Multiple sequence alignment - TraesCS5D01G356800

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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 TraesCS5D01G356800 chr5D 100.000 5608 0 0 1 5608 437812246 437806639 0.000000e+00 10357.0
1 TraesCS5D01G356800 chr5D 88.588 1402 73 26 2761 4121 437695565 437696920 0.000000e+00 1622.0
2 TraesCS5D01G356800 chr5D 88.583 727 62 5 1198 1912 437694017 437694734 0.000000e+00 863.0
3 TraesCS5D01G356800 chr5D 87.121 792 44 25 1955 2737 437694733 437695475 0.000000e+00 845.0
4 TraesCS5D01G356800 chr5D 77.139 1566 235 64 1206 2720 437642089 437643582 0.000000e+00 795.0
5 TraesCS5D01G356800 chr5D 90.468 577 43 6 4174 4750 437697249 437697813 0.000000e+00 750.0
6 TraesCS5D01G356800 chr5D 80.018 1091 154 39 1207 2267 370087243 370088299 0.000000e+00 749.0
7 TraesCS5D01G356800 chr5D 80.357 784 110 28 1963 2723 437566701 437565939 6.350000e-154 555.0
8 TraesCS5D01G356800 chr5D 78.465 808 113 26 1111 1887 437567475 437566698 6.580000e-129 472.0
9 TraesCS5D01G356800 chr5D 88.136 177 20 1 3926 4102 437616826 437616651 5.690000e-50 209.0
10 TraesCS5D01G356800 chr5D 77.850 307 55 7 1578 1873 370089168 370089472 1.610000e-40 178.0
11 TraesCS5D01G356800 chr5A 96.045 5133 104 22 1 5086 552753377 552748297 0.000000e+00 8263.0
12 TraesCS5D01G356800 chr5A 88.914 2219 144 39 1955 4121 552674759 552676927 0.000000e+00 2641.0
13 TraesCS5D01G356800 chr5A 87.989 716 67 4 1206 1912 552674055 552674760 0.000000e+00 828.0
14 TraesCS5D01G356800 chr5A 78.360 1354 185 66 1207 2514 533830403 533831694 0.000000e+00 778.0
15 TraesCS5D01G356800 chr5A 89.848 591 46 8 4161 4750 552677241 552677818 0.000000e+00 747.0
16 TraesCS5D01G356800 chr5A 94.421 484 10 2 5136 5608 552748194 552747717 0.000000e+00 728.0
17 TraesCS5D01G356800 chr5A 79.427 943 117 39 1057 1962 552650650 552651552 3.740000e-166 595.0
18 TraesCS5D01G356800 chr5A 82.353 680 96 9 3252 3925 552630942 552630281 2.270000e-158 569.0
19 TraesCS5D01G356800 chr5A 88.701 177 20 0 3926 4102 552630243 552630067 3.400000e-52 217.0
20 TraesCS5D01G356800 chr5A 78.338 337 43 15 1057 1379 533832010 533832330 2.060000e-44 191.0
21 TraesCS5D01G356800 chr5A 98.077 52 1 0 5084 5135 552748268 552748217 2.150000e-14 91.6
22 TraesCS5D01G356800 chr5B 97.464 3785 40 12 860 4628 531640458 531644202 0.000000e+00 6407.0
23 TraesCS5D01G356800 chr5B 97.995 3192 37 6 27 3213 531708673 531705504 0.000000e+00 5515.0
24 TraesCS5D01G356800 chr5B 93.417 881 45 8 3244 4116 531705507 531704632 0.000000e+00 1293.0
25 TraesCS5D01G356800 chr5B 79.101 1201 162 51 1207 2371 439267589 439268736 0.000000e+00 745.0
