Multiple sequence alignment - TraesCS2A01G592300

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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 TraesCS2A01G592300 chr2A 100.000 2453 0 0 1 2453 779528649 779531101 0.000000e+00 4530
1 TraesCS2A01G592300 chr2A 96.909 1650 49 2 806 2453 779432694 779434343 0.000000e+00 2763
2 TraesCS2A01G592300 chr2A 90.721 1789 97 13 494 2242 779509570 779511329 0.000000e+00 2320
3 TraesCS2A01G592300 chr2A 89.961 1783 102 13 500 2242 779621271 779623016 0.000000e+00 2230
4 TraesCS2A01G592300 chr2A 91.120 1464 88 18 783 2242 779341431 779342856 0.000000e+00 1945
5 TraesCS2A01G592300 chr2A 95.179 809 16 6 1 786 779431931 779432739 0.000000e+00 1256
6 TraesCS2A01G592300 chr2A 90.541 444 41 1 1 444 779619856 779620298 9.770000e-164 586
7 TraesCS2A01G592300 chr2A 90.090 444 43 1 1 444 779339808 779340250 2.120000e-160 575
8 TraesCS2A01G592300 chr2A 90.090 444 43 1 1 444 779507823 779508265 2.120000e-160 575
9 TraesCS2A01G592300 chr2A 92.903 155 9 2 2298 2451 779626704 779626857 8.830000e-55 224
10 TraesCS2A01G592300 chr2A 84.516 155 22 1 2299 2453 779305497 779305649 4.220000e-33 152
11 TraesCS2A01G592300 chr2D 92.083 1402 94 7 807 2194 634155163 634153765 0.000000e+00 1958
12 TraesCS2A01G592300 chr2D 90.896 1406 73 11 377 1731 634149956 634148555 0.000000e+00 1836
13 TraesCS2A01G592300 chr2D 89.277 429 45 1 2 430 634155867 634155440 9.980000e-149 536
14 TraesCS2A01G592300 chr2D 89.694 359 35 2 1 359 634152101 634151745 7.990000e-125 457
15 TraesCS2A01G592300 chr2D 88.141 312 18 5 494 786 634155430 634155119 1.080000e-93 353
16 TraesCS2A01G592300 chr2D 87.889 289 28 2 2012 2299 634148556 634148274 1.410000e-87 333
17 TraesCS2A01G592300 chr2D 88.372 258 28 2 1 256 492202498 492202241 2.370000e-80 309
18 TraesCS2A01G592300 chr2D 96.078 153 6 0 2299 2451 634145461 634145309 1.460000e-62 250
19 TraesCS2A01G592300 chr2D 84.932 146 22 0 2306 2451 634158378 634158233 5.470000e-32 148
20 TraesCS2A01G592300 chr2B 90.263 1407 94 12 805 2194 777143859 777142479 0.000000e+00 1799
21 TraesCS2A01G592300 chr2B 84.161 322 22 10 494 786 777144238 777143917 3.990000e-73 285
22 TraesCS2A01G592300 chr2B 87.692 130 15 1 2299 2428 777145683 777145555 1.520000e-32 150
23 TraesCS2A01G592300 chr2B 92.771 83 5 1 625 707 777143887 777143806 4.280000e-23 119
24 TraesCS2A01G592300 chr2B 86.916 107 6 3 382 481 777144300 777144195 1.990000e-21 113
25 TraesCS2A01G592300 chr5B 87.308 260 30 2 1 257 340535018 340535277 6.630000e-76 294
26 TraesCS2A01G592300 chr3D 86.923 260 32 2 3 261 386736349 386736091 8.580000e-75 291


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 TraesCS2A01G592300 chr2A 779528649 779531101 2452 False 4530.000000 4530 100.00000 1 2453 1 chr2A.!!$F2 2452
1 TraesCS2A01G592300 chr2A 779431931 779434343 2412 False 2009.500000 2763 96.04400 1 2453 2 chr2A.!!$F4 2452
2 TraesCS2A01G592300 chr2A 779507823 779511329 3506 False 1447.500000 2320 90.40550 1 2242 2 chr2A.!!$F5 2241
3 TraesCS2A01G592300 chr2A 779339808 779342856 3048 False 1260.000000 1945 90.60500 1 2242 2 chr2A.!!$F3 2241
4 TraesCS2A01G592300 chr2A 779619856 779626857 7001 False 1013.333333 2230 91.13500 1 2451 3 chr2A.!!$F6 2450
5 TraesCS2A01G592300 chr2D 634145309 634158378 13069 True 733.875000 1958 89.87375 1 2451 8 chr2D.!!$R2 2450
6 TraesCS2A01G592300 chr2B 777142479 777145683 3204 True 493.200000 1799 88.36060 382 2428 5 chr2B.!!$R1 2046

