Multiple sequence alignment - TraesCS6A01G160000

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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 TraesCS6A01G160000 chr6A 100.000 1738 0 0 681 2418 152874272 152872535 0.000000e+00 3210.0
1 TraesCS6A01G160000 chr6A 91.407 1734 111 15 690 2416 152886384 152888086 0.000000e+00 2342.0
2 TraesCS6A01G160000 chr6A 94.288 1103 50 5 1321 2413 152855827 152856926 0.000000e+00 1676.0
3 TraesCS6A01G160000 chr6A 93.313 643 36 4 693 1331 152846593 152847232 0.000000e+00 942.0
4 TraesCS6A01G160000 chr6A 100.000 200 0 0 1 200 152874952 152874753 1.060000e-98 370.0
5 TraesCS6A01G160000 chr6A 97.959 98 2 0 102 199 152885742 152885839 1.150000e-38 171.0
6 TraesCS6A01G160000 chr3A 94.543 1741 89 3 681 2416 383542336 383540597 0.000000e+00 2684.0
7 TraesCS6A01G160000 chr3A 94.072 388 23 0 784 1171 302917619 302918006 7.450000e-165 590.0
8 TraesCS6A01G160000 chr3A 81.870 353 56 8 1639 1988 428000172 428000519 8.460000e-75 291.0
9 TraesCS6A01G160000 chr3A 94.681 94 5 0 11 104 427894677 427894584 1.940000e-31 147.0
10 TraesCS6A01G160000 chr3A 89.815 108 9 1 1 106 84791592 84791699 1.170000e-28 137.0
11 TraesCS6A01G160000 chr3A 85.612 139 11 5 68 199 302916747 302916883 1.170000e-28 137.0
12 TraesCS6A01G160000 chr4A 95.311 1642 74 3 778 2416 209653104 209651463 0.000000e+00 2603.0
13 TraesCS6A01G160000 chr4A 82.286 350 55 7 1642 1988 176009993 176009648 1.820000e-76 296.0
14 TraesCS6A01G160000 chr4A 91.935 124 8 2 77 199 209653639 209653517 3.200000e-39 172.0
15 TraesCS6A01G160000 chr1B 94.912 570 26 3 1783 2350 551651539 551650971 0.000000e+00 889.0
16 TraesCS6A01G160000 chr1B 89.655 609 60 3 1171 1779 551652641 551652036 0.000000e+00 773.0
17 TraesCS6A01G160000 chr1B 93.805 113 7 0 2233 2345 143904864 143904752 1.150000e-38 171.0
18 TraesCS6A01G160000 chr4B 93.728 574 33 3 1780 2350 122751123 122750550 0.000000e+00 857.0
19 TraesCS6A01G160000 chr4B 89.819 609 60 2 1171 1779 122752163 122751557 0.000000e+00 780.0
20 TraesCS6A01G160000 chr2B 91.304 368 32 0 803 1170 186586528 186586895 9.980000e-139 503.0
21 TraesCS6A01G160000 chr2B 90.870 230 21 0 2113 2342 731301496 731301725 2.330000e-80 309.0
22 TraesCS6A01G160000 chr6D 84.000 350 50 6 1642 1988 239344651 239344305 4.980000e-87 331.0
23 TraesCS6A01G160000 chr2D 87.413 286 27 3 1558 1842 322749521 322749244 1.080000e-83 320.0
24 TraesCS6A01G160000 chr2D 93.814 97 6 0 8 104 357413854 357413950 1.940000e-31 147.0
25 TraesCS6A01G160000 chr7D 92.308 104 8 0 1 104 452843373 452843476 5.390000e-32 148.0
26 TraesCS6A01G160000 chr5A 91.589 107 7 1 1 105 133913122 133913228 1.940000e-31 147.0
27 TraesCS6A01G160000 chr5A 90.722 97 6 1 66 162 630213018 630213111 2.520000e-25 126.0
28 TraesCS6A01G160000 chr5A 89.796 98 6 3 69 162 704048415 704048318 3.260000e-24 122.0
29 TraesCS6A01G160000 chr4D 95.652 92 2 1 15 104 277696492 277696401 1.940000e-31 147.0
