Multiple sequence alignment - TraesCS4A01G197900

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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 TraesCS4A01G197900 chr4A 100.000 6146 0 0 1 6146 482139841 482133696 0.000000e+00 11350.0
1 TraesCS4A01G197900 chr4D 94.986 3949 127 24 2218 6146 96519501 96523398 0.000000e+00 6130.0
2 TraesCS4A01G197900 chr4D 91.891 2047 76 27 166 2169 96517505 96519504 0.000000e+00 2778.0
3 TraesCS4A01G197900 chr4B 94.363 3956 149 36 2226 6146 136528384 136532300 0.000000e+00 6002.0
4 TraesCS4A01G197900 chr4B 90.444 2072 97 44 166 2182 136526363 136528388 0.000000e+00 2636.0
5 TraesCS4A01G197900 chr4B 96.855 159 4 1 1 158 667726128 667725970 1.310000e-66 265.0
6 TraesCS4A01G197900 chr5A 79.335 692 104 29 4184 4843 284694273 284694957 3.380000e-122 449.0
7 TraesCS4A01G197900 chr5A 97.484 159 3 1 1 158 210736206 210736048 2.820000e-68 270.0
8 TraesCS4A01G197900 chr5D 78.993 695 105 27 4184 4843 215877603 215878291 2.630000e-118 436.0
9 TraesCS4A01G197900 chr5B 79.507 649 97 25 4228 4843 231731951 231732596 4.400000e-116 429.0
10 TraesCS4A01G197900 chr7B 98.742 159 1 1 1 158 84291493 84291651 1.300000e-71 281.0
11 TraesCS4A01G197900 chr7B 98.113 159 2 1 1 158 130504405 130504563 6.070000e-70 276.0
12 TraesCS4A01G197900 chr7B 97.436 156 4 0 1 156 679597249 679597094 3.650000e-67 267.0
13 TraesCS4A01G197900 chr1A 98.742 159 1 1 1 158 575370791 575370949 1.300000e-71 281.0
14 TraesCS4A01G197900 chr1A 96.855 159 4 1 1 158 164754383 164754541 1.310000e-66 265.0
15 TraesCS4A01G197900 chr6A 97.484 159 3 1 1 158 586578568 586578726 2.820000e-68 270.0
16 TraesCS4A01G197900 chr2A 97.484 159 3 1 1 158 726752242 726752400 2.820000e-68 270.0
17 TraesCS4A01G197900 chr7A 91.304 46 4 0 2439 2484 64131342 64131297 5.140000e-06 63.9


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 TraesCS4A01G197900 chr4A 482133696 482139841 6145 True 11350 11350 100.0000 1 6146 1 chr4A.!!$R1 6145
1 TraesCS4A01G197900 chr4D 96517505 96523398 5893 False 4454 6130 93.4385 166 6146 2 chr4D.!!$F1 5980
2 TraesCS4A01G197900 chr4B 136526363 136532300 5937 False 4319 6002 92.4035 166 6146 2 chr4B.!!$F1 5980
3 TraesCS4A01G197900 chr5A 284694273 284694957 684 False 449 449 79.3350 4184 4843 1 chr5A.!!$F1 659
4 TraesCS4A01G197900 chr5D 215877603 215878291 688 False 436 436 78.9930 4184 4843 1 chr5D.!!$F1 659
5 TraesCS4A01G197900 chr5B 231731951 231732596 645 False 429 429 79.5070 4228 4843 1 chr5B.!!$F1 615

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
914 980 0.250727 CATATCCGGGCCGAATTGGT 60.251 55.000 30.79 9.53 41.21 3.67 F
1658 1744 0.179200 GTACGTTGGCTGGAATTGCG 60.179 55.000 0.00 0.00 0.00 4.85 F
1880 1966 0.322366 TGATGATGGGCACGCTTTGA 60.322 50.000 0.00 0.00 0.00 2.69 F
2214 2300 0.460284 CTTCGCAGCGGTGGTATTCT 60.460 55.000 16.42 0.00 0.00 2.40 F
2215 2301 0.739462 TTCGCAGCGGTGGTATTCTG 60.739 55.000 16.42 0.00 0.00 3.02 F
2286 2372 1.272212 AGCAAACCCACCAAATAAGCG 59.728 47.619 0.00 0.00 0.00 4.68 F
2554 2644 1.330521 TGCATCGCCGCTCTTTATTTC 59.669 47.619 0.00 0.00 0.00 2.17 F
3952 4047 2.418368 AGCTTTATGCCATTCCGACA 57.582 45.000 0.00 0.00 44.23 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2200 2286 0.249120 TGGACAGAATACCACCGCTG 59.751 55.000 0.00 0.00 34.65 5.18 R
3611 3704 1.202651 CGGAACACTGTTTCCTCTGGT 60.203 52.381 15.08 0.00 42.74 4.00 R
3797 3892 6.203338 TCTCCGCATTTATACGAAAAATACCC 59.797 38.462 0.00 0.00 0.00 3.69 R
3956 4051 0.107752 TGTGAGTGCTGCTGTCAACA 60.108 50.000 0.00 2.84 0.00 3.33 R
3957 4052 1.233019 ATGTGAGTGCTGCTGTCAAC 58.767 50.000 0.00 0.00 0.00 3.18 R
4040 4135 6.659824 AGACTGGTTTCCACTAGAAAGAAAA 58.340 36.000 0.00 0.00 45.11 2.29 R
4508 4608 1.871039 GTTTGCTGTTAGGAGAACGCA 59.129 47.619 0.00 0.00 0.00 5.24 R
5808 5945 0.413434 AACCCTGGGAGAAAATGGGG 59.587 55.000 22.23 0.00 42.00 4.96 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
28 29 9.898152 TCACATAACAACACCAATATCATTAGA 57.102 29.630 0.00 0.00 0.00 2.10
35 36 9.857656 ACAACACCAATATCATTAGATTCATCT 57.142 29.630 0.00 0.00 40.86 2.90
38 39 9.293404 ACACCAATATCATTAGATTCATCTTGG 57.707 33.333 0.00 0.00 38.32 3.61
39 40 9.511272 CACCAATATCATTAGATTCATCTTGGA 57.489 33.333 0.00 0.00 38.32 3.53
109 110 9.625747 AATTTCCAATGTAAATTTGGTCAAACT 57.374 25.926 0.00 0.00 43.41 2.66
110 111 9.625747 ATTTCCAATGTAAATTTGGTCAAACTT 57.374 25.926 0.00 0.00 43.41 2.66
113 114 9.535878 TCCAATGTAAATTTGGTCAAACTTAAC 57.464 29.630 0.00 0.00 43.41 2.01
114 115 9.319143 CCAATGTAAATTTGGTCAAACTTAACA 57.681 29.630 0.00 2.71 39.05 2.41
118 119 9.930693 TGTAAATTTGGTCAAACTTAACAAAGT 57.069 25.926 0.00 0.00 34.91 2.66
