Multiple sequence alignment - TraesCS2B01G493100

Loading Multiple Alignment...

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 TraesCS2B01G493100 chr2B 100.000 7816 0 0 1 7816 690942976 690935161 0.000000e+00 14434.0
1 TraesCS2B01G493100 chr2B 92.455 2147 100 19 2693 4808 690938169 690940284 0.000000e+00 3011.0
2 TraesCS2B01G493100 chr2B 100.000 1512 0 0 8228 9739 690934749 690933238 0.000000e+00 2793.0
3 TraesCS2B01G493100 chr2B 98.546 1513 21 1 8228 9739 672018884 672020396 0.000000e+00 2671.0
4 TraesCS2B01G493100 chr2B 91.165 1777 97 30 337 2088 691046803 691048544 0.000000e+00 2357.0
5 TraesCS2B01G493100 chr2B 90.124 1853 124 18 4850 6673 519671693 519669871 0.000000e+00 2353.0
6 TraesCS2B01G493100 chr2B 88.997 1854 150 28 4849 6673 787510400 787512228 0.000000e+00 2244.0
7 TraesCS2B01G493100 chr2B 95.252 1053 36 3 2691 3729 4797018 4798070 0.000000e+00 1655.0
8 TraesCS2B01G493100 chr2B 84.708 1576 196 24 903 2437 691038170 691039741 0.000000e+00 1533.0
9 TraesCS2B01G493100 chr2B 92.462 1048 41 6 3799 4808 4798067 4797020 0.000000e+00 1463.0
10 TraesCS2B01G493100 chr2B 96.115 695 27 0 3035 3729 321311677 321310983 0.000000e+00 1134.0
11 TraesCS2B01G493100 chr2B 86.720 753 73 20 3035 3769 669630705 669629962 0.000000e+00 811.0
12 TraesCS2B01G493100 chr2B 88.358 670 59 14 3113 3769 296480834 296481497 0.000000e+00 787.0
13 TraesCS2B01G493100 chr2B 95.599 409 17 1 4401 4808 72192178 72192586 0.000000e+00 654.0
14 TraesCS2B01G493100 chr2B 94.458 415 22 1 2690 3104 72192589 72192176 1.070000e-178 638.0
15 TraesCS2B01G493100 chr2B 98.701 231 3 0 7586 7816 672018429 672018659 2.530000e-110 411.0
16 TraesCS2B01G493100 chr2B 96.491 228 8 0 7078 7305 672018090 672018317 2.570000e-100 377.0
17 TraesCS2B01G493100 chr2B 93.284 134 8 1 8444 8576 672018983 672019116 7.720000e-46 196.0
18 TraesCS2B01G493100 chr2B 92.537 134 9 1 8327 8460 690934533 690934401 3.590000e-44 191.0
19 TraesCS2B01G493100 chr2B 92.537 134 9 1 8444 8576 690934650 690934517 3.590000e-44 191.0
20 TraesCS2B01G493100 chr2B 95.370 108 4 1 6876 6982 672017589 672017696 4.680000e-38 171.0
21 TraesCS2B01G493100 chr2B 80.874 183 16 11 9559 9739 748324114 748324279 1.030000e-24 126.0
22 TraesCS2B01G493100 chr2B 90.909 88 8 0 9652 9739 748410507 748410594 1.720000e-22 119.0
23 TraesCS2B01G493100 chr2B 96.923 65 2 0 6987 7051 672017814 672017878 1.030000e-19 110.0
24 TraesCS2B01G493100 chr2B 94.286 70 4 0 3760 3829 690939145 690939214 3.720000e-19 108.0
25 TraesCS2B01G493100 chr2A 92.328 2255 103 38 356 2562 713125425 713123193 0.000000e+00 3142.0
26 TraesCS2B01G493100 chr2A 91.540 1643 96 14 474 2086 713189299 713190928 0.000000e+00 2224.0
27 TraesCS2B01G493100 chr2A 92.105 152 9 2 6673 6823 713122957 713122808 2.760000e-50 211.0
28 TraesCS2B01G493100 chr2A 91.781 73 5 1 2581 2653 713123122 713123051 6.220000e-17 100.0
29 TraesCS2B01G493100 chr2A 84.337 83 11 2 6870 6950 241083398 241083480 8.110000e-11 80.5
30 TraesCS2B01G493100 chr2D 91.626 2281 116 43 359 2582 574663463 574661201 0.000000e+00 3085.0
31 TraesCS2B01G493100 chr2D 93.364 1748 93 12 359 2089 575158768 575160509 0.000000e+00 2564.0
32 TraesCS2B01G493100 chr2D 89.771 1662 138 16 4852 6489 52038701 52040354 0.000000e+00 2098.0
33 TraesCS2B01G493100 chr2D 88.661 1658 158 23 4862 6499 107705164 107706811 0.000000e+00 1993.0
34 TraesCS2B01G493100 chr2D 85.154 1199 134 23 1278 2437 574600715 574601908 0.000000e+00 1188.0
35 TraesCS2B01G493100 chr2D 84.641 1224 146 21 1252 2437 574572064 574573283 0.000000e+00 1181.0
36 TraesCS2B01G493100 chr2D 85.899 929 89 21 1547 2437 574597057 574597981 0.000000e+00 952.0
37 TraesCS2B01G493100 chr2D 93.056 216 7 6 6673 6881 574660990 574660776 9.500000e-80 309.0
38 TraesCS2B01G493100 chr2D 93.103 87 6 0 2581 2667 574661163 574661077 2.850000e-25 128.0
39 TraesCS2B01G493100 chr2D 84.043 94 10 2 2022 2114 575167599 575167688 1.740000e-12 86.1
40 TraesCS2B01G493100 chr2D 100.000 39 0 0 4813 4851 574661028 574660990 1.360000e-08 73.1
41 TraesCS2B01G493100 chr3D 97.685 1512 29 3 8228 9739 491172705 491174210 0.000000e+00 2593.0
42 TraesCS2B01G493100 chr3D 97.349 830 22 0 6987 7816 491171653 491172482 0.000000e+00 1411.0
43 TraesCS2B01G493100 chr3D 95.939 197 6 2 1 197 83428548 83428742 1.580000e-82 318.0
44 TraesCS2B01G493100 chr3D 94.975 199 6 4 1 197 282527783 282527587 9.500000e-80 309.0
45 TraesCS2B01G493100 chr3D 82.079 279 19 10 8444 8717 491172804 491173056 9.910000e-50 209.0
46 TraesCS2B01G493100 chr3D 94.030 134 7 1 8327 8460 491172921 491173053 1.660000e-47 202.0
47 TraesCS2B01G493100 chr3D 97.196 107 3 0 6880 6986 491171424 491171530 2.160000e-41 182.0
48 TraesCS2B01G493100 chr4B 89.046 1835 158 26 4852 6664 514036326 514038139 0.000000e+00 2235.0
49 TraesCS2B01G493100 chr4B 93.833 1054 49 3 2691 3729 547266487 547267539 0.000000e+00 1572.0
50 TraesCS2B01G493100 chr4B 87.299 1055 104 26 2690 3729 347894667 347893628 0.000000e+00 1179.0
51 TraesCS2B01G493100 chr4B 90.936 673 57 3 3799 4470 22191483 22192152 0.000000e+00 902.0
52 TraesCS2B01G493100 chr4B 91.616 489 39 2 3036 3524 104108601 104108115 0.000000e+00 675.0
53 TraesCS2B01G493100 chr4B 96.088 409 15 1 4401 4808 510477338 510476930 0.000000e+00 665.0
54 TraesCS2B01G493100 chr4B 94.699 415 21 1 2690 3104 510476927 510477340 2.290000e-180 643.0
55 TraesCS2B01G493100 chr4B 78.199 211 40 5 1558 1765 650599566 650599359 7.940000e-26 130.0
56 TraesCS2B01G493100 chr4B 90.625 64 6 0 6869 6932 544022294 544022357 1.740000e-12 86.1
57 TraesCS2B01G493100 chr4B 100.000 37 0 0 3763 3799 22191513 22191477 1.760000e-07 69.4
58 TraesCS2B01G493100 chr4B 97.500 40 1 0 3760 3799 91349727 91349766 1.760000e-07 69.4
59 TraesCS2B01G493100 chr4B 100.000 37 0 0 3763 3799 347893661 347893625 1.760000e-07 69.4
60 TraesCS2B01G493100 chr5D 90.702 1624 129 16 4852 6462 439600083 439601697 0.000000e+00 2143.0
61 TraesCS2B01G493100 chr5D 88.045 1673 157 28 4852 6499 549988651 549990305 0.000000e+00 1941.0
62 TraesCS2B01G493100 chr5D 95.939 197 6 2 1 197 362106829 362106635 1.580000e-82 318.0
63 TraesCS2B01G493100 chr5D 95.431 197 7 2 1 197 31812391 31812197 7.340000e-81 313.0
64 TraesCS2B01G493100 chr5D 95.431 197 7 2 1 197 426525334 426525528 7.340000e-81 313.0
65 TraesCS2B01G493100 chr5D 86.818 220 21 2 9516 9734 33018412 33018200 1.260000e-58 239.0
66 TraesCS2B01G493100 chr6B 87.771 1848 181 24 4852 6677 53600986 53599162 0.000000e+00 2119.0
67 TraesCS2B01G493100 chr6B 88.439 173 13 3 8587 8752 720764166 720764338 1.660000e-47 202.0
