Multiple sequence alignment - TraesCS6A01G295800

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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 TraesCS6A01G295800 chr6A 100.000 3476 0 0 1 3476 529484379 529487854 0.000000e+00 6420.0
1 TraesCS6A01G295800 chr6A 93.928 3442 146 18 1 3416 529558483 529561887 0.000000e+00 5140.0
2 TraesCS6A01G295800 chr6A 86.647 3108 281 63 1 3028 529286278 529289331 0.000000e+00 3317.0
3 TraesCS6A01G295800 chr6A 94.094 1236 62 5 2192 3425 529374996 529376222 0.000000e+00 1868.0
4 TraesCS6A01G295800 chr6A 73.290 1711 268 103 699 2305 536024983 536023358 1.470000e-123 453.0
5 TraesCS6A01G295800 chr6A 92.157 102 6 2 1 101 529374900 529375000 3.620000e-30 143.0
6 TraesCS6A01G295800 chr6A 97.500 40 1 0 3437 3476 529562142 529562181 6.230000e-08 69.4
7 TraesCS6A01G295800 chr6A 94.595 37 2 0 3440 3476 529376222 529376258 1.350000e-04 58.4
8 TraesCS6A01G295800 chr6D 94.165 3496 162 21 1 3476 385221789 385225262 0.000000e+00 5288.0
9 TraesCS6A01G295800 chr6D 84.968 3100 323 52 1 3028 385164373 385167401 0.000000e+00 3011.0
10 TraesCS6A01G295800 chr6D 87.891 256 27 3 3020 3274 385167424 385167676 7.290000e-77 298.0
11 TraesCS6A01G295800 chr6D 90.732 205 16 3 1 203 385164003 385164206 1.590000e-68 270.0
12 TraesCS6A01G295800 chr6D 88.636 132 13 2 3346 3476 385167677 385167807 3.590000e-35 159.0
13 TraesCS6A01G295800 chr6B 93.129 2649 139 17 550 3180 575320828 575323451 0.000000e+00 3843.0
14 TraesCS6A01G295800 chr6B 85.880 3102 316 61 1 3028 575313751 575316804 0.000000e+00 3190.0
15 TraesCS6A01G295800 chr6B 76.711 833 95 52 1577 2374 583335472 583334704 4.240000e-99 372.0
16 TraesCS6A01G295800 chr6B 90.299 268 23 3 1 266 575320561 575320827 7.140000e-92 348.0
17 TraesCS6A01G295800 chr6B 84.674 261 30 5 3020 3274 575316827 575317083 5.760000e-63 252.0
18 TraesCS6A01G295800 chr6B 95.238 42 2 0 155 196 575320786 575320827 2.240000e-07 67.6
19 TraesCS6A01G295800 chr7A 81.739 115 16 4 3364 3476 720122916 720123027 1.330000e-14 91.6


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 TraesCS6A01G295800 chr6A 529484379 529487854 3475 False 6420.00 6420 100.000000 1 3476 1 chr6A.!!$F2 3475
1 TraesCS6A01G295800 chr6A 529286278 529289331 3053 False 3317.00 3317 86.647000 1 3028 1 chr6A.!!$F1 3027
2 TraesCS6A01G295800 chr6A 529558483 529562181 3698 False 2604.70 5140 95.714000 1 3476 2 chr6A.!!$F4 3475
3 TraesCS6A01G295800 chr6A 529374900 529376258 1358 False 689.80 1868 93.615333 1 3476 3 chr6A.!!$F3 3475
4 TraesCS6A01G295800 chr6A 536023358 536024983 1625 True 453.00 453 73.290000 699 2305 1 chr6A.!!$R1 1606
5 TraesCS6A01G295800 chr6D 385221789 385225262 3473 False 5288.00 5288 94.165000 1 3476 1 chr6D.!!$F1 3475
6 TraesCS6A01G295800 chr6D 385164003 385167807 3804 False 934.50 3011 88.056750 1 3476 4 chr6D.!!$F2 3475
7 TraesCS6A01G295800 chr6B 575313751 575323451 9700 False 1540.12 3843 89.844000 1 3274 5 chr6B.!!$F1 3273
8 TraesCS6A01G295800 chr6B 583334704 583335472 768 True 372.00 372 76.711000 1577 2374 1 chr6B.!!$R1 797

