Multiple sequence alignment - TraesCS2D01G260700

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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 TraesCS2D01G260700 chr2D 100.000 2858 0 0 563 3420 317263478 317266335 0.000000e+00 5278
1 TraesCS2D01G260700 chr2D 100.000 181 0 0 1 181 317262916 317263096 5.470000e-88 335
2 TraesCS2D01G260700 chr2B 95.112 2373 72 22 571 2915 384747828 384750184 0.000000e+00 3699
3 TraesCS2D01G260700 chr2B 96.829 473 12 1 2945 3417 384750181 384750650 0.000000e+00 787
4 TraesCS2D01G260700 chr2B 92.638 163 12 0 1 163 384747500 384747662 5.710000e-58 235
5 TraesCS2D01G260700 chr2B 93.082 159 11 0 3035 3193 780209344 780209502 2.050000e-57 233
6 TraesCS2D01G260700 chr2B 87.356 87 9 2 2771 2856 780209184 780209269 7.810000e-17 99
7 TraesCS2D01G260700 chr2A 94.031 1156 45 14 565 1700 417747537 417746386 0.000000e+00 1731
8 TraesCS2D01G260700 chr2A 93.285 685 26 14 2243 2925 417745598 417744932 0.000000e+00 992
9 TraesCS2D01G260700 chr2A 91.898 469 26 5 2946 3413 417744943 417744486 0.000000e+00 645
10 TraesCS2D01G260700 chr2A 89.394 528 29 7 1696 2222 417746233 417745732 1.030000e-179 640
11 TraesCS2D01G260700 chr2A 92.222 180 14 0 2 181 417747874 417747695 4.380000e-64 255
12 TraesCS2D01G260700 chr5D 93.065 447 29 2 2943 3387 465700125 465700571 0.000000e+00 652
13 TraesCS2D01G260700 chr7B 93.228 443 29 1 2946 3387 662529506 662529064 0.000000e+00 651
14 TraesCS2D01G260700 chr7B 90.780 141 10 2 2786 2925 662529636 662529498 5.830000e-43 185
15 TraesCS2D01G260700 chr1B 90.144 487 34 13 2943 3417 289040055 289040539 3.750000e-174 621
16 TraesCS2D01G260700 chr1B 96.358 302 11 0 2946 3247 553654948 553654647 6.590000e-137 497
17 TraesCS2D01G260700 chr1B 88.272 162 10 4 2766 2925 289039912 289040066 5.830000e-43 185
18 TraesCS2D01G260700 chr5B 83.828 303 49 0 2954 3256 537810690 537810388 4.320000e-74 289


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 TraesCS2D01G260700 chr2D 317262916 317266335 3419 False 2806.500000 5278 100.000000 1 3420 2 chr2D.!!$F1 3419
1 TraesCS2D01G260700 chr2B 384747500 384750650 3150 False 1573.666667 3699 94.859667 1 3417 3 chr2B.!!$F1 3416
2 TraesCS2D01G260700 chr2A 417744486 417747874 3388 True 852.600000 1731 92.166000 2 3413 5 chr2A.!!$R1 3411
3 TraesCS2D01G260700 chr7B 662529064 662529636 572 True 418.000000 651 92.004000 2786 3387 2 chr7B.!!$R1 601
4 TraesCS2D01G260700 chr1B 289039912 289040539 627 False 403.000000 621 89.208000 2766 3417 2 chr1B.!!$F1 651

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
592 593 1.142870 CCATGATATTGGTCCCGGTGT 59.857 52.381 0.0 0.0 31.74 4.16 F
1772 1957 0.400213 ATGTCCGAACCAGCTTTGGA 59.600 50.000 0.0 0.0 39.86 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2362 2663 1.153568 CTTCGGATGCTTCGCCTCA 60.154 57.895 0.0 0.0 0.00 3.86 R
