Multiple sequence alignment - TraesCS6A01G147700

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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 TraesCS6A01G147700 chr6A 100.000 6980 0 0 1 6980 127886824 127879845 0.000000e+00 12890.0
1 TraesCS6A01G147700 chr6A 87.045 934 86 11 2514 3412 364082971 364082038 0.000000e+00 1022.0
2 TraesCS6A01G147700 chr6A 99.419 344 2 0 3415 3758 65438438 65438781 5.940000e-175 625.0
3 TraesCS6A01G147700 chr6A 86.640 247 31 2 169 414 126561217 126560972 8.920000e-69 272.0
4 TraesCS6A01G147700 chr6A 87.607 234 22 7 169 398 356826973 356827203 1.490000e-66 265.0
5 TraesCS6A01G147700 chr6A 83.577 274 43 2 169 441 370755310 370755582 8.980000e-64 255.0
6 TraesCS6A01G147700 chr6A 85.882 170 24 0 3868 4037 262046819 262046988 1.550000e-41 182.0
7 TraesCS6A01G147700 chr6D 96.440 3174 73 11 3816 6980 105576605 105573463 0.000000e+00 5199.0
8 TraesCS6A01G147700 chr6D 94.425 2547 102 15 1 2516 105581308 105578771 0.000000e+00 3880.0
9 TraesCS6A01G147700 chr6D 97.577 908 12 2 2514 3414 105577591 105576687 0.000000e+00 1546.0
10 TraesCS6A01G147700 chr6D 85.379 937 100 17 2514 3414 314506285 314505350 0.000000e+00 937.0
11 TraesCS6A01G147700 chr6D 87.266 267 26 7 2258 2516 365846885 365847151 1.470000e-76 298.0
12 TraesCS6A01G147700 chr6D 86.920 237 29 2 169 404 104606476 104606241 1.490000e-66 265.0
13 TraesCS6A01G147700 chr6D 88.263 213 25 0 3831 4043 424821373 424821585 8.980000e-64 255.0
14 TraesCS6A01G147700 chr6D 84.151 265 37 5 169 431 73493683 73493944 1.160000e-62 252.0
15 TraesCS6A01G147700 chr6D 83.142 261 41 3 172 431 408699891 408699633 1.170000e-57 235.0
16 TraesCS6A01G147700 chr6D 85.778 225 26 2 2258 2481 210769527 210769746 4.210000e-57 233.0
17 TraesCS6A01G147700 chr6D 84.649 228 33 2 2258 2484 126868582 126868356 7.040000e-55 226.0
18 TraesCS6A01G147700 chr6D 81.685 273 47 3 172 443 405898313 405898583 2.530000e-54 224.0
19 TraesCS6A01G147700 chr6D 86.486 185 25 0 3857 4041 438917567 438917383 3.300000e-48 204.0
20 TraesCS6A01G147700 chr6D 85.965 171 24 0 3867 4037 221216330 221216500 4.300000e-42 183.0
21 TraesCS6A01G147700 chr6D 83.030 165 25 1 1 165 285914066 285913905 5.640000e-31 147.0
22 TraesCS6A01G147700 chr6D 86.719 128 14 1 36 163 16123749 16123625 9.440000e-29 139.0
23 TraesCS6A01G147700 chr6D 96.825 63 2 0 3759 3821 105576691 105576629 9.580000e-19 106.0
24 TraesCS6A01G147700 chr6D 94.286 35 1 1 6404 6438 436940692 436940659 1.300000e-02 52.8
25 TraesCS6A01G147700 chr6B 92.034 2109 85 23 4908 6980 191995644 191997705 0.000000e+00 2887.0
26 TraesCS6A01G147700 chr6B 91.461 1745 95 25 795 2504 191990662 191992387 0.000000e+00 2348.0
27 TraesCS6A01G147700 chr6B 89.794 921 66 15 2508 3414 191993149 191994055 0.000000e+00 1155.0
28 TraesCS6A01G147700 chr6B 83.297 928 121 20 2514 3414 664261448 664260528 0.000000e+00 824.0
29 TraesCS6A01G147700 chr6B 93.645 535 29 3 4324 4857 191994777 191995307 0.000000e+00 795.0
30 TraesCS6A01G147700 chr6B 99.133 346 3 0 3415 3760 308521913 308522258 2.140000e-174 623.0
31 TraesCS6A01G147700 chr6B 86.348 586 44 12 3759 4331 191994051 191994613 2.150000e-169 606.0
32 TraesCS6A01G147700 chr6B 86.296 270 36 1 169 437 448001484 448001215 6.850000e-75 292.0
33 TraesCS6A01G147700 chr6B 82.822 163 25 1 1 163 215023983 215024142 7.300000e-30 143.0
34 TraesCS6A01G147700 chr1A 87.248 941 83 14 2514 3418 252516606 252515667 0.000000e+00 1038.0
35 TraesCS6A01G147700 chr1A 99.419 344 2 0 3415 3758 566643949 566644292 5.940000e-175 625.0
36 TraesCS6A01G147700 chr1A 88.646 229 22 3 3816 4043 333876190 333876415 6.900000e-70 276.0
37 TraesCS6A01G147700 chr1A 85.317 252 31 2 2271 2516 520581206 520580955 8.980000e-64 255.0
38 TraesCS6A01G147700 chr1A 82.847 274 44 3 169 441 127663720 127663991 6.990000e-60 243.0
39 TraesCS6A01G147700 chr1A 82.209 163 25 2 1 163 325691037 325691195 3.400000e-28 137.0
40 TraesCS6A01G147700 chr1A 98.214 56 1 0 3765 3820 361357814 361357869 1.600000e-16 99.0
41 TraesCS6A01G147700 chr2A 86.910 932 92 13 2514 3418 520938721 520937793 0.000000e+00 1018.0
42 TraesCS6A01G147700 chr7D 86.481 932 80 21 2514 3418 466053675 466054587 0.000000e+00 981.0
43 TraesCS6A01G147700 chr7D 86.965 491 48 9 2942 3418 474079310 474078822 7.970000e-149 538.0
44 TraesCS6A01G147700 chr7D 91.111 225 20 0 3816 4040 481166528 481166304 8.800000e-79 305.0
45 TraesCS6A01G147700 chr7D 86.891 267 33 2 172 437 230382544 230382279 1.470000e-76 298.0
46 TraesCS6A01G147700 chr7D 86.792 265 28 2 2259 2516 401841612 401841348 8.860000e-74 289.0
47 TraesCS6A01G147700 chr7D 85.401 274 38 2 169 441 472713634 472713362 4.120000e-72 283.0
48 TraesCS6A01G147700 chr7D 83.436 163 27 0 1 163 167346329 167346491 1.210000e-32 152.0
49 TraesCS6A01G147700 chr7D 95.238 63 3 0 3759 3821 199027466 199027404 4.450000e-17 100.0
50 TraesCS6A01G147700 chr4A 86.936 865 84 16 2514 3355 571836475 571837333 0.000000e+00 944.0
