Multiple sequence alignment - TraesCS1B01G475000

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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 TraesCS1B01G475000 chr1B 100.000 4392 0 0 1 4392 683472450 683476841 0.000000e+00 8111.0
1 TraesCS1B01G475000 chr1B 96.599 147 5 0 3561 3707 683472654 683472800 1.220000e-60 244.0
2 TraesCS1B01G475000 chr1B 96.599 147 5 0 205 351 683476010 683476156 1.220000e-60 244.0
3 TraesCS1B01G475000 chr1D 91.374 2446 131 33 1061 3454 491042704 491045121 0.000000e+00 3275.0
4 TraesCS1B01G475000 chr1D 89.045 639 32 13 30 668 491041272 491041872 0.000000e+00 758.0
5 TraesCS1B01G475000 chr1D 85.459 392 18 16 4007 4392 491045860 491046218 5.360000e-99 372.0
6 TraesCS1B01G475000 chr1D 90.182 275 20 5 704 978 491042092 491042359 6.990000e-93 351.0
7 TraesCS1B01G475000 chr1D 83.548 310 30 18 3561 3861 491041441 491041738 2.010000e-68 270.0
8 TraesCS1B01G475000 chr1D 93.605 172 7 2 3698 3869 491045396 491045563 2.030000e-63 254.0
9 TraesCS1B01G475000 chr1D 80.851 235 15 16 440 670 491045480 491045688 1.640000e-34 158.0
10 TraesCS1B01G475000 chr1D 84.615 117 5 6 3881 3985 491045632 491045747 2.160000e-18 104.0
11 TraesCS1B01G475000 chr1D 83.333 114 10 6 4270 4375 491049247 491049359 3.620000e-16 97.1
12 TraesCS1B01G475000 chr1A 91.822 1504 76 25 704 2197 589039892 589041358 0.000000e+00 2052.0
13 TraesCS1B01G475000 chr1A 93.296 1238 47 12 2229 3454 589041354 589042567 0.000000e+00 1794.0
14 TraesCS1B01G475000 chr1A 88.037 326 22 11 30 351 589039154 589039466 1.930000e-98 370.0
15 TraesCS1B01G475000 chr1A 89.270 233 14 4 3561 3782 589039320 589039552 9.300000e-72 281.0
16 TraesCS1B01G475000 chr1A 93.252 163 6 1 3698 3860 589042845 589043002 7.340000e-58 235.0
17 TraesCS1B01G475000 chr1A 90.769 130 7 4 4011 4139 589043271 589043396 7.550000e-38 169.0
18 TraesCS1B01G475000 chr1A 82.796 186 19 6 458 639 589039545 589039721 2.120000e-33 154.0
19 TraesCS1B01G475000 chr1A 86.885 122 13 3 1414 1532 589054294 589054415 2.760000e-27 134.0
20 TraesCS1B01G475000 chr1A 82.963 135 4 10 440 569 589042927 589043047 2.160000e-18 104.0
21 TraesCS1B01G475000 chr6A 90.816 98 9 0 193 290 159242937 159242840 9.910000e-27 132.0
22 TraesCS1B01G475000 chr6A 89.535 86 9 0 3561 3646 159242925 159242840 4.640000e-20 110.0


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 TraesCS1B01G475000 chr1B 683472450 683476841 4391 False 8111.000000 8111 100.000000 1 4392 1 chr1B.!!$F1 4391
1 TraesCS1B01G475000 chr1B 683472654 683476156 3502 False 244.000000 244 96.599000 205 3707 2 chr1B.!!$F2 3502
2 TraesCS1B01G475000 chr1D 491041272 491049359 8087 False 626.566667 3275 86.890222 30 4392 9 chr1D.!!$F1 4362
