Multiple sequence alignment - TraesCS6D01G024000

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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 TraesCS6D01G024000 chr6D 100.000 2842 0 0 1 2842 9113490 9116331 0.000000e+00 5249.0
1 TraesCS6D01G024000 chr6D 81.591 1081 168 16 624 1679 9027229 9028303 0.000000e+00 865.0
2 TraesCS6D01G024000 chr6D 76.667 1050 195 30 660 1679 9215841 9216870 1.160000e-148 536.0
3 TraesCS6D01G024000 chr6D 79.535 430 60 23 2112 2528 9028781 9029195 5.990000e-72 281.0
4 TraesCS6D01G024000 chr6B 95.395 1976 83 5 1 1975 16627629 16629597 0.000000e+00 3138.0
5 TraesCS6D01G024000 chr6B 95.294 1976 84 6 1 1975 16682808 16684775 0.000000e+00 3125.0
6 TraesCS6D01G024000 chr6B 90.042 2360 165 22 538 2842 16995803 16998147 0.000000e+00 2992.0
7 TraesCS6D01G024000 chr6B 95.249 884 34 3 1967 2842 16640921 16641804 0.000000e+00 1393.0
8 TraesCS6D01G024000 chr6B 95.023 884 36 3 1967 2842 16697338 16698221 0.000000e+00 1382.0
9 TraesCS6D01G024000 chr6B 81.071 1083 165 23 624 1679 16547445 16546376 0.000000e+00 828.0
10 TraesCS6D01G024000 chr6B 77.548 775 103 35 1804 2528 16546236 16545483 4.410000e-108 401.0
11 TraesCS6D01G024000 chr6B 91.892 111 9 0 379 489 16985601 16985711 3.790000e-34 156.0
12 TraesCS6D01G024000 chr6B 87.963 108 13 0 2274 2381 17217124 17217231 8.260000e-26 128.0
13 TraesCS6D01G024000 chr6B 85.185 108 16 0 2274 2381 17220801 17220908 8.320000e-21 111.0
14 TraesCS6D01G024000 chr6A 89.528 2311 176 28 586 2842 9946604 9948902 0.000000e+00 2867.0
15 TraesCS6D01G024000 chr6A 89.249 2316 179 28 586 2842 9855895 9858199 0.000000e+00 2833.0
16 TraesCS6D01G024000 chr6A 80.501 1077 173 20 628 1679 9519566 9520630 0.000000e+00 791.0
17 TraesCS6D01G024000 chrUn 94.927 1301 59 4 1 1301 359222925 359224218 0.000000e+00 2030.0
18 TraesCS6D01G024000 chr5D 96.834 379 12 0 1 379 408902107 408901729 3.990000e-178 634.0
19 TraesCS6D01G024000 chr4D 96.561 378 13 0 1 378 499010990 499011367 6.680000e-176 627.0
20 TraesCS6D01G024000 chr3D 94.975 398 18 1 1 398 456893884 456893489 8.650000e-175 623.0
21 TraesCS6D01G024000 chr3D 100.000 29 0 0 390 418 611607523 611607551 1.000000e-03 54.7
22 TraesCS6D01G024000 chr1B 96.073 382 15 0 1 382 660019711 660020092 8.650000e-175 623.0
23 TraesCS6D01G024000 chr1D 95.619 388 16 1 1 387 258836011 258835624 3.110000e-174 621.0
24 TraesCS6D01G024000 chr1A 95.141 391 19 0 1 391 368142536 368142926 4.020000e-173 617.0


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 TraesCS6D01G024000 chr6D 9113490 9116331 2841 False 5249.0 5249 100.0000 1 2842 1 chr6D.!!$F1 2841
1 TraesCS6D01G024000 chr6D 9027229 9029195 1966 False 573.0 865 80.5630 624 2528 2 chr6D.!!$F3 1904
2 TraesCS6D01G024000 chr6D 9215841 9216870 1029 False 536.0 536 76.6670 660 1679 1 chr6D.!!$F2 1019
