Multiple sequence alignment - TraesCS4B01G242400

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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 TraesCS4B01G242400 chr4B 100.000 2550 0 0 1 2550 502213510 502210961 0 4710
1 TraesCS4B01G242400 chr4A 95.744 1997 75 9 559 2550 705529262 705527271 0 3208
2 TraesCS4B01G242400 chr1B 95.735 1993 76 7 565 2550 581717565 581715575 0 3201
3 TraesCS4B01G242400 chr1B 95.464 1984 82 7 570 2550 520844118 520842140 0 3158
4 TraesCS4B01G242400 chr2B 95.379 1991 83 7 564 2550 458657418 458659403 0 3158
5 TraesCS4B01G242400 chr2B 95.148 1999 85 10 561 2550 492636657 492638652 0 3144
6 TraesCS4B01G242400 chr7B 95.267 1986 86 7 570 2550 720989189 720987207 0 3140
7 TraesCS4B01G242400 chr7B 95.169 1987 87 8 570 2550 602142438 602144421 0 3129
8 TraesCS4B01G242400 chr7B 95.073 1989 86 10 570 2550 677862789 677860805 0 3120
9 TraesCS4B01G242400 chr5B 94.850 2000 92 9 558 2550 497276153 497278148 0 3112
10 TraesCS4B01G242400 chr3D 94.542 568 29 2 1 568 250794250 250793685 0 876
11 TraesCS4B01G242400 chr3D 93.849 569 33 2 1 568 507864395 507864962 0 856
12 TraesCS4B01G242400 chr5D 94.366 568 31 1 1 568 71786129 71786695 0 870
13 TraesCS4B01G242400 chr4D 94.366 568 31 1 1 568 45363578 45364144 0 870
14 TraesCS4B01G242400 chr4D 93.849 569 33 2 1 568 294589092 294589659 0 856
15 TraesCS4B01G242400 chr1D 94.025 569 32 2 1 568 384583598 384584165 0 861
16 TraesCS4B01G242400 chr7D 93.849 569 33 2 1 569 408425789 408426355 0 856
17 TraesCS4B01G242400 chr7D 93.849 569 33 2 1 568 586474217 586473650 0 856
18 TraesCS4B01G242400 chr2D 93.849 569 33 2 1 568 539741785 539742352 0 856


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 TraesCS4B01G242400 chr4B 502210961 502213510 2549 True 4710 4710 100.000 1 2550 1 chr4B.!!$R1 2549
1 TraesCS4B01G242400 chr4A 705527271 705529262 1991 True 3208 3208 95.744 559 2550 1 chr4A.!!$R1 1991
2 TraesCS4B01G242400 chr1B 581715575 581717565 1990 True 3201 3201 95.735 565 2550 1 chr1B.!!$R2 1985
3 TraesCS4B01G242400 chr1B 520842140 520844118 1978 True 3158 3158 95.464 570 2550 1 chr1B.!!$R1 1980
4 TraesCS4B01G242400 chr2B 458657418 458659403 1985 False 3158 3158 95.379 564 2550 1 chr2B.!!$F1 1986
5 TraesCS4B01G242400 chr2B 492636657 492638652 1995 False 3144 3144 95.148 561 2550 1 chr2B.!!$F2 1989
6 TraesCS4B01G242400 chr7B 720987207 720989189 1982 True 3140 3140 95.267 570 2550 1 chr7B.!!$R2 1980
7 TraesCS4B01G242400 chr7B 602142438 602144421 1983 False 3129 3129 95.169 570 2550 1 chr7B.!!$F1 1980
