Multiple sequence alignment - TraesCS5A01G107300

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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 TraesCS5A01G107300 chr5A 100.000 5051 0 0 1 5051 180991606 180996656 0.000000e+00 9328.0
1 TraesCS5A01G107300 chr5D 96.998 4763 101 11 1 4761 177169220 177173942 0.000000e+00 7965.0
2 TraesCS5A01G107300 chr5D 88.197 305 21 6 4758 5051 177174019 177174319 2.890000e-92 350.0
3 TraesCS5A01G107300 chr5B 97.410 4131 91 10 1 4125 191958187 191962307 0.000000e+00 7022.0
4 TraesCS5A01G107300 chr5B 91.247 914 52 17 4162 5051 191962318 191963227 0.000000e+00 1219.0
5 TraesCS5A01G107300 chr2D 81.040 327 45 12 2890 3211 598634698 598634384 1.400000e-60 244.0
6 TraesCS5A01G107300 chr2A 80.793 328 46 13 2890 3212 732564433 732564118 1.820000e-59 241.0
7 TraesCS5A01G107300 chr1B 100.000 30 0 0 4308 4337 675897114 675897143 7.060000e-04 56.5
8 TraesCS5A01G107300 chr1A 100.000 29 0 0 4309 4337 360164322 360164294 3.000000e-03 54.7
9 TraesCS5A01G107300 chr1A 100.000 28 0 0 4310 4337 71835399 71835426 9.000000e-03 52.8


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 TraesCS5A01G107300 chr5A 180991606 180996656 5050 False 9328.0 9328 100.0000 1 5051 1 chr5A.!!$F1 5050
1 TraesCS5A01G107300 chr5D 177169220 177174319 5099 False 4157.5 7965 92.5975 1 5051 2 chr5D.!!$F1 5050
2 TraesCS5A01G107300 chr5B 191958187 191963227 5040 False 4120.5 7022 94.3285 1 5051 2 chr5B.!!$F1 5050

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
80 81 0.613777 GACGATCAGGTGACCCCTTT 59.386 55.0 0.00 0.0 42.73 3.11 F
408 410 0.785979 GCGAAATTTGCTGTTGCTGG 59.214 50.0 0.00 0.0 40.48 4.85 F
1246 1255 0.973632 TCGACCAGCTTCTTAAGGCA 59.026 50.0 1.85 0.0 0.00 4.75 F
2549 2558 0.175073 GTACTGTCCGGGTGGTGATC 59.825 60.0 0.00 0.0 36.30 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1014 1022 0.759346 CTTATCTTAGCCCACCGCCT 59.241 55.000 0.00 0.00 38.78 5.52 R
1528 1537 1.270571 TGCACAACGCTTCCATCACTA 60.271 47.619 0.00 0.00 43.06 2.74 R
3025 3036 2.080286 AACAGATGGCGACTACACAC 57.920 50.000 0.00 0.00 0.00 3.82 R
4532 4565 0.196888 ATCATAGGGCCCCATGGAGA 59.803 55.000 27.46 11.15 0.00 3.71 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
80 81 0.613777 GACGATCAGGTGACCCCTTT 59.386 55.000 0.00 0.00 42.73 3.11
81 82 1.829222 GACGATCAGGTGACCCCTTTA 59.171 52.381 0.00 0.00 42.73 1.85
82 83 1.553704 ACGATCAGGTGACCCCTTTAC 59.446 52.381 0.00 0.00 42.73 2.01
