Multiple sequence alignment - TraesCS6D01G284000

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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 TraesCS6D01G284000 chr6D 100.000 3197 0 0 1 3197 391539065 391535869 0.000000e+00 5904
1 TraesCS6D01G284000 chr6D 75.051 489 106 15 1165 1645 16775621 16775141 2.500000e-51 213
2 TraesCS6D01G284000 chr6A 95.739 2253 80 9 346 2587 537662657 537660410 0.000000e+00 3615
3 TraesCS6D01G284000 chr6A 89.757 576 31 9 2630 3197 537660409 537659854 0.000000e+00 712
4 TraesCS6D01G284000 chr6A 85.714 364 38 6 2848 3197 537599733 537599370 3.890000e-99 372
5 TraesCS6D01G284000 chr6A 85.359 362 41 6 2848 3197 537606993 537606632 6.520000e-97 364
6 TraesCS6D01G284000 chr6A 87.324 213 16 5 1 213 537662848 537662647 1.920000e-57 233
7 TraesCS6D01G284000 chr6A 88.112 143 17 0 1167 1309 15700855 15700997 1.520000e-38 171
8 TraesCS6D01G284000 chr6A 88.112 143 17 0 1167 1309 15906812 15906670 1.520000e-38 171
9 TraesCS6D01G284000 chr6A 83.851 161 9 6 2691 2848 537607285 537607139 1.550000e-28 137
10 TraesCS6D01G284000 chr6A 87.963 108 9 2 2693 2797 537600160 537600054 1.200000e-24 124
11 TraesCS6D01G284000 chr6A 97.674 43 1 0 2806 2848 537599919 537599877 1.230000e-09 75
12 TraesCS6D01G284000 chr6B 94.412 2237 68 11 826 3007 584911763 584909529 0.000000e+00 3386
13 TraesCS6D01G284000 chr6B 93.750 192 10 1 3008 3197 584909485 584909294 1.450000e-73 287
14 TraesCS6D01G284000 chr6B 86.207 261 26 3 2861 3111 584684978 584684718 1.130000e-69 274
15 TraesCS6D01G284000 chr6B 97.170 106 3 0 1 106 584911931 584911826 2.530000e-41 180
16 TraesCS6D01G284000 chr6B 85.938 128 11 5 2726 2848 584685245 584685120 2.590000e-26 130
17 TraesCS6D01G284000 chr2D 92.285 687 45 6 108 790 7067619 7068301 0.000000e+00 968
18 TraesCS6D01G284000 chr1B 91.433 712 52 9 104 809 155432601 155433309 0.000000e+00 968
19 TraesCS6D01G284000 chr1B 90.616 714 52 13 112 818 17760655 17759950 0.000000e+00 933
20 TraesCS6D01G284000 chr1D 90.756 714 56 8 104 809 462145903 462145192 0.000000e+00 944
21 TraesCS6D01G284000 chr1D 90.909 704 50 12 112 809 470719027 470718332 0.000000e+00 933
22 TraesCS6D01G284000 chr7D 90.603 713 55 8 104 809 264039006 264039713 0.000000e+00 935
23 TraesCS6D01G284000 chr4D 90.436 711 60 8 104 809 166541853 166542560 0.000000e+00 929
24 TraesCS6D01G284000 chr5D 89.972 718 62 10 104 815 257165438 257166151 0.000000e+00 918
25 TraesCS6D01G284000 chr5D 79.111 225 42 2 1139 1360 356636904 356637126 1.990000e-32 150
