Multiple sequence alignment - TraesCS2A01G335100

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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 TraesCS2A01G335100 chr2A 100.000 5457 0 0 2174 7630 569202508 569197052 0.000000e+00 10078.0
1 TraesCS2A01G335100 chr2A 100.000 1819 0 0 1 1819 569204681 569202863 0.000000e+00 3360.0
2 TraesCS2A01G335100 chr2A 89.683 504 28 3 1 481 620727880 620728382 8.410000e-174 621.0
3 TraesCS2A01G335100 chr2A 89.526 506 27 4 1 481 35940243 35939739 1.090000e-172 617.0
4 TraesCS2A01G335100 chr2A 91.729 266 15 2 479 744 35938168 35937910 5.630000e-96 363.0
5 TraesCS2A01G335100 chr2A 90.545 275 16 5 479 744 293050465 293050738 9.420000e-94 355.0
6 TraesCS2A01G335100 chr2D 95.278 2139 77 7 2216 4335 422760864 422758731 0.000000e+00 3369.0
7 TraesCS2A01G335100 chr2D 94.818 1486 58 8 5674 7157 422758747 422757279 0.000000e+00 2300.0
8 TraesCS2A01G335100 chr2D 93.656 930 39 8 907 1819 422761853 422760927 0.000000e+00 1373.0
9 TraesCS2A01G335100 chr2D 87.982 441 28 12 7211 7628 422757281 422756843 1.480000e-136 497.0
10 TraesCS2A01G335100 chr2B 92.149 1987 106 18 5674 7628 495145373 495143405 0.000000e+00 2760.0
11 TraesCS2A01G335100 chr2B 92.559 1223 62 13 3123 4335 495146560 495145357 0.000000e+00 1727.0
12 TraesCS2A01G335100 chr2B 94.525 968 35 4 2179 3129 495147710 495146744 0.000000e+00 1478.0
13 TraesCS2A01G335100 chr2B 93.542 960 27 13 860 1819 495148701 495147777 0.000000e+00 1397.0
14 TraesCS2A01G335100 chr3A 98.137 1342 18 6 4336 5671 336603161 336604501 0.000000e+00 2333.0
15 TraesCS2A01G335100 chr3A 90.476 378 14 1 126 481 714324182 714323805 5.360000e-131 479.0
16 TraesCS2A01G335100 chr3A 89.170 277 13 5 479 744 509547226 509547496 5.710000e-86 329.0
17 TraesCS2A01G335100 chr3A 81.132 371 56 12 138 497 81659586 81659953 1.250000e-72 285.0
18 TraesCS2A01G335100 chr3D 96.526 1324 31 7 4336 5653 326963129 326961815 0.000000e+00 2176.0
19 TraesCS2A01G335100 chr3D 86.310 504 42 8 1 481 80220233 80219734 2.440000e-144 523.0
20 TraesCS2A01G335100 chr3D 84.711 484 55 12 1 479 1216610 1217079 4.170000e-127 466.0
21 TraesCS2A01G335100 chr3D 84.615 351 43 7 2 346 412823222 412823567 9.480000e-89 339.0
22 TraesCS2A01G335100 chr6D 94.581 1347 61 6 4336 5673 396922722 396924065 0.000000e+00 2073.0
23 TraesCS2A01G335100 chr6D 86.733 505 42 8 1 481 451668155 451667652 8.710000e-149 538.0
24 TraesCS2A01G335100 chr6D 86.263 495 41 5 9 481 108455544 108455055 5.280000e-141 512.0
25 TraesCS2A01G335100 chr6D 83.992 506 50 12 2 481 473051007 473051507 2.510000e-124 457.0
26 TraesCS2A01G335100 chr6D 80.493 446 73 12 47 479 97734933 97735377 5.710000e-86 329.0
27 TraesCS2A01G335100 chr6D 83.636 385 27 15 6 355 99233492 99233109 5.710000e-86 329.0
28 TraesCS2A01G335100 chr6D 87.879 264 26 5 1 258 324750514 324750251 9.620000e-79 305.0
29 TraesCS2A01G335100 chr6D 82.850 379 26 16 479 819 451666051 451665674 3.460000e-78 303.0
30 TraesCS2A01G335100 chr6D 80.916 393 31 21 479 836 108453544 108453161 3.510000e-68 270.0
31 TraesCS2A01G335100 chr6D 90.187 214 7 5 481 680 324749976 324749763 4.540000e-67 267.0
32 TraesCS2A01G335100 chr6D 89.372 207 21 1 273 479 322577707 322577912 7.600000e-65 259.0
33 TraesCS2A01G335100 chr6D 89.286 196 20 1 287 482 414267498 414267304 2.130000e-60 244.0
34 TraesCS2A01G335100 chr7A 94.560 1342 67 3 4336 5672 254418968 254417628 0.000000e+00 2069.0
35 TraesCS2A01G335100 chr7A 90.476 504 17 6 1 481 725469397 725469892 3.000000e-178 636.0
36 TraesCS2A01G335100 chr7A 89.216 510 21 13 1 481 18188818 18188314 2.350000e-169 606.0
37 TraesCS2A01G335100 chr7A 88.642 405 27 7 478 864 725689233 725688830 6.930000e-130 475.0
38 TraesCS2A01G335100 chr7A 86.029 408 28 17 479 862 90657540 90657942 1.980000e-110 411.0
39 TraesCS2A01G335100 chr7A 93.609 266 16 1 479 744 564245236 564244972 5.550000e-106 396.0
40 TraesCS2A01G335100 chr7A 96.373 193 5 1 4336 4528 202984265 202984075 4.440000e-82 316.0
41 TraesCS2A01G335100 chr7A 93.596 203 12 1 4336 4538 155659242 155659041 1.240000e-77 302.0
42 TraesCS2A01G335100 chr7A 94.558 147 8 0 4336 4482 85108585 85108731 2.140000e-55 228.0
43 TraesCS2A01G335100 chr4D 93.022 1347 74 12 4336 5676 206063807 206065139 0.000000e+00 1949.0
44 TraesCS2A01G335100 chr4D 89.059 1243 116 13 4441 5673 346466964 346468196 0.000000e+00 1524.0
45 TraesCS2A01G335100 chr4D 86.083 503 46 10 1 481 386123154 386123654 3.160000e-143 520.0
