Multiple sequence alignment - TraesCS2D01G222500

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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 TraesCS2D01G222500 chr2D 100.000 6160 0 0 1 6160 189533895 189527736 0.000000e+00 11376.0
1 TraesCS2D01G222500 chr2D 93.667 1279 54 13 2621 3887 86068232 86069495 0.000000e+00 1888.0
2 TraesCS2D01G222500 chr2D 92.667 1241 71 10 2657 3892 565161315 565160090 0.000000e+00 1770.0
3 TraesCS2D01G222500 chr2D 94.161 805 39 8 1824 2623 25066953 25066152 0.000000e+00 1219.0
4 TraesCS2D01G222500 chr2D 93.665 805 45 6 1824 2623 79276847 79277650 0.000000e+00 1199.0
5 TraesCS2D01G222500 chr2D 93.540 805 45 6 1824 2623 14886231 14885429 0.000000e+00 1192.0
6 TraesCS2D01G222500 chr2D 91.986 574 30 10 3317 3887 25065929 25065369 0.000000e+00 791.0
7 TraesCS2D01G222500 chr2D 80.186 646 114 13 1168 1810 189389542 189388908 7.230000e-129 472.0
8 TraesCS2D01G222500 chr2D 77.143 560 106 20 1170 1718 188836382 188836930 7.760000e-79 305.0
9 TraesCS2D01G222500 chr2A 95.539 1883 60 12 3962 5828 203328148 203326274 0.000000e+00 2990.0
10 TraesCS2D01G222500 chr2A 95.170 1822 83 5 1 1817 203330012 203328191 0.000000e+00 2872.0
11 TraesCS2D01G222500 chr2A 88.950 1276 105 19 2621 3887 773271953 773273201 0.000000e+00 1543.0
12 TraesCS2D01G222500 chr2A 93.532 804 47 5 1824 2623 25355983 25356785 0.000000e+00 1192.0
13 TraesCS2D01G222500 chr2A 80.526 647 110 13 1168 1810 203321774 203321140 3.340000e-132 483.0
14 TraesCS2D01G222500 chr2A 96.923 130 3 1 5970 6098 203326265 203326136 3.740000e-52 217.0
15 TraesCS2D01G222500 chr2A 100.000 48 0 0 3885 3932 203328201 203328154 8.500000e-14 89.8
16 TraesCS2D01G222500 chr2B 97.200 1643 32 7 4192 5826 245822306 245820670 0.000000e+00 2767.0
17 TraesCS2D01G222500 chr2B 97.404 963 21 2 856 1817 245823646 245822687 0.000000e+00 1637.0
18 TraesCS2D01G222500 chr2B 98.387 310 4 1 3885 4193 245822697 245822388 1.510000e-150 544.0
19 TraesCS2D01G222500 chr2B 79.102 646 109 13 1168 1810 245794066 245793444 7.380000e-114 422.0
20 TraesCS2D01G222500 chr2B 75.313 559 118 18 1170 1718 244934583 244935131 3.690000e-62 250.0
21 TraesCS2D01G222500 chr2B 95.385 130 5 1 5970 6098 245820659 245820530 8.090000e-49 206.0
22 TraesCS2D01G222500 chr2B 94.949 99 1 1 5824 5922 715814806 715814712 1.070000e-32 152.0
23 TraesCS2D01G222500 chr2B 94.845 97 4 1 5826 5921 101490640 101490544 3.850000e-32 150.0
24 TraesCS2D01G222500 chr3D 94.214 1279 50 10 2621 3887 110279210 110280476 0.000000e+00 1930.0
25 TraesCS2D01G222500 chr3D 92.368 1271 79 11 2621 3887 339302312 339301056 0.000000e+00 1794.0
26 TraesCS2D01G222500 chr3D 91.654 1282 78 17 2621 3887 2740778 2742045 0.000000e+00 1748.0
27 TraesCS2D01G222500 chr1D 93.427 1278 60 8 2621 3887 297520379 297519115 0.000000e+00 1873.0
28 TraesCS2D01G222500 chr1D 92.009 876 48 12 3017 3890 240585205 240584350 0.000000e+00 1210.0
29 TraesCS2D01G222500 chr1D 93.649 803 45 6 1824 2623 469045378 469046177 0.000000e+00 1195.0
30 TraesCS2D01G222500 chr1D 91.275 149 6 3 5823 5969 494045183 494045040 4.870000e-46 196.0
31 TraesCS2D01G222500 chr1D 94.792 96 2 1 5879 5971 75879652 75879747 4.980000e-31 147.0
32 TraesCS2D01G222500 chr1D 93.684 95 3 1 5880 5971 75879739 75879645 8.330000e-29 139.0
33 TraesCS2D01G222500 chr1D 77.251 211 42 5 5393 5601 481557584 481557378 1.080000e-22 119.0
34 TraesCS2D01G222500 chr1D 100.000 57 0 0 5824 5880 471188920 471188864 8.440000e-19 106.0
35 TraesCS2D01G222500 chrUn 93.432 1279 47 17 2621 3887 94193599 94194852 0.000000e+00 1862.0
36 TraesCS2D01G222500 chrUn 92.885 1279 67 12 2621 3887 96048458 96049724 0.000000e+00 1836.0
37 TraesCS2D01G222500 chrUn 92.607 1285 56 19 2621 3891 320127113 320128372 0.000000e+00 1810.0
38 TraesCS2D01G222500 chrUn 90.867 1281 88 15 2621 3885 27712043 27713310 0.000000e+00 1690.0
39 TraesCS2D01G222500 chrUn 89.556 1283 109 12 2621 3891 305006623 305007892 0.000000e+00 1604.0
40 TraesCS2D01G222500 chrUn 94.030 804 43 5 1824 2623 94192770 94193572 0.000000e+00 1214.0
41 TraesCS2D01G222500 chrUn 91.201 841 57 9 3048 3887 382211796 382212620 0.000000e+00 1127.0
42 TraesCS2D01G222500 chrUn 93.269 104 4 1 5879 5979 389647839 389647942 3.850000e-32 150.0
43 TraesCS2D01G222500 chrUn 92.632 95 4 1 5880 5971 389647926 389647832 3.870000e-27 134.0
44 TraesCS2D01G222500 chrUn 83.221 149 5 11 5823 5971 128516274 128516402 1.080000e-22 119.0
45 TraesCS2D01G222500 chrUn 83.108 148 5 10 5824 5971 19647286 19647159 3.900000e-22 117.0
46 TraesCS2D01G222500 chrUn 83.108 148 5 10 5824 5971 104559179 104559306 3.900000e-22 117.0
47 TraesCS2D01G222500 chrUn 83.108 148 5 13 5824 5971 154681608 154681481 3.900000e-22 117.0
48 TraesCS2D01G222500 chrUn 82.432 148 6 10 5824 5971 73486536 73486409 1.820000e-20 111.0
49 TraesCS2D01G222500 chrUn 82.432 148 6 10 5824 5971 102887927 102887800 1.820000e-20 111.0
50 TraesCS2D01G222500 chrUn 82.432 148 6 10 5824 5971 254470448 254470575 1.820000e-20 111.0
51 TraesCS2D01G222500 chrUn 81.410 156 9 11 5824 5979 19647154 19647289 6.530000e-20 110.0
52 TraesCS2D01G222500 chrUn 81.699 153 8 11 5827 5979 104559308 104559176 6.530000e-20 110.0
53 TraesCS2D01G222500 chrUn 81.410 156 9 10 5824 5979 154681476 154681611 6.530000e-20 110.0
54 TraesCS2D01G222500 chrUn 81.757 148 7 10 5824 5971 262619269 262619396 8.440000e-19 106.0
55 TraesCS2D01G222500 chrUn 80.769 156 10 11 5824 5979 73486404 73486539 3.040000e-18 104.0
56 TraesCS2D01G222500 chrUn 80.769 156 10 11 5824 5979 102887795 102887930 3.040000e-18 104.0
57 TraesCS2D01G222500 chrUn 98.305 59 1 0 5921 5979 254470503 254470445 3.040000e-18 104.0
58 TraesCS2D01G222500 chrUn 98.305 59 1 0 5921 5979 262619324 262619266 3.040000e-18 104.0
59 TraesCS2D01G222500 chrUn 98.246 57 1 0 5823 5879 87983127 87983183 3.930000e-17 100.0
60 TraesCS2D01G222500 chrUn 87.097 93 6 5 5881 5971 362729149 362729061 3.930000e-17 100.0
61 TraesCS2D01G222500 chrUn 86.170 94 7 5 5880 5971 362729069 362729158 5.080000e-16 97.1
62 TraesCS2D01G222500 chrUn 100.000 43 0 0 5880 5922 19647273 19647231 5.120000e-11 80.5
63 TraesCS2D01G222500 chrUn 100.000 43 0 0 5880 5922 36371391 36371349 5.120000e-11 80.5
64 TraesCS2D01G222500 chrUn 100.000 43 0 0 5880 5922 64149818 64149776 5.120000e-11 80.5
65 TraesCS2D01G222500 chrUn 100.000 43 0 0 5880 5922 66416419 66416461 5.120000e-11 80.5
66 TraesCS2D01G222500 chrUn 100.000 43 0 0 5880 5922 73486523 73486481 5.120000e-11 80.5
67 TraesCS2D01G222500 chr5D 92.763 1285 63 13 2621 3887 374396826 374398098 0.000000e+00 1831.0
68 TraesCS2D01G222500 chr5D 92.796 930 50 11 2965 3892 238113633 238112719 0.000000e+00 1330.0