129 130 7.806149 AAACTTAACAAAGTTTGACTTTCGG 57.194 32.000 22.23 7.59 44.47 4.30
130 131 5.337554 ACTTAACAAAGTTTGACTTTCGGC 58.662 37.500 22.23 0.00 44.47 5.54
131 132 3.859411 AACAAAGTTTGACTTTCGGCA 57.141 38.095 22.23 0.00 44.47 5.69
132 133 3.859411 ACAAAGTTTGACTTTCGGCAA 57.141 38.095 22.23 0.00 44.47 4.52
133 134 4.181309 ACAAAGTTTGACTTTCGGCAAA 57.819 36.364 22.23 0.00 44.47 3.68
134 135 4.754322 ACAAAGTTTGACTTTCGGCAAAT 58.246 34.783 22.23 0.00 44.47 2.32
135 136 5.175127 ACAAAGTTTGACTTTCGGCAAATT 58.825 33.333 22.23 0.00 44.47 1.82
136 137 5.290885 ACAAAGTTTGACTTTCGGCAAATTC 59.709 36.000 22.23 0.00 44.47 2.17
137 138 4.647424 AGTTTGACTTTCGGCAAATTCA 57.353 36.364 0.00 0.00 36.51 2.57
138 139 5.004922 AGTTTGACTTTCGGCAAATTCAA 57.995 34.783 0.00 9.43 38.64 2.69
139 140 5.600696 AGTTTGACTTTCGGCAAATTCAAT 58.399 33.333 12.32 2.12 39.55 2.57
140 141 5.463061 AGTTTGACTTTCGGCAAATTCAATG 59.537 36.000 12.32 0.00 39.55 2.82
141 142 4.582701 TGACTTTCGGCAAATTCAATGT 57.417 36.364 0.00 0.00 30.43 2.71
142 143 4.297510 TGACTTTCGGCAAATTCAATGTG 58.702 39.130 0.00 0.00 30.43 3.21
143 144 3.059166 ACTTTCGGCAAATTCAATGTGC 58.941 40.909 3.63 3.63 37.55 4.57
144 145 2.808523 TTCGGCAAATTCAATGTGCA 57.191 40.000 14.72 0.00 40.12 4.57
145 146 2.350899 TCGGCAAATTCAATGTGCAG 57.649 45.000 14.72 10.54 40.12 4.41
146 147 1.885233 TCGGCAAATTCAATGTGCAGA 59.115 42.857 14.72 12.84 39.61 4.26
147 148 2.095110 TCGGCAAATTCAATGTGCAGAG 60.095 45.455 14.72 5.36 37.52 3.35
148 149 2.352030 CGGCAAATTCAATGTGCAGAGT 60.352 45.455 14.72 0.00 40.12 3.24
149 150 3.119884 CGGCAAATTCAATGTGCAGAGTA 60.120 43.478 14.72 0.00 40.12 2.59
150 151 4.615682 CGGCAAATTCAATGTGCAGAGTAA 60.616 41.667 14.72 0.00 40.12 2.24
151 152 5.229423 GGCAAATTCAATGTGCAGAGTAAA 58.771 37.500 14.72 0.00 40.12 2.01
152 153 5.695816 GGCAAATTCAATGTGCAGAGTAAAA 59.304 36.000 14.72 0.00 40.12 1.52
153 154 6.202570 GGCAAATTCAATGTGCAGAGTAAAAA 59.797 34.615 14.72 0.00 40.12 1.94
154 155 7.285788 GCAAATTCAATGTGCAGAGTAAAAAG 58.714 34.615 7.75 0.00 38.19 2.27
155 156 7.169645 GCAAATTCAATGTGCAGAGTAAAAAGA 59.830 33.333 7.75 0.00 38.19 2.52
156 157 8.482429 CAAATTCAATGTGCAGAGTAAAAAGAC 58.518 33.333 0.00 0.00 0.00 3.01
157 158 5.689383 TCAATGTGCAGAGTAAAAAGACC 57.311 39.130 0.00 0.00 0.00 3.85
158 159 5.376625 TCAATGTGCAGAGTAAAAAGACCT 58.623 37.500 0.00 0.00 0.00 3.85
159 160 6.530120 TCAATGTGCAGAGTAAAAAGACCTA 58.470 36.000 0.00 0.00 0.00 3.08
160 161 6.995686 TCAATGTGCAGAGTAAAAAGACCTAA 59.004 34.615 0.00 0.00 0.00 2.69
161 162 6.803154 ATGTGCAGAGTAAAAAGACCTAAC 57.197 37.500 0.00 0.00 0.00 2.34
162 163 5.676552 TGTGCAGAGTAAAAAGACCTAACA 58.323 37.500 0.00 0.00 0.00 2.41
163 164 6.116806 TGTGCAGAGTAAAAAGACCTAACAA 58.883 36.000 0.00 0.00 0.00 2.83
164 165 6.770785 TGTGCAGAGTAAAAAGACCTAACAAT 59.229 34.615 0.00 0.00 0.00 2.71
208 226 0.297820 CGAAAAGCGATAGTCACGGC 59.702 55.000 0.00 0.00 44.57 5.68
223 241 1.358759 CGGCACCAACCAAACAGTC 59.641 57.895 0.00 0.00 0.00 3.51
225 243 1.358759 GCACCAACCAAACAGTCCG 59.641 57.895 0.00 0.00 0.00 4.79
226 244 1.381165 GCACCAACCAAACAGTCCGT 61.381 55.000 0.00 0.00 0.00 4.69
227 245 0.661020 CACCAACCAAACAGTCCGTC 59.339 55.000 0.00 0.00 0.00 4.79
228 246 0.464916 ACCAACCAAACAGTCCGTCC 60.465 55.000 0.00 0.00 0.00 4.79
229 247 1.503818 CCAACCAAACAGTCCGTCCG 61.504 60.000 0.00 0.00 0.00 4.79
230 248 0.812412 CAACCAAACAGTCCGTCCGT 60.812 55.000 0.00 0.00 0.00 4.69
231 249 0.531311 AACCAAACAGTCCGTCCGTC 60.531 55.000 0.00 0.00 0.00 4.79
232 250 1.666872 CCAAACAGTCCGTCCGTCC 60.667 63.158 0.00 0.00 0.00 4.79
300 318 2.371306 CTCATGGCCACATCACATCAA 58.629 47.619 8.16 0.00 34.35 2.57
345 363 3.135712 AGCTCTCGTCTCTCTCTTGGATA 59.864 47.826 0.00 0.00 0.00 2.59
360 378 7.045416 TCTCTTGGATAGCACGCTTAAATAAA 58.955 34.615 0.00 0.00 0.00 1.40
361 379 7.715249 TCTCTTGGATAGCACGCTTAAATAAAT 59.285 33.333 0.00 0.00 0.00 1.40
363 381 9.332502 TCTTGGATAGCACGCTTAAATAAATAA 57.667 29.630 0.00 0.00 0.00 1.40
364 382 9.382244 CTTGGATAGCACGCTTAAATAAATAAC 57.618 33.333 0.00 0.00 0.00 1.89
365 383 8.671384 TGGATAGCACGCTTAAATAAATAACT 57.329 30.769 0.00 0.00 0.00 2.24
366 384 9.767228 TGGATAGCACGCTTAAATAAATAACTA 57.233 29.630 0.00 0.00 0.00 2.24
371 389 8.943002 AGCACGCTTAAATAAATAACTAACTGT 58.057 29.630 0.00 0.00 0.00 3.55
478 503 8.180267 CACATCATCATCATCATCATCATCTTG 58.820 37.037 0.00 0.00 0.00 3.02
535 572 1.059913 AACTCCAACTCCACCTCCAG 58.940 55.000 0.00 0.00 0.00 3.86
536 573 1.298014 CTCCAACTCCACCTCCAGC 59.702 63.158 0.00 0.00 0.00 4.85
537 574 1.152030 TCCAACTCCACCTCCAGCT 60.152 57.895 0.00 0.00 0.00 4.24
538 575 1.194781 TCCAACTCCACCTCCAGCTC 61.195 60.000 0.00 0.00 0.00 4.09
539 576 1.298014 CAACTCCACCTCCAGCTCC 59.702 63.158 0.00 0.00 0.00 4.70
