Multiple sequence alignment - TraesCS2B01G164500

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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 TraesCS2B01G164500 chr2B 100.000 3472 0 0 1 3472 136639853 136636382 0.000000e+00 6412
1 TraesCS2B01G164500 chr2B 95.078 2580 92 14 729 3282 136815293 136812723 0.000000e+00 4028
2 TraesCS2B01G164500 chr2B 93.392 2618 109 25 691 3280 137622677 137620096 0.000000e+00 3818
3 TraesCS2B01G164500 chr2B 97.518 1410 33 2 729 2137 137014950 137013542 0.000000e+00 2409
4 TraesCS2B01G164500 chr2B 90.749 1135 78 14 2165 3282 137013547 137012423 0.000000e+00 1489
5 TraesCS2B01G164500 chr2B 90.815 969 49 20 2159 3094 135464706 135465667 0.000000e+00 1260
6 TraesCS2B01G164500 chr2B 90.843 961 59 12 2159 3094 182132935 182131979 0.000000e+00 1260
7 TraesCS2B01G164500 chr2B 91.964 112 4 3 386 497 137702655 137702549 6.000000e-33 152
8 TraesCS2B01G164500 chr2B 95.946 74 3 0 3399 3472 137012319 137012246 1.690000e-23 121
9 TraesCS2B01G164500 chr2B 92.405 79 6 0 3099 3177 182131591 182131513 2.830000e-21 113
10 TraesCS2B01G164500 chr2D 94.268 1727 61 11 455 2164 84780833 84779128 0.000000e+00 2606
11 TraesCS2B01G164500 chr2D 96.201 1474 55 1 691 2164 85408973 85407501 0.000000e+00 2410
12 TraesCS2B01G164500 chr2D 95.706 1374 52 4 797 2164 84938076 84936704 0.000000e+00 2204
13 TraesCS2B01G164500 chr2D 95.741 1315 22 11 2159 3472 85250909 85249628 0.000000e+00 2087
14 TraesCS2B01G164500 chr2D 88.551 1415 70 29 376 1750 85252362 85251000 0.000000e+00 1631
15 TraesCS2B01G164500 chr2D 92.000 900 53 2 851 1750 85703786 85702906 0.000000e+00 1245
16 TraesCS2B01G164500 chr2D 86.986 1045 100 26 2159 3193 127820371 127819353 0.000000e+00 1144
17 TraesCS2B01G164500 chr2D 84.981 1052 72 38 2159 3142 83530930 83531963 0.000000e+00 989
18 TraesCS2B01G164500 chr2D 83.476 466 32 13 3028 3472 84777952 84777511 3.250000e-105 392
19 TraesCS2B01G164500 chr2D 86.824 296 10 9 3028 3321 84935524 84935256 1.570000e-78 303
20 TraesCS2B01G164500 chr2D 86.486 296 11 9 3028 3321 85406320 85406052 7.290000e-77 298
21 TraesCS2B01G164500 chr2D 97.183 71 2 0 3402 3472 84935152 84935082 1.690000e-23 121
22 TraesCS2B01G164500 chr2D 94.595 74 2 1 3399 3472 85405951 85405880 2.830000e-21 113
23 TraesCS2B01G164500 chr2A 93.548 1240 49 4 836 2068 85613727 85612512 0.000000e+00 1818
24 TraesCS2B01G164500 chr2A 93.548 1240 49 4 836 2068 85927152 85925937 0.000000e+00 1818
25 TraesCS2B01G164500 chr2A 93.226 1240 53 4 836 2068 85811245 85810030 0.000000e+00 1796
