Multiple sequence alignment - TraesCS2D01G147300

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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 TraesCS2D01G147300 chr2D 100.000 5108 0 0 1 5108 88286866 88291973 0.000000e+00 9433.0
1 TraesCS2D01G147300 chr2D 100.000 2982 0 0 5561 8542 88292426 88295407 0.000000e+00 5507.0
2 TraesCS2D01G147300 chr2D 92.294 1090 41 20 5597 6676 559300406 559299350 0.000000e+00 1507.0
3 TraesCS2D01G147300 chr2D 96.349 630 21 2 4476 5104 559301563 559300935 0.000000e+00 1035.0
4 TraesCS2D01G147300 chr2D 94.099 627 27 4 4472 5089 569252189 569252814 0.000000e+00 944.0
5 TraesCS2D01G147300 chr2D 91.903 247 19 1 4858 5104 21106090 21106335 2.280000e-90 344.0
6 TraesCS2D01G147300 chr2D 93.035 201 14 0 7071 7271 88293837 88294037 2.330000e-75 294.0
7 TraesCS2D01G147300 chr2D 93.035 201 14 0 6972 7172 88293936 88294136 2.330000e-75 294.0
8 TraesCS2D01G147300 chr2D 91.176 170 12 3 3183 3352 79056326 79056160 2.400000e-55 228.0
9 TraesCS2D01G147300 chr2D 80.984 305 21 12 405 674 558242528 558242226 3.130000e-49 207.0
10 TraesCS2D01G147300 chr2D 84.141 227 19 7 424 634 316289976 316290201 4.040000e-48 204.0
11 TraesCS2D01G147300 chr2D 78.247 308 28 9 406 674 35027981 35028288 2.470000e-35 161.0
12 TraesCS2D01G147300 chr2D 93.458 107 3 3 2906 3009 88289664 88289769 1.150000e-33 156.0
13 TraesCS2D01G147300 chr2D 93.458 107 3 3 2799 2904 88289771 88289874 1.150000e-33 156.0
14 TraesCS2D01G147300 chr2D 85.034 147 17 3 4255 4396 547238898 547239044 2.490000e-30 145.0
15 TraesCS2D01G147300 chr2D 90.385 52 3 2 2286 2336 644868142 644868192 5.530000e-07 67.6
16 TraesCS2D01G147300 chr2A 93.402 2895 88 36 737 3578 88661648 88664492 0.000000e+00 4193.0
17 TraesCS2D01G147300 chr2A 96.937 914 19 3 6683 7587 88670724 88671637 0.000000e+00 1524.0
18 TraesCS2D01G147300 chr2A 92.243 593 36 3 5561 6150 72379926 72379341 0.000000e+00 832.0
19 TraesCS2D01G147300 chr2A 98.253 458 8 0 3581 4038 88669524 88669981 0.000000e+00 802.0
20 TraesCS2D01G147300 chr2A 97.511 442 6 2 4038 4478 88670294 88670731 0.000000e+00 750.0
21 TraesCS2D01G147300 chr2A 81.637 855 101 24 3586 4396 41162199 41161357 0.000000e+00 658.0
22 TraesCS2D01G147300 chr2A 95.833 192 7 1 645 836 88661592 88661782 8.330000e-80 309.0
23 TraesCS2D01G147300 chr2A 90.643 171 13 3 3183 3353 79316164 79315997 3.100000e-54 224.0
24 TraesCS2D01G147300 chr2A 92.523 107 7 1 2799 2904 88663805 88663911 1.490000e-32 152.0
25 TraesCS2D01G147300 chr2A 93.137 102 4 2 2906 3004 88663699 88663800 6.910000e-31 147.0
26 TraesCS2D01G147300 chr2A 83.654 104 15 2 1835 1938 88669778 88669879 7.060000e-16 97.1
27 TraesCS2D01G147300 chr2B 96.151 1637 25 7 933 2540 141559004 141560631 0.000000e+00 2639.0
28 TraesCS2D01G147300 chr2B 94.717 1060 28 14 2540 3578 141561513 141562565 0.000000e+00 1622.0
29 TraesCS2D01G147300 chr2B 97.998 899 15 3 3581 4478 141563121 141564017 0.000000e+00 1557.0
30 TraesCS2D01G147300 chr2B 96.078 918 23 3 6683 7587 141564010 141564927 0.000000e+00 1483.0
31 TraesCS2D01G147300 chr2B 90.135 963 64 15 7587 8542 116273575 116272637 0.000000e+00 1223.0
32 TraesCS2D01G147300 chr2B 92.537 335 25 0 46 380 141534864 141535198 1.670000e-131 481.0
33 TraesCS2D01G147300 chr2B 83.221 298 34 9 3821 4104 672333311 672333016 8.510000e-65 259.0
34 TraesCS2D01G147300 chr2B 79.926 269 27 14 674 927 579961315 579961571 1.140000e-38 172.0
