Multiple sequence alignment - TraesCS6B01G292900

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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 TraesCS6B01G292900 chr6B 100.000 3452 0 0 1 3452 526718144 526714693 0.000000e+00 6375
1 TraesCS6B01G292900 chr6D 97.115 2773 62 11 13 2773 352357983 352360749 0.000000e+00 4662
2 TraesCS6B01G292900 chr6D 92.647 680 15 7 2775 3439 352360817 352361476 0.000000e+00 946
3 TraesCS6B01G292900 chr6D 95.062 324 15 1 1324 1647 448792797 448792475 3.070000e-140 508
4 TraesCS6B01G292900 chr6A 93.586 2058 78 14 729 2773 490492311 490490295 0.000000e+00 3020
5 TraesCS6B01G292900 chr6A 90.441 680 24 19 2784 3443 490490218 490489560 0.000000e+00 857
6 TraesCS6B01G292900 chr6A 84.530 724 58 19 31 712 490493097 490492386 0.000000e+00 667


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 TraesCS6B01G292900 chr6B 526714693 526718144 3451 True 6375.000000 6375 100.000 1 3452 1 chr6B.!!$R1 3451
1 TraesCS6B01G292900 chr6D 352357983 352361476 3493 False 2804.000000 4662 94.881 13 3439 2 chr6D.!!$F1 3426
2 TraesCS6B01G292900 chr6A 490489560 490493097 3537 True 1514.666667 3020 89.519 31 3443 3 chr6A.!!$R1 3412

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
136 144 0.242825 CACCATGGCTTGAACTGCTG 59.757 55.000 13.04 0.00 0.0 4.41 F
181 189 1.066430 TGTCTGGGTTCGCATACTTCC 60.066 52.381 6.85 0.00 0.0 3.46 F
611 655 1.807142 GACTTTGGCTAGCTTGGTGTC 59.193 52.381 15.72 12.52 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1611 1721 0.038166 TGGAACCAGCAACATCCTCC 59.962 55.000 0.0 0.0 33.02 4.30 R
2172 2283 1.768275 TCTTGACCTTTCTGCTCACCA 59.232 47.619 0.0 0.0 0.00 4.17 R
2544 2655 0.609131 ATGGCACCACTTTCCTTCCG 60.609 55.000 0.0 0.0 0.00 4.30 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
25 26 4.977347 GTCTAACTAGTATTTCGGAGCTGC 59.023 45.833 0.00 0.00 0.00 5.25
35 36 2.517875 GGAGCTGCCATCGCCATT 60.518 61.111 0.00 0.00 36.34 3.16
53 55 4.168760 CCATTGGAGAAAATCTGAAACGC 58.831 43.478 0.00 0.00 0.00 4.84
63 65 2.386661 TCTGAAACGCCTGAATCCTC 57.613 50.000 0.00 0.00 0.00 3.71
98 106 4.454678 TGCCAGAGGATCAATGTGTATTC 58.545 43.478 0.00 0.00 37.82 1.75
110 118 7.566760 TCAATGTGTATTCTTGCCGATAAAT 57.433 32.000 0.00 0.00 0.00 1.40
136 144 0.242825 CACCATGGCTTGAACTGCTG 59.757 55.000 13.04 0.00 0.00 4.41
142 150 3.701205 TGGCTTGAACTGCTGAGAATA 57.299 42.857 0.00 0.00 0.00 1.75
169 177 6.399639 AATTTATTGAACGTTTGTCTGGGT 57.600 33.333 0.46 0.00 0.00 4.51
