Multiple sequence alignment - TraesCS1D01G017000

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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 TraesCS1D01G017000 chr1D 100.000 2782 0 0 1 2782 7693093 7695874 0.000000e+00 5138.0
1 TraesCS1D01G017000 chr1D 90.855 2001 129 29 1 1968 7040622 7038643 0.000000e+00 2632.0
2 TraesCS1D01G017000 chr1D 85.149 1010 71 41 317 1259 7744311 7745308 0.000000e+00 961.0
3 TraesCS1D01G017000 chr1D 83.801 784 112 13 1260 2035 7755938 7756714 0.000000e+00 730.0
4 TraesCS1D01G017000 chr1D 89.216 102 5 3 46 146 7472968 7472872 3.760000e-24 122.0
5 TraesCS1D01G017000 chr1A 94.145 2801 115 27 18 2782 9155353 9158140 0.000000e+00 4218.0
6 TraesCS1D01G017000 chr1A 96.383 1963 63 5 804 2761 9194294 9196253 0.000000e+00 3225.0
7 TraesCS1D01G017000 chr1A 83.312 779 116 7 995 1764 9104015 9103242 0.000000e+00 706.0
8 TraesCS1D01G017000 chr1A 85.027 187 23 4 1 185 9131209 9131392 4.730000e-43 185.0
9 TraesCS1D01G017000 chr1A 92.157 102 4 3 46 146 9105091 9104993 1.040000e-29 141.0
10 TraesCS1D01G017000 chr1A 100.000 36 0 0 2747 2782 9196367 9196402 1.790000e-07 67.6
11 TraesCS1D01G017000 chrUn 95.302 2320 89 10 478 2782 276780832 276778518 0.000000e+00 3663.0
12 TraesCS1D01G017000 chrUn 96.872 1886 51 6 902 2782 278893720 278891838 0.000000e+00 3149.0
13 TraesCS1D01G017000 chrUn 90.526 285 21 3 518 796 76770494 76770778 3.380000e-99 372.0
14 TraesCS1D01G017000 chrUn 90.741 54 5 0 112 165 276781010 276780957 3.840000e-09 73.1
15 TraesCS1D01G017000 chr1B 90.881 1974 134 31 26 1968 9716724 9714766 0.000000e+00 2606.0
16 TraesCS1D01G017000 chr1B 90.754 822 73 3 1149 1968 9673023 9672203 0.000000e+00 1094.0
17 TraesCS1D01G017000 chr1B 89.399 283 30 0 478 760 9673308 9673026 9.480000e-95 357.0
18 TraesCS1D01G017000 chr1B 90.244 123 7 4 26 146 9844309 9844428 3.710000e-34 156.0
19 TraesCS1D01G017000 chr2B 91.720 157 9 3 2220 2374 523078491 523078337 6.030000e-52 215.0
20 TraesCS1D01G017000 chr2A 88.525 183 11 7 2220 2395 497259510 497259331 2.170000e-51 213.0
21 TraesCS1D01G017000 chr2A 87.701 187 14 8 2220 2399 497257244 497257060 2.810000e-50 209.0
22 TraesCS1D01G017000 chr6B 90.323 155 10 4 2216 2370 706024431 706024580 6.080000e-47 198.0
23 TraesCS1D01G017000 chr6B 90.323 155 10 4 2216 2370 706230371 706230520 6.080000e-47 198.0


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 TraesCS1D01G017000 chr1D 7693093 7695874 2781 False 5138.00 5138 100.0000 1 2782 1 chr1D.!!$F1 2781
1 TraesCS1D01G017000 chr1D 7038643 7040622 1979 True 2632.00 2632 90.8550 1 1968 1 chr1D.!!$R1 1967
2 TraesCS1D01G017000 chr1D 7744311 7745308 997 False 961.00 961 85.1490 317 1259 1 chr1D.!!$F2 942
3 TraesCS1D01G017000 chr1D 7755938 7756714 776 False 730.00 730 83.8010 1260 2035 1 chr1D.!!$F3 775
4 TraesCS1D01G017000 chr1A 9155353 9158140 2787 False 4218.00 4218 94.1450 18 2782 1 chr1A.!!$F2 2764
5 TraesCS1D01G017000 chr1A 9194294 9196402 2108 False 1646.30 3225 98.1915 804 2782 2 chr1A.!!$F3 1978
