS7D01G015200 chr3B 88.554 498 44 8 6 500 690355907 690356394 2.970000e-165 592.0
26 TraesCS7D01G015200 chr3B 74.164 538 124 13 1810 2343 742548475 742549001 3.490000e-50 209.0
27 TraesCS7D01G015200 chr3B 76.757 370 70 12 1979 2343 742710625 742710983 3.520000e-45 193.0
28 TraesCS7D01G015200 chr3B 94.286 35 2 0 530 564 690356391 690356425 2.000000e-03 54.7
29 TraesCS7D01G015200 chr7B 90.357 560 46 2 1 559 666516887 666516335 0.000000e+00 728.0
30 TraesCS7D01G015200 chr7B 90.943 530 38 7 36 564 666510308 666509788 0.000000e+00 704.0
31 TraesCS7D01G015200 chr3A 88.510 557 53 6 6 558 658093267 658093816 0.000000e+00 664.0
32 TraesCS7D01G015200 chr2D 92.638 163 12 0 1005 1167 440617045 440616883 5.760000e-58 235.0
33 TraesCS7D01G015200 chr1D 86.585 82 11 0 1283 1364 18130941 18130860 1.320000e-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 TraesCS7D01G015200 chr7D 6581269 6584722 3453 False 6379.000000 6379 100.000000 1 3454 1 chr7D.!!$F1 3453
1 TraesCS7D01G015200 chr7D 6490878 6493186 2308 False 898.000000 1232 82.377500 845 3054 2 chr7D.!!$F2 2209
2 TraesCS7D01G015200 chr7D 6464617 6465183 566 True 660.000000 660 87.916000 898 1458 1 chr7D.!!$R1 560
3 TraesCS7D01G015200 chr7A 7628688 7636659 7971 False 2087.666667 4462 86.615667 640 3454 3 chr7A.!!$F1 2814
4 TraesCS7D01G015200 chr7A 7667722 7671622 3900 False 1182.666667 2453 86.040333 1 3219 3 chr7A.!!$F2 3218
5 TraesCS7D01G015200 chr4A 733637896 733640546 2650 True 1406.950000 2750 91.567000 776 3454 2 chr4A.!!$R2 2678
6 TraesCS7D01G015200 chr4A 733741277 733742741 1464 False 1391.000000 1391 84.092000 898 2343 1 chr4A.!!$F2 1445
7 TraesCS7D01G015200 chr4A 733661966 733662519 553 True 745.000000 745 90.909000 6 564 1 chr4A.!!$R1 558
8 TraesCS7D01G015200 chr4A 733759891 733762827 2936 False 444.150000 699 83.509750 843 3454 4 chr4A.!!$F3 2611
9 TraesCS7D01G015200 chr4A 733670020 733672323 2303 True 441.150000 1303 87.746250 845 3454 4 chr4A.!!$R3 2609
10 TraesCS7D01G015200 chr3B 225452759 225453306 547 False 769.000000 769 91.906000 10 564 1 chr3B.!!$F1 554
11 TraesCS7D01G015200 chr3B 689984294 689984846 552 False 695.000000 695 89.286000 6 564 1 chr3B.!!$F2 558
12 TraesCS7D01G015200 chr3B 690355907 690356425 518 False 323.350000 592 91.420000 6 564 2 chr3B.!!$F5 558
13 TraesCS7D01G015200 chr3B 742548475 742549001 526 False 209.000000 209 74.164000 1810 2343 1 chr3B.!!$F3 533
14 TraesCS7D01G015200 chr7B 666516335 666516887 552 True 728.000000 728 90.357000 1 559 1 chr7B.!!$R2 558
15 TraesCS7D01G015200 chr7B 666509788 666510308 520 True 704.000000 704 90.943000 36 564 1 chr7B.!!$R1 528
