Multiple sequence alignment - TraesCS4D01G294000

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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 TraesCS4D01G294000 chr4D 100.000 2803 0 0 1 2803 464395686 464392884 0.000000e+00 5177.0
1 TraesCS4D01G294000 chr4D 80.488 205 27 9 2156 2354 465416332 465416529 8.090000e-31 145.0
2 TraesCS4D01G294000 chr4B 93.001 2229 109 19 7 2210 580792448 580790242 0.000000e+00 3208.0
3 TraesCS4D01G294000 chr4B 97.598 333 8 0 2471 2803 580788516 580788184 3.130000e-159 571.0
4 TraesCS4D01G294000 chr4B 95.806 310 12 1 2205 2513 580788821 580788512 1.500000e-137 499.0
5 TraesCS4D01G294000 chr4A 93.589 1669 58 22 567 2211 5706288 5707931 0.000000e+00 2444.0
6 TraesCS4D01G294000 chr4A 91.223 695 45 7 2119 2803 5708188 5708876 0.000000e+00 931.0
7 TraesCS4D01G294000 chr4A 86.063 574 54 15 6 574 5705533 5706085 6.690000e-166 593.0
8 TraesCS4D01G294000 chr3D 76.923 195 37 4 2161 2350 554389934 554390125 1.370000e-18 104.0
9 TraesCS4D01G294000 chr7D 76.142 197 19 16 2158 2345 34231639 34231462 8.320000e-11 78.7
10 TraesCS4D01G294000 chr5D 84.932 73 7 3 2303 2374 521874440 521874509 1.390000e-08 71.3
11 TraesCS4D01G294000 chr7A 88.136 59 4 3 210 266 524698263 524698206 1.800000e-07 67.6
12 TraesCS4D01G294000 chr2B 91.837 49 3 1 2320 2367 432911137 432911089 1.800000e-07 67.6
13 TraesCS4D01G294000 chr2D 93.023 43 1 2 2320 2361 364921207 364921166 8.380000e-06 62.1


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 TraesCS4D01G294000 chr4D 464392884 464395686 2802 True 5177.000000 5177 100.000000 1 2803 1 chr4D.!!$R1 2802
1 TraesCS4D01G294000 chr4B 580788184 580792448 4264 True 1426.000000 3208 95.468333 7 2803 3 chr4B.!!$R1 2796
2 TraesCS4D01G294000 chr4A 5705533 5708876 3343 False 1322.666667 2444 90.291667 6 2803 3 chr4A.!!$F1 2797

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
68 69 0.102663 GCTAGGAACCTCGCCTACAC 59.897 60.000 6.15 0.0 36.96 2.90 F
311 317 0.389757 TCACGATCACCCAACAACGA 59.610 50.000 0.00 0.0 0.00 3.85 F
1757 1999 1.080569 GGCCTTTGTGATTGGCGTG 60.081 57.895 0.00 0.0 46.97 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1766 2008 0.037697 CCCCGTTCATGTTGTCGAGA 60.038 55.000 0.00 0.00 0.00 4.04 R
1781 2023 2.180159 AACACCTCGTGGATTCCCCG 62.180 60.000 11.17 0.62 37.94 5.73 R
2719 4795 3.500343 AGTGGCATTTATCATTAGGGGC 58.500 45.455 0.00 0.00 0.00 5.80 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
68 69 0.102663 GCTAGGAACCTCGCCTACAC 59.897 60.000 6.15 0.00 36.96 2.90
84 85 1.807814 ACACCACCAAGAGGAGTCTT 58.192 50.000 0.00 0.00 44.40 3.01
95 96 1.001406 GAGGAGTCTTGGTCACCACTG 59.999 57.143 0.00 0.00 30.78 3.66
