Multiple sequence alignment - TraesCS1B01G253000

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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 TraesCS1B01G253000 chr1B 100.000 1703 0 0 916 2618 445877856 445879558 0.000000e+00 3145.0
1 TraesCS1B01G253000 chr1B 100.000 726 0 0 1 726 445876941 445877666 0.000000e+00 1341.0
2 TraesCS1B01G253000 chr1D 92.599 1716 89 11 916 2618 331505744 331507434 0.000000e+00 2431.0
3 TraesCS1B01G253000 chr1D 93.989 732 26 8 1 726 331504923 331505642 0.000000e+00 1092.0
4 TraesCS1B01G253000 chr1A 97.276 881 23 1 916 1795 428663719 428664599 0.000000e+00 1493.0
5 TraesCS1B01G253000 chr1A 91.792 731 30 9 1 726 428662912 428663617 0.000000e+00 990.0
6 TraesCS1B01G253000 chr1A 88.911 514 53 4 1846 2359 428664614 428665123 4.750000e-177 630.0
7 TraesCS1B01G253000 chr2D 86.047 86 12 0 1484 1569 77170659 77170574 2.770000e-15 93.5
8 TraesCS1B01G253000 chr2B 82.524 103 15 2 1484 1586 119049476 119049377 1.290000e-13 87.9
9 TraesCS1B01G253000 chr2A 84.884 86 13 0 1484 1569 78183045 78182960 1.290000e-13 87.9
10 TraesCS1B01G253000 chr7A 81.081 111 16 4 1460 1569 547757616 547757510 1.670000e-12 84.2
11 TraesCS1B01G253000 chr7D 88.406 69 3 4 1460 1527 447908014 447908078 7.770000e-11 78.7
12 TraesCS1B01G253000 chr7B 87.879 66 3 4 1460 1524 465216986 465217047 3.610000e-09 73.1


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 TraesCS1B01G253000 chr1B 445876941 445879558 2617 False 2243.000000 3145 100.000000 1 2618 2 chr1B.!!$F1 2617
1 TraesCS1B01G253000 chr1D 331504923 331507434 2511 False 1761.500000 2431 93.294000 1 2618 2 chr1D.!!$F1 2617
2 TraesCS1B01G253000 chr1A 428662912 428665123 2211 False 1037.666667 1493 92.659667 1 2359 3 chr1A.!!$F1 2358

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
696 706 1.340502 TGATATTTGAACAGCCGGCCA 60.341 47.619 26.15 11.55 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2453 2477 0.107214 TCATCGACATTCCCCCAAGC 60.107 55.0 0.0 0.0 0.0 4.01 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
36 37 5.795766 TGCGACATCTAAATTAAAGCGAAG 58.204 37.500 0.00 0.00 0.00 3.79
221 222 3.000082 GCCACAATTATCTTTAGGCGC 58.000 47.619 0.00 0.00 0.00 6.53
268 269 8.548721 AGAAGAAGACAATGTTACGTTACTTTG 58.451 33.333 23.56 23.56 38.45 2.77
480 482 9.911788 ATTCTATCATGGTTGAATGAACTAAGT 57.088 29.630 13.82 0.00 39.90 2.24
487 489 7.724305 TGGTTGAATGAACTAAGTAAGTGAC 57.276 36.000 0.00 0.00 38.88 3.67
555 557 7.050377 TCCATGAGAAGAACCATTCACTAATC 58.950 38.462 0.00 0.00 0.00 1.75
696 706 1.340502 TGATATTTGAACAGCCGGCCA 60.341 47.619 26.15 11.55 0.00 5.36
1419 1429 0.752009 TCCTCCCGGAGTTCATCGAG 60.752 60.000 13.62 0.00 33.30 4.04
