Multiple sequence alignment - TraesCS1B01G343400

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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 TraesCS1B01G343400 chr1B 100.000 2549 0 0 1 2549 571670262 571672810 0 4708
1 TraesCS1B01G343400 chr1B 92.550 1141 71 8 574 1701 154580594 154581733 0 1624
2 TraesCS1B01G343400 chr1B 92.021 1153 77 8 563 1701 663786484 663787635 0 1605
3 TraesCS1B01G343400 chr4D 93.140 1997 114 4 574 2549 43272763 43270769 0 2907
4 TraesCS1B01G343400 chr4D 90.435 575 50 5 1 572 417529813 417530385 0 752
5 TraesCS1B01G343400 chr4D 90.278 576 51 5 1 574 159961337 159961909 0 749
6 TraesCS1B01G343400 chr7B 92.939 1997 114 10 573 2549 523399855 523397866 0 2881
7 TraesCS1B01G343400 chr7B 92.743 1998 117 11 573 2549 523525077 523523087 0 2861
8 TraesCS1B01G343400 chr3B 92.893 1998 112 6 578 2549 548772278 548774271 0 2876
9 TraesCS1B01G343400 chr3B 92.034 1996 118 15 572 2549 599079413 599077441 0 2767
10 TraesCS1B01G343400 chr3B 93.491 1567 79 6 1004 2549 548472452 548474016 0 2307
11 TraesCS1B01G343400 chr3B 94.090 1269 53 5 1302 2549 550862661 550863928 0 1908
12 TraesCS1B01G343400 chr3B 92.651 1143 66 10 573 1701 703251168 703252306 0 1629
13 TraesCS1B01G343400 chr3B 92.476 1143 74 6 574 1704 129332737 129331595 0 1624
14 TraesCS1B01G343400 chr5B 92.579 1900 119 4 671 2549 693448273 693446375 0 2708
15 TraesCS1B01G343400 chr5B 92.751 1145 70 8 570 1701 317969010 317970154 0 1642
16 TraesCS1B01G343400 chr5B 92.489 1145 70 9 574 1704 446193254 446192112 0 1624
17 TraesCS1B01G343400 chr5B 92.476 1143 73 6 572 1701 269389471 269390613 0 1622
18 TraesCS1B01G343400 chr7D 93.792 1643 78 5 930 2549 94497154 94495513 0 2447
19 TraesCS1B01G343400 chr7D 90.767 574 50 3 1 572 375340421 375339849 0 763
20 TraesCS1B01G343400 chr2B 92.583 1146 71 7 573 1704 602077186 602076041 0 1633
21 TraesCS1B01G343400 chr2B 92.174 1150 75 8 569 1704 543889475 543888327 0 1611
22 TraesCS1B01G343400 chr2D 91.289 574 46 4 1 572 174126332 174125761 0 780
23 TraesCS1B01G343400 chr2D 90.767 574 49 4 1 572 196849611 196849040 0 763
24 TraesCS1B01G343400 chr4B 91.115 574 48 3 1 572 180157449 180158021 0 774
25 TraesCS1B01G343400 chr4B 90.609 575 49 5 1 572 588964662 588965234 0 758
26 TraesCS1B01G343400 chr1D 91.115 574 45 6 1 572 309595886 309596455 0 773
27 TraesCS1B01G343400 chr1D 90.592 574 51 3 1 572 473238047 473238619 0 758
28 TraesCS1B01G343400 chr6D 90.957 575 46 5 1 572 392931987 392932558 0 769
29 TraesCS1B01G343400 chr6D 90.592 574 50 4 1 572 104611438 104610867 0 758
30 TraesCS1B01G343400 chr6D 90.592 574 51 3 1 572 120909023 120909595 0 758
