Multiple sequence alignment - TraesCS5B01G230000

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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 TraesCS5B01G230000 chr5B 100.000 5237 0 0 519 5755 406935361 406930125 0.000000e+00 9672.0
1 TraesCS5B01G230000 chr5B 96.347 958 28 4 3306 4259 672860413 672859459 0.000000e+00 1568.0
2 TraesCS5B01G230000 chr5B 92.612 961 54 6 3306 4259 64718694 64717744 0.000000e+00 1365.0
3 TraesCS5B01G230000 chr5B 91.232 901 62 12 3306 4202 404184450 404185337 0.000000e+00 1210.0
4 TraesCS5B01G230000 chr5B 97.414 116 3 0 521 636 406940654 406940539 1.260000e-46 198.0
5 TraesCS5B01G230000 chr5B 84.878 205 16 13 3029 3225 660198448 660198251 5.880000e-45 193.0
6 TraesCS5B01G230000 chr5B 88.272 162 2 5 3081 3225 226284798 226284637 1.650000e-40 178.0
7 TraesCS5B01G230000 chr5B 88.272 162 2 6 3081 3225 592861500 592861339 1.650000e-40 178.0
8 TraesCS5B01G230000 chr5B 100.000 93 0 0 1 93 406935879 406935787 7.670000e-39 172.0
9 TraesCS5B01G230000 chr5B 82.203 236 3 6 3029 3225 672860646 672860411 3.570000e-37 167.0
10 TraesCS5B01G230000 chr5D 98.003 2053 32 3 986 3029 344829361 344831413 0.000000e+00 3555.0
11 TraesCS5B01G230000 chr5D 96.533 1500 30 4 4258 5755 344831410 344832889 0.000000e+00 2462.0
12 TraesCS5B01G230000 chr5D 91.294 402 15 9 637 1026 344828953 344829346 1.100000e-146 531.0
13 TraesCS5B01G230000 chr5D 95.763 118 5 0 519 636 373766767 373766650 2.120000e-44 191.0
14 TraesCS5B01G230000 chr5D 94.915 118 6 0 519 636 373767879 373767762 9.850000e-43 185.0
15 TraesCS5B01G230000 chr5D 94.915 118 4 1 521 636 564923087 564922970 3.540000e-42 183.0
16 TraesCS5B01G230000 chr5D 97.849 93 2 0 1 93 373767215 373767123 1.660000e-35 161.0
17 TraesCS5B01G230000 chr5D 97.674 86 2 0 3222 3307 21789114 21789199 1.290000e-31 148.0
18 TraesCS5B01G230000 chr5D 97.647 85 2 0 1 85 564923417 564923333 4.650000e-31 147.0
19 TraesCS5B01G230000 chr5D 93.814 97 4 2 3214 3309 384349142 384349047 1.670000e-30 145.0
20 TraesCS5B01G230000 chr7A 84.755 1653 214 22 986 2608 16645346 16643702 0.000000e+00 1622.0
21 TraesCS5B01G230000 chr7A 85.965 969 109 17 3306 4259 670171692 670170736 0.000000e+00 1011.0
22 TraesCS5B01G230000 chr7A 80.258 542 87 11 4306 4843 16643272 16642747 1.940000e-104 390.0
23 TraesCS5B01G230000 chr7A 84.127 378 37 9 2670 3025 16643706 16643330 1.540000e-90 344.0
24 TraesCS5B01G230000 chr7A 95.000 120 4 1 519 636 24505526 24505645 2.740000e-43 187.0
25 TraesCS5B01G230000 chr7A 93.396 106 6 1 3203 3308 211640948 211640844 7.720000e-34 156.0
26 TraesCS5B01G230000 chr7D 84.804 1632 211 20 1008 2608 17253106 17251481 0.000000e+00 1605.0
27 TraesCS5B01G230000 chr7D 80.443 542 86 11 4306 4843 17251054 17250529 4.180000e-106 396.0
28 TraesCS5B01G230000 chr7D 84.817 382 35 9 2670 3029 17251485 17251105 4.240000e-96 363.0
29 TraesCS5B01G230000 chr7D 98.305 118 2 0 519 636 490208645 490208528 2.100000e-49 207.0
30 TraesCS5B01G230000 chr7D 95.041 121 5 1 519 639 490213772 490213653 7.610000e-44 189.0
31 TraesCS5B01G230000 chr7D 98.913 92 1 0 1 92 490208798 490208707 1.280000e-36 165.0
32 TraesCS5B01G230000 chr7D 97.826 92 2 0 1 92 479725811 479725720 5.970000e-35 159.0
33 TraesCS5B01G230000 chr7D 97.701 87 2 0 3223 3309 37655869 37655955 3.590000e-32 150.0
34 TraesCS5B01G230000 chr7D 87.755 49 3 3 3025 3070 266255855 266255903 3.000000e-03 54.7
35 TraesCS5B01G230000 chr4B 96.350 959 26 3 3306 4259 668878105 668879059 0.000000e+00 1568.0
36 TraesCS5B01G230000 chr4B 97.917 144 1 1 3082 3225 31987045 31986904 1.240000e-61 248.0
37 TraesCS5B01G230000 chr4B 87.578 161 4 2 3081 3225 185870576 185870736 7.670000e-39 172.0
38 TraesCS5B01G230000 chr4B 86.957 161 4 2 3082 3225 118510958 118510798 1.280000e-36 165.0
39 TraesCS5B01G230000 chr4B 82.439 205 17 15 3027 3225 495357005 495357196 1.660000e-35 161.0
40 TraesCS5B01G230000 chr4B 97.753 89 2 0 3222 3310 273620119 273620207 2.780000e-33 154.0
41 TraesCS5B01G230000 chr4B 100.000 65 0 0 3085 3149 640825477 640825541 2.820000e-23 121.0
42 TraesCS5B01G230000 chr4B 98.333 60 1 0 3027 3086 89003833 89003892 7.890000e-19 106.0
43 TraesCS5B01G230000 chr4B 92.208 77 2 3 3024 3099 423043778 423043705 7.890000e-19 106.0
44 TraesCS5B01G230000 chr4B 96.721 61 2 0 3026 3086 5837598 5837658 1.020000e-17 102.0
45 TraesCS5B01G230000 chr6B 95.657 967 23 5 3306 4261 140095188 140096146 0.000000e+00 1535.0
46 TraesCS5B01G230000 chr6B 95.607 956 23 4 3306 4259 647391816 647392754 0.000000e+00 1515.0
47 TraesCS5B01G230000 chr6B 87.838 222 6 4 3025 3225 591189027 591189248 2.070000e-59 241.0
48 TraesCS5B01G230000 chr6B 98.333 60 1 0 3027 3086 662196462 662196521 7.890000e-19 106.0
49 TraesCS5B01G230000 chr2B 94.444 972 32 5 3306 4259 516958303 516959270 0.000000e+00 1476.0
50 TraesCS5B01G230000 chr2B 88.889 162 1 5 3081 3225 540749957 540750118 3.540000e-42 183.0
51 TraesCS5B01G230000 chr2B 88.889 162 1 6 3081 3225 625250503 625250342 3.540000e-42 183.0
52 TraesCS5B01G230000 chr2B 81.435 237 6 4 3027 3225 688454575 688454339 5.970000e-35 159.0
53 TraesCS5B01G230000 chr2B 98.305 59 1 0 3028 3086 625250577 625250519 2.840000e-18 104.0
54 TraesCS5B01G230000 chr4A 82.912 1621 230 24 1002 2608 717018668 717020255 0.000000e+00 1415.0
55 TraesCS5B01G230000 chr4A 81.999 1611 236 35 1010 2605 676538014 676536443 0.000000e+00 1319.0
56 TraesCS5B01G230000 chr4A 83.161 386 41 9 2658 3022 717020242 717020624 1.200000e-86 331.0
57 TraesCS5B01G230000 chr4A 78.340 494 102 4 4291 4781 717020676 717021167 1.200000e-81 315.0
58 TraesCS5B01G230000 chr4A 78.147 421 75 12 4290 4703 676536086 676535676 9.570000e-63 252.0
59 TraesCS5B01G230000 chr4A 79.037 353 45 13 2671 3016 676536446 676536116 1.260000e-51 215.0
60 TraesCS5B01G230000 chr4A 88.050 159 3 2 3082 3225 670885753 670885596 2.130000e-39 174.0
61 TraesCS5B01G230000 chr4A 96.739 92 2 1 3222 3312 609073907 609073816 9.990000e-33 152.0
62 TraesCS5B01G230000 chr4A 94.792 96 5 0 3216 3311 698479852 698479947 3.590000e-32 150.0
