Multiple sequence alignment - TraesCS5D01G292500

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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 TraesCS5D01G292500 chr5D 100.000 5079 0 0 1 5079 390018395 390023473 0.000000e+00 9380
1 TraesCS5D01G292500 chr5A 95.830 4125 121 16 987 5065 493190942 493195061 0.000000e+00 6617
2 TraesCS5D01G292500 chr5A 92.308 494 22 11 463 950 493190460 493190943 0.000000e+00 688
3 TraesCS5D01G292500 chr5A 92.239 451 25 6 1 447 493189628 493190072 9.280000e-177 630
4 TraesCS5D01G292500 chr5B 95.615 3421 146 4 928 4347 470030451 470033868 0.000000e+00 5483
5 TraesCS5D01G292500 chr5B 93.575 607 20 10 1 595 470029672 470030271 0.000000e+00 887
6 TraesCS5D01G292500 chr5B 89.778 675 43 16 4412 5065 470033995 470034664 0.000000e+00 841
7 TraesCS5D01G292500 chr5B 98.551 69 1 0 4347 4415 470033894 470033962 6.910000e-24 122


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 TraesCS5D01G292500 chr5D 390018395 390023473 5078 False 9380.00 9380 100.00000 1 5079 1 chr5D.!!$F1 5078
1 TraesCS5D01G292500 chr5A 493189628 493195061 5433 False 2645.00 6617 93.45900 1 5065 3 chr5A.!!$F1 5064
2 TraesCS5D01G292500 chr5B 470029672 470034664 4992 False 1833.25 5483 94.37975 1 5065 4 chr5B.!!$F1 5064

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
631 1015 0.038159 CCTGTTGTCCCGTGTCTCTC 60.038 60.0 0.00 0.0 0.00 3.20 F
840 1224 0.107643 TGACGTCCAGGCATTTGACA 59.892 50.0 14.12 0.0 28.76 3.58 F
2436 2827 0.251742 TGGGGAACTTGGCATCCTTG 60.252 55.0 5.64 0.0 35.95 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2412 2803 1.004277 GATGCCAAGTTCCCCACAGTA 59.996 52.381 0.0 0.0 0.00 2.74 R
2830 3221 1.883926 GGTAAACGGCACTTCACCAAT 59.116 47.619 0.0 0.0 0.00 3.16 R
4206 4597 0.769873 AATAGGCTCTGGCATCTGGG 59.230 55.000 0.0 0.0 40.87 4.45 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
177 181 1.736126 CGAAGATGATGCTTGTGCTGT 59.264 47.619 0.00 0.00 40.48 4.40
406 412 2.203408 GATAGCCCTTGCCCCAGC 60.203 66.667 0.00 0.00 38.69 4.85
424 430 1.211709 CGAATGGGAAAACGGTGCC 59.788 57.895 0.00 0.00 0.00 5.01
460 833 5.521735 CGATGGAATCTCACTGTTAGGAAAG 59.478 44.000 0.00 0.00 42.58 2.62
463 836 4.323868 GGAATCTCACTGTTAGGAAAGGCT 60.324 45.833 0.00 0.00 0.00 4.58
570 950 1.925185 GCTAGTCATCGACGGGAAAAC 59.075 52.381 0.00 0.00 37.67 2.43
622 1006 1.600916 GTGTCCTGCCTGTTGTCCC 60.601 63.158 0.00 0.00 0.00 4.46
630 1014 2.050269 CCTGTTGTCCCGTGTCTCT 58.950 57.895 0.00 0.00 0.00 3.10
631 1015 0.038159 CCTGTTGTCCCGTGTCTCTC 60.038 60.000 0.00 0.00 0.00 3.20
