Multiple sequence alignment - TraesCS5D01G130100

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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 TraesCS5D01G130100 chr5D 100.000 9815 0 0 1 9815 205122511 205112697 0.000000e+00 18125.0
1 TraesCS5D01G130100 chr5D 96.027 1334 47 6 4340 5669 241110410 241111741 0.000000e+00 2165.0
2 TraesCS5D01G130100 chr5D 96.099 1333 41 3 4340 5670 464905570 464904247 0.000000e+00 2163.0
3 TraesCS5D01G130100 chr5D 96.003 1326 49 4 4346 5667 412926359 412927684 0.000000e+00 2152.0
4 TraesCS5D01G130100 chr5D 95.659 1336 52 5 4340 5671 481735217 481733884 0.000000e+00 2141.0
5 TraesCS5D01G130100 chr5D 90.492 305 24 4 3454 3756 450144319 450144620 1.990000e-106 398.0
6 TraesCS5D01G130100 chr5D 91.620 179 15 0 3148 3326 512406019 512405841 2.120000e-61 248.0
7 TraesCS5D01G130100 chr5D 91.061 179 16 0 3148 3326 6161804 6161982 9.850000e-60 243.0
8 TraesCS5D01G130100 chr5D 91.061 179 16 0 3148 3326 503306978 503306800 9.850000e-60 243.0
9 TraesCS5D01G130100 chr5D 90.968 155 11 3 9661 9815 495612637 495612486 1.290000e-48 206.0
10 TraesCS5D01G130100 chr5D 90.850 153 13 1 9662 9814 116886087 116885936 4.650000e-48 204.0
11 TraesCS5D01G130100 chr5D 90.385 156 12 3 9660 9815 376833149 376833301 1.670000e-47 202.0
12 TraesCS5D01G130100 chr5D 82.609 230 38 1 9433 9662 381172151 381172378 1.670000e-47 202.0
13 TraesCS5D01G130100 chr5D 93.130 131 7 2 3016 3144 449150442 449150312 3.620000e-44 191.0
14 TraesCS5D01G130100 chr5D 91.129 124 11 0 4193 4316 268905802 268905679 1.700000e-37 169.0
15 TraesCS5D01G130100 chr5D 97.297 37 1 0 9259 9295 167355151 167355115 8.230000e-06 63.9
16 TraesCS5D01G130100 chr5D 97.297 37 1 0 5671 5707 285263078 285263114 8.230000e-06 63.9
17 TraesCS5D01G130100 chr5D 96.970 33 1 0 5671 5703 498667702 498667670 1.000000e-03 56.5
18 TraesCS5D01G130100 chr5B 96.372 3583 98 12 5671 9233 207169661 207173231 0.000000e+00 5867.0
19 TraesCS5D01G130100 chr5B 96.536 2829 84 9 642 3466 207166662 207169480 0.000000e+00 4669.0
20 TraesCS5D01G130100 chr5B 96.483 654 14 6 1 646 207160290 207160942 0.000000e+00 1072.0
21 TraesCS5D01G130100 chr5B 96.774 217 6 1 4101 4316 207169459 207169675 2.610000e-95 361.0
22 TraesCS5D01G130100 chr5B 90.323 124 12 0 4193 4316 304628734 304628611 7.890000e-36 163.0
23 TraesCS5D01G130100 chr5B 90.991 111 9 1 3349 3458 387983735 387983625 2.210000e-31 148.0
24 TraesCS5D01G130100 chr5B 90.991 111 9 1 3349 3458 387985973 387985863 2.210000e-31 148.0
25 TraesCS5D01G130100 chr5B 90.991 111 9 1 3349 3458 576270171 576270061 2.210000e-31 148.0
26 TraesCS5D01G130100 chr5A 96.540 3526 90 9 5671 9169 244757964 244754444 0.000000e+00 5806.0
27 TraesCS5D01G130100 chr5A 95.556 2340 75 17 1 2331 244762494 244760175 0.000000e+00 3718.0
28 TraesCS5D01G130100 chr5A 95.118 1987 75 6 2331 4316 244759915 244757950 0.000000e+00 3112.0
29 TraesCS5D01G130100 chr5A 83.266 496 28 17 9201 9662 244754455 244753981 1.190000e-108 405.0
30 TraesCS5D01G130100 chr5A 92.857 154 10 1 9662 9815 128113912 128114064 1.280000e-53 222.0
31 TraesCS5D01G130100 chr5A 82.251 231 38 3 9433 9662 126103565 126103337 7.780000e-46 196.0
32 TraesCS5D01G130100 chr6D 96.177 1334 45 6 4340 5669 131933347 131932016 0.000000e+00 2176.0
33 TraesCS5D01G130100 chr6D 88.959 317 28 5 3750 4066 12619468 12619777 1.550000e-102 385.0
34 TraesCS5D01G130100 chr6D 91.503 153 12 1 9662 9814 264390017 264389866 9.990000e-50 209.0
35 TraesCS5D01G130100 chr6D 81.624 234 43 0 9433 9666 188467792 188467559 2.800000e-45 195.0
36 TraesCS5D01G130100 chr6D 89.744 156 11 5 9660 9815 368720970 368720820 2.800000e-45 195.0
37 TraesCS5D01G130100 chr6D 82.949 217 33 4 9448 9662 103469288 103469074 1.010000e-44 193.0
38 TraesCS5D01G130100 chr6D 89.610 154 13 3 9662 9815 255529329 255529479 1.010000e-44 193.0
39 TraesCS5D01G130100 chr6D 82.629 213 37 0 9448 9660 117060459 117060247 1.300000e-43 189.0
40 TraesCS5D01G130100 chr6D 88.961 154 15 2 9662 9815 180051783 180051934 1.300000e-43 189.0
41 TraesCS5D01G130100 chr6D 89.103 156 11 2 9660 9815 185183217 185183366 1.300000e-43 189.0
42 TraesCS5D01G130100 chr6D 81.466 232 41 1 9433 9662 204179177 204179408 1.300000e-43 189.0
43 TraesCS5D01G130100 chr6D 82.629 213 37 0 9448 9660 212385375 212385163 1.300000e-43 189.0
44 TraesCS5D01G130100 chr6D 82.629 213 37 0 9448 9660 213975569 213975357 1.300000e-43 189.0
45 TraesCS5D01G130100 chr6D 82.629 213 37 0 9448 9660 238806641 238806429 1.300000e-43 189.0
46 TraesCS5D01G130100 chr6D 89.610 154 9 2 9660 9813 272652061 272651915 1.300000e-43 189.0
47 TraesCS5D01G130100 chr6D 81.579 228 42 0 9435 9662 466934359 466934586 1.300000e-43 189.0
48 TraesCS5D01G130100 chr6D 82.160 213 38 0 9448 9660 138317945 138317733 6.050000e-42 183.0
49 TraesCS5D01G130100 chr6D 81.140 228 43 0 9435 9662 205956714 205956487 6.050000e-42 183.0
50 TraesCS5D01G130100 chr6D 88.961 154 10 6 9662 9815 359009152 359009298 6.050000e-42 183.0
51 TraesCS5D01G130100 chr6D 88.387 155 12 3 9661 9815 185129715 185129863 2.180000e-41 182.0
52 TraesCS5D01G130100 chr6D 88.816 152 11 4 9660 9811 302131302 302131157 2.180000e-41 182.0
53 TraesCS5D01G130100 chr6D 88.462 156 11 5 9658 9813 303147084 303147232 2.180000e-41 182.0
54 TraesCS5D01G130100 chr6D 91.200 125 10 1 4192 4316 249987212 249987089 1.700000e-37 169.0
55 TraesCS5D01G130100 chr6D 97.368 38 1 0 5671 5708 249987103 249987066 2.290000e-06 65.8
56 TraesCS5D01G130100 chr7D 96.174 1333 44 7 4342 5670 150754863 150756192 0.000000e+00 2172.0
57 TraesCS5D01G130100 chr7D 88.308 325 33 2 3746 4070 18114193 18114512 1.550000e-102 385.0
58 TraesCS5D01G130100 chr7D 88.328 317 32 2 3750 4066 629114058 629113747 9.310000e-100 375.0
59 TraesCS5D01G130100 chr7D 88.304 171 12 6 9645 9815 466066222 466066060 2.160000e-46 198.0
60 TraesCS5D01G130100 chr7D 82.018 228 41 0 9435 9662 311832739 311832966 2.800000e-45 195.0
