Multiple sequence alignment - TraesCS5D01G276000

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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 TraesCS5D01G276000 chr5D 100.000 3486 0 0 1 3486 378821656 378818171 0.000000e+00 6438
1 TraesCS5D01G276000 chr2B 95.903 3490 130 8 1 3486 352036640 352040120 0.000000e+00 5640
2 TraesCS5D01G276000 chr2B 95.370 108 5 0 1 108 85868472 85868365 4.630000e-39 172
3 TraesCS5D01G276000 chr6B 95.757 3488 137 6 1 3486 628273441 628269963 0.000000e+00 5611
4 TraesCS5D01G276000 chr6B 98.000 150 3 0 3229 3378 360712037 360711888 9.600000e-66 261
5 TraesCS5D01G276000 chr6B 100.000 114 0 0 3373 3486 360712471 360712358 9.800000e-51 211
6 TraesCS5D01G276000 chr3B 95.300 3489 147 10 1 3486 355963559 355960085 0.000000e+00 5518
7 TraesCS5D01G276000 chr3B 95.737 3237 126 8 1 3234 402665454 402668681 0.000000e+00 5203
8 TraesCS5D01G276000 chr1B 96.753 3234 102 3 1 3231 425399402 425402635 0.000000e+00 5387
9 TraesCS5D01G276000 chr1B 95.269 3192 129 13 52 3234 555898136 555894958 0.000000e+00 5038
10 TraesCS5D01G276000 chr1B 99.333 150 1 0 3229 3378 112026348 112026497 4.430000e-69 272
11 TraesCS5D01G276000 chr1B 98.000 150 3 0 3229 3378 425402820 425402969 9.600000e-66 261
12 TraesCS5D01G276000 chr1B 99.123 114 1 0 3373 3486 425402387 425402500 4.560000e-49 206
13 TraesCS5D01G276000 chr7B 95.675 3237 127 9 1 3234 365271401 365268175 0.000000e+00 5190
14 TraesCS5D01G276000 chr7B 94.823 3187 148 10 56 3234 33969144 33972321 0.000000e+00 4955
15 TraesCS5D01G276000 chr7B 98.000 150 3 0 3229 3378 365267992 365267843 9.600000e-66 261
16 TraesCS5D01G276000 chr7B 99.123 114 1 0 3373 3486 214356694 214356807 4.560000e-49 206
17 TraesCS5D01G276000 chr4B 94.795 3189 154 8 50 3234 425954059 425950879 0.000000e+00 4959
18 TraesCS5D01G276000 chr4B 98.000 150 3 0 3229 3378 379331667 379331518 9.600000e-66 261
19 TraesCS5D01G276000 chr4B 99.123 114 1 0 3373 3486 379332104 379331991 4.560000e-49 206
20 TraesCS5D01G276000 chr4B 99.123 114 1 0 3373 3486 485280310 485280423 4.560000e-49 206
21 TraesCS5D01G276000 chr7D 98.000 150 3 0 3229 3378 341108938 341109087 9.600000e-66 261
22 TraesCS5D01G276000 chr3D 99.123 114 1 0 3373 3486 428374928 428375041 4.560000e-49 206


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 TraesCS5D01G276000 chr5D 378818171 378821656 3485 True 6438.000000 6438 100.000000 1 3486 1 chr5D.!!$R1 3485
1 TraesCS5D01G276000 chr2B 352036640 352040120 3480 False 5640.000000 5640 95.903000 1 3486 1 chr2B.!!$F1 3485
2 TraesCS5D01G276000 chr6B 628269963 628273441 3478 True 5611.000000 5611 95.757000 1 3486 1 chr6B.!!$R1 3485
3 TraesCS5D01G276000 chr6B 360711888 360712471 583 True 236.000000 261 99.000000 3229 3486 2 chr6B.!!$R2 257
4 TraesCS5D01G276000 chr3B 355960085 355963559 3474 True 5518.000000 5518 95.300000 1 3486 1 chr3B.!!$R1 3485
5 TraesCS5D01G276000 chr3B 402665454 402668681 3227 False 5203.000000 5203 95.737000 1 3234 1 chr3B.!!$F1 3233
6 TraesCS5D01G276000 chr1B 555894958 555898136 3178 True 5038.000000 5038 95.269000 52 3234 1 chr1B.!!$R1 3182
7 TraesCS5D01G276000 chr1B 425399402 425402969 3567 False 1951.333333 5387 97.958667 1 3486 3 chr1B.!!$F2 3485
8 TraesCS5D01G276000 chr7B 33969144 33972321 3177 False 4955.000000 4955 94.823000 56 3234 1 chr7B.!!$F1 3178
9 TraesCS5D01G276000 chr7B 365267843 365271401 3558 True 2725.500000 5190 96.837500 1 3378 2 chr7B.!!$R1 3377
10 TraesCS5D01G276000 chr4B 425950879 425954059 3180 True 4959.000000 4959 94.795000 50 3234 1 chr4B.!!$R1 3184
11 TraesCS5D01G276000 chr4B 379331518 379332104 586 True 233.500000 261 98.561500 3229 3486 2 chr4B.!!$R2 257


