Multiple sequence alignment - TraesCS6B01G392200

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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 TraesCS6B01G392200 chr6B 100.000 2348 0 0 1 2348 667344710 667347057 0 4337
1 TraesCS6B01G392200 chr6B 94.985 2353 98 8 1 2348 709805834 709808171 0 3674
2 TraesCS6B01G392200 chr5B 95.495 2353 88 3 1 2348 680875068 680877407 0 3742
3 TraesCS6B01G392200 chr5B 95.348 2042 82 5 315 2348 88393925 88391889 0 3232
4 TraesCS6B01G392200 chr2D 93.631 2355 105 17 1 2348 645076574 645078890 0 3476
5 TraesCS6B01G392200 chr1B 93.461 2355 126 11 1 2346 332058990 332061325 0 3470
6 TraesCS6B01G392200 chr1B 94.861 973 35 5 1390 2348 374516578 374515607 0 1506
7 TraesCS6B01G392200 chr1D 94.580 1808 88 4 1 1808 451667678 451669475 0 2787
8 TraesCS6B01G392200 chr2A 95.312 1749 82 0 2 1750 744587979 744586231 0 2776
9 TraesCS6B01G392200 chr1A 94.800 1750 91 0 1 1750 71334898 71336647 0 2728
10 TraesCS6B01G392200 chr5A 93.719 1815 103 4 1 1808 548405791 548403981 0 2710
11 TraesCS6B01G392200 chrUn 95.473 972 29 5 1390 2348 60563039 60562070 0 1537
12 TraesCS6B01G392200 chrUn 94.439 971 40 5 1390 2348 37351414 37352382 0 1482
13 TraesCS6B01G392200 chr4B 95.052 970 33 6 1390 2348 534918637 534919602 0 1511
14 TraesCS6B01G392200 chr2B 94.547 972 29 8 1390 2348 565223783 565224743 0 1480


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 TraesCS6B01G392200 chr6B 667344710 667347057 2347 False 4337 4337 100.000 1 2348 1 chr6B.!!$F1 2347
1 TraesCS6B01G392200 chr6B 709805834 709808171 2337 False 3674 3674 94.985 1 2348 1 chr6B.!!$F2 2347
2 TraesCS6B01G392200 chr5B 680875068 680877407 2339 False 3742 3742 95.495 1 2348 1 chr5B.!!$F1 2347
3 TraesCS6B01G392200 chr5B 88391889 88393925 2036 True 3232 3232 95.348 315 2348 1 chr5B.!!$R1 2033
4 TraesCS6B01G392200 chr2D 645076574 645078890 2316 False 3476 3476 93.631 1 2348 1 chr2D.!!$F1 2347
5 TraesCS6B01G392200 chr1B 332058990 332061325 2335 False 3470 3470 93.461 1 2346 1 chr1B.!!$F1 2345
6 TraesCS6B01G392200 chr1B 374515607 374516578 971 True 1506 1506 94.861 1390 2348 1 chr1B.!!$R1 958
7 TraesCS6B01G392200 chr1D 451667678 451669475 1797 False 2787 2787 94.580 1 1808 1 chr1D.!!$F1 1807
8 TraesCS6B01G392200 chr2A 744586231 744587979 1748 True 2776 2776 95.312 2 1750 1 chr2A.!!$R1 1748
9 TraesCS6B01G392200 chr1A 71334898 71336647 1749 False 2728 2728 94.800 1 1750 1 chr1A.!!$F1 1749
10 TraesCS6B01G392200 chr5A 548403981 548405791 1810 True 2710 2710 93.719 1 1808 1 chr5A.!!$R1 1807
11 TraesCS6B01G392200 chrUn 60562070 60563039 969 True 1537 1537 95.473 1390 2348 1 chrUn.!!$R1 958
12 TraesCS6B01G392200 chrUn 37351414 37352382 968 False 1482 1482 94.439 1390 2348 1 chrUn.!!$F1 958
13 TraesCS6B01G392200 chr4B 534918637 534919602 965 False 1511 1511 95.052 1390 2348 1 chr4B.!!$F1 958
14 TraesCS6B01G392200 chr2B 565223783 565224743 960 False 1480 1480 94.547 1390 2348 1 chr2B.!!$F1 958