31 TraesCS1B01G343400 chr6D 90.361 581 50 5 1 576 350524916 350525495 0 758
32 TraesCS1B01G343400 chr6D 90.435 575 49 6 1 572 208967157 208967728 0 752
33 TraesCS1B01G343400 chr6D 90.244 574 53 3 1 572 209030477 209031049 0 747
34 TraesCS1B01G343400 chr5D 90.815 577 47 6 1 572 486482863 486482288 0 767
35 TraesCS1B01G343400 chr3D 90.767 574 50 3 1 572 118557256 118557828 0 763
36 TraesCS1B01G343400 chrUn 90.070 574 53 4 1 572 280331675 280332246 0 741
37 TraesCS1B01G343400 chrUn 90.070 574 53 4 1 572 280338701 280339272 0 741
38 TraesCS1B01G343400 chrUn 90.070 574 53 4 1 572 347883171 347882600 0 741
39 TraesCS1B01G343400 chrUn 89.547 574 57 3 1 572 171675774 171675202 0 725
40 TraesCS1B01G343400 chrUn 89.199 574 58 4 1 572 171730558 171731129 0 713
41 TraesCS1B01G343400 chrUn 89.043 575 58 5 1 572 317034971 317035543 0 708
42 TraesCS1B01G343400 chrUn 89.043 575 58 5 1 572 339823151 339823723 0 708
43 TraesCS1B01G343400 chrUn 89.261 568 57 4 7 572 363155139 363154574 0 708
44 TraesCS1B01G343400 chrUn 89.142 571 58 4 1 569 406933907 406934475 0 708


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 TraesCS1B01G343400 chr1B 571670262 571672810 2548 False 4708 4708 100.000 1 2549 1 chr1B.!!$F2 2548
1 TraesCS1B01G343400 chr1B 154580594 154581733 1139 False 1624 1624 92.550 574 1701 1 chr1B.!!$F1 1127
2 TraesCS1B01G343400 chr1B 663786484 663787635 1151 False 1605 1605 92.021 563 1701 1 chr1B.!!$F3 1138
3 TraesCS1B01G343400 chr4D 43270769 43272763 1994 True 2907 2907 93.140 574 2549 1 chr4D.!!$R1 1975
4 TraesCS1B01G343400 chr4D 417529813 417530385 572 False 752 752 90.435 1 572 1 chr4D.!!$F2 571
5 TraesCS1B01G343400 chr4D 159961337 159961909 572 False 749 749 90.278 1 574 1 chr4D.!!$F1 573
6 TraesCS1B01G343400 chr7B 523397866 523399855 1989 True 2881 2881 92.939 573 2549 1 chr7B.!!$R1 1976
7 TraesCS1B01G343400 chr7B 523523087 523525077 1990 True 2861 2861 92.743 573 2549 1 chr7B.!!$R2 1976
8 TraesCS1B01G343400 chr3B 548772278 548774271 1993 False 2876 2876 92.893 578 2549 1 chr3B.!!$F2 1971
9 TraesCS1B01G343400 chr3B 599077441 599079413 1972 True 2767 2767 92.034 572 2549 1 chr3B.!!$R2 1977
10 TraesCS1B01G343400 chr3B 548472452 548474016 1564 False 2307 2307 93.491 1004 2549 1 chr3B.!!$F1 1545
11 TraesCS1B01G343400 chr3B 550862661 550863928 1267 False 1908 1908 94.090 1302 2549 1 chr3B.!!$F3 1247
12 TraesCS1B01G343400 chr3B 703251168 703252306 1138 False 1629 1629 92.651 573 1701 1 chr3B.!!$F4 1128
13 TraesCS1B01G343400 chr3B 129331595 129332737 1142 True 1624 1624 92.476 574 1704 1 chr3B.!!$R1 1130
14 TraesCS1B01G343400 chr5B 693446375 693448273 1898 True 2708 2708 92.579 671 2549 1 chr5B.!!$R2 1878
