Multiple sequence alignment - TraesCS5B01G122600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5B01G122600 chr5B 100.000 8072 0 0 1 8072 220818597 220810526 0.000000e+00 14907.0
1 TraesCS5B01G122600 chr5B 97.909 287 5 1 1 286 634281334 634281620 5.630000e-136 496.0
2 TraesCS5B01G122600 chr5B 83.032 277 19 10 5735 5986 270299937 270300210 8.150000e-55 226.0
3 TraesCS5B01G122600 chr5B 83.128 243 15 6 5762 5980 103323961 103324201 1.780000e-46 198.0
4 TraesCS5B01G122600 chr5B 82.500 200 9 5 5806 5980 80280017 80280215 1.400000e-32 152.0
5 TraesCS5B01G122600 chr5B 94.444 36 1 1 4525 4559 313308108 313308073 4.000000e-03 54.7
6 TraesCS5B01G122600 chr5A 94.472 4631 164 34 1777 6347 267941208 267945806 0.000000e+00 7049.0
7 TraesCS5B01G122600 chr5A 94.759 1164 36 8 6200 7358 267945807 267946950 0.000000e+00 1788.0
8 TraesCS5B01G122600 chr5A 94.651 916 31 8 801 1704 267940296 267941205 0.000000e+00 1404.0
9 TraesCS5B01G122600 chr5A 88.806 670 52 10 7366 8013 267953504 267954172 0.000000e+00 800.0
10 TraesCS5B01G122600 chr5A 86.667 270 12 9 5735 5980 259062963 259062694 2.220000e-70 278.0
11 TraesCS5B01G122600 chr5A 83.333 270 18 7 5735 5980 10801940 10802206 2.930000e-54 224.0
12 TraesCS5B01G122600 chr5A 81.550 271 24 6 5735 5981 514807285 514807017 4.940000e-47 200.0
13 TraesCS5B01G122600 chr5A 85.401 137 11 4 5852 5980 699849791 699849656 5.080000e-27 134.0
14 TraesCS5B01G122600 chr5A 93.671 79 5 0 7994 8072 267954219 267954297 1.420000e-22 119.0
15 TraesCS5B01G122600 chr5A 95.122 41 2 0 7645 7685 355177535 355177495 1.880000e-06 65.8
16 TraesCS5B01G122600 chr5A 92.857 42 2 1 4519 4559 325195151 325195192 8.750000e-05 60.2
17 TraesCS5B01G122600 chr5D 94.254 2280 109 20 3254 5518 207249591 207247319 0.000000e+00 3465.0
18 TraesCS5B01G122600 chr5D 96.454 1523 44 8 1703 3223 207251174 207249660 0.000000e+00 2505.0
19 TraesCS5B01G122600 chr5D 94.050 1479 57 13 6185 7639 207245844 207244373 0.000000e+00 2215.0
20 TraesCS5B01G122600 chr5D 95.071 913 23 9 832 1722 207252416 207251504 0.000000e+00 1417.0
21 TraesCS5B01G122600 chr5D 87.352 253 18 10 5735 5977 50024874 50025122 2.220000e-70 278.0
22 TraesCS5B01G122600 chr5D 85.227 264 30 5 7670 7925 207244301 207244039 6.210000e-66 263.0
23 TraesCS5B01G122600 chr5D 85.199 277 14 7 5733 5984 436255229 436255503 8.040000e-65 259.0
24 TraesCS5B01G122600 chr5D 94.231 156 6 3 5502 5655 207246853 207246699 1.350000e-57 235.0
25 TraesCS5B01G122600 chr5D 92.405 158 9 2 6185 6339 207246046 207245889 1.050000e-53 222.0
26 TraesCS5B01G122600 chr5D 94.118 119 7 0 5733 5851 234210196 234210078 1.790000e-41 182.0
27 TraesCS5B01G122600 chr5D 90.000 80 4 1 5981 6056 207246646 207246567 5.150000e-17 100.0
28 TraesCS5B01G122600 chr5D 89.041 73 6 2 5908 5980 522502506 522502576 1.120000e-13 89.8
29 TraesCS5B01G122600 chr5D 88.462 78 1 4 5911 5980 439492357 439492280 4.010000e-13 87.9
30 TraesCS5B01G122600 chr5D 87.838 74 7 2 5907 5980 72610539 72610610 1.440000e-12 86.1
31 TraesCS5B01G122600 chr5D 89.796 49 5 0 7637 7685 6347772 6347820 6.760000e-06 63.9
32 TraesCS5B01G122600 chrUn 94.063 539 26 6 284 816 301170281 301170819 0.000000e+00 813.0
33 TraesCS5B01G122600 chrUn 93.704 540 27 6 284 816 131818333 131818872 0.000000e+00 802.0
34 TraesCS5B01G122600 chrUn 93.078 549 31 6 284 825 4346119 4345571 0.000000e+00 797.0
35 TraesCS5B01G122600 chrUn 93.506 539 29 5 284 816 287229582 287230120 0.000000e+00 797.0
36 TraesCS5B01G122600 chrUn 93.506 539 29 5 284 816 287481447 287481985 0.000000e+00 797.0
37 TraesCS5B01G122600 chrUn 93.506 539 29 5 284 816 326848479 326849017 0.000000e+00 797.0
38 TraesCS5B01G122600 chrUn 93.078 549 31 6 284 825 378240459 378239911 0.000000e+00 797.0
39 TraesCS5B01G122600 chrUn 85.199 277 15 8 5734 5986 362324467 362324193 2.230000e-65 261.0
40 TraesCS5B01G122600 chrUn 85.240 271 14 6 5734 5980 253448926 253448658 1.040000e-63 255.0
41 TraesCS5B01G122600 chrUn 84.871 271 15 4 5734 5980 60727897 60728165 4.840000e-62 250.0
42 TraesCS5B01G122600 chrUn 84.871 271 15 6 5734 5980 364164308 364164576 4.840000e-62 250.0
43 TraesCS5B01G122600 chrUn 84.871 271 15 6 5734 5980 378881058 378881326 4.840000e-62 250.0
44 TraesCS5B01G122600 chrUn 84.502 271 16 8 5734 5980 60670428 60670696 2.250000e-60 244.0
45 TraesCS5B01G122600 chrUn 84.502 271 16 6 5734 5980 249053690 249053422 2.250000e-60 244.0
46 TraesCS5B01G122600 chrUn 84.502 271 16 7 5734 5980 393591705 393591973 2.250000e-60 244.0
47 TraesCS5B01G122600 chrUn 84.502 271 15 7 5734 5980 411428618 411428351 8.090000e-60 243.0
48 TraesCS5B01G122600 chrUn 84.000 275 18 7 5733 5983 92967746 92968018 2.910000e-59 241.0
49 TraesCS5B01G122600 chrUn 83.643 269 18 11 5737 5979 89675163 89675431 6.300000e-56 230.0
50 TraesCS5B01G122600 chrUn 81.919 271 23 6 5735 5981 54975403 54975135 1.060000e-48 206.0
51 TraesCS5B01G122600 chrUn 93.220 118 7 1 5734 5851 401918159 401918275 1.080000e-38 172.0
52 TraesCS5B01G122600 chrUn 87.591 137 8 4 5852 5980 13920379 13920514 5.050000e-32 150.0
53 TraesCS5B01G122600 chrUn 74.818 274 50 16 4514 4775 225032065 225031799 1.110000e-18 106.0
54 TraesCS5B01G122600 chrUn 85.185 81 3 4 5908 5980 92967748 92967827 3.120000e-09 75.0
55 TraesCS5B01G122600 chrUn 97.500 40 1 0 5941 5980 7865770 7865809 1.450000e-07 69.4
56 TraesCS5B01G122600 chrUn 97.500 40 1 0 5941 5980 49116942 49116981 1.450000e-07 69.4
