Multiple sequence alignment - TraesCS3B01G052600

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 TraesCS3B01G052600 chr3B 100.000 5195 0 0 1 5195 26653841 26648647 0.000000e+00 9594.0
1 TraesCS3B01G052600 chr3B 97.986 5213 45 24 1 5195 14982255 14987425 0.000000e+00 8990.0
2 TraesCS3B01G052600 chr6D 80.910 3164 516 61 1056 4181 456424531 456427644 0.000000e+00 2416.0
3 TraesCS3B01G052600 chr6D 79.691 3176 513 83 1069 4187 456408591 456411691 0.000000e+00 2170.0
4 TraesCS3B01G052600 chr6D 78.121 3236 617 57 997 4187 17500276 17503465 0.000000e+00 1969.0
5 TraesCS3B01G052600 chr6A 80.381 3150 533 50 1068 4181 603081661 603084761 0.000000e+00 2314.0
6 TraesCS3B01G052600 chr6A 80.214 3179 518 63 1056 4181 603091783 603094903 0.000000e+00 2283.0
7 TraesCS3B01G052600 chr6A 78.419 3239 602 64 997 4187 18461143 18464332 0.000000e+00 2019.0
8 TraesCS3B01G052600 chr6A 82.564 1950 285 36 2258 4181 603101949 603103869 0.000000e+00 1666.0
9 TraesCS3B01G052600 chr6A 80.108 1845 304 37 2385 4181 603044208 603046037 0.000000e+00 1315.0
10 TraesCS3B01G052600 chr6A 78.736 348 50 13 512 840 606095944 606095602 1.470000e-50 211.0
11 TraesCS3B01G052600 chr6B 78.191 3283 609 66 955 4187 31690443 31687218 0.000000e+00 1997.0
12 TraesCS3B01G052600 chr6B 78.192 3242 600 71 999 4187 30889721 30892908 0.000000e+00 1971.0
13 TraesCS3B01G052600 chr6B 78.439 3177 571 76 1056 4181 693927135 693930248 0.000000e+00 1967.0
14 TraesCS3B01G052600 chr6B 81.518 1845 287 36 2364 4181 693937002 693938819 0.000000e+00 1469.0
15 TraesCS3B01G052600 chr6B 93.506 77 4 1 5119 5195 366432029 366431954 4.250000e-21 113.0
16 TraesCS3B01G052600 chr2B 80.580 345 38 12 512 830 415997252 415996911 6.720000e-59 239.0
17 TraesCS3B01G052600 chr2B 95.946 74 2 1 5120 5193 118604714 118604642 9.140000e-23 119.0
18 TraesCS3B01G052600 chr1B 81.699 306 33 11 552 838 662163714 662163413 3.130000e-57 233.0
19 TraesCS3B01G052600 chr1B 77.700 287 43 10 550 818 30442931 30442648 6.970000e-34 156.0
20 TraesCS3B01G052600 chr1B 94.805 77 2 2 5120 5195 240710049 240710124 9.140000e-23 119.0
21 TraesCS3B01G052600 chr1D 78.852 331 41 17 534 840 475955217 475954892 4.100000e-46 196.0
22 TraesCS3B01G052600 chr7B 79.725 291 38 11 542 814 589393119 589393406 1.910000e-44 191.0
23 TraesCS3B01G052600 chr7B 84.848 99 14 1 549 646 384192411 384192313 1.190000e-16 99.0
24 TraesCS3B01G052600 chr5D 79.585 289 39 9 547 818 383074485 383074770 6.870000e-44 189.0
25 TraesCS3B01G052600 chr5D 85.542 83 11 1 564 646 236944389 236944470 9.270000e-13 86.1
26 TraesCS3B01G052600 chr5D 80.808 99 18 1 549 646 281011384 281011286 5.580000e-10 76.8
27 TraesCS3B01G052600 chrUn 79.298 285 40 9 550 818 108880266 108879985 1.150000e-41 182.0
