Multiple sequence alignment - TraesCS7B01G336000

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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 TraesCS7B01G336000 chr7B 100.000 2756 0 0 1 2756 591074108 591071353 0.000000e+00 5090.0
1 TraesCS7B01G336000 chr7B 90.123 1468 75 31 788 2226 591577023 591578449 0.000000e+00 1844.0
2 TraesCS7B01G336000 chr7B 95.004 1121 31 3 393 1513 591160031 591158936 0.000000e+00 1736.0
3 TraesCS7B01G336000 chr7B 87.553 1414 139 13 104 1485 591280119 591278711 0.000000e+00 1602.0
4 TraesCS7B01G336000 chr7B 88.539 1143 70 19 780 1913 589916295 589917385 0.000000e+00 1328.0
5 TraesCS7B01G336000 chr7B 90.220 1002 74 9 504 1485 591228579 591227582 0.000000e+00 1286.0
6 TraesCS7B01G336000 chr7B 94.317 739 25 8 1510 2239 591147755 591147025 0.000000e+00 1116.0
7 TraesCS7B01G336000 chr7B 92.486 732 40 7 1515 2239 591227585 591226862 0.000000e+00 1033.0
8 TraesCS7B01G336000 chr7B 92.350 732 41 7 1515 2239 591278714 591277991 0.000000e+00 1027.0
9 TraesCS7B01G336000 chr7B 93.333 450 30 0 2237 2686 458992323 458991874 0.000000e+00 665.0
10 TraesCS7B01G336000 chr7B 93.284 402 27 0 1 402 591186381 591185980 6.570000e-166 593.0
11 TraesCS7B01G336000 chr7B 81.264 459 66 10 1 446 591280944 591280493 1.210000e-93 353.0
12 TraesCS7B01G336000 chr7B 97.333 75 2 0 2682 2756 458991817 458991743 8.010000e-26 128.0
13 TraesCS7B01G336000 chr7D 86.978 2035 155 46 1 1994 548096702 548094737 0.000000e+00 2189.0
14 TraesCS7B01G336000 chr7D 92.326 1277 76 8 966 2234 548089093 548087831 0.000000e+00 1796.0
15 TraesCS7B01G336000 chr7D 81.368 2163 252 66 42 2121 139082746 139084840 0.000000e+00 1622.0
16 TraesCS7B01G336000 chr7D 94.545 440 24 0 2244 2683 527926786 527927225 0.000000e+00 680.0
17 TraesCS7B01G336000 chr7D 96.000 75 3 0 2682 2756 527927285 527927359 3.730000e-24 122.0
18 TraesCS7B01G336000 chr7D 92.308 39 3 0 490 528 58925961 58925923 3.830000e-04 56.5
19 TraesCS7B01G336000 chr7A 86.164 1366 149 25 117 1456 631955617 631954266 0.000000e+00 1439.0
20 TraesCS7B01G336000 chr7A 83.270 1584 148 51 704 2205 138982161 138983709 0.000000e+00 1349.0
21 TraesCS7B01G336000 chr7A 85.567 679 49 22 1541 2206 631954241 631953599 0.000000e+00 665.0
22 TraesCS7B01G336000 chr7A 85.207 676 54 22 1541 2206 630437037 630437676 0.000000e+00 652.0
23 TraesCS7B01G336000 chr7A 76.827 643 110 27 61 671 138981393 138982028 2.650000e-85 326.0
24 TraesCS7B01G336000 chr1B 94.395 446 24 1 2238 2683 356446377 356446821 0.000000e+00 684.0
