Multiple sequence alignment - TraesCS4A01G381300

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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 TraesCS4A01G381300 chr4A 100.000 2718 0 0 1 2718 658923582 658920865 0.000000e+00 5020.0
1 TraesCS4A01G381300 chr4A 98.711 2716 29 5 1 2715 658350765 658353475 0.000000e+00 4817.0
2 TraesCS4A01G381300 chr4A 95.828 839 32 2 1878 2715 658413710 658414546 0.000000e+00 1352.0
3 TraesCS4A01G381300 chr4A 89.130 920 57 11 975 1864 658412601 658413507 0.000000e+00 1105.0
4 TraesCS4A01G381300 chr4A 92.677 437 22 8 1 434 666304455 666304884 2.970000e-174 621.0
5 TraesCS4A01G381300 chr4A 92.677 437 22 8 1 434 666368205 666368634 2.970000e-174 621.0
6 TraesCS4A01G381300 chr4A 79.644 393 32 23 811 1184 658349940 658350303 3.500000e-59 239.0
7 TraesCS4A01G381300 chr4A 79.739 306 55 6 1165 1468 542499332 542499632 5.890000e-52 215.0
8 TraesCS4A01G381300 chr4A 89.011 91 10 0 1628 1718 542499949 542500039 2.210000e-21 113.0
9 TraesCS4A01G381300 chr4A 97.727 44 1 0 1044 1087 658346981 658347024 2.900000e-10 76.8
10 TraesCS4A01G381300 chr7D 85.604 778 57 25 817 1557 45759591 45760350 0.000000e+00 765.0
11 TraesCS4A01G381300 chr7D 85.849 424 54 6 2289 2709 461201525 461201945 1.920000e-121 446.0
12 TraesCS4A01G381300 chr7D 82.326 430 62 8 2292 2709 47425967 47425540 7.150000e-96 361.0
13 TraesCS4A01G381300 chr7D 81.429 420 72 6 2292 2709 118868951 118868536 3.350000e-89 339.0
14 TraesCS4A01G381300 chr7D 81.235 421 72 7 2289 2707 630507391 630507806 1.560000e-87 333.0
15 TraesCS4A01G381300 chr7D 83.562 292 35 8 2016 2297 136596520 136596808 7.460000e-66 261.0
16 TraesCS4A01G381300 chr7D 80.162 247 28 15 1627 1864 45760467 45760701 6.020000e-37 165.0
17 TraesCS4A01G381300 chr4B 97.826 368 7 1 1 368 633946820 633947186 3.820000e-178 634.0
18 TraesCS4A01G381300 chr4B 83.614 415 63 4 2292 2705 423364012 423363602 4.250000e-103 385.0
19 TraesCS4A01G381300 chr4B 98.077 208 4 0 388 595 638162112 638161905 1.990000e-96 363.0
20 TraesCS4A01G381300 chr4B 84.828 290 27 12 2016 2295 182177528 182177246 2.670000e-70 276.0
21 TraesCS4A01G381300 chr4B 78.947 304 53 8 1169 1468 80673251 80672955 2.140000e-46 196.0
22 TraesCS4A01G381300 chr4B 90.217 92 9 0 1627 1718 80672634 80672543 1.320000e-23 121.0
23 TraesCS4A01G381300 chr4B 79.245 106 17 5 2349 2452 542783690 542783792 4.860000e-08 69.4
24 TraesCS4A01G381300 chr5B 92.906 437 22 7 1 434 329434951 329434521 6.390000e-176 627.0
25 TraesCS4A01G381300 chr5B 92.661 436 26 6 1 434 533021160 533020729 8.260000e-175 623.0
26 TraesCS4A01G381300 chr5B 82.339 419 68 6 2294 2709 54508272 54507857 2.570000e-95 359.0
27 TraesCS4A01G381300 chr3B 92.874 435 26 5 1 434 811684554 811684124 6.390000e-176 627.0
28 TraesCS4A01G381300 chr3B 84.775 289 32 5 2018 2295 39464864 39465151 2.060000e-71 279.0
29 TraesCS4A01G381300 chr1B 92.449 437 26 6 1 434 665511487 665511055 3.850000e-173 617.0
30 TraesCS4A01G381300 chr1B 97.642 212 4 1 387 597 669272412 669272623 1.990000e-96 363.0
