Multiple sequence alignment - TraesCS5A01G134300

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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 TraesCS5A01G134300 chr5A 100.000 2216 0 0 1 2216 302990144 302987929 0.000000e+00 4093
1 TraesCS5A01G134300 chr5A 90.229 655 39 2 1 630 475608067 475607413 0.000000e+00 832
2 TraesCS5A01G134300 chr5A 88.021 192 13 9 886 1073 489933001 489933186 3.700000e-53 219
3 TraesCS5A01G134300 chr5A 87.500 160 19 1 2058 2216 256233698 256233857 1.350000e-42 183
4 TraesCS5A01G134300 chr7A 97.163 2221 58 1 1 2216 503325558 503327778 0.000000e+00 3747
5 TraesCS5A01G134300 chr4A 96.406 1892 59 2 1 1887 142904457 142902570 0.000000e+00 3109
6 TraesCS5A01G134300 chr2A 92.599 1081 70 5 1 1072 239932571 239933650 0.000000e+00 1544
7 TraesCS5A01G134300 chr2A 89.940 1004 69 11 1069 2052 684122149 684121158 0.000000e+00 1266
8 TraesCS5A01G134300 chr2A 93.151 292 15 1 344 630 165026526 165026817 7.310000e-115 424
9 TraesCS5A01G134300 chr2A 89.744 195 18 2 437 630 172843127 172843320 4.730000e-62 248
10 TraesCS5A01G134300 chr6B 91.705 1085 75 6 2 1072 389762712 389763795 0.000000e+00 1491
11 TraesCS5A01G134300 chr2B 89.820 1002 79 8 1069 2052 646019654 646018658 0.000000e+00 1264
12 TraesCS5A01G134300 chr2B 91.078 538 41 5 544 1079 391878011 391877479 0.000000e+00 721
13 TraesCS5A01G134300 chr2D 89.474 988 88 8 1069 2044 540639351 540638368 0.000000e+00 1234
14 TraesCS5A01G134300 chr6D 92.585 472 29 2 1 467 162249255 162248785 0.000000e+00 673
15 TraesCS5A01G134300 chr6D 95.833 240 9 1 673 911 162248482 162248243 9.600000e-104 387
16 TraesCS5A01G134300 chr6D 87.500 184 10 6 907 1079 162246656 162246475 1.340000e-47 200
17 TraesCS5A01G134300 chr1B 92.718 412 23 3 89 494 51329209 51329619 2.450000e-164 588
18 TraesCS5A01G134300 chr7B 91.990 412 25 4 89 494 720100904 720100495 2.470000e-159 571
19 TraesCS5A01G134300 chr7B 91.429 245 19 2 645 888 204337716 204337473 3.530000e-88 335
20 TraesCS5A01G134300 chr5B 91.505 412 27 4 89 494 142835899 142836308 5.340000e-156 560
21 TraesCS5A01G134300 chr3A 91.429 245 18 2 645 888 199618473 199618715 1.270000e-87 333
22 TraesCS5A01G134300 chr3A 81.737 334 31 5 320 623 595977459 595977792 3.650000e-63 252
23 TraesCS5A01G134300 chr4B 91.057 246 20 2 645 888 429610675 429610920 4.560000e-87 331
24 TraesCS5A01G134300 chr6A 90.270 185 18 0 437 621 463795675 463795859 2.200000e-60 243
25 TraesCS5A01G134300 chr5D 85.638 188 17 6 886 1073 387250152 387250329 2.900000e-44 189
26 TraesCS5A01G134300 chr3D 87.662 154 18 1 2061 2213 239098004 239097851 6.290000e-41 178


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 TraesCS5A01G134300 chr5A 302987929 302990144 2215 True 4093 4093 100.000000 1 2216 1 chr5A.!!$R1 2215
1 TraesCS5A01G134300 chr5A 475607413 475608067 654 True 832 832 90.229000 1 630 1 chr5A.!!$R2 629
2 TraesCS5A01G134300 chr7A 503325558 503327778 2220 False 3747 3747 97.163000 1 2216 1 chr7A.!!$F1 2215
3 TraesCS5A01G134300 chr4A 142902570 142904457 1887 True 3109 3109 96.406000 1 1887 1 chr4A.!!$R1 1886
4 TraesCS5A01G134300 chr2A 239932571 239933650 1079 False 1544 1544 92.599000 1 1072 1 chr2A.!!$F3 1071
5 TraesCS5A01G134300 chr2A 684121158 684122149 991 True 1266 1266 89.940000 1069 2052 1 chr2A.!!$R1 983
6 TraesCS5A01G134300 chr6B 389762712 389763795 1083 False 1491 1491 91.705000 2 1072 1 chr6B.!!$F1 1070
7 TraesCS5A01G134300 chr2B 646018658 646019654 996 True 1264 1264 89.820000 1069 2052 1 chr2B.!!$R2 983
8 TraesCS5A01G134300 chr2B 391877479 391878011 532 True 721 721 91.078000 544 1079 1 chr2B.!!$R1 535
9 TraesCS5A01G134300 chr2D 540638368 540639351 983 True 1234 1234 89.474000 1069 2044 1 chr2D.!!$R1 975
10 TraesCS5A01G134300 chr6D 162246475 162249255 2780 True 420 673 91.972667 1 1079 3 chr6D.!!$R1 1078

