Multiple sequence alignment - TraesCS2A01G592400

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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 TraesCS2A01G592400 chr2A 100.000 2595 0 0 1 2595 779620724 779623318 0.000000e+00 4793
1 TraesCS2A01G592400 chr2A 96.277 2256 33 12 241 2469 779509274 779511505 0.000000e+00 3653
2 TraesCS2A01G592400 chr2A 95.218 1694 27 7 803 2469 779341366 779343032 0.000000e+00 2630
3 TraesCS2A01G592400 chr2A 89.961 1783 102 13 548 2293 779529148 779530890 0.000000e+00 2230
4 TraesCS2A01G592400 chr2A 90.840 1441 92 7 891 2293 779432694 779434132 0.000000e+00 1893
5 TraesCS2A01G592400 chr2A 96.296 594 18 1 1 594 779340676 779341265 0.000000e+00 972
6 TraesCS2A01G592400 chr2A 93.567 342 21 1 548 889 779432435 779432775 2.300000e-140 508
7 TraesCS2A01G592400 chr2A 97.143 245 7 0 1 245 779508778 779509022 5.170000e-112 414
8 TraesCS2A01G592400 chr2A 95.420 131 6 0 2465 2595 779350982 779351112 2.620000e-50 209
9 TraesCS2A01G592400 chr2A 94.656 131 7 0 2465 2595 779514406 779514536 1.220000e-48 204
10 TraesCS2A01G592400 chr2B 88.914 1768 125 42 541 2245 777144238 777142479 0.000000e+00 2113
11 TraesCS2A01G592400 chr2B 90.476 84 6 2 673 756 777143887 777143806 2.730000e-20 110
12 TraesCS2A01G592400 chr2D 93.053 1310 66 12 504 1789 634149864 634148556 0.000000e+00 1892
13 TraesCS2A01G592400 chr2D 90.994 1399 81 15 892 2245 634155163 634153765 0.000000e+00 1844
14 TraesCS2A01G592400 chr2D 93.017 358 24 1 532 889 634155439 634155083 2.960000e-144 521
15 TraesCS2A01G592400 chr2D 95.167 269 12 1 2325 2593 634148229 634147962 8.580000e-115 424
16 TraesCS2A01G592400 chr2D 94.595 222 12 0 2072 2293 634148553 634148332 6.880000e-91 344
17 TraesCS2A01G592400 chr2D 96.296 81 3 0 892 972 634149560 634149480 1.620000e-27 134
18 TraesCS2A01G592400 chrUn 91.772 316 14 6 193 507 12151030 12151334 1.850000e-116 429
19 TraesCS2A01G592400 chrUn 91.772 316 14 6 193 507 285687180 285687484 1.850000e-116 429
20 TraesCS2A01G592400 chr3A 90.823 316 17 6 193 507 545354772 545355076 1.860000e-111 412
21 TraesCS2A01G592400 chr3A 89.881 168 15 2 1 166 173925812 173925645 5.620000e-52 215
22 TraesCS2A01G592400 chr1B 90.566 318 18 7 192 508 646916627 646916933 6.680000e-111 411
23 TraesCS2A01G592400 chr7D 89.908 327 18 8 192 515 455570659 455570345 8.650000e-110 407
24 TraesCS2A01G592400 chr6B 90.093 323 19 7 186 507 26600094 26600404 8.650000e-110 407
25 TraesCS2A01G592400 chr4B 89.846 325 19 9 189 512 655776896 655777207 3.110000e-109 405
26 TraesCS2A01G592400 chr7B 90.588 170 13 3 1 167 255203680 255203511 3.360000e-54 222
27 TraesCS2A01G592400 chr6A 91.018 167 11 4 1 163 516259036 516259202 3.360000e-54 222
28 TraesCS2A01G592400 chr1A 90.533 169 12 4 1 166 542819116 542818949 1.210000e-53 220
29 TraesCS2A01G592400 chr1A 90.361 166 13 2 1 165 23411905 23411742 5.620000e-52 215
30 TraesCS2A01G592400 chr6D 90.419 167 12 4 1 164 425441480 425441315 1.560000e-52 217
31 TraesCS2A01G592400 chr6D 89.474 171 16 2 1 169 224255333 224255163 5.620000e-52 215


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 TraesCS2A01G592400 chr2A 779620724 779623318 2594 False 4793.000000 4793 100.000000 1 2595 1 chr2A.!!$F3 2594
1 TraesCS2A01G592400 chr2A 779529148 779530890 1742 False 2230.000000 2230 89.961000 548 2293 1 chr2A.!!$F2 1745
2 TraesCS2A01G592400 chr2A 779340676 779343032 2356 False 1801.000000 2630 95.757000 1 2469 2 chr2A.!!$F4 2468
3 TraesCS2A01G592400 chr2A 779508778 779514536 5758 False 1423.666667 3653 96.025333 1 2595 3 chr2A.!!$F6 2594
4 TraesCS2A01G592400 chr2A 779432435 779434132 1697 False 1200.500000 1893 92.203500 548 2293 2 chr2A.!!$F5 1745
5 TraesCS2A01G592400 chr2B 777142479 777144238 1759 True 1111.500000 2113 89.695000 541 2245 2 chr2B.!!$R1 1704
6 TraesCS2A01G592400 chr2D 634153765 634155439 1674 True 1182.500000 1844 92.005500 532 2245 2 chr2D.!!$R2 1713
7 TraesCS2A01G592400 chr2D 634147962 634149864 1902 True 698.500000 1892 94.777750 504 2593 4 chr2D.!!$R1 2089

