Multiple sequence alignment - TraesCS2B01G065100

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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 TraesCS2B01G065100 chr2B 100.000 7860 0 0 1 7860 31587171 31595030 0.000000e+00 14515.0
1 TraesCS2B01G065100 chr2B 86.026 229 20 8 7032 7258 732349662 732349880 1.320000e-57 235.0
2 TraesCS2B01G065100 chr2B 93.333 120 5 2 1 120 31609615 31609731 2.920000e-39 174.0
3 TraesCS2B01G065100 chr2B 79.144 187 23 7 7375 7545 300329210 300329024 1.790000e-21 115.0
4 TraesCS2B01G065100 chr1B 98.968 6882 65 5 384 7260 441990718 441997598 0.000000e+00 12310.0
5 TraesCS2B01G065100 chr1B 90.196 255 24 1 124 378 461905394 461905141 1.630000e-86 331.0
6 TraesCS2B01G065100 chr7A 98.751 6885 77 6 384 7261 721569630 721562748 0.000000e+00 12229.0
7 TraesCS2B01G065100 chr7A 98.613 4110 50 7 3155 7260 691157937 691153831 0.000000e+00 7267.0
8 TraesCS2B01G065100 chr7A 99.475 1143 6 0 1459 2601 660468707 660469849 0.000000e+00 2078.0
9 TraesCS2B01G065100 chr7A 75.708 4133 926 72 1294 5392 19151098 19147010 0.000000e+00 1999.0
10 TraesCS2B01G065100 chr3A 98.421 6903 67 12 384 7260 20021351 20028237 0.000000e+00 12105.0
11 TraesCS2B01G065100 chr3A 98.543 4666 53 7 1788 6442 625211574 625216235 0.000000e+00 8226.0
12 TraesCS2B01G065100 chr3A 86.341 1845 225 23 5418 7257 741114955 741116777 0.000000e+00 1986.0
13 TraesCS2B01G065100 chr3A 86.528 579 64 11 6684 7260 22392866 22392300 6.700000e-175 625.0
14 TraesCS2B01G065100 chr3B 98.737 5621 59 7 1643 7261 762634455 762628845 0.000000e+00 9976.0
15 TraesCS2B01G065100 chr2A 98.579 5419 52 5 1848 7258 117176260 117170859 0.000000e+00 9557.0
16 TraesCS2B01G065100 chr2A 99.161 596 5 0 419 1014 117177534 117176939 0.000000e+00 1074.0
17 TraesCS2B01G065100 chr6B 98.891 4959 52 3 384 5340 586518900 586523857 0.000000e+00 8850.0
18 TraesCS2B01G065100 chr6B 78.495 186 24 7 7375 7544 587744363 587744178 3.000000e-19 108.0
19 TraesCS2B01G065100 chr4A 92.464 5706 411 17 1559 7260 656896071 656901761 0.000000e+00 8137.0
20 TraesCS2B01G065100 chr4A 90.588 255 23 1 124 378 737370247 737370500 3.510000e-88 337.0
21 TraesCS2B01G065100 chr6A 92.991 4979 344 5 384 5360 117404448 117409423 0.000000e+00 7256.0
22 TraesCS2B01G065100 chr2D 87.664 535 53 8 7337 7860 88625015 88624483 1.880000e-170 610.0
23 TraesCS2B01G065100 chr2D 85.213 541 54 14 7332 7860 88709865 88709339 4.180000e-147 532.0
24 TraesCS2B01G065100 chr2D 88.302 265 30 1 125 389 88710230 88709967 4.580000e-82 316.0
25 TraesCS2B01G065100 chr3D 86.916 535 56 4 7338 7860 419619989 419620521 8.790000e-164 588.0
26 TraesCS2B01G065100 chr3D 86.069 524 59 4 7338 7849 355107498 355108019 1.150000e-152 551.0
27 TraesCS2B01G065100 chr3D 86.395 294 37 3 97 389 355107101 355107392 1.270000e-82 318.0
28 TraesCS2B01G065100 chr3D 88.015 267 31 1 123 389 419619618 419619883 1.650000e-81 315.0
29 TraesCS2B01G065100 chr5D 86.355 535 59 4 7338 7860 564879631 564879099 8.850000e-159 571.0
30 TraesCS2B01G065100 chr5D 86.168 535 60 7 7338 7860 90296356 90295824 4.120000e-157 566.0
31 TraesCS2B01G065100 chr5D 88.302 265 30 1 125 389 90296725 90296462 4.580000e-82 316.0
32 TraesCS2B01G065100 chr5D 87.823 271 32 1 119 389 564880006 564879737 4.580000e-82 316.0
33 TraesCS2B01G065100 chr7D 85.794 535 62 7 7338 7860 575661031 575660499 8.910000e-154 555.0
34 TraesCS2B01G065100 chrUn 85.794 535 61 5 7338 7860 70163794 70164325 3.210000e-153 553.0
35 TraesCS2B01G065100 chrUn 89.434 265 27 1 125 389 289849867 289849604 4.550000e-87 333.0
36 TraesCS2B01G065100 chr7B 89.811 265 26 1 125 389 693337138 693336875 9.770000e-89 339.0
37 TraesCS2B01G065100 chr7B 78.093 493 87 10 7375 7850 571566767 571567255 7.710000e-75 292.0
38 TraesCS2B01G065100 chr7B 79.032 186 23 7 7375 7544 345994384 345994199 6.450000e-21 113.0
39 TraesCS2B01G065100 chr5B 79.518 332 53 6 7526 7843 205580714 205581044 1.030000e-53 222.0
40 TraesCS2B01G065100 chr5B 77.419 186 26 7 7375 7544 22031752 22031937 6.490000e-16 97.1
41 TraesCS2B01G065100 chr5B 77.419 186 26 7 7375 7544 463401690 463401875 6.490000e-16 97.1
42 TraesCS2B01G065100 chr5B 77.654 179 23 7 7375 7542 206473723 206473895 8.400000e-15 93.5
43 TraesCS2B01G065100 chr5A 84.091 220 30 4 7524 7740 166879009 166879226 2.870000e-49 207.0
44 TraesCS2B01G065100 chr4B 75.401 187 20 10 7375 7545 152079950 152080126 5.090000e-07 67.6


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 TraesCS2B01G065100 chr2B 31587171 31595030 7859 False 14515.0 14515 100.0000 1 7860 1 chr2B.!!$F1 7859
