Multiple sequence alignment - TraesCS5B01G424600

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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 TraesCS5B01G424600 chr5B 100.000 9672 0 0 1 9672 600650219 600640548 0.000000e+00 17861.0
1 TraesCS5B01G424600 chr5B 80.672 238 31 8 3083 3305 600643333 600643096 4.640000e-38 171.0
2 TraesCS5B01G424600 chr5B 80.672 238 31 8 6887 7124 600647137 600646915 4.640000e-38 171.0
3 TraesCS5B01G424600 chr5B 100.000 60 0 0 6235 6294 600644041 600643982 2.860000e-20 111.0
4 TraesCS5B01G424600 chr5D 97.287 2506 61 4 6236 8739 487983577 487981077 0.000000e+00 4244.0
5 TraesCS5B01G424600 chr5D 97.974 1481 25 5 1 1478 487988162 487986684 0.000000e+00 2564.0
6 TraesCS5B01G424600 chr5D 96.640 1399 39 6 2720 4113 487985455 487984060 0.000000e+00 2316.0
7 TraesCS5B01G424600 chr5D 97.258 1167 27 4 1476 2642 487986611 487985450 0.000000e+00 1973.0
8 TraesCS5B01G424600 chr5D 93.345 571 22 6 5668 6238 487984073 487983519 0.000000e+00 830.0
9 TraesCS5B01G424600 chr5D 92.632 570 30 8 9105 9670 487980626 487980065 0.000000e+00 809.0
10 TraesCS5B01G424600 chr5D 92.381 420 19 5 8734 9142 487981043 487980626 3.890000e-163 586.0
11 TraesCS5B01G424600 chr5D 97.024 168 4 1 1987 2154 198477551 198477385 2.060000e-71 281.0
12 TraesCS5B01G424600 chr5D 83.043 230 24 7 6887 7116 487985091 487984877 2.760000e-45 195.0
13 TraesCS5B01G424600 chr5D 81.092 238 30 8 3083 3305 487982925 487982688 9.980000e-40 176.0
14 TraesCS5B01G424600 chr5D 86.905 84 9 2 7558 7640 541806186 541806268 1.030000e-14 93.5
15 TraesCS5B01G424600 chr5D 94.872 39 2 0 8130 8168 488161803 488161765 2.920000e-05 62.1
16 TraesCS5B01G424600 chr5A 95.893 2508 71 7 6235 8739 608703827 608701349 0.000000e+00 4032.0
17 TraesCS5B01G424600 chr5A 97.308 1486 31 4 1 1478 608708435 608706951 0.000000e+00 2514.0
18 TraesCS5B01G424600 chr5A 96.357 1400 45 4 2720 4113 608705722 608704323 0.000000e+00 2298.0
19 TraesCS5B01G424600 chr5A 97.172 1167 24 6 1476 2642 608706874 608705717 0.000000e+00 1964.0
20 TraesCS5B01G424600 chr5A 95.797 571 22 2 5668 6238 608704336 608703768 0.000000e+00 920.0
21 TraesCS5B01G424600 chr5A 88.961 616 29 18 9011 9602 608701003 608700403 0.000000e+00 725.0
22 TraesCS5B01G424600 chr5A 81.640 561 82 15 7961 8514 608806834 608806288 6.890000e-121 446.0
23 TraesCS5B01G424600 chr5A 91.857 307 12 4 8734 9032 608701316 608701015 5.400000e-112 416.0
24 TraesCS5B01G424600 chr5A 80.734 545 95 7 7959 8498 608813876 608813337 5.400000e-112 416.0
25 TraesCS5B01G424600 chr5A 96.491 171 6 0 1987 2157 585001810 585001640 5.720000e-72 283.0
26 TraesCS5B01G424600 chr5A 90.244 205 12 3 1005 1201 444593095 444593299 2.680000e-65 261.0
27 TraesCS5B01G424600 chr5A 83.478 230 23 8 6887 7116 608705355 608705141 5.920000e-47 200.0
28 TraesCS5B01G424600 chr5A 79.832 238 33 8 3083 3305 608703174 608702937 1.010000e-34 159.0
29 TraesCS5B01G424600 chr5A 80.142 141 22 6 7194 7332 494876218 494876354 6.180000e-17 100.0
30 TraesCS5B01G424600 chr7A 91.356 1018 82 4 4443 5457 302664754 302663740 0.000000e+00 1387.0
31 TraesCS5B01G424600 chr7A 88.785 321 20 3 4132 4451 302672113 302671808 7.090000e-101 379.0
32 TraesCS5B01G424600 chr7A 90.783 217 16 4 5456 5670 302663708 302663494 4.420000e-73 287.0
33 TraesCS5B01G424600 chr7A 95.413 109 5 0 832 940 263351599 263351707 3.590000e-39 174.0
34 TraesCS5B01G424600 chr7A 92.000 100 8 0 1012 1111 263352408 263352507 3.640000e-29 141.0
35 TraesCS5B01G424600 chr6B 93.164 746 50 1 4710 5454 91129319 91130064 0.000000e+00 1094.0
36 TraesCS5B01G424600 chr6B 89.356 714 66 6 4752 5457 308517158 308516447 0.000000e+00 889.0
37 TraesCS5B01G424600 chr6B 77.216 1365 243 55 4130 5457 716579970 716578637 0.000000e+00 736.0
38 TraesCS5B01G424600 chr6B 93.458 214 13 1 5456 5669 91130099 91130311 5.640000e-82 316.0
39 TraesCS5B01G424600 chr6B 89.815 216 18 4 5456 5669 308516415 308516202 3.440000e-69 274.0
40 TraesCS5B01G424600 chr1D 86.614 889 76 16 4130 4998 143994708 143993843 0.000000e+00 942.0
41 TraesCS5B01G424600 chr1D 86.867 830 88 14 4638 5457 52355397 52354579 0.000000e+00 909.0
42 TraesCS5B01G424600 chr1D 81.305 567 95 10 5668 6230 125583465 125584024 5.330000e-122 449.0
43 TraesCS5B01G424600 chr1D 97.041 169 4 1 1985 2152 365727163 365727331 5.720000e-72 283.0
44 TraesCS5B01G424600 chr1D 88.940 217 20 4 5456 5670 52354547 52354333 2.070000e-66 265.0
45 TraesCS5B01G424600 chr1D 91.228 114 5 5 2619 2730 348120756 348120866 6.050000e-32 150.0
46 TraesCS5B01G424600 chr1D 85.047 107 15 1 7531 7636 141705954 141706060 3.690000e-19 108.0
47 TraesCS5B01G424600 chr1D 88.889 81 6 3 7558 7637 298568636 298568558 8.000000e-16 97.1
48 TraesCS5B01G424600 chr1D 76.282 156 28 7 7177 7331 486140963 486141110 3.750000e-09 75.0
49 TraesCS5B01G424600 chr7D 86.774 809 91 13 4656 5454 109789997 109789195 0.000000e+00 887.0
50 TraesCS5B01G424600 chr7D 83.598 567 85 8 5668 6231 310183975 310184536 8.600000e-145 525.0
51 TraesCS5B01G424600 chr7D 87.636 275 9 9 948 1198 166199292 166199019 7.340000e-76 296.0
52 TraesCS5B01G424600 chr7D 92.982 114 5 2 831 943 166200016 166199905 7.770000e-36 163.0
53 TraesCS5B01G424600 chr7D 92.241 116 6 3 2639 2753 26757828 26757941 2.800000e-35 161.0
54 TraesCS5B01G424600 chr7D 82.313 147 21 5 4137 4281 20375149 20375006 1.320000e-23 122.0
55 TraesCS5B01G424600 chr7D 84.536 97 10 5 7546 7638 71314553 71314458 3.720000e-14 91.6
56 TraesCS5B01G424600 chr3D 86.320 826 88 15 4638 5452 519602009 519602820 0.000000e+00 876.0
57 TraesCS5B01G424600 chr3D 83.217 572 87 9 5668 6236 287285270 287285835 5.180000e-142 516.0
58 TraesCS5B01G424600 chr3D 76.061 919 137 55 4131 5018 595864002 595864868 1.510000e-107 401.0
