Multiple sequence alignment - TraesCS3B01G180000

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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 TraesCS3B01G180000 chr3B 100.000 3125 0 0 1 3125 187805472 187802348 0 5771
1 TraesCS3B01G180000 chr3A 89.077 3195 179 90 18 3125 144154301 144151190 0 3810
2 TraesCS3B01G180000 chr3D 92.344 2312 86 40 1 2260 131354010 131351738 0 3205
3 TraesCS3B01G180000 chr3D 94.133 784 31 5 2348 3125 131351674 131350900 0 1179


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 TraesCS3B01G180000 chr3B 187802348 187805472 3124 True 5771 5771 100.0000 1 3125 1 chr3B.!!$R1 3124
1 TraesCS3B01G180000 chr3A 144151190 144154301 3111 True 3810 3810 89.0770 18 3125 1 chr3A.!!$R1 3107
2 TraesCS3B01G180000 chr3D 131350900 131354010 3110 True 2192 3205 93.2385 1 3125 2 chr3D.!!$R1 3124

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
383 429 0.033011 TCTTCTCCTTCCTCCTCCCG 60.033 60.0 0.0 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2315 2435 0.249868 CTCACCGTTCCACAGAGCAA 60.25 55.0 0.0 0.0 0.0 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
94 104 3.626996 CTGCATGCGTCAAGGGGGA 62.627 63.158 14.09 0.00 0.00 4.81
95 105 2.825836 GCATGCGTCAAGGGGGAG 60.826 66.667 0.00 0.00 0.00 4.30
96 106 2.825836 CATGCGTCAAGGGGGAGC 60.826 66.667 0.00 0.00 0.00 4.70
97 107 3.329889 ATGCGTCAAGGGGGAGCA 61.330 61.111 0.00 0.00 42.28 4.26
98 108 2.905996 ATGCGTCAAGGGGGAGCAA 61.906 57.895 0.00 0.00 41.37 3.91
246 268 1.450312 CGAGTGCTCCCACCAATCC 60.450 63.158 0.00 0.00 43.09 3.01
251 280 0.846427 TGCTCCCACCAATCCCTTCT 60.846 55.000 0.00 0.00 0.00 2.85
256 285 1.589414 CCACCAATCCCTTCTCCTCT 58.411 55.000 0.00 0.00 0.00 3.69
274 311 0.519077 CTTGTTTCTTCAGGCGCCTC 59.481 55.000 30.29 14.65 0.00 4.70
296 333 0.036294 CCCGTTCCTTCTTGGAGGAC 60.036 60.000 0.00 0.00 45.30 3.85
298 335 1.071699 CCGTTCCTTCTTGGAGGACAA 59.928 52.381 0.00 0.00 45.30 3.18
308 345 2.762535 TGGAGGACAAGGATTCGAAC 57.237 50.000 0.00 0.00 0.00 3.95
309 346 1.974957 TGGAGGACAAGGATTCGAACA 59.025 47.619 0.00 0.00 0.00 3.18
328 365 5.663795 AACAATTCGATCATCATTCCTCG 57.336 39.130 0.00 0.00 0.00 4.63
370 416 4.151512 CGGCTGTTTCTTCTTCTTCTTCTC 59.848 45.833 0.00 0.00 0.00 2.87
383 429 0.033011 TCTTCTCCTTCCTCCTCCCG 60.033 60.000 0.00 0.00 0.00 5.14
