Multiple sequence alignment - TraesCS6D01G302200

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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 TraesCS6D01G302200 chr6D 100.000 3289 0 0 1 3289 411609565 411612853 0.000000e+00 6074
1 TraesCS6D01G302200 chr6D 100.000 1938 0 0 3640 5577 411613204 411615141 0.000000e+00 3579
2 TraesCS6D01G302200 chr6B 93.960 1871 75 23 1449 3289 618936913 618938775 0.000000e+00 2795
3 TraesCS6D01G302200 chr6B 88.256 1669 148 27 3640 5295 618938831 618940464 0.000000e+00 1953
4 TraesCS6D01G302200 chr6B 92.116 723 41 11 706 1418 618936196 618936912 0.000000e+00 1005
5 TraesCS6D01G302200 chr6B 90.625 256 8 7 5315 5559 618941769 618942019 5.390000e-85 326
6 TraesCS6D01G302200 chr6A 92.674 1870 89 22 1449 3289 556527210 556529060 0.000000e+00 2651
7 TraesCS6D01G302200 chr6A 93.272 1189 52 17 3640 4807 556529115 556530296 0.000000e+00 1727
8 TraesCS6D01G302200 chr6A 91.873 726 40 11 707 1418 556526489 556527209 0.000000e+00 996
9 TraesCS6D01G302200 chr6A 90.374 748 55 13 4824 5559 556530366 556531108 0.000000e+00 966
10 TraesCS6D01G302200 chr6A 88.889 540 54 6 131 666 556525683 556526220 0.000000e+00 660
11 TraesCS6D01G302200 chr2D 83.094 834 80 31 2173 2958 545942587 545941767 0.000000e+00 702
12 TraesCS6D01G302200 chr2D 84.256 578 69 12 1598 2165 545943282 545942717 1.370000e-150 544
13 TraesCS6D01G302200 chr2D 81.157 605 78 17 4942 5523 396668691 396669282 2.370000e-123 453
14 TraesCS6D01G302200 chr2D 89.970 329 27 5 2964 3289 545941721 545941396 2.400000e-113 420
15 TraesCS6D01G302200 chr2D 87.259 259 31 1 3640 3896 545941341 545941083 1.520000e-75 294
16 TraesCS6D01G302200 chr2D 88.362 232 23 2 997 1228 545943774 545943547 5.500000e-70 276
17 TraesCS6D01G302200 chr2D 79.494 356 33 16 4357 4706 545940631 545940310 3.380000e-52 217
18 TraesCS6D01G302200 chr2D 88.356 146 8 7 1 144 460386425 460386563 3.460000e-37 167
19 TraesCS6D01G302200 chr2A 82.885 818 77 35 2190 2958 687004296 687003493 0.000000e+00 676
20 TraesCS6D01G302200 chr2A 84.413 571 57 10 1711 2259 687004882 687004322 2.960000e-147 532
21 TraesCS6D01G302200 chr2A 81.157 605 78 17 4942 5523 534630847 534631438 2.370000e-123 453
22 TraesCS6D01G302200 chr2A 89.394 330 27 7 2964 3289 687003449 687003124 5.200000e-110 409
23 TraesCS6D01G302200 chr2A 85.769 260 33 3 3640 3896 687003069 687002811 7.120000e-69 272
24 TraesCS6D01G302200 chr2A 83.262 233 21 9 4357 4585 687002352 687002134 1.230000e-46 198
25 TraesCS6D01G302200 chr2A 91.473 129 7 4 1 126 227782628 227782755 2.070000e-39 174
26 TraesCS6D01G302200 chr2A 78.810 269 50 6 134 398 644250920 644250655 2.070000e-39 174
27 TraesCS6D01G302200 chr2A 79.227 207 42 1 193 398 620703589 620703795 5.820000e-30 143
28 TraesCS6D01G302200 chr2B 84.956 452 52 7 2519 2958 652620414 652619967 1.430000e-120 444
29 TraesCS6D01G302200 chr2B 91.159 328 25 3 2964 3289 652619921 652619596 5.130000e-120 442
30 TraesCS6D01G302200 chr2B 81.952 543 62 20 5006 5523 470064954 470065485 1.440000e-115 427
31 TraesCS6D01G302200 chr2B 86.873 259 31 2 3640 3896 652619541 652619284 2.540000e-73 287
32 TraesCS6D01G302200 chr2B 88.362 232 23 2 997 1228 652620741 652620514 5.500000e-70 276
33 TraesCS6D01G302200 chr2B 84.817 191 17 4 4395 4585 652618666 652618488 1.230000e-41 182
34 TraesCS6D01G302200 chr4A 84.135 208 31 2 3687 3894 707065268 707065473 3.410000e-47 200
35 TraesCS6D01G302200 chr4A 75.934 241 56 2 141 379 611594916 611595156 7.590000e-24 122
36 TraesCS6D01G302200 chr1B 84.135 208 31 2 3687 3894 360872288 360872083 3.410000e-47 200
37 TraesCS6D01G302200 chr1B 81.683 202 30 5 148 345 623897629 623897431 1.610000e-35 161
38 TraesCS6D01G302200 chr1A 83.173 208 33 2 3687 3894 561151161 561150956 7.380000e-44 189
39 TraesCS6D01G302200 chr1A 87.662 154 12 6 1 148 419055738 419055890 7.430000e-39 172
40 TraesCS6D01G302200 chr3D 95.690 116 2 3 1 115 593752875 593752988 3.430000e-42 183
41 TraesCS6D01G302200 chr3D 94.167 120 4 3 1 119 539928682 539928565 4.440000e-41 180
42 TraesCS6D01G302200 chr1D 95.690 116 2 2 1 113 135769949 135769834 3.430000e-42 183
43 TraesCS6D01G302200 chr1D 79.336 271 47 6 134 398 389330990 389330723 1.230000e-41 182
44 TraesCS6D01G302200 chr4D 92.188 128 2 8 4 128 298741913 298741791 2.070000e-39 174