25 TraesCS7B01G336000 chr1B 96.000 75 3 0 2682 2756 122921215 122921141 3.730000e-24 122.0
26 TraesCS7B01G336000 chr1B 96.000 75 3 0 2682 2756 647534876 647534950 3.730000e-24 122.0
27 TraesCS7B01G336000 chr2D 94.037 436 24 2 2251 2686 635745591 635745158 0.000000e+00 660.0
28 TraesCS7B01G336000 chr2D 97.297 74 2 0 2683 2756 635745101 635745028 2.880000e-25 126.0
29 TraesCS7B01G336000 chr2A 93.080 448 30 1 2239 2686 394619483 394619037 0.000000e+00 654.0
30 TraesCS7B01G336000 chr5D 92.873 449 32 0 2238 2686 455150300 455149852 0.000000e+00 652.0
31 TraesCS7B01G336000 chr5D 92.857 448 31 1 2239 2686 455257950 455257504 0.000000e+00 649.0
32 TraesCS7B01G336000 chr5D 97.333 75 2 0 2682 2756 455149795 455149721 8.010000e-26 128.0
33 TraesCS7B01G336000 chr5D 97.333 75 2 0 2682 2756 455257447 455257373 8.010000e-26 128.0
34 TraesCS7B01G336000 chr2B 93.065 447 28 2 2239 2683 121373181 121373626 0.000000e+00 651.0
35 TraesCS7B01G336000 chr2B 97.333 75 2 0 2682 2756 634621745 634621819 8.010000e-26 128.0
36 TraesCS7B01G336000 chr3A 92.601 446 33 0 2238 2683 711117198 711117643 2.310000e-180 641.0
37 TraesCS7B01G336000 chr3B 97.333 75 2 0 2682 2756 29531576 29531650 8.010000e-26 128.0


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 TraesCS7B01G336000 chr7B 591071353 591074108 2755 True 5090.0 5090 100.000000 1 2756 1 chr7B.!!$R1 2755
1 TraesCS7B01G336000 chr7B 591577023 591578449 1426 False 1844.0 1844 90.123000 788 2226 1 chr7B.!!$F2 1438
2 TraesCS7B01G336000 chr7B 591158936 591160031 1095 True 1736.0 1736 95.004000 393 1513 1 chr7B.!!$R3 1120
3 TraesCS7B01G336000 chr7B 589916295 589917385 1090 False 1328.0 1328 88.539000 780 1913 1 chr7B.!!$F1 1133
4 TraesCS7B01G336000 chr7B 591226862 591228579 1717 True 1159.5 1286 91.353000 504 2239 2 chr7B.!!$R6 1735
5 TraesCS7B01G336000 chr7B 591147025 591147755 730 True 1116.0 1116 94.317000 1510 2239 1 chr7B.!!$R2 729
6 TraesCS7B01G336000 chr7B 591277991 591280944 2953 True 994.0 1602 87.055667 1 2239 3 chr7B.!!$R7 2238
7 TraesCS7B01G336000 chr7B 458991743 458992323 580 True 396.5 665 95.333000 2237 2756 2 chr7B.!!$R5 519
8 TraesCS7B01G336000 chr7D 548094737 548096702 1965 True 2189.0 2189 86.978000 1 1994 1 chr7D.!!$R3 1993
9 TraesCS7B01G336000 chr7D 548087831 548089093 1262 True 1796.0 1796 92.326000 966 2234 1 chr7D.!!$R2 1268
10 TraesCS7B01G336000 chr7D 139082746 139084840 2094 False 1622.0 1622 81.368000 42 2121 1 chr7D.!!$F1 2079