35 TraesCS2D01G147300 chr2B 92.308 104 8 0 3581 3684 672333436 672333333 1.920000e-31 148.0
36 TraesCS2D01G147300 chr2B 93.137 102 4 3 2906 3004 141561772 141561873 6.910000e-31 147.0
37 TraesCS2D01G147300 chr2B 86.364 110 6 2 2799 2899 141561878 141561987 2.520000e-20 111.0
38 TraesCS2D01G147300 chr2B 84.615 104 14 2 1835 1938 141563375 141563476 1.520000e-17 102.0
39 TraesCS2D01G147300 chr3D 95.543 1077 44 3 5603 6676 415663917 415662842 0.000000e+00 1720.0
40 TraesCS2D01G147300 chr3D 94.234 659 30 5 6023 6675 337659641 337658985 0.000000e+00 1000.0
41 TraesCS2D01G147300 chr3D 93.027 631 23 2 4474 5104 415664964 415664355 0.000000e+00 902.0
42 TraesCS2D01G147300 chr3D 92.989 542 37 1 4476 5016 135254649 135255190 0.000000e+00 789.0
43 TraesCS2D01G147300 chr3D 84.016 513 49 15 3581 4062 497491455 497490945 6.040000e-126 462.0
44 TraesCS2D01G147300 chr3D 93.038 158 10 1 3190 3347 288550458 288550614 6.670000e-56 230.0
45 TraesCS2D01G147300 chr3D 92.308 156 11 1 3190 3344 347585233 347585388 4.010000e-53 220.0
46 TraesCS2D01G147300 chr3D 90.798 163 14 1 3183 3345 322435451 322435290 5.190000e-52 217.0
47 TraesCS2D01G147300 chr3D 91.250 160 11 3 3191 3348 315480578 315480420 1.870000e-51 215.0
48 TraesCS2D01G147300 chr3D 82.117 274 24 10 406 655 480421168 480420896 2.420000e-50 211.0
49 TraesCS2D01G147300 chr3D 80.072 276 23 12 404 654 427057069 427056801 8.810000e-40 176.0
50 TraesCS2D01G147300 chr3D 78.906 256 33 12 406 642 31402652 31402399 4.130000e-33 154.0
51 TraesCS2D01G147300 chr7D 93.800 1129 51 6 5561 6676 581388327 581387205 0.000000e+00 1679.0
52 TraesCS2D01G147300 chr7D 93.989 1048 44 8 5635 6676 296506501 296505467 0.000000e+00 1568.0
53 TraesCS2D01G147300 chr7D 95.747 964 31 5 7587 8542 558182775 558181814 0.000000e+00 1544.0
54 TraesCS2D01G147300 chr7D 94.770 631 27 6 4476 5102 581388970 581388342 0.000000e+00 977.0
55 TraesCS2D01G147300 chr7D 94.937 158 7 1 3190 3347 436961795 436961951 6.620000e-61 246.0
56 TraesCS2D01G147300 chr7D 92.857 154 10 1 3190 3343 593035315 593035163 1.120000e-53 222.0
57 TraesCS2D01G147300 chr7D 90.854 164 12 3 3190 3351 74596194 74596032 5.190000e-52 217.0
58 TraesCS2D01G147300 chr7D 90.798 163 14 1 3190 3352 197927008 197927169 5.190000e-52 217.0
59 TraesCS2D01G147300 chr7D 89.017 173 18 1 3190 3362 375400916 375400745 6.720000e-51 213.0
60 TraesCS2D01G147300 chr7D 89.744 78 4 1 717 794 94211398 94211325 7.060000e-16 97.1
61 TraesCS2D01G147300 chr7D 84.946 93 6 5 702 794 94211378 94211294 4.250000e-13 87.9
62 TraesCS2D01G147300 chr7D 91.667 48 3 1 2289 2336 2666238 2666284 1.990000e-06 65.8
63 TraesCS2D01G147300 chr5D 94.722 1042 51 3 5638 6676 230976389 230975349 0.000000e+00 1616.0
64 TraesCS2D01G147300 chr5D 89.592 1153 63 23 1028 2135 530424514 530425654 0.000000e+00 1411.0
65 TraesCS2D01G147300 chr5D 88.864 907 68 14 3581 4468 530426468 530427360 0.000000e+00 1085.0
66 TraesCS2D01G147300 chr5D 94.402 661 30 5 6023 6676 263148239 263148899 0.000000e+00 1009.0
67 TraesCS2D01G147300 chr5D 94.266 593 25 1 4476 5059 230977333 230976741 0.000000e+00 898.0
68 TraesCS2D01G147300 chr5D 91.481 493 38 2 6684 7172 530427362 530427854 0.000000e+00 675.0
69 TraesCS2D01G147300 chr5D 86.667 360 44 4 7071 7428 530427654 530428011 6.210000e-106 396.0
70 TraesCS2D01G147300 chr5D 83.333 282 27 10 410 673 174279225 174279504 8.570000e-60 243.0
71 TraesCS2D01G147300 chr5D 82.492 297 26 13 405 676 399997652 399997357 3.990000e-58 237.0
