Multiple sequence alignment - TraesCS6D01G328600

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 TraesCS6D01G328600 chr6D 100.000 3232 0 0 1 3232 433281660 433278429 0.000000e+00 5969.0
1 TraesCS6D01G328600 chr6D 94.260 2474 118 15 1 2465 433156316 433153858 0.000000e+00 3760.0
2 TraesCS6D01G328600 chr6D 93.849 2276 129 6 195 2465 432932317 432930048 0.000000e+00 3417.0
3 TraesCS6D01G328600 chr6D 89.982 1667 148 9 786 2447 433259321 433257669 0.000000e+00 2135.0
4 TraesCS6D01G328600 chr6D 90.944 1579 124 8 895 2465 432914545 432912978 0.000000e+00 2106.0
5 TraesCS6D01G328600 chr6D 88.303 607 68 3 2623 3227 433153862 433153257 0.000000e+00 725.0
6 TraesCS6D01G328600 chr6D 88.579 359 40 1 2626 2983 432930049 432929691 4.950000e-118 435.0
7 TraesCS6D01G328600 chr6D 80.077 522 83 11 96 612 432915297 432914792 5.090000e-98 368.0
8 TraesCS6D01G328600 chr6D 85.987 314 29 7 2156 2465 433037324 433037022 4.020000e-84 322.0
9 TraesCS6D01G328600 chr6D 86.124 209 28 1 2623 2830 432912982 432912774 1.170000e-54 224.0
10 TraesCS6D01G328600 chr6D 87.838 74 6 1 2346 2416 433548838 433548911 2.070000e-12 84.2
11 TraesCS6D01G328600 chr6D 87.838 74 6 1 2346 2416 433563963 433564036 2.070000e-12 84.2
12 TraesCS6D01G328600 chr6B 95.216 3240 138 11 1 3232 653873632 653870402 0.000000e+00 5108.0
13 TraesCS6D01G328600 chr6B 84.895 2284 265 53 1 2256 653195778 653193547 0.000000e+00 2233.0
14 TraesCS6D01G328600 chr6B 88.994 1690 162 10 786 2465 653715843 653714168 0.000000e+00 2069.0
15 TraesCS6D01G328600 chr6B 88.704 1682 163 13 787 2465 653788972 653787315 0.000000e+00 2028.0
16 TraesCS6D01G328600 chr6B 89.008 1583 153 9 895 2465 653856640 653855067 0.000000e+00 1940.0
17 TraesCS6D01G328600 chr6B 90.101 1485 109 12 1 1482 653700020 653698571 0.000000e+00 1893.0
18 TraesCS6D01G328600 chr6B 84.804 612 81 7 2623 3228 653697620 653697015 3.570000e-169 604.0
19 TraesCS6D01G328600 chr6B 89.157 166 17 1 2461 2625 548811085 548811250 4.230000e-49 206.0
20 TraesCS6D01G328600 chr6B 88.608 79 5 2 2341 2416 655054671 655054748 3.430000e-15 93.5
21 TraesCS6D01G328600 chr6A 94.766 3248 150 10 1 3232 579144132 579140889 0.000000e+00 5038.0
22 TraesCS6D01G328600 chr6A 89.367 1580 147 9 895 2465 579125017 579123450 0.000000e+00 1967.0
23 TraesCS6D01G328600 chr3D 84.518 394 59 2 2841 3232 605638285 605637892 3.910000e-104 388.0
24 TraesCS6D01G328600 chr7D 84.697 379 54 4 2853 3229 479999365 479999741 3.040000e-100 375.0
