Multiple sequence alignment - TraesCS5A01G083100

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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 TraesCS5A01G083100 chr5A 100.000 2931 0 0 1 2931 109278392 109281322 0.000000e+00 5413.0
1 TraesCS5A01G083100 chr5A 80.952 147 23 4 53 197 668269493 668269350 8.590000e-21 111.0
2 TraesCS5A01G083100 chr5A 91.304 69 6 0 53 121 668224069 668224001 8.650000e-16 95.3
3 TraesCS5A01G083100 chr5B 97.858 2614 40 8 321 2931 115074133 115076733 0.000000e+00 4503.0
4 TraesCS5A01G083100 chr5B 86.648 352 17 13 1 351 115073771 115074093 2.150000e-96 363.0
5 TraesCS5A01G083100 chr5B 81.148 122 18 3 75 194 704164012 704163894 3.110000e-15 93.5
6 TraesCS5A01G083100 chr5D 98.563 1948 22 4 321 2268 105103008 105104949 0.000000e+00 3437.0
7 TraesCS5A01G083100 chr5D 96.741 675 16 3 2260 2931 105105079 105105750 0.000000e+00 1120.0
8 TraesCS5A01G083100 chr5D 88.563 341 14 10 1 341 105102616 105102931 9.850000e-105 390.0
9 TraesCS5A01G083100 chr5D 80.833 120 23 0 75 194 558730959 558731078 8.650000e-16 95.3
10 TraesCS5A01G083100 chr3D 86.029 136 18 1 62 197 445311931 445311797 8.470000e-31 145.0
11 TraesCS5A01G083100 chr4A 82.500 120 20 1 75 194 611707329 611707447 1.440000e-18 104.0
12 TraesCS5A01G083100 chr2B 86.076 79 6 2 47 121 787815771 787815694 2.420000e-11 80.5
13 TraesCS5A01G083100 chr1A 97.297 37 1 0 1494 1530 10227983 10227947 2.440000e-06 63.9


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 TraesCS5A01G083100 chr5A 109278392 109281322 2930 False 5413 5413 100.000000 1 2931 1 chr5A.!!$F1 2930
1 TraesCS5A01G083100 chr5B 115073771 115076733 2962 False 2433 4503 92.253000 1 2931 2 chr5B.!!$F1 2930
2 TraesCS5A01G083100 chr5D 105102616 105105750 3134 False 1649 3437 94.622333 1 2931 3 chr5D.!!$F2 2930

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
260 261 0.325016 ACCCGGACGGAGGAAGTAAT 60.325 55.0 13.13 0.0 37.5 1.89 F
1569 1667 0.823460 GCACAGGAGAGGAAGAGGAG 59.177 60.0 0.00 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1657 1755 0.987294 AGCTACTGCCACCATGAAGT 59.013 50.0 0.0 0.0 40.8 3.01 R
2455 2692 0.179067 TTTTGGCTGTTCGACCTCGT 60.179 50.0 0.0 0.0 40.8 4.18 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
27 28 6.754702 TTAACTAGCCAGTACTGAGTACAG 57.245 41.667 24.68 15.80 41.03 2.74
37 38 2.645730 CTGAGTACAGTCCAGTCAGC 57.354 55.000 0.00 0.00 36.83 4.26
38 39 2.166829 CTGAGTACAGTCCAGTCAGCT 58.833 52.381 0.00 0.00 36.83 4.24
