Multiple sequence alignment - TraesCS1B01G171800

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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 TraesCS1B01G171800 chr1B 100.000 4686 0 0 3702 8387 305540339 305545024 0.000000e+00 8654.0
1 TraesCS1B01G171800 chr1B 100.000 3371 0 0 1 3371 305536638 305540008 0.000000e+00 6226.0
2 TraesCS1B01G171800 chr1B 87.037 1188 141 7 6082 7258 302222616 302221431 0.000000e+00 1328.0
3 TraesCS1B01G171800 chr1B 87.800 459 39 6 17 464 415214450 415213998 9.650000e-144 521.0
4 TraesCS1B01G171800 chr1B 92.090 354 21 5 243 596 653809852 653810198 7.560000e-135 492.0
5 TraesCS1B01G171800 chr1B 83.448 435 63 5 5638 6063 302228256 302227822 6.100000e-106 396.0
6 TraesCS1B01G171800 chr1B 89.796 98 7 3 7436 7531 612866162 612866258 1.140000e-23 122.0
7 TraesCS1B01G171800 chr1B 88.764 89 10 0 5264 5352 581199163 581199075 8.900000e-20 110.0
8 TraesCS1B01G171800 chr1B 87.500 96 4 6 4629 4719 603534843 603534751 4.140000e-18 104.0
9 TraesCS1B01G171800 chr1B 87.234 94 6 4 4629 4718 110607342 110607251 1.490000e-17 102.0
10 TraesCS1B01G171800 chr1B 100.000 30 0 0 5214 5243 627939369 627939340 1.000000e-03 56.5
11 TraesCS1B01G171800 chr1A 93.963 2203 98 16 5242 7442 265647855 265645686 0.000000e+00 3299.0
12 TraesCS1B01G171800 chr1A 91.430 1832 68 39 595 2385 265650891 265649108 0.000000e+00 2431.0
13 TraesCS1B01G171800 chr1A 86.152 1632 215 7 5637 7258 265034624 265032994 0.000000e+00 1751.0
14 TraesCS1B01G171800 chr1A 97.822 597 12 1 1 596 119491522 119490926 0.000000e+00 1029.0
15 TraesCS1B01G171800 chr1A 92.781 471 25 5 4709 5171 265648326 265647857 0.000000e+00 673.0
16 TraesCS1B01G171800 chr1A 94.241 382 14 4 4118 4497 265649110 265648735 2.030000e-160 577.0
17 TraesCS1B01G171800 chr1A 87.377 507 51 7 96 596 301862158 301862657 3.400000e-158 569.0
18 TraesCS1B01G171800 chr1A 84.310 529 68 9 7647 8165 543776969 543776446 3.490000e-138 503.0
19 TraesCS1B01G171800 chr1D 94.526 2119 96 13 5241 7357 211305316 211303216 0.000000e+00 3253.0
20 TraesCS1B01G171800 chr1D 93.220 1829 59 25 600 2386 211308332 211306527 0.000000e+00 2630.0
21 TraesCS1B01G171800 chr1D 85.898 1631 219 7 5638 7258 206503730 206502101 0.000000e+00 1727.0
22 TraesCS1B01G171800 chr1D 92.994 471 21 3 4714 5172 211305786 211305316 0.000000e+00 676.0
23 TraesCS1B01G171800 chr1D 82.810 669 81 20 7641 8291 199261465 199262117 1.220000e-157 568.0
24 TraesCS1B01G171800 chr1D 92.798 361 21 3 4118 4474 211306530 211306171 1.250000e-142 518.0
25 TraesCS1B01G171800 chr1D 84.428 533 60 13 7646 8165 447692329 447691807 3.490000e-138 503.0
26 TraesCS1B01G171800 chr1D 86.364 110 6 7 4607 4712 200826086 200825982 2.470000e-20 111.0
27 TraesCS1B01G171800 chr1D 90.698 86 4 3 4629 4712 337895919 337895836 2.470000e-20 111.0
28 TraesCS1B01G171800 chr1D 88.608 79 8 1 5262 5339 77379752 77379830 2.490000e-15 95.3
29 TraesCS1B01G171800 chr1D 92.593 54 4 0 8334 8387 30434009 30434062 2.510000e-10 78.7
30 TraesCS1B01G171800 chr1D 81.707 82 11 4 8306 8386 37799346 37799268 1.950000e-06 65.8
31 TraesCS1B01G171800 chr5B 98.580 986 14 0 2386 3371 422112711 422111726 0.000000e+00 1744.0
32 TraesCS1B01G171800 chr5B 99.070 215 2 0 3702 3916 422111679 422111465 3.670000e-103 387.0
33 TraesCS1B01G171800 chr5B 87.500 104 11 2 7436 7538 659822378 659822276 1.480000e-22 119.0
34 TraesCS1B01G171800 chr5B 86.567 67 7 2 8321 8387 621584198 621584262 1.170000e-08 73.1
35 TraesCS1B01G171800 chr5B 100.000 29 0 0 3758 3786 579516931 579516959 4.000000e-03 54.7
36 TraesCS1B01G171800 chr3A 98.580 986 14 0 2386 3371 704969916 704968931 0.000000e+00 1744.0
37 TraesCS1B01G171800 chr3A 97.251 982 27 0 2386 3367 58863766 58864747 0.000000e+00 1664.0
38 TraesCS1B01G171800 chr3A 97.021 940 28 0 2386 3325 395760550 395759611 0.000000e+00 1581.0
39 TraesCS1B01G171800 chr3A 99.020 408 4 0 3702 4109 704967993 704967586 0.000000e+00 732.0
40 TraesCS1B01G171800 chr3A 98.768 406 5 0 3702 4107 395759172 395758767 0.000000e+00 723.0
41 TraesCS1B01G171800 chr3A 95.181 83 3 1 7436 7517 181675550 181675632 6.830000e-26 130.0
42 TraesCS1B01G171800 chr3A 85.981 107 5 8 4613 4711 465214459 465214563 1.150000e-18 106.0
43 TraesCS1B01G171800 chr3A 87.500 96 4 6 4622 4712 750297133 750297225 4.140000e-18 104.0
44 TraesCS1B01G171800 chr3A 85.149 101 8 5 4629 4725 736118053 736118150 6.930000e-16 97.1
45 TraesCS1B01G171800 chr3A 93.443 61 3 1 5171 5230 527230012 527229952 1.160000e-13 89.8
46 TraesCS1B01G171800 chr3A 100.000 43 0 0 3329 3371 395759261 395759219 6.980000e-11 80.5
47 TraesCS1B01G171800 chr6B 98.479 986 15 0 2386 3371 479070528 479071513 0.000000e+00 1738.0
48 TraesCS1B01G171800 chr6B 98.154 921 17 0 2451 3371 708238816 708239736 0.000000e+00 1607.0
49 TraesCS1B01G171800 chr6B 97.487 597 14 1 1 596 177563004 177563600 0.000000e+00 1018.0
50 TraesCS1B01G171800 chr6B 98.529 408 6 0 3702 4109 708239783 708240190 0.000000e+00 721.0
51 TraesCS1B01G171800 chr6B 87.657 478 48 6 7732 8200 693461208 693461683 5.720000e-151 545.0
52 TraesCS1B01G171800 chr6B 98.305 118 2 0 3702 3819 479071560 479071677 3.070000e-49 207.0
53 TraesCS1B01G171800 chr6B 90.741 108 10 0 8233 8340 693461803 693461910 2.440000e-30 145.0
54 TraesCS1B01G171800 chr6B 88.542 96 5 4 4626 4717 531739476 531739569 2.470000e-20 111.0
55 TraesCS1B01G171800 chr6B 87.368 95 6 4 4629 4719 639915408 639915316 4.140000e-18 104.0
56 TraesCS1B01G171800 chr6B 88.525 61 7 0 8327 8387 192985567 192985507 3.250000e-09 75.0
57 TraesCS1B01G171800 chr6B 85.526 76 6 5 537 609 714644648 714644575 3.250000e-09 75.0
58 TraesCS1B01G171800 chr6A 97.757 981 22 0 2387 3367 602216784 602215804 0.000000e+00 1690.0
59 TraesCS1B01G171800 chr6A 97.052 407 11 1 3702 4107 17902679 17902273 0.000000e+00 684.0
60 TraesCS1B01G171800 chr6A 89.583 96 4 4 4628 4719 613688332 613688239 5.320000e-22 117.0
61 TraesCS1B01G171800 chr6A 86.735 98 7 4 4628 4721 591742031 591741936 4.140000e-18 104.0
62 TraesCS1B01G171800 chr6A 91.667 72 6 0 5269 5340 57749776 57749705 5.360000e-17 100.0
63 TraesCS1B01G171800 chr5A 96.636 981 23 2 2388 3367 657556729 657557700 0.000000e+00 1620.0
64 TraesCS1B01G171800 chr5A 91.411 326 14 7 3785 4109 601719041 601719353 1.290000e-117 435.0
65 TraesCS1B01G171800 chr5A 89.000 100 10 1 7436 7534 35197844 35197943 1.140000e-23 122.0
66 TraesCS1B01G171800 chr5A 89.000 100 10 1 7436 7534 438917577 438917478 1.140000e-23 122.0
67 TraesCS1B01G171800 chr5A 89.130 92 3 5 4624 4711 271053602 271053514 3.200000e-19 108.0
68 TraesCS1B01G171800 chr4A 98.523 880 13 0 2386 3265 699039230 699038351 0.000000e+00 1554.0
69 TraesCS1B01G171800 chr4A 83.948 542 39 20 7821 8332 38326498 38325975 7.620000e-130 475.0
70 TraesCS1B01G171800 chr4A 88.660 97 8 3 5257 5351 613697927 613697832 1.910000e-21 115.0
71 TraesCS1B01G171800 chr7D 92.612 582 34 6 17 596 380734406 380733832 0.000000e+00 828.0
72 TraesCS1B01G171800 chr7D 87.587 572 47 6 7773 8332 139852492 139853051 7.100000e-180 641.0
73 TraesCS1B01G171800 chr7D 94.839 155 8 0 8188 8342 139853039 139853193 8.410000e-60 243.0
74 TraesCS1B01G171800 chr7D 82.051 156 19 7 8187 8342 554910002 554910148 3.180000e-24 124.0
