Multiple sequence alignment - TraesCS2B01G601100

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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 TraesCS2B01G601100 chr2B 100.000 2371 0 0 1 2371 784238515 784240885 0 4379
1 TraesCS2B01G601100 chr3A 97.218 2372 64 2 1 2370 66004937 66002566 0 4013
2 TraesCS2B01G601100 chr6D 97.133 2372 66 2 1 2370 389245626 389243255 0 4002
3 TraesCS2B01G601100 chr5D 97.049 2372 68 2 1 2370 503264580 503262209 0 3991
4 TraesCS2B01G601100 chr5D 97.007 2372 69 2 1 2370 503245468 503247839 0 3986
5 TraesCS2B01G601100 chr3D 97.049 2372 67 3 1 2370 589263330 589260960 0 3989
6 TraesCS2B01G601100 chr2A 97.007 2372 69 2 1 2370 726906259 726903888 0 3986
7 TraesCS2B01G601100 chr2D 96.965 2372 70 2 1 2370 591984805 591987176 0 3980
8 TraesCS2B01G601100 chr1D 96.965 2372 70 2 1 2370 459904521 459902150 0 3980
9 TraesCS2B01G601100 chr7B 96.880 2372 72 2 1 2370 663099229 663096858 0 3969


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 TraesCS2B01G601100 chr2B 784238515 784240885 2370 False 4379 4379 100.000 1 2371 1 chr2B.!!$F1 2370
1 TraesCS2B01G601100 chr3A 66002566 66004937 2371 True 4013 4013 97.218 1 2370 1 chr3A.!!$R1 2369
2 TraesCS2B01G601100 chr6D 389243255 389245626 2371 True 4002 4002 97.133 1 2370 1 chr6D.!!$R1 2369
3 TraesCS2B01G601100 chr5D 503262209 503264580 2371 True 3991 3991 97.049 1 2370 1 chr5D.!!$R1 2369
4 TraesCS2B01G601100 chr5D 503245468 503247839 2371 False 3986 3986 97.007 1 2370 1 chr5D.!!$F1 2369
5 TraesCS2B01G601100 chr3D 589260960 589263330 2370 True 3989 3989 97.049 1 2370 1 chr3D.!!$R1 2369
6 TraesCS2B01G601100 chr2A 726903888 726906259 2371 True 3986 3986 97.007 1 2370 1 chr2A.!!$R1 2369
7 TraesCS2B01G601100 chr2D 591984805 591987176 2371 False 3980 3980 96.965 1 2370 1 chr2D.!!$F1 2369
8 TraesCS2B01G601100 chr1D 459902150 459904521 2371 True 3980 3980 96.965 1 2370 1 chr1D.!!$R1 2369
9 TraesCS2B01G601100 chr7B 663096858 663099229 2371 True 3969 3969 96.880 1 2370 1 chr7B.!!$R1 2369

