Multiple sequence alignment - TraesCS2D01G458500

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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 TraesCS2D01G458500 chr2D 100.000 8369 0 0 1 8369 565472270 565480638 0.000000e+00 15455.0
1 TraesCS2D01G458500 chr2D 93.023 43 3 0 511 553 352119151 352119109 7.010000e-06 63.9
2 TraesCS2D01G458500 chr2D 92.500 40 3 0 513 552 24935267 24935306 3.260000e-04 58.4
3 TraesCS2D01G458500 chr2D 100.000 30 0 0 5688 5717 169967402 169967373 1.000000e-03 56.5
4 TraesCS2D01G458500 chr2A 95.954 2768 85 12 2316 5066 705874380 705877137 0.000000e+00 4466.0
5 TraesCS2D01G458500 chr2A 94.503 2565 88 27 5069 7609 705877187 705879722 0.000000e+00 3906.0
6 TraesCS2D01G458500 chr2A 89.085 1420 79 27 922 2314 705872934 705874304 0.000000e+00 1694.0
7 TraesCS2D01G458500 chr2A 93.485 614 26 4 7626 8235 705879780 705880383 0.000000e+00 900.0
8 TraesCS2D01G458500 chr2A 93.182 44 3 0 510 553 562064544 562064587 1.950000e-06 65.8
9 TraesCS2D01G458500 chr2B 94.783 1955 67 11 3141 5071 677803621 677805564 0.000000e+00 3013.0
10 TraesCS2D01G458500 chr2B 88.889 2529 139 62 5827 8302 677806503 677808942 0.000000e+00 2983.0
11 TraesCS2D01G458500 chr2B 89.822 1572 81 22 782 2315 677801132 677802662 0.000000e+00 1943.0
12 TraesCS2D01G458500 chr2B 95.078 833 29 5 2316 3139 677802737 677803566 0.000000e+00 1301.0
13 TraesCS2D01G458500 chr2B 96.199 763 27 2 5069 5830 677805620 677806381 0.000000e+00 1247.0
14 TraesCS2D01G458500 chr2B 84.485 767 79 22 1 742 677797052 677797803 0.000000e+00 721.0
15 TraesCS2D01G458500 chr2B 87.006 531 40 15 7512 8036 677850975 677851482 9.420000e-159 571.0
16 TraesCS2D01G458500 chr2B 92.982 57 2 1 5024 5078 677805621 677805565 1.940000e-11 82.4
17 TraesCS2D01G458500 chr2B 100.000 31 0 0 5687 5717 383562673 383562703 3.260000e-04 58.4
18 TraesCS2D01G458500 chr2B 100.000 30 0 0 5688 5717 291570972 291570943 1.000000e-03 56.5
19 TraesCS2D01G458500 chr7A 89.520 458 32 7 1301 1744 464241266 464240811 4.380000e-157 566.0
20 TraesCS2D01G458500 chr4A 89.301 458 32 8 1301 1744 701677882 701678336 7.340000e-155 558.0
21 TraesCS2D01G458500 chr4A 83.548 389 29 13 922 1282 701677435 701677816 1.740000e-86 331.0
22 TraesCS2D01G458500 chr3A 88.646 458 35 7 1301 1744 58630751 58631205 7.390000e-150 542.0
23 TraesCS2D01G458500 chr3A 82.609 207 24 6 5715 5917 275289569 275289767 1.120000e-38 172.0
24 TraesCS2D01G458500 chr3A 96.875 32 1 0 5685 5716 335463523 335463554 4.000000e-03 54.7
25 TraesCS2D01G458500 chr5D 82.698 341 49 8 2 340 387292474 387292142 2.280000e-75 294.0
26 TraesCS2D01G458500 chr6D 85.990 207 19 8 5714 5917 276144679 276144878 6.580000e-51 213.0
27 TraesCS2D01G458500 chr6D 93.750 48 1 1 5033 5078 39676414 39676461 4.190000e-08 71.3
28 TraesCS2D01G458500 chr6D 100.000 30 0 0 5688 5717 178882326 178882355 1.000000e-03 56.5
29 TraesCS2D01G458500 chr6A 85.024 207 21 8 5714 5917 399836708 399836509 1.420000e-47 202.0
30 TraesCS2D01G458500 chr6A 80.833 120 21 2 509 626 182327832 182327713 8.940000e-15 93.5
31 TraesCS2D01G458500 chr6B 84.541 207 22 8 5714 5917 438102950 438103149 6.630000e-46 196.0
32 TraesCS2D01G458500 chr7D 83.500 200 24 5 5722 5917 431921366 431921172 2.400000e-40 178.0
33 TraesCS2D01G458500 chr4D 82.609 207 29 4 5715 5918 277395814 277395612 8.630000e-40 176.0
34 TraesCS2D01G458500 chr3D 82.381 210 28 6 5715 5917 210623459 210623252 3.110000e-39 174.0
35 TraesCS2D01G458500 chr3D 95.833 48 0 1 5033 5078 19854375 19854422 9.010000e-10 76.8
36 TraesCS2D01G458500 chr3D 100.000 30 0 0 5688 5717 575560709 575560680 1.000000e-03 56.5
37 TraesCS2D01G458500 chr3D 96.875 32 1 0 5685 5716 254116805 254116774 4.000000e-03 54.7
38 TraesCS2D01G458500 chr3B 73.171 410 89 15 83 476 421578557 421578961 2.450000e-25 128.0
39 TraesCS2D01G458500 chr4B 94.231 52 1 1 5029 5078 67733996 67734047 2.500000e-10 78.7
40 TraesCS2D01G458500 chr4B 97.619 42 1 0 5030 5071 656162615 656162656 1.170000e-08 73.1
41 TraesCS2D01G458500 chr1A 90.741 54 3 1 5026 5077 464858612 464858665 4.190000e-08 71.3
42 TraesCS2D01G458500 chr1A 87.302 63 5 3 5011 5071 566135550 566135611 1.510000e-07 69.4
43 TraesCS2D01G458500 chr1A 97.143 35 1 0 509 543 584586359 584586393 9.070000e-05 60.2
44 TraesCS2D01G458500 chr1B 97.222 36 1 0 510 545 550268075 550268110 2.520000e-05 62.1
45 TraesCS2D01G458500 chr1B 94.737 38 2 0 516 553 555779605 555779568 9.070000e-05 60.2
46 TraesCS2D01G458500 chr1D 97.143 35 1 0 509 543 487134323 487134357 9.070000e-05 60.2


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 TraesCS2D01G458500 chr2D 565472270 565480638 8368 False 15455.0 15455 100.000000 1 8369 1 chr2D.!!$F2 8368
1 TraesCS2D01G458500 chr2A 705872934 705880383 7449 False 2741.5 4466 93.256750 922 8235 4 chr2A.!!$F2 7313
2 TraesCS2D01G458500 chr2B 677797052 677808942 11890 False 1868.0 3013 91.542667 1 8302 6 chr2B.!!$F3 8301
