Multiple sequence alignment - TraesCS7D01G092300

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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 TraesCS7D01G092300 chr7D 100.000 5833 0 0 1 5833 55249102 55254934 0.000000e+00 10772
1 TraesCS7D01G092300 chr7D 96.910 4078 107 15 1335 5403 55267518 55271585 0.000000e+00 6815
2 TraesCS7D01G092300 chr7D 80.983 1383 131 69 348 1647 55386749 55388082 0.000000e+00 976
3 TraesCS7D01G092300 chr7D 81.113 1186 189 22 3589 4765 55390864 55392023 0.000000e+00 917
4 TraesCS7D01G092300 chr7D 80.018 1131 184 24 3592 4718 55378119 55379211 0.000000e+00 798
5 TraesCS7D01G092300 chr7D 82.545 888 120 22 1690 2558 55388234 55389105 0.000000e+00 749
6 TraesCS7D01G092300 chr7D 99.020 408 4 0 5426 5833 55272040 55272447 0.000000e+00 732
7 TraesCS7D01G092300 chr7D 81.922 874 117 27 1659 2517 55375200 55376047 0.000000e+00 701
8 TraesCS7D01G092300 chr7D 82.713 752 70 31 343 1053 55373791 55374523 1.070000e-171 614
9 TraesCS7D01G092300 chr7D 83.080 591 55 29 1067 1648 55374571 55375125 4.060000e-136 496
10 TraesCS7D01G092300 chr7D 91.331 323 11 4 340 652 55266488 55266803 5.400000e-115 425
11 TraesCS7D01G092300 chr7D 88.579 359 15 6 715 1051 55266808 55267162 4.210000e-111 412
12 TraesCS7D01G092300 chr7D 83.824 272 25 10 1067 1338 55267209 55267461 2.100000e-59 241
13 TraesCS7D01G092300 chr7D 89.840 187 17 2 152 338 20408633 20408817 7.550000e-59 239
14 TraesCS7D01G092300 chr7D 90.556 180 16 1 155 334 576857481 576857659 2.720000e-58 237
15 TraesCS7D01G092300 chr7D 75.632 435 66 29 5403 5826 5757212 5757617 4.640000e-41 180
16 TraesCS7D01G092300 chr7D 87.097 155 16 4 1 154 55266343 55266494 7.770000e-39 172
17 TraesCS7D01G092300 chr7D 80.851 188 30 5 5403 5589 213798845 213798663 6.090000e-30 143
18 TraesCS7D01G092300 chr7A 91.098 2797 159 47 714 3453 59201457 59204220 0.000000e+00 3703
19 TraesCS7D01G092300 chr7A 86.864 1553 165 22 3589 5131 59232090 59233613 0.000000e+00 1701
20 TraesCS7D01G092300 chr7A 92.600 973 70 1 3443 4415 59204262 59205232 0.000000e+00 1397
21 TraesCS7D01G092300 chr7A 80.258 1398 129 75 348 1649 59348424 59349770 0.000000e+00 917
22 TraesCS7D01G092300 chr7A 81.006 1153 193 17 3617 4754 59352531 59353672 0.000000e+00 893
23 TraesCS7D01G092300 chr7A 91.806 537 41 1 4864 5400 59216753 59217286 0.000000e+00 745
24 TraesCS7D01G092300 chr7A 82.633 881 115 26 1659 2528 59288314 59289167 0.000000e+00 745
25 TraesCS7D01G092300 chr7A 81.943 875 125 20 1690 2558 59349891 59350738 0.000000e+00 710
26 TraesCS7D01G092300 chr7A 94.575 424 22 1 5403 5826 59217322 59217744 0.000000e+00 654
27 TraesCS7D01G092300 chr7A 89.655 464 42 2 4413 4870 59205493 59205956 2.340000e-163 586
28 TraesCS7D01G092300 chr7A 90.376 426 37 4 5402 5826 59233613 59234035 1.840000e-154 556
29 TraesCS7D01G092300 chr7A 82.456 684 64 26 343 993 59228018 59228678 1.110000e-151 547
30 TraesCS7D01G092300 chr7A 80.857 700 108 15 1831 2523 59229629 59230309 1.440000e-145 527
31 TraesCS7D01G092300 chr7A 80.289 761 74 30 339 1041 59286878 59287620 6.750000e-139 505
32 TraesCS7D01G092300 chr7A 82.373 590 59 29 1069 1649 59287687 59288240 6.840000e-129 472
33 TraesCS7D01G092300 chr7A 92.357 314 16 3 339 652 59201148 59201453 1.930000e-119 440
34 TraesCS7D01G092300 chr7A 86.207 348 23 16 1309 1649 59229055 59229384 2.590000e-93 353
35 TraesCS7D01G092300 chr7A 94.231 156 6 2 1 154 59201001 59201155 9.770000e-58 235
36 TraesCS7D01G092300 chr7A 93.548 155 8 1 1067 1221 59228776 59228928 4.550000e-56 230
37 TraesCS7D01G092300 chr7A 91.803 122 10 0 2673 2794 59230398 59230519 2.790000e-38 171
38 TraesCS7D01G092300 chr4A 90.170 1882 169 10 3508 5387 671526060 671527927 0.000000e+00 2436
39 TraesCS7D01G092300 chr4A 90.858 711 65 0 1813 2523 671524505 671525215 0.000000e+00 953
40 TraesCS7D01G092300 chr4A 81.049 1182 194 16 3630 4804 671601340 671602498 0.000000e+00 915
41 TraesCS7D01G092300 chr4A 80.876 1187 193 22 3622 4798 671642693 671643855 0.000000e+00 904
42 TraesCS7D01G092300 chr4A 83.743 855 112 18 1678 2518 671639834 671640675 0.000000e+00 784
43 TraesCS7D01G092300 chr4A 79.477 1223 148 59 470 1649 671596409 671597571 0.000000e+00 773
44 TraesCS7D01G092300 chr4A 88.822 501 38 13 1320 1814 671523555 671524043 3.010000e-167 599
45 TraesCS7D01G092300 chr4A 83.598 567 72 14 1678 2227 671597726 671598288 4.030000e-141 512
46 TraesCS7D01G092300 chr4A 95.082 305 13 2 5522 5826 671528225 671528527 4.090000e-131 479
47 TraesCS7D01G092300 chr4A 90.149 335 27 2 2520 2854 671525470 671525798 1.160000e-116 431
48 TraesCS7D01G092300 chr4A 78.029 842 67 61 741 1512 671638828 671639621 6.990000e-114 422
49 TraesCS7D01G092300 chr4A 87.397 365 18 6 715 1051 671522852 671523216 1.520000e-105 394
50 TraesCS7D01G092300 chr4A 90.444 293 16 4 366 652 671522561 671522847 5.520000e-100 375
51 TraesCS7D01G092300 chr4A 85.886 333 42 3 349 679 671638467 671638796 3.340000e-92 350
52 TraesCS7D01G092300 chr4A 91.824 159 13 0 1068 1226 671523264 671523422 7.610000e-54 222
