Multiple sequence alignment - TraesCS2A01G188700

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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 TraesCS2A01G188700 chr2A 100.000 3683 0 0 1 3683 154423828 154420146 0.000000e+00 6802
1 TraesCS2A01G188700 chr2A 82.736 1367 226 9 1263 2624 155074674 155073313 0.000000e+00 1208
2 TraesCS2A01G188700 chr2A 86.022 186 23 3 3464 3648 384552328 384552511 2.900000e-46 196
3 TraesCS2A01G188700 chr2D 92.754 2774 132 27 596 3346 147953070 147955797 0.000000e+00 3945
4 TraesCS2A01G188700 chr2D 82.151 1367 234 9 1263 2624 147426250 147427611 0.000000e+00 1164
5 TraesCS2A01G188700 chr2D 93.980 299 16 1 300 598 147948231 147948527 5.610000e-123 451
6 TraesCS2A01G188700 chr2D 92.021 188 14 1 3464 3650 147955803 147955990 2.820000e-66 263
7 TraesCS2A01G188700 chr2D 82.581 310 29 15 1 300 456965747 456966041 2.200000e-62 250
8 TraesCS2A01G188700 chr2D 76.901 342 48 13 3033 3345 375263374 375263035 8.180000e-37 165
9 TraesCS2A01G188700 chr2D 88.710 124 13 1 3223 3345 375262695 375262572 2.290000e-32 150
10 TraesCS2A01G188700 chr2D 88.189 127 13 2 3344 3468 441085766 441085892 2.290000e-32 150
11 TraesCS2A01G188700 chr2D 86.331 139 16 3 3334 3469 95519531 95519669 8.240000e-32 148
12 TraesCS2A01G188700 chr2B 96.225 1881 65 6 911 2789 207481924 207483800 0.000000e+00 3075
13 TraesCS2A01G188700 chr2B 94.472 398 16 3 300 697 207481244 207481635 3.150000e-170 608
14 TraesCS2A01G188700 chr2B 82.154 325 28 17 1 298 456620435 456620756 6.110000e-63 252
15 TraesCS2A01G188700 chr2B 89.231 130 11 3 3338 3465 729806042 729806170 3.810000e-35 159
16 TraesCS2A01G188700 chr2B 86.232 138 13 6 3330 3464 89499080 89498946 1.070000e-30 145
17 TraesCS2A01G188700 chr2B 84.277 159 7 5 696 849 207481739 207481884 4.960000e-29 139
18 TraesCS2A01G188700 chr2B 77.419 279 32 21 44 298 792151237 792150966 1.780000e-28 137
19 TraesCS2A01G188700 chr3B 89.933 1927 136 24 807 2710 64537900 64539791 0.000000e+00 2431
20 TraesCS2A01G188700 chr3B 79.310 261 32 15 61 301 735584620 735584362 2.940000e-36 163
21 TraesCS2A01G188700 chr3B 89.231 130 13 1 3218 3346 794320672 794320801 1.060000e-35 161
22 TraesCS2A01G188700 chr1D 86.671 1673 191 23 1035 2683 483972589 483974253 0.000000e+00 1825
23 TraesCS2A01G188700 chr1D 77.681 345 54 10 3024 3345 313381249 313381593 4.860000e-44 189
24 TraesCS2A01G188700 chr1D 85.106 188 24 4 3464 3650 424526132 424525948 4.860000e-44 189
25 TraesCS2A01G188700 chr1A 86.155 1654 193 23 1055 2683 580988276 580989918 0.000000e+00 1753
26 TraesCS2A01G188700 chr1A 84.768 302 34 12 1 297 451518042 451517748 3.600000e-75 292
27 TraesCS2A01G188700 chr1B 85.741 1592 194 24 1088 2659 673992230 673993808 0.000000e+00 1652
28 TraesCS2A01G188700 chr1B 88.000 1375 159 5 1262 2633 674004544 674003173 0.000000e+00 1620
29 TraesCS2A01G188700 chr1B 89.062 128 14 0 3218 3345 175929103 175929230 3.810000e-35 159
30 TraesCS2A01G188700 chr1B 79.508 244 26 16 67 295 657522595 657522829 6.370000e-33 152
31 TraesCS2A01G188700 chr1B 79.098 244 27 16 67 295 657540719 657540953 2.960000e-31 147
32 TraesCS2A01G188700 chr6D 82.716 324 24 17 1 298 2936813 2936496 3.650000e-65 259
33 TraesCS2A01G188700 chr6D 80.189 318 40 19 2 301 456689595 456689283 2.230000e-52 217
34 TraesCS2A01G188700 chr6D 77.222 360 55 14 3006 3346 182324649 182325000 6.280000e-43 185
35 TraesCS2A01G188700 chr6D 84.043 188 23 6 3464 3649 456371666 456371848 1.360000e-39 174
36 TraesCS2A01G188700 chr6D 86.111 144 16 4 3334 3475 366701097 366701238 6.370000e-33 152
37 TraesCS2A01G188700 chr6D 87.313 134 14 3 3332 3464 142147458 142147589 2.290000e-32 150
38 TraesCS2A01G188700 chr6D 86.131 137 16 3 3342 3476 48675624 48675759 1.070000e-30 145
39 TraesCS2A01G188700 chr6D 90.698 86 8 0 212 297 458096426 458096511 8.360000e-22 115
40 TraesCS2A01G188700 chr7B 82.263 327 22 12 5 298 65307268 65307591 2.200000e-62 250
41 TraesCS2A01G188700 chr7B 84.874 119 14 4 184 299 599254981 599254864 2.320000e-22 117
42 TraesCS2A01G188700 chr5D 87.766 188 21 2 3464 3650 375754058 375753872 6.190000e-53 219
43 TraesCS2A01G188700 chr5D 91.603 131 8 3 3217 3345 216158722 216158851 1.050000e-40 178
44 TraesCS2A01G188700 chr5D 83.871 186 27 3 3464 3648 23652933 23653116 1.360000e-39 174
45 TraesCS2A01G188700 chr5D 87.218 133 14 3 3335 3466 37143263 37143393 8.240000e-32 148
46 TraesCS2A01G188700 chr7D 79.240 342 42 14 3019 3336 535507954 535507618 1.040000e-50 211
47 TraesCS2A01G188700 chr7D 86.096 187 23 3 3464 3650 535507604 535507421 8.070000e-47 198
48 TraesCS2A01G188700 chr4B 87.234 188 21 3 3464 3650 648569043 648568858 1.040000e-50 211
49 TraesCS2A01G188700 chr4B 78.333 360 50 16 3010 3345 592622043 592621688 1.340000e-49 207
50 TraesCS2A01G188700 chr5B 86.170 188 24 2 3464 3650 690698754 690698568 6.240000e-48 202
51 TraesCS2A01G188700 chr5B 76.577 333 37 25 1 301 383156784 383156461 1.070000e-30 145
52 TraesCS2A01G188700 chr4A 84.896 192 18 4 68 248 471164994 471165185 2.260000e-42 183
53 TraesCS2A01G188700 chr4A 86.755 151 17 3 3340 3489 153242615 153242467 8.180000e-37 165
54 TraesCS2A01G188700 chr3A 78.431 306 42 14 3063 3346 623795622 623795925 1.050000e-40 178
55 TraesCS2A01G188700 chr6A 88.976 127 12 2 3220 3346 566447352 566447228 4.920000e-34 156
