Multiple sequence alignment - TraesCS1B01G245500

Loading Multiple Alignment...

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 TraesCS1B01G245500 chr1B 100.000 2762 0 0 1 2762 434643472 434646233 0.000000e+00 5101.0
1 TraesCS1B01G245500 chr1D 92.850 2084 103 26 3 2064 322026394 322028453 0.000000e+00 2981.0
2 TraesCS1B01G245500 chr1D 92.160 625 23 11 1732 2348 322028491 322029097 0.000000e+00 859.0
3 TraesCS1B01G245500 chr1D 90.291 206 17 3 546 751 322002395 322002597 1.630000e-67 267.0
4 TraesCS1B01G245500 chr1D 88.000 150 16 1 2165 2314 398123143 398122996 2.830000e-40 176.0
5 TraesCS1B01G245500 chr1A 92.229 1956 121 21 8 1949 405680967 405682905 0.000000e+00 2741.0
6 TraesCS1B01G245500 chr1A 89.720 214 18 3 537 750 405678159 405678368 1.260000e-68 270.0
7 TraesCS1B01G245500 chr3B 92.891 422 27 1 2344 2762 170981780 170982201 6.540000e-171 610.0
8 TraesCS1B01G245500 chr3B 93.253 415 25 1 2351 2762 170984198 170984612 2.350000e-170 608.0
9 TraesCS1B01G245500 chr5A 93.253 415 25 1 2351 2762 3319739 3320153 2.350000e-170 608.0
10 TraesCS1B01G245500 chr3D 92.736 413 14 3 2351 2762 22265871 22265474 1.430000e-162 582.0
11 TraesCS1B01G245500 chr3D 83.495 309 49 2 101 408 231320103 231320410 1.250000e-73 287.0
12 TraesCS1B01G245500 chr2B 79.587 436 57 22 2351 2761 655981518 655981946 1.620000e-72 283.0
13 TraesCS1B01G245500 chr2B 90.769 65 6 0 344 408 310511135 310511071 1.360000e-13 87.9
14 TraesCS1B01G245500 chr5D 81.672 311 47 4 100 408 50970688 50970386 1.640000e-62 250.0
15 TraesCS1B01G245500 chr6B 81.029 311 49 4 100 408 55120883 55120581 3.550000e-59 239.0
16 TraesCS1B01G245500 chr7A 92.857 42 3 0 2073 2114 17691688 17691647 8.260000e-06 62.1
17 TraesCS1B01G245500 chr5B 88.235 51 6 0 2065 2115 68486117 68486167 8.260000e-06 62.1


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 TraesCS1B01G245500 chr1B 434643472 434646233 2761 False 5101.0 5101 100.0000 1 2762 1 chr1B.!!$F1 2761
1 TraesCS1B01G245500 chr1D 322026394 322029097 2703 False 1920.0 2981 92.5050 3 2348 2 chr1D.!!$F2 2345
2 TraesCS1B01G245500 chr1A 405678159 405682905 4746 False 1505.5 2741 90.9745 8 1949 2 chr1A.!!$F1 1941
3 TraesCS1B01G245500 chr3B 170981780 170984612 2832 False 609.0 610 93.0720 2344 2762 2 chr3B.!!$F1 418

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
