Multiple sequence alignment - TraesCS2D01G143800

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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 TraesCS2D01G143800 chr2D 100.000 3056 0 0 1 3056 84938849 84935794 0.000000e+00 5644.0
1 TraesCS2D01G143800 chr2D 97.329 2284 55 3 774 3056 85408868 85406590 0.000000e+00 3875.0
2 TraesCS2D01G143800 chr2D 96.236 2285 59 10 774 3056 84780481 84778222 0.000000e+00 3718.0
3 TraesCS2D01G143800 chr2D 93.111 900 43 6 833 1732 85703786 85702906 0.000000e+00 1301.0
4 TraesCS2D01G143800 chr2D 92.544 845 51 8 2216 3056 85703010 85702174 0.000000e+00 1201.0
5 TraesCS2D01G143800 chr2D 93.050 777 36 7 1 774 85409685 85408924 0.000000e+00 1120.0
6 TraesCS2D01G143800 chr2D 84.404 327 28 15 411 728 85252467 85252155 1.780000e-77 300.0
7 TraesCS2D01G143800 chr2D 86.310 168 18 4 1 167 85252695 85252532 8.710000e-41 178.0
8 TraesCS2D01G143800 chr2D 94.000 50 3 0 725 774 84780586 84780537 3.270000e-10 76.8
9 TraesCS2D01G143800 chr2B 95.994 1373 48 4 775 2146 136815224 136813858 0.000000e+00 2224.0
10 TraesCS2D01G143800 chr2B 95.706 1374 52 4 774 2146 136639057 136637690 0.000000e+00 2204.0
11 TraesCS2D01G143800 chr2B 95.706 1374 51 3 774 2146 137622572 137621206 0.000000e+00 2204.0
12 TraesCS2D01G143800 chr2B 95.323 1347 54 6 775 2119 137014881 137013542 0.000000e+00 2130.0
13 TraesCS2D01G143800 chr2B 93.112 842 47 6 2216 3056 137348518 137347687 0.000000e+00 1223.0
14 TraesCS2D01G143800 chr2B 92.993 842 48 7 2216 3056 137813679 137812848 0.000000e+00 1218.0
15 TraesCS2D01G143800 chr2B 93.238 488 26 6 265 748 137015432 137014948 0.000000e+00 712.0
16 TraesCS2D01G143800 chr2B 91.068 515 22 9 265 774 137623123 137622628 0.000000e+00 675.0
17 TraesCS2D01G143800 chr2B 91.520 342 20 7 414 748 136815630 136815291 2.150000e-126 462.0
18 TraesCS2D01G143800 chr2B 89.354 263 22 4 774 1035 137130722 137130465 2.940000e-85 326.0
19 TraesCS2D01G143800 chr2B 92.500 200 15 0 1 200 137015621 137015422 1.390000e-73 287.0
20 TraesCS2D01G143800 chr2B 92.000 200 16 0 1 200 137623312 137623113 6.450000e-72 281.0
21 TraesCS2D01G143800 chr2B 89.175 194 9 1 1943 2124 182131328 182131135 6.590000e-57 231.0
22 TraesCS2D01G143800 chr2B 89.005 191 9 1 1943 2121 135466323 135466513 3.070000e-55 226.0
23 TraesCS2D01G143800 chr2B 85.859 198 27 1 1 198 137463313 137463117 3.090000e-50 209.0
24 TraesCS2D01G143800 chr2B 85.377 212 13 6 564 774 137349645 137349451 1.440000e-48 204.0
25 TraesCS2D01G143800 chr2B 85.149 202 23 5 1 198 136815867 136815669 1.860000e-47 200.0
26 TraesCS2D01G143800 chr2B 87.425 167 21 0 1 167 137131713 137131547 3.110000e-45 193.0
27 TraesCS2D01G143800 chr2B 89.404 151 16 0 628 778 137130903 137130753 1.120000e-44 191.0
28 TraesCS2D01G143800 chr2B 80.426 235 14 16 414 632 137702767 137702549 1.900000e-32 150.0
29 TraesCS2D01G143800 chr2B 85.161 155 8 9 509 657 136639478 136639333 8.830000e-31 145.0
30 TraesCS2D01G143800 chr2B 80.423 189 13 9 428 598 137463063 137462881 4.140000e-24 122.0