16 TraesCS7D01G015200 chr3A 658093267 658093816 549 False 664.000000 664 88.510000 6 558 1 chr3A.!!$F1 552

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
631 1284 1.271102 GTTGCAATTTCGTAGGCCCAA 59.729 47.619 0.59 0.0 0.0 4.12 F
741 5255 2.093128 AGCGGACGAAAATTAGGATGGT 60.093 45.455 0.00 0.0 0.0 3.55 F
1761 7173 0.679505 CCTCCTCGACTTGGTTGACA 59.320 55.000 0.00 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1591 6217 1.705337 GGTCATCGGATTGCACACGG 61.705 60.000 4.34 0.0 0.00 4.94 R
1939 7355 1.737355 ATCCGGGCCATCAATTTGCG 61.737 55.000 4.39 0.0 0.00 4.85 R
3425 8986 1.226717 TTCAACGCCACAAAACGGC 60.227 52.632 0.00 0.0 46.62 5.68 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 5.708230 ACTTCGGCTGACAAAATATTACCAA 59.292 36.000 0.00 0.00 0.00 3.67
89 91 5.394115 GGCTGACAAAATATTACCAACAGGG 60.394 44.000 0.00 0.00 44.81 4.45
163 166 2.401766 CCACGCCTGCTTAGCAAGG 61.402 63.158 8.68 12.68 38.41 3.61
206 209 4.486839 GAAATCCCTGAATCCCAATCCAT 58.513 43.478 0.00 0.00 0.00 3.41
208 211 1.421268 TCCCTGAATCCCAATCCATCG 59.579 52.381 0.00 0.00 0.00 3.84
288 291 2.291540 CCTTGCTTCCCCACCAGAATTA 60.292 50.000 0.00 0.00 0.00 1.40
315 318 1.993370 GAGTTTATTCACGTGCTCGCT 59.007 47.619 11.67 3.83 41.18 4.93
503 506 2.836981 GAGCCTACATCAGAGGGCATAT 59.163 50.000 5.62 0.00 46.23 1.78
504 507 2.836981 AGCCTACATCAGAGGGCATATC 59.163 50.000 5.62 0.00 46.23 1.63
505 508 2.417924 GCCTACATCAGAGGGCATATCG 60.418 54.545 0.00 0.00 43.59 2.92
508 511 1.627329 ACATCAGAGGGCATATCGCAT 59.373 47.619 0.00 0.00 45.17 4.73
509 512 2.833943 ACATCAGAGGGCATATCGCATA 59.166 45.455 0.00 0.00 45.17 3.14
564 570 7.039152 TGGGCACTTGAAGAATATTTTTGATCA 60.039 33.333 0.00 0.00 0.00 2.92
579 1231 7.531857 TTTTTGATCATACCCAAGTAAAGCA 57.468 32.000 0.00 0.00 30.59 3.91
584 1236 5.235850 TCATACCCAAGTAAAGCAAGTGA 57.764 39.130 0.00 0.00 30.59 3.41
623 1276 3.071495 CGAAGCGTTGCAATTTCGT 57.929 47.368 23.79 8.78 38.03 3.85
631 1284 1.271102 GTTGCAATTTCGTAGGCCCAA 59.729 47.619 0.59 0.00 0.00 4.12
686 5200 4.330074 CAGCGAAGATAAAATGGTTCGAGT 59.670 41.667 7.46 0.00 43.50 4.18
723 5237 3.824414 AATTTTGGAAGGTACGAAGCG 57.176 42.857 0.00 0.00 0.00 4.68
739 5253 3.302480 CGAAGCGGACGAAAATTAGGATG 60.302 47.826 0.00 0.00 0.00 3.51
740 5254 2.561569 AGCGGACGAAAATTAGGATGG 58.438 47.619 0.00 0.00 0.00 3.51
741 5255 2.093128 AGCGGACGAAAATTAGGATGGT 60.093 45.455 0.00 0.00 0.00 3.55
742 5256 3.133362 AGCGGACGAAAATTAGGATGGTA 59.867 43.478 0.00 0.00 0.00 3.25
882 5413 2.483013 CGGAAGAATCGTGAAGGCCATA 60.483 50.000 5.01 0.00 0.00 2.74
1160 5741 4.205587 CCTCCTCCTCCAATCAATCTTTG 58.794 47.826 0.00 0.00 0.00 2.77