57 TraesCS5B01G122600 chrUn 83.951 81 4 4 5908 5980 98278119 98278040 1.450000e-07 69.4
58 TraesCS5B01G122600 chrUn 91.489 47 3 1 7633 7679 320620113 320620068 6.760000e-06 63.9
59 TraesCS5B01G122600 chr3B 93.866 538 27 5 284 816 515159618 515160154 0.000000e+00 806.0
60 TraesCS5B01G122600 chr3B 93.866 538 25 8 284 816 670193616 670193082 0.000000e+00 804.0
61 TraesCS5B01G122600 chr3B 87.732 269 11 4 5734 5980 335843016 335842748 2.200000e-75 294.0
62 TraesCS5B01G122600 chr3B 84.815 270 15 9 5735 5980 5127702 5127969 1.740000e-61 248.0
63 TraesCS5B01G122600 chr3B 100.000 35 0 0 7645 7679 808987670 808987704 1.880000e-06 65.8
64 TraesCS5B01G122600 chr3B 93.182 44 3 0 7638 7681 829125267 829125224 1.880000e-06 65.8
65 TraesCS5B01G122600 chr3B 89.362 47 4 1 7633 7679 5967918 5967873 3.150000e-04 58.4
66 TraesCS5B01G122600 chr7B 98.258 287 4 1 1 286 424535937 424535651 1.210000e-137 501.0
67 TraesCS5B01G122600 chr7B 97.909 287 5 1 1 286 34125188 34124902 5.630000e-136 496.0
68 TraesCS5B01G122600 chr6B 98.258 287 4 1 1 286 613593729 613593443 1.210000e-137 501.0
69 TraesCS5B01G122600 chr6B 97.909 287 5 1 1 286 188498749 188498463 5.630000e-136 496.0
70 TraesCS5B01G122600 chr6B 85.926 270 14 6 5735 5980 164051943 164052212 4.800000e-67 267.0
71 TraesCS5B01G122600 chr6B 88.060 134 7 4 5852 5977 420770779 420770647 5.050000e-32 150.0
72 TraesCS5B01G122600 chr6B 75.446 224 37 7 7789 8011 157582811 157582605 8.630000e-15 93.5
73 TraesCS5B01G122600 chr6B 91.667 48 3 1 7633 7680 226867912 226867958 1.880000e-06 65.8
74 TraesCS5B01G122600 chr2B 98.258 287 4 1 1 286 229781587 229781301 1.210000e-137 501.0
75 TraesCS5B01G122600 chr2B 87.097 279 12 6 5731 5985 383640263 383639985 2.200000e-75 294.0
76 TraesCS5B01G122600 chr1A 98.258 287 4 1 1 286 451855881 451856167 1.210000e-137 501.0
77 TraesCS5B01G122600 chr1A 83.704 270 18 7 5735 5980 475397590 475397857 1.750000e-56 231.0
78 TraesCS5B01G122600 chr1A 71.443 991 230 42 4719 5684 149869173 149870135 6.350000e-51 213.0
79 TraesCS5B01G122600 chr1A 71.140 991 233 41 4719 5684 149887966 149888928 6.390000e-46 196.0
80 TraesCS5B01G122600 chr1A 80.000 270 28 6 5735 5980 565122749 565123016 8.330000e-40 176.0
81 TraesCS5B01G122600 chr1A 86.585 82 3 5 5907 5980 584579774 584579855 5.190000e-12 84.2
82 TraesCS5B01G122600 chr1A 89.286 56 5 1 4514 4568 429000003 428999948 1.450000e-07 69.4
83 TraesCS5B01G122600 chr4B 98.246 285 4 1 3 286 221094772 221095056 1.560000e-136 497.0
84 TraesCS5B01G122600 chr4B 85.556 270 13 4 5735 5980 2014289 2014022 8.040000e-65 259.0
85 TraesCS5B01G122600 chr4B 84.444 270 16 6 5735 5980 3335655 3335388 8.090000e-60 243.0
86 TraesCS5B01G122600 chr4B 82.721 272 20 10 5734 5980 660199915 660200184 4.910000e-52 217.0
87 TraesCS5B01G122600 chr4B 97.059 34 1 0 7648 7681 496469448 496469415 3.150000e-04 58.4
88 TraesCS5B01G122600 chr4B 97.059 34 1 0 7646 7679 664200732 664200699 3.150000e-04 58.4
89 TraesCS5B01G122600 chr4B 100.000 28 0 0 4525 4552 632867749 632867722 1.500000e-02 52.8
90 TraesCS5B01G122600 chr3A 97.909 287 5 1 1 286 729745192 729745478 5.630000e-136 496.0
91 TraesCS5B01G122600 chr3A 92.857 42 3 0 7638 7679 694102789 694102830 2.430000e-05 62.1
92 TraesCS5B01G122600 chr2D 79.184 490 82 13 3795 4278 29068663 29068188 1.010000e-83 322.0
93 TraesCS5B01G122600 chr2D 86.738 279 13 6 5731 5985 315978343 315978065 1.020000e-73 289.0
94 TraesCS5B01G122600 chr2D 84.615 273 16 6 5733 5981 643067945 643067675 1.740000e-61 248.0
95 TraesCS5B01G122600 chr2A 86.667 270 11 5 5735 5980 102694604 102694872 7.980000e-70 276.0
96 TraesCS5B01G122600 chr2A 84.871 271 16 5 5734 5981 611004074 611003806 4.840000e-62 250.0
97 TraesCS5B01G122600 chr2A 78.261 207 38 4 7762 7961 631535448 631535654 8.500000e-25 126.0
98 TraesCS5B01G122600 chr2A 97.143 35 0 1 4525 4558 552061842 552061808 3.150000e-04 58.4
99 TraesCS5B01G122600 chr1B 86.397 272 11 11 5733 5980 66377926 66377657 2.870000e-69 274.0
100 TraesCS5B01G122600 chr1B 83.525 261 25 3 5736 5980 49140525 49140783 2.270000e-55 228.0
101 TraesCS5B01G122600 chr1B 83.212 274 19 9 5735 5983 472046074 472046345 8.150000e-55 226.0
102 TraesCS5B01G122600 chr1B 90.909 44 4 0 7638 7681 302510067 302510110 8.750000e-05 60.2
103 TraesCS5B01G122600 chr4D 85.662 272 15 5 5734 5981 433698296 433698567 1.730000e-66 265.0
104 TraesCS5B01G122600 chr4D 83.835 266 15 7 5737 5978 86777572 86777311 2.270000e-55 228.0
105 TraesCS5B01G122600 chr4D 83.088 272 20 7 5735 5982 481337531 481337800 2.930000e-54 224.0
106 TraesCS5B01G122600 chr4D 82.156 269 21 7 5732 5975 488877464 488877198 1.060000e-48 206.0
107 TraesCS5B01G122600 chr4D 80.309 259 45 2 7761 8013 400646793 400647051 2.970000e-44 191.0
108 TraesCS5B01G122600 chr4D 89.922 129 4 4 5852 5972 175092438 175092311 3.020000e-34 158.0
109 TraesCS5B01G122600 chr4D 88.148 135 7 4 5852 5978 97449129 97449262 1.400000e-32 152.0
110 TraesCS5B01G122600 chr4D 86.131 137 10 3 5854 5981 445738787 445738651 1.090000e-28 139.0
111 TraesCS5B01G122600 chr4D 90.000 90 8 1 5852 5940 295001979 295002068 1.840000e-21 115.0
112 TraesCS5B01G122600 chr4D 100.000 40 0 0 5941 5980 329665808 329665847 3.120000e-09 75.0
113 TraesCS5B01G122600 chr4D 100.000 35 0 0 7644 7678 373466754 373466788 1.880000e-06 65.8
