Multiple sequence alignment - TraesCS1B01G388300

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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 TraesCS1B01G388300 chr1B 100.000 2798 0 0 1 2798 622312111 622314908 0.000000e+00 5168
1 TraesCS1B01G388300 chr1B 95.905 2808 102 5 3 2798 622357753 622360559 0.000000e+00 4536
2 TraesCS1B01G388300 chr1B 92.617 2167 113 15 649 2798 622217993 622220129 0.000000e+00 3072
3 TraesCS1B01G388300 chr1A 91.307 1806 94 18 625 2383 547238878 547237089 0.000000e+00 2407
4 TraesCS1B01G388300 chr1A 91.206 1808 94 18 625 2383 547216982 547215191 0.000000e+00 2398
5 TraesCS1B01G388300 chr1D 91.006 1779 118 16 625 2383 452262540 452260784 0.000000e+00 2361
6 TraesCS1B01G388300 chr1D 91.545 1372 77 11 647 1997 452270299 452268946 0.000000e+00 1855
7 TraesCS1B01G388300 chr1D 91.172 1382 87 17 631 1997 452265414 452264053 0.000000e+00 1844
8 TraesCS1B01G388300 chr1D 91.974 1059 69 8 953 1997 452337963 452336907 0.000000e+00 1471
9 TraesCS1B01G388300 chr1D 88.051 544 56 8 1 535 132862939 132862396 1.090000e-178 636
10 TraesCS1B01G388300 chr1D 81.994 311 52 2 2481 2791 110975874 110975568 7.690000e-66 261
11 TraesCS1B01G388300 chr1D 92.754 138 9 1 1958 2094 452264047 452263910 6.110000e-47 198
12 TraesCS1B01G388300 chrUn 91.803 1525 78 11 625 2116 246249905 246248395 0.000000e+00 2080
13 TraesCS1B01G388300 chrUn 91.667 1032 57 10 1379 2383 416393732 416394761 0.000000e+00 1402
14 TraesCS1B01G388300 chrUn 91.837 245 12 4 625 863 362688419 362688661 4.470000e-88 335
15 TraesCS1B01G388300 chr2B 86.202 645 64 8 4 625 24827567 24828209 0.000000e+00 675
16 TraesCS1B01G388300 chr3B 86.094 640 68 8 1 630 710395547 710394919 0.000000e+00 669
17 TraesCS1B01G388300 chr2D 85.911 653 63 6 1 624 646431170 646431822 0.000000e+00 669
18 TraesCS1B01G388300 chr2D 79.811 317 60 3 2478 2793 621961575 621961888 7.800000e-56 228
19 TraesCS1B01G388300 chr7D 85.516 649 61 11 1 636 618329979 618329351 0.000000e+00 647
20 TraesCS1B01G388300 chr7D 85.231 650 71 14 1 639 91566400 91565765 0.000000e+00 645
21 TraesCS1B01G388300 chr7D 83.175 315 52 1 2483 2796 428978699 428979013 1.270000e-73 287
22 TraesCS1B01G388300 chr6B 86.106 583 58 9 53 625 506550562 506551131 8.570000e-170 606
23 TraesCS1B01G388300 chr3D 84.146 656 72 10 1 624 348273280 348272625 8.570000e-170 606
24 TraesCS1B01G388300 chr3A 83.920 653 77 9 1 627 222467959 222468609 1.430000e-167 599
25 TraesCS1B01G388300 chr3A 84.144 637 61 16 1 618 682081982 682081367 5.200000e-162 580
26 TraesCS1B01G388300 chr7B 83.937 635 65 19 1 613 43562102 43562721 8.690000e-160 573
27 TraesCS1B01G388300 chr7B 82.595 316 50 5 2478 2791 104298643 104298955 9.870000e-70 274
28 TraesCS1B01G388300 chr5D 83.648 318 51 1 2481 2797 536239838 536240155 5.860000e-77 298
29 TraesCS1B01G388300 chr6D 83.280 311 52 0 2481 2791 20134782 20134472 1.270000e-73 287
