Multiple sequence alignment - TraesCS3A01G218900

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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 TraesCS3A01G218900 chr3A 100.000 4278 0 0 1 4278 401677176 401672899 0 7901
1 TraesCS3A01G218900 chr5D 95.921 4290 156 12 1 4278 3134885 3139167 0 6935
2 TraesCS3A01G218900 chr1B 95.597 4293 169 13 1 4278 683734145 683729858 0 6863
3 TraesCS3A01G218900 chr1B 95.341 4293 171 19 1 4278 49798423 49802701 0 6793
4 TraesCS3A01G218900 chr7B 95.434 4293 177 12 1 4278 698140157 698144445 0 6824
5 TraesCS3A01G218900 chrUn 95.342 4294 179 13 1 4278 40085856 40090144 0 6802
6 TraesCS3A01G218900 chr3B 95.247 4292 186 12 1 4278 92142921 92147208 0 6780
7 TraesCS3A01G218900 chr3B 95.178 4293 187 14 1 4278 92261853 92266140 0 6763
8 TraesCS3A01G218900 chr5B 95.155 4293 187 14 1 4278 713082221 713077935 0 6756


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 TraesCS3A01G218900 chr3A 401672899 401677176 4277 True 7901 7901 100.000 1 4278 1 chr3A.!!$R1 4277
1 TraesCS3A01G218900 chr5D 3134885 3139167 4282 False 6935 6935 95.921 1 4278 1 chr5D.!!$F1 4277
2 TraesCS3A01G218900 chr1B 683729858 683734145 4287 True 6863 6863 95.597 1 4278 1 chr1B.!!$R1 4277
3 TraesCS3A01G218900 chr1B 49798423 49802701 4278 False 6793 6793 95.341 1 4278 1 chr1B.!!$F1 4277
4 TraesCS3A01G218900 chr7B 698140157 698144445 4288 False 6824 6824 95.434 1 4278 1 chr7B.!!$F1 4277
5 TraesCS3A01G218900 chrUn 40085856 40090144 4288 False 6802 6802 95.342 1 4278 1 chrUn.!!$F1 4277
6 TraesCS3A01G218900 chr3B 92142921 92147208 4287 False 6780 6780 95.247 1 4278 1 chr3B.!!$F1 4277
7 TraesCS3A01G218900 chr3B 92261853 92266140 4287 False 6763 6763 95.178 1 4278 1 chr3B.!!$F2 4277
8 TraesCS3A01G218900 chr5B 713077935 713082221 4286 True 6756 6756 95.155 1 4278 1 chr5B.!!$R1 4277

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
38 39 0.036010 ACGAGAGCCCAATCACAAGG 60.036 55.000 0.00 0.00 0.00 3.61 F
1238 1247 2.024414 GGAGTGTTGGTCAAAGCAAGT 58.976 47.619 0.00 0.00 36.14 3.16 F
2181 2196 0.252197 GAATTCCCACTACCGCTGGT 59.748 55.000 5.58 5.58 40.16 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1417 1427 0.179137 CACGCTTCGCTGACCTATCA 60.179 55.0 0.0 0.0 0.0 2.15 R
3107 3129 0.034059 CCACTTCAGTCGTGCTCCTT 59.966 55.0 0.0 0.0 0.0 3.36 R
