Multiple sequence alignment - TraesCS1A01G122300

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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 TraesCS1A01G122300 chr1A 100.000 3924 0 0 1 3924 137408677 137404754 0.000000e+00 7247.0
1 TraesCS1A01G122300 chr1D 97.475 3723 67 13 2 3712 124905717 124902010 0.000000e+00 6329.0
2 TraesCS1A01G122300 chr1B 97.468 3238 53 8 1 3229 188907520 188904303 0.000000e+00 5498.0
3 TraesCS1A01G122300 chr1B 94.256 679 32 5 3251 3924 188828827 188828151 0.000000e+00 1031.0
4 TraesCS1A01G122300 chrUn 97.959 49 1 0 2705 2753 43370833 43370785 6.990000e-13 86.1


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 TraesCS1A01G122300 chr1A 137404754 137408677 3923 True 7247 7247 100.000 1 3924 1 chr1A.!!$R1 3923
1 TraesCS1A01G122300 chr1D 124902010 124905717 3707 True 6329 6329 97.475 2 3712 1 chr1D.!!$R1 3710
2 TraesCS1A01G122300 chr1B 188904303 188907520 3217 True 5498 5498 97.468 1 3229 1 chr1B.!!$R2 3228
3 TraesCS1A01G122300 chr1B 188828151 188828827 676 True 1031 1031 94.256 3251 3924 1 chr1B.!!$R1 673