59 TraesCS5B01G424600 chr3D 94.845 194 9 1 1005 1197 277606398 277606205 1.580000e-77 302.0
60 TraesCS5B01G424600 chr3D 89.831 118 8 4 2628 2742 591879147 591879031 2.180000e-31 148.0
61 TraesCS5B01G424600 chr3D 78.378 185 33 5 7172 7354 199205969 199205790 7.940000e-21 113.0
62 TraesCS5B01G424600 chr3D 87.778 90 10 1 7553 7641 523157470 523157381 4.780000e-18 104.0
63 TraesCS5B01G424600 chr3D 98.305 59 0 1 947 1004 277606481 277606423 1.720000e-17 102.0
64 TraesCS5B01G424600 chr4B 86.347 813 93 12 4656 5457 206810549 206809744 0.000000e+00 870.0
65 TraesCS5B01G424600 chr4B 89.767 215 19 3 5456 5669 206809712 206809500 1.240000e-68 272.0
66 TraesCS5B01G424600 chr4B 93.333 105 7 0 832 936 30854542 30854438 1.300000e-33 156.0
67 TraesCS5B01G424600 chr4B 84.146 82 12 1 7551 7631 270831669 270831750 2.900000e-10 78.7
68 TraesCS5B01G424600 chr2D 85.628 828 94 15 4638 5454 637373572 637372759 0.000000e+00 846.0
69 TraesCS5B01G424600 chr2D 90.323 217 17 4 5456 5670 637372718 637372504 2.060000e-71 281.0
70 TraesCS5B01G424600 chr2D 82.951 305 40 10 3815 4113 404410590 404410292 2.070000e-66 265.0
71 TraesCS5B01G424600 chr2D 82.680 306 40 11 3814 4113 248864665 248864963 9.640000e-65 259.0
72 TraesCS5B01G424600 chr2D 84.536 97 13 2 7553 7648 506776633 506776538 2.880000e-15 95.3
73 TraesCS5B01G424600 chr4D 85.502 807 103 9 4656 5457 136962335 136961538 0.000000e+00 830.0
74 TraesCS5B01G424600 chr4D 86.469 303 31 7 3815 4110 445401995 445402294 3.370000e-84 324.0
75 TraesCS5B01G424600 chr4D 86.622 299 29 8 3822 4113 473172622 473172916 4.360000e-83 320.0
76 TraesCS5B01G424600 chr4D 93.333 195 13 0 1005 1199 432585168 432584974 1.230000e-73 289.0
77 TraesCS5B01G424600 chr4D 95.192 104 2 1 2628 2728 478668916 478669019 2.800000e-35 161.0
78 TraesCS5B01G424600 chr4D 96.809 94 3 0 832 925 432585946 432585853 3.620000e-34 158.0
79 TraesCS5B01G424600 chr4D 95.000 100 3 2 2625 2724 14928659 14928756 1.300000e-33 156.0
80 TraesCS5B01G424600 chrUn 89.251 614 41 9 5062 5668 36514758 36514163 0.000000e+00 745.0
81 TraesCS5B01G424600 chrUn 78.571 364 66 12 4261 4617 8125086 8124728 7.560000e-56 230.0
82 TraesCS5B01G424600 chrUn 82.796 279 20 15 4145 4422 96738388 96738137 3.520000e-54 224.0
83 TraesCS5B01G424600 chrUn 88.073 109 12 1 4126 4234 40894845 40894738 2.840000e-25 128.0
84 TraesCS5B01G424600 chrUn 85.088 114 13 4 4121 4232 222085474 222085585 7.940000e-21 113.0
85 TraesCS5B01G424600 chrUn 83.951 81 12 1 7552 7631 37004709 37004629 1.040000e-09 76.8
86 TraesCS5B01G424600 chrUn 83.951 81 12 1 7552 7631 37371500 37371580 1.040000e-09 76.8
87 TraesCS5B01G424600 chrUn 83.951 81 12 1 7552 7631 196711297 196711377 1.040000e-09 76.8
88 TraesCS5B01G424600 chrUn 83.951 81 12 1 7552 7631 329135011 329135091 1.040000e-09 76.8
89 TraesCS5B01G424600 chrUn 83.951 81 12 1 7552 7631 332576980 332577060 1.040000e-09 76.8
90 TraesCS5B01G424600 chrUn 87.692 65 7 1 7568 7631 341187344 341187280 3.750000e-09 75.0
91 TraesCS5B01G424600 chr6D 84.118 743 93 16 4947 5670 114879449 114878713 0.000000e+00 695.0
92 TraesCS5B01G424600 chr6D 82.986 576 80 16 5668 6236 194228393 194227829 1.120000e-138 505.0
93 TraesCS5B01G424600 chr6D 85.185 297 39 5 3820 4113 227984389 227984095 5.680000e-77 300.0
94 TraesCS5B01G424600 chr6D 98.214 168 2 1 1986 2152 392278576 392278743 9.500000e-75 292.0
95 TraesCS5B01G424600 chr6D 84.385 301 41 5 3815 4113 213020513 213020217 3.420000e-74 291.0
96 TraesCS5B01G424600 chr6D 92.661 109 5 3 2639 2745 248004002 248004109 4.680000e-33 154.0
97 TraesCS5B01G424600 chr6D 77.419 186 32 8 7175 7355 65646351 65646171 1.720000e-17 102.0
98 TraesCS5B01G424600 chr6D 86.420 81 10 1 7558 7637 155602040 155601960 4.810000e-13 87.9
99 TraesCS5B01G424600 chr6D 89.855 69 3 3 7567 7631 24823409 24823341 1.730000e-12 86.1
100 TraesCS5B01G424600 chr6A 83.333 576 80 15 5668 6236 268963351 268962785 1.440000e-142 518.0
101 TraesCS5B01G424600 chr6A 82.404 574 89 12 5669 6238 270605927 270606492 3.140000e-134 490.0
102 TraesCS5B01G424600 chr6A 84.211 304 37 10 3815 4113 268963635 268963338 1.590000e-72 285.0
103 TraesCS5B01G424600 chr6A 91.892 111 7 2 2615 2724 581742856 581742965 4.680000e-33 154.0
104 TraesCS5B01G424600 chr6A 87.654 81 9 1 7558 7637 209391420 209391340 1.030000e-14 93.5
105 TraesCS5B01G424600 chr6A 85.227 88 12 1 7545 7631 14350980 14351067 1.340000e-13 89.8
106 TraesCS5B01G424600 chr1B 81.786 571 90 13 5668 6235 259030311 259030870 5.290000e-127 466.0
107 TraesCS5B01G424600 chr1B 76.146 851 150 40 4200 5018 57135488 57134659 1.960000e-106 398.0
108 TraesCS5B01G424600 chr1B 90.148 203 12 2 1003 1199 238981592 238981792 3.470000e-64 257.0
109 TraesCS5B01G424600 chr1B 93.860 114 6 1 830 943 655842404 655842292 4.640000e-38 171.0
110 TraesCS5B01G424600 chr1B 85.047 107 15 1 7531 7636 195591178 195591284 3.690000e-19 108.0
111 TraesCS5B01G424600 chr1B 98.276 58 1 0 947 1004 238981512 238981569 1.720000e-17 102.0
112 TraesCS5B01G424600 chr3A 80.198 606 81 30 4130 4724 747419262 747418685 1.500000e-112 418.0
113 TraesCS5B01G424600 chr3A 93.264 193 12 1 1006 1197 45156314 45156506 5.720000e-72 283.0
114 TraesCS5B01G424600 chr3A 91.795 195 14 2 1960 2152 66171237 66171043 4.450000e-68 270.0
115 TraesCS5B01G424600 chr3A 79.348 184 34 3 7172 7354 313499416 313499236 1.020000e-24 126.0
116 TraesCS5B01G424600 chr4A 74.087 876 166 44 4163 5018 538909563 538910397 4.390000e-78 303.0
117 TraesCS5B01G424600 chr4A 94.301 193 9 2 1006 1197 714558805 714558996 2.640000e-75 294.0
118 TraesCS5B01G424600 chr4A 97.590 166 3 1 1987 2151 346686995 346686830 5.720000e-72 283.0
119 TraesCS5B01G424600 chr4A 97.849 93 2 0 831 923 714555418 714555510 2.800000e-35 161.0
