Multiple sequence alignment - TraesCS6A01G192300

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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 TraesCS6A01G192300 chr6A 100.000 2913 0 0 1 2913 260119120 260122032 0 5380
1 TraesCS6A01G192300 chr6A 92.732 798 34 9 2061 2837 305446450 305447244 0 1131
2 TraesCS6A01G192300 chr6A 95.094 693 33 1 2061 2752 358789582 358788890 0 1090
3 TraesCS6A01G192300 chr6A 93.914 723 40 4 2045 2764 333919841 333920562 0 1088
4 TraesCS6A01G192300 chr6A 94.350 708 36 2 2058 2764 333926895 333927599 0 1083
5 TraesCS6A01G192300 chr6A 94.334 706 37 3 2060 2763 341542436 341543140 0 1079
6 TraesCS6A01G192300 chr6A 94.184 705 40 1 2061 2764 301245696 301244992 0 1074
7 TraesCS6A01G192300 chr6A 95.921 662 26 1 2061 2721 286492983 286493644 0 1072
8 TraesCS6A01G192300 chr6A 93.539 681 40 4 2061 2738 358782857 358782178 0 1011
9 TraesCS6A01G192300 chrUn 95.663 2098 53 8 1 2060 93414839 93416936 0 3336
10 TraesCS6A01G192300 chrUn 96.588 1612 44 4 1 1601 93412471 93414082 0 2662
11 TraesCS6A01G192300 chr1A 95.635 2085 63 5 1 2060 584780605 584778524 0 3321
12 TraesCS6A01G192300 chr3B 95.544 2087 65 7 1 2060 201524170 201522085 0 3314
13 TraesCS6A01G192300 chr1D 95.461 2093 62 6 1 2060 254523230 254521138 0 3308
14 TraesCS6A01G192300 chr5D 95.372 2096 57 9 1 2060 503215380 503213289 0 3297
15 TraesCS6A01G192300 chr5D 94.530 2084 71 10 1 2060 329122944 329125008 0 3177
16 TraesCS6A01G192300 chr5D 95.511 1782 46 7 313 2060 560881661 560879880 0 2817
17 TraesCS6A01G192300 chr3A 95.204 2085 73 6 1 2060 672912847 672914929 0 3271
18 TraesCS6A01G192300 chr2D 95.172 2092 63 11 1 2058 272796733 272798820 0 3269
19 TraesCS6A01G192300 chr2D 95.477 1813 46 8 1 1778 635585393 635587204 0 2861
20 TraesCS6A01G192300 chr3D 95.630 1968 51 7 1 1933 24168973 24167006 0 3125
21 TraesCS6A01G192300 chr4A 91.608 715 48 12 2059 2766 111323854 111323145 0 977


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 TraesCS6A01G192300 chr6A 260119120 260122032 2912 False 5380 5380 100.0000 1 2913 1 chr6A.!!$F1 2912
1 TraesCS6A01G192300 chr6A 305446450 305447244 794 False 1131 1131 92.7320 2061 2837 1 chr6A.!!$F3 776
2 TraesCS6A01G192300 chr6A 358788890 358789582 692 True 1090 1090 95.0940 2061 2752 1 chr6A.!!$R3 691
3 TraesCS6A01G192300 chr6A 333919841 333920562 721 False 1088 1088 93.9140 2045 2764 1 chr6A.!!$F4 719