31 TraesCS2D01G143800 chr2B 96.721 61 2 0 207 267 368341605 368341665 5.390000e-18 102.0
32 TraesCS2D01G143800 chr2A 94.274 1240 40 10 818 2050 85613727 85612512 0.000000e+00 1868.0
33 TraesCS2D01G143800 chr2A 94.274 1240 40 10 818 2050 85927152 85925937 0.000000e+00 1868.0
34 TraesCS2D01G143800 chr2A 93.952 1240 44 10 818 2050 85811245 85810030 0.000000e+00 1845.0
35 TraesCS2D01G143800 chr2A 91.778 900 52 6 833 1722 86061984 86061097 0.000000e+00 1232.0
36 TraesCS2D01G143800 chr2A 93.103 841 49 4 2216 3056 84229107 84229938 0.000000e+00 1223.0
37 TraesCS2D01G143800 chr2A 92.773 844 49 7 2215 3056 84144427 84145260 0.000000e+00 1210.0
38 TraesCS2D01G143800 chr2A 97.778 45 1 0 725 769 84228161 84228205 9.080000e-11 78.7
39 TraesCS2D01G143800 chr4A 94.113 1240 42 10 818 2050 349806780 349805565 0.000000e+00 1857.0
40 TraesCS2D01G143800 chr7A 93.743 959 47 5 774 1732 618195418 618194473 0.000000e+00 1426.0
41 TraesCS2D01G143800 chr7A 92.637 842 53 6 2216 3056 618194577 618193744 0.000000e+00 1203.0
42 TraesCS2D01G143800 chr7A 91.244 217 11 6 547 757 618195694 618195480 3.860000e-74 289.0
43 TraesCS2D01G143800 chr7A 83.626 171 25 2 1 169 80596854 80596685 1.130000e-34 158.0
44 TraesCS2D01G143800 chr5D 91.815 843 58 6 2216 3056 283109566 283108733 0.000000e+00 1164.0
45 TraesCS2D01G143800 chr5D 88.947 190 12 5 543 728 283110887 283110703 3.070000e-55 226.0
46 TraesCS2D01G143800 chr5D 96.000 50 2 0 725 774 283110574 283110525 7.020000e-12 82.4
47 TraesCS2D01G143800 chr7D 82.719 434 47 13 1804 2211 518766779 518767210 8.060000e-96 361.0
48 TraesCS2D01G143800 chr7B 93.642 173 5 1 2050 2216 588876413 588876241 1.410000e-63 254.0
49 TraesCS2D01G143800 chr7B 100.000 59 0 0 207 265 93581187 93581245 3.220000e-20 110.0
50 TraesCS2D01G143800 chr7B 90.141 71 6 1 199 268 728952988 728952918 1.170000e-14 91.6
51 TraesCS2D01G143800 chr5B 84.579 214 11 10 526 728 321478750 321478548 3.110000e-45 193.0
52 TraesCS2D01G143800 chr5B 100.000 59 0 0 207 265 654502977 654502919 3.220000e-20 110.0
53 TraesCS2D01G143800 chr5B 98.361 61 1 0 207 267 48932955 48933015 1.160000e-19 108.0
54 TraesCS2D01G143800 chr5B 96.000 50 2 0 725 774 321478419 321478370 7.020000e-12 82.4
55 TraesCS2D01G143800 chr4B 100.000 54 0 0 210 263 603576344 603576291 1.940000e-17 100.0
56 TraesCS2D01G143800 chr6B 95.082 61 1 2 207 265 658546603 658546663 9.020000e-16 95.3
57 TraesCS2D01G143800 chr1B 86.842 76 8 2 192 265 605009174 605009249 1.950000e-12 84.2
58 TraesCS2D01G143800 chr5A 90.566 53 2 1 725 774 375377442 375377390 1.970000e-07 67.6


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 TraesCS2D01G143800 chr2D 84935794 84938849 3055 True 5644.000000 5644 100.000000 1 3056 1 chr2D.!!$R1 3055
1 TraesCS2D01G143800 chr2D 85406590 85409685 3095 True 2497.500000 3875 95.189500 1 3056 2 chr2D.!!$R4 3055
2 TraesCS2D01G143800 chr2D 84778222 84780586 2364 True 1897.400000 3718 95.118000 725 3056 2 chr2D.!!$R2 2331