114 TraesCS5B01G122600 chr4D 97.222 36 1 0 7644 7679 37608900 37608935 2.430000e-05 62.1
115 TraesCS5B01G122600 chr4D 92.500 40 3 0 7646 7685 160591727 160591688 3.150000e-04 58.4
116 TraesCS5B01G122600 chr4D 92.683 41 2 1 4513 4552 495629246 495629206 3.150000e-04 58.4
117 TraesCS5B01G122600 chr4D 90.244 41 3 1 4519 4558 223620711 223620751 1.500000e-02 52.8
118 TraesCS5B01G122600 chr6D 85.199 277 15 8 5734 5986 458198986 458198712 2.230000e-65 261.0
119 TraesCS5B01G122600 chr6D 85.199 277 15 8 5734 5986 458229359 458229085 2.230000e-65 261.0
120 TraesCS5B01G122600 chr6D 85.199 277 15 8 5734 5986 458263351 458263077 2.230000e-65 261.0
121 TraesCS5B01G122600 chr6D 85.294 272 16 6 5735 5982 471190595 471190866 8.040000e-65 259.0
122 TraesCS5B01G122600 chr6D 84.838 277 16 8 5734 5986 458293474 458293200 1.040000e-63 255.0
123 TraesCS5B01G122600 chr6D 84.477 277 17 8 5734 5986 458169510 458169236 4.840000e-62 250.0
124 TraesCS5B01G122600 chr6D 84.477 277 17 8 5734 5986 458222497 458222223 4.840000e-62 250.0
125 TraesCS5B01G122600 chr6D 84.133 271 19 4 5734 5980 91817761 91817491 2.910000e-59 241.0
126 TraesCS5B01G122600 chr6D 87.313 134 8 4 5855 5980 469944897 469944765 2.350000e-30 145.0
127 TraesCS5B01G122600 chr6D 73.273 333 62 16 3946 4273 449280731 449281041 6.670000e-16 97.1
128 TraesCS5B01G122600 chr6D 86.420 81 2 4 5908 5980 458143576 458143497 6.720000e-11 80.5
129 TraesCS5B01G122600 chr6D 97.297 37 1 0 7642 7678 144264781 144264817 6.760000e-06 63.9
130 TraesCS5B01G122600 chr6D 91.304 46 3 1 4509 4553 394182464 394182419 2.430000e-05 62.1
131 TraesCS5B01G122600 chr6D 100.000 28 0 0 4526 4553 89171765 89171738 1.500000e-02 52.8
132 TraesCS5B01G122600 chr3D 85.240 271 14 5 5735 5981 603056852 603057120 1.040000e-63 255.0
133 TraesCS5B01G122600 chr3D 84.249 273 17 7 5735 5983 441645862 441645592 8.090000e-60 243.0
134 TraesCS5B01G122600 chr3D 97.222 36 1 0 7646 7681 516651272 516651307 2.430000e-05 62.1
135 TraesCS5B01G122600 chr7A 84.871 271 15 6 5734 5980 123200020 123200288 4.840000e-62 250.0
136 TraesCS5B01G122600 chr7A 75.000 184 40 3 7800 7982 693840322 693840144 6.720000e-11 80.5
137 TraesCS5B01G122600 chr7A 92.857 42 3 0 7638 7679 500130560 500130519 2.430000e-05 62.1
138 TraesCS5B01G122600 chr1D 84.615 273 15 11 5733 5980 45499873 45499603 6.260000e-61 246.0
139 TraesCS5B01G122600 chr1D 83.088 272 18 7 5735 5982 6218337 6218070 1.050000e-53 222.0
140 TraesCS5B01G122600 chr1D 83.077 195 8 4 5808 5978 461756839 461757032 3.900000e-33 154.0
141 TraesCS5B01G122600 chr1D 86.207 145 11 4 5852 5988 482764763 482764620 1.820000e-31 148.0
142 TraesCS5B01G122600 chr1D 85.185 81 3 4 5908 5980 389793658 389793579 3.120000e-09 75.0
143 TraesCS5B01G122600 chr1D 92.857 42 2 1 7645 7685 318714952 318714993 8.750000e-05 60.2
144 TraesCS5B01G122600 chr1D 96.774 31 1 0 7655 7685 11746585 11746555 1.500000e-02 52.8
145 TraesCS5B01G122600 chr1D 90.244 41 3 1 4519 4558 228026098 228026138 1.500000e-02 52.8
146 TraesCS5B01G122600 chr1D 96.774 31 1 0 7655 7685 476758210 476758180 1.500000e-02 52.8
147 TraesCS5B01G122600 chr6A 83.755 277 19 7 5728 5980 99210467 99210741 1.050000e-58 239.0
148 TraesCS5B01G122600 chr7D 83.764 271 16 7 5735 5980 56294881 56295148 1.750000e-56 231.0
149 TraesCS5B01G122600 chr7D 95.349 43 2 0 7637 7679 136315442 136315484 1.450000e-07 69.4
150 TraesCS5B01G122600 chr4A 86.111 144 12 3 5852 5987 450795750 450795893 1.820000e-31 148.0
151 TraesCS5B01G122600 chr4A 76.882 186 38 5 7777 7960 32413511 32413693 5.150000e-17 100.0


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 TraesCS5B01G122600 chr5B 220810526 220818597 8071 True 14907.000000 14907 100.000000 1 8072 1 chr5B.!!$R1 8071
1 TraesCS5B01G122600 chr5A 267940296 267946950 6654 False 3413.666667 7049 94.627333 801 7358 3 chr5A.!!$F3 6557
2 TraesCS5B01G122600 chr5A 267953504 267954297 793 False 459.500000 800 91.238500 7366 8072 2 chr5A.!!$F4 706
3 TraesCS5B01G122600 chr5D 207244039 207252416 8377 True 1302.750000 3465 92.711500 832 7925 8 chr5D.!!$R3 7093
4 TraesCS5B01G122600 chrUn 301170281 301170819 538 False 813.000000 813 94.063000 284 816 1 chrUn.!!$F10 532
5 TraesCS5B01G122600 chrUn 131818333 131818872 539 False 802.000000 802 93.704000 284 816 1 chrUn.!!$F7 532
6 TraesCS5B01G122600 chrUn 4345571 4346119 548 True 797.000000 797 93.078000 284 825 1 chrUn.!!$R1 541
7 TraesCS5B01G122600 chrUn 287229582 287230120 538 False 797.000000 797 93.506000 284 816 1 chrUn.!!$F8 532
8 TraesCS5B01G122600 chrUn 287481447 287481985 538 False 797.000000 797 93.506000 284 816 1 chrUn.!!$F9 532
9 TraesCS5B01G122600 chrUn 326848479 326849017 538 False 797.000000 797 93.506000 284 816 1 chrUn.!!$F11 532
10 TraesCS5B01G122600 chrUn 378239911 378240459 548 True 797.000000 797 93.078000 284 825 1 chrUn.!!$R9 541
11 TraesCS5B01G122600 chr3B 515159618 515160154 536 False 806.000000 806 93.866000 284 816 1 chr3B.!!$F2 532
12 TraesCS5B01G122600 chr3B 670193082 670193616 534 True 804.000000 804 93.866000 284 816 1 chr3B.!!$R3 532
13 TraesCS5B01G122600 chr1A 149869173 149870135 962 False 213.000000 213 71.443000 4719 5684 1 chr1A.!!$F1 965

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
829 839 0.685458 TGCCCTTACCGACCTACTCC 60.685 60.0 0.00 0.00 0.00 3.85 F
1758 2140 0.397941 AGCTGCAGCAAGTAGAACCA 59.602 50.0 38.24 0.00 45.16 3.67 F
