Multiple sequence alignment - TraesCS5D01G273000

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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 TraesCS5D01G273000 chr5D 100.000 4095 0 0 1 4095 375747515 375751609 0.000000e+00 7563.0
1 TraesCS5D01G273000 chr5A 93.720 4124 182 35 1 4095 476850955 476855030 0.000000e+00 6109.0
2 TraesCS5D01G273000 chr5B 93.823 2234 95 15 1 2224 448600325 448602525 0.000000e+00 3321.0
3 TraesCS5D01G273000 chr5B 96.386 1854 56 8 2248 4095 448602520 448604368 0.000000e+00 3042.0
4 TraesCS5D01G273000 chr7A 84.884 86 5 2 1252 1329 202520927 202520842 3.390000e-11 80.5
5 TraesCS5D01G273000 chr7D 100.000 29 0 0 1252 1280 192929259 192929231 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 TraesCS5D01G273000 chr5D 375747515 375751609 4094 False 7563.0 7563 100.0000 1 4095 1 chr5D.!!$F1 4094
1 TraesCS5D01G273000 chr5A 476850955 476855030 4075 False 6109.0 6109 93.7200 1 4095 1 chr5A.!!$F1 4094
2 TraesCS5D01G273000 chr5B 448600325 448604368 4043 False 3181.5 3321 95.1045 1 4095 2 chr5B.!!$F1 4094

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
817 834 1.350019 GGCCCAACTGGTGTTAGTACT 59.650 52.381 0.0 0.0 34.60 2.73 F
1104 1135 0.810426 CCTCATCGTCGTCCTCTCGA 60.810 60.000 0.0 0.0 37.96 4.04 F
2407 2450 1.674441 CTGCTGATGCCAAGGTATGTG 59.326 52.381 0.0 0.0 38.71 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2083 2122 0.512952 CTTCCGCCACAGAAAAGTCG 59.487 55.000 0.00 0.0 0.00 4.18 R
2426 2469 0.676466 CATGCCGCCCACAAAGTAGA 60.676 55.000 0.00 0.0 0.00 2.59 R
3505 3553 1.004862 GGATAGGGCCTAGGCATTTCC 59.995 57.143 34.09 27.5 44.11 3.13 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
206 217 2.169352 ACAGATACAGGCAACAGCTAGG 59.831 50.000 0.00 0.00 41.41 3.02
240 251 2.008242 AGAGATCCATCCGAGAAGGG 57.992 55.000 0.00 0.00 41.52 3.95
485 496 1.648467 GGATGAACTTGCGCTCCACC 61.648 60.000 9.73 0.15 0.00 4.61
738 755 4.124351 CCATGGCTGCTTGCGGTG 62.124 66.667 0.00 0.00 44.05 4.94
783 800 4.689549 TCGGCCTGGGAGACGGAA 62.690 66.667 0.00 0.00 0.00 4.30
817 834 1.350019 GGCCCAACTGGTGTTAGTACT 59.650 52.381 0.00 0.00 34.60 2.73
844 861 3.369366 CCTGTTACATTTTGATTGGGCCC 60.369 47.826 17.59 17.59 0.00 5.80
847 864 4.349342 TGTTACATTTTGATTGGGCCCTTT 59.651 37.500 25.70 10.50 0.00 3.11
848 865 3.421919 ACATTTTGATTGGGCCCTTTG 57.578 42.857 25.70 10.82 0.00 2.77
1009 1034 2.740826 ACGTTTCCATGGTCGCCG 60.741 61.111 12.58 12.27 0.00 6.46
1010 1035 4.160635 CGTTTCCATGGTCGCCGC 62.161 66.667 12.58 0.00 0.00 6.53
1011 1036 3.810896 GTTTCCATGGTCGCCGCC 61.811 66.667 12.58 0.00 0.00 6.13