69 TraesCS2D01G222500 chr5D 93.524 803 43 7 1824 2623 425842803 425843599 0.000000e+00 1186.0
70 TraesCS2D01G222500 chr5D 96.703 91 1 2 5880 5970 462044298 462044386 3.850000e-32 150.0
71 TraesCS2D01G222500 chr5D 97.222 72 2 0 6089 6160 64653844 64653915 8.390000e-24 122.0
72 TraesCS2D01G222500 chr4D 92.547 1288 69 13 2621 3892 8007023 8005747 0.000000e+00 1821.0
73 TraesCS2D01G222500 chr4D 92.416 1279 69 13 2624 3889 505822526 505821263 0.000000e+00 1799.0
74 TraesCS2D01G222500 chr4D 92.410 1278 58 12 2624 3890 502597436 502596187 0.000000e+00 1786.0
75 TraesCS2D01G222500 chr4D 94.059 101 2 1 5879 5979 312648929 312649025 3.850000e-32 150.0
76 TraesCS2D01G222500 chr4D 94.565 92 4 1 5881 5971 333016938 333017029 2.310000e-29 141.0
77 TraesCS2D01G222500 chr4D 93.478 92 2 1 5880 5971 312649009 312648922 3.870000e-27 134.0
78 TraesCS2D01G222500 chr4D 92.473 93 6 1 5880 5971 333017021 333016929 1.390000e-26 132.0
79 TraesCS2D01G222500 chr4D 90.722 97 5 1 5826 5922 10405778 10405870 6.480000e-25 126.0
80 TraesCS2D01G222500 chr4D 92.391 92 2 1 5880 5971 496945858 496945772 6.480000e-25 126.0
81 TraesCS2D01G222500 chr4D 90.625 96 4 1 5880 5975 496945780 496945870 8.390000e-24 122.0
82 TraesCS2D01G222500 chr4D 82.000 150 7 6 5824 5973 407364125 407364254 6.530000e-20 110.0
83 TraesCS2D01G222500 chr4D 87.500 96 6 5 5880 5975 397678215 397678304 8.440000e-19 106.0
84 TraesCS2D01G222500 chr7D 92.344 1280 75 10 2621 3887 570329336 570330605 0.000000e+00 1799.0
85 TraesCS2D01G222500 chr7D 93.905 804 44 5 1824 2623 9964523 9965325 0.000000e+00 1208.0
86 TraesCS2D01G222500 chr7D 98.387 62 1 0 6098 6159 616752976 616752915 6.530000e-20 110.0
87 TraesCS2D01G222500 chr7D 96.825 63 2 0 6097 6159 169033563 169033501 8.440000e-19 106.0
88 TraesCS2D01G222500 chr7D 97.959 49 1 0 6112 6160 169033379 169033331 1.100000e-12 86.1
89 TraesCS2D01G222500 chr6D 92.344 1280 65 15 2621 3887 276127004 276128263 0.000000e+00 1790.0
90 TraesCS2D01G222500 chr6D 87.857 1227 120 18 2621 3841 368142023 368143226 0.000000e+00 1413.0
91 TraesCS2D01G222500 chr6D 92.797 944 54 8 2947 3887 450665480 450666412 0.000000e+00 1354.0
92 TraesCS2D01G222500 chr6D 92.780 928 54 7 2961 3887 23776019 23775104 0.000000e+00 1330.0
93 TraesCS2D01G222500 chr6D 94.140 802 40 6 1825 2623 276126180 276126977 0.000000e+00 1214.0
94 TraesCS2D01G222500 chr6D 97.917 96 1 1 5880 5974 129156600 129156505 1.370000e-36 165.0
95 TraesCS2D01G222500 chr6D 98.925 93 0 1 5880 5971 129156516 129156608 1.370000e-36 165.0
96 TraesCS2D01G222500 chr6D 94.898 98 3 1 5825 5922 312136255 312136350 1.070000e-32 152.0
97 TraesCS2D01G222500 chr6D 83.108 148 5 9 5824 5971 421855390 421855263 3.900000e-22 117.0
98 TraesCS2D01G222500 chr6D 89.888 89 4 2 5833 5921 456337272 456337189 6.530000e-20 110.0
99 TraesCS2D01G222500 chr6D 100.000 57 0 0 5823 5879 445850827 445850883 8.440000e-19 106.0
100 TraesCS2D01G222500 chr6D 98.305 59 1 0 5821 5879 403312402 403312344 3.040000e-18 104.0
101 TraesCS2D01G222500 chr5B 90.966 1273 100 12 2621 3891 10451525 10452784 0.000000e+00 1700.0
102 TraesCS2D01G222500 chr5B 94.231 104 3 1 5879 5979 460590056 460589953 8.270000e-34 156.0
103 TraesCS2D01G222500 chr5B 94.175 103 4 1 5879 5979 663324510 663324408 8.270000e-34 156.0
104 TraesCS2D01G222500 chr5B 90.110 91 9 0 5832 5922 618275056 618275146 1.080000e-22 119.0
105 TraesCS2D01G222500 chr5B 100.000 62 0 0 6097 6158 292194423 292194362 1.400000e-21 115.0
106 TraesCS2D01G222500 chr4A 89.889 1266 110 12 2622 3884 166334039 166335289 0.000000e+00 1613.0
107 TraesCS2D01G222500 chr4A 90.260 154 3 2 5827 5971 278325735 278325885 2.270000e-44 191.0
108 TraesCS2D01G222500 chr4A 83.041 171 29 0 1229 1399 725907051 725906881 8.270000e-34 156.0
109 TraesCS2D01G222500 chr4A 100.000 62 0 0 6097 6158 488011234 488011173 1.400000e-21 115.0
110 TraesCS2D01G222500 chr6A 89.548 1282 112 11 2622 3890 78569527 78568255 0.000000e+00 1605.0
111 TraesCS2D01G222500 chr6A 91.241 137 5 2 5841 5974 200245953 200245821 4.910000e-41 180.0
112 TraesCS2D01G222500 chr6A 98.020 101 1 1 5879 5979 61597805 61597904 2.280000e-39 174.0
113 TraesCS2D01G222500 chr6A 97.826 92 1 1 5880 5971 61597888 61597798 2.300000e-34 158.0
114 TraesCS2D01G222500 chr6A 100.000 62 0 0 6097 6158 561439474 561439535 1.400000e-21 115.0
115 TraesCS2D01G222500 chr6A 100.000 62 0 0 6097 6158 561614408 561614347 1.400000e-21 115.0
116 TraesCS2D01G222500 chr6A 88.172 93 6 1 5827 5919 556981064 556980977 8.440000e-19 106.0
117 TraesCS2D01G222500 chr5A 89.056 1197 110 11 2621 3805 653567284 653568471 0.000000e+00 1465.0
118 TraesCS2D01G222500 chr5A 92.553 94 5 1 5829 5922 25705146 25705055 3.870000e-27 134.0
119 TraesCS2D01G222500 chr3B 75.456 493 93 19 349 820 571999437 571999922 1.340000e-51 215.0
120 TraesCS2D01G222500 chr3B 91.391 151 7 2 5825 5971 732905447 732905299 1.050000e-47 202.0
121 TraesCS2D01G222500 chr3B 95.146 103 3 1 5879 5979 283473991 283474093 1.780000e-35 161.0
122 TraesCS2D01G222500 chr3B 100.000 63 0 0 6096 6158 71553670 71553608 3.900000e-22 117.0
123 TraesCS2D01G222500 chr7B 86.335 161 15 7 5834 5990 593418009 593418166 1.060000e-37 169.0
124 TraesCS2D01G222500 chr7B 94.340 106 1 1 5879 5979 624570254 624570149 2.300000e-34 158.0
125 TraesCS2D01G222500 chr7B 93.617 94 6 0 5827 5920 593417959 593418052 2.310000e-29 141.0
126 TraesCS2D01G222500 chr7B 90.000 100 7 1 5826 5922 392820020 392819921 6.480000e-25 126.0
127 TraesCS2D01G222500 chr7B 100.000 62 0 0 6097 6158 350693656 350693595 1.400000e-21 115.0
128 TraesCS2D01G222500 chr7A 87.097 155 10 7 5823 5971 493700368 493700518 3.820000e-37 167.0
129 TraesCS2D01G222500 chr1A 96.842 95 1 1 5879 5971 202090603 202090509 2.300000e-34 158.0
130 TraesCS2D01G222500 chr1A 96.842 95 1 1 5879 5971 202090516 202090610 2.300000e-34 158.0
131 TraesCS2D01G222500 chr1A 95.918 98 2 1 5827 5922 276575262 276575165 2.300000e-34 158.0
132 TraesCS2D01G222500 chr1A 88.660 97 11 0 5826 5922 95827388 95827484 1.080000e-22 119.0
133 TraesCS2D01G222500 chr1A 79.856 139 25 3 293 429 21835187 21835324 1.410000e-16 99.0
134 TraesCS2D01G222500 chr6B 93.333 105 3 1 5879 5979 174298378 174298274 1.070000e-32 152.0
135 TraesCS2D01G222500 chr1B 91.262 103 4 2 5825 5922 677272745 677272847 1.080000e-27 135.0
136 TraesCS2D01G222500 chr1B 89.000 100 5 3 5827 5920 675092970 675093069 1.080000e-22 119.0
137 TraesCS2D01G222500 chr3A 74.098 305 67 9 1153 1448 719835844 719836145 1.400000e-21 115.0
138 TraesCS2D01G222500 chr4B 96.825 63 1 1 5817 5879 450453463 450453524 3.040000e-18 104.0