28 TraesCS3B01G052600 chr2D 79.371 286 34 12 550 818 514252895 514252618 1.490000e-40 178.0
29 TraesCS3B01G052600 chr2D 78.966 290 38 11 547 818 525514864 525515148 5.350000e-40 176.0
30 TraesCS3B01G052600 chr4D 94.805 77 3 1 5119 5195 449455612 449455687 9.140000e-23 119.0
31 TraesCS3B01G052600 chr4B 95.890 73 3 0 5123 5195 273251782 273251710 9.140000e-23 119.0
32 TraesCS3B01G052600 chr5B 94.737 76 3 1 5120 5195 711237879 711237953 3.290000e-22 117.0
33 TraesCS3B01G052600 chr5B 92.500 80 4 2 5117 5195 665559931 665560009 4.250000e-21 113.0
34 TraesCS3B01G052600 chr5B 85.542 83 11 1 564 646 268293980 268293899 9.270000e-13 86.1
35 TraesCS3B01G052600 chr7D 93.506 77 4 1 5119 5195 444474254 444474329 4.250000e-21 113.0
36 TraesCS3B01G052600 chr5A 87.500 64 7 1 583 646 40157045 40157107 7.220000e-09 73.1


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 TraesCS3B01G052600 chr3B 26648647 26653841 5194 True 9594 9594 100.000 1 5195 1 chr3B.!!$R1 5194
1 TraesCS3B01G052600 chr3B 14982255 14987425 5170 False 8990 8990 97.986 1 5195 1 chr3B.!!$F1 5194
2 TraesCS3B01G052600 chr6D 456424531 456427644 3113 False 2416 2416 80.910 1056 4181 1 chr6D.!!$F3 3125
3 TraesCS3B01G052600 chr6D 456408591 456411691 3100 False 2170 2170 79.691 1069 4187 1 chr6D.!!$F2 3118
4 TraesCS3B01G052600 chr6D 17500276 17503465 3189 False 1969 1969 78.121 997 4187 1 chr6D.!!$F1 3190
5 TraesCS3B01G052600 chr6A 603081661 603084761 3100 False 2314 2314 80.381 1068 4181 1 chr6A.!!$F3 3113
6 TraesCS3B01G052600 chr6A 603091783 603094903 3120 False 2283 2283 80.214 1056 4181 1 chr6A.!!$F4 3125
7 TraesCS3B01G052600 chr6A 18461143 18464332 3189 False 2019 2019 78.419 997 4187 1 chr6A.!!$F1 3190
8 TraesCS3B01G052600 chr6A 603101949 603103869 1920 False 1666 1666 82.564 2258 4181 1 chr6A.!!$F5 1923
9 TraesCS3B01G052600 chr6A 603044208 603046037 1829 False 1315 1315 80.108 2385 4181 1 chr6A.!!$F2 1796
10 TraesCS3B01G052600 chr6B 31687218 31690443 3225 True 1997 1997 78.191 955 4187 1 chr6B.!!$R1 3232
11 TraesCS3B01G052600 chr6B 30889721 30892908 3187 False 1971 1971 78.192 999 4187 1 chr6B.!!$F1 3188
12 TraesCS3B01G052600 chr6B 693927135 693930248 3113 False 1967 1967 78.439 1056 4181 1 chr6B.!!$F2 3125
13 TraesCS3B01G052600 chr6B 693937002 693938819 1817 False 1469 1469 81.518 2364 4181 1 chr6B.!!$F3 1817

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
178 179 0.097150 GCGCGGAAATTCCTCAAGAC 59.903 55.0 8.83 0.0 33.30 3.01 F
179 180 0.727398 CGCGGAAATTCCTCAAGACC 59.273 55.0 10.64 0.0 33.30 3.85 F
1066 1088 0.675633 GGCAACAACATTCAGCCACT 59.324 50.0 0.00 0.0 44.59 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1066 1088 0.994247 AAGGCATCCACATCAGTCCA 59.006 50.000 0.0 0.0 0.00 4.02 R