51 TraesCS6A01G147700 chr4A 84.783 506 60 10 2920 3414 300462676 300462177 6.290000e-135 492.0
52 TraesCS6A01G147700 chr4A 87.938 257 30 1 181 437 103065747 103066002 1.140000e-77 302.0
53 TraesCS6A01G147700 chr4A 84.871 271 38 3 172 441 165180244 165180512 3.210000e-68 270.0
54 TraesCS6A01G147700 chr7B 99.419 344 2 0 3415 3758 368149020 368149363 5.940000e-175 625.0
55 TraesCS6A01G147700 chr7B 99.419 344 2 0 3415 3758 727532614 727532957 5.940000e-175 625.0
56 TraesCS6A01G147700 chr7B 99.130 345 3 0 3415 3759 368151165 368151509 7.690000e-174 621.0
57 TraesCS6A01G147700 chr7B 89.333 225 24 0 3816 4040 506744352 506744128 4.120000e-72 283.0
58 TraesCS6A01G147700 chr7B 83.333 288 40 5 3759 4041 531652309 531652593 6.950000e-65 259.0
59 TraesCS6A01G147700 chr7B 82.209 163 26 1 1 163 245833601 245833442 3.400000e-28 137.0
60 TraesCS6A01G147700 chr7B 81.657 169 26 5 1 168 364753777 364753941 1.220000e-27 135.0
61 TraesCS6A01G147700 chr4B 98.580 352 5 0 3415 3766 386044670 386045021 2.140000e-174 623.0
62 TraesCS6A01G147700 chr4B 89.868 227 23 0 2258 2484 285608306 285608080 6.850000e-75 292.0
63 TraesCS6A01G147700 chr4B 87.719 228 25 3 3816 4043 253687603 253687827 5.370000e-66 263.0
64 TraesCS6A01G147700 chr4B 88.426 216 21 2 3829 4043 270821651 270821863 2.500000e-64 257.0
65 TraesCS6A01G147700 chr4B 86.957 230 26 4 2257 2484 363314903 363314676 8.980000e-64 255.0
66 TraesCS6A01G147700 chr4B 86.784 227 26 3 2259 2484 305486879 305487102 4.180000e-62 250.0
67 TraesCS6A01G147700 chr4B 86.404 228 30 1 3816 4043 54027590 54027816 1.500000e-61 248.0
68 TraesCS6A01G147700 chr4B 86.937 222 27 2 3830 4050 171804373 171804153 1.500000e-61 248.0
69 TraesCS6A01G147700 chr4B 80.444 225 29 9 2306 2516 322280761 322280984 2.610000e-34 158.0
70 TraesCS6A01G147700 chr4B 82.812 128 19 1 36 163 476703595 476703471 2.060000e-20 111.0
71 TraesCS6A01G147700 chr4B 96.491 57 2 0 3759 3815 235393880 235393824 2.070000e-15 95.3
72 TraesCS6A01G147700 chr4B 91.935 62 5 0 3760 3821 273652415 273652476 3.470000e-13 87.9
73 TraesCS6A01G147700 chr4B 91.935 62 5 0 3760 3821 273659193 273659254 3.470000e-13 87.9
74 TraesCS6A01G147700 chr4B 91.935 62 5 0 3760 3821 273665984 273666045 3.470000e-13 87.9
75 TraesCS6A01G147700 chr4B 81.633 98 11 3 2427 2518 237152671 237152767 2.700000e-09 75.0
76 TraesCS6A01G147700 chr4B 100.000 28 0 0 2489 2516 111790478 111790451 1.300000e-02 52.8
77 TraesCS6A01G147700 chr7A 99.130 345 3 0 3414 3758 201420627 201420971 7.690000e-174 621.0
78 TraesCS6A01G147700 chr7A 99.130 345 3 0 3415 3759 383178971 383179315 7.690000e-174 621.0
79 TraesCS6A01G147700 chr7A 83.562 73 12 0 623 695 58212237 58212165 1.260000e-07 69.4
80 TraesCS6A01G147700 chr7A 100.000 28 0 0 2489 2516 107357939 107357912 1.300000e-02 52.8
81 TraesCS6A01G147700 chr3A 87.500 272 32 2 169 439 136414259 136414529 5.260000e-81 313.0
82 TraesCS6A01G147700 chr3A 90.351 228 22 0 3816 4043 732390284 732390057 4.090000e-77 300.0
83 TraesCS6A01G147700 chr3A 89.427 227 22 2 3816 4041 83249611 83249836 1.150000e-72 285.0
84 TraesCS6A01G147700 chr3A 81.887 265 39 3 2258 2516 235375977 235375716 1.520000e-51 215.0
85 TraesCS6A01G147700 chr3A 79.851 134 18 4 2390 2516 182623929 182623798 9.640000e-14 89.8
86 TraesCS6A01G147700 chr3D 87.037 270 33 2 169 437 272489990 272490258 3.160000e-78 303.0
87 TraesCS6A01G147700 chr3D 85.878 262 30 2 2258 2512 175542267 175542006 8.920000e-69 272.0
88 TraesCS6A01G147700 chr3D 88.288 222 21 5 2259 2477 45759759 45759540 1.930000e-65 261.0
89 TraesCS6A01G147700 chr3D 87.281 228 29 0 3816 4043 352639618 352639845 1.930000e-65 261.0
90 TraesCS6A01G147700 chr3D 83.636 275 40 4 169 441 475145317 475145588 3.230000e-63 254.0
91 TraesCS6A01G147700 chr3D 81.347 193 34 2 2258 2449 283324905 283324714 9.370000e-34 156.0
92 TraesCS6A01G147700 chr3D 81.595 163 30 0 1 163 184509561 184509723 1.220000e-27 135.0
93 TraesCS6A01G147700 chr1D 87.594 266 25 3 2258 2516 150939037 150939301 1.140000e-77 302.0
94 TraesCS6A01G147700 chr1D 89.474 228 23 1 3816 4043 268961897 268961671 3.190000e-73 287.0
95 TraesCS6A01G147700 chr1D 83.955 268 39 4 172 437 356706460 356706195 3.230000e-63 254.0
96 TraesCS6A01G147700 chr1D 86.829 205 24 2 3839 4043 183022144 183021943 7.040000e-55 226.0
97 TraesCS6A01G147700 chr1D 86.802 197 23 2 3847 4043 155720064 155720257 4.240000e-52 217.0
98 TraesCS6A01G147700 chr1D 83.436 163 24 1 1 163 313232745 313232586 1.570000e-31 148.0
99 TraesCS6A01G147700 chr1D 82.822 163 25 1 1 163 295486720 295486879 7.300000e-30 143.0
100 TraesCS6A01G147700 chr5A 86.667 270 34 2 169 437 353866253 353865985 1.470000e-76 298.0
101 TraesCS6A01G147700 chr5A 88.144 194 21 2 3851 4043 589238735 589238543 5.450000e-56 230.0
102 TraesCS6A01G147700 chr5A 83.553 152 25 0 1 152 436724881 436724730 7.300000e-30 143.0
