Multiple sequence alignment - TraesCS4A01G487600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4A01G487600 chr4A 100.000 3928 0 0 1600 5527 739861351 739865278 0.000000e+00 7254.0
1 TraesCS4A01G487600 chr4A 100.000 2832 0 0 5827 8658 739865578 739868409 0.000000e+00 5230.0
2 TraesCS4A01G487600 chr4A 86.304 2570 259 55 6150 8658 739650327 739652864 0.000000e+00 2710.0
3 TraesCS4A01G487600 chr4A 86.187 2570 262 55 6150 8658 742055606 742058143 0.000000e+00 2693.0
4 TraesCS4A01G487600 chr4A 87.832 2219 189 33 6483 8658 741795934 741793754 0.000000e+00 2527.0
5 TraesCS4A01G487600 chr4A 100.000 1068 0 0 459 1526 739860210 739861277 0.000000e+00 1973.0
6 TraesCS4A01G487600 chr4A 97.940 1068 11 2 459 1526 740566006 740567062 0.000000e+00 1840.0
7 TraesCS4A01G487600 chr4A 98.418 948 15 0 1600 2547 740567341 740568288 0.000000e+00 1668.0
8 TraesCS4A01G487600 chr4A 86.085 1581 180 18 3448 5018 740928808 740930358 0.000000e+00 1664.0
9 TraesCS4A01G487600 chr4A 89.876 1205 103 8 6513 7701 740456804 740455603 0.000000e+00 1531.0
10 TraesCS4A01G487600 chr4A 87.345 1375 111 25 6487 7854 740303708 740305026 0.000000e+00 1517.0
11 TraesCS4A01G487600 chr4A 87.345 1375 111 25 6487 7854 740346962 740348280 0.000000e+00 1517.0
12 TraesCS4A01G487600 chr4A 87.055 1375 114 26 6487 7854 740269557 740270874 0.000000e+00 1495.0
13 TraesCS4A01G487600 chr4A 89.764 1016 79 13 3352 4358 740572726 740573725 0.000000e+00 1277.0
14 TraesCS4A01G487600 chr4A 89.542 1004 82 5 7676 8658 740455595 740454594 0.000000e+00 1251.0
15 TraesCS4A01G487600 chr4A 89.197 1009 81 9 7676 8658 740578858 740579864 0.000000e+00 1234.0
16 TraesCS4A01G487600 chr4A 93.641 802 51 0 7857 8658 741815614 741814813 0.000000e+00 1199.0
17 TraesCS4A01G487600 chr4A 87.264 1060 100 15 7634 8658 741590157 741591216 0.000000e+00 1177.0
18 TraesCS4A01G487600 chr4A 91.284 849 68 6 7812 8658 740019141 740018297 0.000000e+00 1153.0
19 TraesCS4A01G487600 chr4A 89.111 799 58 15 731 1518 741587948 741588728 0.000000e+00 966.0
20 TraesCS4A01G487600 chr4A 88.529 802 60 7 723 1518 740023002 740022227 0.000000e+00 942.0
21 TraesCS4A01G487600 chr4A 87.160 810 67 19 734 1526 741491489 741490700 0.000000e+00 885.0
22 TraesCS4A01G487600 chr4A 87.600 750 70 12 2606 3346 740568281 740569016 0.000000e+00 848.0
23 TraesCS4A01G487600 chr4A 83.190 928 74 38 619 1526 739642517 739643382 0.000000e+00 774.0
24 TraesCS4A01G487600 chr4A 82.888 935 79 37 619 1526 742047640 742048520 0.000000e+00 765.0
25 TraesCS4A01G487600 chr4A 87.250 549 56 7 983 1521 740926794 740927338 1.600000e-171 614.0
26 TraesCS4A01G487600 chr4A 89.139 488 48 3 1035 1521 740457374 740456891 3.460000e-168 603.0
27 TraesCS4A01G487600 chr4A 86.813 546 61 5 983 1521 740268862 740269403 4.470000e-167 599.0
28 TraesCS4A01G487600 chr4A 86.813 546 58 8 983 1521 740303015 740303553 1.610000e-166 597.0
29 TraesCS4A01G487600 chr4A 100.000 321 0 0 1 321 739859752 739860072 2.080000e-165 593.0
30 TraesCS4A01G487600 chr4A 86.447 546 63 5 983 1521 740346267 740346808 9.680000e-164 588.0
31 TraesCS4A01G487600 chr4A 95.938 320 12 1 1 319 740565525 740565844 1.290000e-142 518.0
32 TraesCS4A01G487600 chr4A 91.848 368 25 3 2606 2971 740927904 740928268 7.750000e-140 508.0
33 TraesCS4A01G487600 chr4A 84.645 521 64 12 3115 3635 739734495 739734999 1.000000e-138 505.0
34 TraesCS4A01G487600 chr4A 84.645 521 65 8 3115 3635 742130988 742131493 1.000000e-138 505.0
35 TraesCS4A01G487600 chr4A 85.275 455 41 7 2101 2547 742129837 742130273 6.170000e-121 446.0
36 TraesCS4A01G487600 chr4A 89.167 360 32 7 4355 4711 740575188 740575543 7.980000e-120 442.0
37 TraesCS4A01G487600 chr4A 88.994 318 35 0 5148 5465 740930373 740930690 2.270000e-105 394.0
38 TraesCS4A01G487600 chr4A 90.598 234 21 1 5925 6158 740576795 740577027 8.440000e-80 309.0
39 TraesCS4A01G487600 chr4A 93.210 162 10 1 619 780 741491648 741491488 4.040000e-58 237.0
40 TraesCS4A01G487600 chr4A 93.210 162 10 1 619 780 741587792 741587952 4.040000e-58 237.0
41 TraesCS4A01G487600 chr4A 94.737 114 5 1 615 727 740023739 740023626 8.930000e-40 176.0
42 TraesCS4A01G487600 chr4A 89.130 138 13 2 3846 3981 739735421 739735558 4.160000e-38 171.0
43 TraesCS4A01G487600 chr4A 89.313 131 14 0 3846 3976 742131916 742132046 1.930000e-36 165.0
44 TraesCS4A01G487600 chr4A 90.083 121 12 0 5978 6098 741486194 741486074 3.240000e-34 158.0
45 TraesCS4A01G487600 chr4A 88.889 117 13 0 5978 6094 739650217 739650333 2.520000e-30 145.0
46 TraesCS4A01G487600 chr4A 85.124 121 9 7 1683 1794 740456945 740456825 1.980000e-21 115.0
47 TraesCS4A01G487600 chr4A 79.878 164 25 7 6183 6342 47456881 47456722 7.100000e-21 113.0
48 TraesCS4A01G487600 chr4A 93.443 61 4 0 1683 1743 742129280 742129340 3.330000e-14 91.6
49 TraesCS4A01G487600 chr4A 92.982 57 4 0 1687 1743 739734036 739734092 5.570000e-12 84.2
50 TraesCS4A01G487600 chr4A 91.803 61 4 1 1683 1742 740303499 740303559 5.570000e-12 84.2
51 TraesCS4A01G487600 chr4A 97.872 47 1 0 1645 1691 742129158 742129204 2.000000e-11 82.4
52 TraesCS4A01G487600 chr4A 94.231 52 3 0 1687 1738 741796347 741796296 7.200000e-11 80.5
53 TraesCS4A01G487600 chr4A 93.333 45 1 1 1752 1794 741588954 741588998 2.020000e-06 65.8
54 TraesCS4A01G487600 chr7A 91.247 2422 168 19 6277 8658 3311037 3313454 0.000000e+00 3258.0
55 TraesCS4A01G487600 chr7A 86.578 2861 293 45 5828 8658 2119547 2116748 0.000000e+00 3072.0
56 TraesCS4A01G487600 chr7A 92.412 1700 105 11 5828 7512 3210003 3208313 0.000000e+00 2403.0
57 TraesCS4A01G487600 chr7A 92.009 1702 114 9 5828 7514 1998496 1996802 0.000000e+00 2370.0
58 TraesCS4A01G487600 chr7A 92.401 1645 91 8 3402 5035 3308419 3310040 0.000000e+00 2314.0
59 TraesCS4A01G487600 chr7A 89.109 1111 100 13 3929 5035 3211576 3210483 0.000000e+00 1362.0
60 TraesCS4A01G487600 chr7A 86.690 1127 99 16 3929 5035 2000304 1999209 0.000000e+00 1203.0