72 TraesCS2D01G147300 chr5D 86.614 127 11 4 7455 7580 530428071 530428192 1.500000e-27 135.0
73 TraesCS2D01G147300 chr5D 97.143 35 0 1 2283 2317 35828575 35828608 3.330000e-04 58.4
74 TraesCS2D01G147300 chr4D 93.681 1092 39 11 5591 6676 14993729 14994796 0.000000e+00 1607.0
75 TraesCS2D01G147300 chr4D 92.593 621 37 4 4476 5089 311909638 311909020 0.000000e+00 883.0
76 TraesCS2D01G147300 chr4D 91.346 624 35 12 4476 5087 472669859 472669243 0.000000e+00 835.0
77 TraesCS2D01G147300 chr4D 92.593 162 12 0 3182 3343 74079512 74079351 5.160000e-57 233.0
78 TraesCS2D01G147300 chr4D 90.323 155 12 3 3190 3343 335774436 335774284 5.230000e-47 200.0
79 TraesCS2D01G147300 chr4D 82.128 235 36 2 405 634 485493726 485493959 6.760000e-46 196.0
80 TraesCS2D01G147300 chr4D 89.610 154 15 1 3190 3343 420141016 420141168 2.430000e-45 195.0
81 TraesCS2D01G147300 chr4D 89.032 155 16 1 3190 3344 82727680 82727527 3.150000e-44 191.0
82 TraesCS2D01G147300 chr4D 87.273 165 17 4 3190 3352 341693403 341693241 1.460000e-42 185.0
83 TraesCS2D01G147300 chr4D 79.928 279 27 12 406 655 113170187 113170465 2.450000e-40 178.0
84 TraesCS2D01G147300 chr4D 80.292 274 22 15 405 648 375650416 375650687 2.450000e-40 178.0
85 TraesCS2D01G147300 chr4D 79.848 263 18 9 406 657 111552631 111552869 8.880000e-35 159.0
86 TraesCS2D01G147300 chr4D 85.047 107 11 2 406 507 12412294 12412400 4.220000e-18 104.0
87 TraesCS2D01G147300 chr4D 100.000 33 0 0 2289 2321 213332165 213332197 2.570000e-05 62.1
88 TraesCS2D01G147300 chr4D 93.023 43 1 1 2279 2321 493836151 493836191 2.570000e-05 62.1
89 TraesCS2D01G147300 chr4D 84.483 58 8 1 620 677 39240681 39240625 1.000000e-03 56.5
90 TraesCS2D01G147300 chr4D 100.000 30 0 0 2288 2317 134540461 134540432 1.000000e-03 56.5
91 TraesCS2D01G147300 chr1D 96.680 964 23 4 7587 8542 412179144 412178182 0.000000e+00 1594.0
92 TraesCS2D01G147300 chr1D 93.086 593 31 3 5561 6150 212715004 212715589 0.000000e+00 859.0
93 TraesCS2D01G147300 chr1D 91.213 569 39 7 4531 5097 297166892 297167451 0.000000e+00 763.0
94 TraesCS2D01G147300 chr1D 82.353 833 97 22 3581 4375 399354009 399354829 0.000000e+00 678.0
95 TraesCS2D01G147300 chr1D 81.330 857 102 26 3586 4396 97777446 97776602 2.010000e-180 643.0
96 TraesCS2D01G147300 chr1D 84.836 244 18 11 681 910 459896083 459895845 2.400000e-55 228.0
97 TraesCS2D01G147300 chr1D 91.875 160 10 3 3185 3344 7349700 7349856 4.010000e-53 220.0
98 TraesCS2D01G147300 chr1D 82.593 270 28 6 422 673 240118995 240119263 4.010000e-53 220.0
99 TraesCS2D01G147300 chr1D 89.759 166 15 2 3190 3354 156133339 156133503 2.420000e-50 211.0
100 TraesCS2D01G147300 chr1D 81.949 277 20 13 405 652 188464206 188464481 3.130000e-49 207.0
101 TraesCS2D01G147300 chr1D 81.560 282 21 14 404 655 393034972 393035252 4.040000e-48 204.0
102 TraesCS2D01G147300 chr1D 88.750 160 17 1 3190 3349 471593832 471593674 2.430000e-45 195.0
103 TraesCS2D01G147300 chr1D 80.000 280 22 16 406 654 386375762 386376038 8.810000e-40 176.0
104 TraesCS2D01G147300 chr1D 80.321 249 27 8 404 630 445570272 445570024 1.470000e-37 169.0
105 TraesCS2D01G147300 chr1D 88.991 109 12 0 422 530 55887021 55887129 1.500000e-27 135.0
106 TraesCS2D01G147300 chr1D 76.512 281 28 15 410 654 431964218 431964496 1.510000e-22 119.0
107 TraesCS2D01G147300 chr1D 82.796 93 8 6 702 794 78088212 78088128 9.190000e-10 76.8