45 TraesCS6D01G302200 chr4D 79.913 229 38 8 134 359 375155720 375155497 1.610000e-35 161
46 TraesCS6D01G302200 chr3A 92.000 125 8 2 1 124 433388226 433388349 2.070000e-39 174
47 TraesCS6D01G302200 chr3A 98.020 101 1 1 1 100 558750052 558750152 2.070000e-39 174
48 TraesCS6D01G302200 chr5D 80.583 206 39 1 152 356 342859085 342858880 2.080000e-34 158
49 TraesCS6D01G302200 chr7A 73.529 476 91 18 142 586 149029364 149028893 1.250000e-31 148
50 TraesCS6D01G302200 chr5B 76.678 283 54 11 134 409 477563596 477563319 4.500000e-31 147


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 TraesCS6D01G302200 chr6D 411609565 411615141 5576 False 4826.500000 6074 100.000000 1 5577 2 chr6D.!!$F1 5576
1 TraesCS6D01G302200 chr6B 618936196 618942019 5823 False 1519.750000 2795 91.239250 706 5559 4 chr6B.!!$F1 4853
2 TraesCS6D01G302200 chr6A 556525683 556531108 5425 False 1400.000000 2651 91.416400 131 5559 5 chr6A.!!$F1 5428
3 TraesCS6D01G302200 chr2D 396668691 396669282 591 False 453.000000 453 81.157000 4942 5523 1 chr2D.!!$F1 581
4 TraesCS6D01G302200 chr2D 545940310 545943774 3464 True 408.833333 702 85.405833 997 4706 6 chr2D.!!$R1 3709
5 TraesCS6D01G302200 chr2A 534630847 534631438 591 False 453.000000 453 81.157000 4942 5523 1 chr2A.!!$F2 581
6 TraesCS6D01G302200 chr2A 687002134 687004882 2748 True 417.400000 676 85.144600 1711 4585 5 chr2A.!!$R2 2874
7 TraesCS6D01G302200 chr2B 470064954 470065485 531 False 427.000000 427 81.952000 5006 5523 1 chr2B.!!$F1 517
8 TraesCS6D01G302200 chr2B 652618488 652620741 2253 True 326.200000 444 87.233400 997 4585 5 chr2B.!!$R1 3588

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
259 261 0.029163 TCCCCCATCATTAGAGGGCA 60.029 55.000 0.00 0.0 44.28 5.36 F
423 426 0.237498 GTTGTTGGCCTTAGCACGAC 59.763 55.000 3.32 0.0 42.56 4.34 F
2100 2369 0.238289 CGGTGTCCATGTTCTTGCAC 59.762 55.000 0.00 0.0 0.00 4.57 F
3948 4472 3.482722 TCCAGTAGTCGTTTTAGCTCG 57.517 47.619 0.00 0.0 0.00 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2081 2350 0.238289 GTGCAAGAACATGGACACCG 59.762 55.000 0.00 0.0 40.88 4.94 R
2336 2780 0.109342 ACAGCCTTGTGAGGAAGTGG 59.891 55.000 0.00 0.0 46.74 4.00 R
4016 4546 2.765807 ATACTCGCCAGGCCAGCT 60.766 61.111 5.87 0.0 0.00 4.24 R
5186 5942 1.354031 TGTCAGGCCCACATGTTACAT 59.646 47.619 0.00 0.0 0.00 2.29 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
24 25 7.490962 TTCCGGTTAATACAATTCTAGCATG 57.509 36.000 0.00 0.00 0.00 4.06
25 26 6.822442 TCCGGTTAATACAATTCTAGCATGA 58.178 36.000 0.00 0.00 0.00 3.07
26 27 7.276658 TCCGGTTAATACAATTCTAGCATGAA 58.723 34.615 0.00 0.00 0.00 2.57
27 28 7.936847 TCCGGTTAATACAATTCTAGCATGAAT 59.063 33.333 0.00 0.00 38.19 2.57
28 29 9.214957 CCGGTTAATACAATTCTAGCATGAATA 57.785 33.333 0.00 0.00 35.82 1.75
86 87 7.881775 AACAACTTTATTATTGCCTCTAGGG 57.118 36.000 0.00 0.00 35.18 3.53
99 100 4.982241 CCTCTAGGGCATATTTCCTTCA 57.018 45.455 0.00 0.00 34.75 3.02
100 101 4.904241 CCTCTAGGGCATATTTCCTTCAG 58.096 47.826 0.00 0.00 34.75 3.02
101 102 4.263243 CCTCTAGGGCATATTTCCTTCAGG 60.263 50.000 0.00 2.64 34.75 3.86
102 103 4.307259 TCTAGGGCATATTTCCTTCAGGT 58.693 43.478 0.00 0.00 34.75 4.00
103 104 3.584733 AGGGCATATTTCCTTCAGGTC 57.415 47.619 0.00 0.00 36.34 3.85
104 105 2.852449 AGGGCATATTTCCTTCAGGTCA 59.148 45.455 0.00 0.00 36.34 4.02
105 106 3.464833 AGGGCATATTTCCTTCAGGTCAT 59.535 43.478 0.00 0.00 36.34 3.06
106 107 4.665009 AGGGCATATTTCCTTCAGGTCATA 59.335 41.667 0.00 0.00 36.34 2.15
107 108 5.006386 GGGCATATTTCCTTCAGGTCATAG 58.994 45.833 0.00 0.00 36.34 2.23
108 109 5.006386 GGCATATTTCCTTCAGGTCATAGG 58.994 45.833 0.00 0.00 36.34 2.57
109 110 5.006386 GCATATTTCCTTCAGGTCATAGGG 58.994 45.833 0.00 0.00 36.34 3.53
110 111 5.221925 GCATATTTCCTTCAGGTCATAGGGA 60.222 44.000 0.00 0.00 36.34 4.20
111 112 6.523150 GCATATTTCCTTCAGGTCATAGGGAT 60.523 42.308 0.00 0.00 36.34 3.85
112 113 4.778213 TTTCCTTCAGGTCATAGGGATG 57.222 45.455 0.00 0.00 36.34 3.51
113 114 3.421394 TCCTTCAGGTCATAGGGATGT 57.579 47.619 0.00 0.00 34.41 3.06
114 115 3.041211 TCCTTCAGGTCATAGGGATGTG 58.959 50.000 0.00 0.00 34.41 3.21
115 116 2.105477 CCTTCAGGTCATAGGGATGTGG 59.895 54.545 0.00 0.00 34.41 4.17
116 117 2.568546 TCAGGTCATAGGGATGTGGT 57.431 50.000 0.00 0.00 34.41 4.16
117 118 2.118679 TCAGGTCATAGGGATGTGGTG 58.881 52.381 0.00 0.00 34.41 4.17
118 119 1.141657 CAGGTCATAGGGATGTGGTGG 59.858 57.143 0.00 0.00 34.41 4.61