31 TraesCS4A01G381300 chr1B 94.714 227 7 2 368 589 656110888 656110662 5.570000e-92 348.0
32 TraesCS4A01G381300 chr6D 82.964 587 75 19 26 592 392602341 392601760 8.680000e-140 507.0
33 TraesCS4A01G381300 chr6D 82.339 419 70 4 2292 2708 10721914 10721498 7.150000e-96 361.0
34 TraesCS4A01G381300 chr6D 84.642 293 26 12 2014 2296 101716934 101716651 9.590000e-70 274.0
35 TraesCS4A01G381300 chr6D 84.247 292 32 9 2016 2296 87389541 87389253 3.450000e-69 272.0
36 TraesCS4A01G381300 chr6D 82.828 297 48 3 2289 2584 12329307 12329601 2.080000e-66 263.0
37 TraesCS4A01G381300 chr6D 82.759 290 37 8 2016 2295 255006741 255007027 2.090000e-61 246.0
38 TraesCS4A01G381300 chr6D 82.653 294 35 8 2015 2295 303469970 303470260 2.090000e-61 246.0
39 TraesCS4A01G381300 chr6D 80.743 296 38 10 2016 2295 299197138 299197430 2.120000e-51 213.0
40 TraesCS4A01G381300 chr6D 80.669 269 47 5 2427 2693 38895579 38895314 1.280000e-48 204.0
41 TraesCS4A01G381300 chr6D 84.434 212 22 6 2016 2217 34337855 34338065 5.940000e-47 198.0
42 TraesCS4A01G381300 chr6D 79.245 159 26 5 2127 2283 26357011 26357164 1.330000e-18 104.0
43 TraesCS4A01G381300 chr6D 83.529 85 8 2 2081 2159 119946296 119946212 1.040000e-09 75.0
44 TraesCS4A01G381300 chr7A 81.733 531 45 21 819 1332 48011934 48012429 1.960000e-106 396.0
45 TraesCS4A01G381300 chr7A 84.247 292 33 8 2016 2295 52986253 52985963 3.450000e-69 272.0
46 TraesCS4A01G381300 chr7A 83.793 290 33 8 2016 2295 105723247 105723532 2.080000e-66 263.0
47 TraesCS4A01G381300 chr7A 76.722 421 48 26 1447 1852 48012427 48012812 3.570000e-44 189.0
48 TraesCS4A01G381300 chr7A 78.884 251 29 12 1621 1864 489704182 489703949 6.060000e-32 148.0
49 TraesCS4A01G381300 chr7B 97.143 210 6 0 387 596 726779153 726778944 3.330000e-94 355.0
50 TraesCS4A01G381300 chr7B 96.714 213 6 1 387 598 60387584 60387796 1.200000e-93 353.0
51 TraesCS4A01G381300 chr7B 80.668 419 77 3 2292 2709 129966225 129966640 3.380000e-84 322.0
52 TraesCS4A01G381300 chr7B 96.392 194 5 2 588 780 200016544 200016736 4.370000e-83 318.0
53 TraesCS4A01G381300 chr7B 84.083 289 33 8 2016 2294 378382478 378382763 1.600000e-67 267.0
54 TraesCS4A01G381300 chrUn 94.714 227 7 2 368 589 342258150 342257924 5.570000e-92 348.0
55 TraesCS4A01G381300 chrUn 94.714 227 7 2 368 589 474378100 474378326 5.570000e-92 348.0
56 TraesCS4A01G381300 chrUn 94.359 195 7 4 588 780 79693272 79693464 2.050000e-76 296.0
57 TraesCS4A01G381300 chrUn 94.359 195 7 4 588 780 79770163 79770355 2.050000e-76 296.0
58 TraesCS4A01G381300 chrUn 94.359 195 7 4 588 780 299935911 299936103 2.050000e-76 296.0
59 TraesCS4A01G381300 chrUn 93.939 198 8 4 588 783 324933282 324933087 2.050000e-76 296.0
60 TraesCS4A01G381300 chrUn 93.939 198 8 4 588 783 354796744 354796549 2.050000e-76 296.0
61 TraesCS4A01G381300 chrUn 80.899 267 38 9 2036 2295 20119384 20119644 5.940000e-47 198.0
62 TraesCS4A01G381300 chrUn 82.553 235 30 5 2018 2242 429089413 429089180 2.140000e-46 196.0