6 TraesCS1D01G017000 chr1A 9103242 9105091 1849 True 423.50 706 87.7345 46 1764 2 chr1A.!!$R1 1718
7 TraesCS1D01G017000 chrUn 278891838 278893720 1882 True 3149.00 3149 96.8720 902 2782 1 chrUn.!!$R1 1880
8 TraesCS1D01G017000 chrUn 276778518 276781010 2492 True 1868.05 3663 93.0215 112 2782 2 chrUn.!!$R2 2670
9 TraesCS1D01G017000 chr1B 9714766 9716724 1958 True 2606.00 2606 90.8810 26 1968 1 chr1B.!!$R1 1942
10 TraesCS1D01G017000 chr1B 9672203 9673308 1105 True 725.50 1094 90.0765 478 1968 2 chr1B.!!$R2 1490
11 TraesCS1D01G017000 chr2A 497257060 497259510 2450 True 211.00 213 88.1130 2220 2399 2 chr2A.!!$R1 179

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
701 979 0.306533 TCTGCAAGAAAACGGCGTTC 59.693 50.0 26.96 14.96 42.31 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2172 2522 0.537188 ACAGCCCACTCGGAATAGTG 59.463 55.0 0.0 0.0 45.33 2.74 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
94 95 9.767684 TGTCGAAAACATTGTACATAATGAATC 57.232 29.630 13.29 7.73 39.79 2.52
149 179 7.978099 AATTTAATTAGGTGCTTGATTCCCT 57.022 32.000 0.00 0.00 0.00 4.20
242 307 7.776500 TGGATTGCATCAAATATTCTGAGAGAA 59.224 33.333 0.00 0.00 38.78 2.87
244 309 9.613957 GATTGCATCAAATATTCTGAGAGAATG 57.386 33.333 8.75 0.00 44.14 2.67
296 361 1.136336 GTCGGTTCGTTTGTCTCATGC 60.136 52.381 0.00 0.00 0.00 4.06
304 369 6.292381 GGTTCGTTTGTCTCATGCTATATGAC 60.292 42.308 0.00 0.00 0.00 3.06
305 370 4.976116 TCGTTTGTCTCATGCTATATGACG 59.024 41.667 0.00 0.00 0.00 4.35
501 731 2.661718 TGTCATGGATGCATGCTTGAT 58.338 42.857 30.28 11.12 35.44 2.57
603 878 1.484240 CTGGGGATGTCAAGGACTCTC 59.516 57.143 0.00 0.00 33.15 3.20
628 903 3.140325 TCTGTTTACTTCCCAGCCTTG 57.860 47.619 0.00 0.00 0.00 3.61
701 979 0.306533 TCTGCAAGAAAACGGCGTTC 59.693 50.000 26.96 14.96 42.31 3.95
719 998 4.437390 GCGTTCACTAATGTTGCTAAGCAT 60.437 41.667 0.00 0.00 38.76 3.79
818 1118 3.879892 GCAGGAAGTCTATTCAATGTCCC 59.120 47.826 0.00 0.00 0.00 4.46
919 1242 8.981672 TCCCATACCCTATATATATCACTCCAT 58.018 37.037 0.00 0.00 0.00 3.41
1200 1538 1.444895 CAACGGCAAGCCAATCTGC 60.445 57.895 12.19 0.00 35.37 4.26
1231 1569 3.808174 CGTCATCCTAGAGTACATCGACA 59.192 47.826 0.00 0.00 0.00 4.35
1318 1656 4.421948 GTTCTGGGTAGACTACATTGACG 58.578 47.826 14.48 0.00 31.21 4.35
1361 1700 7.114882 TGTTTTGTGTTGTTGATTTCACAAG 57.885 32.000 9.00 0.00 46.41 3.16
1643 1987 0.598065 GCAAACCCTTTGACATCGCT 59.402 50.000 0.00 0.00 43.26 4.93
1651 1995 2.615493 CCTTTGACATCGCTAACACCCT 60.615 50.000 0.00 0.00 0.00 4.34
2092 2442 5.049543 CAGAGGTATGGTACGTAGCTTAGAC 60.050 48.000 23.89 16.52 30.62 2.59
2132 2482 8.721133 TGTGCCTTTGATATATAACTCCTCTA 57.279 34.615 0.00 0.00 0.00 2.43
2172 2522 2.224257 GGACAGAAGGAGCTGATGGATC 60.224 54.545 0.00 0.00 39.20 3.36
2215 2565 2.234661 TCTCAACCGCATGACATCTTCT 59.765 45.455 0.00 0.00 0.00 2.85
2230 2580 8.815565 TGACATCTTCTCTCTGTTAGAAGTAT 57.184 34.615 15.96 9.32 46.60 2.12
2231 2581 9.907229 TGACATCTTCTCTCTGTTAGAAGTATA 57.093 33.333 15.96 4.17 46.60 1.47
