Multiple sequence alignment - TraesCS5B01G406000

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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 TraesCS5B01G406000 chr5B 100.000 2786 0 0 1 2786 581830836 581828051 0.000000e+00 5145.0
1 TraesCS5B01G406000 chr5A 89.720 2889 127 65 1 2786 594082732 594079911 0.000000e+00 3533.0
2 TraesCS5B01G406000 chr5D 91.855 1817 66 30 362 2120 474815182 474813390 0.000000e+00 2460.0
3 TraesCS5B01G406000 chr5D 91.845 515 28 7 2280 2786 474813145 474812637 0.000000e+00 706.0
4 TraesCS5B01G406000 chr5D 86.701 391 32 10 2 377 474815583 474815198 1.540000e-112 416.0
5 TraesCS5B01G406000 chr2B 94.737 57 2 1 1855 1910 724698013 724697957 1.370000e-13 87.9


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 TraesCS5B01G406000 chr5B 581828051 581830836 2785 True 5145 5145 100.000000 1 2786 1 chr5B.!!$R1 2785
1 TraesCS5B01G406000 chr5A 594079911 594082732 2821 True 3533 3533 89.720000 1 2786 1 chr5A.!!$R1 2785
2 TraesCS5B01G406000 chr5D 474812637 474815583 2946 True 1194 2460 90.133667 2 2786 3 chr5D.!!$R1 2784

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
117 127 0.179250 CCACTGTCATTTCGCGTTCG 60.179 55.0 5.77 0.0 0.00 3.95 F
1509 1613 0.250727 TCTGCCAAAAGGAGTTCCCG 60.251 55.0 0.00 0.0 40.87 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1717 1827 0.032117 TCCTCATCGTCCTCCCACAT 60.032 55.0 0.0 0.0 0.0 3.21 R
2490 2777 0.988832 ATTCCCCGGCTAAACACAGA 59.011 50.0 0.0 0.0 0.0 3.41 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
21 23 4.719369 ACGAGGCGAAGACCGTGC 62.719 66.667 0.00 0.00 40.61 5.34
52 58 2.082366 CGCATGTGCCAAACGCTTC 61.082 57.895 0.00 0.00 38.78 3.86
83 89 1.140375 GGAACCACTACCGTAGCCG 59.860 63.158 5.42 0.00 0.00 5.52
113 123 1.787847 GACCCACTGTCATTTCGCG 59.212 57.895 0.00 0.00 43.85 5.87
117 127 0.179250 CCACTGTCATTTCGCGTTCG 60.179 55.000 5.77 0.00 0.00 3.95
136 153 1.335872 CGAGTGGCCCAAACAATCAAC 60.336 52.381 0.00 0.00 32.91 3.18
179 200 1.338674 TGCACCACCCTAGATGTTTCG 60.339 52.381 0.00 0.00 0.00 3.46
195 216 2.445453 TTCGCGAAGACAAACACAAC 57.555 45.000 19.38 0.00 0.00 3.32
211 232 0.606401 CAACTCGGATGTTGCACCCT 60.606 55.000 0.00 0.00 40.40 4.34
212 233 0.981183 AACTCGGATGTTGCACCCTA 59.019 50.000 0.00 0.00 0.00 3.53
214 235 0.462047 CTCGGATGTTGCACCCTACC 60.462 60.000 0.00 0.00 0.00 3.18