540 577 1.152030 AACTCCACCTCCAGCTCCA 60.152 57.895 0.00 0.00 0.00 3.86
541 578 1.484444 AACTCCACCTCCAGCTCCAC 61.484 60.000 0.00 0.00 0.00 4.02
542 579 2.607750 TCCACCTCCAGCTCCACC 60.608 66.667 0.00 0.00 0.00 4.61
543 580 2.608988 CCACCTCCAGCTCCACCT 60.609 66.667 0.00 0.00 0.00 4.00
544 581 2.664081 CCACCTCCAGCTCCACCTC 61.664 68.421 0.00 0.00 0.00 3.85
545 582 2.284995 ACCTCCAGCTCCACCTCC 60.285 66.667 0.00 0.00 0.00 4.30
546 583 2.284921 CCTCCAGCTCCACCTCCA 60.285 66.667 0.00 0.00 0.00 3.86
654 693 3.442441 TTTTTGTCCCCAGCGCAG 58.558 55.556 11.47 0.00 0.00 5.18
677 716 3.554337 CCCAGATTAGAATACCCGTTCCG 60.554 52.174 0.00 0.00 0.00 4.30
761 800 2.370445 CCCCGTCCCAGCAATCTCT 61.370 63.158 0.00 0.00 0.00 3.10
878 917 2.520458 CACCACCACCACCACCAT 59.480 61.111 0.00 0.00 0.00 3.55
880 919 2.359850 CCACCACCACCACCATCG 60.360 66.667 0.00 0.00 0.00 3.84
881 920 2.747022 CACCACCACCACCATCGA 59.253 61.111 0.00 0.00 0.00 3.59
882 921 1.375908 CACCACCACCACCATCGAG 60.376 63.158 0.00 0.00 0.00 4.04
883 922 2.268920 CCACCACCACCATCGAGG 59.731 66.667 0.00 0.00 45.67 4.63
894 960 1.902508 ACCATCGAGGAAGAAAGCTCA 59.097 47.619 0.00 0.00 41.22 4.26
897 963 3.529533 CATCGAGGAAGAAAGCTCACAT 58.470 45.455 0.00 0.00 0.00 3.21
898 964 4.442052 CCATCGAGGAAGAAAGCTCACATA 60.442 45.833 0.00 0.00 41.22 2.29
900 966 4.938080 TCGAGGAAGAAAGCTCACATATC 58.062 43.478 0.00 0.00 0.00 1.63
907 973 2.357517 GCTCACATATCCGGGCCG 60.358 66.667 21.46 21.46 0.00 6.13
911 977 0.762418 TCACATATCCGGGCCGAATT 59.238 50.000 30.79 14.00 0.00 2.17
914 980 0.250727 CATATCCGGGCCGAATTGGT 60.251 55.000 30.79 9.53 41.21 3.67
925 991 2.510691 AATTGGTCCTACGCCGCG 60.511 61.111 12.14 12.14 0.00 6.46
973 1039 1.908483 CCCGAGAAGAAGAAGGGGG 59.092 63.158 0.00 0.00 38.44 5.40
1495 1570 4.829064 AAGCTTCGAAAACATGCTTGTA 57.171 36.364 17.67 0.00 41.61 2.41
1508 1584 6.492007 ACATGCTTGTATTTCTGAACTCAG 57.508 37.500 2.92 0.00 38.68 3.35
1543 1619 3.819564 TTCAGTATCATCCAGTTCCCG 57.180 47.619 0.00 0.00 0.00 5.14
1612 1698 5.317808 TGCTACTGTTTGCCTATTTTGGTA 58.682 37.500 0.00 0.00 0.00 3.25
1633 1719 6.824704 TGGTAGTGGTTTTAATCGGGATAAAG 59.175 38.462 0.00 0.00 0.00 1.85
1643 1729 4.785511 ATCGGGATAAAGAGATGGTACG 57.214 45.455 0.00 0.00 0.00 3.67
1658 1744 0.179200 GTACGTTGGCTGGAATTGCG 60.179 55.000 0.00 0.00 0.00 4.85
1692 1778 2.859165 TTGGTCTGAAGCTTGGTAGG 57.141 50.000 2.10 0.00 0.00 3.18
1796 1882 1.112950 CTCCGTAGACTTCTTCCCCC 58.887 60.000 0.00 0.00 0.00 5.40
1880 1966 0.322366 TGATGATGGGCACGCTTTGA 60.322 50.000 0.00 0.00 0.00 2.69
1895 1981 2.746472 GCTTTGAACCACCACTCTGTCT 60.746 50.000 0.00 0.00 0.00 3.41
2167 2253 5.414789 TCTACATTTAGTTACAGCAGCCA 57.585 39.130 0.00 0.00 0.00 4.75
2182 2268 4.157289 CAGCAGCCATTCTGTTCACTTTAT 59.843 41.667 0.00 0.00 44.66 1.40
2183 2269 4.768968 AGCAGCCATTCTGTTCACTTTATT 59.231 37.500 0.00 0.00 44.66 1.40
2184 2270 5.098211 GCAGCCATTCTGTTCACTTTATTC 58.902 41.667 0.00 0.00 44.66 1.75
2185 2271 5.105997 GCAGCCATTCTGTTCACTTTATTCT 60.106 40.000 0.00 0.00 44.66 2.40
2186 2272 6.571150 GCAGCCATTCTGTTCACTTTATTCTT 60.571 38.462 0.00 0.00 44.66 2.52
2187 2273 7.373493 CAGCCATTCTGTTCACTTTATTCTTT 58.627 34.615 0.00 0.00 38.02 2.52
2188 2274 7.869429 CAGCCATTCTGTTCACTTTATTCTTTT 59.131 33.333 0.00 0.00 38.02 2.27
2189 2275 8.084684 AGCCATTCTGTTCACTTTATTCTTTTC 58.915 33.333 0.00 0.00 0.00 2.29
2190 2276 7.329471 GCCATTCTGTTCACTTTATTCTTTTCC 59.671 37.037 0.00 0.00 0.00 3.13
2191 2277 8.579863 CCATTCTGTTCACTTTATTCTTTTCCT 58.420 33.333 0.00 0.00 0.00 3.36
2192 2278 9.403110 CATTCTGTTCACTTTATTCTTTTCCTG 57.597 33.333 0.00 0.00 0.00 3.86
2193 2279 8.519799 TTCTGTTCACTTTATTCTTTTCCTGT 57.480 30.769 0.00 0.00 0.00 4.00
2194 2280 8.154649 TCTGTTCACTTTATTCTTTTCCTGTC 57.845 34.615 0.00 0.00 0.00 3.51
2195 2281 7.228706 TCTGTTCACTTTATTCTTTTCCTGTCC 59.771 37.037 0.00 0.00 0.00 4.02
2196 2282 7.060421 TGTTCACTTTATTCTTTTCCTGTCCT 58.940 34.615 0.00 0.00 0.00 3.85
2197 2283 7.559897 TGTTCACTTTATTCTTTTCCTGTCCTT 59.440 33.333 0.00 0.00 0.00 3.36
2198 2284 7.745620 TCACTTTATTCTTTTCCTGTCCTTC 57.254 36.000 0.00 0.00 0.00 3.46
2199 2285 6.426937 TCACTTTATTCTTTTCCTGTCCTTCG 59.573 38.462 0.00 0.00 0.00 3.79
2200 2286 5.181433 ACTTTATTCTTTTCCTGTCCTTCGC 59.819 40.000 0.00 0.00 0.00 4.70
2201 2287 2.631160 TTCTTTTCCTGTCCTTCGCA 57.369 45.000 0.00 0.00 0.00 5.10
2202 2288 2.169832 TCTTTTCCTGTCCTTCGCAG 57.830 50.000 0.00 0.00 0.00 5.18
2203 2289 0.519077 CTTTTCCTGTCCTTCGCAGC 59.481 55.000 0.00 0.00 32.93 5.25
2204 2290 1.227999 TTTTCCTGTCCTTCGCAGCG 61.228 55.000 9.06 9.06 32.93 5.18
2205 2291 3.589654 TTCCTGTCCTTCGCAGCGG 62.590 63.158 16.42 0.00 32.93 5.52
