Multiple sequence alignment - TraesCS3D01G466200

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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 TraesCS3D01G466200 chr3D 100.000 3293 0 0 1 3293 569882983 569886275 0.000000e+00 6082
1 TraesCS3D01G466200 chr3D 89.096 697 69 4 412 1104 580656356 580657049 0.000000e+00 859
2 TraesCS3D01G466200 chr5D 94.916 1495 64 7 1806 3293 179972287 179970798 0.000000e+00 2329
3 TraesCS3D01G466200 chr5D 89.740 692 57 7 420 1104 59767190 59766506 0.000000e+00 872
4 TraesCS3D01G466200 chr5D 89.535 688 66 4 420 1104 373804917 373804233 0.000000e+00 867
5 TraesCS3D01G466200 chr5D 89.892 277 21 4 1533 1805 427075403 427075130 1.880000e-92 350
6 TraesCS3D01G466200 chr5D 89.209 278 22 4 1533 1805 427015944 427015670 1.130000e-89 340
7 TraesCS3D01G466200 chr7B 94.444 1494 77 6 1802 3293 681764399 681765888 0.000000e+00 2294
8 TraesCS3D01G466200 chr7B 94.602 1482 66 10 1814 3293 678829381 678830850 0.000000e+00 2281
9 TraesCS3D01G466200 chr4D 94.362 1490 70 9 1806 3293 502108132 502106655 0.000000e+00 2274
10 TraesCS3D01G466200 chr4D 90.086 696 58 5 412 1104 8171597 8170910 0.000000e+00 893
11 TraesCS3D01G466200 chr6A 94.031 1491 79 6 1806 3293 563198147 563199630 0.000000e+00 2252
12 TraesCS3D01G466200 chr6A 92.039 716 36 7 1105 1807 49843667 49842960 0.000000e+00 987
13 TraesCS3D01G466200 chr6A 89.209 278 23 4 1534 1805 596781776 596781500 1.130000e-89 340
14 TraesCS3D01G466200 chr7D 94.090 1489 70 11 1807 3293 175932695 175931223 0.000000e+00 2246
15 TraesCS3D01G466200 chr7D 92.818 724 33 8 1103 1807 629192482 629193205 0.000000e+00 1031
16 TraesCS3D01G466200 chr7D 90.809 729 38 5 1105 1805 601583417 601582690 0.000000e+00 948
17 TraesCS3D01G466200 chr7D 93.807 436 23 3 1105 1536 593116915 593116480 0.000000e+00 652
18 TraesCS3D01G466200 chr7D 93.793 435 24 2 1105 1536 9053703 9053269 0.000000e+00 651
19 TraesCS3D01G466200 chr2A 93.850 1496 74 9 1806 3293 704738149 704736664 0.000000e+00 2237
20 TraesCS3D01G466200 chr2A 93.700 1492 88 5 1806 3293 754614776 754616265 0.000000e+00 2230
21 TraesCS3D01G466200 chr3B 93.952 1488 63 14 1806 3291 670040395 670041857 0.000000e+00 2224
22 TraesCS3D01G466200 chr7A 93.417 714 27 6 1105 1806 107015643 107014938 0.000000e+00 1040
23 TraesCS3D01G466200 chr7A 91.389 720 36 7 1105 1806 175071204 175071915 0.000000e+00 963
24 TraesCS3D01G466200 chr7A 92.101 671 26 8 1149 1806 3037156 3036500 0.000000e+00 920
25 TraesCS3D01G466200 chr7A 89.903 723 49 9 1105 1811 663455636 663454922 0.000000e+00 909
26 TraesCS3D01G466200 chr1A 91.243 708 38 9 1102 1805 159528640 159529327 0.000000e+00 942
27 TraesCS3D01G466200 chr3A 90.150 731 38 15 1091 1809 141875653 141874945 0.000000e+00 920
28 TraesCS3D01G466200 chrUn 90.000 700 59 8 413 1104 350530804 350531500 0.000000e+00 894
29 TraesCS3D01G466200 chr1D 89.725 691 59 6 420 1104 278102463 278101779 0.000000e+00 872
30 TraesCS3D01G466200 chr5B 89.550 689 66 4 420 1104 55038746 55038060 0.000000e+00 869
31 TraesCS3D01G466200 chr5B 90.175 285 18 2 1531 1805 192661376 192661660 2.420000e-96 363
32 TraesCS3D01G466200 chr2B 89.322 693 68 4 412 1104 143956018 143956704 0.000000e+00 865
33 TraesCS3D01G466200 chr2B 91.398 279 21 2 1531 1806 790135705 790135427 2.400000e-101 379
34 TraesCS3D01G466200 chr5A 89.275 690 67 5 420 1104 619775384 619774697 0.000000e+00 857
35 TraesCS3D01G466200 chr5A 95.652 230 10 0 1576 1805 4295951 4295722 1.440000e-98 370


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 TraesCS3D01G466200 chr3D 569882983 569886275 3292 False 6082 6082 100.000 1 3293 1 chr3D.!!$F1 3292
1 TraesCS3D01G466200 chr3D 580656356 580657049 693 False 859 859 89.096 412 1104 1 chr3D.!!$F2 692
2 TraesCS3D01G466200 chr5D 179970798 179972287 1489 True 2329 2329 94.916 1806 3293 1 chr5D.!!$R2 1487
3 TraesCS3D01G466200 chr5D 59766506 59767190 684 True 872 872 89.740 420 1104 1 chr5D.!!$R1 684
4 TraesCS3D01G466200 chr5D 373804233 373804917 684 True 867 867 89.535 420 1104 1 chr5D.!!$R3 684
5 TraesCS3D01G466200 chr7B 681764399 681765888 1489 False 2294 2294 94.444 1802 3293 1 chr7B.!!$F2 1491
6 TraesCS3D01G466200 chr7B 678829381 678830850 1469 False 2281 2281 94.602 1814 3293 1 chr7B.!!$F1 1479
7 TraesCS3D01G466200 chr4D 502106655 502108132 1477 True 2274 2274 94.362 1806 3293 1 chr4D.!!$R2 1487
8 TraesCS3D01G466200 chr4D 8170910 8171597 687 True 893 893 90.086 412 1104 1 chr4D.!!$R1 692
9 TraesCS3D01G466200 chr6A 563198147 563199630 1483 False 2252 2252 94.031 1806 3293 1 chr6A.!!$F1 1487
10 TraesCS3D01G466200 chr6A 49842960 49843667 707 True 987 987 92.039 1105 1807 1 chr6A.!!$R1 702
11 TraesCS3D01G466200 chr7D 175931223 175932695 1472 True 2246 2246 94.090 1807 3293 1 chr7D.!!$R2 1486
12 TraesCS3D01G466200 chr7D 629192482 629193205 723 False 1031 1031 92.818 1103 1807 1 chr7D.!!$F1 704
13 TraesCS3D01G466200 chr7D 601582690 601583417 727 True 948 948 90.809 1105 1805 1 chr7D.!!$R4 700
