Multiple sequence alignment - TraesCS6B01G146700

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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 TraesCS6B01G146700 chr6B 100.000 3888 0 0 1 3888 147581352 147585239 0.000000e+00 7180
1 TraesCS6B01G146700 chr6B 100.000 58 0 0 2890 2947 147584186 147584243 1.480000e-19 108
2 TraesCS6B01G146700 chr6B 100.000 58 0 0 2835 2892 147584241 147584298 1.480000e-19 108
3 TraesCS6B01G146700 chr6A 97.608 2634 57 4 263 2892 89592074 89594705 0.000000e+00 4510
4 TraesCS6B01G146700 chr6A 96.318 679 16 4 3215 3888 89595038 89595712 0.000000e+00 1107
5 TraesCS6B01G146700 chr6A 96.040 303 12 0 2890 3192 89594648 89594950 9.700000e-136 494
6 TraesCS6B01G146700 chr6A 97.368 266 7 0 1 266 89591553 89591818 1.650000e-123 453
7 TraesCS6B01G146700 chr6D 97.243 2539 48 8 373 2892 73067830 73070365 0.000000e+00 4281
8 TraesCS6B01G146700 chr6D 97.798 999 19 1 2890 3888 73070308 73071303 0.000000e+00 1720
9 TraesCS6B01G146700 chr6D 96.541 318 11 0 1 318 73067513 73067830 9.570000e-146 527
10 TraesCS6B01G146700 chr6D 80.430 419 72 9 1037 1448 192631095 192630680 1.050000e-80 311
11 TraesCS6B01G146700 chr1B 82.069 435 73 4 1080 1510 511483908 511484341 2.210000e-97 366
12 TraesCS6B01G146700 chr7D 85.276 163 21 3 1435 1596 370399865 370399705 8.640000e-37 165


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 TraesCS6B01G146700 chr6B 147581352 147585239 3887 False 2465.333333 7180 100.0000 1 3888 3 chr6B.!!$F1 3887
1 TraesCS6B01G146700 chr6A 89591553 89595712 4159 False 1641.000000 4510 96.8335 1 3888 4 chr6A.!!$F1 3887
2 TraesCS6B01G146700 chr6D 73067513 73071303 3790 False 2176.000000 4281 97.1940 1 3888 3 chr6D.!!$F1 3887

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
63 64 1.808411 TTGACCTTTCACATCGCCTC 58.192 50.0 0.0 0.0 0.0 4.70 F
1792 2061 1.299541 AACTTGCAACCACTGTCGAG 58.700 50.0 0.0 0.0 0.0 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1833 2102 2.810852 GACTGAAGGCTTTCCACTTCTG 59.189 50.0 6.06 5.03 42.67 3.02 R
3586 3936 0.179084 CATCGGTACCTTCGGTGCAT 60.179 55.0 10.90 0.00 40.07 3.96 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
22 23 4.811908 GAAGGAGTTGAACTCTACCAGTC 58.188 47.826 23.06 6.37 44.46 3.51
63 64 1.808411 TTGACCTTTCACATCGCCTC 58.192 50.000 0.00 0.00 0.00 4.70
173 174 8.736097 AATATGGTGGACATACCTATCACTTA 57.264 34.615 0.00 0.00 44.41 2.24
235 236 2.770164 AGGCTACCAATGTGTCAGTC 57.230 50.000 0.00 0.00 0.00 3.51