3 TraesCS2D01G458500 chr2B 677850975 677851482 507 False 571.0 571 87.006000 7512 8036 1 chr2B.!!$F2 524
4 TraesCS2D01G458500 chr4A 701677435 701678336 901 False 444.5 558 86.424500 922 1744 2 chr4A.!!$F1 822

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
925 4249 0.035056 ACCAGCAAGTATCCCACTGC 60.035 55.000 0.00 0.0 37.63 4.40 F
1904 5348 1.075482 CTTTTGGGCCTCCAGCTGA 59.925 57.895 17.39 0.0 45.04 4.26 F
2914 6441 1.005924 CAGGGTGGAAATACAGGCCTT 59.994 52.381 0.00 0.0 0.00 4.35 F
3219 6799 1.403647 CGTTGATGGGTGCTTCGAGTA 60.404 52.381 0.00 0.0 0.00 2.59 F
3881 7477 2.234168 CCATGGATTCAATGTGTGCCAA 59.766 45.455 5.56 0.0 0.00 4.52 F
4744 8344 3.268330 CTGCAATGACTACATGAGCTGT 58.732 45.455 0.00 0.0 42.13 4.40 F
5717 9382 0.550914 AAGGTTGTGGAGGAGCAACA 59.449 50.000 9.20 0.0 44.70 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2914 6441 0.751277 CTGGAACACTGCCACCAACA 60.751 55.000 0.00 0.0 31.85 3.33 R
3379 6964 1.201429 AACCTTGTGATCTCGGGCCT 61.201 55.000 0.84 0.0 0.00 5.19 R
4744 8344 2.170397 TGAGTGTTTGCAAGAGACCTGA 59.830 45.455 0.00 0.0 0.00 3.86 R
4971 8575 2.490903 ACATGCATGCAGTTTCTTCTCC 59.509 45.455 26.69 0.0 0.00 3.71 R
5560 9222 5.523369 CGGATTCTCCAAAAATTAGATGCC 58.477 41.667 0.00 0.0 35.91 4.40 R
6640 10431 0.033208 CTTTCATTAGCCCCAGCCCA 60.033 55.000 0.00 0.0 41.25 5.36 R
7616 11459 0.036164 ACACACACACACACACAGGT 59.964 50.000 0.00 0.0 0.00 4.00 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 2.621526 ACAAGGTGTTTGACGGAATTCC 59.378 45.455 15.01 15.01 39.21 3.01
28 29 4.069304 CAAGGTGTTTGACGGAATTCCTA 58.931 43.478 22.05 5.93 39.21 2.94
29 30 3.671716 AGGTGTTTGACGGAATTCCTAC 58.328 45.455 22.05 15.22 0.00 3.18
30 31 3.071892 AGGTGTTTGACGGAATTCCTACA 59.928 43.478 22.05 17.44 0.00 2.74
32 33 4.457949 GGTGTTTGACGGAATTCCTACAAT 59.542 41.667 22.05 2.59 32.29 2.71
33 34 5.390613 GTGTTTGACGGAATTCCTACAATG 58.609 41.667 22.05 8.00 32.29 2.82
34 35 5.048991 GTGTTTGACGGAATTCCTACAATGT 60.049 40.000 22.05 11.22 32.29 2.71
37 38 7.392113 TGTTTGACGGAATTCCTACAATGTAAT 59.608 33.333 22.05 0.00 32.29 1.89
40 41 8.343168 TGACGGAATTCCTACAATGTAATTTT 57.657 30.769 22.05 0.00 31.22 1.82
41 42 8.798402 TGACGGAATTCCTACAATGTAATTTTT 58.202 29.630 22.05 0.00 31.22 1.94
125 126 2.828520 AGACGAGTTCATGTGACTCCAT 59.171 45.455 19.26 11.88 0.00 3.41
151 152 1.605710 GCCACGATTCCTCATTGGATG 59.394 52.381 0.00 0.00 45.68 3.51
174 175 2.305927 GGAGTTTGACATGGAGGAGGAA 59.694 50.000 0.00 0.00 0.00 3.36
185 186 2.503356 TGGAGGAGGAAGAAGATCTTGC 59.497 50.000 14.00 4.79 43.95 4.01
186 187 2.503356 GGAGGAGGAAGAAGATCTTGCA 59.497 50.000 14.00 0.00 45.70 4.08
189 190 5.163258 GGAGGAGGAAGAAGATCTTGCATTA 60.163 44.000 14.00 0.00 45.70 1.90
207 208 5.712217 CATTAATCTTGGCAATGCACAAG 57.288 39.130 22.00 22.00 44.09 3.16
218 220 3.854784 GCAATGCACAAGAACAAGAGGTC 60.855 47.826 0.00 0.00 0.00 3.85
223 225 3.458189 CACAAGAACAAGAGGTCGAAGT 58.542 45.455 0.00 0.00 0.00 3.01
227 229 4.457834 AGAACAAGAGGTCGAAGTATGG 57.542 45.455 0.00 0.00 0.00 2.74
233 235 0.611714 AGGTCGAAGTATGGCGGTTT 59.388 50.000 0.00 0.00 0.00 3.27
234 236 1.826720 AGGTCGAAGTATGGCGGTTTA 59.173 47.619 0.00 0.00 0.00 2.01
240 242 4.864247 TCGAAGTATGGCGGTTTAGTTTAC 59.136 41.667 0.00 0.00 0.00 2.01
242 244 4.454728 AGTATGGCGGTTTAGTTTACGA 57.545 40.909 0.00 0.00 0.00 3.43
243 245 4.176271 AGTATGGCGGTTTAGTTTACGAC 58.824 43.478 0.00 0.00 34.33 4.34
244 246 1.794512 TGGCGGTTTAGTTTACGACC 58.205 50.000 0.00 0.00 32.33 4.79
245 247 1.069823 TGGCGGTTTAGTTTACGACCA 59.930 47.619 0.00 0.00 32.33 4.02
247 249 2.134346 GCGGTTTAGTTTACGACCACA 58.866 47.619 0.00 0.00 32.41 4.17
276 278 3.523157 TGTGGAGATAATGGAAAGAGGCA 59.477 43.478 0.00 0.00 0.00 4.75
279 281 4.166725 TGGAGATAATGGAAAGAGGCACAT 59.833 41.667 0.00 0.00 0.00 3.21
284 286 0.401356 TGGAAAGAGGCACATGAGCA 59.599 50.000 17.11 0.00 35.83 4.26
285 287 1.202915 TGGAAAGAGGCACATGAGCAA 60.203 47.619 17.11 0.00 35.83 3.91
286 288 2.097825 GGAAAGAGGCACATGAGCAAT 58.902 47.619 17.11 4.65 35.83 3.56
287 289 2.494870 GGAAAGAGGCACATGAGCAATT 59.505 45.455 17.11 5.32 35.83 2.32
288 290 3.508762 GAAAGAGGCACATGAGCAATTG 58.491 45.455 17.11 0.00 35.83 2.32
289 291 2.502142 AGAGGCACATGAGCAATTGA 57.498 45.000 17.11 0.00 35.83 2.57
290 292 3.014304 AGAGGCACATGAGCAATTGAT 57.986 42.857 17.11 1.34 35.83 2.57
291 293 2.688446 AGAGGCACATGAGCAATTGATG 59.312 45.455 17.11 6.84 35.83 3.07
312 315 3.584834 GCACAACTATTTTGGGCGAAAT 58.415 40.909 0.00 0.00 39.20 2.17
340 343 4.261280 GCTATCCAGAGAGGTACTTTCGAC 60.261 50.000 0.00 0.00 45.01 4.20
346 362 3.932089 AGAGAGGTACTTTCGACGTCTAC 59.068 47.826 14.70 8.57 45.01 2.59
348 364 1.734465 AGGTACTTTCGACGTCTACGG 59.266 52.381 14.70 4.11 39.06 4.02
353 369 2.240040 CTTTCGACGTCTACGGACTTG 58.760 52.381 14.70 0.00 44.95 3.16
398 414 6.690194 ATAAAGCAACATGATCAGTCCTTC 57.310 37.500 0.00 0.00 0.00 3.46
399 415 2.996631 AGCAACATGATCAGTCCTTCC 58.003 47.619 0.00 0.00 0.00 3.46