120 TraesCS5B01G424600 chr4A 89.247 93 8 2 7546 7636 464695917 464695825 2.210000e-21 115.0
121 TraesCS5B01G424600 chr4A 96.552 58 0 1 947 1004 714558724 714558779 2.880000e-15 95.3
122 TraesCS5B01G424600 chr2B 97.143 175 3 2 1987 2160 659694467 659694640 2.640000e-75 294.0
123 TraesCS5B01G424600 chr2B 89.720 214 20 2 5456 5669 743339326 743339537 1.240000e-68 272.0
124 TraesCS5B01G424600 chr2B 77.957 186 34 7 7175 7356 795984302 795984120 1.030000e-19 110.0
125 TraesCS5B01G424600 chr2A 95.050 101 3 2 2625 2725 196359679 196359581 3.620000e-34 158.0
126 TraesCS5B01G424600 chr2A 91.071 112 7 3 825 936 93850780 93850672 2.180000e-31 148.0
127 TraesCS5B01G424600 chr1A 89.344 122 5 7 2629 2748 584082909 584082794 7.830000e-31 147.0
128 TraesCS5B01G424600 chr1A 83.019 159 22 4 7175 7333 64403182 64403335 1.310000e-28 139.0
129 TraesCS5B01G424600 chr1A 86.316 95 12 1 7543 7636 148958984 148958890 1.720000e-17 102.0
130 TraesCS5B01G424600 chr3B 80.108 186 35 2 7169 7353 284420448 284420632 4.710000e-28 137.0


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 TraesCS5B01G424600 chr5B 600640548 600650219 9671 True 17861.000000 17861 100.000000 1 9672 1 chr5B.!!$R1 9671
1 TraesCS5B01G424600 chr5D 487980065 487988162 8097 True 1521.444444 4244 92.405778 1 9670 9 chr5D.!!$R3 9669
2 TraesCS5B01G424600 chr5A 608700403 608708435 8032 True 1469.777778 4032 91.850556 1 9602 9 chr5A.!!$R4 9601
3 TraesCS5B01G424600 chr5A 608806288 608806834 546 True 446.000000 446 81.640000 7961 8514 1 chr5A.!!$R2 553
4 TraesCS5B01G424600 chr5A 608813337 608813876 539 True 416.000000 416 80.734000 7959 8498 1 chr5A.!!$R3 539
5 TraesCS5B01G424600 chr7A 302663494 302664754 1260 True 837.000000 1387 91.069500 4443 5670 2 chr7A.!!$R2 1227
6 TraesCS5B01G424600 chr6B 716578637 716579970 1333 True 736.000000 736 77.216000 4130 5457 1 chr6B.!!$R1 1327
7 TraesCS5B01G424600 chr6B 91129319 91130311 992 False 705.000000 1094 93.311000 4710 5669 2 chr6B.!!$F1 959
8 TraesCS5B01G424600 chr6B 308516202 308517158 956 True 581.500000 889 89.585500 4752 5669 2 chr6B.!!$R2 917
9 TraesCS5B01G424600 chr1D 143993843 143994708 865 True 942.000000 942 86.614000 4130 4998 1 chr1D.!!$R1 868
10 TraesCS5B01G424600 chr1D 52354333 52355397 1064 True 587.000000 909 87.903500 4638 5670 2 chr1D.!!$R3 1032
11 TraesCS5B01G424600 chr1D 125583465 125584024 559 False 449.000000 449 81.305000 5668 6230 1 chr1D.!!$F1 562
12 TraesCS5B01G424600 chr7D 109789195 109789997 802 True 887.000000 887 86.774000 4656 5454 1 chr7D.!!$R3 798
13 TraesCS5B01G424600 chr7D 310183975 310184536 561 False 525.000000 525 83.598000 5668 6231 1 chr7D.!!$F2 563
14 TraesCS5B01G424600 chr7D 166199019 166200016 997 True 229.500000 296 90.309000 831 1198 2 chr7D.!!$R4 367
15 TraesCS5B01G424600 chr3D 519602009 519602820 811 False 876.000000 876 86.320000 4638 5452 1 chr3D.!!$F2 814
16 TraesCS5B01G424600 chr3D 287285270 287285835 565 False 516.000000 516 83.217000 5668 6236 1 chr3D.!!$F1 568
17 TraesCS5B01G424600 chr3D 595864002 595864868 866 False 401.000000 401 76.061000 4131 5018 1 chr3D.!!$F3 887
18 TraesCS5B01G424600 chr4B 206809500 206810549 1049 True 571.000000 870 88.057000 4656 5669 2 chr4B.!!$R2 1013
19 TraesCS5B01G424600 chr2D 637372504 637373572 1068 True 563.500000 846 87.975500 4638 5670 2 chr2D.!!$R3 1032
20 TraesCS5B01G424600 chr4D 136961538 136962335 797 True 830.000000 830 85.502000 4656 5457 1 chr4D.!!$R1 801
21 TraesCS5B01G424600 chr4D 432584974 432585946 972 True 223.500000 289 95.071000 832 1199 2 chr4D.!!$R2 367
22 TraesCS5B01G424600 chrUn 36514163 36514758 595 True 745.000000 745 89.251000 5062 5668 1 chrUn.!!$R2 606
23 TraesCS5B01G424600 chr6D 114878713 114879449 736 True 695.000000 695 84.118000 4947 5670 1 chr6D.!!$R3 723
24 TraesCS5B01G424600 chr6D 194227829 194228393 564 True 505.000000 505 82.986000 5668 6236 1 chr6D.!!$R5 568
25 TraesCS5B01G424600 chr6A 270605927 270606492 565 False 490.000000 490 82.404000 5669 6238 1 chr6A.!!$F2 569
26 TraesCS5B01G424600 chr6A 268962785 268963635 850 True 401.500000 518 83.772000 3815 6236 2 chr6A.!!$R2 2421
27 TraesCS5B01G424600 chr1B 259030311 259030870 559 False 466.000000 466 81.786000 5668 6235 1 chr1B.!!$F2 567
28 TraesCS5B01G424600 chr1B 57134659 57135488 829 True 398.000000 398 76.146000 4200 5018 1 chr1B.!!$R1 818
29 TraesCS5B01G424600 chr3A 747418685 747419262 577 True 418.000000 418 80.198000 4130 4724 1 chr3A.!!$R3 594
30 TraesCS5B01G424600 chr4A 538909563 538910397 834 False 303.000000 303 74.087000 4163 5018 1 chr4A.!!$F1 855

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
82 83 7.122501 TGCATGCAGGTTATAGAATTTCTGAAA 59.877 33.333 18.46 5.15 0.0 2.69 F
1039 1680 2.690778 GCTTCATTGGCGCCGAAGT 61.691 57.895 30.65 13.17 38.7 3.01 F
2424 3227 0.234884 GCCTGTACACAACGCTGAAC 59.765 55.000 0.00 0.00 0.0 3.18 F
3297 4104 0.762418 TGACGGGTGATCTTGGTGTT 59.238 50.000 0.00 0.00 0.0 3.32 F
4654 5488 0.104620 ATATGGCTAGGGTTCGGGGT 60.105 55.000 0.00 0.00 0.0 4.95 F
6499 7496 0.038599 ATGGCATTGCAGTGGTCTCA 59.961 50.000 11.53 0.00 0.0 3.27 F
6799 7797 0.032267 GATCCTCGTTCCCATCCGTC 59.968 60.000 0.00 0.00 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1318 1967 2.753452 TCTCGCTCGTCCTGTAAATTCT 59.247 45.455 0.00 0.00 0.00 2.40 R
2825 3628 0.909610 ACGCCCTCTGATCCCAAGAA 60.910 55.000 0.00 0.00 0.00 2.52 R
3694 4502 0.105453 GGGAGTGGAGGAGATGGCTA 60.105 60.000 0.00 0.00 0.00 3.93 R
4676 5512 0.038744 AGCAACAGCCATACCAAGCT 59.961 50.000 0.00 0.00 40.89 3.74 R
6541 7538 0.032540 CCAAGCCAGCCACAAGAAAC 59.967 55.000 0.00 0.00 0.00 2.78 R
7736 8735 0.546122 GGACAGTCCCCATGCATGTA 59.454 55.000 24.58 7.67 0.00 2.29 R
