Multiple sequence alignment - TraesCS2A01G497100

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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 TraesCS2A01G497100 chr2A 100.000 9071 0 0 1 9071 728020712 728029782 0.000000e+00 16752.0
1 TraesCS2A01G497100 chr2D 91.835 4997 303 38 3532 8473 593226662 593231608 0.000000e+00 6870.0
2 TraesCS2A01G497100 chr2D 89.930 1569 101 35 1988 3534 593225101 593226634 0.000000e+00 1969.0
3 TraesCS2A01G497100 chr2D 90.717 711 34 15 832 1532 593223803 593224491 0.000000e+00 918.0
4 TraesCS2A01G497100 chr2D 81.555 1003 169 12 6270 7268 73123485 73124475 0.000000e+00 813.0
5 TraesCS2A01G497100 chr2D 91.722 302 19 5 1590 1891 593224488 593224783 1.820000e-111 414.0
6 TraesCS2A01G497100 chr2D 82.590 471 57 14 8473 8919 532559990 532560459 8.540000e-105 392.0
7 TraesCS2A01G497100 chr2D 93.208 265 16 2 106 369 360433749 360433486 1.100000e-103 388.0
8 TraesCS2A01G497100 chr2D 97.222 216 6 0 622 837 360433051 360432836 5.180000e-97 366.0
9 TraesCS2A01G497100 chr2D 88.727 275 18 5 95 369 568194087 568194348 3.160000e-84 324.0
10 TraesCS2A01G497100 chr2D 91.469 211 9 2 382 588 360433384 360433179 1.930000e-71 281.0
11 TraesCS2A01G497100 chr2D 93.750 160 9 1 677 835 568197132 568197291 1.180000e-58 239.0
12 TraesCS2A01G497100 chr2D 78.736 348 63 8 7055 7399 70817976 70818315 1.190000e-53 222.0
13 TraesCS2A01G497100 chr2D 85.417 192 14 10 1414 1593 33773719 33773908 4.320000e-43 187.0
14 TraesCS2A01G497100 chr2D 86.335 161 20 2 1447 1605 555946392 555946552 3.370000e-39 174.0
15 TraesCS2A01G497100 chr2B 92.048 2729 140 42 832 3534 719496331 719499008 0.000000e+00 3766.0
16 TraesCS2A01G497100 chr2B 90.148 2771 176 33 3532 6259 719499036 719501752 0.000000e+00 3515.0
17 TraesCS2A01G497100 chr2B 88.279 802 80 2 6768 7569 719515682 719516469 0.000000e+00 948.0
18 TraesCS2A01G497100 chr2B 96.267 375 14 0 7783 8157 719516691 719517065 4.650000e-172 616.0
19 TraesCS2A01G497100 chr2B 89.107 459 39 6 6314 6772 719501755 719502202 2.210000e-155 560.0
20 TraesCS2A01G497100 chr2B 86.466 266 23 7 8203 8468 719517057 719517309 6.940000e-71 279.0
21 TraesCS2A01G497100 chr2B 88.462 208 11 7 7556 7753 719516486 719516690 1.180000e-58 239.0
22 TraesCS2A01G497100 chr2B 78.155 412 63 17 1627 2017 40269556 40269151 4.230000e-58 237.0
23 TraesCS2A01G497100 chr2B 89.796 147 12 3 1450 1593 430221052 430220906 1.560000e-42 185.0
24 TraesCS2A01G497100 chr2B 92.500 40 2 1 7583 7621 716550228 716550189 1.000000e-03 56.5
25 TraesCS2A01G497100 chr7A 96.456 2060 38 9 1890 3937 255920372 255918336 0.000000e+00 3367.0
26 TraesCS2A01G497100 chr7A 96.875 768 17 4 1864 2627 255892516 255891752 0.000000e+00 1279.0
27 TraesCS2A01G497100 chr7A 71.318 645 153 24 5127 5759 693210903 693210279 4.420000e-28 137.0
28 TraesCS2A01G497100 chr7A 98.276 58 1 0 1125 1182 255892733 255892790 1.610000e-17 102.0
29 TraesCS2A01G497100 chr7A 83.117 77 12 1 2352 2427 98096689 98096613 1.630000e-07 69.4
30 TraesCS2A01G497100 chr7A 100.000 29 0 0 7639 7667 605162835 605162807 5.000000e-03 54.7
31 TraesCS2A01G497100 chr6D 85.096 1409 181 17 4496 5882 57169128 57170529 0.000000e+00 1411.0
32 TraesCS2A01G497100 chr6D 95.910 489 18 2 165 653 425085476 425085962 0.000000e+00 791.0
33 TraesCS2A01G497100 chr6D 93.617 188 7 2 652 838 425086056 425086239 8.970000e-70 276.0
34 TraesCS2A01G497100 chr6D 96.094 128 4 1 101 228 425085350 425085476 3.320000e-49 207.0
35 TraesCS2A01G497100 chr6D 88.000 150 14 3 1450 1596 390489553 390489405 3.370000e-39 174.0
36 TraesCS2A01G497100 chr6D 87.919 149 16 2 1450 1596 390732716 390732568 3.370000e-39 174.0
37 TraesCS2A01G497100 chr6D 87.333 150 16 2 1450 1596 390481386 390481237 1.570000e-37 169.0
38 TraesCS2A01G497100 chr6D 78.667 150 26 5 1717 1864 27228402 27228547 2.700000e-15 95.3
39 TraesCS2A01G497100 chr1A 98.641 736 9 1 97 832 568023228 568023962 0.000000e+00 1303.0
40 TraesCS2A01G497100 chr1A 87.800 500 51 7 8472 8968 27348945 27349437 2.200000e-160 577.0
41 TraesCS2A01G497100 chr1A 86.076 158 16 6 1447 1599 483658568 483658724 2.030000e-36 165.0
42 TraesCS2A01G497100 chr1A 84.472 161 18 5 1441 1598 111535595 111535751 1.580000e-32 152.0
43 TraesCS2A01G497100 chr7D 79.730 1406 224 40 4516 5894 180214589 180213218 0.000000e+00 961.0
44 TraesCS2A01G497100 chr7D 84.074 923 145 2 6270 7190 253157184 253158106 0.000000e+00 889.0
45 TraesCS2A01G497100 chr7D 91.216 148 9 3 1450 1593 616210257 616210110 2.000000e-46 198.0
46 TraesCS2A01G497100 chr7D 87.821 156 16 3 1446 1598 312470541 312470386 7.240000e-41 180.0
47 TraesCS2A01G497100 chr7D 88.000 150 15 2 1450 1596 585490117 585489968 3.370000e-39 174.0
48 TraesCS2A01G497100 chr7D 88.462 130 14 1 8775 8903 597083413 597083284 1.220000e-33 156.0
49 TraesCS2A01G497100 chr7B 81.834 1167 188 15 6278 7435 3507870 3509021 0.000000e+00 959.0
50 TraesCS2A01G497100 chr7B 82.604 891 151 4 6266 7152 230215032 230215922 0.000000e+00 784.0
51 TraesCS2A01G497100 chr5A 83.023 966 140 17 6263 7224 379351673 379350728 0.000000e+00 854.0
52 TraesCS2A01G497100 chr5A 88.079 151 15 2 1450 1597 327725260 327725110 9.360000e-40 176.0
53 TraesCS2A01G497100 chr5A 80.645 217 32 7 1652 1865 40158814 40158605 9.430000e-35 159.0
54 TraesCS2A01G497100 chr5A 90.196 51 1 4 3234 3282 457557564 457557516 7.600000e-06 63.9
55 TraesCS2A01G497100 chr5A 100.000 29 0 0 7639 7667 620748611 620748639 5.000000e-03 54.7
56 TraesCS2A01G497100 chr1D 82.759 928 145 14 6270 7190 375982217 375983136 0.000000e+00 813.0
57 TraesCS2A01G497100 chr1D 82.004 928 157 8 6267 7190 326223591 326224512 0.000000e+00 780.0
58 TraesCS2A01G497100 chr1D 76.574 397 68 14 1642 2017 231026876 231027268 2.580000e-45 195.0
59 TraesCS2A01G497100 chr1D 85.161 155 15 6 1450 1598 470035460 470035308 1.580000e-32 152.0
60 TraesCS2A01G497100 chr1D 84.868 152 18 3 1447 1598 246416387 246416533 2.040000e-31 148.0
61 TraesCS2A01G497100 chr6A 90.718 571 50 3 8472 9039 599751432 599752002 0.000000e+00 758.0
62 TraesCS2A01G497100 chr6A 84.639 319 42 6 5567 5882 71933351 71933665 2.460000e-80 311.0
63 TraesCS2A01G497100 chr3A 88.735 577 57 4 8470 9039 23126509 23127084 0.000000e+00 699.0
64 TraesCS2A01G497100 chr3A 83.422 374 54 6 8595 8967 464893139 464893505 3.140000e-89 340.0
65 TraesCS2A01G497100 chr3A 85.890 163 19 3 1437 1596 581251521 581251682 4.360000e-38 171.0
66 TraesCS2A01G497100 chr3A 93.333 75 5 0 1018 1092 647499722 647499648 2.680000e-20 111.0
67 TraesCS2A01G497100 chr3A 97.778 45 1 0 1860 1904 40688896 40688852 2.720000e-10 78.7
68 TraesCS2A01G497100 chr3A 97.778 45 1 0 1860 1904 40739658 40739614 2.720000e-10 78.7
69 TraesCS2A01G497100 chr3A 97.778 45 1 0 1860 1904 40794914 40794870 2.720000e-10 78.7
70 TraesCS2A01G497100 chr3A 95.556 45 2 0 1860 1904 40750931 40750887 1.260000e-08 73.1