336 596 2.226330 TGCACTTACCGCAGAAATGTT 58.774 42.857 0.00 0.00 33.55 2.71
550 810 8.746052 AGGATATTTCCATGTAAAACGAATCA 57.254 30.769 4.92 0.00 45.30 2.57
706 975 7.286087 TGCAGAATACTCATATTCCAAATGCTT 59.714 33.333 14.72 0.00 45.49 3.91
900 1169 3.304928 CCAACTTGCAGAACAGATTCACC 60.305 47.826 0.00 0.00 37.29 4.02
951 1220 8.370493 TGAGAGAAAACATTCTTGAACTACAG 57.630 34.615 0.00 0.00 0.00 2.74
1091 1360 3.197983 GGTACTGGGAGCTATTCTGTTGT 59.802 47.826 0.00 0.00 0.00 3.32
1308 1577 3.249559 GGGAAGCTGAATCTTATGCGAAG 59.750 47.826 0.00 0.00 0.00 3.79
1329 1598 2.604132 GCAGCTTTCTGTTGAGCTTGAC 60.604 50.000 0.00 0.00 46.55 3.18
1359 1628 6.403866 AGAATGCAAGTACACAATTTGGAA 57.596 33.333 0.78 0.00 0.00 3.53
1464 1733 5.012239 AGTGAGCAGCATGGAAGAATAAAA 58.988 37.500 0.00 0.00 35.86 1.52
1510 1779 4.851639 AAAGACCAAGGTGAGCTGATAT 57.148 40.909 0.00 0.00 0.00 1.63
1522 1791 6.317391 AGGTGAGCTGATATAACTTTCTTTGC 59.683 38.462 0.00 0.00 0.00 3.68
1792 2061 1.299541 AACTTGCAACCACTGTCGAG 58.700 50.000 0.00 0.00 0.00 4.04
1833 2102 3.563390 AGCTTGTCTGAAAGTCTTCTTGC 59.437 43.478 0.00 0.00 33.79 4.01
1925 2194 8.596781 AGTCACAAGGAGTACTAATGAACTAT 57.403 34.615 0.00 0.00 0.00 2.12
2352 2622 8.935844 TGTTTTGTATGCAATTTAACACAAACA 58.064 25.926 7.83 4.88 36.07 2.83
2405 2684 6.105657 TGTTTATTCATAGTCACGTGCATG 57.894 37.500 11.67 13.62 0.00 4.06
2446 2725 1.237285 ACAAAGTAAGCCCAGCTGCG 61.237 55.000 8.66 0.00 39.62 5.18
2473 2752 2.202932 CAGATTCGAGGGGCACGG 60.203 66.667 0.00 0.00 0.00 4.94
2491 2770 1.666700 CGGAAAGTCAACAACGACCAA 59.333 47.619 0.00 0.00 36.52 3.67
2884 3165 6.715344 CATGCATTGCTTGTGAGTTTTATT 57.285 33.333 14.59 0.00 0.00 1.40
2885 3166 7.124347 CATGCATTGCTTGTGAGTTTTATTT 57.876 32.000 14.59 0.00 0.00 1.40
2886 3167 6.528014 TGCATTGCTTGTGAGTTTTATTTG 57.472 33.333 10.49 0.00 0.00 2.32
2887 3168 6.279123 TGCATTGCTTGTGAGTTTTATTTGA 58.721 32.000 10.49 0.00 0.00 2.69
2888 3169 6.760298 TGCATTGCTTGTGAGTTTTATTTGAA 59.240 30.769 10.49 0.00 0.00 2.69
2889 3170 7.042590 TGCATTGCTTGTGAGTTTTATTTGAAG 60.043 33.333 10.49 0.00 0.00 3.02
2890 3171 7.569957 GCATTGCTTGTGAGTTTTATTTGAAGG 60.570 37.037 0.16 0.00 0.00 3.46
2891 3172 6.463995 TGCTTGTGAGTTTTATTTGAAGGT 57.536 33.333 0.00 0.00 0.00 3.50
2892 3173 6.272318 TGCTTGTGAGTTTTATTTGAAGGTG 58.728 36.000 0.00 0.00 0.00 4.00
2893 3174 6.127479 TGCTTGTGAGTTTTATTTGAAGGTGT 60.127 34.615 0.00 0.00 0.00 4.16
2894 3175 6.417930 GCTTGTGAGTTTTATTTGAAGGTGTC 59.582 38.462 0.00 0.00 0.00 3.67
