Multiple sequence alignment - TraesCS4A01G303200

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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 TraesCS4A01G303200 chr4A 100.000 4443 0 0 1 4443 599248813 599244371 0.000000e+00 8205
1 TraesCS4A01G303200 chr4A 99.168 4445 33 4 1 4443 599159734 599155292 0.000000e+00 8000
2 TraesCS4A01G303200 chr4A 98.830 4443 49 3 1 4443 599126773 599122334 0.000000e+00 7914
3 TraesCS4A01G303200 chr4A 94.557 2425 124 7 2023 4443 599221997 599219577 0.000000e+00 3740
4 TraesCS4A01G303200 chr4A 94.518 2426 124 7 2023 4443 599178570 599176149 0.000000e+00 3735
5 TraesCS4A01G303200 chr4A 94.173 2437 122 10 2023 4443 599101191 599098759 0.000000e+00 3696
6 TraesCS4A01G303200 chr4A 94.177 2164 123 2 2282 4443 599083271 599081109 0.000000e+00 3295
7 TraesCS4A01G303200 chr4A 94.230 2045 113 4 2203 4245 599144528 599142487 0.000000e+00 3118
8 TraesCS4A01G303200 chr4A 93.399 2030 114 13 1 2025 599103281 599101267 0.000000e+00 2988
9 TraesCS4A01G303200 chr4A 93.350 2030 115 14 1 2025 599180660 599178646 0.000000e+00 2983
10 TraesCS4A01G303200 chr4A 93.300 2030 116 14 1 2025 599224087 599222073 0.000000e+00 2977
11 TraesCS4A01G303200 chr4A 93.039 2040 120 15 1 2035 599085557 599083535 0.000000e+00 2961
12 TraesCS4A01G303200 chr4A 92.956 2030 119 15 1 2025 599147497 599145487 0.000000e+00 2935
13 TraesCS4A01G303200 chrUn 99.341 3337 22 0 1107 4443 216675826 216672490 0.000000e+00 6041
14 TraesCS4A01G303200 chrUn 93.264 1737 96 13 293 2025 360633603 360631884 0.000000e+00 2540
15 TraesCS4A01G303200 chrUn 93.155 1198 71 9 1 1195 216652968 216651779 0.000000e+00 1748
16 TraesCS4A01G303200 chrUn 93.478 368 20 4 4079 4443 360632885 360632519 1.090000e-150 544
17 TraesCS4A01G303200 chr4B 91.429 2100 128 11 2023 4075 7354718 7356812 0.000000e+00 2833
18 TraesCS4A01G303200 chr4B 91.251 2103 126 20 2023 4075 7171746 7173840 0.000000e+00 2811
19 TraesCS4A01G303200 chr6A 94.813 1388 64 3 3063 4443 593024889 593023503 0.000000e+00 2158


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 TraesCS4A01G303200 chr4A 599244371 599248813 4442 True 8205.0 8205 100.0000 1 4443 1 chr4A.!!$R3 4442
1 TraesCS4A01G303200 chr4A 599155292 599159734 4442 True 8000.0 8000 99.1680 1 4443 1 chr4A.!!$R2 4442
2 TraesCS4A01G303200 chr4A 599122334 599126773 4439 True 7914.0 7914 98.8300 1 4443 1 chr4A.!!$R1 4442
3 TraesCS4A01G303200 chr4A 599176149 599180660 4511 True 3359.0 3735 93.9340 1 4443 2 chr4A.!!$R7 4442
4 TraesCS4A01G303200 chr4A 599219577 599224087 4510 True 3358.5 3740 93.9285 1 4443 2 chr4A.!!$R8 4442
5 TraesCS4A01G303200 chr4A 599098759 599103281 4522 True 3342.0 3696 93.7860 1 4443 2 chr4A.!!$R5 4442
6 TraesCS4A01G303200 chr4A 599081109 599085557 4448 True 3128.0 3295 93.6080 1 4443 2 chr4A.!!$R4 4442
7 TraesCS4A01G303200 chr4A 599142487 599147497 5010 True 3026.5 3118 93.5930 1 4245 2 chr4A.!!$R6 4244
8 TraesCS4A01G303200 chrUn 216672490 216675826 3336 True 6041.0 6041 99.3410 1107 4443 1 chrUn.!!$R2 3336
9 TraesCS4A01G303200 chrUn 216651779 216652968 1189 True 1748.0 1748 93.1550 1 1195 1 chrUn.!!$R1 1194
10 TraesCS4A01G303200 chrUn 360631884 360633603 1719 True 1542.0 2540 93.3710 293 4443 2 chrUn.!!$R3 4150
11 TraesCS4A01G303200 chr4B 7354718 7356812 2094 False 2833.0 2833 91.4290 2023 4075 1 chr4B.!!$F2 2052
12 TraesCS4A01G303200 chr4B 7171746 7173840 2094 False 2811.0 2811 91.2510 2023 4075 1 chr4B.!!$F1 2052
13 TraesCS4A01G303200 chr6A 593023503 593024889 1386 True 2158.0 2158 94.8130 3063 4443 1 chr6A.!!$R1 1380