3605 3633 2.030274 TCGTCGAGAAGAATGTTGCTCA 60.030 45.455 0.0 0.0 0.00 4.26 R
4246 4321 3.297830 AAAAAGGACCTGCGTTTATGC 57.702 42.857 0.0 0.0 33.76 3.14 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
89 90 1.852067 GCTAACCAACAGCACACGGG 61.852 60.000 0.00 0.00 38.93 5.28
115 116 1.298014 CTGCTGACCCTCTTGACCC 59.702 63.158 0.00 0.00 0.00 4.46
117 118 2.982130 CTGACCCTCTTGACCCGG 59.018 66.667 0.00 0.00 0.00 5.73
145 146 5.355071 GGTGTAATGTCATGTCATGTCATGT 59.645 40.000 25.46 13.44 43.70 3.21
146 147 6.457392 GGTGTAATGTCATGTCATGTCATGTC 60.457 42.308 25.46 21.68 43.70 3.06
147 148 6.092533 GTGTAATGTCATGTCATGTCATGTCA 59.907 38.462 25.27 25.27 43.48 3.58
162 163 3.785859 TCATGGTGGAGGGAGCGC 61.786 66.667 0.00 0.00 0.00 5.92
178 179 0.097150 GCGCGGAAATTCCTCAAGAC 59.903 55.000 8.83 0.00 33.30 3.01
179 180 0.727398 CGCGGAAATTCCTCAAGACC 59.273 55.000 10.64 0.00 33.30 3.85
180 181 1.676014 CGCGGAAATTCCTCAAGACCT 60.676 52.381 10.64 0.00 33.30 3.85
181 182 2.010497 GCGGAAATTCCTCAAGACCTC 58.990 52.381 10.64 0.00 33.30 3.85
182 183 2.355209 GCGGAAATTCCTCAAGACCTCT 60.355 50.000 10.64 0.00 33.30 3.69
183 184 3.265791 CGGAAATTCCTCAAGACCTCTG 58.734 50.000 10.64 0.00 33.30 3.35
207 208 1.901538 CATCGGTGGATCGATCGATC 58.098 55.000 38.31 38.31 46.59 3.69
367 368 6.098266 TGTCACTTAGCCATATGAGCTCTTAA 59.902 38.462 16.19 9.57 41.83 1.85
516 517 3.404899 GAAAATACACGGGAGTTCCACA 58.595 45.455 0.00 0.00 44.67 4.17
525 526 3.028850 CGGGAGTTCCACACCTCTATAA 58.971 50.000 0.00 0.00 37.91 0.98
661 670 3.161866 GGCAAAGGAAATACTGTCCCAA 58.838 45.455 0.00 0.00 35.59 4.12
973 989 6.136743 CAGGAAAAGCTTACGTTTCTTCTTC 58.863 40.000 0.00 0.00 42.01 2.87
1066 1088 0.675633 GGCAACAACATTCAGCCACT 59.324 50.000 0.00 0.00 44.59 4.00
3605 3633 6.072286 CCAATAATTCACTGTGACTTGAAGCT 60.072 38.462 19.79 0.00 35.25 3.74
3636 3664 3.719924 TCTTCTCGACGAGGATCTAGTC 58.280 50.000 23.92 0.00 33.79 2.59
3766 3794 3.430929 CGCTCCAGGTATAGCTTGACTTT 60.431 47.826 0.55 0.00 36.56 2.66
3770 3798 5.734720 TCCAGGTATAGCTTGACTTTTCTG 58.265 41.667 0.55 0.00 0.00 3.02
4375 4450 1.256812 GCCCTGTTTGGTTAGCATGT 58.743 50.000 0.00 0.00 0.00 3.21
4531 4606 6.489603 TCTAAAGCCAGGAAATTAATGGTGA 58.510 36.000 0.00 0.00 36.43 4.02
4565 4640 7.706281 CATGTAAAAGGCAACATGTGTAAAA 57.294 32.000 0.00 0.00 45.08 1.52
4707 4782 8.690840 GCAAGTAAAGTTGATCAACATAAACAC 58.309 33.333 33.92 22.38 43.47 3.32
4880 4955 2.551938 GGACTCTGAGCTCTGCCTTTTT 60.552 50.000 16.19 0.00 0.00 1.94
4922 4998 4.496360 GAAGGAAGACTTGCTGGTAGTAC 58.504 47.826 10.27 0.00 40.21 2.73
4938 5014 1.699634 AGTACTTGAGCCCTCTTGCAA 59.300 47.619 0.00 0.00 0.00 4.08
4999 5075 8.066612 TGAATTCTTTCACTGAAAACCTCTTT 57.933 30.769 7.05 0.00 36.94 2.52
5029 5107 1.555075 AGAAAACCTGCAGCTCGGATA 59.445 47.619 8.66 0.00 0.00 2.59
