Multiple sequence alignment - TraesCS2A01G165300

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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 TraesCS2A01G165300 chr2A 100.000 2807 0 0 1 2807 117762198 117759392 0.000000e+00 5184.0
1 TraesCS2A01G165300 chr2B 90.434 2164 149 20 686 2804 166810745 166808595 0.000000e+00 2796.0
2 TraesCS2A01G165300 chr2B 88.281 384 43 2 1 384 166834406 166834787 2.550000e-125 459.0
3 TraesCS2A01G165300 chr2B 88.372 258 24 2 375 627 166811020 166810764 3.510000e-79 305.0
4 TraesCS2A01G165300 chr2D 88.645 2369 153 42 464 2807 116591488 116589211 0.000000e+00 2778.0
5 TraesCS2A01G165300 chr2D 90.949 453 34 7 1 449 116592036 116591587 1.110000e-168 603.0
6 TraesCS2A01G165300 chr1B 78.363 171 25 10 149 315 680779987 680780149 1.780000e-17 100.0
7 TraesCS2A01G165300 chr7B 76.263 198 35 11 121 315 56479365 56479553 8.280000e-16 95.3
8 TraesCS2A01G165300 chr6D 77.647 170 28 7 149 315 447512279 447512441 8.280000e-16 95.3


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 TraesCS2A01G165300 chr2A 117759392 117762198 2806 True 5184.0 5184 100.000 1 2807 1 chr2A.!!$R1 2806
1 TraesCS2A01G165300 chr2B 166808595 166811020 2425 True 1550.5 2796 89.403 375 2804 2 chr2B.!!$R1 2429
2 TraesCS2A01G165300 chr2D 116589211 116592036 2825 True 1690.5 2778 89.797 1 2807 2 chr2D.!!$R1 2806

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
287 288 0.670546 AGACAACATTCGCCTCCGTG 60.671 55.0 0.0 0.0 35.54 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2161 2271 3.259902 GTCGAGGGACCTTATTGTGTTC 58.74 50.0 0.0 0.0 37.19 3.18 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
122 123 1.283029 AGATGGTGGCTAAGTGCATGT 59.717 47.619 0.00 0.00 45.15 3.21
192 193 1.595311 TCATCCACCAGCCACCTTAT 58.405 50.000 0.00 0.00 0.00 1.73
196 197 4.167892 TCATCCACCAGCCACCTTATAATT 59.832 41.667 0.00 0.00 0.00 1.40
207 208 3.058016 CACCTTATAATTGATGCCGGCAG 60.058 47.826 35.36 18.29 0.00 4.85
255 256 1.763545 GGAACCAAGGTCCTAGCCTAG 59.236 57.143 0.00 0.00 38.03 3.02
280 281 3.187227 AGTTCATGACAGACAACATTCGC 59.813 43.478 0.00 0.00 0.00 4.70
282 283 2.079158 CATGACAGACAACATTCGCCT 58.921 47.619 0.00 0.00 0.00 5.52
287 288 0.670546 AGACAACATTCGCCTCCGTG 60.671 55.000 0.00 0.00 35.54 4.94
320 321 5.990668 ACAAAAGACACTGAAGTAGGAGTT 58.009 37.500 0.00 0.00 0.00 3.01
322 323 6.316390 ACAAAAGACACTGAAGTAGGAGTTTG 59.684 38.462 0.00 0.00 0.00 2.93
335 336 6.958767 AGTAGGAGTTTGTGGCTAATTGTAT 58.041 36.000 0.00 0.00 0.00 2.29
339 340 5.449177 GGAGTTTGTGGCTAATTGTATGCTC 60.449 44.000 0.00 0.00 0.00 4.26
345 347 5.123820 TGTGGCTAATTGTATGCTCTTCAAC 59.876 40.000 0.00 0.00 0.00 3.18