8 TraesCS4B01G242400 chr7B 677860805 677862789 1984 True 3120 3120 95.073 570 2550 1 chr7B.!!$R1 1980
9 TraesCS4B01G242400 chr5B 497276153 497278148 1995 False 3112 3112 94.850 558 2550 1 chr5B.!!$F1 1992
10 TraesCS4B01G242400 chr3D 250793685 250794250 565 True 876 876 94.542 1 568 1 chr3D.!!$R1 567
11 TraesCS4B01G242400 chr3D 507864395 507864962 567 False 856 856 93.849 1 568 1 chr3D.!!$F1 567
12 TraesCS4B01G242400 chr5D 71786129 71786695 566 False 870 870 94.366 1 568 1 chr5D.!!$F1 567
13 TraesCS4B01G242400 chr4D 45363578 45364144 566 False 870 870 94.366 1 568 1 chr4D.!!$F1 567
14 TraesCS4B01G242400 chr4D 294589092 294589659 567 False 856 856 93.849 1 568 1 chr4D.!!$F2 567
15 TraesCS4B01G242400 chr1D 384583598 384584165 567 False 861 861 94.025 1 568 1 chr1D.!!$F1 567
16 TraesCS4B01G242400 chr7D 408425789 408426355 566 False 856 856 93.849 1 569 1 chr7D.!!$F1 568
17 TraesCS4B01G242400 chr7D 586473650 586474217 567 True 856 856 93.849 1 568 1 chr7D.!!$R1 567
18 TraesCS4B01G242400 chr2D 539741785 539742352 567 False 856 856 93.849 1 568 1 chr2D.!!$F1 567

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
658 664 0.250597 GTTTTGCCCCTAGTCCGTGT 60.251 55.0 0.0 0.0 0.0 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2318 2343 0.468226 AGGAAAACCACTCTCACGCA 59.532 50.0 0.0 0.0 0.0 5.24 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
32 33 3.069586 ACCGAATATTTGCCGATGAGAGA 59.930 43.478 0.00 0.00 0.00 3.10
43 44 3.191371 GCCGATGAGAGATTGTTTTTGGT 59.809 43.478 0.00 0.00 0.00 3.67
65 66 1.484653 CCCACCGTGTATGAATCAGGA 59.515 52.381 0.00 0.00 0.00 3.86
71 72 3.118408 CCGTGTATGAATCAGGAAGGGAA 60.118 47.826 0.00 0.00 0.00 3.97
82 83 1.838077 AGGAAGGGAATCGATTTCGGT 59.162 47.619 12.81 0.82 40.29 4.69
130 131 1.567504 CGTGTATGAATCCGGGTGAC 58.432 55.000 0.00 0.00 0.00 3.67
174 175 3.937079 GTGAAATTACGAACCTACCCCTG 59.063 47.826 0.00 0.00 0.00 4.45
176 177 4.776837 TGAAATTACGAACCTACCCCTGTA 59.223 41.667 0.00 0.00 0.00 2.74
193 194 6.906901 ACCCCTGTAGAAACCTATAGAAATCA 59.093 38.462 0.00 0.00 29.87 2.57
195 196 8.272173 CCCCTGTAGAAACCTATAGAAATCAAA 58.728 37.037 0.00 0.00 29.87 2.69
242 243 3.285484 AGGCAGCAGTAATTTCCATCTG 58.715 45.455 0.00 0.00 0.00 2.90
258 259 3.258872 CCATCTGGCAGATTTTGGTTTCA 59.741 43.478 26.87 0.00 31.32 2.69
304 305 5.212194 GCTTCGTTCAAATTTTGCAGAGTA 58.788 37.500 4.19 0.00 0.00 2.59
658 664 0.250597 GTTTTGCCCCTAGTCCGTGT 60.251 55.000 0.00 0.00 0.00 4.49
