Multiple sequence alignment - TraesCS2A01G255300

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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 TraesCS2A01G255300 chr2A 100.000 6022 0 0 1 6022 389448853 389442832 0.000000e+00 11121.0
1 TraesCS2A01G255300 chr2A 92.152 395 15 4 1 393 389467327 389466947 1.480000e-150 544.0
2 TraesCS2A01G255300 chr2A 97.143 35 0 1 5953 5986 389442872 389442838 2.340000e-04 58.4
3 TraesCS2A01G255300 chr2A 97.143 35 0 1 5982 6016 389442901 389442868 2.340000e-04 58.4
4 TraesCS2A01G255300 chr2D 96.864 6027 131 31 1 5986 308490359 308484350 0.000000e+00 10030.0
5 TraesCS2A01G255300 chr2B 96.921 3443 83 12 590 4026 359608018 359611443 0.000000e+00 5749.0
6 TraesCS2A01G255300 chr2B 95.445 1888 57 15 4104 5986 359611438 359613301 0.000000e+00 2983.0
7 TraesCS2A01G255300 chr2B 93.820 534 23 6 1 525 359607482 359608014 0.000000e+00 795.0
8 TraesCS2A01G255300 chrUn 89.399 283 28 2 1263 1545 77732813 77732533 7.420000e-94 355.0
9 TraesCS2A01G255300 chr3D 84.564 149 16 4 2 145 517683504 517683650 2.260000e-29 141.0
10 TraesCS2A01G255300 chr6A 82.432 148 21 4 2 145 255588528 255588674 2.280000e-24 124.0


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 TraesCS2A01G255300 chr2A 389442832 389448853 6021 True 11121.000000 11121 100.000000 1 6022 1 chr2A.!!$R1 6021
1 TraesCS2A01G255300 chr2D 308484350 308490359 6009 True 10030.000000 10030 96.864000 1 5986 1 chr2D.!!$R1 5985
2 TraesCS2A01G255300 chr2B 359607482 359613301 5819 False 3175.666667 5749 95.395333 1 5986 3 chr2B.!!$F1 5985

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
865 886 0.839853 ACTCCTCCTTGCTTGCCTCT 60.840 55.000 0.0 0.0 0.00 3.69 F
915 936 1.425066 AGCATTCCCTCAAACACCTCA 59.575 47.619 0.0 0.0 0.00 3.86 F
2208 2230 0.627451 TCCTCAAGCATGGGCATTCT 59.373 50.000 0.0 0.0 44.61 2.40 F
2585 2607 4.321899 GCCTTTTGTATGCTCCAAACATCA 60.322 41.667 0.0 0.0 31.88 3.07 F
3362 3388 2.431057 AGTTACAGGCCTTATCTCCACG 59.569 50.000 0.0 0.0 0.00 4.94 F
4712 4742 1.202770 ACGTGCCTAAACTCAAAGCCT 60.203 47.619 0.0 0.0 0.00 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2076 2098 0.681564 CTCTCGGGGACACTGCTACT 60.682 60.000 0.00 0.0 0.00 2.57 R
2397 2419 0.804989 CATTGGTCAAGTCCGCCTTC 59.195 55.000 0.00 0.0 0.00 3.46 R
3241 3267 0.468029 AGTCAAAACAGGCAGGTGGG 60.468 55.000 0.00 0.0 0.00 4.61 R
4573 4603 1.878734 TGCTGATGCGATTTGTTGTGA 59.121 42.857 0.00 0.0 43.34 3.58 R
4786 4816 0.036022 GAGCCTTGCAGAGTTGGACT 59.964 55.000 0.00 0.0 0.00 3.85 R
5636 5689 0.452184 TTCTGGAGACGCGATGAGAC 59.548 55.000 15.93 0.0 0.00 3.36 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
