Multiple sequence alignment - TraesCS3D01G100500

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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 TraesCS3D01G100500 chr3D 100.000 3148 0 0 1 3148 52885030 52881883 0.000000e+00 5814
1 TraesCS3D01G100500 chr3D 84.879 1488 184 25 774 2233 45479650 45481124 0.000000e+00 1463
2 TraesCS3D01G100500 chr5B 94.940 2233 108 5 2 2230 665194810 665197041 0.000000e+00 3493
3 TraesCS3D01G100500 chr5B 89.364 1053 95 11 3 1053 530945137 530946174 0.000000e+00 1308
4 TraesCS3D01G100500 chr6A 94.362 2235 118 8 1 2233 454860633 454862861 0.000000e+00 3422
5 TraesCS3D01G100500 chr2A 84.444 2250 308 36 1 2233 89190432 89188208 0.000000e+00 2178
6 TraesCS3D01G100500 chr2A 87.358 1060 124 8 1182 2233 89184151 89183094 0.000000e+00 1206
7 TraesCS3D01G100500 chr7A 84.542 2083 258 41 176 2233 677257535 677255492 0.000000e+00 2004
8 TraesCS3D01G100500 chr1D 82.931 2279 300 54 8 2222 21462306 21464559 0.000000e+00 1971
9 TraesCS3D01G100500 chr3B 83.606 1897 247 41 4 1882 807606021 807604171 0.000000e+00 1722
10 TraesCS3D01G100500 chr3B 91.248 1154 87 11 37 1187 710174926 710173784 0.000000e+00 1559
11 TraesCS3D01G100500 chr3B 88.769 926 90 13 2233 3148 155182322 155183243 0.000000e+00 1122
12 TraesCS3D01G100500 chr4A 91.508 1154 83 12 37 1187 347507533 347508674 0.000000e+00 1574
13 TraesCS3D01G100500 chr6D 91.033 881 70 9 2234 3107 466220260 466219382 0.000000e+00 1181
14 TraesCS3D01G100500 chr5D 89.924 923 79 12 2234 3148 477586922 477587838 0.000000e+00 1177
15 TraesCS3D01G100500 chr2D 90.190 897 75 11 2234 3121 103452743 103453635 0.000000e+00 1157
16 TraesCS3D01G100500 chr2D 88.732 923 93 10 2234 3148 105990809 105991728 0.000000e+00 1118
17 TraesCS3D01G100500 chr4B 89.286 924 80 14 2234 3148 582146732 582147645 0.000000e+00 1140
18 TraesCS3D01G100500 chr4B 85.538 650 71 10 1 642 630653782 630653148 0.000000e+00 658
19 TraesCS3D01G100500 chr7B 88.853 924 84 14 2234 3148 714568504 714569417 0.000000e+00 1118
20 TraesCS3D01G100500 chr1B 88.581 937 86 18 2224 3148 93564659 93563732 0.000000e+00 1118
21 TraesCS3D01G100500 chr2B 88.757 925 86 15 2234 3148 150920768 150921684 0.000000e+00 1116
22 TraesCS3D01G100500 chrUn 85.714 644 69 10 1 636 233312681 233313309 0.000000e+00 658
23 TraesCS3D01G100500 chr1A 88.147 464 54 1 400 863 126539127 126539589 4.590000e-153 551


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 TraesCS3D01G100500 chr3D 52881883 52885030 3147 True 5814 5814 100.000 1 3148 1 chr3D.!!$R1 3147
1 TraesCS3D01G100500 chr3D 45479650 45481124 1474 False 1463 1463 84.879 774 2233 1 chr3D.!!$F1 1459
2 TraesCS3D01G100500 chr5B 665194810 665197041 2231 False 3493 3493 94.940 2 2230 1 chr5B.!!$F2 2228
