Multiple sequence alignment - TraesCS4D01G160100

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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 TraesCS4D01G160100 chr4D 100.000 3964 0 0 1 3964 234398954 234394991 0.000000e+00 7321.0
1 TraesCS4D01G160100 chr4D 96.847 3774 85 10 29 3795 297889495 297893241 0.000000e+00 6279.0
2 TraesCS4D01G160100 chr4D 100.000 52 0 0 1 52 21719709 21719760 3.260000e-16 97.1
3 TraesCS4D01G160100 chr4D 100.000 52 0 0 1 52 21730997 21730946 3.260000e-16 97.1
4 TraesCS4D01G160100 chr5D 95.993 3943 128 16 29 3964 340330830 340326911 0.000000e+00 6379.0
5 TraesCS4D01G160100 chr5D 92.775 346 25 0 3619 3964 340327086 340326741 5.910000e-138 501.0
6 TraesCS4D01G160100 chr1D 95.771 3949 127 18 29 3964 467310688 467306767 0.000000e+00 6331.0
7 TraesCS4D01G160100 chr1D 96.718 3595 90 10 46 3622 398922847 398926431 0.000000e+00 5960.0
8 TraesCS4D01G160100 chr1D 93.582 3350 138 43 29 3345 400135017 400131712 0.000000e+00 4924.0
9 TraesCS4D01G160100 chr1D 94.690 452 14 3 2953 3395 74541014 74540564 0.000000e+00 693.0
10 TraesCS4D01G160100 chr1D 100.000 52 0 0 1 52 14519730 14519781 3.260000e-16 97.1
11 TraesCS4D01G160100 chr6D 95.810 3938 111 22 46 3964 51478124 51482026 0.000000e+00 6309.0
12 TraesCS4D01G160100 chr6D 96.114 3860 106 12 49 3889 237094042 237090208 0.000000e+00 6257.0
13 TraesCS4D01G160100 chr6D 96.153 3847 106 15 139 3964 293098500 293102325 0.000000e+00 6246.0
14 TraesCS4D01G160100 chr6D 96.431 3362 90 9 1 3345 139921965 139925313 0.000000e+00 5517.0
15 TraesCS4D01G160100 chr6D 93.656 331 21 0 3619 3949 139926371 139926701 2.750000e-136 496.0
16 TraesCS4D01G160100 chr6D 92.219 347 25 2 3619 3964 340206307 340205962 1.280000e-134 490.0
17 TraesCS4D01G160100 chr6D 100.000 52 0 0 1 52 51478043 51478094 3.260000e-16 97.1
18 TraesCS4D01G160100 chr6D 100.000 52 0 0 1 52 237094126 237094075 3.260000e-16 97.1
19 TraesCS4D01G160100 chr6D 100.000 52 0 0 1 52 256712856 256712907 3.260000e-16 97.1
20 TraesCS4D01G160100 chr6D 100.000 52 0 0 1 52 365439512 365439461 3.260000e-16 97.1
21 TraesCS4D01G160100 chr2D 95.753 3932 111 20 52 3962 532015444 532011548 0.000000e+00 6285.0
22 TraesCS4D01G160100 chr2D 93.623 345 20 2 3619 3962 532011401 532011058 7.600000e-142 514.0
23 TraesCS4D01G160100 chr3D 96.637 3776 85 8 29 3786 8677097 8680848 0.000000e+00 6231.0
24 TraesCS4D01G160100 chr3D 96.506 3320 100 8 29 3345 382997624 382994318 0.000000e+00 5474.0
25 TraesCS4D01G160100 chr3D 96.865 3254 77 11 1 3240 82111787 82115029 0.000000e+00 5421.0
26 TraesCS4D01G160100 chr7D 96.512 3612 91 10 29 3622 106887250 106890844 0.000000e+00 5939.0
27 TraesCS4D01G160100 chr7D 96.462 3250 96 6 28 3258 119047288 119044039 0.000000e+00 5347.0
28 TraesCS4D01G160100 chr7D 89.425 643 47 12 3322 3964 174998735 174998114 0.000000e+00 791.0


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 TraesCS4D01G160100 chr4D 234394991 234398954 3963 True 7321.00 7321 100.0000 1 3964 1 chr4D.!!$R2 3963