14 TraesCS3D01G466200 chr2A 704736664 704738149 1485 True 2237 2237 93.850 1806 3293 1 chr2A.!!$R1 1487
15 TraesCS3D01G466200 chr2A 754614776 754616265 1489 False 2230 2230 93.700 1806 3293 1 chr2A.!!$F1 1487
16 TraesCS3D01G466200 chr3B 670040395 670041857 1462 False 2224 2224 93.952 1806 3291 1 chr3B.!!$F1 1485
17 TraesCS3D01G466200 chr7A 107014938 107015643 705 True 1040 1040 93.417 1105 1806 1 chr7A.!!$R2 701
18 TraesCS3D01G466200 chr7A 175071204 175071915 711 False 963 963 91.389 1105 1806 1 chr7A.!!$F1 701
19 TraesCS3D01G466200 chr7A 3036500 3037156 656 True 920 920 92.101 1149 1806 1 chr7A.!!$R1 657
20 TraesCS3D01G466200 chr7A 663454922 663455636 714 True 909 909 89.903 1105 1811 1 chr7A.!!$R3 706
21 TraesCS3D01G466200 chr1A 159528640 159529327 687 False 942 942 91.243 1102 1805 1 chr1A.!!$F1 703
22 TraesCS3D01G466200 chr3A 141874945 141875653 708 True 920 920 90.150 1091 1809 1 chr3A.!!$R1 718
23 TraesCS3D01G466200 chrUn 350530804 350531500 696 False 894 894 90.000 413 1104 1 chrUn.!!$F1 691
24 TraesCS3D01G466200 chr1D 278101779 278102463 684 True 872 872 89.725 420 1104 1 chr1D.!!$R1 684
25 TraesCS3D01G466200 chr5B 55038060 55038746 686 True 869 869 89.550 420 1104 1 chr5B.!!$R1 684
26 TraesCS3D01G466200 chr2B 143956018 143956704 686 False 865 865 89.322 412 1104 1 chr2B.!!$F1 692
27 TraesCS3D01G466200 chr5A 619774697 619775384 687 True 857 857 89.275 420 1104 1 chr5A.!!$R2 684

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
292 293 0.038526 GTCGCGTGAGAAAGGGAGAA 60.039 55.0 5.77 0.00 0.00 2.87 F
326 327 0.102481 GAGCGAGCTCGTGGGAATTA 59.898 55.0 34.46 0.00 42.22 1.40 F
327 328 0.103208 AGCGAGCTCGTGGGAATTAG 59.897 55.0 34.46 5.79 42.22 1.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1998 2095 0.111061 ACATGGCCACTTGCTCTTCA 59.889 50.0 8.16 0.0 40.92 3.02 R
2267 2365 0.512952 GCCTGTGTTAGTGCTCAACG 59.487 55.0 0.00 0.0 0.00 4.10 R
2491 2590 0.320771 ACCAGGTCGACTCATGTTGC 60.321 55.0 16.46 0.0 0.00 4.17 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
54 55 3.680786 CGAGTGTCCCGTGCAGGA 61.681 66.667 8.24 0.00 45.00 3.86
55 56 2.982130 GAGTGTCCCGTGCAGGAT 59.018 61.111 8.24 0.00 45.00 3.24
56 57 1.663379 CGAGTGTCCCGTGCAGGATA 61.663 60.000 8.24 0.00 45.00 2.59
57 58 0.103208 GAGTGTCCCGTGCAGGATAG 59.897 60.000 8.24 0.00 45.00 2.08
58 59 1.144057 GTGTCCCGTGCAGGATAGG 59.856 63.158 8.24 0.58 45.00 2.57
59 60 2.063979 TGTCCCGTGCAGGATAGGG 61.064 63.158 8.24 6.39 45.00 3.53
60 61 3.161450 TCCCGTGCAGGATAGGGC 61.161 66.667 8.24 0.00 45.00 5.19
61 62 4.609018 CCCGTGCAGGATAGGGCG 62.609 72.222 8.24 0.00 45.00 6.13
62 63 3.849951 CCGTGCAGGATAGGGCGT 61.850 66.667 8.24 0.00 45.00 5.68
63 64 2.279517 CGTGCAGGATAGGGCGTC 60.280 66.667 0.00 0.00 0.00 5.19
64 65 2.109181 GTGCAGGATAGGGCGTCC 59.891 66.667 0.00 0.00 35.94 4.79
65 66 2.041922 TGCAGGATAGGGCGTCCT 60.042 61.111 15.76 15.76 46.92 3.85
83 84 3.567473 GCAGTCGGCAGAGGTTTC 58.433 61.111 0.00 0.00 43.97 2.78
84 85 2.035442 GCAGTCGGCAGAGGTTTCC 61.035 63.158 0.00 0.00 43.97 3.13
85 86 1.371183 CAGTCGGCAGAGGTTTCCA 59.629 57.895 0.00 0.00 0.00 3.53
86 87 0.250295 CAGTCGGCAGAGGTTTCCAA 60.250 55.000 0.00 0.00 0.00 3.53
87 88 0.693049 AGTCGGCAGAGGTTTCCAAT 59.307 50.000 0.00 0.00 0.00 3.16
88 89 1.073923 AGTCGGCAGAGGTTTCCAATT 59.926 47.619 0.00 0.00 0.00 2.32
89 90 1.886542 GTCGGCAGAGGTTTCCAATTT 59.113 47.619 0.00 0.00 0.00 1.82
90 91 2.296190 GTCGGCAGAGGTTTCCAATTTT 59.704 45.455 0.00 0.00 0.00 1.82
91 92 2.295909 TCGGCAGAGGTTTCCAATTTTG 59.704 45.455 0.00 0.00 0.00 2.44
100 101 2.810458 CCAATTTTGGCAGCGGCG 60.810 61.111 0.51 0.51 42.21 6.46
101 102 2.810458 CAATTTTGGCAGCGGCGG 60.810 61.111 9.78 0.00 42.47 6.13
102 103 4.740431 AATTTTGGCAGCGGCGGC 62.740 61.111 16.93 16.93 42.47 6.53
122 123 3.539842 CCTACGGAGGGAAGCCTC 58.460 66.667 5.47 0.00 39.48 4.70
131 132 3.181282 GGAAGCCTCCCCTTGGTT 58.819 61.111 0.00 0.00 35.42 3.67
132 133 2.394514 GGAAGCCTCCCCTTGGTTA 58.605 57.895 0.00 0.00 35.42 2.85
133 134 0.256177 GGAAGCCTCCCCTTGGTTAG 59.744 60.000 0.00 0.00 35.42 2.34
134 135 1.286248 GAAGCCTCCCCTTGGTTAGA 58.714 55.000 0.00 0.00 0.00 2.10
135 136 1.210722 GAAGCCTCCCCTTGGTTAGAG 59.789 57.143 0.00 0.00 0.00 2.43
137 138 1.915983 CCTCCCCTTGGTTAGAGGC 59.084 63.158 0.00 0.00 39.54 4.70
138 139 1.522569 CTCCCCTTGGTTAGAGGCG 59.477 63.158 0.00 0.00 32.74 5.52
139 140 2.124695 CCCCTTGGTTAGAGGCGC 60.125 66.667 0.00 0.00 32.74 6.53
140 141 2.511600 CCCTTGGTTAGAGGCGCG 60.512 66.667 0.00 0.00 32.74 6.86
141 142 3.195698 CCTTGGTTAGAGGCGCGC 61.196 66.667 25.94 25.94 0.00 6.86
142 143 3.554692 CTTGGTTAGAGGCGCGCG 61.555 66.667 28.44 28.44 0.00 6.86
157 158 3.686045 GCGCGAGGGATAGGGAGG 61.686 72.222 12.10 0.00 0.00 4.30
158 159 3.686045 CGCGAGGGATAGGGAGGC 61.686 72.222 0.00 0.00 0.00 4.70
159 160 3.686045 GCGAGGGATAGGGAGGCG 61.686 72.222 0.00 0.00 0.00 5.52
160 161 2.992114 CGAGGGATAGGGAGGCGG 60.992 72.222 0.00 0.00 0.00 6.13
