Multiple sequence alignment - TraesCS1A01G349300

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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 TraesCS1A01G349300 chr1A 100.000 3769 0 0 1 3769 534274543 534278311 0.000000e+00 6961.0
1 TraesCS1A01G349300 chr1A 76.193 2096 391 77 601 2629 9533173 9531119 0.000000e+00 1007.0
2 TraesCS1A01G349300 chr1A 86.667 240 25 2 3280 3519 534269035 534269267 3.730000e-65 259.0
3 TraesCS1A01G349300 chr1B 95.230 3061 86 25 1 3007 592367966 592364912 0.000000e+00 4789.0
4 TraesCS1A01G349300 chr1B 78.603 1804 327 48 719 2483 9647399 9649182 0.000000e+00 1138.0
5 TraesCS1A01G349300 chr1B 92.259 788 28 7 3008 3769 592364800 592364020 0.000000e+00 1086.0
6 TraesCS1A01G349300 chr1D 95.251 2843 76 19 1 2796 437293728 437290898 0.000000e+00 4447.0
7 TraesCS1A01G349300 chr1D 77.415 2019 365 71 672 2629 7371994 7373982 0.000000e+00 1118.0
8 TraesCS1A01G349300 chr1D 95.455 110 5 0 2819 2928 437290838 437290729 3.870000e-40 176.0
9 TraesCS1A01G349300 chr1D 97.674 43 1 0 3727 3769 437296516 437296474 1.450000e-09 75.0
10 TraesCS1A01G349300 chr5D 73.721 1271 256 58 719 1936 41878416 41877171 3.480000e-115 425.0
11 TraesCS1A01G349300 chr5D 90.123 81 7 1 2954 3033 366647761 366647681 1.850000e-18 104.0
12 TraesCS1A01G349300 chr5D 71.984 257 61 11 1397 1646 375586275 375586527 8.740000e-07 65.8
13 TraesCS1A01G349300 chr2B 80.962 478 70 13 719 1188 785984525 785984061 3.580000e-95 359.0
14 TraesCS1A01G349300 chr2B 78.044 501 90 16 719 1207 775385775 775386267 7.910000e-77 298.0
15 TraesCS1A01G349300 chr2B 80.952 147 12 5 245 391 772593830 772593700 6.660000e-18 102.0
16 TraesCS1A01G349300 chr2D 77.046 501 95 16 719 1207 631983088 631983580 1.730000e-68 270.0
17 TraesCS1A01G349300 chr3D 72.844 545 117 27 1415 1942 514680439 514679909 1.400000e-34 158.0
18 TraesCS1A01G349300 chr3B 72.364 550 115 28 1415 1944 676967355 676966823 5.080000e-29 139.0
19 TraesCS1A01G349300 chr7B 88.696 115 6 6 33 147 534805774 534805881 2.360000e-27 134.0
20 TraesCS1A01G349300 chr4D 92.857 56 4 0 192 247 368914487 368914432 8.680000e-12 82.4
21 TraesCS1A01G349300 chr5B 72.481 258 58 8 1397 1646 448314635 448314887 1.880000e-08 71.3


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 TraesCS1A01G349300 chr1A 534274543 534278311 3768 False 6961.0 6961 100.000000 1 3769 1 chr1A.!!$F2 3768