75 TraesCS1B01G171800 chr7D 90.000 90 8 1 5262 5350 199607047 199607136 1.910000e-21 115.0
76 TraesCS1B01G171800 chr7D 90.000 90 8 1 5262 5350 485106549 485106460 1.910000e-21 115.0
77 TraesCS1B01G171800 chr7D 90.000 90 8 1 5262 5350 511228101 511228012 1.910000e-21 115.0
78 TraesCS1B01G171800 chr7D 90.164 61 6 0 8326 8386 188342501 188342441 6.980000e-11 80.5
79 TraesCS1B01G171800 chr4B 83.356 721 78 12 7645 8342 454530312 454529611 5.530000e-176 628.0
80 TraesCS1B01G171800 chr4B 89.796 98 7 3 7436 7531 107776873 107776969 1.140000e-23 122.0
81 TraesCS1B01G171800 chr4B 87.037 108 12 2 7426 7531 654697239 654697132 4.110000e-23 121.0
82 TraesCS1B01G171800 chr3D 86.498 474 42 7 17 481 280191098 280190638 1.260000e-137 501.0
83 TraesCS1B01G171800 chr3D 88.308 402 35 10 7642 8041 28964855 28965246 9.850000e-129 472.0
84 TraesCS1B01G171800 chr3D 83.396 530 55 14 7645 8165 10830901 10831406 2.130000e-125 460.0
85 TraesCS1B01G171800 chr3D 85.567 97 8 4 4626 4718 405817981 405817887 6.930000e-16 97.1
86 TraesCS1B01G171800 chr3D 86.076 79 8 3 5149 5224 468976893 468976971 1.940000e-11 82.4
87 TraesCS1B01G171800 chr3D 84.146 82 9 4 5276 5354 441024129 441024049 9.030000e-10 76.8
88 TraesCS1B01G171800 chr3D 88.525 61 7 0 8327 8387 103735407 103735467 3.250000e-09 75.0
89 TraesCS1B01G171800 chr3B 82.462 593 74 14 20 597 103907099 103906522 7.560000e-135 492.0
90 TraesCS1B01G171800 chr3B 92.675 314 23 0 283 596 442087099 442087412 3.570000e-123 453.0
91 TraesCS1B01G171800 chr3B 80.632 253 42 6 7645 7896 15114822 15114576 1.110000e-43 189.0
92 TraesCS1B01G171800 chr3B 80.228 263 39 11 3853 4109 820112315 820112570 1.440000e-42 185.0
93 TraesCS1B01G171800 chr3B 90.816 98 7 2 7436 7531 771996927 771996830 6.830000e-26 130.0
94 TraesCS1B01G171800 chr4D 87.298 433 39 8 55 478 355000807 355001232 1.640000e-131 481.0
95 TraesCS1B01G171800 chr4D 75.835 389 58 25 7961 8325 442565551 442565927 1.870000e-36 165.0
96 TraesCS1B01G171800 chr4D 82.192 146 18 6 8187 8331 432420056 432419918 1.480000e-22 119.0
97 TraesCS1B01G171800 chr4D 84.043 94 13 2 5265 5358 66516846 66516755 1.160000e-13 89.8
98 TraesCS1B01G171800 chr4D 88.406 69 7 1 5164 5231 109074978 109074910 1.940000e-11 82.4
99 TraesCS1B01G171800 chr4D 92.593 54 4 0 8334 8387 427315502 427315449 2.510000e-10 78.7
100 TraesCS1B01G171800 chr2D 85.593 472 43 12 17 478 599455388 599454932 9.850000e-129 472.0
101 TraesCS1B01G171800 chr2D 85.321 327 25 3 3785 4110 142717378 142717682 4.890000e-82 316.0
102 TraesCS1B01G171800 chr2D 81.955 266 33 12 3852 4109 601985524 601985782 2.370000e-50 211.0
103 TraesCS1B01G171800 chr2D 87.912 91 8 3 5262 5350 507261282 507261371 4.140000e-18 104.0
104 TraesCS1B01G171800 chr2D 92.188 64 4 1 5162 5224 7202108 7202045 1.160000e-13 89.8
105 TraesCS1B01G171800 chr2D 91.045 67 4 2 5166 5231 584873580 584873645 1.160000e-13 89.8
106 TraesCS1B01G171800 chr2D 87.671 73 6 3 5154 5224 33786924 33786853 1.940000e-11 82.4
107 TraesCS1B01G171800 chrUn 86.567 402 43 7 7645 8044 36160382 36159990 4.650000e-117 433.0
108 TraesCS1B01G171800 chr5D 84.639 319 26 14 3785 4102 565698761 565698465 6.370000e-76 296.0
109 TraesCS1B01G171800 chr5D 81.250 320 39 18 3805 4109 499443305 499442992 1.090000e-58 239.0
110 TraesCS1B01G171800 chr5D 82.270 141 17 8 8187 8326 259174705 259174572 1.910000e-21 115.0
111 TraesCS1B01G171800 chr5D 82.222 135 16 8 8187 8320 402974670 402974543 8.900000e-20 110.0
112 TraesCS1B01G171800 chr5D 89.855 69 3 4 5166 5231 510940975 510941042 1.500000e-12 86.1
113 TraesCS1B01G171800 chr5D 90.909 44 2 2 5265 5307 333071679 333071721 3.270000e-04 58.4
114 TraesCS1B01G171800 chr7A 89.720 107 9 2 7436 7540 68887575 68887681 1.470000e-27 135.0
115 TraesCS1B01G171800 chr7A 89.888 89 3 4 4628 4712 111835322 111835236 8.900000e-20 110.0
116 TraesCS1B01G171800 chr7A 89.189 74 8 0 8103 8176 684272606 684272679 8.960000e-15 93.5
117 TraesCS1B01G171800 chr7A 89.062 64 6 1 8325 8387 598764604 598764667 2.510000e-10 78.7
118 TraesCS1B01G171800 chr7A 92.727 55 0 4 555 608 261389216 261389165 9.030000e-10 76.8
119 TraesCS1B01G171800 chr7A 97.727 44 0 1 555 598 266903504 266903462 3.250000e-09 75.0
120 TraesCS1B01G171800 chr7B 90.000 90 8 1 5262 5350 540063288 540063199 1.910000e-21 115.0
121 TraesCS1B01G171800 chr7B 87.629 97 6 4 4620 4712 634299379 634299285 3.200000e-19 108.0
122 TraesCS1B01G171800 chr7B 90.909 66 3 3 5168 5231 328714743 328714807 1.500000e-12 86.1
123 TraesCS1B01G171800 chr7B 100.000 32 0 0 5212 5243 641158813 641158782 9.090000e-05 60.2
124 TraesCS1B01G171800 chr2B 82.883 111 17 2 5241 5350 9291176 9291067 1.930000e-16 99.0
125 TraesCS1B01G171800 chr6D 91.935 62 4 1 5170 5230 372879532 372879471 1.500000e-12 86.1
126 TraesCS1B01G171800 chr6D 92.727 55 4 0 8332 8386 141582915 141582861 6.980000e-11 80.5


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 TraesCS1B01G171800 chr1B 305536638 305545024 8386 False 7440.000000 8654 100.000000 1 8387 2 chr1B.!!$F3 8386
1 TraesCS1B01G171800 chr1B 302221431 302222616 1185 True 1328.000000 1328 87.037000 6082 7258 1 chr1B.!!$R2 1176
2 TraesCS1B01G171800 chr1A 265032994 265034624 1630 True 1751.000000 1751 86.152000 5637 7258 1 chr1A.!!$R2 1621
3 TraesCS1B01G171800 chr1A 265645686 265650891 5205 True 1745.000000 3299 93.103750 595 7442 4 chr1A.!!$R4 6847
4 TraesCS1B01G171800 chr1A 119490926 119491522 596 True 1029.000000 1029 97.822000 1 596 1 chr1A.!!$R1 595
5 TraesCS1B01G171800 chr1A 543776446 543776969 523 True 503.000000 503 84.310000 7647 8165 1 chr1A.!!$R3 518
6 TraesCS1B01G171800 chr1D 211303216 211308332 5116 True 1769.250000 3253 93.384500 600 7357 4 chr1D.!!$R6 6757
7 TraesCS1B01G171800 chr1D 206502101 206503730 1629 True 1727.000000 1727 85.898000 5638 7258 1 chr1D.!!$R3 1620
8 TraesCS1B01G171800 chr1D 199261465 199262117 652 False 568.000000 568 82.810000 7641 8291 1 chr1D.!!$F3 650
9 TraesCS1B01G171800 chr1D 447691807 447692329 522 True 503.000000 503 84.428000 7646 8165 1 chr1D.!!$R5 519
10 TraesCS1B01G171800 chr5B 422111465 422112711 1246 True 1065.500000 1744 98.825000 2386 3916 2 chr5B.!!$R2 1530
11 TraesCS1B01G171800 chr3A 58863766 58864747 981 False 1664.000000 1664 97.251000 2386 3367 1 chr3A.!!$F1 981
12 TraesCS1B01G171800 chr3A 704967586 704969916 2330 True 1238.000000 1744 98.800000 2386 4109 2 chr3A.!!$R3 1723
13 TraesCS1B01G171800 chr3A 395758767 395760550 1783 True 794.833333 1581 98.596333 2386 4107 3 chr3A.!!$R2 1721
14 TraesCS1B01G171800 chr6B 708238816 708240190 1374 False 1164.000000 1607 98.341500 2451 4109 2 chr6B.!!$F5 1658
15 TraesCS1B01G171800 chr6B 177563004 177563600 596 False 1018.000000 1018 97.487000 1 596 1 chr6B.!!$F1 595
16 TraesCS1B01G171800 chr6B 479070528 479071677 1149 False 972.500000 1738 98.392000 2386 3819 2 chr6B.!!$F3 1433
17 TraesCS1B01G171800 chr6B 693461208 693461910 702 False 345.000000 545 89.199000 7732 8340 2 chr6B.!!$F4 608
18 TraesCS1B01G171800 chr6A 602215804 602216784 980 True 1690.000000 1690 97.757000 2387 3367 1 chr6A.!!$R4 980
19 TraesCS1B01G171800 chr5A 657556729 657557700 971 False 1620.000000 1620 96.636000 2388 3367 1 chr5A.!!$F3 979