3 TraesCS3D01G100500 chr5B 530945137 530946174 1037 False 1308 1308 89.364 3 1053 1 chr5B.!!$F1 1050
4 TraesCS3D01G100500 chr6A 454860633 454862861 2228 False 3422 3422 94.362 1 2233 1 chr6A.!!$F1 2232
5 TraesCS3D01G100500 chr2A 89188208 89190432 2224 True 2178 2178 84.444 1 2233 1 chr2A.!!$R2 2232
6 TraesCS3D01G100500 chr2A 89183094 89184151 1057 True 1206 1206 87.358 1182 2233 1 chr2A.!!$R1 1051
7 TraesCS3D01G100500 chr7A 677255492 677257535 2043 True 2004 2004 84.542 176 2233 1 chr7A.!!$R1 2057
8 TraesCS3D01G100500 chr1D 21462306 21464559 2253 False 1971 1971 82.931 8 2222 1 chr1D.!!$F1 2214
9 TraesCS3D01G100500 chr3B 807604171 807606021 1850 True 1722 1722 83.606 4 1882 1 chr3B.!!$R2 1878
10 TraesCS3D01G100500 chr3B 710173784 710174926 1142 True 1559 1559 91.248 37 1187 1 chr3B.!!$R1 1150
11 TraesCS3D01G100500 chr3B 155182322 155183243 921 False 1122 1122 88.769 2233 3148 1 chr3B.!!$F1 915
12 TraesCS3D01G100500 chr4A 347507533 347508674 1141 False 1574 1574 91.508 37 1187 1 chr4A.!!$F1 1150
13 TraesCS3D01G100500 chr6D 466219382 466220260 878 True 1181 1181 91.033 2234 3107 1 chr6D.!!$R1 873
14 TraesCS3D01G100500 chr5D 477586922 477587838 916 False 1177 1177 89.924 2234 3148 1 chr5D.!!$F1 914
15 TraesCS3D01G100500 chr2D 103452743 103453635 892 False 1157 1157 90.190 2234 3121 1 chr2D.!!$F1 887
16 TraesCS3D01G100500 chr2D 105990809 105991728 919 False 1118 1118 88.732 2234 3148 1 chr2D.!!$F2 914
17 TraesCS3D01G100500 chr4B 582146732 582147645 913 False 1140 1140 89.286 2234 3148 1 chr4B.!!$F1 914
18 TraesCS3D01G100500 chr4B 630653148 630653782 634 True 658 658 85.538 1 642 1 chr4B.!!$R1 641
19 TraesCS3D01G100500 chr7B 714568504 714569417 913 False 1118 1118 88.853 2234 3148 1 chr7B.!!$F1 914
20 TraesCS3D01G100500 chr1B 93563732 93564659 927 True 1118 1118 88.581 2224 3148 1 chr1B.!!$R1 924
21 TraesCS3D01G100500 chr2B 150920768 150921684 916 False 1116 1116 88.757 2234 3148 1 chr2B.!!$F1 914
22 TraesCS3D01G100500 chrUn 233312681 233313309 628 False 658 658 85.714 1 636 1 chrUn.!!$F1 635

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
47 48 1.078918 CCAGCTTCGCCTCACATCA 60.079 57.895 0.00 0.00 0.0 3.07 F
163 165 1.621814 ACCTTGTTCGATTCCTCGGAA 59.378 47.619 0.11 0.11 45.1 4.30 F
1928 2038 1.952990 CCCACATATTTATGGCGCACA 59.047 47.619 10.83 5.20 38.0 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1273 1372 1.684734 CCACCGGCCTAGTACCAGT 60.685 63.158 0.0 0.0 0.00 4.00 R
2123 2264 0.107214 ACGACATATGGGGTTGCCTG 60.107 55.000 7.8 0.0 0.00 4.85 R
3100 3282 0.036388 TCCGACATTGGAGCTTGGAC 60.036 55.000 0.0 0.0 33.05 4.02 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
47 48 1.078918 CCAGCTTCGCCTCACATCA 60.079 57.895 0.00 0.00 0.00 3.07