71 TraesCS2A01G497100 chr3A 95.556 45 2 0 1860 1904 40806187 40806143 1.260000e-08 73.1
72 TraesCS2A01G497100 chr3A 95.556 45 1 1 1861 1904 40728378 40728334 4.540000e-08 71.3
73 TraesCS2A01G497100 chr4D 80.411 924 171 10 5019 5937 464399773 464400691 0.000000e+00 695.0
74 TraesCS2A01G497100 chr4D 85.253 495 61 7 921 1406 477089563 477089072 4.890000e-137 499.0
75 TraesCS2A01G497100 chr4D 84.010 419 42 9 7849 8267 477087861 477087468 6.650000e-101 379.0
76 TraesCS2A01G497100 chr4D 89.384 292 25 6 3851 4136 477088995 477088704 6.690000e-96 363.0
77 TraesCS2A01G497100 chr4D 82.407 324 34 20 5953 6258 477088439 477088121 2.510000e-65 261.0
78 TraesCS2A01G497100 chr4D 86.364 154 16 3 1447 1596 44750799 44750647 7.290000e-36 163.0
79 TraesCS2A01G497100 chr4D 85.621 153 19 3 1447 1596 362792021 362792173 3.390000e-34 158.0
80 TraesCS2A01G497100 chr4D 84.472 161 20 4 1450 1606 3747557 3747398 4.390000e-33 154.0
81 TraesCS2A01G497100 chr4D 84.416 154 20 4 1447 1596 416425082 416425235 2.040000e-31 148.0
82 TraesCS2A01G497100 chr4D 83.230 161 23 3 1450 1607 93704757 93704598 2.640000e-30 145.0
83 TraesCS2A01G497100 chr4D 95.122 41 1 1 7436 7475 340026279 340026239 7.600000e-06 63.9
84 TraesCS2A01G497100 chr3B 87.114 551 62 9 8472 9018 790591206 790591751 4.650000e-172 616.0
85 TraesCS2A01G497100 chr3B 79.753 405 78 4 5538 5938 591361074 591360670 3.200000e-74 291.0
86 TraesCS2A01G497100 chr3B 93.333 75 5 0 1018 1092 673098168 673098094 2.680000e-20 111.0
87 TraesCS2A01G497100 chr3B 70.287 801 182 48 5161 5938 474369814 474370581 9.630000e-20 110.0
88 TraesCS2A01G497100 chr3B 70.016 637 159 28 5199 5820 772032200 772031581 1.250000e-13 89.8
89 TraesCS2A01G497100 chr3B 84.286 70 6 2 5870 5938 772915114 772915179 7.600000e-06 63.9
90 TraesCS2A01G497100 chr3B 94.737 38 2 0 5900 5937 51151410 51151447 9.840000e-05 60.2
91 TraesCS2A01G497100 chr3B 94.595 37 2 0 5902 5938 722455714 722455678 3.540000e-04 58.4
92 TraesCS2A01G497100 chr4B 79.062 874 161 16 5076 5938 620108968 620109830 1.700000e-161 580.0
93 TraesCS2A01G497100 chr4B 79.038 873 160 17 5076 5938 620192895 620193754 2.200000e-160 577.0
94 TraesCS2A01G497100 chr4B 92.453 159 11 1 677 834 581943330 581943172 9.160000e-55 226.0
95 TraesCS2A01G497100 chr6B 94.722 360 11 1 476 835 578060319 578059968 3.700000e-153 553.0
96 TraesCS2A01G497100 chr6B 95.015 341 13 1 96 436 578060655 578060319 4.820000e-147 532.0
97 TraesCS2A01G497100 chr6B 76.642 137 29 3 5322 5457 664404746 664404880 1.260000e-08 73.1
98 TraesCS2A01G497100 chr6B 100.000 29 0 0 7639 7667 298287881 298287909 5.000000e-03 54.7
99 TraesCS2A01G497100 chr4A 88.419 449 49 3 8472 8917 102440623 102440175 1.040000e-148 538.0
100 TraesCS2A01G497100 chr4A 93.427 213 11 3 95 307 537187010 537187219 6.840000e-81 313.0
101 TraesCS2A01G497100 chr4A 80.896 424 54 17 1001 1409 614014654 614015065 8.850000e-80 309.0
102 TraesCS2A01G497100 chr4A 88.559 236 24 3 7842 8077 614005962 614006194 5.360000e-72 283.0
103 TraesCS2A01G497100 chr4A 79.753 405 59 17 1016 1406 614004509 614004904 1.160000e-68 272.0
104 TraesCS2A01G497100 chr4A 86.864 236 31 0 3901 4136 614004985 614005220 1.940000e-66 265.0
105 TraesCS2A01G497100 chr4A 92.949 156 9 2 677 831 537188016 537188170 9.160000e-55 226.0
106 TraesCS2A01G497100 chr4A 83.471 242 35 5 7825 8065 614016013 614016250 4.260000e-53 220.0
107 TraesCS2A01G497100 chr4A 87.097 155 18 2 1447 1599 515655546 515655700 3.370000e-39 174.0
108 TraesCS2A01G497100 chr4A 86.624 157 17 3 1447 1599 515651857 515652013 4.360000e-38 171.0
109 TraesCS2A01G497100 chr4A 86.364 154 17 3 1450 1600 11366171 11366019 2.030000e-36 165.0
110 TraesCS2A01G497100 chr4A 79.668 241 40 2 3896 4136 622441407 622441176 2.030000e-36 165.0
111 TraesCS2A01G497100 chr4A 79.668 241 40 2 3896 4136 622510474 622510243 2.030000e-36 165.0
112 TraesCS2A01G497100 chr4A 79.668 241 40 2 3896 4136 622559039 622558808 2.030000e-36 165.0
113 TraesCS2A01G497100 chrUn 88.136 295 34 1 8473 8766 26076594 26076888 5.210000e-92 350.0
114 TraesCS2A01G497100 chrUn 88.136 295 34 1 8473 8766 226923682 226923388 5.210000e-92 350.0
115 TraesCS2A01G497100 chrUn 84.667 150 20 2 1450 1596 71546747 71546598 7.340000e-31 147.0
116 TraesCS2A01G497100 chrUn 84.667 150 20 2 1450 1596 268022327 268022178 7.340000e-31 147.0
117 TraesCS2A01G497100 chrUn 83.871 155 21 3 1447 1598 30689269 30689422 2.640000e-30 145.0
118 TraesCS2A01G497100 chrUn 84.106 151 18 6 1450 1596 388800533 388800385 3.410000e-29 141.0
119 TraesCS2A01G497100 chrUn 83.221 149 23 2 1441 1588 290145756 290145903 1.590000e-27 135.0
120 TraesCS2A01G497100 chrUn 82.468 154 20 7 1450 1599 317868733 317868583 2.660000e-25 128.0
121 TraesCS2A01G497100 chrUn 81.633 147 16 6 1450 1596 474962479 474962344 2.680000e-20 111.0
122 TraesCS2A01G497100 chrUn 78.947 152 25 7 1450 1597 74039602 74039454 7.500000e-16 97.1
123 TraesCS2A01G497100 chrUn 94.340 53 3 0 1545 1597 339023907 339023855 2.100000e-11 82.4
124 TraesCS2A01G497100 chrUn 97.778 45 1 0 1860 1904 398674015 398673971 2.720000e-10 78.7
125 TraesCS2A01G497100 chr5B 81.604 424 54 17 1001 1406 696165231 696165648 6.790000e-86 329.0
126 TraesCS2A01G497100 chr5B 89.831 236 18 6 7842 8075 696155971 696156202 1.910000e-76 298.0
127 TraesCS2A01G497100 chr5B 88.073 218 26 0 1189 1406 696154658 696154875 9.040000e-65 259.0
128 TraesCS2A01G497100 chr5B 78.417 417 52 19 1624 2017 292486215 292485814 4.230000e-58 237.0
129 TraesCS2A01G497100 chr5B 83.673 245 33 7 7835 8077 696166646 696166885 3.300000e-54 224.0
130 TraesCS2A01G497100 chr5B 80.851 235 36 1 3902 4136 689646451 689646676 9.360000e-40 176.0
131 TraesCS2A01G497100 chr5B 80.851 235 36 1 3902 4136 689670004 689670229 9.360000e-40 176.0
132 TraesCS2A01G497100 chr5B 85.625 160 20 3 1441 1597 633284233 633284392 2.030000e-36 165.0
133 TraesCS2A01G497100 chr5B 94.737 38 2 0 7639 7676 108903944 108903907 9.840000e-05 60.2
134 TraesCS2A01G497100 chr5B 94.444 36 2 0 7632 7667 13103048 13103083 1.000000e-03 56.5
135 TraesCS2A01G497100 chr5D 89.219 269 11 9 95 362 419216426 419216677 4.090000e-83 320.0
136 TraesCS2A01G497100 chr5D 80.597 402 54 16 1019 1406 554577396 554577005 1.150000e-73 289.0
137 TraesCS2A01G497100 chr5D 88.430 242 22 6 7842 8080 554575593 554575355 4.140000e-73 287.0
138 TraesCS2A01G497100 chr5D 88.479 217 25 0 1190 1406 554521095 554520879 6.980000e-66 263.0
139 TraesCS2A01G497100 chr5D 82.869 251 38 5 7828 8077 554519916 554519670 4.260000e-53 220.0
140 TraesCS2A01G497100 chr5D 96.694 121 4 0 94 214 377300710 377300830 1.540000e-47 202.0
141 TraesCS2A01G497100 chr5D 85.714 161 20 2 1441 1598 488352346 488352506 5.630000e-37 167.0