11 TraesCS7B01G336000 chr7D 527926786 527927359 573 False 401.0 680 95.272500 2244 2756 2 chr7D.!!$F2 512
12 TraesCS7B01G336000 chr7A 631953599 631955617 2018 True 1052.0 1439 85.865500 117 2206 2 chr7A.!!$R1 2089
13 TraesCS7B01G336000 chr7A 138981393 138983709 2316 False 837.5 1349 80.048500 61 2205 2 chr7A.!!$F2 2144
14 TraesCS7B01G336000 chr7A 630437037 630437676 639 False 652.0 652 85.207000 1541 2206 1 chr7A.!!$F1 665
15 TraesCS7B01G336000 chr2D 635745028 635745591 563 True 393.0 660 95.667000 2251 2756 2 chr2D.!!$R1 505
16 TraesCS7B01G336000 chr5D 455149721 455150300 579 True 390.0 652 95.103000 2238 2756 2 chr5D.!!$R1 518
17 TraesCS7B01G336000 chr5D 455257373 455257950 577 True 388.5 649 95.095000 2239 2756 2 chr5D.!!$R2 517

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
23 24 0.105224 CCCGTACAACAGTGGTGTCA 59.895 55.0 19.16 1.53 35.08 3.58 F
324 1063 0.251121 TTCTTCTTTGGGCGCATGGA 60.251 50.0 10.83 3.11 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1215 2132 2.185350 CGCAGCGTCTCAAGGGAT 59.815 61.111 6.65 0.0 0.0 3.85 R
2114 3105 1.152312 ACCTCCGTCCCACAAGAGT 60.152 57.895 0.00 0.0 0.0 3.24 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
23 24 0.105224 CCCGTACAACAGTGGTGTCA 59.895 55.000 19.16 1.53 35.08 3.58
55 56 1.079819 CTGCGACTTCGGATGTGGT 60.080 57.895 0.77 0.00 39.39 4.16
56 57 1.078759 CTGCGACTTCGGATGTGGTC 61.079 60.000 0.77 0.00 39.39 4.02
58 59 1.211969 CGACTTCGGATGTGGTCGT 59.788 57.895 0.77 0.00 44.05 4.34
125 128 0.315568 GAGAATGACCGGCTCGCTAT 59.684 55.000 0.00 0.00 0.00 2.97
180 908 2.203640 AGACCAGTCTCCGCACCA 60.204 61.111 0.00 0.00 34.17 4.17
265 993 2.124193 CATTCATCCGGCCAGCCA 60.124 61.111 9.78 0.00 35.37 4.75
324 1063 0.251121 TTCTTCTTTGGGCGCATGGA 60.251 50.000 10.83 3.11 0.00 3.41
337 1076 1.305129 CATGGAATGGGTGGCCACA 60.305 57.895 35.78 18.54 41.79 4.17
396 1136 2.103538 GGGCGCGTCGTCTATCAA 59.896 61.111 8.43 0.00 0.00 2.57
424 1165 1.383019 GGAGGGTTTTGGGGGAGAC 59.617 63.158 0.00 0.00 0.00 3.36
463 1205 1.378514 CCCCCTGACAAATGGGTCG 60.379 63.158 0.00 0.00 41.82 4.79
555 1301 6.822073 TGAATCACGACGGACAAAATATAG 57.178 37.500 0.00 0.00 0.00 1.31
890 1788 2.427453 AGCGTACTACATCCACAAGAGG 59.573 50.000 0.00 0.00 0.00 3.69
1215 2132 2.047655 GACGACCACATGGCGGAA 60.048 61.111 10.20 0.00 38.43 4.30
1869 2828 0.391597 AATGCAGTTGCTTGCTTGCT 59.608 45.000 5.62 0.65 44.38 3.91
1870 2829 0.391597 ATGCAGTTGCTTGCTTGCTT 59.608 45.000 5.62 8.41 44.38 3.91
1871 2830 0.528901 TGCAGTTGCTTGCTTGCTTG 60.529 50.000 5.62 1.63 44.38 4.01