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
150 2661 1.147376 TGTGAGTGGTGGTTTCGGG 59.853 57.895 0.0 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2099 11477 0.604073 GCGGGGTAAGCTAGATCCTC 59.396 60.0 0.0 0.0 0.0 3.71 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
144 2655 1.502690 TTGTAGGTGTGAGTGGTGGT 58.497 50.000 0.00 0.00 0.00 4.16
150 2661 1.147376 TGTGAGTGGTGGTTTCGGG 59.853 57.895 0.00 0.00 0.00 5.14
163 2674 2.885894 GGTTTCGGGTGGTTTGATGTAA 59.114 45.455 0.00 0.00 0.00 2.41
177 2688 7.122055 TGGTTTGATGTAAGTTTTTGTCAGACT 59.878 33.333 1.31 0.00 0.00 3.24
726 4531 3.371898 TGAGTTATCTGATTGCACGCAAG 59.628 43.478 10.60 0.00 39.47 4.01
804 4731 3.067106 CTCTTTCACTTGGCACGTACAT 58.933 45.455 0.00 0.00 0.00 2.29
856 4784 1.592131 CATCCTCAGCTCGCTCTGC 60.592 63.158 0.00 0.00 34.19 4.26
864 4792 3.086391 GCTCGCTCTGCTCATCCCA 62.086 63.158 0.00 0.00 0.00 4.37
884 4812 3.067106 CACTCTTTCACTTGGCACGTAT 58.933 45.455 0.00 0.00 0.00 3.06
1011 4972 4.741342 CACAGGCCAGAATGAAGATTTTC 58.259 43.478 5.01 0.00 39.69 2.29
1206 5167 1.756538 CAGAAGGGCCACAACAACTTT 59.243 47.619 6.18 0.00 0.00 2.66
1328 5289 2.116827 TGGTTTGTGGACAAAGTCGT 57.883 45.000 5.18 0.00 45.36 4.34
1329 5290 1.740585 TGGTTTGTGGACAAAGTCGTG 59.259 47.619 5.18 0.00 45.36 4.35
1344 5305 1.193874 GTCGTGTTCACCCAAATCGAC 59.806 52.381 0.00 0.00 39.04 4.20
1501 5462 8.077991 CGAATACATCATTTTACATGCCTGAAT 58.922 33.333 0.00 0.00 0.00 2.57
1684 5647 1.067071 CAGTACCTTCCTCGTGGGTTC 60.067 57.143 3.23 0.00 34.86 3.62
1688 5651 1.481056 CCTTCCTCGTGGGTTCCTGT 61.481 60.000 3.23 0.00 36.25 4.00
2011 5980 1.414919 ACACGCTCTCCACAAACCTTA 59.585 47.619 0.00 0.00 0.00 2.69
2099 11477 3.767230 CGCCAGCTTCACGTCACG 61.767 66.667 0.00 0.00 0.00 4.35
2302 15413 1.030457 CCTAGACGTCCGGCTGTATT 58.970 55.000 13.01 0.00 34.01 1.89
2365 15476 2.435069 TCTAGGACAGGGTCTACTCGAG 59.565 54.545 11.84 11.84 32.47 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
144 2655 3.822940 ACTTACATCAAACCACCCGAAA 58.177 40.909 0.00 0.00 0.00 3.46
150 2661 7.220108 GTCTGACAAAAACTTACATCAAACCAC 59.780 37.037 2.24 0.00 0.00 4.16
751 4660 3.363970 GCGTGGTCAACAGATTACTTGTG 60.364 47.826 0.00 0.00 0.00 3.33
804 4731 9.462174 CAGCAGATTACTTTCAAACAAAATACA 57.538 29.630 0.00 0.00 0.00 2.29
856 4784 3.341823 CCAAGTGAAAGAGTGGGATGAG 58.658 50.000 0.00 0.00 0.00 2.90
864 4792 2.902705 TACGTGCCAAGTGAAAGAGT 57.097 45.000 0.00 0.00 0.00 3.24
884 4812 6.016860 ACGTAATGAGGTCTATGCACGTATTA 60.017 38.462 0.00 0.00 39.36 0.98
890 4818 4.928601 TGTACGTAATGAGGTCTATGCAC 58.071 43.478 0.00 0.00 0.00 4.57
969 4929 0.949397 CGTGTAGGATGGCGCTAGTA 59.051 55.000 7.64 0.00 0.00 1.82
1011 4972 1.870167 GCGAGGAGAAATAGGGCGAAG 60.870 57.143 0.00 0.00 0.00 3.79
1206 5167 1.116308 TGTCGGTGTGTCCTTTCTCA 58.884 50.000 0.00 0.00 0.00 3.27
1328 5289 2.350057 TTGGTCGATTTGGGTGAACA 57.650 45.000 0.00 0.00 0.00 3.18
1329 5290 3.719173 TTTTGGTCGATTTGGGTGAAC 57.281 42.857 0.00 0.00 0.00 3.18
1684 5647 7.973388 CAGAGAATACTTCTAAAGTCTCACAGG 59.027 40.741 0.00 0.00 41.77 4.00
1688 5651 6.374613 TCGCAGAGAATACTTCTAAAGTCTCA 59.625 38.462 0.00 0.00 41.77 3.27
1772 5735 3.978687 ACTTTCCTCGTCTATTATGCCG 58.021 45.455 0.00 0.00 0.00 5.69
2011 5980 2.158959 GCGACACGAGCTTATGCGT 61.159 57.895 0.00 5.04 45.42 5.24
2099 11477 0.604073 GCGGGGTAAGCTAGATCCTC 59.396 60.000 0.00 0.00 0.00 3.71
2302 15413 1.211949 CGATTTTCTCCTTGGGCCCTA 59.788 52.381 25.70 15.88 0.00 3.53
2365 15476 4.451150 TCTGCCATGGTCGCGGTC 62.451 66.667 14.67 0.00 34.10 4.79


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

AutoCloner maintained by Alex Coulton.