Multiple sequence alignment - TraesCS2A01G499000

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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 TraesCS2A01G499000 chr2A 100.000 2606 0 0 1 2606 728940455 728943060 0 4813
1 TraesCS2A01G499000 chr2A 99.372 637 3 1 1 636 148608737 148608101 0 1153
2 TraesCS2A01G499000 chr2A 99.057 636 6 0 1 636 752752065 752751430 0 1142
3 TraesCS2A01G499000 chr2D 91.351 1480 59 26 637 2083 594449421 594450864 0 1960
4 TraesCS2A01G499000 chr2D 92.453 477 23 5 2143 2606 594450860 594451336 0 669
5 TraesCS2A01G499000 chr2B 90.873 1501 67 29 637 2089 721715311 721716789 0 1949
6 TraesCS2A01G499000 chr2B 93.151 511 24 2 2107 2606 721716847 721717357 0 739
7 TraesCS2A01G499000 chr3A 99.371 636 4 0 1 636 69954354 69954989 0 1153
8 TraesCS2A01G499000 chr1B 99.214 636 5 0 1 636 443571423 443572058 0 1147
9 TraesCS2A01G499000 chr1B 98.899 636 4 3 1 636 302765688 302765056 0 1133
10 TraesCS2A01G499000 chr7A 99.214 636 3 1 1 636 16011679 16012312 0 1146
11 TraesCS2A01G499000 chr7B 99.057 636 5 1 1 636 133424549 133423915 0 1140
12 TraesCS2A01G499000 chr7B 98.901 637 6 1 1 636 102657056 102657692 0 1136
13 TraesCS2A01G499000 chr3B 98.903 638 7 0 1 638 798605852 798605215 0 1140


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 TraesCS2A01G499000 chr2A 728940455 728943060 2605 False 4813.0 4813 100.000 1 2606 1 chr2A.!!$F1 2605
1 TraesCS2A01G499000 chr2A 148608101 148608737 636 True 1153.0 1153 99.372 1 636 1 chr2A.!!$R1 635
2 TraesCS2A01G499000 chr2A 752751430 752752065 635 True 1142.0 1142 99.057 1 636 1 chr2A.!!$R2 635
3 TraesCS2A01G499000 chr2D 594449421 594451336 1915 False 1314.5 1960 91.902 637 2606 2 chr2D.!!$F1 1969
4 TraesCS2A01G499000 chr2B 721715311 721717357 2046 False 1344.0 1949 92.012 637 2606 2 chr2B.!!$F1 1969
5 TraesCS2A01G499000 chr3A 69954354 69954989 635 False 1153.0 1153 99.371 1 636 1 chr3A.!!$F1 635
6 TraesCS2A01G499000 chr1B 443571423 443572058 635 False 1147.0 1147 99.214 1 636 1 chr1B.!!$F1 635
7 TraesCS2A01G499000 chr1B 302765056 302765688 632 True 1133.0 1133 98.899 1 636 1 chr1B.!!$R1 635
8 TraesCS2A01G499000 chr7A 16011679 16012312 633 False 1146.0 1146 99.214 1 636 1 chr7A.!!$F1 635
9 TraesCS2A01G499000 chr7B 133423915 133424549 634 True 1140.0 1140 99.057 1 636 1 chr7B.!!$R1 635
10 TraesCS2A01G499000 chr7B 102657056 102657692 636 False 1136.0 1136 98.901 1 636 1 chr7B.!!$F1 635
11 TraesCS2A01G499000 chr3B 798605215 798605852 637 True 1140.0 1140 98.903 1 638 1 chr3B.!!$R1 637

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
945 963 0.106719 CCTCCTCCTTCTCTCGCTCT 60.107 60.0 0.0 0.0 0.0 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2475 2603 0.331616 ATAACCACCCCTCAAGCACC 59.668 55.0 0.0 0.0 0.0 5.01 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
615 617 4.019141 TCGGGATTTAGTTTGCCTTAAGGA 60.019 41.667 26.21 7.61 37.39 3.36
