Multiple sequence alignment - TraesCS1D01G026700

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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 TraesCS1D01G026700 chr1D 100.000 5094 0 0 1 5094 10777978 10772885 0.000000e+00 9407.0
1 TraesCS1D01G026700 chr1D 88.713 2277 190 35 2836 5071 10930409 10932659 0.000000e+00 2719.0
2 TraesCS1D01G026700 chr1D 96.752 1170 20 2 1669 2821 370321256 370322424 0.000000e+00 1934.0
3 TraesCS1D01G026700 chr1D 93.756 977 47 3 4132 5094 10762302 10761326 0.000000e+00 1454.0
4 TraesCS1D01G026700 chr1D 89.989 939 29 18 745 1668 10835548 10836436 0.000000e+00 1153.0
5 TraesCS1D01G026700 chr1D 85.271 645 71 16 1669 2297 437265718 437265082 1.200000e-180 643.0
6 TraesCS1D01G026700 chr1D 83.407 452 54 8 2377 2809 437010837 437010388 2.860000e-107 399.0
7 TraesCS1D01G026700 chr1D 80.380 474 68 18 1020 1476 10929929 10930394 2.270000e-88 337.0
8 TraesCS1D01G026700 chr1D 85.714 84 8 2 1563 1642 10763915 10763832 9.090000e-13 86.1
9 TraesCS1D01G026700 chr1A 95.211 2255 90 14 2837 5088 13213036 13215275 0.000000e+00 3550.0
10 TraesCS1D01G026700 chr1A 94.919 2047 91 6 2837 4878 13229647 13231685 0.000000e+00 3192.0
11 TraesCS1D01G026700 chr1A 95.186 1558 68 4 2837 4390 13009260 13007706 0.000000e+00 2455.0
12 TraesCS1D01G026700 chr1A 86.037 2299 200 45 2836 5071 22761543 22759303 0.000000e+00 2355.0
13 TraesCS1D01G026700 chr1A 85.363 936 97 19 4164 5071 13273868 13274791 0.000000e+00 933.0
14 TraesCS1D01G026700 chr1A 94.559 533 16 2 4574 5094 13007698 13007167 0.000000e+00 811.0
15 TraesCS1D01G026700 chr1A 92.000 550 24 10 910 1451 13250303 13250840 0.000000e+00 754.0
16 TraesCS1D01G026700 chr1A 89.760 459 47 0 1061 1519 22818656 22818198 5.680000e-164 588.0
17 TraesCS1D01G026700 chr1A 96.537 231 4 3 1442 1668 13255599 13255829 3.720000e-101 379.0
18 TraesCS1D01G026700 chr1A 81.013 474 70 15 1020 1476 22762028 22761558 4.850000e-95 359.0
19 TraesCS1D01G026700 chr1A 84.182 373 50 8 1674 2039 534097828 534097458 2.260000e-93 353.0
20 TraesCS1D01G026700 chr1A 81.057 454 55 18 2375 2807 534061117 534060674 2.940000e-87 333.0
21 TraesCS1D01G026700 chr1A 84.104 346 52 3 1020 1364 13272079 13272422 1.060000e-86 331.0
22 TraesCS1D01G026700 chr1A 75.168 298 31 29 1355 1636 13006108 13005838 3.250000e-17 100.0
23 TraesCS1D01G026700 chr1A 88.750 80 9 0 1563 1642 13009498 13009419 1.170000e-16 99.0
24 TraesCS1D01G026700 chr1A 88.750 80 9 0 1563 1642 13229409 13229488 1.170000e-16 99.0
25 TraesCS1D01G026700 chr1A 93.443 61 4 0 1582 1642 22790820 22790760 1.950000e-14 91.6
26 TraesCS1D01G026700 chr1A 86.905 84 6 1 788 866 13250221 13250304 7.020000e-14 89.8
27 TraesCS1D01G026700 chr1B 94.601 2278 88 12 2836 5094 16225019 16222758 0.000000e+00 3493.0
28 TraesCS1D01G026700 chr1B 93.864 2021 106 8 2836 4847 23598080 23600091 0.000000e+00 3029.0
29 TraesCS1D01G026700 chr1B 93.815 2021 106 8 2836 4847 23896856 23898866 0.000000e+00 3022.0