53 TraesCS7D01G092300 chr4A 76.905 433 67 24 5403 5826 618181694 618181286 1.270000e-51 215
54 TraesCS7D01G092300 chr4A 75.806 434 70 24 5403 5826 734899433 734899025 2.780000e-43 187
55 TraesCS7D01G092300 chr4A 88.889 144 14 2 1 144 671522101 671522242 6.010000e-40 176
56 TraesCS7D01G092300 chr4A 78.929 280 39 11 2264 2538 671598292 671598556 7.770000e-39 172
57 TraesCS7D01G092300 chr4A 98.305 59 1 0 1591 1649 671639648 671639706 2.880000e-18 104
58 TraesCS7D01G092300 chr6B 78.014 423 76 16 5403 5818 413928688 413929100 3.490000e-62 250
59 TraesCS7D01G092300 chr6B 87.755 196 20 4 140 334 101742757 101742949 5.880000e-55 226
60 TraesCS7D01G092300 chr3D 90.761 184 15 2 155 338 2074322 2074503 1.620000e-60 244
61 TraesCS7D01G092300 chr2B 91.209 182 13 3 147 327 782126779 782126600 1.620000e-60 244
62 TraesCS7D01G092300 chr3A 91.525 177 13 2 158 334 679364330 679364156 5.840000e-60 243
63 TraesCS7D01G092300 chr7B 90.960 177 14 2 158 334 710310874 710310700 2.720000e-58 237
64 TraesCS7D01G092300 chr7B 79.255 188 32 7 5403 5589 187760115 187760296 2.210000e-24 124
65 TraesCS7D01G092300 chr5B 90.556 180 16 1 155 334 52792991 52792813 2.720000e-58 237
66 TraesCS7D01G092300 chr3B 91.011 178 13 3 151 327 765591565 765591740 2.720000e-58 237


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 TraesCS7D01G092300 chr7D 55249102 55254934 5832 False 10772.000000 10772 100.000000 1 5833 1 chr7D.!!$F3 5832
1 TraesCS7D01G092300 chr7D 55266343 55272447 6104 False 1466.166667 6815 91.126833 1 5833 6 chr7D.!!$F5 5832
2 TraesCS7D01G092300 chr7D 55386749 55392023 5274 False 880.666667 976 81.547000 348 4765 3 chr7D.!!$F7 4417
3 TraesCS7D01G092300 chr7D 55373791 55379211 5420 False 652.250000 798 81.933250 343 4718 4 chr7D.!!$F6 4375
4 TraesCS7D01G092300 chr7A 59201001 59205956 4955 False 1272.200000 3703 91.988200 1 4870 5 chr7A.!!$F1 4869
5 TraesCS7D01G092300 chr7A 59348424 59353672 5248 False 840.000000 917 81.069000 348 4754 3 chr7A.!!$F5 4406
6 TraesCS7D01G092300 chr7A 59216753 59217744 991 False 699.500000 745 93.190500 4864 5826 2 chr7A.!!$F2 962
7 TraesCS7D01G092300 chr7A 59228018 59234035 6017 False 583.571429 1701 87.444429 343 5826 7 chr7A.!!$F3 5483
8 TraesCS7D01G092300 chr7A 59286878 59289167 2289 False 574.000000 745 81.765000 339 2528 3 chr7A.!!$F4 2189
9 TraesCS7D01G092300 chr4A 671522101 671528527 6426 False 673.888889 2436 90.403889 1 5826 9 chr4A.!!$F1 5825
10 TraesCS7D01G092300 chr4A 671596409 671602498 6089 False 593.000000 915 80.763250 470 4804 4 chr4A.!!$F2 4334
11 TraesCS7D01G092300 chr4A 671638467 671643855 5388 False 512.800000 904 85.367800 349 4798 5 chr4A.!!$F3 4449

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
182 185 0.105039 AAATAGCGCGCTAAGCCTCT 59.895 50.000 40.90 23.18 44.76 3.69 F
752 1080 0.168128 GCGCACGTTGAAGCCTATTT 59.832 50.000 0.30 0.00 0.00 1.40 F
1014 1422 0.177604 CTGGTGCTGGCTAGAGAAGG 59.822 60.000 0.00 0.00 0.00 3.46 F
1062 1511 0.323908 AGAGGAGGAGAGGGACGTTG 60.324 60.000 0.00 0.00 0.00 4.10 F
2163 3499 0.741221 GTCTCTTTGCGCCTCGGAAT 60.741 55.000 4.18 0.00 37.01 3.01 F
2319 3673 2.202932 GCGTCGGGATGTGCTGAT 60.203 61.111 0.00 0.00 0.00 2.90 F
4408 9527 0.171679 TCACATCGTACGTCGGCAAT 59.828 50.000 16.05 0.00 40.32 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1055 1504 0.034896 TCTCCTTTCTGGCAACGTCC 59.965 55.000 0.00 0.00 42.51 4.79 R
2123 3459 0.779997 AACCCAGGCTCCTTGACATT 59.220 50.000 0.00 0.00 0.00 2.71 R
2756 4411 1.447140 GCACCCTGTTGCGATCGTA 60.447 57.895 17.81 9.90 31.51 3.43 R
3394 8427 4.663636 ACGCAACTGTTAAAGCATCTAC 57.336 40.909 0.00 0.00 0.00 2.59 R
3744 8854 0.393402 GCCTGACATGAGCATGGACA 60.393 55.000 14.35 12.08 42.91 4.02 R
4531 9930 1.812571 CCATTTGGAGAACCGTTCTGG 59.187 52.381 18.59 9.24 40.87 3.86 R
5409 10873 2.781431 ATTTGGGTGACTTCGGCCCC 62.781 60.000 0.00 0.00 41.66 5.80 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
44 45 8.132604 AGCTAGCGAGAAATCATTAGTTTTAC 57.867 34.615 9.55 0.00 0.00 2.01
48 49 8.324163 AGCGAGAAATCATTAGTTTTACTGTT 57.676 30.769 0.00 0.00 0.00 3.16
49 50 8.784043 AGCGAGAAATCATTAGTTTTACTGTTT 58.216 29.630 0.00 0.00 0.00 2.83
171 174 8.979574 ACTACTAATCATAGTTTCAAATAGCGC 58.020 33.333 0.00 0.00 42.39 5.92
172 175 6.877855 ACTAATCATAGTTTCAAATAGCGCG 58.122 36.000 0.00 0.00 39.36 6.86
173 176 3.585748 TCATAGTTTCAAATAGCGCGC 57.414 42.857 26.66 26.66 0.00 6.86
174 177 3.194861 TCATAGTTTCAAATAGCGCGCT 58.805 40.909 38.01 38.01 0.00 5.92
175 178 4.364860 TCATAGTTTCAAATAGCGCGCTA 58.635 39.130 39.72 39.72 0.00 4.26
176 179 4.806775 TCATAGTTTCAAATAGCGCGCTAA 59.193 37.500 40.90 25.64 31.73 3.09
177 180 3.658351 AGTTTCAAATAGCGCGCTAAG 57.342 42.857 40.90 31.32 31.73 2.18
178 181 2.101878 GTTTCAAATAGCGCGCTAAGC 58.898 47.619 40.90 25.39 43.95 3.09
179 182 0.655733 TTCAAATAGCGCGCTAAGCC 59.344 50.000 40.90 8.11 44.76 4.35
180 183 0.179084 TCAAATAGCGCGCTAAGCCT 60.179 50.000 40.90 24.32 44.76 4.58
181 184 0.233332 CAAATAGCGCGCTAAGCCTC 59.767 55.000 40.90 6.44 44.76 4.70
182 185 0.105039 AAATAGCGCGCTAAGCCTCT 59.895 50.000 40.90 23.18 44.76 3.69