2895 3176 7.639113 TTGTGAGTTTTATTTGAAGGTGTCT 57.361 32.000 0.00 0.00 0.00 3.41
2896 3177 7.639113 TGTGAGTTTTATTTGAAGGTGTCTT 57.361 32.000 0.00 0.00 35.62 3.01
2897 3178 7.479980 TGTGAGTTTTATTTGAAGGTGTCTTG 58.520 34.615 0.00 0.00 32.52 3.02
2898 3179 7.338196 TGTGAGTTTTATTTGAAGGTGTCTTGA 59.662 33.333 0.00 0.00 32.52 3.02
2899 3180 8.352942 GTGAGTTTTATTTGAAGGTGTCTTGAT 58.647 33.333 0.00 0.00 32.52 2.57
2900 3181 9.567776 TGAGTTTTATTTGAAGGTGTCTTGATA 57.432 29.630 0.00 0.00 32.52 2.15
2906 3187 9.613428 TTATTTGAAGGTGTCTTGATATACTGG 57.387 33.333 0.00 0.00 32.52 4.00
2907 3188 6.867519 TTGAAGGTGTCTTGATATACTGGA 57.132 37.500 0.00 0.00 32.52 3.86
2908 3189 7.437713 TTGAAGGTGTCTTGATATACTGGAT 57.562 36.000 0.00 0.00 32.52 3.41
2909 3190 8.547481 TTGAAGGTGTCTTGATATACTGGATA 57.453 34.615 0.00 0.00 32.52 2.59
2910 3191 8.183104 TGAAGGTGTCTTGATATACTGGATAG 57.817 38.462 0.00 0.00 32.52 2.08
2911 3192 6.597832 AGGTGTCTTGATATACTGGATAGC 57.402 41.667 0.00 0.00 0.00 2.97
2912 3193 6.077993 AGGTGTCTTGATATACTGGATAGCA 58.922 40.000 0.00 0.00 34.59 3.49
2913 3194 6.728164 AGGTGTCTTGATATACTGGATAGCAT 59.272 38.462 0.00 0.00 36.34 3.79
2914 3195 7.236432 AGGTGTCTTGATATACTGGATAGCATT 59.764 37.037 0.00 0.00 36.34 3.56
2915 3196 7.332926 GGTGTCTTGATATACTGGATAGCATTG 59.667 40.741 0.00 0.00 36.34 2.82
2916 3197 6.875726 TGTCTTGATATACTGGATAGCATTGC 59.124 38.462 0.00 0.00 36.34 3.56
2917 3198 6.875726 GTCTTGATATACTGGATAGCATTGCA 59.124 38.462 11.91 0.00 36.34 4.08
2918 3199 7.551974 GTCTTGATATACTGGATAGCATTGCAT 59.448 37.037 11.91 2.41 36.34 3.96
2919 3200 7.551617 TCTTGATATACTGGATAGCATTGCATG 59.448 37.037 11.91 0.00 36.34 4.06
3068 3349 1.025812 CCTTGGTTAAACGTGGTGCA 58.974 50.000 0.00 0.00 0.00 4.57
3195 3476 9.733556 TTGAGTTGTGTTCACCTTATGTATTAT 57.266 29.630 0.37 0.00 0.00 1.28
3498 3848 8.357402 GTTTGTTACTGAATACCTGAACCAAAT 58.643 33.333 0.00 0.00 0.00 2.32
3595 3945 0.888736 CCCAAGACACATGCACCGAA 60.889 55.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.490115 AGCAGACCTCTCTTAGTTGACG 59.510 50.000 0.00 0.00 0.00 4.35
63 64 3.613952 TTTGCTGAATGCGCTGGCG 62.614 57.895 9.73 10.80 46.63 5.69
173 174 6.260700 TGCTACTGGTTAACATCCCATTAT 57.739 37.500 8.10 0.00 0.00 1.28
186 187 2.787473 TGCTGCTTATGCTACTGGTT 57.213 45.000 0.00 0.00 40.48 3.67
269 529 6.147581 CACAACATCAGTCCAATCTTTTCTG 58.852 40.000 0.00 0.00 0.00 3.02
538 798 5.856126 TGGTCATCTGTGATTCGTTTTAC 57.144 39.130 0.00 0.00 36.60 2.01
670 930 3.255642 TGAGTATTCTGCAAAGGCCAAAC 59.744 43.478 5.01 0.00 40.13 2.93
