Multiple sequence alignment - TraesCS1B01G405000

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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 TraesCS1B01G405000 chr1B 100.000 3365 0 0 1 3365 633716327 633719691 0.000000e+00 6215
1 TraesCS1B01G405000 chr3A 98.324 3162 46 3 1 3156 105557602 105554442 0.000000e+00 5539
2 TraesCS1B01G405000 chr3A 92.504 627 25 9 78 701 673485989 673486596 0.000000e+00 878
3 TraesCS1B01G405000 chr3A 92.105 114 5 1 1 110 746687144 746687257 1.250000e-34 158
4 TraesCS1B01G405000 chr3A 95.652 69 3 0 1 69 673485868 673485936 9.870000e-21 111
5 TraesCS1B01G405000 chr5B 98.262 3165 45 6 1 3156 57515770 57512607 0.000000e+00 5531
6 TraesCS1B01G405000 chr5D 97.606 3174 50 12 1 3156 503338794 503341959 0.000000e+00 5417
7 TraesCS1B01G405000 chr5D 97.170 3180 58 10 1 3156 6253929 6250758 0.000000e+00 5345
8 TraesCS1B01G405000 chr5D 99.537 216 1 0 3150 3365 299969516 299969301 8.750000e-106 394
9 TraesCS1B01G405000 chr5D 99.537 216 1 0 3150 3365 503341915 503342130 8.750000e-106 394
10 TraesCS1B01G405000 chr1D 97.412 3168 53 12 1 3156 254458769 254461919 0.000000e+00 5369
11 TraesCS1B01G405000 chr4A 95.839 3124 108 12 1 3118 309447054 309443947 0.000000e+00 5029
12 TraesCS1B01G405000 chr4D 95.729 3044 104 12 127 3156 19900207 19903238 0.000000e+00 4878
13 TraesCS1B01G405000 chr4D 99.074 216 2 0 3150 3365 134988349 134988134 4.070000e-104 388
14 TraesCS1B01G405000 chr7A 96.131 2895 85 12 276 3156 537841776 537838895 0.000000e+00 4700
15 TraesCS1B01G405000 chr7B 98.488 2579 33 4 1 2577 662755679 662753105 0.000000e+00 4542
16 TraesCS1B01G405000 chr2B 93.860 456 23 1 2706 3156 449192597 449192142 0.000000e+00 682
17 TraesCS1B01G405000 chr2B 94.203 69 4 0 2587 2655 427926166 427926098 4.590000e-19 106
18 TraesCS1B01G405000 chr7D 99.537 216 1 0 3150 3365 203510512 203510727 8.750000e-106 394
19 TraesCS1B01G405000 chr7D 99.537 216 1 0 3150 3365 231556478 231556263 8.750000e-106 394
20 TraesCS1B01G405000 chr7D 99.537 216 1 0 3150 3365 381963240 381963025 8.750000e-106 394
21 TraesCS1B01G405000 chr6D 99.537 216 1 0 3150 3365 283217660 283217875 8.750000e-106 394
22 TraesCS1B01G405000 chr5A 99.537 216 1 0 3150 3365 559029476 559029261 8.750000e-106 394
23 TraesCS1B01G405000 chr1A 99.537 216 1 0 3150 3365 554484495 554484710 8.750000e-106 394


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 TraesCS1B01G405000 chr1B 633716327 633719691 3364 False 6215.0 6215 100.0000 1 3365 1 chr1B.!!$F1 3364
1 TraesCS1B01G405000 chr3A 105554442 105557602 3160 True 5539.0 5539 98.3240 1 3156 1 chr3A.!!$R1 3155
