Multiple sequence alignment - TraesCS6D01G250400

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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 TraesCS6D01G250400 chr6D 100.000 2794 0 0 1 2794 353652073 353649280 0.000000e+00 5160
1 TraesCS6D01G250400 chr6B 93.750 1952 66 23 21 1951 524962107 524964023 0.000000e+00 2878
2 TraesCS6D01G250400 chr6B 93.535 495 9 6 2008 2487 524964027 524964513 0.000000e+00 715
3 TraesCS6D01G250400 chr6B 91.667 276 8 6 2521 2794 524964512 524964774 4.400000e-98 368
4 TraesCS6D01G250400 chr6A 88.867 2021 76 34 703 2639 488604778 488606733 0.000000e+00 2348
5 TraesCS6D01G250400 chr6A 84.068 703 36 30 1 682 488603886 488604533 2.380000e-170 608


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 TraesCS6D01G250400 chr6D 353649280 353652073 2793 True 5160.000000 5160 100.0000 1 2794 1 chr6D.!!$R1 2793
1 TraesCS6D01G250400 chr6B 524962107 524964774 2667 False 1320.333333 2878 92.9840 21 2794 3 chr6B.!!$F1 2773
2 TraesCS6D01G250400 chr6A 488603886 488606733 2847 False 1478.000000 2348 86.4675 1 2639 2 chr6A.!!$F1 2638

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
827 1086 0.957395 CACAAGATCCCGCAGCAACT 60.957 55.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1977 2288 0.169672 CAAGGATGCAAGGCAACGAG 59.83 55.0 0.0 0.0 43.62 4.18 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 95 6.253942 GCACTCCTCGTACTAATCTCTTTTTC 59.746 42.308 0.00 0.00 0.00 2.29
100 115 8.896722 TCTCTTTTTCTAGGGAATACAGTAGT 57.103 34.615 0.00 0.00 0.00 2.73
106 121 9.765295 TTTTCTAGGGAATACAGTAGTAAGAGT 57.235 33.333 0.00 0.00 33.13 3.24
107 122 9.765295 TTTCTAGGGAATACAGTAGTAAGAGTT 57.235 33.333 0.00 0.00 33.13 3.01
109 124 9.844257 TCTAGGGAATACAGTAGTAAGAGTTAC 57.156 37.037 0.00 0.00 33.13 2.50
112 127 9.850198 AGGGAATACAGTAGTAAGAGTTACTAG 57.150 37.037 6.77 0.00 46.29 2.57
412 435 1.709147 ATCTGCGAGATTGCAACCGC 61.709 55.000 25.91 25.91 45.74 5.68
665 696 2.464459 GCCGTTGCTCAGAATCGGG 61.464 63.158 4.21 0.00 41.24 5.14
676 707 2.239654 TCAGAATCGGGCTGGAGATTTT 59.760 45.455 0.00 0.00 37.23 1.82
679 710 3.054065 AGAATCGGGCTGGAGATTTTTCT 60.054 43.478 0.00 0.00 37.23 2.52
691 722 6.248433 TGGAGATTTTTCTAGCCAGATTTGT 58.752 36.000 0.00 0.00 0.00 2.83
711 967 7.658179 TTTGTGCTACAAACAAAACAAATCA 57.342 28.000 9.46 0.00 42.55 2.57
740 996 4.580167 TGTTTCTTTGCTCAGTTGTATGCT 59.420 37.500 0.00 0.00 0.00 3.79
742 998 3.338249 TCTTTGCTCAGTTGTATGCTCC 58.662 45.455 0.00 0.00 0.00 4.70
821 1080 3.545124 AACCGCACAAGATCCCGCA 62.545 57.895 0.00 0.00 0.00 5.69
827 1086 0.957395 CACAAGATCCCGCAGCAACT 60.957 55.000 0.00 0.00 0.00 3.16
845 1104 1.229368 TACTGCCCAGCTGTACCCA 60.229 57.895 13.81 2.99 40.85 4.51
883 1142 2.476051 CGCAAGCTACGTGCCTTG 59.524 61.111 19.59 19.59 44.23 3.61