215 236 1.451387 CGGATGTTGCACCCTACCC 60.451 63.158 0.00 0.00 0.00 3.69
216 237 1.910580 CGGATGTTGCACCCTACCCT 61.911 60.000 0.00 0.00 0.00 4.34
217 238 1.209621 GGATGTTGCACCCTACCCTA 58.790 55.000 0.00 0.00 0.00 3.53
218 239 1.562475 GGATGTTGCACCCTACCCTAA 59.438 52.381 0.00 0.00 0.00 2.69
219 240 2.640184 GATGTTGCACCCTACCCTAAC 58.360 52.381 0.00 0.00 0.00 2.34
220 241 1.436326 TGTTGCACCCTACCCTAACA 58.564 50.000 0.00 0.00 0.00 2.41
221 242 1.775459 TGTTGCACCCTACCCTAACAA 59.225 47.619 0.00 0.00 0.00 2.83
224 245 3.359695 TGCACCCTACCCTAACAATTC 57.640 47.619 0.00 0.00 0.00 2.17
225 246 2.645297 TGCACCCTACCCTAACAATTCA 59.355 45.455 0.00 0.00 0.00 2.57
226 247 3.279434 GCACCCTACCCTAACAATTCAG 58.721 50.000 0.00 0.00 0.00 3.02
227 248 3.279434 CACCCTACCCTAACAATTCAGC 58.721 50.000 0.00 0.00 0.00 4.26
257 285 2.420022 CCCAAAAGATCGACATGTCACC 59.580 50.000 24.93 12.83 0.00 4.02
307 336 8.669243 ACAGCTTCGAAATATTTTTAGAAGGAG 58.331 33.333 25.80 13.84 46.32 3.69
447 515 2.743928 GCTTCCCGCAGTCCACAG 60.744 66.667 0.00 0.00 38.92 3.66
452 520 2.734723 CCGCAGTCCACAGTGACG 60.735 66.667 0.62 0.00 40.26 4.35
545 621 2.437897 CTCCACTTGCCCTGCCTT 59.562 61.111 0.00 0.00 0.00 4.35
546 622 1.975407 CTCCACTTGCCCTGCCTTG 60.975 63.158 0.00 0.00 0.00 3.61
634 725 2.113139 GTCCACCACCCACCACAG 59.887 66.667 0.00 0.00 0.00 3.66
639 731 4.704833 CCACCCACCACAGCGGAG 62.705 72.222 0.00 0.00 38.63 4.63
698 790 1.624813 CCGGTTCCTAACTAACCACCA 59.375 52.381 0.00 0.00 45.59 4.17
700 792 2.691927 GGTTCCTAACTAACCACCACG 58.308 52.381 0.00 0.00 44.83 4.94
733 831 2.356313 CGTCAGCCGAACAGCACT 60.356 61.111 0.00 0.00 39.56 4.40
860 958 0.251832 TCTCACTCCACCACTCCCTC 60.252 60.000 0.00 0.00 0.00 4.30
861 959 0.542938 CTCACTCCACCACTCCCTCA 60.543 60.000 0.00 0.00 0.00 3.86
862 960 0.832135 TCACTCCACCACTCCCTCAC 60.832 60.000 0.00 0.00 0.00 3.51
863 961 1.121407 CACTCCACCACTCCCTCACA 61.121 60.000 0.00 0.00 0.00 3.58
864 962 1.122019 ACTCCACCACTCCCTCACAC 61.122 60.000 0.00 0.00 0.00 3.82
865 963 1.831652 CTCCACCACTCCCTCACACC 61.832 65.000 0.00 0.00 0.00 4.16
866 964 2.146724 CCACCACTCCCTCACACCA 61.147 63.158 0.00 0.00 0.00 4.17
867 965 1.071471 CACCACTCCCTCACACCAC 59.929 63.158 0.00 0.00 0.00 4.16
868 966 1.383943 ACCACTCCCTCACACCACA 60.384 57.895 0.00 0.00 0.00 4.17
