Multiple sequence alignment - TraesCS6D01G186900

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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 TraesCS6D01G186900 chr6D 100.000 9937 0 0 1 9937 249457708 249447772 0.000000e+00 18351.0
1 TraesCS6D01G186900 chr6D 91.620 179 10 4 2966 3141 137159940 137159764 9.970000e-60 243.0
2 TraesCS6D01G186900 chr6D 90.164 183 13 4 2960 3140 418953964 418954143 6.000000e-57 233.0
3 TraesCS6D01G186900 chr6D 89.130 184 15 3 2960 3141 195484538 195484358 3.610000e-54 224.0
4 TraesCS6D01G186900 chr6D 89.888 178 12 4 2960 3133 348280287 348280462 3.610000e-54 224.0
5 TraesCS6D01G186900 chr6D 88.690 168 13 5 2969 3133 219787171 219787335 6.090000e-47 200.0
6 TraesCS6D01G186900 chr6B 96.320 8451 210 39 1012 9412 337239258 337230859 0.000000e+00 13790.0
7 TraesCS6D01G186900 chr6B 91.197 727 60 3 1 725 337279617 337278893 0.000000e+00 985.0
8 TraesCS6D01G186900 chr6B 86.076 395 32 9 7166 7546 222010312 222009927 4.320000e-108 403.0
9 TraesCS6D01G186900 chr6B 90.444 293 27 1 722 1014 337241782 337241491 1.570000e-102 385.0
10 TraesCS6D01G186900 chr6B 92.973 185 8 3 2960 3141 225525372 225525554 2.130000e-66 265.0
11 TraesCS6D01G186900 chr6B 82.188 320 45 9 3251 3562 279907953 279907638 2.130000e-66 265.0
12 TraesCS6D01G186900 chr6B 86.321 212 18 1 9478 9689 337230798 337230598 4.670000e-53 220.0
13 TraesCS6D01G186900 chr6B 76.203 395 83 6 3261 3649 701129526 701129915 2.190000e-46 198.0
14 TraesCS6D01G186900 chr6B 91.803 61 4 1 9396 9456 337230845 337230786 6.400000e-12 84.2
15 TraesCS6D01G186900 chr6A 97.427 6063 93 16 1012 7039 349510443 349516477 0.000000e+00 10274.0
16 TraesCS6D01G186900 chr6A 96.866 2329 48 9 7038 9357 349516638 349518950 0.000000e+00 3873.0
17 TraesCS6D01G186900 chr6A 90.909 550 47 2 467 1014 349494129 349494677 0.000000e+00 736.0
18 TraesCS6D01G186900 chr6A 92.111 469 36 1 1 469 349389343 349389810 0.000000e+00 660.0
19 TraesCS6D01G186900 chr6A 87.636 461 39 6 9478 9937 349519176 349519619 4.110000e-143 520.0
20 TraesCS6D01G186900 chr6A 94.142 239 11 2 9220 9456 349518951 349519188 2.640000e-95 361.0
21 TraesCS6D01G186900 chr6A 91.935 186 10 4 2960 3143 153373065 153372883 1.280000e-63 255.0
22 TraesCS6D01G186900 chr6A 84.462 251 37 2 7967 8216 595187540 595187291 7.710000e-61 246.0
23 TraesCS6D01G186900 chr6A 74.094 552 122 16 3 542 536036332 536035790 3.640000e-49 207.0
24 TraesCS6D01G186900 chr6A 80.769 260 49 1 3337 3596 611305447 611305189 1.690000e-47 202.0
25 TraesCS6D01G186900 chr2D 84.599 1383 141 33 6568 7896 133239543 133238179 0.000000e+00 1308.0
26 TraesCS6D01G186900 chr2D 87.308 717 71 9 6564 7270 284549082 284549788 0.000000e+00 802.0
27 TraesCS6D01G186900 chr2D 90.438 251 21 3 7967 8216 388833913 388833665 2.680000e-85 327.0
28 TraesCS6D01G186900 chr2D 88.372 258 26 4 7960 8216 380416785 380416531 3.490000e-79 307.0
29 TraesCS6D01G186900 chr2D 78.652 445 69 12 3315 3744 174248600 174248167 1.270000e-68 272.0
30 TraesCS6D01G186900 chr2D 77.405 447 72 14 3243 3684 603656516 603656938 1.290000e-58 239.0
31 TraesCS6D01G186900 chr7A 84.226 1008 118 20 6564 7546 195407999 195408990 0.000000e+00 942.0
32 TraesCS6D01G186900 chr7A 80.723 664 106 18 44 699 300365869 300366518 1.930000e-136 497.0
33 TraesCS6D01G186900 chr7A 92.188 192 11 3 2962 3151 83785009 83784820 1.650000e-67 268.0
34 TraesCS6D01G186900 chr7A 97.222 36 0 1 6345 6380 462341092 462341058 1.080000e-04 60.2
35 TraesCS6D01G186900 chr4A 87.887 710 71 7 6571 7270 357684271 357684975 0.000000e+00 821.0
36 TraesCS6D01G186900 chr4A 87.606 710 73 7 6571 7270 48292195 48292899 0.000000e+00 809.0
37 TraesCS6D01G186900 chr4A 87.169 717 76 8 6564 7270 75433468 75434178 0.000000e+00 800.0
38 TraesCS6D01G186900 chr1D 87.308 717 76 7 6564 7270 107620380 107621091 0.000000e+00 806.0
39 TraesCS6D01G186900 chr1D 89.007 282 29 2 7266 7546 218902068 218902348 2.050000e-91 348.0
40 TraesCS6D01G186900 chr1D 89.020 255 25 3 7960 8213 33747864 33747612 7.490000e-81 313.0
41 TraesCS6D01G186900 chr1D 92.818 181 8 4 2960 3138 86918509 86918686 3.560000e-64 257.0
42 TraesCS6D01G186900 chr1D 91.257 183 11 3 2960 3140 317429454 317429633 2.770000e-60 244.0
43 TraesCS6D01G186900 chr1D 75.561 446 90 13 3255 3689 397060027 397059590 1.690000e-47 202.0
44 TraesCS6D01G186900 chr2A 87.169 717 77 7 6564 7270 101856695 101855984 0.000000e+00 800.0
