Multiple sequence alignment - TraesCS5B01G238000

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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 TraesCS5B01G238000 chr5B 100.000 2585 0 0 1 2585 418817072 418814488 0.000000e+00 4774.0
1 TraesCS5B01G238000 chr5D 94.043 2367 70 19 245 2585 354506199 354503878 0.000000e+00 3524.0
2 TraesCS5B01G238000 chr5D 95.102 245 11 1 7 250 354506603 354506359 4.040000e-103 385.0
3 TraesCS5B01G238000 chr5A 92.411 2372 99 36 245 2585 455469347 455467026 0.000000e+00 3308.0
4 TraesCS5B01G238000 chr5A 94.884 215 9 2 7 220 455469848 455469635 4.120000e-88 335.0
5 TraesCS5B01G238000 chr7D 77.913 1313 181 45 414 1683 11677290 11676044 0.000000e+00 717.0
6 TraesCS5B01G238000 chr6A 82.913 357 44 6 2229 2585 42922690 42923029 3.230000e-79 305.0
7 TraesCS5B01G238000 chr7A 80.108 372 51 11 1189 1537 11104939 11104568 3.300000e-64 255.0
8 TraesCS5B01G238000 chr1A 76.190 252 45 13 1922 2163 515838235 515838481 4.520000e-23 119.0
9 TraesCS5B01G238000 chr4A 92.188 64 4 1 7 69 726112039 726112102 3.540000e-14 89.8


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 TraesCS5B01G238000 chr5B 418814488 418817072 2584 True 4774.0 4774 100.0000 1 2585 1 chr5B.!!$R1 2584
1 TraesCS5B01G238000 chr5D 354503878 354506603 2725 True 1954.5 3524 94.5725 7 2585 2 chr5D.!!$R1 2578
2 TraesCS5B01G238000 chr5A 455467026 455469848 2822 True 1821.5 3308 93.6475 7 2585 2 chr5A.!!$R1 2578
3 TraesCS5B01G238000 chr7D 11676044 11677290 1246 True 717.0 717 77.9130 414 1683 1 chr7D.!!$R1 1269

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
391 657 0.678684 TGCCAGTGTGATGCATCTGG 60.679 55.0 26.32 24.12 43.23 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2335 2653 0.106918 ACGGGGTGCAAGAACAAGAA 60.107 50.0 0.0 0.0 0.0 2.52 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
93 95 1.077716 CTCCCCATTTCCACCGTCC 60.078 63.158 0.00 0.00 0.00 4.79
124 126 3.382832 CCTCTTCCGTCCGCTGGT 61.383 66.667 0.00 0.00 0.00 4.00
127 129 4.379243 CTTCCGTCCGCTGGTGCT 62.379 66.667 0.00 0.00 36.97 4.40
136 138 4.416738 GCTGGTGCTCCACTCCCC 62.417 72.222 2.64 0.00 39.03 4.81
221 224 1.692749 TTCCCCCATTCCCCTCTCG 60.693 63.158 0.00 0.00 0.00 4.04
297 563 2.165167 CCATGGTCTGTCTGTGCATTT 58.835 47.619 2.57 0.00 0.00 2.32
387 653 1.592400 GCAGTGCCAGTGTGATGCAT 61.592 55.000 2.85 0.00 37.34 3.96
391 657 0.678684 TGCCAGTGTGATGCATCTGG 60.679 55.000 26.32 24.12 43.23 3.86
