Multiple sequence alignment - TraesCS6B01G241300

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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 TraesCS6B01G241300 chr6B 100.000 7252 0 0 1 7252 423090471 423097722 0.000000e+00 13393.0
1 TraesCS6B01G241300 chr6B 89.474 570 14 10 2282 2824 255099029 255098479 0.000000e+00 678.0
2 TraesCS6B01G241300 chr6B 95.089 224 11 0 1 224 713806078 713805855 3.220000e-93 353.0
3 TraesCS6B01G241300 chr1A 96.613 7056 107 14 223 7212 508964902 508957913 0.000000e+00 11585.0
4 TraesCS6B01G241300 chr1A 88.095 588 20 7 1218 1770 562935714 562935142 0.000000e+00 652.0
5 TraesCS6B01G241300 chr1A 88.579 359 15 8 2183 2523 232346466 232346816 5.240000e-111 412.0
6 TraesCS6B01G241300 chr1A 89.212 241 18 2 6072 6312 568544720 568544952 1.980000e-75 294.0
7 TraesCS6B01G241300 chr1A 94.286 140 6 2 1835 1974 562935149 562935012 5.700000e-51 213.0
8 TraesCS6B01G241300 chr1A 88.194 144 12 1 904 1042 29985800 29985943 4.500000e-37 167.0
9 TraesCS6B01G241300 chr1A 93.056 72 1 1 5249 5320 56507367 56507300 1.290000e-17 102.0
10 TraesCS6B01G241300 chr1A 93.056 72 1 1 5249 5320 472656797 472656864 1.290000e-17 102.0
11 TraesCS6B01G241300 chr6A 96.562 4916 116 11 2365 7252 26328944 26324054 0.000000e+00 8093.0
12 TraesCS6B01G241300 chr6A 95.205 2148 57 14 223 2327 26331081 26328937 0.000000e+00 3354.0
13 TraesCS6B01G241300 chr6A 93.855 179 7 1 4814 4992 464310672 464310846 4.310000e-67 267.0
14 TraesCS6B01G241300 chr1B 92.646 2706 129 30 2028 4702 167562498 167565164 0.000000e+00 3831.0
15 TraesCS6B01G241300 chr1B 90.909 264 15 7 6072 6326 659555753 659556016 5.390000e-91 346.0
16 TraesCS6B01G241300 chr1B 80.844 308 37 15 286 586 47169853 47170145 9.470000e-54 222.0
17 TraesCS6B01G241300 chr1B 83.784 111 14 4 6213 6320 659378752 659378861 1.290000e-17 102.0
18 TraesCS6B01G241300 chr5A 94.397 2231 87 13 2774 4992 510200059 510202263 0.000000e+00 3393.0
19 TraesCS6B01G241300 chr5A 89.767 1935 171 18 2749 4667 296675239 296677162 0.000000e+00 2451.0
20 TraesCS6B01G241300 chr5A 89.297 1878 176 14 2802 4667 591604960 591606824 0.000000e+00 2331.0
21 TraesCS6B01G241300 chr5A 93.084 535 26 3 2083 2614 510199032 510199558 0.000000e+00 773.0
22 TraesCS6B01G241300 chr5A 90.824 534 30 2 1046 1560 296673740 296674273 0.000000e+00 697.0
23 TraesCS6B01G241300 chr5A 92.877 365 26 0 1046 1410 591603792 591604156 1.390000e-146 531.0
24 TraesCS6B01G241300 chr5A 93.750 352 22 0 4641 4992 705522001 705521650 4.980000e-146 529.0
25 TraesCS6B01G241300 chr5A 97.403 308 7 1 5757 6064 280756980 280757286 2.320000e-144 523.0
26 TraesCS6B01G241300 chr5A 94.958 238 9 3 5519 5754 280757740 280757976 3.200000e-98 370.0
27 TraesCS6B01G241300 chr5A 94.468 235 12 1 5021 5254 426285376 426285142 1.920000e-95 361.0
28 TraesCS6B01G241300 chr5A 85.022 227 20 9 6072 6296 673690524 673690738 1.220000e-52 219.0
29 TraesCS6B01G241300 chr5A 96.721 61 2 0 982 1042 591603704 591603764 1.290000e-17 102.0
30 TraesCS6B01G241300 chr5A 92.647 68 5 0 6072 6139 49959955 49960022 1.670000e-16 99.0
31 TraesCS6B01G241300 chr5A 100.000 35 0 0 4763 4797 705521916 705521882 1.690000e-06 65.8
32 TraesCS6B01G241300 chr3A 97.699 1521 31 3 2028 3545 411271271 411269752 0.000000e+00 2612.0
33 TraesCS6B01G241300 chr3A 96.952 1542 32 4 5672 7212 411267642 411266115 0.000000e+00 2573.0
34 TraesCS6B01G241300 chr3A 97.710 1048 19 3 3968 5011 411269754 411268708 0.000000e+00 1797.0
35 TraesCS6B01G241300 chr3A 98.377 616 9 1 5019 5633 411268250 411267635 0.000000e+00 1081.0
36 TraesCS6B01G241300 chr3A 91.734 738 40 7 5019 5754 206100243 206100961 0.000000e+00 1005.0
37 TraesCS6B01G241300 chr3A 93.561 497 22 2 2032 2526 193870880 193870392 0.000000e+00 732.0
38 TraesCS6B01G241300 chr3A 87.676 568 20 7 1238 1770 235348428 235348980 3.720000e-172 616.0
39 TraesCS6B01G241300 chr3A 89.181 342 12 4 1459 1776 30182710 30183050 3.150000e-108 403.0
40 TraesCS6B01G241300 chr3A 95.775 213 7 2 1762 1974 30182996 30183206 6.970000e-90 342.0
41 TraesCS6B01G241300 chr3A 94.286 140 6 2 1835 1974 235348973 235349110 5.700000e-51 213.0
42 TraesCS6B01G241300 chr3A 100.000 44 0 0 1982 2025 411271605 411271562 1.680000e-11 82.4
43 TraesCS6B01G241300 chr3A 100.000 39 0 0 5768 5806 110782070 110782108 1.010000e-08 73.1
44 TraesCS6B01G241300 chr6D 95.929 1523 54 5 2874 4392 79980469 79981987 0.000000e+00 2462.0
45 TraesCS6B01G241300 chr6D 94.846 912 36 4 6351 7252 79982173 79983083 0.000000e+00 1413.0
46 TraesCS6B01G241300 chr6D 83.088 136 5 4 5617 5734 17254931 17255066 2.770000e-19 108.0
47 TraesCS6B01G241300 chr6D 91.304 69 5 1 564 631 121093398 121093330 7.750000e-15 93.5
48 TraesCS6B01G241300 chr4B 90.337 1842 159 10 2846 4677 505153657 505155489 0.000000e+00 2398.0
49 TraesCS6B01G241300 chr4B 95.227 838 25 10 2028 2858 494951179 494950350 0.000000e+00 1312.0