108 109 2.594303 CACTGCAACGAGGGCCAA 60.594 61.111 6.18 0.00 0.00 4.52
115 116 0.606401 CAACGAGGGCCAACACATCT 60.606 55.000 6.18 0.00 0.00 2.90
120 121 1.279271 GAGGGCCAACACATCTACACT 59.721 52.381 6.18 0.00 0.00 3.55
166 167 2.040330 CAGAGATCAGAGCCTCCCG 58.960 63.158 0.00 0.00 0.00 5.14
192 193 3.953775 CCCCTTGCCGTCCACACT 61.954 66.667 0.00 0.00 0.00 3.55
194 195 1.602237 CCCTTGCCGTCCACACTAT 59.398 57.895 0.00 0.00 0.00 2.12
197 198 1.338674 CCTTGCCGTCCACACTATCAA 60.339 52.381 0.00 0.00 0.00 2.57
198 199 2.002586 CTTGCCGTCCACACTATCAAG 58.997 52.381 0.00 0.00 0.00 3.02
226 227 3.068729 GCCTGCCGGAAAGCCAATC 62.069 63.158 5.05 0.00 0.00 2.67
250 251 4.838152 CCACCATCCAGGACCGCG 62.838 72.222 0.00 0.00 41.22 6.46
298 304 1.138883 CGACCATCCACGTCACGAT 59.861 57.895 2.91 0.00 0.00 3.73
302 308 0.806102 CCATCCACGTCACGATCACC 60.806 60.000 2.91 0.00 0.00 4.02
311 317 0.389757 TCACGATCACCCAACAACGA 59.610 50.000 0.00 0.00 0.00 3.85
325 331 4.177026 CAACAACGATAGGAGGAGTGAAG 58.823 47.826 0.00 0.00 43.77 3.02
394 402 4.927425 GCCGAGCGTAAATTAGATGGAATA 59.073 41.667 0.00 0.00 0.00 1.75
477 485 2.026262 ACTCACCGGGCAATGATAAAGT 60.026 45.455 6.32 0.00 0.00 2.66
641 864 6.317088 CGCAATTAGGCATAATCCTTATGTG 58.683 40.000 3.76 1.87 43.81 3.21
686 909 3.665745 AGGCAAAGGCATAAACACAAG 57.334 42.857 0.00 0.00 43.71 3.16
761 992 1.270414 CCATCTCCTGTGGTCCTGCT 61.270 60.000 0.00 0.00 31.96 4.24
827 1062 1.683790 CTTCGTGGAATCGCGTGGTC 61.684 60.000 5.77 1.62 45.94 4.02
828 1063 3.541831 CGTGGAATCGCGTGGTCG 61.542 66.667 5.77 1.38 41.47 4.79
1149 1385 1.444553 GAGGGTCGTCTTCAGCGTG 60.445 63.158 0.00 0.00 0.00 5.34
1567 1804 1.614385 CACGTCGTAGCACAGGTAAG 58.386 55.000 0.00 0.00 0.00 2.34
1615 1852 2.401017 TGAGTCACGAGTTCAGTTCG 57.599 50.000 0.00 0.00 43.38 3.95
1757 1999 1.080569 GGCCTTTGTGATTGGCGTG 60.081 57.895 0.00 0.00 46.97 5.34
1781 2023 2.483877 TGCCATTCTCGACAACATGAAC 59.516 45.455 0.00 0.00 0.00 3.18
1793 2035 0.392461 ACATGAACGGGGAATCCACG 60.392 55.000 23.90 23.90 34.36 4.94
1865 2107 2.943033 GGGACCGATAAGATTGTGTTGG 59.057 50.000 0.00 0.00 0.00 3.77
1903 2145 5.867903 TCTTGATTGATTGTTTGTTGGGT 57.132 34.783 0.00 0.00 0.00 4.51
1905 2147 5.362143 TCTTGATTGATTGTTTGTTGGGTCA 59.638 36.000 0.00 0.00 0.00 4.02
1907 2149 4.648762 TGATTGATTGTTTGTTGGGTCACT 59.351 37.500 0.00 0.00 0.00 3.41
1908 2150 5.128499 TGATTGATTGTTTGTTGGGTCACTT 59.872 36.000 0.00 0.00 0.00 3.16
1909 2151 4.647424 TGATTGTTTGTTGGGTCACTTC 57.353 40.909 0.00 0.00 0.00 3.01
1910 2152 3.383185 TGATTGTTTGTTGGGTCACTTCC 59.617 43.478 0.00 0.00 0.00 3.46
1911 2153 2.516227 TGTTTGTTGGGTCACTTCCA 57.484 45.000 0.00 0.00 0.00 3.53
