Multiple sequence alignment - TraesCS2B01G546900

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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 TraesCS2B01G546900 chr2B 100.000 2632 0 0 1 2632 743729012 743731643 0.000000e+00 4861
1 TraesCS2B01G546900 chr2A 96.965 1285 26 2 1349 2632 742134227 742135499 0.000000e+00 2145
2 TraesCS2B01G546900 chr2A 95.212 1086 22 10 291 1351 742133113 742134193 0.000000e+00 1690
3 TraesCS2B01G546900 chr2A 97.952 293 6 0 1 293 742132783 742133075 2.340000e-140 508
4 TraesCS2B01G546900 chr2A 89.011 91 1 7 358 441 726910964 726911052 1.290000e-18 104
5 TraesCS2B01G546900 chr2D 96.654 1285 30 2 1349 2632 609435594 609436866 0.000000e+00 2122
6 TraesCS2B01G546900 chr2D 94.766 1089 28 5 291 1351 609434473 609435560 0.000000e+00 1668
7 TraesCS2B01G546900 chr2D 97.270 293 8 0 1 293 609434143 609434435 5.060000e-137 497
8 TraesCS2B01G546900 chr2D 89.011 91 1 7 358 441 272795807 272795895 1.290000e-18 104
9 TraesCS2B01G546900 chr7A 89.888 89 2 6 358 441 352183720 352183806 9.960000e-20 108
10 TraesCS2B01G546900 chr6A 88.889 90 2 7 358 441 445904256 445904343 1.290000e-18 104
11 TraesCS2B01G546900 chr3B 89.011 91 1 7 358 441 201525096 201525008 1.290000e-18 104
12 TraesCS2B01G546900 chrUn 88.043 92 1 7 358 441 23290066 23290155 1.670000e-17 100
13 TraesCS2B01G546900 chrUn 88.043 92 1 7 358 441 93411545 93411634 1.670000e-17 100


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 TraesCS2B01G546900 chr2B 743729012 743731643 2631 False 4861.000000 4861 100.000000 1 2632 1 chr2B.!!$F1 2631
1 TraesCS2B01G546900 chr2A 742132783 742135499 2716 False 1447.666667 2145 96.709667 1 2632 3 chr2A.!!$F2 2631
2 TraesCS2B01G546900 chr2D 609434143 609436866 2723 False 1429.000000 2122 96.230000 1 2632 3 chr2D.!!$F2 2631

