Multiple sequence alignment - TraesCS7B01G001900

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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 TraesCS7B01G001900 chr7B 100.000 2619 0 0 1 2619 737786 735168 0.000000e+00 4837.0
1 TraesCS7B01G001900 chr7B 88.382 241 28 0 56 296 737340 737100 9.170000e-75 291.0
2 TraesCS7B01G001900 chr7B 88.382 241 28 0 447 687 737731 737491 9.170000e-75 291.0
3 TraesCS7B01G001900 chr5D 96.654 1913 49 5 1 1910 562038318 562040218 0.000000e+00 3164.0
4 TraesCS7B01G001900 chr5D 87.243 1168 134 6 451 1610 562052172 562053332 0.000000e+00 1317.0
5 TraesCS7B01G001900 chr5D 88.382 241 28 0 56 296 562038761 562039001 9.170000e-75 291.0
6 TraesCS7B01G001900 chr5D 85.268 224 31 1 447 670 562051944 562052165 2.030000e-56 230.0
7 TraesCS7B01G001900 chr5D 87.209 172 21 1 527 697 562051735 562051906 7.400000e-46 195.0
8 TraesCS7B01G001900 chr5B 95.719 1892 63 7 1 1881 712417403 712419287 0.000000e+00 3029.0
9 TraesCS7B01G001900 chr5B 86.939 245 28 1 56 296 712417849 712418093 3.320000e-69 272.0
10 TraesCS7B01G001900 chr5B 87.395 238 27 3 1913 2147 511018049 511018286 1.190000e-68 270.0
11 TraesCS7B01G001900 chr5B 86.307 241 28 5 1911 2147 244519580 244519819 9.300000e-65 257.0
12 TraesCS7B01G001900 chr5B 85.657 251 29 7 1916 2161 659983193 659982945 9.300000e-65 257.0
13 TraesCS7B01G001900 chr5B 100.000 28 0 0 2592 2619 367075014 367074987 5.000000e-03 52.8
14 TraesCS7B01G001900 chr3A 97.107 484 7 3 2140 2619 723331353 723331833 0.000000e+00 809.0
15 TraesCS7B01G001900 chr3A 84.524 672 62 25 1913 2557 19596090 19596746 6.150000e-176 627.0
16 TraesCS7B01G001900 chr3A 94.118 238 11 3 1913 2147 723331093 723331330 2.480000e-95 359.0
17 TraesCS7B01G001900 chr3A 91.781 73 5 1 2548 2619 19605022 19605094 1.660000e-17 100.0
18 TraesCS7B01G001900 chr2A 91.268 481 30 4 2140 2619 62097329 62096860 0.000000e+00 645.0
19 TraesCS7B01G001900 chr2A 94.118 153 8 1 295 447 651820097 651819946 5.640000e-57 231.0
20 TraesCS7B01G001900 chr7A 90.289 484 28 10 2140 2615 564249174 564248702 1.330000e-172 616.0
21 TraesCS7B01G001900 chr6B 87.815 238 26 3 1913 2147 545320443 545320206 2.570000e-70 276.0
22 TraesCS7B01G001900 chr6B 87.029 239 26 5 1913 2147 91855732 91855495 5.560000e-67 265.0
23 TraesCS7B01G001900 chr5A 85.547 256 33 4 1913 2165 700342178 700341924 5.560000e-67 265.0
24 TraesCS7B01G001900 chr5A 89.683 126 8 3 2495 2619 616702338 616702459 3.490000e-34 156.0
25 TraesCS7B01G001900 chr5A 100.000 28 0 0 2592 2619 697855558 697855531 5.000000e-03 52.8
26 TraesCS7B01G001900 chr4B 86.111 252 28 7 1917 2163 653277109 653276860 5.560000e-67 265.0
27 TraesCS7B01G001900 chr4B 94.771 153 7 1 295 447 217725124 217725275 1.210000e-58 237.0
28 TraesCS7B01G001900 chr4B 100.000 28 0 0 2592 2619 649180291 649180264 5.000000e-03 52.8
29 TraesCS7B01G001900 chr3D 86.611 239 27 5 1913 2147 609961314 609961551 2.590000e-65 259.0
30 TraesCS7B01G001900 chr4A 94.771 153 7 1 295 447 511131681 511131530 1.210000e-58 237.0
31 TraesCS7B01G001900 chr4A 94.156 154 8 1 297 450 535039238 535039390 1.570000e-57 233.0
32 TraesCS7B01G001900 chr6A 94.156 154 8 1 294 447 133810163 133810315 1.570000e-57 233.0
33 TraesCS7B01G001900 chr6A 94.702 151 7 1 297 447 339577013 339576864 1.570000e-57 233.0
34 TraesCS7B01G001900 chr2B 95.804 143 5 1 297 439 437240421 437240280 2.030000e-56 230.0
35 TraesCS7B01G001900 chr1D 85.965 57 6 2 632 687 450203669 450203724 2.810000e-05 60.2