68 TraesCS2B01G493100 chr6B 85.714 70 10 0 6881 6950 651424478 651424547 3.770000e-09 75.0
69 TraesCS2B01G493100 chr7B 88.538 1771 169 20 4930 6673 723925101 723926864 0.000000e+00 2115.0
70 TraesCS2B01G493100 chr7B 93.561 1056 51 5 2690 3729 105913194 105912140 0.000000e+00 1557.0
71 TraesCS2B01G493100 chr7B 86.433 1054 102 32 2690 3729 640949961 640950987 0.000000e+00 1116.0
72 TraesCS2B01G493100 chr7B 88.823 841 61 8 3795 4606 654117590 654118426 0.000000e+00 1002.0
73 TraesCS2B01G493100 chr7B 90.828 676 57 5 3795 4470 542914676 542914006 0.000000e+00 900.0
74 TraesCS2B01G493100 chr7B 89.450 654 51 6 6036 6675 191730459 191731108 0.000000e+00 809.0
75 TraesCS2B01G493100 chr7B 94.924 197 8 2 1 197 598955025 598954831 3.420000e-79 307.0
76 TraesCS2B01G493100 chr7B 89.238 223 18 5 6453 6674 700888887 700888670 3.470000e-69 274.0
77 TraesCS2B01G493100 chr7B 85.567 97 13 1 9276 9372 720106367 720106462 6.220000e-17 100.0
78 TraesCS2B01G493100 chr6D 89.455 1669 132 22 4850 6489 464142609 464140956 0.000000e+00 2067.0
79 TraesCS2B01G493100 chr6D 89.905 842 70 12 2896 3729 19118753 19117919 0.000000e+00 1070.0
80 TraesCS2B01G493100 chr6D 85.526 988 111 24 2690 3665 323702023 323702990 0.000000e+00 1003.0
81 TraesCS2B01G493100 chr6D 92.512 641 47 1 3799 4439 424195138 424195777 0.000000e+00 917.0
82 TraesCS2B01G493100 chr6D 84.386 839 102 24 2692 3524 278664724 278665539 0.000000e+00 797.0
83 TraesCS2B01G493100 chr6D 95.939 197 6 2 1 197 256101903 256102097 1.580000e-82 318.0
84 TraesCS2B01G493100 chr6D 95.431 197 7 2 1 197 80113610 80113804 7.340000e-81 313.0
85 TraesCS2B01G493100 chr6D 94.924 197 7 3 1 197 388990634 388990827 1.230000e-78 305.0
86 TraesCS2B01G493100 chr6D 95.745 188 8 0 1 188 926298 926111 4.420000e-78 303.0
87 TraesCS2B01G493100 chr6D 95.745 188 7 1 1 188 26354227 26354041 1.590000e-77 302.0
88 TraesCS2B01G493100 chr6D 94.416 197 9 2 1 197 293889777 293889583 1.590000e-77 302.0
89 TraesCS2B01G493100 chr6D 94.416 197 9 2 1 197 293937024 293936830 1.590000e-77 302.0
90 TraesCS2B01G493100 chr6D 83.178 321 46 6 834 1153 205823288 205823601 4.450000e-73 287.0
91 TraesCS2B01G493100 chr6D 100.000 37 0 0 3763 3799 19117952 19117916 1.760000e-07 69.4
92 TraesCS2B01G493100 chr6D 97.500 40 1 0 3760 3799 278665708 278665747 1.760000e-07 69.4
93 TraesCS2B01G493100 chr6D 100.000 37 0 0 3763 3799 323703045 323703081 1.760000e-07 69.4
94 TraesCS2B01G493100 chr6D 100.000 35 0 0 3731 3765 19117962 19117928 2.270000e-06 65.8
95 TraesCS2B01G493100 chr3B 87.181 1841 166 32 4852 6671 667857186 667858977 0.000000e+00 2028.0
96 TraesCS2B01G493100 chr3B 92.758 1008 47 8 2689 3673 761503903 761502899 0.000000e+00 1434.0
97 TraesCS2B01G493100 chr3B 91.381 963 59 7 3868 4808 761502939 761503899 0.000000e+00 1297.0
98 TraesCS2B01G493100 chr3B 86.897 1015 107 11 3795 4807 27112264 27111274 0.000000e+00 1114.0
99 TraesCS2B01G493100 chr3B 92.251 542 42 0 3124 3665 59723400 59722859 0.000000e+00 769.0
100 TraesCS2B01G493100 chr3B 84.091 132 19 1 488 619 543843768 543843897 1.030000e-24 126.0
101 TraesCS2B01G493100 chrUn 86.853 1856 190 26 4850 6674 47956192 47954360 0.000000e+00 2026.0
102 TraesCS2B01G493100 chrUn 90.438 617 56 3 3049 3664 260673724 260674338 0.000000e+00 809.0
103 TraesCS2B01G493100 chrUn 86.250 640 59 14 3035 3673 108940963 108941574 0.000000e+00 667.0
104 TraesCS2B01G493100 chrUn 95.355 409 18 1 4401 4808 383821457 383821049 0.000000e+00 649.0
105 TraesCS2B01G493100 chrUn 93.976 415 24 1 2690 3104 383821046 383821459 2.310000e-175 627.0
106 TraesCS2B01G493100 chrUn 95.431 197 7 2 1 197 68758091 68758285 7.340000e-81 313.0
107 TraesCS2B01G493100 chrUn 94.924 197 8 2 1 197 108799249 108799443 3.420000e-79 307.0
108 TraesCS2B01G493100 chrUn 94.416 197 9 2 1 197 56941380 56941186 1.590000e-77 302.0
109 TraesCS2B01G493100 chrUn 94.416 197 9 2 1 197 287961108 287960914 1.590000e-77 302.0
110 TraesCS2B01G493100 chrUn 95.652 184 8 0 5 188 460548406 460548589 7.400000e-76 296.0
111 TraesCS2B01G493100 chrUn 94.149 188 11 0 1 188 336901322 336901135 4.450000e-73 287.0
112 TraesCS2B01G493100 chrUn 93.617 188 12 0 1 188 56272668 56272481 2.070000e-71 281.0
113 TraesCS2B01G493100 chrUn 93.617 188 12 0 1 188 336902533 336902346 2.070000e-71 281.0
114 TraesCS2B01G493100 chrUn 92.593 189 13 1 1 188 12121478 12121666 4.480000e-68 270.0
115 TraesCS2B01G493100 chrUn 97.500 40 1 0 3760 3799 260674391 260674430 1.760000e-07 69.4
116 TraesCS2B01G493100 chr4A 87.934 1641 168 19 4845 6462 545781361 545779728 0.000000e+00 1906.0
117 TraesCS2B01G493100 chr4A 92.137 903 49 7 8312 9204 174723939 174724829 0.000000e+00 1254.0
118 TraesCS2B01G493100 chr4A 86.853 753 72 20 3035 3769 430165721 430166464 0.000000e+00 817.0
119 TraesCS2B01G493100 chr4A 95.146 515 25 0 7302 7816 174722768 174723282 0.000000e+00 813.0
120 TraesCS2B01G493100 chr4A 91.560 545 25 6 9202 9739 174724878 174725408 0.000000e+00 732.0
121 TraesCS2B01G493100 chr4A 86.728 648 49 16 6040 6674 663763291 663762668 0.000000e+00 686.0
122 TraesCS2B01G493100 chr4A 82.800 500 67 16 8228 8717 174723716 174724206 6.990000e-116 429.0
123 TraesCS2B01G493100 chr4A 85.714 238 31 3 8444 8680 174723814 174724049 2.100000e-61 248.0
124 TraesCS2B01G493100 chr4A 88.439 173 13 3 8587 8752 726662679 726662851 1.660000e-47 202.0
125 TraesCS2B01G493100 chr4A 91.791 134 10 1 8327 8460 174724071 174724203 1.670000e-42 185.0
126 TraesCS2B01G493100 chr4A 94.690 113 6 0 6987 7099 174722106 174722218 1.010000e-39 176.0
127 TraesCS2B01G493100 chr4A 95.876 97 4 0 6882 6978 174721877 174721973 3.640000e-34 158.0
128 TraesCS2B01G493100 chr4A 100.000 39 0 0 3763 3801 566115452 566115414 1.360000e-08 73.1
129 TraesCS2B01G493100 chr1B 87.879 1518 117 23 5114 6596 658401632 658403117 0.000000e+00 1722.0
130 TraesCS2B01G493100 chr1B 93.750 1056 49 4 2689 3729 3092857 3091804 0.000000e+00 1568.0
131 TraesCS2B01G493100 chr1B 92.751 1007 49 6 2690 3673 638234617 638235622 0.000000e+00 1434.0
132 TraesCS2B01G493100 chr1B 91.134 1049 52 10 3799 4808 3091807 3092853 0.000000e+00 1384.0
133 TraesCS2B01G493100 chr1B 90.788 673 58 3 3799 4470 675379831 675379162 0.000000e+00 896.0
134 TraesCS2B01G493100 chr1B 92.730 619 41 4 4192 4808 657211305 657210689 0.000000e+00 891.0
135 TraesCS2B01G493100 chr1B 92.444 622 45 2 2689 3309 657210685 657211305 0.000000e+00 887.0
136 TraesCS2B01G493100 chr1B 91.681 589 47 2 3078 3665 672768719 672769306 0.000000e+00 815.0
137 TraesCS2B01G493100 chr1B 85.635 181 11 5 8587 8752 512628596 512628416 1.010000e-39 176.0
138 TraesCS2B01G493100 chr1B 84.615 78 9 2 6882 6957 40436354 40436430 3.770000e-09 75.0
