Multiple sequence alignment - TraesCS1B01G045000

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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 TraesCS1B01G045000 chr1B 100.000 3385 0 0 1 3385 24934605 24931221 0.000000e+00 6252.0
1 TraesCS1B01G045000 chr1D 94.868 3410 120 24 1 3385 17170619 17167240 0.000000e+00 5276.0
2 TraesCS1B01G045000 chr1A 92.153 3186 134 39 251 3385 18463021 18459901 0.000000e+00 4392.0
3 TraesCS1B01G045000 chr3B 92.181 243 16 3 1513 1752 828111441 828111683 1.160000e-89 340.0
4 TraesCS1B01G045000 chr3B 86.920 237 27 4 1519 1752 823129941 823129706 2.590000e-66 263.0
5 TraesCS1B01G045000 chr3D 91.770 243 17 3 1513 1752 610544041 610544283 5.410000e-88 335.0
6 TraesCS1B01G045000 chr3D 87.705 244 25 5 1519 1758 613806091 613805849 2.570000e-71 279.0
7 TraesCS1B01G045000 chr3A 90.947 243 19 3 1513 1752 744879511 744879753 1.170000e-84 324.0
8 TraesCS1B01G045000 chr3A 85.448 268 34 4 1496 1758 750298780 750298513 1.200000e-69 274.0
9 TraesCS1B01G045000 chr5B 87.719 228 25 2 1520 1744 112194758 112194531 2.590000e-66 263.0
10 TraesCS1B01G045000 chr7D 97.143 35 1 0 88 122 571979479 571979445 3.650000e-05 60.2
11 TraesCS1B01G045000 chr2A 100.000 29 0 0 5 33 266870277 266870305 2.000000e-03 54.7


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 TraesCS1B01G045000 chr1B 24931221 24934605 3384 True 6252 6252 100.000 1 3385 1 chr1B.!!$R1 3384
1 TraesCS1B01G045000 chr1D 17167240 17170619 3379 True 5276 5276 94.868 1 3385 1 chr1D.!!$R1 3384
2 TraesCS1B01G045000 chr1A 18459901 18463021 3120 True 4392 4392 92.153 251 3385 1 chr1A.!!$R1 3134

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
68 69 0.733150 GAAAATACGAGCACTGGGGC 59.267 55.0 0.0 0.0 0.00 5.80 F
525 542 0.745845 GCACCCCTATGTCTGCACAG 60.746 60.0 0.0 0.0 35.41 3.66 F
1961 1981 0.254178 ACTTCGATGCCATGAGCCTT 59.746 50.0 0.0 0.0 42.71 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1510 1530 0.392863 CGACATGGACATGGGCTTCA 60.393 55.000 15.94 0.00 42.91 3.02 R
2232 2252 1.002900 CGCGTGATGAAACTGTTGGTT 60.003 47.619 0.00 0.00 40.28 3.67 R
2902 2951 1.200519 AGGAAAATGCATGCATGGCT 58.799 45.000 32.79 19.82 36.68 4.75 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
41 42 1.823797 ACGTCTTCTCCGACTAAGCT 58.176 50.000 0.00 0.00 0.00 3.74
