Multiple sequence alignment - TraesCS2D01G170600

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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 TraesCS2D01G170600 chr2D 100.000 4022 0 0 1 4022 114550426 114546405 0.000000e+00 7428.0
1 TraesCS2D01G170600 chr2D 88.123 682 57 18 1924 2589 27763014 27762341 0.000000e+00 789.0
2 TraesCS2D01G170600 chr2D 85.495 717 80 15 1889 2586 27758427 27759138 0.000000e+00 726.0
3 TraesCS2D01G170600 chr2D 86.321 424 46 9 2727 3140 27762220 27761799 6.130000e-123 451.0
4 TraesCS2D01G170600 chr2D 90.566 318 30 0 2726 3043 27759251 27759568 4.810000e-114 422.0
5 TraesCS2D01G170600 chr2D 86.310 168 22 1 1041 1208 27764103 27763937 8.880000e-42 182.0
6 TraesCS2D01G170600 chr2D 76.901 342 53 19 796 1130 27756950 27757272 1.920000e-38 171.0
7 TraesCS2D01G170600 chr2D 80.628 191 29 6 2151 2338 27668691 27668876 1.510000e-29 141.0
8 TraesCS2D01G170600 chr2B 95.189 1455 50 6 1811 3253 165112316 165110870 0.000000e+00 2281.0
9 TraesCS2D01G170600 chr2B 92.406 935 58 11 669 1599 165113454 165112529 0.000000e+00 1321.0
10 TraesCS2D01G170600 chr2B 87.097 713 74 12 1890 2589 43614792 43615499 0.000000e+00 791.0
11 TraesCS2D01G170600 chr2B 86.963 698 68 15 1925 2609 43630853 43630166 0.000000e+00 763.0
12 TraesCS2D01G170600 chr2B 87.828 419 44 6 2727 3140 43630062 43629646 6.040000e-133 484.0
13 TraesCS2D01G170600 chr2B 90.415 313 28 2 2726 3037 43615633 43615944 1.040000e-110 411.0
14 TraesCS2D01G170600 chr2B 77.834 397 60 23 796 1183 43613692 43614069 1.880000e-53 220.0
15 TraesCS2D01G170600 chr2B 94.400 125 5 2 1694 1817 165112484 165112361 1.480000e-44 191.0
16 TraesCS2D01G170600 chr2B 87.333 150 17 2 1066 1213 43631755 43631606 1.920000e-38 171.0
17 TraesCS2D01G170600 chr2B 89.610 77 8 0 130 206 695443356 695443432 9.200000e-17 99.0
18 TraesCS2D01G170600 chr2B 89.610 77 8 0 130 206 736388663 736388739 9.200000e-17 99.0
19 TraesCS2D01G170600 chr2B 88.095 84 9 1 3439 3521 795590524 795590607 9.200000e-17 99.0
20 TraesCS2D01G170600 chr2B 89.474 76 8 0 130 205 210267629 210267704 3.310000e-16 97.1
21 TraesCS2D01G170600 chr2B 95.000 60 2 1 219 277 165115355 165115296 4.280000e-15 93.5
22 TraesCS2D01G170600 chr2A 94.414 1468 66 11 1811 3265 116001259 115999795 0.000000e+00 2242.0
23 TraesCS2D01G170600 chr2A 90.977 931 49 20 750 1672 116002390 116001487 0.000000e+00 1221.0
24 TraesCS2D01G170600 chr2A 85.097 718 80 16 1889 2589 29878412 29877705 0.000000e+00 708.0
25 TraesCS2D01G170600 chr2A 84.807 724 76 21 1890 2584 29871252 29871970 0.000000e+00 697.0
26 TraesCS2D01G170600 chr2A 87.648 421 45 7 2726 3140 29877569 29877150 2.170000e-132 483.0
27 TraesCS2D01G170600 chr2A 89.744 312 32 0 2726 3037 29872083 29872394 2.250000e-107 399.0
28 TraesCS2D01G170600 chr2A 79.887 353 47 21 796 1138 29869855 29870193 1.870000e-58 237.0
29 TraesCS2D01G170600 chr2A 86.528 193 21 4 1018 1208 29879305 29879116 1.460000e-49 207.0
30 TraesCS2D01G170600 chr2A 91.176 68 5 1 10 76 14570975 14571042 1.540000e-14 91.6
31 TraesCS2D01G170600 chr2A 97.619 42 1 0 236 277 116014085 116014044 5.580000e-09 73.1
32 TraesCS2D01G170600 chr7A 96.467 368 9 2 3655 4022 652697152 652697515 4.450000e-169 604.0
33 TraesCS2D01G170600 chr7A 90.667 75 6 1 3451 3525 660463670 660463743 9.200000e-17 99.0
34 TraesCS2D01G170600 chr7A 84.694 98 13 2 3440 3535 200638839 200638742 3.310000e-16 97.1
35 TraesCS2D01G170600 chr4A 95.652 368 12 2 3655 4022 585392233 585392596 4.480000e-164 588.0
36 TraesCS2D01G170600 chr4A 93.455 382 11 3 3655 4022 708546667 708547048 4.540000e-154 555.0
37 TraesCS2D01G170600 chr4A 100.000 32 0 0 3600 3631 708546577 708546608 4.340000e-05 60.2
38 TraesCS2D01G170600 chr1B 95.652 368 12 2 3655 4022 150529768 150530131 4.480000e-164 588.0
39 TraesCS2D01G170600 chr1B 87.356 87 8 2 133 216 589500630 589500544 3.310000e-16 97.1