108 TraesCS2D01G147300 chr1D 88.235 51 5 1 2289 2339 6369874 6369923 9.260000e-05 60.2
109 TraesCS2D01G147300 chr1D 100.000 32 0 0 2288 2319 468194013 468194044 9.260000e-05 60.2
110 TraesCS2D01G147300 chr5B 88.813 1314 82 34 1028 2289 669670037 669671337 0.000000e+00 1552.0
111 TraesCS2D01G147300 chr5B 88.268 912 76 16 3581 4477 669671682 669672577 0.000000e+00 1062.0
112 TraesCS2D01G147300 chr5B 89.109 505 41 6 7071 7563 669672854 669673356 4.380000e-172 616.0
113 TraesCS2D01G147300 chr5B 89.293 495 37 7 6683 7172 669672571 669673054 2.640000e-169 606.0
114 TraesCS2D01G147300 chr5B 90.476 168 12 4 3190 3357 176588228 176588391 1.440000e-52 219.0
115 TraesCS2D01G147300 chr5B 78.007 291 27 14 422 676 482293300 482293011 1.920000e-31 148.0
116 TraesCS2D01G147300 chr5B 84.354 147 17 4 4255 4396 455278846 455278991 1.160000e-28 139.0
117 TraesCS2D01G147300 chr5B 91.860 86 7 0 3747 3832 669671938 669672023 4.190000e-23 121.0
118 TraesCS2D01G147300 chr5B 88.119 101 12 0 6973 7073 669672954 669673054 4.190000e-23 121.0
119 TraesCS2D01G147300 chr5A 91.763 947 44 12 1028 1948 658670231 658671169 0.000000e+00 1286.0
120 TraesCS2D01G147300 chr5A 88.974 916 65 15 3581 4477 658672037 658672935 0.000000e+00 1099.0
121 TraesCS2D01G147300 chr5A 91.896 617 30 7 4476 5089 229765193 229765792 0.000000e+00 845.0
122 TraesCS2D01G147300 chr5A 94.428 341 18 1 6833 7172 658673028 658673368 2.730000e-144 523.0
123 TraesCS2D01G147300 chr5A 88.022 359 34 2 7071 7428 658673168 658673518 4.770000e-112 416.0
124 TraesCS2D01G147300 chr5A 91.975 162 11 2 3184 3344 86662178 86662018 8.630000e-55 226.0
125 TraesCS2D01G147300 chr5A 82.375 261 35 4 406 655 641747232 641746972 5.190000e-52 217.0
126 TraesCS2D01G147300 chr5A 97.059 102 3 0 6972 7073 658673267 658673368 1.140000e-38 172.0
127 TraesCS2D01G147300 chr5A 100.000 36 0 0 2288 2323 344342687 344342722 5.530000e-07 67.6
128 TraesCS2D01G147300 chr4A 94.021 669 30 7 6024 6684 17977287 17977953 0.000000e+00 1005.0
129 TraesCS2D01G147300 chr4A 92.545 550 34 6 4476 5020 381226107 381225560 0.000000e+00 782.0
130 TraesCS2D01G147300 chr4A 86.058 208 18 4 404 601 48526158 48526364 6.720000e-51 213.0
131 TraesCS2D01G147300 chr4A 84.354 147 18 3 4255 4396 615524930 615525076 1.160000e-28 139.0
132 TraesCS2D01G147300 chr4A 100.000 36 0 0 2289 2324 397861322 397861287 5.530000e-07 67.6
133 TraesCS2D01G147300 chr7A 93.155 599 26 5 5561 6150 167262903 167262311 0.000000e+00 865.0
134 TraesCS2D01G147300 chr7A 94.304 158 8 1 3190 3347 486929940 486930096 3.080000e-59 241.0
135 TraesCS2D01G147300 chr6D 92.759 580 32 3 5561 6137 20198551 20197979 0.000000e+00 830.0
136 TraesCS2D01G147300 chr6D 81.544 298 24 18 405 673 323051436 323051141 5.190000e-52 217.0
137 TraesCS2D01G147300 chr6D 89.937 159 14 2 3190 3347 303060007 303059850 4.040000e-48 204.0
138 TraesCS2D01G147300 chr6D 80.392 306 24 16 403 673 423083041 423083345 5.230000e-47 200.0
139 TraesCS2D01G147300 chr6D 88.957 163 15 2 3190 3352 356594218 356594059 1.880000e-46 198.0
140 TraesCS2D01G147300 chr6D 91.971 137 10 1 3207 3343 221843011 221843146 3.150000e-44 191.0
141 TraesCS2D01G147300 chr6D 88.961 154 15 2 3190 3343 320698231 320698080 1.130000e-43 189.0
142 TraesCS2D01G147300 chr6D 87.975 158 17 2 3186 3343 256728605 256728450 1.460000e-42 185.0
143 TraesCS2D01G147300 chr6D 87.975 158 17 2 3186 3343 256729402 256729247 1.460000e-42 185.0
144 TraesCS2D01G147300 chr6D 80.282 284 20 15 406 654 100600615 100600333 1.890000e-41 182.0
