Multiple sequence alignment - TraesCS5A01G258600

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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 TraesCS5A01G258600 chr5A 100.000 2399 0 0 1 2399 473244447 473242049 0.000000e+00 4431.0
1 TraesCS5A01G258600 chr5A 98.883 1433 14 2 1 1431 685966090 685967522 0.000000e+00 2556.0
2 TraesCS5A01G258600 chr5A 100.000 35 0 0 2365 2399 566166493 566166459 5.540000e-07 65.8
3 TraesCS5A01G258600 chr4A 99.930 1433 1 0 1 1433 475389172 475390604 0.000000e+00 2641.0
4 TraesCS5A01G258600 chr1A 99.095 1436 11 2 1 1435 457823408 457821974 0.000000e+00 2579.0
5 TraesCS5A01G258600 chr1A 97.059 34 1 0 2364 2397 313913761 313913794 9.260000e-05 58.4
6 TraesCS5A01G258600 chr6A 99.229 1427 10 1 1 1427 434546735 434548160 0.000000e+00 2573.0
7 TraesCS5A01G258600 chr6A 100.000 35 0 0 2365 2399 357514609 357514575 5.540000e-07 65.8
8 TraesCS5A01G258600 chr7B 99.814 1074 2 0 362 1435 586051083 586052156 0.000000e+00 1973.0
9 TraesCS5A01G258600 chr2D 94.403 1215 62 4 1 1209 634829951 634831165 0.000000e+00 1862.0
10 TraesCS5A01G258600 chr2D 85.620 1370 186 8 66 1429 386814280 386815644 0.000000e+00 1428.0
11 TraesCS5A01G258600 chr2D 91.803 61 5 0 1437 1497 56664712 56664652 4.250000e-13 86.1
12 TraesCS5A01G258600 chr4D 80.571 1436 271 8 2 1433 484147511 484148942 0.000000e+00 1099.0
13 TraesCS5A01G258600 chr2B 79.834 1443 279 12 2 1438 135779086 135780522 0.000000e+00 1042.0
14 TraesCS5A01G258600 chr2B 100.000 33 0 0 2364 2396 714518264 714518232 7.160000e-06 62.1
15 TraesCS5A01G258600 chr2B 100.000 32 0 0 2368 2399 670444163 670444194 2.580000e-05 60.2
16 TraesCS5A01G258600 chr5D 92.478 452 28 5 1919 2368 370633491 370633044 2.010000e-180 641.0
17 TraesCS5A01G258600 chr5D 86.809 470 30 15 1437 1883 370634200 370633740 1.660000e-136 496.0
18 TraesCS5A01G258600 chr5B 90.191 418 38 3 1953 2368 439959593 439959177 2.100000e-150 542.0
19 TraesCS5A01G258600 chr5B 89.030 237 22 4 1595 1828 439959955 439959720 8.390000e-75 291.0
20 TraesCS5A01G258600 chr5B 95.604 91 4 0 1437 1527 439960072 439959982 1.920000e-31 147.0
21 TraesCS5A01G258600 chr5B 100.000 32 0 0 2368 2399 598578044 598578013 2.580000e-05 60.2
22 TraesCS5A01G258600 chr2A 88.136 59 7 0 1437 1495 58031282 58031224 1.190000e-08 71.3
23 TraesCS5A01G258600 chr6B 100.000 34 0 0 2364 2397 434182125 434182158 1.990000e-06 63.9