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
883 952 2.159572 CCCTAAAAATGGACAAGACGCG 60.16 50.0 3.53 3.53 0.0 6.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1730 1836 0.394565 ACACAGAAGGTCAGAGGCAC 59.605 55.0 0.0 0.0 0.0 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
105 106 6.530181 CAGAACAAAAGGAAGTGTTAACAACC 59.470 38.462 10.51 13.68 38.07 3.77
277 278 7.279981 ACTTCTCAAACCTGCAAAATTAAAACC 59.720 33.333 0.00 0.00 0.00 3.27
366 407 9.717942 GCTAGGAATAGATGTGTGAAATCTAAT 57.282 33.333 0.00 0.00 39.46 1.73
877 946 8.499288 AAAGAATAACCCCTAAAAATGGACAA 57.501 30.769 0.00 0.00 0.00 3.18
883 952 2.159572 CCCTAAAAATGGACAAGACGCG 60.160 50.000 3.53 3.53 0.00 6.01
947 1016 5.291905 ACCATATAAGTAGGACCTTGCAC 57.708 43.478 0.00 0.00 0.00 4.57
1200 1269 1.079750 GTCCTCCTTGACGGCTGAC 60.080 63.158 0.00 0.00 0.00 3.51
1270 1339 1.107114 CGAGACAGCCACATACCTCT 58.893 55.000 0.00 0.00 0.00 3.69
1272 1341 2.103373 GAGACAGCCACATACCTCTCA 58.897 52.381 0.00 0.00 0.00 3.27
1385 1490 6.822442 TGAATCATGGATTGCATGCTTTATT 58.178 32.000 20.33 7.69 31.89 1.40
1409 1514 8.667076 TTGATCATATATATGCATGCAGGTAC 57.333 34.615 26.69 8.46 33.76 3.34
1537 1642 1.464198 AGAAGGGGTGCCAGGACTT 60.464 57.895 0.00 0.00 0.00 3.01
1704 1810 5.186198 AGACATGGTGGCTAGTGAATTAAC 58.814 41.667 0.00 0.00 30.85 2.01
1726 1832 1.350071 ATCTAGCAGATGGGAGCCAG 58.650 55.000 0.00 0.00 36.75 4.85
1727 1833 0.262876 TCTAGCAGATGGGAGCCAGA 59.737 55.000 0.00 0.00 36.75 3.86
1728 1834 1.132913 TCTAGCAGATGGGAGCCAGAT 60.133 52.381 0.00 0.00 36.75 2.90
1729 1835 1.275856 CTAGCAGATGGGAGCCAGATC 59.724 57.143 0.00 0.00 36.75 2.75
1730 1836 1.301558 GCAGATGGGAGCCAGATCG 60.302 63.158 0.00 0.00 36.75 3.69
1731 1837 2.037620 GCAGATGGGAGCCAGATCGT 62.038 60.000 0.00 0.00 36.75 3.73
1732 1838 0.249784 CAGATGGGAGCCAGATCGTG 60.250 60.000 0.00 0.00 36.75 4.35
1733 1839 1.596477 GATGGGAGCCAGATCGTGC 60.596 63.158 1.70 1.70 36.75 5.34
1734 1840 3.112205 ATGGGAGCCAGATCGTGCC 62.112 63.158 5.97 0.00 36.75 5.01
1735 1841 3.474570 GGGAGCCAGATCGTGCCT 61.475 66.667 5.97 0.00 0.00 4.75
1736 1842 2.107953 GGAGCCAGATCGTGCCTC 59.892 66.667 5.97 1.30 0.00 4.70
1737 1843 2.430610 GGAGCCAGATCGTGCCTCT 61.431 63.158 5.97 0.00 0.00 3.69
1800 1906 1.397693 GCTAGATAAACATGCTGCGCG 60.398 52.381 0.00 0.00 0.00 6.86
1816 1923 2.288152 TGCGCGACAGATTATGCTATCA 60.288 45.455 12.10 0.00 0.00 2.15
2043 2150 0.036732 AGGTGCAGAAAATCCGCTCA 59.963 50.000 0.00 0.00 0.00 4.26
2100 2207 3.628032 TGAACGACATGGCAAAACTTACA 59.372 39.130 0.00 0.00 0.00 2.41
2102 2209 4.640789 ACGACATGGCAAAACTTACAAA 57.359 36.364 0.00 0.00 0.00 2.83
2103 2210 5.195001 ACGACATGGCAAAACTTACAAAT 57.805 34.783 0.00 0.00 0.00 2.32
2143 2250 3.294627 GCACGAACGAAATGAACGAATTC 59.705 43.478 0.14 0.00 35.18 2.17
2227 2334 8.762426 ACGTAGATTTTCAACTACACTTTCTTC 58.238 33.333 0.00 0.00 38.90 2.87
