Multiple sequence alignment - TraesCS3A01G281300

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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 TraesCS3A01G281300 chr3A 100.000 2198 0 0 1 2198 510006061 510008258 0.000000e+00 4060.0
1 TraesCS3A01G281300 chr3D 90.831 818 51 12 558 1369 389136137 389136936 0.000000e+00 1074.0
2 TraesCS3A01G281300 chr3D 92.679 683 21 10 1521 2198 389139064 389139722 0.000000e+00 957.0
3 TraesCS3A01G281300 chr3D 82.801 564 69 14 1 560 389086667 389087206 1.530000e-131 479.0
4 TraesCS3A01G281300 chr3D 90.780 141 5 5 1374 1511 389138841 389138976 4.820000e-42 182.0
5 TraesCS3A01G281300 chr3D 82.895 76 12 1 600 674 44203188 44203113 1.410000e-07 67.6
6 TraesCS3A01G281300 chr3B 87.312 733 73 9 1 714 506730719 506731450 0.000000e+00 821.0
7 TraesCS3A01G281300 chr3B 90.679 633 24 13 708 1315 506733944 506734566 0.000000e+00 809.0
8 TraesCS3A01G281300 chr3B 92.391 92 7 0 1 92 506730277 506730368 4.920000e-27 132.0
9 TraesCS3A01G281300 chr1B 75.824 182 29 10 1022 1191 669751498 669751676 6.510000e-11 78.7


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 TraesCS3A01G281300 chr3A 510006061 510008258 2197 False 4060.000000 4060 100.000000 1 2198 1 chr3A.!!$F1 2197
1 TraesCS3A01G281300 chr3D 389136137 389139722 3585 False 737.666667 1074 91.430000 558 2198 3 chr3D.!!$F2 1640
2 TraesCS3A01G281300 chr3D 389086667 389087206 539 False 479.000000 479 82.801000 1 560 1 chr3D.!!$F1 559
3 TraesCS3A01G281300 chr3B 506730277 506734566 4289 False 587.333333 821 90.127333 1 1315 3 chr3B.!!$F1 1314

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
527 990 0.464193 GGCGGGCCGACCTATTTTTA 60.464 55.0 33.44 0.0 36.97 1.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1453 6349 2.030562 CCCACGGTGACACCTCAC 59.969 66.667 22.14 2.31 45.54 3.51 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
43 44 3.118112 AGTTGCTCCAATCCTCGATCAAT 60.118 43.478 0.00 0.00 0.00 2.57
45 46 2.435437 TGCTCCAATCCTCGATCAATCA 59.565 45.455 0.00 0.00 0.00 2.57
60 61 5.525012 CGATCAATCAGTTCTTTAGATGCCA 59.475 40.000 0.00 0.00 0.00 4.92
86 529 3.069729 GCCGGTAAAGAGTCCTATGATGT 59.930 47.826 1.90 0.00 0.00 3.06
137 581 1.954927 CCTTTATCTTCTCCGGTGCC 58.045 55.000 0.00 0.00 0.00 5.01
151 595 2.415776 CGGTGCCCGTCTTTACTTTTA 58.584 47.619 5.56 0.00 42.73 1.52
181 625 5.918608 ACACATAGATCATTACCGCTCTTT 58.081 37.500 0.00 0.00 0.00 2.52
184 628 5.986135 ACATAGATCATTACCGCTCTTTCAC 59.014 40.000 0.00 0.00 0.00 3.18
207 651 7.550551 TCACTATTCCAACTAAATCTTCTGCAG 59.449 37.037 7.63 7.63 0.00 4.41