407 673 3.297134 TCTGGTTGGCCTATGATTTCC 57.703 47.619 3.32 0.00 35.27 3.13
410 676 3.631250 TGGTTGGCCTATGATTTCCTTC 58.369 45.455 3.32 0.00 35.27 3.46
441 707 8.792830 ATGTGCTTATATATAATTCCACGCTT 57.207 30.769 5.64 2.28 0.00 4.68
548 814 8.459521 TGTTTATCTTAAATGATGGCGTTTTG 57.540 30.769 0.00 0.00 35.06 2.44
549 815 8.085296 TGTTTATCTTAAATGATGGCGTTTTGT 58.915 29.630 0.00 0.00 35.06 2.83
556 822 1.478510 TGATGGCGTTTTGTTGTTGGT 59.521 42.857 0.00 0.00 0.00 3.67
560 826 1.923864 GGCGTTTTGTTGTTGGTCTTG 59.076 47.619 0.00 0.00 0.00 3.02
561 827 1.923864 GCGTTTTGTTGTTGGTCTTGG 59.076 47.619 0.00 0.00 0.00 3.61
562 828 1.923864 CGTTTTGTTGTTGGTCTTGGC 59.076 47.619 0.00 0.00 0.00 4.52
563 829 2.416701 CGTTTTGTTGTTGGTCTTGGCT 60.417 45.455 0.00 0.00 0.00 4.75
564 830 3.186909 GTTTTGTTGTTGGTCTTGGCTC 58.813 45.455 0.00 0.00 0.00 4.70
565 831 2.136298 TTGTTGTTGGTCTTGGCTCA 57.864 45.000 0.00 0.00 0.00 4.26
586 852 6.206243 GCTCAGGCTCATTTATGTGAATGTAT 59.794 38.462 0.00 0.00 38.04 2.29
587 853 7.572724 GCTCAGGCTCATTTATGTGAATGTATC 60.573 40.741 0.00 0.00 38.04 2.24
588 854 7.281841 TCAGGCTCATTTATGTGAATGTATCA 58.718 34.615 0.00 0.00 38.04 2.15
589 855 7.940688 TCAGGCTCATTTATGTGAATGTATCAT 59.059 33.333 0.00 0.00 40.97 2.45
590 856 8.021396 CAGGCTCATTTATGTGAATGTATCATG 58.979 37.037 0.00 0.00 40.97 3.07
591 857 7.722728 AGGCTCATTTATGTGAATGTATCATGT 59.277 33.333 0.00 0.00 40.97 3.21
592 858 9.002600 GGCTCATTTATGTGAATGTATCATGTA 57.997 33.333 0.00 0.00 40.97 2.29
615 881 2.283145 AACAGCAGAGGCAACAATCT 57.717 45.000 0.00 0.00 44.61 2.40
626 893 6.867816 CAGAGGCAACAATCTATGTCTAGATC 59.132 42.308 0.00 0.00 42.66 2.75
675 942 2.364632 ACGGCAAATGCTAATACTGCA 58.635 42.857 5.25 0.00 44.95 4.41
685 952 3.197766 TGCTAATACTGCAAGCTGTAGGT 59.802 43.478 15.30 9.49 37.60 3.08
749 1021 7.453141 ACAAGGGCTAGAATTAGGAACTATT 57.547 36.000 0.00 0.00 42.38 1.73
792 1065 2.541120 GCATGAGAGCGACATGGCC 61.541 63.158 17.38 0.00 43.39 5.36
798 1071 0.760567 AGAGCGACATGGCCAGGATA 60.761 55.000 26.87 0.00 0.00 2.59
1009 1304 1.826921 CCAGCAGCCATGTCCATCC 60.827 63.158 0.00 0.00 0.00 3.51
1021 1316 3.235750 TGTCCATCCGATCTCTCATCT 57.764 47.619 0.00 0.00 0.00 2.90
1068 1363 0.250234 CCGCTTCCACCATCTCTCAA 59.750 55.000 0.00 0.00 0.00 3.02
1095 1390 3.702048 CCCTCCTCCGCGTTTCCA 61.702 66.667 4.92 0.00 0.00 3.53
1096 1391 2.434359 CCTCCTCCGCGTTTCCAC 60.434 66.667 4.92 0.00 0.00 4.02
1134 1429 5.403897 TTCTTTACAACAGAAGCAGAACG 57.596 39.130 0.00 0.00 0.00 3.95