61 TraesCS4A01G487600 chr7A 93.218 811 53 1 7848 8658 3208020 3207212 0.000000e+00 1192.0
62 TraesCS4A01G487600 chr7A 90.461 912 75 10 7748 8658 3631705 3630805 0.000000e+00 1192.0
63 TraesCS4A01G487600 chr7A 88.644 907 77 11 619 1519 3284931 3285817 0.000000e+00 1081.0
64 TraesCS4A01G487600 chr7A 89.737 799 66 12 2609 3405 3286474 3287258 0.000000e+00 1007.0
65 TraesCS4A01G487600 chr7A 94.286 350 18 2 5148 5495 3310038 3310387 1.280000e-147 534.0
66 TraesCS4A01G487600 chr7A 91.053 380 33 1 5148 5527 1999211 1998833 5.990000e-141 512.0
67 TraesCS4A01G487600 chr7A 90.283 247 24 0 5148 5394 3210485 3210239 3.010000e-84 324.0
68 TraesCS4A01G487600 chr7A 88.426 216 13 1 2045 2260 3213044 3212841 5.190000e-62 250.0
69 TraesCS4A01G487600 chr7A 88.235 170 17 1 2098 2264 2001731 2001562 5.300000e-47 200.0
70 TraesCS4A01G487600 chr7A 85.276 163 18 4 1808 1970 3285868 3286024 6.950000e-36 163.0
71 TraesCS4A01G487600 chr7A 87.313 134 17 0 2414 2547 3286345 3286478 4.190000e-33 154.0
72 TraesCS4A01G487600 chr7A 93.220 59 3 1 1685 1742 3285767 3285825 1.550000e-12 86.1
73 TraesCS4A01G487600 chr7A 92.453 53 4 0 1683 1735 3213526 3213474 9.320000e-10 76.8
74 TraesCS4A01G487600 chr7D 89.331 2540 189 43 6150 8658 3788658 3786170 0.000000e+00 3114.0
75 TraesCS4A01G487600 chr7D 91.953 1628 117 7 5893 7514 3905037 3906656 0.000000e+00 2268.0
76 TraesCS4A01G487600 chr7D 89.701 1806 138 24 5908 7701 2568058 2566289 0.000000e+00 2261.0
77 TraesCS4A01G487600 chr7D 90.109 1375 110 18 6150 7514 3634869 3633511 0.000000e+00 1762.0
78 TraesCS4A01G487600 chr7D 89.695 1310 99 14 3744 5035 3903026 3904317 0.000000e+00 1639.0
79 TraesCS4A01G487600 chr7D 92.415 1147 85 2 6369 7514 2359145 2358000 0.000000e+00 1635.0
80 TraesCS4A01G487600 chr7D 92.848 811 58 0 7848 8658 2609922 2609112 0.000000e+00 1177.0
81 TraesCS4A01G487600 chr7D 92.478 811 61 0 7848 8658 3633185 3632375 0.000000e+00 1160.0
82 TraesCS4A01G487600 chr7D 86.762 1050 90 22 2656 3693 3900440 3901452 0.000000e+00 1123.0
83 TraesCS4A01G487600 chr7D 86.876 1021 85 24 7676 8658 2566281 2565272 0.000000e+00 1098.0
84 TraesCS4A01G487600 chr7D 88.609 834 66 14 4023 4853 2568868 2568061 0.000000e+00 987.0
85 TraesCS4A01G487600 chr7D 86.907 527 57 3 988 1505 2359819 2359296 1.620000e-161 580.0
86 TraesCS4A01G487600 chr7D 89.443 341 34 2 5148 5488 3904315 3904653 6.210000e-116 429.0
87 TraesCS4A01G487600 chr7D 88.201 339 40 0 3634 3972 2569209 2568871 1.050000e-108 405.0
88 TraesCS4A01G487600 chr7D 90.076 262 19 4 2268 2523 3900167 3900427 5.010000e-87 333.0
89 TraesCS4A01G487600 chr7D 85.455 220 16 4 2045 2261 3898284 3898490 1.890000e-51 215.0
90 TraesCS4A01G487600 chr7D 96.748 123 4 0 5030 5152 233649824 233649702 1.140000e-48 206.0
91 TraesCS4A01G487600 chr7D 87.302 126 16 0 5973 6098 3788773 3788648 2.520000e-30 145.0
92 TraesCS4A01G487600 chr7D 93.103 87 6 0 534 620 448711236 448711150 2.540000e-25 128.0
93 TraesCS4A01G487600 chr7D 96.154 52 2 0 1687 1738 2611484 2611433 1.550000e-12 86.1
94 TraesCS4A01G487600 chr7D 92.857 56 4 0 1683 1738 3639967 3639912 2.000000e-11 82.4
95 TraesCS4A01G487600 chr3B 90.333 300 26 3 23 321 412442756 412443053 2.930000e-104 390.0
96 TraesCS4A01G487600 chr3B 95.161 124 5 1 5032 5154 694025014 694025137 2.470000e-45 195.0
97 TraesCS4A01G487600 chr3B 75.581 172 35 6 6176 6343 729936360 729936192 2.590000e-10 78.7
98 TraesCS4A01G487600 chr7B 89.701 301 29 2 23 321 601630207 601630507 4.900000e-102 383.0
99 TraesCS4A01G487600 chr7B 87.879 297 35 1 26 321 663974494 663974198 1.790000e-91 348.0
100 TraesCS4A01G487600 chr7B 86.971 307 35 5 17 321 654172691 654172994 2.990000e-89 340.0
101 TraesCS4A01G487600 chr4B 90.169 295 27 2 24 316 670806752 670807046 4.900000e-102 383.0
102 TraesCS4A01G487600 chr4B 99.145 117 1 0 5034 5150 136675741 136675857 2.450000e-50 211.0
103 TraesCS4A01G487600 chr4B 86.624 157 20 1 4102 4258 438375334 438375179 1.160000e-38 172.0
104 TraesCS4A01G487600 chr4B 86.364 154 20 1 4103 4256 366930148 366930300 5.380000e-37 167.0
105 TraesCS4A01G487600 chr2B 89.562 297 25 4 23 317 777379334 777379626 1.060000e-98 372.0
106 TraesCS4A01G487600 chr2B 98.361 122 2 0 5033 5154 85699389 85699510 1.890000e-51 215.0
107 TraesCS4A01G487600 chr2B 95.833 120 5 0 5033 5152 563855639 563855758 2.470000e-45 195.0
108 TraesCS4A01G487600 chr2B 94.253 87 5 0 534 620 26279909 26279823 5.450000e-27 134.0
109 TraesCS4A01G487600 chr2B 79.268 164 28 5 6183 6340 634082962 634082799 9.190000e-20 110.0
110 TraesCS4A01G487600 chr5B 89.041 292 29 3 26 316 88868620 88868909 8.260000e-95 359.0
111 TraesCS4A01G487600 chr5B 96.667 120 4 0 5034 5153 351460531 351460650 5.300000e-47 200.0
112 TraesCS4A01G487600 chr3D 86.184 304 41 1 19 321 529122046 529121743 2.330000e-85 327.0
113 TraesCS4A01G487600 chr3D 95.041 121 6 0 5032 5152 112723214 112723334 3.190000e-44 191.0
114 TraesCS4A01G487600 chr3D 79.470 151 24 5 6176 6320 51711917 51712066 5.530000e-17 100.0
115 TraesCS4A01G487600 chr1B 96.000 125 4 1 5030 5153 95761643 95761767 1.470000e-47 202.0
116 TraesCS4A01G487600 chr1B 96.610 118 4 0 5033 5150 572677693 572677810 6.860000e-46 196.0
117 TraesCS4A01G487600 chr1B 89.796 98 8 2 529 626 317444366 317444461 3.280000e-24 124.0
118 TraesCS4A01G487600 chr6B 94.253 87 5 0 534 620 100890994 100890908 5.450000e-27 134.0
119 TraesCS4A01G487600 chr1D 94.253 87 4 1 534 620 457823178 457823093 1.960000e-26 132.0
120 TraesCS4A01G487600 chr1D 94.186 86 5 0 534 619 489967253 489967338 1.960000e-26 132.0
121 TraesCS4A01G487600 chr6D 92.857 84 6 0 537 620 82650482 82650399 1.180000e-23 122.0
122 TraesCS4A01G487600 chr2D 91.954 87 7 0 534 620 476013984 476013898 1.180000e-23 122.0


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 TraesCS4A01G487600 chr4A 739859752 739868409 8657 False 3762.500000 7254 100.000000 1 8658 4 chr4A.!!$F6 8657