61 TraesCS5D01G130100 chr7D 81.739 230 42 0 9433 9662 336170937 336170708 1.010000e-44 193.0
62 TraesCS5D01G130100 chr7D 97.143 35 1 0 5671 5705 351584303 351584337 1.060000e-04 60.2
63 TraesCS5D01G130100 chr7D 97.143 35 1 0 5671 5705 356904083 356904049 1.060000e-04 60.2
64 TraesCS5D01G130100 chrUn 95.655 1335 51 2 4341 5674 45206504 45205176 0.000000e+00 2137.0
65 TraesCS5D01G130100 chrUn 93.130 131 7 2 3016 3144 416133439 416133569 3.620000e-44 191.0
66 TraesCS5D01G130100 chrUn 90.476 84 4 3 4121 4200 85062835 85062918 3.750000e-19 108.0
67 TraesCS5D01G130100 chrUn 91.026 78 3 3 4121 4194 85059611 85059688 1.740000e-17 102.0
68 TraesCS5D01G130100 chrUn 97.297 37 1 0 9259 9295 14784794 14784830 8.230000e-06 63.9
69 TraesCS5D01G130100 chrUn 97.297 37 1 0 9259 9295 120020549 120020513 8.230000e-06 63.9
70 TraesCS5D01G130100 chrUn 97.297 37 1 0 9259 9295 125395370 125395334 8.230000e-06 63.9
71 TraesCS5D01G130100 chrUn 97.297 37 1 0 9259 9295 128934033 128934069 8.230000e-06 63.9
72 TraesCS5D01G130100 chrUn 97.297 37 1 0 9259 9295 132654098 132654134 8.230000e-06 63.9
73 TraesCS5D01G130100 chrUn 97.297 37 1 0 9259 9295 149775597 149775561 8.230000e-06 63.9
74 TraesCS5D01G130100 chrUn 97.297 37 1 0 9259 9295 150555208 150555244 8.230000e-06 63.9
75 TraesCS5D01G130100 chrUn 97.297 37 1 0 9259 9295 160869323 160869359 8.230000e-06 63.9
76 TraesCS5D01G130100 chr6B 95.714 1330 54 2 4343 5671 676166010 676164683 0.000000e+00 2137.0
77 TraesCS5D01G130100 chr6B 91.620 179 15 0 3148 3326 450087051 450087229 2.120000e-61 248.0
78 TraesCS5D01G130100 chr6B 91.558 154 12 1 9662 9815 250529868 250529716 2.780000e-50 211.0
79 TraesCS5D01G130100 chr6B 91.870 123 7 3 4195 4316 44661364 44661244 1.700000e-37 169.0
80 TraesCS5D01G130100 chr1D 95.581 1335 55 4 4340 5670 461541676 461543010 0.000000e+00 2135.0
81 TraesCS5D01G130100 chr1D 79.525 337 51 11 9337 9662 195725520 195725191 3.570000e-54 224.0
82 TraesCS5D01G130100 chr1D 92.208 154 9 3 9662 9815 453830373 453830523 2.150000e-51 215.0
83 TraesCS5D01G130100 chr1D 91.667 156 9 3 9660 9815 346708687 346708536 7.720000e-51 213.0
84 TraesCS5D01G130100 chr1D 83.117 231 37 2 9433 9662 204788736 204788965 9.990000e-50 209.0
85 TraesCS5D01G130100 chr1D 91.083 157 11 3 9660 9815 463955087 463954933 9.990000e-50 209.0
86 TraesCS5D01G130100 chr1D 84.286 210 33 0 9453 9662 206947203 206946994 1.290000e-48 206.0
87 TraesCS5D01G130100 chr1D 90.385 156 8 3 9660 9815 407645008 407644860 2.160000e-46 198.0
88 TraesCS5D01G130100 chr1D 93.893 131 6 2 3016 3144 254533676 254533546 7.780000e-46 196.0
89 TraesCS5D01G130100 chr1D 89.744 156 11 2 9660 9815 208063052 208063202 2.800000e-45 195.0
90 TraesCS5D01G130100 chr1D 82.949 217 33 4 9448 9662 165119360 165119574 1.010000e-44 193.0
91 TraesCS5D01G130100 chr1D 90.066 151 10 3 9665 9815 407654173 407654028 3.620000e-44 191.0
92 TraesCS5D01G130100 chr1D 97.297 37 1 0 5671 5707 424738003 424737967 8.230000e-06 63.9
93 TraesCS5D01G130100 chr3D 91.919 297 22 2 3460 3756 150827975 150828269 1.970000e-111 414.0
94 TraesCS5D01G130100 chr3D 89.408 321 29 2 3750 4070 260974258 260974573 5.520000e-107 399.0
95 TraesCS5D01G130100 chr3D 90.909 154 12 2 9662 9815 109746640 109746791 1.290000e-48 206.0
96 TraesCS5D01G130100 chr3D 90.123 162 10 4 9654 9815 330958948 330958793 1.290000e-48 206.0
97 TraesCS5D01G130100 chr3D 97.368 38 1 0 5671 5708 272096141 272096104 2.290000e-06 65.8
98 TraesCS5D01G130100 chr3D 97.297 37 1 0 5671 5707 241667239 241667203 8.230000e-06 63.9
99 TraesCS5D01G130100 chr3D 97.297 37 1 0 5671 5707 335673864 335673900 8.230000e-06 63.9
100 TraesCS5D01G130100 chr3D 97.222 36 1 0 5672 5707 290590210 290590175 2.960000e-05 62.1
101 TraesCS5D01G130100 chr3B 91.946 298 19 4 3461 3755 34646756 34646461 7.090000e-111 412.0
102 TraesCS5D01G130100 chr3B 87.850 321 31 5 3750 4070 821561440 821561128 4.330000e-98 370.0
103 TraesCS5D01G130100 chr3B 91.057 123 10 1 4194 4316 284405191 284405070 2.190000e-36 165.0
104 TraesCS5D01G130100 chr3B 91.743 109 9 0 3349 3457 770117113 770117221 1.710000e-32 152.0
105 TraesCS5D01G130100 chr3B 90.909 77 3 4 4121 4194 571820730 571820655 6.270000e-17 100.0
106 TraesCS5D01G130100 chr3B 97.368 38 1 0 5671 5708 333460437 333460400 2.290000e-06 65.8
107 TraesCS5D01G130100 chr6A 91.611 298 22 3 3461 3756 567346299 567346595 9.180000e-110 409.0
108 TraesCS5D01G130100 chr6A 90.435 115 9 2 3345 3458 2686983 2687096 6.140000e-32 150.0
109 TraesCS5D01G130100 chr6A 90.991 111 9 1 3349 3458 68930757 68930647 2.210000e-31 148.0
110 TraesCS5D01G130100 chr3A 91.156 294 23 2 3461 3752 696209115 696208823 7.140000e-106 396.0
111 TraesCS5D01G130100 chr3A 92.179 179 14 0 3148 3326 435413541 435413719 4.550000e-63 254.0
112 TraesCS5D01G130100 chr3A 97.368 38 1 0 5671 5708 353160576 353160613 2.290000e-06 65.8
113 TraesCS5D01G130100 chr4D 90.604 298 25 2 3461 3756 77293048 77292752 9.240000e-105 392.0
114 TraesCS5D01G130100 chr4D 92.208 154 6 2 9662 9815 267648720 267648867 7.720000e-51 213.0
115 TraesCS5D01G130100 chr4D 83.043 230 38 1 9433 9662 213441986 213441758 3.590000e-49 207.0
116 TraesCS5D01G130100 chr4D 91.026 156 9 3 9660 9815 321910962 321911112 1.290000e-48 206.0
117 TraesCS5D01G130100 chr4D 91.026 156 8 2 9660 9815 458087142 458087291 1.290000e-48 206.0
118 TraesCS5D01G130100 chr4D 90.260 154 13 2 9662 9815 324400085 324399934 6.010000e-47 200.0
119 TraesCS5D01G130100 chr4D 82.251 231 39 2 9433 9662 209523138 209522909 2.160000e-46 198.0
120 TraesCS5D01G130100 chr4D 81.739 230 41 1 9433 9662 271239242 271239470 3.620000e-44 191.0
121 TraesCS5D01G130100 chr4D 93.130 131 7 2 3016 3144 379366099 379365969 3.620000e-44 191.0
122 TraesCS5D01G130100 chr2A 90.635 299 23 3 3454 3748 593500069 593500366 9.240000e-105 392.0
123 TraesCS5D01G130100 chr2A 88.509 322 29 5 3750 4070 4241364 4241050 5.560000e-102 383.0
