Multiple sequence alignment - TraesCS7A01G135300

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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 TraesCS7A01G135300 chr7A 100.000 4095 0 0 1 4095 88178816 88174722 0 7563
1 TraesCS7A01G135300 chr7A 97.012 4117 96 6 1 4095 88128065 88123954 0 6896
2 TraesCS7A01G135300 chr7A 96.738 4139 87 8 1 4095 88014808 88010674 0 6852
3 TraesCS7A01G135300 chr7A 91.562 4160 261 37 1 4095 88442319 88438185 0 5655
4 TraesCS7A01G135300 chr7A 89.375 3454 265 35 719 4095 87456919 87453491 0 4252
5 TraesCS7A01G135300 chr7A 90.226 2568 186 15 4 2530 88324114 88321571 0 3291
6 TraesCS7A01G135300 chr7A 93.283 1444 84 9 2540 3972 88320596 88319155 0 2117
7 TraesCS7A01G135300 chr7D 92.622 4161 221 29 1 4095 87212888 87208748 0 5904
8 TraesCS7A01G135300 chr7D 93.168 3981 221 23 1 3938 86768941 86764969 0 5797
9 TraesCS7A01G135300 chr7D 92.869 3688 211 23 452 4095 86924514 86920835 0 5306
10 TraesCS7A01G135300 chr7D 88.859 3761 321 35 390 4095 86800998 86797281 0 4534
11 TraesCS7A01G135300 chr7D 93.125 2429 130 15 1 2405 86927712 86925297 0 3526
12 TraesCS7A01G135300 chr7D 85.791 2245 254 31 142 2340 86298583 86296358 0 2318
13 TraesCS7A01G135300 chr7B 89.519 3931 305 36 223 4075 35313792 35309891 0 4878
14 TraesCS7A01G135300 chr7B 89.396 3310 242 39 1 3251 35513702 35510443 0 4067
15 TraesCS7A01G135300 chr7B 81.014 2307 330 58 142 2395 35257603 35255352 0 1735


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 TraesCS7A01G135300 chr7A 88174722 88178816 4094 True 7563 7563 100.0000 1 4095 1 chr7A.!!$R4 4094
1 TraesCS7A01G135300 chr7A 88123954 88128065 4111 True 6896 6896 97.0120 1 4095 1 chr7A.!!$R3 4094
2 TraesCS7A01G135300 chr7A 88010674 88014808 4134 True 6852 6852 96.7380 1 4095 1 chr7A.!!$R2 4094
3 TraesCS7A01G135300 chr7A 88438185 88442319 4134 True 5655 5655 91.5620 1 4095 1 chr7A.!!$R5 4094
4 TraesCS7A01G135300 chr7A 87453491 87456919 3428 True 4252 4252 89.3750 719 4095 1 chr7A.!!$R1 3376
5 TraesCS7A01G135300 chr7A 88319155 88324114 4959 True 2704 3291 91.7545 4 3972 2 chr7A.!!$R6 3968
6 TraesCS7A01G135300 chr7D 87208748 87212888 4140 True 5904 5904 92.6220 1 4095 1 chr7D.!!$R4 4094
7 TraesCS7A01G135300 chr7D 86764969 86768941 3972 True 5797 5797 93.1680 1 3938 1 chr7D.!!$R2 3937
8 TraesCS7A01G135300 chr7D 86797281 86800998 3717 True 4534 4534 88.8590 390 4095 1 chr7D.!!$R3 3705
9 TraesCS7A01G135300 chr7D 86920835 86927712 6877 True 4416 5306 92.9970 1 4095 2 chr7D.!!$R5 4094
10 TraesCS7A01G135300 chr7D 86296358 86298583 2225 True 2318 2318 85.7910 142 2340 1 chr7D.!!$R1 2198