63 TraesCS4A01G381300 chr1A 80.615 423 78 4 2289 2709 549591706 549592126 9.390000e-85 324.0
64 TraesCS4A01G381300 chr1A 92.308 195 11 4 588 780 62945397 62945589 9.590000e-70 274.0
65 TraesCS4A01G381300 chr1A 80.412 291 42 8 2016 2296 297046857 297047142 9.860000e-50 207.0
66 TraesCS4A01G381300 chr1A 78.983 295 48 7 2015 2295 350196548 350196254 3.570000e-44 189.0
67 TraesCS4A01G381300 chr5D 81.081 407 72 5 2306 2709 412153225 412152821 1.210000e-83 320.0
68 TraesCS4A01G381300 chr5D 86.254 291 25 10 2016 2295 132472633 132472919 4.400000e-78 302.0
69 TraesCS4A01G381300 chr5D 79.750 400 76 5 2309 2705 549433772 549434169 4.430000e-73 285.0
70 TraesCS4A01G381300 chr5D 83.860 285 30 10 2016 2290 133319934 133320212 9.660000e-65 257.0
71 TraesCS4A01G381300 chr5D 82.131 291 36 7 2018 2295 283351588 283351875 4.520000e-58 235.0
72 TraesCS4A01G381300 chr2B 93.434 198 9 4 588 783 166741405 166741210 9.520000e-75 291.0
73 TraesCS4A01G381300 chr2B 84.536 291 31 9 2015 2295 467860175 467859889 2.670000e-70 276.0
74 TraesCS4A01G381300 chr2D 84.642 293 30 10 2014 2295 325807607 325807319 7.410000e-71 278.0
75 TraesCS4A01G381300 chr1D 83.448 290 33 10 2016 2294 125746768 125746483 3.470000e-64 255.0
76 TraesCS4A01G381300 chr1D 77.966 354 66 10 2289 2631 452189401 452189753 7.620000e-51 211.0
77 TraesCS4A01G381300 chr1D 80.934 257 43 6 2298 2552 365430475 365430223 5.940000e-47 198.0
78 TraesCS4A01G381300 chr1D 79.333 300 41 14 2011 2296 116444099 116443807 9.930000e-45 191.0
79 TraesCS4A01G381300 chr1D 76.793 237 42 11 2295 2525 48025589 48025818 1.320000e-23 121.0
80 TraesCS4A01G381300 chr6A 82.215 298 34 12 2015 2296 570743099 570742805 3.500000e-59 239.0
81 TraesCS4A01G381300 chr3D 82.545 275 33 8 2016 2278 595079687 595079416 7.570000e-56 228.0
82 TraesCS4A01G381300 chr4D 79.412 306 50 10 1168 1468 54621947 54621650 1.280000e-48 204.0
83 TraesCS4A01G381300 chr4D 86.957 184 18 5 2114 2296 465415516 465415338 4.590000e-48 202.0
84 TraesCS4A01G381300 chr4D 79.924 264 49 4 2292 2554 477223103 477222843 9.930000e-45 191.0
85 TraesCS4A01G381300 chr4D 86.184 152 20 1 2559 2709 436986331 436986180 2.170000e-36 163.0
86 TraesCS4A01G381300 chr4D 73.608 413 84 17 2306 2711 58274285 58273891 4.720000e-28 135.0
87 TraesCS4A01G381300 chr4D 89.130 92 10 0 1627 1718 54621342 54621251 6.150000e-22 115.0
88 TraesCS4A01G381300 chr4D 77.049 183 40 2 2370 2552 479414252 479414432 1.330000e-18 104.0


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 TraesCS4A01G381300 chr4A 658920865 658923582 2717 True 5020.000000 5020 100.000000 1 2718 1 chr4A.!!$R1 2717
1 TraesCS4A01G381300 chr4A 658346981 658353475 6494 False 1710.933333 4817 92.027333 1 2715 3 chr4A.!!$F4 2714
2 TraesCS4A01G381300 chr4A 658412601 658414546 1945 False 1228.500000 1352 92.479000 975 2715 2 chr4A.!!$F5 1740
3 TraesCS4A01G381300 chr7D 45759591 45760701 1110 False 465.000000 765 82.883000 817 1864 2 chr7D.!!$F4 1047
4 TraesCS4A01G381300 chr6D 392601760 392602341 581 True 507.000000 507 82.964000 26 592 1 chr6D.!!$R6 566