145 TraesCS2D01G147300 chr6D 78.878 303 24 14 404 673 428619271 428619566 1.470000e-37 169.0
146 TraesCS2D01G147300 chr6D 79.298 285 21 16 406 654 411556340 411556622 1.910000e-36 165.0
147 TraesCS2D01G147300 chr6D 96.667 60 1 1 405 463 812957 812898 1.960000e-16 99.0
148 TraesCS2D01G147300 chr6D 96.970 33 1 0 2288 2320 24033664 24033632 1.000000e-03 56.5
149 TraesCS2D01G147300 chr6D 96.970 33 1 0 2288 2320 329080284 329080252 1.000000e-03 56.5
150 TraesCS2D01G147300 chr6D 100.000 29 0 0 2289 2317 329857492 329857520 4.000000e-03 54.7
151 TraesCS2D01G147300 chr6D 100.000 29 0 0 2289 2317 367991011 367991039 4.000000e-03 54.7
152 TraesCS2D01G147300 chr6D 100.000 29 0 0 2289 2317 395332175 395332203 4.000000e-03 54.7
153 TraesCS2D01G147300 chr6D 100.000 29 0 0 2289 2317 470407791 470407819 4.000000e-03 54.7
154 TraesCS2D01G147300 chr6A 91.568 593 37 6 5561 6147 122686517 122687102 0.000000e+00 806.0
155 TraesCS2D01G147300 chr6A 81.893 856 97 28 3586 4396 207841253 207840411 0.000000e+00 669.0
156 TraesCS2D01G147300 chr6A 82.226 602 72 17 3583 4153 614472868 614473465 3.580000e-133 486.0
157 TraesCS2D01G147300 chr6A 81.229 602 78 16 3583 4153 598684081 598684678 3.640000e-123 453.0
158 TraesCS2D01G147300 chr6A 80.420 286 25 13 402 657 417487903 417487619 1.130000e-43 189.0
159 TraesCS2D01G147300 chr6A 97.436 39 0 1 2285 2323 550721856 550721893 1.990000e-06 65.8
160 TraesCS2D01G147300 chr7B 81.192 856 102 28 3586 4396 114144719 114143878 1.210000e-177 634.0
161 TraesCS2D01G147300 chr7B 94.937 158 7 1 3190 3347 453623290 453623446 6.620000e-61 246.0
162 TraesCS2D01G147300 chr7B 91.824 159 11 2 3190 3348 155471319 155471163 4.010000e-53 220.0
163 TraesCS2D01G147300 chr7B 89.017 173 18 1 3190 3362 369872871 369872700 6.720000e-51 213.0
164 TraesCS2D01G147300 chr7B 80.843 261 26 9 405 642 24005444 24005185 5.270000e-42 183.0
165 TraesCS2D01G147300 chr7B 81.081 259 23 10 401 634 586179772 586179515 5.270000e-42 183.0
166 TraesCS2D01G147300 chr7B 97.222 36 1 0 2288 2323 123310104 123310069 2.570000e-05 62.1
167 TraesCS2D01G147300 chr7B 92.683 41 2 1 2289 2328 33809030 33809070 3.330000e-04 58.4
168 TraesCS2D01G147300 chr3A 82.618 466 59 18 3948 4394 637283448 637283910 8.040000e-105 392.0
169 TraesCS2D01G147300 chr3A 84.848 165 16 4 524 680 52197175 52197338 3.190000e-34 158.0
170 TraesCS2D01G147300 chr3A 83.099 71 6 6 2289 2356 689337427 689337494 9.260000e-05 60.2
171 TraesCS2D01G147300 chr6B 82.373 295 36 11 3821 4101 519221653 519221945 8.570000e-60 243.0
172 TraesCS2D01G147300 chr6B 83.523 176 19 6 410 576 64201212 64201386 1.150000e-33 156.0
173 TraesCS2D01G147300 chr6B 90.385 104 10 0 3581 3684 519221528 519221631 4.160000e-28 137.0
174 TraesCS2D01G147300 chr6B 94.872 39 2 0 2289 2327 563062912 563062874 2.570000e-05 62.1
175 TraesCS2D01G147300 chr6B 94.872 39 1 1 2285 2323 299961344 299961307 9.260000e-05 60.2
176 TraesCS2D01G147300 chr6B 94.872 39 1 1 2289 2327 632814433 632814470 9.260000e-05 60.2
177 TraesCS2D01G147300 chr3B 90.964 166 13 2 3183 3347 328715604 328715440 1.120000e-53 222.0
178 TraesCS2D01G147300 chr3B 80.090 221 26 12 4100 4312 657539470 657539260 1.920000e-31 148.0
179 TraesCS2D01G147300 chr3B 85.714 147 11 7 3909 4046 657541200 657541055 6.910000e-31 147.0
180 TraesCS2D01G147300 chr3B 95.122 41 2 0 2288 2328 277026487 277026447 1.990000e-06 65.8
