Multiple sequence alignment - TraesCS5D01G114800

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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 TraesCS5D01G114800 chr5D 100.000 2806 0 0 1 2806 134569438 134572243 0.000000e+00 5182.0
1 TraesCS5D01G114800 chr5D 97.500 40 0 1 1210 1248 384339721 384339682 1.800000e-07 67.6
2 TraesCS5D01G114800 chr6A 94.912 1926 81 5 157 2071 217782442 217784361 0.000000e+00 2998.0
3 TraesCS5D01G114800 chr6A 95.155 743 28 5 2068 2806 217793013 217793751 0.000000e+00 1166.0
4 TraesCS5D01G114800 chr1D 93.563 901 44 8 1264 2153 267005383 267004486 0.000000e+00 1330.0
5 TraesCS5D01G114800 chr1D 89.158 867 73 10 1 850 267006697 267005835 0.000000e+00 1061.0
6 TraesCS5D01G114800 chr1D 94.865 370 18 1 847 1215 267005756 267005387 6.740000e-161 577.0
7 TraesCS5D01G114800 chr1D 93.458 214 13 1 2594 2806 266995782 266995569 1.620000e-82 316.0
8 TraesCS5D01G114800 chr1D 95.480 177 5 3 2148 2323 266996134 266995960 2.130000e-71 279.0
9 TraesCS5D01G114800 chr1D 80.189 212 26 5 121 332 443425873 443425678 8.100000e-31 145.0
10 TraesCS5D01G114800 chr1D 83.969 131 8 6 2467 2595 266995959 266995840 2.280000e-21 113.0
11 TraesCS5D01G114800 chr4D 88.482 738 80 3 114 850 51010677 51009944 0.000000e+00 887.0
12 TraesCS5D01G114800 chr4D 88.529 741 69 10 1432 2157 51009429 51008690 0.000000e+00 883.0
13 TraesCS5D01G114800 chr4D 93.784 370 22 1 847 1215 51009872 51009503 3.160000e-154 555.0
14 TraesCS5D01G114800 chr4D 75.943 212 35 6 121 332 105010471 105010666 8.270000e-16 95.3
15 TraesCS5D01G114800 chr4D 95.238 42 2 0 1 42 51011695 51011654 1.800000e-07 67.6
16 TraesCS5D01G114800 chr7A 93.570 591 25 5 1264 1844 247277413 247276826 0.000000e+00 869.0
17 TraesCS5D01G114800 chr7A 93.537 557 32 4 291 846 247280254 247279701 0.000000e+00 826.0
18 TraesCS5D01G114800 chr7A 95.418 371 15 2 847 1215 247277787 247277417 8.660000e-165 590.0
19 TraesCS5D01G114800 chr7A 94.860 214 10 1 2594 2806 247276021 247275808 1.610000e-87 333.0
20 TraesCS5D01G114800 chr7A 77.522 347 45 13 1 330 604423426 604423756 7.990000e-41 178.0
21 TraesCS5D01G114800 chr7A 89.815 108 9 2 2217 2323 247276305 247276199 1.360000e-28 137.0
22 TraesCS5D01G114800 chrUn 93.537 557 32 4 291 846 363163557 363164110 0.000000e+00 826.0
23 TraesCS5D01G114800 chrUn 93.529 170 8 2 2182 2350 96546146 96546313 1.670000e-62 250.0
24 TraesCS5D01G114800 chrUn 91.549 71 4 1 2374 2444 96546314 96546382 2.300000e-16 97.1
