Multiple sequence alignment - TraesCS2D01G414300

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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 TraesCS2D01G414300 chr2D 100.000 3431 0 0 1 3431 528474875 528471445 0.000000e+00 6336.0
1 TraesCS2D01G414300 chr2D 87.072 1052 111 13 1104 2153 528590054 528589026 0.000000e+00 1166.0
2 TraesCS2D01G414300 chr2D 80.876 251 18 19 512 746 528590706 528590470 1.640000e-38 171.0
3 TraesCS2D01G414300 chr2D 90.141 71 5 2 834 904 528590313 528590245 1.310000e-14 91.6
4 TraesCS2D01G414300 chr2B 93.283 2933 119 39 545 3431 626652482 626649582 0.000000e+00 4253.0
5 TraesCS2D01G414300 chr2B 86.502 1052 114 15 1104 2153 626884289 626883264 0.000000e+00 1131.0
6 TraesCS2D01G414300 chr2B 87.619 525 38 12 1 521 626653092 626652591 4.930000e-163 584.0
7 TraesCS2D01G414300 chr2A 94.384 2101 83 14 302 2382 673196932 673194847 0.000000e+00 3193.0
8 TraesCS2D01G414300 chr2A 86.977 1052 112 13 1104 2153 673277486 673276458 0.000000e+00 1160.0
9 TraesCS2D01G414300 chr2A 91.916 334 10 7 2744 3073 673194487 673194167 5.220000e-123 451.0
10 TraesCS2D01G414300 chr2A 87.356 261 10 3 3172 3431 673193768 673193530 9.380000e-71 278.0
11 TraesCS2D01G414300 chr2A 88.426 216 15 3 4 215 673197160 673196951 5.680000e-63 252.0
12 TraesCS2D01G414300 chr2A 79.592 245 29 16 512 741 673278161 673277923 4.580000e-34 156.0
13 TraesCS2D01G414300 chr3D 79.747 158 29 3 1566 1723 330062839 330062685 1.010000e-20 111.0
14 TraesCS2D01G414300 chr3B 79.268 164 31 3 1566 1729 427590210 427590050 1.010000e-20 111.0
15 TraesCS2D01G414300 chr7D 82.292 96 11 4 1575 1667 16635709 16635617 1.020000e-10 78.7


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 TraesCS2D01G414300 chr2D 528471445 528474875 3430 True 6336.0 6336 100.000000 1 3431 1 chr2D.!!$R1 3430
1 TraesCS2D01G414300 chr2D 528589026 528590706 1680 True 476.2 1166 86.029667 512 2153 3 chr2D.!!$R2 1641
2 TraesCS2D01G414300 chr2B 626649582 626653092 3510 True 2418.5 4253 90.451000 1 3431 2 chr2B.!!$R2 3430
3 TraesCS2D01G414300 chr2B 626883264 626884289 1025 True 1131.0 1131 86.502000 1104 2153 1 chr2B.!!$R1 1049
4 TraesCS2D01G414300 chr2A 673193530 673197160 3630 True 1043.5 3193 90.520500 4 3431 4 chr2A.!!$R1 3427
5 TraesCS2D01G414300 chr2A 673276458 673278161 1703 True 658.0 1160 83.284500 512 2153 2 chr2A.!!$R2 1641

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
