Multiple sequence alignment - TraesCS4D01G143300

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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 TraesCS4D01G143300 chr4D 100.000 2507 0 0 1 2507 130555332 130552826 0.000000e+00 4630.0
1 TraesCS4D01G143300 chrUn 98.066 2017 17 4 380 2396 55726344 55724350 0.000000e+00 3489.0
2 TraesCS4D01G143300 chrUn 97.494 399 4 3 1 393 55726800 55726402 0.000000e+00 676.0
3 TraesCS4D01G143300 chrUn 97.000 100 3 0 2406 2505 55724306 55724207 4.290000e-38 169.0
4 TraesCS4D01G143300 chr4A 95.448 703 22 5 994 1687 436398266 436398967 0.000000e+00 1112.0
5 TraesCS4D01G143300 chr4A 95.058 344 16 1 2163 2505 436438776 436439119 7.890000e-150 540.0
6 TraesCS4D01G143300 chr4A 96.023 176 4 1 734 909 436398072 436398244 1.470000e-72 283.0
7 TraesCS4D01G143300 chr4A 88.776 196 5 4 1774 1964 436398975 436399158 9.020000e-55 224.0
8 TraesCS4D01G143300 chr4A 93.443 122 6 2 2013 2132 436399155 436399276 1.980000e-41 180.0
9 TraesCS4D01G143300 chr4A 98.718 78 1 0 672 749 436397971 436398048 3.360000e-29 139.0
10 TraesCS4D01G143300 chr4A 96.552 58 2 0 1 58 436396160 436396217 2.050000e-16 97.1
11 TraesCS4D01G143300 chr7D 98.876 89 1 0 1685 1773 84374346 84374258 2.580000e-35 159.0
12 TraesCS4D01G143300 chr3D 95.789 95 4 0 1678 1772 153849497 153849591 1.200000e-33 154.0
13 TraesCS4D01G143300 chr2D 95.789 95 4 0 1682 1776 22958389 22958483 1.200000e-33 154.0
14 TraesCS4D01G143300 chr2B 94.949 99 3 1 1673 1769 33495518 33495616 1.200000e-33 154.0
15 TraesCS4D01G143300 chr2B 100.000 32 0 0 411 442 606037743 606037774 2.690000e-05 60.2
16 TraesCS4D01G143300 chr6D 93.939 99 6 0 1674 1772 380781879 380781781 1.550000e-32 150.0
17 TraesCS4D01G143300 chr6D 92.308 104 8 0 1673 1776 142141258 142141155 5.590000e-32 148.0
18 TraesCS4D01G143300 chr6D 95.652 92 4 0 1685 1776 221219400 221219309 5.590000e-32 148.0
19 TraesCS4D01G143300 chr6D 100.000 28 0 0 402 429 392920508 392920481 5.000000e-03 52.8
20 TraesCS4D01G143300 chr3A 93.069 101 7 0 1675 1775 655640619 655640719 5.590000e-32 148.0


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 TraesCS4D01G143300 chr4D 130552826 130555332 2506 True 4630.000000 4630 100.000000 1 2507 1 chr4D.!!$R1 2506
1 TraesCS4D01G143300 chrUn 55724207 55726800 2593 True 1444.666667 3489 97.520000 1 2505 3 chrUn.!!$R1 2504
2 TraesCS4D01G143300 chr4A 436396160 436399276 3116 False 339.183333 1112 94.826667 1 2132 6 chr4A.!!$F2 2131

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
456 2117 0.105862 ATATTGGGACGGAGGTCGGA 60.106 55.0 0.0 0.0 44.39 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2287 4007 0.887933 TTTGGGAAGGAAAGCATCGC 59.112 50.0 0.0 0.0 0.0 4.58 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
