Multiple sequence alignment - TraesCS7A01G405900

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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 TraesCS7A01G405900 chr7A 100.000 3492 0 0 1 3492 589458032 589454541 0 6449
1 TraesCS7A01G405900 chr7D 91.102 3574 203 56 1 3492 515825639 515822099 0 4732
2 TraesCS7A01G405900 chr7B 90.997 2066 124 30 1474 3492 548165059 548163009 0 2728
3 TraesCS7A01G405900 chr7B 94.139 1399 43 8 1 1382 548166614 548165238 0 2093


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 TraesCS7A01G405900 chr7A 589454541 589458032 3491 True 6449.0 6449 100.000 1 3492 1 chr7A.!!$R1 3491
1 TraesCS7A01G405900 chr7D 515822099 515825639 3540 True 4732.0 4732 91.102 1 3492 1 chr7D.!!$R1 3491
2 TraesCS7A01G405900 chr7B 548163009 548166614 3605 True 2410.5 2728 92.568 1 3492 2 chr7B.!!$R1 3491

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
848 860 1.595382 CGCTCGGGCTTAGGGAATG 60.595 63.158 5.36 0.00 36.09 2.67 F
1772 1908 0.105593 AGACAGACCATATGGCGCTG 59.894 55.000 29.73 29.73 42.86 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1774 1910 0.103026 CCCTCGACGAAGATGATGCA 59.897 55.0 0.0 0.0 0.0 3.96 R
3426 3613 0.379669 CCACAATCATCTTCCGCTGC 59.620 55.0 0.0 0.0 0.0 5.25 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
44 51 4.681025 CCAAACACAACATGATAACAGCAC 59.319 41.667 0.00 0.00 0.00 4.40
51 58 8.615211 ACACAACATGATAACAGCACATATTAG 58.385 33.333 0.00 0.00 0.00 1.73
847 859 2.822399 CGCTCGGGCTTAGGGAAT 59.178 61.111 5.36 0.00 36.09 3.01
848 860 1.595382 CGCTCGGGCTTAGGGAATG 60.595 63.158 5.36 0.00 36.09 2.67
849 861 1.894282 GCTCGGGCTTAGGGAATGC 60.894 63.158 0.00 0.00 35.22 3.56
1144 1165 0.628522 TCCTCTCCTCTCCAGACAGG 59.371 60.000 0.00 0.00 39.47 4.00
1146 1167 1.000993 TCTCCTCTCCAGACAGGGC 59.999 63.158 0.00 0.00 38.24 5.19
1276 1297 2.866762 CGCCTATCTGCAGAAACCTAAC 59.133 50.000 22.50 5.97 0.00 2.34
1367 1390 3.476552 TCTCCTTGCTTTTGTTCGATGT 58.523 40.909 0.00 0.00 0.00 3.06
1378 1401 9.502145 TGCTTTTGTTCGATGTTAATATGATTC 57.498 29.630 0.00 0.00 0.00 2.52
1398 1482 8.821686 TGATTCATTGGTATCTGTTGGTTATT 57.178 30.769 0.00 0.00 0.00 1.40
1536 1647 4.134563 ACTACTTTGTTGAGAATTGCCGT 58.865 39.130 0.00 0.00 0.00 5.68
1564 1675 3.463944 TCCAGTTTGGAACTTTCTCGTC 58.536 45.455 0.00 0.00 45.00 4.20
