Multiple sequence alignment - TraesCS2A01G200100

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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 TraesCS2A01G200100 chr2A 100.000 4300 0 0 541 4840 172554635 172550336 0.000000e+00 7941
1 TraesCS2A01G200100 chr2A 99.353 2165 9 5 541 2702 646835945 646833783 0.000000e+00 3916
2 TraesCS2A01G200100 chr2A 100.000 281 0 0 1 281 172555175 172554895 2.000000e-143 520
3 TraesCS2A01G200100 chr2A 100.000 281 0 0 1 281 646836433 646836153 2.000000e-143 520
4 TraesCS2A01G200100 chr6B 98.634 4320 26 18 541 4837 534000144 534004453 0.000000e+00 7620
5 TraesCS2A01G200100 chr6B 97.114 4228 57 30 541 4733 401412706 401416903 0.000000e+00 7071
6 TraesCS2A01G200100 chr6B 100.000 281 0 0 1 281 533999656 533999936 2.000000e-143 520
7 TraesCS2A01G200100 chr6B 99.288 281 1 1 1 281 401412218 401412497 1.550000e-139 507
8 TraesCS2A01G200100 chr6B 91.875 320 19 6 4521 4840 637161668 637161356 1.600000e-119 440
9 TraesCS2A01G200100 chr6B 91.749 303 19 6 4539 4837 401416619 401416919 2.690000e-112 416
10 TraesCS2A01G200100 chr7A 98.047 4198 28 21 674 4840 286988668 286984494 0.000000e+00 7249
11 TraesCS2A01G200100 chr7A 100.000 281 0 0 1 281 286989227 286988947 2.000000e-143 520
12 TraesCS2A01G200100 chr4A 98.219 3650 27 19 541 4160 627589711 627593352 0.000000e+00 6346
13 TraesCS2A01G200100 chr4A 100.000 281 0 0 1 281 627589223 627589503 2.000000e-143 520
14 TraesCS2A01G200100 chr2B 98.439 3588 29 12 541 4110 91071664 91075242 0.000000e+00 6290
15 TraesCS2A01G200100 chr2B 97.916 2207 20 11 2647 4837 91076083 91078279 0.000000e+00 3797
16 TraesCS2A01G200100 chr2B 91.370 1599 91 29 3042 4616 335406341 335407916 0.000000e+00 2145
17 TraesCS2A01G200100 chr2B 100.000 280 0 0 2 281 91071176 91071455 7.180000e-143 518
18 TraesCS2A01G200100 chr7B 96.032 2520 69 13 541 3046 654101839 654104341 0.000000e+00 4071
19 TraesCS2A01G200100 chr7B 91.935 2517 127 36 541 3033 725143370 725140906 0.000000e+00 3454
20 TraesCS2A01G200100 chr7B 90.473 1711 103 38 3042 4720 725140849 725139167 0.000000e+00 2202
21 TraesCS2A01G200100 chr7B 91.307 1599 92 30 3042 4616 734765674 734767249 0.000000e+00 2139
22 TraesCS2A01G200100 chr7B 96.441 281 10 0 1 281 654101353 654101633 9.490000e-127 464
23 TraesCS2A01G200100 chr7B 93.375 317 16 5 4521 4837 654105735 654106046 9.490000e-127 464
24 TraesCS2A01G200100 chrUn 95.236 2519 95 13 541 3046 12544140 12541634 0.000000e+00 3964
25 TraesCS2A01G200100 chrUn 97.509 281 7 0 1 281 12544628 12544348 9.420000e-132 481
26 TraesCS2A01G200100 chr5B 93.663 2383 117 14 673 3033 3900088 3897718 0.000000e+00 3533
27 TraesCS2A01G200100 chr5A 91.495 1599 88 30 3042 4616 678286709 678288283 0.000000e+00 2156
28 TraesCS2A01G200100 chr1B 91.182 1599 92 30 3042 4616 36520944 36522517 0.000000e+00 2126
29 TraesCS2A01G200100 chr1B 96.085 281 11 0 1 281 36517924 36518204 4.410000e-125 459
30 TraesCS2A01G200100 chr1D 95.306 490 18 1 541 1025 478764845 478764356 0.000000e+00 773
31 TraesCS2A01G200100 chr1A 95.092 489 19 2 541 1025 555101363 555100876 0.000000e+00 765


