Multiple sequence alignment - TraesCS3A01G180400

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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 TraesCS3A01G180400 chr3A 100.000 5267 0 0 1 5267 208242049 208236783 0.000000e+00 9727
1 TraesCS3A01G180400 chr3B 95.195 5224 171 24 85 5267 246153455 246148271 0.000000e+00 8183
2 TraesCS3A01G180400 chr3B 98.824 85 1 0 3 87 246153618 246153534 9.140000e-33 152
3 TraesCS3A01G180400 chr3D 96.406 4313 140 6 960 5267 170674917 170670615 0.000000e+00 7092
4 TraesCS3A01G180400 chr3D 96.064 813 22 4 85 892 170676038 170675231 0.000000e+00 1315
5 TraesCS3A01G180400 chr3D 98.795 83 1 0 3 85 170676200 170676118 1.180000e-31 148
6 TraesCS3A01G180400 chr6A 90.191 418 27 6 124 541 61705646 61706049 2.790000e-147 532


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 TraesCS3A01G180400 chr3A 208236783 208242049 5266 True 9727.000000 9727 100.000000 1 5267 1 chr3A.!!$R1 5266
1 TraesCS3A01G180400 chr3B 246148271 246153618 5347 True 4167.500000 8183 97.009500 3 5267 2 chr3B.!!$R1 5264
2 TraesCS3A01G180400 chr3D 170670615 170676200 5585 True 2851.666667 7092 97.088333 3 5267 3 chr3D.!!$R1 5264

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
951 1038 0.038159 CGCTTGAACGTTCCTCTCCT 60.038 55.000 24.78 0.00 0.00 3.69 F
1399 1732 0.180406 CCTTTCCCCGTCCACCTATG 59.820 60.000 0.00 0.00 0.00 2.23 F
2189 2522 0.250597 GGTGAAACTACCAAGGCCGT 60.251 55.000 0.00 0.00 40.54 5.68 F
2278 2611 0.815734 AGAGGATACGACCGGTGTTG 59.184 55.000 14.63 3.72 46.39 3.33 F
3489 3822 1.606668 ACCCGTGTTTACAACATGCTG 59.393 47.619 3.67 0.00 45.01 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2278 2611 0.106894 AGCCTAGCCTTTATCGCCAC 59.893 55.000 0.00 0.0 0.00 5.01 R
3036 3369 1.224075 CACTGATAGGAATGCTGCCG 58.776 55.000 0.00 0.0 0.00 5.69 R
4061 4394 0.108520 CATGGGTTGCAATGTGCCTC 60.109 55.000 0.59 0.0 44.23 4.70 R
4069 4402 1.699083 TCTCTCTGTCATGGGTTGCAA 59.301 47.619 0.00 0.0 0.00 4.08 R
5098 5469 1.604278 GCTTCTTGTGTCAGGGTTCAC 59.396 52.381 0.00 0.0 35.43 3.18 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
149 231 5.294306 TCAAATTAGCTTAGCCAGAATCACG 59.706 40.000 0.00 0.00 0.00 4.35
185 267 7.867921 TCCCCAACATAATCTAAACATGTACT 58.132 34.615 0.00 0.00 32.70 2.73
186 268 8.994500 TCCCCAACATAATCTAAACATGTACTA 58.006 33.333 0.00 0.00 32.70 1.82
187 269 9.052759 CCCCAACATAATCTAAACATGTACTAC 57.947 37.037 0.00 0.00 32.70 2.73
217 301 4.872691 CCACTATCTCAACAATGTCCTGAC 59.127 45.833 0.00 0.00 0.00 3.51
243 327 1.724545 TTAGGGCATAGGCATACGGT 58.275 50.000 0.15 0.00 43.71 4.83
267 351 0.249911 CCTAGGCATACCGGCAGAAC 60.250 60.000 0.00 0.00 44.47 3.01
