Multiple sequence alignment - TraesCS7B01G475800

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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 TraesCS7B01G475800 chr7B 100.000 3588 0 0 1 3588 732160480 732156893 0.000000e+00 6626.0
1 TraesCS7B01G475800 chr7B 99.192 3588 24 3 1 3588 732202350 732198768 0.000000e+00 6460.0
2 TraesCS7B01G475800 chr7B 93.214 280 18 1 3307 3586 471276391 471276113 9.270000e-111 411.0
3 TraesCS7B01G475800 chr7B 84.564 298 34 9 411 705 697805499 697805787 5.860000e-73 285.0
4 TraesCS7B01G475800 chr7B 82.000 100 17 1 3206 3304 739485043 739485142 2.300000e-12 84.2
5 TraesCS7B01G475800 chr7B 90.000 50 5 0 3259 3308 726158701 726158750 8.320000e-07 65.8
6 TraesCS7B01G475800 chr2B 89.360 1109 106 4 1256 2355 64356686 64357791 0.000000e+00 1384.0
7 TraesCS7B01G475800 chr2B 73.635 861 167 35 1481 2329 1749882 1750694 9.810000e-71 278.0
8 TraesCS7B01G475800 chr2B 73.684 855 152 45 1494 2329 1765057 1765857 7.640000e-67 265.0
9 TraesCS7B01G475800 chr2D 86.847 1072 106 13 1255 2319 37225439 37224396 0.000000e+00 1166.0
10 TraesCS7B01G475800 chr2D 80.693 1010 161 22 1345 2329 3119141 3120141 0.000000e+00 754.0
11 TraesCS7B01G475800 chr2D 79.632 653 113 9 1306 1951 4597623 4596984 5.460000e-123 451.0
12 TraesCS7B01G475800 chr2D 77.723 202 35 7 1 199 323655466 323655660 8.140000e-22 115.0
13 TraesCS7B01G475800 chr2D 78.740 127 24 3 1903 2028 7206716 7206592 8.260000e-12 82.4
14 TraesCS7B01G475800 chr2D 97.368 38 1 0 2742 2779 512904156 512904119 8.320000e-07 65.8
15 TraesCS7B01G475800 chr7D 91.815 281 14 6 3307 3586 629875432 629875704 2.020000e-102 383.0
16 TraesCS7B01G475800 chr7D 90.336 238 21 1 467 704 595688123 595687888 9.670000e-81 311.0
17 TraesCS7B01G475800 chr7D 83.540 322 43 7 719 1032 333633992 333633673 3.500000e-75 292.0
18 TraesCS7B01G475800 chr7D 78.963 328 52 10 2814 3130 628545979 628546300 1.310000e-49 207.0
19 TraesCS7B01G475800 chr7D 83.111 225 22 14 1 219 64729151 64729365 1.310000e-44 191.0
20 TraesCS7B01G475800 chr7D 86.735 98 13 0 3207 3304 213990427 213990330 3.790000e-20 110.0
21 TraesCS7B01G475800 chr7D 97.222 36 1 0 2744 2779 378341774 378341739 1.080000e-05 62.1
22 TraesCS7B01G475800 chr6B 86.154 325 37 4 719 1035 144891369 144891693 9.540000e-91 344.0
23 TraesCS7B01G475800 chr1D 85.404 322 41 2 721 1036 492108219 492107898 2.670000e-86 329.0
24 TraesCS7B01G475800 chr7A 91.213 239 18 2 467 704 721584584 721584348 4.470000e-84 322.0
25 TraesCS7B01G475800 chr7A 80.844 308 53 5 2824 3130 604518876 604518574 1.670000e-58 237.0
26 TraesCS7B01G475800 chr5B 85.266 319 38 6 721 1033 101321152 101321467 1.610000e-83 320.0
27 TraesCS7B01G475800 chr5B 84.950 299 36 6 411 705 696341171 696341464 9.740000e-76 294.0
28 TraesCS7B01G475800 chr5B 72.296 675 130 41 1499 2161 537506318 537506947 1.330000e-34 158.0
29 TraesCS7B01G475800 chr6D 90.000 240 22 1 467 706 18495363 18495600 3.480000e-80 309.0
30 TraesCS7B01G475800 chr6D 75.551 454 69 21 2814 3251 335302253 335301826 6.120000e-43 185.0
31 TraesCS7B01G475800 chr6D 75.000 232 53 5 2850 3079 419589392 419589620 6.340000e-18 102.0
32 TraesCS7B01G475800 chr5D 84.375 320 43 3 721 1033 286475054 286475373 1.250000e-79 307.0
33 TraesCS7B01G475800 chr5D 82.188 320 48 4 721 1033 94024111 94024428 2.120000e-67 267.0
34 TraesCS7B01G475800 chr5D 73.489 728 124 41 1467 2161 441158390 441159081 1.010000e-50 211.0
35 TraesCS7B01G475800 chr5D 72.069 870 175 50 1466 2313 441327294 441328117 7.860000e-47 198.0
36 TraesCS7B01G475800 chr5D 85.185 81 12 0 3206 3286 532007900 532007980 2.300000e-12 84.2
37 TraesCS7B01G475800 chr2A 89.958 239 21 2 467 704 43004462 43004226 4.500000e-79 305.0
38 TraesCS7B01G475800 chr2A 79.808 104 19 2 3204 3307 468596121 468596020 1.380000e-09 75.0
39 TraesCS7B01G475800 chr3D 88.446 251 26 2 454 704 8368169 8367922 2.090000e-77 300.0
40 TraesCS7B01G475800 chr3D 83.471 242 37 3 3342 3581 544894550 544894790 4.660000e-54 222.0
41 TraesCS7B01G475800 chr3D 83.495 103 16 1 3204 3306 64329852 64329751 1.060000e-15 95.3
42 TraesCS7B01G475800 chr3D 100.000 29 0 0 2751 2779 363246586 363246614 2.000000e-03 54.7
43 TraesCS7B01G475800 chr1B 85.050 301 33 9 410 704 497823324 497823618 2.710000e-76 296.0
44 TraesCS7B01G475800 chr1B 83.696 92 13 2 3220 3310 109432097 109432007 6.380000e-13 86.1
45 TraesCS7B01G475800 chr3A 83.077 325 44 6 717 1033 714368759 714369080 5.860000e-73 285.0
46 TraesCS7B01G475800 chr3A 78.191 188 38 2 2814 2999 673712803 673712989 2.260000e-22 117.0
47 TraesCS7B01G475800 chr3A 93.182 44 3 0 2824 2867 589185445 589185488 8.320000e-07 65.8
48 TraesCS7B01G475800 chr3A 100.000 29 0 0 2751 2779 483741724 483741752 2.000000e-03 54.7
49 TraesCS7B01G475800 chr4A 81.677 322 38 7 718 1035 685310660 685310964 7.690000e-62 248.0
50 TraesCS7B01G475800 chr5A 76.221 307 64 8 1968 2270 706559893 706559592 1.730000e-33 154.0
51 TraesCS7B01G475800 chr5A 76.147 218 38 8 2923 3129 268332632 268332418 6.340000e-18 102.0
52 TraesCS7B01G475800 chr3B 74.752 404 70 25 1 395 4518355 4518735 6.200000e-33 152.0
53 TraesCS7B01G475800 chr3B 74.118 340 75 6 2815 3143 31431826 31431489 1.050000e-25 128.0
54 TraesCS7B01G475800 chr1A 88.312 77 7 1 2814 2888 547947424 547947348 1.370000e-14 91.6
55 TraesCS7B01G475800 chr4D 94.231 52 2 1 3207 3258 315515004 315515054 1.070000e-10 78.7