26 TraesCS6D01G284000 chr5A 89.986 719 61 9 104 815 501402107 501401393 0.000000e+00 918
27 TraesCS6D01G284000 chr5A 72.934 484 118 10 1167 1645 456099769 456099294 4.270000e-34 156
28 TraesCS6D01G284000 chr2B 74.333 487 108 12 1166 1645 54016540 54016064 1.170000e-44 191
29 TraesCS6D01G284000 chr2B 74.127 487 109 12 1166 1645 54043892 54043416 5.450000e-43 185


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 TraesCS6D01G284000 chr6D 391535869 391539065 3196 True 5904.000000 5904 100.000000 1 3197 1 chr6D.!!$R2 3196
1 TraesCS6D01G284000 chr6A 537659854 537662848 2994 True 1520.000000 3615 90.940000 1 3197 3 chr6A.!!$R4 3196
2 TraesCS6D01G284000 chr6A 537606632 537607285 653 True 250.500000 364 84.605000 2691 3197 2 chr6A.!!$R3 506
3 TraesCS6D01G284000 chr6B 584909294 584911931 2637 True 1284.333333 3386 95.110667 1 3197 3 chr6B.!!$R2 3196
4 TraesCS6D01G284000 chr6B 584684718 584685245 527 True 202.000000 274 86.072500 2726 3111 2 chr6B.!!$R1 385
5 TraesCS6D01G284000 chr2D 7067619 7068301 682 False 968.000000 968 92.285000 108 790 1 chr2D.!!$F1 682
6 TraesCS6D01G284000 chr1B 155432601 155433309 708 False 968.000000 968 91.433000 104 809 1 chr1B.!!$F1 705
7 TraesCS6D01G284000 chr1B 17759950 17760655 705 True 933.000000 933 90.616000 112 818 1 chr1B.!!$R1 706
8 TraesCS6D01G284000 chr1D 462145192 462145903 711 True 944.000000 944 90.756000 104 809 1 chr1D.!!$R1 705
9 TraesCS6D01G284000 chr1D 470718332 470719027 695 True 933.000000 933 90.909000 112 809 1 chr1D.!!$R2 697
10 TraesCS6D01G284000 chr7D 264039006 264039713 707 False 935.000000 935 90.603000 104 809 1 chr7D.!!$F1 705
11 TraesCS6D01G284000 chr4D 166541853 166542560 707 False 929.000000 929 90.436000 104 809 1 chr4D.!!$F1 705
12 TraesCS6D01G284000 chr5D 257165438 257166151 713 False 918.000000 918 89.972000 104 815 1 chr5D.!!$F1 711
13 TraesCS6D01G284000 chr5A 501401393 501402107 714 True 918.000000 918 89.986000 104 815 1 chr5A.!!$R2 711

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
646 650 0.252789 TGGTGGGGTATTTCCGGAGA 60.253 55.0 3.34 0.0 37.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2424 2490 1.134699 TGGCGATGTCCATCTTCTGTC 60.135 52.381 5.79 0.0 35.72 3.51 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
98 99 7.174253 GGATACCACTCAAAGACATTTGTTACA 59.826 37.037 1.08 0.00 45.06 2.41
109 110 5.301551 AGACATTTGTTACAACTTGCATGGA 59.698 36.000 10.28 0.00 0.00 3.41
611 615 4.610714 TGCTTGGTACGCGGCACA 62.611 61.111 12.47 2.37 0.00 4.57