4 TraesCS6A01G192300 chr6A 333926895 333927599 704 False 1083 1083 94.3500 2058 2764 1 chr6A.!!$F5 706
5 TraesCS6A01G192300 chr6A 341542436 341543140 704 False 1079 1079 94.3340 2060 2763 1 chr6A.!!$F6 703
6 TraesCS6A01G192300 chr6A 301244992 301245696 704 True 1074 1074 94.1840 2061 2764 1 chr6A.!!$R1 703
7 TraesCS6A01G192300 chr6A 286492983 286493644 661 False 1072 1072 95.9210 2061 2721 1 chr6A.!!$F2 660
8 TraesCS6A01G192300 chr6A 358782178 358782857 679 True 1011 1011 93.5390 2061 2738 1 chr6A.!!$R2 677
9 TraesCS6A01G192300 chrUn 93412471 93416936 4465 False 2999 3336 96.1255 1 2060 2 chrUn.!!$F1 2059
10 TraesCS6A01G192300 chr1A 584778524 584780605 2081 True 3321 3321 95.6350 1 2060 1 chr1A.!!$R1 2059
11 TraesCS6A01G192300 chr3B 201522085 201524170 2085 True 3314 3314 95.5440 1 2060 1 chr3B.!!$R1 2059
12 TraesCS6A01G192300 chr1D 254521138 254523230 2092 True 3308 3308 95.4610 1 2060 1 chr1D.!!$R1 2059
13 TraesCS6A01G192300 chr5D 503213289 503215380 2091 True 3297 3297 95.3720 1 2060 1 chr5D.!!$R1 2059
14 TraesCS6A01G192300 chr5D 329122944 329125008 2064 False 3177 3177 94.5300 1 2060 1 chr5D.!!$F1 2059
15 TraesCS6A01G192300 chr5D 560879880 560881661 1781 True 2817 2817 95.5110 313 2060 1 chr5D.!!$R2 1747
16 TraesCS6A01G192300 chr3A 672912847 672914929 2082 False 3271 3271 95.2040 1 2060 1 chr3A.!!$F1 2059
17 TraesCS6A01G192300 chr2D 272796733 272798820 2087 False 3269 3269 95.1720 1 2058 1 chr2D.!!$F1 2057
18 TraesCS6A01G192300 chr2D 635585393 635587204 1811 False 2861 2861 95.4770 1 1778 1 chr2D.!!$F2 1777
19 TraesCS6A01G192300 chr3D 24167006 24168973 1967 True 3125 3125 95.6300 1 1933 1 chr3D.!!$R1 1932
20 TraesCS6A01G192300 chr4A 111323145 111323854 709 True 977 977 91.6080 2059 2766 1 chr4A.!!$R1 707

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
258 263 3.688049 AAAGGGATGTGGATAAAGGGG 57.312 47.619 0.0 0.0 0.0 4.79 F
1018 3397 4.065088 TCTCATGTCCAGTTTTGCAGTAC 58.935 43.478 0.0 0.0 0.0 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1185 3564 0.667487 TTGCTCTTCGTCCTGCTTCG 60.667 55.000 0.0 0.0 0.00 3.79 R
2134 4566 1.203994 GACAAAGATCCGAACCCGAGA 59.796 52.381 0.0 0.0 38.22 4.04 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
23 24 3.706698 GCTATGATTAGCGTGTGACTCA 58.293 45.455 0.00 0.00 41.38 3.41
96 100 9.742144 TTAACTAATAACCAACCTATTGCTTCA 57.258 29.630 0.00 0.00 34.17 3.02
258 263 3.688049 AAAGGGATGTGGATAAAGGGG 57.312 47.619 0.00 0.00 0.00 4.79
