Multiple sequence alignment - TraesCS6A01G248700

Loading Multiple Alignment...

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 TraesCS6A01G248700 chr6A 100.000 2945 0 0 1 2945 461643949 461646893 0.000000e+00 5439
1 TraesCS6A01G248700 chr6B 93.478 2959 121 20 1 2945 499579642 499576742 0.000000e+00 4329
2 TraesCS6A01G248700 chr6D 93.401 2470 80 27 495 2945 324247954 324250359 0.000000e+00 3581
3 TraesCS6A01G248700 chr6D 94.493 454 25 0 1 454 324247179 324247632 0.000000e+00 701
4 TraesCS6A01G248700 chr2B 76.464 956 150 47 993 1918 620861719 620860809 1.610000e-122 449
5 TraesCS6A01G248700 chr2D 76.464 956 144 56 993 1918 524932529 524931625 7.490000e-121 444
6 TraesCS6A01G248700 chr2A 76.249 981 133 64 993 1953 670315092 670314192 2.100000e-116 429


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 TraesCS6A01G248700 chr6A 461643949 461646893 2944 False 5439 5439 100.000 1 2945 1 chr6A.!!$F1 2944
1 TraesCS6A01G248700 chr6B 499576742 499579642 2900 True 4329 4329 93.478 1 2945 1 chr6B.!!$R1 2944
2 TraesCS6A01G248700 chr6D 324247179 324250359 3180 False 2141 3581 93.947 1 2945 2 chr6D.!!$F1 2944
3 TraesCS6A01G248700 chr2B 620860809 620861719 910 True 449 449 76.464 993 1918 1 chr2B.!!$R1 925
4 TraesCS6A01G248700 chr2D 524931625 524932529 904 True 444 444 76.464 993 1918 1 chr2D.!!$R1 925
5 TraesCS6A01G248700 chr2A 670314192 670315092 900 True 429 429 76.249 993 1953 1 chr2A.!!$R1 960

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
188 189 0.252057 TGTTGGTGATCGAGAGGGGA 60.252 55.0 0.0 0.0 0.0 4.81 F
298 299 0.391793 GTTGAGGAAAGAGAGGCCCG 60.392 60.0 0.0 0.0 0.0 6.13 F
469 470 0.679002 AGGCATGGTGTGATGAGTGC 60.679 55.0 0.0 0.0 0.0 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1157 1461 0.436531 CTTCTTGAAGCTGACGTCGC 59.563 55.000 19.92 19.92 0.00 5.19 R
1836 2174 1.153765 GCCAAAGGCTTTGATCGGC 60.154 57.895 35.18 27.02 46.69 5.54 R
2300 2641 0.250467 CTATGCGAACATGGGGAGGG 60.250 60.000 0.00 0.00 37.04 4.30 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
35 36 2.309755 TCTCCAAAGATGTGGCTCCATT 59.690 45.455 0.00 0.00 38.68 3.16
66 67 0.684805 TTGGTGACACCCAACCCAAC 60.685 55.000 22.00 0.00 42.67 3.77
149 150 7.448469 AGAATACATAATATGCCAAACTGGGAC 59.552 37.037 0.00 0.00 41.95 4.46
188 189 0.252057 TGTTGGTGATCGAGAGGGGA 60.252 55.000 0.00 0.00 0.00 4.81