25 TraesCS5D01G114800 chrUn 81.203 133 11 9 435 556 401612671 401612542 8.270000e-16 95.3
26 TraesCS5D01G114800 chr2A 86.923 260 27 7 1901 2157 608927203 608926948 4.570000e-73 285.0
27 TraesCS5D01G114800 chr5A 87.097 217 21 4 2594 2806 416116686 416116899 3.610000e-59 239.0
28 TraesCS5D01G114800 chr4A 94.521 146 4 3 2662 2806 617627177 617627035 3.640000e-54 222.0
29 TraesCS5D01G114800 chr4A 100.000 40 0 0 1211 1250 702429309 702429270 1.080000e-09 75.0
30 TraesCS5D01G114800 chr3A 88.235 170 20 0 1988 2157 406787667 406787836 1.320000e-48 204.0
31 TraesCS5D01G114800 chr3A 91.463 82 6 1 1272 1353 406787539 406787619 8.220000e-21 111.0
32 TraesCS5D01G114800 chr3D 93.939 99 5 1 2709 2806 600092427 600092525 6.260000e-32 148.0
33 TraesCS5D01G114800 chr2B 87.368 95 11 1 859 953 218291814 218291907 1.060000e-19 108.0
34 TraesCS5D01G114800 chr2B 100.000 40 0 0 1211 1250 612672756 612672795 1.080000e-09 75.0
35 TraesCS5D01G114800 chr2B 97.727 44 0 1 1206 1248 713971448 713971405 1.080000e-09 75.0
36 TraesCS5D01G114800 chr2B 93.878 49 1 2 1201 1248 686905230 686905183 3.880000e-09 73.1
37 TraesCS5D01G114800 chr7B 81.203 133 11 9 435 556 680260421 680260292 8.270000e-16 95.3
38 TraesCS5D01G114800 chr6D 100.000 40 0 0 1209 1248 305136532 305136493 1.080000e-09 75.0
39 TraesCS5D01G114800 chr3B 93.878 49 2 1 1200 1248 246117767 246117814 3.880000e-09 73.1
40 TraesCS5D01G114800 chr3B 87.097 62 5 3 1190 1248 523983466 523983405 1.800000e-07 67.6
41 TraesCS5D01G114800 chr3B 100.000 29 0 0 2182 2210 59032672 59032644 1.000000e-03 54.7
42 TraesCS5D01G114800 chr1A 97.619 42 1 0 1 42 174039786 174039745 3.880000e-09 73.1
43 TraesCS5D01G114800 chr1A 95.122 41 1 1 1 41 174042546 174042507 2.330000e-06 63.9


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 TraesCS5D01G114800 chr5D 134569438 134572243 2805 False 5182.000000 5182 100.000000 1 2806 1 chr5D.!!$F1 2805
1 TraesCS5D01G114800 chr6A 217782442 217784361 1919 False 2998.000000 2998 94.912000 157 2071 1 chr6A.!!$F1 1914
2 TraesCS5D01G114800 chr6A 217793013 217793751 738 False 1166.000000 1166 95.155000 2068 2806 1 chr6A.!!$F2 738
3 TraesCS5D01G114800 chr1D 267004486 267006697 2211 True 989.333333 1330 92.528667 1 2153 3 chr1D.!!$R3 2152
4 TraesCS5D01G114800 chr1D 266995569 266996134 565 True 236.000000 316 90.969000 2148 2806 3 chr1D.!!$R2 658
5 TraesCS5D01G114800 chr4D 51008690 51011695 3005 True 598.150000 887 91.508250 1 2157 4 chr4D.!!$R1 2156
