Multiple sequence alignment - TraesCS1B01G035000

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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 TraesCS1B01G035000 chr1B 100.000 2255 0 0 1 2255 16659539 16657285 0.000000e+00 4165.0
1 TraesCS1B01G035000 chr1B 93.099 1710 70 10 1 1685 16503556 16501870 0.000000e+00 2460.0
2 TraesCS1B01G035000 chr1B 89.281 793 64 19 5 786 17332800 17332018 0.000000e+00 974.0
3 TraesCS1B01G035000 chr1B 88.171 820 89 5 533 1351 16668905 16668093 0.000000e+00 970.0
4 TraesCS1B01G035000 chr1D 93.954 1687 89 10 5 1685 11098590 11096911 0.000000e+00 2538.0
5 TraesCS1B01G035000 chr1D 93.835 1687 90 11 5 1685 11051053 11049375 0.000000e+00 2527.0
6 TraesCS1B01G035000 chr1D 93.717 1687 93 10 5 1685 11013256 11011577 0.000000e+00 2516.0
7 TraesCS1B01G035000 chr1D 93.444 1693 74 13 1 1685 11133022 11131359 0.000000e+00 2477.0
8 TraesCS1B01G035000 chr1D 86.157 1387 132 24 84 1438 11137023 11135665 0.000000e+00 1443.0
9 TraesCS1B01G035000 chr1D 85.194 1290 153 29 192 1462 11207139 11205869 0.000000e+00 1290.0
10 TraesCS1B01G035000 chrUn 92.379 1509 71 23 184 1685 159669 158198 0.000000e+00 2109.0
11 TraesCS1B01G035000 chr1A 90.418 1461 121 12 2 1450 22626188 22627641 0.000000e+00 1905.0
12 TraesCS1B01G035000 chr1A 88.616 571 62 3 1685 2255 58376068 58375501 0.000000e+00 691.0
13 TraesCS1B01G035000 chr1A 90.566 53 5 0 1633 1685 22627844 22627896 1.120000e-08 71.3
14 TraesCS1B01G035000 chr7A 95.789 570 23 1 1686 2255 80367704 80367136 0.000000e+00 918.0
15 TraesCS1B01G035000 chr5A 95.455 572 24 2 1684 2255 7964123 7964692 0.000000e+00 911.0
16 TraesCS1B01G035000 chr5A 93.881 572 21 2 1684 2255 8016964 8017521 0.000000e+00 850.0
17 TraesCS1B01G035000 chr5A 93.520 571 23 2 1685 2255 8047903 8048459 0.000000e+00 837.0
18 TraesCS1B01G035000 chr5A 93.357 572 24 2 1684 2255 7988251 7988808 0.000000e+00 833.0
19 TraesCS1B01G035000 chr2B 95.263 570 26 1 1686 2255 128368394 128368962 0.000000e+00 902.0
20 TraesCS1B01G035000 chr3A 92.670 573 41 1 1683 2255 729955502 729954931 0.000000e+00 824.0
21 TraesCS1B01G035000 chr4D 90.893 571 51 1 1685 2255 57060213 57059644 0.000000e+00 765.0
22 TraesCS1B01G035000 chr2A 86.982 169 18 4 1474 1639 135473229 135473396 1.060000e-43 187.0
23 TraesCS1B01G035000 chr2A 86.471 170 19 4 1470 1635 245782648 245782479 1.380000e-42 183.0
24 TraesCS1B01G035000 chr4B 87.578 161 16 4 1474 1631 406391052 406391211 1.380000e-42 183.0
25 TraesCS1B01G035000 chr4B 87.578 161 16 4 1474 1631 406391262 406391421 1.380000e-42 183.0


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 TraesCS1B01G035000 chr1B 16657285 16659539 2254 True 4165.00 4165 100.0000 1 2255 1 chr1B.!!$R2 2254