183 186 0.105039 AATAGCGCGCTAAGCCTCTT 59.895 50.000 40.90 27.25 44.76 2.85
184 187 0.959553 ATAGCGCGCTAAGCCTCTTA 59.040 50.000 40.90 20.62 44.76 2.10
185 188 0.311165 TAGCGCGCTAAGCCTCTTAG 59.689 55.000 36.77 8.76 44.76 2.18
186 189 2.590401 GCGCGCTAAGCCTCTTAGC 61.590 63.158 26.67 22.09 44.76 3.09
190 193 2.874709 GCTAAGCCTCTTAGCGTCG 58.125 57.895 18.95 0.00 38.12 5.12
191 194 0.595310 GCTAAGCCTCTTAGCGTCGG 60.595 60.000 18.95 0.00 38.12 4.79
192 195 1.022735 CTAAGCCTCTTAGCGTCGGA 58.977 55.000 0.00 0.00 38.01 4.55
193 196 0.737219 TAAGCCTCTTAGCGTCGGAC 59.263 55.000 0.00 0.00 38.01 4.79
194 197 1.946475 AAGCCTCTTAGCGTCGGACC 61.946 60.000 1.91 0.00 38.01 4.46
195 198 2.416432 GCCTCTTAGCGTCGGACCT 61.416 63.158 1.91 3.67 0.00 3.85
196 199 1.728672 CCTCTTAGCGTCGGACCTC 59.271 63.158 1.91 0.00 0.00 3.85
197 200 0.748729 CCTCTTAGCGTCGGACCTCT 60.749 60.000 1.91 2.89 0.00 3.69
198 201 1.096416 CTCTTAGCGTCGGACCTCTT 58.904 55.000 1.91 0.00 0.00 2.85
199 202 1.064357 CTCTTAGCGTCGGACCTCTTC 59.936 57.143 1.91 0.00 0.00 2.87
200 203 1.096416 CTTAGCGTCGGACCTCTTCT 58.904 55.000 1.91 0.00 0.00 2.85
201 204 2.093288 TCTTAGCGTCGGACCTCTTCTA 60.093 50.000 1.91 0.00 0.00 2.10
202 205 2.408271 TAGCGTCGGACCTCTTCTAA 57.592 50.000 1.91 0.00 0.00 2.10
203 206 1.542492 AGCGTCGGACCTCTTCTAAA 58.458 50.000 1.91 0.00 0.00 1.85
204 207 2.100989 AGCGTCGGACCTCTTCTAAAT 58.899 47.619 1.91 0.00 0.00 1.40
205 208 2.159226 AGCGTCGGACCTCTTCTAAATG 60.159 50.000 1.91 0.00 0.00 2.32
206 209 2.194271 CGTCGGACCTCTTCTAAATGC 58.806 52.381 1.91 0.00 0.00 3.56
207 210 2.159226 CGTCGGACCTCTTCTAAATGCT 60.159 50.000 1.91 0.00 0.00 3.79
208 211 3.066342 CGTCGGACCTCTTCTAAATGCTA 59.934 47.826 1.91 0.00 0.00 3.49
209 212 4.261656 CGTCGGACCTCTTCTAAATGCTAT 60.262 45.833 1.91 0.00 0.00 2.97
210 213 5.048921 CGTCGGACCTCTTCTAAATGCTATA 60.049 44.000 1.91 0.00 0.00 1.31
211 214 6.383415 GTCGGACCTCTTCTAAATGCTATAG 58.617 44.000 0.00 0.00 0.00 1.31
212 215 6.016108 GTCGGACCTCTTCTAAATGCTATAGT 60.016 42.308 0.84 0.00 0.00 2.12
213 216 6.016192 TCGGACCTCTTCTAAATGCTATAGTG 60.016 42.308 0.84 0.00 0.00 2.74
214 217 6.239064 CGGACCTCTTCTAAATGCTATAGTGT 60.239 42.308 0.84 0.00 0.00 3.55
215 218 6.926272 GGACCTCTTCTAAATGCTATAGTGTG 59.074 42.308 0.84 0.00 0.00 3.82
216 219 6.284459 ACCTCTTCTAAATGCTATAGTGTGC 58.716 40.000 0.84 0.00 0.00 4.57
217 220 6.098982 ACCTCTTCTAAATGCTATAGTGTGCT 59.901 38.462 0.84 0.00 0.00 4.40
218 221 7.287927 ACCTCTTCTAAATGCTATAGTGTGCTA 59.712 37.037 0.84 0.00 0.00 3.49
219 222 8.310382 CCTCTTCTAAATGCTATAGTGTGCTAT 58.690 37.037 0.84 0.00 40.69 2.97
227 230 4.022464 CTATAGTGTGCTATAGCGGAGC 57.978 50.000 19.55 10.19 45.68 4.70
248 251 4.638963 GCTATAGCGCGCTATTTAAAAGG 58.361 43.478 46.76 29.49 39.65 3.11
249 252 4.435651 GCTATAGCGCGCTATTTAAAAGGG 60.436 45.833 46.76 28.44 39.65 3.95
250 253 1.746470 AGCGCGCTATTTAAAAGGGT 58.254 45.000 35.79 2.52 0.00 4.34
251 254 2.089201 AGCGCGCTATTTAAAAGGGTT 58.911 42.857 35.79 1.95 0.00 4.11
252 255 2.490509 AGCGCGCTATTTAAAAGGGTTT 59.509 40.909 35.79 1.11 0.00 3.27
253 256 2.596862 GCGCGCTATTTAAAAGGGTTTG 59.403 45.455 26.67 0.00 0.00 2.93
254 257 3.828786 CGCGCTATTTAAAAGGGTTTGT 58.171 40.909 5.56 0.00 0.00 2.83
255 258 4.231439 CGCGCTATTTAAAAGGGTTTGTT 58.769 39.130 5.56 0.00 0.00 2.83
256 259 4.322539 CGCGCTATTTAAAAGGGTTTGTTC 59.677 41.667 5.56 0.63 0.00 3.18
257 260 5.224135 GCGCTATTTAAAAGGGTTTGTTCA 58.776 37.500 0.00 0.00 0.00 3.18
258 261 5.867174 GCGCTATTTAAAAGGGTTTGTTCAT 59.133 36.000 0.00 0.00 0.00 2.57
259 262 6.367695 GCGCTATTTAAAAGGGTTTGTTCATT 59.632 34.615 0.00 0.00 0.00 2.57
260 263 7.095397 GCGCTATTTAAAAGGGTTTGTTCATTT 60.095 33.333 0.00 0.00 0.00 2.32
261 264 8.220434 CGCTATTTAAAAGGGTTTGTTCATTTG 58.780 33.333 0.00 0.00 0.00 2.32
262 265 9.051679 GCTATTTAAAAGGGTTTGTTCATTTGT 57.948 29.630 0.00 0.00 0.00 2.83
266 269 6.507958 AAAAGGGTTTGTTCATTTGTTTGG 57.492 33.333 0.00 0.00 0.00 3.28
267 270 5.428184 AAGGGTTTGTTCATTTGTTTGGA 57.572 34.783 0.00 0.00 0.00 3.53
268 271 4.765273 AGGGTTTGTTCATTTGTTTGGAC 58.235 39.130 0.00 0.00 0.00 4.02
269 272 3.874543 GGGTTTGTTCATTTGTTTGGACC 59.125 43.478 0.00 0.00 0.00 4.46
270 273 4.508662 GGTTTGTTCATTTGTTTGGACCA 58.491 39.130 0.00 0.00 0.00 4.02
271 274 4.938226 GGTTTGTTCATTTGTTTGGACCAA 59.062 37.500 1.69 1.69 0.00 3.67
272 275 5.588246 GGTTTGTTCATTTGTTTGGACCAAT 59.412 36.000 7.99 0.00 0.00 3.16
273 276 6.458070 GGTTTGTTCATTTGTTTGGACCAATG 60.458 38.462 7.99 2.95 39.19 2.82
274 277 5.350504 TGTTCATTTGTTTGGACCAATGT 57.649 34.783 7.99 0.00 39.01 2.71
275 278 5.355596 TGTTCATTTGTTTGGACCAATGTC 58.644 37.500 7.99 2.92 39.01 3.06
276 279 5.128499 TGTTCATTTGTTTGGACCAATGTCT 59.872 36.000 7.99 0.00 39.01 3.41
277 280 5.867903 TCATTTGTTTGGACCAATGTCTT 57.132 34.783 7.99 0.00 39.01 3.01
278 281 6.232581 TCATTTGTTTGGACCAATGTCTTT 57.767 33.333 7.99 0.00 39.01 2.52
279 282 6.648192 TCATTTGTTTGGACCAATGTCTTTT 58.352 32.000 7.99 0.00 39.01 2.27
280 283 7.786030 TCATTTGTTTGGACCAATGTCTTTTA 58.214 30.769 7.99 0.00 39.01 1.52
281 284 7.925483 TCATTTGTTTGGACCAATGTCTTTTAG 59.075 33.333 7.99 0.00 39.01 1.85