3920 3944 0.109319 GGCACAACAATACCCAAGCG 60.109 55.0 0.0 0.0 0.0 4.68 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
38 39 0.036010 ACGAGAGCCCAATCACAAGG 60.036 55.000 0.00 0.00 0.00 3.61
181 182 2.091541 CCTTTACATGGCCATTCACGT 58.908 47.619 17.92 13.72 0.00 4.49
209 210 3.605749 ATCAACCACTCGTGCCCGG 62.606 63.158 0.00 0.00 33.95 5.73
241 242 4.584325 TCCAATCAAAAACCAGACTTCCAG 59.416 41.667 0.00 0.00 0.00 3.86
369 370 6.403200 GCTCATATTGGTGACGTTATTGTTGT 60.403 38.462 0.00 0.00 0.00 3.32
411 412 4.403752 GCCCAAAATGCCTCTAGAAAGATT 59.596 41.667 0.00 0.00 0.00 2.40
462 464 8.194433 TGTACGTACATGTAAAAACTCAAACA 57.806 30.769 24.10 0.00 0.00 2.83
471 473 8.994429 ATGTAAAAACTCAAACATGACAACAA 57.006 26.923 0.00 0.00 31.56 2.83
754 761 8.104566 TCGAATCTTAATAAAAGGAAGGGTTCA 58.895 33.333 0.00 0.00 0.00 3.18
1045 1053 7.723616 TCTTCTTTTTCATTACTTCCATGGTCA 59.276 33.333 12.58 0.00 0.00 4.02
1053 1061 4.504596 TCCATGGTCATGCCCCGC 62.505 66.667 12.58 0.00 37.49 6.13
1086 1094 5.318630 ACACCCGTACTATTGAAATGGTTT 58.681 37.500 0.00 0.00 32.12 3.27
1089 1097 5.771165 ACCCGTACTATTGAAATGGTTTGTT 59.229 36.000 0.00 0.00 32.12 2.83
1107 1115 4.713824 TGTTAGTAGAGATGTTCCCACG 57.286 45.455 0.00 0.00 0.00 4.94
1238 1247 2.024414 GGAGTGTTGGTCAAAGCAAGT 58.976 47.619 0.00 0.00 36.14 3.16
1258 1267 3.258622 AGTCGCCCTATTCTATTACCAGC 59.741 47.826 0.00 0.00 0.00 4.85
1311 1321 4.681744 TGCTTTATTTCATTCATTCCCGC 58.318 39.130 0.00 0.00 0.00 6.13
1342 1352 6.448369 TTCCTTATTATCGAATCCATGGGT 57.552 37.500 13.02 0.00 0.00 4.51
1371 1381 8.716646 TTGTCATATTTAGAATCTTTCTGCGA 57.283 30.769 0.07 0.00 40.94 5.10
1375 1385 9.416794 TCATATTTAGAATCTTTCTGCGATCTC 57.583 33.333 0.07 0.00 40.94 2.75
1417 1427 4.153835 CGTACTCTCTTCTCTTTACCACGT 59.846 45.833 0.00 0.00 0.00 4.49
1564 1574 4.061131 AGGTTTTGGGCCTATAGCTTTT 57.939 40.909 4.53 0.00 43.05 2.27
1574 1586 0.989212 TATAGCTTTTCCCGCCCCCA 60.989 55.000 0.00 0.00 0.00 4.96
1600 1614 1.014352 GTCGAGTGGTGCTTGTTTGT 58.986 50.000 0.00 0.00 0.00 2.83
1833 1847 4.124351 CGGGCGGCGTGAACTCTA 62.124 66.667 9.37 0.00 0.00 2.43
1871 1885 4.845580 CCCGCCGCTGAGATGCTT 62.846 66.667 0.00 0.00 0.00 3.91
1909 1923 6.302269 ACCTTGATAGGAAGATGGCTTATTG 58.698 40.000 0.00 0.00 45.05 1.90
2073 2087 2.108168 TCCCTAGCAGTACGCAAAGAT 58.892 47.619 11.30 0.00 46.13 2.40
2181 2196 0.252197 GAATTCCCACTACCGCTGGT 59.748 55.000 5.58 5.58 40.16 4.00