1 TraesCS1B01G035000 chr1B 16501870 16503556 1686 True 2460.00 2460 93.0990 1 1685 1 chr1B.!!$R1 1684
2 TraesCS1B01G035000 chr1B 17332018 17332800 782 True 974.00 974 89.2810 5 786 1 chr1B.!!$R4 781
3 TraesCS1B01G035000 chr1B 16668093 16668905 812 True 970.00 970 88.1710 533 1351 1 chr1B.!!$R3 818
4 TraesCS1B01G035000 chr1D 11096911 11098590 1679 True 2538.00 2538 93.9540 5 1685 1 chr1D.!!$R3 1680
5 TraesCS1B01G035000 chr1D 11049375 11051053 1678 True 2527.00 2527 93.8350 5 1685 1 chr1D.!!$R2 1680
6 TraesCS1B01G035000 chr1D 11011577 11013256 1679 True 2516.00 2516 93.7170 5 1685 1 chr1D.!!$R1 1680
7 TraesCS1B01G035000 chr1D 11131359 11137023 5664 True 1960.00 2477 89.8005 1 1685 2 chr1D.!!$R5 1684
8 TraesCS1B01G035000 chr1D 11205869 11207139 1270 True 1290.00 1290 85.1940 192 1462 1 chr1D.!!$R4 1270
9 TraesCS1B01G035000 chrUn 158198 159669 1471 True 2109.00 2109 92.3790 184 1685 1 chrUn.!!$R1 1501
10 TraesCS1B01G035000 chr1A 22626188 22627896 1708 False 988.15 1905 90.4920 2 1685 2 chr1A.!!$F1 1683
11 TraesCS1B01G035000 chr1A 58375501 58376068 567 True 691.00 691 88.6160 1685 2255 1 chr1A.!!$R1 570
12 TraesCS1B01G035000 chr7A 80367136 80367704 568 True 918.00 918 95.7890 1686 2255 1 chr7A.!!$R1 569
13 TraesCS1B01G035000 chr5A 7964123 7964692 569 False 911.00 911 95.4550 1684 2255 1 chr5A.!!$F1 571
14 TraesCS1B01G035000 chr5A 8016964 8017521 557 False 850.00 850 93.8810 1684 2255 1 chr5A.!!$F3 571
15 TraesCS1B01G035000 chr5A 8047903 8048459 556 False 837.00 837 93.5200 1685 2255 1 chr5A.!!$F4 570
16 TraesCS1B01G035000 chr5A 7988251 7988808 557 False 833.00 833 93.3570 1684 2255 1 chr5A.!!$F2 571
17 TraesCS1B01G035000 chr2B 128368394 128368962 568 False 902.00 902 95.2630 1686 2255 1 chr2B.!!$F1 569
18 TraesCS1B01G035000 chr3A 729954931 729955502 571 True 824.00 824 92.6700 1683 2255 1 chr3A.!!$R1 572
19 TraesCS1B01G035000 chr4D 57059644 57060213 569 True 765.00 765 90.8930 1685 2255 1 chr4D.!!$R1 570

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
182 4185 2.552093 AGTACTGCAGGTATGTCCCT 57.448 50.0 19.93 0.0 36.75 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2104 6276 0.391395 CAGGAGCAGTGGCAAGAGAG 60.391 60.0 0.0 0.0 44.61 3.2 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
170 4173 7.538678 CCATGTAGAAACAAATTGAAGTACTGC 59.461 37.037 0.00 0.00 39.58 4.40
182 4185 2.552093 AGTACTGCAGGTATGTCCCT 57.448 50.000 19.93 0.00 36.75 4.20
246 4250 3.139077 CAAGGTACCTCCACTTGTTGTC 58.861 50.000 16.64 0.00 37.43 3.18
357 4367 7.710475 TGCAAACTTGAAGGGAAAGAAATAAAG 59.290 33.333 0.00 0.00 0.00 1.85