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
142 144 0.613777 GGTCGACACCCATCCTCTTT 59.386 55.0 18.91 0.0 36.54 2.52 F
938 2700 0.881796 CCAGCAGTACGTGTCTCTCA 59.118 55.0 0.00 0.0 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1049 2830 0.255318 CTTGAGGCCTTCAGCTCCAT 59.745 55.00 6.77 0.0 43.05 3.41 R
2169 3997 7.446931 ACCATTGGACTTTTTGTTTTGTTCTTT 59.553 29.63 10.37 0.0 0.00 2.52 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
142 144 0.613777 GGTCGACACCCATCCTCTTT 59.386 55.000 18.91 0.0 36.54 2.52
589 759 8.940952 AGAATTGTAAGCATCTTCTGAGTTTAC 58.059 33.333 0.00 0.0 30.61 2.01
603 773 8.578308 TTCTGAGTTTACAATGCTTGAAATTG 57.422 30.769 3.37 0.0 40.23 2.32
611 781 4.229096 CAATGCTTGAAATTGCAGTACGT 58.771 39.130 0.00 0.0 42.74 3.57
668 838 6.460781 TGTTGTTCCCTGTAGTTGTATAGTG 58.539 40.000 0.00 0.0 0.00 2.74
938 2700 0.881796 CCAGCAGTACGTGTCTCTCA 59.118 55.000 0.00 0.0 0.00 3.27
984 2752 1.002544 TCTCTCTCACTCTCTCACGCA 59.997 52.381 0.00 0.0 0.00 5.24
1044 2825 3.535561 AGCCATGCAGTATGACAAGTAC 58.464 45.455 0.00 0.0 39.69 2.73
1049 2830 1.468565 GCAGTATGACAAGTACGGCGA 60.469 52.381 16.62 0.0 39.69 5.54
1115 2896 4.422073 TGTCTCCAAACAGACTTGACAT 57.578 40.909 2.49 0.0 43.00 3.06
1118 2899 1.872952 TCCAAACAGACTTGACATGCG 59.127 47.619 0.00 0.0 0.00 4.73
1569 3372 0.175531 GTTGCCTGCAAGTGTGGTTT 59.824 50.000 4.52 0.0 36.52 3.27
1610 3417 1.002033 GCAAAGTCTCAGCAACCTGTG 60.002 52.381 0.00 0.0 40.09 3.66
1709 3534 8.421249 TTCATATGAAACAAACCTTCTCCATT 57.579 30.769 15.82 0.0 0.00 3.16
1725 3550 6.737720 TCTCCATTAGAGCATCAAGTACAT 57.262 37.500 0.00 0.0 42.90 2.29
1933 3761 4.389992 CGTCATGTGTTAAGTTCTCTGCAT 59.610 41.667 0.00 0.0 0.00 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
626 796 5.144100 ACAACATTGACCAATTCCACCTAA 58.856 37.500 0.00 0.00 0.00 2.69
668 838 3.053455 GGAATCGACGATTGATCTGGAC 58.947 50.000 26.79 10.01 31.89 4.02
813 984 1.268896 GCCGTCGATCCTCGTTGATTA 60.269 52.381 0.00 0.00 41.35 1.75
814 985 0.527817 GCCGTCGATCCTCGTTGATT 60.528 55.000 0.00 0.00 41.35 2.57
938 2700 3.436243 AGAAAGAGAGAAGGACGATGGT 58.564 45.455 0.00 0.00 0.00 3.55
1044 2825 2.587194 CCTTCAGCTCCATCGCCG 60.587 66.667 0.00 0.00 0.00 6.46
1049 2830 0.255318 CTTGAGGCCTTCAGCTCCAT 59.745 55.000 6.77 0.00 43.05 3.41
1115 2896 1.795872 CATTGAACCTTACACGACGCA 59.204 47.619 0.00 0.00 0.00 5.24
1118 2899 2.410730 CGGTCATTGAACCTTACACGAC 59.589 50.000 0.00 0.00 37.15 4.34
1165 2955 1.881252 GCCATACGTCGCACGGATT 60.881 57.895 12.18 0.00 43.81 3.01
1179 2969 1.677217 GCAAGAAGTTCTCCGAGCCAT 60.677 52.381 5.70 0.00 0.00 4.40
1460 3263 5.163540 GCCATCTCTTGCTTCATGAAGAAAT 60.164 40.000 34.43 15.63 40.79 2.17
1569 3372 2.346766 ACATGCACAAAGACAGGTGA 57.653 45.000 0.00 0.00 37.18 4.02
1610 3417 3.251004 CACTGTCTTACAAAGTCAAGGGC 59.749 47.826 0.00 0.00 0.00 5.19
1612 3419 4.273480 CACCACTGTCTTACAAAGTCAAGG 59.727 45.833 0.00 0.00 32.28 3.61
1709 3534 5.045942 TGGGAAACATGTACTTGATGCTCTA 60.046 40.000 15.13 0.00 0.00 2.43
1725 3550 0.703488 TGGCATCTCCATGGGAAACA 59.297 50.000 13.02 6.38 40.72 2.83
2169 3997 7.446931 ACCATTGGACTTTTTGTTTTGTTCTTT 59.553 29.630 10.37 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.