Multiple sequence alignment - TraesCS5D01G203700

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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 TraesCS5D01G203700 chr5D 100.000 2738 0 0 1 2738 308867307 308870044 0.000000e+00 5057
1 TraesCS5D01G203700 chr5D 91.736 2178 154 15 1 2166 333779236 333781399 0.000000e+00 3001
2 TraesCS5D01G203700 chr5D 95.304 575 25 2 2166 2738 20939194 20939768 0.000000e+00 911
3 TraesCS5D01G203700 chr5D 86.900 458 41 14 1 445 433788394 433788845 1.890000e-136 496
4 TraesCS5D01G203700 chr2D 96.869 2172 59 3 1 2163 511169420 511171591 0.000000e+00 3626
5 TraesCS5D01G203700 chr2D 96.644 2175 61 5 1 2166 59122339 59124510 0.000000e+00 3602
6 TraesCS5D01G203700 chr2D 96.324 2176 64 8 1 2166 28466029 28468198 0.000000e+00 3561
7 TraesCS5D01G203700 chr2D 95.986 573 22 1 2167 2738 352593442 352594014 0.000000e+00 929
8 TraesCS5D01G203700 chr2D 95.462 573 25 1 2167 2738 189709401 189708829 0.000000e+00 913
9 TraesCS5D01G203700 chr1D 96.737 2176 59 6 1 2166 355491156 355488983 0.000000e+00 3615
10 TraesCS5D01G203700 chr1D 92.209 2182 145 16 1 2166 393405097 393407269 0.000000e+00 3064
11 TraesCS5D01G203700 chr6D 96.184 2175 70 5 1 2166 345132976 345130806 0.000000e+00 3544
12 TraesCS5D01G203700 chr6D 92.674 2184 128 15 1 2166 284783665 284785834 0.000000e+00 3118
13 TraesCS5D01G203700 chr6D 91.987 911 30 14 1 893 263890405 263889520 0.000000e+00 1238
14 TraesCS5D01G203700 chr6D 95.812 573 22 2 2167 2738 53111734 53111163 0.000000e+00 924
15 TraesCS5D01G203700 chr6D 95.296 574 25 2 2166 2738 52415217 52415789 0.000000e+00 909
16 TraesCS5D01G203700 chr6D 85.714 651 47 32 3 631 379194456 379195082 0.000000e+00 645
17 TraesCS5D01G203700 chr7D 92.057 2178 149 13 1 2166 399528604 399530769 0.000000e+00 3042
18 TraesCS5D01G203700 chr7D 91.663 2195 149 26 1 2166 77997478 77995289 0.000000e+00 3009
19 TraesCS5D01G203700 chrUn 91.797 2182 153 13 1 2166 98422286 98420115 0.000000e+00 3014
20 TraesCS5D01G203700 chrUn 91.632 2187 151 22 1 2166 110605703 110603528 0.000000e+00 2996
21 TraesCS5D01G203700 chrUn 88.940 651 46 18 1 631 355803697 355803053 0.000000e+00 780
22 TraesCS5D01G203700 chr4D 83.104 2184 269 60 1 2166 170802274 170800173 0.000000e+00 1897
23 TraesCS5D01G203700 chr4D 95.819 574 21 3 2167 2738 423723947 423724519 0.000000e+00 924
24 TraesCS5D01G203700 chr4D 95.645 574 22 3 2167 2738 433443568 433444140 0.000000e+00 918
25 TraesCS5D01G203700 chr4D 95.637 573 24 1 2167 2738 502321440 502320868 0.000000e+00 918
26 TraesCS5D01G203700 chr4D 84.557 654 59 24 1 645 53667385 53668005 6.480000e-171 610
27 TraesCS5D01G203700 chr3D 95.312 576 25 1 2165 2738 477136630 477137205 0.000000e+00 913
28 TraesCS5D01G203700 chr7B 84.959 492 52 17 1 475 293325644 293325158 1.910000e-131 479
29 TraesCS5D01G203700 chr7B 83.852 514 53 25 2 494 657642477 657641973 1.920000e-126 462
30 TraesCS5D01G203700 chr6B 84.040 495 50 20 2 475 294003443 294002957 1.500000e-122 449


