Multiple sequence alignment - TraesCS5B01G333600

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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 TraesCS5B01G333600 chr5B 100.000 1483 0 0 1 1483 517502626 517504108 0.000000e+00 2739
1 TraesCS5B01G333600 chr5B 100.000 615 0 0 1806 2420 517504431 517505045 0.000000e+00 1136
2 TraesCS5B01G333600 chr5B 83.794 253 26 6 947 1196 517557148 517557388 2.420000e-55 226
3 TraesCS5B01G333600 chr5D 95.699 1488 55 5 1 1483 428306241 428307724 0.000000e+00 2385
4 TraesCS5B01G333600 chr5D 88.179 626 58 9 1807 2419 428307783 428308405 0.000000e+00 732
5 TraesCS5B01G333600 chr5D 82.126 414 52 16 791 1195 428374745 428375145 3.860000e-88 335
6 TraesCS5B01G333600 chr5A 91.056 1487 105 11 8 1483 543713228 543714697 0.000000e+00 1984
7 TraesCS5B01G333600 chr5A 89.070 613 62 4 1807 2417 543714760 543715369 0.000000e+00 756
8 TraesCS5B01G333600 chr5A 80.144 418 54 15 791 1195 543916279 543916680 3.940000e-73 285


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 TraesCS5B01G333600 chr5B 517502626 517505045 2419 False 1937.5 2739 100.000 1 2420 2 chr5B.!!$F2 2419
1 TraesCS5B01G333600 chr5D 428306241 428308405 2164 False 1558.5 2385 91.939 1 2419 2 chr5D.!!$F2 2418
2 TraesCS5B01G333600 chr5A 543713228 543715369 2141 False 1370.0 1984 90.063 8 2417 2 chr5A.!!$F2 2409

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
184 186 0.394762 TGCCATCCCAGAATGTGCTC 60.395 55.0 0.0 0.0 0.00 4.26 F
690 693 0.463295 CCAGAGCTGATTGGACGCAT 60.463 55.0 0.0 0.0 36.55 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1284 1298 0.028242 CCTCGTCGTCCTCATCTTCG 59.972 60.0 0.0 0.0 0.0 3.79 R
2237 2261 0.038159 AGTTCTACCACACGCAGAGC 60.038 55.0 0.0 0.0 0.0 4.09 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
39 40 2.627699 CGTTTTGGGGGATATTCCATGG 59.372 50.000 4.97 4.97 38.64 3.66
144 145 2.315901 CGAAAAACGGGTGAGAATTGC 58.684 47.619 0.00 0.00 38.46 3.56
146 147 1.698506 AAAACGGGTGAGAATTGCCA 58.301 45.000 0.00 0.00 0.00 4.92
157 158 3.448301 TGAGAATTGCCATGCCCTAAAAG 59.552 43.478 0.00 0.00 0.00 2.27
158 160 3.701040 GAGAATTGCCATGCCCTAAAAGA 59.299 43.478 0.00 0.00 0.00 2.52
182 184 1.117150 ATTGCCATCCCAGAATGTGC 58.883 50.000 0.00 0.00 0.00 4.57
184 186 0.394762 TGCCATCCCAGAATGTGCTC 60.395 55.000 0.00 0.00 0.00 4.26
276 278 3.008049 ACTGACACTTTAGAATTCGGGCT 59.992 43.478 0.00 0.00 0.00 5.19
303 305 2.281484 ACGTGCATGAGGGCGTTT 60.281 55.556 14.17 0.00 33.54 3.60
318 320 4.120589 GGGCGTTTACTGAGAATCCTTAG 58.879 47.826 0.00 0.00 32.76 2.18
383 386 8.871629 TGCTTGGAGTATTTGTTCCTAAATAA 57.128 30.769 0.00 0.00 35.10 1.40