3159 3468 0.828762 ACATGCTGAAGCTTTGGCCA 60.829 50.000 0.0 0.0 42.66 5.36 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
37 38 1.143183 GATGACGCCGAAGCCCTTA 59.857 57.895 0.00 0.00 34.57 2.69
86 87 1.645034 CAAATCGATGAGGTGACGCT 58.355 50.000 0.00 0.00 0.00 5.07
155 156 3.243873 ACGTCGGCATGATATGAAGTGAT 60.244 43.478 0.00 0.00 0.00 3.06
171 172 4.512961 ATGACGCAGCGATGCCGA 62.513 61.111 24.65 4.01 38.22 5.54
176 177 3.857854 GCAGCGATGCCGACACAG 61.858 66.667 16.30 0.00 38.22 3.66
592 593 1.142870 CCATGATATTGGTCCCGGTGT 59.857 52.381 0.00 0.00 31.74 4.16
602 603 4.514577 CCCGGTGTAGCTGCGAGG 62.515 72.222 0.00 0.00 0.00 4.63
621 622 4.083802 CGAGGTTCTTGTCAGAAATCAACC 60.084 45.833 0.00 0.00 40.90 3.77
652 655 7.197703 GGAGACGTTTGTTTCCAGATTAAAAA 58.802 34.615 0.00 0.00 46.21 1.94
653 656 7.865889 GGAGACGTTTGTTTCCAGATTAAAAAT 59.134 33.333 0.00 0.00 46.21 1.82
1148 1163 3.485463 TCTGATCCTGTCGGTGTTTTT 57.515 42.857 0.00 0.00 34.65 1.94
1328 1344 7.171447 TGAATTTGTTGAAATTACGCCTTTG 57.829 32.000 0.00 0.00 41.06 2.77
1365 1381 1.890041 CCCCGTCAGTTGCAACGAA 60.890 57.895 23.21 12.92 41.29 3.85
1466 1484 2.754552 AGCTTATTTCTCAATTGCGCCA 59.245 40.909 4.18 0.00 0.00 5.69
1522 1545 4.262617 CCAGGACTATAGCTAGCGTATCA 58.737 47.826 9.55 0.00 0.00 2.15
1711 1896 5.991606 TGTTTGATGAGTAAGAGACACTTGG 59.008 40.000 0.00 0.00 39.38 3.61
1720 1905 7.120923 AGTAAGAGACACTTGGTAGTTCAAA 57.879 36.000 0.00 0.00 39.38 2.69
1772 1957 0.400213 ATGTCCGAACCAGCTTTGGA 59.600 50.000 0.00 0.00 39.86 3.53
1959 2147 6.624352 TGAGATGCCAAATAGCTACATTTC 57.376 37.500 0.00 0.38 0.00 2.17
1962 2150 6.131961 AGATGCCAAATAGCTACATTTCCTT 58.868 36.000 0.00 0.00 0.00 3.36
1963 2151 7.290061 AGATGCCAAATAGCTACATTTCCTTA 58.710 34.615 0.00 0.00 0.00 2.69
1964 2152 6.693315 TGCCAAATAGCTACATTTCCTTAC 57.307 37.500 0.00 0.00 0.00 2.34
1965 2153 6.423182 TGCCAAATAGCTACATTTCCTTACT 58.577 36.000 0.00 0.00 0.00 2.24
1966 2154 6.318648 TGCCAAATAGCTACATTTCCTTACTG 59.681 38.462 0.00 0.00 0.00 2.74
1967 2155 6.318900 GCCAAATAGCTACATTTCCTTACTGT 59.681 38.462 0.00 0.00 0.00 3.55
1968 2156 7.467403 GCCAAATAGCTACATTTCCTTACTGTC 60.467 40.741 0.00 0.00 0.00 3.51
1969 2157 7.254455 CCAAATAGCTACATTTCCTTACTGTCG 60.254 40.741 0.00 0.00 0.00 4.35
2055 2243 6.835174 AGTGATGTGGCTCTTGATATAATGT 58.165 36.000 0.00 0.00 0.00 2.71
2060 2248 9.884465 GATGTGGCTCTTGATATAATGTAAAAC 57.116 33.333 0.00 0.00 0.00 2.43
2064 2252 9.109393 TGGCTCTTGATATAATGTAAAACTGTC 57.891 33.333 0.00 0.00 0.00 3.51
2623 2930 6.018425 CAGCCTGTTGTGCTACAATATCTTAG 60.018 42.308 5.26 0.00 40.59 2.18
2674 2981 6.639632 AGTCAGTATGCTGTCACAAAATTT 57.360 33.333 10.80 0.00 43.05 1.82
2803 3110 8.946085 TCGAAAGCAAACACAGATTTCTATTAT 58.054 29.630 0.00 0.00 38.76 1.28
2861 3169 1.898574 CAGGTTGCGGAAAGTGGCT 60.899 57.895 0.00 0.00 0.00 4.75
2904 3212 5.144100 CCACTCTCCATATAGACTCCACTT 58.856 45.833 0.00 0.00 0.00 3.16
2914 3222 1.694150 AGACTCCACTTGCAGCTAACA 59.306 47.619 0.00 0.00 0.00 2.41