124 TraesCS5D01G130100 chr2A 93.846 130 7 1 3016 3144 394050799 394050670 2.800000e-45 195.0
125 TraesCS5D01G130100 chr4B 90.236 297 26 2 3460 3754 662764859 662764564 1.550000e-102 385.0
126 TraesCS5D01G130100 chr4B 84.783 230 35 0 9433 9662 310953558 310953329 2.130000e-56 231.0
127 TraesCS5D01G130100 chr4B 91.870 123 7 3 4192 4313 302858993 302859113 1.700000e-37 169.0
128 TraesCS5D01G130100 chr2D 88.644 317 28 5 3750 4065 81980417 81980726 7.190000e-101 379.0
129 TraesCS5D01G130100 chr2D 91.026 156 10 4 9660 9815 588656430 588656581 3.590000e-49 207.0
130 TraesCS5D01G130100 chr2D 93.893 131 6 2 3016 3144 272804179 272804309 7.780000e-46 196.0
131 TraesCS5D01G130100 chr2D 93.130 131 7 2 3016 3144 630266706 630266576 3.620000e-44 191.0
132 TraesCS5D01G130100 chr2D 92.000 125 9 1 4192 4316 388833665 388833788 3.640000e-39 174.0
133 TraesCS5D01G130100 chr2D 97.222 36 1 0 5671 5706 345842398 345842433 2.960000e-05 62.1
134 TraesCS5D01G130100 chr2B 86.997 323 32 7 3744 4066 789129704 789129392 1.210000e-93 355.0
135 TraesCS5D01G130100 chr1A 91.620 179 15 0 3148 3326 554475567 554475389 2.120000e-61 248.0
136 TraesCS5D01G130100 chr1A 97.297 37 1 0 5671 5707 520581110 520581074 8.230000e-06 63.9
137 TraesCS5D01G130100 chr7B 91.061 179 16 0 3148 3326 137679968 137679790 9.850000e-60 243.0
138 TraesCS5D01G130100 chr7B 91.667 156 11 2 9660 9814 738843749 738843903 2.150000e-51 215.0
139 TraesCS5D01G130100 chr7B 90.909 77 4 2 4121 4194 23253670 23253594 6.270000e-17 100.0
140 TraesCS5D01G130100 chr1B 92.308 156 8 4 9660 9815 485971567 485971718 1.660000e-52 219.0
141 TraesCS5D01G130100 chr1B 82.174 230 41 0 9433 9662 231713478 231713707 2.160000e-46 198.0
142 TraesCS5D01G130100 chr1B 90.244 82 6 2 4122 4201 661055640 661055559 1.350000e-18 106.0
143 TraesCS5D01G130100 chr1B 90.667 75 5 2 4122 4194 661057964 661057890 2.260000e-16 99.0
144 TraesCS5D01G130100 chr7A 83.043 230 39 0 9433 9662 379040506 379040277 9.990000e-50 209.0
145 TraesCS5D01G130100 chr7A 90.265 113 11 0 3349 3461 6766240 6766352 2.210000e-31 148.0
146 TraesCS5D01G130100 chr4A 83.117 231 37 2 9433 9662 232504486 232504715 9.990000e-50 209.0
147 TraesCS5D01G130100 chr4A 92.208 77 3 3 4121 4194 701101615 701101539 1.350000e-18 106.0


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 TraesCS5D01G130100 chr5D 205112697 205122511 9814 True 18125.000000 18125 100.000000 1 9815 1 chr5D.!!$R3 9814
1 TraesCS5D01G130100 chr5D 241110410 241111741 1331 False 2165.000000 2165 96.027000 4340 5669 1 chr5D.!!$F2 1329
2 TraesCS5D01G130100 chr5D 464904247 464905570 1323 True 2163.000000 2163 96.099000 4340 5670 1 chr5D.!!$R6 1330
3 TraesCS5D01G130100 chr5D 412926359 412927684 1325 False 2152.000000 2152 96.003000 4346 5667 1 chr5D.!!$F6 1321
4 TraesCS5D01G130100 chr5D 481733884 481735217 1333 True 2141.000000 2141 95.659000 4340 5671 1 chr5D.!!$R7 1331
5 TraesCS5D01G130100 chr5B 207166662 207173231 6569 False 3632.333333 5867 96.560667 642 9233 3 chr5B.!!$F2 8591
6 TraesCS5D01G130100 chr5B 207160290 207160942 652 False 1072.000000 1072 96.483000 1 646 1 chr5B.!!$F1 645
7 TraesCS5D01G130100 chr5A 244753981 244762494 8513 True 3260.250000 5806 92.620000 1 9662 4 chr5A.!!$R2 9661
8 TraesCS5D01G130100 chr6D 131932016 131933347 1331 True 2176.000000 2176 96.177000 4340 5669 1 chr6D.!!$R3 1329
9 TraesCS5D01G130100 chr7D 150754863 150756192 1329 False 2172.000000 2172 96.174000 4342 5670 1 chr7D.!!$F2 1328
10 TraesCS5D01G130100 chrUn 45205176 45206504 1328 True 2137.000000 2137 95.655000 4341 5674 1 chrUn.!!$R1 1333
11 TraesCS5D01G130100 chr6B 676164683 676166010 1327 True 2137.000000 2137 95.714000 4343 5671 1 chr6B.!!$R3 1328
12 TraesCS5D01G130100 chr1D 461541676 461543010 1334 False 2135.000000 2135 95.581000 4340 5670 1 chr1D.!!$F5 1330

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
284 289 0.238289 CATATTTGCGCGGGGCTTAG 59.762 55.000 18.19 0.00 44.05 2.18 F
672 680 0.678950 AACAAATTCCCGGGTTGCTG 59.321 50.000 22.86 16.23 0.00 4.41 F
1128 1138 0.527817 GCGATCAGGTTCTACCCACG 60.528 60.000 0.00 0.00 39.75 4.94 F
1708 1720 0.736053 CTAGTCCTCAGACCTCGCAC 59.264 60.000 0.00 0.00 44.72 5.34 F
3450 3726 1.006519 CTCCAAGTCTCTCTCCCTCCA 59.993 57.143 0.00 0.00 0.00 3.86 F
4321 4599 0.250467 CACACCCCTGTCCAGAGTTG 60.250 60.000 0.00 0.00 0.00 3.16 F
6086 6391 0.385390 AACTCCAAGCTGCAAAACCG 59.615 50.000 1.02 0.00 0.00 4.44 F
6285 6590 0.614294 ATCAAGCAGCAGAGACAGCT 59.386 50.000 0.00 0.00 44.62 4.24 F
6865 7170 0.899720 CAGGCTGGTGGAAATGCAAT 59.100 50.000 6.61 0.00 0.00 3.56 F
7925 8233 0.035317 TTGTCAGCAGCGGAGTTCAT 59.965 50.000 0.00 0.00 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1107 1117 0.824109 TGGGTAGAACCTGATCGCTG 59.176 55.0 0.00 0.0 38.64 5.18 R
1895 1908 1.769026 TCCGGAGAAGACCTGATCTG 58.231 55.0 0.00 0.0 37.88 2.90 R
2507 2783 2.435805 GTCTCATCATGCCTAACCCTCA 59.564 50.0 0.00 0.0 0.00 3.86 R
3614 3891 0.394352 GACATTCGGCACCCCTTCAT 60.394 55.0 0.00 0.0 0.00 2.57 R
5197 5499 1.546589 TACCAAGTACCACCAGCCGG 61.547 60.0 0.00 0.0 38.77 6.13 R
6285 6590 0.110295 TTTCCAGGTGCTGCTTGCTA 59.890 50.0 0.00 0.0 43.37 3.49 R
7200 7505 0.028770 TTTGCACTTCCTCGTTTGCG 59.971 50.0 0.00 0.0 37.82 4.85 R
7339 7644 0.607217 CACAGCTGTGCCTCCAATGA 60.607 55.0 32.39 0.0 39.39 2.57 R
8672 9005 0.036765 CACCGACATTTCCGAGGGAA 60.037 55.0 0.00 0.0 40.27 3.97 R
9150 9492 0.383949 TTCGCAAAAACCTGCACCTC 59.616 50.0 0.00 0.0 42.77 3.85 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
52 57 1.668751 GTGTTCACGGAGTTCTTGCAA 59.331 47.619 0.00 0.00 41.61 4.08
168 173 1.533625 TCTTGGTTTCCGCCATGAAG 58.466 50.000 0.00 0.00 39.00 3.02
179 184 1.936547 CGCCATGAAGTTTCTCTAGCC 59.063 52.381 0.00 0.00 0.00 3.93
210 215 3.262448 TTCTTTCCCCGCTTCCCCG 62.262 63.158 0.00 0.00 0.00 5.73
263 268 1.203125 GGTCTGGATTTGGGGGTTTCA 60.203 52.381 0.00 0.00 0.00 2.69
272 277 4.550076 TTTGGGGGTTTCAGCATATTTG 57.450 40.909 0.00 0.00 0.00 2.32
