Multiple sequence alignment - TraesCS7B01G285500

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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 TraesCS7B01G285500 chr7B 100.000 3440 0 0 1 3440 519783422 519786861 0 6353
1 TraesCS7B01G285500 chr7A 95.813 3463 92 23 1 3440 557552802 557556234 0 5542
2 TraesCS7B01G285500 chr7D 95.418 3470 89 30 1 3440 491245683 491249112 0 5463


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 TraesCS7B01G285500 chr7B 519783422 519786861 3439 False 6353 6353 100.000 1 3440 1 chr7B.!!$F1 3439
1 TraesCS7B01G285500 chr7A 557552802 557556234 3432 False 5542 5542 95.813 1 3440 1 chr7A.!!$F1 3439
2 TraesCS7B01G285500 chr7D 491245683 491249112 3429 False 5463 5463 95.418 1 3440 1 chr7D.!!$F1 3439

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
950 977 0.323542 GTCTTCTCCTCCACCTCCGA 60.324 60.0 0.0 0.0 0.00 4.55 F
1050 1077 0.027063 CCGACACCGACAACAACAAC 59.973 55.0 0.0 0.0 38.22 3.32 F
1672 1699 0.321653 CCACCTCCCTTTCCACTTCG 60.322 60.0 0.0 0.0 0.00 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2316 2343 0.037160 ATGCATGCACAGACCACAGA 59.963 50.0 25.37 0.00 0.00 3.41 R
2317 2344 0.170339 CATGCATGCACAGACCACAG 59.830 55.0 25.37 0.69 0.00 3.66 R
2620 2649 0.677288 ATGCGATCCCCATGCATTTG 59.323 50.0 0.00 0.00 46.55 2.32 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
52 53 4.032703 TGCAGTGAGCTGAAAAGTTTTC 57.967 40.909 19.44 19.44 45.28 2.29
53 54 3.696051 TGCAGTGAGCTGAAAAGTTTTCT 59.304 39.130 24.81 8.77 45.28 2.52
69 70 5.880341 AGTTTTCTTTTTGTTGAGGACTCG 58.120 37.500 0.00 0.00 0.00 4.18
84 85 7.624360 TGAGGACTCGTAAATGCATATTTTT 57.376 32.000 0.00 0.00 37.64 1.94
110 111 7.845037 TCAATCGCTCCATTAGATCATCTTAT 58.155 34.615 0.00 0.00 0.00 1.73
131 132 8.637099 TCTTATGACATTAGAGTGATTCTCCAG 58.363 37.037 0.00 0.00 43.71 3.86
190 197 5.725362 AGCTTAGCGAGACTTAACAGATTT 58.275 37.500 0.00 0.00 0.00 2.17
197 204 5.614887 GCGAGACTTAACAGATTTTGTGGTC 60.615 44.000 0.00 0.00 40.74 4.02
202 209 7.173907 AGACTTAACAGATTTTGTGGTCAGATG 59.826 37.037 0.00 0.00 40.74 2.90
388 395 1.202533 GCCGATCTAAAGCTGCCACTA 60.203 52.381 0.00 0.00 0.00 2.74
432 445 4.036971 GCAGCAACTAGTAGCTAAGCTCTA 59.963 45.833 0.00 0.00 39.50 2.43
651 672 3.007635 GTGCCGAGCAAAATACCTACTT 58.992 45.455 0.00 0.00 41.47 2.24
706 727 2.093764 GCATCTAGTAGGCTATGGCTGG 60.094 54.545 0.00 0.00 39.30 4.85
950 977 0.323542 GTCTTCTCCTCCACCTCCGA 60.324 60.000 0.00 0.00 0.00 4.55
1050 1077 0.027063 CCGACACCGACAACAACAAC 59.973 55.000 0.00 0.00 38.22 3.32