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
60 61 4.284234 TCCAATCATCCATAGCATTCGAGA 59.716 41.667 0.00 0.0 0.00 4.04 F
444 446 7.120579 TGAATATGTTCTCCTTGCATTAAACGT 59.879 33.333 3.72 0.0 35.33 3.99 F
1189 1194 5.408604 ACTTGTAAGCCGAATTACTCTTGTG 59.591 40.000 9.98 0.0 36.73 3.33 F
2142 2147 0.249398 GTCAGGCCATAACTGTCGGT 59.751 55.000 5.01 0.0 37.25 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1067 1072 1.969923 CAAATGAACAAAGGGGGAGCA 59.030 47.619 0.00 0.0 0.00 4.26 R
1313 1318 3.588842 AGTGAAGAATCCATTGAGTCCCA 59.411 43.478 0.00 0.0 36.25 4.37 R
2520 2529 0.311790 CTGCGCCAAACACAAGTCAT 59.688 50.000 4.18 0.0 0.00 3.06 R
3450 3461 0.881118 TCCAATGAGCTTTTCGTGCC 59.119 50.000 0.00 0.0 0.00 5.01 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
60 61 4.284234 TCCAATCATCCATAGCATTCGAGA 59.716 41.667 0.00 0.00 0.00 4.04
444 446 7.120579 TGAATATGTTCTCCTTGCATTAAACGT 59.879 33.333 3.72 0.00 35.33 3.99
1186 1191 7.494952 GGATAACTTGTAAGCCGAATTACTCTT 59.505 37.037 9.98 0.00 36.73 2.85
1189 1194 5.408604 ACTTGTAAGCCGAATTACTCTTGTG 59.591 40.000 9.98 0.00 36.73 3.33
1313 1318 2.103153 TGGAGTTTCTCTCTGGTGGT 57.897 50.000 0.00 0.00 42.40 4.16
1549 1554 5.221843 TGGGCAAGGATGTAATAGACCATAC 60.222 44.000 0.00 0.00 0.00 2.39
2140 2145 2.386661 AAGTCAGGCCATAACTGTCG 57.613 50.000 5.01 0.00 37.25 4.35
2141 2146 0.537188 AGTCAGGCCATAACTGTCGG 59.463 55.000 5.01 0.00 37.25 4.79
2142 2147 0.249398 GTCAGGCCATAACTGTCGGT 59.751 55.000 5.01 0.00 37.25 4.69
2143 2148 0.981183 TCAGGCCATAACTGTCGGTT 59.019 50.000 5.01 1.93 41.54 4.44
2144 2149 1.349688 TCAGGCCATAACTGTCGGTTT 59.650 47.619 5.01 0.00 39.17 3.27
2145 2150 2.159382 CAGGCCATAACTGTCGGTTTT 58.841 47.619 5.01 0.00 39.17 2.43
2508 2517 3.712016 TTGCCTGCCTTATGTGTTCTA 57.288 42.857 0.00 0.00 0.00 2.10
2520 2529 7.334421 GCCTTATGTGTTCTAATTCACTGAAGA 59.666 37.037 0.00 0.00 35.82 2.87
2655 2664 0.976641 TTCATCTCTTGTCGCCAGGT 59.023 50.000 0.00 0.00 0.00 4.00
2809 2818 5.221244 ACACCTTTCCCTTGAAAATCTTTCG 60.221 40.000 0.00 0.00 39.88 3.46
3160 3171 1.476074 CAAAGCTTGCTTTCGCGAAA 58.524 45.000 30.47 30.47 39.65 3.46
3192 3203 6.203813 TGTACCACCCCTATGTAATCTAACA 58.796 40.000 0.00 0.00 0.00 2.41
3201 3212 6.489361 CCCTATGTAATCTAACACCGAGTAGT 59.511 42.308 0.00 0.00 30.75 2.73
3465 3478 0.326264 AGAGGGCACGAAAAGCTCAT 59.674 50.000 0.00 0.00 34.03 2.90
3475 3488 3.502211 ACGAAAAGCTCATTGGACGAATT 59.498 39.130 0.00 0.00 0.00 2.17
3508 3522 1.448985 TCCGTCAAATAGTTGGCAGC 58.551 50.000 8.38 0.00 39.45 5.25
3515 3529 2.684881 CAAATAGTTGGCAGCGGATTCT 59.315 45.455 0.00 0.00 0.00 2.40
3525 3541 1.869767 CAGCGGATTCTCTGGTATTGC 59.130 52.381 0.00 0.00 31.35 3.56
3564 3580 5.591472 CACATCCAATGATACCAACACTCAT 59.409 40.000 0.00 0.00 0.00 2.90
3627 3643 8.650714 GGAAGTTCTCAAAAATATTGTCAATGC 58.349 33.333 8.39 0.00 0.00 3.56
3783 3800 4.706842 GGTTGGTACCATGGTATCATCT 57.293 45.455 33.28 6.35 44.36 2.90
3805 3822 7.681939 TCTAAACCTTGGTTTCATGACATAC 57.318 36.000 19.57 0.00 0.00 2.39
3822 3839 3.927142 ACATACTTTGTCGCACTAAGAGC 59.073 43.478 13.89 0.00 35.14 4.09
3838 3855 1.873591 AGAGCGTGTTTGGTTCATGTC 59.126 47.619 0.00 0.00 0.00 3.06
3860 3877 0.399806 AGGTTGCCCCACCAAAACAT 60.400 50.000 0.09 0.00 39.62 2.71