103 TraesCS6A01G147700 chr1B 90.351 228 21 1 3816 4043 370025650 370025876 1.470000e-76 298.0
104 TraesCS6A01G147700 chr1B 89.520 229 22 2 2258 2485 231642979 231643206 8.860000e-74 289.0
105 TraesCS6A01G147700 chr1B 84.444 270 40 2 172 441 193834930 193834663 1.490000e-66 265.0
106 TraesCS6A01G147700 chr1B 88.106 227 21 5 3819 4043 388764579 388764357 1.490000e-66 265.0
107 TraesCS6A01G147700 chr1B 83.764 271 42 2 169 438 495627971 495628240 8.980000e-64 255.0
108 TraesCS6A01G147700 chr1B 81.788 302 35 13 3759 4043 237007713 237007415 1.170000e-57 235.0
109 TraesCS6A01G147700 chr1B 78.868 265 36 12 2260 2516 213326663 213326915 2.010000e-35 161.0
110 TraesCS6A01G147700 chr3B 86.397 272 33 3 169 437 389255123 389255393 1.900000e-75 294.0
111 TraesCS6A01G147700 chr5D 89.474 228 22 2 3816 4043 118843300 118843525 3.190000e-73 287.0
112 TraesCS6A01G147700 chr5D 87.281 228 29 0 3816 4043 174310409 174310182 1.930000e-65 261.0
113 TraesCS6A01G147700 chr5D 84.091 264 40 2 169 431 507610270 507610532 3.230000e-63 254.0
114 TraesCS6A01G147700 chr5D 83.436 163 24 1 1 163 456300615 456300456 1.570000e-31 148.0
115 TraesCS6A01G147700 chr5D 82.209 163 26 1 1 163 54167991 54167832 3.400000e-28 137.0
116 TraesCS6A01G147700 chr5D 81.595 163 27 1 1 163 349646413 349646254 1.580000e-26 132.0
117 TraesCS6A01G147700 chr5D 96.552 58 2 0 3759 3816 265551394 265551337 5.760000e-16 97.1
118 TraesCS6A01G147700 chr5B 85.926 270 36 2 169 437 300326461 300326729 3.190000e-73 287.0
119 TraesCS6A01G147700 chr5B 86.415 265 29 3 2259 2516 400094363 400094627 4.120000e-72 283.0
120 TraesCS6A01G147700 chr5B 88.158 228 27 0 3816 4043 484886841 484887068 8.920000e-69 272.0
121 TraesCS6A01G147700 chr5B 89.671 213 20 2 2267 2477 211587341 211587129 3.210000e-68 270.0
122 TraesCS6A01G147700 chr5B 83.513 279 40 3 172 445 571247886 571247609 8.980000e-64 255.0
123 TraesCS6A01G147700 chr5B 83.650 263 35 3 2261 2516 138775296 138775557 2.520000e-59 241.0
124 TraesCS6A01G147700 chr5B 82.424 165 26 2 3 167 242365211 242365372 2.620000e-29 141.0
125 TraesCS6A01G147700 chr5B 96.429 56 2 0 3766 3821 223127934 223127879 7.450000e-15 93.5
126 TraesCS6A01G147700 chr2D 86.466 266 27 6 2258 2516 388833666 388833929 4.120000e-72 283.0
127 TraesCS6A01G147700 chr2D 84.644 267 39 2 172 437 392128828 392128563 1.490000e-66 265.0
128 TraesCS6A01G147700 chr2D 82.530 166 27 1 1 164 354357584 354357749 2.030000e-30 145.0
129 TraesCS6A01G147700 chr4D 89.035 228 22 3 3816 4043 210455553 210455777 5.330000e-71 279.0
130 TraesCS6A01G147700 chr4D 88.596 228 25 1 2258 2484 281188406 281188633 6.900000e-70 276.0
131 TraesCS6A01G147700 chr4D 87.773 229 24 4 2257 2484 294454577 294454352 1.490000e-66 265.0
132 TraesCS6A01G147700 chr4D 83.942 274 42 2 169 441 294359511 294359783 1.930000e-65 261.0
133 TraesCS6A01G147700 chr4D 88.073 218 23 3 2260 2476 190482462 190482677 8.980000e-64 255.0
134 TraesCS6A01G147700 chr4D 87.850 214 26 0 3830 4043 295021422 295021635 1.160000e-62 252.0
135 TraesCS6A01G147700 chr4D 86.842 228 24 2 3816 4043 234408101 234408322 4.180000e-62 250.0
136 TraesCS6A01G147700 chr4D 86.404 228 31 0 3816 4043 380241537 380241764 4.180000e-62 250.0
137 TraesCS6A01G147700 chr4D 86.463 229 28 2 2258 2484 248930113 248930340 1.500000e-61 248.0
138 TraesCS6A01G147700 chr4D 83.146 267 43 2 172 437 498200605 498200340 6.990000e-60 243.0
139 TraesCS6A01G147700 chr4D 83.333 264 36 4 2259 2515 163760148 163759886 3.250000e-58 237.0
140 TraesCS6A01G147700 chr4D 82.657 271 44 3 172 441 444579930 444580198 3.250000e-58 237.0
141 TraesCS6A01G147700 chr4D 81.579 304 37 11 3759 4043 294453014 294452711 4.210000e-57 233.0
142 TraesCS6A01G147700 chr4D 81.949 277 42 8 169 441 122583027 122583299 1.960000e-55 228.0
143 TraesCS6A01G147700 chr4D 81.522 276 46 4 169 441 206082961 206083234 9.110000e-54 222.0
144 TraesCS6A01G147700 chr4D 81.387 274 43 8 172 441 186577374 186577105 4.240000e-52 217.0
145 TraesCS6A01G147700 chr4D 81.273 267 40 10 169 431 9061469 9061729 2.550000e-49 207.0
146 TraesCS6A01G147700 chr4D 83.122 237 31 5 2287 2516 70229672 70229438 2.550000e-49 207.0
147 TraesCS6A01G147700 chr4D 83.333 234 30 4 2290 2516 360950614 360950383 2.550000e-49 207.0
148 TraesCS6A01G147700 chr4D 86.702 188 24 1 2270 2456 473136141 473135954 2.550000e-49 207.0
149 TraesCS6A01G147700 chr4D 79.392 296 53 8 156 449 447120629 447120918 1.190000e-47 202.0
150 TraesCS6A01G147700 chr4D 83.333 216 23 6 2314 2516 179876915 179876700 3.320000e-43 187.0
151 TraesCS6A01G147700 chr4D 90.000 140 13 1 2260 2398 287550962 287550823 5.560000e-41 180.0
152 TraesCS6A01G147700 chr4D 96.364 55 2 0 3759 3813 258906095 258906041 2.680000e-14 91.6
153 TraesCS6A01G147700 chr4D 90.476 63 6 0 3759 3821 385742931 385742869 4.490000e-12 84.2
154 TraesCS6A01G147700 chr4D 87.302 63 8 0 3759 3821 210455467 210455529 9.710000e-09 73.1