1209 1502 4.711949 CTCTGCCCCAACTGCGCT 62.712 66.667 9.73 0.00 0.00 5.92
1688 1997 1.541588 CTGTTGCTTTTAGGAGGTGGC 59.458 52.381 0.00 0.00 0.00 5.01
1693 2002 4.689612 TGCTTTTAGGAGGTGGCTATAG 57.310 45.455 0.00 0.00 0.00 1.31
1806 2116 1.080569 CCTGTGATTTGGGCGCAAC 60.081 57.895 16.70 6.01 0.00 4.17
1849 2159 1.373570 CGTCATTTCCTCCCTGCTTC 58.626 55.000 0.00 0.00 0.00 3.86
1962 2273 3.127721 GCTACTTTCTTTCCAGCACCATC 59.872 47.826 0.00 0.00 32.46 3.51
2060 2372 5.189736 TCCTAGGCATGTGAGACAGTTAAAT 59.810 40.000 2.96 0.00 0.00 1.40
2110 2443 2.540101 GCACCACTATCATTAGCGTGTC 59.460 50.000 0.00 0.00 34.10 3.67
2155 2488 1.514678 GGCGGTGTGTTCATTGCTCA 61.515 55.000 0.00 0.00 0.00 4.26
2203 2536 0.337428 TGGAGTGGGGGTACTAGGTC 59.663 60.000 0.00 0.00 0.00 3.85
2204 2537 0.635555 GGAGTGGGGGTACTAGGTCT 59.364 60.000 0.00 0.00 0.00 3.85
2205 2538 1.855599 GGAGTGGGGGTACTAGGTCTA 59.144 57.143 0.00 0.00 0.00 2.59
2206 2539 2.158490 GGAGTGGGGGTACTAGGTCTAG 60.158 59.091 3.65 3.65 39.04 2.43
2207 2540 1.858246 AGTGGGGGTACTAGGTCTAGG 59.142 57.143 9.51 0.00 37.49 3.02
2208 2541 1.572895 GTGGGGGTACTAGGTCTAGGT 59.427 57.143 9.51 0.00 37.49 3.08
2257 2590 1.067416 TGTCGTGCACACTGGTCTC 59.933 57.895 18.64 0.00 0.00 3.36
2415 2751 2.873472 CTCTACTACCTGGTCTAGTGCG 59.127 54.545 0.63 0.00 0.00 5.34
2494 2830 4.364318 GCAGTGAGCTCTCCCCTA 57.636 61.111 16.19 0.00 41.15 3.53
2495 2831 1.819905 GCAGTGAGCTCTCCCCTAC 59.180 63.158 16.19 3.20 41.15 3.18
2496 2832 1.681486 GCAGTGAGCTCTCCCCTACC 61.681 65.000 16.19 0.00 41.15 3.18
2646 2982 3.313803 GGAATCTTTCGGAGAAGATTGCC 59.686 47.826 21.75 18.74 45.90 4.52
2649 2985 2.093447 TCTTTCGGAGAAGATTGCCCTC 60.093 50.000 0.00 0.00 45.90 4.30
2653 2991 0.472044 GGAGAAGATTGCCCTCTCCC 59.528 60.000 6.13 0.00 40.65 4.30
2658 2996 0.543749 AGATTGCCCTCTCCCGAAAG 59.456 55.000 0.00 0.00 0.00 2.62
2672 3010 2.527442 CGAAAGGAAAATGTCTCGCC 57.473 50.000 0.00 0.00 0.00 5.54
2680 3018 0.603569 AAATGTCTCGCCTCGTCACT 59.396 50.000 0.00 0.00 0.00 3.41
2686 3024 1.206610 TCTCGCCTCGTCACTACTACT 59.793 52.381 0.00 0.00 0.00 2.57
2687 3025 2.428530 TCTCGCCTCGTCACTACTACTA 59.571 50.000 0.00 0.00 0.00 1.82
2688 3026 2.796031 CTCGCCTCGTCACTACTACTAG 59.204 54.545 0.00 0.00 0.00 2.57
2689 3027 2.167281 TCGCCTCGTCACTACTACTAGT 59.833 50.000 0.00 0.00 33.01 2.57
2690 3028 3.381590 TCGCCTCGTCACTACTACTAGTA 59.618 47.826 1.89 1.89 31.46 1.82
2774 3112 7.952671 TGCTGTAGAGATAAAATGTAGTAGGG 58.047 38.462 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 1.000506 AGTCGGTCTTGTGCAATACGT 59.999 47.619 0.00 0.00 0.00 3.57
16 17 1.710013 AGTCGGTCTTGTGCAATACG 58.290 50.000 0.00 0.00 0.00 3.06
17 18 3.846360 AGTAGTCGGTCTTGTGCAATAC 58.154 45.455 0.00 0.00 0.00 1.89
18 19 4.460034 TGTAGTAGTCGGTCTTGTGCAATA 59.540 41.667 0.00 0.00 0.00 1.90