39 40 3.348119 CTGAGTACAGTCCAGTCAGCTA 58.652 50.000 0.00 0.00 36.83 3.32
40 41 3.951037 CTGAGTACAGTCCAGTCAGCTAT 59.049 47.826 0.00 0.00 36.83 2.97
41 42 4.344978 TGAGTACAGTCCAGTCAGCTATT 58.655 43.478 0.00 0.00 0.00 1.73
42 43 5.506708 TGAGTACAGTCCAGTCAGCTATTA 58.493 41.667 0.00 0.00 0.00 0.98
43 44 5.357314 TGAGTACAGTCCAGTCAGCTATTAC 59.643 44.000 0.00 0.00 0.00 1.89
44 45 5.511363 AGTACAGTCCAGTCAGCTATTACT 58.489 41.667 0.00 0.00 0.00 2.24
45 46 4.727507 ACAGTCCAGTCAGCTATTACTG 57.272 45.455 13.49 13.49 42.25 2.74
60 61 5.394993 GCTATTACTGGTACTTCCTCCGTTT 60.395 44.000 0.00 0.00 37.07 3.60
182 183 2.572290 ACTTGAAAGAGGTTTCCCACG 58.428 47.619 0.00 0.00 41.37 4.94
191 192 5.446260 AGAGGTTTCCCACGGTATAATTT 57.554 39.130 0.00 0.00 0.00 1.82
245 246 2.348411 ATGGAGAGGCAATAAACCCG 57.652 50.000 0.00 0.00 0.00 5.28
260 261 0.325016 ACCCGGACGGAGGAAGTAAT 60.325 55.000 13.13 0.00 37.50 1.89
276 277 5.889289 GGAAGTAATTGCCTAATTGGTGGTA 59.111 40.000 0.00 0.00 37.12 3.25
277 278 6.039382 GGAAGTAATTGCCTAATTGGTGGTAG 59.961 42.308 0.00 0.00 37.12 3.18
278 279 6.074698 AGTAATTGCCTAATTGGTGGTAGT 57.925 37.500 0.00 0.00 37.12 2.73
279 280 6.490492 AGTAATTGCCTAATTGGTGGTAGTT 58.510 36.000 0.00 0.00 37.12 2.24
280 281 7.635648 AGTAATTGCCTAATTGGTGGTAGTTA 58.364 34.615 0.00 0.00 37.12 2.24
281 282 8.110908 AGTAATTGCCTAATTGGTGGTAGTTAA 58.889 33.333 0.00 0.00 37.12 2.01
282 283 7.784470 AATTGCCTAATTGGTGGTAGTTAAA 57.216 32.000 0.00 0.00 35.26 1.52
283 284 6.578163 TTGCCTAATTGGTGGTAGTTAAAC 57.422 37.500 0.00 0.00 38.35 2.01
284 285 5.632118 TGCCTAATTGGTGGTAGTTAAACA 58.368 37.500 0.00 0.00 38.35 2.83
285 286 5.708230 TGCCTAATTGGTGGTAGTTAAACAG 59.292 40.000 0.00 0.00 38.35 3.16
286 287 5.708697 GCCTAATTGGTGGTAGTTAAACAGT 59.291 40.000 0.00 0.00 38.35 3.55
287 288 6.208007 GCCTAATTGGTGGTAGTTAAACAGTT 59.792 38.462 0.00 0.00 38.35 3.16
288 289 7.590279 CCTAATTGGTGGTAGTTAAACAGTTG 58.410 38.462 0.00 0.00 0.00 3.16
289 290 7.229907 CCTAATTGGTGGTAGTTAAACAGTTGT 59.770 37.037 0.00 0.00 0.00 3.32
293 294 4.025480 GGTGGTAGTTAAACAGTTGTGACG 60.025 45.833 0.00 0.00 0.00 4.35
327 328 8.458052 TGTTATCAACACTCGCAATAATGAATT 58.542 29.630 0.00 0.00 36.25 2.17
414 512 3.876309 AAGGTTTCAGCCTTTCAGGTA 57.124 42.857 0.00 0.00 45.91 3.08
415 513 4.388577 AAGGTTTCAGCCTTTCAGGTAT 57.611 40.909 0.00 0.00 45.91 2.73
444 542 5.393124 TGCAAACAAGAAATATGAAGCTCG 58.607 37.500 0.00 0.00 0.00 5.03