2206 2292 4.379243 CCTGTCCTTCGCAGCGGT 62.379 66.667 16.42 0.00 32.93 5.68
2207 2293 3.114616 CTGTCCTTCGCAGCGGTG 61.115 66.667 16.42 10.98 0.00 4.94
2208 2294 4.680237 TGTCCTTCGCAGCGGTGG 62.680 66.667 16.42 16.96 0.00 4.61
2209 2295 4.681978 GTCCTTCGCAGCGGTGGT 62.682 66.667 16.42 0.00 0.00 4.16
2210 2296 2.992689 TCCTTCGCAGCGGTGGTA 60.993 61.111 16.42 5.22 0.00 3.25
2211 2297 2.186903 CCTTCGCAGCGGTGGTAT 59.813 61.111 16.42 0.00 0.00 2.73
2212 2298 1.449601 CCTTCGCAGCGGTGGTATT 60.450 57.895 16.42 0.00 0.00 1.89
2213 2299 1.429148 CCTTCGCAGCGGTGGTATTC 61.429 60.000 16.42 0.00 0.00 1.75
2214 2300 0.460284 CTTCGCAGCGGTGGTATTCT 60.460 55.000 16.42 0.00 0.00 2.40
2215 2301 0.739462 TTCGCAGCGGTGGTATTCTG 60.739 55.000 16.42 0.00 0.00 3.02
2216 2302 1.447838 CGCAGCGGTGGTATTCTGT 60.448 57.895 17.54 0.00 0.00 3.41
2245 2331 4.469657 TGCTTTAGTGTTCCCATCAACTT 58.530 39.130 0.00 0.00 0.00 2.66
2286 2372 1.272212 AGCAAACCCACCAAATAAGCG 59.728 47.619 0.00 0.00 0.00 4.68
2319 2405 2.294233 ACATCCATGTGTTGTGAAGTGC 59.706 45.455 0.00 0.00 40.03 4.40
2326 2412 2.159268 TGTGTTGTGAAGTGCATGGTTG 60.159 45.455 0.00 0.00 0.00 3.77
2333 2423 5.911752 TGTGAAGTGCATGGTTGTTTTAAT 58.088 33.333 0.00 0.00 0.00 1.40
2510 2600 7.472334 AGGTATTTTTCATTCAGTGCAAGAT 57.528 32.000 0.00 0.00 0.00 2.40
2554 2644 1.330521 TGCATCGCCGCTCTTTATTTC 59.669 47.619 0.00 0.00 0.00 2.17
2560 2650 3.308866 TCGCCGCTCTTTATTTCTTTAGC 59.691 43.478 0.00 0.00 0.00 3.09
2562 2652 3.546218 GCCGCTCTTTATTTCTTTAGCCG 60.546 47.826 0.00 0.00 0.00 5.52
2567 2657 5.220854 GCTCTTTATTTCTTTAGCCGATGCA 60.221 40.000 0.00 0.00 41.13 3.96
2705 2795 9.378551 AGATTATTAAACGCTAAGTCATGTTGA 57.621 29.630 0.00 0.00 0.00 3.18
2735 2826 6.379703 TCAAAGAAGAACTGTTGGGAATTTCA 59.620 34.615 0.00 0.00 0.00 2.69
2785 2876 5.991328 TTGTCTTGATTAGATGATTCCGC 57.009 39.130 0.00 0.00 34.79 5.54
3017 3110 7.856145 AGAATAAGCTAAATGGTTCTCTGTG 57.144 36.000 0.00 0.00 37.56 3.66
3040 3133 4.624604 GCAAGGATGGAATCATTTTGCCTT 60.625 41.667 13.54 0.00 46.42 4.35
3126 3219 4.151883 ACCAACAAAACTGGAGCATATGT 58.848 39.130 4.29 0.00 37.40 2.29
3254 3347 8.349983 ACCGGCACTTAATAATAATGTGAAATC 58.650 33.333 0.00 0.00 0.00 2.17
3513 3606 7.761409 TGTTTATGATTAGTTCCAGTTCATGC 58.239 34.615 0.00 0.00 0.00 4.06
3522 3615 4.072131 GTTCCAGTTCATGCTTCCTTGTA 58.928 43.478 0.00 0.00 0.00 2.41
3537 3630 4.850680 TCCTTGTACTGTTGGTGTTCTTT 58.149 39.130 0.00 0.00 0.00 2.52
3611 3704 6.930722 ACAATCGATGCAGTGTTCATATGATA 59.069 34.615 6.17 0.00 0.00 2.15
3689 3782 2.700897 CAAGGAGGTCTTCGGGTATGAT 59.299 50.000 0.00 0.00 32.41 2.45
3705 3798 8.185505 TCGGGTATGATGTTTTAGCATTTTAAC 58.814 33.333 0.00 0.00 36.64 2.01
3950 4045 3.552132 TGTAGCTTTATGCCATTCCGA 57.448 42.857 0.00 0.00 44.23 4.55
3951 4046 3.202906 TGTAGCTTTATGCCATTCCGAC 58.797 45.455 0.00 0.00 44.23 4.79
3952 4047 2.418368 AGCTTTATGCCATTCCGACA 57.582 45.000 0.00 0.00 44.23 4.35
3953 4048 2.936202 AGCTTTATGCCATTCCGACAT 58.064 42.857 0.00 0.00 44.23 3.06
3954 4049 3.290710 AGCTTTATGCCATTCCGACATT 58.709 40.909 0.00 0.00 44.23 2.71
3955 4050 3.316308 AGCTTTATGCCATTCCGACATTC 59.684 43.478 0.00 0.00 44.23 2.67
3956 4051 3.316308 GCTTTATGCCATTCCGACATTCT 59.684 43.478 0.00 0.00 35.15 2.40
3957 4052 4.790766 GCTTTATGCCATTCCGACATTCTG 60.791 45.833 0.00 0.00 35.15 3.02
4040 4135 3.643320 TCTCAACACTTGTCAGTCCAGAT 59.357 43.478 0.00 0.00 0.00 2.90
4111 4206 3.869065 ACGACTCTTCTGTCCAACAAAA 58.131 40.909 0.00 0.00 33.70 2.44
4508 4608 4.729868 GCTCCAAATATGACCCAGGTAAT 58.270 43.478 0.00 0.00 0.00 1.89
4514 4614 2.038387 ATGACCCAGGTAATGCGTTC 57.962 50.000 0.00 0.00 0.00 3.95
4566 4692 2.159085 GGTGGATACTAACTCTTGCGCT 60.159 50.000 9.73 0.00 37.61 5.92
4574 4700 4.566004 ACTAACTCTTGCGCTCATGTAAA 58.434 39.130 9.73 0.00 0.00 2.01
4690 4816 1.691219 TCCAACCTGGAAGATGCCC 59.309 57.895 0.00 0.00 45.00 5.36
4747 4873 0.104672 TCAGAACCCCAGTCTTCCCA 60.105 55.000 0.00 0.00 0.00 4.37
4860 4986 0.807667 CTCCTGTGGAAGGCGATTCG 60.808 60.000 0.62 0.62 46.92 3.34
4893 5019 2.565391 TGTCCATACAAGTGATGTCCGT 59.435 45.455 0.00 0.00 42.70 4.69
5085 5211 2.355108 CCCTCCAGCTGAAAAATCGAGA 60.355 50.000 17.39 0.00 0.00 4.04
5089 5215 2.079158 CAGCTGAAAAATCGAGAGGCA 58.921 47.619 8.42 0.00 0.00 4.75
5097 5223 0.176680 AATCGAGAGGCACGAGCATT 59.823 50.000 7.26 0.00 44.61 3.56
5354 5481 5.278758 GCCTTTGCTTCCTTTGTTGTACATA 60.279 40.000 0.00 0.00 33.53 2.29
5414 5541 5.163953 CGTCCTGAACATGTGTTATTCTCAC 60.164 44.000 0.00 0.00 38.56 3.51
5495 5622 5.871524 TCATCGCATCAGATAGCTTTATTCC 59.128 40.000 0.00 0.00 0.00 3.01
5496 5623 5.213891 TCGCATCAGATAGCTTTATTCCA 57.786 39.130 0.00 0.00 0.00 3.53
5512 5639 1.452108 CCACCTTCCGCCCTTCATC 60.452 63.158 0.00 0.00 0.00 2.92