189 190 0.902531 GTTGGTGATCGAGAGGGGAA 59.097 55.000 0.00 0.00 0.00 3.97
250 251 0.631212 GTGGGAAAGGGGGATCATGT 59.369 55.000 0.00 0.00 0.00 3.21
298 299 0.391793 GTTGAGGAAAGAGAGGCCCG 60.392 60.000 0.00 0.00 0.00 6.13
342 343 3.427573 TGAAGTCGAGGATTAGGTCACA 58.572 45.455 0.00 0.00 0.00 3.58
359 360 1.315257 ACATTCACCCCATCGCAAGC 61.315 55.000 0.00 0.00 37.18 4.01
445 446 2.361119 TGTAACAAGTCACGCTCACTCT 59.639 45.455 0.00 0.00 0.00 3.24
469 470 0.679002 AGGCATGGTGTGATGAGTGC 60.679 55.000 0.00 0.00 0.00 4.40
560 842 1.635663 CTTGCATTCGACCGTCCACC 61.636 60.000 0.00 0.00 0.00 4.61
561 843 2.107041 TTGCATTCGACCGTCCACCT 62.107 55.000 0.00 0.00 0.00 4.00
910 1195 5.526115 TGTTCCGCTATATTCTAACTTCCG 58.474 41.667 0.00 0.00 0.00 4.30
1412 1722 2.182030 CGACTCCTGGCCTTCGAC 59.818 66.667 3.32 0.00 33.20 4.20
1999 2337 4.282195 GGTGATCCGAGGTGAGATAAATCT 59.718 45.833 0.00 0.00 40.50 2.40
2000 2338 5.477291 GGTGATCCGAGGTGAGATAAATCTA 59.523 44.000 0.00 0.00 37.25 1.98
2001 2339 6.153680 GGTGATCCGAGGTGAGATAAATCTAT 59.846 42.308 0.00 0.00 37.25 1.98
2002 2340 7.254852 GTGATCCGAGGTGAGATAAATCTATC 58.745 42.308 0.00 0.00 37.25 2.08
2003 2341 6.378564 TGATCCGAGGTGAGATAAATCTATCC 59.621 42.308 0.00 0.00 37.25 2.59
2004 2342 5.641155 TCCGAGGTGAGATAAATCTATCCA 58.359 41.667 12.42 0.00 37.25 3.41
2005 2343 6.256819 TCCGAGGTGAGATAAATCTATCCAT 58.743 40.000 12.42 2.49 37.25 3.41
2006 2344 6.378564 TCCGAGGTGAGATAAATCTATCCATC 59.621 42.308 12.42 0.97 37.25 3.51
2007 2345 6.406400 CCGAGGTGAGATAAATCTATCCATCC 60.406 46.154 12.42 4.45 37.25 3.51
2008 2346 6.153510 CGAGGTGAGATAAATCTATCCATCCA 59.846 42.308 12.42 0.00 37.25 3.41
2009 2347 7.147759 CGAGGTGAGATAAATCTATCCATCCAT 60.148 40.741 12.42 0.00 37.25 3.41
2010 2348 8.088463 AGGTGAGATAAATCTATCCATCCATC 57.912 38.462 12.42 0.00 37.25 3.51
2040 2380 5.076873 TCCATCCAAGAAACCAAAAGGTAG 58.923 41.667 0.00 0.00 0.00 3.18
2041 2381 5.076873 CCATCCAAGAAACCAAAAGGTAGA 58.923 41.667 0.00 0.00 0.00 2.59
2118 2459 2.159653 GGCAGTCAATTTGCTCGTACAG 60.160 50.000 0.92 0.00 41.27 2.74
2170 2511 8.476925 GGATTTTAAACTGTTGATGTTCGTTTC 58.523 33.333 0.00 0.00 0.00 2.78
2174 2515 4.191662 ACTGTTGATGTTCGTTTCGTTC 57.808 40.909 0.00 0.00 0.00 3.95
2244 2585 6.280643 TGTTATTGATCCGACGATCTGAATT 58.719 36.000 0.00 0.00 44.61 2.17
2245 2586 6.420903 TGTTATTGATCCGACGATCTGAATTC 59.579 38.462 0.00 0.00 44.61 2.17