413 416 2.503356 TGGGCTGAAAAACCACACATTT 59.497 40.909 0.00 0.00 0.00 2.32
430 433 3.890147 ACATTTAACCGGTAAACCAGCAA 59.110 39.130 8.00 0.00 34.50 3.91
526 529 5.871396 ACCTACTCGTGTGAATATCCAAT 57.129 39.130 0.00 0.00 0.00 3.16
539 542 8.631797 TGTGAATATCCAATGATAACAATGTGG 58.368 33.333 0.00 0.00 37.04 4.17
574 577 5.063564 GCAGAAACAAGTTAACCCTAGATCG 59.936 44.000 0.88 0.00 0.00 3.69
578 581 5.934402 ACAAGTTAACCCTAGATCGTGAT 57.066 39.130 0.88 0.00 0.00 3.06
662 665 1.226802 CAGTCGTCTGATCTGGCGG 60.227 63.158 23.70 6.83 43.76 6.13
690 693 0.463295 CCAGAGCTGATTGGACGCAT 60.463 55.000 0.00 0.00 36.55 4.73
706 709 3.527533 ACGCATTACACGTTGTATCCAT 58.472 40.909 0.00 0.00 41.93 3.41
718 721 3.998913 TGTATCCATCCAAAGCTCACA 57.001 42.857 0.00 0.00 0.00 3.58
776 779 6.401688 GCGCACATTTACACTAGATTACACAA 60.402 38.462 0.30 0.00 0.00 3.33
964 975 3.186613 GCAACCAAAGAAAGAGTAGACGG 59.813 47.826 0.00 0.00 0.00 4.79
1230 1244 3.622826 CGTTCCGTGGACACCCCT 61.623 66.667 0.00 0.00 35.38 4.79
1284 1298 2.668550 GGTTGCGTGGACTGGGAC 60.669 66.667 0.00 0.00 0.00 4.46
1407 1421 1.712977 GCAGCAGCCGGAAGATCAAG 61.713 60.000 5.05 0.00 33.58 3.02
1421 1435 6.699642 CGGAAGATCAAGAAGAAGGAATAGAC 59.300 42.308 0.00 0.00 0.00 2.59
1424 1438 7.411486 AGATCAAGAAGAAGGAATAGACGAA 57.589 36.000 0.00 0.00 0.00 3.85
1455 1469 2.356667 GGAGAGGGGCCAACCTTG 59.643 66.667 4.39 0.00 42.10 3.61
1920 1938 7.737972 TTATTTTGTTCTACTGTTGCTAGCA 57.262 32.000 14.93 14.93 0.00 3.49
1966 1984 2.331893 CGATGGACGGCCTTTGCAA 61.332 57.895 9.82 0.00 40.13 4.08
2001 2019 0.316841 GGCGGAGAGGATCAGATCAC 59.683 60.000 12.66 5.83 37.82 3.06
2002 2020 0.316841 GCGGAGAGGATCAGATCACC 59.683 60.000 12.66 8.47 37.82 4.02
2003 2021 1.993956 CGGAGAGGATCAGATCACCT 58.006 55.000 12.66 7.96 37.82 4.00
2007 2025 0.965439 GAGGATCAGATCACCTCCGG 59.035 60.000 12.66 0.00 42.84 5.14
2008 2026 1.118356 AGGATCAGATCACCTCCGGC 61.118 60.000 12.66 0.00 32.87 6.13
2010 2028 1.383109 ATCAGATCACCTCCGGCCA 60.383 57.895 2.24 0.00 0.00 5.36
2011 2029 1.406065 ATCAGATCACCTCCGGCCAG 61.406 60.000 2.24 0.00 0.00 4.85
2012 2030 2.765807 AGATCACCTCCGGCCAGG 60.766 66.667 7.59 7.59 42.97 4.45
2013 2031 3.866582 GATCACCTCCGGCCAGGG 61.867 72.222 13.51 8.87 41.52 4.45
2014 2032 4.414956 ATCACCTCCGGCCAGGGA 62.415 66.667 13.51 6.64 41.52 4.20
2015 2033 3.721172 ATCACCTCCGGCCAGGGAT 62.721 63.158 13.51 9.84 41.52 3.85
2017 2035 3.090532 ACCTCCGGCCAGGGATTC 61.091 66.667 13.51 0.00 41.52 2.52
2018 2036 4.241555 CCTCCGGCCAGGGATTCG 62.242 72.222 2.24 0.00 41.52 3.34
2019 2037 4.241555 CTCCGGCCAGGGATTCGG 62.242 72.222 2.24 8.29 43.42 4.30