2081 2463 0.530744 CTAGTACGTGCCTCTTGCCA 59.469 55.0 0.00 0.00 40.16 4.92 F
2958 3341 0.744414 AAGATCCATCGCCAACACCG 60.744 55.0 0.00 0.00 0.00 4.94 F
3856 4300 0.464916 AAAACTGAACCGGCGGACTT 60.465 50.0 35.78 18.38 0.00 3.01 F
4995 5449 0.318762 AGAGCCTCACGGACAAAGTC 59.681 55.0 0.00 0.00 0.00 3.01 F
5857 6807 0.877743 GAGTTCAAGACCCTTGCAGC 59.122 55.0 2.04 0.00 0.00 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2072 2454 1.066143 AGAACATACGGTGGCAAGAGG 60.066 52.381 0.00 0.0 0.00 3.69 R
2990 3373 1.135603 GCAAGCAAGCATCGATGAACA 60.136 47.619 29.20 0.0 0.00 3.18 R
3853 4297 1.111277 AGCTTCAAAAACCGCCAAGT 58.889 45.000 0.00 0.0 0.00 3.16 R
4370 4820 0.602905 ACGGTAAGTGACTTGGCAGC 60.603 55.000 8.33 0.0 0.00 5.25 R
5252 5718 0.546122 TGTCTTGGCACAGTCACCTT 59.454 50.000 0.00 0.0 42.39 3.50 R
6118 7402 1.133823 ACAACTTCATGTGCTCCACCA 60.134 47.619 0.00 0.0 32.73 4.17 R
7278 8859 1.098050 AGATCGGTTCAGCAAATGCC 58.902 50.000 0.94 0.0 43.38 4.40 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 3.637273 GGTGGGTGGAGAGGCGTT 61.637 66.667 0.00 0.00 0.00 4.84
24 25 2.358737 GTGGGTGGAGAGGCGTTG 60.359 66.667 0.00 0.00 0.00 4.10
25 26 3.636231 TGGGTGGAGAGGCGTTGG 61.636 66.667 0.00 0.00 0.00 3.77
92 93 4.785453 CTGGGGCTCCGGCTTGAC 62.785 72.222 0.00 0.00 38.73 3.18
131 132 3.519930 GCGGACGAGGAGGAGGAC 61.520 72.222 0.00 0.00 0.00 3.85
132 133 2.829458 CGGACGAGGAGGAGGACC 60.829 72.222 0.00 0.00 0.00 4.46
133 134 2.442458 GGACGAGGAGGAGGACCC 60.442 72.222 0.00 0.00 36.73 4.46
134 135 2.442458 GACGAGGAGGAGGACCCC 60.442 72.222 0.00 0.00 36.73 4.95
135 136 4.077180 ACGAGGAGGAGGACCCCC 62.077 72.222 0.00 0.00 36.73 5.40
152 153 4.899239 CCGGTCTCCATGCGCCTC 62.899 72.222 4.18 0.00 0.00 4.70
154 155 4.899239 GGTCTCCATGCGCCTCGG 62.899 72.222 4.18 2.05 0.00 4.63
155 156 4.899239 GTCTCCATGCGCCTCGGG 62.899 72.222 4.18 0.41 0.00 5.14
188 189 4.735132 CGGCGGCGTGAGAAGGAA 62.735 66.667 24.74 0.00 0.00 3.36
189 190 2.815647 GGCGGCGTGAGAAGGAAG 60.816 66.667 9.37 0.00 0.00 3.46
190 191 2.815647 GCGGCGTGAGAAGGAAGG 60.816 66.667 9.37 0.00 0.00 3.46
191 192 2.125512 CGGCGTGAGAAGGAAGGG 60.126 66.667 0.00 0.00 0.00 3.95
192 193 2.269241 GGCGTGAGAAGGAAGGGG 59.731 66.667 0.00 0.00 0.00 4.79
193 194 2.269241 GCGTGAGAAGGAAGGGGG 59.731 66.667 0.00 0.00 0.00 5.40
194 195 2.291043 GCGTGAGAAGGAAGGGGGA 61.291 63.158 0.00 0.00 0.00 4.81
195 196 1.901085 CGTGAGAAGGAAGGGGGAG 59.099 63.158 0.00 0.00 0.00 4.30
196 197 1.604915 GTGAGAAGGAAGGGGGAGC 59.395 63.158 0.00 0.00 0.00 4.70
197 198 1.990060 TGAGAAGGAAGGGGGAGCG 60.990 63.158 0.00 0.00 0.00 5.03
198 199 2.689034 AGAAGGAAGGGGGAGCGG 60.689 66.667 0.00 0.00 0.00 5.52
199 200 3.798511 GAAGGAAGGGGGAGCGGG 61.799 72.222 0.00 0.00 0.00 6.13
202 203 4.810184 GGAAGGGGGAGCGGGGTA 62.810 72.222 0.00 0.00 0.00 3.69
203 204 3.477346 GAAGGGGGAGCGGGGTAC 61.477 72.222 0.00 0.00 0.00 3.34
204 205 3.997756 GAAGGGGGAGCGGGGTACT 62.998 68.421 0.00 0.00 0.00 2.73
205 206 3.997756 AAGGGGGAGCGGGGTACTC 62.998 68.421 0.00 0.00 0.00 2.59
207 208 4.828296 GGGGAGCGGGGTACTCGA 62.828 72.222 12.01 0.00 34.87 4.04
208 209 3.217743 GGGAGCGGGGTACTCGAG 61.218 72.222 11.84 11.84 34.87 4.04
209 210 3.217743 GGAGCGGGGTACTCGAGG 61.218 72.222 18.41 0.00 34.87 4.63
210 211 3.902086 GAGCGGGGTACTCGAGGC 61.902 72.222 18.41 9.21 0.00 4.70
233 234 3.499737 GTGTTGCCGCCCTCGATG 61.500 66.667 0.00 0.00 38.10 3.84
234 235 4.015406 TGTTGCCGCCCTCGATGT 62.015 61.111 0.00 0.00 38.10 3.06
235 236 2.185867 GTTGCCGCCCTCGATGTA 59.814 61.111 0.00 0.00 38.10 2.29
236 237 2.171725 GTTGCCGCCCTCGATGTAC 61.172 63.158 0.00 0.00 38.10 2.90
237 238 2.355986 TTGCCGCCCTCGATGTACT 61.356 57.895 0.00 0.00 38.10 2.73
238 239 2.027751 GCCGCCCTCGATGTACTC 59.972 66.667 0.00 0.00 38.10 2.59
248 249 1.359475 GATGTACTCGAGGACGGCC 59.641 63.158 22.57 0.00 40.21 6.13
257 258 4.003788 AGGACGGCCTCCAACGTG 62.004 66.667 2.12 0.00 42.19 4.49
345 346 4.093952 GAGGAACGACGACGGCGA 62.094 66.667 32.70 0.00 44.46 5.54
346 347 3.599792 GAGGAACGACGACGGCGAA 62.600 63.158 32.70 0.00 44.46 4.70
352 353 1.133253 CGACGACGGCGAAAGAGTA 59.867 57.895 22.49 0.00 41.64 2.59
644 648 1.429927 TTCGCGCCAAAACAGTTCGA 61.430 50.000 0.00 0.00 0.00 3.71
732 738 4.178861 CGGCGAAAATCGGAGTCA 57.821 55.556 0.00 0.00 40.84 3.41
735 741 1.651987 GGCGAAAATCGGAGTCATGA 58.348 50.000 0.00 0.00 40.84 3.07
826 836 1.340568 GAGATGCCCTTACCGACCTAC 59.659 57.143 0.00 0.00 0.00 3.18
827 837 1.063114 AGATGCCCTTACCGACCTACT 60.063 52.381 0.00 0.00 0.00 2.57
828 838 1.340568 GATGCCCTTACCGACCTACTC 59.659 57.143 0.00 0.00 0.00 2.59
829 839 0.685458 TGCCCTTACCGACCTACTCC 60.685 60.000 0.00 0.00 0.00 3.85
830 840 1.732417 GCCCTTACCGACCTACTCCG 61.732 65.000 0.00 0.00 0.00 4.63
859 869 2.420687 GCCTCCGGTCATCTCTCAAATT 60.421 50.000 0.00 0.00 0.00 1.82
1224 1238 5.818136 TTCCTTGCTTATGTTGCTCATAC 57.182 39.130 2.59 0.00 38.55 2.39
1557 1573 4.527509 TTTGACAAGGTGAGTGCAAAAA 57.472 36.364 0.00 0.00 0.00 1.94
1630 1646 8.061304 ACATGAAACAAAATCTATGGATACCCT 58.939 33.333 0.00 0.00 0.00 4.34
1631 1647 8.917088 CATGAAACAAAATCTATGGATACCCTT 58.083 33.333 0.00 0.00 0.00 3.95
1636 1665 9.547279 AACAAAATCTATGGATACCCTTCTTTT 57.453 29.630 0.00 0.00 0.00 2.27
1679 1712 6.693466 TGGAACTACAAGTGTCGAATTCATA 58.307 36.000 6.22 0.00 0.00 2.15
1692 1725 7.224753 GTGTCGAATTCATAGCTTATTCTCCAA 59.775 37.037 6.22 0.00 0.00 3.53
1758 2140 0.397941 AGCTGCAGCAAGTAGAACCA 59.602 50.000 38.24 0.00 45.16 3.67