50 TraesCS6B01G241300 chr4B 88.854 323 18 8 5430 5734 187541876 187541554 1.480000e-101 381.0
51 TraesCS6B01G241300 chr4B 91.189 227 18 2 4766 4992 410668659 410668435 2.540000e-79 307.0
52 TraesCS6B01G241300 chr4B 84.906 106 16 0 223 328 526168390 526168495 2.770000e-19 108.0
53 TraesCS6B01G241300 chr4B 100.000 32 0 0 5944 5975 170929281 170929312 7.860000e-05 60.2
54 TraesCS6B01G241300 chr5D 90.602 1777 156 8 2935 4700 251072057 251070281 0.000000e+00 2346.0
55 TraesCS6B01G241300 chr5D 89.788 803 43 13 242 1042 395175921 395176686 0.000000e+00 992.0
56 TraesCS6B01G241300 chr5D 91.653 623 29 9 1077 1677 395176821 395177442 0.000000e+00 841.0
57 TraesCS6B01G241300 chr5D 87.340 624 42 20 6447 7066 395251521 395252111 0.000000e+00 680.0
58 TraesCS6B01G241300 chr5D 94.389 303 8 5 1677 1975 395177475 395177772 2.380000e-124 457.0
59 TraesCS6B01G241300 chr5D 92.523 214 5 5 1762 1974 382015235 382015032 5.500000e-76 296.0
60 TraesCS6B01G241300 chr5D 91.346 104 5 2 1677 1776 382015284 382015181 9.810000e-29 139.0
61 TraesCS6B01G241300 chr5D 94.286 70 0 1 5252 5321 555450786 555450851 3.580000e-18 104.0
62 TraesCS6B01G241300 chr5D 96.078 51 2 0 1775 1825 395177532 395177582 4.660000e-12 84.2
63 TraesCS6B01G241300 chr4D 95.050 1313 45 6 383 1677 124258978 124257668 0.000000e+00 2047.0
64 TraesCS6B01G241300 chr4D 95.143 906 35 3 6350 7252 124253817 124252918 0.000000e+00 1421.0
65 TraesCS6B01G241300 chr4D 97.667 300 5 2 1677 1975 124257635 124257337 1.400000e-141 514.0
66 TraesCS6B01G241300 chr4D 91.667 144 11 1 223 365 124259103 124258960 1.600000e-46 198.0
67 TraesCS6B01G241300 chr4D 100.000 28 0 0 5944 5971 109471839 109471866 1.300000e-02 52.8
68 TraesCS6B01G241300 chr3B 92.584 890 39 7 6350 7212 801128333 801129222 0.000000e+00 1253.0
69 TraesCS6B01G241300 chr3B 92.177 882 34 11 6350 7212 534168338 534169203 0.000000e+00 1214.0
70 TraesCS6B01G241300 chr3B 91.379 348 15 4 2597 2940 597105436 597105100 5.130000e-126 462.0
71 TraesCS6B01G241300 chr3B 96.135 207 8 0 1046 1252 534167696 534167902 9.010000e-89 339.0
72 TraesCS6B01G241300 chr3B 79.167 384 51 15 223 586 801123868 801124242 9.400000e-59 239.0
73 TraesCS6B01G241300 chr3B 78.646 384 53 15 223 586 534165906 534166280 2.040000e-55 228.0
74 TraesCS6B01G241300 chr3B 97.059 68 1 1 5997 6064 798657315 798657249 5.950000e-21 113.0
75 TraesCS6B01G241300 chr3B 96.078 51 0 2 2564 2614 158150074 158150122 1.680000e-11 82.4
76 TraesCS6B01G241300 chr3B 97.436 39 1 0 5768 5806 166161402 166161364 4.700000e-07 67.6
77 TraesCS6B01G241300 chr3B 100.000 35 0 0 7218 7252 534169184 534169218 1.690000e-06 65.8
78 TraesCS6B01G241300 chr3B 100.000 35 0 0 7218 7252 801129203 801129237 1.690000e-06 65.8
79 TraesCS6B01G241300 chr3B 97.143 35 1 0 223 257 534169475 534169441 7.860000e-05 60.2
80 TraesCS6B01G241300 chr5B 91.006 934 40 16 6350 7252 672815845 672814925 0.000000e+00 1219.0
81 TraesCS6B01G241300 chr5B 90.426 564 28 9 2037 2582 397292368 397291813 0.000000e+00 719.0
82 TraesCS6B01G241300 chr5B 94.664 431 17 3 1251 1677 672816551 672816123 0.000000e+00 664.0
83 TraesCS6B01G241300 chr5B 85.008 627 49 20 6447 7062 475581882 475582474 4.840000e-166 595.0
84 TraesCS6B01G241300 chr5B 95.781 237 9 1 5019 5254 386568279 386568515 1.480000e-101 381.0
85 TraesCS6B01G241300 chr5B 95.299 234 10 1 5022 5254 655026653 655026886 3.200000e-98 370.0
86 TraesCS6B01G241300 chr5B 95.652 207 9 0 1046 1252 672816825 672816619 4.190000e-87 333.0
87 TraesCS6B01G241300 chr5B 88.000 150 13 1 904 1048 288308375 288308226 9.670000e-39 172.0
88 TraesCS6B01G241300 chrUn 91.109 866 40 17 6350 7212 87097180 87096349 0.000000e+00 1138.0
89 TraesCS6B01G241300 chrUn 95.299 234 10 1 5022 5254 468180670 468180903 3.200000e-98 370.0
90 TraesCS6B01G241300 chrUn 89.873 158 13 1 4529 4683 322336697 322336540 4.440000e-47 200.0
91 TraesCS6B01G241300 chrUn 97.674 43 1 0 7210 7252 87096376 87096334 2.810000e-09 75.0
92 TraesCS6B01G241300 chr7B 89.592 932 48 17 6350 7252 126793150 126794061 0.000000e+00 1138.0
93 TraesCS6B01G241300 chr7B 88.908 568 24 11 1246 1776 126788926 126789491 0.000000e+00 664.0
94 TraesCS6B01G241300 chr7B 92.971 441 16 2 1251 1677 648276347 648276786 4.780000e-176 628.0
95 TraesCS6B01G241300 chr7B 89.164 323 17 8 5430 5734 728776400 728776078 3.170000e-103 387.0
96 TraesCS6B01G241300 chr7B 89.590 317 15 5 5430 5728 734094013 734094329 3.170000e-103 387.0
97 TraesCS6B01G241300 chr7B 95.169 207 10 0 1046 1252 648276073 648276279 1.950000e-85 327.0
98 TraesCS6B01G241300 chr7B 79.602 402 52 19 218 608 126786731 126787113 2.010000e-65 261.0
99 TraesCS6B01G241300 chr7B 86.986 146 12 2 904 1042 148227260 148227405 2.710000e-34 158.0
100 TraesCS6B01G241300 chr1D 93.562 699 26 4 2342 3039 493748165 493748845 0.000000e+00 1024.0