1187 5774 2.093181 TCCATGGAACGGAATCGATTGT 60.093 45.455 16.96 5.25 40.11 2.71
1477 6103 4.514577 CCCGCTGATCGACGCCTT 62.515 66.667 1.88 0.00 41.67 4.35
1591 6217 3.846335 GGACAAGACAAATTCGATTTCGC 59.154 43.478 0.00 0.00 39.60 4.70
1646 7058 2.834549 GCTGCCTCCTATAGAATGGCTA 59.165 50.000 22.10 12.92 43.57 3.93
1761 7173 0.679505 CCTCCTCGACTTGGTTGACA 59.320 55.000 0.00 0.00 0.00 3.58
2143 7577 5.312079 ACTCTTTGAAGAAATGGACTCCAG 58.688 41.667 3.62 0.00 33.56 3.86
2245 7685 1.473434 CCTTACTGACCGGAAGATGGC 60.473 57.143 9.46 0.00 0.00 4.40
2438 7928 5.407995 CCATTTTGTGGCGTTGAATAATGTT 59.592 36.000 0.00 0.00 42.12 2.71
2439 7929 5.896922 TTTTGTGGCGTTGAATAATGTTG 57.103 34.783 0.00 0.00 0.00 3.33
2440 7930 4.576216 TTGTGGCGTTGAATAATGTTGT 57.424 36.364 0.00 0.00 0.00 3.32
2719 8217 4.476297 TGCTGAATATTGATGATGCCCTT 58.524 39.130 0.00 0.00 0.00 3.95
2753 8255 8.288689 ACGGTAATAGAATTTAGCAAATGGTT 57.711 30.769 0.00 0.00 31.48 3.67
2765 8276 4.088634 AGCAAATGGTTTCTTCTATGCCA 58.911 39.130 0.00 0.00 33.19 4.92
2807 8321 9.167311 AGGAGATGTTAGTGTCATTTATGAAAC 57.833 33.333 5.11 5.11 43.78 2.78
2813 8328 9.438228 TGTTAGTGTCATTTATGAAACCGATAA 57.562 29.630 8.99 0.89 44.37 1.75
2818 8333 7.280205 GTGTCATTTATGAAACCGATAAGGAGT 59.720 37.037 2.20 0.00 38.76 3.85
2870 8396 7.307278 GCTTAGCAGATAGAGTGAACATCATTG 60.307 40.741 0.00 0.00 0.00 2.82
2893 8419 6.180472 TGTCTCTTTATTTTGATCAGGGGAC 58.820 40.000 0.00 0.00 0.00 4.46
3155 8712 3.319137 TCTGTGTACTGGATGCACTTC 57.681 47.619 0.00 0.00 43.82 3.01
3235 8792 2.030562 CTTGACCGCCCGTCTTGT 59.969 61.111 0.75 0.00 42.49 3.16
3322 8883 8.723311 CGTGTGATAGGTTTAAACTTTATTCCA 58.277 33.333 17.50 12.22 0.00 3.53
3425 8986 2.634815 ATTATGCTCTCTGGGTGCAG 57.365 50.000 10.29 0.00 45.63 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.499479 CAATAATTGTAGGAAGAGATGTGCTAT 57.501 33.333 0.00 0.00 0.00 2.97
163 166 0.174617 AGCTCTTCAACCTAGCGCTC 59.825 55.000 16.34 0.00 41.19 5.03
206 209 2.092861 TGACCCAACCAAAGTTTCTCGA 60.093 45.455 0.00 0.00 32.45 4.04
208 211 3.636764 ACATGACCCAACCAAAGTTTCTC 59.363 43.478 0.00 0.00 32.45 2.87
288 291 5.348986 AGCACGTGAATAAACTCATACGAT 58.651 37.500 22.23 0.00 35.69 3.73
306 309 1.142778 GAGAGGCTTAAGCGAGCACG 61.143 60.000 20.80 0.00 44.49 5.34
328 331 9.103048 GTTTACTCTATGTCGTGTTTGAAATTG 57.897 33.333 0.00 0.00 0.00 2.32
334 337 8.636843 GTTCTAGTTTACTCTATGTCGTGTTTG 58.363 37.037 0.00 0.00 0.00 2.93
503 506 3.568443 TGATAGGTACTTGGGTATGCGA 58.432 45.455 0.00 0.00 41.75 5.10
504 507 4.537135 ATGATAGGTACTTGGGTATGCG 57.463 45.455 0.00 0.00 41.75 4.73
505 508 5.865085 TGAATGATAGGTACTTGGGTATGC 58.135 41.667 0.00 0.00 41.75 3.14
