Multiple sequence alignment - TraesCS7B01G155200

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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 TraesCS7B01G155200 chr7B 100.000 3444 0 0 1 3444 207971324 207974767 0 6360
1 TraesCS7B01G155200 chr7B 95.048 3453 151 15 1 3444 430145637 430149078 0 5411
2 TraesCS7B01G155200 chr6B 97.188 3449 88 7 1 3444 247392375 247395819 0 5823
3 TraesCS7B01G155200 chr2B 97.072 3449 91 8 1 3444 179064058 179067501 0 5801
4 TraesCS7B01G155200 chr2B 95.397 3454 141 14 1 3444 261018130 261021575 0 5481
5 TraesCS7B01G155200 chr2B 95.368 3454 141 14 1 3444 379155448 379158892 0 5474
6 TraesCS7B01G155200 chr2B 95.306 3451 145 13 1 3444 209875994 209872554 0 5459
7 TraesCS7B01G155200 chr1B 95.742 3452 131 12 1 3444 330756300 330759743 0 5546
8 TraesCS7B01G155200 chr3B 95.251 3453 145 15 1 3444 236260867 236257425 0 5450
9 TraesCS7B01G155200 chr3B 95.082 3457 150 16 1 3444 252185473 252188922 0 5424


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 TraesCS7B01G155200 chr7B 207971324 207974767 3443 False 6360 6360 100.000 1 3444 1 chr7B.!!$F1 3443
1 TraesCS7B01G155200 chr7B 430145637 430149078 3441 False 5411 5411 95.048 1 3444 1 chr7B.!!$F2 3443
2 TraesCS7B01G155200 chr6B 247392375 247395819 3444 False 5823 5823 97.188 1 3444 1 chr6B.!!$F1 3443
3 TraesCS7B01G155200 chr2B 179064058 179067501 3443 False 5801 5801 97.072 1 3444 1 chr2B.!!$F1 3443
4 TraesCS7B01G155200 chr2B 261018130 261021575 3445 False 5481 5481 95.397 1 3444 1 chr2B.!!$F2 3443
5 TraesCS7B01G155200 chr2B 379155448 379158892 3444 False 5474 5474 95.368 1 3444 1 chr2B.!!$F3 3443
6 TraesCS7B01G155200 chr2B 209872554 209875994 3440 True 5459 5459 95.306 1 3444 1 chr2B.!!$R1 3443
7 TraesCS7B01G155200 chr1B 330756300 330759743 3443 False 5546 5546 95.742 1 3444 1 chr1B.!!$F1 3443
8 TraesCS7B01G155200 chr3B 236257425 236260867 3442 True 5450 5450 95.251 1 3444 1 chr3B.!!$R1 3443
9 TraesCS7B01G155200 chr3B 252185473 252188922 3449 False 5424 5424 95.082 1 3444 1 chr3B.!!$F1 3443