155 TraesCS6A01G147700 chrUn 88.318 214 23 2 3831 4043 345538534 345538322 8.980000e-64 255.0
156 TraesCS6A01G147700 chrUn 88.318 214 23 2 3831 4043 380113549 380113337 8.980000e-64 255.0
157 TraesCS6A01G147700 chrUn 87.793 213 26 0 3831 4043 401415219 401415431 4.180000e-62 250.0
158 TraesCS6A01G147700 chrUn 87.793 213 26 0 3831 4043 402130450 402130238 4.180000e-62 250.0
159 TraesCS6A01G147700 chrUn 87.793 213 26 0 3831 4043 430922017 430921805 4.180000e-62 250.0
160 TraesCS6A01G147700 chrUn 87.324 213 27 0 3831 4043 27368301 27368513 1.940000e-60 244.0
161 TraesCS6A01G147700 chrUn 87.324 213 27 0 3831 4043 397598984 397598772 1.940000e-60 244.0
162 TraesCS6A01G147700 chrUn 87.204 211 26 1 3830 4040 111064411 111064620 9.050000e-59 239.0
163 TraesCS6A01G147700 chrUn 87.081 209 27 0 3831 4039 70287526 70287734 3.250000e-58 237.0
164 TraesCS6A01G147700 chrUn 81.203 266 41 7 169 431 28877398 28877657 9.180000e-49 206.0
165 TraesCS6A01G147700 chrUn 80.435 276 47 7 169 441 189503448 189503719 3.300000e-48 204.0
166 TraesCS6A01G147700 chrUn 80.597 268 46 6 169 433 84105075 84105339 1.190000e-47 202.0
167 TraesCS6A01G147700 chrUn 80.364 275 45 7 169 437 469202224 469201953 4.270000e-47 200.0
168 TraesCS6A01G147700 chrUn 80.524 267 43 7 177 441 314235403 314235662 5.520000e-46 196.0
169 TraesCS6A01G147700 chrUn 81.250 240 43 2 176 415 219402142 219401905 7.140000e-45 193.0
170 TraesCS6A01G147700 chrUn 81.250 240 43 2 176 415 320708557 320708320 7.140000e-45 193.0
171 TraesCS6A01G147700 chrUn 79.348 276 51 6 169 441 110826287 110826015 9.240000e-44 189.0
172 TraesCS6A01G147700 chrUn 78.930 299 45 14 151 441 249429955 249429667 3.320000e-43 187.0
173 TraesCS6A01G147700 chrUn 78.547 289 53 9 156 440 241142213 241142496 1.550000e-41 182.0
174 TraesCS6A01G147700 chrUn 94.643 56 3 0 3766 3821 345980767 345980712 3.470000e-13 87.9
175 TraesCS6A01G147700 chr2B 84.496 129 14 5 3294 3418 601188754 601188880 9.510000e-24 122.0
176 TraesCS6A01G147700 chr2B 81.818 110 12 2 2415 2516 385533338 385533447 1.250000e-12 86.1


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 TraesCS6A01G147700 chr6A 127879845 127886824 6979 True 12890.00 12890 100.00000 1 6980 1 chr6A.!!$R2 6979
1 TraesCS6A01G147700 chr6A 364082038 364082971 933 True 1022.00 1022 87.04500 2514 3412 1 chr6A.!!$R3 898
2 TraesCS6A01G147700 chr6D 105573463 105581308 7845 True 2682.75 5199 96.31675 1 6980 4 chr6D.!!$R9 6979
3 TraesCS6A01G147700 chr6D 314505350 314506285 935 True 937.00 937 85.37900 2514 3414 1 chr6D.!!$R5 900
4 TraesCS6A01G147700 chr6B 191990662 191997705 7043 False 1558.20 2887 90.65640 795 6980 5 chr6B.!!$F3 6185
5 TraesCS6A01G147700 chr6B 664260528 664261448 920 True 824.00 824 83.29700 2514 3414 1 chr6B.!!$R2 900
6 TraesCS6A01G147700 chr1A 252515667 252516606 939 True 1038.00 1038 87.24800 2514 3418 1 chr1A.!!$R1 904
7 TraesCS6A01G147700 chr2A 520937793 520938721 928 True 1018.00 1018 86.91000 2514 3418 1 chr2A.!!$R1 904
8 TraesCS6A01G147700 chr7D 466053675 466054587 912 False 981.00 981 86.48100 2514 3418 1 chr7D.!!$F2 904
9 TraesCS6A01G147700 chr4A 571836475 571837333 858 False 944.00 944 86.93600 2514 3355 1 chr4A.!!$F3 841
10 TraesCS6A01G147700 chr7B 368149020 368151509 2489 False 623.00 625 99.27450 3415 3759 2 chr7B.!!$F4 344
11 TraesCS6A01G147700 chr4D 294452711 294454577 1866 True 249.00 265 84.67600 2257 4043 2 chr4D.!!$R11 1786

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
285 286 0.026544 CGAGTTCGTCTAGTCGAGGC 59.973 60.000 11.73 9.35 42.19 4.70 F
542 543 0.321564 CCTCAAGACCGGTTCATGCA 60.322 55.000 9.42 0.00 0.00 3.96 F
662 663 1.001641 CTGGGAGAAAGGTGGCAGG 60.002 63.158 0.00 0.00 0.00 4.85 F
1790 1823 1.612950 TGCCAAGTGCCAACTGTTATG 59.387 47.619 0.00 0.00 40.16 1.90 F
2038 2071 1.745653 GAGGCACCATCAAAGGTAAGC 59.254 52.381 0.00 0.00 40.77 3.09 F
3950 7825 1.349067 AAACGCTGGTAGAGGTCCTT 58.651 50.000 0.00 0.00 0.00 3.36 F
4694 8746 0.692476 CATGTGTGACTTCCTCCCCA 59.308 55.000 0.00 0.00 0.00 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1454 1486 0.329261 CCCTGACTTTGCATCTCCCA 59.671 55.000 0.0 0.0 0.00 4.37 R
1662 1695 0.543749 AAAATCTCCCAGGCCTCTCG 59.456 55.000 0.0 0.0 0.00 4.04 R
2367 2414 0.551377 TTAGCCATGGACAAGGGGGA 60.551 55.000 18.4 0.0 0.00 4.81 R
3092 4743 1.620819 GGAGAGAGAGCACCACTTCAA 59.379 52.381 0.0 0.0 0.00 2.69 R
3986 7861 1.949257 GTGGCAAAGAAGACCACCG 59.051 57.895 0.0 0.0 46.65 4.94 R
5596 9969 0.250901 ACTCCATTGCAGCTTCCGTT 60.251 50.000 0.0 0.0 0.00 4.44 R
6443 10824 0.524392 CTGCCTCTGATCGACGTGTC 60.524 60.000 0.0 0.0 0.00 3.67 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
24 25 3.685139 TCCAAAGAGATGACAGACACC 57.315 47.619 0.00 0.00 0.00 4.16
31 32 1.686587 AGATGACAGACACCAACGTCA 59.313 47.619 0.00 0.00 42.19 4.35
58 59 1.067416 GCCGAGTATGTGGCGATGA 59.933 57.895 0.00 0.00 42.22 2.92