45 TraesCS6D01G186900 chr2A 87.258 361 42 3 7539 7896 716167645 716168004 9.290000e-110 409.0
46 TraesCS6D01G186900 chr2A 90.421 261 23 2 7272 7531 569200098 569199839 9.560000e-90 342.0
47 TraesCS6D01G186900 chrUn 99.490 392 2 0 5413 5804 479294285 479294676 0.000000e+00 713.0
48 TraesCS6D01G186900 chrUn 76.835 436 76 19 3240 3662 82609287 82608864 1.300000e-53 222.0
49 TraesCS6D01G186900 chrUn 75.964 441 80 18 3331 3755 82617790 82617360 4.710000e-48 204.0
50 TraesCS6D01G186900 chrUn 91.946 149 7 4 2964 3110 267270755 267270610 4.710000e-48 204.0
51 TraesCS6D01G186900 chrUn 87.363 182 16 4 2960 3138 416761379 416761556 1.690000e-47 202.0
52 TraesCS6D01G186900 chrUn 87.363 182 16 4 2960 3138 438675664 438675841 1.690000e-47 202.0
53 TraesCS6D01G186900 chrUn 91.275 149 8 4 2964 3110 186911003 186910858 2.190000e-46 198.0
54 TraesCS6D01G186900 chrUn 94.167 120 5 1 2960 3077 477203734 477203853 2.200000e-41 182.0
55 TraesCS6D01G186900 chrUn 88.060 134 14 1 3002 3135 65976804 65976935 3.720000e-34 158.0
56 TraesCS6D01G186900 chrUn 83.851 161 19 5 2980 3138 60420956 60421111 8.040000e-31 147.0
57 TraesCS6D01G186900 chrUn 92.708 96 5 1 2964 3057 400989388 400989483 4.840000e-28 137.0
58 TraesCS6D01G186900 chr7B 81.667 720 111 19 1 708 616639301 616640011 6.690000e-161 579.0
59 TraesCS6D01G186900 chr7B 80.186 646 103 20 42 675 532672334 532671702 2.530000e-125 460.0
60 TraesCS6D01G186900 chr7B 77.358 265 51 6 3399 3662 67684942 67685198 2.240000e-31 148.0
61 TraesCS6D01G186900 chr7B 75.904 332 57 14 3254 3578 323488439 323488754 2.240000e-31 148.0
62 TraesCS6D01G186900 chr7B 86.747 83 10 1 6344 6425 3894366 3894284 3.820000e-14 91.6
63 TraesCS6D01G186900 chr7B 84.286 70 9 1 6348 6415 719076460 719076529 6.440000e-07 67.6
64 TraesCS6D01G186900 chr7B 87.931 58 3 3 6345 6400 413108295 413108240 2.320000e-06 65.8
65 TraesCS6D01G186900 chr2B 77.922 1001 169 43 1 976 396923676 396924649 2.410000e-160 577.0
66 TraesCS6D01G186900 chr2B 81.389 720 108 21 1 708 60156802 60157507 1.870000e-156 564.0
67 TraesCS6D01G186900 chr2B 89.014 355 31 7 7548 7896 451827803 451827451 5.510000e-117 433.0
68 TraesCS6D01G186900 chr2B 78.634 454 83 11 3245 3690 579581380 579580933 1.260000e-73 289.0
69 TraesCS6D01G186900 chr2B 86.441 59 7 1 6425 6483 630743859 630743916 8.330000e-06 63.9
70 TraesCS6D01G186900 chr4D 90.300 433 41 1 4 436 36445195 36444764 5.210000e-157 566.0
71 TraesCS6D01G186900 chr4D 90.069 433 42 1 4 436 36550836 36550405 2.420000e-155 560.0
72 TraesCS6D01G186900 chr4D 89.136 405 43 1 4 408 36451535 36451132 4.140000e-138 503.0
73 TraesCS6D01G186900 chr4D 90.385 260 23 2 7273 7531 248938516 248938258 3.440000e-89 340.0
74 TraesCS6D01G186900 chr4D 88.213 263 23 5 7960 8216 346467927 346468187 3.490000e-79 307.0
75 TraesCS6D01G186900 chr4D 93.478 184 7 4 2960 3141 482703448 482703628 1.650000e-67 268.0
76 TraesCS6D01G186900 chr4D 92.896 183 7 5 2965 3145 100798505 100798683 2.750000e-65 261.0
77 TraesCS6D01G186900 chr4D 91.398 186 10 5 2961 3144 18694834 18694653 5.960000e-62 250.0
78 TraesCS6D01G186900 chr4D 91.005 189 12 4 2960 3146 23322897 23322712 5.960000e-62 250.0
79 TraesCS6D01G186900 chr4D 92.135 178 9 3 2965 3140 65536120 65536294 7.710000e-61 246.0
80 TraesCS6D01G186900 chr4D 90.449 178 11 4 2960 3133 469604531 469604706 7.760000e-56 230.0
81 TraesCS6D01G186900 chr4D 84.091 132 17 2 3345 3473 109913916 109913786 3.770000e-24 124.0
82 TraesCS6D01G186900 chr3B 81.250 720 115 19 1 708 720190184 720189473 1.870000e-156 564.0
83 TraesCS6D01G186900 chr3D 79.975 789 132 22 24 799 5483765 5482990 8.720000e-155 558.0
84 TraesCS6D01G186900 chr3D 87.705 366 37 5 7539 7897 324775173 324775537 4.290000e-113 420.0
85 TraesCS6D01G186900 chr3D 85.866 283 33 6 7960 8241 38502638 38502362 2.710000e-75 294.0
86 TraesCS6D01G186900 chr3D 77.381 504 87 15 3249 3737 543958305 543958796 3.540000e-69 274.0
87 TraesCS6D01G186900 chr3D 93.889 180 6 4 2960 3137 422517617 422517793 5.920000e-67 267.0
88 TraesCS6D01G186900 chr5A 80.833 720 118 18 1 708 661245141 661245852 1.890000e-151 547.0
89 TraesCS6D01G186900 chr5A 88.550 262 26 4 7960 8219 441923168 441922909 2.080000e-81 315.0
90 TraesCS6D01G186900 chr5A 81.463 205 36 2 8014 8216 104255805 104255601 6.170000e-37 167.0
