Multiple sequence alignment - TraesCS6D01G373600

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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 TraesCS6D01G373600 chr6D 100.000 2029 0 0 1 2029 458426349 458424321 0.000000e+00 3747.0
1 TraesCS6D01G373600 chr6D 99.409 2031 10 1 1 2029 458416608 458414578 0.000000e+00 3683.0
2 TraesCS6D01G373600 chr6D 100.000 1405 0 0 2764 4168 458423586 458422182 0.000000e+00 2595.0
3 TraesCS6D01G373600 chr6D 99.573 1405 6 0 2764 4168 458414201 458412797 0.000000e+00 2562.0
4 TraesCS6D01G373600 chr3D 96.697 1635 42 5 1 1633 604384003 604382379 0.000000e+00 2710.0
5 TraesCS6D01G373600 chr3D 95.956 1632 51 8 1 1630 77343712 77345330 0.000000e+00 2634.0
6 TraesCS6D01G373600 chr3D 97.032 977 22 2 2764 3739 77346173 77347143 0.000000e+00 1637.0
7 TraesCS6D01G373600 chr3D 96.923 975 15 2 2764 3738 604381381 604380422 0.000000e+00 1620.0
8 TraesCS6D01G373600 chr3D 96.977 430 10 1 3739 4168 401072774 401073200 0.000000e+00 719.0
9 TraesCS6D01G373600 chr3D 96.744 430 14 0 3739 4168 44115764 44115335 0.000000e+00 717.0
10 TraesCS6D01G373600 chr3D 96.744 430 14 0 3739 4168 434857317 434856888 0.000000e+00 717.0
11 TraesCS6D01G373600 chr3D 94.192 396 12 2 1633 2027 77345403 77345788 9.980000e-166 593.0
12 TraesCS6D01G373600 chr3D 96.667 300 9 1 1633 1931 604382309 604382010 8.050000e-137 497.0
13 TraesCS6D01G373600 chr3D 85.256 156 13 6 757 909 456321767 456321915 7.220000e-33 152.0
14 TraesCS6D01G373600 chr3A 96.453 1635 55 3 1 1633 24109696 24108063 0.000000e+00 2695.0
15 TraesCS6D01G373600 chr3A 95.838 1634 59 8 1 1630 37970066 37971694 0.000000e+00 2632.0
16 TraesCS6D01G373600 chr3A 97.035 978 26 2 2764 3738 24107214 24106237 0.000000e+00 1642.0
17 TraesCS6D01G373600 chr3A 97.304 408 10 1 2764 3171 37972761 37973167 0.000000e+00 691.0
18 TraesCS6D01G373600 chr3A 96.717 396 12 1 1633 2027 24107993 24107598 0.000000e+00 658.0
19 TraesCS6D01G373600 chr3A 96.486 370 12 1 1633 2001 37971766 37972135 9.910000e-171 610.0
20 TraesCS6D01G373600 chr7B 95.474 1635 60 4 1 1633 252388835 252387213 0.000000e+00 2597.0
21 TraesCS6D01G373600 chr7B 96.308 975 35 1 2764 3738 252386365 252385392 0.000000e+00 1600.0
22 TraesCS6D01G373600 chr7B 95.960 396 15 1 1633 2027 252387144 252386749 3.510000e-180 641.0
23 TraesCS6D01G373600 chr7B 85.906 149 17 4 576 723 376350235 376350090 5.580000e-34 156.0
24 TraesCS6D01G373600 chr7D 94.093 1642 78 17 1 1630 540632548 540634182 0.000000e+00 2477.0
25 TraesCS6D01G373600 chr7D 96.977 430 13 0 3739 4168 50605103 50604674 0.000000e+00 723.0
26 TraesCS6D01G373600 chr7D 95.263 380 17 1 1635 2013 540634250 540634629 5.960000e-168 601.0
27 TraesCS6D01G373600 chr7D 85.235 149 18 4 576 723 382117128 382116983 2.600000e-32 150.0
28 TraesCS6D01G373600 chr2B 96.407 974 33 2 2764 3737 742546672 742545701 0.000000e+00 1604.0
29 TraesCS6D01G373600 chr2B 95.916 857 31 4 1 855 742553912 742553058 0.000000e+00 1386.0