281 286 3.595758 GCATATTTGCGCGGGGCT 61.596 61.111 18.19 0.46 44.05 5.19
282 287 3.119193 CATATTTGCGCGGGGCTT 58.881 55.556 18.19 5.87 44.05 4.35
283 288 1.791103 GCATATTTGCGCGGGGCTTA 61.791 55.000 18.19 6.38 44.05 3.09
284 289 0.238289 CATATTTGCGCGGGGCTTAG 59.762 55.000 18.19 0.00 44.05 2.18
285 290 1.515521 ATATTTGCGCGGGGCTTAGC 61.516 55.000 18.19 0.00 44.05 3.09
288 296 4.715523 TGCGCGGGGCTTAGCTTT 62.716 61.111 18.19 0.00 44.05 3.51
291 299 3.140814 GCGGGGCTTAGCTTTGGG 61.141 66.667 3.59 0.00 0.00 4.12
463 471 2.032030 CAGTCGGTGGCTACAACTTTTG 60.032 50.000 1.52 0.00 29.98 2.44
479 487 1.028130 TTTGGAGTGACGCATTGCAA 58.972 45.000 9.69 0.00 30.83 4.08
522 530 2.613977 CGCACCTTCTTCTCCTGATGTT 60.614 50.000 0.00 0.00 0.00 2.71
574 582 3.506067 CCGGCTGTTCTTAGTTGGAATTT 59.494 43.478 0.00 0.00 0.00 1.82
584 592 3.160679 AGTTGGAATTTCTGGACAGGG 57.839 47.619 0.00 0.00 0.00 4.45
602 610 2.916934 AGGGCATAGTTGGGACTTTGTA 59.083 45.455 0.00 0.00 37.23 2.41
604 612 4.017499 AGGGCATAGTTGGGACTTTGTATT 60.017 41.667 0.00 0.00 37.23 1.89
672 680 0.678950 AACAAATTCCCGGGTTGCTG 59.321 50.000 22.86 16.23 0.00 4.41
1068 1078 1.690219 ATAGTCCTGGGGCAAGCGAG 61.690 60.000 0.00 0.00 0.00 5.03
1107 1117 1.818785 GCATCCTCAGTGCTGCTCC 60.819 63.158 0.00 0.00 39.45 4.70
1108 1118 1.600638 CATCCTCAGTGCTGCTCCA 59.399 57.895 0.00 0.00 0.00 3.86
1128 1138 0.527817 GCGATCAGGTTCTACCCACG 60.528 60.000 0.00 0.00 39.75 4.94
1264 1274 6.542821 TGGGCAATGAATTCTAGTATTAGGG 58.457 40.000 7.05 0.00 0.00 3.53
1369 1379 7.628234 AGTTTGATCAGATTCAAGTAGGACAT 58.372 34.615 0.00 0.00 36.97 3.06
1411 1421 2.493278 GTTGAGTACATTGCCATTGCCT 59.507 45.455 0.00 0.00 36.33 4.75
1464 1474 4.261994 GCCAACAGCTTTCAACCTATCAAA 60.262 41.667 0.00 0.00 38.99 2.69
1708 1720 0.736053 CTAGTCCTCAGACCTCGCAC 59.264 60.000 0.00 0.00 44.72 5.34
1855 1868 4.202172 GGTAGCTACCAGAAGGACTTGATC 60.202 50.000 33.64 4.14 45.73 2.92
1857 1870 2.482142 GCTACCAGAAGGACTTGATCGG 60.482 54.545 0.00 0.00 38.69 4.18
2074 2089 3.846588 AGTCCATGTGTATGTTTCCTCCT 59.153 43.478 0.00 0.00 32.21 3.69
2107 2122 8.459635 GGTGAATAATTGACTTCCTAAAGTTCC 58.540 37.037 0.00 0.00 45.80 3.62
2309 2325 5.483811 TGTCATCTATTTACAAACAGGCGA 58.516 37.500 0.00 0.00 0.00 5.54
2507 2783 4.145052 GGTCAATCACCCAAAGTCTCTTT 58.855 43.478 0.00 0.00 39.69 2.52
2542 2818 4.996793 TGATGAGACCCAAGAAATTGGAA 58.003 39.130 8.59 0.00 44.82 3.53
2591 2867 9.455847 GCTAGCATCAAGAGTTAATTTAAATGG 57.544 33.333 10.63 0.00 0.00 3.16
2670 2946 3.251484 AGAGACCAAGGAGACCATGAAA 58.749 45.455 0.00 0.00 0.00 2.69
2810 3086 4.149511 TGATTCCCGCATATGTTCTTGA 57.850 40.909 4.29 0.00 0.00 3.02
2974 3250 8.911247 ATAAGAAAAGGCGCTTACAAATTAAG 57.089 30.769 7.64 0.00 30.17 1.85
3345 3621 8.415950 AGTCCCATATTTCATTTACAACAACA 57.584 30.769 0.00 0.00 0.00 3.33
3346 3622 8.865090 AGTCCCATATTTCATTTACAACAACAA 58.135 29.630 0.00 0.00 0.00 2.83
3347 3623 8.921670 GTCCCATATTTCATTTACAACAACAAC 58.078 33.333 0.00 0.00 0.00 3.32
3422 3698 8.706492 AATCGGTTTAAATCATGTACGACTTA 57.294 30.769 0.00 0.00 31.60 2.24
3450 3726 1.006519 CTCCAAGTCTCTCTCCCTCCA 59.993 57.143 0.00 0.00 0.00 3.86
3515 3792 1.454295 ATCTGGGCGATGCATGCAA 60.454 52.632 26.68 8.49 0.00 4.08
3614 3891 2.179424 GTCCCTACTCCTATCCCCTTGA 59.821 54.545 0.00 0.00 0.00 3.02
3650 3927 4.706842 ATGTCCGAGCCTAATACCAAAT 57.293 40.909 0.00 0.00 0.00 2.32
3658 3935 5.573282 CGAGCCTAATACCAAATAGACATCG 59.427 44.000 0.00 0.00 0.00 3.84
3670 3947 0.613260 AGACATCGCACCAAAGCCTA 59.387 50.000 0.00 0.00 0.00 3.93
3748 4025 4.074526 GCGCACTCTCAGAGGCCA 62.075 66.667 5.01 0.00 33.35 5.36
3772 4049 3.046087 CTGCCGCCCATCGCATAG 61.046 66.667 0.00 0.00 37.30 2.23
3774 4051 4.996434 GCCGCCCATCGCATAGCT 62.996 66.667 0.00 0.00 37.30 3.32
3913 4190 3.757248 ATGGGAGATCCGGCGCAAC 62.757 63.158 10.83 0.00 38.76 4.17
3917 4194 4.162690 AGATCCGGCGCAACCCTC 62.163 66.667 10.83 0.00 33.26 4.30
3944 4221 4.356442 CCCTTTTGGCGTTGGGCG 62.356 66.667 0.00 0.00 44.92 6.13
4115 4392 3.202151 TGAATTCCCCTCCCATGTACTTC 59.798 47.826 2.27 0.00 0.00 3.01
4214 4491 3.525268 ACAACAACAAAGCCTTTCAGG 57.475 42.857 0.00 0.00 38.80 3.86
4284 4562 1.031235 CAAGTCATGGTTGTGGCACA 58.969 50.000 17.96 17.96 0.00 4.57
4316 4594 1.705002 TTCCACACACCCCTGTCCAG 61.705 60.000 0.00 0.00 0.00 3.86
4317 4595 2.146724 CCACACACCCCTGTCCAGA 61.147 63.158 0.00 0.00 0.00 3.86
4318 4596 1.372683 CACACACCCCTGTCCAGAG 59.627 63.158 0.00 0.00 0.00 3.35
4319 4597 1.074471 ACACACCCCTGTCCAGAGT 60.074 57.895 0.00 0.00 0.00 3.24
4320 4598 0.694444 ACACACCCCTGTCCAGAGTT 60.694 55.000 0.00 0.00 0.00 3.01
4321 4599 0.250467 CACACCCCTGTCCAGAGTTG 60.250 60.000 0.00 0.00 0.00 3.16
4322 4600 1.302832 CACCCCTGTCCAGAGTTGC 60.303 63.158 0.00 0.00 0.00 4.17
4323 4601 2.046892 CCCCTGTCCAGAGTTGCG 60.047 66.667 0.00 0.00 0.00 4.85
4324 4602 2.743718 CCCTGTCCAGAGTTGCGT 59.256 61.111 0.00 0.00 0.00 5.24
4325 4603 1.669115 CCCTGTCCAGAGTTGCGTG 60.669 63.158 0.00 0.00 0.00 5.34
4326 4604 1.069765 CCTGTCCAGAGTTGCGTGT 59.930 57.895 0.00 0.00 0.00 4.49
4327 4605 1.224069 CCTGTCCAGAGTTGCGTGTG 61.224 60.000 0.00 0.00 0.00 3.82
4328 4606 1.224069 CTGTCCAGAGTTGCGTGTGG 61.224 60.000 0.00 0.00 0.00 4.17
4329 4607 2.280797 TCCAGAGTTGCGTGTGGC 60.281 61.111 0.00 0.00 43.96 5.01
4338 4616 2.280119 GCGTGTGGCACTCAGACA 60.280 61.111 19.83 0.00 39.36 3.41
4487 4767 2.370633 GGGGCTCTTCCTCCCTCT 59.629 66.667 0.00 0.00 42.25 3.69
4495 4775 1.304217 TTCCTCCCTCTCGCGTCTT 60.304 57.895 5.77 0.00 0.00 3.01
4500 4780 4.237445 CCTCTCGCGTCTTAGGGA 57.763 61.111 5.77 0.00 0.00 4.20
4544 4824 1.437986 GTGCGGCCGATCTAGAAGT 59.562 57.895 33.48 0.00 0.00 3.01
5048 5350 2.203195 TTTGTGGAGCAGCGCTGT 60.203 55.556 35.80 23.48 39.88 4.40
5195 5497 2.705658 TCTTCCAAGGACTTCAAGCTGA 59.294 45.455 0.00 0.00 0.00 4.26
5197 5499 1.163554 CCAAGGACTTCAAGCTGAGC 58.836 55.000 0.00 0.00 0.00 4.26
5215 5517 2.747686 CGGCTGGTGGTACTTGGT 59.252 61.111 0.00 0.00 0.00 3.67