91 TraesCS6D01G186900 chr5A 83.133 83 13 1 6344 6425 691402369 691402451 3.850000e-09 75.0
92 TraesCS6D01G186900 chr5A 100.000 29 0 0 6348 6376 401139687 401139715 5.000000e-03 54.7
93 TraesCS6D01G186900 chr5D 79.070 817 141 24 2 804 11423606 11422806 1.470000e-147 534.0
94 TraesCS6D01G186900 chr5D 87.500 360 42 3 7539 7896 152753338 152753696 7.180000e-111 412.0
95 TraesCS6D01G186900 chr5D 89.123 285 26 4 7266 7546 522047672 522047955 5.710000e-92 350.0
96 TraesCS6D01G186900 chr5D 88.889 261 22 7 7960 8216 360542116 360541859 2.080000e-81 315.0
97 TraesCS6D01G186900 chr5D 92.265 181 9 4 2960 3138 468170646 468170469 1.660000e-62 252.0
98 TraesCS6D01G186900 chr5D 77.064 218 44 6 3294 3508 378895203 378894989 4.870000e-23 121.0
99 TraesCS6D01G186900 chr5D 83.544 79 11 2 3261 3339 436351723 436351799 1.380000e-08 73.1
100 TraesCS6D01G186900 chr4B 80.030 671 111 18 42 706 63934583 63933930 9.030000e-130 475.0
101 TraesCS6D01G186900 chr4B 79.260 622 107 18 42 657 63798333 63797728 2.000000e-111 414.0
102 TraesCS6D01G186900 chr4B 92.432 185 9 4 2960 3141 612274157 612274339 9.900000e-65 259.0
103 TraesCS6D01G186900 chr4B 90.323 186 13 4 2961 3144 30730581 30730399 1.290000e-58 239.0
104 TraesCS6D01G186900 chr7D 87.819 353 37 5 7548 7896 466053788 466053438 9.290000e-110 409.0
105 TraesCS6D01G186900 chr7D 75.399 439 86 12 3254 3678 14781842 14781412 1.020000e-44 193.0
106 TraesCS6D01G186900 chr7D 83.962 106 13 3 7969 8072 264379396 264379499 2.280000e-16 99.0
107 TraesCS6D01G186900 chr7D 87.719 57 4 3 6345 6400 403782696 403782642 8.330000e-06 63.9
108 TraesCS6D01G186900 chr5B 78.648 651 106 27 69 706 113800609 113801239 1.550000e-107 401.0
109 TraesCS6D01G186900 chr5B 89.362 282 24 5 7266 7542 474781719 474781999 5.710000e-92 350.0
110 TraesCS6D01G186900 chr5B 93.370 181 7 4 2960 3138 574956622 574956445 7.650000e-66 263.0
111 TraesCS6D01G186900 chr5B 76.654 257 52 7 3288 3540 67965443 67965695 1.740000e-27 135.0
112 TraesCS6D01G186900 chr5B 79.720 143 26 3 7967 8108 224323485 224323625 6.350000e-17 100.0
113 TraesCS6D01G186900 chr3A 85.459 392 43 9 7539 7917 438363009 438363399 7.230000e-106 396.0
114 TraesCS6D01G186900 chr3A 92.432 185 9 4 2960 3142 353624419 353624600 9.900000e-65 259.0
115 TraesCS6D01G186900 chr3A 97.436 39 1 0 7900 7938 605853507 605853545 6.440000e-07 67.6
116 TraesCS6D01G186900 chr1B 80.550 509 79 11 3245 3737 666553722 666553218 3.390000e-99 374.0
117 TraesCS6D01G186900 chr1B 80.317 315 42 9 7900 8212 111049386 111049090 4.670000e-53 220.0
118 TraesCS6D01G186900 chr1B 75.982 433 87 9 3262 3687 676394130 676394552 3.640000e-49 207.0
119 TraesCS6D01G186900 chr1A 88.189 254 26 4 7960 8210 154011371 154011623 5.830000e-77 300.0
120 TraesCS6D01G186900 chr1A 90.811 185 12 3 2960 3142 398450568 398450749 9.970000e-60 243.0


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 TraesCS6D01G186900 chr6D 249447772 249457708 9936 True 18351.0 18351 100.00000 1 9937 1 chr6D.!!$R3 9936
1 TraesCS6D01G186900 chr6B 337230598 337241782 11184 True 3619.8 13790 91.22200 722 9689 4 chr6B.!!$R4 8967
2 TraesCS6D01G186900 chr6B 337278893 337279617 724 True 985.0 985 91.19700 1 725 1 chr6B.!!$R3 724
3 TraesCS6D01G186900 chr6A 349510443 349519619 9176 False 3757.0 10274 94.01775 1012 9937 4 chr6A.!!$F3 8925
4 TraesCS6D01G186900 chr6A 349494129 349494677 548 False 736.0 736 90.90900 467 1014 1 chr6A.!!$F2 547
5 TraesCS6D01G186900 chr6A 536035790 536036332 542 True 207.0 207 74.09400 3 542 1 chr6A.!!$R2 539
6 TraesCS6D01G186900 chr2D 133238179 133239543 1364 True 1308.0 1308 84.59900 6568 7896 1 chr2D.!!$R1 1328
7 TraesCS6D01G186900 chr2D 284549082 284549788 706 False 802.0 802 87.30800 6564 7270 1 chr2D.!!$F1 706
8 TraesCS6D01G186900 chr7A 195407999 195408990 991 False 942.0 942 84.22600 6564 7546 1 chr7A.!!$F1 982
9 TraesCS6D01G186900 chr7A 300365869 300366518 649 False 497.0 497 80.72300 44 699 1 chr7A.!!$F2 655
10 TraesCS6D01G186900 chr4A 357684271 357684975 704 False 821.0 821 87.88700 6571 7270 1 chr4A.!!$F3 699
11 TraesCS6D01G186900 chr4A 48292195 48292899 704 False 809.0 809 87.60600 6571 7270 1 chr4A.!!$F1 699
12 TraesCS6D01G186900 chr4A 75433468 75434178 710 False 800.0 800 87.16900 6564 7270 1 chr4A.!!$F2 706
13 TraesCS6D01G186900 chr1D 107620380 107621091 711 False 806.0 806 87.30800 6564 7270 1 chr1D.!!$F2 706
