Multiple sequence alignment - TraesCS4D01G183300

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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 TraesCS4D01G183300 chr4D 100.000 8664 0 0 999 9662 320585626 320594289 0.000000e+00 16000.0
1 TraesCS4D01G183300 chr4D 98.889 2521 27 1 1552 4071 507394828 507397348 0.000000e+00 4499.0
2 TraesCS4D01G183300 chr4D 97.593 1620 33 5 6012 7628 507402091 507403707 0.000000e+00 2771.0
3 TraesCS4D01G183300 chr4D 100.000 630 0 0 1 630 320584628 320585257 0.000000e+00 1164.0
4 TraesCS4D01G183300 chr4D 96.435 561 18 2 999 1557 507392553 507393113 0.000000e+00 924.0
5 TraesCS4D01G183300 chr4D 98.707 464 4 1 4652 5115 507397347 507397808 0.000000e+00 822.0
6 TraesCS4D01G183300 chr4D 94.810 289 14 1 7337 7624 28428365 28428077 5.320000e-122 449.0
7 TraesCS4D01G183300 chr4D 97.656 256 6 0 999 1254 9238758 9238503 3.200000e-119 440.0
8 TraesCS4D01G183300 chr4D 97.738 221 5 0 999 1219 508414987 508415207 1.970000e-101 381.0
9 TraesCS4D01G183300 chr4D 95.758 165 7 0 1242 1406 9238487 9238323 5.750000e-67 267.0
10 TraesCS4D01G183300 chr4D 94.771 153 8 0 1254 1406 508415205 508415357 1.250000e-58 239.0
11 TraesCS4D01G183300 chr4D 96.226 106 4 0 524 629 508414505 508414610 3.590000e-39 174.0
12 TraesCS4D01G183300 chr4D 90.351 114 9 1 4036 4147 49767875 49767762 2.170000e-31 148.0
13 TraesCS4D01G183300 chr4D 92.157 102 7 1 9106 9206 252173702 252173803 1.010000e-29 143.0
14 TraesCS4D01G183300 chr4D 92.000 100 5 1 533 629 9239243 9239144 4.710000e-28 137.0
15 TraesCS4D01G183300 chr4D 85.047 107 16 0 524 630 507392078 507392184 1.030000e-19 110.0
16 TraesCS4D01G183300 chr4D 90.741 54 5 0 1833 1886 28440534 28440481 1.350000e-08 73.1
17 TraesCS4D01G183300 chr5D 97.698 3084 58 5 999 4071 458285068 458281987 0.000000e+00 5289.0
18 TraesCS4D01G183300 chr5D 97.816 2976 60 5 4652 7625 458281988 458279016 0.000000e+00 5131.0
19 TraesCS4D01G183300 chr5D 95.101 796 36 3 6830 7624 106686863 106686070 0.000000e+00 1251.0
20 TraesCS4D01G183300 chr5D 95.254 590 25 3 6830 7417 367987703 367987115 0.000000e+00 931.0
21 TraesCS4D01G183300 chr5D 98.409 440 6 1 4655 5094 531280031 531280469 0.000000e+00 773.0
22 TraesCS4D01G183300 chr5D 84.170 518 48 16 7107 7595 355428714 355429226 1.140000e-128 472.0
23 TraesCS4D01G183300 chr5D 96.250 240 9 0 999 1238 35098286 35098525 2.530000e-105 394.0
24 TraesCS4D01G183300 chr5D 95.152 165 8 0 1242 1406 35098889 35099053 2.680000e-65 261.0
25 TraesCS4D01G183300 chr5D 87.755 196 10 1 7409 7604 367986774 367986593 5.880000e-52 217.0
26 TraesCS4D01G183300 chr5D 96.262 107 4 0 524 630 35097788 35097894 9.970000e-40 176.0
27 TraesCS4D01G183300 chr5D 89.565 115 10 1 4035 4147 461620110 461619996 2.810000e-30 145.0
28 TraesCS4D01G183300 chr5D 86.508 126 16 1 44 168 500042756 500042631 4.710000e-28 137.0
29 TraesCS4D01G183300 chr5D 88.235 85 5 1 9458 9537 159411436 159411352 7.990000e-16 97.1
30 TraesCS4D01G183300 chr5D 90.741 54 5 0 1833 1886 469798901 469798954 1.350000e-08 73.1
31 TraesCS4D01G183300 chr6B 96.127 1885 64 5 999 2875 641468693 641470576 0.000000e+00 3068.0
32 TraesCS4D01G183300 chr6B 96.674 1413 38 2 999 2402 671930416 671931828 0.000000e+00 2340.0
33 TraesCS4D01G183300 chr6B 97.047 1287 33 4 2868 4150 641485107 641486392 0.000000e+00 2161.0
34 TraesCS4D01G183300 chr6B 95.323 1176 34 4 2402 3576 671939483 671940638 0.000000e+00 1847.0
35 TraesCS4D01G183300 chr6B 92.233 103 8 0 9100 9202 485061194 485061296 7.820000e-31 147.0
36 TraesCS4D01G183300 chr6B 95.349 86 4 0 3699 3784 19943470 19943385 4.710000e-28 137.0
37 TraesCS4D01G183300 chr6B 95.349 86 4 0 3699 3784 19961593 19961508 4.710000e-28 137.0
38 TraesCS4D01G183300 chr6B 89.189 111 11 1 9097 9206 48874135 48874025 4.710000e-28 137.0
39 TraesCS4D01G183300 chr6B 81.437 167 30 1 1 166 374943741 374943907 1.690000e-27 135.0
40 TraesCS4D01G183300 chr4B 95.926 1399 38 12 7732 9119 399948423 399947033 0.000000e+00 2250.0
41 TraesCS4D01G183300 chr4B 97.510 482 12 0 9181 9662 399946956 399946475 0.000000e+00 824.0
42 TraesCS4D01G183300 chr4B 91.633 502 30 8 4754 5250 419681331 419680837 0.000000e+00 684.0
43 TraesCS4D01G183300 chr4B 94.085 355 14 2 174 525 399958031 399957681 5.140000e-147 532.0
44 TraesCS4D01G183300 chr4B 76.740 503 99 15 34 525 340730324 340729829 2.070000e-66 265.0
45 TraesCS4D01G183300 chr4B 92.529 174 7 2 1 173 399958249 399958081 2.700000e-60 244.0
46 TraesCS4D01G183300 chr4B 84.667 150 13 2 3841 3981 337551940 337551792 3.640000e-29 141.0
47 TraesCS4D01G183300 chr4B 88.393 112 11 1 4038 4147 541692634 541692523 6.090000e-27 134.0
48 TraesCS4D01G183300 chr4B 96.154 52 2 0 7618 7669 399948680 399948629 1.730000e-12 86.1
49 TraesCS4D01G183300 chr4B 94.545 55 3 0 7624 7678 399957681 399957627 1.730000e-12 86.1
50 TraesCS4D01G183300 chr4B 93.333 45 1 2 7690 7733 399948629 399948586 2.250000e-06 65.8