188 194 0.032952 TTTAACGCCACAGACGAGCT 59.967 50.0 0.00 0.00 0.0 4.09 F
189 195 0.032952 TTAACGCCACAGACGAGCTT 59.967 50.0 0.00 0.00 0.0 3.74 F
1124 1417 0.323629 TGGATTTCGCCGGAGAAGTT 59.676 50.0 20.19 12.35 0.0 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2138 2437 1.131126 CACAGCAATTAACCGCCTCTG 59.869 52.381 0.00 0.00 0.00 3.35 R
2162 2464 4.484912 TGTTTATTGGTTAACCCCAGCTT 58.515 39.130 21.97 3.18 35.49 3.74 R
2514 2856 0.102300 GCCACTTTCCGTTTTGCTGT 59.898 50.000 0.00 0.00 0.00 4.40 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
108 110 3.970610 CGTTCATCAAGCAACTGTGAAAG 59.029 43.478 0.00 0.00 31.38 2.62
129 131 2.286891 GGACGTATCAGGTAGAACGAGC 60.287 54.545 0.23 0.00 35.86 5.03
163 169 4.155709 CTCTAATGGCATGGAGGACTAGA 58.844 47.826 17.63 11.04 0.00 2.43
188 194 0.032952 TTTAACGCCACAGACGAGCT 59.967 50.000 0.00 0.00 0.00 4.09
189 195 0.032952 TTAACGCCACAGACGAGCTT 59.967 50.000 0.00 0.00 0.00 3.74
190 196 0.666274 TAACGCCACAGACGAGCTTG 60.666 55.000 0.00 0.00 0.00 4.01
191 197 2.356313 CGCCACAGACGAGCTTGT 60.356 61.111 6.22 6.22 0.00 3.16
192 198 1.080772 CGCCACAGACGAGCTTGTA 60.081 57.895 6.58 0.00 0.00 2.41
193 199 1.073216 CGCCACAGACGAGCTTGTAG 61.073 60.000 6.58 5.52 0.00 2.74
253 259 2.668250 CATTGATATGCATGGCAACGG 58.332 47.619 10.16 6.06 43.62 4.44
258 264 0.534877 TATGCATGGCAACGGGCTAG 60.535 55.000 10.16 0.00 43.62 3.42
259 265 2.438434 GCATGGCAACGGGCTAGT 60.438 61.111 0.00 0.00 44.01 2.57
260 266 2.046285 GCATGGCAACGGGCTAGTT 61.046 57.895 0.00 0.00 44.01 2.24
269 275 3.057104 GCAACGGGCTAGTTTAATTTGGT 60.057 43.478 0.00 0.00 40.25 3.67
289 295 1.462616 TCGCCAATTTGTGCTATGCT 58.537 45.000 7.82 0.00 0.00 3.79
295 301 0.819582 ATTTGTGCTATGCTGGTGCC 59.180 50.000 0.00 0.00 38.71 5.01
296 302 0.539207 TTTGTGCTATGCTGGTGCCA 60.539 50.000 0.00 0.00 38.71 4.92
297 303 0.323633 TTGTGCTATGCTGGTGCCAT 60.324 50.000 0.00 0.00 38.71 4.40
298 304 1.033202 TGTGCTATGCTGGTGCCATG 61.033 55.000 0.00 0.00 38.71 3.66
300 306 1.826921 GCTATGCTGGTGCCATGCT 60.827 57.895 11.72 3.69 38.71 3.79
440 446 4.326278 TCGATCGCTAGTTGTGAACAATTC 59.674 41.667 11.09 0.00 38.81 2.17
528 550 8.076781 ACACTGCGTAGTATAAGAATGATACTG 58.923 37.037 5.64 0.00 42.79 2.74
809 1020 2.860009 CACGATCCCTGGCTAGTACTA 58.140 52.381 1.89 1.89 0.00 1.82
812 1023 2.814919 CGATCCCTGGCTAGTACTACTG 59.185 54.545 0.00 0.00 0.00 2.74