1785 2167 8.511604 AAATGCAGCAAGTACTATAGACATTT 57.488 30.769 6.78 15.10 31.22 2.32
2072 2454 3.057734 AGAAAGTGTTGCTAGTACGTGC 58.942 45.455 0.00 0.00 0.00 5.34
2081 2463 0.530744 CTAGTACGTGCCTCTTGCCA 59.469 55.000 0.00 0.00 40.16 4.92
2084 2466 3.583276 TACGTGCCTCTTGCCACCG 62.583 63.158 0.00 0.00 40.16 4.94
2262 2644 6.817140 AGGGTGATACGAAAATTACAGACTTC 59.183 38.462 0.00 0.00 0.00 3.01
2339 2721 4.642429 ACCGAAACTTCTCTTAGCAACAT 58.358 39.130 0.00 0.00 0.00 2.71
2342 2724 5.352569 CCGAAACTTCTCTTAGCAACATCAT 59.647 40.000 0.00 0.00 0.00 2.45
2737 3120 4.400529 AAAGCTGTTTTCGGAATTTGGT 57.599 36.364 0.00 0.00 0.00 3.67
2765 3148 2.362736 TCGTAGGCGTTCTACATCTGT 58.637 47.619 14.94 0.00 46.61 3.41
2958 3341 0.744414 AAGATCCATCGCCAACACCG 60.744 55.000 0.00 0.00 0.00 4.94
2990 3373 4.924305 TGCATTCAGAAGAGTTTTGCTT 57.076 36.364 5.89 0.00 0.00 3.91
3071 3454 9.070149 GGTAAAGTGACGTCTAGTACAATTAAG 57.930 37.037 17.92 0.00 0.00 1.85
3193 3577 8.972458 TTATGCAGTAAGTATAGGATTTTGCA 57.028 30.769 0.00 0.00 42.36 4.08
3211 3595 8.621532 ATTTTGCAACACTATCTGAGAGTAAA 57.378 30.769 4.40 1.88 0.00 2.01
3256 3640 3.238108 AGTCAACAGATTAGCGGTCTG 57.762 47.619 12.50 12.50 46.60 3.51
3268 3708 3.914426 AGCGGTCTGAGGTGATAATTT 57.086 42.857 0.00 0.00 0.00 1.82
3383 3823 6.951198 TGGGGTTTATTTTGCTCTCTGAAATA 59.049 34.615 0.00 0.00 0.00 1.40
3385 3825 8.311109 GGGGTTTATTTTGCTCTCTGAAATAAA 58.689 33.333 8.38 8.38 40.28 1.40
3386 3826 9.875691 GGGTTTATTTTGCTCTCTGAAATAAAT 57.124 29.630 13.20 0.00 42.42 1.40
3490 3930 2.224281 TGGACTTGGCAGAGTACAACAG 60.224 50.000 10.91 0.00 37.54 3.16
3509 3949 3.244665 ACAGAAGTGTTCATGATCCAGCA 60.245 43.478 0.00 0.00 30.30 4.41
3524 3964 6.417258 TGATCCAGCAGAAAGATTATCACAA 58.583 36.000 0.00 0.00 0.00 3.33
3715 4157 7.701924 TCTTACTGCAGTTGTTTCAATCTTTTG 59.298 33.333 27.06 0.00 0.00 2.44
3759 4203 8.150945 TCCGGGATTCAAAATTCATGTTAAAAA 58.849 29.630 0.00 0.00 0.00 1.94
3853 4297 4.563404 AAAAACTGAACCGGCGGA 57.437 50.000 35.78 9.74 0.00 5.54
3856 4300 0.464916 AAAACTGAACCGGCGGACTT 60.465 50.000 35.78 18.38 0.00 3.01
3867 4311 1.660264 GCGGACTTGGCGGTTTTTG 60.660 57.895 0.00 0.00 0.00 2.44
3874 4318 2.293399 ACTTGGCGGTTTTTGAAGCTAG 59.707 45.455 0.00 0.00 0.00 3.42
3881 4326 3.813166 CGGTTTTTGAAGCTAGAAGACCA 59.187 43.478 13.31 0.00 0.00 4.02
3976 4424 1.975660 TGAACCGGAAAAACCAGGAG 58.024 50.000 9.46 0.00 38.90 3.69
4044 4492 1.202256 CGTGAGTAGTAGGCATTGCGA 60.202 52.381 1.91 0.00 0.00 5.10
4053 4501 2.117156 GGCATTGCGAGCTCATGGT 61.117 57.895 15.40 0.00 0.00 3.55
4133 4581 7.820044 TTTGACCATTGTTTAACACTGTTTC 57.180 32.000 13.06 9.78 28.06 2.78
4255 4704 1.067846 TCACAGGTTCGATCTTCGGTG 60.068 52.381 0.00 0.00 40.88 4.94
4264 4713 3.655486 TCGATCTTCGGTGCAGTTTTTA 58.345 40.909 0.00 0.00 40.88 1.52
4307 4756 8.820153 ATATCTCAGAAAAAGAAATTGGAGCT 57.180 30.769 0.00 0.00 0.00 4.09
4370 4820 3.058501 ACGAATTTACAGGAACTTTGCCG 60.059 43.478 0.00 0.00 34.60 5.69
4448 4898 1.548973 GAATATGAGTGCGCCCGTCG 61.549 60.000 4.18 0.00 42.12 5.12
4599 5051 9.787435 TTAAAGTGCAGGAAAGTAAATAGAAGA 57.213 29.630 0.00 0.00 0.00 2.87
4682 5135 6.156429 AGAGTTAAAAGATCAACGGATAGGGT 59.844 38.462 0.00 0.00 32.67 4.34
4802 5256 7.627300 GCAAGAAGGCCAAAATTTTAAACACAA 60.627 33.333 5.01 0.00 0.00 3.33
4867 5321 1.695242 TCACGTACAGTCCATTGGGTT 59.305 47.619 2.09 0.00 34.93 4.11
4905 5359 1.519455 CTAACCTGAAGAGGCGCCG 60.519 63.158 23.20 7.32 44.33 6.46
4995 5449 0.318762 AGAGCCTCACGGACAAAGTC 59.681 55.000 0.00 0.00 0.00 3.01
5188 5653 4.079253 GAGCTTTTCACAAATGGGAGGTA 58.921 43.478 0.00 0.00 0.00 3.08
5252 5718 3.057547 GCAGAGAAGAGCGCCGAGA 62.058 63.158 2.29 0.00 0.00 4.04
5438 5904 2.168936 GAGCAAATCATGAAATGGCCCA 59.831 45.455 0.00 0.00 46.73 5.36
5490 5956 1.028905 CACGGGTTGAGCCAAAAGAA 58.971 50.000 0.00 0.00 39.65 2.52
5590 6538 1.278127 GAGATCCTTCCCAACGGTCAA 59.722 52.381 0.00 0.00 0.00 3.18
5729 6679 1.970114 CAGGGCAGCAGAAGTGTGG 60.970 63.158 0.00 0.00 0.00 4.17
5732 6682 1.968540 GGCAGCAGAAGTGTGGTCC 60.969 63.158 0.00 0.00 0.00 4.46
5740 6690 1.141053 AGAAGTGTGGTCCCTGTTGAC 59.859 52.381 0.00 0.00 34.42 3.18
5770 6720 5.957771 TGTATTGCCTAGTCTCTTCCATT 57.042 39.130 0.00 0.00 0.00 3.16
5821 6771 4.739046 GCATGCACTTCTACATGGTATC 57.261 45.455 14.21 0.00 43.13 2.24
5826 6776 4.054671 GCACTTCTACATGGTATCAGAGC 58.945 47.826 0.00 0.00 0.00 4.09
5831 6781 2.338577 ACATGGTATCAGAGCCAAGC 57.661 50.000 0.00 0.00 38.38 4.01
5855 6805 2.727123 TTGAGTTCAAGACCCTTGCA 57.273 45.000 2.04 0.00 0.00 4.08
5856 6806 2.260844 TGAGTTCAAGACCCTTGCAG 57.739 50.000 2.04 0.00 0.00 4.41
5857 6807 0.877743 GAGTTCAAGACCCTTGCAGC 59.122 55.000 2.04 0.00 0.00 5.25
5864 6829 1.973812 GACCCTTGCAGCCCACTTC 60.974 63.158 0.00 0.00 0.00 3.01
5882 6847 2.435410 CGGTCCACGTTTAGGCCC 60.435 66.667 0.00 0.00 37.93 5.80
5914 6879 0.939577 CGTGAGTGGGAGTGTTGACG 60.940 60.000 0.00 0.00 0.00 4.35
5918 6883 3.192001 GTGAGTGGGAGTGTTGACGTATA 59.808 47.826 0.00 0.00 0.00 1.47
5936 6901 8.418662 TGACGTATAAATGTATTGCCTAGTCTT 58.581 33.333 0.00 0.00 0.00 3.01
5944 6917 2.943036 TTGCCTAGTCTTTTCCGGTT 57.057 45.000 0.00 0.00 0.00 4.44
6118 7402 0.396435 TGAAGGTGTGCTTCCATCGT 59.604 50.000 0.00 0.00 0.00 3.73
6266 7837 2.990066 AAAGAATGTAGGCCTCCTCG 57.010 50.000 9.68 0.00 34.61 4.63
6273 7844 1.284198 TGTAGGCCTCCTCGTCTAAGT 59.716 52.381 9.68 0.00 34.61 2.24