636 640 4.642488 TCGGGCTGTGGTGGGGTA 62.642 66.667 0.00 0.00 0.00 3.69
646 650 0.252789 TGGTGGGGTATTTCCGGAGA 60.253 55.000 3.34 0.00 37.00 3.71
745 754 2.032376 TTGATGTGCTGCTCGCCA 59.968 55.556 0.00 0.00 38.05 5.69
748 758 2.033141 ATGTGCTGCTCGCCAAGT 59.967 55.556 0.00 0.00 38.05 3.16
752 762 2.666190 GCTGCTCGCCAAGTGTCA 60.666 61.111 0.00 0.00 0.00 3.58
755 765 3.414700 GCTCGCCAAGTGTCACGG 61.415 66.667 0.00 0.00 0.00 4.94
770 780 2.867368 GTCACGGTGTGTACAATGTTGA 59.133 45.455 8.17 0.00 34.79 3.18
783 793 5.021033 ACAATGTTGATTGGTTGCTTTGA 57.979 34.783 0.00 0.00 43.00 2.69
792 802 8.394121 GTTGATTGGTTGCTTTGAAATACAAAA 58.606 29.630 0.00 0.00 45.97 2.44
1258 1307 2.525629 TCGCCCACCTCAAGTCCA 60.526 61.111 0.00 0.00 0.00 4.02
2127 2176 2.783288 CGTAGCCCCCTTCGAGGAC 61.783 68.421 0.00 0.00 37.67 3.85
2346 2408 7.877612 GGTGGATGTTCATAATTTTGGAACTTT 59.122 33.333 13.96 5.72 41.07 2.66
2371 2433 7.819644 TGGAAGTGTTCATTACTGATTGAATG 58.180 34.615 0.00 0.00 34.60 2.67
2399 2463 7.505585 TGGATTTGGTGTAAAACTCTGAGAAAT 59.494 33.333 12.44 3.50 0.00 2.17
2403 2469 7.377766 TGGTGTAAAACTCTGAGAAATATGC 57.622 36.000 12.44 0.00 0.00 3.14
2405 2471 6.183360 GGTGTAAAACTCTGAGAAATATGCCC 60.183 42.308 12.44 0.00 0.00 5.36
2406 2472 5.885912 TGTAAAACTCTGAGAAATATGCCCC 59.114 40.000 12.44 0.00 0.00 5.80
2424 2490 2.362077 CCCCTTTGGTTCTGTCTTGTTG 59.638 50.000 0.00 0.00 0.00 3.33
2481 2558 6.292274 CGTGCAATGCTTCAAAAGTGTTTAAT 60.292 34.615 6.82 0.00 0.00 1.40
2505 2582 4.406069 CAGTGGTCAATTCTTATTGTGCG 58.594 43.478 0.00 0.00 41.54 5.34
2539 2616 4.781934 CTGTTAGCCCTAAAGTAATGCCT 58.218 43.478 0.00 0.00 0.00 4.75
2562 2639 7.679638 GCCTCTGCACAAATGTATTAAACCTAG 60.680 40.741 0.00 0.00 37.47 3.02
2907 3139 3.648339 TTCAAGAGGCTGCATTTTGTC 57.352 42.857 15.58 0.00 0.00 3.18
3049 3332 3.420893 TGCAATTTACCCCTCTGAACTG 58.579 45.455 0.00 0.00 0.00 3.16
3050 3333 3.073798 TGCAATTTACCCCTCTGAACTGA 59.926 43.478 0.00 0.00 0.00 3.41
3051 3334 4.079253 GCAATTTACCCCTCTGAACTGAA 58.921 43.478 0.00 0.00 0.00 3.02
3052 3335 4.156739 GCAATTTACCCCTCTGAACTGAAG 59.843 45.833 0.00 0.00 0.00 3.02
3054 3337 4.618920 TTTACCCCTCTGAACTGAAGAC 57.381 45.455 0.00 0.00 0.00 3.01
3055 3338 1.353091 ACCCCTCTGAACTGAAGACC 58.647 55.000 0.00 0.00 0.00 3.85
3056 3339 0.615850 CCCCTCTGAACTGAAGACCC 59.384 60.000 0.00 0.00 0.00 4.46
3057 3340 1.650528 CCCTCTGAACTGAAGACCCT 58.349 55.000 0.00 0.00 0.00 4.34
3058 3341 1.981495 CCCTCTGAACTGAAGACCCTT 59.019 52.381 0.00 0.00 0.00 3.95