1584 1594 0.679505 CGATATCGGAGGCCAGGAAA 59.320 55.000 17.51 0.00 35.37 3.13
1628 1638 4.671590 TCGGTGAGGCTGGTCGGA 62.672 66.667 0.00 0.00 0.00 4.55
1629 1639 4.135153 CGGTGAGGCTGGTCGGAG 62.135 72.222 0.00 0.00 0.00 4.63
1718 1739 3.897239 TCTCCATCAAGAGAGAGGAGTC 58.103 50.000 13.19 0.00 44.35 3.36
1769 1790 2.038557 ACTAGCGGAAAAGAGGCAAGAA 59.961 45.455 0.00 0.00 0.00 2.52
1798 1819 7.842887 AGATAGTTTAGAAGGAGATGGGTAC 57.157 40.000 0.00 0.00 0.00 3.34
1799 1820 7.363031 AGATAGTTTAGAAGGAGATGGGTACA 58.637 38.462 0.00 0.00 0.00 2.90
1800 1821 7.844779 AGATAGTTTAGAAGGAGATGGGTACAA 59.155 37.037 0.00 0.00 0.00 2.41
1842 1863 9.651718 GTTCTAGTTCATTCAGTTTTGTGTTAG 57.348 33.333 0.00 0.00 0.00 2.34
1850 1871 8.474025 TCATTCAGTTTTGTGTTAGACCAAAAT 58.526 29.630 0.00 0.00 41.17 1.82
1878 1899 5.803967 GGATGCAGTTGAATGAATGAGTTTC 59.196 40.000 0.00 0.00 34.72 2.78
1917 1938 6.151663 TGCAGTTCATCATAATTCCATTGG 57.848 37.500 0.00 0.00 0.00 3.16
1919 1940 6.183360 TGCAGTTCATCATAATTCCATTGGTC 60.183 38.462 1.86 0.00 0.00 4.02
1928 1949 6.331042 TCATAATTCCATTGGTCTGATCTCCT 59.669 38.462 1.86 0.00 0.00 3.69
1958 1979 6.866480 TCCAGCTGGATCATAAAAATGAAAC 58.134 36.000 32.00 0.00 39.78 2.78
1965 1986 8.752005 TGGATCATAAAAATGAAACTAGAGGG 57.248 34.615 0.00 0.00 33.83 4.30
1978 1999 3.371965 ACTAGAGGGCTCAAATTCCGTA 58.628 45.455 0.00 0.00 0.00 4.02
2089 2111 9.483062 GTTCAACATCGAATCTAAAGAATCTTG 57.517 33.333 0.00 0.00 0.00 3.02
2114 2136 5.715439 AGAACACCCCTTGAATATCATGA 57.285 39.130 0.00 0.00 0.00 3.07
2174 2196 2.797156 CTCGGCCTTTGAATGTAGATCG 59.203 50.000 0.00 0.00 0.00 3.69
2226 2248 3.055675 TGTGTAATTACGGGACTCCTTGG 60.056 47.826 10.92 0.00 0.00 3.61
2244 2267 1.337118 GGGGGTTGTCTGCAAATTCA 58.663 50.000 0.00 0.00 36.22 2.57
2274 2297 0.183492 CCCTACCACCATGGGATGTG 59.817 60.000 18.09 4.76 43.37 3.21
2370 2393 2.099062 GCTTGATTGGCGCGTCAG 59.901 61.111 15.27 2.36 0.00 3.51
2397 2420 9.634163 AAGAAAAACGCCCTTACATTATTTAAG 57.366 29.630 0.00 0.00 0.00 1.85
2401 2424 8.514330 AAACGCCCTTACATTATTTAAGATCA 57.486 30.769 0.00 0.00 0.00 2.92
2453 2477 1.596954 GGCTTGTTGCATTATACGCGG 60.597 52.381 12.47 0.00 45.15 6.46
2459 2483 1.163420 TGCATTATACGCGGCTTGGG 61.163 55.000 12.47 0.00 0.00 4.12
2482 2506 1.888215 ATGTCGATGATGTGGCATCC 58.112 50.000 6.65 0.00 41.21 3.51
2483 2507 0.540923 TGTCGATGATGTGGCATCCA 59.459 50.000 6.65 0.00 41.21 3.41
2513 2537 3.034721 TCCGCGTAAGATTGACTGTTT 57.965 42.857 4.92 0.00 43.02 2.83
2515 2539 2.495939 CGCGTAAGATTGACTGTTTGC 58.504 47.619 0.00 0.00 43.02 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 5.198274 CCTTCGCTTTAATTTAGATGTCGC 58.802 41.667 0.00 0.00 0.00 5.19
36 37 3.991121 GGATAGCGCAAGAGAAGATAACC 59.009 47.826 11.47 0.00 43.02 2.85