5039 5117 1.869767 CAGCTCGGATAGGATGCAAAC 59.130 52.381 0.00 0.00 0.00 2.93
5040 5118 1.486310 AGCTCGGATAGGATGCAAACA 59.514 47.619 0.00 0.00 0.00 2.83
5041 5119 2.105477 AGCTCGGATAGGATGCAAACAT 59.895 45.455 0.00 0.00 39.98 2.71
5042 5120 2.225019 GCTCGGATAGGATGCAAACATG 59.775 50.000 0.00 0.00 36.35 3.21
5043 5121 2.221169 TCGGATAGGATGCAAACATGC 58.779 47.619 0.00 0.00 44.45 4.06
5050 5128 3.969117 GGATGCAAACATGCTATTCGA 57.031 42.857 0.00 0.00 41.15 3.71
5051 5129 4.291540 GGATGCAAACATGCTATTCGAA 57.708 40.909 0.00 0.00 41.15 3.71
5052 5130 4.863491 GGATGCAAACATGCTATTCGAAT 58.137 39.130 16.15 16.15 41.15 3.34
5053 5131 6.000891 GGATGCAAACATGCTATTCGAATA 57.999 37.500 16.69 16.69 41.15 1.75
5054 5132 6.082338 GGATGCAAACATGCTATTCGAATAG 58.918 40.000 31.95 31.95 41.15 1.73
5055 5133 5.422666 TGCAAACATGCTATTCGAATAGG 57.577 39.130 34.78 24.63 39.00 2.57
5056 5134 5.122519 TGCAAACATGCTATTCGAATAGGA 58.877 37.500 34.78 33.82 42.35 2.94
5057 5135 5.237127 TGCAAACATGCTATTCGAATAGGAG 59.763 40.000 34.78 27.92 41.62 3.69
5058 5136 5.237344 GCAAACATGCTATTCGAATAGGAGT 59.763 40.000 34.78 28.40 41.62 3.85
5059 5137 6.423905 GCAAACATGCTATTCGAATAGGAGTA 59.576 38.462 34.78 19.62 41.62 2.59
5060 5138 7.569591 GCAAACATGCTATTCGAATAGGAGTAC 60.570 40.741 34.78 22.84 41.62 2.73
5061 5139 6.902771 ACATGCTATTCGAATAGGAGTACT 57.097 37.500 34.78 20.96 41.62 2.73
5062 5140 7.997773 ACATGCTATTCGAATAGGAGTACTA 57.002 36.000 34.78 15.82 41.62 1.82
5063 5141 7.818642 ACATGCTATTCGAATAGGAGTACTAC 58.181 38.462 34.78 21.17 41.62 2.73
5064 5142 7.447545 ACATGCTATTCGAATAGGAGTACTACA 59.552 37.037 34.78 24.79 41.62 2.74
5065 5143 7.436430 TGCTATTCGAATAGGAGTACTACAG 57.564 40.000 34.78 16.49 39.00 2.74
5066 5144 6.996879 TGCTATTCGAATAGGAGTACTACAGT 59.003 38.462 34.78 4.87 39.00 3.55
5067 5145 7.041303 TGCTATTCGAATAGGAGTACTACAGTG 60.041 40.741 34.78 14.44 39.00 3.66
5068 5146 5.496133 TTCGAATAGGAGTACTACAGTGC 57.504 43.478 8.10 0.00 33.70 4.40
5069 5147 4.778579 TCGAATAGGAGTACTACAGTGCT 58.221 43.478 8.10 0.00 43.64 4.40
5144 5222 1.557832 CTCCCTCCGTCCCAAAATGTA 59.442 52.381 0.00 0.00 0.00 2.29
5145 5223 1.986631 TCCCTCCGTCCCAAAATGTAA 59.013 47.619 0.00 0.00 0.00 2.41
5146 5224 2.026636 TCCCTCCGTCCCAAAATGTAAG 60.027 50.000 0.00 0.00 0.00 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
115 116 2.083774 ACATGACATTACACCTTGCCG 58.916 47.619 0.00 0.00 0.00 5.69
117 118 4.156556 ACATGACATGACATTACACCTTGC 59.843 41.667 22.19 0.00 0.00 4.01
145 146 3.785859 GCGCTCCCTCCACCATGA 61.786 66.667 0.00 0.00 0.00 3.07
162 163 3.265791 CAGAGGTCTTGAGGAATTTCCG 58.734 50.000 9.77 0.00 42.75 4.30
178 179 2.503061 CACCGATGGAGGCAGAGG 59.497 66.667 0.00 0.00 33.69 3.69
205 206 4.024048 CGAAGGCCATTAAATAAGCGTGAT 60.024 41.667 5.01 0.00 0.00 3.06