1089 1120 1.007038 CGTTTCCGTCCGTTCCTCA 60.007 57.895 0.00 0.00 0.00 3.86
1101 1132 1.096416 GTTCCTCATCGTCGTCCTCT 58.904 55.000 0.00 0.00 0.00 3.69
1104 1135 0.810426 CCTCATCGTCGTCCTCTCGA 60.810 60.000 0.00 0.00 37.96 4.04
1368 1399 2.487934 CTCCAGCGATCGATCCATTTT 58.512 47.619 21.57 0.00 0.00 1.82
1391 1422 7.490657 TTAGGGTTTGCTTCTACTTATCTCA 57.509 36.000 0.00 0.00 0.00 3.27
1396 1427 6.481644 GGTTTGCTTCTACTTATCTCATCCAG 59.518 42.308 0.00 0.00 0.00 3.86
1441 1472 2.143925 GACCGCCCTATGCTATCAAAC 58.856 52.381 0.00 0.00 38.05 2.93
1484 1515 9.864034 CTGCTGTTTAAACGAGTTATTATATGG 57.136 33.333 13.45 0.00 0.00 2.74
1547 1584 6.855914 CACTAGAACGTTGCACATTTGTATTT 59.144 34.615 5.00 0.00 0.00 1.40
1607 1646 5.997129 TGAATCAGCAATACAAGTGAACAGA 59.003 36.000 0.00 0.00 0.00 3.41
1730 1769 2.175878 AGTGCGACAGCTTCATTTCT 57.824 45.000 0.00 0.00 45.42 2.52
2322 2362 7.959651 GCAGAACAAGAGTTGTATAACATTCAG 59.040 37.037 5.08 0.14 44.59 3.02
2323 2363 9.208022 CAGAACAAGAGTTGTATAACATTCAGA 57.792 33.333 5.08 0.00 44.59 3.27
2324 2364 9.778741 AGAACAAGAGTTGTATAACATTCAGAA 57.221 29.630 5.08 0.00 44.59 3.02
2407 2450 1.674441 CTGCTGATGCCAAGGTATGTG 59.326 52.381 0.00 0.00 38.71 3.21
2415 2458 3.792401 TGCCAAGGTATGTGTTATCTCG 58.208 45.455 0.00 0.00 0.00 4.04
2426 2469 3.940852 TGTGTTATCTCGATGCTTGCATT 59.059 39.130 9.59 0.00 0.00 3.56
2439 2482 2.672195 GCTTGCATTCTACTTTGTGGGC 60.672 50.000 0.00 0.00 0.00 5.36
2445 2488 0.676466 TCTACTTTGTGGGCGGCATG 60.676 55.000 12.47 0.00 0.00 4.06
2465 2509 6.366061 GGCATGTTCTTACAACATTTTTCTCC 59.634 38.462 0.00 0.00 38.69 3.71
2605 2649 7.152645 AGGTTCTACTGTGTGTACATTGTTAG 58.847 38.462 0.00 0.00 35.97 2.34
2909 2953 5.349817 AGAGTATCAGTGCGAAAAACATCTG 59.650 40.000 0.00 0.00 37.82 2.90
2971 3015 8.579863 CCACTCAAAGAGAAATGTTTAAATCCT 58.420 33.333 0.31 0.00 33.32 3.24
3099 3143 6.648725 GCTACAAAGAGATGGATGTAGAATCC 59.351 42.308 14.15 0.00 45.05 3.01
3109 3153 3.531538 GATGTAGAATCCGGACTGCAAA 58.468 45.455 15.15 0.00 33.17 3.68
3123 3167 5.161358 GGACTGCAAAAACTTATTACCAGC 58.839 41.667 0.00 0.00 0.00 4.85
3170 3214 3.455543 TCACCTCATCTCATTATGCCACA 59.544 43.478 0.00 0.00 0.00 4.17
3178 3222 7.761409 TCATCTCATTATGCCACAAAGTTTAC 58.239 34.615 0.00 0.00 0.00 2.01
3190 3234 9.461312 TGCCACAAAGTTTACTGAATATCTTAT 57.539 29.630 0.00 0.00 0.00 1.73
3212 3259 5.947228 TGTCAAAGAAGAAGCAACCTATG 57.053 39.130 0.00 0.00 0.00 2.23
3295 3342 6.060136 TGAATGCATAATTCTTCTCCCTCAG 58.940 40.000 0.00 0.00 44.42 3.35
3463 3511 3.129638 AGACCGTGAGAATCTAGCACTTC 59.870 47.826 1.50 0.00 34.92 3.01
3504 3552 6.314152 TGAACACGTTGAACTAATTGACTGAA 59.686 34.615 0.00 0.00 0.00 3.02