40 TraesCS2D01G170600 chr1B 87.324 71 8 1 10 79 94009505 94009435 3.330000e-11 80.5
41 TraesCS2D01G170600 chr1B 100.000 29 0 0 3600 3628 150529678 150529706 2.000000e-03 54.7
42 TraesCS2D01G170600 chr4B 90.984 366 32 1 3658 4022 433131230 433130865 3.610000e-135 492.0
43 TraesCS2D01G170600 chr3B 89.773 88 5 3 3440 3525 427162233 427162318 4.250000e-20 110.0
44 TraesCS2D01G170600 chr3B 90.541 74 7 0 133 206 784169945 784169872 9.200000e-17 99.0
45 TraesCS2D01G170600 chr3B 89.333 75 8 0 133 207 59236585 59236511 1.190000e-15 95.3
46 TraesCS2D01G170600 chr3B 84.783 92 14 0 3437 3528 412593474 412593383 4.280000e-15 93.5
47 TraesCS2D01G170600 chr3B 87.324 71 8 1 10 79 143152805 143152735 3.330000e-11 80.5
48 TraesCS2D01G170600 chr7B 89.744 78 8 0 130 207 742229801 742229878 2.560000e-17 100.0
49 TraesCS2D01G170600 chr7B 89.474 76 8 0 130 205 24414541 24414616 3.310000e-16 97.1
50 TraesCS2D01G170600 chr7B 86.517 89 11 1 3440 3528 632954049 632953962 3.310000e-16 97.1
51 TraesCS2D01G170600 chr7B 93.878 49 3 0 80 128 462055115 462055067 1.550000e-09 75.0
52 TraesCS2D01G170600 chr5B 89.610 77 8 0 130 206 674377690 674377766 9.200000e-17 99.0
53 TraesCS2D01G170600 chr5D 88.608 79 9 0 3447 3525 309003540 309003618 3.310000e-16 97.1
54 TraesCS2D01G170600 chr5D 84.416 77 11 1 1 76 74150101 74150177 1.550000e-09 75.0
55 TraesCS2D01G170600 chr4D 85.714 91 12 1 3439 3529 370529763 370529674 1.190000e-15 95.3
56 TraesCS2D01G170600 chr5A 84.884 86 13 0 3440 3525 534896779 534896864 1.990000e-13 87.9
57 TraesCS2D01G170600 chr5A 84.810 79 11 1 1 78 44090905 44090983 1.200000e-10 78.7
58 TraesCS2D01G170600 chr6B 87.324 71 8 1 10 79 7959208 7959138 3.330000e-11 80.5
59 TraesCS2D01G170600 chr1D 87.324 71 8 1 10 79 13009258 13009188 3.330000e-11 80.5
60 TraesCS2D01G170600 chr6D 85.915 71 9 1 10 79 435833074 435833004 1.550000e-09 75.0
61 TraesCS2D01G170600 chr3D 85.915 71 9 1 10 79 537680095 537680025 1.550000e-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 TraesCS2D01G170600 chr2D 114546405 114550426 4021 True 7428.000000 7428 100.000000 1 4022 1 chr2D.!!$R1 4021
1 TraesCS2D01G170600 chr2D 27761799 27764103 2304 True 474.000000 789 86.918000 1041 3140 3 chr2D.!!$R2 2099
2 TraesCS2D01G170600 chr2D 27756950 27759568 2618 False 439.666667 726 84.320667 796 3043 3 chr2D.!!$F2 2247
3 TraesCS2D01G170600 chr2B 165110870 165115355 4485 True 971.625000 2281 94.248750 219 3253 4 chr2B.!!$R2 3034
4 TraesCS2D01G170600 chr2B 43613692 43615944 2252 False 474.000000 791 85.115333 796 3037 3 chr2B.!!$F5 2241
5 TraesCS2D01G170600 chr2B 43629646 43631755 2109 True 472.666667 763 87.374667 1066 3140 3 chr2B.!!$R1 2074
6 TraesCS2D01G170600 chr2A 115999795 116002390 2595 True 1731.500000 2242 92.695500 750 3265 2 chr2A.!!$R3 2515
7 TraesCS2D01G170600 chr2A 29877150 29879305 2155 True 466.000000 708 86.424333 1018 3140 3 chr2A.!!$R2 2122
8 TraesCS2D01G170600 chr2A 29869855 29872394 2539 False 444.333333 697 84.812667 796 3037 3 chr2A.!!$F2 2241


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
118 119 0.034756 TAGAGGTTCGCAAAGCAGCA 59.965 50.0 0.00 0.0 35.29 4.41 F
442 659 0.469331 ACAGAACCACACCTCTCCGA 60.469 55.0 0.00 0.0 0.00 4.55 F
1345 3154 0.445436 GCATGTTGACTGCGGAGAAG 59.555 55.0 12.26 0.0 0.00 2.85 F
1527 3355 0.036010 AATGGAGGTTCTGTCAGCGG 60.036 55.0 0.00 0.0 0.00 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1338 3147 1.067565 TGTAACAGAGCAGCTTCTCCG 60.068 52.381 9.94 2.11 33.66 4.63 R
1507 3335 1.207089 CCGCTGACAGAACCTCCATTA 59.793 52.381 6.65 0.00 0.00 1.90 R
2773 5172 0.036010 CTCACGGTCTTCCCTGCAAT 60.036 55.000 0.00 0.00 0.00 3.56 R
3340 5745 0.248289 TAACCCTGTTAGTCGCCTGC 59.752 55.000 0.00 0.00 0.00 4.85 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)



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AutoCloner maintained by Alex Coulton.