139 TraesCS2B01G493100 chr5B 95.270 1057 33 3 2690 3729 610657886 610656830 0.000000e+00 1659.0
140 TraesCS2B01G493100 chr5B 88.230 1045 89 8 3795 4808 586826271 586825230 0.000000e+00 1218.0
141 TraesCS2B01G493100 chr5B 92.251 542 42 0 3124 3665 162880720 162880179 0.000000e+00 769.0
142 TraesCS2B01G493100 chr6A 92.418 1042 59 8 8228 9256 553940499 553939465 0.000000e+00 1469.0
143 TraesCS2B01G493100 chr6A 92.382 827 52 5 6991 7816 553941539 553940723 0.000000e+00 1168.0
144 TraesCS2B01G493100 chr6A 86.034 580 41 18 9166 9739 553939746 553939201 3.920000e-163 586.0
145 TraesCS2B01G493100 chr6A 94.924 197 8 2 1 197 76520926 76520732 3.420000e-79 307.0
146 TraesCS2B01G493100 chr6A 92.537 134 9 1 8327 8460 553940287 553940155 3.590000e-44 191.0
147 TraesCS2B01G493100 chr6A 92.481 133 8 1 8444 8576 553940401 553940271 1.290000e-43 189.0
148 TraesCS2B01G493100 chr6A 93.458 107 7 0 6883 6989 553941761 553941655 1.010000e-34 159.0
149 TraesCS2B01G493100 chr1D 84.898 980 105 22 2689 3665 27473148 27472209 0.000000e+00 950.0
150 TraesCS2B01G493100 chr1D 81.873 993 124 38 2690 3665 373424615 373425568 0.000000e+00 785.0
151 TraesCS2B01G493100 chr1D 97.500 40 1 0 3760 3799 373425620 373425659 1.760000e-07 69.4
152 TraesCS2B01G493100 chr1D 100.000 35 0 0 3731 3765 310158349 310158315 2.270000e-06 65.8
153 TraesCS2B01G493100 chr1D 97.297 37 1 0 3763 3799 310158339 310158303 8.170000e-06 63.9
154 TraesCS2B01G493100 chr1D 100.000 29 0 0 3763 3791 413812544 413812572 5.000000e-03 54.7
155 TraesCS2B01G493100 chr3A 90.639 673 57 4 3799 4470 645349189 645348522 0.000000e+00 889.0
156 TraesCS2B01G493100 chr3A 92.020 589 45 2 3078 3665 47259625 47259038 0.000000e+00 826.0
157 TraesCS2B01G493100 chr3A 88.439 173 13 3 8587 8752 109880946 109881118 1.660000e-47 202.0
158 TraesCS2B01G493100 chr4D 91.572 617 51 1 3049 3665 321944798 321944183 0.000000e+00 850.0
159 TraesCS2B01G493100 chr4D 95.431 197 6 3 1 197 20973469 20973276 2.640000e-80 311.0
160 TraesCS2B01G493100 chr4D 97.297 37 1 0 3763 3799 321944128 321944092 8.170000e-06 63.9
161 TraesCS2B01G493100 chr5A 82.600 1000 123 41 2690 3665 662063219 662062247 0.000000e+00 835.0
162 TraesCS2B01G493100 chr5A 95.604 91 4 0 9649 9739 21424924 21424834 7.880000e-31 147.0
163 TraesCS2B01G493100 chr5A 92.308 52 2 2 3749 3799 474921017 474921067 1.360000e-08 73.1
164 TraesCS2B01G493100 chr7D 95.960 198 5 3 1 197 101582751 101582946 1.580000e-82 318.0
165 TraesCS2B01G493100 chr7D 95.939 197 6 2 1 197 445784715 445784909 1.580000e-82 318.0
166 TraesCS2B01G493100 chr7D 73.069 479 77 28 8916 9363 515215443 515215900 1.330000e-23 122.0
167 TraesCS2B01G493100 chr1A 89.017 173 12 3 8587 8752 22855977 22855805 3.560000e-49 207.0
168 TraesCS2B01G493100 chr7A 91.667 60 5 0 6873 6932 538802123 538802064 6.270000e-12 84.2


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 TraesCS2B01G493100 chr2B 690933238 690942976 9738 True 4402.250000 14434 96.268500 1 9739 4 chr2B.!!$R6 9738
1 TraesCS2B01G493100 chr2B 691046803 691048544 1741 False 2357.000000 2357 91.165000 337 2088 1 chr2B.!!$F5 1751
2 TraesCS2B01G493100 chr2B 519669871 519671693 1822 True 2353.000000 2353 90.124000 4850 6673 1 chr2B.!!$R4 1823
3 TraesCS2B01G493100 chr2B 787510400 787512228 1828 False 2244.000000 2244 88.997000 4849 6673 1 chr2B.!!$F8 1824
4 TraesCS2B01G493100 chr2B 4797018 4798070 1052 False 1655.000000 1655 95.252000 2691 3729 1 chr2B.!!$F1 1038
5 TraesCS2B01G493100 chr2B 690938169 690940284 2115 False 1559.500000 3011 93.370500 2693 4808 2 chr2B.!!$F10 2115
6 TraesCS2B01G493100 chr2B 691038170 691039741 1571 False 1533.000000 1533 84.708000 903 2437 1 chr2B.!!$F4 1534
7 TraesCS2B01G493100 chr2B 4797020 4798067 1047 True 1463.000000 1463 92.462000 3799 4808 1 chr2B.!!$R1 1009
8 TraesCS2B01G493100 chr2B 321310983 321311677 694 True 1134.000000 1134 96.115000 3035 3729 1 chr2B.!!$R3 694
9 TraesCS2B01G493100 chr2B 669629962 669630705 743 True 811.000000 811 86.720000 3035 3769 1 chr2B.!!$R5 734
10 TraesCS2B01G493100 chr2B 296480834 296481497 663 False 787.000000 787 88.358000 3113 3769 1 chr2B.!!$F3 656
11 TraesCS2B01G493100 chr2B 672017589 672020396 2807 False 656.000000 2671 96.552500 6876 9739 6 chr2B.!!$F9 2863
12 TraesCS2B01G493100 chr2A 713189299 713190928 1629 False 2224.000000 2224 91.540000 474 2086 1 chr2A.!!$F2 1612
13 TraesCS2B01G493100 chr2A 713122808 713125425 2617 True 1151.000000 3142 92.071333 356 6823 3 chr2A.!!$R1 6467
14 TraesCS2B01G493100 chr2D 575158768 575160509 1741 False 2564.000000 2564 93.364000 359 2089 1 chr2D.!!$F4 1730
15 TraesCS2B01G493100 chr2D 52038701 52040354 1653 False 2098.000000 2098 89.771000 4852 6489 1 chr2D.!!$F1 1637
16 TraesCS2B01G493100 chr2D 107705164 107706811 1647 False 1993.000000 1993 88.661000 4862 6499 1 chr2D.!!$F2 1637
17 TraesCS2B01G493100 chr2D 574572064 574573283 1219 False 1181.000000 1181 84.641000 1252 2437 1 chr2D.!!$F3 1185
18 TraesCS2B01G493100 chr2D 574597057 574601908 4851 False 1070.000000 1188 85.526500 1278 2437 2 chr2D.!!$F6 1159
19 TraesCS2B01G493100 chr2D 574660776 574663463 2687 True 898.775000 3085 94.446250 359 6881 4 chr2D.!!$R1 6522
20 TraesCS2B01G493100 chr3D 491171424 491174210 2786 False 919.400000 2593 93.667800 6880 9739 5 chr3D.!!$F2 2859
21 TraesCS2B01G493100 chr4B 514036326 514038139 1813 False 2235.000000 2235 89.046000 4852 6664 1 chr4B.!!$F4 1812
22 TraesCS2B01G493100 chr4B 547266487 547267539 1052 False 1572.000000 1572 93.833000 2691 3729 1 chr4B.!!$F6 1038
23 TraesCS2B01G493100 chr4B 22191483 22192152 669 False 902.000000 902 90.936000 3799 4470 1 chr4B.!!$F1 671
24 TraesCS2B01G493100 chr4B 347893625 347894667 1042 True 624.200000 1179 93.649500 2690 3799 2 chr4B.!!$R5 1109
25 TraesCS2B01G493100 chr5D 439600083 439601697 1614 False 2143.000000 2143 90.702000 4852 6462 1 chr5D.!!$F2 1610
26 TraesCS2B01G493100 chr5D 549988651 549990305 1654 False 1941.000000 1941 88.045000 4852 6499 1 chr5D.!!$F3 1647
27 TraesCS2B01G493100 chr6B 53599162 53600986 1824 True 2119.000000 2119 87.771000 4852 6677 1 chr6B.!!$R1 1825
28 TraesCS2B01G493100 chr7B 723925101 723926864 1763 False 2115.000000 2115 88.538000 4930 6673 1 chr7B.!!$F5 1743
29 TraesCS2B01G493100 chr7B 105912140 105913194 1054 True 1557.000000 1557 93.561000 2690 3729 1 chr7B.!!$R1 1039
30 TraesCS2B01G493100 chr7B 640949961 640950987 1026 False 1116.000000 1116 86.433000 2690 3729 1 chr7B.!!$F2 1039
31 TraesCS2B01G493100 chr7B 654117590 654118426 836 False 1002.000000 1002 88.823000 3795 4606 1 chr7B.!!$F3 811