206 207 3.311322 CGAAGGCCATTAAATAAGCGTGA 59.689 43.478 5.01 0.00 0.00 4.35
207 208 3.617669 CGAAGGCCATTAAATAAGCGTG 58.382 45.455 5.01 0.00 0.00 5.34
208 209 2.032924 GCGAAGGCCATTAAATAAGCGT 59.967 45.455 5.01 0.00 0.00 5.07
367 368 4.501400 GGCTTGTTCCAAACAACTGCTAAT 60.501 41.667 13.20 0.00 45.79 1.73
484 485 7.070821 ACTCCCGTGTATTTTCCTTAGACATAT 59.929 37.037 0.00 0.00 0.00 1.78
818 827 4.344104 CCCCCTATGTGAACATGAAGTTT 58.656 43.478 0.00 0.00 41.51 2.66
860 873 8.593945 AAGCCATGAACAAATTAAATCCTAGA 57.406 30.769 0.00 0.00 0.00 2.43
1066 1088 0.994247 AAGGCATCCACATCAGTCCA 59.006 50.000 0.00 0.00 0.00 4.02
3605 3633 2.030274 TCGTCGAGAAGAATGTTGCTCA 60.030 45.455 0.00 0.00 0.00 4.26
3636 3664 4.052229 AAGTCCCCGACGTGAGCG 62.052 66.667 0.00 0.00 44.93 5.03
3766 3794 8.373992 GCAAAATTGTTGTTTAACGTTACAGAA 58.626 29.630 7.70 3.56 39.71 3.02
3770 3798 7.109532 GCATGCAAAATTGTTGTTTAACGTTAC 59.890 33.333 14.21 0.22 39.71 2.50
4246 4321 3.297830 AAAAAGGACCTGCGTTTATGC 57.702 42.857 0.00 0.00 33.76 3.14
4375 4450 3.316029 CACAACTGCAAAGGACAGATCAA 59.684 43.478 0.00 0.00 38.55 2.57
4638 4713 7.275123 CGGTTTTACTGTCAGGTCTTATCTTAC 59.725 40.741 4.53 0.00 0.00 2.34
4639 4714 7.177216 TCGGTTTTACTGTCAGGTCTTATCTTA 59.823 37.037 4.53 0.00 0.00 2.10
4707 4782 1.802960 ACTCTGCATCTTTCAACTGCG 59.197 47.619 0.00 0.00 38.75 5.18
4900 4976 3.686916 ACTACCAGCAAGTCTTCCTTC 57.313 47.619 0.00 0.00 0.00 3.46
4922 4998 0.538057 TGGTTGCAAGAGGGCTCAAG 60.538 55.000 0.00 0.00 34.04 3.02
4938 5014 1.679032 GGAAGAAAGCAGGCGTATGGT 60.679 52.381 0.00 0.00 0.00 3.55
5039 5117 7.817641 TGTAGTACTCCTATTCGAATAGCATG 58.182 38.462 31.30 24.58 37.61 4.06
5040 5118 7.666388 ACTGTAGTACTCCTATTCGAATAGCAT 59.334 37.037 31.30 22.24 37.61 3.79
5041 5119 6.996879 ACTGTAGTACTCCTATTCGAATAGCA 59.003 38.462 31.30 21.14 37.61 3.49
5042 5120 7.299586 CACTGTAGTACTCCTATTCGAATAGC 58.700 42.308 31.30 20.45 37.61 2.97
5043 5121 7.173562 AGCACTGTAGTACTCCTATTCGAATAG 59.826 40.741 30.22 30.22 38.45 1.73
5044 5122 6.996879 AGCACTGTAGTACTCCTATTCGAATA 59.003 38.462 16.69 16.69 0.00 1.75
5045 5123 5.828859 AGCACTGTAGTACTCCTATTCGAAT 59.171 40.000 16.15 16.15 0.00 3.34
5046 5124 5.191426 AGCACTGTAGTACTCCTATTCGAA 58.809 41.667 0.00 0.00 0.00 3.71
5048 5126 4.817464 AGAGCACTGTAGTACTCCTATTCG 59.183 45.833 0.00 0.00 38.83 3.34
5049 5127 7.804843 TTAGAGCACTGTAGTACTCCTATTC 57.195 40.000 0.00 0.00 38.83 1.75
5050 5128 8.591114 TTTTAGAGCACTGTAGTACTCCTATT 57.409 34.615 0.00 0.00 38.83 1.73
5051 5129 8.591114 TTTTTAGAGCACTGTAGTACTCCTAT 57.409 34.615 0.00 0.00 38.83 2.57
5053 5131 6.912951 TTTTTAGAGCACTGTAGTACTCCT 57.087 37.500 0.00 0.88 38.83 3.69
5073 5151 4.406456 TCACCATGGTAGCACATCTTTTT 58.594 39.130 19.28 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.