Multiple sequence alignment - TraesCS7D01G181400

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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 TraesCS7D01G181400 chr7D 100.000 3140 0 0 1 3140 135356355 135359494 0.000000e+00 5799.0
1 TraesCS7D01G181400 chr7D 100.000 244 0 0 984 1227 135356809 135356566 4.780000e-123 451.0
2 TraesCS7D01G181400 chr7D 100.000 244 0 0 212 455 135357581 135357338 4.780000e-123 451.0
3 TraesCS7D01G181400 chr7A 95.305 2705 87 13 467 3140 134490711 134493406 0.000000e+00 4255.0
4 TraesCS7D01G181400 chr7A 95.902 244 3 2 212 455 134491464 134491228 3.800000e-104 388.0
5 TraesCS7D01G181400 chr7A 94.444 216 6 4 1 210 134490450 134490665 8.400000e-86 327.0
6 TraesCS7D01G181400 chr7B 93.153 2731 121 23 457 3140 97191617 97194328 0.000000e+00 3947.0
7 TraesCS7D01G181400 chr7B 91.935 186 10 5 271 455 97192332 97192151 4.020000e-64 255.0
8 TraesCS7D01G181400 chr7B 85.185 216 23 7 1 210 97191390 97191602 2.450000e-51 213.0
9 TraesCS7D01G181400 chr6B 77.038 601 110 23 1221 1801 613610385 613610977 1.410000e-83 320.0
10 TraesCS7D01G181400 chr6B 77.461 386 78 7 1424 1804 614127916 614128297 4.080000e-54 222.0
11 TraesCS7D01G181400 chr6D 78.756 386 73 8 1424 1804 409288380 409288761 1.870000e-62 250.0
12 TraesCS7D01G181400 chr6D 77.922 385 76 6 1425 1804 408945987 408946367 6.770000e-57 231.0
13 TraesCS7D01G181400 chr6A 78.497 386 74 7 1424 1804 554716446 554716827 8.700000e-61 244.0
14 TraesCS7D01G181400 chr3A 81.102 127 20 4 1232 1356 330698437 330698561 7.170000e-17 99.0
15 TraesCS7D01G181400 chr1D 92.188 64 5 0 747 810 118475725 118475662 1.200000e-14 91.6
16 TraesCS7D01G181400 chr1B 77.966 118 26 0 1426 1543 615744798 615744681 1.210000e-09 75.0
17 TraesCS7D01G181400 chr1A 81.609 87 16 0 1447 1533 545009086 545009000 4.340000e-09 73.1


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 TraesCS7D01G181400 chr7D 135356355 135359494 3139 False 5799 5799 100.0000 1 3140 1 chr7D.!!$F1 3139
1 TraesCS7D01G181400 chr7D 135356566 135357581 1015 True 451 451 100.0000 212 1227 2 chr7D.!!$R1 1015
2 TraesCS7D01G181400 chr7A 134490450 134493406 2956 False 2291 4255 94.8745 1 3140 2 chr7A.!!$F1 3139
3 TraesCS7D01G181400 chr7B 97191390 97194328 2938 False 2080 3947 89.1690 1 3140 2 chr7B.!!$F1 3139
4 TraesCS7D01G181400 chr6B 613610385 613610977 592 False 320 320 77.0380 1221 1801 1 chr6B.!!$F1 580