161 162 2.604991 GAGGGATAGGGAGGCGGG 60.605 72.222 0.00 0.00 0.00 6.13
162 163 4.964241 AGGGATAGGGAGGCGGGC 62.964 72.222 0.00 0.00 0.00 6.13
163 164 4.964241 GGGATAGGGAGGCGGGCT 62.964 72.222 2.69 2.69 0.00 5.19
164 165 3.315140 GGATAGGGAGGCGGGCTC 61.315 72.222 22.20 22.20 0.00 4.70
165 166 3.315140 GATAGGGAGGCGGGCTCC 61.315 72.222 35.50 35.50 40.15 4.70
166 167 4.172232 ATAGGGAGGCGGGCTCCA 62.172 66.667 40.50 27.45 42.56 3.86
167 168 4.860881 TAGGGAGGCGGGCTCCAG 62.861 72.222 40.50 0.00 42.56 3.86
220 221 2.266055 GGAAGAGGTCCAGTGCGG 59.734 66.667 0.00 0.00 46.97 5.69
221 222 2.435059 GAAGAGGTCCAGTGCGGC 60.435 66.667 0.00 0.00 33.14 6.53
222 223 2.925170 AAGAGGTCCAGTGCGGCT 60.925 61.111 0.00 0.00 33.14 5.52
223 224 3.245668 AAGAGGTCCAGTGCGGCTG 62.246 63.158 0.00 1.55 44.63 4.85
236 237 4.785453 GGCTGCGTGGGGGAAGAG 62.785 72.222 0.00 0.00 0.00 2.85
237 238 4.785453 GCTGCGTGGGGGAAGAGG 62.785 72.222 0.00 0.00 0.00 3.69
238 239 3.322466 CTGCGTGGGGGAAGAGGT 61.322 66.667 0.00 0.00 0.00 3.85
239 240 3.316573 CTGCGTGGGGGAAGAGGTC 62.317 68.421 0.00 0.00 0.00 3.85
240 241 3.003763 GCGTGGGGGAAGAGGTCT 61.004 66.667 0.00 0.00 0.00 3.85
241 242 2.982130 CGTGGGGGAAGAGGTCTG 59.018 66.667 0.00 0.00 0.00 3.51
242 243 2.660064 CGTGGGGGAAGAGGTCTGG 61.660 68.421 0.00 0.00 0.00 3.86
243 244 1.539124 GTGGGGGAAGAGGTCTGGT 60.539 63.158 0.00 0.00 0.00 4.00
244 245 1.538876 TGGGGGAAGAGGTCTGGTG 60.539 63.158 0.00 0.00 0.00 4.17
245 246 2.671682 GGGGAAGAGGTCTGGTGC 59.328 66.667 0.00 0.00 0.00 5.01
246 247 2.671682 GGGAAGAGGTCTGGTGCC 59.328 66.667 0.00 0.00 0.00 5.01
247 248 1.920835 GGGAAGAGGTCTGGTGCCT 60.921 63.158 0.00 0.00 39.42 4.75
248 249 1.298014 GGAAGAGGTCTGGTGCCTG 59.702 63.158 0.00 0.00 36.29 4.85
249 250 1.376553 GAAGAGGTCTGGTGCCTGC 60.377 63.158 0.00 0.00 36.29 4.85
250 251 2.116983 GAAGAGGTCTGGTGCCTGCA 62.117 60.000 0.00 0.00 36.29 4.41
251 252 2.359230 GAGGTCTGGTGCCTGCAC 60.359 66.667 13.75 13.75 45.49 4.57
252 253 2.851102 AGGTCTGGTGCCTGCACT 60.851 61.111 20.52 0.00 45.52 4.40
253 254 2.113986 GGTCTGGTGCCTGCACTT 59.886 61.111 20.52 0.00 45.52 3.16
254 255 1.968540 GGTCTGGTGCCTGCACTTC 60.969 63.158 20.52 6.87 45.52 3.01
255 256 1.227943 GTCTGGTGCCTGCACTTCA 60.228 57.895 20.52 10.87 45.52 3.02
256 257 0.819259 GTCTGGTGCCTGCACTTCAA 60.819 55.000 20.52 5.09 45.52 2.69
257 258 0.111061 TCTGGTGCCTGCACTTCAAT 59.889 50.000 20.52 0.00 45.52 2.57
258 259 0.963962 CTGGTGCCTGCACTTCAATT 59.036 50.000 20.52 0.00 45.52 2.32
259 260 1.342174 CTGGTGCCTGCACTTCAATTT 59.658 47.619 20.52 0.00 45.52 1.82
260 261 1.761784 TGGTGCCTGCACTTCAATTTT 59.238 42.857 20.52 0.00 45.52 1.82
261 262 2.137523 GGTGCCTGCACTTCAATTTTG 58.862 47.619 20.52 0.00 45.52 2.44
262 263 2.483538 GGTGCCTGCACTTCAATTTTGT 60.484 45.455 20.52 0.00 45.52 2.83
263 264 2.796593 GTGCCTGCACTTCAATTTTGTC 59.203 45.455 14.77 0.00 43.12 3.18
264 265 2.224018 TGCCTGCACTTCAATTTTGTCC 60.224 45.455 0.00 0.00 0.00 4.02
265 266 2.664916 CCTGCACTTCAATTTTGTCCG 58.335 47.619 0.00 0.00 0.00 4.79
266 267 2.053627 CTGCACTTCAATTTTGTCCGC 58.946 47.619 0.00 0.00 0.00 5.54
267 268 1.269517 TGCACTTCAATTTTGTCCGCC 60.270 47.619 0.00 0.00 0.00 6.13
268 269 1.685302 CACTTCAATTTTGTCCGCCG 58.315 50.000 0.00 0.00 0.00 6.46
269 270 1.001815 CACTTCAATTTTGTCCGCCGT 60.002 47.619 0.00 0.00 0.00 5.68
270 271 1.679153 ACTTCAATTTTGTCCGCCGTT 59.321 42.857 0.00 0.00 0.00 4.44
271 272 2.050691 CTTCAATTTTGTCCGCCGTTG 58.949 47.619 0.00 0.00 0.00 4.10
272 273 0.318275 TCAATTTTGTCCGCCGTTGC 60.318 50.000 0.00 0.00 0.00 4.17
284 285 3.391631 CGTTGCGTCGCGTGAGAA 61.392 61.111 13.38 0.00 0.00 2.87
285 286 2.923177 CGTTGCGTCGCGTGAGAAA 61.923 57.895 13.38 0.00 0.00 2.52
286 287 1.154836 GTTGCGTCGCGTGAGAAAG 60.155 57.895 13.38 0.00 0.00 2.62
287 288 2.307309 TTGCGTCGCGTGAGAAAGG 61.307 57.895 13.38 0.00 0.00 3.11
288 289 3.479269 GCGTCGCGTGAGAAAGGG 61.479 66.667 5.77 0.00 0.00 3.95
289 290 2.257371 CGTCGCGTGAGAAAGGGA 59.743 61.111 5.77 0.00 0.00 4.20
290 291 1.801913 CGTCGCGTGAGAAAGGGAG 60.802 63.158 5.77 0.00 0.00 4.30
291 292 1.585006 GTCGCGTGAGAAAGGGAGA 59.415 57.895 5.77 0.00 0.00 3.71
292 293 0.038526 GTCGCGTGAGAAAGGGAGAA 60.039 55.000 5.77 0.00 0.00 2.87
293 294 0.243907 TCGCGTGAGAAAGGGAGAAG 59.756 55.000 5.77 0.00 0.00 2.85
294 295 1.355066 CGCGTGAGAAAGGGAGAAGC 61.355 60.000 0.00 0.00 0.00 3.86
295 296 1.355066 GCGTGAGAAAGGGAGAAGCG 61.355 60.000 0.00 0.00 0.00 4.68
296 297 0.737715 CGTGAGAAAGGGAGAAGCGG 60.738 60.000 0.00 0.00 0.00 5.52
297 298 1.021920 GTGAGAAAGGGAGAAGCGGC 61.022 60.000 0.00 0.00 0.00 6.53
298 299 1.194781 TGAGAAAGGGAGAAGCGGCT 61.195 55.000 0.00 0.00 0.00 5.52
299 300 0.742635 GAGAAAGGGAGAAGCGGCTG 60.743 60.000 1.81 0.00 0.00 4.85
300 301 1.746991 GAAAGGGAGAAGCGGCTGG 60.747 63.158 1.81 0.00 0.00 4.85
301 302 3.273788 AAAGGGAGAAGCGGCTGGG 62.274 63.158 1.81 0.00 0.00 4.45
322 323 3.443925 CTGAGCGAGCTCGTGGGA 61.444 66.667 34.46 16.66 45.48 4.37