20 TraesCS1B01G171800 chr4A 699038351 699039230 879 True 1554.000000 1554 98.523000 2386 3265 1 chr4A.!!$R3 879
21 TraesCS1B01G171800 chr4A 38325975 38326498 523 True 475.000000 475 83.948000 7821 8332 1 chr4A.!!$R1 511
22 TraesCS1B01G171800 chr7D 380733832 380734406 574 True 828.000000 828 92.612000 17 596 1 chr7D.!!$R2 579
23 TraesCS1B01G171800 chr7D 139852492 139853193 701 False 442.000000 641 91.213000 7773 8342 2 chr7D.!!$F3 569
24 TraesCS1B01G171800 chr4B 454529611 454530312 701 True 628.000000 628 83.356000 7645 8342 1 chr4B.!!$R1 697
25 TraesCS1B01G171800 chr3D 10830901 10831406 505 False 460.000000 460 83.396000 7645 8165 1 chr3D.!!$F1 520
26 TraesCS1B01G171800 chr3B 103906522 103907099 577 True 492.000000 492 82.462000 20 597 1 chr3B.!!$R2 577

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
890 938 1.309499 CCTCGCTCCAACTCTCTCGT 61.309 60.0 0.00 0.00 0.00 4.18 F
1056 1105 0.242825 ACATACACGCACGCACTAGT 59.757 50.0 0.00 0.00 0.00 2.57 F
2124 2208 0.675522 AAATTCGCCATTCCGACCGT 60.676 50.0 0.00 0.00 36.90 4.83 F
2327 2417 0.041238 ATTCAGAGGTCAGACGGGGA 59.959 55.0 0.00 0.00 0.00 4.81 F
2328 2418 0.178944 TTCAGAGGTCAGACGGGGAA 60.179 55.0 0.00 0.00 0.00 3.97 F
3095 3186 0.539438 CATAGCTCGAGGAGGAGGCT 60.539 60.0 15.58 6.43 34.56 4.58 F
4785 6500 0.396695 CTTGTCTCCGGCCCCTACTA 60.397 60.0 0.00 0.00 0.00 1.82 F
6641 8387 0.318784 GAGGGCGGTATCATCACGAC 60.319 60.0 0.00 0.00 34.22 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2124 2208 0.035439 GGGGCCAGAATGAAAGACGA 60.035 55.0 4.39 0.0 39.69 4.20 R
2305 2395 0.460987 CCGTCTGACCTCTGAATGCC 60.461 60.0 1.55 0.0 0.00 4.40 R
3095 3186 0.326618 GGGTGGATCCTCTCCCTTCA 60.327 60.0 23.59 0.0 44.23 3.02 R
3265 4247 0.467474 ATCTGTCCCGATCCGTGCTA 60.467 55.0 0.00 0.0 0.00 3.49 R
4188 5517 0.478072 ATGAAACTGGTGTGAGCCCA 59.522 50.0 0.00 0.0 0.00 5.36 R
4817 6532 0.108138 AAGTCGCCCTGAGATTTCCG 60.108 55.0 0.00 0.0 0.00 4.30 R
6735 8481 0.250038 GGCTCATGCGCTCCTTCATA 60.250 55.0 9.73 0.0 40.82 2.15 R
7730 9481 0.250234 AGCGCCTGATGAAGCAACTA 59.750 50.0 2.29 0.0 0.00 2.24 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
53 54 4.839668 TTTTCTGTAATTGTGGAACCGG 57.160 40.909 0.00 0.00 34.36 5.28
471 482 5.049612 GGAACTAGGAAAAAGTTGAGAACCG 60.050 44.000 0.00 0.00 37.31 4.44
487 498 6.216569 TGAGAACCGCATATAAGCTTTAGAG 58.783 40.000 3.20 0.00 0.00 2.43
828 873 6.651225 AGCCGTTTTAAATGAGGAGATATAGC 59.349 38.462 0.00 0.00 0.00 2.97
890 938 1.309499 CCTCGCTCCAACTCTCTCGT 61.309 60.000 0.00 0.00 0.00 4.18
924 972 3.540014 CGCTCGCTCGCTGAGTTG 61.540 66.667 7.27 2.01 35.85 3.16
1040 1088 2.175202 ACCGAGAAGAGAGAAGCACAT 58.825 47.619 0.00 0.00 0.00 3.21
1056 1105 0.242825 ACATACACGCACGCACTAGT 59.757 50.000 0.00 0.00 0.00 2.57
1375 1424 1.202330 CCAATCTCCTCTCCTGCACT 58.798 55.000 0.00 0.00 0.00 4.40
1418 1474 3.982241 GTGGTCGTCCCGTCGGTT 61.982 66.667 11.06 0.00 35.15 4.44
1553 1613 4.754667 GGCCGGACGGACCACTTC 62.755 72.222 15.99 0.00 37.31 3.01
1554 1614 4.754667 GCCGGACGGACCACTTCC 62.755 72.222 15.99 0.00 41.75 3.46
1576 1646 6.328592 TCCCTTCCTCCCTACGAATTATTAT 58.671 40.000 0.00 0.00 0.00 1.28
1615 1685 3.061831 TGTCATTTTTGCTTTTGTGCGTG 59.938 39.130 0.00 0.00 35.36 5.34
1724 1797 1.227249 TTGTTTGTCCCCTTCTCCCA 58.773 50.000 0.00 0.00 0.00 4.37
1725 1798 1.227249 TGTTTGTCCCCTTCTCCCAA 58.773 50.000 0.00 0.00 0.00 4.12
1726 1799 1.133606 TGTTTGTCCCCTTCTCCCAAC 60.134 52.381 0.00 0.00 0.00 3.77
2012 2086 4.877378 ACGTCTTCTACACCATGGTAAA 57.123 40.909 19.28 7.66 0.00 2.01
2013 2087 4.817517 ACGTCTTCTACACCATGGTAAAG 58.182 43.478 19.28 17.42 0.00 1.85
2016 2090 5.393787 CGTCTTCTACACCATGGTAAAGCTA 60.394 44.000 19.28 8.27 0.00 3.32
2078 2162 5.477510 AGTAGTTTGCATGAGTCTCTCAAG 58.522 41.667 0.00 1.01 44.04 3.02
2083 2167 1.654317 CATGAGTCTCTCAAGCTGGC 58.346 55.000 0.65 0.00 44.04 4.85
2084 2168 1.066358 CATGAGTCTCTCAAGCTGGCA 60.066 52.381 0.65 0.00 44.04 4.92
2124 2208 0.675522 AAATTCGCCATTCCGACCGT 60.676 50.000 0.00 0.00 36.90 4.83
2167 2251 2.949177 TGGCAACTTAAGGCTTCAGA 57.051 45.000 15.05 0.00 37.61 3.27
2254 2338 5.940192 AAAAATTCAAATTTTCGAGGGGC 57.060 34.783 12.48 0.00 45.16 5.80
2305 2395 1.446907 CTCCTTGCTGTACTTGCAGG 58.553 55.000 13.54 13.54 41.71 4.85
2324 2414 0.460987 GGCATTCAGAGGTCAGACGG 60.461 60.000 0.00 0.00 0.00 4.79
2325 2415 0.460987 GCATTCAGAGGTCAGACGGG 60.461 60.000 0.00 0.00 0.00 5.28
2326 2416 0.176680 CATTCAGAGGTCAGACGGGG 59.823 60.000 0.00 0.00 0.00 5.73
2327 2417 0.041238 ATTCAGAGGTCAGACGGGGA 59.959 55.000 0.00 0.00 0.00 4.81
2328 2418 0.178944 TTCAGAGGTCAGACGGGGAA 60.179 55.000 0.00 0.00 0.00 3.97
2382 2472 2.697761 GGCCTGCACTGCATGTCTG 61.698 63.158 3.64 0.00 38.13 3.51
2441 2532 2.422276 CATCTGGTCGATGCATACGA 57.578 50.000 14.50 14.50 42.75 3.43
2595 2686 1.302033 CAGACCTCGCAGCCAAACT 60.302 57.895 0.00 0.00 0.00 2.66
2731 2822 5.541868 CCTACCACATATCCATCTTCAGAGT 59.458 44.000 0.00 0.00 0.00 3.24
3095 3186 0.539438 CATAGCTCGAGGAGGAGGCT 60.539 60.000 15.58 6.43 34.56 4.58
3188 4170 4.351054 CGCCAGCCAGGGGTTTCT 62.351 66.667 2.06 0.00 44.93 2.52
4188 5517 2.498167 CACTGGCTTGCTAACTGAACT 58.502 47.619 0.00 0.00 0.00 3.01
4220 5550 3.486841 CCAGTTTCATGCTCGTGTTTTTG 59.513 43.478 0.00 0.00 0.00 2.44
4230 5560 1.819288 TCGTGTTTTTGGCCTGAAACA 59.181 42.857 24.17 24.17 41.84 2.83
4262 5592 3.463127 GTTTCGATTTGAACACGTACCG 58.537 45.455 0.00 0.00 35.97 4.02
4290 5620 1.409427 GAGACGGAACCATTCTCGGAT 59.591 52.381 0.00 0.00 0.00 4.18
4329 5659 6.995686 TGCAGTTCCTATCACTCTTTTTGTTA 59.004 34.615 0.00 0.00 0.00 2.41
4387 5720 1.165270 AGTTGGACATTGCGTAAGGC 58.835 50.000 0.00 0.00 43.96 4.35
4440 5773 6.349300 ACTGTCACCATTATATTCCTCACAC 58.651 40.000 0.00 0.00 0.00 3.82
4498 6206 5.409643 CGGAGCACATGGTTTCTTTATAG 57.590 43.478 0.00 0.00 0.00 1.31
4551 6259 5.903010 ACACCTCATAGTTGTGGGACATATA 59.097 40.000 0.00 0.00 44.52 0.86
4552 6260 6.042093 ACACCTCATAGTTGTGGGACATATAG 59.958 42.308 0.00 0.00 44.52 1.31
4569 6277 6.058183 ACATATAGTCCTTGCATTCTGGAAC 58.942 40.000 0.00 0.00 0.00 3.62
4712 6423 8.822652 ATATTAATTTTTACGGAGGGAGTACG 57.177 34.615 0.00 0.00 0.00 3.67
4713 6424 4.806640 AATTTTTACGGAGGGAGTACGA 57.193 40.909 0.00 0.00 0.00 3.43
4714 6425 4.806640 ATTTTTACGGAGGGAGTACGAA 57.193 40.909 0.00 0.00 0.00 3.85
4715 6426 4.599047 TTTTTACGGAGGGAGTACGAAA 57.401 40.909 0.00 0.00 0.00 3.46
4716 6427 4.806640 TTTTACGGAGGGAGTACGAAAT 57.193 40.909 0.00 0.00 0.00 2.17
4717 6428 5.913137 TTTTACGGAGGGAGTACGAAATA 57.087 39.130 0.00 0.00 0.00 1.40
4718 6429 5.913137 TTTACGGAGGGAGTACGAAATAA 57.087 39.130 0.00 0.00 0.00 1.40
4719 6430 5.505173 TTACGGAGGGAGTACGAAATAAG 57.495 43.478 0.00 0.00 0.00 1.73
4720 6431 3.624777 ACGGAGGGAGTACGAAATAAGA 58.375 45.455 0.00 0.00 0.00 2.10
4721 6432 4.019174 ACGGAGGGAGTACGAAATAAGAA 58.981 43.478 0.00 0.00 0.00 2.52
4785 6500 0.396695 CTTGTCTCCGGCCCCTACTA 60.397 60.000 0.00 0.00 0.00 1.82
4813 6528 3.999001 TCAGTACACAGTGGAGTAGTACG 59.001 47.826 5.31 0.00 39.84 3.67
4817 6532 0.886563 ACAGTGGAGTAGTACGCACC 59.113 55.000 6.37 6.79 0.00 5.01
4915 6636 2.408704 CGCAACAAGTACTGAGTAGCAC 59.591 50.000 0.00 0.00 0.00 4.40
4952 6675 2.223876 ACACCGATGTTAACGTGTCACT 60.224 45.455 4.71 0.00 34.46 3.41