1051 1078 0.722282 CGACACCGACAACAACAACA 59.278 50.000 0.00 0.00 38.22 3.33
1052 1079 1.128878 CGACACCGACAACAACAACAA 59.871 47.619 0.00 0.00 38.22 2.83
1053 1080 2.511879 GACACCGACAACAACAACAAC 58.488 47.619 0.00 0.00 0.00 3.32
1054 1081 1.880675 ACACCGACAACAACAACAACA 59.119 42.857 0.00 0.00 0.00 3.33
1055 1082 2.293677 ACACCGACAACAACAACAACAA 59.706 40.909 0.00 0.00 0.00 2.83
1056 1083 2.659279 CACCGACAACAACAACAACAAC 59.341 45.455 0.00 0.00 0.00 3.32
1057 1084 2.293677 ACCGACAACAACAACAACAACA 59.706 40.909 0.00 0.00 0.00 3.33
1058 1085 3.243434 ACCGACAACAACAACAACAACAA 60.243 39.130 0.00 0.00 0.00 2.83
1244 1271 3.299190 GATCCTCCTCTCCGCGGG 61.299 72.222 27.83 16.54 0.00 6.13
1630 1657 1.005394 CTTCGTACAGGCAACCGGT 60.005 57.895 0.00 0.00 35.79 5.28
1672 1699 0.321653 CCACCTCCCTTTCCACTTCG 60.322 60.000 0.00 0.00 0.00 3.79
2318 2345 4.856607 GCGCGCGCCTTCTACTCT 62.857 66.667 42.83 0.00 34.56 3.24
2319 2346 2.951745 CGCGCGCCTTCTACTCTG 60.952 66.667 27.72 2.72 0.00 3.35
2320 2347 2.182030 GCGCGCCTTCTACTCTGT 59.818 61.111 23.24 0.00 0.00 3.41
2321 2348 2.161486 GCGCGCCTTCTACTCTGTG 61.161 63.158 23.24 0.00 0.00 3.66
2322 2349 1.517257 CGCGCCTTCTACTCTGTGG 60.517 63.158 0.00 0.00 0.00 4.17
2577 2606 4.202398 TGTTAATTTTTCATTGGCTGCCCA 60.202 37.500 17.53 5.33 40.06 5.36
2677 2708 1.884235 ACTTGTGAGGCTGCTACAAC 58.116 50.000 11.50 2.28 31.64 3.32
2722 2753 8.166422 TCTATTTTTCCTCTTTCTTGGTTGTC 57.834 34.615 0.00 0.00 0.00 3.18
2754 2785 4.748600 GCTTAGTTCGTGTTGGAGTAAAGT 59.251 41.667 0.00 0.00 0.00 2.66
2759 2790 7.008440 AGTTCGTGTTGGAGTAAAGTTTTAC 57.992 36.000 6.65 6.65 42.50 2.01
2772 2803 7.570161 AGTAAAGTTTTACGGAGATTTTGTCG 58.430 34.615 8.62 0.00 45.77 4.35
2861 2892 4.031418 TGCTTCTGTTCACAACACATTG 57.969 40.909 0.00 0.00 41.98 2.82
2867 2898 2.692041 TGTTCACAACACATTGCCATGA 59.308 40.909 4.52 0.00 39.66 3.07
2906 2937 4.082081 TGTGATCTTGCAAAATGGATCCAC 60.082 41.667 18.99 16.39 35.18 4.02
2907 2938 3.448301 TGATCTTGCAAAATGGATCCACC 59.552 43.478 18.99 3.96 35.18 4.61
2987 3023 9.249053 TCATTTGTATAGTTAATTTCTTGGGCA 57.751 29.630 0.00 0.00 0.00 5.36
3034 3070 2.223595 GCTCTATAGCTCACTTGCACGA 60.224 50.000 0.00 0.00 45.85 4.35
3039 3075 2.375766 GCTCACTTGCACGACCTCG 61.376 63.158 0.00 0.00 46.33 4.63
3075 3111 6.698008 TCTGACATTTGACTTGAATGTTGT 57.302 33.333 4.23 0.00 45.11 3.32
3090 3126 1.950216 TGTTGTTGCTTGATGCCGTTA 59.050 42.857 0.00 0.00 42.00 3.18
3095 3131 2.276472 TGCTTGATGCCGTTATTTGC 57.724 45.000 0.00 0.00 42.00 3.68