3 TraesCS1B01G475000 chr1A 589039154 589043396 4242 False 644.875000 2052 89.025625 30 4139 8 chr1A.!!$F2 4109

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
138 139 2.880879 CGTCCACATCGTCTGCCG 60.881 66.667 0.0 0.0 38.13 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3728 4435 3.667497 TTCTACAGCAGTCAAGTCTGG 57.333 47.619 0.0 0.0 36.12 3.86 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
104 105 2.992114 AAGACCGCCGACTCTGCT 60.992 61.111 0.00 0.00 0.00 4.24
107 108 3.991536 GACCGCCGACTCTGCTTCC 62.992 68.421 0.00 0.00 0.00 3.46
128 129 4.539083 ACTGCAACGGCGTCCACA 62.539 61.111 15.17 11.25 45.35 4.17
129 130 3.049674 CTGCAACGGCGTCCACAT 61.050 61.111 15.17 0.00 45.35 3.21
138 139 2.880879 CGTCCACATCGTCTGCCG 60.881 66.667 0.00 0.00 38.13 5.69
3730 4437 3.249189 GGAGGCTCACCACCACCA 61.249 66.667 17.69 0.00 45.56 4.17
3731 4438 2.348998 GAGGCTCACCACCACCAG 59.651 66.667 10.25 0.00 39.06 4.00
3732 4439 2.122413 AGGCTCACCACCACCAGA 60.122 61.111 0.00 0.00 39.06 3.86
3733 4440 2.032681 GGCTCACCACCACCAGAC 59.967 66.667 0.00 0.00 35.26 3.51
3734 4441 2.520536 GGCTCACCACCACCAGACT 61.521 63.158 0.00 0.00 35.26 3.24
3735 4442 1.451936 GCTCACCACCACCAGACTT 59.548 57.895 0.00 0.00 0.00 3.01
3753 4460 7.124298 ACCAGACTTGACTGCTGTAGAATAATA 59.876 37.037 0.00 0.00 36.67 0.98
3821 4528 5.082425 AGAATGGCTTGATTGGACTCTTTT 58.918 37.500 0.00 0.00 0.00 2.27
3918 4683 8.477419 AGATAAGGATTTGGTTTGTCTCAAAA 57.523 30.769 0.00 0.00 36.60 2.44
3931 4696 6.522625 TTGTCTCAAAACAAGATGGTCAAA 57.477 33.333 0.00 0.00 34.31 2.69
3932 4697 5.890334 TGTCTCAAAACAAGATGGTCAAAC 58.110 37.500 0.00 0.00 0.00 2.93
3933 4698 5.652014 TGTCTCAAAACAAGATGGTCAAACT 59.348 36.000 0.00 0.00 0.00 2.66
3934 4699 5.973565 GTCTCAAAACAAGATGGTCAAACTG 59.026 40.000 0.00 0.00 0.00 3.16
3935 4700 5.885352 TCTCAAAACAAGATGGTCAAACTGA 59.115 36.000 0.00 0.00 0.00 3.41
3956 4732 6.263842 ACTGATTCATTCATGTGTCACAAGTT 59.736 34.615 10.28 0.00 32.72 2.66
3985 4761 4.318332 TGTTGTCTCTGGATGCAAACTAG 58.682 43.478 0.00 0.00 0.00 2.57
3988 4764 5.073311 TGTCTCTGGATGCAAACTAGTAC 57.927 43.478 0.00 0.49 0.00 2.73
3989 4765 4.772624 TGTCTCTGGATGCAAACTAGTACT 59.227 41.667 0.00 0.00 0.00 2.73
3990 4766 5.949952 TGTCTCTGGATGCAAACTAGTACTA 59.050 40.000 1.89 1.89 0.00 1.82
3992 4768 7.039293 TGTCTCTGGATGCAAACTAGTACTAAA 60.039 37.037 3.76 0.00 0.00 1.85
4073 4946 4.285517 CAGCCTATCTATTCCCATGTCACT 59.714 45.833 0.00 0.00 0.00 3.41
4074 4947 4.285517 AGCCTATCTATTCCCATGTCACTG 59.714 45.833 0.00 0.00 0.00 3.66
4142 5015 4.527509 AGCGAGAGATAGAGAGAGAGAG 57.472 50.000 0.00 0.00 0.00 3.20
4144 5017 4.774726 AGCGAGAGATAGAGAGAGAGAGAT 59.225 45.833 0.00 0.00 0.00 2.75
