Multiple sequence alignment - TraesCS4A01G452100

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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 TraesCS4A01G452100 chr4A 100.000 2861 0 0 1 2861 717282059 717284919 0.000000e+00 5284.0
1 TraesCS4A01G452100 chr4A 95.750 2094 64 6 39 2128 717255589 717257661 0.000000e+00 3350.0
2 TraesCS4A01G452100 chr4A 92.461 1963 100 16 182 2128 717808558 717806628 0.000000e+00 2761.0
3 TraesCS4A01G452100 chr4A 97.500 1560 33 2 575 2128 717220944 717222503 0.000000e+00 2660.0
4 TraesCS4A01G452100 chr4A 96.571 1283 39 4 575 1856 717757373 717756095 0.000000e+00 2121.0
5 TraesCS4A01G452100 chr4A 98.085 731 14 0 2131 2861 717222721 717223451 0.000000e+00 1273.0
6 TraesCS4A01G452100 chr4A 90.587 733 36 6 2129 2861 717806468 717805769 0.000000e+00 941.0
7 TraesCS4A01G452100 chr4A 90.591 457 28 4 2132 2586 717257858 717258301 2.450000e-165 592.0
8 TraesCS4A01G452100 chr4A 98.106 264 5 0 2598 2861 717755220 717754957 7.220000e-126 460.0
9 TraesCS4A01G452100 chr4A 96.029 277 8 1 1855 2128 717756045 717755769 5.620000e-122 448.0
10 TraesCS4A01G452100 chr4A 92.233 309 22 2 39 345 717757829 717757521 1.220000e-118 436.0
11 TraesCS4A01G452100 chr4A 94.697 264 13 1 2598 2861 717258287 717258549 2.650000e-110 409.0
12 TraesCS4A01G452100 chr4A 88.506 174 18 2 358 529 717220760 717220933 2.890000e-50 209.0
13 TraesCS4A01G452100 chr4A 92.742 124 9 0 394 517 717757516 717757393 2.260000e-41 180.0
14 TraesCS4A01G452100 chr4A 96.739 92 3 0 2129 2220 717755545 717755454 1.370000e-33 154.0
15 TraesCS4A01G452100 chr7A 92.802 1820 89 13 39 1847 16436842 16435054 0.000000e+00 2597.0
16 TraesCS4A01G452100 chr7A 92.747 1820 90 13 39 1847 16324706 16322918 0.000000e+00 2591.0
17 TraesCS4A01G452100 chr7A 91.793 1121 76 7 1019 2128 15818715 15819830 0.000000e+00 1546.0
18 TraesCS4A01G452100 chr7A 95.333 900 42 0 566 1465 16432653 16431754 0.000000e+00 1430.0
19 TraesCS4A01G452100 chr7A 94.143 683 34 4 1450 2128 16430456 16429776 0.000000e+00 1035.0
20 TraesCS4A01G452100 chr7A 92.083 720 46 8 1412 2128 16394809 16394098 0.000000e+00 1003.0
21 TraesCS4A01G452100 chr7A 94.737 608 26 6 2259 2861 16317411 16316805 0.000000e+00 941.0
22 TraesCS4A01G452100 chr7A 91.751 594 31 9 373 966 16395387 16394812 0.000000e+00 809.0
23 TraesCS4A01G452100 chr7A 89.382 631 33 11 2238 2861 15820126 15820729 0.000000e+00 763.0
24 TraesCS4A01G452100 chr7A 93.763 497 22 4 42 537 16433141 16432653 0.000000e+00 737.0
25 TraesCS4A01G452100 chr7A 95.423 437 17 1 2150 2586 16429591 16429158 0.000000e+00 693.0
