Multiple sequence alignment - TraesCS3D01G264900

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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 TraesCS3D01G264900 chr3D 100.000 4766 0 0 1 4766 366798266 366803031 0.000000e+00 8802.0
1 TraesCS3D01G264900 chr3D 96.396 333 10 2 1 332 489615582 489615251 9.020000e-152 547.0
2 TraesCS3D01G264900 chr3A 96.306 3952 130 8 329 4275 488993238 488997178 0.000000e+00 6475.0
3 TraesCS3D01G264900 chr3A 94.556 496 14 4 4277 4766 488997289 488997777 0.000000e+00 754.0
4 TraesCS3D01G264900 chr3B 96.568 2797 90 4 875 3667 478011902 478014696 0.000000e+00 4628.0
5 TraesCS3D01G264900 chr3B 95.114 614 26 2 3661 4273 478050205 478050815 0.000000e+00 965.0
6 TraesCS3D01G264900 chr3B 92.308 520 24 4 333 838 478011384 478011901 0.000000e+00 725.0
7 TraesCS3D01G264900 chr3B 91.467 375 19 1 4392 4766 478052707 478053068 1.980000e-138 503.0
8 TraesCS3D01G264900 chr3B 94.309 123 6 1 4274 4395 478050925 478051047 2.260000e-43 187.0
9 TraesCS3D01G264900 chr2B 86.962 1603 199 8 2169 3766 258641893 258643490 0.000000e+00 1794.0
10 TraesCS3D01G264900 chr2B 86.425 221 30 0 1295 1515 258640075 258640295 4.770000e-60 243.0
11 TraesCS3D01G264900 chr2B 89.933 149 15 0 2018 2166 258641655 258641803 4.870000e-45 193.0
12 TraesCS3D01G264900 chr2A 86.800 1606 202 8 2169 3769 278917224 278915624 0.000000e+00 1783.0
13 TraesCS3D01G264900 chr2A 87.156 218 28 0 1298 1515 278919094 278918877 1.020000e-61 248.0
14 TraesCS3D01G264900 chr2A 89.474 152 16 0 2018 2169 278917462 278917311 4.870000e-45 193.0
15 TraesCS3D01G264900 chr2D 86.758 1601 206 5 2169 3766 204495988 204497585 0.000000e+00 1777.0
16 TraesCS3D01G264900 chr2D 95.706 326 12 1 1 324 457661799 457662124 1.520000e-144 523.0
17 TraesCS3D01G264900 chr2D 86.425 221 30 0 1295 1515 204494179 204494399 4.770000e-60 243.0
18 TraesCS3D01G264900 chr2D 89.933 149 15 0 2018 2166 204495751 204495899 4.870000e-45 193.0
19 TraesCS3D01G264900 chr1D 96.605 324 11 0 1 324 463236847 463237170 5.430000e-149 538.0
20 TraesCS3D01G264900 chr1D 91.743 327 21 6 1 324 276210151 276209828 2.620000e-122 449.0
21 TraesCS3D01G264900 chr6D 93.353 331 12 3 1 329 67085058 67085380 9.280000e-132 481.0
22 TraesCS3D01G264900 chr6A 91.018 334 27 2 1 332 138827610 138827278 9.410000e-122 448.0
23 TraesCS3D01G264900 chr4A 89.728 331 28 5 1 326 164317611 164317282 7.380000e-113 418.0
24 TraesCS3D01G264900 chr5A 88.131 337 34 6 1 335 603552910 603553242 3.460000e-106 396.0
25 TraesCS3D01G264900 chr4D 87.761 335 33 6 1 331 319094766 319094436 7.480000e-103 385.0
26 TraesCS3D01G264900 chr4B 88.263 213 24 1 1683 1894 672050112 672049900 2.200000e-63 254.0
27 TraesCS3D01G264900 chr7A 90.141 71 7 0 2181 2251 610963022 610963092 5.080000e-15 93.5


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 TraesCS3D01G264900 chr3D 366798266 366803031 4765 False 8802.000000 8802 100.000000 1 4766 1 chr3D.!!$F1 4765
1 TraesCS3D01G264900 chr3A 488993238 488997777 4539 False 3614.500000 6475 95.431000 329 4766 2 chr3A.!!$F1 4437
2 TraesCS3D01G264900 chr3B 478011384 478014696 3312 False 2676.500000 4628 94.438000 333 3667 2 chr3B.!!$F1 3334
3 TraesCS3D01G264900 chr3B 478050205 478053068 2863 False 551.666667 965 93.630000 3661 4766 3 chr3B.!!$F2 1105
4 TraesCS3D01G264900 chr2B 258640075 258643490 3415 False 743.333333 1794 87.773333 1295 3766 3 chr2B.!!$F1 2471
5 TraesCS3D01G264900 chr2A 278915624 278919094 3470 True 741.333333 1783 87.810000 1298 3769 3 chr2A.!!$R1 2471
6 TraesCS3D01G264900 chr2D 204494179 204497585 3406 False 737.666667 1777 87.705333 1295 3766 3 chr2D.!!$F2 2471

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
51 52 0.036199 GCATGCATTTTCAGGGGCAA 60.036 50.0 14.21 0.0 40.02 4.52 F
60 61 0.106268 TTCAGGGGCAAACAAGCTGA 60.106 50.0 0.00 0.0 34.17 4.26 F
157 158 0.107831 CCTTTGGGGAAGTGACGTGA 59.892 55.0 0.00 0.0 37.23 4.35 F
184 185 0.179200 CCATGTGCGTCGTTTTAGCC 60.179 55.0 0.00 0.0 0.00 3.93 F
1266 1287 0.248134 CGGAGTTCGACGATGAGGAC 60.248 60.0 0.00 0.0 42.43 3.85 F
2399 3489 0.394762 TCATCATCCACCAAGGCTGC 60.395 55.0 0.00 0.0 33.44 5.25 F
3269 4359 0.692419 ACCCTGAAGATCCCGCAGAT 60.692 55.0 8.24 0.0 38.17 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1541 1645 0.033601 ACCTTGGTCACCAACAAGCA 60.034 50.000 4.67 0.0 42.01 3.91 R