813 1024 2.068834 TCCCTGGCTAGTACTACTGC 57.931 55.000 0.00 1.91 0.00 4.40
814 1025 1.569548 TCCCTGGCTAGTACTACTGCT 59.430 52.381 12.39 0.00 0.00 4.24
815 1026 1.957877 CCCTGGCTAGTACTACTGCTC 59.042 57.143 12.39 5.36 0.00 4.26
890 1106 1.987368 ACGACCCCTAAGCCCTAAAAA 59.013 47.619 0.00 0.00 0.00 1.94
1124 1417 0.323629 TGGATTTCGCCGGAGAAGTT 59.676 50.000 20.19 12.35 0.00 2.66
1204 1497 2.237751 CGACGGCGAACCATGATCC 61.238 63.158 16.62 0.00 40.82 3.36
1398 1697 2.203640 ACGTCCCTGAGGCTGTGA 60.204 61.111 0.00 0.00 0.00 3.58
1452 1751 4.767255 GCCAGCCGTCTCCTGTGG 62.767 72.222 0.00 0.00 0.00 4.17
1457 1756 4.007644 CCGTCTCCTGTGGCTGCA 62.008 66.667 0.50 0.00 0.00 4.41
1562 1861 2.743928 GCACCGCTGGAGGACTTG 60.744 66.667 1.50 0.00 34.73 3.16
1931 2230 4.988716 TCGTCCGCCCAGGTGTCT 62.989 66.667 0.00 0.00 41.99 3.41
2138 2437 3.241995 CGCAGCTCACCGTTAGTTAATTC 60.242 47.826 0.00 0.00 0.00 2.17
2160 2462 2.017049 GAGGCGGTTAATTGCTGTGAT 58.983 47.619 2.49 0.00 0.00 3.06
2162 2464 3.616219 AGGCGGTTAATTGCTGTGATTA 58.384 40.909 2.49 0.00 0.00 1.75
2200 2502 7.836842 CCAATAAACAGGCTTTGGTAGTTTAT 58.163 34.615 10.78 10.78 43.37 1.40
2209 2511 5.048013 GGCTTTGGTAGTTTATTTGACAGCT 60.048 40.000 0.00 0.00 0.00 4.24
2465 2796 6.239402 GGCATTGCTTGGGAGTATATGAATTT 60.239 38.462 8.82 0.00 0.00 1.82
2471 2802 9.639563 TGCTTGGGAGTATATGAATTTTAATCA 57.360 29.630 0.00 0.00 0.00 2.57
2663 3005 5.720202 ACGTATGTTTCTGCTCTGATGTTA 58.280 37.500 0.00 0.00 0.00 2.41
2671 3013 7.065085 TGTTTCTGCTCTGATGTTAGCTAATTC 59.935 37.037 9.88 10.44 39.53 2.17
2692 3034 8.594881 AATTCCATCAGACGTACAAAGATATC 57.405 34.615 0.00 0.00 0.00 1.63
2719 3061 1.579698 CTGGATCACTGAATCGCCAG 58.420 55.000 0.00 0.00 39.93 4.85
2742 3088 1.157870 AGGCGGGCGAATAATTGACG 61.158 55.000 0.00 0.00 0.00 4.35
2749 3095 1.668751 GCGAATAATTGACGGCAAGGA 59.331 47.619 10.69 0.00 37.45 3.36
2807 3153 2.627699 CAGAGAAGTCCTCCAGATAGGC 59.372 54.545 0.00 0.00 42.97 3.93
2808 3154 2.246067 AGAGAAGTCCTCCAGATAGGCA 59.754 50.000 0.00 0.00 42.97 4.75
2809 3155 3.034635 GAGAAGTCCTCCAGATAGGCAA 58.965 50.000 0.00 0.00 36.51 4.52
2810 3156 3.452627 GAGAAGTCCTCCAGATAGGCAAA 59.547 47.826 0.00 0.00 36.51 3.68
3054 3406 6.999950 TGCAGGAACTTTCAACAGTATAGTA 58.000 36.000 0.00 0.00 34.60 1.82
3055 3407 6.872020 TGCAGGAACTTTCAACAGTATAGTAC 59.128 38.462 0.00 0.00 34.60 2.73
3056 3408 6.034683 GCAGGAACTTTCAACAGTATAGTACG 59.965 42.308 0.00 0.00 34.60 3.67