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 TraesCS2D01G222500 chr2D 189527736 189533895 6159 True 11376.0 11376 100.0000 1 6160 1 chr2D.!!$R3 6159
1 TraesCS2D01G222500 chr2D 86068232 86069495 1263 False 1888.0 1888 93.6670 2621 3887 1 chr2D.!!$F2 1266
2 TraesCS2D01G222500 chr2D 565160090 565161315 1225 True 1770.0 1770 92.6670 2657 3892 1 chr2D.!!$R4 1235
3 TraesCS2D01G222500 chr2D 79276847 79277650 803 False 1199.0 1199 93.6650 1824 2623 1 chr2D.!!$F1 799
4 TraesCS2D01G222500 chr2D 14885429 14886231 802 True 1192.0 1192 93.5400 1824 2623 1 chr2D.!!$R1 799
5 TraesCS2D01G222500 chr2D 25065369 25066953 1584 True 1005.0 1219 93.0735 1824 3887 2 chr2D.!!$R5 2063
6 TraesCS2D01G222500 chr2D 189388908 189389542 634 True 472.0 472 80.1860 1168 1810 1 chr2D.!!$R2 642
7 TraesCS2D01G222500 chr2D 188836382 188836930 548 False 305.0 305 77.1430 1170 1718 1 chr2D.!!$F3 548
8 TraesCS2D01G222500 chr2A 773271953 773273201 1248 False 1543.0 1543 88.9500 2621 3887 1 chr2A.!!$F2 1266
9 TraesCS2D01G222500 chr2A 203326136 203330012 3876 True 1542.2 2990 96.9080 1 6098 4 chr2A.!!$R2 6097
10 TraesCS2D01G222500 chr2A 25355983 25356785 802 False 1192.0 1192 93.5320 1824 2623 1 chr2A.!!$F1 799
11 TraesCS2D01G222500 chr2A 203321140 203321774 634 True 483.0 483 80.5260 1168 1810 1 chr2A.!!$R1 642
12 TraesCS2D01G222500 chr2B 245820530 245823646 3116 True 1288.5 2767 97.0940 856 6098 4 chr2B.!!$R4 5242
13 TraesCS2D01G222500 chr2B 245793444 245794066 622 True 422.0 422 79.1020 1168 1810 1 chr2B.!!$R2 642
14 TraesCS2D01G222500 chr2B 244934583 244935131 548 False 250.0 250 75.3130 1170 1718 1 chr2B.!!$F1 548
15 TraesCS2D01G222500 chr3D 110279210 110280476 1266 False 1930.0 1930 94.2140 2621 3887 1 chr3D.!!$F2 1266
16 TraesCS2D01G222500 chr3D 339301056 339302312 1256 True 1794.0 1794 92.3680 2621 3887 1 chr3D.!!$R1 1266
17 TraesCS2D01G222500 chr3D 2740778 2742045 1267 False 1748.0 1748 91.6540 2621 3887 1 chr3D.!!$F1 1266
18 TraesCS2D01G222500 chr1D 297519115 297520379 1264 True 1873.0 1873 93.4270 2621 3887 1 chr1D.!!$R3 1266
19 TraesCS2D01G222500 chr1D 240584350 240585205 855 True 1210.0 1210 92.0090 3017 3890 1 chr1D.!!$R2 873
20 TraesCS2D01G222500 chr1D 469045378 469046177 799 False 1195.0 1195 93.6490 1824 2623 1 chr1D.!!$F2 799
21 TraesCS2D01G222500 chrUn 96048458 96049724 1266 False 1836.0 1836 92.8850 2621 3887 1 chrUn.!!$F6 1266
22 TraesCS2D01G222500 chrUn 320127113 320128372 1259 False 1810.0 1810 92.6070 2621 3891 1 chrUn.!!$F14 1270
23 TraesCS2D01G222500 chrUn 27712043 27713310 1267 False 1690.0 1690 90.8670 2621 3885 1 chrUn.!!$F2 1264
24 TraesCS2D01G222500 chrUn 305006623 305007892 1269 False 1604.0 1604 89.5560 2621 3891 1 chrUn.!!$F13 1270
25 TraesCS2D01G222500 chrUn 94192770 94194852 2082 False 1538.0 1862 93.7310 1824 3887 2 chrUn.!!$F18 2063
26 TraesCS2D01G222500 chrUn 382211796 382212620 824 False 1127.0 1127 91.2010 3048 3887 1 chrUn.!!$F16 839
27 TraesCS2D01G222500 chr5D 374396826 374398098 1272 False 1831.0 1831 92.7630 2621 3887 1 chr5D.!!$F2 1266
28 TraesCS2D01G222500 chr5D 238112719 238113633 914 True 1330.0 1330 92.7960 2965 3892 1 chr5D.!!$R1 927
29 TraesCS2D01G222500 chr5D 425842803 425843599 796 False 1186.0 1186 93.5240 1824 2623 1 chr5D.!!$F3 799
30 TraesCS2D01G222500 chr4D 8005747 8007023 1276 True 1821.0 1821 92.5470 2621 3892 1 chr4D.!!$R1 1271
31 TraesCS2D01G222500 chr4D 505821263 505822526 1263 True 1799.0 1799 92.4160 2624 3889 1 chr4D.!!$R6 1265
32 TraesCS2D01G222500 chr4D 502596187 502597436 1249 True 1786.0 1786 92.4100 2624 3890 1 chr4D.!!$R5 1266
33 TraesCS2D01G222500 chr7D 570329336 570330605 1269 False 1799.0 1799 92.3440 2621 3887 1 chr7D.!!$F2 1266
34 TraesCS2D01G222500 chr7D 9964523 9965325 802 False 1208.0 1208 93.9050 1824 2623 1 chr7D.!!$F1 799
35 TraesCS2D01G222500 chr6D 276126180 276128263 2083 False 1502.0 1790 93.2420 1825 3887 2 chr6D.!!$F6 2062
36 TraesCS2D01G222500 chr6D 368142023 368143226 1203 False 1413.0 1413 87.8570 2621 3841 1 chr6D.!!$F3 1220
37 TraesCS2D01G222500 chr6D 450665480 450666412 932 False 1354.0 1354 92.7970 2947 3887 1 chr6D.!!$F5 940
38 TraesCS2D01G222500 chr6D 23775104 23776019 915 True 1330.0 1330 92.7800 2961 3887 1 chr6D.!!$R1 926
39 TraesCS2D01G222500 chr5B 10451525 10452784 1259 False 1700.0 1700 90.9660 2621 3891 1 chr5B.!!$F1 1270
40 TraesCS2D01G222500 chr4A 166334039 166335289 1250 False 1613.0 1613 89.8890 2622 3884 1 chr4A.!!$F1 1262
41 TraesCS2D01G222500 chr6A 78568255 78569527 1272 True 1605.0 1605 89.5480 2622 3890 1 chr6A.!!$R2 1268
42 TraesCS2D01G222500 chr5A 653567284 653568471 1187 False 1465.0 1465 89.0560 2621 3805 1 chr5A.!!$F1 1184

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
91 92 0.389817 TGTTTCGTGGATGAGCCGAG 60.390 55.0 0.00 0.00 40.66 4.63 F
721 725 0.392998 GGTCATGTGCCCTGGTGTAG 60.393 60.0 0.00 0.00 0.00 2.74 F
1821 1830 0.322975 TTCTTCTCAGACAGCTGGCC 59.677 55.0 18.28 8.21 42.53 5.36 F
2683 2730 0.249120 TGTGAGTTCCTGGCATACCG 59.751 55.0 0.00 0.00 39.70 4.02 F
3960 4067 0.888736 CACCAGTGGACATTTCGCCA 60.889 55.0 18.40 0.00 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1816 1825 0.030638 CGATTTTTATGCGGGGCCAG 59.969 55.000 4.39 1.12 0.00 4.85 R
2257 2275 0.249398 GTTGATCACCAGCTACCGGT 59.751 55.000 13.98 13.98 37.16 5.28 R
3330 3398 0.818296 CCGACGTCCAGGAAGAAGAT 59.182 55.000 10.58 0.00 0.00 2.40 R
4247 4445 1.660052 CGGTCAAGTGTGCATTGTTCG 60.660 52.381 0.00 0.00 0.00 3.95 R
5952 6165 0.323451 GCTCCCTCCGTCCCAAAATT 60.323 55.000 0.00 0.00 0.00 1.82 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
19 20 2.426842 ATTGGGAGCTTAGGAAGTGC 57.573 50.000 0.00 0.00 0.00 4.40
37 38 2.280389 AGTGGCTCACGCACACTG 60.280 61.111 0.00 0.00 42.28 3.66
58 59 3.147595 CGCCGTCCATCTCCTCCA 61.148 66.667 0.00 0.00 0.00 3.86
67 68 2.143419 ATCTCCTCCATCCCCGTGC 61.143 63.158 0.00 0.00 0.00 5.34
81 82 2.244382 GTGCGTCGTGTTTCGTGG 59.756 61.111 0.00 0.00 40.80 4.94
91 92 0.389817 TGTTTCGTGGATGAGCCGAG 60.390 55.000 0.00 0.00 40.66 4.63
118 119 5.035784 ACTCAAACTTCTGCGCTTATTTC 57.964 39.130 9.73 0.00 0.00 2.17
171 172 9.878667 TTTGGATTAATTACGAGTCACTAATGA 57.121 29.630 0.00 0.00 0.00 2.57
184 185 7.194607 AGTCACTAATGAATGCCATTATTCG 57.805 36.000 0.00 0.00 44.26 3.34
190 191 6.698008 AATGAATGCCATTATTCGAGACAA 57.302 33.333 0.00 0.00 43.30 3.18
207 208 3.675619 AATGGACCCGGCTACACGC 62.676 63.158 0.00 0.00 38.13 5.34
287 288 2.739932 GCATGCTAACTCTGTCGTGGAT 60.740 50.000 11.37 0.00 0.00 3.41
320 321 4.024670 GACTCCTACCCGGATGCTTATAT 58.975 47.826 0.73 0.00 42.12 0.86
357 358 2.289444 CGGCCAGAGAGAAAACCAACTA 60.289 50.000 2.24 0.00 0.00 2.24
400 401 2.076100 TCGTCATTCACTGTTCCATGC 58.924 47.619 0.00 0.00 0.00 4.06
402 403 2.485426 CGTCATTCACTGTTCCATGCTT 59.515 45.455 0.00 0.00 0.00 3.91