63 TraesCS5B01G230000 chr4A 94.737 95 5 0 3215 3309 532602578 532602484 1.290000e-31 148.0
64 TraesCS5B01G230000 chr4A 93.056 72 1 3 3029 3099 721378172 721378104 1.020000e-17 102.0
65 TraesCS5B01G230000 chr5A 92.841 880 48 10 3389 4259 688857986 688858859 0.000000e+00 1262.0
66 TraesCS5B01G230000 chr5A 94.737 95 5 0 3214 3308 78157118 78157212 1.290000e-31 148.0
67 TraesCS5B01G230000 chr7B 96.575 146 4 1 3081 3225 655571358 655571503 2.070000e-59 241.0
68 TraesCS5B01G230000 chr7B 97.541 122 1 1 519 638 737389496 737389617 2.100000e-49 207.0
69 TraesCS5B01G230000 chr7B 96.721 122 2 1 519 638 737088749 737088870 9.780000e-48 202.0
70 TraesCS5B01G230000 chr7B 96.721 122 2 1 519 638 737315726 737315847 9.780000e-48 202.0
71 TraesCS5B01G230000 chr7B 96.667 120 2 1 519 636 737724583 737724702 1.260000e-46 198.0
72 TraesCS5B01G230000 chr7B 95.902 122 3 1 519 638 737056269 737056390 4.550000e-46 196.0
73 TraesCS5B01G230000 chr7B 95.902 122 3 1 519 638 737610221 737610342 4.550000e-46 196.0
74 TraesCS5B01G230000 chr7B 95.699 93 4 0 3221 3313 736631891 736631983 3.590000e-32 150.0
75 TraesCS5B01G230000 chr1D 98.319 119 2 0 519 637 326556376 326556494 5.840000e-50 209.0
76 TraesCS5B01G230000 chr1D 100.000 93 0 0 1 93 326555918 326556010 7.670000e-39 172.0
77 TraesCS5B01G230000 chr1D 97.701 87 2 0 3223 3309 356580413 356580327 3.590000e-32 150.0
78 TraesCS5B01G230000 chr1D 97.701 87 2 0 3223 3309 485967767 485967853 3.590000e-32 150.0
79 TraesCS5B01G230000 chr1D 96.591 88 3 0 3223 3310 50875274 50875361 4.650000e-31 147.0
80 TraesCS5B01G230000 chr1D 97.647 85 2 0 3223 3307 234329042 234329126 4.650000e-31 147.0
81 TraesCS5B01G230000 chr1D 97.647 85 2 0 3223 3307 439024787 439024871 4.650000e-31 147.0
82 TraesCS5B01G230000 chr1D 92.473 93 7 0 1 93 472344323 472344415 3.620000e-27 134.0
83 TraesCS5B01G230000 chr6D 98.276 116 2 0 519 634 388269446 388269331 2.720000e-48 204.0
84 TraesCS5B01G230000 chr6D 94.068 118 7 0 519 636 238979338 238979221 4.580000e-41 180.0
85 TraesCS5B01G230000 chr6D 94.068 118 5 1 521 636 446958166 446958283 1.650000e-40 178.0
86 TraesCS5B01G230000 chr6D 92.373 118 9 0 519 636 178817860 178817743 9.920000e-38 169.0
87 TraesCS5B01G230000 chr6D 98.925 93 1 0 1 93 178797592 178797500 3.570000e-37 167.0
88 TraesCS5B01G230000 chr6D 97.849 93 2 0 1 93 27060828 27060736 1.660000e-35 161.0
89 TraesCS5B01G230000 chr6D 97.849 93 2 0 1 93 238959650 238959558 1.660000e-35 161.0
90 TraesCS5B01G230000 chr6D 94.845 97 2 2 3212 3307 36675490 36675396 1.290000e-31 148.0
91 TraesCS5B01G230000 chr6D 96.552 87 3 0 3222 3308 199144927 199144841 1.670000e-30 145.0
92 TraesCS5B01G230000 chr6D 96.512 86 3 0 3223 3308 235208726 235208641 6.010000e-30 143.0
93 TraesCS5B01G230000 chr6D 96.471 85 3 0 3223 3307 470635624 470635708 2.160000e-29 141.0
94 TraesCS5B01G230000 chr6D 89.423 104 9 2 3211 3312 248003989 248004092 4.680000e-26 130.0
95 TraesCS5B01G230000 chr6D 88.679 106 10 2 3203 3307 385917045 385916941 1.680000e-25 128.0
96 TraesCS5B01G230000 chr3D 96.610 118 4 0 519 636 246588525 246588408 4.550000e-46 196.0
97 TraesCS5B01G230000 chr3D 96.610 118 4 0 519 636 333240059 333239942 4.550000e-46 196.0
98 TraesCS5B01G230000 chr3D 98.925 93 1 0 1 93 399288682 399288590 3.570000e-37 167.0
99 TraesCS5B01G230000 chr3D 97.849 93 2 0 1 93 19318611 19318703 1.660000e-35 161.0
100 TraesCS5B01G230000 chr3D 96.774 93 3 0 1 93 333240482 333240390 7.720000e-34 156.0
101 TraesCS5B01G230000 chr3D 97.727 88 2 0 3223 3310 37525650 37525563 9.990000e-33 152.0
102 TraesCS5B01G230000 chr2D 96.610 118 4 0 519 636 42035156 42035273 4.550000e-46 196.0
103 TraesCS5B01G230000 chr2D 100.000 93 0 0 1 93 42042600 42042692 7.670000e-39 172.0
104 TraesCS5B01G230000 chr2D 97.753 89 2 0 3222 3310 131465389 131465301 2.780000e-33 154.0
105 TraesCS5B01G230000 chr2D 97.727 88 2 0 3223 3310 548274158 548274245 9.990000e-33 152.0
106 TraesCS5B01G230000 chr2D 86.567 67 2 4 3027 3086 48166984 48167050 3.720000e-07 67.6
107 TraesCS5B01G230000 chr2D 89.130 46 1 2 3027 3068 387196444 387196399 3.000000e-03 54.7
108 TraesCS5B01G230000 chr6A 95.833 120 3 2 519 636 520918198 520918317 5.880000e-45 193.0
109 TraesCS5B01G230000 chr6A 97.849 93 2 0 1 93 520917904 520917996 1.660000e-35 161.0
110 TraesCS5B01G230000 chr6A 95.699 93 4 0 1 93 466675111 466675203 3.590000e-32 150.0
111 TraesCS5B01G230000 chr6A 93.878 98 4 2 3214 3310 617249190 617249286 4.650000e-31 147.0
112 TraesCS5B01G230000 chr1B 90.972 144 10 1 3081 3224 39986843 39986983 2.120000e-44 191.0
113 TraesCS5B01G230000 chr1B 82.427 239 4 7 3025 3225 615016555 615016317 2.130000e-39 174.0
114 TraesCS5B01G230000 chr1B 87.654 162 3 8 3081 3225 613006694 613006855 7.670000e-39 172.0
115 TraesCS5B01G230000 chr1B 98.925 93 1 0 1 93 4766771 4766679 3.570000e-37 167.0
116 TraesCS5B01G230000 chr1B 85.802 162 5 9 3082 3225 667759887 667759726 7.720000e-34 156.0
117 TraesCS5B01G230000 chr1B 95.588 68 1 2 3019 3086 633529003 633529068 2.190000e-19 108.0
118 TraesCS5B01G230000 chr1B 98.276 58 1 0 3029 3086 660825461 660825518 1.020000e-17 102.0
119 TraesCS5B01G230000 chr1B 92.000 75 1 4 3027 3099 677574988 677574917 3.670000e-17 100.0
120 TraesCS5B01G230000 chrUn 95.041 121 4 1 519 637 475632774 475632894 7.610000e-44 189.0
121 TraesCS5B01G230000 chrUn 92.500 120 7 1 519 636 211067812 211067931 2.760000e-38 171.0
122 TraesCS5B01G230000 chrUn 91.667 120 8 2 519 636 211087228 211087347 1.280000e-36 165.0
123 TraesCS5B01G230000 chrUn 96.591 88 3 0 3223 3310 244923812 244923899 4.650000e-31 147.0
124 TraesCS5B01G230000 chrUn 96.591 88 3 0 3223 3310 287095700 287095787 4.650000e-31 147.0
125 TraesCS5B01G230000 chrUn 94.624 93 5 0 1 93 307839277 307839185 1.670000e-30 145.0
126 TraesCS5B01G230000 chrUn 94.624 93 5 0 1 93 328018772 328018680 1.670000e-30 145.0
127 TraesCS5B01G230000 chrUn 94.624 93 5 0 1 93 369208363 369208271 1.670000e-30 145.0
128 TraesCS5B01G230000 chrUn 89.474 114 10 1 519 632 68661332 68661443 6.010000e-30 143.0
129 TraesCS5B01G230000 chrUn 96.471 85 3 0 3223 3307 16901709 16901625 2.160000e-29 141.0