212 656 6.061441 TCCAACTAAATCTTCTGCAGAAACA 58.939 36.000 28.16 18.52 34.16 2.83
236 680 6.715280 AGGGTACTGAATAATATGCATGGAG 58.285 40.000 10.16 0.00 0.00 3.86
266 710 5.435820 CCTAACGTAGGTAGATCCTTGAC 57.564 47.826 0.00 0.00 45.67 3.18
267 711 4.885907 CCTAACGTAGGTAGATCCTTGACA 59.114 45.833 0.00 0.00 45.67 3.58
280 739 1.098050 CTTGACATGGCTACCTTGGC 58.902 55.000 0.00 1.80 37.23 4.52
307 766 1.269569 TGACAGGCCGACATATTAGCG 60.270 52.381 0.00 0.00 0.00 4.26
388 848 3.804193 GCAAGGCTAGGCACGTGC 61.804 66.667 32.15 32.15 41.14 5.34
447 907 4.677584 TCATAGCACACAAACAACCAAAC 58.322 39.130 0.00 0.00 0.00 2.93
453 913 3.130340 CACACAAACAACCAAACTAGGCT 59.870 43.478 0.00 0.00 0.00 4.58
488 951 1.003118 ACAGGCCTAAAATCACGCAGA 59.997 47.619 3.98 0.00 0.00 4.26
491 954 2.500098 AGGCCTAAAATCACGCAGACTA 59.500 45.455 1.29 0.00 0.00 2.59
527 990 0.464193 GGCGGGCCGACCTATTTTTA 60.464 55.000 33.44 0.00 36.97 1.52
541 1004 5.010213 ACCTATTTTTATTGTTGTGGCGTGT 59.990 36.000 0.00 0.00 0.00 4.49
568 1031 4.265056 GAGGTTGGGCACGTGGGT 62.265 66.667 18.88 0.00 0.00 4.51
606 1069 4.386951 CGGGTCATGGCCGACACA 62.387 66.667 10.95 0.00 39.41 3.72
681 1144 3.624900 GACACAGCCCGTTTAGTTTTTC 58.375 45.455 0.00 0.00 0.00 2.29
770 3735 0.887387 TGGTGGGCTAAAAGTGCGAC 60.887 55.000 0.00 0.00 0.00 5.19
804 3769 4.988598 CCTCGTTGTGCCGTGCCT 62.989 66.667 0.00 0.00 0.00 4.75
887 3856 2.287117 TGGCCACCAGATCCCCAT 60.287 61.111 0.00 0.00 0.00 4.00
888 3857 2.386100 TGGCCACCAGATCCCCATC 61.386 63.158 0.00 0.00 0.00 3.51
889 3858 2.111878 GCCACCAGATCCCCATCG 59.888 66.667 0.00 0.00 33.75 3.84
890 3859 2.111878 CCACCAGATCCCCATCGC 59.888 66.667 0.00 0.00 33.75 4.58
891 3860 2.745308 CCACCAGATCCCCATCGCA 61.745 63.158 0.00 0.00 33.75 5.10
1200 4193 1.229359 CCTCTCCCCCGTGTAGCTA 59.771 63.158 0.00 0.00 0.00 3.32
1202 4195 1.705873 CTCTCCCCCGTGTAGCTATT 58.294 55.000 0.00 0.00 0.00 1.73
1326 4320 0.690192 TCCTTGATTGCCACCGAGAA 59.310 50.000 0.00 0.00 0.00 2.87
1332 4326 0.252197 ATTGCCACCGAGAACCTACC 59.748 55.000 0.00 0.00 0.00 3.18
1334 4328 1.218316 GCCACCGAGAACCTACCAG 59.782 63.158 0.00 0.00 0.00 4.00
1338 4332 1.405821 CACCGAGAACCTACCAGCTAG 59.594 57.143 0.00 0.00 0.00 3.42
1344 4338 5.507650 CCGAGAACCTACCAGCTAGTTTATC 60.508 48.000 0.00 0.00 0.00 1.75
1347 4341 5.958987 AGAACCTACCAGCTAGTTTATCTGT 59.041 40.000 0.00 0.00 0.00 3.41
1352 4346 7.730784 ACCTACCAGCTAGTTTATCTGTATGAT 59.269 37.037 0.00 0.00 39.11 2.45
1390 6286 6.852664 GCTACAATTAGTTGCAAATACTGGT 58.147 36.000 6.03 7.76 46.27 4.00
1395 6291 7.335924 ACAATTAGTTGCAAATACTGGTATCGT 59.664 33.333 6.03 0.00 38.96 3.73