729 1113 4.629092 ACTTTCTAAACTCCAACGACTCC 58.371 43.478 0.00 0.00 0.00 3.85
762 1146 1.284408 CGCTAGCATCTCGAGGGAC 59.716 63.158 16.45 1.84 33.28 4.46
785 1169 2.247637 CGTTCATACTTCAGCGTCGAA 58.752 47.619 0.00 0.00 0.00 3.71
833 1217 1.003839 GACCATTGACGTCCAGGCA 60.004 57.895 14.12 0.00 34.88 4.75
840 1224 0.107643 TGACGTCCAGGCATTTGACA 59.892 50.000 14.12 0.00 28.76 3.58
843 1227 1.210155 GTCCAGGCATTTGACACGC 59.790 57.895 0.00 0.00 0.00 5.34
873 1257 3.829601 ACTACAGACAGGGCTATAGATGC 59.170 47.826 3.21 0.00 0.00 3.91
884 1268 4.201970 GGGCTATAGATGCGTGTATCTCTC 60.202 50.000 3.21 0.00 38.35 3.20
886 1270 5.818336 GGCTATAGATGCGTGTATCTCTCTA 59.182 44.000 3.21 0.00 38.35 2.43
887 1271 6.238266 GGCTATAGATGCGTGTATCTCTCTAC 60.238 46.154 3.21 0.00 38.35 2.59
888 1272 6.537301 GCTATAGATGCGTGTATCTCTCTACT 59.463 42.308 3.21 0.00 38.35 2.57
889 1273 7.707464 GCTATAGATGCGTGTATCTCTCTACTA 59.293 40.741 3.21 0.00 38.35 1.82
890 1274 9.244799 CTATAGATGCGTGTATCTCTCTACTAG 57.755 40.741 3.64 0.00 38.35 2.57
967 1352 1.238439 CTTCGTGAGTTGTGGCCATT 58.762 50.000 9.72 0.00 0.00 3.16
970 1355 2.147958 TCGTGAGTTGTGGCCATTAAC 58.852 47.619 21.70 21.70 0.00 2.01
971 1356 1.199097 CGTGAGTTGTGGCCATTAACC 59.801 52.381 24.12 18.05 0.00 2.85
978 1363 3.162147 TGTGGCCATTAACCAAAGCTA 57.838 42.857 9.72 0.00 39.39 3.32
1266 1657 4.117661 GAGAGGGTCGTCGCGCTT 62.118 66.667 5.56 0.00 36.87 4.68
1290 1681 4.003788 AACTCGTCCCACCTGGCG 62.004 66.667 0.00 0.00 35.71 5.69
1523 1914 1.577736 CTCCAAGGTGAGATCCCTGT 58.422 55.000 0.00 0.00 34.11 4.00
1524 1915 1.484240 CTCCAAGGTGAGATCCCTGTC 59.516 57.143 0.00 0.00 34.11 3.51
1678 2069 3.198417 GGCCATTCCATCATCTTTTGGTT 59.802 43.478 0.00 0.00 34.48 3.67
1688 2079 0.762082 TCTTTTGGTTGCATGCCCCA 60.762 50.000 19.24 19.24 0.00 4.96
1914 2305 1.167851 CAAATTCCTCCGAGCTGCAA 58.832 50.000 1.02 0.00 0.00 4.08
2142 2533 3.427243 GTCGATCTCTAACCTGTCAACG 58.573 50.000 0.00 0.00 0.00 4.10
2168 2559 3.927854 TCGTATATCTGTCCCTCTCTCG 58.072 50.000 0.00 0.00 0.00 4.04
2319 2710 1.355720 CTGTCCCTGGGAAGGAACAAT 59.644 52.381 19.06 0.00 34.43 2.71
2322 2713 3.399644 TGTCCCTGGGAAGGAACAATTTA 59.600 43.478 19.06 0.00 34.43 1.40
2336 2727 2.039879 ACAATTTAAGTGGGAGCGTCCT 59.960 45.455 0.00 0.00 36.57 3.85
2383 2774 4.020485 AGTTAAGCAACTTGTATCTCGGGT 60.020 41.667 0.00 0.00 42.51 5.28
2436 2827 0.251742 TGGGGAACTTGGCATCCTTG 60.252 55.000 5.64 0.00 35.95 3.61
2574 2965 6.510157 CGATACCGTCTGAAATTGGAAATCTG 60.510 42.308 0.00 0.00 0.00 2.90