1573 1684 6.847956 TGGAACTTTCTCGTCGAAATAAAA 57.152 33.333 0.00 0.00 40.62 1.52
1643 1779 1.374947 CGTGCCAGGGAGAAGGAAA 59.625 57.895 0.00 0.00 0.00 3.13
1667 1803 4.703575 TGGAGCTGGAATCAAAGATGAAAG 59.296 41.667 0.00 0.00 39.49 2.62
1677 1813 3.822735 TCAAAGATGAAAGCCAGAACCAG 59.177 43.478 0.00 0.00 30.99 4.00
1701 1837 2.656002 TCGAATTGACTCGAGATCCCT 58.344 47.619 21.68 0.00 42.69 4.20
1746 1882 2.023501 ACCAGAGCCCTGTCTCTAAGAT 60.024 50.000 0.00 0.00 41.22 2.40
1762 1898 0.323816 AGATCCAGCGAGACAGACCA 60.324 55.000 0.00 0.00 0.00 4.02
1771 1907 0.390860 GAGACAGACCATATGGCGCT 59.609 55.000 22.18 15.99 39.32 5.92
1772 1908 0.105593 AGACAGACCATATGGCGCTG 59.894 55.000 29.73 29.73 42.86 5.18
1773 1909 0.882042 GACAGACCATATGGCGCTGG 60.882 60.000 32.26 21.29 42.04 4.85
1775 1911 1.146930 AGACCATATGGCGCTGGTG 59.853 57.895 22.28 9.32 45.70 4.17
1776 1912 2.516930 ACCATATGGCGCTGGTGC 60.517 61.111 22.18 0.00 44.06 5.01
1782 1918 0.886043 TATGGCGCTGGTGCATCATC 60.886 55.000 7.64 0.00 39.64 2.92
1818 1954 4.693283 TCACATAGCAGTTCTTATTCGGG 58.307 43.478 0.00 0.00 0.00 5.14
1879 2015 5.462530 TTCTTCGATCAAGGTCAGTTACA 57.537 39.130 0.00 0.00 32.22 2.41
1886 2025 4.713824 TCAAGGTCAGTTACAGTATCCG 57.286 45.455 0.00 0.00 0.00 4.18
1888 2027 5.255687 TCAAGGTCAGTTACAGTATCCGTA 58.744 41.667 0.00 0.00 0.00 4.02
1893 2032 6.015180 AGGTCAGTTACAGTATCCGTAAACAA 60.015 38.462 0.00 0.00 30.96 2.83
1894 2033 6.089954 GGTCAGTTACAGTATCCGTAAACAAC 59.910 42.308 0.00 0.00 30.96 3.32
1896 2035 6.642131 TCAGTTACAGTATCCGTAAACAACAC 59.358 38.462 0.00 0.00 30.96 3.32
1897 2036 6.421501 CAGTTACAGTATCCGTAAACAACACA 59.578 38.462 0.00 0.00 30.96 3.72
1918 2057 9.442047 AACACAGGAGAAATTAAATAGTGAGAG 57.558 33.333 0.00 0.00 0.00 3.20
1997 2158 9.538508 CATGATCATAGTCTTACAATGTTCTCA 57.461 33.333 8.15 0.00 0.00 3.27
2033 2194 6.942532 ATGTGGTTAGCCTATACATTTGTG 57.057 37.500 0.00 0.00 35.27 3.33
2142 2310 2.439507 TGGTTCTAGAATGGATGAGCCC 59.560 50.000 8.75 2.36 34.97 5.19
2145 2313 1.051812 CTAGAATGGATGAGCCCGGT 58.948 55.000 0.00 0.00 34.97 5.28
2165 2333 1.770658 TCCATACCTCAAGCCTCCATG 59.229 52.381 0.00 0.00 0.00 3.66
2170 2338 1.522092 CTCAAGCCTCCATGCGGTA 59.478 57.895 0.00 0.00 36.02 4.02
2186 2354 1.398390 CGGTAGGCAAGACAATTCAGC 59.602 52.381 0.00 0.00 0.00 4.26