1839 2322 0.959372 GAGCAACACTCATGGCAGCT 60.959 55.000 0.00 0.0 45.49 4.24 R
1872 2355 1.665735 CCAAGCACGGTTTCCATTTCG 60.666 52.381 0.00 0.0 0.00 3.46 R
2067 3070 7.631377 GCAGCAACCTTCTTCAATATACCAAAT 60.631 37.037 0.00 0.0 0.00 2.32 R
2983 4073 0.179004 ACTTCATCAACGCACCCCAA 60.179 50.000 0.00 0.0 0.00 4.12 R
3292 4382 0.329261 CAGATGGCCTTCCTCACCAA 59.671 55.000 14.77 0.0 36.94 3.67 R
4159 5256 0.931005 GCCTCGAGCTGAATAAACCG 59.069 55.000 6.99 0.0 38.99 4.44 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
19 20 2.133281 TCATTTCCTGGCACATCTGG 57.867 50.000 0.00 0.00 38.20 3.86
20 21 0.458669 CATTTCCTGGCACATCTGGC 59.541 55.000 0.00 0.00 43.44 4.85
21 22 0.333993 ATTTCCTGGCACATCTGGCT 59.666 50.000 0.00 0.00 43.53 4.75
22 23 0.609957 TTTCCTGGCACATCTGGCTG 60.610 55.000 0.00 0.00 43.53 4.85
24 25 2.672908 CTGGCACATCTGGCTGGA 59.327 61.111 0.00 0.00 43.53 3.86
25 26 1.001764 CTGGCACATCTGGCTGGAA 60.002 57.895 0.00 0.00 43.53 3.53
26 27 0.609957 CTGGCACATCTGGCTGGAAA 60.610 55.000 0.00 0.00 43.53 3.13
27 28 0.609957 TGGCACATCTGGCTGGAAAG 60.610 55.000 0.00 0.00 43.53 2.62
28 29 0.322816 GGCACATCTGGCTGGAAAGA 60.323 55.000 0.00 0.00 39.91 2.52
29 30 1.538047 GCACATCTGGCTGGAAAGAA 58.462 50.000 0.00 0.00 0.00 2.52
30 31 1.888512 GCACATCTGGCTGGAAAGAAA 59.111 47.619 0.00 0.00 0.00 2.52
31 32 2.494870 GCACATCTGGCTGGAAAGAAAT 59.505 45.455 0.00 0.00 0.00 2.17
32 33 3.675228 GCACATCTGGCTGGAAAGAAATG 60.675 47.826 0.00 0.00 0.00 2.32
33 34 2.494870 ACATCTGGCTGGAAAGAAATGC 59.505 45.455 0.00 0.00 0.00 3.56
34 35 2.291209 TCTGGCTGGAAAGAAATGCA 57.709 45.000 0.00 0.00 0.00 3.96
35 36 2.811410 TCTGGCTGGAAAGAAATGCAT 58.189 42.857 0.00 0.00 0.00 3.96
36 37 2.494471 TCTGGCTGGAAAGAAATGCATG 59.506 45.455 0.00 0.00 0.00 4.06
37 38 1.066716 TGGCTGGAAAGAAATGCATGC 60.067 47.619 11.82 11.82 0.00 4.06
38 39 1.066716 GGCTGGAAAGAAATGCATGCA 60.067 47.619 25.04 25.04 0.00 3.96
39 40 2.419574 GGCTGGAAAGAAATGCATGCAT 60.420 45.455 27.46 27.46 38.46 3.96
48 49 2.702592 AATGCATGCATTTTCAGGGG 57.297 45.000 34.78 0.00 43.32 4.79
49 50 0.179468 ATGCATGCATTTTCAGGGGC 59.821 50.000 27.46 0.00 31.82 5.80
50 51 1.192803 TGCATGCATTTTCAGGGGCA 61.193 50.000 18.46 0.00 41.00 5.36
51 52 0.036199 GCATGCATTTTCAGGGGCAA 60.036 50.000 14.21 0.00 40.02 4.52
52 53 1.611148 GCATGCATTTTCAGGGGCAAA 60.611 47.619 14.21 0.00 40.02 3.68
53 54 2.078392 CATGCATTTTCAGGGGCAAAC 58.922 47.619 0.00 0.00 40.02 2.93
54 55 1.126488 TGCATTTTCAGGGGCAAACA 58.874 45.000 0.00 0.00 32.54 2.83
55 56 1.487976 TGCATTTTCAGGGGCAAACAA 59.512 42.857 0.00 0.00 32.54 2.83
56 57 2.145536 GCATTTTCAGGGGCAAACAAG 58.854 47.619 0.00 0.00 0.00 3.16
57 58 2.145536 CATTTTCAGGGGCAAACAAGC 58.854 47.619 0.00 0.00 0.00 4.01
58 59 1.494960 TTTTCAGGGGCAAACAAGCT 58.505 45.000 0.00 0.00 34.17 3.74
59 60 0.752054 TTTCAGGGGCAAACAAGCTG 59.248 50.000 0.00 0.00 34.17 4.24
60 61 0.106268 TTCAGGGGCAAACAAGCTGA 60.106 50.000 0.00 0.00 34.17 4.26
61 62 0.823356 TCAGGGGCAAACAAGCTGAC 60.823 55.000 0.00 0.00 34.17 3.51
62 63 1.898574 AGGGGCAAACAAGCTGACG 60.899 57.895 0.00 0.00 34.17 4.35
63 64 2.050077 GGGCAAACAAGCTGACGC 60.050 61.111 0.00 0.00 34.17 5.19
72 73 3.303189 AGCTGACGCTAGGCACAT 58.697 55.556 0.00 0.00 46.79 3.21
73 74 1.142748 AGCTGACGCTAGGCACATC 59.857 57.895 0.00 0.00 46.79 3.06
74 75 1.153568 GCTGACGCTAGGCACATCA 60.154 57.895 0.00 0.00 0.00 3.07
75 76 0.531532 GCTGACGCTAGGCACATCAT 60.532 55.000 0.00 0.00 0.00 2.45
76 77 1.495878 CTGACGCTAGGCACATCATC 58.504 55.000 0.00 0.00 0.00 2.92
77 78 0.823460 TGACGCTAGGCACATCATCA 59.177 50.000 0.00 0.00 0.00 3.07
78 79 1.206849 TGACGCTAGGCACATCATCAA 59.793 47.619 0.00 0.00 0.00 2.57
79 80 2.279741 GACGCTAGGCACATCATCAAA 58.720 47.619 0.00 0.00 0.00 2.69
80 81 2.283298 ACGCTAGGCACATCATCAAAG 58.717 47.619 0.00 0.00 0.00 2.77
81 82 1.003116 CGCTAGGCACATCATCAAAGC 60.003 52.381 0.00 0.00 0.00 3.51
82 83 2.019249 GCTAGGCACATCATCAAAGCA 58.981 47.619 0.00 0.00 0.00 3.91
83 84 2.621998 GCTAGGCACATCATCAAAGCAT 59.378 45.455 0.00 0.00 0.00 3.79
84 85 3.550233 GCTAGGCACATCATCAAAGCATG 60.550 47.826 0.00 0.00 0.00 4.06
85 86 1.136305 AGGCACATCATCAAAGCATGC 59.864 47.619 10.51 10.51 0.00 4.06
86 87 1.567504 GCACATCATCAAAGCATGCC 58.432 50.000 15.66 0.00 0.00 4.40
87 88 1.134936 GCACATCATCAAAGCATGCCA 60.135 47.619 15.66 0.00 0.00 4.92
88 89 2.809446 CACATCATCAAAGCATGCCAG 58.191 47.619 15.66 4.53 0.00 4.85