130 TraesCS5B01G230000 chrUn 95.455 88 4 0 3221 3308 335557647 335557734 2.160000e-29 141.0
131 TraesCS5B01G230000 chrUn 94.444 90 4 1 3219 3308 478445761 478445673 2.800000e-28 137.0
132 TraesCS5B01G230000 chrUn 95.294 85 4 0 3223 3307 13209427 13209343 1.010000e-27 135.0
133 TraesCS5B01G230000 chrUn 94.318 88 5 0 1 88 211087081 211087168 1.010000e-27 135.0
134 TraesCS5B01G230000 chrUn 94.186 86 5 0 3223 3308 55723612 55723697 1.300000e-26 132.0
135 TraesCS5B01G230000 chrUn 94.118 85 5 0 3223 3307 22143243 22143159 4.680000e-26 130.0
136 TraesCS5B01G230000 chrUn 93.258 89 4 2 528 614 472033698 472033610 4.680000e-26 130.0
137 TraesCS5B01G230000 chrUn 93.103 87 6 0 3222 3308 29391781 29391867 1.680000e-25 128.0
138 TraesCS5B01G230000 chr4D 95.690 116 5 0 521 636 107724962 107725077 2.740000e-43 187.0
139 TraesCS5B01G230000 chr4D 94.915 118 4 2 520 636 282810286 282810170 3.540000e-42 183.0
140 TraesCS5B01G230000 chr4D 94.167 120 5 2 519 636 35127367 35127486 1.270000e-41 182.0
141 TraesCS5B01G230000 chr4D 93.333 120 6 1 519 636 35145356 35145237 5.930000e-40 176.0
142 TraesCS5B01G230000 chr4D 93.220 118 6 1 519 634 211024708 211024591 7.670000e-39 172.0
143 TraesCS5B01G230000 chr4D 96.629 89 3 0 3223 3311 509106377 509106465 1.290000e-31 148.0
144 TraesCS5B01G230000 chr4D 95.604 91 4 0 1 91 107724799 107724889 4.650000e-31 147.0
145 TraesCS5B01G230000 chr4D 96.552 87 3 0 3223 3309 436376801 436376715 1.670000e-30 145.0
146 TraesCS5B01G230000 chr4D 93.548 93 6 0 1 93 175402468 175402560 7.780000e-29 139.0
147 TraesCS5B01G230000 chr4D 90.196 102 9 1 3223 3324 35665566 35665466 1.300000e-26 132.0
148 TraesCS5B01G230000 chr4D 100.000 29 0 0 3026 3054 352545403 352545431 3.000000e-03 54.7
149 TraesCS5B01G230000 chr3A 95.833 96 4 0 3222 3317 646921641 646921546 7.720000e-34 156.0
150 TraesCS5B01G230000 chr3A 93.333 45 3 0 2057 2101 749611967 749611923 3.720000e-07 67.6
151 TraesCS5B01G230000 chr1A 95.789 95 4 0 3217 3311 49249744 49249650 2.780000e-33 154.0
152 TraesCS5B01G230000 chr1A 97.701 87 2 0 3223 3309 498400930 498400844 3.590000e-32 150.0
153 TraesCS5B01G230000 chr2A 96.739 92 2 1 3222 3312 712843623 712843532 9.990000e-33 152.0


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 TraesCS5B01G230000 chr5B 406930125 406935879 5754 True 4922.000000 9672 100.000000 1 5755 2 chr5B.!!$R6 5754
1 TraesCS5B01G230000 chr5B 64717744 64718694 950 True 1365.000000 1365 92.612000 3306 4259 1 chr5B.!!$R1 953
2 TraesCS5B01G230000 chr5B 404184450 404185337 887 False 1210.000000 1210 91.232000 3306 4202 1 chr5B.!!$F1 896
3 TraesCS5B01G230000 chr5B 672859459 672860646 1187 True 867.500000 1568 89.275000 3029 4259 2 chr5B.!!$R7 1230
4 TraesCS5B01G230000 chr5D 344828953 344832889 3936 False 2182.666667 3555 95.276667 637 5755 3 chr5D.!!$F2 5118
5 TraesCS5B01G230000 chr7A 670170736 670171692 956 True 1011.000000 1011 85.965000 3306 4259 1 chr7A.!!$R2 953
6 TraesCS5B01G230000 chr7A 16642747 16645346 2599 True 785.333333 1622 83.046667 986 4843 3 chr7A.!!$R3 3857
7 TraesCS5B01G230000 chr7D 17250529 17253106 2577 True 788.000000 1605 83.354667 1008 4843 3 chr7D.!!$R3 3835
8 TraesCS5B01G230000 chr4B 668878105 668879059 954 False 1568.000000 1568 96.350000 3306 4259 1 chr4B.!!$F7 953
9 TraesCS5B01G230000 chr6B 140095188 140096146 958 False 1535.000000 1535 95.657000 3306 4261 1 chr6B.!!$F1 955
10 TraesCS5B01G230000 chr6B 647391816 647392754 938 False 1515.000000 1515 95.607000 3306 4259 1 chr6B.!!$F3 953
11 TraesCS5B01G230000 chr2B 516958303 516959270 967 False 1476.000000 1476 94.444000 3306 4259 1 chr2B.!!$F1 953
12 TraesCS5B01G230000 chr4A 717018668 717021167 2499 False 687.000000 1415 81.471000 1002 4781 3 chr4A.!!$F2 3779
13 TraesCS5B01G230000 chr4A 676535676 676538014 2338 True 595.333333 1319 79.727667 1010 4703 3 chr4A.!!$R5 3693
14 TraesCS5B01G230000 chr5A 688857986 688858859 873 False 1262.000000 1262 92.841000 3389 4259 1 chr5A.!!$F2 870

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
548 549 0.107654 CCCCGCCTCTAGTTTCCTTG 60.108 60.000 0.0 0.0 0.00 3.61 F
1450 1523 0.035915 GCAGACCTTCAACCTCCTCC 60.036 60.000 0.0 0.0 0.00 4.30 F
1870 1967 0.683504 GGGAGACGCAGAAGACCCTA 60.684 60.000 0.0 0.0 35.03 3.53 F
1871 1968 1.183549 GGAGACGCAGAAGACCCTAA 58.816 55.000 0.0 0.0 0.00 2.69 F
2400 2500 1.875009 TGGCGATGAGATTCATGCTC 58.125 50.000 0.0 0.0 37.20 4.26 F
3545 3733 2.258286 GCATTCGCCAACGCCTTT 59.742 55.556 0.0 0.0 39.84 3.11 F
4499 4758 0.543277 CAGAGCTTGGGATGCACCTA 59.457 55.000 0.0 0.0 38.98 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2400 2500 0.036388 TGGCTCTGCTACCGGAAAAG 60.036 55.000 9.46 3.3 0.00 2.27 R
2405 2505 1.097547 CCATTTGGCTCTGCTACCGG 61.098 60.000 0.00 0.0 0.00 5.28 R
3772 3960 1.166129 AGATGTGTACACGCTCGAGT 58.834 50.000 20.61 0.0 0.00 4.18 R
4013 4225 1.162951 TTCCCCTCTCCCTCTCCCTT 61.163 60.000 0.00 0.0 0.00 3.95 R
4332 4588 0.385473 CGGTTCGTGCATGGTTTGTC 60.385 55.000 5.98 0.0 0.00 3.18 R
4570 4829 1.978617 GTGTTCATGGCCTGGTGGG 60.979 63.158 3.32 0.0 38.36 4.61 R
5691 5957 5.973565 GGCATAGAAACAACATGATAACTGC 59.026 40.000 0.00 0.0 0.00 4.40 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.281761 CCCACCGCTCAGCAGTTT 60.282 61.111 0.00 0.00 0.00 2.66
18 19 2.620112 CCCACCGCTCAGCAGTTTG 61.620 63.158 0.00 0.00 0.00 2.93
19 20 2.253452 CACCGCTCAGCAGTTTGC 59.747 61.111 0.00 0.00 45.46 3.68
20 21 2.980233 ACCGCTCAGCAGTTTGCC 60.980 61.111 0.00 0.00 46.52 4.52
21 22 4.093952 CCGCTCAGCAGTTTGCCG 62.094 66.667 0.00 0.00 46.52 5.69
22 23 3.043713 CGCTCAGCAGTTTGCCGA 61.044 61.111 0.00 0.00 46.52 5.54
23 24 2.393768 CGCTCAGCAGTTTGCCGAT 61.394 57.895 0.00 0.00 46.52 4.18
24 25 1.136147 GCTCAGCAGTTTGCCGATG 59.864 57.895 0.00 0.00 46.52 3.84
25 26 1.580845 GCTCAGCAGTTTGCCGATGT 61.581 55.000 0.00 0.00 46.52 3.06
26 27 0.877071 CTCAGCAGTTTGCCGATGTT 59.123 50.000 0.00 0.00 46.52 2.71
27 28 2.076100 CTCAGCAGTTTGCCGATGTTA 58.924 47.619 0.00 0.00 46.52 2.41
28 29 2.679837 CTCAGCAGTTTGCCGATGTTAT 59.320 45.455 0.00 0.00 46.52 1.89