323 324 2.989253 TGAGCGAGCTCGTGGGAA 60.989 61.111 34.46 15.20 45.48 3.97
324 325 2.290122 CTGAGCGAGCTCGTGGGAAT 62.290 60.000 34.46 15.41 45.48 3.01
325 326 1.153549 GAGCGAGCTCGTGGGAATT 60.154 57.895 34.46 13.37 42.22 2.17
326 327 0.102481 GAGCGAGCTCGTGGGAATTA 59.898 55.000 34.46 0.00 42.22 1.40
327 328 0.103208 AGCGAGCTCGTGGGAATTAG 59.897 55.000 34.46 5.79 42.22 1.73
328 329 1.491505 GCGAGCTCGTGGGAATTAGC 61.492 60.000 34.46 12.23 42.22 3.09
329 330 1.209275 CGAGCTCGTGGGAATTAGCG 61.209 60.000 27.79 0.00 39.94 4.26
330 331 0.876342 GAGCTCGTGGGAATTAGCGG 60.876 60.000 0.00 0.00 39.94 5.52
331 332 1.153429 GCTCGTGGGAATTAGCGGT 60.153 57.895 0.00 0.00 0.00 5.68
332 333 1.429148 GCTCGTGGGAATTAGCGGTG 61.429 60.000 0.00 0.00 0.00 4.94
333 334 0.810031 CTCGTGGGAATTAGCGGTGG 60.810 60.000 0.00 0.00 0.00 4.61
334 335 2.469516 CGTGGGAATTAGCGGTGGC 61.470 63.158 0.00 0.00 40.37 5.01
335 336 1.377987 GTGGGAATTAGCGGTGGCA 60.378 57.895 0.00 0.00 43.41 4.92
336 337 1.077787 TGGGAATTAGCGGTGGCAG 60.078 57.895 0.00 0.00 43.41 4.85
337 338 2.481471 GGGAATTAGCGGTGGCAGC 61.481 63.158 6.62 6.62 43.41 5.25
339 340 1.718757 GGAATTAGCGGTGGCAGCTG 61.719 60.000 15.48 10.11 45.60 4.24
340 341 0.744414 GAATTAGCGGTGGCAGCTGA 60.744 55.000 20.43 5.37 45.60 4.26
341 342 0.745845 AATTAGCGGTGGCAGCTGAG 60.746 55.000 20.43 3.53 45.60 3.35
342 343 3.958147 TTAGCGGTGGCAGCTGAGC 62.958 63.158 20.43 13.60 45.60 4.26
353 354 2.202676 GCTGAGCGAGCTAGCGTT 60.203 61.111 13.42 0.00 45.21 4.84
354 355 2.227568 GCTGAGCGAGCTAGCGTTC 61.228 63.158 13.42 8.83 45.21 3.95
355 356 1.431440 CTGAGCGAGCTAGCGTTCT 59.569 57.895 13.42 7.22 41.26 3.01
356 357 0.865218 CTGAGCGAGCTAGCGTTCTG 60.865 60.000 13.42 8.43 41.26 3.02
357 358 1.305930 TGAGCGAGCTAGCGTTCTGA 61.306 55.000 13.42 0.00 41.26 3.27
358 359 0.179161 GAGCGAGCTAGCGTTCTGAA 60.179 55.000 13.42 0.00 43.00 3.02
359 360 0.457851 AGCGAGCTAGCGTTCTGAAT 59.542 50.000 13.42 0.00 43.00 2.57
360 361 0.849579 GCGAGCTAGCGTTCTGAATC 59.150 55.000 9.55 0.00 0.00 2.52
361 362 1.116436 CGAGCTAGCGTTCTGAATCG 58.884 55.000 9.55 6.71 0.00 3.34
362 363 1.482278 GAGCTAGCGTTCTGAATCGG 58.518 55.000 9.55 0.00 0.00 4.18
363 364 0.528684 AGCTAGCGTTCTGAATCGGC 60.529 55.000 9.55 8.16 0.00 5.54
364 365 1.812214 GCTAGCGTTCTGAATCGGCG 61.812 60.000 0.00 0.00 0.00 6.46
365 366 1.209275 CTAGCGTTCTGAATCGGCGG 61.209 60.000 7.21 0.00 0.00 6.13
366 367 1.940883 TAGCGTTCTGAATCGGCGGT 61.941 55.000 7.21 0.00 37.12 5.68
367 368 3.081133 CGTTCTGAATCGGCGGTG 58.919 61.111 7.21 0.00 0.00 4.94
368 369 2.452813 CGTTCTGAATCGGCGGTGG 61.453 63.158 7.21 0.00 0.00 4.61
369 370 2.435938 TTCTGAATCGGCGGTGGC 60.436 61.111 7.21 0.00 38.90 5.01
386 387 2.811317 CGGCTGAGCTCGTGGTTC 60.811 66.667 9.64 0.00 0.00 3.62
387 388 2.343758 GGCTGAGCTCGTGGTTCA 59.656 61.111 9.64 0.00 34.14 3.18
388 389 1.301716 GGCTGAGCTCGTGGTTCAA 60.302 57.895 9.64 0.00 34.86 2.69
389 390 1.569479 GGCTGAGCTCGTGGTTCAAC 61.569 60.000 9.64 0.00 34.86 3.18
390 391 1.569479 GCTGAGCTCGTGGTTCAACC 61.569 60.000 9.64 0.00 39.22 3.77
391 392 1.284982 CTGAGCTCGTGGTTCAACCG 61.285 60.000 9.64 0.00 42.58 4.44
392 393 2.665185 AGCTCGTGGTTCAACCGC 60.665 61.111 10.38 10.38 45.04 5.68
393 394 2.665185 GCTCGTGGTTCAACCGCT 60.665 61.111 18.08 0.00 46.27 5.52
394 395 2.668280 GCTCGTGGTTCAACCGCTC 61.668 63.158 18.08 3.62 46.27 5.03
395 396 2.355363 TCGTGGTTCAACCGCTCG 60.355 61.111 18.08 14.11 46.27 5.03
396 397 4.072088 CGTGGTTCAACCGCTCGC 62.072 66.667 18.08 0.00 46.27 5.03
397 398 2.665185 GTGGTTCAACCGCTCGCT 60.665 61.111 13.27 0.00 45.06 4.93
398 399 2.664851 TGGTTCAACCGCTCGCTG 60.665 61.111 1.02 0.00 42.58 5.18
399 400 3.423154 GGTTCAACCGCTCGCTGG 61.423 66.667 0.00 0.00 0.00 4.85
400 401 3.423154 GTTCAACCGCTCGCTGGG 61.423 66.667 5.15 0.00 0.00 4.45
403 404 4.451150 CAACCGCTCGCTGGGCTA 62.451 66.667 0.00 0.00 0.00 3.93
404 405 4.148825 AACCGCTCGCTGGGCTAG 62.149 66.667 0.00 0.00 0.00 3.42
406 407 4.277593 CCGCTCGCTGGGCTAGAG 62.278 72.222 0.43 0.00 35.28 2.43
409 410 4.165926 CTCGCTGGGCTAGAGCTA 57.834 61.111 0.43 0.00 41.70 3.32
410 411 1.956043 CTCGCTGGGCTAGAGCTAG 59.044 63.158 0.43 0.13 41.70 3.42
473 474 2.064581 GCGGGAAGGAAGAGGCCTA 61.065 63.158 4.42 0.00 37.26 3.93
495 501 0.478072 TGGTTGCCTGGATTCACTGT 59.522 50.000 0.00 0.00 0.00 3.55
496 502 1.133513 TGGTTGCCTGGATTCACTGTT 60.134 47.619 0.00 0.00 0.00 3.16
497 503 1.270550 GGTTGCCTGGATTCACTGTTG 59.729 52.381 0.00 0.00 0.00 3.33
498 504 1.270550 GTTGCCTGGATTCACTGTTGG 59.729 52.381 0.00 0.00 0.00 3.77
499 505 0.251297 TGCCTGGATTCACTGTTGGG 60.251 55.000 0.00 0.00 0.00 4.12
517 523 3.869272 CCTGCATCGCACGCTTCC 61.869 66.667 0.00 0.00 33.79 3.46
659 666 0.254178 AGATGGAAATCTGGCACGCT 59.746 50.000 0.00 0.00 0.00 5.07
665 672 3.628646 AATCTGGCACGCTGTCCCC 62.629 63.158 0.00 0.00 0.00 4.81
684 694 2.141517 CCGCATCAAATCTAGCCTCAG 58.858 52.381 0.00 0.00 0.00 3.35
816 840 1.557269 AAGAGGCAGCGGATCTGGTT 61.557 55.000 2.75 0.00 43.06 3.67