89 90 2.425668 CACATCATCAAAGCATGCCAGA 59.574 45.455 15.66 10.50 0.00 3.86
90 91 2.688446 ACATCATCAAAGCATGCCAGAG 59.312 45.455 15.66 2.10 0.00 3.35
91 92 1.100510 TCATCAAAGCATGCCAGAGC 58.899 50.000 15.66 0.00 40.48 4.09
92 93 0.248498 CATCAAAGCATGCCAGAGCG 60.248 55.000 15.66 2.12 44.31 5.03
93 94 0.393402 ATCAAAGCATGCCAGAGCGA 60.393 50.000 15.66 3.13 44.31 4.93
94 95 1.136147 CAAAGCATGCCAGAGCGAC 59.864 57.895 15.66 0.00 44.31 5.19
95 96 1.302752 AAAGCATGCCAGAGCGACA 60.303 52.632 15.66 0.00 44.31 4.35
96 97 0.679002 AAAGCATGCCAGAGCGACAT 60.679 50.000 15.66 0.00 44.31 3.06
97 98 1.374343 AAGCATGCCAGAGCGACATG 61.374 55.000 15.66 0.00 44.31 3.21
98 99 2.831366 GCATGCCAGAGCGACATGG 61.831 63.158 6.36 0.00 44.31 3.66
99 100 1.153309 CATGCCAGAGCGACATGGA 60.153 57.895 0.00 0.00 44.31 3.41
100 101 1.145598 ATGCCAGAGCGACATGGAG 59.854 57.895 0.00 0.00 44.31 3.86
101 102 2.894387 GCCAGAGCGACATGGAGC 60.894 66.667 6.56 6.56 39.02 4.70
102 103 2.580815 CCAGAGCGACATGGAGCA 59.419 61.111 15.39 0.00 39.02 4.26
103 104 1.078918 CCAGAGCGACATGGAGCAA 60.079 57.895 15.39 0.00 39.02 3.91
104 105 0.463295 CCAGAGCGACATGGAGCAAT 60.463 55.000 15.39 2.51 39.02 3.56
105 106 0.656259 CAGAGCGACATGGAGCAATG 59.344 55.000 15.39 9.95 35.48 2.82
106 107 0.463295 AGAGCGACATGGAGCAATGG 60.463 55.000 15.39 0.00 35.48 3.16
107 108 2.056481 GAGCGACATGGAGCAATGGC 62.056 60.000 15.39 0.00 41.61 4.40
133 134 3.945434 GGCGCACGATGCATCCAG 61.945 66.667 20.87 14.05 45.36 3.86
134 135 4.602696 GCGCACGATGCATCCAGC 62.603 66.667 20.87 21.41 45.36 4.85
143 144 2.890371 GCATCCAGCAGCCCTTTG 59.110 61.111 0.00 0.00 44.79 2.77
144 145 2.718073 GCATCCAGCAGCCCTTTGG 61.718 63.158 0.00 0.00 44.79 3.28
156 157 2.629002 CCTTTGGGGAAGTGACGTG 58.371 57.895 0.00 0.00 37.23 4.49
157 158 0.107831 CCTTTGGGGAAGTGACGTGA 59.892 55.000 0.00 0.00 37.23 4.35
158 159 1.512926 CTTTGGGGAAGTGACGTGAG 58.487 55.000 0.00 0.00 0.00 3.51
159 160 1.070134 CTTTGGGGAAGTGACGTGAGA 59.930 52.381 0.00 0.00 0.00 3.27
160 161 1.348064 TTGGGGAAGTGACGTGAGAT 58.652 50.000 0.00 0.00 0.00 2.75
161 162 2.225382 TGGGGAAGTGACGTGAGATA 57.775 50.000 0.00 0.00 0.00 1.98
162 163 2.747177 TGGGGAAGTGACGTGAGATAT 58.253 47.619 0.00 0.00 0.00 1.63
163 164 2.693591 TGGGGAAGTGACGTGAGATATC 59.306 50.000 0.00 0.00 0.00 1.63
164 165 2.959707 GGGGAAGTGACGTGAGATATCT 59.040 50.000 4.47 4.47 0.00 1.98
165 166 3.004944 GGGGAAGTGACGTGAGATATCTC 59.995 52.174 23.47 23.47 43.15 2.75
166 167 3.004944 GGGAAGTGACGTGAGATATCTCC 59.995 52.174 26.33 17.44 42.20 3.71
167 168 3.632604 GGAAGTGACGTGAGATATCTCCA 59.367 47.826 26.33 15.73 42.20 3.86
168 169 4.279671 GGAAGTGACGTGAGATATCTCCAT 59.720 45.833 26.33 13.80 42.20 3.41
169 170 4.844998 AGTGACGTGAGATATCTCCATG 57.155 45.455 26.33 20.62 42.20 3.66
170 171 4.211125 AGTGACGTGAGATATCTCCATGT 58.789 43.478 26.33 23.01 42.20 3.21
171 172 4.037327 AGTGACGTGAGATATCTCCATGTG 59.963 45.833 26.33 14.97 42.20 3.21
172 173 3.243535 TGACGTGAGATATCTCCATGTGC 60.244 47.826 26.33 17.79 42.20 4.57
173 174 2.287849 ACGTGAGATATCTCCATGTGCG 60.288 50.000 26.33 20.86 42.20 5.34
174 175 2.287849 CGTGAGATATCTCCATGTGCGT 60.288 50.000 26.33 0.00 42.20 5.24
175 176 3.312828 GTGAGATATCTCCATGTGCGTC 58.687 50.000 26.33 2.72 42.20 5.19
176 177 2.030805 TGAGATATCTCCATGTGCGTCG 60.031 50.000 26.33 0.00 42.20 5.12
177 178 1.957177 AGATATCTCCATGTGCGTCGT 59.043 47.619 0.00 0.00 0.00 4.34
178 179 2.362397 AGATATCTCCATGTGCGTCGTT 59.638 45.455 0.00 0.00 0.00 3.85
179 180 2.665649 TATCTCCATGTGCGTCGTTT 57.334 45.000 0.00 0.00 0.00 3.60
180 181 1.808411 ATCTCCATGTGCGTCGTTTT 58.192 45.000 0.00 0.00 0.00 2.43
181 182 2.442212 TCTCCATGTGCGTCGTTTTA 57.558 45.000 0.00 0.00 0.00 1.52
182 183 2.333926 TCTCCATGTGCGTCGTTTTAG 58.666 47.619 0.00 0.00 0.00 1.85
183 184 0.793861 TCCATGTGCGTCGTTTTAGC 59.206 50.000 0.00 0.00 0.00 3.09
184 185 0.179200 CCATGTGCGTCGTTTTAGCC 60.179 55.000 0.00 0.00 0.00 3.93
185 186 0.796312 CATGTGCGTCGTTTTAGCCT 59.204 50.000 0.00 0.00 0.00 4.58
186 187 1.996898 CATGTGCGTCGTTTTAGCCTA 59.003 47.619 0.00 0.00 0.00 3.93
187 188 1.705256 TGTGCGTCGTTTTAGCCTAG 58.295 50.000 0.00 0.00 0.00 3.02
188 189 1.000060 TGTGCGTCGTTTTAGCCTAGT 60.000 47.619 0.00 0.00 0.00 2.57
189 190 2.064014 GTGCGTCGTTTTAGCCTAGTT 58.936 47.619 0.00 0.00 0.00 2.24
190 191 2.477754 GTGCGTCGTTTTAGCCTAGTTT 59.522 45.455 0.00 0.00 0.00 2.66