25 TraesCS6D01G328600 chr7D 76.245 522 89 22 1 507 500745020 500745521 8.960000e-61 244.0
26 TraesCS6D01G328600 chr7D 88.571 175 17 3 2453 2625 579762512 579762685 3.270000e-50 209.0
27 TraesCS6D01G328600 chr7D 87.293 181 21 2 2460 2638 171316160 171315980 4.230000e-49 206.0
28 TraesCS6D01G328600 chr5A 84.392 378 56 3 2841 3216 589001983 589002359 5.090000e-98 368.0
29 TraesCS6D01G328600 chr2A 83.463 387 59 5 2846 3227 11009105 11009491 3.970000e-94 355.0
30 TraesCS6D01G328600 chr2B 83.247 388 60 5 2843 3227 142674025 142673640 5.130000e-93 351.0
31 TraesCS6D01G328600 chr1B 89.697 165 16 1 2461 2624 626100390 626100554 3.270000e-50 209.0
32 TraesCS6D01G328600 chr5B 88.372 172 19 1 2461 2632 294096604 294096434 4.230000e-49 206.0
33 TraesCS6D01G328600 chr1D 88.235 170 15 3 2461 2629 289532272 289532107 7.070000e-47 198.0
34 TraesCS6D01G328600 chr1D 88.235 170 15 3 2461 2629 289597488 289597323 7.070000e-47 198.0


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 TraesCS6D01G328600 chr6D 433278429 433281660 3231 True 5969.000000 5969 100.0000 1 3232 1 chr6D.!!$R3 3231
1 TraesCS6D01G328600 chr6D 433153257 433156316 3059 True 2242.500000 3760 91.2815 1 3227 2 chr6D.!!$R6 3226
2 TraesCS6D01G328600 chr6D 433257669 433259321 1652 True 2135.000000 2135 89.9820 786 2447 1 chr6D.!!$R2 1661
3 TraesCS6D01G328600 chr6D 432929691 432932317 2626 True 1926.000000 3417 91.2140 195 2983 2 chr6D.!!$R5 2788
4 TraesCS6D01G328600 chr6D 432912774 432915297 2523 True 899.333333 2106 85.7150 96 2830 3 chr6D.!!$R4 2734
5 TraesCS6D01G328600 chr6B 653870402 653873632 3230 True 5108.000000 5108 95.2160 1 3232 1 chr6B.!!$R5 3231
6 TraesCS6D01G328600 chr6B 653193547 653195778 2231 True 2233.000000 2233 84.8950 1 2256 1 chr6B.!!$R1 2255
7 TraesCS6D01G328600 chr6B 653714168 653715843 1675 True 2069.000000 2069 88.9940 786 2465 1 chr6B.!!$R2 1679
8 TraesCS6D01G328600 chr6B 653787315 653788972 1657 True 2028.000000 2028 88.7040 787 2465 1 chr6B.!!$R3 1678
9 TraesCS6D01G328600 chr6B 653855067 653856640 1573 True 1940.000000 1940 89.0080 895 2465 1 chr6B.!!$R4 1570
10 TraesCS6D01G328600 chr6B 653697015 653700020 3005 True 1248.500000 1893 87.4525 1 3228 2 chr6B.!!$R6 3227
11 TraesCS6D01G328600 chr6A 579140889 579144132 3243 True 5038.000000 5038 94.7660 1 3232 1 chr6A.!!$R2 3231
12 TraesCS6D01G328600 chr6A 579123450 579125017 1567 True 1967.000000 1967 89.3670 895 2465 1 chr6A.!!$R1 1570
13 TraesCS6D01G328600 chr7D 500745020 500745521 501 False 244.000000 244 76.2450 1 507 1 chr7D.!!$F2 506

