Multiple sequence alignment - TraesCS5D01G321500

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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 TraesCS5D01G321500 chr5D 100.000 2579 0 0 1 2579 413489656 413492234 0.000000e+00 4763.0
1 TraesCS5D01G321500 chr5D 97.117 2185 29 4 398 2579 413592674 413594827 0.000000e+00 3655.0
2 TraesCS5D01G321500 chr5D 98.512 336 5 0 1 336 413592340 413592675 6.140000e-166 593.0
3 TraesCS5D01G321500 chr5D 79.624 319 47 13 1489 1791 413286966 413287282 2.010000e-51 213.0
4 TraesCS5D01G321500 chr5D 82.800 250 26 12 84 318 413285248 413285495 9.350000e-50 207.0
5 TraesCS5D01G321500 chr5D 97.561 41 1 0 1492 1532 413491108 413491148 1.280000e-08 71.3
6 TraesCS5D01G321500 chr5D 97.561 41 1 0 1453 1493 413491147 413491187 1.280000e-08 71.3
7 TraesCS5D01G321500 chr5D 97.561 41 1 0 1492 1532 413593728 413593768 1.280000e-08 71.3
8 TraesCS5D01G321500 chr5D 97.561 41 1 0 1453 1493 413593767 413593807 1.280000e-08 71.3
9 TraesCS5D01G321500 chr5A 94.414 1450 72 9 48 1493 525724275 525725719 0.000000e+00 2220.0
10 TraesCS5D01G321500 chr5A 93.785 1448 75 8 48 1493 525918333 525919767 0.000000e+00 2161.0
11 TraesCS5D01G321500 chr5A 93.448 1450 80 8 48 1493 525829708 525831146 0.000000e+00 2137.0
12 TraesCS5D01G321500 chr5A 89.625 1253 84 19 48 1285 526264904 526266125 0.000000e+00 1552.0
13 TraesCS5D01G321500 chr5A 92.593 324 20 4 1492 1812 525919727 525920049 1.810000e-126 462.0
14 TraesCS5D01G321500 chr5A 92.500 320 21 3 1492 1810 525831106 525831423 3.030000e-124 455.0
15 TraesCS5D01G321500 chr5A 92.157 306 21 3 1492 1796 525725679 525725982 1.830000e-116 429.0
16 TraesCS5D01G321500 chr5A 93.074 231 13 2 1492 1720 526279433 526279662 4.110000e-88 335.0
17 TraesCS5D01G321500 chr5A 92.157 204 16 0 1281 1484 526279261 526279464 3.250000e-74 289.0
18 TraesCS5D01G321500 chr5B 95.078 447 16 1 55 495 498511395 498511841 0.000000e+00 699.0
19 TraesCS5D01G321500 chr5B 91.004 478 32 5 1016 1493 498722803 498723269 3.620000e-178 634.0
20 TraesCS5D01G321500 chr5B 89.213 445 22 13 1492 1933 498723229 498723650 1.360000e-147 532.0
21 TraesCS5D01G321500 chr5B 87.609 460 48 6 1995 2449 498723653 498724108 2.270000e-145 525.0
22 TraesCS5D01G321500 chr5B 94.081 321 14 4 1492 1808 498512092 498512411 1.390000e-132 483.0
23 TraesCS5D01G321500 chr5B 84.507 497 66 8 2073 2562 206804012 206804504 4.990000e-132 481.0
24 TraesCS5D01G321500 chr5B 93.925 214 12 1 48 260 498722579 498722792 3.200000e-84 322.0
25 TraesCS5D01G321500 chr5B 82.493 337 38 15 76 397 498082200 498082530 2.530000e-70 276.0
26 TraesCS5D01G321500 chr5B 87.607 234 24 2 1264 1493 498511900 498512132 1.520000e-67 267.0
27 TraesCS5D01G321500 chr5B 97.059 68 2 0 521 588 498511832 498511899 5.830000e-22 115.0
28 TraesCS5D01G321500 chr6B 84.423 520 66 9 2066 2577 501111914 501112426 4.960000e-137 497.0
29 TraesCS5D01G321500 chr2D 85.102 490 63 5 2073 2555 386256130 386255644 2.310000e-135 492.0
30 TraesCS5D01G321500 chr4B 84.109 516 69 10 2072 2579 277322495 277323005 1.070000e-133 486.0
31 TraesCS5D01G321500 chr4D 85.417 480 55 9 2072 2544 292915672 292916143 3.860000e-133 484.0
32 TraesCS5D01G321500 chr3D 84.929 491 61 8 2072 2554 96417647 96417162 3.860000e-133 484.0
33 TraesCS5D01G321500 chr3A 84.898 490 62 6 2072 2554 114452369 114451885 3.860000e-133 484.0
34 TraesCS5D01G321500 chr7B 94.231 52 3 0 649 700 668204569 668204620 2.130000e-11 80.5
35 TraesCS5D01G321500 chr6A 94.872 39 2 0 657 695 504479646 504479608 7.710000e-06 62.1