191 192 3.059393 GTGCGTCGTTTTAGCCTAGTTTT 60.059 43.478 0.00 0.00 0.00 2.43
192 193 3.560896 TGCGTCGTTTTAGCCTAGTTTTT 59.439 39.130 0.00 0.00 0.00 1.94
213 214 3.008835 TCAGATGGCCTGATTCTTTGG 57.991 47.619 3.32 0.00 46.38 3.28
214 215 2.029623 CAGATGGCCTGATTCTTTGGG 58.970 52.381 3.32 0.00 45.78 4.12
215 216 1.063417 AGATGGCCTGATTCTTTGGGG 60.063 52.381 3.32 0.00 0.00 4.96
216 217 0.688749 ATGGCCTGATTCTTTGGGGC 60.689 55.000 3.32 0.00 43.45 5.80
217 218 3.621225 GCCTGATTCTTTGGGGCC 58.379 61.111 0.00 0.00 37.12 5.80
218 219 2.060383 GCCTGATTCTTTGGGGCCC 61.060 63.158 18.17 18.17 37.12 5.80
219 220 1.754234 CCTGATTCTTTGGGGCCCG 60.754 63.158 19.83 3.38 0.00 6.13
220 221 1.302949 CTGATTCTTTGGGGCCCGA 59.697 57.895 19.83 14.79 0.00 5.14
221 222 0.323360 CTGATTCTTTGGGGCCCGAA 60.323 55.000 24.06 24.06 0.00 4.30
222 223 0.323360 TGATTCTTTGGGGCCCGAAG 60.323 55.000 37.51 37.51 44.27 3.79
223 224 0.323451 GATTCTTTGGGGCCCGAAGT 60.323 55.000 39.52 27.91 43.57 3.01
224 225 0.996583 ATTCTTTGGGGCCCGAAGTA 59.003 50.000 39.52 34.08 43.57 2.24
225 226 0.772384 TTCTTTGGGGCCCGAAGTAA 59.228 50.000 39.52 30.63 43.57 2.24
226 227 0.326927 TCTTTGGGGCCCGAAGTAAG 59.673 55.000 39.52 25.68 43.57 2.34
227 228 0.326927 CTTTGGGGCCCGAAGTAAGA 59.673 55.000 35.66 11.55 39.52 2.10
228 229 0.996583 TTTGGGGCCCGAAGTAAGAT 59.003 50.000 21.95 0.00 0.00 2.40
229 230 0.254747 TTGGGGCCCGAAGTAAGATG 59.745 55.000 16.38 0.00 0.00 2.90
230 231 0.912487 TGGGGCCCGAAGTAAGATGT 60.912 55.000 19.83 0.00 0.00 3.06
231 232 1.125633 GGGGCCCGAAGTAAGATGTA 58.874 55.000 17.79 0.00 0.00 2.29
232 233 1.697982 GGGGCCCGAAGTAAGATGTAT 59.302 52.381 17.79 0.00 0.00 2.29
233 234 2.105993 GGGGCCCGAAGTAAGATGTATT 59.894 50.000 17.79 0.00 0.00 1.89
234 235 3.139077 GGGCCCGAAGTAAGATGTATTG 58.861 50.000 5.69 0.00 0.00 1.90
235 236 2.548480 GGCCCGAAGTAAGATGTATTGC 59.452 50.000 0.00 0.00 0.00 3.56
236 237 2.548480 GCCCGAAGTAAGATGTATTGCC 59.452 50.000 0.00 0.00 0.00 4.52
237 238 3.744530 GCCCGAAGTAAGATGTATTGCCT 60.745 47.826 0.00 0.00 0.00 4.75
238 239 4.058817 CCCGAAGTAAGATGTATTGCCTC 58.941 47.826 0.00 0.00 0.00 4.70
239 240 4.202264 CCCGAAGTAAGATGTATTGCCTCT 60.202 45.833 0.00 0.00 0.00 3.69
240 241 4.985409 CCGAAGTAAGATGTATTGCCTCTC 59.015 45.833 0.00 0.00 0.00 3.20
241 242 5.221342 CCGAAGTAAGATGTATTGCCTCTCT 60.221 44.000 0.00 0.00 0.00 3.10
242 243 6.276847 CGAAGTAAGATGTATTGCCTCTCTT 58.723 40.000 0.00 0.00 0.00 2.85
243 244 6.758886 CGAAGTAAGATGTATTGCCTCTCTTT 59.241 38.462 0.00 0.00 0.00 2.52
244 245 7.278868 CGAAGTAAGATGTATTGCCTCTCTTTT 59.721 37.037 0.00 0.00 0.00 2.27
245 246 8.499403 AAGTAAGATGTATTGCCTCTCTTTTC 57.501 34.615 0.00 0.00 0.00 2.29
246 247 7.051000 AGTAAGATGTATTGCCTCTCTTTTCC 58.949 38.462 0.00 0.00 0.00 3.13
247 248 5.441718 AGATGTATTGCCTCTCTTTTCCA 57.558 39.130 0.00 0.00 0.00 3.53
248 249 6.011122 AGATGTATTGCCTCTCTTTTCCAT 57.989 37.500 0.00 0.00 0.00 3.41
249 250 5.826737 AGATGTATTGCCTCTCTTTTCCATG 59.173 40.000 0.00 0.00 0.00 3.66
250 251 5.178096 TGTATTGCCTCTCTTTTCCATGA 57.822 39.130 0.00 0.00 0.00 3.07
251 252 5.759059 TGTATTGCCTCTCTTTTCCATGAT 58.241 37.500 0.00 0.00 0.00 2.45
252 253 5.824624 TGTATTGCCTCTCTTTTCCATGATC 59.175 40.000 0.00 0.00 0.00 2.92
253 254 2.910199 TGCCTCTCTTTTCCATGATCG 58.090 47.619 0.00 0.00 0.00 3.69
254 255 1.601430 GCCTCTCTTTTCCATGATCGC 59.399 52.381 0.00 0.00 0.00 4.58
255 256 2.744494 GCCTCTCTTTTCCATGATCGCT 60.744 50.000 0.00 0.00 0.00 4.93
256 257 3.539604 CCTCTCTTTTCCATGATCGCTT 58.460 45.455 0.00 0.00 0.00 4.68
257 258 3.311871 CCTCTCTTTTCCATGATCGCTTG 59.688 47.826 0.00 0.00 0.00 4.01
258 259 4.186926 CTCTCTTTTCCATGATCGCTTGA 58.813 43.478 0.00 0.00 0.00 3.02
259 260 4.774124 TCTCTTTTCCATGATCGCTTGAT 58.226 39.130 0.00 0.00 34.17 2.57
278 279 6.932356 TTGATCAGCATCTGTAATTTCTCC 57.068 37.500 0.00 0.00 32.61 3.71
279 280 5.371526 TGATCAGCATCTGTAATTTCTCCC 58.628 41.667 0.00 0.00 32.61 4.30
280 281 5.131642 TGATCAGCATCTGTAATTTCTCCCT 59.868 40.000 0.00 0.00 32.61 4.20
281 282 4.774124 TCAGCATCTGTAATTTCTCCCTG 58.226 43.478 0.00 0.00 32.61 4.45
282 283 3.314635 CAGCATCTGTAATTTCTCCCTGC 59.685 47.826 0.00 0.00 0.00 4.85
283 284 3.201708 AGCATCTGTAATTTCTCCCTGCT 59.798 43.478 0.00 0.00 32.92 4.24
284 285 4.410228 AGCATCTGTAATTTCTCCCTGCTA 59.590 41.667 0.00 0.00 35.81 3.49
285 286 5.104360 AGCATCTGTAATTTCTCCCTGCTAA 60.104 40.000 0.00 0.00 35.81 3.09