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
532 535 0.463654 GGCATGTAGGCGGTGAATCA 60.464 55.000 0.0 0.0 33.57 2.57 F
860 863 1.815421 CTCGCTGCCAAACGCCTAT 60.815 57.895 0.0 0.0 36.24 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1889 1897 6.736581 TCAGCTCTTCTACCTATGGCTATAT 58.263 40.000 0.0 0.0 0.0 0.86 R
3449 4356 1.421646 CACTCTTCCCCCTTCACTTGT 59.578 52.381 0.0 0.0 0.0 3.16 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
406 408 0.596577 AAGCTCTTACGTCGAGTGCA 59.403 50.000 20.76 0.0 36.40 4.57
504 507 4.378874 GCAAGTACTCTTTGGAATGACTGC 60.379 45.833 0.00 0.0 0.00 4.40
532 535 0.463654 GGCATGTAGGCGGTGAATCA 60.464 55.000 0.00 0.0 33.57 2.57
638 641 5.130477 TGGATGGTCTTCTATTTGTCCCTAC 59.870 44.000 0.00 0.0 0.00 3.18
860 863 1.815421 CTCGCTGCCAAACGCCTAT 60.815 57.895 0.00 0.0 36.24 2.57
884 887 2.997897 GACCCTCGTGAGCCCAGT 60.998 66.667 0.00 0.0 0.00 4.00
1302 1306 2.821245 CGCCCTCTATCATCTCTCCCTT 60.821 54.545 0.00 0.0 0.00 3.95
1510 1514 3.737172 GCCCGCTGCGTCAATGTT 61.737 61.111 21.59 0.0 0.00 2.71
1924 1932 6.096282 AGGTAGAAGAGCTGAGTTTAGTCATC 59.904 42.308 0.00 0.0 33.53 2.92
3449 4356 3.054139 TGGTCCTAACTCCTAAGTAGCGA 60.054 47.826 0.00 0.0 33.48 4.93
3743 4684 9.006215 GTGACTTTGTTTTGTTGTATGTTCTAC 57.994 33.333 0.00 0.0 0.00 2.59
3937 4881 0.764271 TGGTCTGCAAGGTCACATCA 59.236 50.000 0.00 0.0 0.00 3.07
3983 4927 1.996191 GAGACAACGTGAAGAGCATCC 59.004 52.381 0.00 0.0 33.66 3.51
4131 5076 4.658786 ACCGAGGTGAGGCCCCTT 62.659 66.667 0.00 0.0 38.26 3.95
4157 5111 0.032952 TCTAGTCGTGTGGTTGTGGC 59.967 55.000 0.00 0.0 0.00 5.01
4410 5376 9.281371 CATCTTAATTATCTGCTCTGGAAATCA 57.719 33.333 0.00 0.0 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
406 408 6.773200 TCTTCCTCTAGTTATGTCATGATCGT 59.227 38.462 0.00 0.00 0.00 3.73
504 507 1.772063 GCCTACATGCCCTTTACGCG 61.772 60.000 3.53 3.53 0.00 6.01
532 535 5.476945 ACTTTCACAGTTTCACTTTCAACCT 59.523 36.000 0.00 0.00 27.32 3.50
638 641 6.391227 AAACTTAGTCCCTCACAATGTTTG 57.609 37.500 0.00 0.00 0.00 2.93
860 863 1.244697 GCTCACGAGGGTCTCTCACA 61.245 60.000 0.00 0.00 42.55 3.58
884 887 2.037144 GGAGGAGCGGAGGTTGTATAA 58.963 52.381 0.00 0.00 39.88 0.98
1302 1306 1.813178 CAGTACCGAGACAGAGAGCAA 59.187 52.381 0.00 0.00 0.00 3.91
1510 1514 8.978539 GTATAATAAACAGATCTGAATCGCACA 58.021 33.333 29.27 7.32 36.97 4.57
1889 1897 6.736581 TCAGCTCTTCTACCTATGGCTATAT 58.263 40.000 0.00 0.00 0.00 0.86
3449 4356 1.421646 CACTCTTCCCCCTTCACTTGT 59.578 52.381 0.00 0.00 0.00 3.16
3937 4881 1.611673 CCGACAGCTTTGTGATCCCTT 60.612 52.381 0.00 0.00 0.00 3.95
3983 4927 2.024414 GCAAATACACCTAAGCCCAGG 58.976 52.381 0.00 0.00 41.87 4.45
4209 5163 1.676635 CCTCGTCCACGACACCCTA 60.677 63.158 0.00 0.00 44.22 3.53


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

AutoCloner maintained by Alex Coulton.