Multiple sequence alignment - TraesCS4B01G177500

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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 TraesCS4B01G177500 chr4B 100.000 2300 0 0 1 2300 387880948 387883247 0 4248
1 TraesCS4B01G177500 chr4D 95.146 2328 83 5 1 2300 310456526 310458851 0 3646
2 TraesCS4B01G177500 chr4A 94.409 2325 95 8 1 2300 164510787 164508473 0 3541


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 TraesCS4B01G177500 chr4B 387880948 387883247 2299 False 4248 4248 100.000 1 2300 1 chr4B.!!$F1 2299
1 TraesCS4B01G177500 chr4D 310456526 310458851 2325 False 3646 3646 95.146 1 2300 1 chr4D.!!$F1 2299
2 TraesCS4B01G177500 chr4A 164508473 164510787 2314 True 3541 3541 94.409 1 2300 1 chr4A.!!$R1 2299

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
955 958 0.320683 GGGGCCAGACAAATTGTTGC 60.321 55.0 4.39 4.02 38.39 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2015 2047 0.179084 CAGAAGCGCTATTCCGGGAA 60.179 55.0 12.05 12.67 0.0 3.97 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
27 28 6.114767 TCAGAATACATACAAATCAGCTGCA 58.885 36.000 9.47 0.00 0.00 4.41
96 99 2.224161 GGTAGACAGAGATGTGGCATCC 60.224 54.545 5.59 0.00 0.00 3.51
129 132 1.035923 TGATGATCCTCTCGTGCTCC 58.964 55.000 0.00 0.00 0.00 4.70
135 138 1.984570 CCTCTCGTGCTCCTTGGGA 60.985 63.158 0.00 0.00 0.00 4.37
198 201 1.009829 CGCTGCCGAGCTTCTTTATT 58.990 50.000 0.00 0.00 43.77 1.40
360 363 2.215196 TCTTCAGCCGTAAACAACACC 58.785 47.619 0.00 0.00 0.00 4.16
387 390 1.073125 TCGAAAAGATGCAAGTCCCCA 59.927 47.619 0.00 0.00 0.00 4.96
411 414 1.202698 AGTTTGTCAGGAGAGTGCACC 60.203 52.381 14.63 5.12 0.00 5.01
429 432 2.502947 CACCCTCAAGATGGAGTGATGA 59.497 50.000 0.00 0.00 32.91 2.92
480 483 6.290605 TGATATCAATGAAGGCATCGAAGAA 58.709 36.000 1.98 0.00 43.58 2.52
482 485 3.942829 TCAATGAAGGCATCGAAGAAGT 58.057 40.909 0.00 0.00 43.58 3.01
485 488 3.126001 TGAAGGCATCGAAGAAGTTGT 57.874 42.857 0.00 0.00 43.58 3.32
513 516 2.325583 TAAGGCTGGAAATGCTACCG 57.674 50.000 0.00 0.00 0.00 4.02
612 615 0.955178 ACGGTGATGATCCTAGCGAG 59.045 55.000 16.03 0.00 38.53 5.03
618 621 3.254411 GTGATGATCCTAGCGAGACATCA 59.746 47.826 18.62 18.62 41.58 3.07
928 931 5.796424 ATCAGGAAATTTCAGCAAACTGT 57.204 34.783 19.49 5.27 44.77 3.55
955 958 0.320683 GGGGCCAGACAAATTGTTGC 60.321 55.000 4.39 4.02 38.39 4.17
