Multiple sequence alignment - TraesCS2D01G153400

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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 TraesCS2D01G153400 chr2D 100.000 3385 0 0 1 3385 96082493 96085877 0.000000e+00 6252.0
1 TraesCS2D01G153400 chr2D 98.306 2774 36 5 2 2765 96291942 96294714 0.000000e+00 4852.0
2 TraesCS2D01G153400 chr2D 97.525 2182 39 9 1216 3385 95917196 95919374 0.000000e+00 3716.0
3 TraesCS2D01G153400 chr2D 95.468 2074 36 21 705 2765 95786405 95788433 0.000000e+00 3256.0
4 TraesCS2D01G153400 chr2D 94.627 1098 44 10 136 1227 95914331 95915419 0.000000e+00 1687.0
5 TraesCS2D01G153400 chr2D 93.017 401 18 3 2985 3385 95788468 95788858 8.140000e-161 577.0
6 TraesCS2D01G153400 chr2D 92.269 401 21 2 2985 3385 96294749 96295139 8.200000e-156 560.0
7 TraesCS2D01G153400 chr2D 97.761 134 2 1 1 133 95902482 95902615 2.630000e-56 230.0
8 TraesCS2D01G153400 chr2D 84.328 134 17 3 3106 3237 533780162 533780293 9.860000e-26 128.0
9 TraesCS2D01G153400 chr2D 84.127 126 14 6 3114 3237 388170225 388170346 2.130000e-22 117.0
10 TraesCS2D01G153400 chr2D 81.022 137 22 3 3105 3240 524003958 524003825 4.620000e-19 106.0
11 TraesCS2D01G153400 chr2D 87.097 62 5 3 1460 1521 95772769 95772827 2.180000e-07 67.6
12 TraesCS2D01G153400 chr2D 87.500 56 7 0 1450 1505 96679886 96679941 7.840000e-07 65.8
13 TraesCS2D01G153400 chr2D 87.500 56 7 0 1450 1505 96749673 96749728 7.840000e-07 65.8
14 TraesCS2D01G153400 chr2D 100.000 32 0 0 2927 2958 95788432 95788463 3.650000e-05 60.2
15 TraesCS2D01G153400 chr2D 100.000 32 0 0 2927 2958 96294713 96294744 3.650000e-05 60.2
16 TraesCS2D01G153400 chr2A 87.592 2039 164 35 700 2700 94317135 94319122 0.000000e+00 2281.0
17 TraesCS2D01G153400 chr2A 91.472 856 70 2 1593 2448 94447034 94447886 0.000000e+00 1173.0
18 TraesCS2D01G153400 chr2A 92.738 661 45 3 2007 2666 94324405 94325063 0.000000e+00 952.0
19 TraesCS2D01G153400 chr2A 80.061 657 71 26 720 1367 94323815 94324420 1.870000e-117 433.0
20 TraesCS2D01G153400 chr2A 89.474 228 20 3 2479 2702 94447882 94448109 5.530000e-73 285.0
21 TraesCS2D01G153400 chr2A 90.751 173 12 3 2927 3099 94319876 94320044 9.450000e-56 228.0
22 TraesCS2D01G153400 chr2A 87.407 135 15 2 3237 3370 94320679 94320812 1.630000e-33 154.0
23 TraesCS2D01G153400 chr2A 91.150 113 7 3 3238 3348 94449628 94449739 2.100000e-32 150.0
24 TraesCS2D01G153400 chr2A 84.314 153 15 7 2948 3093 95163548 95163698 1.270000e-29 141.0
25 TraesCS2D01G153400 chr2A 96.923 65 2 0 2701 2765 94449400 94449464 3.570000e-20 110.0
26 TraesCS2D01G153400 chr2A 85.135 74 9 2 700 772 94419445 94419517 1.300000e-09 75.0
27 TraesCS2D01G153400 chrUn 90.714 1023 76 12 1583 2601 17383308 17384315 0.000000e+00 1345.0