3 TraesCS2D01G143800 chr2D 85702174 85703786 1612 True 1251.000000 1301 92.827500 833 3056 2 chr2D.!!$R5 2223
4 TraesCS2D01G143800 chr2D 85252155 85252695 540 True 239.000000 300 85.357000 1 728 2 chr2D.!!$R3 727
5 TraesCS2D01G143800 chr2B 137812848 137813679 831 True 1218.000000 1218 92.993000 2216 3056 1 chr2B.!!$R2 840
6 TraesCS2D01G143800 chr2B 136637690 136639478 1788 True 1174.500000 2204 90.433500 509 2146 2 chr2B.!!$R4 1637
7 TraesCS2D01G143800 chr2B 137621206 137623312 2106 True 1053.333333 2204 92.924667 1 2146 3 chr2B.!!$R10 2145
8 TraesCS2D01G143800 chr2B 137013542 137015621 2079 True 1043.000000 2130 93.687000 1 2119 3 chr2B.!!$R6 2118
9 TraesCS2D01G143800 chr2B 136813858 136815867 2009 True 962.000000 2224 90.887667 1 2146 3 chr2B.!!$R5 2145
10 TraesCS2D01G143800 chr2B 137347687 137349645 1958 True 713.500000 1223 89.244500 564 3056 2 chr2B.!!$R8 2492
11 TraesCS2D01G143800 chr2B 137130465 137131713 1248 True 236.666667 326 88.727667 1 1035 3 chr2B.!!$R7 1034
12 TraesCS2D01G143800 chr2A 85612512 85613727 1215 True 1868.000000 1868 94.274000 818 2050 1 chr2A.!!$R1 1232
13 TraesCS2D01G143800 chr2A 85925937 85927152 1215 True 1868.000000 1868 94.274000 818 2050 1 chr2A.!!$R3 1232
14 TraesCS2D01G143800 chr2A 85810030 85811245 1215 True 1845.000000 1845 93.952000 818 2050 1 chr2A.!!$R2 1232
15 TraesCS2D01G143800 chr2A 86061097 86061984 887 True 1232.000000 1232 91.778000 833 1722 1 chr2A.!!$R4 889
16 TraesCS2D01G143800 chr2A 84144427 84145260 833 False 1210.000000 1210 92.773000 2215 3056 1 chr2A.!!$F1 841
17 TraesCS2D01G143800 chr2A 84228161 84229938 1777 False 650.850000 1223 95.440500 725 3056 2 chr2A.!!$F2 2331
18 TraesCS2D01G143800 chr4A 349805565 349806780 1215 True 1857.000000 1857 94.113000 818 2050 1 chr4A.!!$R1 1232
19 TraesCS2D01G143800 chr7A 618193744 618195694 1950 True 972.666667 1426 92.541333 547 3056 3 chr7A.!!$R2 2509
20 TraesCS2D01G143800 chr5D 283108733 283110887 2154 True 490.800000 1164 92.254000 543 3056 3 chr5D.!!$R1 2513

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
200 203 0.321671 CTGAGCGTGGGAAGGAGAAA 59.678 55.0 0.0 0.0 0.0 2.52 F
201 204 0.762418 TGAGCGTGGGAAGGAGAAAA 59.238 50.0 0.0 0.0 0.0 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1871 2724 0.392193 CATCTGCTCCACCTTTCGCT 60.392 55.0 0.00 0.00 0.00 4.93 R
2336 3190 0.598942 TGCGCGCAGAGTTGAAACTA 60.599 50.0 33.09 1.22 39.88 2.24 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
39 40 7.279536 GCAACATCAAGATTAGAGATGAAGTGA 59.720 37.037 8.46 0.00 41.18 3.41
122 123 2.039818 TCTTATGGCGAGAGAGACGT 57.960 50.000 0.00 0.00 0.00 4.34
181 184 2.436646 CACTGGGACCGCCATCAC 60.437 66.667 0.00 0.00 35.15 3.06
195 198 0.742281 CATCACTGAGCGTGGGAAGG 60.742 60.000 0.00 0.00 43.94 3.46
200 203 0.321671 CTGAGCGTGGGAAGGAGAAA 59.678 55.000 0.00 0.00 0.00 2.52
201 204 0.762418 TGAGCGTGGGAAGGAGAAAA 59.238 50.000 0.00 0.00 0.00 2.29
202 205 1.142060 TGAGCGTGGGAAGGAGAAAAA 59.858 47.619 0.00 0.00 0.00 1.94