400 416 2.306805 AGCAACATGATCAGTCCTTCCA 59.693 45.455 0.00 0.00 0.00 3.53
401 417 2.681848 GCAACATGATCAGTCCTTCCAG 59.318 50.000 0.00 0.00 0.00 3.86
402 418 2.681848 CAACATGATCAGTCCTTCCAGC 59.318 50.000 0.00 0.00 0.00 4.85
404 420 2.306805 ACATGATCAGTCCTTCCAGCAA 59.693 45.455 0.00 0.00 0.00 3.91
405 421 3.245016 ACATGATCAGTCCTTCCAGCAAA 60.245 43.478 0.00 0.00 0.00 3.68
406 422 3.063510 TGATCAGTCCTTCCAGCAAAG 57.936 47.619 0.00 0.00 0.00 2.77
407 423 2.639347 TGATCAGTCCTTCCAGCAAAGA 59.361 45.455 0.00 0.00 0.00 2.52
424 440 1.534729 AGAAGGATTTGCACCGGAAC 58.465 50.000 9.46 0.00 0.00 3.62
487 503 2.490903 GCATGATGGCCTATGATGTTCC 59.509 50.000 16.16 0.00 33.49 3.62
489 505 1.072173 TGATGGCCTATGATGTTCCGG 59.928 52.381 3.32 0.00 0.00 5.14
490 506 1.072331 GATGGCCTATGATGTTCCGGT 59.928 52.381 3.32 0.00 0.00 5.28
502 518 4.764308 TGATGTTCCGGTTGATTTCATTGA 59.236 37.500 0.00 0.00 0.00 2.57
514 530 7.201902 GGTTGATTTCATTGATGGCCTATGTTA 60.202 37.037 3.32 0.00 31.38 2.41
652 675 5.739752 TTCGAGATGAAAAGTGCATATGG 57.260 39.130 4.56 0.00 32.37 2.74
654 677 3.562973 CGAGATGAAAAGTGCATATGGCT 59.437 43.478 4.56 0.00 45.15 4.75
667 690 3.573229 TGGCTCTGGGCAGCTGTT 61.573 61.111 16.64 0.00 43.20 3.16
686 709 2.589798 TGGAGACGTCACTTTTTCGT 57.410 45.000 19.50 0.00 40.49 3.85
687 710 3.713858 TGGAGACGTCACTTTTTCGTA 57.286 42.857 19.50 0.00 37.92 3.43
688 711 3.374745 TGGAGACGTCACTTTTTCGTAC 58.625 45.455 19.50 0.00 37.92 3.67
689 712 2.728318 GGAGACGTCACTTTTTCGTACC 59.272 50.000 19.50 0.13 37.92 3.34
690 713 3.374745 GAGACGTCACTTTTTCGTACCA 58.625 45.455 19.50 0.00 37.92 3.25
742 766 1.405105 CCGGTCATTTTAGGTGCCATG 59.595 52.381 0.00 0.00 0.00 3.66
744 768 2.491693 CGGTCATTTTAGGTGCCATGTT 59.508 45.455 0.00 0.00 0.00 2.71
750 1015 6.016276 GTCATTTTAGGTGCCATGTTATAGGG 60.016 42.308 0.00 0.00 0.00 3.53
768 1033 3.973425 AGGGCTGTTATTGAAGATGCTT 58.027 40.909 0.00 0.00 0.00 3.91
774 1039 7.260603 GGCTGTTATTGAAGATGCTTTTATGT 58.739 34.615 0.00 0.00 0.00 2.29
776 1041 9.956720 GCTGTTATTGAAGATGCTTTTATGTAT 57.043 29.630 0.00 0.00 0.00 2.29
904 4220 9.037737 CGGATAAAATCATTTCCGAACTAGTAA 57.962 33.333 3.23 0.00 37.85 2.24
910 4226 8.888579 AATCATTTCCGAACTAGTAATACCAG 57.111 34.615 0.00 0.00 0.00 4.00
911 4227 6.278363 TCATTTCCGAACTAGTAATACCAGC 58.722 40.000 0.00 0.00 0.00 4.85
913 4229 5.664294 TTCCGAACTAGTAATACCAGCAA 57.336 39.130 0.00 0.00 0.00 3.91
925 4249 0.035056 ACCAGCAAGTATCCCACTGC 60.035 55.000 0.00 0.00 37.63 4.40
998 4323 1.668419 GTGTCAGAATTCCCATCCCG 58.332 55.000 0.65 0.00 0.00 5.14
1223 4578 1.590259 GGACGATCTCTTCTGGCGC 60.590 63.158 0.00 0.00 0.00 6.53
1270 4699 4.201950 GGATTTGGATCGATTGTTCTGTGG 60.202 45.833 0.00 0.00 32.84 4.17
1275 4704 3.600388 GATCGATTGTTCTGTGGGTTCT 58.400 45.455 0.00 0.00 0.00 3.01
1279 4708 3.315191 CGATTGTTCTGTGGGTTCTGTTT 59.685 43.478 0.00 0.00 0.00 2.83
1340 4769 4.109050 TGTGAAAGTTTGTTGCGGATTTC 58.891 39.130 0.00 0.00 0.00 2.17
1506 4936 6.465439 TCTTAGAGTTTCAGTTGTCAGACA 57.535 37.500 0.00 0.00 0.00 3.41
1510 4940 5.112686 AGAGTTTCAGTTGTCAGACAGTTC 58.887 41.667 2.82 0.00 0.00 3.01
1518 4948 4.333926 AGTTGTCAGACAGTTCTTTCTTGC 59.666 41.667 2.82 0.00 0.00 4.01
1572 5010 7.012894 CCGATTTCTACAGATCTACAGAACTCT 59.987 40.741 21.19 10.99 29.36 3.24
1679 5123 4.713553 TGTATGGCATAACCCATGTGTAG 58.286 43.478 9.14 0.00 45.03 2.74
1691 5135 4.825085 ACCCATGTGTAGTTGGTTTACTTG 59.175 41.667 0.00 0.00 0.00 3.16
1764 5208 6.473758 ACAGAGGGAGTAGTTTTTATTGGAC 58.526 40.000 0.00 0.00 0.00 4.02
1802 5246 9.506042 TTATGATACATGATGATACCCAGGTAT 57.494 33.333 9.13 9.13 41.22 2.73
1810 5254 2.248950 TGATACCCAGGTATGTCCCTCA 59.751 50.000 14.07 3.05 40.93 3.86
1904 5348 1.075482 CTTTTGGGCCTCCAGCTGA 59.925 57.895 17.39 0.00 45.04 4.26
1958 5402 4.215399 GGATGATTCGTTTGGAGTTCAACA 59.785 41.667 0.00 0.00 34.67 3.33
2210 5654 7.596995 TCAAGCGGAATTTTAATTTAACACCAG 59.403 33.333 0.00 0.00 0.00 4.00
2211 5655 6.988522 AGCGGAATTTTAATTTAACACCAGT 58.011 32.000 0.00 0.00 0.00 4.00
2214 5658 9.361315 GCGGAATTTTAATTTAACACCAGTTAT 57.639 29.630 0.00 0.00 39.78 1.89
2242 5686 6.427547 GGATTTCCATTTTCTGACAATTGCAA 59.572 34.615 5.05 0.00 35.64 4.08
2288 5732 8.379902 GGCAGTAATCATTTTAATTGTTTTCGG 58.620 33.333 0.00 0.00 0.00 4.30
2453 5980 7.489113 CCAAGCATGTACTTTTTGATGTATTCC 59.511 37.037 0.00 0.00 0.00 3.01
2504 6031 8.819974 CAAATTGTTCAGAAAGTTGTTAGCATT 58.180 29.630 0.00 0.00 30.21 3.56
2561 6088 9.448438 TTTAGTAGCAATAGAAAATCAGCTTCA 57.552 29.630 0.00 0.00 33.83 3.02
2884 6411 1.136774 CGACTCGAGACGATTGGCA 59.863 57.895 28.92 0.00 34.61 4.92
2914 6441 1.005924 CAGGGTGGAAATACAGGCCTT 59.994 52.381 0.00 0.00 0.00 4.35
3095 6622 2.355010 ACTTCCTTTCTGTTGCTGCT 57.645 45.000 0.00 0.00 0.00 4.24
3219 6799 1.403647 CGTTGATGGGTGCTTCGAGTA 60.404 52.381 0.00 0.00 0.00 2.59
3239 6819 7.598869 TCGAGTATCCATATTCATGTTTAGCAC 59.401 37.037 0.00 0.00 0.00 4.40