2 TraesCS1B01G405000 chr3A 673485868 673486596 728 False 494.5 878 94.0780 1 701 2 chr3A.!!$F2 700
3 TraesCS1B01G405000 chr5B 57512607 57515770 3163 True 5531.0 5531 98.2620 1 3156 1 chr5B.!!$R1 3155
4 TraesCS1B01G405000 chr5D 6250758 6253929 3171 True 5345.0 5345 97.1700 1 3156 1 chr5D.!!$R1 3155
5 TraesCS1B01G405000 chr5D 503338794 503342130 3336 False 2905.5 5417 98.5715 1 3365 2 chr5D.!!$F1 3364
6 TraesCS1B01G405000 chr1D 254458769 254461919 3150 False 5369.0 5369 97.4120 1 3156 1 chr1D.!!$F1 3155
7 TraesCS1B01G405000 chr4A 309443947 309447054 3107 True 5029.0 5029 95.8390 1 3118 1 chr4A.!!$R1 3117
8 TraesCS1B01G405000 chr4D 19900207 19903238 3031 False 4878.0 4878 95.7290 127 3156 1 chr4D.!!$F1 3029
9 TraesCS1B01G405000 chr7A 537838895 537841776 2881 True 4700.0 4700 96.1310 276 3156 1 chr7A.!!$R1 2880
10 TraesCS1B01G405000 chr7B 662753105 662755679 2574 True 4542.0 4542 98.4880 1 2577 1 chr7B.!!$R1 2576

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
321 371 4.641541 CACCATGAATCCACTAATTGCTGA 59.358 41.667 0.0 0.0 0.0 4.26 F
1831 1901 9.830186 AGATAGAGGATAGGCTCATTACTTAAA 57.170 33.333 0.0 0.0 0.0 1.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2186 2257 9.480538 GTTTTTCAAAATAAAGGGTTTCGTTTC 57.519 29.63 0.0 0.0 33.64 2.78 R
3126 3198 0.101219 GGTGAATCCGCCATTTCAGC 59.899 55.00 0.0 0.0 42.48 4.26 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
156 204 6.884472 TGGAATTCCCTTCTATGTAGTTCA 57.116 37.500 21.90 0.00 34.08 3.18
321 371 4.641541 CACCATGAATCCACTAATTGCTGA 59.358 41.667 0.00 0.00 0.00 4.26
1831 1901 9.830186 AGATAGAGGATAGGCTCATTACTTAAA 57.170 33.333 0.00 0.00 0.00 1.52
2333 2404 4.913345 CCGTACGATTCGTGCTAATATTGA 59.087 41.667 21.40 0.00 41.39 2.57
2366 2437 5.513962 GGTCCCTGGAATGGAAGAGATAATC 60.514 48.000 0.00 0.00 30.32 1.75
2582 2654 2.154462 GGGATGGGATTGCTCGTATTG 58.846 52.381 0.00 0.00 0.00 1.90
2604 2676 8.650143 ATTGTAGGTCTTGGTGAAATAATGTT 57.350 30.769 0.00 0.00 0.00 2.71
2877 2949 4.207165 GCTCCAAGTATAATTTCCAGGCA 58.793 43.478 0.00 0.00 0.00 4.75
2889 2961 3.417069 TTCCAGGCATTCCATATACGG 57.583 47.619 0.00 0.00 33.74 4.02
3002 3074 4.497006 GCAAAATAGCAGTAGCCACAGATG 60.497 45.833 0.00 0.00 43.56 2.90
3063 3135 8.630037 TGTTTATGTAGCTATCGATCAAAGAGA 58.370 33.333 0.00 0.00 0.00 3.10
3082 3154 2.428890 AGAATCCTCCGTAGCTCAAGTG 59.571 50.000 0.00 0.00 0.00 3.16
3118 3190 0.103173 AGGAGGGGGCCATGGAATAT 60.103 55.000 18.40 0.00 0.00 1.28
3119 3191 0.786435 GGAGGGGGCCATGGAATATT 59.214 55.000 18.40 0.00 0.00 1.28
3120 3192 1.550869 GGAGGGGGCCATGGAATATTG 60.551 57.143 18.40 0.00 0.00 1.90
3121 3193 1.147817 GAGGGGGCCATGGAATATTGT 59.852 52.381 18.40 0.00 0.00 2.71