46 TraesCS2A01G335100 chr4D 85.516 504 45 8 1 481 467824014 467823516 1.140000e-137 501.0
47 TraesCS2A01G335100 chr4D 85.622 466 35 18 1 443 439874190 439874646 1.940000e-125 460.0
48 TraesCS2A01G335100 chr4D 85.674 356 23 13 6 338 175189143 175189493 4.380000e-92 350.0
49 TraesCS2A01G335100 chr4D 81.818 429 50 11 76 482 487405104 487404682 1.230000e-87 335.0
50 TraesCS2A01G335100 chr4D 82.834 367 24 14 479 816 175189502 175189858 7.490000e-75 292.0
51 TraesCS2A01G335100 chr4D 85.862 290 12 10 479 740 93441288 93441576 1.620000e-71 281.0
52 TraesCS2A01G335100 chr4D 90.094 212 11 5 479 680 386142488 386142699 4.540000e-67 267.0
53 TraesCS2A01G335100 chr1D 95.826 1198 32 7 4336 5531 218901826 218903007 0.000000e+00 1919.0
54 TraesCS2A01G335100 chr1D 85.149 505 49 10 1 481 470207007 470207509 1.910000e-135 494.0
55 TraesCS2A01G335100 chr1D 85.861 389 27 9 9 374 66765354 66765737 9.280000e-104 388.0
56 TraesCS2A01G335100 chr1D 87.085 271 30 4 1 266 395350067 395349797 1.240000e-77 302.0
57 TraesCS2A01G335100 chr1D 82.418 364 31 14 479 819 395349674 395349321 3.480000e-73 287.0
58 TraesCS2A01G335100 chr5B 91.685 1335 96 8 4336 5664 474781477 474782802 0.000000e+00 1836.0
59 TraesCS2A01G335100 chr6B 95.965 1041 39 2 4636 5673 68109914 68108874 0.000000e+00 1687.0
60 TraesCS2A01G335100 chr6B 84.956 339 41 9 149 481 31581359 31581693 1.230000e-87 335.0
61 TraesCS2A01G335100 chr6A 90.297 505 25 4 1 481 544168659 544168155 2.320000e-179 640.0
62 TraesCS2A01G335100 chr6A 87.327 505 29 13 1 481 93271100 93270607 5.210000e-151 545.0
63 TraesCS2A01G335100 chr6A 85.996 507 41 14 1 481 430315019 430314517 4.080000e-142 516.0
64 TraesCS2A01G335100 chr6A 87.841 403 22 8 479 860 616391130 616391526 1.510000e-121 448.0
65 TraesCS2A01G335100 chr6A 88.131 337 10 4 173 481 585442967 585443301 2.600000e-99 374.0
66 TraesCS2A01G335100 chr6A 91.912 272 14 4 479 744 585444883 585445152 2.600000e-99 374.0
67 TraesCS2A01G335100 chr6A 91.791 268 16 1 479 740 579138777 579139044 1.210000e-97 368.0
68 TraesCS2A01G335100 chr6A 91.045 268 22 2 1 266 616374495 616374762 2.020000e-95 361.0
69 TraesCS2A01G335100 chr6A 89.928 278 15 5 479 744 93269028 93268752 5.670000e-91 346.0
70 TraesCS2A01G335100 chr6A 89.170 277 16 5 479 744 560107124 560106851 4.410000e-87 333.0
71 TraesCS2A01G335100 chr6A 93.665 221 13 1 262 481 560110288 560110068 5.710000e-86 329.0
72 TraesCS2A01G335100 chrUn 89.703 505 28 3 1 481 150817375 150817879 2.340000e-174 623.0
73 TraesCS2A01G335100 chrUn 84.118 510 52 16 1 481 82489611 82490120 4.170000e-127 466.0
74 TraesCS2A01G335100 chrUn 85.488 441 33 12 1 418 332494214 332493782 1.520000e-116 431.0
75 TraesCS2A01G335100 chrUn 85.488 441 33 12 1 418 364365984 364366416 1.520000e-116 431.0
76 TraesCS2A01G335100 chrUn 86.072 359 23 7 9 345 20485935 20485582 2.020000e-95 361.0
77 TraesCS2A01G335100 chrUn 79.574 470 54 24 47 479 89858302 89858766 1.610000e-76 298.0
78 TraesCS2A01G335100 chrUn 77.589 531 62 32 1 482 84334972 84334450 1.260000e-67 268.0
79 TraesCS2A01G335100 chrUn 77.652 528 61 32 1 479 265276804 265277323 1.260000e-67 268.0
80 TraesCS2A01G335100 chrUn 85.603 257 32 4 1 252 1922455 1922711 1.630000e-66 265.0
81 TraesCS2A01G335100 chrUn 89.815 216 8 6 479 680 332492210 332491995 1.630000e-66 265.0
82 TraesCS2A01G335100 chrUn 89.815 216 8 6 479 680 370576383 370576598 1.630000e-66 265.0
83 TraesCS2A01G335100 chrUn 89.815 216 8 6 479 680 396909948 396909733 1.630000e-66 265.0
84 TraesCS2A01G335100 chrUn 90.291 206 13 3 479 679 23659870 23660073 5.870000e-66 263.0
85 TraesCS2A01G335100 chrUn 90.000 210 7 7 479 680 1922743 1922946 7.600000e-65 259.0
86 TraesCS2A01G335100 chrUn 87.225 227 24 4 1 222 418863953 418864179 3.530000e-63 254.0
87 TraesCS2A01G335100 chrUn 84.532 278 10 4 479 744 150818762 150819018 2.130000e-60 244.0
88 TraesCS2A01G335100 chrUn 88.152 211 15 6 479 680 318019820 318020029 7.650000e-60 243.0
89 TraesCS2A01G335100 chrUn 88.152 211 15 6 479 680 421370078 421370287 7.650000e-60 243.0
90 TraesCS2A01G335100 chrUn 84.681 235 31 4 1 230 98078299 98078065 5.960000e-56 230.0
91 TraesCS2A01G335100 chrUn 92.357 157 12 0 262 418 455225767 455225611 2.770000e-54 224.0
92 TraesCS2A01G335100 chrUn 90.476 168 12 3 479 643 324892107 324892273 1.290000e-52 219.0
93 TraesCS2A01G335100 chrUn 90.476 168 12 3 479 643 324895234 324895400 1.290000e-52 219.0
