Multiple sequence alignment - TraesCS2A01G330300

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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 TraesCS2A01G330300 chr2A 100.000 2756 0 0 1 2756 562680363 562683118 0.000000e+00 5090.0
1 TraesCS2A01G330300 chr2A 96.460 904 17 7 1860 2756 702857299 702856404 0.000000e+00 1478.0
2 TraesCS2A01G330300 chr2D 92.180 1867 99 19 1 1834 425495537 425493685 0.000000e+00 2595.0
3 TraesCS2A01G330300 chr2B 91.525 1829 101 19 43 1834 500839353 500837542 0.000000e+00 2470.0
4 TraesCS2A01G330300 chr2B 91.304 46 4 0 4 49 500840734 500840689 2.290000e-06 63.9
5 TraesCS2A01G330300 chr4A 94.481 906 34 11 1860 2756 45375833 45374935 0.000000e+00 1382.0
6 TraesCS2A01G330300 chr3A 94.157 907 36 12 1860 2756 26581193 26582092 0.000000e+00 1365.0
7 TraesCS2A01G330300 chr5A 76.838 272 57 6 1100 1368 475525750 475525482 6.150000e-32 148.0
8 TraesCS2A01G330300 chr5D 76.471 272 58 6 1100 1368 372325198 372324930 2.860000e-30 143.0


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 TraesCS2A01G330300 chr2A 562680363 562683118 2755 False 5090.00 5090 100.0000 1 2756 1 chr2A.!!$F1 2755
1 TraesCS2A01G330300 chr2A 702856404 702857299 895 True 1478.00 1478 96.4600 1860 2756 1 chr2A.!!$R1 896
2 TraesCS2A01G330300 chr2D 425493685 425495537 1852 True 2595.00 2595 92.1800 1 1834 1 chr2D.!!$R1 1833
3 TraesCS2A01G330300 chr2B 500837542 500840734 3192 True 1266.95 2470 91.4145 4 1834 2 chr2B.!!$R1 1830
4 TraesCS2A01G330300 chr4A 45374935 45375833 898 True 1382.00 1382 94.4810 1860 2756 1 chr4A.!!$R1 896
5 TraesCS2A01G330300 chr3A 26581193 26582092 899 False 1365.00 1365 94.1570 1860 2756 1 chr3A.!!$F1 896

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
35 36 0.391528 TCAGCCGTGACATGGACATG 60.392 55.0 18.32 11.9 44.15 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1885 3269 0.106519 AGGGCGCTGCTATGGAAAAT 60.107 50.0 7.64 0.0 0.0 1.82 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
35 36 0.391528 TCAGCCGTGACATGGACATG 60.392 55.000 18.32 11.90 44.15 3.21
54 1397 6.093219 GGACATGTATGCTATTATCTGGCTTG 59.907 42.308 0.00 0.00 31.45 4.01
87 1430 2.265904 TACGTGCGCTGGTGAGACT 61.266 57.895 9.73 0.00 0.00 3.24
214 1564 1.859703 CGTGCATCAGAGATTCAGAGC 59.140 52.381 0.00 0.00 0.00 4.09
