Multiple sequence alignment - TraesCS6B01G157300

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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 TraesCS6B01G157300 chr6B 100.000 2915 0 0 1 2915 159597922 159600836 0.000000e+00 5384.0
1 TraesCS6B01G157300 chr6B 91.200 1909 118 20 617 2504 159406973 159408852 0.000000e+00 2549.0
2 TraesCS6B01G157300 chr6B 91.542 1407 97 13 840 2236 158145805 158144411 0.000000e+00 1919.0
3 TraesCS6B01G157300 chr6B 82.876 619 38 21 1 615 159405537 159406091 7.260000e-136 494.0
4 TraesCS6B01G157300 chr6B 85.167 418 28 12 2503 2915 159408885 159409273 5.850000e-107 398.0
5 TraesCS6B01G157300 chr6B 80.160 499 56 28 1 495 158146868 158146409 1.670000e-87 333.0
6 TraesCS6B01G157300 chr6B 91.855 221 15 2 1 220 159575951 159576169 3.650000e-79 305.0
7 TraesCS6B01G157300 chr6B 83.396 265 12 11 617 867 158145970 158145724 1.760000e-52 217.0
8 TraesCS6B01G157300 chr6A 89.822 1739 124 25 823 2554 100764851 100766543 0.000000e+00 2182.0
9 TraesCS6B01G157300 chr6A 88.384 1782 143 29 681 2432 100811423 100813170 0.000000e+00 2085.0
10 TraesCS6B01G157300 chr6A 88.298 1410 109 26 830 2234 100181345 100179987 0.000000e+00 1639.0
11 TraesCS6B01G157300 chr6A 90.260 308 21 7 2541 2846 100904648 100904948 7.570000e-106 394.0
12 TraesCS6B01G157300 chr6A 92.520 254 15 2 2596 2845 100766543 100766796 7.680000e-96 361.0
13 TraesCS6B01G157300 chr6A 88.182 220 13 2 316 522 100810728 100810947 1.730000e-62 250.0
14 TraesCS6B01G157300 chr6A 79.500 400 42 20 168 554 100182254 100181882 6.240000e-62 248.0
15 TraesCS6B01G157300 chr6A 87.692 195 12 3 316 498 100764092 100764286 1.760000e-52 217.0
16 TraesCS6B01G157300 chr6A 86.700 203 14 8 681 879 100764761 100764954 2.280000e-51 213.0
17 TraesCS6B01G157300 chr6A 82.022 267 21 14 617 879 100181489 100181246 4.930000e-48 202.0
18 TraesCS6B01G157300 chr6A 90.722 97 8 1 2819 2915 100766855 100766950 8.480000e-26 128.0
19 TraesCS6B01G157300 chr6A 89.535 86 3 4 533 613 100764285 100764369 1.430000e-18 104.0
20 TraesCS6B01G157300 chr6A 87.368 95 5 4 777 867 100811569 100811660 5.140000e-18 102.0
21 TraesCS6B01G157300 chr6A 100.000 39 0 0 2627 2665 100813355 100813393 4.030000e-09 73.1
22 TraesCS6B01G157300 chr6A 97.059 34 1 0 2503 2536 100813274 100813307 1.130000e-04 58.4
23 TraesCS6B01G157300 chr6D 85.645 1867 151 41 681 2504 83549859 83551651 0.000000e+00 1855.0