8758 9800 0.987294 CACCATCCAGACTCCCAGTT 59.013 55.000 0.00 0.00 0.00 3.16 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
82 83 7.122501 TGCATGCAGGTTATAGAATTTCTGAAA 59.877 33.333 18.46 5.15 0.00 2.69
205 206 7.550712 AGAATCTGCAAAACCATAAAAGATCC 58.449 34.615 0.00 0.00 0.00 3.36
936 940 9.594478 CCTATATGCGTTTATGTAACATATGGA 57.406 33.333 7.80 0.00 36.50 3.41
1039 1680 2.690778 GCTTCATTGGCGCCGAAGT 61.691 57.895 30.65 13.17 38.70 3.01
1079 1726 4.037565 ACCAACATTGCTATCTATCGACGA 59.962 41.667 0.00 0.00 0.00 4.20
1120 1767 7.565680 AGATCAACCTCGGTATTATGAACTTT 58.434 34.615 0.00 0.00 0.00 2.66
1318 1967 4.653868 TCGTAAAAGAATTAGTGCCCCAA 58.346 39.130 0.00 0.00 0.00 4.12
1358 2007 6.650807 AGCGAGACAGATAAAAGTGAAATCAA 59.349 34.615 0.00 0.00 0.00 2.57
1534 2337 6.134754 TCCTAGAACTCAAGATACTAACCCC 58.865 44.000 0.00 0.00 0.00 4.95
1621 2424 1.322442 GCCTTCTGAGTTGGTTGCTT 58.678 50.000 0.00 0.00 0.00 3.91
1622 2425 1.000938 GCCTTCTGAGTTGGTTGCTTG 60.001 52.381 0.00 0.00 0.00 4.01
1696 2499 8.821686 TCCTGAAATTGATTGGCTATCTTTTA 57.178 30.769 10.19 0.58 34.17 1.52
2060 2863 8.542497 ACTACATACGAAGCAAAATGAGTTAA 57.458 30.769 0.00 0.00 0.00 2.01
2163 2966 5.704978 CGGAGGGAGTAGTAACTATAGAACC 59.295 48.000 6.78 0.00 35.56 3.62
2424 3227 0.234884 GCCTGTACACAACGCTGAAC 59.765 55.000 0.00 0.00 0.00 3.18
2448 3251 2.921121 TGAGCTTATGAGTAACAACGCG 59.079 45.455 3.53 3.53 0.00 6.01
2623 3426 1.816835 ACTCTCCAACATGCAGCATTG 59.183 47.619 4.69 3.20 0.00 2.82
2642 3445 6.030228 GCATTGTGGCTCAATTTAAGTACTC 58.970 40.000 11.81 0.00 43.33 2.59
2643 3446 6.555315 CATTGTGGCTCAATTTAAGTACTCC 58.445 40.000 11.81 0.00 43.33 3.85
2644 3447 4.585879 TGTGGCTCAATTTAAGTACTCCC 58.414 43.478 0.00 0.00 0.00 4.30
2645 3448 4.288626 TGTGGCTCAATTTAAGTACTCCCT 59.711 41.667 0.00 0.00 0.00 4.20
2646 3449 4.876679 GTGGCTCAATTTAAGTACTCCCTC 59.123 45.833 0.00 0.00 0.00 4.30
2647 3450 4.080526 TGGCTCAATTTAAGTACTCCCTCC 60.081 45.833 0.00 0.00 0.00 4.30
2648 3451 4.120589 GCTCAATTTAAGTACTCCCTCCG 58.879 47.826 0.00 0.00 0.00 4.63
2649 3452 4.382793 GCTCAATTTAAGTACTCCCTCCGT 60.383 45.833 0.00 0.00 0.00 4.69
2650 3453 5.163478 GCTCAATTTAAGTACTCCCTCCGTA 60.163 44.000 0.00 0.00 0.00 4.02
2651 3454 6.628844 GCTCAATTTAAGTACTCCCTCCGTAA 60.629 42.308 0.00 0.00 0.00 3.18
2652 3455 7.243604 TCAATTTAAGTACTCCCTCCGTAAA 57.756 36.000 0.00 0.00 0.00 2.01
2653 3456 7.099120 TCAATTTAAGTACTCCCTCCGTAAAC 58.901 38.462 0.00 0.00 0.00 2.01
2654 3457 6.864151 ATTTAAGTACTCCCTCCGTAAACT 57.136 37.500 0.00 0.00 0.00 2.66
2655 3458 7.961326 ATTTAAGTACTCCCTCCGTAAACTA 57.039 36.000 0.00 0.00 0.00 2.24
2656 3459 7.775053 TTTAAGTACTCCCTCCGTAAACTAA 57.225 36.000 0.00 0.00 0.00 2.24
2657 3460 7.961326 TTAAGTACTCCCTCCGTAAACTAAT 57.039 36.000 0.00 0.00 0.00 1.73
2658 3461 9.474313 TTTAAGTACTCCCTCCGTAAACTAATA 57.526 33.333 0.00 0.00 0.00 0.98
2659 3462 9.646522 TTAAGTACTCCCTCCGTAAACTAATAT 57.353 33.333 0.00 0.00 0.00 1.28
2661 3464 9.646522 AAGTACTCCCTCCGTAAACTAATATAA 57.353 33.333 0.00 0.00 0.00 0.98
2662 3465 9.294614 AGTACTCCCTCCGTAAACTAATATAAG 57.705 37.037 0.00 0.00 0.00 1.73
2663 3466 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
2664 3467 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
2665 3468 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
2666 3469 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
2667 3470 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
2668 3471 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
2669 3472 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
2670 3473 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
2671 3474 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
2672 3475 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
2684 3487 9.953697 ATAAGAGCGTTTAGATCACTAAAGTAG 57.046 33.333 0.00 0.00 45.42 2.57
2685 3488 7.393841 AGAGCGTTTAGATCACTAAAGTAGT 57.606 36.000 0.00 0.00 45.42 2.73
2719 3522 9.710818 ACACTCTTATATTAGTTTACAGAGGGA 57.289 33.333 2.59 0.00 34.50 4.20
2721 3524 9.939424 ACTCTTATATTAGTTTACAGAGGGAGT 57.061 33.333 0.00 0.00 32.21 3.85
2825 3628 9.787435 ACACAATACCAATATCCGTATATGTTT 57.213 29.630 0.00 0.00 0.00 2.83
3056 3863 3.246387 ACCCACCCTACTAGGAATTGAGT 60.246 47.826 3.36 0.00 37.67 3.41
3072 3879 1.151899 AGTCTGGCTTGGGTGGGTA 60.152 57.895 0.00 0.00 0.00 3.69
3143 3950 2.650778 CAAGGTGCCCGCTTTTCC 59.349 61.111 0.00 0.00 0.00 3.13
3144 3951 2.197324 AAGGTGCCCGCTTTTCCA 59.803 55.556 0.00 0.00 0.00 3.53
3151 3958 1.250840 GCCCGCTTTTCCACAATCCT 61.251 55.000 0.00 0.00 0.00 3.24
3183 3990 2.284995 GTGGGGTCTCCTGGAGCT 60.285 66.667 19.08 0.00 41.70 4.09
3189 3996 4.704103 TCTCCTGGAGCTGGGCGT 62.704 66.667 19.08 0.00 0.00 5.68
3290 4097 1.123928 GGAGGAATGACGGGTGATCT 58.876 55.000 0.00 0.00 0.00 2.75
3297 4104 0.762418 TGACGGGTGATCTTGGTGTT 59.238 50.000 0.00 0.00 0.00 3.32
3413 4220 1.480212 ATCAGGAGGTGGCACGACAA 61.480 55.000 12.17 0.00 0.00 3.18
3431 4238 4.566987 GACAAAGGACCGAGATAGTTTGT 58.433 43.478 5.67 5.67 40.02 2.83
3493 4300 0.899717 ATTCACAATTGGGGCGCAGT 60.900 50.000 10.83 0.00 0.00 4.40
3658 4466 4.526262 TCTGAGAGAAGTAGAGCTTTGCTT 59.474 41.667 7.32 7.32 39.88 3.91
3708 4516 2.134287 GCGGTAGCCATCTCCTCCA 61.134 63.158 0.00 0.00 37.42 3.86
3818 4626 1.625818 GGCTCTTCTCCCTCTTTGTCA 59.374 52.381 0.00 0.00 0.00 3.58
3850 4658 3.696518 TATGGGACCAGCGAGGCCT 62.697 63.158 3.86 3.86 43.14 5.19
3911 4719 2.480419 GCAAATCTAGCAGTTCACACGT 59.520 45.455 0.00 0.00 0.00 4.49
4099 4909 2.754465 TGGGCCTCCTTTTATAGACGA 58.246 47.619 4.53 0.00 0.00 4.20
4100 4910 3.109151 TGGGCCTCCTTTTATAGACGAA 58.891 45.455 4.53 0.00 0.00 3.85
4101 4911 3.520317 TGGGCCTCCTTTTATAGACGAAA 59.480 43.478 4.53 0.00 0.00 3.46
4102 4912 4.019141 TGGGCCTCCTTTTATAGACGAAAA 60.019 41.667 4.53 0.00 0.00 2.29