3282 6862 4.457466 AGTTCACCGTACCTGTTCAAATT 58.543 39.130 0.00 0.00 0.00 1.82
3292 6872 7.094975 CCGTACCTGTTCAAATTCTTGTTGATA 60.095 37.037 0.00 0.00 35.03 2.15
3379 6964 7.885922 TCCATGTTACTGCTTTCCTTACATTTA 59.114 33.333 0.00 0.00 0.00 1.40
3505 7090 6.511416 TGTTTGGATTTGATGTCGTGAATTT 58.489 32.000 0.00 0.00 0.00 1.82
3606 7200 2.637382 TGTCTGCTGTCAGGTAAATGGA 59.363 45.455 1.14 0.00 40.69 3.41
3682 7276 6.016527 GGAAAATGAAGGGTAAAGTCGTCTTT 60.017 38.462 12.18 12.18 44.72 2.52
3779 7373 4.647424 ATGTTTTCTTTTGAGTTGCCGA 57.353 36.364 0.00 0.00 0.00 5.54
3881 7477 2.234168 CCATGGATTCAATGTGTGCCAA 59.766 45.455 5.56 0.00 0.00 4.52
3892 7488 3.415457 TGTGTGCCAATACAGTGATCA 57.585 42.857 0.00 0.00 0.00 2.92
3913 7509 8.529476 TGATCACTCATATAATCTGGTCATCAG 58.471 37.037 0.00 0.00 44.68 2.90
4547 8145 4.836125 AGCACTTATTTGTTGGTGAGTG 57.164 40.909 0.00 0.00 37.98 3.51
4744 8344 3.268330 CTGCAATGACTACATGAGCTGT 58.732 45.455 0.00 0.00 42.13 4.40
5060 8664 6.269194 TCCCTCCGTCCCATAATATAAGATT 58.731 40.000 0.00 0.00 0.00 2.40
5560 9222 6.940739 AGTTATAGCACAGGATATTAGCCAG 58.059 40.000 0.02 0.00 0.00 4.85
5717 9382 0.550914 AAGGTTGTGGAGGAGCAACA 59.449 50.000 9.20 0.00 44.70 3.33
5840 9630 9.726438 AGACAAAATAAATACTAGACTGCAGTT 57.274 29.630 22.65 13.26 0.00 3.16
5858 9648 7.176865 ACTGCAGTTGTATCTAGAAGTAGTCAA 59.823 37.037 15.25 0.00 0.00 3.18
5968 9758 3.313249 TCGATGTGCAAGCTGATATTTGG 59.687 43.478 0.00 0.00 0.00 3.28
6523 10314 5.745312 TGGCTTCAGTTTCTCAAGATAGA 57.255 39.130 0.00 0.00 0.00 1.98
6524 10315 5.482908 TGGCTTCAGTTTCTCAAGATAGAC 58.517 41.667 0.00 0.00 0.00 2.59
6723 10514 9.914834 AAGTATTTAAATACCATCTTACTGCCA 57.085 29.630 27.21 0.00 41.68 4.92
6757 10548 3.735746 GCACAAATTGTTACTTCAGTGCC 59.264 43.478 0.00 0.00 43.72 5.01
6829 10644 3.187637 GCGCACTTTAATGTTAGGTGTGA 59.812 43.478 0.30 0.00 39.73 3.58
6830 10645 4.669197 GCGCACTTTAATGTTAGGTGTGAG 60.669 45.833 0.30 10.60 39.73 3.51
6831 10646 4.451096 CGCACTTTAATGTTAGGTGTGAGT 59.549 41.667 12.07 0.00 39.73 3.41
6832 10647 5.614668 CGCACTTTAATGTTAGGTGTGAGTG 60.615 44.000 12.07 0.00 39.73 3.51
6833 10648 5.238650 GCACTTTAATGTTAGGTGTGAGTGT 59.761 40.000 0.00 0.00 35.61 3.55
6834 10649 6.658831 CACTTTAATGTTAGGTGTGAGTGTG 58.341 40.000 0.00 0.00 0.00 3.82
6835 10650 6.260050 CACTTTAATGTTAGGTGTGAGTGTGT 59.740 38.462 0.00 0.00 0.00 3.72
6836 10651 6.260050 ACTTTAATGTTAGGTGTGAGTGTGTG 59.740 38.462 0.00 0.00 0.00 3.82
6845 10660 2.935849 GTGTGAGTGTGTGACAATGTCA 59.064 45.455 12.63 12.63 40.50 3.58
6868 10683 7.859377 GTCATATTCTTGACTATTTGTGCATGG 59.141 37.037 0.00 0.00 42.22 3.66
6967 10789 6.240894 AGATTTTCAGTTATGCTCACTTCCA 58.759 36.000 0.00 0.00 0.00 3.53
6984 10806 0.181350 CCATACAACCCTGGAGGAGC 59.819 60.000 0.00 0.00 39.89 4.70
7045 10877 7.216494 AGCTCTGCCTTATTCTTCTTCTTATC 58.784 38.462 0.00 0.00 0.00 1.75
7079 10911 9.160496 AGAACAATACTTCATTTGTTTTTGCAA 57.840 25.926 0.00 0.00 43.95 4.08
7080 10912 9.766277 GAACAATACTTCATTTGTTTTTGCAAA 57.234 25.926 8.05 8.05 43.95 3.68
7082 10914 9.771915 ACAATACTTCATTTGTTTTTGCAAAAG 57.228 25.926 22.78 11.68 41.03 2.27
7088 10920 9.992384 CTTCATTTGTTTTTGCAAAAGAAAAAC 57.008 25.926 25.26 20.30 46.51 2.43
7104 10939 4.220602 AGAAAAACTTGCAGTTGTGTTCCT 59.779 37.500 2.88 0.00 38.66 3.36
7141 10977 4.339748 TGGCTGGTAATTATGCTTGACAA 58.660 39.130 7.61 0.00 0.00 3.18
7262 11103 0.981183 ATTGTCACCGGAGCAGGTAA 59.019 50.000 9.46 0.00 43.89 2.85
7281 11122 7.555195 GCAGGTAAGCTTCTTTTATTTACCCTA 59.445 37.037 0.00 0.00 42.59 3.53
7282 11123 9.628500 CAGGTAAGCTTCTTTTATTTACCCTAT 57.372 33.333 0.00 0.00 42.59 2.57
7288 11129 9.417561 AGCTTCTTTTATTTACCCTATTTACCC 57.582 33.333 0.00 0.00 0.00 3.69
7289 11130 9.417561 GCTTCTTTTATTTACCCTATTTACCCT 57.582 33.333 0.00 0.00 0.00 4.34
7306 11147 4.287766 ACCCTTGAGTATGGAACTGAAC 57.712 45.455 0.00 0.00 39.07 3.18
7340 11181 3.940209 TGTTTTCACCTGATTCATGCC 57.060 42.857 0.00 0.00 0.00 4.40
7497 11339 1.000607 TGTTGTCAGCGTCTGGAGTAC 60.001 52.381 6.95 0.00 31.51 2.73
7588 11431 1.079266 GCACAGGCACCTCAGAGAG 60.079 63.158 0.00 0.00 40.72 3.20
7592 11435 2.050144 ACAGGCACCTCAGAGAGAAAA 58.950 47.619 0.00 0.00 0.00 2.29
7650 11534 2.482336 TGTGTGTGTGTGTGTGAACTTC 59.518 45.455 0.00 0.00 0.00 3.01
7854 11738 5.034852 TGGTCTTCAACAATCACTCTTCA 57.965 39.130 0.00 0.00 0.00 3.02
7980 11874 0.169672 CAAATGAGAAGCGCCACCAG 59.830 55.000 2.29 0.00 0.00 4.00
7981 11875 0.962356 AAATGAGAAGCGCCACCAGG 60.962 55.000 2.29 0.00 38.23 4.45
8053 11948 6.672593 TCCCTATCATCTTGGCACTAAAAAT 58.327 36.000 0.00 0.00 0.00 1.82
8054 11949 7.811282 TCCCTATCATCTTGGCACTAAAAATA 58.189 34.615 0.00 0.00 0.00 1.40
8212 12107 0.955905 GCACGGTTTTTCTAAGGCCA 59.044 50.000 5.01 0.00 0.00 5.36
8226 12121 2.033194 GGCCAAGCTACACGGTGTC 61.033 63.158 18.43 4.33 0.00 3.67
8263 12160 3.209410 GCTGGATTCTGTTACAGGGATG 58.791 50.000 12.79 0.44 31.51 3.51
8302 12199 0.178950 ATGGAGCAGGATCCGAGCTA 60.179 55.000 27.67 17.38 42.77 3.32