15 TraesCS1B01G343400 chr5B 317969010 317970154 1144 False 1642 1642 92.751 570 1701 1 chr5B.!!$F2 1131
16 TraesCS1B01G343400 chr5B 446192112 446193254 1142 True 1624 1624 92.489 574 1704 1 chr5B.!!$R1 1130
17 TraesCS1B01G343400 chr5B 269389471 269390613 1142 False 1622 1622 92.476 572 1701 1 chr5B.!!$F1 1129
18 TraesCS1B01G343400 chr7D 94495513 94497154 1641 True 2447 2447 93.792 930 2549 1 chr7D.!!$R1 1619
19 TraesCS1B01G343400 chr7D 375339849 375340421 572 True 763 763 90.767 1 572 1 chr7D.!!$R2 571
20 TraesCS1B01G343400 chr2B 602076041 602077186 1145 True 1633 1633 92.583 573 1704 1 chr2B.!!$R2 1131
21 TraesCS1B01G343400 chr2B 543888327 543889475 1148 True 1611 1611 92.174 569 1704 1 chr2B.!!$R1 1135
22 TraesCS1B01G343400 chr2D 174125761 174126332 571 True 780 780 91.289 1 572 1 chr2D.!!$R1 571
23 TraesCS1B01G343400 chr2D 196849040 196849611 571 True 763 763 90.767 1 572 1 chr2D.!!$R2 571
24 TraesCS1B01G343400 chr4B 180157449 180158021 572 False 774 774 91.115 1 572 1 chr4B.!!$F1 571
25 TraesCS1B01G343400 chr4B 588964662 588965234 572 False 758 758 90.609 1 572 1 chr4B.!!$F2 571
26 TraesCS1B01G343400 chr1D 309595886 309596455 569 False 773 773 91.115 1 572 1 chr1D.!!$F1 571
27 TraesCS1B01G343400 chr1D 473238047 473238619 572 False 758 758 90.592 1 572 1 chr1D.!!$F2 571
28 TraesCS1B01G343400 chr6D 392931987 392932558 571 False 769 769 90.957 1 572 1 chr6D.!!$F5 571
29 TraesCS1B01G343400 chr6D 104610867 104611438 571 True 758 758 90.592 1 572 1 chr6D.!!$R1 571
30 TraesCS1B01G343400 chr6D 120909023 120909595 572 False 758 758 90.592 1 572 1 chr6D.!!$F1 571
31 TraesCS1B01G343400 chr6D 350524916 350525495 579 False 758 758 90.361 1 576 1 chr6D.!!$F4 575
32 TraesCS1B01G343400 chr6D 208967157 208967728 571 False 752 752 90.435 1 572 1 chr6D.!!$F2 571
33 TraesCS1B01G343400 chr6D 209030477 209031049 572 False 747 747 90.244 1 572 1 chr6D.!!$F3 571
34 TraesCS1B01G343400 chr5D 486482288 486482863 575 True 767 767 90.815 1 572 1 chr5D.!!$R1 571
35 TraesCS1B01G343400 chr3D 118557256 118557828 572 False 763 763 90.767 1 572 1 chr3D.!!$F1 571
36 TraesCS1B01G343400 chrUn 280331675 280332246 571 False 741 741 90.070 1 572 1 chrUn.!!$F2 571
37 TraesCS1B01G343400 chrUn 280338701 280339272 571 False 741 741 90.070 1 572 1 chrUn.!!$F3 571
38 TraesCS1B01G343400 chrUn 347882600 347883171 571 True 741 741 90.070 1 572 1 chrUn.!!$R2 571
39 TraesCS1B01G343400 chrUn 171675202 171675774 572 True 725 725 89.547 1 572 1 chrUn.!!$R1 571
40 TraesCS1B01G343400 chrUn 171730558 171731129 571 False 713 713 89.199 1 572 1 chrUn.!!$F1 571
41 TraesCS1B01G343400 chrUn 317034971 317035543 572 False 708 708 89.043 1 572 1 chrUn.!!$F4 571