29 30 2.419673 TCAGCAGTTTGCCGATGTTATG 59.580 45.455 0.00 0.00 46.52 1.90
30 31 2.419673 CAGCAGTTTGCCGATGTTATGA 59.580 45.455 0.00 0.00 46.52 2.15
31 32 2.420022 AGCAGTTTGCCGATGTTATGAC 59.580 45.455 0.00 0.00 46.52 3.06
32 33 2.477863 GCAGTTTGCCGATGTTATGACC 60.478 50.000 0.00 0.00 37.42 4.02
33 34 2.746904 CAGTTTGCCGATGTTATGACCA 59.253 45.455 0.00 0.00 0.00 4.02
34 35 3.190327 CAGTTTGCCGATGTTATGACCAA 59.810 43.478 0.00 0.00 0.00 3.67
35 36 3.440173 AGTTTGCCGATGTTATGACCAAG 59.560 43.478 0.00 0.00 0.00 3.61
36 37 2.036958 TGCCGATGTTATGACCAAGG 57.963 50.000 0.00 0.00 0.00 3.61
37 38 1.308998 GCCGATGTTATGACCAAGGG 58.691 55.000 0.00 0.00 0.00 3.95
38 39 1.967319 CCGATGTTATGACCAAGGGG 58.033 55.000 0.00 0.00 41.29 4.79
48 49 2.435410 CCAAGGGGTTACCGACGC 60.435 66.667 0.00 0.00 46.96 5.19
53 54 3.287445 GGGTTACCGACGCCTACA 58.713 61.111 0.00 0.00 35.30 2.74
54 55 1.818555 GGGTTACCGACGCCTACAT 59.181 57.895 0.00 0.00 35.30 2.29
55 56 0.176449 GGGTTACCGACGCCTACATT 59.824 55.000 0.00 0.00 35.30 2.71
56 57 1.405933 GGGTTACCGACGCCTACATTT 60.406 52.381 0.00 0.00 35.30 2.32
57 58 1.662122 GGTTACCGACGCCTACATTTG 59.338 52.381 0.00 0.00 0.00 2.32
58 59 2.609350 GTTACCGACGCCTACATTTGA 58.391 47.619 0.00 0.00 0.00 2.69
59 60 2.572191 TACCGACGCCTACATTTGAG 57.428 50.000 0.00 0.00 0.00 3.02
60 61 0.108329 ACCGACGCCTACATTTGAGG 60.108 55.000 0.00 0.00 37.12 3.86
61 62 0.174845 CCGACGCCTACATTTGAGGA 59.825 55.000 0.00 0.00 35.99 3.71
62 63 1.560923 CGACGCCTACATTTGAGGAG 58.439 55.000 0.00 0.00 39.58 3.69
64 65 2.674177 CGACGCCTACATTTGAGGAGTT 60.674 50.000 0.00 0.00 45.85 3.01
65 66 2.930682 GACGCCTACATTTGAGGAGTTC 59.069 50.000 0.00 0.00 45.85 3.01
66 67 2.280628 CGCCTACATTTGAGGAGTTCC 58.719 52.381 0.00 0.00 35.99 3.62
67 68 2.280628 GCCTACATTTGAGGAGTTCCG 58.719 52.381 0.00 0.00 42.08 4.30
68 69 2.906354 CCTACATTTGAGGAGTTCCGG 58.094 52.381 0.00 0.00 42.08 5.14
69 70 2.236395 CCTACATTTGAGGAGTTCCGGT 59.764 50.000 0.00 0.00 42.08 5.28
70 71 2.474410 ACATTTGAGGAGTTCCGGTC 57.526 50.000 0.00 0.00 42.08 4.79
71 72 1.003233 ACATTTGAGGAGTTCCGGTCC 59.997 52.381 0.00 0.22 42.08 4.46
72 73 1.003118 CATTTGAGGAGTTCCGGTCCA 59.997 52.381 11.86 0.00 42.08 4.02
73 74 0.685097 TTTGAGGAGTTCCGGTCCAG 59.315 55.000 11.86 0.00 42.08 3.86
74 75 0.471211 TTGAGGAGTTCCGGTCCAGT 60.471 55.000 11.86 0.00 42.08 4.00
75 76 0.898789 TGAGGAGTTCCGGTCCAGTC 60.899 60.000 11.86 5.10 42.08 3.51
76 77 0.612453 GAGGAGTTCCGGTCCAGTCT 60.612 60.000 11.86 0.00 42.08 3.24
77 78 0.702902 AGGAGTTCCGGTCCAGTCTA 59.297 55.000 11.86 0.00 42.08 2.59
78 79 1.288335 AGGAGTTCCGGTCCAGTCTAT 59.712 52.381 11.86 0.00 42.08 1.98
79 80 1.409427 GGAGTTCCGGTCCAGTCTATG 59.591 57.143 0.00 0.00 33.84 2.23
80 81 0.824759 AGTTCCGGTCCAGTCTATGC 59.175 55.000 0.00 0.00 0.00 3.14
81 82 0.527817 GTTCCGGTCCAGTCTATGCG 60.528 60.000 0.00 0.00 0.00 4.73
82 83 0.968901 TTCCGGTCCAGTCTATGCGT 60.969 55.000 0.00 0.00 0.00 5.24
83 84 1.065928 CCGGTCCAGTCTATGCGTC 59.934 63.158 0.00 0.00 0.00 5.19
84 85 1.663379 CCGGTCCAGTCTATGCGTCA 61.663 60.000 0.00 0.00 0.00 4.35
85 86 0.525668 CGGTCCAGTCTATGCGTCAC 60.526 60.000 0.00 0.00 0.00 3.67
86 87 0.818296 GGTCCAGTCTATGCGTCACT 59.182 55.000 0.00 0.00 0.00 3.41
87 88 1.469940 GGTCCAGTCTATGCGTCACTG 60.470 57.143 9.94 9.94 37.81 3.66
90 91 1.633561 CAGTCTATGCGTCACTGGTG 58.366 55.000 9.26 0.00 34.96 4.17
91 92 1.202348 CAGTCTATGCGTCACTGGTGA 59.798 52.381 9.26 0.00 34.96 4.02
544 545 2.189784 GGCCCCGCCTCTAGTTTC 59.810 66.667 0.00 0.00 46.69 2.78
545 546 2.189784 GCCCCGCCTCTAGTTTCC 59.810 66.667 0.00 0.00 0.00 3.13
546 547 2.368011 GCCCCGCCTCTAGTTTCCT 61.368 63.158 0.00 0.00 0.00 3.36
547 548 1.911702 GCCCCGCCTCTAGTTTCCTT 61.912 60.000 0.00 0.00 0.00 3.36
548 549 0.107654 CCCCGCCTCTAGTTTCCTTG 60.108 60.000 0.00 0.00 0.00 3.61
549 550 0.613777 CCCGCCTCTAGTTTCCTTGT 59.386 55.000 0.00 0.00 0.00 3.16
550 551 1.829222 CCCGCCTCTAGTTTCCTTGTA 59.171 52.381 0.00 0.00 0.00 2.41
551 552 2.434702 CCCGCCTCTAGTTTCCTTGTAT 59.565 50.000 0.00 0.00 0.00 2.29
552 553 3.640029 CCCGCCTCTAGTTTCCTTGTATA 59.360 47.826 0.00 0.00 0.00 1.47
553 554 4.262079 CCCGCCTCTAGTTTCCTTGTATAG 60.262 50.000 0.00 0.00 0.00 1.31
554 555 4.583489 CCGCCTCTAGTTTCCTTGTATAGA 59.417 45.833 0.00 0.00 0.00 1.98
555 556 5.244178 CCGCCTCTAGTTTCCTTGTATAGAT 59.756 44.000 0.00 0.00 0.00 1.98
556 557 6.153067 CGCCTCTAGTTTCCTTGTATAGATG 58.847 44.000 0.00 0.00 0.00 2.90
557 558 6.016192 CGCCTCTAGTTTCCTTGTATAGATGA 60.016 42.308 0.00 0.00 0.00 2.92
558 559 7.375053 GCCTCTAGTTTCCTTGTATAGATGAG 58.625 42.308 0.00 0.00 0.00 2.90
559 560 7.524698 GCCTCTAGTTTCCTTGTATAGATGAGG 60.525 44.444 0.00 0.00 38.19 3.86
560 561 7.291411 TCTAGTTTCCTTGTATAGATGAGGC 57.709 40.000 0.00 0.00 0.00 4.70
561 562 7.069986 TCTAGTTTCCTTGTATAGATGAGGCT 58.930 38.462 0.00 0.00 0.00 4.58
562 563 8.225416 TCTAGTTTCCTTGTATAGATGAGGCTA 58.775 37.037 0.00 0.00 0.00 3.93
563 564 7.676683 AGTTTCCTTGTATAGATGAGGCTAA 57.323 36.000 0.00 0.00 0.00 3.09
564 565 7.731054 AGTTTCCTTGTATAGATGAGGCTAAG 58.269 38.462 0.00 0.00 0.00 2.18
565 566 6.672266 TTCCTTGTATAGATGAGGCTAAGG 57.328 41.667 0.00 0.00 35.83 2.69
566 567 5.087323 TCCTTGTATAGATGAGGCTAAGGG 58.913 45.833 6.98 0.00 35.36 3.95
567 568 4.323104 CCTTGTATAGATGAGGCTAAGGGC 60.323 50.000 0.00 0.00 40.90 5.19
584 585 3.790089 GGGCTGCCCTTGTACTTATAT 57.210 47.619 30.42 0.00 41.34 0.86
585 586 4.903045 GGGCTGCCCTTGTACTTATATA 57.097 45.455 30.42 0.00 41.34 0.86
586 587 4.576879 GGGCTGCCCTTGTACTTATATAC 58.423 47.826 30.42 0.00 41.34 1.47
587 588 4.243270 GGCTGCCCTTGTACTTATATACG 58.757 47.826 7.66 0.00 0.00 3.06
588 589 4.262335 GGCTGCCCTTGTACTTATATACGT 60.262 45.833 7.66 0.00 0.00 3.57
589 590 4.684703 GCTGCCCTTGTACTTATATACGTG 59.315 45.833 0.00 0.00 0.00 4.49
590 591 4.624015 TGCCCTTGTACTTATATACGTGC 58.376 43.478 0.00 1.70 0.00 5.34
591 592 4.099727 TGCCCTTGTACTTATATACGTGCA 59.900 41.667 6.13 6.13 0.00 4.57
592 593 4.446719 GCCCTTGTACTTATATACGTGCAC 59.553 45.833 6.82 6.82 0.00 4.57
593 594 4.986659 CCCTTGTACTTATATACGTGCACC 59.013 45.833 12.15 0.00 0.00 5.01
594 595 4.678287 CCTTGTACTTATATACGTGCACCG 59.322 45.833 12.15 9.19 44.03 4.94