51 TraesCS4D01G183300 chr4A 95.920 1250 34 6 7861 9109 151953791 151952558 0.000000e+00 2010.0
52 TraesCS4D01G183300 chr4A 89.292 1186 93 14 2600 3784 687396146 687397298 0.000000e+00 1456.0
53 TraesCS4D01G183300 chr4A 97.095 482 11 1 9181 9662 151952555 151952077 0.000000e+00 809.0
54 TraesCS4D01G183300 chr4A 88.688 221 21 3 1066 1282 51375401 51375621 5.750000e-67 267.0
55 TraesCS4D01G183300 chr4A 96.364 55 2 0 9539 9593 594030136 594030190 3.720000e-14 91.6
56 TraesCS4D01G183300 chr4A 94.737 57 3 0 9539 9595 618462227 618462171 1.340000e-13 89.8
57 TraesCS4D01G183300 chr4A 87.500 80 6 3 9028 9105 640215000 640215077 1.340000e-13 89.8
58 TraesCS4D01G183300 chr4A 86.076 79 10 1 9030 9108 674339400 674339323 6.220000e-12 84.2
59 TraesCS4D01G183300 chr3B 95.657 944 39 2 2600 3542 798181675 798180733 0.000000e+00 1515.0
60 TraesCS4D01G183300 chr3B 85.316 538 70 8 2073 2604 778165700 778165166 1.830000e-151 547.0
61 TraesCS4D01G183300 chr3B 86.772 378 31 14 6429 6805 745457457 745457816 4.200000e-108 403.0
62 TraesCS4D01G183300 chr3B 88.764 267 22 7 1617 1881 814642543 814642803 4.350000e-83 320.0
63 TraesCS4D01G183300 chr3B 94.737 95 3 2 9107 9200 372246296 372246389 7.820000e-31 147.0
64 TraesCS4D01G183300 chr3B 92.929 99 7 0 9098 9196 802996070 802995972 2.810000e-30 145.0
65 TraesCS4D01G183300 chr3B 90.769 65 6 0 9539 9603 474402033 474402097 4.810000e-13 87.9
66 TraesCS4D01G183300 chr5B 95.339 944 42 2 2600 3542 626288045 626288987 0.000000e+00 1498.0
67 TraesCS4D01G183300 chr5B 88.304 1197 96 14 2600 3784 649868136 649869300 0.000000e+00 1395.0
68 TraesCS4D01G183300 chr5B 94.856 797 39 2 6830 7624 686748699 686747903 0.000000e+00 1243.0
69 TraesCS4D01G183300 chr5B 95.464 463 21 0 3080 3542 704265140 704265602 0.000000e+00 739.0
70 TraesCS4D01G183300 chr5B 91.418 268 18 2 3516 3782 425671131 425671394 7.130000e-96 363.0
71 TraesCS4D01G183300 chr5B 82.558 172 29 1 7688 7859 125830232 125830062 6.040000e-32 150.0
72 TraesCS4D01G183300 chr5B 88.136 118 12 1 4036 4151 441695369 441695486 1.310000e-28 139.0
73 TraesCS4D01G183300 chr5B 93.617 47 3 0 8797 8843 427246224 427246178 4.840000e-08 71.3
74 TraesCS4D01G183300 chr5B 100.000 32 0 0 187 218 206715255 206715286 1.050000e-04 60.2
75 TraesCS4D01G183300 chr2B 95.339 944 42 2 2600 3542 776825567 776824625 0.000000e+00 1498.0
76 TraesCS4D01G183300 chr2B 89.053 1014 75 13 2773 3784 655604371 655603392 0.000000e+00 1225.0
77 TraesCS4D01G183300 chr2B 90.825 861 39 12 3812 4632 616944702 616943842 0.000000e+00 1116.0
78 TraesCS4D01G183300 chr2B 92.645 707 32 5 6919 7624 382235831 382235144 0.000000e+00 1000.0
79 TraesCS4D01G183300 chr2B 90.432 648 55 5 6161 6805 616940789 616940146 0.000000e+00 846.0
80 TraesCS4D01G183300 chr2B 88.491 643 46 10 3057 3696 105839025 105838408 0.000000e+00 752.0
81 TraesCS4D01G183300 chr2B 82.779 511 42 17 4115 4583 747494723 747494217 1.940000e-111 414.0
82 TraesCS4D01G183300 chr2B 75.217 690 82 46 4634 5252 11089774 11089103 2.700000e-60 244.0
83 TraesCS4D01G183300 chr2B 87.755 196 22 2 6612 6805 495886009 495886204 2.710000e-55 228.0
84 TraesCS4D01G183300 chr2B 90.441 136 12 1 6197 6332 495885343 495885477 2.770000e-40 178.0
85 TraesCS4D01G183300 chr2B 97.826 92 2 0 6830 6921 382236918 382236827 1.000000e-34 159.0
86 TraesCS4D01G183300 chr2B 83.125 160 17 2 3841 3991 214579858 214580016 4.710000e-28 137.0
87 TraesCS4D01G183300 chr2B 84.733 131 19 1 44 173 570445816 570445686 7.870000e-26 130.0
88 TraesCS4D01G183300 chr2B 87.069 116 13 1 4038 4151 747494839 747494724 7.870000e-26 130.0
89 TraesCS4D01G183300 chr2B 90.741 54 3 2 8798 8850 584118817 584118765 4.840000e-08 71.3
90 TraesCS4D01G183300 chr2B 100.000 29 0 0 5251 5279 11089092 11089064 5.000000e-03 54.7
91 TraesCS4D01G183300 chr6D 90.354 1130 85 9 2600 3724 66625628 66624518 0.000000e+00 1461.0
92 TraesCS4D01G183300 chr6D 89.646 1130 81 12 2600 3724 66260635 66259537 0.000000e+00 1406.0
93 TraesCS4D01G183300 chr6D 93.103 58 1 3 575 630 450972345 450972401 2.240000e-11 82.4
94 TraesCS4D01G183300 chr1D 89.903 1129 79 13 2600 3724 470457062 470458159 0.000000e+00 1421.0
95 TraesCS4D01G183300 chr1D 94.245 417 14 3 1000 1406 474075095 474075511 6.370000e-176 628.0
96 TraesCS4D01G183300 chr1D 96.296 108 4 0 523 630 474074596 474074703 2.770000e-40 178.0
97 TraesCS4D01G183300 chr1D 86.508 126 16 1 44 168 181816455 181816330 4.710000e-28 137.0
98 TraesCS4D01G183300 chr1D 94.444 54 3 0 9539 9592 216718775 216718722 6.220000e-12 84.2
99 TraesCS4D01G183300 chr1D 92.000 50 2 2 8794 8842 106843161 106843113 1.740000e-07 69.4
100 TraesCS4D01G183300 chr1D 92.105 38 2 1 5270 5307 103692277 103692313 1.800000e-02 52.8
101 TraesCS4D01G183300 chr3D 94.605 797 40 3 6830 7624 375199809 375199014 0.000000e+00 1230.0