56 TraesCS2A01G188700 chr5A 76.821 302 46 14 1 295 618339528 618339244 8.240000e-32 148
57 TraesCS2A01G188700 chr4D 76.393 305 46 18 1 297 231200209 231199923 1.380000e-29 141


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 TraesCS2A01G188700 chr2A 154420146 154423828 3682 True 6802.0 6802 100.0000 1 3683 1 chr2A.!!$R1 3682
1 TraesCS2A01G188700 chr2A 155073313 155074674 1361 True 1208.0 1208 82.7360 1263 2624 1 chr2A.!!$R2 1361
2 TraesCS2A01G188700 chr2D 147953070 147955990 2920 False 2104.0 3945 92.3875 596 3650 2 chr2D.!!$F6 3054
3 TraesCS2A01G188700 chr2D 147426250 147427611 1361 False 1164.0 1164 82.1510 1263 2624 1 chr2D.!!$F2 1361
4 TraesCS2A01G188700 chr2B 207481244 207483800 2556 False 1274.0 3075 91.6580 300 2789 3 chr2B.!!$F3 2489
5 TraesCS2A01G188700 chr3B 64537900 64539791 1891 False 2431.0 2431 89.9330 807 2710 1 chr3B.!!$F1 1903
6 TraesCS2A01G188700 chr1D 483972589 483974253 1664 False 1825.0 1825 86.6710 1035 2683 1 chr1D.!!$F2 1648
7 TraesCS2A01G188700 chr1A 580988276 580989918 1642 False 1753.0 1753 86.1550 1055 2683 1 chr1A.!!$F1 1628
8 TraesCS2A01G188700 chr1B 673992230 673993808 1578 False 1652.0 1652 85.7410 1088 2659 1 chr1B.!!$F4 1571
9 TraesCS2A01G188700 chr1B 674003173 674004544 1371 True 1620.0 1620 88.0000 1262 2633 1 chr1B.!!$R1 1371
10 TraesCS2A01G188700 chr7D 535507421 535507954 533 True 204.5 211 82.6680 3019 3650 2 chr7D.!!$R1 631

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
203 204 0.095245 CTGGCTGTTGCGATTGTACG 59.905 55.000 0.00 0.0 40.82 3.67 F
952 1081 0.392706 ACGGCAGTTCACTCATCACA 59.607 50.000 0.00 0.0 0.00 3.58 F
1164 1307 1.077501 CATGGCCACCATCGTCCTT 60.078 57.895 8.16 0.0 43.15 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1164 1307 0.390603 GCATGTGTGTACCGTAGCCA 60.391 55.000 0.00 0.00 0.0 4.75 R
2643 2822 1.007387 CGCCTTGTCTTTTGTGGCC 60.007 57.895 0.00 0.00 40.4 5.36 R
3034 3225 1.006571 TGAACCGACGGAAGCACTC 60.007 57.895 23.38 7.32 0.0 3.51 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
37 38 9.581099 AAAACAATTTTCGAACATGAACTTAGT 57.419 25.926 0.00 0.00 0.00 2.24
38 39 9.581099 AAACAATTTTCGAACATGAACTTAGTT 57.419 25.926 0.00 0.00 0.00 2.24
39 40 9.581099 AACAATTTTCGAACATGAACTTAGTTT 57.419 25.926 0.00 0.00 0.00 2.66
40 41 9.581099 ACAATTTTCGAACATGAACTTAGTTTT 57.419 25.926 0.00 0.00 0.00 2.43
180 181 3.898517 CCTTCAGAAGGTTCCGAAAAC 57.101 47.619 20.07 0.00 43.95 2.43
181 182 2.552743 CCTTCAGAAGGTTCCGAAAACC 59.447 50.000 20.07 10.67 43.95 3.27
182 183 3.211045 CTTCAGAAGGTTCCGAAAACCA 58.789 45.455 18.25 0.00 42.69 3.67
183 184 2.846193 TCAGAAGGTTCCGAAAACCAG 58.154 47.619 18.25 8.10 42.69 4.00
184 185 1.266989 CAGAAGGTTCCGAAAACCAGC 59.733 52.381 18.25 11.11 42.69 4.85
185 186 1.143073 AGAAGGTTCCGAAAACCAGCT 59.857 47.619 18.25 12.70 42.69 4.24
186 187 1.266989 GAAGGTTCCGAAAACCAGCTG 59.733 52.381 18.25 6.78 42.69 4.24
187 188 0.537371 AGGTTCCGAAAACCAGCTGG 60.537 55.000 31.60 31.60 42.69 4.85
188 189 1.285950 GTTCCGAAAACCAGCTGGC 59.714 57.895 33.06 15.27 39.32 4.85
189 190 1.150536 TTCCGAAAACCAGCTGGCT 59.849 52.632 33.06 19.23 39.32 4.75
190 191 1.172180 TTCCGAAAACCAGCTGGCTG 61.172 55.000 33.06 16.84 43.26 4.85
191 192 1.898574 CCGAAAACCAGCTGGCTGT 60.899 57.895 33.06 16.94 42.15 4.40
192 193 1.455383 CCGAAAACCAGCTGGCTGTT 61.455 55.000 33.06 22.71 42.15 3.16
193 194 0.318107 CGAAAACCAGCTGGCTGTTG 60.318 55.000 33.06 16.23 42.15 3.33
194 195 0.598419 GAAAACCAGCTGGCTGTTGC 60.598 55.000 33.06 18.54 42.15 4.17
195 196 2.354074 AAAACCAGCTGGCTGTTGCG 62.354 55.000 33.06 6.74 42.15 4.85
196 197 3.772853 AACCAGCTGGCTGTTGCGA 62.773 57.895 33.06 0.00 42.15 5.10
197 198 2.749044 CCAGCTGGCTGTTGCGAT 60.749 61.111 22.33 0.00 42.15 4.58
198 199 2.338015 CCAGCTGGCTGTTGCGATT 61.338 57.895 22.33 0.00 42.15 3.34
199 200 1.154093 CAGCTGGCTGTTGCGATTG 60.154 57.895 13.76 0.00 40.82 2.67
200 201 1.601759 AGCTGGCTGTTGCGATTGT 60.602 52.632 0.00 0.00 40.82 2.71
201 202 0.321564 AGCTGGCTGTTGCGATTGTA 60.322 50.000 0.00 0.00 40.82 2.41
202 203 0.179189 GCTGGCTGTTGCGATTGTAC 60.179 55.000 0.00 0.00 40.82 2.90
203 204 0.095245 CTGGCTGTTGCGATTGTACG 59.905 55.000 0.00 0.00 40.82 3.67
215 216 3.479006 CGATTGTACGCTCAAAAACTGG 58.521 45.455 0.00 0.00 0.00 4.00
216 217 3.666902 CGATTGTACGCTCAAAAACTGGG 60.667 47.826 0.00 0.00 0.00 4.45
220 221 2.650778 GCTCAAAAACTGGGCCGG 59.349 61.111 11.83 11.83 46.91 6.13
221 222 2.650778 CTCAAAAACTGGGCCGGC 59.349 61.111 21.18 21.18 0.00 6.13
222 223 2.915137 TCAAAAACTGGGCCGGCC 60.915 61.111 38.57 38.57 0.00 6.13
250 251 4.406173 CTGCTCGGTCGCTCGTGT 62.406 66.667 0.00 0.00 0.00 4.49
251 252 3.035576 CTGCTCGGTCGCTCGTGTA 62.036 63.158 0.00 0.00 0.00 2.90
252 253 2.324332 CTGCTCGGTCGCTCGTGTAT 62.324 60.000 0.00 0.00 0.00 2.29
253 254 1.939785 GCTCGGTCGCTCGTGTATG 60.940 63.158 0.00 0.00 0.00 2.39
254 255 1.298413 CTCGGTCGCTCGTGTATGG 60.298 63.158 0.00 0.00 0.00 2.74
255 256 2.278596 CGGTCGCTCGTGTATGGG 60.279 66.667 0.00 0.00 0.00 4.00
256 257 2.767445 CGGTCGCTCGTGTATGGGA 61.767 63.158 0.00 0.00 0.00 4.37
257 258 1.514087 GGTCGCTCGTGTATGGGAA 59.486 57.895 0.00 0.00 0.00 3.97
258 259 0.527817 GGTCGCTCGTGTATGGGAAG 60.528 60.000 0.00 0.00 0.00 3.46
259 260 1.141019 TCGCTCGTGTATGGGAAGC 59.859 57.895 0.00 0.00 0.00 3.86
