Multiple sequence alignment - TraesCS1A01G305500

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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 TraesCS1A01G305500 chr1A 100.000 3916 0 0 1 3916 498051643 498047728 0.000000e+00 7232
1 TraesCS1A01G305500 chr1B 96.974 1917 48 8 1 1910 540723330 540721417 0.000000e+00 3210
2 TraesCS1A01G305500 chr1B 94.200 2000 94 15 1919 3909 540721377 540719391 0.000000e+00 3031
3 TraesCS1A01G305500 chr1D 95.806 2003 54 10 1919 3916 402825431 402823454 0.000000e+00 3206
4 TraesCS1A01G305500 chr1D 98.285 1458 21 4 456 1910 402826927 402825471 0.000000e+00 2551
5 TraesCS1A01G305500 chr1D 95.538 493 14 5 1 492 402827412 402826927 0.000000e+00 782
6 TraesCS1A01G305500 chr5D 84.127 126 16 4 582 705 505091794 505091671 6.870000e-23 119


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 TraesCS1A01G305500 chr1A 498047728 498051643 3915 True 7232.000000 7232 100.000 1 3916 1 chr1A.!!$R1 3915
1 TraesCS1A01G305500 chr1B 540719391 540723330 3939 True 3120.500000 3210 95.587 1 3909 2 chr1B.!!$R1 3908
2 TraesCS1A01G305500 chr1D 402823454 402827412 3958 True 2179.666667 3206 96.543 1 3916 3 chr1D.!!$R1 3915

