Multiple sequence alignment - TraesCS4D01G063700

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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 TraesCS4D01G063700 chr4D 100.000 2495 0 0 1 2495 39360670 39363164 0 4608
1 TraesCS4D01G063700 chr4B 94.821 1680 66 6 827 2495 57750013 57748344 0 2601
2 TraesCS4D01G063700 chr4B 95.163 827 36 2 1 823 57750911 57750085 0 1303
3 TraesCS4D01G063700 chr4A 91.188 1861 115 19 14 1836 560993625 560995474 0 2483
4 TraesCS4D01G063700 chr4A 88.872 656 49 5 1834 2474 560995577 560996223 0 785


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 TraesCS4D01G063700 chr4D 39360670 39363164 2494 False 4608 4608 100.000 1 2495 1 chr4D.!!$F1 2494
1 TraesCS4D01G063700 chr4B 57748344 57750911 2567 True 1952 2601 94.992 1 2495 2 chr4B.!!$R1 2494
2 TraesCS4D01G063700 chr4A 560993625 560996223 2598 False 1634 2483 90.030 14 2474 2 chr4A.!!$F1 2460

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
262 263 2.305009 GAGATTGGAGATTGGGGCTTG 58.695 52.381 0.0 0.0 0.0 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2047 2273 2.224597 TGGACATCTCAGCAGCTCAAAA 60.225 45.455 0.0 0.0 0.0 2.44 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
47 48 3.763557 ATGGACCATTGACCCTTTCAT 57.236 42.857 0.00 0.00 32.84 2.57
76 77 4.727734 GCATCGATTGTAAAGTGAACGCAT 60.728 41.667 0.00 0.00 0.00 4.73
167 168 8.918202 AAGAAACATGATTGACCTAAACAGTA 57.082 30.769 0.00 0.00 0.00 2.74
222 223 2.686915 CCTGCTGGATTTTAGCTTCCTG 59.313 50.000 2.92 4.48 41.66 3.86
262 263 2.305009 GAGATTGGAGATTGGGGCTTG 58.695 52.381 0.00 0.00 0.00 4.01
330 331 2.882761 GTGATGATGCATACACATGGCT 59.117 45.455 19.34 0.00 34.05 4.75
360 361 3.242739 CGCTATCAAGGGGAAACATTTCG 60.243 47.826 0.00 0.00 38.06 3.46
619 626 5.048434 ACTTCATTTGCCTCTCTAAAGCAAC 60.048 40.000 0.00 0.00 45.57 4.17
641 651 6.560253 ACACTGAAGATCAACATTACCAAC 57.440 37.500 0.00 0.00 0.00 3.77
703 739 6.403200 CCTCACGTTTCAAAAGAAGTTCAAGA 60.403 38.462 5.50 0.00 0.00 3.02
721 757 7.828223 AGTTCAAGACATCTTTGAATCAGCTAT 59.172 33.333 4.02 0.00 33.11 2.97
726 762 8.476064 AGACATCTTTGAATCAGCTATCTAGA 57.524 34.615 0.00 0.00 0.00 2.43
770 807 8.851541 TTTCTTTAAGACCGTGGTATACAAAT 57.148 30.769 5.01 0.00 0.00 2.32
810 847 6.964370 CGATAAATCGCAAAACCAATTGTCTA 59.036 34.615 4.43 0.00 43.84 2.59
855 960 8.839310 AAGAATTGTCCTCCGATAATTATCAG 57.161 34.615 22.22 13.16 39.21 2.90
889 994 6.749118 GCCTTCTCGTTTTATTTACGTAGAGA 59.251 38.462 0.00 0.00 39.84 3.10
890 995 7.253585 GCCTTCTCGTTTTATTTACGTAGAGAC 60.254 40.741 6.45 0.00 39.84 3.36
924 1029 7.010091 CGTATTCAGTTCATAACATGTGCTGTA 59.990 37.037 0.00 0.00 36.98 2.74
927 1032 6.405538 TCAGTTCATAACATGTGCTGTATCA 58.594 36.000 0.00 0.00 36.98 2.15
1006 1111 2.291930 CCCACCAAAACCCTAATGGCTA 60.292 50.000 0.00 0.00 37.77 3.93
1110 1215 4.135153 CGGGTCTCAGGCCTCGTG 62.135 72.222 0.00 0.00 0.00 4.35
1437 1542 3.264845 GGGGTGCCCAAGGAGGAA 61.265 66.667 9.76 0.00 44.65 3.36
1721 1826 3.755905 TGTTTGTTTGAGTGTGAGCAAGA 59.244 39.130 0.00 0.00 0.00 3.02
1869 2079 4.500035 GCTGTTGCTAGGTAGTAGGATGTC 60.500 50.000 0.00 0.00 36.03 3.06
1904 2114 6.402658 GCAGTAACAGGAAGTGAGATTTTAGC 60.403 42.308 0.00 0.00 0.00 3.09