26 TraesCS2B01G164500 chr2A 90.909 1243 78 19 2165 3389 85612506 85611281 0.000000e+00 1637
27 TraesCS2B01G164500 chr2A 90.155 965 59 19 2159 3094 84144623 84145580 0.000000e+00 1223
28 TraesCS2B01G164500 chr2A 89.403 972 76 18 2159 3105 83991119 83992088 0.000000e+00 1199
29 TraesCS2B01G164500 chr2A 89.900 901 79 7 852 1750 84143642 84144532 0.000000e+00 1149
30 TraesCS2B01G164500 chr2A 90.685 365 14 13 356 711 85811593 85811240 5.250000e-128 468
31 TraesCS2B01G164500 chr2A 90.659 364 14 13 357 711 85614074 85613722 1.890000e-127 466
32 TraesCS2B01G164500 chr2A 90.411 365 15 11 356 711 85927500 85927147 2.440000e-126 462
33 TraesCS2B01G164500 chr2A 86.313 358 32 7 1 358 85614490 85614150 1.180000e-99 374
34 TraesCS2B01G164500 chr2A 86.034 358 34 6 1 358 85812008 85811667 1.520000e-98 370
35 TraesCS2B01G164500 chr2A 92.000 100 8 0 3099 3198 84146006 84146105 1.300000e-29 141
36 TraesCS2B01G164500 chr4A 93.387 1240 51 4 836 2068 349806780 349805565 0.000000e+00 1807
37 TraesCS2B01G164500 chr4A 90.685 365 14 13 356 711 349807128 349806775 5.250000e-128 468
38 TraesCS2B01G164500 chr5B 91.949 1267 73 12 512 1750 321478599 321477334 0.000000e+00 1748
39 TraesCS2B01G164500 chr5B 90.076 131 4 5 393 521 321478750 321478627 9.970000e-36 161
40 TraesCS2B01G164500 chr7A 94.887 1017 44 3 734 1750 618195481 618194473 0.000000e+00 1583
41 TraesCS2B01G164500 chr7A 87.807 1058 81 30 2159 3193 618194379 618193347 0.000000e+00 1195
42 TraesCS2B01G164500 chr7A 83.386 319 45 5 43 358 688532796 688532483 4.380000e-74 289
43 TraesCS2B01G164500 chr7A 93.103 116 5 3 407 521 618195695 618195582 2.140000e-37 167
44 TraesCS2B01G164500 chr7A 95.000 80 3 1 2058 2137 627006928 627006850 1.310000e-24 124
45 TraesCS2B01G164500 chr5D 87.310 591 35 26 393 949 283110898 283110314 1.050000e-179 640
46 TraesCS2B01G164500 chrUn 90.685 365 14 13 356 711 354326417 354326064 5.250000e-128 468
47 TraesCS2B01G164500 chr7D 86.297 343 33 6 1822 2151 518766779 518767120 9.160000e-96 361
48 TraesCS2B01G164500 chr5A 87.500 320 29 9 41 358 416027101 416026791 3.290000e-95 359
49 TraesCS2B01G164500 chr5A 84.395 314 40 6 41 353 690429659 690429964 2.030000e-77 300
50 TraesCS2B01G164500 chr6D 86.378 323 29 7 41 358 80092051 80091739 4.290000e-89 339
51 TraesCS2B01G164500 chr6D 84.034 238 31 5 115 351 906450 906219 4.510000e-54 222
52 TraesCS2B01G164500 chr4D 85.000 320 40 6 41 358 434981449 434981762 5.590000e-83 318
53 TraesCS2B01G164500 chr1D 83.439 314 42 7 41 351 10160248 10159942 2.040000e-72 283
54 TraesCS2B01G164500 chr7B 92.233 103 2 1 2068 2164 588876413 588876311 1.300000e-29 141


