Multiple sequence alignment - TraesCS3B01G382200

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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 TraesCS3B01G382200 chr3B 100.000 2240 0 0 1 2240 602302023 602304262 0.000000e+00 4137
1 TraesCS3B01G382200 chr3D 95.914 1860 54 8 384 2240 455864057 455865897 0.000000e+00 2994
2 TraesCS3B01G382200 chr3D 95.331 257 12 0 1 257 455863645 455863901 2.070000e-110 409
3 TraesCS3B01G382200 chr3D 95.652 46 2 0 253 298 455863935 455863980 8.580000e-10 75
4 TraesCS3B01G382200 chr3A 95.668 1870 64 8 384 2240 598548936 598550801 0.000000e+00 2988
5 TraesCS3B01G382200 chr3A 91.946 298 21 2 1 298 598548564 598548858 4.450000e-112 414


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 TraesCS3B01G382200 chr3B 602302023 602304262 2239 False 4137.000000 4137 100.000000 1 2240 1 chr3B.!!$F1 2239
1 TraesCS3B01G382200 chr3D 455863645 455865897 2252 False 1159.333333 2994 95.632333 1 2240 3 chr3D.!!$F1 2239
2 TraesCS3B01G382200 chr3A 598548564 598550801 2237 False 1701.000000 2988 93.807000 1 2240 2 chr3A.!!$F1 2239

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
207 208 0.807496 GCACATGAAGCCTCCTTGAC 59.193 55.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1918 2002 0.458543 CTACATGTCGCGCTCCAACT 60.459 55.0 0.0 0.0 0.0 3.16 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
118 119 2.012673 GTTGCACATCTCATCAGGGTC 58.987 52.381 0.00 0.00 0.00 4.46
207 208 0.807496 GCACATGAAGCCTCCTTGAC 59.193 55.000 0.00 0.00 0.00 3.18
298 337 7.076842 ACATTTGCACTACATAGTTGATCAC 57.923 36.000 0.00 0.00 33.46 3.06
321 398 7.119699 TCACTCTACATCAAATGACCAACAATC 59.880 37.037 0.00 0.00 0.00 2.67
325 402 3.998099 TCAAATGACCAACAATCGCAA 57.002 38.095 0.00 0.00 0.00 4.85
335 412 3.245048 CCAACAATCGCAAAAGTTCCAAC 59.755 43.478 0.00 0.00 0.00 3.77
347 424 1.900486 AGTTCCAACTTACTCCCTCCG 59.100 52.381 0.00 0.00 35.21 4.63
348 425 1.622312 GTTCCAACTTACTCCCTCCGT 59.378 52.381 0.00 0.00 0.00 4.69
349 426 2.827921 GTTCCAACTTACTCCCTCCGTA 59.172 50.000 0.00 0.00 0.00 4.02
350 427 3.173953 TCCAACTTACTCCCTCCGTAA 57.826 47.619 0.00 0.00 0.00 3.18
351 428 3.509442 TCCAACTTACTCCCTCCGTAAA 58.491 45.455 0.00 0.00 0.00 2.01
352 429 4.098894 TCCAACTTACTCCCTCCGTAAAT 58.901 43.478 0.00 0.00 0.00 1.40
353 430 4.081309 TCCAACTTACTCCCTCCGTAAATG 60.081 45.833 0.00 0.00 0.00 2.32
354 431 3.538634 ACTTACTCCCTCCGTAAATGC 57.461 47.619 0.00 0.00 0.00 3.56
355 432 3.105283 ACTTACTCCCTCCGTAAATGCT 58.895 45.455 0.00 0.00 0.00 3.79
356 433 3.132467 ACTTACTCCCTCCGTAAATGCTC 59.868 47.826 0.00 0.00 0.00 4.26
357 434 1.867363 ACTCCCTCCGTAAATGCTCT 58.133 50.000 0.00 0.00 0.00 4.09