101 TraesCS6B01G241300 chr1D 98.382 309 4 1 5756 6064 310161347 310161040 6.400000e-150 542.0
102 TraesCS6B01G241300 chr1D 90.261 421 21 7 5352 5754 399808224 399807806 3.850000e-147 532.0
103 TraesCS6B01G241300 chr1D 94.718 284 15 0 4709 4992 46105475 46105192 6.680000e-120 442.0
104 TraesCS6B01G241300 chr1D 95.618 251 8 2 2028 2276 493747909 493748158 4.080000e-107 399.0
105 TraesCS6B01G241300 chr1D 87.500 248 20 6 6072 6317 474053893 474054131 7.170000e-70 276.0
106 TraesCS6B01G241300 chr1D 98.969 97 1 0 5658 5754 310160479 310160383 2.690000e-39 174.0
107 TraesCS6B01G241300 chr1D 93.056 72 1 1 5249 5320 24596114 24596181 1.290000e-17 102.0
108 TraesCS6B01G241300 chr1D 86.420 81 11 0 6213 6293 474011217 474011297 1.000000e-13 89.8
109 TraesCS6B01G241300 chr1D 100.000 44 0 0 1982 2025 493747577 493747620 1.680000e-11 82.4
110 TraesCS6B01G241300 chr1D 100.000 30 0 0 1854 1883 10351712 10351683 1.000000e-03 56.5
111 TraesCS6B01G241300 chr2A 85.197 608 55 14 6447 7051 655938674 655939249 6.270000e-165 592.0
112 TraesCS6B01G241300 chr2A 93.688 301 18 1 2615 2914 467112008 467111708 3.990000e-122 449.0
113 TraesCS6B01G241300 chr2D 90.141 426 18 8 5352 5754 118800228 118799804 3.850000e-147 532.0
114 TraesCS6B01G241300 chr2D 94.286 70 0 1 5252 5321 197868301 197868236 3.580000e-18 104.0
115 TraesCS6B01G241300 chr2D 97.297 37 1 0 1988 2024 13209528 13209564 6.070000e-06 63.9
116 TraesCS6B01G241300 chr2B 95.089 224 10 1 1 224 373907937 373908159 1.160000e-92 351.0
117 TraesCS6B01G241300 chr2B 79.167 384 51 15 223 586 331218179 331218553 9.400000e-59 239.0
118 TraesCS6B01G241300 chr2B 97.222 36 1 0 222 257 331220096 331220061 2.180000e-05 62.1
119 TraesCS6B01G241300 chr3D 89.686 223 17 5 6 224 331402784 331403004 5.540000e-71 279.0
120 TraesCS6B01G241300 chr3D 100.000 39 0 0 5768 5806 114670568 114670606 1.010000e-08 73.1
121 TraesCS6B01G241300 chr3D 100.000 32 0 0 1988 2019 168502815 168502846 7.860000e-05 60.2
122 TraesCS6B01G241300 chr7A 93.333 180 8 1 4813 4992 662773324 662773149 5.580000e-66 263.0
123 TraesCS6B01G241300 chr7A 78.226 372 61 13 223 586 636231419 636231060 3.410000e-53 220.0
124 TraesCS6B01G241300 chr7A 85.841 113 16 0 222 334 729057200 729057088 3.550000e-23 121.0
125 TraesCS6B01G241300 chr7A 93.182 44 2 1 215 257 636229171 636229214 6.070000e-06 63.9
126 TraesCS6B01G241300 chr4A 100.000 28 0 0 5944 5971 466939371 466939344 1.300000e-02 52.8


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 TraesCS6B01G241300 chr6B 423090471 423097722 7251 False 13393.000000 13393 100.000000 1 7252 1 chr6B.!!$F1 7251
1 TraesCS6B01G241300 chr6B 255098479 255099029 550 True 678.000000 678 89.474000 2282 2824 1 chr6B.!!$R1 542
2 TraesCS6B01G241300 chr1A 508957913 508964902 6989 True 11585.000000 11585 96.613000 223 7212 1 chr1A.!!$R2 6989
3 TraesCS6B01G241300 chr1A 562935012 562935714 702 True 432.500000 652 91.190500 1218 1974 2 chr1A.!!$R3 756
4 TraesCS6B01G241300 chr6A 26324054 26331081 7027 True 5723.500000 8093 95.883500 223 7252 2 chr6A.!!$R1 7029
5 TraesCS6B01G241300 chr1B 167562498 167565164 2666 False 3831.000000 3831 92.646000 2028 4702 1 chr1B.!!$F2 2674
6 TraesCS6B01G241300 chr5A 510199032 510202263 3231 False 2083.000000 3393 93.740500 2083 4992 2 chr5A.!!$F5 2909
7 TraesCS6B01G241300 chr5A 296673740 296677162 3422 False 1574.000000 2451 90.295500 1046 4667 2 chr5A.!!$F4 3621
8 TraesCS6B01G241300 chr5A 591603704 591606824 3120 False 988.000000 2331 92.965000 982 4667 3 chr5A.!!$F6 3685
9 TraesCS6B01G241300 chr5A 280756980 280757976 996 False 446.500000 523 96.180500 5519 6064 2 chr5A.!!$F3 545
10 TraesCS6B01G241300 chr3A 411266115 411271605 5490 True 1629.080000 2612 98.147600 1982 7212 5 chr3A.!!$R2 5230
11 TraesCS6B01G241300 chr3A 206100243 206100961 718 False 1005.000000 1005 91.734000 5019 5754 1 chr3A.!!$F2 735
12 TraesCS6B01G241300 chr3A 235348428 235349110 682 False 414.500000 616 90.981000 1238 1974 2 chr3A.!!$F4 736
13 TraesCS6B01G241300 chr6D 79980469 79983083 2614 False 1937.500000 2462 95.387500 2874 7252 2 chr6D.!!$F2 4378
14 TraesCS6B01G241300 chr4B 505153657 505155489 1832 False 2398.000000 2398 90.337000 2846 4677 1 chr4B.!!$F2 1831
15 TraesCS6B01G241300 chr4B 494950350 494951179 829 True 1312.000000 1312 95.227000 2028 2858 1 chr4B.!!$R3 830
16 TraesCS6B01G241300 chr5D 251070281 251072057 1776 True 2346.000000 2346 90.602000 2935 4700 1 chr5D.!!$R1 1765
17 TraesCS6B01G241300 chr5D 395251521 395252111 590 False 680.000000 680 87.340000 6447 7066 1 chr5D.!!$F1 619
18 TraesCS6B01G241300 chr5D 395175921 395177772 1851 False 593.550000 992 92.977000 242 1975 4 chr5D.!!$F3 1733
19 TraesCS6B01G241300 chr4D 124252918 124259103 6185 True 1045.000000 2047 94.881750 223 7252 4 chr4D.!!$R1 7029
20 TraesCS6B01G241300 chr3B 801128333 801129237 904 False 659.400000 1253 96.292000 6350 7252 2 chr3B.!!$F4 902