26 TraesCS4A01G452100 chr7A 88.831 573 32 9 2295 2861 15791612 15792158 0.000000e+00 675.0
27 TraesCS4A01G452100 chr7A 91.868 455 21 1 2132 2586 16393903 16393465 3.130000e-174 621.0
28 TraesCS4A01G452100 chr7A 96.212 264 9 1 2598 2861 16393479 16393217 5.660000e-117 431.0
29 TraesCS4A01G452100 chr7A 94.318 264 14 1 2598 2861 16429172 16428910 1.230000e-108 403.0
30 TraesCS4A01G452100 chr7A 91.065 291 16 3 1841 2128 16317909 16317626 4.470000e-103 385.0
31 TraesCS4A01G452100 chr7A 92.083 240 17 2 39 276 16395782 16395543 1.270000e-88 337.0
32 TraesCS4A01G452100 chr7A 91.667 84 5 2 83 164 16395459 16395542 6.480000e-22 115.0
33 TraesCS4A01G452100 chr7D 91.708 1797 85 19 358 2128 16756105 16757863 0.000000e+00 2435.0
34 TraesCS4A01G452100 chr7D 93.859 1547 76 6 592 2128 16997783 16996246 0.000000e+00 2313.0
35 TraesCS4A01G452100 chr7D 90.424 731 42 12 2132 2861 17124562 17123859 0.000000e+00 937.0
36 TraesCS4A01G452100 chr7D 96.264 455 15 2 2132 2586 16758061 16758513 0.000000e+00 745.0
37 TraesCS4A01G452100 chr7D 95.076 264 11 2 2132 2395 16996083 16995822 5.700000e-112 414.0
38 TraesCS4A01G452100 chr7D 94.318 264 14 1 2598 2861 16758499 16758761 1.230000e-108 403.0
39 TraesCS4A01G452100 chr7D 87.027 185 24 0 160 344 17126295 17126111 2.890000e-50 209.0
40 TraesCS4A01G452100 chr7D 93.798 129 6 2 39 165 17128258 17128130 2.910000e-45 193.0
41 TraesCS4A01G452100 chr7D 92.623 122 9 0 393 514 17126093 17125972 2.930000e-40 176.0
42 TraesCS4A01G452100 chr7B 90.449 1780 137 20 358 2119 655815574 655813810 0.000000e+00 2314.0
43 TraesCS4A01G452100 chr7B 89.674 736 44 7 2129 2861 655813602 655812896 0.000000e+00 909.0
44 TraesCS4A01G452100 chr2A 81.818 374 34 15 173 539 745558904 745559250 1.680000e-72 283.0
45 TraesCS4A01G452100 chr2A 91.489 47 3 1 85 131 745558833 745558878 2.380000e-06 63.9


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 TraesCS4A01G452100 chr4A 717282059 717284919 2860 False 5284.000000 5284 100.000000 1 2861 1 chr4A.!!$F1 2860
1 TraesCS4A01G452100 chr4A 717805769 717808558 2789 True 1851.000000 2761 91.524000 182 2861 2 chr4A.!!$R2 2679
2 TraesCS4A01G452100 chr4A 717255589 717258549 2960 False 1450.333333 3350 93.679333 39 2861 3 chr4A.!!$F3 2822
3 TraesCS4A01G452100 chr4A 717220760 717223451 2691 False 1380.666667 2660 94.697000 358 2861 3 chr4A.!!$F2 2503
4 TraesCS4A01G452100 chr4A 717754957 717757829 2872 True 633.166667 2121 95.403333 39 2861 6 chr4A.!!$R1 2822
5 TraesCS4A01G452100 chr7A 16322918 16324706 1788 True 2591.000000 2591 92.747000 39 1847 1 chr7A.!!$R1 1808