717 724 2.300152 TCTCTCTCCACCATCACAACAC 59.700 50.000 0.00 0.00 0.00 3.32
737 744 4.415332 CAAAGGCAGCAGCGGCAG 62.415 66.667 19.73 3.80 44.61 4.85
799 810 4.835284 ATCTTCCTCACCTTCTTCTTCC 57.165 45.455 0.00 0.00 0.00 3.46
800 811 3.863086 TCTTCCTCACCTTCTTCTTCCT 58.137 45.455 0.00 0.00 0.00 3.36
903 919 0.252284 TCCCGCCTTTCCTCTCTCTT 60.252 55.000 0.00 0.00 0.00 2.85
910 928 3.428862 GCCTTTCCTCTCTCTTTCTCTCG 60.429 52.174 0.00 0.00 0.00 4.04
935 953 0.933700 CTCTCCTCCTCCTCCTCCTT 59.066 60.000 0.00 0.00 0.00 3.36
936 954 0.930726 TCTCCTCCTCCTCCTCCTTC 59.069 60.000 0.00 0.00 0.00 3.46
941 959 0.548989 TCCTCCTCCTCCTTCTCTCG 59.451 60.000 0.00 0.00 0.00 4.04
944 962 0.106918 TCCTCCTCCTTCTCTCGCTC 60.107 60.000 0.00 0.00 0.00 5.03
945 963 0.106719 CCTCCTCCTTCTCTCGCTCT 60.107 60.000 0.00 0.00 0.00 4.09
958 981 2.433318 GCTCTGCGAGGTGTGGTC 60.433 66.667 7.50 0.00 0.00 4.02
972 995 1.048601 GTGGTCAGTTGAGGTGAGGA 58.951 55.000 0.00 0.00 0.00 3.71
991 1014 0.322546 AGAGGATTTTGGGTGGACGC 60.323 55.000 0.00 0.00 0.00 5.19
993 1016 1.969589 GGATTTTGGGTGGACGCGT 60.970 57.895 13.85 13.85 0.00 6.01
1040 1063 1.628846 GGAGAGCTCAAACCCTAACCA 59.371 52.381 17.77 0.00 0.00 3.67
1209 1232 3.506059 CTACTCCTCCATGGCGCGG 62.506 68.421 8.83 7.55 35.26 6.46
1377 1403 4.070552 GTCGCCCTCGCTCCTGTT 62.071 66.667 0.00 0.00 35.26 3.16
1383 1409 2.125912 CTCGCTCCTGTTGTCGGG 60.126 66.667 0.00 0.00 41.27 5.14
1386 1412 2.743928 GCTCCTGTTGTCGGGCAG 60.744 66.667 0.00 0.00 39.81 4.85
1387 1419 2.743928 CTCCTGTTGTCGGGCAGC 60.744 66.667 0.00 0.00 39.81 5.25
1619 1654 2.490351 GCCAATGATCCATCCAGTCCAT 60.490 50.000 0.00 0.00 0.00 3.41
1620 1655 3.418995 CCAATGATCCATCCAGTCCATC 58.581 50.000 0.00 0.00 0.00 3.51
1621 1656 3.181437 CCAATGATCCATCCAGTCCATCA 60.181 47.826 0.00 0.00 0.00 3.07
1622 1657 4.508584 CCAATGATCCATCCAGTCCATCAT 60.509 45.833 0.00 0.00 36.04 2.45
1623 1658 4.571369 ATGATCCATCCAGTCCATCATC 57.429 45.455 0.00 0.00 29.91 2.92
1624 1659 2.301009 TGATCCATCCAGTCCATCATCG 59.699 50.000 0.00 0.00 0.00 3.84
1687 1722 8.732746 TCTAAATTATTACTTCTTCCTGCACC 57.267 34.615 0.00 0.00 0.00 5.01
1688 1723 6.436843 AAATTATTACTTCTTCCTGCACCG 57.563 37.500 0.00 0.00 0.00 4.94
1689 1724 4.546829 TTATTACTTCTTCCTGCACCGT 57.453 40.909 0.00 0.00 0.00 4.83
1694 1737 0.108804 TTCTTCCTGCACCGTCGATC 60.109 55.000 0.00 0.00 0.00 3.69
1704 1747 2.405357 GCACCGTCGATCGAAATCATAG 59.595 50.000 21.31 7.50 42.86 2.23
1706 1749 2.030185 ACCGTCGATCGAAATCATAGGG 60.030 50.000 21.31 13.16 42.86 3.53
1723 1787 3.876274 AGGGTTCCATGATATCGATCG 57.124 47.619 9.36 9.36 34.49 3.69
1724 1788 2.497675 AGGGTTCCATGATATCGATCGG 59.502 50.000 16.41 0.00 34.49 4.18
1792 1856 4.443725 CGCGCATGATCAATATAGAGGATC 59.556 45.833 8.75 0.00 38.29 3.36
1799 1863 3.779444 TCAATATAGAGGATCACCGGCT 58.221 45.455 0.00 0.00 41.83 5.52