32 TraesCS2B01G493100 chr7B 542914006 542914676 670 True 900.000000 900 90.828000 3795 4470 1 chr7B.!!$R2 675
33 TraesCS2B01G493100 chr7B 191730459 191731108 649 False 809.000000 809 89.450000 6036 6675 1 chr7B.!!$F1 639
34 TraesCS2B01G493100 chr6D 464140956 464142609 1653 True 2067.000000 2067 89.455000 4850 6489 1 chr6D.!!$R5 1639
35 TraesCS2B01G493100 chr6D 424195138 424195777 639 False 917.000000 917 92.512000 3799 4439 1 chr6D.!!$F5 640
36 TraesCS2B01G493100 chr6D 323702023 323703081 1058 False 536.200000 1003 92.763000 2690 3799 2 chr6D.!!$F7 1109
37 TraesCS2B01G493100 chr6D 278664724 278665747 1023 False 433.200000 797 90.943000 2692 3799 2 chr6D.!!$F6 1107
38 TraesCS2B01G493100 chr6D 19117916 19118753 837 True 401.733333 1070 96.635000 2896 3799 3 chr6D.!!$R6 903
39 TraesCS2B01G493100 chr3B 667857186 667858977 1791 False 2028.000000 2028 87.181000 4852 6671 1 chr3B.!!$F2 1819
40 TraesCS2B01G493100 chr3B 761502899 761503903 1004 True 1434.000000 1434 92.758000 2689 3673 1 chr3B.!!$R3 984
41 TraesCS2B01G493100 chr3B 761502939 761503899 960 False 1297.000000 1297 91.381000 3868 4808 1 chr3B.!!$F3 940
42 TraesCS2B01G493100 chr3B 27111274 27112264 990 True 1114.000000 1114 86.897000 3795 4807 1 chr3B.!!$R1 1012
43 TraesCS2B01G493100 chr3B 59722859 59723400 541 True 769.000000 769 92.251000 3124 3665 1 chr3B.!!$R2 541
44 TraesCS2B01G493100 chrUn 47954360 47956192 1832 True 2026.000000 2026 86.853000 4850 6674 1 chrUn.!!$R1 1824
45 TraesCS2B01G493100 chrUn 108940963 108941574 611 False 667.000000 667 86.250000 3035 3673 1 chrUn.!!$F4 638
46 TraesCS2B01G493100 chrUn 260673724 260674430 706 False 439.200000 809 93.969000 3049 3799 2 chrUn.!!$F7 750
47 TraesCS2B01G493100 chrUn 336901135 336902533 1398 True 284.000000 287 93.883000 1 188 2 chrUn.!!$R6 187
48 TraesCS2B01G493100 chr4A 545779728 545781361 1633 True 1906.000000 1906 87.934000 4845 6462 1 chr4A.!!$R1 1617
49 TraesCS2B01G493100 chr4A 430165721 430166464 743 False 817.000000 817 86.853000 3035 3769 1 chr4A.!!$F1 734
50 TraesCS2B01G493100 chr4A 663762668 663763291 623 True 686.000000 686 86.728000 6040 6674 1 chr4A.!!$R3 634
51 TraesCS2B01G493100 chr4A 174721877 174725408 3531 False 499.375000 1254 91.214250 6882 9739 8 chr4A.!!$F3 2857
52 TraesCS2B01G493100 chr1B 658401632 658403117 1485 False 1722.000000 1722 87.879000 5114 6596 1 chr1B.!!$F5 1482
53 TraesCS2B01G493100 chr1B 3091804 3092857 1053 True 1568.000000 1568 93.750000 2689 3729 1 chr1B.!!$R1 1040
54 TraesCS2B01G493100 chr1B 638234617 638235622 1005 False 1434.000000 1434 92.751000 2690 3673 1 chr1B.!!$F3 983
55 TraesCS2B01G493100 chr1B 3091807 3092853 1046 False 1384.000000 1384 91.134000 3799 4808 1 chr1B.!!$F1 1009
56 TraesCS2B01G493100 chr1B 675379162 675379831 669 True 896.000000 896 90.788000 3799 4470 1 chr1B.!!$R4 671
57 TraesCS2B01G493100 chr1B 657210689 657211305 616 True 891.000000 891 92.730000 4192 4808 1 chr1B.!!$R3 616
58 TraesCS2B01G493100 chr1B 657210685 657211305 620 False 887.000000 887 92.444000 2689 3309 1 chr1B.!!$F4 620
59 TraesCS2B01G493100 chr1B 672768719 672769306 587 False 815.000000 815 91.681000 3078 3665 1 chr1B.!!$F6 587
60 TraesCS2B01G493100 chr5B 610656830 610657886 1056 True 1659.000000 1659 95.270000 2690 3729 1 chr5B.!!$R3 1039
61 TraesCS2B01G493100 chr5B 586825230 586826271 1041 True 1218.000000 1218 88.230000 3795 4808 1 chr5B.!!$R2 1013
62 TraesCS2B01G493100 chr5B 162880179 162880720 541 True 769.000000 769 92.251000 3124 3665 1 chr5B.!!$R1 541
63 TraesCS2B01G493100 chr6A 553939201 553941761 2560 True 627.000000 1469 91.551667 6883 9739 6 chr6A.!!$R2 2856
64 TraesCS2B01G493100 chr1D 27472209 27473148 939 True 950.000000 950 84.898000 2689 3665 1 chr1D.!!$R1 976
65 TraesCS2B01G493100 chr1D 373424615 373425659 1044 False 427.200000 785 89.686500 2690 3799 2 chr1D.!!$F2 1109
66 TraesCS2B01G493100 chr3A 645348522 645349189 667 True 889.000000 889 90.639000 3799 4470 1 chr3A.!!$R2 671
67 TraesCS2B01G493100 chr3A 47259038 47259625 587 True 826.000000 826 92.020000 3078 3665 1 chr3A.!!$R1 587
68 TraesCS2B01G493100 chr4D 321944092 321944798 706 True 456.950000 850 94.434500 3049 3799 2 chr4D.!!$R2 750
69 TraesCS2B01G493100 chr5A 662062247 662063219 972 True 835.000000 835 82.600000 2690 3665 1 chr5A.!!$R2 975

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
632 660 0.105224 TGCCCGTCGAGTCTTTTTCA 59.895 50.000 0.00 0.00 0.00 2.69 F
1227 1279 0.390860 GGATGGCAGACTACGCTGAT 59.609 55.000 0.00 0.00 38.14 2.90 F
1332 3714 0.813184 AAGATGGCGAGGCACAATTG 59.187 50.000 3.24 3.24 0.00 2.32 F
3065 5630 0.105913 TCTTTCCCGCCAACCCTTTT 60.106 50.000 0.00 0.00 0.00 2.27 F
3633 6545 0.748005 ATCGACGGATGGCAAAAGGG 60.748 55.000 0.00 0.00 0.00 3.95 F
3937 6874 0.034186 ATTGCCCTTCGAGGATGCAA 60.034 50.000 20.60 20.60 43.36 4.08 F
4142 7103 0.178873 TAGGTCCTTTCAGGCCACCT 60.179 55.000 12.85 12.85 43.03 4.00 F
5350 8459 0.324830 CTTCCCGTTCCTCCCTCTCT 60.325 60.000 0.00 0.00 0.00 3.10 F
5781 8894 0.945813 GGAGTCCATCCTCGAGTACG 59.054 60.000 12.31 0.00 45.64 3.67 F
7014 10471 1.003118 TCGTTCCCTTGTCATTCCCAG 59.997 52.381 0.00 0.00 0.00 4.45 F
7620 11640 1.679977 GCTCCAGCCATTCAAGCCA 60.680 57.895 0.00 0.00 34.31 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1772 4154 1.334869 CACCTTCTTTGTGGTGCTCAC 59.665 52.381 0.00 4.23 45.68 3.51 R
2967 5491 2.159382 CGGCCTACACTTGACCAAAAT 58.841 47.619 0.00 0.00 0.00 1.82 R
3138 5753 3.617284 CGCCTGAAGGGGTTTTTATAGT 58.383 45.455 5.27 0.00 42.54 2.12 R
3883 6795 0.101219 GATGGCAAAAGGACCGCATC 59.899 55.000 0.00 0.00 0.00 3.91 R
4602 7608 0.102300 GTTTTCGGCTGCTGTTTGGT 59.898 50.000 8.55 0.00 0.00 3.67 R
5098 8155 0.382515 GGAACCGAGACGATGAGGAG 59.617 60.000 0.00 0.00 0.00 3.69 R
5422 8531 1.276421 CTTCCTCATGAAGGTCGTGGT 59.724 52.381 0.00 0.00 45.66 4.16 R
7014 10471 1.160329 ACTCTGTTCTGGTTGCGTGC 61.160 55.000 0.00 0.00 0.00 5.34 R
7244 11264 1.808945 ACGTACCGAATCACGAAGACT 59.191 47.619 0.62 0.00 45.77 3.24 R
8404 12589 2.793278 AACCACGAAGAAAATGCACC 57.207 45.000 0.00 0.00 0.00 5.01 R
9510 13761 8.830201 ATCAACATATCTTGAGAGATTACTGC 57.170 34.615 0.00 0.00 42.55 4.40 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 8.188139 CGCATATAAGGTTTGGTAAAAGTCAAT 58.812 33.333 0.00 0.00 0.00 2.57
46 47 8.630037 AGGTTTGGTAAAAGTCAATCTTTGTAG 58.370 33.333 0.00 0.00 44.50 2.74
121 122 8.570488 TCAATATTATCAGATGCACCATGAAAC 58.430 33.333 0.00 0.00 0.00 2.78
196 197 6.820470 ATAAATTTGGTCAAACGTGTTGTG 57.180 33.333 0.00 0.00 32.51 3.33
197 198 4.442375 AATTTGGTCAAACGTGTTGTGA 57.558 36.364 0.00 0.00 32.51 3.58
