Multiple sequence alignment - TraesCS1A01G340500

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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 TraesCS1A01G340500 chr1A 100.000 2474 0 0 1 2474 530725301 530727774 0.000000e+00 4569.0
1 TraesCS1A01G340500 chr1A 93.717 382 9 4 1907 2275 530728111 530727732 2.150000e-155 558.0
2 TraesCS1A01G340500 chr1A 100.000 43 0 0 2432 2474 530727575 530727533 2.040000e-11 80.5
3 TraesCS1A01G340500 chr1B 91.039 1049 53 22 595 1622 583684228 583685256 0.000000e+00 1378.0
4 TraesCS1A01G340500 chr1B 82.068 619 59 9 3 599 583683270 583683858 4.790000e-132 481.0
5 TraesCS1A01G340500 chr1B 75.564 266 40 18 1 261 242711650 242711895 9.360000e-20 108.0
6 TraesCS1A01G340500 chr1D 88.833 1003 40 26 717 1707 432201488 432202430 0.000000e+00 1166.0
7 TraesCS1A01G340500 chr1D 89.034 383 30 9 328 705 432200850 432201225 4.820000e-127 464.0
8 TraesCS1A01G340500 chr1D 94.709 189 10 0 1 189 432200529 432200717 6.690000e-76 294.0
9 TraesCS1A01G340500 chr1D 83.951 162 23 3 1 160 281422085 281421925 4.260000e-33 152.0
10 TraesCS1A01G340500 chr5D 89.696 757 34 12 958 1707 80200983 80201702 0.000000e+00 926.0
11 TraesCS1A01G340500 chr5D 89.696 757 34 12 958 1707 378329147 378329866 0.000000e+00 926.0
12 TraesCS1A01G340500 chr5D 89.065 759 37 14 958 1707 559441907 559441186 0.000000e+00 900.0
13 TraesCS1A01G340500 chr5D 88.933 759 38 16 958 1707 296179875 296179154 0.000000e+00 894.0
14 TraesCS1A01G340500 chr5D 79.795 292 41 16 1 292 164697096 164696823 1.940000e-46 196.0
15 TraesCS1A01G340500 chr3A 95.985 523 8 2 1922 2431 142922906 142922384 0.000000e+00 837.0
16 TraesCS1A01G340500 chr3A 95.111 225 8 2 1707 1928 739742013 739741789 3.910000e-93 351.0
17 TraesCS1A01G340500 chr3A 92.147 191 2 2 1919 2096 142907885 142908075 8.780000e-65 257.0
18 TraesCS1A01G340500 chr3A 97.674 43 1 0 2432 2474 142922540 142922582 9.490000e-10 75.0
19 TraesCS1A01G340500 chr5A 95.211 522 13 6 1922 2431 423039305 423038784 0.000000e+00 815.0
20 TraesCS1A01G340500 chr5A 94.828 522 15 1 1922 2431 662628937 662628416 0.000000e+00 804.0
21 TraesCS1A01G340500 chr5A 91.489 188 3 5 1922 2096 423034426 423034613 1.900000e-61 246.0
22 TraesCS1A01G340500 chr5A 73.653 334 60 24 1 328 376401836 376401525 1.210000e-18 104.0
23 TraesCS1A01G340500 chr5A 100.000 43 0 0 2432 2474 423038940 423038982 2.040000e-11 80.5
24 TraesCS1A01G340500 chr5A 100.000 42 0 0 2433 2474 662628573 662628614 7.340000e-11 78.7
25 TraesCS1A01G340500 chr3D 90.369 488 32 4 1922 2395 497962099 497962585 5.810000e-176 627.0
26 TraesCS1A01G340500 chr3D 89.300 486 38 3 1923 2395 49541381 49541865 4.550000e-167 597.0
27 TraesCS1A01G340500 chr3D 87.958 191 11 4 1922 2100 49546692 49546502 5.360000e-52 215.0
28 TraesCS1A01G340500 chr3D 84.066 182 23 5 1 179 537395117 537395295 1.180000e-38 171.0
29 TraesCS1A01G340500 chr2A 83.305 587 54 25 917 1475 717819464 717818894 3.670000e-138 501.0
30 TraesCS1A01G340500 chr2A 97.183 213 5 1 1707 1919 188909575 188909364 2.340000e-95 359.0
31 TraesCS1A01G340500 chr2A 93.991 233 10 3 1697 1925 526096875 526097107 1.410000e-92 350.0
32 TraesCS1A01G340500 chr2A 95.045 222 8 2 1707 1925 432590429 432590650 1.820000e-91 346.0
33 TraesCS1A01G340500 chr7D 85.072 489 37 11 1921 2395 4250058 4250524 1.340000e-127 466.0
34 TraesCS1A01G340500 chr7D 89.202 213 16 2 1 213 296644494 296644699 2.440000e-65 259.0
35 TraesCS1A01G340500 chr7D 88.318 214 24 1 1 213 31244189 31243976 3.160000e-64 255.0
36 TraesCS1A01G340500 chr7D 87.850 214 25 1 1 213 31233881 31233668 1.470000e-62 250.0
37 TraesCS1A01G340500 chr7D 89.062 192 10 6 1918 2100 4255281 4255092 6.880000e-56 228.0
38 TraesCS1A01G340500 chr7D 76.316 266 38 21 1 261 267934497 267934742 4.320000e-23 119.0
39 TraesCS1A01G340500 chr7D 75.564 266 39 19 1 261 70194205 70194449 9.360000e-20 108.0
40 TraesCS1A01G340500 chr7D 100.000 28 0 0 1048 1075 96663545 96663518 4.000000e-03 52.8
41 TraesCS1A01G340500 chr5B 81.698 530 58 13 1922 2432 676270089 676269580 2.960000e-109 405.0
42 TraesCS1A01G340500 chr7A 86.280 379 31 12 2003 2376 567014726 567014364 2.310000e-105 392.0
43 TraesCS1A01G340500 chr7A 80.992 484 53 29 1922 2388 32830020 32829559 5.060000e-92 348.0
44 TraesCS1A01G340500 chr7A 95.067 223 8 2 1699 1919 120755233 120755454 5.060000e-92 348.0
45 TraesCS1A01G340500 chr7A 92.827 237 14 2 1695 1928 200362073 200361837 8.470000e-90 340.0
46 TraesCS1A01G340500 chr7A 88.172 93 10 1 2315 2406 490993531 490993623 2.600000e-20 110.0
47 TraesCS1A01G340500 chr6A 94.783 230 7 4 1692 1919 564880174 564880400 1.090000e-93 353.0
48 TraesCS1A01G340500 chr6A 95.495 222 7 2 1707 1925 181909849 181910070 3.910000e-93 351.0
49 TraesCS1A01G340500 chr4A 95.045 222 8 2 1707 1925 460894052 460894273 1.820000e-91 346.0
50 TraesCS1A01G340500 chr2D 76.112 787 80 61 952 1707 579963511 579962802 1.850000e-81 313.0
51 TraesCS1A01G340500 chr2D 76.336 262 40 17 4 261 579222247 579222490 1.200000e-23 121.0
52 TraesCS1A01G340500 chr3B 79.599 299 44 11 1 298 178611605 178611323 5.400000e-47 198.0
53 TraesCS1A01G340500 chr3B 77.903 267 36 18 1 263 596102327 596102080 7.130000e-31 145.0
54 TraesCS1A01G340500 chr4B 75.908 303 51 18 1 299 654312360 654312076 4.290000e-28 135.0
55 TraesCS1A01G340500 chr2B 76.190 273 43 18 30 299 680883626 680883373 9.290000e-25 124.0