24 TraesCS6B01G157300 chr6D 85.892 1687 148 34 830 2470 83102789 83101147 0.000000e+00 1714.0
25 TraesCS6B01G157300 chr6D 90.388 1134 95 8 830 1959 84030693 84031816 0.000000e+00 1478.0
26 TraesCS6B01G157300 chr6D 86.520 638 44 17 1 615 83544012 83544630 0.000000e+00 664.0
27 TraesCS6B01G157300 chr6D 87.554 466 27 6 1967 2430 84031787 84032223 7.210000e-141 510.0
28 TraesCS6B01G157300 chr6D 96.296 297 10 1 2619 2915 84064752 84065047 1.210000e-133 486.0
29 TraesCS6B01G157300 chr6D 84.211 475 48 16 38 500 83103920 83103461 1.240000e-118 436.0
30 TraesCS6B01G157300 chr6D 90.939 309 22 5 1 307 83114780 83114476 7.520000e-111 411.0
31 TraesCS6B01G157300 chr6D 88.424 311 25 5 2606 2915 83552755 83553055 5.940000e-97 364.0
32 TraesCS6B01G157300 chr6D 91.450 269 11 3 617 879 84030527 84030789 2.760000e-95 359.0
33 TraesCS6B01G157300 chr6D 92.742 248 17 1 2668 2915 83551948 83552194 9.930000e-95 357.0
34 TraesCS6B01G157300 chr6D 87.540 313 27 6 2606 2915 84065589 84065892 4.620000e-93 351.0
35 TraesCS6B01G157300 chr6D 84.502 271 23 8 617 879 83102954 83102695 1.730000e-62 250.0
36 TraesCS6B01G157300 chr6D 85.774 239 18 6 378 615 84029894 84030117 3.750000e-59 239.0
37 TraesCS6B01G157300 chr6D 96.899 129 1 3 2503 2629 84032313 84032440 2.280000e-51 213.0
38 TraesCS6B01G157300 chr6D 82.915 199 10 6 418 615 83114418 83114243 1.080000e-34 158.0
39 TraesCS6B01G157300 chr5D 83.224 304 39 9 87 382 121090797 121091096 4.790000e-68 268.0
40 TraesCS6B01G157300 chr5A 83.007 306 36 12 87 382 132104169 132104468 2.230000e-66 263.0
41 TraesCS6B01G157300 chr5B 81.518 303 45 8 87 382 134139800 134140098 3.750000e-59 239.0


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 TraesCS6B01G157300 chr6B 159597922 159600836 2914 False 5384.000000 5384 100.000000 1 2915 1 chr6B.!!$F2 2914
1 TraesCS6B01G157300 chr6B 159405537 159409273 3736 False 1147.000000 2549 86.414333 1 2915 3 chr6B.!!$F3 2914
2 TraesCS6B01G157300 chr6B 158144411 158146868 2457 True 823.000000 1919 85.032667 1 2236 3 chr6B.!!$R1 2235
3 TraesCS6B01G157300 chr6A 100179987 100182254 2267 True 696.333333 1639 83.273333 168 2234 3 chr6A.!!$R1 2066
4 TraesCS6B01G157300 chr6A 100764092 100766950 2858 False 534.166667 2182 89.498500 316 2915 6 chr6A.!!$F2 2599
5 TraesCS6B01G157300 chr6A 100810728 100813393 2665 False 513.700000 2085 92.198600 316 2665 5 chr6A.!!$F3 2349