42 TraesCS1B01G343400 chrUn 339823151 339823723 572 False 708 708 89.043 1 572 1 chrUn.!!$F5 571
43 TraesCS1B01G343400 chrUn 363154574 363155139 565 True 708 708 89.261 7 572 1 chrUn.!!$R3 565
44 TraesCS1B01G343400 chrUn 406933907 406934475 568 False 708 708 89.142 1 569 1 chrUn.!!$F6 568

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
707 721 1.006571 GCGTCTCCGTCAGGTCAAA 60.007 57.895 0.0 0.0 39.05 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1738 1786 0.533951 GCTCTGAATTTGGCCCAAGG 59.466 55.0 0.0 0.0 0.0 3.61 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
32 34 6.019559 GGCACTCTTTGAAATTCTTTGTGTTC 60.020 38.462 0.00 0.00 0.00 3.18
102 105 4.908601 ACTCATGGATACTTGTGGTGAA 57.091 40.909 0.00 0.00 42.16 3.18
127 130 6.978674 TTGGAGTATCTAGGTGACATTAGG 57.021 41.667 0.00 0.00 33.73 2.69
188 191 7.802738 ACGAACTCTTAGATAGATCGATTGAG 58.197 38.462 0.00 1.07 37.51 3.02
199 204 9.967451 AGATAGATCGATTGAGAAGGATAACTA 57.033 33.333 0.00 0.00 0.00 2.24
251 256 5.533482 AGATCGATCGGAAAGGATAACTTG 58.467 41.667 19.33 0.00 39.96 3.16
314 321 1.829222 CCGCTAGGTAGGAACTTGGAA 59.171 52.381 0.00 0.00 41.75 3.53
338 345 4.768448 TGATTCTTCATTGCATGTTGAGGT 59.232 37.500 0.00 0.00 0.00 3.85
353 360 7.826252 GCATGTTGAGGTATGGTTATATGATCT 59.174 37.037 0.00 0.00 0.00 2.75
417 425 2.175715 GGACCCTAGGCCTCATTTTCAT 59.824 50.000 9.68 0.00 0.00 2.57
707 721 1.006571 GCGTCTCCGTCAGGTCAAA 60.007 57.895 0.00 0.00 39.05 2.69
772 786 5.587043 ACGGGCAATTTTATTCAGATCGTTA 59.413 36.000 0.00 0.00 0.00 3.18
803 817 2.584391 GCGGGACCCAACAGAGAGT 61.584 63.158 12.15 0.00 0.00 3.24
827 843 1.483424 GAGCATAGAGTCGTTGCGGC 61.483 60.000 12.70 0.00 41.22 6.53
830 846 1.141881 ATAGAGTCGTTGCGGCTGG 59.858 57.895 0.00 0.00 43.67 4.85
909 933 4.167359 GCGAGAGAGCGAGCACGA 62.167 66.667 8.01 0.00 42.66 4.35
912 936 1.724467 GAGAGAGCGAGCACGATGA 59.276 57.895 8.01 0.00 42.66 2.92
1012 1036 0.809241 GAGCTCCATGTCTTCCGCAG 60.809 60.000 0.87 0.00 0.00 5.18
1143 1167 3.181478 GGAACCAGAATCGTCCGTTCTAT 60.181 47.826 0.00 0.00 35.40 1.98
1221 1245 4.161001 GGATCTTTGAGCAATGGGTTGATT 59.839 41.667 0.00 0.00 37.53 2.57
1510 1534 5.133660 TGGGCATTTGTAGGTATGGTAATCT 59.866 40.000 0.00 0.00 0.00 2.40
1552 1576 8.102047 TGAAAATGTATGGAAAGGCATGAATTT 58.898 29.630 0.00 0.00 0.00 1.82
1725 1773 1.627329 TCTGCTCTGCCTTTCTGTCAT 59.373 47.619 0.00 0.00 0.00 3.06
1799 1847 1.005805 ACTAATGGGCCAACTGCATCA 59.994 47.619 11.89 0.00 43.89 3.07
1827 1875 0.328258 CCATTCGGGGGTTCTCTTGT 59.672 55.000 0.00 0.00 0.00 3.16
2108 2156 9.487790 TTTTTAAGGGCATTACATTGAGAAAAG 57.512 29.630 0.00 0.00 0.00 2.27