1452 6348 0.995024 CACCCTTTGAGATGGGAGGT 59.005 55.000 4.93 0.00 46.15 3.85
1453 6349 0.995024 ACCCTTTGAGATGGGAGGTG 59.005 55.000 4.93 0.00 46.15 4.00
1454 6350 0.995024 CCCTTTGAGATGGGAGGTGT 59.005 55.000 0.00 0.00 46.15 4.16
1463 6359 0.473694 ATGGGAGGTGTGAGGTGTCA 60.474 55.000 0.00 0.00 0.00 3.58
1478 6374 4.680237 TCACCGTGGGAGCAAGCG 62.680 66.667 0.00 0.00 0.00 4.68
1498 6395 3.772932 CGCAGGTACGGTGTTTATAAGA 58.227 45.455 0.00 0.00 0.00 2.10
1500 6397 4.807304 CGCAGGTACGGTGTTTATAAGATT 59.193 41.667 0.00 0.00 0.00 2.40
1502 6399 6.509039 CGCAGGTACGGTGTTTATAAGATTTC 60.509 42.308 0.00 0.00 0.00 2.17
1504 6401 7.465513 GCAGGTACGGTGTTTATAAGATTTCTG 60.466 40.741 0.00 0.00 0.00 3.02
1563 6539 9.139174 CTTGCATACATATACAATATGTGACGA 57.861 33.333 18.42 9.26 38.47 4.20
1614 6590 7.964559 CGATGAAAACATGACATCTTGTACAAT 59.035 33.333 9.13 0.00 38.43 2.71
1617 6593 9.500785 TGAAAACATGACATCTTGTACAATAGA 57.499 29.630 9.13 4.07 34.38 1.98
1700 6677 7.918076 TCTTGAACAAGGAAGGTACTCATATT 58.082 34.615 13.46 0.00 36.95 1.28
1777 6754 6.112734 TCCGCTAATTACAGACAAATCACAT 58.887 36.000 0.00 0.00 0.00 3.21
1807 6784 4.714802 GCTTACAGGTAAAATGGGGGAAAT 59.285 41.667 0.00 0.00 0.00 2.17
1808 6785 5.188948 GCTTACAGGTAAAATGGGGGAAATT 59.811 40.000 0.00 0.00 0.00 1.82
1905 6882 9.995594 AATGCTTTGGGGTATATACAATCATAT 57.004 29.630 14.70 0.00 0.00 1.78
1953 6930 8.437575 TCCTCCATATCACCTAAAAATAGAACC 58.562 37.037 0.00 0.00 0.00 3.62
1960 6937 7.837202 TCACCTAAAAATAGAACCGTATGTG 57.163 36.000 0.00 0.00 0.00 3.21
1965 6942 5.773239 AAAATAGAACCGTATGTGTGACG 57.227 39.130 0.00 0.00 40.02 4.35
1998 6975 7.829211 TCCTTTAGATCTAACAATTTGTGAGGG 59.171 37.037 14.85 5.66 29.53 4.30
2013 6990 6.566079 TTGTGAGGGTAAGATTCAGATGAT 57.434 37.500 0.00 0.00 0.00 2.45
2165 7145 7.011389 TGACAGTTAAACACTCAATCTTCAGTG 59.989 37.037 0.00 0.00 44.83 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 5.525012 TGGCATCTAAAGAACTGATTGATCG 59.475 40.000 0.00 0.00 0.00 3.69
43 44 2.354704 CCCGTGGCATCTAAAGAACTGA 60.355 50.000 0.00 0.00 0.00 3.41
45 46 2.403252 CCCGTGGCATCTAAAGAACT 57.597 50.000 0.00 0.00 0.00 3.01
60 61 2.653087 GGACTCTTTACCGGCCCGT 61.653 63.158 0.00 1.41 0.00 5.28
86 529 1.107538 CCTCTCACCCGAATAGGCGA 61.108 60.000 0.00 0.00 39.21 5.54
169 613 5.353394 TGGAATAGTGAAAGAGCGGTAAT 57.647 39.130 0.00 0.00 0.00 1.89
175 619 8.499403 AGATTTAGTTGGAATAGTGAAAGAGC 57.501 34.615 0.00 0.00 0.00 4.09
181 625 7.394016 TGCAGAAGATTTAGTTGGAATAGTGA 58.606 34.615 0.00 0.00 0.00 3.41