119 120 1.009552 AGGTCATAGGGATGTGGTGGA 59.990 52.381 0.00 0.00 34.41 4.02
120 121 2.057922 GGTCATAGGGATGTGGTGGAT 58.942 52.381 0.00 0.00 34.41 3.41
121 122 2.039084 GGTCATAGGGATGTGGTGGATC 59.961 54.545 0.00 0.00 34.41 3.36
122 123 2.975489 GTCATAGGGATGTGGTGGATCT 59.025 50.000 0.00 0.00 34.41 2.75
123 124 3.007398 GTCATAGGGATGTGGTGGATCTC 59.993 52.174 0.00 0.00 34.41 2.75
124 125 2.866923 TAGGGATGTGGTGGATCTCA 57.133 50.000 0.00 0.00 0.00 3.27
125 126 1.971149 AGGGATGTGGTGGATCTCAA 58.029 50.000 0.00 0.00 0.00 3.02
126 127 1.561542 AGGGATGTGGTGGATCTCAAC 59.438 52.381 0.00 0.00 0.00 3.18
127 128 1.408822 GGGATGTGGTGGATCTCAACC 60.409 57.143 0.00 0.00 30.29 3.77
128 129 1.408822 GGATGTGGTGGATCTCAACCC 60.409 57.143 1.23 0.00 30.29 4.11
129 130 1.561542 GATGTGGTGGATCTCAACCCT 59.438 52.381 1.23 0.00 30.29 4.34
130 131 1.444933 TGTGGTGGATCTCAACCCTT 58.555 50.000 1.23 0.00 30.29 3.95
131 132 1.073763 TGTGGTGGATCTCAACCCTTG 59.926 52.381 1.23 0.00 30.29 3.61
132 133 1.351017 GTGGTGGATCTCAACCCTTGA 59.649 52.381 1.23 0.00 38.17 3.02
133 134 2.025887 GTGGTGGATCTCAACCCTTGAT 60.026 50.000 1.23 0.00 39.30 2.57
134 135 2.649312 TGGTGGATCTCAACCCTTGATT 59.351 45.455 1.23 0.00 39.30 2.57
172 173 2.618709 GTTTGTGTCCTGTTCAGGAAGG 59.381 50.000 21.13 0.00 40.06 3.46
173 174 1.507140 TGTGTCCTGTTCAGGAAGGT 58.493 50.000 21.13 0.00 40.06 3.50
200 201 1.144936 GGCGTCTCCCTGAAGATGG 59.855 63.158 0.00 0.00 33.65 3.51
206 207 4.626042 CGTCTCCCTGAAGATGGAATAAG 58.374 47.826 0.00 0.00 0.00 1.73
212 213 7.016072 TCTCCCTGAAGATGGAATAAGATTCTC 59.984 40.741 0.00 0.00 0.00 2.87
215 216 6.044171 CCTGAAGATGGAATAAGATTCTCCCT 59.956 42.308 0.00 0.00 0.00 4.20
230 232 2.352805 CCTGCCAACCCCAGTCTC 59.647 66.667 0.00 0.00 0.00 3.36
259 261 0.029163 TCCCCCATCATTAGAGGGCA 60.029 55.000 0.00 0.00 44.28 5.36
267 269 1.770658 TCATTAGAGGGCATGTGGAGG 59.229 52.381 0.00 0.00 0.00 4.30
281 283 4.436998 GAGGTGTGTCTCCGGCGG 62.437 72.222 22.51 22.51 0.00 6.13
282 284 4.988716 AGGTGTGTCTCCGGCGGA 62.989 66.667 29.14 29.14 0.00 5.54
283 285 3.771160 GGTGTGTCTCCGGCGGAT 61.771 66.667 31.23 0.00 0.00 4.18
284 286 2.202756 GTGTGTCTCCGGCGGATC 60.203 66.667 31.23 24.22 0.00 3.36
285 287 2.362503 TGTGTCTCCGGCGGATCT 60.363 61.111 31.23 0.00 0.00 2.75
286 288 1.982395 TGTGTCTCCGGCGGATCTT 60.982 57.895 31.23 0.00 0.00 2.40
287 289 1.519455 GTGTCTCCGGCGGATCTTG 60.519 63.158 31.23 18.07 0.00 3.02
288 290 2.586357 GTCTCCGGCGGATCTTGC 60.586 66.667 31.23 13.71 0.00 4.01
308 310 2.752903 GCGGGATTCAGTTGGTATTTGT 59.247 45.455 0.00 0.00 0.00 2.83
314 316 5.163754 GGATTCAGTTGGTATTTGTCTTCGG 60.164 44.000 0.00 0.00 0.00 4.30
345 347 1.477700 TGGATCCGGTATTCGTTCGTT 59.522 47.619 7.39 0.00 37.11 3.85
348 350 2.437200 TCCGGTATTCGTTCGTTTGT 57.563 45.000 0.00 0.00 37.11 2.83
360 362 3.484393 CGTTCGTTTGTGTTCATGTGTCA 60.484 43.478 0.00 0.00 0.00 3.58
361 363 3.666883 TCGTTTGTGTTCATGTGTCAC 57.333 42.857 0.00 0.00 0.00 3.67
368 371 2.805671 GTGTTCATGTGTCACGGATTGA 59.194 45.455 0.00 0.00 0.00 2.57
397 400 3.242220 CCGAACATTGCTTCTCTTCATCG 60.242 47.826 0.00 0.00 0.00 3.84
402 405 4.153117 ACATTGCTTCTCTTCATCGACAAC 59.847 41.667 0.00 0.00 0.00 3.32
403 406 3.385193 TGCTTCTCTTCATCGACAACA 57.615 42.857 0.00 0.00 0.00 3.33
420 423 1.318576 ACAGTTGTTGGCCTTAGCAC 58.681 50.000 3.32 0.00 42.56 4.40
423 426 0.237498 GTTGTTGGCCTTAGCACGAC 59.763 55.000 3.32 0.00 42.56 4.34
457 460 4.214545 CCGTCTATTGCAACAAGGTTTGTA 59.785 41.667 0.00 0.00 44.59 2.41
460 463 2.853731 TTGCAACAAGGTTTGTACGG 57.146 45.000 0.00 0.00 44.59 4.02
472 475 3.069729 GGTTTGTACGGCTCCTATGAGAT 59.930 47.826 0.00 0.00 41.42 2.75
474 477 5.462405 GTTTGTACGGCTCCTATGAGATAG 58.538 45.833 0.00 0.00 41.42 2.08
486 489 5.559427 CTATGAGATAGGAGTGATGACGG 57.441 47.826 0.00 0.00 0.00 4.79
489 492 0.664767 GATAGGAGTGATGACGGCGC 60.665 60.000 6.90 0.00 0.00 6.53
512 515 1.986378 CGCTTTCGACTAACTCCAGTG 59.014 52.381 0.00 0.00 38.10 3.66
525 528 2.656646 CAGTGCTGGTAGCCGTCA 59.343 61.111 0.00 0.00 41.51 4.35
536 539 0.330604 TAGCCGTCACTAGGTGGTCT 59.669 55.000 0.00 0.00 33.87 3.85
546 549 1.338337 CTAGGTGGTCTACGAGCATGG 59.662 57.143 0.00 0.00 42.05 3.66
673 677 7.843490 AAAACATTACTGCATACGTATCAGT 57.157 32.000 27.89 27.89 42.89 3.41
675 679 7.843490 AACATTACTGCATACGTATCAGTTT 57.157 32.000 29.00 20.41 40.96 2.66