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 TraesCS5D01G203700 chr5D 308867307 308870044 2737 False 5057 5057 100.000 1 2738 1 chr5D.!!$F2 2737
1 TraesCS5D01G203700 chr5D 333779236 333781399 2163 False 3001 3001 91.736 1 2166 1 chr5D.!!$F3 2165
2 TraesCS5D01G203700 chr5D 20939194 20939768 574 False 911 911 95.304 2166 2738 1 chr5D.!!$F1 572
3 TraesCS5D01G203700 chr2D 511169420 511171591 2171 False 3626 3626 96.869 1 2163 1 chr2D.!!$F4 2162
4 TraesCS5D01G203700 chr2D 59122339 59124510 2171 False 3602 3602 96.644 1 2166 1 chr2D.!!$F2 2165
5 TraesCS5D01G203700 chr2D 28466029 28468198 2169 False 3561 3561 96.324 1 2166 1 chr2D.!!$F1 2165
6 TraesCS5D01G203700 chr2D 352593442 352594014 572 False 929 929 95.986 2167 2738 1 chr2D.!!$F3 571
7 TraesCS5D01G203700 chr2D 189708829 189709401 572 True 913 913 95.462 2167 2738 1 chr2D.!!$R1 571
8 TraesCS5D01G203700 chr1D 355488983 355491156 2173 True 3615 3615 96.737 1 2166 1 chr1D.!!$R1 2165
9 TraesCS5D01G203700 chr1D 393405097 393407269 2172 False 3064 3064 92.209 1 2166 1 chr1D.!!$F1 2165
10 TraesCS5D01G203700 chr6D 345130806 345132976 2170 True 3544 3544 96.184 1 2166 1 chr6D.!!$R3 2165
11 TraesCS5D01G203700 chr6D 284783665 284785834 2169 False 3118 3118 92.674 1 2166 1 chr6D.!!$F2 2165
12 TraesCS5D01G203700 chr6D 263889520 263890405 885 True 1238 1238 91.987 1 893 1 chr6D.!!$R2 892
13 TraesCS5D01G203700 chr6D 53111163 53111734 571 True 924 924 95.812 2167 2738 1 chr6D.!!$R1 571
14 TraesCS5D01G203700 chr6D 52415217 52415789 572 False 909 909 95.296 2166 2738 1 chr6D.!!$F1 572
15 TraesCS5D01G203700 chr6D 379194456 379195082 626 False 645 645 85.714 3 631 1 chr6D.!!$F3 628
16 TraesCS5D01G203700 chr7D 399528604 399530769 2165 False 3042 3042 92.057 1 2166 1 chr7D.!!$F1 2165
17 TraesCS5D01G203700 chr7D 77995289 77997478 2189 True 3009 3009 91.663 1 2166 1 chr7D.!!$R1 2165
18 TraesCS5D01G203700 chrUn 98420115 98422286 2171 True 3014 3014 91.797 1 2166 1 chrUn.!!$R1 2165
19 TraesCS5D01G203700 chrUn 110603528 110605703 2175 True 2996 2996 91.632 1 2166 1 chrUn.!!$R2 2165
20 TraesCS5D01G203700 chrUn 355803053 355803697 644 True 780 780 88.940 1 631 1 chrUn.!!$R3 630
21 TraesCS5D01G203700 chr4D 170800173 170802274 2101 True 1897 1897 83.104 1 2166 1 chr4D.!!$R1 2165
22 TraesCS5D01G203700 chr4D 423723947 423724519 572 False 924 924 95.819 2167 2738 1 chr4D.!!$F2 571
23 TraesCS5D01G203700 chr4D 433443568 433444140 572 False 918 918 95.645 2167 2738 1 chr4D.!!$F3 571
24 TraesCS5D01G203700 chr4D 502320868 502321440 572 True 918 918 95.637 2167 2738 1 chr4D.!!$R2 571
25 TraesCS5D01G203700 chr4D 53667385 53668005 620 False 610 610 84.557 1 645 1 chr4D.!!$F1 644
26 TraesCS5D01G203700 chr3D 477136630 477137205 575 False 913 913 95.312 2165 2738 1 chr3D.!!$F1 573
27 TraesCS5D01G203700 chr7B 657641973 657642477 504 True 462 462 83.852 2 494 1 chr7B.!!$R2 492