1912 2154 2.374184 TGTTTGTTGGGTCACTTCCAG 58.626 47.619 0.00 0.00 35.48 3.86
1924 2166 5.428253 GGTCACTTCCAGTATATTTGCTCA 58.572 41.667 0.00 0.00 0.00 4.26
1934 2176 8.212995 TCCAGTATATTTGCTCATTCTCAATGA 58.787 33.333 0.00 0.00 45.19 2.57
1938 2180 9.985318 GTATATTTGCTCATTCTCAATGATAGC 57.015 33.333 0.00 2.28 46.10 2.97
2003 2255 6.377327 ACAAGCAAATGGTATGTGTATAGC 57.623 37.500 0.00 0.00 37.69 2.97
2014 2266 5.291128 GGTATGTGTATAGCGTTGCATATCC 59.709 44.000 0.00 0.00 0.00 2.59
2094 2347 0.394216 TGATCCTGCCCCAATGTTCG 60.394 55.000 0.00 0.00 0.00 3.95
2128 2381 0.986019 AATACTGTCCGCCATGGGGA 60.986 55.000 29.29 21.97 42.39 4.81
2296 4324 5.724370 TGATTTGAGTATGTGTAGGGGAAGA 59.276 40.000 0.00 0.00 0.00 2.87
2719 4795 6.870439 TCATATGATCAACCTCGCAGATAAAG 59.130 38.462 0.00 0.00 33.89 1.85
2793 4869 5.878669 CCAGTAACACTACAACTAAATCCCC 59.121 44.000 0.00 0.00 0.00 4.81
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.666190 CGGCACCTATGGGCATCG 60.666 66.667 0.00 0.00 35.63 3.84
1 2 2.980233 GCGGCACCTATGGGCATC 60.980 66.667 0.00 0.00 35.63 3.91
2 3 4.586235 GGCGGCACCTATGGGCAT 62.586 66.667 3.07 0.00 35.63 4.40
22 23 1.992233 TTGCATTTCTGGCGCCGATC 61.992 55.000 23.90 11.40 0.00 3.69
23 24 1.594194 TTTGCATTTCTGGCGCCGAT 61.594 50.000 23.90 10.29 0.00 4.18
57 58 1.079127 CTTGGTGGTGTAGGCGAGG 60.079 63.158 0.00 0.00 0.00 4.63
84 85 1.227527 CTCGTTGCAGTGGTGACCA 60.228 57.895 0.00 0.00 0.00 4.02
95 96 2.200170 GATGTGTTGGCCCTCGTTGC 62.200 60.000 0.00 0.00 0.00 4.17
108 109 3.639094 GCCCTGATCTAGTGTAGATGTGT 59.361 47.826 1.10 0.00 45.16 3.72
115 116 1.757118 GCAGTGCCCTGATCTAGTGTA 59.243 52.381 2.85 0.00 41.50 2.90
120 121 1.483827 CTCTTGCAGTGCCCTGATCTA 59.516 52.381 13.72 0.00 41.50 1.98
147 148 1.747774 GGGAGGCTCTGATCTCTGC 59.252 63.158 15.23 0.00 0.00 4.26
150 151 0.753479 TGACGGGAGGCTCTGATCTC 60.753 60.000 15.23 3.25 40.05 2.75
166 167 1.375523 CGGCAAGGGGTGTAGTGAC 60.376 63.158 0.00 0.00 0.00 3.67
226 227 1.746615 CCTGGATGGTGGCTTCACG 60.747 63.158 0.00 0.00 42.09 4.35
278 284 2.813908 GTGACGTGGATGGTCGGC 60.814 66.667 0.00 0.00 37.22 5.54
298 304 1.553248 CCTCCTATCGTTGTTGGGTGA 59.447 52.381 0.00 0.00 0.00 4.02
302 308 2.496070 TCACTCCTCCTATCGTTGTTGG 59.504 50.000 0.00 0.00 0.00 3.77
311 317 1.501582 GTGCCCTTCACTCCTCCTAT 58.498 55.000 0.00 0.00 42.38 2.57
394 402 4.201812 CGTTAATCATGGACACGAGCAAAT 60.202 41.667 0.00 0.00 32.51 2.32
477 485 6.351626 GGGAGGAAGTAAGAAAGATAACCGAA 60.352 42.308 0.00 0.00 0.00 4.30
641 864 2.490903 TGAGGAGTTTACGTCCAGCTAC 59.509 50.000 0.00 0.00 36.43 3.58
686 909 2.046988 GGCCACCAAATTGCAGCC 60.047 61.111 0.00 3.95 0.00 4.85
