Multiple sequence alignment - TraesCS6B01G232400

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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 TraesCS6B01G232400 chr6B 100.000 7421 0 0 1 7421 388079520 388072100 0.000000e+00 13705.0
1 TraesCS6B01G232400 chr6B 96.044 809 32 0 1 809 367629148 367628340 0.000000e+00 1317.0
2 TraesCS6B01G232400 chr6B 95.936 812 33 0 1 812 375229691 375228880 0.000000e+00 1317.0
3 TraesCS6B01G232400 chr6B 95.808 811 34 0 1 811 376411321 376412131 0.000000e+00 1310.0
4 TraesCS6B01G232400 chr6B 95.572 813 34 2 3 813 710114434 710113622 0.000000e+00 1301.0
5 TraesCS6B01G232400 chr6B 94.190 568 18 3 6867 7421 388119287 388118722 0.000000e+00 852.0
6 TraesCS6B01G232400 chr6B 95.349 172 8 0 4331 4502 16450363 16450534 2.640000e-69 274.0
7 TraesCS6B01G232400 chr6B 75.855 468 82 26 6890 7343 386974144 386973694 7.540000e-50 209.0
8 TraesCS6B01G232400 chr6B 82.353 170 16 6 7265 7421 119699204 119699036 1.300000e-27 135.0
9 TraesCS6B01G232400 chr6B 72.978 507 90 37 6871 7351 305500025 305499540 4.670000e-27 134.0
10 TraesCS6B01G232400 chr6B 100.000 31 0 0 6129 6159 388073271 388073241 2.890000e-04 58.4
11 TraesCS6B01G232400 chr6B 100.000 31 0 0 6250 6280 388073392 388073362 2.890000e-04 58.4
12 TraesCS6B01G232400 chr3D 95.932 3294 79 15 1088 4336 208829027 208832310 0.000000e+00 5289.0
13 TraesCS6B01G232400 chr3D 96.146 960 20 4 4695 5639 208834060 208835017 0.000000e+00 1552.0
14 TraesCS6B01G232400 chr3D 97.541 610 13 1 5634 6241 208843569 208844178 0.000000e+00 1042.0
15 TraesCS6B01G232400 chr3D 87.582 459 19 7 6288 6738 208844814 208845242 1.440000e-136 497.0
16 TraesCS6B01G232400 chr3D 92.754 276 15 2 816 1090 208828652 208828923 1.940000e-105 394.0
17 TraesCS6B01G232400 chr3D 93.274 223 12 2 3943 4165 47795274 47795055 7.180000e-85 326.0
18 TraesCS6B01G232400 chr3D 93.103 203 12 2 4496 4696 208832308 208832510 5.630000e-76 296.0
19 TraesCS6B01G232400 chr3D 92.308 182 7 3 4161 4336 47789881 47789701 1.240000e-62 252.0
20 TraesCS6B01G232400 chr3D 94.737 133 7 0 6735 6867 208845272 208845404 2.710000e-49 207.0
21 TraesCS6B01G232400 chr3D 100.000 31 0 0 6250 6280 208844066 208844096 2.890000e-04 58.4
22 TraesCS6B01G232400 chr7D 95.485 3300 76 20 1087 4336 513998092 513994816 0.000000e+00 5201.0
23 TraesCS6B01G232400 chr7D 96.694 847 23 3 4697 5541 513993000 513992157 0.000000e+00 1404.0
24 TraesCS6B01G232400 chr7D 95.545 202 8 1 4496 4696 513994818 513994617 9.290000e-84 322.0
25 TraesCS6B01G232400 chr7D 89.362 188 19 1 2796 2983 40388259 40388445 1.240000e-57 235.0
26 TraesCS6B01G232400 chr7D 89.262 149 14 2 4549 4696 33073224 33073077 1.270000e-42 185.0
27 TraesCS6B01G232400 chr7D 81.319 182 10 11 6541 6700 370865092 370864913 7.820000e-25 126.0
28 TraesCS6B01G232400 chr5B 94.847 2969 90 14 1088 4042 648735074 648737993 0.000000e+00 4577.0
29 TraesCS6B01G232400 chr5B 96.781 932 26 2 3013 3940 359313867 359312936 0.000000e+00 1552.0
30 TraesCS6B01G232400 chr5B 95.583 815 33 3 3 815 323814598 323815411 0.000000e+00 1303.0
31 TraesCS6B01G232400 chr5B 95.360 819 32 4 3 816 483562880 483562063 0.000000e+00 1297.0
32 TraesCS6B01G232400 chr5B 86.299 562 39 13 6317 6867 648738227 648738761 1.800000e-160 577.0
33 TraesCS6B01G232400 chr5B 86.334 461 54 7 4759 5213 460760000 460760457 1.860000e-135 494.0
34 TraesCS6B01G232400 chr5B 82.513 589 69 12 5661 6239 460762416 460762980 3.110000e-133 486.0
35 TraesCS6B01G232400 chr5B 88.953 344 36 2 5214 5556 460760540 460760882 2.480000e-114 424.0
36 TraesCS6B01G232400 chr5B 91.566 249 19 2 843 1090 648734724 648734971 7.130000e-90 342.0
37 TraesCS6B01G232400 chr5B 74.052 501 85 33 6871 7341 180894510 180894995 5.960000e-36 163.0
38 TraesCS6B01G232400 chr2A 95.002 2401 90 13 1088 3481 37030599 37028222 0.000000e+00 3742.0
39 TraesCS6B01G232400 chr2A 96.987 1560 29 4 4697 6239 37026642 37025084 0.000000e+00 2604.0
40 TraesCS6B01G232400 chr2A 87.683 341 24 14 810 1141 37030961 37030630 1.510000e-101 381.0
41 TraesCS6B01G232400 chr2A 97.927 193 4 0 6291 6483 37024433 37024241 1.190000e-87 335.0
42 TraesCS6B01G232400 chr2A 95.858 169 7 0 4331 4499 113822462 113822294 2.640000e-69 274.0
43 TraesCS6B01G232400 chr2A 94.483 145 7 1 4552 4696 37028216 37028073 9.690000e-54 222.0
44 TraesCS6B01G232400 chr2A 100.000 31 0 0 6250 6280 37025194 37025164 2.890000e-04 58.4
45 TraesCS6B01G232400 chr1A 94.975 2408 71 10 1093 3481 561614144 561616520 0.000000e+00 3731.0
46 TraesCS6B01G232400 chr1A 96.991 1562 29 4 4695 6239 561618081 561619641 0.000000e+00 2608.0
47 TraesCS6B01G232400 chr1A 86.486 407 45 8 4815 5213 593648862 593649266 8.840000e-119 438.0
48 TraesCS6B01G232400 chr1A 88.925 307 29 5 818 1119 561613805 561614111 2.530000e-99 374.0
49 TraesCS6B01G232400 chr1A 97.959 196 4 0 6288 6483 561620287 561620482 2.560000e-89 340.0
50 TraesCS6B01G232400 chr1A 95.556 180 8 0 4335 4514 66887374 66887195 9.420000e-74 289.0
51 TraesCS6B01G232400 chr1A 97.163 141 4 0 4552 4692 561616526 561616666 9.620000e-59 239.0
52 TraesCS6B01G232400 chr1A 100.000 31 0 0 6250 6280 561619531 561619561 2.890000e-04 58.4
53 TraesCS6B01G232400 chr3A 93.645 2093 66 23 864 2906 10617464 10619539 0.000000e+00 3066.0
54 TraesCS6B01G232400 chr3A 96.741 1565 28 7 4695 6239 10622823 10624384 0.000000e+00 2586.0
55 TraesCS6B01G232400 chr3A 96.244 1544 36 5 2799 4336 10619536 10621063 0.000000e+00 2510.0
56 TraesCS6B01G232400 chr3A 96.040 202 7 1 4496 4696 10621061 10621262 2.000000e-85 327.0
57 TraesCS6B01G232400 chr3A 93.897 213 11 2 6339 6549 10625075 10625287 3.340000e-83 320.0
58 TraesCS6B01G232400 chr3A 94.828 174 9 0 4325 4498 20900234 20900407 9.490000e-69 272.0
59 TraesCS6B01G232400 chr3A 91.327 196 15 2 6546 6740 10625236 10625430 4.410000e-67 267.0
60 TraesCS6B01G232400 chr3A 94.118 136 8 0 6732 6867 10625455 10625590 2.710000e-49 207.0
61 TraesCS6B01G232400 chr3A 100.000 28 0 0 6288 6315 10625050 10625077 1.300000e-02 52.8
62 TraesCS6B01G232400 chr7A 97.512 1487 31 2 2856 4336 673065899 673067385 0.000000e+00 2536.0
63 TraesCS6B01G232400 chr7A 93.888 998 20 6 1504 2466 673056150 673057141 0.000000e+00 1467.0
64 TraesCS6B01G232400 chr7A 96.467 368 13 0 2496 2863 673064054 673064421 6.370000e-170 608.0
65 TraesCS6B01G232400 chr7A 94.043 235 12 2 817 1050 673032621 673032854 9.160000e-94 355.0
66 TraesCS6B01G232400 chr7A 92.276 246 14 2 1088 1329 673033291 673033535 1.980000e-90 344.0
67 TraesCS6B01G232400 chr7A 96.040 202 7 1 4496 4696 673067383 673067584 2.000000e-85 327.0
68 TraesCS6B01G232400 chr7A 95.161 186 9 0 1324 1509 673042081 673042266 2.020000e-75 294.0
69 TraesCS6B01G232400 chr7A 96.407 167 6 0 4335 4501 285794172 285794006 7.330000e-70 276.0
70 TraesCS6B01G232400 chr7A 78.431 204 23 10 6552 6734 542719025 542719228 6.090000e-21 113.0
71 TraesCS6B01G232400 chr7B 95.591 1565 47 8 4695 6239 263153846 263155408 0.000000e+00 2488.0