5524 5651 2.296190 GCCCTTCATCCTTTTCGTTTGT 59.704 45.455 0.00 0.00 0.00 2.83
5550 5677 3.664107 TCTGTCCCGAGATTTTCACAAG 58.336 45.455 0.00 0.00 0.00 3.16
5553 5680 4.456535 TGTCCCGAGATTTTCACAAGAAA 58.543 39.130 0.00 0.00 41.78 2.52
5611 5738 1.154169 TCGTTCGTCGAATCCACCG 60.154 57.895 11.45 9.57 45.98 4.94
5613 5740 1.670971 CGTTCGTCGAATCCACCGTG 61.671 60.000 11.45 0.00 42.86 4.94
5687 5814 1.712081 CGAGAGGAATTGCAGTGCG 59.288 57.895 11.20 0.00 0.00 5.34
5690 5817 1.537202 GAGAGGAATTGCAGTGCGTTT 59.463 47.619 11.20 6.33 0.00 3.60
5693 5820 1.000274 AGGAATTGCAGTGCGTTTTCC 60.000 47.619 24.94 24.94 35.30 3.13
5770 5902 1.229428 CACTTGACACCAGTGCGATT 58.771 50.000 0.00 0.00 0.00 3.34
5771 5903 1.603802 CACTTGACACCAGTGCGATTT 59.396 47.619 0.00 0.00 0.00 2.17
5789 5921 4.319694 CGATTTTCAGTGACAAGTGCATCA 60.320 41.667 0.00 0.00 0.00 3.07
5790 5922 3.969117 TTTCAGTGACAAGTGCATCAC 57.031 42.857 9.67 9.67 44.64 3.06
5796 5928 2.918571 ACAAGTGCATCACTGGTCG 58.081 52.632 1.34 0.00 44.40 4.79
5799 5936 2.436646 GTGCATCACTGGTCGGGG 60.437 66.667 0.00 0.00 0.00 5.73
5808 5945 2.045731 TGGTCGGGGGAAAATCGC 60.046 61.111 0.00 0.00 0.00 4.58
5857 6001 1.538276 GCGGAATGTGCGAATTTGAG 58.462 50.000 0.00 0.00 30.86 3.02
6004 6155 1.488393 AGCTCTACCTGCAGATTTCCC 59.512 52.381 17.39 0.00 0.00 3.97
6006 6157 2.092699 GCTCTACCTGCAGATTTCCCTT 60.093 50.000 17.39 0.00 0.00 3.95
6007 6158 3.802866 CTCTACCTGCAGATTTCCCTTC 58.197 50.000 17.39 0.00 0.00 3.46
6009 6160 1.376649 ACCTGCAGATTTCCCTTCCT 58.623 50.000 17.39 0.00 0.00 3.36
6020 6171 5.488919 AGATTTCCCTTCCTCTGACATGTTA 59.511 40.000 0.00 0.00 0.00 2.41
6079 6230 4.346730 AGATGCACATTTCCATTTCCTCA 58.653 39.130 0.00 0.00 0.00 3.86
6093 6244 0.322816 TCCTCATCCCAAGTTGCAGC 60.323 55.000 0.00 0.00 0.00 5.25
6116 6267 2.754002 GGAGTATATACCGGCTCCACTC 59.246 54.545 16.17 14.41 45.00 3.51
6123 6274 2.027625 CCGGCTCCACTCGTGAAAC 61.028 63.158 0.00 0.00 0.00 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.898152 TCTAATGATATTGGTGTTGTTATGTGA 57.102 29.630 0.00 0.00 0.00 3.58
9 10 9.857656 AGATGAATCTAATGATATTGGTGTTGT 57.142 29.630 0.00 0.00 34.85 3.32
12 13 9.293404 CCAAGATGAATCTAATGATATTGGTGT 57.707 33.333 0.00 0.00 35.76 4.16
13 14 9.511272 TCCAAGATGAATCTAATGATATTGGTG 57.489 33.333 0.00 0.00 35.76 4.17
92 93 9.930693 ACTTTGTTAAGTTTGACCAAATTTACA 57.069 25.926 9.11 8.40 41.85 2.41
115 116 5.004922 TGAATTTGCCGAAAGTCAAACTT 57.995 34.783 0.00 0.00 41.82 2.66
116 117 4.647424 TGAATTTGCCGAAAGTCAAACT 57.353 36.364 0.00 0.00 41.82 2.66
120 121 4.297510 CACATTGAATTTGCCGAAAGTCA 58.702 39.130 0.00 0.00 42.76 3.41
121 122 3.121778 GCACATTGAATTTGCCGAAAGTC 59.878 43.478 5.03 0.00 36.82 3.01
122 123 3.059166 GCACATTGAATTTGCCGAAAGT 58.941 40.909 5.03 0.00 0.00 2.66
123 124 3.058450 TGCACATTGAATTTGCCGAAAG 58.942 40.909 13.13 0.00 35.26 2.62
124 125 3.058450 CTGCACATTGAATTTGCCGAAA 58.942 40.909 13.13 0.00 35.26 3.46
125 126 2.295629 TCTGCACATTGAATTTGCCGAA 59.704 40.909 13.13 0.00 35.26 4.30
126 127 1.885233 TCTGCACATTGAATTTGCCGA 59.115 42.857 13.13 9.67 35.26 5.54
127 128 2.256174 CTCTGCACATTGAATTTGCCG 58.744 47.619 13.13 7.51 35.26 5.69
128 129 3.308438 ACTCTGCACATTGAATTTGCC 57.692 42.857 13.13 0.00 35.26 4.52
129 130 6.768029 TTTTACTCTGCACATTGAATTTGC 57.232 33.333 9.23 9.23 36.76 3.68
130 131 8.482429 GTCTTTTTACTCTGCACATTGAATTTG 58.518 33.333 0.00 0.00 0.00 2.32
131 132 7.653311 GGTCTTTTTACTCTGCACATTGAATTT 59.347 33.333 0.00 0.00 0.00 1.82
132 133 7.014615 AGGTCTTTTTACTCTGCACATTGAATT 59.985 33.333 0.00 0.00 0.00 2.17
133 134 6.491403 AGGTCTTTTTACTCTGCACATTGAAT 59.509 34.615 0.00 0.00 0.00 2.57
134 135 5.827797 AGGTCTTTTTACTCTGCACATTGAA 59.172 36.000 0.00 0.00 0.00 2.69
135 136 5.376625 AGGTCTTTTTACTCTGCACATTGA 58.623 37.500 0.00 0.00 0.00 2.57
136 137 5.695851 AGGTCTTTTTACTCTGCACATTG 57.304 39.130 0.00 0.00 0.00 2.82
137 138 6.770785 TGTTAGGTCTTTTTACTCTGCACATT 59.229 34.615 0.00 0.00 0.00 2.71
138 139 6.296026 TGTTAGGTCTTTTTACTCTGCACAT 58.704 36.000 0.00 0.00 0.00 3.21
139 140 5.676552 TGTTAGGTCTTTTTACTCTGCACA 58.323 37.500 0.00 0.00 0.00 4.57
140 141 6.613755 TTGTTAGGTCTTTTTACTCTGCAC 57.386 37.500 0.00 0.00 0.00 4.57
141 142 6.770785 ACATTGTTAGGTCTTTTTACTCTGCA 59.229 34.615 0.00 0.00 0.00 4.41
142 143 7.203255 ACATTGTTAGGTCTTTTTACTCTGC 57.797 36.000 0.00 0.00 0.00 4.26
155 156 9.886132 CACTTTTAGGACTATACATTGTTAGGT 57.114 33.333 0.00 0.00 0.00 3.08
156 157 8.827677 GCACTTTTAGGACTATACATTGTTAGG 58.172 37.037 0.00 0.00 0.00 2.69
157 158 9.601217 AGCACTTTTAGGACTATACATTGTTAG 57.399 33.333 0.00 0.10 0.00 2.34
158 159 9.378551 CAGCACTTTTAGGACTATACATTGTTA 57.621 33.333 0.00 0.00 0.00 2.41