1018 3397 4.065088 TCTCATGTCCAGTTTTGCAGTAC 58.935 43.478 0.00 0.00 0.00 2.73
1045 3424 6.433847 TGGAACTAAGAAAGAGAACCATCA 57.566 37.500 0.00 0.00 0.00 3.07
1046 3425 6.231211 TGGAACTAAGAAAGAGAACCATCAC 58.769 40.000 0.00 0.00 0.00 3.06
1072 3451 7.180229 CCTATAACCCCAAAAGAACCAGATTTT 59.820 37.037 0.00 0.00 0.00 1.82
1185 3564 1.406898 TGGATCACAGCGAGACAGATC 59.593 52.381 0.00 0.00 35.52 2.75
1255 3634 8.640063 AAAAATATGGGTACGTATATTTCCCC 57.360 34.615 18.47 11.66 37.59 4.81
1329 3708 0.843984 CCCCCGAATGTTGGGTATCT 59.156 55.000 0.00 0.00 45.86 1.98
1330 3709 2.051692 CCCCCGAATGTTGGGTATCTA 58.948 52.381 0.00 0.00 45.86 1.98
1367 3746 6.464749 GGTCGTATACTTTATGAAATGGGGGA 60.465 42.308 0.56 0.00 0.00 4.81
1384 3763 4.224370 TGGGGGAAGTATCTGAAACTGTAC 59.776 45.833 0.00 0.00 0.00 2.90
1405 3784 5.205517 ACCTAGAGCAGCTATCTCCATAT 57.794 43.478 0.00 0.00 0.00 1.78
1540 3923 7.662604 ATTTCTTTCATCCTTTTGCATTGAC 57.337 32.000 0.00 0.00 0.00 3.18
1601 4005 9.178758 CTTAGACCCTTTTAAATGTAGCAGATT 57.821 33.333 0.00 0.00 0.00 2.40
1680 4107 7.935520 TGTTATTGTTGCTGTAATCAAAGACA 58.064 30.769 0.00 0.00 0.00 3.41
1681 4108 8.409371 TGTTATTGTTGCTGTAATCAAAGACAA 58.591 29.630 0.00 0.00 0.00 3.18
1686 4113 6.700960 TGTTGCTGTAATCAAAGACAAATTGG 59.299 34.615 0.00 0.00 0.00 3.16
1693 4121 7.718753 TGTAATCAAAGACAAATTGGCCAAATT 59.281 29.630 24.71 18.66 40.32 1.82
1799 4227 0.522626 TGATGACAATGCTGCGGTTG 59.477 50.000 13.75 13.75 0.00 3.77
1848 4276 1.154654 CTCGAGTTTTTGGCGCGAC 60.155 57.895 12.10 8.22 34.73 5.19
2134 4566 9.720667 GTTTCCGGCGTTAAGTTAATTTATATT 57.279 29.630 6.01 0.00 0.00 1.28
2146 4578 7.729116 AGTTAATTTATATTCTCGGGTTCGGA 58.271 34.615 0.00 0.00 36.95 4.55
2193 4628 5.993441 TCGTTGTCATGCATCTCATATCATT 59.007 36.000 0.00 0.00 33.19 2.57
2358 4793 0.181587 TTGGACCGAGACTTGCCAAA 59.818 50.000 0.00 0.00 35.82 3.28
2360 4795 0.534203 GGACCGAGACTTGCCAAACA 60.534 55.000 0.00 0.00 0.00 2.83
2438 4873 4.620589 TTGATACTCCAACGGTTAACCA 57.379 40.909 24.14 3.44 35.14 3.67
2508 4943 0.113580 GGCCCAAAACCCACCTAAGA 59.886 55.000 0.00 0.00 0.00 2.10
2660 5097 0.321741 TAAAAATCCACCTCGCGCCA 60.322 50.000 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 100 9.968870 GTTTCTTAGTTAGGATCTCGACAATAT 57.031 33.333 0.00 0.00 0.00 1.28
213 218 5.827797 AGTTTTGCTTCACAACCTAGAATCA 59.172 36.000 0.00 0.00 38.23 2.57
258 263 5.221823 CCTCTTCCTTCTTTCTATCATCCCC 60.222 48.000 0.00 0.00 0.00 4.81
419 424 3.404899 CCGGGCGGCTCTTTATTATTTA 58.595 45.455 9.56 0.00 0.00 1.40