274 358 1.140312 ATACCGGCAGAACATGGGAT 58.860 50.000 0.00 0.00 0.00 3.85
300 384 0.813610 TGTTGTCCACACGCTTCAGG 60.814 55.000 0.00 0.00 0.00 3.86
318 402 1.313091 GGAACCATCCCAGCGGAAAC 61.313 60.000 0.00 0.00 43.10 2.78
320 404 0.112412 AACCATCCCAGCGGAAACTT 59.888 50.000 0.00 0.00 43.10 2.66
724 811 2.288729 TGCGACTGCTGCATCATAATTC 59.711 45.455 1.31 0.00 43.34 2.17
776 863 1.985159 TCATGGTGGACTGGCTAAACT 59.015 47.619 0.00 0.00 0.00 2.66
791 878 4.021456 GGCTAAACTTTGTGGCCATTTACT 60.021 41.667 9.72 0.00 42.08 2.24
855 942 0.704076 TAAACCAAGCTCATGGGCCT 59.296 50.000 15.67 0.00 45.18 5.19
903 990 0.108774 GGATACAGCCCAGCCCTAAC 59.891 60.000 0.00 0.00 0.00 2.34
906 993 1.610554 TACAGCCCAGCCCTAACGAC 61.611 60.000 0.00 0.00 0.00 4.34
938 1025 3.043713 CTTCACTGCGGCGCTTGA 61.044 61.111 33.26 29.01 0.00 3.02
940 1027 2.770587 CTTCACTGCGGCGCTTGAAC 62.771 60.000 31.66 8.84 31.60 3.18
941 1028 4.724697 CACTGCGGCGCTTGAACG 62.725 66.667 33.26 15.46 0.00 3.95
943 1030 4.012895 CTGCGGCGCTTGAACGTT 62.013 61.111 33.26 0.00 34.88 3.99
944 1031 3.911155 CTGCGGCGCTTGAACGTTC 62.911 63.158 33.26 21.42 34.88 3.95
946 1033 3.041940 CGGCGCTTGAACGTTCCT 61.042 61.111 24.78 0.00 34.88 3.36
948 1035 1.668151 GGCGCTTGAACGTTCCTCT 60.668 57.895 24.78 0.00 34.88 3.69
949 1036 1.627550 GGCGCTTGAACGTTCCTCTC 61.628 60.000 24.78 10.63 34.88 3.20
951 1038 0.038159 CGCTTGAACGTTCCTCTCCT 60.038 55.000 24.78 0.00 0.00 3.69
953 1040 1.673329 GCTTGAACGTTCCTCTCCTCC 60.673 57.143 24.78 0.00 0.00 4.30
955 1042 0.903454 TGAACGTTCCTCTCCTCCCC 60.903 60.000 24.78 0.00 0.00 4.81
1092 1425 0.322816 AGCAGCATGTGGACCGAATT 60.323 50.000 0.00 0.00 39.31 2.17
1098 1431 0.462047 ATGTGGACCGAATTCTCGCC 60.462 55.000 3.52 2.42 44.04 5.54
1399 1732 0.180406 CCTTTCCCCGTCCACCTATG 59.820 60.000 0.00 0.00 0.00 2.23
1425 1758 4.048504 TGATTATATCGGAGTTGTGTGCG 58.951 43.478 0.00 0.00 0.00 5.34
1541 1874 1.719063 TTCTCCAAGGCCAGCAAGGT 61.719 55.000 5.01 0.00 40.61 3.50
1564 1897 1.810030 GCCGGCTTGGAGTTCTACG 60.810 63.158 22.15 0.00 42.00 3.51
1635 1968 1.408702 ACTGCGGTTGTGAATTTGCTT 59.591 42.857 0.00 0.00 0.00 3.91
1860 2193 3.031736 TGGGATGTGTAGAGAAGGTAGC 58.968 50.000 0.00 0.00 0.00 3.58
1932 2265 7.042051 GCTAAGCCGAATTTGATCACTTATACA 60.042 37.037 0.00 0.00 0.00 2.29
1949 2282 6.775629 ACTTATACATCACTTGTTGGTGGTTT 59.224 34.615 0.00 0.00 41.17 3.27
1970 2303 2.366916 TCTGCAAGAGGAATAGGCTAGC 59.633 50.000 6.04 6.04 38.67 3.42
2004 2337 5.551233 TCCATAGTGAGGAAACTTGAACAG 58.449 41.667 0.00 0.00 44.43 3.16
2107 2440 2.238144 TCTTTGCTTGGAGAGATGGAGG 59.762 50.000 0.00 0.00 0.00 4.30
2189 2522 0.250597 GGTGAAACTACCAAGGCCGT 60.251 55.000 0.00 0.00 40.54 5.68
2278 2611 0.815734 AGAGGATACGACCGGTGTTG 59.184 55.000 14.63 3.72 46.39 3.33