2231 2246 2.745968 ACAGGCTTCCCAAAAAGTGAA 58.254 42.857 0.00 0.00 0.00 3.18
2417 2433 1.079405 GTCCGAGCCGATTGGTCAA 60.079 57.895 0.00 0.00 41.69 3.18
2462 2483 6.658188 ATATTAGCCGCCTATCCTAGAATC 57.342 41.667 0.00 0.00 0.00 2.52
2475 2496 2.560542 CCTAGAATCGACTGGGATGGAG 59.439 54.545 0.00 0.00 40.28 3.86
2488 2509 2.093658 GGGATGGAGTAGAAAGAACGCA 60.094 50.000 0.00 0.00 0.00 5.24
2492 2513 4.067972 TGGAGTAGAAAGAACGCAAAGT 57.932 40.909 0.00 0.00 0.00 2.66
2623 2644 1.489560 CCCCCTTTCCTGTTCGTCCT 61.490 60.000 0.00 0.00 0.00 3.85
2633 2654 2.915659 TTCGTCCTGACCGGCAGT 60.916 61.111 19.93 0.00 43.33 4.40
2673 2694 0.400594 CCTCAACTTCCCCGGTCTTT 59.599 55.000 0.00 0.00 0.00 2.52
2723 2744 2.674380 ACGTACGGTTCGGAGGCT 60.674 61.111 21.06 0.00 0.00 4.58
2910 2932 6.640907 GTGGGAATTTGATGATTTATAACCGC 59.359 38.462 0.00 0.00 0.00 5.68
2960 2982 4.087510 ACATGATGAATCACTTTGTGCG 57.912 40.909 0.00 0.00 40.03 5.34
3073 3095 6.012745 AGAATTTCTGGTTTAGCATGTTCCT 58.987 36.000 0.00 0.00 0.00 3.36
3079 3101 6.721318 TCTGGTTTAGCATGTTCCTAGAAAT 58.279 36.000 0.00 0.00 0.00 2.17
3145 3167 7.661437 TGAAGTGGCTATACATACAAATCCATC 59.339 37.037 0.00 0.00 0.00 3.51
3262 3284 6.126507 TGGATAGGATTTCTGTTGGCTTCATA 60.127 38.462 0.00 0.00 0.00 2.15
3295 3317 4.293415 CGTAGTTTGTTACGTCAACTCCT 58.707 43.478 0.00 0.00 41.01 3.69
3364 3386 6.719370 TGCATAAAAGGAGTCAAAATAGTGGT 59.281 34.615 0.00 0.00 0.00 4.16
3375 3397 4.973055 TAGTGGTTGCGGCGCGTT 62.973 61.111 28.09 10.78 0.00 4.84
3468 3490 5.338708 CCAATAGAAGTTCACTGACCATCCT 60.339 44.000 5.50 0.00 0.00 3.24
3573 3595 8.336235 TGGAACCATTAGATTAGTGGAAAGAAT 58.664 33.333 4.85 0.00 37.74 2.40
3622 3644 7.461749 ACTTACCAAGAGGAAGAAATGATGAA 58.538 34.615 0.00 0.00 38.69 2.57
3685 3707 6.537301 AGAAGTAATCACAACGTCACTTTTCA 59.463 34.615 0.00 0.00 0.00 2.69
3857 3881 8.429237 TTTCATCCCAAATTGGTATACAAAGT 57.571 30.769 11.52 0.00 43.46 2.66
3980 4004 1.638070 TGGTGATTGGCCTTGTATGGA 59.362 47.619 3.32 0.00 0.00 3.41
4009 4033 5.396772 CCATCCCTTTCAGCAGATGTACTAA 60.397 44.000 0.00 0.00 35.42 2.24
4054 4079 9.823647 ATATCTTAATGCGAGAGTTTATATGGG 57.176 33.333 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.017559 GCTCTCGTGGGCGGATTACT 62.018 60.000 0.00 0.00 38.89 2.24
38 39 3.282021 TGATTGCTTTCTGTATGAGCCC 58.718 45.455 0.00 0.00 35.59 5.19
166 167 1.378514 GGGACGTGAATGGCCATGT 60.379 57.895 21.63 13.07 38.85 3.21