21 TraesCS6B01G241300 chr3B 534165906 534169218 3312 False 461.700000 1214 91.739500 223 7252 4 chr3B.!!$F3 7029
22 TraesCS6B01G241300 chr5B 672814925 672816825 1900 True 738.666667 1219 93.774000 1046 7252 3 chr5B.!!$R3 6206
23 TraesCS6B01G241300 chr5B 397291813 397292368 555 True 719.000000 719 90.426000 2037 2582 1 chr5B.!!$R2 545
24 TraesCS6B01G241300 chr5B 475581882 475582474 592 False 595.000000 595 85.008000 6447 7062 1 chr5B.!!$F2 615
25 TraesCS6B01G241300 chrUn 87096334 87097180 846 True 606.500000 1138 94.391500 6350 7252 2 chrUn.!!$R2 902
26 TraesCS6B01G241300 chr7B 126786731 126794061 7330 False 687.666667 1138 86.034000 218 7252 3 chr7B.!!$F3 7034
27 TraesCS6B01G241300 chr7B 648276073 648276786 713 False 477.500000 628 94.070000 1046 1677 2 chr7B.!!$F4 631
28 TraesCS6B01G241300 chr1D 493747577 493748845 1268 False 501.800000 1024 96.393333 1982 3039 3 chr1D.!!$F4 1057
29 TraesCS6B01G241300 chr1D 310160383 310161347 964 True 358.000000 542 98.675500 5658 6064 2 chr1D.!!$R4 406
30 TraesCS6B01G241300 chr2A 655938674 655939249 575 False 592.000000 592 85.197000 6447 7051 1 chr2A.!!$F1 604

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
718 1052 0.388520 CTCTCGTCATGTCGTTGCCA 60.389 55.000 11.96 0.0 0.00 4.92 F
937 1278 1.200760 TCCCCTCTTGCTGCTTGCTA 61.201 55.000 0.00 0.0 43.37 3.49 F
2026 4052 1.406341 GCCCGTGTTTCCACTGCTATA 60.406 52.381 0.00 0.0 39.55 1.31 F
2985 6238 2.254546 TGTCAAGCATCGGAACAAGT 57.745 45.000 0.00 0.0 0.00 3.16 F
3880 7215 0.396811 AACTTAGGCCTCGCAGTTGT 59.603 50.000 9.68 0.0 0.00 3.32 F
4502 7838 1.366082 TCTCCTTCCATTCCCTCTCCA 59.634 52.381 0.00 0.0 0.00 3.86 F
4503 7839 2.021639 TCTCCTTCCATTCCCTCTCCAT 60.022 50.000 0.00 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1566 3172 4.061596 GCTTGATACTCCACAGATTAGGC 58.938 47.826 0.00 0.00 0.00 3.93 R
2676 4954 4.968259 TGTGAGGCTTGTATGTGTAACTT 58.032 39.130 0.00 0.00 38.04 2.66 R
3121 6452 1.068352 AAGGCTTGAGGGTCTTGGGT 61.068 55.000 0.00 0.00 29.29 4.51 R
4569 7905 0.679002 CCACCTGCAGAAGATGTGGG 60.679 60.000 23.88 10.84 42.16 4.61 R
5590 9826 9.133326 AACTGGGAAAGTTCCGGCTAATTTTAC 62.133 40.741 0.00 0.00 46.60 2.01 R
6238 12324 3.191162 CCAAATCCTTCAAGCAATCGTCA 59.809 43.478 0.00 0.00 0.00 4.35 R
6412 13492 4.098044 GCACTAAGTGTGGCTCTACATCTA 59.902 45.833 2.31 0.00 46.27 1.98 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
26 27 8.394971 TCATATCAAGTTTTCAGAAAAGCTCA 57.605 30.769 8.67 1.87 35.18 4.26
27 28 9.017509 TCATATCAAGTTTTCAGAAAAGCTCAT 57.982 29.630 8.67 7.72 35.18 2.90
28 29 9.286946 CATATCAAGTTTTCAGAAAAGCTCATC 57.713 33.333 8.67 0.00 35.18 2.92
29 30 6.698008 TCAAGTTTTCAGAAAAGCTCATCA 57.302 33.333 8.67 0.00 35.18 3.07
30 31 7.099266 TCAAGTTTTCAGAAAAGCTCATCAA 57.901 32.000 8.67 0.00 35.18 2.57
31 32 7.546358 TCAAGTTTTCAGAAAAGCTCATCAAA 58.454 30.769 8.67 0.00 35.18 2.69
32 33 8.034215 TCAAGTTTTCAGAAAAGCTCATCAAAA 58.966 29.630 8.67 0.00 35.18 2.44
33 34 8.823818 CAAGTTTTCAGAAAAGCTCATCAAAAT 58.176 29.630 8.67 0.00 35.18 1.82
34 35 8.953368 AGTTTTCAGAAAAGCTCATCAAAATT 57.047 26.923 8.67 0.00 31.03 1.82
35 36 8.823818 AGTTTTCAGAAAAGCTCATCAAAATTG 58.176 29.630 8.67 0.00 31.03 2.32
36 37 8.819974 GTTTTCAGAAAAGCTCATCAAAATTGA 58.180 29.630 8.67 0.00 42.14 2.57
37 38 8.945481 TTTCAGAAAAGCTCATCAAAATTGAA 57.055 26.923 0.00 0.00 41.13 2.69
38 39 8.583810 TTCAGAAAAGCTCATCAAAATTGAAG 57.416 30.769 0.00 0.00 41.13 3.02
39 40 7.944061 TCAGAAAAGCTCATCAAAATTGAAGA 58.056 30.769 0.00 0.57 41.13 2.87
40 41 8.415553 TCAGAAAAGCTCATCAAAATTGAAGAA 58.584 29.630 0.00 0.00 41.13 2.52
41 42 9.037737 CAGAAAAGCTCATCAAAATTGAAGAAA 57.962 29.630 0.00 0.00 41.13 2.52
42 43 9.603921 AGAAAAGCTCATCAAAATTGAAGAAAA 57.396 25.926 0.00 0.00 41.13 2.29
43 44 9.859692 GAAAAGCTCATCAAAATTGAAGAAAAG 57.140 29.630 0.00 0.00 41.13 2.27
44 45 8.953368 AAAGCTCATCAAAATTGAAGAAAAGT 57.047 26.923 0.00 0.00 41.13 2.66
45 46 8.953368 AAGCTCATCAAAATTGAAGAAAAGTT 57.047 26.923 0.00 0.00 41.13 2.66
46 47 8.585189 AGCTCATCAAAATTGAAGAAAAGTTC 57.415 30.769 0.00 0.00 41.13 3.01
47 48 8.199449 AGCTCATCAAAATTGAAGAAAAGTTCA 58.801 29.630 0.00 0.00 41.13 3.18
48 49 8.985805 GCTCATCAAAATTGAAGAAAAGTTCAT 58.014 29.630 0.00 0.00 41.13 2.57
64 65 5.560966 AGTTCATCAAACTCAACAAACGT 57.439 34.783 0.00 0.00 45.28 3.99
65 66 5.949735 AGTTCATCAAACTCAACAAACGTT 58.050 33.333 0.00 0.00 45.28 3.99
66 67 6.027749 AGTTCATCAAACTCAACAAACGTTC 58.972 36.000 0.00 0.00 45.28 3.95
67 68 5.553290 TCATCAAACTCAACAAACGTTCA 57.447 34.783 0.00 0.00 0.00 3.18
68 69 6.130298 TCATCAAACTCAACAAACGTTCAT 57.870 33.333 0.00 0.00 0.00 2.57
69 70 6.198687 TCATCAAACTCAACAAACGTTCATC 58.801 36.000 0.00 0.00 0.00 2.92
70 71 5.553290 TCAAACTCAACAAACGTTCATCA 57.447 34.783 0.00 0.00 0.00 3.07
71 72 5.944013 TCAAACTCAACAAACGTTCATCAA 58.056 33.333 0.00 0.00 0.00 2.57