949 3760 0.179148 CGTACACGCACCTGCTGATA 60.179 55.0 0.0 0.0 39.32 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2690 5890 0.039256 CGCAATGAAATATGGCCCGG 60.039 55.0 0.0 0.0 0.0 5.73 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
47 2849 7.917505 GGTGCTTAGATTGATTTTCTATGTTGG 59.082 37.037 0.00 0.00 0.00 3.77
110 2912 4.951715 ACACAATGCCAACATGTATGATCT 59.048 37.500 0.00 0.00 36.36 2.75
165 2967 3.127548 CCAACCATGACAAGCACTATCAC 59.872 47.826 0.00 0.00 0.00 3.06
198 3000 6.477742 TCATCTTATCGTTTTCTGCATTTCG 58.522 36.000 0.00 0.00 0.00 3.46
220 3022 5.659525 TCGAGAGGGGAACAATTTAGACATA 59.340 40.000 0.00 0.00 0.00 2.29
284 3086 3.074412 CACCTGCAGAATAACTCGGTTT 58.926 45.455 17.39 0.00 0.00 3.27
294 3096 9.095065 GCAGAATAACTCGGTTTCTATTTCTTA 57.905 33.333 0.00 0.00 0.00 2.10
304 3106 6.036300 CGGTTTCTATTTCTTACCGTGCATAA 59.964 38.462 0.00 0.00 44.90 1.90
438 3240 5.876357 AGACTTTGCTGAAATACTAACCCA 58.124 37.500 0.00 0.00 0.00 4.51
545 3347 1.228552 GAAGCCATGGGGTGTGTGT 60.229 57.895 15.13 0.00 36.17 3.72
555 3357 1.349688 GGGGTGTGTGTGAGGATTGTA 59.650 52.381 0.00 0.00 0.00 2.41
645 3447 2.727544 GTGGTGCACGTGCCATTT 59.272 55.556 35.72 0.00 41.18 2.32
705 3509 7.011295 TCCTTTTGAACATTTGCAATGAGTTTC 59.989 33.333 0.00 0.14 0.00 2.78
731 3535 4.871822 CATTTAAAGATTCCCACCCCTCT 58.128 43.478 0.00 0.00 0.00 3.69
760 3564 7.169982 CACCTAAAAATATCTAGCGAAGACTGG 59.830 40.741 0.00 0.00 36.93 4.00
819 3623 0.749454 GAGTGCCGCTCCATCCAAAT 60.749 55.000 0.00 0.00 38.27 2.32
944 3755 1.801913 CTCTCGTACACGCACCTGC 60.802 63.158 0.00 0.00 39.60 4.85
946 3757 2.049526 TCGTACACGCACCTGCTG 60.050 61.111 0.00 0.00 39.32 4.41
947 3758 2.049526 CGTACACGCACCTGCTGA 60.050 61.111 0.00 0.00 39.32 4.26
948 3759 1.446099 CGTACACGCACCTGCTGAT 60.446 57.895 0.00 0.00 39.32 2.90
949 3760 0.179148 CGTACACGCACCTGCTGATA 60.179 55.000 0.00 0.00 39.32 2.15
950 3761 1.734377 CGTACACGCACCTGCTGATAA 60.734 52.381 0.00 0.00 39.32 1.75
960 3771 0.924090 CTGCTGATAAACGCCTCGTC 59.076 55.000 0.00 0.00 39.99 4.20
974 3785 2.125512 CGTCCGAGAGCCCAAAGG 60.126 66.667 0.00 0.00 0.00 3.11
1050 3862 2.112297 GACCACCACAAAGGCGGA 59.888 61.111 0.00 0.00 42.62 5.54
1161 3976 0.739112 GCTCCGTCCTTCTGCTTCTG 60.739 60.000 0.00 0.00 0.00 3.02
1361 4188 2.359354 CGTCATCCGCAACCCCAA 60.359 61.111 0.00 0.00 0.00 4.12