2376 2483 6.096846 GGACTTTCAACCCATAACAAGCATAT 59.903 38.462 0.00 0.00 0.00 1.78
2493 2600 5.825593 TGTAGGACTATGGGGATTTCATC 57.174 43.478 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 6.540914 ACTTCATGGTATGTATGGGTTTAACG 59.459 38.462 0.00 0.00 0.00 3.18
105 106 2.820059 TCCTACCAAGATGCTATGCG 57.180 50.000 0.00 0.00 0.00 4.73
277 278 4.143179 GGAGAAAGTGTTTGTAACCGATCG 60.143 45.833 8.51 8.51 0.00 3.69
877 946 2.357517 CAGAAAGTGCCCGCGTCT 60.358 61.111 4.92 0.00 0.00 4.18
883 952 2.552743 GACAGGTTAACAGAAAGTGCCC 59.447 50.000 8.10 0.00 0.00 5.36
1270 1339 5.934043 AGTTGTCATCTTCATCGATGTTTGA 59.066 36.000 24.09 19.12 41.17 2.69
1272 1341 6.427853 TGAAGTTGTCATCTTCATCGATGTTT 59.572 34.615 24.09 5.90 43.88 2.83
1385 1490 6.925165 CGTACCTGCATGCATATATATGATCA 59.075 38.462 22.97 14.40 35.75 2.92
1440 1545 2.023741 CATGTCCAGCGCGATTGC 59.976 61.111 12.10 0.00 37.91 3.56
1537 1642 0.535335 GATGCTCCGGTGTTCTGGTA 59.465 55.000 0.00 0.00 40.77 3.25
1704 1810 2.902486 TGGCTCCCATCTGCTAGATAAG 59.098 50.000 0.00 0.00 32.12 1.73
1726 1832 0.820871 AGAAGGTCAGAGGCACGATC 59.179 55.000 0.00 0.00 0.00 3.69
1727 1833 0.534412 CAGAAGGTCAGAGGCACGAT 59.466 55.000 0.00 0.00 0.00 3.73
1728 1834 0.827925 ACAGAAGGTCAGAGGCACGA 60.828 55.000 0.00 0.00 0.00 4.35
1729 1835 0.668706 CACAGAAGGTCAGAGGCACG 60.669 60.000 0.00 0.00 0.00 5.34
1730 1836 0.394565 ACACAGAAGGTCAGAGGCAC 59.605 55.000 0.00 0.00 0.00 5.01
1731 1837 2.009681 TACACAGAAGGTCAGAGGCA 57.990 50.000 0.00 0.00 0.00 4.75
1732 1838 3.067833 GTTTACACAGAAGGTCAGAGGC 58.932 50.000 0.00 0.00 0.00 4.70
1733 1839 4.608948 AGTTTACACAGAAGGTCAGAGG 57.391 45.455 0.00 0.00 0.00 3.69
1734 1840 5.047660 AGCTAGTTTACACAGAAGGTCAGAG 60.048 44.000 0.00 0.00 0.00 3.35
1735 1841 4.833380 AGCTAGTTTACACAGAAGGTCAGA 59.167 41.667 0.00 0.00 0.00 3.27
1736 1842 4.926238 CAGCTAGTTTACACAGAAGGTCAG 59.074 45.833 0.00 0.00 0.00 3.51
1737 1843 4.587262 TCAGCTAGTTTACACAGAAGGTCA 59.413 41.667 0.00 0.00 0.00 4.02
1800 1906 8.187480 AGTATGACGATGATAGCATAATCTGTC 58.813 37.037 0.00 0.00 34.11 3.51
1804 1910 8.187480 ACTGAGTATGACGATGATAGCATAATC 58.813 37.037 0.00 0.00 38.24 1.75
1816 1923 1.948145 GACCCGACTGAGTATGACGAT 59.052 52.381 0.00 0.00 0.00 3.73
2043 2150 5.178096 TCCAATGTGACATGTTCTATGGT 57.822 39.130 10.51 0.00 0.00 3.55
2100 2207 7.065324 TCGTGCGGAATGATTTTCTTAGTATTT 59.935 33.333 0.00 0.00 0.00 1.40
2102 2209 6.046593 TCGTGCGGAATGATTTTCTTAGTAT 58.953 36.000 0.00 0.00 0.00 2.12
2103 2210 5.412640 TCGTGCGGAATGATTTTCTTAGTA 58.587 37.500 0.00 0.00 0.00 1.82
2143 2250 5.587388 ATGTTAGTGATGAAAGGCAATGG 57.413 39.130 0.00 0.00 0.00 3.16
2200 2307 8.658499 AGAAAGTGTAGTTGAAAATCTACGTT 57.342 30.769 0.00 0.00 39.25 3.99
2376 2483 3.067106 CTCTTTGCCACTTCTAGCGAAA 58.933 45.455 0.00 0.00 32.09 3.46


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

AutoCloner maintained by Alex Coulton.