72 TraesCS6B01G232400 chr7B 96.767 1330 37 4 3013 4336 263150748 263152077 0.000000e+00 2213.0
73 TraesCS6B01G232400 chr7B 95.284 827 38 1 3 828 213288231 213289057 0.000000e+00 1310.0
74 TraesCS6B01G232400 chr7B 88.450 1039 77 26 5211 6239 253909282 253910287 0.000000e+00 1214.0
75 TraesCS6B01G232400 chr7B 88.322 1019 67 23 4695 5666 253908737 253909750 0.000000e+00 1175.0
76 TraesCS6B01G232400 chr7B 84.301 758 78 20 5453 6183 641176676 641177419 0.000000e+00 702.0
77 TraesCS6B01G232400 chr7B 86.092 568 42 14 6334 6880 263156047 263156598 1.800000e-160 577.0
78 TraesCS6B01G232400 chr7B 95.545 202 8 1 4496 4696 263152075 263152276 9.290000e-84 322.0
79 TraesCS6B01G232400 chr7B 87.500 176 16 5 6291 6466 253910953 253911122 1.630000e-46 198.0
80 TraesCS6B01G232400 chr7B 96.117 103 4 0 7239 7341 518613048 518613150 1.280000e-37 169.0
81 TraesCS6B01G232400 chr7B 93.204 103 7 0 7239 7341 518620706 518620808 1.290000e-32 152.0
82 TraesCS6B01G232400 chr7B 83.333 156 13 4 7279 7421 281298554 281298399 1.680000e-26 132.0
83 TraesCS6B01G232400 chr5A 94.754 915 35 6 3016 3919 406672276 406671364 0.000000e+00 1411.0
84 TraesCS6B01G232400 chr5A 89.055 603 28 6 1088 1677 328542152 328542729 0.000000e+00 713.0
85 TraesCS6B01G232400 chr5A 86.347 542 38 12 6337 6868 328544983 328545498 6.500000e-155 558.0
86 TraesCS6B01G232400 chr5A 85.041 488 48 5 1968 2432 110283753 110284238 2.420000e-129 473.0
87 TraesCS6B01G232400 chr5A 85.325 477 46 4 1979 2432 149229692 149229217 8.720000e-129 472.0
88 TraesCS6B01G232400 chr5A 81.306 337 40 11 1303 1632 110282797 110283117 1.240000e-62 252.0
89 TraesCS6B01G232400 chr5D 94.292 911 44 5 3016 3919 312608570 312607661 0.000000e+00 1387.0
90 TraesCS6B01G232400 chr5D 76.817 289 32 12 6552 6805 532664326 532664614 6.040000e-26 130.0
91 TraesCS6B01G232400 chr5D 77.990 209 29 11 6614 6805 100013875 100014083 1.690000e-21 115.0
92 TraesCS6B01G232400 chr4B 95.443 812 35 2 1 811 485482750 485483560 0.000000e+00 1293.0
93 TraesCS6B01G232400 chr4B 95.320 812 38 0 1 812 169838219 169837408 0.000000e+00 1290.0
94 TraesCS6B01G232400 chr4B 74.227 582 98 36 6871 7421 460572463 460571903 5.870000e-46 196.0
95 TraesCS6B01G232400 chr4B 81.768 181 19 9 7254 7421 301971806 301971627 1.000000e-28 139.0
96 TraesCS6B01G232400 chr4B 82.051 156 15 2 7279 7421 593731858 593731703 3.640000e-23 121.0
97 TraesCS6B01G232400 chr4B 71.260 508 95 37 6867 7341 326322067 326322556 1.720000e-11 82.4
98 TraesCS6B01G232400 chr4B 77.344 128 19 7 6870 6992 436160795 436160673 4.810000e-07 67.6
99 TraesCS6B01G232400 chr1B 92.668 641 19 5 3701 4336 372097846 372097229 0.000000e+00 898.0
100 TraesCS6B01G232400 chr1B 96.468 453 13 2 5789 6239 372096506 372096055 0.000000e+00 745.0
101 TraesCS6B01G232400 chr1B 85.350 471 40 21 818 1262 470716108 470715641 1.890000e-125 460.0
102 TraesCS6B01G232400 chr1B 95.735 211 8 1 6288 6498 372095387 372095178 9.220000e-89 339.0
103 TraesCS6B01G232400 chr1B 78.543 508 87 15 6871 7368 236866974 236866479 1.550000e-81 315.0
104 TraesCS6B01G232400 chr1B 87.455 279 28 4 818 1090 372099421 372099144 1.550000e-81 315.0
105 TraesCS6B01G232400 chr1B 94.554 202 10 1 4496 4696 372097231 372097030 2.010000e-80 311.0
106 TraesCS6B01G232400 chr1B 94.318 176 10 0 4331 4506 56487774 56487599 3.410000e-68 270.0
107 TraesCS6B01G232400 chr1B 88.636 220 14 5 1088 1303 372099040 372098828 2.660000e-64 257.0
108 TraesCS6B01G232400 chr1B 90.551 127 11 1 6741 6867 372095113 372094988 4.610000e-37 167.0
109 TraesCS6B01G232400 chr1B 75.111 225 54 2 1334 1557 674391025 674391248 3.660000e-18 104.0
110 TraesCS6B01G232400 chr2D 84.394 833 82 18 5433 6239 461541873 461542683 0.000000e+00 774.0
111 TraesCS6B01G232400 chr2D 83.333 270 26 9 6619 6871 633233990 633234257 1.610000e-56 231.0
112 TraesCS6B01G232400 chr2D 94.309 123 7 0 6416 6538 633233859 633233981 9.830000e-44 189.0
113 TraesCS6B01G232400 chr2D 81.340 209 16 6 6552 6738 515573642 515573435 1.670000e-31 148.0
114 TraesCS6B01G232400 chr2D 79.821 223 21 13 6538 6738 502525304 502525524 2.790000e-29 141.0
115 TraesCS6B01G232400 chr1D 84.293 834 80 23 5433 6239 376893091 376893900 0.000000e+00 767.0
116 TraesCS6B01G232400 chr1D 83.467 375 53 9 6866 7235 369606156 369605786 2.560000e-89 340.0
117 TraesCS6B01G232400 chr1D 76.789 517 78 27 6867 7368 191433124 191433613 1.240000e-62 252.0
118 TraesCS6B01G232400 chr1D 78.698 169 19 9 6554 6707 318891129 318890963 6.130000e-16 97.1
119 TraesCS6B01G232400 chr1D 81.395 129 11 4 6618 6738 327935101 327934978 7.930000e-15 93.5
120 TraesCS6B01G232400 chr6A 86.017 472 36 8 817 1262 12146468 12146001 5.210000e-131 479.0
121 TraesCS6B01G232400 chr6A 79.808 208 22 12 6551 6738 7524517 7524310 4.670000e-27 134.0
122 TraesCS6B01G232400 chr6A 82.500 160 13 6 6558 6702 31038127 31037968 7.820000e-25 126.0
123 TraesCS6B01G232400 chr6A 76.744 215 23 9 6546 6739 556095143 556094935 2.200000e-15 95.3
124 TraesCS6B01G232400 chr3B 85.745 470 37 8 819 1262 806129148 806129613 3.130000e-128 470.0
125 TraesCS6B01G232400 chr3B 85.372 417 54 6 6865 7276 401779971 401779557 6.880000e-115 425.0
126 TraesCS6B01G232400 chr3B 84.634 410 56 5 6872 7276 401772637 401772230 1.160000e-107 401.0
127 TraesCS6B01G232400 chr3B 81.295 417 63 10 6866 7272 157342001 157342412 2.580000e-84 324.0
128 TraesCS6B01G232400 chr3B 96.407 167 6 0 4332 4498 178399254 178399088 7.330000e-70 276.0
129 TraesCS6B01G232400 chr3B 95.833 168 7 0 4331 4498 525060155 525060322 9.490000e-69 272.0
130 TraesCS6B01G232400 chr3B 76.636 428 67 25 6867 7276 457288684 457289096 9.760000e-49 206.0
131 TraesCS6B01G232400 chr3B 81.325 166 18 2 7269 7421 296107046 296106881 1.010000e-23 122.0
132 TraesCS6B01G232400 chr3B 81.325 166 17 4 7269 7421 296114811 296114647 1.010000e-23 122.0
133 TraesCS6B01G232400 chrUn 88.487 304 31 4 6871 7172 382975120 382974819 1.520000e-96 364.0
134 TraesCS6B01G232400 chrUn 83.069 378 43 9 6511 6868 326758259 326757883 2.580000e-84 324.0
135 TraesCS6B01G232400 chrUn 82.812 384 45 9 6505 6868 381260160 381260542 2.580000e-84 324.0
136 TraesCS6B01G232400 chr2B 83.117 385 53 11 6867 7244 645576259 645576638 2.560000e-89 340.0
137 TraesCS6B01G232400 chr2B 82.532 395 53 14 6867 7252 645569118 645569505 4.290000e-87 333.0
138 TraesCS6B01G232400 chr2B 82.090 402 51 18 6867 7258 115964134 115964524 2.580000e-84 324.0
139 TraesCS6B01G232400 chr2B 86.154 195 15 4 7239 7421 577141089 577140895 4.540000e-47 200.0
140 TraesCS6B01G232400 chr4A 95.402 174 8 0 4328 4501 674230655 674230482 2.040000e-70 278.0
141 TraesCS6B01G232400 chr6D 81.343 268 31 6 6551 6808 423793518 423793260 4.540000e-47 200.0
142 TraesCS6B01G232400 chr6D 92.500 40 2 1 6433 6471 7472463 7472424 1.000000e-03 56.5


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 TraesCS6B01G232400 chr6B 388072100 388079520 7420 True 13705.000000 13705 100.000000 1 7421 1 chr6B.!!$R6 7420