84 85 2.236395 CGATCAGGTGACCCCTTTACTT 59.764 50.000 0.00 0.00 42.73 2.24
85 86 3.307480 CGATCAGGTGACCCCTTTACTTT 60.307 47.826 0.00 0.00 42.73 2.66
295 297 1.203001 TCCGGACTGGCATTTTTCCTT 60.203 47.619 0.00 0.00 37.80 3.36
306 308 4.219725 GGCATTTTTCCTTGTAGGTAAGCA 59.780 41.667 0.00 0.00 36.53 3.91
375 377 4.271816 CGAGCTATCCGCGGCTGT 62.272 66.667 23.51 11.70 45.59 4.40
408 410 0.785979 GCGAAATTTGCTGTTGCTGG 59.214 50.000 0.00 0.00 40.48 4.85
511 514 1.202359 TGCCTGGAACGCAAAAAGTTC 60.202 47.619 0.00 0.89 45.16 3.01
514 517 3.115554 CCTGGAACGCAAAAAGTTCTTG 58.884 45.455 8.66 0.00 45.20 3.02
583 586 4.099380 TCGCAAATTTTTATTCCCGGTC 57.901 40.909 0.00 0.00 0.00 4.79
661 664 1.965414 TAGCCTCTTGTTGGGATGGA 58.035 50.000 0.00 0.00 0.00 3.41
749 752 3.179443 TGTGACAGGAACACTTCTGAC 57.821 47.619 0.00 0.00 38.81 3.51
751 754 3.197766 TGTGACAGGAACACTTCTGACTT 59.802 43.478 0.00 0.00 38.81 3.01
777 784 3.713288 TGTTGTACTTCGTGGACTCTTG 58.287 45.455 0.00 0.00 0.00 3.02
778 785 2.433868 TGTACTTCGTGGACTCTTGC 57.566 50.000 0.00 0.00 0.00 4.01
779 786 1.961394 TGTACTTCGTGGACTCTTGCT 59.039 47.619 0.00 0.00 0.00 3.91
780 787 2.364324 TGTACTTCGTGGACTCTTGCTT 59.636 45.455 0.00 0.00 0.00 3.91
788 795 3.369147 CGTGGACTCTTGCTTATCAGTTG 59.631 47.826 0.00 0.00 0.00 3.16
898 905 3.626924 AGGGTGGTCAGTGGCGAC 61.627 66.667 0.57 0.57 35.03 5.19
1131 1140 2.036387 TGAGTCCAACGAAGACTTGGA 58.964 47.619 4.01 0.55 44.55 3.53
1141 1150 2.565841 GAAGACTTGGATAATGCGCCT 58.434 47.619 4.18 0.00 0.00 5.52
1246 1255 0.973632 TCGACCAGCTTCTTAAGGCA 59.026 50.000 1.85 0.00 0.00 4.75
1308 1317 1.657751 GCCGGGGCAGATTCTTTGTC 61.658 60.000 2.18 0.00 41.49 3.18
1358 1367 3.084039 GGGTCATCTCAAATTGCAGTCA 58.916 45.455 0.00 0.00 0.00 3.41
1528 1537 1.280421 GCCTCCTTGATGGTTCAGAGT 59.720 52.381 0.00 0.00 37.07 3.24
1541 1550 3.182967 GTTCAGAGTAGTGATGGAAGCG 58.817 50.000 0.00 0.00 0.00 4.68
1945 1954 5.535030 AGAACAACCTTCACTTGGTAATTCC 59.465 40.000 0.00 0.00 36.69 3.01
2099 2108 1.924731 TGAGAGGTCGTCTGAATGGT 58.075 50.000 0.00 0.00 34.71 3.55
2395 2404 7.771183 TGTTTGCTTTGAAGGTTATGGATATC 58.229 34.615 0.00 0.00 0.00 1.63
2549 2558 0.175073 GTACTGTCCGGGTGGTGATC 59.825 60.000 0.00 0.00 36.30 2.92
2626 2635 7.277098 GCGAGGTACATTTCATTGAGTACTTAA 59.723 37.037 2.16 2.16 37.55 1.85
2653 2662 8.037382 ACTTCAGACATGAACATTCAGTATTG 57.963 34.615 0.00 0.00 40.54 1.90
2658 2667 6.656270 AGACATGAACATTCAGTATTGCAGAA 59.344 34.615 0.00 0.00 41.08 3.02