84 95 9.850198 AGTAACTCTTACTACTGTATTCCCTAG 57.150 37.037 0.00 0.00 44.30 3.02
177 193 3.242518 GCAAAGTCAAAACGATTAGGCC 58.757 45.455 0.00 0.00 0.00 5.19
248 265 2.174969 GTGTGGTTGACGAACGGCA 61.175 57.895 0.00 0.00 32.28 5.69
311 328 0.882474 ACTGACTGACTGACTACGGC 59.118 55.000 0.00 0.00 0.00 5.68
469 500 9.354673 TGTTCCTTTATTTCTCTCAATGAGTTT 57.645 29.630 10.36 0.00 43.13 2.66
470 501 8.924511 TGTTCCTTTATTTCTCTCAATGAGTT 57.075 30.769 10.36 0.00 43.13 3.01
471 502 7.120432 GCTGTTCCTTTATTTCTCTCAATGAGT 59.880 37.037 10.36 0.00 43.13 3.41
472 503 7.414984 GGCTGTTCCTTTATTTCTCTCAATGAG 60.415 40.741 3.38 3.38 43.96 2.90
473 504 6.375455 GGCTGTTCCTTTATTTCTCTCAATGA 59.625 38.462 0.00 0.00 0.00 2.57
474 505 6.558909 GGCTGTTCCTTTATTTCTCTCAATG 58.441 40.000 0.00 0.00 0.00 2.82
477 508 4.253685 CGGCTGTTCCTTTATTTCTCTCA 58.746 43.478 0.00 0.00 0.00 3.27
665 696 3.878778 TCTGGCTAGAAAAATCTCCAGC 58.121 45.455 0.00 1.69 40.51 4.85
676 707 4.551702 TGTAGCACAAATCTGGCTAGAA 57.448 40.909 3.02 0.00 40.50 2.10
691 722 6.255453 GCTTCTGATTTGTTTTGTTTGTAGCA 59.745 34.615 0.00 0.00 0.00 3.49
700 731 7.529880 AAGAAACAGCTTCTGATTTGTTTTG 57.470 32.000 12.70 0.00 44.00 2.44
711 967 3.549794 ACTGAGCAAAGAAACAGCTTCT 58.450 40.909 0.00 0.00 46.92 2.85
740 996 2.225382 TCATTCAGGACGTGTAGGGA 57.775 50.000 0.00 0.00 0.00 4.20
742 998 2.205074 GCATCATTCAGGACGTGTAGG 58.795 52.381 0.00 0.00 0.00 3.18
771 1029 0.179108 CTGTAGCCTAGAACCACCGC 60.179 60.000 0.00 0.00 0.00 5.68
827 1086 0.838554 TTGGGTACAGCTGGGCAGTA 60.839 55.000 19.93 0.00 29.63 2.74
845 1104 2.365582 GTTATTCACGAGGGTGCCATT 58.634 47.619 0.00 0.00 44.03 3.16
883 1142 1.572941 GTTTTTCGGGCACGGAGAC 59.427 57.895 9.32 0.00 39.30 3.36
925 1184 6.183360 GGAGTGTGTAATAAAGGAGGCAATTC 60.183 42.308 0.00 0.00 0.00 2.17
926 1185 5.652452 GGAGTGTGTAATAAAGGAGGCAATT 59.348 40.000 0.00 0.00 0.00 2.32
927 1186 5.193679 GGAGTGTGTAATAAAGGAGGCAAT 58.806 41.667 0.00 0.00 0.00 3.56
928 1187 4.585879 GGAGTGTGTAATAAAGGAGGCAA 58.414 43.478 0.00 0.00 0.00 4.52
1014 1273 3.657835 CTCGCGCTTCTTGGCAAGC 62.658 63.158 22.31 11.01 44.67 4.01
1245 1538 2.835895 GCCGAGGAGGAGGAGGAC 60.836 72.222 0.00 0.00 45.00 3.85
1458 1763 1.827789 CAGCCTCTCCTCCTCCTCG 60.828 68.421 0.00 0.00 0.00 4.63
1461 1766 2.445654 CCCAGCCTCTCCTCCTCC 60.446 72.222 0.00 0.00 0.00 4.30
1660 1965 5.486526 CTCCTAAAAGCAACAGACAGATCT 58.513 41.667 0.00 0.00 34.57 2.75
1806 2116 1.154205 CCAGAGGGTAATTGAGCGCG 61.154 60.000 0.00 0.00 0.00 6.86
1849 2159 0.179056 ACGACACCAAGGGACAACAG 60.179 55.000 0.00 0.00 0.00 3.16
1884 2194 2.097825 GATGGTACTACACGGTGGAGT 58.902 52.381 27.74 27.74 45.18 3.85
1962 2273 3.999769 CAACGAGATTGCAGATTCACAG 58.000 45.455 0.00 0.00 0.00 3.66
1977 2288 0.169672 CAAGGATGCAAGGCAACGAG 59.830 55.000 0.00 0.00 43.62 4.18
2039 2351 5.105513 TCGATTTAACTGTCTCACATGCCTA 60.106 40.000 0.00 0.00 0.00 3.93
