Multiple sequence alignment - TraesCS5D01G348700

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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 TraesCS5D01G348700 chr5D 100.000 2426 0 0 1 2426 434330340 434332765 0.000000e+00 4481.0
1 TraesCS5D01G348700 chr5D 95.922 2060 46 8 1 2050 434383042 434381011 0.000000e+00 3304.0
2 TraesCS5D01G348700 chr5D 80.274 877 139 21 717 1573 435237356 435238218 4.400000e-177 630.0
3 TraesCS5D01G348700 chr5D 80.068 878 142 25 707 1573 434568967 434569822 2.650000e-174 621.0
4 TraesCS5D01G348700 chr5D 74.198 655 130 24 340 970 434674636 434673997 1.120000e-58 237.0
5 TraesCS5D01G348700 chr5D 91.589 107 9 0 2307 2413 433992617 433992723 5.400000e-32 148.0
6 TraesCS5D01G348700 chr5A 95.768 2434 77 10 1 2413 548227702 548225274 0.000000e+00 3901.0
7 TraesCS5D01G348700 chr5B 94.901 2432 67 12 1 2413 527041059 527038666 0.000000e+00 3751.0
8 TraesCS5D01G348700 chr5B 79.884 860 140 22 730 1573 527061063 527060221 1.240000e-167 599.0
9 TraesCS5D01G348700 chr5B 79.475 877 147 21 707 1573 527607516 527608369 2.080000e-165 592.0
10 TraesCS5D01G348700 chr5B 75.687 1201 225 44 340 1520 527772228 527773381 2.740000e-149 538.0
11 TraesCS5D01G348700 chr5B 78.303 825 147 20 765 1571 528524503 528525313 1.000000e-138 503.0
12 TraesCS5D01G348700 chr5B 79.201 726 130 16 861 1573 527059081 527058364 3.630000e-133 484.0
13 TraesCS5D01G348700 chr5B 89.041 73 7 1 340 412 527494965 527495036 3.320000e-14 89.8


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 TraesCS5D01G348700 chr5D 434330340 434332765 2425 False 4481.0 4481 100.0000 1 2426 1 chr5D.!!$F2 2425
1 TraesCS5D01G348700 chr5D 434381011 434383042 2031 True 3304.0 3304 95.9220 1 2050 1 chr5D.!!$R1 2049
2 TraesCS5D01G348700 chr5D 435237356 435238218 862 False 630.0 630 80.2740 717 1573 1 chr5D.!!$F4 856
3 TraesCS5D01G348700 chr5D 434568967 434569822 855 False 621.0 621 80.0680 707 1573 1 chr5D.!!$F3 866
4 TraesCS5D01G348700 chr5D 434673997 434674636 639 True 237.0 237 74.1980 340 970 1 chr5D.!!$R2 630
5 TraesCS5D01G348700 chr5A 548225274 548227702 2428 True 3901.0 3901 95.7680 1 2413 1 chr5A.!!$R1 2412
6 TraesCS5D01G348700 chr5B 527038666 527041059 2393 True 3751.0 3751 94.9010 1 2413 1 chr5B.!!$R1 2412
7 TraesCS5D01G348700 chr5B 527607516 527608369 853 False 592.0 592 79.4750 707 1573 1 chr5B.!!$F2 866
8 TraesCS5D01G348700 chr5B 527058364 527061063 2699 True 541.5 599 79.5425 730 1573 2 chr5B.!!$R2 843
9 TraesCS5D01G348700 chr5B 527772228 527773381 1153 False 538.0 538 75.6870 340 1520 1 chr5B.!!$F3 1180
10 TraesCS5D01G348700 chr5B 528524503 528525313 810 False 503.0 503 78.3030 765 1571 1 chr5B.!!$F4 806