30 TraesCS1B01G388300 chr2A 81.761 318 58 0 2481 2798 729831268 729831585 1.650000e-67 267


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 TraesCS1B01G388300 chr1B 622312111 622314908 2797 False 5168.0 5168 100.00000 1 2798 1 chr1B.!!$F2 2797
1 TraesCS1B01G388300 chr1B 622357753 622360559 2806 False 4536.0 4536 95.90500 3 2798 1 chr1B.!!$F3 2795
2 TraesCS1B01G388300 chr1B 622217993 622220129 2136 False 3072.0 3072 92.61700 649 2798 1 chr1B.!!$F1 2149
3 TraesCS1B01G388300 chr1A 547237089 547238878 1789 True 2407.0 2407 91.30700 625 2383 1 chr1A.!!$R2 1758
4 TraesCS1B01G388300 chr1A 547215191 547216982 1791 True 2398.0 2398 91.20600 625 2383 1 chr1A.!!$R1 1758
5 TraesCS1B01G388300 chr1D 452260784 452270299 9515 True 1564.5 2361 91.61925 625 2383 4 chr1D.!!$R4 1758
6 TraesCS1B01G388300 chr1D 452336907 452337963 1056 True 1471.0 1471 91.97400 953 1997 1 chr1D.!!$R3 1044
7 TraesCS1B01G388300 chr1D 132862396 132862939 543 True 636.0 636 88.05100 1 535 1 chr1D.!!$R2 534
8 TraesCS1B01G388300 chrUn 246248395 246249905 1510 True 2080.0 2080 91.80300 625 2116 1 chrUn.!!$R1 1491
9 TraesCS1B01G388300 chrUn 416393732 416394761 1029 False 1402.0 1402 91.66700 1379 2383 1 chrUn.!!$F2 1004
10 TraesCS1B01G388300 chr2B 24827567 24828209 642 False 675.0 675 86.20200 4 625 1 chr2B.!!$F1 621
11 TraesCS1B01G388300 chr3B 710394919 710395547 628 True 669.0 669 86.09400 1 630 1 chr3B.!!$R1 629
12 TraesCS1B01G388300 chr2D 646431170 646431822 652 False 669.0 669 85.91100 1 624 1 chr2D.!!$F2 623
13 TraesCS1B01G388300 chr7D 618329351 618329979 628 True 647.0 647 85.51600 1 636 1 chr7D.!!$R2 635
14 TraesCS1B01G388300 chr7D 91565765 91566400 635 True 645.0 645 85.23100 1 639 1 chr7D.!!$R1 638
15 TraesCS1B01G388300 chr6B 506550562 506551131 569 False 606.0 606 86.10600 53 625 1 chr6B.!!$F1 572
16 TraesCS1B01G388300 chr3D 348272625 348273280 655 True 606.0 606 84.14600 1 624 1 chr3D.!!$R1 623
17 TraesCS1B01G388300 chr3A 222467959 222468609 650 False 599.0 599 83.92000 1 627 1 chr3A.!!$F1 626
18 TraesCS1B01G388300 chr3A 682081367 682081982 615 True 580.0 580 84.14400 1 618 1 chr3A.!!$R1 617
19 TraesCS1B01G388300 chr7B 43562102 43562721 619 False 573.0 573 83.93700 1 613 1 chr7B.!!$F1 612

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
771 847 0.249911 GGTCTCAAGTTGCCACGTCT 60.25 55.0 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1811 1908 0.250513 GGCTACAACTGGCAGCTAGT 59.749 55.0 15.89 5.4 35.6 2.57 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
189 209 2.173782 TGTAGGTTTGAACTGAAGCCCA 59.826 45.455 0.00 0.00 0.00 5.36
261 284 4.052518 GGTCCAGCAGGGGCATGT 62.053 66.667 0.00 0.00 45.89 3.21
292 316 9.403583 CCCTATTGTTTTAAACTTATGCCTAGA 57.596 33.333 9.33 0.00 0.00 2.43
303 327 8.986929 AAACTTATGCCTAGAAGCTTATGATT 57.013 30.769 3.25 0.00 0.00 2.57
419 487 4.256920 GGACAGATCAAGTACTTGCACAT 58.743 43.478 27.49 17.41 40.24 3.21