216 1566 1.479730 TGCATCAGAGATTCAGAGCGT 59.520 47.619 0.00 0.00 0.00 5.07
217 1567 1.859703 GCATCAGAGATTCAGAGCGTG 59.140 52.381 0.00 0.00 0.00 5.34
218 1568 2.738000 GCATCAGAGATTCAGAGCGTGT 60.738 50.000 0.00 0.00 0.00 4.49
219 1569 3.519579 CATCAGAGATTCAGAGCGTGTT 58.480 45.455 0.00 0.00 0.00 3.32
220 1570 4.676546 CATCAGAGATTCAGAGCGTGTTA 58.323 43.478 0.00 0.00 0.00 2.41
279 1649 7.611079 TCATCATTCATCATACCTGTGTTTTGA 59.389 33.333 0.00 0.00 0.00 2.69
298 1668 2.591429 TTGGCCGACACAGCACTG 60.591 61.111 0.00 0.00 0.00 3.66
381 1751 4.079253 TCTGCATTTTTGTAGAGGGTTCC 58.921 43.478 0.00 0.00 0.00 3.62
402 1772 2.742372 GTGCATTCCGTCGGTGCT 60.742 61.111 22.86 3.30 39.52 4.40
418 1788 4.080807 TCGGTGCTCCCATTTTAATACTCA 60.081 41.667 0.00 0.00 0.00 3.41
419 1789 4.821805 CGGTGCTCCCATTTTAATACTCAT 59.178 41.667 0.00 0.00 0.00 2.90
478 1848 9.733556 TGTACTATTCTATTTTGGAAAAGCTCA 57.266 29.630 0.00 0.00 0.00 4.26
541 1911 2.392181 CCGGCCGTGTAAATCGCAA 61.392 57.895 26.12 0.00 0.00 4.85
599 1969 6.478512 TCATCACAACATAGTACTATGCCA 57.521 37.500 33.26 17.98 45.06 4.92
613 1983 4.666512 ACTATGCCAGAAGGTTTTGACAT 58.333 39.130 0.00 0.00 37.19 3.06
615 1985 1.879380 TGCCAGAAGGTTTTGACATCG 59.121 47.619 0.00 0.00 37.19 3.84
650 2020 3.813724 AGCCCGAGAAAACTTTACTGAAC 59.186 43.478 0.00 0.00 0.00 3.18
682 2052 1.142474 CTGTTTGTTCCGACGTACCC 58.858 55.000 0.00 0.00 0.00 3.69
960 2332 3.842732 TGCTCATCATCTGCACTTTTG 57.157 42.857 0.00 0.00 0.00 2.44
961 2333 3.151554 TGCTCATCATCTGCACTTTTGT 58.848 40.909 0.00 0.00 0.00 2.83
962 2334 4.325972 TGCTCATCATCTGCACTTTTGTA 58.674 39.130 0.00 0.00 0.00 2.41
963 2335 4.393990 TGCTCATCATCTGCACTTTTGTAG 59.606 41.667 0.00 0.00 36.82 2.74
964 2336 4.730035 GCTCATCATCTGCACTTTTGTAGC 60.730 45.833 0.00 0.00 35.52 3.58
966 2338 4.761227 TCATCATCTGCACTTTTGTAGCAA 59.239 37.500 0.00 0.00 36.55 3.91
967 2339 4.754372 TCATCTGCACTTTTGTAGCAAG 57.246 40.909 0.00 0.00 36.55 4.01
976 2348 5.748592 CACTTTTGTAGCAAGTCCTGTAAC 58.251 41.667 0.00 0.00 31.83 2.50
977 2349 4.510340 ACTTTTGTAGCAAGTCCTGTAACG 59.490 41.667 0.00 0.00 27.49 3.18
983 2355 0.865769 CAAGTCCTGTAACGCACACC 59.134 55.000 0.00 0.00 32.33 4.16
984 2356 0.466543 AAGTCCTGTAACGCACACCA 59.533 50.000 0.00 0.00 32.33 4.17