72 73 6.382608 TCAAACTCAACAAACGTTCATCAAA 58.617 32.000 0.00 0.00 0.00 2.69
73 74 7.032580 TCAAACTCAACAAACGTTCATCAAAT 58.967 30.769 0.00 0.00 0.00 2.32
74 75 7.543868 TCAAACTCAACAAACGTTCATCAAATT 59.456 29.630 0.00 0.00 0.00 1.82
75 76 6.810888 ACTCAACAAACGTTCATCAAATTG 57.189 33.333 0.00 0.00 0.00 2.32
76 77 6.559810 ACTCAACAAACGTTCATCAAATTGA 58.440 32.000 0.00 0.00 0.00 2.57
77 78 7.032580 ACTCAACAAACGTTCATCAAATTGAA 58.967 30.769 0.00 0.00 33.32 2.69
78 79 7.220683 ACTCAACAAACGTTCATCAAATTGAAG 59.779 33.333 0.00 0.00 36.34 3.02
79 80 7.254137 TCAACAAACGTTCATCAAATTGAAGA 58.746 30.769 0.00 0.00 36.34 2.87
80 81 7.757173 TCAACAAACGTTCATCAAATTGAAGAA 59.243 29.630 9.27 9.27 36.34 2.52
81 82 8.379161 CAACAAACGTTCATCAAATTGAAGAAA 58.621 29.630 14.13 0.45 36.10 2.52
82 83 8.472683 ACAAACGTTCATCAAATTGAAGAAAA 57.527 26.923 14.13 0.00 36.10 2.29
83 84 8.930760 ACAAACGTTCATCAAATTGAAGAAAAA 58.069 25.926 14.13 0.00 36.10 1.94
111 112 9.999660 TCATCAATTTTGAAAAAGGATCATCAA 57.000 25.926 0.00 0.00 41.13 2.57
128 129 9.443283 GGATCATCAAATTTGATAAGAAGTTCG 57.557 33.333 28.61 15.54 45.62 3.95
129 130 9.994432 GATCATCAAATTTGATAAGAAGTTCGT 57.006 29.630 28.61 10.41 45.62 3.85
130 131 9.994432 ATCATCAAATTTGATAAGAAGTTCGTC 57.006 29.630 28.61 0.00 45.62 4.20
131 132 8.168626 TCATCAAATTTGATAAGAAGTTCGTCG 58.831 33.333 28.61 14.33 45.62 5.12
132 133 7.646446 TCAAATTTGATAAGAAGTTCGTCGA 57.354 32.000 16.91 0.00 31.01 4.20
133 134 8.251750 TCAAATTTGATAAGAAGTTCGTCGAT 57.748 30.769 16.91 0.00 31.01 3.59
134 135 8.717821 TCAAATTTGATAAGAAGTTCGTCGATT 58.282 29.630 16.91 0.00 31.01 3.34
135 136 9.329913 CAAATTTGATAAGAAGTTCGTCGATTT 57.670 29.630 13.08 5.01 0.00 2.17
136 137 9.893305 AAATTTGATAAGAAGTTCGTCGATTTT 57.107 25.926 0.00 0.00 0.00 1.82
137 138 9.893305 AATTTGATAAGAAGTTCGTCGATTTTT 57.107 25.926 0.00 0.00 0.00 1.94
141 142 9.414295 TGATAAGAAGTTCGTCGATTTTTAAGA 57.586 29.630 0.00 0.00 0.00 2.10
149 150 9.199982 AGTTCGTCGATTTTTAAGAAATAGTCA 57.800 29.630 0.00 0.00 0.00 3.41
150 151 9.247562 GTTCGTCGATTTTTAAGAAATAGTCAC 57.752 33.333 0.00 0.00 0.00 3.67
151 152 7.660059 TCGTCGATTTTTAAGAAATAGTCACG 58.340 34.615 0.00 0.00 0.00 4.35
152 153 7.538334 TCGTCGATTTTTAAGAAATAGTCACGA 59.462 33.333 0.00 0.00 0.00 4.35
153 154 8.157813 CGTCGATTTTTAAGAAATAGTCACGAA 58.842 33.333 0.00 0.00 0.00 3.85
154 155 9.968743 GTCGATTTTTAAGAAATAGTCACGAAT 57.031 29.630 0.00 0.00 0.00 3.34
179 180 6.945938 TTTTAGAAAAACATCGAACCAGGA 57.054 33.333 0.00 0.00 0.00 3.86
180 181 6.945938 TTTAGAAAAACATCGAACCAGGAA 57.054 33.333 0.00 0.00 0.00 3.36
181 182 6.554334 TTAGAAAAACATCGAACCAGGAAG 57.446 37.500 0.00 0.00 0.00 3.46
182 183 4.714632 AGAAAAACATCGAACCAGGAAGA 58.285 39.130 0.00 0.00 0.00 2.87
183 184 5.130350 AGAAAAACATCGAACCAGGAAGAA 58.870 37.500 0.00 0.00 0.00 2.52
184 185 5.239525 AGAAAAACATCGAACCAGGAAGAAG 59.760 40.000 0.00 0.00 0.00 2.85
185 186 4.351874 AAACATCGAACCAGGAAGAAGA 57.648 40.909 0.00 0.00 0.00 2.87
186 187 4.559862 AACATCGAACCAGGAAGAAGAT 57.440 40.909 0.00 0.00 0.00 2.40
187 188 4.559862 ACATCGAACCAGGAAGAAGATT 57.440 40.909 0.00 0.00 0.00 2.40
188 189 5.677319 ACATCGAACCAGGAAGAAGATTA 57.323 39.130 0.00 0.00 0.00 1.75
189 190 6.049955 ACATCGAACCAGGAAGAAGATTAA 57.950 37.500 0.00 0.00 0.00 1.40
190 191 6.472887 ACATCGAACCAGGAAGAAGATTAAA 58.527 36.000 0.00 0.00 0.00 1.52
191 192 6.595716 ACATCGAACCAGGAAGAAGATTAAAG 59.404 38.462 0.00 0.00 0.00 1.85
192 193 6.354794 TCGAACCAGGAAGAAGATTAAAGA 57.645 37.500 0.00 0.00 0.00 2.52
193 194 6.765403 TCGAACCAGGAAGAAGATTAAAGAA 58.235 36.000 0.00 0.00 0.00 2.52
194 195 6.874134 TCGAACCAGGAAGAAGATTAAAGAAG 59.126 38.462 0.00 0.00 0.00 2.85
195 196 6.874134 CGAACCAGGAAGAAGATTAAAGAAGA 59.126 38.462 0.00 0.00 0.00 2.87
196 197 7.387948 CGAACCAGGAAGAAGATTAAAGAAGAA 59.612 37.037 0.00 0.00 0.00 2.52
197 198 8.996651 AACCAGGAAGAAGATTAAAGAAGAAA 57.003 30.769 0.00 0.00 0.00 2.52
198 199 8.996651 ACCAGGAAGAAGATTAAAGAAGAAAA 57.003 30.769 0.00 0.00 0.00 2.29
199 200 9.072375 ACCAGGAAGAAGATTAAAGAAGAAAAG 57.928 33.333 0.00 0.00 0.00 2.27
200 201 9.289782 CCAGGAAGAAGATTAAAGAAGAAAAGA 57.710 33.333 0.00 0.00 0.00 2.52
370 461 1.213013 CAACACTCTCTCCCCGACG 59.787 63.158 0.00 0.00 0.00 5.12
371 462 1.074423 AACACTCTCTCCCCGACGA 59.926 57.895 0.00 0.00 0.00 4.20
372 463 1.242665 AACACTCTCTCCCCGACGAC 61.243 60.000 0.00 0.00 0.00 4.34
373 464 2.045143 ACTCTCTCCCCGACGACC 60.045 66.667 0.00 0.00 0.00 4.79
374 465 2.045242 CTCTCTCCCCGACGACCA 60.045 66.667 0.00 0.00 0.00 4.02
375 466 2.360852 TCTCTCCCCGACGACCAC 60.361 66.667 0.00 0.00 0.00 4.16
376 467 2.675423 CTCTCCCCGACGACCACA 60.675 66.667 0.00 0.00 0.00 4.17
377 468 2.203523 TCTCCCCGACGACCACAA 60.204 61.111 0.00 0.00 0.00 3.33
378 469 2.214181 CTCTCCCCGACGACCACAAG 62.214 65.000 0.00 0.00 0.00 3.16
379 470 3.296709 CTCCCCGACGACCACAAGG 62.297 68.421 0.00 0.00 42.21 3.61
