Multiple sequence alignment - TraesCS5D01G255900

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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 TraesCS5D01G255900 chr5D 100.000 3571 0 0 1 3571 362073222 362069652 0.000000e+00 6595
1 TraesCS5D01G255900 chr5D 77.744 328 53 18 587 905 362072693 362072377 2.190000e-42 183
2 TraesCS5D01G255900 chr7B 92.598 2513 100 44 1 2470 328557070 328559539 0.000000e+00 3531
3 TraesCS5D01G255900 chr2B 92.247 2515 105 42 1 2470 84547031 84544562 0.000000e+00 3482
4 TraesCS5D01G255900 chr2B 95.750 1106 47 0 2466 3571 84536860 84535755 0.000000e+00 1783
5 TraesCS5D01G255900 chr2B 93.942 1106 67 0 2466 3571 26198755 26197650 0.000000e+00 1672
6 TraesCS5D01G255900 chr7A 91.512 1508 96 20 983 2472 119518638 119520131 0.000000e+00 2047
7 TraesCS5D01G255900 chr7A 89.873 79 8 0 705 783 119518429 119518507 6.310000e-18 102
8 TraesCS5D01G255900 chr1D 95.364 1100 51 0 2466 3565 431420096 431421195 0.000000e+00 1749
9 TraesCS5D01G255900 chr1D 94.408 769 41 2 1704 2470 431412666 431413434 0.000000e+00 1181
10 TraesCS5D01G255900 chr1D 80.941 1212 127 66 497 1673 431411530 431412672 0.000000e+00 863
11 TraesCS5D01G255900 chr7D 94.818 1100 50 3 2466 3565 587285110 587286202 0.000000e+00 1709
12 TraesCS5D01G255900 chr7D 94.538 769 40 2 1704 2470 587277694 587278462 0.000000e+00 1186
13 TraesCS5D01G255900 chr7D 81.472 1209 120 68 497 1673 587276564 587277700 0.000000e+00 896
14 TraesCS5D01G255900 chr4D 94.128 1107 64 1 2466 3571 422222267 422221161 0.000000e+00 1683
15 TraesCS5D01G255900 chr4D 95.224 691 32 1 1782 2472 422229603 422228914 0.000000e+00 1092
16 TraesCS5D01G255900 chr4D 85.743 1003 80 41 785 1754 422230567 422229595 0.000000e+00 1002
17 TraesCS5D01G255900 chr5B 93.671 1106 70 0 2466 3571 170636860 170635755 0.000000e+00 1655
18 TraesCS5D01G255900 chr5B 91.789 950 70 7 1525 2472 170644474 170643531 0.000000e+00 1315
19 TraesCS5D01G255900 chr5B 86.901 710 89 4 1763 2470 551419392 551420099 0.000000e+00 793
20 TraesCS5D01G255900 chr5B 87.638 542 35 22 928 1447 170645156 170644625 5.100000e-168 601
21 TraesCS5D01G255900 chr1B 91.410 1106 95 0 2466 3571 3169063 3167958 0.000000e+00 1517
22 TraesCS5D01G255900 chr2D 90.506 1106 105 0 2466 3571 589967600 589968705 0.000000e+00 1461
23 TraesCS5D01G255900 chr2D 90.516 1086 101 2 2487 3571 537008265 537007181 0.000000e+00 1434
24 TraesCS5D01G255900 chr6A 87.183 710 87 4 1763 2470 573126212 573125505 0.000000e+00 804
25 TraesCS5D01G255900 chr4A 79.710 483 63 26 989 1455 37297683 37298146 2.070000e-82 316
26 TraesCS5D01G255900 chr5A 78.834 326 60 8 982 1303 603053365 603053045 1.000000e-50 211
