Multiple sequence alignment - TraesCS4B01G368100

Loading Multiple Alignment...

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 TraesCS4B01G368100 chr4B 100.000 2447 0 0 1 2447 654676250 654673804 0.000000e+00 4519
1 TraesCS4B01G368100 chr4B 97.145 2207 57 6 243 2447 654793212 654791010 0.000000e+00 3722
2 TraesCS4B01G368100 chr4B 97.428 2138 53 2 312 2447 605030999 605028862 0.000000e+00 3642
3 TraesCS4B01G368100 chr4B 94.355 248 11 2 1 247 654793755 654793510 6.390000e-101 377
4 TraesCS4B01G368100 chr4B 93.562 233 14 1 1 233 654592897 654592666 1.800000e-91 346
5 TraesCS4B01G368100 chr4B 92.704 233 16 1 1 233 654719979 654719748 3.900000e-88 335
6 TraesCS4B01G368100 chr4B 86.574 216 28 1 18 233 654751880 654751666 1.130000e-58 237
7 TraesCS4B01G368100 chr4B 85.648 216 30 1 18 233 654762119 654761905 2.450000e-55 226
8 TraesCS4B01G368100 chr7B 97.889 2132 44 1 316 2447 743567527 743569657 0.000000e+00 3687
9 TraesCS4B01G368100 chr7B 97.610 2134 49 1 316 2447 640242296 640240163 0.000000e+00 3657
10 TraesCS4B01G368100 chr3B 97.612 2136 47 3 315 2447 24582047 24584181 0.000000e+00 3659
11 TraesCS4B01G368100 chr1B 97.612 2136 46 3 316 2447 647584287 647582153 0.000000e+00 3657
12 TraesCS4B01G368100 chr2B 97.566 2136 48 3 315 2447 793232309 793234443 0.000000e+00 3653
13 TraesCS4B01G368100 chr4A 97.521 2138 44 2 315 2447 715970250 715972383 0.000000e+00 3646
14 TraesCS4B01G368100 chr5B 97.475 2139 45 5 316 2447 641330891 641328755 0.000000e+00 3642
15 TraesCS4B01G368100 chrUn 91.453 234 20 0 1 234 154617492 154617725 3.040000e-84 322
16 TraesCS4B01G368100 chrUn 91.379 232 20 0 1 232 154587005 154587236 3.930000e-83 318
17 TraesCS4B01G368100 chrUn 87.624 202 25 0 33 234 154601705 154601906 4.070000e-58 235
18 TraesCS4B01G368100 chr5A 90.283 247 22 1 1 247 692179652 692179408 3.040000e-84 322


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 TraesCS4B01G368100 chr4B 654673804 654676250 2446 True 4519.0 4519 100.000 1 2447 1 chr4B.!!$R3 2446
1 TraesCS4B01G368100 chr4B 605028862 605030999 2137 True 3642.0 3642 97.428 312 2447 1 chr4B.!!$R1 2135
2 TraesCS4B01G368100 chr4B 654791010 654793755 2745 True 2049.5 3722 95.750 1 2447 2 chr4B.!!$R7 2446
3 TraesCS4B01G368100 chr7B 743567527 743569657 2130 False 3687.0 3687 97.889 316 2447 1 chr7B.!!$F1 2131
4 TraesCS4B01G368100 chr7B 640240163 640242296 2133 True 3657.0 3657 97.610 316 2447 1 chr7B.!!$R1 2131
5 TraesCS4B01G368100 chr3B 24582047 24584181 2134 False 3659.0 3659 97.612 315 2447 1 chr3B.!!$F1 2132
6 TraesCS4B01G368100 chr1B 647582153 647584287 2134 True 3657.0 3657 97.612 316 2447 1 chr1B.!!$R1 2131
7 TraesCS4B01G368100 chr2B 793232309 793234443 2134 False 3653.0 3653 97.566 315 2447 1 chr2B.!!$F1 2132
8 TraesCS4B01G368100 chr4A 715970250 715972383 2133 False 3646.0 3646 97.521 315 2447 1 chr4A.!!$F1 2132
9 TraesCS4B01G368100 chr5B 641328755 641330891 2136 True 3642.0 3642 97.475 316 2447 1 chr5B.!!$R1 2131