2196 2364 1.464997 GACAATTCAGCAAGTCCGGAC 59.535 52.381 27.67 27.67 0.00 4.79
2200 2368 3.114616 CAGCAAGTCCGGACGCAG 61.115 66.667 28.80 22.75 36.20 5.18
2214 2382 2.062519 GACGCAGGAGTGAAAGAAGAC 58.937 52.381 0.00 0.00 0.00 3.01
2311 2479 3.884169 TCGAAGCACAAGCACATAAAAC 58.116 40.909 0.00 0.00 45.49 2.43
2347 2515 1.337260 GCAGCAACCGAGAGAGAAAGA 60.337 52.381 0.00 0.00 0.00 2.52
2352 2520 3.580731 CAACCGAGAGAGAAAGAAGGAC 58.419 50.000 0.00 0.00 0.00 3.85
2357 2525 4.501571 CCGAGAGAGAAAGAAGGACAACAA 60.502 45.833 0.00 0.00 0.00 2.83
2570 2739 2.484264 ACTTCTACTTGGTGATTTGCGC 59.516 45.455 0.00 0.00 0.00 6.09
2637 2806 7.275888 TGCTCTGTTATGTTCTTCATTGTTT 57.724 32.000 0.00 0.00 37.91 2.83
2668 2837 5.105064 TCCCTTCTAAACAATCTACCCTTCG 60.105 44.000 0.00 0.00 0.00 3.79
2756 2926 4.732784 AGGCACATGCAGTAAAATTTACG 58.267 39.130 9.88 6.76 44.36 3.18
2927 3097 2.668632 GGATGCGTGGTTCCTCCA 59.331 61.111 0.00 0.00 45.01 3.86
3009 3180 9.803315 AAATTCAGTTAAGTTTCCTTTCAGAAC 57.197 29.630 0.00 0.00 31.89 3.01
3113 3296 4.022762 TGGTTTCATGTGTACATTTTCCCG 60.023 41.667 0.00 0.00 33.61 5.14
3294 3481 3.060000 GCAGTGCCAGCATCTGCA 61.060 61.111 27.27 4.09 43.57 4.41
3315 3502 6.985117 TGCAAAAGAGAGTTAAAATCAGCAT 58.015 32.000 0.00 0.00 0.00 3.79
3328 3515 3.437795 AGCATTGCTCAGCACGCC 61.438 61.111 15.24 0.00 38.71 5.68
3343 3530 2.303537 CACGCCGTTGTACAAATCAAC 58.696 47.619 10.51 0.00 40.89 3.18
3362 3549 6.653526 TCAACCTAATTATGGCATGATTGG 57.346 37.500 23.26 20.46 0.00 3.16
3365 3552 4.761739 ACCTAATTATGGCATGATTGGTCG 59.238 41.667 23.26 13.09 0.00 4.79
3370 3557 2.998316 TGGCATGATTGGTCGTATCA 57.002 45.000 0.00 0.00 36.53 2.15
3375 3562 3.871006 GCATGATTGGTCGTATCAGTTGA 59.129 43.478 0.00 0.00 35.63 3.18
3376 3563 4.025396 GCATGATTGGTCGTATCAGTTGAG 60.025 45.833 0.00 0.00 35.63 3.02
3377 3564 5.351458 CATGATTGGTCGTATCAGTTGAGA 58.649 41.667 0.00 0.00 35.63 3.27
3378 3565 5.598416 TGATTGGTCGTATCAGTTGAGAT 57.402 39.130 0.00 0.00 0.00 2.75
3379 3566 6.709018 TGATTGGTCGTATCAGTTGAGATA 57.291 37.500 0.00 0.00 0.00 1.98
3380 3567 7.107639 TGATTGGTCGTATCAGTTGAGATAA 57.892 36.000 0.00 0.00 32.64 1.75
3386 3573 7.081349 GGTCGTATCAGTTGAGATAAGATCAG 58.919 42.308 0.00 0.00 39.78 2.90
3399 3586 9.310449 TGAGATAAGATCAGATCAGATCATCAA 57.690 33.333 24.89 12.38 45.39 2.57
3416 3603 5.906073 TCATCAATGAAGAGATCTTGCGTA 58.094 37.500 0.00 0.00 36.11 4.42