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 TraesCS7B01G475800 chr7B 732156893 732160480 3587 True 6626 6626 100.000 1 3588 1 chr7B.!!$R2 3587
1 TraesCS7B01G475800 chr7B 732198768 732202350 3582 True 6460 6460 99.192 1 3588 1 chr7B.!!$R3 3587
2 TraesCS7B01G475800 chr2B 64356686 64357791 1105 False 1384 1384 89.360 1256 2355 1 chr2B.!!$F3 1099
3 TraesCS7B01G475800 chr2B 1749882 1750694 812 False 278 278 73.635 1481 2329 1 chr2B.!!$F1 848
4 TraesCS7B01G475800 chr2B 1765057 1765857 800 False 265 265 73.684 1494 2329 1 chr2B.!!$F2 835
5 TraesCS7B01G475800 chr2D 37224396 37225439 1043 True 1166 1166 86.847 1255 2319 1 chr2D.!!$R3 1064
6 TraesCS7B01G475800 chr2D 3119141 3120141 1000 False 754 754 80.693 1345 2329 1 chr2D.!!$F1 984
7 TraesCS7B01G475800 chr2D 4596984 4597623 639 True 451 451 79.632 1306 1951 1 chr2D.!!$R1 645
8 TraesCS7B01G475800 chr5D 441158390 441159081 691 False 211 211 73.489 1467 2161 1 chr5D.!!$F3 694