286 287 5.590259 GCATCTGTAATTTCTCCCTGCTAAA 59.410 40.000 0.00 0.00 0.00 1.85
287 288 6.264067 GCATCTGTAATTTCTCCCTGCTAAAT 59.736 38.462 0.00 0.00 0.00 1.40
288 289 7.201857 GCATCTGTAATTTCTCCCTGCTAAATT 60.202 37.037 0.00 0.00 36.87 1.82
289 290 9.342308 CATCTGTAATTTCTCCCTGCTAAATTA 57.658 33.333 0.00 0.00 35.20 1.40
290 291 9.920946 ATCTGTAATTTCTCCCTGCTAAATTAA 57.079 29.630 0.00 0.00 37.02 1.40
291 292 9.747898 TCTGTAATTTCTCCCTGCTAAATTAAA 57.252 29.630 0.00 0.00 37.02 1.52
298 299 9.705290 TTTCTCCCTGCTAAATTAAATGAAAAC 57.295 29.630 0.00 0.00 0.00 2.43
299 300 7.836842 TCTCCCTGCTAAATTAAATGAAAACC 58.163 34.615 0.00 0.00 0.00 3.27
300 301 7.453126 TCTCCCTGCTAAATTAAATGAAAACCA 59.547 33.333 0.00 0.00 0.00 3.67
301 302 7.610865 TCCCTGCTAAATTAAATGAAAACCAG 58.389 34.615 0.00 0.00 0.00 4.00
302 303 6.313658 CCCTGCTAAATTAAATGAAAACCAGC 59.686 38.462 0.00 0.00 0.00 4.85
303 304 7.099120 CCTGCTAAATTAAATGAAAACCAGCT 58.901 34.615 0.00 0.00 0.00 4.24
304 305 8.250332 CCTGCTAAATTAAATGAAAACCAGCTA 58.750 33.333 0.00 0.00 0.00 3.32
305 306 8.980143 TGCTAAATTAAATGAAAACCAGCTAC 57.020 30.769 0.00 0.00 0.00 3.58
306 307 7.753132 TGCTAAATTAAATGAAAACCAGCTACG 59.247 33.333 0.00 0.00 0.00 3.51
307 308 6.944557 AAATTAAATGAAAACCAGCTACGC 57.055 33.333 0.00 0.00 0.00 4.42
308 309 5.897377 ATTAAATGAAAACCAGCTACGCT 57.103 34.783 0.00 0.00 40.77 5.07
317 318 3.708210 AGCTACGCTGGCCACTTA 58.292 55.556 0.00 0.00 37.57 2.24
318 319 1.980052 AGCTACGCTGGCCACTTAA 59.020 52.632 0.00 0.00 37.57 1.85
319 320 0.323629 AGCTACGCTGGCCACTTAAA 59.676 50.000 0.00 0.00 37.57 1.52
320 321 1.161843 GCTACGCTGGCCACTTAAAA 58.838 50.000 0.00 0.00 0.00 1.52
321 322 1.538075 GCTACGCTGGCCACTTAAAAA 59.462 47.619 0.00 0.00 0.00 1.94
447 465 0.719015 TCCTCCTCCTCCCATCAGTT 59.281 55.000 0.00 0.00 0.00 3.16
516 534 1.133790 AGCTTGCTTGAATTCATCCGC 59.866 47.619 9.40 12.58 0.00 5.54
524 542 2.432444 TGAATTCATCCGCTCCGTTTT 58.568 42.857 3.38 0.00 0.00 2.43
525 543 2.817258 TGAATTCATCCGCTCCGTTTTT 59.183 40.909 3.38 0.00 0.00 1.94
706 724 0.955919 CGTCCCCACAAGGAAGAAGC 60.956 60.000 0.00 0.00 37.58 3.86
735 753 3.260380 CGGGCATAGATCAGGAGAAATCT 59.740 47.826 0.00 0.00 36.28 2.40
740 758 5.622007 GCATAGATCAGGAGAAATCTCGAGG 60.622 48.000 13.56 0.00 43.76 4.63
777 795 2.808202 CGATGGGAATGGGAAGCTACAG 60.808 54.545 0.00 0.00 0.00 2.74
868 886 5.536161 ACAATGTGTATTCTTTGCCTTCTGT 59.464 36.000 0.00 0.00 0.00 3.41
970 988 4.399303 AGCCGATGGAAAATTTAAGGTCAG 59.601 41.667 0.00 0.00 0.00 3.51
1230 1251 3.196469 TGTTCAGATCAGGAGCTGTTAGG 59.804 47.826 13.59 0.00 44.55 2.69
1266 1287 0.248134 CGGAGTTCGACGATGAGGAC 60.248 60.000 0.00 0.00 42.43 3.85
1385 1406 0.537188 GACCCGACATCTGACATGGT 59.463 55.000 0.00 0.00 0.00 3.55
1484 1505 1.698532 CTGGGAGCTTGCTGGATCTAT 59.301 52.381 0.00 0.00 0.00 1.98
1508 1529 4.097892 GCTAGGACATATTTTGGGTGTTGG 59.902 45.833 0.00 0.00 0.00 3.77
1516 1537 4.576330 ATTTTGGGTGTTGGGAAAACAA 57.424 36.364 0.00 0.00 31.20 2.83
1541 1645 1.836166 ACAGGCTGATGCTGATACTGT 59.164 47.619 23.66 0.00 39.59 3.55
1734 2216 3.133901 GGGAAAATCAAGTGGTTGTGGTT 59.866 43.478 0.00 0.00 34.98 3.67
1839 2322 1.137282 TGCACTCAACCAAGACGTGTA 59.863 47.619 0.00 0.00 0.00 2.90
1872 2355 3.106407 GCTCGGCGTGTCAGTGAC 61.106 66.667 16.68 16.68 0.00 3.67
1935 2418 1.352156 GGTTCGAGGATGTCACGTGC 61.352 60.000 11.67 6.86 0.00 5.34
1937 2420 1.811645 TTCGAGGATGTCACGTGCCA 61.812 55.000 11.67 6.09 0.00 4.92
2396 3486 4.397417 GCTAATATCATCATCCACCAAGGC 59.603 45.833 0.00 0.00 37.29 4.35
2399 3489 0.394762 TCATCATCCACCAAGGCTGC 60.395 55.000 0.00 0.00 33.44 5.25
2403 3493 3.292481 ATCCACCAAGGCTGCAGGG 62.292 63.158 17.12 10.61 37.29 4.45
2475 3565 3.015327 CAAGATCTTTCAGAAGGCAGGG 58.985 50.000 4.86 0.00 33.56 4.45
2721 3811 2.158813 GGAATCCGCTTACCAGGATGAA 60.159 50.000 0.00 0.00 45.78 2.57
2908 3998 2.824071 GAACAATGCTGGCGGCCTTG 62.824 60.000 27.76 27.76 46.85 3.61
2983 4073 2.551270 TGCTTCTCATGGGTAAGGAGT 58.449 47.619 0.00 0.00 0.00 3.85
3018 4108 9.901724 GTTGATGAAGTACTAACAATTGTATCG 57.098 33.333 12.39 5.87 0.00 2.92
3145 4235 3.244353 CCTCAATGTATACCTGCTCTGGG 60.244 52.174 0.00 0.00 0.00 4.45
3162 4252 4.458397 TCTGGGAGTCGAACGAATATAGT 58.542 43.478 0.00 0.00 0.00 2.12
3269 4359 0.692419 ACCCTGAAGATCCCGCAGAT 60.692 55.000 8.24 0.00 38.17 2.90
3273 4363 2.416566 CCTGAAGATCCCGCAGATATCG 60.417 54.545 8.24 0.00 34.42 2.92