260 261 2.230940 CGCTCGTGTATGGGAAGCG 61.231 63.158 0.38 0.38 37.93 4.68
261 262 2.526120 GCTCGTGTATGGGAAGCGC 61.526 63.158 0.00 0.00 0.00 5.92
262 263 2.202690 TCGTGTATGGGAAGCGCG 60.203 61.111 0.00 0.00 37.46 6.86
263 264 3.261951 CGTGTATGGGAAGCGCGG 61.262 66.667 8.83 0.00 33.22 6.46
264 265 2.895372 GTGTATGGGAAGCGCGGG 60.895 66.667 8.83 0.00 0.00 6.13
265 266 4.849310 TGTATGGGAAGCGCGGGC 62.849 66.667 17.92 17.92 40.37 6.13
266 267 4.849310 GTATGGGAAGCGCGGGCA 62.849 66.667 27.20 5.46 43.41 5.36
267 268 4.545706 TATGGGAAGCGCGGGCAG 62.546 66.667 27.20 0.00 43.41 4.85
271 272 4.404654 GGAAGCGCGGGCAGTTTG 62.405 66.667 27.20 0.00 43.41 2.93
272 273 3.353836 GAAGCGCGGGCAGTTTGA 61.354 61.111 27.20 0.00 43.41 2.69
273 274 3.595108 GAAGCGCGGGCAGTTTGAC 62.595 63.158 27.20 5.61 43.41 3.18
278 279 2.718731 CGGGCAGTTTGACGCAAA 59.281 55.556 1.63 1.63 0.00 3.68
279 280 1.370414 CGGGCAGTTTGACGCAAAG 60.370 57.895 5.45 0.00 33.82 2.77
280 281 1.733526 GGGCAGTTTGACGCAAAGT 59.266 52.632 5.45 6.15 37.47 2.66
294 295 3.764885 GCAAAGTGCGTCAAATAGGAT 57.235 42.857 0.00 0.00 31.71 3.24
295 296 4.096732 GCAAAGTGCGTCAAATAGGATT 57.903 40.909 0.00 0.00 31.71 3.01
296 297 4.485163 GCAAAGTGCGTCAAATAGGATTT 58.515 39.130 0.00 0.00 31.71 2.17
297 298 4.558860 GCAAAGTGCGTCAAATAGGATTTC 59.441 41.667 0.00 0.00 31.71 2.17
298 299 4.600012 AAGTGCGTCAAATAGGATTTCG 57.400 40.909 0.00 0.00 0.00 3.46
303 304 3.302740 GCGTCAAATAGGATTTCGCTGAG 60.303 47.826 9.47 0.00 39.26 3.35
332 333 2.510012 CAGCCAGCGATTCAGCGA 60.510 61.111 0.00 0.00 43.00 4.93
341 342 1.944676 GATTCAGCGAGCGTACCCG 60.945 63.158 0.00 0.00 37.07 5.28
445 446 0.663153 AGCAGTCCAAGTTTCAACGC 59.337 50.000 0.00 0.00 0.00 4.84
446 447 0.657368 GCAGTCCAAGTTTCAACGCG 60.657 55.000 3.53 3.53 0.00 6.01
447 448 0.655733 CAGTCCAAGTTTCAACGCGT 59.344 50.000 5.58 5.58 0.00 6.01
448 449 0.655733 AGTCCAAGTTTCAACGCGTG 59.344 50.000 14.98 7.52 0.00 5.34
474 475 1.745489 GTTGAGTGGACATCCGGGC 60.745 63.158 0.00 0.00 39.43 6.13
503 504 1.751351 CATACCAGAGCGGACAAGAGA 59.249 52.381 0.00 0.00 38.63 3.10
511 512 1.515952 CGGACAAGAGAGCAGCGAG 60.516 63.158 0.00 0.00 0.00 5.03
607 608 2.187946 GATGTAGCCAGCCAGCGT 59.812 61.111 0.00 0.00 38.01 5.07
610 611 1.308069 ATGTAGCCAGCCAGCGTTTG 61.308 55.000 0.00 0.00 38.01 2.93
611 612 3.055719 TAGCCAGCCAGCGTTTGC 61.056 61.111 0.00 0.00 43.24 3.68
697 698 0.988832 TTGGGCCACGTTCTTCCTAT 59.011 50.000 5.23 0.00 0.00 2.57
699 805 1.339631 TGGGCCACGTTCTTCCTATTG 60.340 52.381 0.00 0.00 0.00 1.90
773 879 3.696281 TGCACATACATTATGCAGCAC 57.304 42.857 0.00 0.00 44.17 4.40
794 900 4.681942 CACGTCTATGCTACCTGCTAAATC 59.318 45.833 0.00 0.00 43.37 2.17
795 901 4.341235 ACGTCTATGCTACCTGCTAAATCA 59.659 41.667 0.00 0.00 43.37 2.57
878 1007 6.600822 GTGCACCCATATCATAAGAGCATAAT 59.399 38.462 5.22 0.00 0.00 1.28
906 1035 8.489990 TCGGTGTCTATATAAGAGTGCTATAC 57.510 38.462 0.00 0.00 33.88 1.47
907 1036 8.319881 TCGGTGTCTATATAAGAGTGCTATACT 58.680 37.037 0.00 0.00 44.02 2.12
908 1037 9.597170 CGGTGTCTATATAAGAGTGCTATACTA 57.403 37.037 0.00 0.00 40.53 1.82
952 1081 0.392706 ACGGCAGTTCACTCATCACA 59.607 50.000 0.00 0.00 0.00 3.58
958 1088 2.095869 CAGTTCACTCATCACAAGCTGC 60.096 50.000 0.00 0.00 0.00 5.25
972 1102 1.342074 AGCTGCCAGTCTGTCTGTTA 58.658 50.000 0.00 0.00 42.19 2.41
973 1103 1.274728 AGCTGCCAGTCTGTCTGTTAG 59.725 52.381 0.00 1.03 42.19 2.34
1021 1151 4.938226 AGATGAAAATGTCTCCGGAAAGAC 59.062 41.667 15.21 15.21 44.87 3.01
1072 1209 3.326646 ATGGCTTCTGCTGCGCTCT 62.327 57.895 9.73 0.00 39.59 4.09
1164 1307 1.077501 CATGGCCACCATCGTCCTT 60.078 57.895 8.16 0.00 43.15 3.36
1572 1745 3.740397 TACACGGCCGAGGTGTCG 61.740 66.667 35.90 12.70 44.93 4.35
1833 2006 2.600769 AAGACCTCCGACACGCCT 60.601 61.111 0.00 0.00 0.00 5.52
1973 2146 1.359848 GAGCTCATCTTTTCGCCGAA 58.640 50.000 9.40 0.00 0.00 4.30
2112 2285 2.358737 GACAACCACCTGCTCGGG 60.359 66.667 0.00 0.00 36.97 5.14
2643 2822 2.372690 CGTCGAAGCCCAAGACACG 61.373 63.158 0.00 0.00 34.80 4.49
2649 2828 4.947147 GCCCAAGACACGGCCACA 62.947 66.667 2.24 0.00 39.39 4.17
2667 2846 3.108144 CACAAAAGACAAGGCGAAAGTG 58.892 45.455 0.00 0.00 0.00 3.16
2710 2895 3.290948 AAAGTCACCCAACTGTTGCTA 57.709 42.857 14.94 0.00 0.00 3.49
2722 2910 6.112734 CCAACTGTTGCTAATGTACCATAGA 58.887 40.000 14.94 0.00 0.00 1.98
2792 2981 4.082081 TGCTCATTGATGGATTGTTTGGAC 60.082 41.667 0.00 0.00 0.00 4.02
2830 3019 7.972277 AGAATTGTTTCAAGATTGGATCAATCG 59.028 33.333 13.00 3.17 42.77 3.34
2856 3046 4.997905 AACGTTGACATGACATCTCTTG 57.002 40.909 0.00 0.00 0.00 3.02
2860 3050 1.065199 TGACATGACATCTCTTGGCCC 60.065 52.381 0.00 0.00 29.87 5.80
2871 3061 3.346631 CTTGGCCCGTTGATGCTGC 62.347 63.158 0.00 0.00 0.00 5.25
2886 3076 1.293963 GCTGCTCAGCGTGTCATTGA 61.294 55.000 6.08 0.00 45.29 2.57
2887 3077 1.366679 CTGCTCAGCGTGTCATTGAT 58.633 50.000 0.00 0.00 0.00 2.57
2903 3094 6.016860 TGTCATTGATATCCATTAGCACTTGC 60.017 38.462 0.00 0.00 42.49 4.01
2938 3129 5.278660 GGATAGCTTTATCTGGTGGCATTTG 60.279 44.000 0.00 0.00 0.00 2.32
2961 3152 3.849708 GCATTTGTTCGGTTAAATCGTCC 59.150 43.478 0.45 0.00 0.00 4.79
2963 3154 5.695818 CATTTGTTCGGTTAAATCGTCCTT 58.304 37.500 0.45 0.00 0.00 3.36
3050 3241 2.342648 GGAGTGCTTCCGTCGGTT 59.657 61.111 11.88 0.00 35.91 4.44