1012 2384 0.405198 TGCAGAAATGGAGCCCAAGA 59.595 50.000 0.00 0.00 36.95 3.02
1260 2632 4.814294 ATCACCGTCTTCGCGCCC 62.814 66.667 0.00 0.00 35.54 6.13
1364 2736 1.837090 CCATGCCCAGGTACTACCC 59.163 63.158 1.19 0.00 39.75 3.69
1381 2753 3.452786 CGCTCTCGGCCTTCTCCA 61.453 66.667 0.00 0.00 37.74 3.86
1382 2754 2.982130 GCTCTCGGCCTTCTCCAA 59.018 61.111 0.00 0.00 34.27 3.53
1412 2784 2.717044 CGAGCCCGGTGTCCATGTA 61.717 63.158 0.00 0.00 0.00 2.29
1680 3064 3.449042 GACGCCAAGAGTTCGTCG 58.551 61.111 0.00 0.00 42.18 5.12
1728 3112 1.539827 GCATTTGGCTACGTGGTTCTT 59.460 47.619 0.00 0.00 40.25 2.52
1751 3135 1.378514 TCTCCGGGCTTTTGATGGC 60.379 57.895 0.00 0.00 0.00 4.40
1758 3142 0.733150 GGCTTTTGATGGCGTAGTCC 59.267 55.000 0.00 0.00 0.00 3.85
1777 3161 3.002246 GTCCGATAATTCTTTGCATGCGA 59.998 43.478 14.09 8.74 0.00 5.10
1834 3218 8.785101 CGGAAAGTGTTCGTAAATTCATTTATG 58.215 33.333 5.46 5.46 39.46 1.90
1835 3219 9.072294 GGAAAGTGTTCGTAAATTCATTTATGG 57.928 33.333 10.34 1.21 38.91 2.74
1836 3220 8.980143 AAAGTGTTCGTAAATTCATTTATGGG 57.020 30.769 10.34 0.00 38.91 4.00
1837 3221 7.696992 AGTGTTCGTAAATTCATTTATGGGT 57.303 32.000 10.34 0.00 38.91 4.51
1838 3222 7.535139 AGTGTTCGTAAATTCATTTATGGGTG 58.465 34.615 10.34 0.00 38.91 4.61
1839 3223 7.175990 AGTGTTCGTAAATTCATTTATGGGTGT 59.824 33.333 10.34 0.00 38.91 4.16
1840 3224 7.272515 GTGTTCGTAAATTCATTTATGGGTGTG 59.727 37.037 10.34 0.00 38.91 3.82
1841 3225 7.040340 TGTTCGTAAATTCATTTATGGGTGTGT 60.040 33.333 10.34 0.00 38.91 3.72
1842 3226 7.455641 TCGTAAATTCATTTATGGGTGTGTT 57.544 32.000 10.34 0.00 38.91 3.32
1843 3227 7.887381 TCGTAAATTCATTTATGGGTGTGTTT 58.113 30.769 10.34 0.00 38.91 2.83
1844 3228 9.011095 TCGTAAATTCATTTATGGGTGTGTTTA 57.989 29.630 10.34 0.00 38.91 2.01
1845 3229 9.284594 CGTAAATTCATTTATGGGTGTGTTTAG 57.715 33.333 4.23 0.00 36.23 1.85
1849 3233 9.479549 AATTCATTTATGGGTGTGTTTAGATCT 57.520 29.630 0.00 0.00 0.00 2.75
1850 3234 8.506168 TTCATTTATGGGTGTGTTTAGATCTC 57.494 34.615 0.00 0.00 0.00 2.75
1851 3235 7.629157 TCATTTATGGGTGTGTTTAGATCTCA 58.371 34.615 0.00 0.00 0.00 3.27
1852 3236 7.770433 TCATTTATGGGTGTGTTTAGATCTCAG 59.230 37.037 0.00 0.00 0.00 3.35
1853 3237 6.620877 TTATGGGTGTGTTTAGATCTCAGT 57.379 37.500 0.00 0.00 0.00 3.41
1854 3238 4.537135 TGGGTGTGTTTAGATCTCAGTC 57.463 45.455 0.00 0.00 0.00 3.51