3869 3886 1.472480 CCACCAAAACATCGGCTAAGG 59.528 52.381 0.00 0.00 0.00 2.69
3874 3891 4.526650 ACCAAAACATCGGCTAAGGAAAAT 59.473 37.500 0.00 0.00 0.00 1.82
3911 3928 6.003326 TGATGAGTTGGTAAAAGAGCATTGA 58.997 36.000 0.00 0.00 34.92 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
152 154 1.794714 ATGAATCTCCAGGGCGTAGT 58.205 50.000 0.00 0.00 0.00 2.73
156 158 1.134280 ACAGAATGAATCTCCAGGGCG 60.134 52.381 0.00 0.00 39.69 6.13
411 413 9.851686 ATGCAAGGAGAACATATTCACTAAATA 57.148 29.630 0.00 0.00 37.29 1.40
444 446 8.624367 TTAAAAGTTAATGAGGGAACGATGAA 57.376 30.769 0.00 0.00 0.00 2.57
484 486 1.039785 TGTCAGAGAGCAGGGATCCG 61.040 60.000 5.45 0.00 0.00 4.18
801 803 7.761651 ACTTTTCTTTTTCATGAAACTGCTC 57.238 32.000 20.35 0.00 32.72 4.26
1067 1072 1.969923 CAAATGAACAAAGGGGGAGCA 59.030 47.619 0.00 0.00 0.00 4.26
1186 1191 8.102676 TCATTCTATCAGAAGAAAATCACCACA 58.897 33.333 0.00 0.00 37.69 4.17
1189 1194 9.334947 TCATCATTCTATCAGAAGAAAATCACC 57.665 33.333 0.00 0.00 37.69 4.02
1313 1318 3.588842 AGTGAAGAATCCATTGAGTCCCA 59.411 43.478 0.00 0.00 36.25 4.37
1777 1782 7.551617 GGCTTCAACCTAGCTAAGTATAACAAA 59.448 37.037 0.00 0.00 38.67 2.83
1854 1859 6.683974 AAAAGATTCTCGATTACATGGGTG 57.316 37.500 0.00 0.00 0.00 4.61
1934 1939 9.082313 CCCAAAGTAGATTATTAGGCAAATCAT 57.918 33.333 0.00 0.00 35.07 2.45
2197 2203 7.495279 TGCACTAAATATGATTCCATTTTTGGC 59.505 33.333 0.00 0.00 36.45 4.52
2464 2473 2.934553 GGTAAAGTTGTCGGTGATAGCC 59.065 50.000 0.00 0.00 0.00 3.93
2508 2517 6.949352 AACACAAGTCATCTTCAGTGAATT 57.051 33.333 5.91 0.00 34.59 2.17
2520 2529 0.311790 CTGCGCCAAACACAAGTCAT 59.688 50.000 4.18 0.00 0.00 3.06
2655 2664 3.708403 ACAGGTGAGATGAGCAAATCA 57.292 42.857 1.99 0.00 43.70 2.57
3192 3203 1.412453 TTGGGGCACAACTACTCGGT 61.412 55.000 0.00 0.00 33.18 4.69
3201 3212 9.821240 ATTAGTATCATTATATTTGGGGCACAA 57.179 29.630 0.00 0.00 37.28 3.33
3450 3461 0.881118 TCCAATGAGCTTTTCGTGCC 59.119 50.000 0.00 0.00 0.00 5.01
3465 3478 8.671028 GGAAATTAGCTACTTTAATTCGTCCAA 58.329 33.333 8.88 0.00 32.56 3.53
3475 3488 9.880157 ACTATTTGACGGAAATTAGCTACTTTA 57.120 29.630 8.88 0.00 35.74 1.85
3508 3522 2.620251 TGGCAATACCAGAGAATCCG 57.380 50.000 0.00 0.00 46.36 4.18
3564 3580 7.052248 TCAAGAGTTAGTATCACGGTCTGATA 58.948 38.462 0.00 0.00 40.38 2.15
3587 3603 5.820423 TGAGAACTTCCGAGTTTGAAATTCA 59.180 36.000 1.44 0.00 45.88 2.57
3751 3768 1.997606 GGTACCAACCTTCGAATGTCG 59.002 52.381 7.15 3.30 43.08 4.35
3753 3770 3.343617 CATGGTACCAACCTTCGAATGT 58.656 45.455 20.76 0.00 46.91 2.71
3758 3775 3.118555 TGATACCATGGTACCAACCTTCG 60.119 47.826 26.87 5.27 46.91 3.79
3762 3779 4.706842 AGATGATACCATGGTACCAACC 57.293 45.455 26.87 18.32 46.98 3.77
3783 3800 8.356657 CAAAGTATGTCATGAAACCAAGGTTTA 58.643 33.333 16.62 6.74 46.80 2.01
3812 3829 1.226746 ACCAAACACGCTCTTAGTGC 58.773 50.000 0.00 0.00 42.94 4.40
3819 3836 1.069227 GGACATGAACCAAACACGCTC 60.069 52.381 0.00 0.00 0.00 5.03
3820 3837 0.951558 GGACATGAACCAAACACGCT 59.048 50.000 0.00 0.00 0.00 5.07
3822 3839 2.287547 CCTTGGACATGAACCAAACACG 60.288 50.000 21.84 13.98 45.05 4.49
3860 3877 5.510009 GGAAACCAAAATTTTCCTTAGCCGA 60.510 40.000 0.00 0.00 45.94 5.54


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

AutoCloner maintained by Alex Coulton.