3419 3606 4.509230 TCAATGAAGAGATCTTGCGTATGC 59.491 41.667 0.00 0.00 43.20 3.14
3453 3645 3.691609 GGAAGATGATTGTGGTTCTGGTC 59.308 47.826 0.00 0.00 0.00 4.02
3457 3649 3.126001 TGATTGTGGTTCTGGTCTGAC 57.874 47.619 0.00 0.00 0.00 3.51
3459 3651 1.116308 TTGTGGTTCTGGTCTGACGA 58.884 50.000 1.07 0.00 0.00 4.20
3468 3660 2.897326 TCTGGTCTGACGAAGATCCAAA 59.103 45.455 7.50 0.00 34.83 3.28
3469 3661 2.996621 CTGGTCTGACGAAGATCCAAAC 59.003 50.000 1.07 0.00 34.83 2.93
3474 3666 4.750098 GTCTGACGAAGATCCAAACTTTGA 59.250 41.667 2.87 0.00 37.23 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 51 3.741344 GGTGCGCAGTAGGAACTAATATG 59.259 47.826 12.22 0.00 45.48 1.78
51 58 2.813908 CCGGTGCGCAGTAGGAAC 60.814 66.667 12.22 0.00 0.00 3.62
448 455 4.218578 CGCCAGCTGCTCTCCGAT 62.219 66.667 8.66 0.00 38.05 4.18
844 856 2.182842 CCCACGCCTAGCAGCATTC 61.183 63.158 0.00 0.00 0.00 2.67
849 861 4.880537 CGAGCCCACGCCTAGCAG 62.881 72.222 0.00 0.00 34.57 4.24
919 940 1.949631 GCTTCCGCTTCCGTATCCG 60.950 63.158 0.00 0.00 0.00 4.18
923 944 2.998480 TGGGCTTCCGCTTCCGTA 60.998 61.111 0.00 0.00 36.09 4.02
1163 1184 1.223487 CCGTCCCCAAATCCATCGT 59.777 57.895 0.00 0.00 0.00 3.73
1378 1401 7.554118 ACTGAGAATAACCAACAGATACCAATG 59.446 37.037 0.00 0.00 33.53 2.82
1398 1482 3.308401 TCATATTAGCTGGGCACTGAGA 58.692 45.455 0.00 0.00 0.00 3.27
1508 1618 7.965107 GGCAATTCTCAACAAAGTAGTATCTTG 59.035 37.037 0.00 0.00 0.00 3.02
1514 1624 4.134563 ACGGCAATTCTCAACAAAGTAGT 58.865 39.130 0.00 0.00 0.00 2.73
1561 1672 8.488979 ACAAACAGAGAAATTTTATTTCGACG 57.511 30.769 6.52 0.00 33.86 5.12
1562 1673 9.665264 AGACAAACAGAGAAATTTTATTTCGAC 57.335 29.630 6.52 5.74 33.86 4.20
1564 1675 8.420189 GCAGACAAACAGAGAAATTTTATTTCG 58.580 33.333 6.52 0.00 33.86 3.46
1573 1684 3.216800 TGCTGCAGACAAACAGAGAAAT 58.783 40.909 20.43 0.00 35.90 2.17
1643 1779 4.515028 TCATCTTTGATTCCAGCTCCAT 57.485 40.909 0.00 0.00 0.00 3.41
1667 1803 0.321653 ATTCGACCACTGGTTCTGGC 60.322 55.000 1.13 0.00 35.25 4.85
1677 1813 2.631418 TCTCGAGTCAATTCGACCAC 57.369 50.000 13.13 1.08 46.69 4.16
1701 1837 2.875087 TGAGTCGTTCTTCCGTTTCA 57.125 45.000 0.00 0.00 0.00 2.69
1746 1882 1.683385 CATATGGTCTGTCTCGCTGGA 59.317 52.381 0.00 0.00 0.00 3.86
1762 1898 0.251033 ATGATGCACCAGCGCCATAT 60.251 50.000 2.29 0.00 46.23 1.78