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
77 79 1.071605 CACGCTGAAGCTGAAGGTAC 58.928 55.0 0.1 0.0 39.32 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1862 2179 0.108804 TCTTCGCCGTCTTCCATCAC 60.109 55.0 0.0 0.0 0.0 3.06 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
77 79 1.071605 CACGCTGAAGCTGAAGGTAC 58.928 55.000 0.10 0.0 39.32 3.34
81 83 1.687494 CTGAAGCTGAAGGTACGCGC 61.687 60.000 5.73 0.0 0.00 6.86
131 133 3.335534 GCGTGCCGACAAACGAGT 61.336 61.111 0.00 0.0 45.77 4.18
141 143 1.529865 GACAAACGAGTAGTGTTGCCC 59.470 52.381 0.00 0.0 0.00 5.36
223 225 1.880340 CGTCCTCGGCATCAAGCTC 60.880 63.158 0.00 0.0 44.79 4.09
230 232 1.154150 GGCATCAAGCTCAACGTGC 60.154 57.895 0.00 0.0 44.79 5.34
234 236 4.389576 CAAGCTCAACGTGCCCGC 62.390 66.667 0.00 0.0 37.70 6.13
302 604 2.815211 CGGTCCGTGATGTGCCAG 60.815 66.667 2.08 0.0 0.00 4.85
706 1013 2.556622 GTGCTCTAGCTCACCTCCTATC 59.443 54.545 3.26 0.0 42.66 2.08
778 1085 2.167281 CTCTCCAAGCTCGATCTCCAAA 59.833 50.000 0.00 0.0 0.00 3.28
1017 1327 1.663695 CGATGGTTTTGGTATCCGCT 58.336 50.000 0.00 0.0 0.00 5.52
1337 1654 7.609760 TGCGCTTGAAGATTAGAAAGATTAA 57.390 32.000 9.73 0.0 0.00 1.40
1755 2072 3.457749 TGTTGTCCATGCCCTATATGTGA 59.542 43.478 0.00 0.0 0.00 3.58
1780 2097 2.775890 ACGAAGTCTTACTCTGACCGA 58.224 47.619 0.00 0.0 29.74 4.69
1862 2179 1.379527 GCACGGAGAAATAGGGGTTG 58.620 55.000 0.00 0.0 0.00 3.77
2263 2585 5.313712 ACGAAGAAGCTTCCAAAGGATAAA 58.686 37.500 22.81 0.0 0.00 1.40
2383 2708 0.101759 GCGGTGCGTACAAGGATCTA 59.898 55.000 5.86 0.0 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 4.493747 CCGGTCGAAGGCGGAGAC 62.494 72.222 0.00 1.64 38.28 3.36
77 79 2.720750 GTTCAACACGTTGGCGCG 60.721 61.111 0.00 0.00 42.83 6.86
81 83 0.029300 CAGCAGGTTCAACACGTTGG 59.971 55.000 9.90 0.00 40.78 3.77
131 133 0.037326 CTCAGAAGCGGGCAACACTA 60.037 55.000 0.00 0.00 39.74 2.74
230 232 4.619227 ACACAAGGTCACGGCGGG 62.619 66.667 13.24 7.61 0.00 6.13
234 236 6.895607 AAAAATAAAAACACAAGGTCACGG 57.104 33.333 0.00 0.00 0.00 4.94
675 982 2.481952 GAGCTAGAGCACCACAAAGTTG 59.518 50.000 4.01 0.00 45.16 3.16
677 984 1.694150 TGAGCTAGAGCACCACAAAGT 59.306 47.619 4.01 0.00 45.16 2.66
706 1013 1.014044 CCATCGAACACCTCGTGTGG 61.014 60.000 11.45 6.84 46.79 4.17
778 1085 9.401058 CTAGACAAATATTGAGGAAAATGGAGT 57.599 33.333 0.00 0.00 0.00 3.85
981 1291 5.414360 ACCATCGCACTATATAAGATGCAG 58.586 41.667 11.70 6.51 37.97 4.41
1034 1344 4.753516 ACCACATCCGAATCATAGACAA 57.246 40.909 0.00 0.00 0.00 3.18
1337 1654 5.278957 GCCTCGGTATGAATGGCATATTTTT 60.279 40.000 0.00 0.00 41.29 1.94
1755 2072 5.064962 CGGTCAGAGTAAGACTTCGTATTCT 59.935 44.000 0.00 0.00 36.29 2.40
1780 2097 2.965147 CAGGTGGGTGTGAAGGATTTTT 59.035 45.455 0.00 0.00 0.00 1.94
1862 2179 0.108804 TCTTCGCCGTCTTCCATCAC 60.109 55.000 0.00 0.00 0.00 3.06
2241 2563 5.643777 TCTTTATCCTTTGGAAGCTTCTTCG 59.356 40.000 25.05 11.48 34.34 3.79
2263 2585 3.737047 CGTATGTACTGTCGGGCAATTCT 60.737 47.826 0.00 0.00 0.00 2.40
2383 2708 2.770589 GCATACCGGGCATGCGTTT 61.771 57.895 22.63 0.00 39.43 3.60


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

AutoCloner maintained by Alex Coulton.