4103 4913 4.575236 GGGCCTCCTTTTATAGACGAAAAG 59.425 45.833 0.84 0.00 41.54 2.27
4110 4920 6.418585 CTTTTATAGACGAAAAGGGGTCAC 57.581 41.667 0.00 0.00 39.29 3.67
4111 4921 4.476628 TTATAGACGAAAAGGGGTCACC 57.523 45.455 0.00 0.00 35.63 4.02
4112 4922 1.719529 TAGACGAAAAGGGGTCACCA 58.280 50.000 0.00 0.00 43.89 4.17
4113 4923 0.396811 AGACGAAAAGGGGTCACCAG 59.603 55.000 0.00 0.00 43.89 4.00
4114 4924 0.605589 GACGAAAAGGGGTCACCAGG 60.606 60.000 0.00 0.00 43.89 4.45
4115 4925 1.057851 ACGAAAAGGGGTCACCAGGA 61.058 55.000 0.00 0.00 43.89 3.86
4116 4926 0.109723 CGAAAAGGGGTCACCAGGAA 59.890 55.000 0.00 0.00 43.89 3.36
4117 4927 1.271926 CGAAAAGGGGTCACCAGGAAT 60.272 52.381 0.00 0.00 43.89 3.01
4118 4928 2.817839 CGAAAAGGGGTCACCAGGAATT 60.818 50.000 0.00 0.00 43.89 2.17
4119 4929 3.239449 GAAAAGGGGTCACCAGGAATTT 58.761 45.455 0.00 0.00 43.89 1.82
4120 4930 3.344535 AAAGGGGTCACCAGGAATTTT 57.655 42.857 0.00 0.00 43.89 1.82
4121 4931 4.479156 AAAGGGGTCACCAGGAATTTTA 57.521 40.909 0.00 0.00 43.89 1.52
4122 4932 4.692523 AAGGGGTCACCAGGAATTTTAT 57.307 40.909 0.00 0.00 43.89 1.40
4123 4933 4.251103 AGGGGTCACCAGGAATTTTATC 57.749 45.455 0.00 0.00 43.89 1.75
4124 4934 3.596046 AGGGGTCACCAGGAATTTTATCA 59.404 43.478 0.00 0.00 43.89 2.15
4125 4935 4.045334 AGGGGTCACCAGGAATTTTATCAA 59.955 41.667 0.00 0.00 43.89 2.57
4126 4936 4.402474 GGGGTCACCAGGAATTTTATCAAG 59.598 45.833 0.00 0.00 39.85 3.02
4127 4937 5.261216 GGGTCACCAGGAATTTTATCAAGA 58.739 41.667 0.00 0.00 36.50 3.02
4128 4938 5.714806 GGGTCACCAGGAATTTTATCAAGAA 59.285 40.000 0.00 0.00 36.50 2.52
4338 5149 3.314331 CAGCTCCGGACTGGGTGT 61.314 66.667 20.14 0.00 38.76 4.16
4339 5150 3.314331 AGCTCCGGACTGGGTGTG 61.314 66.667 0.00 0.00 38.76 3.82
4437 5248 4.749323 CACATCCTGGTGGTGCAT 57.251 55.556 7.37 0.00 35.13 3.96
4532 5360 3.311110 GTGGTCTGGTGGCGGAGA 61.311 66.667 0.00 0.00 0.00 3.71
4637 5470 0.739462 CGGTGCGCTTGTCTTGGATA 60.739 55.000 9.73 0.00 0.00 2.59
4649 5483 3.391296 TGTCTTGGATATGGCTAGGGTTC 59.609 47.826 0.00 0.00 0.00 3.62
4650 5484 2.632996 TCTTGGATATGGCTAGGGTTCG 59.367 50.000 0.00 0.00 0.00 3.95
4651 5485 1.348064 TGGATATGGCTAGGGTTCGG 58.652 55.000 0.00 0.00 0.00 4.30
4654 5488 0.104620 ATATGGCTAGGGTTCGGGGT 60.105 55.000 0.00 0.00 0.00 4.95
4859 5710 1.134965 ACCTTCGCTTCATCTTCTCGG 60.135 52.381 0.00 0.00 0.00 4.63
4860 5711 1.134965 CCTTCGCTTCATCTTCTCGGT 60.135 52.381 0.00 0.00 0.00 4.69
4865 5716 1.066858 GCTTCATCTTCTCGGTGTCCA 60.067 52.381 0.00 0.00 0.00 4.02
4970 5908 2.731721 CGCGCACGGTGTTGTAGA 60.732 61.111 8.75 0.00 34.97 2.59
5411 6358 1.605753 GTTCCCTTCTTGAAGGCGTT 58.394 50.000 20.71 0.00 38.63 4.84
5495 6481 3.691342 CGTCTTGGAGCCCCACGA 61.691 66.667 0.00 0.00 43.41 4.35
5537 6527 3.118000 TCTCTTCGTGATAGTGCTAGGGA 60.118 47.826 0.00 0.00 0.00 4.20
5577 6567 2.485479 CGCCTATGTATTCTGCCTTGGT 60.485 50.000 0.00 0.00 0.00 3.67
5630 6620 8.562892 GTTTGTATCGGATGATGATGATCTTTT 58.437 33.333 0.00 0.00 35.99 2.27
5804 6796 5.663456 TGATAATGATCCTTTGGCAAAAGC 58.337 37.500 14.43 3.51 41.33 3.51
5829 6821 4.003788 CCTTCTGTGCCGTCGGGT 62.004 66.667 14.38 0.00 34.97 5.28
5904 6897 1.651987 ACTTTATCGTGACATGCCGG 58.348 50.000 0.00 0.00 0.00 6.13
6085 7079 1.815003 GCAACTGGGATCTTGTCCTTG 59.185 52.381 0.00 0.00 46.91 3.61
6222 7218 0.457337 GCAACTGCCTATGCACAAGC 60.457 55.000 0.00 0.00 44.23 4.01
6235 7232 0.673644 CACAAGCCAGGGTACGAAGG 60.674 60.000 0.00 0.00 0.00 3.46
6238 7235 2.349755 GCCAGGGTACGAAGGCAA 59.650 61.111 14.05 0.00 46.26 4.52
6239 7236 1.745489 GCCAGGGTACGAAGGCAAG 60.745 63.158 14.05 0.00 46.26 4.01
6240 7237 1.745489 CCAGGGTACGAAGGCAAGC 60.745 63.158 0.00 0.00 0.00 4.01
6241 7238 1.745489 CAGGGTACGAAGGCAAGCC 60.745 63.158 2.02 2.02 0.00 4.35
6265 7262 3.741476 GCGGGAAGGCTGCAACTG 61.741 66.667 0.50 0.00 0.00 3.16
6266 7263 3.741476 CGGGAAGGCTGCAACTGC 61.741 66.667 0.50 0.00 42.50 4.40
6267 7264 3.376918 GGGAAGGCTGCAACTGCC 61.377 66.667 7.36 7.36 46.61 4.85
6272 7269 2.803479 GGCTGCAACTGCCTATGC 59.197 61.111 8.16 0.00 43.62 3.14
6274 7271 1.138247 GCTGCAACTGCCTATGCAC 59.862 57.895 3.58 0.00 46.87 4.57
6275 7272 1.588824 GCTGCAACTGCCTATGCACA 61.589 55.000 3.58 0.00 46.87 4.57
6276 7273 0.883153 CTGCAACTGCCTATGCACAA 59.117 50.000 3.58 0.00 46.87 3.33
6277 7274 0.883153 TGCAACTGCCTATGCACAAG 59.117 50.000 3.58 0.00 46.87 3.16
6278 7275 0.457337 GCAACTGCCTATGCACAAGC 60.457 55.000 0.00 0.00 44.23 4.01
6279 7276 0.171903 CAACTGCCTATGCACAAGCC 59.828 55.000 0.00 0.00 44.23 4.35
6280 7277 0.251297 AACTGCCTATGCACAAGCCA 60.251 50.000 0.00 0.00 44.23 4.75
6281 7278 0.679002 ACTGCCTATGCACAAGCCAG 60.679 55.000 7.19 7.19 44.23 4.85
6282 7279 1.378911 TGCCTATGCACAAGCCAGG 60.379 57.895 0.00 0.00 44.23 4.45
6283 7280 2.123428 GCCTATGCACAAGCCAGGG 61.123 63.158 0.00 0.00 40.51 4.45
6284 7281 1.304282 CCTATGCACAAGCCAGGGT 59.696 57.895 0.00 0.00 41.13 4.34
6285 7282 0.546122 CCTATGCACAAGCCAGGGTA 59.454 55.000 0.00 0.00 41.13 3.69
6286 7283 1.668419 CTATGCACAAGCCAGGGTAC 58.332 55.000 0.00 0.00 41.13 3.34
6287 7284 0.107897 TATGCACAAGCCAGGGTACG 60.108 55.000 0.00 0.00 41.13 3.67
6288 7285 1.836999 ATGCACAAGCCAGGGTACGA 61.837 55.000 0.00 0.00 41.13 3.43
6289 7286 1.302192 GCACAAGCCAGGGTACGAA 60.302 57.895 0.00 0.00 33.58 3.85
6290 7287 1.298859 GCACAAGCCAGGGTACGAAG 61.299 60.000 0.00 0.00 33.58 3.79
6312 7309 2.027561 GCACCCATGTCTTAGTACACCA 60.028 50.000 0.00 0.00 30.75 4.17
6358 7355 1.973281 GCTTACTGCAGGCTGGCAA 60.973 57.895 19.93 1.18 44.40 4.52
6452 7449 1.940883 CTGCATGATGGGTGGTGCAC 61.941 60.000 8.80 8.80 42.13 4.57
6461 7458 2.427320 GTGGTGCACCTGAGCTGA 59.573 61.111 34.75 11.74 36.82 4.26
6499 7496 0.038599 ATGGCATTGCAGTGGTCTCA 59.961 50.000 11.53 0.00 0.00 3.27