508 511 5.968167 ACCTTGAATGATAGGTACTTGGGTA 59.032 40.000 0.00 0.00 42.87 3.69
509 512 4.788617 ACCTTGAATGATAGGTACTTGGGT 59.211 41.667 0.00 0.00 42.87 4.51
564 570 4.042934 AGGTCACTTGCTTTACTTGGGTAT 59.957 41.667 0.00 0.00 0.00 2.73
567 573 2.863809 AGGTCACTTGCTTTACTTGGG 58.136 47.619 0.00 0.00 0.00 4.12
578 1230 3.429547 CCTGATCCTTCGTAGGTCACTTG 60.430 52.174 8.06 1.14 42.60 3.16
579 1231 2.761208 CCTGATCCTTCGTAGGTCACTT 59.239 50.000 8.06 0.00 42.60 3.16
584 1236 0.325296 TGGCCTGATCCTTCGTAGGT 60.325 55.000 3.32 0.00 42.60 3.08
631 1284 2.936919 TCATCCATCGCTGGCTTAAT 57.063 45.000 0.00 0.00 42.80 1.40
686 5200 3.302365 AATTTTCTTCCGTCCGTCGTA 57.698 42.857 0.00 0.00 37.94 3.43
723 5237 5.032327 ACCTACCATCCTAATTTTCGTCC 57.968 43.478 0.00 0.00 0.00 4.79
739 5253 5.153675 AGGGGCTATTACTTCTTACCTACC 58.846 45.833 0.00 0.00 0.00 3.18
740 5254 6.744175 AAGGGGCTATTACTTCTTACCTAC 57.256 41.667 0.00 0.00 0.00 3.18
741 5255 9.456459 AATAAAGGGGCTATTACTTCTTACCTA 57.544 33.333 0.00 0.00 0.00 3.08
742 5256 7.949468 ATAAAGGGGCTATTACTTCTTACCT 57.051 36.000 0.00 0.00 0.00 3.08
882 5413 2.584391 GGCTGTGTTCCTCGAGGGT 61.584 63.158 30.80 0.00 36.25 4.34
907 5438 2.358737 CGGAAAGGCAAGAGCGGT 60.359 61.111 0.00 0.00 43.41 5.68
1160 5741 1.611519 TTCCGTTCCATGGACCAAAC 58.388 50.000 15.91 9.22 31.86 2.93
1187 5774 4.162320 ACCGAGAAAGATTGATTAGGCTCA 59.838 41.667 0.00 0.00 0.00 4.26
1325 5945 0.105964 ACTGCTTGGACACGCACTTA 59.894 50.000 0.00 0.00 32.01 2.24
1591 6217 1.705337 GGTCATCGGATTGCACACGG 61.705 60.000 4.34 0.00 0.00 4.94
1761 7173 5.323382 TCCCATGAGTATATTGCCACAAT 57.677 39.130 0.00 0.00 0.00 2.71
1939 7355 1.737355 ATCCGGGCCATCAATTTGCG 61.737 55.000 4.39 0.00 0.00 4.85
2143 7577 3.399330 TGGTCACGATCCTTTTCTTCAC 58.601 45.455 0.00 0.00 0.00 3.18
2438 7928 4.345859 AAATCTCTAACGGTGACCAACA 57.654 40.909 1.11 0.00 0.00 3.33
2439 7929 4.514066 ACAAAATCTCTAACGGTGACCAAC 59.486 41.667 1.11 0.00 0.00 3.77
2440 7930 4.710324 ACAAAATCTCTAACGGTGACCAA 58.290 39.130 1.11 0.00 0.00 3.67
2753 8255 6.998074 CCCTTTGTATATGTGGCATAGAAGAA 59.002 38.462 0.00 0.00 0.00 2.52
2765 8276 7.691993 ACATCTCCTTACCCTTTGTATATGT 57.308 36.000 0.00 0.00 0.00 2.29
2870 8396 6.180472 TGTCCCCTGATCAAAATAAAGAGAC 58.820 40.000 0.00 0.00 0.00 3.36
3122 8679 5.089411 CAGTACACAGATCGTAGTTGACAG 58.911 45.833 0.00 0.00 0.00 3.51
3235 8792 2.224744 ACATGTGTAGTGGGTCATGCAA 60.225 45.455 0.00 0.00 40.57 4.08
3384 8945 5.708736 TTTGGAATCATAGGGAGTAAGCA 57.291 39.130 0.00 0.00 0.00 3.91
3425 8986 1.226717 TTCAACGCCACAAAACGGC 60.227 52.632 0.00 0.00 46.62 5.68


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

AutoCloner maintained by Alex Coulton.