Multiple sequence alignment - TraesCS5B01G309400

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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 TraesCS5B01G309400 chr5B 100.000 2264 0 0 1 2264 491840949 491838686 0 4181
1 TraesCS5B01G309400 chr5B 91.746 836 69 0 1429 2264 378066697 378065862 0 1162
2 TraesCS5B01G309400 chr5B 91.148 836 71 3 1429 2264 566133810 566134642 0 1131
3 TraesCS5B01G309400 chr5B 90.562 837 71 5 1429 2264 489173769 489172940 0 1101
4 TraesCS5B01G309400 chr6D 95.238 1428 64 4 1 1426 293060949 293059524 0 2257
5 TraesCS5B01G309400 chr3D 95.175 1430 66 3 1 1428 62370598 62369170 0 2255
6 TraesCS5B01G309400 chr1D 93.697 1428 82 4 1 1426 297552132 297550711 0 2132
7 TraesCS5B01G309400 chr5D 93.366 1432 89 4 1 1426 313383468 313382037 0 2113
8 TraesCS5B01G309400 chr5D 92.087 1428 75 17 1 1426 387840643 387839252 0 1977
9 TraesCS5B01G309400 chr3A 92.717 1428 93 6 1 1426 145558982 145557564 0 2050
10 TraesCS5B01G309400 chr7B 92.509 1415 97 4 14 1426 315602075 315600668 0 2017
11 TraesCS5B01G309400 chr7B 91.036 1428 86 18 1 1426 34282268 34280881 0 1890
12 TraesCS5B01G309400 chr7B 93.134 801 53 2 1 799 315291373 315290573 0 1173
13 TraesCS5B01G309400 chr7B 91.116 833 74 0 1432 2264 55432748 55433580 0 1129
14 TraesCS5B01G309400 chr7B 90.453 838 73 4 1429 2264 75855474 75856306 0 1098
15 TraesCS5B01G309400 chr4A 92.351 1425 97 6 4 1426 664930506 664929092 0 2017
16 TraesCS5B01G309400 chr2D 95.652 920 35 3 508 1426 641205598 641204683 0 1472
17 TraesCS5B01G309400 chr4B 92.721 838 60 1 1427 2264 541441413 541440577 0 1208
18 TraesCS5B01G309400 chr4B 92.252 826 61 3 1429 2252 521497417 521498241 0 1168
19 TraesCS5B01G309400 chr2B 91.527 838 54 8 1 837 596098501 596099322 0 1138
20 TraesCS5B01G309400 chr3B 91.071 840 75 0 1425 2264 658683155 658683994 0 1136
21 TraesCS5B01G309400 chr3B 90.920 837 76 0 1428 2264 177159976 177159140 0 1125


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 TraesCS5B01G309400 chr5B 491838686 491840949 2263 True 4181 4181 100.000 1 2264 1 chr5B.!!$R3 2263
1 TraesCS5B01G309400 chr5B 378065862 378066697 835 True 1162 1162 91.746 1429 2264 1 chr5B.!!$R1 835
2 TraesCS5B01G309400 chr5B 566133810 566134642 832 False 1131 1131 91.148 1429 2264 1 chr5B.!!$F1 835
3 TraesCS5B01G309400 chr5B 489172940 489173769 829 True 1101 1101 90.562 1429 2264 1 chr5B.!!$R2 835
4 TraesCS5B01G309400 chr6D 293059524 293060949 1425 True 2257 2257 95.238 1 1426 1 chr6D.!!$R1 1425
5 TraesCS5B01G309400 chr3D 62369170 62370598 1428 True 2255 2255 95.175 1 1428 1 chr3D.!!$R1 1427
6 TraesCS5B01G309400 chr1D 297550711 297552132 1421 True 2132 2132 93.697 1 1426 1 chr1D.!!$R1 1425
7 TraesCS5B01G309400 chr5D 313382037 313383468 1431 True 2113 2113 93.366 1 1426 1 chr5D.!!$R1 1425
8 TraesCS5B01G309400 chr5D 387839252 387840643 1391 True 1977 1977 92.087 1 1426 1 chr5D.!!$R2 1425
9 TraesCS5B01G309400 chr3A 145557564 145558982 1418 True 2050 2050 92.717 1 1426 1 chr3A.!!$R1 1425
10 TraesCS5B01G309400 chr7B 315600668 315602075 1407 True 2017 2017 92.509 14 1426 1 chr7B.!!$R3 1412