2281 2622 3.671008 ATTGGGGTTTAAAAGGAACGC 57.329 42.857 0.00 0.00 38.70 4.84
2300 2641 2.951726 GCTTTTTCAGCTGAACCATCC 58.048 47.619 28.46 12.22 46.27 3.51
2313 2654 1.289244 ACCATCCCCTCCCCATGTTC 61.289 60.000 0.00 0.00 0.00 3.18
2362 2703 4.282195 ACTGAGACCAAGTAGTTGAGAAGG 59.718 45.833 12.04 0.00 35.46 3.46
2382 2723 2.093235 GGAGTGCTAGAGACCAAAGCAT 60.093 50.000 0.00 0.00 46.99 3.79
2484 2825 1.134431 TGTGCTTTGCTCTGTGTCTGA 60.134 47.619 0.00 0.00 0.00 3.27
2514 2861 2.351455 CCTCCTTTCTTTCGCTCCTTC 58.649 52.381 0.00 0.00 0.00 3.46
2535 2882 1.747355 AGTTGCTGCTGCCATATGAAC 59.253 47.619 13.47 9.30 38.71 3.18
2536 2883 1.473677 GTTGCTGCTGCCATATGAACA 59.526 47.619 13.47 1.15 38.71 3.18
2537 2884 1.385528 TGCTGCTGCCATATGAACAG 58.614 50.000 13.47 16.95 38.71 3.16
2561 2918 2.391389 GCTGCTCGTACCCTTGTGC 61.391 63.158 0.00 0.00 0.00 4.57
2602 2959 7.176690 CACCACTATTTCTTTCATTAACCACCT 59.823 37.037 0.00 0.00 0.00 4.00
2606 2963 9.975218 ACTATTTCTTTCATTAACCACCTATGT 57.025 29.630 0.00 0.00 0.00 2.29
2610 2967 6.650120 TCTTTCATTAACCACCTATGTCTCC 58.350 40.000 0.00 0.00 0.00 3.71
2683 3040 1.033746 AATTGCAGAGGTCATGGCCG 61.034 55.000 11.52 0.00 0.00 6.13
2687 3044 3.790437 AGAGGTCATGGCCGCTGG 61.790 66.667 22.73 0.00 37.29 4.85
2696 3053 1.168407 ATGGCCGCTGGAATCAATCG 61.168 55.000 0.00 0.00 0.00 3.34
2697 3054 1.819632 GGCCGCTGGAATCAATCGT 60.820 57.895 0.00 0.00 0.00 3.73
2698 3055 0.531974 GGCCGCTGGAATCAATCGTA 60.532 55.000 0.00 0.00 0.00 3.43
2730 3087 4.982701 ACAGCCAGCCAACCAGCC 62.983 66.667 0.00 0.00 0.00 4.85
2736 3093 4.673375 AGCCAACCAGCCAGCCAG 62.673 66.667 0.00 0.00 0.00 4.85
2750 3107 1.606668 CAGCCAGCCGTTCTTTGTTTA 59.393 47.619 0.00 0.00 0.00 2.01
2751 3108 2.228822 CAGCCAGCCGTTCTTTGTTTAT 59.771 45.455 0.00 0.00 0.00 1.40
2752 3109 2.228822 AGCCAGCCGTTCTTTGTTTATG 59.771 45.455 0.00 0.00 0.00 1.90
2753 3110 2.671070 GCCAGCCGTTCTTTGTTTATGG 60.671 50.000 0.00 0.00 0.00 2.74
2754 3111 2.817258 CCAGCCGTTCTTTGTTTATGGA 59.183 45.455 0.00 0.00 0.00 3.41
2755 3112 3.119849 CCAGCCGTTCTTTGTTTATGGAG 60.120 47.826 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.280421 ACATCTTTGGAGAGTGGAGCC 59.720 52.381 0.00 0.00 34.85 4.70
188 189 4.332819 CCGAAAGATGAGCGTAATCCTTTT 59.667 41.667 0.00 0.00 0.00 2.27
189 190 3.871594 CCGAAAGATGAGCGTAATCCTTT 59.128 43.478 0.00 0.00 0.00 3.11