361 363 6.072452 GCTCTTCAACCTTACTTTTAGTGCAT 60.072 38.462 0.00 0.00 0.00 3.96
394 398 7.514721 AGATTGGTAGTTACTTTTCAGGTTCA 58.485 34.615 0.00 0.00 0.00 3.18
487 575 7.272037 TCACTTTCTGGAATTTTTCTACCAC 57.728 36.000 0.00 0.00 0.00 4.16
547 635 6.128580 GCAGTTTACATAACAATTTGGCTTGG 60.129 38.462 0.78 0.00 0.00 3.61
583 676 5.773176 ACAAAGTACAAAATTAGTGGGAGGG 59.227 40.000 0.00 0.00 0.00 4.30
793 886 6.039270 TGTTCATCAAACCAATCGAAGAAACT 59.961 34.615 0.00 0.00 37.25 2.66
869 962 5.881777 TCGAAGGATATACCGATGAGAAG 57.118 43.478 0.00 0.00 44.74 2.85
880 973 2.159653 CCGATGAGAAGAACGCCAAAAG 60.160 50.000 0.00 0.00 0.00 2.27
896 989 4.706962 GCCAAAAGTAAGGATCATCCAACT 59.293 41.667 6.42 6.17 39.61 3.16
900 993 4.392921 AGTAAGGATCATCCAACTGACG 57.607 45.455 6.42 0.00 39.61 4.35
1923 2024 4.201910 CGTCCACAATGTGTTCTGACTTTT 60.202 41.667 12.79 0.00 0.00 2.27
2074 2184 1.751351 TGATTTGCGTTGGTTTGGTGA 59.249 42.857 0.00 0.00 0.00 4.02
2236 2362 4.927978 TCTCGGAAGATGGAAAGATCTC 57.072 45.455 0.00 0.00 40.84 2.75
2255 2381 3.205056 TCTCCCCCTTAACGACCACTATA 59.795 47.826 0.00 0.00 0.00 1.31
2258 2384 3.320256 CCCCCTTAACGACCACTATAGTC 59.680 52.174 1.26 0.00 0.00 2.59
2292 2418 1.066752 CGTCACGTCCTTGTCACCA 59.933 57.895 0.00 0.00 0.00 4.17
2301 2427 3.041946 GTCCTTGTCACCATCCTCCTAT 58.958 50.000 0.00 0.00 0.00 2.57
2304 2430 2.454336 TGTCACCATCCTCCTATCGT 57.546 50.000 0.00 0.00 0.00 3.73
2316 2442 0.603569 CCTATCGTAGCCGGCTTGAT 59.396 55.000 37.74 34.78 33.95 2.57
2317 2443 1.000955 CCTATCGTAGCCGGCTTGATT 59.999 52.381 34.74 23.52 33.95 2.57
2330 2456 4.165779 CGGCTTGATTTTGTCAATGGTAC 58.834 43.478 0.00 0.00 45.36 3.34
2332 2458 5.564651 CGGCTTGATTTTGTCAATGGTACTT 60.565 40.000 0.00 0.00 45.36 2.24
2343 2469 7.639113 TGTCAATGGTACTTGGGAAATATTC 57.361 36.000 0.00 0.00 0.00 1.75
2357 2483 4.089065 GGAAATATTCGTATACGTGTCGCC 59.911 45.833 23.67 13.78 40.80 5.54
2363 2489 1.268896 CGTATACGTGTCGCCAAGGAT 60.269 52.381 17.16 0.00 34.11 3.24
2365 2491 0.821517 ATACGTGTCGCCAAGGATCA 59.178 50.000 0.00 0.00 0.00 2.92
2366 2492 0.604073 TACGTGTCGCCAAGGATCAA 59.396 50.000 0.00 0.00 0.00 2.57
2368 2494 1.787847 GTGTCGCCAAGGATCAACG 59.212 57.895 0.00 0.00 0.00 4.10
2370 2496 0.669318 TGTCGCCAAGGATCAACGTC 60.669 55.000 0.00 0.00 0.00 4.34
2372 2498 0.389817 TCGCCAAGGATCAACGTCAG 60.390 55.000 0.00 0.00 0.00 3.51
2374 2500 1.403647 CGCCAAGGATCAACGTCAGTA 60.404 52.381 0.00 0.00 0.00 2.74
2378 2504 4.686554 GCCAAGGATCAACGTCAGTATATC 59.313 45.833 0.00 0.00 0.00 1.63
2382 2508 4.215827 AGGATCAACGTCAGTATATCCGTC 59.784 45.833 0.00 0.00 42.28 4.79
2403 2529 9.058174 TCCGTCAAAGTAATCTAAACAAAATGA 57.942 29.630 0.00 0.00 0.00 2.57
