Multiple sequence alignment - TraesCS1B01G215000

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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 TraesCS1B01G215000 chr1B 100.000 2867 0 0 1 2867 390382206 390379340 0.000000e+00 5295
1 TraesCS1B01G215000 chr1D 95.620 2808 58 19 1 2782 288894060 288891292 0.000000e+00 4444
2 TraesCS1B01G215000 chr1A 90.850 2470 92 55 87 2516 361175301 361172926 0.000000e+00 3186
3 TraesCS1B01G215000 chr1A 89.971 349 25 7 2519 2867 361172881 361172543 2.620000e-120 442
4 TraesCS1B01G215000 chrUn 80.926 367 41 15 1069 1435 365429959 365429622 2.190000e-66 263
5 TraesCS1B01G215000 chr5A 80.654 367 42 15 1069 1435 679875207 679874870 1.020000e-64 257
6 TraesCS1B01G215000 chr4B 80.381 367 43 17 1069 1435 641891305 641890968 4.740000e-63 252
7 TraesCS1B01G215000 chr2D 80.737 353 41 18 1066 1418 500362672 500362997 1.710000e-62 250
8 TraesCS1B01G215000 chr2A 80.453 353 42 18 1066 1418 645311412 645311737 7.930000e-61 244
9 TraesCS1B01G215000 chr2B 80.170 353 43 18 1066 1418 588067408 588067733 3.690000e-59 239
10 TraesCS1B01G215000 chr6D 80.000 350 43 14 1069 1418 342472975 342472653 1.720000e-57 233


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 TraesCS1B01G215000 chr1B 390379340 390382206 2866 True 5295 5295 100.0000 1 2867 1 chr1B.!!$R1 2866
1 TraesCS1B01G215000 chr1D 288891292 288894060 2768 True 4444 4444 95.6200 1 2782 1 chr1D.!!$R1 2781
2 TraesCS1B01G215000 chr1A 361172543 361175301 2758 True 1814 3186 90.4105 87 2867 2 chr1A.!!$R1 2780

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
666 696 0.25051 ACACACACACACACACACCA 60.251 50.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2151 2210 1.335324 GCATGAAGCCATAATCCGTGC 60.335 52.381 0.0 0.0 37.23 5.34 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
47 48 4.281182 ACACACGAGGTAATCCTATCATCC 59.719 45.833 0.00 0.00 45.24 3.51
49 50 4.899457 ACACGAGGTAATCCTATCATCCAA 59.101 41.667 0.00 0.00 45.24 3.53
198 223 7.033530 ACGAATTTTCTGTGGAAATACAACA 57.966 32.000 0.00 0.00 40.57 3.33
252 278 5.488341 TGAGGACCTGTGATAAAAAGCTAC 58.512 41.667 0.00 0.00 0.00 3.58
380 406 2.224867 ACCACAGCTAGCAAACCAATCT 60.225 45.455 18.83 0.00 0.00 2.40
392 418 5.711506 AGCAAACCAATCTGAATCACACATA 59.288 36.000 0.00 0.00 0.00 2.29
393 419 6.379133 AGCAAACCAATCTGAATCACACATAT 59.621 34.615 0.00 0.00 0.00 1.78
394 420 6.694411 GCAAACCAATCTGAATCACACATATC 59.306 38.462 0.00 0.00 0.00 1.63
395 421 6.949352 AACCAATCTGAATCACACATATCC 57.051 37.500 0.00 0.00 0.00 2.59
396 422 5.380043 ACCAATCTGAATCACACATATCCC 58.620 41.667 0.00 0.00 0.00 3.85