48 49 3.283259 TCTCCGACTAAGCTCTGATGA 57.717 47.619 0.00 0.00 0.00 2.92
50 51 3.118223 TCTCCGACTAAGCTCTGATGAGA 60.118 47.826 0.00 0.00 42.73 3.27
64 65 5.105063 TCTGATGAGAAAATACGAGCACTG 58.895 41.667 0.00 0.00 0.00 3.66
66 67 2.972625 TGAGAAAATACGAGCACTGGG 58.027 47.619 0.00 0.00 0.00 4.45
68 69 0.733150 GAAAATACGAGCACTGGGGC 59.267 55.000 0.00 0.00 0.00 5.80
86 87 2.225467 GGCCATGTCTAGGATTTGAGC 58.775 52.381 0.00 0.00 0.00 4.26
185 186 8.330466 TGATTATAAACAATAACCTATGCCCG 57.670 34.615 0.00 0.00 32.86 6.13
438 454 4.142838 GCACCATGGCTTTTTAAATCAAGC 60.143 41.667 13.04 13.85 44.06 4.01
446 462 4.988540 GCTTTTTAAATCAAGCCGGTTCTT 59.011 37.500 11.89 0.00 39.70 2.52
449 465 7.471657 TTTTTAAATCAAGCCGGTTCTTTTC 57.528 32.000 1.90 0.00 0.00 2.29
525 542 0.745845 GCACCCCTATGTCTGCACAG 60.746 60.000 0.00 0.00 35.41 3.66
628 645 5.163447 GCCACATAGAAGGTACATGTCTACA 60.163 44.000 0.00 0.00 30.59 2.74
834 851 3.964031 ACTACCTCCAAGCCTCTATCAAG 59.036 47.826 0.00 0.00 0.00 3.02
876 893 3.885297 ACACACACCAGAATTGAAGGAAG 59.115 43.478 0.00 0.00 0.00 3.46
923 940 1.801178 CTGCACGAAGGAAAGGAGAAC 59.199 52.381 0.00 0.00 0.00 3.01
1071 1089 6.839134 ACCAGGTAATTAATTTCATTCCCCTC 59.161 38.462 5.91 0.00 0.00 4.30
1104 1122 5.221048 CCGGATTTTGTTCACTCTCACTTTT 60.221 40.000 0.00 0.00 0.00 2.27
1105 1123 5.682862 CGGATTTTGTTCACTCTCACTTTTG 59.317 40.000 0.00 0.00 0.00 2.44
1106 1124 5.460091 GGATTTTGTTCACTCTCACTTTTGC 59.540 40.000 0.00 0.00 0.00 3.68
1130 1149 6.633500 TGCACAAGCTCAAATAAAGTTAGT 57.367 33.333 0.00 0.00 42.74 2.24
1191 1210 6.166984 TGCAAAGAGGAGAATGATACTAGG 57.833 41.667 0.00 0.00 0.00 3.02
1192 1211 5.663106 TGCAAAGAGGAGAATGATACTAGGT 59.337 40.000 0.00 0.00 0.00 3.08
1193 1212 6.183360 TGCAAAGAGGAGAATGATACTAGGTC 60.183 42.308 0.00 0.00 0.00 3.85
1326 1346 4.186926 TCTTGATTCTTCTTCTCATGCCG 58.813 43.478 0.00 0.00 0.00 5.69
1327 1347 3.616956 TGATTCTTCTTCTCATGCCGT 57.383 42.857 0.00 0.00 0.00 5.68
1961 1981 0.254178 ACTTCGATGCCATGAGCCTT 59.746 50.000 0.00 0.00 42.71 4.35
1985 2005 4.115199 ACCTTCTCCGGCATGGGC 62.115 66.667 0.00 0.00 38.76 5.36
2131 2151 2.981909 CCAGCAGCACACACTGGG 60.982 66.667 0.00 0.00 45.97 4.45
2132 2152 2.981909 CAGCAGCACACACTGGGG 60.982 66.667 0.00 0.00 38.16 4.96
2195 2215 3.134127 CTAGGCTTGGGCAACGGC 61.134 66.667 0.00 0.00 40.87 5.68