2227 2276 1.740285 CGCTGGTAACCGCTAGGAT 59.260 57.895 0.00 0.00 41.02 3.24
2354 2406 4.842574 AGTGGTTTTCCTTTGTTTTGCAT 58.157 34.783 0.00 0.00 41.38 3.96
2363 2415 8.908172 TTTCCTTTGTTTTGCATTGAAATTTC 57.092 26.923 11.41 11.41 0.00 2.17
2369 2421 4.862902 TTTGCATTGAAATTTCGGAGGA 57.137 36.364 13.34 4.01 0.00 3.71
2385 2437 3.763897 CGGAGGATTGGAAGGTTGAAAAT 59.236 43.478 0.00 0.00 0.00 1.82
2399 2451 7.283625 AGGTTGAAAATGTATGTTTGCACTA 57.716 32.000 0.00 0.00 0.00 2.74
2466 2518 6.325286 AGTGGCACTTGGTTTAGGATTTAAAA 59.675 34.615 15.88 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 7 4.651045 ACAAAGAATTTCAAAGAGTGCCCT 59.349 37.500 0.00 0.00 35.03 5.19
102 105 7.016661 CCCTAATGTCACCTAGATACTCCAATT 59.983 40.741 0.00 0.00 0.00 2.32
127 130 4.083324 CCATATGATACGCATCAACCAACC 60.083 45.833 3.65 0.00 44.27 3.77
199 204 8.095169 CCAAGAGTTTGTACTAAGATAACACCT 58.905 37.037 0.00 0.00 33.84 4.00
417 425 2.234168 AGCACAAATGGTATTGCATGCA 59.766 40.909 18.46 18.46 35.75 3.96
576 590 5.835280 CCACTCAGGGCAAAAGGATAATTAT 59.165 40.000 0.00 0.00 0.00 1.28
595 609 0.610174 TGAGCAGATGGACACCACTC 59.390 55.000 0.00 0.00 35.80 3.51
707 721 1.418637 TGTAAGGGCCGAGTCAAAACT 59.581 47.619 0.00 0.00 38.88 2.66
803 817 2.863739 CAACGACTCTATGCTCAACGA 58.136 47.619 0.00 0.00 0.00 3.85
909 933 2.846206 TCCACAACTAGCTTCCCATCAT 59.154 45.455 0.00 0.00 0.00 2.45
912 936 1.561542 CCTCCACAACTAGCTTCCCAT 59.438 52.381 0.00 0.00 0.00 4.00
940 964 0.835971 TCCACAGCTAGCTTCCCACA 60.836 55.000 16.46 0.00 0.00 4.17
1055 1079 1.996191 GACAGACGAAGACAAGCATCC 59.004 52.381 0.00 0.00 0.00 3.51
1143 1167 0.888736 CCCCATTCTCGTTGCACACA 60.889 55.000 0.00 0.00 0.00 3.72
1221 1245 2.020720 ACCTGCATGAACACGAAACAA 58.979 42.857 0.00 0.00 0.00 2.83
1552 1576 9.709495 CAATTTCAAGATTACAAATTCCTCCAA 57.291 29.630 0.00 0.00 29.17 3.53
1738 1786 0.533951 GCTCTGAATTTGGCCCAAGG 59.466 55.000 0.00 0.00 0.00 3.61
1977 2025 5.560966 ATCACGGTGTATTTGAATTGGAC 57.439 39.130 8.17 0.00 0.00 4.02
2130 2179 2.629336 TTTTGTGCATTTTCCACCCC 57.371 45.000 0.00 0.00 32.30 4.95
2159 2208 3.003763 GGGTTCGAGTCCCCAGCT 61.004 66.667 14.49 0.00 40.88 4.24
2227 2276 4.264253 CCATGTCAAAGTCTTGCCATCTA 58.736 43.478 0.00 0.00 28.75 1.98
2354 2406 4.462483 CCTTCCAATCCTCCGAAATTTCAA 59.538 41.667 17.99 4.73 0.00 2.69
2363 2415 2.489938 TTCAACCTTCCAATCCTCCG 57.510 50.000 0.00 0.00 0.00 4.63
2369 2421 7.173047 GCAAACATACATTTTCAACCTTCCAAT 59.827 33.333 0.00 0.00 0.00 3.16
2385 2437 2.803386 CACGTGGTAGTGCAAACATACA 59.197 45.455 7.95 0.00 35.17 2.29
2466 2518 9.590451 CATGAACTAACATGCAAATTTATTCCT 57.410 29.630 0.00 0.00 40.54 3.36


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

AutoCloner maintained by Alex Coulton.