Multiple sequence alignment - TraesCS3B01G418600

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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 TraesCS3B01G418600 chr3B 100.000 3277 0 0 1 3277 655423834 655420558 0.000000e+00 6052
1 TraesCS3B01G418600 chr3D 93.603 3314 125 36 9 3277 496407882 496404611 0.000000e+00 4865
2 TraesCS3B01G418600 chr3A 91.913 3079 128 51 274 3277 635732398 635729366 0.000000e+00 4194
3 TraesCS3B01G418600 chr3A 91.915 235 19 0 1 235 635732639 635732405 2.440000e-86 329
4 TraesCS3B01G418600 chr2D 89.062 128 9 3 2854 2981 526253317 526253439 1.570000e-33 154
5 TraesCS3B01G418600 chr7D 76.336 262 55 5 1249 1508 404062840 404063096 2.050000e-27 134
6 TraesCS3B01G418600 chr7A 76.336 262 55 5 1249 1508 462984866 462985122 2.050000e-27 134


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 TraesCS3B01G418600 chr3B 655420558 655423834 3276 True 6052.0 6052 100.000 1 3277 1 chr3B.!!$R1 3276
1 TraesCS3B01G418600 chr3D 496404611 496407882 3271 True 4865.0 4865 93.603 9 3277 1 chr3D.!!$R1 3268
2 TraesCS3B01G418600 chr3A 635729366 635732639 3273 True 2261.5 4194 91.914 1 3277 2 chr3A.!!$R1 3276

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
143 144 0.677288 TATCCTAACCCACGATGCCG 59.323 55.0 0.0 0.0 42.5 5.69 F
1184 1214 0.036010 AACATCGTCTTCCCCAGCAG 60.036 55.0 0.0 0.0 0.0 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1530 1578 0.385098 CATTGTGCTGTGCTGTGTCG 60.385 55.0 0.00 0.0 0.00 4.35 R
2847 2921 0.248907 GCGATCCGGAGAATTCGACA 60.249 55.0 25.25 0.0 42.19 4.35 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
103 104 6.254589 GTCTCCTTTCTGATCTATGTTTGTCG 59.745 42.308 0.00 0.00 0.00 4.35
121 122 4.556233 TGTCGACCAATTTCACTAGTCTG 58.444 43.478 14.12 0.00 0.00 3.51
122 123 3.368236 GTCGACCAATTTCACTAGTCTGC 59.632 47.826 3.51 0.00 0.00 4.26
123 124 2.673368 CGACCAATTTCACTAGTCTGCC 59.327 50.000 0.00 0.00 0.00 4.85
143 144 0.677288 TATCCTAACCCACGATGCCG 59.323 55.000 0.00 0.00 42.50 5.69
184 185 3.194005 ACACATATCCGACACCAATCC 57.806 47.619 0.00 0.00 0.00 3.01
196 197 3.573967 GACACCAATCCACCAAACTTCAT 59.426 43.478 0.00 0.00 0.00 2.57
201 202 4.523943 CCAATCCACCAAACTTCATCTTGA 59.476 41.667 0.00 0.00 0.00 3.02
214 215 5.070446 ACTTCATCTTGACGAATATGCCCTA 59.930 40.000 0.00 0.00 0.00 3.53
265 272 3.302156 CGCGAATACGTGCAAATCATACA 60.302 43.478 0.00 0.00 42.78 2.29
270 277 6.545504 AATACGTGCAAATCATACATCCTC 57.454 37.500 0.00 0.00 0.00 3.71
395 404 5.624491 GCATATACGTCCTCGAAACTAACTC 59.376 44.000 0.00 0.00 40.62 3.01