706 975 0.034198 TTCACCGTGAATTCCAGCGA 59.966 50.000 9.99 0.00 30.26 4.93
900 1169 5.414454 TGATTCCAACTCGTTATTTTGGGAG 59.586 40.000 0.00 0.00 40.31 4.30
951 1220 6.279513 TCTTCCTTCTCTTTGATCTCTGAC 57.720 41.667 0.00 0.00 0.00 3.51
1024 1293 7.015682 TCCTTCAATCTCAGAAACTGAACTAGT 59.984 37.037 0.00 0.00 40.18 2.57
1091 1360 9.970395 GATCATATGAAAATAAATGGTTCTGCA 57.030 29.630 9.99 0.00 0.00 4.41
1359 1628 6.882610 TTAAGCAACATCTCAACATGTTCT 57.117 33.333 8.48 0.00 43.75 3.01
1464 1733 3.323115 TGCTCAGTTCATCAGTCAACTCT 59.677 43.478 0.00 0.00 30.06 3.24
1510 1779 9.097257 CAAAGAAATTTCAGGCAAAGAAAGTTA 57.903 29.630 19.99 0.00 41.54 2.24
1522 1791 5.464389 CAGAAGCAACCAAAGAAATTTCAGG 59.536 40.000 19.99 18.63 0.00 3.86
1591 1860 6.208402 ACACCACAACATATAACAAATGCAGA 59.792 34.615 0.00 0.00 0.00 4.26
1611 1880 6.013725 ACCTTCAATCTCTGTACAATACACCA 60.014 38.462 0.00 0.00 34.46 4.17
1792 2061 3.433615 AGCTATGCAACTCGTCAAACTTC 59.566 43.478 0.00 0.00 0.00 3.01
1833 2102 2.810852 GACTGAAGGCTTTCCACTTCTG 59.189 50.000 6.06 5.03 42.67 3.02
1925 2194 5.181245 GCTTGTTGCTATCTTCAGTGGTTAA 59.819 40.000 0.00 0.00 38.95 2.01
2113 2382 3.130264 TTGCACAGCAACCCTCAAT 57.870 47.368 0.00 0.00 43.99 2.57
2399 2678 5.177881 TCTGCATTCAAATTGAAACATGCAC 59.822 36.000 23.48 5.40 41.87 4.57
2405 2684 7.410800 TGTCATTCTGCATTCAAATTGAAAC 57.589 32.000 12.75 8.59 40.12 2.78
2446 2725 2.611518 CCTCGAATCTGAGTGACAACC 58.388 52.381 0.00 0.00 34.04 3.77
2473 2752 4.095610 CAACTTGGTCGTTGTTGACTTTC 58.904 43.478 0.00 0.00 42.35 2.62
2491 2770 5.757320 GTGCATCTCTACATCAATAGCAACT 59.243 40.000 0.00 0.00 0.00 3.16
2500 2779 3.515104 TGTCCTTGTGCATCTCTACATCA 59.485 43.478 0.00 0.00 0.00 3.07
2866 3147 7.439056 CACCTTCAAATAAAACTCACAAGCAAT 59.561 33.333 0.00 0.00 0.00 3.56
2867 3148 6.756074 CACCTTCAAATAAAACTCACAAGCAA 59.244 34.615 0.00 0.00 0.00 3.91
2868 3149 6.127479 ACACCTTCAAATAAAACTCACAAGCA 60.127 34.615 0.00 0.00 0.00 3.91
2869 3150 6.273071 ACACCTTCAAATAAAACTCACAAGC 58.727 36.000 0.00 0.00 0.00 4.01
2870 3151 7.707104 AGACACCTTCAAATAAAACTCACAAG 58.293 34.615 0.00 0.00 0.00 3.16
2871 3152 7.639113 AGACACCTTCAAATAAAACTCACAA 57.361 32.000 0.00 0.00 0.00 3.33
2872 3153 7.338196 TCAAGACACCTTCAAATAAAACTCACA 59.662 33.333 0.00 0.00 0.00 3.58
2873 3154 7.703328 TCAAGACACCTTCAAATAAAACTCAC 58.297 34.615 0.00 0.00 0.00 3.51
2874 3155 7.873719 TCAAGACACCTTCAAATAAAACTCA 57.126 32.000 0.00 0.00 0.00 3.41
2880 3161 9.613428 CCAGTATATCAAGACACCTTCAAATAA 57.387 33.333 0.00 0.00 0.00 1.40
