Multiple sequence alignment - TraesCS2A01G044400

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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 TraesCS2A01G044400 chr2A 100.000 2572 0 0 1 2572 17598872 17596301 0.000000e+00 4750.0
1 TraesCS2A01G044400 chr2A 87.709 2091 206 24 1 2081 17475130 17473081 0.000000e+00 2390.0
2 TraesCS2A01G044400 chr2A 86.954 2131 208 32 1 2116 17534351 17532276 0.000000e+00 2331.0
3 TraesCS2A01G044400 chr2A 90.000 1820 154 10 1 1811 17503287 17501487 0.000000e+00 2327.0
4 TraesCS2A01G044400 chr2A 90.306 1599 145 3 1 1599 17549684 17548096 0.000000e+00 2085.0
5 TraesCS2A01G044400 chr2A 76.598 2081 332 96 1 2040 17413305 17411339 0.000000e+00 1002.0
6 TraesCS2A01G044400 chr2A 87.879 825 70 10 991 1791 17419081 17418263 0.000000e+00 942.0
7 TraesCS2A01G044400 chr2A 77.565 1511 203 63 943 2401 17546054 17544628 0.000000e+00 787.0
8 TraesCS2A01G044400 chr2A 82.950 522 48 16 1464 1969 17559176 17558680 1.410000e-117 433.0
9 TraesCS2A01G044400 chr2A 80.200 601 81 19 1851 2425 17507621 17507033 1.420000e-112 416.0
10 TraesCS2A01G044400 chr2A 80.968 310 28 12 1484 1791 17507924 17507644 1.550000e-52 217.0
11 TraesCS2A01G044400 chr2A 97.561 41 1 0 2496 2536 17417706 17417666 1.280000e-08 71.3
12 TraesCS2A01G044400 chr2B 90.353 1814 155 7 1 1811 27544971 27543175 0.000000e+00 2362.0
13 TraesCS2A01G044400 chr2B 86.566 1995 219 28 134 2117 27617256 27615300 0.000000e+00 2154.0
14 TraesCS2A01G044400 chr2B 87.164 1153 147 1 1 1153 27582376 27581225 0.000000e+00 1308.0
15 TraesCS2A01G044400 chr2B 79.385 325 28 19 2277 2572 27627632 27627318 2.610000e-45 193.0
16 TraesCS2A01G044400 chr2B 87.209 86 11 0 2487 2572 27587734 27587649 5.860000e-17 99.0
17 TraesCS2A01G044400 chr2D 83.302 2156 283 47 1 2116 15472411 15470293 0.000000e+00 1916.0
18 TraesCS2A01G044400 chr2D 88.889 1422 152 3 1 1416 15506718 15505297 0.000000e+00 1746.0
19 TraesCS2A01G044400 chr2D 96.007 1077 28 7 1045 2117 15458328 15457263 0.000000e+00 1736.0
20 TraesCS2A01G044400 chr2D 77.943 2158 349 64 1 2115 15516566 15514493 0.000000e+00 1230.0
21 TraesCS2A01G044400 chr2D 91.921 458 16 9 2136 2572 15457278 15456821 2.810000e-174 621.0
22 TraesCS2A01G044400 chr2D 86.059 581 55 14 1549 2117 15505223 15504657 3.660000e-168 601.0
23 TraesCS2A01G044400 chr2D 84.000 300 36 7 2134 2422 15504674 15504376 7.010000e-71 278.0
24 TraesCS2A01G044400 chr2D 83.893 298 28 9 2134 2422 15470311 15470025 1.520000e-67 267.0
25 TraesCS2A01G044400 chr2D 84.701 268 26 6 2168 2425 15496582 15496320 1.180000e-63 254.0
26 TraesCS2A01G044400 chr2D 83.069 189 31 1 2134 2322 15514508 15514321 1.220000e-38 171.0