6 TraesCS5D01G114800 chr7A 247275808 247280254 4446 True 551.000000 869 93.440000 291 2806 5 chr7A.!!$R1 2515
7 TraesCS5D01G114800 chrUn 363163557 363164110 553 False 826.000000 826 93.537000 291 846 1 chrUn.!!$F1 555

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
119 1026 0.036388 GCCACTGTCTCCATCGGAAA 60.036 55.0 0.00 0.0 0.0 3.13 F
144 1051 0.617820 TTCCGCTTCTTCCTAGGGCT 60.618 55.0 9.46 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1747 4745 1.066858 TCGTCAGCTCATCCCAAAGAC 60.067 52.381 0.0 0.0 0.0 3.01 R
2097 5098 2.049433 CCTCCGTCGCAGTTTCGT 60.049 61.111 0.0 0.0 0.0 3.85 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
69 964 1.571460 CCAGCTGCAAGAACGACAC 59.429 57.895 8.66 0.00 34.07 3.67
70 965 1.159713 CCAGCTGCAAGAACGACACA 61.160 55.000 8.66 0.00 34.07 3.72
71 966 0.041839 CAGCTGCAAGAACGACACAC 60.042 55.000 0.00 0.00 34.07 3.82
72 967 0.461870 AGCTGCAAGAACGACACACA 60.462 50.000 1.02 0.00 34.07 3.72
73 968 0.376852 GCTGCAAGAACGACACACAA 59.623 50.000 0.00 0.00 34.07 3.33
74 969 1.002468 GCTGCAAGAACGACACACAAT 60.002 47.619 0.00 0.00 34.07 2.71
75 970 2.223144 GCTGCAAGAACGACACACAATA 59.777 45.455 0.00 0.00 34.07 1.90
76 971 3.303725 GCTGCAAGAACGACACACAATAA 60.304 43.478 0.00 0.00 34.07 1.40
79 974 3.002862 GCAAGAACGACACACAATAACCA 59.997 43.478 0.00 0.00 0.00 3.67
109 1016 4.320456 CCACCGCTGCCACTGTCT 62.320 66.667 0.00 0.00 0.00 3.41
112 1019 4.007644 CCGCTGCCACTGTCTCCA 62.008 66.667 0.00 0.00 0.00 3.86
118 1025 1.191489 TGCCACTGTCTCCATCGGAA 61.191 55.000 0.00 0.00 0.00 4.30
119 1026 0.036388 GCCACTGTCTCCATCGGAAA 60.036 55.000 0.00 0.00 0.00 3.13
144 1051 0.617820 TTCCGCTTCTTCCTAGGGCT 60.618 55.000 9.46 0.00 0.00 5.19
334 1247 3.511477 TCTCTCCTTTCTAGCACCACTT 58.489 45.455 0.00 0.00 0.00 3.16
720 1634 6.636447 TGCTTTTTCAGATGAACATGTTTACG 59.364 34.615 13.36 1.47 33.13 3.18
730 1644 6.627395 TGAACATGTTTACGAAACCAATCT 57.373 33.333 13.36 0.00 40.67 2.40
886 3870 7.755591 ACATGTGTTAAGATCAGTAGCATTTG 58.244 34.615 0.00 0.94 0.00 2.32
888 3872 7.744087 TGTGTTAAGATCAGTAGCATTTGTT 57.256 32.000 0.00 0.00 0.00 2.83
1106 4092 6.745857 AGATTACCAAAAGGGATTCTCCAAT 58.254 36.000 0.00 0.00 38.64 3.16
1223 4209 4.716794 AGAAGTAGTATGTACTCCCTCCG 58.283 47.826 0.00 0.00 37.73 4.63
1254 4240 1.470098 CTTGTCGGAGAAATTGGCCAG 59.530 52.381 5.11 0.00 39.69 4.85
1471 4459 8.789767 AATCCTTCTTCTATGTCCTTAGATCA 57.210 34.615 0.00 0.00 0.00 2.92