3073 3425 0.883153 ACGACACAACATGCATGCAT 59.117 45.000 27.46 27.46 37.08 3.96
3136 3524 7.184779 CACTTACGTACGTAATCTCAGATTCA 58.815 38.462 33.89 13.21 39.49 2.57
3147 3535 4.039151 TCTCAGATTCAAGCGATGAGAC 57.961 45.455 0.00 0.00 40.98 3.36
3180 3832 2.522060 CTGCAGGACAGTCAACGTC 58.478 57.895 5.57 0.00 41.86 4.34
3273 3925 3.362237 CGAAAGCGATTAATCTAGGCTCG 59.638 47.826 14.31 11.63 40.82 5.03
3302 3954 0.034896 GGTTGATGACTGTGGACCGT 59.965 55.000 0.00 0.00 0.00 4.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 1.305201 GAACCTTGGCTTCACGTCAA 58.695 50.000 0.00 0.00 35.58 3.18
16 17 2.702847 GTGAACCTTGGCTTCACGT 58.297 52.632 14.42 0.00 38.52 4.49
36 37 2.798976 TACGTGTACAACTGGTGGTC 57.201 50.000 0.00 0.00 0.00 4.02
108 110 2.286891 GCTCGTTCTACCTGATACGTCC 60.287 54.545 0.00 0.00 33.88 4.79
129 131 5.698741 TGCCATTAGAGGATATACATGGG 57.301 43.478 0.00 0.00 33.13 4.00
163 169 2.478894 CGTCTGTGGCGTTAAATGAAGT 59.521 45.455 0.00 0.00 0.00 3.01
188 194 4.946157 GGTCCAGTACTACTACAGCTACAA 59.054 45.833 0.00 0.00 0.00 2.41
189 195 4.521146 GGTCCAGTACTACTACAGCTACA 58.479 47.826 0.00 0.00 0.00 2.74
190 196 3.559242 CGGTCCAGTACTACTACAGCTAC 59.441 52.174 0.00 0.00 0.00 3.58
191 197 3.198635 ACGGTCCAGTACTACTACAGCTA 59.801 47.826 0.00 0.00 0.00 3.32
192 198 2.026449 ACGGTCCAGTACTACTACAGCT 60.026 50.000 0.00 0.00 0.00 4.24
193 199 2.097142 CACGGTCCAGTACTACTACAGC 59.903 54.545 0.00 0.00 0.00 4.40
253 259 3.191791 TGGCGAACCAAATTAAACTAGCC 59.808 43.478 0.00 5.31 45.37 3.93
269 275 1.818060 AGCATAGCACAAATTGGCGAA 59.182 42.857 0.00 0.00 34.54 4.70
275 281 1.205417 GGCACCAGCATAGCACAAATT 59.795 47.619 0.00 0.00 44.61 1.82
276 282 0.819582 GGCACCAGCATAGCACAAAT 59.180 50.000 0.00 0.00 44.61 2.32
277 283 0.539207 TGGCACCAGCATAGCACAAA 60.539 50.000 0.00 0.00 44.61 2.83
289 295 4.720902 CCCGTGAGCATGGCACCA 62.721 66.667 3.13 0.00 36.15 4.17
440 446 3.196469 TCACTACTCAGAGATTGCAAGGG 59.804 47.826 4.94 0.00 0.00 3.95
542 564 9.661563 TTTATTCACACAGAAAACGGATATAGT 57.338 29.630 0.00 0.00 40.22 2.12
812 1023 2.815647 GCCGCTGTACTGTGGAGC 60.816 66.667 30.09 15.38 39.82 4.70
813 1024 2.507102 CGCCGCTGTACTGTGGAG 60.507 66.667 30.09 24.45 39.82 3.86
814 1025 4.735132 GCGCCGCTGTACTGTGGA 62.735 66.667 30.09 0.00 39.82 4.02
1124 1417 3.961729 TCGAGAGCGAAGTCGTCA 58.038 55.556 2.25 0.00 44.78 4.35
1551 1850 3.571119 CTTGCGCAAGTCCTCCAG 58.429 61.111 36.23 14.23 41.68 3.86