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 TraesCS2B01G164500 chr2B 136636382 136639853 3471 True 6412.000000 6412 100.000000 1 3472 1 chr2B.!!$R1 3471
1 TraesCS2B01G164500 chr2B 136812723 136815293 2570 True 4028.000000 4028 95.078000 729 3282 1 chr2B.!!$R2 2553
2 TraesCS2B01G164500 chr2B 137620096 137622677 2581 True 3818.000000 3818 93.392000 691 3280 1 chr2B.!!$R3 2589
3 TraesCS2B01G164500 chr2B 137012246 137014950 2704 True 1339.666667 2409 94.737667 729 3472 3 chr2B.!!$R5 2743
4 TraesCS2B01G164500 chr2B 135464706 135465667 961 False 1260.000000 1260 90.815000 2159 3094 1 chr2B.!!$F1 935
5 TraesCS2B01G164500 chr2B 182131513 182132935 1422 True 686.500000 1260 91.624000 2159 3177 2 chr2B.!!$R6 1018
6 TraesCS2B01G164500 chr2D 85249628 85252362 2734 True 1859.000000 2087 92.146000 376 3472 2 chr2D.!!$R5 3096
7 TraesCS2B01G164500 chr2D 84777511 84780833 3322 True 1499.000000 2606 88.872000 455 3472 2 chr2D.!!$R3 3017
8 TraesCS2B01G164500 chr2D 85702906 85703786 880 True 1245.000000 1245 92.000000 851 1750 1 chr2D.!!$R1 899
9 TraesCS2B01G164500 chr2D 127819353 127820371 1018 True 1144.000000 1144 86.986000 2159 3193 1 chr2D.!!$R2 1034
10 TraesCS2B01G164500 chr2D 83530930 83531963 1033 False 989.000000 989 84.981000 2159 3142 1 chr2D.!!$F1 983
11 TraesCS2B01G164500 chr2D 85405880 85408973 3093 True 940.333333 2410 92.427333 691 3472 3 chr2D.!!$R6 2781
12 TraesCS2B01G164500 chr2D 84935082 84938076 2994 True 876.000000 2204 93.237667 797 3472 3 chr2D.!!$R4 2675
13 TraesCS2B01G164500 chr2A 83991119 83992088 969 False 1199.000000 1199 89.403000 2159 3105 1 chr2A.!!$F1 946
14 TraesCS2B01G164500 chr2A 85925937 85927500 1563 True 1140.000000 1818 91.979500 356 2068 2 chr2A.!!$R3 1712
15 TraesCS2B01G164500 chr2A 85611281 85614490 3209 True 1073.750000 1818 90.357250 1 3389 4 chr2A.!!$R1 3388
16 TraesCS2B01G164500 chr2A 85810030 85812008 1978 True 878.000000 1796 89.981667 1 2068 3 chr2A.!!$R2 2067
17 TraesCS2B01G164500 chr2A 84143642 84146105 2463 False 837.666667 1223 90.685000 852 3198 3 chr2A.!!$F2 2346
18 TraesCS2B01G164500 chr4A 349805565 349807128 1563 True 1137.500000 1807 92.036000 356 2068 2 chr4A.!!$R1 1712
19 TraesCS2B01G164500 chr5B 321477334 321478750 1416 True 954.500000 1748 91.012500 393 1750 2 chr5B.!!$R1 1357
20 TraesCS2B01G164500 chr7A 618193347 618195695 2348 True 981.666667 1583 91.932333 407 3193 3 chr7A.!!$R3 2786
21 TraesCS2B01G164500 chr5D 283110314 283110898 584 True 640.000000 640 87.310000 393 949 1 chr5D.!!$R1 556

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