3505 3553 6.287107 ACACGTTGAACTAATTGACTGAAG 57.713 37.500 0.00 0.00 0.00 3.02
3597 3645 0.320946 TAGCCGCCCTGTTACACAAC 60.321 55.000 0.00 0.00 35.06 3.32
3673 3721 5.768317 TGTTTGCTCACCTTTTATGTAAGC 58.232 37.500 0.00 0.00 0.00 3.09
3692 3740 2.744202 AGCGCATTCTACTTCTTTGGTG 59.256 45.455 11.47 0.00 0.00 4.17
3825 3875 9.731819 CATCATTTTCTTACATTTCAGATCAGG 57.268 33.333 0.00 0.00 0.00 3.86
3826 3876 9.690913 ATCATTTTCTTACATTTCAGATCAGGA 57.309 29.630 0.00 0.00 0.00 3.86
3827 3877 9.519191 TCATTTTCTTACATTTCAGATCAGGAA 57.481 29.630 0.00 0.00 0.00 3.36
3895 3948 1.972198 CTCCTGCTGTTGTCCGGTA 59.028 57.895 0.00 0.00 0.00 4.02
3902 3955 2.614983 TGCTGTTGTCCGGTAAAAGAAC 59.385 45.455 13.35 5.07 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
131 140 9.418045 GCTTTTATGGTTTGCTTTCAATTAGTA 57.582 29.630 0.00 0.00 31.33 1.82
206 217 4.195416 GGATCTCTTCCTGGTGATGTTTC 58.805 47.826 0.00 0.00 41.78 2.78
240 251 4.277423 GCTCTACTTCTGATCTAGGTCCAC 59.723 50.000 0.00 0.00 0.00 4.02
243 254 3.824443 GGGCTCTACTTCTGATCTAGGTC 59.176 52.174 0.00 0.00 0.00 3.85
530 541 4.813526 CACCTCGTCCTCGTCGCG 62.814 72.222 0.00 0.00 38.33 5.87
783 800 0.988832 TGGGCCTTATTTGACGTCCT 59.011 50.000 14.12 0.03 0.00 3.85
817 834 4.709397 CCAATCAAAATGTAACAGGGCCTA 59.291 41.667 5.28 0.00 0.00 3.93
844 861 5.303971 CCTATAAGATCAGTCCCTGCAAAG 58.696 45.833 0.00 0.00 0.00 2.77
847 864 2.634940 GCCTATAAGATCAGTCCCTGCA 59.365 50.000 0.00 0.00 0.00 4.41
848 865 2.027653 GGCCTATAAGATCAGTCCCTGC 60.028 54.545 0.00 0.00 0.00 4.85
859 876 5.391256 TCTTTGTAGATCCGGCCTATAAGA 58.609 41.667 17.19 17.19 0.00 2.10
862 879 5.105877 CGAATCTTTGTAGATCCGGCCTATA 60.106 44.000 0.00 0.00 40.26 1.31
865 888 2.224066 CGAATCTTTGTAGATCCGGCCT 60.224 50.000 0.00 0.00 40.26 5.19
905 930 3.049912 GTGGTTTTCGAAATGCCAAGTC 58.950 45.455 26.12 15.79 0.00 3.01
1074 1105 1.246056 ACGATGAGGAACGGACGGAA 61.246 55.000 0.00 0.00 0.00 4.30
1080 1111 1.226603 GGACGACGATGAGGAACGG 60.227 63.158 0.00 0.00 0.00 4.44
1368 1399 7.202011 GGATGAGATAAGTAGAAGCAAACCCTA 60.202 40.741 0.00 0.00 0.00 3.53
1391 1422 7.657761 GTGTATCCAAATAAGATCGAACTGGAT 59.342 37.037 14.87 14.87 43.08 3.41
1396 1427 7.491372 TCACTGTGTATCCAAATAAGATCGAAC 59.509 37.037 7.79 0.00 0.00 3.95
1425 1456 1.264288 GCACGTTTGATAGCATAGGGC 59.736 52.381 0.00 0.00 45.30 5.19
1441 1472 3.062639 CAGCAGAAACTTATACAGGCACG 59.937 47.826 0.00 0.00 0.00 5.34
1501 1532 2.742116 GGTGGAGCCCAATCGCCTA 61.742 63.158 0.00 0.00 34.18 3.93
1504 1535 2.514824 GAGGTGGAGCCCAATCGC 60.515 66.667 0.00 0.00 38.26 4.58
1505 1536 2.190578 GGAGGTGGAGCCCAATCG 59.809 66.667 0.00 0.00 38.26 3.34