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
131 132 2.109480 AGGTGTACCGGCCTATCTATCA 59.891 50.000 0.00 0.0 42.08 2.15 F
398 441 2.358322 TTGAGTTGGGTGAACCTTCC 57.642 50.000 0.00 0.0 41.11 3.46 F
1356 1419 2.429610 GCAATGGGAAATGATCAGCACT 59.570 45.455 0.09 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1051 1113 0.314302 ACTTCCTTCAGGTGTCGTCG 59.686 55.000 0.00 0.0 36.34 5.12 R
1688 1751 1.069204 TGATATCCGCTCCAGCTTCAC 59.931 52.381 0.00 0.0 39.32 3.18 R
2690 2780 1.044790 TCCTCATCATGGAGAGCGCA 61.045 55.000 11.47 0.0 37.05 6.09 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
108 109 2.373502 GGCTAGCAGATGTAGGGGATTT 59.626 50.000 18.24 0.00 0.00 2.17
131 132 2.109480 AGGTGTACCGGCCTATCTATCA 59.891 50.000 0.00 0.00 42.08 2.15
398 441 2.358322 TTGAGTTGGGTGAACCTTCC 57.642 50.000 0.00 0.00 41.11 3.46
424 467 6.773976 ATGTTTAACAACCACCATGATAGG 57.226 37.500 0.66 0.00 31.02 2.57
656 711 3.244112 CCTTAGGTCGTGGTCTTTCACTT 60.244 47.826 0.00 0.00 35.63 3.16
798 857 3.919216 AGTGTGTGATTGCTACTCTGTC 58.081 45.455 0.00 0.00 0.00 3.51
1051 1113 3.568430 ACCGGATGAAGAAACACCTTTTC 59.432 43.478 9.46 0.00 0.00 2.29
1259 1322 2.652095 GCATGGCAGCCCACATTGT 61.652 57.895 9.64 0.00 45.77 2.71
1356 1419 2.429610 GCAATGGGAAATGATCAGCACT 59.570 45.455 0.09 0.00 0.00 4.40
1649 1712 4.216366 ACTACATCATCATCGACGACAG 57.784 45.455 0.00 0.00 0.00 3.51
1688 1751 4.560427 CGATAGCGATGATGACTATGTTGG 59.440 45.833 0.00 0.00 40.82 3.77
1781 1844 9.517868 AGTAGTATTCCTCCATGTACATAGTAC 57.482 37.037 8.32 7.78 0.00 2.73
1883 1950 2.810274 CTCATGTGCATATGGGTAGTGC 59.190 50.000 21.57 0.00 39.26 4.40
1998 2070 2.601240 TCACCCAATTGATCCAGCAA 57.399 45.000 7.12 0.00 0.00 3.91
2198 2282 9.182933 GTCTCCAACGTATCTAGAATTTATGAC 57.817 37.037 0.00 0.00 0.00 3.06
2318 2404 3.634910 GTGCCAGTTTCTGTTTTTCCCTA 59.365 43.478 0.00 0.00 0.00 3.53
2439 2526 0.392998 GTGCACGTCAGGGGATCAAT 60.393 55.000 0.00 0.00 0.00 2.57
2602 2690 2.980233 GTTCCGCTGCCACAAGCT 60.980 61.111 0.00 0.00 44.23 3.74
2690 2780 1.144503 GTGGCCATCTTCATCATCCCT 59.855 52.381 9.72 0.00 0.00 4.20
2704 2794 1.126329 ATCCCTGCGCTCTCCATGAT 61.126 55.000 9.73 0.00 0.00 2.45
2717 2807 3.931241 TCCATGATGAGGAGGGAGTAT 57.069 47.619 0.00 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 86 1.668294 CCCTACATCTGCTAGCCCG 59.332 63.158 13.29 3.30 0.00 6.13
108 109 2.761786 AGATAGGCCGGTACACCTAA 57.238 50.000 9.32 0.00 39.72 2.69
131 132 1.078324 TCCGAAGAGGTCCCCTTAACT 59.922 52.381 0.00 0.00 41.99 2.24
398 441 5.207110 TCATGGTGGTTGTTAAACATTGG 57.793 39.130 0.00 0.00 38.10 3.16
656 711 1.621317 TCAACTCCAACGGCATCACTA 59.379 47.619 0.00 0.00 0.00 2.74
798 857 6.688385 CACGCACAATACTTGAAGGATTTATG 59.312 38.462 0.00 3.59 0.00 1.90
944 1005 7.510549 AATGAGAAGAGAGTAGTGATCTAGC 57.489 40.000 0.00 0.00 0.00 3.42
1051 1113 0.314302 ACTTCCTTCAGGTGTCGTCG 59.686 55.000 0.00 0.00 36.34 5.12
1259 1322 2.242965 ACTTCTCCAATGCATCCCATGA 59.757 45.455 0.00 0.00 33.49 3.07
1316 1379 2.514592 CATCTCGGCGCCCACAAT 60.515 61.111 23.46 6.65 0.00 2.71
1356 1419 3.444034 CGGCAATCGATCTATCCTTCCTA 59.556 47.826 0.00 0.00 42.43 2.94
1649 1712 4.477975 CGTCAGGGTCCGAGTCGC 62.478 72.222 7.12 0.00 0.00 5.19
1688 1751 1.069204 TGATATCCGCTCCAGCTTCAC 59.931 52.381 0.00 0.00 39.32 3.18
1781 1844 7.188157 ACTATCGTTAAAAGAGCTCGAACTAG 58.812 38.462 8.37 11.52 34.38 2.57
1883 1950 9.581099 GAATAGAAAAGAGGTCTAGTGAGAAAG 57.419 37.037 0.00 0.00 31.96 2.62
2439 2526 2.283173 TGCCTCGTGCTCTCCTCA 60.283 61.111 1.74 0.00 42.00 3.86
2602 2690 1.141254 TGGTTTTCGGTGGCTACAGAA 59.859 47.619 11.53 11.53 38.86 3.02
2615 2703 1.304962 AGGGCCCCGATTGGTTTTC 60.305 57.895 21.43 0.00 0.00 2.29
2690 2780 1.044790 TCCTCATCATGGAGAGCGCA 61.045 55.000 11.47 0.00 37.05 6.09
2704 2794 2.478292 GGGTGAAATACTCCCTCCTCA 58.522 52.381 0.00 0.00 45.77 3.86


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

AutoCloner maintained by Alex Coulton.