4965 6688 5.530519 ACGTGTCACTGTTTGCATAATAG 57.469 39.130 0.65 0.00 0.00 1.73
5009 6732 4.093408 TCAGATAATGCGCTTTGTCAAGAC 59.907 41.667 26.69 7.63 30.57 3.01
5148 6873 9.645128 ACCAAATCAATACATTAGGATCATCAA 57.355 29.630 0.00 0.00 0.00 2.57
5164 6889 9.525826 AGGATCATCAATTAATACATTTCCCTC 57.474 33.333 0.00 0.00 0.00 4.30
5175 6900 7.888514 AATACATTTCCCTCCCATATACTCA 57.111 36.000 0.00 0.00 0.00 3.41
5176 6901 5.568620 ACATTTCCCTCCCATATACTCAC 57.431 43.478 0.00 0.00 0.00 3.51
5177 6902 5.227593 ACATTTCCCTCCCATATACTCACT 58.772 41.667 0.00 0.00 0.00 3.41
5178 6903 5.308237 ACATTTCCCTCCCATATACTCACTC 59.692 44.000 0.00 0.00 0.00 3.51
5179 6904 3.544698 TCCCTCCCATATACTCACTCC 57.455 52.381 0.00 0.00 0.00 3.85
5180 6905 2.171840 CCCTCCCATATACTCACTCCG 58.828 57.143 0.00 0.00 0.00 4.63
5181 6906 2.491086 CCCTCCCATATACTCACTCCGT 60.491 54.545 0.00 0.00 0.00 4.69
5182 6907 3.231818 CCTCCCATATACTCACTCCGTT 58.768 50.000 0.00 0.00 0.00 4.44
5183 6908 3.641906 CCTCCCATATACTCACTCCGTTT 59.358 47.826 0.00 0.00 0.00 3.60
5184 6909 4.262079 CCTCCCATATACTCACTCCGTTTC 60.262 50.000 0.00 0.00 0.00 2.78
5185 6910 4.283337 TCCCATATACTCACTCCGTTTCA 58.717 43.478 0.00 0.00 0.00 2.69
5186 6911 4.712829 TCCCATATACTCACTCCGTTTCAA 59.287 41.667 0.00 0.00 0.00 2.69
5187 6912 5.188163 TCCCATATACTCACTCCGTTTCAAA 59.812 40.000 0.00 0.00 0.00 2.69
5188 6913 5.878116 CCCATATACTCACTCCGTTTCAAAA 59.122 40.000 0.00 0.00 0.00 2.44
5189 6914 6.542370 CCCATATACTCACTCCGTTTCAAAAT 59.458 38.462 0.00 0.00 0.00 1.82
5190 6915 7.713507 CCCATATACTCACTCCGTTTCAAAATA 59.286 37.037 0.00 0.00 0.00 1.40
5191 6916 8.765219 CCATATACTCACTCCGTTTCAAAATAG 58.235 37.037 0.00 0.00 0.00 1.73
5192 6917 9.529325 CATATACTCACTCCGTTTCAAAATAGA 57.471 33.333 0.00 0.00 0.00 1.98
5194 6919 6.727824 ACTCACTCCGTTTCAAAATAGATG 57.272 37.500 0.00 0.00 0.00 2.90
5195 6920 6.464222 ACTCACTCCGTTTCAAAATAGATGA 58.536 36.000 0.00 0.00 0.00 2.92
5196 6921 6.369065 ACTCACTCCGTTTCAAAATAGATGAC 59.631 38.462 0.00 0.00 0.00 3.06
5197 6922 6.464222 TCACTCCGTTTCAAAATAGATGACT 58.536 36.000 0.00 0.00 0.00 3.41
5198 6923 6.590292 TCACTCCGTTTCAAAATAGATGACTC 59.410 38.462 0.00 0.00 0.00 3.36
5199 6924 6.368791 CACTCCGTTTCAAAATAGATGACTCA 59.631 38.462 0.00 0.00 0.00 3.41
5200 6925 6.934645 ACTCCGTTTCAAAATAGATGACTCAA 59.065 34.615 0.00 0.00 0.00 3.02
5201 6926 7.095187 ACTCCGTTTCAAAATAGATGACTCAAC 60.095 37.037 0.00 0.00 0.00 3.18
5202 6927 6.934645 TCCGTTTCAAAATAGATGACTCAACT 59.065 34.615 0.00 0.00 0.00 3.16
5203 6928 7.444183 TCCGTTTCAAAATAGATGACTCAACTT 59.556 33.333 0.00 0.00 0.00 2.66
5204 6929 8.076178 CCGTTTCAAAATAGATGACTCAACTTT 58.924 33.333 0.00 0.00 0.00 2.66
5205 6930 8.895845 CGTTTCAAAATAGATGACTCAACTTTG 58.104 33.333 0.00 0.00 0.00 2.77
5206 6931 9.736023 GTTTCAAAATAGATGACTCAACTTTGT 57.264 29.630 0.00 0.00 0.00 2.83
5209 6934 9.778741 TCAAAATAGATGACTCAACTTTGTACT 57.221 29.630 0.00 0.00 0.00 2.73
5216 6941 9.915629 AGATGACTCAACTTTGTACTAACTTAG 57.084 33.333 0.00 0.00 0.00 2.18
5217 6942 9.909644 GATGACTCAACTTTGTACTAACTTAGA 57.090 33.333 2.65 0.00 0.00 2.10
5219 6944 9.909644 TGACTCAACTTTGTACTAACTTAGATC 57.090 33.333 2.65 0.00 0.00 2.75
5220 6945 9.909644 GACTCAACTTTGTACTAACTTAGATCA 57.090 33.333 2.65 0.00 0.00 2.92
5224 6949 9.813080 CAACTTTGTACTAACTTAGATCAAAGC 57.187 33.333 26.78 0.00 43.82 3.51
5225 6950 9.780186 AACTTTGTACTAACTTAGATCAAAGCT 57.220 29.630 26.78 20.57 43.82 3.74
5236 6961 9.553064 AACTTAGATCAAAGCTAATATGTGGAG 57.447 33.333 0.00 0.00 0.00 3.86
5237 6962 8.709308 ACTTAGATCAAAGCTAATATGTGGAGT 58.291 33.333 0.00 0.00 0.00 3.85
5326 7052 5.057149 ACTTAGGTCAAAGCTAATATGCGG 58.943 41.667 0.00 0.00 37.52 5.69
5335 7061 8.936864 GTCAAAGCTAATATGCGGAGTAAATAT 58.063 33.333 0.00 0.00 38.13 1.28
5377 7105 6.713792 TGATCGAATGAAAACGTGTATTGA 57.286 33.333 0.00 0.00 0.00 2.57
5384 7112 9.405083 CGAATGAAAACGTGTATTGATAAGTAC 57.595 33.333 0.00 0.00 0.00 2.73
5391 7119 7.978982 AACGTGTATTGATAAGTACTCGTACT 58.021 34.615 11.77 3.97 44.89 2.73
5392 7120 8.648557 ACGTGTATTGATAAGTACTCGTACTA 57.351 34.615 10.18 0.82 44.96 1.82
5393 7121 8.759641 ACGTGTATTGATAAGTACTCGTACTAG 58.240 37.037 10.18 0.00 44.96 2.57
5429 7157 2.704572 AGCTGGACTTGTTAGTGATGC 58.295 47.619 0.00 0.00 33.84 3.91
5467 7195 5.181690 TGAATAAAGTGTGCCACAAGTTC 57.818 39.130 0.00 0.96 36.74 3.01
5496 7224 4.457466 AGTAAGATTTGTTGGTCACGGTT 58.543 39.130 0.00 0.00 0.00 4.44
5500 7228 1.670791 TTTGTTGGTCACGGTTCCTC 58.329 50.000 0.00 0.00 0.00 3.71
5504 7232 2.435069 TGTTGGTCACGGTTCCTCTTTA 59.565 45.455 0.00 0.00 0.00 1.85
5507 7235 5.221682 TGTTGGTCACGGTTCCTCTTTATTA 60.222 40.000 0.00 0.00 0.00 0.98
5508 7236 5.687166 TGGTCACGGTTCCTCTTTATTAT 57.313 39.130 0.00 0.00 0.00 1.28
5726 7463 3.465403 CAGGGGGCTCTCCGTGAG 61.465 72.222 2.43 0.00 43.25 3.51
5848 7585 1.006571 GTCGTCGTTGAGAAGGGCA 60.007 57.895 0.00 0.00 0.00 5.36
6543 8289 2.897207 CACATCGGCCGGAACCTA 59.103 61.111 27.83 4.46 0.00 3.08
6630 8376 2.036890 AAGTCCTACGAGGGCGGT 59.963 61.111 0.00 0.00 46.90 5.68
6641 8387 0.318784 GAGGGCGGTATCATCACGAC 60.319 60.000 0.00 0.00 34.22 4.34
6684 8430 4.286320 ATCATCGAGACGCCGGCC 62.286 66.667 23.46 7.92 0.00 6.13
7049 8795 3.131478 GACGGCGGACAAATGGGG 61.131 66.667 13.24 0.00 0.00 4.96
7266 9012 1.079819 CGAGTCCATGACCAACGCT 60.080 57.895 0.00 0.00 32.18 5.07
7289 9035 7.473027 CTCAGAAGCACTACTAGAGTACTAC 57.527 44.000 0.00 0.00 35.64 2.73
7291 9037 7.042950 TCAGAAGCACTACTAGAGTACTACAG 58.957 42.308 0.00 0.00 35.64 2.74
7292 9038 6.819649 CAGAAGCACTACTAGAGTACTACAGT 59.180 42.308 12.22 12.22 35.64 3.55
7293 9039 7.980662 CAGAAGCACTACTAGAGTACTACAGTA 59.019 40.741 12.97 12.97 35.64 2.74
7317 9067 1.485480 ACTAGTCGATCGAGTCAGGGA 59.515 52.381 27.84 10.22 0.00 4.20
7364 9114 0.804989 GGTGCACTTGTCTGGCATAC 59.195 55.000 17.98 0.00 40.05 2.39
7365 9115 0.804989 GTGCACTTGTCTGGCATACC 59.195 55.000 10.32 0.00 40.05 2.73
7367 9117 1.982073 GCACTTGTCTGGCATACCGC 61.982 60.000 0.17 0.00 39.70 5.68
7368 9118 0.673333 CACTTGTCTGGCATACCGCA 60.673 55.000 0.17 0.00 45.17 5.69
7369 9119 0.253044 ACTTGTCTGGCATACCGCAT 59.747 50.000 0.17 0.00 45.17 4.73
7370 9120 1.484653 ACTTGTCTGGCATACCGCATA 59.515 47.619 0.17 0.00 45.17 3.14
7371 9121 2.093181 ACTTGTCTGGCATACCGCATAA 60.093 45.455 0.17 0.00 45.17 1.90
7372 9122 2.700722 TGTCTGGCATACCGCATAAA 57.299 45.000 0.17 0.00 45.17 1.40
7373 9123 2.285083 TGTCTGGCATACCGCATAAAC 58.715 47.619 0.17 0.00 45.17 2.01
7374 9124 2.093181 TGTCTGGCATACCGCATAAACT 60.093 45.455 0.17 0.00 45.17 2.66
7375 9125 2.287915 GTCTGGCATACCGCATAAACTG 59.712 50.000 0.00 0.00 45.17 3.16
7376 9126 2.093181 TCTGGCATACCGCATAAACTGT 60.093 45.455 0.00 0.00 45.17 3.55
7377 9127 2.682856 CTGGCATACCGCATAAACTGTT 59.317 45.455 0.00 0.00 45.17 3.16
7442 9192 5.169295 ACTCGCTTATGTTTGTTACTCCTC 58.831 41.667 0.00 0.00 0.00 3.71
7443 9193 4.501071 TCGCTTATGTTTGTTACTCCTCC 58.499 43.478 0.00 0.00 0.00 4.30
7444 9194 3.306166 CGCTTATGTTTGTTACTCCTCCG 59.694 47.826 0.00 0.00 0.00 4.63
7445 9195 4.251268 GCTTATGTTTGTTACTCCTCCGT 58.749 43.478 0.00 0.00 0.00 4.69
7446 9196 4.694037 GCTTATGTTTGTTACTCCTCCGTT 59.306 41.667 0.00 0.00 0.00 4.44