56 TraesCS1A01G340500 chr2B 75.094 265 43 17 1 261 239664025 239663780 4.350000e-18 102.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G340500 chr1A 530725301 530727774 2473 False 4569.000000 4569 100.000000 1 2474 1 chr1A.!!$F1 2473
1 TraesCS1A01G340500 chr1A 530727533 530728111 578 True 319.250000 558 96.858500 1907 2474 2 chr1A.!!$R1 567
2 TraesCS1A01G340500 chr1B 583683270 583685256 1986 False 929.500000 1378 86.553500 3 1622 2 chr1B.!!$F2 1619
3 TraesCS1A01G340500 chr1D 432200529 432202430 1901 False 641.333333 1166 90.858667 1 1707 3 chr1D.!!$F1 1706
4 TraesCS1A01G340500 chr5D 80200983 80201702 719 False 926.000000 926 89.696000 958 1707 1 chr5D.!!$F1 749
5 TraesCS1A01G340500 chr5D 378329147 378329866 719 False 926.000000 926 89.696000 958 1707 1 chr5D.!!$F2 749
6 TraesCS1A01G340500 chr5D 559441186 559441907 721 True 900.000000 900 89.065000 958 1707 1 chr5D.!!$R3 749
7 TraesCS1A01G340500 chr5D 296179154 296179875 721 True 894.000000 894 88.933000 958 1707 1 chr5D.!!$R2 749
8 TraesCS1A01G340500 chr3A 142922384 142922906 522 True 837.000000 837 95.985000 1922 2431 1 chr3A.!!$R1 509
9 TraesCS1A01G340500 chr5A 423038784 423039305 521 True 815.000000 815 95.211000 1922 2431 1 chr5A.!!$R2 509
10 TraesCS1A01G340500 chr5A 662628416 662628937 521 True 804.000000 804 94.828000 1922 2431 1 chr5A.!!$R3 509
11 TraesCS1A01G340500 chr2A 717818894 717819464 570 True 501.000000 501 83.305000 917 1475 1 chr2A.!!$R2 558
12 TraesCS1A01G340500 chr5B 676269580 676270089 509 True 405.000000 405 81.698000 1922 2432 1 chr5B.!!$R1 510
13 TraesCS1A01G340500 chr2D 579962802 579963511 709 True 313.000000 313 76.112000 952 1707 1 chr2D.!!$R1 755

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
125 126 0.38852 CTCCATCGAGTTCACGTGCA 60.389 55.0 11.67 0.0 34.7 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1892 2654 0.031585 TCAGGATTTCCGGCGATACG 59.968 55.0 9.3 0.0 42.08 3.06 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
125 126 0.388520 CTCCATCGAGTTCACGTGCA 60.389 55.000 11.67 0.00 34.70 4.57
164 166 9.180678 CTTTACTTTGTGCTTGTTATTACCTTG 57.819 33.333 0.00 0.00 0.00 3.61
165 167 6.709018 ACTTTGTGCTTGTTATTACCTTGT 57.291 33.333 0.00 0.00 0.00 3.16
166 168 7.107639 ACTTTGTGCTTGTTATTACCTTGTT 57.892 32.000 0.00 0.00 0.00 2.83
167 169 6.978080 ACTTTGTGCTTGTTATTACCTTGTTG 59.022 34.615 0.00 0.00 0.00 3.33
168 170 6.458232 TTGTGCTTGTTATTACCTTGTTGT 57.542 33.333 0.00 0.00 0.00 3.32
169 171 6.458232 TGTGCTTGTTATTACCTTGTTGTT 57.542 33.333 0.00 0.00 0.00 2.83
170 172 6.269315 TGTGCTTGTTATTACCTTGTTGTTG 58.731 36.000 0.00 0.00 0.00 3.33
171 173 6.127591 TGTGCTTGTTATTACCTTGTTGTTGT 60.128 34.615 0.00 0.00 0.00 3.32
172 174 6.754675 GTGCTTGTTATTACCTTGTTGTTGTT 59.245 34.615 0.00 0.00 0.00 2.83
173 175 6.754209 TGCTTGTTATTACCTTGTTGTTGTTG 59.246 34.615 0.00 0.00 0.00 3.33
174 176 6.754675 GCTTGTTATTACCTTGTTGTTGTTGT 59.245 34.615 0.00 0.00 0.00 3.32
175 177 7.276878 GCTTGTTATTACCTTGTTGTTGTTGTT 59.723 33.333 0.00 0.00 0.00 2.83
176 178 8.467402 TTGTTATTACCTTGTTGTTGTTGTTG 57.533 30.769 0.00 0.00 0.00 3.33
177 179 7.603651 TGTTATTACCTTGTTGTTGTTGTTGT 58.396 30.769 0.00 0.00 0.00 3.32
178 180 8.088981 TGTTATTACCTTGTTGTTGTTGTTGTT 58.911 29.630 0.00 0.00 0.00 2.83
179 181 6.959671 ATTACCTTGTTGTTGTTGTTGTTG 57.040 33.333 0.00 0.00 0.00 3.33
180 182 4.329462 ACCTTGTTGTTGTTGTTGTTGT 57.671 36.364 0.00 0.00 0.00 3.32
181 183 4.698575 ACCTTGTTGTTGTTGTTGTTGTT 58.301 34.783 0.00 0.00 0.00 2.83
182 184 4.509600 ACCTTGTTGTTGTTGTTGTTGTTG 59.490 37.500 0.00 0.00 0.00 3.33
183 185 4.509600 CCTTGTTGTTGTTGTTGTTGTTGT 59.490 37.500 0.00 0.00 0.00 3.32
184 186 5.007136 CCTTGTTGTTGTTGTTGTTGTTGTT 59.993 36.000 0.00 0.00 0.00 2.83
185 187 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
186 188 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
187 189 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
226 228 7.686438 TGTTGTTGTTGAGCTTGTCATATAT 57.314 32.000 0.00 0.00 34.17 0.86
231 233 6.682423 TGTTGAGCTTGTCATATATGTTGG 57.318 37.500 12.42 3.67 34.17 3.77
256 258 7.437748 GTCACCTAGTTGCATATCTAGACAAT 58.562 38.462 17.11 0.00 36.66 2.71
258 260 6.870965 CACCTAGTTGCATATCTAGACAATCC 59.129 42.308 17.11 0.00 36.66 3.01
286 288 9.830975 ATTATTTTGTTGAGCCTAAAGTTTGTT 57.169 25.926 0.00 0.00 0.00 2.83
319 321 6.819397 AAAGTTTTGTTAGTCAGCTATCCC 57.181 37.500 0.00 0.00 0.00 3.85
375 407 3.467803 GGGAACTCCGAGTGATTTATGG 58.532 50.000 0.65 0.00 36.71 2.74
376 408 2.872858 GGAACTCCGAGTGATTTATGGC 59.127 50.000 0.65 0.00 0.00 4.40
377 409 2.622064 ACTCCGAGTGATTTATGGCC 57.378 50.000 0.00 0.00 0.00 5.36
384 416 3.131396 GAGTGATTTATGGCCCGTGTAG 58.869 50.000 0.00 0.00 0.00 2.74
400 432 4.446719 CCGTGTAGGCGTTTAGGAATATTC 59.553 45.833 6.93 6.93 0.00 1.75
525 558 7.577616 GCTTCCTTACATTTGAACTTGCCTATT 60.578 37.037 0.00 0.00 0.00 1.73
527 560 8.276252 TCCTTACATTTGAACTTGCCTATTAC 57.724 34.615 0.00 0.00 0.00 1.89
528 561 7.885922 TCCTTACATTTGAACTTGCCTATTACA 59.114 33.333 0.00 0.00 0.00 2.41
541 574 7.663905 ACTTGCCTATTACAGTGTTTATTGTCA 59.336 33.333 0.00 0.00 0.00 3.58
543 576 8.574251 TGCCTATTACAGTGTTTATTGTCATT 57.426 30.769 0.00 0.00 0.00 2.57
544 577 8.673711 TGCCTATTACAGTGTTTATTGTCATTC 58.326 33.333 0.00 0.00 0.00 2.67
545 578 7.850982 GCCTATTACAGTGTTTATTGTCATTCG 59.149 37.037 0.00 0.00 0.00 3.34
549 582 6.612247 ACAGTGTTTATTGTCATTCGTTCA 57.388 33.333 0.00 0.00 0.00 3.18
631 1041 6.469410 TGTTTGTAAGATCGGGTAGATTGTT 58.531 36.000 0.00 0.00 40.26 2.83