235 236 2.091885 TGCCTAACATGATCCCCCTTTC 60.092 50.000 0.00 0.00 0.00 2.62
270 271 3.005897 TCTCTTTCCTCAACTCTTCACGG 59.994 47.826 0.00 0.00 0.00 4.94
298 299 1.676635 TGCATGGCAGAAGGTGAGC 60.677 57.895 0.00 0.00 33.32 4.26
310 311 0.392863 TCGACTTCATGGGTGCATGG 60.393 55.000 0.00 0.00 33.61 3.66
342 343 1.001020 TGCTTGCGATGGGGTGAAT 60.001 52.632 0.00 0.00 0.00 2.57
359 360 0.944386 CTCAAACCCTTCACGGTGTG 59.056 55.000 8.17 2.74 41.87 3.82
445 446 4.218200 CACTCATCACACCATGCCTTTTAA 59.782 41.667 0.00 0.00 0.00 1.52
484 495 7.599245 CGATTACTATCATCCTTTACAACTCCC 59.401 40.741 0.00 0.00 0.00 4.30
487 498 7.861372 CGACGATTACTATCATCCTTTACAACT 59.139 37.037 0.00 0.00 0.00 3.16
489 500 7.709947 ACGACGATTACTATCATCCTTTACAA 58.290 34.615 0.00 0.00 0.00 2.41
501 783 4.092383 GCAACCACAAACGACGATTACTAT 59.908 41.667 0.00 0.00 0.00 2.12
588 870 7.865385 AGTAATAAGTTAACACGGTGTAACGAA 59.135 33.333 15.11 11.80 38.12 3.85
705 987 2.200373 TTCCAGCCTTAACTCCTTGC 57.800 50.000 0.00 0.00 0.00 4.01
735 1017 3.304190 GCATATCAAATCACAGATGCGCA 60.304 43.478 14.96 14.96 31.33 6.09
738 1020 4.227538 GCAGCATATCAAATCACAGATGC 58.772 43.478 0.00 0.00 39.94 3.91
796 1079 2.653890 CGTTGACACTTTCCATTGCTG 58.346 47.619 0.00 0.00 0.00 4.41
910 1195 2.433318 AAACGAGAGAGCTGCGGC 60.433 61.111 10.33 10.33 39.06 6.53
1157 1461 0.436531 CTTCTTGAAGCTGACGTCGC 59.563 55.000 19.92 19.92 0.00 5.19
1506 1838 3.345808 CCGCACTGGAACCGTGTG 61.346 66.667 16.19 16.19 42.00 3.82
1618 1950 3.443479 AGGAGGAGGGGGAGCGAT 61.443 66.667 0.00 0.00 0.00 4.58
1836 2174 1.153765 GCCAAAGGCTTTGATCGGC 60.154 57.895 35.18 27.02 46.69 5.54
1999 2337 3.817959 TGGATGGATGGATGGATGGATA 58.182 45.455 0.00 0.00 0.00 2.59
2000 2338 2.651190 TGGATGGATGGATGGATGGAT 58.349 47.619 0.00 0.00 0.00 3.41
2001 2339 2.136974 TGGATGGATGGATGGATGGA 57.863 50.000 0.00 0.00 0.00 3.41
2002 2340 2.357881 GGATGGATGGATGGATGGATGG 60.358 54.545 0.00 0.00 0.00 3.51
2003 2341 2.310647 TGGATGGATGGATGGATGGATG 59.689 50.000 0.00 0.00 0.00 3.51
2004 2342 2.651190 TGGATGGATGGATGGATGGAT 58.349 47.619 0.00 0.00 0.00 3.41
2005 2343 2.136974 TGGATGGATGGATGGATGGA 57.863 50.000 0.00 0.00 0.00 3.41
2006 2344 2.377531 TCTTGGATGGATGGATGGATGG 59.622 50.000 0.00 0.00 0.00 3.51
2007 2345 3.801307 TCTTGGATGGATGGATGGATG 57.199 47.619 0.00 0.00 0.00 3.51
2008 2346 4.477249 GTTTCTTGGATGGATGGATGGAT 58.523 43.478 0.00 0.00 0.00 3.41