610 640 6.187727 TGTATTGTTCCTGACCTTTTCTCT 57.812 37.500 0.00 0.00 0.00 3.10
611 641 6.231211 TGTATTGTTCCTGACCTTTTCTCTC 58.769 40.000 0.00 0.00 0.00 3.20
656 686 3.006537 ACTCATACCCACTACACACACAC 59.993 47.826 0.00 0.00 0.00 3.82
657 687 2.966516 TCATACCCACTACACACACACA 59.033 45.455 0.00 0.00 0.00 3.72
658 688 2.894763 TACCCACTACACACACACAC 57.105 50.000 0.00 0.00 0.00 3.82
659 689 0.906066 ACCCACTACACACACACACA 59.094 50.000 0.00 0.00 0.00 3.72
660 690 1.295792 CCCACTACACACACACACAC 58.704 55.000 0.00 0.00 0.00 3.82
661 691 1.406205 CCCACTACACACACACACACA 60.406 52.381 0.00 0.00 0.00 3.72
662 692 1.663643 CCACTACACACACACACACAC 59.336 52.381 0.00 0.00 0.00 3.82
663 693 2.342179 CACTACACACACACACACACA 58.658 47.619 0.00 0.00 0.00 3.72
664 694 2.093625 CACTACACACACACACACACAC 59.906 50.000 0.00 0.00 0.00 3.82
665 695 1.663643 CTACACACACACACACACACC 59.336 52.381 0.00 0.00 0.00 4.16
666 696 0.250510 ACACACACACACACACACCA 60.251 50.000 0.00 0.00 0.00 4.17
667 697 0.877743 CACACACACACACACACCAA 59.122 50.000 0.00 0.00 0.00 3.67
668 698 1.135717 CACACACACACACACACCAAG 60.136 52.381 0.00 0.00 0.00 3.61
669 699 1.271108 ACACACACACACACACCAAGA 60.271 47.619 0.00 0.00 0.00 3.02
670 700 2.016318 CACACACACACACACCAAGAT 58.984 47.619 0.00 0.00 0.00 2.40
677 707 3.213506 CACACACACCAAGATCCAAGAA 58.786 45.455 0.00 0.00 0.00 2.52
740 770 2.677228 CCCCCGTTTCTGGCATCT 59.323 61.111 0.00 0.00 0.00 2.90
775 805 4.450082 TGGCATAATCGCATATCGTAGT 57.550 40.909 0.00 0.00 39.67 2.73
839 871 4.404715 TCGGAGGCCCATATTATAGTAAGC 59.595 45.833 0.00 0.00 0.00 3.09
970 1005 4.821589 CGAGCTCGGGAGGTTGGC 62.822 72.222 28.40 0.00 39.57 4.52
1116 1151 4.353437 GTGACCCCGAGCGACGTT 62.353 66.667 0.00 0.00 40.78 3.99
1179 1214 1.404843 GCTACTTCCCTCTCGATGGT 58.595 55.000 4.27 0.00 0.00 3.55
1459 1494 1.520787 GCTTACAGCGCCACCGTAT 60.521 57.895 2.29 0.00 36.67 3.06
1635 1670 4.393155 CCAGCGGCTGTGGTGCTA 62.393 66.667 26.79 0.00 37.15 3.49
1735 1770 1.591863 GTGAACCTCGATAGCCCGC 60.592 63.158 0.00 0.00 0.00 6.13
1799 1852 4.400961 GACGCTCCTGCTGCCCTT 62.401 66.667 0.00 0.00 36.97 3.95
2151 2210 4.626172 CCTCTGCATCATGAGATACATTCG 59.374 45.833 0.09 0.00 37.07 3.34
2208 2268 2.614829 TATGGCTTCCCTTCGTTAGC 57.385 50.000 0.00 0.00 0.00 3.09
2218 2278 6.399639 TTCCCTTCGTTAGCAAAAGAAAAT 57.600 33.333 0.00 0.00 33.56 1.82
2249 2309 3.671702 GCTTCCCTTCATTCGCAAAAGAG 60.672 47.826 0.00 0.00 0.00 2.85
2298 2369 3.430042 ACACTACAGTCTCGTTCCCTA 57.570 47.619 0.00 0.00 0.00 3.53
2362 2437 3.688694 ACTCATGCTTGGGTACGTTTA 57.311 42.857 2.71 0.00 33.71 2.01
2407 2482 0.039978 CGTTCTGGAGATCGATCCCG 60.040 60.000 21.66 16.37 38.99 5.14