607 608 2.358125 CACCGTGCACCCGATCAA 60.358 61.111 12.15 0.00 0.00 2.57
608 609 1.745115 CACCGTGCACCCGATCAAT 60.745 57.895 12.15 0.00 0.00 2.57
609 610 0.461163 CACCGTGCACCCGATCAATA 60.461 55.000 12.15 0.00 0.00 1.90
610 611 0.461339 ACCGTGCACCCGATCAATAC 60.461 55.000 12.15 0.00 0.00 1.89
611 612 0.461163 CCGTGCACCCGATCAATACA 60.461 55.000 12.15 0.00 0.00 2.29
612 613 1.581934 CGTGCACCCGATCAATACAT 58.418 50.000 12.15 0.00 0.00 2.29
613 614 1.526887 CGTGCACCCGATCAATACATC 59.473 52.381 12.15 0.00 0.00 3.06
614 615 2.560504 GTGCACCCGATCAATACATCA 58.439 47.619 5.22 0.00 0.00 3.07
615 616 2.942376 GTGCACCCGATCAATACATCAA 59.058 45.455 5.22 0.00 0.00 2.57
616 617 3.002656 GTGCACCCGATCAATACATCAAG 59.997 47.826 5.22 0.00 0.00 3.02
617 618 3.118445 TGCACCCGATCAATACATCAAGA 60.118 43.478 0.00 0.00 0.00 3.02
618 619 3.496130 GCACCCGATCAATACATCAAGAG 59.504 47.826 0.00 0.00 0.00 2.85
619 620 4.697514 CACCCGATCAATACATCAAGAGT 58.302 43.478 0.00 0.00 0.00 3.24
620 621 5.118990 CACCCGATCAATACATCAAGAGTT 58.881 41.667 0.00 0.00 0.00 3.01
621 622 5.007039 CACCCGATCAATACATCAAGAGTTG 59.993 44.000 0.00 0.00 0.00 3.16
622 623 4.024556 CCCGATCAATACATCAAGAGTTGC 60.025 45.833 0.00 0.00 0.00 4.17
623 624 4.571984 CCGATCAATACATCAAGAGTTGCA 59.428 41.667 0.00 0.00 0.00 4.08
624 625 5.237996 CCGATCAATACATCAAGAGTTGCAT 59.762 40.000 0.00 0.00 0.00 3.96
625 626 6.238566 CCGATCAATACATCAAGAGTTGCATT 60.239 38.462 0.00 0.00 0.00 3.56
626 627 6.631636 CGATCAATACATCAAGAGTTGCATTG 59.368 38.462 0.00 0.00 0.00 2.82
627 628 5.643664 TCAATACATCAAGAGTTGCATTGC 58.356 37.500 0.46 0.46 0.00 3.56
628 629 4.644103 ATACATCAAGAGTTGCATTGCC 57.356 40.909 6.12 0.00 0.00 4.52
629 630 2.522185 ACATCAAGAGTTGCATTGCCT 58.478 42.857 6.12 0.00 0.00 4.75
630 631 2.895404 ACATCAAGAGTTGCATTGCCTT 59.105 40.909 6.12 0.00 0.00 4.35
631 632 3.057033 ACATCAAGAGTTGCATTGCCTTC 60.057 43.478 6.12 1.34 0.00 3.46
632 633 2.585330 TCAAGAGTTGCATTGCCTTCA 58.415 42.857 6.12 0.00 0.00 3.02
633 634 2.957680 TCAAGAGTTGCATTGCCTTCAA 59.042 40.909 6.12 0.00 36.51 2.69
634 635 3.054878 CAAGAGTTGCATTGCCTTCAAC 58.945 45.455 6.12 3.90 40.08 3.18
635 636 2.309613 AGAGTTGCATTGCCTTCAACA 58.690 42.857 6.12 0.00 41.67 3.33
674 675 4.867599 GGTCGACGGGCGCCTTAG 62.868 72.222 28.56 20.05 40.61 2.18
678 679 4.452733 GACGGGCGCCTTAGCACT 62.453 66.667 28.56 2.36 38.66 4.40
679 680 3.952628 GACGGGCGCCTTAGCACTT 62.953 63.158 28.56 0.71 38.66 3.16
680 681 3.195698 CGGGCGCCTTAGCACTTC 61.196 66.667 28.56 4.75 38.66 3.01
699 700 6.753744 GCACTTCCTTAATTAATTCCTGCAAG 59.246 38.462 3.39 2.56 0.00 4.01
721 722 3.008485 GCCTCCTATTCAACCCCATCTAG 59.992 52.174 0.00 0.00 0.00 2.43
732 733 1.683917 CCCCATCTAGTCAGTTCCTCG 59.316 57.143 0.00 0.00 0.00 4.63
799 805 7.941795 ATATTTAGAGTATTCCGTTTGGTCG 57.058 36.000 0.00 0.00 36.30 4.79
800 806 4.789012 TTAGAGTATTCCGTTTGGTCGT 57.211 40.909 0.00 0.00 36.30 4.34
856 865 1.876714 GATGAAGGCGCGCGTAAGA 60.877 57.895 32.35 13.90 43.02 2.10
862 871 1.083401 GGCGCGCGTAAGATCAATG 60.083 57.895 32.35 0.00 43.02 2.82
864 873 0.300491 GCGCGCGTAAGATCAATGAA 59.700 50.000 32.35 0.00 43.02 2.57
910 919 8.856153 TCACTTTTATATTGCACCTTCAGTTA 57.144 30.769 0.00 0.00 0.00 2.24
937 946 3.306019 GCCGGTTCTGAACATTTCCAAAT 60.306 43.478 21.01 0.00 0.00 2.32
1281 1354 1.139058 GGACTGATGCAACTATCGGGT 59.861 52.381 0.00 0.00 37.69 5.28
1323 1396 2.594592 GTGTGGGCGGTTCTGCTT 60.595 61.111 3.62 0.00 34.52 3.91
1450 1523 0.035915 GCAGACCTTCAACCTCCTCC 60.036 60.000 0.00 0.00 0.00 4.30
1549 1622 3.077359 ACTAACAACCAAGAGAGCATGC 58.923 45.455 10.51 10.51 0.00 4.06
1580 1653 3.894427 AGTGACTACATGAGCTATGAGGG 59.106 47.826 0.00 3.42 39.21 4.30
1596 1669 1.375268 GGGCGATCTATCTGCTGGC 60.375 63.158 0.00 0.00 0.00 4.85
1712 1803 1.569072 AGGGGGAACAAGAACACTGTT 59.431 47.619 0.00 0.00 0.00 3.16
1809 1900 2.407090 CACAAGAATCAGCTCGTCACA 58.593 47.619 0.00 0.00 0.00 3.58
1827 1918 2.679837 CACAGTGGACAAGATATGGCAC 59.320 50.000 0.00 0.00 39.66 5.01
1829 1920 1.134401 AGTGGACAAGATATGGCACGG 60.134 52.381 0.00 0.00 39.66 4.94
1856 1947 1.990160 AACGGCAGGTTGTTGGGAGA 61.990 55.000 0.00 0.00 37.50 3.71
1862 1953 1.070786 GGTTGTTGGGAGACGCAGA 59.929 57.895 0.00 0.00 0.00 4.26
1870 1967 0.683504 GGGAGACGCAGAAGACCCTA 60.684 60.000 0.00 0.00 35.03 3.53
1871 1968 1.183549 GGAGACGCAGAAGACCCTAA 58.816 55.000 0.00 0.00 0.00 2.69
2109 2206 2.357760 GTGTTTGCCGGCGGACTA 60.358 61.111 33.44 15.19 0.00 2.59
2124 2221 2.292794 GACTAATGGTGCCGCTCCGA 62.293 60.000 6.97 0.00 0.00 4.55
2160 2257 4.243008 TCTTTGGCCACGGCGACA 62.243 61.111 16.62 3.86 43.06 4.35
2400 2500 1.875009 TGGCGATGAGATTCATGCTC 58.125 50.000 0.00 0.00 37.20 4.26
2405 2505 4.525686 GCGATGAGATTCATGCTCTTTTC 58.474 43.478 0.00 0.00 37.20 2.29
3025 3158 8.117813 TGAGGTAATCAAAGAAATTAACCACC 57.882 34.615 0.00 0.00 34.02 4.61
3026 3159 7.947890 TGAGGTAATCAAAGAAATTAACCACCT 59.052 33.333 0.00 0.00 34.02 4.00
3027 3160 8.721133 AGGTAATCAAAGAAATTAACCACCTT 57.279 30.769 0.00 0.00 28.36 3.50
3228 3400 7.907214 ATTGCATAGATTAAACGATACTCCC 57.093 36.000 0.00 0.00 0.00 4.30
3229 3401 6.665992 TGCATAGATTAAACGATACTCCCT 57.334 37.500 0.00 0.00 0.00 4.20
3230 3402 6.688578 TGCATAGATTAAACGATACTCCCTC 58.311 40.000 0.00 0.00 0.00 4.30
3231 3403 6.100668 GCATAGATTAAACGATACTCCCTCC 58.899 44.000 0.00 0.00 0.00 4.30
3232 3404 4.850347 AGATTAAACGATACTCCCTCCG 57.150 45.455 0.00 0.00 0.00 4.63
3233 3405 4.213513 AGATTAAACGATACTCCCTCCGT 58.786 43.478 0.00 0.00 36.77 4.69
3234 3406 5.380043 AGATTAAACGATACTCCCTCCGTA 58.620 41.667 0.00 0.00 34.60 4.02
3235 3407 5.829924 AGATTAAACGATACTCCCTCCGTAA 59.170 40.000 0.00 0.00 34.60 3.18
3236 3408 5.913137 TTAAACGATACTCCCTCCGTAAA 57.087 39.130 0.00 0.00 34.60 2.01
3237 3409 3.790152 AACGATACTCCCTCCGTAAAC 57.210 47.619 0.00 0.00 34.60 2.01
3238 3410 3.010200 ACGATACTCCCTCCGTAAACT 57.990 47.619 0.00 0.00 33.13 2.66
3239 3411 4.156455 ACGATACTCCCTCCGTAAACTA 57.844 45.455 0.00 0.00 33.13 2.24
3240 3412 4.526970 ACGATACTCCCTCCGTAAACTAA 58.473 43.478 0.00 0.00 33.13 2.24
3241 3413 5.136105 ACGATACTCCCTCCGTAAACTAAT 58.864 41.667 0.00 0.00 33.13 1.73