645 1055 6.317893 GGGTAGATTGTTTGGTAACCACATAG 59.682 42.308 0.00 0.00 30.78 2.23
768 1445 1.599518 GGTCATGTGTGGCAACGGA 60.600 57.895 0.00 0.00 42.51 4.69
773 1450 1.298157 ATGTGTGGCAACGGACGATG 61.298 55.000 0.00 0.00 42.51 3.84
913 1593 2.624822 CCCCCACCTTATAAACCCCAAC 60.625 54.545 0.00 0.00 0.00 3.77
915 1595 2.313643 CCCACCTTATAAACCCCAACCT 59.686 50.000 0.00 0.00 0.00 3.50
1188 1915 4.564116 CGCCGATTCGTACGCCCT 62.564 66.667 11.24 0.00 0.00 5.19
1230 1959 5.966636 TCGATCGATCTGGTGTTTATTTG 57.033 39.130 22.43 3.10 0.00 2.32
1231 1960 5.416083 TCGATCGATCTGGTGTTTATTTGT 58.584 37.500 22.43 0.00 0.00 2.83
1232 1961 5.872617 TCGATCGATCTGGTGTTTATTTGTT 59.127 36.000 22.43 0.00 0.00 2.83
1233 1962 6.370442 TCGATCGATCTGGTGTTTATTTGTTT 59.630 34.615 22.43 0.00 0.00 2.83
1234 1963 7.021196 CGATCGATCTGGTGTTTATTTGTTTT 58.979 34.615 22.43 0.00 0.00 2.43
1235 1964 7.537306 CGATCGATCTGGTGTTTATTTGTTTTT 59.463 33.333 22.43 0.00 0.00 1.94
1536 2283 2.673523 GCTGTCTCCACCTGCCAT 59.326 61.111 0.00 0.00 0.00 4.40
1592 2339 2.550830 TGTGGCTTCTTCAGTCTTCC 57.449 50.000 0.00 0.00 0.00 3.46
1607 2354 3.053455 GTCTTCCTGTTGTCTTCAGTCG 58.947 50.000 0.00 0.00 0.00 4.18
1608 2355 2.956333 TCTTCCTGTTGTCTTCAGTCGA 59.044 45.455 0.00 0.00 0.00 4.20
1609 2356 3.004839 TCTTCCTGTTGTCTTCAGTCGAG 59.995 47.826 0.00 0.00 0.00 4.04
1610 2357 2.307768 TCCTGTTGTCTTCAGTCGAGT 58.692 47.619 0.00 0.00 0.00 4.18
1623 2381 4.142790 TCAGTCGAGTTTCCTCTGTACTT 58.857 43.478 0.00 0.00 35.43 2.24
1666 2428 1.766143 GCGATGCCTTGTGATCCGAC 61.766 60.000 0.00 0.00 0.00 4.79
1673 2435 0.525455 CTTGTGATCCGACGCGATGA 60.525 55.000 15.93 6.24 0.00 2.92
1707 2469 7.278135 TCTCAGTATAATCTTTGCTGCATCTT 58.722 34.615 1.84 0.00 0.00 2.40
1708 2470 7.772292 TCTCAGTATAATCTTTGCTGCATCTTT 59.228 33.333 1.84 0.00 0.00 2.52
1709 2471 8.284945 TCAGTATAATCTTTGCTGCATCTTTT 57.715 30.769 1.84 0.00 0.00 2.27
1710 2472 8.742777 TCAGTATAATCTTTGCTGCATCTTTTT 58.257 29.630 1.84 0.00 0.00 1.94
1732 2494 7.561021 TTTTTGAGCATAAGTACAGACACAA 57.439 32.000 0.00 0.00 0.00 3.33
1733 2495 6.785488 TTTGAGCATAAGTACAGACACAAG 57.215 37.500 0.00 0.00 0.00 3.16
1734 2496 4.245660 TGAGCATAAGTACAGACACAAGC 58.754 43.478 0.00 0.00 0.00 4.01
1735 2497 3.254060 AGCATAAGTACAGACACAAGCG 58.746 45.455 0.00 0.00 0.00 4.68
1736 2498 2.222819 GCATAAGTACAGACACAAGCGC 60.223 50.000 0.00 0.00 0.00 5.92
1737 2499 3.254060 CATAAGTACAGACACAAGCGCT 58.746 45.455 2.64 2.64 0.00 5.92
1738 2500 1.784525 AAGTACAGACACAAGCGCTC 58.215 50.000 12.06 0.00 0.00 5.03
1739 2501 0.673985 AGTACAGACACAAGCGCTCA 59.326 50.000 12.06 0.00 0.00 4.26
1740 2502 1.273606 AGTACAGACACAAGCGCTCAT 59.726 47.619 12.06 0.00 0.00 2.90
1741 2503 2.492088 AGTACAGACACAAGCGCTCATA 59.508 45.455 12.06 0.00 0.00 2.15
1742 2504 2.680312 ACAGACACAAGCGCTCATAT 57.320 45.000 12.06 0.00 0.00 1.78
1743 2505 3.801114 ACAGACACAAGCGCTCATATA 57.199 42.857 12.06 0.00 0.00 0.86
1744 2506 3.448686 ACAGACACAAGCGCTCATATAC 58.551 45.455 12.06 1.00 0.00 1.47
1745 2507 3.119137 ACAGACACAAGCGCTCATATACA 60.119 43.478 12.06 0.00 0.00 2.29
1746 2508 3.243877 CAGACACAAGCGCTCATATACAC 59.756 47.826 12.06 0.00 0.00 2.90
1747 2509 2.193447 ACACAAGCGCTCATATACACG 58.807 47.619 12.06 0.00 0.00 4.49
1751 2513 3.916439 CGCTCATATACACGCGCA 58.084 55.556 5.73 0.00 39.11 6.09
1752 2514 2.434688 CGCTCATATACACGCGCAT 58.565 52.632 5.73 0.00 39.11 4.73
1753 2515 1.613270 CGCTCATATACACGCGCATA 58.387 50.000 5.73 1.53 39.11 3.14
1754 2516 1.317611 CGCTCATATACACGCGCATAC 59.682 52.381 5.73 0.00 39.11 2.39
1755 2517 2.324860 GCTCATATACACGCGCATACA 58.675 47.619 5.73 0.00 0.00 2.29
1756 2518 2.090658 GCTCATATACACGCGCATACAC 59.909 50.000 5.73 0.00 0.00 2.90
1757 2519 3.565516 CTCATATACACGCGCATACACT 58.434 45.455 5.73 0.00 0.00 3.55
1758 2520 3.561503 TCATATACACGCGCATACACTC 58.438 45.455 5.73 0.00 0.00 3.51
1759 2521 3.003897 TCATATACACGCGCATACACTCA 59.996 43.478 5.73 0.00 0.00 3.41
1760 2522 1.556564 ATACACGCGCATACACTCAC 58.443 50.000 5.73 0.00 0.00 3.51
1761 2523 0.457166 TACACGCGCATACACTCACC 60.457 55.000 5.73 0.00 0.00 4.02
1762 2524 2.125673 ACGCGCATACACTCACCC 60.126 61.111 5.73 0.00 0.00 4.61
1763 2525 2.184322 CGCGCATACACTCACCCT 59.816 61.111 8.75 0.00 0.00 4.34
1764 2526 1.447838 CGCGCATACACTCACCCTT 60.448 57.895 8.75 0.00 0.00 3.95
1765 2527 0.179121 CGCGCATACACTCACCCTTA 60.179 55.000 8.75 0.00 0.00 2.69
1766 2528 1.538204 CGCGCATACACTCACCCTTAT 60.538 52.381 8.75 0.00 0.00 1.73
1767 2529 2.287970 CGCGCATACACTCACCCTTATA 60.288 50.000 8.75 0.00 0.00 0.98
1768 2530 3.724374 GCGCATACACTCACCCTTATAA 58.276 45.455 0.30 0.00 0.00 0.98
1769 2531 4.124238 GCGCATACACTCACCCTTATAAA 58.876 43.478 0.30 0.00 0.00 1.40
1770 2532 4.025145 GCGCATACACTCACCCTTATAAAC 60.025 45.833 0.30 0.00 0.00 2.01
1771 2533 4.208460 CGCATACACTCACCCTTATAAACG 59.792 45.833 0.00 0.00 0.00 3.60
1772 2534 4.025145 GCATACACTCACCCTTATAAACGC 60.025 45.833 0.00 0.00 0.00 4.84
1773 2535 3.688694 ACACTCACCCTTATAAACGCA 57.311 42.857 0.00 0.00 0.00 5.24
1774 2536 3.332034 ACACTCACCCTTATAAACGCAC 58.668 45.455 0.00 0.00 0.00 5.34
1775 2537 3.244284 ACACTCACCCTTATAAACGCACA 60.244 43.478 0.00 0.00 0.00 4.57
1776 2538 3.124636 CACTCACCCTTATAAACGCACAC 59.875 47.826 0.00 0.00 0.00 3.82
1777 2539 3.244284 ACTCACCCTTATAAACGCACACA 60.244 43.478 0.00 0.00 0.00 3.72
1778 2540 3.068560 TCACCCTTATAAACGCACACAC 58.931 45.455 0.00 0.00 0.00 3.82
1779 2541 2.809119 CACCCTTATAAACGCACACACA 59.191 45.455 0.00 0.00 0.00 3.72