24 TraesCS5A01G258600 chr1B 100.000 32 0 0 2368 2399 289282427 289282396 2.580000e-05 60.2
25 TraesCS5A01G258600 chr1D 100.000 31 0 0 2365 2395 99522892 99522862 9.260000e-05 58.4


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 TraesCS5A01G258600 chr5A 473242049 473244447 2398 True 4431.000000 4431 100.000000 1 2399 1 chr5A.!!$R1 2398
1 TraesCS5A01G258600 chr5A 685966090 685967522 1432 False 2556.000000 2556 98.883000 1 1431 1 chr5A.!!$F1 1430
2 TraesCS5A01G258600 chr4A 475389172 475390604 1432 False 2641.000000 2641 99.930000 1 1433 1 chr4A.!!$F1 1432
3 TraesCS5A01G258600 chr1A 457821974 457823408 1434 True 2579.000000 2579 99.095000 1 1435 1 chr1A.!!$R1 1434
4 TraesCS5A01G258600 chr6A 434546735 434548160 1425 False 2573.000000 2573 99.229000 1 1427 1 chr6A.!!$F1 1426
5 TraesCS5A01G258600 chr7B 586051083 586052156 1073 False 1973.000000 1973 99.814000 362 1435 1 chr7B.!!$F1 1073
6 TraesCS5A01G258600 chr2D 634829951 634831165 1214 False 1862.000000 1862 94.403000 1 1209 1 chr2D.!!$F2 1208
7 TraesCS5A01G258600 chr2D 386814280 386815644 1364 False 1428.000000 1428 85.620000 66 1429 1 chr2D.!!$F1 1363
8 TraesCS5A01G258600 chr4D 484147511 484148942 1431 False 1099.000000 1099 80.571000 2 1433 1 chr4D.!!$F1 1431
9 TraesCS5A01G258600 chr2B 135779086 135780522 1436 False 1042.000000 1042 79.834000 2 1438 1 chr2B.!!$F1 1436
10 TraesCS5A01G258600 chr5D 370633044 370634200 1156 True 568.500000 641 89.643500 1437 2368 2 chr5D.!!$R1 931
11 TraesCS5A01G258600 chr5B 439959177 439960072 895 True 326.666667 542 91.608333 1437 2368 3 chr5B.!!$R2 931

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
1456 1468 0.403271 AATGAAGTCAGTGCCCTGCT 59.597 50.0 0.0 0.0 38.66 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2335 2598 0.60762 TGCCGACATGTCACATGAGA 59.392 50.0 24.98 0.0 0.0 3.27 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
1456 1468 0.403271 AATGAAGTCAGTGCCCTGCT 59.597 50.000 0.00 0.0 38.66 4.24
1532 1544 3.567585 CCTGATCTAGCTTCATCTCGTCA 59.432 47.826 0.00 0.0 0.00 4.35
1557 1569 5.652014 TCGAAGCCTGGAATTGTTGATAAAT 59.348 36.000 0.00 0.0 0.00 1.40
1562 1574 6.211184 AGCCTGGAATTGTTGATAAATGAACA 59.789 34.615 0.00 0.0 32.15 3.18
1564 1576 6.532657 CCTGGAATTGTTGATAAATGAACAGC 59.467 38.462 0.00 0.0 35.43 4.40
1567 1579 7.043565 GGAATTGTTGATAAATGAACAGCCAT 58.956 34.615 0.00 0.0 35.43 4.40