3242 3414 6.299141 ACGATACTCCCTCCGTAAACTAATA 58.701 40.000 0.00 0.00 33.13 0.98
3243 3415 6.944862 ACGATACTCCCTCCGTAAACTAATAT 59.055 38.462 0.00 0.00 33.13 1.28
3244 3416 8.103305 ACGATACTCCCTCCGTAAACTAATATA 58.897 37.037 0.00 0.00 33.13 0.86
3245 3417 8.950210 CGATACTCCCTCCGTAAACTAATATAA 58.050 37.037 0.00 0.00 0.00 0.98
3248 3420 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
3249 3421 8.003629 ACTCCCTCCGTAAACTAATATAAGAGT 58.996 37.037 0.00 0.00 0.00 3.24
3250 3422 8.174733 TCCCTCCGTAAACTAATATAAGAGTG 57.825 38.462 0.00 0.00 0.00 3.51
3251 3423 7.781693 TCCCTCCGTAAACTAATATAAGAGTGT 59.218 37.037 0.00 0.00 0.00 3.55
3252 3424 8.419442 CCCTCCGTAAACTAATATAAGAGTGTT 58.581 37.037 0.00 0.00 0.00 3.32
3253 3425 9.813446 CCTCCGTAAACTAATATAAGAGTGTTT 57.187 33.333 0.00 0.00 0.00 2.83
3545 3733 2.258286 GCATTCGCCAACGCCTTT 59.742 55.556 0.00 0.00 39.84 3.11
3898 4086 4.083862 GAGGGCGAGCCGGAGTTT 62.084 66.667 5.05 0.00 36.85 2.66
4162 4386 2.600122 TTTCCGCGTGCGCTTGTTTT 62.600 50.000 9.73 0.00 39.32 2.43
4499 4758 0.543277 CAGAGCTTGGGATGCACCTA 59.457 55.000 0.00 0.00 38.98 3.08
4661 4920 4.383861 CTGTGGGCGCTGCTCTCA 62.384 66.667 7.64 0.00 31.57 3.27
4764 5024 8.270799 CAGTACAAAATGCATGAAAAGTTCTTG 58.729 33.333 0.00 0.75 37.74 3.02
4849 5113 7.067532 TGGTATTTGTTCGTACTGCTATTTG 57.932 36.000 0.00 0.00 0.00 2.32
5102 5366 6.446318 TGCAGCCTTTTATTTTTAGTGTCTG 58.554 36.000 0.00 0.00 0.00 3.51
5288 5552 1.274703 ATGGAAGGAGATGTGGCCGT 61.275 55.000 0.00 0.00 0.00 5.68
5395 5659 4.226427 TGCAAAGATAGAGATGGTTGCT 57.774 40.909 7.59 0.00 41.43 3.91
5514 5778 9.862149 ACCCTCATTCGGTTATTTTAATTATCT 57.138 29.630 0.00 0.00 0.00 1.98
5645 5911 9.305925 ACATTTTGATGTCTTTCTCAGTTTTTC 57.694 29.630 0.00 0.00 0.00 2.29
5649 5915 7.206981 TGATGTCTTTCTCAGTTTTTCATCC 57.793 36.000 0.00 0.00 0.00 3.51
5656 5922 8.721478 TCTTTCTCAGTTTTTCATCCTTATTCG 58.279 33.333 0.00 0.00 0.00 3.34
5657 5923 7.979444 TTCTCAGTTTTTCATCCTTATTCGT 57.021 32.000 0.00 0.00 0.00 3.85
5658 5924 7.979444 TCTCAGTTTTTCATCCTTATTCGTT 57.021 32.000 0.00 0.00 0.00 3.85
5659 5925 8.029642 TCTCAGTTTTTCATCCTTATTCGTTC 57.970 34.615 0.00 0.00 0.00 3.95
5660 5926 7.659799 TCTCAGTTTTTCATCCTTATTCGTTCA 59.340 33.333 0.00 0.00 0.00 3.18
5661 5927 8.160521 TCAGTTTTTCATCCTTATTCGTTCAA 57.839 30.769 0.00 0.00 0.00 2.69
5662 5928 8.625651 TCAGTTTTTCATCCTTATTCGTTCAAA 58.374 29.630 0.00 0.00 0.00 2.69
5663 5929 9.410556 CAGTTTTTCATCCTTATTCGTTCAAAT 57.589 29.630 0.00 0.00 0.00 2.32
5664 5930 9.981114 AGTTTTTCATCCTTATTCGTTCAAATT 57.019 25.926 0.00 0.00 0.00 1.82
5696 5962 7.168219 TCAGTTTTATCTTGGTCTATGCAGTT 58.832 34.615 0.00 0.00 0.00 3.16
5714 5980 6.554419 TGCAGTTATCATGTTGTTTCTATGC 58.446 36.000 0.00 0.00 0.00 3.14
5722 5988 6.112734 TCATGTTGTTTCTATGCCGTAATCT 58.887 36.000 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.420022 GTCATAACATCGGCAAACTGCT 59.580 45.455 0.00 0.00 44.28 4.24
11 12 2.477863 GGTCATAACATCGGCAAACTGC 60.478 50.000 0.00 0.00 44.08 4.40
12 13 2.746904 TGGTCATAACATCGGCAAACTG 59.253 45.455 0.00 0.00 0.00 3.16
13 14 3.066291 TGGTCATAACATCGGCAAACT 57.934 42.857 0.00 0.00 0.00 2.66
14 15 3.427503 CCTTGGTCATAACATCGGCAAAC 60.428 47.826 0.00 0.00 0.00 2.93
15 16 2.752354 CCTTGGTCATAACATCGGCAAA 59.248 45.455 0.00 0.00 0.00 3.68
16 17 2.364632 CCTTGGTCATAACATCGGCAA 58.635 47.619 0.00 0.00 0.00 4.52
17 18 1.408127 CCCTTGGTCATAACATCGGCA 60.408 52.381 0.00 0.00 0.00 5.69
18 19 1.308998 CCCTTGGTCATAACATCGGC 58.691 55.000 0.00 0.00 0.00 5.54
19 20 1.211949 ACCCCTTGGTCATAACATCGG 59.788 52.381 0.00 0.00 43.06 4.18
20 21 2.710096 ACCCCTTGGTCATAACATCG 57.290 50.000 0.00 0.00 43.06 3.84
31 32 2.435410 GCGTCGGTAACCCCTTGG 60.435 66.667 0.00 0.00 37.80 3.61
32 33 1.606885 TAGGCGTCGGTAACCCCTTG 61.607 60.000 0.00 0.00 37.37 3.61
33 34 1.305213 TAGGCGTCGGTAACCCCTT 60.305 57.895 0.00 0.00 37.37 3.95
34 35 2.054453 GTAGGCGTCGGTAACCCCT 61.054 63.158 0.00 0.00 39.56 4.79
35 36 1.679559 ATGTAGGCGTCGGTAACCCC 61.680 60.000 0.00 0.00 0.00 4.95
36 37 0.176449 AATGTAGGCGTCGGTAACCC 59.824 55.000 0.00 0.00 0.00 4.11
37 38 1.662122 CAAATGTAGGCGTCGGTAACC 59.338 52.381 0.00 0.00 0.00 2.85
38 39 2.601763 CTCAAATGTAGGCGTCGGTAAC 59.398 50.000 0.00 0.00 0.00 2.50
39 40 2.417651 CCTCAAATGTAGGCGTCGGTAA 60.418 50.000 0.00 0.00 0.00 2.85
40 41 1.135527 CCTCAAATGTAGGCGTCGGTA 59.864 52.381 0.00 0.00 0.00 4.02
41 42 0.108329 CCTCAAATGTAGGCGTCGGT 60.108 55.000 0.00 0.00 0.00 4.69
42 43 0.174845 TCCTCAAATGTAGGCGTCGG 59.825 55.000 0.00 0.00 33.84 4.79
43 44 1.135083 ACTCCTCAAATGTAGGCGTCG 60.135 52.381 0.00 0.00 33.84 5.12
44 45 2.674796 ACTCCTCAAATGTAGGCGTC 57.325 50.000 0.00 0.00 33.84 5.19
45 46 2.354805 GGAACTCCTCAAATGTAGGCGT 60.355 50.000 0.00 0.00 33.49 5.68
46 47 2.280628 GGAACTCCTCAAATGTAGGCG 58.719 52.381 0.00 0.00 33.84 5.52
47 48 2.280628 CGGAACTCCTCAAATGTAGGC 58.719 52.381 0.00 0.00 33.84 3.93
48 49 2.236395 ACCGGAACTCCTCAAATGTAGG 59.764 50.000 9.46 0.00 35.26 3.18
49 50 3.522553 GACCGGAACTCCTCAAATGTAG 58.477 50.000 9.46 0.00 0.00 2.74
50 51 2.235402 GGACCGGAACTCCTCAAATGTA 59.765 50.000 9.46 0.00 0.00 2.29
51 52 1.003233 GGACCGGAACTCCTCAAATGT 59.997 52.381 9.46 0.00 0.00 2.71
52 53 1.003118 TGGACCGGAACTCCTCAAATG 59.997 52.381 9.46 0.00 0.00 2.32
53 54 1.279271 CTGGACCGGAACTCCTCAAAT 59.721 52.381 9.46 0.00 0.00 2.32
54 55 0.685097 CTGGACCGGAACTCCTCAAA 59.315 55.000 9.46 0.00 0.00 2.69
55 56 0.471211 ACTGGACCGGAACTCCTCAA 60.471 55.000 9.46 0.00 0.00 3.02
56 57 0.898789 GACTGGACCGGAACTCCTCA 60.899 60.000 9.46 0.00 0.00 3.86
57 58 0.612453 AGACTGGACCGGAACTCCTC 60.612 60.000 9.46 0.00 0.00 3.71
58 59 0.702902 TAGACTGGACCGGAACTCCT 59.297 55.000 9.46 0.00 0.00 3.69
59 60 1.409427 CATAGACTGGACCGGAACTCC 59.591 57.143 9.46 5.31 0.00 3.85
60 61 1.202428 GCATAGACTGGACCGGAACTC 60.202 57.143 9.46 0.00 0.00 3.01
61 62 0.824759 GCATAGACTGGACCGGAACT 59.175 55.000 9.46 8.50 0.00 3.01
62 63 0.527817 CGCATAGACTGGACCGGAAC 60.528 60.000 9.46 0.00 0.00 3.62
63 64 0.968901 ACGCATAGACTGGACCGGAA 60.969 55.000 9.46 0.00 0.00 4.30