460 558 2.096909 AGCTCGTGAATTTGAAACGACG 60.097 45.455 0.00 0.00 41.08 5.12
830 928 2.693074 GTCAGCTTCCTTCTCTCCCTAG 59.307 54.545 0.00 0.00 0.00 3.02
849 947 6.670027 TCCCTAGTAGCTTCATTCTTCTTCTT 59.330 38.462 0.00 0.00 0.00 2.52
850 948 6.983890 CCCTAGTAGCTTCATTCTTCTTCTTC 59.016 42.308 0.00 0.00 0.00 2.87
851 949 7.147742 CCCTAGTAGCTTCATTCTTCTTCTTCT 60.148 40.741 0.00 0.00 0.00 2.85
852 950 8.257306 CCTAGTAGCTTCATTCTTCTTCTTCTT 58.743 37.037 0.00 0.00 0.00 2.52
900 998 0.832135 TCGTCCTGAAACTGGAGCCT 60.832 55.000 0.00 0.00 32.29 4.58
933 1031 4.696479 AAGGAAGAAGAGCAAGAAGACA 57.304 40.909 0.00 0.00 0.00 3.41
1569 1667 0.823460 GCACAGGAGAGGAAGAGGAG 59.177 60.000 0.00 0.00 0.00 3.69
1583 1681 2.048127 GGAGCGTGTCACCCTCAC 60.048 66.667 17.34 5.48 0.00 3.51
1657 1755 1.378514 GGGAATTGGCGAGCAGGAA 60.379 57.895 0.00 0.00 0.00 3.36
1822 1920 3.795041 CCCTCTGGCCCTCTGCTG 61.795 72.222 0.00 0.00 40.92 4.41
2123 2221 2.664402 ATGCAAGGACACTTCCACTT 57.336 45.000 0.00 0.00 45.72 3.16
2188 2286 4.331108 TGCAAACATGATTAGCAGGTGTA 58.669 39.130 0.00 0.00 41.31 2.90
2310 2546 5.166398 GCTGAAGATTGCTTTGCATTAACT 58.834 37.500 0.00 0.00 38.76 2.24
2311 2547 5.061808 GCTGAAGATTGCTTTGCATTAACTG 59.938 40.000 0.00 0.00 38.76 3.16
2375 2611 7.499232 GTGATACTATTCCATAGTGGCAACTTT 59.501 37.037 0.00 0.00 45.24 2.66
2388 2624 2.031420 GGCAACTTTCAAGTTACGGGAC 60.031 50.000 4.61 0.00 46.89 4.46
2435 2672 0.254178 GTCAGGAGCCACATGTCCAT 59.746 55.000 0.00 0.00 35.02 3.41
2455 2692 8.038351 TGTCCATGACGTCTTGAAGATAAAATA 58.962 33.333 27.68 0.00 34.95 1.40
2685 2925 3.578282 TGAACAAGTCATACAGCTGGAGA 59.422 43.478 19.93 9.77 0.00 3.71
2742 2982 9.950496 AAGACAAAATAGTGAACTCTGACATAT 57.050 29.630 0.00 0.00 0.00 1.78
2855 3095 8.475331 AAATGCGTAACCATATATGCTACTAC 57.525 34.615 7.24 4.88 38.38 2.73
2902 3142 2.439409 TGAATGTTGTGCTGGGAGATG 58.561 47.619 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 5.221283 GGAGGAAGTACCAGTAATAGCTGAC 60.221 48.000 0.00 0.00 42.04 3.51
34 35 4.261656 CGGAGGAAGTACCAGTAATAGCTG 60.262 50.000 0.00 0.00 42.04 4.24
35 36 3.890147 CGGAGGAAGTACCAGTAATAGCT 59.110 47.826 0.00 0.00 42.04 3.32
36 37 3.635836 ACGGAGGAAGTACCAGTAATAGC 59.364 47.826 0.00 0.00 42.04 2.97
37 38 5.848833 AACGGAGGAAGTACCAGTAATAG 57.151 43.478 0.00 0.00 42.04 1.73
38 39 5.105228 CCAAACGGAGGAAGTACCAGTAATA 60.105 44.000 0.00 0.00 42.04 0.98
39 40 4.323257 CCAAACGGAGGAAGTACCAGTAAT 60.323 45.833 0.00 0.00 42.04 1.89