94 TraesCS2A01G335100 chrUn 90.058 171 13 3 479 646 406870703 406870534 1.290000e-52 219.0
95 TraesCS2A01G335100 chrUn 79.259 270 50 6 1 265 221515819 221516087 4.700000e-42 183.0
96 TraesCS2A01G335100 chrUn 83.838 198 27 4 287 482 340719054 340718860 4.700000e-42 183.0
97 TraesCS2A01G335100 chrUn 94.595 37 2 0 325 361 335315334 335315298 2.970000e-04 58.4
98 TraesCS2A01G335100 chr5A 89.881 504 22 6 1 481 589306727 589307224 8.410000e-174 621.0
99 TraesCS2A01G335100 chr5A 88.824 510 28 3 1 481 35645331 35644822 3.940000e-167 599.0
100 TraesCS2A01G335100 chr5A 88.000 400 25 9 479 864 556781518 556781908 1.170000e-122 451.0
101 TraesCS2A01G335100 chr5A 89.736 341 13 11 163 481 650676051 650676391 4.260000e-112 416.0
102 TraesCS2A01G335100 chr5A 85.459 392 33 14 479 860 566142799 566142422 3.340000e-103 387.0
103 TraesCS2A01G335100 chr5A 92.279 272 13 3 479 744 35643271 35643002 5.590000e-101 379.0
104 TraesCS2A01G335100 chr1A 88.538 506 30 5 1 481 520128493 520127991 8.530000e-164 588.0
105 TraesCS2A01G335100 chr1A 88.797 482 29 7 6 462 509010835 509010354 1.110000e-157 568.0
106 TraesCS2A01G335100 chr1A 87.921 505 30 6 1 481 420530766 420530269 4.000000e-157 566.0
107 TraesCS2A01G335100 chr1A 88.702 416 21 4 1 391 131255326 131254912 1.150000e-132 484.0
108 TraesCS2A01G335100 chr1A 85.542 415 27 17 479 860 514134403 514134817 3.320000e-108 403.0
109 TraesCS2A01G335100 chr1A 93.750 272 10 4 479 744 131254786 131254516 1.190000e-107 401.0
110 TraesCS2A01G335100 chr1A 85.122 410 35 10 479 863 509010000 509009592 5.550000e-106 396.0
111 TraesCS2A01G335100 chr1A 92.336 274 9 3 479 740 499978065 499978338 5.590000e-101 379.0
112 TraesCS2A01G335100 chr1A 89.542 306 10 1 198 481 477752885 477753190 1.210000e-97 368.0
113 TraesCS2A01G335100 chr1A 89.769 303 9 2 201 481 514133543 514133845 1.210000e-97 368.0
114 TraesCS2A01G335100 chr1A 89.145 304 11 1 200 481 499976164 499976467 7.280000e-95 359.0
115 TraesCS2A01G335100 chr1A 83.582 402 33 20 479 860 18105535 18105923 5.670000e-91 346.0
116 TraesCS2A01G335100 chr1A 88.849 278 17 5 479 744 420528771 420528496 5.710000e-86 329.0
117 TraesCS2A01G335100 chr1A 92.889 225 14 2 520 744 539747611 539747389 7.380000e-85 326.0
118 TraesCS2A01G335100 chr1A 91.031 223 20 0 262 484 582755432 582755210 1.240000e-77 302.0
119 TraesCS2A01G335100 chr1A 81.250 400 42 19 479 863 520126379 520125998 7.490000e-75 292.0
120 TraesCS2A01G335100 chr1A 95.062 81 3 1 664 744 49966803 49966882 8.040000e-25 126.0
121 TraesCS2A01G335100 chr1A 87.069 116 7 7 756 863 103311314 103311429 2.890000e-24 124.0
122 TraesCS2A01G335100 chr4A 87.795 508 35 4 1 481 684298189 684298696 3.090000e-158 569.0
123 TraesCS2A01G335100 chr4A 89.011 364 18 1 140 481 322656117 322656480 1.520000e-116 431.0
124 TraesCS2A01G335100 chr4A 86.603 418 23 21 478 862 584779390 584779807 1.520000e-116 431.0
125 TraesCS2A01G335100 chr4A 87.139 381 24 9 479 834 322658073 322658453 7.130000e-110 409.0
126 TraesCS2A01G335100 chr4A 87.316 339 30 12 149 481 612663032 612663363 7.230000e-100 375.0
127 TraesCS2A01G335100 chr4A 91.367 278 11 3 479 744 612664884 612665160 1.210000e-97 368.0
128 TraesCS2A01G335100 chr7B 81.579 494 70 14 1 480 646057362 646057848 9.280000e-104 388.0
129 TraesCS2A01G335100 chr5D 89.591 269 23 4 1 266 559069877 559069611 3.410000e-88 337.0


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 TraesCS2A01G335100 chr2A 569197052 569204681 7629 True 6719.00 10078 100.00000 1 7630 2 chr2A.!!$R2 7629
1 TraesCS2A01G335100 chr2A 620727880 620728382 502 False 621.00 621 89.68300 1 481 1 chr2A.!!$F2 480
2 TraesCS2A01G335100 chr2A 35937910 35940243 2333 True 490.00 617 90.62750 1 744 2 chr2A.!!$R1 743
3 TraesCS2A01G335100 chr2D 422756843 422761853 5010 True 1884.75 3369 92.93350 907 7628 4 chr2D.!!$R1 6721
4 TraesCS2A01G335100 chr2B 495143405 495148701 5296 True 1840.50 2760 93.19375 860 7628 4 chr2B.!!$R1 6768
5 TraesCS2A01G335100 chr3A 336603161 336604501 1340 False 2333.00 2333 98.13700 4336 5671 1 chr3A.!!$F2 1335
6 TraesCS2A01G335100 chr3D 326961815 326963129 1314 True 2176.00 2176 96.52600 4336 5653 1 chr3D.!!$R2 1317
7 TraesCS2A01G335100 chr6D 396922722 396924065 1343 False 2073.00 2073 94.58100 4336 5673 1 chr6D.!!$F3 1337
8 TraesCS2A01G335100 chr6D 473051007 473051507 500 False 457.00 457 83.99200 2 481 1 chr6D.!!$F4 479
9 TraesCS2A01G335100 chr6D 451665674 451668155 2481 True 420.50 538 84.79150 1 819 2 chr6D.!!$R5 818