142 TraesCS2A01G497100 chr5D 79.583 240 38 3 3896 4134 546566456 546566685 2.620000e-35 161.0
143 TraesCS2A01G497100 chr5D 84.177 158 20 5 1446 1599 443898161 443898317 2.040000e-31 148.0
144 TraesCS2A01G497100 chr5D 79.630 216 28 7 1725 1926 50827985 50827772 3.410000e-29 141.0
145 TraesCS2A01G497100 chr5D 94.521 73 4 0 1015 1087 410278074 410278146 7.440000e-21 113.0
146 TraesCS2A01G497100 chr5D 95.652 46 2 0 7588 7633 472740089 472740134 3.510000e-09 75.0
147 TraesCS2A01G497100 chr3D 86.093 151 18 3 1451 1598 64764588 64764438 9.430000e-35 159.0
148 TraesCS2A01G497100 chr3D 85.906 149 19 2 1453 1599 526977758 526977610 3.390000e-34 158.0
149 TraesCS2A01G497100 chr3D 93.333 75 5 0 1018 1092 511444272 511444198 2.680000e-20 111.0
150 TraesCS2A01G497100 chr1B 93.421 76 5 0 1018 1093 637368589 637368664 7.440000e-21 113.0


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 TraesCS2A01G497100 chr2A 728020712 728029782 9070 False 16752.000000 16752 100.000000 1 9071 1 chr2A.!!$F1 9070
1 TraesCS2A01G497100 chr2D 593223803 593231608 7805 False 2542.750000 6870 91.051000 832 8473 4 chr2D.!!$F7 7641
2 TraesCS2A01G497100 chr2D 73123485 73124475 990 False 813.000000 813 81.555000 6270 7268 1 chr2D.!!$F3 998
3 TraesCS2A01G497100 chr2D 360432836 360433749 913 True 345.000000 388 93.966333 106 837 3 chr2D.!!$R1 731
4 TraesCS2A01G497100 chr2D 568194087 568197291 3204 False 281.500000 324 91.238500 95 835 2 chr2D.!!$F6 740
5 TraesCS2A01G497100 chr2B 719496331 719502202 5871 False 2613.666667 3766 90.434333 832 6772 3 chr2B.!!$F1 5940
6 TraesCS2A01G497100 chr2B 719515682 719517309 1627 False 520.500000 948 89.868500 6768 8468 4 chr2B.!!$F2 1700
7 TraesCS2A01G497100 chr7A 255918336 255920372 2036 True 3367.000000 3367 96.456000 1890 3937 1 chr7A.!!$R3 2047
8 TraesCS2A01G497100 chr7A 255891752 255892516 764 True 1279.000000 1279 96.875000 1864 2627 1 chr7A.!!$R2 763
9 TraesCS2A01G497100 chr6D 57169128 57170529 1401 False 1411.000000 1411 85.096000 4496 5882 1 chr6D.!!$F2 1386
10 TraesCS2A01G497100 chr6D 425085350 425086239 889 False 424.666667 791 95.207000 101 838 3 chr6D.!!$F3 737
11 TraesCS2A01G497100 chr1A 568023228 568023962 734 False 1303.000000 1303 98.641000 97 832 1 chr1A.!!$F4 735
12 TraesCS2A01G497100 chr7D 180213218 180214589 1371 True 961.000000 961 79.730000 4516 5894 1 chr7D.!!$R1 1378
13 TraesCS2A01G497100 chr7D 253157184 253158106 922 False 889.000000 889 84.074000 6270 7190 1 chr7D.!!$F1 920
14 TraesCS2A01G497100 chr7B 3507870 3509021 1151 False 959.000000 959 81.834000 6278 7435 1 chr7B.!!$F1 1157
15 TraesCS2A01G497100 chr7B 230215032 230215922 890 False 784.000000 784 82.604000 6266 7152 1 chr7B.!!$F2 886
16 TraesCS2A01G497100 chr5A 379350728 379351673 945 True 854.000000 854 83.023000 6263 7224 1 chr5A.!!$R3 961
17 TraesCS2A01G497100 chr1D 375982217 375983136 919 False 813.000000 813 82.759000 6270 7190 1 chr1D.!!$F4 920
18 TraesCS2A01G497100 chr1D 326223591 326224512 921 False 780.000000 780 82.004000 6267 7190 1 chr1D.!!$F3 923
19 TraesCS2A01G497100 chr6A 599751432 599752002 570 False 758.000000 758 90.718000 8472 9039 1 chr6A.!!$F2 567
20 TraesCS2A01G497100 chr3A 23126509 23127084 575 False 699.000000 699 88.735000 8470 9039 1 chr3A.!!$F1 569
21 TraesCS2A01G497100 chr4D 464399773 464400691 918 False 695.000000 695 80.411000 5019 5937 1 chr4D.!!$F3 918
22 TraesCS2A01G497100 chr4D 477087468 477089563 2095 True 375.500000 499 85.263500 921 8267 4 chr4D.!!$R5 7346
23 TraesCS2A01G497100 chr3B 790591206 790591751 545 False 616.000000 616 87.114000 8472 9018 1 chr3B.!!$F4 546
24 TraesCS2A01G497100 chr4B 620108968 620109830 862 False 580.000000 580 79.062000 5076 5938 1 chr4B.!!$F1 862
25 TraesCS2A01G497100 chr4B 620192895 620193754 859 False 577.000000 577 79.038000 5076 5938 1 chr4B.!!$F2 862
26 TraesCS2A01G497100 chr6B 578059968 578060655 687 True 542.500000 553 94.868500 96 835 2 chr6B.!!$R1 739
27 TraesCS2A01G497100 chr4A 614004509 614006194 1685 False 273.333333 283 85.058667 1016 8077 3 chr4A.!!$F3 7061
28 TraesCS2A01G497100 chr4A 537187010 537188170 1160 False 269.500000 313 93.188000 95 831 2 chr4A.!!$F2 736
29 TraesCS2A01G497100 chr4A 614014654 614016250 1596 False 264.500000 309 82.183500 1001 8065 2 chr4A.!!$F4 7064
30 TraesCS2A01G497100 chr5B 696154658 696156202 1544 False 278.500000 298 88.952000 1189 8075 2 chr5B.!!$F5 6886
31 TraesCS2A01G497100 chr5B 696165231 696166885 1654 False 276.500000 329 82.638500 1001 8077 2 chr5B.!!$F6 7076
32 TraesCS2A01G497100 chr5D 554575355 554577396 2041 True 288.000000 289 84.513500 1019 8080 2 chr5D.!!$R3 7061
33 TraesCS2A01G497100 chr5D 554519670 554521095 1425 True 241.500000 263 85.674000 1190 8077 2 chr5D.!!$R2 6887

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
65 66 0.110056 CAGCGTCATGTTTGCCTCAC 60.110 55.000 0.00 0.00 0.00 3.51 F
76 77 0.770499 TTGCCTCACCCATGAAGTCA 59.230 50.000 0.00 0.00 33.30 3.41 F
77 78 0.994247 TGCCTCACCCATGAAGTCAT 59.006 50.000 0.00 0.00 33.30 3.06 F
995 3759 1.063567 ACATAGGAGAAGCGAGAGGGT 60.064 52.381 0.00 0.00 0.00 4.34 F
1117 3897 1.135632 CACACATGCATGCATTCACGA 60.136 47.619 30.32 1.61 33.90 4.35 F
2579 5644 1.407656 ATCACACACCGACCACCAGT 61.408 55.000 0.00 0.00 0.00 4.00 F
3520 6600 1.603456 ATTGCACGGTCACAACATCA 58.397 45.000 0.00 0.00 0.00 3.07 F
4730 8037 0.474854 TTGGCTACTGGAGGGGAACA 60.475 55.000 0.00 0.00 0.00 3.18 F
5373 8766 0.106819 GTCTGCATGATTGGCCCTCT 60.107 55.000 0.00 0.00 0.00 3.69 F
5813 9214 0.179148 CGGTAGCATAGTCGTGTGCA 60.179 55.000 0.00 0.00 43.04 4.57 F
5938 9340 0.249699 CGGGGCAAAAACCTGTTTCC 60.250 55.000 0.00 0.00 31.45 3.13 F
6805 10313 1.304052 CCAAAACGATGCCCCCAGA 60.304 57.895 0.00 0.00 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1311 4137 1.001974 TGGAAACATCACAGACGGAGG 59.998 52.381 0.00 0.00 33.40 4.30 R
1633 4466 1.990060 GAGCACCCAGGCACTCCTA 60.990 63.158 0.00 0.00 41.93 2.94 R
1778 4612 6.588204 ACTGTATTTTCCTCGCCACATATAA 58.412 36.000 0.00 0.00 0.00 0.98 R
2579 5644 1.069513 ACATTTTGACCTCGGTGTCGA 59.930 47.619 0.00 0.00 43.86 4.20 R
2608 5673 1.203523 TGTTTGTTGTGGAGTTGTGGC 59.796 47.619 0.00 0.00 0.00 5.01 R
3977 7165 0.834612 TCGACTCCAAGTTGGTGGTT 59.165 50.000 24.08 7.69 39.03 3.67 R
5003 8342 0.612453 AGGAGAGGAACCTCACGACC 60.612 60.000 20.84 16.69 44.99 4.79 R
6305 9806 1.033202 TGGCTGCATGCATCGTTCAT 61.033 50.000 22.97 0.00 45.15 2.57 R
6758 10264 0.978146 TAGCTGGAGGGGACAAGAGC 60.978 60.000 0.00 0.00 0.00 4.09 R
7477 10988 0.908198 ACACCATCAAGAGAGCCCTC 59.092 55.000 0.00 0.00 39.72 4.30 R
7478 10989 1.834263 GTACACCATCAAGAGAGCCCT 59.166 52.381 0.00 0.00 0.00 5.19 R
8661 12556 0.244450 ACCATGCTGTTTTCCATGCG 59.756 50.000 0.00 0.00 37.96 4.73 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
22 23 5.689383 CAAAAGAGAAGGGAAATCGACAA 57.311 39.130 0.00 0.00 0.00 3.18