184 628 8.498054 TTCTGCAGAAGATTTAGTTGGAATAG 57.502 34.615 25.16 0.00 33.93 1.73
207 651 7.801716 TGCATATTATTCAGTACCCTGTTTC 57.198 36.000 0.00 0.00 39.82 2.78
212 656 6.702449 TCCATGCATATTATTCAGTACCCT 57.298 37.500 0.00 0.00 0.00 4.34
236 680 1.821258 CCTACGTTAGGTGAGGGGC 59.179 63.158 0.00 0.00 41.18 5.80
254 698 3.643792 AGGTAGCCATGTCAAGGATCTAC 59.356 47.826 0.00 1.33 0.00 2.59
280 739 2.046023 TCGGCCTGTCAAGCATGG 60.046 61.111 0.00 0.00 0.00 3.66
282 741 0.541392 TATGTCGGCCTGTCAAGCAT 59.459 50.000 0.00 0.00 0.00 3.79
286 745 2.801699 CGCTAATATGTCGGCCTGTCAA 60.802 50.000 0.00 0.00 0.00 3.18
350 810 1.227380 CTCATGCACGACCCTAGGC 60.227 63.158 2.05 0.00 0.00 3.93
388 848 2.026014 GGTTGTGTTGTGCCAGCG 59.974 61.111 0.00 0.00 0.00 5.18
462 925 4.007659 CGTGATTTTAGGCCTGTTAAGGT 58.992 43.478 17.99 0.02 46.43 3.50
466 929 3.006940 CTGCGTGATTTTAGGCCTGTTA 58.993 45.455 17.99 0.00 0.00 2.41
469 932 1.398390 GTCTGCGTGATTTTAGGCCTG 59.602 52.381 17.99 0.00 0.00 4.85
488 951 0.618981 GGCAGGTTTAGCCCACTAGT 59.381 55.000 0.00 0.00 46.50 2.57
521 984 4.981674 CAGACACGCCACAACAATAAAAAT 59.018 37.500 0.00 0.00 0.00 1.82
522 985 4.355437 CAGACACGCCACAACAATAAAAA 58.645 39.130 0.00 0.00 0.00 1.94
527 990 1.172180 CCCAGACACGCCACAACAAT 61.172 55.000 0.00 0.00 0.00 2.71
541 1004 2.935481 CCAACCTCCAGGCCCAGA 60.935 66.667 0.00 0.00 39.32 3.86
665 1128 5.135383 ACTAAAGGAAAAACTAAACGGGCT 58.865 37.500 0.00 0.00 0.00 5.19
666 1129 5.443185 ACTAAAGGAAAAACTAAACGGGC 57.557 39.130 0.00 0.00 0.00 6.13
770 3735 0.609131 AGGAAATGGGCCGACAACAG 60.609 55.000 0.00 0.00 0.00 3.16
811 3776 4.596585 CCCGGGTGCCCAGTGTTT 62.597 66.667 14.18 0.00 35.37 2.83
887 3856 0.324738 AGAGGAGGTTCAGGATGCGA 60.325 55.000 0.00 0.00 34.76 5.10
888 3857 0.103937 GAGAGGAGGTTCAGGATGCG 59.896 60.000 0.00 0.00 34.76 4.73
889 3858 0.467804 GGAGAGGAGGTTCAGGATGC 59.532 60.000 0.00 0.00 34.76 3.91
890 3859 2.038659 GAGGAGAGGAGGTTCAGGATG 58.961 57.143 0.00 0.00 37.54 3.51
891 3860 1.936631 AGAGGAGAGGAGGTTCAGGAT 59.063 52.381 0.00 0.00 0.00 3.24
1200 4193 2.900337 GATCGGGCCGCGGAAAAT 60.900 61.111 33.48 16.05 0.00 1.82
1249 4242 7.803189 CGAAATTATTGGGGAGAAATACGAATG 59.197 37.037 0.00 0.00 0.00 2.67
1253 4246 6.854496 TCGAAATTATTGGGGAGAAATACG 57.146 37.500 0.00 0.00 0.00 3.06
1326 4320 7.067421 TCATACAGATAAACTAGCTGGTAGGT 58.933 38.462 17.30 8.74 45.96 3.08
1363 4359 7.189512 CAGTATTTGCAACTAATTGTAGCTCC 58.810 38.462 0.00 0.00 38.17 4.70
1369 4365 7.335924 ACGATACCAGTATTTGCAACTAATTGT 59.664 33.333 0.00 2.30 38.17 2.71
1370 4366 7.639850 CACGATACCAGTATTTGCAACTAATTG 59.360 37.037 0.00 0.00 38.99 2.32