667 673 2.137425 CTAGTCCGTGTGCACCGACA 62.137 60.000 23.58 10.79 40.42 4.35
672 678 3.095032 GTGTGCACCGACACGTTT 58.905 55.556 15.69 0.00 43.74 3.60
734 740 0.546747 CCCTTACAGGTGGGACCAGA 60.547 60.000 0.00 0.00 46.15 3.86
736 742 1.348064 CTTACAGGTGGGACCAGACA 58.652 55.000 0.00 0.00 41.95 3.41
773 779 0.319986 TATTCAGACCGTTGCACGCA 60.320 50.000 0.00 0.00 40.91 5.24
931 941 1.070914 GGTGGGAAGCTAGCTATGGAC 59.929 57.143 19.70 12.43 0.00 4.02
955 965 1.040646 CGATGGTGGGAAGCTAGCTA 58.959 55.000 19.70 0.00 0.00 3.32
1009 1019 0.614697 TCCGAGCTCCATGTCTTCCA 60.615 55.000 8.47 0.00 0.00 3.53
1014 1024 1.980765 AGCTCCATGTCTTCCACAAGA 59.019 47.619 0.00 0.00 38.97 3.02
1111 1121 1.944430 GCGTTGATCGGAGGGTTTCTT 60.944 52.381 0.00 0.00 40.26 2.52
1195 1205 1.460359 CAATTGCACCATTTTCGTGGC 59.540 47.619 0.00 0.00 43.27 5.01
1254 1264 1.241165 TGCAGGTGACATGCTTCTTG 58.759 50.000 23.05 0.00 44.17 3.02
1255 1265 0.524862 GCAGGTGACATGCTTCTTGG 59.475 55.000 15.63 0.00 40.59 3.61
1256 1266 1.901591 CAGGTGACATGCTTCTTGGT 58.098 50.000 0.00 0.00 0.00 3.67
1259 1269 2.887152 AGGTGACATGCTTCTTGGTTTC 59.113 45.455 0.00 0.00 0.00 2.78
1269 1279 0.682852 TCTTGGTTTCGGGTCGATGT 59.317 50.000 0.00 0.00 35.23 3.06
1516 1526 6.468333 TTTGTAGGTATGGTAATCGCACTA 57.532 37.500 0.00 0.00 0.00 2.74
1721 1733 8.717821 CAGAAACTTTTGATCAATGAAATGCAT 58.282 29.630 9.40 0.00 39.43 3.96
1867 1880 2.305635 TGGAAAATGTGCCTCAGCTCTA 59.694 45.455 0.00 0.00 40.80 2.43
2035 2054 0.035598 TGGTGTTTAAGGCTGCGCTA 59.964 50.000 9.73 0.00 0.00 4.26
2085 2104 3.119319 TGACATGGGTAGGGAAGCAATA 58.881 45.455 0.00 0.00 0.00 1.90
2087 2106 4.074970 GACATGGGTAGGGAAGCAATATG 58.925 47.826 0.00 0.00 0.00 1.78
2198 2220 2.095372 GCGTGGATTAGTGGTGTTTAGC 59.905 50.000 0.00 0.00 0.00 3.09
2287 2309 5.998454 AGTGAGACTGTGAAATTTGTCAG 57.002 39.130 14.04 14.04 32.41 3.51
2318 2343 2.226437 GAGACCGTGAATGTTTGCACAT 59.774 45.455 0.00 0.00 46.34 3.21
2398 2423 0.590682 CGTATGTTTGCACTGCCACA 59.409 50.000 5.77 5.77 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 0.615850 TGATTCATACACGGTGGGCA 59.384 50.000 13.48 0.00 0.00 5.36
65 66 1.479323 TCGACCGAAATCGATTCCCTT 59.521 47.619 11.83 0.00 45.84 3.95
82 83 2.276201 CAAAACACAGTGTGTCCTCGA 58.724 47.619 28.32 0.00 46.79 4.04
130 131 1.136085 CAAACGTGACATAACCGCCTG 60.136 52.381 0.00 0.00 0.00 4.85
162 163 3.179685 AGGTTTCTACAGGGGTAGGTTC 58.820 50.000 2.37 0.00 45.76 3.62
193 194 5.212532 TGCCATGCAAAGACTATTTGTTT 57.787 34.783 0.00 0.00 34.76 2.83
195 196 3.194116 CCTGCCATGCAAAGACTATTTGT 59.806 43.478 0.00 0.00 38.41 2.83
