Multiple sequence alignment - TraesCS6B01G068900

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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 TraesCS6B01G068900 chr6B 100.000 2585 0 0 1 2585 46653670 46656254 0.000000e+00 4774.0
1 TraesCS6B01G068900 chr6B 93.060 1686 95 11 24 1708 37653228 37651564 0.000000e+00 2446.0
2 TraesCS6B01G068900 chr6B 97.305 1410 35 3 713 2121 38565233 38563826 0.000000e+00 2390.0
3 TraesCS6B01G068900 chr6B 87.282 1376 138 14 250 1615 37035438 37036786 0.000000e+00 1537.0
4 TraesCS6B01G068900 chr6B 87.226 1370 145 17 250 1616 38541483 38540141 0.000000e+00 1533.0
5 TraesCS6B01G068900 chr6B 87.135 1368 154 12 250 1616 37645020 37643674 0.000000e+00 1531.0
6 TraesCS6B01G068900 chr6B 94.201 707 35 5 17 723 38566396 38565696 0.000000e+00 1074.0
7 TraesCS6B01G068900 chr6B 85.753 737 86 11 881 1615 37775429 37774710 0.000000e+00 761.0
8 TraesCS6B01G068900 chr6B 87.747 253 29 2 2113 2364 38563795 38563544 7.000000e-76 294.0
9 TraesCS6B01G068900 chr6B 93.717 191 9 2 2391 2581 37650532 37650345 1.510000e-72 283.0
10 TraesCS6B01G068900 chr6B 93.717 191 9 2 2391 2581 38562640 38562453 1.510000e-72 283.0
11 TraesCS6B01G068900 chr6B 82.270 141 18 5 2134 2269 37643403 37643265 5.850000e-22 115.0
12 TraesCS6B01G068900 chr6B 83.051 118 15 3 2156 2269 38539843 38539727 4.550000e-18 102.0
13 TraesCS6B01G068900 chr6B 95.349 43 2 0 2002 2044 38563905 38563863 4.620000e-08 69.4
14 TraesCS6B01G068900 chr6B 95.349 43 2 0 2042 2084 38563945 38563903 4.620000e-08 69.4
15 TraesCS6B01G068900 chr6B 95.349 43 2 0 2042 2084 46655671 46655713 4.620000e-08 69.4
16 TraesCS6B01G068900 chr6B 95.349 43 2 0 2002 2044 46655711 46655753 4.620000e-08 69.4
17 TraesCS6B01G068900 chr6B 96.875 32 0 1 1926 1957 37036855 37036885 5.000000e-03 52.8
18 TraesCS6B01G068900 chr6D 93.122 1672 98 7 38 1708 23642452 23640797 0.000000e+00 2435.0
19 TraesCS6B01G068900 chr6D 87.354 1368 144 15 250 1615 23632187 23630847 0.000000e+00 1541.0
20 TraesCS6B01G068900 chr6D 92.670 191 14 0 2391 2581 23639445 23639255 2.530000e-70 276.0
21 TraesCS6B01G068900 chr6D 92.517 147 9 2 1974 2118 23638653 23638507 2.610000e-50 209.0
22 TraesCS6B01G068900 chr6D 90.667 150 12 2 2123 2272 23638469 23638322 5.640000e-47 198.0
23 TraesCS6B01G068900 chr6D 95.349 43 2 0 2042 2084 23638623 23638581 4.620000e-08 69.4
24 TraesCS6B01G068900 chr6D 93.023 43 3 0 2002 2044 23638583 23638541 2.150000e-06 63.9
25 TraesCS6B01G068900 chr6D 96.875 32 1 0 1926 1957 23640707 23640676 1.000000e-03 54.7
26 TraesCS6B01G068900 chr6A 92.835 1605 92 10 70 1666 22201203 22199614 0.000000e+00 2305.0
