Multiple sequence alignment - TraesCS1A01G035500

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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 TraesCS1A01G035500 chr1A 100.000 3797 0 0 1 3797 18992804 18989008 0.000000e+00 6938.0
1 TraesCS1A01G035500 chr1A 99.679 3119 8 2 1 3117 18821603 18818485 0.000000e+00 5703.0
2 TraesCS1A01G035500 chr1A 100.000 475 0 0 3128 3602 18898592 18898118 0.000000e+00 878.0
3 TraesCS1A01G035500 chr1A 99.579 475 2 0 3128 3602 18815997 18815523 0.000000e+00 867.0
4 TraesCS1A01G035500 chr1A 97.689 476 10 1 3128 3602 30623955 30624430 0.000000e+00 817.0
5 TraesCS1A01G035500 chr1A 97.059 476 13 1 3128 3602 572713012 572713487 0.000000e+00 800.0
6 TraesCS1A01G035500 chr1A 98.378 185 3 0 3613 3797 41929405 41929221 3.660000e-85 326.0
7 TraesCS1A01G035500 chr1A 86.667 210 16 8 2044 2251 326024369 326024568 4.940000e-54 222.0
8 TraesCS1A01G035500 chr1A 86.190 210 17 8 2044 2251 289542653 289542454 2.300000e-52 217.0
9 TraesCS1A01G035500 chr1A 100.000 77 0 0 1 77 18904654 18904578 3.950000e-30 143.0
10 TraesCS1A01G035500 chr1A 79.577 142 18 6 1076 1217 586369802 586369932 1.450000e-14 91.6
11 TraesCS1A01G035500 chr1A 95.000 40 1 1 2266 2305 313910428 313910466 1.140000e-05 62.1
12 TraesCS1A01G035500 chrUn 99.735 1512 4 0 1606 3117 393223993 393225504 0.000000e+00 2771.0
13 TraesCS1A01G035500 chrUn 99.592 490 2 0 1115 1604 475170739 475170250 0.000000e+00 894.0
14 TraesCS1A01G035500 chrUn 100.000 475 0 0 3128 3602 368817126 368816652 0.000000e+00 878.0
15 TraesCS1A01G035500 chrUn 99.459 185 1 0 3613 3797 383072064 383072248 1.690000e-88 337.0
16 TraesCS1A01G035500 chrUn 98.919 185 2 0 3613 3797 355210109 355210293 7.860000e-87 331.0
17 TraesCS1A01G035500 chrUn 98.378 185 3 0 3613 3797 13258085 13257901 3.660000e-85 326.0
18 TraesCS1A01G035500 chrUn 100.000 77 0 0 1 77 367814710 367814786 3.950000e-30 143.0
19 TraesCS1A01G035500 chrUn 100.000 77 0 0 1 77 368977812 368977736 3.950000e-30 143.0
20 TraesCS1A01G035500 chrUn 100.000 77 0 0 1 77 371121715 371121639 3.950000e-30 143.0
21 TraesCS1A01G035500 chrUn 92.683 41 1 2 2259 2298 265419650 265419611 1.470000e-04 58.4
22 TraesCS1A01G035500 chrUn 85.000 60 5 4 2239 2295 357360946 357360888 1.470000e-04 58.4
23 TraesCS1A01G035500 chrUn 100.000 30 0 0 2266 2295 21367962 21367991 5.300000e-04 56.5
24 TraesCS1A01G035500 chrUn 100.000 30 0 0 2266 2295 79245873 79245902 5.300000e-04 56.5
25 TraesCS1A01G035500 chrUn 100.000 30 0 0 2266 2295 100780097 100780126 5.300000e-04 56.5
26 TraesCS1A01G035500 chrUn 100.000 30 0 0 2266 2295 311530625 311530596 5.300000e-04 56.5
27 TraesCS1A01G035500 chrUn 100.000 30 0 0 2266 2295 324196769 324196798 5.300000e-04 56.5
28 TraesCS1A01G035500 chrUn 94.286 35 2 0 2266 2300 96464946 96464980 2.000000e-03 54.7
29 TraesCS1A01G035500 chrUn 96.875 32 1 0 2265 2296 349616288 349616257 2.000000e-03 54.7
30 TraesCS1A01G035500 chrUn 92.105 38 1 1 2265 2302 158278 158243 7.000000e-03 52.8
31 TraesCS1A01G035500 chrUn 90.244 41 3 1 2266 2305 11569640 11569600 7.000000e-03 52.8
32 TraesCS1A01G035500 chrUn 94.286 35 1 1 2262 2296 90117524 90117557 7.000000e-03 52.8
