Multiple sequence alignment - TraesCS6D01G209700

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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 TraesCS6D01G209700 chr6D 100.000 2609 0 0 1 2609 296349171 296346563 0.000000e+00 4819
1 TraesCS6D01G209700 chr6D 85.891 404 53 4 1130 1531 452722160 452721759 6.670000e-116 427
2 TraesCS6D01G209700 chr6B 94.214 2385 66 31 256 2609 460927818 460930161 0.000000e+00 3574
3 TraesCS6D01G209700 chr6B 86.139 404 52 4 1130 1531 687525397 687524996 1.430000e-117 433
4 TraesCS6D01G209700 chr6B 97.122 139 4 0 32 170 460927309 460927447 4.340000e-58 235
5 TraesCS6D01G209700 chr6B 100.000 40 0 0 203 242 460927786 460927825 1.000000e-09 75
6 TraesCS6D01G209700 chr6A 92.736 2423 79 41 272 2609 422329538 422327128 0.000000e+00 3410
7 TraesCS6D01G209700 chr6A 86.139 404 52 4 1130 1531 598619720 598619319 1.430000e-117 433
8 TraesCS6D01G209700 chr6A 95.098 204 7 2 1 202 422330150 422329948 4.190000e-83 318
9 TraesCS6D01G209700 chr2D 89.111 450 46 3 1112 1558 483256327 483255878 8.160000e-155 556
10 TraesCS6D01G209700 chr2A 88.839 448 48 2 1112 1558 626589683 626589237 1.360000e-152 549
11 TraesCS6D01G209700 chr2B 88.521 453 49 3 1109 1558 568275133 568275585 1.770000e-151 545
12 TraesCS6D01G209700 chr1D 84.901 404 61 0 1125 1528 214068338 214067935 2.420000e-110 409


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 TraesCS6D01G209700 chr6D 296346563 296349171 2608 True 4819.000000 4819 100.000 1 2609 1 chr6D.!!$R1 2608
1 TraesCS6D01G209700 chr6B 460927309 460930161 2852 False 1294.666667 3574 97.112 32 2609 3 chr6B.!!$F1 2577
2 TraesCS6D01G209700 chr6A 422327128 422330150 3022 True 1864.000000 3410 93.917 1 2609 2 chr6A.!!$R2 2608