4160 5033 8.732746 AGAGAGAGATAGAGAGTTACTGAAAC 57.267 38.462 0.00 0.00 38.46 2.78
4162 5035 8.871629 AGAGAGATAGAGAGTTACTGAAACAA 57.128 34.615 0.00 0.00 40.83 2.83
4163 5036 9.474313 AGAGAGATAGAGAGTTACTGAAACAAT 57.526 33.333 0.00 0.00 40.83 2.71
4164 5037 9.730420 GAGAGATAGAGAGTTACTGAAACAATC 57.270 37.037 0.00 0.00 40.83 2.67
4165 5038 8.691797 AGAGATAGAGAGTTACTGAAACAATCC 58.308 37.037 0.00 0.00 40.83 3.01
4166 5039 7.787028 AGATAGAGAGTTACTGAAACAATCCC 58.213 38.462 0.00 0.00 40.83 3.85
4169 5042 6.468543 AGAGAGTTACTGAAACAATCCCTTC 58.531 40.000 0.00 0.00 40.83 3.46
4190 5063 5.993748 TCCATTCATTCAGTTAAAACCCC 57.006 39.130 0.00 0.00 0.00 4.95
4195 5068 0.955905 TTCAGTTAAAACCCCGCAGC 59.044 50.000 0.00 0.00 0.00 5.25
4216 5094 1.804151 CCGGTGTAAGTGTCATTGTGG 59.196 52.381 0.00 0.00 0.00 4.17
4218 5096 2.808933 CGGTGTAAGTGTCATTGTGGGT 60.809 50.000 0.00 0.00 0.00 4.51
4226 5104 2.622942 GTGTCATTGTGGGTGTGAATGT 59.377 45.455 0.00 0.00 0.00 2.71
4258 5136 0.104671 GCAACAGCAGGAGCCAAAAA 59.895 50.000 0.00 0.00 43.56 1.94
4282 5160 3.631453 CTCCTTGCTGGTGCTTACA 57.369 52.632 0.00 0.00 40.48 2.41
4283 5161 1.446907 CTCCTTGCTGGTGCTTACAG 58.553 55.000 0.00 0.00 40.48 2.74
4284 5162 1.002430 CTCCTTGCTGGTGCTTACAGA 59.998 52.381 6.99 0.00 38.20 3.41
4285 5163 1.160137 CCTTGCTGGTGCTTACAGAC 58.840 55.000 6.99 0.63 38.20 3.51
4286 5164 1.543208 CCTTGCTGGTGCTTACAGACA 60.543 52.381 6.99 2.76 38.20 3.41
4312 5190 3.441572 ACACATCCAAGCTGCTTGAATAC 59.558 43.478 36.69 0.00 43.42 1.89
4315 5193 3.370840 TCCAAGCTGCTTGAATACCAT 57.629 42.857 36.69 1.13 43.42 3.55
4327 5205 5.698545 GCTTGAATACCATCCACTAGCTTAG 59.301 44.000 0.00 0.00 0.00 2.18
4328 5206 5.215252 TGAATACCATCCACTAGCTTAGC 57.785 43.478 0.00 0.00 0.00 3.09
4329 5207 4.901849 TGAATACCATCCACTAGCTTAGCT 59.098 41.667 12.67 12.67 43.41 3.32
4344 5222 2.124778 GCTGCTGCTCCTCCTTCC 60.125 66.667 8.53 0.00 36.03 3.46
4359 5237 2.707791 TCCTTCCCCATGCTCTAAGATG 59.292 50.000 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 9.135189 TGCCAAGCAAGAGTGATTAATAATAAT 57.865 29.630 0.00 0.00 34.76 1.28
12 13 8.518430 TGCCAAGCAAGAGTGATTAATAATAA 57.482 30.769 0.00 0.00 34.76 1.40
13 14 8.518430 TTGCCAAGCAAGAGTGATTAATAATA 57.482 30.769 0.00 0.00 43.99 0.98
14 15 7.408756 TTGCCAAGCAAGAGTGATTAATAAT 57.591 32.000 0.00 0.00 43.99 1.28
15 16 6.832520 TTGCCAAGCAAGAGTGATTAATAA 57.167 33.333 0.00 0.00 43.99 1.40
28 29 3.131155 CTGCAGGTTGCCAAGCAA 58.869 55.556 5.57 0.00 46.80 3.91
51 52 1.401199 GTAGTAGGTCCTGACGAGCAC 59.599 57.143 0.00 0.00 41.71 4.40
145 146 4.436998 GGTCAGTGGACTCGGCGG 62.437 72.222 7.21 0.00 43.77 6.13
146 147 4.436998 GGGTCAGTGGACTCGGCG 62.437 72.222 0.00 0.00 43.77 6.46