11 TraesCS7A01G135300 chr7B 35309891 35313792 3901 True 4878 4878 89.5190 223 4075 1 chr7B.!!$R2 3852
12 TraesCS7A01G135300 chr7B 35510443 35513702 3259 True 4067 4067 89.3960 1 3251 1 chr7B.!!$R3 3250
13 TraesCS7A01G135300 chr7B 35255352 35257603 2251 True 1735 1735 81.0140 142 2395 1 chr7B.!!$R1 2253

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
576 635 1.715785 AACCATGGTTTGGGTCTTGG 58.284 50.0 24.86 0.0 44.50 3.61 F
1258 4106 2.429610 ACCCATGTTACTAGTGGTAGCG 59.570 50.0 5.39 0.0 34.91 4.26 F
1810 4673 0.908198 AGGCACAAGAGGATGAGGAC 59.092 55.0 0.00 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1570 4424 1.269413 GGACGAACGTGTTCCTTCTCA 60.269 52.381 4.19 0.0 36.27 3.27 R
2686 6573 1.348064 CAGGGGTCTTAGTGGTGACA 58.652 55.000 0.00 0.0 35.11 3.58 R
3642 7560 0.586319 CCACAACGTAGCAACACCAG 59.414 55.000 0.00 0.0 0.00 4.00 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
56 58 4.646945 CGTGGTCCCATATGATAGCTAGAT 59.353 45.833 3.65 0.00 0.00 1.98
338 369 8.443176 AGAAATCTGCCTATAGATGGAATTTCA 58.557 33.333 18.81 0.00 37.48 2.69
576 635 1.715785 AACCATGGTTTGGGTCTTGG 58.284 50.000 24.86 0.00 44.50 3.61
648 709 8.701895 TCCTATCTATCTACACCGAAATTGTTT 58.298 33.333 0.00 0.00 0.00 2.83
665 726 9.952188 GAAATTGTTTAATACTCAATAGGCCTC 57.048 33.333 9.68 0.00 32.52 4.70
794 862 8.349568 AGGTCAACTTAAAATAGTTTGGGATC 57.650 34.615 0.00 0.00 36.24 3.36
981 3826 8.226819 TCATACTCCTCATAATTCTATAGCGG 57.773 38.462 0.00 0.00 0.00 5.52
1203 4051 9.632807 GTAACAGATCTTTATATTGATCTCGCT 57.367 33.333 12.39 5.85 45.13 4.93
1258 4106 2.429610 ACCCATGTTACTAGTGGTAGCG 59.570 50.000 5.39 0.00 34.91 4.26
1308 4159 3.845178 TGTCAACGGTAACTATGAGCTG 58.155 45.455 0.00 0.00 30.72 4.24
1408 4262 2.606725 CGAGAGGAGTGCAACAATCATC 59.393 50.000 1.87 1.87 39.09 2.92
1449 4303 6.058183 CCTTTGGTTGTCCTATGGAGAATAG 58.942 44.000 0.00 0.00 37.32 1.73
1570 4424 3.324556 CACATCAATGGGGTTTTTGGACT 59.675 43.478 0.00 0.00 0.00 3.85
1573 4427 3.230134 TCAATGGGGTTTTTGGACTGAG 58.770 45.455 0.00 0.00 0.00 3.35
1810 4673 0.908198 AGGCACAAGAGGATGAGGAC 59.092 55.000 0.00 0.00 0.00 3.85
1834 4697 7.296856 ACACAACCATGGATGATAATGGATTA 58.703 34.615 27.18 0.00 45.29 1.75
1869 4750 4.406972 CAGACTGGAGGATACAAGAATCCA 59.593 45.833 5.72 0.00 46.81 3.41
1967 4848 1.213537 GCTGTTGCCGCACATCAAT 59.786 52.632 0.00 0.00 0.00 2.57
2292 5197 7.726216 GGCAGTAAAATAGGCCATTAAATTCT 58.274 34.615 5.01 0.00 45.70 2.40
2503 5425 2.025589 TGCGTTGTTGTAGTGGTTCA 57.974 45.000 0.00 0.00 0.00 3.18
2686 6573 6.041979 ACTGGAAAAACATATCCAAGCACTTT 59.958 34.615 0.00 0.00 44.77 2.66