3 TraesCS6D01G024000 chr6B 16627629 16629597 1968 False 3138.0 3138 95.3950 1 1975 1 chr6B.!!$F1 1974
4 TraesCS6D01G024000 chr6B 16682808 16684775 1967 False 3125.0 3125 95.2940 1 1975 1 chr6B.!!$F3 1974
5 TraesCS6D01G024000 chr6B 16995803 16998147 2344 False 2992.0 2992 90.0420 538 2842 1 chr6B.!!$F6 2304
6 TraesCS6D01G024000 chr6B 16640921 16641804 883 False 1393.0 1393 95.2490 1967 2842 1 chr6B.!!$F2 875
7 TraesCS6D01G024000 chr6B 16697338 16698221 883 False 1382.0 1382 95.0230 1967 2842 1 chr6B.!!$F4 875
8 TraesCS6D01G024000 chr6B 16545483 16547445 1962 True 614.5 828 79.3095 624 2528 2 chr6B.!!$R1 1904
9 TraesCS6D01G024000 chr6A 9946604 9948902 2298 False 2867.0 2867 89.5280 586 2842 1 chr6A.!!$F3 2256
10 TraesCS6D01G024000 chr6A 9855895 9858199 2304 False 2833.0 2833 89.2490 586 2842 1 chr6A.!!$F2 2256
11 TraesCS6D01G024000 chr6A 9519566 9520630 1064 False 791.0 791 80.5010 628 1679 1 chr6A.!!$F1 1051
12 TraesCS6D01G024000 chrUn 359222925 359224218 1293 False 2030.0 2030 94.9270 1 1301 1 chrUn.!!$F1 1300

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
345 346 0.030638 CACTTGGAAGCCCAACAACG 59.969 55.000 0.00 0.00 46.94 4.10 F
425 426 1.152008 GGTAGGGGCCTAGGCATCT 60.152 63.158 34.09 28.84 44.11 2.90 F
520 521 1.191489 TCATCACGAGGGCCTGAACA 61.191 55.000 12.95 0.00 0.00 3.18 F
1563 1592 0.747644 CCATATGTCACTGGCGGCAA 60.748 55.000 14.48 0.00 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1524 1553 0.252513 TGCCTGGGCTTGGTAGACTA 60.253 55.000 13.05 0.0 42.51 2.59 R
1563 1592 0.833287 CATCGAAGACCCCATGTCCT 59.167 55.000 0.00 0.0 45.68 3.85 R
1606 1638 1.141657 GCCATGTCAAGCTATCCCTCA 59.858 52.381 0.00 0.0 0.00 3.86 R
2720 2862 6.648879 TTTGAAAATGGAAATCCTTCGAGT 57.351 33.333 0.44 0.0 36.82 4.18 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
20 21 3.933861 AAGTATGAACCCTAGGCCTTG 57.066 47.619 12.58 9.54 0.00 3.61
135 136 6.486657 ACCATACATATTGCACTTGTATCACC 59.513 38.462 10.79 0.00 35.04 4.02
137 138 7.175467 CCATACATATTGCACTTGTATCACCAT 59.825 37.037 10.79 0.00 35.04 3.55
150 151 0.108804 TCACCATCTCTTCGCCGAAC 60.109 55.000 0.00 0.00 0.00 3.95
151 152 0.108615 CACCATCTCTTCGCCGAACT 60.109 55.000 0.00 0.00 0.00 3.01
152 153 1.134367 CACCATCTCTTCGCCGAACTA 59.866 52.381 0.00 0.00 0.00 2.24
164 165 2.223641 CGCCGAACTAGTGCACCTATAA 60.224 50.000 14.63 0.00 0.00 0.98
173 174 6.335777 ACTAGTGCACCTATAAAGTTTACCG 58.664 40.000 14.63 0.00 0.00 4.02
185 186 5.694231 AAAGTTTACCGTTGTATTGGGTC 57.306 39.130 0.00 0.00 35.28 4.46
189 190 2.467566 ACCGTTGTATTGGGTCTGTC 57.532 50.000 0.00 0.00 0.00 3.51
223 224 5.827797 AGAGACTCTTTGTTATTTGGTTGCA 59.172 36.000 0.00 0.00 0.00 4.08
264 265 0.105039 CTTCATCCTACGCCTCCCAC 59.895 60.000 0.00 0.00 0.00 4.61
297 298 2.840651 CCTTAGGTCATCCACTTGAGGT 59.159 50.000 0.00 0.00 35.89 3.85
308 309 6.945435 TCATCCACTTGAGGTAAATTTGCTAA 59.055 34.615 6.23 0.00 0.00 3.09