2707 2716 9.760077 TTTCTTTACTCGAAGTAATCAGTTTCT 57.240 29.630 7.86 0.00 40.08 2.52
2785 2794 2.851263 TGTTGGCTCGGTTTATGACT 57.149 45.000 0.00 0.00 0.00 3.41
2973 2984 5.903810 CCACTTTAGAGAGGCGTATTTAGT 58.096 41.667 0.00 0.00 0.00 2.24
2974 2985 7.035840 CCACTTTAGAGAGGCGTATTTAGTA 57.964 40.000 0.00 0.00 0.00 1.82
2975 2986 6.916932 CCACTTTAGAGAGGCGTATTTAGTAC 59.083 42.308 0.00 0.00 0.00 2.73
3025 3036 6.655062 TGTTCTAATAACTCTGTTTTGCACG 58.345 36.000 0.00 0.00 0.00 5.34
3858 3869 4.240888 GGAAGAAGAAAGAAGGCAAATGC 58.759 43.478 0.00 0.00 41.14 3.56
3915 3926 4.009370 AGTTTTCTAGTGAGGTCTTGGC 57.991 45.455 0.00 0.00 0.00 4.52
4074 4085 2.206576 AAGGAACAATCAGAGCCCAC 57.793 50.000 0.00 0.00 0.00 4.61
4077 4088 0.321653 GAACAATCAGAGCCCACGGT 60.322 55.000 0.00 0.00 0.00 4.83
4131 4142 6.461370 CCAGTTGATCTAGTGATCTCTTCCTG 60.461 46.154 12.83 0.00 46.84 3.86
4146 4157 0.537143 TCCTGTTGTGCAGCCGAATT 60.537 50.000 0.00 0.00 43.71 2.17
4163 4174 1.760192 ATTCTTGGAGGAGCATGCAC 58.240 50.000 21.98 14.31 0.00 4.57
4181 4192 3.012518 GCACATCCACTGTTTCTGCTAT 58.987 45.455 0.00 0.00 35.29 2.97
4200 4211 1.668826 TGGGCAAGAGGGTGATTACT 58.331 50.000 0.00 0.00 0.00 2.24
4309 4320 8.536175 ACAAAAACATCCTTTTTCTTACTCCAA 58.464 29.630 0.00 0.00 30.00 3.53
4321 4332 4.955335 TCTTACTCCAAATACTCCCTCCA 58.045 43.478 0.00 0.00 0.00 3.86
4339 4371 5.183904 CCCTCCATTCACTTTTGTAAGGAAG 59.816 44.000 0.00 0.00 35.61 3.46
4358 4390 4.636206 GGAAGGCCTTACAATAGTGAACAG 59.364 45.833 23.74 0.00 0.00 3.16
4367 4399 7.070074 CCTTACAATAGTGAACAGAGGGAGTAT 59.930 40.741 0.00 0.00 0.00 2.12
4604 4637 2.862541 TGTGGTGTTGGATCCAGAAAG 58.137 47.619 15.53 0.00 34.16 2.62
4687 4720 5.738693 CACGATTTATGATGCGTCACATTTT 59.261 36.000 11.65 0.00 39.84 1.82
4761 4794 2.026636 GGTGAGGGTTATGCCTTGTACA 60.027 50.000 0.00 0.00 37.43 2.90
4762 4795 3.560453 GGTGAGGGTTATGCCTTGTACAA 60.560 47.826 8.28 8.28 37.43 2.41
4763 4796 4.270008 GTGAGGGTTATGCCTTGTACAAT 58.730 43.478 9.13 0.00 37.43 2.71
4764 4797 4.335594 GTGAGGGTTATGCCTTGTACAATC 59.664 45.833 9.13 4.98 37.43 2.67
4778 4891 8.827677 GCCTTGTACAATCTAAGGTGTTTATAG 58.172 37.037 9.13 0.00 42.30 1.31
4923 5039 2.171341 TACGCACCTTGCATTGTACA 57.829 45.000 0.00 0.00 45.36 2.90
4927 5043 3.694072 ACGCACCTTGCATTGTACATTAT 59.306 39.130 0.00 0.00 45.36 1.28
4928 5044 4.878971 ACGCACCTTGCATTGTACATTATA 59.121 37.500 0.00 0.00 45.36 0.98