6297 7870 2.812358 AACCTTTTGACCGAAATGCC 57.188 45.000 0.00 0.00 0.00 4.40
6307 7880 1.094785 CCGAAATGCCGTTTCCTGAT 58.905 50.000 3.88 0.00 42.63 2.90
6324 7897 4.946784 CTGATTACAGGCAAACCAGTAC 57.053 45.455 0.00 0.00 37.63 2.73
6325 7898 4.579869 CTGATTACAGGCAAACCAGTACT 58.420 43.478 0.00 0.00 37.63 2.73
6326 7899 4.575885 TGATTACAGGCAAACCAGTACTC 58.424 43.478 0.00 0.00 37.63 2.59
6327 7900 4.041075 TGATTACAGGCAAACCAGTACTCA 59.959 41.667 0.00 4.35 41.94 3.41
6328 7901 2.256117 ACAGGCAAACCAGTACTCAC 57.744 50.000 0.00 0.00 39.06 3.51
6410 7983 9.675464 TTTCTTTTCCGTATATTGGTACTCAAT 57.325 29.630 12.34 12.34 46.79 2.57
6468 8041 5.410746 CAGATGTCTGAGTGCATGTTTACTT 59.589 40.000 3.96 0.00 46.59 2.24
6674 8252 5.723887 CAGGTAGAGGAATATCTTGGGCTAT 59.276 44.000 0.00 0.00 0.00 2.97
6698 8276 4.627611 TTCTCTCGTAGTAACCAATCCG 57.372 45.455 0.00 0.00 0.00 4.18
6701 8279 4.100707 TCTCGTAGTAACCAATCCGTTG 57.899 45.455 0.00 0.00 35.05 4.10
6713 8291 3.443681 CCAATCCGTTGCTGTATTTTCCT 59.556 43.478 0.00 0.00 33.90 3.36
6999 8580 0.681243 GCACATGGGGAAGAAGGGAC 60.681 60.000 0.00 0.00 0.00 4.46
7278 8859 2.500509 TTTGTGCTTTTTACTGCCGG 57.499 45.000 0.00 0.00 0.00 6.13
7292 8873 2.573340 CCGGGCATTTGCTGAACC 59.427 61.111 2.12 0.00 41.70 3.62
7322 8903 9.976511 CTATCATGCATGTTATCTTTCCATTTT 57.023 29.630 25.43 0.00 0.00 1.82
7379 8960 8.915057 ACATTGAGGTATTGGAATCTATTCAG 57.085 34.615 5.15 0.00 38.53 3.02
7385 8966 6.995091 AGGTATTGGAATCTATTCAGTTGAGC 59.005 38.462 5.15 0.00 38.53 4.26
7393 8974 9.008683 GGAATCTATTCAGTTGAGCCTCAACAC 62.009 44.444 32.69 13.62 45.02 3.32
7411 8999 6.524734 TCAACACAGTCTACAATGAACTGAT 58.475 36.000 17.07 6.57 33.15 2.90
7479 9067 4.137116 TGAATGACGGGGAGACATTTAG 57.863 45.455 0.00 0.00 43.26 1.85
7534 9131 8.972262 AACTGCATATGTTAGATATACGACAG 57.028 34.615 13.74 6.42 0.00 3.51
7590 9189 1.538687 AACCCAGCCTCTGCATTTGC 61.539 55.000 0.00 0.00 41.13 3.68
7591 9190 2.718073 CCCAGCCTCTGCATTTGCC 61.718 63.158 0.00 0.00 41.13 4.52
7640 9239 3.129988 AGCAAATCATCCAAACAGCTAGC 59.870 43.478 6.62 6.62 0.00 3.42
7643 9242 2.472695 TCATCCAAACAGCTAGCGTT 57.527 45.000 15.93 15.93 0.00 4.84
7653 9252 4.727235 ACAGCTAGCGTTAAAAACACTC 57.273 40.909 9.55 0.00 0.00 3.51
7695 9335 5.430089 GGGAGTAGATGATAAGGGCCATTAT 59.570 44.000 22.12 22.12 0.00 1.28
7710 9350 3.333804 CCATTATGGCCAAAACACAACC 58.666 45.455 10.96 0.00 0.00 3.77
7776 9418 6.672266 TGAGAAGGTGTCTAGAACTCAATT 57.328 37.500 0.00 0.00 36.41 2.32
7786 9428 6.040955 TGTCTAGAACTCAATTGACTGTGACT 59.959 38.462 20.11 15.66 0.00 3.41
7826 9470 4.871557 ACGTCAGTGTAGTTGTTTTGCTAA 59.128 37.500 0.00 0.00 0.00 3.09
7888 9538 1.005766 CGCAACAACTTTGCAAGCAAG 60.006 47.619 7.60 0.00 45.14 4.01
7893 9543 2.431782 ACAACTTTGCAAGCAAGGACAT 59.568 40.909 21.42 6.40 36.65 3.06
7911 9561 2.296190 ACATCTAACGCTGCATCCGATA 59.704 45.455 13.01 5.54 0.00 2.92
7958 9608 1.080093 GATGTTGCGACCGGTGAGA 60.080 57.895 14.63 0.00 0.00 3.27
7960 9610 3.103911 GTTGCGACCGGTGAGACG 61.104 66.667 14.63 11.10 0.00 4.18
7969 9619 3.127533 GGTGAGACGGCATGCCAC 61.128 66.667 34.93 26.49 35.37 5.01
7974 9624 2.040213 GAGACGGCATGCCACGATTG 62.040 60.000 34.93 20.23 35.37 2.67
7985 9635 1.215382 CACGATTGACGAGGGCAGA 59.785 57.895 0.00 0.00 45.77 4.26
7990 9640 2.481276 CGATTGACGAGGGCAGATGTTA 60.481 50.000 0.00 0.00 45.77 2.41
7999 9716 1.134521 GGGCAGATGTTATGACCGTGA 60.135 52.381 0.00 0.00 35.73 4.35
8032 9749 0.107703 GAGATCCATTGGACGGTGCA 60.108 55.000 7.76 0.00 32.98 4.57
8038 9755 0.603707 CATTGGACGGTGCACAGTCT 60.604 55.000 37.17 22.54 40.23 3.24
8065 9782 6.454186 GCACGAATCTCCATGCAAAATTTAAC 60.454 38.462 0.00 0.00 38.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.637273 AACGCCTCTCCACCCACC 61.637 66.667 0.00 0.00 0.00 4.61
7 8 2.358737 CAACGCCTCTCCACCCAC 60.359 66.667 0.00 0.00 0.00 4.61
8 9 3.636231 CCAACGCCTCTCCACCCA 61.636 66.667 0.00 0.00 0.00 4.51
75 76 4.785453 GTCAAGCCGGAGCCCCAG 62.785 72.222 5.05 0.00 41.25 4.45
114 115 3.519930 GTCCTCCTCCTCGTCCGC 61.520 72.222 0.00 0.00 0.00 5.54
115 116 2.829458 GGTCCTCCTCCTCGTCCG 60.829 72.222 0.00 0.00 0.00 4.79
116 117 2.442458 GGGTCCTCCTCCTCGTCC 60.442 72.222 0.00 0.00 0.00 4.79
117 118 2.442458 GGGGTCCTCCTCCTCGTC 60.442 72.222 0.00 0.00 35.33 4.20
135 136 4.899239 GAGGCGCATGGAGACCGG 62.899 72.222 10.83 0.00 0.00 5.28
137 138 4.899239 CCGAGGCGCATGGAGACC 62.899 72.222 10.83 0.00 0.00 3.85
138 139 4.899239 CCCGAGGCGCATGGAGAC 62.899 72.222 10.83 0.00 0.00 3.36
171 172 4.735132 TTCCTTCTCACGCCGCCG 62.735 66.667 0.00 0.00 41.14 6.46
172 173 2.815647 CTTCCTTCTCACGCCGCC 60.816 66.667 0.00 0.00 0.00 6.13
173 174 2.815647 CCTTCCTTCTCACGCCGC 60.816 66.667 0.00 0.00 0.00 6.53
174 175 2.125512 CCCTTCCTTCTCACGCCG 60.126 66.667 0.00 0.00 0.00 6.46
175 176 2.269241 CCCCTTCCTTCTCACGCC 59.731 66.667 0.00 0.00 0.00 5.68
176 177 2.245438 CTCCCCCTTCCTTCTCACGC 62.245 65.000 0.00 0.00 0.00 5.34
177 178 1.901085 CTCCCCCTTCCTTCTCACG 59.099 63.158 0.00 0.00 0.00 4.35
178 179 1.604915 GCTCCCCCTTCCTTCTCAC 59.395 63.158 0.00 0.00 0.00 3.51
179 180 1.990060 CGCTCCCCCTTCCTTCTCA 60.990 63.158 0.00 0.00 0.00 3.27
180 181 2.736826 CCGCTCCCCCTTCCTTCTC 61.737 68.421 0.00 0.00 0.00 2.87
181 182 2.689034 CCGCTCCCCCTTCCTTCT 60.689 66.667 0.00 0.00 0.00 2.85
182 183 3.798511 CCCGCTCCCCCTTCCTTC 61.799 72.222 0.00 0.00 0.00 3.46
185 186 4.810184 TACCCCGCTCCCCCTTCC 62.810 72.222 0.00 0.00 0.00 3.46