30 TraesCS1D01G026700 chr1B 89.619 2100 183 23 2837 4915 39814791 39816876 0.000000e+00 2638.0
31 TraesCS1D01G026700 chr1B 90.218 2014 145 28 2957 4948 16400916 16402899 0.000000e+00 2580.0
32 TraesCS1D01G026700 chr1B 93.171 1435 93 4 2836 4268 39732855 39734286 0.000000e+00 2102.0
33 TraesCS1D01G026700 chr1B 97.311 781 19 2 1 779 16397366 16398146 0.000000e+00 1325.0
34 TraesCS1D01G026700 chr1B 95.098 714 23 4 955 1668 23774888 23775589 0.000000e+00 1114.0
35 TraesCS1D01G026700 chr1B 95.753 518 18 2 776 1289 16399953 16400470 0.000000e+00 832.0
36 TraesCS1D01G026700 chr1B 92.280 557 35 2 4294 4847 39734285 39734836 0.000000e+00 784.0
37 TraesCS1D01G026700 chr1B 87.452 526 44 13 4576 5094 39808732 39809242 2.040000e-163 586.0
38 TraesCS1D01G026700 chr1B 80.835 814 82 28 4295 5088 23776968 23777727 5.720000e-159 571.0
39 TraesCS1D01G026700 chr1B 90.179 336 26 4 955 1289 39813033 39813362 1.010000e-116 431.0
40 TraesCS1D01G026700 chr1B 96.585 205 4 1 1372 1573 16400485 16400689 2.270000e-88 337.0
41 TraesCS1D01G026700 chr1B 79.487 390 52 18 1091 1452 39806246 39806635 8.470000e-63 252.0
42 TraesCS1D01G026700 chr1B 94.595 148 0 1 1529 1668 16400700 16400847 6.640000e-54 222.0
43 TraesCS1D01G026700 chr1B 92.357 157 9 1 1330 1486 39814524 39814677 2.390000e-53 220.0
44 TraesCS1D01G026700 chr4D 98.874 1155 12 1 1668 2822 455761523 455762676 0.000000e+00 2060.0
45 TraesCS1D01G026700 chr2D 98.786 1153 14 0 1669 2821 81972149 81970997 0.000000e+00 2052.0
46 TraesCS1D01G026700 chr2D 85.714 266 36 1 2556 2821 592035001 592035264 3.880000e-71 279.0
47 TraesCS1D01G026700 chr5D 98.699 1153 15 0 1669 2821 400282397 400283549 0.000000e+00 2047.0
48 TraesCS1D01G026700 chr5D 83.007 306 41 11 2521 2825 98667563 98667268 3.020000e-67 267.0
49 TraesCS1D01G026700 chr6A 94.719 1174 41 6 1669 2826 84048769 84049937 0.000000e+00 1805.0
50 TraesCS1D01G026700 chr3B 87.343 1193 108 14 1664 2832 800935237 800934064 0.000000e+00 1327.0
51 TraesCS1D01G026700 chr5A 95.716 747 27 4 1 744 708204408 708205152 0.000000e+00 1197.0
52 TraesCS1D01G026700 chr5A 96.278 403 14 1 1 403 622108688 622108287 0.000000e+00 660.0
53 TraesCS1D01G026700 chr5A 86.038 530 64 7 1674 2202 337648262 337647742 1.240000e-155 560.0
54 TraesCS1D01G026700 chr7A 94.868 760 32 6 1 755 636728189 636727432 0.000000e+00 1181.0
55 TraesCS1D01G026700 chr2A 93.833 681 32 8 1 674 726584384 726583707 0.000000e+00 1016.0
56 TraesCS1D01G026700 chr2A 95.455 286 10 3 2537 2821 602690236 602690519 2.160000e-123 453.0
57 TraesCS1D01G026700 chr2A 94.737 266 14 0 1944 2209 602689512 602689777 1.020000e-111 414.0
58 TraesCS1D01G026700 chr2A 94.958 238 12 0 1669 1906 602689276 602689513 1.730000e-99 374.0
59 TraesCS1D01G026700 chr5B 96.114 386 12 2 1 385 81180942 81181325 1.200000e-175 627.0
60 TraesCS1D01G026700 chr5B 88.830 376 15 6 374 745 81184055 81184407 2.180000e-118 436.0
61 TraesCS1D01G026700 chr3A 96.491 285 8 2 2537 2821 682752936 682752654 2.150000e-128 470.0