396 442 1.978580 TCCTCCCGCTTTCTTCTTCTT 59.021 47.619 0.00 0.00 0.00 2.52
397 443 2.028020 TCCTCCCGCTTTCTTCTTCTTC 60.028 50.000 0.00 0.00 0.00 2.87
398 444 2.027653 CCTCCCGCTTTCTTCTTCTTCT 60.028 50.000 0.00 0.00 0.00 2.85
399 445 3.258228 CTCCCGCTTTCTTCTTCTTCTC 58.742 50.000 0.00 0.00 0.00 2.87
433 491 5.354842 AGTCAGATCATGCATGAGAAGAA 57.645 39.130 31.36 14.79 40.64 2.52
434 492 5.361427 AGTCAGATCATGCATGAGAAGAAG 58.639 41.667 31.36 18.20 40.64 2.85
438 496 5.992217 CAGATCATGCATGAGAAGAAGATCA 59.008 40.000 31.36 7.12 40.64 2.92
439 497 6.652900 CAGATCATGCATGAGAAGAAGATCAT 59.347 38.462 31.36 12.58 40.64 2.45
440 498 6.876789 AGATCATGCATGAGAAGAAGATCATC 59.123 38.462 31.36 19.65 40.64 2.92
441 499 4.989168 TCATGCATGAGAAGAAGATCATCG 59.011 41.667 25.42 0.00 33.91 3.84
442 500 4.660789 TGCATGAGAAGAAGATCATCGA 57.339 40.909 0.00 0.00 33.91 3.59
443 501 5.211174 TGCATGAGAAGAAGATCATCGAT 57.789 39.130 0.00 0.00 33.91 3.59
481 539 5.737757 GTGTCGTTTCTTCTTTCAGGAAAAC 59.262 40.000 0.00 0.00 32.00 2.43
521 590 2.421739 GGGTGGGATCGTGATCGG 59.578 66.667 3.91 0.00 38.69 4.18
538 615 3.088194 TCGGAAATCGAATACCCGAAG 57.912 47.619 15.77 0.00 45.08 3.79
597 677 3.566742 TCCATTCAGCATTGATCCATTCG 59.433 43.478 0.00 0.00 32.27 3.34
619 706 4.602006 GCTTCTTTCTTCTTTGGTGACAC 58.398 43.478 0.00 0.00 42.67 3.67
633 720 1.157257 TGACACGCTGACGCAATTGT 61.157 50.000 7.40 0.00 45.53 2.71
701 788 5.643777 CCCAAACAATTCTGGTCTACTAGTG 59.356 44.000 5.39 0.00 0.00 2.74
757 845 6.545504 TGTGCACTCTTAATTTCTCTTCAC 57.454 37.500 19.41 0.00 0.00 3.18
802 892 7.712205 GCCTTCAATTATTGCAATTCTTACCAT 59.288 33.333 18.75 0.00 0.00 3.55
843 933 6.289064 CCTTTTCTTCCCATATAAGCGTACT 58.711 40.000 0.00 0.00 0.00 2.73
844 934 7.439381 CCTTTTCTTCCCATATAAGCGTACTA 58.561 38.462 0.00 0.00 0.00 1.82
845 935 7.384387 CCTTTTCTTCCCATATAAGCGTACTAC 59.616 40.741 0.00 0.00 0.00 2.73
846 936 5.972107 TCTTCCCATATAAGCGTACTACC 57.028 43.478 0.00 0.00 0.00 3.18
898 988 2.481854 CTCCAAGATCTCATTGCTCCG 58.518 52.381 0.00 0.00 0.00 4.63
916 1006 2.256461 CAAGCGTTTCAGGCCAGC 59.744 61.111 5.01 0.00 0.00 4.85
951 1041 2.029838 ATCAAATCCTCGCCTCACAC 57.970 50.000 0.00 0.00 0.00 3.82
954 1044 2.521958 AAATCCTCGCCTCACACCCG 62.522 60.000 0.00 0.00 0.00 5.28
955 1045 3.957435 ATCCTCGCCTCACACCCGA 62.957 63.158 0.00 0.00 0.00 5.14
1185 1275 4.736896 GACTCCCCGTCGCACCAC 62.737 72.222 0.00 0.00 32.04 4.16