33 TraesCS1A01G035500 chrUn 90.000 40 4 0 2266 2305 309880498 309880459 7.000000e-03 52.8
34 TraesCS1A01G035500 chrUn 100.000 28 0 0 2266 2293 317211751 317211778 7.000000e-03 52.8
35 TraesCS1A01G035500 chr2B 96.708 729 14 3 2393 3117 306175582 306174860 0.000000e+00 1205.0
36 TraesCS1A01G035500 chr2B 96.433 729 16 3 2393 3117 190630195 190630917 0.000000e+00 1194.0
37 TraesCS1A01G035500 chr2B 97.679 474 7 4 1 470 130057216 130057689 0.000000e+00 811.0
38 TraesCS1A01G035500 chr2B 97.059 204 5 1 2044 2247 193951092 193951294 3.630000e-90 342.0
39 TraesCS1A01G035500 chr2B 98.837 86 1 0 2263 2348 193952311 193952396 1.830000e-33 154.0
40 TraesCS1A01G035500 chr2B 95.238 42 1 1 2259 2300 198072253 198072293 8.800000e-07 65.8
41 TraesCS1A01G035500 chr4A 96.571 729 12 3 2393 3117 375966539 375965820 0.000000e+00 1195.0
42 TraesCS1A01G035500 chr4A 97.479 476 11 1 3128 3602 621279134 621278659 0.000000e+00 811.0
43 TraesCS1A01G035500 chr4A 97.059 476 13 1 3128 3602 505500361 505500836 0.000000e+00 800.0
44 TraesCS1A01G035500 chr4A 98.919 185 2 0 3613 3797 680083274 680083090 7.860000e-87 331.0
45 TraesCS1A01G035500 chr4A 98.907 183 2 0 3615 3797 24390768 24390586 1.020000e-85 327.0
46 TraesCS1A01G035500 chr5B 96.433 729 16 3 2393 3117 678063884 678064606 0.000000e+00 1194.0
47 TraesCS1A01G035500 chr5B 83.871 62 5 4 2239 2297 322206611 322206670 2.000000e-03 54.7
48 TraesCS1A01G035500 chr5B 96.875 32 0 1 2266 2297 242031366 242031396 7.000000e-03 52.8
49 TraesCS1A01G035500 chr3B 96.433 729 16 3 2393 3117 655539407 655540129 0.000000e+00 1194.0
50 TraesCS1A01G035500 chr3B 98.097 473 6 3 1 470 162675169 162675641 0.000000e+00 821.0
51 TraesCS1A01G035500 chr3B 98.529 204 2 1 2044 2247 366405683 366405481 3.610000e-95 359.0
52 TraesCS1A01G035500 chr3B 97.549 204 5 0 2044 2247 51486754 51486957 2.170000e-92 350.0
53 TraesCS1A01G035500 chr3B 100.000 86 0 0 2263 2348 366404467 366404382 3.930000e-35 159.0
54 TraesCS1A01G035500 chr3B 84.615 65 5 5 2239 2299 32446007 32445944 4.100000e-05 60.2
55 TraesCS1A01G035500 chr4B 96.022 729 19 3 2393 3117 17910284 17909562 0.000000e+00 1177.0
56 TraesCS1A01G035500 chr4B 87.544 859 74 18 922 1774 387820133 387819302 0.000000e+00 963.0
57 TraesCS1A01G035500 chr4B 90.617 373 31 4 1 371 387820704 387820334 3.410000e-135 492.0
58 TraesCS1A01G035500 chr4B 97.059 204 4 2 2044 2247 233692874 233693075 3.630000e-90 342.0
59 TraesCS1A01G035500 chr4B 88.889 270 25 2 1773 2038 387819190 387818922 1.020000e-85 327.0
60 TraesCS1A01G035500 chr4B 94.083 169 8 2 2949 3117 528801719 528801553 4.870000e-64 255.0
61 TraesCS1A01G035500 chr4B 92.308 169 13 0 2949 3117 330519029 330518861 1.360000e-59 241.0
62 TraesCS1A01G035500 chr4B 86.364 220 18 6 1826 2044 258741241 258741033 2.950000e-56 230.0
63 TraesCS1A01G035500 chr4B 94.964 139 7 0 2975 3113 623663849 623663987 6.390000e-53 219.0
64 TraesCS1A01G035500 chr4B 96.639 119 4 0 2999 3117 258711592 258711474 8.320000e-47 198.0
65 TraesCS1A01G035500 chr4B 98.837 86 1 0 2263 2348 233694091 233694176 1.830000e-33 154.0