1 TraesCS4A01G487600 chr4A 742055606 742058143 2537 False 2693.000000 2693 86.187000 6150 8658 1 chr4A.!!$F3 2508
2 TraesCS4A01G487600 chr4A 739650217 739652864 2647 False 1427.500000 2710 87.596500 5978 8658 2 chr4A.!!$F4 2680
3 TraesCS4A01G487600 chr4A 741793754 741796347 2593 True 1303.750000 2527 91.031500 1687 8658 2 chr4A.!!$R7 6971
4 TraesCS4A01G487600 chr4A 741814813 741815614 801 True 1199.000000 1199 93.641000 7857 8658 1 chr4A.!!$R3 801
5 TraesCS4A01G487600 chr4A 740346267 740348280 2013 False 1052.500000 1517 86.896000 983 7854 2 chr4A.!!$F9 6871
6 TraesCS4A01G487600 chr4A 740268862 740270874 2012 False 1047.000000 1495 86.934000 983 7854 2 chr4A.!!$F7 6871
7 TraesCS4A01G487600 chr4A 740565525 740579864 14339 False 1017.000000 1840 92.327750 1 8658 8 chr4A.!!$F10 8657
8 TraesCS4A01G487600 chr4A 740454594 740457374 2780 True 875.000000 1531 88.420250 1035 8658 4 chr4A.!!$R5 7623
9 TraesCS4A01G487600 chr4A 740926794 740930690 3896 False 795.000000 1664 88.544250 983 5465 4 chr4A.!!$F11 4482
10 TraesCS4A01G487600 chr4A 739642517 739643382 865 False 774.000000 774 83.190000 619 1526 1 chr4A.!!$F1 907
11 TraesCS4A01G487600 chr4A 742047640 742048520 880 False 765.000000 765 82.888000 619 1526 1 chr4A.!!$F2 907
12 TraesCS4A01G487600 chr4A 740018297 740023739 5442 True 757.000000 1153 91.516667 615 8658 3 chr4A.!!$R4 8043
13 TraesCS4A01G487600 chr4A 740303015 740305026 2011 False 732.733333 1517 88.653667 983 7854 3 chr4A.!!$F8 6871
14 TraesCS4A01G487600 chr4A 741587792 741591216 3424 False 611.450000 1177 90.729500 619 8658 4 chr4A.!!$F12 8039
15 TraesCS4A01G487600 chr4A 741490700 741491648 948 True 561.000000 885 90.185000 619 1526 2 chr4A.!!$R6 907
16 TraesCS4A01G487600 chr4A 742129158 742132046 2888 False 258.000000 505 90.109600 1645 3976 5 chr4A.!!$F13 2331
17 TraesCS4A01G487600 chr4A 739734036 739735558 1522 False 253.400000 505 88.919000 1687 3981 3 chr4A.!!$F5 2294
18 TraesCS4A01G487600 chr7A 2116748 2119547 2799 True 3072.000000 3072 86.578000 5828 8658 1 chr7A.!!$R1 2830
19 TraesCS4A01G487600 chr7A 3308419 3313454 5035 False 2035.333333 3258 92.644667 3402 8658 3 chr7A.!!$F2 5256
20 TraesCS4A01G487600 chr7A 3630805 3631705 900 True 1192.000000 1192 90.461000 7748 8658 1 chr7A.!!$R2 910
21 TraesCS4A01G487600 chr7A 1996802 2001731 4929 True 1071.250000 2370 89.496750 2098 7514 4 chr7A.!!$R3 5416
22 TraesCS4A01G487600 chr7A 3207212 3213526 6314 True 934.633333 2403 90.983500 1683 8658 6 chr7A.!!$R4 6975
23 TraesCS4A01G487600 chr7A 3284931 3287258 2327 False 498.220000 1081 88.838000 619 3405 5 chr7A.!!$F1 2786
24 TraesCS4A01G487600 chr7D 3786170 3788773 2603 True 1629.500000 3114 88.316500 5973 8658 2 chr7D.!!$R8 2685
25 TraesCS4A01G487600 chr7D 3632375 3634869 2494 True 1461.000000 1762 91.293500 6150 8658 2 chr7D.!!$R7 2508
26 TraesCS4A01G487600 chr7D 2565272 2569209 3937 True 1187.750000 2261 88.346750 3634 8658 4 chr7D.!!$R5 5024
27 TraesCS4A01G487600 chr7D 2358000 2359819 1819 True 1107.500000 1635 89.661000 988 7514 2 chr7D.!!$R4 6526
28 TraesCS4A01G487600 chr7D 3898284 3906656 8372 False 1001.166667 2268 88.897333 2045 7514 6 chr7D.!!$F1 5469
29 TraesCS4A01G487600 chr7D 2609112 2611484 2372 True 631.550000 1177 94.501000 1687 8658 2 chr7D.!!$R6 6971

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
319 321 0.031449 CGGAATTTTTGTGCACCCGT 59.969 50.000 15.69 0.00 0.00 5.28 F
320 322 1.537135 CGGAATTTTTGTGCACCCGTT 60.537 47.619 15.69 2.03 0.00 4.44 F
2449 6404 1.078848 CTGCCACAGTGGTAGGCTC 60.079 63.158 26.15 7.64 45.08 4.70 F
2871 6829 0.111061 ATTGGTCACAGCAGAGGCAA 59.889 50.000 0.00 0.00 44.61 4.52 F
3091 7058 0.178068 CCATACCACTAGCCACGCTT 59.822 55.000 0.00 0.00 40.44 4.68 F
5008 16544 0.036732 CTTGGCTAACAGTGAGGGCA 59.963 55.000 0.00 1.97 0.00 5.36 F
5052 16589 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17 F
5053 16590 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40 F
5055 16592 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12 F
6680 19362 0.111061 TGGATGCAAGCTGACCAAGT 59.889 50.000 0.00 0.00 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2449 6404 1.105167 ATGACAATGCTGATGGCCCG 61.105 55.000 0.00 0.00 40.92 6.13 R
2471 6426 2.863484 TTGGCCCAGGGATGGTGT 60.863 61.111 10.89 0.00 0.00 4.16 R
3762 13699 0.107312 ACTGCCTCATCACCATCTGC 60.107 55.000 0.00 0.00 0.00 4.26 R
4925 16460 0.032615 AGAAAACAGGGTGGTTGCCA 60.033 50.000 0.00 0.00 0.00 4.92 R
5034 16571 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85 R
5840 17417 0.464373 TGCTAACCTATGCCTGCAGC 60.464 55.000 8.66 4.57 44.14 5.25 R
6198 18700 1.094785 ACACACACACAGGCAAAGAC 58.905 50.000 0.00 0.00 0.00 3.01 R
6680 19362 1.138859 CTGCGACCTATCATTGACCCA 59.861 52.381 0.00 0.00 0.00 4.51 R
6779 19582 1.163554 GCCTCTTTCTTCCAGCACTG 58.836 55.000 0.00 0.00 0.00 3.66 R
7712 21132 0.671796 TGTCCGTTGACTCGACACAT 59.328 50.000 0.00 0.00 42.28 3.21 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
23 24 5.726980 TCAATAAAATGCAGTCAAAGCCT 57.273 34.783 0.00 0.00 0.00 4.58
105 107 0.514691 CGAACAGCTCCAGCAGAAAC 59.485 55.000 0.48 0.00 45.16 2.78
119 121 3.433615 AGCAGAAACTGTAGCGCTAAAAG 59.566 43.478 20.73 20.98 33.43 2.27
142 144 2.729491 GGGTGCGCGCTGAAAAAC 60.729 61.111 33.29 20.28 0.00 2.43
181 183 0.829602 TTTTGGCTTCGGATTGGGCA 60.830 50.000 0.00 0.00 0.00 5.36
196 198 1.268352 TGGGCACGCTTCACAATTTAC 59.732 47.619 0.00 0.00 0.00 2.01
219 221 2.026879 GTTCTTTTTGGGCGCGCA 59.973 55.556 34.42 24.55 0.00 6.09
319 321 0.031449 CGGAATTTTTGTGCACCCGT 59.969 50.000 15.69 0.00 0.00 5.28
320 322 1.537135 CGGAATTTTTGTGCACCCGTT 60.537 47.619 15.69 2.03 0.00 4.44
552 576 7.646548 ACTGCTATGACTTGATTGTACTCTA 57.353 36.000 0.00 0.00 0.00 2.43
571 595 6.226787 ACTCTATACTGCTATGTTTGATGCC 58.773 40.000 0.00 0.00 0.00 4.40
606 630 7.888424 GCTTTATAATATAAAGCGGGGGAAAA 58.112 34.615 30.20 0.57 46.31 2.29