869 967 1.071471 CCACTCCCTCACACCACAC 59.929 63.158 0.00 0.00 0.00 3.82
949 1050 1.576421 CACCGCACAAGGAAGAAGC 59.424 57.895 0.00 0.00 34.73 3.86
1071 1175 4.379243 CTGGACGTTGAGGCGGCT 62.379 66.667 13.09 13.09 40.27 5.52
1200 1304 1.067749 CTGCCTCCTCATGCTCTCG 59.932 63.158 0.00 0.00 0.00 4.04
1317 1421 4.435970 TCCTACCAGGCGCTCGGA 62.436 66.667 20.29 8.77 34.61 4.55
1360 1464 3.914551 AAGCAGCCGTCTCCTCCCT 62.915 63.158 0.00 0.00 0.00 4.20
1371 1475 3.160047 CCTCCCTCTGATGCCGCT 61.160 66.667 0.00 0.00 0.00 5.52
1509 1613 0.250727 TCTGCCAAAAGGAGTTCCCG 60.251 55.000 0.00 0.00 40.87 5.14
1512 1616 0.250770 GCCAAAAGGAGTTCCCGACT 60.251 55.000 0.00 0.00 42.70 4.18
1668 1775 0.322546 GGGCCTTCGACCTGAACATT 60.323 55.000 0.84 0.00 31.87 2.71
1731 1841 2.094100 AGATGATGTGGGAGGACGAT 57.906 50.000 0.00 0.00 0.00 3.73
1836 1957 2.685897 TCCAAAGTTTTTGGTCCAGTCG 59.314 45.455 17.46 0.00 40.40 4.18
1956 2089 7.997223 AGCCATATACGTAGATATAGGCAGTAA 59.003 37.037 23.87 0.00 37.85 2.24
1957 2090 8.291032 GCCATATACGTAGATATAGGCAGTAAG 58.709 40.741 19.55 0.00 36.72 2.34
1971 2117 3.052036 GCAGTAAGTTGTAACGACGGAA 58.948 45.455 0.00 0.00 0.00 4.30
2000 2146 3.415212 TGCTTCCTCTTTCAGATGTTGG 58.585 45.455 0.00 0.00 0.00 3.77
2045 2191 5.158101 AGTCGACAGTTCATACATACTCG 57.842 43.478 19.50 0.00 0.00 4.18
2067 2213 5.650703 TCGTACAGAGATTGGTCATGAACTA 59.349 40.000 12.94 4.54 0.00 2.24
2073 2219 5.658634 AGAGATTGGTCATGAACTAGCAGTA 59.341 40.000 12.94 0.00 0.00 2.74
2088 2234 6.327934 ACTAGCAGTACCGTGTAACATAAAG 58.672 40.000 0.00 0.00 35.74 1.85
2155 2322 9.809096 TGCACTTGTTTTATCAATTTAACTTCA 57.191 25.926 0.00 0.00 0.00 3.02
2173 2340 2.416747 TCAGTGGCTCGATGAAACTTG 58.583 47.619 0.00 0.00 0.00 3.16
2230 2501 5.832568 TGCGTACACTGTAACTTGTATTG 57.167 39.130 0.00 0.00 31.05 1.90
2243 2514 1.816074 TGTATTGGCCACGAAGGAAC 58.184 50.000 3.88 0.00 41.22 3.62
2308 2579 6.715347 ACTGTAACTTGCAAGAAGGAAAAT 57.285 33.333 32.50 4.68 0.00 1.82
2325 2596 1.270907 AATGAGACGGAAGCCTCTGT 58.729 50.000 0.00 0.00 44.26 3.41
2440 2725 1.560860 GCAAGACTGCTCACCACGTC 61.561 60.000 0.00 0.00 45.74 4.34
2445 2730 3.633094 CTGCTCACCACGTCTCCGG 62.633 68.421 0.00 0.00 38.78 5.14
2478 2765 8.276325 GTGATTAGCTCGACGAATAATCAAATT 58.724 33.333 28.82 8.03 42.90 1.82
2479 2766 8.826710 TGATTAGCTCGACGAATAATCAAATTT 58.173 29.630 26.90 6.17 40.09 1.82