181 182 0.400213 AGTGGTTGATCTTTGCGGGA 59.600 50.000 0.00 0.00 0.00 5.14
187 188 1.523758 GGCACGAGTGGTTGATCTTT 58.476 50.000 5.32 0.00 0.00 2.52
241 242 1.691434 GGGTCTGAGTGAGATGGATCC 59.309 57.143 4.20 4.20 31.63 3.36
369 370 3.255642 GGGCACTGCTTCTTTGATTACAA 59.744 43.478 0.00 0.00 0.00 2.41
411 412 4.325119 ACAGCTCGTCTTACTTCTGTCTA 58.675 43.478 0.00 0.00 29.81 2.59
493 495 5.246981 TCCTTCTTGATCAATGACAACCT 57.753 39.130 8.96 0.00 0.00 3.50
876 884 7.036220 ACCATTAATGACTAGTTCGAAGACTG 58.964 38.462 17.23 0.00 34.32 3.51
877 885 7.171630 ACCATTAATGACTAGTTCGAAGACT 57.828 36.000 17.23 0.00 34.32 3.24
1086 1094 3.446161 CCGTGGGAACATCTCTACTAACA 59.554 47.826 0.00 0.00 46.14 2.41
1089 1097 2.024655 ACCCGTGGGAACATCTCTACTA 60.025 50.000 13.01 0.00 46.14 1.82
1107 1115 1.467920 CATTGGAAGAAGAGGCACCC 58.532 55.000 0.00 0.00 0.00 4.61
1190 1199 3.642141 TGCTCTGTCCATGGAGTGTATA 58.358 45.455 16.81 0.00 32.67 1.47
1195 1204 2.957402 TTTTGCTCTGTCCATGGAGT 57.043 45.000 16.81 0.00 32.67 3.85
1238 1247 2.565834 GGCTGGTAATAGAATAGGGCGA 59.434 50.000 0.00 0.00 0.00 5.54
1258 1267 3.631227 GGATGAGCTTCTCTCCATTTTGG 59.369 47.826 0.00 0.00 41.18 3.28
1304 1314 3.372440 AAGGAAATGAAGAGCGGGAAT 57.628 42.857 0.00 0.00 0.00 3.01
1311 1321 9.494271 TGGATTCGATAATAAGGAAATGAAGAG 57.506 33.333 0.00 0.00 0.00 2.85
1371 1381 7.162082 ACGAAAGAATTGTAAACAGAGGAGAT 58.838 34.615 0.00 0.00 0.00 2.75
1375 1385 7.599245 AGAGTACGAAAGAATTGTAAACAGAGG 59.401 37.037 0.00 0.00 0.00 3.69
1417 1427 0.179137 CACGCTTCGCTGACCTATCA 60.179 55.000 0.00 0.00 0.00 2.15
1449 1459 3.067601 CCGAAGTGTTTGGCCTTTACTTT 59.932 43.478 3.32 0.00 32.23 2.66
1574 1586 4.039357 CACCACTCGACGAGCGGT 62.039 66.667 27.65 27.65 44.73 5.68
1577 1589 2.049063 AAGCACCACTCGACGAGC 60.049 61.111 24.38 11.23 32.04 5.03
1797 1811 4.204012 CCCGCCCTGAACAAATAGAATAA 58.796 43.478 0.00 0.00 0.00 1.40
1833 1847 4.324267 GGATTGAATACCCGGATCGAATT 58.676 43.478 0.73 0.00 0.00 2.17
1871 1885 7.186972 TCCTATCAAGGTTAAGGAGTCAACTA 58.813 38.462 0.00 0.00 44.09 2.24
1909 1923 3.230743 ACCCTTATGCACGAATTTTGC 57.769 42.857 6.13 6.13 40.63 3.68
2061 2075 2.751259 TCACGACCTATCTTTGCGTACT 59.249 45.455 0.00 0.00 33.45 2.73
2125 2139 1.055849 AAAAGGGTTGGTTGGATGCC 58.944 50.000 0.00 0.00 0.00 4.40
2159 2174 1.482593 CAGCGGTAGTGGGAATTCTCT 59.517 52.381 6.92 5.41 0.00 3.10