181 TraesCS2D01G147300 chr1A 90.798 163 13 2 3190 3351 155857859 155857698 5.190000e-52 217.0
182 TraesCS2D01G147300 chr1A 91.613 155 11 2 3190 3343 298614248 298614401 6.720000e-51 213.0
183 TraesCS2D01G147300 chr1A 95.122 123 4 2 720 841 551611081 551610960 8.750000e-45 193.0
184 TraesCS2D01G147300 chr1A 80.287 279 26 11 401 655 385669915 385670188 5.270000e-42 183.0
185 TraesCS2D01G147300 chr1A 79.211 279 32 11 422 676 555644788 555645064 4.100000e-38 171.0
186 TraesCS2D01G147300 chr1A 80.000 240 29 7 422 642 59512467 59512228 8.880000e-35 159.0
187 TraesCS2D01G147300 chr1A 79.412 238 24 10 406 642 547297628 547297415 2.490000e-30 145.0
188 TraesCS2D01G147300 chr1A 100.000 31 0 0 2289 2319 27378100 27378130 3.330000e-04 58.4
189 TraesCS2D01G147300 chr1A 100.000 31 0 0 2289 2319 332051613 332051583 3.330000e-04 58.4
190 TraesCS2D01G147300 chr1A 92.308 39 2 1 2279 2317 546328984 546329021 4.000000e-03 54.7
191 TraesCS2D01G147300 chr1A 94.444 36 1 1 2285 2320 547002317 547002283 4.000000e-03 54.7
192 TraesCS2D01G147300 chr4B 90.361 166 11 5 3192 3357 510827662 510827822 6.720000e-51 213.0
193 TraesCS2D01G147300 chr4B 91.558 154 12 1 3190 3343 106227561 106227409 2.420000e-50 211.0
194 TraesCS2D01G147300 chr4B 89.759 166 13 4 3190 3354 510849249 510849087 8.690000e-50 209.0
195 TraesCS2D01G147300 chr4B 90.566 159 12 3 3189 3347 483582140 483581985 3.130000e-49 207.0
196 TraesCS2D01G147300 chr4B 89.157 166 16 2 3183 3348 658773057 658773220 1.120000e-48 206.0
197 TraesCS2D01G147300 chr4B 79.924 264 20 16 422 655 659385952 659385692 6.860000e-36 163.0
198 TraesCS2D01G147300 chr4B 90.090 111 8 3 556 666 191650556 191650663 3.210000e-29 141.0
199 TraesCS2D01G147300 chr4B 77.407 270 30 14 403 642 6934473 6934741 1.930000e-26 132.0
200 TraesCS2D01G147300 chr4B 100.000 34 0 0 2288 2321 258738039 258738072 7.160000e-06 63.9
201 TraesCS2D01G147300 chr4B 100.000 34 0 0 2288 2321 387804554 387804587 7.160000e-06 63.9
202 TraesCS2D01G147300 chr4B 100.000 33 0 0 2289 2321 69147516 69147548 2.570000e-05 62.1
203 TraesCS2D01G147300 chr1B 85.000 220 17 13 681 894 632007572 632007363 8.690000e-50 209.0
204 TraesCS2D01G147300 chr1B 82.927 246 15 13 725 961 173133144 173132917 6.760000e-46 196.0
205 TraesCS2D01G147300 chrUn 90.968 155 13 1 3190 3344 96471030 96471183 3.130000e-49 207.0
206 TraesCS2D01G147300 chrUn 90.260 154 14 1 3190 3343 126680478 126680630 5.230000e-47 200.0
207 TraesCS2D01G147300 chrUn 90.667 150 13 1 3194 3343 50619843 50619991 1.880000e-46 198.0
208 TraesCS2D01G147300 chrUn 88.125 160 18 1 3192 3351 81694230 81694072 1.130000e-43 189.0
209 TraesCS2D01G147300 chrUn 85.882 170 19 4 3183 3352 277499567 277499731 8.810000e-40 176.0
210 TraesCS2D01G147300 chrUn 80.303 264 24 12 404 642 23672513 23672773 3.170000e-39 174.0
211 TraesCS2D01G147300 chrUn 86.928 153 17 3 3191 3343 40642977 40642828 1.470000e-37 169.0
212 TraesCS2D01G147300 chrUn 86.928 153 17 3 3191 3343 319944400 319944251 1.470000e-37 169.0
213 TraesCS2D01G147300 chrUn 88.722 133 13 2 3209 3341 12585659 12585789 2.470000e-35 161.0
214 TraesCS2D01G147300 chrUn 79.487 273 20 13 405 648 255617640 255617905 2.470000e-35 161.0
215 TraesCS2D01G147300 chrUn 79.211 279 22 13 405 654 445390559 445390288 2.470000e-35 161.0
216 TraesCS2D01G147300 chrUn 81.595 163 21 6 3189 3343 90452953 90453114 9.000000e-25 126.0
217 TraesCS2D01G147300 chrUn 76.512 281 27 18 406 647 48395166 48395446 5.420000e-22 117.0