2575 2866 1.301401 GTACAAGACACCGCTGGCA 60.301 57.895 0.00 0.00 0.00 4.92
2773 3074 4.054455 TCGCTTTCGACGCAACGC 62.054 61.111 6.68 0.00 40.21 4.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 23 1.019278 ACATGCGTGTAGAAAGCCGG 61.019 55.000 10.57 0.00 36.63 6.13
30 32 1.571953 CGTTTGGCACATGCGTGTA 59.428 52.632 12.10 0.00 45.50 2.90
52 58 2.051345 GTTCCGGTGCTGCAAACG 60.051 61.111 17.67 17.67 0.00 3.60
83 89 0.251787 AGTGGGTCAAATGAAGGGGC 60.252 55.000 0.00 0.00 0.00 5.80
113 123 0.958822 ATTGTTTGGGCCACTCGAAC 59.041 50.000 5.23 9.02 0.00 3.95
117 127 1.000843 GGTTGATTGTTTGGGCCACTC 59.999 52.381 5.23 2.42 0.00 3.51
179 200 1.332904 CCGAGTTGTGTTTGTCTTCGC 60.333 52.381 0.00 0.00 0.00 4.70
195 216 0.462047 GGTAGGGTGCAACATCCGAG 60.462 60.000 3.06 0.00 40.09 4.63
207 228 3.190439 AGCTGAATTGTTAGGGTAGGGT 58.810 45.455 0.00 0.00 0.00 4.34
209 230 6.590234 AAAAAGCTGAATTGTTAGGGTAGG 57.410 37.500 0.00 0.00 0.00 3.18
246 274 3.542875 CGTACGTACTAGGTGACATGTCG 60.543 52.174 22.55 8.60 0.00 4.35
282 310 7.641802 GCTCCTTCTAAAAATATTTCGAAGCTG 59.358 37.037 19.34 16.07 42.55 4.24
286 314 6.596497 ACGGCTCCTTCTAAAAATATTTCGAA 59.404 34.615 0.10 0.00 31.66 3.71
299 328 1.757118 CTCATTGGACGGCTCCTTCTA 59.243 52.381 0.00 0.00 37.48 2.10
300 329 0.539051 CTCATTGGACGGCTCCTTCT 59.461 55.000 0.00 0.00 37.48 2.85
304 333 0.460987 CACTCTCATTGGACGGCTCC 60.461 60.000 0.00 0.00 37.04 4.70
307 336 0.460987 CCTCACTCTCATTGGACGGC 60.461 60.000 0.00 0.00 0.00 5.68
639 731 2.200337 GGTTGTGGGTCACTTGGGC 61.200 63.158 0.00 0.00 35.11 5.36
725 823 4.609018 ACGAGGCGCAGTGCTGTT 62.609 61.111 14.33 0.00 45.43 3.16
860 958 1.377856 TGTGGTGTGGTGTGGTGTG 60.378 57.895 0.00 0.00 0.00 3.82
861 959 1.377987 GTGTGGTGTGGTGTGGTGT 60.378 57.895 0.00 0.00 0.00 4.16
862 960 2.118404 GGTGTGGTGTGGTGTGGTG 61.118 63.158 0.00 0.00 0.00 4.17
863 961 2.274104 GGTGTGGTGTGGTGTGGT 59.726 61.111 0.00 0.00 0.00 4.16
864 962 2.518349 GGGTGTGGTGTGGTGTGG 60.518 66.667 0.00 0.00 0.00 4.17
865 963 1.823470 CTGGGTGTGGTGTGGTGTG 60.823 63.158 0.00 0.00 0.00 3.82
866 964 2.595095 CTGGGTGTGGTGTGGTGT 59.405 61.111 0.00 0.00 0.00 4.16
867 965 2.050836 TAGCTGGGTGTGGTGTGGTG 62.051 60.000 0.00 0.00 0.00 4.17
868 966 1.768482 TAGCTGGGTGTGGTGTGGT 60.768 57.895 0.00 0.00 0.00 4.16
869 967 1.003355 CTAGCTGGGTGTGGTGTGG 60.003 63.158 0.00 0.00 0.00 4.17