23 24 5.693814 CAAAAGAGAAGGGAAATCGACAAG 58.306 41.667 0.00 0.00 0.00 3.16
24 25 4.625607 AAGAGAAGGGAAATCGACAAGT 57.374 40.909 0.00 0.00 0.00 3.16
25 26 5.740290 AAGAGAAGGGAAATCGACAAGTA 57.260 39.130 0.00 0.00 0.00 2.24
26 27 5.941555 AGAGAAGGGAAATCGACAAGTAT 57.058 39.130 0.00 0.00 0.00 2.12
27 28 7.419711 AAGAGAAGGGAAATCGACAAGTATA 57.580 36.000 0.00 0.00 0.00 1.47
28 29 6.807789 AGAGAAGGGAAATCGACAAGTATAC 58.192 40.000 0.00 0.00 0.00 1.47
29 30 6.380274 AGAGAAGGGAAATCGACAAGTATACA 59.620 38.462 5.50 0.00 0.00 2.29
30 31 6.942976 AGAAGGGAAATCGACAAGTATACAA 58.057 36.000 5.50 0.00 0.00 2.41
31 32 7.565680 AGAAGGGAAATCGACAAGTATACAAT 58.434 34.615 5.50 0.00 0.00 2.71
32 33 8.047310 AGAAGGGAAATCGACAAGTATACAATT 58.953 33.333 5.50 0.00 0.00 2.32
33 34 7.553881 AGGGAAATCGACAAGTATACAATTG 57.446 36.000 3.24 3.24 0.00 2.32
34 35 6.038271 AGGGAAATCGACAAGTATACAATTGC 59.962 38.462 5.05 0.00 0.00 3.56
35 36 6.183360 GGGAAATCGACAAGTATACAATTGCA 60.183 38.462 5.05 0.00 0.00 4.08
36 37 7.417612 GGAAATCGACAAGTATACAATTGCAT 58.582 34.615 5.05 0.00 0.00 3.96
37 38 7.587757 GGAAATCGACAAGTATACAATTGCATC 59.412 37.037 5.05 0.00 0.00 3.91
38 39 5.984233 TCGACAAGTATACAATTGCATCC 57.016 39.130 5.05 0.00 0.00 3.51
39 40 4.814234 TCGACAAGTATACAATTGCATCCC 59.186 41.667 5.05 0.00 0.00 3.85
40 41 4.574421 CGACAAGTATACAATTGCATCCCA 59.426 41.667 5.05 0.00 0.00 4.37
41 42 5.504010 CGACAAGTATACAATTGCATCCCAC 60.504 44.000 5.05 0.00 0.00 4.61
42 43 4.335315 ACAAGTATACAATTGCATCCCACG 59.665 41.667 5.05 0.00 0.00 4.94
43 44 4.150897 AGTATACAATTGCATCCCACGT 57.849 40.909 5.05 0.00 0.00 4.49
44 45 5.284861 AGTATACAATTGCATCCCACGTA 57.715 39.130 5.05 0.00 0.00 3.57
45 46 5.297547 AGTATACAATTGCATCCCACGTAG 58.702 41.667 5.05 0.00 0.00 3.51
46 47 1.094785 ACAATTGCATCCCACGTAGC 58.905 50.000 5.05 0.00 0.00 3.58
47 48 1.093972 CAATTGCATCCCACGTAGCA 58.906 50.000 0.00 0.00 34.79 3.49
48 49 1.064505 CAATTGCATCCCACGTAGCAG 59.935 52.381 0.00 0.00 38.35 4.24
49 50 1.097547 ATTGCATCCCACGTAGCAGC 61.098 55.000 0.00 0.00 38.35 5.25
50 51 3.264897 GCATCCCACGTAGCAGCG 61.265 66.667 0.00 0.00 37.94 5.18
51 52 2.184322 CATCCCACGTAGCAGCGT 59.816 61.111 0.00 0.00 46.88 5.07
52 53 1.878522 CATCCCACGTAGCAGCGTC 60.879 63.158 2.60 0.00 43.83 5.19
53 54 2.348104 ATCCCACGTAGCAGCGTCA 61.348 57.895 2.60 0.00 43.83 4.35
54 55 1.676678 ATCCCACGTAGCAGCGTCAT 61.677 55.000 2.60 0.00 43.83 3.06
55 56 2.167219 CCCACGTAGCAGCGTCATG 61.167 63.158 2.60 0.00 43.83 3.07
56 57 1.446099 CCACGTAGCAGCGTCATGT 60.446 57.895 2.60 0.00 43.83 3.21
57 58 1.014044 CCACGTAGCAGCGTCATGTT 61.014 55.000 2.60 0.00 43.83 2.71
58 59 0.790207 CACGTAGCAGCGTCATGTTT 59.210 50.000 2.60 0.00 43.83 2.83
59 60 0.790207 ACGTAGCAGCGTCATGTTTG 59.210 50.000 0.00 0.00 41.71 2.93
60 61 0.519175 CGTAGCAGCGTCATGTTTGC 60.519 55.000 0.00 0.00 36.83 3.68
61 62 0.179189 GTAGCAGCGTCATGTTTGCC 60.179 55.000 0.00 0.00 37.26 4.52
62 63 0.321564 TAGCAGCGTCATGTTTGCCT 60.322 50.000 0.00 0.00 37.26 4.75
63 64 1.154150 GCAGCGTCATGTTTGCCTC 60.154 57.895 0.00 0.00 0.00 4.70
64 65 1.855213 GCAGCGTCATGTTTGCCTCA 61.855 55.000 0.00 0.00 0.00 3.86
65 66 0.110056 CAGCGTCATGTTTGCCTCAC 60.110 55.000 0.00 0.00 0.00 3.51
66 67 1.210155 GCGTCATGTTTGCCTCACC 59.790 57.895 0.00 0.00 0.00 4.02
67 68 1.875963 CGTCATGTTTGCCTCACCC 59.124 57.895 0.00 0.00 0.00 4.61
68 69 0.888736 CGTCATGTTTGCCTCACCCA 60.889 55.000 0.00 0.00 0.00 4.51
69 70 1.549203 GTCATGTTTGCCTCACCCAT 58.451 50.000 0.00 0.00 0.00 4.00
70 71 1.203052 GTCATGTTTGCCTCACCCATG 59.797 52.381 0.00 0.00 35.39 3.66
71 72 1.075212 TCATGTTTGCCTCACCCATGA 59.925 47.619 0.00 0.00 39.51 3.07
72 73 1.894466 CATGTTTGCCTCACCCATGAA 59.106 47.619 0.00 0.00 35.96 2.57
73 74 1.619654 TGTTTGCCTCACCCATGAAG 58.380 50.000 0.00 0.00 33.30 3.02
74 75 1.133513 TGTTTGCCTCACCCATGAAGT 60.134 47.619 0.00 0.00 33.30 3.01
75 76 1.541588 GTTTGCCTCACCCATGAAGTC 59.458 52.381 0.00 0.00 33.30 3.01
76 77 0.770499 TTGCCTCACCCATGAAGTCA 59.230 50.000 0.00 0.00 33.30 3.41
77 78 0.994247 TGCCTCACCCATGAAGTCAT 59.006 50.000 0.00 0.00 33.30 3.06
90 91 5.936054 CATGAAGTCATGTTCACTTTCTCC 58.064 41.667 12.30 0.00 46.40 3.71
91 92 5.034852 TGAAGTCATGTTCACTTTCTCCA 57.965 39.130 0.32 0.00 34.10 3.86
92 93 5.059161 TGAAGTCATGTTCACTTTCTCCAG 58.941 41.667 0.32 0.00 34.10 3.86
93 94 3.406764 AGTCATGTTCACTTTCTCCAGC 58.593 45.455 0.00 0.00 0.00 4.85
260 323 3.119096 GCGAGAAACTGGCGGACC 61.119 66.667 0.00 0.00 0.00 4.46
380 443 1.517832 CTTGAGGCGAGTCCGGATT 59.482 57.895 7.81 1.79 40.77 3.01
463 671 2.878406 GGCGGCTGTGTCATACAAATAT 59.122 45.455 0.00 0.00 39.20 1.28
557 767 1.725665 CACCGAGCCGACGAATAGA 59.274 57.895 0.00 0.00 35.09 1.98
847 3607 1.742768 CCTTAGTGGAGGCGGCTAG 59.257 63.158 13.24 4.04 38.35 3.42
859 3619 2.820037 GGCTAGGCCTGCAACGTC 60.820 66.667 17.99 0.20 46.69 4.34
883 3646 5.108254 CGACAGCTTATTTTGTTGCACTTTC 60.108 40.000 0.00 0.00 0.00 2.62
884 3647 5.906073 ACAGCTTATTTTGTTGCACTTTCT 58.094 33.333 0.00 0.00 0.00 2.52
885 3648 5.750067 ACAGCTTATTTTGTTGCACTTTCTG 59.250 36.000 0.00 0.00 0.00 3.02
886 3649 5.176223 CAGCTTATTTTGTTGCACTTTCTGG 59.824 40.000 0.00 0.00 0.00 3.86
890 3653 7.532682 TTATTTTGTTGCACTTTCTGGTTTC 57.467 32.000 0.00 0.00 0.00 2.78
902 3665 1.856265 CTGGTTTCTGCGTGCCTTCC 61.856 60.000 0.00 0.00 0.00 3.46
978 3742 2.283388 CACCCAAGCCAGCCACAT 60.283 61.111 0.00 0.00 0.00 3.21
995 3759 1.063567 ACATAGGAGAAGCGAGAGGGT 60.064 52.381 0.00 0.00 0.00 4.34
1117 3897 1.135632 CACACATGCATGCATTCACGA 60.136 47.619 30.32 1.61 33.90 4.35
1142 3934 4.210120 CGCATGCCTCTCTTAATTCTACAC 59.790 45.833 13.15 0.00 0.00 2.90
1143 3935 5.118990 GCATGCCTCTCTTAATTCTACACA 58.881 41.667 6.36 0.00 0.00 3.72
1152 3944 5.304778 TCTTAATTCTACACAAGTGCAGCA 58.695 37.500 0.00 0.00 0.00 4.41
1175 3994 8.189460 AGCAAGTACTCGTAAATTACTTCCTAG 58.811 37.037 0.00 0.00 34.50 3.02
1406 4232 6.153851 TGGCAAGCTTGACATACTAGTAAGTA 59.846 38.462 31.26 3.19 42.34 2.24
1443 4276 8.706322 TTATTGGTATGTCTAGAGCATAGTGA 57.294 34.615 12.49 5.36 30.45 3.41
1445 4278 8.885693 ATTGGTATGTCTAGAGCATAGTGATA 57.114 34.615 12.49 2.62 30.45 2.15
1448 4281 9.975218 TGGTATGTCTAGAGCATAGTGATATAA 57.025 33.333 12.49 0.00 30.45 0.98
1479 4312 8.043113 TGCATATCTAAGTGACTCAATCAAACT 58.957 33.333 0.00 0.00 39.72 2.66
1480 4313 9.534565 GCATATCTAAGTGACTCAATCAAACTA 57.465 33.333 0.00 0.00 39.72 2.24
1485 4318 9.698309 TCTAAGTGACTCAATCAAACTAGAAAG 57.302 33.333 0.00 0.00 39.72 2.62
1486 4319 9.698309 CTAAGTGACTCAATCAAACTAGAAAGA 57.302 33.333 0.00 0.00 39.72 2.52
1487 4320 8.964476 AAGTGACTCAATCAAACTAGAAAGAA 57.036 30.769 0.00 0.00 39.72 2.52
1488 4321 8.964476 AGTGACTCAATCAAACTAGAAAGAAA 57.036 30.769 0.00 0.00 39.72 2.52
1489 4322 9.050601 AGTGACTCAATCAAACTAGAAAGAAAG 57.949 33.333 0.00 0.00 39.72 2.62
1539 4372 7.904977 CACGAATCTTCACGTAAAATCAATGAT 59.095 33.333 0.00 0.00 40.76 2.45