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
165 166 0.036875 GCTTGCGGGGGATATAGCTT 59.963 55.0 0.0 0.0 0.0 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1816 1819 0.802607 CTTTCGCTACGGCTCTGGTC 60.803 60.0 0.0 0.0 36.09 4.02 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
29 30 2.196595 TCTCTCCCGATTGGTTGGATT 58.803 47.619 0.00 0.00 34.77 3.01
142 143 4.763073 TGACTCTTTCATGCATACTCCAG 58.237 43.478 0.00 0.00 0.00 3.86
149 150 2.025981 TCATGCATACTCCAGTTGGCTT 60.026 45.455 0.00 0.00 34.44 4.35
151 152 0.453390 GCATACTCCAGTTGGCTTGC 59.547 55.000 0.00 0.00 34.44 4.01
165 166 0.036875 GCTTGCGGGGGATATAGCTT 59.963 55.000 0.00 0.00 0.00 3.74
215 216 0.038435 TCGTTGCGATTACGGGTTGA 60.038 50.000 0.00 0.00 39.38 3.18
258 259 7.523380 GCGGTAATGATAGTATCTTGTACCTGT 60.523 40.741 21.99 4.02 0.00 4.00
312 313 2.906389 AGAGGACTGAAACATGCCACTA 59.094 45.455 0.00 0.00 0.00 2.74
342 343 2.519013 ACTGAGACAAAAAGATGGGCC 58.481 47.619 0.00 0.00 0.00 5.80
423 424 1.725665 CGATAGTTGGAGTCGGCGA 59.274 57.895 4.99 4.99 0.00 5.54
481 482 0.779997 AGGATCAAGTTGGCCCTTGT 59.220 50.000 17.98 8.45 42.01 3.16
603 604 0.544357 ACGAGATCACCCCAAGGACA 60.544 55.000 0.00 0.00 36.73 4.02
605 606 1.280457 GAGATCACCCCAAGGACACT 58.720 55.000 0.00 0.00 36.73 3.55
755 756 0.895530 AAGATCAAAGAGTCGGGCGA 59.104 50.000 0.00 0.00 0.00 5.54
840 841 6.745857 AATCCTTAGAATGGGATTCCAACTT 58.254 36.000 0.00 0.00 45.84 2.66
905 906 5.386958 AGAGCACAGTACGATGAAAGTTA 57.613 39.130 3.82 0.00 0.00 2.24
913 914 6.255887 ACAGTACGATGAAAGTTATAAGCTGC 59.744 38.462 0.00 0.00 0.00 5.25
946 948 6.042208 GGGAGTTATTGTCTATAGTCAGCCTT 59.958 42.308 0.00 0.00 0.00 4.35
960 962 3.054655 GTCAGCCTTTATGGTAGAACCCA 60.055 47.826 0.00 0.00 37.50 4.51
1044 1046 0.608640 CTCCAGCCCGTGAACTTAGT 59.391 55.000 0.00 0.00 0.00 2.24
1176 1178 3.881089 GGCATAGCCTTAACGTTAATGGT 59.119 43.478 24.48 24.48 46.69 3.55
1216 1218 1.410004 CTTGCGGTGGATACCTAGGA 58.590 55.000 17.98 0.00 45.22 2.94
1226 1228 3.273886 TGGATACCTAGGAACCCAGAGAA 59.726 47.826 17.98 0.00 0.00 2.87
1316 1319 8.226112 TCCCAAATAGGTCAACCTTTTAAACTA 58.774 33.333 7.07 0.00 46.09 2.24
1323 1326 5.999600 GGTCAACCTTTTAAACTACCTGCTA 59.000 40.000 0.00 0.00 0.00 3.49
1362 1365 0.868406 GACAACCTGGCGAACTGAAG 59.132 55.000 0.00 0.00 0.00 3.02
1653 1656 4.474113 GGTGACCGATAGCGAAATAGTAG 58.526 47.826 0.00 0.00 40.82 2.57
1758 1761 1.213013 GTGATCTCTGACCGCGTGT 59.787 57.895 4.92 1.93 0.00 4.49
1816 1819 0.035176 TGGTTAAGGGAACGGAACCG 59.965 55.000 11.83 11.83 46.81 4.44
1820 1823 0.831288 TAAGGGAACGGAACCGACCA 60.831 55.000 20.14 4.86 42.83 4.02
1898 1901 3.246301 CCTGGGTGATCTATCCATGACT 58.754 50.000 0.00 0.00 0.00 3.41
1936 1939 6.183360 GGATGAAACTAAGTAGAGGTCCGAAT 60.183 42.308 0.00 0.00 0.00 3.34
1971 1974 3.930336 AGAATCAGCGAATGAGTTGTGA 58.070 40.909 0.00 0.00 42.53 3.58
2114 2117 3.695830 ACCAAATCGAGGCAAACTCTA 57.304 42.857 0.00 0.00 44.33 2.43
2153 2156 4.346709 CCAAAAATAACAGGGGTCAAGGTT 59.653 41.667 0.00 0.00 0.00 3.50
2156 2159 0.774908 TAACAGGGGTCAAGGTTGGG 59.225 55.000 0.00 0.00 0.00 4.12
2186 2189 2.038952 CGATGGGGGATAAGCTTCATCA 59.961 50.000 18.34 6.04 32.88 3.07
2201 2204 4.507710 CTTCATCATCGAGAGGGAAACAA 58.492 43.478 0.00 0.00 0.00 2.83