1261 1557 4.329545 GGGCTTGGACCACTCGCA 62.330 66.667 10.69 0.00 0.00 5.10
1262 1558 2.045926 GGCTTGGACCACTCGCAT 60.046 61.111 10.69 0.00 0.00 4.73
1290 1603 0.532573 AGGTACAGTCTGTGATGCCG 59.467 55.000 16.03 0.00 0.00 5.69
1330 1643 5.632347 GTGGAAAGAGCTGAATGAATTGTTG 59.368 40.000 0.00 0.00 0.00 3.33
1381 1694 3.875727 CAGTAGCAGATGTCAATTCAGGG 59.124 47.826 0.00 0.00 0.00 4.45
1664 1982 2.422597 TGGTCCGAGTAAATGCAAGTG 58.577 47.619 0.00 0.00 0.00 3.16
1738 2056 6.101997 TCTATCTAGGCGATACATTGCATTG 58.898 40.000 7.04 7.04 38.98 2.82
2001 2319 0.109723 ACTTAGGCAAGGGTTCGCAA 59.890 50.000 0.00 0.00 35.97 4.85
2353 2671 0.310854 GTTCTTGTTCTTGCACCCCG 59.689 55.000 0.00 0.00 0.00 5.73
2494 2813 6.071051 GGTTTTAGAAACTATGGATTTGGGCA 60.071 38.462 3.85 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
221 224 1.063567 TGAGAGGGAGAGAGGGTTAGC 60.064 57.143 0.00 0.00 0.00 3.09
297 563 1.358152 AAGTCCCAAATCAGGTCGGA 58.642 50.000 0.00 0.00 0.00 4.55
334 600 2.530701 ACTAAGGTAGTCAGCAGCAGT 58.469 47.619 0.00 0.00 32.47 4.40
387 653 2.852449 AGGAAATCATAGGCCAACCAGA 59.148 45.455 5.01 0.00 39.06 3.86
391 657 5.930135 TCTAGAAGGAAATCATAGGCCAAC 58.070 41.667 5.01 0.00 0.00 3.77
430 696 4.022416 TGCAATCAGTTTAAGCGTGGAATT 60.022 37.500 0.00 0.00 0.00 2.17
464 730 8.644216 ACATGGCATCATCATACATAAACAATT 58.356 29.630 0.00 0.00 0.00 2.32
465 731 8.185506 ACATGGCATCATCATACATAAACAAT 57.814 30.769 0.00 0.00 0.00 2.71
466 732 7.503230 AGACATGGCATCATCATACATAAACAA 59.497 33.333 0.00 0.00 0.00 2.83
548 814 0.954452 CCTGAGCCAAGACCAACAAC 59.046 55.000 0.00 0.00 0.00 3.32
549 815 0.823356 GCCTGAGCCAAGACCAACAA 60.823 55.000 0.00 0.00 0.00 2.83
556 822 3.054139 ACATAAATGAGCCTGAGCCAAGA 60.054 43.478 0.00 0.00 41.25 3.02
560 826 2.923121 TCACATAAATGAGCCTGAGCC 58.077 47.619 0.00 0.00 41.25 4.70
561 827 4.337555 ACATTCACATAAATGAGCCTGAGC 59.662 41.667 3.78 0.00 38.64 4.26
562 828 7.443272 TGATACATTCACATAAATGAGCCTGAG 59.557 37.037 3.78 0.00 38.64 3.35
563 829 7.281841 TGATACATTCACATAAATGAGCCTGA 58.718 34.615 3.78 0.00 38.64 3.86
564 830 7.500720 TGATACATTCACATAAATGAGCCTG 57.499 36.000 3.78 0.00 38.64 4.85
565 831 7.722728 ACATGATACATTCACATAAATGAGCCT 59.277 33.333 0.00 0.00 38.64 4.58
586 852 4.842574 TGCCTCTGCTGTTTTATACATGA 58.157 39.130 0.00 0.00 35.85 3.07
587 853 5.106197 TGTTGCCTCTGCTGTTTTATACATG 60.106 40.000 0.00 0.00 35.85 3.21
588 854 5.009631 TGTTGCCTCTGCTGTTTTATACAT 58.990 37.500 0.00 0.00 35.85 2.29
589 855 4.393834 TGTTGCCTCTGCTGTTTTATACA 58.606 39.130 0.00 0.00 38.71 2.29