5 TraesCS4A01G381300 chr7A 48011934 48012812 878 False 292.500000 396 79.227500 819 1852 2 chr7A.!!$F2 1033

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
169 3954 7.212274 GGACCGCTAAACCTAGACAAATATTA 58.788 38.462 0.0 0.0 0.0 0.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2098 6228 6.257849 TCACGAGCAGATGGACATTTATTTAC 59.742 38.462 0.0 0.0 0.0 2.01 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
169 3954 7.212274 GGACCGCTAAACCTAGACAAATATTA 58.788 38.462 0.00 0.00 0.00 0.98
2091 6221 6.886459 AGCTTGTGACCTGACAATAATAATGT 59.114 34.615 0.00 0.00 35.32 2.71
2098 6228 8.676401 TGACCTGACAATAATAATGTGATTGTG 58.324 33.333 4.32 0.00 42.40 3.33
2312 6443 9.280174 AGTAGAGATTCACCGAAAATACAAAAA 57.720 29.630 0.00 0.00 0.00 1.94
2414 6546 1.950484 GCTGATGTCGTCACCCCAATT 60.950 52.381 0.00 0.00 32.22 2.32
2437 6569 4.436998 GCCGGTCTGACCCAGTCG 62.437 72.222 20.68 8.65 33.75 4.18
2483 6615 3.015145 GCCCCCTAAGGACCAGCA 61.015 66.667 0.00 0.00 38.24 4.41
2506 6638 1.446099 GGAGCTGCAATCGTCGTCA 60.446 57.895 0.00 0.00 0.00 4.35
2622 6754 2.271800 CAGAAATCTACGCCGAAGCTT 58.728 47.619 0.00 0.00 36.60 3.74
2662 6794 1.762957 GATGAACTTGGGGAGGATCGA 59.237 52.381 0.00 0.00 34.37 3.59
2710 6842 0.039527 GTTGCCATCCGTCCAAACAC 60.040 55.000 0.00 0.00 0.00 3.32
2715 6847 2.773487 CCATCCGTCCAAACACTGTAA 58.227 47.619 0.00 0.00 0.00 2.41
2716 6848 2.482721 CCATCCGTCCAAACACTGTAAC 59.517 50.000 0.00 0.00 0.00 2.50
2717 6849 3.399330 CATCCGTCCAAACACTGTAACT 58.601 45.455 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
169 3954 2.110721 ACCTCCAAGCTCCATTTTCCTT 59.889 45.455 0.00 0.0 0.00 3.36
2091 6221 8.190122 GCAGATGGACATTTATTTACACAATCA 58.810 33.333 0.00 0.0 0.00 2.57
2098 6228 6.257849 TCACGAGCAGATGGACATTTATTTAC 59.742 38.462 0.00 0.0 0.00 2.01
2160 6290 8.250143 ACCTTCTGAACCAATTTCACTTTTAT 57.750 30.769 0.00 0.0 39.45 1.40
2278 6408 9.985730 TTTTCGGTGAATCTCTACTTACTTTAA 57.014 29.630 0.00 0.0 0.00 1.52
2281 6411 9.583765 GTATTTTCGGTGAATCTCTACTTACTT 57.416 33.333 0.00 0.0 0.00 2.24
2282 6412 8.746530 TGTATTTTCGGTGAATCTCTACTTACT 58.253 33.333 0.00 0.0 0.00 2.24
2283 6413 8.922058 TGTATTTTCGGTGAATCTCTACTTAC 57.078 34.615 0.00 0.0 0.00 2.34
2284 6414 9.932207 TTTGTATTTTCGGTGAATCTCTACTTA 57.068 29.630 0.00 0.0 0.00 2.24
2285 6415 8.842358 TTTGTATTTTCGGTGAATCTCTACTT 57.158 30.769 0.00 0.0 0.00 2.24
2348 6480 0.179040 ACAATGGTCGTTCGGTGGTT 60.179 50.000 0.00 0.0 0.00 3.67
2427 6559 1.471287 CGACTATCAACGACTGGGTCA 59.529 52.381 0.00 0.0 32.09 4.02
2437 6569 3.119566 ACGAAGACTTCCCGACTATCAAC 60.120 47.826 9.63 0.0 0.00 3.18
2483 6615 2.109799 CGATTGCAGCTCCGGGAT 59.890 61.111 0.00 0.0 0.00 3.85
2494 6626 2.609459 AGGATTCAATGACGACGATTGC 59.391 45.455 0.00 0.0 31.89 3.56
2506 6638 9.565090 TTCTTCATATCGATTCAAGGATTCAAT 57.435 29.630 1.71 0.0 0.00 2.57
2662 6794 1.822990 TCGAGTCAGTATTTCGGGCTT 59.177 47.619 0.00 0.0 35.21 4.35


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

AutoCloner maintained by Alex Coulton.