403 412 6.632035 CGTCCTCGAAACTAACTCACATATAC 59.368 42.308 0.00 0.00 39.71 1.47
433 444 3.288809 CTGGACAGCATATCGATCGAA 57.711 47.619 23.50 11.90 0.00 3.71
476 488 0.889638 AGAAGACTCGCGTGTCTCCA 60.890 55.000 35.51 2.61 45.49 3.86
536 548 3.047796 CACACGCTACGTACTTCAAACT 58.952 45.455 0.00 0.00 38.32 2.66
542 554 3.428589 GCTACGTACTTCAAACTCGGGAT 60.429 47.826 0.00 0.00 0.00 3.85
557 569 2.185238 GGATATCCTCCCTCTCGCG 58.815 63.158 14.97 0.00 38.19 5.87
593 611 1.455248 CCTCGATCCCTATCTCGGTC 58.545 60.000 0.00 0.00 35.64 4.79
594 612 1.003812 CCTCGATCCCTATCTCGGTCT 59.996 57.143 0.00 0.00 35.64 3.85
595 613 2.352388 CTCGATCCCTATCTCGGTCTC 58.648 57.143 0.00 0.00 35.64 3.36
651 669 1.079405 CACGTTACCACCGCCATCT 60.079 57.895 0.00 0.00 0.00 2.90
669 687 1.076332 CTTGGGAAACACCGATCGAC 58.924 55.000 18.66 0.58 40.11 4.20
726 744 1.913722 CCTCTCTCCATGGCTTGCT 59.086 57.895 6.96 0.00 0.00 3.91
737 755 2.684843 GGCTTGCTCGTGAAGGCTG 61.685 63.158 0.00 0.00 41.56 4.85
874 898 2.187707 CGTTTAAATCCGTCGACCGAT 58.812 47.619 12.80 12.80 39.56 4.18
979 1009 2.023461 CGTTTTGTTGCGTGGCGA 59.977 55.556 0.00 0.00 0.00 5.54
1159 1189 1.125093 CACCCAGTACACCAGGACCA 61.125 60.000 0.00 0.00 0.00 4.02
1160 1190 0.178873 ACCCAGTACACCAGGACCAT 60.179 55.000 0.00 0.00 0.00 3.55
1184 1214 0.036010 AACATCGTCTTCCCCAGCAG 60.036 55.000 0.00 0.00 0.00 4.24
1187 1217 2.249413 ATCGTCTTCCCCAGCAGCAG 62.249 60.000 0.00 0.00 0.00 4.24
1197 1227 4.962836 AGCAGCAGCACCACCACC 62.963 66.667 3.17 0.00 45.49 4.61
1200 1230 4.935495 AGCAGCACCACCACCGTG 62.935 66.667 0.00 0.00 39.91 4.94
1203 1233 1.959226 CAGCACCACCACCGTGTAC 60.959 63.158 0.00 0.00 38.41 2.90
1266 1314 2.152699 GCACGACATGACGGACGAG 61.153 63.158 20.92 7.09 37.61 4.18
1269 1317 1.443702 CGACATGACGGACGAGCAA 60.444 57.895 9.78 0.00 0.00 3.91
1401 1449 4.082523 TGGGAGCGCTTCTTCCGG 62.083 66.667 16.97 0.00 44.03 5.14
1407 1455 2.438434 CGCTTCTTCCGGGGCAAT 60.438 61.111 0.00 0.00 0.00 3.56
1514 1562 1.356527 CCAAGCCAGGTACGTAACGC 61.357 60.000 4.68 3.54 0.00 4.84
1536 1584 2.583868 GCCACACGACACGACACA 60.584 61.111 0.00 0.00 0.00 3.72
1615 1672 1.149987 AATTCTTTTCCGCGTGCGTA 58.850 45.000 13.70 0.00 37.81 4.42
1880 1941 1.601759 GCTGCAGCAGTGGAGGAAA 60.602 57.895 33.36 0.00 42.29 3.13
1901 1962 1.079543 CTCCCAGTGGTTCGAGCTG 60.080 63.158 8.74 0.72 0.00 4.24
1956 2017 1.822990 CCAAGTACTACCCGCTCTTCA 59.177 52.381 0.00 0.00 0.00 3.02
2014 2075 3.760035 CCTCCCGACCACCGTGAG 61.760 72.222 0.00 0.00 41.48 3.51