827 1062 3.849123 TGTACGTACGTGATTATCGTCG 58.151 45.455 30.25 7.73 41.72 5.12
828 1063 3.656719 GCTGTACGTACGTGATTATCGTC 59.343 47.826 30.25 9.53 41.72 4.20
1149 1385 2.591715 ATAATGCCGCAGCCGTCC 60.592 61.111 0.00 0.00 38.69 4.79
1212 1448 4.080638 ACCTTCTTGTGGATGAAGAGGATC 60.081 45.833 0.00 0.00 41.38 3.36
1449 1686 3.308705 GGGTTCGACGGTGACCCT 61.309 66.667 20.63 0.00 37.63 4.34
1567 1804 4.445452 TGACTTATCACGTGGTAGAACC 57.555 45.455 17.00 4.39 39.22 3.62
1603 1840 6.389622 TGTAATTGAATCGAACTGAACTCG 57.610 37.500 0.00 0.00 37.66 4.18
1647 1889 9.701098 AATCTAGTTCACACGTTATTAGAAACA 57.299 29.630 0.00 0.00 0.00 2.83
1648 1890 9.953825 CAATCTAGTTCACACGTTATTAGAAAC 57.046 33.333 0.00 0.00 0.00 2.78
1649 1891 9.146984 CCAATCTAGTTCACACGTTATTAGAAA 57.853 33.333 0.00 0.00 0.00 2.52
1650 1892 8.525316 TCCAATCTAGTTCACACGTTATTAGAA 58.475 33.333 0.00 0.00 0.00 2.10
1651 1893 8.058667 TCCAATCTAGTTCACACGTTATTAGA 57.941 34.615 0.00 0.00 0.00 2.10
1652 1894 7.974501 ACTCCAATCTAGTTCACACGTTATTAG 59.025 37.037 0.00 0.00 0.00 1.73
1757 1999 3.374988 TCATGTTGTCGAGAATGGCAATC 59.625 43.478 0.00 0.00 0.00 2.67
1766 2008 0.037697 CCCCGTTCATGTTGTCGAGA 60.038 55.000 0.00 0.00 0.00 4.04
1781 2023 2.180159 AACACCTCGTGGATTCCCCG 62.180 60.000 11.17 0.62 37.94 5.73
1793 2035 4.156008 CCCACTTTGTAGCATTAACACCTC 59.844 45.833 0.00 0.00 0.00 3.85
1907 2149 8.843262 CATTGAGAATGAGCAAATATACTGGAA 58.157 33.333 0.00 0.00 41.46 3.53
1908 2150 8.212995 TCATTGAGAATGAGCAAATATACTGGA 58.787 33.333 0.00 0.00 42.69 3.86
1909 2151 8.387190 TCATTGAGAATGAGCAAATATACTGG 57.613 34.615 0.00 0.00 42.69 4.00
1924 2166 3.979347 ACCTCCAGGCTATCATTGAGAAT 59.021 43.478 0.00 0.00 39.32 2.40
1934 2176 4.475016 ACAGTAATTTCACCTCCAGGCTAT 59.525 41.667 0.00 0.00 39.32 2.97
1938 2180 7.703058 AATTTACAGTAATTTCACCTCCAGG 57.297 36.000 0.00 0.00 42.17 4.45
2094 2347 5.642491 GGACAGTATTAAAGTCACCTCCAAC 59.358 44.000 0.00 0.00 34.04 3.77
2128 2381 3.117776 AGGAAAGGTCACCGGTACTTTTT 60.118 43.478 23.59 15.68 33.66 1.94
2202 2804 8.908786 ATGTCGGATATGATTTATGTTGAAGT 57.091 30.769 0.00 0.00 0.00 3.01
2219 4247 5.623956 TGGGTGTAAGATTTATGTCGGAT 57.376 39.130 0.00 0.00 0.00 4.18
2283 4311 5.450453 TCAAAAATTGTCTTCCCCTACACA 58.550 37.500 0.00 0.00 0.00 3.72
2289 4317 6.873605 CACCTAAATCAAAAATTGTCTTCCCC 59.126 38.462 0.00 0.00 0.00 4.81
2296 4324 6.326323 ACCACCTCACCTAAATCAAAAATTGT 59.674 34.615 0.00 0.00 0.00 2.71
2691 4767 4.827284 TCTGCGAGGTTGATCATATGAGTA 59.173 41.667 11.78 0.00 0.00 2.59
2719 4795 3.500343 AGTGGCATTTATCATTAGGGGC 58.500 45.455 0.00 0.00 0.00 5.80


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

AutoCloner maintained by Alex Coulton.