Multiple sequence alignment - TraesCS4A01G070300

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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 TraesCS4A01G070300 chr4A 100.000 1496 0 0 1410 2905 67599027 67597532 0 2763
1 TraesCS4A01G070300 chr4A 100.000 1173 0 0 1 1173 67600436 67599264 0 2167
2 TraesCS4A01G070300 chr5A 98.660 1493 20 0 1410 2902 19246593 19248085 0 2647
3 TraesCS4A01G070300 chr5A 98.384 1176 16 2 1 1173 19245368 19246543 0 2063
4 TraesCS4A01G070300 chr5A 97.956 1174 23 1 1 1173 238819335 238820508 0 2034
5 TraesCS4A01G070300 chr7D 98.529 1496 22 0 1410 2905 381926251 381924756 0 2641
6 TraesCS4A01G070300 chr7D 98.463 1496 23 0 1410 2905 382052329 382050834 0 2636
7 TraesCS4A01G070300 chr7D 98.392 1493 21 1 1410 2902 381971520 381973009 0 2621
8 TraesCS4A01G070300 chr7D 98.262 1496 26 0 1410 2905 203502249 203500754 0 2619
9 TraesCS4A01G070300 chr7D 98.467 1174 17 1 1 1173 382053552 382052379 0 2067
10 TraesCS4A01G070300 chr7D 98.211 1174 20 1 1 1173 203503472 203502299 0 2050
11 TraesCS4A01G070300 chr7D 98.128 1175 20 2 1 1173 381970291 381971465 0 2047
12 TraesCS4A01G070300 chr7D 97.956 1174 23 1 1 1173 381927474 381926301 0 2034
13 TraesCS4A01G070300 chr7B 98.526 1493 22 0 1410 2902 716876531 716878023 0 2636
14 TraesCS4A01G070300 chr7B 98.259 1493 26 0 1410 2902 716836320 716837812 0 2614
15 TraesCS4A01G070300 chr1A 98.459 1493 23 0 1410 2902 498688977 498690469 0 2630
16 TraesCS4A01G070300 chr6D 98.262 1496 26 0 1410 2905 124519772 124518277 0 2619
17 TraesCS4A01G070300 chr6D 98.129 1176 19 3 1 1173 124520997 124519822 0 2047
18 TraesCS4A01G070300 chr7A 97.872 1175 18 3 1 1173 60282782 60281613 0 2025
19 TraesCS4A01G070300 chr1D 97.785 1174 25 1 1 1173 43233242 43234415 0 2023


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 TraesCS4A01G070300 chr4A 67597532 67600436 2904 True 2465.0 2763 100.0000 1 2905 2 chr4A.!!$R1 2904
1 TraesCS4A01G070300 chr5A 19245368 19248085 2717 False 2355.0 2647 98.5220 1 2902 2 chr5A.!!$F2 2901
2 TraesCS4A01G070300 chr5A 238819335 238820508 1173 False 2034.0 2034 97.9560 1 1173 1 chr5A.!!$F1 1172
3 TraesCS4A01G070300 chr7D 382050834 382053552 2718 True 2351.5 2636 98.4650 1 2905 2 chr7D.!!$R3 2904
4 TraesCS4A01G070300 chr7D 381924756 381927474 2718 True 2337.5 2641 98.2425 1 2905 2 chr7D.!!$R2 2904
5 TraesCS4A01G070300 chr7D 203500754 203503472 2718 True 2334.5 2619 98.2365 1 2905 2 chr7D.!!$R1 2904
6 TraesCS4A01G070300 chr7D 381970291 381973009 2718 False 2334.0 2621 98.2600 1 2902 2 chr7D.!!$F1 2901
7 TraesCS4A01G070300 chr7B 716876531 716878023 1492 False 2636.0 2636 98.5260 1410 2902 1 chr7B.!!$F2 1492
8 TraesCS4A01G070300 chr7B 716836320 716837812 1492 False 2614.0 2614 98.2590 1410 2902 1 chr7B.!!$F1 1492
9 TraesCS4A01G070300 chr1A 498688977 498690469 1492 False 2630.0 2630 98.4590 1410 2902 1 chr1A.!!$F1 1492
10 TraesCS4A01G070300 chr6D 124518277 124520997 2720 True 2333.0 2619 98.1955 1 2905 2 chr6D.!!$R1 2904
11 TraesCS4A01G070300 chr7A 60281613 60282782 1169 True 2025.0 2025 97.8720 1 1173 1 chr7A.!!$R1 1172
12 TraesCS4A01G070300 chr1D 43233242 43234415 1173 False 2023.0 2023 97.7850 1 1173 1 chr1D.!!$F1 1172