3132 3168 4.402851 TGCTTTGCCCAGCACTAG 57.597 55.556 2.83 0.00 45.14 2.57
3228 3264 6.437928 CAACTTGCAGCAGTCTAACAAATTA 58.562 36.000 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 4.454728 AAACTTTTCAGCTCACTGCAAA 57.545 36.364 0.00 0.00 44.10 3.68
30 31 4.158394 AGAAAACTTTTCAGCTCACTGCAA 59.842 37.500 15.17 0.00 44.10 4.08
31 32 3.696051 AGAAAACTTTTCAGCTCACTGCA 59.304 39.130 15.17 0.00 44.10 4.41
34 35 7.154656 ACAAAAAGAAAACTTTTCAGCTCACT 58.845 30.769 15.17 0.00 35.72 3.41
52 53 5.625311 GCATTTACGAGTCCTCAACAAAAAG 59.375 40.000 0.00 0.00 0.00 2.27
53 54 5.066634 TGCATTTACGAGTCCTCAACAAAAA 59.933 36.000 0.00 0.00 0.00 1.94
59 60 7.624360 AAAATATGCATTTACGAGTCCTCAA 57.376 32.000 3.54 0.00 33.09 3.02
60 61 7.624360 AAAAATATGCATTTACGAGTCCTCA 57.376 32.000 3.54 0.00 33.09 3.86
84 85 6.106648 AGATGATCTAATGGAGCGATTGAA 57.893 37.500 0.00 0.00 32.20 2.69
85 86 5.735285 AGATGATCTAATGGAGCGATTGA 57.265 39.130 0.00 0.00 32.20 2.57
86 87 7.763071 TCATAAGATGATCTAATGGAGCGATTG 59.237 37.037 0.00 0.00 33.59 2.67
110 111 7.904558 ATACTGGAGAATCACTCTAATGTCA 57.095 36.000 0.00 0.00 44.37 3.58
151 152 5.145059 GCTAAGCTTTTGACGGTTTAACTC 58.855 41.667 3.20 0.00 0.00 3.01
152 153 4.319261 CGCTAAGCTTTTGACGGTTTAACT 60.319 41.667 3.20 0.00 0.00 2.24
153 154 3.904234 CGCTAAGCTTTTGACGGTTTAAC 59.096 43.478 3.20 0.00 0.00 2.01
190 197 3.676049 GCGTCTATCACATCTGACCACAA 60.676 47.826 0.00 0.00 0.00 3.33
197 204 5.536554 AAAACTTGCGTCTATCACATCTG 57.463 39.130 0.00 0.00 0.00 2.90
202 209 8.813643 ATATAGGTAAAACTTGCGTCTATCAC 57.186 34.615 0.00 0.00 0.00 3.06
226 233 9.653516 TTTTGAGGTGATTCTCTCTCTCTATAT 57.346 33.333 8.35 0.00 34.98 0.86
231 238 6.226787 TGTTTTTGAGGTGATTCTCTCTCTC 58.773 40.000 8.35 0.00 34.98 3.20
235 242 7.651808 TCAAATGTTTTTGAGGTGATTCTCTC 58.348 34.615 0.00 0.00 44.81 3.20
432 445 1.112113 ATGGACGAGGTTCATACGCT 58.888 50.000 0.00 0.00 28.71 5.07
651 672 1.648568 ACAGATGAGAGAGGGAGGGAA 59.351 52.381 0.00 0.00 0.00 3.97
706 727 5.107453 CCAGCTACGCTACTACAAATAATGC 60.107 44.000 0.00 0.00 36.40 3.56
1050 1077 1.470699 CGGCGTTGCTGTTGTTGTTG 61.471 55.000 0.00 0.00 0.00 3.33
1051 1078 1.226547 CGGCGTTGCTGTTGTTGTT 60.227 52.632 0.00 0.00 0.00 2.83
1052 1079 2.109739 TCGGCGTTGCTGTTGTTGT 61.110 52.632 6.85 0.00 36.18 3.32
1053 1080 1.654137 GTCGGCGTTGCTGTTGTTG 60.654 57.895 6.85 0.00 36.18 3.33
1054 1081 2.713154 GTCGGCGTTGCTGTTGTT 59.287 55.556 6.85 0.00 36.18 2.83
1055 1082 3.276846 GGTCGGCGTTGCTGTTGT 61.277 61.111 6.85 0.00 36.18 3.32