14 TraesCS6D01G186900 chr2A 101855984 101856695 711 True 800.0 800 87.16900 6564 7270 1 chr2A.!!$R1 706
15 TraesCS6D01G186900 chr7B 616639301 616640011 710 False 579.0 579 81.66700 1 708 1 chr7B.!!$F3 707
16 TraesCS6D01G186900 chr7B 532671702 532672334 632 True 460.0 460 80.18600 42 675 1 chr7B.!!$R3 633
17 TraesCS6D01G186900 chr2B 396923676 396924649 973 False 577.0 577 77.92200 1 976 1 chr2B.!!$F2 975
18 TraesCS6D01G186900 chr2B 60156802 60157507 705 False 564.0 564 81.38900 1 708 1 chr2B.!!$F1 707
19 TraesCS6D01G186900 chr3B 720189473 720190184 711 True 564.0 564 81.25000 1 708 1 chr3B.!!$R1 707
20 TraesCS6D01G186900 chr3D 5482990 5483765 775 True 558.0 558 79.97500 24 799 1 chr3D.!!$R1 775
21 TraesCS6D01G186900 chr5A 661245141 661245852 711 False 547.0 547 80.83300 1 708 1 chr5A.!!$F2 707
22 TraesCS6D01G186900 chr5D 11422806 11423606 800 True 534.0 534 79.07000 2 804 1 chr5D.!!$R1 802
23 TraesCS6D01G186900 chr4B 63933930 63934583 653 True 475.0 475 80.03000 42 706 1 chr4B.!!$R3 664
24 TraesCS6D01G186900 chr4B 63797728 63798333 605 True 414.0 414 79.26000 42 657 1 chr4B.!!$R2 615
25 TraesCS6D01G186900 chr5B 113800609 113801239 630 False 401.0 401 78.64800 69 706 1 chr5B.!!$F2 637
26 TraesCS6D01G186900 chr1B 666553218 666553722 504 True 374.0 374 80.55000 3245 3737 1 chr1B.!!$R2 492

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
252 258 0.103026 CATCGTCTTGGGAGCATCGA 59.897 55.000 0.00 0.00 34.37 3.59 F
483 499 0.108281 GTGACGCCTAAGGAGGGAAC 60.108 60.000 0.00 0.00 43.97 3.62 F
699 735 0.769247 ACCAACACCCAACTCCTACC 59.231 55.000 0.00 0.00 0.00 3.18 F
713 756 1.064166 TCCTACCCGGTCGAAGAAGAT 60.064 52.381 0.00 0.00 39.69 2.40 F
2168 4457 1.070758 TGGACTTGTCTTCCAGAGTGC 59.929 52.381 0.61 0.00 38.28 4.40 F
3089 5379 0.109913 AAAGTGGTCGAACCCTTCCC 59.890 55.000 0.00 0.00 37.50 3.97 F
3090 5380 0.767060 AAGTGGTCGAACCCTTCCCT 60.767 55.000 0.00 0.00 37.50 4.20 F
3795 6122 1.153046 CCAACACACCCACCTCGTT 60.153 57.895 0.00 0.00 0.00 3.85 F
5707 8064 0.736672 GGAACCTTCTCCGACTTCGC 60.737 60.000 0.00 0.00 38.18 4.70 F
6724 9081 0.752009 ACGGAGCAGATCGCCTTCTA 60.752 55.000 6.02 0.00 44.04 2.10 F
7695 10270 0.609957 TTGGGGTCAATGCTGCAGAG 60.610 55.000 20.43 3.58 0.00 3.35 F
8130 10707 0.527600 TTAGCTATGCACGTGCGAGG 60.528 55.000 33.22 24.67 45.83 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2103 4392 3.154710 CATGAGCATGGCAGGAACATAT 58.845 45.455 1.99 0.00 35.24 1.78 R
2372 4661 3.519913 CCTTACTTCAAACTCCTAGCCCT 59.480 47.826 0.00 0.00 0.00 5.19 R
2706 4996 1.308069 GCAGGTGTGCCATTCGTGAT 61.308 55.000 0.00 0.00 44.72 3.06 R
2747 5037 1.155155 GGTTGGGAGGGGCTTTTGA 59.845 57.895 0.00 0.00 0.00 2.69 R
3530 5828 0.174389 CGTAGTGTGATGCTCCAGCT 59.826 55.000 0.00 0.00 42.66 4.24 R
4193 6528 1.840635 AGGCTGTCAGGAATAACTCCC 59.159 52.381 1.14 0.00 46.81 4.30 R
4875 7232 4.628661 AGACCTTATAGGGGTGAAGAGT 57.371 45.455 5.79 0.00 40.58 3.24 R
5816 8173 1.298859 GGAAGCCGCATTCAGAACGT 61.299 55.000 0.00 0.00 0.00 3.99 R
7433 9989 0.039764 AAGGGCTCAAAGCTAACCCC 59.960 55.000 5.97 3.46 41.99 4.95 R
7868 10445 1.000274 GAACTGTTGGACATGTTGCCC 60.000 52.381 0.00 0.00 0.00 5.36 R
8921 11500 1.002069 TTGGTCATCTTGGGCCAGAT 58.998 50.000 6.23 9.44 33.44 2.90 R
9774 12526 0.751643 ACCGGCAATTGCATCTACCC 60.752 55.000 30.32 11.22 44.36 3.69 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
22 23 2.222027 GTAGCAAGAACAGCACAACCT 58.778 47.619 0.00 0.00 0.00 3.50
252 258 0.103026 CATCGTCTTGGGAGCATCGA 59.897 55.000 0.00 0.00 34.37 3.59
296 302 3.371097 GATCAACTCGGGCCAGCGA 62.371 63.158 4.39 4.15 0.00 4.93
417 430 2.358737 CGGACCAAGGCTTTCGCT 60.359 61.111 0.00 0.00 36.09 4.93
442 455 1.070105 CCACAACCCGACCGAGAAA 59.930 57.895 0.00 0.00 0.00 2.52
449 462 1.511768 CCGACCGAGAAAGGGAGAC 59.488 63.158 0.00 0.00 35.02 3.36
483 499 0.108281 GTGACGCCTAAGGAGGGAAC 60.108 60.000 0.00 0.00 43.97 3.62
523 550 1.608025 CGTCACTAGCTCCAGCCAAAA 60.608 52.381 0.00 0.00 43.38 2.44
581 608 1.211949 CACCCCTACCATCGGATTTGT 59.788 52.381 0.00 0.00 0.00 2.83
633 669 2.274437 CAACACCTCCTCGTCATGATG 58.726 52.381 8.74 8.74 0.00 3.07
699 735 0.769247 ACCAACACCCAACTCCTACC 59.231 55.000 0.00 0.00 0.00 3.18
713 756 1.064166 TCCTACCCGGTCGAAGAAGAT 60.064 52.381 0.00 0.00 39.69 2.40
750 794 1.451567 CTCCAGCACTGCCCAGATG 60.452 63.158 1.69 0.00 0.00 2.90