2009 2347 3.373001 GGTTTCTTGGATGGATGGATGGA 60.373 47.826 0.00 0.00 0.00 3.41
2010 2348 2.961062 GGTTTCTTGGATGGATGGATGG 59.039 50.000 0.00 0.00 0.00 3.51
2118 2459 4.663636 AAAACAGATCAACGGAATCGAC 57.336 40.909 0.00 0.00 40.11 4.20
2170 2511 4.205323 AGCTTTTAAACGAACAGGAACG 57.795 40.909 0.00 0.00 0.00 3.95
2174 2515 5.873179 TCCATAGCTTTTAAACGAACAGG 57.127 39.130 0.00 0.00 0.00 4.00
2244 2585 4.263199 CCCCAATTCTGATGCTATAGCTGA 60.263 45.833 24.61 14.31 42.66 4.26
2245 2586 4.008330 CCCCAATTCTGATGCTATAGCTG 58.992 47.826 24.61 12.01 42.66 4.24
2281 2622 2.232208 GGGGATGGTTCAGCTGAAAAAG 59.768 50.000 29.99 0.00 35.58 2.27
2300 2641 0.250467 CTATGCGAACATGGGGAGGG 60.250 60.000 0.00 0.00 37.04 4.30
2313 2654 2.176273 GTGTGCTCTGGGCTATGCG 61.176 63.158 0.00 0.00 42.39 4.73
2362 2703 2.751166 TGCTTTGGTCTCTAGCACTC 57.249 50.000 0.00 0.00 39.79 3.51
2484 2825 0.179018 AGAAAGGAGGCAACGCAACT 60.179 50.000 0.00 0.00 46.39 3.16
2514 2861 1.385528 TCATATGGCAGCAGCAACTG 58.614 50.000 2.65 1.82 44.61 3.16
2561 2918 0.184933 TGGTGGGGAACAAACAGGAG 59.815 55.000 0.00 0.00 0.00 3.69
2602 2959 2.494445 CACGCGCAGGGAGACATA 59.506 61.111 5.73 0.00 46.37 2.29
2641 2998 2.418628 TGCAACCTAGTACCGTACGTAC 59.581 50.000 15.90 15.90 46.69 3.67
2696 3053 6.263516 TGGCTGTTATCATCCGTATACTAC 57.736 41.667 0.56 0.00 33.03 2.73
2697 3054 5.105877 GCTGGCTGTTATCATCCGTATACTA 60.106 44.000 0.56 0.00 33.03 1.82
2698 3055 4.322049 GCTGGCTGTTATCATCCGTATACT 60.322 45.833 0.56 0.00 33.03 2.12
2730 3087 0.385390 AAACAAAGAACGGCTGGCTG 59.615 50.000 0.00 0.00 0.00 4.85
2736 3093 4.438744 CCATCTCCATAAACAAAGAACGGC 60.439 45.833 0.00 0.00 0.00 5.68
2737 3094 4.941263 TCCATCTCCATAAACAAAGAACGG 59.059 41.667 0.00 0.00 0.00 4.44
2738 3095 5.874810 TCTCCATCTCCATAAACAAAGAACG 59.125 40.000 0.00 0.00 0.00 3.95
2739 3096 7.687941 TTCTCCATCTCCATAAACAAAGAAC 57.312 36.000 0.00 0.00 0.00 3.01
2750 3107 0.911769 TGCCGTTTCTCCATCTCCAT 59.088 50.000 0.00 0.00 0.00 3.41
2751 3108 0.250234 CTGCCGTTTCTCCATCTCCA 59.750 55.000 0.00 0.00 0.00 3.86
2752 3109 0.250513 ACTGCCGTTTCTCCATCTCC 59.749 55.000 0.00 0.00 0.00 3.71
2753 3110 1.646189 GACTGCCGTTTCTCCATCTC 58.354 55.000 0.00 0.00 0.00 2.75
2754 3111 0.108615 CGACTGCCGTTTCTCCATCT 60.109 55.000 0.00 0.00 0.00 2.90
2755 3112 2.373938 CGACTGCCGTTTCTCCATC 58.626 57.895 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.