676 680 7.843490 ACATTACTGCATACGTATCAGTTTT 57.157 32.000 29.00 20.09 40.96 2.43
742 974 6.691388 GCAACTACCTTCTAAAAACACACAAG 59.309 38.462 0.00 0.00 0.00 3.16
744 976 6.420638 ACTACCTTCTAAAAACACACAAGGT 58.579 36.000 6.42 6.42 44.60 3.50
756 988 2.808543 CACACAAGGTCTTGCTAAGGAC 59.191 50.000 10.31 0.00 44.03 3.85
762 994 1.439679 GTCTTGCTAAGGACAACCCG 58.560 55.000 0.00 0.00 40.87 5.28
773 1006 2.882761 AGGACAACCCGCTAAGAAAAAC 59.117 45.455 0.00 0.00 40.87 2.43
836 1070 2.739784 CTAGAGATGGCCAGCCCG 59.260 66.667 19.48 0.00 35.87 6.13
851 1085 4.170062 CCGCTTCGACCGACGCTA 62.170 66.667 16.61 0.00 42.26 4.26
852 1086 2.202388 CGCTTCGACCGACGCTAA 60.202 61.111 16.61 0.00 42.26 3.09
989 1234 0.688087 CCCTAGGGTTTCCGCTCTCT 60.688 60.000 20.88 0.00 38.33 3.10
1225 1471 1.622607 CCGGCCATCACCACCTCTAA 61.623 60.000 2.24 0.00 0.00 2.10
1259 1505 2.124983 CCTGGTCTGGTGGCATCG 60.125 66.667 0.00 0.00 0.00 3.84
1286 1532 6.187682 CAGTGAACCCTTATTTTGGATAGGT 58.812 40.000 0.00 0.00 0.00 3.08
1331 1578 4.014406 GGGTTTTACCACATCAAGGTAGG 58.986 47.826 0.00 0.00 42.22 3.18
1430 1679 1.406205 GCTGGGGCTGACTTCTCTAAC 60.406 57.143 0.00 0.00 35.22 2.34
1435 1684 3.070302 GGGGCTGACTTCTCTAACATAGG 59.930 52.174 0.00 0.00 0.00 2.57
1438 1687 4.500716 GGCTGACTTCTCTAACATAGGAGC 60.501 50.000 0.00 0.00 0.00 4.70
1439 1688 4.340950 GCTGACTTCTCTAACATAGGAGCT 59.659 45.833 0.00 0.00 0.00 4.09
1440 1689 5.533154 GCTGACTTCTCTAACATAGGAGCTA 59.467 44.000 0.00 0.00 0.00 3.32
1442 1691 6.664714 TGACTTCTCTAACATAGGAGCTAGT 58.335 40.000 0.00 0.00 31.78 2.57
1443 1692 6.768861 TGACTTCTCTAACATAGGAGCTAGTC 59.231 42.308 0.06 0.06 39.08 2.59
1444 1693 6.664714 ACTTCTCTAACATAGGAGCTAGTCA 58.335 40.000 0.00 0.00 0.00 3.41
1479 1728 5.873179 TTTGTTTGACGCTTTAGGATAGG 57.127 39.130 0.00 0.00 0.00 2.57
1480 1729 3.267483 TGTTTGACGCTTTAGGATAGGC 58.733 45.455 0.00 0.00 0.00 3.93
1486 1735 2.553172 ACGCTTTAGGATAGGCTCTACG 59.447 50.000 0.00 0.00 0.00 3.51
1493 1742 1.604185 GGATAGGCTCTACGCTGCTTG 60.604 57.143 0.00 0.00 39.13 4.01
1548 1797 3.992943 ATGTTACCTGTGATTTCGGGA 57.007 42.857 0.00 0.00 37.31 5.14
1549 1798 3.773418 TGTTACCTGTGATTTCGGGAA 57.227 42.857 0.00 0.00 37.31 3.97
1562 1824 7.447238 TGTGATTTCGGGAAAGAATTAGTTTCT 59.553 33.333 10.91 0.00 46.92 2.52
1632 1895 8.257602 TCTACCCAAATGAAGCTATGTGTATA 57.742 34.615 0.00 0.00 0.00 1.47
1697 1961 1.275573 ACCGAGTTCTAACTTGCCTCC 59.724 52.381 4.78 0.00 39.88 4.30
1698 1962 1.405661 CCGAGTTCTAACTTGCCTCCC 60.406 57.143 4.78 0.00 39.88 4.30
1746 2012 5.741388 ATGTAATTTCCGCATGTCTCTTC 57.259 39.130 0.00 0.00 0.00 2.87
1765 2031 7.485595 GTCTCTTCGAGGTAATCTAACAAGTTC 59.514 40.741 0.00 0.00 0.00 3.01
1956 2222 2.356382 TGAACGTGGAATTGGTGTTGTC 59.644 45.455 0.00 0.00 0.00 3.18
2100 2369 0.238289 CGGTGTCCATGTTCTTGCAC 59.762 55.000 0.00 0.00 0.00 4.57
2132 2401 5.105513 GGTTTAATCGTTCATTTCCATGGGT 60.106 40.000 13.02 0.00 0.00 4.51
2154 2427 7.054124 GGGTTCTATCATTGTTCTAATGTGGA 58.946 38.462 0.00 0.00 0.00 4.02
2184 2472 9.595823 GCAGTAGGATCACTTAGTTTTAACATA 57.404 33.333 0.00 0.00 0.00 2.29
2248 2655 7.865706 AAATATTTGTGGTAGAGTGGCTTAG 57.134 36.000 0.00 0.00 0.00 2.18
2270 2678 6.683974 AGTTGCATGTGTCTATTTGATACC 57.316 37.500 0.00 0.00 36.17 2.73
2271 2679 5.590259 AGTTGCATGTGTCTATTTGATACCC 59.410 40.000 0.00 0.00 36.17 3.69
2282 2690 7.770433 TGTCTATTTGATACCCACTCTTGATTG 59.230 37.037 0.00 0.00 0.00 2.67
2283 2691 7.987458 GTCTATTTGATACCCACTCTTGATTGA 59.013 37.037 0.00 0.00 0.00 2.57
2300 2731 8.514594 TCTTGATTGAATGGTTGAATGAACTAC 58.485 33.333 0.00 0.00 34.66 2.73
2311 2742 7.173218 TGGTTGAATGAACTACTGAAGAATGAC 59.827 37.037 0.00 0.00 34.66 3.06
2343 2787 6.919721 TGCAACTATTTTATTGTCCACTTCC 58.080 36.000 0.00 0.00 0.00 3.46
2364 2808 3.989817 CCTCACAAGGCTGTTAATTTTGC 59.010 43.478 0.00 0.00 35.37 3.68
2789 3235 5.163884 GCTTGACTTCCTTTATTACCGTGTC 60.164 44.000 0.00 0.00 0.00 3.67
2898 3356 4.181051 GGCTTGACTGCCCTTGTT 57.819 55.556 0.00 0.00 46.82 2.83
2949 3407 9.461312 AAGTCTTTGAATATATTGCAGGTTACA 57.539 29.630 1.78 0.00 0.00 2.41
2971 3468 7.907214 ACATCTGAGTACCTTACATTGTTTC 57.093 36.000 0.00 0.00 0.00 2.78
2983 3480 7.012894 ACCTTACATTGTTTCGTTTTCATGAGA 59.987 33.333 0.00 0.00 0.00 3.27
3214 3711 8.224389 TCATAATTCATGGTCTAAATGTGTGG 57.776 34.615 0.00 0.00 35.16 4.17
3948 4472 3.482722 TCCAGTAGTCGTTTTAGCTCG 57.517 47.619 0.00 0.00 0.00 5.03