6 TraesCS6B01G157300 chr6D 83549859 83553055 3196 False 858.666667 1855 88.937000 681 2915 3 chr6D.!!$F2 2234
7 TraesCS6B01G157300 chr6D 83101147 83103920 2773 True 800.000000 1714 84.868333 38 2470 3 chr6D.!!$R1 2432
8 TraesCS6B01G157300 chr6D 83544012 83544630 618 False 664.000000 664 86.520000 1 615 1 chr6D.!!$F1 614
9 TraesCS6B01G157300 chr6D 84029894 84032440 2546 False 559.800000 1478 90.413000 378 2629 5 chr6D.!!$F3 2251
10 TraesCS6B01G157300 chr6D 84064752 84065892 1140 False 418.500000 486 91.918000 2606 2915 2 chr6D.!!$F4 309
11 TraesCS6B01G157300 chr6D 83114243 83114780 537 True 284.500000 411 86.927000 1 615 2 chr6D.!!$R2 614

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
411 435 1.103987 TGGTTGGCGTAAAAGCAGCA 61.104 50.0 0.0 0.0 39.27 4.41 F
1410 2800 0.173481 TCTTCTCGAACAGGCCGATG 59.827 55.0 0.0 0.0 35.35 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1627 3017 0.250338 GACCTTCCTGGACGTGCTTT 60.250 55.0 8.99 0.0 39.71 3.51 R
2449 3932 0.745486 CATCCATGGAGCAGCGTTGA 60.745 55.0 21.33 0.0 0.00 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
25 26 7.296628 TGCAACTTACTGTAAATGGGAAAAT 57.703 32.000 12.29 0.00 0.00 1.82
26 27 8.410673 TGCAACTTACTGTAAATGGGAAAATA 57.589 30.769 12.29 0.00 0.00 1.40
62 63 3.096092 TGGAAAGAAACACTGCAACCTT 58.904 40.909 0.00 0.00 0.00 3.50
148 153 6.018433 ACAAATATCCCAGGCAAGACTATT 57.982 37.500 0.00 0.00 0.00 1.73
160 165 5.945784 AGGCAAGACTATTAAAGCATGTCAA 59.054 36.000 0.00 0.00 0.00 3.18
163 168 7.221452 GGCAAGACTATTAAAGCATGTCAAATG 59.779 37.037 0.00 0.00 0.00 2.32
166 171 7.253422 AGACTATTAAAGCATGTCAAATGTGC 58.747 34.615 0.00 0.00 39.10 4.57
220 226 2.076863 CAAGGTACTGTGGTTGCTAGC 58.923 52.381 8.10 8.10 40.86 3.42
307 313 7.475015 CAACCAGATGTTACATTTGGTATCTG 58.525 38.462 31.69 24.29 41.08 2.90
327 339 2.149578 GCTCTACCTACGATAAGCGGA 58.850 52.381 0.00 0.00 46.49 5.54
411 435 1.103987 TGGTTGGCGTAAAAGCAGCA 61.104 50.000 0.00 0.00 39.27 4.41
471 539 1.497991 TCAGTTCGCAGTGTTAGTGC 58.502 50.000 0.00 0.00 41.02 4.40
488 556 3.519579 AGTGCGAGAGACATTGATTCAG 58.480 45.455 0.00 0.00 0.00 3.02
615 730 1.525535 AGAGCTTGATGATGGCCGC 60.526 57.895 0.00 0.00 0.00 6.53
754 2051 3.449737 AGTGCCAAGCTCGGTAATACTAA 59.550 43.478 0.00 0.00 0.00 2.24
794 2097 5.948842 TCATGTCCACCTAGCTACATACTA 58.051 41.667 0.00 0.00 31.55 1.82
795 2098 5.768662 TCATGTCCACCTAGCTACATACTAC 59.231 44.000 0.00 0.00 31.55 2.73
