Multiple sequence alignment - TraesCS3D01G490800

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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 TraesCS3D01G490800 chr3D 100.000 3008 0 0 1 3008 584752787 584749780 0.000000e+00 5555.0
1 TraesCS3D01G490800 chr3D 89.666 1587 82 38 653 2167 551375785 551374209 0.000000e+00 1947.0
2 TraesCS3D01G490800 chr3D 88.456 641 37 23 2379 3006 551373304 551372688 0.000000e+00 739.0
3 TraesCS3D01G490800 chr3D 87.850 642 40 23 2379 3006 32371325 32371942 0.000000e+00 719.0
4 TraesCS3D01G490800 chr3D 96.000 275 11 0 1 275 520183498 520183224 5.920000e-122 448.0
5 TraesCS3D01G490800 chr1D 97.678 3014 56 7 1 3008 33570794 33567789 0.000000e+00 5166.0
6 TraesCS3D01G490800 chr1D 90.909 1309 59 22 852 2133 21343840 21345115 0.000000e+00 1703.0
7 TraesCS3D01G490800 chr1D 89.724 1158 53 24 852 1949 404205400 404206551 0.000000e+00 1419.0
8 TraesCS3D01G490800 chr1D 93.236 754 42 6 1978 2723 404206550 404207302 0.000000e+00 1101.0
9 TraesCS3D01G490800 chr1D 94.631 298 16 0 2709 3006 404207330 404207627 2.110000e-126 462.0
10 TraesCS3D01G490800 chr1D 94.595 296 15 1 2709 3004 21346275 21346569 9.830000e-125 457.0
11 TraesCS3D01G490800 chr1D 94.237 295 15 2 1 294 404204028 404204321 1.640000e-122 449.0
12 TraesCS3D01G490800 chr1D 90.845 284 16 3 653 936 21343600 21343873 3.660000e-99 372.0
13 TraesCS3D01G490800 chr1D 84.956 339 23 14 603 937 404205129 404205443 4.840000e-83 318.0
14 TraesCS3D01G490800 chr5D 94.062 3048 102 21 1 3006 520988100 520985090 0.000000e+00 4553.0
15 TraesCS3D01G490800 chr5D 88.612 641 36 22 2379 3006 348510869 348511485 0.000000e+00 745.0
16 TraesCS3D01G490800 chr5D 92.351 353 19 3 2378 2723 494291692 494292043 2.080000e-136 496.0
17 TraesCS3D01G490800 chr5D 88.353 249 22 5 2762 3006 489241439 489241684 2.930000e-75 292.0
18 TraesCS3D01G490800 chr5D 96.226 53 2 0 2227 2279 161438871 161438819 1.490000e-13 87.9
19 TraesCS3D01G490800 chr2D 91.689 2190 93 30 603 2723 556372300 556374469 0.000000e+00 2953.0
20 TraesCS3D01G490800 chr2D 91.257 1567 62 28 653 2167 46907919 46906376 0.000000e+00 2065.0
21 TraesCS3D01G490800 chr2D 87.832 641 41 22 2379 3006 6566127 6565511 0.000000e+00 717.0
22 TraesCS3D01G490800 chr2D 93.750 352 14 5 2379 2723 46905375 46905025 3.440000e-144 521.0
23 TraesCS3D01G490800 chr2D 95.973 298 12 0 2709 3006 556374497 556374794 4.510000e-133 484.0
24 TraesCS3D01G490800 chr2D 94.966 298 15 0 2709 3006 46904997 46904700 4.540000e-128 468.0
25 TraesCS3D01G490800 chr2D 89.455 275 29 0 1 275 318423005 318422731 6.170000e-92 348.0
26 TraesCS3D01G490800 chr2D 89.157 249 20 6 2762 3006 385381940 385382185 1.350000e-78 303.0
27 TraesCS3D01G490800 chr7D 92.830 1576 62 20 852 2382 66521815 66520246 0.000000e+00 2237.0
28 TraesCS3D01G490800 chr7D 92.351 353 19 4 2378 2723 459875828 459875477 2.080000e-136 496.0
29 TraesCS3D01G490800 chr7D 89.820 334 14 3 606 939 66522092 66521779 7.760000e-111 411.0
30 TraesCS3D01G490800 chr7D 92.674 273 19 1 3 275 12035466 12035195 2.810000e-105 392.0