2413 5036 3.225177 TCTATACGCTCTAGTGGGCTT 57.775 47.619 8.62 0.18 0.00 4.35
2519 5144 1.975660 TCACGACTTTTTCCCAAGGG 58.024 50.000 0.00 0.00 0.00 3.95
2535 5160 2.101640 AGGGAGGCAAATTTTGTGGT 57.898 45.000 10.65 0.00 0.00 4.16
2579 5204 0.446222 CAATTTACCTGCGACGGTGG 59.554 55.000 6.35 0.00 37.93 4.61
2580 5205 1.303091 AATTTACCTGCGACGGTGGC 61.303 55.000 8.28 8.28 37.93 5.01
2581 5206 2.457743 ATTTACCTGCGACGGTGGCA 62.458 55.000 16.91 16.91 37.93 4.92
2741 5368 5.349809 GCATTAATATACTCCTACGAGGCC 58.650 45.833 0.00 0.00 40.77 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 95 5.243981 CCTATCAACCTGCAGAATCCATAG 58.756 45.833 17.39 12.76 0.00 2.23
101 102 1.289160 AGCCCTATCAACCTGCAGAA 58.711 50.000 17.39 0.00 0.00 3.02
103 104 2.171448 AGTTAGCCCTATCAACCTGCAG 59.829 50.000 6.78 6.78 0.00 4.41
105 106 4.417426 TTAGTTAGCCCTATCAACCTGC 57.583 45.455 0.00 0.00 0.00 4.85
106 107 8.974060 TTAAATTAGTTAGCCCTATCAACCTG 57.026 34.615 0.00 0.00 0.00 4.00
296 361 6.761099 ATGTAGCTAAGGTCCGTCATATAG 57.239 41.667 0.00 0.00 0.00 1.31
603 878 5.501156 AGGCTGGGAAGTAAACAGATTAAG 58.499 41.667 0.00 0.00 34.21 1.85
628 903 7.066374 GACATTAGTCATTGTCTTGGAGAAC 57.934 40.000 0.00 0.00 44.34 3.01
684 962 0.248296 GTGAACGCCGTTTTCTTGCA 60.248 50.000 3.07 0.00 0.00 4.08
696 974 3.120338 TGCTTAGCAACATTAGTGAACGC 60.120 43.478 3.67 0.00 34.76 4.84
698 976 6.611381 TCAATGCTTAGCAACATTAGTGAAC 58.389 36.000 12.08 0.00 43.62 3.18
701 979 6.615088 ACTTCAATGCTTAGCAACATTAGTG 58.385 36.000 12.08 0.00 43.62 2.74
818 1118 6.834959 ATTCTGCACAATCACTTAGTATCG 57.165 37.500 0.00 0.00 0.00 2.92
999 1336 1.813859 CTCGTCTTCACCGGCCATA 59.186 57.895 0.00 0.00 0.00 2.74
1361 1700 7.442364 ACATTAATCAGCTCACCACATACATAC 59.558 37.037 0.00 0.00 0.00 2.39
1643 1987 1.278127 GCCAGCAGAAGTAGGGTGTTA 59.722 52.381 0.00 0.00 0.00 2.41
1651 1995 2.214216 ACCCACGCCAGCAGAAGTA 61.214 57.895 0.00 0.00 0.00 2.24
2092 2442 1.666888 GGCACATTTCTTGCGACAAGG 60.667 52.381 16.13 6.09 41.18 3.61
2106 2456 8.212259 AGAGGAGTTATATATCAAAGGCACAT 57.788 34.615 0.00 0.00 0.00 3.21
2107 2457 7.618019 AGAGGAGTTATATATCAAAGGCACA 57.382 36.000 0.00 0.00 0.00 4.57
2109 2459 8.762645 CCATAGAGGAGTTATATATCAAAGGCA 58.237 37.037 0.00 0.00 41.22 4.75
2132 2482 2.311542 TCCTGGTCCTGTATTTTGCCAT 59.688 45.455 0.00 0.00 0.00 4.40
2140 2490 2.044492 TCCTTCTGTCCTGGTCCTGTAT 59.956 50.000 0.00 0.00 0.00 2.29
2172 2522 0.537188 ACAGCCCACTCGGAATAGTG 59.463 55.000 0.00 0.00 45.33 2.74
2231 2581 9.760077 CTCCTAATCCATAACTAACACGTTTAT 57.240 33.333 0.00 0.00 0.00 1.40
2519 5144 3.187022 GCATCAACCACAAAATTTGCCTC 59.813 43.478 5.52 0.00 0.00 4.70
2535 5160 2.548707 CCTCGCCTAGCTAATGCATCAA 60.549 50.000 0.00 0.00 42.74 2.57
2579 5204 3.126858 TGCGAAAGTGAAATATGGTCTGC 59.873 43.478 0.00 0.00 0.00 4.26
2580 5205 4.944962 TGCGAAAGTGAAATATGGTCTG 57.055 40.909 0.00 0.00 0.00 3.51
2581 5206 7.807977 AATATGCGAAAGTGAAATATGGTCT 57.192 32.000 0.00 0.00 0.00 3.85
2582 5207 8.856490 AAAATATGCGAAAGTGAAATATGGTC 57.144 30.769 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.