1583 4580 8.575589 CGGAATGGTGAAATTTGGAATATGATA 58.424 33.333 0.00 0.00 0.00 2.15
1722 4720 5.781818 AGTGGAGTTGATTGGGATGAAATTT 59.218 36.000 0.00 0.00 0.00 1.82
1739 4737 4.804868 AATTTGGTGCATGATACAAGCA 57.195 36.364 0.00 0.00 35.71 3.91
1747 4745 3.310501 TGCATGATACAAGCAGATGAACG 59.689 43.478 0.00 0.00 33.12 3.95
1768 4766 1.066858 TCTTTGGGATGAGCTGACGAC 60.067 52.381 0.00 0.00 0.00 4.34
1774 4772 2.094182 GGGATGAGCTGACGACTGTAAA 60.094 50.000 0.00 0.00 0.00 2.01
1917 4916 5.762279 AGTTCAAGTCCAAACCTTTTCCTA 58.238 37.500 0.00 0.00 0.00 2.94
2065 5066 5.751990 CCGTTATAACTTGACATCCACTACC 59.248 44.000 13.56 0.00 0.00 3.18
2097 5098 5.003160 ACAGATTGCTAGTGTTGCACATAA 58.997 37.500 2.01 0.00 40.40 1.90
2110 5111 1.782023 GCACATAACGAAACTGCGACG 60.782 52.381 0.00 0.00 34.83 5.12
2210 5211 4.885907 AGAAACAGACTCCATGGCATATTG 59.114 41.667 6.96 4.29 0.00 1.90
2213 5214 4.603131 ACAGACTCCATGGCATATTGTTT 58.397 39.130 6.96 0.00 0.00 2.83
2214 5215 5.018809 ACAGACTCCATGGCATATTGTTTT 58.981 37.500 6.96 0.00 0.00 2.43
2215 5216 5.481473 ACAGACTCCATGGCATATTGTTTTT 59.519 36.000 6.96 0.00 0.00 1.94
2317 5464 9.003658 CAACTTTTCATCTTCTAGTATGTTGGT 57.996 33.333 0.00 0.00 0.00 3.67
2335 5482 6.851609 TGTTGGTCACATTAGCAATATGTTC 58.148 36.000 0.00 0.00 38.93 3.18
2336 5483 5.733226 TGGTCACATTAGCAATATGTTCG 57.267 39.130 0.00 0.00 34.11 3.95
2360 5507 4.027674 TGGCAATCCACTTAGCAAACTA 57.972 40.909 0.00 0.00 37.47 2.24
2526 5673 3.435671 GGAACTGGTCGACTTTTACATGG 59.564 47.826 16.46 0.00 0.00 3.66
2542 5689 2.174210 ACATGGCAATGAGGCTGTAGAT 59.826 45.455 8.45 0.00 44.55 1.98
2613 5819 7.118245 CAGAGAACTGCATTGTACTATGTTTGA 59.882 37.037 16.86 1.25 37.33 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 63 1.159713 TGTGTCGTTCTTGCAGCTGG 61.160 55.000 17.12 0.00 0.00 4.85
69 964 1.593006 GCGACGGAGATGGTTATTGTG 59.407 52.381 0.00 0.00 0.00 3.33
70 965 1.472728 GGCGACGGAGATGGTTATTGT 60.473 52.381 0.00 0.00 0.00 2.71
71 966 1.217882 GGCGACGGAGATGGTTATTG 58.782 55.000 0.00 0.00 0.00 1.90
72 967 3.680842 GGCGACGGAGATGGTTATT 57.319 52.632 0.00 0.00 0.00 1.40
94 989 4.008933 GGAGACAGTGGCAGCGGT 62.009 66.667 0.00 0.00 0.00 5.68
105 1012 6.434661 GGAATCAGGTTTCCGATGGAGACA 62.435 50.000 8.55 0.00 38.39 3.41
109 1016 2.710096 GGAATCAGGTTTCCGATGGA 57.290 50.000 0.00 0.00 36.12 3.41
118 1025 1.630878 AGGAAGAAGCGGAATCAGGTT 59.369 47.619 0.00 0.00 0.00 3.50
119 1026 1.280457 AGGAAGAAGCGGAATCAGGT 58.720 50.000 0.00 0.00 0.00 4.00