2915 3223 1.801178 GACTCCACTTGCAGCTAACAC 59.199 52.381 0.00 0.00 0.00 3.32
2916 3224 1.140852 ACTCCACTTGCAGCTAACACA 59.859 47.619 0.00 0.00 0.00 3.72
2917 3225 2.224621 ACTCCACTTGCAGCTAACACAT 60.225 45.455 0.00 0.00 0.00 3.21
2918 3226 3.007940 ACTCCACTTGCAGCTAACACATA 59.992 43.478 0.00 0.00 0.00 2.29
2919 3227 4.194640 CTCCACTTGCAGCTAACACATAT 58.805 43.478 0.00 0.00 0.00 1.78
2920 3228 3.940852 TCCACTTGCAGCTAACACATATG 59.059 43.478 0.00 0.00 0.00 1.78
2921 3229 3.691118 CCACTTGCAGCTAACACATATGT 59.309 43.478 1.41 1.41 42.46 2.29
2930 3238 4.462394 CACATATGTGCTCCCCCG 57.538 61.111 22.27 0.00 39.39 5.73
2931 3239 1.893808 CACATATGTGCTCCCCCGC 60.894 63.158 22.27 0.00 39.39 6.13
2932 3240 2.374525 ACATATGTGCTCCCCCGCA 61.375 57.895 7.78 0.00 37.62 5.69
2933 3241 1.152984 CATATGTGCTCCCCCGCAA 60.153 57.895 0.00 0.00 42.32 4.85
2934 3242 0.751277 CATATGTGCTCCCCCGCAAA 60.751 55.000 0.00 0.00 42.32 3.68
2935 3243 0.033601 ATATGTGCTCCCCCGCAAAA 60.034 50.000 0.00 0.00 42.32 2.44
2936 3244 0.251386 TATGTGCTCCCCCGCAAAAA 60.251 50.000 0.00 0.00 42.32 1.94
3058 3366 3.265791 AGTGCCTAAAGCTGAAAGATCG 58.734 45.455 0.00 0.00 44.23 3.69
3136 3445 4.100479 TGGCAGCCCAAATGAGTG 57.900 55.556 9.64 0.00 38.46 3.51
3159 3468 4.096984 GGCAGTAATAGTTGCTTGCTGAAT 59.903 41.667 5.17 0.00 38.23 2.57
3178 3487 0.828762 TGGCCAAAGCTTCAGCATGT 60.829 50.000 19.03 0.00 45.16 3.21
3351 3661 4.870363 TCCACTTATGTTTTGCTTGCTTC 58.130 39.130 0.00 0.00 0.00 3.86
3378 3688 4.962155 TCTCTTCCTTCTTTGTCTTGTCC 58.038 43.478 0.00 0.00 0.00 4.02
3379 3689 4.656112 TCTCTTCCTTCTTTGTCTTGTCCT 59.344 41.667 0.00 0.00 0.00 3.85
3380 3690 5.131142 TCTCTTCCTTCTTTGTCTTGTCCTT 59.869 40.000 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 2.177594 CTCGGCTGGCTCAAGGAGTT 62.178 60.000 0.00 0.00 31.39 3.01
86 87 2.052690 GGCTGACGTGAGGGCTCTA 61.053 63.158 3.66 0.00 0.00 2.43
121 122 2.184322 CGACGTCCACCATCCCAG 59.816 66.667 10.58 0.00 0.00 4.45
562 563 2.287769 CAATATCATGGTGCCACGTCA 58.712 47.619 0.00 0.00 0.00 4.35
563 564 1.603802 CCAATATCATGGTGCCACGTC 59.396 52.381 0.00 0.00 35.65 4.34
564 565 1.679139 CCAATATCATGGTGCCACGT 58.321 50.000 0.00 0.00 35.65 4.49
592 593 0.966179 TGACAAGAACCTCGCAGCTA 59.034 50.000 0.00 0.00 0.00 3.32
602 603 4.319549 GGACGGTTGATTTCTGACAAGAAC 60.320 45.833 0.00 0.00 42.20 3.01
652 655 6.144080 GGAATCGATAAAAATCTGACGTCGAT 59.856 38.462 11.62 13.29 45.74 3.59
653 656 5.457799 GGAATCGATAAAAATCTGACGTCGA 59.542 40.000 11.62 11.52 40.32 4.20
702 705 3.267031 AGCTGTAAGAAAACTGGGCCTAT 59.733 43.478 4.53 0.00 34.07 2.57
706 709 5.416013 AGAAATAGCTGTAAGAAAACTGGGC 59.584 40.000 0.00 0.00 34.07 5.36
1148 1163 1.208052 CCCTGCGAAGGATCAGAAGAA 59.792 52.381 12.53 0.00 32.26 2.52
1281 1296 1.402259 AGATAACAGTCTCGTCAGCGG 59.598 52.381 0.00 0.00 38.89 5.52
1283 1298 3.495670 ACAGATAACAGTCTCGTCAGC 57.504 47.619 0.00 0.00 0.00 4.26