1 TraesCS2B01G065100 chr1B 441990718 441997598 6880 False 12310.0 12310 98.9680 384 7260 1 chr1B.!!$F1 6876
2 TraesCS2B01G065100 chr7A 721562748 721569630 6882 True 12229.0 12229 98.7510 384 7261 1 chr7A.!!$R3 6877
3 TraesCS2B01G065100 chr7A 691153831 691157937 4106 True 7267.0 7267 98.6130 3155 7260 1 chr7A.!!$R2 4105
4 TraesCS2B01G065100 chr7A 660468707 660469849 1142 False 2078.0 2078 99.4750 1459 2601 1 chr7A.!!$F1 1142
5 TraesCS2B01G065100 chr7A 19147010 19151098 4088 True 1999.0 1999 75.7080 1294 5392 1 chr7A.!!$R1 4098
6 TraesCS2B01G065100 chr3A 20021351 20028237 6886 False 12105.0 12105 98.4210 384 7260 1 chr3A.!!$F1 6876
7 TraesCS2B01G065100 chr3A 625211574 625216235 4661 False 8226.0 8226 98.5430 1788 6442 1 chr3A.!!$F2 4654
8 TraesCS2B01G065100 chr3A 741114955 741116777 1822 False 1986.0 1986 86.3410 5418 7257 1 chr3A.!!$F3 1839
9 TraesCS2B01G065100 chr3A 22392300 22392866 566 True 625.0 625 86.5280 6684 7260 1 chr3A.!!$R1 576
10 TraesCS2B01G065100 chr3B 762628845 762634455 5610 True 9976.0 9976 98.7370 1643 7261 1 chr3B.!!$R1 5618
11 TraesCS2B01G065100 chr2A 117170859 117177534 6675 True 5315.5 9557 98.8700 419 7258 2 chr2A.!!$R1 6839
12 TraesCS2B01G065100 chr6B 586518900 586523857 4957 False 8850.0 8850 98.8910 384 5340 1 chr6B.!!$F1 4956
13 TraesCS2B01G065100 chr4A 656896071 656901761 5690 False 8137.0 8137 92.4640 1559 7260 1 chr4A.!!$F1 5701
14 TraesCS2B01G065100 chr6A 117404448 117409423 4975 False 7256.0 7256 92.9910 384 5360 1 chr6A.!!$F1 4976
15 TraesCS2B01G065100 chr2D 88624483 88625015 532 True 610.0 610 87.6640 7337 7860 1 chr2D.!!$R1 523
16 TraesCS2B01G065100 chr2D 88709339 88710230 891 True 424.0 532 86.7575 125 7860 2 chr2D.!!$R2 7735
17 TraesCS2B01G065100 chr3D 419619618 419620521 903 False 451.5 588 87.4655 123 7860 2 chr3D.!!$F2 7737
18 TraesCS2B01G065100 chr3D 355107101 355108019 918 False 434.5 551 86.2320 97 7849 2 chr3D.!!$F1 7752
19 TraesCS2B01G065100 chr5D 564879099 564880006 907 True 443.5 571 87.0890 119 7860 2 chr5D.!!$R2 7741
20 TraesCS2B01G065100 chr5D 90295824 90296725 901 True 441.0 566 87.2350 125 7860 2 chr5D.!!$R1 7735
21 TraesCS2B01G065100 chr7D 575660499 575661031 532 True 555.0 555 85.7940 7338 7860 1 chr7D.!!$R1 522
22 TraesCS2B01G065100 chrUn 70163794 70164325 531 False 553.0 553 85.7940 7338 7860 1 chrUn.!!$F1 522

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
175 176 0.179108 GCCGAGAGTAAGCCAATCGT 60.179 55.000 0.00 0.0 0.00 3.73 F
294 295 1.006805 GGATGGCCGATGTCTCTCG 60.007 63.158 0.00 0.0 38.37 4.04 F
1698 1724 3.778265 AGAAAGGGCATGTTGTTATGGT 58.222 40.909 0.00 0.0 0.00 3.55 F
2960 3038 2.236395 CCCTCTCTTTAACATGGGACGT 59.764 50.000 0.00 0.0 36.90 4.34 F
3697 3779 6.042638 TCTACTTGGGTTGAGAGAGATTTG 57.957 41.667 0.00 0.0 0.00 2.32 F
4361 4447 4.986054 TGAGGGCACTAAAAACCTTCTA 57.014 40.909 0.00 0.0 32.42 2.10 F
4991 5078 2.631062 TGACTGTCATAGGAAACGTGGT 59.369 45.455 6.36 0.0 0.00 4.16 F
5732 5830 4.468510 TGGTTAAGTGGACGAGGATATGTT 59.531 41.667 0.00 0.0 0.00 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1698 1724 1.346395 TCCTTCAGAGGCAAGCGTTTA 59.654 47.619 0.0 0.0 43.21 2.01 R
1802 1828 6.319658 GCATCTTTTCTCTATGGGAATGTTGA 59.680 38.462 0.0 0.0 0.00 3.18 R
3356 3434 0.252239 GCCACCAGATTTCCCCCTTT 60.252 55.000 0.0 0.0 0.00 3.11 R
4034 4120 3.225940 CAAATTAGATCCCCAGCCCTTC 58.774 50.000 0.0 0.0 0.00 3.46 R
4991 5078 5.536916 CCACCCACACCACTTAGAATTAAAA 59.463 40.000 0.0 0.0 0.00 1.52 R
5993 6091 0.687354 GCCCACGGATCATACCAGAT 59.313 55.000 0.0 0.0 0.00 2.90 R
6093 6191 3.369471 GCCCAGCTCATAGTTGTTAGTCA 60.369 47.826 0.0 0.0 0.00 3.41 R
7529 7649 0.036306 AAGGAAGAAATCGCACCGGT 59.964 50.000 0.0 0.0 0.00 5.28 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
31 32 4.840005 GCTCCTACGCCAGCCACC 62.840 72.222 0.00 0.00 0.00 4.61
32 33 3.390521 CTCCTACGCCAGCCACCA 61.391 66.667 0.00 0.00 0.00 4.17
33 34 3.376935 CTCCTACGCCAGCCACCAG 62.377 68.421 0.00 0.00 0.00 4.00
34 35 3.706373 CCTACGCCAGCCACCAGT 61.706 66.667 0.00 0.00 0.00 4.00
35 36 2.434884 CTACGCCAGCCACCAGTG 60.435 66.667 0.00 0.00 0.00 3.66
56 57 4.803426 GCAGAGCTACAGGCGCGT 62.803 66.667 8.43 0.00 45.35 6.01
57 58 2.580867 CAGAGCTACAGGCGCGTC 60.581 66.667 0.21 0.21 45.35 5.19
58 59 3.827898 AGAGCTACAGGCGCGTCC 61.828 66.667 7.31 9.59 45.35 4.79
61 62 4.183686 GCTACAGGCGCGTCCGTA 62.184 66.667 7.31 6.91 40.77 4.02
62 63 2.277756 CTACAGGCGCGTCCGTAC 60.278 66.667 7.31 0.00 40.77 3.67
93 94 2.413351 CAGCCAGCTGCATCATGC 59.587 61.111 8.66 1.35 44.83 4.06