358 435 1.757699 ACTCCCTCCGTAAATGCTCTC 59.242 52.381 0.00 0.00 0.00 3.20
359 436 1.757118 CTCCCTCCGTAAATGCTCTCA 59.243 52.381 0.00 0.00 0.00 3.27
360 437 2.366916 CTCCCTCCGTAAATGCTCTCAT 59.633 50.000 0.00 0.00 33.53 2.90
361 438 3.572642 TCCCTCCGTAAATGCTCTCATA 58.427 45.455 0.00 0.00 31.46 2.15
362 439 4.160329 TCCCTCCGTAAATGCTCTCATAT 58.840 43.478 0.00 0.00 31.46 1.78
363 440 4.593206 TCCCTCCGTAAATGCTCTCATATT 59.407 41.667 0.00 0.00 31.46 1.28
364 441 5.071788 TCCCTCCGTAAATGCTCTCATATTT 59.928 40.000 0.00 0.00 31.46 1.40
365 442 5.765182 CCCTCCGTAAATGCTCTCATATTTT 59.235 40.000 0.00 0.00 31.46 1.82
366 443 6.263168 CCCTCCGTAAATGCTCTCATATTTTT 59.737 38.462 0.00 0.00 31.46 1.94
425 509 1.953686 TCGTCGTATCATCATGGCAGA 59.046 47.619 0.00 0.00 0.00 4.26
455 539 2.033602 GGAAGGGTTGGGTGTCGG 59.966 66.667 0.00 0.00 0.00 4.79
621 705 4.899239 CAGATGAGCCCGGACGCC 62.899 72.222 0.73 0.00 0.00 5.68
1023 1107 2.187946 GTCCCGATGACCTGGCTG 59.812 66.667 0.00 0.00 38.09 4.85
1103 1187 3.148279 GGAGGCGGTGGAGACGAT 61.148 66.667 0.00 0.00 0.00 3.73
1227 1311 1.671379 GAAGTTGGTCTCGGCCACC 60.671 63.158 2.24 3.10 38.42 4.61
1621 1705 2.615618 GAATAGAGCGTGCGTGCG 59.384 61.111 0.00 0.00 40.67 5.34
1644 1728 2.280183 GCATGTCTCGTCGAAATCTGTC 59.720 50.000 0.00 0.00 0.00 3.51
1659 1743 1.201647 TCTGTCGGTCGATCAGAAACC 59.798 52.381 16.81 0.00 35.65 3.27
1672 1756 1.263217 CAGAAACCACGCACCTTGTAC 59.737 52.381 0.00 0.00 0.00 2.90
1767 1851 1.779092 CCACATGAATCCCCAGGAGAT 59.221 52.381 0.00 0.00 34.05 2.75
1888 1972 5.230942 AGTATCACACAACACAAGTAGCTC 58.769 41.667 0.00 0.00 0.00 4.09
1918 2002 6.830838 TGATCATCTCTAGCAAGTAGTTCTCA 59.169 38.462 0.00 0.00 0.00 3.27
1926 2010 2.739379 GCAAGTAGTTCTCAGTTGGAGC 59.261 50.000 0.00 0.00 43.70 4.70
1940 2024 0.179137 TGGAGCGCGACATGTAGAAG 60.179 55.000 12.10 4.01 0.00 2.85
1941 2026 0.100682 GGAGCGCGACATGTAGAAGA 59.899 55.000 12.10 0.00 0.00 2.87
2009 2098 1.457346 GGAAGAAGGTCATGCCACAG 58.543 55.000 8.58 0.00 40.61 3.66
2042 2131 5.433526 CCGGAGTAAAACCATTGGAAGATA 58.566 41.667 10.37 0.00 0.00 1.98
2069 2158 0.890996 AAAAGCTTCCCAGGCACGAG 60.891 55.000 0.00 0.00 0.00 4.18
2102 2191 4.127171 GAGACACTTGCTTCCTGTGTTAA 58.873 43.478 0.00 0.00 43.81 2.01
2122 2211 7.462844 TGTTAAGAAACAGAGGCACTCCAATC 61.463 42.308 0.00 0.00 44.53 2.67
2129 2218 2.622064 AGGCACTCCAATCGATTACC 57.378 50.000 10.97 5.94 33.74 2.85
2170 2259 0.107831 TGTTGCTTGCTACCGGAGTT 59.892 50.000 9.46 0.00 0.00 3.01
2171 2260 0.517316 GTTGCTTGCTACCGGAGTTG 59.483 55.000 9.46 0.00 0.00 3.16
2172 2261 0.394938 TTGCTTGCTACCGGAGTTGA 59.605 50.000 9.46 0.00 0.00 3.18