203 204 1.133699 CCTATCCCTGCCATGCAAAGA 60.134 52.381 0.00 0.00 38.41 2.52
242 243 1.669795 CGCCTGAAACCAAAATCTGCC 60.670 52.381 0.00 0.00 0.00 4.85
258 259 0.669625 GAAAGTCGCAGTAACCGCCT 60.670 55.000 0.00 0.00 0.00 5.52
304 305 1.877443 GAGTTGGCATGGTAAACGTGT 59.123 47.619 0.00 0.00 38.39 4.49
410 415 7.754069 TCTTTGTTGTGCTTTTGAAAGTATG 57.246 32.000 5.47 0.00 38.28 2.39
658 664 1.019805 TCACAAAACGTGTCGGTGCA 61.020 50.000 5.78 0.00 46.44 4.57
667 673 3.130340 AGATGCCAAAGTTCACAAAACGT 59.870 39.130 0.00 0.00 0.00 3.99
672 678 1.879380 CGGAGATGCCAAAGTTCACAA 59.121 47.619 0.00 0.00 35.94 3.33
734 740 3.574074 AATTGGCCGCCTCTGCTGT 62.574 57.895 11.61 0.00 34.43 4.40
736 742 0.323360 TAAAATTGGCCGCCTCTGCT 60.323 50.000 11.61 0.00 34.43 4.24
773 779 4.431131 CTGGGTCCCGCAAGCCAT 62.431 66.667 2.65 0.00 45.28 4.40
1009 1019 4.778143 GGTGGCGCGGGATCTTGT 62.778 66.667 8.83 0.00 0.00 3.16
1049 1059 1.911357 TGAAGACAGGCATCTCCACAT 59.089 47.619 0.00 0.00 37.29 3.21
1111 1121 1.121378 TTGTGGTTCCTCGGTGTGTA 58.879 50.000 0.00 0.00 0.00 2.90
1195 1205 0.940126 CGATTGCTCAAAGATCCCGG 59.060 55.000 0.00 0.00 0.00 5.73
1254 1264 1.076332 CAGAACATCGACCCGAAACC 58.924 55.000 0.00 0.00 39.99 3.27
1255 1265 1.076332 CCAGAACATCGACCCGAAAC 58.924 55.000 0.00 0.00 39.99 2.78
1256 1266 0.672401 GCCAGAACATCGACCCGAAA 60.672 55.000 0.00 0.00 39.99 3.46
1259 1269 2.511600 GGCCAGAACATCGACCCG 60.512 66.667 0.00 0.00 0.00 5.28
1269 1279 4.908601 TTTATCAGAGTCTTGGCCAGAA 57.091 40.909 5.11 0.00 31.28 3.02
1603 1613 8.499162 CAACATTTAAACAACTTTGACCAACAA 58.501 29.630 0.00 0.00 36.65 2.83
1636 1648 7.730364 TTAAATGTTGGTCACTTCTTCTCTC 57.270 36.000 0.00 0.00 0.00 3.20
1721 1733 7.833682 TGTTTGGCTCTGGAATAATTCATTAGA 59.166 33.333 0.00 0.00 0.00 2.10
1867 1880 4.775780 TGGCACTAGGTGTAAACATCTACT 59.224 41.667 0.00 0.00 38.47 2.57
1993 2012 2.593436 CCACGCGGTCTTGGGTTT 60.593 61.111 12.47 0.00 32.02 3.27
2035 2054 2.032620 CCATCTGTCCTAGCGGTTACT 58.967 52.381 0.00 0.00 0.00 2.24
2085 2104 8.939929 CAAATTTCACAGTCTCACTATGTACAT 58.060 33.333 13.93 13.93 0.00 2.29
2087 2106 8.311650 ACAAATTTCACAGTCTCACTATGTAC 57.688 34.615 0.00 0.00 0.00 2.90
2152 2174 0.543410 TTGGTTCGAGTCCCTAGCCA 60.543 55.000 6.32 0.00 0.00 4.75
2157 2179 0.685660 GGTCTTTGGTTCGAGTCCCT 59.314 55.000 6.32 0.00 0.00 4.20
2318 2343 0.468226 AGGAAAACCACTCTCACGCA 59.532 50.000 0.00 0.00 0.00 5.24
2398 2423 2.890945 GTGCCACTCTAACCAAAACCAT 59.109 45.455 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.