435 503 3.569277 TGCACATAATCAAACAGCTGTGT 59.431 39.130 22.49 13.18 39.19 3.72
478 546 1.807377 GCACAAACACAGGCAAGCAAT 60.807 47.619 0.00 0.00 0.00 3.56
561 630 3.957591 TTTTTGCCTGCATATGCTCAA 57.042 38.095 27.13 22.52 42.66 3.02
694 769 5.641155 ACATGTGATCCATCATCCAATCAT 58.359 37.500 0.00 0.00 39.30 2.45
771 847 0.249911 GGTCTCAAGTTGCCACGTCT 60.250 55.000 0.00 0.00 0.00 4.18
952 1049 1.813178 CTCCACACTCGCTCTTCAGTA 59.187 52.381 0.00 0.00 0.00 2.74
1032 1129 0.396417 CCATGTCCCTCTCCTCGACT 60.396 60.000 0.00 0.00 0.00 4.18
1039 1136 1.595993 CCTCTCCTCGACTTTCGCCA 61.596 60.000 0.00 0.00 40.21 5.69
1046 1143 0.531974 TCGACTTTCGCCAGCAAGTT 60.532 50.000 0.00 0.00 40.21 2.66
1143 1240 1.000396 GGTTTCATCAGGCAGCCCT 60.000 57.895 8.22 0.00 44.25 5.19
1218 1315 0.669625 GCTACTTGACCGGCGAGTTT 60.670 55.000 19.63 3.68 41.55 2.66
1758 1855 1.142060 TCCGACCCTGTCAACAACAAT 59.858 47.619 0.00 0.00 37.45 2.71
1842 1949 1.791103 TTGTAGCCACAAACTGCGGC 61.791 55.000 0.00 0.00 45.50 6.53
1912 2034 4.096681 AGGATCTTTGGGGAAATGGTTTC 58.903 43.478 0.00 0.00 38.94 2.78
2022 2188 0.603569 AAGTCGCTCTTCGTGATGGT 59.396 50.000 0.00 0.00 39.67 3.55
2043 2209 7.615582 TGGTAACTTATGCTCTCATTTTCTG 57.384 36.000 0.00 0.00 33.65 3.02
2231 10130 4.866327 ACCTAGAGGCTTGAGTACTAGT 57.134 45.455 0.00 0.00 39.32 2.57
2232 10131 4.784177 ACCTAGAGGCTTGAGTACTAGTC 58.216 47.826 0.00 0.00 39.32 2.59
2329 10230 6.410942 TTCTCCATGTAGTATGTGGATGAG 57.589 41.667 6.86 0.00 40.96 2.90
2334 10235 3.111484 TGTAGTATGTGGATGAGGGCAA 58.889 45.455 0.00 0.00 0.00 4.52
2401 10306 3.318839 TGTACTAGCAAATATACCCGCGT 59.681 43.478 4.92 0.00 0.00 6.01
2417 10322 0.657368 GCGTGTTGCAACGGAAGAAG 60.657 55.000 23.79 9.87 45.45 2.85
2440 10345 4.946784 AGATTGACAACGCTTGATTACC 57.053 40.909 5.01 0.00 0.00 2.85
2441 10346 3.370978 AGATTGACAACGCTTGATTACCG 59.629 43.478 5.01 0.00 0.00 4.02
2504 10409 0.251916 ATCCGAGCGAATCCACCAAA 59.748 50.000 0.00 0.00 0.00 3.28
2525 10430 0.396435 ACAAATCTGCCGGAGACACA 59.604 50.000 5.05 0.00 31.75 3.72
2549 10454 2.182284 CACGCCCACCGACGATAA 59.818 61.111 0.00 0.00 41.02 1.75
2569 10474 2.234896 TAGACACACCACCGGGATAA 57.765 50.000 6.32 0.00 38.05 1.75
2584 10489 1.713297 GATAAGGGCTAGACGGGGAA 58.287 55.000 0.00 0.00 0.00 3.97
2605 10510 7.062957 GGGAAAATCTTATTCCATCTTCAGGA 58.937 38.462 7.53 0.00 46.69 3.86
2641 10546 0.756294 TCTTCCAAAGCAGGACACGA 59.244 50.000 0.00 0.00 37.42 4.35
2685 10590 3.181478 ACGTCTAAAAATAGAGCCCTCCG 60.181 47.826 0.00 0.00 0.00 4.63
2709 10614 2.204291 AAGGGCCAGGATCCACCA 60.204 61.111 15.82 0.00 42.04 4.17
2791 10696 2.557056 GCGGAGAAAACCTAGGCTTTTT 59.443 45.455 11.42 10.28 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 3.997064 GAGTGATGTCGCTGGCGCT 62.997 63.158 7.64 0.26 36.74 5.92
189 209 2.866762 GTTGACAGCAAAAGAGACGACT 59.133 45.455 0.00 0.00 35.42 4.18
261 284 7.978975 GCATAAGTTTAAAACAATAGGGCATCA 59.021 33.333 0.00 0.00 0.00 3.07