79 80 1.635817 GCCAAGACTCCTGCCCCATA 61.636 60.000 0.00 0.00 0.00 2.74
102 103 4.361971 TCACTCGAGCCTCCCCGT 62.362 66.667 13.61 0.00 0.00 5.28
163 165 1.621814 ACCTTGTTCGATTCCTCGGAA 59.378 47.619 0.11 0.11 45.10 4.30
183 193 2.370281 TTTTCTCACTCGCTAGGCTG 57.630 50.000 0.00 0.00 0.00 4.85
199 214 3.118531 AGGCTGTCCCATCTACTGAATT 58.881 45.455 0.00 0.00 35.39 2.17
279 296 5.643379 AATTGCGGCTCTATTTTTGAAGA 57.357 34.783 0.00 0.00 0.00 2.87
289 306 6.152638 TCTATTTTTGAAGATCCCCAACCT 57.847 37.500 0.00 0.00 0.00 3.50
293 310 3.439857 TTGAAGATCCCCAACCTTGAG 57.560 47.619 0.00 0.00 0.00 3.02
294 311 2.631384 TGAAGATCCCCAACCTTGAGA 58.369 47.619 0.00 0.00 0.00 3.27
402 423 8.689061 TCCTTCAGATGGATGAAAATTGTTATG 58.311 33.333 0.65 0.00 38.66 1.90
591 630 7.979537 GCTAAATTTGTTAGGATTACCCCTTTG 59.020 37.037 0.00 0.00 37.74 2.77
669 710 6.550481 TGCAGCCTAAATTCCATGATTCAATA 59.450 34.615 0.00 0.00 0.00 1.90
696 737 5.773176 ACAAAATTCCTTCGTAATTGTCCCT 59.227 36.000 0.00 0.00 0.00 4.20
783 850 4.226394 TCCTGGCACCAAGCTTACTTATTA 59.774 41.667 0.00 0.00 44.79 0.98
804 876 3.468770 ACAATACCATGCGCCGTATTTA 58.531 40.909 17.19 0.00 33.84 1.40
1046 1139 2.689983 TGCAGAGTCGATATTCAGCTGA 59.310 45.455 13.74 13.74 0.00 4.26
1105 1203 3.288809 GGAAAGACCTCATTTGCACAC 57.711 47.619 0.00 0.00 35.41 3.82
1150 1249 2.291209 TGGCAAATTCTCAGCTCCAA 57.709 45.000 0.00 0.00 0.00 3.53
1170 1269 4.166919 CCAAAGGGTCTCCTAGAATGGATT 59.833 45.833 0.00 0.00 44.07 3.01
1183 1282 5.110814 AGAATGGATTGTTGACCGGATTA 57.889 39.130 9.46 0.00 0.00 1.75
1323 1422 3.380637 GCAAGCATGAAGAATCACCTCAT 59.619 43.478 0.00 0.00 38.69 2.90
1576 1675 7.609146 AGCAAATTCTCAAAGATGTCATGTCTA 59.391 33.333 0.00 0.00 0.00 2.59
1580 1679 5.423015 TCTCAAAGATGTCATGTCTAAGGC 58.577 41.667 0.00 0.00 0.00 4.35
1905 2014 4.678044 CGCTGATAAAAGTAGACTGAGCCA 60.678 45.833 0.00 0.00 0.00 4.75
1928 2038 1.952990 CCCACATATTTATGGCGCACA 59.047 47.619 10.83 5.20 38.00 4.57
2139 2280 0.552848 CCTCAGGCAACCCCATATGT 59.447 55.000 1.24 0.00 35.39 2.29
2264 2405 0.974010 AACCGGCAGATCTCGGGTAA 60.974 55.000 22.66 0.00 45.54 2.85
2373 2515 5.807011 CCCTAAATGCTGCTTTTGATTGTAC 59.193 40.000 19.95 0.00 0.00 2.90
2381 2523 6.206438 TGCTGCTTTTGATTGTACTTGATGTA 59.794 34.615 0.00 0.00 0.00 2.29
2477 2627 7.066404 GTCATAATGATCTATCGACTAGCCTGA 59.934 40.741 0.00 0.00 0.00 3.86
2517 2667 3.460825 ACCAGAGGCCTAGGATAACAAA 58.539 45.455 26.29 0.00 0.00 2.83
2538 2688 0.940126 GTCCTAGTCGAATACGCCGA 59.060 55.000 0.00 0.00 39.58 5.54
2555 2706 1.529309 GATGGGGAGGAGTCCTTGC 59.471 63.158 14.41 0.53 43.36 4.01
2622 2774 1.746615 CCGAACTGGCCCATGAGTG 60.747 63.158 0.00 0.00 0.00 3.51
2637 2789 3.404438 GTGTACGGCCATGGGGGA 61.404 66.667 15.13 0.00 40.01 4.81
