Multiple sequence alignment - TraesCS6A01G221200

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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 TraesCS6A01G221200 chr6A 100.000 3389 0 0 1 3389 410895988 410892600 0.000000e+00 6259.0
1 TraesCS6A01G221200 chr6A 93.506 2002 86 14 1130 3124 441435761 441437725 0.000000e+00 2937.0
2 TraesCS6A01G221200 chr6A 95.687 997 26 6 67 1061 441434454 441435435 0.000000e+00 1587.0
3 TraesCS6A01G221200 chr6D 97.505 3326 63 10 67 3389 304286959 304290267 0.000000e+00 5664.0
4 TraesCS6A01G221200 chr6D 97.101 69 2 0 1 69 304286423 304286491 2.140000e-22 117.0
5 TraesCS6A01G221200 chr6B 95.800 3333 106 15 67 3389 470131098 470134406 0.000000e+00 5349.0
6 TraesCS6A01G221200 chr4A 97.727 44 1 0 3341 3384 546004049 546004006 3.630000e-10 76.8
7 TraesCS6A01G221200 chr3A 83.750 80 9 3 3305 3384 275567728 275567653 4.690000e-09 73.1
8 TraesCS6A01G221200 chr1B 80.612 98 14 4 3288 3384 518875764 518875671 1.690000e-08 71.3
9 TraesCS6A01G221200 chr7A 97.222 36 1 0 3349 3384 310303892 310303927 1.020000e-05 62.1
10 TraesCS6A01G221200 chr5B 97.222 36 1 0 3349 3384 692810586 692810551 1.020000e-05 62.1
11 TraesCS6A01G221200 chr5B 97.222 36 1 0 3349 3384 692812666 692812631 1.020000e-05 62.1
12 TraesCS6A01G221200 chr2D 94.444 36 2 0 3349 3384 101464920 101464885 4.720000e-04 56.5


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 TraesCS6A01G221200 chr6A 410892600 410895988 3388 True 6259.0 6259 100.0000 1 3389 1 chr6A.!!$R1 3388
1 TraesCS6A01G221200 chr6A 441434454 441437725 3271 False 2262.0 2937 94.5965 67 3124 2 chr6A.!!$F1 3057
2 TraesCS6A01G221200 chr6D 304286423 304290267 3844 False 2890.5 5664 97.3030 1 3389 2 chr6D.!!$F1 3388
3 TraesCS6A01G221200 chr6B 470131098 470134406 3308 False 5349.0 5349 95.8000 67 3389 1 chr6B.!!$F1 3322