2452 2785 5.831525 ACCGTCACCTATCATACACTCATAA 59.168 40.000 0.00 0.00 0.00 1.90
2510 2843 6.653183 CAGTTGAGTTGTTTGATGAGTACAG 58.347 40.000 0.00 0.00 0.00 2.74
2556 2889 2.557924 TGTTGTTCACAATGGCCTGATC 59.442 45.455 3.32 0.00 38.24 2.92
2601 2934 2.163010 GGTCACCATTGCTGATCAAGTG 59.837 50.000 0.00 0.00 38.22 3.16
2685 3018 3.465871 TGCAAATTTCAAAGAAGGTGGC 58.534 40.909 0.00 0.00 0.00 5.01
2711 3044 6.403866 ACAAGGTGTGCTAAATTTCATTCA 57.596 33.333 0.00 0.00 0.00 2.57
2905 3238 2.228582 CGCAATGGAAATGAACAGGTCA 59.771 45.455 0.00 0.00 41.67 4.02
2925 3258 6.879458 AGGTCATAGAACCATTGTTAAGTGAC 59.121 38.462 10.09 10.09 42.12 3.67
3036 3369 4.675114 CGGTTTTCAAGTAACATGAACAGC 59.325 41.667 0.00 0.00 36.57 4.40
3239 3572 6.152932 AGACTTGTGTGAAAGCATGAAAAT 57.847 33.333 0.00 0.00 0.00 1.82
3349 3682 7.119846 GGCTCTTTGATTACTTAGAAAGAAGCA 59.880 37.037 0.48 0.00 34.78 3.91
3356 3689 8.730680 TGATTACTTAGAAAGAAGCAACATTCC 58.269 33.333 0.00 0.00 0.00 3.01
3449 3782 9.865321 ATATGAATTGTTTCAGAAAATGTCCAG 57.135 29.630 0.00 0.00 44.75 3.86
3489 3822 1.606668 ACCCGTGTTTACAACATGCTG 59.393 47.619 3.67 0.00 45.01 4.41
3494 3827 5.086058 CCGTGTTTACAACATGCTGATAAC 58.914 41.667 2.44 7.05 45.01 1.89
3891 4224 5.419155 TGAGGTTGTGACTATCCTAAGTGAG 59.581 44.000 0.00 0.00 0.00 3.51
3961 4294 3.118261 ACTTGGTCAGTTCAAGAAGCTGA 60.118 43.478 10.30 9.48 42.94 4.26
4069 4402 1.299976 GGAAGTTCCCGAGGCACAT 59.700 57.895 11.17 0.00 0.00 3.21
4108 4441 7.547019 CAGAGAGAACTGATAGTTTATGCACAA 59.453 37.037 0.00 0.00 38.80 3.33
4112 4445 7.584987 AGAACTGATAGTTTATGCACAACAAC 58.415 34.615 12.07 2.90 38.80 3.32
4529 4868 0.111253 AAGGAGGAAACCAGTGGCAG 59.889 55.000 9.78 0.00 0.00 4.85
4649 4990 2.414559 CGCGAGAGAAAATGGTGCAAAT 60.415 45.455 0.00 0.00 0.00 2.32
4678 5019 1.009829 GTAAGAGCAATGGACCTGCG 58.990 55.000 0.36 0.00 44.75 5.18
4749 5090 4.402056 TTCACTTTCTAGCCCTATTCGG 57.598 45.455 0.00 0.00 0.00 4.30
4754 5095 7.179966 TCACTTTCTAGCCCTATTCGGATATA 58.820 38.462 0.00 0.00 33.16 0.86
4762 5103 6.890293 AGCCCTATTCGGATATATTTCCTTC 58.110 40.000 10.10 0.00 33.30 3.46
4862 5211 0.904394 TGCCTTTCCATTTGCCCCTC 60.904 55.000 0.00 0.00 0.00 4.30
4875 5224 3.085952 TGCCCCTCTACAAATTTCTGG 57.914 47.619 0.00 0.00 0.00 3.86
4896 5245 4.887071 TGGAAATGGCACCTTGTACATATC 59.113 41.667 0.00 0.00 0.00 1.63
4956 5305 1.944709 GCGGCCGTTTATTAGATGGTT 59.055 47.619 28.70 0.00 0.00 3.67
5098 5469 8.859156 CATTTTGGGTGTTGTAAAGAAATATCG 58.141 33.333 0.00 0.00 0.00 2.92
5227 5599 5.639506 TCAGCTAATTAGTGACTTCAAGCAC 59.360 40.000 13.91 4.35 35.30 4.40
5232 5604 1.876322 AGTGACTTCAAGCACAGAGC 58.124 50.000 12.60 0.00 46.19 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 1.419762 TCTGCTTGGCCTAGTTTGTCA 59.580 47.619 15.85 3.90 0.00 3.58