218 TraesCS2D01G147300 chrUn 92.105 76 1 1 403 473 2934924 2934999 1.520000e-17 102.0
219 TraesCS2D01G147300 chrUn 85.714 98 13 1 557 653 346548210 346548307 1.520000e-17 102.0
220 TraesCS2D01G147300 chrUn 91.667 72 5 1 402 473 256594198 256594128 1.960000e-16 99.0
221 TraesCS2D01G147300 chrUn 100.000 30 0 0 2288 2317 62073553 62073524 1.000000e-03 56.5
222 TraesCS2D01G147300 chrUn 96.970 33 1 0 2288 2320 87725776 87725744 1.000000e-03 56.5
223 TraesCS2D01G147300 chrUn 96.875 32 1 0 2289 2320 118800925 118800894 4.000000e-03 54.7
224 TraesCS2D01G147300 chrUn 100.000 28 0 0 439 466 326758250 326758223 1.500000e-02 52.8
225 TraesCS2D01G147300 chrUn 88.372 43 5 0 424 466 381260160 381260202 1.500000e-02 52.8


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 TraesCS2D01G147300 chr2D 88286866 88295407 8541 False 2640.000000 9433 95.497667 1 8542 6 chr2D.!!$F7 8541
1 TraesCS2D01G147300 chr2D 559299350 559301563 2213 True 1271.000000 1507 94.321500 4476 6676 2 chr2D.!!$R3 2200
2 TraesCS2D01G147300 chr2D 569252189 569252814 625 False 944.000000 944 94.099000 4472 5089 1 chr2D.!!$F5 617
3 TraesCS2D01G147300 chr2A 88661592 88664492 2900 False 1200.250000 4193 93.723750 645 3578 4 chr2A.!!$F1 2933
4 TraesCS2D01G147300 chr2A 72379341 72379926 585 True 832.000000 832 92.243000 5561 6150 1 chr2A.!!$R2 589
5 TraesCS2D01G147300 chr2A 88669524 88671637 2113 False 793.275000 1524 94.088750 1835 7587 4 chr2A.!!$F2 5752
6 TraesCS2D01G147300 chr2A 41161357 41162199 842 True 658.000000 658 81.637000 3586 4396 1 chr2A.!!$R1 810
7 TraesCS2D01G147300 chr2B 116272637 116273575 938 True 1223.000000 1223 90.135000 7587 8542 1 chr2B.!!$R1 955
8 TraesCS2D01G147300 chr2B 141559004 141564927 5923 False 1094.428571 2639 92.722857 933 7587 7 chr2B.!!$F3 6654
9 TraesCS2D01G147300 chr3D 415662842 415664964 2122 True 1311.000000 1720 94.285000 4474 6676 2 chr3D.!!$R8 2202
10 TraesCS2D01G147300 chr3D 337658985 337659641 656 True 1000.000000 1000 94.234000 6023 6675 1 chr3D.!!$R4 652
11 TraesCS2D01G147300 chr3D 135254649 135255190 541 False 789.000000 789 92.989000 4476 5016 1 chr3D.!!$F1 540
12 TraesCS2D01G147300 chr3D 497490945 497491455 510 True 462.000000 462 84.016000 3581 4062 1 chr3D.!!$R7 481
13 TraesCS2D01G147300 chr7D 296505467 296506501 1034 True 1568.000000 1568 93.989000 5635 6676 1 chr7D.!!$R2 1041
14 TraesCS2D01G147300 chr7D 558181814 558182775 961 True 1544.000000 1544 95.747000 7587 8542 1 chr7D.!!$R4 955
15 TraesCS2D01G147300 chr7D 581387205 581388970 1765 True 1328.000000 1679 94.285000 4476 6676 2 chr7D.!!$R7 2200
16 TraesCS2D01G147300 chr5D 230975349 230977333 1984 True 1257.000000 1616 94.494000 4476 6676 2 chr5D.!!$R2 2200
17 TraesCS2D01G147300 chr5D 263148239 263148899 660 False 1009.000000 1009 94.402000 6023 6676 1 chr5D.!!$F3 653
18 TraesCS2D01G147300 chr5D 530424514 530428192 3678 False 740.400000 1411 88.643600 1028 7580 5 chr5D.!!$F4 6552
19 TraesCS2D01G147300 chr4D 14993729 14994796 1067 False 1607.000000 1607 93.681000 5591 6676 1 chr4D.!!$F2 1085
20 TraesCS2D01G147300 chr4D 311909020 311909638 618 True 883.000000 883 92.593000 4476 5089 1 chr4D.!!$R5 613
21 TraesCS2D01G147300 chr4D 472669243 472669859 616 True 835.000000 835 91.346000 4476 5087 1 chr4D.!!$R8 611
22 TraesCS2D01G147300 chr1D 412178182 412179144 962 True 1594.000000 1594 96.680000 7587 8542 1 chr1D.!!$R3 955