822 866 2.519541 CTCGGAGCGATCCAGGGA 60.520 66.667 21.44 8.09 34.61 4.20
856 900 2.136878 CCATAGCACCTCGCCTCCT 61.137 63.158 0.00 0.00 44.04 3.69
878 925 4.112341 GCGACGAGCGTACCCACT 62.112 66.667 0.00 0.00 43.41 4.00
1025 3311 2.168106 CCTCTGCAGCTTGTATCTGTCT 59.832 50.000 9.47 0.00 34.21 3.41
1374 3660 4.523943 TCTGGATGCAATGCACTAGTTTTT 59.476 37.500 11.23 0.00 40.85 1.94
1399 3685 5.865085 TCAAACTGTAGACTGGCACTTAAT 58.135 37.500 0.00 0.00 0.00 1.40
1414 3700 6.772233 TGGCACTTAATACATCTTACATGCAT 59.228 34.615 0.00 0.00 0.00 3.96
1504 3791 4.421948 ACTCTAATCGTTTGGTGTCGATC 58.578 43.478 0.00 0.00 44.29 3.69
1831 4119 2.025155 TCGAGTAGCCCTTCATCAGTC 58.975 52.381 0.00 0.00 0.00 3.51
1846 4134 4.162888 TCATCAGTCTGTGCCTGATATTGT 59.837 41.667 0.00 0.00 45.52 2.71
2103 4392 5.117355 ACTTCGAACTATGTCTTTCGTCA 57.883 39.130 0.00 0.00 44.00 4.35
2109 4398 7.255569 TCGAACTATGTCTTTCGTCATATGTT 58.744 34.615 1.90 0.00 44.00 2.71
2168 4457 1.070758 TGGACTTGTCTTCCAGAGTGC 59.929 52.381 0.61 0.00 38.28 4.40
2706 4996 4.020573 ACCCTTCACACGAGTTATGATTGA 60.021 41.667 0.00 0.00 0.00 2.57
2747 5037 6.252995 TGCCTCCTAAATTTTACTCCAATGT 58.747 36.000 0.00 0.00 0.00 2.71
2866 5156 3.056821 CCGTACAGACAAGATCCTTGTGA 60.057 47.826 16.01 0.00 31.96 3.58
2915 5205 5.232838 CGATGAAGCTTCAAATATTTTGGGC 59.767 40.000 31.55 9.18 41.13 5.36
3037 5327 3.751767 TGGAAACAGCCTCTTGCAT 57.248 47.368 0.00 0.00 44.83 3.96
3089 5379 0.109913 AAAGTGGTCGAACCCTTCCC 59.890 55.000 0.00 0.00 37.50 3.97
3090 5380 0.767060 AAGTGGTCGAACCCTTCCCT 60.767 55.000 0.00 0.00 37.50 4.20
3169 5461 5.280011 CCAGAAACTCTGTAACCTATGTGGT 60.280 44.000 3.15 0.00 46.46 4.16
3171 5463 7.364762 CCAGAAACTCTGTAACCTATGTGGTAT 60.365 40.741 3.15 0.00 44.97 2.73
3172 5464 7.492669 CAGAAACTCTGTAACCTATGTGGTATG 59.507 40.741 0.00 0.00 43.04 2.39
3530 5828 6.398095 TCTAGAAATCGCTGAAGAAACATCA 58.602 36.000 0.00 0.00 0.00 3.07
3698 6006 7.118390 CCTTGATAGACACACAAACTAAAGAGG 59.882 40.741 0.00 0.00 0.00 3.69
3784 6100 5.629133 GCTGGATAGACCTTATTCCAACACA 60.629 44.000 0.00 0.00 39.86 3.72
3795 6122 1.153046 CCAACACACCCACCTCGTT 60.153 57.895 0.00 0.00 0.00 3.85
3829 6156 4.500205 GGGAAACAAAACGTTAGGGAAAGG 60.500 45.833 0.00 0.00 36.59 3.11
3834 6161 6.474140 ACAAAACGTTAGGGAAAGGAAAAT 57.526 33.333 0.00 0.00 0.00 1.82
3878 6205 2.540910 TGGGAGAGGAGGGGGACT 60.541 66.667 0.00 0.00 0.00 3.85
4063 6398 7.313646 TCCTCACTTTTAAATGTCTCTCTACG 58.686 38.462 3.86 0.00 0.00 3.51
4193 6528 6.073276 TGGATTTGTATCTGAACAAGTTCACG 60.073 38.462 11.34 8.34 43.90 4.35
4389 6745 5.909621 ATGAGGCTTACGAACTAGTGTTA 57.090 39.130 0.00 0.00 36.39 2.41
4569 6925 4.463539 TGTCATGCAGATTAAGTGCCAATT 59.536 37.500 9.49 0.00 40.43 2.32
4708 7065 3.630769 GTCGGGTCAAATTCCTAAATCCC 59.369 47.826 0.00 0.00 0.00 3.85
4875 7232 3.181329 TCCATCTACTGGCTCCTTTTCA 58.819 45.455 0.00 0.00 45.52 2.69
5159 7516 2.094675 AGATGGCACTTTGGTACATGC 58.905 47.619 0.00 0.00 40.71 4.06
5707 8064 0.736672 GGAACCTTCTCCGACTTCGC 60.737 60.000 0.00 0.00 38.18 4.70
5804 8161 3.432592 GCGAGGTACTTTGTTCTTTCCTC 59.567 47.826 0.00 0.00 41.55 3.71
5816 8173 9.720769 CTTTGTTCTTTCCTCTAATACCTAACA 57.279 33.333 0.00 0.00 0.00 2.41
6334 8691 7.175119 GCTTCTTGACTGGGTAAATACTTCTTT 59.825 37.037 0.00 0.00 0.00 2.52
6390 8747 7.929785 AGAAATATTTCAGCCATAGCCAAAATG 59.070 33.333 26.02 0.00 39.61 2.32
6455 8812 3.738791 GCGATTTTGGTTTTCATTTCGGT 59.261 39.130 0.00 0.00 0.00 4.69
6489 8846 7.599998 CCAAAGTTTCCACTTGAATTAGATTGG 59.400 37.037 0.00 0.00 42.89 3.16
6666 9023 3.382278 AGATGGCCAAGATCTGAGAGAA 58.618 45.455 10.96 0.00 0.00 2.87
6724 9081 0.752009 ACGGAGCAGATCGCCTTCTA 60.752 55.000 6.02 0.00 44.04 2.10
6837 9196 3.181490 TGGACGACTCCTTTGATGATACG 60.181 47.826 0.00 0.00 37.48 3.06
7082 9609 4.326548 GCAGGATGTTCGAAGTTGTACTAC 59.673 45.833 0.00 0.00 39.31 2.73
7083 9610 4.863131 CAGGATGTTCGAAGTTGTACTACC 59.137 45.833 0.00 0.00 0.00 3.18
7432 9988 6.757897 TTGATTAAAATAGGACTGCACCAG 57.242 37.500 0.00 0.00 37.52 4.00
7433 9989 5.192927 TGATTAAAATAGGACTGCACCAGG 58.807 41.667 0.00 0.00 35.51 4.45
7460 10018 6.602009 GGTTAGCTTTGAGCCCTTATCTTTTA 59.398 38.462 0.00 0.00 43.77 1.52
7475 10033 9.627123 CCTTATCTTTTACTTTGGTGATGGATA 57.373 33.333 0.00 0.00 0.00 2.59
7695 10270 0.609957 TTGGGGTCAATGCTGCAGAG 60.610 55.000 20.43 3.58 0.00 3.35
7760 10335 0.611618 ATGGATGAAGTGGCGCCAAA 60.612 50.000 34.66 17.93 31.53 3.28