1780 2542 2.809696 ACCCTTATAAACGCACACACAC 59.190 45.455 0.00 0.00 0.00 3.82
1781 2543 2.809119 CCCTTATAAACGCACACACACA 59.191 45.455 0.00 0.00 0.00 3.72
1782 2544 3.364565 CCCTTATAAACGCACACACACAC 60.365 47.826 0.00 0.00 0.00 3.82
1783 2545 3.364565 CCTTATAAACGCACACACACACC 60.365 47.826 0.00 0.00 0.00 4.16
1784 2546 0.948678 ATAAACGCACACACACACCC 59.051 50.000 0.00 0.00 0.00 4.61
1785 2547 0.107606 TAAACGCACACACACACCCT 60.108 50.000 0.00 0.00 0.00 4.34
1786 2548 0.107606 AAACGCACACACACACCCTA 60.108 50.000 0.00 0.00 0.00 3.53
1787 2549 0.812412 AACGCACACACACACCCTAC 60.812 55.000 0.00 0.00 0.00 3.18
1788 2550 1.959226 CGCACACACACACCCTACC 60.959 63.158 0.00 0.00 0.00 3.18
1789 2551 1.599797 GCACACACACACCCTACCC 60.600 63.158 0.00 0.00 0.00 3.69
1790 2552 1.072505 CACACACACACCCTACCCC 59.927 63.158 0.00 0.00 0.00 4.95
1791 2553 1.074014 ACACACACACCCTACCCCT 60.074 57.895 0.00 0.00 0.00 4.79
1792 2554 0.191563 ACACACACACCCTACCCCTA 59.808 55.000 0.00 0.00 0.00 3.53
1793 2555 1.203389 ACACACACACCCTACCCCTAT 60.203 52.381 0.00 0.00 0.00 2.57
1794 2556 1.209504 CACACACACCCTACCCCTATG 59.790 57.143 0.00 0.00 0.00 2.23
1795 2557 1.079825 ACACACACCCTACCCCTATGA 59.920 52.381 0.00 0.00 0.00 2.15
1796 2558 1.762957 CACACACCCTACCCCTATGAG 59.237 57.143 0.00 0.00 0.00 2.90
1797 2559 0.759346 CACACCCTACCCCTATGAGC 59.241 60.000 0.00 0.00 0.00 4.26
1798 2560 0.341961 ACACCCTACCCCTATGAGCA 59.658 55.000 0.00 0.00 0.00 4.26
1799 2561 0.759346 CACCCTACCCCTATGAGCAC 59.241 60.000 0.00 0.00 0.00 4.40
1800 2562 0.400093 ACCCTACCCCTATGAGCACC 60.400 60.000 0.00 0.00 0.00 5.01
1801 2563 0.104934 CCCTACCCCTATGAGCACCT 60.105 60.000 0.00 0.00 0.00 4.00
1802 2564 1.343069 CCTACCCCTATGAGCACCTC 58.657 60.000 0.00 0.00 0.00 3.85
1803 2565 1.343069 CTACCCCTATGAGCACCTCC 58.657 60.000 0.00 0.00 0.00 4.30
1804 2566 0.469331 TACCCCTATGAGCACCTCCG 60.469 60.000 0.00 0.00 0.00 4.63
1805 2567 1.457643 CCCCTATGAGCACCTCCGA 60.458 63.158 0.00 0.00 0.00 4.55
1806 2568 1.467678 CCCCTATGAGCACCTCCGAG 61.468 65.000 0.00 0.00 0.00 4.63
1807 2569 0.468214 CCCTATGAGCACCTCCGAGA 60.468 60.000 0.00 0.00 0.00 4.04
1808 2570 0.958091 CCTATGAGCACCTCCGAGAG 59.042 60.000 0.00 0.00 0.00 3.20
1809 2571 1.477740 CCTATGAGCACCTCCGAGAGA 60.478 57.143 0.00 0.00 0.00 3.10
1810 2572 1.606668 CTATGAGCACCTCCGAGAGAC 59.393 57.143 0.00 0.00 0.00 3.36
1811 2573 0.033601 ATGAGCACCTCCGAGAGACT 60.034 55.000 0.00 0.00 0.00 3.24
1812 2574 0.962855 TGAGCACCTCCGAGAGACTG 60.963 60.000 0.00 0.22 0.00 3.51
1813 2575 0.678366 GAGCACCTCCGAGAGACTGA 60.678 60.000 0.00 0.00 0.00 3.41
1814 2576 0.679640 AGCACCTCCGAGAGACTGAG 60.680 60.000 0.00 0.00 0.00 3.35
1815 2577 1.806568 CACCTCCGAGAGACTGAGC 59.193 63.158 0.00 0.00 0.00 4.26
1816 2578 1.379309 ACCTCCGAGAGACTGAGCC 60.379 63.158 0.00 0.00 0.00 4.70
1817 2579 2.477176 CCTCCGAGAGACTGAGCCG 61.477 68.421 0.00 0.00 0.00 5.52
1818 2580 2.438614 TCCGAGAGACTGAGCCGG 60.439 66.667 0.00 0.00 41.36 6.13
1819 2581 4.200283 CCGAGAGACTGAGCCGGC 62.200 72.222 21.89 21.89 33.47 6.13
1820 2582 3.443925 CGAGAGACTGAGCCGGCA 61.444 66.667 31.54 7.98 0.00 5.69
1821 2583 2.780094 CGAGAGACTGAGCCGGCAT 61.780 63.158 31.54 14.28 0.00 4.40
1822 2584 1.448119 CGAGAGACTGAGCCGGCATA 61.448 60.000 31.54 16.21 0.00 3.14
1823 2585 0.965439 GAGAGACTGAGCCGGCATAT 59.035 55.000 31.54 8.11 0.00 1.78
1824 2586 0.965439 AGAGACTGAGCCGGCATATC 59.035 55.000 31.54 18.63 0.00 1.63
1825 2587 0.676184 GAGACTGAGCCGGCATATCA 59.324 55.000 31.54 22.44 0.00 2.15
1826 2588 1.274728 GAGACTGAGCCGGCATATCAT 59.725 52.381 31.54 13.17 0.00 2.45
1827 2589 1.274728 AGACTGAGCCGGCATATCATC 59.725 52.381 31.54 19.98 0.00 2.92
1828 2590 1.274728 GACTGAGCCGGCATATCATCT 59.725 52.381 31.54 11.40 0.00 2.90
1829 2591 1.696336 ACTGAGCCGGCATATCATCTT 59.304 47.619 31.54 3.33 0.00 2.40
1830 2592 2.074576 CTGAGCCGGCATATCATCTTG 58.925 52.381 31.54 7.95 0.00 3.02
1831 2593 1.693606 TGAGCCGGCATATCATCTTGA 59.306 47.619 31.54 0.00 0.00 3.02
1832 2594 2.289257 TGAGCCGGCATATCATCTTGAG 60.289 50.000 31.54 0.00 0.00 3.02
1833 2595 1.973515 AGCCGGCATATCATCTTGAGA 59.026 47.619 31.54 0.00 0.00 3.27
1834 2596 2.570752 AGCCGGCATATCATCTTGAGAT 59.429 45.455 31.54 0.00 34.56 2.75
1835 2597 3.008813 AGCCGGCATATCATCTTGAGATT 59.991 43.478 31.54 0.00 31.21 2.40
1836 2598 3.755378 GCCGGCATATCATCTTGAGATTT 59.245 43.478 24.80 0.00 31.21 2.17
1837 2599 4.937620 GCCGGCATATCATCTTGAGATTTA 59.062 41.667 24.80 0.00 31.21 1.40
1838 2600 5.163814 GCCGGCATATCATCTTGAGATTTAC 60.164 44.000 24.80 0.00 31.21 2.01
1839 2601 5.062683 CCGGCATATCATCTTGAGATTTACG 59.937 44.000 0.00 0.00 31.21 3.18
1840 2602 5.863935 CGGCATATCATCTTGAGATTTACGA 59.136 40.000 0.00 0.00 31.21 3.43
1841 2603 6.366061 CGGCATATCATCTTGAGATTTACGAA 59.634 38.462 0.00 0.00 31.21 3.85
1842 2604 7.411264 CGGCATATCATCTTGAGATTTACGAAG 60.411 40.741 0.00 0.00 31.21 3.79
1843 2605 7.386299 GGCATATCATCTTGAGATTTACGAAGT 59.614 37.037 0.00 0.00 37.29 3.01
1844 2606 8.431593 GCATATCATCTTGAGATTTACGAAGTC 58.568 37.037 0.00 0.00 35.39 3.01
1845 2607 9.468532 CATATCATCTTGAGATTTACGAAGTCA 57.531 33.333 0.00 0.00 35.39 3.41
1846 2608 7.763172 ATCATCTTGAGATTTACGAAGTCAC 57.237 36.000 0.00 0.00 35.39 3.67
1847 2609 6.100004 TCATCTTGAGATTTACGAAGTCACC 58.900 40.000 0.00 0.00 35.39 4.02
1848 2610 4.482386 TCTTGAGATTTACGAAGTCACCG 58.518 43.478 0.00 0.00 43.93 4.94
1849 2611 3.928727 TGAGATTTACGAAGTCACCGT 57.071 42.857 0.00 0.00 43.93 4.83