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
772 777 0.037697 TCTTTGCTCGCGTACCACAT 60.038 50.0 5.77 0.0 0.0 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1662 1680 1.363744 CCATCACTTTGCTCCTCGTC 58.636 55.0 0.0 0.0 0.0 4.2 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
170 171 2.032071 AGTTGCCTACGGTGTGCC 59.968 61.111 0.00 0.00 0.00 5.01
259 264 5.657826 CAATGGGTTGGTCATTCATACAA 57.342 39.130 0.00 0.00 33.08 2.41
266 271 5.359576 GGTTGGTCATTCATACAAATGCCTA 59.640 40.000 0.00 0.00 36.72 3.93
304 309 1.604604 CGTGGACAATGTGTTCCCTT 58.395 50.000 0.00 0.00 0.00 3.95
305 310 1.953686 CGTGGACAATGTGTTCCCTTT 59.046 47.619 0.00 0.00 0.00 3.11
402 407 4.013728 ACAATTTATGGCCAGCGTCTTTA 58.986 39.130 13.05 0.00 0.00 1.85
408 413 0.521735 GGCCAGCGTCTTTAACTTGG 59.478 55.000 0.00 0.00 34.87 3.61
554 559 8.260818 AGTTGACTATGTGCACAATAATCTAGT 58.739 33.333 25.72 23.64 0.00 2.57
579 584 3.005472 AGTCTTTCAACTCAACGATCCGA 59.995 43.478 0.00 0.00 0.00 4.55
667 672 0.906066 TTACCGTGCAGGAATAGCCA 59.094 50.000 8.24 0.00 45.00 4.75
700 705 2.712384 TGGGCCACATTATCATCCCTA 58.288 47.619 0.00 0.00 34.89 3.53
763 768 1.800586 TGAACATGACTCTTTGCTCGC 59.199 47.619 0.00 0.00 0.00 5.03
772 777 0.037697 TCTTTGCTCGCGTACCACAT 60.038 50.000 5.77 0.00 0.00 3.21
773 778 0.796312 CTTTGCTCGCGTACCACATT 59.204 50.000 5.77 0.00 0.00 2.71
849 854 2.810852 AGAAGCTAGAACTTGCAGTTGC 59.189 45.455 10.31 0.00 38.80 4.17
918 923 0.252284 TCACTTCTCTCCCAGGTCCC 60.252 60.000 0.00 0.00 0.00 4.46
1176 1181 0.603065 GTGGGTCTGGTCATTTTGGC 59.397 55.000 0.00 0.00 0.00 4.52
1218 1223 1.002251 GATGTAGCGTTCGGAGAGAGG 60.002 57.143 0.00 0.00 38.43 3.69
1291 1296 7.096884 ACAGATGATGAAAATGATGGTCAAG 57.903 36.000 0.00 0.00 0.00 3.02
1306 1311 0.035152 TCAAGAGCCGGTTGCATCAT 60.035 50.000 1.90 0.00 44.83 2.45
1331 1336 3.933332 GAGGATTTTGACGAGGTTCGAAT 59.067 43.478 0.00 0.00 43.74 3.34
1403 1408 6.830324 CCTCCAAATAATGATTCAAGTGAGGA 59.170 38.462 0.00 0.00 0.00 3.71
1498 1512 3.635373 ACCTTCTGTCGTTGTGAGTTCTA 59.365 43.478 0.00 0.00 0.00 2.10
1509 1523 6.028368 CGTTGTGAGTTCTACTAGGTATGTG 58.972 44.000 0.00 0.00 0.00 3.21
1517 1531 8.596781 AGTTCTACTAGGTATGTGAATCTTGT 57.403 34.615 0.00 0.00 0.00 3.16
1586 1604 3.243839 ACCCTTTATGTTTTGCACAGCTG 60.244 43.478 13.48 13.48 39.40 4.24
1820 1845 7.943079 TTGACATGATGTAATCTGTTGGATT 57.057 32.000 0.00 0.00 45.81 3.01
1840 1865 6.377712 TGGATTATGTTTGAATGAGCACATGA 59.622 34.615 0.00 0.00 36.79 3.07
1847 1872 6.985059 TGTTTGAATGAGCACATGATTTTTCA 59.015 30.769 0.00 0.00 36.79 2.69
1850 1876 7.589574 TGAATGAGCACATGATTTTTCATTG 57.410 32.000 0.00 0.00 35.92 2.82
1981 2011 6.515272 TCCTTCTTAGTCAATCCAAAATGC 57.485 37.500 0.00 0.00 0.00 3.56
1999 2029 1.133945 TGCAGCTGTGGTGAGGTTTTA 60.134 47.619 16.64 0.00 32.22 1.52
