Multiple sequence alignment - TraesCS7A01G114200

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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 TraesCS7A01G114200 chr7A 100.000 4823 0 0 1 4823 70239836 70235014 0.000000e+00 8907.0
1 TraesCS7A01G114200 chr7A 83.040 1138 155 28 185 1291 728849496 728848366 0.000000e+00 998.0
2 TraesCS7A01G114200 chr7A 89.353 742 58 11 3615 4351 70246087 70245362 0.000000e+00 913.0
3 TraesCS7A01G114200 chr7A 90.815 577 35 6 3619 4188 70214142 70213577 0.000000e+00 756.0
4 TraesCS7A01G114200 chr7A 81.962 887 101 31 1568 2431 74856686 74857536 0.000000e+00 697.0
5 TraesCS7A01G114200 chr7A 77.690 1264 148 61 1655 2860 70194799 70195986 0.000000e+00 649.0
6 TraesCS7A01G114200 chr7A 81.124 890 86 40 1561 2431 70247926 70247100 5.260000e-179 638.0
7 TraesCS7A01G114200 chr7A 80.367 871 129 26 1647 2477 86466395 86467263 1.470000e-174 623.0
8 TraesCS7A01G114200 chr7A 78.610 1108 108 59 2490 3554 74857558 74858579 8.870000e-172 614.0
9 TraesCS7A01G114200 chr7A 90.575 435 35 5 3758 4188 70197164 70197596 5.420000e-159 571.0
10 TraesCS7A01G114200 chr7A 79.015 853 132 28 1655 2474 85199072 85198234 1.530000e-149 540.0
11 TraesCS7A01G114200 chr7A 76.510 1209 128 71 2235 3389 70215326 70214220 2.570000e-142 516.0
12 TraesCS7A01G114200 chr7A 78.984 709 132 11 1655 2359 70767385 70766690 7.310000e-128 468.0
13 TraesCS7A01G114200 chr7A 87.468 391 23 9 3609 3987 74858681 74859057 1.240000e-115 427.0
14 TraesCS7A01G114200 chr7A 86.828 372 40 7 23 385 97388128 97388499 1.620000e-109 407.0
15 TraesCS7A01G114200 chr7A 85.934 391 33 18 4452 4823 130299976 130300363 9.730000e-107 398.0
16 TraesCS7A01G114200 chr7A 97.826 230 5 0 4594 4823 592060110 592059881 9.730000e-107 398.0
17 TraesCS7A01G114200 chr7A 80.702 513 95 3 1806 2317 634349283 634348774 3.500000e-106 396.0
18 TraesCS7A01G114200 chr7A 97.391 230 6 0 4594 4823 42970725 42970496 4.530000e-105 392.0
19 TraesCS7A01G114200 chr7A 76.493 787 137 29 1635 2392 74883332 74884099 7.570000e-103 385.0
20 TraesCS7A01G114200 chr7A 76.694 738 95 40 2679 3389 70246998 70246311 5.980000e-89 339.0
21 TraesCS7A01G114200 chr7A 78.503 521 100 6 1668 2182 70737192 70736678 1.000000e-86 331.0
22 TraesCS7A01G114200 chr7A 81.592 402 54 14 3209 3608 74594060 74594443 1.010000e-81 315.0
23 TraesCS7A01G114200 chr7A 79.901 403 53 14 3209 3608 634347911 634347534 2.210000e-68 270.0
24 TraesCS7A01G114200 chr7A 85.185 216 21 8 2241 2452 74548714 74548922 1.360000e-50 211.0
25 TraesCS7A01G114200 chr7A 77.603 317 58 6 2633 2949 74549042 74549345 3.840000e-41 180.0
26 TraesCS7A01G114200 chr7A 76.984 252 44 7 3359 3608 47020712 47020473 1.090000e-26 132.0
27 TraesCS7A01G114200 chr7A 80.153 131 19 4 2822 2952 483184678 483184555 1.850000e-14 91.6
28 TraesCS7A01G114200 chr7A 77.381 168 28 5 2785 2952 681276906 681276749 1.850000e-14 91.6
29 TraesCS7A01G114200 chr3A 94.984 1216 52 8 1 1212 58070654 58069444 0.000000e+00 1899.0
30 TraesCS7A01G114200 chr3A 97.826 230 5 0 4594 4823 742380381 742380152 9.730000e-107 398.0
31 TraesCS7A01G114200 chr3A 93.846 260 13 2 4351 4607 181138430 181138689 5.850000e-104 388.0
32 TraesCS7A01G114200 chr1B 90.008 1301 115 11 1 1291 561717652 561716357 0.000000e+00 1668.0
33 TraesCS7A01G114200 chr1B 75.161 777 136 34 1648 2391 678116399 678115647 3.620000e-81 313.0
34 TraesCS7A01G114200 chr1B 94.737 95 4 1 1328 1422 561716365 561716272 3.890000e-31 147.0
35 TraesCS7A01G114200 chr7B 89.530 1299 116 17 1 1291 588260899 588259613 0.000000e+00 1628.0
36 TraesCS7A01G114200 chr7B 87.882 883 67 19 1 877 394863870 394863022 0.000000e+00 1002.0
37 TraesCS7A01G114200 chr7B 88.256 579 52 5 3615 4188 233207346 233206779 0.000000e+00 678.0
38 TraesCS7A01G114200 chr7B 87.209 602 45 14 1 599 394912035 394911463 0.000000e+00 656.0
39 TraesCS7A01G114200 chr7B 87.253 455 43 4 3615 4064 3487769 3487325 5.570000e-139 505.0
40 TraesCS7A01G114200 chr7B 88.389 422 41 5 877 1291 394908337 394907917 7.210000e-138 501.0
41 TraesCS7A01G114200 chr7B 88.152 422 42 5 877 1291 394860397 394859977 3.350000e-136 496.0
42 TraesCS7A01G114200 chr7B 78.799 783 116 30 1655 2401 32898642 32897874 9.390000e-132 481.0
43 TraesCS7A01G114200 chr7B 81.552 580 88 10 1806 2372 34889120 34889693 1.220000e-125 460.0
44 TraesCS7A01G114200 chr7B 77.143 840 140 26 1561 2350 592419069 592418232 1.590000e-119 440.0
45 TraesCS7A01G114200 chr7B 77.933 716 126 19 1667 2372 10880955 10881648 7.470000e-113 418.0
46 TraesCS7A01G114200 chr7B 78.487 595 115 9 1806 2392 10946589 10947178 1.270000e-100 377.0
47 TraesCS7A01G114200 chr7B 76.923 754 113 28 1655 2363 592427404 592426667 5.900000e-99 372.0
48 TraesCS7A01G114200 chr7B 80.049 406 74 5 1667 2071 10891996 10892395 1.310000e-75 294.0
49 TraesCS7A01G114200 chr7B 83.729 295 37 6 3209 3494 8447185 8446893 7.960000e-68 268.0
50 TraesCS7A01G114200 chr7B 91.534 189 16 0 3876 4064 672195790 672195602 1.330000e-65 261.0
51 TraesCS7A01G114200 chr7B 88.532 218 19 5 2241 2452 8448146 8447929 4.790000e-65 259.0
52 TraesCS7A01G114200 chr7B 75.929 565 86 22 1908 2452 10061114 10061648 1.340000e-60 244.0
53 TraesCS7A01G114200 chr7B 78.358 402 68 13 3209 3608 648443133 648443517 4.820000e-60 243.0
54 TraesCS7A01G114200 chr7B 79.006 362 58 13 3248 3608 715226357 715226013 1.040000e-56 231.0
55 TraesCS7A01G114200 chr7B 80.851 282 40 9 3325 3606 32896336 32896069 4.890000e-50 209.0
56 TraesCS7A01G114200 chr7B 73.770 549 111 21 1736 2264 491084294 491083759 8.240000e-43 185.0
57 TraesCS7A01G114200 chr7B 84.865 185 17 7 3611 3794 34891014 34891188 4.960000e-40 176.0
58 TraesCS7A01G114200 chr7B 78.689 244 46 3 2633 2876 8447838 8447601 1.800000e-34 158.0
59 TraesCS7A01G114200 chr7B 88.182 110 11 1 1655 1762 10916482 10916591 3.920000e-26 130.0
60 TraesCS7A01G114200 chr7B 100.000 32 0 0 3778 3809 10918849 10918880 5.210000e-05 60.2
61 TraesCS7A01G114200 chr6B 90.419 1242 102 13 57 1291 638240795 638239564 0.000000e+00 1618.0
62 TraesCS7A01G114200 chr6B 78.999 1438 232 45 13 1422 638561148 638559753 0.000000e+00 918.0
63 TraesCS7A01G114200 chr6B 89.915 585 50 7 1 579 593070409 593069828 0.000000e+00 745.0
64 TraesCS7A01G114200 chr6B 89.109 404 37 3 3666 4064 669522827 669523228 3.350000e-136 496.0
65 TraesCS7A01G114200 chr6B 87.465 359 36 4 933 1291 593069827 593069478 5.810000e-109 405.0
66 TraesCS7A01G114200 chr6B 94.000 100 6 0 1328 1427 593069486 593069387 8.360000e-33 152.0
67 TraesCS7A01G114200 chr3B 89.162 1301 123 12 1 1291 323381724 323383016 0.000000e+00 1605.0
68 TraesCS7A01G114200 chr3B 87.832 452 40 4 3615 4061 109039559 109040000 2.570000e-142 516.0
69 TraesCS7A01G114200 chr3B 80.964 394 58 11 3216 3608 276908650 276909027 3.650000e-76 296.0
70 TraesCS7A01G114200 chr3B 80.711 394 59 11 3216 3608 276882034 276882411 1.700000e-74 291.0
71 TraesCS7A01G114200 chr3B 77.976 168 27 7 2785 2952 751774316 751774159 3.970000e-16 97.1
72 TraesCS7A01G114200 chr3B 87.097 62 4 3 4298 4357 62012508 62012449 3.120000e-07 67.6
73 TraesCS7A01G114200 chr1D 86.018 1316 150 25 1 1291 3952871 3954177 0.000000e+00 1380.0
74 TraesCS7A01G114200 chr1D 82.024 1324 190 29 1 1291 476817976 476819284 0.000000e+00 1083.0
75 TraesCS7A01G114200 chr1D 78.420 519 93 14 782 1291 409008064 409008572 2.170000e-83 320.0
76 TraesCS7A01G114200 chr1D 74.935 774 134 35 1648 2391 486926553 486925810 2.820000e-77 300.0