840 864 0.320073 CCTTGCTGTTGGCCATTGTG 60.320 55.000 6.09 0.00 40.92 3.33
884 908 2.044650 CCCCCTACGTCGTCCTCA 60.045 66.667 0.00 0.00 0.00 3.86
962 987 2.167693 CGTTTGGCTAGGTGTAGGATCA 59.832 50.000 0.00 0.00 0.00 2.92
991 1016 2.029380 ACTGAATGAACCGTCGATGTCA 60.029 45.455 3.52 2.07 0.00 3.58
1006 1031 4.707934 TCGATGTCAACTAGGTTATGGACA 59.292 41.667 1.54 1.54 39.31 4.02
1029 1054 4.202398 ACACGGATGAGGCTGATAATTCAT 60.202 41.667 0.00 0.00 33.23 2.57
1199 1233 2.374525 CCCATCCCCATCACCGTGA 61.375 63.158 3.10 3.10 0.00 4.35
1344 1412 4.114073 CAAAACAAGCACATTTCAGCAGA 58.886 39.130 0.00 0.00 0.00 4.26
1358 1426 6.579666 TTTCAGCAGAATAACTTGAGCAAT 57.420 33.333 0.00 0.00 32.89 3.56
1469 1539 6.431852 TCAGATTTCAGCAACAAAGATGATCA 59.568 34.615 0.00 0.00 33.44 2.92
1470 1540 6.747739 CAGATTTCAGCAACAAAGATGATCAG 59.252 38.462 0.09 0.00 33.44 2.90
1471 1541 6.657966 AGATTTCAGCAACAAAGATGATCAGA 59.342 34.615 0.09 0.00 33.44 3.27
1472 1542 6.829229 TTTCAGCAACAAAGATGATCAGAT 57.171 33.333 0.09 0.00 33.44 2.90
1473 1543 6.829229 TTCAGCAACAAAGATGATCAGATT 57.171 33.333 0.09 0.00 33.44 2.40
1474 1544 6.829229 TCAGCAACAAAGATGATCAGATTT 57.171 33.333 0.09 1.75 0.00 2.17
1475 1545 6.849502 TCAGCAACAAAGATGATCAGATTTC 58.150 36.000 0.09 0.00 0.00 2.17
1510 1587 5.982516 GGTTCAACAAGATGTGCAATTACAA 59.017 36.000 0.00 0.00 33.69 2.41
1552 1630 3.469863 TTTGGCCTTCGACGCTGGT 62.470 57.895 3.32 0.00 0.00 4.00
1738 1834 1.503818 CGGGGATGAAAATACGCCCG 61.504 60.000 0.00 0.00 39.75 6.13
1895 1991 5.793817 ACTACATCTACAACTGCAATGACA 58.206 37.500 6.19 0.00 0.00 3.58
2267 2365 5.973565 GGCTTGATATGCTTGTATTGTTCAC 59.026 40.000 0.00 0.00 0.00 3.18
2491 2590 4.261072 GCATGATGCTAACATTCTCAGTGG 60.261 45.833 10.72 0.00 40.96 4.00
2509 2608 1.021390 GGCAACATGAGTCGACCTGG 61.021 60.000 13.01 2.10 0.00 4.45
2597 2696 2.783510 TCTTCCACCCTTCAGGAAAACT 59.216 45.455 0.00 0.00 42.91 2.66
2680 2779 2.889512 TCTCAGACACTCCAGCCTTAA 58.110 47.619 0.00 0.00 0.00 1.85
2730 2831 8.317776 AGCTCTGAAGAATAGGTTTAAGATCT 57.682 34.615 0.00 0.00 0.00 2.75
2763 2864 2.242196 CCATTCCACCCATACTCCACTT 59.758 50.000 0.00 0.00 0.00 3.16
2765 2866 4.104738 CCATTCCACCCATACTCCACTTAT 59.895 45.833 0.00 0.00 0.00 1.73
2785 2886 8.289618 CACTTATGTTAAGCTTGTTCTTGCTTA 58.710 33.333 9.86 3.68 46.19 3.09
2856 2957 0.033991 TGAGGAGGAAGAGGTCGAGG 60.034 60.000 0.00 0.00 0.00 4.63
2863 2964 1.587933 GAAGAGGTCGAGGCTGACGT 61.588 60.000 10.56 10.56 39.83 4.34
2900 3001 2.104967 CATGGTGTGGAGGCATTTGAT 58.895 47.619 0.00 0.00 0.00 2.57
2968 3069 2.494059 GCTTAACAGAGGTCAGTGCAA 58.506 47.619 0.00 0.00 0.00 4.08
2980 3081 4.276926 AGGTCAGTGCAAGATTTGAAGAAC 59.723 41.667 0.00 0.00 0.00 3.01
3024 3136 4.283212 AGAAGAAGAAGCAGTAGCAGAAGT 59.717 41.667 0.00 0.00 45.49 3.01
3058 3182 4.162131 GCAGAAGAAGAGGAAGAGGAAGAT 59.838 45.833 0.00 0.00 0.00 2.40
3075 3199 4.343526 GGAAGATGAAGATCTGGTAGCAGA 59.656 45.833 25.72 25.72 39.04 4.26
3083 3207 1.045407 TCTGGTAGCAGAAACACCGT 58.955 50.000 21.91 0.00 34.94 4.83
3184 3308 4.312443 TGTTTAACTAGCTGGCACTACAC 58.688 43.478 0.00 0.00 0.00 2.90
3205 3329 4.034626 CACGTTCAGATTGTGTGTGGTAAA 59.965 41.667 0.00 0.00 0.00 2.01
3274 3398 3.193056 CCAAACACCATGTCATATGTGCA 59.807 43.478 12.36 4.05 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 1.663379 TATCCTGCACGGGACACTCG 61.663 60.000 0.00 0.00 38.30 4.18
38 39 0.103208 CTATCCTGCACGGGACACTC 59.897 60.000 0.00 0.00 38.30 3.51
39 40 1.330655 CCTATCCTGCACGGGACACT 61.331 60.000 0.00 0.00 38.30 3.55
40 41 1.144057 CCTATCCTGCACGGGACAC 59.856 63.158 0.00 0.00 38.30 3.67
41 42 2.063979 CCCTATCCTGCACGGGACA 61.064 63.158 0.00 0.00 39.08 4.02
42 43 2.822399 CCCTATCCTGCACGGGAC 59.178 66.667 0.00 0.00 39.08 4.46
43 44 3.161450 GCCCTATCCTGCACGGGA 61.161 66.667 0.00 0.00 39.08 5.14
44 45 4.609018 CGCCCTATCCTGCACGGG 62.609 72.222 2.86 0.00 39.76 5.28
45 46 3.792053 GACGCCCTATCCTGCACGG 62.792 68.421 0.00 0.00 0.00 4.94
46 47 2.279517 GACGCCCTATCCTGCACG 60.280 66.667 0.00 0.00 0.00 5.34
47 48 2.109181 GGACGCCCTATCCTGCAC 59.891 66.667 0.00 0.00 33.03 4.57
48 49 2.041922 AGGACGCCCTATCCTGCA 60.042 61.111 0.00 0.00 45.29 4.41
52 53 2.370647 GACTGCAGGACGCCCTATCC 62.371 65.000 19.93 0.00 42.02 2.59
53 54 1.068250 GACTGCAGGACGCCCTATC 59.932 63.158 19.93 0.00 42.02 2.08
54 55 2.786495 CGACTGCAGGACGCCCTAT 61.786 63.158 19.93 0.00 42.02 2.57
55 56 3.449227 CGACTGCAGGACGCCCTA 61.449 66.667 19.93 0.00 42.02 3.53
66 67 2.035442 GGAAACCTCTGCCGACTGC 61.035 63.158 0.00 0.00 41.77 4.40
67 68 0.250295 TTGGAAACCTCTGCCGACTG 60.250 55.000 0.00 0.00 0.00 3.51
68 69 0.693049 ATTGGAAACCTCTGCCGACT 59.307 50.000 0.00 0.00 0.00 4.18
69 70 1.534729 AATTGGAAACCTCTGCCGAC 58.465 50.000 0.00 0.00 0.00 4.79
70 71 2.286365 AAATTGGAAACCTCTGCCGA 57.714 45.000 0.00 0.00 0.00 5.54
71 72 2.676076 CAAAATTGGAAACCTCTGCCG 58.324 47.619 0.00 0.00 0.00 5.69
84 85 2.810458 CCGCCGCTGCCAAAATTG 60.810 61.111 0.00 0.00 0.00 2.32
85 86 4.740431 GCCGCCGCTGCCAAAATT 62.740 61.111 0.00 0.00 0.00 1.82
