Multiple sequence alignment - TraesCS2B01G010700

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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 TraesCS2B01G010700 chr2B 100.000 3100 0 0 1 3100 5787189 5784090 0.000000e+00 5725
1 TraesCS2B01G010700 chr2B 93.944 1833 71 10 1070 2886 6120409 6122217 0.000000e+00 2734
2 TraesCS2B01G010700 chr2B 90.159 2134 115 22 774 2886 6022539 6024598 0.000000e+00 2689
3 TraesCS2B01G010700 chr2B 92.467 1208 53 21 774 1961 6004529 6005718 0.000000e+00 1692
4 TraesCS2B01G010700 chr2B 93.426 1080 58 10 2 1072 6119211 6120286 0.000000e+00 1589
5 TraesCS2B01G010700 chr2B 98.915 737 7 1 121 856 6003797 6004533 0.000000e+00 1315
6 TraesCS2B01G010700 chr2B 92.324 938 39 12 1982 2899 6005842 6006766 0.000000e+00 1303
7 TraesCS2B01G010700 chr2B 87.437 597 49 6 1548 2136 6065048 6065626 0.000000e+00 664
8 TraesCS2B01G010700 chr2B 89.796 392 18 9 466 856 6022173 6022543 1.670000e-132 483
9 TraesCS2B01G010700 chr2B 89.030 237 22 4 2866 3100 6122268 6122502 1.090000e-74 291
10 TraesCS2B01G010700 chr2B 96.667 150 4 1 549 697 6003652 6003801 6.640000e-62 248
11 TraesCS2B01G010700 chr2D 92.373 2255 112 25 661 2886 5425675 5423452 0.000000e+00 3157
12 TraesCS2B01G010700 chr2D 80.938 320 40 10 2025 2327 5401898 5401583 1.860000e-57 233
13 TraesCS2B01G010700 chr2D 86.111 108 12 3 1865 1969 5402013 5401906 2.530000e-21 113
14 TraesCS2B01G010700 chr2A 92.205 2091 117 20 825 2886 4047829 4045756 0.000000e+00 2916
15 TraesCS2B01G010700 chr2A 95.455 132 5 1 661 791 4047962 4047831 3.130000e-50 209
16 TraesCS2B01G010700 chr2A 89.109 101 8 3 87 185 456496638 456496737 4.200000e-24 122
17 TraesCS2B01G010700 chr4B 93.182 88 4 2 87 174 612271406 612271491 9.020000e-26 128
18 TraesCS2B01G010700 chr5A 92.135 89 7 0 87 175 390156987 390157075 3.250000e-25 126
19 TraesCS2B01G010700 chr1D 92.135 89 7 0 84 172 90207943 90208031 3.250000e-25 126
20 TraesCS2B01G010700 chr1D 80.420 143 22 5 309 449 469057571 469057433 1.520000e-18 104
21 TraesCS2B01G010700 chr7A 91.209 91 8 0 82 172 728022269 728022359 1.170000e-24 124
22 TraesCS2B01G010700 chr6D 90.426 94 8 1 83 175 59623171 59623264 4.200000e-24 122
23 TraesCS2B01G010700 chr4A 91.011 89 8 0 83 171 440964911 440964823 1.510000e-23 121


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 TraesCS2B01G010700 chr2B 5784090 5787189 3099 True 5725.0 5725 100.000000 1 3100 1 chr2B.!!$R1 3099
1 TraesCS2B01G010700 chr2B 6022173 6024598 2425 False 1586.0 2689 89.977500 466 2886 2 chr2B.!!$F3 2420