2232 2252 0.530744 CCATGAAGACGACGGAGGAA 59.469 55.000 0.00 0.00 0.00 3.36
2375 2395 0.609131 ATGCTGCCACAGGTAACCAC 60.609 55.000 0.00 0.00 37.17 4.16
2474 2494 5.363939 GTGCTGTGAGATATAGAAAAGGCT 58.636 41.667 0.00 0.00 0.00 4.58
2650 2670 7.868415 TGCTGTCTTTCTTCTACTTCTTCTTAC 59.132 37.037 0.00 0.00 0.00 2.34
2661 2681 7.183460 TCTACTTCTTCTTACTTAGGGCTCTT 58.817 38.462 0.00 0.00 0.00 2.85
2703 2730 6.826741 GGGGTGAAGTTATGTGTGTATTGTAT 59.173 38.462 0.00 0.00 0.00 2.29
2775 2811 5.927030 TGTACAATTCTCGCATTTCTGTTC 58.073 37.500 0.00 0.00 0.00 3.18
2821 2861 2.932614 GTGATCCAAGAGTGTGAATCCG 59.067 50.000 0.00 0.00 0.00 4.18
2871 2911 6.095432 TGTCACCAAAATTGTTATCCAAGG 57.905 37.500 0.00 0.00 36.25 3.61
2891 2940 6.281405 CAAGGTACTACATTCTACATGGACC 58.719 44.000 0.00 0.00 38.49 4.46
2899 2948 4.957954 ACATTCTACATGGACCAAATGCAT 59.042 37.500 13.48 0.00 40.63 3.96
2902 2951 5.109500 TCTACATGGACCAAATGCATACA 57.891 39.130 0.00 0.00 37.23 2.29
2903 2952 5.125356 TCTACATGGACCAAATGCATACAG 58.875 41.667 0.00 0.00 37.23 2.74
2906 2955 1.272369 TGGACCAAATGCATACAGCCA 60.272 47.619 0.00 1.69 44.83 4.75
2944 3004 8.055181 TCCTTTTGGAGAATACATATGAGCTTT 58.945 33.333 10.38 0.00 45.19 3.51
2949 3009 7.337938 TGGAGAATACATATGAGCTTTGTCAA 58.662 34.615 10.38 0.00 0.00 3.18
3024 3090 5.592054 TGATATGCCACTCTTCTAACTTCG 58.408 41.667 0.00 0.00 0.00 3.79
3081 3147 6.729187 ACATGTGTAAGCAGAAAGAGAAAAC 58.271 36.000 0.00 0.00 0.00 2.43
3280 3346 0.523072 AATGTTGATCACGGCTGCAC 59.477 50.000 0.50 0.00 0.00 4.57
3284 3350 3.197790 GATCACGGCTGCACGCAT 61.198 61.111 0.50 0.00 41.67 4.73
3338 3404 4.275196 AGCAAGGTCGGTTCTTTAGTTTTC 59.725 41.667 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 3.629855 TCATCAGAGCTTAGTCGGAGAAG 59.370 47.826 0.00 0.00 39.69 2.85
33 34 7.197017 TCGTATTTTCTCATCAGAGCTTAGTC 58.803 38.462 0.00 0.00 41.81 2.59
37 38 4.808364 GCTCGTATTTTCTCATCAGAGCTT 59.192 41.667 6.84 0.00 44.35 3.74
41 42 5.105063 CAGTGCTCGTATTTTCTCATCAGA 58.895 41.667 0.00 0.00 0.00 3.27
48 49 1.679032 GCCCCAGTGCTCGTATTTTCT 60.679 52.381 0.00 0.00 0.00 2.52
50 51 0.679960 GGCCCCAGTGCTCGTATTTT 60.680 55.000 0.00 0.00 0.00 1.82
64 65 1.494721 TCAAATCCTAGACATGGCCCC 59.505 52.381 0.00 0.00 0.00 5.80
66 67 2.225467 GCTCAAATCCTAGACATGGCC 58.775 52.381 0.00 0.00 0.00 5.36