26 TraesCS5D01G356800 chr5B 90.150 599 22 19 5035 5608 531644720 531645306 0.000000e+00 745.0
27 TraesCS5D01G356800 chr5B 90.401 573 43 6 4178 4750 531704350 531703790 0.000000e+00 743.0
28 TraesCS5D01G356800 chr5B 82.430 683 107 7 3252 3925 531621387 531620709 8.100000e-163 584.0
29 TraesCS5D01G356800 chr5B 75.637 1178 175 60 789 1887 531627858 531626714 3.040000e-132 483.0
30 TraesCS5D01G356800 chr5B 89.277 401 6 5 4568 4956 531644203 531644578 8.510000e-128 468.0
31 TraesCS5D01G356800 chr5B 97.321 224 6 0 1 224 16161291 16161068 1.140000e-101 381.0
32 TraesCS5D01G356800 chr5B 93.694 222 4 2 1 222 250487011 250487222 1.950000e-84 324.0
33 TraesCS5D01G356800 chr5B 90.533 169 16 0 3926 4094 531620671 531620503 2.030000e-54 224.0
34 TraesCS5D01G356800 chr5B 84.783 230 19 7 1198 1412 531639743 531639971 3.400000e-52 217.0
35 TraesCS5D01G356800 chr5B 100.000 44 0 0 4955 4998 531644682 531644725 1.290000e-11 82.4
36 TraesCS5D01G356800 chr5B 86.441 59 8 0 3245 3303 342873401 342873459 1.300000e-06 65.8
37 TraesCS5D01G356800 chr6B 82.284 683 108 7 3252 3925 607132877 607132199 3.770000e-161 579.0
38 TraesCS5D01G356800 chr6B 76.217 1274 194 61 1057 2270 608187668 608186444 1.750000e-159 573.0
39 TraesCS5D01G356800 chr6B 80.488 779 105 28 1963 2717 608188420 608187665 2.280000e-153 553.0
40 TraesCS5D01G356800 chr6B 80.025 786 109 29 1963 2723 607136311 607135549 6.390000e-149 538.0
41 TraesCS5D01G356800 chr6B 76.174 1171 171 52 789 1887 607137442 607136308 8.330000e-143 518.0
42 TraesCS5D01G356800 chr6B 82.293 593 93 8 3252 3836 608184692 608184104 2.330000e-138 503.0
43 TraesCS5D01G356800 chr6B 76.657 1041 148 46 909 1887 608189424 608188417 6.530000e-134 488.0
44 TraesCS5D01G356800 chr6B 90.533 169 16 0 3926 4094 607132161 607131993 2.030000e-54 224.0
45 TraesCS5D01G356800 chr4B 97.321 224 6 0 1 224 632313142 632312919 1.140000e-101 381.0
46 TraesCS5D01G356800 chr4B 95.536 224 10 0 1 224 213360088 213360311 5.340000e-95 359.0
47 TraesCS5D01G356800 chr2B 96.875 224 7 0 1 224 710589480 710589257 5.300000e-100 375.0
48 TraesCS5D01G356800 chr2B 93.750 224 4 2 1 224 222792202 222791989 1.510000e-85 327.0
49 TraesCS5D01G356800 chrUn 93.304 224 5 2 1 224 328845432 328845645 7.010000e-84 322.0
50 TraesCS5D01G356800 chr1B 93.750 208 3 2 17 224 601564170 601563973 2.540000e-78 303.0
51 TraesCS5D01G356800 chr1B 91.477 176 5 2 1 176 54766895 54767060 3.380000e-57 233.0
52 TraesCS5D01G356800 chr1B 91.477 176 5 2 1 176 54771800 54771965 3.380000e-57 233.0
53 TraesCS5D01G356800 chr3D 84.914 232 33 2 301 531 442162463 442162693 3.380000e-57 233.0


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 TraesCS5D01G356800 chr5D 437806639 437812246 5607 True 10357.000000 10357 100.000000 1 5608 1 chr5D.!!$R2 5607