10 TraesCS2A01G335100 chr6D 108453161 108455544 2383 True 391.00 512 83.58950 9 836 2 chr6D.!!$R3 827
11 TraesCS2A01G335100 chr6D 324749763 324750514 751 True 286.00 305 89.03300 1 680 2 chr6D.!!$R4 679
12 TraesCS2A01G335100 chr7A 254417628 254418968 1340 True 2069.00 2069 94.56000 4336 5672 1 chr7A.!!$R4 1336
13 TraesCS2A01G335100 chr7A 18188314 18188818 504 True 606.00 606 89.21600 1 481 1 chr7A.!!$R1 480
14 TraesCS2A01G335100 chr4D 206063807 206065139 1332 False 1949.00 1949 93.02200 4336 5676 1 chr4D.!!$F2 1340
15 TraesCS2A01G335100 chr4D 346466964 346468196 1232 False 1524.00 1524 89.05900 4441 5673 1 chr4D.!!$F3 1232
16 TraesCS2A01G335100 chr4D 386123154 386123654 500 False 520.00 520 86.08300 1 481 1 chr4D.!!$F4 480
17 TraesCS2A01G335100 chr4D 175189143 175189858 715 False 321.00 350 84.25400 6 816 2 chr4D.!!$F7 810
18 TraesCS2A01G335100 chr1D 218901826 218903007 1181 False 1919.00 1919 95.82600 4336 5531 1 chr1D.!!$F2 1195
19 TraesCS2A01G335100 chr1D 470207007 470207509 502 False 494.00 494 85.14900 1 481 1 chr1D.!!$F3 480
20 TraesCS2A01G335100 chr1D 395349321 395350067 746 True 294.50 302 84.75150 1 819 2 chr1D.!!$R1 818
21 TraesCS2A01G335100 chr5B 474781477 474782802 1325 False 1836.00 1836 91.68500 4336 5664 1 chr5B.!!$F1 1328
22 TraesCS2A01G335100 chr6B 68108874 68109914 1040 True 1687.00 1687 95.96500 4636 5673 1 chr6B.!!$R1 1037
23 TraesCS2A01G335100 chr6A 544168155 544168659 504 True 640.00 640 90.29700 1 481 1 chr6A.!!$R2 480
24 TraesCS2A01G335100 chr6A 430314517 430315019 502 True 516.00 516 85.99600 1 481 1 chr6A.!!$R1 480
25 TraesCS2A01G335100 chr6A 93268752 93271100 2348 True 445.50 545 88.62750 1 744 2 chr6A.!!$R3 743
26 TraesCS2A01G335100 chr6A 585442967 585445152 2185 False 374.00 374 90.02150 173 744 2 chr6A.!!$F4 571
27 TraesCS2A01G335100 chr6A 560106851 560110288 3437 True 331.00 333 91.41750 262 744 2 chr6A.!!$R4 482
28 TraesCS2A01G335100 chrUn 82489611 82490120 509 False 466.00 466 84.11800 1 481 1 chrUn.!!$F2 480
29 TraesCS2A01G335100 chrUn 150817375 150819018 1643 False 433.50 623 87.11750 1 744 2 chrUn.!!$F12 743
30 TraesCS2A01G335100 chrUn 332491995 332494214 2219 True 348.00 431 87.65150 1 680 2 chrUn.!!$R9 679
31 TraesCS2A01G335100 chrUn 84334450 84334972 522 True 268.00 268 77.58900 1 482 1 chrUn.!!$R2 481
32 TraesCS2A01G335100 chrUn 265276804 265277323 519 False 268.00 268 77.65200 1 479 1 chrUn.!!$F5 478
33 TraesCS2A01G335100 chrUn 324892107 324895400 3293 False 219.00 219 90.47600 479 643 2 chrUn.!!$F13 164
34 TraesCS2A01G335100 chr5A 35643002 35645331 2329 True 489.00 599 90.55150 1 744 2 chr5A.!!$R2 743
35 TraesCS2A01G335100 chr1A 509009592 509010835 1243 True 482.00 568 86.95950 6 863 2 chr1A.!!$R5 857
36 TraesCS2A01G335100 chr1A 420528496 420530766 2270 True 447.50 566 88.38500 1 744 2 chr1A.!!$R4 743
37 TraesCS2A01G335100 chr1A 131254516 131255326 810 True 442.50 484 91.22600 1 744 2 chr1A.!!$R3 743
38 TraesCS2A01G335100 chr1A 520125998 520128493 2495 True 440.00 588 84.89400 1 863 2 chr1A.!!$R6 862
39 TraesCS2A01G335100 chr1A 514133543 514134817 1274 False 385.50 403 87.65550 201 860 2 chr1A.!!$F6 659
40 TraesCS2A01G335100 chr1A 499976164 499978338 2174 False 369.00 379 90.74050 200 740 2 chr1A.!!$F5 540
41 TraesCS2A01G335100 chr4A 684298189 684298696 507 False 569.00 569 87.79500 1 481 1 chr4A.!!$F2 480
42 TraesCS2A01G335100 chr4A 322656117 322658453 2336 False 420.00 431 88.07500 140 834 2 chr4A.!!$F3 694
43 TraesCS2A01G335100 chr4A 612663032 612665160 2128 False 371.50 375 89.34150 149 744 2 chr4A.!!$F4 595

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
508 5511 0.611200 TTCATCTTCGGAGGCGGAAA 59.389 50.000 0.00 0.00 0.00 3.13 F
961 6112 1.244019 ACAAATCGAGCCCAAGTGCC 61.244 55.000 0.00 0.00 0.00 5.01 F
2210 8290 2.832838 TCCTAGCCAGTTCTGGATTGA 58.167 47.619 21.32 12.52 0.00 2.57 F
2281 8361 1.153469 CTTCCCTCGCAAGGAGCTC 60.153 63.158 4.71 4.71 46.67 4.09 F
3391 9679 1.195115 TGCTCCTGACCGCTTCTATT 58.805 50.000 0.00 0.00 0.00 1.73 F
3887 10231 1.072331 AGATGGCCGACTGAGTTGTTT 59.928 47.619 0.00 0.00 0.00 2.83 F
4342 10691 3.181491 GCTTATGCGCAAATTACAAGGGA 60.181 43.478 17.11 0.00 0.00 4.20 F
5999 12466 0.517316 GCTTTAACAGCGGGACAGTG 59.483 55.000 0.00 0.00 39.29 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1494 7558 1.308998 AGGACCAACGAACAAAGCTG 58.691 50.000 0.00 0.00 0.00 4.24 R
2228 8308 2.029560 GCCTGCCCAGAAGAAGAAAAAG 60.030 50.000 0.00 0.00 0.00 2.27 R