4053 4591 7.446013 CGAGTATGGTCTTTCCTCTAGACTTAT 59.554 40.741 0.00 0.00 41.37 1.73
4187 4854 6.483307 TGACTTGTCGATTTTCAGAAAGTGAT 59.517 34.615 0.00 0.00 34.17 3.06
4253 4921 7.168804 GCTCTGCATATCTGAAAATTTTTAGGC 59.831 37.037 19.27 15.31 0.00 3.93
4289 4962 9.952030 TTAGATATTGGACACTGACATAAAACA 57.048 29.630 0.00 0.00 0.00 2.83
4337 5010 5.178096 TGAGTTATGATTCTGCTGGGAAA 57.822 39.130 0.00 0.00 0.00 3.13
4383 5063 7.670364 ACTTTCTTGAATGGTTAAATTCCCAG 58.330 34.615 0.00 0.00 35.98 4.45
4384 5064 7.290014 ACTTTCTTGAATGGTTAAATTCCCAGT 59.710 33.333 0.00 0.00 35.98 4.00
4386 5066 7.696992 TCTTGAATGGTTAAATTCCCAGTAC 57.303 36.000 0.00 0.00 35.98 2.73
4387 5067 6.661805 TCTTGAATGGTTAAATTCCCAGTACC 59.338 38.462 0.00 0.00 35.98 3.34
4389 5069 3.353370 TGGTTAAATTCCCAGTACCCG 57.647 47.619 0.00 0.00 0.00 5.28
4421 5105 2.616510 GGACAACTCTATTGGCAGTGCT 60.617 50.000 16.11 0.00 0.00 4.40
4451 5135 3.874543 ACAGTCAGCAACGTTATTGACAA 59.125 39.130 30.11 6.92 41.74 3.18
4455 5140 4.846137 GTCAGCAACGTTATTGACAATCAC 59.154 41.667 26.66 3.08 39.67 3.06
4462 5147 6.569228 ACGTTATTGACAATCACATACTCG 57.431 37.500 3.36 0.00 0.00 4.18
4495 5182 2.327200 GGTATCGGCTTACCTTTGCT 57.673 50.000 6.32 0.00 38.89 3.91
4577 5264 2.031314 TTGCTGCCGCCGACTAAA 59.969 55.556 0.00 0.00 34.43 1.85
4794 5484 5.422970 AGGTTTAGGTGATGTATGGACGTAA 59.577 40.000 0.00 0.00 0.00 3.18
4827 5570 8.421002 TGCTACAATACATTTCTATGCAGTAGA 58.579 33.333 0.00 0.00 37.65 2.59
4868 5611 7.429162 CAACTAATTAGGTTGCGCAGTATTGC 61.429 42.308 11.31 0.00 39.75 3.56
4918 5661 5.734855 TTCGTTTTGATCAGCTATTAGGC 57.265 39.130 0.00 0.00 0.00 3.93
4978 5721 7.757941 TCTTTGAACATGATACATTGTCCAA 57.242 32.000 0.00 0.00 0.00 3.53
5099 5855 4.032960 TGCTGAAGGAACCATAACACAT 57.967 40.909 0.00 0.00 0.00 3.21
5162 5918 7.231519 TCACTATTCTGTAGGTGGTGATATCAG 59.768 40.741 5.42 0.00 0.00 2.90
5264 6020 2.095110 TCATTCCAAAGCGTGATTGCAG 60.095 45.455 0.00 0.00 37.31 4.41
5271 6027 4.379813 CCAAAGCGTGATTGCAGAATTACT 60.380 41.667 0.00 0.00 37.31 2.24
5295 6052 4.650754 TTACGATAAGCTTGAGAGTCCC 57.349 45.455 9.86 0.00 0.00 4.46
5532 7589 7.438160 GTGGGCTAGGTGCAAAATAAATAAATC 59.562 37.037 0.00 0.00 45.15 2.17
5558 7615 8.729756 CAATCAAACTTGTACTGATTATGTGGA 58.270 33.333 6.89 0.00 37.63 4.02
5559 7616 7.667043 TCAAACTTGTACTGATTATGTGGAC 57.333 36.000 0.00 0.00 0.00 4.02
5560 7617 6.653320 TCAAACTTGTACTGATTATGTGGACC 59.347 38.462 0.00 0.00 0.00 4.46
5561 7618 5.755409 ACTTGTACTGATTATGTGGACCA 57.245 39.130 0.00 0.00 0.00 4.02
5562 7619 6.121776 ACTTGTACTGATTATGTGGACCAA 57.878 37.500 0.00 0.00 0.00 3.67
5563 7620 6.721318 ACTTGTACTGATTATGTGGACCAAT 58.279 36.000 0.00 0.00 0.00 3.16
5564 7621 7.175104 ACTTGTACTGATTATGTGGACCAATT 58.825 34.615 0.00 0.00 0.00 2.32
5565 7622 7.669722 ACTTGTACTGATTATGTGGACCAATTT 59.330 33.333 0.00 0.00 0.00 1.82
5566 7623 9.173021 CTTGTACTGATTATGTGGACCAATTTA 57.827 33.333 0.00 0.00 0.00 1.40
5567 7624 9.521841 TTGTACTGATTATGTGGACCAATTTAA 57.478 29.630 0.00 0.00 0.00 1.52
5568 7625 9.173021 TGTACTGATTATGTGGACCAATTTAAG 57.827 33.333 0.00 0.00 0.00 1.85
5569 7626 9.174166 GTACTGATTATGTGGACCAATTTAAGT 57.826 33.333 0.00 0.00 0.00 2.24
5571 7628 9.920946 ACTGATTATGTGGACCAATTTAAGTAT 57.079 29.630 0.00 0.00 0.00 2.12
5576 7633 9.747898 TTATGTGGACCAATTTAAGTATTGAGT 57.252 29.630 0.00 0.00 37.65 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 6.822442 TCATGCTAGAATTGTATTAACCGGA 58.178 36.000 9.46 0.00 0.00 5.14
2 3 7.490962 TTCATGCTAGAATTGTATTAACCGG 57.509 36.000 0.00 0.00 0.00 5.28
60 61 9.574516 CCCTAGAGGCAATAATAAAGTTGTTAT 57.425 33.333 0.00 0.00 0.00 1.89
61 62 8.974060 CCCTAGAGGCAATAATAAAGTTGTTA 57.026 34.615 0.00 0.00 0.00 2.41
62 63 7.881775 CCCTAGAGGCAATAATAAAGTTGTT 57.118 36.000 0.00 0.00 0.00 2.83
78 79 4.263243 CCTGAAGGAAATATGCCCTAGAGG 60.263 50.000 0.00 0.00 37.39 3.69
79 80 4.349342 ACCTGAAGGAAATATGCCCTAGAG 59.651 45.833 2.62 0.00 38.94 2.43
80 81 4.307259 ACCTGAAGGAAATATGCCCTAGA 58.693 43.478 2.62 0.00 38.94 2.43
81 82 4.103153 TGACCTGAAGGAAATATGCCCTAG 59.897 45.833 2.62 0.00 38.94 3.02
82 83 4.044308 TGACCTGAAGGAAATATGCCCTA 58.956 43.478 2.62 0.00 38.94 3.53
83 84 2.852449 TGACCTGAAGGAAATATGCCCT 59.148 45.455 2.62 0.00 38.94 5.19
84 85 3.297134 TGACCTGAAGGAAATATGCCC 57.703 47.619 2.62 0.00 38.94 5.36
85 86 5.006386 CCTATGACCTGAAGGAAATATGCC 58.994 45.833 2.62 0.00 38.94 4.40