104 105 2.759538 GCATCATGCAGAGCTTCTTC 57.240 50.000 4.20 0.00 44.26 2.87
106 107 2.683867 GCATCATGCAGAGCTTCTTCTT 59.316 45.455 4.20 0.00 44.26 2.52
107 108 3.242804 GCATCATGCAGAGCTTCTTCTTC 60.243 47.826 4.20 0.00 44.26 2.87
110 111 4.649692 TCATGCAGAGCTTCTTCTTCTTT 58.350 39.130 0.00 0.00 0.00 2.52
117 118 6.037062 GCAGAGCTTCTTCTTCTTTATCCTTC 59.963 42.308 0.00 0.00 0.00 3.46
118 119 7.330262 CAGAGCTTCTTCTTCTTTATCCTTCT 58.670 38.462 0.00 0.00 0.00 2.85
121 122 9.476202 GAGCTTCTTCTTCTTTATCCTTCTATC 57.524 37.037 0.00 0.00 0.00 2.08
173 174 2.993539 GGCCGAGAGTAAGCCAATC 58.006 57.895 0.00 0.00 46.34 2.67
174 175 0.876342 GGCCGAGAGTAAGCCAATCG 60.876 60.000 0.00 0.00 46.34 3.34
175 176 0.179108 GCCGAGAGTAAGCCAATCGT 60.179 55.000 0.00 0.00 0.00 3.73
176 177 1.739371 GCCGAGAGTAAGCCAATCGTT 60.739 52.381 0.00 0.00 0.00 3.85
177 178 2.480759 GCCGAGAGTAAGCCAATCGTTA 60.481 50.000 0.00 0.00 0.00 3.18
178 179 3.799232 GCCGAGAGTAAGCCAATCGTTAT 60.799 47.826 0.00 0.00 0.00 1.89
179 180 4.558095 GCCGAGAGTAAGCCAATCGTTATA 60.558 45.833 0.00 0.00 0.00 0.98
180 181 5.526115 CCGAGAGTAAGCCAATCGTTATAA 58.474 41.667 0.00 0.00 0.00 0.98
181 182 5.629849 CCGAGAGTAAGCCAATCGTTATAAG 59.370 44.000 0.00 0.00 0.00 1.73
182 183 6.436261 CGAGAGTAAGCCAATCGTTATAAGA 58.564 40.000 0.00 0.00 0.00 2.10
183 184 6.579292 CGAGAGTAAGCCAATCGTTATAAGAG 59.421 42.308 0.00 0.00 0.00 2.85
184 185 7.349412 AGAGTAAGCCAATCGTTATAAGAGT 57.651 36.000 0.00 0.00 0.00 3.24
185 186 7.203910 AGAGTAAGCCAATCGTTATAAGAGTG 58.796 38.462 5.79 5.79 33.97 3.51
186 187 6.875076 AGTAAGCCAATCGTTATAAGAGTGT 58.125 36.000 9.76 0.00 32.50 3.55
187 188 6.757010 AGTAAGCCAATCGTTATAAGAGTGTG 59.243 38.462 9.76 5.09 32.50 3.82
188 189 3.871594 AGCCAATCGTTATAAGAGTGTGC 59.128 43.478 9.76 11.15 32.50 4.57
189 190 3.621268 GCCAATCGTTATAAGAGTGTGCA 59.379 43.478 13.74 0.00 33.49 4.57
190 191 4.273480 GCCAATCGTTATAAGAGTGTGCAT 59.727 41.667 0.00 0.00 33.49 3.96
191 192 5.220854 GCCAATCGTTATAAGAGTGTGCATT 60.221 40.000 0.00 0.00 33.49 3.56
192 193 6.018262 GCCAATCGTTATAAGAGTGTGCATTA 60.018 38.462 0.00 0.00 33.49 1.90
193 194 7.466725 GCCAATCGTTATAAGAGTGTGCATTAA 60.467 37.037 0.00 0.00 33.49 1.40
194 195 7.850982 CCAATCGTTATAAGAGTGTGCATTAAC 59.149 37.037 0.00 0.00 32.50 2.01
195 196 8.387354 CAATCGTTATAAGAGTGTGCATTAACA 58.613 33.333 0.00 0.00 0.00 2.41
196 197 8.662781 ATCGTTATAAGAGTGTGCATTAACAT 57.337 30.769 0.00 0.00 31.49 2.71
197 198 9.758651 ATCGTTATAAGAGTGTGCATTAACATA 57.241 29.630 0.00 0.00 31.49 2.29
198 199 9.758651 TCGTTATAAGAGTGTGCATTAACATAT 57.241 29.630 0.00 0.00 31.49 1.78
219 220 9.113838 ACATATTGATGTTCGAAAAGAATAGCT 57.886 29.630 0.00 0.00 44.18 3.32
220 221 9.591404 CATATTGATGTTCGAAAAGAATAGCTC 57.409 33.333 0.00 0.00 41.49 4.09
221 222 7.615582 ATTGATGTTCGAAAAGAATAGCTCA 57.384 32.000 0.00 0.00 41.49 4.26
222 223 7.615582 TTGATGTTCGAAAAGAATAGCTCAT 57.384 32.000 0.00 0.00 41.49 2.90
223 224 8.716646 TTGATGTTCGAAAAGAATAGCTCATA 57.283 30.769 0.00 0.00 41.49 2.15
224 225 8.893219 TGATGTTCGAAAAGAATAGCTCATAT 57.107 30.769 0.00 0.00 41.49 1.78
225 226 9.981114 TGATGTTCGAAAAGAATAGCTCATATA 57.019 29.630 0.00 0.00 41.49 0.86
227 228 9.988815 ATGTTCGAAAAGAATAGCTCATATACT 57.011 29.630 0.00 0.00 41.49 2.12
261 262 9.884465 GTAAGTACATAAGATTGGAAATGATGC 57.116 33.333 0.00 0.00 0.00 3.91
262 263 8.523915 AAGTACATAAGATTGGAAATGATGCA 57.476 30.769 0.00 0.00 0.00 3.96
263 264 7.934457 AGTACATAAGATTGGAAATGATGCAC 58.066 34.615 0.00 0.00 0.00 4.57
264 265 7.776969 AGTACATAAGATTGGAAATGATGCACT 59.223 33.333 0.00 0.00 0.00 4.40
265 266 9.056005 GTACATAAGATTGGAAATGATGCACTA 57.944 33.333 0.00 0.00 0.00 2.74
266 267 8.523915 ACATAAGATTGGAAATGATGCACTAA 57.476 30.769 0.00 0.00 0.00 2.24
267 268 8.970020 ACATAAGATTGGAAATGATGCACTAAA 58.030 29.630 0.00 0.00 0.00 1.85
268 269 9.459640 CATAAGATTGGAAATGATGCACTAAAG 57.540 33.333 0.00 0.00 0.00 1.85
269 270 7.472334 AAGATTGGAAATGATGCACTAAAGT 57.528 32.000 0.00 0.00 0.00 2.66
270 271 7.093322 AGATTGGAAATGATGCACTAAAGTC 57.907 36.000 0.00 0.00 0.00 3.01
271 272 6.660521 AGATTGGAAATGATGCACTAAAGTCA 59.339 34.615 0.00 0.00 0.00 3.41
272 273 6.839124 TTGGAAATGATGCACTAAAGTCAT 57.161 33.333 0.00 0.00 32.99 3.06
273 274 6.198650 TGGAAATGATGCACTAAAGTCATG 57.801 37.500 0.00 0.00 32.07 3.07
274 275 5.711506 TGGAAATGATGCACTAAAGTCATGT 59.288 36.000 0.00 0.00 32.07 3.21
275 276 6.883756 TGGAAATGATGCACTAAAGTCATGTA 59.116 34.615 0.00 0.00 32.07 2.29
276 277 7.066163 TGGAAATGATGCACTAAAGTCATGTAG 59.934 37.037 0.00 0.00 32.07 2.74