66 TraesCS1A01G035500 chr1B 95.885 729 20 3 2393 3117 86567872 86567150 0.000000e+00 1171.0
67 TraesCS1A01G035500 chr1B 96.585 205 6 1 2044 2247 169363797 169364001 4.700000e-89 339.0
68 TraesCS1A01G035500 chr1B 97.619 84 2 0 2265 2348 169365011 169365094 1.100000e-30 145.0
69 TraesCS1A01G035500 chr1B 80.282 142 13 7 1063 1200 545162609 545162739 4.040000e-15 93.5
70 TraesCS1A01G035500 chr1B 94.737 57 3 0 922 978 473223668 473223724 5.220000e-14 89.8
71 TraesCS1A01G035500 chr2A 97.484 477 10 2 3128 3602 58119790 58119314 0.000000e+00 813.0
72 TraesCS1A01G035500 chr2A 89.623 318 17 6 609 923 2873677 2873373 1.280000e-104 390.0
73 TraesCS1A01G035500 chr2A 98.039 204 3 1 2044 2247 743976751 743976549 1.680000e-93 353.0
74 TraesCS1A01G035500 chr2A 93.750 96 6 0 923 1018 2873231 2873136 1.100000e-30 145.0
75 TraesCS1A01G035500 chr2A 96.491 57 2 0 922 978 751645751 751645695 1.120000e-15 95.3
76 TraesCS1A01G035500 chr6A 97.269 476 12 1 3128 3602 357260986 357260511 0.000000e+00 806.0
77 TraesCS1A01G035500 chr6A 98.919 185 2 0 3613 3797 52882195 52882011 7.860000e-87 331.0
78 TraesCS1A01G035500 chr6A 80.137 146 16 9 1073 1217 237733369 237733236 3.120000e-16 97.1
79 TraesCS1A01G035500 chr6A 97.222 36 1 0 889 924 189430363 189430328 1.140000e-05 62.1
80 TraesCS1A01G035500 chr5A 97.059 476 12 2 3128 3602 496137230 496137704 0.000000e+00 800.0
81 TraesCS1A01G035500 chr5A 81.541 753 87 28 922 1660 573871440 573870726 1.180000e-159 573.0
82 TraesCS1A01G035500 chr5A 82.796 465 46 17 1210 1660 332449229 332449673 5.950000e-103 385.0
83 TraesCS1A01G035500 chr5A 98.919 185 2 0 3613 3797 4333949 4334133 7.860000e-87 331.0
84 TraesCS1A01G035500 chr5A 98.919 185 2 0 3613 3797 567987749 567987933 7.860000e-87 331.0
85 TraesCS1A01G035500 chr5A 88.128 219 17 7 1826 2044 573870669 573870460 6.300000e-63 252.0
86 TraesCS1A01G035500 chr5A 88.690 168 13 5 1875 2042 332449801 332449962 2.310000e-47 200.0
87 TraesCS1A01G035500 chr5A 88.732 71 3 2 1851 1921 332449731 332449796 8.740000e-12 82.4
88 TraesCS1A01G035500 chr3A 94.514 401 16 3 1553 1951 55051797 55051401 6.970000e-172 614.0
89 TraesCS1A01G035500 chr3A 97.549 204 4 1 2044 2247 358267184 358266982 7.810000e-92 348.0
90 TraesCS1A01G035500 chr3A 97.549 204 4 1 2044 2247 630361221 630361019 7.810000e-92 348.0
91 TraesCS1A01G035500 chr3A 95.283 106 5 0 1936 2041 55051372 55051267 6.520000e-38 169.0
92 TraesCS1A01G035500 chr3A 100.000 67 0 0 2265 2331 358265963 358265897 1.430000e-24 124.0
93 TraesCS1A01G035500 chr7D 83.801 463 52 7 1210 1660 8994183 8994634 5.870000e-113 418.0
94 TraesCS1A01G035500 chr7D 87.912 182 16 3 4 180 597590820 597590640 3.840000e-50 209.0
95 TraesCS1A01G035500 chr7B 97.044 203 6 0 2045 2247 655259627 655259829 3.630000e-90 342.0
96 TraesCS1A01G035500 chr7B 98.837 86 1 0 2263 2348 655260845 655260930 1.830000e-33 154.0
97 TraesCS1A01G035500 chr7B 83.696 92 13 2 922 1012 715810565 715810475 6.760000e-13 86.1
98 TraesCS1A01G035500 chr7B 97.297 37 1 0 2266 2302 378419417 378419453 3.170000e-06 63.9
99 TraesCS1A01G035500 chr2D 98.919 185 2 0 3613 3797 647321850 647322034 7.860000e-87 331.0