102 TraesCS4D01G183300 chr3D 90.435 115 9 1 4035 4147 477825133 477825019 6.040000e-32 150.0
103 TraesCS4D01G183300 chr3D 83.846 130 10 5 3846 3965 19091475 19091603 7.930000e-21 113.0
104 TraesCS4D01G183300 chr7D 94.981 777 37 2 6830 7604 417781317 417780541 0.000000e+00 1218.0
105 TraesCS4D01G183300 chr7D 90.686 816 54 10 6830 7624 142139147 142139961 0.000000e+00 1066.0
106 TraesCS4D01G183300 chr7D 84.972 539 71 9 2073 2604 45009198 45008663 1.100000e-148 538.0
107 TraesCS4D01G183300 chr7D 82.953 569 47 25 6236 6803 60467109 60467628 1.470000e-127 468.0
108 TraesCS4D01G183300 chr7D 94.483 290 15 1 7337 7625 3717744 3718033 6.880000e-121 446.0
109 TraesCS4D01G183300 chr7D 89.338 272 24 4 6333 6601 531769287 531769018 4.320000e-88 337.0
110 TraesCS4D01G183300 chr7D 92.553 94 7 0 533 626 571735668 571735575 1.690000e-27 135.0
111 TraesCS4D01G183300 chr7D 91.139 79 6 1 9030 9108 60438250 60438327 1.330000e-18 106.0
112 TraesCS4D01G183300 chr7D 88.889 72 8 0 9030 9101 136249745 136249816 1.340000e-13 89.8
113 TraesCS4D01G183300 chr7D 94.118 51 2 1 8800 8849 127000932 127000982 1.040000e-09 76.8
114 TraesCS4D01G183300 chr2D 91.036 859 37 9 3812 4632 616019555 616018699 0.000000e+00 1123.0
115 TraesCS4D01G183300 chr2D 89.747 790 49 14 4603 5367 616018692 616017910 0.000000e+00 981.0
116 TraesCS4D01G183300 chr2D 94.013 451 25 2 7152 7601 14400069 14400518 0.000000e+00 682.0
117 TraesCS4D01G183300 chr2D 89.905 525 39 5 5432 5955 616017585 616017074 0.000000e+00 664.0
118 TraesCS4D01G183300 chr2D 89.381 452 38 6 6358 6805 615993402 615992957 2.360000e-155 560.0
119 TraesCS4D01G183300 chr2D 83.174 523 39 26 4936 5434 285136 284639 5.360000e-117 433.0
120 TraesCS4D01G183300 chr2D 96.947 131 4 0 5947 6077 616013800 616013670 4.540000e-53 220.0
121 TraesCS4D01G183300 chr2D 96.703 91 3 0 6236 6326 615993493 615993403 1.680000e-32 152.0
122 TraesCS4D01G183300 chr2D 97.701 87 2 0 9107 9193 643235909 643235823 6.040000e-32 150.0
123 TraesCS4D01G183300 chr2D 86.290 124 16 1 46 168 425983159 425983036 6.090000e-27 134.0
124 TraesCS4D01G183300 chr2D 100.000 67 0 0 5366 5432 616017786 616017720 3.660000e-24 124.0
125 TraesCS4D01G183300 chr2D 91.429 70 6 0 4769 4838 285402 285333 7.990000e-16 97.1
126 TraesCS4D01G183300 chr2D 88.000 75 5 1 9466 9536 467973899 467973825 1.730000e-12 86.1
127 TraesCS4D01G183300 chr2D 91.379 58 2 3 575 630 27049632 27049576 1.040000e-09 76.8
128 TraesCS4D01G183300 chr2D 97.561 41 1 0 6124 6164 616013671 616013631 4.840000e-08 71.3
129 TraesCS4D01G183300 chr2D 92.857 42 2 1 4714 4755 285484 285444 1.050000e-04 60.2
130 TraesCS4D01G183300 chr6A 91.049 648 51 5 6161 6805 595913638 595914281 0.000000e+00 869.0
131 TraesCS4D01G183300 chr6A 90.432 648 55 5 6161 6805 420588786 420588143 0.000000e+00 846.0
132 TraesCS4D01G183300 chr6A 87.500 80 5 1 9463 9537 607845428 607845507 4.810000e-13 87.9
133 TraesCS4D01G183300 chr6A 96.000 50 2 0 3987 4036 556974138 556974089 2.240000e-11 82.4
134 TraesCS4D01G183300 chr3A 90.363 633 54 5 6161 6790 699788799 699789427 0.000000e+00 824.0
135 TraesCS4D01G183300 chr3A 91.026 78 7 0 9030 9107 13151550 13151627 1.330000e-18 106.0
136 TraesCS4D01G183300 chr3A 89.231 65 6 1 9539 9603 485595233 485595296 8.040000e-11 80.5
137 TraesCS4D01G183300 chr3A 89.231 65 6 1 9539 9603 485679854 485679917 8.040000e-11 80.5
138 TraesCS4D01G183300 chr3A 97.436 39 1 0 9029 9067 20020377 20020415 6.260000e-07 67.6
139 TraesCS4D01G183300 chr1B 87.778 450 27 13 4607 5030 6237251 6236804 1.450000e-137 501.0
140 TraesCS4D01G183300 chr1B 87.556 450 28 13 4607 5030 7483197 7482750 6.740000e-136 496.0
141 TraesCS4D01G183300 chr1B 91.878 197 12 1 4440 4632 6237458 6237262 1.240000e-68 272.0
142 TraesCS4D01G183300 chr1B 96.703 91 3 0 9106 9196 181305285 181305375 1.680000e-32 152.0
143 TraesCS4D01G183300 chr1B 96.703 91 3 0 9106 9196 679324607 679324517 1.680000e-32 152.0
144 TraesCS4D01G183300 chr1B 81.714 175 30 1 1 173 301114823 301114649 2.810000e-30 145.0
145 TraesCS4D01G183300 chr1B 88.235 85 4 2 9460 9538 687798700 687798616 7.990000e-16 97.1
146 TraesCS4D01G183300 chr2A 84.938 405 28 21 4896 5278 250610 251003 7.080000e-101 379.0
147 TraesCS4D01G183300 chr2A 93.000 100 4 3 9100 9198 699439201 699439298 1.010000e-29 143.0
148 TraesCS4D01G183300 chr2A 87.234 94 11 1 2070 2162 762712297 762712390 1.330000e-18 106.0
149 TraesCS4D01G183300 chr2A 86.250 80 6 2 9461 9535 171955813 171955734 2.240000e-11 82.4
150 TraesCS4D01G183300 chr2A 87.013 77 5 1 9466 9537 582635130 582635054 2.240000e-11 82.4
151 TraesCS4D01G183300 chr2A 93.878 49 3 0 4769 4817 250444 250492 3.740000e-09 75.0
152 TraesCS4D01G183300 chr2A 94.000 50 2 1 8799 8848 66844889 66844937 3.740000e-09 75.0
153 TraesCS4D01G183300 chr2A 94.872 39 1 1 4714 4752 250362 250399 1.050000e-04 60.2
154 TraesCS4D01G183300 chr7A 88.768 276 24 6 1607 1881 222575090 222575359 2.010000e-86 331.0