86 87 5.006386 CCCTATGACCTGAAGGAAATATGC 58.994 45.833 2.62 0.00 38.94 3.14
87 88 6.439636 TCCCTATGACCTGAAGGAAATATG 57.560 41.667 2.62 0.00 38.94 1.78
88 89 6.564152 ACATCCCTATGACCTGAAGGAAATAT 59.436 38.462 2.62 0.00 36.19 1.28
89 90 5.911178 ACATCCCTATGACCTGAAGGAAATA 59.089 40.000 2.62 0.15 36.19 1.40
90 91 4.728860 ACATCCCTATGACCTGAAGGAAAT 59.271 41.667 2.62 0.00 36.19 2.17
91 92 4.080356 CACATCCCTATGACCTGAAGGAAA 60.080 45.833 2.62 0.00 36.19 3.13
92 93 3.455910 CACATCCCTATGACCTGAAGGAA 59.544 47.826 2.62 0.00 36.19 3.36
93 94 3.041211 CACATCCCTATGACCTGAAGGA 58.959 50.000 2.62 0.00 36.19 3.36
94 95 2.105477 CCACATCCCTATGACCTGAAGG 59.895 54.545 0.00 0.00 37.62 3.46
95 96 2.774234 ACCACATCCCTATGACCTGAAG 59.226 50.000 0.00 0.00 36.54 3.02
96 97 2.505407 CACCACATCCCTATGACCTGAA 59.495 50.000 0.00 0.00 36.54 3.02
97 98 2.118679 CACCACATCCCTATGACCTGA 58.881 52.381 0.00 0.00 36.54 3.86
98 99 1.141657 CCACCACATCCCTATGACCTG 59.858 57.143 0.00 0.00 36.54 4.00
99 100 1.009552 TCCACCACATCCCTATGACCT 59.990 52.381 0.00 0.00 36.54 3.85
100 101 1.507140 TCCACCACATCCCTATGACC 58.493 55.000 0.00 0.00 36.54 4.02
101 102 2.975489 AGATCCACCACATCCCTATGAC 59.025 50.000 0.00 0.00 36.54 3.06
102 103 3.242867 GAGATCCACCACATCCCTATGA 58.757 50.000 0.00 0.00 36.54 2.15
103 104 2.974794 TGAGATCCACCACATCCCTATG 59.025 50.000 0.00 0.00 39.17 2.23
104 105 3.350992 TGAGATCCACCACATCCCTAT 57.649 47.619 0.00 0.00 0.00 2.57
105 106 2.771943 GTTGAGATCCACCACATCCCTA 59.228 50.000 0.00 0.00 0.00 3.53
106 107 1.561542 GTTGAGATCCACCACATCCCT 59.438 52.381 0.00 0.00 0.00 4.20
107 108 1.408822 GGTTGAGATCCACCACATCCC 60.409 57.143 0.00 0.00 0.00 3.85
108 109 1.408822 GGGTTGAGATCCACCACATCC 60.409 57.143 5.54 0.00 0.00 3.51
109 110 1.561542 AGGGTTGAGATCCACCACATC 59.438 52.381 5.54 0.00 0.00 3.06
110 111 1.673767 AGGGTTGAGATCCACCACAT 58.326 50.000 5.54 0.00 0.00 3.21
111 112 1.073763 CAAGGGTTGAGATCCACCACA 59.926 52.381 5.54 0.00 0.00 4.17
112 113 1.351017 TCAAGGGTTGAGATCCACCAC 59.649 52.381 5.54 0.00 34.08 4.16
113 114 1.741028 TCAAGGGTTGAGATCCACCA 58.259 50.000 5.54 0.00 34.08 4.17
114 115 3.372440 AATCAAGGGTTGAGATCCACC 57.628 47.619 0.00 0.00 43.98 4.61
115 116 5.728637 AAAAATCAAGGGTTGAGATCCAC 57.271 39.130 0.00 0.00 43.98 4.02
142 143 5.473846 TGAACAGGACACAAACACTAAACAA 59.526 36.000 0.00 0.00 0.00 2.83
145 146 5.811399 CTGAACAGGACACAAACACTAAA 57.189 39.130 0.00 0.00 0.00 1.85
189 190 6.237154 GGAGAATCTTATTCCATCTTCAGGG 58.763 44.000 0.00 0.00 33.73 4.45
200 201 3.885901 GGTTGGCAGGGAGAATCTTATTC 59.114 47.826 0.00 0.00 33.73 1.75
206 207 1.076705 GGGGTTGGCAGGGAGAATC 60.077 63.158 0.00 0.00 0.00 2.52
212 213 3.260100 AGACTGGGGTTGGCAGGG 61.260 66.667 0.00 0.00 0.00 4.45
215 216 3.636231 CCGAGACTGGGGTTGGCA 61.636 66.667 0.00 0.00 0.00 4.92
267 269 2.202756 GATCCGCCGGAGACACAC 60.203 66.667 13.12 0.00 34.05 3.82
279 281 0.179073 ACTGAATCCCGCAAGATCCG 60.179 55.000 0.00 0.00 43.02 4.18
281 283 1.672881 CCAACTGAATCCCGCAAGATC 59.327 52.381 0.00 0.00 43.02 2.75
282 284 1.004745 ACCAACTGAATCCCGCAAGAT 59.995 47.619 0.00 0.00 43.02 2.40
283 285 0.400213 ACCAACTGAATCCCGCAAGA 59.600 50.000 0.00 0.00 43.02 3.02
284 286 2.107950 TACCAACTGAATCCCGCAAG 57.892 50.000 0.00 0.00 0.00 4.01
285 287 2.799126 ATACCAACTGAATCCCGCAA 57.201 45.000 0.00 0.00 0.00 4.85
286 288 2.752354 CAAATACCAACTGAATCCCGCA 59.248 45.455 0.00 0.00 0.00 5.69
287 289 2.752903 ACAAATACCAACTGAATCCCGC 59.247 45.455 0.00 0.00 0.00 6.13
288 290 4.261801 AGACAAATACCAACTGAATCCCG 58.738 43.478 0.00 0.00 0.00 5.14
323 325 2.058798 CGAACGAATACCGGATCCATG 58.941 52.381 9.46 4.51 43.93 3.66
324 326 1.684983 ACGAACGAATACCGGATCCAT 59.315 47.619 9.46 1.11 43.93 3.41
345 347 2.317530 TCCGTGACACATGAACACAA 57.682 45.000 6.37 0.00 34.69 3.33
348 350 3.118905 TCAATCCGTGACACATGAACA 57.881 42.857 6.37 0.00 0.00 3.18
368 371 3.690460 AGAAGCAATGTTCGGAAGGAAT 58.310 40.909 0.00 0.00 36.92 3.01
379 382 3.930336 TGTCGATGAAGAGAAGCAATGT 58.070 40.909 0.00 0.00 0.00 2.71
402 405 0.238289 CGTGCTAAGGCCAACAACTG 59.762 55.000 5.01 0.00 37.74 3.16
403 406 0.107831 TCGTGCTAAGGCCAACAACT 59.892 50.000 5.01 0.00 37.74 3.16
413 416 2.745886 CGAAAAGTCGTCGTGCTAAG 57.254 50.000 0.00 0.00 42.53 2.18
435 438 4.223320 ACAAACCTTGTTGCAATAGACG 57.777 40.909 0.59 0.00 42.22 4.18