134 142 1.495509 GTTGCAACGCACGAGCATA 59.504 52.632 14.90 5.07 38.71 3.14
280 293 4.488126 TCTTTGAAATGGAGCTTGTTCG 57.512 40.909 0.00 0.00 0.00 3.95
341 354 1.909302 TCGGCTCCAAGAGAAAAGGAT 59.091 47.619 0.00 0.00 0.00 3.24
559 575 3.373565 GAAACCAAGCGGGCCCAG 61.374 66.667 24.92 16.07 42.05 4.45
753 770 3.003763 GGACGGCTGGAAGAGGGT 61.004 66.667 0.00 0.00 34.07 4.34
754 771 2.266055 GACGGCTGGAAGAGGGTG 59.734 66.667 0.00 0.00 34.07 4.61
865 886 0.839853 ACTCCTCCTTGCTTGCCTCT 60.840 55.000 0.00 0.00 0.00 3.69
878 899 3.827898 CCTCTCCCACGTCTCCGC 61.828 72.222 0.00 0.00 37.70 5.54
915 936 1.425066 AGCATTCCCTCAAACACCTCA 59.575 47.619 0.00 0.00 0.00 3.86
1456 1478 2.091278 TCATCGGGGAATCTGACTAGGT 60.091 50.000 0.00 0.00 32.83 3.08
1947 1969 6.105333 GGCAGCATTGATGGTTATGTTTTTA 58.895 36.000 3.80 0.00 36.17 1.52
2076 2098 0.915872 ATCCTGTGGCCTCATCACCA 60.916 55.000 8.18 0.00 34.46 4.17
2208 2230 0.627451 TCCTCAAGCATGGGCATTCT 59.373 50.000 0.00 0.00 44.61 2.40
2300 2322 7.078228 AGTATCAACAAAGTTTCAAGCGAATC 58.922 34.615 0.00 0.00 0.00 2.52
2397 2419 4.848562 TCTGTCCTACAAGTATATGCCG 57.151 45.455 0.00 0.00 0.00 5.69
2562 2584 6.966632 CACCATTCGTTCACAGGTATTTTATG 59.033 38.462 0.00 0.00 0.00 1.90
2564 2586 5.554822 TTCGTTCACAGGTATTTTATGCC 57.445 39.130 0.00 0.00 34.96 4.40
2585 2607 4.321899 GCCTTTTGTATGCTCCAAACATCA 60.322 41.667 0.00 0.00 31.88 3.07
2586 2608 5.782047 CCTTTTGTATGCTCCAAACATCAA 58.218 37.500 0.00 0.00 31.88 2.57
2886 2912 9.429359 GAATTGACCTGATGTAGAAGTATATGG 57.571 37.037 0.00 0.00 0.00 2.74
3241 3267 9.469807 CATAATTGGTAGTAGTCATCTTCTGTC 57.530 37.037 0.00 0.00 0.00 3.51
3362 3388 2.431057 AGTTACAGGCCTTATCTCCACG 59.569 50.000 0.00 0.00 0.00 4.94
3514 3540 6.545508 TGATGATAAATTTGAAGTGCGACTG 58.454 36.000 0.00 0.00 0.00 3.51
3826 3852 8.361139 CGATGACCCTATGTATAGAAAAGAAGT 58.639 37.037 0.51 0.00 32.05 3.01
4010 4037 3.760738 TGCACACCAAATAAGGACATGA 58.239 40.909 0.00 0.00 0.00 3.07
4069 4099 3.126001 TCTAGGACTGCAAACTGTTGG 57.874 47.619 0.00 0.00 35.10 3.77
4092 4122 6.209192 TGGTTGCAGAAACATCAGTGAATAAT 59.791 34.615 0.00 0.00 40.86 1.28
4206 4236 4.828939 TCTGTTGTCTTGAGCAAATTCCAT 59.171 37.500 0.00 0.00 0.00 3.41
4389 4419 7.607607 TCCGCATGCTACTTTCATAATTGATAT 59.392 33.333 17.13 0.00 0.00 1.63
4390 4420 8.882736 CCGCATGCTACTTTCATAATTGATATA 58.117 33.333 17.13 0.00 0.00 0.86
4469 4499 3.994853 GGCCCACCAGCAACTTGC 61.995 66.667 5.55 5.55 45.46 4.01
4712 4742 1.202770 ACGTGCCTAAACTCAAAGCCT 60.203 47.619 0.00 0.00 0.00 4.58
4796 4826 1.481056 CGGGTTCCCAGTCCAACTCT 61.481 60.000 8.70 0.00 0.00 3.24