1850 2612 5.181811 TCTTGAGATTTACGAAGTCACCGTA 59.818 40.000 0.00 0.00 43.93 4.02
1851 2613 4.978186 TGAGATTTACGAAGTCACCGTAG 58.022 43.478 0.00 0.00 43.93 3.51
1863 2625 3.494336 CCGTAGGCGTCTCGTCGT 61.494 66.667 0.00 0.00 46.14 4.34
1864 2626 2.021106 CGTAGGCGTCTCGTCGTC 59.979 66.667 0.00 0.00 36.23 4.20
1865 2627 2.021106 GTAGGCGTCTCGTCGTCG 59.979 66.667 0.00 0.00 40.52 5.12
1866 2628 2.125952 TAGGCGTCTCGTCGTCGA 60.126 61.111 4.42 4.42 44.12 4.20
1867 2629 2.447887 TAGGCGTCTCGTCGTCGAC 61.448 63.158 15.51 15.51 41.35 4.20
1886 2648 2.363297 GGGAACGTCTCCTTCCACT 58.637 57.895 13.94 0.00 44.68 4.00
1887 2649 0.037232 GGGAACGTCTCCTTCCACTG 60.037 60.000 13.94 0.00 44.68 3.66
1888 2650 0.966920 GGAACGTCTCCTTCCACTGA 59.033 55.000 8.87 0.00 41.61 3.41
1889 2651 1.343465 GGAACGTCTCCTTCCACTGAA 59.657 52.381 8.87 0.00 41.61 3.02
1890 2652 2.224209 GGAACGTCTCCTTCCACTGAAA 60.224 50.000 8.87 0.00 41.61 2.69
1891 2653 2.821991 ACGTCTCCTTCCACTGAAAG 57.178 50.000 0.00 0.00 42.29 2.62
1892 2654 1.270358 ACGTCTCCTTCCACTGAAAGC 60.270 52.381 0.00 0.00 37.60 3.51
1893 2655 1.433534 GTCTCCTTCCACTGAAAGCG 58.566 55.000 0.00 0.00 37.60 4.68
1894 2656 1.048601 TCTCCTTCCACTGAAAGCGT 58.951 50.000 0.00 0.00 37.60 5.07
1895 2657 2.029290 GTCTCCTTCCACTGAAAGCGTA 60.029 50.000 0.00 0.00 37.60 4.42
1896 2658 2.832129 TCTCCTTCCACTGAAAGCGTAT 59.168 45.455 0.00 0.00 37.60 3.06
1897 2659 3.119101 TCTCCTTCCACTGAAAGCGTATC 60.119 47.826 0.00 0.00 37.60 2.24
1898 2660 1.927174 CCTTCCACTGAAAGCGTATCG 59.073 52.381 0.00 0.00 37.60 2.92
1910 2672 2.517598 CGTATCGCCGGAAATCCTG 58.482 57.895 5.05 0.00 0.00 3.86
1911 2673 0.031585 CGTATCGCCGGAAATCCTGA 59.968 55.000 5.05 0.00 0.00 3.86
1912 2674 1.537348 CGTATCGCCGGAAATCCTGAA 60.537 52.381 5.05 0.00 0.00 3.02
1913 2675 2.557317 GTATCGCCGGAAATCCTGAAA 58.443 47.619 5.05 0.00 0.00 2.69
1914 2676 2.348411 ATCGCCGGAAATCCTGAAAT 57.652 45.000 5.05 0.00 0.00 2.17
1915 2677 2.992124 TCGCCGGAAATCCTGAAATA 57.008 45.000 5.05 0.00 0.00 1.40
1916 2678 3.269538 TCGCCGGAAATCCTGAAATAA 57.730 42.857 5.05 0.00 0.00 1.40
1917 2679 3.611970 TCGCCGGAAATCCTGAAATAAA 58.388 40.909 5.05 0.00 0.00 1.40
1918 2680 4.204012 TCGCCGGAAATCCTGAAATAAAT 58.796 39.130 5.05 0.00 0.00 1.40
1919 2681 4.642885 TCGCCGGAAATCCTGAAATAAATT 59.357 37.500 5.05 0.00 0.00 1.82
1920 2682 4.976116 CGCCGGAAATCCTGAAATAAATTC 59.024 41.667 5.05 0.00 38.60 2.17
2006 2783 5.102967 ACCAGTTAACTAATCCCCTACCAA 58.897 41.667 8.04 0.00 0.00 3.67
2103 2880 2.675371 GCTTGGTAGGGTGGGTCC 59.325 66.667 0.00 0.00 0.00 4.46
2124 2901 2.093106 GAGACTTAACTGCTCCTCCGA 58.907 52.381 0.00 0.00 0.00 4.55
2223 3000 4.103103 CAGCGCGACGACTCCAGA 62.103 66.667 12.10 0.00 0.00 3.86
2288 3065 6.577800 CACGTACTTCTCTGTGTTAACTACAG 59.422 42.308 22.04 22.04 45.30 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
125 126 7.942894 AGCACAAAGTAAAGGACCTAAATAACT 59.057 33.333 0.00 0.00 0.00 2.24
164 166 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
165 167 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
166 168 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
167 169 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
168 170 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
169 171 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
170 172 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
171 173 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
172 174 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
173 175 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
174 176 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
175 177 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
176 178 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
177 179 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
178 180 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
179 181 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
180 182 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
181 183 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
182 184 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
183 185 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
184 186 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
185 187 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
186 188 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
187 189 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
226 228 2.949177 ATGCAACTAGGTGACCAACA 57.051 45.000 13.29 0.00 0.00 3.33
231 233 6.392625 TGTCTAGATATGCAACTAGGTGAC 57.607 41.667 13.29 3.44 37.34 3.67
256 258 9.528489 AACTTTAGGCTCAACAAAATAATAGGA 57.472 29.630 0.00 0.00 0.00 2.94
299 301 3.945921 GGGGGATAGCTGACTAACAAAAC 59.054 47.826 0.00 0.00 30.45 2.43
363 395 2.038387 ACACGGGCCATAAATCACTC 57.962 50.000 4.39 0.00 0.00 3.51
376 408 0.247185 TTCCTAAACGCCTACACGGG 59.753 55.000 0.00 0.00 37.37 5.28
377 409 2.304751 ATTCCTAAACGCCTACACGG 57.695 50.000 0.00 0.00 37.37 4.94
384 416 3.678548 CGGCTAGAATATTCCTAAACGCC 59.321 47.826 11.92 12.65 0.00 5.68
422 455 3.053991 TCACCACAACTCCCTCTTTCAAA 60.054 43.478 0.00 0.00 0.00 2.69
424 457 2.123589 TCACCACAACTCCCTCTTTCA 58.876 47.619 0.00 0.00 0.00 2.69
425 458 2.930826 TCACCACAACTCCCTCTTTC 57.069 50.000 0.00 0.00 0.00 2.62
428 461 2.289694 CGAATTCACCACAACTCCCTCT 60.290 50.000 6.22 0.00 0.00 3.69
430 463 1.271379 CCGAATTCACCACAACTCCCT 60.271 52.381 6.22 0.00 0.00 4.20
431 464 1.165270 CCGAATTCACCACAACTCCC 58.835 55.000 6.22 0.00 0.00 4.30