758 1465 2.100605 ATCCCAGTGCTTCGAAAGAC 57.899 50.000 0.00 0.00 41.84 3.01
2408 6363 4.828072 ACCTTGTCTCTCTCCCATTTAC 57.172 45.455 0.00 0.00 0.00 2.01
2449 6404 1.078848 CTGCCACAGTGGTAGGCTC 60.079 63.158 26.15 7.64 45.08 4.70
2471 6426 2.487805 GGGCCATCAGCATTGTCATAGA 60.488 50.000 4.39 0.00 46.50 1.98
2524 6479 6.437928 GGTTTGAAAGAAAATCATTTTGGCC 58.562 36.000 0.00 0.00 31.94 5.36
2539 6494 0.981183 TGGCCATGGTCGTTCTAACT 59.019 50.000 12.67 0.00 0.00 2.24
2540 6495 2.181125 TGGCCATGGTCGTTCTAACTA 58.819 47.619 12.67 0.00 0.00 2.24
2541 6496 2.568062 TGGCCATGGTCGTTCTAACTAA 59.432 45.455 12.67 0.00 0.00 2.24
2542 6497 3.008157 TGGCCATGGTCGTTCTAACTAAA 59.992 43.478 12.67 0.00 0.00 1.85
2543 6498 4.196971 GGCCATGGTCGTTCTAACTAAAT 58.803 43.478 14.67 0.00 0.00 1.40
2544 6499 5.104859 TGGCCATGGTCGTTCTAACTAAATA 60.105 40.000 12.67 0.00 0.00 1.40
2545 6500 5.995897 GGCCATGGTCGTTCTAACTAAATAT 59.004 40.000 14.67 0.00 0.00 1.28
2546 6501 7.156673 GGCCATGGTCGTTCTAACTAAATATA 58.843 38.462 14.67 0.00 0.00 0.86
2547 6502 7.822822 GGCCATGGTCGTTCTAACTAAATATAT 59.177 37.037 14.67 0.00 0.00 0.86
2548 6503 9.865321 GCCATGGTCGTTCTAACTAAATATATA 57.135 33.333 14.67 0.00 0.00 0.86
2691 6646 8.186821 ACATACTAGTGGTAAAGAACATACGAC 58.813 37.037 5.39 0.00 33.68 4.34
2870 6828 0.607217 CATTGGTCACAGCAGAGGCA 60.607 55.000 0.00 0.00 44.61 4.75
2871 6829 0.111061 ATTGGTCACAGCAGAGGCAA 59.889 50.000 0.00 0.00 44.61 4.52
3013 6980 3.357079 GCACGGCCTGTTGACCAG 61.357 66.667 0.00 0.00 41.15 4.00
3066 7033 3.243035 CGGCATCATGGCTATTTTTCGAA 60.243 43.478 9.90 0.00 41.25 3.71
3068 7035 3.732721 GCATCATGGCTATTTTTCGAAGC 59.267 43.478 0.00 0.00 35.47 3.86
3069 7036 4.734402 GCATCATGGCTATTTTTCGAAGCA 60.734 41.667 8.22 0.00 38.01 3.91
3070 7037 5.526115 CATCATGGCTATTTTTCGAAGCAT 58.474 37.500 8.22 2.86 38.01 3.79
3071 7038 6.671190 CATCATGGCTATTTTTCGAAGCATA 58.329 36.000 8.22 3.82 38.01 3.14
3072 7039 6.060028 TCATGGCTATTTTTCGAAGCATAC 57.940 37.500 8.22 0.00 38.01 2.39
3091 7058 0.178068 CCATACCACTAGCCACGCTT 59.822 55.000 0.00 0.00 40.44 4.68
3195 7491 1.955080 GCTAACGCTAGAGGCTCCTTA 59.045 52.381 11.71 0.00 39.13 2.69
3232 7532 0.301687 CACCATTGTCGATGCGCTAC 59.698 55.000 9.73 1.09 34.25 3.58
3233 7533 0.810031 ACCATTGTCGATGCGCTACC 60.810 55.000 9.73 0.00 34.25 3.18
3234 7534 1.559814 CATTGTCGATGCGCTACCG 59.440 57.895 9.73 9.68 37.57 4.02
3349 7649 4.767255 GGGCAGTGTCCCTCAGCG 62.767 72.222 0.88 0.00 43.13 5.18
3355 11359 1.598130 GTGTCCCTCAGCGTGCTTT 60.598 57.895 0.00 0.00 0.00 3.51
3435 11439 1.077930 AGCAGCAACATCAGCCGAT 60.078 52.632 0.00 0.00 0.00 4.18
3520 11800 1.336240 GGCAACATGGTGTCAGCTTTC 60.336 52.381 11.31 0.00 33.56 2.62
3521 11801 1.337703 GCAACATGGTGTCAGCTTTCA 59.662 47.619 13.35 0.00 31.36 2.69
3536 11832 2.799412 GCTTTCATAGCCGATGTCTGAG 59.201 50.000 0.00 0.00 44.48 3.35
3550 11846 2.905736 TGTCTGAGGACATCCATCAACA 59.094 45.455 0.00 6.17 46.19 3.33
3677 12091 4.808414 TGCATGTCCTATAGATAGCACC 57.192 45.455 0.00 0.00 0.00 5.01
3762 13699 4.487948 TGACAAATACGGTAGGAAACTCG 58.512 43.478 0.00 0.00 43.67 4.18
3783 13720 1.208776 CAGATGGTGATGAGGCAGTGA 59.791 52.381 0.00 0.00 0.00 3.41
3804 13743 1.654954 TAGAAGCGACGAGGAGGCAC 61.655 60.000 0.00 0.00 0.00 5.01
3841 13780 3.488489 CGGCGTTTTCTCCTACATTTTG 58.512 45.455 0.00 0.00 0.00 2.44
3848 13879 1.564348 TCTCCTACATTTTGCCCCTCC 59.436 52.381 0.00 0.00 0.00 4.30
3936 13981 6.546772 TCATATATGGTTGTGCACATCAACAT 59.453 34.615 22.18 22.18 44.53 2.71
4018 14064 0.672342 CCTAGGATACGACCCAACCG 59.328 60.000 1.05 0.00 46.39 4.44
4327 14373 2.683211 ATTGACCCAAAACAGAGGCT 57.317 45.000 0.00 0.00 0.00 4.58
4426 15939 9.515020 TTTGAATTTCTAGCTTTGTTGTTGTAG 57.485 29.630 0.00 0.00 0.00 2.74
4490 16003 8.938801 TCCCTCATAGTATATGTAAACGGTTA 57.061 34.615 0.00 0.00 0.00 2.85
4527 16040 2.367241 TCGAACACATTGTCTCCCAAGA 59.633 45.455 0.00 0.00 36.25 3.02
4563 16093 6.839124 TCAAAATTGTGCCTATGAAGACAT 57.161 33.333 0.00 0.00 40.16 3.06
4587 16117 5.179368 TCAAACACTCGAGAACAAATGATCC 59.821 40.000 21.68 0.00 0.00 3.36
4790 16325 3.327404 GTCGGTGGGGGTGGATGT 61.327 66.667 0.00 0.00 0.00 3.06
4793 16328 2.998949 GGTGGGGGTGGATGTCTC 59.001 66.667 0.00 0.00 0.00 3.36
4821 16356 1.227943 GAAGGCAGCACAGGTGTCA 60.228 57.895 3.56 0.00 38.18 3.58
4877 16412 1.296392 CATCCAGGCGACCAACTCA 59.704 57.895 0.00 0.00 0.00 3.41
4916 16451 0.827089 CACCCACCTTGTTCATGGCA 60.827 55.000 0.00 0.00 31.66 4.92
4940 16475 1.120795 CCATTGGCAACCACCCTGTT 61.121 55.000 0.00 0.00 30.78 3.16
4993 16529 2.911143 CGGGGATCCCAGTCTTGG 59.089 66.667 32.07 7.93 45.83 3.61
5008 16544 0.036732 CTTGGCTAACAGTGAGGGCA 59.963 55.000 0.00 1.97 0.00 5.36
5034 16571 4.794648 GGGCGGCTGTGGCATGTA 62.795 66.667 9.56 0.00 40.87 2.29
5035 16572 3.508840 GGCGGCTGTGGCATGTAC 61.509 66.667 0.00 0.00 40.87 2.90
5036 16573 2.436646 GCGGCTGTGGCATGTACT 60.437 61.111 0.00 0.00 40.87 2.73
5037 16574 2.464459 GCGGCTGTGGCATGTACTC 61.464 63.158 0.00 0.00 40.87 2.59
5038 16575 1.815421 CGGCTGTGGCATGTACTCC 60.815 63.158 0.00 0.30 40.87 3.85
5039 16576 1.452108 GGCTGTGGCATGTACTCCC 60.452 63.158 0.00 0.00 40.87 4.30
5040 16577 1.604378 GCTGTGGCATGTACTCCCT 59.396 57.895 0.00 0.00 38.54 4.20
5041 16578 0.462759 GCTGTGGCATGTACTCCCTC 60.463 60.000 0.00 0.00 38.54 4.30
5042 16579 0.179000 CTGTGGCATGTACTCCCTCC 59.821 60.000 0.00 0.00 0.00 4.30
5043 16580 1.144057 GTGGCATGTACTCCCTCCG 59.856 63.158 0.00 0.00 0.00 4.63
5044 16581 1.305802 TGGCATGTACTCCCTCCGT 60.306 57.895 0.00 0.00 0.00 4.69
5045 16582 1.327690 TGGCATGTACTCCCTCCGTC 61.328 60.000 0.00 0.00 0.00 4.79
5046 16583 1.442148 GCATGTACTCCCTCCGTCC 59.558 63.158 0.00 0.00 0.00 4.79
5047 16584 1.734137 CATGTACTCCCTCCGTCCG 59.266 63.158 0.00 0.00 0.00 4.79
5048 16585 1.455217 ATGTACTCCCTCCGTCCGG 60.455 63.158 0.00 0.00 0.00 5.14
5049 16586 1.929860 ATGTACTCCCTCCGTCCGGA 61.930 60.000 0.00 0.00 42.90 5.14
5050 16587 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