7447 9197 5.180680 GCTTATGTTTGTTACTCCTCCGTTT 59.819 40.000 0.00 0.00 0.00 3.60
7448 9198 6.620089 GCTTATGTTTGTTACTCCTCCGTTTC 60.620 42.308 0.00 0.00 0.00 2.78
7449 9199 4.139859 TGTTTGTTACTCCTCCGTTTCA 57.860 40.909 0.00 0.00 0.00 2.69
7450 9200 4.515361 TGTTTGTTACTCCTCCGTTTCAA 58.485 39.130 0.00 0.00 0.00 2.69
7451 9201 4.942483 TGTTTGTTACTCCTCCGTTTCAAA 59.058 37.500 0.00 0.00 0.00 2.69
7452 9202 5.415077 TGTTTGTTACTCCTCCGTTTCAAAA 59.585 36.000 0.00 0.00 0.00 2.44
7453 9203 6.095720 TGTTTGTTACTCCTCCGTTTCAAAAT 59.904 34.615 0.00 0.00 0.00 1.82
7454 9204 7.282675 TGTTTGTTACTCCTCCGTTTCAAAATA 59.717 33.333 0.00 0.00 0.00 1.40
7455 9205 7.429636 TTGTTACTCCTCCGTTTCAAAATAG 57.570 36.000 0.00 0.00 0.00 1.73
7456 9206 6.761312 TGTTACTCCTCCGTTTCAAAATAGA 58.239 36.000 0.00 0.00 0.00 1.98
7457 9207 7.391620 TGTTACTCCTCCGTTTCAAAATAGAT 58.608 34.615 0.00 0.00 0.00 1.98
7458 9208 7.333423 TGTTACTCCTCCGTTTCAAAATAGATG 59.667 37.037 0.00 0.00 0.00 2.90
7459 9209 6.049955 ACTCCTCCGTTTCAAAATAGATGA 57.950 37.500 0.00 0.00 0.00 2.92
7460 9210 5.875359 ACTCCTCCGTTTCAAAATAGATGAC 59.125 40.000 0.00 0.00 0.00 3.06
7461 9211 5.183228 TCCTCCGTTTCAAAATAGATGACC 58.817 41.667 0.00 0.00 0.00 4.02
7462 9212 4.335594 CCTCCGTTTCAAAATAGATGACCC 59.664 45.833 0.00 0.00 0.00 4.46
7463 9213 4.912586 TCCGTTTCAAAATAGATGACCCA 58.087 39.130 0.00 0.00 0.00 4.51
7464 9214 5.317808 TCCGTTTCAAAATAGATGACCCAA 58.682 37.500 0.00 0.00 0.00 4.12
7465 9215 5.770663 TCCGTTTCAAAATAGATGACCCAAA 59.229 36.000 0.00 0.00 0.00 3.28
7466 9216 6.435904 TCCGTTTCAAAATAGATGACCCAAAT 59.564 34.615 0.00 0.00 0.00 2.32
7467 9217 7.039363 TCCGTTTCAAAATAGATGACCCAAATT 60.039 33.333 0.00 0.00 0.00 1.82
7468 9218 7.602265 CCGTTTCAAAATAGATGACCCAAATTT 59.398 33.333 0.00 0.00 0.00 1.82
7469 9219 9.632807 CGTTTCAAAATAGATGACCCAAATTTA 57.367 29.630 0.00 0.00 0.00 1.40
7526 9276 9.793259 TTGAGTCATCTATTTTAAAACTGAGGT 57.207 29.630 1.97 0.00 0.00 3.85
7541 9291 8.843885 AAAACTGAGGTAGTACTTATTGTTCC 57.156 34.615 0.00 0.00 39.18 3.62
7542 9292 7.549147 AACTGAGGTAGTACTTATTGTTCCA 57.451 36.000 0.00 0.00 39.18 3.53
7543 9293 7.735326 ACTGAGGTAGTACTTATTGTTCCAT 57.265 36.000 0.00 0.00 38.04 3.41
7544 9294 8.834004 ACTGAGGTAGTACTTATTGTTCCATA 57.166 34.615 0.00 0.00 38.04 2.74
7545 9295 9.263446 ACTGAGGTAGTACTTATTGTTCCATAA 57.737 33.333 0.00 0.00 38.04 1.90
7589 9339 5.961272 TCTTTTTGAAAAGACCAGTTGTCC 58.039 37.500 13.38 0.00 46.80 4.02
7590 9340 5.478679 TCTTTTTGAAAAGACCAGTTGTCCA 59.521 36.000 13.38 0.00 46.80 4.02
7591 9341 5.930837 TTTTGAAAAGACCAGTTGTCCAT 57.069 34.783 0.00 0.00 45.68 3.41
7592 9342 5.930837 TTTGAAAAGACCAGTTGTCCATT 57.069 34.783 0.00 0.00 45.68 3.16
7593 9343 5.930837 TTGAAAAGACCAGTTGTCCATTT 57.069 34.783 0.00 0.00 45.68 2.32
7594 9344 5.930837 TGAAAAGACCAGTTGTCCATTTT 57.069 34.783 0.00 0.00 45.68 1.82
7595 9345 6.293004 TGAAAAGACCAGTTGTCCATTTTT 57.707 33.333 0.00 0.00 45.68 1.94
7618 9368 9.638239 TTTTTCATTTCATTCGGATTTCCTTAG 57.362 29.630 0.00 0.00 0.00 2.18
7619 9369 6.377327 TCATTTCATTCGGATTTCCTTAGC 57.623 37.500 0.00 0.00 0.00 3.09
7620 9370 6.122277 TCATTTCATTCGGATTTCCTTAGCT 58.878 36.000 0.00 0.00 0.00 3.32
7621 9371 6.603201 TCATTTCATTCGGATTTCCTTAGCTT 59.397 34.615 0.00 0.00 0.00 3.74
7622 9372 7.773224 TCATTTCATTCGGATTTCCTTAGCTTA 59.227 33.333 0.00 0.00 0.00 3.09
7623 9373 7.553881 TTTCATTCGGATTTCCTTAGCTTAG 57.446 36.000 0.00 0.00 0.00 2.18
7624 9374 6.479972 TCATTCGGATTTCCTTAGCTTAGA 57.520 37.500 0.16 0.00 0.00 2.10
7625 9375 7.067496 TCATTCGGATTTCCTTAGCTTAGAT 57.933 36.000 0.16 0.00 0.00 1.98
7626 9376 7.155328 TCATTCGGATTTCCTTAGCTTAGATC 58.845 38.462 0.16 0.00 0.00 2.75
7627 9377 5.122512 TCGGATTTCCTTAGCTTAGATCG 57.877 43.478 0.16 0.00 0.00 3.69
7628 9378 3.675698 CGGATTTCCTTAGCTTAGATCGC 59.324 47.826 0.16 0.00 0.00 4.58
7629 9379 4.559704 CGGATTTCCTTAGCTTAGATCGCT 60.560 45.833 0.16 0.00 41.35 4.93
7630 9380 4.688413 GGATTTCCTTAGCTTAGATCGCTG 59.312 45.833 0.16 0.00 38.38 5.18
7631 9381 3.735237 TTCCTTAGCTTAGATCGCTGG 57.265 47.619 0.16 0.00 38.38 4.85
7632 9382 1.341531 TCCTTAGCTTAGATCGCTGGC 59.658 52.381 0.16 0.25 38.38 4.85
7633 9383 1.342819 CCTTAGCTTAGATCGCTGGCT 59.657 52.381 0.16 7.17 38.38 4.75
7634 9384 2.224161 CCTTAGCTTAGATCGCTGGCTT 60.224 50.000 0.16 0.00 38.38 4.35
7635 9385 3.462021 CTTAGCTTAGATCGCTGGCTTT 58.538 45.455 0.00 0.00 38.38 3.51
7636 9386 1.946745 AGCTTAGATCGCTGGCTTTC 58.053 50.000 0.00 0.00 36.15 2.62
7637 9387 1.484240 AGCTTAGATCGCTGGCTTTCT 59.516 47.619 0.00 0.00 36.15 2.52
7638 9388 2.093235 AGCTTAGATCGCTGGCTTTCTT 60.093 45.455 0.00 0.00 36.15 2.52
7639 9389 2.680339 GCTTAGATCGCTGGCTTTCTTT 59.320 45.455 0.00 0.00 0.00 2.52
7670 9420 3.382591 TTCAACACACGCGCGCAAA 62.383 52.632 32.58 10.69 0.00 3.68
7709 9460 4.485024 TTTTTACAGCGCCGAAATAACA 57.515 36.364 2.29 0.00 0.00 2.41
7730 9481 1.191647 CTTTTGCGCGTCGAACTAGTT 59.808 47.619 8.13 8.13 0.00 2.24
7749 9500 0.250234 TAGTTGCTTCATCAGGCGCT 59.750 50.000 7.64 0.00 0.00 5.92
7754 9505 0.737219 GCTTCATCAGGCGCTCAAAT 59.263 50.000 7.64 0.00 0.00 2.32
7807 9558 1.287425 GCGGTAAAATAGAGCGTGCT 58.713 50.000 0.00 0.00 39.88 4.40
7852 9604 8.820933 ACAATACATACAAGATGATCTCAAACG 58.179 33.333 0.00 0.00 0.00 3.60
7861 9613 6.824305 AGATGATCTCAAACGTCCAAAATT 57.176 33.333 0.00 0.00 0.00 1.82
7916 9670 9.961265 CAAACATCAATGAGAAACATAGCATAT 57.039 29.630 0.00 0.00 38.38 1.78
7976 9743 4.555313 CGCACAAACAAGATGATCACAAGT 60.555 41.667 0.00 0.00 0.00 3.16
7987 9754 8.890718 CAAGATGATCACAAGTAAGTTCATGAT 58.109 33.333 0.00 0.00 0.00 2.45
8117 9909 2.027192 TCTCCTTCATTGGAAACTCGGG 60.027 50.000 0.00 0.00 35.43 5.14
8220 10186 3.466836 TGAGAGACGCAAAACTCATGTT 58.533 40.909 0.00 0.00 38.16 2.71
8247 10279 1.127343 GTAGCTCCCATGGAAGCTCT 58.873 55.000 30.75 9.66 37.38 4.09
8311 10343 1.003003 GAAGCTCCTATGCCTCCCATC 59.997 57.143 0.00 0.00 35.34 3.51
8313 10345 1.978473 CTCCTATGCCTCCCATCGG 59.022 63.158 0.00 0.00 37.96 4.18
8314 10346 0.833834 CTCCTATGCCTCCCATCGGT 60.834 60.000 0.00 0.00 37.86 4.69
8343 10375 1.047002 CCTCTCATAGGTGCTCCCTG 58.953 60.000 0.00 0.00 45.81 4.45
8344 10376 1.412217 CCTCTCATAGGTGCTCCCTGA 60.412 57.143 0.00 4.49 45.81 3.86
8345 10377 2.607499 CTCTCATAGGTGCTCCCTGAT 58.393 52.381 0.00 0.00 45.81 2.90
8346 10378 2.299582 CTCTCATAGGTGCTCCCTGATG 59.700 54.545 0.00 3.65 45.81 3.07
8347 10379 2.091111 TCTCATAGGTGCTCCCTGATGA 60.091 50.000 0.00 7.67 45.81 2.92
8348 10380 2.702478 CTCATAGGTGCTCCCTGATGAA 59.298 50.000 12.90 2.38 45.81 2.57
8349 10381 3.114606 TCATAGGTGCTCCCTGATGAAA 58.885 45.455 10.59 0.00 45.81 2.69
8350 10382 3.523157 TCATAGGTGCTCCCTGATGAAAA 59.477 43.478 10.59 0.00 45.81 2.29
8351 10383 4.166725 TCATAGGTGCTCCCTGATGAAAAT 59.833 41.667 10.59 0.00 45.81 1.82
8352 10384 2.731572 AGGTGCTCCCTGATGAAAATG 58.268 47.619 0.00 0.00 44.08 2.32
8353 10385 2.042162 AGGTGCTCCCTGATGAAAATGT 59.958 45.455 0.00 0.00 44.08 2.71
8354 10386 3.266772 AGGTGCTCCCTGATGAAAATGTA 59.733 43.478 0.00 0.00 44.08 2.29
8355 10387 3.378427 GGTGCTCCCTGATGAAAATGTAC 59.622 47.826 0.00 0.00 0.00 2.90
8356 10388 3.378427 GTGCTCCCTGATGAAAATGTACC 59.622 47.826 0.00 0.00 0.00 3.34
8357 10389 2.952310 GCTCCCTGATGAAAATGTACCC 59.048 50.000 0.00 0.00 0.00 3.69