3274 4364 1.067565 TGAAGATCCCGCAGATATCGC 60.068 52.381 8.81 8.81 34.42 4.58
3384 4474 3.334891 TGCCGTAATGGGGTGCCT 61.335 61.111 0.00 0.00 38.63 4.75
3641 4731 1.486997 AAGCTGAGGCAGGAGCAAGA 61.487 55.000 0.00 0.00 44.61 3.02
3673 4766 0.980231 CAGAGTGAAGGGGAGGGAGG 60.980 65.000 0.00 0.00 0.00 4.30
3674 4767 1.156322 AGAGTGAAGGGGAGGGAGGA 61.156 60.000 0.00 0.00 0.00 3.71
3753 4849 2.877154 ATCTTAGGCCCAGAAGGAGA 57.123 50.000 6.34 0.00 38.24 3.71
3804 4900 7.492669 AGTGAGTATGTTTGTATGTGCTGATAC 59.507 37.037 0.00 0.00 0.00 2.24
3942 5039 6.338146 TGCTAATTTCTTAGTAGTGCGACAT 58.662 36.000 0.00 0.00 37.30 3.06
3943 5040 6.816640 TGCTAATTTCTTAGTAGTGCGACATT 59.183 34.615 0.00 0.00 37.30 2.71
3944 5041 7.119997 GCTAATTTCTTAGTAGTGCGACATTG 58.880 38.462 0.00 0.00 37.30 2.82
4159 5256 1.871126 GAGCCTGCTGTTGCTTTCCC 61.871 60.000 0.00 0.00 38.11 3.97
4175 5272 1.187974 TCCCGGTTTATTCAGCTCGA 58.812 50.000 0.00 0.00 0.00 4.04
4176 5273 1.136305 TCCCGGTTTATTCAGCTCGAG 59.864 52.381 8.45 8.45 0.00 4.04
4217 5314 6.636850 CCACATTACAACAAGTTTAAGTGAGC 59.363 38.462 0.00 0.00 0.00 4.26
4275 5372 5.761726 TCATATGGATGCAGAAACATCAGTC 59.238 40.000 2.13 0.00 46.81 3.51
4336 5543 8.746922 TGCAACTTCATTGTAGATTCAAATTC 57.253 30.769 0.00 0.00 40.77 2.17
4570 7446 9.547753 TCACATTAAATAGTAGGCTGAATTCTC 57.452 33.333 7.05 0.00 0.00 2.87
4649 7525 4.787598 ACAAACTCTAATTTCAGCAAGCG 58.212 39.130 0.00 0.00 0.00 4.68
4701 7577 9.844790 CATCTACTCTCTGCTTAATCTGATAAG 57.155 37.037 0.00 0.00 36.24 1.73
4711 7587 7.382110 TGCTTAATCTGATAAGAGATGCTACC 58.618 38.462 9.55 0.00 35.35 3.18
4712 7588 6.816140 GCTTAATCTGATAAGAGATGCTACCC 59.184 42.308 9.55 0.00 35.35 3.69
4713 7589 5.753721 AATCTGATAAGAGATGCTACCCC 57.246 43.478 0.00 0.00 32.77 4.95
4714 7590 3.511477 TCTGATAAGAGATGCTACCCCC 58.489 50.000 0.00 0.00 0.00 5.40
4740 7616 1.869754 GCTGCTGTCTGTCGAGTTGAA 60.870 52.381 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.956636 GCCAGATGTGCCAGGAAATGA 60.957 52.381 0.00 0.00 0.00 2.57
2 3 0.333993 AGCCAGATGTGCCAGGAAAT 59.666 50.000 0.00 0.00 0.00 2.17
3 4 0.609957 CAGCCAGATGTGCCAGGAAA 60.610 55.000 0.00 0.00 0.00 3.13
4 5 1.001764 CAGCCAGATGTGCCAGGAA 60.002 57.895 0.00 0.00 0.00 3.36
5 6 2.672908 CAGCCAGATGTGCCAGGA 59.327 61.111 0.00 0.00 0.00 3.86
6 7 2.439701 CCAGCCAGATGTGCCAGG 60.440 66.667 0.00 0.00 0.00 4.45
7 8 0.609957 TTTCCAGCCAGATGTGCCAG 60.610 55.000 0.00 0.00 0.00 4.85
8 9 0.609957 CTTTCCAGCCAGATGTGCCA 60.610 55.000 0.00 0.00 0.00 4.92
9 10 0.322816 TCTTTCCAGCCAGATGTGCC 60.323 55.000 0.00 0.00 0.00 5.01
10 11 1.538047 TTCTTTCCAGCCAGATGTGC 58.462 50.000 0.00 0.00 0.00 4.57
11 12 3.675228 GCATTTCTTTCCAGCCAGATGTG 60.675 47.826 0.00 0.00 0.00 3.21
12 13 2.494870 GCATTTCTTTCCAGCCAGATGT 59.505 45.455 0.00 0.00 0.00 3.06
13 14 2.494471 TGCATTTCTTTCCAGCCAGATG 59.506 45.455 0.00 0.00 0.00 2.90
14 15 2.811410 TGCATTTCTTTCCAGCCAGAT 58.189 42.857 0.00 0.00 0.00 2.90
15 16 2.291209 TGCATTTCTTTCCAGCCAGA 57.709 45.000 0.00 0.00 0.00 3.86
16 17 2.888594 CATGCATTTCTTTCCAGCCAG 58.111 47.619 0.00 0.00 0.00 4.85
17 18 1.066716 GCATGCATTTCTTTCCAGCCA 60.067 47.619 14.21 0.00 0.00 4.75
18 19 1.066716 TGCATGCATTTCTTTCCAGCC 60.067 47.619 18.46 0.00 0.00 4.85
19 20 2.373540 TGCATGCATTTCTTTCCAGC 57.626 45.000 18.46 0.00 0.00 4.85
30 31 0.179468 GCCCCTGAAAATGCATGCAT 59.821 50.000 27.46 27.46 38.46 3.96
31 32 1.192803 TGCCCCTGAAAATGCATGCA 61.193 50.000 25.04 25.04 0.00 3.96
32 33 0.036199 TTGCCCCTGAAAATGCATGC 60.036 50.000 11.82 11.82 33.08 4.06
33 34 2.078392 GTTTGCCCCTGAAAATGCATG 58.922 47.619 0.00 0.00 33.08 4.06
34 35 1.698532 TGTTTGCCCCTGAAAATGCAT 59.301 42.857 0.00 0.00 33.08 3.96
35 36 1.126488 TGTTTGCCCCTGAAAATGCA 58.874 45.000 0.00 0.00 0.00 3.96
36 37 2.145536 CTTGTTTGCCCCTGAAAATGC 58.854 47.619 0.00 0.00 0.00 3.56
37 38 2.145536 GCTTGTTTGCCCCTGAAAATG 58.854 47.619 0.00 0.00 0.00 2.32
38 39 2.049372 AGCTTGTTTGCCCCTGAAAAT 58.951 42.857 0.00 0.00 0.00 1.82
39 40 1.138661 CAGCTTGTTTGCCCCTGAAAA 59.861 47.619 0.00 0.00 0.00 2.29
40 41 0.752054 CAGCTTGTTTGCCCCTGAAA 59.248 50.000 0.00 0.00 0.00 2.69
41 42 0.106268 TCAGCTTGTTTGCCCCTGAA 60.106 50.000 0.00 0.00 30.30 3.02
42 43 0.823356 GTCAGCTTGTTTGCCCCTGA 60.823 55.000 0.00 0.00 0.00 3.86
43 44 1.662044 GTCAGCTTGTTTGCCCCTG 59.338 57.895 0.00 0.00 0.00 4.45
44 45 1.898574 CGTCAGCTTGTTTGCCCCT 60.899 57.895 0.00 0.00 0.00 4.79