58 59 4.156008 CCAAGTGCCAGGATAAAACTGTAC 59.844 45.833 0.00 0.00 34.16 2.90
393 1981 1.136110 GTAGCCAAGCACTCTCCTCTC 59.864 57.143 0.00 0.00 0.00 3.20
394 1982 0.543883 AGCCAAGCACTCTCCTCTCA 60.544 55.000 0.00 0.00 0.00 3.27
420 2079 6.406370 TCATGCATAAATTATACTCCCTCCG 58.594 40.000 0.00 0.00 0.00 4.63
439 2100 6.296026 CCTCCGTCCCAAAAATGATCTTATA 58.704 40.000 0.00 0.00 0.00 0.98
450 2111 7.986085 AAAATGATCTTATATTGGGACGGAG 57.014 36.000 0.00 0.00 0.00 4.63
451 2112 5.683876 ATGATCTTATATTGGGACGGAGG 57.316 43.478 0.00 0.00 0.00 4.30
452 2113 4.489737 TGATCTTATATTGGGACGGAGGT 58.510 43.478 0.00 0.00 0.00 3.85
453 2114 4.527038 TGATCTTATATTGGGACGGAGGTC 59.473 45.833 0.00 0.00 42.66 3.85
454 2115 2.889045 TCTTATATTGGGACGGAGGTCG 59.111 50.000 0.00 0.00 44.39 4.79
455 2116 1.624336 TATATTGGGACGGAGGTCGG 58.376 55.000 0.00 0.00 44.39 4.79
456 2117 0.105862 ATATTGGGACGGAGGTCGGA 60.106 55.000 0.00 0.00 44.39 4.55
567 2228 9.511144 CAGTAAACGTTTGAAAGAAAATAGGTT 57.489 29.630 23.46 0.00 0.00 3.50
1446 3151 2.290577 GGAGAATGAGAAGGCCAACTGT 60.291 50.000 5.01 0.00 0.00 3.55
1607 3319 4.079253 TCAAAAGGTGATAGCCCAAAGTC 58.921 43.478 0.00 0.00 0.00 3.01
1846 3563 6.949352 TGATATGCTTTCCCATTCTCTTTC 57.051 37.500 0.00 0.00 0.00 2.62
1847 3564 5.829924 TGATATGCTTTCCCATTCTCTTTCC 59.170 40.000 0.00 0.00 0.00 3.13
1848 3565 2.807676 TGCTTTCCCATTCTCTTTCCC 58.192 47.619 0.00 0.00 0.00 3.97
1849 3566 2.109834 TGCTTTCCCATTCTCTTTCCCA 59.890 45.455 0.00 0.00 0.00 4.37
1850 3567 3.245730 TGCTTTCCCATTCTCTTTCCCAT 60.246 43.478 0.00 0.00 0.00 4.00
1851 3568 3.771479 GCTTTCCCATTCTCTTTCCCATT 59.229 43.478 0.00 0.00 0.00 3.16
1979 3697 2.093711 TGTAGACATGACCCGTCAATGG 60.094 50.000 0.00 0.00 43.58 3.16
2287 4007 3.068590 AGTGCTGTTCCAACAAGATTTGG 59.931 43.478 0.00 0.00 46.64 3.28
2401 4121 4.539726 TCCCTCAGAATGGATCAAATTGG 58.460 43.478 0.00 0.00 36.16 3.16
2402 4122 4.230272 TCCCTCAGAATGGATCAAATTGGA 59.770 41.667 0.00 0.00 36.16 3.53
2403 4123 5.103387 TCCCTCAGAATGGATCAAATTGGAT 60.103 40.000 0.00 0.00 36.16 3.41
2404 4124 5.601313 CCCTCAGAATGGATCAAATTGGATT 59.399 40.000 0.00 0.00 36.16 3.01
2452 4206 0.394899 GCCAAACCATAGAGCCTGCT 60.395 55.000 0.00 0.00 0.00 4.24
2456 4210 1.577736 AACCATAGAGCCTGCTCACT 58.422 50.000 20.38 4.19 44.99 3.41
2480 4234 3.471570 TACACCCACCCCGACAGGT 62.472 63.158 0.00 0.00 42.40 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 1667 1.211949 CCTTTAATGAGAAGGGCGGGA 59.788 52.381 0.00 0.00 39.99 5.14
91 1668 1.211949 TCCTTTAATGAGAAGGGCGGG 59.788 52.381 3.30 0.00 43.13 6.13