2192 2253 4.052229 AACCAGAGGCCGACGTCG 62.052 66.667 30.33 30.33 35.81 5.12
2281 2342 1.619332 GGTCATGGGGTACTAGCTAGC 59.381 57.143 20.91 6.62 0.00 3.42
2344 2405 7.918076 TCTTCCATGTTTGTAACTTAGGATCT 58.082 34.615 0.00 0.00 0.00 2.75
2345 2406 9.042450 TCTTCCATGTTTGTAACTTAGGATCTA 57.958 33.333 0.00 0.00 0.00 1.98
2370 2431 1.071987 CAGCAGCCTCTTGACCACA 59.928 57.895 0.00 0.00 0.00 4.17
2371 2432 0.322277 CAGCAGCCTCTTGACCACAT 60.322 55.000 0.00 0.00 0.00 3.21
2444 2505 4.365899 TGTCGAATTCGCTACAGTATGT 57.634 40.909 22.90 0.00 46.47 2.29
2449 2510 6.071928 TCGAATTCGCTACAGTATGTATGGC 61.072 44.000 22.90 0.00 44.14 4.40
2462 2523 2.985896 TGTATGGCCTTCGAAAAGAGG 58.014 47.619 3.32 0.00 34.14 3.69
2464 2525 0.034089 ATGGCCTTCGAAAAGAGGGG 60.034 55.000 3.32 0.00 45.45 4.79
2465 2526 1.131303 TGGCCTTCGAAAAGAGGGGA 61.131 55.000 3.32 0.00 45.45 4.81
2466 2527 0.037734 GGCCTTCGAAAAGAGGGGAA 59.962 55.000 0.00 0.00 45.45 3.97
2467 2528 1.546998 GGCCTTCGAAAAGAGGGGAAA 60.547 52.381 0.00 0.00 45.45 3.13
2496 2558 7.873195 AGAAGGAAGGTTAGTTTAGGCATAAT 58.127 34.615 0.00 0.00 0.00 1.28
2510 2572 3.255888 AGGCATAATCATTCAGCAGCATG 59.744 43.478 0.00 0.00 40.87 4.06
2659 2723 3.357079 GGCACTGAACCACCGCAG 61.357 66.667 0.00 0.00 38.10 5.18
2764 2828 2.686915 CAACCATCAATTCCAGCTCCTC 59.313 50.000 0.00 0.00 0.00 3.71
2765 2829 1.213926 ACCATCAATTCCAGCTCCTCC 59.786 52.381 0.00 0.00 0.00 4.30
2766 2830 1.493871 CCATCAATTCCAGCTCCTCCT 59.506 52.381 0.00 0.00 0.00 3.69
2767 2831 2.486907 CCATCAATTCCAGCTCCTCCTC 60.487 54.545 0.00 0.00 0.00 3.71
2768 2832 1.207791 TCAATTCCAGCTCCTCCTCC 58.792 55.000 0.00 0.00 0.00 4.30
2846 2920 1.838112 TCATTGCCATGGTCCAGTTC 58.162 50.000 14.67 0.00 0.00 3.01
2847 2921 1.355381 TCATTGCCATGGTCCAGTTCT 59.645 47.619 14.67 0.00 0.00 3.01
2984 3061 1.582968 CACCACCAGCATCAACAGC 59.417 57.895 0.00 0.00 0.00 4.40
2993 3070 1.000843 AGCATCAACAGCGTGTCAGTA 59.999 47.619 0.00 0.00 37.01 2.74
3100 3186 2.734492 GCACGCTAGTAACTGACGGAAT 60.734 50.000 0.00 0.00 0.00 3.01
3126 3212 3.438087 CACCAATTAACTGCACTCTGAGG 59.562 47.826 9.85 0.00 0.00 3.86
3128 3214 4.074970 CCAATTAACTGCACTCTGAGGTT 58.925 43.478 9.85 6.01 0.00 3.50
3146 3244 7.337689 TCTGAGGTTGTTAATGGAATGAATGAG 59.662 37.037 0.00 0.00 0.00 2.90
3261 3359 4.553547 GCTTGGCTCACGTTTCATCATATC 60.554 45.833 0.00 0.00 0.00 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 104 3.944087 AGGCAGACTAGTGAAATTGGTC 58.056 45.455 0.00 0.00 0.00 4.02
121 122 1.608283 GCATCGTGGGTTAGGATAGGC 60.608 57.143 0.00 0.00 32.87 3.93