77 TraesCS7A01G114200 chr1D 93.814 97 6 0 1329 1425 476817852 476817756 3.890000e-31 147.0
78 TraesCS7A01G114200 chr1D 91.089 101 9 0 1322 1422 3954163 3954263 2.340000e-28 137.0
79 TraesCS7A01G114200 chr1D 91.089 101 9 0 1322 1422 454902121 454902221 2.340000e-28 137.0
80 TraesCS7A01G114200 chr1D 92.391 92 7 0 1331 1422 476819279 476819370 1.090000e-26 132.0
81 TraesCS7A01G114200 chr1D 78.571 196 28 6 2163 2351 491971622 491971810 3.050000e-22 117.0
82 TraesCS7A01G114200 chr7D 85.920 1250 150 18 64 1291 178883137 178884382 0.000000e+00 1310.0
83 TraesCS7A01G114200 chr7D 81.300 877 124 24 1635 2477 85345121 85345991 0.000000e+00 675.0
84 TraesCS7A01G114200 chr7D 81.308 856 125 21 1 835 61755039 61755880 0.000000e+00 662.0
85 TraesCS7A01G114200 chr7D 77.641 1297 145 70 1600 2866 65814745 65813564 0.000000e+00 654.0
86 TraesCS7A01G114200 chr7D 87.805 574 40 6 3615 4188 65792290 65791747 0.000000e+00 645.0
87 TraesCS7A01G114200 chr7D 81.158 812 104 22 1650 2432 68901798 68902589 1.480000e-169 606.0
88 TraesCS7A01G114200 chr7D 80.266 902 76 45 1561 2431 65824644 65823814 1.930000e-163 586.0
89 TraesCS7A01G114200 chr7D 88.981 481 38 10 3883 4351 65822656 65822179 9.000000e-162 580.0
90 TraesCS7A01G114200 chr7D 79.140 791 122 30 1667 2425 66105579 66104800 1.550000e-139 507.0
91 TraesCS7A01G114200 chr7D 79.640 722 114 20 1655 2350 548812960 548812246 5.610000e-134 488.0
92 TraesCS7A01G114200 chr7D 79.028 720 126 12 1668 2371 65940346 65939636 2.030000e-128 470.0
93 TraesCS7A01G114200 chr7D 82.739 533 86 1 1807 2339 66348226 66347700 2.030000e-128 470.0
94 TraesCS7A01G114200 chr7D 78.591 724 119 23 1667 2372 69041551 69042256 3.420000e-121 446.0
95 TraesCS7A01G114200 chr7D 78.243 740 98 35 1648 2379 66517251 66516567 2.690000e-112 416.0
96 TraesCS7A01G114200 chr7D 84.848 396 35 12 3016 3389 65792917 65792525 4.560000e-100 375.0
97 TraesCS7A01G114200 chr7D 81.390 446 67 10 2045 2477 85281750 85282192 2.760000e-92 350.0
98 TraesCS7A01G114200 chr7D 76.104 657 98 24 1806 2452 68897597 68898204 6.110000e-74 289.0
99 TraesCS7A01G114200 chr7D 79.004 462 60 21 2677 3128 65823714 65823280 1.020000e-71 281.0
100 TraesCS7A01G114200 chr7D 80.196 409 50 16 3209 3608 66546607 66546221 1.320000e-70 278.0
101 TraesCS7A01G114200 chr7D 82.131 291 35 13 1663 1938 85281465 85281753 2.900000e-57 233.0
102 TraesCS7A01G114200 chr7D 82.332 283 32 12 3328 3608 83600652 83600386 3.750000e-56 230.0
103 TraesCS7A01G114200 chr7D 86.256 211 18 5 3188 3389 65823270 65823062 8.130000e-53 219.0
104 TraesCS7A01G114200 chr7D 83.412 211 29 6 3669 3877 85283452 85283658 1.770000e-44 191.0
105 TraesCS7A01G114200 chr7D 79.359 281 40 7 3209 3488 580779470 580779733 1.070000e-41 182.0
106 TraesCS7A01G114200 chr7D 86.164 159 13 2 3633 3791 65822831 65822682 3.860000e-36 163.0
107 TraesCS7A01G114200 chr7D 79.098 244 45 1 2633 2876 68898310 68898547 3.860000e-36 163.0
108 TraesCS7A01G114200 chr7D 75.938 320 63 9 2633 2952 66547283 66546978 8.360000e-33 152.0
109 TraesCS7A01G114200 chr7D 80.000 95 15 4 3774 3866 66101517 66101425 3.120000e-07 67.6
110 TraesCS7A01G114200 chr4D 85.897 1248 150 18 64 1291 25425624 25424383 0.000000e+00 1306.0
111 TraesCS7A01G114200 chr4D 79.541 523 89 10 785 1291 403126806 403126286 1.650000e-94 357.0
112 TraesCS7A01G114200 chr4D 95.652 92 4 0 1331 1422 25424388 25424297 1.080000e-31 148.0
113 TraesCS7A01G114200 chr2B 87.366 1116 119 13 75 1173 770763209 770764319 0.000000e+00 1260.0
114 TraesCS7A01G114200 chr2B 86.813 455 44 8 3615 4064 697426379 697426822 1.210000e-135 494.0
115 TraesCS7A01G114200 chr2B 84.337 166 26 0 3329 3494 76515675 76515510 3.860000e-36 163.0
116 TraesCS7A01G114200 chr2B 91.346 104 9 0 1329 1432 625180084 625179981 5.030000e-30 143.0
117 TraesCS7A01G114200 chr2B 88.889 117 11 2 1306 1422 625181149 625181263 5.030000e-30 143.0
118 TraesCS7A01G114200 chr6A 84.058 1311 168 31 1 1291 52039406 52040695 0.000000e+00 1225.0
119 TraesCS7A01G114200 chr6A 94.253 261 12 2 4350 4607 60159595 60159335 3.500000e-106 396.0
120 TraesCS7A01G114200 chr6A 86.352 381 28 14 4464 4823 40587808 40587431 1.260000e-105 394.0
121 TraesCS7A01G114200 chr6A 97.807 228 5 0 4594 4821 514048734 514048507 1.260000e-105 394.0
122 TraesCS7A01G114200 chr6A 93.870 261 13 2 4350 4607 453823893 453823633 1.630000e-104 390.0
123 TraesCS7A01G114200 chr6A 94.737 95 5 0 1328 1422 52040687 52040781 1.080000e-31 148.0
124 TraesCS7A01G114200 chr4A 81.179 1323 201 33 1 1291 659230350 659231656 0.000000e+00 1020.0
125 TraesCS7A01G114200 chr4A 95.385 260 9 2 4351 4607 574837144 574836885 1.250000e-110 411.0
126 TraesCS7A01G114200 chr4A 95.918 245 10 0 4352 4596 668744064 668744308 9.730000e-107 398.0
127 TraesCS7A01G114200 chr4A 95.200 250 12 0 4347 4596 609652600 609652849 3.500000e-106 396.0
128 TraesCS7A01G114200 chr4A 97.391 230 6 0 4594 4823 520123195 520123424 4.530000e-105 392.0
129 TraesCS7A01G114200 chr5B 81.747 1019 142 27 1 988 503531916 503532921 0.000000e+00 811.0
130 TraesCS7A01G114200 chr5B 88.428 579 52 5 3615 4188 589021873 589021305 0.000000e+00 684.0
131 TraesCS7A01G114200 chr5B 92.929 99 7 0 1328 1426 711388606 711388508 1.400000e-30 145.0
132 TraesCS7A01G114200 chr5B 93.684 95 6 0 1328 1422 503531793 503531699 5.030000e-30 143.0
133 TraesCS7A01G114200 chr5B 91.262 103 9 0 1322 1424 711390028 711390130 1.810000e-29 141.0
134 TraesCS7A01G114200 chr5B 100.000 36 0 0 2325 2360 13371508 13371473 3.120000e-07 67.6
135 TraesCS7A01G114200 chrUn 77.793 716 127 19 1667 2372 305654325 305655018 3.470000e-111 412.0
136 TraesCS7A01G114200 chrUn 78.621 580 101 12 1807 2378 308151859 308151295 3.550000e-96 363.0
137 TraesCS7A01G114200 chrUn 78.621 580 101 12 1807 2378 308155967 308155403 3.550000e-96 363.0
138 TraesCS7A01G114200 chrUn 81.416 452 58 14 1 435 295539049 295538607 3.570000e-91 346.0
139 TraesCS7A01G114200 chrUn 81.416 452 58 14 1 435 329606463 329606021 3.570000e-91 346.0
140 TraesCS7A01G114200 chrUn 81.416 452 58 14 1 435 363944116 363944558 3.570000e-91 346.0
141 TraesCS7A01G114200 chrUn 92.632 95 7 0 1328 1422 295538064 295537970 2.340000e-28 137.0
142 TraesCS7A01G114200 chrUn 92.632 95 7 0 1328 1422 329605478 329605384 2.340000e-28 137.0
143 TraesCS7A01G114200 chrUn 91.089 101 9 0 1322 1422 363945095 363945195 2.340000e-28 137.0
144 TraesCS7A01G114200 chr1A 87.332 371 27 17 4471 4823 361379621 361379253 1.620000e-109 407.0
145 TraesCS7A01G114200 chr1A 95.565 248 11 0 4349 4596 361379800 361379553 9.730000e-107 398.0
146 TraesCS7A01G114200 chr1A 94.141 256 12 2 4355 4607 14151745 14151490 2.110000e-103 387.0
147 TraesCS7A01G114200 chr1A 92.473 93 7 0 1330 1422 446808546 446808638 3.030000e-27 134.0
148 TraesCS7A01G114200 chr1A 94.444 36 2 0 2325 2360 424485143 424485108 6.740000e-04 56.5
149 TraesCS7A01G114200 chr5A 85.934 391 33 18 4452 4823 426267345 426266958 9.730000e-107 398.0
150 TraesCS7A01G114200 chr5A 94.253 261 12 2 4350 4607 568332318 568332058 3.500000e-106 396.0
151 TraesCS7A01G114200 chr4B 91.720 157 13 0 3908 4064 106278419 106278575 8.130000e-53 219.0
152 TraesCS7A01G114200 chr4B 81.509 265 30 8 3615 3874 106278210 106278460 2.940000e-47 200.0
153 TraesCS7A01G114200 chr2D 92.233 103 8 0 1322 1424 590220751 590220853 3.890000e-31 147.0
154 TraesCS7A01G114200 chr6D 90.179 112 8 3 1328 1437 445855886 445855776 5.030000e-30 143.0