198 199 2.904011 TTGGTCAAACGTGTTGTGAC 57.096 45.000 11.46 11.46 40.77 3.67
200 201 2.428491 TGGTCAAACGTGTTGTGACTT 58.572 42.857 16.64 0.00 41.17 3.01
201 202 2.417239 TGGTCAAACGTGTTGTGACTTC 59.583 45.455 16.64 6.58 41.17 3.01
202 203 2.223180 GGTCAAACGTGTTGTGACTTCC 60.223 50.000 16.64 3.03 41.17 3.46
203 204 2.676342 GTCAAACGTGTTGTGACTTCCT 59.324 45.455 12.25 0.00 38.87 3.36
204 205 2.933906 TCAAACGTGTTGTGACTTCCTC 59.066 45.455 0.00 0.00 0.00 3.71
206 207 2.684001 ACGTGTTGTGACTTCCTCAA 57.316 45.000 0.00 0.00 0.00 3.02
207 208 3.194005 ACGTGTTGTGACTTCCTCAAT 57.806 42.857 0.00 0.00 31.84 2.57
208 209 4.330944 ACGTGTTGTGACTTCCTCAATA 57.669 40.909 0.00 0.00 31.84 1.90
209 210 4.307432 ACGTGTTGTGACTTCCTCAATAG 58.693 43.478 0.00 0.00 31.84 1.73
210 211 4.038763 ACGTGTTGTGACTTCCTCAATAGA 59.961 41.667 0.00 0.00 31.84 1.98
211 212 4.623167 CGTGTTGTGACTTCCTCAATAGAG 59.377 45.833 0.00 0.00 41.72 2.43
225 226 6.214191 CTCAATAGAGGTGAGTGTATGTGT 57.786 41.667 0.00 0.00 38.16 3.72
226 227 5.965922 TCAATAGAGGTGAGTGTATGTGTG 58.034 41.667 0.00 0.00 0.00 3.82
228 229 6.661805 TCAATAGAGGTGAGTGTATGTGTGTA 59.338 38.462 0.00 0.00 0.00 2.90
229 230 7.342026 TCAATAGAGGTGAGTGTATGTGTGTAT 59.658 37.037 0.00 0.00 0.00 2.29
230 231 8.630037 CAATAGAGGTGAGTGTATGTGTGTATA 58.370 37.037 0.00 0.00 0.00 1.47
231 232 8.941995 ATAGAGGTGAGTGTATGTGTGTATAT 57.058 34.615 0.00 0.00 0.00 0.86
232 233 7.043961 AGAGGTGAGTGTATGTGTGTATATG 57.956 40.000 0.00 0.00 0.00 1.78
234 235 5.128663 AGGTGAGTGTATGTGTGTATATGCA 59.871 40.000 0.00 0.00 0.00 3.96
235 236 5.991606 GGTGAGTGTATGTGTGTATATGCAT 59.008 40.000 3.79 3.79 0.00 3.96
236 237 6.073602 GGTGAGTGTATGTGTGTATATGCATG 60.074 42.308 10.16 0.00 0.00 4.06
238 239 7.386025 GTGAGTGTATGTGTGTATATGCATGAT 59.614 37.037 10.16 1.78 0.00 2.45
239 240 7.385752 TGAGTGTATGTGTGTATATGCATGATG 59.614 37.037 10.16 0.00 0.00 3.07
240 241 7.219322 AGTGTATGTGTGTATATGCATGATGT 58.781 34.615 10.16 0.00 0.00 3.06
241 242 7.716560 AGTGTATGTGTGTATATGCATGATGTT 59.283 33.333 10.16 0.00 0.00 2.71
242 243 8.011673 GTGTATGTGTGTATATGCATGATGTTC 58.988 37.037 10.16 0.00 0.00 3.18
243 244 5.655893 TGTGTGTATATGCATGATGTTCG 57.344 39.130 10.16 0.00 0.00 3.95
244 245 4.024977 TGTGTGTATATGCATGATGTTCGC 60.025 41.667 10.16 3.19 0.00 4.70
245 246 4.212004 GTGTGTATATGCATGATGTTCGCT 59.788 41.667 10.16 0.00 0.00 4.93
246 247 4.815846 TGTGTATATGCATGATGTTCGCTT 59.184 37.500 10.16 0.00 0.00 4.68
247 248 5.050159 TGTGTATATGCATGATGTTCGCTTC 60.050 40.000 10.16 0.00 0.00 3.86
248 249 5.178252 GTGTATATGCATGATGTTCGCTTCT 59.822 40.000 10.16 0.00 0.00 2.85
249 250 4.744136 ATATGCATGATGTTCGCTTCTG 57.256 40.909 10.16 0.00 0.00 3.02
250 251 1.812235 TGCATGATGTTCGCTTCTGT 58.188 45.000 0.00 0.00 0.00 3.41
251 252 2.971307 TGCATGATGTTCGCTTCTGTA 58.029 42.857 0.00 0.00 0.00 2.74
252 253 2.672874 TGCATGATGTTCGCTTCTGTAC 59.327 45.455 0.00 0.00 0.00 2.90
253 254 2.932614 GCATGATGTTCGCTTCTGTACT 59.067 45.455 0.00 0.00 0.00 2.73
254 255 3.242220 GCATGATGTTCGCTTCTGTACTG 60.242 47.826 0.00 0.00 0.00 2.74
255 256 3.660501 TGATGTTCGCTTCTGTACTGT 57.339 42.857 0.00 0.00 0.00 3.55
256 257 3.317150 TGATGTTCGCTTCTGTACTGTG 58.683 45.455 0.00 0.00 0.00 3.66
257 258 2.882927 TGTTCGCTTCTGTACTGTGT 57.117 45.000 0.00 0.00 0.00 3.72
258 259 3.173668 TGTTCGCTTCTGTACTGTGTT 57.826 42.857 0.00 0.00 0.00 3.32
260 261 3.936453 TGTTCGCTTCTGTACTGTGTTTT 59.064 39.130 0.00 0.00 0.00 2.43
261 262 4.393680 TGTTCGCTTCTGTACTGTGTTTTT 59.606 37.500 0.00 0.00 0.00 1.94
285 286 8.776061 TTTTTCTAAAGAATCTTTTCCAGGGA 57.224 30.769 13.89 1.43 33.54 4.20
286 287 8.776061 TTTTCTAAAGAATCTTTTCCAGGGAA 57.224 30.769 13.89 0.00 33.54 3.97
287 288 7.761038 TTCTAAAGAATCTTTTCCAGGGAAC 57.239 36.000 13.89 0.00 33.41 3.62
288 289 6.848069 TCTAAAGAATCTTTTCCAGGGAACA 58.152 36.000 13.89 0.00 33.41 3.18
290 291 6.410942 AAAGAATCTTTTCCAGGGAACAAG 57.589 37.500 1.80 8.10 33.41 3.16
292 293 4.106341 AGAATCTTTTCCAGGGAACAAGGA 59.894 41.667 16.12 5.54 35.33 3.36
293 294 3.223674 TCTTTTCCAGGGAACAAGGAC 57.776 47.619 16.12 0.00 36.65 3.85
296 297 3.680777 TTTCCAGGGAACAAGGACTTT 57.319 42.857 0.00 0.00 36.65 2.66
320 321 7.876896 TGTTTTCCTGTTATAATTTTTCCGC 57.123 32.000 0.00 0.00 0.00 5.54
322 323 7.382759 TGTTTTCCTGTTATAATTTTTCCGCAC 59.617 33.333 0.00 0.00 0.00 5.34
323 324 6.576662 TTCCTGTTATAATTTTTCCGCACA 57.423 33.333 0.00 0.00 0.00 4.57
324 325 6.189677 TCCTGTTATAATTTTTCCGCACAG 57.810 37.500 0.00 0.00 0.00 3.66
325 326 4.798387 CCTGTTATAATTTTTCCGCACAGC 59.202 41.667 0.00 0.00 30.99 4.40
327 328 5.157781 TGTTATAATTTTTCCGCACAGCAC 58.842 37.500 0.00 0.00 0.00 4.40
328 329 2.323939 TAATTTTTCCGCACAGCACG 57.676 45.000 0.00 0.00 0.00 5.34
329 330 0.383949 AATTTTTCCGCACAGCACGT 59.616 45.000 0.00 0.00 0.00 4.49
396 399 0.548510 AGCCTAGTTTCTCATGGGCC 59.451 55.000 0.00 0.00 40.32 5.80
416 419 4.467735 GCCGATTTCACTGAAAACTCTTC 58.532 43.478 8.28 0.94 35.11 2.87
422 425 8.737648 CGATTTCACTGAAAACTCTTCTTTTTC 58.262 33.333 8.28 1.44 41.44 2.29
423 426 8.932945 ATTTCACTGAAAACTCTTCTTTTTCC 57.067 30.769 8.28 0.00 40.71 3.13
424 427 7.703058 TTCACTGAAAACTCTTCTTTTTCCT 57.297 32.000 5.38 0.00 40.71 3.36
425 428 7.088589 TCACTGAAAACTCTTCTTTTTCCTG 57.911 36.000 5.38 2.17 40.71 3.86
428 437 4.099419 TGAAAACTCTTCTTTTTCCTGCCC 59.901 41.667 5.38 0.00 40.71 5.36
432 441 2.200170 CTTCTTTTTCCTGCCCGCCG 62.200 60.000 0.00 0.00 0.00 6.46
590 603 4.467084 TGCGGGATTGCGTCCTCC 62.467 66.667 7.76 0.00 46.91 4.30
632 660 0.105224 TGCCCGTCGAGTCTTTTTCA 59.895 50.000 0.00 0.00 0.00 2.69
719 760 3.975168 TCTTTAGTGTTGGGTAGGCTC 57.025 47.619 0.00 0.00 0.00 4.70
906 951 6.826668 TGAAACCTGTTGATCTCTCAGTTTA 58.173 36.000 0.00 0.00 31.68 2.01
1056 1108 2.028476 CCAACTACCCAAGACATCGTCA 60.028 50.000 0.00 0.00 34.60 4.35
1143 1195 2.983030 ATCGGCGTTGGCAAGCAA 60.983 55.556 18.66 9.79 42.47 3.91
1227 1279 0.390860 GGATGGCAGACTACGCTGAT 59.609 55.000 0.00 0.00 38.14 2.90
1332 3714 0.813184 AAGATGGCGAGGCACAATTG 59.187 50.000 3.24 3.24 0.00 2.32
1595 3977 3.667360 CAGATGTGACATTCAGTGTGGA 58.333 45.455 0.00 0.00 42.36 4.02
1772 4154 2.695666 ACACAGATTCCCTGATAGTCGG 59.304 50.000 0.00 0.00 45.78 4.79
2062 4450 3.334583 TGGTCATGAAGGAGTTACTGC 57.665 47.619 0.00 0.00 0.00 4.40
2080 4469 2.429930 CATGGTGTCCCGTGGTGT 59.570 61.111 0.00 0.00 43.05 4.16
2619 5112 9.772973 AAGGAAGGGTGTTAAATAATGTTTTTC 57.227 29.630 0.00 0.00 0.00 2.29
2685 5194 4.753233 CCAACTCTCACTACTGAATCTGG 58.247 47.826 0.00 0.00 0.00 3.86
2686 5195 4.180057 CAACTCTCACTACTGAATCTGGC 58.820 47.826 0.00 0.00 0.00 4.85
2687 5196 2.763448 ACTCTCACTACTGAATCTGGCC 59.237 50.000 0.00 0.00 0.00 5.36