1 TraesCS4D01G160100 chr4D 297889495 297893241 3746 False 6279.00 6279 96.8470 29 3795 1 chr4D.!!$F2 3766
2 TraesCS4D01G160100 chr5D 340326741 340330830 4089 True 3440.00 6379 94.3840 29 3964 2 chr5D.!!$R1 3935
3 TraesCS4D01G160100 chr1D 467306767 467310688 3921 True 6331.00 6331 95.7710 29 3964 1 chr1D.!!$R3 3935
4 TraesCS4D01G160100 chr1D 398922847 398926431 3584 False 5960.00 5960 96.7180 46 3622 1 chr1D.!!$F2 3576
5 TraesCS4D01G160100 chr1D 400131712 400135017 3305 True 4924.00 4924 93.5820 29 3345 1 chr1D.!!$R2 3316
6 TraesCS4D01G160100 chr6D 293098500 293102325 3825 False 6246.00 6246 96.1530 139 3964 1 chr6D.!!$F2 3825
7 TraesCS4D01G160100 chr6D 51478043 51482026 3983 False 3203.05 6309 97.9050 1 3964 2 chr6D.!!$F3 3963
8 TraesCS4D01G160100 chr6D 237090208 237094126 3918 True 3177.05 6257 98.0570 1 3889 2 chr6D.!!$R3 3888
9 TraesCS4D01G160100 chr6D 139921965 139926701 4736 False 3006.50 5517 95.0435 1 3949 2 chr6D.!!$F4 3948
10 TraesCS4D01G160100 chr2D 532011058 532015444 4386 True 3399.50 6285 94.6880 52 3962 2 chr2D.!!$R1 3910
11 TraesCS4D01G160100 chr3D 8677097 8680848 3751 False 6231.00 6231 96.6370 29 3786 1 chr3D.!!$F1 3757
12 TraesCS4D01G160100 chr3D 382994318 382997624 3306 True 5474.00 5474 96.5060 29 3345 1 chr3D.!!$R1 3316
13 TraesCS4D01G160100 chr3D 82111787 82115029 3242 False 5421.00 5421 96.8650 1 3240 1 chr3D.!!$F2 3239
14 TraesCS4D01G160100 chr7D 106887250 106890844 3594 False 5939.00 5939 96.5120 29 3622 1 chr7D.!!$F1 3593
15 TraesCS4D01G160100 chr7D 119044039 119047288 3249 True 5347.00 5347 96.4620 28 3258 1 chr7D.!!$R1 3230
16 TraesCS4D01G160100 chr7D 174998114 174998735 621 True 791.00 791 89.4250 3322 3964 1 chr7D.!!$R2 642

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
877 953 0.106149 CACCGTATGTAAGGGAGGCC 59.894 60.0 0.0 0.0 36.57 5.19 F
2103 2183 0.026803 GACGGTTTCGATGATGCTGC 59.973 55.0 0.0 0.0 40.11 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2413 2493 0.251354 TCATCACTGGAGCTGAAGGC 59.749 55.0 0.0 0.00 42.19 4.35 R
3750 4176 0.249489 CTGTATAGTGTGGCGCCTCC 60.249 60.0 29.7 18.65 0.00 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
877 953 0.106149 CACCGTATGTAAGGGAGGCC 59.894 60.000 0.00 0.00 36.57 5.19
929 1006 2.258013 CGACGCCACCCAACAATGT 61.258 57.895 0.00 0.00 0.00 2.71
1224 1303 1.001633 TCGAACTTCAGTACTTGCCCC 59.998 52.381 0.00 0.00 0.00 5.80
1360 1439 1.683790 GGCGTTGACCGTCTTCGATG 61.684 60.000 15.95 0.00 38.41 3.84
1422 1501 6.932400 TGTATCGACAGGTATGAAGTTGTTTT 59.068 34.615 0.00 0.00 0.00 2.43
1595 1674 0.170561 CGATTGGACGACCGAAGACT 59.829 55.000 0.00 0.00 39.42 3.24
1629 1708 0.748450 TTGGGACGACAAAGACGACT 59.252 50.000 0.00 0.00 34.70 4.18
1811 1890 9.669353 GTAACTCGATATCAATTTTGCATTCAT 57.331 29.630 3.12 0.00 0.00 2.57
1887 1966 3.964031 ACCCTATAGAGTTCAGGCTGAAG 59.036 47.826 29.22 15.70 37.00 3.02
1928 2007 1.674221 GGATCTCTGGCATATGCGGTC 60.674 57.143 21.04 12.53 43.26 4.79