3053 3244 1.282930 GAGTGCTTCCGTCGGTTCAC 61.283 60.000 11.88 16.17 0.00 3.18
3054 3245 2.029964 TGCTTCCGTCGGTTCACC 59.970 61.111 11.88 0.00 0.00 4.02
3073 3266 6.489127 TCACCGTCACACCATTTTATAAAG 57.511 37.500 0.00 0.00 0.00 1.85
3075 3268 6.882140 TCACCGTCACACCATTTTATAAAGAT 59.118 34.615 0.00 0.00 0.00 2.40
3076 3269 7.065324 TCACCGTCACACCATTTTATAAAGATC 59.935 37.037 0.00 0.00 0.00 2.75
3081 3274 7.996644 GTCACACCATTTTATAAAGATCCCCTA 59.003 37.037 0.00 0.00 0.00 3.53
3086 3279 9.588096 ACCATTTTATAAAGATCCCCTATGTTC 57.412 33.333 0.00 0.00 0.00 3.18
3248 3462 5.822519 TCAGTTAATCAATCCGCAGCTTATT 59.177 36.000 0.00 0.00 0.00 1.40
3252 3466 8.129211 AGTTAATCAATCCGCAGCTTATTTAAC 58.871 33.333 0.00 0.00 0.00 2.01
3355 3570 9.836179 AGAATCTAAATATGATACTCCCTCTGT 57.164 33.333 0.00 0.00 0.00 3.41
3357 3572 8.602472 ATCTAAATATGATACTCCCTCTGTCC 57.398 38.462 0.00 0.00 0.00 4.02
3358 3573 5.730296 AAATATGATACTCCCTCTGTCCG 57.270 43.478 0.00 0.00 0.00 4.79
3359 3574 4.659529 ATATGATACTCCCTCTGTCCGA 57.340 45.455 0.00 0.00 0.00 4.55
3360 3575 2.820728 TGATACTCCCTCTGTCCGAA 57.179 50.000 0.00 0.00 0.00 4.30
3361 3576 3.095912 TGATACTCCCTCTGTCCGAAA 57.904 47.619 0.00 0.00 0.00 3.46
3362 3577 3.437213 TGATACTCCCTCTGTCCGAAAA 58.563 45.455 0.00 0.00 0.00 2.29
3363 3578 4.030913 TGATACTCCCTCTGTCCGAAAAT 58.969 43.478 0.00 0.00 0.00 1.82
3364 3579 5.205821 TGATACTCCCTCTGTCCGAAAATA 58.794 41.667 0.00 0.00 0.00 1.40
3365 3580 3.889520 ACTCCCTCTGTCCGAAAATAC 57.110 47.619 0.00 0.00 0.00 1.89
3366 3581 3.442076 ACTCCCTCTGTCCGAAAATACT 58.558 45.455 0.00 0.00 0.00 2.12
3367 3582 3.838903 ACTCCCTCTGTCCGAAAATACTT 59.161 43.478 0.00 0.00 0.00 2.24
3368 3583 4.184629 CTCCCTCTGTCCGAAAATACTTG 58.815 47.826 0.00 0.00 0.00 3.16
3369 3584 3.581332 TCCCTCTGTCCGAAAATACTTGT 59.419 43.478 0.00 0.00 0.00 3.16
3370 3585 3.933332 CCCTCTGTCCGAAAATACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
3371 3586 4.562757 CCCTCTGTCCGAAAATACTTGTCA 60.563 45.833 0.00 0.00 0.00 3.58
3372 3587 4.389077 CCTCTGTCCGAAAATACTTGTCAC 59.611 45.833 0.00 0.00 0.00 3.67
3373 3588 5.209818 TCTGTCCGAAAATACTTGTCACT 57.790 39.130 0.00 0.00 0.00 3.41
3374 3589 4.988540 TCTGTCCGAAAATACTTGTCACTG 59.011 41.667 0.00 0.00 0.00 3.66
3375 3590 4.951254 TGTCCGAAAATACTTGTCACTGA 58.049 39.130 0.00 0.00 0.00 3.41
3376 3591 5.361427 TGTCCGAAAATACTTGTCACTGAA 58.639 37.500 0.00 0.00 0.00 3.02
3377 3592 5.818336 TGTCCGAAAATACTTGTCACTGAAA 59.182 36.000 0.00 0.00 0.00 2.69
3378 3593 6.485313 TGTCCGAAAATACTTGTCACTGAAAT 59.515 34.615 0.00 0.00 0.00 2.17
3379 3594 6.797033 GTCCGAAAATACTTGTCACTGAAATG 59.203 38.462 0.00 0.00 0.00 2.32
3380 3595 6.072728 TCCGAAAATACTTGTCACTGAAATGG 60.073 38.462 0.00 0.00 0.00 3.16
3381 3596 6.072728 CCGAAAATACTTGTCACTGAAATGGA 60.073 38.462 0.00 0.00 0.00 3.41
3382 3597 7.362056 CCGAAAATACTTGTCACTGAAATGGAT 60.362 37.037 0.00 0.00 0.00 3.41
3383 3598 7.482743 CGAAAATACTTGTCACTGAAATGGATG 59.517 37.037 0.00 0.00 0.00 3.51
3384 3599 8.408043 AAAATACTTGTCACTGAAATGGATGA 57.592 30.769 0.00 0.00 0.00 2.92
3385 3600 8.408043 AAATACTTGTCACTGAAATGGATGAA 57.592 30.769 0.00 0.00 0.00 2.57
3386 3601 8.408043 AATACTTGTCACTGAAATGGATGAAA 57.592 30.769 0.00 0.00 0.00 2.69
3387 3602 6.076981 ACTTGTCACTGAAATGGATGAAAC 57.923 37.500 0.00 0.00 0.00 2.78
3388 3603 4.747540 TGTCACTGAAATGGATGAAACG 57.252 40.909 0.00 0.00 0.00 3.60
3389 3604 4.384940 TGTCACTGAAATGGATGAAACGA 58.615 39.130 0.00 0.00 0.00 3.85
3390 3605 4.819088 TGTCACTGAAATGGATGAAACGAA 59.181 37.500 0.00 0.00 0.00 3.85
3391 3606 5.473162 TGTCACTGAAATGGATGAAACGAAT 59.527 36.000 0.00 0.00 0.00 3.34
3392 3607 5.796935 GTCACTGAAATGGATGAAACGAATG 59.203 40.000 0.00 0.00 0.00 2.67
3393 3608 5.473162 TCACTGAAATGGATGAAACGAATGT 59.527 36.000 0.00 0.00 0.00 2.71
3394 3609 6.652900 TCACTGAAATGGATGAAACGAATGTA 59.347 34.615 0.00 0.00 0.00 2.29
3395 3610 6.963242 CACTGAAATGGATGAAACGAATGTAG 59.037 38.462 0.00 0.00 0.00 2.74
3396 3611 6.655003 ACTGAAATGGATGAAACGAATGTAGT 59.345 34.615 0.00 0.00 0.00 2.73
3397 3612 7.174946 ACTGAAATGGATGAAACGAATGTAGTT 59.825 33.333 0.00 0.00 0.00 2.24
3398 3613 8.554835 TGAAATGGATGAAACGAATGTAGTTA 57.445 30.769 0.00 0.00 0.00 2.24
3399 3614 8.664798 TGAAATGGATGAAACGAATGTAGTTAG 58.335 33.333 0.00 0.00 0.00 2.34
3400 3615 8.786826 AAATGGATGAAACGAATGTAGTTAGA 57.213 30.769 0.00 0.00 0.00 2.10
3401 3616 8.786826 AATGGATGAAACGAATGTAGTTAGAA 57.213 30.769 0.00 0.00 0.00 2.10
3402 3617 7.591006 TGGATGAAACGAATGTAGTTAGAAC 57.409 36.000 0.00 0.00 0.00 3.01
3403 3618 7.383687 TGGATGAAACGAATGTAGTTAGAACT 58.616 34.615 0.00 0.00 42.91 3.01
3404 3619 8.525316 TGGATGAAACGAATGTAGTTAGAACTA 58.475 33.333 0.00 0.00 40.37 2.24
3405 3620 9.362539 GGATGAAACGAATGTAGTTAGAACTAA 57.637 33.333 3.72 0.00 42.66 2.24
3433 3648 6.332735 TGTCTAGATACATCCATTTCTCCG 57.667 41.667 0.00 0.00 0.00 4.63
3434 3649 6.068670 TGTCTAGATACATCCATTTCTCCGA 58.931 40.000 0.00 0.00 0.00 4.55
3435 3650 6.016192 TGTCTAGATACATCCATTTCTCCGAC 60.016 42.308 0.00 0.00 0.00 4.79
3436 3651 6.016192 GTCTAGATACATCCATTTCTCCGACA 60.016 42.308 0.00 0.00 0.00 4.35
3437 3652 5.614324 AGATACATCCATTTCTCCGACAA 57.386 39.130 0.00 0.00 0.00 3.18
3438 3653 5.605534 AGATACATCCATTTCTCCGACAAG 58.394 41.667 0.00 0.00 0.00 3.16
3439 3654 3.703001 ACATCCATTTCTCCGACAAGT 57.297 42.857 0.00 0.00 0.00 3.16
