Multiple sequence alignment - TraesCS4A01G155500

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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 TraesCS4A01G155500 chr4A 100.000 2255 0 0 1 2255 310762407 310764661 0.000000e+00 4165
1 TraesCS4A01G155500 chr3B 95.841 2260 89 3 1 2255 201560773 201558514 0.000000e+00 3648
2 TraesCS4A01G155500 chr3B 92.934 651 32 4 1609 2255 260376862 260377502 0.000000e+00 935
3 TraesCS4A01G155500 chr3A 95.341 2275 82 8 1 2255 672878431 672876161 0.000000e+00 3592
4 TraesCS4A01G155500 chr2D 95.120 2295 65 5 1 2255 630270294 630272581 0.000000e+00 3574
5 TraesCS4A01G155500 chr2D 94.952 2298 66 6 1 2255 33933817 33936107 0.000000e+00 3555
6 TraesCS4A01G155500 chr5B 94.195 2274 98 7 1 2255 432876725 432878983 0.000000e+00 3437
7 TraesCS4A01G155500 chr5B 94.675 1690 67 6 589 2255 413608024 413609713 0.000000e+00 2601
8 TraesCS4A01G155500 chr1B 95.701 2047 83 4 1 2044 633728863 633726819 0.000000e+00 3288
9 TraesCS4A01G155500 chr5D 94.301 2123 97 9 1 2103 432292717 432290599 0.000000e+00 3229
10 TraesCS4A01G155500 chr4D 93.840 2094 109 4 180 2255 245648863 245650954 0.000000e+00 3134
11 TraesCS4A01G155500 chr1A 92.794 1013 64 5 1 1010 371831415 371832421 0.000000e+00 1458
12 TraesCS4A01G155500 chr3D 88.306 667 33 16 1609 2255 182097139 182097780 0.000000e+00 758
13 TraesCS4A01G155500 chr5A 95.495 222 9 1 2035 2255 482027333 482027112 9.910000e-94 353
14 TraesCS4A01G155500 chrUn 93.333 225 11 2 2035 2255 451362730 451362954 1.670000e-86 329


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 TraesCS4A01G155500 chr4A 310762407 310764661 2254 False 4165 4165 100.000 1 2255 1 chr4A.!!$F1 2254
1 TraesCS4A01G155500 chr3B 201558514 201560773 2259 True 3648 3648 95.841 1 2255 1 chr3B.!!$R1 2254
2 TraesCS4A01G155500 chr3B 260376862 260377502 640 False 935 935 92.934 1609 2255 1 chr3B.!!$F1 646
3 TraesCS4A01G155500 chr3A 672876161 672878431 2270 True 3592 3592 95.341 1 2255 1 chr3A.!!$R1 2254
4 TraesCS4A01G155500 chr2D 630270294 630272581 2287 False 3574 3574 95.120 1 2255 1 chr2D.!!$F2 2254
5 TraesCS4A01G155500 chr2D 33933817 33936107 2290 False 3555 3555 94.952 1 2255 1 chr2D.!!$F1 2254
6 TraesCS4A01G155500 chr5B 432876725 432878983 2258 False 3437 3437 94.195 1 2255 1 chr5B.!!$F2 2254
7 TraesCS4A01G155500 chr5B 413608024 413609713 1689 False 2601 2601 94.675 589 2255 1 chr5B.!!$F1 1666
8 TraesCS4A01G155500 chr1B 633726819 633728863 2044 True 3288 3288 95.701 1 2044 1 chr1B.!!$R1 2043
9 TraesCS4A01G155500 chr5D 432290599 432292717 2118 True 3229 3229 94.301 1 2103 1 chr5D.!!$R1 2102
10 TraesCS4A01G155500 chr4D 245648863 245650954 2091 False 3134 3134 93.840 180 2255 1 chr4D.!!$F1 2075
11 TraesCS4A01G155500 chr1A 371831415 371832421 1006 False 1458 1458 92.794 1 1010 1 chr1A.!!$F1 1009
12 TraesCS4A01G155500 chr3D 182097139 182097780 641 False 758 758 88.306 1609 2255 1 chr3D.!!$F1 646