27 TraesCS6B01G068900 chr6A 87.125 1367 149 15 250 1615 22193499 22192159 0.000000e+00 1524.0
28 TraesCS6B01G068900 chr6A 89.474 171 17 1 2412 2581 22198204 22198034 5.600000e-52 215.0
29 TraesCS6B01G068900 chr6A 90.826 109 9 1 2113 2221 22199147 22199040 7.460000e-31 145.0
30 TraesCS6B01G068900 chr6A 100.000 29 0 0 2557 2585 22441879 22441851 1.000000e-03 54.7
31 TraesCS6B01G068900 chr3B 92.045 88 4 2 1957 2041 744915505 744915418 1.260000e-23 121.0
32 TraesCS6B01G068900 chr3B 91.358 81 6 1 2501 2581 744913761 744913682 2.720000e-20 110.0
33 TraesCS6B01G068900 chr3B 88.750 80 9 0 2042 2121 744915457 744915378 5.890000e-17 99.0
34 TraesCS6B01G068900 chr3B 94.915 59 2 1 1848 1906 744915764 744915707 9.850000e-15 91.6
35 TraesCS6B01G068900 chr7D 84.615 78 8 2 1769 1846 11610606 11610533 9.920000e-10 75.0
36 TraesCS6B01G068900 chr4D 97.368 38 1 0 12 49 423078242 423078205 5.970000e-07 65.8
37 TraesCS6B01G068900 chr4B 97.368 38 1 0 12 49 311122933 311122896 5.970000e-07 65.8
38 TraesCS6B01G068900 chr3D 97.368 38 1 0 12 49 309671140 309671103 5.970000e-07 65.8
39 TraesCS6B01G068900 chr1D 97.368 38 1 0 12 49 208679035 208679072 5.970000e-07 65.8
40 TraesCS6B01G068900 chr1D 97.368 38 1 0 12 49 304333080 304333117 5.970000e-07 65.8
41 TraesCS6B01G068900 chr1D 97.368 38 1 0 12 49 438366985 438367022 5.970000e-07 65.8
42 TraesCS6B01G068900 chr5B 85.246 61 7 2 12 70 591057298 591057238 7.720000e-06 62.1


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 TraesCS6B01G068900 chr6B 46653670 46656254 2584 False 1637.600000 4774 96.899333 1 2585 3 chr6B.!!$F2 2584
1 TraesCS6B01G068900 chr6B 37650345 37653228 2883 True 1364.500000 2446 93.388500 24 2581 2 chr6B.!!$R3 2557
2 TraesCS6B01G068900 chr6B 37643265 37645020 1755 True 823.000000 1531 84.702500 250 2269 2 chr6B.!!$R2 2019
3 TraesCS6B01G068900 chr6B 38539727 38541483 1756 True 817.500000 1533 85.138500 250 2269 2 chr6B.!!$R4 2019
4 TraesCS6B01G068900 chr6B 37035438 37036885 1447 False 794.900000 1537 92.078500 250 1957 2 chr6B.!!$F1 1707
5 TraesCS6B01G068900 chr6B 37774710 37775429 719 True 761.000000 761 85.753000 881 1615 1 chr6B.!!$R1 734
6 TraesCS6B01G068900 chr6B 38562453 38566396 3943 True 696.633333 2390 93.944667 17 2581 6 chr6B.!!$R5 2564
7 TraesCS6B01G068900 chr6D 23630847 23632187 1340 True 1541.000000 1541 87.354000 250 1615 1 chr6D.!!$R1 1365
8 TraesCS6B01G068900 chr6D 23638322 23642452 4130 True 472.285714 2435 93.460429 38 2581 7 chr6D.!!$R2 2543
9 TraesCS6B01G068900 chr6A 22192159 22193499 1340 True 1524.000000 1524 87.125000 250 1615 1 chr6A.!!$R1 1365
10 TraesCS6B01G068900 chr6A 22198034 22201203 3169 True 888.333333 2305 91.045000 70 2581 3 chr6A.!!$R3 2511