277 278 6.932356 AATGATGCACTAAAGTCATGTAGG 57.068 37.500 0.00 0.00 32.07 3.18
278 279 5.675684 TGATGCACTAAAGTCATGTAGGA 57.324 39.130 0.00 0.00 0.00 2.94
279 280 6.239217 TGATGCACTAAAGTCATGTAGGAT 57.761 37.500 0.00 0.00 0.00 3.24
280 281 6.051074 TGATGCACTAAAGTCATGTAGGATG 58.949 40.000 0.00 0.00 0.00 3.51
281 282 4.769688 TGCACTAAAGTCATGTAGGATGG 58.230 43.478 0.00 0.00 0.00 3.51
282 283 3.561725 GCACTAAAGTCATGTAGGATGGC 59.438 47.826 0.00 0.00 0.00 4.40
283 284 4.130118 CACTAAAGTCATGTAGGATGGCC 58.870 47.826 0.00 0.00 0.00 5.36
284 285 2.332063 AAAGTCATGTAGGATGGCCG 57.668 50.000 0.00 0.00 39.96 6.13
285 286 1.496060 AAGTCATGTAGGATGGCCGA 58.504 50.000 0.00 0.00 39.96 5.54
286 287 1.722034 AGTCATGTAGGATGGCCGAT 58.278 50.000 0.00 0.00 39.96 4.18
287 288 1.345741 AGTCATGTAGGATGGCCGATG 59.654 52.381 0.00 0.00 39.96 3.84
288 289 1.070758 GTCATGTAGGATGGCCGATGT 59.929 52.381 0.00 0.00 39.96 3.06
289 290 1.344438 TCATGTAGGATGGCCGATGTC 59.656 52.381 0.00 0.00 39.96 3.06
290 291 1.345741 CATGTAGGATGGCCGATGTCT 59.654 52.381 0.00 0.00 39.96 3.41
291 292 1.040646 TGTAGGATGGCCGATGTCTC 58.959 55.000 0.00 0.00 39.96 3.36
292 293 1.333177 GTAGGATGGCCGATGTCTCT 58.667 55.000 0.00 0.00 39.96 3.10
293 294 1.271102 GTAGGATGGCCGATGTCTCTC 59.729 57.143 0.00 0.00 39.96 3.20
294 295 1.006805 GGATGGCCGATGTCTCTCG 60.007 63.158 0.00 0.00 38.37 4.04
308 309 7.998141 CGATGTCTCTCGGAAAGATAAATAAC 58.002 38.462 0.00 0.00 35.03 1.89
309 310 7.115095 CGATGTCTCTCGGAAAGATAAATAACC 59.885 40.741 0.00 0.00 35.03 2.85
310 311 7.419711 TGTCTCTCGGAAAGATAAATAACCT 57.580 36.000 0.00 0.00 32.19 3.50
311 312 7.848128 TGTCTCTCGGAAAGATAAATAACCTT 58.152 34.615 0.00 0.00 32.19 3.50
312 313 8.319146 TGTCTCTCGGAAAGATAAATAACCTTT 58.681 33.333 0.00 0.00 32.19 3.11
313 314 8.819015 GTCTCTCGGAAAGATAAATAACCTTTC 58.181 37.037 0.00 0.00 42.85 2.62
314 315 8.759782 TCTCTCGGAAAGATAAATAACCTTTCT 58.240 33.333 0.00 0.00 43.03 2.52
840 865 4.700365 CGAGACGCACACCTCGCA 62.700 66.667 0.00 0.00 44.35 5.10
1698 1724 3.778265 AGAAAGGGCATGTTGTTATGGT 58.222 40.909 0.00 0.00 0.00 3.55
1802 1828 2.649816 AGAAAGCATGGGTTAGGGTTCT 59.350 45.455 0.00 0.00 29.49 3.01
2461 2539 4.503123 CCTCACCTCTGTTTATGTGTCACA 60.503 45.833 8.40 8.40 0.00 3.58
2960 3038 2.236395 CCCTCTCTTTAACATGGGACGT 59.764 50.000 0.00 0.00 36.90 4.34
3697 3779 6.042638 TCTACTTGGGTTGAGAGAGATTTG 57.957 41.667 0.00 0.00 0.00 2.32
4361 4447 4.986054 TGAGGGCACTAAAAACCTTCTA 57.014 40.909 0.00 0.00 32.42 2.10
4469 4555 7.396907 CAGGATGAGATGATTACTCCTAGTGAT 59.603 40.741 0.00 0.00 39.69 3.06
4505 4591 5.780984 ACTCGACCTTTTTCGTTAGAAGAT 58.219 37.500 0.00 0.00 40.07 2.40
4880 4967 9.799106 GGAATCCTATCTCTCCATGAAATTTTA 57.201 33.333 0.00 0.00 0.00 1.52
4991 5078 2.631062 TGACTGTCATAGGAAACGTGGT 59.369 45.455 6.36 0.00 0.00 4.16
5732 5830 4.468510 TGGTTAAGTGGACGAGGATATGTT 59.531 41.667 0.00 0.00 0.00 2.71
6093 6191 4.079446 CACGGTTGCATCTTGGGT 57.921 55.556 0.00 0.00 0.00 4.51
6201 6299 1.971357 ACTGTCGTTGAATGACTCCCT 59.029 47.619 17.45 0.00 35.24 4.20
7305 7414 8.980143 ATAGTAAATGGGAAAACAAAATCGTG 57.020 30.769 0.00 0.00 0.00 4.35
7306 7415 5.694458 AGTAAATGGGAAAACAAAATCGTGC 59.306 36.000 0.00 0.00 0.00 5.34
7307 7416 2.517650 TGGGAAAACAAAATCGTGCC 57.482 45.000 0.00 0.00 0.00 5.01
7308 7417 2.035632 TGGGAAAACAAAATCGTGCCT 58.964 42.857 0.00 0.00 0.00 4.75
7309 7418 2.432510 TGGGAAAACAAAATCGTGCCTT 59.567 40.909 0.00 0.00 0.00 4.35
7310 7419 2.799978 GGGAAAACAAAATCGTGCCTTG 59.200 45.455 0.00 0.00 0.00 3.61
7311 7420 2.220824 GGAAAACAAAATCGTGCCTTGC 59.779 45.455 0.00 0.00 0.00 4.01
7312 7421 2.593346 AAACAAAATCGTGCCTTGCA 57.407 40.000 0.00 0.00 35.60 4.08
7313 7422 2.593346 AACAAAATCGTGCCTTGCAA 57.407 40.000 0.00 0.00 41.47 4.08
7314 7423 2.593346 ACAAAATCGTGCCTTGCAAA 57.407 40.000 0.00 0.00 41.47 3.68
7315 7424 3.110447 ACAAAATCGTGCCTTGCAAAT 57.890 38.095 0.00 0.00 41.47 2.32
7316 7425 3.465871 ACAAAATCGTGCCTTGCAAATT 58.534 36.364 0.00 0.00 41.47 1.82
7317 7426 3.876320 ACAAAATCGTGCCTTGCAAATTT 59.124 34.783 0.00 0.00 41.47 1.82
7318 7427 4.335037 ACAAAATCGTGCCTTGCAAATTTT 59.665 33.333 10.16 10.16 41.95 1.82
7319 7428 5.163673 ACAAAATCGTGCCTTGCAAATTTTT 60.164 32.000 12.38 8.47 40.66 1.94
7320 7429 4.471157 AATCGTGCCTTGCAAATTTTTG 57.529 36.364 0.00 0.00 41.47 2.44
7321 7430 2.898705 TCGTGCCTTGCAAATTTTTGT 58.101 38.095 0.00 0.00 41.47 2.83
7322 7431 3.265791 TCGTGCCTTGCAAATTTTTGTT 58.734 36.364 0.00 0.00 41.47 2.83
7323 7432 3.686726 TCGTGCCTTGCAAATTTTTGTTT 59.313 34.783 0.00 0.00 41.47 2.83