1 TraesCS6B01G232400 chr6B 367628340 367629148 808 True 1317.000000 1317 96.044000 1 809 1 chr6B.!!$R3 808
2 TraesCS6B01G232400 chr6B 375228880 375229691 811 True 1317.000000 1317 95.936000 1 812 1 chr6B.!!$R4 811
3 TraesCS6B01G232400 chr6B 376411321 376412131 810 False 1310.000000 1310 95.808000 1 811 1 chr6B.!!$F2 810
4 TraesCS6B01G232400 chr6B 710113622 710114434 812 True 1301.000000 1301 95.572000 3 813 1 chr6B.!!$R8 810
5 TraesCS6B01G232400 chr6B 388118722 388119287 565 True 852.000000 852 94.190000 6867 7421 1 chr6B.!!$R7 554
6 TraesCS6B01G232400 chr3D 208828652 208835017 6365 False 1882.750000 5289 94.483750 816 5639 4 chr3D.!!$F1 4823
7 TraesCS6B01G232400 chr3D 208843569 208845404 1835 False 451.100000 1042 94.965000 5634 6867 4 chr3D.!!$F2 1233
8 TraesCS6B01G232400 chr7D 513992157 513998092 5935 True 2309.000000 5201 95.908000 1087 5541 3 chr7D.!!$R3 4454
9 TraesCS6B01G232400 chr5B 648734724 648738761 4037 False 1832.000000 4577 90.904000 843 6867 3 chr5B.!!$F4 6024
10 TraesCS6B01G232400 chr5B 359312936 359313867 931 True 1552.000000 1552 96.781000 3013 3940 1 chr5B.!!$R1 927
11 TraesCS6B01G232400 chr5B 323814598 323815411 813 False 1303.000000 1303 95.583000 3 815 1 chr5B.!!$F2 812
12 TraesCS6B01G232400 chr5B 483562063 483562880 817 True 1297.000000 1297 95.360000 3 816 1 chr5B.!!$R2 813
13 TraesCS6B01G232400 chr5B 460760000 460762980 2980 False 468.000000 494 85.933333 4759 6239 3 chr5B.!!$F3 1480
14 TraesCS6B01G232400 chr2A 37024241 37030961 6720 True 1223.733333 3742 95.347000 810 6483 6 chr2A.!!$R2 5673
15 TraesCS6B01G232400 chr1A 561613805 561620482 6677 False 1225.066667 3731 96.002167 818 6483 6 chr1A.!!$F2 5665
16 TraesCS6B01G232400 chr3A 10617464 10625590 8126 False 1166.975000 3066 95.251500 864 6867 8 chr3A.!!$F2 6003
17 TraesCS6B01G232400 chr7A 673056150 673057141 991 False 1467.000000 1467 93.888000 1504 2466 1 chr7A.!!$F3 962
18 TraesCS6B01G232400 chr7A 673064054 673067584 3530 False 1157.000000 2536 96.673000 2496 4696 3 chr7A.!!$F5 2200
19 TraesCS6B01G232400 chr7A 673032621 673033535 914 False 349.500000 355 93.159500 817 1329 2 chr7A.!!$F4 512
20 TraesCS6B01G232400 chr7B 263150748 263156598 5850 False 1400.000000 2488 93.498750 3013 6880 4 chr7B.!!$F6 3867
21 TraesCS6B01G232400 chr7B 213288231 213289057 826 False 1310.000000 1310 95.284000 3 828 1 chr7B.!!$F1 825
22 TraesCS6B01G232400 chr7B 253908737 253911122 2385 False 862.333333 1214 88.090667 4695 6466 3 chr7B.!!$F5 1771
23 TraesCS6B01G232400 chr7B 641176676 641177419 743 False 702.000000 702 84.301000 5453 6183 1 chr7B.!!$F4 730
24 TraesCS6B01G232400 chr5A 406671364 406672276 912 True 1411.000000 1411 94.754000 3016 3919 1 chr5A.!!$R2 903
25 TraesCS6B01G232400 chr5A 328542152 328545498 3346 False 635.500000 713 87.701000 1088 6868 2 chr5A.!!$F2 5780
26 TraesCS6B01G232400 chr5A 110282797 110284238 1441 False 362.500000 473 83.173500 1303 2432 2 chr5A.!!$F1 1129
27 TraesCS6B01G232400 chr5D 312607661 312608570 909 True 1387.000000 1387 94.292000 3016 3919 1 chr5D.!!$R1 903
28 TraesCS6B01G232400 chr4B 485482750 485483560 810 False 1293.000000 1293 95.443000 1 811 1 chr4B.!!$F2 810
29 TraesCS6B01G232400 chr4B 169837408 169838219 811 True 1290.000000 1290 95.320000 1 812 1 chr4B.!!$R1 811
30 TraesCS6B01G232400 chr1B 372094988 372099421 4433 True 433.142857 898 92.295286 818 6867 7 chr1B.!!$R4 6049
31 TraesCS6B01G232400 chr2D 461541873 461542683 810 False 774.000000 774 84.394000 5433 6239 1 chr2D.!!$F1 806
32 TraesCS6B01G232400 chr1D 376893091 376893900 809 False 767.000000 767 84.293000 5433 6239 1 chr1D.!!$F2 806

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
880 886 0.524414 GGCCACGTCGCCTTTAATTT 59.476 50.000 17.69 0.00 46.10 1.82 F
1454 1987 0.464373 CAGGGCCACGACAGCATAAT 60.464 55.000 6.18 0.00 0.00 1.28 F
1949 2850 3.456644 TCCATTTAGGCCTGTTTATCCGA 59.543 43.478 17.99 0.00 37.29 4.55 F
2742 3826 5.295152 AGTTCGGTTGTAGAAGAACGAAAT 58.705 37.500 7.85 5.22 45.27 2.17 F
4350 7517 0.042131 ATGTACTCCCTCCGTTCCCA 59.958 55.000 0.00 0.00 0.00 4.37 F
4452 7619 0.034756 TTGTGCCGCATGTAGTCACT 59.965 50.000 0.00 0.00 0.00 3.41 F
4455 7622 0.034756 TGCCGCATGTAGTCACTTGT 59.965 50.000 0.00 0.00 33.46 3.16 F
4920 9729 0.981183 TAGGTGTGATGGTGGTGGTC 59.019 55.000 0.00 0.00 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2527 3610 1.370900 CTTGTGACAAAGCGGCTGC 60.371 57.895 10.33 10.33 43.24 5.25 R
2742 3826 2.104622 TGACTTCCTGATGTGTGCTTCA 59.895 45.455 0.00 0.00 0.00 3.02 R
3148 5821 3.433740 GGTGTGAAAGGTTCTTGAGGAGT 60.434 47.826 0.00 0.00 0.00 3.85 R
4433 7600 0.034756 AGTGACTACATGCGGCACAA 59.965 50.000 20.04 0.00 32.16 3.33 R
6242 13025 1.072391 CGCATGCTGGTACAACGTTA 58.928 50.000 17.13 0.00 38.70 3.18 R
6247 13030 1.375853 GATGCCGCATGCTGGTACAA 61.376 55.000 23.32 11.71 42.00 2.41 R
6265 13048 1.550072 TCTCAAGCATCATGTCACCGA 59.450 47.619 0.00 0.00 0.00 4.69 R
6512 14247 0.671251 TTGCGTTAGGCTTTGGTTGG 59.329 50.000 0.00 0.00 44.05 3.77 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
49 50 2.295885 GGCAGCAGAGCTAAATCATGT 58.704 47.619 0.00 0.00 36.40 3.21
89 90 0.811616 GATCGGCTGTGGCTCGAATT 60.812 55.000 0.00 0.00 41.55 2.17
151 152 3.710209 AGACTTCCAAATCTGACCTGG 57.290 47.619 0.00 0.00 0.00 4.45
155 156 1.198094 TCCAAATCTGACCTGGCGGA 61.198 55.000 0.00 0.00 0.00 5.54
264 265 0.763223 AAAGTCTCACCCTGGACCGT 60.763 55.000 0.00 0.00 33.39 4.83
301 302 1.346068 GAAGGAGCCATCGAGCCTATT 59.654 52.381 0.00 0.00 0.00 1.73
373 374 1.075450 GGTGGATCTCGGGTAGGGT 60.075 63.158 0.00 0.00 0.00 4.34
545 546 4.371681 AGATCAAGGAGGCTAAACCCTAA 58.628 43.478 0.00 0.00 40.58 2.69
637 643 3.206866 AGGGCTAGGGTTACATAGAGTCA 59.793 47.826 0.00 0.00 0.00 3.41
653 659 7.565398 ACATAGAGTCAGTTACAATGGTAGGAT 59.435 37.037 0.00 0.00 0.00 3.24
680 686 2.902705 TATCCGTATCGCCAAGCTTT 57.097 45.000 0.00 0.00 0.00 3.51
758 764 3.964411 TCTTCATAGTCTTGGAGTCCGA 58.036 45.455 4.30 0.84 0.00 4.55
834 840 5.660417 ACATGGCATTGAACATATAAACCCA 59.340 36.000 0.00 0.00 0.00 4.51
880 886 0.524414 GGCCACGTCGCCTTTAATTT 59.476 50.000 17.69 0.00 46.10 1.82
904 910 3.603532 CATGAACAGTACTCATGCCACT 58.396 45.455 9.80 0.00 42.63 4.00
1031 1038 4.779733 GCCTCCCCCTCCTCGTCA 62.780 72.222 0.00 0.00 0.00 4.35
1201 1638 1.381327 GGAGGGGTGGATGAGACGA 60.381 63.158 0.00 0.00 0.00 4.20
1204 1641 1.381327 GGGGTGGATGAGACGAGGA 60.381 63.158 0.00 0.00 0.00 3.71
1232 1669 2.043248 GGAGAGAGTGGGGGCGTA 60.043 66.667 0.00 0.00 0.00 4.42
1320 1830 1.610673 AGCCTGTGGGATGTCGACT 60.611 57.895 17.92 1.84 33.58 4.18
1339 1872 3.838271 GACCGGCAGCGATGGAGA 61.838 66.667 0.00 0.00 0.00 3.71
1422 1955 1.967535 CGACCACCTGAGCTTCTCA 59.032 57.895 0.00 0.00 38.25 3.27
1454 1987 0.464373 CAGGGCCACGACAGCATAAT 60.464 55.000 6.18 0.00 0.00 1.28
1632 2185 5.477291 TGGTTACTTGTGGAGAGTAGAAGAG 59.523 44.000 0.00 0.00 31.74 2.85
1679 2234 5.146010 AGATGAACAAGGTGAACTCTCTC 57.854 43.478 0.00 0.00 0.00 3.20