5759 6064 7.320443 TGATGGATTGTATTTCTGCAAGTAC 57.680 36.000 0.00 0.00 30.17 2.73
6086 6391 0.385390 AACTCCAAGCTGCAAAACCG 59.615 50.000 1.02 0.00 0.00 4.44
6175 6480 5.105392 CCTGATCTACAAGAGAAGCTTCAGT 60.105 44.000 27.57 20.32 36.47 3.41
6260 6565 6.930731 AGATACTCTCACTGGAAAAAGACTC 58.069 40.000 0.00 0.00 0.00 3.36
6285 6590 0.614294 ATCAAGCAGCAGAGACAGCT 59.386 50.000 0.00 0.00 44.62 4.24
6450 6755 3.599343 TGACAGTGCAGAATGTATGGTC 58.401 45.455 0.00 0.00 39.31 4.02
6698 7003 7.118088 GTGACGAGAAACAACTCTTCTAAAAC 58.882 38.462 0.00 0.00 36.55 2.43
6855 7160 2.270986 GGCAAGGAACAGGCTGGTG 61.271 63.158 20.34 9.41 0.00 4.17
6865 7170 0.899720 CAGGCTGGTGGAAATGCAAT 59.100 50.000 6.61 0.00 0.00 3.56
6920 7225 1.267574 GCTCTGGGAGATGTGGACCA 61.268 60.000 0.00 0.00 0.00 4.02
7035 7340 7.117379 GGAGAAAATGCAGAAAAGAAGGAATTG 59.883 37.037 0.00 0.00 0.00 2.32
7200 7505 3.003480 GTTGGAGACACAGCTGTATTCC 58.997 50.000 25.39 25.39 42.67 3.01
7208 7513 1.075542 CAGCTGTATTCCGCAAACGA 58.924 50.000 5.25 0.00 43.93 3.85
7289 7594 2.729862 ACTGCGCGACGAACTCAC 60.730 61.111 12.10 0.00 0.00 3.51
7290 7595 3.470567 CTGCGCGACGAACTCACC 61.471 66.667 12.10 0.00 0.00 4.02
7339 7644 4.401925 AGCTGTTGAGGCTGTTAAAGAAT 58.598 39.130 0.00 0.00 38.73 2.40
7387 7692 4.667519 AACACCGAAGTAGAGAAACTGT 57.332 40.909 0.00 0.00 0.00 3.55
7662 7970 6.090483 TCTCTTTCTGTGGAGTCTGTTAAG 57.910 41.667 0.00 0.00 0.00 1.85
7749 8057 0.877071 CGCTTGAGCATGAAGTGGTT 59.123 50.000 0.00 0.00 36.14 3.67
7862 8170 0.815615 CAGGATGCCCGGAAGCTTAC 60.816 60.000 0.73 0.00 37.58 2.34
7925 8233 0.035317 TTGTCAGCAGCGGAGTTCAT 59.965 50.000 0.00 0.00 0.00 2.57
8206 8514 8.762645 TCTCTTTATACTGAATCTGGTGATTGT 58.237 33.333 0.00 0.00 42.43 2.71
8212 8520 2.040145 TGAATCTGGTGATTGTGGCTCA 59.960 45.455 0.00 0.00 42.43 4.26
8548 8881 1.500474 CAGTGATCCTGGCCTCCTTA 58.500 55.000 3.32 0.00 37.54 2.69
8619 8952 1.486726 GATCTTGACCTTCCGGATGGT 59.513 52.381 35.41 35.41 41.00 3.55
8672 9005 0.976073 ATTCGACCGTCATCACCCCT 60.976 55.000 0.00 0.00 0.00 4.79
8775 9108 8.843885 TGATGGATGATTAGAATGTCAAGATC 57.156 34.615 0.00 0.00 0.00 2.75
8780 9113 9.645059 GGATGATTAGAATGTCAAGATCGATTA 57.355 33.333 0.00 0.00 0.00 1.75
8906 9244 7.811117 AGAGGTAGTAGATCAGTGTACATTC 57.189 40.000 0.00 0.00 0.00 2.67
8927 9265 7.667219 ACATTCACAGAAACTGATTGGTAGATT 59.333 33.333 5.76 0.00 35.18 2.40
9065 9405 0.249699 CGGTGTACTGGCTGTGTTGA 60.250 55.000 7.34 0.00 0.00 3.18
9101 9441 1.534163 GGTTTGGTGCGGTTTCTACTC 59.466 52.381 0.00 0.00 0.00 2.59
9113 9455 0.109735 TTCTACTCGCTGTGTGCTCG 60.110 55.000 0.00 0.00 40.11 5.03
9150 9492 3.817084 TGTTTGAGGCTGATTCAGACAAG 59.183 43.478 21.42 0.00 42.99 3.16
9165 9507 2.689983 AGACAAGAGGTGCAGGTTTTTG 59.310 45.455 0.00 0.00 0.00 2.44
9193 9535 4.767409 GCTTTCCTTAATCAACAAGGGAGT 59.233 41.667 1.50 0.00 42.47 3.85
9196 9538 7.362142 GCTTTCCTTAATCAACAAGGGAGTTAG 60.362 40.741 1.50 0.00 42.47 2.34
9203 9545 5.499004 TCAACAAGGGAGTTAGCTAACAT 57.501 39.130 32.48 20.08 38.62 2.71
9249 9591 7.205297 ACATCATTAGCCATGTTTAGAAATGC 58.795 34.615 0.00 0.00 34.06 3.56
9254 9596 3.509575 AGCCATGTTTAGAAATGCGGAAA 59.490 39.130 0.00 0.00 0.00 3.13
9255 9597 3.612423 GCCATGTTTAGAAATGCGGAAAC 59.388 43.478 0.00 0.00 33.37 2.78
9261 9603 4.576216 TTAGAAATGCGGAAACTGCAAA 57.424 36.364 9.27 0.00 41.66 3.68
9268 9610 3.146066 TGCGGAAACTGCAAAGACTTAT 58.854 40.909 2.65 0.00 37.03 1.73
9269 9611 3.058293 TGCGGAAACTGCAAAGACTTATG 60.058 43.478 2.65 0.00 37.03 1.90
9378 9727 4.726583 TGGGAGAGTATAGCGTAGACAAT 58.273 43.478 0.00 0.00 0.00 2.71
9381 9730 5.241064 GGGAGAGTATAGCGTAGACAATGAA 59.759 44.000 0.00 0.00 0.00 2.57
9384 9733 7.868415 GGAGAGTATAGCGTAGACAATGAATTT 59.132 37.037 0.00 0.00 0.00 1.82
9501 9877 5.830912 TCTTGGTGATGAATTTGTGTCAAC 58.169 37.500 0.00 0.00 0.00 3.18
9502 9878 4.582701 TGGTGATGAATTTGTGTCAACC 57.417 40.909 0.00 0.00 0.00 3.77
9605 9981 8.570488 TGATATGGTTTAATGATGAGCATTGTC 58.430 33.333 6.14 0.00 46.38 3.18
9606 9982 6.778834 ATGGTTTAATGATGAGCATTGTCA 57.221 33.333 6.14 0.00 46.38 3.58
9607 9983 6.198650 TGGTTTAATGATGAGCATTGTCAG 57.801 37.500 6.14 0.00 46.38 3.51
9608 9984 5.711506 TGGTTTAATGATGAGCATTGTCAGT 59.288 36.000 6.14 0.00 46.38 3.41
9609 9985 6.032094 GGTTTAATGATGAGCATTGTCAGTG 58.968 40.000 6.14 0.00 46.38 3.66
9610 9986 6.349611 GGTTTAATGATGAGCATTGTCAGTGT 60.350 38.462 6.14 0.00 46.38 3.55
9611 9987 6.822667 TTAATGATGAGCATTGTCAGTGTT 57.177 33.333 6.14 0.00 46.38 3.32
9612 9988 5.717078 AATGATGAGCATTGTCAGTGTTT 57.283 34.783 0.00 0.00 45.27 2.83
9613 9989 4.492791 TGATGAGCATTGTCAGTGTTTG 57.507 40.909 0.00 0.00 0.00 2.93
9614 9990 4.136051 TGATGAGCATTGTCAGTGTTTGA 58.864 39.130 0.00 0.00 0.00 2.69
9615 9991 4.579753 TGATGAGCATTGTCAGTGTTTGAA 59.420 37.500 0.00 0.00 37.61 2.69
9616 9992 5.242171 TGATGAGCATTGTCAGTGTTTGAAT 59.758 36.000 0.00 0.00 37.61 2.57
9617 9993 5.112220 TGAGCATTGTCAGTGTTTGAATC 57.888 39.130 0.00 0.00 37.61 2.52
9618 9994 4.823442 TGAGCATTGTCAGTGTTTGAATCT 59.177 37.500 0.00 0.00 37.61 2.40
9619 9995 5.997129 TGAGCATTGTCAGTGTTTGAATCTA 59.003 36.000 0.00 0.00 37.61 1.98
9633 10009 9.766277 GTGTTTGAATCTAAATAAGAGCTTCAG 57.234 33.333 0.00 0.00 35.60 3.02
9683 10059 9.784531 ATATTGAAAGAATCGATATGGTTGACT 57.215 29.630 0.00 0.00 41.62 3.41
9685 10061 8.648557 TTGAAAGAATCGATATGGTTGACTAG 57.351 34.615 0.00 0.00 0.00 2.57
9686 10062 8.007405 TGAAAGAATCGATATGGTTGACTAGA 57.993 34.615 0.00 0.00 0.00 2.43
9687 10063 8.138074 TGAAAGAATCGATATGGTTGACTAGAG 58.862 37.037 0.00 0.00 0.00 2.43
9688 10064 6.582677 AGAATCGATATGGTTGACTAGAGG 57.417 41.667 0.00 0.00 0.00 3.69
9689 10065 5.478679 AGAATCGATATGGTTGACTAGAGGG 59.521 44.000 0.00 0.00 0.00 4.30
9690 10066 3.497332 TCGATATGGTTGACTAGAGGGG 58.503 50.000 0.00 0.00 0.00 4.79
9691 10067 2.563179 CGATATGGTTGACTAGAGGGGG 59.437 54.545 0.00 0.00 0.00 5.40
9707 10083 1.140312 GGGGGAGTGATGAATAGGCA 58.860 55.000 0.00 0.00 0.00 4.75
9708 10084 1.494721 GGGGGAGTGATGAATAGGCAA 59.505 52.381 0.00 0.00 0.00 4.52