155 TraesCS4D01G183300 chr7A 87.500 96 9 3 2070 2163 55390966 55391060 3.690000e-19 108.0
156 TraesCS4D01G183300 chr7A 100.000 40 0 0 8802 8841 603130259 603130298 3.740000e-09 75.0
157 TraesCS4D01G183300 chr1A 88.172 279 28 3 1607 1881 543394186 543394463 2.600000e-85 327.0
158 TraesCS4D01G183300 chr5A 84.795 171 19 4 7688 7857 119864613 119864449 2.160000e-36 165.0
159 TraesCS4D01G183300 chr5A 96.296 54 2 0 9539 9592 59700851 59700798 1.340000e-13 89.8
160 TraesCS4D01G183300 chr5A 97.826 46 1 0 3989 4034 150395777 150395822 8.040000e-11 80.5
161 TraesCS4D01G183300 chr5A 84.524 84 8 2 9459 9537 451589965 451589882 2.890000e-10 78.7
162 TraesCS4D01G183300 chr7B 88.034 117 13 1 44 159 361554832 361554948 4.710000e-28 137.0
163 TraesCS4D01G183300 chr7B 89.394 66 3 4 9030 9093 99108796 99108859 8.040000e-11 80.5
164 TraesCS4D01G183300 chr7B 95.455 44 2 0 8799 8842 450642113 450642156 4.840000e-08 71.3
165 TraesCS4D01G183300 chrUn 91.304 46 4 0 9029 9074 37398661 37398616 8.100000e-06 63.9
166 TraesCS4D01G183300 chrUn 97.222 36 1 0 5402 5437 267468460 267468425 2.910000e-05 62.1


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 TraesCS4D01G183300 chr4D 320584628 320594289 9661 False 8582.000000 16000 100.000000 1 9662 2 chr4D.!!$F3 9661
1 TraesCS4D01G183300 chr4D 507402091 507403707 1616 False 2771.000000 2771 97.593000 6012 7628 1 chr4D.!!$F2 1616
2 TraesCS4D01G183300 chr4D 507392078 507397808 5730 False 1588.750000 4499 94.769500 524 5115 4 chr4D.!!$F4 4591
3 TraesCS4D01G183300 chr4D 9238323 9239243 920 True 281.333333 440 95.138000 533 1406 3 chr4D.!!$R4 873
4 TraesCS4D01G183300 chr4D 508414505 508415357 852 False 264.666667 381 96.245000 524 1406 3 chr4D.!!$F5 882
5 TraesCS4D01G183300 chr5D 458279016 458285068 6052 True 5210.000000 5289 97.757000 999 7625 2 chr5D.!!$R6 6626
6 TraesCS4D01G183300 chr5D 106686070 106686863 793 True 1251.000000 1251 95.101000 6830 7624 1 chr5D.!!$R1 794
7 TraesCS4D01G183300 chr5D 367986593 367987703 1110 True 574.000000 931 91.504500 6830 7604 2 chr5D.!!$R5 774
8 TraesCS4D01G183300 chr5D 355428714 355429226 512 False 472.000000 472 84.170000 7107 7595 1 chr5D.!!$F1 488
9 TraesCS4D01G183300 chr5D 35097788 35099053 1265 False 277.000000 394 95.888000 524 1406 3 chr5D.!!$F4 882
10 TraesCS4D01G183300 chr6B 641468693 641470576 1883 False 3068.000000 3068 96.127000 999 2875 1 chr6B.!!$F3 1876
11 TraesCS4D01G183300 chr6B 671930416 671931828 1412 False 2340.000000 2340 96.674000 999 2402 1 chr6B.!!$F5 1403
12 TraesCS4D01G183300 chr6B 641485107 641486392 1285 False 2161.000000 2161 97.047000 2868 4150 1 chr6B.!!$F4 1282
13 TraesCS4D01G183300 chr6B 671939483 671940638 1155 False 1847.000000 1847 95.323000 2402 3576 1 chr6B.!!$F6 1174
14 TraesCS4D01G183300 chr4B 399946475 399948680 2205 True 806.475000 2250 95.730750 7618 9662 4 chr4B.!!$R5 2044
15 TraesCS4D01G183300 chr4B 399957627 399958249 622 True 287.366667 532 93.719667 1 7678 3 chr4B.!!$R6 7677
16 TraesCS4D01G183300 chr4A 687396146 687397298 1152 False 1456.000000 1456 89.292000 2600 3784 1 chr4A.!!$F4 1184
17 TraesCS4D01G183300 chr4A 151952077 151953791 1714 True 1409.500000 2010 96.507500 7861 9662 2 chr4A.!!$R3 1801
18 TraesCS4D01G183300 chr3B 798180733 798181675 942 True 1515.000000 1515 95.657000 2600 3542 1 chr3B.!!$R2 942
19 TraesCS4D01G183300 chr3B 778165166 778165700 534 True 547.000000 547 85.316000 2073 2604 1 chr3B.!!$R1 531
20 TraesCS4D01G183300 chr5B 626288045 626288987 942 False 1498.000000 1498 95.339000 2600 3542 1 chr5B.!!$F4 942
21 TraesCS4D01G183300 chr5B 649868136 649869300 1164 False 1395.000000 1395 88.304000 2600 3784 1 chr5B.!!$F5 1184
22 TraesCS4D01G183300 chr5B 686747903 686748699 796 True 1243.000000 1243 94.856000 6830 7624 1 chr5B.!!$R3 794
23 TraesCS4D01G183300 chr2B 776824625 776825567 942 True 1498.000000 1498 95.339000 2600 3542 1 chr2B.!!$R5 942
24 TraesCS4D01G183300 chr2B 655603392 655604371 979 True 1225.000000 1225 89.053000 2773 3784 1 chr2B.!!$R4 1011
25 TraesCS4D01G183300 chr2B 616940146 616944702 4556 True 981.000000 1116 90.628500 3812 6805 2 chr2B.!!$R8 2993
26 TraesCS4D01G183300 chr2B 105838408 105839025 617 True 752.000000 752 88.491000 3057 3696 1 chr2B.!!$R1 639
27 TraesCS4D01G183300 chr2B 382235144 382236918 1774 True 579.500000 1000 95.235500 6830 7624 2 chr2B.!!$R7 794
28 TraesCS4D01G183300 chr2B 747494217 747494839 622 True 272.000000 414 84.924000 4038 4583 2 chr2B.!!$R9 545
29 TraesCS4D01G183300 chr2B 495885343 495886204 861 False 203.000000 228 89.098000 6197 6805 2 chr2B.!!$F2 608
30 TraesCS4D01G183300 chr6D 66624518 66625628 1110 True 1461.000000 1461 90.354000 2600 3724 1 chr6D.!!$R2 1124
31 TraesCS4D01G183300 chr6D 66259537 66260635 1098 True 1406.000000 1406 89.646000 2600 3724 1 chr6D.!!$R1 1124