114 115 0.256177 CTAACCAAGGGGAGGCTTCC 59.744 60.000 6.25 6.25 43.23 3.46
115 116 1.210722 CTCTAACCAAGGGGAGGCTTC 59.789 57.143 0.00 0.00 38.05 3.86
116 117 1.290134 CTCTAACCAAGGGGAGGCTT 58.710 55.000 0.00 0.00 38.05 4.35
117 118 3.013682 CTCTAACCAAGGGGAGGCT 57.986 57.895 0.00 0.00 38.05 4.58
123 124 2.511600 CGCGCCTCTAACCAAGGG 60.512 66.667 0.00 0.00 34.26 3.95
124 125 3.195698 GCGCGCCTCTAACCAAGG 61.196 66.667 23.24 0.00 36.95 3.61
125 126 3.554692 CGCGCGCCTCTAACCAAG 61.555 66.667 27.72 2.72 0.00 3.61
139 140 4.044484 CTCCCTATCCCTCGCGCG 62.044 72.222 26.76 26.76 0.00 6.86
140 141 3.686045 CCTCCCTATCCCTCGCGC 61.686 72.222 0.00 0.00 0.00 6.86
141 142 3.686045 GCCTCCCTATCCCTCGCG 61.686 72.222 0.00 0.00 0.00 5.87
142 143 3.686045 CGCCTCCCTATCCCTCGC 61.686 72.222 0.00 0.00 0.00 5.03
143 144 2.992114 CCGCCTCCCTATCCCTCG 60.992 72.222 0.00 0.00 0.00 4.63
144 145 2.604991 CCCGCCTCCCTATCCCTC 60.605 72.222 0.00 0.00 0.00 4.30
145 146 4.964241 GCCCGCCTCCCTATCCCT 62.964 72.222 0.00 0.00 0.00 4.20
146 147 4.964241 AGCCCGCCTCCCTATCCC 62.964 72.222 0.00 0.00 0.00 3.85
147 148 3.315140 GAGCCCGCCTCCCTATCC 61.315 72.222 0.00 0.00 34.35 2.59
191 192 3.077556 TCTTCCTCCGGCCTCTGC 61.078 66.667 0.00 0.00 0.00 4.26
192 193 2.430610 CCTCTTCCTCCGGCCTCTG 61.431 68.421 0.00 0.00 0.00 3.35
193 194 2.042435 CCTCTTCCTCCGGCCTCT 60.042 66.667 0.00 0.00 0.00 3.69
194 195 2.364448 ACCTCTTCCTCCGGCCTC 60.364 66.667 0.00 0.00 0.00 4.70
195 196 2.364448 GACCTCTTCCTCCGGCCT 60.364 66.667 0.00 0.00 0.00 5.19
196 197 3.471806 GGACCTCTTCCTCCGGCC 61.472 72.222 0.00 0.00 41.95 6.13
197 198 2.683933 TGGACCTCTTCCTCCGGC 60.684 66.667 0.00 0.00 46.10 6.13
198 199 1.305381 ACTGGACCTCTTCCTCCGG 60.305 63.158 0.00 0.00 46.10 5.14
199 200 1.893786 CACTGGACCTCTTCCTCCG 59.106 63.158 0.00 0.00 46.10 4.63
200 201 1.599576 GCACTGGACCTCTTCCTCC 59.400 63.158 0.00 0.00 46.10 4.30
201 202 1.216710 CGCACTGGACCTCTTCCTC 59.783 63.158 0.00 0.00 46.10 3.71
202 203 2.286523 CCGCACTGGACCTCTTCCT 61.287 63.158 0.00 0.00 46.10 3.36
203 204 2.266055 CCGCACTGGACCTCTTCC 59.734 66.667 0.00 0.00 46.13 3.46
204 205 2.435059 GCCGCACTGGACCTCTTC 60.435 66.667 0.00 0.00 42.00 2.87
205 206 2.925170 AGCCGCACTGGACCTCTT 60.925 61.111 0.00 0.00 42.00 2.85
206 207 3.699894 CAGCCGCACTGGACCTCT 61.700 66.667 0.00 0.00 43.19 3.69
219 220 4.785453 CTCTTCCCCCACGCAGCC 62.785 72.222 0.00 0.00 0.00 4.85
220 221 4.785453 CCTCTTCCCCCACGCAGC 62.785 72.222 0.00 0.00 0.00 5.25
221 222 3.316573 GACCTCTTCCCCCACGCAG 62.317 68.421 0.00 0.00 0.00 5.18
222 223 3.319198 GACCTCTTCCCCCACGCA 61.319 66.667 0.00 0.00 0.00 5.24
223 224 3.003763 AGACCTCTTCCCCCACGC 61.004 66.667 0.00 0.00 0.00 5.34
224 225 2.660064 CCAGACCTCTTCCCCCACG 61.660 68.421 0.00 0.00 0.00 4.94
225 226 1.539124 ACCAGACCTCTTCCCCCAC 60.539 63.158 0.00 0.00 0.00 4.61
226 227 1.538876 CACCAGACCTCTTCCCCCA 60.539 63.158 0.00 0.00 0.00 4.96
227 228 2.972819 GCACCAGACCTCTTCCCCC 61.973 68.421 0.00 0.00 0.00 5.40
228 229 2.671682 GCACCAGACCTCTTCCCC 59.328 66.667 0.00 0.00 0.00 4.81
229 230 1.920835 AGGCACCAGACCTCTTCCC 60.921 63.158 0.00 0.00 28.76 3.97
230 231 1.298014 CAGGCACCAGACCTCTTCC 59.702 63.158 0.00 0.00 34.42 3.46
231 232 1.376553 GCAGGCACCAGACCTCTTC 60.377 63.158 0.00 0.00 34.42 2.87
232 233 2.149383 TGCAGGCACCAGACCTCTT 61.149 57.895 0.00 0.00 34.42 2.85
233 234 2.527624 TGCAGGCACCAGACCTCT 60.528 61.111 0.00 0.00 34.42 3.69
234 235 2.359230 GTGCAGGCACCAGACCTC 60.359 66.667 13.28 0.00 40.79 3.85
242 243 2.796593 GACAAAATTGAAGTGCAGGCAC 59.203 45.455 16.29 16.29 46.50 5.01
243 244 2.224018 GGACAAAATTGAAGTGCAGGCA 60.224 45.455 0.00 0.00 0.00 4.75
244 245 2.407090 GGACAAAATTGAAGTGCAGGC 58.593 47.619 0.00 0.00 0.00 4.85
245 246 2.664916 CGGACAAAATTGAAGTGCAGG 58.335 47.619 0.00 0.00 0.00 4.85
246 247 2.053627 GCGGACAAAATTGAAGTGCAG 58.946 47.619 0.00 0.00 0.00 4.41
247 248 1.269517 GGCGGACAAAATTGAAGTGCA 60.270 47.619 0.00 0.00 0.00 4.57
248 249 1.418373 GGCGGACAAAATTGAAGTGC 58.582 50.000 0.00 0.00 0.00 4.40
249 250 1.001815 ACGGCGGACAAAATTGAAGTG 60.002 47.619 13.24 0.00 0.00 3.16
250 251 1.314730 ACGGCGGACAAAATTGAAGT 58.685 45.000 13.24 0.00 0.00 3.01
251 252 2.050691 CAACGGCGGACAAAATTGAAG 58.949 47.619 13.24 0.00 0.00 3.02
252 253 1.866063 GCAACGGCGGACAAAATTGAA 60.866 47.619 13.24 0.00 0.00 2.69
253 254 0.318275 GCAACGGCGGACAAAATTGA 60.318 50.000 13.24 0.00 0.00 2.57
254 255 2.140923 GCAACGGCGGACAAAATTG 58.859 52.632 13.24 5.77 0.00 2.32
255 256 4.645692 GCAACGGCGGACAAAATT 57.354 50.000 13.24 0.00 0.00 1.82
267 268 2.780338 CTTTCTCACGCGACGCAACG 62.780 60.000 21.35 6.13 0.00 4.10
268 269 1.154836 CTTTCTCACGCGACGCAAC 60.155 57.895 21.35 0.00 0.00 4.17
269 270 2.307309 CCTTTCTCACGCGACGCAA 61.307 57.895 21.35 2.73 0.00 4.85
270 271 2.733218 CCTTTCTCACGCGACGCA 60.733 61.111 21.35 0.00 0.00 5.24
271 272 3.479269 CCCTTTCTCACGCGACGC 61.479 66.667 15.93 10.49 0.00 5.19
272 273 1.801913 CTCCCTTTCTCACGCGACG 60.802 63.158 15.93 2.89 0.00 5.12