8303 12200 0.178950 TGGAGCAGGATCCGAGCTAT 60.179 55.000 27.67 12.72 42.77 2.97
8304 12201 0.530288 GGAGCAGGATCCGAGCTATC 59.470 60.000 27.67 20.38 39.02 2.08
8305 12202 1.252175 GAGCAGGATCCGAGCTATCA 58.748 55.000 27.67 0.00 39.02 2.15
8306 12203 0.965439 AGCAGGATCCGAGCTATCAC 59.035 55.000 26.84 3.31 36.73 3.06
8307 12204 0.037790 GCAGGATCCGAGCTATCACC 60.038 60.000 20.77 0.00 0.00 4.02
8308 12205 1.332195 CAGGATCCGAGCTATCACCA 58.668 55.000 5.98 0.00 0.00 4.17
8309 12206 1.898472 CAGGATCCGAGCTATCACCAT 59.102 52.381 5.98 0.00 0.00 3.55
8310 12207 1.898472 AGGATCCGAGCTATCACCATG 59.102 52.381 5.98 0.00 0.00 3.66
8311 12208 1.620819 GGATCCGAGCTATCACCATGT 59.379 52.381 0.00 0.00 0.00 3.21
8312 12209 2.826128 GGATCCGAGCTATCACCATGTA 59.174 50.000 0.00 0.00 0.00 2.29
8313 12210 3.258372 GGATCCGAGCTATCACCATGTAA 59.742 47.826 0.00 0.00 0.00 2.41
8314 12211 4.262463 GGATCCGAGCTATCACCATGTAAA 60.262 45.833 0.00 0.00 0.00 2.01
8315 12212 4.746535 TCCGAGCTATCACCATGTAAAA 57.253 40.909 0.00 0.00 0.00 1.52
8316 12213 4.439057 TCCGAGCTATCACCATGTAAAAC 58.561 43.478 0.00 0.00 0.00 2.43
8317 12214 4.081365 TCCGAGCTATCACCATGTAAAACA 60.081 41.667 0.00 0.00 0.00 2.83
8318 12215 4.034048 CCGAGCTATCACCATGTAAAACAC 59.966 45.833 0.00 0.00 0.00 3.32
8319 12216 4.870426 CGAGCTATCACCATGTAAAACACT 59.130 41.667 0.00 0.00 0.00 3.55
8320 12217 5.220472 CGAGCTATCACCATGTAAAACACTG 60.220 44.000 0.00 0.00 0.00 3.66
8321 12218 4.943705 AGCTATCACCATGTAAAACACTGG 59.056 41.667 0.00 6.85 34.84 4.00
8322 12219 4.438744 GCTATCACCATGTAAAACACTGGC 60.439 45.833 0.00 0.00 33.19 4.85
8323 12220 3.222173 TCACCATGTAAAACACTGGCT 57.778 42.857 0.00 0.00 33.19 4.75
8324 12221 3.146066 TCACCATGTAAAACACTGGCTC 58.854 45.455 0.00 0.00 33.19 4.70
8325 12222 3.149196 CACCATGTAAAACACTGGCTCT 58.851 45.455 0.00 0.00 33.19 4.09
8326 12223 3.058016 CACCATGTAAAACACTGGCTCTG 60.058 47.826 0.00 0.00 33.19 3.35
8327 12224 2.489329 CCATGTAAAACACTGGCTCTGG 59.511 50.000 0.00 0.00 0.00 3.86
8328 12225 3.411446 CATGTAAAACACTGGCTCTGGA 58.589 45.455 0.00 0.00 0.00 3.86
8329 12226 2.846193 TGTAAAACACTGGCTCTGGAC 58.154 47.619 0.00 0.00 0.00 4.02
8330 12227 2.171659 TGTAAAACACTGGCTCTGGACA 59.828 45.455 0.00 0.00 0.00 4.02
8331 12228 2.664402 AAAACACTGGCTCTGGACAT 57.336 45.000 0.00 0.00 0.00 3.06
8332 12229 1.901591 AAACACTGGCTCTGGACATG 58.098 50.000 0.00 0.00 0.00 3.21
8333 12230 0.607489 AACACTGGCTCTGGACATGC 60.607 55.000 0.00 0.00 0.00 4.06
8334 12231 1.002990 CACTGGCTCTGGACATGCA 60.003 57.895 0.00 0.00 0.00 3.96
8335 12232 0.607217 CACTGGCTCTGGACATGCAA 60.607 55.000 0.00 0.00 0.00 4.08
8336 12233 0.322277 ACTGGCTCTGGACATGCAAG 60.322 55.000 0.00 0.00 34.18 4.01
8337 12234 0.322277 CTGGCTCTGGACATGCAAGT 60.322 55.000 0.00 0.00 0.00 3.16
8338 12235 0.321919 TGGCTCTGGACATGCAAGTC 60.322 55.000 13.60 13.60 37.80 3.01
8346 12243 0.445436 GACATGCAAGTCCTGAAGCG 59.555 55.000 10.98 0.00 32.36 4.68
8347 12244 0.035317 ACATGCAAGTCCTGAAGCGA 59.965 50.000 0.00 0.00 0.00 4.93
8348 12245 0.725686 CATGCAAGTCCTGAAGCGAG 59.274 55.000 0.00 0.00 0.00 5.03
8349 12246 1.023513 ATGCAAGTCCTGAAGCGAGC 61.024 55.000 0.00 0.00 0.00 5.03
8350 12247 2.394563 GCAAGTCCTGAAGCGAGCC 61.395 63.158 0.00 0.00 0.00 4.70
8351 12248 2.097038 CAAGTCCTGAAGCGAGCCG 61.097 63.158 0.00 0.00 0.00 5.52
8352 12249 3.302347 AAGTCCTGAAGCGAGCCGG 62.302 63.158 0.00 0.00 0.00 6.13
8353 12250 3.760035 GTCCTGAAGCGAGCCGGA 61.760 66.667 5.05 0.00 0.00 5.14
8354 12251 3.452786 TCCTGAAGCGAGCCGGAG 61.453 66.667 5.05 0.00 0.00 4.63
8355 12252 3.764466 CCTGAAGCGAGCCGGAGT 61.764 66.667 5.05 0.00 0.00 3.85
8356 12253 2.262915 CTGAAGCGAGCCGGAGTT 59.737 61.111 5.05 0.00 0.00 3.01
8357 12254 2.048222 TGAAGCGAGCCGGAGTTG 60.048 61.111 5.05 0.00 0.00 3.16
8358 12255 3.491652 GAAGCGAGCCGGAGTTGC 61.492 66.667 5.05 7.06 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 7.931578 AAATTACATTGTAGGAATTCCGTCA 57.068 32.000 18.82 17.59 42.08 4.35
40 41 4.512944 TGCAAAGAAAAGCACAACAACAAA 59.487 33.333 0.00 0.00 35.51 2.83
41 42 4.060900 TGCAAAGAAAAGCACAACAACAA 58.939 34.783 0.00 0.00 35.51 2.83
42 43 3.657634 TGCAAAGAAAAGCACAACAACA 58.342 36.364 0.00 0.00 35.51 3.33
43 44 4.863152 ATGCAAAGAAAAGCACAACAAC 57.137 36.364 0.00 0.00 44.49 3.32
107 108 5.362556 AAAAATGGAGTCACATGAACTCG 57.637 39.130 19.55 0.00 0.00 4.18
146 147 2.912295 TCCATGTCAAACTCCTCATCCA 59.088 45.455 0.00 0.00 0.00 3.41
151 152 2.093235 CCTCCTCCATGTCAAACTCCTC 60.093 54.545 0.00 0.00 0.00 3.71
174 175 5.889853 TGCCAAGATTAATGCAAGATCTTCT 59.110 36.000 4.57 0.00 37.88 2.85
185 186 5.412640 TCTTGTGCATTGCCAAGATTAATG 58.587 37.500 25.62 10.37 39.22 1.90
186 187 5.664294 TCTTGTGCATTGCCAAGATTAAT 57.336 34.783 25.62 0.00 39.22 1.40
189 190 3.069872 TGTTCTTGTGCATTGCCAAGATT 59.930 39.130 27.86 0.00 41.53 2.40
202 203 3.458189 ACTTCGACCTCTTGTTCTTGTG 58.542 45.455 0.00 0.00 0.00 3.33
207 208 2.930682 GCCATACTTCGACCTCTTGTTC 59.069 50.000 0.00 0.00 0.00 3.18