30 TraesCS6D01G373600 chr2B 94.891 783 31 2 851 1633 742548288 742547515 0.000000e+00 1216.0
31 TraesCS6D01G373600 chr2B 93.924 395 13 2 1633 2026 742547445 742547061 1.670000e-163 586.0
32 TraesCS6D01G373600 chr2B 78.986 690 109 19 3057 3738 438722528 438723189 4.950000e-119 438.0
33 TraesCS6D01G373600 chr4B 91.701 976 78 2 2764 3738 133362007 133362980 0.000000e+00 1351.0
34 TraesCS6D01G373600 chr4B 87.225 728 57 19 38 745 133359746 133360457 0.000000e+00 797.0
35 TraesCS6D01G373600 chr4B 88.101 395 37 7 1633 2022 133360957 133361346 1.060000e-125 460.0
36 TraesCS6D01G373600 chr4B 85.894 397 32 3 1187 1563 133360453 133360845 6.490000e-108 401.0
37 TraesCS6D01G373600 chr2D 91.086 976 68 6 2764 3738 615215696 615216653 0.000000e+00 1303.0
38 TraesCS6D01G373600 chr2D 87.468 774 54 19 1 745 615213246 615214005 0.000000e+00 852.0
39 TraesCS6D01G373600 chr2D 87.284 464 35 3 1187 1630 615214001 615214460 3.720000e-140 508.0
40 TraesCS6D01G373600 chr2D 89.620 395 31 6 1633 2022 615214531 615214920 1.040000e-135 494.0
41 TraesCS6D01G373600 chr6A 88.176 888 87 8 2764 3644 113085885 113086761 0.000000e+00 1042.0
42 TraesCS6D01G373600 chr6A 81.509 795 77 39 1 744 113306719 113307494 1.290000e-164 590.0
43 TraesCS6D01G373600 chr6A 82.775 627 56 36 150 745 113070362 113070967 2.870000e-141 512.0
44 TraesCS6D01G373600 chr6A 88.350 309 27 4 1633 1939 113071515 113071816 3.060000e-96 363.0
45 TraesCS6D01G373600 chr6A 82.326 430 38 13 1225 1633 113071035 113071447 5.160000e-89 339.0
46 TraesCS6D01G373600 chr6A 82.394 426 37 8 1225 1630 113307547 113307954 1.860000e-88 337.0
47 TraesCS6D01G373600 chr6A 83.333 66 8 2 735 798 30878118 30878054 1.620000e-04 58.4
48 TraesCS6D01G373600 chr4D 97.209 430 12 0 3739 4168 94963060 94963489 0.000000e+00 728.0
49 TraesCS6D01G373600 chr4D 96.977 430 13 0 3739 4168 123879740 123880169 0.000000e+00 723.0
50 TraesCS6D01G373600 chr4D 85.161 310 35 5 758 1067 470110655 470110357 1.460000e-79 307.0
51 TraesCS6D01G373600 chr4D 87.791 172 15 4 758 929 72485753 72485918 3.290000e-46 196.0
52 TraesCS6D01G373600 chr4D 89.796 147 13 2 923 1068 72486661 72486806 1.980000e-43 187.0
53 TraesCS6D01G373600 chr4D 86.957 115 15 0 1066 1180 72486836 72486950 3.380000e-26 130.0
54 TraesCS6D01G373600 chr4D 95.918 49 2 0 1339 1387 274418908 274418956 3.450000e-11 80.5
55 TraesCS6D01G373600 chr1D 96.759 432 12 1 3739 4168 101792116 101792547 0.000000e+00 719.0
56 TraesCS6D01G373600 chr1D 100.000 31 0 0 1152 1182 270219624 270219594 1.620000e-04 58.4
57 TraesCS6D01G373600 chr5D 96.956 427 13 0 3739 4165 182860763 182861189 0.000000e+00 717.0
58 TraesCS6D01G373600 chr5D 85.714 308 38 3 758 1064 218946908 218946606 1.870000e-83 320.0
59 TraesCS6D01G373600 chr5D 86.719 128 12 4 758 882 326367171 326367296 2.020000e-28 137.0
60 TraesCS6D01G373600 chr7A 88.065 310 30 4 758 1067 109848450 109848148 1.100000e-95 361.0
61 TraesCS6D01G373600 chr7A 85.231 325 40 6 745 1068 732632937 732633254 1.120000e-85 327.0