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
701 712 2.860735 GCAGATCGTAAGTACAGCTTGG 59.139 50.0 0.0 0.0 38.05 3.61 F
2255 2280 0.673644 CGACTCCTTGGCCGATGTTT 60.674 55.0 0.0 0.0 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2306 2331 1.152756 ACAGTTTGTGGTCTGCCCC 60.153 57.895 0.00 0.00 35.37 5.80 R
3117 3153 3.766051 GGGAATGTGAATTGAAGCTTCCT 59.234 43.478 23.42 8.36 32.98 3.36 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
380 387 3.775202 TGTGACACCAAATTTCAAACCG 58.225 40.909 2.45 0.00 0.00 4.44
432 439 7.058023 TCACACAGTACTAAACCATAAGTGT 57.942 36.000 0.00 0.00 38.11 3.55
701 712 2.860735 GCAGATCGTAAGTACAGCTTGG 59.139 50.000 0.00 0.00 38.05 3.61
1068 1083 1.153745 GAGCAGCAACCTCGTCGAT 60.154 57.895 0.00 0.00 0.00 3.59
1183 1198 2.811317 CAGACAAGGCCGACGAGC 60.811 66.667 0.00 0.00 0.00 5.03
1245 1260 3.489229 CGAGCTTCATCGGAGTTGATGTA 60.489 47.826 3.90 0.00 44.82 2.29
1431 1446 6.884280 AACTTGTTTCCCAACTAGATGAAG 57.116 37.500 0.79 0.00 37.81 3.02
1436 1451 6.464222 TGTTTCCCAACTAGATGAAGTACTG 58.536 40.000 0.79 0.00 33.58 2.74
1613 1629 5.205988 GCATAGATTCTGATCTTGATGCG 57.794 43.478 7.85 0.00 41.18 4.73
1617 1633 4.953667 AGATTCTGATCTTGATGCGCTAA 58.046 39.130 9.73 0.09 39.63 3.09
1699 1715 7.451501 TCTTGATGCACATGTTTCTCAAATA 57.548 32.000 0.00 0.00 0.00 1.40
2255 2280 0.673644 CGACTCCTTGGCCGATGTTT 60.674 55.000 0.00 0.00 0.00 2.83
2306 2331 2.611292 GGCATGAAGAAGAAGATGGACG 59.389 50.000 0.00 0.00 0.00 4.79
2477 2502 2.301870 CCCTACTACCACTGCAACTTCA 59.698 50.000 0.00 0.00 0.00 3.02
2548 2573 5.362430 TGCCTGTCCTTAATCTTGTTGTTTT 59.638 36.000 0.00 0.00 0.00 2.43
2607 2632 5.499004 ACCTTATGTTATGTGTGTCAGGT 57.501 39.130 0.00 0.00 0.00 4.00
2771 2796 9.480053 CACAAGTCATGGAGAAACAAAAATAAT 57.520 29.630 0.00 0.00 0.00 1.28
2826 2858 5.049612 GTGGCAGACTAACTAAGGACAAAAC 60.050 44.000 0.00 0.00 0.00 2.43
2844 2876 6.016555 ACAAAACCAAATAGTAGCCTTGGAT 58.983 36.000 12.95 1.91 41.88 3.41
3153 3189 4.819630 TCACATTCCCTAAAACAGTGACAC 59.180 41.667 0.00 0.00 30.43 3.67
3292 3520 8.333226 AGTTATGAACTTAATAGGGCTACCTT 57.667 34.615 0.00 0.00 41.33 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
380 387 4.349663 TTGTAATTTCATACAGCGCACC 57.650 40.909 11.47 0.00 37.13 5.01
572 581 7.858382 CGTGTGGATGTTAAGTATTGTTTTTCA 59.142 33.333 0.00 0.00 0.00 2.69
701 712 2.079158 TGCTGCACTGATTAGTCTTGC 58.921 47.619 0.00 5.74 34.07 4.01
1245 1260 5.104485 AGGTTCTTCTTTGTTGGTGTACTCT 60.104 40.000 0.00 0.00 0.00 3.24
1431 1446 5.107065 GCATCCACTTCACAAACTACAGTAC 60.107 44.000 0.00 0.00 0.00 2.73
1436 1451 3.363970 CGTGCATCCACTTCACAAACTAC 60.364 47.826 0.00 0.00 39.86 2.73
2227 2252 3.067180 CGGCCAAGGAGTCGTAGTATTTA 59.933 47.826 2.24 0.00 0.00 1.40
2255 2280 4.451150 GTGGATGACGCCGCCTGA 62.451 66.667 0.00 0.00 32.25 3.86
2306 2331 1.152756 ACAGTTTGTGGTCTGCCCC 60.153 57.895 0.00 0.00 35.37 5.80
2477 2502 2.715749 TTCATGCATCTTCATCCCGT 57.284 45.000 0.00 0.00 0.00 5.28
2548 2573 8.995220 ACATAACGAAAGCAAACTACAAATCTA 58.005 29.630 0.00 0.00 0.00 1.98
2607 2632 6.463995 AGACATAGGCAAACTTGTTCAAAA 57.536 33.333 0.00 0.00 0.00 2.44
2826 2858 3.817647 GAGCATCCAAGGCTACTATTTGG 59.182 47.826 0.00 0.00 42.78 3.28
2844 2876 3.511540 ACATGTCTAAGCTGTACTGAGCA 59.488 43.478 7.83 0.00 41.83 4.26
2934 2970 2.897969 AGTACTGAATGTTGTCCTCGGT 59.102 45.455 0.00 0.00 33.34 4.69
2981 3017 8.094798 TCCTGTTGCAGTACTTAGTAAATTTG 57.905 34.615 0.00 0.00 0.00 2.32
3117 3153 3.766051 GGGAATGTGAATTGAAGCTTCCT 59.234 43.478 23.42 8.36 32.98 3.36



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

AutoCloner maintained by Alex Coulton.