1833 1897 2.356780 GGTACGGTGGAGGTGGAGG 61.357 68.421 0.00 0.00 0.00 4.30
1839 1903 1.554583 GGTGGAGGTGGAGGGAAGAC 61.555 65.000 0.00 0.00 0.00 3.01
2017 2081 9.684448 ATCGATCGATATGGATTTACATATGTC 57.316 33.333 28.45 0.00 42.48 3.06
2096 2160 9.114952 TGTTCTTGATTGAACTACAAACACATA 57.885 29.630 8.52 0.00 44.63 2.29
2099 2163 9.283768 TCTTGATTGAACTACAAACACATATGT 57.716 29.630 1.41 1.41 40.11 2.29
2130 2234 3.141398 CCATGTCATGTGGGTGCTATAC 58.859 50.000 11.84 0.00 32.98 1.47
2166 2270 4.965814 AGATGTGTAGGTTATGAGGCATG 58.034 43.478 0.00 0.00 0.00 4.06
2191 2295 6.015265 GTCTGTACTCTTCCCTTTCTGTTACT 60.015 42.308 0.00 0.00 0.00 2.24
2194 2298 7.215085 TGTACTCTTCCCTTTCTGTTACTTTC 58.785 38.462 0.00 0.00 0.00 2.62
2220 2324 8.367660 TCTCTTGTAGGTCTATCTGTGAATTT 57.632 34.615 0.00 0.00 0.00 1.82
2234 2338 6.506147 TCTGTGAATTTTGATTGGTGAACAG 58.494 36.000 0.00 0.00 34.13 3.16
2405 2528 1.535462 CAAAAGGTAGTTCCCTGCACG 59.465 52.381 0.00 0.00 34.19 5.34
2465 2588 0.394352 TAGCTAGCTGCCTTTTGCCC 60.394 55.000 27.68 0.00 44.23 5.36
2475 2603 1.478105 GCCTTTTGCCCTGTGATTAGG 59.522 52.381 0.00 0.00 37.59 2.69
2506 2634 3.054213 GGGGTGGTTATGCTTAGGTTGTA 60.054 47.826 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
717 724 4.047059 CCGCTGCTGCCTTTGTGG 62.047 66.667 10.24 0.20 39.35 4.17
747 758 1.600916 ACAAAGCGGGGAGAGCAAC 60.601 57.895 0.00 0.00 37.01 4.17
799 810 1.075600 GGGTGGGGGAGAGAGAGAG 60.076 68.421 0.00 0.00 0.00 3.20
800 811 1.452226 TTGGGTGGGGGAGAGAGAGA 61.452 60.000 0.00 0.00 0.00 3.10
903 919 1.749638 GGAGAGGGCGACGAGAGAA 60.750 63.158 0.00 0.00 0.00 2.87
910 928 2.835895 GGAGGAGGAGAGGGCGAC 60.836 72.222 0.00 0.00 0.00 5.19
944 962 1.069765 AACTGACCACACCTCGCAG 59.930 57.895 0.00 0.00 0.00 5.18
945 963 1.227527 CAACTGACCACACCTCGCA 60.228 57.895 0.00 0.00 0.00 5.10
958 981 1.930251 TCCTCTCCTCACCTCAACTG 58.070 55.000 0.00 0.00 0.00 3.16
972 995 0.322546 GCGTCCACCCAAAATCCTCT 60.323 55.000 0.00 0.00 0.00 3.69
993 1016 0.953471 CCTTGGCGTCCATCAAACGA 60.953 55.000 0.00 0.00 42.62 3.85
1040 1063 2.732094 GTACGCTGGCAACGACGT 60.732 61.111 18.16 12.86 42.22 4.34
1188 1211 2.434843 CGCCATGGAGGAGTAGGCA 61.435 63.158 18.40 0.00 45.47 4.75
1361 1387 4.069232 CAACAGGAGCGAGGGCGA 62.069 66.667 0.00 0.00 46.35 5.54
1366 1392 2.125912 CCCGACAACAGGAGCGAG 60.126 66.667 0.00 0.00 0.00 5.03
1367 1393 4.373116 GCCCGACAACAGGAGCGA 62.373 66.667 0.00 0.00 0.00 4.93
1377 1403 4.451150 GACGATGGCTGCCCGACA 62.451 66.667 21.39 1.47 33.07 4.35
1619 1654 3.997762 TGCATGATGATGATGACGATGA 58.002 40.909 0.00 0.00 0.00 2.92
1620 1655 4.201822 GGATGCATGATGATGATGACGATG 60.202 45.833 2.46 0.00 0.00 3.84
1621 1656 3.939592 GGATGCATGATGATGATGACGAT 59.060 43.478 2.46 0.00 0.00 3.73
1622 1657 3.007614 AGGATGCATGATGATGATGACGA 59.992 43.478 2.46 0.00 0.00 4.20
1623 1658 3.335579 AGGATGCATGATGATGATGACG 58.664 45.455 2.46 0.00 0.00 4.35