1 TraesCS5D01G356800 chr5D 437694017 437697813 3796 False 1020.000000 1622 88.690000 1198 4750 4 chr5D.!!$F3 3552
2 TraesCS5D01G356800 chr5D 437642089 437643582 1493 False 795.000000 795 77.139000 1206 2720 1 chr5D.!!$F1 1514
3 TraesCS5D01G356800 chr5D 437565939 437567475 1536 True 513.500000 555 79.411000 1111 2723 2 chr5D.!!$R3 1612
4 TraesCS5D01G356800 chr5D 370087243 370089472 2229 False 463.500000 749 78.934000 1207 2267 2 chr5D.!!$F2 1060
5 TraesCS5D01G356800 chr5A 552747717 552753377 5660 True 3027.533333 8263 96.181000 1 5608 3 chr5A.!!$R2 5607
6 TraesCS5D01G356800 chr5A 552674055 552677818 3763 False 1405.333333 2641 88.917000 1206 4750 3 chr5A.!!$F3 3544
7 TraesCS5D01G356800 chr5A 552650650 552651552 902 False 595.000000 595 79.427000 1057 1962 1 chr5A.!!$F1 905
8 TraesCS5D01G356800 chr5A 533830403 533832330 1927 False 484.500000 778 78.349000 1057 2514 2 chr5A.!!$F2 1457
9 TraesCS5D01G356800 chr5A 552630067 552630942 875 True 393.000000 569 85.527000 3252 4102 2 chr5A.!!$R1 850
10 TraesCS5D01G356800 chr5B 531703790 531708673 4883 True 2517.000000 5515 93.937667 27 4750 3 chr5B.!!$R4 4723
11 TraesCS5D01G356800 chr5B 531639743 531645306 5563 False 1583.880000 6407 92.334800 860 5608 5 chr5B.!!$F4 4748
12 TraesCS5D01G356800 chr5B 439267589 439268736 1147 False 745.000000 745 79.101000 1207 2371 1 chr5B.!!$F3 1164
13 TraesCS5D01G356800 chr5B 531626714 531627858 1144 True 483.000000 483 75.637000 789 1887 1 chr5B.!!$R2 1098
14 TraesCS5D01G356800 chr5B 531620503 531621387 884 True 404.000000 584 86.481500 3252 4094 2 chr5B.!!$R3 842
15 TraesCS5D01G356800 chr6B 608184104 608189424 5320 True 529.250000 573 78.913750 909 3836 4 chr6B.!!$R2 2927
16 TraesCS5D01G356800 chr6B 607131993 607137442 5449 True 464.750000 579 82.254000 789 4094 4 chr6B.!!$R1 3305

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
834 842 2.445145 TCAACCCACCAATTCCTCAGAA 59.555 45.455 0.00 0.00 36.15 3.02 F
1195 1271 1.750780 AGCGAGATCGGACAGCTCA 60.751 57.895 4.18 0.00 40.23 4.26 F
2092 2334 2.626266 TGAACTGCTCTCGTACCAGAAA 59.374 45.455 3.46 0.00 0.00 2.52 F
2838 6784 1.090052 GCCTTTTCGACGAGATGGGG 61.090 60.000 18.30 9.34 0.00 4.96 F
4057 8952 1.141053 GCCGAGGGATGTTATTCACCT 59.859 52.381 0.00 0.00 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2092 2334 1.271217 GCACGTAGGGGGTCTTTTTCT 60.271 52.381 0.0 0.0 0.00 2.52 R
2528 2814 3.255642 GCAAATTAGTGAACAAGGGAGCA 59.744 43.478 0.0 0.0 0.00 4.26 R
3817 8671 2.186076 CGTGGAGACGCATAGTTCTTC 58.814 52.381 0.0 0.0 42.37 2.87 R
4578 10080 0.107945 CACTGCCTCCTAACCAGCTC 60.108 60.000 0.0 0.0 0.00 4.09 R