32 TraesCS4D01G183300 chr1D 470457062 470458159 1097 False 1421.000000 1421 89.903000 2600 3724 1 chr1D.!!$F2 1124
33 TraesCS4D01G183300 chr1D 474074596 474075511 915 False 403.000000 628 95.270500 523 1406 2 chr1D.!!$F3 883
34 TraesCS4D01G183300 chr3D 375199014 375199809 795 True 1230.000000 1230 94.605000 6830 7624 1 chr3D.!!$R1 794
35 TraesCS4D01G183300 chr7D 417780541 417781317 776 True 1218.000000 1218 94.981000 6830 7604 1 chr7D.!!$R2 774
36 TraesCS4D01G183300 chr7D 142139147 142139961 814 False 1066.000000 1066 90.686000 6830 7624 1 chr7D.!!$F6 794
37 TraesCS4D01G183300 chr7D 45008663 45009198 535 True 538.000000 538 84.972000 2073 2604 1 chr7D.!!$R1 531
38 TraesCS4D01G183300 chr7D 60467109 60467628 519 False 468.000000 468 82.953000 6236 6803 1 chr7D.!!$F3 567
39 TraesCS4D01G183300 chr2D 616013631 616019555 5924 True 530.550000 1123 94.199333 3812 6164 6 chr2D.!!$R7 2352
40 TraesCS4D01G183300 chr2D 615992957 615993493 536 True 356.000000 560 93.042000 6236 6805 2 chr2D.!!$R6 569
41 TraesCS4D01G183300 chr6A 595913638 595914281 643 False 869.000000 869 91.049000 6161 6805 1 chr6A.!!$F1 644
42 TraesCS4D01G183300 chr6A 420588143 420588786 643 True 846.000000 846 90.432000 6161 6805 1 chr6A.!!$R1 644
43 TraesCS4D01G183300 chr3A 699788799 699789427 628 False 824.000000 824 90.363000 6161 6790 1 chr3A.!!$F5 629
44 TraesCS4D01G183300 chr1B 6236804 6237458 654 True 386.500000 501 89.828000 4440 5030 2 chr1B.!!$R5 590

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
283 334 0.958091 GCATACAGGTTGTTGTGGCA 59.042 50.000 0.00 0.00 34.69 4.92 F
1278 1723 0.179032 TTGCTTCTCCCGAACTGCAA 60.179 50.000 0.00 0.00 37.73 4.08 F
1350 1795 1.137086 GTCTTCTGCGATGGCTTCCTA 59.863 52.381 0.15 0.00 40.82 2.94 F
1478 1923 2.487762 GCAGATTCGTCCATTTTCACCA 59.512 45.455 0.00 0.00 0.00 4.17 F
1969 4138 3.349022 TGGTGTTCGTTTTTCCTTGTCT 58.651 40.909 0.00 0.00 0.00 3.41 F
3583 5790 2.240921 TGGTGCCTGCTATTGGTCATAA 59.759 45.455 0.00 0.00 0.00 1.90 F
4611 6924 2.226437 GCTTGCTTCTTCATCGAACCAA 59.774 45.455 0.00 0.00 0.00 3.67 F
5362 8857 7.540400 CGATAGATAACAGAGGCTTCACTATTG 59.460 40.741 0.00 0.00 39.76 1.90 F
5877 10527 1.264749 AACCCGCTATGGTGAGCTCA 61.265 55.000 13.74 13.74 40.51 4.26 F
7423 17025 1.071542 TGGTGGAGCAGAATGACGAAA 59.928 47.619 0.00 0.00 39.69 3.46 F
7984 17781 0.106708 TATGCCTGGCTCGGATGAAC 59.893 55.000 21.03 0.00 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1544 1989 0.878416 GCGTCATAGGTGTTTGGCAA 59.122 50.000 0.00 0.00 0.00 4.52 R
2920 5099 1.156736 AATTTCAGCCGGAGAACACG 58.843 50.000 5.05 0.00 0.00 4.49 R
3179 5370 3.615155 GCTAGAAAGGTGAGGCAGAATT 58.385 45.455 0.00 0.00 0.00 2.17 R
3410 5604 8.774586 ACATTTGACAATATATTTCTACCGAGC 58.225 33.333 0.00 0.00 0.00 5.03 R
3642 5853 0.183492 ACTGAACCAAGCAGCTGGAA 59.817 50.000 17.12 3.07 38.96 3.53 R
4623 6936 2.413310 TCCAATCTAAAACTCGCCCC 57.587 50.000 0.00 0.00 0.00 5.80 R
5877 10527 2.103263 GGCGTAATCCAGAGGTGAAGAT 59.897 50.000 0.00 0.00 0.00 2.40 R
7325 16567 3.565482 GGTCCATGGTGTAAGTATGCATG 59.435 47.826 12.58 0.00 0.00 4.06 R
7682 17303 0.037303 CAGTGGCAGATCACCCTGTT 59.963 55.000 0.00 0.00 38.34 3.16 R
8318 18116 1.896465 CCTGAGATTCCCGGATAGGAC 59.104 57.143 0.73 0.00 45.00 3.85 R
9238 19052 2.159028 GGCTGGGTGTTTTGCTTGTTTA 60.159 45.455 0.00 0.00 0.00 2.01 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
23 24 4.226427 TCTTTAGTGAGGTAGAGGCGTA 57.774 45.455 0.00 0.00 0.00 4.42
43 44 1.024579 GGCGTGGTGTGTAGGGATTG 61.025 60.000 0.00 0.00 0.00 2.67
93 94 4.216257 ACAACCACAAGAATATGAGTGTGC 59.784 41.667 7.19 0.00 40.02 4.57
99 100 4.080129 ACAAGAATATGAGTGTGCCCATCT 60.080 41.667 0.00 0.00 0.00 2.90
103 104 1.283347 ATGAGTGTGCCCATCTGAGT 58.717 50.000 0.00 0.00 0.00 3.41
152 154 4.370917 CCCAAACATCAAAAGGTTCACAG 58.629 43.478 0.00 0.00 0.00 3.66
168 170 9.751542 AAGGTTCACAGACTAGATTATAATTCG 57.248 33.333 0.00 0.00 0.00 3.34
283 334 0.958091 GCATACAGGTTGTTGTGGCA 59.042 50.000 0.00 0.00 34.69 4.92
287 338 1.102978 ACAGGTTGTTGTGGCACTTC 58.897 50.000 19.83 11.90 0.00 3.01
311 362 3.703420 GAGAATGGCATTCATCTTGTGC 58.297 45.455 34.54 11.51 41.71 4.57
329 380 1.967779 TGCTGTAGAACACACTGCCTA 59.032 47.619 0.00 0.00 39.36 3.93
368 419 2.184533 TGCCGGTAGAGAAAAGGATCA 58.815 47.619 1.90 0.00 0.00 2.92
454 505 6.346096 GTGGCATATACTTCCTTACAAGACA 58.654 40.000 0.00 0.00 0.00 3.41
455 506 6.480320 GTGGCATATACTTCCTTACAAGACAG 59.520 42.308 0.00 0.00 0.00 3.51
456 507 6.156256 TGGCATATACTTCCTTACAAGACAGT 59.844 38.462 0.00 0.00 0.00 3.55
457 508 7.048512 GGCATATACTTCCTTACAAGACAGTT 58.951 38.462 0.00 0.00 0.00 3.16
481 532 6.759497 AGTATAATCTGCAAACCAAGGTTC 57.241 37.500 4.73 0.00 37.35 3.62
512 566 8.492673 TTTAATCATAGCTAAACACTCACCTG 57.507 34.615 0.00 0.00 0.00 4.00
569 623 1.602377 CCCGAGCGTTTTCAGAGTTTT 59.398 47.619 0.00 0.00 0.00 2.43
1172 1257 1.270907 GCTCCTCCAGGAAGAAGACA 58.729 55.000 0.00 0.00 44.91 3.41
