Multiple sequence alignment - TraesCS4A01G181000

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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 TraesCS4A01G181000 chr4A 100.000 2254 0 0 1 2254 455273622 455271369 0.000000e+00 4163.0
1 TraesCS4A01G181000 chr4D 95.242 1135 42 7 1122 2254 118374437 118375561 0.000000e+00 1786.0
2 TraesCS4A01G181000 chr4D 92.586 1133 55 11 1 1119 118373223 118374340 0.000000e+00 1600.0
3 TraesCS4A01G181000 chr4D 94.650 486 23 1 1 486 114198176 114197694 0.000000e+00 750.0
4 TraesCS4A01G181000 chr4B 91.449 1111 59 13 1 1096 180560172 180561261 0.000000e+00 1493.0
5 TraesCS4A01G181000 chr4B 91.529 850 31 19 1148 1972 180561262 180562095 0.000000e+00 1133.0
6 TraesCS4A01G181000 chr4B 92.913 127 5 2 1983 2107 180562182 180562306 4.950000e-42 182.0
7 TraesCS4A01G181000 chr4B 85.625 160 9 1 2095 2254 180562630 180562775 3.000000e-34 156.0
8 TraesCS4A01G181000 chr5A 81.250 288 37 9 993 1263 330199701 330199414 1.360000e-52 217.0
9 TraesCS4A01G181000 chr5A 96.875 32 1 0 1295 1326 330199364 330199333 1.000000e-03 54.7
10 TraesCS4A01G181000 chr5D 80.364 275 39 10 993 1263 246303625 246303362 6.350000e-46 195.0
11 TraesCS4A01G181000 chr5D 100.000 29 0 0 1295 1323 246303312 246303284 1.000000e-03 54.7
12 TraesCS4A01G181000 chr5B 77.807 374 39 27 993 1326 280987914 280987545 8.220000e-45 191.0


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 TraesCS4A01G181000 chr4A 455271369 455273622 2253 True 4163 4163 100.000 1 2254 1 chr4A.!!$R1 2253
1 TraesCS4A01G181000 chr4D 118373223 118375561 2338 False 1693 1786 93.914 1 2254 2 chr4D.!!$F1 2253
2 TraesCS4A01G181000 chr4B 180560172 180562775 2603 False 741 1493 90.379 1 2254 4 chr4B.!!$F1 2253

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
224 225 0.460284 AGCGGCCGTCTTTCATAGTG 60.46 55.0 28.7 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1990 2212 0.539986 TTCTAGGACCCACCGATTGC 59.46 55.0 0.0 0.0 44.74 3.56 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
50 51 6.748333 TTCTTCATTGACATCAACCTGATC 57.252 37.500 0.00 0.00 38.86 2.92
171 172 5.639506 CAGGTTTATATCACGACCATGGATC 59.360 44.000 21.47 11.37 34.60 3.36
187 188 3.033909 TGGATCTGATCATCGTTGTCCT 58.966 45.455 18.64 0.00 0.00 3.85
190 191 1.405463 TCTGATCATCGTTGTCCTCCG 59.595 52.381 0.00 0.00 0.00 4.63
192 193 1.134367 TGATCATCGTTGTCCTCCGTC 59.866 52.381 0.00 0.00 0.00 4.79
224 225 0.460284 AGCGGCCGTCTTTCATAGTG 60.460 55.000 28.70 0.00 0.00 2.74
231 232 2.098607 CCGTCTTTCATAGTGGTAGCGA 59.901 50.000 0.00 0.00 0.00 4.93
245 246 2.609491 GGTAGCGATTCATGGCGTGATA 60.609 50.000 10.74 2.29 36.54 2.15