2750 5260 5.592054 TCGGAAACTATAGCACAGAATGAG 58.408 41.667 0.00 0.00 39.69 2.90
2771 5284 7.288810 TGAGAAAAATGCAAAACTATGACCT 57.711 32.000 0.00 0.00 0.00 3.85
2967 5491 4.880696 GTCTACTCTAGGCCGAAAAGTAGA 59.119 45.833 24.34 24.34 43.64 2.59
3065 5630 0.105913 TCTTTCCCGCCAACCCTTTT 60.106 50.000 0.00 0.00 0.00 2.27
3138 5753 2.355716 CCCGCCATTTTCTCCTCTGTAA 60.356 50.000 0.00 0.00 0.00 2.41
3596 6387 1.339438 GGCAAGAGTTCTGCATCCTCA 60.339 52.381 9.31 0.00 0.00 3.86
3633 6545 0.748005 ATCGACGGATGGCAAAAGGG 60.748 55.000 0.00 0.00 0.00 3.95
3729 6641 6.699366 TGTATTCCAGTTGTACCGTTTCATA 58.301 36.000 0.00 0.00 0.00 2.15
3730 6642 7.160049 TGTATTCCAGTTGTACCGTTTCATAA 58.840 34.615 0.00 0.00 0.00 1.90
3731 6643 5.927954 TTCCAGTTGTACCGTTTCATAAC 57.072 39.130 0.00 0.00 0.00 1.89
3732 6644 5.217978 TCCAGTTGTACCGTTTCATAACT 57.782 39.130 0.00 0.00 31.89 2.24
3733 6645 5.613329 TCCAGTTGTACCGTTTCATAACTT 58.387 37.500 0.00 0.00 31.89 2.66
3735 6647 5.467399 CCAGTTGTACCGTTTCATAACTTCA 59.533 40.000 0.00 0.00 31.89 3.02
3736 6648 6.148811 CCAGTTGTACCGTTTCATAACTTCAT 59.851 38.462 0.00 0.00 31.89 2.57
3737 6649 7.015289 CAGTTGTACCGTTTCATAACTTCATG 58.985 38.462 0.00 0.00 31.89 3.07
3738 6650 6.708949 AGTTGTACCGTTTCATAACTTCATGT 59.291 34.615 0.00 0.00 31.89 3.21
3739 6651 7.874016 AGTTGTACCGTTTCATAACTTCATGTA 59.126 33.333 0.00 0.00 31.89 2.29
3740 6652 7.821595 TGTACCGTTTCATAACTTCATGTAG 57.178 36.000 0.00 0.00 31.89 2.74
3741 6653 7.380536 TGTACCGTTTCATAACTTCATGTAGT 58.619 34.615 0.00 0.00 31.89 2.73
3742 6654 8.522003 TGTACCGTTTCATAACTTCATGTAGTA 58.478 33.333 5.32 0.00 31.89 1.82
3745 6657 8.038944 ACCGTTTCATAACTTCATGTAGTATGT 58.961 33.333 5.32 0.00 31.89 2.29
3773 6685 9.770097 AGATGTATTCCAGTTGTATGTAAGATG 57.230 33.333 0.00 0.00 0.00 2.90
3781 6693 8.204160 TCCAGTTGTATGTAAGATGTATTCCAG 58.796 37.037 0.00 0.00 0.00 3.86
3782 6694 7.987458 CCAGTTGTATGTAAGATGTATTCCAGT 59.013 37.037 0.00 0.00 0.00 4.00
3783 6695 9.383519 CAGTTGTATGTAAGATGTATTCCAGTT 57.616 33.333 0.00 0.00 0.00 3.16
3784 6696 9.383519 AGTTGTATGTAAGATGTATTCCAGTTG 57.616 33.333 0.00 0.00 0.00 3.16
3785 6697 9.162764 GTTGTATGTAAGATGTATTCCAGTTGT 57.837 33.333 0.00 0.00 0.00 3.32
3787 6699 9.811995 TGTATGTAAGATGTATTCCAGTTGTAC 57.188 33.333 0.00 0.00 0.00 2.90
3788 6700 9.257651 GTATGTAAGATGTATTCCAGTTGTACC 57.742 37.037 0.00 0.00 0.00 3.34
3790 6702 5.416271 AAGATGTATTCCAGTTGTACCGT 57.584 39.130 0.00 0.00 0.00 4.83
3791 6703 5.416271 AGATGTATTCCAGTTGTACCGTT 57.584 39.130 0.00 0.00 0.00 4.44
3792 6704 5.801380 AGATGTATTCCAGTTGTACCGTTT 58.199 37.500 0.00 0.00 0.00 3.60
3793 6705 5.873164 AGATGTATTCCAGTTGTACCGTTTC 59.127 40.000 0.00 0.00 0.00 2.78
3794 6706 4.958509 TGTATTCCAGTTGTACCGTTTCA 58.041 39.130 0.00 0.00 0.00 2.69
3795 6707 5.553123 TGTATTCCAGTTGTACCGTTTCAT 58.447 37.500 0.00 0.00 0.00 2.57
3797 6709 5.622770 ATTCCAGTTGTACCGTTTCATTC 57.377 39.130 0.00 0.00 0.00 2.67
3877 6789 3.345028 ATGCAGCCCTCTTGCCCT 61.345 61.111 0.00 0.00 0.00 5.19
3880 6792 2.643232 GCAGCCCTCTTGCCCTTTG 61.643 63.158 0.00 0.00 0.00 2.77
3881 6793 1.075482 CAGCCCTCTTGCCCTTTGA 59.925 57.895 0.00 0.00 0.00 2.69
3882 6794 1.075659 AGCCCTCTTGCCCTTTGAC 59.924 57.895 0.00 0.00 0.00 3.18
3883 6795 2.335712 GCCCTCTTGCCCTTTGACG 61.336 63.158 0.00 0.00 0.00 4.35
3884 6796 1.374947 CCCTCTTGCCCTTTGACGA 59.625 57.895 0.00 0.00 0.00 4.20
3885 6797 0.035056 CCCTCTTGCCCTTTGACGAT 60.035 55.000 0.00 0.00 0.00 3.73
3886 6798 1.089920 CCTCTTGCCCTTTGACGATG 58.910 55.000 0.00 0.00 0.00 3.84
3887 6799 0.449388 CTCTTGCCCTTTGACGATGC 59.551 55.000 0.00 0.00 0.00 3.91
3888 6800 1.135315 CTTGCCCTTTGACGATGCG 59.865 57.895 0.00 0.00 0.00 4.73
3890 6802 2.746277 GCCCTTTGACGATGCGGT 60.746 61.111 0.00 0.00 0.00 5.68
3937 6874 0.034186 ATTGCCCTTCGAGGATGCAA 60.034 50.000 20.60 20.60 43.36 4.08
4118 7079 7.295322 ACCTAAGAAGTTCTTTACGTACCTT 57.705 36.000 22.66 0.00 37.89 3.50
4142 7103 0.178873 TAGGTCCTTTCAGGCCACCT 60.179 55.000 12.85 12.85 43.03 4.00
4217 7178 1.420430 TCGTCCCATGGAACTATCCC 58.580 55.000 15.22 0.00 45.95 3.85
4242 7203 3.203716 GTCCATCCTGAAATCGGTAACC 58.796 50.000 0.00 0.00 0.00 2.85
4395 7357 0.899720 TGGCGGGAAAGAACGACTAT 59.100 50.000 0.00 0.00 39.30 2.12
4602 7608 5.646577 TTTGACCAAAAAGACCTTTTCGA 57.353 34.783 8.04 0.00 41.45 3.71
4710 7716 2.933573 TGGCCGAAAACTACCTTTTCA 58.066 42.857 0.00 0.00 45.74 2.69
4718 7724 5.411669 CGAAAACTACCTTTTCAGCCTACAT 59.588 40.000 6.41 0.00 45.74 2.29
4750 7757 7.296628 ACAGGGTCATAGTTTTGCATTTTTA 57.703 32.000 0.00 0.00 0.00 1.52
5052 8107 1.212616 CATTTTTGGCGCGAAAACCA 58.787 45.000 26.79 15.70 30.74 3.67
5098 8155 0.800300 CTCTTCTCGCTGCTTCGTCC 60.800 60.000 0.00 0.00 0.00 4.79
5311 8384 0.738389 CCGGTGAAGCACAAACACTT 59.262 50.000 0.00 0.00 35.86 3.16
5350 8459 0.324830 CTTCCCGTTCCTCCCTCTCT 60.325 60.000 0.00 0.00 0.00 3.10
5728 8841 1.130054 AGGCTCAACTCTGAAGGCCA 61.130 55.000 5.01 0.00 42.66 5.36
5781 8894 0.945813 GGAGTCCATCCTCGAGTACG 59.054 60.000 12.31 0.00 45.64 3.67
6150 9273 2.680352 ACGAGATGGTCCGGCAGT 60.680 61.111 0.00 0.00 0.00 4.40
6637 9948 1.451387 CTGGGCGGCGATTTTAGGT 60.451 57.895 12.98 0.00 0.00 3.08
6690 10001 6.269307 TGCTCTAAGTAGGTAAGTTTGAGGTT 59.731 38.462 6.29 0.00 39.42 3.50
6745 10056 6.292542 GGTCGTTTGGTTCTAGTTGTAAGTTC 60.293 42.308 0.00 0.00 0.00 3.01
6839 10157 5.046663 TCCTTTTCTGGGTTTATCCAAATGC 60.047 40.000 0.00 0.00 36.21 3.56
6982 10300 2.017782 GTCTGATCTCTCGCTACCACA 58.982 52.381 0.00 0.00 0.00 4.17
7014 10471 1.003118 TCGTTCCCTTGTCATTCCCAG 59.997 52.381 0.00 0.00 0.00 4.45
7291 11311 3.278574 CGTTTTTGCCTGGATCCTCATA 58.721 45.455 14.23 1.17 0.00 2.15
7397 11417 3.064958 TCGAATCTTGTACTCACGGCTAG 59.935 47.826 0.00 0.00 0.00 3.42
7470 11490 3.388308 CGGCTGATTGAATCTCTAGGTG 58.612 50.000 6.73 0.00 0.00 4.00
7500 11520 3.001838 TCGAACACACTGGATTCGTTTTG 59.998 43.478 13.54 0.00 44.28 2.44
7519 11539 5.534207 TTTGCAGTGTCTTCAAATCCATT 57.466 34.783 0.00 0.00 0.00 3.16
7620 11640 1.679977 GCTCCAGCCATTCAAGCCA 60.680 57.895 0.00 0.00 34.31 4.75
7801 11822 7.247456 TGTTGGTTGTAATGTAGGATCAGTA 57.753 36.000 0.00 0.00 0.00 2.74
8535 12720 4.994852 CGGAGTTCCAGTGTATTTTCTTCA 59.005 41.667 0.00 0.00 35.14 3.02
8852 13039 5.933463 TGGGTTTAGTGTAATTGACGGTAAG 59.067 40.000 0.00 0.00 0.00 2.34
9510 13761 8.020819 ACCAAGTTGTAATGTGACAAAATATCG 58.979 33.333 1.45 0.00 40.88 2.92
9585 13836 7.448469 ACAGTGTGTAGCTTAAGAAATTTGGAT 59.552 33.333 6.67 0.00 0.00 3.41
9666 13924 2.038426 CACATGACAGTTACTGGGGTCA 59.962 50.000 17.21 11.46 43.61 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 7.079182 TGACTTTTACCAAACCTTATATGCG 57.921 36.000 0.00 0.00 0.00 4.73