444 446 4.111016 CGCCAGCCATGTGCACAG 62.111 66.667 25.84 13.66 44.83 3.66
446 448 2.675423 CCAGCCATGTGCACAGCT 60.675 61.111 25.84 24.64 44.83 4.24
447 449 2.566529 CAGCCATGTGCACAGCTG 59.433 61.111 33.41 33.41 45.92 4.24
465 467 1.743252 GAACGGGAGAGCAAGCCTG 60.743 63.158 0.00 0.00 36.60 4.85
472 474 1.377536 GAGAGCAAGCCTGTGGAATC 58.622 55.000 0.00 0.00 0.00 2.52
505 507 2.754375 CTGCACCGGGTTAAGGGT 59.246 61.111 6.32 0.00 36.87 4.34
533 535 1.537814 TTTTAGGGAGCGTCTCGGCA 61.538 55.000 0.00 0.00 34.64 5.69
559 561 1.007038 TCCCGGTTCGTTCTTGTCG 60.007 57.895 0.00 0.00 0.00 4.35
595 597 4.116961 CAACTACTTTTCTGACACCGACA 58.883 43.478 0.00 0.00 0.00 4.35
682 686 1.559682 AGTCACTGGCGGGTATGATTT 59.440 47.619 0.00 0.00 0.00 2.17
685 689 1.670811 CACTGGCGGGTATGATTTGTC 59.329 52.381 0.00 0.00 0.00 3.18
694 698 3.490348 GGTATGATTTGTCCATCCCCTG 58.510 50.000 0.00 0.00 0.00 4.45
700 704 4.044065 TGATTTGTCCATCCCCTGTTTACT 59.956 41.667 0.00 0.00 0.00 2.24
702 706 3.433306 TGTCCATCCCCTGTTTACTTG 57.567 47.619 0.00 0.00 0.00 3.16
712 716 2.228822 CCTGTTTACTTGGTCATGTGCC 59.771 50.000 0.00 0.00 0.00 5.01
714 718 2.158534 TGTTTACTTGGTCATGTGCCCT 60.159 45.455 6.61 0.00 0.00 5.19
721 725 0.392998 GGTCATGTGCCCTGGTGTAG 60.393 60.000 0.00 0.00 0.00 2.74
782 786 3.190535 GGGCTCACATGTTTATGTTTCGT 59.809 43.478 0.00 0.00 45.01 3.85
800 804 6.597672 TGTTTCGTTATGAGCTTCATACCAAT 59.402 34.615 5.65 0.00 38.92 3.16
805 809 7.967854 TCGTTATGAGCTTCATACCAATTTTTG 59.032 33.333 5.65 0.00 38.92 2.44
838 843 6.930731 TGATTTACTTTGGGATTAAAGTGCC 58.069 36.000 12.65 0.00 46.98 5.01
850 855 7.125507 TGGGATTAAAGTGCCAACATATTCAAT 59.874 33.333 0.00 0.00 36.59 2.57
1044 1049 0.944311 CTTCTTCACCGACCACACCG 60.944 60.000 0.00 0.00 0.00 4.94
1748 1756 1.048724 CCAAGTATCTCAGCGGGGGA 61.049 60.000 0.00 0.00 0.00 4.81
1758 1767 4.176752 GCGGGGGAAGAGCGGAAT 62.177 66.667 0.00 0.00 0.00 3.01
1808 1817 5.963594 GGTACGAGTTGTATCCTTTCTTCT 58.036 41.667 0.00 0.00 35.02 2.85
1809 1818 6.035217 GGTACGAGTTGTATCCTTTCTTCTC 58.965 44.000 0.00 0.00 35.02 2.87
1810 1819 5.723672 ACGAGTTGTATCCTTTCTTCTCA 57.276 39.130 0.00 0.00 0.00 3.27
1811 1820 5.715070 ACGAGTTGTATCCTTTCTTCTCAG 58.285 41.667 0.00 0.00 0.00 3.35
1812 1821 5.477291 ACGAGTTGTATCCTTTCTTCTCAGA 59.523 40.000 0.00 0.00 0.00 3.27
1813 1822 5.802956 CGAGTTGTATCCTTTCTTCTCAGAC 59.197 44.000 0.00 0.00 0.00 3.51
1814 1823 6.570571 CGAGTTGTATCCTTTCTTCTCAGACA 60.571 42.308 0.00 0.00 0.00 3.41
1815 1824 6.696411 AGTTGTATCCTTTCTTCTCAGACAG 58.304 40.000 0.00 0.00 0.00 3.51
1816 1825 5.078411 TGTATCCTTTCTTCTCAGACAGC 57.922 43.478 0.00 0.00 0.00 4.40
1817 1826 4.774726 TGTATCCTTTCTTCTCAGACAGCT 59.225 41.667 0.00 0.00 0.00 4.24
1818 1827 3.674528 TCCTTTCTTCTCAGACAGCTG 57.325 47.619 13.48 13.48 43.67 4.24
1819 1828 2.301296 TCCTTTCTTCTCAGACAGCTGG 59.699 50.000 19.93 0.00 42.53 4.85
1820 1829 2.075338 CTTTCTTCTCAGACAGCTGGC 58.925 52.381 19.93 16.91 42.53 4.85
1821 1830 0.322975 TTCTTCTCAGACAGCTGGCC 59.677 55.000 18.28 8.21 42.53 5.36
1822 1831 1.078567 CTTCTCAGACAGCTGGCCC 60.079 63.158 18.28 5.36 42.53 5.80
1839 1848 1.106944 CCCCGCATAAAAATCGCCCT 61.107 55.000 0.00 0.00 0.00 5.19
1846 1855 3.808728 CATAAAAATCGCCCTCTGGAGA 58.191 45.455 0.00 0.00 45.10 3.71
1885 1898 3.223589 GCTGGGGCGGTTTTGTGT 61.224 61.111 0.00 0.00 0.00 3.72
1915 1930 0.684153 CCCCAGGCATCGAAATTGGT 60.684 55.000 0.00 0.00 0.00 3.67
1928 1943 5.841810 TCGAAATTGGTTCATTTTTCAGCT 58.158 33.333 0.00 0.00 35.83 4.24
1970 1985 3.272574 CCATATGGGCGAGAATATGCT 57.727 47.619 14.52 0.00 36.05 3.79
1988 2003 1.859080 GCTCATATTCGACGTGGTTCC 59.141 52.381 0.00 0.00 0.00 3.62
1995 2010 4.309950 GACGTGGTTCCCCGTGCT 62.310 66.667 3.90 0.00 37.44 4.40
1996 2011 4.619227 ACGTGGTTCCCCGTGCTG 62.619 66.667 0.00 0.00 35.69 4.41
2008 2025 1.393539 CCCGTGCTGACGTTCAATTAG 59.606 52.381 0.00 0.00 44.54 1.73
2017 2034 6.128035 TGCTGACGTTCAATTAGCAATGTAAT 60.128 34.615 0.00 0.00 40.99 1.89
2172 2190 0.400525 CCCCCTTGAGCCTCCATAGA 60.401 60.000 0.00 0.00 0.00 1.98
2220 2238 3.612247 ATGCACCTGTGGGTCTCGC 62.612 63.158 0.00 0.00 45.41 5.03
2254 2272 2.836636 ACTGAGATAGGCAGTCCAGA 57.163 50.000 0.00 0.00 42.62 3.86
2257 2275 4.809193 ACTGAGATAGGCAGTCCAGATTA 58.191 43.478 0.00 0.00 42.62 1.75
2281 2299 1.661112 GTAGCTGGTGATCAACTTCGC 59.339 52.381 12.94 11.70 0.00 4.70
2349 2367 1.406898 TCTTGCTCGCTCTCGATGATT 59.593 47.619 0.00 0.00 44.56 2.57
2377 2395 1.136141 GCAAGATGACACAGCAAGTCG 60.136 52.381 0.00 0.00 38.83 4.18
2683 2730 0.249120 TGTGAGTTCCTGGCATACCG 59.751 55.000 0.00 0.00 39.70 4.02
3129 3189 6.176183 GGAATTCACAATTCTGAGGAAGAGA 58.824 40.000 7.93 0.00 45.17 3.10
3213 3275 1.186200 AGTCGGAGTAGAGCATGCAA 58.814 50.000 21.98 1.32 0.00 4.08
3214 3276 1.134965 AGTCGGAGTAGAGCATGCAAC 60.135 52.381 21.98 14.61 0.00 4.17
3330 3398 1.144716 GGCGAGCACCATCAGATGA 59.855 57.895 12.41 0.00 0.00 2.92
3656 3742 1.004200 GGAAAGCGAGTCGGGGAAA 60.004 57.895 15.52 0.00 0.00 3.13
3960 4067 0.888736 CACCAGTGGACATTTCGCCA 60.889 55.000 18.40 0.00 0.00 5.69
3989 4096 1.228003 TGGACATTTCACCGCCGTT 60.228 52.632 0.00 0.00 0.00 4.44
4112 4226 5.261209 TGGTGTTTGTCAAATTTCCTCAG 57.739 39.130 0.40 0.00 0.00 3.35
4247 4445 7.824779 ACAAAACTGGATAAGATACTGAAGGTC 59.175 37.037 0.00 0.00 0.00 3.85
4302 4506 4.690748 CACTGACGACTGACCAATAAACAT 59.309 41.667 0.00 0.00 0.00 2.71
4881 5085 3.762288 ACTGAATCAGCTGCACAATGAAT 59.238 39.130 9.47 0.00 34.37 2.57
5029 5233 5.756918 TGGTAATTTCATCCGGAATTACCA 58.243 37.500 34.60 34.60 45.18 3.25
5042 5246 4.552767 CGGAATTACCAATCGAGCATGAAC 60.553 45.833 0.00 0.00 38.90 3.18
5043 5247 4.335315 GGAATTACCAATCGAGCATGAACA 59.665 41.667 0.00 0.00 38.79 3.18
5102 5307 4.853924 ATTGTCCGTGCTCTGAAAATTT 57.146 36.364 0.00 0.00 0.00 1.82
5103 5308 4.647424 TTGTCCGTGCTCTGAAAATTTT 57.353 36.364 2.28 2.28 0.00 1.82
5240 5450 9.547753 TGTGATAAGACCAAGAAATATTAGAGC 57.452 33.333 0.00 0.00 0.00 4.09
5433 5643 6.494835 GGAATTGCCAAGGGAATATTGTATCT 59.505 38.462 6.26 0.00 35.12 1.98
5434 5644 7.015584 GGAATTGCCAAGGGAATATTGTATCTT 59.984 37.037 6.26 0.00 35.12 2.40
5511 5721 4.771590 TTTGCTGGATGAGAACATGAAC 57.228 40.909 0.00 0.00 36.82 3.18
5520 5730 6.723515 TGGATGAGAACATGAACCCAAAAATA 59.276 34.615 0.00 0.00 36.82 1.40
5556 5766 1.573108 CAAGGCTGTTAGGAGGAGGA 58.427 55.000 0.00 0.00 0.00 3.71
5828 6041 6.637658 GTGAATCTCCTAAGCGATGTAAGTAC 59.362 42.308 0.00 0.00 0.00 2.73
5830 6043 6.563222 ATCTCCTAAGCGATGTAAGTACTC 57.437 41.667 0.00 0.00 0.00 2.59
5832 6045 3.887716 TCCTAAGCGATGTAAGTACTCCC 59.112 47.826 0.00 0.00 0.00 4.30
5834 6047 4.023021 CCTAAGCGATGTAAGTACTCCCTC 60.023 50.000 0.00 0.00 0.00 4.30