1255 1700 2.229792 CCCGATTCTCTCTCTCTCTGG 58.770 57.143 0.00 0.00 0.00 3.86
1278 1723 0.179032 TTGCTTCTCCCGAACTGCAA 60.179 50.000 0.00 0.00 37.73 4.08
1317 1762 3.306502 GGTGTCAACCGTCCTTGATCTAA 60.307 47.826 0.00 0.00 36.51 2.10
1350 1795 1.137086 GTCTTCTGCGATGGCTTCCTA 59.863 52.381 0.15 0.00 40.82 2.94
1424 1869 6.875195 GCTAGGTATGTCTCTATTCTAGACGT 59.125 42.308 0.00 0.00 45.19 4.34
1453 1898 5.164041 CGTCTCTGATTTTCGTCTTCCTTTC 60.164 44.000 0.00 0.00 0.00 2.62
1478 1923 2.487762 GCAGATTCGTCCATTTTCACCA 59.512 45.455 0.00 0.00 0.00 4.17
1544 1989 8.368668 GGATTTATAGGTAAGTAGCACACAGAT 58.631 37.037 0.00 0.00 0.00 2.90
1740 3909 7.536281 GGTTAGCTAGGTTTATTTGTTTGTTCG 59.464 37.037 0.00 0.00 0.00 3.95
1813 3982 4.041567 TGTTCTCTATCTGGCTTTGTTGGA 59.958 41.667 0.00 0.00 0.00 3.53
1969 4138 3.349022 TGGTGTTCGTTTTTCCTTGTCT 58.651 40.909 0.00 0.00 0.00 3.41
2195 4365 5.349543 GTGGAACATGAGCAAATTTTCATCC 59.650 40.000 0.00 4.02 44.52 3.51
2249 4419 9.603921 CTTATTTCCTATTTGGTTCATGCATTT 57.396 29.630 0.00 0.00 37.07 2.32
2346 4516 5.107337 GGCTGTTGCTTTATTTTCTTTCTGC 60.107 40.000 0.00 0.00 39.59 4.26
2513 4686 3.864789 ATTCGACTATGAAATGGGCCT 57.135 42.857 4.53 0.00 21.44 5.19
2920 5099 5.165676 TGTTGTTGTCGTGTCCTATATCAC 58.834 41.667 0.00 0.00 0.00 3.06
3179 5370 3.904965 TGTAGGTACAAATCTGGGTGTCA 59.095 43.478 0.00 0.00 32.40 3.58
3283 5474 6.675565 TCCCCCATTTATTTTACTTAGGTCC 58.324 40.000 0.00 0.00 0.00 4.46
3467 5661 6.818644 GCAACTGTAATTAGAGATCAAGGTCA 59.181 38.462 16.03 0.00 0.00 4.02
3583 5790 2.240921 TGGTGCCTGCTATTGGTCATAA 59.759 45.455 0.00 0.00 0.00 1.90
4325 6614 7.506114 TGGTAATCTACATTCTGTATGAACCC 58.494 38.462 1.04 0.00 37.52 4.11
4379 6670 3.152341 CCCCATGAGAAGCCATCATAAC 58.848 50.000 0.00 0.00 35.64 1.89
4383 6675 4.514441 CCATGAGAAGCCATCATAACAGAC 59.486 45.833 0.00 0.00 35.64 3.51
4429 6721 6.630045 CGTCAACGATGTATATCAAGTCGTTA 59.370 38.462 10.53 0.00 44.51 3.18
4550 6859 4.635833 TGTATACTGCGGTTAATGACGA 57.364 40.909 1.99 0.00 0.00 4.20
4605 6918 4.118410 ACTCTATGCTTGCTTCTTCATCG 58.882 43.478 0.00 0.00 0.00 3.84
4611 6924 2.226437 GCTTGCTTCTTCATCGAACCAA 59.774 45.455 0.00 0.00 0.00 3.67
5362 8857 7.540400 CGATAGATAACAGAGGCTTCACTATTG 59.460 40.741 0.00 0.00 39.76 1.90
5519 9909 7.660030 TCCATGTCTGACATAGAACAATCTA 57.340 36.000 21.88 0.00 42.23 1.98
5877 10527 1.264749 AACCCGCTATGGTGAGCTCA 61.265 55.000 13.74 13.74 40.51 4.26
6036 13969 4.282496 ACTGGTTTGTTGTTGGTTATGGA 58.718 39.130 0.00 0.00 0.00 3.41
6973 16212 4.644685 CCCCAAACAAGTATGGTCTATTGG 59.355 45.833 0.00 0.00 36.65 3.16
7200 16442 5.129320 TGCTCAGAGTCTCTTTATTGCCATA 59.871 40.000 0.00 0.00 0.00 2.74
7227 16469 7.011109 TGTTTTCTGAAGTTAGTCTCGAAAAGG 59.989 37.037 0.00 0.00 32.72 3.11
7229 16471 4.038763 TCTGAAGTTAGTCTCGAAAAGGCA 59.961 41.667 0.00 0.00 29.30 4.75
7325 16567 4.488126 TGCTTAATCTGTGTTGTTCTGC 57.512 40.909 0.00 0.00 0.00 4.26
7341 16583 3.625649 TCTGCATGCATACTTACACCA 57.374 42.857 22.97 0.00 0.00 4.17
7423 17025 1.071542 TGGTGGAGCAGAATGACGAAA 59.928 47.619 0.00 0.00 39.69 3.46
7424 17026 2.290260 TGGTGGAGCAGAATGACGAAAT 60.290 45.455 0.00 0.00 39.69 2.17
7558 17179 4.148079 TGGTTATGTTCTGGTGCAAATGA 58.852 39.130 0.00 0.00 0.00 2.57
7582 17203 2.401766 CCATGTGAGTTGCTCGCCC 61.402 63.158 7.16 0.00 39.93 6.13
7684 17305 9.477484 ACGTGATGGATACTCATTTATTAGAAC 57.523 33.333 0.00 0.00 37.61 3.01
7685 17306 9.476202 CGTGATGGATACTCATTTATTAGAACA 57.524 33.333 0.00 0.00 37.61 3.18
7688 17309 9.442047 GATGGATACTCATTTATTAGAACAGGG 57.558 37.037 0.00 0.00 37.61 4.45
7720 17341 2.033194 GGTTGTCTTCGCCCCTTCG 61.033 63.158 0.00 0.00 0.00 3.79
7727 17348 1.033574 CTTCGCCCCTTCGATCTACT 58.966 55.000 0.00 0.00 38.37 2.57
7728 17349 2.158711 TCTTCGCCCCTTCGATCTACTA 60.159 50.000 0.00 0.00 38.37 1.82
7729 17350 2.581216 TCGCCCCTTCGATCTACTAT 57.419 50.000 0.00 0.00 33.02 2.12
7784 17569 1.532505 CGAATCAAATGAGGCTTGGCG 60.533 52.381 0.00 0.00 0.00 5.69
7791 17576 0.179000 ATGAGGCTTGGCGTCCTTAG 59.821 55.000 9.23 0.00 41.92 2.18
7900 17697 8.246180 TGAATGAAGAAAGGCAGTAATTTCATC 58.754 33.333 0.00 0.00 37.78 2.92
7984 17781 0.106708 TATGCCTGGCTCGGATGAAC 59.893 55.000 21.03 0.00 0.00 3.18
8020 17817 2.600792 GCAAGAGACTGCGACAAAAGTG 60.601 50.000 0.00 0.00 31.50 3.16
8318 18116 0.809385 TTCTCACGAACTAGGCTCCG 59.191 55.000 0.00 0.00 0.00 4.63
8398 18197 0.533755 GCTTGCCATATCAGCTCCGT 60.534 55.000 0.00 0.00 0.00 4.69
8608 18407 4.087892 CCCTCACCAGGACAGGCG 62.088 72.222 0.00 0.00 43.65 5.52
8648 18447 5.954150 ACATAGATGAAAGGCAATCAAGGTT 59.046 36.000 0.00 0.00 0.00 3.50
8710 18509 9.766277 CAAGAGATTGAACTTTTAAGCACTATC 57.234 33.333 0.00 0.00 0.00 2.08
8808 18607 9.403583 TCATTTATTTATTCACAACTACTCCCC 57.596 33.333 0.00 0.00 0.00 4.81
8859 18658 6.934083 TGACACTGAGTATATTGCAACAGAAA 59.066 34.615 16.69 0.00 0.00 2.52
8926 18725 6.002653 TCCTACTGCTCATACTAGAGTCAA 57.997 41.667 0.00 0.00 37.94 3.18