6 TraesCS4A01G452100 chr7A 15818715 15820729 2014 False 1154.500000 1546 90.587500 1019 2861 2 chr7A.!!$F3 1842
7 TraesCS4A01G452100 chr7A 16428910 16436842 7932 True 1149.166667 2597 94.297000 39 2861 6 chr7A.!!$R4 2822
8 TraesCS4A01G452100 chr7A 15791612 15792158 546 False 675.000000 675 88.831000 2295 2861 1 chr7A.!!$F1 566
9 TraesCS4A01G452100 chr7A 16316805 16317909 1104 True 663.000000 941 92.901000 1841 2861 2 chr7A.!!$R2 1020
10 TraesCS4A01G452100 chr7A 16393217 16395782 2565 True 640.200000 1003 92.799400 39 2861 5 chr7A.!!$R3 2822
11 TraesCS4A01G452100 chr7D 16995822 16997783 1961 True 1363.500000 2313 94.467500 592 2395 2 chr7D.!!$R1 1803
12 TraesCS4A01G452100 chr7D 16756105 16758761 2656 False 1194.333333 2435 94.096667 358 2861 3 chr7D.!!$F1 2503
13 TraesCS4A01G452100 chr7D 17123859 17128258 4399 True 378.750000 937 90.968000 39 2861 4 chr7D.!!$R2 2822
14 TraesCS4A01G452100 chr7B 655812896 655815574 2678 True 1611.500000 2314 90.061500 358 2861 2 chr7B.!!$R1 2503

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
765 2742 0.445436 CCGTTGTCGCTCTACTACGT 59.555 55.0 13.31 0.0 43.78 3.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2234 9554 1.661617 TGTTTGGTTGTCGAACACTCG 59.338 47.619 0.0 0.0 42.98 4.18 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
19 20 3.129792 GTGAAGAAGGAGCACGAGG 57.870 57.895 0.00 0.00 0.00 4.63
20 21 1.016653 GTGAAGAAGGAGCACGAGGC 61.017 60.000 0.00 0.00 45.30 4.70
21 22 1.448717 GAAGAAGGAGCACGAGGCC 60.449 63.158 0.00 0.00 46.50 5.19
22 23 2.172483 GAAGAAGGAGCACGAGGCCA 62.172 60.000 5.01 0.00 46.50 5.36
23 24 1.557269 AAGAAGGAGCACGAGGCCAT 61.557 55.000 5.01 0.00 46.50 4.40
24 25 1.817099 GAAGGAGCACGAGGCCATG 60.817 63.158 5.01 0.49 46.50 3.66
25 26 3.984193 AAGGAGCACGAGGCCATGC 62.984 63.158 16.59 16.59 46.50 4.06
38 39 4.569023 CATGCTCGCCGCCTACGA 62.569 66.667 0.00 0.00 43.93 3.43
75 76 4.202461 TGCAAGTAGGGATTAAGGCATAGG 60.202 45.833 0.00 0.00 0.00 2.57
245 2088 4.350368 TTTCTGTCAGCATGGACACTTA 57.650 40.909 1.13 0.00 42.56 2.24
283 2209 7.681939 TTGTTTGAGAAATACTAGGCGATTT 57.318 32.000 0.00 0.00 0.00 2.17
564 2521 4.553330 TCATCTTGGTAACTCCTGTTCC 57.447 45.455 0.00 0.00 37.59 3.62
620 2583 5.739752 AACCTTTTTCTTGAATTTGCTGC 57.260 34.783 0.00 0.00 0.00 5.25
765 2742 0.445436 CCGTTGTCGCTCTACTACGT 59.555 55.000 13.31 0.00 43.78 3.57
2079 9145 3.050089 TGGAGTTTTCTTGTACCTGGGA 58.950 45.455 0.00 0.00 0.00 4.37
2234 9554 4.306600 CACCAACAAAAATTAGGCAGACC 58.693 43.478 0.00 0.00 0.00 3.85
2509 9834 5.254115 GGGAGTAATTAACAAGGTTCAGCT 58.746 41.667 0.00 0.00 0.00 4.24