1194 1284 1.296715 GTCGCACCACTCCTCCATT 59.703 57.895 0.00 0.00 0.00 3.16
1416 1506 2.525629 TCGGTTCTGGTCCTGGCA 60.526 61.111 0.00 0.00 0.00 4.92
1485 1575 1.006102 CAGCGTCCTCGTCAAGGTT 60.006 57.895 0.00 0.00 46.32 3.50
1525 1615 5.396436 CCGTCACCTTAAATTCAGTATCCCT 60.396 44.000 0.00 0.00 0.00 4.20
1640 1730 1.593209 GCCGACCAAGTTCGTCACA 60.593 57.895 1.50 0.00 37.29 3.58
1687 1777 0.609131 CACAACCCCTCCACCATGTC 60.609 60.000 0.00 0.00 0.00 3.06
1730 1820 4.155709 CCTCCATCCAGCTCTACTATTCA 58.844 47.826 0.00 0.00 0.00 2.57
1763 1853 0.034896 CCAGCGGTCAGGTAGTGTTT 59.965 55.000 0.00 0.00 0.00 2.83
1776 1866 4.080526 AGGTAGTGTTTATTAGCACCCCAG 60.081 45.833 7.44 0.00 36.35 4.45
1787 1877 1.318158 GCACCCCAGAAAGCATCAGG 61.318 60.000 0.00 0.00 34.56 3.86
1788 1878 1.000396 ACCCCAGAAAGCATCAGGC 60.000 57.895 0.00 0.00 45.30 4.85
1802 1906 3.298619 CATCAGGCAATACCCATTTCCA 58.701 45.455 0.00 0.00 40.58 3.53
1812 1916 6.041296 GCAATACCCATTTCCATCAGAATTCT 59.959 38.462 0.88 0.88 33.44 2.40
1822 1926 6.239217 TCCATCAGAATTCTGCTAGCTAAA 57.761 37.500 27.45 10.64 43.46 1.85
1823 1927 6.835174 TCCATCAGAATTCTGCTAGCTAAAT 58.165 36.000 27.45 12.35 43.46 1.40
1845 1957 1.000866 TCCTCCTGCTGCTGCTCTA 59.999 57.895 17.00 1.07 40.48 2.43
1954 2066 0.690762 GGCTACCTTTGTCCTCACCA 59.309 55.000 0.00 0.00 0.00 4.17
2135 2247 5.181009 CAGCTACTCTTGATTTGGTGATCA 58.819 41.667 0.00 0.00 34.37 2.92
2151 2263 5.945191 TGGTGATCAATTGCTTGAGATGTTA 59.055 36.000 0.00 0.00 44.32 2.41
2315 2435 1.145738 ACATGCTGTTTGAGGGGAGTT 59.854 47.619 0.00 0.00 0.00 3.01
2328 2448 1.239347 GGGAGTTTGCTCTGTGGAAC 58.761 55.000 0.00 0.00 41.38 3.62
2337 2463 0.962489 CTCTGTGGAACGGTGAGACT 59.038 55.000 0.00 0.00 45.64 3.24
2469 2621 1.133025 CAAACAATGGCCGCCTCTTAG 59.867 52.381 11.61 0.00 0.00 2.18
2513 2665 2.625737 GCTGATGCTGTGACTGTACAT 58.374 47.619 0.00 0.00 36.03 2.29
2535 2687 1.228675 ACCCTGCTTCTGCCTTTGG 60.229 57.895 0.00 0.00 38.71 3.28
2553 2705 1.110518 GGTTCCTGCAAAACCCCGAA 61.111 55.000 16.43 0.00 40.29 4.30
2555 2707 1.460273 TTCCTGCAAAACCCCGAAGC 61.460 55.000 0.00 0.00 0.00 3.86
2715 2870 0.539051 CACTGGCTCTTCCGGATCTT 59.461 55.000 4.15 0.00 44.37 2.40
2716 2871 0.827368 ACTGGCTCTTCCGGATCTTC 59.173 55.000 4.15 0.00 44.37 2.87
2725 2880 1.448540 CCGGATCTTCGCAGCTTGT 60.449 57.895 0.00 0.00 0.00 3.16