27 TraesCS5D01G255900 chr1A 78.834 326 60 8 982 1303 501995364 501995044 1.000000e-50 211


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 TraesCS5D01G255900 chr5D 362069652 362073222 3570 True 3389.0 6595 88.8720 1 3571 2 chr5D.!!$R1 3570
1 TraesCS5D01G255900 chr7B 328557070 328559539 2469 False 3531.0 3531 92.5980 1 2470 1 chr7B.!!$F1 2469
2 TraesCS5D01G255900 chr2B 84544562 84547031 2469 True 3482.0 3482 92.2470 1 2470 1 chr2B.!!$R3 2469
3 TraesCS5D01G255900 chr2B 84535755 84536860 1105 True 1783.0 1783 95.7500 2466 3571 1 chr2B.!!$R2 1105
4 TraesCS5D01G255900 chr2B 26197650 26198755 1105 True 1672.0 1672 93.9420 2466 3571 1 chr2B.!!$R1 1105
5 TraesCS5D01G255900 chr7A 119518429 119520131 1702 False 1074.5 2047 90.6925 705 2472 2 chr7A.!!$F1 1767
6 TraesCS5D01G255900 chr1D 431420096 431421195 1099 False 1749.0 1749 95.3640 2466 3565 1 chr1D.!!$F1 1099
7 TraesCS5D01G255900 chr1D 431411530 431413434 1904 False 1022.0 1181 87.6745 497 2470 2 chr1D.!!$F2 1973
8 TraesCS5D01G255900 chr7D 587285110 587286202 1092 False 1709.0 1709 94.8180 2466 3565 1 chr7D.!!$F1 1099
9 TraesCS5D01G255900 chr7D 587276564 587278462 1898 False 1041.0 1186 88.0050 497 2470 2 chr7D.!!$F2 1973
10 TraesCS5D01G255900 chr4D 422221161 422222267 1106 True 1683.0 1683 94.1280 2466 3571 1 chr4D.!!$R1 1105
11 TraesCS5D01G255900 chr4D 422228914 422230567 1653 True 1047.0 1092 90.4835 785 2472 2 chr4D.!!$R2 1687
12 TraesCS5D01G255900 chr5B 170635755 170636860 1105 True 1655.0 1655 93.6710 2466 3571 1 chr5B.!!$R1 1105
13 TraesCS5D01G255900 chr5B 170643531 170645156 1625 True 958.0 1315 89.7135 928 2472 2 chr5B.!!$R2 1544
14 TraesCS5D01G255900 chr5B 551419392 551420099 707 False 793.0 793 86.9010 1763 2470 1 chr5B.!!$F1 707
15 TraesCS5D01G255900 chr1B 3167958 3169063 1105 True 1517.0 1517 91.4100 2466 3571 1 chr1B.!!$R1 1105
16 TraesCS5D01G255900 chr2D 589967600 589968705 1105 False 1461.0 1461 90.5060 2466 3571 1 chr2D.!!$F1 1105
17 TraesCS5D01G255900 chr2D 537007181 537008265 1084 True 1434.0 1434 90.5160 2487 3571 1 chr2D.!!$R1 1084
18 TraesCS5D01G255900 chr6A 573125505 573126212 707 True 804.0 804 87.1830 1763 2470 1 chr6A.!!$R1 707

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
312 321 4.941873 GGTGCTAGCCTTTTACAGTGTAAT 59.058 41.667 16.26 4.13 0.0 1.89 F
2165 2510 0.035458 CTCCCGTGTCCTTCTTTGCT 59.965 55.000 0.00 0.00 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2191 2536 2.996631 AGACATCTTCATCAGGCAACC 58.003 47.619 0.0 0.0 37.17 3.77 R
3333 3679 5.233050 GTGAGGTCAAGAATGATGTATGACG 59.767 44.000 0.0 0.0 40.92 4.35 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