3440 3655 4.819105 ACATCCATTTCTCCGACAAGTA 57.181 40.909 0.00 0.00 0.00 2.24
3441 3656 5.359194 ACATCCATTTCTCCGACAAGTAT 57.641 39.130 0.00 0.00 0.00 2.12
3442 3657 5.745227 ACATCCATTTCTCCGACAAGTATT 58.255 37.500 0.00 0.00 0.00 1.89
3443 3658 6.180472 ACATCCATTTCTCCGACAAGTATTT 58.820 36.000 0.00 0.00 0.00 1.40
3444 3659 6.316390 ACATCCATTTCTCCGACAAGTATTTC 59.684 38.462 0.00 0.00 0.00 2.17
3445 3660 5.183228 TCCATTTCTCCGACAAGTATTTCC 58.817 41.667 0.00 0.00 0.00 3.13
3446 3661 4.034048 CCATTTCTCCGACAAGTATTTCCG 59.966 45.833 0.00 0.00 0.00 4.30
3447 3662 2.953466 TCTCCGACAAGTATTTCCGG 57.047 50.000 0.00 0.00 41.36 5.14
3448 3663 2.449464 TCTCCGACAAGTATTTCCGGA 58.551 47.619 0.00 0.00 45.74 5.14
3449 3664 3.028850 TCTCCGACAAGTATTTCCGGAT 58.971 45.455 4.15 0.00 46.53 4.18
3450 3665 3.123804 CTCCGACAAGTATTTCCGGATG 58.876 50.000 4.15 0.97 46.53 3.51
3451 3666 2.159014 TCCGACAAGTATTTCCGGATGG 60.159 50.000 4.15 0.00 43.47 3.51
3452 3667 2.159014 CCGACAAGTATTTCCGGATGGA 60.159 50.000 4.15 0.00 44.61 3.41
3461 3676 2.329111 TCCGGATGGAGGGAGTACT 58.671 57.895 0.00 0.00 40.17 2.73
3462 3677 1.526315 TCCGGATGGAGGGAGTACTA 58.474 55.000 0.00 0.00 40.17 1.82
3522 3738 5.872617 TGCAAACTTAATCTATAGTGCACGT 59.127 36.000 12.01 7.12 0.00 4.49
3553 3769 1.044611 TTCATACCGGCGATGATCCA 58.955 50.000 17.81 3.67 33.41 3.41
3559 3775 1.024271 CCGGCGATGATCCAAATTGT 58.976 50.000 9.30 0.00 0.00 2.71
3572 3788 9.874205 ATGATCCAAATTGTAAATAAACACCTG 57.126 29.630 0.00 0.00 0.00 4.00
3587 3803 9.936759 AATAAACACCTGTTAAAACCATATTGG 57.063 29.630 0.00 0.00 39.54 3.16
3650 3866 3.165498 CCTCGCGAGGGAAAAACG 58.835 61.111 41.47 17.83 44.87 3.60
3651 3867 3.023591 CCTCGCGAGGGAAAAACGC 62.024 63.158 41.47 0.00 44.87 4.84
3673 3889 4.167359 GCGCACGCGAGAGAGAGA 62.167 66.667 15.93 0.00 42.83 3.10
3674 3890 2.022623 CGCACGCGAGAGAGAGAG 59.977 66.667 15.93 0.00 42.83 3.20
3675 3891 2.456948 CGCACGCGAGAGAGAGAGA 61.457 63.158 15.93 0.00 42.83 3.10
3676 3892 1.351707 GCACGCGAGAGAGAGAGAG 59.648 63.158 15.93 0.00 33.96 3.20
3677 3893 1.087202 GCACGCGAGAGAGAGAGAGA 61.087 60.000 15.93 0.00 33.96 3.10
3678 3894 0.930310 CACGCGAGAGAGAGAGAGAG 59.070 60.000 15.93 0.00 33.96 3.20
3679 3895 0.821517 ACGCGAGAGAGAGAGAGAGA 59.178 55.000 15.93 0.00 33.96 3.10
3680 3896 1.202417 ACGCGAGAGAGAGAGAGAGAG 60.202 57.143 15.93 0.00 33.96 3.20
3681 3897 1.067060 CGCGAGAGAGAGAGAGAGAGA 59.933 57.143 0.00 0.00 0.00 3.10
3682 3898 2.748605 GCGAGAGAGAGAGAGAGAGAG 58.251 57.143 0.00 0.00 0.00 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 9.581099 ACTAAGTTCATGTTCGAAAATTGTTTT 57.419 25.926 0.00 0.00 35.12 2.43
12 13 9.581099 AACTAAGTTCATGTTCGAAAATTGTTT 57.419 25.926 0.00 0.00 0.00 2.83
13 14 9.581099 AAACTAAGTTCATGTTCGAAAATTGTT 57.419 25.926 0.00 0.00 0.00 2.83
14 15 9.581099 AAAACTAAGTTCATGTTCGAAAATTGT 57.419 25.926 0.00 0.00 0.00 2.71
150 151 2.784347 CCTTCTGAAGGTTCCCTGAAC 58.216 52.381 25.13 0.00 43.95 3.18
163 164 2.846193 CTGGTTTTCGGAACCTTCTGA 58.154 47.619 18.26 0.00 40.88 3.27
164 165 1.266989 GCTGGTTTTCGGAACCTTCTG 59.733 52.381 18.26 9.82 40.88 3.02
165 166 1.143073 AGCTGGTTTTCGGAACCTTCT 59.857 47.619 18.26 13.20 40.88 2.85
166 167 1.266989 CAGCTGGTTTTCGGAACCTTC 59.733 52.381 18.26 11.71 40.88 3.46
167 168 1.318576 CAGCTGGTTTTCGGAACCTT 58.681 50.000 18.26 5.91 40.88 3.50
168 169 0.537371 CCAGCTGGTTTTCGGAACCT 60.537 55.000 25.53 1.17 40.88 3.50
169 170 1.956802 CCAGCTGGTTTTCGGAACC 59.043 57.895 25.53 12.84 40.67 3.62
170 171 1.172812 AGCCAGCTGGTTTTCGGAAC 61.173 55.000 32.81 13.48 37.57 3.62
171 172 1.150536 AGCCAGCTGGTTTTCGGAA 59.849 52.632 32.81 0.00 37.57 4.30
172 173 1.600636 CAGCCAGCTGGTTTTCGGA 60.601 57.895 32.81 0.00 40.17 4.55
173 174 1.455383 AACAGCCAGCTGGTTTTCGG 61.455 55.000 32.81 18.91 41.95 4.30
174 175 0.318107 CAACAGCCAGCTGGTTTTCG 60.318 55.000 32.81 18.16 41.95 3.46
175 176 0.598419 GCAACAGCCAGCTGGTTTTC 60.598 55.000 32.81 16.86 41.95 2.29
176 177 1.442987 GCAACAGCCAGCTGGTTTT 59.557 52.632 32.81 18.83 41.95 2.43
177 178 2.848858 CGCAACAGCCAGCTGGTTT 61.849 57.895 32.81 20.42 41.95 3.27
178 179 3.289834 CGCAACAGCCAGCTGGTT 61.290 61.111 32.81 25.91 41.95 3.67
179 180 3.557903 ATCGCAACAGCCAGCTGGT 62.558 57.895 32.81 17.48 46.17 4.00
182 183 0.321564 TACAATCGCAACAGCCAGCT 60.322 50.000 0.00 0.00 0.00 4.24
183 184 0.179189 GTACAATCGCAACAGCCAGC 60.179 55.000 0.00 0.00 0.00 4.85
184 185 0.095245 CGTACAATCGCAACAGCCAG 59.905 55.000 0.00 0.00 0.00 4.85
185 186 2.158300 CGTACAATCGCAACAGCCA 58.842 52.632 0.00 0.00 0.00 4.75
194 195 3.479006 CCAGTTTTTGAGCGTACAATCG 58.521 45.455 0.00 0.00 0.00 3.34
195 196 3.821841 CCCAGTTTTTGAGCGTACAATC 58.178 45.455 0.00 0.00 0.00 2.67
196 197 2.030274 GCCCAGTTTTTGAGCGTACAAT 60.030 45.455 0.00 0.00 0.00 2.71
197 198 1.335496 GCCCAGTTTTTGAGCGTACAA 59.665 47.619 0.00 0.00 0.00 2.41
198 199 0.948678 GCCCAGTTTTTGAGCGTACA 59.051 50.000 0.00 0.00 0.00 2.90
199 200 0.240145 GGCCCAGTTTTTGAGCGTAC 59.760 55.000 0.00 0.00 29.94 3.67
200 201 1.231958 CGGCCCAGTTTTTGAGCGTA 61.232 55.000 0.00 0.00 29.94 4.42
201 202 2.551912 CGGCCCAGTTTTTGAGCGT 61.552 57.895 0.00 0.00 29.94 5.07
202 203 2.255252 CGGCCCAGTTTTTGAGCG 59.745 61.111 0.00 0.00 29.94 5.03
203 204 2.650778 CCGGCCCAGTTTTTGAGC 59.349 61.111 0.00 0.00 0.00 4.26