2427 2553 8.289618 TGAGACTTTATTTGGACAAAAAGATCG 58.710 33.333 13.31 0.77 33.56 3.69
2429 2555 9.014297 AGACTTTATTTGGACAAAAAGATCGAT 57.986 29.630 13.31 0.00 33.56 3.59
2430 2556 9.278734 GACTTTATTTGGACAAAAAGATCGATC 57.721 33.333 17.91 17.91 33.56 3.69
2435 2561 7.979444 TTTGGACAAAAAGATCGATCTTAGT 57.021 32.000 34.56 30.30 45.83 2.24
2437 2563 6.697395 TGGACAAAAAGATCGATCTTAGTGA 58.303 36.000 35.01 22.54 45.83 3.41
2441 2567 6.528423 ACAAAAAGATCGATCTTAGTGAGACG 59.472 38.462 35.01 23.12 45.83 4.18
2444 2572 4.443621 AGATCGATCTTAGTGAGACGTGA 58.556 43.478 22.32 0.00 37.17 4.35
2454 2582 4.585955 AGTGAGACGTGAAACATGTAGT 57.414 40.909 0.00 0.00 35.74 2.73
2462 2590 5.117584 ACGTGAAACATGTAGTGGTAACAA 58.882 37.500 0.00 0.00 45.33 2.83
2517 2645 1.740297 TACACAACAACGTGCAAGGT 58.260 45.000 4.26 0.00 40.73 3.50
2563 2691 2.165167 CACTACGGACAGGGTTGTAGA 58.835 52.381 13.27 0.00 37.76 2.59
2567 2714 2.880443 ACGGACAGGGTTGTAGAAGTA 58.120 47.619 0.00 0.00 37.76 2.24
2586 2733 7.514721 AGAAGTAATGTCTGTTTTGAACCCTA 58.485 34.615 0.00 0.00 0.00 3.53
2625 2772 1.269448 CAAACGAACCCCACATCCAAG 59.731 52.381 0.00 0.00 0.00 3.61
2652 2799 7.235606 TCCCTGAAATTGATACCCTATACTCAG 59.764 40.741 0.00 0.00 0.00 3.35
2655 2802 6.041637 TGAAATTGATACCCTATACTCAGCGT 59.958 38.462 0.00 0.00 0.00 5.07
2727 2874 1.351017 TCCTGGATGGGATTAATCGCC 59.649 52.381 24.85 18.80 38.81 5.54
2744 2891 2.032528 CACTCCCACATGCACCGT 59.967 61.111 0.00 0.00 0.00 4.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
166 167 1.632920 TGGCTGGTGGATGATGTAACA 59.367 47.619 0.00 0.00 0.00 2.41
174 175 3.576078 TTATAAGGTGGCTGGTGGATG 57.424 47.619 0.00 0.00 0.00 3.51
175 176 4.167892 TCAATTATAAGGTGGCTGGTGGAT 59.832 41.667 0.00 0.00 0.00 3.41
192 193 0.819259 GGAGCTGCCGGCATCAATTA 60.819 55.000 32.87 4.54 44.79 1.40
196 197 4.166888 GAGGAGCTGCCGGCATCA 62.167 66.667 32.87 7.31 44.79 3.07
207 208 0.548031 TCCACCATGGATTGAGGAGC 59.452 55.000 21.47 0.00 42.67 4.70
255 256 5.445142 CGAATGTTGTCTGTCATGAACTAGC 60.445 44.000 0.00 0.00 0.00 3.42
280 281 2.605295 TACACCACCCCACGGAGG 60.605 66.667 0.00 0.00 45.09 4.30
282 283 1.343431 TTTGTACACCACCCCACGGA 61.343 55.000 0.00 0.00 0.00 4.69
287 288 1.951602 GTGTCTTTTGTACACCACCCC 59.048 52.381 0.00 0.00 41.10 4.95
291 292 4.839121 ACTTCAGTGTCTTTTGTACACCA 58.161 39.130 0.00 0.00 46.77 4.17
296 297 6.726490 ACTCCTACTTCAGTGTCTTTTGTA 57.274 37.500 0.00 0.00 0.00 2.41
320 321 5.252547 TGAAGAGCATACAATTAGCCACAA 58.747 37.500 0.00 0.00 0.00 3.33
322 323 5.449177 GGTTGAAGAGCATACAATTAGCCAC 60.449 44.000 0.00 0.00 0.00 5.01
335 336 5.238650 GCACTAAAAGTAAGGTTGAAGAGCA 59.761 40.000 0.00 0.00 0.00 4.26
365 367 8.657712 ACCTGAAAAGTAACTACCAATCTACTT 58.342 33.333 0.00 0.00 36.41 2.24