1855 3239 3.901222 TGGGTGTGTTTAGATCTCAGTCA 59.099 43.478 0.00 0.00 0.00 3.41
1856 3240 4.346709 TGGGTGTGTTTAGATCTCAGTCAA 59.653 41.667 0.00 0.00 0.00 3.18
1857 3241 4.691216 GGGTGTGTTTAGATCTCAGTCAAC 59.309 45.833 0.00 0.00 0.00 3.18
1858 3242 5.511545 GGGTGTGTTTAGATCTCAGTCAACT 60.512 44.000 0.00 0.00 0.00 3.16
2122 3511 6.030548 TCTTGTTTTGTTGACAAACCATCA 57.969 33.333 8.70 4.49 44.56 3.07
2148 3540 4.156008 GGACCACAAAATATTCGCTCACTT 59.844 41.667 0.00 0.00 0.00 3.16
2149 3541 5.335661 GGACCACAAAATATTCGCTCACTTT 60.336 40.000 0.00 0.00 0.00 2.66
2150 3542 6.084326 ACCACAAAATATTCGCTCACTTTT 57.916 33.333 0.00 0.00 0.00 2.27
2182 3574 7.346751 AGCTGAAGAAAAAGGTAAACAATGA 57.653 32.000 0.00 0.00 0.00 2.57
2211 3603 4.388378 ACTAGAGGAAAAGGATGTACGC 57.612 45.455 0.00 0.00 0.00 4.42
2223 3615 3.938963 AGGATGTACGCGTTGAATCATTT 59.061 39.130 20.78 5.49 0.00 2.32
2345 3737 3.430651 CGCCCTAACAATGGAAATGCAAT 60.431 43.478 0.00 0.00 0.00 3.56
2380 3774 1.877637 ATGTGTATGTGTGTGTGCGT 58.122 45.000 0.00 0.00 0.00 5.24
2476 3870 7.098477 GGTGTATGTGGTGTTTGTATGTACTA 58.902 38.462 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 4.583871 AGCCAAGCCAGATAATAGCATAC 58.416 43.478 0.00 0.00 0.00 2.39
41 1384 4.621510 CGAGCATAGCCAAGCCAGATAATA 60.622 45.833 0.00 0.00 0.00 0.98
176 1526 1.205064 GTAGTTGTGCTGCACTGCG 59.795 57.895 30.43 0.00 35.11 5.18
252 1622 7.943079 AAACACAGGTATGATGAATGATGAA 57.057 32.000 0.00 0.00 0.00 2.57
253 1623 7.611079 TCAAAACACAGGTATGATGAATGATGA 59.389 33.333 0.00 0.00 0.00 2.92
254 1624 7.764331 TCAAAACACAGGTATGATGAATGATG 58.236 34.615 0.00 0.00 0.00 3.07
255 1625 7.613022 ACTCAAAACACAGGTATGATGAATGAT 59.387 33.333 0.00 0.00 0.00 2.45
271 1641 0.736053 TGTCGGCCAACTCAAAACAC 59.264 50.000 2.24 0.00 0.00 3.32
279 1649 2.591715 GTGCTGTGTCGGCCAACT 60.592 61.111 2.24 0.00 34.37 3.16
381 1751 3.853330 CCGACGGAATGCACAGCG 61.853 66.667 8.64 0.00 0.00 5.18
402 1772 6.494666 AGACCGATGAGTATTAAAATGGGA 57.505 37.500 0.00 0.00 0.00 4.37
418 1788 9.967451 TTATCTAGAGAATAGATCAAGACCGAT 57.033 33.333 0.00 0.00 35.95 4.18
419 1789 9.967451 ATTATCTAGAGAATAGATCAAGACCGA 57.033 33.333 10.87 0.00 35.95 4.69
468 1838 6.720012 TGTTTTTGAAAACTGAGCTTTTCC 57.280 33.333 17.33 3.84 46.37 3.13