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 TraesCS5D01G321500 chr5D 413489656 413492234 2578 False 1635.20 4763 98.37400 1 2579 3 chr5D.!!$F2 2578
1 TraesCS5D01G321500 chr5D 413592340 413594827 2487 False 1097.65 3655 97.68775 1 2579 4 chr5D.!!$F3 2578
2 TraesCS5D01G321500 chr5D 413285248 413287282 2034 False 210.00 213 81.21200 84 1791 2 chr5D.!!$F1 1707
3 TraesCS5D01G321500 chr5A 526264904 526266125 1221 False 1552.00 1552 89.62500 48 1285 1 chr5A.!!$F1 1237
4 TraesCS5D01G321500 chr5A 525724275 525725982 1707 False 1324.50 2220 93.28550 48 1796 2 chr5A.!!$F2 1748
5 TraesCS5D01G321500 chr5A 525918333 525920049 1716 False 1311.50 2161 93.18900 48 1812 2 chr5A.!!$F4 1764
6 TraesCS5D01G321500 chr5A 525829708 525831423 1715 False 1296.00 2137 92.97400 48 1810 2 chr5A.!!$F3 1762
7 TraesCS5D01G321500 chr5B 498722579 498724108 1529 False 503.25 634 90.43775 48 2449 4 chr5B.!!$F4 2401
8 TraesCS5D01G321500 chr5B 498511395 498512411 1016 False 391.00 699 93.45625 55 1808 4 chr5B.!!$F3 1753
9 TraesCS5D01G321500 chr6B 501111914 501112426 512 False 497.00 497 84.42300 2066 2577 1 chr6B.!!$F1 511
10 TraesCS5D01G321500 chr4B 277322495 277323005 510 False 486.00 486 84.10900 2072 2579 1 chr4B.!!$F1 507