155 TraesCS7A01G114200 chr6D 79.259 135 13 7 1569 1701 473377683 473377804 4.000000e-11 80.5
156 TraesCS7A01G114200 chr5D 93.684 95 6 0 1328 1422 209499017 209498923 5.030000e-30 143.0
157 TraesCS7A01G114200 chr5D 93.684 95 6 0 1328 1422 330595330 330595236 5.030000e-30 143.0
158 TraesCS7A01G114200 chr5D 93.684 95 6 0 1328 1422 330629009 330628915 5.030000e-30 143.0
159 TraesCS7A01G114200 chr5D 77.576 165 30 4 2785 2949 504123989 504124146 5.140000e-15 93.5
160 TraesCS7A01G114200 chr2A 77.976 168 25 6 2785 2952 46537469 46537314 1.430000e-15 95.3


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 TraesCS7A01G114200 chr7A 70235014 70239836 4822 True 8907.000000 8907 100.000000 1 4823 1 chr7A.!!$R3 4822
1 TraesCS7A01G114200 chr7A 728848366 728849496 1130 True 998.000000 998 83.040000 185 1291 1 chr7A.!!$R10 1106
2 TraesCS7A01G114200 chr7A 70213577 70215326 1749 True 636.000000 756 83.662500 2235 4188 2 chr7A.!!$R11 1953
3 TraesCS7A01G114200 chr7A 70245362 70247926 2564 True 630.000000 913 82.390333 1561 4351 3 chr7A.!!$R12 2790
4 TraesCS7A01G114200 chr7A 86466395 86467263 868 False 623.000000 623 80.367000 1647 2477 1 chr7A.!!$F3 830
5 TraesCS7A01G114200 chr7A 70194799 70197596 2797 False 610.000000 649 84.132500 1655 4188 2 chr7A.!!$F6 2533
6 TraesCS7A01G114200 chr7A 74856686 74859057 2371 False 579.333333 697 82.680000 1568 3987 3 chr7A.!!$F8 2419
7 TraesCS7A01G114200 chr7A 85198234 85199072 838 True 540.000000 540 79.015000 1655 2474 1 chr7A.!!$R6 819
8 TraesCS7A01G114200 chr7A 70766690 70767385 695 True 468.000000 468 78.984000 1655 2359 1 chr7A.!!$R5 704
9 TraesCS7A01G114200 chr7A 74883332 74884099 767 False 385.000000 385 76.493000 1635 2392 1 chr7A.!!$F2 757
10 TraesCS7A01G114200 chr7A 634347534 634349283 1749 True 333.000000 396 80.301500 1806 3608 2 chr7A.!!$R13 1802
11 TraesCS7A01G114200 chr7A 70736678 70737192 514 True 331.000000 331 78.503000 1668 2182 1 chr7A.!!$R4 514
12 TraesCS7A01G114200 chr3A 58069444 58070654 1210 True 1899.000000 1899 94.984000 1 1212 1 chr3A.!!$R1 1211
13 TraesCS7A01G114200 chr1B 561716272 561717652 1380 True 907.500000 1668 92.372500 1 1422 2 chr1B.!!$R2 1421
14 TraesCS7A01G114200 chr1B 678115647 678116399 752 True 313.000000 313 75.161000 1648 2391 1 chr1B.!!$R1 743
15 TraesCS7A01G114200 chr7B 588259613 588260899 1286 True 1628.000000 1628 89.530000 1 1291 1 chr7B.!!$R4 1290
16 TraesCS7A01G114200 chr7B 394859977 394863870 3893 True 749.000000 1002 88.017000 1 1291 2 chr7B.!!$R11 1290
17 TraesCS7A01G114200 chr7B 233206779 233207346 567 True 678.000000 678 88.256000 3615 4188 1 chr7B.!!$R2 573
18 TraesCS7A01G114200 chr7B 394907917 394912035 4118 True 578.500000 656 87.799000 1 1291 2 chr7B.!!$R12 1290
19 TraesCS7A01G114200 chr7B 592418232 592419069 837 True 440.000000 440 77.143000 1561 2350 1 chr7B.!!$R5 789
20 TraesCS7A01G114200 chr7B 10880955 10881648 693 False 418.000000 418 77.933000 1667 2372 1 chr7B.!!$F2 705
21 TraesCS7A01G114200 chr7B 10946589 10947178 589 False 377.000000 377 78.487000 1806 2392 1 chr7B.!!$F4 586
22 TraesCS7A01G114200 chr7B 592426667 592427404 737 True 372.000000 372 76.923000 1655 2363 1 chr7B.!!$R6 708
23 TraesCS7A01G114200 chr7B 32896069 32898642 2573 True 345.000000 481 79.825000 1655 3606 2 chr7B.!!$R10 1951
24 TraesCS7A01G114200 chr7B 34889120 34891188 2068 False 318.000000 460 83.208500 1806 3794 2 chr7B.!!$F7 1988
25 TraesCS7A01G114200 chr7B 10061114 10061648 534 False 244.000000 244 75.929000 1908 2452 1 chr7B.!!$F1 544
26 TraesCS7A01G114200 chr7B 8446893 8448146 1253 True 228.333333 268 83.650000 2241 3494 3 chr7B.!!$R9 1253
27 TraesCS7A01G114200 chr6B 638239564 638240795 1231 True 1618.000000 1618 90.419000 57 1291 1 chr6B.!!$R1 1234
28 TraesCS7A01G114200 chr6B 638559753 638561148 1395 True 918.000000 918 78.999000 13 1422 1 chr6B.!!$R2 1409
29 TraesCS7A01G114200 chr6B 593069387 593070409 1022 True 434.000000 745 90.460000 1 1427 3 chr6B.!!$R3 1426
30 TraesCS7A01G114200 chr3B 323381724 323383016 1292 False 1605.000000 1605 89.162000 1 1291 1 chr3B.!!$F4 1290
31 TraesCS7A01G114200 chr1D 3952871 3954263 1392 False 758.500000 1380 88.553500 1 1422 2 chr1D.!!$F4 1421
32 TraesCS7A01G114200 chr1D 476817976 476819370 1394 False 607.500000 1083 87.207500 1 1422 2 chr1D.!!$F5 1421
33 TraesCS7A01G114200 chr1D 409008064 409008572 508 False 320.000000 320 78.420000 782 1291 1 chr1D.!!$F1 509
34 TraesCS7A01G114200 chr1D 486925810 486926553 743 True 300.000000 300 74.935000 1648 2391 1 chr1D.!!$R2 743
35 TraesCS7A01G114200 chr7D 178883137 178884382 1245 False 1310.000000 1310 85.920000 64 1291 1 chr7D.!!$F4 1227
36 TraesCS7A01G114200 chr7D 85345121 85345991 870 False 675.000000 675 81.300000 1635 2477 1 chr7D.!!$F3 842
37 TraesCS7A01G114200 chr7D 61755039 61755880 841 False 662.000000 662 81.308000 1 835 1 chr7D.!!$F1 834
38 TraesCS7A01G114200 chr7D 65813564 65814745 1181 True 654.000000 654 77.641000 1600 2866 1 chr7D.!!$R1 1266
39 TraesCS7A01G114200 chr7D 65791747 65792917 1170 True 510.000000 645 86.326500 3016 4188 2 chr7D.!!$R7 1172
40 TraesCS7A01G114200 chr7D 548812246 548812960 714 True 488.000000 488 79.640000 1655 2350 1 chr7D.!!$R6 695
41 TraesCS7A01G114200 chr7D 65939636 65940346 710 True 470.000000 470 79.028000 1668 2371 1 chr7D.!!$R2 703
42 TraesCS7A01G114200 chr7D 66347700 66348226 526 True 470.000000 470 82.739000 1807 2339 1 chr7D.!!$R3 532
43 TraesCS7A01G114200 chr7D 69041551 69042256 705 False 446.000000 446 78.591000 1667 2372 1 chr7D.!!$F2 705
44 TraesCS7A01G114200 chr7D 66516567 66517251 684 True 416.000000 416 78.243000 1648 2379 1 chr7D.!!$R4 731
45 TraesCS7A01G114200 chr7D 65822179 65824644 2465 True 365.800000 586 84.134200 1561 4351 5 chr7D.!!$R8 2790
46 TraesCS7A01G114200 chr7D 68897597 68902589 4992 False 352.666667 606 78.786667 1650 2876 3 chr7D.!!$F6 1226
47 TraesCS7A01G114200 chr7D 66101425 66105579 4154 True 287.300000 507 79.570000 1667 3866 2 chr7D.!!$R9 2199
48 TraesCS7A01G114200 chr7D 85281465 85283658 2193 False 258.000000 350 82.311000 1663 3877 3 chr7D.!!$F7 2214
49 TraesCS7A01G114200 chr7D 66546221 66547283 1062 True 215.000000 278 78.067000 2633 3608 2 chr7D.!!$R10 975
50 TraesCS7A01G114200 chr4D 25424297 25425624 1327 True 727.000000 1306 90.774500 64 1422 2 chr4D.!!$R2 1358
51 TraesCS7A01G114200 chr4D 403126286 403126806 520 True 357.000000 357 79.541000 785 1291 1 chr4D.!!$R1 506
52 TraesCS7A01G114200 chr2B 770763209 770764319 1110 False 1260.000000 1260 87.366000 75 1173 1 chr2B.!!$F3 1098
53 TraesCS7A01G114200 chr6A 52039406 52040781 1375 False 686.500000 1225 89.397500 1 1422 2 chr6A.!!$F1 1421
54 TraesCS7A01G114200 chr4A 659230350 659231656 1306 False 1020.000000 1020 81.179000 1 1291 1 chr4A.!!$F3 1290
55 TraesCS7A01G114200 chr5B 503531916 503532921 1005 False 811.000000 811 81.747000 1 988 1 chr5B.!!$F1 987
56 TraesCS7A01G114200 chr5B 589021305 589021873 568 True 684.000000 684 88.428000 3615 4188 1 chr5B.!!$R3 573
57 TraesCS7A01G114200 chrUn 305654325 305655018 693 False 412.000000 412 77.793000 1667 2372 1 chrUn.!!$F1 705
58 TraesCS7A01G114200 chrUn 308151295 308155967 4672 True 363.000000 363 78.621000 1807 2378 2 chrUn.!!$R2 571
59 TraesCS7A01G114200 chrUn 295537970 295539049 1079 True 241.500000 346 87.024000 1 1422 2 chrUn.!!$R1 1421
60 TraesCS7A01G114200 chrUn 329605384 329606463 1079 True 241.500000 346 87.024000 1 1422 2 chrUn.!!$R3 1421