137 1715 8.079203 TGTTGTTAACATGCAAATTACTACCAG 58.921 33.333 9.56 0.00 36.25 4.00
393 1981 7.335422 GGAGGGAGTATAATTTATGCATGAGTG 59.665 40.741 10.16 0.00 0.00 3.51
394 1982 7.398024 GGAGGGAGTATAATTTATGCATGAGT 58.602 38.462 10.16 0.00 0.00 3.41
420 2079 8.477419 TCCCAATATAAGATCATTTTTGGGAC 57.523 34.615 22.25 0.00 35.98 4.46
439 2100 2.038329 TCCGACCTCCGTCCCAAT 59.962 61.111 0.00 0.00 35.40 3.16
450 2111 7.167535 GTCCTATATATATACTCCCTCCGACC 58.832 46.154 0.00 0.00 0.00 4.79
451 2112 7.743749 TGTCCTATATATATACTCCCTCCGAC 58.256 42.308 0.00 0.00 0.00 4.79
452 2113 7.793222 TCTGTCCTATATATATACTCCCTCCGA 59.207 40.741 0.00 0.00 0.00 4.55
453 2114 7.975608 TCTGTCCTATATATATACTCCCTCCG 58.024 42.308 0.00 0.00 0.00 4.63
454 2115 9.577222 GTTCTGTCCTATATATATACTCCCTCC 57.423 40.741 0.00 0.00 0.00 4.30
455 2116 9.275398 CGTTCTGTCCTATATATATACTCCCTC 57.725 40.741 0.00 0.00 0.00 4.30
456 2117 8.219178 CCGTTCTGTCCTATATATATACTCCCT 58.781 40.741 0.00 0.00 0.00 4.20
660 2321 6.114187 ACAGAAACATGACTGTCCAGATTA 57.886 37.500 15.05 0.00 42.61 1.75
934 2634 4.068599 CGCTCTTCTTTCCCTCTCTTTTT 58.931 43.478 0.00 0.00 0.00 1.94
935 2635 3.325135 TCGCTCTTCTTTCCCTCTCTTTT 59.675 43.478 0.00 0.00 0.00 2.27
936 2636 2.900546 TCGCTCTTCTTTCCCTCTCTTT 59.099 45.455 0.00 0.00 0.00 2.52
937 2637 2.495669 CTCGCTCTTCTTTCCCTCTCTT 59.504 50.000 0.00 0.00 0.00 2.85
938 2638 2.099405 CTCGCTCTTCTTTCCCTCTCT 58.901 52.381 0.00 0.00 0.00 3.10
1446 3151 1.826054 CACTGGTTTTGGTCCGGCA 60.826 57.895 0.00 0.00 34.93 5.69
1840 3557 5.990120 ATCTTGACCAAAATGGGAAAGAG 57.010 39.130 16.24 3.21 42.44 2.85
1841 3558 9.713684 ATATTATCTTGACCAAAATGGGAAAGA 57.286 29.630 14.50 14.50 43.37 2.52
1993 3711 9.539825 AATATCTATTACTGCAAGAGACAACAG 57.460 33.333 0.00 0.00 37.31 3.16
2287 4007 0.887933 TTTGGGAAGGAAAGCATCGC 59.112 50.000 0.00 0.00 0.00 4.58
2319 4039 6.816134 TTCATGTCTAAATTTAGCACTGCA 57.184 33.333 18.68 12.32 0.00 4.41
2396 4116 3.053917 AGGCGTAACCACCTAATCCAATT 60.054 43.478 0.00 0.00 43.14 2.32
2397 4117 2.508300 AGGCGTAACCACCTAATCCAAT 59.492 45.455 0.00 0.00 43.14 3.16
2398 4118 1.910671 AGGCGTAACCACCTAATCCAA 59.089 47.619 0.00 0.00 43.14 3.53
2401 4121 3.064931 GCATAGGCGTAACCACCTAATC 58.935 50.000 0.00 0.00 41.76 1.75
2402 4122 2.436542 TGCATAGGCGTAACCACCTAAT 59.563 45.455 0.00 0.00 45.35 1.73
2403 4123 1.832366 TGCATAGGCGTAACCACCTAA 59.168 47.619 0.00 0.00 45.35 2.69
2404 4124 1.487300 TGCATAGGCGTAACCACCTA 58.513 50.000 0.00 0.00 45.35 3.08
2452 4206 1.972795 GGGTGGGTGTAGTGTAAGTGA 59.027 52.381 0.00 0.00 0.00 3.41
2456 4210 0.178938 TCGGGGTGGGTGTAGTGTAA 60.179 55.000 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.