3059 3342 2.027653 CCCTCTGAACTGAAGACCCTTC 60.028 54.545 0.00 0.00 0.00 3.46
3060 3343 2.903135 CCTCTGAACTGAAGACCCTTCT 59.097 50.000 8.02 0.00 0.00 2.85
3061 3344 3.326297 CCTCTGAACTGAAGACCCTTCTT 59.674 47.826 8.02 0.00 45.35 2.52
3062 3345 4.202409 CCTCTGAACTGAAGACCCTTCTTT 60.202 45.833 8.02 2.18 42.53 2.52
3063 3346 5.372373 CTCTGAACTGAAGACCCTTCTTTT 58.628 41.667 8.02 1.88 42.53 2.27
3064 3347 5.755849 TCTGAACTGAAGACCCTTCTTTTT 58.244 37.500 8.02 0.00 42.53 1.94
3065 3348 6.895782 TCTGAACTGAAGACCCTTCTTTTTA 58.104 36.000 8.02 0.00 42.53 1.52
3066 3349 7.518188 TCTGAACTGAAGACCCTTCTTTTTAT 58.482 34.615 8.02 0.00 42.53 1.40
3075 3358 6.178324 AGACCCTTCTTTTTATAACCCTTCG 58.822 40.000 0.00 0.00 0.00 3.79
3085 3383 9.783256 CTTTTTATAACCCTTCGTCCTTATTTG 57.217 33.333 0.00 0.00 0.00 2.32
3124 3422 7.284074 TGTTTGACTCCAATTTTGTCCTAGTA 58.716 34.615 0.00 0.00 31.46 1.82
3131 3429 6.607019 TCCAATTTTGTCCTAGTAAGTGGTT 58.393 36.000 0.00 0.00 37.13 3.67
3186 3486 4.467795 TCATTTCTCCCTCCTCACAACTAG 59.532 45.833 0.00 0.00 0.00 2.57
3189 3489 3.432378 TCTCCCTCCTCACAACTAGAAC 58.568 50.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 99 3.055719 CCGCCGTCCATGCAAGTT 61.056 61.111 0.00 0.00 0.00 2.66
448 452 3.049674 CGCCGGTGTCACTGCATT 61.050 61.111 6.91 0.00 0.00 3.56
636 640 2.512515 GCTGCGCTCTCCGGAAAT 60.513 61.111 9.73 0.00 36.65 2.17
713 722 3.057736 CACATCAAGCCCAAAGACAGAAG 60.058 47.826 0.00 0.00 0.00 2.85
745 754 2.676632 TTGTACACACCGTGACACTT 57.323 45.000 5.28 0.00 36.96 3.16
748 758 2.605837 ACATTGTACACACCGTGACA 57.394 45.000 5.28 0.00 36.96 3.58
752 762 3.252215 CCAATCAACATTGTACACACCGT 59.748 43.478 0.00 0.00 38.22 4.83
755 765 4.444056 GCAACCAATCAACATTGTACACAC 59.556 41.667 0.00 0.00 38.22 3.82
770 780 6.018343 CCGTTTTGTATTTCAAAGCAACCAAT 60.018 34.615 7.61 0.00 45.14 3.16
1581 1630 2.637383 GGAGACGTTGGGCTCGACT 61.637 63.158 1.61 0.00 36.27 4.18
2036 2085 2.052104 TCTTCCTCGATCAGCCGCA 61.052 57.895 0.00 0.00 0.00 5.69
2112 2161 2.164332 TACAGTCCTCGAAGGGGGCT 62.164 60.000 0.00 0.00 39.67 5.19
2346 2408 7.665145 TCATTCAATCAGTAATGAACACTTCCA 59.335 33.333 0.00 0.00 38.74 3.53
2371 2433 6.655003 TCTCAGAGTTTTACACCAAATCCATC 59.345 38.462 0.00 0.00 0.00 3.51
2399 2463 1.992557 AGACAGAACCAAAGGGGCATA 59.007 47.619 0.00 0.00 42.05 3.14
2403 2469 2.362077 CAACAAGACAGAACCAAAGGGG 59.638 50.000 0.00 0.00 44.81 4.79
2405 2471 4.292977 GTCAACAAGACAGAACCAAAGG 57.707 45.455 0.00 0.00 46.77 3.11