7324 7433 4.154918 TCGTGCCTTGCAAATTTTTGTTTT 59.845 33.333 0.00 0.00 41.47 2.43
7325 7434 4.855937 CGTGCCTTGCAAATTTTTGTTTTT 59.144 33.333 0.00 0.00 41.47 1.94
7351 7460 4.570772 GGCAAAGGAAAAGAAACACCTTTC 59.429 41.667 0.00 0.00 46.59 2.62
7359 7468 1.947456 AGAAACACCTTTCTGTTCCGC 59.053 47.619 0.00 0.00 43.84 5.54
7380 7489 7.255569 TCCGCGTATATGGAGATAAGTATTTG 58.744 38.462 4.92 0.00 0.00 2.32
7390 7499 5.517299 GGAGATAAGTATTTGGATGGCCCAT 60.517 44.000 0.00 0.00 46.10 4.00
7398 7507 7.248237 AGTATTTGGATGGCCCATATGTTATT 58.752 34.615 0.00 0.00 46.10 1.40
7405 7514 3.141083 TGGCCCATATGTTATTTAGCCCA 59.859 43.478 0.00 0.00 38.40 5.36
7460 7580 2.894387 GGCAGCGAGCTGATCCAC 60.894 66.667 27.09 9.79 46.30 4.02
7465 7585 3.069980 GCGAGCTGATCCACCGAGT 62.070 63.158 0.00 0.00 0.00 4.18
7466 7586 1.513158 CGAGCTGATCCACCGAGTT 59.487 57.895 0.00 0.00 0.00 3.01
7470 7590 1.079503 GCTGATCCACCGAGTTTGTC 58.920 55.000 0.00 0.00 0.00 3.18
7520 7640 2.383527 GCGTCAGAGGCGTTTCCAG 61.384 63.158 0.00 0.00 37.29 3.86
7529 7649 4.735132 CGTTTCCAGAGCCGCCGA 62.735 66.667 0.00 0.00 0.00 5.54
7544 7664 1.740296 CCGACCGGTGCGATTTCTT 60.740 57.895 14.63 0.00 0.00 2.52
7546 7666 1.693083 CGACCGGTGCGATTTCTTCC 61.693 60.000 14.63 0.00 0.00 3.46
7547 7667 0.391263 GACCGGTGCGATTTCTTCCT 60.391 55.000 14.63 0.00 0.00 3.36
7549 7669 0.727398 CCGGTGCGATTTCTTCCTTC 59.273 55.000 0.00 0.00 0.00 3.46
7576 7696 9.513906 TTCTGATTTTGGATTTGTCTACATGTA 57.486 29.630 5.25 5.25 0.00 2.29
7585 7705 9.337396 TGGATTTGTCTACATGTATGGATTTAC 57.663 33.333 5.91 0.00 0.00 2.01
7612 7732 7.707624 TTGATTTATCTGGAACTTGCATCTT 57.292 32.000 0.00 0.00 0.00 2.40
7621 7741 5.332743 TGGAACTTGCATCTTCCCTATTTT 58.667 37.500 16.59 0.00 35.91 1.82
7626 7746 5.047092 ACTTGCATCTTCCCTATTTTTGTGG 60.047 40.000 0.00 0.00 0.00 4.17
7642 7762 1.923395 TGGCGATTTCCACCCCTCT 60.923 57.895 0.00 0.00 0.00 3.69
7679 7799 6.425210 AGGCATTATAGATCTTGTGCTGTA 57.575 37.500 0.00 0.00 33.38 2.74
7682 7802 7.605691 AGGCATTATAGATCTTGTGCTGTAATC 59.394 37.037 0.00 0.00 29.54 1.75
7732 7853 4.260497 GGAAGTAAATCGCCGTGGTTATTC 60.260 45.833 0.00 0.00 0.00 1.75
7765 7886 7.815549 TGTCATTGTTTTGATTGAAGATCCATG 59.184 33.333 0.00 0.00 0.00 3.66
7770 7891 8.991243 TGTTTTGATTGAAGATCCATGATTTC 57.009 30.769 0.00 0.00 0.00 2.17
7792 7913 4.011517 GTTCCTGCGACGGGGGAA 62.012 66.667 0.00 0.00 36.86 3.97
7832 7953 2.094286 CGATCCTGTGGATATCAGCTCC 60.094 54.545 4.83 0.00 43.27 4.70
7849 7970 0.684535 TCCGATGGAAGCACTGACAA 59.315 50.000 0.00 0.00 0.00 3.18
7850 7971 0.798776 CCGATGGAAGCACTGACAAC 59.201 55.000 0.00 0.00 0.00 3.32
7856 7977 0.871057 GAAGCACTGACAACAGCTCC 59.129 55.000 0.00 0.00 46.95 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 4.840005 GGTGGCTGGCGTAGGAGC 62.840 72.222 0.00 0.00 34.23 4.70
15 16 3.376935 CTGGTGGCTGGCGTAGGAG 62.377 68.421 0.00 0.00 0.00 3.69
16 17 3.390521 CTGGTGGCTGGCGTAGGA 61.391 66.667 0.00 0.00 0.00 2.94
17 18 3.706373 ACTGGTGGCTGGCGTAGG 61.706 66.667 0.00 0.00 0.00 3.18
18 19 2.434884 CACTGGTGGCTGGCGTAG 60.435 66.667 0.00 0.00 0.00 3.51
19 20 4.015406 CCACTGGTGGCTGGCGTA 62.015 66.667 6.84 0.00 44.73 4.42
30 31 3.774528 TAGCTCTGCGCCCACTGG 61.775 66.667 4.18 0.00 40.39 4.00
31 32 2.510238 GTAGCTCTGCGCCCACTG 60.510 66.667 4.18 0.00 40.39 3.66
32 33 2.997315 TGTAGCTCTGCGCCCACT 60.997 61.111 4.18 0.00 40.39 4.00
33 34 2.510238 CTGTAGCTCTGCGCCCAC 60.510 66.667 4.18 0.00 40.39 4.61
34 35 3.774528 CCTGTAGCTCTGCGCCCA 61.775 66.667 4.18 0.00 40.39 5.36
39 40 4.803426 ACGCGCCTGTAGCTCTGC 62.803 66.667 5.73 0.00 40.39 4.26
40 41 2.580867 GACGCGCCTGTAGCTCTG 60.581 66.667 5.73 0.00 40.39 3.35
41 42 3.827898 GGACGCGCCTGTAGCTCT 61.828 66.667 5.73 0.00 40.39 4.09
44 45 4.183686 TACGGACGCGCCTGTAGC 62.184 66.667 10.25 0.00 38.52 3.58
45 46 2.277756 GTACGGACGCGCCTGTAG 60.278 66.667 14.75 2.88 0.00 2.74
46 47 4.164664 CGTACGGACGCGCCTGTA 62.165 66.667 7.51 10.25 43.21 2.74
72 73 3.823330 GATGCAGCTGGCTGTGGC 61.823 66.667 21.34 9.86 45.24 5.01
73 74 1.753078 ATGATGCAGCTGGCTGTGG 60.753 57.895 21.34 0.00 45.24 4.17
74 75 1.433471 CATGATGCAGCTGGCTGTG 59.567 57.895 21.34 9.48 45.24 3.66
75 76 2.415608 GCATGATGCAGCTGGCTGT 61.416 57.895 21.34 5.06 44.26 4.40
76 77 2.413351 GCATGATGCAGCTGGCTG 59.587 61.111 17.12 17.16 44.26 4.85
85 86 2.290464 AGAAGAAGCTCTGCATGATGC 58.710 47.619 11.12 11.12 45.29 3.91
86 87 4.193090 AGAAGAAGAAGCTCTGCATGATG 58.807 43.478 0.00 0.00 0.00 3.07
87 88 4.490899 AGAAGAAGAAGCTCTGCATGAT 57.509 40.909 0.00 0.00 0.00 2.45
88 89 3.977134 AGAAGAAGAAGCTCTGCATGA 57.023 42.857 0.00 0.00 0.00 3.07