1681 2236 4.592485 TGAACAAGGTGAACTCTCTCTC 57.408 45.455 0.00 0.00 0.00 3.20
1682 2237 4.219115 TGAACAAGGTGAACTCTCTCTCT 58.781 43.478 0.00 0.00 0.00 3.10
1683 2238 4.279671 TGAACAAGGTGAACTCTCTCTCTC 59.720 45.833 0.00 0.00 0.00 3.20
1922 2519 4.724293 TCATAATTGTACATCCACCCTCCA 59.276 41.667 0.00 0.00 0.00 3.86
1927 2524 4.396357 TGTACATCCACCCTCCATTTTT 57.604 40.909 0.00 0.00 0.00 1.94
1949 2850 3.456644 TCCATTTAGGCCTGTTTATCCGA 59.543 43.478 17.99 0.00 37.29 4.55
2301 3379 7.039011 TGTCCTGTGTACTCATTCTAAACAGAT 60.039 37.037 0.00 0.00 36.51 2.90
2347 3430 8.268850 TGCTTTACAGTTAATCCTCTCAAATC 57.731 34.615 0.00 0.00 0.00 2.17
2367 3450 9.179552 TCAAATCAAATACAGTGAAATCAAACG 57.820 29.630 0.00 0.00 0.00 3.60
2521 3604 6.699575 ACCCTTCTTAATTGTCACATATGC 57.300 37.500 1.58 0.00 0.00 3.14
2527 3610 7.543947 TCTTAATTGTCACATATGCACAGAG 57.456 36.000 1.58 3.98 0.00 3.35
2742 3826 5.295152 AGTTCGGTTGTAGAAGAACGAAAT 58.705 37.500 7.85 5.22 45.27 2.17
2802 3886 8.745837 CAACAACAACAAAAGTAAGTGATGATC 58.254 33.333 0.00 0.00 0.00 2.92
3148 5821 6.240549 AGAGAACTTGAGGAAGAAGTGAAA 57.759 37.500 0.00 0.00 33.85 2.69
3190 5863 5.130350 CACCCCAATATTGTGGTTAGTAGG 58.870 45.833 18.76 7.15 36.78 3.18
3358 6035 2.427453 GGTCTATCCAGTCGCTTCTTGA 59.573 50.000 0.00 0.00 35.97 3.02
3439 6117 4.848562 TTGACTCGCAGAAGAGAAACTA 57.151 40.909 0.62 0.00 40.57 2.24
3447 6125 5.694910 TCGCAGAAGAGAAACTAATTCGTTT 59.305 36.000 7.74 7.74 43.15 3.60
3481 6159 9.877222 TGATCAGGTCATTAGGAAGTATACTAA 57.123 33.333 5.65 0.00 34.07 2.24
3509 6187 5.659440 TTTTGCAAGGGTTGGAATATCTC 57.341 39.130 0.00 0.00 40.72 2.75
3529 6207 6.726258 TCTCCATAGCAATGCAATAATACG 57.274 37.500 8.35 0.00 0.00 3.06
3623 6306 7.056006 TGTGCTAATTATCTTGGTGATCATGT 58.944 34.615 0.00 0.00 36.65 3.21
3682 6440 1.226773 GGCTGCATTAAGCTTGCCG 60.227 57.895 9.86 2.29 46.93 5.69
3744 6502 9.399797 AGATTGATGTTCAATATGCTGTTAAGA 57.600 29.630 2.87 0.00 46.20 2.10
3932 7093 3.644966 AGTGTGAGTTTGGTTCCAAGA 57.355 42.857 4.44 0.00 0.00 3.02
3954 7115 6.963322 AGAAGGCTTATGGTAATGTTCTCTT 58.037 36.000 0.00 0.00 0.00 2.85
4333 7500 5.820131 TCTTCGCTGTAATTATTTGCCATG 58.180 37.500 0.00 0.00 0.00 3.66
4334 7501 5.356751 TCTTCGCTGTAATTATTTGCCATGT 59.643 36.000 0.00 0.00 0.00 3.21
4335 7502 6.540551 TCTTCGCTGTAATTATTTGCCATGTA 59.459 34.615 0.00 0.00 0.00 2.29
4336 7503 6.055231 TCGCTGTAATTATTTGCCATGTAC 57.945 37.500 0.00 0.00 0.00 2.90
4337 7504 5.820423 TCGCTGTAATTATTTGCCATGTACT 59.180 36.000 0.00 0.00 0.00 2.73
4338 7505 6.018262 TCGCTGTAATTATTTGCCATGTACTC 60.018 38.462 0.00 0.00 0.00 2.59
4339 7506 6.438763 GCTGTAATTATTTGCCATGTACTCC 58.561 40.000 0.00 0.00 0.00 3.85
4340 7507 6.515035 GCTGTAATTATTTGCCATGTACTCCC 60.515 42.308 0.00 0.00 0.00 4.30
4341 7508 6.668645 TGTAATTATTTGCCATGTACTCCCT 58.331 36.000 0.00 0.00 0.00 4.20
4342 7509 6.770785 TGTAATTATTTGCCATGTACTCCCTC 59.229 38.462 0.00 0.00 0.00 4.30
4343 7510 2.736670 ATTTGCCATGTACTCCCTCC 57.263 50.000 0.00 0.00 0.00 4.30
4344 7511 0.251916 TTTGCCATGTACTCCCTCCG 59.748 55.000 0.00 0.00 0.00 4.63
4345 7512 0.907704 TTGCCATGTACTCCCTCCGT 60.908 55.000 0.00 0.00 0.00 4.69
4346 7513 0.907704 TGCCATGTACTCCCTCCGTT 60.908 55.000 0.00 0.00 0.00 4.44
4347 7514 0.179081 GCCATGTACTCCCTCCGTTC 60.179 60.000 0.00 0.00 0.00 3.95
4348 7515 0.464452 CCATGTACTCCCTCCGTTCC 59.536 60.000 0.00 0.00 0.00 3.62
4349 7516 0.464452 CATGTACTCCCTCCGTTCCC 59.536 60.000 0.00 0.00 0.00 3.97
4350 7517 0.042131 ATGTACTCCCTCCGTTCCCA 59.958 55.000 0.00 0.00 0.00 4.37
4351 7518 0.178926 TGTACTCCCTCCGTTCCCAA 60.179 55.000 0.00 0.00 0.00 4.12
4352 7519 0.978907 GTACTCCCTCCGTTCCCAAA 59.021 55.000 0.00 0.00 0.00 3.28
4353 7520 1.558294 GTACTCCCTCCGTTCCCAAAT 59.442 52.381 0.00 0.00 0.00 2.32
4354 7521 1.961133 ACTCCCTCCGTTCCCAAATA 58.039 50.000 0.00 0.00 0.00 1.40
4355 7522 1.558294 ACTCCCTCCGTTCCCAAATAC 59.442 52.381 0.00 0.00 0.00 1.89
4356 7523 1.838077 CTCCCTCCGTTCCCAAATACT 59.162 52.381 0.00 0.00 0.00 2.12
4357 7524 2.238898 CTCCCTCCGTTCCCAAATACTT 59.761 50.000 0.00 0.00 0.00 2.24
4358 7525 2.026636 TCCCTCCGTTCCCAAATACTTG 60.027 50.000 0.00 0.00 0.00 3.16
4359 7526 2.290705 CCCTCCGTTCCCAAATACTTGT 60.291 50.000 0.00 0.00 0.00 3.16
4360 7527 3.007635 CCTCCGTTCCCAAATACTTGTC 58.992 50.000 0.00 0.00 0.00 3.18
4361 7528 3.007635 CTCCGTTCCCAAATACTTGTCC 58.992 50.000 0.00 0.00 0.00 4.02
4362 7529 2.640826 TCCGTTCCCAAATACTTGTCCT 59.359 45.455 0.00 0.00 0.00 3.85
4363 7530 3.073356 TCCGTTCCCAAATACTTGTCCTT 59.927 43.478 0.00 0.00 0.00 3.36
4364 7531 3.439129 CCGTTCCCAAATACTTGTCCTTC 59.561 47.826 0.00 0.00 0.00 3.46
4365 7532 4.324267 CGTTCCCAAATACTTGTCCTTCT 58.676 43.478 0.00 0.00 0.00 2.85
4366 7533 5.484715 CGTTCCCAAATACTTGTCCTTCTA 58.515 41.667 0.00 0.00 0.00 2.10
4367 7534 5.581085 CGTTCCCAAATACTTGTCCTTCTAG 59.419 44.000 0.00 0.00 0.00 2.43
4368 7535 5.693769 TCCCAAATACTTGTCCTTCTAGG 57.306 43.478 0.00 0.00 36.46 3.02
4369 7536 4.080526 TCCCAAATACTTGTCCTTCTAGGC 60.081 45.833 0.00 0.00 34.61 3.93
4370 7537 4.324254 CCCAAATACTTGTCCTTCTAGGCA 60.324 45.833 0.00 0.00 34.61 4.75
4371 7538 5.440610 CCAAATACTTGTCCTTCTAGGCAT 58.559 41.667 0.00 0.00 34.61 4.40
4372 7539 5.888161 CCAAATACTTGTCCTTCTAGGCATT 59.112 40.000 0.00 0.00 34.61 3.56
4373 7540 6.378280 CCAAATACTTGTCCTTCTAGGCATTT 59.622 38.462 0.00 0.00 34.61 2.32
4374 7541 7.415653 CCAAATACTTGTCCTTCTAGGCATTTC 60.416 40.741 0.00 0.00 34.61 2.17
4375 7542 4.640771 ACTTGTCCTTCTAGGCATTTCA 57.359 40.909 0.00 0.00 34.61 2.69
4376 7543 4.985538 ACTTGTCCTTCTAGGCATTTCAA 58.014 39.130 0.00 0.00 34.61 2.69
4377 7544 5.385198 ACTTGTCCTTCTAGGCATTTCAAA 58.615 37.500 0.00 0.00 34.61 2.69
4378 7545 6.012745 ACTTGTCCTTCTAGGCATTTCAAAT 58.987 36.000 0.00 0.00 34.61 2.32
4379 7546 5.902613 TGTCCTTCTAGGCATTTCAAATG 57.097 39.130 5.68 5.68 34.61 2.32
4380 7547 4.706476 TGTCCTTCTAGGCATTTCAAATGG 59.294 41.667 12.14 0.00 34.61 3.16
4381 7548 4.949856 GTCCTTCTAGGCATTTCAAATGGA 59.050 41.667 12.14 0.00 34.61 3.41
4382 7549 4.949856 TCCTTCTAGGCATTTCAAATGGAC 59.050 41.667 12.14 0.00 34.61 4.02
4383 7550 4.952335 CCTTCTAGGCATTTCAAATGGACT 59.048 41.667 12.14 3.08 0.00 3.85
4384 7551 5.067023 CCTTCTAGGCATTTCAAATGGACTC 59.933 44.000 12.14 0.00 0.00 3.36
4385 7552 5.178096 TCTAGGCATTTCAAATGGACTCA 57.822 39.130 12.14 0.00 0.00 3.41
4386 7553 5.569355 TCTAGGCATTTCAAATGGACTCAA 58.431 37.500 12.14 0.00 0.00 3.02
4387 7554 4.525912 AGGCATTTCAAATGGACTCAAC 57.474 40.909 12.14 0.00 0.00 3.18
4388 7555 3.896888 AGGCATTTCAAATGGACTCAACA 59.103 39.130 12.14 0.00 0.00 3.33
4389 7556 4.529377 AGGCATTTCAAATGGACTCAACAT 59.471 37.500 12.14 0.00 0.00 2.71
4390 7557 5.716228 AGGCATTTCAAATGGACTCAACATA 59.284 36.000 12.14 0.00 0.00 2.29
4391 7558 5.807011 GGCATTTCAAATGGACTCAACATAC 59.193 40.000 12.14 0.00 0.00 2.39
4392 7559 5.512788 GCATTTCAAATGGACTCAACATACG 59.487 40.000 12.14 0.00 0.00 3.06
4393 7560 5.621197 TTTCAAATGGACTCAACATACGG 57.379 39.130 0.00 0.00 0.00 4.02