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
566 577 0.037326 ATCAACACCGACGCTGACAT 60.037 50.0 0.0 0.0 0.0 3.06 F
2113 2141 2.674796 AGCTGAAGTTGTCCGGTATC 57.325 50.0 0.0 0.0 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2285 2313 0.403271 ATGAGGTTGTCTGGCAGCTT 59.597 50.000 10.34 0.0 0.00 3.74 R
3065 3102 4.335647 CTGCGCCTGACCTTGGGT 62.336 66.667 4.18 0.0 39.44 4.51 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
309 315 3.081061 TCCCAATTCAGAAACACCATCG 58.919 45.455 0.00 0.00 0.00 3.84
566 577 0.037326 ATCAACACCGACGCTGACAT 60.037 50.000 0.00 0.00 0.00 3.06
749 760 4.020039 ACATGGACGGTTAGTTATTCCACA 60.020 41.667 0.00 0.00 0.00 4.17
769 780 3.575247 ACCATCCGTGCCACCCAA 61.575 61.111 0.00 0.00 0.00 4.12
1384 1402 4.099266 TCATTTGCCCTGCATATGGTTTAC 59.901 41.667 15.99 0.00 44.12 2.01
1942 1967 8.893727 ACTACTTCATGGATTAATTGCTTGTAC 58.106 33.333 0.00 0.00 0.00 2.90
2113 2141 2.674796 AGCTGAAGTTGTCCGGTATC 57.325 50.000 0.00 0.00 0.00 2.24
2333 2361 1.007618 GGAGTAGATGCGTACGCCC 60.008 63.158 35.11 26.03 37.00 6.13
2368 2396 5.917462 TGGTTCATGATCGACTACATCAAT 58.083 37.500 0.00 0.00 33.94 2.57
2418 2446 2.367567 AGGCTGAAAACTTCTACGACCA 59.632 45.455 0.00 0.00 0.00 4.02
2500 2528 3.922850 GCTTGTGCTTGCCTTTTATCTTC 59.077 43.478 0.00 0.00 36.03 2.87
2614 2642 7.816640 TCAAGTACAATGTTTTGCTTATCTCC 58.183 34.615 0.00 0.00 36.22 3.71
2774 2802 5.049886 CGTGTCAGTACAACTCAGTACACTA 60.050 44.000 6.97 0.00 45.25 2.74
2781 2809 3.128938 ACAACTCAGTACACTAGATCGGC 59.871 47.826 0.00 0.00 0.00 5.54
2825 2855 9.696917 AATAAAAAGTACAAAAGAAGCATCAGG 57.303 29.630 0.00 0.00 0.00 3.86
2855 2885 4.686091 GCGCTACTATGAATGCACTATCAA 59.314 41.667 0.00 0.00 0.00 2.57
2904 2934 5.124457 CCATAGTTCTGAAAATGACACCAGG 59.876 44.000 12.96 0.00 0.00 4.45
2911 2941 1.981256 AAATGACACCAGGACACACC 58.019 50.000 0.00 0.00 39.35 4.16
3001 3033 6.535150 TCACACAAAACTGACAAGAACTAGAG 59.465 38.462 0.00 0.00 0.00 2.43
3113 3150 6.631016 ACAATGCTAGATACTTGAACTCGAA 58.369 36.000 0.00 0.00 0.00 3.71
3145 3182 4.642429 GAATCCCTAGTAATCCGCACAAT 58.358 43.478 0.00 0.00 0.00 2.71
3183 3220 1.484444 GGCCCACAGGTCAAGAGAGT 61.484 60.000 0.00 0.00 37.86 3.24
3234 3271 1.614413 AGTGTTCAGAGGAGTTCGACC 59.386 52.381 0.00 0.00 0.00 4.79
3236 3273 0.597072 GTTCAGAGGAGTTCGACCGT 59.403 55.000 0.00 0.00 0.00 4.83
3309 3346 1.810030 GGACTAAACCCAGAGCGCG 60.810 63.158 0.00 0.00 0.00 6.86
3424 3463 2.916934 AGCCCAGGTATACAAACCAGAA 59.083 45.455 5.01 0.00 42.40 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
309 315 8.682710 TGCTTGAGGTAATTATTTTCATGTACC 58.317 33.333 0.00 0.00 32.77 3.34
469 480 3.575256 ACGTACCAAATACCAGTGAGACA 59.425 43.478 0.00 0.00 0.00 3.41
566 577 1.825090 CTGCTTATCCCACTTGCACA 58.175 50.000 0.00 0.00 0.00 4.57
670 681 4.184629 GTCAAGCTGTACTTATGACCTGG 58.815 47.826 1.71 0.00 36.04 4.45
769 780 0.606401 CCCTTGTGTCAACCGCTCAT 60.606 55.000 0.00 0.00 0.00 2.90
1090 1106 0.466543 AGGGTTGTTGTGTACTCGCA 59.533 50.000 0.00 0.00 0.00 5.10
1452 1470 4.432712 GTGCATCCACTTTTTCACAAACT 58.567 39.130 0.00 0.00 38.93 2.66
1649 1670 9.813080 GAAAATACTTCACTACATCAAGTTCAC 57.187 33.333 0.00 0.00 32.56 3.18
2083 2111 4.517285 ACAACTTCAGCTTCTCTTTGTCA 58.483 39.130 0.00 0.00 0.00 3.58
2113 2141 2.185004 ACTTGTTGGGGTTGATCTCG 57.815 50.000 0.00 0.00 0.00 4.04
2285 2313 0.403271 ATGAGGTTGTCTGGCAGCTT 59.597 50.000 10.34 0.00 0.00 3.74
2333 2361 3.595173 TCATGAACCATGACTTGTACGG 58.405 45.455 5.61 0.00 44.60 4.02
2368 2396 0.456628 TCGCATATTCCGAACCGTCA 59.543 50.000 0.00 0.00 0.00 4.35
2418 2446 1.001631 GCAAAGGGGCAATAGGGGT 59.998 57.895 0.00 0.00 0.00 4.95
2500 2528 9.736023 AAGAGCAAACTACTAATTTGAAACAAG 57.264 29.630 1.76 0.00 39.01 3.16
2774 2802 3.961408 AGTAAGAATGTACTGGCCGATCT 59.039 43.478 0.00 0.00 32.97 2.75
2814 2844 0.462759 GCTTACGGCCTGATGCTTCT 60.463 55.000 0.00 0.00 40.92 2.85
2825 2855 2.129823 TTCATAGTAGCGCTTACGGC 57.870 50.000 18.68 0.98 40.57 5.68
2855 2885 6.022163 ACTTGCGTGTAGACTAAGTTGTAT 57.978 37.500 4.40 0.00 0.00 2.29
2904 2934 6.801539 TTTGTGATTATTCTCAGGTGTGTC 57.198 37.500 0.00 0.00 0.00 3.67
2911 2941 9.299963 TGTGTTTGTTTTTGTGATTATTCTCAG 57.700 29.630 0.00 0.00 0.00 3.35
3001 3033 4.627467 CACCAGTAGACTGATACTTGTTGC 59.373 45.833 11.31 0.00 46.59 4.17
3065 3102 4.335647 CTGCGCCTGACCTTGGGT 62.336 66.667 4.18 0.00 39.44 4.51


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

AutoCloner maintained by Alex Coulton.