64 65 1.379443 ACGCATAGACTGGACCGGA 60.379 57.895 9.46 0.00 0.00 5.14
65 66 1.065928 GACGCATAGACTGGACCGG 59.934 63.158 0.00 0.00 0.00 5.28
66 67 0.525668 GTGACGCATAGACTGGACCG 60.526 60.000 0.00 0.00 0.00 4.79
67 68 0.818296 AGTGACGCATAGACTGGACC 59.182 55.000 0.00 0.00 0.00 4.46
68 69 1.914634 CAGTGACGCATAGACTGGAC 58.085 55.000 0.00 0.00 34.63 4.02
71 72 1.202348 TCACCAGTGACGCATAGACTG 59.798 52.381 0.00 0.00 37.45 3.51
72 73 1.545841 TCACCAGTGACGCATAGACT 58.454 50.000 0.00 0.00 34.14 3.24
528 529 1.911702 AAGGAAACTAGAGGCGGGGC 61.912 60.000 0.00 0.00 42.68 5.80
529 530 0.107654 CAAGGAAACTAGAGGCGGGG 60.108 60.000 0.00 0.00 42.68 5.73
530 531 0.613777 ACAAGGAAACTAGAGGCGGG 59.386 55.000 0.00 0.00 42.68 6.13
531 532 3.821421 ATACAAGGAAACTAGAGGCGG 57.179 47.619 0.00 0.00 42.68 6.13
532 533 5.769484 TCTATACAAGGAAACTAGAGGCG 57.231 43.478 0.00 0.00 42.68 5.52
533 534 7.291411 TCATCTATACAAGGAAACTAGAGGC 57.709 40.000 0.00 0.00 42.68 4.70
534 535 7.524698 GCCTCATCTATACAAGGAAACTAGAGG 60.525 44.444 0.00 0.00 42.68 3.69
535 536 7.232534 AGCCTCATCTATACAAGGAAACTAGAG 59.767 40.741 0.00 0.00 42.68 2.43
536 537 7.069986 AGCCTCATCTATACAAGGAAACTAGA 58.930 38.462 0.00 0.00 42.68 2.43
537 538 7.296628 AGCCTCATCTATACAAGGAAACTAG 57.703 40.000 0.00 0.00 42.68 2.57
538 539 8.777578 TTAGCCTCATCTATACAAGGAAACTA 57.222 34.615 0.00 0.00 42.68 2.24
540 541 6.931840 CCTTAGCCTCATCTATACAAGGAAAC 59.068 42.308 0.00 0.00 0.00 2.78
541 542 6.043243 CCCTTAGCCTCATCTATACAAGGAAA 59.957 42.308 0.00 0.00 0.00 3.13
542 543 5.544176 CCCTTAGCCTCATCTATACAAGGAA 59.456 44.000 0.00 0.00 0.00 3.36
543 544 5.087323 CCCTTAGCCTCATCTATACAAGGA 58.913 45.833 0.00 0.00 0.00 3.36
544 545 4.323104 GCCCTTAGCCTCATCTATACAAGG 60.323 50.000 0.00 0.00 34.35 3.61
545 546 4.530161 AGCCCTTAGCCTCATCTATACAAG 59.470 45.833 0.00 0.00 45.47 3.16
546 547 4.284490 CAGCCCTTAGCCTCATCTATACAA 59.716 45.833 0.00 0.00 45.47 2.41
547 548 3.834813 CAGCCCTTAGCCTCATCTATACA 59.165 47.826 0.00 0.00 45.47 2.29
548 549 3.368948 GCAGCCCTTAGCCTCATCTATAC 60.369 52.174 0.00 0.00 45.47 1.47
549 550 2.834549 GCAGCCCTTAGCCTCATCTATA 59.165 50.000 0.00 0.00 45.47 1.31
550 551 1.627834 GCAGCCCTTAGCCTCATCTAT 59.372 52.381 0.00 0.00 45.47 1.98
551 552 1.051812 GCAGCCCTTAGCCTCATCTA 58.948 55.000 0.00 0.00 45.47 1.98
552 553 1.835693 GCAGCCCTTAGCCTCATCT 59.164 57.895 0.00 0.00 45.47 2.90
553 554 4.471761 GCAGCCCTTAGCCTCATC 57.528 61.111 0.00 0.00 45.47 2.92
564 565 3.790089 ATATAAGTACAAGGGCAGCCC 57.210 47.619 24.90 24.90 45.90 5.19
565 566 4.243270 CGTATATAAGTACAAGGGCAGCC 58.757 47.826 1.26 1.26 0.00 4.85
566 567 4.684703 CACGTATATAAGTACAAGGGCAGC 59.315 45.833 0.76 0.00 0.00 5.25
567 568 4.684703 GCACGTATATAAGTACAAGGGCAG 59.315 45.833 0.76 0.00 0.00 4.85
568 569 4.099727 TGCACGTATATAAGTACAAGGGCA 59.900 41.667 0.76 3.56 0.00 5.36
569 570 4.446719 GTGCACGTATATAAGTACAAGGGC 59.553 45.833 0.00 2.41 0.00 5.19
570 571 4.986659 GGTGCACGTATATAAGTACAAGGG 59.013 45.833 11.45 0.00 0.00 3.95
571 572 4.678287 CGGTGCACGTATATAAGTACAAGG 59.322 45.833 11.45 0.00 37.93 3.61
572 573 5.801176 CGGTGCACGTATATAAGTACAAG 57.199 43.478 11.45 0.00 37.93 3.16
590 591 0.461163 TATTGATCGGGTGCACGGTG 60.461 55.000 11.45 3.15 0.00 4.94
591 592 0.461339 GTATTGATCGGGTGCACGGT 60.461 55.000 11.45 0.00 0.00 4.83
592 593 0.461163 TGTATTGATCGGGTGCACGG 60.461 55.000 11.45 5.41 0.00 4.94
593 594 1.526887 GATGTATTGATCGGGTGCACG 59.473 52.381 11.45 0.00 0.00 5.34
594 595 2.560504 TGATGTATTGATCGGGTGCAC 58.439 47.619 8.80 8.80 0.00 4.57
595 596 2.998316 TGATGTATTGATCGGGTGCA 57.002 45.000 0.00 0.00 0.00 4.57
596 597 3.466836 TCTTGATGTATTGATCGGGTGC 58.533 45.455 0.00 0.00 0.00 5.01
597 598 4.697514 ACTCTTGATGTATTGATCGGGTG 58.302 43.478 0.00 0.00 0.00 4.61
598 599 5.118990 CAACTCTTGATGTATTGATCGGGT 58.881 41.667 0.00 0.00 0.00 5.28
599 600 4.024556 GCAACTCTTGATGTATTGATCGGG 60.025 45.833 0.00 0.00 0.00 5.14
600 601 4.571984 TGCAACTCTTGATGTATTGATCGG 59.428 41.667 0.00 0.00 0.00 4.18
601 602 5.723492 TGCAACTCTTGATGTATTGATCG 57.277 39.130 0.00 0.00 0.00 3.69
602 603 6.417044 GCAATGCAACTCTTGATGTATTGATC 59.583 38.462 16.96 0.00 36.74 2.92
603 604 6.270815 GCAATGCAACTCTTGATGTATTGAT 58.729 36.000 16.96 0.00 36.74 2.57
604 605 5.393352 GGCAATGCAACTCTTGATGTATTGA 60.393 40.000 16.96 0.00 36.74 2.57
605 606 4.802039 GGCAATGCAACTCTTGATGTATTG 59.198 41.667 7.79 10.81 36.74 1.90
606 607 4.708421 AGGCAATGCAACTCTTGATGTATT 59.292 37.500 7.79 0.00 33.21 1.89
607 608 4.275810 AGGCAATGCAACTCTTGATGTAT 58.724 39.130 7.79 0.00 0.00 2.29
608 609 3.689347 AGGCAATGCAACTCTTGATGTA 58.311 40.909 7.79 0.00 0.00 2.29
609 610 2.522185 AGGCAATGCAACTCTTGATGT 58.478 42.857 7.79 0.00 0.00 3.06
610 611 3.057104 TGAAGGCAATGCAACTCTTGATG 60.057 43.478 7.79 0.00 0.00 3.07
611 612 3.159472 TGAAGGCAATGCAACTCTTGAT 58.841 40.909 7.79 0.00 0.00 2.57
612 613 2.585330 TGAAGGCAATGCAACTCTTGA 58.415 42.857 7.79 0.00 0.00 3.02
613 614 3.054878 GTTGAAGGCAATGCAACTCTTG 58.945 45.455 7.79 0.00 38.96 3.02
614 615 2.694628 TGTTGAAGGCAATGCAACTCTT 59.305 40.909 7.79 0.26 41.71 2.85
615 616 2.295349 CTGTTGAAGGCAATGCAACTCT 59.705 45.455 7.79 0.00 41.71 3.24
616 617 2.608752 CCTGTTGAAGGCAATGCAACTC 60.609 50.000 7.79 0.32 41.71 3.01
617 618 1.342174 CCTGTTGAAGGCAATGCAACT 59.658 47.619 7.79 0.00 41.71 3.16
618 619 1.340889 TCCTGTTGAAGGCAATGCAAC 59.659 47.619 7.79 3.26 46.92 4.17
619 620 1.340889 GTCCTGTTGAAGGCAATGCAA 59.659 47.619 7.79 0.00 46.92 4.08
620 621 0.961019 GTCCTGTTGAAGGCAATGCA 59.039 50.000 7.79 0.00 46.92 3.96
621 622 1.068055 CAGTCCTGTTGAAGGCAATGC 60.068 52.381 0.00 0.00 46.92 3.56
622 623 2.227388 GTCAGTCCTGTTGAAGGCAATG 59.773 50.000 0.00 0.00 46.92 2.82
623 624 2.508526 GTCAGTCCTGTTGAAGGCAAT 58.491 47.619 0.00 0.00 46.92 3.56
624 625 1.476833 GGTCAGTCCTGTTGAAGGCAA 60.477 52.381 0.00 0.00 46.92 4.52
625 626 0.108585 GGTCAGTCCTGTTGAAGGCA 59.891 55.000 0.00 0.00 46.92 4.75
626 627 0.398318 AGGTCAGTCCTGTTGAAGGC 59.602 55.000 0.00 0.00 46.92 4.35
672 673 7.116075 TGCAGGAATTAATTAAGGAAGTGCTA 58.884 34.615 16.72 6.92 0.00 3.49
673 674 5.951747 TGCAGGAATTAATTAAGGAAGTGCT 59.048 36.000 16.72 0.89 0.00 4.40