525 1895 1.427819 CCTTGCGATTTACACGGCC 59.572 57.895 0.00 0.00 0.00 6.13
527 1897 0.519519 TTGCCTTGCGATTTACACGG 59.480 50.000 0.00 0.00 0.00 4.94
541 1911 0.322906 GCTTAGCCCTTCAGTTGCCT 60.323 55.000 0.00 0.00 0.00 4.75
599 1969 2.851195 ACAGCGATGTCAAAACCTTCT 58.149 42.857 0.00 0.00 0.00 2.85
633 2003 5.977725 GCTTTGGGTTCAGTAAAGTTTTCTC 59.022 40.000 0.00 0.00 34.69 2.87
650 2020 0.527565 CAAACAGGATCCGCTTTGGG 59.472 55.000 21.20 5.27 38.76 4.12
674 2044 3.177249 GAACGCTGCGGGTACGTC 61.177 66.667 26.95 9.32 43.45 4.34
697 2069 6.361748 GTGACTGCAATTTTGTTCTTCTGATC 59.638 38.462 0.00 0.00 0.00 2.92
960 2332 1.725164 GTGCGTTACAGGACTTGCTAC 59.275 52.381 0.00 0.00 0.00 3.58
961 2333 1.341852 TGTGCGTTACAGGACTTGCTA 59.658 47.619 0.00 0.00 33.42 3.49
962 2334 0.105964 TGTGCGTTACAGGACTTGCT 59.894 50.000 0.00 0.00 33.42 3.91
963 2335 0.234884 GTGTGCGTTACAGGACTTGC 59.765 55.000 0.00 0.00 40.69 4.01
964 2336 0.865769 GGTGTGCGTTACAGGACTTG 59.134 55.000 0.00 0.00 40.69 3.16
966 2338 0.685097 ATGGTGTGCGTTACAGGACT 59.315 50.000 0.00 0.00 40.69 3.85
967 2339 1.076332 GATGGTGTGCGTTACAGGAC 58.924 55.000 0.00 0.00 40.69 3.85
976 2348 1.130955 GCAAAACTTGATGGTGTGCG 58.869 50.000 0.00 0.00 0.00 5.34
977 2349 2.129607 CTGCAAAACTTGATGGTGTGC 58.870 47.619 0.00 0.00 34.01 4.57
983 2355 4.387862 GCTCCATTTCTGCAAAACTTGATG 59.612 41.667 0.00 0.00 0.00 3.07
984 2356 4.562143 GGCTCCATTTCTGCAAAACTTGAT 60.562 41.667 0.00 0.00 0.00 2.57
1297 2669 1.147376 CGGTGGTGAGGTTGGACAA 59.853 57.895 0.00 0.00 0.00 3.18
1364 2736 2.897641 CTTGGAGAAGGCCGAGAGCG 62.898 65.000 0.00 0.00 45.17 5.03
1412 2784 0.936297 GACGTTCACCTTGTACGCGT 60.936 55.000 19.17 19.17 43.43 6.01
1711 3095 2.489971 CAGAAGAACCACGTAGCCAAA 58.510 47.619 0.00 0.00 0.00 3.28
1728 3112 1.125093 TCAAAAGCCCGGAGACCAGA 61.125 55.000 0.73 0.00 0.00 3.86
1751 3135 5.670097 CATGCAAAGAATTATCGGACTACG 58.330 41.667 0.00 0.00 46.11 3.51
1758 3142 3.910170 CCATCGCATGCAAAGAATTATCG 59.090 43.478 19.57 0.00 0.00 2.92
1785 3169 5.231991 CGGAAGGAAATAAAAATTCATGGCG 59.768 40.000 0.00 0.00 0.00 5.69
1834 3218 4.537135 TGACTGAGATCTAAACACACCC 57.463 45.455 0.00 0.00 0.00 4.61
1835 3219 5.542779 AGTTGACTGAGATCTAAACACACC 58.457 41.667 0.00 0.00 0.00 4.16
1836 3220 7.371936 ACTAGTTGACTGAGATCTAAACACAC 58.628 38.462 0.00 0.00 0.00 3.82
