Multiple sequence alignment - TraesCS4B01G214900

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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 TraesCS4B01G214900 chr4B 100.000 2330 0 0 1 2330 454522061 454524390 0.000000e+00 4303
1 TraesCS4B01G214900 chr2B 93.309 1614 101 3 718 2330 589255464 589257071 0.000000e+00 2375
2 TraesCS4B01G214900 chr2B 90.884 724 61 2 1 724 589254723 589255441 0.000000e+00 966
3 TraesCS4B01G214900 chr4A 89.838 1604 156 6 726 2327 565825434 565827032 0.000000e+00 2052
4 TraesCS4B01G214900 chr4A 87.870 709 85 1 16 724 565824695 565825402 0.000000e+00 832
5 TraesCS4B01G214900 chr6A 82.065 2353 350 43 22 2330 522519593 522521917 0.000000e+00 1941
6 TraesCS4B01G214900 chr6A 80.381 1626 274 39 723 2330 380202752 380201154 0.000000e+00 1194
7 TraesCS4B01G214900 chr5D 87.167 1613 197 9 722 2330 400275141 400273535 0.000000e+00 1823
8 TraesCS4B01G214900 chr5D 93.939 66 4 0 659 724 400275233 400275168 1.470000e-17 100
9 TraesCS4B01G214900 chr5B 80.859 2351 396 32 18 2330 263539038 263541372 0.000000e+00 1799
10 TraesCS4B01G214900 chr6B 90.487 1335 124 1 996 2330 55648829 55647498 0.000000e+00 1759
11 TraesCS4B01G214900 chr3A 82.343 1869 289 23 496 2330 456799502 456797641 0.000000e+00 1585
12 TraesCS4B01G214900 chr1D 86.555 1309 170 5 1023 2330 229404510 229403207 0.000000e+00 1437
13 TraesCS4B01G214900 chr7D 81.728 405 64 10 725 1123 632376222 632376622 1.730000e-86 329


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 TraesCS4B01G214900 chr4B 454522061 454524390 2329 False 4303.0 4303 100.0000 1 2330 1 chr4B.!!$F1 2329
1 TraesCS4B01G214900 chr2B 589254723 589257071 2348 False 1670.5 2375 92.0965 1 2330 2 chr2B.!!$F1 2329
2 TraesCS4B01G214900 chr4A 565824695 565827032 2337 False 1442.0 2052 88.8540 16 2327 2 chr4A.!!$F1 2311
3 TraesCS4B01G214900 chr6A 522519593 522521917 2324 False 1941.0 1941 82.0650 22 2330 1 chr6A.!!$F1 2308
4 TraesCS4B01G214900 chr6A 380201154 380202752 1598 True 1194.0 1194 80.3810 723 2330 1 chr6A.!!$R1 1607
5 TraesCS4B01G214900 chr5D 400273535 400275233 1698 True 961.5 1823 90.5530 659 2330 2 chr5D.!!$R1 1671
6 TraesCS4B01G214900 chr5B 263539038 263541372 2334 False 1799.0 1799 80.8590 18 2330 1 chr5B.!!$F1 2312
7 TraesCS4B01G214900 chr6B 55647498 55648829 1331 True 1759.0 1759 90.4870 996 2330 1 chr6B.!!$R1 1334
8 TraesCS4B01G214900 chr3A 456797641 456799502 1861 True 1585.0 1585 82.3430 496 2330 1 chr3A.!!$R1 1834
9 TraesCS4B01G214900 chr1D 229403207 229404510 1303 True 1437.0 1437 86.5550 1023 2330 1 chr1D.!!$R1 1307