1654 4487 3.909086 GAGTGCCTGGGTGCTCCAC 62.909 68.421 7.20 0.00 41.46 4.02
1791 4625 6.377327 ACCAGAAAATTTATATGTGGCGAG 57.623 37.500 4.81 0.00 0.00 5.03
1818 4652 9.406828 GAAAATACAGTCCAAACTAAAATCCAC 57.593 33.333 0.00 0.00 33.25 4.02
1935 4773 3.718723 TCATATCCCAAAACCCCCAAAG 58.281 45.455 0.00 0.00 0.00 2.77
2058 5113 2.359230 GTCCTCCTGGTGCAGTGC 60.359 66.667 8.58 8.58 34.23 4.40
2510 5575 2.989909 TGGCTCATGTGGATGTTACAG 58.010 47.619 0.00 0.00 0.00 2.74
2579 5644 1.407656 ATCACACACCGACCACCAGT 61.408 55.000 0.00 0.00 0.00 4.00
2608 5673 6.582295 CACCGAGGTCAAAATGTTTAAAGATG 59.418 38.462 0.00 0.00 0.00 2.90
2649 5714 4.770010 ACAACTCCACTCTCCTCTTAGAAG 59.230 45.833 0.00 0.00 0.00 2.85
3459 6539 4.645588 GCTAAGGGAGTGAGCTAACTTAGA 59.354 45.833 4.84 0.00 40.17 2.10
3520 6600 1.603456 ATTGCACGGTCACAACATCA 58.397 45.000 0.00 0.00 0.00 3.07
3558 6668 4.505039 GGCCGAAATATGTAAGGACTCCAT 60.505 45.833 0.00 0.00 0.00 3.41
3685 6801 7.118496 AGACAAAACCATGACATAAAAACCA 57.882 32.000 0.00 0.00 0.00 3.67
4302 7603 5.867174 AGTTCGATTGAATGTATTGTCACGA 59.133 36.000 0.00 0.00 36.29 4.35
4389 7693 2.351276 CCACCTTCAACCTCCCCG 59.649 66.667 0.00 0.00 0.00 5.73
4481 7786 1.990060 CCTCTTCCCCTTCCTCGCA 60.990 63.158 0.00 0.00 0.00 5.10
4506 7811 3.041940 GGCGTGGGACAACGACAG 61.042 66.667 2.95 0.00 44.16 3.51
4508 7813 2.022129 GCGTGGGACAACGACAGAG 61.022 63.158 2.95 0.00 44.16 3.35
4642 7948 1.272536 GGCCTAGATCTGGATCGGGTA 60.273 57.143 7.81 3.97 42.48 3.69
4663 7969 1.048724 ATGCTCTAGCCGGCTACCAA 61.049 55.000 32.24 18.51 41.18 3.67
4698 8005 4.813235 GGCAACATGGGCCGGCTA 62.813 66.667 28.56 16.71 42.39 3.93
4728 8035 0.991920 CTTTGGCTACTGGAGGGGAA 59.008 55.000 0.00 0.00 0.00 3.97
4730 8037 0.474854 TTGGCTACTGGAGGGGAACA 60.475 55.000 0.00 0.00 0.00 3.18
4806 8114 3.866582 GTCCGGGGAGCAGATGGG 61.867 72.222 0.00 0.00 0.00 4.00
4838 8146 0.882927 GTAGGTGGCGCTTGTGTTCA 60.883 55.000 7.64 0.00 0.00 3.18
4962 8301 2.126424 GAGTCGGAGTTCGCGCTT 60.126 61.111 5.56 0.00 39.05 4.68
5005 8344 4.003788 CGGAAGGTGCTCGTGGGT 62.004 66.667 0.00 0.00 0.00 4.51
5006 8345 2.047179 GGAAGGTGCTCGTGGGTC 60.047 66.667 0.00 0.00 0.00 4.46
5007 8346 2.432628 GAAGGTGCTCGTGGGTCG 60.433 66.667 0.00 0.00 41.41 4.79
5008 8347 3.222354 GAAGGTGCTCGTGGGTCGT 62.222 63.158 0.00 0.00 40.80 4.34
5009 8348 3.515316 AAGGTGCTCGTGGGTCGTG 62.515 63.158 0.00 0.00 40.80 4.35
5010 8349 3.986006 GGTGCTCGTGGGTCGTGA 61.986 66.667 0.00 0.00 40.80 4.35
5011 8350 2.430921 GTGCTCGTGGGTCGTGAG 60.431 66.667 0.00 0.00 40.80 3.51
5012 8351 3.680786 TGCTCGTGGGTCGTGAGG 61.681 66.667 0.00 0.00 40.80 3.86
5013 8352 3.681835 GCTCGTGGGTCGTGAGGT 61.682 66.667 0.00 0.00 40.80 3.85
5014 8353 3.048602 CTCGTGGGTCGTGAGGTT 58.951 61.111 0.00 0.00 40.80 3.50
5015 8354 1.080705 CTCGTGGGTCGTGAGGTTC 60.081 63.158 0.00 0.00 40.80 3.62
5016 8355 2.048503 CGTGGGTCGTGAGGTTCC 60.049 66.667 0.00 0.00 34.52 3.62
5017 8356 2.571216 CGTGGGTCGTGAGGTTCCT 61.571 63.158 0.00 0.00 34.52 3.36
5018 8357 1.292541 GTGGGTCGTGAGGTTCCTC 59.707 63.158 11.53 11.53 0.00 3.71
5019 8358 1.155390 TGGGTCGTGAGGTTCCTCT 59.845 57.895 18.07 0.00 34.42 3.69
5020 8359 0.898789 TGGGTCGTGAGGTTCCTCTC 60.899 60.000 18.07 13.90 34.42 3.20
5021 8360 1.605971 GGGTCGTGAGGTTCCTCTCC 61.606 65.000 18.07 14.07 34.42 3.71
5074 8461 0.685097 GCTCCACTACACTGTTGGGA 59.315 55.000 0.85 1.81 0.00 4.37
5102 8489 4.025401 CAACGGCCACGGTCAAGC 62.025 66.667 2.24 0.00 46.48 4.01
5143 8530 4.429212 CGGCCGTCGGTCATCACA 62.429 66.667 19.50 0.00 34.75 3.58
5278 8671 3.580895 GTGTCTCCTTTTCTCCTCCTTCT 59.419 47.826 0.00 0.00 0.00 2.85
5312 8705 0.250124 GTGATGTGGACGGTTGGTGA 60.250 55.000 0.00 0.00 0.00 4.02
5326 8719 1.728323 TGGTGAAGTCCTGGACATGA 58.272 50.000 27.48 8.47 34.60 3.07
5337 8730 1.275421 TGGACATGAATGCCGGGGTA 61.275 55.000 2.18 0.00 0.00 3.69
5369 8762 3.113745 CGGTCTGCATGATTGGCC 58.886 61.111 0.00 0.00 0.00 5.36
5373 8766 0.106819 GTCTGCATGATTGGCCCTCT 60.107 55.000 0.00 0.00 0.00 3.69
5400 8793 4.127744 CATGGTGGCGGGGATGGT 62.128 66.667 0.00 0.00 0.00 3.55
5416 8809 2.973694 TGGTATTACCTCTTGGTCGC 57.026 50.000 13.90 0.00 44.78 5.19
5467 8860 1.961277 CGGGCGTGCTCTTTGTCTT 60.961 57.895 0.00 0.00 0.00 3.01
5472 8865 1.330521 GCGTGCTCTTTGTCTTTGACA 59.669 47.619 0.00 0.00 41.09 3.58
5517 8910 3.243670 CTGGAAGATCTATGCTCTTCGCA 60.244 47.826 0.00 5.57 46.24 5.10
5526 8919 1.079127 GCTCTTCGCACTTGCCCTA 60.079 57.895 0.00 0.00 38.92 3.53
5534 8927 0.615850 GCACTTGCCCTAGAGACCTT 59.384 55.000 0.00 0.00 34.31 3.50
5612 9008 3.320078 CTCGCGGGCGTCGTTATG 61.320 66.667 13.21 0.00 41.72 1.90
5650 9046 2.347322 GGCGCTCCTCTCTGTGTCT 61.347 63.158 7.64 0.00 0.00 3.41
5668 9065 1.214175 TCTGGGTTCTGGCTGAAAACA 59.786 47.619 8.48 9.51 36.30 2.83
5722 9119 2.280186 CGCCGTTATCCCTCCTGC 60.280 66.667 0.00 0.00 0.00 4.85
5813 9214 0.179148 CGGTAGCATAGTCGTGTGCA 60.179 55.000 0.00 0.00 43.04 4.57
5841 9242 4.166050 CGTGATCCGATCATCTTGGGATG 61.166 52.174 14.15 0.09 43.80 3.51
5855 9256 1.076549 GGATGGGCAGTGTTTGGGA 59.923 57.895 0.00 0.00 0.00 4.37
5938 9340 0.249699 CGGGGCAAAAACCTGTTTCC 60.250 55.000 0.00 0.00 31.45 3.13
6024 9499 2.104170 TCGGTGCCCTTGTTTCTTTTT 58.896 42.857 0.00 0.00 0.00 1.94
6025 9500 2.100087 TCGGTGCCCTTGTTTCTTTTTC 59.900 45.455 0.00 0.00 0.00 2.29
6259 9757 7.063593 TGGTAGCTCTGAGATAGTAAGTTCAT 58.936 38.462 9.28 0.00 0.00 2.57
6305 9806 2.041922 ACCTCCGGCCTCTGCATA 60.042 61.111 0.00 0.00 40.13 3.14
6437 9943 3.904800 TTGATGAAGAGGTGCCGATTA 57.095 42.857 0.00 0.00 0.00 1.75
6490 9996 4.462483 CCAAAGCCTAACATCTAAAGCCAA 59.538 41.667 0.00 0.00 0.00 4.52
6495 10001 4.600062 CCTAACATCTAAAGCCAAAGGGT 58.400 43.478 0.00 0.00 36.17 4.34
6523 10029 2.046023 CGCATTGCTGGGTCTGGA 60.046 61.111 7.12 0.00 0.00 3.86
6573 10079 3.379445 ACCGCCGTCGTCTTCCAT 61.379 61.111 0.00 0.00 0.00 3.41
6586 10092 4.056740 CGTCTTCCATCAATCCATCTCTG 58.943 47.826 0.00 0.00 0.00 3.35
6689 10195 1.569003 CATCAACACGCGCTTGTCA 59.431 52.632 20.59 10.37 0.00 3.58
6725 10231 4.592192 ATGCCACCGAGATCCGCG 62.592 66.667 0.00 0.00 36.84 6.46
6758 10264 3.195610 TGGTAGATGTAACACTGCTCCTG 59.804 47.826 0.00 0.00 0.00 3.86
6805 10313 1.304052 CCAAAACGATGCCCCCAGA 60.304 57.895 0.00 0.00 0.00 3.86
6844 10352 2.726180 GCCGTCATCGTCCGATCG 60.726 66.667 8.51 8.51 31.62 3.69
6878 10386 2.967201 TCTAGGGTTTCCTCGTGAACAA 59.033 45.455 0.00 0.00 43.66 2.83
7007 10516 3.872728 CGCGTCGTCCCGATCTCA 61.873 66.667 0.00 0.00 38.42 3.27
7068 10577 3.066190 CCGCCACCAGTACTCCGA 61.066 66.667 0.00 0.00 0.00 4.55
7138 10648 1.445582 ACGCGAAGAATGGACGACC 60.446 57.895 15.93 0.00 0.00 4.79
7145 10655 2.762535 AGAATGGACGACCGATTTGT 57.237 45.000 0.00 0.00 39.42 2.83
7307 10818 4.552365 CCCGGTCGAGCCATGCAT 62.552 66.667 9.39 0.00 36.97 3.96
7308 10819 3.274586 CCGGTCGAGCCATGCATG 61.275 66.667 20.19 20.19 36.97 4.06