62 TraesCS1D01G026700 chr3A 96.617 266 9 0 1944 2209 682753664 682753399 4.680000e-120 442.0
63 TraesCS1D01G026700 chr3A 94.561 239 13 0 1668 1906 682753901 682753663 2.240000e-98 370.0
64 TraesCS1D01G026700 chrUn 85.455 330 26 9 4759 5071 261630582 261630258 1.770000e-84 324.0


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 TraesCS1D01G026700 chr1D 10772885 10777978 5093 True 9407.000000 9407 100.000000 1 5094 1 chr1D.!!$R1 5093
1 TraesCS1D01G026700 chr1D 370321256 370322424 1168 False 1934.000000 1934 96.752000 1669 2821 1 chr1D.!!$F2 1152
2 TraesCS1D01G026700 chr1D 10929929 10932659 2730 False 1528.000000 2719 84.546500 1020 5071 2 chr1D.!!$F3 4051
3 TraesCS1D01G026700 chr1D 10835548 10836436 888 False 1153.000000 1153 89.989000 745 1668 1 chr1D.!!$F1 923
4 TraesCS1D01G026700 chr1D 10761326 10763915 2589 True 770.050000 1454 89.735000 1563 5094 2 chr1D.!!$R4 3531
5 TraesCS1D01G026700 chr1D 437265082 437265718 636 True 643.000000 643 85.271000 1669 2297 1 chr1D.!!$R3 628
6 TraesCS1D01G026700 chr1A 13213036 13215275 2239 False 3550.000000 3550 95.211000 2837 5088 1 chr1A.!!$F1 2251
7 TraesCS1D01G026700 chr1A 13229409 13231685 2276 False 1645.500000 3192 91.834500 1563 4878 2 chr1A.!!$F3 3315
8 TraesCS1D01G026700 chr1A 22759303 22762028 2725 True 1357.000000 2355 83.525000 1020 5071 2 chr1A.!!$R6 4051
9 TraesCS1D01G026700 chr1A 13005838 13009498 3660 True 866.250000 2455 88.415750 1355 5094 4 chr1A.!!$R5 3739
10 TraesCS1D01G026700 chr1A 13272079 13274791 2712 False 632.000000 933 84.733500 1020 5071 2 chr1A.!!$F5 4051
11 TraesCS1D01G026700 chr1A 13250221 13250840 619 False 421.900000 754 89.452500 788 1451 2 chr1A.!!$F4 663
12 TraesCS1D01G026700 chr1B 16222758 16225019 2261 True 3493.000000 3493 94.601000 2836 5094 1 chr1B.!!$R1 2258
13 TraesCS1D01G026700 chr1B 23598080 23600091 2011 False 3029.000000 3029 93.864000 2836 4847 1 chr1B.!!$F1 2011
14 TraesCS1D01G026700 chr1B 23896856 23898866 2010 False 3022.000000 3022 93.815000 2836 4847 1 chr1B.!!$F2 2011
15 TraesCS1D01G026700 chr1B 39732855 39734836 1981 False 1443.000000 2102 92.725500 2836 4847 2 chr1B.!!$F5 2011
16 TraesCS1D01G026700 chr1B 16397366 16402899 5533 False 1059.200000 2580 94.892400 1 4948 5 chr1B.!!$F3 4947
17 TraesCS1D01G026700 chr1B 23774888 23777727 2839 False 842.500000 1114 87.966500 955 5088 2 chr1B.!!$F4 4133
18 TraesCS1D01G026700 chr1B 39806246 39816876 10630 False 825.400000 2638 87.818800 955 5094 5 chr1B.!!$F6 4139
19 TraesCS1D01G026700 chr4D 455761523 455762676 1153 False 2060.000000 2060 98.874000 1668 2822 1 chr4D.!!$F1 1154
20 TraesCS1D01G026700 chr2D 81970997 81972149 1152 True 2052.000000 2052 98.786000 1669 2821 1 chr2D.!!$R1 1152
21 TraesCS1D01G026700 chr5D 400282397 400283549 1152 False 2047.000000 2047 98.699000 1669 2821 1 chr5D.!!$F1 1152
22 TraesCS1D01G026700 chr6A 84048769 84049937 1168 False 1805.000000 1805 94.719000 1669 2826 1 chr6A.!!$F1 1157