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
60 61 0.304098 GCAAGCTGCATCGAGACATC 59.696 55.0 1.02 0.0 44.26 3.06 F
957 1026 0.388134 CGTCGTCGTTCAATCCTGGT 60.388 55.0 0.00 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1328 1397 0.879765 CCCGTAGACTGTCGTCAACT 59.120 55.000 1.52 0.0 42.73 3.16 R
1953 2023 1.918609 GGTCGACGTTCTTGTGCTATC 59.081 52.381 9.92 0.0 0.00 2.08 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
59 60 1.426816 CGCAAGCTGCATCGAGACAT 61.427 55.000 1.02 0.00 45.36 3.06
60 61 0.304098 GCAAGCTGCATCGAGACATC 59.696 55.000 1.02 0.00 44.26 3.06
123 124 3.243053 TTCGAGGGGGCCAAACGA 61.243 61.111 4.39 10.01 0.00 3.85
147 148 3.387225 GACTCCACCTAAGCGCCCC 62.387 68.421 2.29 0.00 0.00 5.80
211 212 1.214175 TCAACAAGCCCCTCAGTTTCA 59.786 47.619 0.00 0.00 0.00 2.69
212 213 2.158475 TCAACAAGCCCCTCAGTTTCAT 60.158 45.455 0.00 0.00 0.00 2.57
255 256 3.696518 ATCGCTGGACCTAGGGCCA 62.697 63.158 35.06 35.06 0.00 5.36
256 257 3.399181 CGCTGGACCTAGGGCCAA 61.399 66.667 36.36 20.36 30.91 4.52
301 302 4.293648 CCACCACGACCTCGCACA 62.294 66.667 0.00 0.00 44.43 4.57
404 405 2.163815 CGACACTCCCGTTCTTCACTAT 59.836 50.000 0.00 0.00 0.00 2.12
535 536 2.274948 ATCATCAGTGCCCCATGCGT 62.275 55.000 0.00 0.00 45.60 5.24
538 539 1.626356 ATCAGTGCCCCATGCGTAGT 61.626 55.000 0.00 0.00 45.60 2.73
540 541 2.824041 GTGCCCCATGCGTAGTGG 60.824 66.667 0.00 0.00 45.60 4.00
570 572 2.215625 TTTGGTGCATGGCCTTGGG 61.216 57.895 19.47 0.10 0.00 4.12
571 573 2.669744 TTTGGTGCATGGCCTTGGGA 62.670 55.000 19.47 0.00 0.00 4.37
572 574 2.042639 GGTGCATGGCCTTGGGAT 60.043 61.111 19.47 0.00 0.00 3.85
573 575 1.686800 GGTGCATGGCCTTGGGATT 60.687 57.895 19.47 0.00 0.00 3.01
574 576 1.266867 GGTGCATGGCCTTGGGATTT 61.267 55.000 19.47 0.00 0.00 2.17
757 824 4.138290 AGATTCTCACCGTAGTCGATGAT 58.862 43.478 0.00 0.00 39.02 2.45
800 867 7.930325 GGTGAAGTTAGGAAGTAGTTTGTTAGT 59.070 37.037 0.00 0.00 0.00 2.24
884 951 4.813235 GCCTATTGGTGGCCGCCA 62.813 66.667 34.47 34.47 44.32 5.69
916 984 2.880443 TGGTAGGGAAGTGTACTCGTT 58.120 47.619 0.00 0.00 0.00 3.85
927 995 7.254863 GGGAAGTGTACTCGTTGTTATTTTCAA 60.255 37.037 0.00 0.00 0.00 2.69
957 1026 0.388134 CGTCGTCGTTCAATCCTGGT 60.388 55.000 0.00 0.00 0.00 4.00
958 1027 1.347320 GTCGTCGTTCAATCCTGGTC 58.653 55.000 0.00 0.00 0.00 4.02
1059 1128 2.116125 GGCCTGAACAACCCAGCT 59.884 61.111 0.00 0.00 0.00 4.24
1079 1148 2.494918 GCGATCCGTAGTGCAGGT 59.505 61.111 0.00 0.00 0.00 4.00
1115 1184 2.048222 CCTCGCCGTTCTCTGCAA 60.048 61.111 0.00 0.00 0.00 4.08
1154 1223 2.526432 AGAGTGGACACCAGTAATCGT 58.474 47.619 0.00 0.00 37.30 3.73
1305 1374 1.116536 TCACGGCCAAGGTCACTGTA 61.117 55.000 2.24 0.00 0.00 2.74