28 TraesCS2D01G153400 chrUn 87.991 916 63 20 700 1579 17382370 17383274 0.000000e+00 1038.0
29 TraesCS2D01G153400 chrUn 100.000 407 0 0 2162 2568 477994025 477993619 0.000000e+00 752.0
30 TraesCS2D01G153400 chr7D 87.821 312 33 3 283 592 630765844 630765536 8.930000e-96 361.0
31 TraesCS2D01G153400 chr7D 86.032 315 39 5 280 592 632095853 632095542 1.950000e-87 333.0
32 TraesCS2D01G153400 chr7D 92.021 188 15 0 2756 2943 202716852 202716665 7.200000e-67 265.0
33 TraesCS2D01G153400 chr4A 87.781 311 30 6 284 591 535261387 535261082 1.160000e-94 357.0
34 TraesCS2D01G153400 chr4A 94.857 175 9 0 2764 2938 581869016 581868842 1.200000e-69 274.0
35 TraesCS2D01G153400 chr4B 86.859 312 36 4 282 591 92021766 92021458 8.990000e-91 344.0
36 TraesCS2D01G153400 chr4B 95.322 171 8 0 2762 2932 80990815 80990645 4.300000e-69 272.0
37 TraesCS2D01G153400 chr4B 74.747 198 34 11 53 246 416545200 416545015 1.300000e-09 75.0
38 TraesCS2D01G153400 chr6B 86.392 316 39 3 284 599 130939760 130940071 3.230000e-90 342.0
39 TraesCS2D01G153400 chr5D 86.731 309 38 2 284 591 491336202 491335896 1.160000e-89 340.0
40 TraesCS2D01G153400 chr5D 100.000 28 0 0 210 237 36491432 36491459 6.000000e-03 52.8
41 TraesCS2D01G153400 chr3D 86.207 319 39 4 284 600 559081078 559080763 1.160000e-89 340.0
42 TraesCS2D01G153400 chr3D 85.606 132 16 3 3106 3236 145566331 145566202 5.890000e-28 135.0
43 TraesCS2D01G153400 chr4D 96.988 166 5 0 2763 2928 404108577 404108742 2.570000e-71 279.0
44 TraesCS2D01G153400 chr1D 95.376 173 6 2 2760 2931 112940488 112940317 1.200000e-69 274.0
45 TraesCS2D01G153400 chr1D 95.376 173 6 2 2760 2931 321444818 321444989 1.200000e-69 274.0
46 TraesCS2D01G153400 chr1D 84.211 133 18 2 3106 3237 340178924 340178794 3.550000e-25 126.0
47 TraesCS2D01G153400 chr3B 94.350 177 9 1 2757 2933 571752518 571752693 1.550000e-68 270.0
48 TraesCS2D01G153400 chr6D 92.063 189 14 1 2740 2928 271602751 271602938 7.200000e-67 265.0
49 TraesCS2D01G153400 chr2B 82.759 145 15 5 2959 3100 148043035 148043172 1.650000e-23 121.0
50 TraesCS2D01G153400 chr2B 87.500 56 7 0 1450 1505 147830231 147830286 7.840000e-07 65.8
51 TraesCS2D01G153400 chr5B 82.707 133 18 5 3105 3236 356177199 356177071 2.760000e-21 113.0
52 TraesCS2D01G153400 chr7B 76.471 170 34 5 1675 1841 535614669 535614835 1.670000e-13 87.9
53 TraesCS2D01G153400 chr3A 81.308 107 18 2 1677 1782 628219824 628219719 6.020000e-13 86.1
54 TraesCS2D01G153400 chr3A 79.091 110 13 8 146 251 506779121 506779224 2.180000e-07 67.6
55 TraesCS2D01G153400 chr7A 80.734 109 19 2 1675 1782 574754198 574754305 2.160000e-12 84.2
56 TraesCS2D01G153400 chr5A 100.000 29 0 0 211 239 69358080 69358052 2.000000e-03 54.7