4394 7561 4.545208 TCAAATGGACTCAACATACGGA 57.455 40.909 0.00 0.00 0.00 4.69
4395 7562 5.097742 TCAAATGGACTCAACATACGGAT 57.902 39.130 0.00 0.00 0.00 4.18
4396 7563 4.875536 TCAAATGGACTCAACATACGGATG 59.124 41.667 5.94 5.94 39.16 3.51
4398 7565 5.607939 AATGGACTCAACATACGGATGTA 57.392 39.130 15.10 0.00 45.93 2.29
4399 7566 5.808366 ATGGACTCAACATACGGATGTAT 57.192 39.130 15.10 0.00 45.93 2.29
4400 7567 6.911250 ATGGACTCAACATACGGATGTATA 57.089 37.500 15.10 4.17 45.93 1.47
4401 7568 6.911250 TGGACTCAACATACGGATGTATAT 57.089 37.500 15.10 0.00 45.93 0.86
4402 7569 8.589701 ATGGACTCAACATACGGATGTATATA 57.410 34.615 15.10 0.00 45.93 0.86
4403 7570 8.051901 TGGACTCAACATACGGATGTATATAG 57.948 38.462 15.10 11.28 45.93 1.31
4404 7571 7.886446 TGGACTCAACATACGGATGTATATAGA 59.114 37.037 15.10 6.65 45.93 1.98
4405 7572 8.182881 GGACTCAACATACGGATGTATATAGAC 58.817 40.741 15.10 9.13 45.93 2.59
4406 7573 8.631480 ACTCAACATACGGATGTATATAGACA 57.369 34.615 15.10 2.07 45.93 3.41
4407 7574 9.244292 ACTCAACATACGGATGTATATAGACAT 57.756 33.333 15.10 12.70 45.93 3.06
4438 7605 8.524870 AAAGTGTAGATTCATTCATTTTGTGC 57.475 30.769 0.00 0.00 0.00 4.57
4439 7606 6.624423 AGTGTAGATTCATTCATTTTGTGCC 58.376 36.000 0.00 0.00 0.00 5.01
4440 7607 5.512788 GTGTAGATTCATTCATTTTGTGCCG 59.487 40.000 0.00 0.00 0.00 5.69
4441 7608 3.514645 AGATTCATTCATTTTGTGCCGC 58.485 40.909 0.00 0.00 0.00 6.53
4442 7609 2.808523 TTCATTCATTTTGTGCCGCA 57.191 40.000 0.00 0.00 0.00 5.69
4443 7610 3.316071 TTCATTCATTTTGTGCCGCAT 57.684 38.095 0.00 0.00 0.00 4.73
4444 7611 2.608268 TCATTCATTTTGTGCCGCATG 58.392 42.857 0.00 0.00 0.00 4.06
4445 7612 2.029200 TCATTCATTTTGTGCCGCATGT 60.029 40.909 0.00 0.00 0.00 3.21
4446 7613 3.192212 TCATTCATTTTGTGCCGCATGTA 59.808 39.130 0.00 0.00 0.00 2.29
4447 7614 2.917701 TCATTTTGTGCCGCATGTAG 57.082 45.000 0.00 0.00 0.00 2.74
4448 7615 2.158559 TCATTTTGTGCCGCATGTAGT 58.841 42.857 0.00 0.00 0.00 2.73
4449 7616 2.161410 TCATTTTGTGCCGCATGTAGTC 59.839 45.455 0.00 0.00 0.00 2.59
4450 7617 1.598882 TTTTGTGCCGCATGTAGTCA 58.401 45.000 0.00 0.00 0.00 3.41
4451 7618 0.871722 TTTGTGCCGCATGTAGTCAC 59.128 50.000 0.00 0.00 0.00 3.67
4452 7619 0.034756 TTGTGCCGCATGTAGTCACT 59.965 50.000 0.00 0.00 0.00 3.41
4453 7620 0.034756 TGTGCCGCATGTAGTCACTT 59.965 50.000 0.00 0.00 0.00 3.16
4454 7621 0.443869 GTGCCGCATGTAGTCACTTG 59.556 55.000 0.00 0.00 33.92 3.16
4455 7622 0.034756 TGCCGCATGTAGTCACTTGT 59.965 50.000 0.00 0.00 33.46 3.16
4456 7623 1.156736 GCCGCATGTAGTCACTTGTT 58.843 50.000 0.00 0.00 33.46 2.83
4457 7624 1.135972 GCCGCATGTAGTCACTTGTTG 60.136 52.381 0.00 0.00 33.46 3.33
4458 7625 2.412870 CCGCATGTAGTCACTTGTTGA 58.587 47.619 0.00 0.00 33.46 3.18
4459 7626 2.805671 CCGCATGTAGTCACTTGTTGAA 59.194 45.455 0.00 0.00 35.39 2.69
4460 7627 3.249799 CCGCATGTAGTCACTTGTTGAAA 59.750 43.478 0.00 0.00 35.39 2.69
4461 7628 4.083324 CCGCATGTAGTCACTTGTTGAAAT 60.083 41.667 0.00 0.00 35.39 2.17
4462 7629 5.082059 CGCATGTAGTCACTTGTTGAAATC 58.918 41.667 0.00 0.00 35.39 2.17
4463 7630 5.106948 CGCATGTAGTCACTTGTTGAAATCT 60.107 40.000 0.00 0.00 35.39 2.40
4464 7631 6.310197 GCATGTAGTCACTTGTTGAAATCTC 58.690 40.000 0.00 0.00 35.39 2.75
4465 7632 6.148480 GCATGTAGTCACTTGTTGAAATCTCT 59.852 38.462 0.00 0.00 35.39 3.10
4466 7633 7.331934 GCATGTAGTCACTTGTTGAAATCTCTA 59.668 37.037 0.00 0.00 35.39 2.43
4467 7634 9.208022 CATGTAGTCACTTGTTGAAATCTCTAA 57.792 33.333 0.00 0.00 35.39 2.10
4468 7635 9.778741 ATGTAGTCACTTGTTGAAATCTCTAAA 57.221 29.630 0.00 0.00 35.39 1.85
4469 7636 9.607988 TGTAGTCACTTGTTGAAATCTCTAAAA 57.392 29.630 0.00 0.00 35.39 1.52
4472 7639 9.396022 AGTCACTTGTTGAAATCTCTAAAAAGA 57.604 29.630 0.00 0.00 35.39 2.52
4473 7640 9.439537 GTCACTTGTTGAAATCTCTAAAAAGAC 57.560 33.333 0.00 0.00 35.39 3.01
4474 7641 9.173021 TCACTTGTTGAAATCTCTAAAAAGACA 57.827 29.630 0.00 0.00 0.00 3.41
4475 7642 9.787532 CACTTGTTGAAATCTCTAAAAAGACAA 57.212 29.630 0.00 0.00 0.00 3.18
4492 7659 8.622948 AAAAGACAAGTATTTAGGAACAGAGG 57.377 34.615 0.00 0.00 0.00 3.69
4493 7660 6.301169 AGACAAGTATTTAGGAACAGAGGG 57.699 41.667 0.00 0.00 0.00 4.30
4494 7661 6.023603 AGACAAGTATTTAGGAACAGAGGGA 58.976 40.000 0.00 0.00 0.00 4.20
4535 7703 7.977853 ACATGTCAAAATATGCTTTGAAGATCC 59.022 33.333 4.51 0.00 44.66 3.36
4547 7715 5.851703 GCTTTGAAGATCCGTTTCTTACAAC 59.148 40.000 0.00 0.00 36.10 3.32
4660 7828 6.764308 ATCACAAACCCTCAATAATGTCTG 57.236 37.500 0.00 0.00 0.00 3.51
4661 7829 5.630121 TCACAAACCCTCAATAATGTCTGT 58.370 37.500 0.00 0.00 0.00 3.41
4692 7878 6.808321 TTTACCAGCTCTGAGGTATTACAT 57.192 37.500 9.32 0.00 39.92 2.29
4693 7879 4.679373 ACCAGCTCTGAGGTATTACATG 57.321 45.455 9.32 0.00 36.07 3.21
4777 9583 5.418840 TGCTTATCTTTGGAAATCTTCACCC 59.581 40.000 0.00 0.00 0.00 4.61
4920 9729 0.981183 TAGGTGTGATGGTGGTGGTC 59.019 55.000 0.00 0.00 0.00 4.02
5473 10528 8.727149 TGATATGAAAGGGGAAATAGACAGAAT 58.273 33.333 0.00 0.00 0.00 2.40
5493 10548 9.632638 ACAGAATAGTGAAAATTATGTGGCTAT 57.367 29.630 0.00 0.00 37.38 2.97
6161 12942 1.227645 ATCGGTGACATGATGCCGG 60.228 57.895 19.90 0.00 43.87 6.13
6241 13024 3.044305 GCAGCGGCTCGAGTTGTT 61.044 61.111 15.13 1.78 36.96 2.83
6242 13025 2.607892 GCAGCGGCTCGAGTTGTTT 61.608 57.895 15.13 0.00 36.96 2.83
6243 13026 1.289109 GCAGCGGCTCGAGTTGTTTA 61.289 55.000 15.13 0.00 36.96 2.01
6245 13028 1.136336 CAGCGGCTCGAGTTGTTTAAC 60.136 52.381 15.13 0.00 37.06 2.01
6247 13030 1.134226 CGGCTCGAGTTGTTTAACGT 58.866 50.000 15.13 0.00 41.71 3.99
6248 13031 1.523934 CGGCTCGAGTTGTTTAACGTT 59.476 47.619 15.13 5.88 41.71 3.99
6249 13032 2.658224 CGGCTCGAGTTGTTTAACGTTG 60.658 50.000 15.13 0.00 41.71 4.10
6250 13033 2.286025 GGCTCGAGTTGTTTAACGTTGT 59.714 45.455 15.13 0.00 41.71 3.32
6251 13034 3.490526 GGCTCGAGTTGTTTAACGTTGTA 59.509 43.478 15.13 0.00 41.71 2.41
6252 13035 4.440068 GCTCGAGTTGTTTAACGTTGTAC 58.560 43.478 15.13 9.24 41.71 2.90
6253 13036 4.606894 GCTCGAGTTGTTTAACGTTGTACC 60.607 45.833 15.13 0.00 41.71 3.34
6255 13038 4.503734 TCGAGTTGTTTAACGTTGTACCAG 59.496 41.667 11.99 0.00 41.71 4.00
6256 13039 4.521010 GAGTTGTTTAACGTTGTACCAGC 58.479 43.478 11.99 4.62 41.71 4.85
6257 13040 3.940221 AGTTGTTTAACGTTGTACCAGCA 59.060 39.130 11.99 0.00 41.71 4.41
6262 13045 1.573829 AACGTTGTACCAGCATGCGG 61.574 55.000 21.83 21.83 31.97 5.69
6263 13046 2.485122 GTTGTACCAGCATGCGGC 59.515 61.111 22.90 11.90 45.30 6.53
6273 13056 2.819154 CATGCGGCATCGGTGACA 60.819 61.111 13.53 0.00 36.79 3.58
6274 13057 2.182181 CATGCGGCATCGGTGACAT 61.182 57.895 13.53 0.00 36.79 3.06
6275 13058 2.182181 ATGCGGCATCGGTGACATG 61.182 57.895 10.23 0.00 36.79 3.21
6277 13060 1.889105 GCGGCATCGGTGACATGAT 60.889 57.895 0.57 0.00 36.79 2.45
6282 13065 2.750301 CATCGGTGACATGATGCTTG 57.250 50.000 0.00 0.00 35.97 4.01
6283 13066 2.282407 CATCGGTGACATGATGCTTGA 58.718 47.619 0.00 0.00 35.97 3.02
6284 13067 2.014335 TCGGTGACATGATGCTTGAG 57.986 50.000 0.00 0.00 0.00 3.02
6286 13069 2.028203 TCGGTGACATGATGCTTGAGAA 60.028 45.455 0.00 0.00 0.00 2.87