31 TraesCS3D01G490800 chr7A 89.152 719 51 14 1392 2097 56063966 56064670 0.000000e+00 870.0
32 TraesCS3D01G490800 chr3A 89.718 603 57 3 842 1441 710765527 710764927 0.000000e+00 765.0
33 TraesCS3D01G490800 chr3A 92.898 352 17 6 2379 2723 71576574 71576924 3.460000e-139 505.0
34 TraesCS3D01G490800 chr3A 87.356 87 4 2 620 699 666688614 666688700 3.190000e-15 93.5
35 TraesCS3D01G490800 chr5A 86.221 733 52 17 1392 2097 596892296 596893006 0.000000e+00 749.0
36 TraesCS3D01G490800 chr4D 88.300 641 38 22 2379 3006 434988802 434988186 0.000000e+00 734.0
37 TraesCS3D01G490800 chr4D 92.308 52 4 0 2227 2278 261240643 261240592 1.160000e-09 75.0
38 TraesCS3D01G490800 chr4B 89.474 532 50 6 1571 2097 554164077 554163547 0.000000e+00 667.0
39 TraesCS3D01G490800 chr1B 92.593 297 14 4 2378 2667 665223568 665223273 1.290000e-113 420.0
40 TraesCS3D01G490800 chr1B 88.095 252 24 5 31 280 663657007 663656760 8.150000e-76 294.0
41 TraesCS3D01G490800 chr6D 92.336 274 13 3 2378 2644 463820302 463820030 1.690000e-102 383.0
42 TraesCS3D01G490800 chr4A 92.308 273 13 4 2378 2643 677662055 677661784 6.080000e-102 381.0
43 TraesCS3D01G490800 chr4A 94.231 52 3 0 2227 2278 381396106 381396055 2.490000e-11 80.5
44 TraesCS3D01G490800 chr6B 87.755 245 27 2 31 273 720541988 720542231 1.770000e-72 283.0
45 TraesCS3D01G490800 chr3B 86.992 246 27 4 31 273 139623857 139624100 3.820000e-69 272.0
46 TraesCS3D01G490800 chr2B 80.000 215 10 13 727 939 87173415 87173232 8.750000e-26 128.0
47 TraesCS3D01G490800 chr1A 92.308 52 4 0 2227 2278 580782231 580782282 1.160000e-09 75.0


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 TraesCS3D01G490800 chr3D 584749780 584752787 3007 True 5555.0 5555 100.000000 1 3008 1 chr3D.!!$R2 3007
1 TraesCS3D01G490800 chr3D 551372688 551375785 3097 True 1343.0 1947 89.061000 653 3006 2 chr3D.!!$R3 2353
2 TraesCS3D01G490800 chr3D 32371325 32371942 617 False 719.0 719 87.850000 2379 3006 1 chr3D.!!$F1 627
3 TraesCS3D01G490800 chr1D 33567789 33570794 3005 True 5166.0 5166 97.678000 1 3008 1 chr1D.!!$R1 3007
4 TraesCS3D01G490800 chr1D 21343600 21346569 2969 False 844.0 1703 92.116333 653 3004 3 chr1D.!!$F1 2351
5 TraesCS3D01G490800 chr1D 404204028 404207627 3599 False 749.8 1419 91.356800 1 3006 5 chr1D.!!$F2 3005
6 TraesCS3D01G490800 chr5D 520985090 520988100 3010 True 4553.0 4553 94.062000 1 3006 1 chr5D.!!$R2 3005
7 TraesCS3D01G490800 chr5D 348510869 348511485 616 False 745.0 745 88.612000 2379 3006 1 chr5D.!!$F1 627
8 TraesCS3D01G490800 chr2D 556372300 556374794 2494 False 1718.5 2953 93.831000 603 3006 2 chr2D.!!$F2 2403
9 TraesCS3D01G490800 chr2D 46904700 46907919 3219 True 1018.0 2065 93.324333 653 3006 3 chr2D.!!$R3 2353
10 TraesCS3D01G490800 chr2D 6565511 6566127 616 True 717.0 717 87.832000 2379 3006 1 chr2D.!!$R1 627
11 TraesCS3D01G490800 chr7D 66520246 66522092 1846 True 1324.0 2237 91.325000 606 2382 2 chr7D.!!$R3 1776
12 TraesCS3D01G490800 chr7A 56063966 56064670 704 False 870.0 870 89.152000 1392 2097 1 chr7A.!!$F1 705