984 987 5.411781 ACATTGAACTCTACAAGATCGTCC 58.588 41.667 0.00 0.00 29.59 4.79
1071 1074 3.159213 AGCTTGGTGATTGATGTTGGA 57.841 42.857 0.00 0.00 0.00 3.53
1098 1101 2.955660 CCCAGTAAAGTTGTTCAGGCAA 59.044 45.455 0.00 0.00 0.00 4.52
1137 1140 1.736645 ACTCAAACGACCGATGCCG 60.737 57.895 0.00 0.00 0.00 5.69
1194 1197 9.189723 GAAAGATCAAGAAATGAAAGGTTTGAG 57.810 33.333 0.00 0.00 42.54 3.02
1330 1333 7.573843 GCTTAGCTGCTGTAAAGAGATTTTTCA 60.574 37.037 13.43 0.00 0.00 2.69
1427 1430 5.277731 GCAATTCTCCTGCTAGCAAGTTATC 60.278 44.000 19.86 0.00 36.84 1.75
1471 1474 4.522789 GCCTCAAAAATTGGGTAGTCTGAA 59.477 41.667 0.00 0.00 0.00 3.02
1692 1695 2.093658 ACGCCTAATTGGACCTGTGTAG 60.094 50.000 0.00 0.00 38.35 2.74
1737 1762 6.052840 AGTAATCGCAACACATCATCATTC 57.947 37.500 0.00 0.00 0.00 2.67
1757 1782 7.706159 TCATTCACAAACATAGTATGGATTGC 58.294 34.615 21.53 0.00 35.75 3.56
1767 1792 1.599542 GTATGGATTGCTTCGGTGCTC 59.400 52.381 2.64 0.00 0.00 4.26
1769 1794 0.674581 TGGATTGCTTCGGTGCTCTG 60.675 55.000 2.64 0.00 0.00 3.35
1789 1814 2.227194 GGAGGTTATTATGGCAACGGG 58.773 52.381 0.00 0.00 42.51 5.28
1794 1819 4.401202 AGGTTATTATGGCAACGGGAAAAG 59.599 41.667 0.00 0.00 42.51 2.27
1878 1909 3.150848 GCATAAGGCAAAAGTGGTAGC 57.849 47.619 0.00 0.00 43.97 3.58
1916 1948 9.850628 GTTTAATAAGGGAAAGCTTAAAACGAT 57.149 29.630 0.00 0.00 0.00 3.73
1919 1951 8.757164 AATAAGGGAAAGCTTAAAACGATTTG 57.243 30.769 0.00 0.00 0.00 2.32
2099 2131 7.059156 CCTTGAGGGAGATCATGAAGTTAAAT 58.941 38.462 0.00 0.00 37.23 1.40
2183 2215 3.258225 CGTCGGATCGCTCTCAAAT 57.742 52.632 0.00 0.00 0.00 2.32
2282 2314 1.609501 CAGGGACCCCGAGAACTGA 60.610 63.158 7.00 0.00 41.95 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 7.927629 CAGCTCTCTCTAAATCAAATTCTAGCT 59.072 37.037 0.00 0.00 34.59 3.32
41 42 5.361285 GGTAATGGTTCTCAGCTCTCTCTAA 59.639 44.000 0.00 0.00 0.00 2.10
42 43 4.890581 GGTAATGGTTCTCAGCTCTCTCTA 59.109 45.833 0.00 0.00 0.00 2.43
96 99 8.296211 AGAGGATCATCATATCAGACTATGTG 57.704 38.462 10.44 0.00 37.82 3.21
129 132 0.831307 GCTACTACTGGGGTCCCAAG 59.169 60.000 11.27 11.27 46.63 3.61
135 138 1.757340 GCGAGGCTACTACTGGGGT 60.757 63.158 0.00 0.00 0.00 4.95
198 201 3.066203 GCAAGAAAGAGTTTTCCCGTGAA 59.934 43.478 0.00 0.00 42.99 3.18
387 390 2.746472 GCACTCTCCTGACAAACTGGTT 60.746 50.000 0.00 0.00 38.50 3.67
411 414 3.136077 ACCATCATCACTCCATCTTGAGG 59.864 47.826 0.00 0.00 36.66 3.86