282 285 5.195001 TGTTTGGACCAATGTCTTTTAGC 57.805 39.130 7.99 0.00 41.47 3.09
283 286 4.226761 GTTTGGACCAATGTCTTTTAGCG 58.773 43.478 7.99 0.00 41.47 4.26
284 287 1.810151 TGGACCAATGTCTTTTAGCGC 59.190 47.619 0.00 0.00 41.47 5.92
285 288 1.810151 GGACCAATGTCTTTTAGCGCA 59.190 47.619 11.47 0.00 41.47 6.09
286 289 2.227865 GGACCAATGTCTTTTAGCGCAA 59.772 45.455 11.47 0.00 41.47 4.85
287 290 3.492313 GACCAATGTCTTTTAGCGCAAG 58.508 45.455 11.47 4.65 38.53 4.01
288 291 3.146066 ACCAATGTCTTTTAGCGCAAGA 58.854 40.909 11.47 7.46 43.02 3.02
295 298 5.486095 GTCTTTTAGCGCAAGACATTTTG 57.514 39.130 25.71 1.89 46.48 2.44
296 299 4.976116 GTCTTTTAGCGCAAGACATTTTGT 59.024 37.500 25.71 0.00 46.48 2.83
297 300 6.140110 GTCTTTTAGCGCAAGACATTTTGTA 58.860 36.000 25.71 0.00 46.48 2.41
298 301 6.635239 GTCTTTTAGCGCAAGACATTTTGTAA 59.365 34.615 25.71 4.15 46.48 2.41
299 302 7.166804 GTCTTTTAGCGCAAGACATTTTGTAAA 59.833 33.333 25.71 9.36 46.48 2.01
300 303 7.865385 TCTTTTAGCGCAAGACATTTTGTAAAT 59.135 29.630 11.47 0.00 43.02 1.40
301 304 6.926280 TTAGCGCAAGACATTTTGTAAATG 57.074 33.333 11.47 9.86 43.02 2.32
302 305 3.674753 AGCGCAAGACATTTTGTAAATGC 59.325 39.130 11.47 3.21 43.02 3.56
303 306 3.674753 GCGCAAGACATTTTGTAAATGCT 59.325 39.130 0.30 7.37 43.02 3.79
304 307 4.856487 GCGCAAGACATTTTGTAAATGCTA 59.144 37.500 0.30 0.00 43.02 3.49
305 308 5.516339 GCGCAAGACATTTTGTAAATGCTAT 59.484 36.000 0.30 0.00 43.02 2.97
306 309 6.690957 GCGCAAGACATTTTGTAAATGCTATA 59.309 34.615 0.30 0.00 43.02 1.31
307 310 7.096885 GCGCAAGACATTTTGTAAATGCTATAG 60.097 37.037 0.30 0.00 43.02 1.31
308 311 7.096885 CGCAAGACATTTTGTAAATGCTATAGC 60.097 37.037 18.18 18.18 43.02 2.97
309 312 7.917505 GCAAGACATTTTGTAAATGCTATAGCT 59.082 33.333 24.61 8.18 42.66 3.32
310 313 9.443283 CAAGACATTTTGTAAATGCTATAGCTC 57.557 33.333 24.61 9.55 42.66 4.09
311 314 8.159344 AGACATTTTGTAAATGCTATAGCTCC 57.841 34.615 24.61 9.00 42.66 4.70
312 315 6.959361 ACATTTTGTAAATGCTATAGCTCCG 58.041 36.000 24.61 3.95 42.66 4.63
313 316 5.418310 TTTTGTAAATGCTATAGCTCCGC 57.582 39.130 24.61 11.84 42.66 5.54
314 317 4.336889 TTGTAAATGCTATAGCTCCGCT 57.663 40.909 24.61 8.15 43.41 5.52
315 318 5.462530 TTGTAAATGCTATAGCTCCGCTA 57.537 39.130 24.61 4.45 45.55 4.26
334 337 5.292671 GCTATAGCGGGCTATTTAAAACC 57.707 43.478 17.49 0.00 39.65 3.27
335 338 4.758165 GCTATAGCGGGCTATTTAAAACCA 59.242 41.667 17.49 0.00 39.65 3.67
336 339 5.414765 GCTATAGCGGGCTATTTAAAACCAT 59.585 40.000 17.49 0.00 39.65 3.55
337 340 5.705609 ATAGCGGGCTATTTAAAACCATG 57.294 39.130 7.36 0.00 35.92 3.66
491 796 8.841300 AGACATATATGTATGAGCGATTACGAT 58.159 33.333 18.28 0.00 41.95 3.73
513 821 2.029649 TGAACTTCCTCTAACGAACGGG 60.030 50.000 0.00 0.00 0.00 5.28
572 882 1.269998 CTTGACGAAAGAGTCTCCCGT 59.730 52.381 16.48 16.48 41.47 5.28
593 903 3.537795 TCTATAATAGTGGGCCGAGGT 57.462 47.619 0.00 0.00 0.00 3.85
657 977 0.904865 ATCAACGCCAGAGGAGGACA 60.905 55.000 0.00 0.00 0.00 4.02
705 1033 3.427863 GGACGCGCATCTTAGTTATAACC 59.572 47.826 5.73 0.00 0.00 2.85
708 1036 2.735134 GCGCATCTTAGTTATAACCGGG 59.265 50.000 12.05 0.00 0.00 5.73
709 1037 3.323243 CGCATCTTAGTTATAACCGGGG 58.677 50.000 12.05 1.29 0.00 5.73
710 1038 3.072211 GCATCTTAGTTATAACCGGGGC 58.928 50.000 12.05 5.58 0.00 5.80
711 1039 3.671716 CATCTTAGTTATAACCGGGGCC 58.328 50.000 12.05 0.00 0.00 5.80
712 1040 2.761809 TCTTAGTTATAACCGGGGCCA 58.238 47.619 12.05 0.00 0.00 5.36
752 1080 0.168128 GCGCACGTTGAAGCCTATTT 59.832 50.000 0.30 0.00 0.00 1.40
844 1204 2.009774 AGTGCGGCTATGTTTGACATC 58.990 47.619 0.00 0.00 39.88 3.06
963 1359 2.036992 CCATGGTCTAGGCTTCTAGCTG 59.963 54.545 2.57 0.00 41.99 4.24
990 1390 5.372343 CCTATATATACAAGGCCATGGCA 57.628 43.478 36.56 17.73 44.11 4.92
992 1392 5.824624 CCTATATATACAAGGCCATGGCAAG 59.175 44.000 36.56 26.23 44.11 4.01
994 1394 0.336048 ATACAAGGCCATGGCAAGGT 59.664 50.000 36.56 29.33 44.11 3.50
996 1396 1.304713 CAAGGCCATGGCAAGGTCT 60.305 57.895 36.56 21.67 44.57 3.85
999 1399 2.036256 GCCATGGCAAGGTCTGGT 59.964 61.111 32.08 0.00 41.49 4.00
1000 1400 2.345760 GCCATGGCAAGGTCTGGTG 61.346 63.158 32.08 0.00 41.49 4.17
1001 1401 2.345760 CCATGGCAAGGTCTGGTGC 61.346 63.158 0.00 0.00 40.14 5.01
1002 1402 1.303888 CATGGCAAGGTCTGGTGCT 60.304 57.895 0.00 0.00 40.70 4.40
1014 1422 0.177604 CTGGTGCTGGCTAGAGAAGG 59.822 60.000 0.00 0.00 0.00 3.46
1018 1426 1.552792 GTGCTGGCTAGAGAAGGAAGT 59.447 52.381 0.00 0.00 0.00 3.01
1055 1504 5.269189 AGAAACTAGAAAGAGGAGGAGAGG 58.731 45.833 0.00 0.00 0.00 3.69
1059 1508 1.107945 GAAAGAGGAGGAGAGGGACG 58.892 60.000 0.00 0.00 0.00 4.79
1060 1509 0.410270 AAAGAGGAGGAGAGGGACGT 59.590 55.000 0.00 0.00 0.00 4.34
1061 1510 0.410270 AAGAGGAGGAGAGGGACGTT 59.590 55.000 0.00 0.00 0.00 3.99
1062 1511 0.323908 AGAGGAGGAGAGGGACGTTG 60.324 60.000 0.00 0.00 0.00 4.10
1063 1512 1.950973 GAGGAGGAGAGGGACGTTGC 61.951 65.000 0.00 0.00 0.00 4.17
1064 1513 2.579738 GAGGAGAGGGACGTTGCC 59.420 66.667 0.00 0.00 0.00 4.52
1065 1514 2.203788 AGGAGAGGGACGTTGCCA 60.204 61.111 0.00 0.00 0.00 4.92