78 79 4.529731 GCCATGGAGCCCCTTCCC 62.530 72.222 18.40 0.00 36.35 3.97
174 175 5.948992 AGTCTTTGTTTAGAGCATTGGTC 57.051 39.130 7.79 7.79 0.00 4.02
198 199 5.674525 TGTCCATCACATCATTCTCCTAAC 58.325 41.667 0.00 0.00 0.00 2.34
285 286 0.026544 CGAGTTCGTCTAGTCGAGGC 59.973 60.000 11.73 9.35 42.19 4.70
289 290 1.085091 TTCGTCTAGTCGAGGCTCAC 58.915 55.000 15.95 11.62 40.86 3.51
294 295 1.141254 TCTAGTCGAGGCTCACTAGGG 59.859 57.143 31.26 19.91 41.70 3.53
299 300 1.810532 GAGGCTCACTAGGGACACG 59.189 63.158 10.25 0.00 0.00 4.49
300 301 0.680280 GAGGCTCACTAGGGACACGA 60.680 60.000 10.25 0.00 0.00 4.35
313 314 3.190535 AGGGACACGATGTTTGTTTATGC 59.809 43.478 0.00 0.00 0.00 3.14
337 338 9.013229 TGCATCCACATATATATTTGAGTTTCC 57.987 33.333 9.95 0.00 0.00 3.13
340 341 7.741785 TCCACATATATATTTGAGTTTCCGGT 58.258 34.615 9.95 0.00 0.00 5.28
401 402 7.781324 AGAACAAGGGAAATGTGATAACAAT 57.219 32.000 0.00 0.00 0.00 2.71
463 464 2.157834 TGTGATTTGTAAGTCGGCGT 57.842 45.000 6.85 0.00 0.00 5.68
503 504 3.900601 GGTAGGGTGATGATGAGAGTCAT 59.099 47.826 0.00 0.00 40.34 3.06
509 510 7.244558 AGGGTGATGATGAGAGTCATAGATTA 58.755 38.462 0.00 0.00 37.20 1.75
531 532 3.056328 GGGGCGCAACCTCAAGAC 61.056 66.667 10.83 0.00 39.64 3.01
532 533 3.056328 GGGCGCAACCTCAAGACC 61.056 66.667 10.83 0.00 39.10 3.85
541 542 0.321653 ACCTCAAGACCGGTTCATGC 60.322 55.000 9.42 0.00 0.00 4.06
542 543 0.321564 CCTCAAGACCGGTTCATGCA 60.322 55.000 9.42 0.00 0.00 3.96
571 572 4.378978 CGCTTATGTCGATTTTGGACCAAA 60.379 41.667 15.89 15.89 33.46 3.28
576 577 9.632807 CTTATGTCGATTTTGGACCAAATTTTA 57.367 29.630 20.22 6.01 33.19 1.52
608 609 3.244946 GGCCAACTCTCTTTTAACTCCCT 60.245 47.826 0.00 0.00 0.00 4.20
610 611 4.505039 GCCAACTCTCTTTTAACTCCCTGA 60.505 45.833 0.00 0.00 0.00 3.86
615 616 7.138054 ACTCTCTTTTAACTCCCTGAAAAGA 57.862 36.000 8.33 8.33 43.45 2.52
616 617 7.574607 ACTCTCTTTTAACTCCCTGAAAAGAA 58.425 34.615 9.55 2.62 44.40 2.52
620 621 6.824704 TCTTTTAACTCCCTGAAAAGAAACGA 59.175 34.615 6.57 0.00 42.98 3.85
621 622 5.996669 TTAACTCCCTGAAAAGAAACGAC 57.003 39.130 0.00 0.00 0.00 4.34
625 626 4.275936 ACTCCCTGAAAAGAAACGACAATG 59.724 41.667 0.00 0.00 0.00 2.82
631 632 5.823353 TGAAAAGAAACGACAATGTTACCC 58.177 37.500 0.00 0.00 0.00 3.69
653 654 1.938016 GCTAACGTTCGCTGGGAGAAA 60.938 52.381 16.78 0.00 0.00 2.52
662 663 1.001641 CTGGGAGAAAGGTGGCAGG 60.002 63.158 0.00 0.00 0.00 4.85
692 693 4.034742 CCATTTGATGGCAATTTTAGCTGC 59.965 41.667 0.00 0.00 44.70 5.25
727 728 4.278975 ACAAGGGCAGTTTGAAAACAAA 57.721 36.364 8.53 0.00 41.30 2.83
728 729 4.646572 ACAAGGGCAGTTTGAAAACAAAA 58.353 34.783 8.53 0.00 41.30 2.44
789 792 7.500227 TCATTTTATCACAACCAAAAATGCCAA 59.500 29.630 12.30 0.00 43.80 4.52
798 801 3.558006 ACCAAAAATGCCAACTAAAACGC 59.442 39.130 0.00 0.00 0.00 4.84
799 802 3.059257 CCAAAAATGCCAACTAAAACGCC 60.059 43.478 0.00 0.00 0.00 5.68
803 806 2.910345 GCCAACTAAAACGCCCGCA 61.910 57.895 0.00 0.00 0.00 5.69
807 810 2.098443 CCAACTAAAACGCCCGCATATT 59.902 45.455 0.00 0.00 0.00 1.28
1114 1140 3.876589 CTACGGCGTTGGCACCACT 62.877 63.158 21.24 0.00 42.47 4.00
1375 1407 5.830000 AAGCCGAGTGGTATAATTTTTCC 57.170 39.130 0.00 0.00 37.67 3.13
1380 1412 6.750501 GCCGAGTGGTATAATTTTTCCTTTTC 59.249 38.462 0.00 0.00 37.67 2.29
1387 1419 8.811994 TGGTATAATTTTTCCTTTTCCTCCAAG 58.188 33.333 0.00 0.00 0.00 3.61
1434 1466 7.549134 CAGTATGGTCTCTTTATGTTACTGCAA 59.451 37.037 0.00 0.00 31.88 4.08
1456 1488 2.943033 ACGTCTGAAGTTTGGTTTCTGG 59.057 45.455 0.00 0.00 0.00 3.86
1478 1510 3.573967 GGAGATGCAAAGTCAGGGAAAAA 59.426 43.478 0.00 0.00 0.00 1.94
1481 1513 5.787380 AGATGCAAAGTCAGGGAAAAATTC 58.213 37.500 0.00 0.00 0.00 2.17
1564 1597 7.415095 CGTTGGGTGATTTCATTGCTTTCTATA 60.415 37.037 0.00 0.00 0.00 1.31
1565 1598 8.416329 GTTGGGTGATTTCATTGCTTTCTATAT 58.584 33.333 0.00 0.00 0.00 0.86
1599 1632 3.288092 ACCCTTCCACAGTTCAACTTTC 58.712 45.455 0.00 0.00 0.00 2.62
1609 1642 4.597507 ACAGTTCAACTTTCCCCTCATCTA 59.402 41.667 0.00 0.00 0.00 1.98
1612 1645 5.104318 AGTTCAACTTTCCCCTCATCTATCC 60.104 44.000 0.00 0.00 0.00 2.59
1636 1669 6.343703 CAGAACAGAATGAGATGTGGTGATA 58.656 40.000 0.00 0.00 39.69 2.15
1662 1695 5.185828 AGTTTAGAAGGATGTTTCAATGGCC 59.814 40.000 0.00 0.00 0.00 5.36
1790 1823 1.612950 TGCCAAGTGCCAACTGTTATG 59.387 47.619 0.00 0.00 40.16 1.90
1900 1933 6.398918 TCTGATTTGTTCTTCAGGTACTAGC 58.601 40.000 0.00 0.00 39.84 3.42
2038 2071 1.745653 GAGGCACCATCAAAGGTAAGC 59.254 52.381 0.00 0.00 40.77 3.09
2143 2177 3.374220 TCAAATGAAACCAGCTGCAAG 57.626 42.857 8.66 0.00 0.00 4.01
2202 2236 6.071784 AGCTGTGCACTGATCAATTTGATTTA 60.072 34.615 25.94 5.47 37.20 1.40
2266 2304 1.895131 GTGGAGATGGGCAACAACAAT 59.105 47.619 0.00 0.00 39.74 2.71
2367 2414 3.039011 ACGTGGATAGCTAACCTCCATT 58.961 45.455 19.69 7.22 40.96 3.16
2700 4329 3.722147 GTCGATTAGCACCACATCATCT 58.278 45.455 0.00 0.00 0.00 2.90
2725 4354 4.357918 AAGAGCATACACCATGGGATAC 57.642 45.455 18.09 1.20 34.97 2.24