3367 9654 0.668535 AAGCGGTCAGGAGCAAAAAC 59.331 50.000 0.00 0.00 35.48 2.43 R
3423 9711 1.066605 AGCAAGTTTCACAAGCAGCAG 59.933 47.619 0.00 0.00 0.00 4.24 R
4325 10674 2.192664 TCTCCCTTGTAATTTGCGCA 57.807 45.000 5.66 5.66 0.00 6.09 R
5635 12102 3.636764 ACAACAAAGCCTTTAGTCCCAAG 59.363 43.478 0.00 0.00 0.00 3.61 R
6146 12613 2.100631 CGTTACTGAAGCTGGGCCG 61.101 63.158 0.00 0.00 0.00 6.13 R
7158 13638 0.178938 TGAGCCCAAGCCAAATCCAA 60.179 50.000 0.00 0.00 41.25 3.53 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
51 56 4.803908 CCTCCAAAGCCTCCCGCC 62.804 72.222 0.00 0.00 38.78 6.13
156 198 2.670251 CGCCGCCACAAACCCTAA 60.670 61.111 0.00 0.00 0.00 2.69
462 2192 2.354539 GGCGCGCACAACATGTTT 60.355 55.556 34.42 0.00 0.00 2.83
508 5511 0.611200 TTCATCTTCGGAGGCGGAAA 59.389 50.000 0.00 0.00 0.00 3.13
585 5612 9.883142 TTTCCTTTGTGTATTGAACTTGATTTT 57.117 25.926 0.00 0.00 0.00 1.82
635 5663 5.069648 TGTGGGCATGATTTTAAACTTGTGA 59.930 36.000 0.00 0.00 0.00 3.58
659 5695 7.013178 TGAGCATGAACTTCATCAACTTGTTTA 59.987 33.333 0.00 0.00 34.28 2.01
761 5902 1.296288 CGCGCGCGCTGTATTTTAA 60.296 52.632 45.97 0.00 39.32 1.52
961 6112 1.244019 ACAAATCGAGCCCAAGTGCC 61.244 55.000 0.00 0.00 0.00 5.01
1479 7543 4.282703 CACCAGTACCTAATAATACGCCCT 59.717 45.833 0.00 0.00 0.00 5.19
1505 7572 6.408039 CGTTTACTATATTGCAGCTTTGTTCG 59.592 38.462 0.00 0.00 0.00 3.95
1660 7727 8.904834 CAGAGAGTTAGCACTTATAAGACCTTA 58.095 37.037 19.38 5.78 31.22 2.69
1668 7735 8.738645 AGCACTTATAAGACCTTATTTTGGAG 57.261 34.615 19.38 2.96 37.07 3.86
1689 7756 5.297569 AGAGCCAATCCCTTGTTATCTAC 57.702 43.478 0.00 0.00 0.00 2.59
1707 7774 9.465985 GTTATCTACATAAAAGACCAGTAGCTC 57.534 37.037 0.00 0.00 33.86 4.09
1713 7780 4.762289 AAAAGACCAGTAGCTCCATAGG 57.238 45.455 0.00 0.00 0.00 2.57
2210 8290 2.832838 TCCTAGCCAGTTCTGGATTGA 58.167 47.619 21.32 12.52 0.00 2.57
2281 8361 1.153469 CTTCCCTCGCAAGGAGCTC 60.153 63.158 4.71 4.71 46.67 4.09
2390 8470 4.159135 GCTTCCATGAAGGTGACATCATTT 59.841 41.667 6.03 0.00 45.93 2.32
2633 8728 5.762825 AAATGTACTGCATCATGATGGAC 57.237 39.130 31.62 19.97 39.16 4.02
2803 8898 6.152831 AGTTAGGAAGCAATAAATTCACCACC 59.847 38.462 0.00 0.00 0.00 4.61
2804 8899 4.415596 AGGAAGCAATAAATTCACCACCA 58.584 39.130 0.00 0.00 0.00 4.17
2878 8973 9.868277 GATGGGTTTACATCACATCAATTAAAA 57.132 29.630 3.70 0.00 45.11 1.52
2917 9012 4.660303 AGTCCTGACATATCCAATGCCTTA 59.340 41.667 0.00 0.00 0.00 2.69
2922 9017 7.564660 TCCTGACATATCCAATGCCTTAAAATT 59.435 33.333 0.00 0.00 0.00 1.82
2923 9018 8.206189 CCTGACATATCCAATGCCTTAAAATTT 58.794 33.333 0.00 0.00 0.00 1.82
2930 9025 7.309770 TCCAATGCCTTAAAATTTAGTGGTT 57.690 32.000 3.55 0.00 0.00 3.67
2961 9056 3.124297 GCTAGTTTGTGTCTGTCTCATGC 59.876 47.826 0.00 0.00 0.00 4.06
3020 9117 5.354234 ACAGCCAACGATAATTCAGTTTAGG 59.646 40.000 0.00 0.00 0.00 2.69
3053 9150 2.744202 GGATGTGGATACCGATTGATGC 59.256 50.000 0.00 0.00 0.00 3.91
3195 9482 8.779354 AACTTTAGAGACCTCATGTATGTTTC 57.221 34.615 0.00 0.00 0.00 2.78
3225 9512 5.384336 TGGTGAGGATGAAACATCAGAAAA 58.616 37.500 12.66 0.00 31.41 2.29
3313 9600 3.823873 TCCCTATTGAAAATTGCACACGT 59.176 39.130 0.00 0.00 0.00 4.49
3316 9603 5.118510 CCCTATTGAAAATTGCACACGTTTC 59.881 40.000 0.00 0.00 0.00 2.78
3340 9627 7.660112 TCACTTTAGATTGAATGTTGCATTGT 58.340 30.769 0.00 0.00 0.00 2.71
3341 9628 8.143193 TCACTTTAGATTGAATGTTGCATTGTT 58.857 29.630 0.00 0.00 0.00 2.83
3355 9642 3.130869 TGCATTGTTGTTGCTTTCTGTCT 59.869 39.130 0.00 0.00 40.77 3.41
3358 9645 6.206438 TGCATTGTTGTTGCTTTCTGTCTATA 59.794 34.615 0.00 0.00 40.77 1.31
3382 9670 4.590850 AAATCTGTTTTTGCTCCTGACC 57.409 40.909 0.00 0.00 0.00 4.02
3391 9679 1.195115 TGCTCCTGACCGCTTCTATT 58.805 50.000 0.00 0.00 0.00 1.73
3393 9681 2.027192 TGCTCCTGACCGCTTCTATTTT 60.027 45.455 0.00 0.00 0.00 1.82
3423 9711 3.002656 CACCGGTAGATTGAATGATGCAC 59.997 47.826 6.87 0.00 0.00 4.57
3426 9714 3.303593 CGGTAGATTGAATGATGCACTGC 60.304 47.826 0.00 0.00 0.00 4.40
3458 9746 9.034544 GTGAAACTTGCTCATATGTTTTTCTTT 57.965 29.630 1.90 0.00 33.49 2.52
3628 9972 4.566360 GTGCAAGAAGATCTACTCAGAAGC 59.434 45.833 0.00 0.00 33.50 3.86
3636 9980 6.603940 AGATCTACTCAGAAGCAGAAAAGT 57.396 37.500 0.00 0.00 33.50 2.66
3733 10077 6.812160 GTCACAGTTGTTTCCTAGGTATACTG 59.188 42.308 20.33 20.33 38.12 2.74
3797 10141 2.043664 TGTCTCTCCTGATGAGGTTCCT 59.956 50.000 0.00 0.00 41.76 3.36
3811 10155 8.106462 TGATGAGGTTCCTCTATATACTGAGAG 58.894 40.741 18.07 4.01 39.18 3.20