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
373 376 3.934068 TCGAGGGTGAATCCACTTTAAC 58.066 45.455 0.0 0.0 42.77 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1516 1529 3.153919 AGTTTTCTTATTGCCGAGCCAA 58.846 40.909 0.0 0.0 0.0 4.52 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
241 244 7.369607 TCATGAGTTATGGTCAACAAACAATG 58.630 34.615 0.00 0.0 37.39 2.82
269 272 6.438108 TGCTACAAGGTACATAGGTCAAAGTA 59.562 38.462 0.00 0.0 0.00 2.24
352 355 5.705609 AATCAATTACACCAGAGCGTTTT 57.294 34.783 0.00 0.0 0.00 2.43
371 374 4.627284 TTTCGAGGGTGAATCCACTTTA 57.373 40.909 0.00 0.0 42.77 1.85
373 376 3.934068 TCGAGGGTGAATCCACTTTAAC 58.066 45.455 0.00 0.0 42.77 2.01
532 539 5.528043 TTTGTGGCAATTGTGTTGAGTAT 57.472 34.783 7.40 0.0 0.00 2.12
626 633 8.865590 TTACAACCAAATTTCTTTAAGTCAGC 57.134 30.769 0.00 0.0 0.00 4.26
637 644 6.605471 TCTTTAAGTCAGCTACCAATCTCA 57.395 37.500 0.00 0.0 0.00 3.27
638 645 7.187824 TCTTTAAGTCAGCTACCAATCTCAT 57.812 36.000 0.00 0.0 0.00 2.90
732 739 9.611284 TTTGAATTCAAGAACGATTACTGATTG 57.389 29.630 19.64 0.0 37.15 2.67
959 968 7.390718 TCCTTGAATCCTTTAGTTTTAGTCAGC 59.609 37.037 0.00 0.0 0.00 4.26
1023 1032 7.645058 AATGGATTTACTTGGACCAATACAG 57.355 36.000 7.54 0.0 34.28 2.74
1063 1072 6.652205 TTGGGGGATTTGTTCTTCTACTAT 57.348 37.500 0.00 0.0 0.00 2.12
1069 1078 6.100714 GGGATTTGTTCTTCTACTATGGGGTA 59.899 42.308 0.00 0.0 0.00 3.69
1252 1265 5.220854 GCTGTAATGTTCGTAAATGGCTCAT 60.221 40.000 0.00 0.0 0.00 2.90
1393 1406 6.262273 TCTTTGGACTACAAGATCAAACCAAC 59.738 38.462 0.00 0.0 40.82 3.77
1449 1462 8.776470 CAACAAATTGGAATTCATTTAGCAACT 58.224 29.630 7.93 0.0 31.63 3.16
1451 1464 6.973229 AATTGGAATTCATTTAGCAACTGC 57.027 33.333 7.93 0.0 42.49 4.40
1734 1747 8.737168 TTGAAATGAATCGAGATTGATAAGGT 57.263 30.769 2.72 0.0 0.00 3.50
1740 1753 6.701841 TGAATCGAGATTGATAAGGTGTTAGC 59.298 38.462 2.72 0.0 0.00 3.09
1910 1926 4.944962 TCTGTTTGATAGTCGCCAATTG 57.055 40.909 0.00 0.0 0.00 2.32
1919 1935 3.140325 AGTCGCCAATTGAAAGGAGAA 57.860 42.857 7.12 0.0 35.47 2.87
1926 1942 5.928264 CGCCAATTGAAAGGAGAAATTTTCT 59.072 36.000 11.40 11.4 44.21 2.52
1960 1976 2.359107 CCTTGCGGCTGCTGAAGA 60.359 61.111 20.27 0.0 43.34 2.87
2073 2123 3.567478 ATCCTCTAAAGAAAGGCGCAT 57.433 42.857 10.83 0.0 32.37 4.73
2074 2124 2.632377 TCCTCTAAAGAAAGGCGCATG 58.368 47.619 10.83 0.0 32.37 4.06
