Multiple sequence alignment - TraesCS1D01G169500

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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 TraesCS1D01G169500 chr1D 100.000 3978 0 0 1 3978 244196410 244192433 0.000000e+00 7347
1 TraesCS1D01G169500 chr1D 95.865 3990 129 18 1 3978 244763606 244759641 0.000000e+00 6421
2 TraesCS1D01G169500 chr1D 95.132 4006 150 28 1 3978 254471909 254467921 0.000000e+00 6276
3 TraesCS1D01G169500 chr5D 95.138 4011 146 26 1 3978 503326002 503322008 0.000000e+00 6281
4 TraesCS1D01G169500 chr5D 94.426 4001 168 27 1 3978 6240793 6244761 0.000000e+00 6102
5 TraesCS1D01G169500 chr5D 94.024 1573 76 13 1 1565 444305968 444307530 0.000000e+00 2368
6 TraesCS1D01G169500 chr2B 94.094 4047 161 32 1 3978 683740950 683736913 0.000000e+00 6078
7 TraesCS1D01G169500 chr4A 92.154 4002 263 32 1 3978 205016909 205020883 0.000000e+00 5603
8 TraesCS1D01G169500 chr4A 93.597 3139 164 27 856 3978 309398995 309402112 0.000000e+00 4649
9 TraesCS1D01G169500 chr7B 94.735 3609 142 28 1 3572 662742519 662746116 0.000000e+00 5568
10 TraesCS1D01G169500 chr7B 80.531 226 32 9 1250 1473 52950696 52950911 3.180000e-36 163
11 TraesCS1D01G169500 chr3A 95.026 2513 106 14 1 2501 524023685 524021180 0.000000e+00 3930
12 TraesCS1D01G169500 chrUn 94.761 2367 84 22 1240 3572 298932655 298935015 0.000000e+00 3648
13 TraesCS1D01G169500 chrUn 93.548 1085 33 14 2930 3978 359776170 359775087 0.000000e+00 1581
14 TraesCS1D01G169500 chr3B 94.761 2367 84 22 1240 3572 201483719 201481359 0.000000e+00 3648
15 TraesCS1D01G169500 chr3B 94.523 1844 80 13 1 1830 201488223 201486387 0.000000e+00 2826
16 TraesCS1D01G169500 chr7A 94.379 2384 101 16 1 2372 12217379 12219741 0.000000e+00 3629
17 TraesCS1D01G169500 chr1A 94.632 2012 82 14 1 1994 554453234 554455237 0.000000e+00 3094
18 TraesCS1D01G169500 chr5A 80.531 226 32 8 1250 1473 162144166 162144381 3.180000e-36 163
19 TraesCS1D01G169500 chr1B 79.204 226 35 11 1250 1473 286060970 286061185 3.200000e-31 147


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 TraesCS1D01G169500 chr1D 244192433 244196410 3977 True 7347 7347 100.000 1 3978 1 chr1D.!!$R1 3977
1 TraesCS1D01G169500 chr1D 244759641 244763606 3965 True 6421 6421 95.865 1 3978 1 chr1D.!!$R2 3977
2 TraesCS1D01G169500 chr1D 254467921 254471909 3988 True 6276 6276 95.132 1 3978 1 chr1D.!!$R3 3977
3 TraesCS1D01G169500 chr5D 503322008 503326002 3994 True 6281 6281 95.138 1 3978 1 chr5D.!!$R1 3977
4 TraesCS1D01G169500 chr5D 6240793 6244761 3968 False 6102 6102 94.426 1 3978 1 chr5D.!!$F1 3977
5 TraesCS1D01G169500 chr5D 444305968 444307530 1562 False 2368 2368 94.024 1 1565 1 chr5D.!!$F2 1564
6 TraesCS1D01G169500 chr2B 683736913 683740950 4037 True 6078 6078 94.094 1 3978 1 chr2B.!!$R1 3977
7 TraesCS1D01G169500 chr4A 205016909 205020883 3974 False 5603 5603 92.154 1 3978 1 chr4A.!!$F1 3977
8 TraesCS1D01G169500 chr4A 309398995 309402112 3117 False 4649 4649 93.597 856 3978 1 chr4A.!!$F2 3122
9 TraesCS1D01G169500 chr7B 662742519 662746116 3597 False 5568 5568 94.735 1 3572 1 chr7B.!!$F2 3571
10 TraesCS1D01G169500 chr3A 524021180 524023685 2505 True 3930 3930 95.026 1 2501 1 chr3A.!!$R1 2500
11 TraesCS1D01G169500 chrUn 298932655 298935015 2360 False 3648 3648 94.761 1240 3572 1 chrUn.!!$F1 2332
12 TraesCS1D01G169500 chrUn 359775087 359776170 1083 True 1581 1581 93.548 2930 3978 1 chrUn.!!$R1 1048
13 TraesCS1D01G169500 chr3B 201481359 201488223 6864 True 3237 3648 94.642 1 3572 2 chr3B.!!$R1 3571
14 TraesCS1D01G169500 chr7A 12217379 12219741 2362 False 3629 3629 94.379 1 2372 1 chr7A.!!$F1 2371
15 TraesCS1D01G169500 chr1A 554453234 554455237 2003 False 3094 3094 94.632 1 1994 1 chr1A.!!$F1 1993