1185 1697 9.955208 CTCTTGATTTTGTGCTTTGCATATATA 57.045 29.630 0.00 0.00 41.91 0.86
1222 1758 8.620533 AAGAGTTTGATTCTTTTTCTTGAACG 57.379 30.769 0.00 0.00 30.98 3.95
1239 1777 3.708563 AACGAGTGTTCATTTGGTTGG 57.291 42.857 0.00 0.00 30.83 3.77
1240 1778 2.925724 ACGAGTGTTCATTTGGTTGGA 58.074 42.857 0.00 0.00 0.00 3.53
1241 1779 3.486383 ACGAGTGTTCATTTGGTTGGAT 58.514 40.909 0.00 0.00 0.00 3.41
1242 1780 3.253188 ACGAGTGTTCATTTGGTTGGATG 59.747 43.478 0.00 0.00 0.00 3.51
1243 1781 3.501828 CGAGTGTTCATTTGGTTGGATGA 59.498 43.478 0.00 0.00 0.00 2.92
1244 1782 4.378770 CGAGTGTTCATTTGGTTGGATGAG 60.379 45.833 0.00 0.00 34.10 2.90
1245 1783 4.473444 AGTGTTCATTTGGTTGGATGAGT 58.527 39.130 0.00 0.00 34.10 3.41
1246 1784 5.630121 AGTGTTCATTTGGTTGGATGAGTA 58.370 37.500 0.00 0.00 34.10 2.59
1254 1792 7.936847 TCATTTGGTTGGATGAGTATATGGTAC 59.063 37.037 0.00 0.00 0.00 3.34
1256 1794 4.243270 GGTTGGATGAGTATATGGTACGC 58.757 47.826 0.00 0.00 0.00 4.42
1262 1800 5.418209 GGATGAGTATATGGTACGCCTAGTT 59.582 44.000 0.00 0.00 35.27 2.24
1289 1834 3.810386 GGACTGAAGACTTGGTTGAGTTC 59.190 47.826 0.00 0.00 0.00 3.01
1307 1852 1.078567 CCTCTCTTGTCTGGCCTGC 60.079 63.158 3.32 0.30 0.00 4.85
1310 1855 3.965539 CTCTTGTCTGGCCTGCGGG 62.966 68.421 7.41 7.41 0.00 6.13
1312 1857 3.850098 CTTGTCTGGCCTGCGGGTT 62.850 63.158 14.55 0.00 34.45 4.11
1313 1858 4.641645 TGTCTGGCCTGCGGGTTG 62.642 66.667 14.55 3.83 34.45 3.77
1318 1930 4.424711 GGCCTGCGGGTTGGATGA 62.425 66.667 14.55 0.00 34.45 2.92
1331 1950 4.310769 GGTTGGATGAGTATCTTGATCCG 58.689 47.826 0.00 0.00 37.75 4.18
1341 1976 6.179906 AGTATCTTGATCCGTGAATGGAAT 57.820 37.500 0.00 0.00 42.46 3.01
1342 1977 5.994054 AGTATCTTGATCCGTGAATGGAATG 59.006 40.000 0.00 0.00 42.46 2.67
1343 1978 3.544684 TCTTGATCCGTGAATGGAATGG 58.455 45.455 0.00 0.00 42.46 3.16
1344 1979 2.346766 TGATCCGTGAATGGAATGGG 57.653 50.000 0.00 0.00 42.46 4.00
1359 1994 1.813102 ATGGGATCAGGGACTTCTCC 58.187 55.000 0.00 0.00 34.60 3.71
1388 2025 8.891671 TGATCGATGTCAAAATCAATCAGATA 57.108 30.769 0.54 0.00 35.39 1.98
1582 2268 4.402155 AGATAAGAGATGATCATCGAGCCC 59.598 45.833 26.09 16.09 42.48 5.19
1588 2274 1.216710 GATCATCGAGCCCCGGATC 59.783 63.158 0.73 0.00 39.14 3.36
1589 2275 1.533994 ATCATCGAGCCCCGGATCA 60.534 57.895 0.73 0.00 39.14 2.92
1708 2553 3.012274 TCCTAATTGCCCTGAAATTCCCA 59.988 43.478 0.00 0.00 0.00 4.37
1885 3221 7.227314 TGCTTTGCTTCACCAATGAGTATATAG 59.773 37.037 0.00 0.00 35.83 1.31
1900 3236 8.874744 TGAGTATATAGCTAATAACGGGTCTT 57.125 34.615 0.00 0.00 0.00 3.01
1969 3305 1.687612 CACAAGGGCAGAGATGGGT 59.312 57.895 0.00 0.00 0.00 4.51
2012 3348 2.026542 AGGCTGAAGATGATGCTGTCAA 60.027 45.455 0.00 0.00 40.97 3.18
2014 3350 3.268330 GCTGAAGATGATGCTGTCAAGA 58.732 45.455 0.00 0.00 40.97 3.02
2055 3391 1.471684 CCTTCAGAAGCAGTTGGATGC 59.528 52.381 4.41 0.00 46.88 3.91
2123 3459 1.514678 GCACACATCGCCTTCCAACA 61.515 55.000 0.00 0.00 0.00 3.33
2163 3499 0.741221 GTCTCTTTGCGCCTCGGAAT 60.741 55.000 4.18 0.00 37.01 3.01
2319 3673 2.202932 GCGTCGGGATGTGCTGAT 60.203 61.111 0.00 0.00 0.00 2.90
2920 6756 2.355756 GGCGATCAGTGTACCTAACGTA 59.644 50.000 0.00 0.00 0.00 3.57
3364 7323 5.125417 GCAGGGATTTGCACTTGAACTAATA 59.875 40.000 0.00 0.00 43.53 0.98
3497 8593 6.091034 TGTTAGTAATTTGCGACGAATTAGCA 59.909 34.615 0.00 0.00 39.33 3.49
3744 8854 2.281070 CACCACTTCTGCCGCTGT 60.281 61.111 0.00 0.00 0.00 4.40
4408 9527 0.171679 TCACATCGTACGTCGGCAAT 59.828 50.000 16.05 0.00 40.32 3.56
4531 9930 1.735559 GTCGTCAACGGTAGCCACC 60.736 63.158 2.31 0.00 41.93 4.61
4740 10164 5.860641 GCATAATTGCTGAAAATGTGTTGG 58.139 37.500 0.00 0.00 45.77 3.77
4807 10232 6.200665 TGTTTGTGACAAGCTATTTGCATTTC 59.799 34.615 13.18 0.00 40.59 2.17
4847 10272 6.758416 GTGCACTGATCATATGAGACAAACTA 59.242 38.462 10.32 0.15 0.00 2.24
4961 10386 7.596248 CCTGTTGAATTAGCACATAATTATGGC 59.404 37.037 25.45 23.35 42.84 4.40
5409 10873 2.763448 TGGAACCCTTTCACAAAACCAG 59.237 45.455 0.00 0.00 32.80 4.00
5454 11312 6.942532 TCTTCCACTATTATCAAATGTGGC 57.057 37.500 0.00 0.00 40.43 5.01
5551 11410 6.670695 AACAAGATTAGGGTTTGCAAGAAT 57.329 33.333 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
146 149 8.156553 CGCGCTATTTGAAACTATGATTAGTAG 58.843 37.037 5.56 0.00 37.70 2.57
149 152 5.785599 GCGCGCTATTTGAAACTATGATTAG 59.214 40.000 26.67 0.00 0.00 1.73
150 153 5.465390 AGCGCGCTATTTGAAACTATGATTA 59.535 36.000 35.79 0.00 0.00 1.75
151 154 4.273480 AGCGCGCTATTTGAAACTATGATT 59.727 37.500 35.79 0.18 0.00 2.57
153 156 3.194861 AGCGCGCTATTTGAAACTATGA 58.805 40.909 35.79 0.00 0.00 2.15
154 157 3.592381 AGCGCGCTATTTGAAACTATG 57.408 42.857 35.79 0.00 0.00 2.23
155 158 4.318831 GCTTAGCGCGCTATTTGAAACTAT 60.319 41.667 38.51 13.72 0.00 2.12
156 159 3.000925 GCTTAGCGCGCTATTTGAAACTA 59.999 43.478 38.51 20.65 0.00 2.24
157 160 2.223044 GCTTAGCGCGCTATTTGAAACT 60.223 45.455 38.51 14.50 0.00 2.66
158 161 2.101878 GCTTAGCGCGCTATTTGAAAC 58.898 47.619 38.51 18.80 0.00 2.78
159 162 1.063469 GGCTTAGCGCGCTATTTGAAA 59.937 47.619 38.51 24.43 40.44 2.69
160 163 0.655733 GGCTTAGCGCGCTATTTGAA 59.344 50.000 38.51 25.16 40.44 2.69