6541 7538 4.007940 CGAACGGTGTGTTGCGGG 62.008 66.667 0.00 0.00 42.09 6.13
6608 7605 4.056125 CTCTGGTGGCGAGTGCGA 62.056 66.667 0.00 0.00 44.10 5.10
6610 7607 4.363990 CTGGTGGCGAGTGCGAGT 62.364 66.667 0.00 0.00 44.10 4.18
6691 7689 4.408821 GCATGGCCCGTGGAGTCA 62.409 66.667 4.84 0.00 0.00 3.41
6793 7791 2.355986 CCGGTGATCCTCGTTCCCA 61.356 63.158 0.00 0.00 0.00 4.37
6799 7797 0.032267 GATCCTCGTTCCCATCCGTC 59.968 60.000 0.00 0.00 0.00 4.79
6857 7855 1.228245 GGTGTCATGTGTGTGGGCT 60.228 57.895 0.00 0.00 0.00 5.19
7673 8672 7.090173 GCAACTACAAAAATGCTAAATGGAGA 58.910 34.615 0.00 0.00 35.93 3.71
7695 8694 3.279434 TCAGACTCGATGCAGCTAGTAA 58.721 45.455 9.32 0.00 0.00 2.24
7748 8747 6.885918 TCATGAATACTATTACATGCATGGGG 59.114 38.462 29.41 15.97 39.60 4.96
7873 8873 4.577693 ACATCATGATTGCGCTTCTTGTAT 59.422 37.500 9.73 7.25 0.00 2.29
7915 8915 2.031245 CGAAACATAACACTGCAGGCAA 60.031 45.455 19.93 0.30 0.00 4.52
7943 8943 0.098376 GTCGTCGCCAGTACTACCTG 59.902 60.000 0.00 0.00 0.00 4.00
8357 9357 1.456287 GAGGGCTTGACCACCAACT 59.544 57.895 0.00 0.00 42.05 3.16
8426 9429 0.108615 ATTGAGTGAGAAGGTCGCCG 60.109 55.000 0.00 0.00 36.18 6.46
8533 9536 3.148279 AGGGACGATCCGCAGACC 61.148 66.667 0.00 0.00 37.43 3.85
8539 9542 1.358402 CGATCCGCAGACCTCAGAG 59.642 63.158 0.00 0.00 0.00 3.35
8586 9589 0.252881 AGCTTCTCAGATGGGGGACA 60.253 55.000 0.00 0.00 0.00 4.02
8629 9632 1.546961 GAAGAGAGGACGGAGGACAA 58.453 55.000 0.00 0.00 0.00 3.18
8657 9660 3.267900 GCGGCGAGCTTGTTAGATA 57.732 52.632 12.98 0.00 44.04 1.98
8658 9661 1.567504 GCGGCGAGCTTGTTAGATAA 58.432 50.000 12.98 0.00 44.04 1.75
8843 9893 1.143889 CCCTATCCTTTCCTTCTGGCC 59.856 57.143 0.00 0.00 0.00 5.36
8875 9925 4.142795 GGCTTAGTTGCAGCTAGTCTTTTC 60.143 45.833 10.34 0.00 37.43 2.29
8888 9938 3.019564 AGTCTTTTCAGCTGCTGTTTGT 58.980 40.909 27.24 6.22 32.61 2.83
8892 9942 4.640201 TCTTTTCAGCTGCTGTTTGTACTT 59.360 37.500 27.24 0.00 32.61 2.24
8922 9972 8.848474 TCTTTTTAGCTGCTTGTAAGAACTAT 57.152 30.769 7.79 0.00 0.00 2.12
8923 9973 9.938280 TCTTTTTAGCTGCTTGTAAGAACTATA 57.062 29.630 7.79 0.00 0.00 1.31
8956 10006 4.897140 TCTTTTAACGGAAATCGAGGGAA 58.103 39.130 0.00 0.00 42.43 3.97
8959 10009 2.381725 AACGGAAATCGAGGGAAGAC 57.618 50.000 0.00 0.00 42.43 3.01
9195 10333 6.148811 TCGTCAGATTTGATTTTCCAAGTACC 59.851 38.462 0.00 0.00 35.39 3.34
9211 10349 5.478679 CCAAGTACCCACCATGTTAATTTGA 59.521 40.000 0.00 0.00 0.00 2.69
9312 10454 8.943594 TTCCCTAAAGCTTCCTTTGTTATTTA 57.056 30.769 0.00 0.00 41.24 1.40
9313 10455 9.541884 TTCCCTAAAGCTTCCTTTGTTATTTAT 57.458 29.630 0.00 0.00 41.24 1.40
9340 10483 3.250762 TGAAACTCAAGCCACTCAAATCG 59.749 43.478 0.00 0.00 0.00 3.34
9392 10535 6.576662 TTTGCCATAAGGTAATCGAACAAA 57.423 33.333 0.00 0.00 39.36 2.83
9602 10746 3.655276 TCTCGTGTTCTTTCTGTACCC 57.345 47.619 0.00 0.00 0.00 3.69
9603 10747 2.960384 TCTCGTGTTCTTTCTGTACCCA 59.040 45.455 0.00 0.00 0.00 4.51
9608 10752 5.591067 TCGTGTTCTTTCTGTACCCATTTTT 59.409 36.000 0.00 0.00 0.00 1.94
9625 10769 9.492973 ACCCATTTTTAAATGTGAATCAAAGAG 57.507 29.630 12.70 0.00 43.24 2.85
9632 10776 6.855763 AAATGTGAATCAAAGAGGCCATAA 57.144 33.333 5.01 0.00 0.00 1.90
9637 10781 5.529060 GTGAATCAAAGAGGCCATAAGGTAG 59.471 44.000 5.01 0.00 37.19 3.18
9638 10782 4.713792 ATCAAAGAGGCCATAAGGTAGG 57.286 45.455 5.01 0.00 37.19 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 83 6.911250 TTGTAGGTGATCGATACCATATGT 57.089 37.500 19.59 7.13 40.74 2.29
422 425 3.475575 TGTGTTGCACTCACATATGTGT 58.524 40.909 30.03 13.57 40.26 3.72
711 714 7.749377 TCATCCTAGTTTCCCTCTAATTCAA 57.251 36.000 0.00 0.00 0.00 2.69
925 929 9.379791 GTGGGCTTATATACTTCCATATGTTAC 57.620 37.037 1.24 0.00 0.00 2.50
936 940 4.141041 TGGCAATGGTGGGCTTATATACTT 60.141 41.667 0.00 0.00 0.00 2.24
1039 1680 4.876679 TGTTGGTGTTGATGTCGAACTTAA 59.123 37.500 0.00 0.00 0.00 1.85
1079 1726 6.324770 AGGTTGATCTTGAACTTGGTTTTCAT 59.675 34.615 0.00 0.00 33.03 2.57
1120 1767 9.862371 TGCTTCACAACAAAGTAAGAAATAAAA 57.138 25.926 0.00 0.00 0.00 1.52
1124 1771 8.770438 TTTTGCTTCACAACAAAGTAAGAAAT 57.230 26.923 0.00 0.00 38.23 2.17
1298 1947 6.584185 TTCTTGGGGCACTAATTCTTTTAC 57.416 37.500 0.00 0.00 0.00 2.01
1318 1967 2.753452 TCTCGCTCGTCCTGTAAATTCT 59.247 45.455 0.00 0.00 0.00 2.40
1358 2007 8.938883 ACTGATGATAAGGTACCATTCTAATGT 58.061 33.333 15.94 0.34 34.60 2.71
1696 2499 7.229106 ACTTCTAAGTTCTAACAGAGAAGACGT 59.771 37.037 26.82 13.74 45.06 4.34
1757 2560 6.204688 GTGTCATTGGTGAATGTTCAGTCTAA 59.795 38.462 0.00 0.00 40.09 2.10
1918 2721 4.079970 TCTTGGTGTTAGTCTCGTGAGAT 58.920 43.478 2.42 0.00 39.97 2.75
2305 3108 2.548920 GGTGTGTCTGGACTGAGAAAGG 60.549 54.545 2.38 0.00 0.00 3.11
2424 3227 4.317418 GCGTTGTTACTCATAAGCTCATCG 60.317 45.833 0.00 0.00 0.00 3.84
2448 3251 1.305930 GGGATTTCGTCCTGGTGCAC 61.306 60.000 8.80 8.80 46.91 4.57
2623 3426 4.844884 AGGGAGTACTTAAATTGAGCCAC 58.155 43.478 0.00 0.00 0.00 5.01
2642 3445 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
2643 3446 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
2644 3447 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
2645 3448 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
2646 3449 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
2658 3461 9.953697 CTACTTTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 40.05 1.73
2659 3462 8.954350 ACTACTTTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 40.05 2.10
2660 3463 7.828712 ACTACTTTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 40.05 2.85
2661 3464 7.393841 ACTACTTTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 40.05 4.09
2693 3496 9.710818 TCCCTCTGTAAACTAATATAAGAGTGT 57.289 33.333 0.00 0.00 0.00 3.55
2695 3498 9.939424 ACTCCCTCTGTAAACTAATATAAGAGT 57.061 33.333 0.00 0.00 0.00 3.24