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 TraesCS2D01G153400 chr2D 96082493 96085877 3384 False 6252.000000 6252 100.000000 1 3385 1 chr2D.!!$F3 3384
1 TraesCS2D01G153400 chr2D 95914331 95919374 5043 False 2701.500000 3716 96.076000 136 3385 2 chr2D.!!$F9 3249
2 TraesCS2D01G153400 chr2D 96291942 96295139 3197 False 1824.066667 4852 96.858333 2 3385 3 chr2D.!!$F10 3383
3 TraesCS2D01G153400 chr2D 95786405 95788858 2453 False 1297.733333 3256 96.161667 705 3385 3 chr2D.!!$F8 2680
4 TraesCS2D01G153400 chr2A 94317135 94325063 7928 False 809.600000 2281 87.709800 700 3370 5 chr2A.!!$F3 2670
5 TraesCS2D01G153400 chr2A 94447034 94449739 2705 False 429.500000 1173 92.254750 1593 3348 4 chr2A.!!$F4 1755
6 TraesCS2D01G153400 chrUn 17382370 17384315 1945 False 1191.500000 1345 89.352500 700 2601 2 chrUn.!!$F1 1901

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
221 223 0.039888 CGGTCGAAAATTTGCGGGTT 60.04 50.0 18.38 0.0 0.00 4.11 F
703 710 0.529992 GCGAAGGATACAGAACGGGG 60.53 60.0 0.00 0.0 41.41 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2052 3928 2.654877 CTTCCCAGCGTACGTGGT 59.345 61.111 25.1 8.21 32.62 4.16 R
2630 4515 5.169295 GGATAACGCATACCTAAGGATGTC 58.831 45.833 0.0 0.00 0.00 3.06 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
221 223 0.039888 CGGTCGAAAATTTGCGGGTT 60.040 50.000 18.38 0.00 0.00 4.11
528 535 5.261209 TGTTAGCTTGCAAAACAGTCATT 57.739 34.783 10.41 0.00 0.00 2.57
609 616 1.753956 ACGATTTTTCGCAGCACAAC 58.246 45.000 0.00 0.00 36.44 3.32
703 710 0.529992 GCGAAGGATACAGAACGGGG 60.530 60.000 0.00 0.00 41.41 5.73
954 976 4.726416 CAAGTTTTCTTCATCCCATCGTG 58.274 43.478 0.00 0.00 38.17 4.35
1266 3093 1.534476 TTCACCTCCACCGGCTACA 60.534 57.895 0.00 0.00 0.00 2.74
2052 3928 1.873270 CTCCACCACGTCGATGGACA 61.873 60.000 12.02 0.00 43.02 4.02
2630 4515 7.101700 TGGCAATATATATCTTCTCTGCTGTG 58.898 38.462 12.33 0.00 0.00 3.66
2796 6005 7.281549 TCCGTTCCTAAATATTTGCCTTTCTAC 59.718 37.037 11.05 0.00 0.00 2.59
2811 6020 8.044060 TGCCTTTCTACAGATTTCAATAAGTG 57.956 34.615 0.00 0.00 0.00 3.16
3224 6494 1.805345 GAAGTCTCAGTCGACCGAGAA 59.195 52.381 28.40 13.29 39.88 2.87
3356 7068 0.329261 AAATGCCTAGCTGCCTGTCA 59.671 50.000 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 0.103208 TGCAAACACGCCGGATTTTT 59.897 45.000 5.05 0.00 0.00 1.94
25 26 2.176546 CTCATGCAAACACGCCGG 59.823 61.111 0.00 0.00 0.00 6.13
264 266 7.039853 AGGGAGTACTTGTAAACTACTGAGTTC 60.040 40.741 0.00 0.00 45.50 3.01
345 352 8.545229 TTTTTGCATCAATTATTGTTAGTGGG 57.455 30.769 4.77 0.00 0.00 4.61
360 367 8.836268 AGAAAGCATCTTTAATTTTTGCATCA 57.164 26.923 0.00 0.00 33.39 3.07
703 710 6.080648 TGTGTCGGTAGGTAATGATATCAC 57.919 41.667 7.78 0.00 0.00 3.06
954 976 3.023950 CTCGATCGAGGGACGTCC 58.976 66.667 32.81 27.04 43.13 4.79
1128 1162 3.732849 GGAGGTGGGGAAGGGCTG 61.733 72.222 0.00 0.00 0.00 4.85
2052 3928 2.654877 CTTCCCAGCGTACGTGGT 59.345 61.111 25.10 8.21 32.62 4.16
2630 4515 5.169295 GGATAACGCATACCTAAGGATGTC 58.831 45.833 0.00 0.00 0.00 3.06
2811 6020 6.763135 TCACTCATTTTGCTCCATATGTAGTC 59.237 38.462 1.24 0.00 0.00 2.59
2911 6122 5.522641 AGTTTATTACTCCCTCCGTTCCTA 58.477 41.667 0.00 0.00 28.23 2.94
3212 6482 1.471119 TGGCTAATTCTCGGTCGACT 58.529 50.000 16.46 0.00 0.00 4.18
3224 6494 6.334202 TGTTTTTCGTTTCAGTTTGGCTAAT 58.666 32.000 0.00 0.00 0.00 1.73
3356 7068 2.688794 GGCGAGACGAGAAGACGGT 61.689 63.158 0.00 0.00 37.61 4.83


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

AutoCloner maintained by Alex Coulton.