1727 2026 5.001874 ACCTCGTTTGGGAAGTTTAGAATC 58.998 41.667 0.00 0.00 0.00 2.52
1733 2032 1.589803 CGACCTCGTTTGGGAAGTTT 58.410 50.000 0.00 0.00 34.11 2.66
1919 2218 3.636231 TCCCAAGACACCTGGGCG 61.636 66.667 2.83 0.00 42.46 6.13
2138 2437 1.131126 CACAGCAATTAACCGCCTCTG 59.869 52.381 0.00 0.00 0.00 3.35
2160 2462 6.075984 TGTTTATTGGTTAACCCCAGCTTAA 58.924 36.000 21.97 7.92 35.49 1.85
2162 2464 4.484912 TGTTTATTGGTTAACCCCAGCTT 58.515 39.130 21.97 3.18 35.49 3.74
2200 2502 1.471287 GAGATGCATGCAGCTGTCAAA 59.529 47.619 40.55 7.16 43.23 2.69
2414 2716 7.041440 CCATTTACAGCAAATATCACATCCGTA 60.041 37.037 0.00 0.00 34.99 4.02
2416 2718 6.144854 CCATTTACAGCAAATATCACATCCG 58.855 40.000 0.00 0.00 34.99 4.18
2514 2856 0.102300 GCCACTTTCCGTTTTGCTGT 59.898 50.000 0.00 0.00 0.00 4.40
2663 3005 5.339008 TTGTACGTCTGATGGAATTAGCT 57.661 39.130 0.00 0.00 28.56 3.32
2671 3013 8.353684 ACTTAGATATCTTTGTACGTCTGATGG 58.646 37.037 11.25 0.00 0.00 3.51
2692 3034 3.616956 TTCAGTGATCCAGGCACTTAG 57.383 47.619 0.00 0.00 43.67 2.18
2719 3061 1.135689 CAATTATTCGCCCGCCTATGC 60.136 52.381 0.00 0.00 0.00 3.14
2730 3072 3.126171 TGTTCCTTGCCGTCAATTATTCG 59.874 43.478 0.00 0.00 0.00 3.34
2742 3088 2.362077 ACTGATGTTTGTGTTCCTTGCC 59.638 45.455 0.00 0.00 0.00 4.52
2749 3095 5.359576 TCCTTTGCTTACTGATGTTTGTGTT 59.640 36.000 0.00 0.00 0.00 3.32
2807 3153 6.018994 AGTGTAAGCTACGAAAACTCAGTTTG 60.019 38.462 2.78 0.00 35.80 2.93
2808 3154 6.047231 AGTGTAAGCTACGAAAACTCAGTTT 58.953 36.000 0.00 0.00 37.34 2.66
2809 3155 5.598769 AGTGTAAGCTACGAAAACTCAGTT 58.401 37.500 0.00 0.00 0.00 3.16
2810 3156 5.197682 AGTGTAAGCTACGAAAACTCAGT 57.802 39.130 0.00 0.00 0.00 3.41
3054 3406 0.883153 ATGCATGCATGTTGTGTCGT 59.117 45.000 31.74 4.69 35.03 4.34
3055 3407 1.131693 AGATGCATGCATGTTGTGTCG 59.868 47.619 36.73 0.03 36.70 4.35
3056 3408 2.933495 AGATGCATGCATGTTGTGTC 57.067 45.000 36.73 21.17 36.70 3.67
3094 3460 6.000219 CGTAAGTGGAGCTAAGTACCCTATA 59.000 44.000 0.00 0.00 0.00 1.31
3136 3524 2.625737 CACTCATTGGTCTCATCGCTT 58.374 47.619 0.00 0.00 0.00 4.68
3147 3535 2.617308 CCTGCAGATTAGCACTCATTGG 59.383 50.000 17.39 0.00 40.11 3.16
3183 3835 4.778415 CCGAGAGACCGCCACGTG 62.778 72.222 9.08 9.08 0.00 4.49
3273 3925 1.482593 AGTCATCAACCTGACCCGATC 59.517 52.381 0.82 0.00 45.41 3.69
3302 3954 2.631580 CCGGCCGGCTTGCTTTAAA 61.632 57.895 34.96 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.