420 512 2.311854 CCCTGCCCAGATCCCTTGT 61.312 63.158 0.00 0.00 0.00 3.16
655 908 2.029666 CCGGAGCAGCGGGAATAG 59.970 66.667 0.00 0.00 39.22 1.73
698 1032 6.516860 GCTCTTACTTTGTGTAGTCCTCTTCA 60.517 42.308 0.00 0.00 32.08 3.02
718 1052 0.388520 CTCTCGTCATGTCGTTGCCA 60.389 55.000 11.96 0.00 0.00 4.92
752 1092 1.456705 GAGAGCCTGTCGGAGGGAT 60.457 63.158 3.88 0.00 43.07 3.85
816 1157 3.829601 CTCCAGGTCAGTTCACTACTCTT 59.170 47.826 0.00 0.00 33.85 2.85
937 1278 1.200760 TCCCCTCTTGCTGCTTGCTA 61.201 55.000 0.00 0.00 43.37 3.49
1097 2438 1.843376 CAGACTGGTCCTGGTGGGT 60.843 63.158 0.33 0.00 36.25 4.51
1305 2890 8.638629 AATCTTAGTAAGCGGATACTCATAGT 57.361 34.615 4.93 0.00 37.34 2.12
1339 2924 8.744568 TTTGGATGCACATATAGTTTGTATCA 57.255 30.769 0.00 0.00 34.93 2.15
1622 3228 2.086869 GCCAATTGCTTGCTCTGTAGA 58.913 47.619 0.00 0.00 36.87 2.59
1637 3248 6.147821 TGCTCTGTAGAAACTTTTATGTGCTC 59.852 38.462 0.00 0.00 0.00 4.26
1954 3655 3.066291 ACTCTCGCTCTCTTCTCTTCA 57.934 47.619 0.00 0.00 0.00 3.02
2026 4052 1.406341 GCCCGTGTTTCCACTGCTATA 60.406 52.381 0.00 0.00 39.55 1.31
2985 6238 2.254546 TGTCAAGCATCGGAACAAGT 57.745 45.000 0.00 0.00 0.00 3.16
3000 6277 4.699257 GGAACAAGTCTCATCTCAAGCATT 59.301 41.667 0.00 0.00 0.00 3.56
3121 6452 4.099573 GCATGTTAGTCTTGGAGGTAGCTA 59.900 45.833 0.00 0.00 0.00 3.32
3177 6508 6.987557 TGTGGTATTTTATACCCATTTCCCT 58.012 36.000 12.14 0.00 36.79 4.20
3267 6598 4.170468 TCATAGCCTTCAAATTCCTCCC 57.830 45.455 0.00 0.00 0.00 4.30
3569 6900 5.046304 CAGGAACTCCCTCATCACTTTTCTA 60.046 44.000 0.00 0.00 45.60 2.10
3670 7002 1.843851 TGGCCAGATACCGATTTTCCT 59.156 47.619 0.00 0.00 0.00 3.36
3880 7215 0.396811 AACTTAGGCCTCGCAGTTGT 59.603 50.000 9.68 0.00 0.00 3.32
3898 7233 4.081752 AGTTGTTGTTGTTGCCTCATCAAA 60.082 37.500 4.20 0.00 31.68 2.69
3899 7234 4.462508 TGTTGTTGTTGCCTCATCAAAA 57.537 36.364 4.20 0.00 31.68 2.44
4030 7366 3.116096 AGTAGGCTACATCCCAGTTGA 57.884 47.619 25.48 0.00 0.00 3.18
4357 7693 2.706952 TACCAACTTGCCCAGCACCC 62.707 60.000 0.00 0.00 38.71 4.61
4481 7817 6.442952 TGTACCTGGATTTTGAACAATTTCG 58.557 36.000 0.00 0.00 34.04 3.46
4502 7838 1.366082 TCTCCTTCCATTCCCTCTCCA 59.634 52.381 0.00 0.00 0.00 3.86
4503 7839 2.021639 TCTCCTTCCATTCCCTCTCCAT 60.022 50.000 0.00 0.00 0.00 3.41
4569 7905 7.424227 TTTTCTGCATTTTCATCCATTTCAC 57.576 32.000 0.00 0.00 0.00 3.18
5406 9642 7.878547 AGAGATTAGTTGGTGTAGTACTACC 57.121 40.000 26.41 17.51 35.26 3.18
6238 12324 6.875972 AGGACACTTCTTTCCTGTATATGT 57.124 37.500 0.00 0.00 40.98 2.29
6517 13598 9.248291 AGTAATTTGTTTGCAAGAGTACAATTG 57.752 29.630 13.61 3.24 35.82 2.32
6622 13703 2.334838 CAATTTTCTGCTCCTTGCTGC 58.665 47.619 0.00 0.00 43.37 5.25
6623 13704 1.920610 ATTTTCTGCTCCTTGCTGCT 58.079 45.000 0.00 0.00 43.37 4.24
6624 13705 1.242076 TTTTCTGCTCCTTGCTGCTC 58.758 50.000 0.00 0.00 43.37 4.26
6625 13706 0.607489 TTTCTGCTCCTTGCTGCTCC 60.607 55.000 0.00 0.00 43.37 4.70
6626 13707 1.486997 TTCTGCTCCTTGCTGCTCCT 61.487 55.000 0.00 0.00 43.37 3.69
6627 13708 1.002379 CTGCTCCTTGCTGCTCCTT 60.002 57.895 0.00 0.00 43.37 3.36
6628 13709 1.303074 TGCTCCTTGCTGCTCCTTG 60.303 57.895 0.00 0.00 43.37 3.61
6629 13710 2.698763 GCTCCTTGCTGCTCCTTGC 61.699 63.158 0.00 0.00 43.25 4.01
6630 13711 1.002379 CTCCTTGCTGCTCCTTGCT 60.002 57.895 0.00 0.00 43.37 3.91
6761 13877 4.525996 TGGCTATCAATTCAAGCTTGCTA 58.474 39.130 21.99 12.21 36.48 3.49
6931 14076 2.847234 TTGGTCAGTGCGGGGAGT 60.847 61.111 0.00 0.00 0.00 3.85
7105 14256 0.251354 GAGCTCCAGTGCCTGAATCA 59.749 55.000 0.87 0.00 32.44 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.849168 TGAGCTTTTCTGAAAACTTGATATGAA 58.151 29.630 11.33 0.00 0.00 2.57
1 2 8.394971 TGAGCTTTTCTGAAAACTTGATATGA 57.605 30.769 11.33 0.00 0.00 2.15
2 3 9.286946 GATGAGCTTTTCTGAAAACTTGATATG 57.713 33.333 11.33 1.54 0.00 1.78
5 6 7.281040 TGATGAGCTTTTCTGAAAACTTGAT 57.719 32.000 11.33 1.62 0.00 2.57
6 7 6.698008 TGATGAGCTTTTCTGAAAACTTGA 57.302 33.333 11.33 6.20 0.00 3.02
7 8 7.760131 TTTGATGAGCTTTTCTGAAAACTTG 57.240 32.000 11.33 4.18 0.00 3.16
8 9 8.953368 ATTTTGATGAGCTTTTCTGAAAACTT 57.047 26.923 11.33 3.21 0.00 2.66
9 10 8.823818 CAATTTTGATGAGCTTTTCTGAAAACT 58.176 29.630 11.33 12.82 0.00 2.66
10 11 8.819974 TCAATTTTGATGAGCTTTTCTGAAAAC 58.180 29.630 11.33 8.84 31.01 2.43
11 12 8.945481 TCAATTTTGATGAGCTTTTCTGAAAA 57.055 26.923 14.31 14.31 31.01 2.29
12 13 8.945481 TTCAATTTTGATGAGCTTTTCTGAAA 57.055 26.923 0.00 0.00 37.00 2.69
13 14 8.415553 TCTTCAATTTTGATGAGCTTTTCTGAA 58.584 29.630 5.14 0.00 36.72 3.02
14 15 7.944061 TCTTCAATTTTGATGAGCTTTTCTGA 58.056 30.769 5.14 0.00 36.72 3.27
15 16 8.583810 TTCTTCAATTTTGATGAGCTTTTCTG 57.416 30.769 8.37 0.00 40.82 3.02
16 17 9.603921 TTTTCTTCAATTTTGATGAGCTTTTCT 57.396 25.926 8.37 0.00 40.82 2.52
17 18 9.859692 CTTTTCTTCAATTTTGATGAGCTTTTC 57.140 29.630 8.37 0.00 40.82 2.29
18 19 9.387257 ACTTTTCTTCAATTTTGATGAGCTTTT 57.613 25.926 8.37 0.00 40.82 2.27