3865 10209 3.517296 TGTATTGGGAGTTTCAGCCAA 57.483 42.857 0.00 0.00 0.00 4.52
3887 10231 1.072331 AGATGGCCGACTGAGTTGTTT 59.928 47.619 0.00 0.00 0.00 2.83
4189 10533 3.340814 AGTCGAGGCAGATGAAACAAT 57.659 42.857 0.00 0.00 0.00 2.71
4332 10681 6.852858 TTAGTATACATGCTTATGCGCAAA 57.147 33.333 17.11 9.55 44.06 3.68
4333 10682 5.947228 AGTATACATGCTTATGCGCAAAT 57.053 34.783 17.11 0.00 44.06 2.32
4334 10683 6.317789 AGTATACATGCTTATGCGCAAATT 57.682 33.333 17.11 0.00 44.06 1.82
4342 10691 3.181491 GCTTATGCGCAAATTACAAGGGA 60.181 43.478 17.11 0.00 0.00 4.20
5635 12102 0.909623 TCTAGCCTACCCCAACTTGC 59.090 55.000 0.00 0.00 0.00 4.01
5752 12219 6.441274 TCAGTACAGTTACTTGGTTTAGTCG 58.559 40.000 0.00 0.00 36.31 4.18
5957 12424 9.467258 CTAGAGATGAATAAGAAGCTGAAGAAG 57.533 37.037 0.00 0.00 0.00 2.85
5999 12466 0.517316 GCTTTAACAGCGGGACAGTG 59.483 55.000 0.00 0.00 39.29 3.66
6176 12643 4.556898 GCTTCAGTAACGACAGTCTTCTCA 60.557 45.833 0.00 0.00 0.00 3.27
6293 12760 3.515602 ATTTCAGTCTTGCACCCTCTT 57.484 42.857 0.00 0.00 0.00 2.85
6371 12838 3.055602 ACATCTGCAGCTCATCTGTAACA 60.056 43.478 9.47 0.00 44.66 2.41
6450 12917 1.476891 GAGGTGAGAACGTAGATGCCA 59.523 52.381 0.00 0.00 0.00 4.92
6460 12927 1.303309 GTAGATGCCAGTGATGCACC 58.697 55.000 0.00 0.00 42.38 5.01
6493 12960 1.595609 GTTCTTGATGAAACTGCGCG 58.404 50.000 0.00 0.00 36.30 6.86
6621 13088 0.741915 GTTCGGCAAACAAACCAGGA 59.258 50.000 0.00 0.00 37.82 3.86
6725 13192 7.687941 AAGAGGATTTGTTTTGTCGATGTAT 57.312 32.000 0.00 0.00 0.00 2.29
6798 13265 2.479049 CCTTGTACTGATGCAGCAATGC 60.479 50.000 5.96 0.00 34.37 3.56
6828 13296 7.496529 TTTTTCCTGATCTCAGTTACAAGTG 57.503 36.000 6.46 0.00 42.27 3.16
6829 13297 6.419484 TTTCCTGATCTCAGTTACAAGTGA 57.581 37.500 6.46 0.00 42.27 3.41
6830 13298 6.419484 TTCCTGATCTCAGTTACAAGTGAA 57.581 37.500 6.46 0.00 42.27 3.18
6831 13299 6.030548 TCCTGATCTCAGTTACAAGTGAAG 57.969 41.667 6.46 0.00 42.27 3.02
6865 13340 4.901250 TCATATGCCATCCTCTGTTCACTA 59.099 41.667 0.00 0.00 0.00 2.74
6905 13380 2.886523 TGCTTCTGAAGTTCATGGGTTG 59.113 45.455 17.97 0.00 0.00 3.77
6976 13454 5.703130 AGTGTAAGAAGCTTCCATTCTGTTC 59.297 40.000 22.81 5.36 37.10 3.18
6988 13466 6.317789 TCCATTCTGTTCAAGTTTTGCTAG 57.682 37.500 0.00 0.00 0.00 3.42
7033 13512 3.866910 TGACTAAAACAGACCGTGACAAC 59.133 43.478 0.00 0.00 0.00 3.32
7035 13514 4.510571 ACTAAAACAGACCGTGACAACTT 58.489 39.130 0.00 0.00 0.00 2.66
7036 13515 4.939439 ACTAAAACAGACCGTGACAACTTT 59.061 37.500 0.00 0.00 0.00 2.66
7037 13516 4.776795 AAAACAGACCGTGACAACTTTT 57.223 36.364 0.00 0.00 0.00 2.27
7038 13517 4.776795 AAACAGACCGTGACAACTTTTT 57.223 36.364 0.00 0.00 0.00 1.94
7069 13548 2.603075 TAGCCAAAGTTCCAGCCAAT 57.397 45.000 0.00 0.00 0.00 3.16
7085 13564 3.997021 AGCCAATTACAGTTCACTTCTCG 59.003 43.478 0.00 0.00 0.00 4.04
7138 13618 7.229506 CCAAAACCTTAACCAAAAATATTGGCA 59.770 33.333 7.12 0.00 43.23 4.92
7155 13635 4.205065 TGGCAAGCCAAATTTTGATAGG 57.795 40.909 12.11 0.00 44.12 2.57
7156 13636 3.837146 TGGCAAGCCAAATTTTGATAGGA 59.163 39.130 12.11 0.00 44.12 2.94
7157 13637 4.470664 TGGCAAGCCAAATTTTGATAGGAT 59.529 37.500 12.11 0.00 44.12 3.24
7158 13638 5.045724 TGGCAAGCCAAATTTTGATAGGATT 60.046 36.000 12.11 0.00 44.12 3.01
7159 13639 5.882000 GGCAAGCCAAATTTTGATAGGATTT 59.118 36.000 10.72 0.00 35.81 2.17
7200 13680 1.337728 CCAAGCACGACCATCACACTA 60.338 52.381 0.00 0.00 0.00 2.74
7220 13700 0.099436 GGCTGCTTAGGAATGTTGCG 59.901 55.000 0.00 0.00 0.00 4.85
7224 13704 0.524180 GCTTAGGAATGTTGCGCTGC 60.524 55.000 9.73 1.25 0.00 5.25
7255 13735 1.332375 TGGTTTCGGTTTGCTTCTTCG 59.668 47.619 0.00 0.00 0.00 3.79
7300 13781 3.351416 GGCGTCGGTGTGTTTCCC 61.351 66.667 0.00 0.00 0.00 3.97
7308 13789 1.202245 CGGTGTGTTTCCCTTTGTGTG 60.202 52.381 0.00 0.00 0.00 3.82
7315 13796 3.068873 TGTTTCCCTTTGTGTGTATTGGC 59.931 43.478 0.00 0.00 0.00 4.52
7389 13888 5.523916 CCGTCTCGATGTAAATCAATTCCTT 59.476 40.000 0.00 0.00 0.00 3.36
7426 13925 5.546621 ACAGAAGACAAACCAGCTTACTA 57.453 39.130 0.00 0.00 0.00 1.82
7466 13965 4.055360 CACTTTCGTGATCTACACCAACA 58.945 43.478 0.00 0.00 45.73 3.33
7507 14006 5.414789 TTCCTTTCACATGTCTTCCGATA 57.585 39.130 0.00 0.00 0.00 2.92
7508 14007 5.614324 TCCTTTCACATGTCTTCCGATAT 57.386 39.130 0.00 0.00 0.00 1.63
7511 14010 8.417273 TCCTTTCACATGTCTTCCGATATATA 57.583 34.615 0.00 0.00 0.00 0.86
7629 14133 3.334583 TTCTGTAGAACATCAGTGGCC 57.665 47.619 0.00 0.00 33.89 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 105 1.410004 CTATAGGACGGGGTGAGCAA 58.590 55.000 0.00 0.00 0.00 3.91