2726 2881 1.424493 CCGGATCTTCGCAGCTTGTC 61.424 60.000 0.00 0.00 0.00 3.18
2727 2882 0.737367 CGGATCTTCGCAGCTTGTCA 60.737 55.000 0.00 0.00 0.00 3.58
2728 2883 1.661341 GGATCTTCGCAGCTTGTCAT 58.339 50.000 0.00 0.00 0.00 3.06
2729 2884 1.596727 GGATCTTCGCAGCTTGTCATC 59.403 52.381 0.00 0.00 0.00 2.92
2730 2885 1.257415 GATCTTCGCAGCTTGTCATCG 59.743 52.381 0.00 0.00 0.00 3.84
2891 3052 2.511145 GCTCTGCTTCGGCCTGAG 60.511 66.667 0.00 0.00 40.70 3.35
3029 3190 1.909302 CATCTTCCTGTACACCCTGGT 59.091 52.381 0.00 0.00 0.00 4.00
3045 3206 1.302511 GGTGGCGTTGTCCATGTCT 60.303 57.895 0.00 0.00 38.57 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
124 138 1.347817 GGCTCGAAACTGCTCGTCTG 61.348 60.000 0.00 0.00 39.84 3.51
125 139 1.080434 GGCTCGAAACTGCTCGTCT 60.080 57.895 0.00 0.00 39.84 4.18
133 147 4.035102 GGGCTGGGGCTCGAAACT 62.035 66.667 0.00 0.00 38.73 2.66
246 268 4.322567 CCTGAAGAAACAAGAGGAGAAGG 58.677 47.826 0.00 0.00 0.00 3.46
251 280 1.878102 GCGCCTGAAGAAACAAGAGGA 60.878 52.381 0.00 0.00 0.00 3.71
256 285 0.179032 TGAGGCGCCTGAAGAAACAA 60.179 50.000 38.41 5.40 0.00 2.83
308 345 4.151335 GGACGAGGAATGATGATCGAATTG 59.849 45.833 0.00 0.00 38.50 2.32
309 346 4.202253 TGGACGAGGAATGATGATCGAATT 60.202 41.667 0.00 0.00 38.50 2.17
328 365 0.735287 GGTACGGTCTTCGCTTGGAC 60.735 60.000 0.00 0.00 43.89 4.02
370 416 1.222113 GAAAGCGGGAGGAGGAAGG 59.778 63.158 0.00 0.00 0.00 3.46
383 429 1.391826 CCGCGAGAAGAAGAAGAAAGC 59.608 52.381 8.23 0.00 0.00 3.51
433 491 4.277174 GCGGACAGGATATATCGATGATCT 59.723 45.833 18.45 3.17 0.00 2.75
434 492 4.541779 GCGGACAGGATATATCGATGATC 58.458 47.826 18.45 10.54 0.00 2.92
438 496 2.097629 CACGCGGACAGGATATATCGAT 59.902 50.000 12.47 2.16 0.00 3.59
439 497 1.467342 CACGCGGACAGGATATATCGA 59.533 52.381 12.47 0.00 0.00 3.59
440 498 1.199327 ACACGCGGACAGGATATATCG 59.801 52.381 12.47 0.00 0.00 2.92
441 499 2.728225 CGACACGCGGACAGGATATATC 60.728 54.545 12.47 3.96 36.03 1.63
442 500 1.199327 CGACACGCGGACAGGATATAT 59.801 52.381 12.47 0.00 36.03 0.86
443 501 0.589708 CGACACGCGGACAGGATATA 59.410 55.000 12.47 0.00 36.03 0.86
481 539 3.693245 CGAATCGCCGGAGAAGTG 58.307 61.111 13.28 0.32 0.00 3.16
506 568 2.135933 GATTTCCGATCACGATCCCAC 58.864 52.381 1.50 0.00 42.66 4.61
521 590 5.526111 TCAAATCCTTCGGGTATTCGATTTC 59.474 40.000 0.00 0.00 39.03 2.17