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
67 68 0.107831 TTTCTTCCTGGGTCACCACG 59.892 55.0 0.0 0.0 43.37 4.94 F
77 78 0.247736 GGTCACCACGCTCATCTCTT 59.752 55.0 0.0 0.0 0.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1215 1554 2.169352 TCAGGCTCTTGATAACCAGCTC 59.831 50.00 0.0 0.0 32.14 4.09 R
1674 2017 4.277476 ACAGTGGAAACCAAAGATGAACA 58.723 39.13 0.0 0.0 34.18 3.18 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
40 41 2.886124 GCCTAGGTTCACGCGCTC 60.886 66.667 11.31 0.00 0.00 5.03
67 68 0.107831 TTTCTTCCTGGGTCACCACG 59.892 55.000 0.00 0.00 43.37 4.94
77 78 0.247736 GGTCACCACGCTCATCTCTT 59.752 55.000 0.00 0.00 0.00 2.85
338 595 2.950975 TGCATGCAAAGAAACTGAGTGA 59.049 40.909 20.30 0.00 0.00 3.41
545 802 3.120321 TGCGTGTCCTAAACTGTGATT 57.880 42.857 0.00 0.00 0.00 2.57
731 998 9.715121 ATTTTGTTTGACAATTAATCTGCTGAT 57.285 25.926 0.00 0.00 38.00 2.90
734 1001 8.058667 TGTTTGACAATTAATCTGCTGATCAT 57.941 30.769 6.55 0.00 31.51 2.45
748 1015 3.811098 GCTGATCATGCCATCCTCATCTT 60.811 47.826 0.00 0.00 0.00 2.40
997 1303 4.833380 ACCTGCATAGACCTCATTACGTAT 59.167 41.667 0.00 0.00 0.00 3.06
1139 1478 6.183360 ACGCACAGTGCAAATTCGTTATATTA 60.183 34.615 25.19 0.00 45.36 0.98
1145 1484 8.387354 CAGTGCAAATTCGTTATATTAGTCACA 58.613 33.333 0.00 0.00 0.00 3.58
1201 1540 4.320129 CCGTATATCTCTGTCAGTGAGCAG 60.320 50.000 10.20 13.44 0.00 4.24
1215 1554 2.812178 GCAGCGCAAATGGCAAGG 60.812 61.111 11.47 0.00 45.17 3.61
1530 1869 4.080582 CCAAGTAACCACCTATGTCCATGA 60.081 45.833 0.00 0.00 0.00 3.07
1747 2090 0.834687 ACCTTCCTCGTGGGTTGCTA 60.835 55.000 3.23 0.00 36.25 3.49
1853 2196 7.375053 GTCTAGGCATAATAGACAGAGAAAGG 58.625 42.308 7.97 0.00 45.57 3.11
2084 2436 3.740115 ACCTTGCTCATAAGTTCGTGTT 58.260 40.909 0.00 0.00 0.00 3.32
2539 5885 2.428569 TTCGTCAGTGTCGAGCGC 60.429 61.111 12.06 0.00 38.52 5.92
2563 5909 0.178068 GGAGATAGAAAGGTGCGGCA 59.822 55.000 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 6.566141 GTGAACCTAGGCAAAACTTTTAACA 58.434 36.000 9.30 0.00 0.00 2.41
40 41 1.089920 CCCAGGAAGAAACGATGCTG 58.910 55.000 0.00 0.00 35.08 4.41
77 78 6.876789 TGATGTGGCGAGTTATTTAAGAAGAA 59.123 34.615 0.00 0.00 0.00 2.52
115 116 0.804989 ATGTGCTAAGCTTTCCACGC 59.195 50.000 3.20 0.84 0.00 5.34
338 595 7.108841 TCATAATGACGGTAAGCTACTTCTT 57.891 36.000 0.00 0.00 0.00 2.52
545 802 4.496360 TGACGCGTGTTCAATAGGATAAA 58.504 39.130 20.70 0.00 0.00 1.40
686 953 5.904362 AAATACAGGTCTTCCAGCATTTC 57.096 39.130 0.00 0.00 35.89 2.17
731 998 1.493446 AGCAAGATGAGGATGGCATGA 59.507 47.619 3.81 0.00 0.00 3.07
734 1001 1.134189 CAGAGCAAGATGAGGATGGCA 60.134 52.381 0.00 0.00 0.00 4.92
748 1015 4.186926 GTGCAATCAGATAACTCAGAGCA 58.813 43.478 0.00 0.00 0.00 4.26
997 1303 7.598869 CACAAATGCGAGGTCTATTTATAGCTA 59.401 37.037 0.00 0.00 0.00 3.32
1139 1478 6.611613 TCATCTTTATCTCCTGTTGTGACT 57.388 37.500 0.00 0.00 0.00 3.41
1145 1484 5.374921 CCTGCATCATCTTTATCTCCTGTT 58.625 41.667 0.00 0.00 0.00 3.16
1201 1540 2.507769 GCTCCTTGCCATTTGCGC 60.508 61.111 0.00 0.00 45.60 6.09
1215 1554 2.169352 TCAGGCTCTTGATAACCAGCTC 59.831 50.000 0.00 0.00 32.14 4.09
1415 1754 6.920448 TGAATGTCTTCTCCTTTTGGGACAAT 60.920 38.462 0.00 0.00 39.35 2.71
1674 2017 4.277476 ACAGTGGAAACCAAAGATGAACA 58.723 39.130 0.00 0.00 34.18 3.18
1747 2090 6.557110 GCAGAGAATACTTCTAAAGTCTCGT 58.443 40.000 0.00 0.00 41.77 4.18
2084 2436 0.817634 CCGTGGACACTTTGGAAGCA 60.818 55.000 0.56 0.00 0.00 3.91
2539 5885 2.280628 GCACCTTTCTATCTCCAACGG 58.719 52.381 0.00 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.