171 179 3.982576 ATTGAACGTTTGTCTGGGTTC 57.017 42.857 0.46 0.00 39.29 3.62
181 189 1.066430 TGTCTGGGTTCGCATACTTCC 60.066 52.381 6.85 0.00 0.00 3.46
212 220 7.519032 AAGAATTCTTCCGGTTTACATTTCA 57.481 32.000 15.11 0.00 0.00 2.69
223 232 9.413048 TCCGGTTTACATTTCATTAATTTTGAC 57.587 29.630 0.00 0.00 0.00 3.18
611 655 1.807142 GACTTTGGCTAGCTTGGTGTC 59.193 52.381 15.72 12.52 0.00 3.67
646 690 5.431765 TCTCTGTTTTGAGCTTCAGTTTCT 58.568 37.500 0.00 0.00 34.29 2.52
759 863 5.633601 TGACTGTTATGCTTGTTTCTCGTAG 59.366 40.000 0.00 0.00 0.00 3.51
938 1042 6.374333 TCTCGCTATTTGTTCTTTATTTGGCT 59.626 34.615 0.00 0.00 0.00 4.75
1774 1885 3.698539 CCTCAGTGAGAAGATCAGCACTA 59.301 47.826 22.09 0.91 39.40 2.74
2172 2283 7.213178 ACCAGAAGATACTGAAATGGGTAAT 57.787 36.000 0.00 0.00 39.94 1.89
2178 2289 6.595682 AGATACTGAAATGGGTAATGGTGAG 58.404 40.000 0.00 0.00 0.00 3.51
2186 2297 2.290896 TGGGTAATGGTGAGCAGAAAGG 60.291 50.000 0.00 0.00 0.00 3.11
2386 2497 0.034089 AAGCAGCCCTGTAACCATCC 60.034 55.000 0.00 0.00 0.00 3.51
2543 2654 7.326645 GTTGTCGATGTGTTGTTGTTTTATTG 58.673 34.615 0.00 0.00 0.00 1.90
2544 2655 5.457148 TGTCGATGTGTTGTTGTTTTATTGC 59.543 36.000 0.00 0.00 0.00 3.56
2563 2674 0.609131 CGGAAGGAAAGTGGTGCCAT 60.609 55.000 0.00 0.00 0.00 4.40
2655 2766 7.280769 GCGGTGTATTTTCATTTGTTCTTTTC 58.719 34.615 0.00 0.00 0.00 2.29
2728 2839 5.936187 ACCATTTGAATATGCAACATCCA 57.064 34.783 0.00 0.00 0.00 3.41
2737 2848 0.826672 TGCAACATCCACACCATGCA 60.827 50.000 0.00 0.00 41.08 3.96
2741 2852 1.927487 ACATCCACACCATGCATTGT 58.073 45.000 0.00 0.00 0.00 2.71
2745 2862 1.175654 CCACACCATGCATTGTGCTA 58.824 50.000 26.18 0.00 45.31 3.49
2746 2863 1.545136 CCACACCATGCATTGTGCTAA 59.455 47.619 26.18 0.00 45.31 3.09
2762 2879 4.994852 TGTGCTAATAGTTGAAGTGTGGAC 59.005 41.667 0.00 0.00 0.00 4.02
2768 2885 1.837439 AGTTGAAGTGTGGACCAGACA 59.163 47.619 22.75 2.43 29.61 3.41
2773 2890 3.214328 GAAGTGTGGACCAGACAAACAT 58.786 45.455 22.75 4.43 29.61 2.71
2778 2961 2.948979 GTGGACCAGACAAACATGACAA 59.051 45.455 0.00 0.00 0.00 3.18
2780 2963 3.569277 TGGACCAGACAAACATGACAATG 59.431 43.478 0.00 0.00 39.89 2.82
2792 2975 9.394767 ACAAACATGACAATGTATAAGCAGATA 57.605 29.630 0.00 0.00 46.58 1.98
2916 3104 2.281762 GCTGCACAAGTACAGTATACGC 59.718 50.000 0.00 0.00 36.26 4.42
2917 3105 3.507786 CTGCACAAGTACAGTATACGCA 58.492 45.455 0.00 0.00 0.00 5.24
2918 3106 3.507786 TGCACAAGTACAGTATACGCAG 58.492 45.455 0.00 0.00 0.00 5.18