2178 2511 2.408565 AGTACCCCCACTCCATACATG 58.591 52.381 0.00 0.00 0.00 3.21
2203 2536 2.606725 CCGTCACGTACTACTCACCTAG 59.393 54.545 0.00 0.00 0.00 3.02
2204 2537 2.621338 CCGTCACGTACTACTCACCTA 58.379 52.381 0.00 0.00 0.00 3.08
2205 2538 1.446907 CCGTCACGTACTACTCACCT 58.553 55.000 0.00 0.00 0.00 4.00
2206 2539 0.449388 CCCGTCACGTACTACTCACC 59.551 60.000 0.00 0.00 0.00 4.02
2207 2540 1.442769 TCCCGTCACGTACTACTCAC 58.557 55.000 0.00 0.00 0.00 3.51
2208 2541 2.408271 ATCCCGTCACGTACTACTCA 57.592 50.000 0.00 0.00 0.00 3.41
2257 2590 2.972505 ACCCAAAGCAGCACGACG 60.973 61.111 0.00 0.00 0.00 5.12
2489 2825 0.981943 AACGTGAAGAAGGGTAGGGG 59.018 55.000 0.00 0.00 0.00 4.79
2490 2826 1.346722 ACAACGTGAAGAAGGGTAGGG 59.653 52.381 0.00 0.00 0.00 3.53
2491 2827 2.413837 CACAACGTGAAGAAGGGTAGG 58.586 52.381 0.00 0.00 35.23 3.18
2492 2828 2.224209 ACCACAACGTGAAGAAGGGTAG 60.224 50.000 0.00 0.00 35.23 3.18
2493 2829 1.764134 ACCACAACGTGAAGAAGGGTA 59.236 47.619 0.00 0.00 35.23 3.69
2494 2830 0.544697 ACCACAACGTGAAGAAGGGT 59.455 50.000 0.00 0.00 35.23 4.34
2495 2831 1.202651 AGACCACAACGTGAAGAAGGG 60.203 52.381 0.00 0.00 35.23 3.95
2496 2832 2.240493 AGACCACAACGTGAAGAAGG 57.760 50.000 0.00 0.00 35.23 3.46
2646 2982 3.010420 GACATTTTCCTTTCGGGAGAGG 58.990 50.000 0.00 0.00 46.01 3.69
2649 2985 2.673368 CGAGACATTTTCCTTTCGGGAG 59.327 50.000 0.00 0.00 46.01 4.30
2653 2991 2.076863 AGGCGAGACATTTTCCTTTCG 58.923 47.619 0.00 0.00 0.00 3.46
2658 2996 1.000145 GACGAGGCGAGACATTTTCC 59.000 55.000 0.00 0.00 0.00 3.13
2672 3010 7.857389 CAGTACTCTACTAGTAGTAGTGACGAG 59.143 44.444 31.73 24.09 46.01 4.18
2686 3024 6.829298 AGCTCAAATACTGCAGTACTCTACTA 59.171 38.462 28.28 6.42 37.23 1.82
2687 3025 5.654650 AGCTCAAATACTGCAGTACTCTACT 59.345 40.000 28.28 17.62 40.28 2.57
2688 3026 5.746245 CAGCTCAAATACTGCAGTACTCTAC 59.254 44.000 28.28 15.80 32.72 2.59
2689 3027 5.419155 ACAGCTCAAATACTGCAGTACTCTA 59.581 40.000 28.28 8.88 37.42 2.43
2690 3028 4.221703 ACAGCTCAAATACTGCAGTACTCT 59.778 41.667 28.28 13.28 37.42 3.24
2691 3029 4.499183 ACAGCTCAAATACTGCAGTACTC 58.501 43.478 28.28 13.19 37.42 2.59
2692 3030 4.543590 ACAGCTCAAATACTGCAGTACT 57.456 40.909 28.28 16.07 37.42 2.73
2693 3031 4.690748 TGAACAGCTCAAATACTGCAGTAC 59.309 41.667 28.28 14.50 37.42 2.73
2694 3032 4.690748 GTGAACAGCTCAAATACTGCAGTA 59.309 41.667 27.91 27.91 37.42 2.74
2695 3033 3.499918 GTGAACAGCTCAAATACTGCAGT 59.500 43.478 25.12 25.12 37.42 4.40
2696 3034 3.120060 GGTGAACAGCTCAAATACTGCAG 60.120 47.826 13.48 13.48 37.42 4.41
2697 3035 2.813754 GGTGAACAGCTCAAATACTGCA 59.186 45.455 0.00 0.00 37.42 4.41
2698 3036 2.159653 CGGTGAACAGCTCAAATACTGC 60.160 50.000 2.70 0.00 37.42 4.40


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

AutoCloner maintained by Alex Coulton.