432 465 1.892209 ACCGAATTCACCACAACTCC 58.108 50.000 6.22 0.00 0.00 3.85
498 531 3.914364 GCAAGTTCAAATGTAAGGAAGCG 59.086 43.478 0.00 0.00 0.00 4.68
508 541 6.913170 ACACTGTAATAGGCAAGTTCAAATG 58.087 36.000 0.00 0.00 0.00 2.32
525 558 7.716768 TGAACGAATGACAATAAACACTGTA 57.283 32.000 0.00 0.00 0.00 2.74
527 560 6.032775 GCATGAACGAATGACAATAAACACTG 59.967 38.462 0.00 0.00 0.00 3.66
528 561 6.072508 AGCATGAACGAATGACAATAAACACT 60.073 34.615 0.00 0.00 0.00 3.55
541 574 2.483877 TCGAAGCAAAGCATGAACGAAT 59.516 40.909 0.00 0.00 0.00 3.34
543 576 1.194547 GTCGAAGCAAAGCATGAACGA 59.805 47.619 0.00 0.00 0.00 3.85
544 577 1.069973 TGTCGAAGCAAAGCATGAACG 60.070 47.619 0.00 0.00 0.00 3.95
545 578 2.686558 TGTCGAAGCAAAGCATGAAC 57.313 45.000 0.00 0.00 0.00 3.18
549 582 1.542915 AGCAATGTCGAAGCAAAGCAT 59.457 42.857 0.00 0.00 0.00 3.79
631 1041 1.348366 ACGGTGCTATGTGGTTACCAA 59.652 47.619 5.33 0.00 34.18 3.67
722 1392 2.432874 CGTTGGGTCCAGGATGTGTATA 59.567 50.000 0.00 0.00 0.00 1.47
725 1395 1.374947 CGTTGGGTCCAGGATGTGT 59.625 57.895 0.00 0.00 0.00 3.72
731 1401 2.978010 GTGCACGTTGGGTCCAGG 60.978 66.667 0.00 0.00 0.00 4.45
895 1573 3.626475 GGAGGTTGGGGTTTATAAGGTGG 60.626 52.174 0.00 0.00 0.00 4.61
913 1593 1.522569 GTGGACGGAGGATTGGAGG 59.477 63.158 0.00 0.00 0.00 4.30
915 1595 0.620410 ATGGTGGACGGAGGATTGGA 60.620 55.000 0.00 0.00 0.00 3.53
986 1671 1.133513 TCCTCATGGCTCTCTCTCTCC 60.134 57.143 0.00 0.00 0.00 3.71
1022 1713 2.436824 GCTGCCGGAAGAAGGACC 60.437 66.667 15.89 0.00 0.00 4.46
1146 1861 4.517815 GATTGGGCGTACGGCGGA 62.518 66.667 31.81 23.55 44.92 5.54
1188 1915 2.815211 GAGCAGTCAATCCGCGCA 60.815 61.111 8.75 0.00 0.00 6.09
1235 1964 5.291614 GCAGAAGCAACAACAGATTGAAAAA 59.708 36.000 0.00 0.00 41.58 1.94
1521 2268 0.842030 AGGAATGGCAGGTGGAGACA 60.842 55.000 0.00 0.00 38.70 3.41
1536 2283 0.606604 GTAGGCAGAACCACGAGGAA 59.393 55.000 5.68 0.00 43.14 3.36
1592 2339 3.491267 GGAAACTCGACTGAAGACAACAG 59.509 47.826 0.00 0.00 40.68 3.16
1609 2356 3.064931 CGACCCAAAGTACAGAGGAAAC 58.935 50.000 0.00 0.00 0.00 2.78
1610 2357 2.967201 TCGACCCAAAGTACAGAGGAAA 59.033 45.455 0.00 0.00 0.00 3.13
1623 2381 2.669133 CCCAGCAGGATCGACCCAA 61.669 63.158 0.00 0.00 40.05 4.12
1666 2428 7.977490 ATACTGAGATTAATACATCATCGCG 57.023 36.000 0.00 0.00 0.00 5.87
1708 2470 7.561021 TTGTGTCTGTACTTATGCTCAAAAA 57.439 32.000 0.00 0.00 0.00 1.94
1709 2471 6.293407 GCTTGTGTCTGTACTTATGCTCAAAA 60.293 38.462 0.00 0.00 0.00 2.44
1710 2472 5.179368 GCTTGTGTCTGTACTTATGCTCAAA 59.821 40.000 0.00 0.00 0.00 2.69
1711 2473 4.690748 GCTTGTGTCTGTACTTATGCTCAA 59.309 41.667 0.00 0.00 0.00 3.02
1712 2474 4.245660 GCTTGTGTCTGTACTTATGCTCA 58.754 43.478 0.00 0.00 0.00 4.26
1713 2475 3.304559 CGCTTGTGTCTGTACTTATGCTC 59.695 47.826 0.00 0.00 0.00 4.26
1714 2476 3.254060 CGCTTGTGTCTGTACTTATGCT 58.746 45.455 0.00 0.00 0.00 3.79
1715 2477 2.222819 GCGCTTGTGTCTGTACTTATGC 60.223 50.000 0.00 0.00 0.00 3.14
1716 2478 3.254060 AGCGCTTGTGTCTGTACTTATG 58.746 45.455 2.64 0.00 0.00 1.90
1717 2479 3.056821 TGAGCGCTTGTGTCTGTACTTAT 60.057 43.478 13.26 0.00 0.00 1.73
1718 2480 2.295070 TGAGCGCTTGTGTCTGTACTTA 59.705 45.455 13.26 0.00 0.00 2.24
1719 2481 1.068588 TGAGCGCTTGTGTCTGTACTT 59.931 47.619 13.26 0.00 0.00 2.24
1720 2482 0.673985 TGAGCGCTTGTGTCTGTACT 59.326 50.000 13.26 0.00 0.00 2.73
1721 2483 1.714794 ATGAGCGCTTGTGTCTGTAC 58.285 50.000 13.26 0.00 0.00 2.90
1722 2484 3.801114 ATATGAGCGCTTGTGTCTGTA 57.199 42.857 13.26 0.00 0.00 2.74
1723 2485 2.680312 ATATGAGCGCTTGTGTCTGT 57.320 45.000 13.26 0.00 0.00 3.41
1724 2486 3.243877 GTGTATATGAGCGCTTGTGTCTG 59.756 47.826 13.26 0.00 0.00 3.51
1725 2487 3.448686 GTGTATATGAGCGCTTGTGTCT 58.551 45.455 13.26 0.00 0.00 3.41
1726 2488 2.216488 CGTGTATATGAGCGCTTGTGTC 59.784 50.000 13.26 0.00 0.00 3.67
1727 2489 2.193447 CGTGTATATGAGCGCTTGTGT 58.807 47.619 13.26 4.27 0.00 3.72
1728 2490 1.071239 GCGTGTATATGAGCGCTTGTG 60.071 52.381 13.26 0.00 45.48 3.33
1729 2491 1.209128 GCGTGTATATGAGCGCTTGT 58.791 50.000 13.26 5.98 45.48 3.16
1730 2492 0.159554 CGCGTGTATATGAGCGCTTG 59.840 55.000 13.26 0.00 46.56 4.01
1731 2493 2.506544 CGCGTGTATATGAGCGCTT 58.493 52.632 13.26 0.00 46.56 4.68
1732 2494 4.228451 CGCGTGTATATGAGCGCT 57.772 55.556 11.27 11.27 46.56 5.92
1735 2497 2.090658 GTGTATGCGCGTGTATATGAGC 59.909 50.000 13.61 0.41 38.85 4.26
1736 2498 3.565516 AGTGTATGCGCGTGTATATGAG 58.434 45.455 13.61 0.00 0.00 2.90
1737 2499 3.003897 TGAGTGTATGCGCGTGTATATGA 59.996 43.478 13.61 0.00 0.00 2.15
1738 2500 3.119628 GTGAGTGTATGCGCGTGTATATG 59.880 47.826 13.61 0.00 0.00 1.78
1739 2501 3.305964 GTGAGTGTATGCGCGTGTATAT 58.694 45.455 13.61 0.00 0.00 0.86
1740 2502 2.542205 GGTGAGTGTATGCGCGTGTATA 60.542 50.000 13.61 2.40 0.00 1.47
1741 2503 1.556564 GTGAGTGTATGCGCGTGTAT 58.443 50.000 13.61 4.63 0.00 2.29
1742 2504 0.457166 GGTGAGTGTATGCGCGTGTA 60.457 55.000 13.61 0.00 0.00 2.90
1743 2505 1.736645 GGTGAGTGTATGCGCGTGT 60.737 57.895 13.61 0.00 0.00 4.49
1744 2506 2.452813 GGGTGAGTGTATGCGCGTG 61.453 63.158 13.61 0.00 0.00 5.34
1745 2507 2.125673 GGGTGAGTGTATGCGCGT 60.126 61.111 8.43 7.55 0.00 6.01
1746 2508 0.179121 TAAGGGTGAGTGTATGCGCG 60.179 55.000 0.00 0.00 0.00 6.86
1747 2509 2.240493 ATAAGGGTGAGTGTATGCGC 57.760 50.000 0.00 0.00 0.00 6.09
1748 2510 4.208460 CGTTTATAAGGGTGAGTGTATGCG 59.792 45.833 0.00 0.00 0.00 4.73
1749 2511 4.025145 GCGTTTATAAGGGTGAGTGTATGC 60.025 45.833 0.00 0.00 0.00 3.14