1626 4453 4.238654 TTCGTGTCCGGGCCGTTT 62.239 61.111 26.32 0.00 33.95 3.60
1677 4504 2.809601 GACATGCTCGTCGGCGTT 60.810 61.111 10.18 0.00 39.49 4.84
1756 4583 1.672854 CCCCTCCTGCAACGTCGATA 61.673 60.000 0.00 0.00 0.00 2.92
1758 4585 1.611977 CCCTCCTGCAACGTCGATATA 59.388 52.381 0.00 0.00 0.00 0.86
1801 4990 2.508439 CCTGCGGCGTCGTTACAT 60.508 61.111 12.58 0.00 38.89 2.29
1802 4991 2.098233 CCTGCGGCGTCGTTACATT 61.098 57.895 12.58 0.00 38.89 2.71
1803 4992 1.058748 CTGCGGCGTCGTTACATTG 59.941 57.895 12.58 0.00 38.89 2.82
1804 4993 2.276430 GCGGCGTCGTTACATTGC 60.276 61.111 12.58 0.00 38.89 3.56
1805 4994 3.017656 GCGGCGTCGTTACATTGCA 62.018 57.895 12.58 0.00 38.89 4.08
1806 4995 1.713246 CGGCGTCGTTACATTGCAT 59.287 52.632 0.00 0.00 0.00 3.96
1807 4996 0.315059 CGGCGTCGTTACATTGCATC 60.315 55.000 0.00 0.00 0.00 3.91
1808 4997 0.724549 GGCGTCGTTACATTGCATCA 59.275 50.000 0.00 0.00 0.00 3.07
1809 4998 1.267532 GGCGTCGTTACATTGCATCAG 60.268 52.381 0.00 0.00 0.00 2.90
1810 4999 1.658596 GCGTCGTTACATTGCATCAGA 59.341 47.619 0.00 0.00 0.00 3.27
1811 5000 2.534939 GCGTCGTTACATTGCATCAGAC 60.535 50.000 0.00 0.00 0.00 3.51
1812 5001 2.666022 CGTCGTTACATTGCATCAGACA 59.334 45.455 0.00 0.00 0.00 3.41
1813 5002 3.122780 CGTCGTTACATTGCATCAGACAA 59.877 43.478 0.00 0.00 0.00 3.18
1828 5017 0.454196 GACAAACAACTTGGCCGTGT 59.546 50.000 0.00 0.00 37.02 4.49
1962 5158 1.893137 ACGAGCAGGAGTTGTACATCA 59.107 47.619 6.70 0.00 0.00 3.07
1963 5159 2.263077 CGAGCAGGAGTTGTACATCAC 58.737 52.381 6.70 0.00 0.00 3.06
2100 5297 7.686438 AAACAAAGCAAAAGACTTCCATTTT 57.314 28.000 0.00 0.00 0.00 1.82
2152 5349 1.204792 GCGAGCGGCAAAAAGAAAAA 58.795 45.000 1.45 0.00 42.87 1.94
2163 5360 4.735338 GCAAAAAGAAAAAGTCCACTCTCG 59.265 41.667 0.00 0.00 0.00 4.04
2165 5362 1.784525 AGAAAAAGTCCACTCTCGCG 58.215 50.000 0.00 0.00 0.00 5.87
2211 5408 2.490903 CTCCTGCCAAACTCCAAAGATG 59.509 50.000 0.00 0.00 0.00 2.90
2233 5430 7.619302 AGATGGGTCTCCTTTATTATTTTTGCA 59.381 33.333 0.00 0.00 0.00 4.08
2252 5449 4.880759 TGCAATAACAATGGAAGTTGGTG 58.119 39.130 0.00 0.00 33.40 4.17
2289 5486 0.250901 ATCCTTGCGTTGTGCTCCTT 60.251 50.000 0.00 0.00 46.63 3.36
2314 5511 6.209986 TCCAAATTTCTCATGAGACAAGCATT 59.790 34.615 25.07 14.20 37.14 3.56
2322 5519 7.082287 TCTCATGAGACAAGCATTAGGCAATT 61.082 38.462 21.67 0.00 37.49 2.32