1837 3221 7.526142 ACTAGTTGACTGAGATCTAAACACA 57.474 36.000 0.00 0.00 0.00 3.72
1838 3222 6.743627 CGACTAGTTGACTGAGATCTAAACAC 59.256 42.308 3.81 0.00 0.00 3.32
1839 3223 6.653740 TCGACTAGTTGACTGAGATCTAAACA 59.346 38.462 8.87 0.00 0.00 2.83
1840 3224 7.074507 TCGACTAGTTGACTGAGATCTAAAC 57.925 40.000 8.87 0.00 0.00 2.01
1841 3225 7.553044 TCATCGACTAGTTGACTGAGATCTAAA 59.447 37.037 15.25 0.00 0.00 1.85
1842 3226 7.011576 GTCATCGACTAGTTGACTGAGATCTAA 59.988 40.741 15.25 0.00 43.04 2.10
1843 3227 6.480651 GTCATCGACTAGTTGACTGAGATCTA 59.519 42.308 15.25 0.00 43.04 1.98
1844 3228 5.295787 GTCATCGACTAGTTGACTGAGATCT 59.704 44.000 15.25 0.00 43.04 2.75
1845 3229 5.507077 GTCATCGACTAGTTGACTGAGATC 58.493 45.833 15.25 5.72 43.04 2.75
1846 3230 4.034626 CGTCATCGACTAGTTGACTGAGAT 59.965 45.833 15.25 0.00 43.76 2.75
1847 3231 3.371285 CGTCATCGACTAGTTGACTGAGA 59.629 47.826 15.25 8.33 43.76 3.27
1848 3232 3.125487 ACGTCATCGACTAGTTGACTGAG 59.875 47.826 15.25 9.81 43.76 3.35
1849 3233 3.072211 ACGTCATCGACTAGTTGACTGA 58.928 45.455 15.25 15.48 43.76 3.41
1850 3234 3.120304 TGACGTCATCGACTAGTTGACTG 60.120 47.826 15.76 13.69 43.76 3.51
1851 3235 3.072211 TGACGTCATCGACTAGTTGACT 58.928 45.455 15.76 6.44 43.76 3.41
1852 3236 3.466712 TGACGTCATCGACTAGTTGAC 57.533 47.619 15.76 14.45 42.96 3.18
1853 3237 4.274421 GATGACGTCATCGACTAGTTGA 57.726 45.455 35.44 15.29 42.66 3.18
1883 3267 1.953686 GGGCGCTGCTATGGAAAATAA 59.046 47.619 7.64 0.00 0.00 1.40
1884 3268 1.142870 AGGGCGCTGCTATGGAAAATA 59.857 47.619 7.64 0.00 0.00 1.40
1885 3269 0.106519 AGGGCGCTGCTATGGAAAAT 60.107 50.000 7.64 0.00 0.00 1.82
2122 3511 4.192317 GAGCGAATATTTTGTGGTCCTCT 58.808 43.478 0.00 0.00 0.00 3.69
2148 3540 8.691661 ACCTTTTTCTTCAGCTTCTATGTAAA 57.308 30.769 0.00 0.00 0.00 2.01
2149 3541 9.787435 TTACCTTTTTCTTCAGCTTCTATGTAA 57.213 29.630 0.00 0.00 0.00 2.41
2150 3542 9.787435 TTTACCTTTTTCTTCAGCTTCTATGTA 57.213 29.630 0.00 0.00 0.00 2.29
2345 3737 6.377996 ACATACACATAGACTAACCCACGTTA 59.622 38.462 0.00 0.00 33.17 3.18
2519 3913 6.088824 GCGATCAACTTTTGAATTCATGAGT 58.911 36.000 9.40 12.87 43.95 3.41
2713 4113 1.134670 GGTGAGAGGGGATTGTCTTCG 60.135 57.143 0.00 0.00 0.00 3.79


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

AutoCloner maintained by Alex Coulton.