255 256 5.929697 TCATGGCGTGATAATCATTTCTC 57.070 39.130 5.03 0.00 0.00 2.87
262 263 6.295110 GCGTGATAATCATTTCTCGATGAAG 58.705 40.000 7.67 0.00 39.33 3.02
366 367 4.936411 GCTGCTGCTGATGATGAATAGTAT 59.064 41.667 10.92 0.00 36.03 2.12
427 431 4.559063 CATGCCAGCTCCCCCTCG 62.559 72.222 0.00 0.00 0.00 4.63
462 466 2.000447 CTAGTGCCAAACCTAGTTCGC 59.000 52.381 0.00 0.00 0.00 4.70
480 484 4.437682 TCGCCATCCAAGGAGATTAATT 57.562 40.909 0.00 0.00 32.24 1.40
710 718 1.135094 GATGGAAGGGGAGATGAGCA 58.865 55.000 0.00 0.00 0.00 4.26
764 774 5.464722 GTGACCTATGATGACTGCACATAAG 59.535 44.000 0.00 0.00 0.00 1.73
766 776 5.851720 ACCTATGATGACTGCACATAAGAG 58.148 41.667 0.00 0.00 0.00 2.85
770 780 3.443681 TGATGACTGCACATAAGAGTCGA 59.556 43.478 0.00 0.00 39.23 4.20
800 811 6.430864 TCAGGGCAAAATATACTGAATCCAA 58.569 36.000 0.00 0.00 35.45 3.53
801 812 6.894654 TCAGGGCAAAATATACTGAATCCAAA 59.105 34.615 0.00 0.00 35.45 3.28
802 813 7.068593 TCAGGGCAAAATATACTGAATCCAAAG 59.931 37.037 0.00 0.00 35.45 2.77
803 814 6.324770 AGGGCAAAATATACTGAATCCAAAGG 59.675 38.462 0.00 0.00 0.00 3.11
820 844 3.463048 AAGGAGGGCTGTGAAATTCAT 57.537 42.857 0.00 0.00 0.00 2.57
823 847 2.686915 GGAGGGCTGTGAAATTCATGAG 59.313 50.000 0.00 0.00 0.00 2.90
847 871 2.372074 GGACATACCCTGGCCGGAA 61.372 63.158 15.09 0.00 45.37 4.30
891 915 0.911769 ATCTGAAGGCCCATCGTCAA 59.088 50.000 0.00 0.00 0.00 3.18
912 936 8.263950 CGTCAATTAATTGCAGAATTAGCATTG 58.736 33.333 21.15 7.34 42.33 2.82
938 962 3.509442 TGCAAAGGGGAATCAGTGAAAT 58.491 40.909 0.00 0.00 0.00 2.17
971 995 2.786578 GCAAAAGACGACGATGCAAAAA 59.213 40.909 0.00 0.00 37.00 1.94
1070 1094 1.271379 GGACCAGCTTAGGAGTTGCAA 60.271 52.381 0.00 0.00 33.24 4.08
1103 1127 7.065216 AGATGAACATCAAGTTAACATGTCG 57.935 36.000 15.63 4.77 41.51 4.35
1106 1130 6.830736 TGAACATCAAGTTAACATGTCGATG 58.169 36.000 8.61 13.00 41.51 3.84
1119 1143 9.533253 TTAACATGTCGATGGATGCATATATAG 57.467 33.333 0.00 0.00 33.39 1.31
1120 1144 5.987953 ACATGTCGATGGATGCATATATAGC 59.012 40.000 0.00 0.00 33.39 2.97
1127 1245 7.452813 TCGATGGATGCATATATAGCTAGGATT 59.547 37.037 0.00 0.00 0.00 3.01
1136 1254 9.401058 GCATATATAGCTAGGATTGTGGAAAAT 57.599 33.333 0.00 0.00 0.00 1.82
1151 1269 4.567159 GTGGAAAATGAGAGTAGGCTTACG 59.433 45.833 0.00 0.00 34.88 3.18
1203 1327 1.676384 GAAGCAGTGGTGGAGCTCT 59.324 57.895 14.64 0.00 37.70 4.09
1239 1363 1.609580 CGGGGATTCTTGGAACGAACA 60.610 52.381 0.00 0.00 0.00 3.18
1251 1375 2.180159 AACGAACATAGGGGCGCACT 62.180 55.000 10.74 9.64 0.00 4.40
1417 1541 0.249238 ATGATCGAGGCGCTTGAGAC 60.249 55.000 7.64 2.71 0.00 3.36