2323 5520 8.500290 TCTCATGAGACAAGCATTAGGCAATTT 61.500 37.037 21.67 0.00 37.49 1.82
2348 5545 2.125106 GCGGTCACCTCCACCATC 60.125 66.667 0.00 0.00 32.89 3.51
2349 5546 2.584608 CGGTCACCTCCACCATCC 59.415 66.667 0.00 0.00 32.89 3.51
2472 5669 4.387343 CTGCCCCAGGTGCCCAAT 62.387 66.667 0.00 0.00 0.00 3.16
2527 5724 7.026562 TCAAACAACACAGATAACAAACACAG 58.973 34.615 0.00 0.00 0.00 3.66
2548 5745 6.988580 CACAGCTCAAATAAGATCACCTGATA 59.011 38.462 0.00 0.00 34.37 2.15
2688 5888 7.773489 TCAATTCACCAAGGTTCAAATATCA 57.227 32.000 0.00 0.00 0.00 2.15
2690 5890 5.643379 TTCACCAAGGTTCAAATATCAGC 57.357 39.130 0.00 0.00 0.00 4.26
2696 5896 0.668535 GTTCAAATATCAGCCGGGCC 59.331 55.000 17.02 0.00 0.00 5.80
2699 5899 1.702401 TCAAATATCAGCCGGGCCATA 59.298 47.619 17.02 12.84 0.00 2.74
2705 5905 0.478072 TCAGCCGGGCCATATTTCAT 59.522 50.000 17.02 0.00 0.00 2.57
2713 5913 2.414559 GGGCCATATTTCATTGCGATCG 60.415 50.000 11.69 11.69 0.00 3.69
2714 5914 2.226437 GGCCATATTTCATTGCGATCGT 59.774 45.455 17.81 0.00 0.00 3.73
2723 5923 1.922135 ATTGCGATCGTGTGTTGGCC 61.922 55.000 17.81 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 4.406456 TCAATCTAAGCACCAACACCAAT 58.594 39.130 0.00 0.00 0.00 3.16
47 2849 1.609208 ATTCATGCCCTATTCACGGC 58.391 50.000 0.00 0.00 45.92 5.68
110 2912 7.681679 TGTTGTGAGTCCTTATTGGTATACAA 58.318 34.615 5.01 0.00 44.54 2.41
198 3000 7.125792 TCTATGTCTAAATTGTTCCCCTCTC 57.874 40.000 0.00 0.00 0.00 3.20
284 3086 8.583810 GTGTATTATGCACGGTAAGAAATAGA 57.416 34.615 0.00 0.00 0.00 1.98
545 3347 6.665248 TCAGATCTGAAGAAGTACAATCCTCA 59.335 38.462 23.17 0.00 36.53 3.86
555 3357 3.066064 CGACCGATCAGATCTGAAGAAGT 59.934 47.826 28.40 21.47 43.58 3.01
644 3446 7.441890 TGGAAATTAAGAACGCATACTGAAA 57.558 32.000 0.00 0.00 0.00 2.69
645 3447 7.041030 TGTTGGAAATTAAGAACGCATACTGAA 60.041 33.333 0.00 0.00 0.00 3.02
681 3483 7.912383 AGAAACTCATTGCAAATGTTCAAAAG 58.088 30.769 1.71 0.00 0.00 2.27
705 3509 4.383010 GGGGTGGGAATCTTTAAATGCAAG 60.383 45.833 0.00 0.00 0.00 4.01
731 3535 6.325545 TCTTCGCTAGATATTTTTAGGTGGGA 59.674 38.462 0.00 0.00 0.00 4.37
760 3564 0.729140 CCGCAAGCAAAATCGGTGAC 60.729 55.000 0.00 0.00 37.33 3.67
819 3623 2.053865 GGGTGTCCGATCGGTGGTA 61.054 63.158 32.15 11.81 36.47 3.25
894 3700 1.159713 TCACAAGCTGCTGTGTTCCG 61.160 55.000 22.42 10.86 45.70 4.30