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
328 330 3.742385 TCGAACCCTCGGTAAACAAAAT 58.258 40.909 0.00 0.0 45.49 1.82 F
847 877 4.226427 AGGATACAATTTGAGCTGAGCA 57.774 40.909 7.39 0.0 41.41 4.26 F
2106 5423 0.577269 GCCGTGATCTGTCATTACGC 59.423 55.000 0.00 0.0 36.60 4.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1481 4797 0.619255 TTCCCAGCCCTGATACCGAA 60.619 55.000 0.0 0.0 0.00 4.30 R
2807 6150 0.549950 TCTCCTCGGTCGGAATAGGT 59.450 55.000 0.0 0.0 31.44 3.08 R
3577 6974 1.607148 ACCCGCAACTGTCTTTTTAGC 59.393 47.619 0.0 0.0 0.00 3.09 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
163 164 9.733556 ATGTGTCTTTTTCATACCACAGTAATA 57.266 29.630 0.00 0.00 36.39 0.98
328 330 3.742385 TCGAACCCTCGGTAAACAAAAT 58.258 40.909 0.00 0.00 45.49 1.82
520 528 8.370940 TCATCTAAGTGGAAGGATACATGATTC 58.629 37.037 0.00 0.00 41.41 2.52
521 529 7.921041 TCTAAGTGGAAGGATACATGATTCT 57.079 36.000 0.00 0.00 41.41 2.40
522 530 8.324191 TCTAAGTGGAAGGATACATGATTCTT 57.676 34.615 0.00 0.00 35.91 2.52
660 680 7.134815 CCTTAGAATTCGGTTTGCATAAGATG 58.865 38.462 0.00 0.00 0.00 2.90
847 877 4.226427 AGGATACAATTTGAGCTGAGCA 57.774 40.909 7.39 0.00 41.41 4.26
1007 1045 4.551215 ATGGGTTGGGAATTATGCCTAA 57.449 40.909 0.00 0.00 38.04 2.69
1011 1049 5.147767 GGGTTGGGAATTATGCCTAAATCT 58.852 41.667 0.00 0.00 38.04 2.40
1128 1169 9.778741 TTTACTTATTATGGAGATGGTGTGATC 57.221 33.333 0.00 0.00 0.00 2.92
1130 1171 8.038862 ACTTATTATGGAGATGGTGTGATCTT 57.961 34.615 0.00 0.00 32.57 2.40
1178 1225 5.002516 CCTACCTATACCTCAGTCTTACGG 58.997 50.000 0.00 0.00 0.00 4.02
1222 1278 6.002062 AGAGAGAACCAAATTTGTAAAGCG 57.998 37.500 16.73 3.16 0.00 4.68
1330 4645 8.791327 TCAATTGTAGATTTGAGTATTGAGCA 57.209 30.769 5.13 0.00 0.00 4.26
1367 4682 6.566079 ACAGGATATGGTATGGTATGGATG 57.434 41.667 0.00 0.00 0.00 3.51
1481 4797 6.208840 TGTTAGAAATTACCCCTTTCCTGT 57.791 37.500 0.00 0.00 33.93 4.00
1627 4943 7.554118 TGAGAACAAGGAAATTATTGGAGCTAG 59.446 37.037 0.00 0.00 0.00 3.42
1628 4944 7.406104 AGAACAAGGAAATTATTGGAGCTAGT 58.594 34.615 0.00 0.00 0.00 2.57
1630 4946 5.888161 ACAAGGAAATTATTGGAGCTAGTGG 59.112 40.000 0.00 0.00 0.00 4.00
1739 5056 4.513442 CCCTTTCGGTTCATAATGAGACA 58.487 43.478 0.00 0.00 0.00 3.41
1871 5188 5.539582 TTTTGAATAGAATGAACGACCGG 57.460 39.130 0.00 0.00 0.00 5.28
2106 5423 0.577269 GCCGTGATCTGTCATTACGC 59.423 55.000 0.00 0.00 36.60 4.42
2357 5687 2.295253 GACTGGGTCGATACAACTGG 57.705 55.000 0.00 0.00 0.00 4.00
2362 5695 4.069304 CTGGGTCGATACAACTGGAAAAA 58.931 43.478 0.00 0.00 0.00 1.94
2772 6115 5.116180 CAATTTCTGAGCCGTATGAGGTAA 58.884 41.667 0.00 0.00 0.00 2.85
2773 6116 5.552870 ATTTCTGAGCCGTATGAGGTAAT 57.447 39.130 0.00 0.00 0.00 1.89
2790 6133 7.837863 TGAGGTAATAAACTCTCAAGTACAGG 58.162 38.462 0.00 0.00 34.47 4.00
2807 6150 4.415224 ACAGGTCTAAGGGAAGGAACTA 57.585 45.455 0.00 0.00 38.49 2.24