6335 14065 2.623878 TGTTCGGGTGACAAGCTTTA 57.376 45.000 0.00 0.00 0.00 1.85
6486 14221 4.348168 CACTACTATACTTGGCCATCCCTT 59.652 45.833 6.09 0.00 0.00 3.95
6520 14255 4.958897 CGGACCGGGCCAACCAAA 62.959 66.667 30.17 0.00 40.22 3.28
6521 14256 2.989253 GGACCGGGCCAACCAAAG 60.989 66.667 25.88 0.00 40.22 2.77
6522 14257 3.680786 GACCGGGCCAACCAAAGC 61.681 66.667 6.32 0.00 40.22 3.51
6528 14263 1.584495 GGCCAACCAAAGCCTAACG 59.416 57.895 0.00 0.00 46.14 3.18
6529 14264 1.080772 GCCAACCAAAGCCTAACGC 60.081 57.895 0.00 0.00 37.98 4.84
6530 14265 1.801309 GCCAACCAAAGCCTAACGCA 61.801 55.000 0.00 0.00 41.38 5.24
6531 14266 0.671251 CCAACCAAAGCCTAACGCAA 59.329 50.000 0.00 0.00 41.38 4.85
6532 14267 1.067821 CCAACCAAAGCCTAACGCAAA 59.932 47.619 0.00 0.00 41.38 3.68
6533 14268 2.482142 CCAACCAAAGCCTAACGCAAAA 60.482 45.455 0.00 0.00 41.38 2.44
6534 14269 3.190874 CAACCAAAGCCTAACGCAAAAA 58.809 40.909 0.00 0.00 41.38 1.94
6548 14283 2.520968 AAAAACCCAGGCTCGGCT 59.479 55.556 0.00 0.00 0.00 5.52
6549 14284 1.903404 AAAAACCCAGGCTCGGCTG 60.903 57.895 12.99 12.99 0.00 4.85
6550 14285 2.640581 AAAAACCCAGGCTCGGCTGT 62.641 55.000 17.62 0.00 0.00 4.40
6551 14286 3.553095 AAACCCAGGCTCGGCTGTC 62.553 63.158 17.62 0.00 0.00 3.51
6649 14465 0.679640 CCCATCACGCTAAAAGCCCA 60.680 55.000 0.00 0.00 38.18 5.36
6691 14507 4.276431 TCTTCCTTAAACGGCGAAAACAAT 59.724 37.500 16.62 0.00 0.00 2.71
6734 14550 1.172180 TGCTTCGGGCTCAAAACCTG 61.172 55.000 3.33 0.00 42.39 4.00
6769 14619 1.118965 TTTCAGCCCGAGTCTGGTCA 61.119 55.000 2.26 0.00 32.63 4.02
6835 14710 4.686091 CCATCATCGCTTCTAATTCGCTTA 59.314 41.667 0.00 0.00 0.00 3.09
6915 14791 4.673580 GCTCATAGGATGCACACACAAAAG 60.674 45.833 0.00 0.00 0.00 2.27
6936 14812 4.561105 AGGCAACGAAAAAGACAAAACAA 58.439 34.783 0.00 0.00 46.39 2.83
6981 14857 9.645059 GCAGATTAACATCATATAGCACTCTTA 57.355 33.333 0.00 0.00 0.00 2.10
7026 14902 1.483415 GGATCCAAACAAGCATGGCAT 59.517 47.619 6.95 0.00 36.62 4.40
7105 14981 1.306148 CGGAGCTACATACACGGAGA 58.694 55.000 0.00 0.00 0.00 3.71
7118 14994 2.170397 ACACGGAGATATGGCATGACAA 59.830 45.455 4.70 0.00 0.00 3.18
7121 14997 3.134623 ACGGAGATATGGCATGACAAAGA 59.865 43.478 4.70 0.00 0.00 2.52
7122 14998 3.744942 CGGAGATATGGCATGACAAAGAG 59.255 47.826 4.70 0.00 0.00 2.85
7152 15028 8.356657 CACAAAATGTCATAAAACAGGGACTTA 58.643 33.333 0.00 0.00 34.60 2.24
7163 15039 3.744660 ACAGGGACTTAGCAGTTTTCTG 58.255 45.455 0.00 0.00 44.55 3.02
7237 15114 3.731728 GGGCTCACCATGGGCTCA 61.732 66.667 18.09 0.00 45.79 4.26
7262 15139 2.690510 AAGGAGGAGGAGGCAGGC 60.691 66.667 0.00 0.00 0.00 4.85
7263 15140 4.814041 AGGAGGAGGAGGCAGGCC 62.814 72.222 0.97 0.97 0.00 5.19
7411 15300 1.451028 GGCAGCAAGGAAGATCGCT 60.451 57.895 0.00 0.00 34.29 4.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 2.261361 CCGCACTGTCACGATGGA 59.739 61.111 0.00 0.00 0.00 3.41
89 90 2.671351 GCGGAGACTTGATCTTCAACGA 60.671 50.000 0.00 0.00 38.00 3.85
155 156 1.614241 ATCGAAAGCTACGCCCCTGT 61.614 55.000 8.11 0.00 0.00 4.00
216 217 2.034812 GGACAGATCTTCGTATTCGGCT 59.965 50.000 0.00 0.00 37.69 5.52
264 265 2.993220 CCTTCGATCATCAACAACGACA 59.007 45.455 0.00 0.00 32.89 4.35
301 302 2.230508 GAGTTCCTATGTGTCGTCACCA 59.769 50.000 10.28 0.00 43.26 4.17
314 315 4.041567 TGGTGCTTTCATTGAGAGTTCCTA 59.958 41.667 15.14 5.45 0.00 2.94
347 348 1.024579 CCGAGATCCACCGGTTTTGG 61.025 60.000 2.97 3.06 40.78 3.28
373 374 1.174078 TAGACGCACAGTTCGGGACA 61.174 55.000 0.00 0.00 0.00 4.02
545 546 6.192970 ACAATCATACCATAGGCTAGCTTT 57.807 37.500 15.72 6.10 0.00 3.51
653 659 5.220989 GCTTGGCGATACGGATATGTAGATA 60.221 44.000 0.00 0.00 0.00 1.98
680 686 1.975680 ACTTTCCTTGGCGTAGAAGGA 59.024 47.619 7.59 7.59 45.99 3.36
801 807 1.355381 TCAATGCCATGTGAGGGAGTT 59.645 47.619 0.00 0.00 30.31 3.01
834 840 5.707242 TCGTTGTGACTATGAGTTCTTCT 57.293 39.130 0.00 0.00 0.00 2.85
904 910 0.885196 GGGCACGAAAATAACAGGCA 59.115 50.000 0.00 0.00 0.00 4.75
1031 1038 2.127708 GAGAGAGAGAGAGAGGAGGGT 58.872 57.143 0.00 0.00 0.00 4.34
1127 1554 3.141488 GGAGGCGAGCTTCTCCGA 61.141 66.667 13.50 0.00 39.95 4.55
1201 1638 0.933700 CTCTCCTCCTCCTCCTTCCT 59.066 60.000 0.00 0.00 0.00 3.36
1204 1641 1.287739 CACTCTCTCCTCCTCCTCCTT 59.712 57.143 0.00 0.00 0.00 3.36
1361 1894 3.710722 CCAGCTTCTCCCGCCTGT 61.711 66.667 0.00 0.00 0.00 4.00
1422 1955 2.703007 GTGGCCCTGTCTAGATCAATCT 59.297 50.000 0.00 0.00 40.86 2.40
1470 2003 1.973812 GTGGCTTCAGAGGGTTGCC 60.974 63.158 0.00 0.00 43.49 4.52
1597 2150 6.878317 TCCACAAGTAACCAGAATATGAGAG 58.122 40.000 0.00 0.00 0.00 3.20
1679 2234 8.612619 GTGACTGTATTTAAGAGAGAGAGAGAG 58.387 40.741 0.00 0.00 0.00 3.20
1681 2236 7.406553 CGTGACTGTATTTAAGAGAGAGAGAG 58.593 42.308 0.00 0.00 0.00 3.20
1682 2237 6.183360 GCGTGACTGTATTTAAGAGAGAGAGA 60.183 42.308 0.00 0.00 0.00 3.10
1683 2238 5.968848 GCGTGACTGTATTTAAGAGAGAGAG 59.031 44.000 0.00 0.00 0.00 3.20
1922 2519 7.564793 GGATAAACAGGCCTAAATGGAAAAAT 58.435 34.615 3.98 0.00 38.35 1.82
1927 2524 3.456644 TCGGATAAACAGGCCTAAATGGA 59.543 43.478 3.98 0.00 38.35 3.41
1974 3007 9.342308 TGGCTGATTACTAATTTCCTAAATCTG 57.658 33.333 0.00 0.00 0.00 2.90
2301 3379 6.115446 AGCATCGTTAGATTCCTGAATTTGA 58.885 36.000 0.00 0.00 34.23 2.69
2367 3450 7.063426 GGAAACAAACAGCCAAGCTATTAAATC 59.937 37.037 0.00 0.00 36.40 2.17
2527 3610 1.370900 CTTGTGACAAAGCGGCTGC 60.371 57.895 10.33 10.33 43.24 5.25
2637 3720 8.308207 TCGATGGATGGTAATTATATTCGAACA 58.692 33.333 0.00 0.00 0.00 3.18
2742 3826 2.104622 TGACTTCCTGATGTGTGCTTCA 59.895 45.455 0.00 0.00 0.00 3.02
2802 3886 8.455903 AACAACCATATCAGAGATAAACATGG 57.544 34.615 0.00 5.42 37.93 3.66
3148 5821 3.433740 GGTGTGAAAGGTTCTTGAGGAGT 60.434 47.826 0.00 0.00 0.00 3.85
3439 6117 7.094975 TGACCTGATCAAAATACGAAACGAATT 60.095 33.333 0.00 0.00 33.02 2.17
3447 6125 7.119709 TCCTAATGACCTGATCAAAATACGA 57.880 36.000 0.00 0.00 41.93 3.43
3509 6187 7.545615 TCTCTACGTATTATTGCATTGCTATGG 59.454 37.037 14.61 3.19 32.15 2.74
3529 6207 9.924650 TCAGAGTTTTTACCTTAATGTCTCTAC 57.075 33.333 0.00 0.00 0.00 2.59
3623 6306 4.160439 TGTTTGCACCCTGTAAAACAATCA 59.840 37.500 0.00 0.00 33.94 2.57
3682 6440 6.564328 CAACTTACTTAGATGCCCCAAAATC 58.436 40.000 0.00 0.00 0.00 2.17
3932 7093 6.721318 TGAAGAGAACATTACCATAAGCCTT 58.279 36.000 0.00 0.00 0.00 4.35
3954 7115 6.486657 GCAGGAACTATAATGCAAATACCTGA 59.513 38.462 20.53 0.00 42.22 3.86
4333 7500 0.978907 TTTGGGAACGGAGGGAGTAC 59.021 55.000 0.00 0.00 0.00 2.73
4334 7501 1.961133 ATTTGGGAACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
4335 7502 1.558294 GTATTTGGGAACGGAGGGAGT 59.442 52.381 0.00 0.00 0.00 3.85
4336 7503 1.838077 AGTATTTGGGAACGGAGGGAG 59.162 52.381 0.00 0.00 0.00 4.30
4337 7504 1.961133 AGTATTTGGGAACGGAGGGA 58.039 50.000 0.00 0.00 0.00 4.20
4338 7505 2.290705 ACAAGTATTTGGGAACGGAGGG 60.291 50.000 2.81 0.00 38.66 4.30
4339 7506 3.007635 GACAAGTATTTGGGAACGGAGG 58.992 50.000 2.81 0.00 38.66 4.30
4340 7507 3.007635 GGACAAGTATTTGGGAACGGAG 58.992 50.000 2.81 0.00 38.66 4.63