19 20 8.953368 ACTTTTCTTCAATTTTGATGAGCTTT 57.047 26.923 8.37 0.00 40.82 3.51
20 21 8.953368 AACTTTTCTTCAATTTTGATGAGCTT 57.047 26.923 8.37 0.00 40.82 3.74
21 22 8.199449 TGAACTTTTCTTCAATTTTGATGAGCT 58.801 29.630 8.37 0.00 40.82 4.09
22 23 8.356533 TGAACTTTTCTTCAATTTTGATGAGC 57.643 30.769 8.37 0.00 40.82 4.26
40 41 7.061789 GAACGTTTGTTGAGTTTGATGAACTTT 59.938 33.333 0.46 0.00 42.83 2.66
41 42 6.526674 GAACGTTTGTTGAGTTTGATGAACTT 59.473 34.615 0.46 0.00 42.83 2.66
42 43 6.027749 GAACGTTTGTTGAGTTTGATGAACT 58.972 36.000 0.46 0.00 44.29 3.01
43 44 5.797934 TGAACGTTTGTTGAGTTTGATGAAC 59.202 36.000 0.46 0.00 38.78 3.18
44 45 5.944013 TGAACGTTTGTTGAGTTTGATGAA 58.056 33.333 0.46 0.00 38.78 2.57
45 46 5.553290 TGAACGTTTGTTGAGTTTGATGA 57.447 34.783 0.46 0.00 38.78 2.92
46 47 5.970612 TGATGAACGTTTGTTGAGTTTGATG 59.029 36.000 0.46 0.00 38.78 3.07
47 48 6.130298 TGATGAACGTTTGTTGAGTTTGAT 57.870 33.333 0.46 0.00 38.78 2.57
48 49 5.553290 TGATGAACGTTTGTTGAGTTTGA 57.447 34.783 0.46 0.00 38.78 2.69
49 50 6.624710 TTTGATGAACGTTTGTTGAGTTTG 57.375 33.333 0.46 0.00 38.78 2.93
50 51 7.543868 TCAATTTGATGAACGTTTGTTGAGTTT 59.456 29.630 0.46 0.00 38.78 2.66
51 52 7.032580 TCAATTTGATGAACGTTTGTTGAGTT 58.967 30.769 0.46 0.00 38.78 3.01
52 53 6.559810 TCAATTTGATGAACGTTTGTTGAGT 58.440 32.000 0.46 0.00 38.78 3.41
53 54 7.431960 TCTTCAATTTGATGAACGTTTGTTGAG 59.568 33.333 0.46 0.00 38.78 3.02
54 55 7.254137 TCTTCAATTTGATGAACGTTTGTTGA 58.746 30.769 0.46 3.44 38.78 3.18
55 56 7.448588 TCTTCAATTTGATGAACGTTTGTTG 57.551 32.000 0.46 1.16 38.78 3.33
56 57 8.472683 TTTCTTCAATTTGATGAACGTTTGTT 57.527 26.923 21.01 0.00 39.33 2.83
57 58 8.472683 TTTTCTTCAATTTGATGAACGTTTGT 57.527 26.923 21.01 0.00 39.33 2.83
85 86 9.999660 TTGATGATCCTTTTTCAAAATTGATGA 57.000 25.926 0.00 0.00 37.00 2.92
102 103 9.443283 CGAACTTCTTATCAAATTTGATGATCC 57.557 33.333 33.94 17.62 46.68 3.36
103 104 9.994432 ACGAACTTCTTATCAAATTTGATGATC 57.006 29.630 33.94 22.08 46.68 2.92
104 105 9.994432 GACGAACTTCTTATCAAATTTGATGAT 57.006 29.630 33.94 18.12 46.68 2.45
105 106 8.168626 CGACGAACTTCTTATCAAATTTGATGA 58.831 33.333 33.94 27.37 46.68 2.92
106 107 8.168626 TCGACGAACTTCTTATCAAATTTGATG 58.831 33.333 33.94 22.44 46.68 3.07
108 109 7.646446 TCGACGAACTTCTTATCAAATTTGA 57.354 32.000 22.52 22.52 42.14 2.69
109 110 8.880768 AATCGACGAACTTCTTATCAAATTTG 57.119 30.769 12.15 12.15 0.00 2.32
110 111 9.893305 AAAATCGACGAACTTCTTATCAAATTT 57.107 25.926 0.00 0.00 0.00 1.82
111 112 9.893305 AAAAATCGACGAACTTCTTATCAAATT 57.107 25.926 0.00 0.00 0.00 1.82
115 116 9.414295 TCTTAAAAATCGACGAACTTCTTATCA 57.586 29.630 0.00 0.00 0.00 2.15
123 124 9.199982 TGACTATTTCTTAAAAATCGACGAACT 57.800 29.630 0.00 0.00 0.00 3.01
124 125 9.247562 GTGACTATTTCTTAAAAATCGACGAAC 57.752 33.333 0.00 0.00 0.00 3.95
125 126 8.157813 CGTGACTATTTCTTAAAAATCGACGAA 58.842 33.333 0.00 0.00 0.00 3.85
126 127 7.538334 TCGTGACTATTTCTTAAAAATCGACGA 59.462 33.333 0.00 0.00 0.00 4.20
127 128 7.660059 TCGTGACTATTTCTTAAAAATCGACG 58.340 34.615 0.00 0.00 0.00 5.12
128 129 9.968743 ATTCGTGACTATTTCTTAAAAATCGAC 57.031 29.630 0.00 0.00 0.00 4.20
155 156 7.336161 TCCTGGTTCGATGTTTTTCTAAAAA 57.664 32.000 0.00 0.00 35.67 1.94
156 157 6.945938 TCCTGGTTCGATGTTTTTCTAAAA 57.054 33.333 0.00 0.00 0.00 1.52
157 158 6.768861 TCTTCCTGGTTCGATGTTTTTCTAAA 59.231 34.615 0.00 0.00 0.00 1.85
158 159 6.292923 TCTTCCTGGTTCGATGTTTTTCTAA 58.707 36.000 0.00 0.00 0.00 2.10
159 160 5.860611 TCTTCCTGGTTCGATGTTTTTCTA 58.139 37.500 0.00 0.00 0.00 2.10
160 161 4.714632 TCTTCCTGGTTCGATGTTTTTCT 58.285 39.130 0.00 0.00 0.00 2.52
161 162 5.238650 TCTTCTTCCTGGTTCGATGTTTTTC 59.761 40.000 0.00 0.00 0.00 2.29
162 163 5.130350 TCTTCTTCCTGGTTCGATGTTTTT 58.870 37.500 0.00 0.00 0.00 1.94
163 164 4.714632 TCTTCTTCCTGGTTCGATGTTTT 58.285 39.130 0.00 0.00 0.00 2.43
164 165 4.351874 TCTTCTTCCTGGTTCGATGTTT 57.648 40.909 0.00 0.00 0.00 2.83
165 166 4.559862 ATCTTCTTCCTGGTTCGATGTT 57.440 40.909 0.00 0.00 0.00 2.71
166 167 4.559862 AATCTTCTTCCTGGTTCGATGT 57.440 40.909 0.00 0.00 0.00 3.06
167 168 6.818644 TCTTTAATCTTCTTCCTGGTTCGATG 59.181 38.462 0.00 0.00 0.00 3.84
168 169 6.947464 TCTTTAATCTTCTTCCTGGTTCGAT 58.053 36.000 0.00 0.00 0.00 3.59
169 170 6.354794 TCTTTAATCTTCTTCCTGGTTCGA 57.645 37.500 0.00 0.00 0.00 3.71
170 171 6.874134 TCTTCTTTAATCTTCTTCCTGGTTCG 59.126 38.462 0.00 0.00 0.00 3.95
171 172 8.622948 TTCTTCTTTAATCTTCTTCCTGGTTC 57.377 34.615 0.00 0.00 0.00 3.62
172 173 8.996651 TTTCTTCTTTAATCTTCTTCCTGGTT 57.003 30.769 0.00 0.00 0.00 3.67
173 174 8.996651 TTTTCTTCTTTAATCTTCTTCCTGGT 57.003 30.769 0.00 0.00 0.00 4.00
174 175 9.289782 TCTTTTCTTCTTTAATCTTCTTCCTGG 57.710 33.333 0.00 0.00 0.00 4.45
201 202 9.914131 GGAGTATTATTGTCTGCTTTTCTTTTT 57.086 29.630 0.00 0.00 0.00 1.94
202 203 8.523658 GGGAGTATTATTGTCTGCTTTTCTTTT 58.476 33.333 0.00 0.00 0.00 2.27