2703 3506 9.850198 CTAGTAGTACTCCCTCTGTAAACTAAT 57.150 37.037 5.96 0.00 0.00 1.73
2704 3507 9.051259 TCTAGTAGTACTCCCTCTGTAAACTAA 57.949 37.037 5.96 0.00 0.00 2.24
2705 3508 8.615360 TCTAGTAGTACTCCCTCTGTAAACTA 57.385 38.462 5.96 0.00 0.00 2.24
2706 3509 7.507797 TCTAGTAGTACTCCCTCTGTAAACT 57.492 40.000 5.96 0.00 0.00 2.66
2707 3510 8.572855 TTTCTAGTAGTACTCCCTCTGTAAAC 57.427 38.462 5.96 0.00 0.00 2.01
2711 3514 8.504409 ACATATTTCTAGTAGTACTCCCTCTGT 58.496 37.037 5.96 1.21 0.00 3.41
2712 3515 8.927675 ACATATTTCTAGTAGTACTCCCTCTG 57.072 38.462 5.96 0.62 0.00 3.35
2825 3628 0.909610 ACGCCCTCTGATCCCAAGAA 60.910 55.000 0.00 0.00 0.00 2.52
3056 3863 2.602676 GCTACCCACCCAAGCCAGA 61.603 63.158 0.00 0.00 0.00 3.86
3144 3951 1.003355 CGCCAGGACACAGGATTGT 60.003 57.895 0.00 0.00 38.31 2.71
3151 3958 4.624364 CACAGCCGCCAGGACACA 62.624 66.667 0.00 0.00 41.02 3.72
3165 3972 2.607750 GCTCCAGGAGACCCCACA 60.608 66.667 21.89 0.00 37.41 4.17
3189 3996 3.083349 CTCACCATCCAGGGCCGA 61.083 66.667 0.00 0.00 43.89 5.54
3290 4097 3.243468 TGACGAACTCACGATAACACCAA 60.243 43.478 0.00 0.00 37.03 3.67
3297 4104 5.290885 CCATTGAATTGACGAACTCACGATA 59.709 40.000 0.00 0.00 37.03 2.92
3413 4220 4.618920 AACACAAACTATCTCGGTCCTT 57.381 40.909 0.00 0.00 0.00 3.36
3431 4238 1.979855 ACAAGCATGTGCACCTAACA 58.020 45.000 15.69 0.00 45.16 2.41
3493 4300 2.104359 ATTGGGATTGTGGGGTGCCA 62.104 55.000 0.00 0.00 33.74 4.92
3658 4466 1.337071 GTGGACGAGTGACACAAGAGA 59.663 52.381 8.59 0.00 35.30 3.10
3694 4502 0.105453 GGGAGTGGAGGAGATGGCTA 60.105 60.000 0.00 0.00 0.00 3.93
3708 4516 0.621862 GGACAGGGATGGAAGGGAGT 60.622 60.000 0.00 0.00 0.00 3.85
3740 4548 4.704103 AGAGGGTCCTGGCAGCGA 62.704 66.667 9.56 5.23 0.00 4.93
3818 4626 1.422781 TCCCATAGATCGTCGTACCCT 59.577 52.381 0.00 0.00 0.00 4.34
3911 4719 2.968574 GCCTGAACCTGGATAGATCTCA 59.031 50.000 0.00 0.00 0.00 3.27
3945 4753 6.677076 ACCATAGAACAGGAGTAGGGTTTTAT 59.323 38.462 0.00 0.00 0.00 1.40
4099 4909 3.344535 AAATTCCTGGTGACCCCTTTT 57.655 42.857 0.00 0.00 0.00 2.27
4100 4910 3.344535 AAAATTCCTGGTGACCCCTTT 57.655 42.857 0.00 0.00 0.00 3.11
4101 4911 4.045334 TGATAAAATTCCTGGTGACCCCTT 59.955 41.667 0.00 0.00 0.00 3.95
4102 4912 3.596046 TGATAAAATTCCTGGTGACCCCT 59.404 43.478 0.00 0.00 0.00 4.79
4103 4913 3.976015 TGATAAAATTCCTGGTGACCCC 58.024 45.455 0.00 0.00 0.00 4.95
4104 4914 5.261216 TCTTGATAAAATTCCTGGTGACCC 58.739 41.667 0.00 0.00 0.00 4.46
4105 4915 6.834168 TTCTTGATAAAATTCCTGGTGACC 57.166 37.500 0.00 0.00 0.00 4.02
4106 4916 7.598869 GGTTTTCTTGATAAAATTCCTGGTGAC 59.401 37.037 0.00 0.00 31.43 3.67
4107 4917 7.508977 AGGTTTTCTTGATAAAATTCCTGGTGA 59.491 33.333 0.00 0.00 31.43 4.02
4108 4918 7.670364 AGGTTTTCTTGATAAAATTCCTGGTG 58.330 34.615 0.00 0.00 31.43 4.17
4109 4919 7.855784 AGGTTTTCTTGATAAAATTCCTGGT 57.144 32.000 0.00 0.00 31.43 4.00
4113 4923 9.817809 GGGATAAGGTTTTCTTGATAAAATTCC 57.182 33.333 0.00 0.00 36.93 3.01
4114 4924 9.817809 GGGGATAAGGTTTTCTTGATAAAATTC 57.182 33.333 0.00 0.00 36.93 2.17
4115 4925 9.560860 AGGGGATAAGGTTTTCTTGATAAAATT 57.439 29.630 0.00 0.00 36.93 1.82
4116 4926 9.201989 GAGGGGATAAGGTTTTCTTGATAAAAT 57.798 33.333 0.00 0.00 36.93 1.82
4117 4927 7.618117 GGAGGGGATAAGGTTTTCTTGATAAAA 59.382 37.037 0.00 0.00 36.93 1.52
4118 4928 7.123383 GGAGGGGATAAGGTTTTCTTGATAAA 58.877 38.462 0.00 0.00 36.93 1.40
4119 4929 6.354477 GGGAGGGGATAAGGTTTTCTTGATAA 60.354 42.308 0.00 0.00 36.93 1.75
4120 4930 5.133830 GGGAGGGGATAAGGTTTTCTTGATA 59.866 44.000 0.00 0.00 36.93 2.15
4121 4931 4.079154 GGGAGGGGATAAGGTTTTCTTGAT 60.079 45.833 0.00 0.00 36.93 2.57
4122 4932 3.268595 GGGAGGGGATAAGGTTTTCTTGA 59.731 47.826 0.00 0.00 36.93 3.02
4123 4933 3.632333 GGGAGGGGATAAGGTTTTCTTG 58.368 50.000 0.00 0.00 36.93 3.02
4124 4934 2.241430 CGGGAGGGGATAAGGTTTTCTT 59.759 50.000 0.00 0.00 39.40 2.52
4125 4935 1.844497 CGGGAGGGGATAAGGTTTTCT 59.156 52.381 0.00 0.00 0.00 2.52
4126 4936 1.749635 GCGGGAGGGGATAAGGTTTTC 60.750 57.143 0.00 0.00 0.00 2.29
4127 4937 0.257905 GCGGGAGGGGATAAGGTTTT 59.742 55.000 0.00 0.00 0.00 2.43
4128 4938 1.920532 GCGGGAGGGGATAAGGTTT 59.079 57.895 0.00 0.00 0.00 3.27
4508 5336 2.258591 CACCAGACCACGACGAGG 59.741 66.667 9.97 9.97 0.00 4.63
4621 5454 1.667236 CCATATCCAAGACAAGCGCA 58.333 50.000 11.47 0.00 0.00 6.09
4631 5464 1.697432 CCGAACCCTAGCCATATCCAA 59.303 52.381 0.00 0.00 0.00 3.53
4637 5470 2.042261 ACCCCGAACCCTAGCCAT 59.958 61.111 0.00 0.00 0.00 4.40
4676 5512 0.038744 AGCAACAGCCATACCAAGCT 59.961 50.000 0.00 0.00 40.89 3.74
4859 5710 0.173708 CGGAAGTAGAGCCTGGACAC 59.826 60.000 0.00 0.00 0.00 3.67
4860 5711 0.251653 ACGGAAGTAGAGCCTGGACA 60.252 55.000 0.00 0.00 46.88 4.02
5495 6481 1.206745 CGAAGCCGCATACGACGAAT 61.207 55.000 0.00 0.00 43.93 3.34
5577 6567 1.237954 ACCACAACACACGCACACAA 61.238 50.000 0.00 0.00 0.00 3.33
5804 6796 1.216710 GGCACAGAAGGAGAGACGG 59.783 63.158 0.00 0.00 0.00 4.79
5829 6821 0.838987 AGAAGGTAGGGTTCGGCCAA 60.839 55.000 2.24 0.00 39.65 4.52
5904 6897 0.807667 AAGATCATCAGGACGCGTGC 60.808 55.000 24.26 24.26 0.00 5.34
6222 7218 1.745489 GCTTGCCTTCGTACCCTGG 60.745 63.158 0.00 0.00 0.00 4.45
6248 7245 3.741476 CAGTTGCAGCCTTCCCGC 61.741 66.667 0.00 0.00 0.00 6.13
6249 7246 3.741476 GCAGTTGCAGCCTTCCCG 61.741 66.667 0.00 0.00 41.59 5.14
6265 7262 2.123428 CCCTGGCTTGTGCATAGGC 61.123 63.158 9.16 9.16 41.07 3.93
6266 7263 0.546122 TACCCTGGCTTGTGCATAGG 59.454 55.000 0.00 0.00 41.65 2.57
6267 7264 1.668419 GTACCCTGGCTTGTGCATAG 58.332 55.000 0.00 0.00 41.91 2.23
6268 7265 0.107897 CGTACCCTGGCTTGTGCATA 60.108 55.000 0.00 0.00 41.91 3.14
6269 7266 1.377202 CGTACCCTGGCTTGTGCAT 60.377 57.895 0.00 0.00 41.91 3.96
6270 7267 2.031919 CGTACCCTGGCTTGTGCA 59.968 61.111 0.00 0.00 41.91 4.57