2 TraesCS2B01G010700 chr2B 6119211 6122502 3291 False 1538.0 2734 92.133333 2 3100 3 chr2B.!!$F4 3098
3 TraesCS2B01G010700 chr2B 6003652 6006766 3114 False 1139.5 1692 95.093250 121 2899 4 chr2B.!!$F2 2778
4 TraesCS2B01G010700 chr2B 6065048 6065626 578 False 664.0 664 87.437000 1548 2136 1 chr2B.!!$F1 588
5 TraesCS2B01G010700 chr2D 5423452 5425675 2223 True 3157.0 3157 92.373000 661 2886 1 chr2D.!!$R1 2225
6 TraesCS2B01G010700 chr2A 4045756 4047962 2206 True 1562.5 2916 93.830000 661 2886 2 chr2A.!!$R1 2225

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
860 963 0.584396 ACCATACGTTTGTGTGCGTG 59.416 50.0 5.27 0.0 41.68 5.34 F
997 1104 0.905357 TCTGAGGTTAGCTCCAAGCC 59.095 55.0 9.04 0.0 43.77 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1857 2107 2.238144 ACTGTGCCAGTCAGCATATTCT 59.762 45.455 2.38 0.0 41.21 2.40 R
2940 3423 0.873054 GAGAGATGAATGGCCATGCG 59.127 55.000 21.63 0.0 0.00 4.73 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
21 22 1.134965 AGAGACGCCACTATCAAGCAC 60.135 52.381 0.00 0.00 0.00 4.40
88 89 4.222886 CAGATCGACACGATGGAATCTAC 58.777 47.826 11.26 0.00 47.00 2.59
233 259 1.938577 CTTGATCGGTTGCATGAGGAG 59.061 52.381 0.00 0.00 0.00 3.69
541 567 9.630098 CACAGCTCAGATGTATTTTATTGTTTT 57.370 29.630 0.00 0.00 0.00 2.43
625 652 5.183140 GCAACTAAAGCACCCAGATAAAGAA 59.817 40.000 0.00 0.00 0.00 2.52
755 782 6.981762 ATCACTCTCTGCAAGACTAAAATG 57.018 37.500 0.00 0.00 38.67 2.32
832 935 2.972625 TGCCCTTCATTACGTCAGAAG 58.027 47.619 14.25 14.25 38.72 2.85
838 941 5.292101 CCCTTCATTACGTCAGAAGAACATC 59.708 44.000 19.90 0.00 40.85 3.06
860 963 0.584396 ACCATACGTTTGTGTGCGTG 59.416 50.000 5.27 0.00 41.68 5.34
923 1028 3.321968 AGGGAAATTTCCTTCTGCACAAC 59.678 43.478 31.23 14.15 46.72 3.32
981 1088 5.221422 ACCACCAACCAAAATAACACATCTG 60.221 40.000 0.00 0.00 0.00 2.90
985 1092 5.243730 CCAACCAAAATAACACATCTGAGGT 59.756 40.000 0.00 0.00 0.00 3.85
997 1104 0.905357 TCTGAGGTTAGCTCCAAGCC 59.095 55.000 9.04 0.00 43.77 4.35
1003 1110 1.340991 GGTTAGCTCCAAGCCCAATGA 60.341 52.381 0.00 0.00 43.77 2.57
1079 1311 3.064207 CAAGCTGCAACGTAGAAGGTAA 58.936 45.455 1.02 0.00 0.00 2.85
1273 1510 1.662629 CATGTCTTTTGCTCGAGCGAT 59.337 47.619 30.75 11.52 45.83 4.58
1811 2060 4.573900 ACAGACAAGGTGCAATCTTCTAG 58.426 43.478 0.00 0.00 0.00 2.43
1966 2337 9.097257 CTCATTTCAAACACCACATTACTTTTT 57.903 29.630 0.00 0.00 0.00 1.94
2080 2455 2.464782 AGGCACTGTCAGATCATCTCA 58.535 47.619 6.91 0.00 37.18 3.27
2086 2461 1.550072 TGTCAGATCATCTCAACGGCA 59.450 47.619 0.00 0.00 0.00 5.69
2506 2910 1.474077 CATTTGGTAGTGCTCTTGGGC 59.526 52.381 0.00 0.00 0.00 5.36