7840 10417 3.006940 GGCGATTTGACCTGTGATGTTA 58.993 45.455 0.00 0.00 0.00 2.41
7868 10445 4.414852 CGATGAATGTTGGCCAACTAAAG 58.585 43.478 40.40 24.09 41.67 1.85
8012 10589 2.169978 TGCTGATGATGTCAAGAGAGGG 59.830 50.000 0.00 0.00 36.14 4.30
8130 10707 0.527600 TTAGCTATGCACGTGCGAGG 60.528 55.000 33.22 24.67 45.83 4.63
8568 11147 3.633065 TGTATCACATGTGGGATGCATTG 59.367 43.478 25.16 0.00 43.85 2.82
8921 11500 4.124351 CTCCGCGCCGTGGAACTA 62.124 66.667 21.15 0.00 41.98 2.24
9202 11781 4.202050 GCAATGTGTTATTCTGTGATCCCC 60.202 45.833 0.00 0.00 0.00 4.81
9357 12078 6.332735 TGATATCGAGGGAGTAAATCACAG 57.667 41.667 0.00 0.00 31.63 3.66
9388 12109 2.976185 TCAAACCCTATCCAGTGTGTGA 59.024 45.455 0.00 0.00 0.00 3.58
9438 12189 0.813610 CCGGCTGACGCAAATGGATA 60.814 55.000 0.00 0.00 42.52 2.59
9442 12193 3.403038 GGCTGACGCAAATGGATATAGT 58.597 45.455 0.00 0.00 38.10 2.12
9443 12194 3.815401 GGCTGACGCAAATGGATATAGTT 59.185 43.478 0.00 0.00 38.10 2.24
9444 12195 4.275936 GGCTGACGCAAATGGATATAGTTT 59.724 41.667 0.00 0.00 38.10 2.66
9445 12196 5.221048 GGCTGACGCAAATGGATATAGTTTT 60.221 40.000 0.00 0.00 38.10 2.43
9446 12197 6.265577 GCTGACGCAAATGGATATAGTTTTT 58.734 36.000 0.00 0.00 35.78 1.94
9447 12198 6.197096 GCTGACGCAAATGGATATAGTTTTTG 59.803 38.462 0.00 0.00 35.78 2.44
9448 12199 7.151999 TGACGCAAATGGATATAGTTTTTGT 57.848 32.000 0.00 0.00 31.56 2.83
9449 12200 8.270080 TGACGCAAATGGATATAGTTTTTGTA 57.730 30.769 0.00 0.00 31.56 2.41
9450 12201 8.898761 TGACGCAAATGGATATAGTTTTTGTAT 58.101 29.630 0.00 0.00 31.56 2.29
9451 12202 9.169468 GACGCAAATGGATATAGTTTTTGTATG 57.831 33.333 0.00 0.00 31.56 2.39
9452 12203 7.647715 ACGCAAATGGATATAGTTTTTGTATGC 59.352 33.333 0.00 0.00 31.56 3.14
9453 12204 7.862372 CGCAAATGGATATAGTTTTTGTATGCT 59.138 33.333 0.00 0.00 31.56 3.79
9454 12205 9.533253 GCAAATGGATATAGTTTTTGTATGCTT 57.467 29.630 0.00 0.00 31.56 3.91
9476 12227 8.599774 TGCTTTTTGTCTATAGTTTTTGTTTGC 58.400 29.630 0.00 0.00 0.00 3.68
9498 12249 4.202010 GCTTTTTGTCTGTTTGAGTGGCTA 60.202 41.667 0.00 0.00 0.00 3.93
9507 12258 3.077359 GTTTGAGTGGCTAAGCAGATGT 58.923 45.455 0.00 0.00 0.00 3.06
9532 12283 2.920724 CCCGGTTTTTGATTTGGGTT 57.079 45.000 0.00 0.00 31.82 4.11
9534 12285 2.158885 CCCGGTTTTTGATTTGGGTTGT 60.159 45.455 0.00 0.00 31.82 3.32
9538 12289 4.062293 GGTTTTTGATTTGGGTTGTAGGC 58.938 43.478 0.00 0.00 0.00 3.93
9565 12316 2.534019 CGCGGCCGATGCATTAGTT 61.534 57.895 33.48 0.00 40.13 2.24
9733 12485 1.316706 ACTAGCCCAGCTCTGACGTC 61.317 60.000 9.11 9.11 40.44 4.34
9737 12489 2.653115 CCAGCTCTGACGTCTGCA 59.347 61.111 17.92 5.85 0.00 4.41
9742 12494 1.735920 CTCTGACGTCTGCAGGTGC 60.736 63.158 17.92 3.84 42.50 5.01
9743 12495 3.108289 CTGACGTCTGCAGGTGCG 61.108 66.667 17.92 17.69 45.83 5.34
9796 12548 1.064060 GTAGATGCAATTGCCGGTCAC 59.936 52.381 26.94 14.28 41.18 3.67
9797 12549 0.608856 AGATGCAATTGCCGGTCACA 60.609 50.000 26.94 7.41 41.18 3.58
9803 12555 0.108585 AATTGCCGGTCACACAGAGT 59.891 50.000 1.90 0.00 0.00 3.24
9813 12565 2.743928 CACAGAGTTGGAGCGCCC 60.744 66.667 2.29 5.76 0.00 6.13
9817 12569 3.081409 GAGTTGGAGCGCCCCCTA 61.081 66.667 5.13 0.35 0.00 3.53
9818 12570 3.387225 GAGTTGGAGCGCCCCCTAC 62.387 68.421 18.39 18.39 0.00 3.18
9867 12619 1.005332 AGAGTCTCCTCTAGTGCAGCA 59.995 52.381 0.00 0.00 46.39 4.41
9876 12628 2.692557 CTCTAGTGCAGCATGGTACTCT 59.307 50.000 0.00 4.46 35.31 3.24
9889 12641 0.246635 GTACTCTGCCTTCGCCTTCA 59.753 55.000 0.00 0.00 0.00 3.02
9890 12642 1.134670 GTACTCTGCCTTCGCCTTCAT 60.135 52.381 0.00 0.00 0.00 2.57
9893 12645 0.036732 TCTGCCTTCGCCTTCATGTT 59.963 50.000 0.00 0.00 0.00 2.71
9902 12654 2.552315 TCGCCTTCATGTTCTTTTCACC 59.448 45.455 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 4.253685 TCTGTTGATTAGCTAGGTTGTGC 58.746 43.478 0.00 0.00 0.00 4.57
225 230 3.494398 GCTCCCAAGACGATGGCTTTATA 60.494 47.826 0.00 0.00 39.26 0.98
252 258 1.299541 GGCGCTATGTATGCAGTTGT 58.700 50.000 7.64 0.00 0.00 3.32
296 302 2.172505 TGGTGTGATTCTCTGGTGTTGT 59.827 45.455 0.00 0.00 0.00 3.32
442 455 4.681978 GTGCGTTGGCGTCTCCCT 62.682 66.667 0.00 0.00 44.10 4.20
502 526 0.898326 TTGGCTGGAGCTAGTGACGA 60.898 55.000 0.00 0.00 41.70 4.20
509 533 1.743772 GCTCGATTTTGGCTGGAGCTA 60.744 52.381 4.23 0.00 44.99 3.32
523 550 3.565764 TGGATGAAAATCCTGCTCGAT 57.434 42.857 6.33 0.00 41.29 3.59
622 657 1.583856 CGACGGTTTCATCATGACGAG 59.416 52.381 0.00 0.00 0.00 4.18