2021 2039 3.560251 CCGGCCAGGGATTCGGAT 61.560 66.667 2.24 0.00 44.69 4.18
2038 2056 0.382515 GATTGGTAGCTCGCGACTCT 59.617 55.000 3.71 8.13 0.00 3.24
2057 2075 2.586079 CGCCTGCGGTCGATCAAT 60.586 61.111 3.07 0.00 35.56 2.57
2058 2076 2.173669 CGCCTGCGGTCGATCAATT 61.174 57.895 3.07 0.00 35.56 2.32
2079 2103 1.735571 CCTGCCTGCATGCAATTTTTC 59.264 47.619 22.88 7.58 41.51 2.29
2104 2128 2.332063 AACTATTCCCTGTCGCATGG 57.668 50.000 0.00 0.00 0.00 3.66
2124 2148 1.201855 GCGAGTTGCGATTCACTGAAG 60.202 52.381 0.00 0.00 44.57 3.02
2173 2197 4.520874 TGGTGCTTTGTTTATCGGATTTGA 59.479 37.500 0.00 0.00 0.00 2.69
2176 2200 4.217334 TGCTTTGTTTATCGGATTTGAGCA 59.783 37.500 0.00 2.00 34.42 4.26
2183 2207 2.401195 GGATTTGAGCAGCGACGC 59.599 61.111 13.03 13.03 0.00 5.19
2225 2249 5.429130 CTGGTTTGGGAGTCCTATTTCTAC 58.571 45.833 9.58 0.00 0.00 2.59
2283 2307 1.973515 CAGTAGATATGGCCCTGCAGA 59.026 52.381 17.39 0.00 0.00 4.26
2284 2308 1.974236 AGTAGATATGGCCCTGCAGAC 59.026 52.381 17.39 6.73 0.00 3.51
2285 2309 1.002544 GTAGATATGGCCCTGCAGACC 59.997 57.143 17.39 16.84 0.00 3.85
2287 2311 2.738213 GATATGGCCCTGCAGACCGG 62.738 65.000 17.39 9.41 0.00 5.28
2315 2339 4.481112 CCGCCGGCAGTTGCAATC 62.481 66.667 28.98 0.00 44.36 2.67
2333 2357 1.420430 TCTCTTGTTCTCCGGTGGTT 58.580 50.000 0.00 0.00 0.00 3.67
2336 2360 2.036733 CTCTTGTTCTCCGGTGGTTGTA 59.963 50.000 0.00 0.00 0.00 2.41
2351 2376 5.284079 GTGGTTGTACAACTCTAGTTCGAA 58.716 41.667 31.82 0.00 40.94 3.71
2354 2379 5.163982 GGTTGTACAACTCTAGTTCGAATGC 60.164 44.000 31.82 11.32 40.94 3.56
2376 2401 4.551388 CTCGATATAACACCTGCCTCTTC 58.449 47.826 0.00 0.00 0.00 2.87
2379 2404 4.559704 CGATATAACACCTGCCTCTTCTCC 60.560 50.000 0.00 0.00 0.00 3.71
2387 2412 3.037549 CCTGCCTCTTCTCCTCATACTT 58.962 50.000 0.00 0.00 0.00 2.24
2396 2421 4.553330 TCTCCTCATACTTGTTTGGTCC 57.447 45.455 0.00 0.00 0.00 4.46
2402 2427 7.235079 TCCTCATACTTGTTTGGTCCATTTAA 58.765 34.615 0.00 0.00 0.00 1.52
2410 2435 3.695830 TTGGTCCATTTAAGCGAGTCT 57.304 42.857 0.00 0.00 0.00 3.24
2417 2442 6.539103 GGTCCATTTAAGCGAGTCTAATTTCT 59.461 38.462 0.00 0.00 0.00 2.52
2419 2444 7.905493 GTCCATTTAAGCGAGTCTAATTTCTTG 59.095 37.037 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 1.055338 GCAATTCTTCGTGCTGCAAC 58.945 50.000 2.77 0.00 37.78 4.17
144 145 4.872124 GCAATTTCTTCTTTTAGGGCATGG 59.128 41.667 0.00 0.00 0.00 3.66
146 147 4.531732 TGGCAATTTCTTCTTTTAGGGCAT 59.468 37.500 0.00 0.00 0.00 4.40
157 158 4.161001 ACATTCTGGGATGGCAATTTCTTC 59.839 41.667 0.00 0.00 0.00 2.87
158 160 4.081309 CACATTCTGGGATGGCAATTTCTT 60.081 41.667 0.00 0.00 0.00 2.52