2173 2262 0.037326 TGCTTGCTACCGGAGTTGAG 60.037 55.000 9.46 1.03 0.00 3.02
2174 2263 1.362406 GCTTGCTACCGGAGTTGAGC 61.362 60.000 9.46 8.36 35.43 4.26
2175 2264 0.037326 CTTGCTACCGGAGTTGAGCA 60.037 55.000 9.46 11.95 42.98 4.26
2200 2289 3.861840 GCAGTAGCTAGGTTTCATGTGA 58.138 45.455 0.00 0.00 37.91 3.58
2201 2290 3.619038 GCAGTAGCTAGGTTTCATGTGAC 59.381 47.826 0.00 0.00 37.91 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 0.878416 TTGCCAACACGCACTATTCC 59.122 50.000 0.00 0.00 38.83 3.01
118 119 1.699730 AAACCCGGAGAAACCAAAGG 58.300 50.000 0.73 0.00 38.90 3.11
207 208 4.778579 AGTGGATCAGATGAATCAACAGG 58.221 43.478 0.00 0.00 0.00 4.00
298 337 6.481134 CGATTGTTGGTCATTTGATGTAGAG 58.519 40.000 0.00 0.00 0.00 2.43
310 387 3.490078 GGAACTTTTGCGATTGTTGGTCA 60.490 43.478 0.00 0.00 0.00 4.02
321 398 3.304458 GGGAGTAAGTTGGAACTTTTGCG 60.304 47.826 9.95 0.00 46.52 4.85
325 402 3.244457 CGGAGGGAGTAAGTTGGAACTTT 60.244 47.826 9.95 0.00 46.52 2.66
335 412 3.385111 AGAGCATTTACGGAGGGAGTAAG 59.615 47.826 0.00 0.00 35.75 2.34
339 416 1.757118 TGAGAGCATTTACGGAGGGAG 59.243 52.381 0.00 0.00 0.00 4.30
340 417 1.860641 TGAGAGCATTTACGGAGGGA 58.139 50.000 0.00 0.00 0.00 4.20
341 418 2.918712 ATGAGAGCATTTACGGAGGG 57.081 50.000 0.00 0.00 0.00 4.30
342 419 6.867662 AAAATATGAGAGCATTTACGGAGG 57.132 37.500 0.00 0.00 35.94 4.30
364 441 4.495565 TGTACTCCCTCCCTCTGTAAAAA 58.504 43.478 0.00 0.00 0.00 1.94
365 442 4.136341 TGTACTCCCTCCCTCTGTAAAA 57.864 45.455 0.00 0.00 0.00 1.52
366 443 3.839323 TGTACTCCCTCCCTCTGTAAA 57.161 47.619 0.00 0.00 0.00 2.01
367 444 3.643237 CATGTACTCCCTCCCTCTGTAA 58.357 50.000 0.00 0.00 0.00 2.41
368 445 2.690026 GCATGTACTCCCTCCCTCTGTA 60.690 54.545 0.00 0.00 0.00 2.74
369 446 1.967274 GCATGTACTCCCTCCCTCTGT 60.967 57.143 0.00 0.00 0.00 3.41
370 447 0.755686 GCATGTACTCCCTCCCTCTG 59.244 60.000 0.00 0.00 0.00 3.35
371 448 0.639392 AGCATGTACTCCCTCCCTCT 59.361 55.000 0.00 0.00 0.00 3.69
372 449 2.383442 TAGCATGTACTCCCTCCCTC 57.617 55.000 0.00 0.00 0.00 4.30
373 450 2.180086 TGATAGCATGTACTCCCTCCCT 59.820 50.000 0.00 0.00 0.00 4.20
374 451 2.300437 GTGATAGCATGTACTCCCTCCC 59.700 54.545 0.00 0.00 0.00 4.30
375 452 3.235200 AGTGATAGCATGTACTCCCTCC 58.765 50.000 0.00 0.00 0.00 4.30
376 453 5.317808 TCTAGTGATAGCATGTACTCCCTC 58.682 45.833 0.00 0.00 0.00 4.30
377 454 5.326283 TCTAGTGATAGCATGTACTCCCT 57.674 43.478 0.00 0.00 0.00 4.20
378 455 5.712446 TGATCTAGTGATAGCATGTACTCCC 59.288 44.000 0.00 0.00 32.19 4.30
379 456 6.825944 TGATCTAGTGATAGCATGTACTCC 57.174 41.667 0.00 0.00 32.19 3.85
380 457 7.825681 ACATGATCTAGTGATAGCATGTACTC 58.174 38.462 10.35 0.00 41.87 2.59
381 458 7.361628 CGACATGATCTAGTGATAGCATGTACT 60.362 40.741 11.65 0.00 42.79 2.73