1566 1605 9.787532 TGCTGATTCAACAAGCTATAAAATAAC 57.212 29.630 0.00 0.00 0.00 1.89
1570 1609 9.787532 GTATTGCTGATTCAACAAGCTATAAAA 57.212 29.630 8.34 0.00 0.00 1.52
1607 1646 5.403246 TGCACAACGAAAACATTACTTTGT 58.597 33.333 0.00 0.00 0.00 2.83
1730 1769 3.714798 ACTCAACCTTTTCACTCTGGGTA 59.285 43.478 0.00 0.00 0.00 3.69
2083 2122 0.512952 CTTCCGCCACAGAAAAGTCG 59.487 55.000 0.00 0.00 0.00 4.18
2092 2132 4.634004 CACAAAATAGATACTTCCGCCACA 59.366 41.667 0.00 0.00 0.00 4.17
2140 2180 3.458189 GAGGTGTATATGACCAGCACAC 58.542 50.000 8.12 2.16 38.97 3.82
2322 2362 4.335037 GCATCCTTCTCTTCACATTCCTTC 59.665 45.833 0.00 0.00 0.00 3.46
2323 2363 4.263639 TGCATCCTTCTCTTCACATTCCTT 60.264 41.667 0.00 0.00 0.00 3.36
2324 2364 3.265221 TGCATCCTTCTCTTCACATTCCT 59.735 43.478 0.00 0.00 0.00 3.36
2407 2450 5.694006 AGTAGAATGCAAGCATCGAGATAAC 59.306 40.000 8.14 1.28 35.31 1.89
2415 2458 4.418392 CCACAAAGTAGAATGCAAGCATC 58.582 43.478 8.14 2.60 35.31 3.91
2426 2469 0.676466 CATGCCGCCCACAAAGTAGA 60.676 55.000 0.00 0.00 0.00 2.59
2439 2482 5.920273 AGAAAAATGTTGTAAGAACATGCCG 59.080 36.000 3.17 0.00 40.43 5.69
2445 2488 9.366216 ACAAAAGGAGAAAAATGTTGTAAGAAC 57.634 29.630 0.00 0.00 0.00 3.01
2465 2509 6.304356 TCTGCAATTCTCTACACACAAAAG 57.696 37.500 0.00 0.00 0.00 2.27
2620 2664 5.192327 AGTCAGCATTTCACCTGAAAAAG 57.808 39.130 4.61 2.70 45.81 2.27
2848 2892 1.152247 ACAGTCTCCTGGAGTGCCA 60.152 57.895 22.50 0.91 46.38 4.92
2909 2953 3.760684 ACTGATGATTTTGCTGGAGGAAC 59.239 43.478 0.00 0.00 0.00 3.62
2971 3015 5.246429 ACCAACCAAACTTGTTTCCACTTTA 59.754 36.000 0.00 0.00 0.00 1.85
3099 3143 5.365403 TGGTAATAAGTTTTTGCAGTCCG 57.635 39.130 0.00 0.00 0.00 4.79
3123 3167 7.849804 ATTCAAGCATAAACAGTGTACCTAG 57.150 36.000 0.00 0.00 0.00 3.02
3190 3234 5.620206 TCATAGGTTGCTTCTTCTTTGACA 58.380 37.500 0.00 0.00 0.00 3.58
3212 3259 6.855836 TGAACTGAACAGAATGGCATATTTC 58.144 36.000 0.00 2.08 43.62 2.17
3433 3481 5.674933 AGATTCTCACGGTCTTGAAAAAC 57.325 39.130 0.00 0.00 0.00 2.43
3463 3511 6.534059 ACGTGTTCATTTGACAGAATAATCG 58.466 36.000 0.00 0.00 0.00 3.34
3505 3553 1.004862 GGATAGGGCCTAGGCATTTCC 59.995 57.143 34.09 27.50 44.11 3.13
3517 3565 2.183679 CAGAGTATCAGGGGATAGGGC 58.816 57.143 0.00 0.00 36.69 5.19
3597 3645 2.302157 AGAAGTGTCGTCCTAAAAGGGG 59.698 50.000 0.00 0.00 35.59 4.79
3673 3721 4.631377 TCATCACCAAAGAAGTAGAATGCG 59.369 41.667 0.00 0.00 0.00 4.73
3825 3875 5.009710 CCTAACCAACCAACTTCCTTTCTTC 59.990 44.000 0.00 0.00 0.00 2.87
3826 3876 4.893524 CCTAACCAACCAACTTCCTTTCTT 59.106 41.667 0.00 0.00 0.00 2.52
3827 3877 4.167307 TCCTAACCAACCAACTTCCTTTCT 59.833 41.667 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.