30 TraesCS6A01G160000 chr6B 84.177 158 15 6 13 162 200917405 200917560 6.970000e-31 145.0
31 TraesCS6A01G160000 chr6B 88.136 118 12 2 1047 1164 317682283 317682398 3.240000e-29 139.0
32 TraesCS6A01G160000 chr6B 89.899 99 9 1 69 166 21774259 21774161 2.520000e-25 126.0
33 TraesCS6A01G160000 chr1A 91.262 103 5 2 6 104 378939160 378939058 1.170000e-28 137.0
34 TraesCS6A01G160000 chr3D 89.815 108 7 1 1 104 353315285 353315392 4.190000e-28 135.0
35 TraesCS6A01G160000 chr5B 89.796 98 5 5 70 163 268994423 268994327 1.170000e-23 121.0
36 TraesCS6A01G160000 chr5D 86.607 112 7 6 69 174 236048451 236048560 1.520000e-22 117.0
37 TraesCS6A01G160000 chr7B 88.136 59 5 1 728 784 613701583 613701525 4.310000e-08 69.4


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 TraesCS6A01G160000 chr6A 152872535 152874952 2417 True 1790.0 3210 100.0000 1 2418 2 chr6A.!!$R1 2417
1 TraesCS6A01G160000 chr6A 152855827 152856926 1099 False 1676.0 1676 94.2880 1321 2413 1 chr6A.!!$F2 1092
2 TraesCS6A01G160000 chr6A 152885742 152888086 2344 False 1256.5 2342 94.6830 102 2416 2 chr6A.!!$F3 2314
3 TraesCS6A01G160000 chr6A 152846593 152847232 639 False 942.0 942 93.3130 693 1331 1 chr6A.!!$F1 638
4 TraesCS6A01G160000 chr3A 383540597 383542336 1739 True 2684.0 2684 94.5430 681 2416 1 chr3A.!!$R1 1735
5 TraesCS6A01G160000 chr3A 302916747 302918006 1259 False 363.5 590 89.8420 68 1171 2 chr3A.!!$F3 1103
6 TraesCS6A01G160000 chr4A 209651463 209653639 2176 True 1387.5 2603 93.6230 77 2416 2 chr4A.!!$R2 2339
7 TraesCS6A01G160000 chr1B 551650971 551652641 1670 True 831.0 889 92.2835 1171 2350 2 chr1B.!!$R2 1179
8 TraesCS6A01G160000 chr4B 122750550 122752163 1613 True 818.5 857 91.7735 1171 2350 2 chr4B.!!$R1 1179

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
751 815 0.624795 GATCCCCCACCTTCTTCCCT 60.625 60.0 0.0 0.0 0.0 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1713 2227 1.133025 GAAGCTGCACACACAAACTGT 59.867 47.619 1.02 0.0 0.0 3.55 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
23 24 6.345920 ACTTGTAAACTTCGTCAGTTCAAG 57.654 37.500 18.96 18.96 45.77 3.02
24 25 5.873164 ACTTGTAAACTTCGTCAGTTCAAGT 59.127 36.000 19.73 19.73 46.22 3.16
25 26 6.730960 TTGTAAACTTCGTCAGTTCAAGTT 57.269 33.333 3.69 0.00 45.77 2.66
26 27 6.102006 TGTAAACTTCGTCAGTTCAAGTTG 57.898 37.500 0.00 0.00 45.77 3.16
27 28 4.616181 AAACTTCGTCAGTTCAAGTTGG 57.384 40.909 2.34 0.00 45.77 3.77
28 29 2.561569 ACTTCGTCAGTTCAAGTTGGG 58.438 47.619 2.34 0.00 27.32 4.12
29 30 2.093128 ACTTCGTCAGTTCAAGTTGGGT 60.093 45.455 2.34 0.00 27.32 4.51
30 31 3.133362 ACTTCGTCAGTTCAAGTTGGGTA 59.867 43.478 2.34 0.00 27.32 3.69
31 32 3.823281 TCGTCAGTTCAAGTTGGGTAA 57.177 42.857 2.34 0.00 0.00 2.85
32 33 3.460103 TCGTCAGTTCAAGTTGGGTAAC 58.540 45.455 2.34 0.41 37.06 2.50
33 34 3.118702 TCGTCAGTTCAAGTTGGGTAACA 60.119 43.478 2.34 0.00 39.30 2.41
34 35 3.247648 CGTCAGTTCAAGTTGGGTAACAG 59.752 47.826 2.34 0.00 39.30 3.16