674 675 6.207691 TGCAGGAATTAATTAAGGAAGTGC 57.792 37.500 0.00 9.06 0.00 4.40
675 676 6.753744 GCTTGCAGGAATTAATTAAGGAAGTG 59.246 38.462 19.63 5.70 0.00 3.16
676 677 6.127338 GGCTTGCAGGAATTAATTAAGGAAGT 60.127 38.462 19.63 0.00 0.00 3.01
677 678 6.097412 AGGCTTGCAGGAATTAATTAAGGAAG 59.903 38.462 16.81 16.81 0.00 3.46
678 679 5.957774 AGGCTTGCAGGAATTAATTAAGGAA 59.042 36.000 0.00 1.41 0.00 3.36
679 680 5.518865 AGGCTTGCAGGAATTAATTAAGGA 58.481 37.500 0.00 0.00 0.00 3.36
680 681 5.221322 GGAGGCTTGCAGGAATTAATTAAGG 60.221 44.000 0.00 0.00 0.00 2.69
699 700 1.777272 AGATGGGGTTGAATAGGAGGC 59.223 52.381 0.00 0.00 0.00 4.70
721 722 2.168521 TGAATGGATCCGAGGAACTGAC 59.831 50.000 7.39 0.00 41.55 3.51
732 733 7.562454 TTCTTAATTACCGTTGAATGGATCC 57.438 36.000 11.00 4.20 0.00 3.36
773 779 8.823818 CGACCAAACGGAATACTCTAAATATTT 58.176 33.333 5.89 5.89 0.00 1.40
799 805 8.303876 TGTTAATTATCAAGGCTTTGGAAGAAC 58.696 33.333 8.88 11.28 34.97 3.01
800 806 8.415950 TGTTAATTATCAAGGCTTTGGAAGAA 57.584 30.769 8.88 0.00 34.97 2.52
892 901 7.172532 CGGCTATTTAACTGAAGGTGCAATATA 59.827 37.037 0.00 0.00 0.00 0.86
910 919 4.157840 GGAAATGTTCAGAACCGGCTATTT 59.842 41.667 10.93 9.12 0.00 1.40
937 946 3.388024 AGAGTTCAGTTGGTACTTGCTGA 59.612 43.478 8.82 8.82 36.35 4.26
1281 1354 3.243636 GGAAGTAGTCGTTCACCTTCACA 60.244 47.826 0.00 0.00 34.58 3.58
1323 1396 1.371183 GCTGTACTGCAGGGTGACA 59.629 57.895 19.93 14.59 45.14 3.58
1549 1622 0.532573 ATGTAGTCACTCACCAGCCG 59.467 55.000 0.00 0.00 0.00 5.52
1580 1653 1.735920 CCGCCAGCAGATAGATCGC 60.736 63.158 0.00 0.00 0.00 4.58
1809 1900 1.134401 CCGTGCCATATCTTGTCCACT 60.134 52.381 0.00 0.00 0.00 4.00
1856 1947 2.158871 TGTTTGTTAGGGTCTTCTGCGT 60.159 45.455 0.00 0.00 0.00 5.24
1862 1953 1.235724 GCGCTGTTTGTTAGGGTCTT 58.764 50.000 0.00 0.00 0.00 3.01
1870 1967 0.751643 AGGTCCTTGCGCTGTTTGTT 60.752 50.000 9.73 0.00 0.00 2.83
1871 1968 1.152963 AGGTCCTTGCGCTGTTTGT 60.153 52.632 9.73 0.00 0.00 2.83
2109 2206 2.436646 CTTCGGAGCGGCACCATT 60.437 61.111 16.65 0.00 0.00 3.16
2160 2257 3.434053 AGGATACGCGATGTACCCT 57.566 52.632 15.93 7.27 42.85 4.34
2400 2500 0.036388 TGGCTCTGCTACCGGAAAAG 60.036 55.000 9.46 3.30 0.00 2.27
2405 2505 1.097547 CCATTTGGCTCTGCTACCGG 61.098 60.000 0.00 0.00 0.00 5.28
3025 3158 2.093288 TGGCTGTTGGAGATGCTCTAAG 60.093 50.000 0.00 0.00 31.92 2.18
3026 3159 1.908619 TGGCTGTTGGAGATGCTCTAA 59.091 47.619 0.00 0.00 0.00 2.10
3027 3160 1.208052 GTGGCTGTTGGAGATGCTCTA 59.792 52.381 0.00 0.00 0.00 2.43
3203 3375 8.157476 AGGGAGTATCGTTTAATCTATGCAATT 58.843 33.333 0.00 0.00 34.37 2.32
3222 3394 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
3223 3395 8.003629 ACTCTTATATTAGTTTACGGAGGGAGT 58.996 37.037 0.00 0.00 0.00 3.85
3224 3396 8.298140 CACTCTTATATTAGTTTACGGAGGGAG 58.702 40.741 0.00 0.00 0.00 4.30
3225 3397 7.781693 ACACTCTTATATTAGTTTACGGAGGGA 59.218 37.037 0.00 0.00 0.00 4.20
3226 3398 7.949434 ACACTCTTATATTAGTTTACGGAGGG 58.051 38.462 0.00 0.00 0.00 4.30
3227 3399 9.813446 AAACACTCTTATATTAGTTTACGGAGG 57.187 33.333 0.00 0.00 0.00 4.30
3287 3459 9.097946 ACCTTTGTACTACCTCTGTAAACTAAT 57.902 33.333 0.00 0.00 0.00 1.73
3288 3460 8.482852 ACCTTTGTACTACCTCTGTAAACTAA 57.517 34.615 0.00 0.00 0.00 2.24
3289 3461 9.759473 ATACCTTTGTACTACCTCTGTAAACTA 57.241 33.333 0.00 0.00 0.00 2.24
3290 3462 6.990908 ACCTTTGTACTACCTCTGTAAACT 57.009 37.500 0.00 0.00 0.00 2.66
3291 3463 9.716531 AAATACCTTTGTACTACCTCTGTAAAC 57.283 33.333 0.00 0.00 0.00 2.01
3295 3467 8.873144 TGTAAAATACCTTTGTACTACCTCTGT 58.127 33.333 0.00 0.00 0.00 3.41
3296 3468 9.886132 ATGTAAAATACCTTTGTACTACCTCTG 57.114 33.333 0.00 0.00 0.00 3.35
3298 3470 9.322773 GGATGTAAAATACCTTTGTACTACCTC 57.677 37.037 0.00 0.00 0.00 3.85
3299 3471 7.983484 CGGATGTAAAATACCTTTGTACTACCT 59.017 37.037 0.00 0.00 0.00 3.08
3300 3472 7.981225 TCGGATGTAAAATACCTTTGTACTACC 59.019 37.037 0.00 0.00 0.00 3.18
3301 3473 8.931385 TCGGATGTAAAATACCTTTGTACTAC 57.069 34.615 0.00 0.00 0.00 2.73
3302 3474 9.941325 TTTCGGATGTAAAATACCTTTGTACTA 57.059 29.630 0.00 0.00 0.00 1.82
3303 3475 8.724229 GTTTCGGATGTAAAATACCTTTGTACT 58.276 33.333 0.00 0.00 0.00 2.73
3304 3476 8.505625 TGTTTCGGATGTAAAATACCTTTGTAC 58.494 33.333 0.00 0.00 0.00 2.90
3772 3960 1.166129 AGATGTGTACACGCTCGAGT 58.834 50.000 20.61 0.00 0.00 4.18
4013 4225 1.162951 TTCCCCTCTCCCTCTCCCTT 61.163 60.000 0.00 0.00 0.00 3.95
4088 4310 4.101790 CAAGATTTGGCGCGCCGT 62.102 61.111 41.73 30.89 39.42 5.68
4332 4588 0.385473 CGGTTCGTGCATGGTTTGTC 60.385 55.000 5.98 0.00 0.00 3.18
4499 4758 3.215975 GTCGCCTCTATACACCTCTCTT 58.784 50.000 0.00 0.00 0.00 2.85
4570 4829 1.978617 GTGTTCATGGCCTGGTGGG 60.979 63.158 3.32 0.00 38.36 4.61
4576 4835 2.434884 CGCTCGTGTTCATGGCCT 60.435 61.111 3.32 0.00 0.00 5.19
4764 5024 2.970974 GCGGTGCAAGGAGTCAAGC 61.971 63.158 0.00 0.00 0.00 4.01
4849 5113 8.807581 CAATTACCAAAAGTGAAAGTGAAAGAC 58.192 33.333 0.00 0.00 0.00 3.01
5000 5264 7.128077 ACTTGGAATCTGTGGAATGGATAAAT 58.872 34.615 0.00 0.00 0.00 1.40
5002 5266 6.078456 ACTTGGAATCTGTGGAATGGATAA 57.922 37.500 0.00 0.00 0.00 1.75
5482 5746 6.658188 AAATAACCGAATGAGGGTTTGAAA 57.342 33.333 1.09 0.00 45.25 2.69
5667 5933 9.679661 TGCATAGACCAAGATAAAACTGAATAA 57.320 29.630 0.00 0.00 0.00 1.40
5668 5934 9.330063 CTGCATAGACCAAGATAAAACTGAATA 57.670 33.333 0.00 0.00 0.00 1.75
5669 5935 7.831193 ACTGCATAGACCAAGATAAAACTGAAT 59.169 33.333 0.00 0.00 0.00 2.57
5670 5936 7.168219 ACTGCATAGACCAAGATAAAACTGAA 58.832 34.615 0.00 0.00 0.00 3.02
5671 5937 6.711277 ACTGCATAGACCAAGATAAAACTGA 58.289 36.000 0.00 0.00 0.00 3.41
5672 5938 6.992063 ACTGCATAGACCAAGATAAAACTG 57.008 37.500 0.00 0.00 0.00 3.16
5680 5946 6.239217 ACATGATAACTGCATAGACCAAGA 57.761 37.500 0.00 0.00 0.00 3.02
5684 5950 6.683974 AACAACATGATAACTGCATAGACC 57.316 37.500 0.00 0.00 0.00 3.85
5690 5956 6.404623 GGCATAGAAACAACATGATAACTGCA 60.405 38.462 0.00 0.00 0.00 4.41
5691 5957 5.973565 GGCATAGAAACAACATGATAACTGC 59.026 40.000 0.00 0.00 0.00 4.40
5696 5962 7.931407 AGATTACGGCATAGAAACAACATGATA 59.069 33.333 0.00 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.