23 TraesCS1D01G026700 chr3B 800934064 800935237 1173 True 1327.000000 1327 87.343000 1664 2832 1 chr3B.!!$R1 1168
24 TraesCS1D01G026700 chr5A 708204408 708205152 744 False 1197.000000 1197 95.716000 1 744 1 chr5A.!!$F1 743
25 TraesCS1D01G026700 chr5A 337647742 337648262 520 True 560.000000 560 86.038000 1674 2202 1 chr5A.!!$R1 528
26 TraesCS1D01G026700 chr7A 636727432 636728189 757 True 1181.000000 1181 94.868000 1 755 1 chr7A.!!$R1 754
27 TraesCS1D01G026700 chr2A 726583707 726584384 677 True 1016.000000 1016 93.833000 1 674 1 chr2A.!!$R1 673
28 TraesCS1D01G026700 chr2A 602689276 602690519 1243 False 413.666667 453 95.050000 1669 2821 3 chr2A.!!$F1 1152
29 TraesCS1D01G026700 chr5B 81180942 81184407 3465 False 531.500000 627 92.472000 1 745 2 chr5B.!!$F1 744
30 TraesCS1D01G026700 chr3A 682752654 682753901 1247 True 427.333333 470 95.889667 1668 2821 3 chr3A.!!$R1 1153

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
900 2720 5.894807 CACGAACAAAGACGAAAAGAGTTAC 59.105 40.000 0.00 0.0 0.00 2.50 F
1305 8711 1.070445 GTGGCCTCCATCTCCATCG 59.930 63.158 3.32 0.0 35.28 3.84 F
2777 10888 1.504359 TTAGCGAGTTGGTGGTTTCG 58.496 50.000 0.00 0.0 36.23 3.46 F
3062 11250 2.045926 ATTGCAGCGTCTGTCCCC 60.046 61.111 8.32 0.0 33.43 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2777 10888 0.243636 ATTTGCGGCTAGGTTTGCAC 59.756 50.000 0.00 0.0 37.01 4.57 R
3235 11438 2.133553 CACGCTGGCAATCATCTCTAG 58.866 52.381 0.00 0.0 0.00 2.43 R
3582 11854 1.194781 TGGCCTGTCTGGAACTCCTC 61.195 60.000 3.32 0.0 38.35 3.71 R
4346 13189 4.331717 ACAAATGTTCGTATTTCCGCCTAG 59.668 41.667 0.00 0.0 0.00 3.02 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
900 2720 5.894807 CACGAACAAAGACGAAAAGAGTTAC 59.105 40.000 0.00 0.00 0.00 2.50
1075 7390 1.747709 TAGTGAGGAGTACGTGGAGC 58.252 55.000 0.00 0.00 0.00 4.70
1305 8711 1.070445 GTGGCCTCCATCTCCATCG 59.930 63.158 3.32 0.00 35.28 3.84
1364 8800 7.912056 TTCTGATGTCTGGAAACTGAATTAG 57.088 36.000 0.00 0.00 40.22 1.73
1365 8801 7.009179 TCTGATGTCTGGAAACTGAATTAGT 57.991 36.000 0.00 0.00 42.89 2.24
1366 8802 8.134202 TCTGATGTCTGGAAACTGAATTAGTA 57.866 34.615 0.00 0.00 39.18 1.82
1392 8834 3.626930 ACAGTAGGATGTCTCTCACCTC 58.373 50.000 0.00 0.00 32.67 3.85
1497 8943 7.297936 TGGGTCATATGTATCACTTAACGAT 57.702 36.000 1.90 0.00 0.00 3.73
2777 10888 1.504359 TTAGCGAGTTGGTGGTTTCG 58.496 50.000 0.00 0.00 36.23 3.46
2822 10933 3.319122 GTGGTTTCTTGCAATTGACTCCT 59.681 43.478 10.34 0.00 0.00 3.69
2830 10941 6.888105 TCTTGCAATTGACTCCTCATATGTA 58.112 36.000 10.34 0.00 0.00 2.29
2834 10945 5.698545 GCAATTGACTCCTCATATGTACTCC 59.301 44.000 10.34 0.00 0.00 3.85
2910 11024 5.407995 GCTACAAATGGTGAGATGATAGCTC 59.592 44.000 0.00 0.00 31.84 4.09
2941 11056 8.603242 TGAAGTTAACTCAGTAAGTGAAATCC 57.397 34.615 8.95 0.00 38.58 3.01
3062 11250 2.045926 ATTGCAGCGTCTGTCCCC 60.046 61.111 8.32 0.00 33.43 4.81
3077 11280 4.975132 CCCCCAATGCGATACACA 57.025 55.556 0.00 0.00 0.00 3.72