3122 3194 2.378547 GAGGGGGCCATGGAATATTGTA 59.621 50.000 18.40 0.00 0.00 2.41
3123 3195 2.379907 AGGGGGCCATGGAATATTGTAG 59.620 50.000 18.40 0.00 0.00 2.74
3124 3196 2.110011 GGGGGCCATGGAATATTGTAGT 59.890 50.000 18.40 0.00 0.00 2.73
3125 3197 3.332485 GGGGGCCATGGAATATTGTAGTA 59.668 47.826 18.40 0.00 0.00 1.82
3126 3198 4.567747 GGGGGCCATGGAATATTGTAGTAG 60.568 50.000 18.40 0.00 0.00 2.57
3127 3199 4.010349 GGGCCATGGAATATTGTAGTAGC 58.990 47.826 18.40 0.00 0.00 3.58
3128 3200 4.263506 GGGCCATGGAATATTGTAGTAGCT 60.264 45.833 18.40 0.00 0.00 3.32
3129 3201 4.697352 GGCCATGGAATATTGTAGTAGCTG 59.303 45.833 18.40 0.00 0.00 4.24
3130 3202 5.513094 GGCCATGGAATATTGTAGTAGCTGA 60.513 44.000 18.40 0.00 0.00 4.26
3131 3203 5.997746 GCCATGGAATATTGTAGTAGCTGAA 59.002 40.000 18.40 0.00 0.00 3.02
3132 3204 6.486657 GCCATGGAATATTGTAGTAGCTGAAA 59.513 38.462 18.40 0.00 0.00 2.69
3133 3205 7.175641 GCCATGGAATATTGTAGTAGCTGAAAT 59.824 37.037 18.40 0.00 0.00 2.17
3134 3206 8.509690 CCATGGAATATTGTAGTAGCTGAAATG 58.490 37.037 5.56 0.00 0.00 2.32
3135 3207 8.509690 CATGGAATATTGTAGTAGCTGAAATGG 58.490 37.037 0.00 0.00 0.00 3.16
3136 3208 6.486657 TGGAATATTGTAGTAGCTGAAATGGC 59.513 38.462 0.00 0.00 0.00 4.40
3137 3209 6.347725 GGAATATTGTAGTAGCTGAAATGGCG 60.348 42.308 0.00 0.00 34.52 5.69
3138 3210 2.309528 TGTAGTAGCTGAAATGGCGG 57.690 50.000 0.00 0.00 34.52 6.13
3139 3211 1.828595 TGTAGTAGCTGAAATGGCGGA 59.171 47.619 0.00 0.00 34.52 5.54
3140 3212 2.434336 TGTAGTAGCTGAAATGGCGGAT 59.566 45.455 0.00 0.00 34.52 4.18
3141 3213 2.717639 AGTAGCTGAAATGGCGGATT 57.282 45.000 0.00 0.00 34.52 3.01
3142 3214 2.565841 AGTAGCTGAAATGGCGGATTC 58.434 47.619 0.00 0.00 34.52 2.52
3143 3215 2.092968 AGTAGCTGAAATGGCGGATTCA 60.093 45.455 0.00 0.56 34.57 2.57
3144 3216 1.098050 AGCTGAAATGGCGGATTCAC 58.902 50.000 0.00 0.00 32.46 3.18
3145 3217 0.101219 GCTGAAATGGCGGATTCACC 59.899 55.000 0.00 0.00 32.46 4.02
3146 3218 1.755179 CTGAAATGGCGGATTCACCT 58.245 50.000 0.00 0.00 36.31 4.00
3147 3219 1.402968 CTGAAATGGCGGATTCACCTG 59.597 52.381 0.00 0.00 36.31 4.00
3148 3220 0.101219 GAAATGGCGGATTCACCTGC 59.899 55.000 0.00 0.00 37.42 4.85
3149 3221 0.323725 AAATGGCGGATTCACCTGCT 60.324 50.000 0.00 0.00 37.93 4.24
3150 3222 0.546122 AATGGCGGATTCACCTGCTA 59.454 50.000 0.00 0.00 37.93 3.49
3153 3225 0.179045 GGCGGATTCACCTGCTACAT 60.179 55.000 0.00 0.00 37.93 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
321 371 2.426024 CCAGCAGCAATAACAGAAGCAT 59.574 45.455 0.00 0.00 0.00 3.79
1093 1149 6.932960 ACACCAACCACTACAGTTAGATTTAC 59.067 38.462 0.00 0.00 0.00 2.01
2186 2257 9.480538 GTTTTTCAAAATAAAGGGTTTCGTTTC 57.519 29.630 0.00 0.00 33.64 2.78