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
708 709 0.38423 CACAAGTTGATTCGCGCGTT 60.384 50.0 30.98 18.81 0.0 4.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2647 2739 0.180406 GAGTACCGCATTGGATGGGT 59.82 55.0 4.61 5.6 42.0 4.51 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
95 96 1.831652 CTCCAAGGTTGAGGACGGCT 61.832 60.000 0.00 0.00 0.00 5.52
99 100 1.831652 AAGGTTGAGGACGGCTGGAG 61.832 60.000 0.00 0.00 0.00 3.86
188 189 9.212641 CTCTGTATACCATGTAGAATTTGATGG 57.787 37.037 0.00 0.00 41.11 3.51
209 210 2.750141 AGCGTTCCTACTCCCTCATA 57.250 50.000 0.00 0.00 0.00 2.15
377 378 8.742777 AGCTGAGTTGAGATTAAATGCAAAATA 58.257 29.630 0.00 0.00 0.00 1.40
559 560 4.107051 ACCGTAACCGCCTCGTCG 62.107 66.667 0.00 0.00 0.00 5.12
618 619 5.449862 CGCCGGAAATCCTCAAATAAATTCA 60.450 40.000 5.05 0.00 0.00 2.57
708 709 0.384230 CACAAGTTGATTCGCGCGTT 60.384 50.000 30.98 18.81 0.00 4.84
962 963 0.738389 AAGCAATATTGTTCCCGGCG 59.262 50.000 16.61 0.00 0.00 6.46
1989 2065 1.749638 CGAGTACTGGGAGGCGAGT 60.750 63.158 0.00 0.00 0.00 4.18
2439 2531 2.041485 TGGCCATCACATTCTTCCTCAA 59.959 45.455 0.00 0.00 0.00 3.02
2524 2616 2.821969 AGAGTTGGGCATCAAACACATC 59.178 45.455 0.00 0.00 37.08 3.06
2647 2739 0.037512 CAAATCGGGCCACATTGCAA 60.038 50.000 4.39 0.00 0.00 4.08
2648 2740 0.037419 AAATCGGGCCACATTGCAAC 60.037 50.000 4.39 0.00 0.00 4.17
2649 2741 1.887344 AATCGGGCCACATTGCAACC 61.887 55.000 4.39 0.00 0.00 3.77
2650 2742 4.067913 CGGGCCACATTGCAACCC 62.068 66.667 4.39 11.25 37.19 4.11
2740 2832 7.147828 TGCAAACTAGTAGAATCTCTGCTACAT 60.148 37.037 3.59 0.00 40.04 2.29
2775 2867 5.300969 TCTTCTTTGAAGCAATGGATTCG 57.699 39.130 2.71 0.00 42.27 3.34
3221 3313 2.034999 TGTTGGATGGCCGGTTCC 59.965 61.111 1.90 11.33 36.79 3.62
3234 3326 2.818274 GTTCCCGCATCCGTGTCC 60.818 66.667 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 1.004745 CAAGAAGCTAGCAAGGGGGAA 59.995 52.381 18.83 0.0 0.00 3.97
95 96 1.003580 GCCATGTCTTCCACTTCTCCA 59.996 52.381 0.00 0.0 0.00 3.86
99 100 1.363744 CTCGCCATGTCTTCCACTTC 58.636 55.000 0.00 0.0 0.00 3.01
188 189 1.183549 TGAGGGAGTAGGAACGCTTC 58.816 55.000 0.00 0.0 0.00 3.86
209 210 4.815533 AGTATATTCATGCGGCTCTCAT 57.184 40.909 0.00 0.0 0.00 2.90
377 378 5.344066 CAACGCACTGTTAGACATAGAGAT 58.656 41.667 0.00 0.0 39.29 2.75
418 419 5.404366 GCTTACGTCTGTACTCATTGTTTCA 59.596 40.000 0.00 0.0 0.00 2.69
460 461 0.531090 GGGTGTGCGTGTGTTGAGTA 60.531 55.000 0.00 0.0 0.00 2.59
618 619 3.786656 TGCTGCTCGCATTATTCCT 57.213 47.368 0.00 0.0 45.47 3.36
708 709 3.449018 GGAGATGCTCTAAGTCAACTCCA 59.551 47.826 11.90 0.0 45.80 3.86
851 852 4.499188 GCCTAATATATCCTGCGTGCGATA 60.499 45.833 0.00 0.0 0.00 2.92
2009 2094 1.136500 CCTCGTACCTAAGGAACAGCC 59.864 57.143 0.00 0.0 34.35 4.85
2439 2531 1.884235 CAGGAAGAAAGCGAAGGTGT 58.116 50.000 0.00 0.0 39.47 4.16
2647 2739 0.180406 GAGTACCGCATTGGATGGGT 59.820 55.000 4.61 5.6 42.00 4.51
2648 2740 0.535102 GGAGTACCGCATTGGATGGG 60.535 60.000 0.00 0.0 42.00 4.00
2649 2741 0.469917 AGGAGTACCGCATTGGATGG 59.530 55.000 0.00 0.0 42.00 3.51
2650 2742 2.213499 GAAGGAGTACCGCATTGGATG 58.787 52.381 0.00 0.0 42.00 3.51
3505 3597 6.884836 AGGAAACATTGTGGTTAGTATCTTCC 59.115 38.462 0.00 0.0 0.00 3.46


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

AutoCloner maintained by Alex Coulton.