292 316 6.091713 GCAAAGAACATGCAAATCATAAGCTT 59.908 34.615 3.48 3.48 43.29 3.74
303 327 4.389890 AGAACAAGCAAAGAACATGCAA 57.610 36.364 0.00 0.00 46.22 4.08
478 546 1.187974 CCCAGATGGCTGCAAATTGA 58.812 50.000 0.50 0.00 40.91 2.57
694 769 0.684535 TGTTGGAGAATGGAGACGCA 59.315 50.000 0.00 0.00 0.00 5.24
771 847 2.954989 CAGAGATCTCGTCATCCCTCAA 59.045 50.000 16.97 0.00 34.09 3.02
854 931 0.676184 GAGCTCTGGTCTGTGTGTGA 59.324 55.000 6.43 0.00 0.00 3.58
952 1049 5.882557 ACTGTGTGTTCTCAAAAGAGTGAAT 59.117 36.000 0.00 0.00 31.75 2.57
1032 1129 0.749818 TCACCAACTTGCTGGCGAAA 60.750 50.000 0.00 0.00 40.45 3.46
1039 1136 1.670811 CACGTTCTTCACCAACTTGCT 59.329 47.619 0.00 0.00 0.00 3.91
1046 1143 0.179234 TGAAGCCACGTTCTTCACCA 59.821 50.000 20.14 5.05 43.34 4.17
1152 1249 4.111016 TAGAGCACACGGTCGGCG 62.111 66.667 0.00 0.00 44.60 6.46
1195 1292 2.882876 GCCGGTCAAGTAGCTCGA 59.117 61.111 1.90 0.00 0.00 4.04
1265 1362 0.821711 CCGGTTCTTGGCAAAGGTCA 60.822 55.000 0.00 0.00 33.90 4.02
1810 1907 1.480954 GGCTACAACTGGCAGCTAGTA 59.519 52.381 15.89 13.43 35.60 1.82
1811 1908 0.250513 GGCTACAACTGGCAGCTAGT 59.749 55.000 15.89 5.40 35.60 2.57
1820 1917 1.334059 CGCAGTTTGTGGCTACAACTG 60.334 52.381 26.21 26.21 45.91 3.16
1912 2034 1.381928 ATGAAGCAAGCGGGCAGATG 61.382 55.000 5.46 0.00 35.83 2.90
2022 2188 8.049117 ACCATCAGAAAATGAGAGCATAAGTTA 58.951 33.333 0.00 0.00 42.53 2.24
2231 10130 6.151648 CACTATGCTTTCAGAATTCCTTTGGA 59.848 38.462 0.65 0.00 0.00 3.53
2232 10131 6.151648 TCACTATGCTTTCAGAATTCCTTTGG 59.848 38.462 0.65 0.00 0.00 3.28
2329 10230 4.396790 TGTCCATAAAATACGTCTTTGCCC 59.603 41.667 0.00 0.00 0.00 5.36
2334 10235 7.871463 GCTATACCTGTCCATAAAATACGTCTT 59.129 37.037 0.00 0.00 0.00 3.01
2401 10306 2.912771 TCTTCTTCTTCCGTTGCAACA 58.087 42.857 28.01 7.99 0.00 3.33
2417 10322 5.324697 GGTAATCAAGCGTTGTCAATCTTC 58.675 41.667 0.00 0.00 0.00 2.87
2440 10345 4.429212 TGTCGCCACGTCCATCCG 62.429 66.667 0.00 0.00 0.00 4.18
2441 10346 2.813908 GTGTCGCCACGTCCATCC 60.814 66.667 0.00 0.00 0.00 3.51
2504 10409 0.976641 TGTCTCCGGCAGATTTGTCT 59.023 50.000 0.00 0.00 32.08 3.41
2525 10430 4.697756 CGGTGGGCGTGTGGATGT 62.698 66.667 0.00 0.00 0.00 3.06
2549 10454 2.464796 TATCCCGGTGGTGTGTCTAT 57.535 50.000 0.00 0.00 0.00 1.98
2569 10474 0.837940 GATTTTCCCCGTCTAGCCCT 59.162 55.000 0.00 0.00 0.00 5.19
2584 10489 7.067494 CGGTTTCCTGAAGATGGAATAAGATTT 59.933 37.037 0.00 0.00 42.41 2.17
2605 10510 1.372623 GACGAGACGAAGGCGGTTT 60.373 57.895 0.00 0.00 43.17 3.27
2607 10512 2.197643 GAAGACGAGACGAAGGCGGT 62.198 60.000 0.00 0.00 43.17 5.68
2641 10546 6.128200 ACGTTTCTTCGAGTTTTGTTAGGTTT 60.128 34.615 0.00 0.00 34.70 3.27
2685 10590 2.900671 GATCCTGGCCCTTGCAGACC 62.901 65.000 0.00 0.00 40.13 3.85
2709 10614 3.385749 CTTAGGGCCATGGCGACGT 62.386 63.158 29.90 20.05 43.06 4.34


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

AutoCloner maintained by Alex Coulton.