161 164 0.179084 AGGCTTAGCGCGCTATTTGA 60.179 50.000 38.51 23.89 40.44 2.69
162 165 0.233332 GAGGCTTAGCGCGCTATTTG 59.767 55.000 38.51 29.50 40.44 2.32
163 166 0.105039 AGAGGCTTAGCGCGCTATTT 59.895 50.000 38.51 24.06 40.44 1.40
164 167 0.105039 AAGAGGCTTAGCGCGCTATT 59.895 50.000 38.51 26.01 40.44 1.73
165 168 0.959553 TAAGAGGCTTAGCGCGCTAT 59.040 50.000 38.51 25.42 40.44 2.97
166 169 0.311165 CTAAGAGGCTTAGCGCGCTA 59.689 55.000 35.48 35.48 40.44 4.26
167 170 1.066587 CTAAGAGGCTTAGCGCGCT 59.933 57.895 38.01 38.01 40.44 5.92
168 171 2.590401 GCTAAGAGGCTTAGCGCGC 61.590 63.158 26.66 26.66 38.12 6.86
169 172 3.619054 GCTAAGAGGCTTAGCGCG 58.381 61.111 19.61 0.00 38.12 6.86
172 175 0.595310 CCGACGCTAAGAGGCTTAGC 60.595 60.000 22.75 22.75 42.82 3.09
173 176 1.022735 TCCGACGCTAAGAGGCTTAG 58.977 55.000 9.30 9.30 0.00 2.18
174 177 0.737219 GTCCGACGCTAAGAGGCTTA 59.263 55.000 0.00 0.00 0.00 3.09
175 178 1.511768 GTCCGACGCTAAGAGGCTT 59.488 57.895 0.00 0.00 0.00 4.35
176 179 2.416432 GGTCCGACGCTAAGAGGCT 61.416 63.158 0.00 0.00 0.00 4.58
177 180 2.104530 GGTCCGACGCTAAGAGGC 59.895 66.667 0.00 0.00 0.00 4.70
178 181 0.748729 AGAGGTCCGACGCTAAGAGG 60.749 60.000 0.00 0.00 0.00 3.69
179 182 1.064357 GAAGAGGTCCGACGCTAAGAG 59.936 57.143 0.00 0.00 0.00 2.85
180 183 1.093159 GAAGAGGTCCGACGCTAAGA 58.907 55.000 0.00 0.00 0.00 2.10
181 184 1.096416 AGAAGAGGTCCGACGCTAAG 58.904 55.000 0.00 0.00 0.00 2.18
182 185 2.408271 TAGAAGAGGTCCGACGCTAA 57.592 50.000 0.00 0.00 0.00 3.09
183 186 2.408271 TTAGAAGAGGTCCGACGCTA 57.592 50.000 0.00 0.00 0.00 4.26
184 187 1.542492 TTTAGAAGAGGTCCGACGCT 58.458 50.000 0.00 0.00 0.00 5.07
185 188 2.194271 CATTTAGAAGAGGTCCGACGC 58.806 52.381 0.00 0.00 0.00 5.19
186 189 2.159226 AGCATTTAGAAGAGGTCCGACG 60.159 50.000 0.00 0.00 0.00 5.12
187 190 3.528597 AGCATTTAGAAGAGGTCCGAC 57.471 47.619 0.00 0.00 0.00 4.79
188 191 6.016192 CACTATAGCATTTAGAAGAGGTCCGA 60.016 42.308 0.00 0.00 0.00 4.55
189 192 6.153067 CACTATAGCATTTAGAAGAGGTCCG 58.847 44.000 0.00 0.00 0.00 4.79
190 193 6.926272 CACACTATAGCATTTAGAAGAGGTCC 59.074 42.308 0.00 0.00 0.00 4.46
191 194 6.422400 GCACACTATAGCATTTAGAAGAGGTC 59.578 42.308 0.00 0.00 0.00 3.85
192 195 6.098982 AGCACACTATAGCATTTAGAAGAGGT 59.901 38.462 0.00 0.00 0.00 3.85
193 196 6.520272 AGCACACTATAGCATTTAGAAGAGG 58.480 40.000 0.00 0.00 0.00 3.69
207 210 3.687125 AGCTCCGCTATAGCACACTATA 58.313 45.455 23.99 0.78 42.62 1.31
208 211 2.520069 AGCTCCGCTATAGCACACTAT 58.480 47.619 23.99 2.78 42.62 2.12
209 212 1.982660 AGCTCCGCTATAGCACACTA 58.017 50.000 23.99 3.77 42.62 2.74
210 213 1.982660 TAGCTCCGCTATAGCACACT 58.017 50.000 23.99 16.32 42.62 3.55
219 222 2.868196 CGCGCTATAGCTCCGCTA 59.132 61.111 21.98 0.00 45.55 4.26
222 225 0.179161 AATAGCGCGCTATAGCTCCG 60.179 55.000 43.81 22.32 43.44 4.63
223 226 1.997669 AAATAGCGCGCTATAGCTCC 58.002 50.000 43.81 10.26 43.44 4.70
224 227 5.444745 CCTTTTAAATAGCGCGCTATAGCTC 60.445 44.000 43.81 13.77 43.44 4.09
225 228 4.389077 CCTTTTAAATAGCGCGCTATAGCT 59.611 41.667 43.81 33.17 46.53 3.32
226 229 4.435651 CCCTTTTAAATAGCGCGCTATAGC 60.436 45.833 43.81 15.09 38.20 2.97
227 230 4.689345 ACCCTTTTAAATAGCGCGCTATAG 59.311 41.667 43.81 35.53 38.20 1.31
228 231 4.634199 ACCCTTTTAAATAGCGCGCTATA 58.366 39.130 43.81 31.08 38.20 1.31
229 232 3.473625 ACCCTTTTAAATAGCGCGCTAT 58.526 40.909 40.32 40.32 40.63 2.97
230 233 2.908916 ACCCTTTTAAATAGCGCGCTA 58.091 42.857 39.72 39.72 0.00 4.26
231 234 1.746470 ACCCTTTTAAATAGCGCGCT 58.254 45.000 38.01 38.01 0.00 5.92
232 235 2.554806 AACCCTTTTAAATAGCGCGC 57.445 45.000 26.66 26.66 0.00 6.86
233 236 3.828786 ACAAACCCTTTTAAATAGCGCG 58.171 40.909 0.00 0.00 0.00 6.86
234 237 5.224135 TGAACAAACCCTTTTAAATAGCGC 58.776 37.500 0.00 0.00 0.00 5.92
235 238 7.883229 AATGAACAAACCCTTTTAAATAGCG 57.117 32.000 0.00 0.00 0.00 4.26
236 239 9.051679 ACAAATGAACAAACCCTTTTAAATAGC 57.948 29.630 0.00 0.00 0.00 2.97
240 243 8.515414 CCAAACAAATGAACAAACCCTTTTAAA 58.485 29.630 0.00 0.00 0.00 1.52
241 244 7.883311 TCCAAACAAATGAACAAACCCTTTTAA 59.117 29.630 0.00 0.00 0.00 1.52
242 245 7.334671 GTCCAAACAAATGAACAAACCCTTTTA 59.665 33.333 0.00 0.00 0.00 1.52
243 246 6.150307 GTCCAAACAAATGAACAAACCCTTTT 59.850 34.615 0.00 0.00 0.00 2.27
244 247 5.645929 GTCCAAACAAATGAACAAACCCTTT 59.354 36.000 0.00 0.00 0.00 3.11
245 248 5.182487 GTCCAAACAAATGAACAAACCCTT 58.818 37.500 0.00 0.00 0.00 3.95
246 249 4.383661 GGTCCAAACAAATGAACAAACCCT 60.384 41.667 0.00 0.00 0.00 4.34
247 250 3.874543 GGTCCAAACAAATGAACAAACCC 59.125 43.478 0.00 0.00 0.00 4.11
248 251 4.508662 TGGTCCAAACAAATGAACAAACC 58.491 39.130 0.00 0.00 0.00 3.27
249 252 6.093357 ACATTGGTCCAAACAAATGAACAAAC 59.907 34.615 8.75 0.00 45.97 2.93
250 253 6.176183 ACATTGGTCCAAACAAATGAACAAA 58.824 32.000 8.75 0.00 45.97 2.83
251 254 5.738909 ACATTGGTCCAAACAAATGAACAA 58.261 33.333 8.75 0.00 45.97 2.83
252 255 5.128499 AGACATTGGTCCAAACAAATGAACA 59.872 36.000 8.75 0.00 45.97 3.18
253 256 5.600696 AGACATTGGTCCAAACAAATGAAC 58.399 37.500 8.75 2.92 45.97 3.18
254 257 5.867903 AGACATTGGTCCAAACAAATGAA 57.132 34.783 8.75 0.00 45.97 2.57