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
808 1175 0.248054 GGCCGTTTCGCATGTGTATG 60.248 55.0 6.09 1.73 37.36 2.39 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2141 2582 0.538584 AGGTGAAGATGATGCTCGCA 59.461 50.0 0.0 0.0 0.0 5.1 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
53 54 2.284995 AGAGACTGGGACTGGGGC 60.285 66.667 0.00 0.00 0.00 5.80
242 550 1.569548 TCCGTCCTACCATCTCCTCTT 59.430 52.381 0.00 0.00 0.00 2.85
243 551 2.024273 TCCGTCCTACCATCTCCTCTTT 60.024 50.000 0.00 0.00 0.00 2.52
244 552 2.362717 CCGTCCTACCATCTCCTCTTTC 59.637 54.545 0.00 0.00 0.00 2.62
245 553 3.292460 CGTCCTACCATCTCCTCTTTCT 58.708 50.000 0.00 0.00 0.00 2.52
246 554 3.316868 CGTCCTACCATCTCCTCTTTCTC 59.683 52.174 0.00 0.00 0.00 2.87
247 555 4.542697 GTCCTACCATCTCCTCTTTCTCT 58.457 47.826 0.00 0.00 0.00 3.10
248 556 4.583073 GTCCTACCATCTCCTCTTTCTCTC 59.417 50.000 0.00 0.00 0.00 3.20
249 557 4.480537 TCCTACCATCTCCTCTTTCTCTCT 59.519 45.833 0.00 0.00 0.00 3.10
250 558 4.827284 CCTACCATCTCCTCTTTCTCTCTC 59.173 50.000 0.00 0.00 0.00 3.20
251 559 4.608170 ACCATCTCCTCTTTCTCTCTCT 57.392 45.455 0.00 0.00 0.00 3.10
252 560 4.536765 ACCATCTCCTCTTTCTCTCTCTC 58.463 47.826 0.00 0.00 0.00 3.20
253 561 4.230502 ACCATCTCCTCTTTCTCTCTCTCT 59.769 45.833 0.00 0.00 0.00 3.10
254 562 4.823989 CCATCTCCTCTTTCTCTCTCTCTC 59.176 50.000 0.00 0.00 0.00 3.20
255 563 5.398353 CCATCTCCTCTTTCTCTCTCTCTCT 60.398 48.000 0.00 0.00 0.00 3.10
256 564 5.359194 TCTCCTCTTTCTCTCTCTCTCTC 57.641 47.826 0.00 0.00 0.00 3.20
257 565 5.032846 TCTCCTCTTTCTCTCTCTCTCTCT 58.967 45.833 0.00 0.00 0.00 3.10
258 566 5.129485 TCTCCTCTTTCTCTCTCTCTCTCTC 59.871 48.000 0.00 0.00 0.00 3.20
259 567 5.032846 TCCTCTTTCTCTCTCTCTCTCTCT 58.967 45.833 0.00 0.00 0.00 3.10
260 568 5.129485 TCCTCTTTCTCTCTCTCTCTCTCTC 59.871 48.000 0.00 0.00 0.00 3.20
261 569 5.130145 CCTCTTTCTCTCTCTCTCTCTCTCT 59.870 48.000 0.00 0.00 0.00 3.10
262 570 6.227298 TCTTTCTCTCTCTCTCTCTCTCTC 57.773 45.833 0.00 0.00 0.00 3.20
263 571 5.960811 TCTTTCTCTCTCTCTCTCTCTCTCT 59.039 44.000 0.00 0.00 0.00 3.10
375 718 2.365582 ACCCACCTAAAAATAGCAGCG 58.634 47.619 0.00 0.00 0.00 5.18
515 866 3.653344 TGAGCAACAGCAACTACTACTG 58.347 45.455 0.00 0.00 37.45 2.74
603 966 6.068140 CCCTATATATCTACCTCTTCCACCCT 60.068 46.154 0.00 0.00 0.00 4.34
725 1088 3.912745 AAAAAGGGATCGGCCGCGT 62.913 57.895 23.51 12.10 37.63 6.01
806 1173 2.384309 CGGCCGTTTCGCATGTGTA 61.384 57.895 19.50 0.00 0.00 2.90
808 1175 0.248054 GGCCGTTTCGCATGTGTATG 60.248 55.000 6.09 1.73 37.36 2.39
849 1221 5.424757 TGTTTGGTAGATACATCCCTTTCG 58.575 41.667 0.00 0.00 0.00 3.46
869 1241 1.889105 ACACGCACACAGAGCCAAG 60.889 57.895 0.00 0.00 0.00 3.61
900 1274 0.395586 AGTGTGCACCAGCTCCAAAA 60.396 50.000 15.69 0.00 42.74 2.44
910 1284 2.091541 CAGCTCCAAAATTAAGGGCGA 58.908 47.619 0.00 0.00 0.00 5.54
948 1322 3.120615 GCATTCATCAGCTAGCTTCATCG 60.121 47.826 16.46 3.22 0.00 3.84
1011 1385 1.281867 GGTTGATCCATGGACCTGTCA 59.718 52.381 18.99 14.33 35.97 3.58
1958 2334 9.244799 CTGCTCATTAAAACACGTACATATAGA 57.755 33.333 0.00 0.00 0.00 1.98
1962 2338 8.533965 TCATTAAAACACGTACATATAGAACGC 58.466 33.333 0.00 0.00 40.18 4.84
1968 2344 7.425577 ACACGTACATATAGAACGCACTATA 57.574 36.000 10.23 10.23 40.18 1.31
1983 2363 9.472361 GAACGCACTATATCCTGAAGTTTATAA 57.528 33.333 0.00 0.00 0.00 0.98
2141 2582 0.105964 TGTAGTCTTGTGGCGCACTT 59.894 50.000 10.83 0.00 35.11 3.16
2169 2610 3.855255 TCATCTTCACCTTGGTGTTGA 57.145 42.857 18.05 16.36 0.00 3.18
2233 2678 0.959553 ATCCGCCACATAGGAGTACG 59.040 55.000 0.00 0.00 40.26 3.67
2270 2715 2.039818 TTGCGTTGGTTCCTTGTGTA 57.960 45.000 0.00 0.00 0.00 2.90
2304 2749 4.261031 CCGCCTTATTTTCTTGTATTCCCG 60.261 45.833 0.00 0.00 0.00 5.14
2364 2819 2.582498 GGCGGCGCTGTACTGTAG 60.582 66.667 32.30 0.00 0.00 2.74
2365 2820 2.181021 GCGGCGCTGTACTGTAGT 59.819 61.111 26.86 0.00 0.00 2.73