303 307 1.479323 ACAGAAATGGATGCCATGTGC 59.521 47.619 0.00 0.00 44.40 4.57
309 313 1.630223 TGGATGCCATGTGCTGAAAA 58.370 45.000 7.54 0.00 42.00 2.29
409 415 5.580911 ATGAAAGCTTTTCATTCGCAAAC 57.419 34.783 14.05 0.00 35.79 2.93
463 472 6.741992 TGATTATTGTTGTGGAGTGTGATC 57.258 37.500 0.00 0.00 0.00 2.92
474 485 9.313118 GTTGTGGAGTGTGATCTTTTTAAATTT 57.687 29.630 0.00 0.00 0.00 1.82
769 1420 3.585990 GATGGAATGGCCGTGGCG 61.586 66.667 0.00 0.00 43.06 5.69
1230 2029 4.415332 TTCCAGCGCCGTCTCGAC 62.415 66.667 2.29 0.00 0.00 4.20
1397 2244 1.487452 CGTGTCTGGTGTGTCAACCG 61.487 60.000 0.00 0.00 43.73 4.44
1458 2305 2.305343 GGATGCCTCTGATATTGCCTCT 59.695 50.000 0.00 0.00 0.00 3.69
1498 2345 4.408821 CCACCTTGCCGGCTGCTA 62.409 66.667 29.70 3.37 42.00 3.49
2336 3190 3.007398 GGTGTGAAGAAGATGACTCCAGT 59.993 47.826 0.00 0.00 0.00 4.00
2390 3244 1.407162 GGAGCTCAGCTGCAAGATTCT 60.407 52.381 14.30 0.00 46.16 2.40
2553 3410 2.287608 GGTTCTGCACTTGCTTACCAAC 60.288 50.000 2.33 0.00 42.66 3.77
2894 3756 4.689071 TGAACTTGTCGATACACACAGTT 58.311 39.130 0.00 0.00 34.61 3.16
3008 3872 4.097286 GGTGAGTTAAAGTTGCAGTTTCCA 59.903 41.667 0.00 0.00 0.00 3.53
3026 3890 6.017687 AGTTTCCAACGAGTAACATTGGTTAC 60.018 38.462 9.16 9.16 46.01 2.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 6.441274 CGTGTATACGTGGTTATAGATGGTT 58.559 40.000 3.56 0.00 44.99 3.67
181 184 0.321671 TTTCTCCTTCCCACGCTCAG 59.678 55.000 0.00 0.00 0.00 3.35
201 204 2.188062 TTGGCGTACCCTCGATTTTT 57.812 45.000 0.00 0.00 33.59 1.94
202 205 2.081462 CTTTGGCGTACCCTCGATTTT 58.919 47.619 0.00 0.00 33.59 1.82
203 206 1.677820 CCTTTGGCGTACCCTCGATTT 60.678 52.381 0.00 0.00 33.59 2.17
204 207 0.107848 CCTTTGGCGTACCCTCGATT 60.108 55.000 0.00 0.00 33.59 3.34
205 208 1.520666 CCTTTGGCGTACCCTCGAT 59.479 57.895 0.00 0.00 33.59 3.59
309 313 2.997986 CCACGCACTATTACGTCCTTTT 59.002 45.455 0.00 0.00 41.32 2.27
323 327 2.264794 CCCTGGAGTACCACGCAC 59.735 66.667 0.00 0.00 41.77 5.34
351 355 7.395489 GGGATCATTACAATCTGCCTCATAAAT 59.605 37.037 0.00 0.00 0.00 1.40
450 459 9.883142 AAAAATTTAAAAAGATCACACTCCACA 57.117 25.926 0.00 0.00 0.00 4.17
626 653 2.124942 CTTTGCTCCGGCCTCTCC 60.125 66.667 0.00 0.00 37.74 3.71
934 1726 0.108615 ACGAATCGAGTTGGAGCCAG 60.109 55.000 10.55 0.00 0.00 4.85
1287 2086 3.770040 CGCCCTCCATGGTCGACA 61.770 66.667 18.91 3.91 0.00 4.35
1367 2166 1.153823 CAGACACGGACGGGATCAC 60.154 63.158 0.00 0.00 0.00 3.06
1498 2345 3.941188 CACGGGGTCAGCACCAGT 61.941 66.667 0.00 0.00 45.94 4.00
1871 2724 0.392193 CATCTGCTCCACCTTTCGCT 60.392 55.000 0.00 0.00 0.00 4.93
2336 3190 0.598942 TGCGCGCAGAGTTGAAACTA 60.599 50.000 33.09 1.22 39.88 2.24
2390 3244 0.736053 GGTGACACGGTTTTGCTTCA 59.264 50.000 0.00 0.00 0.00 3.02
2553 3410 6.149474 ACGGGATTCAAAGAACACTAGAAATG 59.851 38.462 0.00 0.00 0.00 2.32
2894 3756 1.000171 CGCTAGGCAGCTCACATGATA 60.000 52.381 0.00 0.00 46.26 2.15
3026 3890 4.083324 ACAAACACACACACAAGAGTTCAG 60.083 41.667 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.