824 2184 3.280295 AGCTTCAATCTTGCTGATCAGG 58.720 45.455 23.89 7.93 35.54 3.86
847 2207 2.916640 ACTCCACCTAGCTACGTACTC 58.083 52.381 0.00 0.00 0.00 2.59
872 2232 5.132502 TGAAAACAGCTTCAATCTCCTTGA 58.867 37.500 0.00 0.00 42.15 3.02
886 2246 5.883685 TCTCCTTGATGATCAGCATACTT 57.116 39.130 15.50 0.00 37.34 2.24
894 2254 8.828688 TTGATGATCAGCATACTTATCTTCTG 57.171 34.615 15.50 0.00 37.34 3.02
919 2282 6.080406 GCTACATACTGAAAACAGCTTCAAC 58.920 40.000 0.00 0.00 34.96 3.18
920 2283 5.438761 ACATACTGAAAACAGCTTCAACC 57.561 39.130 0.00 0.00 34.96 3.77
921 2284 5.133221 ACATACTGAAAACAGCTTCAACCT 58.867 37.500 0.00 0.00 34.96 3.50
1102 2468 2.176273 CCAGCGAAGAAGGATGCCG 61.176 63.158 0.00 0.00 0.00 5.69
1103 2469 2.512515 AGCGAAGAAGGATGCCGC 60.513 61.111 0.00 0.00 45.39 6.53
1104 2470 3.577313 GCGAAGAAGGATGCCGCC 61.577 66.667 0.00 0.00 39.97 6.13
1204 2576 1.522092 GATGCCTCCATCACGGTCA 59.478 57.895 0.00 0.00 45.75 4.02
1237 2609 1.812686 CTTCTCCGACCGGTCAACCA 61.813 60.000 32.80 12.04 36.47 3.67
1240 2624 2.667199 CCGACCGGTCAACCAACC 60.667 66.667 32.80 5.45 35.14 3.77
1291 2678 2.881734 AGTCTGTCACCATCTCAGTCA 58.118 47.619 0.00 0.00 0.00 3.41
1301 2688 2.964464 CCATCTCAGTCATAGGCTCTGT 59.036 50.000 0.00 0.00 0.00 3.41
1409 2799 0.895530 TTCTTCTCGAACAGGCCGAT 59.104 50.000 0.00 0.00 35.35 4.18
1410 2800 0.173481 TCTTCTCGAACAGGCCGATG 59.827 55.000 0.00 0.00 35.35 3.84
1547 2937 1.550130 TTTTCCCTCGGCGTCTCCAT 61.550 55.000 6.85 0.00 34.01 3.41
1659 3049 3.576232 AGGTCGGCCTTGTCCTTT 58.424 55.556 0.35 0.00 44.18 3.11
1810 3200 2.814604 TCGCAGCGACATGGCTAT 59.185 55.556 15.11 0.00 42.53 2.97
2134 3534 0.250124 AACCACGCAATCCGAGTTCA 60.250 50.000 0.00 0.00 41.02 3.18
2362 3828 1.276421 AGTCGCAGCTGTAAGAACCAT 59.724 47.619 16.64 0.00 34.07 3.55
2443 3926 1.915078 TTGCTGCTCTTCCTAGGCCC 61.915 60.000 2.96 0.00 0.00 5.80
2449 3932 3.474570 CTTCCTAGGCCCGCTGCT 61.475 66.667 2.96 0.00 40.92 4.24
2451 3934 4.777854 TCCTAGGCCCGCTGCTCA 62.778 66.667 2.96 0.00 40.92 4.26
2504 4001 5.116074 CGCTTGTCAAGTGTTTGATGAAATC 59.884 40.000 16.52 0.00 44.62 2.17
2577 4155 7.334421 AGTGTGTTACGAATATGATTTTCAGCT 59.666 33.333 0.00 0.00 0.00 4.24
2578 4156 8.600625 GTGTGTTACGAATATGATTTTCAGCTA 58.399 33.333 0.00 0.00 0.00 3.32
2579 4157 9.157104 TGTGTTACGAATATGATTTTCAGCTAA 57.843 29.630 0.00 0.00 0.00 3.09
2585 4163 9.002600 ACGAATATGATTTTCAGCTAATATGCA 57.997 29.630 0.00 0.00 34.99 3.96