273 274 0.038526 TTCTCCCTTTCTCACGCGAC 60.039 55.000 15.93 0.00 0.00 5.19
274 275 0.243907 CTTCTCCCTTTCTCACGCGA 59.756 55.000 15.93 0.00 0.00 5.87
275 276 1.355066 GCTTCTCCCTTTCTCACGCG 61.355 60.000 3.53 3.53 0.00 6.01
276 277 1.355066 CGCTTCTCCCTTTCTCACGC 61.355 60.000 0.00 0.00 0.00 5.34
277 278 0.737715 CCGCTTCTCCCTTTCTCACG 60.738 60.000 0.00 0.00 0.00 4.35
278 279 1.021920 GCCGCTTCTCCCTTTCTCAC 61.022 60.000 0.00 0.00 0.00 3.51
279 280 1.194781 AGCCGCTTCTCCCTTTCTCA 61.195 55.000 0.00 0.00 0.00 3.27
280 281 0.742635 CAGCCGCTTCTCCCTTTCTC 60.743 60.000 0.00 0.00 0.00 2.87
281 282 1.298014 CAGCCGCTTCTCCCTTTCT 59.702 57.895 0.00 0.00 0.00 2.52
282 283 1.746991 CCAGCCGCTTCTCCCTTTC 60.747 63.158 0.00 0.00 0.00 2.62
283 284 2.352805 CCAGCCGCTTCTCCCTTT 59.647 61.111 0.00 0.00 0.00 3.11
284 285 3.721706 CCCAGCCGCTTCTCCCTT 61.722 66.667 0.00 0.00 0.00 3.95
305 306 2.290122 ATTCCCACGAGCTCGCTCAG 62.290 60.000 34.83 21.29 42.86 3.35
306 307 1.888436 AATTCCCACGAGCTCGCTCA 61.888 55.000 34.83 15.53 42.86 4.26
307 308 0.102481 TAATTCCCACGAGCTCGCTC 59.898 55.000 34.83 8.82 44.43 5.03
308 309 0.103208 CTAATTCCCACGAGCTCGCT 59.897 55.000 34.83 19.51 44.43 4.93
309 310 1.491505 GCTAATTCCCACGAGCTCGC 61.492 60.000 34.83 11.50 44.43 5.03
310 311 1.209275 CGCTAATTCCCACGAGCTCG 61.209 60.000 33.45 33.45 46.33 5.03
311 312 0.876342 CCGCTAATTCCCACGAGCTC 60.876 60.000 2.73 2.73 32.60 4.09
312 313 1.144057 CCGCTAATTCCCACGAGCT 59.856 57.895 0.00 0.00 32.60 4.09
313 314 1.153429 ACCGCTAATTCCCACGAGC 60.153 57.895 0.00 0.00 0.00 5.03
314 315 0.810031 CCACCGCTAATTCCCACGAG 60.810 60.000 0.00 0.00 0.00 4.18
315 316 1.219664 CCACCGCTAATTCCCACGA 59.780 57.895 0.00 0.00 0.00 4.35
316 317 2.469516 GCCACCGCTAATTCCCACG 61.470 63.158 0.00 0.00 0.00 4.94
317 318 1.376609 CTGCCACCGCTAATTCCCAC 61.377 60.000 0.00 0.00 35.36 4.61
318 319 1.077787 CTGCCACCGCTAATTCCCA 60.078 57.895 0.00 0.00 35.36 4.37
319 320 2.481471 GCTGCCACCGCTAATTCCC 61.481 63.158 0.00 0.00 35.36 3.97
320 321 1.452108 AGCTGCCACCGCTAATTCC 60.452 57.895 0.00 0.00 35.63 3.01
321 322 0.744414 TCAGCTGCCACCGCTAATTC 60.744 55.000 9.47 0.00 35.63 2.17
322 323 0.745845 CTCAGCTGCCACCGCTAATT 60.746 55.000 9.47 0.00 35.63 1.40
323 324 1.153289 CTCAGCTGCCACCGCTAAT 60.153 57.895 9.47 0.00 35.63 1.73
324 325 2.265739 CTCAGCTGCCACCGCTAA 59.734 61.111 9.47 0.00 35.63 3.09
325 326 4.457496 GCTCAGCTGCCACCGCTA 62.457 66.667 9.47 0.00 35.63 4.26
337 338 0.865218 CAGAACGCTAGCTCGCTCAG 60.865 60.000 13.93 0.00 0.00 3.35
338 339 1.137614 CAGAACGCTAGCTCGCTCA 59.862 57.895 13.93 0.00 0.00 4.26
339 340 0.179161 TTCAGAACGCTAGCTCGCTC 60.179 55.000 13.93 3.78 0.00 5.03
340 341 0.457851 ATTCAGAACGCTAGCTCGCT 59.542 50.000 13.93 3.71 0.00 4.93
341 342 0.849579 GATTCAGAACGCTAGCTCGC 59.150 55.000 13.93 0.00 0.00 5.03
342 343 1.116436 CGATTCAGAACGCTAGCTCG 58.884 55.000 13.93 8.71 0.00 5.03
343 344 1.482278 CCGATTCAGAACGCTAGCTC 58.518 55.000 13.93 4.36 0.00 4.09
344 345 0.528684 GCCGATTCAGAACGCTAGCT 60.529 55.000 13.93 0.00 0.00 3.32
345 346 1.812214 CGCCGATTCAGAACGCTAGC 61.812 60.000 4.06 4.06 0.00 3.42
346 347 1.209275 CCGCCGATTCAGAACGCTAG 61.209 60.000 0.00 0.00 0.00 3.42
347 348 1.226859 CCGCCGATTCAGAACGCTA 60.227 57.895 0.00 0.00 0.00 4.26
348 349 2.509336 CCGCCGATTCAGAACGCT 60.509 61.111 0.00 0.00 0.00 5.07
349 350 2.813908 ACCGCCGATTCAGAACGC 60.814 61.111 0.00 0.00 0.00 4.84
350 351 2.452813 CCACCGCCGATTCAGAACG 61.453 63.158 0.00 0.00 0.00 3.95
351 352 2.750888 GCCACCGCCGATTCAGAAC 61.751 63.158 0.00 0.00 0.00 3.01
352 353 2.435938 GCCACCGCCGATTCAGAA 60.436 61.111 0.00 0.00 0.00 3.02
353 354 4.812476 CGCCACCGCCGATTCAGA 62.812 66.667 0.00 0.00 0.00 3.27
369 370 2.811317 GAACCACGAGCTCAGCCG 60.811 66.667 15.40 2.30 0.00 5.52
370 371 1.301716 TTGAACCACGAGCTCAGCC 60.302 57.895 15.40 0.00 0.00 4.85
371 372 1.569479 GGTTGAACCACGAGCTCAGC 61.569 60.000 15.40 0.00 38.42 4.26
372 373 1.284982 CGGTTGAACCACGAGCTCAG 61.285 60.000 15.58 9.21 38.47 3.35
373 374 1.300620 CGGTTGAACCACGAGCTCA 60.301 57.895 15.58 0.00 38.47 4.26
374 375 2.668280 GCGGTTGAACCACGAGCTC 61.668 63.158 15.58 2.73 38.47 4.09
375 376 2.665185 GCGGTTGAACCACGAGCT 60.665 61.111 15.58 0.00 38.47 4.09
376 377 2.665185 AGCGGTTGAACCACGAGC 60.665 61.111 15.58 9.43 38.47 5.03
377 378 2.372690 CGAGCGGTTGAACCACGAG 61.373 63.158 15.58 0.00 38.47 4.18
378 379 2.355363 CGAGCGGTTGAACCACGA 60.355 61.111 15.58 0.00 38.47 4.35
379 380 4.072088 GCGAGCGGTTGAACCACG 62.072 66.667 15.58 16.34 38.47 4.94
380 381 2.665185 AGCGAGCGGTTGAACCAC 60.665 61.111 15.58 4.46 38.47 4.16
381 382 2.664851 CAGCGAGCGGTTGAACCA 60.665 61.111 15.58 0.00 38.47 3.67
382 383 3.423154 CCAGCGAGCGGTTGAACC 61.423 66.667 3.76 3.76 34.05 3.62
383 384 3.423154 CCCAGCGAGCGGTTGAAC 61.423 66.667 5.91 0.00 0.00 3.18
386 387 4.451150 TAGCCCAGCGAGCGGTTG 62.451 66.667 0.00 0.00 34.64 3.77
387 388 4.148825 CTAGCCCAGCGAGCGGTT 62.149 66.667 0.00 0.00 34.64 4.44