8358 10390 3.372025 GCTCCCTGATGAAAATGTACCCT 60.372 47.826 0.00 0.00 0.00 4.34
8359 10391 4.141482 GCTCCCTGATGAAAATGTACCCTA 60.141 45.833 0.00 0.00 0.00 3.53
8360 10392 5.615289 CTCCCTGATGAAAATGTACCCTAG 58.385 45.833 0.00 0.00 0.00 3.02
8361 10393 5.285401 TCCCTGATGAAAATGTACCCTAGA 58.715 41.667 0.00 0.00 0.00 2.43
8362 10394 5.366768 TCCCTGATGAAAATGTACCCTAGAG 59.633 44.000 0.00 0.00 0.00 2.43
8363 10395 5.455326 CCCTGATGAAAATGTACCCTAGAGG 60.455 48.000 0.00 0.00 43.78 3.69
8364 10396 5.036117 TGATGAAAATGTACCCTAGAGGC 57.964 43.478 0.00 0.00 40.58 4.70
8365 10397 4.473196 TGATGAAAATGTACCCTAGAGGCA 59.527 41.667 0.00 0.00 40.58 4.75
8366 10398 4.919774 TGAAAATGTACCCTAGAGGCAA 57.080 40.909 0.00 0.00 40.58 4.52
8367 10399 5.450818 TGAAAATGTACCCTAGAGGCAAT 57.549 39.130 0.00 0.00 40.58 3.56
8368 10400 6.569127 TGAAAATGTACCCTAGAGGCAATA 57.431 37.500 0.00 0.00 40.58 1.90
8369 10401 6.964464 TGAAAATGTACCCTAGAGGCAATAA 58.036 36.000 0.00 0.00 40.58 1.40
8370 10402 7.582719 TGAAAATGTACCCTAGAGGCAATAAT 58.417 34.615 0.00 0.00 40.58 1.28
8371 10403 8.719596 TGAAAATGTACCCTAGAGGCAATAATA 58.280 33.333 0.00 0.00 40.58 0.98
8372 10404 9.569122 GAAAATGTACCCTAGAGGCAATAATAA 57.431 33.333 0.00 0.00 40.58 1.40
8373 10405 9.930158 AAAATGTACCCTAGAGGCAATAATAAA 57.070 29.630 0.00 0.00 40.58 1.40
8374 10406 9.930158 AAATGTACCCTAGAGGCAATAATAAAA 57.070 29.630 0.00 0.00 40.58 1.52
8376 10408 8.918202 TGTACCCTAGAGGCAATAATAAAATG 57.082 34.615 0.00 0.00 40.58 2.32
8377 10409 7.942341 TGTACCCTAGAGGCAATAATAAAATGG 59.058 37.037 0.00 0.00 40.58 3.16
8378 10410 6.922540 ACCCTAGAGGCAATAATAAAATGGT 58.077 36.000 0.00 0.00 40.58 3.55
8379 10411 7.362234 ACCCTAGAGGCAATAATAAAATGGTT 58.638 34.615 0.00 0.00 40.58 3.67
8380 10412 8.507761 ACCCTAGAGGCAATAATAAAATGGTTA 58.492 33.333 0.00 0.00 40.58 2.85
8381 10413 9.533831 CCCTAGAGGCAATAATAAAATGGTTAT 57.466 33.333 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.000727 GTTTTGACATGTACTCCCTCCG 58.999 50.000 0.00 0.00 0.00 4.63
53 54 2.029020 GGGAACATTTCAGCTCCAAACC 60.029 50.000 0.00 0.00 0.00 3.27
487 498 9.538508 AACATGATACCGGTTTTAGATAGTTAC 57.461 33.333 15.04 0.00 0.00 2.50
496 507 6.988622 ATTCGAAACATGATACCGGTTTTA 57.011 33.333 15.04 0.85 35.08 1.52
598 616 9.667500 GTTACGTCTAAGCTTCTTTTTATAACG 57.332 33.333 0.00 3.84 0.00 3.18
602 620 9.654663 ATCAGTTACGTCTAAGCTTCTTTTTAT 57.345 29.630 0.00 0.00 0.00 1.40
668 688 1.017177 TATGAGCCGTTGGTTGCGAC 61.017 55.000 0.00 0.00 0.00 5.19
692 712 2.271800 CCACCATCTTCGTCTACAAGC 58.728 52.381 0.00 0.00 0.00 4.01
719 739 3.112580 GCGATCTTCTTCTGCTACTGTC 58.887 50.000 0.00 0.00 0.00 3.51
724 744 1.472878 ACGTGCGATCTTCTTCTGCTA 59.527 47.619 0.00 0.00 0.00 3.49
727 747 1.982612 TGACGTGCGATCTTCTTCTG 58.017 50.000 0.00 0.00 0.00 3.02
828 873 2.863853 CGACGATGCGCATCTGTGG 61.864 63.158 38.93 32.55 35.72 4.17
924 972 3.670377 GCTGGTGCACCCGTTTCC 61.670 66.667 32.62 10.04 39.41 3.13
1040 1088 0.524414 ATCACTAGTGCGTGCGTGTA 59.476 50.000 18.45 0.00 34.92 2.90
1056 1105 4.819761 GCGCGCCTCACAGGATCA 62.820 66.667 23.24 0.00 37.67 2.92
1083 1132 1.992277 GCCTTCTCCTCCTCCTGCA 60.992 63.158 0.00 0.00 0.00 4.41
1375 1424 1.153349 TGCATATTGGCGTGGCGTA 60.153 52.632 0.00 0.00 36.28 4.42
1416 1472 4.759516 TCAAGGCGATTAAACCAAGAAC 57.240 40.909 0.00 0.00 0.00 3.01
1418 1474 7.054124 AGAATATCAAGGCGATTAAACCAAGA 58.946 34.615 0.00 0.00 35.39 3.02
1553 1613 4.976540 AATAATTCGTAGGGAGGAAGGG 57.023 45.455 0.00 0.00 33.20 3.95
1554 1614 7.241042 TGATAATAATTCGTAGGGAGGAAGG 57.759 40.000 0.00 0.00 33.20 3.46
1588 1658 4.094590 CACAAAAGCAAAAATGACAAGGCA 59.905 37.500 0.00 0.00 0.00 4.75
1590 1660 4.590226 GCACAAAAGCAAAAATGACAAGG 58.410 39.130 0.00 0.00 0.00 3.61
1592 1662 3.681897 ACGCACAAAAGCAAAAATGACAA 59.318 34.783 0.00 0.00 0.00 3.18
1594 1664 3.543852 CCACGCACAAAAGCAAAAATGAC 60.544 43.478 0.00 0.00 0.00 3.06
1595 1665 2.606725 CCACGCACAAAAGCAAAAATGA 59.393 40.909 0.00 0.00 0.00 2.57
1597 1667 1.330213 GCCACGCACAAAAGCAAAAAT 59.670 42.857 0.00 0.00 0.00 1.82
1598 1668 0.723981 GCCACGCACAAAAGCAAAAA 59.276 45.000 0.00 0.00 0.00 1.94
1604 1674 4.341502 CCGGGCCACGCACAAAAG 62.342 66.667 4.39 0.00 42.52 2.27
1615 1685 1.403647 GCTACAAAATCAAACCGGGCC 60.404 52.381 6.32 0.00 0.00 5.80
1737 1811 2.887568 GTCACCATCAGCTCCGCG 60.888 66.667 0.00 0.00 0.00 6.46
2012 2086 1.912043 ACCAAGAAGAGGTGCATAGCT 59.088 47.619 0.00 0.00 38.13 3.32
2013 2087 2.409948 ACCAAGAAGAGGTGCATAGC 57.590 50.000 0.00 0.00 38.13 2.97
2016 2090 7.806180 AGTAATATTACCAAGAAGAGGTGCAT 58.194 34.615 19.74 0.00 40.26 3.96
2056 2133 5.776519 CTTGAGAGACTCATGCAAACTAC 57.223 43.478 5.02 0.00 40.39 2.73
2124 2208 0.035439 GGGGCCAGAATGAAAGACGA 60.035 55.000 4.39 0.00 39.69 4.20
2167 2251 6.264518 CGTGGCCAGGTATTTAATTTTATCCT 59.735 38.462 17.47 0.00 0.00 3.24
2242 2326 2.683475 CCCCAGCCCCTCGAAAAT 59.317 61.111 0.00 0.00 0.00 1.82
2305 2395 0.460987 CCGTCTGACCTCTGAATGCC 60.461 60.000 1.55 0.00 0.00 4.40
2324 2414 4.495844 CCGATTAATTTCAAGCGTCTTCCC 60.496 45.833 0.00 0.00 35.63 3.97
2325 2415 4.588278 CCGATTAATTTCAAGCGTCTTCC 58.412 43.478 0.00 0.00 35.63 3.46
2326 2416 4.029043 GCCGATTAATTTCAAGCGTCTTC 58.971 43.478 0.00 0.00 35.63 2.87
2327 2417 3.181500 GGCCGATTAATTTCAAGCGTCTT 60.181 43.478 0.00 0.00 35.63 3.01
2328 2418 2.354821 GGCCGATTAATTTCAAGCGTCT 59.645 45.455 0.00 0.00 35.63 4.18
2731 2822 2.873472 CAAGGCCGTTACAACAGTACAA 59.127 45.455 0.00 0.00 0.00 2.41
3095 3186 0.326618 GGGTGGATCCTCTCCCTTCA 60.327 60.000 23.59 0.00 44.23 3.02
3265 4247 0.467474 ATCTGTCCCGATCCGTGCTA 60.467 55.000 0.00 0.00 0.00 3.49
4109 5437 0.618680 AGAGCACTATGCCCCTCACA 60.619 55.000 0.00 0.00 46.52 3.58
4110 5438 1.414158 TAGAGCACTATGCCCCTCAC 58.586 55.000 0.00 0.00 46.52 3.51
4111 5439 1.762957 GTTAGAGCACTATGCCCCTCA 59.237 52.381 0.00 0.00 46.52 3.86
4112 5440 2.043227 AGTTAGAGCACTATGCCCCTC 58.957 52.381 0.00 0.00 46.52 4.30
4113 5441 2.182516 AGTTAGAGCACTATGCCCCT 57.817 50.000 0.00 0.00 46.52 4.79
4114 5442 2.170607 TGAAGTTAGAGCACTATGCCCC 59.829 50.000 0.00 0.00 46.52 5.80
4115 5443 3.543680 TGAAGTTAGAGCACTATGCCC 57.456 47.619 0.00 0.00 46.52 5.36
4116 5444 4.446371 ACATGAAGTTAGAGCACTATGCC 58.554 43.478 0.00 0.00 46.52 4.40
4188 5517 0.478072 ATGAAACTGGTGTGAGCCCA 59.522 50.000 0.00 0.00 0.00 5.36
4220 5550 0.762842 AACCCCCTTTGTTTCAGGCC 60.763 55.000 0.00 0.00 0.00 5.19
4230 5560 2.367241 CAAATCGAAACCAACCCCCTTT 59.633 45.455 0.00 0.00 0.00 3.11
4262 5592 1.535833 TGGTTCCGTCTCTGTCTCTC 58.464 55.000 0.00 0.00 0.00 3.20
4329 5659 1.404843 GGGCGAAGGATAGTCTGACT 58.595 55.000 15.57 15.57 0.00 3.41
4387 5720 3.102052 AGTGCCATTTTCAAGCAAGTG 57.898 42.857 0.00 0.00 38.45 3.16
4498 6206 1.453148 GCATGTGCTCGCTTTTCAAAC 59.547 47.619 0.00 0.00 38.21 2.93
4551 6259 2.957402 TGTTCCAGAATGCAAGGACT 57.043 45.000 0.00 0.00 31.97 3.85
4552 6260 3.565905 CTTGTTCCAGAATGCAAGGAC 57.434 47.619 0.00 0.00 35.87 3.85
4562 6270 2.949177 TGCTTTAGCCTTGTTCCAGA 57.051 45.000 0.00 0.00 41.18 3.86
4564 6272 2.825532 GGAATGCTTTAGCCTTGTTCCA 59.174 45.455 14.79 0.00 41.18 3.53
4569 6277 3.025978 TCATGGGAATGCTTTAGCCTTG 58.974 45.455 0.00 0.00 41.18 3.61
4686 6397 9.912634 CGTACTCCCTCCGTAAAAATTAATATA 57.087 33.333 0.00 0.00 0.00 0.86