204 205 2.650778 GCCGGCCCAGTTTTTGAG 59.349 61.111 18.11 0.00 0.00 3.02
205 206 2.915137 GGCCGGCCCAGTTTTTGA 60.915 61.111 36.64 0.00 0.00 2.69
233 234 2.324332 ATACACGAGCGACCGAGCAG 62.324 60.000 3.95 0.00 40.15 4.24
234 235 2.404186 ATACACGAGCGACCGAGCA 61.404 57.895 3.95 0.00 40.15 4.26
235 236 1.939785 CATACACGAGCGACCGAGC 60.940 63.158 3.95 0.00 37.41 5.03
236 237 1.298413 CCATACACGAGCGACCGAG 60.298 63.158 3.95 0.00 0.00 4.63
237 238 2.767445 CCCATACACGAGCGACCGA 61.767 63.158 3.95 0.00 0.00 4.69
238 239 2.274232 TTCCCATACACGAGCGACCG 62.274 60.000 0.00 0.00 0.00 4.79
239 240 0.527817 CTTCCCATACACGAGCGACC 60.528 60.000 0.00 0.00 0.00 4.79
240 241 1.146358 GCTTCCCATACACGAGCGAC 61.146 60.000 0.00 0.00 0.00 5.19
241 242 1.141019 GCTTCCCATACACGAGCGA 59.859 57.895 0.00 0.00 0.00 4.93
242 243 3.706140 GCTTCCCATACACGAGCG 58.294 61.111 0.00 0.00 0.00 5.03
243 244 2.526120 GCGCTTCCCATACACGAGC 61.526 63.158 0.00 0.00 0.00 5.03
244 245 2.230940 CGCGCTTCCCATACACGAG 61.231 63.158 5.56 0.00 0.00 4.18
245 246 2.202690 CGCGCTTCCCATACACGA 60.203 61.111 5.56 0.00 0.00 4.35
246 247 3.261951 CCGCGCTTCCCATACACG 61.262 66.667 5.56 0.00 0.00 4.49
247 248 2.895372 CCCGCGCTTCCCATACAC 60.895 66.667 5.56 0.00 0.00 2.90
248 249 4.849310 GCCCGCGCTTCCCATACA 62.849 66.667 5.56 0.00 0.00 2.29
249 250 4.849310 TGCCCGCGCTTCCCATAC 62.849 66.667 5.56 0.00 35.36 2.39
250 251 4.545706 CTGCCCGCGCTTCCCATA 62.546 66.667 5.56 0.00 35.36 2.74
254 255 4.404654 CAAACTGCCCGCGCTTCC 62.405 66.667 5.56 0.00 35.36 3.46
255 256 3.353836 TCAAACTGCCCGCGCTTC 61.354 61.111 5.56 0.00 35.36 3.86
256 257 3.660111 GTCAAACTGCCCGCGCTT 61.660 61.111 5.56 0.00 35.36 4.68
260 261 3.477224 TTTGCGTCAAACTGCCCGC 62.477 57.895 0.00 0.00 45.92 6.13
261 262 1.370414 CTTTGCGTCAAACTGCCCG 60.370 57.895 1.63 0.00 0.00 6.13
262 263 0.594796 CACTTTGCGTCAAACTGCCC 60.595 55.000 1.63 0.00 0.00 5.36
263 264 1.208642 GCACTTTGCGTCAAACTGCC 61.209 55.000 17.47 7.48 37.27 4.85
264 265 2.207177 GCACTTTGCGTCAAACTGC 58.793 52.632 15.22 15.22 36.57 4.40
274 275 3.764885 ATCCTATTTGACGCACTTTGC 57.235 42.857 0.00 0.00 40.69 3.68
275 276 4.788100 CGAAATCCTATTTGACGCACTTTG 59.212 41.667 0.00 0.00 0.00 2.77
276 277 4.671766 GCGAAATCCTATTTGACGCACTTT 60.672 41.667 0.00 0.00 43.18 2.66
277 278 3.181510 GCGAAATCCTATTTGACGCACTT 60.182 43.478 0.00 0.00 43.18 3.16
278 279 2.351726 GCGAAATCCTATTTGACGCACT 59.648 45.455 0.00 0.00 43.18 4.40
279 280 2.351726 AGCGAAATCCTATTTGACGCAC 59.648 45.455 15.98 0.00 45.47 5.34
280 281 2.351418 CAGCGAAATCCTATTTGACGCA 59.649 45.455 15.98 0.00 45.47 5.24
281 282 2.607635 TCAGCGAAATCCTATTTGACGC 59.392 45.455 0.00 0.00 43.84 5.19
282 283 3.865745 ACTCAGCGAAATCCTATTTGACG 59.134 43.478 0.00 0.00 0.00 4.35
283 284 4.271291 GGACTCAGCGAAATCCTATTTGAC 59.729 45.833 0.00 0.00 0.00 3.18
284 285 4.081142 TGGACTCAGCGAAATCCTATTTGA 60.081 41.667 0.00 0.00 32.06 2.69
285 286 4.191544 TGGACTCAGCGAAATCCTATTTG 58.808 43.478 0.00 0.00 32.06 2.32
286 287 4.487714 TGGACTCAGCGAAATCCTATTT 57.512 40.909 0.00 0.00 32.06 1.40
287 288 4.487714 TTGGACTCAGCGAAATCCTATT 57.512 40.909 0.00 0.00 32.06 1.73
288 289 4.080863 ACTTTGGACTCAGCGAAATCCTAT 60.081 41.667 0.00 0.00 32.06 2.57
289 290 3.260884 ACTTTGGACTCAGCGAAATCCTA 59.739 43.478 0.00 0.00 32.06 2.94
290 291 2.039084 ACTTTGGACTCAGCGAAATCCT 59.961 45.455 0.00 0.00 32.06 3.24
291 292 2.416893 GACTTTGGACTCAGCGAAATCC 59.583 50.000 0.00 0.00 0.00 3.01
292 293 3.067106 TGACTTTGGACTCAGCGAAATC 58.933 45.455 0.00 0.00 0.00 2.17
293 294 3.070018 CTGACTTTGGACTCAGCGAAAT 58.930 45.455 0.00 0.00 0.00 2.17
294 295 2.483876 CTGACTTTGGACTCAGCGAAA 58.516 47.619 0.00 0.00 0.00 3.46
295 296 2.154854 CTGACTTTGGACTCAGCGAA 57.845 50.000 0.00 0.00 0.00 4.70
296 297 3.894257 CTGACTTTGGACTCAGCGA 57.106 52.632 0.00 0.00 0.00 4.93
303 304 1.860484 GCTGGCTGCTGACTTTGGAC 61.860 60.000 9.31 0.00 38.95 4.02
323 324 1.944676 CGGGTACGCTCGCTGAATC 60.945 63.158 8.43 0.00 0.00 2.52
332 333 1.291272 GTTTCTGGTCGGGTACGCT 59.709 57.895 8.43 0.00 40.69 5.07
341 342 5.854866 GCATTTAAACCTTACGTTTCTGGTC 59.145 40.000 0.00 0.00 43.75 4.02
445 446 0.880278 CCACTCAACCTGTCACCACG 60.880 60.000 0.00 0.00 0.00 4.94
446 447 0.468226 TCCACTCAACCTGTCACCAC 59.532 55.000 0.00 0.00 0.00 4.16
447 448 0.468226 GTCCACTCAACCTGTCACCA 59.532 55.000 0.00 0.00 0.00 4.17
448 449 0.468226 TGTCCACTCAACCTGTCACC 59.532 55.000 0.00 0.00 0.00 4.02
503 504 0.101399 CTTGGATACGTCTCGCTGCT 59.899 55.000 0.00 0.00 42.51 4.24
511 512 1.258982 CGCAAGATGCTTGGATACGTC 59.741 52.381 9.01 0.00 42.25 4.34
559 560 4.735132 ATCACCCGTGGTCGCGTG 62.735 66.667 5.77 0.00 44.15 5.34
697 698 4.649674 ACTGCCGATCTTATCTTAGACCAA 59.350 41.667 0.00 0.00 0.00 3.67
699 805 4.614078 CGACTGCCGATCTTATCTTAGACC 60.614 50.000 0.00 0.00 41.76 3.85
714 820 1.361668 CCAGTGATTTCCGACTGCCG 61.362 60.000 0.00 0.00 38.64 5.69
795 901 9.914834 TGCCCACTTATTTTAATACAGATTAGT 57.085 29.630 0.00 0.00 0.00 2.24
878 1007 7.997773 AGCACTCTTATATAGACACCGATTA 57.002 36.000 0.00 0.00 0.00 1.75
906 1035 7.273598 CCTGTGTTGCGCAGTATATTATACTAG 59.726 40.741 11.31 12.67 39.99 2.57
907 1036 7.040271 TCCTGTGTTGCGCAGTATATTATACTA 60.040 37.037 11.31 0.00 39.99 1.82
908 1037 5.926542 CCTGTGTTGCGCAGTATATTATACT 59.073 40.000 11.31 10.04 39.99 2.12