88 89 9.784680 GGTGCATCTGATAATATTGATTTCATC 57.215 33.333 0.00 0.00 0.00 2.92
93 94 8.873186 TCATGGTGCATCTGATAATATTGATT 57.127 30.769 0.00 0.00 0.00 2.57
188 189 4.556233 TCTATTGAGGAAGTCACAACACG 58.444 43.478 0.00 0.00 33.71 4.49
202 203 6.038985 CACACATACACTCACCTCTATTGAG 58.961 44.000 0.00 0.00 45.21 3.02
203 204 5.480422 ACACACATACACTCACCTCTATTGA 59.520 40.000 0.00 0.00 0.00 2.57
204 205 5.724328 ACACACATACACTCACCTCTATTG 58.276 41.667 0.00 0.00 0.00 1.90
206 207 8.797438 CATATACACACATACACTCACCTCTAT 58.203 37.037 0.00 0.00 0.00 1.98
207 208 7.255486 GCATATACACACATACACTCACCTCTA 60.255 40.741 0.00 0.00 0.00 2.43
208 209 6.461648 GCATATACACACATACACTCACCTCT 60.462 42.308 0.00 0.00 0.00 3.69
209 210 5.692204 GCATATACACACATACACTCACCTC 59.308 44.000 0.00 0.00 0.00 3.85
210 211 5.128663 TGCATATACACACATACACTCACCT 59.871 40.000 0.00 0.00 0.00 4.00
211 212 5.356426 TGCATATACACACATACACTCACC 58.644 41.667 0.00 0.00 0.00 4.02
212 213 6.701400 TCATGCATATACACACATACACTCAC 59.299 38.462 0.00 0.00 0.00 3.51
214 215 7.386025 ACATCATGCATATACACACATACACTC 59.614 37.037 0.00 0.00 0.00 3.51
215 216 7.219322 ACATCATGCATATACACACATACACT 58.781 34.615 0.00 0.00 0.00 3.55
216 217 7.425577 ACATCATGCATATACACACATACAC 57.574 36.000 0.00 0.00 0.00 2.90
219 220 6.128580 GCGAACATCATGCATATACACACATA 60.129 38.462 0.00 0.00 0.00 2.29
220 221 5.334337 GCGAACATCATGCATATACACACAT 60.334 40.000 0.00 0.00 0.00 3.21
221 222 4.024977 GCGAACATCATGCATATACACACA 60.025 41.667 0.00 0.00 0.00 3.72
224 225 4.997905 AGCGAACATCATGCATATACAC 57.002 40.909 0.00 0.00 0.00 2.90
225 226 5.178067 CAGAAGCGAACATCATGCATATACA 59.822 40.000 0.00 0.00 0.00 2.29
226 227 5.178252 ACAGAAGCGAACATCATGCATATAC 59.822 40.000 0.00 0.00 0.00 1.47
228 229 4.132336 ACAGAAGCGAACATCATGCATAT 58.868 39.130 0.00 0.00 0.00 1.78
229 230 3.534554 ACAGAAGCGAACATCATGCATA 58.465 40.909 0.00 0.00 0.00 3.14
230 231 2.362736 ACAGAAGCGAACATCATGCAT 58.637 42.857 0.00 0.00 0.00 3.96
231 232 1.812235 ACAGAAGCGAACATCATGCA 58.188 45.000 0.00 0.00 0.00 3.96
232 233 2.932614 AGTACAGAAGCGAACATCATGC 59.067 45.455 0.00 0.00 0.00 4.06
234 235 3.928992 CACAGTACAGAAGCGAACATCAT 59.071 43.478 0.00 0.00 0.00 2.45
235 236 3.243737 ACACAGTACAGAAGCGAACATCA 60.244 43.478 0.00 0.00 0.00 3.07
236 237 3.318017 ACACAGTACAGAAGCGAACATC 58.682 45.455 0.00 0.00 0.00 3.06
238 239 2.882927 ACACAGTACAGAAGCGAACA 57.117 45.000 0.00 0.00 0.00 3.18
239 240 4.531659 AAAACACAGTACAGAAGCGAAC 57.468 40.909 0.00 0.00 0.00 3.95
260 261 8.776061 TCCCTGGAAAAGATTCTTTAGAAAAA 57.224 30.769 11.92 0.00 37.61 1.94
261 262 8.638873 GTTCCCTGGAAAAGATTCTTTAGAAAA 58.361 33.333 11.92 2.52 35.29 2.29
262 263 7.782644 TGTTCCCTGGAAAAGATTCTTTAGAAA 59.217 33.333 11.92 2.80 35.29 2.52
264 265 6.848069 TGTTCCCTGGAAAAGATTCTTTAGA 58.152 36.000 11.92 1.24 35.75 2.10
265 266 7.309438 CCTTGTTCCCTGGAAAAGATTCTTTAG 60.309 40.741 11.92 6.31 35.75 1.85
267 268 5.305386 CCTTGTTCCCTGGAAAAGATTCTTT 59.695 40.000 5.82 5.82 35.75 2.52
268 269 4.835056 CCTTGTTCCCTGGAAAAGATTCTT 59.165 41.667 16.03 0.00 35.75 2.52
269 270 4.106341 TCCTTGTTCCCTGGAAAAGATTCT 59.894 41.667 16.03 0.00 35.75 2.40
270 271 4.218635 GTCCTTGTTCCCTGGAAAAGATTC 59.781 45.833 16.03 0.76 35.75 2.52
273 274 2.783510 AGTCCTTGTTCCCTGGAAAAGA 59.216 45.455 16.03 4.39 35.75 2.52
274 275 3.229697 AGTCCTTGTTCCCTGGAAAAG 57.770 47.619 0.00 6.95 35.75 2.27
276 277 3.295973 CAAAGTCCTTGTTCCCTGGAAA 58.704 45.455 0.00 0.00 35.75 3.13
277 278 2.243736 ACAAAGTCCTTGTTCCCTGGAA 59.756 45.455 0.00 0.00 46.49 3.53
278 279 1.850345 ACAAAGTCCTTGTTCCCTGGA 59.150 47.619 0.00 0.00 46.49 3.86
279 280 2.364972 ACAAAGTCCTTGTTCCCTGG 57.635 50.000 0.00 0.00 46.49 4.45
287 288 9.981114 AATTATAACAGGAAAACAAAGTCCTTG 57.019 29.630 0.00 0.00 41.73 3.61
296 297 7.382759 GTGCGGAAAAATTATAACAGGAAAACA 59.617 33.333 0.00 0.00 0.00 2.83
298 299 7.434492 TGTGCGGAAAAATTATAACAGGAAAA 58.566 30.769 0.00 0.00 0.00 2.29
300 301 6.576662 TGTGCGGAAAAATTATAACAGGAA 57.423 33.333 0.00 0.00 0.00 3.36
301 302 5.392595 GCTGTGCGGAAAAATTATAACAGGA 60.393 40.000 0.00 0.00 35.47 3.86
302 303 4.798387 GCTGTGCGGAAAAATTATAACAGG 59.202 41.667 0.00 0.00 35.47 4.00
305 306 4.262045 CGTGCTGTGCGGAAAAATTATAAC 59.738 41.667 0.00 0.00 0.00 1.89
306 307 4.083217 ACGTGCTGTGCGGAAAAATTATAA 60.083 37.500 0.00 0.00 0.00 0.98
307 308 3.437395 ACGTGCTGTGCGGAAAAATTATA 59.563 39.130 0.00 0.00 0.00 0.98
308 309 2.227865 ACGTGCTGTGCGGAAAAATTAT 59.772 40.909 0.00 0.00 0.00 1.28
309 310 1.604755 ACGTGCTGTGCGGAAAAATTA 59.395 42.857 0.00 0.00 0.00 1.40
310 311 0.383949 ACGTGCTGTGCGGAAAAATT 59.616 45.000 0.00 0.00 0.00 1.82
311 312 0.317770 CACGTGCTGTGCGGAAAAAT 60.318 50.000 0.82 0.00 42.70 1.82
312 313 1.063327 CACGTGCTGTGCGGAAAAA 59.937 52.632 0.82 0.00 42.70 1.94
317 318 8.021992 CTTATATAAGATCACGTGCTGTGCGG 62.022 46.154 16.21 0.00 40.83 5.69
318 319 5.164148 CTTATATAAGATCACGTGCTGTGCG 60.164 44.000 16.21 0.00 40.83 5.34
319 320 5.920840 TCTTATATAAGATCACGTGCTGTGC 59.079 40.000 19.23 0.00 41.50 4.57
334 335 9.131791 GGGCTTCAGTTTTTCCATCTTATATAA 57.868 33.333 0.00 0.00 0.00 0.98
335 336 8.278639 TGGGCTTCAGTTTTTCCATCTTATATA 58.721 33.333 0.00 0.00 0.00 0.86
338 339 5.332743 TGGGCTTCAGTTTTTCCATCTTAT 58.667 37.500 0.00 0.00 0.00 1.73
341 342 3.243359 TGGGCTTCAGTTTTTCCATCT 57.757 42.857 0.00 0.00 0.00 2.90
370 371 1.272536 TGAGAAACTAGGCTCGGTCCT 60.273 52.381 0.00 2.14 40.21 3.85
396 399 8.620533 AAAAAGAAGAGTTTTCAGTGAAATCG 57.379 30.769 18.69 0.00 31.34 3.34
416 419 4.419939 GCGGCGGGCAGGAAAAAG 62.420 66.667 9.78 0.00 42.87 2.27
428 437 0.807667 AGAGATGCTACTTTGCGGCG 60.808 55.000 0.51 0.51 35.36 6.46
432 441 1.939255 GGCTGAGAGATGCTACTTTGC 59.061 52.381 0.00 0.00 0.00 3.68
434 443 1.137872 CGGGCTGAGAGATGCTACTTT 59.862 52.381 0.00 0.00 0.00 2.66
509 522 1.073923 GCTGAGAGGAAGAAACCCCAA 59.926 52.381 0.00 0.00 0.00 4.12
719 760 7.519970 CGGGGAAAATATTTAAGATCTGAACCG 60.520 40.741 0.01 0.00 0.00 4.44
906 951 4.952335 ACAAGCTAGCAAATATGAGCCTTT 59.048 37.500 18.83 0.00 35.45 3.11
1056 1108 1.070758 ACACTCTCCGTCAAGCATGTT 59.929 47.619 0.00 0.00 0.00 2.71
1227 1279 6.811665 CACGGTCAAGAAAGACTGATGTATAA 59.188 38.462 9.67 0.00 45.66 0.98
1332 3714 9.926158 ACATGATCTATCTCATCACATTTAGTC 57.074 33.333 0.00 0.00 33.59 2.59
1566 3948 1.576577 ATGTCACATCTGCTCCCTGA 58.423 50.000 0.00 0.00 0.00 3.86
1595 3977 1.615392 GAGCTTTGAACAGTTGGCCAT 59.385 47.619 6.09 0.00 0.00 4.40
1603 3985 2.812591 AGCATCTGTGAGCTTTGAACAG 59.187 45.455 11.47 11.47 42.17 3.16
1772 4154 1.334869 CACCTTCTTTGTGGTGCTCAC 59.665 52.381 0.00 4.23 45.68 3.51
2062 4450 2.359850 CACCACGGGACACCATGG 60.360 66.667 11.19 11.19 37.34 3.66