255 258 5.867903 AAGACATTGGTCCAAACAAATGA 57.132 34.783 8.75 0.00 45.97 2.57
257 260 6.705825 GCTAAAAGACATTGGTCCAAACAAAT 59.294 34.615 8.75 0.00 45.48 2.32
258 261 6.045955 GCTAAAAGACATTGGTCCAAACAAA 58.954 36.000 8.75 0.00 45.48 2.83
259 262 5.596845 GCTAAAAGACATTGGTCCAAACAA 58.403 37.500 8.75 0.00 45.48 2.83
260 263 4.261405 CGCTAAAAGACATTGGTCCAAACA 60.261 41.667 8.75 0.00 45.48 2.83
261 264 4.226761 CGCTAAAAGACATTGGTCCAAAC 58.773 43.478 8.75 3.71 45.48 2.93
262 265 3.305064 GCGCTAAAAGACATTGGTCCAAA 60.305 43.478 8.75 0.00 45.48 3.28
263 266 2.227865 GCGCTAAAAGACATTGGTCCAA 59.772 45.455 6.80 6.80 45.48 3.53
264 267 1.810151 GCGCTAAAAGACATTGGTCCA 59.190 47.619 0.00 0.00 45.48 4.02
265 268 1.810151 TGCGCTAAAAGACATTGGTCC 59.190 47.619 9.73 0.00 45.48 4.46
266 269 3.188460 TCTTGCGCTAAAAGACATTGGTC 59.812 43.478 9.73 0.00 44.66 4.02
267 270 3.146066 TCTTGCGCTAAAAGACATTGGT 58.854 40.909 9.73 0.00 0.00 3.67
268 271 3.829886 TCTTGCGCTAAAAGACATTGG 57.170 42.857 9.73 0.00 0.00 3.16
274 277 5.181690 ACAAAATGTCTTGCGCTAAAAGA 57.818 34.783 9.73 6.78 0.00 2.52
275 278 6.984740 TTACAAAATGTCTTGCGCTAAAAG 57.015 33.333 9.73 3.98 0.00 2.27
276 279 7.568497 GCATTTACAAAATGTCTTGCGCTAAAA 60.568 33.333 9.73 0.00 0.00 1.52
277 280 6.128956 GCATTTACAAAATGTCTTGCGCTAAA 60.129 34.615 9.73 0.46 0.00 1.85
278 281 5.344665 GCATTTACAAAATGTCTTGCGCTAA 59.655 36.000 9.73 0.00 0.00 3.09
279 282 4.856487 GCATTTACAAAATGTCTTGCGCTA 59.144 37.500 9.73 0.00 0.00 4.26
280 283 3.674753 GCATTTACAAAATGTCTTGCGCT 59.325 39.130 9.73 0.00 0.00 5.92
281 284 3.674753 AGCATTTACAAAATGTCTTGCGC 59.325 39.130 0.00 0.00 35.86 6.09
282 285 7.096885 GCTATAGCATTTACAAAATGTCTTGCG 60.097 37.037 20.01 0.00 41.59 4.85
283 286 7.917505 AGCTATAGCATTTACAAAATGTCTTGC 59.082 33.333 26.07 12.93 45.16 4.01
284 287 9.443283 GAGCTATAGCATTTACAAAATGTCTTG 57.557 33.333 26.07 6.85 45.16 3.02
285 288 8.624776 GGAGCTATAGCATTTACAAAATGTCTT 58.375 33.333 26.07 0.00 45.16 3.01
286 289 7.041780 CGGAGCTATAGCATTTACAAAATGTCT 60.042 37.037 26.07 11.87 45.16 3.41
287 290 7.072030 CGGAGCTATAGCATTTACAAAATGTC 58.928 38.462 26.07 9.90 45.16 3.06
288 291 6.959361 CGGAGCTATAGCATTTACAAAATGT 58.041 36.000 26.07 0.58 45.16 2.71
312 315 4.758165 TGGTTTTAAATAGCCCGCTATAGC 59.242 41.667 15.09 15.09 38.20 2.97
313 316 6.622896 GCATGGTTTTAAATAGCCCGCTATAG 60.623 42.308 9.56 0.00 38.20 1.31
314 317 5.182380 GCATGGTTTTAAATAGCCCGCTATA 59.818 40.000 9.56 0.00 38.20 1.31
315 318 4.022329 GCATGGTTTTAAATAGCCCGCTAT 60.022 41.667 3.31 3.31 40.63 2.97
316 319 3.316868 GCATGGTTTTAAATAGCCCGCTA 59.683 43.478 0.00 0.00 0.00 4.26
317 320 2.100749 GCATGGTTTTAAATAGCCCGCT 59.899 45.455 0.00 0.00 0.00 5.52
318 321 2.100749 AGCATGGTTTTAAATAGCCCGC 59.899 45.455 0.00 0.00 0.00 6.13
319 322 4.578928 AGTAGCATGGTTTTAAATAGCCCG 59.421 41.667 1.12 0.00 0.00 6.13
320 323 7.576861 TTAGTAGCATGGTTTTAAATAGCCC 57.423 36.000 1.12 0.00 0.00 5.19
329 332 9.509956 TGTACTTGTTATTAGTAGCATGGTTTT 57.490 29.630 1.12 0.00 0.00 2.43
330 333 8.943002 GTGTACTTGTTATTAGTAGCATGGTTT 58.057 33.333 1.12 0.00 0.00 3.27
331 334 7.551617 GGTGTACTTGTTATTAGTAGCATGGTT 59.448 37.037 1.12 0.00 0.00 3.67
332 335 7.046033 GGTGTACTTGTTATTAGTAGCATGGT 58.954 38.462 1.62 1.62 0.00 3.55
333 336 6.200286 CGGTGTACTTGTTATTAGTAGCATGG 59.800 42.308 0.00 0.00 0.00 3.66
334 337 6.755141 ACGGTGTACTTGTTATTAGTAGCATG 59.245 38.462 0.00 0.00 0.00 4.06
335 338 6.870769 ACGGTGTACTTGTTATTAGTAGCAT 58.129 36.000 0.00 0.00 0.00 3.79
336 339 6.271488 ACGGTGTACTTGTTATTAGTAGCA 57.729 37.500 0.00 0.00 0.00 3.49
337 340 5.453587 CGACGGTGTACTTGTTATTAGTAGC 59.546 44.000 0.00 0.00 0.00 3.58
433 725 1.002069 ATGAGATTTGGTGAGGGGCA 58.998 50.000 0.00 0.00 0.00 5.36
434 726 2.149973 AATGAGATTTGGTGAGGGGC 57.850 50.000 0.00 0.00 0.00 5.80
488 793 4.030306 CGTTCGTTAGAGGAAGTTCAATCG 59.970 45.833 5.01 1.25 0.00 3.34
491 796 3.553508 CCCGTTCGTTAGAGGAAGTTCAA 60.554 47.826 5.01 0.00 0.00 2.69
513 821 3.421844 ACCAAATTTCAGTCCTGTAGGC 58.578 45.455 0.00 0.00 34.44 3.93
572 882 3.576982 CACCTCGGCCCACTATTATAGAA 59.423 47.826 6.21 0.00 0.00 2.10
619 932 4.083862 AAGCTTCCCGCGAGTCCC 62.084 66.667 8.23 0.00 45.59 4.46
657 977 4.783841 GCGTACGTCGTCGAGCGT 62.784 66.667 17.90 20.67 44.02 5.07
674 994 1.959899 GATGCGCGTCCAGACTGTTG 61.960 60.000 19.11 0.00 0.00 3.33
709 1037 3.432588 CTGCTGCTGTCTGCTGGC 61.433 66.667 0.00 10.62 43.37 4.85
710 1038 3.432588 GCTGCTGCTGTCTGCTGG 61.433 66.667 8.53 1.94 43.37 4.85
711 1039 2.041115 ATGCTGCTGCTGTCTGCTG 61.041 57.895 17.00 3.90 43.37 4.41
712 1040 2.041115 CATGCTGCTGCTGTCTGCT 61.041 57.895 17.00 0.00 43.37 4.24
752 1080 4.321008 GGAGACTGAGATTTACGTGTGTCA 60.321 45.833 0.00 0.00 0.00 3.58
990 1390 0.545309 TCTAGCCAGCACCAGACCTT 60.545 55.000 0.00 0.00 0.00 3.50
992 1392 0.972983 TCTCTAGCCAGCACCAGACC 60.973 60.000 0.00 0.00 0.00 3.85
994 1394 1.189752 CTTCTCTAGCCAGCACCAGA 58.810 55.000 0.00 0.00 0.00 3.86
996 1396 0.252239 TCCTTCTCTAGCCAGCACCA 60.252 55.000 0.00 0.00 0.00 4.17
999 1399 1.552337 CACTTCCTTCTCTAGCCAGCA 59.448 52.381 0.00 0.00 0.00 4.41