2424 2490 1.134699 TGGCGATGTCCATCTTCTGTC 60.135 52.381 5.79 0.00 35.72 3.51
2435 2501 2.413765 GCATATGCAAGATGGCGATGTC 60.414 50.000 22.84 0.00 41.59 3.06
2481 2558 4.321156 GCACAATAAGAATTGACCACTGCA 60.321 41.667 5.18 0.00 44.50 4.41
2505 2582 3.118592 AGGGCTAACAGCAACTCAGATAC 60.119 47.826 0.00 0.00 44.75 2.24
2549 2626 9.298250 CAGCTACTCCTATCTAGGTTTAATACA 57.702 37.037 3.25 0.00 44.02 2.29
2550 2627 8.741841 CCAGCTACTCCTATCTAGGTTTAATAC 58.258 40.741 3.25 0.00 44.02 1.89
2551 2628 7.396623 GCCAGCTACTCCTATCTAGGTTTAATA 59.603 40.741 3.25 0.00 44.02 0.98
2562 2639 2.962421 ACTGAAGCCAGCTACTCCTATC 59.038 50.000 0.00 0.00 44.16 2.08
2890 3122 3.755378 CACTAGACAAAATGCAGCCTCTT 59.245 43.478 0.00 0.00 0.00 2.85
2907 3139 7.856145 ATCCAACTTAAGAAGCAATCACTAG 57.144 36.000 10.09 0.00 0.00 2.57
3032 3315 4.019231 GGTCTTCAGTTCAGAGGGGTAAAT 60.019 45.833 0.00 0.00 0.00 1.40
3049 3332 7.148289 CGAAGGGTTATAAAAAGAAGGGTCTTC 60.148 40.741 0.00 0.00 43.59 2.87
3050 3333 6.657966 CGAAGGGTTATAAAAAGAAGGGTCTT 59.342 38.462 0.00 0.00 46.47 3.01
3051 3334 6.178324 CGAAGGGTTATAAAAAGAAGGGTCT 58.822 40.000 0.00 0.00 34.72 3.85
3052 3335 5.942236 ACGAAGGGTTATAAAAAGAAGGGTC 59.058 40.000 0.00 0.00 0.00 4.46
3054 3337 5.356190 GGACGAAGGGTTATAAAAAGAAGGG 59.644 44.000 0.00 0.00 0.00 3.95
3055 3338 6.178324 AGGACGAAGGGTTATAAAAAGAAGG 58.822 40.000 0.00 0.00 0.00 3.46
3056 3339 7.683437 AAGGACGAAGGGTTATAAAAAGAAG 57.317 36.000 0.00 0.00 0.00 2.85
3057 3340 9.743581 AATAAGGACGAAGGGTTATAAAAAGAA 57.256 29.630 0.00 0.00 0.00 2.52
3058 3341 9.743581 AAATAAGGACGAAGGGTTATAAAAAGA 57.256 29.630 0.00 0.00 0.00 2.52
3059 3342 9.783256 CAAATAAGGACGAAGGGTTATAAAAAG 57.217 33.333 0.00 0.00 0.00 2.27
3060 3343 8.741841 CCAAATAAGGACGAAGGGTTATAAAAA 58.258 33.333 0.00 0.00 0.00 1.94
3061 3344 7.148035 GCCAAATAAGGACGAAGGGTTATAAAA 60.148 37.037 0.00 0.00 0.00 1.52
3062 3345 6.319405 GCCAAATAAGGACGAAGGGTTATAAA 59.681 38.462 0.00 0.00 0.00 1.40
3063 3346 5.824097 GCCAAATAAGGACGAAGGGTTATAA 59.176 40.000 0.00 0.00 0.00 0.98
3064 3347 5.370679 GCCAAATAAGGACGAAGGGTTATA 58.629 41.667 0.00 0.00 0.00 0.98
3065 3348 4.204799 GCCAAATAAGGACGAAGGGTTAT 58.795 43.478 0.00 0.00 0.00 1.89
3066 3349 3.613030 GCCAAATAAGGACGAAGGGTTA 58.387 45.455 0.00 0.00 0.00 2.85
3075 3358 2.559231 TCAAAACCGGCCAAATAAGGAC 59.441 45.455 0.00 0.00 0.00 3.85
3124 3422 2.779755 TATGCGATGTGGAACCACTT 57.220 45.000 21.98 16.75 46.30 3.16
3131 3429 3.476552 GGGAGAAAATATGCGATGTGGA 58.523 45.455 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.