1568 1580 7.223387 GGAATTGTTGATAAATGAACAGCCATC 59.777 37.037 0.00 0.0 35.43 3.51
1569 1581 6.587206 TTGTTGATAAATGAACAGCCATCA 57.413 33.333 0.00 0.0 35.43 3.07
1570 1582 6.198650 TGTTGATAAATGAACAGCCATCAG 57.801 37.500 0.00 0.0 30.55 2.90
1571 1583 5.711506 TGTTGATAAATGAACAGCCATCAGT 59.288 36.000 0.00 0.0 30.55 3.41
1582 1594 4.147321 ACAGCCATCAGTGAATCAAAAGT 58.853 39.130 0.00 0.0 0.00 2.66
1590 1602 7.824289 CCATCAGTGAATCAAAAGTAGTTCCTA 59.176 37.037 0.00 0.0 0.00 2.94
1629 1644 7.391554 TCTGCTGCAAAAGAATTAGATAGTTGT 59.608 33.333 3.02 0.0 0.00 3.32
1776 1791 8.801715 TGCAAACTAAAATAGAAGCTGAAAAG 57.198 30.769 0.00 0.0 0.00 2.27
1777 1792 7.382218 TGCAAACTAAAATAGAAGCTGAAAAGC 59.618 33.333 0.00 0.0 0.00 3.51
1820 1843 2.627945 TCATATGGTCTTTGACGGTGC 58.372 47.619 2.13 0.0 32.65 5.01
1849 1895 2.495155 TGCATGTGTCCATTAGCACT 57.505 45.000 0.00 0.0 36.63 4.40
1871 1917 1.120437 CGCGCCTCAAAACTCAAAAC 58.880 50.000 0.00 0.0 0.00 2.43
1885 1931 7.513371 AAACTCAAAACGGAACATATTACCA 57.487 32.000 0.00 0.0 0.00 3.25
1886 1932 7.513371 AACTCAAAACGGAACATATTACCAA 57.487 32.000 0.00 0.0 0.00 3.67
1887 1933 7.513371 ACTCAAAACGGAACATATTACCAAA 57.487 32.000 0.00 0.0 0.00 3.28
1888 1934 7.942990 ACTCAAAACGGAACATATTACCAAAA 58.057 30.769 0.00 0.0 0.00 2.44
1889 1935 8.414778 ACTCAAAACGGAACATATTACCAAAAA 58.585 29.630 0.00 0.0 0.00 1.94
1891 1937 8.414778 TCAAAACGGAACATATTACCAAAAACT 58.585 29.630 0.00 0.0 0.00 2.66
1893 1939 7.754851 AACGGAACATATTACCAAAAACTCT 57.245 32.000 0.00 0.0 0.00 3.24
1895 1941 6.373495 ACGGAACATATTACCAAAAACTCTCC 59.627 38.462 0.00 0.0 0.00 3.71
1896 1942 6.183360 CGGAACATATTACCAAAAACTCTCCC 60.183 42.308 0.00 0.0 0.00 4.30
1898 1944 6.147437 ACATATTACCAAAAACTCTCCCCA 57.853 37.500 0.00 0.0 0.00 4.96
1899 1945 6.741724 ACATATTACCAAAAACTCTCCCCAT 58.258 36.000 0.00 0.0 0.00 4.00
1901 1947 2.604912 ACCAAAAACTCTCCCCATCC 57.395 50.000 0.00 0.0 0.00 3.51
1902 1948 2.073776 ACCAAAAACTCTCCCCATCCT 58.926 47.619 0.00 0.0 0.00 3.24
1903 1949 2.225117 ACCAAAAACTCTCCCCATCCTG 60.225 50.000 0.00 0.0 0.00 3.86
1905 1951 1.075601 AAAACTCTCCCCATCCTGCA 58.924 50.000 0.00 0.0 0.00 4.41
1906 1952 1.302907 AAACTCTCCCCATCCTGCAT 58.697 50.000 0.00 0.0 0.00 3.96
1908 1954 1.059006 ACTCTCCCCATCCTGCATCC 61.059 60.000 0.00 0.0 0.00 3.51
1910 1956 2.778278 TCCCCATCCTGCATCCCC 60.778 66.667 0.00 0.0 0.00 4.81