1872 2831 1.828331 GCAGTTGCTTGCTTGCTTGC 61.828 55.000 0.00 6.72 40.89 4.01
1977 2952 4.761739 TCTTCATGTTGGGAAAGATGTGTC 59.238 41.667 0.00 0.00 0.00 3.67
2079 3056 2.035449 TGTCCGTGTTCAGACTTGTAGG 59.965 50.000 0.00 0.00 34.02 3.18
2132 3123 0.113776 TACTCTTGTGGGACGGAGGT 59.886 55.000 0.00 0.00 0.00 3.85
2135 3133 3.901797 CTTGTGGGACGGAGGTGGC 62.902 68.421 0.00 0.00 0.00 5.01
2236 3256 3.994392 ACAGGTAGCATACAAAACTGTCG 59.006 43.478 0.00 0.00 45.43 4.35
2239 3259 5.049680 CAGGTAGCATACAAAACTGTCGTTT 60.050 40.000 0.00 0.00 45.43 3.60
2444 3464 4.398319 TGAAGTTTCCCAGAAACCTGATC 58.602 43.478 14.82 9.88 33.56 2.92
2477 3497 4.404073 GCTTCCTTCTTGAGGTCTATGAGA 59.596 45.833 0.00 0.00 46.39 3.27
2531 3551 0.168788 AAGCCATGAACGCACAATCG 59.831 50.000 0.00 0.00 0.00 3.34
2552 3572 8.356657 CAATCGGTTTCCAAAATAATAGGCATA 58.643 33.333 0.00 0.00 0.00 3.14
2596 3616 0.462581 CCAGCTAGGCATGCTCGAAA 60.463 55.000 18.92 0.00 38.92 3.46
2630 3650 3.371487 CCACACCAGAGCATAACCCAATA 60.371 47.826 0.00 0.00 0.00 1.90
2633 3653 5.184864 CACACCAGAGCATAACCCAATAAAA 59.815 40.000 0.00 0.00 0.00 1.52
2660 3680 6.465464 CCCAAGATGAGACAATGATATCACCT 60.465 42.308 7.78 3.15 0.00 4.00
2737 3818 4.069304 TCACAACAGTATTACTTGCACCC 58.931 43.478 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.575532 CACCTCAATGACACCACTGTT 58.424 47.619 0.00 0.00 0.00 3.16
14 15 0.603707 CGCACCTCAATGACACCACT 60.604 55.000 0.00 0.00 0.00 4.00
16 17 1.965930 GCGCACCTCAATGACACCA 60.966 57.895 0.30 0.00 0.00 4.17
23 24 3.437795 GCAGCAGCGCACCTCAAT 61.438 61.111 11.47 0.00 0.00 2.57
45 46 3.445687 CCCGACGACCACATCCGA 61.446 66.667 0.00 0.00 0.00 4.55
186 914 2.813179 CGAGGCTATGTGCGGCAAC 61.813 63.158 3.23 0.00 44.05 4.17
192 920 2.233654 CGCAGTCGAGGCTATGTGC 61.234 63.158 7.34 0.00 38.38 4.57
265 993 1.739338 CGAAGTAGAGGGCCGCAGAT 61.739 60.000 10.70 0.00 0.00 2.90
324 1063 1.114722 CAACAGTGTGGCCACCCATT 61.115 55.000 32.62 16.86 44.51 3.16
424 1165 1.019278 CGTCCACTCCATTTCCACCG 61.019 60.000 0.00 0.00 0.00 4.94
555 1301 0.935196 AGACGCAAACGAACCTGTTC 59.065 50.000 0.00 0.00 43.93 3.18
613 1359 1.091771 CCATTTCATCAGCCGCGTCT 61.092 55.000 4.92 0.00 0.00 4.18
890 1788 4.083590 GGCGATCAAGGAAAGCTATGAATC 60.084 45.833 0.00 0.00 0.00 2.52
1215 2132 2.185350 CGCAGCGTCTCAAGGGAT 59.815 61.111 6.65 0.00 0.00 3.85
1869 2828 5.017294 TCGATCATGTACATAACAGGCAA 57.983 39.130 8.32 0.00 42.70 4.52
1870 2829 4.664150 TCGATCATGTACATAACAGGCA 57.336 40.909 8.32 0.00 42.70 4.75
1871 2830 4.449068 CCTTCGATCATGTACATAACAGGC 59.551 45.833 8.32 0.00 42.70 4.85