2333 2404 0.546747 TTCCAGGGACCCGAGAATGT 60.547 55.000 12.78 0.00 0.00 2.71
2366 2437 9.788960 GTAGAAGTTCAAGGCCTAATTAATTTG 57.211 33.333 5.16 4.28 0.00 2.32
2440 2512 5.472137 GGTTGCCATTAGTGTTTCTTGACTA 59.528 40.000 0.00 0.00 0.00 2.59
2582 2654 7.827729 ACCTAACATTATTTCACCAAGACCTAC 59.172 37.037 0.00 0.00 0.00 3.18
2604 2676 7.994425 TCTGCAAATTTGACTAATTCACCTA 57.006 32.000 22.31 0.00 35.39 3.08
2877 2949 6.126883 TGTTTGAAGAGGTCCGTATATGGAAT 60.127 38.462 15.48 7.42 40.44 3.01
2889 2961 2.278332 AAGCCCTGTTTGAAGAGGTC 57.722 50.000 6.23 0.00 37.75 3.85
2939 3011 0.530744 ATTAACTCTCGCTGACCGCA 59.469 50.000 0.00 0.00 39.08 5.69
3002 3074 4.317488 TGCCCTTTTTGATTGAGAATTGC 58.683 39.130 0.00 0.00 0.00 3.56
3054 3126 3.964031 AGCTACGGAGGATTCTCTTTGAT 59.036 43.478 0.00 0.00 39.86 2.57
3063 3135 1.482593 CCACTTGAGCTACGGAGGATT 59.517 52.381 0.00 0.00 0.00 3.01
3082 3154 4.141688 CCCTCCTCATGGAAAGTAGTTACC 60.142 50.000 0.00 0.00 42.66 2.85
3118 3190 2.235155 TCCGCCATTTCAGCTACTACAA 59.765 45.455 0.00 0.00 0.00 2.41
3119 3191 1.828595 TCCGCCATTTCAGCTACTACA 59.171 47.619 0.00 0.00 0.00 2.74
3120 3192 2.596904 TCCGCCATTTCAGCTACTAC 57.403 50.000 0.00 0.00 0.00 2.73
3121 3193 3.133901 TGAATCCGCCATTTCAGCTACTA 59.866 43.478 0.00 0.00 0.00 1.82
3122 3194 2.092968 TGAATCCGCCATTTCAGCTACT 60.093 45.455 0.00 0.00 0.00 2.57
3123 3195 2.032178 GTGAATCCGCCATTTCAGCTAC 59.968 50.000 0.00 0.00 32.79 3.58
3124 3196 2.288666 GTGAATCCGCCATTTCAGCTA 58.711 47.619 0.00 0.00 32.79 3.32
3125 3197 1.098050 GTGAATCCGCCATTTCAGCT 58.902 50.000 0.00 0.00 32.79 4.24
3126 3198 0.101219 GGTGAATCCGCCATTTCAGC 59.899 55.000 0.00 0.00 42.48 4.26
3127 3199 1.402968 CAGGTGAATCCGCCATTTCAG 59.597 52.381 0.00 0.00 45.32 3.02
3128 3200 1.462616 CAGGTGAATCCGCCATTTCA 58.537 50.000 0.00 0.00 45.32 2.69
3129 3201 0.101219 GCAGGTGAATCCGCCATTTC 59.899 55.000 0.00 0.00 45.32 2.17
3130 3202 0.323725 AGCAGGTGAATCCGCCATTT 60.324 50.000 0.00 0.00 45.32 2.32
3131 3203 0.546122 TAGCAGGTGAATCCGCCATT 59.454 50.000 0.00 0.00 45.32 3.16
3132 3204 0.179045 GTAGCAGGTGAATCCGCCAT 60.179 55.000 0.00 0.00 45.32 4.40
3133 3205 1.220749 GTAGCAGGTGAATCCGCCA 59.779 57.895 0.00 0.00 45.32 5.69
3134 3206 0.179045 ATGTAGCAGGTGAATCCGCC 60.179 55.000 0.00 0.00 43.25 6.13
3135 3207 1.668419 AATGTAGCAGGTGAATCCGC 58.332 50.000 0.00 0.00 41.99 5.54
3136 3208 4.816385 ACAATAATGTAGCAGGTGAATCCG 59.184 41.667 0.00 0.00 38.24 4.18
3149 3221 7.170828 CGCCATTTCAGCTACTACAATAATGTA 59.829 37.037 0.00 0.00 41.05 2.29
3150 3222 6.017934 CGCCATTTCAGCTACTACAATAATGT 60.018 38.462 0.00 0.00 43.74 2.71
3153 3225 4.814234 CCGCCATTTCAGCTACTACAATAA 59.186 41.667 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.