2919 3107 2.281762 GCACAAGTACAGTATACGCAGC 59.718 50.000 0.00 0.00 0.00 5.25
2920 3108 3.770666 CACAAGTACAGTATACGCAGCT 58.229 45.455 0.00 0.00 0.00 4.24
2921 3109 3.547868 CACAAGTACAGTATACGCAGCTG 59.452 47.826 10.11 10.11 36.41 4.24
2922 3110 2.493713 AGTACAGTATACGCAGCTGC 57.506 50.000 29.12 29.12 33.87 5.25
2923 3111 1.749063 AGTACAGTATACGCAGCTGCA 59.251 47.619 36.03 20.16 42.21 4.41
2924 3112 2.362397 AGTACAGTATACGCAGCTGCAT 59.638 45.455 36.03 26.43 42.21 3.96
2925 3113 3.568430 AGTACAGTATACGCAGCTGCATA 59.432 43.478 36.03 27.82 42.21 3.14
2926 3114 3.018598 ACAGTATACGCAGCTGCATAG 57.981 47.619 36.03 23.12 42.21 2.23
2995 3183 5.468540 AGGAGCCACAAAAATTTAAGGTC 57.531 39.130 0.00 0.00 0.00 3.85
3126 3324 2.616842 AGACCAAGTCAAAACGCGAATT 59.383 40.909 15.93 4.26 34.60 2.17
3129 3327 2.467305 CCAAGTCAAAACGCGAATTGTG 59.533 45.455 15.93 11.22 36.88 3.33
3157 3355 2.267188 AAGCACGCGACGACTATTTA 57.733 45.000 15.93 0.00 0.00 1.40
3158 3356 2.486951 AGCACGCGACGACTATTTAT 57.513 45.000 15.93 0.00 0.00 1.40
3160 3358 2.787680 AGCACGCGACGACTATTTATTC 59.212 45.455 15.93 0.00 0.00 1.75
3161 3359 2.532723 GCACGCGACGACTATTTATTCA 59.467 45.455 15.93 0.00 0.00 2.57
3164 3362 4.206404 CACGCGACGACTATTTATTCACAT 59.794 41.667 15.93 0.00 0.00 3.21
3165 3363 4.206404 ACGCGACGACTATTTATTCACATG 59.794 41.667 15.93 0.00 0.00 3.21
3166 3364 4.439776 CGCGACGACTATTTATTCACATGA 59.560 41.667 0.00 0.00 0.00 3.07
3443 3651 2.117156 CGCTGCATCTTGGGAAGGG 61.117 63.158 0.00 0.00 0.00 3.95
3444 3652 1.000396 GCTGCATCTTGGGAAGGGT 60.000 57.895 0.00 0.00 0.00 4.34
3445 3653 0.613012 GCTGCATCTTGGGAAGGGTT 60.613 55.000 0.00 0.00 0.00 4.11
3446 3654 1.180029 CTGCATCTTGGGAAGGGTTG 58.820 55.000 0.00 0.00 0.00 3.77
3447 3655 0.899717 TGCATCTTGGGAAGGGTTGC 60.900 55.000 0.00 0.00 33.16 4.17
3448 3656 0.613012 GCATCTTGGGAAGGGTTGCT 60.613 55.000 0.00 0.00 0.00 3.91
3449 3657 1.180029 CATCTTGGGAAGGGTTGCTG 58.820 55.000 0.00 0.00 0.00 4.41
3450 3658 0.779997 ATCTTGGGAAGGGTTGCTGT 59.220 50.000 0.00 0.00 0.00 4.40
3451 3659 0.110486 TCTTGGGAAGGGTTGCTGTC 59.890 55.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.561614 CAGCTCCGAAATACTAGTTAGACAA 58.438 40.000 0.00 0.00 0.00 3.18
1 2 5.450137 GCAGCTCCGAAATACTAGTTAGACA 60.450 44.000 0.00 0.00 0.00 3.41
2 3 4.977347 GCAGCTCCGAAATACTAGTTAGAC 59.023 45.833 0.00 0.00 0.00 2.59
3 4 4.037684 GGCAGCTCCGAAATACTAGTTAGA 59.962 45.833 0.00 0.00 0.00 2.10