5836 6049 1.001597 GCGATGTAAGTACTCCCTCCG 60.002 57.143 0.00 0.00 0.00 4.63
5837 6050 2.295885 CGATGTAAGTACTCCCTCCGT 58.704 52.381 0.00 0.00 0.00 4.69
5839 6052 2.134789 TGTAAGTACTCCCTCCGTCC 57.865 55.000 0.00 0.00 0.00 4.79
5840 6053 1.341383 TGTAAGTACTCCCTCCGTCCC 60.341 57.143 0.00 0.00 0.00 4.46
5841 6054 1.002069 TAAGTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
5842 6055 0.115745 AAGTACTCCCTCCGTCCCAA 59.884 55.000 0.00 0.00 0.00 4.12
5843 6056 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
5844 6057 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
5845 6058 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
5846 6059 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
5847 6060 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
5848 6061 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
5849 6062 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
5850 6063 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
5851 6064 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
5852 6065 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
5853 6066 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
5854 6067 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
5855 6068 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
5856 6069 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
5857 6070 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
5858 6071 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
5859 6072 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
5860 6073 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
5861 6074 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
5862 6075 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
5863 6076 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
5864 6077 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
5872 6085 8.622157 TCTTGTCTTAGATTTGTCTAGATACGG 58.378 37.037 0.00 0.00 0.00 4.02
5873 6086 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
5874 6087 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
5875 6088 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
5876 6089 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
5877 6090 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
5880 6093 8.410673 AGATTTGTCTAGATACGGATGTATGT 57.589 34.615 0.00 0.00 41.37 2.29
5881 6094 8.516234 AGATTTGTCTAGATACGGATGTATGTC 58.484 37.037 0.00 0.00 41.37 3.06
5882 6095 6.570672 TTGTCTAGATACGGATGTATGTCC 57.429 41.667 0.00 0.00 41.37 4.02
5883 6096 5.008331 TGTCTAGATACGGATGTATGTCCC 58.992 45.833 0.00 0.00 41.37 4.46
5884 6097 5.008331 GTCTAGATACGGATGTATGTCCCA 58.992 45.833 0.00 0.00 41.37 4.37
5885 6098 5.475909 GTCTAGATACGGATGTATGTCCCAA 59.524 44.000 0.00 0.00 41.37 4.12
5886 6099 6.015688 GTCTAGATACGGATGTATGTCCCAAA 60.016 42.308 0.00 0.00 41.37 3.28
5887 6100 5.623956 AGATACGGATGTATGTCCCAAAA 57.376 39.130 0.00 0.00 41.37 2.44
5888 6101 6.187727 AGATACGGATGTATGTCCCAAAAT 57.812 37.500 0.00 0.00 41.37 1.82
5889 6102 6.601332 AGATACGGATGTATGTCCCAAAATT 58.399 36.000 0.00 0.00 41.37 1.82
5890 6103 6.710744 AGATACGGATGTATGTCCCAAAATTC 59.289 38.462 0.00 0.00 41.37 2.17
5891 6104 4.855340 ACGGATGTATGTCCCAAAATTCT 58.145 39.130 0.00 0.00 34.67 2.40
5892 6105 5.261216 ACGGATGTATGTCCCAAAATTCTT 58.739 37.500 0.00 0.00 34.67 2.52
5893 6106 5.125417 ACGGATGTATGTCCCAAAATTCTTG 59.875 40.000 0.00 0.00 34.67 3.02
5894 6107 5.125417 CGGATGTATGTCCCAAAATTCTTGT 59.875 40.000 0.00 0.00 34.67 3.16
5895 6108 6.564328 GGATGTATGTCCCAAAATTCTTGTC 58.436 40.000 0.00 0.00 31.82 3.18
5896 6109 6.378280 GGATGTATGTCCCAAAATTCTTGTCT 59.622 38.462 0.00 0.00 31.82 3.41
5897 6110 7.093771 GGATGTATGTCCCAAAATTCTTGTCTT 60.094 37.037 0.00 0.00 31.82 3.01
5898 6111 8.877864 ATGTATGTCCCAAAATTCTTGTCTTA 57.122 30.769 0.00 0.00 0.00 2.10
5899 6112 8.335532 TGTATGTCCCAAAATTCTTGTCTTAG 57.664 34.615 0.00 0.00 0.00 2.18
5900 6113 8.160765 TGTATGTCCCAAAATTCTTGTCTTAGA 58.839 33.333 0.00 0.00 0.00 2.10
5901 6114 9.178758 GTATGTCCCAAAATTCTTGTCTTAGAT 57.821 33.333 0.00 0.00 0.00 1.98
5902 6115 8.655935 ATGTCCCAAAATTCTTGTCTTAGATT 57.344 30.769 0.00 0.00 0.00 2.40
5903 6116 8.477419 TGTCCCAAAATTCTTGTCTTAGATTT 57.523 30.769 0.00 0.00 0.00 2.17
5904 6117 8.359642 TGTCCCAAAATTCTTGTCTTAGATTTG 58.640 33.333 0.00 0.00 29.84 2.32
5905 6118 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
5906 6119 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
5907 6120 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
5915 6128 8.622157 TCTTGTCTTAGATTTGTCTAGATACGG 58.378 37.037 0.00 0.00 0.00 4.02
5916 6129 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
5917 6130 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
5918 6131 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
5919 6132 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
5920 6133 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
5924 6137 9.516546 AGATTTGTCTAGATACGGATGTATACA 57.483 33.333 8.27 8.27 41.37 2.29
5943 6156 9.516546 TGTATACATCCGTATCTAGACAAATCT 57.483 33.333 0.08 0.00 39.17 2.40
5947 6160 8.693120 ACATCCGTATCTAGACAAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
5948 6161 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
5949 6162 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
5950 6163 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
5951 6164 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
5952 6165 8.622157 CCGTATCTAGACAAATCTAAGACAAGA 58.378 37.037 0.00 0.00 36.98 3.02
5960 6173 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
5961 6174 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
5962 6175 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
5963 6176 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
5964 6177 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
5965 6178 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
5966 6179 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
5967 6180 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
5968 6181 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
5969 6182 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
5970 6183 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
5971 6184 0.323451 AATTTTGGGACGGAGGGAGC 60.323 55.000 0.00 0.00 0.00 4.70
6053 6266 3.909995 TGCCAGGTATATAACTGCTGGAT 59.090 43.478 20.56 0.00 38.94 3.41
6098 6311 6.500684 AGTTGACAAATCGCTCAATGTATT 57.499 33.333 0.00 0.00 0.00 1.89
6099 6312 6.913170 AGTTGACAAATCGCTCAATGTATTT 58.087 32.000 0.00 0.00 0.00 1.40
6100 6313 8.039603 AGTTGACAAATCGCTCAATGTATTTA 57.960 30.769 0.00 0.00 0.00 1.40
6101 6314 7.962918 AGTTGACAAATCGCTCAATGTATTTAC 59.037 33.333 0.00 0.00 0.00 2.01