40 41 3.007182 CCAAACGGAGGAAGTACCAGTAA 59.993 47.826 0.00 0.00 42.04 2.24
41 42 2.564062 CCAAACGGAGGAAGTACCAGTA 59.436 50.000 0.00 0.00 42.04 2.74
42 43 1.346722 CCAAACGGAGGAAGTACCAGT 59.653 52.381 0.00 0.00 42.04 4.00
43 44 1.338769 CCCAAACGGAGGAAGTACCAG 60.339 57.143 0.00 0.00 42.04 4.00
44 45 0.688487 CCCAAACGGAGGAAGTACCA 59.312 55.000 0.00 0.00 42.04 3.25
45 46 0.689055 ACCCAAACGGAGGAAGTACC 59.311 55.000 0.00 0.00 35.10 3.34
46 47 2.556144 AACCCAAACGGAGGAAGTAC 57.444 50.000 0.00 0.00 34.64 2.73
47 48 4.914177 ATAAACCCAAACGGAGGAAGTA 57.086 40.909 0.00 0.00 34.64 2.24
60 61 1.864559 AGGGGGCCCAATAAACCCA 60.865 57.895 26.86 0.00 46.21 4.51
210 211 7.093068 TGCCTCTCCATTTAACTACATCAGTTA 60.093 37.037 0.00 0.00 45.93 2.24
214 215 5.692115 TGCCTCTCCATTTAACTACATCA 57.308 39.130 0.00 0.00 0.00 3.07
227 228 0.254747 CCGGGTTTATTGCCTCTCCA 59.745 55.000 0.00 0.00 0.00 3.86
245 246 1.209747 AGGCAATTACTTCCTCCGTCC 59.790 52.381 0.00 0.00 0.00 4.79
260 261 6.069331 TGTTTAACTACCACCAATTAGGCAA 58.931 36.000 0.00 0.00 43.14 4.52
276 277 3.547054 TCCCGTCACAACTGTTTAACT 57.453 42.857 0.00 0.00 0.00 2.24
277 278 4.823790 ATTCCCGTCACAACTGTTTAAC 57.176 40.909 0.00 0.00 0.00 2.01
278 279 5.838531 AAATTCCCGTCACAACTGTTTAA 57.161 34.783 0.00 0.00 0.00 1.52
279 280 5.125739 ACAAAATTCCCGTCACAACTGTTTA 59.874 36.000 0.00 0.00 0.00 2.01
280 281 4.081917 ACAAAATTCCCGTCACAACTGTTT 60.082 37.500 0.00 0.00 0.00 2.83
281 282 3.445805 ACAAAATTCCCGTCACAACTGTT 59.554 39.130 0.00 0.00 0.00 3.16
282 283 3.020984 ACAAAATTCCCGTCACAACTGT 58.979 40.909 0.00 0.00 0.00 3.55
283 284 3.708563 ACAAAATTCCCGTCACAACTG 57.291 42.857 0.00 0.00 0.00 3.16
284 285 5.533154 TGATAACAAAATTCCCGTCACAACT 59.467 36.000 0.00 0.00 0.00 3.16
285 286 5.764131 TGATAACAAAATTCCCGTCACAAC 58.236 37.500 0.00 0.00 0.00 3.32
286 287 6.183360 TGTTGATAACAAAATTCCCGTCACAA 60.183 34.615 0.00 0.00 38.72 3.33
287 288 5.299531 TGTTGATAACAAAATTCCCGTCACA 59.700 36.000 0.00 0.00 38.72 3.58
288 289 5.627780 GTGTTGATAACAAAATTCCCGTCAC 59.372 40.000 0.00 0.00 44.16 3.67
289 290 5.533154 AGTGTTGATAACAAAATTCCCGTCA 59.467 36.000 0.00 0.00 44.16 4.35
293 294 4.857037 GCGAGTGTTGATAACAAAATTCCC 59.143 41.667 0.00 0.00 44.16 3.97
327 328 7.031415 AGTTGAATATCATATGCCCACCATA 57.969 36.000 0.00 0.00 40.52 2.74
381 479 4.537015 CTGAAACCTTTTAGCTTTGGTCG 58.463 43.478 0.00 0.00 31.64 4.79
415 513 9.787532 GCTTCATATTTCTTGTTTGCAACTATA 57.212 29.630 0.00 0.00 0.00 1.31