442 445 0.382515 GCCGTACAAACCTTGTTGCA 59.617 50.000 0.00 0.00 42.22 4.08
472 475 2.782222 GGCGCCGTCATCACTCCTA 61.782 63.158 12.58 0.00 0.00 2.94
474 477 4.451150 TGGCGCCGTCATCACTCC 62.451 66.667 23.90 0.00 0.00 3.85
489 492 1.336517 TGGAGTTAGTCGAAAGCGTGG 60.337 52.381 0.00 0.00 38.98 4.94
493 496 1.727335 GCACTGGAGTTAGTCGAAAGC 59.273 52.381 0.00 0.00 0.00 3.51
495 498 3.026630 CAGCACTGGAGTTAGTCGAAA 57.973 47.619 0.00 0.00 0.00 3.46
512 515 1.321074 ACCTAGTGACGGCTACCAGC 61.321 60.000 0.00 0.00 41.46 4.85
517 520 0.330604 AGACCACCTAGTGACGGCTA 59.669 55.000 0.00 0.00 35.23 3.93
520 523 0.731417 CGTAGACCACCTAGTGACGG 59.269 60.000 0.00 0.00 35.23 4.79
525 528 2.025155 CATGCTCGTAGACCACCTAGT 58.975 52.381 0.00 0.00 0.00 2.57
679 683 8.152898 CCTGATGATAGGTATGATTGTCTCAAA 58.847 37.037 0.00 0.00 33.56 2.69
680 684 7.674120 CCTGATGATAGGTATGATTGTCTCAA 58.326 38.462 0.00 0.00 33.56 3.02
681 685 7.237209 CCTGATGATAGGTATGATTGTCTCA 57.763 40.000 0.00 0.00 34.02 3.27
694 698 5.946377 GCCCCTTTTATTACCTGATGATAGG 59.054 44.000 0.00 0.00 43.71 2.57
695 699 6.542821 TGCCCCTTTTATTACCTGATGATAG 58.457 40.000 0.00 0.00 0.00 2.08
697 701 5.402054 TGCCCCTTTTATTACCTGATGAT 57.598 39.130 0.00 0.00 0.00 2.45
699 703 4.956075 AGTTGCCCCTTTTATTACCTGATG 59.044 41.667 0.00 0.00 0.00 3.07
700 704 5.206905 AGTTGCCCCTTTTATTACCTGAT 57.793 39.130 0.00 0.00 0.00 2.90
702 706 4.643334 GGTAGTTGCCCCTTTTATTACCTG 59.357 45.833 0.00 0.00 0.00 4.00
742 974 1.822506 GGGTTGTCCTTAGCAAGACC 58.177 55.000 0.00 0.00 0.00 3.85
744 976 0.321298 GCGGGTTGTCCTTAGCAAGA 60.321 55.000 0.00 0.00 0.00 3.02
756 988 2.603652 CCGTGTTTTTCTTAGCGGGTTG 60.604 50.000 0.00 0.00 36.05 3.77
762 994 2.381589 GTGTGCCGTGTTTTTCTTAGC 58.618 47.619 0.00 0.00 0.00 3.09
797 1030 2.361737 GAGCCCAGTTCAAGCCCC 60.362 66.667 0.00 0.00 0.00 5.80
843 1077 2.048597 TGTGGTGCTTAGCGTCGG 60.049 61.111 0.00 0.00 0.00 4.79
850 1084 0.766674 AGTGGGGACTGTGGTGCTTA 60.767 55.000 0.00 0.00 34.14 3.09
851 1085 2.056906 GAGTGGGGACTGTGGTGCTT 62.057 60.000 0.00 0.00 34.14 3.91
852 1086 2.448542 AGTGGGGACTGTGGTGCT 60.449 61.111 0.00 0.00 34.14 4.40
1225 1471 4.443266 GCAGCGGCCGAAGAGTCT 62.443 66.667 33.48 12.84 0.00 3.24
1248 1494 0.246360 TCACTGTACGATGCCACCAG 59.754 55.000 0.00 0.00 0.00 4.00
1254 1500 2.094762 AAGGGTTCACTGTACGATGC 57.905 50.000 0.00 0.00 0.00 3.91
1259 1505 7.282450 CCTATCCAAAATAAGGGTTCACTGTAC 59.718 40.741 0.00 0.00 0.00 2.90
1286 1532 1.978455 AACCCGTCCAGCACAGAACA 61.978 55.000 0.00 0.00 0.00 3.18
1323 1569 2.569853 TCCACACACCATACCTACCTTG 59.430 50.000 0.00 0.00 0.00 3.61
1331 1578 2.396590 ACCGAATCCACACACCATAC 57.603 50.000 0.00 0.00 0.00 2.39
1430 1679 7.448777 TCCTACTGTAAATGACTAGCTCCTATG 59.551 40.741 0.00 0.00 0.00 2.23
1435 1684 7.982354 ACAAATCCTACTGTAAATGACTAGCTC 59.018 37.037 0.00 0.00 0.00 4.09
1440 1689 8.784043 GTCAAACAAATCCTACTGTAAATGACT 58.216 33.333 0.00 0.00 34.39 3.41
1442 1691 7.572353 GCGTCAAACAAATCCTACTGTAAATGA 60.572 37.037 0.00 0.00 0.00 2.57
1443 1692 6.523201 GCGTCAAACAAATCCTACTGTAAATG 59.477 38.462 0.00 0.00 0.00 2.32
1444 1693 6.430000 AGCGTCAAACAAATCCTACTGTAAAT 59.570 34.615 0.00 0.00 0.00 1.40
1486 1735 0.801251 CCAGTCACTAAGCAAGCAGC 59.199 55.000 0.00 0.00 46.19 5.25
1493 1742 4.022849 ACTGCAAATTTCCAGTCACTAAGC 60.023 41.667 9.03 0.00 37.77 3.09
1548 1797 7.499232 ACAGCTACACACAGAAACTAATTCTTT 59.501 33.333 0.00 0.00 46.39 2.52
1549 1798 6.992715 ACAGCTACACACAGAAACTAATTCTT 59.007 34.615 0.00 0.00 46.39 2.52
1562 1824 4.694982 CCAATATGACAACAGCTACACACA 59.305 41.667 0.00 0.00 0.00 3.72
1613 1876 6.260714 TGGCAGTATACACATAGCTTCATTTG 59.739 38.462 5.50 0.00 0.00 2.32
1632 1895 3.638160 ACAATCTCAAAATGTGTGGCAGT 59.362 39.130 0.00 0.00 0.00 4.40
1680 1944 3.704800 AAGGGAGGCAAGTTAGAACTC 57.295 47.619 0.00 0.00 38.57 3.01
1746 2012 6.811665 TGACATGAACTTGTTAGATTACCTCG 59.188 38.462 0.00 0.00 0.00 4.63
1956 2222 0.829333 AGTCCTGTATCTGCTGCCTG 59.171 55.000 0.00 0.00 0.00 4.85
2060 2329 2.283821 ACCCCCACGCATGCAATT 60.284 55.556 19.57 0.00 0.00 2.32
2081 2350 0.238289 GTGCAAGAACATGGACACCG 59.762 55.000 0.00 0.00 40.88 4.94
2100 2369 1.129811 GAACGATTAAACCTGGCACGG 59.870 52.381 0.00 2.01 0.00 4.94
2132 2401 9.166173 CAGTTCCACATTAGAACAATGATAGAA 57.834 33.333 6.44 1.91 44.91 2.10
2154 2427 5.746990 AACTAAGTGATCCTACTGCAGTT 57.253 39.130 27.06 6.57 34.50 3.16