4687 6398 8.641541 TCGTACTCCCTCCGTAAAAATTAATAT 58.358 33.333 0.00 0.00 0.00 1.28
4688 6399 8.006298 TCGTACTCCCTCCGTAAAAATTAATA 57.994 34.615 0.00 0.00 0.00 0.98
4689 6400 6.877236 TCGTACTCCCTCCGTAAAAATTAAT 58.123 36.000 0.00 0.00 0.00 1.40
4690 6401 6.279513 TCGTACTCCCTCCGTAAAAATTAA 57.720 37.500 0.00 0.00 0.00 1.40
4691 6402 5.913137 TCGTACTCCCTCCGTAAAAATTA 57.087 39.130 0.00 0.00 0.00 1.40
4692 6403 4.806640 TCGTACTCCCTCCGTAAAAATT 57.193 40.909 0.00 0.00 0.00 1.82
4693 6404 4.806640 TTCGTACTCCCTCCGTAAAAAT 57.193 40.909 0.00 0.00 0.00 1.82
4694 6405 4.599047 TTTCGTACTCCCTCCGTAAAAA 57.401 40.909 0.00 0.00 0.00 1.94
4695 6406 4.806640 ATTTCGTACTCCCTCCGTAAAA 57.193 40.909 0.00 0.00 0.00 1.52
4696 6407 5.652014 TCTTATTTCGTACTCCCTCCGTAAA 59.348 40.000 0.00 0.00 0.00 2.01
4697 6408 5.192927 TCTTATTTCGTACTCCCTCCGTAA 58.807 41.667 0.00 0.00 0.00 3.18
4698 6409 4.780815 TCTTATTTCGTACTCCCTCCGTA 58.219 43.478 0.00 0.00 0.00 4.02
4699 6410 3.624777 TCTTATTTCGTACTCCCTCCGT 58.375 45.455 0.00 0.00 0.00 4.69
4700 6411 4.142315 TGTTCTTATTTCGTACTCCCTCCG 60.142 45.833 0.00 0.00 0.00 4.63
4701 6412 5.334724 TGTTCTTATTTCGTACTCCCTCC 57.665 43.478 0.00 0.00 0.00 4.30
4702 6413 6.570692 TGATGTTCTTATTTCGTACTCCCTC 58.429 40.000 0.00 0.00 0.00 4.30
4703 6414 6.407074 CCTGATGTTCTTATTTCGTACTCCCT 60.407 42.308 0.00 0.00 0.00 4.20
4704 6415 5.753921 CCTGATGTTCTTATTTCGTACTCCC 59.246 44.000 0.00 0.00 0.00 4.30
4705 6416 6.476053 GTCCTGATGTTCTTATTTCGTACTCC 59.524 42.308 0.00 0.00 0.00 3.85
4706 6417 7.033791 TGTCCTGATGTTCTTATTTCGTACTC 58.966 38.462 0.00 0.00 0.00 2.59
4707 6418 6.931838 TGTCCTGATGTTCTTATTTCGTACT 58.068 36.000 0.00 0.00 0.00 2.73
4708 6419 7.591006 TTGTCCTGATGTTCTTATTTCGTAC 57.409 36.000 0.00 0.00 0.00 3.67
4709 6420 7.148474 GCTTTGTCCTGATGTTCTTATTTCGTA 60.148 37.037 0.00 0.00 0.00 3.43
4710 6421 6.348540 GCTTTGTCCTGATGTTCTTATTTCGT 60.349 38.462 0.00 0.00 0.00 3.85
4711 6422 6.024049 GCTTTGTCCTGATGTTCTTATTTCG 58.976 40.000 0.00 0.00 0.00 3.46
4712 6423 7.150783 AGCTTTGTCCTGATGTTCTTATTTC 57.849 36.000 0.00 0.00 0.00 2.17
4713 6424 7.373493 CAAGCTTTGTCCTGATGTTCTTATTT 58.627 34.615 0.00 0.00 0.00 1.40
4714 6425 6.071728 CCAAGCTTTGTCCTGATGTTCTTATT 60.072 38.462 0.00 0.00 0.00 1.40
4715 6426 5.416952 CCAAGCTTTGTCCTGATGTTCTTAT 59.583 40.000 0.00 0.00 0.00 1.73
4716 6427 4.761739 CCAAGCTTTGTCCTGATGTTCTTA 59.238 41.667 0.00 0.00 0.00 2.10
4717 6428 3.571401 CCAAGCTTTGTCCTGATGTTCTT 59.429 43.478 0.00 0.00 0.00 2.52
4718 6429 3.152341 CCAAGCTTTGTCCTGATGTTCT 58.848 45.455 0.00 0.00 0.00 3.01
4719 6430 3.149196 TCCAAGCTTTGTCCTGATGTTC 58.851 45.455 0.00 0.00 0.00 3.18
4720 6431 3.228188 TCCAAGCTTTGTCCTGATGTT 57.772 42.857 0.00 0.00 0.00 2.71
4721 6432 2.957402 TCCAAGCTTTGTCCTGATGT 57.043 45.000 0.00 0.00 0.00 3.06
4785 6500 0.615331 CCACTGTGTACTGATGGCCT 59.385 55.000 3.32 0.00 0.00 5.19
4813 6528 2.115291 GCCCTGAGATTTCCGGTGC 61.115 63.158 0.00 0.00 0.00 5.01
4817 6532 0.108138 AAGTCGCCCTGAGATTTCCG 60.108 55.000 0.00 0.00 0.00 4.30
4915 6636 7.035004 ACATCGGTGTTCCATTCATTTATTTG 58.965 34.615 0.00 0.00 34.01 2.32
4981 6704 5.584251 TGACAAAGCGCATTATCTGATTGTA 59.416 36.000 11.47 0.00 0.00 2.41
5009 6732 8.187480 CAGAGACCGGATGATACTAATTGATAG 58.813 40.741 9.46 0.00 37.66 2.08
5119 6844 6.777091 TGATCCTAATGTATTGATTTGGTGGG 59.223 38.462 0.00 0.00 32.08 4.61
5164 6889 4.665833 TGAAACGGAGTGAGTATATGGG 57.334 45.455 0.00 0.00 45.00 4.00
5172 6897 6.591834 AGTCATCTATTTTGAAACGGAGTGAG 59.408 38.462 0.00 0.00 45.00 3.51
5173 6898 6.464222 AGTCATCTATTTTGAAACGGAGTGA 58.536 36.000 0.00 0.00 45.00 3.41
5174 6899 6.368791 TGAGTCATCTATTTTGAAACGGAGTG 59.631 38.462 0.00 0.00 45.00 3.51
5176 6901 6.968131 TGAGTCATCTATTTTGAAACGGAG 57.032 37.500 0.00 0.00 0.00 4.63
5177 6902 6.934645 AGTTGAGTCATCTATTTTGAAACGGA 59.065 34.615 1.70 0.00 0.00 4.69
5178 6903 7.133891 AGTTGAGTCATCTATTTTGAAACGG 57.866 36.000 1.70 0.00 0.00 4.44
5179 6904 8.895845 CAAAGTTGAGTCATCTATTTTGAAACG 58.104 33.333 4.14 0.00 38.91 3.60
5180 6905 9.736023 ACAAAGTTGAGTCATCTATTTTGAAAC 57.264 29.630 15.99 0.00 38.91 2.78
5183 6908 9.778741 AGTACAAAGTTGAGTCATCTATTTTGA 57.221 29.630 15.99 3.46 38.91 2.69
5190 6915 9.915629 CTAAGTTAGTACAAAGTTGAGTCATCT 57.084 33.333 1.40 0.00 0.00 2.90
5191 6916 9.909644 TCTAAGTTAGTACAAAGTTGAGTCATC 57.090 33.333 9.71 0.00 0.00 2.92
5193 6918 9.909644 GATCTAAGTTAGTACAAAGTTGAGTCA 57.090 33.333 9.71 0.00 0.00 3.41
5194 6919 9.909644 TGATCTAAGTTAGTACAAAGTTGAGTC 57.090 33.333 9.71 0.00 0.00 3.36
5198 6923 9.813080 GCTTTGATCTAAGTTAGTACAAAGTTG 57.187 33.333 32.65 23.03 43.09 3.16
5199 6924 9.780186 AGCTTTGATCTAAGTTAGTACAAAGTT 57.220 29.630 32.65 29.59 43.09 2.66
5210 6935 9.553064 CTCCACATATTAGCTTTGATCTAAGTT 57.447 33.333 16.58 13.64 30.51 2.66
5211 6936 8.709308 ACTCCACATATTAGCTTTGATCTAAGT 58.291 33.333 16.58 7.67 30.51 2.24
5229 6954 8.978874 TGCAATAACAGATATTTACTCCACAT 57.021 30.769 0.00 0.00 31.69 3.21
5230 6955 8.800370 TTGCAATAACAGATATTTACTCCACA 57.200 30.769 0.00 0.00 31.69 4.17
5305 7031 5.163343 ACTCCGCATATTAGCTTTGACCTAA 60.163 40.000 0.00 0.00 0.00 2.69
5335 7061 9.777297 TTCGATCATTCATACTCCATTCATTTA 57.223 29.630 0.00 0.00 0.00 1.40
5386 7114 9.874205 AGCTAGGATAATCTTACTACTAGTACG 57.126 37.037 0.00 0.00 28.93 3.67
5474 7202 4.081322 ACCGTGACCAACAAATCTTACT 57.919 40.909 0.00 0.00 0.00 2.24
5507 7235 9.476202 GCAAACAGGTTTCTTTCTTTATGTTAT 57.524 29.630 0.00 0.00 0.00 1.89
5508 7236 7.923878 GGCAAACAGGTTTCTTTCTTTATGTTA 59.076 33.333 0.00 0.00 0.00 2.41
5739 7476 4.522689 TCGCACTGCACCGTGTGT 62.523 61.111 16.45 0.00 43.81 3.72
5848 7585 1.518572 CATCGGCGGCGAAGTAGTT 60.519 57.895 37.73 17.98 0.00 2.24
6012 7749 4.649705 TGCAAGACCTCCCCCGGA 62.650 66.667 0.73 0.00 0.00 5.14
6216 7953 1.079127 CCCGCAGTAGTGTCCCTTG 60.079 63.158 0.00 0.00 0.00 3.61
6217 7954 1.229082 TCCCGCAGTAGTGTCCCTT 60.229 57.895 0.00 0.00 0.00 3.95
6261 7998 4.136511 TCGGTGCCGCGCTTATCA 62.137 61.111 5.56 0.00 39.59 2.15
6630 8376 1.537990 CGGTGCATGGTCGTGATGATA 60.538 52.381 0.00 0.00 0.00 2.15
6735 8481 0.250038 GGCTCATGCGCTCCTTCATA 60.250 55.000 9.73 0.00 40.82 2.15
7049 8795 3.471806 GGGCCGAGGAGAAGACCC 61.472 72.222 0.00 0.00 0.00 4.46
7197 8943 3.682436 CGGACTGAATGGTGATCATTGGA 60.682 47.826 0.00 0.00 45.36 3.53
7289 9035 4.041049 ACTCGATCGACTAGTACGTACTG 58.959 47.826 33.23 24.68 37.10 2.74
7291 9037 4.038361 TGACTCGATCGACTAGTACGTAC 58.962 47.826 18.10 18.10 0.00 3.67
7292 9038 4.286101 CTGACTCGATCGACTAGTACGTA 58.714 47.826 15.15 0.00 0.00 3.57
7293 9039 3.114809 CTGACTCGATCGACTAGTACGT 58.885 50.000 15.15 8.75 0.00 3.57
7294 9040 2.472115 CCTGACTCGATCGACTAGTACG 59.528 54.545 15.15 5.16 0.00 3.67
7364 9114 1.266718 ACAGTGCAACAGTTTATGCGG 59.733 47.619 0.00 0.00 45.47 5.69
7365 9115 2.686558 ACAGTGCAACAGTTTATGCG 57.313 45.000 0.00 0.00 45.47 4.73
7372 9122 9.358872 CGAATCATATATATACAGTGCAACAGT 57.641 33.333 0.00 0.00 41.43 3.55
7373 9123 9.358872 ACGAATCATATATATACAGTGCAACAG 57.641 33.333 0.00 0.00 41.43 3.16
7374 9124 9.705290 AACGAATCATATATATACAGTGCAACA 57.295 29.630 0.00 0.00 41.43 3.33
7424 9174 6.425721 TGAAACGGAGGAGTAACAAACATAAG 59.574 38.462 0.00 0.00 0.00 1.73
7439 9189 4.335594 GGGTCATCTATTTTGAAACGGAGG 59.664 45.833 0.00 0.00 0.00 4.30