368 370 8.653191 TGAACCTGAAAAGTAACTACCAATCTA 58.347 33.333 0.00 0.00 0.00 1.98
369 371 7.514721 TGAACCTGAAAAGTAACTACCAATCT 58.485 34.615 0.00 0.00 0.00 2.40
370 372 7.739498 TGAACCTGAAAAGTAACTACCAATC 57.261 36.000 0.00 0.00 0.00 2.67
371 373 8.706322 ATTGAACCTGAAAAGTAACTACCAAT 57.294 30.769 0.00 0.00 0.00 3.16
372 374 8.528044 AATTGAACCTGAAAAGTAACTACCAA 57.472 30.769 0.00 0.00 0.00 3.67
373 375 9.280174 CTAATTGAACCTGAAAAGTAACTACCA 57.720 33.333 0.00 0.00 0.00 3.25
374 376 9.498176 TCTAATTGAACCTGAAAAGTAACTACC 57.502 33.333 0.00 0.00 0.00 3.18
441 445 8.200792 AGTGAACTTCTATAAACATGCTCCTAG 58.799 37.037 0.00 0.00 0.00 3.02
459 547 8.414003 GGTAGAAAAATTCCAGAAAGTGAACTT 58.586 33.333 0.00 0.00 37.91 2.66
487 575 3.384555 TAGGCCACCCTACCCTCGG 62.385 68.421 5.01 0.00 42.87 4.63
525 613 6.459923 TCCCAAGCCAAATTGTTATGTAAAC 58.540 36.000 0.00 0.00 0.00 2.01
532 620 7.826744 GGAAATAAATCCCAAGCCAAATTGTTA 59.173 33.333 0.00 0.00 33.05 2.41
538 626 4.594920 TGTGGAAATAAATCCCAAGCCAAA 59.405 37.500 0.00 0.00 38.82 3.28
583 676 7.819900 ACAGAGTCATCTTTATTGTACTTGGAC 59.180 37.037 0.00 0.00 31.64 4.02
682 775 2.165437 AGAGATTTCAGGCTCACTCGTC 59.835 50.000 0.00 0.00 33.62 4.20
684 777 2.094286 ACAGAGATTTCAGGCTCACTCG 60.094 50.000 0.00 0.00 33.62 4.18
793 886 6.875948 TTCTTCTGCTGCATTGTTTACTTA 57.124 33.333 1.31 0.00 0.00 2.24
841 934 3.770046 TCGGTATATCCTTCGATTGGGA 58.230 45.455 5.33 5.19 35.96 4.37
849 942 6.087522 CGTTCTTCTCATCGGTATATCCTTC 58.912 44.000 0.00 0.00 0.00 3.46
869 962 4.201920 GGATGATCCTTACTTTTGGCGTTC 60.202 45.833 3.71 0.00 32.53 3.95
880 973 2.866762 GCGTCAGTTGGATGATCCTTAC 59.133 50.000 13.44 10.64 37.46 2.34
896 989 1.596752 ATTTGCCAGTGACGCGTCA 60.597 52.632 36.40 36.40 37.24 4.35
900 993 2.126346 GCCATTTGCCAGTGACGC 60.126 61.111 0.00 0.00 0.00 5.19
967 1060 1.519013 CTGCCTCTGCGAAGAGAGC 60.519 63.158 22.84 21.69 41.78 4.09
1732 1825 3.357079 CTTGACCACCAGGCACGC 61.357 66.667 0.00 0.00 39.06 5.34
1978 2087 9.289782 GGATGAAGCACCTCTGTATTATTTTAT 57.710 33.333 0.00 0.00 0.00 1.40
2074 2184 9.985730 TCAAAAAGAAAAACATGAGCAATAGAT 57.014 25.926 0.00 0.00 0.00 1.98
2124 2234 7.681679 TGGGTGTTTTATACTACTGATGAACA 58.318 34.615 0.00 0.00 0.00 3.18
2161 2271 3.259902 GTCGAGGGACCTTATTGTGTTC 58.740 50.000 0.00 0.00 37.19 3.18
2236 2362 3.303049 ACTATAGTGGTCGTTAAGGGGG 58.697 50.000 4.10 0.00 0.00 5.40
2301 2427 1.083489 CAAAATCAAGCCGGCTACGA 58.917 50.000 33.07 28.72 44.60 3.43
2304 2430 2.192664 TGACAAAATCAAGCCGGCTA 57.807 45.000 33.07 16.93 33.02 3.93
2316 2442 6.739331 ATTTCCCAAGTACCATTGACAAAA 57.261 33.333 0.00 0.00 31.55 2.44
2317 2443 8.429237 AATATTTCCCAAGTACCATTGACAAA 57.571 30.769 0.00 0.00 31.55 2.83