5051 16588 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
5052 16589 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
5053 16590 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
5054 16591 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
5055 16592 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
5056 16593 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
5057 16594 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
5058 16595 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
5059 16596 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
5060 16597 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
5061 16598 1.274596 CGTCCGGAAATACTTGTCGG 58.725 55.000 5.23 0.00 41.80 4.79
5062 16599 1.135315 CGTCCGGAAATACTTGTCGGA 60.135 52.381 5.23 0.00 46.06 4.55
5064 16601 3.681593 TCCGGAAATACTTGTCGGAAA 57.318 42.857 0.00 0.00 45.40 3.13
5065 16602 4.005487 TCCGGAAATACTTGTCGGAAAA 57.995 40.909 0.00 0.00 45.40 2.29
5066 16603 4.387598 TCCGGAAATACTTGTCGGAAAAA 58.612 39.130 0.00 0.00 45.40 1.94
5067 16604 5.005094 TCCGGAAATACTTGTCGGAAAAAT 58.995 37.500 0.00 0.00 45.40 1.82
5068 16605 5.092781 CCGGAAATACTTGTCGGAAAAATG 58.907 41.667 0.00 0.00 42.94 2.32
5069 16606 5.092781 CGGAAATACTTGTCGGAAAAATGG 58.907 41.667 0.00 0.00 0.00 3.16
5070 16607 5.106475 CGGAAATACTTGTCGGAAAAATGGA 60.106 40.000 0.00 0.00 0.00 3.41
5071 16608 6.404293 CGGAAATACTTGTCGGAAAAATGGAT 60.404 38.462 0.00 0.00 0.00 3.41
5072 16609 6.751888 GGAAATACTTGTCGGAAAAATGGATG 59.248 38.462 0.00 0.00 0.00 3.51
5073 16610 6.834168 AATACTTGTCGGAAAAATGGATGT 57.166 33.333 0.00 0.00 0.00 3.06
5074 16611 7.931578 AATACTTGTCGGAAAAATGGATGTA 57.068 32.000 0.00 0.00 0.00 2.29
5075 16612 8.519799 AATACTTGTCGGAAAAATGGATGTAT 57.480 30.769 0.00 0.00 0.00 2.29
5076 16613 6.436843 ACTTGTCGGAAAAATGGATGTATC 57.563 37.500 0.00 0.00 0.00 2.24
5077 16614 6.180472 ACTTGTCGGAAAAATGGATGTATCT 58.820 36.000 0.00 0.00 0.00 1.98
5078 16615 7.335627 ACTTGTCGGAAAAATGGATGTATCTA 58.664 34.615 0.00 0.00 0.00 1.98
5079 16616 7.495934 ACTTGTCGGAAAAATGGATGTATCTAG 59.504 37.037 0.00 0.00 0.00 2.43
5080 16617 7.119709 TGTCGGAAAAATGGATGTATCTAGA 57.880 36.000 0.00 0.00 0.00 2.43
5081 16618 6.984474 TGTCGGAAAAATGGATGTATCTAGAC 59.016 38.462 0.00 0.00 0.00 2.59
5082 16619 6.984474 GTCGGAAAAATGGATGTATCTAGACA 59.016 38.462 0.00 0.00 0.00 3.41
5083 16620 7.657761 GTCGGAAAAATGGATGTATCTAGACAT 59.342 37.037 0.00 0.00 42.82 3.06
5084 16621 8.866093 TCGGAAAAATGGATGTATCTAGACATA 58.134 33.333 0.00 0.00 40.18 2.29
5085 16622 9.658799 CGGAAAAATGGATGTATCTAGACATAT 57.341 33.333 0.00 0.00 40.18 1.78
5123 16660 7.088589 ACATCCACTTTTATCAATTTCTCCG 57.911 36.000 0.00 0.00 0.00 4.63
5124 16661 6.884295 ACATCCACTTTTATCAATTTCTCCGA 59.116 34.615 0.00 0.00 0.00 4.55
5125 16662 6.737254 TCCACTTTTATCAATTTCTCCGAC 57.263 37.500 0.00 0.00 0.00 4.79
5126 16663 6.234920 TCCACTTTTATCAATTTCTCCGACA 58.765 36.000 0.00 0.00 0.00 4.35
5127 16664 6.712998 TCCACTTTTATCAATTTCTCCGACAA 59.287 34.615 0.00 0.00 0.00 3.18
5128 16665 7.023575 CCACTTTTATCAATTTCTCCGACAAG 58.976 38.462 0.00 0.00 0.00 3.16
5129 16666 7.308589 CCACTTTTATCAATTTCTCCGACAAGT 60.309 37.037 0.00 0.00 0.00 3.16
5130 16667 8.717821 CACTTTTATCAATTTCTCCGACAAGTA 58.282 33.333 0.00 0.00 0.00 2.24
5131 16668 9.449719 ACTTTTATCAATTTCTCCGACAAGTAT 57.550 29.630 0.00 0.00 0.00 2.12
5136 16673 6.908825 TCAATTTCTCCGACAAGTATTTTGG 58.091 36.000 0.00 0.00 0.00 3.28
5137 16674 5.897377 ATTTCTCCGACAAGTATTTTGGG 57.103 39.130 0.00 0.00 0.00 4.12
5138 16675 4.627284 TTCTCCGACAAGTATTTTGGGA 57.373 40.909 0.00 0.00 0.00 4.37
5139 16676 3.934068 TCTCCGACAAGTATTTTGGGAC 58.066 45.455 0.00 0.00 0.00 4.46
5140 16677 2.671396 CTCCGACAAGTATTTTGGGACG 59.329 50.000 0.00 0.00 0.00 4.79
5141 16678 1.735571 CCGACAAGTATTTTGGGACGG 59.264 52.381 0.00 0.00 0.00 4.79
5142 16679 2.613474 CCGACAAGTATTTTGGGACGGA 60.613 50.000 0.00 0.00 37.12 4.69
5143 16680 2.671396 CGACAAGTATTTTGGGACGGAG 59.329 50.000 0.00 0.00 0.00 4.63
5144 16681 3.007635 GACAAGTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
5145 16682 2.290705 ACAAGTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
5146 16683 1.961133 AGTATTTTGGGACGGAGGGA 58.039 50.000 0.00 0.00 0.00 4.20
5147 16684 1.838077 AGTATTTTGGGACGGAGGGAG 59.162 52.381 0.00 0.00 0.00 4.30
5148 16685 1.558294 GTATTTTGGGACGGAGGGAGT 59.442 52.381 0.00 0.00 0.00 3.85
5166 16703 2.089980 AGTATTAGGCAGTGTCGTCGT 58.910 47.619 0.00 0.00 0.00 4.34
5241 16779 3.773860 TCAACTGTGCAAAATCGTGTT 57.226 38.095 0.00 0.00 0.00 3.32
5254 16792 6.141685 GCAAAATCGTGTTAACTTTGTTCGAT 59.858 34.615 14.89 12.66 38.00 3.59
5262 16800 7.515528 CGTGTTAACTTTGTTCGATACAGTTCA 60.516 37.037 7.22 0.00 38.19 3.18
5398 16937 2.099141 ACACCACACAGATTCATCCG 57.901 50.000 0.00 0.00 0.00 4.18
5432 16972 3.674753 GGTAAGACATTGCACACAATTGC 59.325 43.478 5.05 0.00 44.21 3.56
5470 17010 1.266446 CGATGTGCAAACCATCACACA 59.734 47.619 14.15 0.00 44.74 3.72
5496 17036 7.910162 ACATGATTTTTATAATGTGTGTCTCGC 59.090 33.333 0.00 0.00 32.18 5.03
5846 17423 3.631145 ACACAATTTACACTGCTGCAG 57.369 42.857 27.02 27.02 37.52 4.41
5864 17441 2.477863 GCAGGCATAGGTTAGCAAAACG 60.478 50.000 0.00 0.00 0.00 3.60
5961 18460 9.555727 TTGCCCTTATATTACAGAGTAATTGTC 57.444 33.333 7.61 0.00 0.00 3.18
6169 18671 4.055360 GGCCAAACTGGTTGAATAAACAC 58.945 43.478 7.08 0.00 40.46 3.32
6170 18672 4.442192 GGCCAAACTGGTTGAATAAACACA 60.442 41.667 7.08 0.00 40.46 3.72
6198 18700 7.642669 TGAGCTTCTGTCTTTTATGAACTTTG 58.357 34.615 0.00 0.00 0.00 2.77
6253 18916 0.322187 GTTGGTTGTGGGCGTCCTAT 60.322 55.000 7.97 0.00 0.00 2.57
6270 18935 0.463654 TATCCATGCAGACAACGGGC 60.464 55.000 0.00 0.00 0.00 6.13
6293 18958 4.662145 GTGTGCTTATTGTGCTTGTATCC 58.338 43.478 0.00 0.00 0.00 2.59
6382 19058 9.371136 TGTTTGTTCAGCAATTTTAATGTGTTA 57.629 25.926 0.00 0.00 36.89 2.41