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 TraesCS2A01G044400 chr2A 17596301 17598872 2571 True 4750.000000 4750 100.000000 1 2572 1 chr2A.!!$R5 2571
1 TraesCS2A01G044400 chr2A 17473081 17475130 2049 True 2390.000000 2390 87.709000 1 2081 1 chr2A.!!$R2 2080
2 TraesCS2A01G044400 chr2A 17532276 17534351 2075 True 2331.000000 2331 86.954000 1 2116 1 chr2A.!!$R3 2115
3 TraesCS2A01G044400 chr2A 17544628 17549684 5056 True 1436.000000 2085 83.935500 1 2401 2 chr2A.!!$R8 2400
4 TraesCS2A01G044400 chr2A 17411339 17413305 1966 True 1002.000000 1002 76.598000 1 2040 1 chr2A.!!$R1 2039
5 TraesCS2A01G044400 chr2A 17501487 17507924 6437 True 986.666667 2327 83.722667 1 2425 3 chr2A.!!$R7 2424
6 TraesCS2A01G044400 chr2A 17417666 17419081 1415 True 506.650000 942 92.720000 991 2536 2 chr2A.!!$R6 1545
7 TraesCS2A01G044400 chr2B 27543175 27544971 1796 True 2362.000000 2362 90.353000 1 1811 1 chr2B.!!$R1 1810
8 TraesCS2A01G044400 chr2B 27615300 27617256 1956 True 2154.000000 2154 86.566000 134 2117 1 chr2B.!!$R4 1983
9 TraesCS2A01G044400 chr2B 27581225 27582376 1151 True 1308.000000 1308 87.164000 1 1153 1 chr2B.!!$R2 1152
10 TraesCS2A01G044400 chr2D 15456821 15458328 1507 True 1178.500000 1736 93.964000 1045 2572 2 chr2D.!!$R2 1527
11 TraesCS2A01G044400 chr2D 15470025 15472411 2386 True 1091.500000 1916 83.597500 1 2422 2 chr2D.!!$R3 2421
12 TraesCS2A01G044400 chr2D 15504376 15506718 2342 True 875.000000 1746 86.316000 1 2422 3 chr2D.!!$R4 2421
13 TraesCS2A01G044400 chr2D 15514321 15516566 2245 True 700.500000 1230 80.506000 1 2322 2 chr2D.!!$R5 2321