334 335 2.435372 ACAAACCTCTGCACTTGGAA 57.565 45.000 2.33 0.00 0.00 3.53
345 346 0.030638 CACTTGGAAGCCCAACAACG 59.969 55.000 0.00 0.00 46.94 4.10
372 373 3.870633 AGAAGAAGGTTGCGTAGTAGG 57.129 47.619 0.00 0.00 0.00 3.18
374 375 1.263356 AGAAGGTTGCGTAGTAGGCA 58.737 50.000 13.34 13.34 37.19 4.75
377 378 1.191535 AGGTTGCGTAGTAGGCATCA 58.808 50.000 17.60 1.86 38.88 3.07
425 426 1.152008 GGTAGGGGCCTAGGCATCT 60.152 63.158 34.09 28.84 44.11 2.90
427 428 1.562783 GTAGGGGCCTAGGCATCTAG 58.437 60.000 34.09 0.00 44.11 2.43
434 435 2.604139 GCCTAGGCATCTAGTCTTCCT 58.396 52.381 29.33 0.00 40.98 3.36
495 496 1.637553 AGACATGCAGGATGAAGGGTT 59.362 47.619 4.84 0.00 39.69 4.11
507 508 6.261826 CAGGATGAAGGGTTTTATCTCATCAC 59.738 42.308 11.32 3.01 39.69 3.06
520 521 1.191489 TCATCACGAGGGCCTGAACA 61.191 55.000 12.95 0.00 0.00 3.18
603 604 4.164796 TCCATCAGTATGCAAGTCAAGGAT 59.835 41.667 0.00 0.00 34.76 3.24
783 785 2.401583 TACGATGCATGTGCCTCTTT 57.598 45.000 2.46 0.00 41.18 2.52
811 813 7.418378 AGAAACCTTCCATACATTTTATCCCA 58.582 34.615 0.00 0.00 0.00 4.37
817 819 8.526147 CCTTCCATACATTTTATCCCATGATTC 58.474 37.037 0.00 0.00 32.18 2.52
819 821 8.640063 TCCATACATTTTATCCCATGATTCAG 57.360 34.615 0.00 0.00 32.18 3.02
972 996 1.271163 GCAGGCCCGCCACTATAAATA 60.271 52.381 8.74 0.00 38.92 1.40
989 1013 8.470939 ACTATAAATATACCCTACCTCCCTTGT 58.529 37.037 0.00 0.00 0.00 3.16
1025 1050 6.464322 CCCAAACTAGCAATTTTCCTTCCTTT 60.464 38.462 0.00 0.00 0.00 3.11
1026 1051 6.424812 CCAAACTAGCAATTTTCCTTCCTTTG 59.575 38.462 0.00 0.00 0.00 2.77
1524 1553 2.983725 AAAAGAAGTGGGCAGCCGCT 62.984 55.000 5.00 3.03 38.60 5.52
1563 1592 0.747644 CCATATGTCACTGGCGGCAA 60.748 55.000 14.48 0.00 0.00 4.52
1601 1633 1.021390 GTATCAGGCGTTGCAGCAGT 61.021 55.000 0.24 0.00 39.27 4.40
1606 1638 2.401766 GGCGTTGCAGCAGTAGCAT 61.402 57.895 17.01 0.00 45.49 3.79
1889 1968 7.081976 AGGCAATTTTAGTCGTTGTTATTGTC 58.918 34.615 0.00 0.00 0.00 3.18
2079 2177 0.812811 AGATGCACACTGCCTATGCG 60.813 55.000 0.00 0.00 44.23 4.73
2096 2194 6.128526 GCCTATGCGAATCCTTAATAGTTGTC 60.129 42.308 0.00 0.00 0.00 3.18
2241 2364 3.321111 ACAATTAGGTGACTGTGTCGACT 59.679 43.478 17.92 0.00 43.88 4.18
2270 2393 4.898829 TCATTAATCAAGTTCCATGCCG 57.101 40.909 0.00 0.00 0.00 5.69
2539 2677 1.882623 CTTTGGACTGAGTGAAAGGGC 59.117 52.381 0.00 0.00 0.00 5.19
2684 2826 0.804364 ACATCGCGTACCGTAGTCAA 59.196 50.000 5.77 0.00 38.35 3.18
2720 2862 8.141298 TGTAGTCCTTTATAGAACACATCCAA 57.859 34.615 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.987220 ACGGTATTGCAATGCTTCAAAAC 59.013 39.130 24.03 11.07 0.00 2.43
115 116 6.359804 AGATGGTGATACAAGTGCAATATGT 58.640 36.000 0.00 0.00 0.00 2.29
135 136 2.455032 CACTAGTTCGGCGAAGAGATG 58.545 52.381 28.47 19.11 0.00 2.90
137 138 0.170561 GCACTAGTTCGGCGAAGAGA 59.829 55.000 28.47 15.42 0.00 3.10
150 151 6.335777 ACGGTAAACTTTATAGGTGCACTAG 58.664 40.000 17.98 7.33 34.56 2.57