2081 2131 7.011828 TCTAAAGAAAGGCGCATGTATTAAC 57.988 36.000 10.83 0.0 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
209 212 3.054434 TGACCATAACTCATGAACCCAGG 60.054 47.826 0.00 0.00 36.69 4.45
241 244 2.159142 ACCTATGTACCTTGTAGCACGC 60.159 50.000 0.00 0.00 0.00 5.34
269 272 7.446106 TTGTGTGGGATAAGGTAGTTATGAT 57.554 36.000 0.00 0.00 30.93 2.45
352 355 3.581332 AGTTAAAGTGGATTCACCCTCGA 59.419 43.478 0.00 0.00 44.64 4.04
371 374 9.979578 TTCACAAGCAATACATTTATCAAAGTT 57.020 25.926 0.00 0.00 0.00 2.66
373 376 9.630098 ACTTCACAAGCAATACATTTATCAAAG 57.370 29.630 0.00 0.00 0.00 2.77
532 539 5.843673 TTGATAAACAGCTTGTTGGACAA 57.156 34.783 2.88 6.62 40.14 3.18
607 614 7.214467 TGGTAGCTGACTTAAAGAAATTTGG 57.786 36.000 0.00 0.00 0.00 3.28
614 621 6.605471 TGAGATTGGTAGCTGACTTAAAGA 57.395 37.500 0.00 0.00 0.00 2.52
624 631 5.608437 TCTCCCATTAATGAGATTGGTAGCT 59.392 40.000 17.23 0.00 32.84 3.32
638 645 9.083422 TGTTTGAATTGTGTAATCTCCCATTAA 57.917 29.630 0.00 0.00 0.00 1.40
708 715 7.119699 AGCAATCAGTAATCGTTCTTGAATTCA 59.880 33.333 3.38 3.38 0.00 2.57
1010 1019 5.779241 AAGAATCTCCTGTATTGGTCCAA 57.221 39.130 6.80 6.80 0.00 3.53
1023 1032 5.012893 CCCCCAAATAGCATAAGAATCTCC 58.987 45.833 0.00 0.00 0.00 3.71
1063 1072 8.394040 GGTAAGTAATACTACTCCTATACCCCA 58.606 40.741 0.00 0.00 37.39 4.96
1069 1078 7.732140 GGGGTTGGTAAGTAATACTACTCCTAT 59.268 40.741 2.69 0.00 37.39 2.57
1105 1114 3.263425 AGAACTAATCCCAGCGAAAAGGA 59.737 43.478 0.00 0.00 0.00 3.36
1165 1178 1.948104 TGTGCGACAGCTACAAAGTT 58.052 45.000 0.00 0.00 45.42 2.66
1292 1305 6.982141 AGTTATACAAACGAGTGAAGTGAACA 59.018 34.615 0.00 0.00 0.00 3.18
1346 1359 4.931661 ATTCCATACCACGACGTATCTT 57.068 40.909 0.00 0.00 0.00 2.40
1449 1462 6.038825 TGAGTTCAAACGGAAGATAAAAAGCA 59.961 34.615 0.00 0.00 35.82 3.91
1451 1464 9.463443 AAATGAGTTCAAACGGAAGATAAAAAG 57.537 29.630 0.00 0.00 35.82 2.27
1516 1529 3.153919 AGTTTTCTTATTGCCGAGCCAA 58.846 40.909 0.00 0.00 0.00 4.52
1734 1747 8.109705 ACATGTTCAAACATCATTAGCTAACA 57.890 30.769 8.70 0.18 46.10 2.41
1869 1885 9.653287 AAACAGATCAGAAAATGTTACGAGATA 57.347 29.630 0.00 0.00 34.92 1.98
1892 1908 5.095490 CCTTTCAATTGGCGACTATCAAAC 58.905 41.667 5.42 0.00 0.00 2.93
1926 1942 5.406649 CGCAAGGGCTATAACAAAAATTGA 58.593 37.500 0.00 0.00 38.10 2.57


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

AutoCloner maintained by Alex Coulton.