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
898 1372 1.293179 GCCCAACACTGGCCATTTC 59.707 57.895 5.51 0.0 43.33 2.17 F
899 1373 1.974543 CCCAACACTGGCCATTTCC 59.025 57.895 5.51 0.0 41.99 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1776 2512 0.679505 TCACCTGGAGAACACCTTCG 59.320 55.0 0.0 0.0 0.0 3.79 R
2505 3241 0.685097 GCATCCCACGAGCCCTTATA 59.315 55.0 0.0 0.0 0.0 0.98 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
154 626 6.293626 CCAGAAATTCGGCACAGATAAATAGG 60.294 42.308 0.00 0.00 0.00 2.57
158 630 7.639113 AATTCGGCACAGATAAATAGGAAAA 57.361 32.000 0.00 0.00 0.00 2.29
376 850 2.599281 TCCACGTCCTTCTCCGCA 60.599 61.111 0.00 0.00 0.00 5.69
693 1167 2.735772 CGATGGGGACTGGGGAGTG 61.736 68.421 0.00 0.00 0.00 3.51
733 1207 1.454722 CTTAAGCGCTACGACGAGTC 58.545 55.000 12.05 0.00 34.06 3.36
897 1371 3.470433 GCCCAACACTGGCCATTT 58.530 55.556 5.51 0.00 43.33 2.32
898 1372 1.293179 GCCCAACACTGGCCATTTC 59.707 57.895 5.51 0.00 43.33 2.17
899 1373 1.974543 CCCAACACTGGCCATTTCC 59.025 57.895 5.51 0.00 41.99 3.13
934 1413 4.233789 CTCTTGTTCTGTACTCTGTGCTC 58.766 47.826 0.00 0.00 0.00 4.26
938 1417 3.243535 TGTTCTGTACTCTGTGCTCTGTG 60.244 47.826 0.00 0.00 0.00 3.66
939 1418 2.587522 TCTGTACTCTGTGCTCTGTGT 58.412 47.619 0.00 5.82 0.00 3.72
940 1419 2.294512 TCTGTACTCTGTGCTCTGTGTG 59.705 50.000 9.66 0.00 0.00 3.82
1200 1936 2.517402 CTCTCCGCCGGCTCTACT 60.517 66.667 26.68 0.00 0.00 2.57
1776 2512 2.409870 CGGACTCAATGGCAAGCCC 61.410 63.158 8.89 0.00 34.56 5.19
2116 2852 3.516300 TGAGGCGAAGGAGGTTATTTACA 59.484 43.478 0.00 0.00 0.00 2.41
2214 2950 2.176247 ACGGAGATACAACCCCTCAT 57.824 50.000 0.00 0.00 0.00 2.90
2307 3043 1.584380 CTGCTGCTGAGGAAACAGGC 61.584 60.000 0.00 0.00 38.22 4.85
2313 3049 0.034059 CTGAGGAAACAGGCGTGTCT 59.966 55.000 13.21 5.71 35.08 3.41
2504 3240 3.430333 CACTAAGGTGTTGCCGTTTTT 57.570 42.857 0.00 0.00 43.70 1.94
2628 3364 0.527565 ATTGTTCCGGTGATGCTTGC 59.472 50.000 0.00 0.00 0.00 4.01
2762 3498 0.029834 GTGTGCAGTGAAACCAGCAG 59.970 55.000 0.00 0.00 46.75 4.24
2889 3632 7.260387 TCCATGAACTACCTGTGGTAATAAA 57.740 36.000 0.00 0.00 37.76 1.40
2890 3633 7.691213 TCCATGAACTACCTGTGGTAATAAAA 58.309 34.615 0.00 0.00 37.76 1.52
2891 3634 8.164733 TCCATGAACTACCTGTGGTAATAAAAA 58.835 33.333 0.00 0.00 37.76 1.94
3084 3827 7.992608 TGGCATTGCATAATTAGAAGAAGAGTA 59.007 33.333 11.39 0.00 0.00 2.59
3195 3939 6.176183 CAAGACATTAGGGACAGAAAGTGAT 58.824 40.000 0.00 0.00 0.00 3.06
3221 3965 6.678568 ATCCAGATATCCTACTTCACAAGG 57.321 41.667 0.00 0.00 0.00 3.61
3250 4002 5.580691 TGATACAATCACTGATTCACCGTTC 59.419 40.000 0.92 0.55 33.59 3.95
3257 4009 5.109210 TCACTGATTCACCGTTCATGATAC 58.891 41.667 0.00 0.00 0.00 2.24
3275 4027 9.787435 TCATGATACTGGTGTTAGTTTTACTTT 57.213 29.630 0.00 0.00 32.19 2.66