61 TraesCS7A01G114200 chrUn 363944116 363945195 1079 False 241.500000 346 86.252500 1 1422 2 chrUn.!!$F2 1421
62 TraesCS7A01G114200 chr1A 361379253 361379800 547 True 402.500000 407 91.448500 4349 4823 2 chr1A.!!$R3 474

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
78 79 1.940613 GCTAAGATTTGAACCGGCGAT 59.059 47.619 9.30 0.0 0.0 4.58 F
1235 4202 0.378610 CGCTCGCATGTCTAGTCAGA 59.621 55.000 0.00 0.0 0.0 3.27 F
1459 4427 0.037975 CCAACATTCAAGCACAGCCC 60.038 55.000 0.00 0.0 0.0 5.19 F
1764 4816 0.179000 CAAGAACTCATCCTCCCCGG 59.821 60.000 0.00 0.0 0.0 5.73 F
2228 5480 0.179156 CAGGCCATCAACAACATCGC 60.179 55.000 5.01 0.0 0.0 4.58 F
3522 10542 0.040351 ACTCCTAGGACTGCTGCTCA 59.960 55.000 7.62 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1440 4408 0.037975 GGGCTGTGCTTGAATGTTGG 60.038 55.0 0.00 0.0 0.00 3.77 R
2211 5463 0.243365 TTGCGATGTTGTTGATGGCC 59.757 50.0 0.00 0.0 0.00 5.36 R
2796 7369 0.252103 TCCTAGTTCCTCGGCAGGTT 60.252 55.0 3.45 0.0 41.28 3.50 R
3515 10535 0.034616 AGAGGTGAACACTGAGCAGC 59.965 55.0 4.96 0.0 0.00 5.25 R
3609 10641 0.797542 TTTAAACCGGGATGCGAACG 59.202 50.0 6.32 0.0 0.00 3.95 R
4466 13947 0.665835 GTTGAACGCCCACACATCAA 59.334 50.0 0.00 0.0 0.00 2.57 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
78 79 1.940613 GCTAAGATTTGAACCGGCGAT 59.059 47.619 9.30 0.00 0.00 4.58
130 131 3.329520 ACATGACCAGGGCAAGTAAGTTA 59.670 43.478 0.00 0.00 0.00 2.24
604 638 7.866729 TCTTCTCTCAGAACTAATATGCGTAG 58.133 38.462 0.00 0.00 29.89 3.51
1012 3925 4.330894 GGCTTTACCGGATATATAAACCGC 59.669 45.833 9.46 2.93 44.45 5.68
1052 3965 8.850156 AGACTGCAAAATTATATGGGTGTATTC 58.150 33.333 0.00 0.00 0.00 1.75
1235 4202 0.378610 CGCTCGCATGTCTAGTCAGA 59.621 55.000 0.00 0.00 0.00 3.27
1282 4250 5.075858 TCGAACCGTATTTGAACCATACT 57.924 39.130 0.00 0.00 0.00 2.12
1283 4251 4.865925 TCGAACCGTATTTGAACCATACTG 59.134 41.667 0.00 0.00 0.00 2.74
1284 4252 4.628333 CGAACCGTATTTGAACCATACTGT 59.372 41.667 0.00 0.00 0.00 3.55
1285 4253 5.220340 CGAACCGTATTTGAACCATACTGTC 60.220 44.000 0.00 0.00 0.00 3.51
1286 4254 5.155278 ACCGTATTTGAACCATACTGTCA 57.845 39.130 0.00 0.00 0.00 3.58
1287 4255 5.553123 ACCGTATTTGAACCATACTGTCAA 58.447 37.500 0.00 0.00 0.00 3.18
1288 4256 5.642063 ACCGTATTTGAACCATACTGTCAAG 59.358 40.000 0.00 0.00 0.00 3.02
1289 4257 5.642063 CCGTATTTGAACCATACTGTCAAGT 59.358 40.000 0.00 0.00 40.67 3.16
1290 4258 6.148811 CCGTATTTGAACCATACTGTCAAGTT 59.851 38.462 0.00 0.00 37.88 2.66
1291 4259 7.308348 CCGTATTTGAACCATACTGTCAAGTTT 60.308 37.037 0.00 0.00 37.88 2.66
1292 4260 8.073768 CGTATTTGAACCATACTGTCAAGTTTT 58.926 33.333 0.00 0.00 37.88 2.43
1293 4261 9.744468 GTATTTGAACCATACTGTCAAGTTTTT 57.256 29.630 0.00 0.00 37.88 1.94
1311 4279 3.831651 TTTTTGCGGGGAGAAAGGA 57.168 47.368 0.00 0.00 0.00 3.36
1312 4280 2.302587 TTTTTGCGGGGAGAAAGGAT 57.697 45.000 0.00 0.00 0.00 3.24
1313 4281 3.443145 TTTTTGCGGGGAGAAAGGATA 57.557 42.857 0.00 0.00 0.00 2.59
1314 4282 3.662759 TTTTGCGGGGAGAAAGGATAT 57.337 42.857 0.00 0.00 0.00 1.63
1315 4283 3.662759 TTTGCGGGGAGAAAGGATATT 57.337 42.857 0.00 0.00 0.00 1.28
1316 4284 3.662759 TTGCGGGGAGAAAGGATATTT 57.337 42.857 0.00 0.00 0.00 1.40
1317 4285 3.662759 TGCGGGGAGAAAGGATATTTT 57.337 42.857 0.00 0.00 0.00 1.82
1318 4286 4.781775 TGCGGGGAGAAAGGATATTTTA 57.218 40.909 0.00 0.00 0.00 1.52
1319 4287 5.319043 TGCGGGGAGAAAGGATATTTTAT 57.681 39.130 0.00 0.00 0.00 1.40
1320 4288 5.701224 TGCGGGGAGAAAGGATATTTTATT 58.299 37.500 0.00 0.00 0.00 1.40
1321 4289 5.768164 TGCGGGGAGAAAGGATATTTTATTC 59.232 40.000 0.00 0.00 0.00 1.75
1322 4290 5.183331 GCGGGGAGAAAGGATATTTTATTCC 59.817 44.000 0.00 0.00 0.00 3.01
1323 4291 6.303839 CGGGGAGAAAGGATATTTTATTCCA 58.696 40.000 0.00 0.00 30.04 3.53
1324 4292 6.206829 CGGGGAGAAAGGATATTTTATTCCAC 59.793 42.308 0.00 0.00 30.04 4.02
1325 4293 7.066781 GGGGAGAAAGGATATTTTATTCCACA 58.933 38.462 0.00 0.00 30.04 4.17
1326 4294 7.563556 GGGGAGAAAGGATATTTTATTCCACAA 59.436 37.037 0.00 0.00 30.04 3.33
1373 4341 8.091449 TCGGTGTATTTTTCAAATTTAGGCATT 58.909 29.630 0.00 0.00 0.00 3.56
1427 4395 6.015180 ACCACTAGTGTTATTACCTCGACAAA 60.015 38.462 21.18 0.00 0.00 2.83
1428 4396 6.869913 CCACTAGTGTTATTACCTCGACAAAA 59.130 38.462 21.18 0.00 0.00 2.44
1429 4397 7.385752 CCACTAGTGTTATTACCTCGACAAAAA 59.614 37.037 21.18 0.00 0.00 1.94
1452 4420 7.581011 AAACGATTTAATCCAACATTCAAGC 57.419 32.000 0.00 0.00 0.00 4.01
1453 4421 6.266168 ACGATTTAATCCAACATTCAAGCA 57.734 33.333 0.00 0.00 0.00 3.91
1454 4422 6.092748 ACGATTTAATCCAACATTCAAGCAC 58.907 36.000 0.00 0.00 0.00 4.40
1455 4423 6.092092 CGATTTAATCCAACATTCAAGCACA 58.908 36.000 0.00 0.00 0.00 4.57
1456 4424 6.252015 CGATTTAATCCAACATTCAAGCACAG 59.748 38.462 0.00 0.00 0.00 3.66
1457 4425 3.308438 AATCCAACATTCAAGCACAGC 57.692 42.857 0.00 0.00 0.00 4.40
1458 4426 0.961019 TCCAACATTCAAGCACAGCC 59.039 50.000 0.00 0.00 0.00 4.85
1459 4427 0.037975 CCAACATTCAAGCACAGCCC 60.038 55.000 0.00 0.00 0.00 5.19
1460 4428 0.675083 CAACATTCAAGCACAGCCCA 59.325 50.000 0.00 0.00 0.00 5.36
1461 4429 1.068895 CAACATTCAAGCACAGCCCAA 59.931 47.619 0.00 0.00 0.00 4.12
1462 4430 1.636148 ACATTCAAGCACAGCCCAAT 58.364 45.000 0.00 0.00 0.00 3.16
1463 4431 1.547372 ACATTCAAGCACAGCCCAATC 59.453 47.619 0.00 0.00 0.00 2.67
1464 4432 0.813184 ATTCAAGCACAGCCCAATCG 59.187 50.000 0.00 0.00 0.00 3.34
1465 4433 0.250684 TTCAAGCACAGCCCAATCGA 60.251 50.000 0.00 0.00 0.00 3.59
1466 4434 0.674581 TCAAGCACAGCCCAATCGAG 60.675 55.000 0.00 0.00 0.00 4.04
1467 4435 2.042831 AAGCACAGCCCAATCGAGC 61.043 57.895 0.00 0.00 0.00 5.03
1468 4436 3.869272 GCACAGCCCAATCGAGCG 61.869 66.667 0.00 0.00 0.00 5.03
1469 4437 3.197790 CACAGCCCAATCGAGCGG 61.198 66.667 0.00 0.00 0.00 5.52
1470 4438 3.706373 ACAGCCCAATCGAGCGGT 61.706 61.111 0.00 0.00 32.37 5.68
1471 4439 2.892425 CAGCCCAATCGAGCGGTC 60.892 66.667 4.06 4.06 0.00 4.79
1485 4453 4.807039 GGTCGGCGAGCGGCTTAA 62.807 66.667 23.96 0.00 42.94 1.85
1486 4454 2.585247 GTCGGCGAGCGGCTTAAT 60.585 61.111 11.20 0.00 42.94 1.40
1487 4455 2.171725 GTCGGCGAGCGGCTTAATT 61.172 57.895 11.20 0.00 42.94 1.40
1488 4456 0.872881 GTCGGCGAGCGGCTTAATTA 60.873 55.000 11.20 0.00 42.94 1.40
1489 4457 0.179105 TCGGCGAGCGGCTTAATTAA 60.179 50.000 4.99 0.00 42.94 1.40
1490 4458 0.865769 CGGCGAGCGGCTTAATTAAT 59.134 50.000 14.40 0.00 42.94 1.40
1491 4459 1.263217 CGGCGAGCGGCTTAATTAATT 59.737 47.619 14.40 5.89 42.94 1.40
1492 4460 2.477375 CGGCGAGCGGCTTAATTAATTA 59.523 45.455 14.40 3.71 42.94 1.40
1493 4461 3.124636 CGGCGAGCGGCTTAATTAATTAT 59.875 43.478 14.40 0.00 42.94 1.28
1494 4462 4.378046 CGGCGAGCGGCTTAATTAATTATT 60.378 41.667 14.40 0.00 42.94 1.40
1495 4463 5.458015 GGCGAGCGGCTTAATTAATTATTT 58.542 37.500 2.97 0.00 42.94 1.40
1496 4464 5.918576 GGCGAGCGGCTTAATTAATTATTTT 59.081 36.000 2.97 0.00 42.94 1.82
1497 4465 6.419710 GGCGAGCGGCTTAATTAATTATTTTT 59.580 34.615 2.97 0.00 42.94 1.94
1498 4466 7.358105 GGCGAGCGGCTTAATTAATTATTTTTC 60.358 37.037 2.97 2.95 42.94 2.29
1499 4467 7.166804 GCGAGCGGCTTAATTAATTATTTTTCA 59.833 33.333 2.97 0.00 39.11 2.69
1500 4468 9.180678 CGAGCGGCTTAATTAATTATTTTTCAT 57.819 29.630 2.97 0.00 0.00 2.57
1510 4478 9.651913 AATTAATTATTTTTCATTCACTGGCGT 57.348 25.926 0.00 0.00 0.00 5.68
1511 4479 8.682128 TTAATTATTTTTCATTCACTGGCGTC 57.318 30.769 0.00 0.00 0.00 5.19
1512 4480 5.697473 TTATTTTTCATTCACTGGCGTCA 57.303 34.783 0.00 0.00 0.00 4.35
1513 4481 3.624326 TTTTTCATTCACTGGCGTCAG 57.376 42.857 17.12 17.12 46.10 3.51