2366 2821 1.430632 GCGGCGCTGTACTGTAGTA 59.569 57.895 26.86 0.00 0.00 1.82
2455 2912 2.046217 GTTCTTCCTCGGCCACCC 60.046 66.667 2.24 0.00 0.00 4.61
2495 2954 1.800586 CTAGCTTGTGTGCGTGACATT 59.199 47.619 0.00 0.00 36.78 2.71
2504 2963 2.741517 TGTGCGTGACATTGTGAATAGG 59.258 45.455 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 4.040755 ACCACCTCCATTTGTATAGCTCT 58.959 43.478 0.00 0.00 0.00 4.09
74 76 1.517475 GGAGGAGAAAGCGAGCGAC 60.517 63.158 0.00 0.00 0.00 5.19
242 550 5.523588 AGAGAGAGAGAGAGAGAGAGAGAA 58.476 45.833 0.00 0.00 0.00 2.87
243 551 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
244 552 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
245 553 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
246 554 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
247 555 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
248 556 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
249 557 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
250 558 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
251 559 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
252 560 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
253 561 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
254 562 5.049060 CGTAGAGAGAGAGAGAGAGAGAGAG 60.049 52.000 0.00 0.00 0.00 3.20
255 563 4.822350 CGTAGAGAGAGAGAGAGAGAGAGA 59.178 50.000 0.00 0.00 0.00 3.10
256 564 4.580995 ACGTAGAGAGAGAGAGAGAGAGAG 59.419 50.000 0.00 0.00 0.00 3.20
257 565 4.533815 ACGTAGAGAGAGAGAGAGAGAGA 58.466 47.826 0.00 0.00 0.00 3.10
258 566 4.554919 CGACGTAGAGAGAGAGAGAGAGAG 60.555 54.167 0.00 0.00 0.00 3.20
259 567 3.314357 CGACGTAGAGAGAGAGAGAGAGA 59.686 52.174 0.00 0.00 0.00 3.10
260 568 3.629058 CGACGTAGAGAGAGAGAGAGAG 58.371 54.545 0.00 0.00 0.00 3.20
261 569 2.223641 GCGACGTAGAGAGAGAGAGAGA 60.224 54.545 0.00 0.00 0.00 3.10
262 570 2.124903 GCGACGTAGAGAGAGAGAGAG 58.875 57.143 0.00 0.00 0.00 3.20
263 571 1.752498 AGCGACGTAGAGAGAGAGAGA 59.248 52.381 0.00 0.00 0.00 3.10
515 866 3.804193 GCCACTTACCGCAGCAGC 61.804 66.667 0.00 0.00 37.42 5.25
603 966 2.501316 TCGAGAATTTGATCTGCAGGGA 59.499 45.455 15.13 0.00 0.00 4.20
725 1088 4.697756 CCTTTCCTCACGGCGGCA 62.698 66.667 13.24 0.00 0.00 5.69
828 1195 4.080807 TGCGAAAGGGATGTATCTACCAAA 60.081 41.667 0.00 0.00 0.00 3.28
838 1210 2.325082 GCGTGTGCGAAAGGGATGT 61.325 57.895 0.00 0.00 41.33 3.06
849 1221 4.017877 GGCTCTGTGTGCGTGTGC 62.018 66.667 0.00 0.00 43.20 4.57
869 1241 3.775654 CACACTCCGCTCCCTCCC 61.776 72.222 0.00 0.00 0.00 4.30
910 1284 0.963355 ATGCGTGCGTATTTGGGGTT 60.963 50.000 0.00 0.00 0.00 4.11
948 1322 3.968649 TCCGCCATTATAGTACACGAAC 58.031 45.455 0.00 0.00 0.00 3.95
1011 1385 3.647771 GGGCTCTCGGGGTTTGGT 61.648 66.667 0.00 0.00 0.00 3.67
1958 2334 9.826574 TTTATAAACTTCAGGATATAGTGCGTT 57.173 29.630 0.00 0.00 0.00 4.84
1968 2344 7.171678 GCACGCTATCTTTATAAACTTCAGGAT 59.828 37.037 0.00 0.00 0.00 3.24
1983 2363 2.444624 CGCACACGCACGCTATCTT 61.445 57.895 0.00 0.00 38.40 2.40
2141 2582 0.538584 AGGTGAAGATGATGCTCGCA 59.461 50.000 0.00 0.00 0.00 5.10
2270 2715 3.933861 AATAAGGCGGAAAGGATCACT 57.066 42.857 0.00 0.00 0.00 3.41
2319 2768 3.499737 CGGACACTCATTGGCGGC 61.500 66.667 0.00 0.00 31.40 6.53
2322 2771 3.134127 GGCCGGACACTCATTGGC 61.134 66.667 5.05 0.00 44.98 4.52
2364 2819 2.349886 ACGTCGTCCTCTTCATACGTAC 59.650 50.000 0.00 0.00 41.30 3.67
2365 2820 2.621338 ACGTCGTCCTCTTCATACGTA 58.379 47.619 0.00 0.00 41.30 3.57
2366 2821 1.446907 ACGTCGTCCTCTTCATACGT 58.553 50.000 0.00 0.00 38.61 3.57
2455 2912 2.049475 CTAGAGAACGAGACGCGGGG 62.049 65.000 12.47 0.00 46.49 5.73
2495 2954 6.646653 CGTAGTACGTCCTATACCTATTCACA 59.353 42.308 14.62 0.00 36.74 3.58
2504 2963 2.159907 GCGCTCGTAGTACGTCCTATAC 60.160 54.545 21.38 3.82 43.14 1.47


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

AutoCloner maintained by Alex Coulton.