6650 19332 6.820656 CCTACTTAAGAAGCTTGACATGATGT 59.179 38.462 10.09 0.00 0.00 3.06
6680 19362 0.111061 TGGATGCAAGCTGACCAAGT 59.889 50.000 0.00 0.00 0.00 3.16
6731 19413 7.070946 TCAGAGATGATCTTGAAGAAATAGGCT 59.929 37.037 0.00 0.00 35.47 4.58
6746 19428 8.497910 AGAAATAGGCTCATACCTTGAAGATA 57.502 34.615 0.00 0.00 41.50 1.98
6928 19737 2.161211 GCTCAAGTGGCAGAAACAGATC 59.839 50.000 0.00 0.00 0.00 2.75
7008 19817 1.841302 ATTCGTGCTCCCAGGAAGCA 61.841 55.000 0.00 0.00 45.62 3.91
7213 20022 5.243954 CCTAGTAATTGATGGTCGGATGAGA 59.756 44.000 0.00 0.00 0.00 3.27
7225 20034 5.874810 TGGTCGGATGAGAAAGTTTATCAAG 59.125 40.000 16.30 11.01 0.00 3.02
7268 20080 1.233285 GCAGCTCAAGGTGGTGTCTG 61.233 60.000 10.90 0.00 43.24 3.51
7303 20115 6.259550 AGATGTCTTGGTAAAACAATGCTC 57.740 37.500 0.00 0.00 0.00 4.26
7335 20147 9.936329 AGTGTTGTATAATAAAATTGGGAGGAT 57.064 29.630 0.00 0.00 0.00 3.24
7505 20317 4.457257 GGAATTATCTACATGGCAAGAGGC 59.543 45.833 0.00 0.00 43.74 4.70
7623 20553 5.170748 ACAGGTTGCTCTTTTGTTTTTGAG 58.829 37.500 0.00 0.00 0.00 3.02
7682 20616 6.710692 AAGTTGTTTTTCAGACAAGCTTTG 57.289 33.333 0.00 0.00 37.65 2.77
7713 21133 6.674694 CTAGAAAAGCTTCAGTACATGCAT 57.325 37.500 0.00 0.00 33.64 3.96
7737 21157 3.752747 TGTCGAGTCAACGGACATTAGTA 59.247 43.478 6.14 0.00 46.80 1.82
7741 21161 7.137426 GTCGAGTCAACGGACATTAGTATTAT 58.863 38.462 0.00 0.00 46.80 1.28
7773 21193 1.541147 GCACTAACTTGATGCTGGCAA 59.459 47.619 0.00 0.00 36.40 4.52
7850 22539 7.541122 AATTCATTCTTTTCTAGCGTACCTC 57.459 36.000 0.00 0.00 0.00 3.85
7855 22548 2.624316 TTTCTAGCGTACCTCACACG 57.376 50.000 0.00 0.00 42.24 4.49
8110 22803 0.533951 GGCAGGATTTTTGGCTCTGG 59.466 55.000 0.00 0.00 38.03 3.86
8113 22806 2.299867 GCAGGATTTTTGGCTCTGGAAA 59.700 45.455 0.00 0.00 0.00 3.13
8115 22808 4.752146 CAGGATTTTTGGCTCTGGAAATC 58.248 43.478 0.00 0.00 37.63 2.17
8116 22809 3.445096 AGGATTTTTGGCTCTGGAAATCG 59.555 43.478 0.00 0.00 38.66 3.34
8400 23108 5.383476 CAGAGGGCTCCATAATCTTCAAAT 58.617 41.667 0.00 0.00 0.00 2.32
8493 23202 6.150976 AGTTGCAGGAATGTATTTCGATGAAA 59.849 34.615 0.00 0.00 35.94 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 1.737838 CGCCTGTTGGAATGCTCTAA 58.262 50.000 0.00 0.00 34.57 2.10
84 86 0.319900 TTCTGCTGGAGCTGTTCGAC 60.320 55.000 0.00 0.00 42.66 4.20
105 107 4.226761 CCCAAAAACTTTTAGCGCTACAG 58.773 43.478 18.63 18.01 0.00 2.74
119 121 2.945398 TTCAGCGCGCACCCAAAAAC 62.945 55.000 35.10 0.00 0.00 2.43
165 167 2.361104 GTGCCCAATCCGAAGCCA 60.361 61.111 0.00 0.00 0.00 4.75
181 183 3.625764 ACACAGTGTAAATTGTGAAGCGT 59.374 39.130 14.96 0.00 45.79 5.07
196 198 1.838913 CGCCCAAAAAGAACACAGTG 58.161 50.000 0.00 0.00 0.00 3.66
219 221 2.297315 GCTTTAGCAGAAGCCCAAAAGT 59.703 45.455 11.71 0.00 44.85 2.66
276 278 3.064408 GCCCTAAAATAGTTTTAGCGCGT 59.936 43.478 8.43 0.00 46.75 6.01
552 576 4.139786 CCAGGCATCAAACATAGCAGTAT 58.860 43.478 0.00 0.00 0.00 2.12
602 626 4.965762 CAGACGTTACGAAAAAGGGTTTTC 59.034 41.667 13.03 2.51 46.17 2.29
606 630 2.486918 CCAGACGTTACGAAAAAGGGT 58.513 47.619 13.03 0.00 0.00 4.34
719 753 5.779771 GGGATTAGACTGGAGAAGATCTCAT 59.220 44.000 9.40 0.00 45.12 2.90
758 1465 5.169561 GCGCTCGATTAAATTATGTTGTGTG 59.830 40.000 0.00 0.00 0.00 3.82
834 1557 1.300931 GTGCCTCTTCTGTCGTGCA 60.301 57.895 0.00 0.00 0.00 4.57
2449 6404 1.105167 ATGACAATGCTGATGGCCCG 61.105 55.000 0.00 0.00 40.92 6.13
2471 6426 2.863484 TTGGCCCAGGGATGGTGT 60.863 61.111 10.89 0.00 0.00 4.16
2691 6646 2.456119 CCGCAGCTTCACTAAGGCG 61.456 63.158 4.02 4.02 40.74 5.52
2846 6804 3.820467 CCTCTGCTGTGACCAATGTTTTA 59.180 43.478 0.00 0.00 0.00 1.52
2870 6828 1.885163 GATCGACGTGGGAGGTGGTT 61.885 60.000 0.00 0.00 0.00 3.67
2871 6829 2.283676 ATCGACGTGGGAGGTGGT 60.284 61.111 0.00 0.00 0.00 4.16
2881 6839 2.488153 TGTGTTGATGAGAGATCGACGT 59.512 45.455 0.00 0.00 35.66 4.34
2964 6931 1.044231 ACACACAGTACCGGTCACCA 61.044 55.000 12.40 0.00 0.00 4.17
3004 6971 1.625315 CCATCTCCACTCTGGTCAACA 59.375 52.381 0.00 0.00 39.03 3.33
3013 6980 0.173708 GACGACACCCATCTCCACTC 59.826 60.000 0.00 0.00 0.00 3.51
3066 7033 2.368875 GTGGCTAGTGGTATGGTATGCT 59.631 50.000 0.00 0.00 0.00 3.79
3068 7035 2.866460 GCGTGGCTAGTGGTATGGTATG 60.866 54.545 0.00 0.00 0.00 2.39
3069 7036 1.343465 GCGTGGCTAGTGGTATGGTAT 59.657 52.381 0.00 0.00 0.00 2.73
3070 7037 0.748450 GCGTGGCTAGTGGTATGGTA 59.252 55.000 0.00 0.00 0.00 3.25
3071 7038 0.976073 AGCGTGGCTAGTGGTATGGT 60.976 55.000 0.00 0.00 36.99 3.55
3072 7039 0.178068 AAGCGTGGCTAGTGGTATGG 59.822 55.000 0.00 0.00 38.25 2.74
3144 7440 1.765904 TGTCACCAACACAAGCTCCTA 59.234 47.619 0.00 0.00 31.20 2.94
3195 7491 6.672946 ATGGTGAGAGGAGGAGATATAGAT 57.327 41.667 0.00 0.00 0.00 1.98
3232 7532 1.228245 CCATGGAGGTTATGCCCGG 60.228 63.158 5.56 0.00 38.26 5.73
3233 7533 4.481195 CCATGGAGGTTATGCCCG 57.519 61.111 5.56 0.00 38.26 6.13
3289 7589 1.749033 CCCACGAAGATAGGGCCTC 59.251 63.158 10.74 0.00 35.44 4.70
3325 7625 1.761174 GGGACACTGCCCTCTTCAA 59.239 57.895 0.00 0.00 45.12 2.69
3346 7646 1.901650 GCGCTAGTCAAAAGCACGCT 61.902 55.000 0.00 0.00 41.50 5.07
3347 7647 1.509995 GCGCTAGTCAAAAGCACGC 60.510 57.895 0.00 0.00 40.08 5.34
3348 7648 0.451135 GTGCGCTAGTCAAAAGCACG 60.451 55.000 9.73 0.00 46.54 5.34
3355 11359 1.153901 GCTACGGTGCGCTAGTCAA 60.154 57.895 9.73 0.00 0.00 3.18
3435 11439 1.883275 CTGGATACCGGCACAAAAACA 59.117 47.619 0.00 0.00 0.00 2.83
3520 11800 2.430546 GTCCTCAGACATCGGCTATG 57.569 55.000 0.00 0.00 42.99 2.23
3536 11832 3.440173 ACAATCGTTGTTGATGGATGTCC 59.560 43.478 5.28 0.00 42.22 4.02
3550 11846 3.871594 GCATAGCTCCACTTACAATCGTT 59.128 43.478 0.00 0.00 0.00 3.85
3762 13699 0.107312 ACTGCCTCATCACCATCTGC 60.107 55.000 0.00 0.00 0.00 4.26
3783 13720 1.378124 GCCTCCTCGTCGCTTCTAGT 61.378 60.000 0.00 0.00 0.00 2.57
3804 13743 1.750399 CCGGAAGCATGTTCAGGGG 60.750 63.158 14.74 7.78 31.44 4.79
3848 13879 5.105797 TGCTCAACAAATTGGCCTACATAAG 60.106 40.000 3.32 0.00 36.39 1.73