1969 2187 6.410540 ACTAGACCAAAAGCTTTGATCTAGG 58.589 40.000 32.51 23.39 38.87 3.02
2087 2314 5.240623 TGTCCAAGGTACATTTAACTGCAAG 59.759 40.000 0.00 0.00 42.29 4.01
2157 2384 2.081462 GGGTGTTGTTGGAGATAACCG 58.919 52.381 0.00 0.00 0.00 4.44
2160 2387 2.095919 GTGTTGTTGGAGATAACCGCAC 60.096 50.000 0.00 0.00 31.90 5.34
2222 2449 7.887996 TGATTATGTTTGTGAAAATTCTGCC 57.112 32.000 0.00 0.00 0.00 4.85
2229 2456 3.013921 TGTGAAAATTCTGCCCGGTATC 58.986 45.455 0.00 0.00 0.00 2.24
2298 2527 1.715785 ATTGGTTTGTGGGGTCAAGG 58.284 50.000 0.00 0.00 0.00 3.61
2407 2641 4.878397 GCTTAGCATAGACACTGGAAACAT 59.122 41.667 0.00 0.00 41.51 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.948979 GGTCAATGGTCCATATTTGCGA 59.051 45.455 4.33 0.00 0.00 5.10
47 48 7.464045 CGTTCACTTTACAATCGATGCAAGATA 60.464 37.037 0.00 0.00 0.00 1.98
76 77 4.080919 AGTTTCACTATAGTCCTGCATGCA 60.081 41.667 21.29 21.29 0.00 3.96
167 168 7.123355 TCATCAAAAGACAAAGGAACCATTT 57.877 32.000 0.00 0.00 0.00 2.32
262 263 2.027469 ACCCCCTAATCACGTGAAAGTC 60.027 50.000 24.13 0.00 0.00 3.01
307 308 3.215975 CCATGTGTATGCATCATCACCA 58.784 45.455 19.54 12.08 32.79 4.17
330 331 1.347707 CCCCTTGATAGCGATTAGGCA 59.652 52.381 0.00 0.00 34.64 4.75
360 361 2.531942 AGACCCCTCACCCCCAAC 60.532 66.667 0.00 0.00 0.00 3.77
619 626 6.205464 AGTGTTGGTAATGTTGATCTTCAGTG 59.795 38.462 0.00 0.00 0.00 3.66
641 651 5.398169 TGTGACAAAAACTTGTTAGCAGTG 58.602 37.500 0.00 0.00 34.90 3.66
721 757 4.530388 CGGCGTACGTCAATAAATCTAGA 58.470 43.478 21.20 0.00 37.93 2.43
823 860 2.031157 CGGAGGACAATTCTTTTGCGTT 60.031 45.455 0.00 0.00 0.00 4.84
824 861 1.535462 CGGAGGACAATTCTTTTGCGT 59.465 47.619 0.00 0.00 0.00 5.24
855 960 2.563471 AACGAGAAGGCGTATCTGAC 57.437 50.000 0.00 0.00 44.86 3.51
924 1029 2.131023 GTGGGGGAGAAGGAAGATGAT 58.869 52.381 0.00 0.00 0.00 2.45
927 1032 1.626631 GGAGTGGGGGAGAAGGAAGAT 60.627 57.143 0.00 0.00 0.00 2.40
1110 1215 3.492311 GAGGCCGCAGATCTCGTCC 62.492 68.421 0.00 9.26 0.00 4.79
1143 1248 3.849951 GCATCGGCGAGGGAGGAA 61.850 66.667 23.65 0.00 0.00 3.36
1329 1434 4.040952 GCCCTCAGCTCCTTGATAATCTTA 59.959 45.833 0.00 0.00 38.99 2.10
1500 1605 3.453717 AGCAAAGGCATACAGAGATCTCA 59.546 43.478 24.39 4.53 44.61 3.27
1721 1826 6.371271 GCTCTGTTCTAAGAAAAGCATTCTCT 59.629 38.462 5.38 0.00 0.00 3.10
1802 1907 6.498303 AGATGCATTACCTAGATACCATGTGA 59.502 38.462 0.00 0.00 0.00 3.58
1807 1912 7.373617 TGAAAGATGCATTACCTAGATACCA 57.626 36.000 0.00 0.00 0.00 3.25
1869 2079 2.869801 TCCTGTTACTGCAAACTTCACG 59.130 45.455 3.11 0.00 0.00 4.35
1904 2114 4.036498 ACTGACGGACATAATAAGACCTCG 59.964 45.833 0.00 0.00 0.00 4.63
2047 2273 2.224597 TGGACATCTCAGCAGCTCAAAA 60.225 45.455 0.00 0.00 0.00 2.44
2087 2314 8.243426 TCTCATTTCAACCACAACATAAATAGC 58.757 33.333 0.00 0.00 0.00 2.97
2157 2384 4.071961 TCCACATAGTCATACCATGTGC 57.928 45.455 11.55 0.00 45.24 4.57
2160 2387 5.048504 GCCATTTCCACATAGTCATACCATG 60.049 44.000 0.00 0.00 0.00 3.66
2253 2482 9.725019 TTAACATAGGCCATCTGAGTATAATTG 57.275 33.333 5.01 0.00 0.00 2.32
2298 2527 4.739587 AGGGATAGTTTCGGAACTTCTC 57.260 45.455 15.75 11.82 43.48 2.87
2407 2641 6.206634 CCAAAGCATACAAAGAAGTGGTTCTA 59.793 38.462 0.00 0.00 42.59 2.10


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

AutoCloner maintained by Alex Coulton.