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
91 92 4.522022 CGGTCTCCTTATACGAGGGTAAAT 59.478 45.833 0.0 0.0 37.41 1.40 F
630 845 5.499004 AGTTGACTAGGGTTTTCTATGCA 57.501 39.130 0.0 0.0 0.00 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1108 1604 1.039856 GCAAAAACAGCTGGGAGGAA 58.960 50.0 19.93 0.0 0.0 3.36 R
2520 3068 0.884704 GGTTGGCAAGTGCTCTTCGA 60.885 55.0 0.00 0.0 41.7 3.71 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
91 92 4.522022 CGGTCTCCTTATACGAGGGTAAAT 59.478 45.833 0.00 0.00 37.41 1.40
630 845 5.499004 AGTTGACTAGGGTTTTCTATGCA 57.501 39.130 0.00 0.00 0.00 3.96
843 1294 8.873215 TCTTGAGACATAAAACCGAAGATATC 57.127 34.615 0.00 0.00 0.00 1.63
1108 1604 1.299976 GGGATGGCGGAACTCAGTT 59.700 57.895 0.00 0.00 0.00 3.16
1390 1898 0.392998 CTATGTCTGTGTGGTGGCCC 60.393 60.000 0.00 0.00 0.00 5.80
1825 2354 4.596585 CCCCACCACCACCACCAC 62.597 72.222 0.00 0.00 0.00 4.16
1826 2355 4.596585 CCCACCACCACCACCACC 62.597 72.222 0.00 0.00 0.00 4.61
1827 2356 3.814906 CCACCACCACCACCACCA 61.815 66.667 0.00 0.00 0.00 4.17
1828 2357 2.518349 CACCACCACCACCACCAC 60.518 66.667 0.00 0.00 0.00 4.16
1829 2358 3.816090 ACCACCACCACCACCACC 61.816 66.667 0.00 0.00 0.00 4.61
1830 2359 3.814906 CCACCACCACCACCACCA 61.815 66.667 0.00 0.00 0.00 4.17
1831 2360 2.518349 CACCACCACCACCACCAC 60.518 66.667 0.00 0.00 0.00 4.16
1832 2361 3.816090 ACCACCACCACCACCACC 61.816 66.667 0.00 0.00 0.00 4.61
1994 2528 2.240500 GGCAACTCTATCTGGCGCG 61.241 63.158 0.00 0.00 0.00 6.86
1995 2529 1.226974 GCAACTCTATCTGGCGCGA 60.227 57.895 12.10 0.00 0.00 5.87
1996 2530 1.211818 GCAACTCTATCTGGCGCGAG 61.212 60.000 12.10 13.90 0.00 5.03
1997 2531 0.596083 CAACTCTATCTGGCGCGAGG 60.596 60.000 19.80 5.34 0.00 4.63
2056 2592 2.904866 GGCGTTGAGGTGGTGCAA 60.905 61.111 0.00 0.00 0.00 4.08
2232 2778 9.860898 GCTAAGGAATGATATTGACAAAACTTT 57.139 29.630 0.00 0.00 0.00 2.66
2303 2849 7.834181 TCCATAGGGAAGCCAATATTATTAAGC 59.166 37.037 0.00 3.51 41.32 3.09
2357 2903 5.177327 GCTCAAGTGCTTAGAGATATTGCTC 59.823 44.000 12.28 0.00 35.11 4.26
2520 3068 0.769776 AGATGGCCCTTCGATCCCAT 60.770 55.000 0.00 6.41 40.60 4.00
2548 3096 2.301346 CACTTGCCAACCTTCTCTTGT 58.699 47.619 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
630 845 7.781693 AGGGAGTATCACATTTTAGAATTGCAT 59.218 33.333 0.00 0.0 45.06 3.96
1108 1604 1.039856 GCAAAAACAGCTGGGAGGAA 58.960 50.000 19.93 0.0 0.00 3.36
1810 2339 3.814906 TGGTGGTGGTGGTGGTGG 61.815 66.667 0.00 0.0 0.00 4.61
1811 2340 2.518349 GTGGTGGTGGTGGTGGTG 60.518 66.667 0.00 0.0 0.00 4.17
1812 2341 3.816090 GGTGGTGGTGGTGGTGGT 61.816 66.667 0.00 0.0 0.00 4.16
1813 2342 3.814906 TGGTGGTGGTGGTGGTGG 61.815 66.667 0.00 0.0 0.00 4.61
1814 2343 2.518349 GTGGTGGTGGTGGTGGTG 60.518 66.667 0.00 0.0 0.00 4.17
1815 2344 3.816090 GGTGGTGGTGGTGGTGGT 61.816 66.667 0.00 0.0 0.00 4.16
1816 2345 3.814906 TGGTGGTGGTGGTGGTGG 61.815 66.667 0.00 0.0 0.00 4.61
1817 2346 2.518349 GTGGTGGTGGTGGTGGTG 60.518 66.667 0.00 0.0 0.00 4.17
1818 2347 3.816090 GGTGGTGGTGGTGGTGGT 61.816 66.667 0.00 0.0 0.00 4.16
1819 2348 3.814906 TGGTGGTGGTGGTGGTGG 61.815 66.667 0.00 0.0 0.00 4.61
1820 2349 2.518349 GTGGTGGTGGTGGTGGTG 60.518 66.667 0.00 0.0 0.00 4.17
1821 2350 3.816090 GGTGGTGGTGGTGGTGGT 61.816 66.667 0.00 0.0 0.00 4.16
1822 2351 3.814906 TGGTGGTGGTGGTGGTGG 61.815 66.667 0.00 0.0 0.00 4.61
1823 2352 2.518349 GTGGTGGTGGTGGTGGTG 60.518 66.667 0.00 0.0 0.00 4.17
1824 2353 3.816090 GGTGGTGGTGGTGGTGGT 61.816 66.667 0.00 0.0 0.00 4.16
1825 2354 4.596585 GGGTGGTGGTGGTGGTGG 62.597 72.222 0.00 0.0 0.00 4.61
1826 2355 4.947147 CGGGTGGTGGTGGTGGTG 62.947 72.222 0.00 0.0 0.00 4.17
1994 2528 4.767255 CTGGCCACCTCACGCCTC 62.767 72.222 0.00 0.0 45.90 4.70
1996 2530 4.101448 ATCTGGCCACCTCACGCC 62.101 66.667 0.00 0.0 45.92 5.68
1997 2531 2.821366 CATCTGGCCACCTCACGC 60.821 66.667 0.00 0.0 0.00 5.34
1998 2532 1.742880 CACATCTGGCCACCTCACG 60.743 63.158 0.00 0.0 0.00 4.35
1999 2533 1.377725 CCACATCTGGCCACCTCAC 60.378 63.158 0.00 0.0 0.00 3.51
2000 2534 1.847506 ACCACATCTGGCCACCTCA 60.848 57.895 0.00 0.0 42.08 3.86
2303 2849 2.418368 TGATCAAAACCTCATCCCCG 57.582 50.000 0.00 0.0 0.00 5.73
2357 2903 2.162681 GGGTGTGACTGAGGATTTTGG 58.837 52.381 0.00 0.0 0.00 3.28
2470 3018 4.511082 ACCGAGACGCTAGAGTTTAGATAC 59.489 45.833 0.00 0.0 0.00 2.24
2520 3068 0.884704 GGTTGGCAAGTGCTCTTCGA 60.885 55.000 0.00 0.0 41.70 3.71


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

AutoCloner maintained by Alex Coulton.