382 459 6.744993 CGACATGATCTAGTGATAGCATGTAC 59.255 42.308 11.65 6.51 42.79 2.90
383 460 6.431234 ACGACATGATCTAGTGATAGCATGTA 59.569 38.462 11.65 0.00 42.79 2.29
384 461 5.242615 ACGACATGATCTAGTGATAGCATGT 59.757 40.000 11.53 11.53 44.10 3.21
425 509 3.207044 ACCCTTCCTGACCTGTAGATT 57.793 47.619 0.00 0.00 0.00 2.40
455 539 1.078143 AAGTCCCGATGAAGGCTGC 60.078 57.895 0.00 0.00 0.00 5.25
576 660 1.485978 GGGCTCTTCTCCATCCCCTAT 60.486 57.143 0.00 0.00 0.00 2.57
690 774 2.400798 GCCATCGACATGTGCGTG 59.599 61.111 1.15 7.90 0.00 5.34
814 898 2.281070 CTTCGTGCTGGCACTGGT 60.281 61.111 20.97 0.00 44.16 4.00
819 903 2.669569 GGCTTCTTCGTGCTGGCA 60.670 61.111 0.00 0.00 0.00 4.92
1621 1705 2.028523 CAGATTTCGACGAGACATGCAC 59.971 50.000 0.00 0.00 0.00 4.57
1624 1708 2.527887 CGACAGATTTCGACGAGACATG 59.472 50.000 0.00 0.00 41.78 3.21
1625 1709 2.478031 CCGACAGATTTCGACGAGACAT 60.478 50.000 0.00 0.00 41.78 3.06
1626 1710 1.135774 CCGACAGATTTCGACGAGACA 60.136 52.381 0.00 0.00 41.78 3.41
1627 1711 1.135746 ACCGACAGATTTCGACGAGAC 60.136 52.381 0.00 0.00 41.78 3.36
1628 1712 1.129998 GACCGACAGATTTCGACGAGA 59.870 52.381 0.00 0.00 41.78 4.04
1644 1728 1.683790 GCGTGGTTTCTGATCGACCG 61.684 60.000 0.00 0.00 36.22 4.79
1659 1743 1.595929 AACGGGTACAAGGTGCGTG 60.596 57.895 0.00 0.00 0.00 5.34
1672 1756 2.913765 TTTGCGTGGCATCAACGGG 61.914 57.895 4.91 0.00 38.76 5.28
1888 1972 5.518848 ACTTGCTAGAGATGATCAGTGAG 57.481 43.478 0.09 0.00 0.00 3.51
1918 2002 0.458543 CTACATGTCGCGCTCCAACT 60.459 55.000 0.00 0.00 0.00 3.16
1926 2010 2.809446 TCCATTCTTCTACATGTCGCG 58.191 47.619 0.00 0.00 0.00 5.87
1940 2024 3.751698 GCGGGTAACTTATCCATCCATTC 59.248 47.826 0.00 0.00 0.00 2.67
1941 2026 3.751518 GCGGGTAACTTATCCATCCATT 58.248 45.455 0.00 0.00 0.00 3.16
1985 2074 1.373570 GCATGACCTTCTTCCCTTCG 58.626 55.000 0.00 0.00 0.00 3.79
2042 2131 3.160269 CCTGGGAAGCTTTTTCATGTCT 58.840 45.455 0.00 0.00 0.00 3.41
2069 2158 2.935201 GCAAGTGTCTCTGATGATCCAC 59.065 50.000 0.00 0.00 0.00 4.02
2102 2191 2.613977 CGATTGGAGTGCCTCTGTTTCT 60.614 50.000 2.79 0.00 34.31 2.52
2122 2211 1.762708 AATGCTGGGTTGGGTAATCG 58.237 50.000 0.00 0.00 0.00 3.34
2129 2218 5.829924 ACAAGATAAGATAATGCTGGGTTGG 59.170 40.000 0.00 0.00 0.00 3.77
2198 2287 2.674852 CACGTACGGAGCTACTAAGTCA 59.325 50.000 21.06 0.00 0.00 3.41
2199 2288 2.538535 GCACGTACGGAGCTACTAAGTC 60.539 54.545 21.06 0.00 0.00 3.01
2200 2289 1.399791 GCACGTACGGAGCTACTAAGT 59.600 52.381 21.06 0.00 0.00 2.24
2201 2290 1.669779 AGCACGTACGGAGCTACTAAG 59.330 52.381 28.40 4.91 36.73 2.18


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

AutoCloner maintained by Alex Coulton.