487 4504 6.110411 AGAAAAGTTCTTTATCCGTCTGGA 57.890 37.500 0.00 0.00 42.96 3.86
658 4682 6.222038 TCGAGGTAGATAAGCATCACTTTT 57.778 37.500 0.00 0.00 39.97 2.27
692 4718 6.956299 GTGTAGGCACGTAATTCTCTAAAA 57.044 37.500 0.00 0.00 35.75 1.52
758 4807 3.901844 TGAAGTTAGCAAGGAGTACACCT 59.098 43.478 5.96 5.96 42.69 4.00
822 4871 6.939163 AGTTGAGCCTGATTGCCTATAAATAG 59.061 38.462 0.00 0.00 0.00 1.73
837 4886 7.824779 GCCTATAAATAGACATTAAGGTGAGGG 59.175 40.741 0.00 0.00 32.05 4.30
854 4903 3.008923 TGAGGGCATGACAGTTCAACATA 59.991 43.478 0.00 0.00 34.61 2.29
858 4907 4.581824 GGGCATGACAGTTCAACATATCAT 59.418 41.667 0.00 0.00 34.61 2.45
868 4917 7.877612 ACAGTTCAACATATCATAGTCACACAA 59.122 33.333 0.00 0.00 0.00 3.33
905 4954 4.692625 CCTCATAGGTTAGTATGTGCATGC 59.307 45.833 11.82 11.82 32.93 4.06
958 5007 5.754890 GCAGGTGATTTTCTGTGACAATTTT 59.245 36.000 0.00 0.00 33.81 1.82
959 5008 6.258507 GCAGGTGATTTTCTGTGACAATTTTT 59.741 34.615 0.00 0.00 33.81 1.94
1009 5059 2.826128 AGCGTCACAAGGATGAGTTCTA 59.174 45.455 0.00 0.00 34.22 2.10
1018 5068 5.121811 CAAGGATGAGTTCTATGGTGAAGG 58.878 45.833 0.00 0.00 0.00 3.46
1021 5071 4.651503 GGATGAGTTCTATGGTGAAGGAGA 59.348 45.833 0.00 0.00 0.00 3.71
1046 5096 1.766496 GGGAGGGAACACCGATATTGA 59.234 52.381 0.00 0.00 46.96 2.57
1049 5099 3.403038 GAGGGAACACCGATATTGATGG 58.597 50.000 0.00 0.00 46.96 3.51
1081 5131 0.390998 GAAGACAGAGTGGCCAGAGC 60.391 60.000 5.11 0.00 38.76 4.09
1092 5142 3.170362 CCAGAGCTGGTGGGGAAA 58.830 61.111 8.38 0.00 45.53 3.13
1271 5321 4.864704 GCTAGCAAGCCTAAGATCTAGT 57.135 45.455 10.63 0.00 43.40 2.57
1332 5382 6.810911 TCTTCTTGGATATAGCAAGACTGAC 58.189 40.000 0.00 0.00 35.05 3.51
1432 5487 8.988546 ATATGGTTATGGTTTGTATGTAAGCA 57.011 30.769 0.00 0.00 37.23 3.91
1573 5745 5.594317 AGTGTAGGTTCACTCATTTTGCTTT 59.406 36.000 0.00 0.00 44.07 3.51
1622 5794 9.321562 CGCTAAAAGGACTTATATTTAGGAACA 57.678 33.333 0.00 0.00 36.39 3.18
1631 5803 8.024145 ACTTATATTTAGGAACAGAGGGAGTG 57.976 38.462 0.00 0.00 0.00 3.51
1635 5807 4.618920 TTAGGAACAGAGGGAGTGTTTC 57.381 45.455 0.00 0.00 38.26 2.78
1903 6075 5.136828 CCCATCTCTTTGCTCTCTAGTAGA 58.863 45.833 0.00 0.00 0.00 2.59
1977 6149 7.281999 TGCATTTGAACTATCCGATTCAATGTA 59.718 33.333 0.62 0.22 42.72 2.29
2104 6276 2.802816 CGCTATAAAGTCACCATGCTCC 59.197 50.000 0.00 0.00 0.00 4.70
2109 6281 1.949799 AAGTCACCATGCTCCTCTCT 58.050 50.000 0.00 0.00 0.00 3.10
2128 6300 1.414866 TTGCCACTGCTCCTGTACCA 61.415 55.000 0.00 0.00 38.71 3.25
2167 6339 4.378356 GCACTGAAAGATGCGTCAACATTA 60.378 41.667 8.99 0.00 37.43 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
281 4286 8.344831 TGCACCAAAATATCTTCATTTCTATCG 58.655 33.333 0.00 0.00 0.00 2.92