1514 4482 0.874390 TTTCATTCACTGGCGTCAGC 59.126 50.000 18.84 0.00 44.59 4.26
1533 4501 3.458872 CGGAGGATTTGTAGCAGCA 57.541 52.632 0.00 0.00 0.00 4.41
1534 4502 1.293924 CGGAGGATTTGTAGCAGCAG 58.706 55.000 0.00 0.00 0.00 4.24
1535 4503 1.406069 CGGAGGATTTGTAGCAGCAGT 60.406 52.381 0.00 0.00 0.00 4.40
1536 4504 2.284190 GGAGGATTTGTAGCAGCAGTC 58.716 52.381 0.00 0.00 0.00 3.51
1537 4505 2.355108 GGAGGATTTGTAGCAGCAGTCA 60.355 50.000 0.00 0.00 0.00 3.41
1538 4506 3.338249 GAGGATTTGTAGCAGCAGTCAA 58.662 45.455 0.00 0.00 0.00 3.18
1539 4507 3.753272 GAGGATTTGTAGCAGCAGTCAAA 59.247 43.478 10.51 10.51 34.95 2.69
1540 4508 4.144297 AGGATTTGTAGCAGCAGTCAAAA 58.856 39.130 11.63 0.00 34.32 2.44
1541 4509 4.584325 AGGATTTGTAGCAGCAGTCAAAAA 59.416 37.500 11.63 0.00 34.32 1.94
1573 4541 4.275196 CGTGGACGATCTGGATCTAACTTA 59.725 45.833 8.65 0.00 43.02 2.24
1581 4549 2.037772 CTGGATCTAACTTATGCGGGCT 59.962 50.000 0.00 0.00 0.00 5.19
1596 4564 1.338973 CGGGCTGATGGATGGATTTTG 59.661 52.381 0.00 0.00 0.00 2.44
1617 4585 3.537388 GCCCATAAGCCCGCAAAT 58.463 55.556 0.00 0.00 0.00 2.32
1622 4590 0.670162 CATAAGCCCGCAAATCCAGG 59.330 55.000 0.00 0.00 0.00 4.45
1664 4640 3.701205 TCTCAGGCAGCTTGAAATACA 57.299 42.857 8.79 0.00 0.00 2.29
1665 4641 4.019792 TCTCAGGCAGCTTGAAATACAA 57.980 40.909 8.79 0.00 36.97 2.41
1706 4699 1.939934 CGTCTCAACCAACAGCTTTCA 59.060 47.619 0.00 0.00 0.00 2.69
1764 4816 0.179000 CAAGAACTCATCCTCCCCGG 59.821 60.000 0.00 0.00 0.00 5.73
1765 4817 1.627297 AAGAACTCATCCTCCCCGGC 61.627 60.000 0.00 0.00 0.00 6.13
1766 4818 3.447025 GAACTCATCCTCCCCGGCG 62.447 68.421 0.00 0.00 0.00 6.46
1870 4964 1.005037 CAGCTTGGCACGTACCTGA 60.005 57.895 6.34 0.00 0.00 3.86
1871 4965 1.016130 CAGCTTGGCACGTACCTGAG 61.016 60.000 6.34 5.47 0.00 3.35
1970 5204 3.357079 GGGCCAGAACGTGCAGTG 61.357 66.667 4.39 0.00 0.00 3.66
1987 5221 1.228988 TGTCTGCTCCTCCTCAGCA 60.229 57.895 0.00 0.00 44.80 4.41
1996 5230 2.283604 TCCTCAGCACCGCCTACA 60.284 61.111 0.00 0.00 0.00 2.74
2007 5241 2.901042 GCCTACAGCGGCTACCTT 59.099 61.111 0.26 0.00 46.63 3.50
2111 5348 1.571955 ATCCTTTGGTTTGCCATCCC 58.428 50.000 0.00 0.00 45.56 3.85
2112 5349 0.486879 TCCTTTGGTTTGCCATCCCT 59.513 50.000 0.00 0.00 45.56 4.20
2210 5462 2.735478 CAACGGCGTTAGCGTCCA 60.735 61.111 26.32 0.00 46.35 4.02
2211 5463 2.431942 AACGGCGTTAGCGTCCAG 60.432 61.111 25.63 7.55 46.35 3.86
2212 5464 3.927163 AACGGCGTTAGCGTCCAGG 62.927 63.158 25.63 0.00 46.35 4.45
2215 5467 4.752879 GCGTTAGCGTCCAGGCCA 62.753 66.667 5.01 0.00 40.81 5.36
2216 5468 2.186903 CGTTAGCGTCCAGGCCAT 59.813 61.111 5.01 0.00 0.00 4.40
2217 5469 1.883084 CGTTAGCGTCCAGGCCATC 60.883 63.158 5.01 0.00 0.00 3.51
2218 5470 1.220749 GTTAGCGTCCAGGCCATCA 59.779 57.895 5.01 0.00 0.00 3.07
2221 5473 1.549243 TAGCGTCCAGGCCATCAACA 61.549 55.000 5.01 0.00 0.00 3.33
2228 5480 0.179156 CAGGCCATCAACAACATCGC 60.179 55.000 5.01 0.00 0.00 4.58
2267 5550 2.357517 CTGGGTCGTGGAGCACAC 60.358 66.667 1.81 1.81 46.78 3.82
2309 5617 2.286523 CCCTTCCAGCTCCGACTGT 61.287 63.158 0.00 0.00 35.83 3.55
2392 5731 2.612672 TGTTGTTAACATGCGTCGGAAA 59.387 40.909 9.56 0.00 36.25 3.13
2479 5841 1.542915 GCCAGATTTGAGCTTCTTGCA 59.457 47.619 4.73 0.00 45.94 4.08
2482 5844 3.442625 CCAGATTTGAGCTTCTTGCATGA 59.557 43.478 0.00 0.00 45.94 3.07
2483 5845 4.098044 CCAGATTTGAGCTTCTTGCATGAT 59.902 41.667 2.75 0.00 45.94 2.45
2484 5846 5.394224 CCAGATTTGAGCTTCTTGCATGATT 60.394 40.000 2.75 0.00 45.94 2.57
2485 5847 6.100004 CAGATTTGAGCTTCTTGCATGATTT 58.900 36.000 2.75 0.00 45.94 2.17
2486 5848 6.035005 CAGATTTGAGCTTCTTGCATGATTTG 59.965 38.462 2.75 0.00 45.94 2.32
2487 5849 5.456548 TTTGAGCTTCTTGCATGATTTGA 57.543 34.783 2.75 0.00 45.94 2.69
2566 5995 1.224069 GCGACTCAGTTGCAGCTTCA 61.224 55.000 12.63 0.00 42.10 3.02
2591 6023 2.126346 GCCGCCATGTTGCTGAAC 60.126 61.111 0.00 0.00 0.00 3.18
2592 6024 2.176546 CCGCCATGTTGCTGAACG 59.823 61.111 0.00 0.00 34.49 3.95
2593 6025 2.616330 CCGCCATGTTGCTGAACGT 61.616 57.895 0.00 0.00 34.49 3.99
2594 6026 1.440850 CGCCATGTTGCTGAACGTG 60.441 57.895 0.00 2.83 45.29 4.49
2596 6028 4.539152 CATGTTGCTGAACGTGGC 57.461 55.556 0.00 0.00 42.98 5.01
2597 6029 1.081242 CATGTTGCTGAACGTGGCC 60.081 57.895 0.00 0.00 42.98 5.36
2598 6030 1.528076 ATGTTGCTGAACGTGGCCA 60.528 52.632 0.00 0.00 34.49 5.36
2629 6061 0.318360 CACTACGTGTGGCTGAACGA 60.318 55.000 12.72 0.00 42.32 3.85
2654 6086 3.917760 GACGGGCCCCTCATCGAG 61.918 72.222 18.66 0.96 0.00 4.04
2660 6092 3.147595 CCCCTCATCGAGCACGGA 61.148 66.667 3.11 0.00 40.21 4.69
2662 6094 2.121538 CCCTCATCGAGCACGGAGA 61.122 63.158 10.44 5.33 40.21 3.71
2796 7369 1.255667 GCTTACCCCACTCCTCGTCA 61.256 60.000 0.00 0.00 0.00 4.35
2807 7380 2.125912 CTCGTCAACCTGCCGAGG 60.126 66.667 0.00 0.00 43.20 4.63
2876 7458 1.760029 GAGAGGCCCTCAACTTCCTAG 59.240 57.143 14.46 0.00 41.58 3.02
2877 7459 1.079658 AGAGGCCCTCAACTTCCTAGT 59.920 52.381 14.46 0.00 35.68 2.57
2886 7479 4.096682 CCTCAACTTCCTAGTTCCTACTCG 59.903 50.000 0.00 0.00 42.67 4.18
2893 7486 4.515361 TCCTAGTTCCTACTCGTCTTCTG 58.485 47.826 0.00 0.00 35.78 3.02
2916 7516 8.946085 TCTGTGGCAAGAAACTTATATTTACAG 58.054 33.333 0.00 0.00 0.00 2.74
2945 7592 5.885230 TGAACTTGTCCAGATATTTGCAG 57.115 39.130 0.00 0.00 0.00 4.41
2949 7640 4.878397 ACTTGTCCAGATATTTGCAGTAGC 59.122 41.667 0.00 0.00 42.57 3.58
2952 7646 4.653801 TGTCCAGATATTTGCAGTAGCCTA 59.346 41.667 0.00 0.00 41.13 3.93
2953 7647 5.221521 TGTCCAGATATTTGCAGTAGCCTAG 60.222 44.000 0.00 0.00 41.13 3.02
2954 7648 4.901849 TCCAGATATTTGCAGTAGCCTAGT 59.098 41.667 0.00 0.00 41.13 2.57
2955 7649 4.993584 CCAGATATTTGCAGTAGCCTAGTG 59.006 45.833 2.01 2.01 41.13 2.74
2981 7675 0.814010 AAGCGTTCGAACCTGTTGCT 60.814 50.000 22.07 19.91 0.00 3.91
2987 7681 3.181530 CGTTCGAACCTGTTGCTAATCTG 60.182 47.826 22.07 0.00 0.00 2.90
3016 7710 6.496144 AGTTTACTGGAACTGGTTTAGTCT 57.504 37.500 7.31 0.00 39.18 3.24
3029 7739 6.096846 ACTGGTTTAGTCTGAAACTTTTGCAT 59.903 34.615 0.00 0.00 39.55 3.96
3042 7753 7.862372 TGAAACTTTTGCATATCTCTGTTTCAC 59.138 33.333 16.76 3.34 43.53 3.18
3044 7755 6.906659 ACTTTTGCATATCTCTGTTTCACTG 58.093 36.000 0.00 0.00 0.00 3.66
3056 9077 4.524714 TCTGTTTCACTGAGGAGTTAGGAG 59.475 45.833 0.00 0.00 0.00 3.69
3071 9099 6.261158 GGAGTTAGGAGTTGGAAATATTCTGC 59.739 42.308 0.00 0.00 0.00 4.26
3075 9103 6.313519 AGGAGTTGGAAATATTCTGCACTA 57.686 37.500 0.00 0.00 0.00 2.74
3085 9117 7.600752 GGAAATATTCTGCACTACTGTAGGATC 59.399 40.741 18.38 7.78 31.17 3.36
3100 9132 8.402798 ACTGTAGGATCATAGACATCAGTAAG 57.597 38.462 5.97 0.00 32.95 2.34
3105 9145 8.177119 AGGATCATAGACATCAGTAAGAGTTC 57.823 38.462 0.00 0.00 0.00 3.01
3123 9163 4.082125 AGTTCCTGAATCAAATCCACACC 58.918 43.478 0.00 0.00 0.00 4.16
3183 9878 9.138062 TCAATTTTCATATGTCAAAAATCCACG 57.862 29.630 11.78 4.83 32.84 4.94
3200 9988 3.007506 TCCACGCTGAAGAAACTATTGGA 59.992 43.478 0.00 0.00 0.00 3.53
3292 10256 9.127277 AGCCTACTGTAGTTTGTTTCAAATAAA 57.873 29.630 13.42 0.00 0.00 1.40
3300 10264 9.233232 GTAGTTTGTTTCAAATAAAGTGTGGAG 57.767 33.333 9.36 0.00 0.00 3.86
3305 10269 8.925161 TGTTTCAAATAAAGTGTGGAGAAAAG 57.075 30.769 0.00 0.00 0.00 2.27
3313 10277 3.545703 AGTGTGGAGAAAAGTCAGGTTG 58.454 45.455 0.00 0.00 0.00 3.77
3367 10376 4.519540 TTGTATGGCAGCTTTCCTTTTC 57.480 40.909 0.00 0.00 0.00 2.29
3399 10408 6.952773 ATTTAAACTTGTTGCAGTACCTGA 57.047 33.333 0.00 0.00 32.44 3.86
3415 10430 2.093288 ACCTGACACACATGATGCCTAG 60.093 50.000 0.00 0.00 0.00 3.02