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
207 208 1.082206 CCCAGTTCCAGGGTAGGGA 59.918 63.158 0.00 0.00 41.61 4.20 F
652 653 1.865788 GCGATCAAGCTTGTGGGCAA 61.866 55.000 25.19 6.03 34.17 4.52 F
1534 2017 2.885861 CCGTGGTCGAGGAGAAGG 59.114 66.667 0.00 0.00 39.71 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1534 2017 0.593128 AGGAACAATGTTGTGCTCGC 59.407 50.000 2.2 0.0 41.31 5.03 R
1554 2037 1.208052 AGAGGATTGACCACATGACCG 59.792 52.381 0.0 0.0 42.04 4.79 R
2381 3106 3.599730 AGCAGATGATGTCGTTGAAGA 57.400 42.857 0.0 0.0 0.00 2.87 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
77 78 4.662961 GCACAGCCGTTTTGCCCC 62.663 66.667 0.00 0.00 0.00 5.80
207 208 1.082206 CCCAGTTCCAGGGTAGGGA 59.918 63.158 0.00 0.00 41.61 4.20
247 248 2.954684 ATCTCCGGCGCTCAACCAA 61.955 57.895 7.64 0.00 0.00 3.67
652 653 1.865788 GCGATCAAGCTTGTGGGCAA 61.866 55.000 25.19 6.03 34.17 4.52
1128 1610 4.556697 TCTACATGCTTATCCTTCTCCCA 58.443 43.478 0.00 0.00 0.00 4.37
1534 2017 2.885861 CCGTGGTCGAGGAGAAGG 59.114 66.667 0.00 0.00 39.71 3.46
1554 2037 1.400242 GCGAGCACAACATTGTTCCTC 60.400 52.381 0.00 5.41 39.91 3.71
1695 2187 5.187967 ACAGAAATGTCCTAATTCGAGGAGT 59.812 40.000 0.00 0.00 46.54 3.85
1781 2273 0.461163 GGTGGGTGTGTTTTGGTTGC 60.461 55.000 0.00 0.00 0.00 4.17
1820 2312 4.833380 TGGTTTCGTTAATGAAATTGGGGA 59.167 37.500 22.33 0.00 39.80 4.81
1827 2319 7.120051 TCGTTAATGAAATTGGGGAAAGGATA 58.880 34.615 0.00 0.00 36.99 2.59
1871 2363 4.367450 GACTGAGTGCTGATCTCCATTAC 58.633 47.826 0.00 0.00 0.00 1.89
2204 2927 6.505048 TGTAGATCAATGAGGATCCAACAT 57.495 37.500 15.82 15.69 43.79 2.71
2230 2953 1.757682 AGAACTGTTCGGGCAACAAA 58.242 45.000 14.35 0.00 44.71 2.83
2232 2955 2.693074 AGAACTGTTCGGGCAACAAAAT 59.307 40.909 14.35 0.00 44.71 1.82
2240 2963 1.476085 CGGGCAACAAAATGGATGCTA 59.524 47.619 9.28 0.00 35.53 3.49
2269 2993 8.797266 AAAGAAACTAAATTTTGTTCTAGCCG 57.203 30.769 16.53 0.00 0.00 5.52
2289 3013 2.806244 CGGTGAACTGGAGTACTTTTGG 59.194 50.000 0.00 0.00 0.00 3.28
2296 3020 4.228824 ACTGGAGTACTTTTGGACAGGTA 58.771 43.478 0.00 0.00 0.00 3.08
2302 3026 3.121738 ACTTTTGGACAGGTAAGTCGG 57.878 47.619 0.00 0.00 39.42 4.79
2308 3033 2.224670 TGGACAGGTAAGTCGGCAAAAT 60.225 45.455 0.00 0.00 39.42 1.82
2309 3034 2.161609 GGACAGGTAAGTCGGCAAAATG 59.838 50.000 0.00 0.00 39.42 2.32
2313 3038 4.156008 ACAGGTAAGTCGGCAAAATGAATC 59.844 41.667 0.00 0.00 0.00 2.52
2319 3044 5.597813 AGTCGGCAAAATGAATCGATATC 57.402 39.130 0.00 0.00 32.46 1.63
2331 3056 6.223138 TGAATCGATATCGTAAATGCAACC 57.777 37.500 23.61 4.73 40.80 3.77
2370 3095 7.750229 ACATGTTTATGTTCTGTCACATCTT 57.250 32.000 0.00 0.00 45.01 2.40