159 160 7.148239 GCAGCACTTTTAGGACTATACATTGTT 60.148 37.037 0.00 0.00 0.00 2.83
160 161 6.316390 GCAGCACTTTTAGGACTATACATTGT 59.684 38.462 0.00 0.00 0.00 2.71
161 162 6.238484 GGCAGCACTTTTAGGACTATACATTG 60.238 42.308 0.00 0.00 0.00 2.82
162 163 5.823045 GGCAGCACTTTTAGGACTATACATT 59.177 40.000 0.00 0.00 0.00 2.71
163 164 5.104527 TGGCAGCACTTTTAGGACTATACAT 60.105 40.000 0.00 0.00 0.00 2.29
164 165 4.224147 TGGCAGCACTTTTAGGACTATACA 59.776 41.667 0.00 0.00 0.00 2.29
208 226 0.661020 GACGGACTGTTTGGTTGGTG 59.339 55.000 0.00 0.00 0.00 4.17
223 241 4.456253 CGACTGACGGACGGACGG 62.456 72.222 6.00 0.00 38.80 4.79
225 243 0.797249 CATTCGACTGACGGACGGAC 60.797 60.000 6.32 0.00 42.82 4.79
226 244 0.956902 TCATTCGACTGACGGACGGA 60.957 55.000 0.65 0.00 42.82 4.69
227 245 0.109458 TTCATTCGACTGACGGACGG 60.109 55.000 4.77 0.00 42.82 4.79
228 246 1.846782 GATTCATTCGACTGACGGACG 59.153 52.381 4.77 0.00 42.82 4.79
229 247 2.876091 TGATTCATTCGACTGACGGAC 58.124 47.619 4.77 0.00 42.82 4.79
230 248 3.056821 ACTTGATTCATTCGACTGACGGA 60.057 43.478 4.77 0.00 42.82 4.69
231 249 3.254060 ACTTGATTCATTCGACTGACGG 58.746 45.455 4.77 0.00 42.82 4.79
232 250 4.857037 TGTACTTGATTCATTCGACTGACG 59.143 41.667 4.77 0.00 44.09 4.35
267 285 5.105797 TGTGGCCATGAGCAAATTAACTAAG 60.106 40.000 9.72 0.00 46.50 2.18
300 318 8.211629 AGCTAAATTAACCCGAGAGTAATGATT 58.788 33.333 0.00 0.00 0.00 2.57
345 363 8.943002 ACAGTTAGTTATTTATTTAAGCGTGCT 58.057 29.630 0.00 0.00 0.00 4.40
375 393 7.545965 CGGTTCTTCTCTTCTTTCTGCTATTTA 59.454 37.037 0.00 0.00 0.00 1.40
377 395 5.872070 CGGTTCTTCTCTTCTTTCTGCTATT 59.128 40.000 0.00 0.00 0.00 1.73
382 403 3.185391 GTGCGGTTCTTCTCTTCTTTCTG 59.815 47.826 0.00 0.00 0.00 3.02
535 572 1.168714 GATTTGTGTGGAGGTGGAGC 58.831 55.000 0.00 0.00 0.00 4.70
536 573 1.352352 AGGATTTGTGTGGAGGTGGAG 59.648 52.381 0.00 0.00 0.00 3.86
537 574 1.444933 AGGATTTGTGTGGAGGTGGA 58.555 50.000 0.00 0.00 0.00 4.02
538 575 3.545703 GATAGGATTTGTGTGGAGGTGG 58.454 50.000 0.00 0.00 0.00 4.61
539 576 3.054434 TGGATAGGATTTGTGTGGAGGTG 60.054 47.826 0.00 0.00 0.00 4.00
540 577 3.054361 GTGGATAGGATTTGTGTGGAGGT 60.054 47.826 0.00 0.00 0.00 3.85
541 578 3.545703 GTGGATAGGATTTGTGTGGAGG 58.454 50.000 0.00 0.00 0.00 4.30
542 579 3.054434 TGGTGGATAGGATTTGTGTGGAG 60.054 47.826 0.00 0.00 0.00 3.86
543 580 2.916269 TGGTGGATAGGATTTGTGTGGA 59.084 45.455 0.00 0.00 0.00 4.02
544 581 3.364460 TGGTGGATAGGATTTGTGTGG 57.636 47.619 0.00 0.00 0.00 4.17
545 582 5.299279 GGTAATGGTGGATAGGATTTGTGTG 59.701 44.000 0.00 0.00 0.00 3.82
546 583 5.445964 GGTAATGGTGGATAGGATTTGTGT 58.554 41.667 0.00 0.00 0.00 3.72
654 693 3.400255 GAACGGGTATTCTAATCTGGGC 58.600 50.000 0.00 0.00 0.00 5.36
761 800 1.686325 GCTCCGGTGGCTCTCCATTA 61.686 60.000 0.00 0.00 45.62 1.90
878 917 4.202161 GGATATGTGAGCTTTCTTCCTCGA 60.202 45.833 0.00 0.00 0.00 4.04
880 919 4.054671 CGGATATGTGAGCTTTCTTCCTC 58.945 47.826 0.00 0.00 0.00 3.71
881 920 3.181461 CCGGATATGTGAGCTTTCTTCCT 60.181 47.826 0.00 0.00 0.00 3.36
882 921 3.134458 CCGGATATGTGAGCTTTCTTCC 58.866 50.000 0.00 0.00 0.00 3.46
883 922 3.134458 CCCGGATATGTGAGCTTTCTTC 58.866 50.000 0.73 0.00 0.00 2.87
894 960 0.250727 CCAATTCGGCCCGGATATGT 60.251 55.000 0.73 0.00 0.00 2.29
897 963 1.448497 GACCAATTCGGCCCGGATA 59.552 57.895 0.73 0.00 39.03 2.59
898 964 2.192175 GACCAATTCGGCCCGGAT 59.808 61.111 0.73 0.00 39.03 4.18
900 966 2.737881 TAGGACCAATTCGGCCCGG 61.738 63.158 1.90 0.00 43.70 5.73
907 973 2.522638 CGCGGCGTAGGACCAATTC 61.523 63.158 15.36 0.00 0.00 2.17
1136 1208 2.285969 ATCCTGCAGGGCTCTGGT 60.286 61.111 32.23 7.40 41.19 4.00
1407 1482 3.372554 GACGGACCTAGCACTGGGC 62.373 68.421 0.00 0.00 45.30 5.36
1416 1491 3.200593 GAGAGCGCGACGGACCTA 61.201 66.667 12.10 0.00 0.00 3.08
1508 1584 9.823098 GATGATACTGAATATGCAGAAACATTC 57.177 33.333 18.17 3.63 39.20 2.67
1543 1619 8.560374 AGTGAAAACTACTTCAGAAATAACAGC 58.440 33.333 0.00 0.00 36.01 4.40
1581 1661 9.799106 AAATAGGCAAACAGTAGCATCTAATAT 57.201 29.630 0.83 0.00 0.00 1.28
1582 1662 9.627123 AAAATAGGCAAACAGTAGCATCTAATA 57.373 29.630 0.83 0.00 0.00 0.98
1584 1664 7.148086 CCAAAATAGGCAAACAGTAGCATCTAA 60.148 37.037 0.83 0.00 0.00 2.10
1585 1665 6.318648 CCAAAATAGGCAAACAGTAGCATCTA 59.681 38.462 0.83 0.00 0.00 1.98
1586 1666 5.126061 CCAAAATAGGCAAACAGTAGCATCT 59.874 40.000 0.83 0.00 0.00 2.90
1587 1667 5.105756 ACCAAAATAGGCAAACAGTAGCATC 60.106 40.000 0.83 0.00 0.00 3.91
1588 1668 4.772100 ACCAAAATAGGCAAACAGTAGCAT 59.228 37.500 0.83 0.00 0.00 3.79
1591 1671 6.128007 CCACTACCAAAATAGGCAAACAGTAG 60.128 42.308 0.00 0.00 0.00 2.57
1612 1698 6.954232 TCTCTTTATCCCGATTAAAACCACT 58.046 36.000 0.00 0.00 0.00 4.00
1633 1719 0.535335 TCCAGCCAACGTACCATCTC 59.465 55.000 0.00 0.00 0.00 2.75