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 TraesCS6D01G373600 chr6D 458422182 458426349 4167 True 3171.000000 3747 100.000000 1 4168 2 chr6D.!!$R2 4167
1 TraesCS6D01G373600 chr6D 458412797 458416608 3811 True 3122.500000 3683 99.491000 1 4168 2 chr6D.!!$R1 4167
2 TraesCS6D01G373600 chr3D 77343712 77347143 3431 False 1621.333333 2634 95.726667 1 3739 3 chr3D.!!$F3 3738
3 TraesCS6D01G373600 chr3D 604380422 604384003 3581 True 1609.000000 2710 96.762333 1 3738 3 chr3D.!!$R3 3737
4 TraesCS6D01G373600 chr3A 24106237 24109696 3459 True 1665.000000 2695 96.735000 1 3738 3 chr3A.!!$R1 3737
5 TraesCS6D01G373600 chr3A 37970066 37973167 3101 False 1311.000000 2632 96.542667 1 3171 3 chr3A.!!$F1 3170
6 TraesCS6D01G373600 chr7B 252385392 252388835 3443 True 1612.666667 2597 95.914000 1 3738 3 chr7B.!!$R2 3737
7 TraesCS6D01G373600 chr7D 540632548 540634629 2081 False 1539.000000 2477 94.678000 1 2013 2 chr7D.!!$F1 2012
8 TraesCS6D01G373600 chr2B 742553058 742553912 854 True 1386.000000 1386 95.916000 1 855 1 chr2B.!!$R1 854
9 TraesCS6D01G373600 chr2B 742545701 742548288 2587 True 1135.333333 1604 95.074000 851 3737 3 chr2B.!!$R2 2886
10 TraesCS6D01G373600 chr2B 438722528 438723189 661 False 438.000000 438 78.986000 3057 3738 1 chr2B.!!$F1 681
11 TraesCS6D01G373600 chr4B 133359746 133362980 3234 False 752.250000 1351 88.230250 38 3738 4 chr4B.!!$F1 3700
12 TraesCS6D01G373600 chr2D 615213246 615216653 3407 False 789.250000 1303 88.864500 1 3738 4 chr2D.!!$F1 3737
13 TraesCS6D01G373600 chr6A 113085885 113086761 876 False 1042.000000 1042 88.176000 2764 3644 1 chr6A.!!$F1 880
14 TraesCS6D01G373600 chr6A 113306719 113307954 1235 False 463.500000 590 81.951500 1 1630 2 chr6A.!!$F3 1629
15 TraesCS6D01G373600 chr6A 113070362 113071816 1454 False 404.666667 512 84.483667 150 1939 3 chr6A.!!$F2 1789

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
1080 1185 4.758251 CGTGCACATGGAGGCCGA 62.758 66.667 18.64 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3244 3822 8.409371 TGCAATCTACTACAATGTTTGAAACAA 58.591 29.63 15.31 0.0 45.86 2.83 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
1080 1185 4.758251 CGTGCACATGGAGGCCGA 62.758 66.667 18.64 0.0 0.0 5.54
1184 1289 4.442052 CGAGGATCTCATGCCAAACTTAGA 60.442 45.833 0.00 0.0 0.0 2.10
1185 1290 5.619220 GAGGATCTCATGCCAAACTTAGAT 58.381 41.667 0.00 0.0 0.0 1.98
3900 4487 4.440880 CATAGAGGGAGCAGAAAAGTCAG 58.559 47.826 0.00 0.0 0.0 3.51
3953 4540 3.817084 CACAAGAAAGAAGAGGATGCACA 59.183 43.478 0.00 0.0 0.0 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1080 1185 4.657824 CTTCCCACGACCACGCGT 62.658 66.667 5.58 5.58 46.88 6.01
3244 3822 8.409371 TGCAATCTACTACAATGTTTGAAACAA 58.591 29.630 15.31 0.00 45.86 2.83
3900 4487 4.320129 GCCTCTCTTTTCTTGAGTGCTTTC 60.320 45.833 0.00 0.00 33.59 2.62


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

AutoCloner maintained by Alex Coulton.