3093 11296 7.393515 TGCGATACACAGATAGTATCTACCAAT 59.606 37.037 12.38 4.95 43.48 3.16
3168 11371 2.114616 CAGATGTAGGCTTCCCAGTCT 58.885 52.381 0.00 0.00 38.95 3.24
3235 11438 3.126858 TGCATTTATCTCTTTCACCGCAC 59.873 43.478 0.00 0.00 0.00 5.34
3294 11499 7.904205 TCCTTCCTTCTAAGTTCGTTCTAATT 58.096 34.615 0.00 0.00 0.00 1.40
3320 11525 5.923684 GGTTTCGTTTTATTTGAAGATGCCA 59.076 36.000 0.00 0.00 0.00 4.92
3322 11527 7.411804 GGTTTCGTTTTATTTGAAGATGCCATG 60.412 37.037 0.00 0.00 0.00 3.66
3472 11705 5.045942 TGTTTGGATGAGCATACTCTAACCA 60.046 40.000 0.00 0.00 43.85 3.67
3736 12011 0.318699 CTGTCCTGAACGCAGTCGAA 60.319 55.000 0.00 0.00 45.00 3.71
4286 13117 7.055667 TGGCTTGTTATACCAAATTTGTTGA 57.944 32.000 16.73 2.24 0.00 3.18
4346 13189 4.735662 TGGCGTTTTGTTAGACATGTAC 57.264 40.909 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
696 700 5.509771 CACGTCTCAAACATTGTTCAATCA 58.490 37.500 1.83 0.00 0.00 2.57
753 757 3.311596 GCACGTTTTTCTTGTAGGTCACT 59.688 43.478 0.00 0.00 0.00 3.41
900 2720 0.972983 TCGAGGCTTCTTGAGGGGAG 60.973 60.000 0.00 0.00 0.00 4.30
1075 7390 3.274586 CGCATCCGCCACCATCTG 61.275 66.667 0.00 0.00 33.11 2.90
1364 8800 5.583854 TGAGAGACATCCTACTGTAACGTAC 59.416 44.000 0.00 0.00 0.00 3.67
1365 8801 5.583854 GTGAGAGACATCCTACTGTAACGTA 59.416 44.000 0.00 0.00 0.00 3.57
1366 8802 4.395542 GTGAGAGACATCCTACTGTAACGT 59.604 45.833 0.00 0.00 0.00 3.99
2297 10146 1.415200 GTGCCCTTCTCCTACCCTAG 58.585 60.000 0.00 0.00 0.00 3.02
2777 10888 0.243636 ATTTGCGGCTAGGTTTGCAC 59.756 50.000 0.00 0.00 37.01 4.57
2834 10945 5.500290 GCGATTCCTGTTGTTAAGTGATACG 60.500 44.000 0.00 0.00 0.00 3.06
2887 11000 6.757237 AGAGCTATCATCTCACCATTTGTAG 58.243 40.000 0.00 0.00 33.15 2.74
2910 11024 8.353684 TCACTTACTGAGTTAACTTCAAGAGAG 58.646 37.037 10.02 12.25 36.10 3.20
2940 11055 8.765219 CACTGAGTTAAACCATCTAATATTCGG 58.235 37.037 0.00 0.00 0.00 4.30
2941 11056 8.765219 CCACTGAGTTAAACCATCTAATATTCG 58.235 37.037 0.00 0.00 0.00 3.34
3062 11250 3.995199 ACTATCTGTGTATCGCATTGGG 58.005 45.455 0.00 0.00 0.00 4.12
3093 11296 6.586344 CAGAGTCTTCTAGCCCAAATTCATA 58.414 40.000 0.00 0.00 30.73 2.15
3168 11371 3.727726 CAATGACACGGCCATAGACATA 58.272 45.455 2.24 0.00 0.00 2.29
3235 11438 2.133553 CACGCTGGCAATCATCTCTAG 58.866 52.381 0.00 0.00 0.00 2.43
3294 11499 5.923684 GCATCTTCAAATAAAACGAAACCCA 59.076 36.000 0.00 0.00 0.00 4.51
3472 11705 5.245531 TCCTATGAAAAGAATTGCACGAGT 58.754 37.500 0.00 0.00 0.00 4.18
3582 11854 1.194781 TGGCCTGTCTGGAACTCCTC 61.195 60.000 3.32 0.00 38.35 3.71
3736 12011 3.575256 TGAGCTTGATTTCAAAGGTGCAT 59.425 39.130 0.00 0.00 35.15 3.96
4261 13092 7.116233 GTCAACAAATTTGGTATAACAAGCCAG 59.884 37.037 21.74 0.00 33.41 4.85
4346 13189 4.331717 ACAAATGTTCGTATTTCCGCCTAG 59.668 41.667 0.00 0.00 0.00 3.02
4826 13692 4.732285 AAATCAACACAGATGTCGTCAC 57.268 40.909 0.00 0.00 38.45 3.67


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

AutoCloner maintained by Alex Coulton.