3936 13981 1.008327 TCAATCCCTGCCCTCTAGACA 59.992 52.381 0.00 0.00 0.00 3.41
3985 14031 6.537301 TCGTATCCTAGGCATTTTGTTAGTTG 59.463 38.462 2.96 0.00 0.00 3.16
3988 14034 5.465724 GGTCGTATCCTAGGCATTTTGTTAG 59.534 44.000 2.96 0.00 0.00 2.34
4228 14274 6.522054 TCCCTCCGTTCACAAATATAAGATC 58.478 40.000 0.00 0.00 0.00 2.75
4285 14331 3.997021 AGAGCTACTTCGGTTTTCATGTG 59.003 43.478 0.00 0.00 0.00 3.21
4327 14373 3.766591 TGGACTTTCTTTTTCCTTGTGCA 59.233 39.130 0.00 0.00 0.00 4.57
4359 14405 9.520515 ACAGAAGTTGTTTCTCCATTAATATGT 57.479 29.630 0.00 0.00 44.34 2.29
4360 14406 9.778993 CACAGAAGTTGTTTCTCCATTAATATG 57.221 33.333 0.00 0.00 44.34 1.78
4361 14407 9.739276 TCACAGAAGTTGTTTCTCCATTAATAT 57.261 29.630 0.00 0.00 44.34 1.28
4362 14408 9.739276 ATCACAGAAGTTGTTTCTCCATTAATA 57.261 29.630 0.00 0.00 44.34 0.98
4363 14409 8.641498 ATCACAGAAGTTGTTTCTCCATTAAT 57.359 30.769 0.00 0.00 44.34 1.40
4364 14410 8.463930 AATCACAGAAGTTGTTTCTCCATTAA 57.536 30.769 0.00 0.00 44.34 1.40
4426 15939 8.995906 GCGTTTATACACTACATTCATTCAAAC 58.004 33.333 0.00 0.00 0.00 2.93
4490 16003 3.572682 TGTTCGATCATAGCGGGAGTTAT 59.427 43.478 0.00 0.00 36.66 1.89
4527 16040 5.585390 CACAATTTTGAAGTGCACTCTTCT 58.415 37.500 21.95 3.63 42.76 2.85
4563 16093 5.179368 GGATCATTTGTTCTCGAGTGTTTGA 59.821 40.000 13.13 9.65 0.00 2.69
4587 16117 7.905604 TTTTGCCCTCTTGTATATCGATATG 57.094 36.000 24.99 10.51 0.00 1.78
4790 16325 1.191489 TGCCTTCCATGACACCGAGA 61.191 55.000 0.00 0.00 0.00 4.04
4793 16328 2.401766 GCTGCCTTCCATGACACCG 61.402 63.158 0.00 0.00 0.00 4.94
4821 16356 2.092538 CAGTCATTCAGAATGGGAGGCT 60.093 50.000 20.91 10.07 38.62 4.58
4916 16451 0.827507 GGTGGTTGCCAATGGAGTGT 60.828 55.000 2.05 0.00 34.18 3.55
4925 16460 0.032615 AGAAAACAGGGTGGTTGCCA 60.033 50.000 0.00 0.00 0.00 4.92
4927 16462 1.692411 AGAGAAAACAGGGTGGTTGC 58.308 50.000 0.00 0.00 0.00 4.17
4993 16529 0.674895 CCTGTGCCCTCACTGTTAGC 60.675 60.000 0.00 0.00 43.49 3.09
5034 16571 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
5035 16572 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
5036 16573 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
5037 16574 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
5038 16575 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
5039 16576 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
5040 16577 1.135315 CGACAAGTATTTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
5041 16578 1.274596 CGACAAGTATTTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
5042 16579 1.135315 TCCGACAAGTATTTCCGGACG 60.135 52.381 1.83 0.00 43.47 4.79
5043 16580 2.660189 TCCGACAAGTATTTCCGGAC 57.340 50.000 1.83 0.00 43.47 4.79
5044 16581 3.681593 TTTCCGACAAGTATTTCCGGA 57.318 42.857 0.00 0.00 46.18 5.14
5045 16582 4.752661 TTTTTCCGACAAGTATTTCCGG 57.247 40.909 0.00 0.00 41.36 5.14
5046 16583 5.092781 CCATTTTTCCGACAAGTATTTCCG 58.907 41.667 0.00 0.00 0.00 4.30
5047 16584 6.262193 TCCATTTTTCCGACAAGTATTTCC 57.738 37.500 0.00 0.00 0.00 3.13
5048 16585 7.312899 ACATCCATTTTTCCGACAAGTATTTC 58.687 34.615 0.00 0.00 0.00 2.17
5049 16586 7.227049 ACATCCATTTTTCCGACAAGTATTT 57.773 32.000 0.00 0.00 0.00 1.40
5050 16587 6.834168 ACATCCATTTTTCCGACAAGTATT 57.166 33.333 0.00 0.00 0.00 1.89
5051 16588 7.993183 AGATACATCCATTTTTCCGACAAGTAT 59.007 33.333 0.00 0.00 0.00 2.12
5052 16589 7.335627 AGATACATCCATTTTTCCGACAAGTA 58.664 34.615 0.00 0.00 0.00 2.24
5053 16590 6.180472 AGATACATCCATTTTTCCGACAAGT 58.820 36.000 0.00 0.00 0.00 3.16
5054 16591 6.683974 AGATACATCCATTTTTCCGACAAG 57.316 37.500 0.00 0.00 0.00 3.16
5055 16592 7.494625 GTCTAGATACATCCATTTTTCCGACAA 59.505 37.037 0.00 0.00 0.00 3.18
5056 16593 6.984474 GTCTAGATACATCCATTTTTCCGACA 59.016 38.462 0.00 0.00 0.00 4.35
5057 16594 6.984474 TGTCTAGATACATCCATTTTTCCGAC 59.016 38.462 0.00 0.00 0.00 4.79
5058 16595 7.119709 TGTCTAGATACATCCATTTTTCCGA 57.880 36.000 0.00 0.00 0.00 4.55
5059 16596 7.969536 ATGTCTAGATACATCCATTTTTCCG 57.030 36.000 0.00 0.00 35.08 4.30
5097 16634 8.840321 CGGAGAAATTGATAAAAGTGGATGTAT 58.160 33.333 0.00 0.00 0.00 2.29
5098 16635 8.044309 TCGGAGAAATTGATAAAAGTGGATGTA 58.956 33.333 0.00 0.00 0.00 2.29
5099 16636 6.884295 TCGGAGAAATTGATAAAAGTGGATGT 59.116 34.615 0.00 0.00 0.00 3.06
5100 16637 7.148255 TGTCGGAGAAATTGATAAAAGTGGATG 60.148 37.037 0.00 0.00 39.69 3.51
5101 16638 6.884295 TGTCGGAGAAATTGATAAAAGTGGAT 59.116 34.615 0.00 0.00 39.69 3.41
5102 16639 6.234920 TGTCGGAGAAATTGATAAAAGTGGA 58.765 36.000 0.00 0.00 39.69 4.02
5103 16640 6.494893 TGTCGGAGAAATTGATAAAAGTGG 57.505 37.500 0.00 0.00 39.69 4.00
5104 16641 7.584987 ACTTGTCGGAGAAATTGATAAAAGTG 58.415 34.615 0.00 0.00 39.69 3.16
5105 16642 7.745620 ACTTGTCGGAGAAATTGATAAAAGT 57.254 32.000 0.00 0.00 39.69 2.66
5110 16647 8.673711 CCAAAATACTTGTCGGAGAAATTGATA 58.326 33.333 0.00 0.00 39.69 2.15
5111 16648 7.362920 CCCAAAATACTTGTCGGAGAAATTGAT 60.363 37.037 0.00 0.00 39.69 2.57
5112 16649 6.072175 CCCAAAATACTTGTCGGAGAAATTGA 60.072 38.462 0.00 0.00 39.69 2.57
5113 16650 6.072175 TCCCAAAATACTTGTCGGAGAAATTG 60.072 38.462 0.00 0.00 39.69 2.32
5114 16651 6.007703 TCCCAAAATACTTGTCGGAGAAATT 58.992 36.000 0.00 0.00 39.69 1.82
5115 16652 5.414765 GTCCCAAAATACTTGTCGGAGAAAT 59.585 40.000 0.00 0.00 39.69 2.17
5116 16653 4.758165 GTCCCAAAATACTTGTCGGAGAAA 59.242 41.667 0.00 0.00 39.69 2.52
5117 16654 4.320870 GTCCCAAAATACTTGTCGGAGAA 58.679 43.478 0.00 0.00 39.69 2.87
5118 16655 3.615592 CGTCCCAAAATACTTGTCGGAGA 60.616 47.826 0.00 0.00 0.00 3.71
5119 16656 2.671396 CGTCCCAAAATACTTGTCGGAG 59.329 50.000 0.00 0.00 0.00 4.63
5120 16657 2.613474 CCGTCCCAAAATACTTGTCGGA 60.613 50.000 0.00 0.00 38.03 4.55
5121 16658 1.735571 CCGTCCCAAAATACTTGTCGG 59.264 52.381 0.00 0.00 0.00 4.79
5122 16659 2.671396 CTCCGTCCCAAAATACTTGTCG 59.329 50.000 0.00 0.00 0.00 4.35
5123 16660 3.007635 CCTCCGTCCCAAAATACTTGTC 58.992 50.000 0.00 0.00 0.00 3.18
5124 16661 2.290705 CCCTCCGTCCCAAAATACTTGT 60.291 50.000 0.00 0.00 0.00 3.16