1911 1957 3.907130 CCCCATCCTGCATCCCCC 61.907 72.222 0.00 0.0 0.00 5.40
1912 1958 2.780040 CCCATCCTGCATCCCCCT 60.780 66.667 0.00 0.0 0.00 4.79
1913 1959 2.838467 CCCATCCTGCATCCCCCTC 61.838 68.421 0.00 0.0 0.00 4.30
1914 1960 2.838467 CCATCCTGCATCCCCCTCC 61.838 68.421 0.00 0.0 0.00 4.30
1980 2240 1.286880 CGGCAGGGCTGTTCTTTTG 59.713 57.895 0.00 0.0 0.00 2.44
2016 2276 0.631753 TGGGTTTCTGTTTGGGTGGA 59.368 50.000 0.00 0.0 0.00 4.02
2082 2342 7.771927 AGCCCTGATTGATTCCTTATTAATG 57.228 36.000 0.00 0.0 0.00 1.90
2083 2343 6.723052 AGCCCTGATTGATTCCTTATTAATGG 59.277 38.462 0.00 0.0 0.00 3.16
2156 2417 5.126222 TGCAAGACAACCAAACACTATTTCA 59.874 36.000 0.00 0.0 0.00 2.69
2181 2442 9.057089 CATAACTAGGACTTTCAGACAACTTTT 57.943 33.333 0.00 0.0 0.00 2.27
2288 2551 3.574284 TTGCATGTGATTTTCCTTCCG 57.426 42.857 0.00 0.0 0.00 4.30
2335 2598 2.989422 GCGTTAGCAAACCACTTCAT 57.011 45.000 0.00 0.0 44.35 2.57
2354 2617 0.607620 TCTCATGTGACATGTCGGCA 59.392 50.000 23.39 20.4 0.00 5.69
2368 2631 4.963276 TGTCGGCATCTATTCCAAAAAG 57.037 40.909 0.00 0.0 0.00 2.27
2369 2632 3.694072 TGTCGGCATCTATTCCAAAAAGG 59.306 43.478 0.00 0.0 39.47 3.11
2370 2633 2.687935 TCGGCATCTATTCCAAAAAGGC 59.312 45.455 0.00 0.0 37.29 4.35
2371 2634 2.223805 CGGCATCTATTCCAAAAAGGCC 60.224 50.000 0.00 0.0 37.29 5.19
2372 2635 2.103094 GGCATCTATTCCAAAAAGGCCC 59.897 50.000 0.00 0.0 37.29 5.80
2373 2636 2.103094 GCATCTATTCCAAAAAGGCCCC 59.897 50.000 0.00 0.0 37.29 5.80
2374 2637 2.543037 TCTATTCCAAAAAGGCCCCC 57.457 50.000 0.00 0.0 37.29 5.40
2375 2638 1.111277 CTATTCCAAAAAGGCCCCCG 58.889 55.000 0.00 0.0 37.29 5.73
2376 2639 0.973496 TATTCCAAAAAGGCCCCCGC 60.973 55.000 0.00 0.0 37.29 6.13
2379 2642 4.050934 CAAAAAGGCCCCCGCGTC 62.051 66.667 4.92 0.0 35.02 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1472 1484 8.830580 CCTATGTGTATTTGTGATGTTTCCTAG 58.169 37.037 0.00 0.00 0.00 3.02
1532 1544 3.071874 TCAACAATTCCAGGCTTCGAT 57.928 42.857 0.00 0.00 0.00 3.59
1557 1569 3.421919 TGATTCACTGATGGCTGTTCA 57.578 42.857 0.00 0.00 0.00 3.18
1562 1574 5.564550 ACTACTTTTGATTCACTGATGGCT 58.435 37.500 0.00 0.00 0.00 4.75
1564 1576 6.656693 AGGAACTACTTTTGATTCACTGATGG 59.343 38.462 0.00 0.00 36.02 3.51
1567 1579 9.621629 TTTTAGGAACTACTTTTGATTCACTGA 57.378 29.630 0.00 0.00 42.67 3.41
1568 1580 9.884465 CTTTTAGGAACTACTTTTGATTCACTG 57.116 33.333 0.00 0.00 42.67 3.66
1569 1581 9.628500 ACTTTTAGGAACTACTTTTGATTCACT 57.372 29.630 0.00 0.00 42.67 3.41