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
266 271 1.003718 ACCACACGCTTCTTAGGGC 60.004 57.895 0.0 0.0 37.83 5.19 F
969 1020 1.067776 CGCTACGTTGGAGACCTTCTT 60.068 52.381 0.0 0.0 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1191 1251 1.054231 CCATCCAGCTCTCATGCCTA 58.946 55.0 0.0 0.0 0.0 3.93 R
2800 2879 0.534203 GTGGGTTGAACGAGCAGGAA 60.534 55.0 0.0 0.0 0.0 3.36 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
185 189 3.365364 GCTTTGCATGGTGTGTCTACTTC 60.365 47.826 0.00 0.00 0.00 3.01
266 271 1.003718 ACCACACGCTTCTTAGGGC 60.004 57.895 0.00 0.00 37.83 5.19
432 459 5.577164 CACGGAGTCCATACAGAACTTAAAG 59.423 44.000 10.49 0.00 41.61 1.85
465 493 1.608590 ACCAAGCATTGTTTGGACTCG 59.391 47.619 31.44 10.96 46.99 4.18
780 831 8.413229 CAAACTTATATATTTTGTCCCCCTGTG 58.587 37.037 0.00 0.00 0.00 3.66
867 918 1.652167 GCAAGCACTTCCAGCTAGGC 61.652 60.000 0.00 0.00 42.53 3.93
969 1020 1.067776 CGCTACGTTGGAGACCTTCTT 60.068 52.381 0.00 0.00 0.00 2.52
1191 1251 0.615331 ATGACTTGTCGATGGTGGCT 59.385 50.000 0.00 0.00 0.00 4.75
1265 1325 1.604278 GAAGGCATACCGATTTGAGGC 59.396 52.381 0.00 0.00 42.76 4.70
1274 1334 1.340017 CCGATTTGAGGCCTTCAAGGA 60.340 52.381 7.98 0.00 46.01 3.36
1407 1467 2.880963 GGTACAAACCAAGCTTGCAA 57.119 45.000 21.43 0.00 45.98 4.08
1463 1523 1.078497 TCGATGCACTTCCGGCAAT 60.078 52.632 0.00 0.00 45.60 3.56
2062 2127 2.045926 GGCAAGACCAGCGATGGT 60.046 61.111 28.26 28.26 46.40 3.55
2065 2130 1.421410 GCAAGACCAGCGATGGTACG 61.421 60.000 27.93 17.71 43.24 3.67
2230 2295 0.179100 CGCCGCATATCCTCCTATGG 60.179 60.000 0.00 0.00 31.11 2.74
2464 2540 9.060347 CCTTCATGCATACATAATGAACTACTT 57.940 33.333 0.00 0.00 37.86 2.24
2597 2675 9.766277 GCAATCTACAGTGAAATCTCTAAAAAG 57.234 33.333 0.00 0.00 0.00 2.27
2619 2697 7.672122 AAGACTTATATTTAGGAACGGAGGT 57.328 36.000 0.00 0.00 0.00 3.85
2762 2840 7.921786 TGTCAATTCGTAAATCTTGAGGAAT 57.078 32.000 0.00 0.00 32.92 3.01
2800 2879 4.785376 ACATCCTCTCTCCCATTGTTACTT 59.215 41.667 0.00 0.00 0.00 2.24
2806 2885 3.686016 TCTCCCATTGTTACTTTCCTGC 58.314 45.455 0.00 0.00 0.00 4.85
2831 2910 1.000993 AACCCACAACACCAGCCAA 59.999 52.632 0.00 0.00 0.00 4.52
2880 2962 0.036388 CAAGGCGACTAGGGAAAGCA 60.036 55.000 0.00 0.00 42.68 3.91
2983 3066 0.250338 GTTTCTGGTGCCTCGGTTCT 60.250 55.000 0.00 0.00 0.00 3.01
3017 3100 2.169978 GGTAGGGTTTTAGTCCTCGCAT 59.830 50.000 0.00 0.00 34.75 4.73
3142 3225 3.677424 GCGTAGATTCCTGTCAGCTTTCT 60.677 47.826 0.00 0.00 0.00 2.52