2807 4438 4.404640 CCGATCCTTGGTGTAGTCCTATA 58.595 47.826 0.00 0.00 0.00 1.31
3092 4743 5.913137 TTTGGTCACACTTGTCATTCTTT 57.087 34.783 0.00 0.00 0.00 2.52
3098 4749 6.404734 GGTCACACTTGTCATTCTTTTGAAGT 60.405 38.462 0.00 0.00 42.30 3.01
3501 7328 9.262358 GTTATCTTAGGCAAGTTATCTTAGGTG 57.738 37.037 0.00 0.00 33.20 4.00
3634 7461 2.252072 CTAGCCGCCAACAGCCCTAA 62.252 60.000 0.00 0.00 38.78 2.69
3759 7586 5.447757 GGTAGAGTACTTGATCCTACCAGT 58.552 45.833 23.37 1.99 45.25 4.00
3760 7587 5.532032 GGTAGAGTACTTGATCCTACCAGTC 59.468 48.000 23.37 5.42 45.25 3.51
3761 7588 4.538738 AGAGTACTTGATCCTACCAGTCC 58.461 47.826 0.00 0.00 0.00 3.85
3762 7589 4.017407 AGAGTACTTGATCCTACCAGTCCA 60.017 45.833 0.00 0.00 0.00 4.02
3806 7633 2.746362 CTCTCCATTGAACAGCTTGTCC 59.254 50.000 0.00 0.00 0.00 4.02
3950 7825 1.349067 AAACGCTGGTAGAGGTCCTT 58.651 50.000 0.00 0.00 0.00 3.36
3986 7861 2.420642 TGCTTCACTCACATCTTGCTC 58.579 47.619 0.00 0.00 0.00 4.26
3987 7862 1.392853 GCTTCACTCACATCTTGCTCG 59.607 52.381 0.00 0.00 0.00 5.03
4121 7996 3.581332 TCCGTTGAGACCTTAAACTCCAT 59.419 43.478 0.00 0.00 32.84 3.41
4196 8071 7.930865 ACATTAGATTGAGACTAATCAAGAGCC 59.069 37.037 0.00 0.00 42.20 4.70
4694 8746 0.692476 CATGTGTGACTTCCTCCCCA 59.308 55.000 0.00 0.00 0.00 4.96
4761 8813 7.415206 GCGAACTAATCAAGGTATGTTTGGAAT 60.415 37.037 0.00 0.00 0.00 3.01
4827 8880 3.189285 GCTGTGTGCATTCTTGTGTTTT 58.811 40.909 0.00 0.00 42.31 2.43
4958 9313 6.578919 GCAACTTTCTACTGTTAAACTGATGC 59.421 38.462 0.00 0.00 0.00 3.91
5275 9632 6.373216 TGCACTTTACAACCCACTATTCATAC 59.627 38.462 0.00 0.00 0.00 2.39
5347 9706 8.635765 AATGTAATCACAGTGTAGGAACATTT 57.364 30.769 15.22 5.71 38.30 2.32
5469 9842 4.395231 GCAGACTACCCTGGTTTTCATTAC 59.605 45.833 0.00 0.00 34.82 1.89
5715 10095 7.744087 TTGTTTGTATCAGCAGAGTTAATGT 57.256 32.000 0.00 0.00 0.00 2.71
5737 10117 7.962964 TGTGATAACTACCAAGCTATAATGC 57.037 36.000 0.00 0.00 0.00 3.56
5815 10195 2.031163 GCACACCAGAGGAGCGTT 59.969 61.111 0.00 0.00 0.00 4.84
5837 10217 0.524862 GGTGTGAATCCTGCTGCTTG 59.475 55.000 0.00 0.00 0.00 4.01
5907 10287 1.952296 CAATCTAATGACCTGCAGGCC 59.048 52.381 33.06 23.59 39.32 5.19
6094 10474 1.021390 AGCATCGGTTAGCTGTGCAC 61.021 55.000 10.75 10.75 40.13 4.57
6097 10477 0.458543 ATCGGTTAGCTGTGCACGAG 60.459 55.000 13.13 11.71 33.64 4.18
6329 10709 2.981898 ACACGGCTTAAACCTATGGTC 58.018 47.619 0.00 0.00 33.12 4.02
6466 10847 0.733150 CGTCGATCAGAGGCAGTGTA 59.267 55.000 0.00 0.00 0.00 2.90
6467 10848 1.532090 CGTCGATCAGAGGCAGTGTAC 60.532 57.143 0.00 0.00 0.00 2.90
6468 10849 1.746220 GTCGATCAGAGGCAGTGTACT 59.254 52.381 0.00 0.00 0.00 2.73
6469 10850 1.745653 TCGATCAGAGGCAGTGTACTG 59.254 52.381 7.64 7.64 46.40 2.74
6470 10851 1.474478 CGATCAGAGGCAGTGTACTGT 59.526 52.381 13.08 0.00 45.45 3.55
6630 11018 3.126073 CGTCTCCATGTGATGTGTATGG 58.874 50.000 0.00 0.00 42.12 2.74
6714 11102 0.741221 GGCGTGAGACCCATCAACTC 60.741 60.000 0.00 0.00 0.00 3.01
6715 11103 1.078759 GCGTGAGACCCATCAACTCG 61.079 60.000 0.00 0.00 33.93 4.18
6716 11104 0.243907 CGTGAGACCCATCAACTCGT 59.756 55.000 0.00 0.00 33.93 4.18
6717 11105 1.471287 CGTGAGACCCATCAACTCGTA 59.529 52.381 0.00 0.00 33.93 3.43
6718 11106 2.099263 CGTGAGACCCATCAACTCGTAT 59.901 50.000 0.00 0.00 33.93 3.06
6719 11107 3.428999 CGTGAGACCCATCAACTCGTATT 60.429 47.826 0.00 0.00 33.93 1.89
6720 11108 4.504858 GTGAGACCCATCAACTCGTATTT 58.495 43.478 0.00 0.00 33.93 1.40
6721 11109 4.567159 GTGAGACCCATCAACTCGTATTTC 59.433 45.833 0.00 0.00 33.93 2.17
6722 11110 4.221924 TGAGACCCATCAACTCGTATTTCA 59.778 41.667 0.00 0.00 33.93 2.69
6723 11111 5.104941 TGAGACCCATCAACTCGTATTTCAT 60.105 40.000 0.00 0.00 33.93 2.57
6724 11112 5.118990 AGACCCATCAACTCGTATTTCATG 58.881 41.667 0.00 0.00 0.00 3.07
6725 11113 4.199310 ACCCATCAACTCGTATTTCATGG 58.801 43.478 0.00 0.00 0.00 3.66
6726 11114 4.080582 ACCCATCAACTCGTATTTCATGGA 60.081 41.667 0.00 0.00 32.51 3.41
6727 11115 4.881273 CCCATCAACTCGTATTTCATGGAA 59.119 41.667 0.00 0.00 32.51 3.53
6728 11116 5.008019 CCCATCAACTCGTATTTCATGGAAG 59.992 44.000 0.00 0.00 32.51 3.46
6729 11117 5.817296 CCATCAACTCGTATTTCATGGAAGA 59.183 40.000 0.00 0.00 32.51 2.87
6730 11118 6.316140 CCATCAACTCGTATTTCATGGAAGAA 59.684 38.462 0.00 0.00 32.51 2.52
6731 11119 7.148255 CCATCAACTCGTATTTCATGGAAGAAA 60.148 37.037 0.00 0.00 41.31 2.52
6732 11120 7.921786 TCAACTCGTATTTCATGGAAGAAAT 57.078 32.000 7.06 7.06 46.69 2.17
6733 11121 7.751732 TCAACTCGTATTTCATGGAAGAAATG 58.248 34.615 11.09 0.00 45.20 2.32
6734 11122 7.390440 TCAACTCGTATTTCATGGAAGAAATGT 59.610 33.333 11.09 0.00 45.20 2.71
6735 11123 7.687941 ACTCGTATTTCATGGAAGAAATGTT 57.312 32.000 11.09 0.00 45.20 2.71
6759 11147 7.537596 TGTGTATTTCATGGAAGAAATGGTT 57.462 32.000 11.09 0.00 45.20 3.67
6947 11339 9.599322 CAAAGTAGTGTGACATTATTCAACTTC 57.401 33.333 0.00 0.00 27.58 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 0.539986 ACCTTGACGTTGGTGTCTGT 59.460 50.000 7.82 0.00 39.64 3.41