218 220 4.259530 CGTAAACTAAACCGCCATACTTCG 60.260 45.833 0.00 0.00 0.00 3.79
223 225 3.056250 TGGTCGTAAACTAAACCGCCATA 60.056 43.478 0.00 0.00 34.39 2.74
227 229 2.134346 TGTGGTCGTAAACTAAACCGC 58.866 47.619 0.00 0.00 41.59 5.68
247 249 9.401058 CTCTTTCCATTATCTCCACAAATACTT 57.599 33.333 0.00 0.00 0.00 2.24
262 264 3.282021 GCTCATGTGCCTCTTTCCATTA 58.718 45.455 8.59 0.00 0.00 1.90
265 267 0.401356 TGCTCATGTGCCTCTTTCCA 59.599 50.000 16.62 0.00 0.00 3.53
284 286 4.937015 GCCCAAAATAGTTGTGCATCAATT 59.063 37.500 0.00 0.00 38.38 2.32
285 287 4.506758 GCCCAAAATAGTTGTGCATCAAT 58.493 39.130 0.00 0.00 38.38 2.57
286 288 3.613671 CGCCCAAAATAGTTGTGCATCAA 60.614 43.478 0.00 0.00 0.00 2.57
287 289 2.094803 CGCCCAAAATAGTTGTGCATCA 60.095 45.455 0.00 0.00 0.00 3.07
288 290 2.163412 TCGCCCAAAATAGTTGTGCATC 59.837 45.455 0.00 0.00 0.00 3.91
289 291 2.166829 TCGCCCAAAATAGTTGTGCAT 58.833 42.857 0.00 0.00 0.00 3.96
290 292 1.610363 TCGCCCAAAATAGTTGTGCA 58.390 45.000 0.00 0.00 0.00 4.57
291 293 2.715737 TTCGCCCAAAATAGTTGTGC 57.284 45.000 0.00 0.00 0.00 4.57
293 295 4.086457 AGGATTTCGCCCAAAATAGTTGT 58.914 39.130 0.00 0.00 0.00 3.32
294 296 4.672409 GAGGATTTCGCCCAAAATAGTTG 58.328 43.478 0.00 0.00 0.00 3.16
295 297 3.377172 CGAGGATTTCGCCCAAAATAGTT 59.623 43.478 0.00 0.00 43.22 2.24
297 299 3.609103 CGAGGATTTCGCCCAAAATAG 57.391 47.619 0.00 0.00 43.22 1.73
308 311 4.173036 CTCTCTGGATAGCGAGGATTTC 57.827 50.000 0.00 0.00 33.19 2.17
323 326 2.743126 AGACGTCGAAAGTACCTCTCTG 59.257 50.000 10.46 0.00 0.00 3.35
359 375 8.087136 TGTTGCTTTATAGAATTGCAAATGTGA 58.913 29.630 1.71 0.00 43.72 3.58
375 391 5.591877 GGAAGGACTGATCATGTTGCTTTAT 59.408 40.000 0.00 0.00 0.00 1.40
377 393 3.760684 GGAAGGACTGATCATGTTGCTTT 59.239 43.478 0.00 0.00 0.00 3.51
378 394 3.245016 TGGAAGGACTGATCATGTTGCTT 60.245 43.478 0.00 0.54 0.00 3.91
380 396 2.681848 CTGGAAGGACTGATCATGTTGC 59.318 50.000 0.00 0.00 0.00 4.17
402 418 1.885887 TCCGGTGCAAATCCTTCTTTG 59.114 47.619 0.00 0.00 38.79 2.77
404 420 1.886542 GTTCCGGTGCAAATCCTTCTT 59.113 47.619 0.00 0.00 0.00 2.52
405 421 1.534729 GTTCCGGTGCAAATCCTTCT 58.465 50.000 0.00 0.00 0.00 2.85
406 422 0.168128 CGTTCCGGTGCAAATCCTTC 59.832 55.000 0.00 0.00 0.00 3.46
407 423 1.862602 GCGTTCCGGTGCAAATCCTT 61.863 55.000 0.00 0.00 0.00 3.36
412 428 2.718731 CAAGCGTTCCGGTGCAAA 59.281 55.556 16.16 0.00 37.73 3.68
419 435 1.154225 GCAATGACCAAGCGTTCCG 60.154 57.895 0.00 0.00 0.00 4.30
420 436 0.387239 GTGCAATGACCAAGCGTTCC 60.387 55.000 0.00 0.00 0.00 3.62
424 440 0.167470 CTCAGTGCAATGACCAAGCG 59.833 55.000 13.76 0.00 0.00 4.68
435 451 2.297315 CTGTGACCTTCTACTCAGTGCA 59.703 50.000 0.00 0.00 0.00 4.57
487 503 2.428171 AGGCCATCAATGAAATCAACCG 59.572 45.455 5.01 0.00 0.00 4.44
489 505 6.152932 ACATAGGCCATCAATGAAATCAAC 57.847 37.500 5.01 0.00 0.00 3.18
490 506 6.795144 AACATAGGCCATCAATGAAATCAA 57.205 33.333 5.01 0.00 0.00 2.57
502 518 6.554784 TCATCAAATCCATAACATAGGCCAT 58.445 36.000 5.01 0.00 0.00 4.40
558 581 9.566530 GTCCAAAACAAACAAAGCAATAATTTT 57.433 25.926 0.00 0.00 0.00 1.82
652 675 3.060615 CCAACAGCTGCCCAGAGC 61.061 66.667 15.27 0.00 44.14 4.09
654 677 1.842920 TCTCCAACAGCTGCCCAGA 60.843 57.895 15.27 7.39 0.00 3.86
667 690 2.589798 ACGAAAAAGTGACGTCTCCA 57.410 45.000 17.92 0.00 35.33 3.86
725 749 6.016276 CCCTATAACATGGCACCTAAAATGAC 60.016 42.308 0.00 0.00 0.00 3.06
728 752 4.832823 GCCCTATAACATGGCACCTAAAAT 59.167 41.667 0.00 0.00 44.70 1.82
742 766 6.712547 AGCATCTTCAATAACAGCCCTATAAC 59.287 38.462 0.00 0.00 0.00 1.89
744 768 6.439636 AGCATCTTCAATAACAGCCCTATA 57.560 37.500 0.00 0.00 0.00 1.31
750 1015 9.956720 ATACATAAAAGCATCTTCAATAACAGC 57.043 29.630 0.00 0.00 0.00 4.40
904 4220 2.158755 GCAGTGGGATACTTGCTGGTAT 60.159 50.000 0.00 2.66 37.60 2.73
908 4224 0.035152 TGGCAGTGGGATACTTGCTG 60.035 55.000 0.00 0.00 37.60 4.41
910 4226 0.035056 ACTGGCAGTGGGATACTTGC 60.035 55.000 21.37 0.00 37.60 4.01
911 4227 1.278985 TGACTGGCAGTGGGATACTTG 59.721 52.381 27.45 0.00 37.60 3.16
913 4229 1.656587 TTGACTGGCAGTGGGATACT 58.343 50.000 27.45 0.00 41.36 2.12
925 4249 2.372690 CGACCTCGCGTTTGACTGG 61.373 63.158 5.77 1.03 0.00 4.00
1010 4343 1.755008 GAGTGGGAGAGGAGGGACG 60.755 68.421 0.00 0.00 0.00 4.79
1100 4437 2.440817 GGATGAACGGACGGGGGAT 61.441 63.158 0.00 0.00 0.00 3.85
1163 4500 2.284151 GAGGAGGAGGGGAGGACC 59.716 72.222 0.00 0.00 39.11 4.46
1223 4578 3.244044 GGCAAGATAGAGCTCCTTACCAG 60.244 52.174 10.93 0.00 0.00 4.00
1270 4699 4.584743 AGAAAGATCCCACAAAACAGAACC 59.415 41.667 0.00 0.00 0.00 3.62
1275 4704 4.405358 AGCAAAGAAAGATCCCACAAAACA 59.595 37.500 0.00 0.00 0.00 2.83
1279 4708 2.297033 GCAGCAAAGAAAGATCCCACAA 59.703 45.455 0.00 0.00 0.00 3.33
1518 4948 7.768120 GGAGCCATATCAATCTTGGTTCTATAG 59.232 40.741 5.26 0.00 39.76 1.31
1572 5010 0.035820 GTCCCCTACATTTCGCCACA 60.036 55.000 0.00 0.00 0.00 4.17
1679 5123 4.267690 GCTTTGCTCAACAAGTAAACCAAC 59.732 41.667 0.00 0.00 40.06 3.77