11 TraesCS5B01G309400 chr7B 34280881 34282268 1387 True 1890 1890 91.036 1 1426 1 chr7B.!!$R1 1425
12 TraesCS5B01G309400 chr7B 315290573 315291373 800 True 1173 1173 93.134 1 799 1 chr7B.!!$R2 798
13 TraesCS5B01G309400 chr7B 55432748 55433580 832 False 1129 1129 91.116 1432 2264 1 chr7B.!!$F1 832
14 TraesCS5B01G309400 chr7B 75855474 75856306 832 False 1098 1098 90.453 1429 2264 1 chr7B.!!$F2 835
15 TraesCS5B01G309400 chr4A 664929092 664930506 1414 True 2017 2017 92.351 4 1426 1 chr4A.!!$R1 1422
16 TraesCS5B01G309400 chr2D 641204683 641205598 915 True 1472 1472 95.652 508 1426 1 chr2D.!!$R1 918
17 TraesCS5B01G309400 chr4B 541440577 541441413 836 True 1208 1208 92.721 1427 2264 1 chr4B.!!$R1 837
18 TraesCS5B01G309400 chr4B 521497417 521498241 824 False 1168 1168 92.252 1429 2252 1 chr4B.!!$F1 823
19 TraesCS5B01G309400 chr2B 596098501 596099322 821 False 1138 1138 91.527 1 837 1 chr2B.!!$F1 836
20 TraesCS5B01G309400 chr3B 658683155 658683994 839 False 1136 1136 91.071 1425 2264 1 chr3B.!!$F1 839
21 TraesCS5B01G309400 chr3B 177159140 177159976 836 True 1125 1125 90.920 1428 2264 1 chr3B.!!$R1 836

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
166 168 0.098552 CGCATTTGATAACGGCAGCA 59.901 50.0 0.0 0.0 0.00 4.41 F
870 884 0.321741 TCGGCCTTCGGTTATTTGCA 60.322 50.0 0.0 0.0 39.77 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1003 1018 0.613777 GTCCTGGAACCGGATGAAGT 59.386 55.000 9.46 0.0 32.25 3.01 R
1812 1834 1.271488 GGGGACACGATGTTTACCCAA 60.271 52.381 0.00 0.0 38.30 4.12 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
57 58 2.335369 GTGGCACGACACGAGACT 59.665 61.111 0.00 0.00 0.00 3.24
90 91 0.467844 TGGTGCTGCATTTGAGGTGT 60.468 50.000 5.27 0.00 0.00 4.16
166 168 0.098552 CGCATTTGATAACGGCAGCA 59.901 50.000 0.00 0.00 0.00 4.41
269 272 1.202348 CGCCTTGATTTCACCCTTTCC 59.798 52.381 0.00 0.00 0.00 3.13
315 318 4.662966 ATCATGGCCCTCATATTAAGCA 57.337 40.909 0.00 0.00 34.12 3.91
361 364 5.160386 ACCAAGGGTAGAAGGAGAACTAAA 58.840 41.667 0.00 0.00 32.11 1.85
376 379 3.503800 ACTAAAAGGTTCAGGGGTGAC 57.496 47.619 0.00 0.00 0.00 3.67
643 651 2.032681 GACAGAGGTGGTGGTGGC 59.967 66.667 0.00 0.00 0.00 5.01
660 668 3.111939 CGGTCGTAGAGGGAGCAG 58.888 66.667 0.00 0.00 36.95 4.24
677 685 2.007360 CAGAAGTGCTAGAGGTGCTG 57.993 55.000 0.00 0.00 0.00 4.41
692 700 2.722201 GCTGGTGGTCGTAGAGGGG 61.722 68.421 0.00 0.00 36.95 4.79
756 770 1.982395 CTAGAGGCGGTGGTGGTCA 60.982 63.158 0.00 0.00 0.00 4.02
757 771 1.305802 TAGAGGCGGTGGTGGTCAT 60.306 57.895 0.00 0.00 0.00 3.06
790 804 1.157513 TGCTAGAGGTGGTGGTGGA 59.842 57.895 0.00 0.00 0.00 4.02
870 884 0.321741 TCGGCCTTCGGTTATTTGCA 60.322 50.000 0.00 0.00 39.77 4.08
1028 1043 4.796231 CGGTTCCAGGACGAGGCG 62.796 72.222 0.00 0.00 0.00 5.52
1520 1536 7.531857 TGAAGATACAAGACTGAAGACTCTT 57.468 36.000 0.00 0.00 0.00 2.85
1625 1641 3.502051 TGTACAACCCTAATCCCCTCT 57.498 47.619 0.00 0.00 0.00 3.69
1694 1714 9.331466 ACATACTCAATCATAATCCTCATAGGT 57.669 33.333 0.00 0.00 36.53 3.08
1812 1834 1.123928 CGATAGAGAGGGCCCAAACT 58.876 55.000 27.56 20.01 39.76 2.66