186 187 3.477346 GTACCCCGCTCCCCCTTC 61.477 72.222 0.00 0.00 0.00 3.46
187 188 3.997756 GAGTACCCCGCTCCCCCTT 62.998 68.421 0.00 0.00 0.00 3.95
188 189 4.477119 GAGTACCCCGCTCCCCCT 62.477 72.222 0.00 0.00 0.00 4.79
190 191 4.828296 TCGAGTACCCCGCTCCCC 62.828 72.222 0.88 0.00 0.00 4.81
191 192 3.217743 CTCGAGTACCCCGCTCCC 61.218 72.222 3.62 0.00 0.00 4.30
192 193 3.217743 CCTCGAGTACCCCGCTCC 61.218 72.222 12.31 0.00 0.00 4.70
193 194 3.902086 GCCTCGAGTACCCCGCTC 61.902 72.222 12.31 0.00 0.00 5.03
216 217 2.845752 TACATCGAGGGCGGCAACAC 62.846 60.000 12.47 0.00 38.28 3.32
217 218 2.651105 TACATCGAGGGCGGCAACA 61.651 57.895 12.47 0.00 38.28 3.33
218 219 2.171725 GTACATCGAGGGCGGCAAC 61.172 63.158 12.47 2.63 38.28 4.17
219 220 2.185867 GTACATCGAGGGCGGCAA 59.814 61.111 12.47 0.00 38.28 4.52
220 221 2.758327 AGTACATCGAGGGCGGCA 60.758 61.111 12.47 0.00 38.28 5.69
221 222 2.027751 GAGTACATCGAGGGCGGC 59.972 66.667 0.00 0.00 38.28 6.53
230 231 1.102222 AGGCCGTCCTCGAGTACATC 61.102 60.000 12.31 0.00 38.72 3.06
231 232 1.076923 AGGCCGTCCTCGAGTACAT 60.077 57.895 12.31 0.00 38.72 2.29
232 233 2.353958 AGGCCGTCCTCGAGTACA 59.646 61.111 12.31 0.00 38.72 2.90
291 292 2.742710 TTCGCCGTCTCCAGTTCACG 62.743 60.000 0.00 0.00 0.00 4.35
345 346 2.093106 ACTCGGCGACTCATACTCTTT 58.907 47.619 4.99 0.00 0.00 2.52
346 347 1.402259 CACTCGGCGACTCATACTCTT 59.598 52.381 4.99 0.00 0.00 2.85
527 531 1.403249 GCGAATCAATGCCAAAGCTGT 60.403 47.619 0.00 0.00 40.80 4.40
728 734 2.182791 CAGTCGCGCCTCATGACT 59.817 61.111 8.81 8.81 43.43 3.41
729 735 2.887568 CCAGTCGCGCCTCATGAC 60.888 66.667 0.00 2.53 0.00 3.06
804 814 0.105039 GGTCGGTAAGGGCATCTCAG 59.895 60.000 0.00 0.00 0.00 3.35
805 815 0.325296 AGGTCGGTAAGGGCATCTCA 60.325 55.000 0.00 0.00 0.00 3.27
846 856 6.283694 CGATAGTCCCAAATTTGAGAGATGA 58.716 40.000 19.86 6.07 0.00 2.92
859 869 1.220749 GCCAGTGCGATAGTCCCAA 59.779 57.895 0.00 0.00 39.35 4.12
1479 1495 9.769677 ATGGACTGGTACATAAATAGCTCTATA 57.230 33.333 0.00 0.00 38.20 1.31
1557 1573 9.759473 AGCTTATGGCATATGGACTATAAATTT 57.241 29.630 18.65 0.00 44.79 1.82
1558 1574 9.182214 CAGCTTATGGCATATGGACTATAAATT 57.818 33.333 18.65 0.00 44.79 1.82
1559 1575 8.551440 TCAGCTTATGGCATATGGACTATAAAT 58.449 33.333 18.65 0.00 44.79 1.40
1640 1669 9.965824 CTTGTAGTTCCATGTGAAAGTTAATTT 57.034 29.630 0.00 0.00 33.94 1.82
1679 1712 9.678260 CTATAGGCATTAATTGGAGAATAAGCT 57.322 33.333 0.00 0.00 0.00 3.74
1758 2140 6.878317 TGTCTATAGTACTTGCTGCATTTCT 58.122 36.000 1.84 2.98 0.00 2.52
1785 2167 6.976934 AAAGAGAATAAGCTTGGTCCAAAA 57.023 33.333 9.86 0.00 0.00 2.44
1841 2223 3.475566 TCTGTTGTCTCCTTTCCTGTG 57.524 47.619 0.00 0.00 0.00 3.66
1850 2232 8.729805 AATCTCATTAAGAATCTGTTGTCTCC 57.270 34.615 0.00 0.00 37.61 3.71
2072 2454 1.066143 AGAACATACGGTGGCAAGAGG 60.066 52.381 0.00 0.00 0.00 3.69
2081 2463 4.402793 AGAGCTAACATCAGAACATACGGT 59.597 41.667 0.00 0.00 0.00 4.83
2084 2466 9.534565 TTGAATAGAGCTAACATCAGAACATAC 57.465 33.333 0.00 0.00 0.00 2.39
2262 2644 1.270094 TGCAGTCCAGAAGTTACACCG 60.270 52.381 0.00 0.00 0.00 4.94
2342 2724 9.595823 GTCCACTTAATACTATTTAGAACAGCA 57.404 33.333 2.50 0.00 0.00 4.41
2737 3120 5.081888 GTAGAACGCCTACGAAAAACAAA 57.918 39.130 0.00 0.00 43.93 2.83
2765 3148 9.509956 TTCTAAATCCAGTAGAAATTCGGAAAA 57.490 29.630 0.00 0.00 35.22 2.29
2958 3341 4.096833 TCTTCTGAATGCATATGTTGTGGC 59.903 41.667 0.00 0.00 0.00 5.01
2990 3373 1.135603 GCAAGCAAGCATCGATGAACA 60.136 47.619 29.20 0.00 0.00 3.18
3071 3454 6.219302 TCGTATCGTTTCTCTTGAAAAACC 57.781 37.500 0.00 0.00 42.94 3.27
3142 3526 4.086457 AGTTTATCACTCCCCGCAAAAAT 58.914 39.130 0.00 0.00 0.00 1.82
3193 3577 8.465999 CATCAGACTTTACTCTCAGATAGTGTT 58.534 37.037 0.00 0.00 33.96 3.32
3211 3595 3.518705 AGAGCTGAAACATCCATCAGACT 59.481 43.478 6.95 3.77 44.64 3.24
3276 3716 5.818136 AACAATTCAACATATGAGACCGG 57.182 39.130 10.38 0.00 39.77 5.28
3490 3930 3.603532 TCTGCTGGATCATGAACACTTC 58.396 45.455 0.00 0.00 0.00 3.01
3509 3949 9.182214 ACATGTGCTATTTGTGATAATCTTTCT 57.818 29.630 0.00 0.00 0.00 2.52
3524 3964 6.708054 GCTATTAGGAACTCACATGTGCTATT 59.292 38.462 21.38 13.95 41.75 1.73
3616 4057 5.314923 ACATCATTGTATGTGAACTTGCC 57.685 39.130 0.00 0.00 38.65 4.52
3617 4058 6.470235 GCTAACATCATTGTATGTGAACTTGC 59.530 38.462 0.00 0.00 39.98 4.01
3715 4157 3.561725 CCGGATAGCAAGAAACCAGATTC 59.438 47.826 0.00 0.00 0.00 2.52
3853 4297 1.111277 AGCTTCAAAAACCGCCAAGT 58.889 45.000 0.00 0.00 0.00 3.16
3856 4300 2.264005 TCTAGCTTCAAAAACCGCCA 57.736 45.000 0.00 0.00 0.00 5.69
3867 4311 3.866651 TGCAGAATGGTCTTCTAGCTTC 58.133 45.455 0.00 0.00 35.86 3.86
3874 4318 3.119352 GGTCCAATTGCAGAATGGTCTTC 60.119 47.826 12.50 4.75 35.86 2.87
3881 4326 1.281867 TCTCCGGTCCAATTGCAGAAT 59.718 47.619 0.00 0.00 0.00 2.40
4024 4472 1.200483 CGCAATGCCTACTACTCACG 58.800 55.000 0.00 0.00 0.00 4.35
4053 4501 1.619827 ACGTCCGAGTTGGTTATTGGA 59.380 47.619 0.00 0.00 39.52 3.53
4133 4581 5.106317 ACGTTTAGTAGACAATGGCCAAATG 60.106 40.000 10.96 15.36 0.00 2.32
4255 4704 5.293560 TGTGGCCATAGTTTTAAAAACTGC 58.706 37.500 9.72 0.00 0.00 4.40
4264 4713 7.573710 TGAGATATACTTGTGGCCATAGTTTT 58.426 34.615 23.49 15.74 0.00 2.43
4307 4756 2.379972 ACCACAAATCACGTTTTCCCA 58.620 42.857 0.00 0.00 0.00 4.37
4370 4820 0.602905 ACGGTAAGTGACTTGGCAGC 60.603 55.000 8.33 0.00 0.00 5.25
4643 5096 3.867771 CTCTGCGGAGTCTTGTGC 58.132 61.111 14.84 0.00 35.03 4.57
4802 5256 1.945394 CTTGCAGTGTGCTTCTGACTT 59.055 47.619 0.00 0.00 45.31 3.01