537 614 2.205074 CTAGCGCACGAATCAAATCCT 58.795 47.619 11.47 0.00 0.00 3.24
538 615 1.333258 GCTAGCGCACGAATCAAATCC 60.333 52.381 11.47 0.00 35.78 3.01
597 677 4.602006 GTGTCACCAAAGAAGAAAGAAGC 58.398 43.478 0.00 0.00 0.00 3.86
633 720 1.939934 GATGAAATCATGAACCCGCGA 59.060 47.619 8.23 0.00 44.70 5.87
642 729 3.304458 CCCAGCACATCGATGAAATCATG 60.304 47.826 31.33 18.18 45.97 3.07
701 788 6.651225 AGAGCGGACCAAAATATAATCTTAGC 59.349 38.462 0.00 0.00 0.00 3.09
802 892 2.243602 AGGGAAAACGTGAACGCTTA 57.756 45.000 2.11 0.00 44.43 3.09
843 933 5.620206 TCTGAAGATTGCAAGTTTGAGGTA 58.380 37.500 4.94 0.00 0.00 3.08
844 934 4.464008 TCTGAAGATTGCAAGTTTGAGGT 58.536 39.130 4.94 0.00 0.00 3.85
845 935 5.182570 TCATCTGAAGATTGCAAGTTTGAGG 59.817 40.000 4.94 6.07 31.21 3.86
846 936 6.250344 TCATCTGAAGATTGCAAGTTTGAG 57.750 37.500 4.94 5.62 31.21 3.02
898 988 2.256461 CTGGCCTGAAACGCTTGC 59.744 61.111 3.32 0.00 0.00 4.01
916 1006 5.448360 GGATTTGATTTCTTGGAGAAGCTCG 60.448 44.000 0.00 0.00 35.37 5.03
985 1075 4.847516 CATCGTCCCTTCGCGCGA 62.848 66.667 31.40 31.40 37.76 5.87
993 1083 1.079819 CGTGTGCTTCATCGTCCCT 60.080 57.895 0.00 0.00 0.00 4.20
1185 1275 4.113815 TGCGGGCCAATGGAGGAG 62.114 66.667 2.05 0.00 0.00 3.69
1416 1506 1.901085 GAGGCAGACGAGGGTGAAT 59.099 57.895 0.00 0.00 0.00 2.57
1485 1575 2.036604 TGACGGAGCAGTCAAATGTACA 59.963 45.455 0.00 0.00 46.81 2.90
1525 1615 5.798132 TCTAAGGTGTTACTGTACGAGAGA 58.202 41.667 0.00 0.00 0.00 3.10
1640 1730 0.610174 TCTCCAGCGAGCAGTTCATT 59.390 50.000 0.00 0.00 35.94 2.57
1687 1777 0.740737 GGAAGAAACATGGATGCCGG 59.259 55.000 0.00 0.00 0.00 6.13
1730 1820 1.447643 GCTGGCGATGGGTATCTGT 59.552 57.895 0.00 0.00 0.00 3.41
1763 1853 3.201930 TGATGCTTTCTGGGGTGCTAATA 59.798 43.478 0.00 0.00 0.00 0.98
1776 1866 2.378038 TGGGTATTGCCTGATGCTTTC 58.622 47.619 0.00 0.00 42.00 2.62
1787 1877 5.796424 ATTCTGATGGAAATGGGTATTGC 57.204 39.130 0.00 0.00 37.49 3.56
1788 1878 7.431249 CAGAATTCTGATGGAAATGGGTATTG 58.569 38.462 28.13 0.00 46.59 1.90
1790 1880 5.537674 GCAGAATTCTGATGGAAATGGGTAT 59.462 40.000 34.43 0.00 46.59 2.73
1791 1881 4.889409 GCAGAATTCTGATGGAAATGGGTA 59.111 41.667 34.43 0.00 46.59 3.69
1793 1883 3.958798 AGCAGAATTCTGATGGAAATGGG 59.041 43.478 34.43 8.00 46.59 4.00
1795 1885 5.531659 AGCTAGCAGAATTCTGATGGAAATG 59.468 40.000 33.08 17.75 46.59 2.32