7385 10896 2.203070 GCCTATGCCGGTGACAGG 60.203 66.667 1.90 6.24 0.00 4.00
7418 10929 4.043200 GCGTCTTGGTTGGCTGCC 62.043 66.667 12.87 12.87 0.00 4.85
7476 10987 3.129502 CGTCGCGAGGGGTCACTA 61.130 66.667 20.58 0.00 0.00 2.74
7477 10988 2.799371 GTCGCGAGGGGTCACTAG 59.201 66.667 10.24 0.00 0.00 2.57
7478 10989 1.748122 GTCGCGAGGGGTCACTAGA 60.748 63.158 10.24 0.00 0.00 2.43
7506 11018 4.763279 TCTCTTGATGGTGTACTTACGACA 59.237 41.667 0.00 0.00 0.00 4.35
7545 11058 9.628500 AAGTTCACTTTACCTGAGTAGAAAAAT 57.372 29.630 0.00 0.00 30.82 1.82
7578 11124 7.549839 CATCCAAAATGATGTGGTAGTTTCAT 58.450 34.615 0.00 0.00 37.85 2.57
7597 11143 6.814954 TTCATCAAAATAGCTACTCCCTCT 57.185 37.500 0.00 0.00 0.00 3.69
7676 11236 1.275573 ACGGAGGGAGTTGCTCTTAAC 59.724 52.381 0.00 0.00 0.00 2.01
7679 11239 3.385111 CGGAGGGAGTTGCTCTTAACTAT 59.615 47.826 0.00 0.00 40.78 2.12
7704 11266 9.678260 ATTTGAAGAGAGCACTAGTGATTTTAT 57.322 29.630 27.08 8.34 0.00 1.40
7705 11267 9.507329 TTTGAAGAGAGCACTAGTGATTTTATT 57.493 29.630 27.08 15.28 0.00 1.40
7816 11686 9.716507 AATTTGATGTATTTATTCGTCTTTCCG 57.283 29.630 0.00 0.00 0.00 4.30
7837 11725 8.736751 TTCCGTCTAAGATTATTTTGCAAAAC 57.263 30.769 26.05 13.68 0.00 2.43
8261 12152 5.106712 CGCAAATTTCTGCCTAGTCTTTGTA 60.107 40.000 0.00 0.00 39.26 2.41
8265 12156 5.801531 TTTCTGCCTAGTCTTTGTACTGA 57.198 39.130 0.00 0.00 0.00 3.41
8328 12219 7.945134 AGATGGATTGTAATGTCTTTTATGCC 58.055 34.615 0.00 0.00 0.00 4.40
8396 12289 4.838986 AGCTGGAGGACTACTGTTCTTAAA 59.161 41.667 0.00 0.00 30.76 1.52
8397 12290 5.307196 AGCTGGAGGACTACTGTTCTTAAAA 59.693 40.000 0.00 0.00 30.76 1.52
8462 12356 5.505780 TCCTCACTTGAAAACTTGAAAGGA 58.494 37.500 0.00 0.00 0.00 3.36
8639 12534 5.007034 TCGTATGACCATTTTTGGTGATGT 58.993 37.500 1.66 0.00 43.24 3.06
8702 12597 5.245075 GGTCCATGATGTTTTGACCCTAAAA 59.755 40.000 7.18 0.00 39.65 1.52
8755 12650 0.590481 GACAAAACGCCACGAACCAC 60.590 55.000 0.00 0.00 0.00 4.16
8771 12666 3.491405 ACGGGGTTTTGGACGGGT 61.491 61.111 0.00 0.00 0.00 5.28
8803 12699 1.496060 AGACCATGGCGTCTTCCATA 58.504 50.000 13.04 0.00 44.63 2.74
8817 12713 3.576550 TCTTCCATACAACCAAAAAGCCC 59.423 43.478 0.00 0.00 0.00 5.19
8913 12816 5.815222 AGGTCAAAATAGTGGTTTTGTTTGC 59.185 36.000 10.71 0.00 45.04 3.68
8935 12838 4.378774 CAAATTGATTGTTGGGTTGCAGA 58.621 39.130 0.00 0.00 34.16 4.26
8989 12892 3.862267 TGCAATGGTTTTTGTTGAAGTCG 59.138 39.130 0.00 0.00 0.00 4.18
9039 12942 7.751047 ATGTTAGTTACATATGACACGTGTC 57.249 36.000 36.01 36.01 45.62 3.67
9040 12943 6.094719 TGTTAGTTACATATGACACGTGTCC 58.905 40.000 38.12 23.28 44.15 4.02
9041 12944 4.119442 AGTTACATATGACACGTGTCCC 57.881 45.455 38.12 21.25 44.15 4.46
9042 12945 3.118884 AGTTACATATGACACGTGTCCCC 60.119 47.826 38.12 20.55 44.15 4.81
9043 12946 0.539986 ACATATGACACGTGTCCCCC 59.460 55.000 38.12 20.20 44.15 5.40
9060 12963 2.692741 CCCCCTCCACCTCCCTTC 60.693 72.222 0.00 0.00 0.00 3.46
9061 12964 2.456840 CCCCTCCACCTCCCTTCT 59.543 66.667 0.00 0.00 0.00 2.85
9062 12965 1.997874 CCCCTCCACCTCCCTTCTG 60.998 68.421 0.00 0.00 0.00 3.02
9063 12966 2.674220 CCCTCCACCTCCCTTCTGC 61.674 68.421 0.00 0.00 0.00 4.26
9064 12967 1.920325 CCTCCACCTCCCTTCTGCA 60.920 63.158 0.00 0.00 0.00 4.41
9065 12968 1.298014 CTCCACCTCCCTTCTGCAC 59.702 63.158 0.00 0.00 0.00 4.57
9066 12969 2.190488 CTCCACCTCCCTTCTGCACC 62.190 65.000 0.00 0.00 0.00 5.01
9067 12970 2.352805 CACCTCCCTTCTGCACCC 59.647 66.667 0.00 0.00 0.00 4.61
9068 12971 2.936032 ACCTCCCTTCTGCACCCC 60.936 66.667 0.00 0.00 0.00 4.95
9069 12972 2.935481 CCTCCCTTCTGCACCCCA 60.935 66.667 0.00 0.00 0.00 4.96
9070 12973 2.352805 CTCCCTTCTGCACCCCAC 59.647 66.667 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.625607 ACTTGTCGATTTCCCTTCTCTT 57.374 40.909 0.00 0.00 0.00 2.85
5 6 6.570692 TGTATACTTGTCGATTTCCCTTCTC 58.429 40.000 4.17 0.00 0.00 2.87
6 7 6.540438 TGTATACTTGTCGATTTCCCTTCT 57.460 37.500 4.17 0.00 0.00 2.85
8 9 7.415206 GCAATTGTATACTTGTCGATTTCCCTT 60.415 37.037 7.40 0.00 0.00 3.95
9 10 6.038271 GCAATTGTATACTTGTCGATTTCCCT 59.962 38.462 7.40 0.00 0.00 4.20
10 11 6.183360 TGCAATTGTATACTTGTCGATTTCCC 60.183 38.462 7.40 0.00 0.00 3.97
11 12 6.781138 TGCAATTGTATACTTGTCGATTTCC 58.219 36.000 7.40 0.00 0.00 3.13
13 14 7.417612 GGATGCAATTGTATACTTGTCGATTT 58.582 34.615 11.21 0.00 0.00 2.17
14 15 6.017109 GGGATGCAATTGTATACTTGTCGATT 60.017 38.462 17.09 0.00 0.00 3.34
15 16 5.470098 GGGATGCAATTGTATACTTGTCGAT 59.530 40.000 17.09 0.00 0.00 3.59
16 17 4.814234 GGGATGCAATTGTATACTTGTCGA 59.186 41.667 17.09 0.00 0.00 4.20
17 18 4.574421 TGGGATGCAATTGTATACTTGTCG 59.426 41.667 17.09 0.00 0.00 4.35
18 19 5.504010 CGTGGGATGCAATTGTATACTTGTC 60.504 44.000 17.09 2.80 0.00 3.18
19 20 4.335315 CGTGGGATGCAATTGTATACTTGT 59.665 41.667 17.09 0.00 0.00 3.16
20 21 4.335315 ACGTGGGATGCAATTGTATACTTG 59.665 41.667 17.09 10.22 0.00 3.16
21 22 4.523083 ACGTGGGATGCAATTGTATACTT 58.477 39.130 17.09 0.72 0.00 2.24
22 23 4.150897 ACGTGGGATGCAATTGTATACT 57.849 40.909 17.09 0.00 0.00 2.12
23 24 4.084013 GCTACGTGGGATGCAATTGTATAC 60.084 45.833 10.11 10.11 0.00 1.47
24 25 4.062293 GCTACGTGGGATGCAATTGTATA 58.938 43.478 9.16 0.00 0.00 1.47
25 26 2.878406 GCTACGTGGGATGCAATTGTAT 59.122 45.455 8.93 8.93 0.00 2.29
26 27 2.285083 GCTACGTGGGATGCAATTGTA 58.715 47.619 7.40 2.30 0.00 2.41
27 28 1.094785 GCTACGTGGGATGCAATTGT 58.905 50.000 7.40 0.00 0.00 2.71
28 29 1.064505 CTGCTACGTGGGATGCAATTG 59.935 52.381 0.00 0.00 34.90 2.32
29 30 1.382522 CTGCTACGTGGGATGCAATT 58.617 50.000 0.00 0.00 34.90 2.32
30 31 1.097547 GCTGCTACGTGGGATGCAAT 61.098 55.000 0.00 0.00 34.90 3.56
31 32 1.745115 GCTGCTACGTGGGATGCAA 60.745 57.895 0.00 0.00 34.90 4.08
32 33 2.125147 GCTGCTACGTGGGATGCA 60.125 61.111 0.00 0.00 0.00 3.96
33 34 3.264897 CGCTGCTACGTGGGATGC 61.265 66.667 0.00 1.36 0.00 3.91
34 35 2.184322 ACGCTGCTACGTGGGATG 59.816 61.111 0.00 0.00 46.28 3.51
41 42 0.519175 GCAAACATGACGCTGCTACG 60.519 55.000 0.00 0.00 39.50 3.51
42 43 0.179189 GGCAAACATGACGCTGCTAC 60.179 55.000 0.00 0.00 35.13 3.58
43 44 0.321564 AGGCAAACATGACGCTGCTA 60.322 50.000 0.00 0.00 35.13 3.49
44 45 1.580845 GAGGCAAACATGACGCTGCT 61.581 55.000 0.00 0.00 35.13 4.24
45 46 1.154150 GAGGCAAACATGACGCTGC 60.154 57.895 0.00 2.07 0.00 5.25
46 47 0.110056 GTGAGGCAAACATGACGCTG 60.110 55.000 0.00 0.00 0.00 5.18
47 48 1.237285 GGTGAGGCAAACATGACGCT 61.237 55.000 0.00 0.00 0.00 5.07
48 49 1.210155 GGTGAGGCAAACATGACGC 59.790 57.895 0.00 0.00 0.00 5.19
49 50 0.888736 TGGGTGAGGCAAACATGACG 60.889 55.000 0.00 0.00 0.00 4.35
50 51 1.203052 CATGGGTGAGGCAAACATGAC 59.797 52.381 0.00 0.00 40.92 3.06
51 52 1.075212 TCATGGGTGAGGCAAACATGA 59.925 47.619 0.00 0.00 43.83 3.07
52 53 1.548081 TCATGGGTGAGGCAAACATG 58.452 50.000 0.00 0.00 40.06 3.21
53 54 2.173519 CTTCATGGGTGAGGCAAACAT 58.826 47.619 0.00 0.00 35.39 2.71