6102 6315 6.781138 TGACAAATCGCTCAATGTATTTACC 58.219 36.000 0.00 0.00 0.00 2.85
6103 6316 6.597672 TGACAAATCGCTCAATGTATTTACCT 59.402 34.615 0.00 0.00 0.00 3.08
6104 6317 7.120579 TGACAAATCGCTCAATGTATTTACCTT 59.879 33.333 0.00 0.00 0.00 3.50
6105 6318 8.500753 ACAAATCGCTCAATGTATTTACCTTA 57.499 30.769 0.00 0.00 0.00 2.69
6106 6319 9.120538 ACAAATCGCTCAATGTATTTACCTTAT 57.879 29.630 0.00 0.00 0.00 1.73
6127 6340 8.451908 CTTATAAAGGATGAAGGGGTTGTTAG 57.548 38.462 0.00 0.00 0.00 2.34
6128 6341 4.741928 AAAGGATGAAGGGGTTGTTAGT 57.258 40.909 0.00 0.00 0.00 2.24
6129 6342 4.302559 AAGGATGAAGGGGTTGTTAGTC 57.697 45.455 0.00 0.00 0.00 2.59
6130 6343 3.256704 AGGATGAAGGGGTTGTTAGTCA 58.743 45.455 0.00 0.00 0.00 3.41
6131 6344 3.009143 AGGATGAAGGGGTTGTTAGTCAC 59.991 47.826 0.00 0.00 0.00 3.67
6132 6345 2.536761 TGAAGGGGTTGTTAGTCACG 57.463 50.000 0.00 0.00 0.00 4.35
6133 6346 2.040939 TGAAGGGGTTGTTAGTCACGA 58.959 47.619 0.00 0.00 0.00 4.35
6134 6347 2.224113 TGAAGGGGTTGTTAGTCACGAC 60.224 50.000 0.00 0.00 38.94 4.34
6139 6352 2.943843 GTTGTTAGTCACGACCAAGC 57.056 50.000 0.00 0.00 33.94 4.01
6140 6353 1.529865 GTTGTTAGTCACGACCAAGCC 59.470 52.381 0.00 0.00 33.94 4.35
6141 6354 0.753867 TGTTAGTCACGACCAAGCCA 59.246 50.000 0.00 0.00 0.00 4.75
6142 6355 1.346395 TGTTAGTCACGACCAAGCCAT 59.654 47.619 0.00 0.00 0.00 4.40
6143 6356 2.000447 GTTAGTCACGACCAAGCCATC 59.000 52.381 0.00 0.00 0.00 3.51
6144 6357 0.535335 TAGTCACGACCAAGCCATCC 59.465 55.000 0.00 0.00 0.00 3.51
6145 6358 1.003839 GTCACGACCAAGCCATCCA 60.004 57.895 0.00 0.00 0.00 3.41
6146 6359 1.003839 TCACGACCAAGCCATCCAC 60.004 57.895 0.00 0.00 0.00 4.02
6147 6360 2.047274 ACGACCAAGCCATCCACG 60.047 61.111 0.00 0.00 0.00 4.94
6148 6361 2.047274 CGACCAAGCCATCCACGT 60.047 61.111 0.00 0.00 0.00 4.49
6149 6362 2.100631 CGACCAAGCCATCCACGTC 61.101 63.158 0.00 0.00 0.00 4.34
6150 6363 2.047274 ACCAAGCCATCCACGTCG 60.047 61.111 0.00 0.00 0.00 5.12
6151 6364 2.819595 CCAAGCCATCCACGTCGG 60.820 66.667 0.00 0.00 0.00 4.79
6152 6365 3.499737 CAAGCCATCCACGTCGGC 61.500 66.667 6.70 6.70 46.62 5.54
6155 6368 2.421739 GCCATCCACGTCGGCTAT 59.578 61.111 7.40 0.00 42.78 2.97
6156 6369 1.956170 GCCATCCACGTCGGCTATG 60.956 63.158 7.40 4.04 42.78 2.23
6157 6370 1.739667 CCATCCACGTCGGCTATGA 59.260 57.895 0.00 0.00 33.14 2.15
6158 6371 0.319040 CCATCCACGTCGGCTATGAG 60.319 60.000 0.00 0.00 33.14 2.90
6159 6372 0.941463 CATCCACGTCGGCTATGAGC 60.941 60.000 0.00 0.00 41.46 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.615850 ACTGCACTTCCTAAGCTCCC 59.384 55.000 0.00 0.00 0.00 4.30
67 68 0.708370 CTCATCCACGAAACACGACG 59.292 55.000 0.00 0.00 45.77 5.12
81 82 2.970576 GAGTTCAGCTCGGCTCATC 58.029 57.895 0.00 0.00 36.40 2.92
91 92 1.661460 GCGCAGAAGTTTGAGTTCAGC 60.661 52.381 0.30 3.62 36.90 4.26
118 119 2.749076 TGAACCATTTCTGATCGGCAAG 59.251 45.455 0.00 0.00 32.36 4.01
171 172 5.009010 GTCCATTGTCTCGAATAATGGCATT 59.991 40.000 18.01 18.01 46.56 3.56
184 185 0.179081 GTAGCCGGGTCCATTGTCTC 60.179 60.000 10.79 0.00 0.00 3.36
190 191 4.157120 GCGTGTAGCCGGGTCCAT 62.157 66.667 10.79 0.00 40.81 3.41
207 208 3.877508 GGGTAGGTTCAAATCTGAATCGG 59.122 47.826 0.00 0.00 45.82 4.18
208 209 3.555956 CGGGTAGGTTCAAATCTGAATCG 59.444 47.826 0.00 0.00 45.82 3.34
214 215 2.354805 GCAGTCGGGTAGGTTCAAATCT 60.355 50.000 0.00 0.00 0.00 2.40
263 264 2.069273 ACGACAGAGTTAGCATGCAAC 58.931 47.619 21.98 20.23 0.00 4.17
264 265 2.068519 CACGACAGAGTTAGCATGCAA 58.931 47.619 21.98 9.44 0.00 4.08
287 288 2.508300 GGGTAGGAGTCATGGGCTAAAA 59.492 50.000 0.00 0.00 0.00 1.52
320 321 1.741327 GCCGACCAACGCCTCCTATA 61.741 60.000 0.00 0.00 41.07 1.31
341 342 6.273495 AGGAGGAATTAGTTGGTTTTCTCTCT 59.727 38.462 0.00 0.00 0.00 3.10
357 358 1.218316 GGTCGTGCGAGGAGGAATT 59.782 57.895 0.00 0.00 0.00 2.17
400 401 1.135315 CCGTCGGATGCAGCAAAAG 59.865 57.895 4.91 0.00 0.00 2.27
402 403 2.031919 ACCGTCGGATGCAGCAAA 59.968 55.556 20.51 0.00 0.00 3.68
410 412 2.842936 GGGATGGGACCGTCGGAT 60.843 66.667 20.51 0.00 33.03 4.18
444 446 2.394563 GCTTGCTCTCCCGTTCAGC 61.395 63.158 0.00 0.00 0.00 4.26
446 448 2.217038 AGGCTTGCTCTCCCGTTCA 61.217 57.895 0.00 0.00 0.00 3.18
447 449 1.743252 CAGGCTTGCTCTCCCGTTC 60.743 63.158 0.00 0.00 0.00 3.95
465 467 1.278127 TCTCAAAGGACGGGATTCCAC 59.722 52.381 4.80 0.00 38.25 4.02
472 474 0.462759 GCAGGATCTCAAAGGACGGG 60.463 60.000 0.00 0.00 0.00 5.28
505 507 4.222145 AGACGCTCCCTAAAAACACTATCA 59.778 41.667 0.00 0.00 0.00 2.15
533 535 4.052229 CGAACCGGGAGCAGTCGT 62.052 66.667 6.32 0.00 0.00 4.34
542 544 1.280206 GACGACAAGAACGAACCGGG 61.280 60.000 6.32 0.00 34.70 5.73
559 561 7.821846 AGAAAAGTAGTTGAATCTGAGGATGAC 59.178 37.037 0.00 0.00 31.75 3.06
595 597 0.865769 GCGACGTCTTCAACCATTGT 59.134 50.000 14.70 0.00 0.00 2.71
664 667 1.280710 ACAAATCATACCCGCCAGTGA 59.719 47.619 0.00 0.00 0.00 3.41
671 675 2.504367 GGGATGGACAAATCATACCCG 58.496 52.381 0.00 0.00 39.21 5.28
682 686 2.041081 CCAAGTAAACAGGGGATGGACA 59.959 50.000 0.00 0.00 0.00 4.02
685 689 2.041081 TGACCAAGTAAACAGGGGATGG 59.959 50.000 0.00 0.00 0.00 3.51
702 706 0.392998 CTACACCAGGGCACATGACC 60.393 60.000 0.00 0.00 46.16 4.02
712 716 5.705441 ACATTTATGAACACACTACACCAGG 59.295 40.000 0.00 0.00 0.00 4.45
714 718 7.283354 TGAAACATTTATGAACACACTACACCA 59.717 33.333 0.00 0.00 0.00 4.17
759 763 3.727673 CGAAACATAAACATGTGAGCCCG 60.728 47.826 0.00 0.00 34.56 6.13
782 786 7.609960 TGCAAAAATTGGTATGAAGCTCATAA 58.390 30.769 7.24 0.00 40.64 1.90
800 804 8.719648 CCAAAGTAAATCATAAGCATGCAAAAA 58.280 29.630 21.98 1.80 31.73 1.94
805 809 6.147864 TCCCAAAGTAAATCATAAGCATGC 57.852 37.500 10.51 10.51 31.73 4.06
850 855 6.367969 GTGTCAAGCTCGAGGATTTTTAACTA 59.632 38.462 15.58 0.00 0.00 2.24
859 864 0.820871 GGAGTGTCAAGCTCGAGGAT 59.179 55.000 15.58 0.00 34.00 3.24
1524 1532 1.879430 CGTTGTCGAACACCACCGT 60.879 57.895 0.00 0.00 39.71 4.83
1748 1756 1.273327 CCAAAAAGCCATTCCGCTCTT 59.727 47.619 0.00 0.00 38.44 2.85
1758 1767 0.817013 GCATCGGATCCAAAAAGCCA 59.183 50.000 13.41 0.00 0.00 4.75
1806 1815 3.005539 GGGGCCAGCTGTCTGAGA 61.006 66.667 13.81 0.00 42.95 3.27
1807 1816 4.463879 CGGGGCCAGCTGTCTGAG 62.464 72.222 13.81 0.00 42.95 3.35
1811 1820 3.697439 TTATGCGGGGCCAGCTGTC 62.697 63.158 28.43 0.00 35.28 3.51
1812 1821 2.779742 TTTTATGCGGGGCCAGCTGT 62.780 55.000 28.43 19.08 35.28 4.40
1813 1822 1.603236 TTTTTATGCGGGGCCAGCTG 61.603 55.000 28.43 6.78 35.28 4.24
1814 1823 0.687427 ATTTTTATGCGGGGCCAGCT 60.687 50.000 28.43 16.44 35.28 4.24
1815 1824 0.249447 GATTTTTATGCGGGGCCAGC 60.249 55.000 22.43 22.43 0.00 4.85
1816 1825 0.030638 CGATTTTTATGCGGGGCCAG 59.969 55.000 4.39 1.12 0.00 4.85
1817 1826 2.010582 GCGATTTTTATGCGGGGCCA 62.011 55.000 4.39 0.00 0.00 5.36