100 101 9.569122 AGTGTTGACTGTTGGTTAAGTATATTT 57.431 29.630 0.00 0.00 0.00 1.40
136 137 8.556194 TGTTTTGTTCTGTAGTTCATGTCATAC 58.444 33.333 0.00 0.00 0.00 2.39
150 151 9.764363 GTTCATGTCATACTTTCAGTATATCCA 57.236 33.333 0.00 0.00 39.26 3.41
193 197 7.012421 GTGTATTTTTCTGACTTTCTGTGTCCT 59.988 37.037 0.00 0.00 33.83 3.85
209 213 5.942961 TGTGTCCTTTTTGTCCCAGTATTA 58.057 37.500 0.00 0.00 0.00 0.98
224 228 8.204836 GTCCCAGTATTACAATGTAATGTCTCT 58.795 37.037 24.31 15.14 34.75 3.10
241 245 7.964604 ATGTCTCTTAGGTTTTACAGTGTTC 57.035 36.000 0.00 0.00 0.00 3.18
306 315 6.992715 AGTATAATGGTGCTAGCCTTTTACAG 59.007 38.462 13.29 0.00 0.00 2.74
312 321 4.941873 GGTGCTAGCCTTTTACAGTGTAAT 59.058 41.667 16.26 4.13 0.00 1.89
313 322 5.414765 GGTGCTAGCCTTTTACAGTGTAATT 59.585 40.000 16.26 3.80 0.00 1.40
314 323 6.072119 GGTGCTAGCCTTTTACAGTGTAATTT 60.072 38.462 16.26 4.10 0.00 1.82
315 324 7.021790 GTGCTAGCCTTTTACAGTGTAATTTC 58.978 38.462 16.26 6.74 0.00 2.17
316 325 6.940298 TGCTAGCCTTTTACAGTGTAATTTCT 59.060 34.615 16.26 12.67 0.00 2.52
317 326 7.094805 TGCTAGCCTTTTACAGTGTAATTTCTG 60.095 37.037 16.26 5.60 37.65 3.02
318 327 6.575162 AGCCTTTTACAGTGTAATTTCTGG 57.425 37.500 16.26 13.71 36.17 3.86
319 328 6.068670 AGCCTTTTACAGTGTAATTTCTGGT 58.931 36.000 16.26 6.91 36.17 4.00
320 329 7.228590 AGCCTTTTACAGTGTAATTTCTGGTA 58.771 34.615 16.26 0.00 36.17 3.25
321 330 7.390718 AGCCTTTTACAGTGTAATTTCTGGTAG 59.609 37.037 16.26 4.85 36.17 3.18
322 331 7.174426 GCCTTTTACAGTGTAATTTCTGGTAGT 59.826 37.037 16.26 0.00 36.17 2.73
323 332 9.063615 CCTTTTACAGTGTAATTTCTGGTAGTT 57.936 33.333 16.26 0.00 36.17 2.24
329 338 9.398538 ACAGTGTAATTTCTGGTAGTTTTTACA 57.601 29.630 0.00 0.00 36.17 2.41
417 427 8.899771 AGTTGTGCTTAGTTTTACACTGTAATT 58.100 29.630 2.41 0.00 35.97 1.40
420 430 9.116067 TGTGCTTAGTTTTACACTGTAATTTCT 57.884 29.630 2.41 4.91 35.97 2.52
424 434 9.382244 CTTAGTTTTACACTGTAATTTCTGTGC 57.618 33.333 17.91 5.64 39.64 4.57
426 436 7.940850 AGTTTTACACTGTAATTTCTGTGCAT 58.059 30.769 17.91 6.33 39.64 3.96
427 437 8.413229 AGTTTTACACTGTAATTTCTGTGCATT 58.587 29.630 17.91 5.77 39.64 3.56
428 438 9.030301 GTTTTACACTGTAATTTCTGTGCATTT 57.970 29.630 17.91 5.49 39.64 2.32
439 449 7.656707 ATTTCTGTGCATTTTTGTCCAATAC 57.343 32.000 0.00 0.00 0.00 1.89
448 458 6.735694 GCATTTTTGTCCAATACTCACAGTGT 60.736 38.462 0.00 0.00 0.00 3.55
464 474 5.293324 TCACAGTGTAGTTGTGCTAGTTTTG 59.707 40.000 0.00 0.00 44.27 2.44
602 696 6.539649 TGTTCAATTACAGTGTAGTTCTGC 57.460 37.500 7.99 2.94 36.50 4.26
603 697 6.288294 TGTTCAATTACAGTGTAGTTCTGCT 58.712 36.000 7.99 0.00 36.50 4.24
604 698 7.438564 TGTTCAATTACAGTGTAGTTCTGCTA 58.561 34.615 7.99 0.00 36.50 3.49