203 204 7.890655 AGGGAGTATTATTGTCTGCTTTTCTTT 59.109 33.333 0.00 0.00 0.00 2.52
204 205 7.406104 AGGGAGTATTATTGTCTGCTTTTCTT 58.594 34.615 0.00 0.00 0.00 2.52
205 206 6.963322 AGGGAGTATTATTGTCTGCTTTTCT 58.037 36.000 0.00 0.00 0.00 2.52
206 207 7.011857 CAGAGGGAGTATTATTGTCTGCTTTTC 59.988 40.741 0.00 0.00 0.00 2.29
207 208 6.825721 CAGAGGGAGTATTATTGTCTGCTTTT 59.174 38.462 0.00 0.00 0.00 2.27
208 209 6.069963 ACAGAGGGAGTATTATTGTCTGCTTT 60.070 38.462 0.00 0.00 34.55 3.51
209 210 5.426833 ACAGAGGGAGTATTATTGTCTGCTT 59.573 40.000 0.00 0.00 34.55 3.91
210 211 4.965532 ACAGAGGGAGTATTATTGTCTGCT 59.034 41.667 0.00 0.00 34.55 4.24
211 212 5.283457 ACAGAGGGAGTATTATTGTCTGC 57.717 43.478 0.00 0.00 34.55 4.26
212 213 6.127054 TGGAACAGAGGGAGTATTATTGTCTG 60.127 42.308 0.00 0.00 36.77 3.51
213 214 5.964477 TGGAACAGAGGGAGTATTATTGTCT 59.036 40.000 0.00 0.00 0.00 3.41
214 215 6.235231 TGGAACAGAGGGAGTATTATTGTC 57.765 41.667 0.00 0.00 0.00 3.18
215 216 6.636454 TTGGAACAGAGGGAGTATTATTGT 57.364 37.500 0.00 0.00 42.39 2.71
216 217 7.938140 TTTTGGAACAGAGGGAGTATTATTG 57.062 36.000 0.00 0.00 42.39 1.90
221 222 6.893020 ACTATTTTGGAACAGAGGGAGTAT 57.107 37.500 0.00 0.00 42.39 2.12
388 479 2.363147 AGGGAGGAGCGAGTGGTC 60.363 66.667 0.00 0.00 41.93 4.02
389 480 2.681778 CAGGGAGGAGCGAGTGGT 60.682 66.667 0.00 0.00 0.00 4.16
390 481 4.154347 GCAGGGAGGAGCGAGTGG 62.154 72.222 0.00 0.00 0.00 4.00
698 1032 3.025168 TGGCAACGACATGACGAGAGT 62.025 52.381 23.72 0.00 46.95 3.24
752 1092 4.349503 AACTGGCCATGGCGCTCA 62.350 61.111 29.90 20.74 43.06 4.26
937 1278 8.373981 TCTCTTCTTCAGTCTTGAAATTGAGAT 58.626 33.333 9.55 0.00 42.48 2.75
1042 2307 0.878961 GAGTGGTTGTCGTCCGCTTT 60.879 55.000 0.00 0.00 44.49 3.51
1097 2438 4.166888 GCCAGAGCGCCCTCATCA 62.167 66.667 2.29 0.00 40.68 3.07
1305 2890 6.698008 ATATGTGCATCCAAAAGAATTCGA 57.302 33.333 0.00 0.00 0.00 3.71
1566 3172 4.061596 GCTTGATACTCCACAGATTAGGC 58.938 47.826 0.00 0.00 0.00 3.93
1622 3228 7.553334 TCCTATACTCGAGCACATAAAAGTTT 58.447 34.615 13.61 0.00 0.00 2.66
1637 3248 5.753438 TGCTAAACAGCAAATCCTATACTCG 59.247 40.000 0.00 0.00 42.40 4.18
1954 3655 7.791029 ACTGAAAAGAGAAGAGAAAGAGAAGT 58.209 34.615 0.00 0.00 0.00 3.01
2375 4490 4.998051 AGAAGAGAGAAGAGAAGTCCTGT 58.002 43.478 0.00 0.00 0.00 4.00
2676 4954 4.968259 TGTGAGGCTTGTATGTGTAACTT 58.032 39.130 0.00 0.00 38.04 2.66
2985 6238 4.192429 TGTTCGAATGCTTGAGATGAGA 57.808 40.909 0.00 0.00 0.00 3.27
3000 6277 2.932622 GCTTGAGATGAGGCTTGTTCGA 60.933 50.000 0.00 0.00 0.00 3.71
3121 6452 1.068352 AAGGCTTGAGGGTCTTGGGT 61.068 55.000 0.00 0.00 29.29 4.51
3177 6508 1.485895 TGAGATCATGAACCATGCGGA 59.514 47.619 0.00 0.00 41.18 5.54
3267 6598 4.037923 ACAAGACCTTATTGCAGGTGTTTG 59.962 41.667 0.00 7.42 45.91 2.93
3569 6900 6.702329 AGAGACAAAGTCAATAAAGGTCGAT 58.298 36.000 0.00 0.00 34.60 3.59
3880 7215 4.744137 CGATTTTTGATGAGGCAACAACAA 59.256 37.500 4.07 4.07 41.41 2.83
3898 7233 9.927668 ATAGGATGAATTTTTGTTTGTCGATTT 57.072 25.926 0.00 0.00 0.00 2.17
3899 7234 9.573133 GATAGGATGAATTTTTGTTTGTCGATT 57.427 29.630 0.00 0.00 0.00 3.34
4030 7366 6.943718 GGTCTACTATTAGATCACTAGCCTGT 59.056 42.308 0.00 0.00 35.71 4.00
4357 7693 3.249799 TCTTTGTTGTATGTCTTGGTGCG 59.750 43.478 0.00 0.00 0.00 5.34
4481 7817 1.765904 GGAGAGGGAATGGAAGGAGAC 59.234 57.143 0.00 0.00 0.00 3.36
4502 7838 6.513947 AGGAGATGATATGGAAGGAGATGAT 58.486 40.000 0.00 0.00 0.00 2.45
4503 7839 5.913277 AGGAGATGATATGGAAGGAGATGA 58.087 41.667 0.00 0.00 0.00 2.92
4569 7905 0.679002 CCACCTGCAGAAGATGTGGG 60.679 60.000 23.88 10.84 42.16 4.61
5406 9642 9.557338 GTACTACACTAAGTAATGTCACTTCAG 57.443 37.037 0.00 0.00 39.45 3.02
5590 9826 9.133326 AACTGGGAAAGTTCCGGCTAATTTTAC 62.133 40.741 0.00 0.00 46.60 2.01
6238 12324 3.191162 CCAAATCCTTCAAGCAATCGTCA 59.809 43.478 0.00 0.00 0.00 4.35
6412 13492 4.098044 GCACTAAGTGTGGCTCTACATCTA 59.902 45.833 2.31 0.00 46.27 1.98
6517 13598 4.691860 AATTCAGTGTACTCATGCTTGC 57.308 40.909 0.00 0.00 0.00 4.01
6622 13703 1.380524 CAGCAAGGATCAGCAAGGAG 58.619 55.000 6.77 0.00 0.00 3.69
6623 13704 0.679002 GCAGCAAGGATCAGCAAGGA 60.679 55.000 6.77 0.00 0.00 3.36
6624 13705 0.680280 AGCAGCAAGGATCAGCAAGG 60.680 55.000 0.00 0.00 0.00 3.61
6625 13706 0.733729 GAGCAGCAAGGATCAGCAAG 59.266 55.000 0.00 1.02 0.00 4.01
6626 13707 0.679002 GGAGCAGCAAGGATCAGCAA 60.679 55.000 0.00 0.00 0.00 3.91
6627 13708 1.077930 GGAGCAGCAAGGATCAGCA 60.078 57.895 0.00 0.00 0.00 4.41
6628 13709 0.394080 AAGGAGCAGCAAGGATCAGC 60.394 55.000 0.00 0.00 0.00 4.26
6629 13710 1.380524 CAAGGAGCAGCAAGGATCAG 58.619 55.000 0.00 0.00 0.00 2.90
6630 13711 0.679002 GCAAGGAGCAGCAAGGATCA 60.679 55.000 0.00 0.00 44.79 2.92
6761 13877 2.834549 AGGACGTCTTCTCACCAATCAT 59.165 45.455 16.46 0.00 0.00 2.45
7024 14175 1.895707 GACCAACAGCAGCAGCAGT 60.896 57.895 3.17 0.00 45.49 4.40


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

AutoCloner maintained by Alex Coulton.