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
680 1083 1.002087 GGAACAACAGAGACCGGATGT 59.998 52.381 9.46 4.31 0.0 3.06 F
1112 1570 0.531974 GGTGACGACAAGAAGGCACA 60.532 55.000 3.77 0.00 0.0 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2416 9536 0.034477 TTCTTCGATGGGGCCTTTCC 60.034 55.0 0.84 0.0 0.0 3.13 R
2823 9971 0.345502 TGGGGTGGCTAGAATAGGGT 59.654 55.0 0.00 0.0 39.7 4.34 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
110 112 8.784043 CATTACACCCCTATATTAAAAGTGCTC 58.216 37.037 0.00 0.00 0.00 4.26
190 564 1.017177 GTGCATAGCGACGGTTTCCA 61.017 55.000 4.26 0.00 0.00 3.53
291 665 5.587043 ACAAATCTGTCAAAAGTCCGTTGTA 59.413 36.000 0.00 0.00 0.00 2.41
680 1083 1.002087 GGAACAACAGAGACCGGATGT 59.998 52.381 9.46 4.31 0.00 3.06
739 1149 7.176165 GGGTAACTCTAACAAACTGCCTTAATT 59.824 37.037 0.00 0.00 0.00 1.40
842 1263 2.511637 CCTCCTCCTCTTTTTATGCCCT 59.488 50.000 0.00 0.00 0.00 5.19
843 1264 3.549794 CTCCTCCTCTTTTTATGCCCTG 58.450 50.000 0.00 0.00 0.00 4.45
847 1270 1.114627 CTCTTTTTATGCCCTGCCCC 58.885 55.000 0.00 0.00 0.00 5.80
898 1321 1.077828 ACCACCATCCAGTCTCTCTCA 59.922 52.381 0.00 0.00 0.00 3.27
944 1373 9.559732 CCACCATACTGAAATATAGATTGACAA 57.440 33.333 0.00 0.00 0.00 3.18
1112 1570 0.531974 GGTGACGACAAGAAGGCACA 60.532 55.000 3.77 0.00 0.00 4.57
1202 1663 6.712276 CCTATCTAAAGAGGGACACTTTTGT 58.288 40.000 0.00 0.00 46.41 2.83
1456 1934 2.789213 TGCTTTCCGATGTGAATTCCA 58.211 42.857 2.27 0.97 0.00 3.53
1800 2335 6.757897 TTTAGAGGAATGTTCGATGCAAAT 57.242 33.333 0.00 0.00 0.00 2.32
1963 2516 5.047306 GTCCTCTTTTAATTTTGGTCCCTGG 60.047 44.000 0.00 0.00 0.00 4.45
2085 2645 6.952358 GTCTAAGACACCATATATACTCCCCA 59.048 42.308 0.00 0.00 32.09 4.96
2416 9536 4.292178 GCTCCCTCAGATCCCGCG 62.292 72.222 0.00 0.00 0.00 6.46
2418 9538 4.137615 TCCCTCAGATCCCGCGGA 62.138 66.667 30.73 13.82 35.55 5.54
2547 9677 8.333235 TGGTACAATCTCCACCATATTTAAACT 58.667 33.333 0.00 0.00 37.42 2.66
2643 9791 4.332543 CGTTTTGTTGCTGATATGGAGCTA 59.667 41.667 0.00 0.00 37.35 3.32
2669 9817 6.151985 CGAGATATTTACCTCCATAGTCTGCT 59.848 42.308 0.00 0.00 0.00 4.24
2732 9880 5.411361 GCACAATAACCATGTTCTCTGTGTA 59.589 40.000 12.99 0.00 36.24 2.90
2766 9914 0.036388 CTTGCACCCATACTGTCGGT 60.036 55.000 0.00 0.00 0.00 4.69
2820 9968 0.394899 CCTCCCTCCTTGTGGATTGC 60.395 60.000 0.00 0.00 42.29 3.56
2823 9971 0.251916 CCCTCCTTGTGGATTGCGTA 59.748 55.000 0.00 0.00 42.29 4.42
3037 10233 1.077930 ATCTGCTGCGGTGCAAGAT 60.078 52.632 8.55 0.12 42.83 2.40
3116 10312 1.690985 GGGCTAGCCTCCCTTGAGT 60.691 63.158 32.18 0.00 40.66 3.41
3159 10355 2.351244 ACTTCTCATGGCTCCGCGA 61.351 57.895 8.23 0.00 0.00 5.87
3160 10356 1.591059 CTTCTCATGGCTCCGCGAG 60.591 63.158 8.23 4.18 0.00 5.03