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
960 966 0.032815 GCTTCGATAGGCTCCACTCC 59.967 60.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2221 2227 0.395312 CGCAGGAATACCCCCGTTAT 59.605 55.0 0.0 0.0 36.73 1.89 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
102 103 3.623960 CACGCCCGTATCAATCCTTTAAA 59.376 43.478 0.00 0.00 0.00 1.52
103 104 4.274950 CACGCCCGTATCAATCCTTTAAAT 59.725 41.667 0.00 0.00 0.00 1.40
224 228 2.073816 TCGGAGAATCGGCTGAAAAAC 58.926 47.619 0.00 0.00 35.13 2.43
225 229 1.804151 CGGAGAATCGGCTGAAAAACA 59.196 47.619 0.00 0.00 34.37 2.83
250 255 4.454504 GGAATTGTCTTCGCCTTTGTAAGA 59.545 41.667 0.00 0.00 0.00 2.10
480 485 7.666804 TCCATTGGTTCATATAGAATCCATGTG 59.333 37.037 1.86 0.00 36.48 3.21
628 633 1.406751 CCATCATACGGCTCACCAACA 60.407 52.381 0.00 0.00 34.57 3.33
739 745 6.459066 AGATGATTCTTTCTTTGTCGAGACA 58.541 36.000 1.24 1.24 39.98 3.41
795 801 4.892934 TGAGTCTGTTTTGCCCACTTTATT 59.107 37.500 0.00 0.00 0.00 1.40
926 932 3.117963 AGAATGAAGAGGAGCCAAGGATG 60.118 47.826 0.00 0.00 0.00 3.51
960 966 0.032815 GCTTCGATAGGCTCCACTCC 59.967 60.000 0.00 0.00 0.00 3.85
964 970 0.178975 CGATAGGCTCCACTCCCTCT 60.179 60.000 0.00 0.00 32.65 3.69
1026 1032 4.288531 GGATAACGAGTCGACGATTGAAT 58.711 43.478 21.50 1.01 37.03 2.57
1153 1159 0.532573 GGATCACTCCAGTGCTTCGA 59.467 55.000 1.49 0.00 45.25 3.71
1161 1167 2.747989 CTCCAGTGCTTCGAGTACTACA 59.252 50.000 0.00 0.00 39.17 2.74
1576 1582 3.965888 AAGCGAAGGGAATGAGCTT 57.034 47.368 0.00 0.00 42.51 3.74
1619 1625 3.520317 TCTTTATTTCTCCGTGCCCCTTA 59.480 43.478 0.00 0.00 0.00 2.69
1627 1633 2.749839 GTGCCCCTTACGCATGCA 60.750 61.111 19.57 0.00 38.76 3.96
1633 1639 1.019278 CCCTTACGCATGCACTTCGT 61.019 55.000 19.57 9.46 39.88 3.85
1981 1987 2.651455 ACAAGGATATGGAGTCGACGA 58.349 47.619 10.46 0.00 0.00 4.20
2011 2017 1.613925 CAGACTCGACCCTGTCTTTCA 59.386 52.381 2.51 0.00 41.06 2.69
2068 2074 2.125673 GCTACGTGTCCGGTGCAT 60.126 61.111 0.00 0.00 38.78 3.96
2078 2084 0.893270 TCCGGTGCATGGAAAACTGG 60.893 55.000 8.09 0.00 41.03 4.00
2532 2538 3.262915 GGCCAGTGCTCCTAAGATCATAT 59.737 47.826 0.00 0.00 37.74 1.78
2560 2566 7.878477 CAATGCTGCAGAAAAAGAAGATTTA 57.122 32.000 20.43 0.00 0.00 1.40
2647 2653 3.004752 AGGCGCAATAGAAAGGAATGT 57.995 42.857 10.83 0.00 0.00 2.71
2831 2843 5.843019 AAGGGAAGGACTTATTCTCAACA 57.157 39.130 0.00 0.00 28.99 3.33
2902 2914 3.799232 GCTGTTCACGTAACTCCACTCTT 60.799 47.826 0.00 0.00 38.99 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 2.180159 ATACGGGCGTGCTTCCTTGT 62.180 55.000 0.00 0.00 0.00 3.16
102 103 4.102838 TCCTAACGCTAGTCTAGTCTCCAT 59.897 45.833 8.68 0.00 0.00 3.41
103 104 3.453717 TCCTAACGCTAGTCTAGTCTCCA 59.546 47.826 8.68 0.00 0.00 3.86
224 228 1.156736 AAGGCGAAGACAATTCCGTG 58.843 50.000 0.00 0.00 39.87 4.94
225 229 1.535462 CAAAGGCGAAGACAATTCCGT 59.465 47.619 0.00 0.00 39.87 4.69
250 255 6.963322 AGATAGGCTTTACTGGACATTTTCT 58.037 36.000 0.00 0.00 0.00 2.52
628 633 1.216990 CCCCCTTAGAGGCAAGTGAT 58.783 55.000 0.00 0.00 32.73 3.06
795 801 5.612261 TGATCATTTTGATAGAGGGGGATGA 59.388 40.000 0.00 0.00 37.20 2.92
1026 1032 3.172106 TGGCAGAACGTTGGGGGA 61.172 61.111 5.00 0.00 0.00 4.81
1153 1159 2.146920 GGCAGAGGGTCTGTAGTACT 57.853 55.000 0.00 0.00 45.94 2.73
1576 1582 3.650950 GTGGGGGAGAAGCAGCCA 61.651 66.667 0.00 0.00 0.00 4.75
1627 1633 3.737172 GCCAATGGCGCACGAAGT 61.737 61.111 9.14 0.00 40.21 3.01
1746 1752 0.965439 CTCATTTGGGGCGGAAAACA 59.035 50.000 0.00 0.00 0.00 2.83
1838 1844 2.208619 TGCTCCCCGTCGGTTGTTA 61.209 57.895 11.06 0.00 0.00 2.41
1981 1987 4.038522 CAGGGTCGAGTCTGATACATCAAT 59.961 45.833 8.75 0.00 36.18 2.57
2011 2017 3.154710 CACAGATGGGAATGCATGCTAT 58.845 45.455 20.33 7.43 0.00 2.97
2068 2074 0.472471 AGACCGAAGCCAGTTTTCCA 59.528 50.000 0.00 0.00 0.00 3.53
2134 2140 1.751924 CAGTGGGAGTAGTGACTAGCC 59.248 57.143 0.00 0.00 35.45 3.93
2221 2227 0.395312 CGCAGGAATACCCCCGTTAT 59.605 55.000 0.00 0.00 36.73 1.89
2560 2566 5.457633 GCTTCCTATGGGGGTACATTACAAT 60.458 44.000 0.00 0.00 35.33 2.71


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

AutoCloner maintained by Alex Coulton.