1056 1083 2.954753 GAGGTCGGCGTTGCTGTTG 61.955 63.158 6.85 0.00 36.18 3.33
1057 1084 2.665185 GAGGTCGGCGTTGCTGTT 60.665 61.111 6.85 0.00 36.18 3.16
1058 1085 3.865929 CTGAGGTCGGCGTTGCTGT 62.866 63.158 6.85 0.00 36.18 4.40
2316 2343 0.037160 ATGCATGCACAGACCACAGA 59.963 50.000 25.37 0.00 0.00 3.41
2317 2344 0.170339 CATGCATGCACAGACCACAG 59.830 55.000 25.37 0.69 0.00 3.66
2318 2345 2.259281 CATGCATGCACAGACCACA 58.741 52.632 25.37 0.00 0.00 4.17
2340 2367 2.879462 CTGTTCGTAGTCGCCGGC 60.879 66.667 19.07 19.07 36.96 6.13
2577 2606 7.833285 ATCAACAGTAAATAACCAACCAACT 57.167 32.000 0.00 0.00 0.00 3.16
2609 2638 3.055963 CCCATGCATTTGTAAGCTTTCCA 60.056 43.478 3.20 0.00 0.00 3.53
2620 2649 0.677288 ATGCGATCCCCATGCATTTG 59.323 50.000 0.00 0.00 46.55 2.32
2722 2753 2.993899 ACACGAACTAAGCGAGAAATGG 59.006 45.455 0.00 0.00 0.00 3.16
2754 2785 8.657074 ATCATATCGACAAAATCTCCGTAAAA 57.343 30.769 0.00 0.00 0.00 1.52
2759 2790 6.530913 ACAATCATATCGACAAAATCTCCG 57.469 37.500 0.00 0.00 0.00 4.63
2772 2803 6.294176 GGTGCATTAGGTCCAACAATCATATC 60.294 42.308 0.00 0.00 0.00 1.63
2816 2847 3.993920 AGCAACAAATCCGCAAAATTCT 58.006 36.364 0.00 0.00 0.00 2.40
2861 2892 7.227314 TCACACATCTCACTTAAATATCATGGC 59.773 37.037 0.00 0.00 0.00 4.40
2867 2898 8.834465 GCAAGATCACACATCTCACTTAAATAT 58.166 33.333 0.00 0.00 0.00 1.28
2906 2937 2.393764 GTGGTCGCAAAAAGTTCATGG 58.606 47.619 0.00 0.00 0.00 3.66
2907 2938 2.223688 TGGTGGTCGCAAAAAGTTCATG 60.224 45.455 0.00 0.00 0.00 3.07
2908 2939 2.028130 TGGTGGTCGCAAAAAGTTCAT 58.972 42.857 0.00 0.00 0.00 2.57
2909 2940 1.464734 TGGTGGTCGCAAAAAGTTCA 58.535 45.000 0.00 0.00 0.00 3.18
2910 2941 2.570442 TTGGTGGTCGCAAAAAGTTC 57.430 45.000 0.00 0.00 0.00 3.01
2911 2942 3.535280 AATTGGTGGTCGCAAAAAGTT 57.465 38.095 0.00 0.00 0.00 2.66
2913 2944 6.538189 AAAATAATTGGTGGTCGCAAAAAG 57.462 33.333 0.00 0.00 0.00 2.27
2987 3023 2.729132 AGATCCTCCTCCTGATCTCCAT 59.271 50.000 0.00 0.00 43.15 3.41
3055 3091 5.750067 AGCAACAACATTCAAGTCAAATGTC 59.250 36.000 2.29 0.00 44.44 3.06
3090 3126 9.184062 CACGCATGATTAGTTATAAATGCAAAT 57.816 29.630 14.66 0.19 36.72 2.32
3095 3131 8.684655 CAAAGCACGCATGATTAGTTATAAATG 58.315 33.333 0.00 0.00 31.79 2.32
3132 3168 6.673154 AAATAACGGACACTAGTTTATGGC 57.327 37.500 0.00 0.00 0.00 4.40
3251 3287 7.668525 AACACTAGGTTTGTTAGCATCTTAC 57.331 36.000 0.00 0.00 35.82 2.34
3330 3367 1.742308 AGAACACAAGCCCCCTTCTA 58.258 50.000 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.