182 184 4.052159 ACTGATCACAATCTAAGCGGAG 57.948 45.455 0.00 0.00 32.75 4.63
184 186 5.006746 GGTTAACTGATCACAATCTAAGCGG 59.993 44.000 5.42 0.00 32.75 5.52
276 278 0.036858 TCATGCACGTCGGATTCCAA 60.037 50.000 3.09 0.00 0.00 3.53
383 386 7.606073 GTGTGGTTTTTCAGCCCATAAAATATT 59.394 33.333 0.00 0.00 0.00 1.28
413 416 2.228925 GGTTTGCTGGTTTACCGGTTA 58.771 47.619 15.04 0.00 44.34 2.85
430 433 6.488683 TCGATTCAGGTTTTTACTGATTGGTT 59.511 34.615 0.00 0.00 43.82 3.67
526 529 7.392953 TGCTTAGTTTCATCCACATTGTTATCA 59.607 33.333 0.00 0.00 0.00 2.15
539 542 9.170584 GTTAACTTGTTTCTGCTTAGTTTCATC 57.829 33.333 0.00 0.00 31.94 2.92
644 647 1.226802 CCGCCAGATCAGACGACTG 60.227 63.158 8.68 8.68 44.66 3.51
671 674 0.463295 ATGCGTCCAATCAGCTCTGG 60.463 55.000 0.29 0.29 0.00 3.86
674 677 2.030946 GTGTAATGCGTCCAATCAGCTC 59.969 50.000 0.00 0.00 0.00 4.09
706 709 2.618241 GTGACACATTGTGAGCTTTGGA 59.382 45.455 23.12 0.00 36.96 3.53
776 779 2.827921 GGCCTGACCAAGATTTGACATT 59.172 45.455 0.00 0.00 38.86 2.71
964 975 2.547007 GCTAATTTCGCCTCCTCTCTCC 60.547 54.545 0.00 0.00 0.00 3.71
1284 1298 0.028242 CCTCGTCGTCCTCATCTTCG 59.972 60.000 0.00 0.00 0.00 3.79
1320 1334 2.509336 CGGTAGCGCTTCACCCTG 60.509 66.667 18.68 2.16 0.00 4.45
1402 1416 7.340743 TCTCTTCGTCTATTCCTTCTTCTTGAT 59.659 37.037 0.00 0.00 0.00 2.57
1403 1417 6.659668 TCTCTTCGTCTATTCCTTCTTCTTGA 59.340 38.462 0.00 0.00 0.00 3.02
1404 1418 6.857956 TCTCTTCGTCTATTCCTTCTTCTTG 58.142 40.000 0.00 0.00 0.00 3.02
1407 1421 6.687081 TCTCTCTTCGTCTATTCCTTCTTC 57.313 41.667 0.00 0.00 0.00 2.87
1421 1435 2.158682 TCTCCCCTCTCATCTCTCTTCG 60.159 54.545 0.00 0.00 0.00 3.79
1424 1438 1.782752 CCTCTCCCCTCTCATCTCTCT 59.217 57.143 0.00 0.00 0.00 3.10
1453 1467 7.309133 CCCTAGCAATCACTTGAATTACAACAA 60.309 37.037 0.00 0.00 34.04 2.83
1455 1469 6.404734 CCCCTAGCAATCACTTGAATTACAAC 60.405 42.308 0.00 0.00 34.04 3.32
1907 1925 1.339055 CCAAGCCTGCTAGCAACAGTA 60.339 52.381 19.86 0.00 33.09 2.74
1910 1928 1.973281 GCCAAGCCTGCTAGCAACA 60.973 57.895 19.86 0.00 34.23 3.33
1920 1938 2.739996 CCGAGATCCAGCCAAGCCT 61.740 63.158 0.00 0.00 0.00 4.58
2002 2020 4.241555 CCGAATCCCTGGCCGGAG 62.242 72.222 15.09 0.00 44.29 4.63
2004 2022 3.120086 AATCCGAATCCCTGGCCGG 62.120 63.158 3.88 3.88 43.02 6.13
2005 2023 1.893808 CAATCCGAATCCCTGGCCG 60.894 63.158 0.00 0.00 0.00 6.13
2006 2024 1.529244 CCAATCCGAATCCCTGGCC 60.529 63.158 0.00 0.00 0.00 5.36
2007 2025 0.472471 TACCAATCCGAATCCCTGGC 59.528 55.000 0.00 0.00 0.00 4.85
2008 2026 1.543429 GCTACCAATCCGAATCCCTGG 60.543 57.143 0.00 0.00 0.00 4.45
2010 2028 1.694696 GAGCTACCAATCCGAATCCCT 59.305 52.381 0.00 0.00 0.00 4.20