2881 3162 8.988060 TCCAGTATATCAAGACACCTTCAAATA 58.012 33.333 0.00 0.00 0.00 1.40
2882 3163 7.861629 TCCAGTATATCAAGACACCTTCAAAT 58.138 34.615 0.00 0.00 0.00 2.32
2883 3164 7.252612 TCCAGTATATCAAGACACCTTCAAA 57.747 36.000 0.00 0.00 0.00 2.69
2884 3165 6.867519 TCCAGTATATCAAGACACCTTCAA 57.132 37.500 0.00 0.00 0.00 2.69
2885 3166 7.255977 GCTATCCAGTATATCAAGACACCTTCA 60.256 40.741 0.00 0.00 0.00 3.02
2886 3167 7.093992 GCTATCCAGTATATCAAGACACCTTC 58.906 42.308 0.00 0.00 0.00 3.46
2887 3168 6.554982 TGCTATCCAGTATATCAAGACACCTT 59.445 38.462 0.00 0.00 0.00 3.50
2888 3169 6.077993 TGCTATCCAGTATATCAAGACACCT 58.922 40.000 0.00 0.00 0.00 4.00
2889 3170 6.346477 TGCTATCCAGTATATCAAGACACC 57.654 41.667 0.00 0.00 0.00 4.16
2890 3171 7.148507 GCAATGCTATCCAGTATATCAAGACAC 60.149 40.741 0.00 0.00 0.00 3.67
2891 3172 6.875726 GCAATGCTATCCAGTATATCAAGACA 59.124 38.462 0.00 0.00 0.00 3.41
2892 3173 6.875726 TGCAATGCTATCCAGTATATCAAGAC 59.124 38.462 6.82 0.00 0.00 3.01
2893 3174 7.008021 TGCAATGCTATCCAGTATATCAAGA 57.992 36.000 6.82 0.00 0.00 3.02
2894 3175 7.694886 CATGCAATGCTATCCAGTATATCAAG 58.305 38.462 6.82 0.00 37.62 3.02
2895 3176 7.619964 CATGCAATGCTATCCAGTATATCAA 57.380 36.000 6.82 0.00 37.62 2.57
2916 3197 6.715344 AATAAAACTCACAAGCAATGCATG 57.285 33.333 8.35 8.72 33.24 4.06
2917 3198 6.930164 TCAAATAAAACTCACAAGCAATGCAT 59.070 30.769 8.35 0.00 0.00 3.96
2918 3199 6.279123 TCAAATAAAACTCACAAGCAATGCA 58.721 32.000 8.35 0.00 0.00 3.96
2919 3200 6.768029 TCAAATAAAACTCACAAGCAATGC 57.232 33.333 0.00 0.00 0.00 3.56
2920 3201 7.439056 ACCTTCAAATAAAACTCACAAGCAATG 59.561 33.333 0.00 0.00 0.00 2.82
2964 3245 4.577283 TGAAGCTTACTAAAACGGTTGCTT 59.423 37.500 5.95 5.95 37.67 3.91
3002 3283 6.261381 AGGCTATAACAGTTCAAACGTGAAAA 59.739 34.615 0.00 0.00 45.29 2.29
3008 3289 4.403453 GCAAGGCTATAACAGTTCAAACG 58.597 43.478 0.00 0.00 0.00 3.60
3195 3476 1.647545 GCATGCCGCTCAACAGCTTA 61.648 55.000 6.36 0.00 44.40 3.09
3498 3848 4.699735 ACAAAAATGATACGCAGATGACCA 59.300 37.500 0.00 0.00 0.00 4.02
3586 3936 0.179084 CATCGGTACCTTCGGTGCAT 60.179 55.000 10.90 0.00 40.07 3.96
3595 3945 3.306780 CCAGTTCTGTTTCATCGGTACCT 60.307 47.826 10.90 0.00 0.00 3.08
3638 3988 4.101741 AGACTATGTACAGGGGATCTTTGC 59.898 45.833 0.33 0.00 0.00 3.68
3639 3989 5.363868 TGAGACTATGTACAGGGGATCTTTG 59.636 44.000 0.33 0.00 0.00 2.77
3640 3990 5.529289 TGAGACTATGTACAGGGGATCTTT 58.471 41.667 0.33 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.