100 TraesCS1A01G035500 chr2D 89.362 47 3 2 2266 2310 578600873 578600919 1.470000e-04 58.4
101 TraesCS1A01G035500 chr2D 84.483 58 5 4 2239 2293 396056429 396056373 2.000000e-03 54.7
102 TraesCS1A01G035500 chr1D 87.143 210 16 7 2044 2251 253348830 253349030 1.060000e-55 228.0
103 TraesCS1A01G035500 chr1D 81.646 158 13 5 1065 1218 405281334 405281479 2.400000e-22 117.0
104 TraesCS1A01G035500 chr1D 97.917 48 1 0 2301 2348 253351013 253351060 2.430000e-12 84.2
105 TraesCS1A01G035500 chr1D 78.322 143 17 8 1076 1217 12647124 12647253 3.140000e-11 80.5
106 TraesCS1A01G035500 chr1D 94.595 37 2 0 2266 2302 330529591 330529555 1.470000e-04 58.4
107 TraesCS1A01G035500 chr6B 93.636 110 5 1 2138 2247 268717397 268717504 3.030000e-36 163.0
108 TraesCS1A01G035500 chr6B 98.837 86 1 0 2263 2348 268718521 268718606 1.830000e-33 154.0
109 TraesCS1A01G035500 chr6B 97.436 39 1 0 1073 1111 291759949 291759911 2.450000e-07 67.6
110 TraesCS1A01G035500 chr6D 83.146 89 15 0 2990 3078 386751379 386751291 8.740000e-12 82.4
111 TraesCS1A01G035500 chr6D 77.083 144 18 7 1075 1217 175710965 175710836 6.810000e-08 69.4
112 TraesCS1A01G035500 chr6D 100.000 31 0 0 2266 2296 69785466 69785496 1.470000e-04 58.4
113 TraesCS1A01G035500 chr6D 97.059 34 1 0 2266 2299 346251408 346251375 1.470000e-04 58.4
114 TraesCS1A01G035500 chr6D 94.737 38 1 1 2262 2299 425931280 425931316 1.470000e-04 58.4
115 TraesCS1A01G035500 chr6D 94.444 36 2 0 2265 2300 194248253 194248218 5.300000e-04 56.5
116 TraesCS1A01G035500 chr6D 92.308 39 1 2 2259 2297 204160147 204160183 2.000000e-03 54.7
117 TraesCS1A01G035500 chr4D 78.512 121 24 1 2997 3117 128999265 128999383 1.130000e-10 78.7
118 TraesCS1A01G035500 chr4D 97.143 35 1 0 2266 2300 216298796 216298762 4.100000e-05 60.2
119 TraesCS1A01G035500 chr4D 94.737 38 1 1 2259 2296 416432003 416432039 1.470000e-04 58.4
120 TraesCS1A01G035500 chr5D 97.222 36 1 0 2266 2301 117356017 117355982 1.140000e-05 62.1
121 TraesCS1A01G035500 chr5D 94.737 38 1 1 2259 2296 343243197 343243161 1.470000e-04 58.4
122 TraesCS1A01G035500 chr3D 92.683 41 2 1 2259 2299 22092908 22092869 1.470000e-04 58.4
123 TraesCS1A01G035500 chr3D 92.683 41 1 2 2259 2297 130015392 130015432 1.470000e-04 58.4
124 TraesCS1A01G035500 chr3D 90.698 43 4 0 2259 2301 391318883 391318925 1.470000e-04 58.4
125 TraesCS1A01G035500 chr3D 89.362 47 3 2 2266 2311 392055306 392055261 1.470000e-04 58.4
126 TraesCS1A01G035500 chr3D 92.683 41 2 1 2259 2299 507038710 507038749 1.470000e-04 58.4


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 TraesCS1A01G035500 chr1A 18989008 18992804 3796 True 6938.000000 6938 100.000000 1 3797 1 chr1A.!!$R3 3796
1 TraesCS1A01G035500 chr1A 18815523 18821603 6080 True 3285.000000 5703 99.629000 1 3602 2 chr1A.!!$R6 3601
2 TraesCS1A01G035500 chrUn 393223993 393225504 1511 False 2771.000000 2771 99.735000 1606 3117 1 chrUn.!!$F11 1511
3 TraesCS1A01G035500 chr2B 306174860 306175582 722 True 1205.000000 1205 96.708000 2393 3117 1 chr2B.!!$R1 724
4 TraesCS1A01G035500 chr2B 190630195 190630917 722 False 1194.000000 1194 96.433000 2393 3117 1 chr2B.!!$F2 724