5008 5132 6.509418 TTGTGGATTTGGAAGCTATAACAC 57.491 37.500 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 5.750352 ATCGACCTAAAAGGGACAAAGTA 57.250 39.130 0.00 0.00 40.58 2.24
81 82 4.635699 ATCGACCTAAAAGGGACAAAGT 57.364 40.909 0.00 0.00 40.58 2.66
82 83 4.092968 CGAATCGACCTAAAAGGGACAAAG 59.907 45.833 0.00 0.00 40.58 2.77
84 85 3.007182 ACGAATCGACCTAAAAGGGACAA 59.993 43.478 10.55 0.00 40.58 3.18
85 86 2.564062 ACGAATCGACCTAAAAGGGACA 59.436 45.455 10.55 0.00 40.58 4.02
230 232 4.436998 GGAGTGGGGTGTCTCGCG 62.437 72.222 0.00 0.00 0.00 5.87
234 236 2.997897 GAGCGGAGTGGGGTGTCT 60.998 66.667 0.00 0.00 0.00 3.41
295 297 2.353889 GAGACGACGATGCTTACCTACA 59.646 50.000 0.00 0.00 0.00 2.74
306 308 0.393132 TCCAGAGCAGAGACGACGAT 60.393 55.000 0.00 0.00 0.00 3.73
375 377 1.793258 TTTCGCGGTTAATTCGTCCA 58.207 45.000 6.13 0.00 0.00 4.02
408 410 4.863925 GAGCCTCCACGAGCTCGC 62.864 72.222 34.83 17.90 45.44 5.03
511 514 0.039764 GGAGGGAGGGGGAAAACAAG 59.960 60.000 0.00 0.00 0.00 3.16
514 517 2.980177 CGGGAGGGAGGGGGAAAAC 61.980 68.421 0.00 0.00 0.00 2.43
558 561 5.164954 CCGGGAATAAAAATTTGCGAGAAA 58.835 37.500 0.00 0.00 0.00 2.52
583 586 2.571611 GATGCAACGCAAGCGACG 60.572 61.111 22.30 12.00 43.62 5.12
661 664 1.995542 TGGGAGAAGAGGGCAAGATTT 59.004 47.619 0.00 0.00 0.00 2.17
749 752 5.236478 AGTCCACGAAGTACAACAAATGAAG 59.764 40.000 0.00 0.00 41.61 3.02
751 754 4.699637 AGTCCACGAAGTACAACAAATGA 58.300 39.130 0.00 0.00 41.61 2.57
824 831 6.527722 GCAATAGCAACATTTCTCGAAAATGA 59.472 34.615 25.90 12.82 38.95 2.57
827 834 5.160641 GGCAATAGCAACATTTCTCGAAAA 58.839 37.500 0.00 0.00 44.61 2.29
956 964 3.806949 ATTGTGCCTTTTAGGGAGACA 57.193 42.857 0.00 0.00 35.94 3.41
1014 1022 0.759346 CTTATCTTAGCCCACCGCCT 59.241 55.000 0.00 0.00 38.78 5.52
1075 1084 3.387091 CCGGACGACCCCATCACA 61.387 66.667 0.00 0.00 0.00 3.58
1131 1140 1.308998 GCCACTAACAGGCGCATTAT 58.691 50.000 10.83 0.00 43.15 1.28
1141 1150 1.005037 CACGCTGGAGCCACTAACA 60.005 57.895 0.00 0.00 37.91 2.41
1246 1255 4.694339 GACGGTAAGTCCTGCTATCAATT 58.306 43.478 0.00 0.00 43.95 2.32
1308 1317 2.578495 GTGTCTTTTGAGCATGCTTCG 58.422 47.619 23.61 8.80 0.00 3.79
1528 1537 1.270571 TGCACAACGCTTCCATCACTA 60.271 47.619 0.00 0.00 43.06 2.74
1541 1550 8.430063 CAAGTTCTTTTTATCATCATGCACAAC 58.570 33.333 0.00 0.00 0.00 3.32
1808 1817 5.958321 TCTGGATGGACTATCATCAGTAGT 58.042 41.667 0.88 0.00 43.82 2.73
1945 1954 9.255304 GAAGAGCAGAATTTAGTACTATTGGAG 57.745 37.037 2.79 0.00 0.00 3.86