605 699 7.598869 TGTTCAATTACAGTGTAGTTCTGCTAG 59.401 37.037 7.99 0.00 36.50 3.42
606 700 7.228314 TCAATTACAGTGTAGTTCTGCTAGT 57.772 36.000 7.99 0.00 36.50 2.57
900 1062 9.672086 GTTGTGCTAGTTTTTACAATGTAATGA 57.328 29.630 6.67 0.00 35.72 2.57
1366 1563 5.211454 TGATGCGTGATAGTTGTGTTTTTG 58.789 37.500 0.00 0.00 0.00 2.44
1476 1677 8.195617 TGTTTTCAGCAATTTTTACTTTCTGG 57.804 30.769 0.00 0.00 0.00 3.86
1805 2148 2.689553 AGAGGCAGAAAAGCTCTAGC 57.310 50.000 0.00 0.00 42.49 3.42
2165 2510 0.035458 CTCCCGTGTCCTTCTTTGCT 59.965 55.000 0.00 0.00 0.00 3.91
2185 2530 5.768317 TGCTAACAAGCTAAAATCAACCAC 58.232 37.500 0.00 0.00 35.49 4.16
2191 2536 3.074412 AGCTAAAATCAACCACAGTCGG 58.926 45.455 0.00 0.00 0.00 4.79
2740 3085 5.677319 TCCGGTCATACTCTCTCAAAAAT 57.323 39.130 0.00 0.00 0.00 1.82
2848 3194 6.262273 GGAAGAATTTGTCCTTGAAGTACACA 59.738 38.462 0.00 0.00 0.00 3.72
2983 3329 2.554032 GTTGTCCACAATGTCCTGGAAG 59.446 50.000 0.00 0.00 38.33 3.46
3118 3464 0.601558 CTGCTTGCATTGCCTTGTCT 59.398 50.000 6.12 0.00 0.00 3.41
3264 3610 2.142356 TGTGGGGATATGCCAACAAG 57.858 50.000 20.47 0.00 38.95 3.16
3333 3679 5.824904 AAACTGATGCAATCTCCACATAC 57.175 39.130 0.00 0.00 45.81 2.39
3506 3852 4.023792 TGTCTCTGTTAATTGTTGCTGCAG 60.024 41.667 10.11 10.11 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 101 5.446143 ACAGAACAAAACAACAACACTCA 57.554 34.783 0.00 0.00 0.00 3.41
164 167 9.561069 ACACAGAAAGTCAGAAAAATACACTAT 57.439 29.630 0.00 0.00 0.00 2.12
185 189 2.654863 ACTGGGACAAAAAGGACACAG 58.345 47.619 0.00 0.00 38.70 3.66
209 213 9.787435 TGTAAAACCTAAGAGACATTACATTGT 57.213 29.630 0.00 0.00 29.62 2.71
224 228 8.030106 CCACAAAAAGAACACTGTAAAACCTAA 58.970 33.333 0.00 0.00 0.00 2.69
241 245 5.167845 ACACTGCAAAACTACCACAAAAAG 58.832 37.500 0.00 0.00 0.00 2.27
282 291 6.766467 ACTGTAAAAGGCTAGCACCATTATAC 59.234 38.462 18.24 10.02 0.00 1.47
289 298 2.779506 ACACTGTAAAAGGCTAGCACC 58.220 47.619 18.24 0.00 0.00 5.01
328 337 8.289618 ACTGTACAAACTAGCACAATTACATTG 58.710 33.333 0.00 0.00 45.59 2.82
329 338 8.289618 CACTGTACAAACTAGCACAATTACATT 58.710 33.333 0.00 0.00 0.00 2.71
330 339 7.444183 ACACTGTACAAACTAGCACAATTACAT 59.556 33.333 0.00 0.00 0.00 2.29
331 340 6.764085 ACACTGTACAAACTAGCACAATTACA 59.236 34.615 0.00 0.00 0.00 2.41
332 341 7.186021 ACACTGTACAAACTAGCACAATTAC 57.814 36.000 0.00 0.00 0.00 1.89
333 342 8.890124 TTACACTGTACAAACTAGCACAATTA 57.110 30.769 0.00 0.00 0.00 1.40
334 343 7.795482 TTACACTGTACAAACTAGCACAATT 57.205 32.000 0.00 0.00 0.00 2.32
335 344 7.878127 AGATTACACTGTACAAACTAGCACAAT 59.122 33.333 0.00 0.00 0.00 2.71
376 385 7.653767 AAGCACAACTACACTGTAATAGAAC 57.346 36.000 5.53 0.00 0.00 3.01