122 123 1.002087 GGCATCGTGGGTTAGGATAGG 59.998 57.143 0.00 0.00 32.87 2.57
123 124 1.336887 CGGCATCGTGGGTTAGGATAG 60.337 57.143 0.00 0.00 32.87 2.08
143 144 5.907391 GTGTAATCTGGCGCAAATGTATAAC 59.093 40.000 10.83 0.00 0.00 1.89
184 185 4.811555 TTCGTCAAGATGAAGTTTGGTG 57.188 40.909 0.73 0.00 32.92 4.17
196 197 3.664107 GCATAGGGCATATTCGTCAAGA 58.336 45.455 0.00 0.00 43.97 3.02
214 215 2.086869 CGACAACTTCAAGGATGGCAT 58.913 47.619 0.00 0.00 0.00 4.40
246 253 6.347725 GGAGGATGTATGATTTGCACGTATTC 60.348 42.308 0.00 0.00 0.00 1.75
248 255 4.997395 GGAGGATGTATGATTTGCACGTAT 59.003 41.667 0.00 0.00 0.00 3.06
252 259 4.581824 ACATGGAGGATGTATGATTTGCAC 59.418 41.667 0.00 0.00 43.96 4.57
256 263 7.935755 CAGAAGTACATGGAGGATGTATGATTT 59.064 37.037 0.00 0.00 46.88 2.17
289 296 6.483640 GGAAGCTTCCTCAAAATACATATCGT 59.516 38.462 33.98 0.00 44.11 3.73
395 404 2.483876 CAGCTTGACGGGGTATATGTG 58.516 52.381 0.00 0.00 0.00 3.21
403 412 2.046892 CTGTCCAGCTTGACGGGG 60.047 66.667 17.17 5.21 37.87 5.73
433 444 3.646637 GGTAATGTCAGCCCTAGGTATGT 59.353 47.826 8.29 0.00 0.00 2.29
556 568 3.431725 GAACAAGAAGGGGGCGCG 61.432 66.667 0.00 0.00 0.00 6.86
557 569 3.062466 GGAACAAGAAGGGGGCGC 61.062 66.667 0.00 0.00 0.00 6.53
567 585 3.235200 AGATAGGGATCGAGGGAACAAG 58.765 50.000 0.00 0.00 37.15 3.16
593 611 1.304617 GCCAAAAGGAGGGGAGGAG 59.695 63.158 0.00 0.00 0.00 3.69
594 612 2.238701 GGCCAAAAGGAGGGGAGGA 61.239 63.158 0.00 0.00 0.00 3.71
595 613 2.360585 GGCCAAAAGGAGGGGAGG 59.639 66.667 0.00 0.00 0.00 4.30
651 669 0.320946 GGTCGATCGGTGTTTCCCAA 60.321 55.000 16.41 0.00 0.00 4.12
726 744 2.579201 GCTAGCCAGCCTTCACGA 59.421 61.111 2.29 0.00 42.37 4.35
737 755 2.105806 CTGATTCCCGGGAGCTAGCC 62.106 65.000 25.26 10.67 0.00 3.93
874 898 1.299392 CTGCCGCTTGATCGATCGA 60.299 57.895 21.86 21.86 0.00 3.59
884 908 3.780173 GGGAGAGCTCTGCCGCTT 61.780 66.667 34.91 3.48 44.51 4.68
965 995 3.959975 GCCTCGCCACGCAACAAA 61.960 61.111 0.00 0.00 0.00 2.83
979 1009 3.764466 CGAGCTCCCTTGTCGCCT 61.764 66.667 8.47 0.00 0.00 5.52
1159 1189 2.039746 TGGGGAAGACGATGTTGTTGAT 59.960 45.455 0.00 0.00 0.00 2.57
1160 1190 1.418264 TGGGGAAGACGATGTTGTTGA 59.582 47.619 0.00 0.00 0.00 3.18
1266 1314 4.451652 GCGCGCCAGAAGAGTTGC 62.452 66.667 23.24 0.00 0.00 4.17
1401 1449 2.044946 AAGCGGTCCTCATTGCCC 60.045 61.111 0.00 0.00 0.00 5.36
1407 1455 2.282958 ACGGAGAAGCGGTCCTCA 60.283 61.111 2.53 0.00 31.14 3.86
1468 1516 2.577593 GCCGTAGAAGGGCGAGTT 59.422 61.111 0.00 0.00 39.53 3.01