97 106 1.113517 GCTATAGGACGGGGTGAGCA 61.114 60.000 1.04 0.00 0.00 4.26
462 2192 0.322456 CCCTTGGAGGCATTTCGTCA 60.322 55.000 0.00 0.00 32.73 4.35
523 5526 0.034380 TCCTCGTCCTCGTCCTCATT 60.034 55.000 0.00 0.00 38.33 2.57
585 5612 6.098124 AGTTCATCCAACCAAGTTCAAAATGA 59.902 34.615 0.00 0.00 35.28 2.57
635 5663 5.779529 AACAAGTTGATGAAGTTCATGCT 57.220 34.783 22.93 14.08 37.20 3.79
789 5930 1.743623 ATCGGTTGATTTGGCGCGA 60.744 52.632 12.10 0.00 0.00 5.87
816 5957 0.724453 CGCGCAAAAACACATACGCT 60.724 50.000 8.75 0.00 43.85 5.07
819 5960 1.323791 GGTCGCGCAAAAACACATAC 58.676 50.000 8.75 0.00 0.00 2.39
823 5964 2.001880 GTCGGTCGCGCAAAAACAC 61.002 57.895 8.75 0.00 0.00 3.32
1479 7543 6.978343 ACAAAGCTGCAATATAGTAAACGA 57.022 33.333 1.02 0.00 0.00 3.85
1494 7558 1.308998 AGGACCAACGAACAAAGCTG 58.691 50.000 0.00 0.00 0.00 4.24
1505 7572 2.678190 GCAGTGGATGTCTAGGACCAAC 60.678 54.545 0.00 0.00 34.11 3.77
1568 7635 5.163581 GCAACAGATCATTGGAAGCTAATGT 60.164 40.000 10.68 0.00 36.97 2.71
1668 7735 5.036117 TGTAGATAACAAGGGATTGGCTC 57.964 43.478 0.00 0.00 34.29 4.70
1689 7756 6.183361 ACCTATGGAGCTACTGGTCTTTTATG 60.183 42.308 0.00 0.00 40.29 1.90
1707 7774 3.069300 CCATCTCAGTCAGTGACCTATGG 59.931 52.174 19.71 20.18 32.46 2.74
2173 8253 7.345691 TGGCTAGGAACTGAAATCATGAAATA 58.654 34.615 0.00 0.00 41.52 1.40
2174 8254 6.189859 TGGCTAGGAACTGAAATCATGAAAT 58.810 36.000 0.00 0.00 41.52 2.17
2175 8255 5.569355 TGGCTAGGAACTGAAATCATGAAA 58.431 37.500 0.00 0.00 41.52 2.69
2176 8256 5.178096 TGGCTAGGAACTGAAATCATGAA 57.822 39.130 0.00 0.00 41.52 2.57
2177 8257 4.225942 ACTGGCTAGGAACTGAAATCATGA 59.774 41.667 0.85 0.00 41.52 3.07
2195 8275 7.507786 GACAAAAGGTCAATCCAGAACTGGC 62.508 48.000 15.20 2.01 46.81 4.85
2210 8290 8.237811 AGAAAAAGTATGTCATGACAAAAGGT 57.762 30.769 31.00 17.27 45.41 3.50
2228 8308 2.029560 GCCTGCCCAGAAGAAGAAAAAG 60.030 50.000 0.00 0.00 0.00 2.27
2281 8361 4.053983 CGTGAGATGAACTGTCATATGGG 58.946 47.826 2.13 0.00 44.83 4.00
2803 8898 7.035004 TGAAGAAAACTGTCTGAAATTGGTTG 58.965 34.615 0.00 0.00 0.00 3.77
2804 8899 7.169158 TGAAGAAAACTGTCTGAAATTGGTT 57.831 32.000 0.00 0.00 0.00 3.67
2917 9012 5.200368 CTGTCCAGCAACCACTAAATTTT 57.800 39.130 0.00 0.00 0.00 1.82
2947 9042 2.254459 CTGTACGCATGAGACAGACAC 58.746 52.381 17.64 2.74 42.65 3.67
2983 9080 3.004315 CGTTGGCTGTATTTTCACAAGGT 59.996 43.478 0.00 0.00 0.00 3.50
3020 9117 2.989909 TCCACATCCACACACATCATC 58.010 47.619 0.00 0.00 0.00 2.92
3053 9150 6.373779 ACGTTGAAGAATATGCAACAGAAAG 58.626 36.000 0.00 0.00 41.34 2.62
3195 9482 6.375174 TGATGTTTCATCCTCACCAAATGTAG 59.625 38.462 7.18 0.00 0.00 2.74
3225 9512 8.021973 CGTTGTTGTCTGTATAAACTACTCTCT 58.978 37.037 0.00 0.00 30.59 3.10
3313 9600 8.980610 CAATGCAACATTCAATCTAAAGTGAAA 58.019 29.630 0.00 0.00 42.21 2.69
3316 9603 7.878477 ACAATGCAACATTCAATCTAAAGTG 57.122 32.000 0.00 0.00 0.00 3.16
3358 9645 6.570378 CGGTCAGGAGCAAAAACAGATTTATT 60.570 38.462 0.00 0.00 0.00 1.40
3367 9654 0.668535 AAGCGGTCAGGAGCAAAAAC 59.331 50.000 0.00 0.00 35.48 2.43
3382 9670 4.260375 CGGTGAATCCAGAAAATAGAAGCG 60.260 45.833 0.00 0.00 35.57 4.68
3391 9679 4.224147 TCAATCTACCGGTGAATCCAGAAA 59.776 41.667 19.93 0.00 35.57 2.52
3393 9681 3.371034 TCAATCTACCGGTGAATCCAGA 58.629 45.455 19.93 11.55 35.57 3.86
3423 9711 1.066605 AGCAAGTTTCACAAGCAGCAG 59.933 47.619 0.00 0.00 0.00 4.24
3426 9714 3.637998 ATGAGCAAGTTTCACAAGCAG 57.362 42.857 0.00 0.00 0.00 4.24
3628 9972 6.738114 TGCTGATTCCACTTTTACTTTTCTG 58.262 36.000 0.00 0.00 0.00 3.02
3636 9980 7.285401 GGATTCCTATTGCTGATTCCACTTTTA 59.715 37.037 0.00 0.00 33.34 1.52
3832 10176 5.672194 ACTCCCAATACATCAGGAAGGTAAT 59.328 40.000 0.00 0.00 0.00 1.89
3842 10186 3.010027 TGGCTGAAACTCCCAATACATCA 59.990 43.478 0.00 0.00 0.00 3.07
3865 10209 2.111384 ACAACTCAGTCGGCCATCTAT 58.889 47.619 2.24 0.00 0.00 1.98
3938 10282 6.030727 AGAGGCCCAATAAATTTGGAGTAT 57.969 37.500 0.00 0.00 42.06 2.12
3980 10324 3.495331 TCTGTTGATAGCCAAGGCAAAA 58.505 40.909 14.40 0.00 44.88 2.44
4189 10533 2.175931 ACAACCCAGGACAAACCATACA 59.824 45.455 0.00 0.00 42.04 2.29
4321 10670 4.335315 TCTCCCTTGTAATTTGCGCATAAG 59.665 41.667 12.75 9.22 0.00 1.73
4322 10671 4.265893 TCTCCCTTGTAATTTGCGCATAA 58.734 39.130 12.75 9.32 0.00 1.90
4323 10672 3.879998 TCTCCCTTGTAATTTGCGCATA 58.120 40.909 12.75 7.07 0.00 3.14
4324 10673 2.722094 TCTCCCTTGTAATTTGCGCAT 58.278 42.857 12.75 0.00 0.00 4.73