89 90 6.238429 GGATAAAGAAGAAGAAGCTCTGCATG 60.238 42.308 0.00 0.00 0.00 4.06
90 91 5.821995 GGATAAAGAAGAAGAAGCTCTGCAT 59.178 40.000 0.00 0.00 0.00 3.96
91 92 5.046014 AGGATAAAGAAGAAGAAGCTCTGCA 60.046 40.000 0.00 0.00 0.00 4.41
92 93 5.427378 AGGATAAAGAAGAAGAAGCTCTGC 58.573 41.667 0.00 0.00 0.00 4.26
93 94 7.330262 AGAAGGATAAAGAAGAAGAAGCTCTG 58.670 38.462 0.00 0.00 0.00 3.35
94 95 7.494922 AGAAGGATAAAGAAGAAGAAGCTCT 57.505 36.000 0.00 0.00 0.00 4.09
95 96 9.476202 GATAGAAGGATAAAGAAGAAGAAGCTC 57.524 37.037 0.00 0.00 0.00 4.09
110 111 8.047911 CGGGTCATCTAGTTAGATAGAAGGATA 58.952 40.741 1.52 0.00 40.91 2.59
117 118 5.462405 GCAACGGGTCATCTAGTTAGATAG 58.538 45.833 1.52 0.00 40.91 2.08
118 119 4.023450 CGCAACGGGTCATCTAGTTAGATA 60.023 45.833 1.52 0.00 40.91 1.98
121 122 2.460918 CGCAACGGGTCATCTAGTTAG 58.539 52.381 0.00 0.00 0.00 2.34
162 163 6.757010 CACACTCTTATAACGATTGGCTTACT 59.243 38.462 0.00 0.00 0.00 2.24
170 171 8.487313 TGTTAATGCACACTCTTATAACGATT 57.513 30.769 0.00 0.00 0.00 3.34
171 172 8.662781 ATGTTAATGCACACTCTTATAACGAT 57.337 30.769 0.00 0.00 0.00 3.73
172 173 9.758651 ATATGTTAATGCACACTCTTATAACGA 57.241 29.630 0.00 0.00 0.00 3.85
178 179 9.394767 ACATCAATATGTTAATGCACACTCTTA 57.605 29.630 0.00 0.00 44.07 2.10
179 180 8.284945 ACATCAATATGTTAATGCACACTCTT 57.715 30.769 0.00 0.00 44.07 2.85
180 181 7.870509 ACATCAATATGTTAATGCACACTCT 57.129 32.000 0.00 0.00 44.07 3.24
194 195 9.591404 GAGCTATTCTTTTCGAACATCAATATG 57.409 33.333 0.00 0.00 39.17 1.78
195 196 9.330063 TGAGCTATTCTTTTCGAACATCAATAT 57.670 29.630 0.00 0.00 33.72 1.28
196 197 8.716646 TGAGCTATTCTTTTCGAACATCAATA 57.283 30.769 0.00 0.00 33.72 1.90
197 198 7.615582 TGAGCTATTCTTTTCGAACATCAAT 57.384 32.000 0.00 0.00 33.72 2.57
198 199 7.615582 ATGAGCTATTCTTTTCGAACATCAA 57.384 32.000 0.00 0.00 33.72 2.57
199 200 8.893219 ATATGAGCTATTCTTTTCGAACATCA 57.107 30.769 0.00 0.00 33.72 3.07
201 202 9.988815 AGTATATGAGCTATTCTTTTCGAACAT 57.011 29.630 0.00 0.00 33.72 2.71
235 236 9.884465 GCATCATTTCCAATCTTATGTACTTAC 57.116 33.333 0.00 0.00 0.00 2.34
236 237 9.625747 TGCATCATTTCCAATCTTATGTACTTA 57.374 29.630 0.00 0.00 0.00 2.24
237 238 8.408601 GTGCATCATTTCCAATCTTATGTACTT 58.591 33.333 0.00 0.00 0.00 2.24
238 239 7.776969 AGTGCATCATTTCCAATCTTATGTACT 59.223 33.333 0.00 0.00 35.09 2.73
239 240 7.934457 AGTGCATCATTTCCAATCTTATGTAC 58.066 34.615 0.00 0.00 0.00 2.90
240 241 9.625747 TTAGTGCATCATTTCCAATCTTATGTA 57.374 29.630 0.00 0.00 0.00 2.29
241 242 8.523915 TTAGTGCATCATTTCCAATCTTATGT 57.476 30.769 0.00 0.00 0.00 2.29
242 243 9.459640 CTTTAGTGCATCATTTCCAATCTTATG 57.540 33.333 0.00 0.00 0.00 1.90
243 244 9.193806 ACTTTAGTGCATCATTTCCAATCTTAT 57.806 29.630 0.00 0.00 0.00 1.73
244 245 8.579850 ACTTTAGTGCATCATTTCCAATCTTA 57.420 30.769 0.00 0.00 0.00 2.10
245 246 7.177216 TGACTTTAGTGCATCATTTCCAATCTT 59.823 33.333 0.00 0.00 0.00 2.40
246 247 6.660521 TGACTTTAGTGCATCATTTCCAATCT 59.339 34.615 0.00 0.00 0.00 2.40
247 248 6.855836 TGACTTTAGTGCATCATTTCCAATC 58.144 36.000 0.00 0.00 0.00 2.67
248 249 6.839124 TGACTTTAGTGCATCATTTCCAAT 57.161 33.333 0.00 0.00 0.00 3.16
249 250 6.209192 ACATGACTTTAGTGCATCATTTCCAA 59.791 34.615 0.00 0.00 29.25 3.53
250 251 5.711506 ACATGACTTTAGTGCATCATTTCCA 59.288 36.000 0.00 0.00 29.25 3.53
251 252 6.199937 ACATGACTTTAGTGCATCATTTCC 57.800 37.500 0.00 0.00 29.25 3.13
252 253 7.280876 TCCTACATGACTTTAGTGCATCATTTC 59.719 37.037 0.00 0.00 29.25 2.17
253 254 7.112122 TCCTACATGACTTTAGTGCATCATTT 58.888 34.615 0.00 0.00 29.25 2.32
254 255 6.653020 TCCTACATGACTTTAGTGCATCATT 58.347 36.000 0.00 0.00 29.25 2.57
255 256 6.239217 TCCTACATGACTTTAGTGCATCAT 57.761 37.500 0.00 0.00 31.93 2.45
256 257 5.675684 TCCTACATGACTTTAGTGCATCA 57.324 39.130 0.00 0.00 0.00 3.07
257 258 5.468072 CCATCCTACATGACTTTAGTGCATC 59.532 44.000 0.00 0.00 0.00 3.91
258 259 5.371526 CCATCCTACATGACTTTAGTGCAT 58.628 41.667 0.00 0.00 0.00 3.96
259 260 4.769688 CCATCCTACATGACTTTAGTGCA 58.230 43.478 0.00 0.00 0.00 4.57
260 261 3.561725 GCCATCCTACATGACTTTAGTGC 59.438 47.826 0.00 0.00 0.00 4.40
261 262 4.130118 GGCCATCCTACATGACTTTAGTG 58.870 47.826 0.00 0.00 0.00 2.74
262 263 3.181465 CGGCCATCCTACATGACTTTAGT 60.181 47.826 2.24 0.00 0.00 2.24
263 264 3.069586 TCGGCCATCCTACATGACTTTAG 59.930 47.826 2.24 0.00 0.00 1.85
264 265 3.035363 TCGGCCATCCTACATGACTTTA 58.965 45.455 2.24 0.00 0.00 1.85
265 266 1.837439 TCGGCCATCCTACATGACTTT 59.163 47.619 2.24 0.00 0.00 2.66
266 267 1.496060 TCGGCCATCCTACATGACTT 58.504 50.000 2.24 0.00 0.00 3.01
267 268 1.345741 CATCGGCCATCCTACATGACT 59.654 52.381 2.24 0.00 0.00 3.41