4341 7508 2.640826 AGGACAAGTATTTGGGAACGGA 59.359 45.455 2.81 0.00 38.66 4.69
4342 7509 3.067684 AGGACAAGTATTTGGGAACGG 57.932 47.619 2.81 0.00 38.66 4.44
4343 7510 4.324267 AGAAGGACAAGTATTTGGGAACG 58.676 43.478 2.81 0.00 38.66 3.95
4344 7511 5.880887 CCTAGAAGGACAAGTATTTGGGAAC 59.119 44.000 2.81 0.00 37.67 3.62
4345 7512 5.572885 GCCTAGAAGGACAAGTATTTGGGAA 60.573 44.000 2.81 0.00 37.67 3.97
4346 7513 4.080526 GCCTAGAAGGACAAGTATTTGGGA 60.081 45.833 2.81 0.00 37.67 4.37
4347 7514 4.200092 GCCTAGAAGGACAAGTATTTGGG 58.800 47.826 2.81 0.00 37.67 4.12
4348 7515 4.843728 TGCCTAGAAGGACAAGTATTTGG 58.156 43.478 2.81 0.00 37.67 3.28
4349 7516 7.121168 TGAAATGCCTAGAAGGACAAGTATTTG 59.879 37.037 0.00 0.00 37.67 2.32
4350 7517 7.175104 TGAAATGCCTAGAAGGACAAGTATTT 58.825 34.615 0.00 0.00 37.67 1.40
4351 7518 6.721318 TGAAATGCCTAGAAGGACAAGTATT 58.279 36.000 0.00 0.00 37.67 1.89
4352 7519 6.313519 TGAAATGCCTAGAAGGACAAGTAT 57.686 37.500 0.00 0.00 37.67 2.12
4353 7520 5.755409 TGAAATGCCTAGAAGGACAAGTA 57.245 39.130 0.00 0.00 37.67 2.24
4354 7521 4.640771 TGAAATGCCTAGAAGGACAAGT 57.359 40.909 0.00 0.00 37.67 3.16
4355 7522 5.964958 TTTGAAATGCCTAGAAGGACAAG 57.035 39.130 0.00 0.00 37.67 3.16
4356 7523 5.185635 CCATTTGAAATGCCTAGAAGGACAA 59.814 40.000 12.26 0.00 37.67 3.18
4357 7524 4.706476 CCATTTGAAATGCCTAGAAGGACA 59.294 41.667 12.26 0.00 37.67 4.02
4358 7525 4.949856 TCCATTTGAAATGCCTAGAAGGAC 59.050 41.667 12.26 0.00 37.67 3.85
4359 7526 4.949856 GTCCATTTGAAATGCCTAGAAGGA 59.050 41.667 12.26 0.00 37.67 3.36
4360 7527 4.952335 AGTCCATTTGAAATGCCTAGAAGG 59.048 41.667 12.26 0.00 38.80 3.46
4361 7528 5.649395 TGAGTCCATTTGAAATGCCTAGAAG 59.351 40.000 12.26 0.00 0.00 2.85
4362 7529 5.569355 TGAGTCCATTTGAAATGCCTAGAA 58.431 37.500 12.26 0.00 0.00 2.10
4363 7530 5.178096 TGAGTCCATTTGAAATGCCTAGA 57.822 39.130 12.26 1.83 0.00 2.43
4364 7531 5.183713 TGTTGAGTCCATTTGAAATGCCTAG 59.816 40.000 12.26 0.00 0.00 3.02
4365 7532 5.076182 TGTTGAGTCCATTTGAAATGCCTA 58.924 37.500 12.26 0.00 0.00 3.93
4366 7533 3.896888 TGTTGAGTCCATTTGAAATGCCT 59.103 39.130 12.26 9.70 0.00 4.75
4367 7534 4.255833 TGTTGAGTCCATTTGAAATGCC 57.744 40.909 12.26 5.23 0.00 4.40
4368 7535 5.512788 CGTATGTTGAGTCCATTTGAAATGC 59.487 40.000 12.26 0.23 0.00 3.56
4369 7536 6.029607 CCGTATGTTGAGTCCATTTGAAATG 58.970 40.000 10.84 10.84 0.00 2.32
4370 7537 5.943416 TCCGTATGTTGAGTCCATTTGAAAT 59.057 36.000 0.00 0.00 0.00 2.17
4371 7538 5.309638 TCCGTATGTTGAGTCCATTTGAAA 58.690 37.500 0.00 0.00 0.00 2.69
4372 7539 4.900684 TCCGTATGTTGAGTCCATTTGAA 58.099 39.130 0.00 0.00 0.00 2.69
4373 7540 4.545208 TCCGTATGTTGAGTCCATTTGA 57.455 40.909 0.00 0.00 0.00 2.69
4374 7541 4.635765 ACATCCGTATGTTGAGTCCATTTG 59.364 41.667 0.00 0.00 44.07 2.32
4375 7542 4.843728 ACATCCGTATGTTGAGTCCATTT 58.156 39.130 0.00 0.00 44.07 2.32
4376 7543 4.487714 ACATCCGTATGTTGAGTCCATT 57.512 40.909 0.00 0.00 44.07 3.16
4377 7544 5.808366 ATACATCCGTATGTTGAGTCCAT 57.192 39.130 0.00 0.00 44.07 3.41
4378 7545 6.911250 ATATACATCCGTATGTTGAGTCCA 57.089 37.500 0.00 0.00 44.07 4.02
4379 7546 8.182881 GTCTATATACATCCGTATGTTGAGTCC 58.817 40.741 0.00 0.00 44.07 3.85
4380 7547 8.727910 TGTCTATATACATCCGTATGTTGAGTC 58.272 37.037 0.00 0.00 44.07 3.36
4381 7548 8.631480 TGTCTATATACATCCGTATGTTGAGT 57.369 34.615 0.00 0.00 44.07 3.41
4412 7579 9.624697 GCACAAAATGAATGAATCTACACTTTA 57.375 29.630 0.00 0.00 0.00 1.85
4413 7580 7.599998 GGCACAAAATGAATGAATCTACACTTT 59.400 33.333 0.00 0.00 0.00 2.66
4414 7581 7.092716 GGCACAAAATGAATGAATCTACACTT 58.907 34.615 0.00 0.00 0.00 3.16
4415 7582 6.623549 CGGCACAAAATGAATGAATCTACACT 60.624 38.462 0.00 0.00 0.00 3.55
4416 7583 5.512788 CGGCACAAAATGAATGAATCTACAC 59.487 40.000 0.00 0.00 0.00 2.90
4417 7584 5.639757 CGGCACAAAATGAATGAATCTACA 58.360 37.500 0.00 0.00 0.00 2.74
4418 7585 4.500477 GCGGCACAAAATGAATGAATCTAC 59.500 41.667 0.00 0.00 0.00 2.59
4419 7586 4.157472 TGCGGCACAAAATGAATGAATCTA 59.843 37.500 0.00 0.00 0.00 1.98
4420 7587 3.056678 TGCGGCACAAAATGAATGAATCT 60.057 39.130 0.00 0.00 0.00 2.40
4421 7588 3.252400 TGCGGCACAAAATGAATGAATC 58.748 40.909 0.00 0.00 0.00 2.52
4422 7589 3.316071 TGCGGCACAAAATGAATGAAT 57.684 38.095 0.00 0.00 0.00 2.57
4423 7590 2.808523 TGCGGCACAAAATGAATGAA 57.191 40.000 0.00 0.00 0.00 2.57
4424 7591 2.029200 ACATGCGGCACAAAATGAATGA 60.029 40.909 4.03 0.00 0.00 2.57
4425 7592 2.339418 ACATGCGGCACAAAATGAATG 58.661 42.857 4.03 0.00 0.00 2.67
4426 7593 2.747396 ACATGCGGCACAAAATGAAT 57.253 40.000 4.03 0.00 0.00 2.57
4427 7594 2.556189 ACTACATGCGGCACAAAATGAA 59.444 40.909 4.03 0.00 0.00 2.57
4428 7595 2.158559 ACTACATGCGGCACAAAATGA 58.841 42.857 4.03 0.00 0.00 2.57
4429 7596 2.095314 TGACTACATGCGGCACAAAATG 60.095 45.455 4.03 1.18 0.00 2.32
4430 7597 2.095263 GTGACTACATGCGGCACAAAAT 60.095 45.455 14.78 0.00 0.00 1.82
4431 7598 1.265635 GTGACTACATGCGGCACAAAA 59.734 47.619 14.78 0.00 0.00 2.44
4432 7599 0.871722 GTGACTACATGCGGCACAAA 59.128 50.000 14.78 0.00 0.00 2.83
4433 7600 0.034756 AGTGACTACATGCGGCACAA 59.965 50.000 20.04 0.00 32.16 3.33
4434 7601 0.034756 AAGTGACTACATGCGGCACA 59.965 50.000 20.04 0.00 32.16 4.57
4435 7602 0.443869 CAAGTGACTACATGCGGCAC 59.556 55.000 4.03 12.42 0.00 5.01
4436 7603 0.034756 ACAAGTGACTACATGCGGCA 59.965 50.000 4.58 4.58 0.00 5.69
4437 7604 1.135972 CAACAAGTGACTACATGCGGC 60.136 52.381 0.00 0.00 0.00 6.53
4438 7605 2.412870 TCAACAAGTGACTACATGCGG 58.587 47.619 0.00 0.00 0.00 5.69
4439 7606 4.466567 TTTCAACAAGTGACTACATGCG 57.533 40.909 0.00 0.00 35.39 4.73
4440 7607 6.148480 AGAGATTTCAACAAGTGACTACATGC 59.852 38.462 0.00 0.00 35.39 4.06
4441 7608 7.664082 AGAGATTTCAACAAGTGACTACATG 57.336 36.000 0.00 0.00 35.39 3.21
4442 7609 9.778741 TTTAGAGATTTCAACAAGTGACTACAT 57.221 29.630 0.00 0.00 35.39 2.29
4443 7610 9.607988 TTTTAGAGATTTCAACAAGTGACTACA 57.392 29.630 0.00 0.00 35.39 2.74
4446 7613 9.396022 TCTTTTTAGAGATTTCAACAAGTGACT 57.604 29.630 0.00 0.00 35.39 3.41
4447 7614 9.439537 GTCTTTTTAGAGATTTCAACAAGTGAC 57.560 33.333 0.00 0.00 35.39 3.67
4448 7615 9.173021 TGTCTTTTTAGAGATTTCAACAAGTGA 57.827 29.630 0.00 0.00 0.00 3.41
4449 7616 9.787532 TTGTCTTTTTAGAGATTTCAACAAGTG 57.212 29.630 0.00 0.00 0.00 3.16
4466 7633 9.067986 CCTCTGTTCCTAAATACTTGTCTTTTT 57.932 33.333 0.00 0.00 0.00 1.94
4467 7634 7.665974 CCCTCTGTTCCTAAATACTTGTCTTTT 59.334 37.037 0.00 0.00 0.00 2.27
4468 7635 7.017254 TCCCTCTGTTCCTAAATACTTGTCTTT 59.983 37.037 0.00 0.00 0.00 2.52
4469 7636 6.500751 TCCCTCTGTTCCTAAATACTTGTCTT 59.499 38.462 0.00 0.00 0.00 3.01
4470 7637 6.023603 TCCCTCTGTTCCTAAATACTTGTCT 58.976 40.000 0.00 0.00 0.00 3.41
4471 7638 6.070710 ACTCCCTCTGTTCCTAAATACTTGTC 60.071 42.308 0.00 0.00 0.00 3.18
4472 7639 5.785940 ACTCCCTCTGTTCCTAAATACTTGT 59.214 40.000 0.00 0.00 0.00 3.16
4473 7640 6.301169 ACTCCCTCTGTTCCTAAATACTTG 57.699 41.667 0.00 0.00 0.00 3.16
4474 7641 8.445361 TTTACTCCCTCTGTTCCTAAATACTT 57.555 34.615 0.00 0.00 0.00 2.24
4475 7642 8.445361 TTTTACTCCCTCTGTTCCTAAATACT 57.555 34.615 0.00 0.00 0.00 2.12