2371 3096 8.169977 ACATGTTTATGTTCTGTCACATCTTT 57.830 30.769 0.00 0.00 45.01 2.52
2372 3097 8.077991 ACATGTTTATGTTCTGTCACATCTTTG 58.922 33.333 0.00 0.00 45.01 2.77
2373 3098 7.566760 TGTTTATGTTCTGTCACATCTTTGT 57.433 32.000 0.00 0.00 38.40 2.83
2375 3100 8.128582 TGTTTATGTTCTGTCACATCTTTGTTC 58.871 33.333 0.00 0.00 38.40 3.18
2376 3101 8.345565 GTTTATGTTCTGTCACATCTTTGTTCT 58.654 33.333 0.00 0.00 38.40 3.01
2378 3103 9.725019 TTATGTTCTGTCACATCTTTGTTCTAT 57.275 29.630 0.00 0.00 38.40 1.98
2381 3106 8.902806 TGTTCTGTCACATCTTTGTTCTATTTT 58.097 29.630 0.00 0.00 32.34 1.82
2383 3108 8.908786 TCTGTCACATCTTTGTTCTATTTTCT 57.091 30.769 0.00 0.00 32.34 2.52
2384 3109 9.342308 TCTGTCACATCTTTGTTCTATTTTCTT 57.658 29.630 0.00 0.00 32.34 2.52
2387 3112 9.950680 GTCACATCTTTGTTCTATTTTCTTCAA 57.049 29.630 0.00 0.00 32.34 2.69
2388 3113 9.950680 TCACATCTTTGTTCTATTTTCTTCAAC 57.049 29.630 0.00 0.00 32.34 3.18
2389 3114 8.895845 CACATCTTTGTTCTATTTTCTTCAACG 58.104 33.333 0.00 0.00 32.34 4.10
2401 4007 3.599730 TCTTCAACGACATCATCTGCT 57.400 42.857 0.00 0.00 0.00 4.24
2403 4009 5.268118 TCTTCAACGACATCATCTGCTAT 57.732 39.130 0.00 0.00 0.00 2.97
2458 4064 4.923893 TGCTCTTTTTGGCAATATGATCG 58.076 39.130 0.00 0.00 35.40 3.69
2479 4085 3.865745 CGGTACATCTTCTGCAAACTAGG 59.134 47.826 0.00 0.00 0.00 3.02
2581 4187 2.422832 GGCTGGCAATTCAGAAAGAGAG 59.577 50.000 0.00 0.00 36.93 3.20
2582 4188 2.159407 GCTGGCAATTCAGAAAGAGAGC 60.159 50.000 0.00 0.00 36.93 4.09
2583 4189 3.345414 CTGGCAATTCAGAAAGAGAGCT 58.655 45.455 0.00 0.00 36.93 4.09
2584 4190 3.341823 TGGCAATTCAGAAAGAGAGCTC 58.658 45.455 5.27 5.27 0.00 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
154 155 2.481568 GCGTTAGGGTTAGGTGAACAAC 59.518 50.000 0.00 0.00 40.09 3.32
247 248 5.780282 TGGTAAGATTCGGATAGGATCACAT 59.220 40.000 0.00 0.00 0.00 3.21
313 314 2.650116 GCCAAGCAGAGGAGGACGA 61.650 63.158 0.00 0.00 0.00 4.20
411 412 3.807538 GTCGCTCGCTACCGGTGA 61.808 66.667 19.93 4.93 34.56 4.02
1128 1610 1.216710 GCTTAGAGTGCCGCTGTCT 59.783 57.895 0.00 0.00 0.00 3.41
1343 1826 2.765807 AGAGCCGTCCATCCCCAG 60.766 66.667 0.00 0.00 0.00 4.45
1426 1909 1.131638 ATCATGACTATGGCCGTGGT 58.868 50.000 14.71 14.71 34.97 4.16
1534 2017 0.593128 AGGAACAATGTTGTGCTCGC 59.407 50.000 2.20 0.00 41.31 5.03
1554 2037 1.208052 AGAGGATTGACCACATGACCG 59.792 52.381 0.00 0.00 42.04 4.79
1695 2187 1.768684 GCCAACCCACTCACTCCTGA 61.769 60.000 0.00 0.00 0.00 3.86
1781 2273 5.293569 ACGAAACCAAGTAGTCTTGTTCTTG 59.706 40.000 7.11 0.00 46.70 3.02
1807 2299 5.532155 AGCTATCCTTTCCCCAATTTCATT 58.468 37.500 0.00 0.00 0.00 2.57