5 TraesCS1A01G035500 chr2B 193951092 193952396 1304 False 248.000000 342 97.948000 2044 2348 2 chr2B.!!$F4 304
6 TraesCS1A01G035500 chr4A 375965820 375966539 719 True 1195.000000 1195 96.571000 2393 3117 1 chr4A.!!$R2 724
7 TraesCS1A01G035500 chr5B 678063884 678064606 722 False 1194.000000 1194 96.433000 2393 3117 1 chr5B.!!$F3 724
8 TraesCS1A01G035500 chr3B 655539407 655540129 722 False 1194.000000 1194 96.433000 2393 3117 1 chr3B.!!$F3 724
9 TraesCS1A01G035500 chr3B 366404382 366405683 1301 True 259.000000 359 99.264500 2044 2348 2 chr3B.!!$R2 304
10 TraesCS1A01G035500 chr4B 17909562 17910284 722 True 1177.000000 1177 96.022000 2393 3117 1 chr4B.!!$R1 724
11 TraesCS1A01G035500 chr4B 387818922 387820704 1782 True 594.000000 963 89.016667 1 2038 3 chr4B.!!$R6 2037
12 TraesCS1A01G035500 chr4B 233692874 233694176 1302 False 248.000000 342 97.948000 2044 2348 2 chr4B.!!$F2 304
13 TraesCS1A01G035500 chr1B 86567150 86567872 722 True 1171.000000 1171 95.885000 2393 3117 1 chr1B.!!$R1 724
14 TraesCS1A01G035500 chr1B 169363797 169365094 1297 False 242.000000 339 97.102000 2044 2348 2 chr1B.!!$F3 304
15 TraesCS1A01G035500 chr2A 2873136 2873677 541 True 267.500000 390 91.686500 609 1018 2 chr2A.!!$R4 409
16 TraesCS1A01G035500 chr5A 573870460 573871440 980 True 412.500000 573 84.834500 922 2044 2 chr5A.!!$R1 1122
17 TraesCS1A01G035500 chr5A 332449229 332449962 733 False 222.466667 385 86.739333 1210 2042 3 chr5A.!!$F4 832
18 TraesCS1A01G035500 chr3A 55051267 55051797 530 True 391.500000 614 94.898500 1553 2041 2 chr3A.!!$R2 488
19 TraesCS1A01G035500 chr3A 358265897 358267184 1287 True 236.000000 348 98.774500 2044 2331 2 chr3A.!!$R3 287
20 TraesCS1A01G035500 chr7B 655259627 655260930 1303 False 248.000000 342 97.940500 2045 2348 2 chr7B.!!$F2 303

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
746 750 1.134521 GTACAATGCGGGAGGATCACA 60.135 52.381 0.0 0.0 39.81 3.58 F
1351 1512 0.397675 TGATCTCATGACCCTCGCCT 60.398 55.000 0.0 0.0 0.00 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2496 3888 7.023575 GCTCGACTATGAACAAAATTGAACAT 58.976 34.615 0.0 7.4 34.35 2.71 R
3225 7104 5.689383 TGCATACTGAACAAAAAGAGGTC 57.311 39.130 0.0 0.0 0.00 3.85 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)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
746 750 1.134521 GTACAATGCGGGAGGATCACA 60.135 52.381 0.0 0.0 39.81 3.58
1351 1512 0.397675 TGATCTCATGACCCTCGCCT 60.398 55.000 0.0 0.0 0.00 5.52
3340 7219 8.831550 CCTAATTGTTTAGAGAGCTAAATGACC 58.168 37.037 0.0 0.0 45.47 4.02
3638 7517 9.623000 AACTAGTAAGTGTTTAATGTTTCACCT 57.377 29.630 0.0 0.0 35.62 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
746 750 4.386049 CGAAAACTGAAACAGCGACTCTAT 59.614 41.667 0.00 0.0 34.37 1.98
2496 3888 7.023575 GCTCGACTATGAACAAAATTGAACAT 58.976 34.615 0.00 7.4 34.35 2.71
3225 7104 5.689383 TGCATACTGAACAAAAAGAGGTC 57.311 39.130 0.00 0.0 0.00 3.85
3340 7219 9.782028 CATTTTGTAGTGATTTTCAATTTCACG 57.218 29.630 2.41 0.0 43.49 4.35
3612 7491 9.623000 AGGTGAAACATTAAACACTTACTAGTT 57.377 29.630 0.00 0.0 39.98 2.24


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

AutoCloner maintained by Alex Coulton.