Multiple sequence alignment - TraesCS1B01G040300

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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 TraesCS1B01G040300 chr1B 100.000 3188 0 0 1 3188 19952416 19949229 0.000000e+00 5888
1 TraesCS1B01G040300 chr1B 98.620 3189 42 2 1 3188 19840540 19837353 0.000000e+00 5644
2 TraesCS1B01G040300 chr1B 98.589 3189 43 2 1 3188 19620987 19617800 0.000000e+00 5638
3 TraesCS1B01G040300 chr1B 98.064 3203 45 4 1 3188 19720946 19717746 0.000000e+00 5555
4 TraesCS1B01G040300 chr1B 98.111 3123 48 3 67 3188 19781501 19778389 0.000000e+00 5430
5 TraesCS1B01G040300 chr1B 99.198 2243 18 0 946 3188 19892022 19889780 0.000000e+00 4043
6 TraesCS1B01G040300 chr1B 90.699 2602 195 20 225 2819 20048532 20045971 0.000000e+00 3421
7 TraesCS1B01G040300 chr1B 91.387 2322 168 21 218 2533 20554500 20556795 0.000000e+00 3151
8 TraesCS1B01G040300 chr1B 89.245 530 48 5 2654 3183 20556820 20557340 0.000000e+00 654
9 TraesCS1B01G040300 chr1B 93.048 187 10 3 13 197 20554192 20554377 1.460000e-68 270
10 TraesCS1B01G040300 chr1D 93.666 2447 138 11 424 2863 13729091 13726655 0.000000e+00 3644
11 TraesCS1B01G040300 chr1D 93.901 2361 127 12 510 2863 13818154 13815804 0.000000e+00 3546
12 TraesCS1B01G040300 chr1D 89.159 535 48 6 2654 3188 13810529 13810005 0.000000e+00 658
13 TraesCS1B01G040300 chr1D 88.785 535 50 6 2654 3188 13721770 13721246 0.000000e+00 647
14 TraesCS1B01G040300 chr1D 86.594 276 19 6 19 278 13508744 13508471 4.020000e-74 289
15 TraesCS1B01G040300 chr1D 84.642 293 21 11 13 289 13818908 13818624 1.460000e-68 270
16 TraesCS1B01G040300 chr1D 95.270 148 5 2 13 159 13729238 13729092 1.910000e-57 233
17 TraesCS1B01G040300 chr1A 91.756 2620 160 26 570 3188 14792339 14789775 0.000000e+00 3591
18 TraesCS1B01G040300 chr1A 82.482 411 50 17 2611 3003 14836682 14836276 1.100000e-89 340
19 TraesCS1B01G040300 chr1A 84.290 331 51 1 260 590 14840903 14840574 3.970000e-84 322
20 TraesCS1B01G040300 chr1A 87.719 228 21 5 218 444 14795266 14795045 3.150000e-65 259


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 TraesCS1B01G040300 chr1B 19949229 19952416 3187 True 5888.000000 5888 100.000000 1 3188 1 chr1B.!!$R6 3187
1 TraesCS1B01G040300 chr1B 19837353 19840540 3187 True 5644.000000 5644 98.620000 1 3188 1 chr1B.!!$R4 3187
2 TraesCS1B01G040300 chr1B 19617800 19620987 3187 True 5638.000000 5638 98.589000 1 3188 1 chr1B.!!$R1 3187
3 TraesCS1B01G040300 chr1B 19717746 19720946 3200 True 5555.000000 5555 98.064000 1 3188 1 chr1B.!!$R2 3187
4 TraesCS1B01G040300 chr1B 19778389 19781501 3112 True 5430.000000 5430 98.111000 67 3188 1 chr1B.!!$R3 3121
5 TraesCS1B01G040300 chr1B 19889780 19892022 2242 True 4043.000000 4043 99.198000 946 3188 1 chr1B.!!$R5 2242
6 TraesCS1B01G040300 chr1B 20045971 20048532 2561 True 3421.000000 3421 90.699000 225 2819 1 chr1B.!!$R7 2594
7 TraesCS1B01G040300 chr1B 20554192 20557340 3148 False 1358.333333 3151 91.226667 13 3183 3 chr1B.!!$F1 3170
8 TraesCS1B01G040300 chr1D 13726655 13729238 2583 True 1938.500000 3644 94.468000 13 2863 2 chr1D.!!$R4 2850
9 TraesCS1B01G040300 chr1D 13815804 13818908 3104 True 1908.000000 3546 89.271500 13 2863 2 chr1D.!!$R5 2850
10 TraesCS1B01G040300 chr1D 13810005 13810529 524 True 658.000000 658 89.159000 2654 3188 1 chr1D.!!$R3 534
11 TraesCS1B01G040300 chr1D 13721246 13721770 524 True 647.000000 647 88.785000 2654 3188 1 chr1D.!!$R2 534
12 TraesCS1B01G040300 chr1A 14789775 14795266 5491 True 1925.000000 3591 89.737500 218 3188 2 chr1A.!!$R1 2970
13 TraesCS1B01G040300 chr1A 14836276 14840903 4627 True 331.000000 340 83.386000 260 3003 2 chr1A.!!$R2 2743