154 236 7.846066 TGTTTAGATTATGTTGGGGAAATTGG 58.154 34.615 0.00 0.00 0.00 3.16
186 268 9.988815 GACATTGTTGAGATAGTGGATATTAGT 57.011 33.333 0.00 0.00 0.00 2.24
187 269 9.429359 GGACATTGTTGAGATAGTGGATATTAG 57.571 37.037 0.00 0.00 0.00 1.73
192 274 5.426509 TCAGGACATTGTTGAGATAGTGGAT 59.573 40.000 0.00 0.00 0.00 3.41
217 301 5.812642 CGTATGCCTATGCCCTAAATCTAAG 59.187 44.000 0.00 0.00 36.33 2.18
243 327 1.155390 CCGGTATGCCTAGGGGAGA 59.845 63.158 11.72 0.00 33.58 3.71
267 351 2.292267 GACAACAGCCACTATCCCATG 58.708 52.381 0.00 0.00 0.00 3.66
300 384 0.322546 AGTTTCCGCTGGGATGGTTC 60.323 55.000 0.00 0.00 43.41 3.62
318 402 3.512033 TCGTTTGGTTTGGGAAACAAG 57.488 42.857 0.00 0.00 42.95 3.16
320 404 3.952323 TGTATCGTTTGGTTTGGGAAACA 59.048 39.130 0.00 0.00 43.15 2.83
531 615 2.179517 CTCGAGGCGCTCTTCGTT 59.820 61.111 21.87 0.00 41.07 3.85
776 863 4.693566 CGACTCTAAGTAAATGGCCACAAA 59.306 41.667 8.16 0.00 0.00 2.83
791 878 1.339631 CCAACAATGGGCCGACTCTAA 60.340 52.381 0.00 0.00 43.51 2.10
855 942 7.710907 GCTCACTTGTATTTGAGACATGGTATA 59.289 37.037 0.00 0.00 41.65 1.47
864 951 3.509967 TCCGAGCTCACTTGTATTTGAGA 59.490 43.478 15.40 0.00 41.65 3.27
938 1025 1.612739 GGGGGAGGAGAGGAACGTT 60.613 63.158 0.00 0.00 0.00 3.99
955 1042 2.357517 GTGTGAGTGCGAGTGGGG 60.358 66.667 0.00 0.00 0.00 4.96
957 1044 2.734723 CGGTGTGAGTGCGAGTGG 60.735 66.667 0.00 0.00 0.00 4.00
1267 1600 3.917760 GAGGCGACGGGATGAGGG 61.918 72.222 0.00 0.00 0.00 4.30
1269 1602 2.415010 CAGAGGCGACGGGATGAG 59.585 66.667 0.00 0.00 0.00 2.90
1399 1732 5.234329 CACACAACTCCGATATAATCACACC 59.766 44.000 0.00 0.00 0.00 4.16
1403 1736 4.048504 CGCACACAACTCCGATATAATCA 58.951 43.478 0.00 0.00 0.00 2.57
1413 1746 4.012895 CCACGCGCACACAACTCC 62.013 66.667 5.73 0.00 0.00 3.85
1548 1881 2.617308 TCTATCGTAGAACTCCAAGCCG 59.383 50.000 0.00 0.00 43.58 5.52
1564 1897 3.888930 CTGACCTCCTTCCTCACTCTATC 59.111 52.174 0.00 0.00 0.00 2.08
1635 1968 1.230281 AATTCTCCCCTGCCTCCCA 60.230 57.895 0.00 0.00 0.00 4.37
1860 2193 0.396811 ACCCCTTCACTTTCTCCACG 59.603 55.000 0.00 0.00 0.00 4.94
1932 2265 2.362077 GCAGAAACCACCAACAAGTGAT 59.638 45.455 0.00 0.00 40.34 3.06
1949 2282 2.366916 GCTAGCCTATTCCTCTTGCAGA 59.633 50.000 2.29 0.00 0.00 4.26
1970 2303 2.874701 CTCACTATGGAAAAGGCATCCG 59.125 50.000 0.00 0.00 39.98 4.18
2004 2337 1.899814 TCATCCACCACTACACCTGTC 59.100 52.381 0.00 0.00 0.00 3.51
2107 2440 1.257750 CCAGCTTTTACCCCCTTGCC 61.258 60.000 0.00 0.00 0.00 4.52
2189 2522 5.063204 CAGTAACACCTTCAGACATTTCCA 58.937 41.667 0.00 0.00 0.00 3.53
2278 2611 0.106894 AGCCTAGCCTTTATCGCCAC 59.893 55.000 0.00 0.00 0.00 5.01