268 269 1.070758 ACATCGGCCATCCTACATGAC 59.929 52.381 2.24 0.00 0.00 3.06
269 270 1.344438 GACATCGGCCATCCTACATGA 59.656 52.381 2.24 0.00 0.00 3.07
270 271 1.345741 AGACATCGGCCATCCTACATG 59.654 52.381 2.24 0.00 0.00 3.21
271 272 1.620819 GAGACATCGGCCATCCTACAT 59.379 52.381 2.24 0.00 0.00 2.29
272 273 1.040646 GAGACATCGGCCATCCTACA 58.959 55.000 2.24 0.00 0.00 2.74
273 274 1.271102 GAGAGACATCGGCCATCCTAC 59.729 57.143 2.24 0.00 0.00 3.18
274 275 1.621992 GAGAGACATCGGCCATCCTA 58.378 55.000 2.24 0.00 0.00 2.94
275 276 1.459455 CGAGAGACATCGGCCATCCT 61.459 60.000 2.24 0.00 39.04 3.24
276 277 1.006805 CGAGAGACATCGGCCATCC 60.007 63.158 2.24 0.00 39.04 3.51
277 278 4.643733 CGAGAGACATCGGCCATC 57.356 61.111 2.24 0.00 39.04 3.51
283 284 7.115095 GGTTATTTATCTTTCCGAGAGACATCG 59.885 40.741 0.00 0.00 42.36 3.84
284 285 8.145122 AGGTTATTTATCTTTCCGAGAGACATC 58.855 37.037 0.00 0.00 37.93 3.06
285 286 8.024145 AGGTTATTTATCTTTCCGAGAGACAT 57.976 34.615 0.00 0.00 37.93 3.06
286 287 7.419711 AGGTTATTTATCTTTCCGAGAGACA 57.580 36.000 0.00 0.00 37.93 3.41
287 288 8.719560 AAAGGTTATTTATCTTTCCGAGAGAC 57.280 34.615 0.00 0.00 37.93 3.36
288 289 8.759782 AGAAAGGTTATTTATCTTTCCGAGAGA 58.240 33.333 5.10 0.00 44.23 3.10
289 290 8.950208 AGAAAGGTTATTTATCTTTCCGAGAG 57.050 34.615 5.10 0.00 44.23 3.20
368 369 8.786898 CATGGAACTTGAATTTCTCTTACAGAA 58.213 33.333 0.00 0.00 39.56 3.02
369 370 8.156820 TCATGGAACTTGAATTTCTCTTACAGA 58.843 33.333 0.00 0.00 0.00 3.41
370 371 8.327941 TCATGGAACTTGAATTTCTCTTACAG 57.672 34.615 0.00 0.00 0.00 2.74
371 372 8.733458 CATCATGGAACTTGAATTTCTCTTACA 58.267 33.333 0.00 0.00 0.00 2.41
372 373 8.186821 CCATCATGGAACTTGAATTTCTCTTAC 58.813 37.037 0.00 0.00 40.96 2.34
373 374 7.148018 GCCATCATGGAACTTGAATTTCTCTTA 60.148 37.037 8.30 0.00 40.96 2.10
374 375 6.350780 GCCATCATGGAACTTGAATTTCTCTT 60.351 38.462 8.30 0.00 40.96 2.85
375 376 5.126707 GCCATCATGGAACTTGAATTTCTCT 59.873 40.000 8.30 0.00 40.96 3.10
376 377 5.346522 GCCATCATGGAACTTGAATTTCTC 58.653 41.667 8.30 0.00 40.96 2.87
377 378 4.142315 CGCCATCATGGAACTTGAATTTCT 60.142 41.667 8.30 0.00 40.96 2.52
378 379 4.107622 CGCCATCATGGAACTTGAATTTC 58.892 43.478 8.30 0.00 40.96 2.17
379 380 3.763360 TCGCCATCATGGAACTTGAATTT 59.237 39.130 8.30 0.00 40.96 1.82
380 381 3.355378 TCGCCATCATGGAACTTGAATT 58.645 40.909 8.30 0.00 40.96 2.17
381 382 2.947652 CTCGCCATCATGGAACTTGAAT 59.052 45.455 8.30 0.00 40.96 2.57
382 383 2.290260 ACTCGCCATCATGGAACTTGAA 60.290 45.455 8.30 0.00 40.96 2.69
386 387 1.278985 TCAACTCGCCATCATGGAACT 59.721 47.619 8.30 0.00 40.96 3.01
450 451 0.104855 GCGCATCCACTATGACTCCA 59.895 55.000 0.30 0.00 37.86 3.86
840 865 3.390639 CCCATAGATGCTTGAAGAGAGGT 59.609 47.826 0.00 0.00 0.00 3.85
1210 1235 2.357517 CTTGTCCTTGGTCGCGCT 60.358 61.111 5.56 0.00 0.00 5.92
1224 1249 4.697756 TTGGAGCCCGCCGTCTTG 62.698 66.667 0.00 0.00 0.00 3.02
1698 1724 1.346395 TCCTTCAGAGGCAAGCGTTTA 59.654 47.619 0.00 0.00 43.21 2.01
1802 1828 6.319658 GCATCTTTTCTCTATGGGAATGTTGA 59.680 38.462 0.00 0.00 0.00 3.18
2461 2539 7.902920 AAGCATTCCCATAAGTATTCACATT 57.097 32.000 0.00 0.00 0.00 2.71
2960 3038 8.089625 TGGTTCTTCAATATCTCCACTATCAA 57.910 34.615 0.00 0.00 0.00 2.57
3356 3434 0.252239 GCCACCAGATTTCCCCCTTT 60.252 55.000 0.00 0.00 0.00 3.11
3697 3779 3.332034 GTGTAACACCCACCAGTCATAC 58.668 50.000 0.00 0.00 36.32 2.39
4034 4120 3.225940 CAAATTAGATCCCCAGCCCTTC 58.774 50.000 0.00 0.00 0.00 3.46
4464 4550 7.070074 AGGTCGAGTTAATTCCTCATTATCACT 59.930 37.037 0.00 0.00 0.00 3.41
4469 4555 8.857694 AAAAAGGTCGAGTTAATTCCTCATTA 57.142 30.769 0.00 0.00 0.00 1.90
4505 4591 8.109705 TCATGCTAAACAAAGCTTTCTTGATA 57.890 30.769 9.23 0.00 43.19 2.15
4880 4967 6.769822 CCTGCCTTCTGAAATGAGTATAATGT 59.230 38.462 0.00 0.00 0.00 2.71
4991 5078 5.536916 CCACCCACACCACTTAGAATTAAAA 59.463 40.000 0.00 0.00 0.00 1.52
5732 5830 1.919654 TCCCCCAATCCTTTTCGATCA 59.080 47.619 0.00 0.00 0.00 2.92
5844 5942 7.067615 TGTTCCTGAAGTATCTAGCTCTTACAG 59.932 40.741 0.00 0.00 0.00 2.74
5993 6091 0.687354 GCCCACGGATCATACCAGAT 59.313 55.000 0.00 0.00 0.00 2.90
6093 6191 3.369471 GCCCAGCTCATAGTTGTTAGTCA 60.369 47.826 0.00 0.00 0.00 3.41
7279 7388 9.418045 CACGATTTTGTTTTCCCATTTACTATT 57.582 29.630 0.00 0.00 0.00 1.73
7280 7389 7.544217 GCACGATTTTGTTTTCCCATTTACTAT 59.456 33.333 0.00 0.00 0.00 2.12
7281 7390 6.864165 GCACGATTTTGTTTTCCCATTTACTA 59.136 34.615 0.00 0.00 0.00 1.82
7282 7391 5.694458 GCACGATTTTGTTTTCCCATTTACT 59.306 36.000 0.00 0.00 0.00 2.24
7283 7392 5.107259 GGCACGATTTTGTTTTCCCATTTAC 60.107 40.000 0.00 0.00 0.00 2.01