2670 3061 7.933577 TGCGAGATTCTCCAAAACATATATCTT 59.066 33.333 8.09 0.00 0.00 2.40
2769 3160 5.180271 AGCAACAAATTATCAGGCCAAATG 58.820 37.500 5.01 0.00 0.00 2.32
2830 3221 8.202461 TCTAAACCTCTCCTTCAATAACTTCA 57.798 34.615 0.00 0.00 0.00 3.02
3080 3471 1.068474 CGTAACCCTTCGACTGCAAG 58.932 55.000 0.00 0.00 42.29 4.01
3189 3580 6.238759 GCACTTTTGGCTCTGTATATAAAGGG 60.239 42.308 0.00 0.00 0.00 3.95
3519 3910 5.604231 TGCACTGGATTATCTTCACTCCTAT 59.396 40.000 0.00 0.00 0.00 2.57
3651 4042 5.854010 GAAACTCTTTTCCCCAAAACTCT 57.146 39.130 0.00 0.00 35.92 3.24
3654 4045 4.386711 ACTCTTTTCCCCAAAACTCTACG 58.613 43.478 0.00 0.00 0.00 3.51
3660 4051 1.630148 CCCAAAACTCTACGAGCTCG 58.370 55.000 33.45 33.45 46.33 5.03
3711 4102 1.610624 GCTCCAGGTTTGTCCGATTCA 60.611 52.381 0.00 0.00 41.99 2.57
3856 4247 8.207545 AGCTACGGAATTCTCATCTTAGAAATT 58.792 33.333 5.23 0.00 38.90 1.82
4042 4433 5.651530 TCAAGAACGTATGATCCTTCTGAC 58.348 41.667 0.00 0.00 0.00 3.51
4061 4452 1.895798 ACGAGAGAAGGATTGACTGCA 59.104 47.619 0.00 0.00 0.00 4.41
4189 4580 4.037858 TCGCGTAGAGGAAGGTTTAATC 57.962 45.455 5.77 0.00 0.00 1.75
4206 4597 7.279313 AGGTTTAATCTTTTGATGAATGCATGC 59.721 33.333 11.82 11.82 39.48 4.06
4228 4619 2.219458 CAGATGCCAGAGCCTATTGTG 58.781 52.381 0.00 0.00 38.69 3.33
4235 4626 3.872240 GCCAGAGCCTATTGTGTTTACCA 60.872 47.826 0.00 0.00 0.00 3.25
4571 5026 6.435430 TCATATGTTTCCATGAAAGAACCG 57.565 37.500 1.90 0.00 31.87 4.44
4732 5199 4.250464 CACCACACAAGAATACGTACCAT 58.750 43.478 0.00 0.00 0.00 3.55
4739 5206 4.036027 ACAAGAATACGTACCATCGTCGAT 59.964 41.667 0.75 0.75 43.12 3.59
4822 5307 3.984838 GCAATGGGCTTGAAACACA 57.015 47.368 0.00 0.00 40.25 3.72
4996 5484 3.934068 TCCGTACCTTGATTCCTTGAAC 58.066 45.455 0.00 0.00 0.00 3.18
5029 5519 0.895100 ACAATGCCGGTGAAGCACAT 60.895 50.000 1.90 0.00 44.40 3.21
5042 5532 2.764314 GCACATAAGCAGCCGTGGG 61.764 63.158 0.00 0.00 0.00 4.61
5065 5555 1.031571 TCTCATGCATTCAACCGCCC 61.032 55.000 0.00 0.00 0.00 6.13
5066 5556 1.303970 TCATGCATTCAACCGCCCA 60.304 52.632 0.00 0.00 0.00 5.36
5067 5557 0.683828 TCATGCATTCAACCGCCCAT 60.684 50.000 0.00 0.00 0.00 4.00
5068 5558 0.528901 CATGCATTCAACCGCCCATG 60.529 55.000 0.00 0.00 0.00 3.66
5069 5559 2.202783 GCATTCAACCGCCCATGC 60.203 61.111 0.00 0.00 35.59 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 76 9.243105 CCATTTACCCCCTTCATTACAATATAG 57.757 37.037 0.00 0.00 0.00 1.31
97 101 2.307496 ATGCAGACATTTTCCACCCA 57.693 45.000 0.00 0.00 30.07 4.51
135 139 3.250040 GGTGTGTCGAAAGTGCTGTTTAT 59.750 43.478 0.00 0.00 0.00 1.40