2330 2456 6.129273 CGACACGTATACGAATATTTCCCAAG 60.129 42.308 30.77 6.94 43.02 3.61
2332 2458 5.214417 CGACACGTATACGAATATTTCCCA 58.786 41.667 30.77 0.00 43.02 4.37
2343 2469 0.099259 TCCTTGGCGACACGTATACG 59.901 55.000 23.24 23.24 42.67 3.06
2357 2483 4.917998 CGGATATACTGACGTTGATCCTTG 59.082 45.833 0.00 0.00 33.89 3.61
2363 2489 4.968812 TTGACGGATATACTGACGTTGA 57.031 40.909 0.00 0.00 39.95 3.18
2365 2491 5.320549 ACTTTGACGGATATACTGACGTT 57.679 39.130 0.00 0.00 39.95 3.99
2366 2492 4.978083 ACTTTGACGGATATACTGACGT 57.022 40.909 0.00 0.00 42.88 4.34
2378 2504 9.329913 CTCATTTTGTTTAGATTACTTTGACGG 57.670 33.333 0.00 0.00 0.00 4.79
2403 2529 8.391075 TCGATCTTTTTGTCCAAATAAAGTCT 57.609 30.769 0.00 0.00 0.00 3.24
2424 2550 5.106277 TGTTTCACGTCTCACTAAGATCGAT 60.106 40.000 0.00 0.00 36.11 3.59
2425 2551 4.214758 TGTTTCACGTCTCACTAAGATCGA 59.785 41.667 0.00 0.00 36.11 3.59
2427 2553 5.864474 ACATGTTTCACGTCTCACTAAGATC 59.136 40.000 0.00 0.00 36.11 2.75
2429 2555 5.196341 ACATGTTTCACGTCTCACTAAGA 57.804 39.130 0.00 0.00 0.00 2.10
2430 2556 6.088217 CACTACATGTTTCACGTCTCACTAAG 59.912 42.308 2.30 0.00 0.00 2.18
2432 2558 5.458015 CACTACATGTTTCACGTCTCACTA 58.542 41.667 2.30 0.00 0.00 2.74
2433 2559 4.299155 CACTACATGTTTCACGTCTCACT 58.701 43.478 2.30 0.00 0.00 3.41
2434 2560 3.428870 CCACTACATGTTTCACGTCTCAC 59.571 47.826 2.30 0.00 0.00 3.51
2435 2561 3.069016 ACCACTACATGTTTCACGTCTCA 59.931 43.478 2.30 0.00 0.00 3.27
2437 2563 3.746045 ACCACTACATGTTTCACGTCT 57.254 42.857 2.30 0.00 0.00 4.18
2441 2567 8.132362 TCAATTTGTTACCACTACATGTTTCAC 58.868 33.333 2.30 0.00 0.00 3.18
2444 2572 9.691362 GATTCAATTTGTTACCACTACATGTTT 57.309 29.630 2.30 0.00 0.00 2.83
2454 2582 7.415095 CCGCTAATCTGATTCAATTTGTTACCA 60.415 37.037 6.10 0.00 0.00 3.25
2462 2590 3.316308 GCCACCGCTAATCTGATTCAATT 59.684 43.478 6.10 0.00 0.00 2.32
2563 2691 8.528044 TTTAGGGTTCAAAACAGACATTACTT 57.472 30.769 0.00 0.00 0.00 2.24
2567 2714 7.093509 ACAACTTTAGGGTTCAAAACAGACATT 60.094 33.333 0.00 0.00 0.00 2.71
2586 2733 1.070134 TGTGCCGCTCTCTACAACTTT 59.930 47.619 0.00 0.00 0.00 2.66
2625 2772 7.016268 TGAGTATAGGGTATCAATTTCAGGGAC 59.984 40.741 0.00 0.00 0.00 4.46
2652 2799 3.370276 GGTCTAGATTTACCGAGAACGC 58.630 50.000 0.00 0.00 38.29 4.84
2655 2802 3.958798 CCAGGGTCTAGATTTACCGAGAA 59.041 47.826 0.00 0.00 36.57 2.87
2698 2845 3.870538 TCCCATCCAGGATCATCTTTG 57.129 47.619 0.00 0.00 41.22 2.77
2727 2874 2.032528 ACGGTGCATGTGGGAGTG 59.967 61.111 0.00 0.00 0.00 3.51
2744 2891 0.968405 GGCAAAAGAGGCAACCATGA 59.032 50.000 0.00 0.00 37.17 3.07


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

AutoCloner maintained by Alex Coulton.