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 TraesCS2A01G200100 chr2A 172550336 172555175 4839 True 4230.500000 7941 100.000000 1 4840 2 chr2A.!!$R1 4839
1 TraesCS2A01G200100 chr2A 646833783 646836433 2650 True 2218.000000 3916 99.676500 1 2702 2 chr2A.!!$R2 2701
2 TraesCS2A01G200100 chr6B 533999656 534004453 4797 False 4070.000000 7620 99.317000 1 4837 2 chr6B.!!$F2 4836
3 TraesCS2A01G200100 chr6B 401412218 401416919 4701 False 2664.666667 7071 96.050333 1 4837 3 chr6B.!!$F1 4836
4 TraesCS2A01G200100 chr7A 286984494 286989227 4733 True 3884.500000 7249 99.023500 1 4840 2 chr7A.!!$R1 4839
5 TraesCS2A01G200100 chr4A 627589223 627593352 4129 False 3433.000000 6346 99.109500 1 4160 2 chr4A.!!$F1 4159
6 TraesCS2A01G200100 chr2B 91071176 91078279 7103 False 3535.000000 6290 98.785000 2 4837 3 chr2B.!!$F2 4835
7 TraesCS2A01G200100 chr2B 335406341 335407916 1575 False 2145.000000 2145 91.370000 3042 4616 1 chr2B.!!$F1 1574
8 TraesCS2A01G200100 chr7B 725139167 725143370 4203 True 2828.000000 3454 91.204000 541 4720 2 chr7B.!!$R1 4179
9 TraesCS2A01G200100 chr7B 734765674 734767249 1575 False 2139.000000 2139 91.307000 3042 4616 1 chr7B.!!$F1 1574
10 TraesCS2A01G200100 chr7B 654101353 654106046 4693 False 1666.333333 4071 95.282667 1 4837 3 chr7B.!!$F2 4836
11 TraesCS2A01G200100 chrUn 12541634 12544628 2994 True 2222.500000 3964 96.372500 1 3046 2 chrUn.!!$R1 3045
12 TraesCS2A01G200100 chr5B 3897718 3900088 2370 True 3533.000000 3533 93.663000 673 3033 1 chr5B.!!$R1 2360
13 TraesCS2A01G200100 chr5A 678286709 678288283 1574 False 2156.000000 2156 91.495000 3042 4616 1 chr5A.!!$F1 1574
14 TraesCS2A01G200100 chr1B 36517924 36522517 4593 False 1292.500000 2126 93.633500 1 4616 2 chr1B.!!$F1 4615

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
1227 1269 5.070847 ACCTTCTGTTTTTGCTTCATCCATT 59.929 36.000 0.0 0.0 0.00 3.16 F
1229 1271 7.153985 CCTTCTGTTTTTGCTTCATCCATTTA 58.846 34.615 0.0 0.0 0.00 1.40 F
2753 2811 3.807071 CACTAACCATTTTTGTTGTGGCC 59.193 43.478 0.0 0.0 36.47 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2751 2809 3.205784 AGCATCTACTTGAAGGATGGC 57.794 47.619 11.6 1.44 37.78 4.40 R
2752 2810 5.543507 AGTAGCATCTACTTGAAGGATGG 57.456 43.478 11.6 0.00 37.78 3.51 R
4580 7135 5.860941 TTTGGAAAACATGGTTGAAGCTA 57.139 34.783 0.0 0.00 0.00 3.32 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
1227 1269 5.070847 ACCTTCTGTTTTTGCTTCATCCATT 59.929 36.000 0.00 0.0 0.00 3.16
1229 1271 7.153985 CCTTCTGTTTTTGCTTCATCCATTTA 58.846 34.615 0.00 0.0 0.00 1.40
2751 2809 5.290643 CACACACTAACCATTTTTGTTGTGG 59.709 40.000 0.00 0.0 38.96 4.17
2752 2810 4.269844 CACACTAACCATTTTTGTTGTGGC 59.730 41.667 0.00 0.0 36.47 5.01
2753 2811 3.807071 CACTAACCATTTTTGTTGTGGCC 59.193 43.478 0.00 0.0 36.47 5.36
3465 3593 9.283768 ACCTGTGAGTTTTCTTTTTGAATTTTT 57.716 25.926 0.00 0.0 34.24 1.94
3601 3731 7.174413 TCAAATATGTGGAGAACTTTGATGGA 58.826 34.615 0.00 0.0 29.99 3.41
4155 6615 2.775911 TCAAGGGAATCTCTGTGCAG 57.224 50.000 0.00 0.0 0.00 4.41
4508 7063 6.227298 TGTTTCCAAAAGCTTCAACCATTA 57.773 33.333 0.00 0.0 0.00 1.90
4580 7135 3.071312 TGGCTTCAACCATTGCTTGAAAT 59.929 39.130 8.16 0.0 37.22 2.17
4837 7399 8.292448 GCTTTTTCACAGAGATTCTAAACATGA 58.708 33.333 0.00 0.0 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2751 2809 3.205784 AGCATCTACTTGAAGGATGGC 57.794 47.619 11.60 1.44 37.78 4.40
2752 2810 5.543507 AGTAGCATCTACTTGAAGGATGG 57.456 43.478 11.60 0.00 37.78 3.51
2753 2811 8.821894 GTTTTAGTAGCATCTACTTGAAGGATG 58.178 37.037 11.24 6.97 39.59 3.51
3601 3731 7.286316 ACCTGATTGAACTCTTTCATTGACTTT 59.714 33.333 0.00 0.00 41.50 2.66
4580 7135 5.860941 TTTGGAAAACATGGTTGAAGCTA 57.139 34.783 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.