590 856 5.371115 TTGTTGCCTCTGCTGTTTTATAC 57.629 39.130 0.00 0.00 38.71 1.47
591 857 5.945784 AGATTGTTGCCTCTGCTGTTTTATA 59.054 36.000 0.00 0.00 38.71 0.98
592 858 4.768968 AGATTGTTGCCTCTGCTGTTTTAT 59.231 37.500 0.00 0.00 38.71 1.40
593 859 4.144297 AGATTGTTGCCTCTGCTGTTTTA 58.856 39.130 0.00 0.00 38.71 1.52
594 860 2.961062 AGATTGTTGCCTCTGCTGTTTT 59.039 40.909 0.00 0.00 38.71 2.43
601 867 6.154203 TCTAGACATAGATTGTTGCCTCTG 57.846 41.667 0.00 0.00 39.18 3.35
615 881 9.397280 CCGTCCATCTAAATAGATCTAGACATA 57.603 37.037 8.70 0.00 40.91 2.29
675 942 1.956477 CAGCAACCAAACCTACAGCTT 59.044 47.619 0.00 0.00 0.00 3.74
685 952 2.229062 TGAACACGAAACAGCAACCAAA 59.771 40.909 0.00 0.00 0.00 3.28
1009 1304 1.135431 GGATGCGGAGATGAGAGATCG 60.135 57.143 0.00 0.00 0.00 3.69
1021 1316 0.105709 TATCTGGACCTGGATGCGGA 60.106 55.000 0.00 1.07 0.00 5.54
1095 1390 0.241481 GAAAGAGCTCGTGGAGTCGT 59.759 55.000 8.37 0.00 31.39 4.34
1096 1391 0.523966 AGAAAGAGCTCGTGGAGTCG 59.476 55.000 8.37 0.00 31.39 4.18
1097 1392 2.734276 AAGAAAGAGCTCGTGGAGTC 57.266 50.000 8.37 0.00 31.39 3.36
1098 1393 3.321111 TGTAAAGAAAGAGCTCGTGGAGT 59.679 43.478 8.37 0.00 31.39 3.85
1099 1394 3.914312 TGTAAAGAAAGAGCTCGTGGAG 58.086 45.455 8.37 0.00 0.00 3.86
1100 1395 4.056050 GTTGTAAAGAAAGAGCTCGTGGA 58.944 43.478 8.37 0.00 0.00 4.02
1101 1396 3.807622 TGTTGTAAAGAAAGAGCTCGTGG 59.192 43.478 8.37 0.00 0.00 4.94
1102 1397 4.745125 TCTGTTGTAAAGAAAGAGCTCGTG 59.255 41.667 8.37 0.00 0.00 4.35
1103 1398 4.945246 TCTGTTGTAAAGAAAGAGCTCGT 58.055 39.130 8.37 1.01 0.00 4.18
1134 1429 9.875675 GATCAGTTCAAAATATAGTGAATCAGC 57.124 33.333 4.74 0.00 36.23 4.26
1261 1557 1.831736 AGACTGTACCTAAAGGCGCAT 59.168 47.619 10.83 0.00 39.32 4.73
1262 1558 1.067142 CAGACTGTACCTAAAGGCGCA 60.067 52.381 10.83 0.00 39.32 6.09
1330 1643 1.869767 GAGCTGCACACATATAGCACC 59.130 52.381 1.02 0.00 38.59 5.01
1381 1694 1.078426 CCCTTCCATGACACGGACC 60.078 63.158 0.00 0.00 30.29 4.46
1522 1835 2.439701 CAGCACATCAGCCAGGGG 60.440 66.667 0.00 0.00 34.23 4.79
1664 1982 7.655490 AGCATTCTGGTTTGATTATCTAATGC 58.345 34.615 0.00 0.00 44.24 3.56
2001 2319 6.042777 CGTATGGATGTCAGATTACAGTGTT 58.957 40.000 0.00 0.00 31.70 3.32
2335 2653 0.106918 ACGGGGTGCAAGAACAAGAA 60.107 50.000 0.00 0.00 0.00 2.52
2353 2671 0.250513 GTGACAGACATGGGGAGGAC 59.749 60.000 0.00 0.00 0.00 3.85
2494 2813 2.845659 TGGTACCATCCCAACAGAGAT 58.154 47.619 11.60 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.