115 116 3.200483 CGTGATCATTGATTGCCAGAGA 58.800 45.455 0.00 0.00 0.00 3.10
116 117 2.941064 ACGTGATCATTGATTGCCAGAG 59.059 45.455 0.00 0.00 0.00 3.35
117 118 2.989909 ACGTGATCATTGATTGCCAGA 58.010 42.857 0.00 0.00 0.00 3.86
236 237 5.107453 CGTAACATTGTCTTCTTCTGGTGAC 60.107 44.000 0.00 0.00 0.00 3.67
242 243 8.548721 CAAAGTAACGTAACATTGTCTTCTTCT 58.451 33.333 0.00 0.00 0.00 2.85
268 269 1.285578 GCTTGCGAGAGAAGACATCC 58.714 55.000 4.70 0.00 0.00 3.51
477 479 2.700897 ACAGTGCTCCAGTCACTTACTT 59.299 45.455 0.00 0.00 42.38 2.24
478 480 2.320781 ACAGTGCTCCAGTCACTTACT 58.679 47.619 0.00 0.00 42.38 2.24
479 481 2.821991 ACAGTGCTCCAGTCACTTAC 57.178 50.000 0.00 0.00 42.38 2.34
480 482 4.149598 TCTAACAGTGCTCCAGTCACTTA 58.850 43.478 0.00 0.00 42.38 2.24
481 483 2.965831 TCTAACAGTGCTCCAGTCACTT 59.034 45.455 0.00 0.00 42.38 3.16
487 489 3.599730 TGACATCTAACAGTGCTCCAG 57.400 47.619 0.00 0.00 0.00 3.86
646 653 9.639601 CAGTTGACCTTAGTTTTTCTTTTTCTT 57.360 29.630 0.00 0.00 0.00 2.52
647 654 8.803235 ACAGTTGACCTTAGTTTTTCTTTTTCT 58.197 29.630 0.00 0.00 0.00 2.52
648 655 8.981724 ACAGTTGACCTTAGTTTTTCTTTTTC 57.018 30.769 0.00 0.00 0.00 2.29
657 664 5.568620 ATCAGGACAGTTGACCTTAGTTT 57.431 39.130 0.30 0.00 38.11 2.66
696 706 8.410912 GGGTGTTATTTTACTCAAAAGTTGACT 58.589 33.333 0.00 0.00 37.08 3.41
1155 1165 3.062466 CCGGAGCAGACGAGGTGA 61.062 66.667 0.00 0.00 0.00 4.02
1229 1239 2.875322 GAAGTAGGTCCTCCCCGCCT 62.875 65.000 0.00 0.00 36.47 5.52
1237 1247 0.971447 GGGAGCACGAAGTAGGTCCT 60.971 60.000 10.08 0.00 46.95 3.85
1419 1429 0.797249 CGTCGGACGTGATCACCTTC 60.797 60.000 21.68 15.51 36.74 3.46
1584 1594 0.692419 ATGTCGGCATCCTTCTCCCT 60.692 55.000 0.00 0.00 0.00 4.20
1628 1638 4.572389 CGGCTGCTAATGTTATCTTGAACT 59.428 41.667 0.00 0.00 0.00 3.01
1629 1639 4.786609 GCGGCTGCTAATGTTATCTTGAAC 60.787 45.833 11.21 0.00 38.39 3.18
1665 1685 1.056700 AGAAGACACCACACCTGGCT 61.057 55.000 0.00 0.00 42.08 4.75
1718 1739 6.366332 ACAATTAAGCGAGACTGAAACACTAG 59.634 38.462 0.00 0.00 0.00 2.57
1769 1790 7.222872 CCATCTCCTTCTAAACTATCTTGCAT 58.777 38.462 0.00 0.00 0.00 3.96
1850 1871 6.604396 ACTCATTCATTCAACTGCATCCAATA 59.396 34.615 0.00 0.00 0.00 1.90
1878 1899 4.430137 ACTGCAGCAAAGTATCAATGTG 57.570 40.909 15.27 0.00 0.00 3.21
1917 1938 0.463620 GGACCAGCAGGAGATCAGAC 59.536 60.000 0.35 0.00 38.69 3.51
1919 1940 0.464870 CTGGACCAGCAGGAGATCAG 59.535 60.000 8.99 0.09 38.69 2.90
1958 1979 2.990066 ACGGAATTTGAGCCCTCTAG 57.010 50.000 0.00 0.00 0.00 2.43
1988 2009 7.750229 ACTTATTGGTACGGTCGATATTAGA 57.250 36.000 0.00 0.00 0.00 2.10
1989 2010 7.540055 GGAACTTATTGGTACGGTCGATATTAG 59.460 40.741 0.00 0.00 0.00 1.73