1 TraesCS1A01G349300 chr1A 9531119 9533173 2054 True 1007.0 1007 76.193000 601 2629 1 chr1A.!!$R1 2028
2 TraesCS1A01G349300 chr1B 592364020 592367966 3946 True 2937.5 4789 93.744500 1 3769 2 chr1B.!!$R1 3768
3 TraesCS1A01G349300 chr1B 9647399 9649182 1783 False 1138.0 1138 78.603000 719 2483 1 chr1B.!!$F1 1764
4 TraesCS1A01G349300 chr1D 437290729 437296516 5787 True 1566.0 4447 96.126667 1 3769 3 chr1D.!!$R1 3768
5 TraesCS1A01G349300 chr1D 7371994 7373982 1988 False 1118.0 1118 77.415000 672 2629 1 chr1D.!!$F1 1957
6 TraesCS1A01G349300 chr5D 41877171 41878416 1245 True 425.0 425 73.721000 719 1936 1 chr5D.!!$R1 1217


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
430 3253 1.008206 AGAGGCCTGGAGAGAAGATGT 59.992 52.381 12.00 0.0 0.00 3.06 F
1197 4053 0.877743 GTGGCAGCCTTCAAAGTCTC 59.122 55.000 14.15 0.0 0.00 3.36 F
1231 4087 2.724174 GCACTGCGTTACAAAATGGAAC 59.276 45.455 0.00 0.0 37.83 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2188 5089 0.706433 AGCATGGAAGGGTGGTGAAT 59.294 50.000 0.00 0.0 0.0 2.57 R
2732 5643 0.892755 TACCAACCACGAAGCGATCT 59.107 50.000 0.00 0.0 0.0 2.75 R
3123 6182 1.340248 CCTATGTAGTACTGGCCCACG 59.660 57.143 5.39 0.0 0.0 4.94 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
55 2844 3.285484 CCCATCTCCCATTCTTTGTCTG 58.715 50.000 0.00 0.00 0.00 3.51
83 2874 6.959671 TTTTTGTTTCATTCTTCGTTTGCT 57.040 29.167 0.00 0.00 0.00 3.91
127 2918 3.968265 ACATGGTAAGTTGGATCTTGGG 58.032 45.455 0.00 0.00 0.00 4.12
151 2943 6.967199 GGTGCACTGTTCTTTAGTATATTTGC 59.033 38.462 17.98 0.00 0.00 3.68
278 3071 3.861113 GCATTTTCTGTGCATGGTACATG 59.139 43.478 4.92 4.92 42.08 3.21
371 3164 3.636282 AATTCGGTTTCCACTTTTCCG 57.364 42.857 0.00 0.00 42.12 4.30
411 3204 3.633573 AAAAACGAACAACGCCCAG 57.366 47.368 0.00 0.00 46.94 4.45
430 3253 1.008206 AGAGGCCTGGAGAGAAGATGT 59.992 52.381 12.00 0.00 0.00 3.06
464 3287 8.184192 AGCCAGTTTGTCATATTTATTTCTTCG 58.816 33.333 0.00 0.00 0.00 3.79
488 3311 5.337813 GGCATTGTTTCTCTTTCCATTCCAT 60.338 40.000 0.00 0.00 0.00 3.41
490 3313 6.753744 GCATTGTTTCTCTTTCCATTCCATAC 59.246 38.462 0.00 0.00 0.00 2.39
506 3329 7.335673 CCATTCCATACACCGCATATATGTTTA 59.664 37.037 14.14 0.21 0.00 2.01
639 3464 8.907222 ATCAGGTGTTTTGCTATTTTCAAAAT 57.093 26.923 0.02 0.02 42.89 1.82
847 3697 1.824852 CAGTTTATTTGGGGGCAGACC 59.175 52.381 0.00 0.00 39.11 3.85