4325 10674 2.192664 TCTCCCTTGTAATTTGCGCA 57.807 45.000 5.66 5.66 0.00 6.09
4327 10676 4.155826 TGAACATCTCCCTTGTAATTTGCG 59.844 41.667 0.00 0.00 0.00 4.85
4328 10677 5.415701 TCTGAACATCTCCCTTGTAATTTGC 59.584 40.000 0.00 0.00 0.00 3.68
4329 10678 6.656693 ACTCTGAACATCTCCCTTGTAATTTG 59.343 38.462 0.00 0.00 0.00 2.32
4332 10681 6.176183 CAACTCTGAACATCTCCCTTGTAAT 58.824 40.000 0.00 0.00 0.00 1.89
4333 10682 5.071788 ACAACTCTGAACATCTCCCTTGTAA 59.928 40.000 0.00 0.00 0.00 2.41
4334 10683 4.593206 ACAACTCTGAACATCTCCCTTGTA 59.407 41.667 0.00 0.00 0.00 2.41
4342 10691 7.974501 CGGTAATTAGTACAACTCTGAACATCT 59.025 37.037 0.00 0.00 34.01 2.90
5635 12102 3.636764 ACAACAAAGCCTTTAGTCCCAAG 59.363 43.478 0.00 0.00 0.00 3.61
5709 12176 4.005650 CTGAAGATGGAAAGCTAACAGCA 58.994 43.478 0.38 0.00 45.56 4.41
5775 12242 7.602753 CAGGGTTAGGGAAACAAATAAAAGAG 58.397 38.462 0.00 0.00 40.08 2.85
5957 12424 4.917906 AGGGGGCAGAAGATTGATATAC 57.082 45.455 0.00 0.00 0.00 1.47
5993 12460 2.480419 AGTACGCAAATCAAGCACTGTC 59.520 45.455 0.00 0.00 0.00 3.51
5999 12466 3.429085 CATTCCAGTACGCAAATCAAGC 58.571 45.455 0.00 0.00 0.00 4.01
6146 12613 2.100631 CGTTACTGAAGCTGGGCCG 61.101 63.158 0.00 0.00 0.00 6.13
6176 12643 3.265791 GAGAACAGCAGTGGAATCGATT 58.734 45.455 11.20 11.20 0.00 3.34
6234 12701 2.354704 CCAACGTAGCCTTCAGATCCAA 60.355 50.000 0.00 0.00 0.00 3.53
6293 12760 7.446106 TTGGCCTCCTTCTAATATAGTTGAA 57.554 36.000 3.32 0.00 0.00 2.69
6450 12917 0.179004 TTTGTTCCCGGTGCATCACT 60.179 50.000 0.00 0.00 34.40 3.41
6460 12927 2.739913 TCAAGAACGCTATTTGTTCCCG 59.260 45.455 2.48 0.00 45.33 5.14
6493 12960 2.084546 CTGCCTGCTTTACCAAGGTAC 58.915 52.381 0.00 0.00 0.00 3.34
6580 13047 4.121317 CAAAGTTTTGCCATCTTGAAGCA 58.879 39.130 0.00 0.00 33.97 3.91
6827 13295 5.476254 TGGCATATGAAACAATCACACTTCA 59.524 36.000 6.97 0.00 41.93 3.02
6828 13296 5.953183 TGGCATATGAAACAATCACACTTC 58.047 37.500 6.97 0.00 41.93 3.01
6829 13297 5.981088 TGGCATATGAAACAATCACACTT 57.019 34.783 6.97 0.00 41.93 3.16
6830 13298 5.068198 GGATGGCATATGAAACAATCACACT 59.932 40.000 6.97 0.00 41.93 3.55
6831 13299 5.068198 AGGATGGCATATGAAACAATCACAC 59.932 40.000 6.97 0.00 41.93 3.82
6905 13380 7.506328 ACTAATCTGGGTTGTGTTAGTTTTC 57.494 36.000 0.00 0.00 33.19 2.29
6976 13454 8.981647 ACATTAGCAAATTTCTAGCAAAACTTG 58.018 29.630 2.29 0.00 0.00 3.16
6988 13466 6.873076 TCACCATCCAAACATTAGCAAATTTC 59.127 34.615 0.00 0.00 0.00 2.17
7045 13524 1.745653 GCTGGAACTTTGGCTATGACC 59.254 52.381 0.00 0.00 0.00 4.02
7046 13525 1.745653 GGCTGGAACTTTGGCTATGAC 59.254 52.381 0.00 0.00 0.00 3.06
7050 13529 2.603075 ATTGGCTGGAACTTTGGCTA 57.397 45.000 0.00 0.00 0.00 3.93
7062 13541 4.143030 CGAGAAGTGAACTGTAATTGGCTG 60.143 45.833 0.00 0.00 0.00 4.85
7069 13548 5.163530 TGTTGGTACGAGAAGTGAACTGTAA 60.164 40.000 0.00 0.00 0.00 2.41
7103 13582 7.893124 TTGGTTAAGGTTTTGGTTGTACATA 57.107 32.000 0.00 0.00 0.00 2.29
7104 13583 6.793505 TTGGTTAAGGTTTTGGTTGTACAT 57.206 33.333 0.00 0.00 0.00 2.29
7105 13584 6.600882 TTTGGTTAAGGTTTTGGTTGTACA 57.399 33.333 0.00 0.00 0.00 2.90
7106 13585 7.902387 TTTTTGGTTAAGGTTTTGGTTGTAC 57.098 32.000 0.00 0.00 0.00 2.90
7108 13587 9.688091 AATATTTTTGGTTAAGGTTTTGGTTGT 57.312 25.926 0.00 0.00 0.00 3.32
7154 13634 1.407299 GCCCAAGCCAAATCCAAATCC 60.407 52.381 0.00 0.00 0.00 3.01
7155 13635 1.556451 AGCCCAAGCCAAATCCAAATC 59.444 47.619 0.00 0.00 41.25 2.17
7156 13636 1.556451 GAGCCCAAGCCAAATCCAAAT 59.444 47.619 0.00 0.00 41.25 2.32
7157 13637 0.975887 GAGCCCAAGCCAAATCCAAA 59.024 50.000 0.00 0.00 41.25 3.28
7158 13638 0.178938 TGAGCCCAAGCCAAATCCAA 60.179 50.000 0.00 0.00 41.25 3.53
7159 13639 0.178938 TTGAGCCCAAGCCAAATCCA 60.179 50.000 0.00 0.00 41.25 3.41
7200 13680 1.467920 GCAACATTCCTAAGCAGCCT 58.532 50.000 0.00 0.00 0.00 4.58
7224 13704 2.333581 GAAACCAACAACCGCCCG 59.666 61.111 0.00 0.00 0.00 6.13
7228 13708 1.551145 CAAACCGAAACCAACAACCG 58.449 50.000 0.00 0.00 0.00 4.44
7229 13709 1.134936 AGCAAACCGAAACCAACAACC 60.135 47.619 0.00 0.00 0.00 3.77
7300 13781 0.525761 CCCCGCCAATACACACAAAG 59.474 55.000 0.00 0.00 0.00 2.77
7308 13789 1.149627 TATGCCACCCCGCCAATAC 59.850 57.895 0.00 0.00 0.00 1.89
7315 13796 2.906897 GCCATGTATGCCACCCCG 60.907 66.667 0.00 0.00 0.00 5.73
7466 13965 6.933514 AGGAAACAAATAATGAATGTGGGT 57.066 33.333 0.00 0.00 0.00 4.51
7520 14019 6.420638 TCTCCACACTGATCATGAAATCAAT 58.579 36.000 0.00 0.00 35.32 2.57


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

AutoCloner maintained by Alex Coulton.