6271 7268 1.298859 CTTCGTACCCTGGCTTGTGC 61.299 60.000 0.00 0.00 38.76 4.57
6272 7269 0.673644 CCTTCGTACCCTGGCTTGTG 60.674 60.000 0.00 0.00 0.00 3.33
6273 7270 1.677552 CCTTCGTACCCTGGCTTGT 59.322 57.895 0.00 0.00 0.00 3.16
6274 7271 1.745489 GCCTTCGTACCCTGGCTTG 60.745 63.158 9.55 0.00 41.92 4.01
6275 7272 2.221299 TGCCTTCGTACCCTGGCTT 61.221 57.895 15.56 0.00 45.11 4.35
6276 7273 2.606519 TGCCTTCGTACCCTGGCT 60.607 61.111 15.56 0.00 45.11 4.75
6277 7274 2.436115 GTGCCTTCGTACCCTGGC 60.436 66.667 9.81 9.81 45.10 4.85
6278 7275 2.267961 GGTGCCTTCGTACCCTGG 59.732 66.667 0.00 0.00 38.75 4.45
6282 7279 0.743345 GACATGGGTGCCTTCGTACC 60.743 60.000 0.00 0.00 43.65 3.34
6283 7280 0.249398 AGACATGGGTGCCTTCGTAC 59.751 55.000 0.00 0.00 0.00 3.67
6284 7281 0.981183 AAGACATGGGTGCCTTCGTA 59.019 50.000 0.00 0.00 0.00 3.43
6285 7282 0.981183 TAAGACATGGGTGCCTTCGT 59.019 50.000 0.00 0.00 30.30 3.85
6286 7283 1.066143 ACTAAGACATGGGTGCCTTCG 60.066 52.381 0.00 0.00 30.30 3.79
6287 7284 2.789409 ACTAAGACATGGGTGCCTTC 57.211 50.000 0.00 0.00 30.30 3.46
6288 7285 2.910319 TGTACTAAGACATGGGTGCCTT 59.090 45.455 0.00 0.00 32.51 4.35
6289 7286 2.236395 GTGTACTAAGACATGGGTGCCT 59.764 50.000 0.00 0.00 0.00 4.75
6290 7287 2.629051 GTGTACTAAGACATGGGTGCC 58.371 52.381 0.00 0.00 0.00 5.01
6353 7350 3.483788 TAGCACAACGCCCTTGCCA 62.484 57.895 0.00 0.00 44.04 4.92
6377 7374 1.675714 GCAGATTCACCGTCATGTCCA 60.676 52.381 0.00 0.00 0.00 4.02
6426 7423 1.077285 CCCATCATGCAGCCTCACA 60.077 57.895 0.00 0.00 0.00 3.58
6490 7487 1.069765 CACGCCACTTGAGACCACT 59.930 57.895 0.00 0.00 0.00 4.00
6541 7538 0.032540 CCAAGCCAGCCACAAGAAAC 59.967 55.000 0.00 0.00 0.00 2.78
6607 7604 1.490910 CCCAAACCCTAGATCCCACTC 59.509 57.143 0.00 0.00 0.00 3.51
6608 7605 1.596496 CCCAAACCCTAGATCCCACT 58.404 55.000 0.00 0.00 0.00 4.00
6610 7607 1.632018 CGCCCAAACCCTAGATCCCA 61.632 60.000 0.00 0.00 0.00 4.37
6799 7797 2.592993 ATATGGATCCGGCCCCACG 61.593 63.158 15.45 0.00 34.92 4.94
7673 8672 2.305928 ACTAGCTGCATCGAGTCTGAT 58.694 47.619 1.02 0.00 0.00 2.90
7695 8694 9.539194 TCTATATGGTAGCAGCAGCATATATAT 57.461 33.333 22.91 12.14 44.59 0.86
7735 8734 1.064758 GGACAGTCCCCATGCATGTAA 60.065 52.381 24.58 7.33 0.00 2.41
7736 8735 0.546122 GGACAGTCCCCATGCATGTA 59.454 55.000 24.58 7.67 0.00 2.29
7737 8736 1.304282 GGACAGTCCCCATGCATGT 59.696 57.895 24.58 6.23 0.00 3.21
7748 8747 3.679389 AGGAATGACACAATGGACAGTC 58.321 45.455 0.00 0.00 0.00 3.51
7873 8873 2.164422 GTGTCATGATCTCACGGTCTGA 59.836 50.000 0.00 0.00 0.00 3.27
8079 9079 3.796443 CGGCCGTCTTCTCGTCGA 61.796 66.667 19.50 0.00 0.00 4.20
8215 9215 2.978452 GATCATAGGTGCGCGCCACT 62.978 60.000 39.02 27.13 44.08 4.00
8357 9357 6.866770 CACAAGGTAGAGTTATCGAGTTTTGA 59.133 38.462 0.00 0.00 0.00 2.69
8533 9536 1.358402 CGTCTGCGGATCCTCTGAG 59.642 63.158 11.23 0.00 0.00 3.35
8539 9542 1.226717 GTCTGACGTCTGCGGATCC 60.227 63.158 17.92 0.00 43.45 3.36
8629 9632 1.593750 GCTCGCCGCATCTGAATCT 60.594 57.895 0.00 0.00 38.92 2.40
8657 9660 4.993028 TGGGTAAGCTATGTTTCAACCTT 58.007 39.130 0.00 0.00 0.00 3.50
8658 9661 4.650972 TGGGTAAGCTATGTTTCAACCT 57.349 40.909 0.00 0.00 0.00 3.50
8758 9800 0.987294 CACCATCCAGACTCCCAGTT 59.013 55.000 0.00 0.00 0.00 3.16
8843 9893 0.097674 GCAACTAAGCCATCACAGCG 59.902 55.000 0.00 0.00 34.64 5.18
8875 9925 4.558538 AAAGAAGTACAAACAGCAGCTG 57.441 40.909 21.54 21.54 37.52 4.24
8888 9938 7.996385 ACAAGCAGCTAAAAAGAAAAGAAGTA 58.004 30.769 0.00 0.00 0.00 2.24
8892 9942 8.220755 TCTTACAAGCAGCTAAAAAGAAAAGA 57.779 30.769 0.00 0.00 0.00 2.52
8942 9992 0.527817 CGGTCTTCCCTCGATTTCCG 60.528 60.000 0.00 0.00 40.25 4.30
8989 10039 4.832248 CAAAATAGGTACCTCAGCACTGA 58.168 43.478 20.32 0.00 38.06 3.41
8990 10040 3.375299 GCAAAATAGGTACCTCAGCACTG 59.625 47.826 20.32 10.60 0.00 3.66
8991 10041 3.610911 GCAAAATAGGTACCTCAGCACT 58.389 45.455 20.32 0.00 0.00 4.40
8992 10042 2.683362 GGCAAAATAGGTACCTCAGCAC 59.317 50.000 20.32 4.94 0.00 4.40
8993 10043 2.307392 TGGCAAAATAGGTACCTCAGCA 59.693 45.455 20.32 0.00 0.00 4.41
8994 10044 2.945668 CTGGCAAAATAGGTACCTCAGC 59.054 50.000 20.32 15.50 0.00 4.26
8995 10045 4.487714 TCTGGCAAAATAGGTACCTCAG 57.512 45.455 20.32 17.13 0.00 3.35
8996 10046 6.569127 TTATCTGGCAAAATAGGTACCTCA 57.431 37.500 20.32 7.39 0.00 3.86
8997 10047 7.502561 ACAATTATCTGGCAAAATAGGTACCTC 59.497 37.037 20.32 2.06 0.00 3.85
8998 10048 7.354312 ACAATTATCTGGCAAAATAGGTACCT 58.646 34.615 20.57 20.57 0.00 3.08
9113 10195 5.228012 GTGAGAAGAAAAGAAAAACAGCACG 59.772 40.000 0.00 0.00 0.00 5.34
9195 10333 4.981806 ACCGATCAAATTAACATGGTGG 57.018 40.909 0.00 0.00 0.00 4.61
9211 10349 2.162681 CAAAGGAGGCTTGAAACCGAT 58.837 47.619 0.00 0.00 0.00 4.18
9312 10454 8.579850 TTTGAGTGGCTTGAGTTTCATATAAT 57.420 30.769 0.00 0.00 0.00 1.28
9313 10455 7.994425 TTTGAGTGGCTTGAGTTTCATATAA 57.006 32.000 0.00 0.00 0.00 0.98
9340 10483 6.315393 TGATAAACCGAGGATTCTTTACAAGC 59.685 38.462 0.00 0.00 0.00 4.01
9377 10520 5.735070 GCACCAAAGTTTGTTCGATTACCTT 60.735 40.000 14.36 0.00 0.00 3.50
9386 10529 2.953020 TGTGTGCACCAAAGTTTGTTC 58.047 42.857 15.69 3.90 0.00 3.18
9392 10535 2.166829 TGAGTTTGTGTGCACCAAAGT 58.833 42.857 27.13 27.13 0.00 2.66
9442 10586 3.227614 TCCATTTCGGATCGTATGGAGA 58.772 45.455 16.41 3.77 40.75 3.71
9603 10747 8.156165 TGGCCTCTTTGATTCACATTTAAAAAT 58.844 29.630 3.32 0.00 0.00 1.82
9608 10752 7.068593 CCTTATGGCCTCTTTGATTCACATTTA 59.931 37.037 3.32 0.00 0.00 1.40
9624 10768 2.127708 CAAGACCCTACCTTATGGCCT 58.872 52.381 3.32 0.00 36.63 5.19
9625 10769 1.844497 ACAAGACCCTACCTTATGGCC 59.156 52.381 0.00 0.00 36.63 5.36
9632 10776 4.513406 TTTTTGTCACAAGACCCTACCT 57.487 40.909 0.00 0.00 44.33 3.08


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

AutoCloner maintained by Alex Coulton.