13 TraesCS3D01G490800 chr3A 710764927 710765527 600 True 765.0 765 89.718000 842 1441 1 chr3A.!!$R1 599
14 TraesCS3D01G490800 chr5A 596892296 596893006 710 False 749.0 749 86.221000 1392 2097 1 chr5A.!!$F1 705
15 TraesCS3D01G490800 chr4D 434988186 434988802 616 True 734.0 734 88.300000 2379 3006 1 chr4D.!!$R2 627
16 TraesCS3D01G490800 chr4B 554163547 554164077 530 True 667.0 667 89.474000 1571 2097 1 chr4B.!!$R1 526

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
974 1535 1.070604 ATGGCGGAGGAATCATGGAT 58.929 50.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2866 4545 0.465097 ATGTGTATGGGCAGCAGCTC 60.465 55.0 0.0 0.0 43.38 4.09 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
199 200 1.415672 GGTGGGGACTGTTGAGTGGA 61.416 60.000 0.00 0.00 30.16 4.02
241 242 4.141274 TGGGTGGGTGAGTTATATTGATGG 60.141 45.833 0.00 0.00 0.00 3.51
578 837 2.366916 CCTTCGTATCCATCCTTGAGCT 59.633 50.000 0.00 0.00 0.00 4.09
701 1202 3.869065 TGTTTCAGAAACAGGAGAACGT 58.131 40.909 22.53 0.00 45.79 3.99
709 1210 1.080025 CAGGAGAACGTCGGGGTTC 60.080 63.158 10.34 10.34 45.19 3.62
844 1345 1.850345 TGGGTTTTCTTCCAGTCCAGT 59.150 47.619 0.00 0.00 0.00 4.00
856 1357 1.204941 CAGTCCAGTTAACTCCCCTCG 59.795 57.143 4.77 0.00 0.00 4.63
898 1409 1.457455 CTCCCTCTGCCTCCCTCTC 60.457 68.421 0.00 0.00 0.00 3.20
974 1535 1.070604 ATGGCGGAGGAATCATGGAT 58.929 50.000 0.00 0.00 0.00 3.41
1233 1794 0.260230 AGATCAGGAAGAGGCTCGGA 59.740 55.000 9.22 3.77 0.00 4.55
1293 1854 1.289066 CAGCGAAGACGAACCTCCA 59.711 57.895 0.00 0.00 42.66 3.86
1387 1948 8.014517 CCAAATGGTAAAAACATACATTTGTGC 58.985 33.333 20.30 0.00 35.44 4.57
1388 1949 8.554528 CAAATGGTAAAAACATACATTTGTGCA 58.445 29.630 16.14 0.00 34.30 4.57
1389 1950 7.887996 ATGGTAAAAACATACATTTGTGCAG 57.112 32.000 0.00 0.00 0.00 4.41
1390 1951 6.810911 TGGTAAAAACATACATTTGTGCAGT 58.189 32.000 0.00 0.00 0.00 4.40
1403 1964 4.882671 TTGTGCAGTTTCTGAAGTTCTC 57.117 40.909 4.17 0.00 32.44 2.87
1446 2044 7.492994 AGTTTCTGAAGTTTCTGTAGTTCTCAC 59.507 37.037 0.00 0.00 0.00 3.51
1459 2057 7.227314 TCTGTAGTTCTCACGTTTCTGTACTTA 59.773 37.037 0.00 0.00 0.00 2.24
1554 2215 4.884247 AGTTTCTGAACTGGCTGTACTAC 58.116 43.478 0.00 0.00 44.27 2.73
1763 2460 1.072331 TGGAAAGAGGTGGCAGTCTTC 59.928 52.381 11.43 6.51 31.61 2.87
2026 2741 0.819582 AGTTGCTTGTGCTTGTGCTT 59.180 45.000 0.00 0.00 40.48 3.91
2027 2742 0.925466 GTTGCTTGTGCTTGTGCTTG 59.075 50.000 0.00 0.00 40.48 4.01
2028 2743 0.531657 TTGCTTGTGCTTGTGCTTGT 59.468 45.000 0.00 0.00 40.48 3.16
2029 2744 0.179132 TGCTTGTGCTTGTGCTTGTG 60.179 50.000 0.00 0.00 40.48 3.33
2030 2745 1.485032 GCTTGTGCTTGTGCTTGTGC 61.485 55.000 0.00 0.00 40.48 4.57
2135 2850 7.310664 TCAGTGATCATTTTGAAGATGCTTTC 58.689 34.615 0.00 0.00 0.00 2.62
2340 3481 4.263068 CCCACTTGTCAATGAGTTAGGACT 60.263 45.833 0.00 0.00 39.32 3.85
2402 3913 2.529744 AACACCCTGTCCTCCTGGC 61.530 63.158 0.00 0.00 0.00 4.85
2442 3958 5.940470 GGACATCTTCAACTAGTTTGTCCAT 59.060 40.000 32.68 12.33 42.48 3.41
2636 4158 3.313526 AGCTTCCTGCAATATAGCAAACG 59.686 43.478 11.00 0.00 45.13 3.60