35 36 4.448210 GTCAGTTCAAGTTGGGTAACAGA 58.552 43.478 2.34 0.37 39.30 3.41
36 37 4.879545 GTCAGTTCAAGTTGGGTAACAGAA 59.120 41.667 2.34 0.00 39.30 3.02
37 38 5.531287 GTCAGTTCAAGTTGGGTAACAGAAT 59.469 40.000 2.34 0.00 39.30 2.40
38 39 6.708949 GTCAGTTCAAGTTGGGTAACAGAATA 59.291 38.462 2.34 0.00 39.30 1.75
39 40 7.227910 GTCAGTTCAAGTTGGGTAACAGAATAA 59.772 37.037 2.34 0.00 39.30 1.40
40 41 7.942341 TCAGTTCAAGTTGGGTAACAGAATAAT 59.058 33.333 2.34 0.00 39.30 1.28
41 42 9.226606 CAGTTCAAGTTGGGTAACAGAATAATA 57.773 33.333 2.34 0.00 39.30 0.98
42 43 9.975218 AGTTCAAGTTGGGTAACAGAATAATAT 57.025 29.630 2.34 0.00 39.30 1.28
56 57 7.853377 CAGAATAATATTCTGTTACGCGAGA 57.147 36.000 26.63 0.90 40.63 4.04
57 58 7.712119 CAGAATAATATTCTGTTACGCGAGAC 58.288 38.462 26.63 11.62 40.63 3.36
58 59 7.378728 CAGAATAATATTCTGTTACGCGAGACA 59.621 37.037 26.63 15.94 40.63 3.41
59 60 7.591795 AGAATAATATTCTGTTACGCGAGACAG 59.408 37.037 28.11 28.11 43.54 3.51
64 65 4.274421 TCTGTTACGCGAGACAGAATAG 57.726 45.455 31.47 16.52 46.64 1.73
65 66 2.784380 CTGTTACGCGAGACAGAATAGC 59.216 50.000 29.28 8.05 44.65 2.97
66 67 2.117910 GTTACGCGAGACAGAATAGCC 58.882 52.381 15.93 0.00 0.00 3.93
183 192 2.866523 CTACTCCGCCTACCCCCACA 62.867 65.000 0.00 0.00 0.00 4.17
189 198 2.622447 GCCTACCCCCACAACCCAT 61.622 63.158 0.00 0.00 0.00 4.00
199 208 2.272146 CAACCCATCACTCCCCCG 59.728 66.667 0.00 0.00 0.00 5.73
751 815 0.624795 GATCCCCCACCTTCTTCCCT 60.625 60.000 0.00 0.00 0.00 4.20
952 1463 5.507315 CCGCCACAAATCTAAAACAAGACTT 60.507 40.000 0.00 0.00 0.00 3.01
1073 1585 2.434884 CGCGCCACATCTCACCTT 60.435 61.111 0.00 0.00 0.00 3.50
1301 1815 3.785859 GGCGCCCTGACCTCATCA 61.786 66.667 18.11 0.00 35.45 3.07
1351 1865 1.153667 GCGTCTGCTCTTCTCCCTG 60.154 63.158 0.00 0.00 38.39 4.45
1368 1882 1.899437 CTGGACCCTTTGCTAGCCGA 61.899 60.000 13.29 0.00 0.00 5.54
1377 1891 3.450115 GCTAGCCGACGTCACCCT 61.450 66.667 17.16 10.30 0.00 4.34
1437 1951 2.997315 CAGTGCTCCCCGAGGTGA 60.997 66.667 0.00 0.00 0.00 4.02
1467 1981 1.875419 GCGTGCGTGCAATCCAAAAC 61.875 55.000 0.00 0.00 34.15 2.43
1536 2050 0.464735 CCTCGATCCCGTCTCTCTGT 60.465 60.000 0.00 0.00 37.05 3.41
1592 2106 2.507944 GCTCCATCACCGGCATCT 59.492 61.111 0.00 0.00 0.00 2.90
1622 2136 2.343758 GAGCAGCAACGGAGGACA 59.656 61.111 0.00 0.00 0.00 4.02
1883 2892 6.527722 CACTATGGAATTCGAATTTGGTGTTG 59.472 38.462 23.49 13.46 0.00 3.33
2081 3100 2.032071 AAACTTGGCGAGGTCCCG 59.968 61.111 6.71 0.00 0.00 5.14
2103 3122 1.175654 CACCCACAGCATGCAATACA 58.824 50.000 21.98 0.00 42.53 2.29
2260 3280 4.183865 GTTTTTGCATCTAGGATTTGCCC 58.816 43.478 0.00 0.00 37.37 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 8.744465 TGTTACCCAACTTGAACTGACGAAGT 62.744 42.308 0.00 0.00 38.61 3.01
9 10 2.561569 ACCCAACTTGAACTGACGAAG 58.438 47.619 0.00 0.00 0.00 3.79
10 11 2.702592 ACCCAACTTGAACTGACGAA 57.297 45.000 0.00 0.00 0.00 3.85
11 12 3.118702 TGTTACCCAACTTGAACTGACGA 60.119 43.478 0.00 0.00 35.56 4.20
12 13 3.199677 TGTTACCCAACTTGAACTGACG 58.800 45.455 0.00 0.00 35.56 4.35