7442 9192 5.637006 TTGGGTCATCTATTTTGAAACGG 57.363 39.130 0.00 0.00 0.00 4.44
7443 9193 8.532977 AAATTTGGGTCATCTATTTTGAAACG 57.467 30.769 0.00 0.00 0.00 3.60
7500 9250 9.793259 ACCTCAGTTTTAAAATAGATGACTCAA 57.207 29.630 3.52 0.00 0.00 3.02
7515 9265 9.933723 GGAACAATAAGTACTACCTCAGTTTTA 57.066 33.333 0.00 0.00 38.80 1.52
7516 9266 8.434392 TGGAACAATAAGTACTACCTCAGTTTT 58.566 33.333 0.00 0.00 34.89 2.43
7517 9267 7.970102 TGGAACAATAAGTACTACCTCAGTTT 58.030 34.615 0.00 0.00 34.89 2.66
7518 9268 7.549147 TGGAACAATAAGTACTACCTCAGTT 57.451 36.000 0.00 0.00 34.89 3.16
7567 9317 5.719173 TGGACAACTGGTCTTTTCAAAAAG 58.281 37.500 8.60 8.60 46.16 2.27
7568 9318 5.730296 TGGACAACTGGTCTTTTCAAAAA 57.270 34.783 0.00 0.00 46.16 1.94
7569 9319 5.930837 ATGGACAACTGGTCTTTTCAAAA 57.069 34.783 0.00 0.00 46.16 2.44
7570 9320 5.930837 AATGGACAACTGGTCTTTTCAAA 57.069 34.783 0.00 0.00 46.16 2.69
7571 9321 5.930837 AAATGGACAACTGGTCTTTTCAA 57.069 34.783 0.00 0.00 46.16 2.69
7572 9322 5.930837 AAAATGGACAACTGGTCTTTTCA 57.069 34.783 0.00 0.00 46.16 2.69
7592 9342 9.638239 CTAAGGAAATCCGAATGAAATGAAAAA 57.362 29.630 0.00 0.00 42.08 1.94
7593 9343 7.759433 GCTAAGGAAATCCGAATGAAATGAAAA 59.241 33.333 0.00 0.00 42.08 2.29
7594 9344 7.122650 AGCTAAGGAAATCCGAATGAAATGAAA 59.877 33.333 0.00 0.00 42.08 2.69
7595 9345 6.603201 AGCTAAGGAAATCCGAATGAAATGAA 59.397 34.615 0.00 0.00 42.08 2.57
7596 9346 6.122277 AGCTAAGGAAATCCGAATGAAATGA 58.878 36.000 0.00 0.00 42.08 2.57
7597 9347 6.382869 AGCTAAGGAAATCCGAATGAAATG 57.617 37.500 0.00 0.00 42.08 2.32
7598 9348 7.993183 TCTAAGCTAAGGAAATCCGAATGAAAT 59.007 33.333 0.00 0.00 42.08 2.17
7599 9349 7.335627 TCTAAGCTAAGGAAATCCGAATGAAA 58.664 34.615 0.00 0.00 42.08 2.69
7600 9350 6.884832 TCTAAGCTAAGGAAATCCGAATGAA 58.115 36.000 0.00 0.00 42.08 2.57
7601 9351 6.479972 TCTAAGCTAAGGAAATCCGAATGA 57.520 37.500 0.00 0.00 42.08 2.57
7602 9352 6.090088 CGATCTAAGCTAAGGAAATCCGAATG 59.910 42.308 0.00 0.00 42.08 2.67
7603 9353 6.159988 CGATCTAAGCTAAGGAAATCCGAAT 58.840 40.000 0.00 0.00 42.08 3.34
7604 9354 5.529791 CGATCTAAGCTAAGGAAATCCGAA 58.470 41.667 0.00 0.00 42.08 4.30
7605 9355 4.558898 GCGATCTAAGCTAAGGAAATCCGA 60.559 45.833 0.00 0.00 42.08 4.55
7606 9356 3.675698 GCGATCTAAGCTAAGGAAATCCG 59.324 47.826 0.00 0.00 42.08 4.18
7607 9357 4.688413 CAGCGATCTAAGCTAAGGAAATCC 59.312 45.833 0.00 0.00 44.06 3.01
7608 9358 4.688413 CCAGCGATCTAAGCTAAGGAAATC 59.312 45.833 0.00 0.00 44.06 2.17
7609 9359 4.636249 CCAGCGATCTAAGCTAAGGAAAT 58.364 43.478 0.00 0.00 44.06 2.17
7610 9360 3.741388 GCCAGCGATCTAAGCTAAGGAAA 60.741 47.826 0.00 0.00 44.06 3.13
7611 9361 2.224066 GCCAGCGATCTAAGCTAAGGAA 60.224 50.000 0.00 0.00 44.06 3.36
7612 9362 1.341531 GCCAGCGATCTAAGCTAAGGA 59.658 52.381 0.00 0.00 44.06 3.36
7613 9363 1.342819 AGCCAGCGATCTAAGCTAAGG 59.657 52.381 0.00 0.00 44.06 2.69
7614 9364 2.810439 AGCCAGCGATCTAAGCTAAG 57.190 50.000 0.00 0.00 44.06 2.18
7615 9365 3.133003 AGAAAGCCAGCGATCTAAGCTAA 59.867 43.478 0.00 0.00 44.06 3.09
7616 9366 2.695666 AGAAAGCCAGCGATCTAAGCTA 59.304 45.455 0.00 0.00 44.06 3.32
7618 9368 1.946745 AGAAAGCCAGCGATCTAAGC 58.053 50.000 0.00 0.00 0.00 3.09
7619 9369 4.633565 AGAAAAGAAAGCCAGCGATCTAAG 59.366 41.667 0.00 0.00 0.00 2.18
7620 9370 4.579869 AGAAAAGAAAGCCAGCGATCTAA 58.420 39.130 0.00 0.00 0.00 2.10
7621 9371 4.207891 AGAAAAGAAAGCCAGCGATCTA 57.792 40.909 0.00 0.00 0.00 1.98
7622 9372 3.064900 AGAAAAGAAAGCCAGCGATCT 57.935 42.857 0.00 0.00 0.00 2.75
7623 9373 3.839051 AAGAAAAGAAAGCCAGCGATC 57.161 42.857 0.00 0.00 0.00 3.69
7624 9374 4.579869 TCTAAGAAAAGAAAGCCAGCGAT 58.420 39.130 0.00 0.00 0.00 4.58
7625 9375 3.997021 CTCTAAGAAAAGAAAGCCAGCGA 59.003 43.478 0.00 0.00 0.00 4.93
7626 9376 3.425492 GCTCTAAGAAAAGAAAGCCAGCG 60.425 47.826 0.00 0.00 0.00 5.18
7627 9377 3.503748 TGCTCTAAGAAAAGAAAGCCAGC 59.496 43.478 0.00 0.00 0.00 4.85
7628 9378 5.647225 AGATGCTCTAAGAAAAGAAAGCCAG 59.353 40.000 0.00 0.00 0.00 4.85
7629 9379 5.564550 AGATGCTCTAAGAAAAGAAAGCCA 58.435 37.500 0.00 0.00 0.00 4.75
7630 9380 6.150140 TGAAGATGCTCTAAGAAAAGAAAGCC 59.850 38.462 0.00 0.00 0.00 4.35
7631 9381 7.138692 TGAAGATGCTCTAAGAAAAGAAAGC 57.861 36.000 0.00 0.00 0.00 3.51
7632 9382 8.562892 TGTTGAAGATGCTCTAAGAAAAGAAAG 58.437 33.333 0.00 0.00 0.00 2.62
7633 9383 8.345565 GTGTTGAAGATGCTCTAAGAAAAGAAA 58.654 33.333 0.00 0.00 0.00 2.52
7634 9384 7.498900 TGTGTTGAAGATGCTCTAAGAAAAGAA 59.501 33.333 0.00 0.00 0.00 2.52
7635 9385 6.992123 TGTGTTGAAGATGCTCTAAGAAAAGA 59.008 34.615 0.00 0.00 0.00 2.52
7636 9386 7.074502 GTGTGTTGAAGATGCTCTAAGAAAAG 58.925 38.462 0.00 0.00 0.00 2.27
7637 9387 6.292865 CGTGTGTTGAAGATGCTCTAAGAAAA 60.293 38.462 0.00 0.00 0.00 2.29
7638 9388 5.177511 CGTGTGTTGAAGATGCTCTAAGAAA 59.822 40.000 0.00 0.00 0.00 2.52
7639 9389 4.686091 CGTGTGTTGAAGATGCTCTAAGAA 59.314 41.667 0.00 0.00 0.00 2.52
7707 9458 1.011574 GTTCGACGCGCAAAAGTGT 60.012 52.632 5.73 0.00 37.59 3.55
7709 9460 0.782384 CTAGTTCGACGCGCAAAAGT 59.218 50.000 5.73 3.10 0.00 2.66
7730 9481 0.250234 AGCGCCTGATGAAGCAACTA 59.750 50.000 2.29 0.00 0.00 2.24
7768 9519 4.189188 CTGCTGAAGCGGCATGCC 62.189 66.667 27.67 27.67 45.18 4.40
7813 9564 0.727793 GTATTGTTTGTGCACCGGCG 60.728 55.000 15.69 0.00 45.35 6.46
7852 9604 6.549952 TGTGTGAAATTTGCAAATTTTGGAC 58.450 32.000 37.43 31.90 45.70 4.02
7861 9613 6.592994 TCATCTTGTTTGTGTGAAATTTGCAA 59.407 30.769 0.00 0.00 0.00 4.08
7925 9679 8.739039 ACTTTGCATATTTTGAACTATGCTACA 58.261 29.630 19.90 7.72 46.64 2.74
7926 9680 9.573133 AACTTTGCATATTTTGAACTATGCTAC 57.427 29.630 19.90 1.34 46.64 3.58
7994 9761 8.751335 GTTGATGTTTAATTCGTTTGTGTGAAT 58.249 29.630 0.00 0.00 36.41 2.57
8158 9950 2.045926 GCTTCCGGTGTGCCTCAT 60.046 61.111 0.00 0.00 0.00 2.90
8247 10279 2.190313 GTGGCATCGGAGGCATGA 59.810 61.111 17.05 0.00 46.23 3.07
8311 10343 3.746949 GAGAGGCATGGGAGCACCG 62.747 68.421 0.00 0.00 44.64 4.94
8313 10345 0.761187 TATGAGAGGCATGGGAGCAC 59.239 55.000 0.00 0.00 37.87 4.40
8314 10346 1.054231 CTATGAGAGGCATGGGAGCA 58.946 55.000 0.00 0.00 37.87 4.26
8342 10374 4.473196 TGCCTCTAGGGTACATTTTCATCA 59.527 41.667 0.00 0.00 37.43 3.07
8343 10375 5.036117 TGCCTCTAGGGTACATTTTCATC 57.964 43.478 0.00 0.00 37.43 2.92
8344 10376 5.450818 TTGCCTCTAGGGTACATTTTCAT 57.549 39.130 0.00 0.00 37.43 2.57
8345 10377 4.919774 TTGCCTCTAGGGTACATTTTCA 57.080 40.909 0.00 0.00 37.43 2.69
8346 10378 9.569122 TTATTATTGCCTCTAGGGTACATTTTC 57.431 33.333 0.00 0.00 37.43 2.29
8347 10379 9.930158 TTTATTATTGCCTCTAGGGTACATTTT 57.070 29.630 0.00 0.00 37.43 1.82
8348 10380 9.930158 TTTTATTATTGCCTCTAGGGTACATTT 57.070 29.630 0.00 0.00 37.43 2.32
8350 10382 9.520515 CATTTTATTATTGCCTCTAGGGTACAT 57.479 33.333 0.00 0.00 37.43 2.29
8351 10383 7.942341 CCATTTTATTATTGCCTCTAGGGTACA 59.058 37.037 0.00 0.00 37.43 2.90
8352 10384 7.942894 ACCATTTTATTATTGCCTCTAGGGTAC 59.057 37.037 0.00 0.00 37.43 3.34
8353 10385 8.052621 ACCATTTTATTATTGCCTCTAGGGTA 57.947 34.615 0.00 0.00 37.43 3.69
8354 10386 6.922540 ACCATTTTATTATTGCCTCTAGGGT 58.077 36.000 0.00 0.00 37.43 4.34
8355 10387 7.839680 AACCATTTTATTATTGCCTCTAGGG 57.160 36.000 0.00 0.00 35.18 3.53


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

AutoCloner maintained by Alex Coulton.