8927 18726 5.823570 TCCTACTGCTCATACTAGAGTCAAC 59.176 44.000 0.00 0.00 37.94 3.18
9026 18825 6.071108 TGCCAGGAGAACTAAGAGATATATGC 60.071 42.308 0.00 0.00 0.00 3.14
9044 18843 2.119655 CACTACTCCCTCCGTCCCG 61.120 68.421 0.00 0.00 0.00 5.14
9056 18855 4.142227 CCCTCCGTCCCGTAATATAAGATG 60.142 50.000 0.00 0.00 0.00 2.90
9134 18933 8.425703 ACTCCCTCTGTAAAGAAATATAAGAGC 58.574 37.037 0.00 0.00 0.00 4.09
9135 18934 8.319057 TCCCTCTGTAAAGAAATATAAGAGCA 57.681 34.615 0.00 0.00 0.00 4.26
9136 18935 8.938883 TCCCTCTGTAAAGAAATATAAGAGCAT 58.061 33.333 0.00 0.00 0.00 3.79
9137 18936 9.566432 CCCTCTGTAAAGAAATATAAGAGCATT 57.434 33.333 0.00 0.00 0.00 3.56
9238 19052 8.303876 ACACGAAAACATGCTAAAAATTCCTAT 58.696 29.630 0.00 0.00 0.00 2.57
9569 19383 5.682943 AACATAGCTTGCAAAAACGTCTA 57.317 34.783 0.00 0.00 0.00 2.59
9635 19449 8.725405 TTCCTAAAATATGACGCTATTTGTGA 57.275 30.769 0.62 0.00 32.88 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 1.198759 AATCCCTACACACCACGCCT 61.199 55.000 0.00 0.00 0.00 5.52
64 65 9.599866 CACTCATATTCTTGTGGTTGTAGATTA 57.400 33.333 0.00 0.00 0.00 1.75
65 66 8.103305 ACACTCATATTCTTGTGGTTGTAGATT 58.897 33.333 0.00 0.00 35.02 2.40
66 67 7.550551 CACACTCATATTCTTGTGGTTGTAGAT 59.449 37.037 0.00 0.00 36.51 1.98
67 68 6.873605 CACACTCATATTCTTGTGGTTGTAGA 59.126 38.462 0.00 0.00 36.51 2.59
68 69 6.402550 GCACACTCATATTCTTGTGGTTGTAG 60.403 42.308 8.65 0.00 39.83 2.74
93 94 1.271379 ACCGTTTTGGACTCAGATGGG 60.271 52.381 0.00 0.00 42.00 4.00
99 100 0.547075 TTGGGACCGTTTTGGACTCA 59.453 50.000 0.00 0.00 41.36 3.41
103 104 2.366640 TCATTTGGGACCGTTTTGGA 57.633 45.000 0.00 0.00 42.00 3.53
168 170 0.645868 GCGCACAGATTCGTTCCTAC 59.354 55.000 0.30 0.00 0.00 3.18
186 237 1.457346 CCCACACTCTTCAAGGATGC 58.543 55.000 0.00 0.00 0.00 3.91
273 324 1.138069 TCTCGAGAAGTGCCACAACAA 59.862 47.619 14.01 0.00 0.00 2.83
283 334 3.616956 TGAATGCCATTCTCGAGAAGT 57.383 42.857 29.89 16.78 39.96 3.01
287 338 3.875727 ACAAGATGAATGCCATTCTCGAG 59.124 43.478 17.73 5.93 39.96 4.04
311 362 4.820897 TGATTAGGCAGTGTGTTCTACAG 58.179 43.478 0.00 0.00 40.69 2.74
329 380 2.517959 CATGGGCCGGATAACATGATT 58.482 47.619 5.05 0.00 42.39 2.57
454 505 7.402862 ACCTTGGTTTGCAGATTATACTAACT 58.597 34.615 0.00 0.00 0.00 2.24
455 506 7.625828 ACCTTGGTTTGCAGATTATACTAAC 57.374 36.000 0.00 0.00 0.00 2.34
456 507 7.065324 CGAACCTTGGTTTGCAGATTATACTAA 59.935 37.037 6.49 0.00 0.00 2.24
457 508 6.537301 CGAACCTTGGTTTGCAGATTATACTA 59.463 38.462 6.49 0.00 0.00 1.82
499 553 3.714798 AGTCCTTTCCAGGTGAGTGTTTA 59.285 43.478 0.00 0.00 41.69 2.01
504 558 2.103153 TGAGTCCTTTCCAGGTGAGT 57.897 50.000 0.00 0.00 41.69 3.41
512 566 6.360618 ACATATTTCTGGATGAGTCCTTTCC 58.639 40.000 0.00 0.00 45.32 3.13
559 613 4.460382 GGCCAGAATGATCAAAACTCTGAA 59.540 41.667 20.52 0.00 39.69 3.02
569 623 0.534873 TCGAACGGCCAGAATGATCA 59.465 50.000 2.24 0.00 39.69 2.92
1172 1257 4.660938 GGCGGCTCACCTTGGGTT 62.661 66.667 0.00 0.00 31.02 4.11
1255 1700 2.358247 TTCGGGAGAAGCAACGGC 60.358 61.111 0.00 0.00 45.39 5.68
1310 1755 4.107149 AGACCTAGGAGGAGCATTAGATCA 59.893 45.833 17.98 0.00 37.67 2.92
1317 1762 2.676748 CAGAAGACCTAGGAGGAGCAT 58.323 52.381 17.98 0.00 37.67 3.79
1355 1800 1.522355 CATCTCAACCAGCGCCGAT 60.522 57.895 2.29 0.00 0.00 4.18
1424 1869 2.987149 GACGAAAATCAGAGACGAGCAA 59.013 45.455 0.00 0.00 0.00 3.91
1453 1898 3.191162 TGAAAATGGACGAATCTGCAAGG 59.809 43.478 0.00 0.00 0.00 3.61
1544 1989 0.878416 GCGTCATAGGTGTTTGGCAA 59.122 50.000 0.00 0.00 0.00 4.52
1740 3909 7.925483 AGCTAGACATGAGAATATTCTTGACAC 59.075 37.037 18.88 10.90 37.73 3.67
1969 4138 4.862574 CGACATTCATTCCTTACACTCGAA 59.137 41.667 0.00 0.00 0.00 3.71
2195 4365 3.425892 CGTCTAACTGGTCCTTGTCTACG 60.426 52.174 0.00 0.00 0.00 3.51
2346 4516 3.604875 AAAGGAAAAGCATGCATGAGG 57.395 42.857 30.64 4.30 0.00 3.86
2603 4778 4.021368 ACGTGTACACTTTCAGATAAGCCT 60.021 41.667 23.01 0.00 0.00 4.58
2920 5099 1.156736 AATTTCAGCCGGAGAACACG 58.843 50.000 5.05 0.00 0.00 4.49
3107 5298 6.758254 ACAAATAAAGTTTTGATCCCCTGTG 58.242 36.000 4.10 0.00 38.58 3.66
3179 5370 3.615155 GCTAGAAAGGTGAGGCAGAATT 58.385 45.455 0.00 0.00 0.00 2.17
3283 5474 9.745880 ACAACAAACTATACCTAGAATGTATCG 57.254 33.333 0.00 0.00 31.65 2.92
3410 5604 8.774586 ACATTTGACAATATATTTCTACCGAGC 58.225 33.333 0.00 0.00 0.00 5.03
3640 5851 1.891150 CTGAACCAAGCAGCTGGAATT 59.109 47.619 17.12 2.44 38.96 2.17
3641 5852 1.202976 ACTGAACCAAGCAGCTGGAAT 60.203 47.619 17.12 5.99 38.96 3.01
3642 5853 0.183492 ACTGAACCAAGCAGCTGGAA 59.817 50.000 17.12 3.07 38.96 3.53
3643 5854 0.535780 CACTGAACCAAGCAGCTGGA 60.536 55.000 17.12 0.00 38.96 3.86
3648 5859 0.602638 TACGGCACTGAACCAAGCAG 60.603 55.000 0.00 0.00 39.26 4.24
4221 6495 5.239359 TGCATGCTATGTTCTTTGATGAC 57.761 39.130 20.33 0.00 0.00 3.06
4259 6548 8.494016 ACATGTTTCTATAAGTACCTCAAAGC 57.506 34.615 0.00 0.00 0.00 3.51