7284 7393 4.991687 GGCACGATTTTGTTTTCCCATTTA 59.008 37.500 0.00 0.00 0.00 1.40
7285 7394 3.812609 GGCACGATTTTGTTTTCCCATTT 59.187 39.130 0.00 0.00 0.00 2.32
7286 7395 3.070878 AGGCACGATTTTGTTTTCCCATT 59.929 39.130 0.00 0.00 0.00 3.16
7287 7396 2.632512 AGGCACGATTTTGTTTTCCCAT 59.367 40.909 0.00 0.00 0.00 4.00
7288 7397 2.035632 AGGCACGATTTTGTTTTCCCA 58.964 42.857 0.00 0.00 0.00 4.37
7289 7398 2.799978 CAAGGCACGATTTTGTTTTCCC 59.200 45.455 0.00 0.00 0.00 3.97
7290 7399 2.220824 GCAAGGCACGATTTTGTTTTCC 59.779 45.455 0.00 0.00 0.00 3.13
7291 7400 2.863137 TGCAAGGCACGATTTTGTTTTC 59.137 40.909 0.00 0.00 31.71 2.29
7292 7401 2.898705 TGCAAGGCACGATTTTGTTTT 58.101 38.095 0.00 0.00 31.71 2.43
7293 7402 2.593346 TGCAAGGCACGATTTTGTTT 57.407 40.000 0.00 0.00 31.71 2.83
7294 7403 2.593346 TTGCAAGGCACGATTTTGTT 57.407 40.000 0.00 0.00 38.71 2.83
7295 7404 2.593346 TTTGCAAGGCACGATTTTGT 57.407 40.000 0.00 0.00 38.71 2.83
7296 7405 4.471157 AAATTTGCAAGGCACGATTTTG 57.529 36.364 0.00 0.00 38.71 2.44
7297 7406 5.163673 ACAAAAATTTGCAAGGCACGATTTT 60.164 32.000 10.16 10.16 41.67 1.82
7298 7407 4.335037 ACAAAAATTTGCAAGGCACGATTT 59.665 33.333 0.00 0.00 41.79 2.17
7299 7408 3.876320 ACAAAAATTTGCAAGGCACGATT 59.124 34.783 0.00 0.00 41.79 3.34
7300 7409 3.465871 ACAAAAATTTGCAAGGCACGAT 58.534 36.364 0.00 0.00 41.79 3.73
7301 7410 2.898705 ACAAAAATTTGCAAGGCACGA 58.101 38.095 0.00 0.00 41.79 4.35
7302 7411 3.672028 AACAAAAATTTGCAAGGCACG 57.328 38.095 0.00 0.00 41.79 5.34
7322 7431 6.596106 GGTGTTTCTTTTCCTTTGCCTAAAAA 59.404 34.615 0.00 0.00 0.00 1.94
7323 7432 6.070481 AGGTGTTTCTTTTCCTTTGCCTAAAA 60.070 34.615 0.00 0.00 0.00 1.52
7324 7433 5.423931 AGGTGTTTCTTTTCCTTTGCCTAAA 59.576 36.000 0.00 0.00 0.00 1.85
7325 7434 4.959839 AGGTGTTTCTTTTCCTTTGCCTAA 59.040 37.500 0.00 0.00 0.00 2.69
7326 7435 4.542697 AGGTGTTTCTTTTCCTTTGCCTA 58.457 39.130 0.00 0.00 0.00 3.93
7327 7436 3.374764 AGGTGTTTCTTTTCCTTTGCCT 58.625 40.909 0.00 0.00 0.00 4.75
7328 7437 3.819564 AGGTGTTTCTTTTCCTTTGCC 57.180 42.857 0.00 0.00 0.00 4.52
7329 7438 5.718649 GAAAGGTGTTTCTTTTCCTTTGC 57.281 39.130 11.87 2.39 46.16 3.68
7351 7460 3.577649 ATCTCCATATACGCGGAACAG 57.422 47.619 12.47 0.00 0.00 3.16
7357 7466 7.255569 TCCAAATACTTATCTCCATATACGCG 58.744 38.462 3.53 3.53 0.00 6.01
7359 7468 9.534565 CCATCCAAATACTTATCTCCATATACG 57.465 37.037 0.00 0.00 0.00 3.06
7380 7489 4.402474 GGCTAAATAACATATGGGCCATCC 59.598 45.833 25.07 9.57 38.35 3.51
7390 7499 3.746114 CGTGGGCTGGGCTAAATAACATA 60.746 47.826 0.00 0.00 0.00 2.29
7398 7507 0.468226 CTATTCGTGGGCTGGGCTAA 59.532 55.000 0.00 0.00 0.00 3.09
7426 7546 0.871057 GCCGCTTCATATTCAGCTCC 59.129 55.000 0.00 0.00 33.52 4.70
7452 7572 2.751166 AGACAAACTCGGTGGATCAG 57.249 50.000 0.00 0.00 0.00 2.90
7453 7573 3.132289 GGATAGACAAACTCGGTGGATCA 59.868 47.826 0.00 0.00 0.00 2.92
7460 7580 3.197983 AGAAAGGGGATAGACAAACTCGG 59.802 47.826 0.00 0.00 0.00 4.63
7465 7585 4.081087 CGAGGAAGAAAGGGGATAGACAAA 60.081 45.833 0.00 0.00 0.00 2.83
7466 7586 3.451178 CGAGGAAGAAAGGGGATAGACAA 59.549 47.826 0.00 0.00 0.00 3.18
7470 7590 3.301274 AGACGAGGAAGAAAGGGGATAG 58.699 50.000 0.00 0.00 0.00 2.08
7529 7649 0.036306 AAGGAAGAAATCGCACCGGT 59.964 50.000 0.00 0.00 0.00 5.28
7544 7664 7.006509 AGACAAATCCAAAATCAGAAGAAGGA 58.993 34.615 0.00 0.00 0.00 3.36
7546 7666 8.786898 TGTAGACAAATCCAAAATCAGAAGAAG 58.213 33.333 0.00 0.00 0.00 2.85
7547 7667 8.690203 TGTAGACAAATCCAAAATCAGAAGAA 57.310 30.769 0.00 0.00 0.00 2.52
7549 7669 8.517878 ACATGTAGACAAATCCAAAATCAGAAG 58.482 33.333 0.00 0.00 0.00 2.85
7576 7696 9.713684 TTCCAGATAAATCAAAGGTAAATCCAT 57.286 29.630 0.00 0.00 39.02 3.41
7585 7705 6.271488 TGCAAGTTCCAGATAAATCAAAGG 57.729 37.500 0.00 0.00 0.00 3.11
7612 7732 3.445805 GGAAATCGCCACAAAAATAGGGA 59.554 43.478 0.00 0.00 0.00 4.20
7626 7746 0.322546 ACAAGAGGGGTGGAAATCGC 60.323 55.000 0.00 0.00 0.00 4.58
7701 7822 2.105993 GGCGATTTACTTCCCTATGGGT 59.894 50.000 2.25 0.00 44.74 4.51
7739 7860 7.287512 TGGATCTTCAATCAAAACAATGACA 57.712 32.000 0.00 0.00 30.82 3.58
7741 7862 8.124808 TCATGGATCTTCAATCAAAACAATGA 57.875 30.769 0.00 0.00 0.00 2.57
7765 7886 1.925185 GTCGCAGGAACCTACGAAATC 59.075 52.381 16.24 2.96 42.50 2.17
7770 7891 2.202570 CCGTCGCAGGAACCTACG 60.203 66.667 7.11 7.11 34.41 3.51
7792 7913 1.123928 GGTTCGAGATCCCCTCATGT 58.876 55.000 0.00 0.00 42.06 3.21
7832 7953 1.462283 CTGTTGTCAGTGCTTCCATCG 59.538 52.381 0.00 0.00 36.97 3.84


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

AutoCloner maintained by Alex Coulton.