151 152 6.284891 ACGGTAAACTTTATAGGTGCACTA 57.715 37.500 17.98 7.61 35.80 2.74
152 153 5.156608 ACGGTAAACTTTATAGGTGCACT 57.843 39.130 17.98 5.41 0.00 4.40
164 165 4.758165 CAGACCCAATACAACGGTAAACTT 59.242 41.667 0.00 0.00 32.19 2.66
173 174 1.677820 CCCCGACAGACCCAATACAAC 60.678 57.143 0.00 0.00 0.00 3.32
185 186 0.038159 GTCTCTTGTGTCCCCGACAG 60.038 60.000 0.00 0.00 43.57 3.51
189 190 0.969894 AAGAGTCTCTTGTGTCCCCG 59.030 55.000 14.48 0.00 34.98 5.73
223 224 2.408565 TGGTCTCTCTCAAACAACCCT 58.591 47.619 0.00 0.00 0.00 4.34
264 265 5.701290 GGATGACCTAAGGTTTATCAATCCG 59.299 44.000 0.00 0.00 35.25 4.18
297 298 8.644374 AGGTTTGTAGGACATTAGCAAATTTA 57.356 30.769 0.00 0.00 32.71 1.40
308 309 2.639839 AGTGCAGAGGTTTGTAGGACAT 59.360 45.455 0.00 0.00 0.00 3.06
334 335 1.414919 TCTTGTAGACGTTGTTGGGCT 59.585 47.619 0.00 0.00 0.00 5.19
345 346 3.391049 ACGCAACCTTCTTCTTGTAGAC 58.609 45.455 0.00 0.00 0.00 2.59
372 373 1.596477 GAGCCGTGGAGGATGATGC 60.596 63.158 0.00 0.00 39.82 3.91
374 375 1.383109 TGGAGCCGTGGAGGATGAT 60.383 57.895 0.00 0.00 39.82 2.45
377 378 0.325296 TAAGTGGAGCCGTGGAGGAT 60.325 55.000 0.00 0.00 44.48 3.24
425 426 7.904558 ATGACAGATGTTGATAGGAAGACTA 57.095 36.000 0.00 0.00 35.80 2.59
427 428 8.363390 TCATATGACAGATGTTGATAGGAAGAC 58.637 37.037 9.76 0.00 0.00 3.01
507 508 2.325082 CGGTTTGTTCAGGCCCTCG 61.325 63.158 0.00 0.00 0.00 4.63
520 521 2.290641 GTGCACATGAGAAGAACGGTTT 59.709 45.455 13.17 0.00 0.00 3.27
783 785 9.847224 GGATAAAATGTATGGAAGGTTTCTCTA 57.153 33.333 0.00 0.00 0.00 2.43
811 813 7.331026 TCAATACGAACTTTCTCCTGAATCAT 58.669 34.615 0.00 0.00 31.56 2.45
817 819 6.368791 TGTCAATCAATACGAACTTTCTCCTG 59.631 38.462 0.00 0.00 0.00 3.86
819 821 6.721571 TGTCAATCAATACGAACTTTCTCC 57.278 37.500 0.00 0.00 0.00 3.71
899 902 2.037121 GCCAAACTTAATTGTGCCCAGT 59.963 45.455 0.00 0.00 0.00 4.00
972 996 3.199289 CGAAAACAAGGGAGGTAGGGTAT 59.801 47.826 0.00 0.00 0.00 2.73
989 1013 3.135994 GCTAGTTTGGGTGAGTCGAAAA 58.864 45.455 0.00 0.00 0.00 2.29
1025 1050 6.928348 TGTCACCTAAGGAGAAAATCTACA 57.072 37.500 0.00 0.00 26.62 2.74
1026 1051 7.281100 CCATTGTCACCTAAGGAGAAAATCTAC 59.719 40.741 0.00 0.00 29.87 2.59
1159 1188 1.196104 AGGCCTTGGCATTGCACAAT 61.196 50.000 14.04 0.00 0.00 2.71
1524 1553 0.252513 TGCCTGGGCTTGGTAGACTA 60.253 55.000 13.05 0.00 42.51 2.59
1563 1592 0.833287 CATCGAAGACCCCATGTCCT 59.167 55.000 0.00 0.00 45.68 3.85
1601 1633 3.308401 TGTCAAGCTATCCCTCATGCTA 58.692 45.455 0.00 0.00 35.09 3.49
1606 1638 1.141657 GCCATGTCAAGCTATCCCTCA 59.858 52.381 0.00 0.00 0.00 3.86
2079 2177 8.889717 TCATTTTCCGACAACTATTAAGGATTC 58.110 33.333 0.00 0.00 0.00 2.52
2096 2194 3.935203 AGTACATGTGCTCTCATTTTCCG 59.065 43.478 11.03 0.00 0.00 4.30
2720 2862 6.648879 TTTGAAAATGGAAATCCTTCGAGT 57.351 33.333 0.44 0.00 36.82 4.18


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

AutoCloner maintained by Alex Coulton.