68 69 2.441001 AGGGCTCAAATCCTAGACATGG 59.559 50.000 0.00 0.00 0.00 3.66
124 125 2.097142 ACGCGAACTGATAGTACCTCAC 59.903 50.000 15.93 0.00 0.00 3.51
170 171 5.766150 TCAATTTCGGGCATAGGTTATTG 57.234 39.130 0.00 0.00 0.00 1.90
184 185 7.621832 TTTTGAACAAGCACTATCAATTTCG 57.378 32.000 0.00 0.00 32.35 3.46
359 360 4.737578 TCTACCCTGGTTAAGCTCGATAT 58.262 43.478 6.19 0.00 0.00 1.63
373 374 5.649395 TCAAAATTGAGCATTCTCTACCCTG 59.351 40.000 0.00 0.00 40.03 4.45
438 454 6.509418 TTAGATGGATTTGAAAAGAACCGG 57.491 37.500 0.00 0.00 0.00 5.28
446 462 7.171848 TCGACTCGTTTTTAGATGGATTTGAAA 59.828 33.333 0.00 0.00 0.00 2.69
449 465 6.403333 TCGACTCGTTTTTAGATGGATTTG 57.597 37.500 0.00 0.00 0.00 2.32
525 542 1.658114 GGGACACCTTGCCGTTTTC 59.342 57.895 0.00 0.00 0.00 2.29
628 645 5.954752 GGATGAGGGAGAAAAAGAAGGAAAT 59.045 40.000 0.00 0.00 0.00 2.17
789 806 1.823041 GATGAGAGGGCAAGCTGGC 60.823 63.158 3.79 3.79 42.88 4.85
790 807 0.179051 GAGATGAGAGGGCAAGCTGG 60.179 60.000 0.00 0.00 0.00 4.85
791 808 0.179051 GGAGATGAGAGGGCAAGCTG 60.179 60.000 0.00 0.00 0.00 4.24
792 809 1.344191 GGGAGATGAGAGGGCAAGCT 61.344 60.000 0.00 0.00 0.00 3.74
834 851 1.579429 CGGCTAAAGGTTGTGGTGC 59.421 57.895 0.00 0.00 0.00 5.01
876 893 4.629115 GGCCTTGTGCGTGTGTGC 62.629 66.667 0.00 0.00 42.61 4.57
909 926 3.500299 GCTCTTGTGTTCTCCTTTCCTTC 59.500 47.826 0.00 0.00 0.00 3.46
913 930 3.304324 GCAAGCTCTTGTGTTCTCCTTTC 60.304 47.826 10.86 0.00 42.31 2.62
923 940 0.032540 GGGTTTGGCAAGCTCTTGTG 59.967 55.000 13.83 0.00 42.31 3.33
1057 1075 5.026121 GGGAAAAGAGAGGGGAATGAAATT 58.974 41.667 0.00 0.00 40.93 1.82
1058 1076 4.572870 GGGGAAAAGAGAGGGGAATGAAAT 60.573 45.833 0.00 0.00 0.00 2.17
1059 1077 3.245622 GGGGAAAAGAGAGGGGAATGAAA 60.246 47.826 0.00 0.00 0.00 2.69
1060 1078 2.311841 GGGGAAAAGAGAGGGGAATGAA 59.688 50.000 0.00 0.00 0.00 2.57
1071 1089 3.572255 TGAACAAAATCCGGGGAAAAGAG 59.428 43.478 0.00 0.00 0.00 2.85
1106 1124 6.580041 CACTAACTTTATTTGAGCTTGTGCAG 59.420 38.462 0.00 0.00 42.74 4.41
1130 1149 1.071699 CCCGAACAACTTTCTCCTCCA 59.928 52.381 0.00 0.00 0.00 3.86
1191 1210 5.833082 TCAGAATATTTAGCCAGAGACGAC 58.167 41.667 0.00 0.00 0.00 4.34
1192 1211 6.656632 ATCAGAATATTTAGCCAGAGACGA 57.343 37.500 0.00 0.00 0.00 4.20
1193 1212 6.925718 TGAATCAGAATATTTAGCCAGAGACG 59.074 38.462 0.00 0.00 0.00 4.18