4867 5321 2.299013 AGTGTTCGCAGTGATTACCTGA 59.701 45.455 0.00 0.00 0.00 3.86
4905 5359 1.474498 CCAAACATACCGGTAGGAGGC 60.474 57.143 31.44 0.00 41.02 4.70
5123 5588 1.881973 CTTTGTTTGGCAGCTGCTCTA 59.118 47.619 35.82 20.50 41.70 2.43
5188 5653 2.279918 GCGTCGACCCTTGTGTGT 60.280 61.111 10.58 0.00 0.00 3.72
5252 5718 0.546122 TGTCTTGGCACAGTCACCTT 59.454 50.000 0.00 0.00 42.39 3.50
5438 5904 2.677003 CGTTGCGTGCCGAATTCCT 61.677 57.895 0.00 0.00 0.00 3.36
5729 6679 7.627340 CAATACATTTATACGTCAACAGGGAC 58.373 38.462 0.00 0.00 34.42 4.46
5732 6682 6.260050 AGGCAATACATTTATACGTCAACAGG 59.740 38.462 0.00 0.00 0.00 4.00
5740 6690 9.130312 GAAGAGACTAGGCAATACATTTATACG 57.870 37.037 0.00 0.00 0.00 3.06
5770 6720 5.538053 TCAATGCAACCAAAAGACCAATCTA 59.462 36.000 0.00 0.00 33.57 1.98
5821 6771 3.571119 CAAGACCGCTTGGCTCTG 58.429 61.111 0.00 0.00 46.13 3.35
5850 6800 3.058160 CCGGAAGTGGGCTGCAAG 61.058 66.667 0.00 0.00 0.00 4.01
5851 6801 3.842925 GACCGGAAGTGGGCTGCAA 62.843 63.158 9.46 0.00 32.64 4.08
5852 6802 4.329545 GACCGGAAGTGGGCTGCA 62.330 66.667 9.46 0.00 32.64 4.41
5854 6804 3.636231 TGGACCGGAAGTGGGCTG 61.636 66.667 9.46 0.00 37.14 4.85
5855 6805 3.637273 GTGGACCGGAAGTGGGCT 61.637 66.667 9.46 0.00 37.14 5.19
5857 6807 2.669777 AAACGTGGACCGGAAGTGGG 62.670 60.000 9.46 0.00 42.24 4.61
5864 6829 2.435410 GGCCTAAACGTGGACCGG 60.435 66.667 0.00 0.00 42.24 5.28
5882 6847 3.633094 CTCACGTGTGGCTCCCTCG 62.633 68.421 16.51 0.00 0.00 4.63
5901 6866 5.155278 ACATTTATACGTCAACACTCCCA 57.845 39.130 0.00 0.00 0.00 4.37
5918 6883 5.357032 CCGGAAAAGACTAGGCAATACATTT 59.643 40.000 0.00 0.00 0.00 2.32
5944 6917 3.554752 GCTCTAGCCAATGCAACCAAAAA 60.555 43.478 0.00 0.00 41.13 1.94
5960 6933 4.358851 GAGTGTAGAAGTGCATGCTCTAG 58.641 47.826 21.70 0.00 0.00 2.43
6034 7011 3.050275 GTGGTTCGTGCAGGAGCC 61.050 66.667 28.98 28.98 41.13 4.70
6080 7364 3.567397 TCATTTTTCCTTTCGGGTTCCA 58.433 40.909 0.00 0.00 36.25 3.53
6118 7402 1.133823 ACAACTTCATGTGCTCCACCA 60.134 47.619 0.00 0.00 32.73 4.17
6266 7837 7.092716 TCGGTCAAAAGGTTATACACTTAGAC 58.907 38.462 0.00 0.00 34.15 2.59
6273 7844 5.106078 GGCATTTCGGTCAAAAGGTTATACA 60.106 40.000 0.00 0.00 0.00 2.29
6307 7880 3.389983 AGTGAGTACTGGTTTGCCTGTAA 59.610 43.478 0.00 0.00 46.22 2.41
6326 7899 9.608617 GCAGATCACATATTCAATATCAAAGTG 57.391 33.333 0.00 0.94 0.00 3.16
6327 7900 8.790718 GGCAGATCACATATTCAATATCAAAGT 58.209 33.333 0.00 0.00 0.00 2.66
6328 7901 9.011095 AGGCAGATCACATATTCAATATCAAAG 57.989 33.333 0.00 0.00 0.00 2.77
6491 8064 5.219343 ACCTAACTAACGCTACCAAACTT 57.781 39.130 0.00 0.00 0.00 2.66
6511 8084 6.458232 AGTCATGTAGATGAGTAGTTGACC 57.542 41.667 8.39 0.00 40.00 4.02
6613 8191 6.892485 TGTCCATAGAATGACTTCATGTGAT 58.108 36.000 0.00 0.00 36.56 3.06
6674 8252 5.620654 CGGATTGGTTACTACGAGAGAAACA 60.621 44.000 0.00 0.00 0.00 2.83
6698 8276 3.735746 GCACAACAGGAAAATACAGCAAC 59.264 43.478 0.00 0.00 0.00 4.17
6701 8279 3.641437 TGCACAACAGGAAAATACAGC 57.359 42.857 0.00 0.00 0.00 4.40
6713 8291 5.278758 GGAAGCTAAGGTATTTTGCACAACA 60.279 40.000 0.00 0.00 39.56 3.33
6819 8398 8.510243 AATATCATGTCAATAAGTCTGCACAA 57.490 30.769 0.00 0.00 0.00 3.33
6999 8580 2.417339 TCCAGAAACTCGAACACTCG 57.583 50.000 0.00 0.00 46.87 4.18
7278 8859 1.098050 AGATCGGTTCAGCAAATGCC 58.902 50.000 0.94 0.00 43.38 4.40
7292 8873 7.332678 TGGAAAGATAACATGCATGATAGATCG 59.667 37.037 32.75 4.14 0.00 3.69
7385 8966 5.178252 CAGTTCATTGTAGACTGTGTTGAGG 59.822 44.000 0.00 0.00 0.00 3.86
7393 8974 7.043125 CCGATGTTATCAGTTCATTGTAGACTG 60.043 40.741 9.66 9.66 0.00 3.51
7411 8999 4.693283 CAGAGAGGCAATAACCGATGTTA 58.307 43.478 0.00 0.00 41.03 2.41
7479 9067 1.472878 GGAAAGCTTTTCCCCGTCATC 59.527 52.381 14.05 0.00 32.48 2.92
7666 9265 5.524535 GCCCTTATCATCTACTCCCTCTAT 58.475 45.833 0.00 0.00 0.00 1.98
7695 9335 1.668101 GGTCGGTTGTGTTTTGGCCA 61.668 55.000 0.00 0.00 0.00 5.36
7710 9350 8.017587 TGAATCATTATTGTTGATATCGGTCG 57.982 34.615 0.00 0.00 33.52 4.79
7756 9396 6.367422 CAGTCAATTGAGTTCTAGACACCTTC 59.633 42.308 13.25 0.00 0.00 3.46
7786 9428 1.289800 CGTCACTCGACCGAGACTGA 61.290 60.000 24.03 15.50 44.53 3.41
7826 9470 2.835431 ATCTAGCCGTGCCGCTCT 60.835 61.111 0.00 0.00 40.39 4.09
7888 9538 1.221414 GGATGCAGCGTTAGATGTCC 58.779 55.000 0.00 0.00 35.92 4.02
7893 9543 2.556622 TCATATCGGATGCAGCGTTAGA 59.443 45.455 0.00 0.00 0.00 2.10
7911 9561 4.827692 TGACGGTTGTAGCATTTAGTCAT 58.172 39.130 0.00 0.00 33.20 3.06
7958 9608 2.046411 TCAATCGTGGCATGCCGT 60.046 55.556 30.87 14.51 39.42 5.68
7960 9610 2.040213 CTCGTCAATCGTGGCATGCC 62.040 60.000 30.54 30.54 40.80 4.40
7963 9613 4.521075 CCTCGTCAATCGTGGCAT 57.479 55.556 0.00 0.00 44.23 4.40
7969 9619 0.179100 ACATCTGCCCTCGTCAATCG 60.179 55.000 0.00 0.00 41.41 3.34
7974 9624 2.474816 GTCATAACATCTGCCCTCGTC 58.525 52.381 0.00 0.00 0.00 4.20
7985 9635 5.391950 GCATTTTGTCTCACGGTCATAACAT 60.392 40.000 0.00 0.00 0.00 2.71
7990 9640 2.485426 CAGCATTTTGTCTCACGGTCAT 59.515 45.455 0.00 0.00 0.00 3.06
7995 9645 0.512518 TCGCAGCATTTTGTCTCACG 59.487 50.000 0.00 0.00 0.00 4.35
7999 9716 2.012673 GGATCTCGCAGCATTTTGTCT 58.987 47.619 0.00 0.00 0.00 3.41
8032 9749 2.447443 TGGAGATTCGTGCTAGACTGT 58.553 47.619 0.00 0.00 0.00 3.55
8038 9755 2.689553 TTGCATGGAGATTCGTGCTA 57.310 45.000 6.85 0.00 46.57 3.49


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

AutoCloner maintained by Alex Coulton.