1750 2512 5.006358 GTGCGTTTATAAGGGTGAGTGTATG 59.994 44.000 0.00 0.00 0.00 2.39
1751 2513 5.114081 GTGCGTTTATAAGGGTGAGTGTAT 58.886 41.667 0.00 0.00 0.00 2.29
1752 2514 4.021280 TGTGCGTTTATAAGGGTGAGTGTA 60.021 41.667 0.00 0.00 0.00 2.90
1753 2515 3.244284 TGTGCGTTTATAAGGGTGAGTGT 60.244 43.478 0.00 0.00 0.00 3.55
1754 2516 3.124636 GTGTGCGTTTATAAGGGTGAGTG 59.875 47.826 0.00 0.00 0.00 3.51
1755 2517 3.244284 TGTGTGCGTTTATAAGGGTGAGT 60.244 43.478 0.00 0.00 0.00 3.41
1756 2518 3.124636 GTGTGTGCGTTTATAAGGGTGAG 59.875 47.826 0.00 0.00 0.00 3.51
1757 2519 3.068560 GTGTGTGCGTTTATAAGGGTGA 58.931 45.455 0.00 0.00 0.00 4.02
1758 2520 2.809119 TGTGTGTGCGTTTATAAGGGTG 59.191 45.455 0.00 0.00 0.00 4.61
1759 2521 2.809696 GTGTGTGTGCGTTTATAAGGGT 59.190 45.455 0.00 0.00 0.00 4.34
1760 2522 2.809119 TGTGTGTGTGCGTTTATAAGGG 59.191 45.455 0.00 0.00 0.00 3.95
1761 2523 3.364565 GGTGTGTGTGTGCGTTTATAAGG 60.365 47.826 0.00 0.00 0.00 2.69
1762 2524 3.364565 GGGTGTGTGTGTGCGTTTATAAG 60.365 47.826 0.00 0.00 0.00 1.73
1763 2525 2.548904 GGGTGTGTGTGTGCGTTTATAA 59.451 45.455 0.00 0.00 0.00 0.98
1764 2526 2.144730 GGGTGTGTGTGTGCGTTTATA 58.855 47.619 0.00 0.00 0.00 0.98
1765 2527 0.948678 GGGTGTGTGTGTGCGTTTAT 59.051 50.000 0.00 0.00 0.00 1.40
1766 2528 0.107606 AGGGTGTGTGTGTGCGTTTA 60.108 50.000 0.00 0.00 0.00 2.01
1767 2529 0.107606 TAGGGTGTGTGTGTGCGTTT 60.108 50.000 0.00 0.00 0.00 3.60
1768 2530 0.812412 GTAGGGTGTGTGTGTGCGTT 60.812 55.000 0.00 0.00 0.00 4.84
1769 2531 1.227438 GTAGGGTGTGTGTGTGCGT 60.227 57.895 0.00 0.00 0.00 5.24
1770 2532 1.959226 GGTAGGGTGTGTGTGTGCG 60.959 63.158 0.00 0.00 0.00 5.34
1771 2533 1.599797 GGGTAGGGTGTGTGTGTGC 60.600 63.158 0.00 0.00 0.00 4.57
1772 2534 1.072505 GGGGTAGGGTGTGTGTGTG 59.927 63.158 0.00 0.00 0.00 3.82
1773 2535 0.191563 TAGGGGTAGGGTGTGTGTGT 59.808 55.000 0.00 0.00 0.00 3.72
1774 2536 1.209504 CATAGGGGTAGGGTGTGTGTG 59.790 57.143 0.00 0.00 0.00 3.82
1775 2537 1.079825 TCATAGGGGTAGGGTGTGTGT 59.920 52.381 0.00 0.00 0.00 3.72
1776 2538 1.762957 CTCATAGGGGTAGGGTGTGTG 59.237 57.143 0.00 0.00 0.00 3.82
1777 2539 1.970226 GCTCATAGGGGTAGGGTGTGT 60.970 57.143 0.00 0.00 0.00 3.72
1778 2540 0.759346 GCTCATAGGGGTAGGGTGTG 59.241 60.000 0.00 0.00 0.00 3.82
1779 2541 0.341961 TGCTCATAGGGGTAGGGTGT 59.658 55.000 0.00 0.00 0.00 4.16
1780 2542 0.759346 GTGCTCATAGGGGTAGGGTG 59.241 60.000 0.00 0.00 0.00 4.61
1781 2543 0.400093 GGTGCTCATAGGGGTAGGGT 60.400 60.000 0.00 0.00 0.00 4.34
1782 2544 0.104934 AGGTGCTCATAGGGGTAGGG 60.105 60.000 0.00 0.00 0.00 3.53
1783 2545 1.343069 GAGGTGCTCATAGGGGTAGG 58.657 60.000 0.00 0.00 0.00 3.18
1784 2546 1.343069 GGAGGTGCTCATAGGGGTAG 58.657 60.000 0.00 0.00 31.08 3.18
1785 2547 0.469331 CGGAGGTGCTCATAGGGGTA 60.469 60.000 0.00 0.00 31.08 3.69
1786 2548 1.762460 CGGAGGTGCTCATAGGGGT 60.762 63.158 0.00 0.00 31.08 4.95
1787 2549 1.457643 TCGGAGGTGCTCATAGGGG 60.458 63.158 0.00 0.00 31.08 4.79
1788 2550 0.468214 TCTCGGAGGTGCTCATAGGG 60.468 60.000 4.96 0.00 31.08 3.53
1789 2551 0.958091 CTCTCGGAGGTGCTCATAGG 59.042 60.000 4.96 0.00 31.08 2.57
1790 2552 1.606668 GTCTCTCGGAGGTGCTCATAG 59.393 57.143 4.96 0.00 31.08 2.23
1791 2553 1.213182 AGTCTCTCGGAGGTGCTCATA 59.787 52.381 4.96 0.00 31.08 2.15
1792 2554 0.033601 AGTCTCTCGGAGGTGCTCAT 60.034 55.000 4.96 0.00 31.08 2.90
1793 2555 0.962855 CAGTCTCTCGGAGGTGCTCA 60.963 60.000 4.96 0.00 31.08 4.26
1794 2556 0.678366 TCAGTCTCTCGGAGGTGCTC 60.678 60.000 4.96 0.00 0.00 4.26
1795 2557 0.679640 CTCAGTCTCTCGGAGGTGCT 60.680 60.000 4.96 0.00 35.32 4.40
1796 2558 1.806568 CTCAGTCTCTCGGAGGTGC 59.193 63.158 4.96 0.00 35.32 5.01
1797 2559 1.662438 GGCTCAGTCTCTCGGAGGTG 61.662 65.000 4.96 0.00 38.48 4.00
1798 2560 1.379309 GGCTCAGTCTCTCGGAGGT 60.379 63.158 4.96 0.00 38.48 3.85
1799 2561 2.477176 CGGCTCAGTCTCTCGGAGG 61.477 68.421 4.96 0.00 38.48 4.30
1800 2562 2.477176 CCGGCTCAGTCTCTCGGAG 61.477 68.421 0.00 0.00 42.94 4.63
1801 2563 2.438614 CCGGCTCAGTCTCTCGGA 60.439 66.667 0.00 0.00 42.94 4.55
1802 2564 4.200283 GCCGGCTCAGTCTCTCGG 62.200 72.222 22.15 0.00 43.13 4.63
1803 2565 1.448119 TATGCCGGCTCAGTCTCTCG 61.448 60.000 29.70 0.00 0.00 4.04
1804 2566 0.965439 ATATGCCGGCTCAGTCTCTC 59.035 55.000 29.70 0.00 0.00 3.20
1805 2567 0.965439 GATATGCCGGCTCAGTCTCT 59.035 55.000 29.70 3.16 0.00 3.10
1806 2568 0.676184 TGATATGCCGGCTCAGTCTC 59.324 55.000 29.70 15.31 0.00 3.36
1807 2569 1.274728 GATGATATGCCGGCTCAGTCT 59.725 52.381 29.70 8.26 0.00 3.24
1808 2570 1.274728 AGATGATATGCCGGCTCAGTC 59.725 52.381 29.70 19.55 0.00 3.51
1809 2571 1.346062 AGATGATATGCCGGCTCAGT 58.654 50.000 29.70 13.44 0.00 3.41
1810 2572 2.074576 CAAGATGATATGCCGGCTCAG 58.925 52.381 29.70 7.35 0.00 3.35
1811 2573 1.693606 TCAAGATGATATGCCGGCTCA 59.306 47.619 29.70 23.34 0.00 4.26
1812 2574 2.028658 TCTCAAGATGATATGCCGGCTC 60.029 50.000 29.70 17.89 0.00 4.70
1813 2575 1.973515 TCTCAAGATGATATGCCGGCT 59.026 47.619 29.70 15.76 0.00 5.52
1814 2576 2.462456 TCTCAAGATGATATGCCGGC 57.538 50.000 22.73 22.73 0.00 6.13
1815 2577 5.062683 CGTAAATCTCAAGATGATATGCCGG 59.937 44.000 0.00 0.00 34.49 6.13
1816 2578 5.863935 TCGTAAATCTCAAGATGATATGCCG 59.136 40.000 0.00 0.00 34.49 5.69
1817 2579 7.386299 ACTTCGTAAATCTCAAGATGATATGCC 59.614 37.037 0.00 0.00 34.49 4.40
1818 2580 8.304202 ACTTCGTAAATCTCAAGATGATATGC 57.696 34.615 0.00 0.00 34.49 3.14
1819 2581 9.468532 TGACTTCGTAAATCTCAAGATGATATG 57.531 33.333 0.00 0.00 34.49 1.78