1643 1729 1.212751 GGTCGCAATTCCAGCCAAC 59.787 57.895 0.00 0.00 0.00 3.77
1658 1744 1.604278 GACCAAAAGCACACAGAGGTC 59.396 52.381 0.00 0.00 37.50 3.85
1796 1882 0.883833 CAGCCAAGTACCAGCAAAGG 59.116 55.000 2.65 0.00 0.00 3.11
1880 1966 5.780793 ACTATTTCTAGACAGAGTGGTGGTT 59.219 40.000 5.40 0.00 30.73 3.67
1895 1981 7.040686 GGGAAAACTCAGCACAAACTATTTCTA 60.041 37.037 0.00 0.00 0.00 2.10
1979 2065 2.030274 ACCCGTTACAGAAAAGCAATGC 60.030 45.455 0.00 0.00 0.00 3.56
2046 2132 1.089920 CTGTTCCATTTCCAGCCTCG 58.910 55.000 0.00 0.00 0.00 4.63
2167 2253 9.136323 ACAGGAAAAGAATAAAGTGAACAGAAT 57.864 29.630 0.00 0.00 0.00 2.40
2182 2268 2.494059 CTGCGAAGGACAGGAAAAGAA 58.506 47.619 0.00 0.00 0.00 2.52
2183 2269 1.878102 GCTGCGAAGGACAGGAAAAGA 60.878 52.381 0.00 0.00 35.62 2.52
2184 2270 0.519077 GCTGCGAAGGACAGGAAAAG 59.481 55.000 0.00 0.00 35.62 2.27
2185 2271 1.227999 CGCTGCGAAGGACAGGAAAA 61.228 55.000 18.66 0.00 35.62 2.29
2186 2272 1.667830 CGCTGCGAAGGACAGGAAA 60.668 57.895 18.66 0.00 35.62 3.13
2187 2273 2.048222 CGCTGCGAAGGACAGGAA 60.048 61.111 18.66 0.00 35.62 3.36
2188 2274 4.069232 CCGCTGCGAAGGACAGGA 62.069 66.667 25.45 0.00 35.62 3.86
2189 2275 4.379243 ACCGCTGCGAAGGACAGG 62.379 66.667 25.45 6.36 35.62 4.00
2190 2276 3.114616 CACCGCTGCGAAGGACAG 61.115 66.667 25.45 7.16 38.22 3.51
2191 2277 4.680237 CCACCGCTGCGAAGGACA 62.680 66.667 25.45 0.00 0.00 4.02
2192 2278 2.573609 ATACCACCGCTGCGAAGGAC 62.574 60.000 29.83 0.00 0.00 3.85
2193 2279 1.895020 AATACCACCGCTGCGAAGGA 61.895 55.000 29.83 14.67 0.00 3.36
2194 2280 1.429148 GAATACCACCGCTGCGAAGG 61.429 60.000 25.45 24.72 0.00 3.46
2195 2281 0.460284 AGAATACCACCGCTGCGAAG 60.460 55.000 25.45 14.82 0.00 3.79
2196 2282 0.739462 CAGAATACCACCGCTGCGAA 60.739 55.000 25.45 3.54 0.00 4.70
2197 2283 1.153647 CAGAATACCACCGCTGCGA 60.154 57.895 25.45 2.65 0.00 5.10
2198 2284 1.421410 GACAGAATACCACCGCTGCG 61.421 60.000 16.34 16.34 31.74 5.18
2199 2285 1.090052 GGACAGAATACCACCGCTGC 61.090 60.000 0.00 0.00 31.74 5.25
2200 2286 0.249120 TGGACAGAATACCACCGCTG 59.751 55.000 0.00 0.00 34.65 5.18
2201 2287 1.134401 CATGGACAGAATACCACCGCT 60.134 52.381 0.00 0.00 39.06 5.52
2202 2288 1.299541 CATGGACAGAATACCACCGC 58.700 55.000 0.00 0.00 39.06 5.68
2203 2289 2.677836 CAACATGGACAGAATACCACCG 59.322 50.000 0.00 0.00 39.06 4.94
2204 2290 2.423538 GCAACATGGACAGAATACCACC 59.576 50.000 0.00 0.00 39.06 4.61
2205 2291 3.347216 AGCAACATGGACAGAATACCAC 58.653 45.455 0.00 0.00 39.06 4.16
2206 2292 3.719268 AGCAACATGGACAGAATACCA 57.281 42.857 0.00 0.00 40.57 3.25
2207 2293 5.648092 ACTAAAGCAACATGGACAGAATACC 59.352 40.000 0.00 0.00 0.00 2.73
2208 2294 6.149474 ACACTAAAGCAACATGGACAGAATAC 59.851 38.462 0.00 0.00 0.00 1.89
2209 2295 6.237901 ACACTAAAGCAACATGGACAGAATA 58.762 36.000 0.00 0.00 0.00 1.75
2210 2296 5.072741 ACACTAAAGCAACATGGACAGAAT 58.927 37.500 0.00 0.00 0.00 2.40
2211 2297 4.460263 ACACTAAAGCAACATGGACAGAA 58.540 39.130 0.00 0.00 0.00 3.02
2212 2298 4.085357 ACACTAAAGCAACATGGACAGA 57.915 40.909 0.00 0.00 0.00 3.41
2213 2299 4.320494 GGAACACTAAAGCAACATGGACAG 60.320 45.833 0.00 0.00 0.00 3.51
2214 2300 3.568007 GGAACACTAAAGCAACATGGACA 59.432 43.478 0.00 0.00 0.00 4.02
2215 2301 3.057526 GGGAACACTAAAGCAACATGGAC 60.058 47.826 0.00 0.00 0.00 4.02
2216 2302 3.153919 GGGAACACTAAAGCAACATGGA 58.846 45.455 0.00 0.00 0.00 3.41
2245 2331 7.036996 TGCTTACAAGTCAAAACATGATTCA 57.963 32.000 0.00 0.00 40.97 2.57
2313 2399 4.621034 CCGATTAAAACAACCATGCACTTC 59.379 41.667 0.00 0.00 0.00 3.01
2319 2405 4.490743 GGAACCCGATTAAAACAACCATG 58.509 43.478 0.00 0.00 0.00 3.66
2510 2600 1.842052 TACAGGCACCATCGAGTACA 58.158 50.000 0.00 0.00 0.00 2.90
2554 2644 2.228822 ACAAAAGGTGCATCGGCTAAAG 59.771 45.455 0.00 0.00 41.91 1.85
2560 2650 1.472082 TGCATACAAAAGGTGCATCGG 59.528 47.619 0.00 0.00 43.30 4.18
2705 2795 6.129179 TCCCAACAGTTCTTCTTTGATCTTT 58.871 36.000 0.00 0.00 0.00 2.52
2735 2826 9.818270 ATATGTCCATTCTCCATTGTAAATCAT 57.182 29.630 0.00 0.00 0.00 2.45
2785 2876 5.359009 AGACAAATGATAATGAGCAAGGTGG 59.641 40.000 0.00 0.00 0.00 4.61
2864 2955 2.575532 CTCAAGAGGACCACAAAGCAA 58.424 47.619 0.00 0.00 0.00 3.91
2865 2956 2.260844 CTCAAGAGGACCACAAAGCA 57.739 50.000 0.00 0.00 0.00 3.91
2937 3029 6.350445 CCTGGAATTCCCAAGACAAACAATAG 60.350 42.308 21.90 6.85 46.07 1.73
3017 3110 3.118519 AGGCAAAATGATTCCATCCTTGC 60.119 43.478 12.76 12.76 43.54 4.01
3040 3133 6.707440 TTGTGCCACTTTATCTTCTTTTCA 57.293 33.333 0.00 0.00 0.00 2.69
3105 3198 4.022068 ACACATATGCTCCAGTTTTGTTGG 60.022 41.667 1.58 0.00 37.04 3.77
3126 3219 4.096231 CCCGATTATTGAATGAGCACAACA 59.904 41.667 0.00 0.00 0.00 3.33