78 79 0.172352 CCGAGTTCCAGTGCTCTCTC 59.828 60.000 0.0 0.0 0.00 3.20 F
871 1015 2.092838 CGAGTTCGAGTTCATTTCCAGC 59.907 50.000 0.0 0.0 43.02 4.85 F
2075 2618 1.066002 GATGCAAATCCACGGGTGATG 59.934 52.381 0.0 0.0 0.00 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2075 2618 3.693085 TGATGATTTCTTGCTCTGCTTCC 59.307 43.478 0.0 0.0 0.00 3.46 R
2083 2626 2.163815 GCACTGCTGATGATTTCTTGCT 59.836 45.455 0.0 0.0 0.00 3.91 R
2942 3890 6.441274 CAGAGCAGCAGAATGTTTTAAGAAA 58.559 36.000 0.0 0.0 39.31 2.52 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
53 54 3.623060 TGATTTTATGAGAGAGGCGTTGC 59.377 43.478 0.00 0.00 0.00 4.17
78 79 0.172352 CCGAGTTCCAGTGCTCTCTC 59.828 60.000 0.00 0.00 0.00 3.20
93 94 8.939929 CAGTGCTCTCTCTATTTGAACAATTTA 58.060 33.333 0.00 0.00 0.00 1.40
120 121 6.698359 TTTGTGTTTCGGAAGTTTCAAAAG 57.302 33.333 0.00 0.00 0.00 2.27
122 123 6.015027 TGTGTTTCGGAAGTTTCAAAAGAA 57.985 33.333 0.00 0.00 0.00 2.52
123 124 6.626302 TGTGTTTCGGAAGTTTCAAAAGAAT 58.374 32.000 0.00 0.00 0.00 2.40
124 125 6.529829 TGTGTTTCGGAAGTTTCAAAAGAATG 59.470 34.615 0.00 0.00 0.00 2.67
125 126 6.530181 GTGTTTCGGAAGTTTCAAAAGAATGT 59.470 34.615 0.00 0.00 0.00 2.71
126 127 6.529829 TGTTTCGGAAGTTTCAAAAGAATGTG 59.470 34.615 0.00 0.00 0.00 3.21
128 129 6.633500 TCGGAAGTTTCAAAAGAATGTGAT 57.367 33.333 0.00 0.00 0.00 3.06
129 130 7.038154 TCGGAAGTTTCAAAAGAATGTGATT 57.962 32.000 0.00 0.00 0.00 2.57
130 131 7.488322 TCGGAAGTTTCAAAAGAATGTGATTT 58.512 30.769 0.00 0.00 0.00 2.17
211 212 9.528489 AGTCTTATTTTGTTTTGGGCTATAGAA 57.472 29.630 3.21 0.00 0.00 2.10
252 253 5.705905 ACAGTATACAGAAGAAAAAGGGTGC 59.294 40.000 5.50 0.00 0.00 5.01
253 254 5.705441 CAGTATACAGAAGAAAAAGGGTGCA 59.295 40.000 5.50 0.00 0.00 4.57
265 266 4.751767 AAAGGGTGCAATTTCTGTCAAA 57.248 36.364 0.00 0.00 0.00 2.69
266 267 4.751767 AAGGGTGCAATTTCTGTCAAAA 57.248 36.364 0.00 0.00 0.00 2.44
267 268 4.751767 AGGGTGCAATTTCTGTCAAAAA 57.248 36.364 0.00 0.00 0.00 1.94
309 310 9.892130 TGTATTTCCCAAAACACAAAGTATTTT 57.108 25.926 0.00 0.00 35.03 1.82
338 339 5.893824 CAGATTTTTACCAGGCCTTAGGAAT 59.106 40.000 15.94 4.99 0.00 3.01
346 347 4.913968 ACCAGGCCTTAGGAATATGTGTAT 59.086 41.667 15.94 0.00 0.00 2.29
347 348 5.221925 ACCAGGCCTTAGGAATATGTGTATG 60.222 44.000 15.94 0.00 0.00 2.39
384 462 5.105797 TGCAGGCATTTTTCGTGATTCTATT 60.106 36.000 0.00 0.00 0.00 1.73
871 1015 2.092838 CGAGTTCGAGTTCATTTCCAGC 59.907 50.000 0.00 0.00 43.02 4.85
1542 1720 3.809013 GACCCCGTGGATGCCCAT 61.809 66.667 0.00 0.00 45.68 4.00
1647 1825 3.951769 AATCTGCCTGCCTGCCACC 62.952 63.158 0.00 0.00 0.00 4.61