1990 2011 7.014134 TGGAACTTATTGGTACGGTCGATATTA 59.986 37.037 0.00 0.00 0.00 0.98
1992 2013 5.302568 TGGAACTTATTGGTACGGTCGATAT 59.697 40.000 0.00 0.00 0.00 1.63
1993 2014 4.644234 TGGAACTTATTGGTACGGTCGATA 59.356 41.667 0.00 0.00 0.00 2.92
1994 2015 3.448301 TGGAACTTATTGGTACGGTCGAT 59.552 43.478 0.00 0.00 0.00 3.59
1995 2016 2.824936 TGGAACTTATTGGTACGGTCGA 59.175 45.455 0.00 0.00 0.00 4.20
1996 2017 3.235157 TGGAACTTATTGGTACGGTCG 57.765 47.619 0.00 0.00 0.00 4.79
1997 2018 5.644636 TCATTTGGAACTTATTGGTACGGTC 59.355 40.000 0.00 0.00 0.00 4.79
1998 2019 5.413523 GTCATTTGGAACTTATTGGTACGGT 59.586 40.000 0.00 0.00 0.00 4.83
1999 2020 5.163693 GGTCATTTGGAACTTATTGGTACGG 60.164 44.000 0.00 0.00 0.00 4.02
2000 2021 5.646360 AGGTCATTTGGAACTTATTGGTACG 59.354 40.000 0.00 0.00 42.28 3.67
2005 2026 6.430925 TCAGACAGGTCATTTGGAACTTATTG 59.569 38.462 1.84 0.00 42.28 1.90
2086 2108 6.434028 TGATATTCAAGGGGTGTTCTTTCAAG 59.566 38.462 0.00 0.00 0.00 3.02
2089 2111 6.603201 TCATGATATTCAAGGGGTGTTCTTTC 59.397 38.462 0.00 0.00 0.00 2.62
2129 2151 1.354040 CGCTAGAGCACCTGAACTTG 58.646 55.000 1.89 0.00 42.21 3.16
2150 2172 2.027192 TCTACATTCAAAGGCCGAGCTT 60.027 45.455 0.00 0.00 0.00 3.74
2160 2182 6.560711 TCTGATCGTTCGATCTACATTCAAA 58.439 36.000 27.33 10.01 41.00 2.69
2174 2196 5.277825 CAGTAACTCCTCATCTGATCGTTC 58.722 45.833 0.00 0.00 0.00 3.95
2226 2248 2.299867 ACATGAATTTGCAGACAACCCC 59.700 45.455 0.00 0.00 34.87 4.95
2244 2267 1.490574 GTGGTAGGGAGAGCTCACAT 58.509 55.000 17.77 8.67 34.87 3.21
2274 2297 3.682292 AAGCTCGGCCGTTGGATCC 62.682 63.158 27.15 4.20 0.00 3.36
2282 2305 0.526524 CTACAGAAGAAGCTCGGCCG 60.527 60.000 22.12 22.12 0.00 6.13
2329 2352 5.412384 CTGGTCTTAGGGGGAAATATCCTA 58.588 45.833 0.00 0.00 45.77 2.94
2370 2393 9.628746 TTAAATAATGTAAGGGCGTTTTTCTTC 57.371 29.630 0.00 0.00 0.00 2.87
2445 2469 1.412453 ATTCCCCCAAGCCGCGTATA 61.412 55.000 4.92 0.00 0.00 1.47
2446 2470 2.752807 ATTCCCCCAAGCCGCGTAT 61.753 57.895 4.92 0.00 0.00 3.06
2453 2477 0.107214 TCATCGACATTCCCCCAAGC 60.107 55.000 0.00 0.00 0.00 4.01
2459 2483 0.947244 GCCACATCATCGACATTCCC 59.053 55.000 0.00 0.00 0.00 3.97
2482 2506 1.061131 CTTACGCGGATTGCTGAGTTG 59.939 52.381 12.47 0.00 43.27 3.16
2483 2507 1.067142 TCTTACGCGGATTGCTGAGTT 60.067 47.619 12.47 0.00 43.27 3.01
2503 2527 0.831711 GGGTGGGGCAAACAGTCAAT 60.832 55.000 0.00 0.00 0.00 2.57
2513 2537 1.006813 ATGTTCTATTGGGTGGGGCA 58.993 50.000 0.00 0.00 0.00 5.36
2515 2539 1.411501 CCCATGTTCTATTGGGTGGGG 60.412 57.143 0.26 0.00 46.38 4.96
2560 2584 8.934023 TCCTATTTACAGAAGTTTGTTCCATT 57.066 30.769 0.00 0.00 32.56 3.16


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

AutoCloner maintained by Alex Coulton.