2464 2543 1.048601 GGAGGTCAGGTGTCAGAACA 58.951 55.000 0.00 0.00 0.00 3.18
2517 2599 4.277423 TCGATCGGCTATGAACATTGTCTA 59.723 41.667 16.41 0.00 0.00 2.59
2604 2728 2.001361 ATGCCGCAAATCTCTGCAGC 62.001 55.000 9.47 0.00 44.40 5.25
2638 2762 2.679837 CGTCTGAAATTATGCCAGCTGT 59.320 45.455 13.81 0.00 0.00 4.40
2689 2813 3.648067 AGCTAGCCAAGTAGCCATATCAA 59.352 43.478 12.13 0.00 45.74 2.57
2693 2817 4.962155 AGCCAAGTAGCCATATCAAGTAC 58.038 43.478 0.00 0.00 0.00 2.73
2695 2819 5.072329 AGCCAAGTAGCCATATCAAGTACAT 59.928 40.000 0.00 0.00 0.00 2.29
2696 2820 6.270000 AGCCAAGTAGCCATATCAAGTACATA 59.730 38.462 0.00 0.00 0.00 2.29
2697 2821 7.038017 AGCCAAGTAGCCATATCAAGTACATAT 60.038 37.037 0.00 0.00 0.00 1.78
2698 2822 8.258007 GCCAAGTAGCCATATCAAGTACATATA 58.742 37.037 0.00 0.00 0.00 0.86
2800 2926 5.183904 AGTTCAAATATTCTTCAGGGCACAC 59.816 40.000 0.00 0.00 0.00 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 3.628017 CGGGTGAACATGTGTTTCTTTC 58.372 45.455 0.00 0.00 38.56 2.62
198 223 2.093447 GGATGGATGACCGAAGAGTTGT 60.093 50.000 0.00 0.00 39.42 3.32
252 278 3.000925 GTGTGGGCACGATATTTTCTACG 59.999 47.826 0.00 0.00 35.75 3.51
392 418 5.130705 TCGGTCAGCTCTATATATGGGAT 57.869 43.478 0.00 0.00 0.00 3.85
393 419 4.586306 TCGGTCAGCTCTATATATGGGA 57.414 45.455 0.00 0.00 0.00 4.37
394 420 4.889995 TGATCGGTCAGCTCTATATATGGG 59.110 45.833 0.00 0.00 0.00 4.00
395 421 5.358160 TGTGATCGGTCAGCTCTATATATGG 59.642 44.000 0.00 0.00 34.36 2.74
396 422 6.127897 TGTGTGATCGGTCAGCTCTATATATG 60.128 42.308 0.00 0.00 34.36 1.78
402 428 1.472878 GTGTGTGATCGGTCAGCTCTA 59.527 52.381 0.00 0.00 34.36 2.43
498 524 1.145819 GAGAGATGGCTGTGAGGGC 59.854 63.158 0.00 0.00 0.00 5.19
610 640 8.630091 AGTGTATGTATATGGGATAAGGTAGGA 58.370 37.037 0.00 0.00 0.00 2.94
611 641 8.840200 AGTGTATGTATATGGGATAAGGTAGG 57.160 38.462 0.00 0.00 0.00 3.18
656 686 2.849942 TCTTGGATCTTGGTGTGTGTG 58.150 47.619 0.00 0.00 0.00 3.82
657 687 3.214328 GTTCTTGGATCTTGGTGTGTGT 58.786 45.455 0.00 0.00 0.00 3.72
658 688 2.554032 GGTTCTTGGATCTTGGTGTGTG 59.446 50.000 0.00 0.00 0.00 3.82
659 689 2.174639 TGGTTCTTGGATCTTGGTGTGT 59.825 45.455 0.00 0.00 0.00 3.72
660 690 2.862541 TGGTTCTTGGATCTTGGTGTG 58.137 47.619 0.00 0.00 0.00 3.82
661 691 3.138283 TCTTGGTTCTTGGATCTTGGTGT 59.862 43.478 0.00 0.00 0.00 4.16
662 692 3.754965 TCTTGGTTCTTGGATCTTGGTG 58.245 45.455 0.00 0.00 0.00 4.17
663 693 4.145052 GTTCTTGGTTCTTGGATCTTGGT 58.855 43.478 0.00 0.00 0.00 3.67
664 694 3.507622 GGTTCTTGGTTCTTGGATCTTGG 59.492 47.826 0.00 0.00 0.00 3.61
665 695 4.401925 AGGTTCTTGGTTCTTGGATCTTG 58.598 43.478 0.00 0.00 0.00 3.02