1923 1945 2.627699 ACCGACATTGGTGCTTTCATTT 59.372 40.909 0.00 0.00 41.85 2.32
1933 1955 3.751698 GGTGCTTTCATTTAGAGTTCCGT 59.248 43.478 0.00 0.00 0.00 4.69
2076 2099 1.067060 CCATCGAGCGGACAATGACTA 59.933 52.381 0.00 0.00 0.00 2.59
2170 2193 7.117812 GTCATCTTTAAACGAACTCCTTGATCA 59.882 37.037 0.00 0.00 0.00 2.92
2178 2201 1.198713 ACTCCTTGATCACATCGCCT 58.801 50.000 0.00 0.00 0.00 5.52
2199 2222 1.982395 CTGGGGGTCGCTACAGACA 60.982 63.158 6.37 0.00 42.62 3.41
2256 2279 2.187958 TCAAATCTCCACCGATCACCT 58.812 47.619 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 7.254455 CCACCATATTGAAAATAGTCTCGTGTC 60.254 40.741 0.00 0.00 0.00 3.67
57 58 4.708909 TGCAGCACCACCATATTGAAAATA 59.291 37.500 0.00 0.00 0.00 1.40
269 272 1.492176 AGGCCACTATGATTGGTCCAG 59.508 52.381 5.01 0.00 39.83 3.86
361 364 0.405585 CCATGTCACCCCTGAACCTT 59.594 55.000 0.00 0.00 0.00 3.50
376 379 0.477204 ATCCAGCCAGGTCATCCATG 59.523 55.000 0.00 0.00 39.02 3.66
463 467 4.980805 TGTCGCCCTTCACCGCAC 62.981 66.667 0.00 0.00 0.00 5.34
643 651 1.030488 TTCTGCTCCCTCTACGACCG 61.030 60.000 0.00 0.00 0.00 4.79
660 668 0.610687 ACCAGCACCTCTAGCACTTC 59.389 55.000 0.00 0.00 0.00 3.01
677 685 3.468140 GCCCCCTCTACGACCACC 61.468 72.222 0.00 0.00 0.00 4.61
692 700 1.017387 GCACCTATAGCACTTGTGCC 58.983 55.000 20.39 4.86 44.89 5.01
705 713 0.115547 TCTACCACCACCAGCACCTA 59.884 55.000 0.00 0.00 0.00 3.08
745 759 1.137086 CTTCCTCTATGACCACCACCG 59.863 57.143 0.00 0.00 0.00 4.94
756 770 4.026744 TCTAGCACTTGTGCTTCCTCTAT 58.973 43.478 29.37 8.95 43.52 1.98
757 771 3.431415 TCTAGCACTTGTGCTTCCTCTA 58.569 45.455 29.37 12.41 43.52 2.43
790 804 1.605712 GCACTTGTGCTTCCTCTACGT 60.606 52.381 17.36 0.00 0.00 3.57
811 825 1.183030 TACGACCACCACCACCTCTG 61.183 60.000 0.00 0.00 0.00 3.35
956 970 4.626042 AGCACAAGACACAAAGAGAGTAG 58.374 43.478 0.00 0.00 0.00 2.57
1003 1018 0.613777 GTCCTGGAACCGGATGAAGT 59.386 55.000 9.46 0.00 32.25 3.01
1028 1043 3.041940 CTTGGTCCGTGCACGACC 61.042 66.667 39.10 36.19 43.02 4.79
1131 1146 0.738389 ACACCTTCACCTTGCAAACG 59.262 50.000 0.00 0.00 0.00 3.60
1226 1241 2.093181 AGGTCATATGCGTTAGTTGGCA 60.093 45.455 0.00 0.00 44.29 4.92
1400 1416 4.499188 CCTCCGTAAGCAATCTCGATGTTA 60.499 45.833 0.00 0.00 0.00 2.41
1465 1481 0.916086 TCCGGCCCACATCAATAGTT 59.084 50.000 0.00 0.00 0.00 2.24
1540 1556 1.303643 GCCTTCCACACCAAGGAGG 60.304 63.158 2.52 0.00 42.94 4.30
1625 1641 2.635915 CCTCCGGTTTATATAGGCACCA 59.364 50.000 0.00 0.00 0.00 4.17
1694 1714 6.886178 AATGGCTAAACCCTAGAAGTCTAA 57.114 37.500 0.00 0.00 37.83 2.10
1808 1830 3.566742 GGACACGATGTTTACCCAAGTTT 59.433 43.478 0.00 0.00 0.00 2.66
1812 1834 1.271488 GGGGACACGATGTTTACCCAA 60.271 52.381 0.00 0.00 38.30 4.12
1923 1945 2.815503 TCGATGTCACAACGGAACTCTA 59.184 45.455 7.69 0.00 30.83 2.43
1933 1955 6.220726 TCAATCCTATCTTCGATGTCACAA 57.779 37.500 0.00 0.00 0.00 3.33
2065 2088 1.822990 TGACCCGAGTAGTCATTGTCC 59.177 52.381 0.00 0.00 39.29 4.02
2076 2099 1.922570 CGATTTTCGATGACCCGAGT 58.077 50.000 0.00 0.00 43.74 4.18
2199 2222 3.694566 GGTTTAAGCCCGATCTGATTGTT 59.305 43.478 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.