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 TraesCS7B01G001900 chr7B 735168 737786 2618 True 1806.333333 4837 92.254667 1 2619 3 chr7B.!!$R1 2618
1 TraesCS7B01G001900 chr5D 562038318 562040218 1900 False 1727.500000 3164 92.518000 1 1910 2 chr5D.!!$F1 1909
2 TraesCS7B01G001900 chr5D 562051735 562053332 1597 False 580.666667 1317 86.573333 447 1610 3 chr5D.!!$F2 1163
3 TraesCS7B01G001900 chr5B 712417403 712419287 1884 False 1650.500000 3029 91.329000 1 1881 2 chr5B.!!$F3 1880
4 TraesCS7B01G001900 chr3A 19596090 19596746 656 False 627.000000 627 84.524000 1913 2557 1 chr3A.!!$F1 644
5 TraesCS7B01G001900 chr3A 723331093 723331833 740 False 584.000000 809 95.612500 1913 2619 2 chr3A.!!$F3 706

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
406 407 1.063806 CCGCTAGATGCTTATCGTGC 58.936 55.0 0.0 0.0 40.11 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1910 1931 0.320374 AGAACAGTGATTTCGGCCGA 59.68 50.0 27.28 27.28 0.0 5.54 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
118 119 4.082625 TCCATGATCAAGTTGTGTTGCATC 60.083 41.667 0.00 0.00 0.00 3.91
130 131 7.105588 AGTTGTGTTGCATCAATGAGTCTATA 58.894 34.615 0.00 0.00 0.00 1.31
226 227 4.458397 ACGATGAGATCCAAAATGAGCAT 58.542 39.130 0.00 0.00 0.00 3.79
406 407 1.063806 CCGCTAGATGCTTATCGTGC 58.936 55.000 0.00 0.00 40.11 5.34
440 441 5.287752 GCACATATTTGTCATCTGCAAAGTG 59.712 40.000 0.00 0.00 38.91 3.16
452 453 1.133407 TGCAAAGTGGTTCCGTTTCAC 59.867 47.619 0.00 0.00 0.00 3.18
1012 1029 5.906073 GCCTTCTAACAATGGCAATAATGT 58.094 37.500 0.00 0.00 44.34 2.71
1035 1052 2.383855 CCGACCTCCATCTTCTTCTCT 58.616 52.381 0.00 0.00 0.00 3.10
1098 1115 3.640407 GGTGGCTCTGGCAGTGGA 61.640 66.667 15.27 0.00 39.19 4.02
1149 1166 2.110213 TGCAAGAACGCTTCGGGT 59.890 55.556 0.00 0.00 30.14 5.28
1200 1217 1.124780 TCTGTTTGTCGACCCTCCAA 58.875 50.000 14.12 0.00 0.00 3.53
1215 1232 1.079127 CCAATCGGACAAGCGGAGT 60.079 57.895 0.00 0.00 0.00 3.85
1320 1337 4.737765 GTCAAGAAAATGCTACAAAACGCA 59.262 37.500 0.00 0.00 40.87 5.24
1321 1338 5.231147 GTCAAGAAAATGCTACAAAACGCAA 59.769 36.000 0.00 0.00 39.89 4.85
1758 1776 7.296856 TGGATGGTTATGATTATCCACACAAT 58.703 34.615 0.00 0.00 42.96 2.71
1848 1869 8.570068 TCTGGCACGTCTACACAATATATATA 57.430 34.615 0.00 0.00 0.00 0.86
1910 1931 3.064324 GAGCAAGGCGGGCATTGT 61.064 61.111 17.81 6.42 39.55 2.71
1911 1932 3.056313 GAGCAAGGCGGGCATTGTC 62.056 63.158 17.81 10.94 39.55 3.18
1964 1985 7.043565 AGCAATCTTTGTCACAAAATGAACTT 58.956 30.769 4.13 0.00 39.72 2.66
2010 2033 1.336755 CCTTTTAGCAACGCCACAGTT 59.663 47.619 0.00 0.00 34.15 3.16