480 483 4.019321 TCCAGCCTTAAAGATAGCACAACT 60.019 41.667 0.00 0.00 0.00 3.16
482 485 4.568072 TCCAGCCTTAAAGATAGCACAA 57.432 40.909 0.00 0.00 0.00 3.33
485 488 4.339247 GCATTTCCAGCCTTAAAGATAGCA 59.661 41.667 0.00 0.00 0.00 3.49
576 579 1.107114 CGTCTGCAGAGTATGGAGGT 58.893 55.000 18.89 0.00 46.76 3.85
612 615 5.100259 CCAAGTTCTGAAATGCATGATGTC 58.900 41.667 0.00 0.00 0.00 3.06
618 621 7.001099 AGAAATTCCAAGTTCTGAAATGCAT 57.999 32.000 1.33 0.00 41.27 3.96
928 931 4.011517 GTCTGGCCCCGTTCCGAA 62.012 66.667 0.00 0.00 0.00 4.30
945 948 8.246908 AGTTCAATGTATCATGCAACAATTTG 57.753 30.769 0.00 5.91 35.62 2.32
955 958 8.697960 CGATCTTGTAGAGTTCAATGTATCATG 58.302 37.037 0.00 0.00 0.00 3.07
984 987 1.372683 CATACCTGATGGCCTCCCG 59.627 63.158 3.32 0.00 36.63 5.14
1071 1074 5.453198 CCTGAACAACTTTACTGGGCAAATT 60.453 40.000 0.00 0.00 0.00 1.82
1098 1101 3.573967 GTGGATTGGTGTTGTTGGATCTT 59.426 43.478 0.00 0.00 0.00 2.40
1194 1197 3.321111 TGTCAGTTCTTCCTGTACAGACC 59.679 47.826 24.68 5.08 33.69 3.85
1276 1279 9.103861 GACCTATCTTAATCTTTCAGGAAACAG 57.896 37.037 0.00 0.00 0.00 3.16
1427 1430 4.096081 GGCTGACTTCATTGAGGATTTCTG 59.904 45.833 2.39 0.00 0.00 3.02
1737 1762 6.194463 CGAAGCAATCCATACTATGTTTGTG 58.806 40.000 9.21 0.00 0.00 3.33
1757 1782 0.895530 TAACCTCCAGAGCACCGAAG 59.104 55.000 0.00 0.00 0.00 3.79
1767 1792 2.878406 CCGTTGCCATAATAACCTCCAG 59.122 50.000 0.00 0.00 0.00 3.86
1769 1794 2.158726 TCCCGTTGCCATAATAACCTCC 60.159 50.000 0.00 0.00 0.00 4.30
1789 1814 6.416455 TGCATGTATTGAACACGTTTCTTTTC 59.584 34.615 10.41 0.00 42.09 2.29
1794 1819 5.629020 ACAATGCATGTATTGAACACGTTTC 59.371 36.000 34.22 0.00 42.09 2.78
1878 1909 5.406175 TCCCTTATTAAACTTGTCGTTCGTG 59.594 40.000 0.00 0.00 33.90 4.35
1957 1989 4.832248 CAACCAGCTCACAGGTAGATTTA 58.168 43.478 0.00 0.00 33.91 1.40
2015 2047 0.179084 CAGAAGCGCTATTCCGGGAA 60.179 55.000 12.05 12.67 0.00 3.97
2021 2053 2.545946 GTCCATTCCAGAAGCGCTATTC 59.454 50.000 12.05 5.45 0.00 1.75
2099 2131 1.746322 TTAGTGGCAACGTCCCGTCA 61.746 55.000 0.00 0.00 39.99 4.35
2115 2147 3.469899 TGCAAGTTACAATGCGCTTAG 57.530 42.857 9.73 0.00 45.47 2.18
2178 2210 1.340017 GCTGTCAGGGCCAGTATTTGA 60.340 52.381 6.18 0.00 32.41 2.69
2183 2215 1.200760 ATGTGCTGTCAGGGCCAGTA 61.201 55.000 6.18 0.00 32.41 2.74


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

AutoCloner maintained by Alex Coulton.