3330 4083 7.822822 GTCTGGTTAGTGGTAATCTATTTGTGT 59.177 37.037 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.541588 GACATTGGCTCCCTTTGACAC 59.458 52.381 0.00 0.00 0.00 3.67
17 18 4.743018 CCGACATTGGCTCCCTTT 57.257 55.556 0.00 0.00 0.00 3.11
148 620 7.773099 ACTATCTCCCCTTCTTTTCCTATTT 57.227 36.000 0.00 0.00 0.00 1.40
154 626 5.990668 TGCTTACTATCTCCCCTTCTTTTC 58.009 41.667 0.00 0.00 0.00 2.29
158 630 3.712218 GGTTGCTTACTATCTCCCCTTCT 59.288 47.826 0.00 0.00 0.00 2.85
352 826 3.003763 AAGGACGTGGAGGAGGCC 61.004 66.667 0.00 0.00 0.00 5.19
604 1078 3.124686 CCTCCTACTCGAGCTGCC 58.875 66.667 13.61 0.00 0.00 4.85
693 1167 2.760385 CCTCTCCCCCGACCTCAC 60.760 72.222 0.00 0.00 0.00 3.51
894 1368 5.707066 AAGAGGAGTCTTGCTATGGAAAT 57.293 39.130 0.00 0.00 41.78 2.17
919 1398 2.294512 CACACAGAGCACAGAGTACAGA 59.705 50.000 0.00 0.00 0.00 3.41
934 1413 2.740055 GGGCGACAGAGCACACAG 60.740 66.667 0.00 0.00 40.96 3.66
938 1417 1.282875 GTTTTGGGCGACAGAGCAC 59.717 57.895 0.00 0.00 41.82 4.40
939 1418 1.896660 GGTTTTGGGCGACAGAGCA 60.897 57.895 0.00 0.00 39.27 4.26
940 1419 0.321298 TAGGTTTTGGGCGACAGAGC 60.321 55.000 0.00 0.00 0.00 4.09
1275 2011 1.077429 GGAAGCTGGGATGTGGGAC 60.077 63.158 0.00 0.00 0.00 4.46
1713 2449 4.120331 GCATGGTCCGGCTTGCAC 62.120 66.667 12.94 0.00 35.22 4.57
1776 2512 0.679505 TCACCTGGAGAACACCTTCG 59.320 55.000 0.00 0.00 0.00 3.79
2116 2852 3.588842 TCAGGGAACTTCTTCATCACCAT 59.411 43.478 0.00 0.00 40.21 3.55
2214 2950 3.683365 TCTTCAGCTGTACATTCTGCA 57.317 42.857 14.67 8.29 35.31 4.41
2307 3043 5.346522 TCATCATCAGATTCTTCAGACACG 58.653 41.667 0.00 0.00 30.20 4.49
2313 3049 6.238293 GCGTTTCATCATCATCAGATTCTTCA 60.238 38.462 0.00 0.00 30.20 3.02
2445 3181 9.142515 CAAAGCAGCATTAACAATTCTTCAATA 57.857 29.630 0.00 0.00 0.00 1.90
2504 3240 1.071699 GCATCCCACGAGCCCTTATAA 59.928 52.381 0.00 0.00 0.00 0.98
2505 3241 0.685097 GCATCCCACGAGCCCTTATA 59.315 55.000 0.00 0.00 0.00 0.98
2628 3364 7.680113 GCAATGCCCAATGATTTTAATTGAAGG 60.680 37.037 0.00 0.00 37.22 3.46
2762 3498 1.003116 CACTTCACTCACTTGCAGTGC 60.003 52.381 8.58 8.58 45.54 4.40
2951 3694 1.900498 AAACCTGGCAGCTGCAGAC 60.900 57.895 37.63 22.24 44.36 3.51
3084 3827 8.106462 CCCAAATTACCAAGTTATTCCCATTTT 58.894 33.333 0.00 0.00 0.00 1.82
3195 3939 7.202038 CCTTGTGAAGTAGGATATCTGGATTCA 60.202 40.741 2.05 6.33 0.00 2.57
3221 3965 7.420800 GGTGAATCAGTGATTGTATCAATTCC 58.579 38.462 22.93 8.59 41.69 3.01
3250 4002 9.825972 CAAAGTAAAACTAACACCAGTATCATG 57.174 33.333 0.00 0.00 0.00 3.07
3257 4009 8.626526 ACATTACCAAAGTAAAACTAACACCAG 58.373 33.333 0.00 0.00 41.68 4.00
3275 4027 4.286032 GGCATACCATCTCCTACATTACCA 59.714 45.833 0.00 0.00 35.26 3.25


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

AutoCloner maintained by Alex Coulton.