1629 1644 5.503002 AGGTTGATGATGATCATGTGAACA 58.497 37.500 14.30 4.61 37.20 3.18
1697 1712 4.036852 GCAAGGCCAGTAGGAATTTATGAC 59.963 45.833 5.01 0.00 36.89 3.06
1773 1788 7.895759 TCCTTTGCTCATTGTATTTAAGCTTT 58.104 30.769 3.20 0.00 34.11 3.51
1776 1791 7.975616 TGATTCCTTTGCTCATTGTATTTAAGC 59.024 33.333 0.00 0.00 0.00 3.09
1785 1808 6.264744 AGACCATATGATTCCTTTGCTCATTG 59.735 38.462 3.65 0.00 32.20 2.82
1820 1843 0.028505 GACACATGCAAGCATAGCGG 59.971 55.000 7.29 0.00 34.91 5.52
1849 1895 1.719725 TTGAGTTTTGAGGCGCGCAA 61.720 50.000 34.42 16.51 0.00 4.85
1856 1902 4.364415 TGTTCCGTTTTGAGTTTTGAGG 57.636 40.909 0.00 0.00 0.00 3.86
1871 1917 6.183360 GGGAGAGTTTTTGGTAATATGTTCCG 60.183 42.308 0.00 0.00 0.00 4.30
1885 1931 1.428912 TGCAGGATGGGGAGAGTTTTT 59.571 47.619 0.00 0.00 35.86 1.94
1886 1932 1.075601 TGCAGGATGGGGAGAGTTTT 58.924 50.000 0.00 0.00 35.86 2.43
1887 1933 1.213926 GATGCAGGATGGGGAGAGTTT 59.786 52.381 0.00 0.00 35.86 2.66
1888 1934 0.842635 GATGCAGGATGGGGAGAGTT 59.157 55.000 0.00 0.00 35.86 3.01
1889 1935 1.059006 GGATGCAGGATGGGGAGAGT 61.059 60.000 0.00 0.00 35.86 3.24
1891 1937 1.771746 GGGATGCAGGATGGGGAGA 60.772 63.158 0.00 0.00 35.86 3.71
1893 1939 2.778278 GGGGATGCAGGATGGGGA 60.778 66.667 0.00 0.00 35.86 4.81
1895 1941 2.780040 AGGGGGATGCAGGATGGG 60.780 66.667 0.00 0.00 35.86 4.00
1896 1942 2.838467 GGAGGGGGATGCAGGATGG 61.838 68.421 0.00 0.00 35.86 3.51
1898 1944 2.451294 GGGAGGGGGATGCAGGAT 60.451 66.667 0.00 0.00 0.00 3.24
1899 1945 4.843331 GGGGAGGGGGATGCAGGA 62.843 72.222 0.00 0.00 0.00 3.86
1917 2176 4.222847 GCGCTAGGGTTCCCTCCG 62.223 72.222 14.24 17.54 37.64 4.63
1980 2240 1.743394 CCCAATTAGTTCGTTGCTCCC 59.257 52.381 0.00 0.00 0.00 4.30
2118 2378 3.947196 TGTCTTGCAATGTCTCACAACTT 59.053 39.130 0.00 0.00 0.00 2.66
2156 2417 9.628500 AAAAAGTTGTCTGAAAGTCCTAGTTAT 57.372 29.630 0.00 0.00 33.76 1.89
2181 2442 2.083774 CTTGCCATCGAGCCTTAACAA 58.916 47.619 0.00 0.00 0.00 2.83
2210 2472 9.550811 CAAAAACCCTAATTACGAAATAGTGTC 57.449 33.333 0.00 0.00 0.00 3.67
2316 2579 2.484264 AGATGAAGTGGTTTGCTAACGC 59.516 45.455 4.95 1.17 35.00 4.84
2335 2598 0.607620 TGCCGACATGTCACATGAGA 59.392 50.000 24.98 0.00 0.00 3.27
2354 2617 2.689723 CGGGGGCCTTTTTGGAATAGAT 60.690 50.000 0.84 0.00 38.35 1.98


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

AutoCloner maintained by Alex Coulton.