9709 10085 2.576615 GGGGAGTGATGAATAGGCAAC 58.423 52.381 0.00 0.00 0.00 4.17
9753 10129 9.436957 TTTTTGACAAATTAGGTTTAGCAACAA 57.563 25.926 0.50 0.00 34.15 2.83
9754 10130 9.436957 TTTTGACAAATTAGGTTTAGCAACAAA 57.563 25.926 0.50 0.00 34.15 2.83
9755 10131 9.606631 TTTGACAAATTAGGTTTAGCAACAAAT 57.393 25.926 0.00 0.00 34.15 2.32
9757 10133 9.906660 TGACAAATTAGGTTTAGCAACAAATAG 57.093 29.630 0.00 0.00 34.15 1.73
9758 10134 9.353999 GACAAATTAGGTTTAGCAACAAATAGG 57.646 33.333 0.00 0.00 34.15 2.57
9759 10135 8.866093 ACAAATTAGGTTTAGCAACAAATAGGT 58.134 29.630 0.00 0.00 34.15 3.08
9760 10136 9.705290 CAAATTAGGTTTAGCAACAAATAGGTT 57.295 29.630 0.00 0.00 34.15 3.50
9779 10155 9.950496 AATAGGTTGTCTAGATATGCAATTAGG 57.050 33.333 0.00 0.00 0.00 2.69
9780 10156 7.380423 AGGTTGTCTAGATATGCAATTAGGT 57.620 36.000 0.00 0.00 0.00 3.08
9781 10157 7.220030 AGGTTGTCTAGATATGCAATTAGGTG 58.780 38.462 0.00 0.00 0.00 4.00
9782 10158 7.071196 AGGTTGTCTAGATATGCAATTAGGTGA 59.929 37.037 0.00 0.00 0.00 4.02
9783 10159 7.386299 GGTTGTCTAGATATGCAATTAGGTGAG 59.614 40.741 0.00 0.00 0.00 3.51
9784 10160 6.459066 TGTCTAGATATGCAATTAGGTGAGC 58.541 40.000 0.00 0.00 0.00 4.26
9785 10161 6.041979 TGTCTAGATATGCAATTAGGTGAGCA 59.958 38.462 0.00 0.00 41.73 4.26
9786 10162 6.931281 GTCTAGATATGCAATTAGGTGAGCAA 59.069 38.462 0.00 0.00 40.76 3.91
9787 10163 6.931281 TCTAGATATGCAATTAGGTGAGCAAC 59.069 38.462 0.00 0.00 40.76 4.17
9808 10184 9.003658 AGCAACCTATATGATGCTAACAATAAC 57.996 33.333 10.37 0.00 46.61 1.89
9809 10185 8.783093 GCAACCTATATGATGCTAACAATAACA 58.217 33.333 3.51 0.00 35.93 2.41
9812 10188 9.845740 ACCTATATGATGCTAACAATAACAACA 57.154 29.630 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 5.476945 ACACAACACTCCACTTCTTTTCTTT 59.523 36.000 0.00 0.00 0.00 2.52
156 161 2.859165 AGAGAAACTTCATGGCGGAA 57.141 45.000 0.00 0.00 0.00 4.30
168 173 0.174617 AGCAGAGCGGCTAGAGAAAC 59.825 55.000 0.60 0.00 43.70 2.78
179 184 2.095516 GGGAAAGAAGAAAAGCAGAGCG 60.096 50.000 0.00 0.00 0.00 5.03
272 277 4.179579 CAAAGCTAAGCCCCGCGC 62.180 66.667 0.00 0.00 37.98 6.86
277 282 1.005569 ACCTAACCCAAAGCTAAGCCC 59.994 52.381 0.00 0.00 0.00 5.19
280 285 4.399303 CCAATCACCTAACCCAAAGCTAAG 59.601 45.833 0.00 0.00 0.00 2.18
281 286 4.340617 CCAATCACCTAACCCAAAGCTAA 58.659 43.478 0.00 0.00 0.00 3.09
282 287 3.876156 GCCAATCACCTAACCCAAAGCTA 60.876 47.826 0.00 0.00 0.00 3.32
283 288 2.807676 CCAATCACCTAACCCAAAGCT 58.192 47.619 0.00 0.00 0.00 3.74
284 289 1.204704 GCCAATCACCTAACCCAAAGC 59.795 52.381 0.00 0.00 0.00 3.51
285 290 1.472480 CGCCAATCACCTAACCCAAAG 59.528 52.381 0.00 0.00 0.00 2.77
288 296 0.251916 CTCGCCAATCACCTAACCCA 59.748 55.000 0.00 0.00 0.00 4.51
291 299 1.473434 CCTCCTCGCCAATCACCTAAC 60.473 57.143 0.00 0.00 0.00 2.34
409 417 6.795590 TCCCCCAAATAGAATAGAAACACAA 58.204 36.000 0.00 0.00 0.00 3.33
413 421 7.116736 TCAACTCCCCCAAATAGAATAGAAAC 58.883 38.462 0.00 0.00 0.00 2.78
463 471 0.593128 AAGTTGCAATGCGTCACTCC 59.407 50.000 0.59 0.00 0.00 3.85
552 560 2.178912 TTCCAACTAAGAACAGCCGG 57.821 50.000 0.00 0.00 0.00 6.13
574 582 0.911769 CCAACTATGCCCTGTCCAGA 59.088 55.000 0.00 0.00 0.00 3.86
584 592 4.705023 ACCAATACAAAGTCCCAACTATGC 59.295 41.667 0.00 0.00 33.48 3.14
602 610 3.356290 GGCAAGACCAATACTGACCAAT 58.644 45.455 0.00 0.00 38.86 3.16
604 612 1.004277 GGGCAAGACCAATACTGACCA 59.996 52.381 0.00 0.00 42.05 4.02
1068 1078 2.433318 GACACGGGCACAGAGCTC 60.433 66.667 5.27 5.27 44.79 4.09
1107 1117 0.824109 TGGGTAGAACCTGATCGCTG 59.176 55.000 0.00 0.00 38.64 5.18
1108 1118 0.824759 GTGGGTAGAACCTGATCGCT 59.175 55.000 0.00 0.00 38.64 4.93
1128 1138 3.193267 TGCAGGATACAAAATGAAGGCAC 59.807 43.478 0.00 0.00 41.41 5.01
1175 1185 8.554528 CATGATAAGAATGTGCTAACTACCTTG 58.445 37.037 0.00 0.00 0.00 3.61
1177 1187 7.220030 CCATGATAAGAATGTGCTAACTACCT 58.780 38.462 0.00 0.00 0.00 3.08
1369 1379 6.039159 TCAACAAACATTAGCATCTGAACACA 59.961 34.615 0.00 0.00 0.00 3.72
1411 1421 9.434275 TCTCTATCACAAGATTTCCCACTAATA 57.566 33.333 0.00 0.00 35.67 0.98
1464 1474 9.436957 CTTACACAACTGGAACTAATCTTACAT 57.563 33.333 0.00 0.00 0.00 2.29
1708 1720 4.097418 AGTAGCCTATGCCCTATAGTTGG 58.903 47.826 0.00 0.00 37.62 3.77
1855 1868 4.371786 AGCATACTGTATTCACATCACCG 58.628 43.478 0.00 0.00 33.14 4.94
1857 1870 7.770801 TGTAAGCATACTGTATTCACATCAC 57.229 36.000 0.00 0.00 33.14 3.06
1895 1908 1.769026 TCCGGAGAAGACCTGATCTG 58.231 55.000 0.00 0.00 37.88 2.90
2074 2089 5.885912 GGAAGTCAATTATTCACCTAAGGCA 59.114 40.000 0.00 0.00 0.00 4.75
2103 2118 6.651225 AGTTAGAATAGTTTGACTGCAGGAAC 59.349 38.462 19.93 18.22 0.00 3.62
2107 2122 8.087982 TCAAAGTTAGAATAGTTTGACTGCAG 57.912 34.615 13.48 13.48 40.64 4.41
2166 2181 7.170277 ACCAAACGGTACTATTTTCACCTTAT 58.830 34.615 0.00 0.00 33.92 1.73
2215 2231 7.553881 TTTGTAGGAGCATGCTAATAGAAAC 57.446 36.000 22.74 12.23 42.04 2.78
2309 2325 9.383519 CATACTACATCACATGAAAAAGTACCT 57.616 33.333 0.00 0.00 0.00 3.08
2507 2783 2.435805 GTCTCATCATGCCTAACCCTCA 59.564 50.000 0.00 0.00 0.00 3.86
2542 2818 6.375455 AGCTTCTCATTCGACAATTTTGGTAT 59.625 34.615 0.00 0.00 0.00 2.73
2670 2946 5.045872 GCAGCAAGTTTTTCATTCAGACTT 58.954 37.500 0.00 0.00 0.00 3.01
2838 3114 4.878397 ACAGAAACAGAACAGTCCTTTCAG 59.122 41.667 0.00 0.00 0.00 3.02
2839 3115 4.843728 ACAGAAACAGAACAGTCCTTTCA 58.156 39.130 0.00 0.00 0.00 2.69
3262 3538 1.810412 CGCAAAGGGGCTGTAGATACC 60.810 57.143 0.00 0.00 0.00 2.73
3422 3698 2.923629 AGAGAGACTTGGAGTAGAGGGT 59.076 50.000 0.00 0.00 0.00 4.34
3486 3763 3.473647 CCCAGATGCAGAGGCCGA 61.474 66.667 0.00 0.00 40.13 5.54
3533 3810 9.988350 GATGTATTACTTTGTAAGGTCATTGTG 57.012 33.333 0.00 0.00 0.00 3.33
3596 3873 4.133526 TCATCAAGGGGATAGGAGTAGG 57.866 50.000 0.00 0.00 33.95 3.18
3614 3891 0.394352 GACATTCGGCACCCCTTCAT 60.394 55.000 0.00 0.00 0.00 2.57
3650 3927 0.613260 AGGCTTTGGTGCGATGTCTA 59.387 50.000 0.00 0.00 0.00 2.59
3658 3935 4.675408 GCTTTAGATGTTAGGCTTTGGTGC 60.675 45.833 0.00 0.00 0.00 5.01