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
418 421 0.392706 TCTTTCACGCTCCAAGCAGA 59.607 50.000 0.0 0.0 42.58 4.26 F
419 422 1.002430 TCTTTCACGCTCCAAGCAGAT 59.998 47.619 0.0 0.0 42.58 2.90 F
1635 1679 1.227823 CCGGAACAAGTGTGCCAGA 60.228 57.895 9.2 0.0 44.37 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1653 1697 1.004044 ACTTCTCTGGCTGTGGAATGG 59.996 52.381 0.0 0.0 0.0 3.16 R
1815 1860 4.737578 AGTAGTTTCAGTACCTCACCTCA 58.262 43.478 0.0 0.0 0.0 3.86 R
3624 3710 0.750546 TGCCTTGCCTGATGCTGATC 60.751 55.000 0.0 0.0 42.0 2.92 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
168 169 9.801714 CAGAATAAATTGACAGAAAAATTGTGC 57.198 29.630 0.00 0.00 0.00 4.57
277 279 4.749099 GCACATACTGCATTCCTCTAAGAG 59.251 45.833 0.00 0.00 46.29 2.85
330 332 9.211485 GAACCAGCAACACTAAACTAAATACTA 57.789 33.333 0.00 0.00 0.00 1.82
331 333 8.773404 ACCAGCAACACTAAACTAAATACTAG 57.227 34.615 0.00 0.00 0.00 2.57
332 334 8.373220 ACCAGCAACACTAAACTAAATACTAGT 58.627 33.333 0.00 0.00 0.00 2.57
333 335 9.865321 CCAGCAACACTAAACTAAATACTAGTA 57.135 33.333 4.77 4.77 0.00 1.82
418 421 0.392706 TCTTTCACGCTCCAAGCAGA 59.607 50.000 0.00 0.00 42.58 4.26
419 422 1.002430 TCTTTCACGCTCCAAGCAGAT 59.998 47.619 0.00 0.00 42.58 2.90
956 998 4.538490 TGGTTAGATCTTTAAGCCCTCCAA 59.462 41.667 0.00 0.00 31.67 3.53
1104 1146 3.100671 AGGAAGTACGCAAGGAGATTCT 58.899 45.455 0.00 0.00 46.39 2.40
1176 1218 5.052304 CGAGTTACATCAGCGATTTGTAGAC 60.052 44.000 0.00 0.00 0.00 2.59
1635 1679 1.227823 CCGGAACAAGTGTGCCAGA 60.228 57.895 9.20 0.00 44.37 3.86
1653 1697 5.009310 TGCCAGAGATGATCAATACAAATGC 59.991 40.000 0.00 0.00 0.00 3.56
1815 1860 6.183360 TGCAGAGACAATTAAACGAACAACTT 60.183 34.615 0.00 0.00 0.00 2.66
1836 1881 5.010820 ACTTGAGGTGAGGTACTGAAACTAC 59.989 44.000 0.00 0.00 41.55 2.73
1910 1955 7.723172 AGATGGAAATCAAGATAACCTGAATCC 59.277 37.037 0.00 0.00 0.00 3.01
1911 1956 6.973642 TGGAAATCAAGATAACCTGAATCCT 58.026 36.000 7.73 0.00 0.00 3.24
1912 1957 7.413446 TGGAAATCAAGATAACCTGAATCCTT 58.587 34.615 7.73 0.00 0.00 3.36
1913 1958 8.556589 TGGAAATCAAGATAACCTGAATCCTTA 58.443 33.333 7.73 0.00 0.00 2.69
1914 1959 9.579932 GGAAATCAAGATAACCTGAATCCTTAT 57.420 33.333 0.00 0.00 0.00 1.73
2119 2196 6.801539 TGTCAAATTCCAGCTAAGTAACAG 57.198 37.500 0.00 0.00 0.00 3.16
2365 2442 2.988493 CAAATGAATGTTTCGGCAGTGG 59.012 45.455 0.00 0.00 0.00 4.00
2411 2488 1.678627 AGTATGCACAGACTAGAGCCG 59.321 52.381 0.00 0.00 30.03 5.52
2615 2692 2.163412 GCGTAAGATGGGTCATTTGCAA 59.837 45.455 0.00 0.00 43.02 4.08
2772 2849 7.487484 TGCAGACAGACTATATCTTGAAGAAG 58.513 38.462 0.00 0.00 34.41 2.85
2804 2881 1.880027 AGACAAGCGGTTGAACATTCC 59.120 47.619 32.17 11.99 37.10 3.01
2835 2912 3.573967 GCATCCAAGTTCTGGGAAGAAAA 59.426 43.478 0.00 0.00 46.44 2.29
3018 3095 7.833285 ATTTGGTGATTAAACTGTGTAGGTT 57.167 32.000 0.00 0.00 37.63 3.50
3022 3099 7.737869 TGGTGATTAAACTGTGTAGGTTAAGA 58.262 34.615 4.18 0.00 46.21 2.10
3098 3176 8.260818 TGTTATAGCTCAGCAGTTTAAATCTCT 58.739 33.333 0.00 0.00 0.00 3.10
3111 3189 9.372369 CAGTTTAAATCTCTATTTCGAGAGGTT 57.628 33.333 0.82 0.00 46.72 3.50
3335 3414 3.310141 GGGACTACCAGAACCTTACCCTA 60.310 52.174 0.00 0.00 39.85 3.53
3389 3468 2.503895 AGCTATCCCTGCCATTATGC 57.496 50.000 0.00 0.00 0.00 3.14
3393 3472 0.700564 ATCCCTGCCATTATGCGGAT 59.299 50.000 0.00 0.00 40.15 4.18
3434 3520 7.227711 ACAGCTTAAAACAAAACCAAACAGTTT 59.772 29.630 0.00 0.00 41.67 2.66
3438 3524 9.894439 CTTAAAACAAAACCAAACAGTTTATCG 57.106 29.630 0.00 0.00 39.00 2.92
3466 3552 2.285834 GCAGACTTCACGAACACAACTG 60.286 50.000 0.00 0.00 0.00 3.16
3482 3568 3.323115 ACAACTGACATCTCAGAGAAGCA 59.677 43.478 3.63 2.40 46.32 3.91
3577 3663 3.622612 TGCATCTATTCATCCACACAACG 59.377 43.478 0.00 0.00 0.00 4.10
3619 3705 1.401552 TCCATCGCAGCACTTATTTGC 59.598 47.619 0.00 0.00 43.34 3.68