1771 1907 0.530288 TCGACGAAGATGATGCACCA 59.470 50.000 0.00 0.00 0.00 4.17
1772 1908 1.203928 CTCGACGAAGATGATGCACC 58.796 55.000 0.00 0.00 0.00 5.01
1773 1909 1.203928 CCTCGACGAAGATGATGCAC 58.796 55.000 0.00 0.00 0.00 4.57
1774 1910 0.103026 CCCTCGACGAAGATGATGCA 59.897 55.000 0.00 0.00 0.00 3.96
1775 1911 0.385751 TCCCTCGACGAAGATGATGC 59.614 55.000 0.00 0.00 0.00 3.91
1776 1912 3.243535 TGAATCCCTCGACGAAGATGATG 60.244 47.826 9.99 0.00 0.00 3.07
1782 1918 2.586258 ATGTGAATCCCTCGACGAAG 57.414 50.000 0.00 0.00 0.00 3.79
1818 1954 3.631046 CTAGCCCATCCTCCCGGC 61.631 72.222 0.00 0.00 43.35 6.13
1879 2015 4.525487 TCTCCTGTGTTGTTTACGGATACT 59.475 41.667 0.00 0.00 0.00 2.12
1888 2027 9.965824 CACTATTTAATTTCTCCTGTGTTGTTT 57.034 29.630 0.00 0.00 0.00 2.83
1893 2032 8.816894 TCTCTCACTATTTAATTTCTCCTGTGT 58.183 33.333 0.00 0.00 0.00 3.72
1894 2033 9.658799 TTCTCTCACTATTTAATTTCTCCTGTG 57.341 33.333 0.00 0.00 0.00 3.66
1961 2106 9.817809 GTAAGACTATGATCATGGAAAGTACAA 57.182 33.333 24.25 3.65 0.00 2.41
1970 2117 8.899427 AGAACATTGTAAGACTATGATCATGG 57.101 34.615 18.72 17.72 36.29 3.66
1997 2158 7.402862 AGGCTAACCACATTTCTTAGTACAAT 58.597 34.615 0.00 0.00 39.06 2.71
2000 2161 9.473640 GTATAGGCTAACCACATTTCTTAGTAC 57.526 37.037 0.00 0.00 39.06 2.73
2003 2164 9.561069 AATGTATAGGCTAACCACATTTCTTAG 57.439 33.333 18.95 0.00 36.96 2.18
2014 2175 5.007724 GCAGACACAAATGTATAGGCTAACC 59.992 44.000 0.00 0.00 39.95 2.85
2145 2313 1.770658 CATGGAGGCTTGAGGTATGGA 59.229 52.381 0.00 0.00 0.00 3.41
2165 2333 1.398390 CTGAATTGTCTTGCCTACCGC 59.602 52.381 0.00 0.00 38.31 5.68
2170 2338 2.555757 GACTTGCTGAATTGTCTTGCCT 59.444 45.455 0.00 0.00 0.00 4.75
2186 2354 2.125912 CTCCTGCGTCCGGACTTG 60.126 66.667 30.92 18.21 0.00 3.16
2196 2364 1.433534 GGTCTTCTTTCACTCCTGCG 58.566 55.000 0.00 0.00 0.00 5.18
2200 2368 2.689646 CTTCCGGTCTTCTTTCACTCC 58.310 52.381 0.00 0.00 0.00 3.85
2311 2479 5.403466 GGTTGCTGCTATTGTTCTTTTCTTG 59.597 40.000 0.00 0.00 0.00 3.02
2352 2520 3.004734 GGTGATGTTTGGACCTCTTGTTG 59.995 47.826 0.00 0.00 0.00 3.33
2357 2525 1.073923 GGTGGTGATGTTTGGACCTCT 59.926 52.381 0.00 0.00 0.00 3.69
2637 2806 5.017490 AGATTGTTTAGAAGGGAGAGACGA 58.983 41.667 0.00 0.00 0.00 4.20
2741 2911 5.236911 ACTTCGTTCCGTAAATTTTACTGCA 59.763 36.000 15.38 0.00 0.00 4.41