150 151 4.436998 CGGCGGGTCAGTGGACTC 62.437 72.222 0.00 0.00 43.77 3.36
3728 4435 3.667497 TTCTACAGCAGTCAAGTCTGG 57.333 47.619 0.00 0.00 36.12 3.86
3729 4436 8.932945 TTATTATTCTACAGCAGTCAAGTCTG 57.067 34.615 0.00 0.00 38.35 3.51
3730 4437 9.593134 CTTTATTATTCTACAGCAGTCAAGTCT 57.407 33.333 0.00 0.00 0.00 3.24
3731 4438 9.372369 ACTTTATTATTCTACAGCAGTCAAGTC 57.628 33.333 0.00 0.00 0.00 3.01
3732 4439 9.726438 AACTTTATTATTCTACAGCAGTCAAGT 57.274 29.630 0.00 0.00 0.00 3.16
3733 4440 9.979270 CAACTTTATTATTCTACAGCAGTCAAG 57.021 33.333 0.00 0.00 0.00 3.02
3734 4441 9.502091 ACAACTTTATTATTCTACAGCAGTCAA 57.498 29.630 0.00 0.00 0.00 3.18
3735 4442 9.151471 GACAACTTTATTATTCTACAGCAGTCA 57.849 33.333 0.00 0.00 0.00 3.41
3753 4460 3.554934 TCAATCAGGCAGTGACAACTTT 58.445 40.909 0.00 0.00 38.28 2.66
3918 4683 6.491062 TGAATGAATCAGTTTGACCATCTTGT 59.509 34.615 0.00 0.00 33.04 3.16
3931 4696 5.766670 ACTTGTGACACATGAATGAATCAGT 59.233 36.000 23.91 11.38 42.53 3.41
3932 4697 6.250344 ACTTGTGACACATGAATGAATCAG 57.750 37.500 23.91 10.81 42.53 2.90
3933 4698 6.638096 AACTTGTGACACATGAATGAATCA 57.362 33.333 23.91 0.00 43.67 2.57
3934 4699 7.935338 AAAACTTGTGACACATGAATGAATC 57.065 32.000 23.91 0.00 0.00 2.52
3956 4732 4.159321 TGCATCCAGAGACAACAACAAAAA 59.841 37.500 0.00 0.00 0.00 1.94
4002 4817 2.033801 CACAGGGAACAACTCAAGCTTG 59.966 50.000 20.81 20.81 0.00 4.01
4017 4832 1.420138 ACTGTAAGAACACCCACAGGG 59.580 52.381 0.00 0.00 43.74 4.45
4073 4946 5.851720 TGCTGCATTGGACTTAAAATTTCA 58.148 33.333 0.00 0.00 0.00 2.69
4074 4947 6.973229 ATGCTGCATTGGACTTAAAATTTC 57.027 33.333 9.81 0.00 0.00 2.17
4117 4990 6.119536 TCTCTCTCTCTATCTCTCGCTTTTT 58.880 40.000 0.00 0.00 0.00 1.94
4121 4994 4.152647 TCTCTCTCTCTCTATCTCTCGCT 58.847 47.826 0.00 0.00 0.00 4.93
4122 4995 4.521130 TCTCTCTCTCTCTATCTCTCGC 57.479 50.000 0.00 0.00 0.00 5.03
4123 4996 7.554476 TCTCTATCTCTCTCTCTCTATCTCTCG 59.446 44.444 0.00 0.00 0.00 4.04
4124 4997 8.815565 TCTCTATCTCTCTCTCTCTATCTCTC 57.184 42.308 0.00 0.00 0.00 3.20
4125 4998 8.397957 ACTCTCTATCTCTCTCTCTCTATCTCT 58.602 40.741 0.00 0.00 0.00 3.10
4126 4999 8.588290 ACTCTCTATCTCTCTCTCTCTATCTC 57.412 42.308 0.00 0.00 0.00 2.75
4127 5000 8.964533 AACTCTCTATCTCTCTCTCTCTATCT 57.035 38.462 0.00 0.00 0.00 1.98
4129 5002 9.830186 AGTAACTCTCTATCTCTCTCTCTCTAT 57.170 37.037 0.00 0.00 0.00 1.98
4130 5003 9.078990 CAGTAACTCTCTATCTCTCTCTCTCTA 57.921 40.741 0.00 0.00 0.00 2.43
4131 5004 7.785028 TCAGTAACTCTCTATCTCTCTCTCTCT 59.215 40.741 0.00 0.00 0.00 3.10
4132 5005 7.952671 TCAGTAACTCTCTATCTCTCTCTCTC 58.047 42.308 0.00 0.00 0.00 3.20
4133 5006 7.914427 TCAGTAACTCTCTATCTCTCTCTCT 57.086 40.000 0.00 0.00 0.00 3.10
