Multiple sequence alignment - TraesCS2B01G483600

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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 TraesCS2B01G483600 chr2B 100.000 2456 0 0 1000 3455 680769699 680767244 0.000000e+00 4536
1 TraesCS2B01G483600 chr2B 100.000 517 0 0 1 517 680770698 680770182 0.000000e+00 955
2 TraesCS2B01G483600 chr2D 95.772 2460 73 12 1000 3455 568232163 568229731 0.000000e+00 3938
3 TraesCS2B01G483600 chr2D 96.339 519 16 2 1 517 568232742 568232225 0.000000e+00 850
4 TraesCS2B01G483600 chr2A 96.040 2222 67 8 1000 3213 707750914 707748706 0.000000e+00 3596
5 TraesCS2B01G483600 chr2A 87.129 505 47 10 25 517 707751476 707750978 1.080000e-154 556
6 TraesCS2B01G483600 chr2A 90.995 211 7 6 3243 3452 707748710 707748511 1.220000e-69 274
7 TraesCS2B01G483600 chr6D 89.695 262 21 1 1021 1276 67518504 67518243 2.570000e-86 329
8 TraesCS2B01G483600 chr6B 88.462 260 21 3 1021 1271 142503344 142503085 4.330000e-79 305
9 TraesCS2B01G483600 chr6A 89.778 225 16 2 1052 1276 85023323 85023106 7.300000e-72 281


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 TraesCS2B01G483600 chr2B 680767244 680770698 3454 True 2745.500000 4536 100.0000 1 3455 2 chr2B.!!$R1 3454
1 TraesCS2B01G483600 chr2D 568229731 568232742 3011 True 2394.000000 3938 96.0555 1 3455 2 chr2D.!!$R1 3454
2 TraesCS2B01G483600 chr2A 707748511 707751476 2965 True 1475.333333 3596 91.3880 25 3452 3 chr2A.!!$R1 3427