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
831 870 0.322008 GTCCCTGGCCAACTCTTCAG 60.322 60.0 7.01 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2271 4208 1.126846 CAGAATGGTTCAGACGTTCGC 59.873 52.381 0.0 0.0 0.0 4.7 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
140 141 6.099990 CAGGGGAGAGAGAATATATGATGCAT 59.900 42.308 0.00 0.00 0.00 3.96
209 210 2.420022 ACAACACACTCAGCAGAAACAC 59.580 45.455 0.00 0.00 0.00 3.32
210 211 2.401583 ACACACTCAGCAGAAACACA 57.598 45.000 0.00 0.00 0.00 3.72
253 264 2.038557 GCAGAACACTTGACCCTCCTAA 59.961 50.000 0.00 0.00 0.00 2.69
516 538 5.236282 ACTGATCAACAACACATCTGAGAG 58.764 41.667 0.00 0.00 0.00 3.20
697 728 2.223805 TGCATCGCAGAATAGATCGTGT 60.224 45.455 0.00 0.00 43.58 4.49
831 870 0.322008 GTCCCTGGCCAACTCTTCAG 60.322 60.000 7.01 0.00 0.00 3.02
926 989 2.801111 CCATCACTTCATCAGCTCATCG 59.199 50.000 0.00 0.00 0.00 3.84
1031 1099 2.421619 GAAGAGACTTGCTCAACTGGG 58.578 52.381 0.00 0.00 46.45 4.45
1044 1112 2.031120 CAACTGGGAAAGAAGTGGCAA 58.969 47.619 0.00 0.00 0.00 4.52
1139 1208 0.811281 GTAAAGGGCCACTGCATCAC 59.189 55.000 6.18 0.00 40.13 3.06
2056 3985 0.892755 CATGGTTTGCAGCTGGTCAT 59.107 50.000 17.12 0.00 0.00 3.06
2079 4008 0.321653 ACCCATCGGAAAGTGCAGAC 60.322 55.000 0.00 0.00 0.00 3.51
2148 4080 7.948278 ACTAAGATACAACACTGTTCAAGTC 57.052 36.000 0.00 0.00 36.83 3.01
2168 4100 3.123621 GTCGTGTTCCTTGCATCAACTAG 59.876 47.826 0.00 0.00 0.00 2.57
2169 4101 3.067106 CGTGTTCCTTGCATCAACTAGT 58.933 45.455 0.00 0.00 0.00 2.57
2170 4102 3.123621 CGTGTTCCTTGCATCAACTAGTC 59.876 47.826 0.00 0.00 0.00 2.59
2171 4103 4.319177 GTGTTCCTTGCATCAACTAGTCT 58.681 43.478 0.00 0.00 0.00 3.24
2269 4206 7.615365 TCACCTGCTAAAATAAGACCATTGAAT 59.385 33.333 0.00 0.00 0.00 2.57
2271 4208 9.125026 ACCTGCTAAAATAAGACCATTGAATAG 57.875 33.333 0.00 0.00 0.00 1.73
2292 4229 2.672714 CGAACGTCTGAACCATTCTGA 58.327 47.619 0.00 0.00 35.61 3.27
2396 4333 2.508361 CCAGTTTGCATGGGATCCC 58.492 57.895 25.22 25.22 33.94 3.85
2406 4343 3.643398 GGGATCCCCGTGCTACTT 58.357 61.111 21.42 0.00 32.13 2.24
2413 4350 0.828022 CCCCGTGCTACTTATCCACA 59.172 55.000 0.00 0.00 0.00 4.17
2414 4351 1.416401 CCCCGTGCTACTTATCCACAT 59.584 52.381 0.00 0.00 0.00 3.21
2415 4352 2.483876 CCCGTGCTACTTATCCACATG 58.516 52.381 0.00 0.00 0.00 3.21
2416 4353 2.158957 CCCGTGCTACTTATCCACATGT 60.159 50.000 0.00 0.00 0.00 3.21
2417 4354 3.531538 CCGTGCTACTTATCCACATGTT 58.468 45.455 0.00 0.00 0.00 2.71
2418 4355 3.309682 CCGTGCTACTTATCCACATGTTG 59.690 47.826 0.00 0.00 0.00 3.33
2419 4356 4.180817 CGTGCTACTTATCCACATGTTGA 58.819 43.478 1.57 1.57 0.00 3.18
2420 4357 4.629634 CGTGCTACTTATCCACATGTTGAA 59.370 41.667 3.42 0.00 0.00 2.69