1820 2582 9.469807 GTGACTTCGTAAATCTCAAGATGATAT 57.530 33.333 0.00 0.00 34.49 1.63
1821 2583 7.921214 GGTGACTTCGTAAATCTCAAGATGATA 59.079 37.037 0.00 0.00 34.49 2.15
1822 2584 6.758886 GGTGACTTCGTAAATCTCAAGATGAT 59.241 38.462 0.00 0.00 34.49 2.45
1823 2585 6.100004 GGTGACTTCGTAAATCTCAAGATGA 58.900 40.000 0.00 0.00 34.49 2.92
1824 2586 5.004821 CGGTGACTTCGTAAATCTCAAGATG 59.995 44.000 0.00 0.00 34.49 2.90
1825 2587 5.103000 CGGTGACTTCGTAAATCTCAAGAT 58.897 41.667 0.00 0.00 36.07 2.40
1826 2588 4.022589 ACGGTGACTTCGTAAATCTCAAGA 60.023 41.667 0.00 0.00 39.22 3.02
1827 2589 4.235360 ACGGTGACTTCGTAAATCTCAAG 58.765 43.478 0.00 0.00 39.22 3.02
1828 2590 4.247267 ACGGTGACTTCGTAAATCTCAA 57.753 40.909 0.00 0.00 39.22 3.02
1829 2591 3.928727 ACGGTGACTTCGTAAATCTCA 57.071 42.857 0.00 0.00 39.22 3.27
1830 2592 4.349501 CCTACGGTGACTTCGTAAATCTC 58.650 47.826 0.00 0.00 41.62 2.75
1831 2593 3.428589 GCCTACGGTGACTTCGTAAATCT 60.429 47.826 0.00 0.00 41.62 2.40
1832 2594 2.856557 GCCTACGGTGACTTCGTAAATC 59.143 50.000 0.00 0.00 41.62 2.17
1833 2595 2.733227 CGCCTACGGTGACTTCGTAAAT 60.733 50.000 0.00 0.00 41.62 1.40
1834 2596 1.401409 CGCCTACGGTGACTTCGTAAA 60.401 52.381 0.00 0.00 41.62 2.01
1835 2597 0.168788 CGCCTACGGTGACTTCGTAA 59.831 55.000 0.00 0.00 41.62 3.18
1836 2598 0.955428 ACGCCTACGGTGACTTCGTA 60.955 55.000 0.00 0.00 46.04 3.43
1837 2599 2.192608 GACGCCTACGGTGACTTCGT 62.193 60.000 0.00 0.00 46.04 3.85
1838 2600 1.513586 GACGCCTACGGTGACTTCG 60.514 63.158 0.00 0.00 46.04 3.79
1839 2601 0.179169 GAGACGCCTACGGTGACTTC 60.179 60.000 0.00 0.00 46.04 3.01
1840 2602 1.881602 GAGACGCCTACGGTGACTT 59.118 57.895 0.00 0.00 46.04 3.01
1841 2603 2.396955 CGAGACGCCTACGGTGACT 61.397 63.158 0.00 0.00 46.04 3.41
1842 2604 2.099831 CGAGACGCCTACGGTGAC 59.900 66.667 0.00 0.00 46.04 3.67
1843 2605 2.359107 ACGAGACGCCTACGGTGA 60.359 61.111 0.00 0.00 46.04 4.02
1844 2606 2.099831 GACGAGACGCCTACGGTG 59.900 66.667 0.00 0.00 46.04 4.94
1845 2607 3.494336 CGACGAGACGCCTACGGT 61.494 66.667 0.00 0.00 46.04 4.83
1846 2608 3.431683 GACGACGAGACGCCTACGG 62.432 68.421 0.00 0.00 46.04 4.02
1847 2609 3.747514 CGACGACGAGACGCCTACG 62.748 68.421 0.00 0.00 43.40 3.51
1848 2610 2.021106 CGACGACGAGACGCCTAC 59.979 66.667 0.00 0.00 42.66 3.18
1849 2611 2.125952 TCGACGACGAGACGCCTA 60.126 61.111 5.75 0.00 43.81 3.93
1870 2632 2.814280 TTCAGTGGAAGGAGACGTTC 57.186 50.000 0.00 0.00 0.00 3.95
1871 2633 2.807108 GCTTTCAGTGGAAGGAGACGTT 60.807 50.000 13.22 0.00 32.18 3.99
1872 2634 1.270358 GCTTTCAGTGGAAGGAGACGT 60.270 52.381 13.22 0.00 32.18 4.34
1873 2635 1.433534 GCTTTCAGTGGAAGGAGACG 58.566 55.000 13.22 0.00 32.18 4.18
1874 2636 1.270358 ACGCTTTCAGTGGAAGGAGAC 60.270 52.381 13.22 0.00 34.35 3.36
1875 2637 1.048601 ACGCTTTCAGTGGAAGGAGA 58.951 50.000 13.22 0.00 34.35 3.71
1876 2638 2.743636 TACGCTTTCAGTGGAAGGAG 57.256 50.000 13.22 0.84 36.28 3.69
1877 2639 2.416836 CGATACGCTTTCAGTGGAAGGA 60.417 50.000 13.22 0.00 32.18 3.36
1878 2640 1.927174 CGATACGCTTTCAGTGGAAGG 59.073 52.381 13.22 5.80 33.82 3.46
1892 2654 0.031585 TCAGGATTTCCGGCGATACG 59.968 55.000 9.30 0.00 42.08 3.06
1893 2655 2.234300 TTCAGGATTTCCGGCGATAC 57.766 50.000 9.30 0.00 42.08 2.24
1894 2656 2.992124 TTTCAGGATTTCCGGCGATA 57.008 45.000 9.30 0.00 42.08 2.92
1895 2657 2.348411 ATTTCAGGATTTCCGGCGAT 57.652 45.000 9.30 0.00 42.08 4.58
1896 2658 2.992124 TATTTCAGGATTTCCGGCGA 57.008 45.000 9.30 0.00 42.08 5.54
1897 2659 4.568152 ATTTATTTCAGGATTTCCGGCG 57.432 40.909 0.00 0.00 42.08 6.46
1898 2660 4.976116 CGAATTTATTTCAGGATTTCCGGC 59.024 41.667 0.00 0.00 42.08 6.13
1899 2661 6.371809 TCGAATTTATTTCAGGATTTCCGG 57.628 37.500 0.00 0.00 42.08 5.14
1900 2662 8.181573 TCTTTCGAATTTATTTCAGGATTTCCG 58.818 33.333 0.00 0.00 42.08 4.30
1901 2663 9.855021 TTCTTTCGAATTTATTTCAGGATTTCC 57.145 29.630 0.00 0.00 33.66 3.13
1905 2667 8.678199 GGACTTCTTTCGAATTTATTTCAGGAT 58.322 33.333 0.00 0.00 33.66 3.24
1906 2668 7.663905 TGGACTTCTTTCGAATTTATTTCAGGA 59.336 33.333 0.00 0.00 33.66 3.86
1907 2669 7.750903 GTGGACTTCTTTCGAATTTATTTCAGG 59.249 37.037 0.00 0.00 33.66 3.86
1908 2670 8.289618 TGTGGACTTCTTTCGAATTTATTTCAG 58.710 33.333 0.00 0.00 33.66 3.02
1909 2671 8.160521 TGTGGACTTCTTTCGAATTTATTTCA 57.839 30.769 0.00 0.00 33.66 2.69
1910 2672 9.278734 GATGTGGACTTCTTTCGAATTTATTTC 57.721 33.333 0.00 0.00 0.00 2.17
1911 2673 8.792633 TGATGTGGACTTCTTTCGAATTTATTT 58.207 29.630 0.00 0.00 0.00 1.40
1912 2674 8.237267 GTGATGTGGACTTCTTTCGAATTTATT 58.763 33.333 0.00 0.00 0.00 1.40
1913 2675 7.148239 GGTGATGTGGACTTCTTTCGAATTTAT 60.148 37.037 0.00 0.00 0.00 1.40
1914 2676 6.148811 GGTGATGTGGACTTCTTTCGAATTTA 59.851 38.462 0.00 0.00 0.00 1.40
1915 2677 5.048713 GGTGATGTGGACTTCTTTCGAATTT 60.049 40.000 0.00 0.00 0.00 1.82
1916 2678 4.455877 GGTGATGTGGACTTCTTTCGAATT 59.544 41.667 0.00 0.00 0.00 2.17
1917 2679 4.003648 GGTGATGTGGACTTCTTTCGAAT 58.996 43.478 0.00 0.00 0.00 3.34
1918 2680 3.399330 GGTGATGTGGACTTCTTTCGAA 58.601 45.455 0.00 0.00 0.00 3.71
1919 2681 2.289444 GGGTGATGTGGACTTCTTTCGA 60.289 50.000 0.00 0.00 0.00 3.71
1920 2682 2.076863 GGGTGATGTGGACTTCTTTCG 58.923 52.381 0.00 0.00 0.00 3.46
2006 2783 1.580994 GGATTAGGGGGTGCCTTGGT 61.581 60.000 0.00 0.00 0.00 3.67
2103 2880 1.202200 CGGAGGAGCAGTTAAGTCTCG 60.202 57.143 0.00 0.00 0.00 4.04
2124 2901 1.818674 GGAGACGATGCCCAAACAAAT 59.181 47.619 0.00 0.00 0.00 2.32
2223 3000 1.192146 TGAGCGCCTAACCTGGACTT 61.192 55.000 2.29 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.