1691 5135 5.234757 TGTTCAAATTCATGCTTTGCTCAAC 59.765 36.000 12.95 12.43 34.36 3.18
1802 5246 4.721274 TCAATCCATATTGAGTGAGGGACA 59.279 41.667 3.05 0.00 45.17 4.02
1904 5348 5.067674 TGTTGTGCTTCTTTTGTTGCTATCT 59.932 36.000 0.00 0.00 0.00 1.98
1936 5380 5.356882 TGTTGAACTCCAAACGAATCATC 57.643 39.130 0.00 0.00 36.36 2.92
1958 5402 1.600485 CCGCAGAACCAAAAGTACGTT 59.400 47.619 0.00 0.00 0.00 3.99
2220 5664 8.772705 GTTATTGCAATTGTCAGAAAATGGAAA 58.227 29.630 18.75 0.00 0.00 3.13
2242 5686 6.014499 ACTGCCACTTCAGTACTACTTGTTAT 60.014 38.462 0.00 0.00 44.77 1.89
2286 5730 1.135689 GCAACCACTACAAATCAGCCG 60.136 52.381 0.00 0.00 0.00 5.52
2288 5732 3.504863 CATGCAACCACTACAAATCAGC 58.495 45.455 0.00 0.00 0.00 4.26
2504 6031 5.038651 TCATGAGACATCCAATGCATACA 57.961 39.130 0.00 0.00 0.00 2.29
2561 6088 2.322355 ATGAAGCGCTACATTCTGCT 57.678 45.000 12.05 0.00 39.89 4.24
2690 6217 7.880160 AGTTTGCTGCATGAGGTATTATTAA 57.120 32.000 1.84 0.00 0.00 1.40
2884 6411 2.715763 TTCCACCCTGAGGAACTACT 57.284 50.000 0.00 0.00 41.55 2.57
2914 6441 0.751277 CTGGAACACTGCCACCAACA 60.751 55.000 0.00 0.00 31.85 3.33
3219 6799 9.224267 GTGATAGTGCTAAACATGAATATGGAT 57.776 33.333 0.00 0.00 38.66 3.41
3267 6847 6.055231 TCAACAAGAATTTGAACAGGTACG 57.945 37.500 0.00 0.00 37.73 3.67
3282 6862 9.897744 GATGAACAGAAAAACATATCAACAAGA 57.102 29.630 0.00 0.00 0.00 3.02
3292 6872 9.736023 GTCTAAAACAGATGAACAGAAAAACAT 57.264 29.630 0.00 0.00 35.17 2.71
3343 6928 5.999044 AGCAGTAACATGGAAATCTCAGAT 58.001 37.500 0.00 0.00 0.00 2.90
3379 6964 1.201429 AACCTTGTGATCTCGGGCCT 61.201 55.000 0.84 0.00 0.00 5.19
3606 7200 5.594317 ACAACCAGCTTCACAAGTAAGAATT 59.406 36.000 0.00 0.00 0.00 2.17
3682 7276 6.846505 AGAACAGAATCATAGAGGGAATACCA 59.153 38.462 0.00 0.00 43.89 3.25
3776 7370 2.710096 ATGGGTCAATGGTAACTCGG 57.290 50.000 0.00 0.00 37.61 4.63
3881 7477 9.319060 ACCAGATTATATGAGTGATCACTGTAT 57.681 33.333 32.50 26.86 42.66 2.29
4309 7907 6.405278 TTCTCTTGATGGAGCATCGTAATA 57.595 37.500 0.00 0.00 43.14 0.98
4547 8145 7.845066 AGAAGGGAAATAGTTTGTATTCGAC 57.155 36.000 0.00 0.00 0.00 4.20
4744 8344 2.170397 TGAGTGTTTGCAAGAGACCTGA 59.830 45.455 0.00 0.00 0.00 3.86
4971 8575 2.490903 ACATGCATGCAGTTTCTTCTCC 59.509 45.455 26.69 0.00 0.00 3.71
5060 8664 8.715191 ACAATATTCTGTTTTCTTGCAAAACA 57.285 26.923 13.13 13.13 44.85 2.83
5077 8739 8.741101 TGTACAATGCAGTCAAAACAATATTC 57.259 30.769 0.00 0.00 0.00 1.75
5560 9222 5.523369 CGGATTCTCCAAAAATTAGATGCC 58.477 41.667 0.00 0.00 35.91 4.40
5596 9260 7.471721 TGGCAAAATCTAAAGATTCACGTATG 58.528 34.615 5.71 1.63 43.41 2.39
5752 9417 8.844244 GCCATGAGTAGAATGTTGAATCTTAAT 58.156 33.333 0.00 0.00 0.00 1.40
5954 9744 5.331902 CGTTAACCACCAAATATCAGCTTG 58.668 41.667 0.00 0.00 0.00 4.01
5968 9758 0.735287 GGAGACTCGGCGTTAACCAC 60.735 60.000 6.85 0.00 0.00 4.16
6012 9802 4.622701 ATTTTTCGAGCACTTCATAGCC 57.377 40.909 0.00 0.00 0.00 3.93
6013 9803 7.183580 AGATATTTTTCGAGCACTTCATAGC 57.816 36.000 0.00 0.00 0.00 2.97
6640 10431 0.033208 CTTTCATTAGCCCCAGCCCA 60.033 55.000 0.00 0.00 41.25 5.36
6719 10510 3.947841 GCGCGAACACAAGTGGCA 61.948 61.111 12.10 0.00 34.19 4.92
6720 10511 3.947841 TGCGCGAACACAAGTGGC 61.948 61.111 12.10 0.00 34.19 5.01
6783 10574 8.499162 CGCCATAGTCTAAAGGAATTGAAATAG 58.501 37.037 6.03 0.00 0.00 1.73
6794 10585 2.604046 AGTGCGCCATAGTCTAAAGG 57.396 50.000 4.18 0.00 0.00 3.11
6795 10586 6.037172 ACATTAAAGTGCGCCATAGTCTAAAG 59.963 38.462 4.18 0.00 0.00 1.85
6797 10588 5.424757 ACATTAAAGTGCGCCATAGTCTAA 58.575 37.500 4.18 0.00 0.00 2.10
6798 10589 5.018539 ACATTAAAGTGCGCCATAGTCTA 57.981 39.130 4.18 0.00 0.00 2.59
6829 10644 6.936335 TCAAGAATATGACATTGTCACACACT 59.064 34.615 21.19 14.77 45.65 3.55
6830 10645 7.017645 GTCAAGAATATGACATTGTCACACAC 58.982 38.462 21.19 13.01 45.65 3.82
6831 10646 7.132694 GTCAAGAATATGACATTGTCACACA 57.867 36.000 21.19 10.29 45.65 3.72
6845 10660 6.321945 TGCCATGCACAAATAGTCAAGAATAT 59.678 34.615 0.00 0.00 31.71 1.28
6868 10683 1.269174 TGTGGCACAACACACATATGC 59.731 47.619 19.74 0.00 45.70 3.14
6967 10789 1.972660 GCGCTCCTCCAGGGTTGTAT 61.973 60.000 0.00 0.00 37.39 2.29
6984 10806 0.297230 CCAACGTTGCACAAAAAGCG 59.703 50.000 22.93 1.10 33.85 4.68
7088 10920 2.851195 AGGTAGGAACACAACTGCAAG 58.149 47.619 0.00 0.00 42.29 4.01
7104 10939 4.422984 ACCAGCCAACTAGTAGAAAGGTA 58.577 43.478 3.59 0.00 0.00 3.08
7141 10977 6.646240 GCACCTGATCACAATACAACATTTTT 59.354 34.615 0.00 0.00 0.00 1.94
7186 11027 8.170730 AGAATTGAGTTAGGGTCCATTAACTTT 58.829 33.333 15.40 8.89 39.52 2.66
7262 11103 9.417561 GGGTAAATAGGGTAAATAAAAGAAGCT 57.582 33.333 0.00 0.00 0.00 3.74
7281 11122 6.636454 TCAGTTCCATACTCAAGGGTAAAT 57.364 37.500 0.00 0.00 33.85 1.40
7282 11123 6.043938 AGTTCAGTTCCATACTCAAGGGTAAA 59.956 38.462 0.00 0.00 33.85 2.01
7283 11124 5.546499 AGTTCAGTTCCATACTCAAGGGTAA 59.454 40.000 0.00 0.00 33.85 2.85
7284 11125 5.091552 AGTTCAGTTCCATACTCAAGGGTA 58.908 41.667 0.00 0.00 33.85 3.69