666 696 4.731313 AGGTTCTTGGTTCTTGGATCTT 57.269 40.909 0.00 0.00 0.00 2.40
667 697 4.104738 TGAAGGTTCTTGGTTCTTGGATCT 59.895 41.667 0.00 0.00 0.00 2.75
668 698 4.398319 TGAAGGTTCTTGGTTCTTGGATC 58.602 43.478 0.00 0.00 0.00 3.36
669 699 4.453480 TGAAGGTTCTTGGTTCTTGGAT 57.547 40.909 0.00 0.00 0.00 3.41
670 700 3.943671 TGAAGGTTCTTGGTTCTTGGA 57.056 42.857 0.00 0.00 0.00 3.53
677 707 2.887152 GAGCACAATGAAGGTTCTTGGT 59.113 45.455 0.00 0.00 0.00 3.67
737 767 4.987963 TGCCATGGATGAACAGATAGAT 57.012 40.909 18.40 0.00 0.00 1.98
738 768 4.987963 ATGCCATGGATGAACAGATAGA 57.012 40.909 18.40 0.00 0.00 1.98
739 769 6.036844 CGATTATGCCATGGATGAACAGATAG 59.963 42.308 18.40 0.00 0.00 2.08
740 770 5.876460 CGATTATGCCATGGATGAACAGATA 59.124 40.000 18.40 0.00 0.00 1.98
775 805 6.774673 TGGAAAACTGGAATAGATGTGTGTA 58.225 36.000 0.00 0.00 0.00 2.90
839 871 4.472833 AGAATTAGGGCTATGGCTATCAGG 59.527 45.833 0.00 0.00 38.73 3.86
991 1026 0.394899 GAGAACTCCATGGCCTTGGG 60.395 60.000 31.62 24.58 37.37 4.12
992 1027 0.745845 CGAGAACTCCATGGCCTTGG 60.746 60.000 28.04 28.04 38.18 3.61
993 1028 1.372087 GCGAGAACTCCATGGCCTTG 61.372 60.000 6.96 11.68 0.00 3.61
994 1029 1.078143 GCGAGAACTCCATGGCCTT 60.078 57.895 6.96 0.00 0.00 4.35
995 1030 2.586792 GCGAGAACTCCATGGCCT 59.413 61.111 6.96 0.90 0.00 5.19
996 1031 2.514824 GGCGAGAACTCCATGGCC 60.515 66.667 6.96 0.00 0.00 5.36
997 1032 1.377202 TTGGCGAGAACTCCATGGC 60.377 57.895 6.96 0.00 30.62 4.40
1104 1139 4.367023 TTCCCAACGTCGCTCGGG 62.367 66.667 7.70 7.70 44.69 5.14
1107 1142 2.048127 AGCTTCCCAACGTCGCTC 60.048 61.111 0.00 0.00 0.00 5.03
1116 1151 3.249189 AGGCGGTTCAGCTTCCCA 61.249 61.111 0.00 0.00 37.29 4.37
2151 2210 1.335324 GCATGAAGCCATAATCCGTGC 60.335 52.381 0.00 0.00 37.23 5.34
2208 2268 9.671279 AGGGAAGCCATAAATAATTTTCTTTTG 57.329 29.630 0.00 0.00 0.00 2.44
2218 2278 5.009610 GCGAATGAAGGGAAGCCATAAATAA 59.990 40.000 0.00 0.00 0.00 1.40
2230 2290 3.417069 TCTCTTTTGCGAATGAAGGGA 57.583 42.857 4.02 0.00 0.00 4.20
2249 2309 9.914131 GTGATAAAGGGAAGCCATAAATATTTC 57.086 33.333 3.39 0.00 0.00 2.17
2298 2369 4.712051 TTGTTATCATATGCAGGGAGCT 57.288 40.909 0.00 0.00 45.94 4.09
2362 2437 6.096001 ACACTGCTTCAAGAAACTTGAAAGAT 59.904 34.615 21.58 11.76 37.89 2.40
2464 2543 8.958506 GGATATCTGTACGTGTAGAAGGATTAT 58.041 37.037 0.00 0.00 0.00 1.28
2604 2728 2.971430 TCAGACGAGTCTTGAACGAG 57.029 50.000 2.55 0.00 37.98 4.18
2800 2926 8.367911 TGGACTGAAGGTGCTATATACAAATAG 58.632 37.037 0.00 0.00 37.18 1.73


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

AutoCloner maintained by Alex Coulton.