3670 3947 1.680338 GGCATCCGGCTTTAGATGTT 58.320 50.000 0.00 0.00 41.60 2.71
3771 4048 0.466124 GGTTGGATTCTCCGCTAGCT 59.534 55.000 13.93 0.00 40.17 3.32
3772 4049 0.876342 CGGTTGGATTCTCCGCTAGC 60.876 60.000 4.06 4.06 40.17 3.42
3773 4050 0.249489 CCGGTTGGATTCTCCGCTAG 60.249 60.000 0.00 0.00 40.17 3.42
3774 4051 0.685131 TCCGGTTGGATTCTCCGCTA 60.685 55.000 0.00 0.00 40.17 4.26
3782 4059 0.673644 CGAAGTGCTCCGGTTGGATT 60.674 55.000 0.00 0.00 45.33 3.01
3787 4064 3.883744 CTGGCGAAGTGCTCCGGTT 62.884 63.158 0.00 0.00 45.43 4.44
3798 4075 2.361104 GAACCCATGGCTGGCGAA 60.361 61.111 6.09 0.00 41.64 4.70
3895 4172 3.479203 TTGCGCCGGATCTCCCAT 61.479 61.111 5.05 0.00 34.14 4.00
3913 4190 4.505970 AGGGCTAGGGCAGGAGGG 62.506 72.222 0.00 0.00 40.87 4.30
3917 4194 1.380380 CCAAAAGGGCTAGGGCAGG 60.380 63.158 0.00 0.00 40.87 4.85
4070 4347 2.477845 CAAGGAAAATTGGCCCCTTG 57.522 50.000 18.23 18.23 46.36 3.61
4071 4348 2.116869 ACAAGGAAAATTGGCCCCTT 57.883 45.000 0.00 0.67 39.42 3.95
4277 4555 3.199880 AGTTAGCTATCCATGTGCCAC 57.800 47.619 0.00 0.00 0.00 5.01
4284 4562 4.384208 GGTGTGTGGAAGTTAGCTATCCAT 60.384 45.833 15.86 0.00 44.55 3.41
4321 4599 2.280119 TGTCTGAGTGCCACACGC 60.280 61.111 0.00 0.00 39.64 5.34
4322 4600 3.630204 GTGTCTGAGTGCCACACG 58.370 61.111 0.00 0.00 39.64 4.49
4323 4601 2.598632 GCGTGTCTGAGTGCCACAC 61.599 63.158 0.00 0.00 37.63 3.82
4324 4602 2.280119 GCGTGTCTGAGTGCCACA 60.280 61.111 0.00 0.00 0.00 4.17
4325 4603 3.044305 GGCGTGTCTGAGTGCCAC 61.044 66.667 9.21 0.00 46.76 5.01
4487 4767 2.812499 GCCATCCCTAAGACGCGA 59.188 61.111 15.93 0.00 0.00 5.87
4544 4824 4.287781 TCGAAGCCAACGCCGTCA 62.288 61.111 0.00 0.00 34.57 4.35
4788 5089 1.763968 TCGAGATCCGATCACCAAGT 58.236 50.000 11.01 0.00 43.23 3.16
5048 5350 1.561643 CACCTCCTGCCTCTGACTTA 58.438 55.000 0.00 0.00 0.00 2.24
5195 5497 2.928396 AAGTACCACCAGCCGGCT 60.928 61.111 27.08 27.08 34.57 5.52
5197 5499 1.546589 TACCAAGTACCACCAGCCGG 61.547 60.000 0.00 0.00 38.77 6.13
5674 5979 0.550147 AACTAGCCATGGACAGGGGT 60.550 55.000 18.40 12.50 45.59 4.95
5675 5980 0.181350 GAACTAGCCATGGACAGGGG 59.819 60.000 18.40 0.95 31.86 4.79
5676 5981 1.207791 AGAACTAGCCATGGACAGGG 58.792 55.000 18.40 0.00 34.91 4.45
5677 5982 3.012518 CAAAGAACTAGCCATGGACAGG 58.987 50.000 18.40 4.37 0.00 4.00
5678 5983 3.679389 ACAAAGAACTAGCCATGGACAG 58.321 45.455 18.40 13.68 0.00 3.51
5679 5984 3.788227 ACAAAGAACTAGCCATGGACA 57.212 42.857 18.40 0.00 0.00 4.02
5680 5985 4.072131 TCAACAAAGAACTAGCCATGGAC 58.928 43.478 18.40 7.03 0.00 4.02
5681 5986 4.365514 TCAACAAAGAACTAGCCATGGA 57.634 40.909 18.40 0.00 0.00 3.41
5682 5987 6.949352 ATATCAACAAAGAACTAGCCATGG 57.051 37.500 7.63 7.63 0.00 3.66
5683 5988 8.461222 TCAAATATCAACAAAGAACTAGCCATG 58.539 33.333 0.00 0.00 0.00 3.66
5684 5989 8.579850 TCAAATATCAACAAAGAACTAGCCAT 57.420 30.769 0.00 0.00 0.00 4.40
5759 6064 3.909776 TGCAGAAATGAAGCTGAACAG 57.090 42.857 0.00 0.00 34.06 3.16
5919 6224 7.233553 TGACCCTCGAGATAATCATTTCTATGT 59.766 37.037 15.71 0.00 33.34 2.29
6086 6391 3.672028 GCTTCTTCAGCTCAGCAATAC 57.328 47.619 0.00 0.00 46.27 1.89
6111 6416 1.973138 CTTCTGATTTGGTTGCTGCG 58.027 50.000 0.00 0.00 0.00 5.18
6175 6480 5.468540 TCCAAGTTCTCTTTCTCGATTGA 57.531 39.130 0.00 0.00 0.00 2.57
6260 6565 0.374063 CTCTGCTGCTTGATTGCTCG 59.626 55.000 0.00 0.00 0.00 5.03
6285 6590 0.110295 TTTCCAGGTGCTGCTTGCTA 59.890 50.000 0.00 0.00 43.37 3.49
6359 6664 4.998671 TTGACCAATGCTGTTTTCTGAA 57.001 36.364 0.00 0.00 0.00 3.02
6450 6755 5.784750 TTCTCAATTCACTATCAACAGCG 57.215 39.130 0.00 0.00 0.00 5.18
6558 6863 3.133003 CCATTAGGTCGATCTCAACAGGT 59.867 47.826 0.00 0.00 0.00 4.00
6698 7003 2.595536 CGCCGCAATTCTTCATTTTCAG 59.404 45.455 0.00 0.00 0.00 3.02
6740 7045 4.215399 CGCTTTCAACTATTTCAACCCTCA 59.785 41.667 0.00 0.00 0.00 3.86
6865 7170 4.215827 GTCATTTGCCAAATCCAATTGCAA 59.784 37.500 0.00 0.00 0.00 4.08
6920 7225 2.820197 GCCTTTTTCTCCGAGTCCAATT 59.180 45.455 0.00 0.00 0.00 2.32
7068 7373 2.210013 AGTCACCCGAAGCTCTGCA 61.210 57.895 0.00 0.00 0.00 4.41
7200 7505 0.028770 TTTGCACTTCCTCGTTTGCG 59.971 50.000 0.00 0.00 37.82 4.85
7289 7594 4.713824 ATCTTCAGCAATGATTGTGTGG 57.286 40.909 7.05 2.99 0.00 4.17
7290 7595 5.705902 TCAATCTTCAGCAATGATTGTGTG 58.294 37.500 18.73 5.32 44.16 3.82
7339 7644 0.607217 CACAGCTGTGCCTCCAATGA 60.607 55.000 32.39 0.00 39.39 2.57
7387 7692 4.702831 TCTAATGCTTCGATAATGCCACA 58.297 39.130 0.00 0.00 0.00 4.17
7450 7755 2.827921 TCTTCATGTCTAGCTGTGCTGA 59.172 45.455 0.00 0.00 40.10 4.26
7453 7758 4.186926 TCAATCTTCATGTCTAGCTGTGC 58.813 43.478 0.00 0.00 0.00 4.57
7662 7970 2.948315 GAGTTCTGCCTCCAATGATTCC 59.052 50.000 0.00 0.00 0.00 3.01
7749 8057 4.831155 TCGTCAGAGAACTCCTTTTCCTTA 59.169 41.667 0.00 0.00 0.00 2.69
7862 8170 3.202906 TCAAACAACTCAACCTTCTCCG 58.797 45.455 0.00 0.00 0.00 4.63
7925 8233 1.815408 GCACAGACTCTTCCTTGGCAA 60.815 52.381 0.00 0.00 0.00 4.52
8206 8514 5.301551 ACAAAACACAAGTTCATATGAGCCA 59.698 36.000 15.17 0.00 36.84 4.75
8212 8520 9.988350 GATAATCGACAAAACACAAGTTCATAT 57.012 29.630 0.00 0.00 36.84 1.78
8619 8952 2.250939 CGAAAAGCAGCCCACGTCA 61.251 57.895 0.00 0.00 0.00 4.35
8672 9005 0.036765 CACCGACATTTCCGAGGGAA 60.037 55.000 0.00 0.00 40.27 3.97
8775 9108 5.045215 TCCATAAACTGTTAGCGGTAATCG 58.955 41.667 10.69 7.26 42.76 3.34
8780 9113 3.596214 CTGTCCATAAACTGTTAGCGGT 58.404 45.455 0.00 0.00 35.32 5.68
8906 9244 7.080099 CACAAATCTACCAATCAGTTTCTGTG 58.920 38.462 0.00 0.00 32.61 3.66
8927 9265 3.320541 AGAATGGAATTTTCGGCACACAA 59.679 39.130 0.00 0.00 36.07 3.33
8966 9306 1.348696 TCTTCATCAAGCAGGCTGTGA 59.651 47.619 17.16 13.17 0.00 3.58
9065 9405 4.464597 ACCAAACCACCATAAATGCGTATT 59.535 37.500 0.00 0.00 0.00 1.89
9113 9455 5.351740 GCCTCAAACAGACCTAACTATTCAC 59.648 44.000 0.00 0.00 0.00 3.18
9150 9492 0.383949 TTCGCAAAAACCTGCACCTC 59.616 50.000 0.00 0.00 42.77 3.85
9165 9507 4.419522 TGTTGATTAAGGAAAGCTTCGC 57.580 40.909 0.00 0.00 0.00 4.70
9167 9509 5.476945 TCCCTTGTTGATTAAGGAAAGCTTC 59.523 40.000 0.00 0.00 46.08 3.86