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
147 4785 0.179 AGATCAGCACCGTCCAATCC 59.821 55.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1964 9490 0.463295 GGAGAGCAGCAGCATAGCAA 60.463 55.0 3.17 0.0 45.49 3.91 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
147 4785 0.179000 AGATCAGCACCGTCCAATCC 59.821 55.000 0.00 0.0 0.00 3.01
260 4898 0.679640 TTAGGCACCAGGCGAATTGG 60.680 55.000 0.00 0.0 46.16 3.16
332 4970 1.673665 CGCTTCTGCCCTTTCAGCT 60.674 57.895 0.00 0.0 34.19 4.24
502 5153 1.730501 GCAAGCTGTCAGTGCTATCA 58.269 50.000 7.93 0.0 40.22 2.15
554 5205 4.290942 CCACCTATTCCTACTCCAAGTCT 58.709 47.826 0.00 0.0 0.00 3.24
636 5296 5.004726 GCAACAACACAACACTCAAAGAATC 59.995 40.000 0.00 0.0 0.00 2.52
708 5369 4.129380 TGTTGTATGTGCATGATAGCTCC 58.871 43.478 0.00 0.0 34.99 4.70
727 5388 0.389817 CTCCATCACTTGCGTTCCGA 60.390 55.000 0.00 0.0 0.00 4.55
864 5525 2.437281 CCTGTCTACATTCTGGGCATCT 59.563 50.000 0.00 0.0 0.00 2.90
896 5557 1.136305 GGCGTGCTACATCTGGAACTA 59.864 52.381 0.00 0.0 0.00 2.24
1011 5672 2.965831 GTCTGAGCATATGGACACCCTA 59.034 50.000 4.56 0.0 0.00 3.53
1323 6008 4.671590 TGGGACGGTCTCGAGGCA 62.672 66.667 20.37 0.0 40.11 4.75
1798 9311 6.279882 TGATTTGGTTTGGTTTGTCTTGATC 58.720 36.000 0.00 0.0 0.00 2.92
1806 9319 7.762159 GGTTTGGTTTGTCTTGATCTTGTTTAA 59.238 33.333 0.00 0.0 0.00 1.52
1824 9337 4.852134 TTAATTTGCTCAGCTTTGCTCA 57.148 36.364 0.00 0.0 36.40 4.26
1964 9490 2.045242 CCTGCCTGCTCATGCTGT 60.045 61.111 0.00 0.0 40.48 4.40
1995 9535 3.132646 TGCTGCTCTCCATTTGTTTGTTT 59.867 39.130 0.00 0.0 0.00 2.83
1996 9536 3.737774 GCTGCTCTCCATTTGTTTGTTTC 59.262 43.478 0.00 0.0 0.00 2.78
2050 9592 9.754382 ATTATTGTAATGCTAAGCAATTCCTTG 57.246 29.630 0.00 0.0 43.62 3.61
2118 9664 9.529325 AAACTGTAGCTTTTTATTTTGTTCTCC 57.471 29.630 0.00 0.0 0.00 3.71
2119 9665 8.465273 ACTGTAGCTTTTTATTTTGTTCTCCT 57.535 30.769 0.00 0.0 0.00 3.69
2120 9666 8.914011 ACTGTAGCTTTTTATTTTGTTCTCCTT 58.086 29.630 0.00 0.0 0.00 3.36
2121 9667 9.750125 CTGTAGCTTTTTATTTTGTTCTCCTTT 57.250 29.630 0.00 0.0 0.00 3.11
2124 9670 8.352752 AGCTTTTTATTTTGTTCTCCTTTTCG 57.647 30.769 0.00 0.0 0.00 3.46
2125 9671 8.194769 AGCTTTTTATTTTGTTCTCCTTTTCGA 58.805 29.630 0.00 0.0 0.00 3.71
2126 9672 8.813282 GCTTTTTATTTTGTTCTCCTTTTCGAA 58.187 29.630 0.00 0.0 0.00 3.71
2410 10030 6.412362 AGTAGTAGCAGTATGGAATCCTTG 57.588 41.667 0.00 0.0 35.86 3.61
2425 10047 8.280258 TGGAATCCTTGTTCTTATCCATATCT 57.720 34.615 0.00 0.0 30.90 1.98
2426 10048 8.727149 TGGAATCCTTGTTCTTATCCATATCTT 58.273 33.333 0.00 0.0 30.90 2.40
2427 10049 9.225436 GGAATCCTTGTTCTTATCCATATCTTC 57.775 37.037 0.00 0.0 0.00 2.87
2433 10055 9.674824 CTTGTTCTTATCCATATCTTCATTTGC 57.325 33.333 0.00 0.0 0.00 3.68
2434 10056 8.169977 TGTTCTTATCCATATCTTCATTTGCC 57.830 34.615 0.00 0.0 0.00 4.52
2481 10130 1.266786 CGACGTGTGTCTTCGTGACC 61.267 60.000 0.00 2.5 44.75 4.02
2489 10138 1.406180 TGTCTTCGTGACCTTTCGACA 59.594 47.619 8.36 0.0 44.75 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 4648 2.301583 GAGCTTCCACTTCTCTGAGGTT 59.698 50.000 4.59 0.00 0.00 3.50
147 4785 2.820059 TATTCTGGCTAGGTGATGCG 57.180 50.000 0.00 0.00 0.00 4.73
502 5153 0.773644 ATCCAGCTGGTCACACCTTT 59.226 50.000 31.58 4.63 39.58 3.11
636 5296 4.865365 GGAGCTAAAGCAACACTAGTACTG 59.135 45.833 5.39 0.00 45.16 2.74
727 5388 2.203538 CCTTGCACCTTGTGGGCT 60.204 61.111 0.00 0.00 39.10 5.19
864 5525 3.094062 GCACGCCATAGGGAGCTGA 62.094 63.158 0.00 0.00 39.06 4.26
896 5557 5.357257 CGCTTGGTTGGTATATTGTACTCT 58.643 41.667 0.00 0.00 0.00 3.24
1011 5672 1.305381 AAGCGTCTCCAGGCTAGGT 60.305 57.895 0.00 0.00 43.08 3.08
1446 6131 4.566987 AGTAAGTTGGCTAGCACACTAAC 58.433 43.478 18.24 12.42 0.00 2.34
1798 9311 5.464389 AGCAAAGCTGAGCAAATTAAACAAG 59.536 36.000 7.39 0.00 37.57 3.16
1806 9319 3.257375 TCATTGAGCAAAGCTGAGCAAAT 59.743 39.130 7.39 8.88 39.88 2.32
1824 9337 6.095440 ACTTTGACGCTTATATGGCTTTCATT 59.905 34.615 0.00 0.00 37.30 2.57
1964 9490 0.463295 GGAGAGCAGCAGCATAGCAA 60.463 55.000 3.17 0.00 45.49 3.91
1995 9535 1.202639 AGCTGACAAATCACACACCGA 60.203 47.619 0.00 0.00 0.00 4.69
1996 9536 1.229428 AGCTGACAAATCACACACCG 58.771 50.000 0.00 0.00 0.00 4.94
2050 9592 6.315393 ACGAATCACCATTTGTATACAAGTCC 59.685 38.462 17.36 2.88 35.16 3.85
2129 9675 6.686679 GCGCAGAACAAAATAAAAAGCTTTTT 59.313 30.769 33.06 33.06 42.51 1.94
2130 9676 6.037062 AGCGCAGAACAAAATAAAAAGCTTTT 59.963 30.769 18.74 18.74 0.00 2.27
2131 9677 5.523552 AGCGCAGAACAAAATAAAAAGCTTT 59.476 32.000 11.47 5.69 0.00 3.51
2132 9678 5.049828 AGCGCAGAACAAAATAAAAAGCTT 58.950 33.333 11.47 0.00 0.00 3.74
2133 9679 4.445385 CAGCGCAGAACAAAATAAAAAGCT 59.555 37.500 11.47 0.00 0.00 3.74
2334 9940 2.808543 CAACACCTCCAGTCTTGCTAAC 59.191 50.000 0.00 0.00 0.00 2.34
2410 10030 7.309438 GGGGCAAATGAAGATATGGATAAGAAC 60.309 40.741 0.00 0.00 0.00 3.01
2481 10130 6.593978 AGAAATCGTCTGAATTTGTCGAAAG 58.406 36.000 0.00 0.00 34.29 2.62


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

AutoCloner maintained by Alex Coulton.