45 46 2.644992 CGTCAGCTTGTTTGCCCC 59.355 61.111 0.00 0.00 0.00 5.80
46 47 2.050077 GCGTCAGCTTGTTTGCCC 60.050 61.111 0.00 0.00 41.01 5.36
56 57 0.531532 ATGATGTGCCTAGCGTCAGC 60.532 55.000 0.00 0.00 45.58 4.26
57 58 1.202452 TGATGATGTGCCTAGCGTCAG 60.202 52.381 0.00 0.00 0.00 3.51
58 59 0.823460 TGATGATGTGCCTAGCGTCA 59.177 50.000 0.00 0.00 0.00 4.35
59 60 1.939974 TTGATGATGTGCCTAGCGTC 58.060 50.000 0.00 0.00 0.00 5.19
60 61 2.283298 CTTTGATGATGTGCCTAGCGT 58.717 47.619 0.00 0.00 0.00 5.07
61 62 1.003116 GCTTTGATGATGTGCCTAGCG 60.003 52.381 0.00 0.00 0.00 4.26
62 63 2.019249 TGCTTTGATGATGTGCCTAGC 58.981 47.619 0.00 0.00 0.00 3.42
63 64 3.550233 GCATGCTTTGATGATGTGCCTAG 60.550 47.826 11.37 0.00 0.00 3.02
64 65 2.359848 GCATGCTTTGATGATGTGCCTA 59.640 45.455 11.37 0.00 0.00 3.93
65 66 1.136305 GCATGCTTTGATGATGTGCCT 59.864 47.619 11.37 0.00 0.00 4.75
66 67 1.567504 GCATGCTTTGATGATGTGCC 58.432 50.000 11.37 0.00 0.00 5.01
67 68 1.134936 TGGCATGCTTTGATGATGTGC 60.135 47.619 18.92 0.00 0.00 4.57
68 69 2.425668 TCTGGCATGCTTTGATGATGTG 59.574 45.455 18.92 0.00 0.00 3.21
69 70 2.688446 CTCTGGCATGCTTTGATGATGT 59.312 45.455 18.92 0.00 0.00 3.06
70 71 2.543861 GCTCTGGCATGCTTTGATGATG 60.544 50.000 18.92 3.27 38.54 3.07
71 72 1.681793 GCTCTGGCATGCTTTGATGAT 59.318 47.619 18.92 0.00 38.54 2.45
72 73 1.100510 GCTCTGGCATGCTTTGATGA 58.899 50.000 18.92 6.21 38.54 2.92
73 74 0.248498 CGCTCTGGCATGCTTTGATG 60.248 55.000 18.92 4.76 38.60 3.07
74 75 0.393402 TCGCTCTGGCATGCTTTGAT 60.393 50.000 18.92 0.00 38.60 2.57
75 76 1.003476 TCGCTCTGGCATGCTTTGA 60.003 52.632 18.92 11.99 38.60 2.69
76 77 1.136147 GTCGCTCTGGCATGCTTTG 59.864 57.895 18.92 8.15 38.60 2.77
77 78 0.679002 ATGTCGCTCTGGCATGCTTT 60.679 50.000 18.92 0.00 38.60 3.51
78 79 1.077930 ATGTCGCTCTGGCATGCTT 60.078 52.632 18.92 0.00 38.60 3.91
79 80 1.818363 CATGTCGCTCTGGCATGCT 60.818 57.895 18.92 0.00 38.60 3.79
80 81 2.713770 CATGTCGCTCTGGCATGC 59.286 61.111 9.90 9.90 38.60 4.06
81 82 1.153309 TCCATGTCGCTCTGGCATG 60.153 57.895 2.61 2.61 39.54 4.06
82 83 1.145598 CTCCATGTCGCTCTGGCAT 59.854 57.895 0.00 0.00 38.60 4.40
83 84 2.580815 CTCCATGTCGCTCTGGCA 59.419 61.111 0.00 0.00 38.60 4.92
84 85 2.894387 GCTCCATGTCGCTCTGGC 60.894 66.667 0.00 0.00 32.30 4.85
85 86 0.463295 ATTGCTCCATGTCGCTCTGG 60.463 55.000 5.26 0.00 0.00 3.86
86 87 0.656259 CATTGCTCCATGTCGCTCTG 59.344 55.000 5.26 0.21 0.00 3.35
87 88 0.463295 CCATTGCTCCATGTCGCTCT 60.463 55.000 5.26 0.00 0.00 4.09
88 89 2.020131 CCATTGCTCCATGTCGCTC 58.980 57.895 5.26 0.00 0.00 5.03
89 90 2.117156 GCCATTGCTCCATGTCGCT 61.117 57.895 5.26 0.00 33.53 4.93
90 91 2.410469 GCCATTGCTCCATGTCGC 59.590 61.111 0.00 0.00 33.53 5.19
91 92 1.815003 TCGCCATTGCTCCATGTCG 60.815 57.895 0.00 0.00 34.43 4.35
92 93 0.745845 AGTCGCCATTGCTCCATGTC 60.746 55.000 0.00 0.00 34.43 3.06
93 94 0.745845 GAGTCGCCATTGCTCCATGT 60.746 55.000 0.00 0.00 34.43 3.21
94 95 1.769098 CGAGTCGCCATTGCTCCATG 61.769 60.000 0.00 0.00 34.43 3.66
95 96 1.522355 CGAGTCGCCATTGCTCCAT 60.522 57.895 0.00 0.00 34.43 3.41
96 97 2.125552 CGAGTCGCCATTGCTCCA 60.126 61.111 0.00 0.00 34.43 3.86
126 127 2.718073 CCAAAGGGCTGCTGGATGC 61.718 63.158 0.00 0.00 43.25 3.91
127 128 2.056223 CCCAAAGGGCTGCTGGATG 61.056 63.158 7.18 0.00 35.35 3.51
128 129 2.361771 CCCAAAGGGCTGCTGGAT 59.638 61.111 7.18 0.00 35.35 3.41
138 139 0.107831 TCACGTCACTTCCCCAAAGG 59.892 55.000 0.00 0.00 39.47 3.11
139 140 1.070134 TCTCACGTCACTTCCCCAAAG 59.930 52.381 0.00 0.00 41.08 2.77
140 141 1.124780 TCTCACGTCACTTCCCCAAA 58.875 50.000 0.00 0.00 0.00 3.28
141 142 1.348064 ATCTCACGTCACTTCCCCAA 58.652 50.000 0.00 0.00 0.00 4.12
142 143 2.225382 TATCTCACGTCACTTCCCCA 57.775 50.000 0.00 0.00 0.00 4.96
143 144 2.959707 AGATATCTCACGTCACTTCCCC 59.040 50.000 0.00 0.00 0.00 4.81
144 145 3.004944 GGAGATATCTCACGTCACTTCCC 59.995 52.174 29.33 8.66 44.60 3.97
145 146 3.632604 TGGAGATATCTCACGTCACTTCC 59.367 47.826 29.33 12.83 44.60 3.46
146 147 4.902443 TGGAGATATCTCACGTCACTTC 57.098 45.455 29.33 12.49 44.60 3.01
147 148 4.646945 ACATGGAGATATCTCACGTCACTT 59.353 41.667 29.33 10.08 44.60 3.16
148 149 4.037327 CACATGGAGATATCTCACGTCACT 59.963 45.833 29.33 8.41 44.60 3.41
149 150 4.294232 CACATGGAGATATCTCACGTCAC 58.706 47.826 29.33 14.36 44.60 3.67
150 151 3.243535 GCACATGGAGATATCTCACGTCA 60.244 47.826 29.33 19.73 44.60 4.35
151 152 3.312828 GCACATGGAGATATCTCACGTC 58.687 50.000 29.33 15.32 44.60 4.34