3202 10398 6.208797 GGGGACACTATAACTTTGCTTTCTTT 59.791 38.462 0.00 0.00 0.00 2.52
3323 10519 1.405463 TCCATCACTTCTCCGACATCG 59.595 52.381 0.00 0.00 39.44 3.84
3398 10594 8.196378 ACCTTGATACTTGAGAGAACTAACTT 57.804 34.615 0.00 0.00 0.00 2.66
3416 10612 3.093814 ACTTTCACGGAAACCAAAAGGT 58.906 40.909 0.00 0.00 32.53 3.50
3445 10875 2.225382 TGTCCGATGTAAGAGGGTGA 57.775 50.000 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 112 5.048364 TGTGTTCACTCGAATATTTTTGGGG 60.048 40.000 4.59 0.0 32.61 4.96
153 156 2.744494 GCACTGGCCTAGATCAAGGAAG 60.744 54.545 3.32 0.0 39.15 3.46
190 564 3.719268 TTTGACAGATATGTGGGCTGT 57.281 42.857 0.00 0.0 44.87 4.40
397 779 1.681666 CGAGATATGGGGGCTGCAT 59.318 57.895 0.50 0.0 0.00 3.96
506 907 6.737254 AGGAAACACATTATTACGAACCAG 57.263 37.500 0.00 0.0 0.00 4.00
842 1263 3.327404 GAGGAACGGGAAGGGGCA 61.327 66.667 0.00 0.0 0.00 5.36
843 1264 4.111053 GGAGGAACGGGAAGGGGC 62.111 72.222 0.00 0.0 0.00 5.80
847 1270 2.368011 GGGGAGGAGGAACGGGAAG 61.368 68.421 0.00 0.0 0.00 3.46
898 1321 2.368548 GGCCTTTGTGTCCCAAGATTTT 59.631 45.455 0.00 0.0 33.75 1.82
1013 1447 4.315588 GCACAATGCTCCTCTGCT 57.684 55.556 0.00 0.0 40.96 4.24
1095 1529 0.874175 CGTGTGCCTTCTTGTCGTCA 60.874 55.000 0.00 0.0 0.00 4.35
1197 1658 0.893270 CCATCCACAGCCCGACAAAA 60.893 55.000 0.00 0.0 0.00 2.44
1800 2335 4.640771 AGTAACATGCTGAGGGAAAAGA 57.359 40.909 0.00 0.0 0.00 2.52
1963 2516 6.988580 TGAGACAGGACATTTCATACATGATC 59.011 38.462 0.00 0.0 36.56 2.92
2115 2675 4.343231 ACAACAACTCATATGATTGGGCA 58.657 39.130 21.51 0.0 0.00 5.36
2280 9381 4.578516 TGTCACAAACATCTCCAACGAATT 59.421 37.500 0.00 0.0 31.20 2.17
2416 9536 0.034477 TTCTTCGATGGGGCCTTTCC 60.034 55.000 0.84 0.0 0.00 3.13
2418 9538 0.698818 ACTTCTTCGATGGGGCCTTT 59.301 50.000 0.84 0.0 0.00 3.11
2547 9677 2.764010 AGCTTGTATACATGGACGGACA 59.236 45.455 17.67 0.0 0.00 4.02
2643 9791 6.071840 GCAGACTATGGAGGTAAATATCTCGT 60.072 42.308 0.00 0.0 34.24 4.18
2732 9880 1.490490 TGCAAGACCTCTCAACTTGGT 59.510 47.619 0.00 0.0 40.57 3.67
2766 9914 2.434185 CGAGGCCAAGCTACGCAA 60.434 61.111 5.01 0.0 0.00 4.85
2820 9968 1.617357 GGGTGGCTAGAATAGGGTACG 59.383 57.143 0.00 0.0 39.70 3.67
2823 9971 0.345502 TGGGGTGGCTAGAATAGGGT 59.654 55.000 0.00 0.0 39.70 4.34
2928 10084 7.416022 CGTGAGTAGATACGATAAAAGGAGTT 58.584 38.462 0.00 0.0 42.54 3.01
3116 10312 1.006825 CGTTGTCGAGCGATGGAACA 61.007 55.000 0.00 0.0 41.13 3.18
3416 10612 5.000591 TCTTACATCGGACATTGCAAAGAA 58.999 37.500 8.96 0.0 0.00 2.52
3445 10875 4.019174 CAAGATATCCAAGCAAACCTGGT 58.981 43.478 0.00 0.0 33.72 4.00


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

AutoCloner maintained by Alex Coulton.