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
792 958 2.923020 CCATAAAGTGAACGCAAATGCC 59.077 45.455 0.0 0.0 37.91 4.40 F
1613 1979 1.197721 CAACCTTCGGCAGTTCATCAC 59.802 52.381 0.0 0.0 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1674 2043 0.596577 GTGACTGCACGTACTGGAGA 59.403 55.000 16.58 0.0 40.82 3.71 R
2789 3183 1.468054 CGGCATGTTTTTCAGCTAGCC 60.468 52.381 12.13 0.0 37.54 3.93 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
164 166 9.844257 AAAGCATACTGAAATTAAGCTCTATCT 57.156 29.630 0.00 0.00 0.00 1.98
169 174 9.771534 ATACTGAAATTAAGCTCTATCTGGTTC 57.228 33.333 0.00 0.00 0.00 3.62
210 218 5.374921 CATACAGGCTCAGATGAAAAGGAT 58.625 41.667 0.00 0.00 0.00 3.24
792 958 2.923020 CCATAAAGTGAACGCAAATGCC 59.077 45.455 0.00 0.00 37.91 4.40
1613 1979 1.197721 CAACCTTCGGCAGTTCATCAC 59.802 52.381 0.00 0.00 0.00 3.06
1625 1991 3.504906 CAGTTCATCACTCAGCAACCATT 59.495 43.478 0.00 0.00 30.92 3.16
1714 2083 1.447489 CTTCACTCTGCAGCCTCCG 60.447 63.158 9.47 0.00 0.00 4.63
1942 2311 6.545666 ACATAACAATGTTGAAACCAGTGAGA 59.454 34.615 9.15 0.00 0.00 3.27
1968 2337 1.882989 GCAGCGAGGGAGAGAACAGT 61.883 60.000 0.00 0.00 0.00 3.55
1972 2341 0.741915 CGAGGGAGAGAACAGTAGCC 59.258 60.000 0.00 0.00 0.00 3.93
1981 2350 3.648545 AGAGAACAGTAGCCAGAAAAGGT 59.351 43.478 0.00 0.00 0.00 3.50
1982 2351 3.997681 GAGAACAGTAGCCAGAAAAGGTC 59.002 47.826 0.00 0.00 0.00 3.85
2064 2433 1.143684 ACCATCAGCACCTCAAACTGT 59.856 47.619 0.00 0.00 33.12 3.55
2124 2493 3.131933 TCCTACTTGATGAAGAGCTGCTC 59.868 47.826 21.72 21.72 32.98 4.26
2125 2494 3.132646 CCTACTTGATGAAGAGCTGCTCT 59.867 47.826 25.80 25.80 43.37 4.09
2142 2511 0.448990 TCTGCGAGTTTGCATGATGC 59.551 50.000 11.12 11.12 45.26 3.91
2387 2756 3.181443 TGGGTTGTTCTTCCTTTCTCTCC 60.181 47.826 0.00 0.00 0.00 3.71
2451 2822 7.494625 CCTAGTTGCTCGAAAATAGGTCATTTA 59.505 37.037 12.97 0.00 41.07 1.40
2452 2823 7.073342 AGTTGCTCGAAAATAGGTCATTTAC 57.927 36.000 0.00 0.00 35.74 2.01
2575 2969 5.368256 AAGCTTGACTGATTGCACTTTAG 57.632 39.130 0.00 0.00 0.00 1.85
2789 3183 5.185056 AGGAATTACAGGAAAATCCCAAACG 59.815 40.000 0.00 0.00 37.19 3.60
2889 3285 1.555075 TGTTAGGGTCAGCATGTCCTC 59.445 52.381 0.00 0.00 44.10 3.71
2940 3336 5.772169 CCTTTTCCTCCAAGAAATTGACTCT 59.228 40.000 0.00 0.00 35.74 3.24
2943 3339 5.157940 TCCTCCAAGAAATTGACTCTGAG 57.842 43.478 2.45 2.45 0.00 3.35
3026 3429 3.664947 CCAAAAATGCAAAAGCGCAAATC 59.335 39.130 11.47 0.00 46.87 2.17
3027 3430 4.529446 CAAAAATGCAAAAGCGCAAATCT 58.471 34.783 11.47 0.00 46.87 2.40
3058 3461 3.365832 GTGCATATCTTCATTGCAACCG 58.634 45.455 0.00 0.00 46.91 4.44
3083 3486 6.572314 GCCAATTACTCCACTTGCAAAATACT 60.572 38.462 0.00 0.00 0.00 2.12
3130 3533 6.392625 TCACTACTTTAAGAGAGCGCATAT 57.607 37.500 11.47 0.00 0.00 1.78
3133 3536 8.237949 TCACTACTTTAAGAGAGCGCATATATC 58.762 37.037 11.47 0.00 0.00 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