1934 2013 2.594592 GCATATGCGGTCCCCACC 60.595 66.667 12.82 0.00 39.69 4.61
1995 2075 1.677052 GTGTTCCGCCAGTTTGGTTTA 59.323 47.619 0.00 0.00 40.46 2.01
2011 2091 0.402504 TTTATTCCAGCCACACCCGT 59.597 50.000 0.00 0.00 0.00 5.28
2103 2183 0.026803 GACGGTTTCGATGATGCTGC 59.973 55.000 0.00 0.00 40.11 5.25
2128 2208 5.751243 TTCTGTTTCTAACTTGCAGGTTC 57.249 39.130 18.41 3.95 0.00 3.62
2217 2297 3.141398 CTCTTAGTGTGGAGCAAGCAAA 58.859 45.455 0.00 0.00 0.00 3.68
2448 2528 3.821033 GTGATGAACTTTGTGGTTAGCCT 59.179 43.478 0.00 0.00 35.27 4.58
2459 2540 4.837972 TGTGGTTAGCCTTTTTGCTTTTT 58.162 34.783 0.00 0.00 42.75 1.94
2683 2764 3.425359 CGTTCCATGTCTCATTCACTTGC 60.425 47.826 0.00 0.00 0.00 4.01
2716 2801 2.009681 CCAGGGCCAAAAGTTAAGGT 57.990 50.000 6.18 0.00 0.00 3.50
2728 2813 6.015434 CCAAAAGTTAAGGTGGCTATCAAACT 60.015 38.462 0.00 0.00 0.00 2.66
2762 2847 2.957006 GTGACCCCGAGTATGTATCACT 59.043 50.000 0.00 0.00 33.74 3.41
2767 2852 5.642165 ACCCCGAGTATGTATCACTAGAAT 58.358 41.667 0.00 0.00 0.00 2.40
2951 3039 7.879677 CCATATCTTCTGTTGATGCATAGGTTA 59.120 37.037 0.00 0.00 0.00 2.85
2969 3057 4.649674 AGGTTACTGATGATATGACCGTGT 59.350 41.667 0.00 0.00 0.00 4.49
3031 3119 3.435671 GGAAGGGAATCAACAAGTACACG 59.564 47.826 0.00 0.00 0.00 4.49
3336 3591 2.971660 TGTCGTTGAACTTGGAGTGA 57.028 45.000 0.00 0.00 0.00 3.41
3352 3607 7.173562 ACTTGGAGTGATCGTAGCTATTAGTAG 59.826 40.741 0.00 0.00 0.00 2.57
3613 4039 2.912986 CAAGGCGTTGCACTGTAGA 58.087 52.632 6.16 0.00 0.00 2.59
3614 4040 0.792640 CAAGGCGTTGCACTGTAGAG 59.207 55.000 6.16 0.00 0.00 2.43
3615 4041 0.393077 AAGGCGTTGCACTGTAGAGT 59.607 50.000 0.00 0.00 0.00 3.24
3718 4144 2.761208 GCCTACCTTCTGTTGCTCTCTA 59.239 50.000 0.00 0.00 0.00 2.43
3764 4190 3.449227 CTCGGAGGCGCCACACTA 61.449 66.667 31.54 10.49 35.94 2.74
3767 4193 1.299926 CGGAGGCGCCACACTATAC 60.300 63.158 31.54 6.17 35.94 1.47
3780 4920 3.159353 CACTATACAGTGCAACGCCTA 57.841 47.619 0.00 0.00 45.44 3.93
3805 4945 0.804989 AAGGCGTTGCATTGTAGAGC 59.195 50.000 0.00 0.00 29.25 4.09
3810 4950 1.156736 GTTGCATTGTAGAGCGTGGT 58.843 50.000 0.00 0.00 0.00 4.16
3841 4981 1.945662 GGCGCTGCACAAACACTTG 60.946 57.895 7.64 0.00 38.61 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
504 579 7.037438 TCCAAAGCATTTTTCTCAATATGAGC 58.963 34.615 2.48 0.00 39.46 4.26
877 953 3.412386 ACTGAATGAAAGGGAAAGTCCG 58.588 45.455 0.00 0.00 37.43 4.79
1224 1303 3.324117 CATGTCCTCATTAGCATCCTCG 58.676 50.000 0.00 0.00 31.15 4.63
1314 1393 3.824133 CCACATCCATGGAGCATTCTTA 58.176 45.455 21.33 0.00 43.02 2.10
1360 1439 0.608130 GAACCCCAACTCCATTTGCC 59.392 55.000 0.00 0.00 0.00 4.52
1578 1657 0.966920 ACAGTCTTCGGTCGTCCAAT 59.033 50.000 0.00 0.00 0.00 3.16
1595 1674 2.232941 GTCCCAATCCTCGTACTTCACA 59.767 50.000 0.00 0.00 0.00 3.58
1629 1708 1.229082 AAGTGGGGAGCCGTAGTGA 60.229 57.895 0.00 0.00 0.00 3.41
1811 1890 2.094100 TTCCACCTGCAAAATGGGAA 57.906 45.000 9.94 5.95 34.03 3.97
1887 1966 0.679505 TATCCCTAGTGCACATCGGC 59.320 55.000 21.04 0.00 0.00 5.54