3434 10449 9.907229 ATGCCTAGCTACTTAACTATTTTTCTT 57.093 29.630 0.00 0.00 0.00 2.52
3453 10469 1.153449 CTAATTCAGCCCACGCGGA 60.153 57.895 12.47 0.00 41.18 5.54
3488 10504 3.577848 GGATGTCCATGCAGAGTAGAGAT 59.422 47.826 0.00 0.00 35.64 2.75
3513 10533 1.754226 CAGAGCAAGGACTCCTAGGAC 59.246 57.143 7.62 0.00 37.39 3.85
3515 10535 1.754226 GAGCAAGGACTCCTAGGACTG 59.246 57.143 7.62 1.28 31.13 3.51
3517 10537 1.859302 CAAGGACTCCTAGGACTGCT 58.141 55.000 7.62 7.02 31.13 4.24
3518 10538 1.480137 CAAGGACTCCTAGGACTGCTG 59.520 57.143 7.62 0.00 31.13 4.41
3519 10539 0.686112 AGGACTCCTAGGACTGCTGC 60.686 60.000 7.62 0.00 28.47 5.25
3520 10540 0.686112 GGACTCCTAGGACTGCTGCT 60.686 60.000 7.62 0.00 0.00 4.24
3521 10541 0.744281 GACTCCTAGGACTGCTGCTC 59.256 60.000 7.62 0.00 0.00 4.26
3522 10542 0.040351 ACTCCTAGGACTGCTGCTCA 59.960 55.000 7.62 0.00 0.00 4.26
3548 10568 3.566351 TCACCTCTTCAGAAGTGTCAGA 58.434 45.455 10.09 2.97 37.65 3.27
3579 10599 3.198068 CACGATGACATTAGAACCCAGG 58.802 50.000 0.00 0.00 0.00 4.45
3598 10622 4.096984 CCAGGTCCTTTTGTTGAGATATGC 59.903 45.833 0.00 0.00 0.00 3.14
3608 10640 4.183865 TGTTGAGATATGCGTTCAGGAAG 58.816 43.478 0.00 0.00 0.00 3.46
3609 10641 2.826428 TGAGATATGCGTTCAGGAAGC 58.174 47.619 0.00 0.00 0.00 3.86
3610 10642 1.789464 GAGATATGCGTTCAGGAAGCG 59.211 52.381 0.00 0.00 0.00 4.68
3613 10725 1.355971 TATGCGTTCAGGAAGCGTTC 58.644 50.000 0.00 0.00 0.00 3.95
3698 10819 6.061441 AGTCTGTAATGTGTTTGACAATGGA 58.939 36.000 0.00 0.00 38.36 3.41
3750 10876 5.540337 TCTCTTAGGTGTTGAGACAGATGTT 59.460 40.000 0.00 0.00 36.20 2.71
3821 11431 5.930837 AGTTTCAGTCCATTAGAGGAGAG 57.069 43.478 0.00 0.00 38.64 3.20
3903 11648 5.524281 GGACACTCTGCCTATAAGTTTTAGC 59.476 44.000 0.00 0.00 0.00 3.09
3943 11688 7.716560 CACCTATAATTCTGAACATGGTGATGA 59.283 37.037 17.30 0.00 43.39 2.92
3973 11718 6.166279 CACCTATGCTTACTCAACTGAAAGA 58.834 40.000 0.00 0.00 37.43 2.52
4027 11774 8.771766 CACCTATCATCTGAATAACATGTGAAG 58.228 37.037 0.00 0.00 0.00 3.02
4132 11881 5.931441 AACTGTCTTGTTGATCTAACTGC 57.069 39.130 0.00 0.00 40.05 4.40
4139 11888 7.661437 TGTCTTGTTGATCTAACTGCTGTTTAT 59.339 33.333 14.54 8.71 40.05 1.40
4295 13765 8.821147 TCATGATTCTTTTGTGAATTTTCAGG 57.179 30.769 0.00 0.00 37.98 3.86
4303 13773 8.934825 TCTTTTGTGAATTTTCAGGAAAAAGTG 58.065 29.630 20.96 9.63 42.71 3.16
4469 13950 1.972198 CCACGTAGGACTGGCTTGA 59.028 57.895 0.00 0.00 41.22 3.02
4478 13959 1.589716 GACTGGCTTGATGTGTGGGC 61.590 60.000 0.00 0.00 0.00 5.36
4484 13965 0.950836 CTTGATGTGTGGGCGTTCAA 59.049 50.000 0.00 0.00 0.00 2.69
4516 13997 2.258013 CGGCCGTTTCACCACACAT 61.258 57.895 19.50 0.00 0.00 3.21
4573 14054 2.336088 GCCACTTTGCACGCACAT 59.664 55.556 0.00 0.00 0.00 3.21
4616 14170 1.376466 CAACTGCCCCTAGTGTGCT 59.624 57.895 0.00 0.00 0.00 4.40
4732 14287 4.039488 TGGCAACTCTCTTTTACCGAGTTA 59.961 41.667 3.87 0.00 43.85 2.24
4778 14346 1.586154 AACTGCCCTAACGTGCATGC 61.586 55.000 11.82 11.82 36.79 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 79 0.320421 GGTCCTTTACAGCGCACAGA 60.320 55.000 11.47 0.00 0.00 3.41
130 131 3.873910 AGGTTAGCGATGCATTACAGTT 58.126 40.909 0.00 0.00 0.00 3.16
583 617 8.858003 TTTTCTACGCATATTAGTTCTGAGAG 57.142 34.615 0.00 0.00 0.00 3.20
932 3826 9.218440 CCATTTTCCACATGTTAGCTTTTTATT 57.782 29.630 0.00 0.00 0.00 1.40
934 3828 7.158021 CCCATTTTCCACATGTTAGCTTTTTA 58.842 34.615 0.00 0.00 0.00 1.52
1012 3925 3.057019 TGCAGTCTTTTACGCACTACAG 58.943 45.455 0.00 0.00 34.31 2.74
1052 3965 1.497278 CGAAGGACATGCACCAACG 59.503 57.895 11.29 11.23 0.00 4.10
1187 4124 2.987547 CCACTTGCAGTGCAGGGG 60.988 66.667 28.38 25.34 44.63 4.79
1255 4222 3.367025 GGTTCAAATACGGTTCGAGTCAG 59.633 47.826 0.00 0.00 0.00 3.51
1259 4226 5.005394 CAGTATGGTTCAAATACGGTTCGAG 59.995 44.000 0.00 0.00 35.95 4.04
1293 4261 2.302587 ATCCTTTCTCCCCGCAAAAA 57.697 45.000 0.00 0.00 0.00 1.94
1294 4262 3.662759 ATATCCTTTCTCCCCGCAAAA 57.337 42.857 0.00 0.00 0.00 2.44
1295 4263 3.662759 AATATCCTTTCTCCCCGCAAA 57.337 42.857 0.00 0.00 0.00 3.68
1296 4264 3.662759 AAATATCCTTTCTCCCCGCAA 57.337 42.857 0.00 0.00 0.00 4.85
1297 4265 3.662759 AAAATATCCTTTCTCCCCGCA 57.337 42.857 0.00 0.00 0.00 5.69
1298 4266 5.183331 GGAATAAAATATCCTTTCTCCCCGC 59.817 44.000 0.00 0.00 32.75 6.13
1299 4267 6.206829 GTGGAATAAAATATCCTTTCTCCCCG 59.793 42.308 0.00 0.00 36.64 5.73
1300 4268 7.066781 TGTGGAATAAAATATCCTTTCTCCCC 58.933 38.462 0.00 0.00 36.64 4.81
1301 4269 8.533569 TTGTGGAATAAAATATCCTTTCTCCC 57.466 34.615 0.00 0.00 36.64 4.30
1302 4270 9.971922 CATTGTGGAATAAAATATCCTTTCTCC 57.028 33.333 0.00 0.00 36.64 3.71
1303 4271 9.468532 GCATTGTGGAATAAAATATCCTTTCTC 57.531 33.333 0.00 0.00 36.64 2.87
1304 4272 8.424133 GGCATTGTGGAATAAAATATCCTTTCT 58.576 33.333 0.00 0.00 36.64 2.52
1305 4273 8.203485 TGGCATTGTGGAATAAAATATCCTTTC 58.797 33.333 0.00 0.00 36.64 2.62
1306 4274 8.088463 TGGCATTGTGGAATAAAATATCCTTT 57.912 30.769 0.00 0.00 36.64 3.11
1307 4275 7.673641 TGGCATTGTGGAATAAAATATCCTT 57.326 32.000 0.00 0.00 36.64 3.36
1308 4276 7.345392 ACTTGGCATTGTGGAATAAAATATCCT 59.655 33.333 0.00 0.00 36.64 3.24
1309 4277 7.500141 ACTTGGCATTGTGGAATAAAATATCC 58.500 34.615 0.00 0.00 36.21 2.59
1310 4278 8.947055 AACTTGGCATTGTGGAATAAAATATC 57.053 30.769 0.00 0.00 0.00 1.63
1314 4282 9.249053 TCTATAACTTGGCATTGTGGAATAAAA 57.751 29.630 0.00 0.00 0.00 1.52
1315 4283 8.815565 TCTATAACTTGGCATTGTGGAATAAA 57.184 30.769 0.00 0.00 0.00 1.40
1316 4284 8.682710 GTTCTATAACTTGGCATTGTGGAATAA 58.317 33.333 0.00 0.00 32.54 1.40
1317 4285 7.284489 GGTTCTATAACTTGGCATTGTGGAATA 59.716 37.037 0.00 0.00 35.81 1.75
1318 4286 6.096846 GGTTCTATAACTTGGCATTGTGGAAT 59.903 38.462 0.00 0.00 35.81 3.01
1319 4287 5.417580 GGTTCTATAACTTGGCATTGTGGAA 59.582 40.000 0.00 0.00 35.81 3.53
1320 4288 4.947388 GGTTCTATAACTTGGCATTGTGGA 59.053 41.667 0.00 0.00 35.81 4.02
1321 4289 4.704540 TGGTTCTATAACTTGGCATTGTGG 59.295 41.667 0.00 0.00 35.81 4.17
1322 4290 5.415701 ACTGGTTCTATAACTTGGCATTGTG 59.584 40.000 0.00 0.00 35.81 3.33
1323 4291 5.570320 ACTGGTTCTATAACTTGGCATTGT 58.430 37.500 0.00 0.00 35.81 2.71
1324 4292 6.515272 AACTGGTTCTATAACTTGGCATTG 57.485 37.500 0.00 0.00 35.81 2.82
1325 4293 5.354234 CGAACTGGTTCTATAACTTGGCATT 59.646 40.000 11.03 0.00 37.44 3.56
1326 4294 4.876107 CGAACTGGTTCTATAACTTGGCAT 59.124 41.667 11.03 0.00 37.44 4.40
1363 4331 5.640357 TCGACGTTCACTTTAATGCCTAAAT 59.360 36.000 0.00 0.00 0.00 1.40
1373 4341 2.442212 TGCCATCGACGTTCACTTTA 57.558 45.000 0.00 0.00 0.00 1.85
1427 4395 7.655328 TGCTTGAATGTTGGATTAAATCGTTTT 59.345 29.630 0.00 0.00 0.00 2.43
1428 4396 7.116233 GTGCTTGAATGTTGGATTAAATCGTTT 59.884 33.333 0.00 0.00 0.00 3.60
1429 4397 6.586082 GTGCTTGAATGTTGGATTAAATCGTT 59.414 34.615 0.00 0.00 0.00 3.85
1430 4398 6.092748 GTGCTTGAATGTTGGATTAAATCGT 58.907 36.000 0.00 0.00 0.00 3.73
1431 4399 6.092092 TGTGCTTGAATGTTGGATTAAATCG 58.908 36.000 0.00 0.00 0.00 3.34
1432 4400 6.035327 GCTGTGCTTGAATGTTGGATTAAATC 59.965 38.462 0.00 0.00 0.00 2.17
1433 4401 5.870978 GCTGTGCTTGAATGTTGGATTAAAT 59.129 36.000 0.00 0.00 0.00 1.40
1434 4402 5.229423 GCTGTGCTTGAATGTTGGATTAAA 58.771 37.500 0.00 0.00 0.00 1.52
1435 4403 4.321899 GGCTGTGCTTGAATGTTGGATTAA 60.322 41.667 0.00 0.00 0.00 1.40
1436 4404 3.193267 GGCTGTGCTTGAATGTTGGATTA 59.807 43.478 0.00 0.00 0.00 1.75
1437 4405 2.028748 GGCTGTGCTTGAATGTTGGATT 60.029 45.455 0.00 0.00 0.00 3.01
1438 4406 1.547372 GGCTGTGCTTGAATGTTGGAT 59.453 47.619 0.00 0.00 0.00 3.41