420 425 2.227194 CCGGGCGGCTCTTTATTATTT 58.773 47.619 9.56 0.00 0.00 1.40
675 680 2.360844 TCAATAAGAATTTCGCGGGCA 58.639 42.857 6.13 0.00 0.00 5.36
956 966 2.874701 CCTCGCGAATGGAATGAGAAAT 59.125 45.455 11.33 0.00 0.00 2.17
1018 3397 6.467677 TGGTTCTCTTTCTTAGTTCCATCTG 58.532 40.000 0.00 0.00 0.00 2.90
1045 3424 4.604490 TCTGGTTCTTTTGGGGTTATAGGT 59.396 41.667 0.00 0.00 0.00 3.08
1046 3425 5.187621 TCTGGTTCTTTTGGGGTTATAGG 57.812 43.478 0.00 0.00 0.00 2.57
1072 3451 6.003326 TCATTCTTCCTCTATGTTGTTTGCA 58.997 36.000 0.00 0.00 0.00 4.08
1185 3564 0.667487 TTGCTCTTCGTCCTGCTTCG 60.667 55.000 0.00 0.00 0.00 3.79
1255 3634 3.495753 GGTCTTAGTGTAACCGGTTTGTG 59.504 47.826 27.64 9.19 37.80 3.33
1319 3698 6.888088 ACCAGGTTTAACAATAGATACCCAAC 59.112 38.462 0.00 0.00 0.00 3.77
1330 3709 9.895138 ATAAAGTATACGACCAGGTTTAACAAT 57.105 29.630 0.00 0.00 0.00 2.71
1367 3746 6.663953 TGCTCTAGGTACAGTTTCAGATACTT 59.336 38.462 0.00 0.00 0.00 2.24
1384 3763 5.300034 CAGATATGGAGATAGCTGCTCTAGG 59.700 48.000 4.91 0.00 40.68 3.02
1405 3784 4.100344 TCGTATGGGCATTTTACTAGCAGA 59.900 41.667 0.00 0.00 0.00 4.26
1577 3981 8.956426 CAAATCTGCTACATTTAAAAGGGTCTA 58.044 33.333 0.00 0.00 0.00 2.59
1601 4005 4.499865 GCAGCTCCTATGACTCGAATACAA 60.500 45.833 0.00 0.00 0.00 2.41
1651 4078 8.969121 TTTGATTACAGCAACAATAACATCAG 57.031 30.769 0.00 0.00 0.00 2.90
1680 4107 6.725834 TCTTTCTAGAGGAATTTGGCCAATTT 59.274 34.615 21.26 21.91 35.02 1.82
1681 4108 6.256053 TCTTTCTAGAGGAATTTGGCCAATT 58.744 36.000 21.26 13.64 37.84 2.32
1686 4113 4.513318 CGGATCTTTCTAGAGGAATTTGGC 59.487 45.833 0.00 0.00 32.92 4.52
1693 4121 7.899648 AATTACTTCGGATCTTTCTAGAGGA 57.100 36.000 0.00 0.00 32.92 3.71
1799 4227 7.903995 TTGGATTGCCTTTTTGATCAATTAC 57.096 32.000 9.40 0.00 34.31 1.89
1848 4276 4.703575 TCAATTCTCTCAATTCCTTGGCAG 59.296 41.667 0.00 0.00 32.95 4.85
2134 4566 1.203994 GACAAAGATCCGAACCCGAGA 59.796 52.381 0.00 0.00 38.22 4.04
2146 4578 6.146184 CGATAACAACACACAGAGACAAAGAT 59.854 38.462 0.00 0.00 0.00 2.40
2193 4628 3.372514 GCAAATGCAATGCACATGATGAA 59.627 39.130 21.43 0.00 43.04 2.57
2250 4685 2.351253 CGGAATGCAAAATGGACAACGA 60.351 45.455 0.00 0.00 0.00 3.85
2438 4873 1.379146 GAGGCCTTTTCGGTCCCTT 59.621 57.895 6.77 0.00 38.54 3.95
2508 4943 5.278907 CGAATGCTCTAGATGATGGAGAAGT 60.279 44.000 0.00 0.00 38.78 3.01


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

AutoCloner maintained by Alex Coulton.