2166 2197 0.749649 ATGTGCGCTGGTTTTTCCAA 59.250 45.000 9.73 0.00 46.59 3.53
2215 2255 5.592282 TGCTCATTTCTGGTCAAACTTAACA 59.408 36.000 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
170 171 1.065782 TCTCCTCAGACTCTGTCTCCG 60.066 57.143 5.94 0.00 41.37 4.63
219 220 1.148273 GGGATGTGCAATAGCCCGA 59.852 57.895 9.53 0.00 41.13 5.14
259 264 5.476945 CCACTTCTAAACCTTTGTAGGCATT 59.523 40.000 0.00 0.00 46.22 3.56
266 271 2.227194 CGGCCACTTCTAAACCTTTGT 58.773 47.619 2.24 0.00 0.00 2.83
402 407 2.945668 GTGCTTCTTCACACTCCAAGTT 59.054 45.455 0.00 0.00 36.97 2.66
408 413 3.495001 GGTAGTTGTGCTTCTTCACACTC 59.505 47.826 0.00 0.00 45.58 3.51
554 559 5.619309 CGGATCGTTGAGTTGAAAGACTCTA 60.619 44.000 6.59 0.00 44.99 2.43
579 584 6.210584 CCACCACATAATGACCCTTTAGTTTT 59.789 38.462 0.00 0.00 0.00 2.43
651 656 1.097547 CCTTGGCTATTCCTGCACGG 61.098 60.000 0.00 0.00 35.26 4.94
667 672 1.003464 GTGGCCCATGAATTTTGCCTT 59.997 47.619 0.00 0.00 42.62 4.35
700 705 2.744202 GCTTCAGTTCATTCATCACGGT 59.256 45.455 0.00 0.00 0.00 4.83
849 854 1.679680 CCAGTTATCTGCCATTGCCTG 59.320 52.381 0.00 0.00 40.09 4.85
918 923 1.808411 ACTGTTGTATGTTCCCTGCG 58.192 50.000 0.00 0.00 0.00 5.18
956 961 1.761784 TGGCTTTGAACCTTGCAACAT 59.238 42.857 0.00 0.00 0.00 2.71
1034 1039 3.495124 GCGCAAAGCTTGAATCCAA 57.505 47.368 0.30 0.00 44.04 3.53
1055 1060 2.495270 CCTGCTGCTCTCTTCAGAACTA 59.505 50.000 0.00 0.00 33.54 2.24
1123 1128 0.319083 TTACGCTTCCTCGCTCCAAA 59.681 50.000 0.00 0.00 0.00 3.28
1201 1206 0.810016 AACCTCTCTCCGAACGCTAC 59.190 55.000 0.00 0.00 0.00 3.58
1202 1207 1.093159 GAACCTCTCTCCGAACGCTA 58.907 55.000 0.00 0.00 0.00 4.26
1291 1296 1.802960 CTCATATGATGCAACCGGCTC 59.197 52.381 5.72 0.00 45.15 4.70
1306 1311 4.158949 TCGAACCTCGTCAAAATCCTCATA 59.841 41.667 0.00 0.00 41.35 2.15
1331 1336 2.221169 GCGGCTATTGACCATCATCAA 58.779 47.619 0.00 0.00 42.62 2.57
1485 1499 6.028368 CACATACCTAGTAGAACTCACAACG 58.972 44.000 0.00 0.00 0.00 4.10
1498 1512 6.672657 ACCCTTACAAGATTCACATACCTAGT 59.327 38.462 0.00 0.00 0.00 2.57
1509 1523 9.099454 CAGTAGTATTTGACCCTTACAAGATTC 57.901 37.037 0.00 0.00 0.00 2.52
1586 1604 5.810587 TGCGTCTTCTTCAAACCTATCATAC 59.189 40.000 0.00 0.00 0.00 2.39
1662 1680 1.363744 CCATCACTTTGCTCCTCGTC 58.636 55.000 0.00 0.00 0.00 4.20
1820 1845 9.142515 GAAAAATCATGTGCTCATTCAAACATA 57.857 29.630 0.00 0.00 32.15 2.29
1882 1912 6.884280 AAGTTAGGTTTGACCAGAATTCAG 57.116 37.500 8.44 0.00 41.95 3.02
1981 2011 3.126001 TCTAAAACCTCACCACAGCTG 57.874 47.619 13.48 13.48 0.00 4.24
2092 2123 6.977213 TGTTTAGGAAAGTTATTTGGCTGAC 58.023 36.000 0.00 0.00 0.00 3.51
2139 2170 3.566853 CAGCGCACATAGCCCGTG 61.567 66.667 11.47 0.00 41.38 4.94


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

AutoCloner maintained by Alex Coulton.