2080 4469 2.625737 CTCTGAACGTACCGGACTAGA 58.374 52.381 9.46 0.79 0.00 2.43
2313 4747 6.663093 TGAACTGAATAATAAACTGCATGGGT 59.337 34.615 0.00 0.00 0.00 4.51
2451 4888 8.862325 ATGAATCTGAAGTTACCATTTACACA 57.138 30.769 0.00 0.00 0.00 3.72
2550 4990 6.663093 TGGCTCATATGTGGTAGAACAAATTT 59.337 34.615 1.90 0.00 32.81 1.82
2555 4995 4.835284 TTGGCTCATATGTGGTAGAACA 57.165 40.909 1.90 0.00 0.00 3.18
2585 5078 7.669089 ATTTAACACCCTTCCTTTTCTTTCA 57.331 32.000 0.00 0.00 0.00 2.69
2619 5112 2.219458 CATGCTATGCTCCCTTGAGTG 58.781 52.381 0.00 0.00 40.95 3.51
2750 5260 7.358352 CGACAAGGTCATAGTTTTGCATTTTTC 60.358 37.037 0.00 0.00 32.09 2.29
2967 5491 2.159382 CGGCCTACACTTGACCAAAAT 58.841 47.619 0.00 0.00 0.00 1.82
3138 5753 3.617284 CGCCTGAAGGGGTTTTTATAGT 58.383 45.455 5.27 0.00 42.54 2.12
3596 6387 2.684881 CGATGCAGAACTATTGCCCTTT 59.315 45.455 0.00 0.00 40.81 3.11
3633 6545 4.179579 GCCCTTTGACGATGCGGC 62.180 66.667 0.00 0.00 34.27 6.53
3748 6660 9.547753 ACATCTTACATACAACTGGAATACATC 57.452 33.333 0.00 0.00 0.00 3.06
3753 6665 9.561069 GGAATACATCTTACATACAACTGGAAT 57.439 33.333 0.00 0.00 0.00 3.01
3756 6668 7.987458 ACTGGAATACATCTTACATACAACTGG 59.013 37.037 0.00 0.00 0.00 4.00
3759 6671 9.162764 ACAACTGGAATACATCTTACATACAAC 57.837 33.333 0.00 0.00 0.00 3.32
3761 6673 9.811995 GTACAACTGGAATACATCTTACATACA 57.188 33.333 0.00 0.00 0.00 2.29
3762 6674 9.257651 GGTACAACTGGAATACATCTTACATAC 57.742 37.037 0.00 0.00 0.00 2.39
3763 6675 8.139350 CGGTACAACTGGAATACATCTTACATA 58.861 37.037 0.00 0.00 0.00 2.29
3764 6676 6.984474 CGGTACAACTGGAATACATCTTACAT 59.016 38.462 0.00 0.00 0.00 2.29
3767 6679 6.534475 ACGGTACAACTGGAATACATCTTA 57.466 37.500 0.00 0.00 0.00 2.10
3770 6682 5.640357 TGAAACGGTACAACTGGAATACATC 59.360 40.000 0.00 0.00 0.00 3.06
3772 6684 4.958509 TGAAACGGTACAACTGGAATACA 58.041 39.130 0.00 0.00 0.00 2.29
3773 6685 6.148150 TGAATGAAACGGTACAACTGGAATAC 59.852 38.462 0.00 0.00 0.00 1.89
3775 6687 5.067273 TGAATGAAACGGTACAACTGGAAT 58.933 37.500 0.00 0.00 0.00 3.01
3778 6690 4.822036 TTGAATGAAACGGTACAACTGG 57.178 40.909 0.00 0.00 0.00 4.00
3790 6702 4.882427 TCCAGTTGTACCGTTTGAATGAAA 59.118 37.500 0.00 0.00 0.00 2.69
3791 6703 4.452825 TCCAGTTGTACCGTTTGAATGAA 58.547 39.130 0.00 0.00 0.00 2.57
3792 6704 4.074627 TCCAGTTGTACCGTTTGAATGA 57.925 40.909 0.00 0.00 0.00 2.57
3793 6705 4.822036 TTCCAGTTGTACCGTTTGAATG 57.178 40.909 0.00 0.00 0.00 2.67
3794 6706 5.998981 TGTATTCCAGTTGTACCGTTTGAAT 59.001 36.000 0.00 0.00 0.00 2.57
3795 6707 5.366460 TGTATTCCAGTTGTACCGTTTGAA 58.634 37.500 0.00 0.00 0.00 2.69
3797 6709 5.642063 AGATGTATTCCAGTTGTACCGTTTG 59.358 40.000 0.00 0.00 0.00 2.93
3877 6789 1.265635 CAAAAGGACCGCATCGTCAAA 59.734 47.619 0.00 0.00 34.24 2.69
3880 6792 1.134694 GCAAAAGGACCGCATCGTC 59.865 57.895 0.00 0.00 0.00 4.20
3881 6793 2.332654 GGCAAAAGGACCGCATCGT 61.333 57.895 0.00 0.00 0.00 3.73
3882 6794 1.656818 ATGGCAAAAGGACCGCATCG 61.657 55.000 0.00 0.00 0.00 3.84
3883 6795 0.101219 GATGGCAAAAGGACCGCATC 59.899 55.000 0.00 0.00 0.00 3.91
3884 6796 1.322538 GGATGGCAAAAGGACCGCAT 61.323 55.000 0.00 0.00 0.00 4.73
3885 6797 1.976474 GGATGGCAAAAGGACCGCA 60.976 57.895 0.00 0.00 0.00 5.69
3886 6798 2.885113 GGATGGCAAAAGGACCGC 59.115 61.111 0.00 0.00 0.00 5.68
3887 6799 1.644786 GACGGATGGCAAAAGGACCG 61.645 60.000 0.00 0.00 44.77 4.79
3888 6800 1.644786 CGACGGATGGCAAAAGGACC 61.645 60.000 0.00 0.00 0.00 4.46
3890 6802 0.251916 ATCGACGGATGGCAAAAGGA 59.748 50.000 0.00 0.00 0.00 3.36
3937 6874 1.056660 TCCTCGAAGGGCAAGAGTTT 58.943 50.000 0.00 0.00 35.59 2.66
4001 6962 5.618236 CATCTTTATGGATTGAGGAGAGCA 58.382 41.667 0.00 0.00 0.00 4.26
4142 7103 3.382546 GGCTCACCAATTACGTAGGTCTA 59.617 47.826 2.16 0.00 32.15 2.59
4217 7178 3.282021 ACCGATTTCAGGATGGACAATG 58.718 45.455 0.00 0.00 36.16 2.82
4395 7357 1.377463 CCGTTTCCCGCCAATACCA 60.377 57.895 0.00 0.00 34.38 3.25
4602 7608 0.102300 GTTTTCGGCTGCTGTTTGGT 59.898 50.000 8.55 0.00 0.00 3.67
4718 7724 1.610967 TATGACCCTGTCGGCCACA 60.611 57.895 2.24 5.66 34.95 4.17
4750 7757 8.902540 TTTCGGAAACTATAGCACATAATGAT 57.097 30.769 0.00 0.00 0.00 2.45
4913 7939 2.254350 GCGACTGGGCCGTTTTTC 59.746 61.111 0.00 0.00 0.00 2.29
5098 8155 0.382515 GGAACCGAGACGATGAGGAG 59.617 60.000 0.00 0.00 0.00 3.69
5305 8378 2.380410 GCGTCGGCGATGAAGTGTT 61.380 57.895 31.53 0.00 41.33 3.32
5350 8459 2.282958 AACTGGAGACGGCGAGGA 60.283 61.111 16.62 0.00 41.93 3.71
5422 8531 1.276421 CTTCCTCATGAAGGTCGTGGT 59.724 52.381 0.00 0.00 45.66 4.16
5781 8894 2.480555 CATGTTGCCGCCTTCGAC 59.519 61.111 0.00 0.00 38.10 4.20
5797 8910 3.009115 GGTACTCCAGCCTGGGCA 61.009 66.667 11.68 0.00 44.88 5.36
6055 9178 2.426651 GCTATGGCCTCGTACTCCA 58.573 57.895 3.32 0.00 0.00 3.86
6150 9273 1.984570 CCTCTTCCAGGTCTCGGCA 60.985 63.158 0.00 0.00 37.53 5.69
6444 9614 9.651718 GCGAGTTCATAAAATATTTTACAGAGG 57.348 33.333 20.21 5.03 35.65 3.69
6445 9615 9.651718 GGCGAGTTCATAAAATATTTTACAGAG 57.348 33.333 20.21 11.96 35.65 3.35
6446 9616 8.332464 CGGCGAGTTCATAAAATATTTTACAGA 58.668 33.333 20.21 17.60 35.65 3.41
6447 9617 8.332464 TCGGCGAGTTCATAAAATATTTTACAG 58.668 33.333 20.21 15.96 35.65 2.74
6448 9618 8.199176 TCGGCGAGTTCATAAAATATTTTACA 57.801 30.769 20.21 9.38 35.65 2.41
6573 9882 3.961414 GGGCGAGTTGGTCCCCAA 61.961 66.667 0.00 0.00 41.69 4.12
6690 10001 1.860240 AGGAGCCCTACCAGATACTGA 59.140 52.381 0.00 0.00 28.82 3.41
6756 10071 9.494271 GGATGCATGTGTAATATTAAGAGAGAA 57.506 33.333 2.46 0.00 0.00 2.87
6808 10126 9.640952 TGGATAAACCCAGAAAAGGATATTTAG 57.359 33.333 0.00 0.00 38.00 1.85
6824 10142 4.636249 TGTTTGTGCATTTGGATAAACCC 58.364 39.130 17.24 0.48 43.20 4.11
6982 10300 2.647158 GGAACGAGAGGAAGGCCGT 61.647 63.158 0.00 0.00 39.96 5.68
7014 10471 1.160329 ACTCTGTTCTGGTTGCGTGC 61.160 55.000 0.00 0.00 0.00 5.34
7244 11264 1.808945 ACGTACCGAATCACGAAGACT 59.191 47.619 0.62 0.00 45.77 3.24
7291 11311 9.959721 AAATCCTACACAGAACTTACAATACAT 57.040 29.630 0.00 0.00 0.00 2.29
7397 11417 3.056749 CCACAGAGTACACACCCTAGAAC 60.057 52.174 0.00 0.00 0.00 3.01
7470 11490 2.933906 TCCAGTGTGTTCGAACTCAAAC 59.066 45.455 28.74 19.03 34.62 2.93
7500 11520 5.531634 TGAAAATGGATTTGAAGACACTGC 58.468 37.500 0.00 0.00 0.00 4.40
7519 11539 5.505985 GCGTACAAAACCTACAACCATGAAA 60.506 40.000 0.00 0.00 0.00 2.69
8404 12589 2.793278 AACCACGAAGAAAATGCACC 57.207 45.000 0.00 0.00 0.00 5.01
8535 12720 9.598517 CCAAATATAATTACAGTGCAAAACCAT 57.401 29.630 0.00 0.00 0.00 3.55
9510 13761 8.830201 ATCAACATATCTTGAGAGATTACTGC 57.170 34.615 0.00 0.00 42.55 4.40
9666 13924 8.635765 TGACCAACTTAATTCTCTTGCTATTT 57.364 30.769 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.