2756 2926 2.234300 TCTGGTTGTCACTTCGTTCC 57.766 50.000 0.00 0.00 0.00 3.62
3006 3177 7.316544 TCTCAAACTTAACTGACCTTTGTTC 57.683 36.000 0.00 0.00 0.00 3.18
3009 3180 6.263168 ACCATCTCAAACTTAACTGACCTTTG 59.737 38.462 0.00 0.00 0.00 2.77
3282 3469 1.132643 CTCTCTTTTGCAGATGCTGGC 59.867 52.381 6.35 0.00 42.66 4.85
3283 3470 2.434428 ACTCTCTTTTGCAGATGCTGG 58.566 47.619 6.35 0.00 42.66 4.85
3294 3481 7.664758 AGCAATGCTGATTTTAACTCTCTTTT 58.335 30.769 7.07 0.00 37.57 2.27
3315 3502 2.980213 TACAACGGCGTGCTGAGCAA 62.980 55.000 15.70 0.00 41.47 3.91
3328 3515 7.431084 GCCATAATTAGGTTGATTTGTACAACG 59.569 37.037 8.07 0.00 45.56 4.10
3343 3530 4.761739 ACGACCAATCATGCCATAATTAGG 59.238 41.667 0.00 0.00 0.00 2.69
3362 3549 7.866729 TCTGATCTTATCTCAACTGATACGAC 58.133 38.462 0.00 0.00 32.54 4.34
3365 3552 9.844790 CTGATCTGATCTTATCTCAACTGATAC 57.155 37.037 17.82 0.00 0.00 2.24
3370 3557 8.709272 TGATCTGATCTGATCTTATCTCAACT 57.291 34.615 30.92 4.20 42.30 3.16
3378 3565 9.930693 CTTCATTGATGATCTGATCTGATCTTA 57.069 33.333 30.92 19.13 42.30 2.10
3379 3566 8.652290 TCTTCATTGATGATCTGATCTGATCTT 58.348 33.333 30.92 26.95 42.30 2.40
3380 3567 8.196378 TCTTCATTGATGATCTGATCTGATCT 57.804 34.615 30.92 21.23 42.30 2.75
3386 3573 8.931775 CAAGATCTCTTCATTGATGATCTGATC 58.068 37.037 19.09 10.72 41.78 2.92
3419 3606 1.469703 TCATCTTCCGCTGCAATTGTG 59.530 47.619 7.40 1.87 0.00 3.33
3421 3608 3.113322 CAATCATCTTCCGCTGCAATTG 58.887 45.455 0.00 0.00 0.00 2.32
3423 3610 2.098607 CACAATCATCTTCCGCTGCAAT 59.901 45.455 0.00 0.00 0.00 3.56
3426 3613 0.379669 CCACAATCATCTTCCGCTGC 59.620 55.000 0.00 0.00 0.00 5.25
3431 3618 3.690460 ACCAGAACCACAATCATCTTCC 58.310 45.455 0.00 0.00 0.00 3.46
3438 3630 2.069273 CGTCAGACCAGAACCACAATC 58.931 52.381 0.00 0.00 0.00 2.67
3442 3634 1.340248 TCTTCGTCAGACCAGAACCAC 59.660 52.381 0.00 0.00 0.00 4.16
3453 3645 4.511454 TGTCAAAGTTTGGATCTTCGTCAG 59.489 41.667 15.47 0.00 0.00 3.51
3457 3649 3.058224 GGGTGTCAAAGTTTGGATCTTCG 60.058 47.826 15.47 0.00 0.00 3.79
3459 3651 3.909732 TGGGTGTCAAAGTTTGGATCTT 58.090 40.909 15.47 0.00 0.00 2.40
3468 3660 4.506802 GGGTAGAGAAATGGGTGTCAAAGT 60.507 45.833 0.00 0.00 0.00 2.66
3469 3661 4.010349 GGGTAGAGAAATGGGTGTCAAAG 58.990 47.826 0.00 0.00 0.00 2.77


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

AutoCloner maintained by Alex Coulton.