7285 11126 3.910627 AGTTCAGTTCCATACTCAAGGGT 59.089 43.478 0.00 0.00 33.85 4.34
7286 11127 4.559862 AGTTCAGTTCCATACTCAAGGG 57.440 45.455 0.00 0.00 33.85 3.95
7287 11128 6.037786 TGTAGTTCAGTTCCATACTCAAGG 57.962 41.667 0.00 0.00 33.85 3.61
7288 11129 8.553459 AAATGTAGTTCAGTTCCATACTCAAG 57.447 34.615 0.00 0.00 33.85 3.02
7289 11130 8.918202 AAAATGTAGTTCAGTTCCATACTCAA 57.082 30.769 0.00 0.00 33.85 3.02
7306 11147 6.646240 CAGGTGAAAACATTGGGAAAATGTAG 59.354 38.462 4.27 0.00 39.73 2.74
7340 11181 1.871039 CCTGTTGGTGTAGAAACCGTG 59.129 52.381 0.00 0.00 43.73 4.94
7417 11259 5.068987 ACAGACAGATCTCTTCTATCCAAGC 59.931 44.000 0.00 0.00 27.13 4.01
7460 11302 7.096065 GCTGACAACAACAGGAATTTTATTCAC 60.096 37.037 0.00 0.00 36.09 3.18
7462 11304 6.088085 CGCTGACAACAACAGGAATTTTATTC 59.912 38.462 0.00 0.00 36.09 1.75
7497 11339 9.941664 GATGTCCATCTGAATAATTGTTTACAG 57.058 33.333 0.00 0.00 35.04 2.74
7612 11455 2.625790 ACACACACACACACAGGTTTTT 59.374 40.909 0.00 0.00 0.00 1.94
7615 11458 1.164411 CACACACACACACACAGGTT 58.836 50.000 0.00 0.00 0.00 3.50
7616 11459 0.036164 ACACACACACACACACAGGT 59.964 50.000 0.00 0.00 0.00 4.00
7617 11460 0.447406 CACACACACACACACACAGG 59.553 55.000 0.00 0.00 0.00 4.00
7620 11500 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
7905 11789 4.669206 TGCAGAATGTTTTGGTGATGTT 57.331 36.364 0.00 0.00 39.31 2.71
7908 11792 7.342799 AGGTAATATGCAGAATGTTTTGGTGAT 59.657 33.333 0.00 0.00 39.31 3.06
7980 11874 5.578336 GGAGCTTGAGATTTTTGTTAATGCC 59.422 40.000 0.00 0.00 0.00 4.40
7981 11875 5.578336 GGGAGCTTGAGATTTTTGTTAATGC 59.422 40.000 0.00 0.00 0.00 3.56
8054 11949 9.342308 CATGTATTAGTACCACATTCTGGAATT 57.658 33.333 0.00 0.00 43.95 2.17
8235 12132 4.065088 TGTAACAGAATCCAGCACAGTTC 58.935 43.478 0.00 0.00 0.00 3.01
8236 12133 4.067896 CTGTAACAGAATCCAGCACAGTT 58.932 43.478 0.00 0.00 32.44 3.16
8244 12141 3.843619 TCACATCCCTGTAACAGAATCCA 59.156 43.478 0.00 0.00 33.14 3.41
8247 12144 3.264193 TGCTCACATCCCTGTAACAGAAT 59.736 43.478 0.00 0.00 33.14 2.40
8263 12160 1.266718 TCTCCGCAAAAATGTGCTCAC 59.733 47.619 0.00 0.00 42.62 3.51
8279 12176 0.829602 TCGGATCCTGCTCCATCTCC 60.830 60.000 10.75 0.00 34.78 3.71
8280 12177 0.602562 CTCGGATCCTGCTCCATCTC 59.397 60.000 10.75 0.00 34.78 2.75
8302 12199 3.758554 GAGCCAGTGTTTTACATGGTGAT 59.241 43.478 0.00 0.00 32.79 3.06
8303 12200 3.146066 GAGCCAGTGTTTTACATGGTGA 58.854 45.455 0.00 0.00 32.79 4.02
8304 12201 3.058016 CAGAGCCAGTGTTTTACATGGTG 60.058 47.826 0.00 0.00 32.79 4.17
8305 12202 3.149196 CAGAGCCAGTGTTTTACATGGT 58.851 45.455 0.00 0.00 32.79 3.55
8306 12203 2.489329 CCAGAGCCAGTGTTTTACATGG 59.511 50.000 0.00 0.00 33.12 3.66
8307 12204 3.189287 GTCCAGAGCCAGTGTTTTACATG 59.811 47.826 0.00 0.00 0.00 3.21
8308 12205 3.181445 TGTCCAGAGCCAGTGTTTTACAT 60.181 43.478 0.00 0.00 0.00 2.29
8309 12206 2.171659 TGTCCAGAGCCAGTGTTTTACA 59.828 45.455 0.00 0.00 0.00 2.41
8310 12207 2.846193 TGTCCAGAGCCAGTGTTTTAC 58.154 47.619 0.00 0.00 0.00 2.01
8311 12208 3.411446 CATGTCCAGAGCCAGTGTTTTA 58.589 45.455 0.00 0.00 0.00 1.52
8312 12209 2.233271 CATGTCCAGAGCCAGTGTTTT 58.767 47.619 0.00 0.00 0.00 2.43
8313 12210 1.901591 CATGTCCAGAGCCAGTGTTT 58.098 50.000 0.00 0.00 0.00 2.83
8314 12211 0.607489 GCATGTCCAGAGCCAGTGTT 60.607 55.000 0.00 0.00 0.00 3.32
8315 12212 1.002868 GCATGTCCAGAGCCAGTGT 60.003 57.895 0.00 0.00 0.00 3.55
8316 12213 0.607217 TTGCATGTCCAGAGCCAGTG 60.607 55.000 0.00 0.00 0.00 3.66
8317 12214 0.322277 CTTGCATGTCCAGAGCCAGT 60.322 55.000 0.00 0.00 0.00 4.00
8318 12215 0.322277 ACTTGCATGTCCAGAGCCAG 60.322 55.000 0.00 0.00 0.00 4.85
8319 12216 0.321919 GACTTGCATGTCCAGAGCCA 60.322 55.000 19.37 0.00 0.00 4.75
8320 12217 2.475666 GACTTGCATGTCCAGAGCC 58.524 57.895 19.37 0.00 0.00 4.70
8327 12224 0.445436 CGCTTCAGGACTTGCATGTC 59.555 55.000 21.33 21.33 36.31 3.06
8328 12225 0.035317 TCGCTTCAGGACTTGCATGT 59.965 50.000 4.68 4.68 0.00 3.21
8329 12226 0.725686 CTCGCTTCAGGACTTGCATG 59.274 55.000 0.00 0.00 0.00 4.06
8330 12227 1.023513 GCTCGCTTCAGGACTTGCAT 61.024 55.000 0.00 0.00 0.00 3.96
8331 12228 1.669115 GCTCGCTTCAGGACTTGCA 60.669 57.895 0.00 0.00 0.00 4.08
8332 12229 2.394563 GGCTCGCTTCAGGACTTGC 61.395 63.158 0.00 0.00 0.00 4.01
8333 12230 2.097038 CGGCTCGCTTCAGGACTTG 61.097 63.158 0.00 0.00 0.00 3.16
8334 12231 2.262915 CGGCTCGCTTCAGGACTT 59.737 61.111 0.00 0.00 0.00 3.01
8335 12232 3.764466 CCGGCTCGCTTCAGGACT 61.764 66.667 0.00 0.00 0.00 3.85
8336 12233 3.708220 CTCCGGCTCGCTTCAGGAC 62.708 68.421 0.00 0.00 0.00 3.85
8337 12234 3.452786 CTCCGGCTCGCTTCAGGA 61.453 66.667 0.00 0.00 0.00 3.86
8338 12235 3.302347 AACTCCGGCTCGCTTCAGG 62.302 63.158 0.00 0.00 0.00 3.86
8339 12236 2.097038 CAACTCCGGCTCGCTTCAG 61.097 63.158 0.00 0.00 0.00 3.02
8340 12237 2.048222 CAACTCCGGCTCGCTTCA 60.048 61.111 0.00 0.00 0.00 3.02
8341 12238 3.491652 GCAACTCCGGCTCGCTTC 61.492 66.667 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.