2662 3066 5.766590 TCATCCAGGATACACTCAAGACTA 58.233 41.667 0.00 0.00 41.41 2.59
2671 3075 6.752815 GGATACACTCAAGACTACAAGCTAAC 59.247 42.308 0.00 0.00 0.00 2.34
2736 3148 7.835634 AGATTAGTCTTTTACAGCTGTTAGC 57.164 36.000 27.06 14.71 42.84 3.09
2737 3149 6.819146 AGATTAGTCTTTTACAGCTGTTAGCC 59.181 38.462 27.06 10.23 43.77 3.93
2738 3150 3.326747 AGTCTTTTACAGCTGTTAGCCG 58.673 45.455 27.06 10.32 43.77 5.52
2739 3151 3.064931 GTCTTTTACAGCTGTTAGCCGT 58.935 45.455 27.06 0.00 43.77 5.68
2740 3152 4.021719 AGTCTTTTACAGCTGTTAGCCGTA 60.022 41.667 27.06 0.99 43.77 4.02
2741 3153 4.326548 GTCTTTTACAGCTGTTAGCCGTAG 59.673 45.833 27.06 12.55 43.77 3.51
2906 3389 7.730084 AGTATATGCAATGACATACTCAGTGT 58.270 34.615 0.00 0.00 45.16 3.55
2940 3423 1.135333 GTCGGTCAATCCTCTCACCTC 59.865 57.143 0.00 0.00 0.00 3.85
2994 3478 4.626042 CGTGATGTTGAAATTTTGGGGAA 58.374 39.130 0.00 0.00 0.00 3.97
3001 3485 4.540359 TGAAATTTTGGGGAAGATGCAG 57.460 40.909 0.00 0.00 0.00 4.41
3012 3496 3.618351 GGAAGATGCAGATATCATGGGG 58.382 50.000 5.32 0.00 0.00 4.96
3025 3509 1.000896 ATGGGGAAAGCGGGTTCAG 60.001 57.895 0.00 0.00 0.00 3.02
3034 3518 0.325296 AGCGGGTTCAGGATAGACCA 60.325 55.000 0.00 0.00 42.04 4.02
3036 3520 0.464452 CGGGTTCAGGATAGACCACC 59.536 60.000 0.00 0.00 42.04 4.61
3038 3522 1.580059 GGTTCAGGATAGACCACCCA 58.420 55.000 0.00 0.00 42.04 4.51
3043 3527 3.256704 TCAGGATAGACCACCCAAAACT 58.743 45.455 0.00 0.00 42.04 2.66
3048 3532 4.948004 GGATAGACCACCCAAAACTTTAGG 59.052 45.833 0.00 0.00 38.79 2.69
3082 3566 8.797266 AATAGGTTCATTCGTGTTTCTTTTTC 57.203 30.769 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 2.429610 AGCTTGCTTGGCAGATTTATGG 59.570 45.455 0.00 0.00 40.61 2.74
35 36 3.119245 ACAGCTTGCTTGGCAGATTTATG 60.119 43.478 0.00 0.00 40.61 1.90
36 37 3.094572 ACAGCTTGCTTGGCAGATTTAT 58.905 40.909 0.00 0.00 40.61 1.40
88 89 1.966845 ATATTATGGGACGGAGGGGG 58.033 55.000 0.00 0.00 0.00 5.40
233 259 3.757248 CTACCGGTGGGCATGGAGC 62.757 68.421 19.93 0.00 44.65 4.70
541 567 2.987149 CACGAGCGCTAGAAAAGAAAGA 59.013 45.455 24.88 0.00 0.00 2.52
625 652 1.445066 CTCGCGAGCACACATGAGT 60.445 57.895 25.07 0.00 0.00 3.41
832 935 6.304126 CACACAAACGTATGGTTAGATGTTC 58.696 40.000 0.00 0.00 38.08 3.18
838 941 2.477375 ACGCACACAAACGTATGGTTAG 59.523 45.455 0.00 0.00 41.48 2.34
923 1028 2.011222 TGGAAGGCTTTTTATACGCGG 58.989 47.619 12.47 0.00 0.00 6.46
981 1088 0.328258 TTGGGCTTGGAGCTAACCTC 59.672 55.000 0.00 0.00 41.99 3.85
985 1092 1.678728 CGTCATTGGGCTTGGAGCTAA 60.679 52.381 0.00 0.00 41.99 3.09
997 1104 1.872952 TGCAAAGTGAGTCGTCATTGG 59.127 47.619 0.00 0.00 34.36 3.16