5192 10925 0.834612 TCCGTCTCTCTCTCTCTCCC 59.165 60.000 0.0 0.0 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
84 85 2.622942 TGTTTGCTTGATGGACACCTTC 59.377 45.455 0.00 0.00 0.00 3.46
138 139 7.426929 ACTGTTGATCTGTTCTGTATTTCAC 57.573 36.000 0.00 0.00 0.00 3.18
834 842 2.445145 TCAACCCACCAATTCCTCAGAA 59.555 45.455 0.00 0.00 36.15 3.02
1195 1271 1.750780 AGCGAGATCGGACAGCTCA 60.751 57.895 4.18 0.00 40.23 4.26
1724 1870 5.668866 GCGTGTAAGTCTTGATTGTGACATC 60.669 44.000 0.00 0.00 35.81 3.06
2092 2334 2.626266 TGAACTGCTCTCGTACCAGAAA 59.374 45.455 3.46 0.00 0.00 2.52
2345 2620 4.082245 CCAAAAACTGCCCCACTAGTATTG 60.082 45.833 0.00 0.00 0.00 1.90
2528 2814 9.683069 CTGCTGTGAAATTTCTGTAACTAATTT 57.317 29.630 18.64 0.00 34.98 1.82
2529 2815 9.462174 TGCTGTGAAATTTCTGTAACTAATTTG 57.538 29.630 18.64 0.00 33.08 2.32
2530 2816 8.427774 GCTGTGAAATTTCTGTAACTAATTTGC 58.572 33.333 18.64 5.14 33.08 3.68
2531 2817 9.683069 CTGTGAAATTTCTGTAACTAATTTGCT 57.317 29.630 18.64 0.00 33.08 3.91
2533 2819 9.129209 GTGAAATTTCTGTAACTAATTTGCTCC 57.871 33.333 18.64 0.00 33.08 4.70
2534 2820 8.303876 TGAAATTTCTGTAACTAATTTGCTCCC 58.696 33.333 18.64 0.00 33.08 4.30
2537 2823 6.817765 TTCTGTAACTAATTTGCTCCCTTG 57.182 37.500 0.00 0.00 0.00 3.61
2539 2825 6.303839 TCTGTAACTAATTTGCTCCCTTGTT 58.696 36.000 0.00 0.00 0.00 2.83
2540 2826 6.430000 TCTGTAACTAATTTGCTCCCTTGTTC 59.570 38.462 0.00 0.00 0.00 3.18
2541 2827 6.065374 TGTAACTAATTTGCTCCCTTGTTCA 58.935 36.000 0.00 0.00 0.00 3.18
2542 2828 5.453567 AACTAATTTGCTCCCTTGTTCAC 57.546 39.130 0.00 0.00 0.00 3.18
2546 2832 6.948309 ACTAATTTGCTCCCTTGTTCACTAAT 59.052 34.615 0.00 0.00 0.00 1.73
2628 4789 5.967674 GCATCTTGTCTTTGTGGATTTATCG 59.032 40.000 0.00 0.00 0.00 2.92
2838 6784 1.090052 GCCTTTTCGACGAGATGGGG 61.090 60.000 18.30 9.34 0.00 4.96
3528 8381 9.391006 CTGAGGGTTGTTACTGCTATTTATTTA 57.609 33.333 0.00 0.00 0.00 1.40
3741 8594 6.116711 TGTAAAAGTGTAATAGCTGTGGGA 57.883 37.500 0.00 0.00 0.00 4.37
4057 8952 1.141053 GCCGAGGGATGTTATTCACCT 59.859 52.381 0.00 0.00 0.00 4.00
4578 10080 7.262772 TGAACCTACTACATTGGATTTCTACG 58.737 38.462 0.00 0.00 0.00 3.51
4768 10331 5.589367 AGTACTACCTCCGTCCCATAATA 57.411 43.478 0.00 0.00 0.00 0.98
4871 10434 5.277058 GCAGAGACCTGAATAATTTGCTACG 60.277 44.000 0.00 0.00 43.02 3.51
5053 10733 6.152154 ACTCCCTAAAATTACCCGAACATTTG 59.848 38.462 0.00 0.00 0.00 2.32
5067 10747 7.603024 ACCCGAACATTTGTTTCAAAGTTAAAA 59.397 29.630 0.00 0.00 38.56 1.52
5069 10749 8.436200 CCGAACATTTGTTTCAAAGTTAAAACA 58.564 29.630 10.76 10.76 42.07 2.83
5192 10925 4.548513 CGGGAGGGAGGGAGGGAG 62.549 77.778 0.00 0.00 0.00 4.30