24 25 1.008538 GGCAAGCACCTTGACGTTG 60.009 57.895 9.01 0.00 43.42 4.10
31 32 0.324943 ACATACTCGGCAAGCACCTT 59.675 50.000 0.00 0.00 0.00 3.50
58 59 1.075748 GAAGGGGCTCCATGGCATT 60.076 57.895 4.79 0.00 43.83 3.56
174 175 4.418973 AGGAGAATGATGTGATGGACAG 57.581 45.455 0.00 0.00 38.23 3.51
198 199 8.061125 TGTCATTTAATAACGAGATCACATCG 57.939 34.615 0.00 0.00 45.54 3.84
285 286 3.254060 CAAACATCGTGTCCCTAGTGAG 58.746 50.000 0.00 0.00 0.00 3.51
289 290 5.447279 GCATAAACAAACATCGTGTCCCTAG 60.447 44.000 0.00 0.00 0.00 3.02
294 295 4.793216 GGATGCATAAACAAACATCGTGTC 59.207 41.667 0.00 0.00 39.83 3.67
313 314 8.668353 CCGGAAACTCAAATATATATGTGGATG 58.332 37.037 12.16 6.52 0.00 3.51
423 424 8.394971 TCACATGAAGACTGTTGAAAATATGT 57.605 30.769 0.00 0.00 0.00 2.29
431 432 7.498900 ACTTACAAATCACATGAAGACTGTTGA 59.501 33.333 0.00 0.00 0.00 3.18
463 464 1.507630 CATACGACCCGAACCGTCA 59.492 57.895 0.00 0.00 39.86 4.35
476 477 3.826729 TCTCATCATCACCCTACCATACG 59.173 47.826 0.00 0.00 0.00 3.06
503 504 0.759959 TTGCGCCCCGGAATAATCTA 59.240 50.000 0.73 0.00 31.36 1.98
509 510 4.796495 GAGGTTGCGCCCCGGAAT 62.796 66.667 0.73 0.00 39.60 3.01
531 532 2.827051 CGAGGCATGCATGAACCGG 61.827 63.158 30.64 15.10 0.00 5.28
532 533 2.711311 CGAGGCATGCATGAACCG 59.289 61.111 30.64 22.30 0.00 4.44
541 542 1.788258 ATCGACATAAGCGAGGCATG 58.212 50.000 0.00 0.00 41.49 4.06
542 543 2.533266 AATCGACATAAGCGAGGCAT 57.467 45.000 0.00 0.00 41.49 4.40
571 572 7.778382 AGAGAGTTGGCCGGTTAATAATAAAAT 59.222 33.333 1.90 0.00 0.00 1.82
576 577 4.772886 AGAGAGTTGGCCGGTTAATAAT 57.227 40.909 1.90 0.00 0.00 1.28
608 609 5.357314 TGGGTAACATTGTCGTTTCTTTTCA 59.643 36.000 0.00 0.00 39.74 2.69
610 611 5.735070 GCTGGGTAACATTGTCGTTTCTTTT 60.735 40.000 0.00 0.00 39.74 2.27
615 616 2.858745 AGCTGGGTAACATTGTCGTTT 58.141 42.857 0.00 0.00 39.74 3.60
616 617 2.561478 AGCTGGGTAACATTGTCGTT 57.439 45.000 0.00 0.00 39.74 3.85
620 621 3.412237 ACGTTAGCTGGGTAACATTGT 57.588 42.857 18.47 8.78 33.20 2.71
621 622 3.181524 CGAACGTTAGCTGGGTAACATTG 60.182 47.826 18.47 9.50 33.20 2.82
625 626 0.717784 GCGAACGTTAGCTGGGTAAC 59.282 55.000 23.81 11.29 0.00 2.50
646 647 2.361737 GCCTGCCACCTTTCTCCC 60.362 66.667 0.00 0.00 0.00 4.30
662 663 4.382728 CCATCAAATGGCGTTCGC 57.617 55.556 8.75 8.75 44.70 4.70
692 693 4.367450 TGCCCTTGTTTGATTTTTCTTCG 58.633 39.130 0.00 0.00 0.00 3.79
758 759 8.417780 TTTTTGGTTGTGATAAAATGACAGTG 57.582 30.769 0.00 0.00 0.00 3.66
769 771 5.543507 AGTTGGCATTTTTGGTTGTGATA 57.456 34.783 0.00 0.00 0.00 2.15
789 792 1.944709 GGAATATGCGGGCGTTTTAGT 59.055 47.619 0.00 0.00 0.00 2.24
798 801 0.035056 GGGAGGATGGAATATGCGGG 60.035 60.000 0.00 0.00 0.00 6.13
799 802 0.987294 AGGGAGGATGGAATATGCGG 59.013 55.000 0.00 0.00 0.00 5.69
803 806 3.260269 TCGTCAGGGAGGATGGAATAT 57.740 47.619 0.00 0.00 0.00 1.28
807 810 1.320344 CGTTCGTCAGGGAGGATGGA 61.320 60.000 0.00 0.00 0.00 3.41
1141 1167 0.747644 TCGGGGAATAGTACGCGTCA 60.748 55.000 18.63 1.98 42.62 4.35
1375 1407 5.982890 TTAAATGGAGCTTGGAGGAAAAG 57.017 39.130 0.00 0.00 0.00 2.27
1380 1412 7.587037 TTATCATTTAAATGGAGCTTGGAGG 57.413 36.000 24.40 0.00 37.03 4.30
1426 1458 4.201871 CCAAACTTCAGACGTTTGCAGTAA 60.202 41.667 21.67 0.00 45.99 2.24
1434 1466 3.377172 CCAGAAACCAAACTTCAGACGTT 59.623 43.478 0.00 0.00 0.00 3.99
1454 1486 0.329261 CCCTGACTTTGCATCTCCCA 59.671 55.000 0.00 0.00 0.00 4.37
1456 1488 2.496899 TTCCCTGACTTTGCATCTCC 57.503 50.000 0.00 0.00 0.00 3.71
1481 1513 3.750130 CCGCTAGATGGAAATTCATCAGG 59.250 47.826 9.18 4.26 44.30 3.86
1564 1597 7.027874 TGTGGAAGGGTCTTAATTAACAGAT 57.972 36.000 0.00 0.00 0.00 2.90
1565 1598 6.043938 ACTGTGGAAGGGTCTTAATTAACAGA 59.956 38.462 11.59 0.00 35.89 3.41
1599 1632 3.581101 TCTGTTCTGGATAGATGAGGGG 58.419 50.000 0.00 0.00 31.81 4.79
1609 1642 4.226846 ACCACATCTCATTCTGTTCTGGAT 59.773 41.667 0.00 0.00 0.00 3.41
1612 1645 4.572909 TCACCACATCTCATTCTGTTCTG 58.427 43.478 0.00 0.00 0.00 3.02
1636 1669 7.068716 GGCCATTGAAACATCCTTCTAAACTAT 59.931 37.037 0.00 0.00 0.00 2.12
1662 1695 0.543749 AAAATCTCCCAGGCCTCTCG 59.456 55.000 0.00 0.00 0.00 4.04
1685 1718 7.054124 TCTGCACCCGAGATATAAAAGAAAAT 58.946 34.615 0.00 0.00 0.00 1.82
1686 1719 6.411376 TCTGCACCCGAGATATAAAAGAAAA 58.589 36.000 0.00 0.00 0.00 2.29
1687 1720 5.984725 TCTGCACCCGAGATATAAAAGAAA 58.015 37.500 0.00 0.00 0.00 2.52
1688 1721 5.607939 TCTGCACCCGAGATATAAAAGAA 57.392 39.130 0.00 0.00 0.00 2.52
1689 1722 5.808366 ATCTGCACCCGAGATATAAAAGA 57.192 39.130 0.00 0.00 0.00 2.52
1817 1850 6.202379 CACTCTGCATGTGACTCCATTTATAG 59.798 42.308 12.86 0.00 37.60 1.31
1835 1868 3.250762 TCAAAGTACACATTGCACTCTGC 59.749 43.478 0.00 0.00 45.29 4.26
1900 1933 4.971830 CAGAATGCGCCTTGTACATTTATG 59.028 41.667 4.18 0.00 34.28 1.90
2038 2071 6.363357 GCAAAAGAGTAAAGGCATGTAACTTG 59.637 38.462 0.00 0.00 0.00 3.16
2117 2151 3.318839 CAGCTGGTTTCATTTGAACAGGA 59.681 43.478 5.57 0.00 32.19 3.86