1592 1735 3.197333 ACAGAAGTGAGCTCATGCATACT 59.803 43.478 21.47 8.14 42.74 2.12
1593 1736 3.803231 CAGAAGTGAGCTCATGCATACTC 59.197 47.826 21.47 13.83 42.74 2.59
1594 1737 2.906691 AGTGAGCTCATGCATACTCC 57.093 50.000 21.47 3.18 42.74 3.85
1595 1738 2.396608 AGTGAGCTCATGCATACTCCT 58.603 47.619 21.47 5.75 42.74 3.69
1596 1739 3.570540 AGTGAGCTCATGCATACTCCTA 58.429 45.455 21.47 0.00 42.74 2.94
1597 1740 3.320541 AGTGAGCTCATGCATACTCCTAC 59.679 47.826 21.47 1.59 42.74 3.18
1674 1817 4.013267 AGTGAGGTGGTGAAAGATTGAG 57.987 45.455 0.00 0.00 0.00 3.02
1740 1884 6.366340 TGTATACCTAAGGAGAGAAGGACAG 58.634 44.000 0.00 0.00 34.34 3.51
1856 2000 4.816925 GTGTGGCTTTCACTTTCTCTAGTT 59.183 41.667 0.00 0.00 46.20 2.24
1889 2033 1.761784 AGAGATCTAAGGCCAGCACTG 59.238 52.381 5.01 0.00 0.00 3.66
2039 2261 0.041312 ACATCACAAGCGCACGTTTC 60.041 50.000 11.47 0.00 0.00 2.78
2043 2265 0.771756 CACAAGCGCACGTTTCATTG 59.228 50.000 11.47 5.06 0.00 2.82
2076 2299 0.674895 GCAGATCAGTGCCGACCTTT 60.675 55.000 0.00 0.00 37.49 3.11
2077 2300 1.813513 CAGATCAGTGCCGACCTTTT 58.186 50.000 0.00 0.00 0.00 2.27
2218 2778 6.694447 AGGTCAATCGTTTGCTTAGTAGTAA 58.306 36.000 1.18 0.00 32.61 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 3.931468 ACAAGCAGAAGAAGATGATGACG 59.069 43.478 0.00 0.00 0.00 4.35
171 172 1.135139 ACGGAGGACAACGATGATCAG 59.865 52.381 0.09 0.00 0.00 2.90
187 188 2.126071 GCAAGCTGCTACGACGGA 60.126 61.111 0.90 0.00 40.96 4.69
224 225 0.529773 TCACGCCATGAATCGCTACC 60.530 55.000 0.00 0.00 33.02 3.18
231 232 6.347969 CGAGAAATGATTATCACGCCATGAAT 60.348 38.462 0.00 0.00 41.93 2.57
245 246 7.507829 AGAATCCTCTTCATCGAGAAATGATT 58.492 34.615 0.00 4.10 35.65 2.57
255 256 4.399004 AGTCCAAGAATCCTCTTCATCG 57.601 45.455 0.00 0.00 40.05 3.84
262 263 5.526846 CAGCTTTGATAGTCCAAGAATCCTC 59.473 44.000 0.00 0.00 0.00 3.71
366 367 4.036971 CACCGTTTACTTGGATCAAAACCA 59.963 41.667 0.00 0.00 35.47 3.67
427 431 2.224161 GCACTAGACCATGTCCTCCATC 60.224 54.545 0.00 0.00 32.18 3.51
462 466 7.512992 ACTGACTAATTAATCTCCTTGGATGG 58.487 38.462 0.00 0.00 0.00 3.51
615 623 5.649782 AAATTGCCCTCTACACATTCAAG 57.350 39.130 0.00 0.00 0.00 3.02
710 718 6.684538 ACAGGGAGGACAAGTCTATAACTAT 58.315 40.000 0.00 0.00 37.17 2.12
764 774 1.323271 TGCCCTGATCTGGTCGACTC 61.323 60.000 16.46 5.51 0.00 3.36
766 776 0.036388 TTTGCCCTGATCTGGTCGAC 60.036 55.000 16.63 7.13 0.00 4.20
770 780 5.132648 TCAGTATATTTTGCCCTGATCTGGT 59.867 40.000 16.63 0.70 0.00 4.00
800 811 2.978156 TGAATTTCACAGCCCTCCTT 57.022 45.000 0.00 0.00 0.00 3.36
801 812 2.309755 TCATGAATTTCACAGCCCTCCT 59.690 45.455 0.15 0.00 0.00 3.69