5193 10926 4.179599 GGGAGGGAGGGAGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
5352 11085 4.530857 GCTACAGGCGCATCCGGT 62.531 66.667 10.83 0.00 45.41 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 9.893305 ATACTGAAAACCTTTTGAACTATTTCG 57.107 29.630 0.00 0.0 34.04 3.46
138 139 3.005684 TGACTAAAATGCTTTGCAGGTGG 59.994 43.478 0.00 0.0 43.65 4.61
834 842 3.361977 GTTGTGCGGCCCAATCGT 61.362 61.111 0.31 0.0 0.00 3.73
1195 1271 4.021925 GCGCCTGGACTGGGTTCT 62.022 66.667 0.00 0.0 0.00 3.01
2092 2334 1.271217 GCACGTAGGGGGTCTTTTTCT 60.271 52.381 0.00 0.0 0.00 2.52
2251 2504 9.562408 TGATACACCTTACACAAACTCAAATAA 57.438 29.630 0.00 0.0 0.00 1.40
2252 2505 9.733556 ATGATACACCTTACACAAACTCAAATA 57.266 29.630 0.00 0.0 0.00 1.40
2528 2814 3.255642 GCAAATTAGTGAACAAGGGAGCA 59.744 43.478 0.00 0.0 0.00 4.26
2529 2815 3.507622 AGCAAATTAGTGAACAAGGGAGC 59.492 43.478 0.00 0.0 0.00 4.70
2530 2816 4.156739 GGAGCAAATTAGTGAACAAGGGAG 59.843 45.833 0.00 0.0 0.00 4.30
2531 2817 4.079253 GGAGCAAATTAGTGAACAAGGGA 58.921 43.478 0.00 0.0 0.00 4.20
2533 2819 4.082125 AGGGAGCAAATTAGTGAACAAGG 58.918 43.478 0.00 0.0 0.00 3.61
2534 2820 5.010012 ACAAGGGAGCAAATTAGTGAACAAG 59.990 40.000 0.00 0.0 0.00 3.16
2537 2823 5.241728 AGAACAAGGGAGCAAATTAGTGAAC 59.758 40.000 0.00 0.0 0.00 3.18
2539 2825 4.761739 CAGAACAAGGGAGCAAATTAGTGA 59.238 41.667 0.00 0.0 0.00 3.41
2540 2826 4.520492 ACAGAACAAGGGAGCAAATTAGTG 59.480 41.667 0.00 0.0 0.00 2.74
2541 2827 4.729868 ACAGAACAAGGGAGCAAATTAGT 58.270 39.130 0.00 0.0 0.00 2.24
2542 2828 7.396540 AATACAGAACAAGGGAGCAAATTAG 57.603 36.000 0.00 0.0 0.00 1.73
2546 2832 4.522789 GGAAATACAGAACAAGGGAGCAAA 59.477 41.667 0.00 0.0 0.00 3.68
2628 4789 3.669023 GCACAATGTAGAAAGCTCACTGC 60.669 47.826 0.00 0.0 43.29 4.40
2838 6784 6.696441 AGCAAGAGGAAATGATTCTGATTC 57.304 37.500 0.00 0.0 35.79 2.52
3817 8671 2.186076 CGTGGAGACGCATAGTTCTTC 58.814 52.381 0.00 0.0 42.37 2.87
4057 8952 9.807921 ATCCTTTATTTAAGTTCAACAAGAGGA 57.192 29.630 0.00 0.0 31.56 3.71
4116 9011 5.663106 ACAGAGGAGTAGATATTTTGCCAGA 59.337 40.000 0.00 0.0 0.00 3.86
4578 10080 0.107945 CACTGCCTCCTAACCAGCTC 60.108 60.000 0.00 0.0 0.00 4.09
4768 10331 7.880195 AGAACATAGCTTACAAAAGTGTCTCAT 59.120 33.333 0.00 0.0 39.30 2.90
5189 10922 1.202651 CGTCTCTCTCTCTCTCCCTCC 60.203 61.905 0.00 0.0 0.00 4.30
5190 10923 1.202651 CCGTCTCTCTCTCTCTCCCTC 60.203 61.905 0.00 0.0 0.00 4.30
5191 10924 0.837272 CCGTCTCTCTCTCTCTCCCT 59.163 60.000 0.00 0.0 0.00 4.20
5192 10925 0.834612 TCCGTCTCTCTCTCTCTCCC 59.165 60.000 0.00 0.0 0.00 4.30
5193 10926 1.202651 CCTCCGTCTCTCTCTCTCTCC 60.203 61.905 0.00 0.0 0.00 3.71


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

AutoCloner maintained by Alex Coulton.