906 3759 3.156293 CCAGGATGTCACCATTGAAACA 58.844 45.455 0.00 0.00 31.90 2.83
1102 3958 2.884012 TCCATTGGTAAACACAGTGCAG 59.116 45.455 0.00 0.00 0.00 4.41
1152 4008 9.821662 GTGTTTGTTACTGGAATTATCAAGTAC 57.178 33.333 0.00 0.00 40.97 2.73
1197 4053 0.877743 GTGGCAGCCTTCAAAGTCTC 59.122 55.000 14.15 0.00 0.00 3.36
1226 4082 3.501828 TCAGATGCACTGCGTTACAAAAT 59.498 39.130 10.36 0.00 45.38 1.82
1231 4087 2.724174 GCACTGCGTTACAAAATGGAAC 59.276 45.455 0.00 0.00 37.83 3.62
1719 4584 3.255888 TCGGATATCCAAGGACGATGAAG 59.744 47.826 21.70 0.62 35.14 3.02
1957 4849 8.547173 AGATTAGTCTCTTGACATTTGATTCCT 58.453 33.333 0.00 0.00 45.20 3.36
2113 5005 8.592809 GTGAATCTTCCCATTCAGATATAGAGT 58.407 37.037 0.00 0.00 42.26 3.24
2566 5470 4.465660 CCATGGAAGATCAGATATCGGACT 59.534 45.833 5.56 5.17 0.00 3.85
2598 5504 3.560896 GGTAAGTGCGTTTGACCACTTTA 59.439 43.478 10.76 0.00 46.86 1.85
2652 5563 7.067859 CAGAAAAGATTGCTCCATGGATCTTTA 59.932 37.037 28.85 12.54 37.37 1.85
2653 5564 7.783596 AGAAAAGATTGCTCCATGGATCTTTAT 59.216 33.333 28.85 21.41 37.37 1.40
2654 5565 7.909485 AAAGATTGCTCCATGGATCTTTATT 57.091 32.000 28.08 13.26 36.82 1.40
2862 5810 7.040478 TGCTATTTTCTGCTTATTGTGTCTGTT 60.040 33.333 0.00 0.00 0.00 3.16
2912 5860 1.732259 AGCGGACTTTTGTGCTATTCG 59.268 47.619 0.00 0.00 38.72 3.34
2946 5894 3.236816 GTCACATTGTGGAATTTGCGAG 58.763 45.455 16.46 0.00 33.87 5.03
2952 5900 7.281999 TCACATTGTGGAATTTGCGAGATTATA 59.718 33.333 16.46 0.00 33.87 0.98
3083 6142 8.737168 TGGATTGTAAGATTCCATCTAGTTTG 57.263 34.615 0.00 0.00 39.08 2.93
3132 6191 2.620251 TGAATTAGATCGTGGGCCAG 57.380 50.000 6.40 0.73 0.00 4.85
3281 6342 2.412323 ATGTGCGAGCAAGGCATGG 61.412 57.895 0.00 0.00 43.19 3.66
3388 6449 7.867909 TCTGTCAGTTTTATCTTATCGCTATGG 59.132 37.037 0.00 0.00 0.00 2.74
3397 6458 4.693283 TCTTATCGCTATGGTCCACTTTG 58.307 43.478 0.00 0.00 0.00 2.77
3400 6461 2.422597 TCGCTATGGTCCACTTTGTTG 58.577 47.619 0.00 0.00 0.00 3.33
3442 6503 3.890756 TCTGCACAGACAAATCCATGTTT 59.109 39.130 0.00 0.00 32.57 2.83
3502 6563 7.501559 CCATGTCTAGTTCATCATTTCTTCCAT 59.498 37.037 0.00 0.00 0.00 3.41
3504 6565 8.868522 TGTCTAGTTCATCATTTCTTCCATTT 57.131 30.769 0.00 0.00 0.00 2.32
3523 6584 2.708386 TTGGGTTTAACGAAATGGCG 57.292 45.000 0.00 0.00 37.29 5.69
3584 6669 1.067776 ACCGAGATTCGTTGGTCACTC 60.068 52.381 0.00 0.00 38.40 3.51