802 813 2.686915 CTCATGAATTTCACAGCCCTCC 59.313 50.000 0.15 0.00 0.00 4.30
803 814 3.350833 ACTCATGAATTTCACAGCCCTC 58.649 45.455 0.15 0.00 0.00 4.30
820 844 1.548719 CAGGGTATGTCCACGAACTCA 59.451 52.381 0.00 0.00 38.11 3.41
823 847 0.743345 GCCAGGGTATGTCCACGAAC 60.743 60.000 0.00 0.00 38.11 3.95
847 871 4.573900 ACAGAAGCAAGAAGATTGACGAT 58.426 39.130 0.00 0.00 0.00 3.73
891 915 5.176223 GCGCAATGCTAATTCTGCAATTAAT 59.824 36.000 0.30 0.00 44.01 1.40
912 936 1.227060 GATTCCCCTTTGCATGCGC 60.227 57.895 14.09 0.00 39.24 6.09
938 962 2.096466 CGTCTTTTGCTGTGCGTTCATA 60.096 45.455 0.00 0.00 0.00 2.15
971 995 6.757010 CAGGTACGCATCACTTTACTTCTTAT 59.243 38.462 0.00 0.00 0.00 1.73
1054 1078 1.198637 GCAGTTGCAACTCCTAAGCTG 59.801 52.381 28.97 16.72 41.59 4.24
1070 1094 4.581824 ACTTGATGTTCATCTTTGTGCAGT 59.418 37.500 12.94 3.06 0.00 4.40
1080 1104 7.060600 TCGACATGTTAACTTGATGTTCATC 57.939 36.000 23.89 10.77 39.89 2.92
1103 1127 8.373981 ACAATCCTAGCTATATATGCATCCATC 58.626 37.037 0.19 0.00 32.85 3.51
1106 1130 6.933521 CCACAATCCTAGCTATATATGCATCC 59.066 42.308 0.19 0.00 0.00 3.51
1119 1143 5.189180 ACTCTCATTTTCCACAATCCTAGC 58.811 41.667 0.00 0.00 0.00 3.42
1120 1144 6.989169 CCTACTCTCATTTTCCACAATCCTAG 59.011 42.308 0.00 0.00 0.00 3.02
1127 1245 4.640771 AAGCCTACTCTCATTTTCCACA 57.359 40.909 0.00 0.00 0.00 4.17
1136 1254 3.632604 CCAAGATCGTAAGCCTACTCTCA 59.367 47.826 0.00 0.00 37.18 3.27
1137 1255 3.551250 GCCAAGATCGTAAGCCTACTCTC 60.551 52.174 0.00 0.00 37.18 3.20
1138 1256 2.362717 GCCAAGATCGTAAGCCTACTCT 59.637 50.000 0.00 0.00 37.18 3.24
1239 1363 2.758327 TCGTCAGTGCGCCCCTAT 60.758 61.111 4.18 0.00 0.00 2.57
1417 1541 2.624838 ACAACAACAGCCTCAAATCAGG 59.375 45.455 0.00 0.00 36.50 3.86
1563 1706 2.036475 TGAGCTCACTTCTGTTGTCTCC 59.964 50.000 13.74 0.00 0.00 3.71
1592 1735 7.684317 TCCAAAGTCCACATATAATGTAGGA 57.316 36.000 6.95 6.95 42.70 2.94
1593 1736 7.445402 CCTTCCAAAGTCCACATATAATGTAGG 59.555 40.741 0.00 0.00 42.70 3.18
1594 1737 8.210946 TCCTTCCAAAGTCCACATATAATGTAG 58.789 37.037 0.00 0.00 42.70 2.74
1595 1738 8.096621 TCCTTCCAAAGTCCACATATAATGTA 57.903 34.615 0.00 0.00 42.70 2.29
1596 1739 6.969043 TCCTTCCAAAGTCCACATATAATGT 58.031 36.000 0.00 0.00 46.22 2.71
1597 1740 7.469181 GCTTCCTTCCAAAGTCCACATATAATG 60.469 40.741 0.00 0.00 0.00 1.90
1856 2000 6.476378 CCTTAGATCTCTCTTTTCCAAACCA 58.524 40.000 0.00 0.00 32.66 3.67
1889 2033 6.862711 AGCTGGACTTTTTAGTTAGTGTTC 57.137 37.500 0.00 0.00 0.00 3.18
1990 2212 0.539986 TTCTAGGACCCACCGATTGC 59.460 55.000 0.00 0.00 44.74 3.56
2169 2729 4.679373 ATGATGTCTACCCTGTGATGTC 57.321 45.455 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.