1818 1827 1.299850 GCGATTTTTATGCGGGGCC 60.300 57.895 0.00 0.00 0.00 5.80
1819 1828 1.299850 GGCGATTTTTATGCGGGGC 60.300 57.895 0.00 0.00 0.00 5.80
1820 1829 1.106944 AGGGCGATTTTTATGCGGGG 61.107 55.000 0.00 0.00 0.00 5.73
1821 1830 0.310854 GAGGGCGATTTTTATGCGGG 59.689 55.000 0.00 0.00 0.00 6.13
1822 1831 1.002468 CAGAGGGCGATTTTTATGCGG 60.002 52.381 0.00 0.00 0.00 5.69
1839 1848 3.531207 CGCCGGCTCATCTCCAGA 61.531 66.667 26.68 0.00 0.00 3.86
1846 1855 4.838152 ATTGCGTCGCCGGCTCAT 62.838 61.111 26.68 3.94 33.68 2.90
1905 1920 5.841810 AGCTGAAAAATGAACCAATTTCGA 58.158 33.333 0.00 0.00 36.97 3.71
1915 1930 4.808558 CCGAAATGGAGCTGAAAAATGAA 58.191 39.130 0.00 0.00 42.00 2.57
1928 1943 2.294074 CCCTTTATTCGCCGAAATGGA 58.706 47.619 2.60 0.00 42.00 3.41
1967 1982 2.536365 GAACCACGTCGAATATGAGCA 58.464 47.619 0.00 0.00 0.00 4.26
1994 2009 8.673626 AAATTACATTGCTAATTGAACGTCAG 57.326 30.769 0.00 0.00 0.00 3.51
1995 2010 9.469807 AAAAATTACATTGCTAATTGAACGTCA 57.530 25.926 0.00 0.00 0.00 4.35
2123 2141 2.347568 CGCGACGTGTGATGAAATATGG 60.348 50.000 0.00 0.00 0.00 2.74
2220 2238 2.620585 TCTCAGTATGCGTCAGGAGATG 59.379 50.000 0.00 0.00 34.76 2.90
2254 2272 2.394632 TGATCACCAGCTACCGGTAAT 58.605 47.619 16.65 3.94 34.02 1.89
2257 2275 0.249398 GTTGATCACCAGCTACCGGT 59.751 55.000 13.98 13.98 37.16 5.28
2281 2299 0.261991 TACAGGCAGGGTCCTCTAGG 59.738 60.000 0.00 0.00 33.25 3.02
2349 2367 3.189080 GCTGTGTCATCTTGCACAACATA 59.811 43.478 0.00 0.00 43.81 2.29
2377 2395 6.538742 TCGAAAGATCAAATGTGGGAGATTAC 59.461 38.462 0.00 0.00 33.31 1.89
2459 2477 1.379977 AGGAAGGATGTCGAGCGGA 60.380 57.895 0.00 0.00 0.00 5.54
2576 2594 5.774179 ACAACAAGGGGTACTATCTAGCTA 58.226 41.667 0.00 0.00 0.00 3.32
2683 2730 2.751806 CTGGATTTGGCACTCCTTCTTC 59.248 50.000 14.52 0.00 32.47 2.87
2856 2914 2.049063 GCGGAAGACACTGCTCGT 60.049 61.111 0.00 0.00 38.89 4.18
3129 3189 2.800544 CCGTTATCGAATGAGCCGAAAT 59.199 45.455 0.00 0.00 39.62 2.17
3213 3275 1.153745 GCATCGTCTCGAAGGCTGT 60.154 57.895 10.30 0.00 39.99 4.40
3214 3276 1.880340 GGCATCGTCTCGAAGGCTG 60.880 63.158 12.15 1.06 44.35 4.85
3330 3398 0.818296 CCGACGTCCAGGAAGAAGAT 59.182 55.000 10.58 0.00 0.00 2.40
3411 3483 3.409959 ATTTCGCCGATTTGCCCGC 62.410 57.895 0.00 0.00 0.00 6.13
3412 3484 1.298339 GATTTCGCCGATTTGCCCG 60.298 57.895 0.00 0.00 0.00 6.13
3424 3496 1.202031 GCAAGGTGTTAGGCGATTTCG 60.202 52.381 0.00 0.00 43.27 3.46
3425 3497 2.544480 GCAAGGTGTTAGGCGATTTC 57.456 50.000 0.00 0.00 0.00 2.17
3509 3585 2.752358 CCTCCAACAGCAGCTGGA 59.248 61.111 26.38 14.05 37.67 3.86
3656 3742 6.183360 CCCTCAGGTGAAAAGTCAAGATTTTT 60.183 38.462 3.38 3.38 34.87 1.94
3841 3939 4.529731 GCCCCCTCCAGGCCATTC 62.530 72.222 5.01 0.00 45.16 2.67
3879 3986 2.268167 GAGGGCTGCCTGAGAGCATT 62.268 60.000 19.68 0.00 43.09 3.56
3989 4096 8.682710 GTGCCATGTTATTACCTCTTTTATTCA 58.317 33.333 0.00 0.00 0.00 2.57
4112 4226 3.512680 GAGTAGCATGTGGACTGTGTAC 58.487 50.000 0.00 0.00 0.00 2.90
4247 4445 1.660052 CGGTCAAGTGTGCATTGTTCG 60.660 52.381 0.00 0.00 0.00 3.95
4351 4555 6.761312 TGTGATTCCGTCCTAAGACTTTTTA 58.239 36.000 0.00 0.00 41.16 1.52
4809 5013 1.884579 CACTGCCACTTCTTGCTCATT 59.115 47.619 0.00 0.00 0.00 2.57
4881 5085 1.067516 GAGCTGAGCCAAAACTTGCAA 59.932 47.619 0.00 0.00 0.00 4.08
5029 5233 3.896648 AAAACGTGTTCATGCTCGATT 57.103 38.095 0.00 0.00 0.00 3.34
5042 5246 7.906010 TGACAAGTTAGTTATGACAAAAACGTG 59.094 33.333 11.60 11.60 34.34 4.49
5043 5247 7.976826 TGACAAGTTAGTTATGACAAAAACGT 58.023 30.769 0.00 0.00 0.00 3.99
5114 5319 9.420118 TCCTTATGCACATTACAAATTATTCCT 57.580 29.630 0.00 0.00 0.00 3.36
5138 5348 8.693542 AGATTCGAAATCAACAAATTCATTCC 57.306 30.769 0.00 0.00 0.00 3.01
5240 5450 9.961265 AATGATGATGATGCACTTAAAATACAG 57.039 29.630 0.00 0.00 0.00 2.74
5433 5643 6.398095 TCTTATGCTCGAGTCTTCATGAAAA 58.602 36.000 15.13 0.00 0.00 2.29
5434 5644 5.965922 TCTTATGCTCGAGTCTTCATGAAA 58.034 37.500 15.13 0.79 0.00 2.69
5511 5721 2.423538 CCCGAAGTCTGCTATTTTTGGG 59.576 50.000 3.53 3.53 37.77 4.12
5520 5730 2.032681 GCCAACCCGAAGTCTGCT 59.967 61.111 0.00 0.00 0.00 4.24
5556 5766 3.169099 AGCTGTCTTGGTCTGAGTATGT 58.831 45.455 0.00 0.00 0.00 2.29
5590 5800 6.595716 AGTCAATCTGTTTCCACTTACTATGC 59.404 38.462 0.00 0.00 0.00 3.14
5828 6041 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
5830 6043 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
5832 6045 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
5834 6047 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
5836 6049 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
5837 6050 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
5846 6059 8.622157 CCGTATCTAGACAAATCTAAGACAAGA 58.378 37.037 0.00 0.00 36.98 3.02
5847 6060 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
5848 6061 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
5849 6062 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
5850 6063 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
5851 6064 8.693120 ACATCCGTATCTAGACAAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
5854 6067 9.516546 ACATACATCCGTATCTAGACAAATCTA 57.483 33.333 0.00 0.00 36.11 1.98
5855 6068 8.410673 ACATACATCCGTATCTAGACAAATCT 57.589 34.615 0.00 0.00 36.11 2.40
5856 6069 7.755822 GGACATACATCCGTATCTAGACAAATC 59.244 40.741 0.00 0.00 36.11 2.17
5857 6070 7.309867 GGGACATACATCCGTATCTAGACAAAT 60.310 40.741 0.00 0.00 39.97 2.32
5858 6071 6.015688 GGGACATACATCCGTATCTAGACAAA 60.016 42.308 0.00 0.00 39.97 2.83
5859 6072 5.475909 GGGACATACATCCGTATCTAGACAA 59.524 44.000 0.00 0.00 39.97 3.18
5860 6073 5.008331 GGGACATACATCCGTATCTAGACA 58.992 45.833 0.00 0.00 39.97 3.41
5861 6074 5.008331 TGGGACATACATCCGTATCTAGAC 58.992 45.833 0.00 0.00 39.97 2.59
5862 6075 5.251182 TGGGACATACATCCGTATCTAGA 57.749 43.478 0.00 0.00 39.97 2.43
5863 6076 5.977489 TTGGGACATACATCCGTATCTAG 57.023 43.478 0.00 0.00 39.97 2.43
5864 6077 6.734502 TTTTGGGACATACATCCGTATCTA 57.265 37.500 0.00 0.00 39.97 1.98
5865 6078 5.623956 TTTTGGGACATACATCCGTATCT 57.376 39.130 0.00 0.00 39.97 1.98
5866 6079 6.710744 AGAATTTTGGGACATACATCCGTATC 59.289 38.462 0.00 0.00 39.97 2.24
5867 6080 6.601332 AGAATTTTGGGACATACATCCGTAT 58.399 36.000 0.00 0.00 39.97 3.06
5868 6081 5.996644 AGAATTTTGGGACATACATCCGTA 58.003 37.500 0.00 0.00 39.97 4.02
5869 6082 4.855340 AGAATTTTGGGACATACATCCGT 58.145 39.130 0.00 0.00 39.97 4.69
5870 6083 5.125417 ACAAGAATTTTGGGACATACATCCG 59.875 40.000 5.68 0.00 39.97 4.18
5871 6084 6.378280 AGACAAGAATTTTGGGACATACATCC 59.622 38.462 5.68 0.00 39.30 3.51
5872 6085 7.396540 AGACAAGAATTTTGGGACATACATC 57.603 36.000 5.68 0.00 39.30 3.06
5873 6086 7.781324 AAGACAAGAATTTTGGGACATACAT 57.219 32.000 5.68 0.00 39.30 2.29