2214 2217 1.611519 GAAACAACCCGGATCACCAA 58.388 50.000 0.73 0.00 35.59 3.67
2304 2307 3.175438 AGAAGCAGCCACCCTTTAAAT 57.825 42.857 0.00 0.00 0.00 1.40
2363 2366 3.217626 GAAGATGAATGGGGCTAAGTGG 58.782 50.000 0.00 0.00 0.00 4.00
2370 2373 2.602676 GGGGCTAAGTGGTCTGCCA 61.603 63.158 5.21 0.00 46.53 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.031870 GCCCCTACAATCCAACCAATC 58.968 52.381 0.00 0.0 0.00 2.67
29 30 3.452990 TGAAGTAAATCATCGCCCCTACA 59.547 43.478 0.00 0.0 0.00 2.74
88 89 0.251341 ATTCTTTTCCCTGGCGCAGT 60.251 50.000 10.83 0.0 0.00 4.40
142 143 0.109723 TATATCCCCCGCAAGCCAAC 59.890 55.000 0.00 0.0 0.00 3.77
149 150 2.301870 CAACTAAGCTATATCCCCCGCA 59.698 50.000 0.00 0.0 0.00 5.69
151 152 2.904434 ACCAACTAAGCTATATCCCCCG 59.096 50.000 0.00 0.0 0.00 5.73
215 216 1.066143 CCGCCTGGACAATTAGACAGT 60.066 52.381 0.00 0.0 37.49 3.55
258 259 1.418637 AGAAAAAGTGAGCCACCGGTA 59.581 47.619 6.87 0.0 34.49 4.02
312 313 9.050601 CATCTTTTTGTCTCAGTAGAGTCTTTT 57.949 33.333 0.00 0.0 42.66 2.27
342 343 3.679824 ACCTCCTCTACCTTTTTGACG 57.320 47.619 0.00 0.0 0.00 4.35
423 424 1.011595 TGAGGGAAGCCTAGGAGAGT 58.988 55.000 14.75 0.0 0.00 3.24
481 482 6.100279 AGGGAGATAGTGCATCAAGTTATTCA 59.900 38.462 0.00 0.0 35.96 2.57
840 841 7.551585 TCAAAATCTCAAAACAAAAGGTGCTA 58.448 30.769 0.00 0.0 0.00 3.49
905 906 2.189521 CCCCCGAACGCAGCTTAT 59.810 61.111 0.00 0.0 0.00 1.73
937 939 3.200165 GGGTTCTACCATAAAGGCTGACT 59.800 47.826 0.00 0.0 41.02 3.41
940 942 3.644966 TGGGTTCTACCATAAAGGCTG 57.355 47.619 0.00 0.0 41.02 4.85
960 962 2.123077 CTCTCAGGCCTCCCCGAT 60.123 66.667 0.00 0.0 39.21 4.18
1044 1046 5.299531 GGTGCTATCGCTATCATAGTATCCA 59.700 44.000 0.00 0.0 36.97 3.41
1087 1089 7.482654 TGAATGTGAAATCATAGATCGAACC 57.517 36.000 0.00 0.0 0.00 3.62
1176 1178 3.117512 AGCCTTTCCTCTTTTGAACCTCA 60.118 43.478 0.00 0.0 0.00 3.86
1216 1218 1.662686 CCCTTCCTCTTCTCTGGGTT 58.337 55.000 0.00 0.0 0.00 4.11
1226 1228 1.901085 CTTGCTACGCCCTTCCTCT 59.099 57.895 0.00 0.0 0.00 3.69
1323 1326 2.025605 TCTCTTGCCTGCTCATGGATTT 60.026 45.455 0.00 0.0 0.00 2.17
1362 1365 4.408182 TTTCCTCTGGCTACTAAGATGC 57.592 45.455 0.00 0.0 0.00 3.91
1647 1650 2.431057 CACCTTTCCCTCACGCTACTAT 59.569 50.000 0.00 0.0 0.00 2.12
1653 1656 1.266989 CTTTTCACCTTTCCCTCACGC 59.733 52.381 0.00 0.0 0.00 5.34
1758 1761 2.688507 GCCGACTCATTCTTCAACAGA 58.311 47.619 0.00 0.0 0.00 3.41
1816 1819 0.802607 CTTTCGCTACGGCTCTGGTC 60.803 60.000 0.00 0.0 36.09 4.02
1820 1823 2.202623 CGCTTTCGCTACGGCTCT 60.203 61.111 0.00 0.0 36.09 4.09
1898 1901 5.441718 AGTTTCATCCAAGCTTCATCCTA 57.558 39.130 0.00 0.0 0.00 2.94
1936 1939 3.928992 GCTGATTCTTCAACATCAGTCGA 59.071 43.478 10.14 0.0 45.69 4.20
1960 1963 4.927267 TCACCCCTAATCACAACTCATT 57.073 40.909 0.00 0.0 0.00 2.57
1971 1974 2.683742 CGAGTGGCATTTCACCCCTAAT 60.684 50.000 0.00 0.0 38.34 1.73
2153 2156 2.659063 CCCATCGTCTCACTGCCCA 61.659 63.158 0.00 0.0 0.00 5.36
2156 2159 1.690219 ATCCCCCATCGTCTCACTGC 61.690 60.000 0.00 0.0 0.00 4.40
2186 2189 0.249398 CGGGTTGTTTCCCTCTCGAT 59.751 55.000 0.25 0.0 44.95 3.59
2201 2204 0.909623 CCTTAGTTGGTGATCCGGGT 59.090 55.000 0.00 0.0 36.30 5.28
2214 2217 1.489230 CGGTCATTTAGGGGCCTTAGT 59.511 52.381 0.84 0.0 0.00 2.24


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

AutoCloner maintained by Alex Coulton.