136 140 2.610374 GGTGTGTCGAAAGTGCTGTTTA 59.390 45.455 0.00 0.00 0.00 2.01
137 141 1.400494 GGTGTGTCGAAAGTGCTGTTT 59.600 47.619 0.00 0.00 0.00 2.83
138 142 1.014352 GGTGTGTCGAAAGTGCTGTT 58.986 50.000 0.00 0.00 0.00 3.16
139 143 1.151777 CGGTGTGTCGAAAGTGCTGT 61.152 55.000 0.00 0.00 0.00 4.40
406 412 1.211709 GGCACCGTTTTCCCATTCG 59.788 57.895 0.00 0.00 0.00 3.34
424 430 0.105658 TTCCATCGACTAGGGGAGGG 60.106 60.000 9.07 9.07 35.51 4.30
622 1006 6.018588 CAGGTAACACTAGATAGAGAGACACG 60.019 46.154 0.00 0.00 41.41 4.49
630 1014 6.058833 CAGAGAGCAGGTAACACTAGATAGA 58.941 44.000 0.00 0.00 41.41 1.98
631 1015 5.240623 CCAGAGAGCAGGTAACACTAGATAG 59.759 48.000 0.00 0.00 41.41 2.08
687 1071 1.229082 TTGTCCCCTGACCTAGCGT 60.229 57.895 0.00 0.00 41.01 5.07
729 1113 0.867746 TAGCGCTGCAAACTTGACTG 59.132 50.000 22.90 0.00 0.00 3.51
762 1146 1.578023 GACGCTGAAGTATGAACGTCG 59.422 52.381 0.00 0.00 40.20 5.12
785 1169 3.191162 CGGTTCACATTGATGATGTTGGT 59.809 43.478 0.00 0.00 46.80 3.67
806 1190 1.076533 CGTCAATGGTCCGGTCTTCG 61.077 60.000 0.00 0.00 38.88 3.79
833 1217 5.294356 TGTAGTCAAGTAAGCGTGTCAAAT 58.706 37.500 0.00 0.00 0.00 2.32
840 1224 3.057456 CCTGTCTGTAGTCAAGTAAGCGT 60.057 47.826 0.00 0.00 0.00 5.07
843 1227 3.511934 AGCCCTGTCTGTAGTCAAGTAAG 59.488 47.826 0.00 0.00 0.00 2.34
873 1257 6.347079 GCAAGCTACTAGTAGAGAGATACACG 60.347 46.154 30.09 9.10 35.21 4.49
884 1268 3.452474 CCTTGCAGCAAGCTACTAGTAG 58.548 50.000 27.32 23.25 45.94 2.57
886 1270 1.677217 GCCTTGCAGCAAGCTACTAGT 60.677 52.381 27.32 0.00 45.94 2.57
887 1271 1.012841 GCCTTGCAGCAAGCTACTAG 58.987 55.000 27.32 14.69 45.94 2.57
888 1272 0.615331 AGCCTTGCAGCAAGCTACTA 59.385 50.000 27.32 0.00 45.94 1.82
889 1273 0.959372 CAGCCTTGCAGCAAGCTACT 60.959 55.000 27.32 20.21 45.94 2.57
890 1274 1.505353 CAGCCTTGCAGCAAGCTAC 59.495 57.895 27.32 18.49 45.94 3.58
978 1363 3.007723 TCGGTCGTAGGATAGATAGCAGT 59.992 47.826 0.00 0.00 0.00 4.40
1120 1511 4.514577 ATTGAGCTCGTCGGCCGG 62.515 66.667 27.83 10.69 37.11 6.13
1137 1528 2.594131 TCCGACTTGAACAAGAGGAGA 58.406 47.619 19.35 8.69 40.64 3.71
1266 1657 0.971386 GGTGGGACGAGTTGAGGTTA 59.029 55.000 0.00 0.00 0.00 2.85
1299 1690 2.809601 CCCAAGAACGGCGAGACG 60.810 66.667 16.62 0.00 40.31 4.18
1524 1915 1.511613 TTTCCAGGGAGCCTATCTGG 58.488 55.000 6.50 6.50 46.91 3.86
1678 2069 1.792757 AAAGAGAGGTGGGGCATGCA 61.793 55.000 21.36 0.00 0.00 3.96
1914 2305 3.695830 TTGTACCCGAGCTCAATTCTT 57.304 42.857 15.40 0.00 0.00 2.52