2248 2655 5.356751 TGGGTATCAAATAGACACATGCAAC 59.643 40.000 0.00 0.00 24.27 4.17
2271 2679 6.916440 TCATTCAACCATTCAATCAAGAGTG 58.084 36.000 0.00 0.00 0.00 3.51
2282 2690 7.672983 TCTTCAGTAGTTCATTCAACCATTC 57.327 36.000 0.00 0.00 35.28 2.67
2283 2691 8.517878 CATTCTTCAGTAGTTCATTCAACCATT 58.482 33.333 0.00 0.00 35.28 3.16
2300 2731 7.246311 AGTTGCAATAAATCGTCATTCTTCAG 58.754 34.615 0.59 0.00 0.00 3.02
2336 2780 0.109342 ACAGCCTTGTGAGGAAGTGG 59.891 55.000 0.00 0.00 46.74 4.00
2343 2787 4.619973 TGCAAAATTAACAGCCTTGTGAG 58.380 39.130 0.00 0.00 37.67 3.51
2810 3256 7.817962 GCCCTCATACTCGTACATATACAAAAT 59.182 37.037 0.00 0.00 0.00 1.82
2833 3291 4.459337 AGAACAAGCATAAACTTAGTGCCC 59.541 41.667 0.00 0.00 39.62 5.36
2898 3356 5.408880 TCATGTCACCATTACTTAACCGA 57.591 39.130 0.00 0.00 0.00 4.69
2949 3407 6.698380 ACGAAACAATGTAAGGTACTCAGAT 58.302 36.000 0.00 0.00 38.49 2.90
2971 3468 6.668541 AAGGTACATCATCTCATGAAAACG 57.331 37.500 0.00 0.00 43.50 3.60
2983 3480 5.241506 CAGTGTCAAACCAAAGGTACATCAT 59.758 40.000 0.00 0.00 33.12 2.45
3214 3711 6.799512 AGATAAGGACACAAATTGCATTAGC 58.200 36.000 0.00 0.00 42.57 3.09
3688 4188 4.681744 TGAACACAAACCTGCAAGAAATC 58.318 39.130 0.00 0.00 34.07 2.17
3948 4472 4.755411 TGAGCTATGGTAACTACTTGTGC 58.245 43.478 0.00 0.00 37.61 4.57
4016 4546 2.765807 ATACTCGCCAGGCCAGCT 60.766 61.111 5.87 0.00 0.00 4.24
4187 4854 8.651391 TTACTTCAACGAAACATGTAGAGAAA 57.349 30.769 0.00 0.00 0.00 2.52
4253 4921 6.072286 AGTGTCCAATATCTAATACGGTACCG 60.072 42.308 32.22 32.22 46.03 4.02
4289 4962 9.506042 AAATACCCAGAAATATTTCCAAGGATT 57.494 29.630 24.74 18.07 37.92 3.01
4337 5010 5.452255 AGTCATGAAAATGGCCATCATACT 58.548 37.500 21.08 17.77 34.44 2.12
4383 5063 1.205655 GTCCTACTTTGTCCCGGGTAC 59.794 57.143 22.86 17.66 0.00 3.34
4384 5064 1.203162 TGTCCTACTTTGTCCCGGGTA 60.203 52.381 22.86 8.42 0.00 3.69
4386 5066 0.688487 TTGTCCTACTTTGTCCCGGG 59.312 55.000 16.85 16.85 0.00 5.73
4387 5067 1.346722 AGTTGTCCTACTTTGTCCCGG 59.653 52.381 0.00 0.00 0.00 5.73
4389 5069 5.678955 ATAGAGTTGTCCTACTTTGTCCC 57.321 43.478 0.00 0.00 0.00 4.46
4392 5072 5.221843 TGCCAATAGAGTTGTCCTACTTTGT 60.222 40.000 0.00 0.00 0.00 2.83
4393 5073 5.245531 TGCCAATAGAGTTGTCCTACTTTG 58.754 41.667 0.00 0.00 0.00 2.77
4421 5105 3.006940 ACGTTGCTGACTGTTTGAAGAA 58.993 40.909 0.00 0.00 0.00 2.52
4451 5135 4.152402 GCACAGAAAACACGAGTATGTGAT 59.848 41.667 17.93 0.00 42.55 3.06
4455 5140 3.120546 CCTGCACAGAAAACACGAGTATG 60.121 47.826 0.00 0.00 0.00 2.39
4462 5147 2.159627 CCGATACCTGCACAGAAAACAC 59.840 50.000 0.00 0.00 0.00 3.32
4495 5182 1.879380 AGCTGCAGTTTATCGTTGCAA 59.121 42.857 16.64 0.00 46.08 4.08
4577 5264 2.053244 TGGTGGGCCATTTTGTTCAAT 58.947 42.857 10.70 0.00 40.46 2.57
4742 5432 6.851222 ACAATCAGTTACAGTTCAGTTCTG 57.149 37.500 0.00 0.00 38.68 3.02
4794 5484 5.195940 AGAAATGTATTGTAGCATGCACCT 58.804 37.500 21.98 1.04 0.00 4.00
4827 5570 9.429359 CTAATTAGTTGAGTTGTGAATGACTCT 57.571 33.333 4.18 0.00 0.00 3.24
4899 5642 6.856895 ACAAAGCCTAATAGCTGATCAAAAC 58.143 36.000 0.00 0.00 44.11 2.43
4949 5692 8.627208 ACAATGTATCATGTTCAAAGAAGAGT 57.373 30.769 0.00 0.00 0.00 3.24
4978 5721 8.542132 CGAATTATCGCCATCAAATTCATTTTT 58.458 29.630 7.25 0.00 42.96 1.94
5024 5767 9.325198 GGAACTTTATTTCCAGTGTTGATTTTT 57.675 29.630 0.00 0.00 44.14 1.94
5186 5942 1.354031 TGTCAGGCCCACATGTTACAT 59.646 47.619 0.00 0.00 0.00 2.29
5192 5948 2.726821 AGTAAATGTCAGGCCCACATG 58.273 47.619 16.82 0.94 34.59 3.21
5193 5949 3.091545 CAAGTAAATGTCAGGCCCACAT 58.908 45.455 11.46 11.46 35.94 3.21
5198 5954 3.674997 TGTCTCAAGTAAATGTCAGGCC 58.325 45.455 0.00 0.00 0.00 5.19
5271 6027 5.873164 GGGACTCTCAAGCTTATCGTAAAAA 59.127 40.000 0.00 0.00 0.00 1.94
5309 6081 8.641541 TGCTGTCCTTCAAATTCTTTAATTCTT 58.358 29.630 0.00 0.00 34.12 2.52
5310 6082 8.181904 TGCTGTCCTTCAAATTCTTTAATTCT 57.818 30.769 0.00 0.00 34.12 2.40
5311 6083 8.816640 TTGCTGTCCTTCAAATTCTTTAATTC 57.183 30.769 0.00 0.00 34.12 2.17
5312 6084 9.264719 CTTTGCTGTCCTTCAAATTCTTTAATT 57.735 29.630 0.00 0.00 36.87 1.40
5313 6085 8.424133 ACTTTGCTGTCCTTCAAATTCTTTAAT 58.576 29.630 0.00 0.00 32.51 1.40
5385 7435 7.849804 TTAGATCTAAATTTCACTGGTCAGC 57.150 36.000 12.87 0.00 0.00 4.26
5532 7589 8.729756 TCCACATAATCAGTACAAGTTTGATTG 58.270 33.333 14.37 5.36 40.63 2.67


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

AutoCloner maintained by Alex Coulton.