4357 6648 1.229131 ATGATGGCTTCTCATGGGGT 58.771 50.000 0.00 0.00 32.20 4.95
4358 6649 3.152341 GTTATGATGGCTTCTCATGGGG 58.848 50.000 0.00 0.00 35.12 4.96
4405 6697 6.807708 AACGACTTGATATACATCGTTGAC 57.192 37.500 9.30 0.00 45.84 3.18
4429 6721 2.421107 CCATAGGAACTGCAGCATGAGT 60.421 50.000 15.27 0.00 41.52 3.41
4570 6879 7.768120 AGCAAGCATAGAGTATATTTAGATGCC 59.232 37.037 0.00 0.00 39.17 4.40
4623 6936 2.413310 TCCAATCTAAAACTCGCCCC 57.587 50.000 0.00 0.00 0.00 5.80
5362 8857 3.146847 GGGGGCAGCAAACTACATATAC 58.853 50.000 0.00 0.00 0.00 1.47
5519 9909 8.320396 TCGATAACGACTATAATGAGTAGCTT 57.680 34.615 0.00 0.00 43.81 3.74
5877 10527 2.103263 GGCGTAATCCAGAGGTGAAGAT 59.897 50.000 0.00 0.00 0.00 2.40
6036 13969 4.943705 CCACATGCTAAACCTACAACATCT 59.056 41.667 0.00 0.00 0.00 2.90
6810 15051 7.201741 GGGAAAATAGAACTGAAGAATGTAGCC 60.202 40.741 0.00 0.00 0.00 3.93
7121 16362 9.108284 CAAAGTCCAAAAATCACAATTACCTTT 57.892 29.630 0.00 0.00 0.00 3.11
7200 16442 8.433421 TTTTCGAGACTAACTTCAGAAAACAT 57.567 30.769 0.00 0.00 34.90 2.71
7325 16567 3.565482 GGTCCATGGTGTAAGTATGCATG 59.435 47.826 12.58 0.00 0.00 4.06
7365 16616 4.744631 GTGAATCACATTGGTTTGGTTCAC 59.255 41.667 8.74 13.09 37.92 3.18
7558 17179 3.612479 GCGAGCAACTCACATGGAAAAAT 60.612 43.478 0.00 0.00 0.00 1.82
7609 17230 9.262358 CTGTTCTAATAAACTAGATAAGTGGCC 57.738 37.037 0.00 0.00 38.88 5.36
7675 17296 4.473196 TGGCAGATCACCCTGTTCTAATAA 59.527 41.667 0.00 0.00 36.57 1.40
7678 17299 2.027192 GTGGCAGATCACCCTGTTCTAA 60.027 50.000 0.00 0.00 36.57 2.10
7679 17300 1.555075 GTGGCAGATCACCCTGTTCTA 59.445 52.381 0.00 0.00 36.57 2.10
7680 17301 0.326264 GTGGCAGATCACCCTGTTCT 59.674 55.000 0.00 0.00 36.57 3.01
7681 17302 0.326264 AGTGGCAGATCACCCTGTTC 59.674 55.000 0.00 0.00 38.34 3.18
7682 17303 0.037303 CAGTGGCAGATCACCCTGTT 59.963 55.000 0.00 0.00 38.34 3.16
7683 17304 1.681666 CAGTGGCAGATCACCCTGT 59.318 57.895 0.00 0.00 38.34 4.00
7684 17305 1.077930 CCAGTGGCAGATCACCCTG 60.078 63.158 0.00 6.00 38.34 4.45
7685 17306 2.304056 CCCAGTGGCAGATCACCCT 61.304 63.158 2.61 0.00 38.34 4.34
7686 17307 2.142292 AACCCAGTGGCAGATCACCC 62.142 60.000 2.61 0.00 38.34 4.61
7687 17308 0.962356 CAACCCAGTGGCAGATCACC 60.962 60.000 2.61 0.00 38.34 4.02
7688 17309 0.250901 ACAACCCAGTGGCAGATCAC 60.251 55.000 2.61 0.00 37.89 3.06
7727 17348 8.306313 TGCTCCAAGAGTTAGATTTGTAGATA 57.694 34.615 0.00 0.00 31.39 1.98
7728 17349 7.187824 TGCTCCAAGAGTTAGATTTGTAGAT 57.812 36.000 0.00 0.00 31.39 1.98
7729 17350 6.605471 TGCTCCAAGAGTTAGATTTGTAGA 57.395 37.500 0.00 0.00 31.39 2.59
7784 17569 8.718102 TGCATTATCTTCTTACAACTAAGGAC 57.282 34.615 0.00 0.00 31.60 3.85
7791 17576 6.030228 GTGCCTTGCATTATCTTCTTACAAC 58.970 40.000 0.00 0.00 41.91 3.32
7900 17697 1.134098 AGGTGTCTGTCCAACAACTGG 60.134 52.381 0.00 0.00 42.94 4.00
7984 17781 5.879223 AGTCTCTTGCCATGAACTATTTCTG 59.121 40.000 0.00 0.00 32.36 3.02
8020 17817 5.628193 CCCACGATTGTATTCTGATACGTAC 59.372 44.000 0.00 0.00 40.85 3.67
8318 18116 1.896465 CCTGAGATTCCCGGATAGGAC 59.104 57.143 0.73 0.00 45.00 3.85
8398 18197 3.096852 TCTGCGATCAGAAAGTAGGGAA 58.903 45.455 0.00 0.00 45.69 3.97
8608 18407 9.770097 TTCATCTATGTATGTTTCTCCAGATTC 57.230 33.333 0.00 0.00 0.00 2.52
8648 18447 6.605471 TTTCAATAGAGTAACTCCTGCTGA 57.395 37.500 0.00 0.00 0.00 4.26
8710 18509 2.198827 TAATGGGCTTGGTGACACAG 57.801 50.000 8.08 0.00 42.67 3.66
8873 18672 8.447924 AGGATCATCTTCTGTAAATCATGTTG 57.552 34.615 0.00 0.00 0.00 3.33
8926 18725 3.609853 TCAGCTTCAGTGTTGTCTTTGT 58.390 40.909 0.00 0.00 0.00 2.83
8927 18726 4.825546 ATCAGCTTCAGTGTTGTCTTTG 57.174 40.909 0.00 0.00 0.00 2.77
9011 18810 7.704727 AGGGAGTAGTGCATATATCTCTTAGT 58.295 38.462 0.00 0.00 0.00 2.24
9026 18825 3.936535 GGGACGGAGGGAGTAGTG 58.063 66.667 0.00 0.00 0.00 2.74
9162 18961 8.822805 TCCCTCCGTAAATAAATATAAGAGCAT 58.177 33.333 0.00 0.00 0.00 3.79
9163 18962 8.197592 TCCCTCCGTAAATAAATATAAGAGCA 57.802 34.615 0.00 0.00 0.00 4.26
9164 18963 8.312564 ACTCCCTCCGTAAATAAATATAAGAGC 58.687 37.037 0.00 0.00 0.00 4.09
9176 18975 9.939802 GATTTATTATGTACTCCCTCCGTAAAT 57.060 33.333 0.00 0.00 0.00 1.40
9177 18976 8.370182 GGATTTATTATGTACTCCCTCCGTAAA 58.630 37.037 0.00 0.00 0.00 2.01
9178 18977 7.510001 TGGATTTATTATGTACTCCCTCCGTAA 59.490 37.037 0.00 0.00 0.00 3.18
9179 18978 7.011994 TGGATTTATTATGTACTCCCTCCGTA 58.988 38.462 0.00 0.00 0.00 4.02
9238 19052 2.159028 GGCTGGGTGTTTTGCTTGTTTA 60.159 45.455 0.00 0.00 0.00 2.01
9399 19213 4.745620 CGCCATAGTTTAGAAAGGTAGCTC 59.254 45.833 0.00 0.00 0.00 4.09
9445 19259 9.862149 GGAGGGATTATTAGGAAGATTACAAAA 57.138 33.333 0.00 0.00 0.00 2.44
9515 19329 2.170607 CCTCCGTCCCACAATGTAAGAT 59.829 50.000 0.00 0.00 0.00 2.40
9569 19383 3.407209 ACTCCCTCCATCCCACAATATT 58.593 45.455 0.00 0.00 0.00 1.28
9635 19449 3.639099 CACTTCTGGTGCCTCATGT 57.361 52.632 0.00 0.00 39.22 3.21


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

AutoCloner maintained by Alex Coulton.