4476 7643 7.280428 GCTTTTACTCCCTCTGTTCCTAAATAC 59.720 40.741 0.00 0.00 0.00 1.89
4477 7644 7.336396 GCTTTTACTCCCTCTGTTCCTAAATA 58.664 38.462 0.00 0.00 0.00 1.40
4478 7645 6.181190 GCTTTTACTCCCTCTGTTCCTAAAT 58.819 40.000 0.00 0.00 0.00 1.40
4479 7646 5.514310 GGCTTTTACTCCCTCTGTTCCTAAA 60.514 44.000 0.00 0.00 0.00 1.85
4480 7647 4.019591 GGCTTTTACTCCCTCTGTTCCTAA 60.020 45.833 0.00 0.00 0.00 2.69
4481 7648 3.518303 GGCTTTTACTCCCTCTGTTCCTA 59.482 47.826 0.00 0.00 0.00 2.94
4482 7649 2.306219 GGCTTTTACTCCCTCTGTTCCT 59.694 50.000 0.00 0.00 0.00 3.36
4483 7650 2.039879 TGGCTTTTACTCCCTCTGTTCC 59.960 50.000 0.00 0.00 0.00 3.62
4484 7651 3.418684 TGGCTTTTACTCCCTCTGTTC 57.581 47.619 0.00 0.00 0.00 3.18
4485 7652 3.876309 TTGGCTTTTACTCCCTCTGTT 57.124 42.857 0.00 0.00 0.00 3.16
4486 7653 4.202567 TGAATTGGCTTTTACTCCCTCTGT 60.203 41.667 0.00 0.00 0.00 3.41
4487 7654 4.156739 GTGAATTGGCTTTTACTCCCTCTG 59.843 45.833 0.00 0.00 0.00 3.35
4488 7655 4.202567 TGTGAATTGGCTTTTACTCCCTCT 60.203 41.667 0.00 0.00 0.00 3.69
4489 7656 4.079253 TGTGAATTGGCTTTTACTCCCTC 58.921 43.478 0.00 0.00 0.00 4.30
4490 7657 4.112634 TGTGAATTGGCTTTTACTCCCT 57.887 40.909 0.00 0.00 0.00 4.20
4491 7658 4.220602 ACATGTGAATTGGCTTTTACTCCC 59.779 41.667 0.00 0.00 0.00 4.30
4492 7659 5.048083 TGACATGTGAATTGGCTTTTACTCC 60.048 40.000 1.15 0.00 0.00 3.85
4493 7660 6.012658 TGACATGTGAATTGGCTTTTACTC 57.987 37.500 1.15 0.00 0.00 2.59
4494 7661 6.403866 TTGACATGTGAATTGGCTTTTACT 57.596 33.333 1.15 0.00 0.00 2.24
4547 7715 8.316640 AGAAGCAAGAGTTTCACTATTACAAG 57.683 34.615 0.00 0.00 37.43 3.16
4684 7852 6.205853 TCCACAAACAGTTCCACATGTAATAC 59.794 38.462 0.00 0.00 0.00 1.89
4692 7878 3.080300 ACTTCCACAAACAGTTCCACA 57.920 42.857 0.00 0.00 0.00 4.17
4693 7879 4.196971 ACTACTTCCACAAACAGTTCCAC 58.803 43.478 0.00 0.00 0.00 4.02
4777 9583 1.536766 AGACCAATGCACAACACATCG 59.463 47.619 0.00 0.00 0.00 3.84
4920 9729 6.820335 TCCAGACATATAAATCTGTGGTCAG 58.180 40.000 13.00 0.00 40.70 3.51
4974 9783 7.432869 CAATTTATTGAAGGAAGAACACCACA 58.567 34.615 0.00 0.00 40.14 4.17
5473 10528 8.210946 AGCACTATAGCCACATAATTTTCACTA 58.789 33.333 0.00 0.00 34.23 2.74
6161 12942 1.566563 CGCGATAGTGCCATTGCTC 59.433 57.895 0.00 0.00 41.13 4.26
6241 13024 1.461512 CGCATGCTGGTACAACGTTAA 59.538 47.619 17.13 0.00 38.70 2.01
6242 13025 1.072391 CGCATGCTGGTACAACGTTA 58.928 50.000 17.13 0.00 38.70 3.18
6243 13026 1.573829 CCGCATGCTGGTACAACGTT 61.574 55.000 17.13 0.00 38.70 3.99
6245 13028 2.784596 CCGCATGCTGGTACAACG 59.215 61.111 17.13 0.00 38.70 4.10
6247 13030 1.375853 GATGCCGCATGCTGGTACAA 61.376 55.000 23.32 11.71 42.00 2.41
6248 13031 1.819208 GATGCCGCATGCTGGTACA 60.819 57.895 23.32 16.42 42.00 2.90
6249 13032 2.885676 CGATGCCGCATGCTGGTAC 61.886 63.158 23.32 15.73 42.00 3.34
6250 13033 2.588596 CGATGCCGCATGCTGGTA 60.589 61.111 23.32 20.79 42.00 3.25
6253 13036 4.246206 CACCGATGCCGCATGCTG 62.246 66.667 17.13 10.87 42.00 4.41
6255 13038 4.241999 GTCACCGATGCCGCATGC 62.242 66.667 11.49 7.91 41.77 4.06
6256 13039 2.182181 ATGTCACCGATGCCGCATG 61.182 57.895 11.49 0.00 0.00 4.06
6257 13040 2.182181 CATGTCACCGATGCCGCAT 61.182 57.895 5.28 5.28 0.00 4.73
6263 13046 2.282407 TCAAGCATCATGTCACCGATG 58.718 47.619 8.96 8.96 41.62 3.84
6264 13047 2.169144 TCTCAAGCATCATGTCACCGAT 59.831 45.455 0.00 0.00 0.00 4.18
6265 13048 1.550072 TCTCAAGCATCATGTCACCGA 59.450 47.619 0.00 0.00 0.00 4.69
6267 13050 2.421424 GGTTCTCAAGCATCATGTCACC 59.579 50.000 0.00 0.00 0.00 4.02
6269 13052 3.708403 AGGTTCTCAAGCATCATGTCA 57.292 42.857 0.00 0.00 0.00 3.58
6270 13053 3.755378 ACAAGGTTCTCAAGCATCATGTC 59.245 43.478 0.00 0.00 0.00 3.06
6271 13054 3.759581 ACAAGGTTCTCAAGCATCATGT 58.240 40.909 0.00 0.00 0.00 3.21
6273 13056 4.147321 ACAACAAGGTTCTCAAGCATCAT 58.853 39.130 0.00 0.00 0.00 2.45
6274 13057 3.554934 ACAACAAGGTTCTCAAGCATCA 58.445 40.909 0.00 0.00 0.00 3.07
6275 13058 4.574599 AACAACAAGGTTCTCAAGCATC 57.425 40.909 0.00 0.00 0.00 3.91
6277 13060 5.646606 GTTAAACAACAAGGTTCTCAAGCA 58.353 37.500 0.00 0.00 0.00 3.91
6279 13062 4.733405 GCGTTAAACAACAAGGTTCTCAAG 59.267 41.667 0.00 0.00 0.00 3.02
6280 13063 4.156190 TGCGTTAAACAACAAGGTTCTCAA 59.844 37.500 0.00 0.00 0.00 3.02
6282 13065 4.281525 TGCGTTAAACAACAAGGTTCTC 57.718 40.909 0.00 0.00 0.00 2.87
6283 13066 4.705337 TTGCGTTAAACAACAAGGTTCT 57.295 36.364 0.00 0.00 0.00 3.01
6284 13067 5.959652 ATTTGCGTTAAACAACAAGGTTC 57.040 34.783 0.00 0.00 0.00 3.62
6286 13069 8.426881 AAAATATTTGCGTTAAACAACAAGGT 57.573 26.923 0.39 0.00 0.00 3.50
6335 14065 7.725397 TCTTATCTATATTGGCCACAAAAGCAT 59.275 33.333 3.88 0.00 40.55 3.79
6503 14238 4.958897 TTTGGTTGGCCCGGTCCG 62.959 66.667 3.60 3.60 35.15 4.79
6504 14239 2.989253 CTTTGGTTGGCCCGGTCC 60.989 66.667 0.00 0.00 35.15 4.46
6505 14240 3.680786 GCTTTGGTTGGCCCGGTC 61.681 66.667 0.00 0.00 35.15 4.79
6511 14246 1.080772 GCGTTAGGCTTTGGTTGGC 60.081 57.895 0.00 0.00 39.11 4.52
6512 14247 0.671251 TTGCGTTAGGCTTTGGTTGG 59.329 50.000 0.00 0.00 44.05 3.77
6513 14248 2.500509 TTTGCGTTAGGCTTTGGTTG 57.499 45.000 0.00 0.00 44.05 3.77
6514 14249 3.528597 TTTTTGCGTTAGGCTTTGGTT 57.471 38.095 0.00 0.00 44.05 3.67
6531 14266 1.903404 CAGCCGAGCCTGGGTTTTT 60.903 57.895 0.00 0.00 37.73 1.94
6532 14267 2.282462 CAGCCGAGCCTGGGTTTT 60.282 61.111 0.00 0.00 37.73 2.43
6533 14268 3.553095 GACAGCCGAGCCTGGGTTT 62.553 63.158 0.00 0.00 37.73 3.27
6534 14269 4.021925 GACAGCCGAGCCTGGGTT 62.022 66.667 0.00 0.00 37.73 4.11
6703 14519 2.345760 CGAAGCATTGGCAAGGGCT 61.346 57.895 19.74 19.74 44.61 5.19
6734 14550 4.678743 AAAAGCCCGACCCAGCCC 62.679 66.667 0.00 0.00 0.00 5.19
6915 14791 4.150804 TGTTGTTTTGTCTTTTTCGTTGCC 59.849 37.500 0.00 0.00 0.00 4.52
6936 14812 7.986085 ATCTGCTGAAACTGTTATAACTTGT 57.014 32.000 16.33 11.89 0.00 3.16
6981 14857 5.263599 TCTTGATGCCCTTATCATTGTTGT 58.736 37.500 0.00 0.00 36.97 3.32
6985 14861 5.074804 TCCATCTTGATGCCCTTATCATTG 58.925 41.667 5.16 0.00 36.97 2.82
6986 14862 5.329191 TCCATCTTGATGCCCTTATCATT 57.671 39.130 5.16 0.00 36.97 2.57
7026 14902 7.833682 TGAGATGCTCTTAATTTGGTTCCATTA 59.166 33.333 0.00 0.00 0.00 1.90
7054 14930 9.022915 CGTGCATGATATATCAAAATGTTTGTT 57.977 29.630 19.03 0.00 40.69 2.83
7057 14933 7.201835 TGCGTGCATGATATATCAAAATGTTT 58.798 30.769 19.03 0.00 40.69 2.83
7105 14981 2.954318 GCACCTCTTTGTCATGCCATAT 59.046 45.455 0.00 0.00 0.00 1.78
7118 14994 6.403866 TTTATGACATTTTGTGCACCTCTT 57.596 33.333 15.69 0.00 0.00 2.85
7121 14997 5.911752 TGTTTTATGACATTTTGTGCACCT 58.088 33.333 15.69 0.00 0.00 4.00
7122 14998 5.177327 CCTGTTTTATGACATTTTGTGCACC 59.823 40.000 15.69 0.00 0.00 5.01
7176 15053 3.245284 GCATTTTAGTATTCTCTCGCGCA 59.755 43.478 8.75 0.00 0.00 6.09
7237 15114 2.041928 CCTCCTCCTTCCTGGGCT 59.958 66.667 0.00 0.00 36.20 5.19
7400 15289 1.467678 CCGGATCCAGCGATCTTCCT 61.468 60.000 13.41 0.00 43.90 3.36


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

AutoCloner maintained by Alex Coulton.