3254 3347 3.003394 TCACCATAAAGATGTGGGCAG 57.997 47.619 0.00 0.00 41.86 4.85
3415 3508 5.722021 AGGTCAAGGCATATTTCGTTTTT 57.278 34.783 0.00 0.00 0.00 1.94
3416 3509 6.433093 ACTTAGGTCAAGGCATATTTCGTTTT 59.567 34.615 0.00 0.00 38.70 2.43
3417 3510 5.944007 ACTTAGGTCAAGGCATATTTCGTTT 59.056 36.000 0.00 0.00 38.70 3.60
3418 3511 5.354234 CACTTAGGTCAAGGCATATTTCGTT 59.646 40.000 0.00 0.00 38.70 3.85
3419 3512 4.876107 CACTTAGGTCAAGGCATATTTCGT 59.124 41.667 0.00 0.00 38.70 3.85
3513 3606 4.451900 AGAACACCAACAGTACAAGGAAG 58.548 43.478 0.00 0.00 0.00 3.46
3522 3615 4.150897 TCAGCTAAAGAACACCAACAGT 57.849 40.909 0.00 0.00 0.00 3.55
3537 3630 6.016024 ACTGCATTTGAAGTTTGAATCAGCTA 60.016 34.615 0.00 0.00 26.38 3.32
3611 3704 1.202651 CGGAACACTGTTTCCTCTGGT 60.203 52.381 15.08 0.00 42.74 4.00
3797 3892 6.203338 TCTCCGCATTTATACGAAAAATACCC 59.797 38.462 0.00 0.00 0.00 3.69
3951 4046 1.878088 AGTGCTGCTGTCAACAGAATG 59.122 47.619 14.20 4.16 46.59 2.67
3952 4047 2.149578 GAGTGCTGCTGTCAACAGAAT 58.850 47.619 14.20 0.00 46.59 2.40
3953 4048 1.134431 TGAGTGCTGCTGTCAACAGAA 60.134 47.619 14.20 2.25 46.59 3.02
3954 4049 0.465287 TGAGTGCTGCTGTCAACAGA 59.535 50.000 14.20 0.00 46.59 3.41
3955 4050 0.585357 GTGAGTGCTGCTGTCAACAG 59.415 55.000 5.77 5.77 46.40 3.16
3956 4051 0.107752 TGTGAGTGCTGCTGTCAACA 60.108 50.000 0.00 2.84 0.00 3.33
3957 4052 1.233019 ATGTGAGTGCTGCTGTCAAC 58.767 50.000 0.00 0.00 0.00 3.18
4040 4135 6.659824 AGACTGGTTTCCACTAGAAAGAAAA 58.340 36.000 0.00 0.00 45.11 2.29
4508 4608 1.871039 GTTTGCTGTTAGGAGAACGCA 59.129 47.619 0.00 0.00 0.00 5.24
4514 4614 4.065088 TGTTGCTAGTTTGCTGTTAGGAG 58.935 43.478 0.00 0.00 0.00 3.69
4566 4692 3.273434 GTCTGCCATCTGCTTTACATGA 58.727 45.455 0.00 0.00 42.00 3.07
4574 4700 0.323178 CAAAGGGTCTGCCATCTGCT 60.323 55.000 0.00 0.00 42.00 4.24
4690 4816 0.895559 GGGTCCTTCTGTGGCAAAGG 60.896 60.000 9.71 9.71 42.89 3.11
4747 4873 8.112183 AGATGTTTCTTCAGGTTGAGGATTAAT 58.888 33.333 0.00 0.00 32.38 1.40
4860 4986 2.093869 TGTATGGACAACGGAAGCTACC 60.094 50.000 0.00 0.00 30.68 3.18
4893 5019 3.379445 GACCCCTCCACGCTCGAA 61.379 66.667 0.00 0.00 0.00 3.71
5062 5188 1.614317 CGATTTTTCAGCTGGAGGGGT 60.614 52.381 15.13 0.00 0.00 4.95
5064 5190 2.012673 CTCGATTTTTCAGCTGGAGGG 58.987 52.381 15.13 0.00 0.00 4.30
5085 5211 2.037136 GCTCACAATGCTCGTGCCT 61.037 57.895 7.05 0.00 38.71 4.75
5089 5215 2.244117 ATCCGGCTCACAATGCTCGT 62.244 55.000 0.00 0.00 0.00 4.18
5354 5481 2.040412 GGTCCAGGGAGTGAAGAAATGT 59.960 50.000 0.00 0.00 0.00 2.71
5414 5541 2.289945 CCTCACTTCAGAAAGGTCAGGG 60.290 54.545 0.00 0.00 36.78 4.45
5495 5622 1.452108 GGATGAAGGGCGGAAGGTG 60.452 63.158 0.00 0.00 0.00 4.00
5496 5623 1.208165 AAGGATGAAGGGCGGAAGGT 61.208 55.000 0.00 0.00 0.00 3.50
5512 5639 4.976116 GGACAGATTCAACAAACGAAAAGG 59.024 41.667 0.00 0.00 0.00 3.11
5524 5651 4.695455 GTGAAAATCTCGGGACAGATTCAA 59.305 41.667 5.71 0.00 41.45 2.69
5611 5738 5.028375 CGTGAAAACTGGAAAAGAGTTCAC 58.972 41.667 0.00 0.00 42.90 3.18
5613 5740 4.334481 TCCGTGAAAACTGGAAAAGAGTTC 59.666 41.667 0.00 0.00 32.33 3.01
5683 5810 2.094130 AGCTAGGTAGAGGAAAACGCAC 60.094 50.000 0.00 0.00 0.00 5.34
5687 5814 4.632251 GCAGAAAGCTAGGTAGAGGAAAAC 59.368 45.833 0.00 0.00 41.15 2.43
5690 5817 2.766828 GGCAGAAAGCTAGGTAGAGGAA 59.233 50.000 0.00 0.00 44.79 3.36
5693 5820 2.763448 ACAGGCAGAAAGCTAGGTAGAG 59.237 50.000 0.00 0.00 44.79 2.43
5770 5902 3.969117 GTGATGCACTTGTCACTGAAA 57.031 42.857 10.29 0.00 41.10 2.69
5789 5921 1.298667 CGATTTTCCCCCGACCAGT 59.701 57.895 0.00 0.00 0.00 4.00
5790 5922 2.112815 GCGATTTTCCCCCGACCAG 61.113 63.158 0.00 0.00 0.00 4.00
5791 5923 2.045731 GCGATTTTCCCCCGACCA 60.046 61.111 0.00 0.00 0.00 4.02
5792 5924 2.827190 GGCGATTTTCCCCCGACC 60.827 66.667 0.00 0.00 0.00 4.79
5793 5925 2.827190 GGGCGATTTTCCCCCGAC 60.827 66.667 0.00 0.00 37.81 4.79
5799 5936 2.159099 GGAGAAAATGGGGCGATTTTCC 60.159 50.000 20.88 15.20 46.72 3.13
5808 5945 0.413434 AACCCTGGGAGAAAATGGGG 59.587 55.000 22.23 0.00 42.00 4.96
5939 6084 3.119531 TCGCACAAATTTGATGGTGATCC 60.120 43.478 24.64 4.95 33.16 3.36
6004 6155 3.875727 CCTGCATAACATGTCAGAGGAAG 59.124 47.826 12.56 1.85 36.90 3.46
6006 6157 2.420547 GCCTGCATAACATGTCAGAGGA 60.421 50.000 12.56 0.00 36.90 3.71
6007 6158 1.945394 GCCTGCATAACATGTCAGAGG 59.055 52.381 12.56 8.78 36.90 3.69
6009 6160 1.281577 TGGCCTGCATAACATGTCAGA 59.718 47.619 12.56 0.00 36.90 3.27
6020 6171 1.677966 CTTCAGCACTGGCCTGCAT 60.678 57.895 18.35 2.00 42.56 3.96
6079 6230 0.323178 CTCCTGCTGCAACTTGGGAT 60.323 55.000 3.02 0.00 0.00 3.85
6116 6267 2.748461 TTCAGGCTTTTCGTTTCACG 57.252 45.000 0.00 0.00 44.19 4.35


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

AutoCloner maintained by Alex Coulton.