4134 5007 8.827677 GTTTCAGTAACTCTCTATCTCTCTCTC 58.172 40.741 0.00 0.00 33.79 3.20
4142 5015 7.787028 AGGGATTGTTTCAGTAACTCTCTATC 58.213 38.462 0.00 0.00 37.64 2.08
4144 5017 7.310485 GGAAGGGATTGTTTCAGTAACTCTCTA 60.310 40.741 0.00 0.00 37.64 2.43
4160 5033 5.927281 AACTGAATGAATGGAAGGGATTG 57.073 39.130 0.00 0.00 0.00 2.67
4162 5035 7.093333 GGTTTTAACTGAATGAATGGAAGGGAT 60.093 37.037 0.00 0.00 0.00 3.85
4163 5036 6.210584 GGTTTTAACTGAATGAATGGAAGGGA 59.789 38.462 0.00 0.00 0.00 4.20
4164 5037 6.398095 GGTTTTAACTGAATGAATGGAAGGG 58.602 40.000 0.00 0.00 0.00 3.95
4165 5038 6.398095 GGGTTTTAACTGAATGAATGGAAGG 58.602 40.000 0.00 0.00 0.00 3.46
4166 5039 6.398095 GGGGTTTTAACTGAATGAATGGAAG 58.602 40.000 0.00 0.00 0.00 3.46
4169 5042 4.743493 CGGGGTTTTAACTGAATGAATGG 58.257 43.478 0.00 0.00 0.00 3.16
4190 5063 3.118454 CACTTACACCGGGCTGCG 61.118 66.667 6.32 0.00 0.00 5.18
4195 5068 1.804151 CACAATGACACTTACACCGGG 59.196 52.381 6.32 0.00 0.00 5.73
4216 5094 1.003118 TCACAGGCCTACATTCACACC 59.997 52.381 3.98 0.00 0.00 4.16
4218 5096 2.356022 CCATCACAGGCCTACATTCACA 60.356 50.000 3.98 0.00 0.00 3.58
4273 5151 0.250295 TGTGGCTGTCTGTAAGCACC 60.250 55.000 6.66 0.00 42.69 5.01
4277 5155 2.289631 TGGATGTGTGGCTGTCTGTAAG 60.290 50.000 0.00 0.00 0.00 2.34
4278 5156 1.696884 TGGATGTGTGGCTGTCTGTAA 59.303 47.619 0.00 0.00 0.00 2.41
4279 5157 1.347062 TGGATGTGTGGCTGTCTGTA 58.653 50.000 0.00 0.00 0.00 2.74
4280 5158 0.473755 TTGGATGTGTGGCTGTCTGT 59.526 50.000 0.00 0.00 0.00 3.41
4281 5159 1.162698 CTTGGATGTGTGGCTGTCTG 58.837 55.000 0.00 0.00 0.00 3.51
4282 5160 0.607489 GCTTGGATGTGTGGCTGTCT 60.607 55.000 0.00 0.00 0.00 3.41
4283 5161 0.607489 AGCTTGGATGTGTGGCTGTC 60.607 55.000 0.00 0.00 31.68 3.51
4284 5162 0.892358 CAGCTTGGATGTGTGGCTGT 60.892 55.000 0.00 0.00 43.44 4.40
4285 5163 1.880894 CAGCTTGGATGTGTGGCTG 59.119 57.895 0.00 0.00 43.03 4.85
4286 5164 1.975407 GCAGCTTGGATGTGTGGCT 60.975 57.895 0.00 0.00 0.00 4.75
4312 5190 1.415659 AGCAGCTAAGCTAGTGGATGG 59.584 52.381 0.00 0.00 44.50 3.51
4315 5193 0.176680 GCAGCAGCTAAGCTAGTGGA 59.823 55.000 0.00 0.00 44.54 4.02
4327 5205 2.124778 GGAAGGAGGAGCAGCAGC 60.125 66.667 0.00 0.00 42.56 5.25
4328 5206 2.588989 GGGAAGGAGGAGCAGCAG 59.411 66.667 0.00 0.00 0.00 4.24
4329 5207 3.011517 GGGGAAGGAGGAGCAGCA 61.012 66.667 0.00 0.00 0.00 4.41
4336 5214 1.419387 CTTAGAGCATGGGGAAGGAGG 59.581 57.143 0.00 0.00 0.00 4.30
4337 5215 2.402564 TCTTAGAGCATGGGGAAGGAG 58.597 52.381 0.00 0.00 0.00 3.69
4344 5222 4.378774 CAGTTCTCATCTTAGAGCATGGG 58.621 47.826 0.00 0.00 35.59 4.00
4359 5237 0.980423 ACTGAAGCCCTCCAGTTCTC 59.020 55.000 0.00 0.00 40.40 2.87


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

AutoCloner maintained by Alex Coulton.