2775 6662 0.955428 GCATCGTCAGGGACAAAGCA 60.955 55.000 0.00 0.00 32.09 3.91
3144 7035 3.066760 GCCATGTTTGGAATACTAGCCAC 59.933 47.826 0.00 0.00 46.92 5.01
3659 7577 1.134640 TGTCTGGTGTTGCTACGTTGT 60.135 47.619 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
338 369 5.203528 CCATTCTTCCCACATCCAACTTAT 58.796 41.667 0.00 0.00 0.00 1.73
576 635 4.489810 ACATGTGTTCTCATCTTCGAGTC 58.510 43.478 0.00 0.00 34.46 3.36
608 667 2.760650 AGATAGGACACGCATCTTGTGA 59.239 45.455 0.00 0.00 39.73 3.58
648 709 4.038763 CACACGGAGGCCTATTGAGTATTA 59.961 45.833 4.42 0.00 0.00 0.98
665 726 3.498397 AGATTGCTAGAAACAACACACGG 59.502 43.478 0.00 0.00 0.00 4.94
981 3826 4.003648 CCATGAGAAAGTGGGTAGTTGAC 58.996 47.826 0.00 0.00 0.00 3.18
1203 4051 3.378861 TGGGTCATATGCATTTCCACA 57.621 42.857 3.54 0.00 0.00 4.17
1258 4106 3.942539 AAAGGTGAAAATGTTTTGCGC 57.057 38.095 0.00 0.00 0.00 6.09
1308 4159 1.396653 CACCATTCTCCTCCATTGGC 58.603 55.000 0.00 0.00 0.00 4.52
1396 4250 5.356470 TCCATTATTGTCGATGATTGTTGCA 59.644 36.000 0.00 0.00 0.00 4.08
1449 4303 4.157120 CCGTCACCGTGATCCCCC 62.157 72.222 4.13 0.00 0.00 5.40
1570 4424 1.269413 GGACGAACGTGTTCCTTCTCA 60.269 52.381 4.19 0.00 36.27 3.27
1573 4427 1.459592 CATGGACGAACGTGTTCCTTC 59.540 52.381 4.19 4.26 36.27 3.46
1810 4673 6.659745 AATCCATTATCATCCATGGTTGTG 57.340 37.500 19.92 13.63 40.90 3.33
1834 4697 3.508793 CCTCCAGTCTGCAACAAAATGAT 59.491 43.478 0.00 0.00 0.00 2.45
1869 4750 4.347865 GAGCCTCCTCCGTCTTCT 57.652 61.111 0.00 0.00 31.68 2.85
1967 4848 4.605183 TCCTCTTTGGTCCAAAACTTTCA 58.395 39.130 17.70 0.00 32.75 2.69
2155 5045 9.693739 TGCAGGGATTAGTATTTCTCAAAAATA 57.306 29.630 0.00 0.00 0.00 1.40
2292 5197 4.664150 TGCGACAAGACATACCATATCA 57.336 40.909 0.00 0.00 0.00 2.15
2302 5207 3.202097 TCTGTTTGATTGCGACAAGACA 58.798 40.909 0.00 0.00 0.00 3.41
2503 5425 5.128663 AGCAAACTACCAATTTGACAGGTTT 59.871 36.000 0.00 1.90 39.01 3.27
2686 6573 1.348064 CAGGGGTCTTAGTGGTGACA 58.652 55.000 0.00 0.00 35.11 3.58
2775 6662 4.277672 GCCTGACATCATTGATGCTGTAAT 59.722 41.667 23.43 5.81 43.15 1.89
2823 6710 4.638865 GCCGGGTGACAGAACTATTATTTT 59.361 41.667 2.18 0.00 0.00 1.82
2913 6800 5.181811 TGAGCTTGGTTGTTCATGACTATTG 59.818 40.000 0.00 0.00 0.00 1.90
2916 6803 4.202357 ACTGAGCTTGGTTGTTCATGACTA 60.202 41.667 0.00 0.00 0.00 2.59
3361 7272 7.657336 TGAGACATCATGTACGCTTTCATATA 58.343 34.615 0.00 0.00 0.00 0.86
3642 7560 0.586319 CCACAACGTAGCAACACCAG 59.414 55.000 0.00 0.00 0.00 4.00
3917 7858 8.322091 CCCAATCTAGGTCTCTAAAAGAAGAAA 58.678 37.037 0.00 0.00 35.21 2.52
3938 7879 0.988832 TTCCAAGCCTACGTCCCAAT 59.011 50.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.