5125 16662 2.026636 TCCCTCCGTCCCAAAATACTTG 60.027 50.000 0.00 0.00 0.00 3.16
5126 16663 2.238898 CTCCCTCCGTCCCAAAATACTT 59.761 50.000 0.00 0.00 0.00 2.24
5127 16664 1.838077 CTCCCTCCGTCCCAAAATACT 59.162 52.381 0.00 0.00 0.00 2.12
5128 16665 1.558294 ACTCCCTCCGTCCCAAAATAC 59.442 52.381 0.00 0.00 0.00 1.89
5129 16666 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
5130 16667 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
5131 16668 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
5132 16669 1.961133 AATACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
5133 16670 2.674420 CTAATACTCCCTCCGTCCCAA 58.326 52.381 0.00 0.00 0.00 4.12
5134 16671 1.133262 CCTAATACTCCCTCCGTCCCA 60.133 57.143 0.00 0.00 0.00 4.37
5135 16672 1.630223 CCTAATACTCCCTCCGTCCC 58.370 60.000 0.00 0.00 0.00 4.46
5136 16673 0.967662 GCCTAATACTCCCTCCGTCC 59.032 60.000 0.00 0.00 0.00 4.79
5137 16674 1.614413 CTGCCTAATACTCCCTCCGTC 59.386 57.143 0.00 0.00 0.00 4.79
5138 16675 1.063114 ACTGCCTAATACTCCCTCCGT 60.063 52.381 0.00 0.00 0.00 4.69
5139 16676 1.341531 CACTGCCTAATACTCCCTCCG 59.658 57.143 0.00 0.00 0.00 4.63
5140 16677 2.365941 GACACTGCCTAATACTCCCTCC 59.634 54.545 0.00 0.00 0.00 4.30
5141 16678 2.034812 CGACACTGCCTAATACTCCCTC 59.965 54.545 0.00 0.00 0.00 4.30
5142 16679 2.032620 CGACACTGCCTAATACTCCCT 58.967 52.381 0.00 0.00 0.00 4.20
5143 16680 1.755380 ACGACACTGCCTAATACTCCC 59.245 52.381 0.00 0.00 0.00 4.30
5144 16681 2.541178 CGACGACACTGCCTAATACTCC 60.541 54.545 0.00 0.00 0.00 3.85
5145 16682 2.097142 ACGACGACACTGCCTAATACTC 59.903 50.000 0.00 0.00 0.00 2.59
5146 16683 2.089980 ACGACGACACTGCCTAATACT 58.910 47.619 0.00 0.00 0.00 2.12
5147 16684 2.182825 CACGACGACACTGCCTAATAC 58.817 52.381 0.00 0.00 0.00 1.89
5148 16685 1.814394 ACACGACGACACTGCCTAATA 59.186 47.619 0.00 0.00 0.00 0.98
5241 16779 7.204604 TGTCTGAACTGTATCGAACAAAGTTA 58.795 34.615 6.06 0.00 37.74 2.24
5382 16921 4.142687 GGTTAAACGGATGAATCTGTGTGG 60.143 45.833 5.55 0.00 45.23 4.17
5432 16972 0.179145 CGCCCACGGTCACTAGTAAG 60.179 60.000 0.00 0.00 34.97 2.34
5470 17010 7.910162 GCGAGACACACATTATAAAAATCATGT 59.090 33.333 0.00 0.00 0.00 3.21
5496 17036 3.379057 TGCTAGTGATGAACAATGCATGG 59.621 43.478 0.00 0.00 30.67 3.66
5826 17366 2.294233 CCTGCAGCAGTGTAAATTGTGT 59.706 45.455 21.26 0.00 0.00 3.72
5827 17367 2.923605 GCCTGCAGCAGTGTAAATTGTG 60.924 50.000 21.26 2.79 42.97 3.33
5828 17368 1.270550 GCCTGCAGCAGTGTAAATTGT 59.729 47.619 21.26 0.00 42.97 2.71
5829 17369 1.986698 GCCTGCAGCAGTGTAAATTG 58.013 50.000 21.26 4.24 42.97 2.32
5840 17417 0.464373 TGCTAACCTATGCCTGCAGC 60.464 55.000 8.66 4.57 44.14 5.25
5841 17418 2.042686 TTGCTAACCTATGCCTGCAG 57.957 50.000 6.78 6.78 0.00 4.41
5846 17423 5.744666 TTATCGTTTTGCTAACCTATGCC 57.255 39.130 0.00 0.00 0.00 4.40
5864 17441 7.175293 AGTCGGGTCTCATCTAGTGTTATTATC 59.825 40.741 0.00 0.00 0.00 1.75
5926 18425 9.030452 TCTGTAATATAAGGGCAACAAATTTGT 57.970 29.630 18.13 18.13 44.72 2.83
5961 18460 3.079578 GGTACTCCCCTTTTCGGAAAAG 58.920 50.000 28.16 28.16 45.78 2.27
5985 18485 2.623878 CATCTTCTGATGCAGAGGCT 57.376 50.000 0.00 0.00 41.75 4.58
6102 18603 6.582636 TGTGGATGAGGTATGTAATCTTGTC 58.417 40.000 0.00 0.00 0.00 3.18
6147 18648 4.055360 GTGTTTATTCAACCAGTTTGGCC 58.945 43.478 0.00 0.00 42.67 5.36
6169 18671 6.791887 TCATAAAAGACAGAAGCTCAACTG 57.208 37.500 12.01 12.01 39.65 3.16
6170 18672 6.995091 AGTTCATAAAAGACAGAAGCTCAACT 59.005 34.615 0.00 0.00 0.00 3.16
6198 18700 1.094785 ACACACACACAGGCAAAGAC 58.905 50.000 0.00 0.00 0.00 3.01
6253 18916 2.359850 GCCCGTTGTCTGCATGGA 60.360 61.111 0.00 0.00 0.00 3.41
6270 18935 2.686558 ACAAGCACAATAAGCACACG 57.313 45.000 0.00 0.00 0.00 4.49
6293 18958 8.975410 TTATTGACTCAAAATGAAGCATCAAG 57.025 30.769 0.00 0.00 39.49 3.02
6382 19058 5.946942 ACACTTCACTCATCATATCCACT 57.053 39.130 0.00 0.00 0.00 4.00
6526 19205 5.840940 AAAACATAGACGAGAAAGAACGG 57.159 39.130 0.00 0.00 0.00 4.44
6680 19362 1.138859 CTGCGACCTATCATTGACCCA 59.861 52.381 0.00 0.00 0.00 4.51
6731 19413 8.642432 CACCTCTAACATATCTTCAAGGTATGA 58.358 37.037 22.36 2.21 34.22 2.15
6746 19428 3.207044 AGGGTCTTCCACCTCTAACAT 57.793 47.619 0.00 0.00 45.95 2.71
6779 19582 1.163554 GCCTCTTTCTTCCAGCACTG 58.836 55.000 0.00 0.00 0.00 3.66
6789 19592 1.640917 TAACTCCCGTGCCTCTTTCT 58.359 50.000 0.00 0.00 0.00 2.52
6928 19737 2.479275 CACATCAGGAGCTGCATATTCG 59.521 50.000 8.35 0.00 0.00 3.34
7008 19817 3.173965 ACTATCTGCTGGTACCACTTGT 58.826 45.455 11.60 0.53 0.00 3.16
7268 20080 5.923204 ACCAAGACATCTAGATCCATGAAC 58.077 41.667 1.03 0.00 0.00 3.18
7303 20115 8.591312 CCAATTTTATTATACAACACTTTGGCG 58.409 33.333 0.00 0.00 37.00 5.69
7335 20147 2.285083 CGAAAGCCCGACAATGGAATA 58.715 47.619 0.00 0.00 0.00 1.75
7597 20527 5.914898 AAAACAAAAGAGCAACCTGTAGT 57.085 34.783 0.00 0.00 0.00 2.73
7662 20596 4.564041 TGCAAAGCTTGTCTGAAAAACAA 58.436 34.783 0.00 0.00 35.44 2.83
7712 21132 0.671796 TGTCCGTTGACTCGACACAT 59.328 50.000 0.00 0.00 42.28 3.21
7713 21133 0.671796 ATGTCCGTTGACTCGACACA 59.328 50.000 0.00 0.00 42.28 3.72
7737 21157 8.854614 AAGTTAGTGCTGACTTGAAGAATAAT 57.145 30.769 8.30 0.00 37.89 1.28
7850 22539 4.263016 CACGCATGTCATATTTACGTGTG 58.737 43.478 14.79 14.79 45.51 3.82
7855 22548 5.751680 AGAATGCACGCATGTCATATTTAC 58.248 37.500 5.06 0.00 36.68 2.01
8110 22803 6.241207 TGAATTCTTCAGGACAACGATTTC 57.759 37.500 7.05 0.00 34.08 2.17
8113 22806 5.530915 TGTTTGAATTCTTCAGGACAACGAT 59.469 36.000 7.05 0.00 41.38 3.73
8115 22808 5.168526 TGTTTGAATTCTTCAGGACAACG 57.831 39.130 7.05 0.00 41.38 4.10
8116 22809 6.564328 ACTTGTTTGAATTCTTCAGGACAAC 58.436 36.000 7.05 6.21 39.94 3.32
8493 23202 6.071728 GGTTGGATGAATCTTCTGTCAACAAT 60.072 38.462 13.97 0.00 35.14 2.71
8585 23294 1.139654 TCTTCTGCAGACTTGTGTGCT 59.860 47.619 18.03 0.00 40.54 4.40


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

AutoCloner maintained by Alex Coulton.