1055 1156 4.680237 CAGCCGCCTCAACGTCCA 62.680 66.667 0.00 0.00 0.00 4.02
1077 1181 4.994471 CTGGTGGCGCTGCTGACA 62.994 66.667 7.64 0.00 0.00 3.58
1314 1418 2.125912 CTCGTCTTGTGGCCTCCG 60.126 66.667 3.32 0.00 0.00 4.63
1317 1421 3.241530 TGGCTCGTCTTGTGGCCT 61.242 61.111 3.32 0.00 44.36 5.19
1462 1566 0.946221 CTGTGGACTCTGTTGGTCGC 60.946 60.000 0.00 0.00 34.82 5.19
1524 1628 4.697756 TTCCTCTTGTGCCCGCCG 62.698 66.667 0.00 0.00 0.00 6.46
1717 1827 0.032117 TCCTCATCGTCCTCCCACAT 60.032 55.000 0.00 0.00 0.00 3.21
1718 1828 0.684479 CTCCTCATCGTCCTCCCACA 60.684 60.000 0.00 0.00 0.00 4.17
1719 1829 1.395826 CCTCCTCATCGTCCTCCCAC 61.396 65.000 0.00 0.00 0.00 4.61
1731 1841 3.005539 GGGCTCTGCACCTCCTCA 61.006 66.667 0.00 0.00 0.00 3.86
1792 1909 0.327259 ATCGATGGGATCCATGCAGG 59.673 55.000 15.23 0.00 45.26 4.85
1836 1957 3.751175 TGAACGAATTTCACCACTGGATC 59.249 43.478 0.71 0.00 39.45 3.36
1956 2089 3.817647 AGTACTCTTCCGTCGTTACAACT 59.182 43.478 0.00 0.00 0.00 3.16
1957 2090 4.152607 AGTACTCTTCCGTCGTTACAAC 57.847 45.455 0.00 0.00 0.00 3.32
1971 2117 4.835615 TCTGAAAGAGGAAGCAAGTACTCT 59.164 41.667 0.00 0.00 38.67 3.24
2000 2146 5.702349 AGTACAATATACTGACGCCTACC 57.298 43.478 0.00 0.00 0.00 3.18
2045 2191 5.751028 GCTAGTTCATGACCAATCTCTGTAC 59.249 44.000 0.00 0.00 0.00 2.90
2067 2213 3.930848 GCTTTATGTTACACGGTACTGCT 59.069 43.478 0.23 0.00 0.00 4.24
2073 2219 3.945346 TCCATGCTTTATGTTACACGGT 58.055 40.909 0.00 0.00 34.87 4.83
2088 2234 6.872020 CCAATAATCTCCAATTTCATCCATGC 59.128 38.462 0.00 0.00 0.00 4.06
2155 2322 2.839486 TCAAGTTTCATCGAGCCACT 57.161 45.000 0.00 0.00 0.00 4.00
2230 2501 3.647771 AGGGGTTCCTTCGTGGCC 61.648 66.667 0.00 0.00 41.56 5.36
2243 2514 0.883833 CTTGCAAGTTACAGCAGGGG 59.116 55.000 18.65 0.00 42.39 4.79
2308 2579 1.048601 AAACAGAGGCTTCCGTCTCA 58.951 50.000 0.00 0.00 44.38 3.27
2334 2609 1.719600 GCAGAGGCTAAGTGTCACAG 58.280 55.000 5.62 0.00 36.96 3.66
2440 2725 3.709880 TAATCACGCCACGCCGGAG 62.710 63.158 5.05 3.72 41.15 4.63
2445 2730 2.860628 CGAGCTAATCACGCCACGC 61.861 63.158 0.00 0.00 0.00 5.34
2450 2735 1.478137 ATTCGTCGAGCTAATCACGC 58.522 50.000 0.00 0.00 34.50 5.34
2490 2777 0.988832 ATTCCCCGGCTAAACACAGA 59.011 50.000 0.00 0.00 0.00 3.41
2575 2866 1.676006 CGAGGTTTGTTTCCACTTGCT 59.324 47.619 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.