1439 4407 0.961019 GGCTGTGCTTGAATGTTGGA 59.039 50.000 0.00 0.00 0.00 3.53
1440 4408 0.037975 GGGCTGTGCTTGAATGTTGG 60.038 55.000 0.00 0.00 0.00 3.77
1441 4409 0.675083 TGGGCTGTGCTTGAATGTTG 59.325 50.000 0.00 0.00 0.00 3.33
1442 4410 1.412079 TTGGGCTGTGCTTGAATGTT 58.588 45.000 0.00 0.00 0.00 2.71
1443 4411 1.547372 GATTGGGCTGTGCTTGAATGT 59.453 47.619 0.00 0.00 0.00 2.71
1444 4412 1.468565 CGATTGGGCTGTGCTTGAATG 60.469 52.381 0.00 0.00 0.00 2.67
1445 4413 0.813184 CGATTGGGCTGTGCTTGAAT 59.187 50.000 0.00 0.00 0.00 2.57
1446 4414 0.250684 TCGATTGGGCTGTGCTTGAA 60.251 50.000 0.00 0.00 0.00 2.69
1447 4415 0.674581 CTCGATTGGGCTGTGCTTGA 60.675 55.000 0.00 0.00 0.00 3.02
1448 4416 1.798735 CTCGATTGGGCTGTGCTTG 59.201 57.895 0.00 0.00 0.00 4.01
1449 4417 2.042831 GCTCGATTGGGCTGTGCTT 61.043 57.895 0.00 0.00 0.00 3.91
1450 4418 2.437359 GCTCGATTGGGCTGTGCT 60.437 61.111 0.00 0.00 0.00 4.40
1451 4419 3.869272 CGCTCGATTGGGCTGTGC 61.869 66.667 2.61 0.00 0.00 4.57
1452 4420 3.197790 CCGCTCGATTGGGCTGTG 61.198 66.667 2.61 0.00 0.00 3.66
1453 4421 3.665675 GACCGCTCGATTGGGCTGT 62.666 63.158 0.76 0.76 0.00 4.40
1454 4422 2.892425 GACCGCTCGATTGGGCTG 60.892 66.667 2.61 0.00 0.00 4.85
1455 4423 4.514577 CGACCGCTCGATTGGGCT 62.515 66.667 2.61 0.00 43.06 5.19
1459 4427 4.847516 TCGCCGACCGCTCGATTG 62.848 66.667 0.71 0.00 43.06 2.67
1460 4428 4.554363 CTCGCCGACCGCTCGATT 62.554 66.667 0.71 0.00 43.06 3.34
1468 4436 4.807039 TTAAGCCGCTCGCCGACC 62.807 66.667 0.00 0.00 40.02 4.79
1469 4437 0.872881 TAATTAAGCCGCTCGCCGAC 60.873 55.000 0.00 0.00 40.02 4.79
1470 4438 0.179105 TTAATTAAGCCGCTCGCCGA 60.179 50.000 0.00 0.00 40.02 5.54
1471 4439 0.865769 ATTAATTAAGCCGCTCGCCG 59.134 50.000 3.94 0.00 38.78 6.46
1472 4440 4.680171 ATAATTAATTAAGCCGCTCGCC 57.320 40.909 11.80 0.00 38.78 5.54
1473 4441 6.986424 AAAATAATTAATTAAGCCGCTCGC 57.014 33.333 11.80 0.00 37.98 5.03
1474 4442 8.555166 TGAAAAATAATTAATTAAGCCGCTCG 57.445 30.769 11.80 0.00 0.00 5.03
1484 4452 9.651913 ACGCCAGTGAATGAAAAATAATTAATT 57.348 25.926 5.89 5.89 0.00 1.40
1485 4453 9.301153 GACGCCAGTGAATGAAAAATAATTAAT 57.699 29.630 0.00 0.00 0.00 1.40
1486 4454 8.300286 TGACGCCAGTGAATGAAAAATAATTAA 58.700 29.630 0.00 0.00 0.00 1.40
1487 4455 7.821652 TGACGCCAGTGAATGAAAAATAATTA 58.178 30.769 0.00 0.00 0.00 1.40
1488 4456 6.686630 TGACGCCAGTGAATGAAAAATAATT 58.313 32.000 0.00 0.00 0.00 1.40
1489 4457 6.266168 TGACGCCAGTGAATGAAAAATAAT 57.734 33.333 0.00 0.00 0.00 1.28
1490 4458 5.697473 TGACGCCAGTGAATGAAAAATAA 57.303 34.783 0.00 0.00 0.00 1.40
1491 4459 4.379394 GCTGACGCCAGTGAATGAAAAATA 60.379 41.667 0.00 0.00 42.35 1.40
1492 4460 3.612479 GCTGACGCCAGTGAATGAAAAAT 60.612 43.478 0.00 0.00 42.35 1.82
1493 4461 2.287547 GCTGACGCCAGTGAATGAAAAA 60.288 45.455 0.00 0.00 42.35 1.94
1494 4462 1.266718 GCTGACGCCAGTGAATGAAAA 59.733 47.619 0.00 0.00 42.35 2.29
1495 4463 0.874390 GCTGACGCCAGTGAATGAAA 59.126 50.000 0.00 0.00 42.35 2.69
1496 4464 2.543578 GCTGACGCCAGTGAATGAA 58.456 52.632 0.00 0.00 42.35 2.57
1497 4465 4.284123 GCTGACGCCAGTGAATGA 57.716 55.556 0.00 0.00 42.35 2.57
1507 4475 2.125106 AAATCCTCCGGCTGACGC 60.125 61.111 0.00 0.00 42.52 5.19
1508 4476 0.174845 TACAAATCCTCCGGCTGACG 59.825 55.000 0.00 0.00 43.80 4.35
1509 4477 1.941325 CTACAAATCCTCCGGCTGAC 58.059 55.000 0.00 0.00 0.00 3.51
1510 4478 0.178068 GCTACAAATCCTCCGGCTGA 59.822 55.000 0.00 0.00 0.00 4.26
1511 4479 0.107703 TGCTACAAATCCTCCGGCTG 60.108 55.000 0.00 0.00 0.00 4.85
1512 4480 0.179000 CTGCTACAAATCCTCCGGCT 59.821 55.000 0.00 0.00 0.00 5.52
1513 4481 1.440145 GCTGCTACAAATCCTCCGGC 61.440 60.000 0.00 0.00 0.00 6.13
1514 4482 0.107703 TGCTGCTACAAATCCTCCGG 60.108 55.000 0.00 0.00 0.00 5.14
1515 4483 1.293924 CTGCTGCTACAAATCCTCCG 58.706 55.000 0.00 0.00 0.00 4.63
1516 4484 2.284190 GACTGCTGCTACAAATCCTCC 58.716 52.381 0.00 0.00 0.00 4.30
1517 4485 2.977914 TGACTGCTGCTACAAATCCTC 58.022 47.619 0.00 0.00 0.00 3.71
1518 4486 3.423539 TTGACTGCTGCTACAAATCCT 57.576 42.857 0.00 0.00 0.00 3.24
1519 4487 4.503741 TTTTGACTGCTGCTACAAATCC 57.496 40.909 15.35 0.00 33.38 3.01
1542 4510 1.531149 CAGATCGTCCACGCTGTTTTT 59.469 47.619 0.00 0.00 39.60 1.94
1543 4511 1.148310 CAGATCGTCCACGCTGTTTT 58.852 50.000 0.00 0.00 39.60 2.43
1544 4512 0.670546 CCAGATCGTCCACGCTGTTT 60.671 55.000 0.00 0.00 39.60 2.83
1545 4513 1.079819 CCAGATCGTCCACGCTGTT 60.080 57.895 0.00 0.00 39.60 3.16
1546 4514 1.323271 ATCCAGATCGTCCACGCTGT 61.323 55.000 0.00 0.00 39.60 4.40
1547 4515 0.596083 GATCCAGATCGTCCACGCTG 60.596 60.000 0.00 0.00 39.60 5.18
1548 4516 0.753479 AGATCCAGATCGTCCACGCT 60.753 55.000 2.08 0.00 42.48 5.07
1549 4517 0.952280 TAGATCCAGATCGTCCACGC 59.048 55.000 2.08 0.00 42.48 5.34
1550 4518 2.619177 AGTTAGATCCAGATCGTCCACG 59.381 50.000 2.08 0.00 42.48 4.94
1551 4519 4.657436 AAGTTAGATCCAGATCGTCCAC 57.343 45.455 2.08 0.00 42.48 4.02
1552 4520 5.279006 GCATAAGTTAGATCCAGATCGTCCA 60.279 44.000 2.08 0.00 42.48 4.02
1553 4521 5.164954 GCATAAGTTAGATCCAGATCGTCC 58.835 45.833 2.08 0.00 42.48 4.79
1554 4522 4.854291 CGCATAAGTTAGATCCAGATCGTC 59.146 45.833 2.08 0.00 42.48 4.20
1555 4523 4.321304 CCGCATAAGTTAGATCCAGATCGT 60.321 45.833 2.08 0.00 42.48 3.73
1556 4524 4.169508 CCGCATAAGTTAGATCCAGATCG 58.830 47.826 2.08 0.00 42.48 3.69
1557 4525 4.499183 CCCGCATAAGTTAGATCCAGATC 58.501 47.826 0.00 0.00 38.09 2.75
1558 4526 3.307059 GCCCGCATAAGTTAGATCCAGAT 60.307 47.826 0.00 0.00 0.00 2.90
1559 4527 2.037251 GCCCGCATAAGTTAGATCCAGA 59.963 50.000 0.00 0.00 0.00 3.86
1573 4541 1.786407 ATCCATCCATCAGCCCGCAT 61.786 55.000 0.00 0.00 0.00 4.73
1581 4549 3.565307 GGCCTACAAAATCCATCCATCA 58.435 45.455 0.00 0.00 0.00 3.07
1617 4585 2.429930 CTTTCGGCACCACCTGGA 59.570 61.111 0.00 0.00 38.94 3.86
1706 4699 0.252742 ACGGGGAGAAGATGGGAAGT 60.253 55.000 0.00 0.00 0.00 3.01
1970 5204 1.217779 GTGCTGAGGAGGAGCAGAC 59.782 63.158 0.00 0.00 46.95 3.51
2111 5348 2.234908 ACTTCGTCCCCAGATTCTGAAG 59.765 50.000 15.36 11.20 37.83 3.02
2112 5349 2.233922 GACTTCGTCCCCAGATTCTGAA 59.766 50.000 15.36 0.00 32.44 3.02
2202 5454 1.220749 GTTGATGGCCTGGACGCTA 59.779 57.895 3.32 0.00 0.00 4.26
2210 5462 0.608856 TGCGATGTTGTTGATGGCCT 60.609 50.000 3.32 0.00 0.00 5.19
2211 5463 0.243365 TTGCGATGTTGTTGATGGCC 59.757 50.000 0.00 0.00 0.00 5.36
2212 5464 1.720852 GTTTGCGATGTTGTTGATGGC 59.279 47.619 0.00 0.00 0.00 4.40
2213 5465 1.978097 CGTTTGCGATGTTGTTGATGG 59.022 47.619 0.00 0.00 41.33 3.51
2214 5466 2.649516 ACGTTTGCGATGTTGTTGATG 58.350 42.857 0.00 0.00 42.00 3.07
2215 5467 2.289274 TGACGTTTGCGATGTTGTTGAT 59.711 40.909 0.00 0.00 42.00 2.57
2216 5468 1.666189 TGACGTTTGCGATGTTGTTGA 59.334 42.857 0.00 0.00 42.00 3.18
2217 5469 1.772966 GTGACGTTTGCGATGTTGTTG 59.227 47.619 0.00 0.00 42.00 3.33
2218 5470 1.268335 GGTGACGTTTGCGATGTTGTT 60.268 47.619 0.00 0.00 42.00 2.83
2221 5473 0.306533 GTGGTGACGTTTGCGATGTT 59.693 50.000 0.00 0.00 42.00 2.71
2228 5480 1.464023 GCATCATCGTGGTGACGTTTG 60.464 52.381 0.00 0.00 46.20 2.93
2309 5617 4.408821 GGCATGGCGGACTCACCA 62.409 66.667 2.41 0.00 41.06 4.17
2404 5743 7.627949 CGAATGAAATTAACACGATTTGCAATG 59.372 33.333 0.00 0.00 36.07 2.82
2456 5818 3.368116 GCAAGAAGCTCAAATCTGGCAAT 60.368 43.478 7.51 0.00 41.40 3.56
2479 5841 7.477945 AGAAGCCAAAGAAATCTCAAATCAT 57.522 32.000 0.00 0.00 0.00 2.45
2482 5844 5.930569 GCAAGAAGCCAAAGAAATCTCAAAT 59.069 36.000 0.00 0.00 37.23 2.32
2483 5845 5.291971 GCAAGAAGCCAAAGAAATCTCAAA 58.708 37.500 0.00 0.00 37.23 2.69