2143 2177 2.084546 GGTCTACATCAGGCACCAAAC 58.915 52.381 0.00 0.00 0.00 2.93
2266 2304 2.105134 TGTTCGGGACTGAAAGGCTTTA 59.895 45.455 13.37 1.00 46.21 1.85
2367 2414 0.551377 TTAGCCATGGACAAGGGGGA 60.551 55.000 18.40 0.00 0.00 4.81
2725 4354 4.566488 GGTCATAAGGGATATGCAAGGAGG 60.566 50.000 0.00 0.00 41.08 4.30
2807 4438 7.094205 GGTGACACTGATGACTTTCCAATTAAT 60.094 37.037 5.39 0.00 0.00 1.40
3092 4743 1.620819 GGAGAGAGAGCACCACTTCAA 59.379 52.381 0.00 0.00 0.00 2.69
3098 4749 2.031624 GCTATGGGAGAGAGAGCACCA 61.032 57.143 0.00 0.00 35.39 4.17
3198 4875 2.272146 GCCGGAAGAATGGAGGCA 59.728 61.111 5.05 0.00 46.48 4.75
3634 7461 4.772231 TAGGAGAAGGGCGGCGGT 62.772 66.667 9.78 0.00 0.00 5.68
3759 7586 3.445008 AGAGCTCTACCATTGAGTTGGA 58.555 45.455 16.50 0.00 39.25 3.53
3760 7587 3.196469 TGAGAGCTCTACCATTGAGTTGG 59.804 47.826 18.25 0.00 42.82 3.77
3761 7588 4.462508 TGAGAGCTCTACCATTGAGTTG 57.537 45.455 18.25 0.00 34.30 3.16
3762 7589 5.424895 AGAATGAGAGCTCTACCATTGAGTT 59.575 40.000 26.78 10.45 34.30 3.01
3806 7633 2.672478 CGGCTTCTGGTGAGAGTACTTG 60.672 54.545 0.00 0.00 0.00 3.16
3950 7825 4.169696 CAAGGGGTCGGGCGCATA 62.170 66.667 10.83 0.00 0.00 3.14
3986 7861 1.949257 GTGGCAAAGAAGACCACCG 59.051 57.895 0.00 0.00 46.65 4.94
4121 7996 0.178932 AGGCCACCACTGTCTCTACA 60.179 55.000 5.01 0.00 0.00 2.74
4196 8071 1.987770 GTGTGCCAAAATGCAATCTCG 59.012 47.619 0.00 0.00 44.11 4.04
4411 8462 5.659048 AAGAAACAGAAGTAGTTTGAGCG 57.341 39.130 0.00 0.00 39.15 5.03
4694 8746 8.378565 TCAATCTCAGTCCTAAAAGAAACAGAT 58.621 33.333 0.00 0.00 0.00 2.90
4811 8864 7.518731 TTAAGTTCAAAACACAAGAATGCAC 57.481 32.000 0.00 0.00 0.00 4.57
4827 8880 3.064207 GCACAGGTCGACATTAAGTTCA 58.936 45.455 18.91 0.00 0.00 3.18
4983 9338 2.119801 AAGATACCACAAGCTGCAGG 57.880 50.000 17.12 0.00 0.00 4.85
4984 9339 4.002982 TGTAAAGATACCACAAGCTGCAG 58.997 43.478 10.11 10.11 0.00 4.41
5365 9724 4.631813 GGGTATAGCACAAGAACTCACAAG 59.368 45.833 4.02 0.00 0.00 3.16
5596 9969 0.250901 ACTCCATTGCAGCTTCCGTT 60.251 50.000 0.00 0.00 0.00 4.44
5715 10095 6.755206 ACGCATTATAGCTTGGTAGTTATCA 58.245 36.000 0.00 0.00 31.28 2.15
5737 10117 7.325694 TCTGGAAGTAAAGAAAGGGTATAACG 58.674 38.462 0.00 0.00 33.76 3.18
5907 10287 3.008835 TCAGCCATCCTTTCCTTCATG 57.991 47.619 0.00 0.00 0.00 3.07
6094 10474 1.419374 GTGTCCACAGTTACAGCTCG 58.581 55.000 0.00 0.00 0.00 5.03
6097 10477 1.202651 ACAGGTGTCCACAGTTACAGC 60.203 52.381 6.83 6.83 42.87 4.40
6259 10639 5.168569 CCAAAGAGTACTCTATTCGCAACA 58.831 41.667 25.42 0.00 39.39 3.33
6372 10752 8.409358 AAAATGTAGACTGCCTCAAAAAGTAT 57.591 30.769 0.00 0.00 0.00 2.12
6421 10802 1.137697 TCATGATGATGCAGAGGCCT 58.862 50.000 3.86 3.86 40.13 5.19
6443 10824 0.524392 CTGCCTCTGATCGACGTGTC 60.524 60.000 0.00 0.00 0.00 3.67
6448 10829 1.746220 AGTACACTGCCTCTGATCGAC 59.254 52.381 0.00 0.00 0.00 4.20
6511 10892 7.180229 TCTGACTTTTGTATTCTACCATGAGGA 59.820 37.037 0.00 0.00 38.69 3.71
6517 10900 6.295688 GGGTCTCTGACTTTTGTATTCTACCA 60.296 42.308 0.00 0.00 32.47 3.25
6630 11018 2.792542 GCACGCAGATGCTTAATTGGAC 60.793 50.000 2.95 0.00 42.62 4.02
6714 11102 7.083858 ACACAACATTTCTTCCATGAAATACG 58.916 34.615 0.00 0.00 42.63 3.06
6718 11106 9.474920 GAAATACACAACATTTCTTCCATGAAA 57.525 29.630 0.00 0.00 38.69 2.69
6719 11107 8.637099 TGAAATACACAACATTTCTTCCATGAA 58.363 29.630 0.00 0.00 41.13 2.57
6720 11108 8.175925 TGAAATACACAACATTTCTTCCATGA 57.824 30.769 0.00 0.00 41.13 3.07
6721 11109 8.865978 CATGAAATACACAACATTTCTTCCATG 58.134 33.333 8.71 0.00 41.13 3.66
6722 11110 8.036575 CCATGAAATACACAACATTTCTTCCAT 58.963 33.333 0.00 0.00 41.13 3.41
6723 11111 7.232330 TCCATGAAATACACAACATTTCTTCCA 59.768 33.333 0.00 0.00 41.13 3.53
6724 11112 7.601856 TCCATGAAATACACAACATTTCTTCC 58.398 34.615 0.00 0.00 41.13 3.46
6725 11113 9.132521 CTTCCATGAAATACACAACATTTCTTC 57.867 33.333 0.00 0.00 41.13 2.87
6726 11114 8.859090 TCTTCCATGAAATACACAACATTTCTT 58.141 29.630 0.00 1.31 41.13 2.52
6727 11115 8.408043 TCTTCCATGAAATACACAACATTTCT 57.592 30.769 0.00 0.00 41.13 2.52
6728 11116 9.474920 TTTCTTCCATGAAATACACAACATTTC 57.525 29.630 0.00 0.00 40.99 2.17
6730 11118 9.426837 CATTTCTTCCATGAAATACACAACATT 57.573 29.630 0.00 0.00 42.63 2.71
6731 11119 8.036575 CCATTTCTTCCATGAAATACACAACAT 58.963 33.333 0.00 0.00 42.63 2.71
6732 11120 7.015098 ACCATTTCTTCCATGAAATACACAACA 59.985 33.333 0.00 0.00 42.63 3.33
6733 11121 7.378181 ACCATTTCTTCCATGAAATACACAAC 58.622 34.615 0.00 0.00 42.63 3.32
6734 11122 7.537596 ACCATTTCTTCCATGAAATACACAA 57.462 32.000 0.00 0.00 42.63 3.33
6735 11123 7.537596 AACCATTTCTTCCATGAAATACACA 57.462 32.000 0.00 0.00 42.63 3.72
6759 11147 3.840890 AAGAATTCATACGGCGCAAAA 57.159 38.095 10.83 0.00 0.00 2.44
6818 11206 3.651206 TCATCGTACGGTGCTGTAAAAA 58.349 40.909 23.61 0.57 0.00 1.94
6929 11321 9.897744 GAAAATCAGAAGTTGAATAATGTCACA 57.102 29.630 0.00 0.00 39.77 3.58


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

AutoCloner maintained by Alex Coulton.