2586 4164 9.830294 CGAATATGATTTTCAGCTAATATGCAA 57.170 29.630 0.00 0.00 34.99 4.08
2591 4169 8.133754 TGATTTTCAGCTAATATGCAATTTGC 57.866 30.769 14.49 14.49 45.29 3.68
2592 4170 6.907206 TTTTCAGCTAATATGCAATTTGCC 57.093 33.333 18.27 1.49 44.23 4.52
2593 4171 5.857471 TTCAGCTAATATGCAATTTGCCT 57.143 34.783 18.27 11.33 44.23 4.75
2594 4172 6.957920 TTCAGCTAATATGCAATTTGCCTA 57.042 33.333 18.27 13.16 44.23 3.93
2595 4173 7.528996 TTCAGCTAATATGCAATTTGCCTAT 57.471 32.000 18.27 14.78 44.23 2.57
2727 4486 3.914426 AGCCACCTACGATTCTCAAAT 57.086 42.857 0.00 0.00 0.00 2.32
2764 4524 3.253188 TGCATTTCTCAGTTACTGTTGGC 59.747 43.478 12.41 9.13 32.61 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 8.275632 GCAGTGTTTCTTTCCAAATCATTTTAC 58.724 33.333 0.00 0.00 0.00 2.01
148 153 3.365868 GGACGCACATTTGACATGCTTTA 60.366 43.478 0.00 0.00 37.20 1.85
160 165 2.487762 CCACAACTTATGGACGCACATT 59.512 45.455 0.00 0.00 39.87 2.71
163 168 0.802494 CCCACAACTTATGGACGCAC 59.198 55.000 0.00 0.00 39.87 5.34
166 171 4.006989 TGAAATCCCACAACTTATGGACG 58.993 43.478 0.00 0.00 39.87 4.79
220 226 2.231235 GGGTAAGTTCAACCAGGCATTG 59.769 50.000 0.00 0.00 38.87 2.82
307 313 2.149578 TCCGCTTATCGTAGGTAGAGC 58.850 52.381 0.00 0.00 36.19 4.09
444 512 5.940192 AACACTGCGAACTGAAATTATGA 57.060 34.783 0.00 0.00 0.00 2.15
452 520 1.497991 GCACTAACACTGCGAACTGA 58.502 50.000 0.00 0.00 0.00 3.41
471 539 3.551082 GTCTGCTGAATCAATGTCTCTCG 59.449 47.826 0.00 0.00 0.00 4.04
488 556 2.113986 ACCAGCCACCAAGTCTGC 59.886 61.111 0.00 0.00 0.00 4.26
626 1895 4.488126 GCAAAGTGCAAACAGAGACATA 57.512 40.909 0.00 0.00 44.26 2.29
754 2051 6.834969 TGGACATGATGAATACAATCACCATT 59.165 34.615 0.00 0.00 30.82 3.16
769 2071 4.613925 ATGTAGCTAGGTGGACATGATG 57.386 45.455 9.08 0.00 31.41 3.07
824 2184 4.640364 AGTACGTAGCTAGGTGGAGTATC 58.360 47.826 25.46 9.43 0.00 2.24
847 2207 5.564259 CAAGGAGATTGAAGCTGTTTTCAGG 60.564 44.000 0.00 0.00 43.50 3.86
872 2232 6.013553 AGCCAGAAGATAAGTATGCTGATCAT 60.014 38.462 10.51 0.00 35.45 2.45
886 2246 7.847096 TGTTTTCAGTATGTAGCCAGAAGATA 58.153 34.615 0.00 0.00 37.40 1.98
919 2282 3.014623 TGCTCATTGATCAGCAAGAAGG 58.985 45.455 4.98 0.00 42.74 3.46
1014 2380 1.524621 CATCATGTCGCCAGACCCC 60.525 63.158 0.00 0.00 46.51 4.95
1020 2386 0.460109 CGACCTTCATCATGTCGCCA 60.460 55.000 0.00 0.00 44.29 5.69
1056 2422 3.861797 ATGGTGTCGCCGGATCCC 61.862 66.667 5.05 0.00 41.21 3.85
1059 2425 0.815213 CATTCATGGTGTCGCCGGAT 60.815 55.000 5.05 0.00 41.21 4.18