2484 5846 4.557296 CGCAAGAAGCCAAAGAAATCTCAA 60.557 41.667 0.00 0.00 41.38 3.02
2485 5847 3.058016 CGCAAGAAGCCAAAGAAATCTCA 60.058 43.478 0.00 0.00 41.38 3.27
2486 5848 3.496155 CGCAAGAAGCCAAAGAAATCTC 58.504 45.455 0.00 0.00 41.38 2.75
2487 5849 2.352127 GCGCAAGAAGCCAAAGAAATCT 60.352 45.455 0.30 0.00 41.38 2.40
2538 5943 2.032178 GCAACTGAGTCGCAAAGAACTT 59.968 45.455 0.00 0.00 0.00 2.66
2539 5944 1.599542 GCAACTGAGTCGCAAAGAACT 59.400 47.619 0.00 0.00 0.00 3.01
2643 6075 3.144120 CTCCGTGCTCGATGAGGGG 62.144 68.421 10.21 0.00 39.71 4.79
2654 6086 1.336056 ACGAAGAAGAACTCTCCGTGC 60.336 52.381 0.00 0.00 31.02 5.34
2660 6092 2.300437 CCTCCCAACGAAGAAGAACTCT 59.700 50.000 0.00 0.00 35.13 3.24
2662 6094 2.037381 GACCTCCCAACGAAGAAGAACT 59.963 50.000 0.00 0.00 0.00 3.01
2673 6105 1.302271 GGAACACGGACCTCCCAAC 60.302 63.158 0.00 0.00 34.14 3.77
2722 7265 2.202932 AGACGTCCATGATGGCGC 60.203 61.111 21.99 16.26 39.47 6.53
2796 7369 0.252103 TCCTAGTTCCTCGGCAGGTT 60.252 55.000 3.45 0.00 41.28 3.50
2824 7397 2.906719 GCGATGACGACGACGATGC 61.907 63.158 15.32 6.29 42.66 3.91
2876 7458 2.671632 GCCACAGAAGACGAGTAGGAAC 60.672 54.545 0.00 0.00 0.00 3.62
2877 7459 1.544691 GCCACAGAAGACGAGTAGGAA 59.455 52.381 0.00 0.00 0.00 3.36
2886 7479 5.948992 ATAAGTTTCTTGCCACAGAAGAC 57.051 39.130 0.00 0.00 34.22 3.01
2916 7516 8.660373 CAAATATCTGGACAAGTTCAAGACTAC 58.340 37.037 0.00 0.00 37.09 2.73
2956 7650 2.031683 ACAGGTTCGAACGCTTTTCAAG 59.968 45.455 21.34 9.31 0.00 3.02
3006 7700 5.906113 TGCAAAAGTTTCAGACTAAACCA 57.094 34.783 0.00 0.00 39.66 3.67
3007 7701 8.515414 AGATATGCAAAAGTTTCAGACTAAACC 58.485 33.333 0.00 0.00 39.66 3.27
3008 7702 9.548208 GAGATATGCAAAAGTTTCAGACTAAAC 57.452 33.333 0.00 0.00 37.72 2.01
3009 7703 9.507329 AGAGATATGCAAAAGTTTCAGACTAAA 57.493 29.630 0.00 0.00 37.72 1.85
3010 7704 8.939929 CAGAGATATGCAAAAGTTTCAGACTAA 58.060 33.333 0.00 0.00 37.72 2.24
3011 7705 8.097038 ACAGAGATATGCAAAAGTTTCAGACTA 58.903 33.333 0.00 0.00 37.72 2.59
3012 7706 6.939163 ACAGAGATATGCAAAAGTTTCAGACT 59.061 34.615 0.00 0.00 41.47 3.24
3013 7707 7.138692 ACAGAGATATGCAAAAGTTTCAGAC 57.861 36.000 0.00 0.00 0.00 3.51
3014 7708 7.750229 AACAGAGATATGCAAAAGTTTCAGA 57.250 32.000 0.00 0.00 0.00 3.27
3015 7709 8.077991 TGAAACAGAGATATGCAAAAGTTTCAG 58.922 33.333 18.34 3.46 44.74 3.02
3016 7710 7.862372 GTGAAACAGAGATATGCAAAAGTTTCA 59.138 33.333 18.34 18.34 46.31 2.69
3042 7753 4.891992 TTTCCAACTCCTAACTCCTCAG 57.108 45.455 0.00 0.00 0.00 3.35
3044 7755 7.713073 CAGAATATTTCCAACTCCTAACTCCTC 59.287 40.741 0.00 0.00 0.00 3.71
3056 9077 6.743575 ACAGTAGTGCAGAATATTTCCAAC 57.256 37.500 0.00 0.00 0.00 3.77
3071 9099 7.446931 ACTGATGTCTATGATCCTACAGTAGTG 59.553 40.741 6.84 0.00 34.95 2.74
3075 9103 8.221251 TCTTACTGATGTCTATGATCCTACAGT 58.779 37.037 0.00 0.00 39.03 3.55
3085 9117 7.340122 TCAGGAACTCTTACTGATGTCTATG 57.660 40.000 0.00 0.00 34.60 2.23
3100 9132 4.156739 GGTGTGGATTTGATTCAGGAACTC 59.843 45.833 0.00 0.00 34.60 3.01
3105 9145 2.710377 TCGGTGTGGATTTGATTCAGG 58.290 47.619 0.00 0.00 0.00 3.86
3123 9163 7.359262 TCTGTACATAAATCAAACAGGTTCG 57.641 36.000 0.00 0.00 38.44 3.95
3183 9878 8.246180 TGAATCAAATCCAATAGTTTCTTCAGC 58.754 33.333 0.00 0.00 0.00 4.26
3200 9988 7.039882 GCCAGACTGAATCATTTGAATCAAAT 58.960 34.615 14.86 14.86 43.71 2.32
3210 9998 3.265791 GAACTCGCCAGACTGAATCATT 58.734 45.455 3.32 0.00 0.00 2.57
3277 10241 8.696410 TTCTCCACACTTTATTTGAAACAAAC 57.304 30.769 0.00 0.00 0.00 2.93
3292 10256 3.054361 ACAACCTGACTTTTCTCCACACT 60.054 43.478 0.00 0.00 0.00 3.55
3300 10264 4.394729 TGTGGGATACAACCTGACTTTTC 58.605 43.478 0.00 0.00 36.06 2.29
3305 10269 1.003118 TGCTGTGGGATACAACCTGAC 59.997 52.381 0.00 0.00 39.20 3.51
3313 10277 4.640201 ACAATGTAATGTGCTGTGGGATAC 59.360 41.667 0.00 0.00 30.82 2.24
3351 10359 2.880443 AGATGAAAAGGAAAGCTGCCA 58.120 42.857 8.45 0.00 0.00 4.92
3352 10360 3.509184 AGAAGATGAAAAGGAAAGCTGCC 59.491 43.478 0.00 0.00 0.00 4.85
3367 10376 9.683069 ACTGCAACAAGTTTAAATAAGAAGATG 57.317 29.630 0.00 0.00 0.00 2.90
3399 10408 2.768527 AGTAGCTAGGCATCATGTGTGT 59.231 45.455 0.00 0.00 0.00 3.72
3434 10449 1.153449 CCGCGTGGGCTGAATTAGA 60.153 57.895 7.26 0.00 36.88 2.10
3499 10515 1.859302 CAGCAGTCCTAGGAGTCCTT 58.141 55.000 19.06 1.34 34.61 3.36
3515 10535 0.034616 AGAGGTGAACACTGAGCAGC 59.965 55.000 4.96 0.00 0.00 5.25
3517 10537 1.762370 TGAAGAGGTGAACACTGAGCA 59.238 47.619 4.96 0.00 0.00 4.26
3518 10538 2.036475 TCTGAAGAGGTGAACACTGAGC 59.964 50.000 4.96 0.00 0.00 4.26
3519 10539 4.202202 ACTTCTGAAGAGGTGAACACTGAG 60.202 45.833 23.36 0.00 32.85 3.35
3520 10540 3.706594 ACTTCTGAAGAGGTGAACACTGA 59.293 43.478 23.36 0.00 32.85 3.41
3521 10541 4.065321 ACTTCTGAAGAGGTGAACACTG 57.935 45.455 23.36 0.00 32.85 3.66
3579 10599 4.946784 ACGCATATCTCAACAAAAGGAC 57.053 40.909 0.00 0.00 0.00 3.85
3598 10622 1.626654 ATGCGAACGCTTCCTGAACG 61.627 55.000 19.32 0.00 42.51 3.95
3608 10640 1.637478 TTAAACCGGGATGCGAACGC 61.637 55.000 6.32 12.33 42.35 4.84
3609 10641 0.797542 TTTAAACCGGGATGCGAACG 59.202 50.000 6.32 0.00 0.00 3.95
3610 10642 2.993449 TTTTAAACCGGGATGCGAAC 57.007 45.000 6.32 0.00 0.00 3.95
3613 10725 3.183754 GGAATTTTTAAACCGGGATGCG 58.816 45.455 6.32 0.00 0.00 4.73
3662 10774 2.953466 TACAGACTAATGTCACCGGC 57.047 50.000 0.00 0.00 45.20 6.13
3663 10775 4.566759 CACATTACAGACTAATGTCACCGG 59.433 45.833 0.00 0.00 43.80 5.28
3664 10776 5.168569 ACACATTACAGACTAATGTCACCG 58.831 41.667 1.33 0.00 43.80 4.94
3665 10777 7.172532 TCAAACACATTACAGACTAATGTCACC 59.827 37.037 1.33 0.00 43.80 4.02
3666 10778 8.009974 GTCAAACACATTACAGACTAATGTCAC 58.990 37.037 1.33 0.00 43.80 3.67
3667 10779 7.713073 TGTCAAACACATTACAGACTAATGTCA 59.287 33.333 1.33 0.00 43.80 3.58
3668 10780 8.083462 TGTCAAACACATTACAGACTAATGTC 57.917 34.615 1.33 0.00 43.80 3.06
3669 10781 8.445275 TTGTCAAACACATTACAGACTAATGT 57.555 30.769 0.00 0.00 45.77 2.71
3698 10819 4.692625 CAGCTAGCAACATTGAAGTAGTGT 59.307 41.667 18.83 0.00 0.00 3.55
3750 10876 2.016318 CAACTCACTGCAAGAACCACA 58.984 47.619 0.00 0.00 37.43 4.17
3812 11422 9.973450 CGAATCAGAAATTTATTCTCTCCTCTA 57.027 33.333 9.42 0.00 0.00 2.43
3813 11423 8.700051 TCGAATCAGAAATTTATTCTCTCCTCT 58.300 33.333 9.42 0.00 0.00 3.69
3903 11648 8.899771 AGAATTATAGGTGTTAATGAAAACGGG 58.100 33.333 0.00 0.00 31.76 5.28
3916 11661 6.957631 TCACCATGTTCAGAATTATAGGTGT 58.042 36.000 16.33 0.00 43.28 4.16
3973 11718 6.705863 AGCATCTTCAGTTTCAGTTTTCTT 57.294 33.333 0.00 0.00 0.00 2.52
4117 11864 7.977789 TGATAAACAGCAGTTAGATCAACAA 57.022 32.000 13.72 0.00 37.32 2.83
4351 13832 2.312348 GTGTGGGCGTTAACATTTTCG 58.688 47.619 6.39 0.00 0.00 3.46
4352 13833 2.287129 ACGTGTGGGCGTTAACATTTTC 60.287 45.455 6.39 0.00 43.04 2.29
4353 13834 1.677052 ACGTGTGGGCGTTAACATTTT 59.323 42.857 6.39 0.00 43.04 1.82
4466 13947 0.665835 GTTGAACGCCCACACATCAA 59.334 50.000 0.00 0.00 0.00 2.57
4469 13950 2.258013 CGGTTGAACGCCCACACAT 61.258 57.895 0.00 0.00 0.00 3.21
4499 13980 1.169661 TCATGTGTGGTGAAACGGCC 61.170 55.000 0.00 0.00 38.12 6.13
4516 13997 2.519622 CCCACACACCAGCTCCTCA 61.520 63.158 0.00 0.00 0.00 3.86
4545 14026 4.555709 AAGTGGCGTGTGGGCGAA 62.556 61.111 0.00 0.00 46.04 4.70
4573 14054 0.981183 CCCACACACTAGCCCTTGTA 59.019 55.000 0.00 0.00 0.00 2.41
4616 14170 4.662278 AGAGTTGCCACCTGCTTATAAAA 58.338 39.130 0.00 0.00 42.00 1.52


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

AutoCloner maintained by Alex Coulton.