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
284 402 0.250467 CCCGCCTCCCTAATGACATG 60.250 60.000 0.00 0.0 0.00 3.21 F
494 907 1.051008 ATGGCGCATCTCATCTACCA 58.949 50.000 10.83 0.0 0.00 3.25 F
1439 4792 1.559682 AGGTGCCGACTACCAATTGAT 59.440 47.619 7.12 0.0 40.74 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1434 4787 1.525535 GCCGAGCAGCCTCATCAAT 60.526 57.895 0.00 0.00 38.00 2.57 R
1719 5072 1.746220 GTCTGTCTCGCTGATACCAGT 59.254 52.381 0.00 0.00 42.35 4.00 R
3008 7994 0.106708 TATCGGGAGCATGCTCAACC 59.893 55.000 40.37 32.43 44.40 3.77 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
248 366 2.047061 TGAGCACCACTACCTTGACTT 58.953 47.619 0.00 0.0 0.00 3.01
284 402 0.250467 CCCGCCTCCCTAATGACATG 60.250 60.000 0.00 0.0 0.00 3.21
494 907 1.051008 ATGGCGCATCTCATCTACCA 58.949 50.000 10.83 0.0 0.00 3.25
1275 4628 2.606213 TCCCACATGGAGCCGTCA 60.606 61.111 0.00 0.0 38.61 4.35
1434 4787 3.065306 CCAGGTGCCGACTACCAA 58.935 61.111 0.00 0.0 40.74 3.67
1439 4792 1.559682 AGGTGCCGACTACCAATTGAT 59.440 47.619 7.12 0.0 40.74 2.57
1734 5087 1.847328 TCCAACTGGTATCAGCGAGA 58.153 50.000 1.90 0.0 44.59 4.04
2401 5755 8.368668 GCTCCTGATGTACCTAGTGTATTTTAT 58.631 37.037 0.00 0.0 0.00 1.40
2662 7625 0.610232 CTGCAGGGGCTAGTGCTTTT 60.610 55.000 5.57 0.0 40.54 2.27
3008 7994 6.371825 GGAGTTTGGTGTTATGGTTTAGAGAG 59.628 42.308 0.00 0.0 0.00 3.20
3134 8120 7.218228 AGTACATGTGAGCATTCATTTTTCA 57.782 32.000 9.11 0.0 35.39 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
248 366 2.933906 GCGGGTTCTCGATTTATGTTCA 59.066 45.455 0.00 0.00 0.00 3.18
284 402 0.237498 GTTGTCGGTTGCCAGTTAGC 59.763 55.000 0.00 0.00 0.00 3.09
320 724 2.115911 TTCTTGGCACGCGGTTTGT 61.116 52.632 12.47 0.00 0.00 2.83
494 907 1.485066 AGAACTCGTCAAACACAGGGT 59.515 47.619 0.00 0.00 0.00 4.34
979 4332 1.003580 TGATCAGCACCAAGGAGTTCC 59.996 52.381 0.00 0.00 0.00 3.62
1434 4787 1.525535 GCCGAGCAGCCTCATCAAT 60.526 57.895 0.00 0.00 38.00 2.57
1719 5072 1.746220 GTCTGTCTCGCTGATACCAGT 59.254 52.381 0.00 0.00 42.35 4.00
1734 5087 2.284625 TCGGGCAGGATGGTCTGT 60.285 61.111 0.00 0.00 37.12 3.41
2567 5945 4.314121 GCTTTTGCAACCCAAACATATGA 58.686 39.130 10.38 0.00 42.81 2.15
2662 7625 9.196139 CCTGAATGTCCCTATATTTAAAAACCA 57.804 33.333 0.00 0.00 0.00 3.67
3008 7994 0.106708 TATCGGGAGCATGCTCAACC 59.893 55.000 40.37 32.43 44.40 3.77
3134 8120 4.081087 ACGGATTCACTGCTTATTACCAGT 60.081 41.667 0.00 0.00 42.67 4.00


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

AutoCloner maintained by Alex Coulton.