2099 2108 5.362430 AGCACTCACCTTTTTCCAATGTTAA 59.638 36.000 0.00 0.00 0.00 2.01
2395 2404 7.769220 TCTTTTTCCTACTAATCAGGTACTCG 58.231 38.462 0.00 0.00 34.60 4.18
2626 2635 6.949352 ACTGAATGTTCATGTCTGAAGTTT 57.051 33.333 0.00 0.00 41.96 2.66
2634 2643 6.426980 TCTGCAATACTGAATGTTCATGTC 57.573 37.500 0.00 0.00 36.46 3.06
2785 2794 7.505585 AGGAAATTTGGAACATCAAGAACTACA 59.494 33.333 0.00 0.00 39.30 2.74
2926 2937 7.232534 TGGCATCCTTAAAGTTGAAAAGTACAT 59.767 33.333 0.00 0.00 0.00 2.29
3025 3036 2.080286 AACAGATGGCGACTACACAC 57.920 50.000 0.00 0.00 0.00 3.82
3858 3869 1.153349 GGCGCTCCTAAAGTCCAGG 60.153 63.158 7.64 0.00 34.20 4.45
3867 3878 4.507916 AGCTCCTCGGCGCTCCTA 62.508 66.667 7.64 0.00 29.26 2.94
3915 3926 3.983344 GGCAGAAATTGTGCTAAACTGTG 59.017 43.478 14.70 0.00 40.97 3.66
4046 4057 7.378181 GGCTCTGATTGTTCCTTTCAATTAAA 58.622 34.615 0.00 0.00 35.94 1.52
4077 4088 2.588027 TAGACGCAACGGCAATGATA 57.412 45.000 0.00 0.00 37.34 2.15
4131 4142 1.666888 CCAAGAATTCGGCTGCACAAC 60.667 52.381 0.50 0.00 0.00 3.32
4146 4157 0.622136 ATGTGCATGCTCCTCCAAGA 59.378 50.000 20.33 0.00 0.00 3.02
4163 4174 2.947652 CCCATAGCAGAAACAGTGGATG 59.052 50.000 0.00 0.00 0.00 3.51
4181 4192 1.668826 AGTAATCACCCTCTTGCCCA 58.331 50.000 0.00 0.00 0.00 5.36
4200 4211 0.887933 GCGCCCATTTGAGAGGAAAA 59.112 50.000 0.00 0.00 0.00 2.29
4309 4320 5.892348 ACAAAAGTGAATGGAGGGAGTATT 58.108 37.500 0.00 0.00 0.00 1.89
4321 4332 4.740902 AGGCCTTCCTTACAAAAGTGAAT 58.259 39.130 0.00 0.00 40.66 2.57
4339 4371 4.192317 CCTCTGTTCACTATTGTAAGGCC 58.808 47.826 0.00 0.00 0.00 5.19
4349 4381 6.681729 AAAACATACTCCCTCTGTTCACTA 57.318 37.500 0.00 0.00 32.18 2.74
4532 4565 0.196888 ATCATAGGGCCCCATGGAGA 59.803 55.000 27.46 11.15 0.00 3.71
4604 4637 3.054361 ACCCCAGTTGTTACATCTCCATC 60.054 47.826 0.00 0.00 0.00 3.51
4687 4720 3.327464 TCACATGTTCCCACATCTTCTCA 59.673 43.478 0.00 0.00 42.14 3.27
4799 4912 8.147244 ACCCTCTACAAATAAATACTCAGTGT 57.853 34.615 0.00 0.00 0.00 3.55
4889 5002 6.420913 AGGTGCGTAAGGAGATATGTAAAT 57.579 37.500 0.00 0.00 39.66 1.40
4896 5009 2.596904 GCAAGGTGCGTAAGGAGATA 57.403 50.000 0.00 0.00 39.66 1.98
4923 5039 7.824289 ACATGGCGATTAGTAGCAACATATAAT 59.176 33.333 0.00 0.00 34.54 1.28
4927 5043 4.956085 ACATGGCGATTAGTAGCAACATA 58.044 39.130 0.00 0.00 34.54 2.29
4928 5044 3.808728 ACATGGCGATTAGTAGCAACAT 58.191 40.909 0.00 0.00 34.54 2.71
5008 5132 1.016627 AATCATGGCATTGTCGGTCG 58.983 50.000 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.