2452 2785 4.735369 TCCCCAAGTTTACACATCATGTT 58.265 39.130 0.00 0.00 43.19 2.71
2510 2843 7.655328 CAGTACTGGAGAATGATGTATCTTTCC 59.345 40.741 15.49 4.91 40.08 3.13
2556 2889 2.628178 TCCTCCATTACATAGTGCTCCG 59.372 50.000 0.00 0.00 0.00 4.63
2685 3018 4.854399 TGAAATTTAGCACACCTTGTTCG 58.146 39.130 0.00 0.00 0.00 3.95
2711 3044 8.997734 AGTCCATTTCTAGTTCTTCCATCTTAT 58.002 33.333 0.00 0.00 0.00 1.73
2721 3054 8.697507 ATGAAAACAAGTCCATTTCTAGTTCT 57.302 30.769 0.00 0.00 34.84 3.01
2905 3238 9.520515 AATGAAGTCACTTAACAATGGTTCTAT 57.479 29.630 0.00 0.00 38.45 1.98
2925 3258 4.340097 TGCAGGCCATGAATCTTAATGAAG 59.660 41.667 5.01 0.00 0.00 3.02
3036 3369 1.224075 CACTGATAGGAATGCTGCCG 58.776 55.000 0.00 0.00 0.00 5.69
3239 3572 5.732331 AATGGTTGGATGAATCCCTTCTA 57.268 39.130 6.87 0.00 46.59 2.10
3349 3682 7.781324 AAGTTATCATTGTTGGAGGAATGTT 57.219 32.000 0.00 0.00 32.40 2.71
3489 3822 9.662947 AAACCATAGTTACAGTAACCAGTTATC 57.337 33.333 18.27 0.00 39.47 1.75
3494 3827 7.277981 CAGCTAAACCATAGTTACAGTAACCAG 59.722 40.741 18.27 9.43 39.47 4.00
3929 4262 8.208224 TCTTGAACTGACCAAGTGTATTAGAAA 58.792 33.333 0.00 0.00 39.81 2.52
3949 4282 5.282055 TCAGTTCTCTTCAGCTTCTTGAA 57.718 39.130 0.00 0.00 35.83 2.69
3961 4294 4.903054 TCACAAGCATCATCAGTTCTCTT 58.097 39.130 0.00 0.00 0.00 2.85
4061 4394 0.108520 CATGGGTTGCAATGTGCCTC 60.109 55.000 0.59 0.00 44.23 4.70
4069 4402 1.699083 TCTCTCTGTCATGGGTTGCAA 59.301 47.619 0.00 0.00 0.00 4.08
4112 4445 9.223099 TGCCATTGTCAATATCAGTATTATCAG 57.777 33.333 0.00 0.00 0.00 2.90
4620 4961 2.512485 TTTTCTCTCGCGTGGTGTTA 57.488 45.000 5.77 0.00 0.00 2.41
4629 4970 2.704725 TTTGCACCATTTTCTCTCGC 57.295 45.000 0.00 0.00 0.00 5.03
4649 4990 5.643777 GTCCATTGCTCTTACAAGCTTTCTA 59.356 40.000 0.00 0.00 42.94 2.10
4762 5103 7.485595 TGCATCATTACATTGTCAAAGATTTCG 59.514 33.333 0.00 0.00 0.00 3.46
4862 5211 5.047092 AGGTGCCATTTCCAGAAATTTGTAG 60.047 40.000 2.86 0.00 38.84 2.74
4875 5224 6.095440 AGTTGATATGTACAAGGTGCCATTTC 59.905 38.462 0.00 0.00 0.00 2.17
4896 5245 3.796504 GCAAGGGTGATTGTGTTCAGTTG 60.797 47.826 0.00 0.00 32.56 3.16
4977 5326 5.067805 GGCTAACCTCACCCAATTGAATTAG 59.932 44.000 7.12 5.28 32.34 1.73
5047 5396 7.012894 TGACACGTAGGTTTCTTGAAAATCATT 59.987 33.333 3.62 0.00 0.00 2.57
5098 5469 1.604278 GCTTCTTGTGTCAGGGTTCAC 59.396 52.381 0.00 0.00 35.43 3.18
5136 5508 5.229423 GCATTTCATAAACTGGTTGCTTCA 58.771 37.500 0.00 0.00 0.00 3.02
5212 5584 2.289072 GGCTCTGTGCTTGAAGTCACTA 60.289 50.000 16.50 7.68 42.39 2.74
5227 5599 7.226325 CAGAGAGGAATTTATTTGTAGGCTCTG 59.774 40.741 0.00 0.00 38.67 3.35
5232 5604 6.261826 CCAGCAGAGAGGAATTTATTTGTAGG 59.738 42.308 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.