2142 2533 2.152830 AGGGACAGATATACGAGCGAC 58.847 52.381 0.00 0.00 0.00 5.19
2168 2559 5.047731 GGTATGTTCCCTAGTATCCGGTTAC 60.048 48.000 13.82 13.82 0.00 2.50
2319 2710 1.053424 ACAGGACGCTCCCACTTAAA 58.947 50.000 1.06 0.00 37.19 1.52
2322 2713 1.071471 CAACAGGACGCTCCCACTT 59.929 57.895 1.06 0.00 37.19 3.16
2336 2727 5.160607 AGTAAGATTTCCGATGGTCAACA 57.839 39.130 0.00 0.00 0.00 3.33
2383 2774 4.459390 TGCTACCGCTGAAAGTATTGTA 57.541 40.909 0.00 0.00 35.30 2.41
2412 2803 1.004277 GATGCCAAGTTCCCCACAGTA 59.996 52.381 0.00 0.00 0.00 2.74
2436 2827 7.315142 TGTTGGTTGAGAAATCAATATTCAGC 58.685 34.615 0.00 0.00 31.79 4.26
2574 2965 5.391449 GCTCGGAATTCTACAAGGTTTTTC 58.609 41.667 5.23 0.00 0.00 2.29
2670 3061 6.133356 ACTACCTTCCAGGAAATTGTTTTGA 58.867 36.000 2.72 0.00 37.67 2.69
2769 3160 2.035961 GAGGTCCTCCAAAAACTTTGGC 59.964 50.000 7.78 0.28 39.38 4.52
2830 3221 1.883926 GGTAAACGGCACTTCACCAAT 59.116 47.619 0.00 0.00 0.00 3.16
3061 3452 1.068474 CTTGCAGTCGAAGGGTTACG 58.932 55.000 0.00 0.00 0.00 3.18
3080 3471 2.528041 CGAAGGGTAGCCTTGGATAC 57.472 55.000 30.29 14.31 0.00 2.24
3189 3580 1.619332 CCCCTATCTCCGCCTAAGTTC 59.381 57.143 0.00 0.00 0.00 3.01
3651 4042 3.483421 TCTAAATCCCATCGAGCTCGTA 58.517 45.455 33.33 21.14 40.80 3.43
3654 4045 2.028567 CCCTCTAAATCCCATCGAGCTC 60.029 54.545 2.73 2.73 0.00 4.09
3660 4051 4.829492 CCAATTGTCCCTCTAAATCCCATC 59.171 45.833 4.43 0.00 0.00 3.51
3711 4102 3.903530 AGGAAACATGGGGAAGAAAGT 57.096 42.857 0.00 0.00 0.00 2.66
3856 4247 2.383608 GGGCCTCTTCCCAGTTACA 58.616 57.895 0.84 0.00 45.82 2.41
3980 4371 4.035102 GGCTGGCGACCCCTTCTT 62.035 66.667 0.00 0.00 0.00 2.52
4042 4433 2.094286 AGTGCAGTCAATCCTTCTCTCG 60.094 50.000 0.00 0.00 0.00 4.04
4061 4452 3.754323 CGAGTCTAAGAAGTGAGGTCAGT 59.246 47.826 0.00 0.00 0.00 3.41
4189 4580 3.118920 TCTGGGCATGCATTCATCAAAAG 60.119 43.478 21.36 2.20 0.00 2.27
4206 4597 0.769873 AATAGGCTCTGGCATCTGGG 59.230 55.000 0.00 0.00 40.87 4.45
4228 4619 9.124807 GTGCTCAAAATACTTTGTATGGTAAAC 57.875 33.333 0.00 0.00 42.26 2.01
4414 4869 3.562182 TGGTCATGGAAGTCGAGCTATA 58.438 45.455 0.00 0.00 0.00 1.31
4415 4870 2.363680 CTGGTCATGGAAGTCGAGCTAT 59.636 50.000 0.00 0.00 0.00 2.97
4647 5110 0.193069 ATCCTAGCTCAGCCCCTGAT 59.807 55.000 0.00 0.00 39.92 2.90
4848 5333 5.331906 TGTTCCAATGATTGAAGGATGGAA 58.668 37.500 6.76 0.00 42.84 3.53
4996 5484 4.858692 CCGGCATTGTAAATCAACTTCAAG 59.141 41.667 0.00 0.00 38.97 3.02
5042 5532 1.329906 CGGTTGAATGCATGAGAGAGC 59.670 52.381 0.00 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.