3221 3305 9.884465 GTCAAATTATTCAGATCGATTTAAGGG 57.116 33.333 0.00 0.00 0.00 3.95
3229 3313 4.868171 CAGATCGATTTAAGGGTTCAACGA 59.132 41.667 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
266 271 2.012414 CGTGGTGTGTGTACGGTCG 61.012 63.158 0.00 0.00 34.43 4.79
272 277 0.110101 CGACGATCGTGGTGTGTGTA 60.110 55.000 28.12 0.00 34.72 2.90
332 355 1.221466 CCACGCAGACGCTCTTTTCA 61.221 55.000 0.00 0.00 45.53 2.69
421 445 9.575783 GGTACTCATCTTCTACTTTAAGTTCTG 57.424 37.037 1.94 0.00 0.00 3.02
432 459 6.109359 ACAATGCTTGGTACTCATCTTCTAC 58.891 40.000 0.00 0.00 34.12 2.59
560 589 1.198759 GGGACTAGGAGGGCAACACA 61.199 60.000 0.00 0.00 39.74 3.72
817 868 9.389755 TGATGTTGACGGATTTTTCTATCAATA 57.610 29.630 0.00 0.00 0.00 1.90
867 918 5.301805 GGGATGGTGGTATAAATCAAACAGG 59.698 44.000 0.00 0.00 0.00 4.00
1191 1251 1.054231 CCATCCAGCTCTCATGCCTA 58.946 55.000 0.00 0.00 0.00 3.93
1265 1325 1.271379 ACCCGACATTGTCCTTGAAGG 60.271 52.381 4.45 4.45 36.46 3.46
1274 1334 1.275291 ACTCGATGAACCCGACATTGT 59.725 47.619 0.00 0.00 32.71 2.71
1407 1467 1.831736 CTGAATCTGGTAGGAACCCGT 59.168 52.381 0.00 0.00 46.16 5.28
1463 1523 3.107601 CCTTTGGTCCTCCAGTCTATGA 58.892 50.000 0.00 0.00 45.22 2.15
1705 1770 1.202405 TCACCATGGACATCACGATCG 60.202 52.381 21.47 14.88 0.00 3.69
1709 1774 2.002586 GTCTTCACCATGGACATCACG 58.997 52.381 21.47 0.00 0.00 4.35
2062 2127 6.987992 AGTTCTTCAACAACCAATACTTCGTA 59.012 34.615 0.00 0.00 34.60 3.43
2065 2130 7.259290 TGAGTTCTTCAACAACCAATACTTC 57.741 36.000 0.00 0.00 34.60 3.01
2238 2303 4.153475 GTGGACGTGTGCAATTATGTACTT 59.847 41.667 0.00 0.00 42.06 2.24
2240 2305 3.682858 AGTGGACGTGTGCAATTATGTAC 59.317 43.478 0.00 0.00 41.92 2.90
2464 2540 4.966805 AGACTTATATTTGGGAACGGAGGA 59.033 41.667 0.00 0.00 0.00 3.71
2565 2642 8.427276 AGAGATTTCACTGTAGATTGCATATGA 58.573 33.333 6.97 0.00 0.00 2.15
2597 2675 8.175925 ACTACCTCCGTTCCTAAATATAAGTC 57.824 38.462 0.00 0.00 0.00 3.01
2762 2840 7.809238 AGAGAGGATGTTCCATCATAATTCAA 58.191 34.615 6.56 0.00 39.61 2.69
2781 2859 4.226168 AGGAAAGTAACAATGGGAGAGAGG 59.774 45.833 0.00 0.00 0.00 3.69
2800 2879 0.534203 GTGGGTTGAACGAGCAGGAA 60.534 55.000 0.00 0.00 0.00 3.36
2806 2885 0.661020 GGTGTTGTGGGTTGAACGAG 59.339 55.000 0.00 0.00 0.00 4.18
2831 2910 5.257262 GGGAAAGAAAAGCTATCTCTGGTT 58.743 41.667 2.68 0.00 0.00 3.67
2880 2962 1.418334 CGGAGATTGAGGGGAGACAT 58.582 55.000 0.00 0.00 0.00 3.06
2983 3066 1.503784 ACCCTACCTATCTGCTAGCCA 59.496 52.381 13.29 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.