169 174 4.586841 TGTATGGTTTTTGGAACAGAAGGG 59.413 41.667 0.00 0.00 42.39 3.95
210 218 4.609301 ACCATATTTTTCTTGCAGGCCTA 58.391 39.130 3.98 0.00 0.00 3.93
456 464 9.687210 CGATCATGAAATTGAATAATTGATGGT 57.313 29.630 0.00 0.00 36.65 3.55
457 465 9.687210 ACGATCATGAAATTGAATAATTGATGG 57.313 29.630 0.00 0.00 36.65 3.51
465 473 9.075519 GCTTTTGAACGATCATGAAATTGAATA 57.924 29.630 0.00 0.00 34.96 1.75
473 481 5.830912 AGTTTGCTTTTGAACGATCATGAA 58.169 33.333 0.00 0.00 34.96 2.57
792 958 4.272489 TGGAAAAGACTGATATGCCCTTG 58.728 43.478 0.00 0.00 0.00 3.61
1356 1698 3.682718 GCAGTGGATGTAGGTGCAGTTAT 60.683 47.826 0.00 0.00 34.18 1.89
1613 1979 1.747355 GGTCATCCAATGGTTGCTGAG 59.253 52.381 5.49 0.00 0.00 3.35
1625 1991 2.756400 GGGCAGTGTGGTCATCCA 59.244 61.111 0.00 0.00 42.05 3.41
1674 2043 0.596577 GTGACTGCACGTACTGGAGA 59.403 55.000 16.58 0.00 40.82 3.71
1829 2198 1.072965 GCCCTGCTAAGTCTATGCCAT 59.927 52.381 0.00 0.00 0.00 4.40
1953 2322 0.741915 GGCTACTGTTCTCTCCCTCG 59.258 60.000 0.00 0.00 0.00 4.63
1968 2337 3.323979 AGAGAAACGACCTTTTCTGGCTA 59.676 43.478 6.28 0.00 44.27 3.93
1972 2341 4.621991 TCAGAGAGAAACGACCTTTTCTG 58.378 43.478 6.28 3.60 44.27 3.02
1981 2350 3.641906 AGGGAGTTTTCAGAGAGAAACGA 59.358 43.478 0.00 0.00 45.48 3.85
1982 2351 3.996480 AGGGAGTTTTCAGAGAGAAACG 58.004 45.455 0.00 0.00 45.48 3.60
2064 2433 2.683859 CGGACTACTGACGCCGTCA 61.684 63.158 20.04 20.04 40.50 4.35
2124 2493 2.939782 GCATCATGCAAACTCGCAG 58.060 52.632 4.20 0.00 46.99 5.18
2142 2511 3.955471 TCAAGCTAGGGAATTCAGGTTG 58.045 45.455 21.39 21.39 44.93 3.77
2281 2650 6.090483 TCTCATGCTTGTAGGCTTATCTAC 57.910 41.667 0.00 0.00 39.86 2.59
2387 2756 5.279708 CCAGGAACTAAGATATAGTGGCAGG 60.280 48.000 0.00 0.00 36.02 4.85
2451 2822 5.777802 TCGCACCATTTGTATCAAAATTGT 58.222 33.333 0.00 0.00 0.00 2.71
2452 2823 6.530887 TCATCGCACCATTTGTATCAAAATTG 59.469 34.615 0.00 0.00 0.00 2.32
2499 2870 4.215613 AGTGAGCGGTATTTTTCTTTCACC 59.784 41.667 0.00 0.00 35.50 4.02
2560 2954 1.815003 GCTGCCTAAAGTGCAATCAGT 59.185 47.619 0.00 0.00 38.46 3.41
2575 2969 3.194329 AGGAAAAGCATTTAGAAGCTGCC 59.806 43.478 0.00 0.00 41.70 4.85
2672 3066 1.800586 TCTTCTGCATGCTCGTGTTTC 59.199 47.619 20.33 0.00 0.00 2.78
2789 3183 1.468054 CGGCATGTTTTTCAGCTAGCC 60.468 52.381 12.13 0.00 37.54 3.93
2872 3266 1.676678 GCGAGGACATGCTGACCCTA 61.677 60.000 0.00 0.00 32.57 3.53
2889 3285 2.973945 ACTTTTACCTGCTCTAAGGCG 58.026 47.619 0.00 0.00 41.46 5.52
2940 3336 6.995686 TGCTACCTCTTTAAAACATGTTCTCA 59.004 34.615 12.39 0.00 0.00 3.27
2943 3339 6.861572 GGTTGCTACCTCTTTAAAACATGTTC 59.138 38.462 12.39 0.00 41.53 3.18
3026 3429 9.406828 CAATGAAGATATGCACCATGATTTAAG 57.593 33.333 0.00 0.00 0.00 1.85
3027 3430 7.868922 GCAATGAAGATATGCACCATGATTTAA 59.131 33.333 0.00 0.00 39.81 1.52
3058 3461 3.658757 TTTGCAAGTGGAGTAATTGGC 57.341 42.857 0.00 0.00 35.03 4.52


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

AutoCloner maintained by Alex Coulton.