699 735 0.457851 AGCTCATCTTCTTCGACCGG 59.542 55.000 0.00 0.00 0.00 5.28
713 756 1.194781 GGAGGTTGGTCTGGAGCTCA 61.195 60.000 17.19 0.61 41.05 4.26
822 866 2.049063 GGTCTCTCGCGTGCAAGT 60.049 61.111 5.77 0.00 0.00 3.16
871 915 1.046472 CGGGATGTGCCTAGTGGGTA 61.046 60.000 0.00 0.00 37.43 3.69
878 925 4.201679 CGCGTCGGGATGTGCCTA 62.202 66.667 2.62 0.00 36.66 3.93
1001 1052 2.093816 CAGATACAAGCTGCAGAGGTCA 60.094 50.000 20.43 0.00 0.00 4.02
1003 1054 1.905215 ACAGATACAAGCTGCAGAGGT 59.095 47.619 20.43 13.92 36.86 3.85
1025 3311 4.530161 ACAAAAGGTAAATTAGCATGGGCA 59.470 37.500 4.96 0.00 44.61 5.36
1128 3414 7.504238 TGAAACCATGTACAAGGATTAACAAGT 59.496 33.333 23.41 0.00 28.71 3.16
1374 3660 4.150897 AGTGCCAGTCTACAGTTTGAAA 57.849 40.909 0.00 0.00 0.00 2.69
1504 3791 4.864806 AGTACAATAGATGCAAGTCACACG 59.135 41.667 0.00 0.00 0.00 4.49
1831 4119 6.932356 AGTTCATAACAATATCAGGCACAG 57.068 37.500 0.00 0.00 0.00 3.66
1846 4134 7.282201 GAGGAAACCTTCGACGAAGTTCATAA 61.282 42.308 30.09 0.00 34.85 1.90
2103 4392 3.154710 CATGAGCATGGCAGGAACATAT 58.845 45.455 1.99 0.00 35.24 1.78
2168 4457 4.627467 GTGCAATATTCTCCTATACAGCCG 59.373 45.833 0.00 0.00 0.00 5.52
2372 4661 3.519913 CCTTACTTCAAACTCCTAGCCCT 59.480 47.826 0.00 0.00 0.00 5.19
2706 4996 1.308069 GCAGGTGTGCCATTCGTGAT 61.308 55.000 0.00 0.00 44.72 3.06
2747 5037 1.155155 GGTTGGGAGGGGCTTTTGA 59.845 57.895 0.00 0.00 0.00 2.69
2866 5156 4.957296 AGGTTCAGTTCACTATCGTTGTT 58.043 39.130 0.00 0.00 0.00 2.83
3037 5327 2.026636 ACGCAGCCTTTCCCTACATTTA 60.027 45.455 0.00 0.00 0.00 1.40
3089 5379 2.435586 CTTGCGCAGGGTCCAGAG 60.436 66.667 12.39 0.00 0.00 3.35
3090 5380 4.704833 GCTTGCGCAGGGTCCAGA 62.705 66.667 21.88 0.00 35.78 3.86
3169 5461 7.720957 AGCAAATCTACAAGGATTATGCACATA 59.279 33.333 17.34 0.00 39.36 2.29
3171 5463 5.887598 AGCAAATCTACAAGGATTATGCACA 59.112 36.000 17.34 0.00 39.36 4.57
3172 5464 6.382869 AGCAAATCTACAAGGATTATGCAC 57.617 37.500 17.34 0.00 39.36 4.57
3173 5465 7.496529 GTAGCAAATCTACAAGGATTATGCA 57.503 36.000 17.34 0.00 45.47 3.96
3201 5493 6.258947 GGACATTTCTGATAGTCCTAGCAAAC 59.741 42.308 13.31 0.00 45.46 2.93
3247 5539 2.378547 TCTAAGATGCCCTTTGGGTGTT 59.621 45.455 4.42 0.00 46.51 3.32
3530 5828 0.174389 CGTAGTGTGATGCTCCAGCT 59.826 55.000 0.00 0.00 42.66 4.24
3715 6023 0.890996 GGGCCTGTCAGAGTTTGTGG 60.891 60.000 0.84 0.00 0.00 4.17
3784 6100 2.351276 GGCATCAACGAGGTGGGT 59.649 61.111 0.00 0.00 0.00 4.51
3795 6122 0.326595 TTGTTTCCCTAGCGGCATCA 59.673 50.000 1.45 0.00 0.00 3.07
3829 6156 4.340263 GCCTCGTCATCCGTTTTATTTTC 58.660 43.478 0.00 0.00 37.94 2.29
3834 6161 0.458889 CGGCCTCGTCATCCGTTTTA 60.459 55.000 0.00 0.00 38.47 1.52
3878 6205 3.680786 CTCCACGCCGTCACCTCA 61.681 66.667 0.00 0.00 0.00 3.86
4047 6382 7.656137 AGTTTTCAAGCGTAGAGAGACATTTAA 59.344 33.333 0.00 0.00 0.00 1.52
4063 6398 6.259550 AGGAACACATATCAGTTTTCAAGC 57.740 37.500 0.00 0.00 31.51 4.01
4193 6528 1.840635 AGGCTGTCAGGAATAACTCCC 59.159 52.381 1.14 0.00 46.81 4.30
4708 7065 7.995289 ACTTGAAGAGTAGTGATATCAGTCAG 58.005 38.462 16.40 5.00 36.65 3.51
4875 7232 4.628661 AGACCTTATAGGGGTGAAGAGT 57.371 45.455 5.79 0.00 40.58 3.24
5602 7959 6.346896 ACGTTCCTCTTTTAGTCTTTTCACT 58.653 36.000 0.00 0.00 0.00 3.41
5707 8064 2.552315 AGTAGGTGTCATGCAAAAACCG 59.448 45.455 6.24 0.00 35.99 4.44
5804 8161 6.291637 CGCATTCAGAACGTGTTAGGTATTAG 60.292 42.308 0.00 0.00 0.00 1.73
5816 8173 1.298859 GGAAGCCGCATTCAGAACGT 61.299 55.000 0.00 0.00 0.00 3.99
6334 8691 8.632679 ACTGAAATTCAAAACTATGCTCTTGAA 58.367 29.630 0.00 0.00 40.85 2.69
6390 8747 8.352942 ACCACTAAATTTCAGTGAAATTCAGTC 58.647 33.333 31.47 0.00 43.11 3.51
6455 8812 1.760029 GTGGAAACTTTGGCCCTTTGA 59.240 47.619 0.00 0.00 0.00 2.69
6539 8896 6.622028 GCAACTACGGTAGTATGCACAAATTT 60.622 38.462 29.48 10.78 39.90 1.82
6666 9023 1.550976 GGTTGACATCCCTCGTCTTCT 59.449 52.381 0.00 0.00 34.37 2.85
6724 9081 3.784178 TCTCCTCATCTTGTCCTTCACT 58.216 45.455 0.00 0.00 0.00 3.41
6759 9116 7.047891 TGAACAACTTGTCAAAGTACTCTCAT 58.952 34.615 0.00 0.00 46.15 2.90
7082 9609 5.541845 TCATCAGCTTAATTCCACGATAGG 58.458 41.667 0.00 0.00 43.77 2.57
7083 9610 5.119898 GCTCATCAGCTTAATTCCACGATAG 59.880 44.000 0.00 0.00 43.09 2.08
7407 9963 7.156876 TGGTGCAGTCCTATTTTAATCAAAG 57.843 36.000 0.00 0.00 0.00 2.77
7432 9988 1.379977 GGGCTCAAAGCTAACCCCC 60.380 63.158 0.00 0.00 41.99 5.40
7433 9989 0.039764 AAGGGCTCAAAGCTAACCCC 59.960 55.000 5.97 3.46 41.99 4.95