1565 1635 5.807011 AGATCAAATGCAAAAATAGGCGTTC 59.193 36.000 0.00 0.00 38.23 3.95
1630 1700 3.953612 AGACAAGTTTTTCTGCACCATCA 59.046 39.130 0.00 0.00 0.00 3.07
1765 1835 3.826157 TCGTTTTGAATCTTTCTGGCCAT 59.174 39.130 5.51 0.00 0.00 4.40
1868 1938 2.899900 TCAAGATGCATCGGGTAGCTAT 59.100 45.455 20.67 0.00 0.00 2.97
2259 2329 0.537188 CTAGGCAGAACCGACCACAT 59.463 55.000 0.00 0.00 46.52 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.001514 CAGGGACCTGGACATGGG 58.998 66.667 10.55 0.00 40.17 4.00
59 60 1.044790 TGCAGATGAGGAGGATGCGA 61.045 55.000 0.00 0.00 39.74 5.10
60 61 0.879400 GTGCAGATGAGGAGGATGCG 60.879 60.000 0.00 0.00 39.74 4.73
211 212 3.834799 GCCCCCGTCTTCGTCGAT 61.835 66.667 0.00 0.00 35.01 3.59
255 256 4.988598 CGCACCAGGGACAGCGTT 62.989 66.667 13.38 0.00 44.67 4.84
535 536 0.475044 AAACGGAAGGTTGCCCACTA 59.525 50.000 0.00 0.00 41.31 2.74
570 572 2.781681 TCTCCTTCGGTCCCAAAATC 57.218 50.000 0.00 0.00 0.00 2.17
571 573 2.642807 TCTTCTCCTTCGGTCCCAAAAT 59.357 45.455 0.00 0.00 0.00 1.82
572 574 2.051692 TCTTCTCCTTCGGTCCCAAAA 58.948 47.619 0.00 0.00 0.00 2.44
573 575 1.724545 TCTTCTCCTTCGGTCCCAAA 58.275 50.000 0.00 0.00 0.00 3.28
574 576 1.555075 CATCTTCTCCTTCGGTCCCAA 59.445 52.381 0.00 0.00 0.00 4.12
614 622 4.717629 CGAAGCGACGGGTGAGCA 62.718 66.667 0.00 0.00 0.00 4.26
800 867 1.731613 CAACTCGCAAGCCGTACGA 60.732 57.895 18.76 0.00 38.35 3.43
884 951 2.375345 CCTACCATCCGGGGTTGCT 61.375 63.158 7.77 0.00 42.42 3.91
927 995 6.932901 TTGAACGACGACGATTACTTTTAT 57.067 33.333 15.32 0.00 42.66 1.40
958 1027 4.729918 GACTGGCCCTGGGTGCAG 62.730 72.222 15.56 4.11 0.00 4.41
1079 1148 2.465299 CGGTGTGTGTTTGCCGTGA 61.465 57.895 0.00 0.00 39.41 4.35
1105 1174 1.609072 GGTTTCCTGGTTGCAGAGAAC 59.391 52.381 0.00 0.00 0.00 3.01
1115 1184 2.091885 TCTTCAAGCTTGGTTTCCTGGT 60.092 45.455 25.73 0.00 0.00 4.00
1154 1223 1.003051 GGGCCTCCTACTTCCCTGA 59.997 63.158 0.84 0.00 35.87 3.86
1323 1392 4.615961 CCGTAGACTGTCGTCAACTAAAAG 59.384 45.833 1.52 0.00 42.73 2.27
1328 1397 0.879765 CCCGTAGACTGTCGTCAACT 59.120 55.000 1.52 0.00 42.73 3.16
1565 1635 1.517257 CGCTCGCTACTCCAAGTGG 60.517 63.158 0.00 0.00 0.00 4.00
1840 1910 2.684374 CCCGATGCATCTTGATGTTCAA 59.316 45.455 23.73 0.00 34.79 2.69
1868 1938 7.093465 ACGATCTACTCCAAATCTTTAAGTCCA 60.093 37.037 0.00 0.00 0.00 4.02
1953 2023 1.918609 GGTCGACGTTCTTGTGCTATC 59.081 52.381 9.92 0.00 0.00 2.08
2063 2133 3.244561 CCGTAGCCATGTTATCCTGGATT 60.245 47.826 15.55 0.00 34.24 3.01
2259 2329 3.995048 CGATGTAGCTCCAGTCGATAGTA 59.005 47.826 0.00 0.00 34.46 1.82


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

AutoCloner maintained by Alex Coulton.