5111 5141 0.742505 CATCGGATGTGCATGGCTTT 59.257 50.000 9.85 0.00 0.00 3.51
5116 5146 1.824230 GGATGTGCATGGCTTTGGTTA 59.176 47.619 0.00 0.00 0.00 2.85
5971 6024 2.813908 GCCTTCGTCGACCGCATT 60.814 61.111 10.58 0.00 36.19 3.56
5983 6036 3.902063 CGCATTGTCGTCGGAGCG 61.902 66.667 0.00 0.00 39.17 5.03
5984 6037 4.210304 GCATTGTCGTCGGAGCGC 62.210 66.667 0.00 0.00 0.00 5.92
5986 6039 3.760035 ATTGTCGTCGGAGCGCCT 61.760 61.111 2.29 0.00 0.00 5.52
5987 6040 3.296709 ATTGTCGTCGGAGCGCCTT 62.297 57.895 2.29 0.00 0.00 4.35
5988 6041 3.909258 TTGTCGTCGGAGCGCCTTC 62.909 63.158 2.29 0.00 0.00 3.46
6000 6053 2.813908 GCCTTCGTCGACCGCATT 60.814 61.111 10.58 0.00 36.19 3.56
6001 6054 3.081133 CCTTCGTCGACCGCATTG 58.919 61.111 10.58 0.00 36.19 2.82
6002 6055 1.736645 CCTTCGTCGACCGCATTGT 60.737 57.895 10.58 0.00 36.19 2.71
6003 6056 1.683790 CCTTCGTCGACCGCATTGTC 61.684 60.000 10.58 0.00 36.19 3.18
6009 6062 2.126228 GACCGCATTGTCGTCGGA 60.126 61.111 6.91 0.00 45.53 4.55
6010 6063 2.126071 ACCGCATTGTCGTCGGAG 60.126 61.111 6.91 0.00 45.53 4.63
6011 6064 3.554692 CCGCATTGTCGTCGGAGC 61.555 66.667 0.00 0.00 45.53 4.70
6012 6065 3.554692 CGCATTGTCGTCGGAGCC 61.555 66.667 0.00 0.00 0.00 4.70
6013 6066 3.554692 GCATTGTCGTCGGAGCCG 61.555 66.667 1.74 1.74 41.35 5.52
6014 6067 3.554692 CATTGTCGTCGGAGCCGC 61.555 66.667 3.59 0.00 39.59 6.53
6015 6068 4.814294 ATTGTCGTCGGAGCCGCC 62.814 66.667 3.59 0.00 39.59 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 71 4.023536 ACACACCCGACAATATCAACAAAC 60.024 41.667 0.00 0.00 0.00 2.93
189 199 6.949578 TTGTGAAAGCTCAAACAAGAAAAG 57.050 33.333 4.45 0.00 31.88 2.27
191 201 6.454795 ACTTTGTGAAAGCTCAAACAAGAAA 58.545 32.000 7.76 0.00 42.27 2.52
248 260 8.043113 AGCTCCATTTCAAAGAAAAAGAAAGTT 58.957 29.630 0.00 0.00 35.05 2.66
341 354 0.966920 GGCTAAGCTATCGGCCAGTA 59.033 55.000 2.24 0.00 43.59 2.74
533 549 4.038080 CTTGGTTTCCACGCGGGC 62.038 66.667 12.47 0.00 36.21 6.13
534 550 4.038080 GCTTGGTTTCCACGCGGG 62.038 66.667 12.47 6.05 38.91 6.13
559 575 1.856265 CGCTGGGTTTCACTGGCTTC 61.856 60.000 0.00 0.00 0.00 3.86
569 585 4.660938 GTGAGGGGCGCTGGGTTT 62.661 66.667 9.52 0.00 0.00 3.27
753 770 0.035317 AAGAGCGATGTTCTGTGGCA 59.965 50.000 0.00 0.00 0.00 4.92
754 771 1.160137 AAAGAGCGATGTTCTGTGGC 58.840 50.000 0.00 0.00 0.00 5.01
1456 1478 1.535444 TGTTCCCGGAGAGGAGCAA 60.535 57.895 0.73 0.00 43.32 3.91
1947 1969 4.757594 TCAAACAGAAAAGCAATGCAACT 58.242 34.783 8.35 0.00 0.00 3.16
2076 2098 0.681564 CTCTCGGGGACACTGCTACT 60.682 60.000 0.00 0.00 0.00 2.57
2177 2199 2.306805 TGCTTGAGGAGGTTGTCATCAT 59.693 45.455 0.00 0.00 45.18 2.45
2208 2230 3.529734 ACACACCATGGTAAATATCCCCA 59.470 43.478 19.28 0.00 0.00 4.96