54 55 1.133513 ACTTCATGGGTGAGGCAAACA 60.134 47.619 0.00 0.00 35.01 2.83
55 56 1.541588 GACTTCATGGGTGAGGCAAAC 59.458 52.381 0.00 0.00 35.01 2.93
56 57 1.144708 TGACTTCATGGGTGAGGCAAA 59.855 47.619 0.00 0.00 35.01 3.68
57 58 0.770499 TGACTTCATGGGTGAGGCAA 59.230 50.000 0.00 0.00 35.01 4.52
58 59 0.994247 ATGACTTCATGGGTGAGGCA 59.006 50.000 0.00 0.00 35.01 4.75
59 60 3.890527 ATGACTTCATGGGTGAGGC 57.109 52.632 0.00 0.00 35.01 4.70
68 69 5.624159 TGGAGAAAGTGAACATGACTTCAT 58.376 37.500 0.00 0.00 32.33 2.57
69 70 5.034852 TGGAGAAAGTGAACATGACTTCA 57.965 39.130 0.00 0.00 32.33 3.02
70 71 4.083590 GCTGGAGAAAGTGAACATGACTTC 60.084 45.833 0.00 0.00 32.33 3.01
71 72 3.817647 GCTGGAGAAAGTGAACATGACTT 59.182 43.478 0.00 0.00 35.08 3.01
72 73 3.072184 AGCTGGAGAAAGTGAACATGACT 59.928 43.478 0.00 0.00 0.00 3.41
73 74 3.406764 AGCTGGAGAAAGTGAACATGAC 58.593 45.455 0.00 0.00 0.00 3.06
74 75 3.777106 AGCTGGAGAAAGTGAACATGA 57.223 42.857 0.00 0.00 0.00 3.07
75 76 3.937706 CCTAGCTGGAGAAAGTGAACATG 59.062 47.826 0.00 0.00 38.35 3.21
76 77 3.584848 ACCTAGCTGGAGAAAGTGAACAT 59.415 43.478 0.00 0.00 39.71 2.71
77 78 2.972713 ACCTAGCTGGAGAAAGTGAACA 59.027 45.455 0.00 0.00 39.71 3.18
78 79 3.330267 CACCTAGCTGGAGAAAGTGAAC 58.670 50.000 0.00 0.00 39.71 3.18
79 80 2.303022 CCACCTAGCTGGAGAAAGTGAA 59.697 50.000 0.00 0.00 39.71 3.18
80 81 1.902508 CCACCTAGCTGGAGAAAGTGA 59.097 52.381 0.00 0.00 39.71 3.41
81 82 1.677217 GCCACCTAGCTGGAGAAAGTG 60.677 57.143 8.36 0.00 39.71 3.16
82 83 0.615850 GCCACCTAGCTGGAGAAAGT 59.384 55.000 8.36 0.00 39.71 2.66
83 84 0.460987 CGCCACCTAGCTGGAGAAAG 60.461 60.000 8.36 0.00 39.71 2.62
84 85 1.192146 ACGCCACCTAGCTGGAGAAA 61.192 55.000 14.09 0.00 39.71 2.52
85 86 1.192146 AACGCCACCTAGCTGGAGAA 61.192 55.000 14.09 0.00 39.71 2.87
86 87 1.192146 AAACGCCACCTAGCTGGAGA 61.192 55.000 14.09 0.00 39.71 3.71
87 88 1.021390 CAAACGCCACCTAGCTGGAG 61.021 60.000 8.36 7.27 39.71 3.86
88 89 1.003839 CAAACGCCACCTAGCTGGA 60.004 57.895 8.36 0.00 39.71 3.86
89 90 2.040544 CCAAACGCCACCTAGCTGG 61.041 63.158 0.00 0.00 42.93 4.85
90 91 0.889186 AACCAAACGCCACCTAGCTG 60.889 55.000 0.00 0.00 0.00 4.24
91 92 0.605589 GAACCAAACGCCACCTAGCT 60.606 55.000 0.00 0.00 0.00 3.32
92 93 0.605589 AGAACCAAACGCCACCTAGC 60.606 55.000 0.00 0.00 0.00 3.42
93 94 1.156736 CAGAACCAAACGCCACCTAG 58.843 55.000 0.00 0.00 0.00 3.02
463 671 0.393944 AGATCGAGCTACACCGTCCA 60.394 55.000 0.00 0.00 0.00 4.02
557 767 2.363406 GGGGCTGGCTTGCTGATT 60.363 61.111 0.00 0.00 0.00 2.57
847 3607 3.414700 CTGTCGACGTTGCAGGCC 61.415 66.667 11.62 0.00 0.00 5.19
852 3612 2.875080 AAATAAGCTGTCGACGTTGC 57.125 45.000 11.62 14.64 0.00 4.17
859 3619 3.888934 AGTGCAACAAAATAAGCTGTCG 58.111 40.909 0.00 0.00 41.43 4.35
883 3646 1.576421 GAAGGCACGCAGAAACCAG 59.424 57.895 0.00 0.00 0.00 4.00
884 3647 1.896660 GGAAGGCACGCAGAAACCA 60.897 57.895 0.00 0.00 0.00 3.67
885 3648 1.856265 CTGGAAGGCACGCAGAAACC 61.856 60.000 0.00 0.00 0.00 3.27
886 3649 1.166531 ACTGGAAGGCACGCAGAAAC 61.167 55.000 0.00 0.00 39.30 2.78
902 3665 9.915629 GAATTTATATATAGCCGGATAGGACTG 57.084 37.037 5.05 0.00 45.00 3.51
978 3742 2.933573 CTAACCCTCTCGCTTCTCCTA 58.066 52.381 0.00 0.00 0.00 2.94
995 3759 2.560504 CATAGTCAACCGCCATGCTAA 58.439 47.619 0.00 0.00 0.00 3.09
1117 3897 3.878778 AGAATTAAGAGAGGCATGCGTT 58.121 40.909 15.04 3.38 0.00 4.84
1142 3934 1.502231 ACGAGTACTTGCTGCACTTG 58.498 50.000 10.23 2.59 31.22 3.16
1143 3935 3.380479 TTACGAGTACTTGCTGCACTT 57.620 42.857 10.23 0.00 0.00 3.16
1175 3994 4.354587 GCATGCCTAGCACAAATTAAGAC 58.645 43.478 6.36 0.00 43.04 3.01
1311 4137 1.001974 TGGAAACATCACAGACGGAGG 59.998 52.381 0.00 0.00 33.40 4.30
1419 4245 8.885693 ATCACTATGCTCTAGACATACCAATA 57.114 34.615 9.58 0.00 0.00 1.90
1496 4329 8.895932 AGATTCGTGTAAACATTTTCATTAGC 57.104 30.769 0.00 0.00 0.00 3.09
1512 4345 6.533819 TTGATTTTACGTGAAGATTCGTGT 57.466 33.333 0.00 0.00 40.50 4.49
1545 4378 6.356556 TGCCATAAGTATTGCACATCTAAGT 58.643 36.000 0.00 0.00 30.49 2.24
1633 4466 1.990060 GAGCACCCAGGCACTCCTA 60.990 63.158 0.00 0.00 41.93 2.94
1654 4487 8.240267 TCCAAATTTAATTTTCGTATAGGGGG 57.760 34.615 0.00 0.00 0.00 5.40
1773 4607 9.744468 GTATTTTCCTCGCCACATATAAATTTT 57.256 29.630 0.00 0.00 0.00 1.82
1778 4612 6.588204 ACTGTATTTTCCTCGCCACATATAA 58.412 36.000 0.00 0.00 0.00 0.98
1791 4625 8.581578 TGGATTTTAGTTTGGACTGTATTTTCC 58.418 33.333 0.00 0.00 36.60 3.13
2510 5575 5.469421 TGAAACCATGGAATTGAATTGTTGC 59.531 36.000 21.47 0.00 0.00 4.17
2579 5644 1.069513 ACATTTTGACCTCGGTGTCGA 59.930 47.619 0.00 0.00 43.86 4.20
2608 5673 1.203523 TGTTTGTTGTGGAGTTGTGGC 59.796 47.619 0.00 0.00 0.00 5.01
2649 5714 3.117046 GTGCTGCTAGAGACGGTATTTC 58.883 50.000 0.00 0.00 0.00 2.17
2696 5762 6.993308 GGGTTTTAATTATGTTTTGGTGGTGT 59.007 34.615 0.00 0.00 0.00 4.16
3106 6181 8.402798 TCATAGTCCTTTTAAATGCTCACAAA 57.597 30.769 0.00 0.00 0.00 2.83
3459 6539 2.739996 CCGGCCCATGAAGCTCTCT 61.740 63.158 0.00 0.00 0.00 3.10
3520 6600 1.913419 TCGGCCTTGGAGGTCTTATTT 59.087 47.619 0.00 0.00 38.01 1.40
3558 6668 2.769663 AGTGGAGTTGTAAGGTGTGTGA 59.230 45.455 0.00 0.00 0.00 3.58
3685 6801 5.617252 TCTCGAGGAAAAGTTATTGTGGTT 58.383 37.500 13.56 0.00 0.00 3.67
3977 7165 0.834612 TCGACTCCAAGTTGGTGGTT 59.165 50.000 24.08 7.69 39.03 3.67
4259 7559 7.431249 TCGAACTGTAACTAAAAGAGACACAT 58.569 34.615 0.00 0.00 0.00 3.21
4405 7710 3.799755 GTGTTCCGATGGTGGCGC 61.800 66.667 0.00 0.00 0.00 6.53
4806 8114 2.207924 ACCTACCCATCGATCCGCC 61.208 63.158 0.00 0.00 0.00 6.13
4838 8146 1.109920 ACTGGCAGAGACACGACACT 61.110 55.000 23.66 0.00 0.00 3.55
4867 8192 1.286248 GCTTAGAACCAGGGGAGGAA 58.714 55.000 0.00 0.00 0.00 3.36
4931 8270 3.909086 GACTCACCCTGGGCACTGC 62.909 68.421 14.08 0.00 0.00 4.40
4940 8279 2.637383 GCGAACTCCGACTCACCCT 61.637 63.158 0.00 0.00 41.76 4.34
4962 8301 2.652095 CCCAAGCGTACCTTCCCGA 61.652 63.158 0.00 0.00 0.00 5.14
4991 8330 3.231736 ACGACCCACGAGCACCTT 61.232 61.111 0.00 0.00 45.77 3.50
4998 8337 2.567497 GGAACCTCACGACCCACGA 61.567 63.158 0.00 0.00 45.77 4.35
5002 8341 1.605971 GGAGAGGAACCTCACGACCC 61.606 65.000 20.84 10.64 44.99 4.46
5003 8342 0.612453 AGGAGAGGAACCTCACGACC 60.612 60.000 20.84 16.69 44.99 4.79
5004 8343 2.964343 AGGAGAGGAACCTCACGAC 58.036 57.895 20.84 9.09 44.99 4.34
5021 8360 4.487412 GTCCACCGTACCCGCGAG 62.487 72.222 8.23 0.00 0.00 5.03
5074 8461 1.375523 GGCCGTTGACACCGATCTT 60.376 57.895 0.00 0.00 0.00 2.40
5312 8705 1.679944 CGGCATTCATGTCCAGGACTT 60.680 52.381 20.82 11.72 33.15 3.01
5369 8762 1.372683 CCATGATACCCGCCAGAGG 59.627 63.158 0.00 0.00 0.00 3.69
5373 8766 2.915079 CCACCATGATACCCGCCA 59.085 61.111 0.00 0.00 0.00 5.69
5380 8773 1.760527 CATCCCCGCCACCATGATA 59.239 57.895 0.00 0.00 0.00 2.15
5517 8910 3.041946 CCATAAGGTCTCTAGGGCAAGT 58.958 50.000 0.00 0.00 0.00 3.16
5534 8927 2.731571 GCTCCCCTGCGTCACCATA 61.732 63.158 0.00 0.00 0.00 2.74