2421 4358 5.445939 CGTGCTACTTATCCACATGTTGAAC 60.446 44.000 3.42 0.00 0.00 3.18
2422 4359 4.941263 TGCTACTTATCCACATGTTGAACC 59.059 41.667 3.42 0.00 0.00 3.62
2423 4360 4.335594 GCTACTTATCCACATGTTGAACCC 59.664 45.833 3.42 0.00 0.00 4.11
2424 4361 4.380843 ACTTATCCACATGTTGAACCCA 57.619 40.909 3.42 0.00 0.00 4.51
2425 4362 4.335416 ACTTATCCACATGTTGAACCCAG 58.665 43.478 3.42 1.06 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 93 1.952990 TCTGATTTCCGCAGTTTGCAA 59.047 42.857 0.00 0.00 45.36 4.08
104 105 4.223923 TCTCTCTCCCCTGTTTCTGATTTC 59.776 45.833 0.00 0.00 0.00 2.17
140 141 5.836358 AGTAATTTTGGCAACTAGTTTCCCA 59.164 36.000 19.84 18.28 37.61 4.37
209 210 5.801947 GCAACTTGCCATAAATTACTGAGTG 59.198 40.000 1.95 0.00 37.42 3.51
210 211 5.476599 TGCAACTTGCCATAAATTACTGAGT 59.523 36.000 11.29 0.00 44.23 3.41
253 264 6.123651 TGTCCAAAGTTGTACCATGTTTAGT 58.876 36.000 0.00 0.00 0.00 2.24
516 538 2.357034 TCGCCGCTGAACCTTCAC 60.357 61.111 0.00 0.00 32.90 3.18
645 676 6.534436 GGATGGATTCAGTTGAGATATCATCG 59.466 42.308 5.32 0.00 0.00 3.84
697 728 4.694760 AGTGGTAGCAATAGCATCATGA 57.305 40.909 0.00 0.00 45.49 3.07
831 870 4.551388 CTGGTGAAGAGTAGTTGTCACTC 58.449 47.826 12.00 0.00 42.30 3.51
926 989 1.070134 TGTAGTGCTCAGTTGGTGGTC 59.930 52.381 0.00 0.00 0.00 4.02
995 1063 4.631813 GTCTCTTCGTGCTAATCATGGTTT 59.368 41.667 0.00 0.00 32.54 3.27
1031 1099 1.341209 CCACCCTTTGCCACTTCTTTC 59.659 52.381 0.00 0.00 0.00 2.62
1044 1112 4.974721 CCAAGTGCCGCCACCCTT 62.975 66.667 0.00 0.00 43.09 3.95
1139 1208 4.403137 TTCCGTCGGCCGTGTACG 62.403 66.667 27.15 26.37 39.44 3.67
1498 3424 9.601810 TTCCTATTGCCTATTATCTAACTCTCA 57.398 33.333 0.00 0.00 0.00 3.27
1596 3523 6.449635 AAGTAAAACAATGACAGCTTGTGA 57.550 33.333 0.00 0.00 36.95 3.58
2056 3985 1.557371 TGCACTTTCCGATGGGTCATA 59.443 47.619 0.00 0.00 33.83 2.15
2066 3995 1.165907 TGCCTTGTCTGCACTTTCCG 61.166 55.000 0.00 0.00 32.85 4.30
2067 3996 2.719376 TGCCTTGTCTGCACTTTCC 58.281 52.632 0.00 0.00 32.85 3.13
2079 4008 3.181483 GGCATCCATTTCTTAGTGCCTTG 60.181 47.826 6.92 0.00 46.44 3.61
2148 4080 3.067106 ACTAGTTGATGCAAGGAACACG 58.933 45.455 0.00 0.00 0.00 4.49
2195 4132 7.323656 GTGATTGTGCTTAATGTGTGTTCTTAC 59.676 37.037 0.00 0.00 0.00 2.34
2269 4206 2.230508 AGAATGGTTCAGACGTTCGCTA 59.769 45.455 0.00 0.00 0.00 4.26
2271 4208 1.126846 CAGAATGGTTCAGACGTTCGC 59.873 52.381 0.00 0.00 0.00 4.70
2292 4229 1.774894 TTGCCACGGGGAAAGCTAGT 61.775 55.000 8.67 0.00 35.59 2.57
2396 4333 3.179443 ACATGTGGATAAGTAGCACGG 57.821 47.619 0.00 0.00 0.00 4.94
2398 4335 5.163754 GGTTCAACATGTGGATAAGTAGCAC 60.164 44.000 3.10 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.