4 5 4.202121 TGGCAGCTCCGAAATACTAGTTAG 60.202 45.833 0.00 0.00 37.80 2.34
5 6 3.702548 TGGCAGCTCCGAAATACTAGTTA 59.297 43.478 0.00 0.00 37.80 2.24
6 7 2.500098 TGGCAGCTCCGAAATACTAGTT 59.500 45.455 0.00 0.00 37.80 2.24
7 8 2.108168 TGGCAGCTCCGAAATACTAGT 58.892 47.619 0.00 0.00 37.80 2.57
8 9 2.890808 TGGCAGCTCCGAAATACTAG 57.109 50.000 0.00 0.00 37.80 2.57
9 10 2.288213 CGATGGCAGCTCCGAAATACTA 60.288 50.000 0.00 0.00 37.80 1.82
10 11 1.539065 CGATGGCAGCTCCGAAATACT 60.539 52.381 0.00 0.00 37.80 2.12
11 12 0.861837 CGATGGCAGCTCCGAAATAC 59.138 55.000 0.00 0.00 37.80 1.89
25 26 2.954318 AGATTTTCTCCAATGGCGATGG 59.046 45.455 0.00 2.15 39.41 3.51
35 36 2.813754 CAGGCGTTTCAGATTTTCTCCA 59.186 45.455 0.00 0.00 0.00 3.86
53 55 3.891049 AGGGAAATTTCGAGGATTCAGG 58.109 45.455 11.95 0.00 0.00 3.86
63 65 2.094545 CCTCTGGCAAAGGGAAATTTCG 60.095 50.000 11.95 0.00 0.00 3.46
98 106 4.216042 TGGTGCATCATATTTATCGGCAAG 59.784 41.667 0.00 0.00 0.00 4.01
110 118 2.689471 GTTCAAGCCATGGTGCATCATA 59.311 45.455 13.21 0.00 0.00 2.15
142 150 8.026607 CCCAGACAAACGTTCAATAAATTACAT 58.973 33.333 0.00 0.00 0.00 2.29
154 162 0.041576 GCGAACCCAGACAAACGTTC 60.042 55.000 0.00 0.00 32.97 3.95
155 163 0.745128 TGCGAACCCAGACAAACGTT 60.745 50.000 0.00 0.00 0.00 3.99
161 169 1.066430 GGAAGTATGCGAACCCAGACA 60.066 52.381 0.00 0.00 29.67 3.41
169 177 3.973206 TTCCTCTTGGAAGTATGCGAA 57.027 42.857 0.00 0.00 46.57 4.70
212 220 5.413309 TGCCGAAATGGGTCAAAATTAAT 57.587 34.783 0.00 0.00 38.63 1.40
223 232 3.730662 CGAAACTGTAATGCCGAAATGGG 60.731 47.826 0.00 0.00 38.63 4.00
404 445 3.648339 AATGGTTGTTCATGTGAGCAC 57.352 42.857 0.00 0.00 35.01 4.40
646 690 1.202475 GCCAAAGGAAAAGGCGAAACA 60.202 47.619 0.00 0.00 38.86 2.83
759 863 3.191371 ACCTCATCCAATTTCGCAAACTC 59.809 43.478 0.00 0.00 0.00 3.01
938 1042 8.842358 AAAAGGTGTCGAATATACTTCTTTCA 57.158 30.769 0.00 0.00 0.00 2.69
1611 1721 0.038166 TGGAACCAGCAACATCCTCC 59.962 55.000 0.00 0.00 33.02 4.30
2172 2283 1.768275 TCTTGACCTTTCTGCTCACCA 59.232 47.619 0.00 0.00 0.00 4.17
2178 2289 2.430465 TCAGCATCTTGACCTTTCTGC 58.570 47.619 0.00 0.00 0.00 4.26
2186 2297 3.476295 TTGCGATTTCAGCATCTTGAC 57.524 42.857 0.00 0.00 44.74 3.18
2286 2397 4.516698 TCAGTCATCAGAAAACTTTCAGGC 59.483 41.667 5.07 0.00 39.61 4.85
2386 2497 4.415150 AGTGGCCATGCAGACGGG 62.415 66.667 9.72 0.00 0.00 5.28
2517 2628 2.730183 ACAACAACACATCGACAACG 57.270 45.000 0.00 0.00 41.26 4.10