2075 2618 1.066002 GATGCAAATCCACGGGTGATG 59.934 52.381 0.00 0.00 0.00 3.07
2083 2626 1.296392 CACGGGTGATGGAAGCAGA 59.704 57.895 0.00 0.00 24.12 4.26
2085 2628 1.817099 CGGGTGATGGAAGCAGAGC 60.817 63.158 0.00 0.00 24.12 4.09
2118 2662 0.313043 CAGTGCAAGCTTCTTGGTGG 59.687 55.000 0.00 0.00 0.00 4.61
2789 3616 2.009774 AGTGAACTCTTGTGTGTGTGC 58.990 47.619 0.00 0.00 0.00 4.57
2790 3617 1.737236 GTGAACTCTTGTGTGTGTGCA 59.263 47.619 0.00 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 6.830324 TCTCATAAAATCATCCCAACTTCCAG 59.170 38.462 0.00 0.00 0.00 3.86
36 37 1.740380 GCTGCAACGCCTCTCTCATAA 60.740 52.381 0.00 0.00 0.00 1.90
53 54 1.669115 CACTGGAACTCGGGTGCTG 60.669 63.158 0.00 0.00 0.00 4.41
64 65 5.012046 TGTTCAAATAGAGAGAGCACTGGAA 59.988 40.000 0.00 0.00 0.00 3.53
93 94 7.659652 TTGAAACTTCCGAAACACAAATTTT 57.340 28.000 0.00 0.00 0.00 1.82
99 100 5.630661 TCTTTTGAAACTTCCGAAACACA 57.369 34.783 0.00 0.00 0.00 3.72
100 101 6.530181 ACATTCTTTTGAAACTTCCGAAACAC 59.470 34.615 0.00 0.00 42.31 3.32
106 107 7.698836 AAATCACATTCTTTTGAAACTTCCG 57.301 32.000 0.00 0.00 42.31 4.30
151 152 6.055588 ACTTTCCACGGGTATTCAGAATATG 58.944 40.000 6.14 0.99 0.00 1.78
153 154 5.687166 ACTTTCCACGGGTATTCAGAATA 57.313 39.130 0.00 0.00 0.00 1.75
157 158 4.320935 CCAAAACTTTCCACGGGTATTCAG 60.321 45.833 0.00 0.00 0.00 3.02
236 237 5.464389 CAGAAATTGCACCCTTTTTCTTCTG 59.536 40.000 0.00 0.00 36.54 3.02
239 240 5.104982 TGACAGAAATTGCACCCTTTTTCTT 60.105 36.000 0.00 0.00 36.54 2.52
309 310 4.488770 AGGCCTGGTAAAAATCTGGAAAA 58.511 39.130 3.11 0.00 0.00 2.29
338 339 5.566032 GCAGCTACGGGAATACATACACATA 60.566 44.000 0.00 0.00 0.00 2.29
346 347 0.464036 CCTGCAGCTACGGGAATACA 59.536 55.000 8.66 0.00 38.48 2.29
347 348 0.880718 GCCTGCAGCTACGGGAATAC 60.881 60.000 16.64 0.00 38.48 1.89
353 354 0.527565 AAAAATGCCTGCAGCTACGG 59.472 50.000 8.66 0.00 44.23 4.02
384 462 4.079253 GTGCTTGGGAAATAAAGACAGGA 58.921 43.478 0.00 0.00 0.00 3.86
882 1033 0.530870 GGACTCGGATTACCAGCTGC 60.531 60.000 8.66 0.00 35.59 5.25
2075 2618 3.693085 TGATGATTTCTTGCTCTGCTTCC 59.307 43.478 0.00 0.00 0.00 3.46
2083 2626 2.163815 GCACTGCTGATGATTTCTTGCT 59.836 45.455 0.00 0.00 0.00 3.91
2085 2628 3.842732 TGCACTGCTGATGATTTCTTG 57.157 42.857 1.98 0.00 0.00 3.02
2118 2662 6.826741 ACTCTTCTCCTCTGATGTAAGACTAC 59.173 42.308 0.00 0.00 0.00 2.73
2335 3154 4.072131 TCTGCTGACACCCTTGTAAAATC 58.928 43.478 0.00 0.00 35.47 2.17
2942 3890 6.441274 CAGAGCAGCAGAATGTTTTAAGAAA 58.559 36.000 0.00 0.00 39.31 2.52
3156 4632 7.333323 TCAAATGAGAAGCTAACATGATCTGA 58.667 34.615 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.