1796 1886 5.692928 AGCTAGCAGAATTCTGATGGAAAT 58.307 37.500 33.08 18.62 46.59 2.17
1798 1902 4.767578 AGCTAGCAGAATTCTGATGGAA 57.232 40.909 33.08 15.98 46.59 3.53
1802 1906 5.472820 GGCATTTAGCTAGCAGAATTCTGAT 59.527 40.000 34.43 31.05 44.27 2.90
1812 1916 1.417890 GGAGGAGGCATTTAGCTAGCA 59.582 52.381 18.83 0.00 44.79 3.49
1822 1926 2.691623 AGCAGCAGGAGGAGGCAT 60.692 61.111 0.00 0.00 0.00 4.40
1823 1927 3.714001 CAGCAGCAGGAGGAGGCA 61.714 66.667 0.00 0.00 0.00 4.75
1845 1957 3.244249 GCTGGTAGAACTTCTCCAACTGT 60.244 47.826 0.00 0.00 0.00 3.55
1854 1966 3.056749 TCTTCTTCGGCTGGTAGAACTTC 60.057 47.826 6.85 0.00 0.00 3.01
1944 2056 1.444250 GTCGGTGTTGGTGAGGACA 59.556 57.895 0.00 0.00 0.00 4.02
2162 2274 9.745880 CGATCACAACCATTATAGTACTTACTT 57.254 33.333 0.00 0.00 37.73 2.24
2163 2275 8.910944 ACGATCACAACCATTATAGTACTTACT 58.089 33.333 0.00 0.00 40.24 2.24
2164 2276 8.965172 CACGATCACAACCATTATAGTACTTAC 58.035 37.037 0.00 0.00 0.00 2.34
2315 2435 0.249868 CTCACCGTTCCACAGAGCAA 60.250 55.000 0.00 0.00 0.00 3.91
2328 2448 2.921634 TCGATTCAGAAGTCTCACCG 57.078 50.000 0.00 0.00 0.00 4.94
2337 2463 4.452114 CACACATTGGTCTTCGATTCAGAA 59.548 41.667 0.00 0.00 0.00 3.02
2440 2592 1.340889 GGCCATTGTTTGCTGTTCAGA 59.659 47.619 0.00 0.00 0.00 3.27
2469 2621 3.557228 ATCAAGATGGTCTTCCTCAGC 57.443 47.619 0.00 0.00 33.78 4.26
2513 2665 3.650950 GGCAGAAGCAGGGTGGGA 61.651 66.667 0.00 0.00 44.61 4.37
2535 2687 0.313987 CTTCGGGGTTTTGCAGGAAC 59.686 55.000 6.51 6.51 0.00 3.62
2553 2705 4.127040 CAGCTCCGACTGCGAGCT 62.127 66.667 6.51 6.51 45.24 4.09
2555 2707 2.202544 GTCAGCTCCGACTGCGAG 60.203 66.667 0.00 0.00 40.82 5.03
2598 2750 2.749441 TTTGCATCATCGGCGCCA 60.749 55.556 28.98 14.46 0.00 5.69
2684 2839 3.052082 CCAGTGAGCAGGCAACGG 61.052 66.667 0.00 0.00 46.39 4.44
2715 2870 1.801512 CGACGATGACAAGCTGCGA 60.802 57.895 0.00 0.00 0.00 5.10
2716 2871 2.002963 GACGACGATGACAAGCTGCG 62.003 60.000 0.00 0.00 0.00 5.18
2725 2880 2.434709 TCCCGACGACGACGATGA 60.435 61.111 20.63 13.30 42.66 2.92
2726 2881 2.277120 GTCCCGACGACGACGATG 60.277 66.667 20.63 11.30 42.66 3.84
2823 2984 1.079127 CGTCGGCCTGGTCAAGAAT 60.079 57.895 0.00 0.00 0.00 2.40
3029 3190 1.965930 GCAGACATGGACAACGCCA 60.966 57.895 0.00 0.00 43.23 5.69


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

AutoCloner maintained by Alex Coulton.