2814 10181 0.606401 ACTCCTCATGTTGGTTGCCG 60.606 55.000 7.23 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.293498 GCCTCGTGCTCCTTCTTCA 59.707 57.895 0.00 0.00 36.87 3.02
3 4 1.448717 GGCCTCGTGCTCCTTCTTC 60.449 63.158 0.00 0.00 40.92 2.87
4 5 1.557269 ATGGCCTCGTGCTCCTTCTT 61.557 55.000 3.32 0.00 40.92 2.52
5 6 1.992277 ATGGCCTCGTGCTCCTTCT 60.992 57.895 3.32 0.00 40.92 2.85
6 7 1.817099 CATGGCCTCGTGCTCCTTC 60.817 63.158 3.32 0.00 40.92 3.46
7 8 2.270205 CATGGCCTCGTGCTCCTT 59.730 61.111 3.32 0.00 40.92 3.36
30 31 2.898840 TAGGCGGTCTCGTAGGCG 60.899 66.667 0.00 0.00 38.89 5.52
31 32 1.453762 ATGTAGGCGGTCTCGTAGGC 61.454 60.000 0.00 0.00 38.89 3.93
32 33 0.592148 GATGTAGGCGGTCTCGTAGG 59.408 60.000 0.00 0.00 38.89 3.18
33 34 1.264557 CAGATGTAGGCGGTCTCGTAG 59.735 57.143 0.00 0.00 38.89 3.51
34 35 1.306148 CAGATGTAGGCGGTCTCGTA 58.694 55.000 0.00 0.00 38.89 3.43
35 36 2.005960 GCAGATGTAGGCGGTCTCGT 62.006 60.000 0.00 0.00 38.89 4.18
36 37 1.299468 GCAGATGTAGGCGGTCTCG 60.299 63.158 0.00 0.00 39.81 4.04
37 38 0.175760 TTGCAGATGTAGGCGGTCTC 59.824 55.000 0.00 0.00 0.00 3.36
38 39 0.176680 CTTGCAGATGTAGGCGGTCT 59.823 55.000 0.00 0.00 0.00 3.85
39 40 0.108138 ACTTGCAGATGTAGGCGGTC 60.108 55.000 0.00 0.00 0.00 4.79
40 41 1.137086 CTACTTGCAGATGTAGGCGGT 59.863 52.381 12.77 0.00 34.24 5.68
41 42 1.539065 CCTACTTGCAGATGTAGGCGG 60.539 57.143 21.43 7.44 46.01 6.13
42 43 1.858091 CCTACTTGCAGATGTAGGCG 58.142 55.000 21.43 7.26 46.01 5.52
75 76 4.564769 CGAGACTAAGCAGAAAGAATCCAC 59.435 45.833 0.00 0.00 0.00 4.02
125 126 6.642733 TGTTGGAGATCTAAAGAGGGAAAT 57.357 37.500 0.00 0.00 0.00 2.17
190 2032 6.017026 CAGAGCACATATGAATTTCAGAGCAT 60.017 38.462 10.38 0.00 0.00 3.79
245 2088 8.918202 TTTCTCAAACAAATACTGTATCTGGT 57.082 30.769 6.13 0.00 37.23 4.00
283 2209 7.717436 TCTTTGTTCATACAGATTACACACCAA 59.283 33.333 0.00 0.00 35.28 3.67
542 2499 4.597507 AGGAACAGGAGTTACCAAGATGAA 59.402 41.667 0.00 0.00 39.54 2.57
620 2583 2.202492 CGCTCTCCCTGTTCGACG 60.202 66.667 0.00 0.00 0.00 5.12
673 2636 3.006323 GCAAAGAGTGAGGAGACAGAAGA 59.994 47.826 0.00 0.00 0.00 2.87
2079 9145 3.555966 GCCTAGCCCATGTTATCAAGTT 58.444 45.455 0.00 0.00 0.00 2.66
2207 9525 4.333926 TGCCTAATTTTTGTTGGTGCAAAC 59.666 37.500 0.00 0.00 37.98 2.93
2234 9554 1.661617 TGTTTGGTTGTCGAACACTCG 59.338 47.619 0.00 0.00 42.98 4.18
2289 9609 4.338964 ACAGAGACAATCAAATGCACACAA 59.661 37.500 0.00 0.00 0.00 3.33
2509 9834 5.067153 ACTTGTGCTACATGTTGCTGTTTTA 59.933 36.000 28.07 8.47 33.38 1.52
2814 10181 7.035840 TCGAGTATTTTCATACCCAGTAGAC 57.964 40.000 0.00 0.00 36.63 2.59


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

AutoCloner maintained by Alex Coulton.