5874 6087 8.160765 TCTAAGACAAGAATTTTGGGACATACA 58.839 33.333 5.68 0.00 39.30 2.29
5875 6088 8.561738 TCTAAGACAAGAATTTTGGGACATAC 57.438 34.615 5.68 0.00 39.30 2.39
5876 6089 9.753674 AATCTAAGACAAGAATTTTGGGACATA 57.246 29.630 5.68 0.00 39.30 2.29
5877 6090 8.655935 AATCTAAGACAAGAATTTTGGGACAT 57.344 30.769 5.68 0.00 39.30 3.06
5878 6091 8.359642 CAAATCTAAGACAAGAATTTTGGGACA 58.640 33.333 5.68 0.00 28.49 4.02
5879 6092 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
5880 6093 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
5881 6094 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
5889 6102 8.622157 CCGTATCTAGACAAATCTAAGACAAGA 58.378 37.037 0.00 0.00 36.98 3.02
5890 6103 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
5891 6104 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
5892 6105 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
5893 6106 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
5894 6107 8.693120 ACATCCGTATCTAGACAAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
5898 6111 9.516546 TGTATACATCCGTATCTAGACAAATCT 57.483 33.333 0.08 0.00 39.17 2.40
5917 6130 9.516546 AGATTTGTCTAGATACGGATGTATACA 57.483 33.333 8.27 8.27 41.37 2.29
5921 6134 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
5922 6135 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
5923 6136 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
5924 6137 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
5925 6138 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
5926 6139 8.622157 TCTTGTCTTAGATTTGTCTAGATACGG 58.378 37.037 0.00 0.00 0.00 4.02
5934 6147 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
5935 6148 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
5936 6149 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
5937 6150 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
5938 6151 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
5939 6152 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
5940 6153 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
5941 6154 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
5942 6155 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
5943 6156 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
5944 6157 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
5945 6158 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
5946 6159 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
5947 6160 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
5948 6161 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
5949 6162 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
5950 6163 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
5951 6164 1.751437 CTCCCTCCGTCCCAAAATTC 58.249 55.000 0.00 0.00 0.00 2.17
5952 6165 0.323451 GCTCCCTCCGTCCCAAAATT 60.323 55.000 0.00 0.00 0.00 1.82
5953 6166 1.303282 GCTCCCTCCGTCCCAAAAT 59.697 57.895 0.00 0.00 0.00 1.82
5954 6167 2.150719 TGCTCCCTCCGTCCCAAAA 61.151 57.895 0.00 0.00 0.00 2.44
5955 6168 2.528127 TGCTCCCTCCGTCCCAAA 60.528 61.111 0.00 0.00 0.00 3.28
5956 6169 3.319198 GTGCTCCCTCCGTCCCAA 61.319 66.667 0.00 0.00 0.00 4.12
5957 6170 3.846405 AAGTGCTCCCTCCGTCCCA 62.846 63.158 0.00 0.00 0.00 4.37
5958 6171 1.262640 TAAAGTGCTCCCTCCGTCCC 61.263 60.000 0.00 0.00 0.00 4.46
5959 6172 0.831307 ATAAAGTGCTCCCTCCGTCC 59.169 55.000 0.00 0.00 0.00 4.79
5960 6173 2.694109 ACTATAAAGTGCTCCCTCCGTC 59.306 50.000 0.00 0.00 33.57 4.79
5961 6174 2.431057 CACTATAAAGTGCTCCCTCCGT 59.569 50.000 0.00 0.00 46.28 4.69
5962 6175 3.099267 CACTATAAAGTGCTCCCTCCG 57.901 52.381 0.00 0.00 46.28 4.63
6102 6315 8.053355 ACTAACAACCCCTTCATCCTTTATAAG 58.947 37.037 0.00 0.00 0.00 1.73
6103 6316 7.935405 ACTAACAACCCCTTCATCCTTTATAA 58.065 34.615 0.00 0.00 0.00 0.98
6104 6317 7.183112 TGACTAACAACCCCTTCATCCTTTATA 59.817 37.037 0.00 0.00 0.00 0.98
6105 6318 6.011981 TGACTAACAACCCCTTCATCCTTTAT 60.012 38.462 0.00 0.00 0.00 1.40
6106 6319 5.311121 TGACTAACAACCCCTTCATCCTTTA 59.689 40.000 0.00 0.00 0.00 1.85
6107 6320 4.105697 TGACTAACAACCCCTTCATCCTTT 59.894 41.667 0.00 0.00 0.00 3.11
6108 6321 3.655777 TGACTAACAACCCCTTCATCCTT 59.344 43.478 0.00 0.00 0.00 3.36
6109 6322 3.009143 GTGACTAACAACCCCTTCATCCT 59.991 47.826 0.00 0.00 0.00 3.24
6110 6323 3.344515 GTGACTAACAACCCCTTCATCC 58.655 50.000 0.00 0.00 0.00 3.51
6111 6324 3.000727 CGTGACTAACAACCCCTTCATC 58.999 50.000 0.00 0.00 0.00 2.92
6112 6325 2.635915 TCGTGACTAACAACCCCTTCAT 59.364 45.455 0.00 0.00 0.00 2.57
6113 6326 2.040939 TCGTGACTAACAACCCCTTCA 58.959 47.619 0.00 0.00 0.00 3.02
6114 6327 2.410939 GTCGTGACTAACAACCCCTTC 58.589 52.381 0.00 0.00 0.00 3.46
6115 6328 1.071228 GGTCGTGACTAACAACCCCTT 59.929 52.381 0.00 0.00 0.00 3.95
6116 6329 0.683412 GGTCGTGACTAACAACCCCT 59.317 55.000 0.00 0.00 0.00 4.79
6117 6330 0.393820 TGGTCGTGACTAACAACCCC 59.606 55.000 0.00 0.00 30.63 4.95
6118 6331 2.140717 CTTGGTCGTGACTAACAACCC 58.859 52.381 0.00 0.00 30.63 4.11
6119 6332 1.529865 GCTTGGTCGTGACTAACAACC 59.470 52.381 0.00 0.00 31.91 3.77
6120 6333 1.529865 GGCTTGGTCGTGACTAACAAC 59.470 52.381 0.00 0.00 0.00 3.32
6121 6334 1.139256 TGGCTTGGTCGTGACTAACAA 59.861 47.619 0.00 0.00 0.00 2.83
6122 6335 0.753867 TGGCTTGGTCGTGACTAACA 59.246 50.000 0.00 0.00 0.00 2.41
6123 6336 2.000447 GATGGCTTGGTCGTGACTAAC 59.000 52.381 0.00 0.00 0.00 2.34
6124 6337 1.066430 GGATGGCTTGGTCGTGACTAA 60.066 52.381 0.00 0.00 0.00 2.24
6125 6338 0.535335 GGATGGCTTGGTCGTGACTA 59.465 55.000 0.00 0.00 0.00 2.59
6126 6339 1.296715 GGATGGCTTGGTCGTGACT 59.703 57.895 0.00 0.00 0.00 3.41
6127 6340 1.003839 TGGATGGCTTGGTCGTGAC 60.004 57.895 0.00 0.00 0.00 3.67
6128 6341 1.003839 GTGGATGGCTTGGTCGTGA 60.004 57.895 0.00 0.00 0.00 4.35
6129 6342 2.390599 CGTGGATGGCTTGGTCGTG 61.391 63.158 0.00 0.00 0.00 4.35
6130 6343 2.047274 CGTGGATGGCTTGGTCGT 60.047 61.111 0.00 0.00 0.00 4.34
6131 6344 2.047274 ACGTGGATGGCTTGGTCG 60.047 61.111 0.00 0.00 0.00 4.79
6132 6345 2.100631 CGACGTGGATGGCTTGGTC 61.101 63.158 0.00 0.00 0.00 4.02
6133 6346 2.047274 CGACGTGGATGGCTTGGT 60.047 61.111 0.00 0.00 0.00 3.67
6134 6347 2.819595 CCGACGTGGATGGCTTGG 60.820 66.667 0.00 0.00 42.00 3.61
6135 6348 3.499737 GCCGACGTGGATGGCTTG 61.500 66.667 0.00 0.00 45.40 4.01
6139 6352 0.319040 CTCATAGCCGACGTGGATGG 60.319 60.000 0.00 0.00 42.00 3.51
6140 6353 0.941463 GCTCATAGCCGACGTGGATG 60.941 60.000 0.00 0.00 42.00 3.51
6141 6354 1.364171 GCTCATAGCCGACGTGGAT 59.636 57.895 0.00 0.00 42.00 3.41
6142 6355 2.805546 GCTCATAGCCGACGTGGA 59.194 61.111 0.00 0.00 42.00 4.02


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

AutoCloner maintained by Alex Coulton.