2300 2322 3.875727 TGAGTACCTCGAATAGAAGTCCG 59.124 47.826 0.00 0.00 32.35 4.79
2397 2419 0.804989 CATTGGTCAAGTCCGCCTTC 59.195 55.000 0.00 0.00 0.00 3.46
2562 2584 3.658757 TGTTTGGAGCATACAAAAGGC 57.341 42.857 2.67 0.00 39.29 4.35
2564 2586 6.183360 GCATTGATGTTTGGAGCATACAAAAG 60.183 38.462 2.67 0.00 39.29 2.27
2654 2676 9.901172 ACCCCAGAAAGTATAAACTAAATGTAG 57.099 33.333 0.00 0.00 33.75 2.74
3241 3267 0.468029 AGTCAAAACAGGCAGGTGGG 60.468 55.000 0.00 0.00 0.00 4.61
3311 3337 1.618837 TGACCTCACCTACTGACAAGC 59.381 52.381 0.00 0.00 0.00 4.01
3514 3540 4.389077 GCGCATATGTTACTCATACTTCCC 59.611 45.833 0.30 0.00 41.13 3.97
3625 3651 7.394016 TCTTCTAAGCCTATCACAAAACATGA 58.606 34.615 0.00 0.00 0.00 3.07
3893 3920 8.107399 ACCAGTAAAATTAGTAAGAAAGTGGC 57.893 34.615 9.47 0.00 30.80 5.01
4010 4037 7.778382 AGTAAACAACTCCAAATTCCTTACTGT 59.222 33.333 0.00 0.00 30.33 3.55
4069 4099 7.307694 TCATTATTCACTGATGTTTCTGCAAC 58.692 34.615 0.00 0.00 35.71 4.17
4110 4140 6.463360 ACCAACCACCAATCAATCAAAATAC 58.537 36.000 0.00 0.00 0.00 1.89
4469 4499 5.220662 CCCAAAGCAGTAAACATCGTATGAG 60.221 44.000 2.48 0.00 0.00 2.90
4572 4602 2.245096 GCTGATGCGATTTGTTGTGAC 58.755 47.619 0.00 0.00 0.00 3.67
4573 4603 1.878734 TGCTGATGCGATTTGTTGTGA 59.121 42.857 0.00 0.00 43.34 3.58
4712 4742 2.172483 GAGCAGAGGGACGCCTTGAA 62.172 60.000 0.00 0.00 0.00 2.69
4786 4816 0.036022 GAGCCTTGCAGAGTTGGACT 59.964 55.000 0.00 0.00 0.00 3.85
5111 5141 3.709653 ACACTTCTGACCTTGAGTAACCA 59.290 43.478 0.00 0.00 0.00 3.67
5116 5146 1.486310 TGCACACTTCTGACCTTGAGT 59.514 47.619 0.00 0.00 0.00 3.41
5309 5341 1.697432 ACCTTCGACCCAGAACAATCA 59.303 47.619 0.00 0.00 0.00 2.57
5455 5495 6.616237 TTTTTAACTGTTTGGGGGTTAACA 57.384 33.333 8.10 0.00 35.87 2.41
5490 5543 1.609555 AGCGAGGTTTAGCTCTATCCG 59.390 52.381 7.29 0.00 39.98 4.18
5636 5689 0.452184 TTCTGGAGACGCGATGAGAC 59.548 55.000 15.93 0.00 0.00 3.36
5971 6024 4.415332 GAAGGCGCTCCGACGACA 62.415 66.667 7.64 0.00 46.03 4.35
5992 6045 2.126228 TCCGACGACAATGCGGTC 60.126 61.111 0.00 0.00 45.02 4.79
5993 6046 2.126071 CTCCGACGACAATGCGGT 60.126 61.111 0.00 0.00 45.02 5.68
5994 6047 3.554692 GCTCCGACGACAATGCGG 61.555 66.667 0.00 0.00 46.08 5.69
5995 6048 3.554692 GGCTCCGACGACAATGCG 61.555 66.667 0.00 0.00 37.29 4.73
5996 6049 3.554692 CGGCTCCGACGACAATGC 61.555 66.667 1.35 0.00 42.83 3.56
5997 6050 3.554692 GCGGCTCCGACGACAATG 61.555 66.667 13.11 0.00 42.83 2.82
5998 6051 4.814294 GGCGGCTCCGACGACAAT 62.814 66.667 13.11 0.00 44.48 2.71


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

AutoCloner maintained by Alex Coulton.