909 1038 5.924254 TCCTGTGTTGCGCAGTATATTATAC 59.076 40.000 11.31 2.74 39.99 1.47
910 1039 5.924254 GTCCTGTGTTGCGCAGTATATTATA 59.076 40.000 11.31 0.00 39.99 0.98
911 1040 4.750098 GTCCTGTGTTGCGCAGTATATTAT 59.250 41.667 11.31 0.00 39.99 1.28
1021 1151 4.521062 CTTGCCCTCCGCTCCTCG 62.521 72.222 0.00 0.00 38.78 4.63
1164 1307 0.390603 GCATGTGTGTACCGTAGCCA 60.391 55.000 0.00 0.00 0.00 4.75
1729 1902 2.778679 GAACACCATGAGCGCGAC 59.221 61.111 12.10 2.99 0.00 5.19
1916 2089 1.463674 CTGGCCGCCTTTTGTCTTAT 58.536 50.000 11.61 0.00 0.00 1.73
2055 2228 2.663852 AACACGCGTGGGCTGTAC 60.664 61.111 39.21 0.00 36.88 2.90
2643 2822 1.007387 CGCCTTGTCTTTTGTGGCC 60.007 57.895 0.00 0.00 40.40 5.36
2649 2828 2.099098 CACCACTTTCGCCTTGTCTTTT 59.901 45.455 0.00 0.00 0.00 2.27
2667 2846 2.159028 GGCTCACTAGTTCATCTCCACC 60.159 54.545 0.00 0.00 0.00 4.61
2722 2910 5.344743 ACCACGTTGATCAGATACATCTT 57.655 39.130 0.00 0.00 34.22 2.40
2762 2951 1.210234 TCCATCAATGAGCACCACGAT 59.790 47.619 0.00 0.00 0.00 3.73
2818 3007 3.881220 ACGTTTACCCGATTGATCCAAT 58.119 40.909 0.00 0.00 36.72 3.16
2830 3019 4.000988 AGATGTCATGTCAACGTTTACCC 58.999 43.478 9.98 0.00 0.00 3.69
2856 3046 3.512516 GAGCAGCATCAACGGGCC 61.513 66.667 0.00 0.00 0.00 5.80
2871 3061 3.721035 TGGATATCAATGACACGCTGAG 58.279 45.455 4.83 0.00 0.00 3.35
2879 3069 6.016860 TGCAAGTGCTAATGGATATCAATGAC 60.017 38.462 4.83 0.00 42.66 3.06
2903 3094 7.251281 CAGATAAAGCTATCCATCATGCAATG 58.749 38.462 0.00 0.00 39.33 2.82
2938 3129 3.828786 ACGATTTAACCGAACAAATGCC 58.171 40.909 0.00 0.00 0.00 4.40
2943 3134 4.815308 TGAAAGGACGATTTAACCGAACAA 59.185 37.500 0.00 0.00 0.00 2.83
3032 3223 2.430382 GAACCGACGGAAGCACTCCA 62.430 60.000 23.38 0.00 45.74 3.86
3034 3225 1.006571 TGAACCGACGGAAGCACTC 60.007 57.895 23.38 7.32 0.00 3.51
3047 3238 1.314730 AAATGGTGTGACGGTGAACC 58.685 50.000 0.00 0.00 0.00 3.62
3048 3239 4.759516 ATAAAATGGTGTGACGGTGAAC 57.240 40.909 0.00 0.00 0.00 3.18
3050 3241 6.231951 TCTTTATAAAATGGTGTGACGGTGA 58.768 36.000 0.00 0.00 0.00 4.02
3053 3244 6.238648 GGGATCTTTATAAAATGGTGTGACGG 60.239 42.308 0.00 0.00 0.00 4.79
3054 3245 6.238648 GGGGATCTTTATAAAATGGTGTGACG 60.239 42.308 0.00 0.00 0.00 4.35
3055 3246 6.833933 AGGGGATCTTTATAAAATGGTGTGAC 59.166 38.462 0.00 0.00 0.00 3.67
3058 3249 8.511126 ACATAGGGGATCTTTATAAAATGGTGT 58.489 33.333 0.00 0.00 0.00 4.16
3073 3266 9.274206 GTTAATTTACAGAGAACATAGGGGATC 57.726 37.037 0.00 0.00 0.00 3.36
3075 3268 7.366191 GGGTTAATTTACAGAGAACATAGGGGA 60.366 40.741 0.00 0.00 0.00 4.81
3076 3269 6.771267 GGGTTAATTTACAGAGAACATAGGGG 59.229 42.308 0.00 0.00 0.00 4.79
3081 3274 8.650143 ATTGTGGGTTAATTTACAGAGAACAT 57.350 30.769 0.00 0.00 0.00 2.71
3086 3279 7.118680 ACGTGTATTGTGGGTTAATTTACAGAG 59.881 37.037 0.00 0.00 0.00 3.35
3137 3330 7.508977 TGTCAGGGGATCTTTTAAGAAAATGTT 59.491 33.333 0.00 0.00 38.77 2.71
3213 3408 9.840427 CGGATTGATTAACTGAAATGTTAAACT 57.160 29.630 4.34 0.00 43.02 2.66
3214 3409 8.583765 GCGGATTGATTAACTGAAATGTTAAAC 58.416 33.333 4.34 3.12 43.02 2.01
3216 3411 7.821652 TGCGGATTGATTAACTGAAATGTTAA 58.178 30.769 0.00 0.00 43.63 2.01
3217 3412 7.384439 TGCGGATTGATTAACTGAAATGTTA 57.616 32.000 0.00 0.00 0.00 2.41
3218 3413 6.266168 TGCGGATTGATTAACTGAAATGTT 57.734 33.333 0.00 0.00 0.00 2.71
3221 3435 4.641989 AGCTGCGGATTGATTAACTGAAAT 59.358 37.500 0.00 0.00 0.00 2.17
3238 3452 8.531530 GGATAATTTTGTGTTAAATAAGCTGCG 58.468 33.333 0.00 0.00 0.00 5.18
3346 3561 4.184629 CAAGTATTTTCGGACAGAGGGAG 58.815 47.826 0.00 0.00 0.00 4.30
3348 3563 3.933332 GACAAGTATTTTCGGACAGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
3349 3564 4.389077 GTGACAAGTATTTTCGGACAGAGG 59.611 45.833 0.00 0.00 0.00 3.69
3350 3565 5.119279 CAGTGACAAGTATTTTCGGACAGAG 59.881 44.000 0.00 0.00 0.00 3.35
3351 3566 4.988540 CAGTGACAAGTATTTTCGGACAGA 59.011 41.667 0.00 0.00 0.00 3.41
3352 3567 4.988540 TCAGTGACAAGTATTTTCGGACAG 59.011 41.667 0.00 0.00 0.00 3.51
3353 3568 4.951254 TCAGTGACAAGTATTTTCGGACA 58.049 39.130 0.00 0.00 0.00 4.02
3354 3569 5.917541 TTCAGTGACAAGTATTTTCGGAC 57.082 39.130 0.00 0.00 0.00 4.79
3355 3570 6.072728 CCATTTCAGTGACAAGTATTTTCGGA 60.073 38.462 0.00 0.00 0.00 4.55
3356 3571 6.072728 TCCATTTCAGTGACAAGTATTTTCGG 60.073 38.462 0.00 0.00 0.00 4.30
3357 3572 6.898041 TCCATTTCAGTGACAAGTATTTTCG 58.102 36.000 0.00 0.00 0.00 3.46
3358 3573 8.514594 TCATCCATTTCAGTGACAAGTATTTTC 58.485 33.333 0.00 0.00 0.00 2.29
3359 3574 8.408043 TCATCCATTTCAGTGACAAGTATTTT 57.592 30.769 0.00 0.00 0.00 1.82
3360 3575 8.408043 TTCATCCATTTCAGTGACAAGTATTT 57.592 30.769 0.00 0.00 0.00 1.40
3361 3576 8.299570 GTTTCATCCATTTCAGTGACAAGTATT 58.700 33.333 0.00 0.00 0.00 1.89
3362 3577 7.361201 CGTTTCATCCATTTCAGTGACAAGTAT 60.361 37.037 0.00 0.00 0.00 2.12
3363 3578 6.073276 CGTTTCATCCATTTCAGTGACAAGTA 60.073 38.462 0.00 0.00 0.00 2.24
3364 3579 5.277974 CGTTTCATCCATTTCAGTGACAAGT 60.278 40.000 0.00 0.00 0.00 3.16
3365 3580 5.049474 TCGTTTCATCCATTTCAGTGACAAG 60.049 40.000 0.00 0.00 0.00 3.16
3366 3581 4.819088 TCGTTTCATCCATTTCAGTGACAA 59.181 37.500 0.00 0.00 0.00 3.18
3367 3582 4.384940 TCGTTTCATCCATTTCAGTGACA 58.615 39.130 0.00 0.00 0.00 3.58
3368 3583 5.356882 TTCGTTTCATCCATTTCAGTGAC 57.643 39.130 0.00 0.00 0.00 3.67
3369 3584 5.473162 ACATTCGTTTCATCCATTTCAGTGA 59.527 36.000 0.00 0.00 0.00 3.41