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
441 448 0.233590 TTGGTCGACAATTTGACGCG 59.766 50.0 18.91 3.53 37.04 6.01 F
474 481 0.251121 TGGATTTGCCTCCAAAGCGA 60.251 50.0 0.00 0.00 45.69 4.93 F
1595 1611 0.389948 GATCGAGAAGTTGGCGGTGT 60.390 55.0 0.00 0.00 0.00 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1734 1750 0.249868 TCTCACTTCTGTGTTGGCCG 60.250 55.0 0.00 0.0 44.14 6.13 R
1922 1938 1.709147 GCCGCGCTCAATGTCAATCT 61.709 55.0 5.56 0.0 0.00 2.40 R
3270 3291 0.179702 TCAGGACATCAGCCATGAGC 59.820 55.0 0.00 0.0 39.29 4.26 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
427 433 2.327940 GTGTGCACGCAGTTGGTC 59.672 61.111 25.05 0.00 41.61 4.02
437 444 1.262950 CGCAGTTGGTCGACAATTTGA 59.737 47.619 18.91 0.00 41.95 2.69
441 448 0.233590 TTGGTCGACAATTTGACGCG 59.766 50.000 18.91 3.53 37.04 6.01
474 481 0.251121 TGGATTTGCCTCCAAAGCGA 60.251 50.000 0.00 0.00 45.69 4.93
1319 1335 1.151668 CTTGCAGACGGAGAAACTGG 58.848 55.000 0.00 0.00 33.00 4.00
1358 1374 1.002468 CGGAAATCATGATGGTTCGGC 60.002 52.381 9.46 0.00 0.00 5.54
1363 1379 2.198827 TCATGATGGTTCGGCTGTTT 57.801 45.000 0.00 0.00 0.00 2.83
1516 1532 3.711190 TGCCACTATTGCAATCTCTAGGA 59.289 43.478 16.86 0.84 35.40 2.94
1595 1611 0.389948 GATCGAGAAGTTGGCGGTGT 60.390 55.000 0.00 0.00 0.00 4.16
1734 1750 1.798813 GCCAATGCCGTTAATGCTGAC 60.799 52.381 2.24 0.00 0.00 3.51
1765 1781 4.202295 ACAGAAGTGAGACATGTGTGACAT 60.202 41.667 14.71 2.53 39.91 3.06
1850 1866 5.410067 CACTGAAAATGTTGAAGTTGGTGT 58.590 37.500 0.00 0.00 0.00 4.16
1870 1886 3.146847 GTTGTTACTGGAGAAGGTTGGG 58.853 50.000 0.00 0.00 0.00 4.12
1922 1938 5.543714 TGCTTATACAGAAACGGAACTCAA 58.456 37.500 0.00 0.00 0.00 3.02
1993 2009 2.038557 GGTTCTGTTGGTCAAGGAGCTA 59.961 50.000 0.00 0.00 0.00 3.32
2094 2110 0.179020 CCATCACCATACCGCCACAT 60.179 55.000 0.00 0.00 0.00 3.21
2702 2719 1.352083 ACCACTGAGCTGGTGTGTAT 58.648 50.000 13.27 0.00 43.38 2.29
2800 2817 2.762887 CTGCAGAGATGAGTACTTGGGA 59.237 50.000 8.42 0.00 0.00 4.37
2861 2878 9.541143 TTTTTCTTGATTGGATTTACAAACTCC 57.459 29.630 0.00 0.00 33.48 3.85
2906 2923 4.825634 ACATTGCTCATATTCCACTCCATG 59.174 41.667 0.00 0.00 0.00 3.66
2922 2939 5.693104 CACTCCATGTCTTCAAATTTTGGTG 59.307 40.000 9.18 3.84 0.00 4.17
3058 3077 3.255642 TGAAATGTGGCCTCTGCTAAAAC 59.744 43.478 3.32 0.00 37.74 2.43
3088 3107 7.332430 ACCATGTCAATTTTCACAAGCATATTG 59.668 33.333 0.00 0.00 0.00 1.90
3116 3135 6.169557 ACCGGCTATCACAGTATGATTTAA 57.830 37.500 0.00 0.00 46.54 1.52
3156 3175 5.048083 ACCCATACACAACATACAGCAAAAG 60.048 40.000 0.00 0.00 0.00 2.27
3227 3248 2.352127 GCATGACAAGGCCTTTTCAGAC 60.352 50.000 31.86 23.94 33.44 3.51
3270 3291 4.568359 CGTGGACATCAGTATTTTCCTGAG 59.432 45.833 0.00 0.00 41.91 3.35
3278 3299 3.314635 CAGTATTTTCCTGAGCTCATGGC 59.685 47.826 18.63 6.95 42.19 4.40
3311 3332 8.449397 CCTGATGTTCTATGCATCTAAAATAGC 58.551 37.037 0.19 0.00 42.21 2.97
3405 3426 8.781196 CATCTGAAATTATTATCCTGGACACAG 58.219 37.037 0.00 0.00 44.51 3.66
3452 3474 7.510675 TCTATTACCTCTGTCCCAAAATTCT 57.489 36.000 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 9.918630 AAGAATGTTCACATTATTTCAAGGAAG 57.081 29.630 5.14 0.00 42.92 3.46