13 14 4.448210 TCTGTTACCCAACTTGAACTGAC 58.552 43.478 0.00 0.00 35.56 3.51
14 15 4.764050 TCTGTTACCCAACTTGAACTGA 57.236 40.909 0.00 0.00 35.56 3.41
15 16 7.504924 TTATTCTGTTACCCAACTTGAACTG 57.495 36.000 0.00 0.00 35.56 3.16
16 17 9.975218 ATATTATTCTGTTACCCAACTTGAACT 57.025 29.630 0.00 0.00 35.56 3.01
33 34 7.423199 TGTCTCGCGTAACAGAATATTATTCT 58.577 34.615 12.26 12.26 0.00 2.40
34 35 7.590322 TCTGTCTCGCGTAACAGAATATTATTC 59.410 37.037 30.13 8.14 46.59 1.75
35 36 7.423199 TCTGTCTCGCGTAACAGAATATTATT 58.577 34.615 30.13 0.00 46.59 1.40
36 37 6.967135 TCTGTCTCGCGTAACAGAATATTAT 58.033 36.000 30.13 0.00 46.59 1.28
37 38 6.367686 TCTGTCTCGCGTAACAGAATATTA 57.632 37.500 30.13 15.59 46.59 0.98
38 39 5.244785 TCTGTCTCGCGTAACAGAATATT 57.755 39.130 30.13 0.00 46.59 1.28
39 40 4.895224 TCTGTCTCGCGTAACAGAATAT 57.105 40.909 30.13 0.00 46.59 1.28
44 45 2.784380 GCTATTCTGTCTCGCGTAACAG 59.216 50.000 26.64 26.64 43.41 3.16
45 46 2.479049 GGCTATTCTGTCTCGCGTAACA 60.479 50.000 5.77 11.01 0.00 2.41
46 47 2.117910 GGCTATTCTGTCTCGCGTAAC 58.882 52.381 5.77 6.33 0.00 2.50
47 48 1.066605 GGGCTATTCTGTCTCGCGTAA 59.933 52.381 5.77 0.00 0.00 3.18
48 49 0.666913 GGGCTATTCTGTCTCGCGTA 59.333 55.000 5.77 0.00 0.00 4.42
49 50 1.320344 TGGGCTATTCTGTCTCGCGT 61.320 55.000 5.77 0.00 0.00 6.01
50 51 0.032678 ATGGGCTATTCTGTCTCGCG 59.967 55.000 0.00 0.00 0.00 5.87
51 52 3.601443 ATATGGGCTATTCTGTCTCGC 57.399 47.619 0.00 0.00 0.00 5.03
729 792 1.984288 GAAGAAGGTGGGGGATCGGG 61.984 65.000 0.00 0.00 0.00 5.14
941 1452 1.170290 CCCCGCCGAAGTCTTGTTTT 61.170 55.000 0.00 0.00 0.00 2.43
1073 1585 1.082954 CCTGGGAAGGAGGGAAGGA 59.917 63.158 0.00 0.00 0.00 3.36
1221 1733 2.125269 GGTGGCCGCGAACTACAT 60.125 61.111 8.23 0.00 0.00 2.29
1293 1807 2.591753 CATGGCCGGTGATGAGGT 59.408 61.111 1.90 0.00 0.00 3.85
1351 1865 1.449778 GTCGGCTAGCAAAGGGTCC 60.450 63.158 18.24 0.00 0.00 4.46
1459 1973 1.755179 CATGCCTCCGAGTTTTGGAT 58.245 50.000 0.00 0.00 34.32 3.41
1536 2050 0.885879 ATGTGAGTAGTTGCCGTCGA 59.114 50.000 0.00 0.00 0.00 4.20
1622 2136 3.005539 AGCACGGGATCTGCAGGT 61.006 61.111 15.13 6.50 37.08 4.00
1713 2227 1.133025 GAAGCTGCACACACAAACTGT 59.867 47.619 1.02 0.00 0.00 3.55
1827 2836 6.775629 ACCAAATTGCTAACTAAGAGGTTCAA 59.224 34.615 0.00 0.00 0.00 2.69
1976 2987 8.915654 CAATAAAGAATGTTAAAAGCACCAGAC 58.084 33.333 0.00 0.00 0.00 3.51
1978 2989 8.816640 ACAATAAAGAATGTTAAAAGCACCAG 57.183 30.769 0.00 0.00 0.00 4.00
2091 3110 2.947652 GTCACCATCTGTATTGCATGCT 59.052 45.455 20.33 1.26 0.00 3.79
2103 3122 3.939837 CTGCACGGCGTCACCATCT 62.940 63.158 10.85 0.00 39.03 2.90
2173 3192 4.516698 ACTGTACTGCATCCTGAAAAACAG 59.483 41.667 0.00 0.00 45.36 3.16
2226 3246 6.645790 AGATGCAAAAACAGATTTCTGAGT 57.354 33.333 14.29 0.00 46.59 3.41
2260 3280 6.094603 CCACAAGGATTTAGACAATCTCCAAG 59.905 42.308 0.00 0.00 36.89 3.61


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

AutoCloner maintained by Alex Coulton.