1521 1569 1.876263 TGCTGTGTCGTGTCGTGTG 60.876 57.895 0.00 0.00 0.00 3.82
1526 1574 1.882625 TGCTGTGCTGTGTCGTGTC 60.883 57.895 0.00 0.00 0.00 3.67
1527 1575 2.173669 GTGCTGTGCTGTGTCGTGT 61.174 57.895 0.00 0.00 0.00 4.49
1528 1576 1.704387 TTGTGCTGTGCTGTGTCGTG 61.704 55.000 0.00 0.00 0.00 4.35
1529 1577 0.815213 ATTGTGCTGTGCTGTGTCGT 60.815 50.000 0.00 0.00 0.00 4.34
1530 1578 0.385098 CATTGTGCTGTGCTGTGTCG 60.385 55.000 0.00 0.00 0.00 4.35
1861 1922 3.889134 TTCCTCCACTGCTGCAGCG 62.889 63.158 32.11 27.01 45.83 5.18
1867 1928 1.682257 GAGCCTTTCCTCCACTGCT 59.318 57.895 0.00 0.00 0.00 4.24
1880 1941 2.203788 TCGAACCACTGGGAGCCT 60.204 61.111 0.00 0.00 38.05 4.58
2094 2155 3.403057 CACGTTCTCGGCCGTGTG 61.403 66.667 27.15 21.05 46.87 3.82
2192 2253 0.955428 TGGCGAACAGGAAGCACATC 60.955 55.000 0.00 0.00 0.00 3.06
2344 2405 5.543790 TGGTCAAGAGGCTGCTGAATATATA 59.456 40.000 0.00 0.00 0.00 0.86
2345 2406 4.349048 TGGTCAAGAGGCTGCTGAATATAT 59.651 41.667 0.00 0.00 0.00 0.86
2370 2431 4.319911 CGTTTTATGTTCACGGGTCACAAT 60.320 41.667 0.00 0.00 0.00 2.71
2371 2432 3.002451 CGTTTTATGTTCACGGGTCACAA 59.998 43.478 0.00 0.00 0.00 3.33
2444 2505 1.211949 CCCCTCTTTTCGAAGGCCATA 59.788 52.381 5.01 0.00 0.00 2.74
2467 2528 6.837048 TGCCTAAACTAACCTTCCTTCTTTTT 59.163 34.615 0.00 0.00 0.00 1.94
2472 2533 7.773690 TGATTATGCCTAAACTAACCTTCCTTC 59.226 37.037 0.00 0.00 0.00 3.46
2496 2558 1.279846 TGGAGACATGCTGCTGAATGA 59.720 47.619 17.86 0.00 35.71 2.57
2510 2572 0.600255 CCAGTCAACGTGGTGGAGAC 60.600 60.000 0.00 0.00 31.04 3.36
2764 2828 3.700350 AGGTGAGGGGAGGGGAGG 61.700 72.222 0.00 0.00 0.00 4.30
2765 2829 2.041405 GAGGTGAGGGGAGGGGAG 60.041 72.222 0.00 0.00 0.00 4.30
2766 2830 2.874245 TGAGGTGAGGGGAGGGGA 60.874 66.667 0.00 0.00 0.00 4.81
2767 2831 2.366167 CTGAGGTGAGGGGAGGGG 60.366 72.222 0.00 0.00 0.00 4.79
2768 2832 2.243774 TAGCTGAGGTGAGGGGAGGG 62.244 65.000 0.00 0.00 0.00 4.30
2846 2920 1.759994 CGATCCGGAGAATTCGACAG 58.240 55.000 18.16 0.00 42.19 3.51
2847 2921 0.248907 GCGATCCGGAGAATTCGACA 60.249 55.000 25.25 0.00 42.19 4.35
2993 3070 1.479389 CCCAGCTTTTCCTTGTCACCT 60.479 52.381 0.00 0.00 0.00 4.00
3100 3186 2.813754 GAGTGCAGTTAATTGGTGCTCA 59.186 45.455 0.00 0.00 38.09 4.26
3126 3212 6.038356 CCAGCTCATTCATTCCATTAACAAC 58.962 40.000 0.00 0.00 0.00 3.32
3128 3214 5.508567 TCCAGCTCATTCATTCCATTAACA 58.491 37.500 0.00 0.00 0.00 2.41
3146 3244 1.823041 GCCTCTTGATGCCTCCAGC 60.823 63.158 0.00 0.00 44.14 4.85


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

AutoCloner maintained by Alex Coulton.