23 TraesCS2D01G147300 chr1D 212715004 212715589 585 False 859.000000 859 93.086000 5561 6150 1 chr1D.!!$F6 589
24 TraesCS2D01G147300 chr1D 297166892 297167451 559 False 763.000000 763 91.213000 4531 5097 1 chr1D.!!$F8 566
25 TraesCS2D01G147300 chr1D 399354009 399354829 820 False 678.000000 678 82.353000 3581 4375 1 chr1D.!!$F11 794
26 TraesCS2D01G147300 chr1D 97776602 97777446 844 True 643.000000 643 81.330000 3586 4396 1 chr1D.!!$R2 810
27 TraesCS2D01G147300 chr5B 669670037 669673356 3319 False 679.666667 1552 89.243667 1028 7563 6 chr5B.!!$F3 6535
28 TraesCS2D01G147300 chr5A 229765193 229765792 599 False 845.000000 845 91.896000 4476 5089 1 chr5A.!!$F1 613
29 TraesCS2D01G147300 chr5A 658670231 658673518 3287 False 699.200000 1286 92.049200 1028 7428 5 chr5A.!!$F3 6400
30 TraesCS2D01G147300 chr4A 17977287 17977953 666 False 1005.000000 1005 94.021000 6024 6684 1 chr4A.!!$F1 660
31 TraesCS2D01G147300 chr4A 381225560 381226107 547 True 782.000000 782 92.545000 4476 5020 1 chr4A.!!$R1 544
32 TraesCS2D01G147300 chr7A 167262311 167262903 592 True 865.000000 865 93.155000 5561 6150 1 chr7A.!!$R1 589
33 TraesCS2D01G147300 chr6D 20197979 20198551 572 True 830.000000 830 92.759000 5561 6137 1 chr6D.!!$R2 576
34 TraesCS2D01G147300 chr6A 122686517 122687102 585 False 806.000000 806 91.568000 5561 6147 1 chr6A.!!$F1 586
35 TraesCS2D01G147300 chr6A 207840411 207841253 842 True 669.000000 669 81.893000 3586 4396 1 chr6A.!!$R1 810
36 TraesCS2D01G147300 chr6A 614472868 614473465 597 False 486.000000 486 82.226000 3583 4153 1 chr6A.!!$F4 570
37 TraesCS2D01G147300 chr6A 598684081 598684678 597 False 453.000000 453 81.229000 3583 4153 1 chr6A.!!$F3 570
38 TraesCS2D01G147300 chr7B 114143878 114144719 841 True 634.000000 634 81.192000 3586 4396 1 chr7B.!!$R2 810

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
371 372 0.037697 CACTCGTCCCCAATCAACGA 60.038 55.000 0.00 0.0 42.59 3.85 F
417 418 0.108585 CCGCAACTATACCTGGCCAT 59.891 55.000 5.51 0.0 0.00 4.40 F
1840 1890 0.040499 AGAAGAAGAGGGAGGAGCGT 59.960 55.000 0.00 0.0 0.00 5.07 F
3057 4284 1.272147 ACTCTTGGGTTTGGGATGCTC 60.272 52.381 0.00 0.0 0.00 4.26 F
3892 5846 1.301716 GTCGTGGAGCTTCCTGCAA 60.302 57.895 0.00 0.0 41.30 4.08 F
4771 7106 1.478510 AGCTTCGGTTCGATCATGTCT 59.521 47.619 0.00 0.0 35.23 3.41 F
4781 7116 0.460284 GATCATGTCTTCACCGCCGT 60.460 55.000 0.00 0.0 0.00 5.68 F
4918 7254 0.912487 TGTTCTTGGCCGGGTCCTAT 60.912 55.000 2.18 0.0 0.00 2.57 F
6115 8473 0.811219 TCATTCTCCATCGCAAGCCG 60.811 55.000 0.00 0.0 38.61 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1840 1890 1.305219 GGAAAGCATAGCACACGCCA 61.305 55.000 0.00 0.0 39.83 5.69 R
2170 2500 2.363306 TGAGGCAGGTTGTGAATTGT 57.637 45.000 0.00 0.0 0.00 2.71 R
3747 5694 2.426522 GAAAGCATAGCAGACACCACA 58.573 47.619 0.00 0.0 0.00 4.17 R
4714 7049 0.676184 TATGGCGCTGCTAGAAGGAG 59.324 55.000 7.64 0.0 36.68 3.69 R
4781 7116 1.117142 AACGGAAGAGACGGGTTGGA 61.117 55.000 0.00 0.0 35.23 3.53 R
6011 8364 0.178970 GCATGCCCAAGATCCCTGAT 60.179 55.000 6.36 0.0 0.00 2.90 R
6115 8473 0.951040 CCGCACAGGAAAGAGTGGAC 60.951 60.000 0.00 0.0 45.00 4.02 R
6649 11871 2.725312 CGCTGCTAGAAGGAGGGCA 61.725 63.158 0.00 0.0 39.48 5.36 R
7882 13154 0.469892 ATTTCGGATGGGGAATGGGC 60.470 55.000 0.00 0.0 0.00 5.36 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)


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

AutoCloner maintained by Alex Coulton.