3370 3585 5.702865 ACATTCGTTTCATCCATTTCAGTG 58.297 37.500 0.00 0.00 0.00 3.66
3371 3586 5.964958 ACATTCGTTTCATCCATTTCAGT 57.035 34.783 0.00 0.00 0.00 3.41
3372 3587 7.076842 ACTACATTCGTTTCATCCATTTCAG 57.923 36.000 0.00 0.00 0.00 3.02
3373 3588 7.447374 AACTACATTCGTTTCATCCATTTCA 57.553 32.000 0.00 0.00 0.00 2.69
3374 3589 8.879759 TCTAACTACATTCGTTTCATCCATTTC 58.120 33.333 0.00 0.00 0.00 2.17
3375 3590 8.786826 TCTAACTACATTCGTTTCATCCATTT 57.213 30.769 0.00 0.00 0.00 2.32
3376 3591 8.665685 GTTCTAACTACATTCGTTTCATCCATT 58.334 33.333 0.00 0.00 0.00 3.16
3377 3592 8.041323 AGTTCTAACTACATTCGTTTCATCCAT 58.959 33.333 0.00 0.00 37.52 3.41
3378 3593 7.383687 AGTTCTAACTACATTCGTTTCATCCA 58.616 34.615 0.00 0.00 37.52 3.41
3379 3594 7.829378 AGTTCTAACTACATTCGTTTCATCC 57.171 36.000 0.00 0.00 37.52 3.51
3407 3622 8.690884 CGGAGAAATGGATGTATCTAGACATAT 58.309 37.037 0.00 0.00 40.18 1.78
3408 3623 7.888546 TCGGAGAAATGGATGTATCTAGACATA 59.111 37.037 0.00 0.00 40.18 2.29
3409 3624 6.721668 TCGGAGAAATGGATGTATCTAGACAT 59.278 38.462 0.00 0.00 42.82 3.06
3410 3625 6.016192 GTCGGAGAAATGGATGTATCTAGACA 60.016 42.308 0.00 0.00 39.69 3.41
3411 3626 6.016192 TGTCGGAGAAATGGATGTATCTAGAC 60.016 42.308 0.00 0.00 39.69 2.59
3412 3627 6.068670 TGTCGGAGAAATGGATGTATCTAGA 58.931 40.000 0.00 0.00 39.69 2.43
3413 3628 6.332735 TGTCGGAGAAATGGATGTATCTAG 57.667 41.667 0.00 0.00 39.69 2.43
3414 3629 6.323996 ACTTGTCGGAGAAATGGATGTATCTA 59.676 38.462 0.00 0.00 39.69 1.98
3415 3630 5.129485 ACTTGTCGGAGAAATGGATGTATCT 59.871 40.000 0.00 0.00 39.69 1.98
3416 3631 5.360591 ACTTGTCGGAGAAATGGATGTATC 58.639 41.667 0.00 0.00 39.69 2.24
3417 3632 5.359194 ACTTGTCGGAGAAATGGATGTAT 57.641 39.130 0.00 0.00 39.69 2.29
3418 3633 4.819105 ACTTGTCGGAGAAATGGATGTA 57.181 40.909 0.00 0.00 39.69 2.29
3419 3634 3.703001 ACTTGTCGGAGAAATGGATGT 57.297 42.857 0.00 0.00 39.69 3.06
3420 3635 6.238484 GGAAATACTTGTCGGAGAAATGGATG 60.238 42.308 0.00 0.00 39.69 3.51
3421 3636 5.823045 GGAAATACTTGTCGGAGAAATGGAT 59.177 40.000 0.00 0.00 39.69 3.41
3422 3637 5.183228 GGAAATACTTGTCGGAGAAATGGA 58.817 41.667 0.00 0.00 39.69 3.41
3423 3638 4.034048 CGGAAATACTTGTCGGAGAAATGG 59.966 45.833 0.00 0.00 39.69 3.16
3424 3639 4.034048 CCGGAAATACTTGTCGGAGAAATG 59.966 45.833 0.00 0.00 42.94 2.32
3425 3640 4.081309 TCCGGAAATACTTGTCGGAGAAAT 60.081 41.667 0.00 0.00 43.84 2.17
3426 3641 3.258872 TCCGGAAATACTTGTCGGAGAAA 59.741 43.478 0.00 0.00 43.84 2.52
3427 3642 2.827322 TCCGGAAATACTTGTCGGAGAA 59.173 45.455 0.00 0.00 43.84 2.87
3428 3643 2.449464 TCCGGAAATACTTGTCGGAGA 58.551 47.619 0.00 0.00 43.84 3.71
3429 3644 2.953466 TCCGGAAATACTTGTCGGAG 57.047 50.000 0.00 0.00 43.84 4.63
3431 3646 2.159014 TCCATCCGGAAATACTTGTCGG 60.159 50.000 9.01 0.00 38.83 4.79
3432 3647 3.123804 CTCCATCCGGAAATACTTGTCG 58.876 50.000 9.01 0.00 42.21 4.35
3433 3648 3.467803 CCTCCATCCGGAAATACTTGTC 58.532 50.000 9.01 0.00 42.21 3.18
3434 3649 2.172717 CCCTCCATCCGGAAATACTTGT 59.827 50.000 9.01 0.00 42.21 3.16
3435 3650 2.438021 TCCCTCCATCCGGAAATACTTG 59.562 50.000 9.01 0.00 42.21 3.16
3436 3651 2.706190 CTCCCTCCATCCGGAAATACTT 59.294 50.000 9.01 0.00 42.21 2.24
3437 3652 2.330216 CTCCCTCCATCCGGAAATACT 58.670 52.381 9.01 0.00 42.21 2.12
3438 3653 2.047830 ACTCCCTCCATCCGGAAATAC 58.952 52.381 9.01 0.00 42.21 1.89
3439 3654 2.489528 ACTCCCTCCATCCGGAAATA 57.510 50.000 9.01 0.00 42.21 1.40
3440 3655 2.047830 GTACTCCCTCCATCCGGAAAT 58.952 52.381 9.01 0.00 42.21 2.17
3441 3656 1.007963 AGTACTCCCTCCATCCGGAAA 59.992 52.381 9.01 0.00 42.21 3.13
3442 3657 0.635009 AGTACTCCCTCCATCCGGAA 59.365 55.000 9.01 0.00 42.21 4.30
3443 3658 1.526315 TAGTACTCCCTCCATCCGGA 58.474 55.000 6.61 6.61 39.79 5.14
3444 3659 2.606751 ATAGTACTCCCTCCATCCGG 57.393 55.000 0.00 0.00 0.00 5.14
3445 3660 4.082136 GCTAAATAGTACTCCCTCCATCCG 60.082 50.000 0.00 0.00 0.00 4.18
3446 3661 5.046950 CAGCTAAATAGTACTCCCTCCATCC 60.047 48.000 0.00 0.00 0.00 3.51
3447 3662 5.540719 ACAGCTAAATAGTACTCCCTCCATC 59.459 44.000 0.00 0.00 0.00 3.51
3448 3663 5.468658 ACAGCTAAATAGTACTCCCTCCAT 58.531 41.667 0.00 0.00 0.00 3.41
3449 3664 4.880164 ACAGCTAAATAGTACTCCCTCCA 58.120 43.478 0.00 0.00 0.00 3.86
3450 3665 5.873146 AACAGCTAAATAGTACTCCCTCC 57.127 43.478 0.00 0.00 0.00 4.30
3479 3694 9.260002 AGTTTGCACCAAAACAATATTTTAGAG 57.740 29.630 2.09 0.00 41.56 2.43
3491 3706 9.341899 CACTATAGATTAAGTTTGCACCAAAAC 57.658 33.333 6.78 0.00 39.80 2.43
3522 3738 3.058085 GCCGGTATGAAAGAAAAACGGAA 60.058 43.478 1.90 0.00 42.42 4.30
3572 3788 6.666113 TCCTTTCCTCCCAATATGGTTTTAAC 59.334 38.462 0.00 0.00 35.17 2.01
3587 3803 4.575236 GGTTATCGATGTTTCCTTTCCTCC 59.425 45.833 8.54 0.00 0.00 4.30
3656 3872 4.167359 TCTCTCTCTCGCGTGCGC 62.167 66.667 9.79 0.00 39.59 6.09
3657 3873 2.022623 CTCTCTCTCTCGCGTGCG 59.977 66.667 5.77 8.14 41.35 5.34
3658 3874 1.087202 TCTCTCTCTCTCTCGCGTGC 61.087 60.000 5.77 0.00 0.00 5.34
3659 3875 0.930310 CTCTCTCTCTCTCTCGCGTG 59.070 60.000 5.77 3.13 0.00 5.34
3660 3876 0.821517 TCTCTCTCTCTCTCTCGCGT 59.178 55.000 5.77 0.00 0.00 6.01
3661 3877 1.067060 TCTCTCTCTCTCTCTCTCGCG 59.933 57.143 0.00 0.00 0.00 5.87
3662 3878 2.748605 CTCTCTCTCTCTCTCTCTCGC 58.251 57.143 0.00 0.00 0.00 5.03


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

AutoCloner maintained by Alex Coulton.