2011 2029 1.605712 CGAGCTACCAATCCGAATCCC 60.606 57.143 0.00 0.00 0.00 3.85
2012 2030 1.784525 CGAGCTACCAATCCGAATCC 58.215 55.000 0.00 0.00 0.00 3.01
2013 2031 1.140816 GCGAGCTACCAATCCGAATC 58.859 55.000 0.00 0.00 0.00 2.52
2014 2032 0.597637 CGCGAGCTACCAATCCGAAT 60.598 55.000 0.00 0.00 0.00 3.34
2015 2033 1.226859 CGCGAGCTACCAATCCGAA 60.227 57.895 0.00 0.00 0.00 4.30
2017 2035 1.944676 GTCGCGAGCTACCAATCCG 60.945 63.158 10.24 0.00 0.00 4.18
2018 2036 0.595310 GAGTCGCGAGCTACCAATCC 60.595 60.000 10.24 0.00 0.00 3.01
2019 2037 0.382515 AGAGTCGCGAGCTACCAATC 59.617 55.000 10.24 0.00 0.00 2.67
2020 2038 0.101399 CAGAGTCGCGAGCTACCAAT 59.899 55.000 10.24 0.00 0.00 3.16
2021 2039 1.506718 CAGAGTCGCGAGCTACCAA 59.493 57.895 10.24 0.00 0.00 3.67
2057 2075 0.978151 AAATTGCATGCAGGCAGGAA 59.022 45.000 26.27 12.68 45.88 3.36
2058 2076 0.978151 AAAATTGCATGCAGGCAGGA 59.022 45.000 26.27 13.49 45.88 3.86
2079 2103 5.811399 TGCGACAGGGAATAGTTAATTTG 57.189 39.130 0.00 0.00 0.00 2.32
2104 2128 0.790207 TTCAGTGAATCGCAACTCGC 59.210 50.000 0.08 0.00 38.27 5.03
2109 2133 2.094234 TCGATCCTTCAGTGAATCGCAA 60.094 45.455 18.25 4.25 0.00 4.85
2136 2160 4.536364 AAGCACCATATTTCACGAATCG 57.464 40.909 0.00 0.00 0.00 3.34
2149 2173 5.184864 TCAAATCCGATAAACAAAGCACCAT 59.815 36.000 0.00 0.00 0.00 3.55
2183 2207 2.633657 GCAGACAACAGTGCACCG 59.366 61.111 14.63 5.70 39.62 4.94
2193 2217 2.192861 CCCAAACCAGCGCAGACAA 61.193 57.895 11.47 0.00 0.00 3.18
2225 2249 0.179171 CGCAGAGCAAGCATTTCTGG 60.179 55.000 10.54 0.34 38.94 3.86
2234 2258 0.038251 TCTACCACACGCAGAGCAAG 60.038 55.000 0.00 0.00 0.00 4.01
2237 2261 0.038159 AGTTCTACCACACGCAGAGC 60.038 55.000 0.00 0.00 0.00 4.09
2276 2300 4.436998 GACGGTCCGGTCTGCAGG 62.437 72.222 17.28 0.00 34.09 4.85
2299 2323 3.386867 GAGATTGCAACTGCCGGCG 62.387 63.158 23.90 18.98 41.18 6.46
2306 2330 3.070018 CGGAGAACAAGAGATTGCAACT 58.930 45.455 0.00 0.56 0.00 3.16
2315 2339 1.202651 ACAACCACCGGAGAACAAGAG 60.203 52.381 9.46 0.00 0.00 2.85
2333 2357 5.386958 AGCATTCGAACTAGAGTTGTACA 57.613 39.130 0.00 0.00 38.56 2.90
2351 2376 2.634940 AGGCAGGTGTTATATCGAGCAT 59.365 45.455 0.00 0.00 0.00 3.79
2354 2379 4.279671 AGAAGAGGCAGGTGTTATATCGAG 59.720 45.833 0.00 0.00 0.00 4.04
2358 2383 4.561752 AGGAGAAGAGGCAGGTGTTATAT 58.438 43.478 0.00 0.00 0.00 0.86
2376 2401 4.286297 TGGACCAAACAAGTATGAGGAG 57.714 45.455 0.00 0.00 0.00 3.69
2379 2404 7.029563 GCTTAAATGGACCAAACAAGTATGAG 58.970 38.462 0.00 0.00 0.00 2.90
2387 2412 3.482436 ACTCGCTTAAATGGACCAAACA 58.518 40.909 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.