1372 4368 7.045416 TCACGATACCAGTATTTGCAACTAAT 58.955 34.615 0.00 0.00 0.00 1.73
1390 6286 8.904099 TGAGACTCTAATACATTCTCACGATA 57.096 34.615 3.68 0.00 38.20 2.92
1395 6291 7.201741 CGTCCTTGAGACTCTAATACATTCTCA 60.202 40.741 3.68 0.00 43.91 3.27
1408 6304 2.250348 CGAACTCGTCCTTGAGACTC 57.750 55.000 0.00 0.00 43.91 3.36
1453 6349 2.030562 CCCACGGTGACACCTCAC 59.969 66.667 22.14 2.31 45.54 3.51
1454 6350 2.123208 TCCCACGGTGACACCTCA 60.123 61.111 22.14 0.00 35.66 3.86
1478 6374 6.537660 AGAAATCTTATAAACACCGTACCTGC 59.462 38.462 0.00 0.00 0.00 4.85
1498 6395 9.293404 CTCCCAAATACATCATACATCAGAAAT 57.707 33.333 0.00 0.00 0.00 2.17
1500 6397 7.805163 ACTCCCAAATACATCATACATCAGAA 58.195 34.615 0.00 0.00 0.00 3.02
1502 6399 8.588472 TCTACTCCCAAATACATCATACATCAG 58.412 37.037 0.00 0.00 0.00 2.90
1504 6401 9.778741 TTTCTACTCCCAAATACATCATACATC 57.221 33.333 0.00 0.00 0.00 3.06
1511 6408 9.899226 GCATTAATTTCTACTCCCAAATACATC 57.101 33.333 0.00 0.00 0.00 3.06
1512 6409 9.646522 AGCATTAATTTCTACTCCCAAATACAT 57.353 29.630 0.00 0.00 0.00 2.29
1513 6410 9.474313 AAGCATTAATTTCTACTCCCAAATACA 57.526 29.630 0.00 0.00 0.00 2.29
1514 6411 9.736023 CAAGCATTAATTTCTACTCCCAAATAC 57.264 33.333 0.00 0.00 0.00 1.89
1516 6413 7.093377 TGCAAGCATTAATTTCTACTCCCAAAT 60.093 33.333 0.00 0.00 0.00 2.32
1519 6416 5.260424 TGCAAGCATTAATTTCTACTCCCA 58.740 37.500 0.00 0.00 0.00 4.37
1571 6547 9.997482 GTTTTCATCGCACCTTATCTTTAATTA 57.003 29.630 0.00 0.00 0.00 1.40
1576 6552 5.957842 TGTTTTCATCGCACCTTATCTTT 57.042 34.783 0.00 0.00 0.00 2.52
1717 6694 9.161629 TGTACAATGGTGATTCTTAGTAATGTG 57.838 33.333 0.00 0.00 0.00 3.21
1718 6695 9.905713 ATGTACAATGGTGATTCTTAGTAATGT 57.094 29.630 0.00 0.00 0.00 2.71
1807 6784 9.513906 CATCCCCAACATGTTATGTGTATATAA 57.486 33.333 11.53 0.00 44.07 0.98
1808 6785 8.885346 TCATCCCCAACATGTTATGTGTATATA 58.115 33.333 11.53 0.00 44.07 0.86
1905 6882 5.872617 GGACAATATACGCAGCAATGGTATA 59.127 40.000 0.00 0.00 34.62 1.47
1906 6883 4.695455 GGACAATATACGCAGCAATGGTAT 59.305 41.667 0.00 0.00 0.00 2.73
1953 6930 3.560481 AGGAGACTATCGTCACACATACG 59.440 47.826 0.00 0.00 42.73 3.06
1960 6937 6.870971 AGATCTAAAGGAGACTATCGTCAC 57.129 41.667 0.00 0.00 42.68 3.67
2078 7055 7.015877 ACAACTCTATAGACAAACCACCTGTAA 59.984 37.037 0.00 0.00 0.00 2.41
2134 7111 8.281212 AGATTGAGTGTTTAACTGTCAAACTT 57.719 30.769 7.97 0.00 40.07 2.66
2140 7117 7.348201 CACTGAAGATTGAGTGTTTAACTGTC 58.652 38.462 4.26 0.00 40.07 3.51
2165 7145 3.735746 GCACCTGAACAAACAACTAATGC 59.264 43.478 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.