1284 1299 5.048153 TCAACAGATAACAGTCTCGTCAG 57.952 43.478 0.00 0.00 0.00 3.51
1285 1300 5.447624 TTCAACAGATAACAGTCTCGTCA 57.552 39.130 0.00 0.00 0.00 4.35
1365 1381 6.153680 CCTATCGAGAAATAGGCTACCAATCT 59.846 42.308 0.00 0.00 41.33 2.40
1466 1484 4.911390 ACATGATTCCCTTCGTTTCTCTT 58.089 39.130 0.00 0.00 0.00 2.85
1965 2153 4.196193 AGAATTTTTCACCTGTGTCGACA 58.804 39.130 15.76 15.76 0.00 4.35
1966 2154 4.813296 AGAATTTTTCACCTGTGTCGAC 57.187 40.909 9.11 9.11 0.00 4.20
1967 2155 5.607477 ACTAGAATTTTTCACCTGTGTCGA 58.393 37.500 0.00 0.00 0.00 4.20
1968 2156 5.696724 AGACTAGAATTTTTCACCTGTGTCG 59.303 40.000 0.00 0.00 0.00 4.35
1969 2157 6.931840 AGAGACTAGAATTTTTCACCTGTGTC 59.068 38.462 0.00 0.00 0.00 3.67
2012 2200 8.784043 ACATCACTTTGTTACTAATTCAAGGTC 58.216 33.333 0.00 0.00 31.05 3.85
2055 2243 7.987750 TTATACACTGCAATGGACAGTTTTA 57.012 32.000 0.00 0.00 46.01 1.52
2060 2248 7.712639 AGACTAATTATACACTGCAATGGACAG 59.287 37.037 0.00 0.00 41.08 3.51
2064 2252 8.338259 GTCAAGACTAATTATACACTGCAATGG 58.662 37.037 0.00 0.00 0.00 3.16
2362 2663 1.153568 CTTCGGATGCTTCGCCTCA 60.154 57.895 0.00 0.00 0.00 3.86
2436 2737 7.127186 TCTCTCTCTCTTTTATCTCTCTCTCCA 59.873 40.741 0.00 0.00 0.00 3.86
2674 2981 9.988350 GAAGCGAGAAACATTATCAAAAAGATA 57.012 29.630 0.00 0.00 38.19 1.98
2686 2993 2.094545 GCCATTGGAAGCGAGAAACATT 60.095 45.455 6.95 0.00 0.00 2.71
2778 3085 9.003112 CATAATAGAAATCTGTGTTTGCTTTCG 57.997 33.333 0.00 0.00 32.47 3.46
2803 3110 2.632512 TGATATGGCCAGCGAGTAATCA 59.367 45.455 13.05 8.46 0.00 2.57
2861 3169 1.338337 GCTGCTATGAGACTCGGCTTA 59.662 52.381 13.38 0.00 0.00 3.09
2914 3222 2.374525 TGCGGGGGAGCACATATGT 61.375 57.895 1.41 1.41 42.92 2.29
2915 3223 2.510411 TGCGGGGGAGCACATATG 59.490 61.111 0.00 0.00 42.92 1.78
2941 3249 7.361116 GGTTGCAATAAAGCAGCACATATTTTT 60.361 33.333 0.59 0.00 46.00 1.94
2942 3250 6.092533 GGTTGCAATAAAGCAGCACATATTTT 59.907 34.615 0.59 0.00 46.00 1.82
2943 3251 5.581874 GGTTGCAATAAAGCAGCACATATTT 59.418 36.000 0.59 0.00 46.00 1.40
2944 3252 5.111293 GGTTGCAATAAAGCAGCACATATT 58.889 37.500 0.59 0.00 46.00 1.28
3058 3366 8.095937 AGGAAGCAATAACAAGTAACAACTAC 57.904 34.615 0.00 0.00 0.00 2.73
3136 3445 3.009723 TCAGCAAGCAACTATTACTGCC 58.990 45.455 0.00 0.00 39.47 4.85
3159 3468 0.828762 ACATGCTGAAGCTTTGGCCA 60.829 50.000 0.00 0.00 42.66 5.36
3178 3487 5.662657 TCTGAATCATGTCTCCAGTCCATTA 59.337 40.000 0.00 0.00 0.00 1.90
3262 3572 5.453339 CCTTTACTGGAGAAACACACTCAGA 60.453 44.000 0.00 0.00 36.26 3.27
3351 3661 5.419239 AGACAAAGAAGGAAGAGATGAGG 57.581 43.478 0.00 0.00 0.00 3.86
3378 3688 6.617879 TCATCTTCAATTGACTTGCATGAAG 58.382 36.000 7.89 14.88 41.64 3.02
3379 3689 6.578163 TCATCTTCAATTGACTTGCATGAA 57.422 33.333 7.89 1.53 34.66 2.57
3380 3690 6.769134 ATCATCTTCAATTGACTTGCATGA 57.231 33.333 7.89 11.10 34.66 3.07


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

AutoCloner maintained by Alex Coulton.