2012 2035 1.669604 TTTAGCAACGCCACAGTTCA 58.330 45.000 0.00 0.00 30.96 3.18
2066 2089 2.357034 TCGCGTTTCAGCTCCACC 60.357 61.111 5.77 0.00 34.40 4.61
2079 2102 1.028905 CTCCACCTTCAAACGCCAAA 58.971 50.000 0.00 0.00 0.00 3.28
2282 2338 1.142531 CGCTCTAGCTGCATGGTCA 59.857 57.895 1.02 0.00 39.32 4.02
2531 2591 5.479375 AGCTAGTGTTGGCAGTAAACTAGTA 59.521 40.000 14.91 0.00 41.46 1.82
2532 2592 5.805994 GCTAGTGTTGGCAGTAAACTAGTAG 59.194 44.000 14.91 0.00 41.46 2.57
2533 2593 5.803237 AGTGTTGGCAGTAAACTAGTAGT 57.197 39.130 0.00 0.00 0.00 2.73
2585 2645 3.190953 GTCGGCATCCAGTAGTATCTACC 59.809 52.174 3.69 0.00 0.00 3.18
2590 2650 6.153000 CGGCATCCAGTAGTATCTACCTATTT 59.847 42.308 3.69 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
226 227 6.873605 CCGTAGAATGCACAAGGATATATCAA 59.126 38.462 14.60 0.00 0.00 2.57
406 407 2.483877 ACAAATATGTGCACGACCACTG 59.516 45.455 13.13 7.64 38.69 3.66
440 441 7.254795 CCATAGATTCATTAGTGAAACGGAACC 60.255 40.741 4.64 0.00 46.67 3.62
594 599 5.008415 GGTGCTCATTTTGTATCTCATCAGG 59.992 44.000 0.00 0.00 0.00 3.86
1012 1029 0.970937 AAGAAGATGGAGGTCGGCGA 60.971 55.000 4.99 4.99 0.00 5.54
1035 1052 1.827344 AGGAGCATGAAGACGATCACA 59.173 47.619 0.00 0.00 30.82 3.58
1149 1166 1.080354 ATCGGGGTCTTGGGTCTCA 59.920 57.895 0.00 0.00 0.00 3.27
1200 1217 2.125512 GCACTCCGCTTGTCCGAT 60.126 61.111 0.00 0.00 37.77 4.18
1215 1232 1.898154 GAGGTCTTTAGCCTCGGCA 59.102 57.895 11.02 0.00 42.46 5.69
1338 1355 5.102313 CACAAATACTGAGAGCGTACATCA 58.898 41.667 0.00 0.00 0.00 3.07
1493 1510 2.086054 AGATCAGTTTGGCACTCGTC 57.914 50.000 0.00 0.00 30.92 4.20
1758 1776 9.529325 CTTACTCATTTCTGTCCGTGATTAATA 57.471 33.333 0.00 0.00 0.00 0.98
1891 1912 2.753043 AATGCCCGCCTTGCTCTG 60.753 61.111 0.00 0.00 0.00 3.35
1910 1931 0.320374 AGAACAGTGATTTCGGCCGA 59.680 50.000 27.28 27.28 0.00 5.54
1911 1932 0.443869 CAGAACAGTGATTTCGGCCG 59.556 55.000 22.12 22.12 0.00 6.13
2010 2033 2.787473 ATGGAGAAGAAACGCCATGA 57.213 45.000 0.00 0.00 45.73 3.07
2066 2089 3.121778 GCAAGCTATTTTGGCGTTTGAAG 59.878 43.478 0.00 0.00 34.52 3.02
2531 2591 8.085296 GCACATACAGATAAACTAGCTGATACT 58.915 37.037 5.98 0.00 44.59 2.12
2532 2592 7.867909 TGCACATACAGATAAACTAGCTGATAC 59.132 37.037 5.98 0.00 44.59 2.24
2533 2593 7.951591 TGCACATACAGATAAACTAGCTGATA 58.048 34.615 5.98 0.00 44.59 2.15
2585 2645 3.546815 GGCTTGCATGCACGAGTAAATAG 60.547 47.826 26.71 15.91 34.04 1.73
2590 2650 1.745115 GGGCTTGCATGCACGAGTA 60.745 57.895 26.71 8.61 34.04 2.59


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

AutoCloner maintained by Alex Coulton.