1000 1400 1.742071 GCACTTCCTTCTCTAGCCAGC 60.742 57.143 0.00 0.00 0.00 4.85
1001 1401 1.830477 AGCACTTCCTTCTCTAGCCAG 59.170 52.381 0.00 0.00 0.00 4.85
1002 1402 1.552337 CAGCACTTCCTTCTCTAGCCA 59.448 52.381 0.00 0.00 0.00 4.75
1014 1422 1.827969 TCTCTAGCCTTCCAGCACTTC 59.172 52.381 0.00 0.00 34.23 3.01
1018 1426 2.260822 AGTTTCTCTAGCCTTCCAGCA 58.739 47.619 0.00 0.00 34.23 4.41
1055 1504 0.034896 TCTCCTTTCTGGCAACGTCC 59.965 55.000 0.00 0.00 42.51 4.79
1059 1508 2.093973 TCTCGATCTCCTTTCTGGCAAC 60.094 50.000 0.00 0.00 35.26 4.17
1060 1509 2.179427 TCTCGATCTCCTTTCTGGCAA 58.821 47.619 0.00 0.00 35.26 4.52
1061 1510 1.852633 TCTCGATCTCCTTTCTGGCA 58.147 50.000 0.00 0.00 35.26 4.92
1062 1511 2.363680 TCATCTCGATCTCCTTTCTGGC 59.636 50.000 0.00 0.00 35.26 4.85
1063 1512 4.808558 GATCATCTCGATCTCCTTTCTGG 58.191 47.826 0.00 0.00 46.16 3.86
1100 1608 3.565961 TTCATGGCCGCCAAGCTGA 62.566 57.895 18.00 13.23 36.95 4.26
1222 1758 4.520492 ACTCATCCAACCAAATGAACACTC 59.480 41.667 0.00 0.00 31.81 3.51
1232 1770 5.740803 GCGTACCATATACTCATCCAACCAA 60.741 44.000 0.00 0.00 0.00 3.67
1237 1775 3.774734 AGGCGTACCATATACTCATCCA 58.225 45.455 0.00 0.00 39.06 3.41
1238 1776 4.948621 ACTAGGCGTACCATATACTCATCC 59.051 45.833 0.00 0.00 39.06 3.51
1239 1777 6.512342 AACTAGGCGTACCATATACTCATC 57.488 41.667 0.00 0.00 39.06 2.92
1240 1778 8.591114 AATAACTAGGCGTACCATATACTCAT 57.409 34.615 0.00 0.00 39.06 2.90
1241 1779 9.170734 CTAATAACTAGGCGTACCATATACTCA 57.829 37.037 0.00 0.00 39.06 3.41
1242 1780 8.619546 CCTAATAACTAGGCGTACCATATACTC 58.380 40.741 0.00 0.00 41.02 2.59
1243 1781 8.331740 TCCTAATAACTAGGCGTACCATATACT 58.668 37.037 0.00 0.00 46.33 2.12
1244 1782 8.401709 GTCCTAATAACTAGGCGTACCATATAC 58.598 40.741 0.00 0.00 46.33 1.47
1245 1783 8.331740 AGTCCTAATAACTAGGCGTACCATATA 58.668 37.037 0.00 0.00 46.33 0.86
1246 1784 7.122353 CAGTCCTAATAACTAGGCGTACCATAT 59.878 40.741 0.00 0.00 46.33 1.78
1254 1792 5.299782 AGTCTTCAGTCCTAATAACTAGGCG 59.700 44.000 0.00 0.00 46.33 5.52
1262 1800 6.497259 ACTCAACCAAGTCTTCAGTCCTAATA 59.503 38.462 0.00 0.00 0.00 0.98
1289 1834 1.078567 GCAGGCCAGACAAGAGAGG 60.079 63.158 5.01 0.00 0.00 3.69
1307 1852 3.819564 TCAAGATACTCATCCAACCCG 57.180 47.619 0.00 0.00 0.00 5.28
1310 1855 4.747108 CACGGATCAAGATACTCATCCAAC 59.253 45.833 0.00 0.00 35.42 3.77
1312 1857 4.215109 TCACGGATCAAGATACTCATCCA 58.785 43.478 0.00 0.00 35.42 3.41
1313 1858 4.855715 TCACGGATCAAGATACTCATCC 57.144 45.455 0.00 0.00 32.75 3.51
1318 1930 5.614324 TTCCATTCACGGATCAAGATACT 57.386 39.130 0.00 0.00 34.19 2.12
1331 1950 2.175499 TCCCTGATCCCATTCCATTCAC 59.825 50.000 0.00 0.00 0.00 3.18
1341 1976 0.719015 AGGAGAAGTCCCTGATCCCA 59.281 55.000 0.00 0.00 45.26 4.37
1342 1977 1.765904 GAAGGAGAAGTCCCTGATCCC 59.234 57.143 0.00 0.00 45.26 3.85
1343 1978 2.433970 CAGAAGGAGAAGTCCCTGATCC 59.566 54.545 0.00 0.00 45.26 3.36
1344 1979 3.370104 TCAGAAGGAGAAGTCCCTGATC 58.630 50.000 0.00 0.00 45.26 2.92
1359 1994 7.691158 TGATTGATTTTGACATCGATCAGAAG 58.309 34.615 8.85 0.00 44.30 2.85
1388 2025 5.163152 GGATCTGTGGTCCCTAAAGATGATT 60.163 44.000 0.00 0.00 0.00 2.57
1477 2133 7.123098 ACAGCATGAATTTATTGGATGACAAGA 59.877 33.333 0.00 0.00 40.16 3.02
1671 2514 8.195436 GGGCAATTAGGAAATTTAAAGACTACC 58.805 37.037 0.00 0.00 32.87 3.18
1676 2519 8.429237 TTCAGGGCAATTAGGAAATTTAAAGA 57.571 30.769 0.00 0.00 32.87 2.52
1688 2531 5.419239 TTTGGGAATTTCAGGGCAATTAG 57.581 39.130 0.00 0.00 0.00 1.73
1694 2537 4.650734 TGAATTTTTGGGAATTTCAGGGC 58.349 39.130 0.00 0.00 29.75 5.19
1800 2655 7.256286 GTGTGTAGGTACTATTTGACTACTGG 58.744 42.308 0.00 0.00 45.60 4.00
1885 3221 2.629051 ACAGCAAGACCCGTTATTAGC 58.371 47.619 0.00 0.00 0.00 3.09
1929 3265 3.182967 GACGCGATCTTGTCTTCTTGAT 58.817 45.455 15.93 0.00 32.37 2.57
1969 3305 5.508153 CCTCTCGTTCTCTTTTCTGACTTCA 60.508 44.000 0.00 0.00 0.00 3.02
2055 3391 2.045536 GCCCTTGCTGGTGGAGAG 60.046 66.667 0.00 0.00 33.53 3.20
2123 3459 0.779997 AACCCAGGCTCCTTGACATT 59.220 50.000 0.00 0.00 0.00 2.71
2459 3816 2.036256 CACCCTGGCCTTCTTGGG 59.964 66.667 3.32 10.37 44.89 4.12
2756 4411 1.447140 GCACCCTGTTGCGATCGTA 60.447 57.895 17.81 9.90 31.51 3.43
3394 8427 4.663636 ACGCAACTGTTAAAGCATCTAC 57.336 40.909 0.00 0.00 0.00 2.59
3601 8706 7.148590 GGAAAAACATAAATGCATGGTCACTTC 60.149 37.037 0.00 0.00 0.00 3.01
3744 8854 0.393402 GCCTGACATGAGCATGGACA 60.393 55.000 14.35 12.08 42.91 4.02
4235 9354 2.808315 CTGGTAGAGCGATGCCGT 59.192 61.111 0.00 0.00 38.24 5.68
4408 9527 2.599281 TCGCCTCCTGTTGTCGGA 60.599 61.111 0.00 0.00 0.00 4.55
4531 9930 1.812571 CCATTTGGAGAACCGTTCTGG 59.187 52.381 18.59 9.24 40.87 3.86
4740 10164 2.821969 AGGCTGTGAATGGTGAATCAAC 59.178 45.455 0.00 0.00 0.00 3.18
4847 10272 8.471609 GCCTAGTTACTCTCTTATCTGAGTTTT 58.528 37.037 0.00 0.00 42.67 2.43
4961 10386 9.559958 GATTACTTGTTTCCACTGTATTTCATG 57.440 33.333 0.00 0.00 0.00 3.07
5409 10873 2.781431 ATTTGGGTGACTTCGGCCCC 62.781 60.000 0.00 0.00 41.66 5.80
5551 11410 5.222233 TGGGTGAGATTGTTTCAATCCCTTA 60.222 40.000 15.81 5.07 33.52 2.69


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

AutoCloner maintained by Alex Coulton.