2668 2820 1.141881 CCAACTGATCGGGAGACGG 59.858 63.158 6.47 0.00 44.82 4.79
2730 2883 3.072476 CCCCTGAACCAGTCTTCAAGTTA 59.928 47.826 0.00 0.00 29.66 2.24
2804 2958 8.093927 TCTTGAAAACTGGTTCAACAAATCTTT 58.906 29.630 5.09 0.00 41.45 2.52
2805 2959 7.826260 TGAAAACTGGTTCAACAAATCTTTC 57.174 32.000 0.00 0.00 34.59 2.62
2806 2960 6.816140 TGAAAACTGGTTCAACAAATCTTTCC 59.184 34.615 0.00 0.00 34.59 3.13
2857 3011 3.928727 ATCCGAAGAGTTTACACGTCA 57.071 42.857 0.00 0.00 0.00 4.35
2950 3107 4.595538 AGTGTTTCCGTGCGGCGA 62.596 61.111 12.98 0.00 44.77 5.54
2961 3118 4.194720 GCGGCGATGTCCTCTCGT 62.195 66.667 12.98 0.00 38.37 4.18
2984 3141 1.642037 CGAGCTCCAACGTCGGACTA 61.642 60.000 8.47 0.00 0.00 2.59
3002 3159 7.977853 GTCGGACTACATTTGAGGTATCTTTTA 59.022 37.037 0.00 0.00 0.00 1.52
3019 3176 2.372040 TTACAGCCGAGCACCAACGT 62.372 55.000 0.00 0.00 0.00 3.99
3076 3257 0.754217 AGCTCCAACGCCGGACTATA 60.754 55.000 5.05 0.00 0.00 1.31
3096 3278 2.278013 CGAGCTCTAACGCCGGAC 60.278 66.667 12.85 0.00 0.00 4.79
3098 3280 1.434622 CGAGCTCTAACGCCGGACTA 61.435 60.000 12.85 0.00 0.00 2.59
3100 3282 0.669077 AGCTCTAACGCCGGACTATG 59.331 55.000 5.05 0.00 0.00 2.23
3115 3297 3.878778 GACTATGTCCAAGCTCCAATGT 58.121 45.455 0.00 0.00 0.00 2.71
3127 3309 2.101582 GCTCCAATGTCGGACTGTATCT 59.898 50.000 9.88 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 0.044855 AGGAACTATGGGGCAGGAGT 59.955 55.000 0.00 0.00 36.02 3.85
102 103 2.358372 TGGTAGCCATGCTGCTCGA 61.358 57.895 0.00 0.00 41.68 4.04
163 165 2.234908 ACAGCCTAGCGAGTGAGAAAAT 59.765 45.455 0.00 0.00 0.00 1.82
183 193 3.209410 CAGCCAATTCAGTAGATGGGAC 58.791 50.000 0.00 0.00 33.45 4.46
199 214 1.998444 AATCGATGGGGATGCAGCCA 61.998 55.000 24.75 2.71 0.00 4.75
279 296 2.225117 CCTTTGTCTCAAGGTTGGGGAT 60.225 50.000 0.00 0.00 0.00 3.85
289 306 3.146066 GGTGCACATACCTTTGTCTCAA 58.854 45.455 20.43 0.00 37.74 3.02
402 423 0.885196 TAGGCCGGCAATGAACAAAC 59.115 50.000 30.85 6.30 0.00 2.93
591 630 4.741321 TTGATGGAAGCATGGAAATTCC 57.259 40.909 4.79 4.79 42.38 3.01
648 689 8.196771 TGTGTTATTGAATCATGGAATTTAGGC 58.803 33.333 0.00 0.00 0.00 3.93
669 710 6.921307 GGACAATTACGAAGGAATTTTGTGTT 59.079 34.615 0.00 0.00 35.06 3.32
783 850 1.961793 AATACGGCGCATGGTATTGT 58.038 45.000 22.00 6.82 37.79 2.71
804 876 6.258727 CAGAAGCACGAAAATATGGACACTAT 59.741 38.462 0.00 0.00 0.00 2.12
879 964 7.615365 TCTGGAATTAGTTGTATGGAAGCAATT 59.385 33.333 0.00 0.00 0.00 2.32
1046 1139 8.045720 ACCCTTGACAATATCATGTAACCTAT 57.954 34.615 0.00 0.00 37.11 2.57
1132 1231 2.094338 CCTTTGGAGCTGAGAATTTGCC 60.094 50.000 0.00 0.00 0.00 4.52
1150 1249 4.375313 ACAATCCATTCTAGGAGACCCTT 58.625 43.478 0.00 0.00 40.78 3.95
1170 1269 3.536548 CGGGTTAATCCGGTCAACA 57.463 52.632 19.83 0.00 45.78 3.33