1258 1277 3.944015 CCAAGAACCAGAATTCAGGCTAG 59.056 47.826 16.30 3.23 0.00 3.42
1326 1346 5.818136 TGCTGCTCAAAATCCAACTATAC 57.182 39.130 0.00 0.00 0.00 1.47
1327 1347 5.221106 GCATGCTGCTCAAAATCCAACTATA 60.221 40.000 11.37 0.00 40.96 1.31
1510 1530 0.392863 CGACATGGACATGGGCTTCA 60.393 55.000 15.94 0.00 42.91 3.02
1595 1615 1.109323 AGCAGAACTTGGTGTTGGCC 61.109 55.000 0.00 0.00 39.30 5.36
1940 1960 1.162800 GGCTCATGGCATCGAAGTCC 61.163 60.000 0.00 0.00 44.01 3.85
1961 1981 3.003173 CCGGAGAAGGTGGAGCCA 61.003 66.667 0.00 0.00 40.61 4.75
2232 2252 1.002900 CGCGTGATGAAACTGTTGGTT 60.003 47.619 0.00 0.00 40.28 3.67
2375 2395 4.272991 GCTTAGCTCATTCATCACAAGAGG 59.727 45.833 0.00 0.00 0.00 3.69
2630 2650 9.863845 CCCTAAGTAAGAAGAAGTAGAAGAAAG 57.136 37.037 0.00 0.00 0.00 2.62
2703 2730 9.685276 ATATAAGATTGTCATGAACCAAAGTGA 57.315 29.630 0.00 0.00 0.00 3.41
2796 2836 5.416952 GGATTCACACTCTTGGATCACATTT 59.583 40.000 0.00 0.00 0.00 2.32
2849 2889 6.096673 ACCTTGGATAACAATTTTGGTGAC 57.903 37.500 0.00 0.00 38.65 3.67
2850 2890 7.007723 AGTACCTTGGATAACAATTTTGGTGA 58.992 34.615 0.00 0.00 38.65 4.02
2863 2903 8.008332 TCCATGTAGAATGTAGTACCTTGGATA 58.992 37.037 0.00 0.00 30.93 2.59
2871 2911 7.254795 GCATTTGGTCCATGTAGAATGTAGTAC 60.255 40.741 12.65 0.00 0.00 2.73
2899 2948 2.159071 GGAAAATGCATGCATGGCTGTA 60.159 45.455 32.79 2.83 36.68 2.74
2902 2951 1.200519 AGGAAAATGCATGCATGGCT 58.799 45.000 32.79 19.82 36.68 4.75
2903 2952 2.032680 AAGGAAAATGCATGCATGGC 57.967 45.000 32.79 22.84 36.68 4.40
2906 2955 4.020039 TCTCCAAAAGGAAAATGCATGCAT 60.020 37.500 27.46 27.46 38.46 3.96
2944 3004 5.408299 CACCTGTCGATTCAAGTTATTGACA 59.592 40.000 7.99 7.99 45.07 3.58
2949 3009 3.937814 TGCACCTGTCGATTCAAGTTAT 58.062 40.909 0.00 0.00 0.00 1.89
3024 3090 5.755861 GGCTCCTACTATGATTTTGAGTGAC 59.244 44.000 0.00 0.00 0.00 3.67
3081 3147 1.546923 TGCATGGCATCTTCACTTTGG 59.453 47.619 0.00 0.00 31.71 3.28
3280 3346 4.755411 TCTTTGACTAGTCCCTTTATGCG 58.245 43.478 20.11 0.00 0.00 4.73
3284 3350 5.783360 TGACCATCTTTGACTAGTCCCTTTA 59.217 40.000 20.11 0.00 0.00 1.85
3338 3404 1.532604 GGCCGGGAAAGGAAAAGGTG 61.533 60.000 2.18 0.00 0.00 4.00
3360 3426 6.806751 TCTATCGATCAGTGTAAAAAGAGGG 58.193 40.000 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.