144 1051 2.448542 GGGGGAGATGGCCAGCTA 60.449 66.667 26.37 0.00 0.00 3.32
334 1247 3.006940 GGGAACACGAGACAATAATGCA 58.993 45.455 0.00 0.00 0.00 3.96
608 1522 4.201657 CCATCCTATTTCTGCATGACACA 58.798 43.478 0.00 0.00 0.00 3.72
720 1634 6.375455 ACAACATGGTCATCTAGATTGGTTTC 59.625 38.462 1.33 0.00 0.00 2.78
730 1644 7.676004 TCAGAACTAAACAACATGGTCATCTA 58.324 34.615 0.00 0.00 0.00 1.98
904 3888 8.523658 GGAAGCAAGATTAAACAGAGGTAAAAT 58.476 33.333 0.00 0.00 0.00 1.82
1223 4209 2.165030 TCTCCGACAAGTATTTCCGGAC 59.835 50.000 1.83 0.00 43.47 4.79
1288 4274 9.529325 GTTATAAAACTCAAAAGCCAAAGTCTT 57.471 29.630 0.00 0.00 32.54 3.01
1471 4459 1.925255 TCCATTGGGCTCTGGATTTCT 59.075 47.619 2.09 0.00 36.63 2.52
1722 4720 2.785540 TCTGCTTGTATCATGCACCA 57.214 45.000 6.28 0.00 39.10 4.17
1739 4737 3.866651 CTCATCCCAAAGACGTTCATCT 58.133 45.455 0.00 0.00 0.00 2.90
1747 4745 1.066858 TCGTCAGCTCATCCCAAAGAC 60.067 52.381 0.00 0.00 0.00 3.01
1768 4766 8.055279 TGAAATTAGGAGGAAAGCATTTACAG 57.945 34.615 0.00 0.00 42.95 2.74
1774 4772 7.286316 CCAATACTGAAATTAGGAGGAAAGCAT 59.714 37.037 0.00 0.00 0.00 3.79
1835 4833 6.195600 AGGGGTGATAGAAGTTAAACAACA 57.804 37.500 0.00 0.00 0.00 3.33
1871 4870 8.421249 ACTTATTGATCCTCAAACCAAATGAA 57.579 30.769 0.00 0.00 40.12 2.57
1882 4881 6.373005 TGGACTTGAACTTATTGATCCTCA 57.627 37.500 0.00 0.00 0.00 3.86
2065 5066 2.133553 CTAGCAATCTGTGATGGCTCG 58.866 52.381 12.16 3.76 36.10 5.03
2097 5098 2.049433 CCTCCGTCGCAGTTTCGT 60.049 61.111 0.00 0.00 0.00 3.85
2110 5111 5.242615 AGAAAAGCTTTGATTGACTTCCTCC 59.757 40.000 13.54 0.00 0.00 4.30
2210 5211 4.682787 CTTCACAAGGAACAGGGAAAAAC 58.317 43.478 0.00 0.00 28.39 2.43
2213 5214 2.306847 GCTTCACAAGGAACAGGGAAA 58.693 47.619 0.00 0.00 28.39 3.13
2214 5215 1.214175 TGCTTCACAAGGAACAGGGAA 59.786 47.619 0.00 0.00 0.00 3.97
2215 5216 0.843309 TGCTTCACAAGGAACAGGGA 59.157 50.000 0.00 0.00 0.00 4.20
2317 5464 6.550843 CCAAACGAACATATTGCTAATGTGA 58.449 36.000 10.82 0.00 37.62 3.58
2335 5482 9.795923 TTAGTTTGCTAAGTGGATTGCCAAACG 62.796 40.741 0.00 0.00 42.20 3.60
2336 5483 6.737346 TTAGTTTGCTAAGTGGATTGCCAAAC 60.737 38.462 0.00 0.00 40.16 2.93
2360 5507 5.072741 ACAGGACATATTTTGCACTCACTT 58.927 37.500 0.00 0.00 0.00 3.16
2465 5612 6.282930 ACTGCATTGCTCACAACTAAATTTT 58.717 32.000 10.49 0.00 38.99 1.82
2526 5673 4.878397 ACTTGTTATCTACAGCCTCATTGC 59.122 41.667 0.00 0.00 38.19 3.56
2613 5819 3.034635 CACCTAGCTACCTCCAGTGAAT 58.965 50.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.