7460 10018 4.042809 TGTGACCTTATCCATCACCAAAGT 59.957 41.667 1.45 0.00 41.71 2.66
7475 10033 3.736094 TGGGATATCTCCTTGTGACCTT 58.264 45.455 0.00 0.00 41.74 3.50
7695 10270 4.090761 TCTTCATTGCTATCACCATCCC 57.909 45.455 0.00 0.00 0.00 3.85
7760 10335 1.040646 TCACAGAGAACGCCAGAAGT 58.959 50.000 0.00 0.00 0.00 3.01
7840 10417 1.888512 GGCCAACATTCATCGCCATAT 59.111 47.619 0.00 0.00 39.50 1.78
7868 10445 1.000274 GAACTGTTGGACATGTTGCCC 60.000 52.381 0.00 0.00 0.00 5.36
8012 10589 2.563702 TGTTAAGTTTGGTCACCCGAC 58.436 47.619 0.00 0.00 41.80 4.79
8333 10911 8.464404 AGAAAAACATTAGATGTGGTGATGATG 58.536 33.333 0.00 0.00 44.07 3.07
8468 11047 2.497138 CAGCTTGTCACTCACCAATGA 58.503 47.619 0.00 0.00 0.00 2.57
8921 11500 1.002069 TTGGTCATCTTGGGCCAGAT 58.998 50.000 6.23 9.44 33.44 2.90
9202 11781 3.261580 TGAATGTCTATGCACCGACAAG 58.738 45.455 19.88 0.00 42.73 3.16
9340 12061 1.802880 CGGCTGTGATTTACTCCCTCG 60.803 57.143 0.00 0.00 0.00 4.63
9357 12078 2.314415 TAGGGTTTGATACGGCCGGC 62.314 60.000 31.76 21.18 0.00 6.13
9388 12109 3.198853 GCCCTAACACCTCTTTGATCTCT 59.801 47.826 0.00 0.00 0.00 3.10
9450 12201 8.599774 GCAAACAAAAACTATAGACAAAAAGCA 58.400 29.630 6.78 0.00 0.00 3.91
9451 12202 8.817100 AGCAAACAAAAACTATAGACAAAAAGC 58.183 29.630 6.78 0.58 0.00 3.51
9457 12208 9.646427 ACAAAAAGCAAACAAAAACTATAGACA 57.354 25.926 6.78 0.00 0.00 3.41
9461 12212 9.646427 ACAGACAAAAAGCAAACAAAAACTATA 57.354 25.926 0.00 0.00 0.00 1.31
9462 12213 8.546597 ACAGACAAAAAGCAAACAAAAACTAT 57.453 26.923 0.00 0.00 0.00 2.12
9463 12214 7.954788 ACAGACAAAAAGCAAACAAAAACTA 57.045 28.000 0.00 0.00 0.00 2.24
9464 12215 6.859420 ACAGACAAAAAGCAAACAAAAACT 57.141 29.167 0.00 0.00 0.00 2.66
9465 12216 7.641802 TCAAACAGACAAAAAGCAAACAAAAAC 59.358 29.630 0.00 0.00 0.00 2.43
9466 12217 7.697691 TCAAACAGACAAAAAGCAAACAAAAA 58.302 26.923 0.00 0.00 0.00 1.94
9467 12218 7.011857 ACTCAAACAGACAAAAAGCAAACAAAA 59.988 29.630 0.00 0.00 0.00 2.44
9468 12219 6.481644 ACTCAAACAGACAAAAAGCAAACAAA 59.518 30.769 0.00 0.00 0.00 2.83
9469 12220 5.988561 ACTCAAACAGACAAAAAGCAAACAA 59.011 32.000 0.00 0.00 0.00 2.83
9470 12221 5.404968 CACTCAAACAGACAAAAAGCAAACA 59.595 36.000 0.00 0.00 0.00 2.83
9471 12222 5.163963 CCACTCAAACAGACAAAAAGCAAAC 60.164 40.000 0.00 0.00 0.00 2.93
9472 12223 4.928615 CCACTCAAACAGACAAAAAGCAAA 59.071 37.500 0.00 0.00 0.00 3.68
9473 12224 4.493547 CCACTCAAACAGACAAAAAGCAA 58.506 39.130 0.00 0.00 0.00 3.91
9474 12225 3.675775 GCCACTCAAACAGACAAAAAGCA 60.676 43.478 0.00 0.00 0.00 3.91
9475 12226 2.860136 GCCACTCAAACAGACAAAAAGC 59.140 45.455 0.00 0.00 0.00 3.51
9476 12227 4.376340 AGCCACTCAAACAGACAAAAAG 57.624 40.909 0.00 0.00 0.00 2.27
9498 12249 1.221840 CGGGTAGGCACATCTGCTT 59.778 57.895 0.00 0.00 43.66 3.91
9507 12258 2.296073 AATCAAAAACCGGGTAGGCA 57.704 45.000 6.32 0.00 46.52 4.75
9510 12261 2.894765 ACCCAAATCAAAAACCGGGTAG 59.105 45.455 6.32 0.00 45.13 3.18
9513 12264 2.158885 ACAACCCAAATCAAAAACCGGG 60.159 45.455 6.32 0.00 39.72 5.73
9550 12301 1.949525 ACATGAACTAATGCATCGGCC 59.050 47.619 0.00 0.00 40.13 6.13
9551 12302 2.287188 CCACATGAACTAATGCATCGGC 60.287 50.000 0.00 0.00 41.68 5.54
9552 12303 2.945008 ACCACATGAACTAATGCATCGG 59.055 45.455 0.00 0.00 0.00 4.18
9554 12305 7.761409 TCTAAAACCACATGAACTAATGCATC 58.239 34.615 0.00 0.00 0.00 3.91
9555 12306 7.701539 TCTAAAACCACATGAACTAATGCAT 57.298 32.000 0.00 0.00 0.00 3.96
9723 12475 1.735920 CACCTGCAGACGTCAGAGC 60.736 63.158 17.39 18.22 33.54 4.09
9774 12526 0.751643 ACCGGCAATTGCATCTACCC 60.752 55.000 30.32 11.22 44.36 3.69
9781 12533 1.794151 CTGTGTGACCGGCAATTGCA 61.794 55.000 30.32 8.07 44.36 4.08
9796 12548 2.743928 GGGCGCTCCAACTCTGTG 60.744 66.667 7.64 0.00 35.00 3.66
9797 12549 4.021925 GGGGCGCTCCAACTCTGT 62.022 66.667 24.98 0.00 37.22 3.41
9803 12555 3.399181 CTGTAGGGGGCGCTCCAA 61.399 66.667 31.11 13.45 37.22 3.53
9813 12565 1.315257 GCACACAATGGCCTGTAGGG 61.315 60.000 3.32 0.00 35.18 3.53
9865 12617 1.432270 GCGAAGGCAGAGTACCATGC 61.432 60.000 10.65 10.65 41.80 4.06
9889 12641 1.608590 CGCCAGTGGTGAAAAGAACAT 59.391 47.619 18.34 0.00 34.74 2.71
9890 12642 1.021202 CGCCAGTGGTGAAAAGAACA 58.979 50.000 18.34 0.00 34.74 3.18
9893 12645 1.896660 GCCGCCAGTGGTGAAAAGA 60.897 57.895 24.62 0.00 34.74 2.52


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

AutoCloner maintained by Alex Coulton.