2263 2279 2.044352 ACAACATTAGGGCCGCCC 60.044 61.111 22.09 22.09 45.90 6.13
2264 2280 1.248101 AACACAACATTAGGGCCGCC 61.248 55.000 0.00 0.00 0.00 6.13
2265 2281 0.109319 CAACACAACATTAGGGCCGC 60.109 55.000 0.00 0.00 0.00 6.53
2417 2433 9.542462 AATATAATATGTGCAGTAGTCGTTGTT 57.458 29.630 0.00 0.00 0.00 2.83
2462 2483 3.024547 TCTTTCTACTCCATCCCAGTCG 58.975 50.000 0.00 0.00 0.00 4.18
2475 2496 4.985044 TGCTACTTTGCGTTCTTTCTAC 57.015 40.909 0.00 0.00 35.36 2.59
2488 2509 3.350833 CTCATCCCTTGCTTGCTACTTT 58.649 45.455 0.00 0.00 0.00 2.66
2492 2513 0.462581 CGCTCATCCCTTGCTTGCTA 60.463 55.000 0.00 0.00 0.00 3.49
2523 2544 3.244156 CAGCAAGAAAACATATGCGCAA 58.756 40.909 17.11 4.13 43.39 4.85
2623 2644 1.823169 GACCCAACTACTGCCGGTCA 61.823 60.000 1.90 0.00 42.17 4.02
2673 2694 2.434843 CCTCATACAGCTCGGGCCA 61.435 63.158 2.00 0.00 39.73 5.36
2723 2744 1.579140 TATTGCATGGGTGGGGCTCA 61.579 55.000 0.00 0.00 0.00 4.26
2735 2756 1.113788 AAGCCGCACCATTATTGCAT 58.886 45.000 0.00 0.00 40.20 3.96
2910 2932 2.746277 CCTTTCGCTCGTTGGGGG 60.746 66.667 0.00 0.00 0.00 5.40
2955 2977 4.947147 GGGCAACAGGTCCGCACA 62.947 66.667 0.00 0.00 39.74 4.57
2960 2982 2.215942 AGTTTATGGGCAACAGGTCC 57.784 50.000 0.00 0.00 43.63 4.46
3107 3129 0.034059 CCACTTCAGTCGTGCTCCTT 59.966 55.000 0.00 0.00 0.00 3.36
3237 3259 4.018506 TGAAGCCAACAGAAATCCTATCCA 60.019 41.667 0.00 0.00 0.00 3.41
3262 3284 1.982938 AAACTACGCGAGCCTCCCT 60.983 57.895 15.93 0.00 0.00 4.20
3295 3317 6.826231 TCGATTCCAATGCAACTTATCCTTTA 59.174 34.615 0.00 0.00 0.00 1.85
3375 3397 3.772572 TCGATATCAAAGGTTGACCCTCA 59.227 43.478 3.12 0.00 45.47 3.86
3468 3490 5.074115 CCTACCTTGGGTTATGTTTGACAA 58.926 41.667 0.00 0.00 37.09 3.18
3573 3595 3.078837 GCTGGTTTCTTCCCATTCGTTA 58.921 45.455 0.00 0.00 0.00 3.18
3576 3598 0.811281 GGCTGGTTTCTTCCCATTCG 59.189 55.000 0.00 0.00 0.00 3.34
3685 3707 4.569719 AAACTACCATGAAATCTCCGGT 57.430 40.909 0.00 0.00 32.55 5.28
3875 3899 6.747414 AATGTTCCTGCATAGTCATACCTA 57.253 37.500 0.00 0.00 0.00 3.08
3920 3944 0.109319 GGCACAACAATACCCAAGCG 60.109 55.000 0.00 0.00 0.00 4.68
3980 4004 1.075748 GCTGAAAGGGATGGGGCAT 60.076 57.895 0.00 0.00 0.00 4.40
4041 4066 8.560903 AGATTGTTTCTTCCCCATATAAACTCT 58.439 33.333 0.00 0.00 32.57 3.24


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

AutoCloner maintained by Alex Coulton.