2747 4348 8.784043 ACTACCTCAAGTAAAATTTAGCAACTG 58.216 33.333 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 2.431683 GTCTGCAGCTGGTTCCCA 59.568 61.111 17.12 3.13 0.00 4.37
199 200 4.467084 CGCACCGCCCACCACTAT 62.467 66.667 0.00 0.00 0.00 2.12
241 242 1.006571 TTCGCGTTCCCACTCACTC 60.007 57.895 5.77 0.00 0.00 3.51
265 266 5.488341 GTTGCAATTAACTCCTCCACTCTA 58.512 41.667 0.59 0.00 0.00 2.43
578 837 0.601057 TCGAGCAAGTTCATCCACGA 59.399 50.000 0.00 0.00 0.00 4.35
701 1202 1.070786 GCAAGTGTCAGAACCCCGA 59.929 57.895 0.00 0.00 0.00 5.14
709 1210 1.581934 TGGTTTCTCGCAAGTGTCAG 58.418 50.000 0.00 0.00 39.48 3.51
710 1211 2.031258 TTGGTTTCTCGCAAGTGTCA 57.969 45.000 0.00 0.00 39.48 3.58
844 1345 4.685030 GCAATGGAATACGAGGGGAGTTAA 60.685 45.833 0.00 0.00 0.00 2.01
856 1357 1.537202 GATGGAGCGGCAATGGAATAC 59.463 52.381 1.45 0.00 0.00 1.89
898 1409 1.144503 CAATGGAATGAGGAGGGAGGG 59.855 57.143 0.00 0.00 0.00 4.30
974 1535 1.203087 TGACAGACGGAGGGGAGTTAA 60.203 52.381 0.00 0.00 0.00 2.01
1326 1887 5.326283 TGTGGTATACTAGGCAGAGATCT 57.674 43.478 0.00 0.00 0.00 2.75
1380 1941 5.357878 TGAGAACTTCAGAAACTGCACAAAT 59.642 36.000 0.00 0.00 0.00 2.32
1381 1942 4.699735 TGAGAACTTCAGAAACTGCACAAA 59.300 37.500 0.00 0.00 0.00 2.83
1382 1943 4.260985 TGAGAACTTCAGAAACTGCACAA 58.739 39.130 0.00 0.00 0.00 3.33
1383 1944 3.872696 TGAGAACTTCAGAAACTGCACA 58.127 40.909 0.00 0.00 0.00 4.57
1384 1945 4.333926 ACTTGAGAACTTCAGAAACTGCAC 59.666 41.667 0.00 0.00 37.07 4.57
1385 1946 4.517285 ACTTGAGAACTTCAGAAACTGCA 58.483 39.130 0.00 0.00 37.07 4.41
1386 1947 5.491635 AACTTGAGAACTTCAGAAACTGC 57.508 39.130 0.00 0.00 37.07 4.40
1387 1948 7.148340 ACAGAAACTTGAGAACTTCAGAAACTG 60.148 37.037 0.00 0.00 37.07 3.16
1388 1949 6.881602 ACAGAAACTTGAGAACTTCAGAAACT 59.118 34.615 0.00 0.00 37.07 2.66
1389 1950 7.078011 ACAGAAACTTGAGAACTTCAGAAAC 57.922 36.000 0.00 0.00 37.07 2.78
1390 1951 8.964476 ATACAGAAACTTGAGAACTTCAGAAA 57.036 30.769 0.00 0.00 37.07 2.52
1446 2044 6.415867 TCAGAAACTTCGTAAGTACAGAAACG 59.584 38.462 0.00 0.00 41.91 3.60
1459 2057 5.875359 AGTTCAGAAACTTCAGAAACTTCGT 59.125 36.000 0.00 0.00 43.28 3.85
1554 2215 7.840342 AATTCATCTACTGCAGAAACTACAG 57.160 36.000 23.35 5.51 36.67 2.74
2026 2741 6.230472 ACAAAGTGAGACACATAATAGCACA 58.770 36.000 4.75 0.00 36.74 4.57
2027 2742 6.727824 ACAAAGTGAGACACATAATAGCAC 57.272 37.500 4.75 0.00 36.74 4.40
2028 2743 7.611770 ACTACAAAGTGAGACACATAATAGCA 58.388 34.615 4.75 0.00 36.74 3.49
2029 2744 8.480643 AACTACAAAGTGAGACACATAATAGC 57.519 34.615 4.75 0.00 36.74 2.97
2135 2850 4.461781 AGCTCCATCAAAATCCAGTTCAAG 59.538 41.667 0.00 0.00 0.00 3.02
2402 3913 5.191426 AGATGTCCATCAACTTCTCAATGG 58.809 41.667 9.76 0.00 40.22 3.16
2442 3958 5.786264 AGAAGAGAAAAGGACAACTACGA 57.214 39.130 0.00 0.00 0.00 3.43
2747 4348 0.875059 GGACACTTAGTTGGCAGTGC 59.125 55.000 6.55 6.55 43.72 4.40
2866 4545 0.465097 ATGTGTATGGGCAGCAGCTC 60.465 55.000 0.00 0.00 43.38 4.09


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

AutoCloner maintained by Alex Coulton.