2853 6196 4.042062 TGCCATTCTATAGGGTGATTCAGG 59.958 45.833 0.00 0.00 0.00 3.86
3023 6367 1.187087 TGGGTGGTTTGGTTGTTGAC 58.813 50.000 0.00 0.00 0.00 3.18
3179 6524 5.779771 AGTGAATAAAAAGAAGGGGCAATCA 59.220 36.000 0.00 0.00 0.00 2.57
3514 6879 9.440761 AGAAGGATGGTAGATAGTAAAGAACAT 57.559 33.333 0.00 0.00 0.00 2.71
3752 7150 2.237392 CAAGAACACTAGCTAAGGGCCT 59.763 50.000 0.00 0.00 43.05 5.19
3772 7170 4.141711 GCCTTGATACTACCACTTGGATCA 60.142 45.833 1.14 0.00 38.94 2.92
3806 7204 5.047188 TGCTAATGCTCACGATTTCGATAA 58.953 37.500 7.01 0.00 40.49 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 0.770948 AGTTCGGGGAAAGGGGAAGT 60.771 55.000 0.00 0.00 0.00 3.01
148 149 9.975218 TCTCTATAGCATATTACTGTGGTATGA 57.025 33.333 14.52 6.47 37.62 2.15
522 530 5.768317 AGCAAGCGCAATTTCTAGTAAAAA 58.232 33.333 11.47 0.00 42.27 1.94
633 653 4.701956 ATGCAAACCGAATTCTAAGGTG 57.298 40.909 3.52 0.00 38.44 4.00
660 680 2.983402 TCGATAGTATGGTGTAGCGC 57.017 50.000 0.00 0.00 37.40 5.92
1007 1045 9.357652 CAATGAATTTTCCATTTACACGAGATT 57.642 29.630 0.00 0.00 32.40 2.40
1114 1155 5.606348 AAGAGTAAGATCACACCATCTCC 57.394 43.478 0.00 0.00 31.44 3.71
1147 1193 4.995536 TGAGGTATAGGTAGGGCTAGAAC 58.004 47.826 0.00 0.00 0.00 3.01
1178 1225 1.995376 TGCCAACCCCTTCTCTTTTC 58.005 50.000 0.00 0.00 0.00 2.29
1222 1278 1.281656 CCGAAGCGTGGGTTTGTTC 59.718 57.895 0.00 0.00 0.00 3.18
1481 4797 0.619255 TTCCCAGCCCTGATACCGAA 60.619 55.000 0.00 0.00 0.00 4.30
1627 4943 8.910351 ATTCTATTAATGCTAGAGGAAACCAC 57.090 34.615 0.00 0.00 0.00 4.16
1628 4944 9.561069 GAATTCTATTAATGCTAGAGGAAACCA 57.439 33.333 0.00 0.00 0.00 3.67
1871 5188 1.401905 GGATTGAGGCAACATCCGTTC 59.598 52.381 0.00 0.00 41.41 3.95
1883 5200 4.319766 CGCATAATTTCCTTCGGATTGAGG 60.320 45.833 0.00 0.00 0.00 3.86
2106 5423 5.608676 TTTCTATAGTGGAGATAGTCGCG 57.391 43.478 0.00 0.00 0.00 5.87
2356 5686 7.346751 TCATGGGATAAGTAAGCATTTTTCC 57.653 36.000 0.00 0.00 0.00 3.13
2557 5896 9.832445 ATATAGAGCCTTCGTTCAAATTTTCTA 57.168 29.630 0.00 0.00 0.00 2.10
2734 6077 7.019774 TCAGAAATTGCTATCTGAATTTCCG 57.980 36.000 11.82 4.95 46.67 4.30
2772 6115 7.124448 CCCTTAGACCTGTACTTGAGAGTTTAT 59.876 40.741 0.00 0.00 37.33 1.40
2773 6116 6.436532 CCCTTAGACCTGTACTTGAGAGTTTA 59.563 42.308 0.00 0.00 37.33 2.01
2790 6133 6.041865 GGAATAGGTAGTTCCTTCCCTTAGAC 59.958 46.154 0.00 0.00 45.67 2.59
2807 6150 0.549950 TCTCCTCGGTCGGAATAGGT 59.450 55.000 0.00 0.00 31.44 3.08
2853 6196 4.320608 TCAAACCAAGCTTCCACAATTC 57.679 40.909 0.00 0.00 0.00 2.17
3577 6974 1.607148 ACCCGCAACTGTCTTTTTAGC 59.393 47.619 0.00 0.00 0.00 3.09
3752 7150 5.277250 TCCTGATCCAAGTGGTAGTATCAA 58.723 41.667 0.00 0.00 36.34 2.57
3772 7170 3.455910 TGAGCATTAGCATGTAGGTTCCT 59.544 43.478 0.00 0.00 45.49 3.36
3806 7204 4.971282 TCTCCTCCAAATCACCAGTATGAT 59.029 41.667 0.00 0.00 41.20 2.45


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

AutoCloner maintained by Alex Coulton.