1003 1110 1.341531 AGCTACTGCAAAGTGAGTCGT 59.658 47.619 0.00 0.00 42.74 4.34
1079 1311 1.768870 GACCATGGGCATGTACCTACT 59.231 52.381 14.59 0.00 37.11 2.57
1758 2000 6.071503 TGGTTTCACATACAATGATGCAATGA 60.072 34.615 0.00 0.00 31.19 2.57
1777 2026 4.023193 CACCTTGTCTGTATTGGTGGTTTC 60.023 45.833 0.00 0.00 43.01 2.78
1857 2107 2.238144 ACTGTGCCAGTCAGCATATTCT 59.762 45.455 2.38 0.00 41.21 2.40
1967 2338 9.768662 GACCGGGAATAAATAGAAACATTAGTA 57.231 33.333 6.32 0.00 0.00 1.82
1977 2348 5.943349 TCAACTGACCGGGAATAAATAGA 57.057 39.130 6.32 0.00 0.00 1.98
2080 2455 3.895656 TGCTTATATACCTCTCTGCCGTT 59.104 43.478 0.00 0.00 0.00 4.44
2204 2594 7.776933 ACAGTAGTGTCTACATGCAAATATG 57.223 36.000 0.00 0.00 26.76 1.78
2206 2596 7.832769 TGTACAGTAGTGTCTACATGCAAATA 58.167 34.615 6.44 0.00 38.19 1.40
2271 2663 8.245195 TGCTTTATGTATCACCTAGTACATGA 57.755 34.615 11.92 3.72 40.63 3.07
2519 2923 4.742438 TCAAAGGTGTAGATCGCAAAAC 57.258 40.909 0.00 0.00 0.00 2.43
2600 3004 5.045872 GGATGCCAAGTGAGCAATTATTTC 58.954 41.667 0.00 0.00 44.83 2.17
2634 3038 5.955961 TGAGTGTATCCTGGATGATGAAA 57.044 39.130 19.42 0.00 0.00 2.69
2662 3066 6.567602 ATTTCTAGATCCTGGTTAGCTTGT 57.432 37.500 0.00 0.00 0.00 3.16
2671 3075 6.939163 CCAGTTCCATTATTTCTAGATCCTGG 59.061 42.308 0.00 0.00 0.00 4.45
2736 3148 3.329929 AAACTTTAGCTGTCCCTACGG 57.670 47.619 0.00 0.00 34.87 4.02
2737 3149 6.916932 GTCTATAAACTTTAGCTGTCCCTACG 59.083 42.308 0.00 0.00 0.00 3.51
2738 3150 7.069702 AGGTCTATAAACTTTAGCTGTCCCTAC 59.930 40.741 0.00 0.00 0.00 3.18
2739 3151 7.130775 AGGTCTATAAACTTTAGCTGTCCCTA 58.869 38.462 0.00 0.00 0.00 3.53
2740 3152 5.965091 AGGTCTATAAACTTTAGCTGTCCCT 59.035 40.000 0.00 0.00 0.00 4.20
2741 3153 6.236558 AGGTCTATAAACTTTAGCTGTCCC 57.763 41.667 0.00 0.00 0.00 4.46
2742 3154 9.833917 AATTAGGTCTATAAACTTTAGCTGTCC 57.166 33.333 0.00 0.00 0.00 4.02
2920 3403 1.135333 GAGGTGAGAGGATTGACCGAC 59.865 57.143 0.00 0.00 44.74 4.79
2926 3409 1.579698 CATGCGAGGTGAGAGGATTG 58.420 55.000 0.00 0.00 0.00 2.67
2940 3423 0.873054 GAGAGATGAATGGCCATGCG 59.127 55.000 21.63 0.00 0.00 4.73
2994 3478 4.810033 GCTTTCCCCATGATATCTGCATCT 60.810 45.833 3.98 0.00 0.00 2.90
3001 3485 1.073923 ACCCGCTTTCCCCATGATATC 59.926 52.381 0.00 0.00 0.00 1.63
3012 3496 2.552031 GTCTATCCTGAACCCGCTTTC 58.448 52.381 0.00 0.00 0.00 2.62
3025 3509 4.948004 CCTAAAGTTTTGGGTGGTCTATCC 59.052 45.833 8.09 0.00 34.45 2.59
3069 3553 9.118236 GAGAAATTGATAGGAAAAAGAAACACG 57.882 33.333 0.00 0.00 0.00 4.49


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

AutoCloner maintained by Alex Coulton.