1872 2831 5.842907 TCCTTCGATCATGTACATAACAGG 58.157 41.667 8.32 8.38 42.70 4.00
2040 3016 9.787532 ACACGGACATAATAAGAATTCAAATTG 57.212 29.630 8.44 0.45 0.00 2.32
2043 3019 9.004717 TGAACACGGACATAATAAGAATTCAAA 57.995 29.630 8.44 0.00 0.00 2.69
2044 3020 8.554835 TGAACACGGACATAATAAGAATTCAA 57.445 30.769 8.44 0.00 0.00 2.69
2045 3021 8.038351 TCTGAACACGGACATAATAAGAATTCA 58.962 33.333 8.44 0.00 0.00 2.57
2046 3022 8.328864 GTCTGAACACGGACATAATAAGAATTC 58.671 37.037 0.00 0.00 39.09 2.17
2047 3023 8.041323 AGTCTGAACACGGACATAATAAGAATT 58.959 33.333 10.99 0.00 40.99 2.17
2048 3024 7.556844 AGTCTGAACACGGACATAATAAGAAT 58.443 34.615 10.99 0.00 40.99 2.40
2050 3026 6.525578 AGTCTGAACACGGACATAATAAGA 57.474 37.500 10.99 0.00 40.99 2.10
2051 3027 6.590292 ACAAGTCTGAACACGGACATAATAAG 59.410 38.462 10.99 0.00 40.99 1.73
2054 3031 4.894784 ACAAGTCTGAACACGGACATAAT 58.105 39.130 10.99 0.00 40.99 1.28
2056 3033 4.082408 CCTACAAGTCTGAACACGGACATA 60.082 45.833 10.99 1.58 40.99 2.29
2079 3056 9.120422 GTCAATTTTGATTGAATTCAAATTGGC 57.880 29.630 26.86 24.51 43.20 4.52
2106 3096 3.933332 CCGTCCCACAAGAGTAGAATTTC 59.067 47.826 0.00 0.00 0.00 2.17
2114 3105 1.152312 ACCTCCGTCCCACAAGAGT 60.152 57.895 0.00 0.00 0.00 3.24
2132 3123 3.004171 GGTTTGTCGTACATATGTGCCA 58.996 45.455 18.81 8.54 0.00 4.92
2135 3133 6.603237 ATCATGGTTTGTCGTACATATGTG 57.397 37.500 18.81 2.62 0.00 3.21
2239 3259 4.021368 TGGACGGGTGTTTTTCAAAAAGAA 60.021 37.500 0.00 0.00 0.00 2.52
2240 3260 3.510360 TGGACGGGTGTTTTTCAAAAAGA 59.490 39.130 0.00 0.00 0.00 2.52
2241 3261 3.851098 TGGACGGGTGTTTTTCAAAAAG 58.149 40.909 0.00 0.00 0.00 2.27
2289 3309 2.095853 CGCCTGCTGTTATGAACGATTT 59.904 45.455 0.00 0.00 0.00 2.17
2390 3410 7.978975 TCAAAAATAAATAGAAGGGCCAATTCG 59.021 33.333 6.18 0.00 0.00 3.34
2420 3440 4.605183 TCAGGTTTCTGGGAAACTTCAAA 58.395 39.130 18.44 2.03 41.23 2.69
2477 3497 4.963318 TGAAAGTTGTGACAGATCCTCT 57.037 40.909 0.00 0.00 0.00 3.69
2552 3572 9.668497 GGGCTTTATATCGGTATTTCTCTTAAT 57.332 33.333 0.00 0.00 0.00 1.40
2596 3616 1.296715 GGTGTGGATGAAGCGGAGT 59.703 57.895 0.00 0.00 0.00 3.85
2630 3650 9.075678 GATATCATTGTCTCATCTTGGGATTTT 57.924 33.333 0.00 0.00 0.00 1.82
2633 3653 7.166851 GTGATATCATTGTCTCATCTTGGGAT 58.833 38.462 9.02 0.00 0.00 3.85
2660 3680 2.592993 GGTGGCCAGGAGCTGTACA 61.593 63.158 5.11 0.00 43.05 2.90
2737 3818 1.151450 AGAGGTGGTGGCTGGTTTG 59.849 57.895 0.00 0.00 0.00 2.93


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

AutoCloner maintained by Alex Coulton.