2518 2629 7.326645 CAATAAAACAACAACACATCGACAAC 58.673 34.615 0.00 0.00 0.00 3.32
2543 2654 2.626780 GGCACCACTTTCCTTCCGC 61.627 63.158 0.00 0.00 0.00 5.54
2544 2655 0.609131 ATGGCACCACTTTCCTTCCG 60.609 55.000 0.00 0.00 0.00 4.30
2655 2766 1.213537 CATTTGTGGCAAGGCTCGG 59.786 57.895 0.00 0.00 0.00 4.63
2737 2848 6.149474 GTCCACACTTCAACTATTAGCACAAT 59.851 38.462 0.00 0.00 0.00 2.71
2741 2852 4.041075 TGGTCCACACTTCAACTATTAGCA 59.959 41.667 0.00 0.00 0.00 3.49
2745 2862 4.102524 TGTCTGGTCCACACTTCAACTATT 59.897 41.667 0.00 0.00 0.00 1.73
2746 2863 3.646162 TGTCTGGTCCACACTTCAACTAT 59.354 43.478 0.00 0.00 0.00 2.12
2762 2879 6.968904 GCTTATACATTGTCATGTTTGTCTGG 59.031 38.462 0.00 0.00 41.16 3.86
2918 3106 4.213666 TGCACTCAGCTATGCAGC 57.786 55.556 13.80 3.38 46.63 5.25
2921 3109 4.621068 TGTAATTTGCACTCAGCTATGC 57.379 40.909 9.31 9.31 45.94 3.14
2922 3110 5.438117 CGATGTAATTTGCACTCAGCTATG 58.562 41.667 0.00 0.00 45.94 2.23
2923 3111 4.024556 GCGATGTAATTTGCACTCAGCTAT 60.025 41.667 0.00 0.00 45.94 2.97
2924 3112 3.309682 GCGATGTAATTTGCACTCAGCTA 59.690 43.478 0.00 0.00 45.94 3.32
2925 3113 2.096496 GCGATGTAATTTGCACTCAGCT 59.904 45.455 0.00 0.00 45.94 4.24
2926 3114 2.444351 GCGATGTAATTTGCACTCAGC 58.556 47.619 0.00 0.00 45.96 4.26
2927 3115 2.697363 CGCGATGTAATTTGCACTCAG 58.303 47.619 0.00 0.00 0.00 3.35
2928 3116 1.202020 GCGCGATGTAATTTGCACTCA 60.202 47.619 12.10 0.00 0.00 3.41
2929 3117 1.062587 AGCGCGATGTAATTTGCACTC 59.937 47.619 12.10 0.00 0.00 3.51
2930 3118 1.086696 AGCGCGATGTAATTTGCACT 58.913 45.000 12.10 0.00 0.00 4.40
2995 3183 3.753797 TCTCGCATCAGCTAGTATACCAG 59.246 47.826 0.00 0.00 39.10 4.00
3126 3324 0.884704 GCGTGCTTTCCCTTCTCACA 60.885 55.000 0.00 0.00 0.00 3.58
3129 3327 1.374252 TCGCGTGCTTTCCCTTCTC 60.374 57.895 5.77 0.00 0.00 2.87
3157 3355 5.131067 CCACAGATCCAGATTCATGTGAAT 58.869 41.667 16.72 7.91 46.54 2.57
3158 3356 4.520179 CCACAGATCCAGATTCATGTGAA 58.480 43.478 16.72 0.00 40.27 3.18
3160 3358 2.617308 GCCACAGATCCAGATTCATGTG 59.383 50.000 11.59 11.59 38.17 3.21
3161 3359 2.422519 GGCCACAGATCCAGATTCATGT 60.423 50.000 0.00 0.00 0.00 3.21
3164 3362 1.288188 TGGCCACAGATCCAGATTCA 58.712 50.000 0.00 0.00 0.00 2.57
3165 3363 2.228059 CATGGCCACAGATCCAGATTC 58.772 52.381 8.16 0.00 35.57 2.52
3166 3364 1.133575 CCATGGCCACAGATCCAGATT 60.134 52.381 8.16 0.00 35.57 2.40


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

AutoCloner maintained by Alex Coulton.