1624 1659 3.690139 GGAGGATGCATGATGATGATGAC 59.310 47.826 2.46 0.00 0.00 3.06
1687 1722 3.284323 ACCCTATGATTTCGATCGACG 57.716 47.619 19.26 0.52 44.09 5.12
1688 1723 3.988517 GGAACCCTATGATTTCGATCGAC 59.011 47.826 19.26 7.33 0.00 4.20
1689 1724 3.639561 TGGAACCCTATGATTTCGATCGA 59.360 43.478 15.15 15.15 0.00 3.59
1694 1737 7.545362 GATATCATGGAACCCTATGATTTCG 57.455 40.000 9.04 0.00 42.37 3.46
1704 1747 2.233922 ACCGATCGATATCATGGAACCC 59.766 50.000 18.66 0.00 31.93 4.11
1706 1749 3.056821 TCCACCGATCGATATCATGGAAC 60.057 47.826 18.66 0.00 41.10 3.62
1723 1787 3.686726 GTCACATGAACAAGAGATCCACC 59.313 47.826 0.00 0.00 0.00 4.61
1724 1788 4.318332 TGTCACATGAACAAGAGATCCAC 58.682 43.478 0.00 0.00 0.00 4.02
1799 1863 0.714180 TACCTAACTCTCCCCTGCCA 59.286 55.000 0.00 0.00 0.00 4.92
1833 1897 6.919775 ACATATATACTCCACCAGTCTTCC 57.080 41.667 0.00 0.00 36.43 3.46
1839 1903 6.162079 CAGCTCAACATATATACTCCACCAG 58.838 44.000 0.00 0.00 0.00 4.00
2016 2080 5.337250 CCCAACAACACTGCACTAGTATAGA 60.337 44.000 11.35 0.00 42.77 1.98
2017 2081 4.870426 CCCAACAACACTGCACTAGTATAG 59.130 45.833 0.00 0.00 46.50 1.31
2089 2153 9.440773 GACATGGTATCATATCACATATGTGTT 57.559 33.333 30.03 25.01 42.49 3.32
2091 2155 9.609346 ATGACATGGTATCATATCACATATGTG 57.391 33.333 26.83 26.83 39.32 3.21
2093 2157 9.609346 ACATGACATGGTATCATATCACATATG 57.391 33.333 19.39 0.00 39.32 1.78
2096 2160 6.882678 CCACATGACATGGTATCATATCACAT 59.117 38.462 19.39 0.00 39.32 3.21
2097 2161 6.232692 CCACATGACATGGTATCATATCACA 58.767 40.000 19.39 0.00 39.32 3.58
2098 2162 5.645067 CCCACATGACATGGTATCATATCAC 59.355 44.000 19.39 0.00 39.32 3.06
2099 2163 5.310331 ACCCACATGACATGGTATCATATCA 59.690 40.000 19.39 0.00 40.58 2.15
2103 2167 3.824133 CACCCACATGACATGGTATCAT 58.176 45.455 19.39 0.00 37.27 2.45
2104 2168 2.683447 GCACCCACATGACATGGTATCA 60.683 50.000 19.39 0.00 35.23 2.15
2166 2270 4.875561 ACAGAAAGGGAAGAGTACAGAC 57.124 45.455 0.00 0.00 0.00 3.51
2191 2295 7.175797 TCACAGATAGACCTACAAGAGAGAAA 58.824 38.462 0.00 0.00 0.00 2.52
2194 2298 7.581213 ATTCACAGATAGACCTACAAGAGAG 57.419 40.000 0.00 0.00 0.00 3.20
2220 2324 8.429237 AATTAATTACCCTGTTCACCAATCAA 57.571 30.769 0.00 0.00 0.00 2.57
2234 2338 8.060689 TGGTAAAGTTCCCCTAATTAATTACCC 58.939 37.037 3.71 0.00 39.16 3.69
2389 2505 1.671742 CACGTGCAGGGAACTACCT 59.328 57.895 11.67 0.00 43.08 3.08
2390 2506 2.033194 GCACGTGCAGGGAACTACC 61.033 63.158 34.52 0.19 40.21 3.18
2410 2533 2.791655 CATCATCCAGCTATGCATGGT 58.208 47.619 10.16 2.08 37.84 3.55
2416 2539 3.196039 AGCTAGAGCATCATCCAGCTATG 59.804 47.826 4.01 0.00 45.16 2.23
2465 2588 2.636830 CCTCAAGCACCCTAATCACAG 58.363 52.381 0.00 0.00 0.00 3.66
2475 2603 0.331616 ATAACCACCCCTCAAGCACC 59.668 55.000 0.00 0.00 0.00 5.01
2506 2634 5.279456 GCTTGGAAAATAAACACTCCACCAT 60.279 40.000 0.00 0.00 37.69 3.55


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

AutoCloner maintained by Alex Coulton.