1183 1282 3.344515 GAAATTCACCTAGCTTCGGGTT 58.655 45.455 0.00 0.00 32.95 4.11
1273 1372 1.684734 CCACCGGCCTAGTACCAGT 60.685 63.158 0.00 0.00 0.00 4.00
1323 1422 5.130292 AGTCCGTTTTGTAGAATTCTCGA 57.870 39.130 12.24 1.14 0.00 4.04
1576 1675 3.963129 TCTTTTGGAATGTATCGGCCTT 58.037 40.909 0.00 0.00 0.00 4.35
1580 1679 6.985188 TCTTCTTCTTTTGGAATGTATCGG 57.015 37.500 0.00 0.00 33.01 4.18
1905 2014 3.027412 TGCGCCATAAATATGTGGGTTT 58.973 40.909 4.18 0.00 38.22 3.27
1928 2038 6.487331 TCATAATTTGTTGTGTCTTACCGGTT 59.513 34.615 15.04 0.00 0.00 4.44
2123 2264 0.107214 ACGACATATGGGGTTGCCTG 60.107 55.000 7.80 0.00 0.00 4.85
2139 2280 2.563620 TGGTAGATTGGCACTACAACGA 59.436 45.455 14.84 0.00 41.08 3.85
2264 2405 2.520968 GCACAACTTGGGACCCCT 59.479 61.111 8.45 0.00 36.94 4.79
2336 2478 6.091441 GCAGCATTTAGGGTATTATCTCTTCG 59.909 42.308 0.00 0.00 0.00 3.79
2354 2496 6.088016 TCAAGTACAATCAAAAGCAGCATT 57.912 33.333 0.00 0.00 0.00 3.56
2381 2523 7.093727 CGGGGTAGATCAACTCTGTAATCATAT 60.094 40.741 0.00 0.00 35.28 1.78
2477 2627 6.014647 TCTGGTATGTTATATAAGCCGAGGT 58.985 40.000 0.00 0.00 0.00 3.85
2517 2667 1.332997 CGGCGTATTCGACTAGGACTT 59.667 52.381 0.00 0.00 43.80 3.01
2538 2688 2.003548 GGCAAGGACTCCTCCCCAT 61.004 63.158 0.00 0.00 37.25 4.00
2622 2774 4.185286 GGTCCCCCATGGCCGTAC 62.185 72.222 6.09 1.09 0.00 3.67
2637 2789 0.615544 CAGTTGGATTGGGCCATGGT 60.616 55.000 14.67 0.00 37.86 3.55
2640 2792 1.751733 CGATCAGTTGGATTGGGCCAT 60.752 52.381 7.26 0.00 37.86 4.40
2804 2958 3.032265 TCCTCAAGATCGAAGATGGGA 57.968 47.619 0.00 0.00 45.12 4.37
2805 2959 4.063689 CAATCCTCAAGATCGAAGATGGG 58.936 47.826 0.00 0.00 45.12 4.00
2806 2960 3.497640 GCAATCCTCAAGATCGAAGATGG 59.502 47.826 0.00 0.00 45.12 3.51
2857 3011 1.962570 AAGGGGCTCCTCGGATACCT 61.963 60.000 5.00 0.00 44.07 3.08
2961 3118 1.725665 CGACGTTGGAGCTCGGATA 59.274 57.895 7.83 0.00 0.00 2.59
2984 3141 5.354234 CGGCTGTAAAAGATACCTCAAATGT 59.646 40.000 0.00 0.00 0.00 2.71
3002 3159 4.235762 ACGTTGGTGCTCGGCTGT 62.236 61.111 0.00 0.00 0.00 4.40
3076 3257 2.722487 CGGCGTTAGAGCTCGGAT 59.278 61.111 8.37 0.00 37.29 4.18
3085 3266 3.564455 GGACATAGTCCGGCGTTAG 57.436 57.895 6.01 0.00 43.14 2.34
3096 3278 2.868583 CGACATTGGAGCTTGGACATAG 59.131 50.000 0.00 0.00 0.00 2.23
3098 3280 1.679944 CCGACATTGGAGCTTGGACAT 60.680 52.381 0.00 0.00 0.00 3.06
3100 3282 0.036388 TCCGACATTGGAGCTTGGAC 60.036 55.000 0.00 0.00 33.05 4.02
3104 3286 0.687354 ACAGTCCGACATTGGAGCTT 59.313 50.000 0.40 0.00 39.14 3.74
3113 3295 2.092323 CACCTCAGATACAGTCCGACA 58.908 52.381 0.40 0.00 0.00 4.35
3115 3297 2.290705 TGACACCTCAGATACAGTCCGA 60.291 50.000 0.00 0.00 0.00 4.55


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

AutoCloner maintained by Alex Coulton.