9219 9561 8.121305 TCTAAACATGGCTAATGATGTTTGTT 57.879 30.769 17.99 1.13 46.97 2.83
9249 9591 3.670627 GCCATAAGTCTTTGCAGTTTCCG 60.671 47.826 0.00 0.00 0.00 4.30
9254 9596 3.424703 ACATGCCATAAGTCTTTGCAGT 58.575 40.909 9.19 5.90 35.10 4.40
9255 9597 4.445452 AACATGCCATAAGTCTTTGCAG 57.555 40.909 9.19 5.47 35.10 4.41
9261 9603 6.780457 AATAAGCAAACATGCCATAAGTCT 57.220 33.333 0.00 0.00 34.90 3.24
9351 9700 5.004448 TCTACGCTATACTCTCCCATCAAG 58.996 45.833 0.00 0.00 0.00 3.02
9353 9702 4.202430 TGTCTACGCTATACTCTCCCATCA 60.202 45.833 0.00 0.00 0.00 3.07
9354 9703 4.325119 TGTCTACGCTATACTCTCCCATC 58.675 47.826 0.00 0.00 0.00 3.51
9355 9704 4.368565 TGTCTACGCTATACTCTCCCAT 57.631 45.455 0.00 0.00 0.00 4.00
9357 9706 4.760715 TCATTGTCTACGCTATACTCTCCC 59.239 45.833 0.00 0.00 0.00 4.30
9464 9840 7.901029 TCATCACCAAGATTAGAGGTCATATC 58.099 38.462 0.00 0.00 33.72 1.63
9476 9852 6.653526 TGACACAAATTCATCACCAAGATT 57.346 33.333 0.00 0.00 33.72 2.40
9479 9855 4.984161 GGTTGACACAAATTCATCACCAAG 59.016 41.667 0.00 0.00 0.00 3.61
9501 9877 3.829886 AGCAAACATGTAACATGTCGG 57.170 42.857 0.00 0.00 0.00 4.79
9502 9878 7.795431 AAATAAGCAAACATGTAACATGTCG 57.205 32.000 0.00 0.00 0.00 4.35
9511 9887 8.802267 ACCACATACTTAAATAAGCAAACATGT 58.198 29.630 0.00 0.00 36.79 3.21
9576 9952 7.275888 TGCTCATCATTAAACCATATCAACC 57.724 36.000 0.00 0.00 0.00 3.77
9582 9958 7.557358 ACTGACAATGCTCATCATTAAACCATA 59.443 33.333 0.00 0.00 43.21 2.74
9605 9981 9.766277 GAAGCTCTTATTTAGATTCAAACACTG 57.234 33.333 0.00 0.00 38.82 3.66
9606 9982 9.507329 TGAAGCTCTTATTTAGATTCAAACACT 57.493 29.630 1.62 0.00 44.04 3.55
9607 9983 9.766277 CTGAAGCTCTTATTTAGATTCAAACAC 57.234 33.333 5.44 0.00 45.65 3.32
9608 9984 9.507329 ACTGAAGCTCTTATTTAGATTCAAACA 57.493 29.630 5.44 0.00 45.65 2.83
9662 10038 7.596995 CCTCTAGTCAACCATATCGATTCTTTC 59.403 40.741 1.71 0.00 0.00 2.62
9663 10039 7.437748 CCTCTAGTCAACCATATCGATTCTTT 58.562 38.462 1.71 0.00 0.00 2.52
9664 10040 6.015010 CCCTCTAGTCAACCATATCGATTCTT 60.015 42.308 1.71 0.00 0.00 2.52
9665 10041 5.478679 CCCTCTAGTCAACCATATCGATTCT 59.521 44.000 1.71 0.00 0.00 2.40
9666 10042 5.336849 CCCCTCTAGTCAACCATATCGATTC 60.337 48.000 1.71 0.00 0.00 2.52
9667 10043 4.528596 CCCCTCTAGTCAACCATATCGATT 59.471 45.833 1.71 0.00 0.00 3.34
9668 10044 4.090090 CCCCTCTAGTCAACCATATCGAT 58.910 47.826 2.16 2.16 0.00 3.59
9669 10045 3.497332 CCCCTCTAGTCAACCATATCGA 58.503 50.000 0.00 0.00 0.00 3.59
9670 10046 2.563179 CCCCCTCTAGTCAACCATATCG 59.437 54.545 0.00 0.00 0.00 2.92
9688 10064 1.140312 TGCCTATTCATCACTCCCCC 58.860 55.000 0.00 0.00 0.00 5.40
9689 10065 2.173569 AGTTGCCTATTCATCACTCCCC 59.826 50.000 0.00 0.00 0.00 4.81
9690 10066 3.567478 AGTTGCCTATTCATCACTCCC 57.433 47.619 0.00 0.00 0.00 4.30
9691 10067 4.141711 TGGTAGTTGCCTATTCATCACTCC 60.142 45.833 0.00 0.00 0.00 3.85
9692 10068 5.023533 TGGTAGTTGCCTATTCATCACTC 57.976 43.478 0.00 0.00 0.00 3.51
9693 10069 5.435686 TTGGTAGTTGCCTATTCATCACT 57.564 39.130 0.00 0.00 0.00 3.41
9694 10070 6.699575 AATTGGTAGTTGCCTATTCATCAC 57.300 37.500 0.00 0.00 30.24 3.06
9695 10071 7.716799 AAAATTGGTAGTTGCCTATTCATCA 57.283 32.000 0.00 0.00 33.93 3.07
9696 10072 9.736023 CTAAAAATTGGTAGTTGCCTATTCATC 57.264 33.333 0.00 0.00 33.93 2.92
9697 10073 9.255029 ACTAAAAATTGGTAGTTGCCTATTCAT 57.745 29.630 0.00 0.00 33.93 2.57
9698 10074 8.644374 ACTAAAAATTGGTAGTTGCCTATTCA 57.356 30.769 0.00 0.00 33.93 2.57
9699 10075 9.923143 AAACTAAAAATTGGTAGTTGCCTATTC 57.077 29.630 12.46 0.00 39.81 1.75
9727 10103 9.436957 TTGTTGCTAAACCTAATTTGTCAAAAA 57.563 25.926 1.31 0.00 35.25 1.94
9728 10104 9.436957 TTTGTTGCTAAACCTAATTTGTCAAAA 57.563 25.926 1.31 0.00 35.25 2.44
9729 10105 9.606631 ATTTGTTGCTAAACCTAATTTGTCAAA 57.393 25.926 0.00 0.00 35.25 2.69
9731 10107 9.906660 CTATTTGTTGCTAAACCTAATTTGTCA 57.093 29.630 0.00 0.00 35.25 3.58
9732 10108 9.353999 CCTATTTGTTGCTAAACCTAATTTGTC 57.646 33.333 0.00 0.00 35.25 3.18
9733 10109 8.866093 ACCTATTTGTTGCTAAACCTAATTTGT 58.134 29.630 0.00 0.00 35.25 2.83
9734 10110 9.705290 AACCTATTTGTTGCTAAACCTAATTTG 57.295 29.630 0.00 0.00 35.25 2.32
9735 10111 9.705290 CAACCTATTTGTTGCTAAACCTAATTT 57.295 29.630 0.00 0.00 39.19 1.82
9753 10129 9.950496 CCTAATTGCATATCTAGACAACCTATT 57.050 33.333 0.00 0.00 0.00 1.73
9754 10130 9.105844 ACCTAATTGCATATCTAGACAACCTAT 57.894 33.333 0.00 0.00 0.00 2.57
9755 10131 8.367911 CACCTAATTGCATATCTAGACAACCTA 58.632 37.037 0.00 0.00 0.00 3.08
9756 10132 7.071196 TCACCTAATTGCATATCTAGACAACCT 59.929 37.037 0.00 0.00 0.00 3.50
9757 10133 7.217200 TCACCTAATTGCATATCTAGACAACC 58.783 38.462 0.00 0.00 0.00 3.77
9758 10134 7.095439 GCTCACCTAATTGCATATCTAGACAAC 60.095 40.741 0.00 0.00 0.00 3.32
9759 10135 6.931281 GCTCACCTAATTGCATATCTAGACAA 59.069 38.462 0.00 0.00 0.00 3.18
9760 10136 6.041979 TGCTCACCTAATTGCATATCTAGACA 59.958 38.462 0.00 0.00 0.00 3.41
9761 10137 6.459066 TGCTCACCTAATTGCATATCTAGAC 58.541 40.000 0.00 0.00 0.00 2.59
9762 10138 6.670695 TGCTCACCTAATTGCATATCTAGA 57.329 37.500 0.00 0.00 0.00 2.43
9763 10139 6.148480 GGTTGCTCACCTAATTGCATATCTAG 59.852 42.308 0.00 0.00 43.29 2.43
9764 10140 5.997746 GGTTGCTCACCTAATTGCATATCTA 59.002 40.000 0.00 0.00 43.29 1.98
9765 10141 4.823989 GGTTGCTCACCTAATTGCATATCT 59.176 41.667 0.00 0.00 43.29 1.98
9766 10142 5.113502 GGTTGCTCACCTAATTGCATATC 57.886 43.478 0.00 0.00 43.29 1.63
9779 10155 5.991606 TGTTAGCATCATATAGGTTGCTCAC 59.008 40.000 22.37 21.14 43.94 3.51
9780 10156 6.173427 TGTTAGCATCATATAGGTTGCTCA 57.827 37.500 22.37 14.38 43.94 4.26
9781 10157 7.678947 ATTGTTAGCATCATATAGGTTGCTC 57.321 36.000 22.37 12.35 43.94 4.26
9782 10158 9.003658 GTTATTGTTAGCATCATATAGGTTGCT 57.996 33.333 22.35 22.35 46.51 3.91
9783 10159 8.783093 TGTTATTGTTAGCATCATATAGGTTGC 58.217 33.333 11.54 11.54 35.34 4.17
9786 10162 9.845740 TGTTGTTATTGTTAGCATCATATAGGT 57.154 29.630 0.00 0.00 0.00 3.08


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

AutoCloner maintained by Alex Coulton.