1846 2338 1.830477 GGAGATCAGCACTCAGTCCTT 59.170 52.381 0.00 0.00 36.26 3.36
1847 2339 1.272928 TGGAGATCAGCACTCAGTCCT 60.273 52.381 0.00 0.00 36.26 3.85
2204 2927 1.603678 GCCCGAACAGTTCTACGTTCA 60.604 52.381 11.60 0.00 41.28 3.18
2257 2981 2.489971 CAGTTCACCGGCTAGAACAAA 58.510 47.619 26.75 0.88 44.94 2.83
2269 2993 3.813724 GTCCAAAAGTACTCCAGTTCACC 59.186 47.826 0.00 0.00 0.00 4.02
2289 3013 3.071479 TCATTTTGCCGACTTACCTGTC 58.929 45.455 0.00 0.00 0.00 3.51
2296 3020 5.333339 CGATATCGATTCATTTTGCCGACTT 60.333 40.000 20.50 0.00 43.02 3.01
2302 3026 7.323416 TGCATTTACGATATCGATTCATTTTGC 59.677 33.333 30.75 23.08 43.02 3.68
2308 3033 5.755861 TGGTTGCATTTACGATATCGATTCA 59.244 36.000 30.75 12.16 43.02 2.57
2309 3034 6.223138 TGGTTGCATTTACGATATCGATTC 57.777 37.500 30.75 9.72 43.02 2.52
2313 3038 4.272504 ACCTTGGTTGCATTTACGATATCG 59.727 41.667 23.18 23.18 46.33 2.92
2319 3044 4.214545 TGAAGTACCTTGGTTGCATTTACG 59.785 41.667 0.00 0.00 0.00 3.18
2331 3056 5.418310 AAACATGTCGTTGAAGTACCTTG 57.582 39.130 0.00 0.00 38.07 3.61
2349 3074 7.566760 ACAAAGATGTGACAGAACATAAACA 57.433 32.000 0.00 0.00 40.87 2.83
2364 3089 8.836413 TCGTTGAAGAAAATAGAACAAAGATGT 58.164 29.630 0.00 0.00 43.14 3.06
2367 3092 8.203937 TGTCGTTGAAGAAAATAGAACAAAGA 57.796 30.769 0.00 0.00 0.00 2.52
2368 3093 9.107367 GATGTCGTTGAAGAAAATAGAACAAAG 57.893 33.333 0.00 0.00 0.00 2.77
2370 3095 8.148807 TGATGTCGTTGAAGAAAATAGAACAA 57.851 30.769 0.00 0.00 0.00 2.83
2371 3096 7.722795 TGATGTCGTTGAAGAAAATAGAACA 57.277 32.000 0.00 0.00 0.00 3.18
2372 3097 8.660373 AGATGATGTCGTTGAAGAAAATAGAAC 58.340 33.333 0.00 0.00 0.00 3.01
2373 3098 8.659491 CAGATGATGTCGTTGAAGAAAATAGAA 58.341 33.333 0.00 0.00 0.00 2.10
2375 3100 6.904011 GCAGATGATGTCGTTGAAGAAAATAG 59.096 38.462 0.00 0.00 0.00 1.73
2376 3101 6.595326 AGCAGATGATGTCGTTGAAGAAAATA 59.405 34.615 0.00 0.00 0.00 1.40
2378 3103 4.756642 AGCAGATGATGTCGTTGAAGAAAA 59.243 37.500 0.00 0.00 0.00 2.29
2381 3106 3.599730 AGCAGATGATGTCGTTGAAGA 57.400 42.857 0.00 0.00 0.00 2.87
2383 3108 7.264947 TCTAAATAGCAGATGATGTCGTTGAA 58.735 34.615 0.00 0.00 0.00 2.69
2384 3109 6.805713 TCTAAATAGCAGATGATGTCGTTGA 58.194 36.000 0.00 0.00 0.00 3.18
2387 3112 7.436933 TGAATCTAAATAGCAGATGATGTCGT 58.563 34.615 0.00 0.00 33.03 4.34
2388 3113 7.811713 TCTGAATCTAAATAGCAGATGATGTCG 59.188 37.037 0.00 0.00 33.03 4.35
2389 3114 8.924691 GTCTGAATCTAAATAGCAGATGATGTC 58.075 37.037 0.00 0.00 37.84 3.06
2458 4064 4.833390 ACCTAGTTTGCAGAAGATGTACC 58.167 43.478 0.00 0.00 0.00 3.34
2479 4085 8.243289 CATTTTGTGGATTCCATTAACTGAAC 57.757 34.615 9.01 0.00 35.28 3.18


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

AutoCloner maintained by Alex Coulton.