389 390 4.277593 CTCTAGCCCAGCGAGCGG 62.278 72.222 0.00 0.00 31.54 5.52
390 391 4.940593 GCTCTAGCCCAGCGAGCG 62.941 72.222 0.00 0.00 40.48 5.03
392 393 1.956043 CTAGCTCTAGCCCAGCGAG 59.044 63.158 0.00 0.00 42.14 5.03
393 394 4.165926 CTAGCTCTAGCCCAGCGA 57.834 61.111 0.00 0.00 42.14 4.93
401 402 5.221880 CAAACATGCTCTAGCTAGCTCTAG 58.778 45.833 23.26 19.89 43.19 2.43
402 403 4.038522 CCAAACATGCTCTAGCTAGCTCTA 59.961 45.833 23.26 9.72 43.19 2.43
403 404 3.181467 CCAAACATGCTCTAGCTAGCTCT 60.181 47.826 23.26 0.00 43.19 4.09
404 405 3.129871 CCAAACATGCTCTAGCTAGCTC 58.870 50.000 23.26 7.43 43.19 4.09
405 406 2.503356 ACCAAACATGCTCTAGCTAGCT 59.497 45.455 23.12 23.12 43.19 3.32
406 407 2.911484 ACCAAACATGCTCTAGCTAGC 58.089 47.619 16.35 6.62 43.08 3.42
407 408 3.064545 GCAACCAAACATGCTCTAGCTAG 59.935 47.826 15.01 15.01 42.66 3.42
408 409 3.009723 GCAACCAAACATGCTCTAGCTA 58.990 45.455 3.26 0.00 42.66 3.32
409 410 1.815003 GCAACCAAACATGCTCTAGCT 59.185 47.619 3.26 0.00 42.66 3.32
410 411 1.135286 GGCAACCAAACATGCTCTAGC 60.135 52.381 0.00 0.00 42.20 3.42
454 455 2.815684 TAGGCCTCTTCCTTCCCGCA 62.816 60.000 9.68 0.00 37.66 5.69
473 474 2.564062 CAGTGAATCCAGGCAACCAAAT 59.436 45.455 0.00 0.00 37.17 2.32
517 523 1.035932 CAGGCTCTGGGATGCTTTGG 61.036 60.000 0.00 0.00 0.00 3.28
606 612 4.947147 GCCCTCACGTTGCACCCA 62.947 66.667 0.00 0.00 0.00 4.51
659 666 1.475034 GCTAGATTTGATGCGGGGACA 60.475 52.381 0.00 0.00 0.00 4.02
665 672 1.530293 GCTGAGGCTAGATTTGATGCG 59.470 52.381 0.00 0.00 35.22 4.73
669 676 0.839946 GGGGCTGAGGCTAGATTTGA 59.160 55.000 5.84 0.00 38.73 2.69
684 694 1.527433 GGTGAGCAAGTGAAAGGGGC 61.527 60.000 0.00 0.00 0.00 5.80
796 820 1.227497 CCAGATCCGCTGCCTCTTC 60.227 63.158 0.00 0.00 43.50 2.87
797 821 1.557269 AACCAGATCCGCTGCCTCTT 61.557 55.000 0.00 0.00 43.50 2.85
798 822 1.965754 GAACCAGATCCGCTGCCTCT 61.966 60.000 0.00 0.00 43.50 3.69
799 823 1.522580 GAACCAGATCCGCTGCCTC 60.523 63.158 0.00 0.00 43.50 4.70
800 824 1.965754 GAGAACCAGATCCGCTGCCT 61.966 60.000 0.00 0.00 43.50 4.75
801 825 1.522580 GAGAACCAGATCCGCTGCC 60.523 63.158 0.00 0.00 43.50 4.85
804 828 2.066999 GGGGAGAACCAGATCCGCT 61.067 63.158 1.41 0.00 43.34 5.52
816 840 2.436109 GCCAACAGCAAGGGGAGA 59.564 61.111 0.00 0.00 42.97 3.71
840 864 1.222115 GCACAGACAAGGTCGACCAC 61.222 60.000 35.00 21.78 37.67 4.16
884 908 1.069823 CTGCTTACCGGCATCAGAGAT 59.930 52.381 0.00 0.00 41.63 2.75
945 970 4.141482 GGAAATTGATCCTACACCTAGCCA 60.141 45.833 0.00 0.00 36.50 4.75
962 987 3.496331 ACGGTTCATTCAGTGGGAAATT 58.504 40.909 0.00 0.00 39.39 1.82
991 1016 3.167485 TCCGTGTGTCCATAACCTAGTT 58.833 45.455 0.00 0.00 0.00 2.24
1006 1031 3.134623 TGAATTATCAGCCTCATCCGTGT 59.865 43.478 0.00 0.00 0.00 4.49
1029 1054 1.445871 CACTAATCAGTGCTGCTGCA 58.554 50.000 14.93 14.93 45.44 4.41
1050 1075 3.053768 TGAACATGACCCATGCCTGAATA 60.054 43.478 0.00 0.00 44.80 1.75
1199 1233 2.267961 CGGAAAACTAGCCCCGCT 59.732 61.111 0.00 0.00 43.41 5.52
1276 1344 9.163899 TGTCGCCACTATGTTTGTTTAAATATA 57.836 29.630 0.00 0.00 31.28 0.86
1738 1834 2.755980 CCTATTAGGGGACGGGGAC 58.244 63.158 1.37 0.00 0.00 4.46
1823 1919 4.133820 CGGATAAACAATGGACCATAGCA 58.866 43.478 7.59 0.00 0.00 3.49
1895 1991 1.047596 AGCATCCACAGAGCCTCGAT 61.048 55.000 0.00 0.00 0.00 3.59
1939 2035 1.819288 CTCAAGGTCTCGACAAGCCTA 59.181 52.381 0.00 0.00 33.01 3.93
1998 2095 0.111061 ACATGGCCACTTGCTCTTCA 59.889 50.000 8.16 0.00 40.92 3.02
2267 2365 0.512952 GCCTGTGTTAGTGCTCAACG 59.487 55.000 0.00 0.00 0.00 4.10
2491 2590 0.320771 ACCAGGTCGACTCATGTTGC 60.321 55.000 16.46 0.00 0.00 4.17
2597 2696 4.597004 AGAACTCGTTGAGATGGTACCTA 58.403 43.478 14.36 0.00 33.32 3.08
2680 2779 4.373156 AATGCCCTCTCAACAGTTACTT 57.627 40.909 0.00 0.00 0.00 2.24
2730 2831 2.621407 GGTGGAATGGCTTCTGATCCAA 60.621 50.000 3.73 0.00 41.54 3.53
2814 2915 1.234615 ACGTGTTCATCAAAGCCCCG 61.235 55.000 0.00 0.00 0.00 5.73
2856 2957 2.096713 CAGAGCTAACAACAACGTCAGC 60.097 50.000 0.00 0.00 0.00 4.26
2863 2964 2.161855 CATGGCCAGAGCTAACAACAA 58.838 47.619 13.05 0.00 39.73 2.83
2900 3001 5.278266 CCTTTTGTTCTTCCAAGCGTCATTA 60.278 40.000 0.00 0.00 0.00 1.90
2968 3069 7.941238 TCTTCTTCTTCCATGTTCTTCAAATCT 59.059 33.333 0.00 0.00 0.00 2.40
2980 3081 7.877097 TCTTCTTCTTCTTCTTCTTCTTCCATG 59.123 37.037 0.00 0.00 0.00 3.66
3024 3136 2.564504 TCTTCTTCTGCTTCTGCTGCTA 59.435 45.455 0.00 0.00 40.48 3.49
3058 3182 4.563580 GGTGTTTCTGCTACCAGATCTTCA 60.564 45.833 0.00 0.00 46.84 3.02
3075 3199 2.374170 AGGGGATAGTTCAACGGTGTTT 59.626 45.455 0.00 0.00 0.00 2.83
3083 3207 6.584471 TTGGCTAAATAGGGGATAGTTCAA 57.416 37.500 0.00 0.00 0.00 2.69
3136 3260 9.823647 AAATGACAGTTCATCCTAACTACTATG 57.176 33.333 0.00 0.00 42.00 2.23
3184 3308 4.272504 AGTTTACCACACACAATCTGAACG 59.727 41.667 0.00 0.00 0.00 3.95
3274 3398 1.379710 TGCCCGCATTGCATTAGGT 60.380 52.632 9.69 0.00 32.85 3.08


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

AutoCloner maintained by Alex Coulton.