1083 2449 1.221840 GGCATCCTTCTTCGCTGGA 59.778 57.895 0.00 0.00 0.00 3.86
1102 2468 1.045911 ATGAAGGAGGACTCGGAGGC 61.046 60.000 10.23 6.05 0.00 4.70
1103 2469 1.036707 GATGAAGGAGGACTCGGAGG 58.963 60.000 10.23 0.00 0.00 4.30
1104 2470 2.065899 AGATGAAGGAGGACTCGGAG 57.934 55.000 2.83 2.83 0.00 4.63
1204 2576 1.064832 GGAGAAGAAGCCAATGCCTCT 60.065 52.381 0.00 0.00 40.02 3.69
1258 2642 1.734477 CAGACTTGGAGGCGTCACG 60.734 63.158 8.91 0.00 32.68 4.35
1291 2678 2.955660 CGGAGAAGAAGACAGAGCCTAT 59.044 50.000 0.00 0.00 0.00 2.57
1627 3017 0.250338 GACCTTCCTGGACGTGCTTT 60.250 55.000 8.99 0.00 39.71 3.51
1810 3200 2.106338 TCCTGTGTTTTGCAGAGATGGA 59.894 45.455 0.00 0.00 40.58 3.41
2362 3828 2.917227 TGCTGCGACTCCTCACCA 60.917 61.111 0.00 0.00 0.00 4.17
2400 3871 1.238439 CGCAGGAGGAAAGCAAGAAA 58.762 50.000 0.00 0.00 0.00 2.52
2449 3932 0.745486 CATCCATGGAGCAGCGTTGA 60.745 55.000 21.33 0.00 0.00 3.18
2451 3934 4.230603 CATCCATGGAGCAGCGTT 57.769 55.556 21.33 0.00 0.00 4.84
2504 4001 6.573664 TGATTGAAAGGAGTGTACCAATTG 57.426 37.500 0.00 0.00 0.00 2.32
2583 4161 9.748708 TCTATTAACATTGAATAGGCAAATTGC 57.251 29.630 9.87 9.87 44.08 3.56
2585 4163 9.971922 GCTCTATTAACATTGAATAGGCAAATT 57.028 29.630 0.00 0.00 37.44 1.82
2586 4164 8.292448 CGCTCTATTAACATTGAATAGGCAAAT 58.708 33.333 13.08 0.00 37.44 2.32
2587 4165 7.497579 TCGCTCTATTAACATTGAATAGGCAAA 59.502 33.333 13.08 4.72 37.44 3.68
2588 4166 6.989759 TCGCTCTATTAACATTGAATAGGCAA 59.010 34.615 13.08 0.00 37.44 4.52
2589 4167 6.521162 TCGCTCTATTAACATTGAATAGGCA 58.479 36.000 13.08 0.00 37.44 4.75
2590 4168 7.360438 CCTTCGCTCTATTAACATTGAATAGGC 60.360 40.741 0.00 0.95 37.44 3.93
2591 4169 7.118390 CCCTTCGCTCTATTAACATTGAATAGG 59.882 40.741 0.00 0.00 37.44 2.57
2592 4170 7.360438 GCCCTTCGCTCTATTAACATTGAATAG 60.360 40.741 0.00 0.00 37.96 1.73
2593 4171 6.426937 GCCCTTCGCTCTATTAACATTGAATA 59.573 38.462 0.00 0.00 0.00 1.75
2594 4172 5.239525 GCCCTTCGCTCTATTAACATTGAAT 59.760 40.000 0.00 0.00 0.00 2.57
2595 4173 4.574828 GCCCTTCGCTCTATTAACATTGAA 59.425 41.667 0.00 0.00 0.00 2.69
2727 4486 4.597079 GAAATGCAGTTTCGACTGTTCAA 58.403 39.130 0.00 0.00 39.76 2.69
2764 4524 5.232626 CCATCATGGAATTAACAAATGCACG 59.767 40.000 0.00 0.00 40.96 5.34
2795 4555 0.887387 TGGAAGCCGCCAAGTTACAC 60.887 55.000 0.00 0.00 34.31 2.90


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

AutoCloner maintained by Alex Coulton.