3624 3710 2.030335 TCGCAGCACTTATTTGCATACG 59.970 45.455 0.00 0.00 45.62 3.06
3651 3737 0.694771 TCAGGCAAGGCAAGAGTCAT 59.305 50.000 0.00 0.00 0.00 3.06
3656 3742 4.883585 CAGGCAAGGCAAGAGTCATTTATA 59.116 41.667 0.00 0.00 0.00 0.98
3660 3746 5.009410 GCAAGGCAAGAGTCATTTATAGCAT 59.991 40.000 0.00 0.00 0.00 3.79
3661 3747 6.205464 GCAAGGCAAGAGTCATTTATAGCATA 59.795 38.462 0.00 0.00 0.00 3.14
3662 3748 7.255242 GCAAGGCAAGAGTCATTTATAGCATAA 60.255 37.037 0.00 0.00 0.00 1.90
3716 3802 5.183904 GCAAAGCTATGTATAATCTTGGGGG 59.816 44.000 0.00 0.00 0.00 5.40
3783 3869 6.445139 TCCTTTGTTCCTCTCCTTATTCTCAT 59.555 38.462 0.00 0.00 0.00 2.90
3827 3913 7.543868 GCAAGAGCACTGTATTATAGAGTATGG 59.456 40.741 1.63 0.00 41.58 2.74
3828 3914 8.797438 CAAGAGCACTGTATTATAGAGTATGGA 58.203 37.037 1.63 0.00 30.30 3.41
3889 3986 0.811616 GCCGGTGTCATCCACTCATC 60.812 60.000 1.90 0.00 43.94 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
168 169 5.777802 AGAGTGACATCTTACACACAGAAG 58.222 41.667 0.00 0.00 39.18 2.85
330 332 6.214399 CAACTTCTCTGTTACCTTCGTTACT 58.786 40.000 0.00 0.00 0.00 2.24
331 333 5.107568 GCAACTTCTCTGTTACCTTCGTTAC 60.108 44.000 0.00 0.00 0.00 2.50
332 334 4.986659 GCAACTTCTCTGTTACCTTCGTTA 59.013 41.667 0.00 0.00 0.00 3.18
333 335 3.808174 GCAACTTCTCTGTTACCTTCGTT 59.192 43.478 0.00 0.00 0.00 3.85
335 337 3.184581 GTGCAACTTCTCTGTTACCTTCG 59.815 47.826 0.00 0.00 0.00 3.79
336 338 4.127171 TGTGCAACTTCTCTGTTACCTTC 58.873 43.478 0.00 0.00 38.04 3.46
450 453 3.571401 ACTGGAGCAATTTGTCTTTCTGG 59.429 43.478 0.00 0.00 0.00 3.86
459 462 6.515272 AATACCTACAACTGGAGCAATTTG 57.485 37.500 0.00 0.00 0.00 2.32
946 988 3.308401 ACAACAGAAATTTGGAGGGCTT 58.692 40.909 0.00 0.00 0.00 4.35
1104 1146 0.895530 CGGTTGAGAGAACTAGCCCA 59.104 55.000 0.00 0.00 0.00 5.36
1176 1218 0.179166 CACCCAATTGATTGACCGCG 60.179 55.000 7.12 0.00 40.14 6.46
1635 1679 6.551975 TGGAATGGCATTTGTATTGATCATCT 59.448 34.615 14.93 0.00 0.00 2.90
1653 1697 1.004044 ACTTCTCTGGCTGTGGAATGG 59.996 52.381 0.00 0.00 0.00 3.16
1815 1860 4.737578 AGTAGTTTCAGTACCTCACCTCA 58.262 43.478 0.00 0.00 0.00 3.86
1836 1881 8.443937 GTCTTGGTTAAGAGCTTATTACACAAG 58.556 37.037 18.09 18.09 43.29 3.16
2130 2207 7.254590 GCACTGATGGATATGTTTTAGTCACTC 60.255 40.741 0.00 0.00 0.00 3.51
2615 2692 5.301551 TGCTTTGTGGTACTCATTCACATTT 59.698 36.000 3.23 0.00 40.49 2.32
2772 2849 1.763634 GCTTGTCTCTTGCAGTTTGC 58.236 50.000 0.00 0.00 45.29 3.68
2804 2881 2.554032 AGAACTTGGATGCTCAAAACCG 59.446 45.455 0.00 0.00 0.00 4.44
2835 2912 6.543465 TCAGTGTTTTGAGTGTTCAGATCAAT 59.457 34.615 0.00 0.00 34.15 2.57
3078 3156 7.010923 CGAAATAGAGATTTAAACTGCTGAGCT 59.989 37.037 5.83 0.00 35.33 4.09
3166 3245 8.572855 GCCTTCTGCATTCTATTCCTATATTT 57.427 34.615 0.00 0.00 40.77 1.40
3389 3468 3.325870 TGTGTTGAGCTGAAAGTATCCG 58.674 45.455 0.00 0.00 35.30 4.18
3434 3520 4.044426 CGTGAAGTCTGCATCAATCGATA 58.956 43.478 0.00 0.00 0.00 2.92
3438 3524 3.433274 TGTTCGTGAAGTCTGCATCAATC 59.567 43.478 0.00 0.00 0.00 2.67
3466 3552 3.859443 ACACATGCTTCTCTGAGATGTC 58.141 45.455 18.36 12.56 0.00 3.06
3557 3643 3.622612 TGCGTTGTGTGGATGAATAGATG 59.377 43.478 0.00 0.00 0.00 2.90
3577 3663 5.401376 GGACTTTACCTCAAAAATCGTTTGC 59.599 40.000 0.00 0.00 0.00 3.68
3619 3705 2.159327 TGCCTGATGCTGATCGTATG 57.841 50.000 0.00 0.00 42.00 2.39
3624 3710 0.750546 TGCCTTGCCTGATGCTGATC 60.751 55.000 0.00 0.00 42.00 2.92
3662 3748 9.868277 TCCATTTGCAGTTTTTAATCGAATTAT 57.132 25.926 0.00 0.00 0.00 1.28
3669 3755 6.646240 TGCTCTTCCATTTGCAGTTTTTAATC 59.354 34.615 0.00 0.00 0.00 1.75
3687 3773 8.502387 CCAAGATTATACATAGCTTTGCTCTTC 58.498 37.037 3.86 0.00 40.44 2.87
3783 3869 4.551702 TTGCTCTTGTGGCAAGTATAGA 57.448 40.909 8.48 0.00 43.50 1.98
3889 3986 5.293814 TCAAGAAGTAGTAGTAGTAGCAGCG 59.706 44.000 0.00 0.00 0.00 5.18


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

AutoCloner maintained by Alex Coulton.