3599 6684 4.141597 TGGTCACTCCAAGTTGTGTATGAA 60.142 41.667 1.45 0.00 44.12 2.57
3601 6686 5.057149 GTCACTCCAAGTTGTGTATGAACT 58.943 41.667 1.45 0.00 35.08 3.01
3659 6744 6.728632 TGTGGGTATAGGCATATGACTTCATA 59.271 38.462 18.25 6.67 42.38 2.15
3661 6746 6.156256 TGGGTATAGGCATATGACTTCATACC 59.844 42.308 28.55 28.55 41.16 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 2796 2.361119 ACTACGTTGACTTGAGTGCTCA 59.639 45.455 3.44 0.00 37.91 4.26
127 2918 7.752695 AGCAAATATACTAAAGAACAGTGCAC 58.247 34.615 9.40 9.40 0.00 4.57
151 2943 6.630443 GCAGTTGCATCGAATAAAATCAGTAG 59.370 38.462 0.00 0.00 41.59 2.57
215 3008 9.656040 TTGACAGCATGCATATTTTAAAGAAAT 57.344 25.926 21.98 0.00 42.53 2.17
395 3188 1.164041 CCTCTGGGCGTTGTTCGTTT 61.164 55.000 0.00 0.00 42.13 3.60
409 3202 1.413445 CATCTTCTCTCCAGGCCTCTG 59.587 57.143 0.00 0.00 40.59 3.35
410 3203 1.008206 ACATCTTCTCTCCAGGCCTCT 59.992 52.381 0.00 0.00 0.00 3.69
411 3204 1.494960 ACATCTTCTCTCCAGGCCTC 58.505 55.000 0.00 0.00 0.00 4.70
464 3287 4.021192 TGGAATGGAAAGAGAAACAATGCC 60.021 41.667 0.00 0.00 0.00 4.40
488 3311 7.042321 GCAAAGACTAAACATATATGCGGTGTA 60.042 37.037 12.79 0.00 0.00 2.90
490 3313 6.017934 AGCAAAGACTAAACATATATGCGGTG 60.018 38.462 12.79 4.10 36.45 4.94
639 3464 8.946085 GTATAAGTTGGATGATTCAGTGTGAAA 58.054 33.333 0.00 0.00 40.12 2.69
906 3759 6.040054 GTGGTTGGGTTCTTGTAAGTATGTTT 59.960 38.462 0.00 0.00 0.00 2.83
1102 3958 0.741221 CTACCCGCAAGCAGAAGGTC 60.741 60.000 0.00 0.00 31.89 3.85
1152 4008 3.056536 TGAGAGACCATGTTCTTTCTCCG 60.057 47.826 11.35 0.00 35.99 4.63
1197 4053 1.146957 GCAGTGCATCTGAGCTCTCG 61.147 60.000 16.19 6.27 46.27 4.04
1226 4082 1.339055 CGATTCCTTCAGGCAGTTCCA 60.339 52.381 0.00 0.00 37.29 3.53
1231 4087 1.094073 CCAGCGATTCCTTCAGGCAG 61.094 60.000 0.00 0.00 34.44 4.85
1957 4849 7.732140 TGGCCATTCATTGGGTTTATCAATATA 59.268 33.333 0.00 0.00 46.55 0.86
2103 4995 9.201989 TCACTTGTACCATGAAACTCTATATCT 57.798 33.333 0.00 0.00 0.00 1.98
2113 5005 6.723298 ACCAAATTCACTTGTACCATGAAA 57.277 33.333 0.00 0.00 36.03 2.69
2173 5074 6.349860 GGGTGGTGAATGAAAAGGTACATTAC 60.350 42.308 0.00 0.00 36.94 1.89
2188 5089 0.706433 AGCATGGAAGGGTGGTGAAT 59.294 50.000 0.00 0.00 0.00 2.57
2566 5470 1.475280 ACGCACTTACCGATTAGCAGA 59.525 47.619 0.00 0.00 0.00 4.26
2659 5570 9.878599 TGCTTTTCAAAATAAAAACGAAACAAA 57.121 22.222 0.00 0.00 0.00 2.83