379 388 8.758633 AACTAAGCACAACTACACTGTAATAG 57.241 34.615 0.00 0.00 0.00 1.73
384 394 6.819649 TGTAAAACTAAGCACAACTACACTGT 59.180 34.615 0.00 0.00 0.00 3.55
392 402 9.511144 AAATTACAGTGTAAAACTAAGCACAAC 57.489 29.630 19.19 0.00 36.83 3.32
417 427 6.040278 TGAGTATTGGACAAAAATGCACAGAA 59.960 34.615 0.00 0.00 0.00 3.02
420 430 5.068329 TGTGAGTATTGGACAAAAATGCACA 59.932 36.000 0.00 0.00 0.00 4.57
424 434 6.738114 ACACTGTGAGTATTGGACAAAAATG 58.262 36.000 15.86 0.00 0.00 2.32
426 436 7.051623 ACTACACTGTGAGTATTGGACAAAAA 58.948 34.615 15.86 0.00 0.00 1.94
427 437 6.588204 ACTACACTGTGAGTATTGGACAAAA 58.412 36.000 15.86 0.00 0.00 2.44
428 438 6.169557 ACTACACTGTGAGTATTGGACAAA 57.830 37.500 15.86 0.00 0.00 2.83
439 449 4.244425 ACTAGCACAACTACACTGTGAG 57.756 45.455 15.86 9.88 45.80 3.51
448 458 4.037327 TGCAATGCAAAACTAGCACAACTA 59.963 37.500 5.01 0.00 45.95 2.24
464 474 5.170021 TGTAAATGAGTGGATTTGCAATGC 58.830 37.500 0.00 0.00 35.70 3.56
476 486 7.792374 AGCACCATTATACTGTAAATGAGTG 57.208 36.000 20.72 20.72 37.35 3.51
577 671 7.445402 AGCAGAACTACACTGTAATTGAACAAT 59.555 33.333 0.00 0.00 37.64 2.71
582 676 7.228314 ACTAGCAGAACTACACTGTAATTGA 57.772 36.000 0.00 0.00 37.64 2.57
583 677 7.891183 AACTAGCAGAACTACACTGTAATTG 57.109 36.000 0.00 0.00 37.64 2.32
753 848 7.677747 GCACTGTAAAAACTAGCACAAGTACAA 60.678 37.037 0.00 0.00 0.00 2.41
892 1054 7.395190 ACAACATAATGCACTGTCATTACAT 57.605 32.000 11.94 4.63 40.48 2.29
900 1062 9.613428 ATGTAAGTATACAACATAATGCACTGT 57.387 29.630 17.56 0.00 44.81 3.55
1038 1219 8.722394 TCAGCACTATCTAAAGATGATACTACG 58.278 37.037 2.66 0.00 36.05 3.51
1366 1563 9.476202 AGGCATTTTACTTTCTGAAAACATAAC 57.524 29.630 4.18 0.00 0.00 1.89
1462 1661 9.836864 AGCATTTTTCTTCCAGAAAGTAAAAAT 57.163 25.926 6.46 11.16 44.14 1.82
1476 1677 9.905171 AAGATAGAACTTCAAGCATTTTTCTTC 57.095 29.630 0.00 0.00 0.00 2.87
1805 2148 4.650754 AGTAGCACAAGTAGGGTAATCG 57.349 45.455 0.00 0.00 0.00 3.34
2165 2510 6.293190 CGACTGTGGTTGATTTTAGCTTGTTA 60.293 38.462 0.00 0.00 0.00 2.41
2191 2536 2.996631 AGACATCTTCATCAGGCAACC 58.003 47.619 0.00 0.00 37.17 3.77
2740 3085 7.655521 TGGAGCTAAATTTAGTGCTACTAGA 57.344 36.000 22.94 2.53 37.29 2.43
2848 3194 5.070446 GGAAAACAGGAAAAAGTTCATCCCT 59.930 40.000 3.83 0.00 35.25 4.20
3118 3464 9.948964 CATCCTATATCAATCATTACAGACCAA 57.051 33.333 0.00 0.00 0.00 3.67
3287 3633 6.854496 TGACACTACATTCCTAACAAACAC 57.146 37.500 0.00 0.00 0.00 3.32
3333 3679 5.233050 GTGAGGTCAAGAATGATGTATGACG 59.767 44.000 0.00 0.00 40.92 4.35
3506 3852 6.092748 ACACAAAGAAACATGTCACAAACTC 58.907 36.000 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.