427 433 2.763461 CGTTTATCGCGTCAAATTGTCG 59.237 45.455 5.77 8.17 32.37 4.35
437 444 0.165079 CAGTTTGCCGTTTATCGCGT 59.835 50.000 5.77 0.00 38.35 6.01
474 481 2.683572 GGGGGCCTTTTGCGGAAT 60.684 61.111 0.84 0.00 42.61 3.01
1319 1335 3.365265 CAAGGGAGGCGCCAACAC 61.365 66.667 31.54 23.06 38.95 3.32
1358 1374 1.239968 GCCAGTCTGCCCAGAAACAG 61.240 60.000 0.00 0.00 39.48 3.16
1363 1379 0.909133 TGTATGCCAGTCTGCCCAGA 60.909 55.000 0.00 0.00 34.56 3.86
1516 1532 2.683211 AATCCTTCACCACCAGCTTT 57.317 45.000 0.00 0.00 0.00 3.51
1595 1611 6.710278 TCACCATTAGAGTCACATTCAATGA 58.290 36.000 3.79 0.00 0.00 2.57
1734 1750 0.249868 TCTCACTTCTGTGTTGGCCG 60.250 55.000 0.00 0.00 44.14 6.13
1765 1781 4.840680 AGGCAGATCAGCATGTACCTTATA 59.159 41.667 12.54 0.00 37.40 0.98
1850 1866 2.488347 GCCCAACCTTCTCCAGTAACAA 60.488 50.000 0.00 0.00 0.00 2.83
1870 1886 4.173256 CACTTTTCCATATTTTCCACGGC 58.827 43.478 0.00 0.00 0.00 5.68
1913 1929 4.436584 GCTCAATGTCAATCTTGAGTTCCG 60.437 45.833 13.59 0.00 46.48 4.30
1922 1938 1.709147 GCCGCGCTCAATGTCAATCT 61.709 55.000 5.56 0.00 0.00 2.40
1993 2009 4.184629 GTGACAGTAAAGCCATTCGAGAT 58.815 43.478 0.00 0.00 0.00 2.75
2702 2719 7.013559 ACACATCATGTTCAGAGTCATCAAAAA 59.986 33.333 0.00 0.00 38.98 1.94
2861 2878 4.654091 ACTCTTGGTTTTGTTGACATGG 57.346 40.909 0.00 0.00 0.00 3.66
2906 2923 6.538381 ACATGTTTCCACCAAAATTTGAAGAC 59.462 34.615 7.37 0.00 0.00 3.01
2922 2939 6.366315 TGCACCGTAATATTACATGTTTCC 57.634 37.500 22.27 11.08 33.28 3.13
2939 2956 4.757657 AGAGTGATAGTAGAGTATGCACCG 59.242 45.833 0.00 0.00 0.00 4.94
3029 3048 4.201657 CAGAGGCCACATTTCATATGACA 58.798 43.478 5.01 0.00 0.00 3.58
3058 3077 6.183360 TGCTTGTGAAAATTGACATGGTTTTG 60.183 34.615 0.00 0.00 0.00 2.44
3088 3107 1.883084 CTGTGATAGCCGGTTCGCC 60.883 63.158 1.90 0.00 0.00 5.54
3116 3135 7.888021 TGTGTATGGGTTAATCAAGAGAACATT 59.112 33.333 0.00 0.00 0.00 2.71
3156 3175 3.002348 GCTAAACCACAATCTGATACGCC 59.998 47.826 0.00 0.00 0.00 5.68
3227 3248 6.756542 TCCACGATCATACAGTTCAATAACAG 59.243 38.462 0.00 0.00 38.12 3.16
3270 3291 0.179702 TCAGGACATCAGCCATGAGC 59.820 55.000 0.00 0.00 39.29 4.26
3278 3299 4.700700 TGCATAGAACATCAGGACATCAG 58.299 43.478 0.00 0.00 0.00 2.90
3279 3300 4.758773 TGCATAGAACATCAGGACATCA 57.241 40.909 0.00 0.00 0.00 3.07
3280 3301 5.549347 AGATGCATAGAACATCAGGACATC 58.451 41.667 0.00 0.00 45.19 3.06
3281 3302 5.563876 AGATGCATAGAACATCAGGACAT 57.436 39.130 0.00 0.00 45.19 3.06
3282 3303 6.484364 TTAGATGCATAGAACATCAGGACA 57.516 37.500 0.00 0.00 45.19 4.02
3283 3304 7.792374 TTTTAGATGCATAGAACATCAGGAC 57.208 36.000 0.00 0.00 45.19 3.85
3284 3305 9.716531 CTATTTTAGATGCATAGAACATCAGGA 57.283 33.333 0.00 0.00 45.19 3.86
3285 3306 8.449397 GCTATTTTAGATGCATAGAACATCAGG 58.551 37.037 0.00 0.00 45.19 3.86
3311 3332 1.291877 CGAGACTCTGGTTTTGGGCG 61.292 60.000 0.03 0.00 0.00 6.13
3392 3413 4.348461 TGTGGTTAAACTGTGTCCAGGATA 59.652 41.667 0.00 0.00 43.36 2.59
3393 3414 3.137544 TGTGGTTAAACTGTGTCCAGGAT 59.862 43.478 0.00 0.00 43.36 3.24
3394 3415 2.506231 TGTGGTTAAACTGTGTCCAGGA 59.494 45.455 0.00 0.00 43.36 3.86


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

AutoCloner maintained by Alex Coulton.