396 4408 5.825679 TCAAGGCAAGCTAAGAAGTTTGTAA 59.174 36.000 0.00 0.00 43.63 2.41
487 4504 4.136796 ACACAACACTGCATACAACTCAT 58.863 39.130 0.00 0.00 0.00 2.90
692 4718 4.956075 ACGAAGATATCCCATTTGGCTTTT 59.044 37.500 0.00 0.00 0.00 2.27
758 4807 5.588648 AGTTCTGCACACAAAGTAAGCTAAA 59.411 36.000 0.00 0.00 0.00 1.85
822 4871 2.945668 GTCATGCCCTCACCTTAATGTC 59.054 50.000 0.00 0.00 0.00 3.06
837 4886 7.225341 TGACTATGATATGTTGAACTGTCATGC 59.775 37.037 15.57 8.99 32.48 4.06
854 4903 7.495606 TGATTAAATCGCTTGTGTGACTATGAT 59.504 33.333 0.00 0.00 35.34 2.45
858 4907 5.063438 GCTGATTAAATCGCTTGTGTGACTA 59.937 40.000 0.00 0.00 35.34 2.59
868 4917 4.040952 ACCTATGAGGCTGATTAAATCGCT 59.959 41.667 0.00 0.00 39.63 4.93
958 5007 8.568676 TCCTATGATCAAAACAAATAACCGAA 57.431 30.769 0.00 0.00 0.00 4.30
959 5008 8.568676 TTCCTATGATCAAAACAAATAACCGA 57.431 30.769 0.00 0.00 0.00 4.69
979 5029 1.608025 CCTTGTGACGCTTGCTTCCTA 60.608 52.381 0.00 0.00 0.00 2.94
1009 5059 0.978146 CCCTCCGTCTCCTTCACCAT 60.978 60.000 0.00 0.00 0.00 3.55
1018 5068 1.305046 TGTTCCCTCCCTCCGTCTC 60.305 63.158 0.00 0.00 0.00 3.36
1021 5071 2.606826 GGTGTTCCCTCCCTCCGT 60.607 66.667 0.00 0.00 0.00 4.69
1046 5096 1.355381 TCTTCTGGTTGTGATGGCCAT 59.645 47.619 20.96 20.96 0.00 4.40
1049 5099 1.808945 CTGTCTTCTGGTTGTGATGGC 59.191 52.381 0.00 0.00 0.00 4.40
1081 5131 1.378514 CCACCGATTTCCCCACCAG 60.379 63.158 0.00 0.00 0.00 4.00
1092 5142 2.285368 TTGGCCTCCTCCACCGAT 60.285 61.111 3.32 0.00 35.50 4.18
1260 5310 3.255642 GCCAGGAGCAGACTAGATCTTAG 59.744 52.174 0.00 0.00 42.97 2.18
1271 5321 1.704641 ACATATACGCCAGGAGCAGA 58.295 50.000 0.00 0.00 44.04 4.26
1432 5487 7.992608 TGTAAACAGATATATGACACCAAGCAT 59.007 33.333 3.93 0.00 0.00 3.79
1465 5637 2.431057 AGAACGGATGGAGTGTATGGTC 59.569 50.000 0.00 0.00 0.00 4.02
1505 5677 6.012337 TCCCATGCAGTCCTTATTGAAATA 57.988 37.500 0.00 0.00 0.00 1.40
1622 5794 2.695585 ACCTTCTGAAACACTCCCTCT 58.304 47.619 0.00 0.00 0.00 3.69
1631 5803 8.951243 AGCTATTTCAATTCTACCTTCTGAAAC 58.049 33.333 0.00 0.00 38.45 2.78
1842 6014 7.280205 CGAAATATGAAGTAAGTAACTGCCCTT 59.720 37.037 0.00 0.00 38.88 3.95
1903 6075 0.618458 TGGGACAAGAAGCGGCTATT 59.382 50.000 1.35 0.00 31.92 1.73
1977 6149 5.583457 GGCAAGATTGGTTGTAACGTAGTAT 59.417 40.000 0.00 0.00 45.00 2.12
1983 6155 2.668279 GCTGGCAAGATTGGTTGTAACG 60.668 50.000 0.00 0.00 0.00 3.18
2104 6276 0.391395 CAGGAGCAGTGGCAAGAGAG 60.391 60.000 0.00 0.00 44.61 3.20
2109 6281 1.374947 GGTACAGGAGCAGTGGCAA 59.625 57.895 0.00 0.00 44.61 4.52
2167 6339 5.185828 GCCAATGAGAGGAGTGGTTAAAATT 59.814 40.000 0.00 0.00 33.45 1.82


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

AutoCloner maintained by Alex Coulton.