5612 9008 3.181516 GCCATGACGATGTCTTCAAGAAC 60.182 47.826 0.00 0.00 33.15 3.01
5650 9046 2.158475 AGATGTTTTCAGCCAGAACCCA 60.158 45.455 0.00 0.00 36.83 4.51
5688 9085 4.496670 GCTAGGCGTCGTCATTGT 57.503 55.556 0.00 0.00 0.00 2.71
5722 9119 4.025401 GCTCCACAACAACGCCCG 62.025 66.667 0.00 0.00 0.00 6.13
5813 9214 2.298446 AGATGATCGGATCACGCAGAAT 59.702 45.455 22.09 5.31 43.01 2.40
5841 9242 2.991540 GGCTCCCAAACACTGCCC 60.992 66.667 0.00 0.00 37.81 5.36
5855 9256 2.090267 AGATAGAAGGAGATGGGTGGCT 60.090 50.000 0.00 0.00 0.00 4.75
6007 9479 3.384789 AGAGGAAAAAGAAACAAGGGCAC 59.615 43.478 0.00 0.00 0.00 5.01
6024 9499 1.550327 AGCACAACGATGAGAGAGGA 58.450 50.000 0.00 0.00 0.00 3.71
6025 9500 2.094286 AGAAGCACAACGATGAGAGAGG 60.094 50.000 0.00 0.00 0.00 3.69
6204 9693 9.407514 CAAATTAAATTCGTGTGTTGTTCTTTG 57.592 29.630 0.00 0.00 0.00 2.77
6305 9806 1.033202 TGGCTGCATGCATCGTTCAT 61.033 50.000 22.97 0.00 45.15 2.57
6379 9885 3.943381 GACAGATGTTGCCAAGATGATGA 59.057 43.478 0.00 0.00 0.00 2.92
6437 9943 4.702131 GTCTGTTTGGTATTTGGCTCAGAT 59.298 41.667 0.00 0.00 34.15 2.90
6465 9971 4.096532 GGCTTTAGATGTTAGGCTTTGGTC 59.903 45.833 0.00 0.00 0.00 4.02
6490 9996 2.115266 CGGCTTGGTTGGACCCTT 59.885 61.111 0.00 0.00 37.50 3.95
6495 10001 2.929903 GCAATGCGGCTTGGTTGGA 61.930 57.895 0.00 0.00 0.00 3.53
6523 10029 2.421739 GTCAGACCGGTGTGTGCT 59.578 61.111 28.90 9.34 35.79 4.40
6573 10079 1.767088 CCTGCTCCAGAGATGGATTGA 59.233 52.381 0.00 0.00 37.34 2.57
6586 10092 1.871408 CGATGCATCAGTACCTGCTCC 60.871 57.143 25.70 0.00 39.16 4.70
6600 10106 2.046023 CCTGGCAAGGTCGATGCA 60.046 61.111 11.32 0.00 45.60 3.96
6725 10231 1.549170 ACATCTACCACAAGACCGACC 59.451 52.381 0.00 0.00 0.00 4.79
6731 10237 4.283467 AGCAGTGTTACATCTACCACAAGA 59.717 41.667 0.00 0.00 0.00 3.02
6758 10264 0.978146 TAGCTGGAGGGGACAAGAGC 60.978 60.000 0.00 0.00 0.00 4.09
6805 10313 3.416156 GCCTTCAGTGTCATTCTTCCTT 58.584 45.455 0.00 0.00 0.00 3.36
6878 10386 1.211969 CACGTCAACTCGATCGGGT 59.788 57.895 16.63 16.63 34.70 5.28
7116 10626 4.590487 TCCATTCTTCGCGTGGAC 57.410 55.556 11.01 0.00 37.12 4.02
7138 10648 1.452110 TCTGGATGCCACACAAATCG 58.548 50.000 0.00 0.00 0.00 3.34
7145 10655 2.190313 GCGGATCTGGATGCCACA 59.810 61.111 3.14 0.00 0.00 4.17
7200 10710 2.671070 CCATGGTCGCTGGGAACT 59.329 61.111 11.23 0.00 31.85 3.01
7293 10804 1.890979 CCTCATGCATGGCTCGACC 60.891 63.158 25.97 0.00 39.84 4.79
7299 10810 2.123428 GGTGACCCTCATGCATGGC 61.123 63.158 25.97 3.51 0.00 4.40
7477 10988 0.908198 ACACCATCAAGAGAGCCCTC 59.092 55.000 0.00 0.00 39.72 4.30
7478 10989 1.834263 GTACACCATCAAGAGAGCCCT 59.166 52.381 0.00 0.00 0.00 5.19
7488 11000 4.859304 AAGTGTCGTAAGTACACCATCA 57.141 40.909 0.00 0.00 44.17 3.07
7569 11115 7.988028 AGGGAGTAGCTATTTTGATGAAACTAC 59.012 37.037 0.00 0.00 30.36 2.73
7575 11121 5.663106 ACAGAGGGAGTAGCTATTTTGATGA 59.337 40.000 0.00 0.00 0.00 2.92
7578 11124 5.273208 AGACAGAGGGAGTAGCTATTTTGA 58.727 41.667 0.00 0.00 0.00 2.69
7639 11185 6.273730 TCCCTCCGTCCCATAATATAAAACAT 59.726 38.462 0.00 0.00 0.00 2.71
7640 11186 5.607592 TCCCTCCGTCCCATAATATAAAACA 59.392 40.000 0.00 0.00 0.00 2.83
7676 11236 8.715191 AAATCACTAGTGCTCTCTTCAAATAG 57.285 34.615 18.45 0.00 0.00 1.73
7679 11239 9.507329 AATAAAATCACTAGTGCTCTCTTCAAA 57.493 29.630 18.45 0.00 0.00 2.69
7721 11283 2.266554 CCGACAGTCTCTGAATCTTGC 58.733 52.381 3.70 0.00 35.18 4.01
7792 11358 8.259049 ACGGAAAGACGAATAAATACATCAAA 57.741 30.769 0.00 0.00 37.61 2.69
7882 11773 4.410492 GTGCAATCCACACAAGAACTAG 57.590 45.455 0.00 0.00 44.06 2.57
8163 12054 5.339990 GTGCGAGTTATTTGTTGGCATTAT 58.660 37.500 0.00 0.00 0.00 1.28
8164 12055 4.380023 GGTGCGAGTTATTTGTTGGCATTA 60.380 41.667 0.00 0.00 0.00 1.90
8165 12056 3.574614 GTGCGAGTTATTTGTTGGCATT 58.425 40.909 0.00 0.00 0.00 3.56
8166 12057 2.094752 GGTGCGAGTTATTTGTTGGCAT 60.095 45.455 0.00 0.00 0.00 4.40
8261 12152 9.770097 CTAGAATCACCATTACATATGTTCAGT 57.230 33.333 14.77 4.30 0.00 3.41
8328 12219 5.805994 GGGTAACTAGAGTCTTGTTCATTCG 59.194 44.000 20.90 0.00 32.46 3.34
8365 12258 3.401002 AGTAGTCCTCCAGCTATCTCCAT 59.599 47.826 0.00 0.00 0.00 3.41
8375 12268 9.372369 CTAATTTTAAGAACAGTAGTCCTCCAG 57.628 37.037 0.00 0.00 0.00 3.86
8413 12306 2.282180 TCGTGGAAAAGCAGGGGC 60.282 61.111 0.00 0.00 41.61 5.80
8414 12307 2.325082 CGTCGTGGAAAAGCAGGGG 61.325 63.158 0.00 0.00 0.00 4.79
8415 12308 1.291877 CTCGTCGTGGAAAAGCAGGG 61.292 60.000 0.00 0.00 0.00 4.45
8416 12309 0.319555 TCTCGTCGTGGAAAAGCAGG 60.320 55.000 0.00 0.00 0.00 4.85
8417 12310 1.063806 CTCTCGTCGTGGAAAAGCAG 58.936 55.000 0.00 0.00 0.00 4.24
8418 12311 0.944311 GCTCTCGTCGTGGAAAAGCA 60.944 55.000 0.00 0.00 0.00 3.91
8462 12356 7.519843 CGCGACAGTTTCTAGTATACTATGAT 58.480 38.462 12.98 0.56 0.00 2.45
8497 12391 5.052481 GTCCCTATAATTAAAGAACGGCGT 58.948 41.667 6.77 6.77 0.00 5.68
8613 12508 5.496556 TCACCAAAAATGGTCATACGAGAT 58.503 37.500 0.00 0.00 40.85 2.75
8618 12513 6.266168 TGACATCACCAAAAATGGTCATAC 57.734 37.500 0.00 0.00 40.85 2.39
8639 12534 1.979855 CCAAGTGTCATGGGTGTTGA 58.020 50.000 0.00 0.00 34.15 3.18
8654 12549 0.958091 TGTTTTCCATGCGACCCAAG 59.042 50.000 0.00 0.00 0.00 3.61
8661 12556 0.244450 ACCATGCTGTTTTCCATGCG 59.756 50.000 0.00 0.00 37.96 4.73
8702 12597 1.882352 GCCAAGTCACACGGGAGAAAT 60.882 52.381 0.00 0.00 0.00 2.17
8755 12650 2.981350 CACCCGTCCAAAACCCCG 60.981 66.667 0.00 0.00 0.00 5.73
8782 12678 0.535335 TGGAAGACGCCATGGTCTAC 59.465 55.000 14.67 6.80 46.21 2.59
8803 12699 2.771372 ACATTCAGGGCTTTTTGGTTGT 59.229 40.909 0.00 0.00 0.00 3.32
8856 12752 2.568509 AGCATGATTTGACCCCCTTTTG 59.431 45.455 0.00 0.00 0.00 2.44
8857 12753 2.906568 AGCATGATTTGACCCCCTTTT 58.093 42.857 0.00 0.00 0.00 2.27
8913 12816 4.211794 GTCTGCAACCCAACAATCAATTTG 59.788 41.667 0.00 0.00 41.36 2.32
8935 12838 9.672673 AAACACTGAGTCTAGCATAATTAATGT 57.327 29.630 0.00 0.00 37.93 2.71
8989 12892 4.225267 TCTTTCCCCTCACATCTAAACTCC 59.775 45.833 0.00 0.00 0.00 3.85
9043 12946 2.692741 GAAGGGAGGTGGAGGGGG 60.693 72.222 0.00 0.00 0.00 5.40
9044 12947 1.997874 CAGAAGGGAGGTGGAGGGG 60.998 68.421 0.00 0.00 0.00 4.79
9045 12948 2.674220 GCAGAAGGGAGGTGGAGGG 61.674 68.421 0.00 0.00 0.00 4.30
9046 12949 1.920325 TGCAGAAGGGAGGTGGAGG 60.920 63.158 0.00 0.00 0.00 4.30
9047 12950 1.298014 GTGCAGAAGGGAGGTGGAG 59.702 63.158 0.00 0.00 0.00 3.86
9048 12951 2.224159 GGTGCAGAAGGGAGGTGGA 61.224 63.158 0.00 0.00 0.00 4.02
9049 12952 2.352805 GGTGCAGAAGGGAGGTGG 59.647 66.667 0.00 0.00 0.00 4.61
9050 12953 2.352805 GGGTGCAGAAGGGAGGTG 59.647 66.667 0.00 0.00 0.00 4.00
9051 12954 2.936032 GGGGTGCAGAAGGGAGGT 60.936 66.667 0.00 0.00 0.00 3.85
9052 12955 2.935481 TGGGGTGCAGAAGGGAGG 60.935 66.667 0.00 0.00 0.00 4.30
9053 12956 2.352805 GTGGGGTGCAGAAGGGAG 59.647 66.667 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.