944 3755 0.099968 TCGGACGAGGCGTTTATCAG 59.900 55.000 0.00 0.00 41.37 2.90
946 3757 0.379669 TCTCGGACGAGGCGTTTATC 59.620 55.000 20.17 0.00 41.37 1.75
947 3758 0.381089 CTCTCGGACGAGGCGTTTAT 59.619 55.000 20.17 0.00 41.37 1.40
948 3759 1.798735 CTCTCGGACGAGGCGTTTA 59.201 57.895 20.17 0.61 41.37 2.01
949 3760 2.567049 CTCTCGGACGAGGCGTTT 59.433 61.111 20.17 0.00 41.37 3.60
950 3761 4.117661 GCTCTCGGACGAGGCGTT 62.118 66.667 20.17 0.00 41.37 4.84
960 3771 1.153349 GCTACCTTTGGGCTCTCGG 60.153 63.158 0.00 0.00 35.63 4.63
1030 3842 2.203294 GCCTTTGTGGTGGTCGGT 60.203 61.111 0.00 0.00 38.35 4.69
1790 4979 1.658596 TCTGATGCAATGTAACGACGC 59.341 47.619 0.00 0.00 0.00 5.19
1798 4987 4.924305 AGTTGTTTGTCTGATGCAATGT 57.076 36.364 0.00 0.00 0.00 2.71
1799 4988 4.446385 CCAAGTTGTTTGTCTGATGCAATG 59.554 41.667 1.45 0.00 34.87 2.82
1800 4989 4.624015 CCAAGTTGTTTGTCTGATGCAAT 58.376 39.130 1.45 0.00 34.87 3.56
1801 4990 3.737663 GCCAAGTTGTTTGTCTGATGCAA 60.738 43.478 1.45 0.00 34.87 4.08
1802 4991 2.223782 GCCAAGTTGTTTGTCTGATGCA 60.224 45.455 1.45 0.00 34.87 3.96
1803 4992 2.397549 GCCAAGTTGTTTGTCTGATGC 58.602 47.619 1.45 0.00 34.87 3.91
1804 4993 2.605338 CGGCCAAGTTGTTTGTCTGATG 60.605 50.000 2.24 0.00 34.87 3.07
1805 4994 1.608590 CGGCCAAGTTGTTTGTCTGAT 59.391 47.619 2.24 0.00 34.87 2.90
1806 4995 1.021202 CGGCCAAGTTGTTTGTCTGA 58.979 50.000 2.24 0.00 34.87 3.27
1807 4996 0.738389 ACGGCCAAGTTGTTTGTCTG 59.262 50.000 2.24 0.00 34.87 3.51
1808 4997 0.738389 CACGGCCAAGTTGTTTGTCT 59.262 50.000 2.24 0.00 34.87 3.41
1809 4998 0.454196 ACACGGCCAAGTTGTTTGTC 59.546 50.000 2.24 0.00 34.87 3.18
1810 4999 0.172352 CACACGGCCAAGTTGTTTGT 59.828 50.000 2.24 0.00 34.87 2.83
1811 5000 0.172352 ACACACGGCCAAGTTGTTTG 59.828 50.000 2.24 0.00 36.50 2.93
1812 5001 0.454196 GACACACGGCCAAGTTGTTT 59.546 50.000 2.24 0.00 0.00 2.83
1813 5002 1.381165 GGACACACGGCCAAGTTGTT 61.381 55.000 2.24 0.00 0.00 2.83
1962 5158 3.252458 GGAACTCGTAAATGTTTGCAGGT 59.748 43.478 0.00 0.00 0.00 4.00
1963 5159 3.252215 TGGAACTCGTAAATGTTTGCAGG 59.748 43.478 0.00 0.00 0.00 4.85
2082 5279 6.819284 TCAATGAAAATGGAAGTCTTTTGCT 58.181 32.000 0.00 0.00 0.00 3.91
2152 5349 1.460504 TTATGTCGCGAGAGTGGACT 58.539 50.000 10.24 0.00 43.49 3.85
2163 5360 5.095490 AGCAGCTTTGTATTTTTATGTCGC 58.905 37.500 0.00 0.00 0.00 5.19