444 542 1.002251 TGGGCGTCGTTTCAAATTCAC 60.002 47.619 0.00 0.00 0.00 3.18
460 558 7.165460 AGTAAATTGGTTGTTAATAGTGGGC 57.835 36.000 0.00 0.00 0.00 5.36
504 602 1.072648 GGGGCTTACAAGGTACACACA 59.927 52.381 0.00 0.00 0.00 3.72
591 689 6.017605 AGCTATATTGCAACTTCATAGTGTGC 60.018 38.462 11.72 0.00 38.13 4.57
686 784 4.140543 TGGAGCTCCCATAAAGACCCTATA 60.141 45.833 29.95 1.94 40.82 1.31
830 928 6.876257 TGGAAGAAGAAGAAGAATGAAGCTAC 59.124 38.462 0.00 0.00 0.00 3.58
849 947 3.454447 TGAACTCCAGTCTGTTTGGAAGA 59.546 43.478 0.00 0.00 43.79 2.87
850 948 3.808728 TGAACTCCAGTCTGTTTGGAAG 58.191 45.455 0.00 2.99 43.79 3.46
851 949 3.924114 TGAACTCCAGTCTGTTTGGAA 57.076 42.857 0.00 0.00 43.79 3.53
852 950 3.390967 TGATGAACTCCAGTCTGTTTGGA 59.609 43.478 0.00 3.59 42.30 3.53
900 998 5.290493 TCTTCTTCCTTTGAGTGCTTGTA 57.710 39.130 0.00 0.00 0.00 2.41
1569 1667 1.741770 GATGGTGAGGGTGACACGC 60.742 63.158 14.45 14.45 38.90 5.34
1583 1681 3.900966 TGTCACTGAGGATGAAGATGG 57.099 47.619 0.00 0.00 0.00 3.51
1657 1755 0.987294 AGCTACTGCCACCATGAAGT 59.013 50.000 0.00 0.00 40.80 3.01
2188 2286 9.309516 CAATCTGCAAGCATTTAAGTTGATATT 57.690 29.630 0.00 0.00 0.00 1.28
2310 2546 1.420138 GTTCCAGTTGACTTCTCCCCA 59.580 52.381 0.00 0.00 0.00 4.96
2311 2547 1.700186 AGTTCCAGTTGACTTCTCCCC 59.300 52.381 0.00 0.00 0.00 4.81
2375 2611 3.842007 TTTTCCTGTCCCGTAACTTGA 57.158 42.857 0.00 0.00 0.00 3.02
2435 2672 6.750501 CCTCGTATTTTATCTTCAAGACGTCA 59.249 38.462 19.50 0.00 0.00 4.35
2455 2692 0.179067 TTTTGGCTGTTCGACCTCGT 60.179 50.000 0.00 0.00 40.80 4.18
2685 2925 8.408043 TGTAACCATGATTCTGAAATCTTGTT 57.592 30.769 0.00 0.00 41.81 2.83
2742 2982 0.665298 TGCGTGCTTGTGTTGCATTA 59.335 45.000 0.00 0.00 42.69 1.90
2801 3041 4.380655 CCGAACCACTGTTTCTAGGTAGAG 60.381 50.000 0.00 0.00 33.97 2.43
2802 3042 3.508793 CCGAACCACTGTTTCTAGGTAGA 59.491 47.826 0.00 0.00 33.97 2.59
2855 3095 3.921119 TTGCCTGCTGTAACTTTCATG 57.079 42.857 0.00 0.00 0.00 3.07
2862 3102 3.253188 TCATGAACTTTGCCTGCTGTAAC 59.747 43.478 0.00 0.00 0.00 2.50
2866 3106 3.250744 CATTCATGAACTTTGCCTGCTG 58.749 45.455 11.07 0.00 0.00 4.41
2867 3107 2.895404 ACATTCATGAACTTTGCCTGCT 59.105 40.909 11.07 0.00 0.00 4.24
2868 3108 3.308438 ACATTCATGAACTTTGCCTGC 57.692 42.857 11.07 0.00 0.00 4.85
2902 3142 7.116948 GGTCTTTTACTTAACGAAGGAAGTACC 59.883 40.741 0.00 0.00 38.93 3.34


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

AutoCloner maintained by Alex Coulton.