2732 5643 0.892755 TACCAACCACGAAGCGATCT 59.107 50.000 0.00 0.00 0.00 2.75
2912 5860 5.975344 CCACAATGTGACATCATAATTCAGC 59.025 40.000 15.91 0.00 35.23 4.26
3014 6073 8.408601 GGTACTTATACTCCAGTCGTTCATTTA 58.591 37.037 0.00 0.00 0.00 1.40
3105 6164 5.509163 GCCCACGATCTAATTCAAGCTAGTA 60.509 44.000 0.00 0.00 0.00 1.82
3123 6182 1.340248 CCTATGTAGTACTGGCCCACG 59.660 57.143 5.39 0.00 0.00 4.94
3132 6191 3.705072 ACCAAGGCTGTCCTATGTAGTAC 59.295 47.826 0.00 0.00 43.40 2.73
3232 6293 3.138884 TGTTGTGCAGCCTTTATCTCA 57.861 42.857 0.00 0.00 0.00 3.27
3281 6342 5.799213 AGCACAGCTAATATCTTGGGTATC 58.201 41.667 0.00 0.00 36.99 2.24
3344 6405 5.521372 TGACAGATAAATCTTCATGCACTCG 59.479 40.000 0.00 0.00 34.22 4.18
3375 6436 4.161565 ACAAAGTGGACCATAGCGATAAGA 59.838 41.667 0.00 0.00 0.00 2.10
3376 6437 4.442706 ACAAAGTGGACCATAGCGATAAG 58.557 43.478 0.00 0.00 0.00 1.73
3377 6438 4.481368 ACAAAGTGGACCATAGCGATAA 57.519 40.909 0.00 0.00 0.00 1.75
3378 6439 4.188462 CAACAAAGTGGACCATAGCGATA 58.812 43.478 0.00 0.00 0.00 2.92
3379 6440 3.009723 CAACAAAGTGGACCATAGCGAT 58.990 45.455 0.00 0.00 0.00 4.58
3380 6441 2.224426 ACAACAAAGTGGACCATAGCGA 60.224 45.455 0.00 0.00 0.00 4.93
3381 6442 2.151202 ACAACAAAGTGGACCATAGCG 58.849 47.619 0.00 0.00 0.00 4.26
3388 6449 2.033424 GCAAGAGGACAACAAAGTGGAC 59.967 50.000 0.00 0.00 0.00 4.02
3397 6458 3.316308 ACAATCAACTGCAAGAGGACAAC 59.684 43.478 0.00 0.00 37.43 3.32
3400 6461 3.817647 AGAACAATCAACTGCAAGAGGAC 59.182 43.478 0.00 0.00 37.43 3.85
3442 6503 1.691219 GAGCCCTGGAACATCCCAA 59.309 57.895 0.00 0.00 38.20 4.12
3488 6549 8.720562 GTTAAACCCAAAATGGAAGAAATGATG 58.279 33.333 0.00 0.00 40.96 3.07
3502 6563 3.181478 ACGCCATTTCGTTAAACCCAAAA 60.181 39.130 0.00 0.00 40.07 2.44
3504 6565 1.955080 ACGCCATTTCGTTAAACCCAA 59.045 42.857 0.00 0.00 40.07 4.12
3588 6673 9.509855 TCATAAACAAACAAGTTCATACACAAC 57.490 29.630 0.00 0.00 0.00 3.32
3630 6715 4.019321 GTCATATGCCTATACCCACACCAT 60.019 45.833 0.00 0.00 0.00 3.55
3659 6744 8.506168 AAAATGTGTCATCGTTAATGATAGGT 57.494 30.769 9.85 0.00 45.94 3.08
3661 6746 9.855361 GAGAAAATGTGTCATCGTTAATGATAG 57.145 33.333 9.85 5.54 45.94 2.08
3671 6756 5.349543 TGACATGAGAGAAAATGTGTCATCG 59.650 40.000 0.00 0.00 40.47 3.84



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

AutoCloner maintained by Alex Coulton.