2165 5362 6.183360 GCCAAGCAGCTTTGTATTTTTATGTC 60.183 38.462 4.38 0.00 0.00 3.06
2201 5398 3.728385 AAAGGAGACCCATCTTTGGAG 57.272 47.619 0.00 0.00 46.92 3.86
2224 5421 8.997323 CCAACTTCCATTGTTATTGCAAAAATA 58.003 29.630 1.71 0.00 31.63 1.40
2226 5423 6.825721 ACCAACTTCCATTGTTATTGCAAAAA 59.174 30.769 1.71 0.00 31.63 1.94
2231 5428 3.679502 GCACCAACTTCCATTGTTATTGC 59.320 43.478 0.00 0.00 31.71 3.56
2233 5430 3.056891 CCGCACCAACTTCCATTGTTATT 60.057 43.478 0.00 0.00 0.00 1.40
2243 5440 1.523758 AATGTCTCCGCACCAACTTC 58.476 50.000 0.00 0.00 0.00 3.01
2289 5486 5.072055 TGCTTGTCTCATGAGAAATTTGGA 58.928 37.500 26.70 12.88 39.48 3.53
2348 5545 1.001181 CAACAACCAAATGAGGCCTGG 59.999 52.381 12.00 8.56 36.24 4.45
2349 5546 1.001181 CCAACAACCAAATGAGGCCTG 59.999 52.381 12.00 0.00 0.00 4.85
2405 5602 5.163216 GGATCTCATGAGAACAGGGAAATCT 60.163 44.000 28.40 8.09 41.36 2.40
2437 5634 2.840974 GTGGAACATCTCCCACGTG 58.159 57.895 9.08 9.08 44.69 4.49
2448 5645 2.776526 ACCTGGGGCAGTGGAACA 60.777 61.111 0.00 0.00 41.43 3.18
2472 5669 2.525592 CCTCCCCCTTGTTGCCAA 59.474 61.111 0.00 0.00 0.00 4.52
2481 5678 0.627768 GGATTTCCTTCCCTCCCCCT 60.628 60.000 0.00 0.00 0.00 4.79
2527 5724 8.388484 ACATTATCAGGTGATCTTATTTGAGC 57.612 34.615 0.00 0.00 36.05 4.26
2554 5751 4.644685 GCCCTTGGATCTTAATTGCTACAA 59.355 41.667 0.00 0.00 0.00 2.41
2556 5753 4.464947 AGCCCTTGGATCTTAATTGCTAC 58.535 43.478 0.00 0.00 0.00 3.58
2557 5754 4.718961 GAGCCCTTGGATCTTAATTGCTA 58.281 43.478 0.00 0.00 34.95 3.49
2570 5767 0.329261 TTGTGGATCAGAGCCCTTGG 59.671 55.000 1.14 0.00 0.00 3.61
2650 5850 6.009589 TGGTGAATTGATGGTTATCAGTTGT 58.990 36.000 3.27 0.00 41.56 3.32
2657 5857 6.015918 TGAACCTTGGTGAATTGATGGTTAT 58.984 36.000 0.00 0.00 36.59 1.89
2688 5888 1.331214 CAATGAAATATGGCCCGGCT 58.669 50.000 9.86 0.00 0.00 5.52
2690 5890 0.039256 CGCAATGAAATATGGCCCGG 60.039 55.000 0.00 0.00 0.00 5.73
2696 5896 4.836455 ACACACGATCGCAATGAAATATG 58.164 39.130 16.60 4.19 0.00 1.78
2699 5899 3.491356 CAACACACGATCGCAATGAAAT 58.509 40.909 16.60 1.12 0.00 2.17
2705 5905 2.612567 GGCCAACACACGATCGCAA 61.613 57.895 16.60 0.00 0.00 4.85
2713 5913 6.079424 TGAAAATAGTTTAGGCCAACACAC 57.921 37.500 5.01 0.00 0.00 3.82
2714 5914 6.266558 ACATGAAAATAGTTTAGGCCAACACA 59.733 34.615 5.01 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.