1928 2007 0.819259 CCAGTTGCATATCGGTGGGG 60.819 60.000 0.00 0.00 0.00 4.96
1934 2013 1.095228 AACCGCCCAGTTGCATATCG 61.095 55.000 0.00 0.00 0.00 2.92
1995 2075 2.351276 GACGGGTGTGGCTGGAAT 59.649 61.111 0.00 0.00 0.00 3.01
2011 2091 2.675423 CGTGTCCTCCCACTCCGA 60.675 66.667 0.00 0.00 33.07 4.55
2102 2182 5.412904 ACCTGCAAGTTAGAAACAGAATAGC 59.587 40.000 0.00 0.00 0.00 2.97
2103 2183 7.440523 AACCTGCAAGTTAGAAACAGAATAG 57.559 36.000 0.00 0.00 0.00 1.73
2128 2208 3.682858 TCTTCCGTTGCTTTTTCCTATCG 59.317 43.478 0.00 0.00 0.00 2.92
2413 2493 0.251354 TCATCACTGGAGCTGAAGGC 59.749 55.000 0.00 0.00 42.19 4.35
2448 2528 7.223582 TGAATAGTGCGAATGAAAAAGCAAAAA 59.776 29.630 0.00 0.00 41.56 1.94
2459 2540 4.504097 CGAAGATGTGAATAGTGCGAATGA 59.496 41.667 0.00 0.00 0.00 2.57
2683 2764 2.126618 CTGGCGCTGCAACATGTG 60.127 61.111 7.64 0.00 0.00 3.21
2716 2801 4.339814 ACAACCGAAAAAGTTTGATAGCCA 59.660 37.500 0.00 0.00 0.00 4.75
2728 2813 1.015868 GGGTCACGACAACCGAAAAA 58.984 50.000 0.00 0.00 41.76 1.94
2762 2847 1.134007 TCGCCGACCTAGACCATTCTA 60.134 52.381 0.00 0.00 32.75 2.10
2767 2852 2.034532 TGTCGCCGACCTAGACCA 59.965 61.111 15.60 0.00 34.24 4.02
2815 2901 3.107601 TCCTCATCCTCGAAAGGTTCAT 58.892 45.455 0.00 0.00 43.82 2.57
2897 2985 4.583489 ACCGTGTGTGAGGATATAGTTAGG 59.417 45.833 0.00 0.00 0.00 2.69
2951 3039 3.031013 TCCACACGGTCATATCATCAGT 58.969 45.455 0.00 0.00 0.00 3.41
2969 3057 3.066190 CCGAGCCTGGTACGTCCA 61.066 66.667 0.00 0.00 45.01 4.02
3031 3119 1.882623 CTTTGGGTGAAGTCTTCAGGC 59.117 52.381 15.71 5.17 41.01 4.85
3165 3300 3.794028 CCTCTTGACGCTTATCTTCTTCG 59.206 47.826 0.00 0.00 0.00 3.79
3336 3591 7.762588 ATTCCACACTACTAATAGCTACGAT 57.237 36.000 0.00 0.00 30.75 3.73
3352 3607 3.569250 ACGGCATAACAAATTCCACAC 57.431 42.857 0.00 0.00 0.00 3.82
3369 3624 0.944386 CACCACTCCAAGTTCAACGG 59.056 55.000 0.00 0.00 0.00 4.44
3444 3699 4.473196 AGGTTCAAAAAGGGTTCACCAAAT 59.527 37.500 0.00 0.00 43.89 2.32
3612 4038 0.878523 TACAGTGCAACGCCACACTC 60.879 55.000 2.15 0.00 45.15 3.51
3614 4040 0.878523 TCTACAGTGCAACGCCACAC 60.879 55.000 0.00 0.00 45.86 3.82
3615 4041 0.599991 CTCTACAGTGCAACGCCACA 60.600 55.000 0.00 0.00 45.86 4.17
3616 4042 0.600255 ACTCTACAGTGCAACGCCAC 60.600 55.000 0.00 0.00 45.86 5.01
3617 4043 0.599991 CACTCTACAGTGCAACGCCA 60.600 55.000 0.00 0.00 43.77 5.69
3718 4144 3.430098 GCTGCACAAGTCTGTAGCTATCT 60.430 47.826 0.00 0.00 44.12 1.98
3750 4176 0.249489 CTGTATAGTGTGGCGCCTCC 60.249 60.000 29.70 18.65 0.00 4.30
3764 4190 0.462047 GGCTAGGCGTTGCACTGTAT 60.462 55.000 14.42 0.00 0.00 2.29
3767 4193 3.490759 CGGCTAGGCGTTGCACTG 61.491 66.667 28.87 0.00 0.00 3.66
3786 4926 0.804989 GCTCTACAATGCAACGCCTT 59.195 50.000 0.00 0.00 0.00 4.35
3797 4937 1.292223 GAGGCACCACGCTCTACAA 59.708 57.895 0.00 0.00 41.91 2.41
3841 4981 1.265635 GTTTGGGGCAAAAATTTCGCC 59.734 47.619 18.84 18.84 45.47 5.54


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

AutoCloner maintained by Alex Coulton.