152 153 2.287849 CGCACATGGAGATATCTCACGT 60.288 50.000 29.33 20.48 44.60 4.49
153 154 2.287849 ACGCACATGGAGATATCTCACG 60.288 50.000 29.33 22.72 44.60 4.35
154 155 3.312828 GACGCACATGGAGATATCTCAC 58.687 50.000 29.33 20.12 44.60 3.51
155 156 2.030805 CGACGCACATGGAGATATCTCA 60.031 50.000 29.33 17.89 44.60 3.27
156 157 2.030717 ACGACGCACATGGAGATATCTC 60.031 50.000 22.41 22.41 42.14 2.75
157 158 1.957177 ACGACGCACATGGAGATATCT 59.043 47.619 4.47 4.47 0.00 1.98
158 159 2.423926 ACGACGCACATGGAGATATC 57.576 50.000 0.00 0.00 0.00 1.63
159 160 2.890808 AACGACGCACATGGAGATAT 57.109 45.000 0.00 0.00 0.00 1.63
160 161 2.665649 AAACGACGCACATGGAGATA 57.334 45.000 0.00 0.00 0.00 1.98
161 162 1.808411 AAAACGACGCACATGGAGAT 58.192 45.000 0.00 0.00 0.00 2.75
162 163 2.333926 CTAAAACGACGCACATGGAGA 58.666 47.619 0.00 0.00 0.00 3.71
163 164 1.201921 GCTAAAACGACGCACATGGAG 60.202 52.381 0.00 0.00 0.00 3.86
164 165 0.793861 GCTAAAACGACGCACATGGA 59.206 50.000 0.00 0.00 0.00 3.41
165 166 0.179200 GGCTAAAACGACGCACATGG 60.179 55.000 0.00 0.00 0.00 3.66
166 167 0.796312 AGGCTAAAACGACGCACATG 59.204 50.000 0.00 0.00 0.00 3.21
167 168 2.268298 CTAGGCTAAAACGACGCACAT 58.732 47.619 0.00 0.00 0.00 3.21
168 169 1.000060 ACTAGGCTAAAACGACGCACA 60.000 47.619 0.00 0.00 0.00 4.57
169 170 1.706443 ACTAGGCTAAAACGACGCAC 58.294 50.000 0.00 0.00 0.00 5.34
170 171 2.443887 AACTAGGCTAAAACGACGCA 57.556 45.000 0.00 0.00 0.00 5.24
171 172 3.800929 AAAACTAGGCTAAAACGACGC 57.199 42.857 0.00 0.00 0.00 5.19
194 195 2.029623 CCCAAAGAATCAGGCCATCTG 58.970 52.381 5.01 0.00 44.68 2.90
195 196 1.063417 CCCCAAAGAATCAGGCCATCT 60.063 52.381 5.01 0.00 0.00 2.90
196 197 1.406903 CCCCAAAGAATCAGGCCATC 58.593 55.000 5.01 0.00 0.00 3.51
197 198 0.688749 GCCCCAAAGAATCAGGCCAT 60.689 55.000 5.01 0.00 37.66 4.40
198 199 1.305213 GCCCCAAAGAATCAGGCCA 60.305 57.895 5.01 0.00 37.66 5.36
199 200 3.621225 GCCCCAAAGAATCAGGCC 58.379 61.111 0.00 0.00 37.66 5.19
200 201 2.060383 GGGCCCCAAAGAATCAGGC 61.060 63.158 12.23 0.00 43.09 4.85
201 202 1.754234 CGGGCCCCAAAGAATCAGG 60.754 63.158 18.66 0.00 0.00 3.86
202 203 0.323360 TTCGGGCCCCAAAGAATCAG 60.323 55.000 18.66 0.00 0.00 2.90
203 204 0.323360 CTTCGGGCCCCAAAGAATCA 60.323 55.000 21.95 0.00 0.00 2.57
204 205 0.323451 ACTTCGGGCCCCAAAGAATC 60.323 55.000 29.59 0.00 0.00 2.52
205 206 0.996583 TACTTCGGGCCCCAAAGAAT 59.003 50.000 29.59 15.83 0.00 2.40
206 207 0.772384 TTACTTCGGGCCCCAAAGAA 59.228 50.000 29.59 20.31 0.00 2.52
207 208 0.326927 CTTACTTCGGGCCCCAAAGA 59.673 55.000 29.59 14.76 0.00 2.52
208 209 0.326927 TCTTACTTCGGGCCCCAAAG 59.673 55.000 23.85 23.85 0.00 2.77
209 210 0.996583 ATCTTACTTCGGGCCCCAAA 59.003 50.000 18.66 10.37 0.00 3.28
210 211 0.254747 CATCTTACTTCGGGCCCCAA 59.745 55.000 18.66 9.51 0.00 4.12
211 212 0.912487 ACATCTTACTTCGGGCCCCA 60.912 55.000 18.66 0.00 0.00 4.96
212 213 1.125633 TACATCTTACTTCGGGCCCC 58.874 55.000 18.66 0.00 0.00 5.80
213 214 3.139077 CAATACATCTTACTTCGGGCCC 58.861 50.000 13.57 13.57 0.00 5.80
214 215 2.548480 GCAATACATCTTACTTCGGGCC 59.452 50.000 0.00 0.00 0.00 5.80
215 216 2.548480 GGCAATACATCTTACTTCGGGC 59.452 50.000 0.00 0.00 0.00 6.13
216 217 4.058817 GAGGCAATACATCTTACTTCGGG 58.941 47.826 0.00 0.00 0.00 5.14
217 218 4.950050 AGAGGCAATACATCTTACTTCGG 58.050 43.478 0.00 0.00 0.00 4.30
218 219 5.837437 AGAGAGGCAATACATCTTACTTCG 58.163 41.667 0.00 0.00 0.00 3.79
219 220 8.499403 AAAAGAGAGGCAATACATCTTACTTC 57.501 34.615 0.00 0.00 30.30 3.01
220 221 7.554476 GGAAAAGAGAGGCAATACATCTTACTT 59.446 37.037 0.00 0.00 30.30 2.24
221 222 7.051000 GGAAAAGAGAGGCAATACATCTTACT 58.949 38.462 0.00 0.00 30.30 2.24
222 223 6.823689 TGGAAAAGAGAGGCAATACATCTTAC 59.176 38.462 0.00 0.00 30.30 2.34
223 224 6.957631 TGGAAAAGAGAGGCAATACATCTTA 58.042 36.000 0.00 0.00 30.30 2.10
224 225 5.819991 TGGAAAAGAGAGGCAATACATCTT 58.180 37.500 0.00 0.00 0.00 2.40
225 226 5.441718 TGGAAAAGAGAGGCAATACATCT 57.558 39.130 0.00 0.00 0.00 2.90
226 227 5.824624 TCATGGAAAAGAGAGGCAATACATC 59.175 40.000 0.00 0.00 0.00 3.06
227 228 5.759059 TCATGGAAAAGAGAGGCAATACAT 58.241 37.500 0.00 0.00 0.00 2.29
228 229 5.178096 TCATGGAAAAGAGAGGCAATACA 57.822 39.130 0.00 0.00 0.00 2.29
229 230 5.049818 CGATCATGGAAAAGAGAGGCAATAC 60.050 44.000 0.00 0.00 0.00 1.89
230 231 5.059161 CGATCATGGAAAAGAGAGGCAATA 58.941 41.667 0.00 0.00 0.00 1.90
231 232 3.881688 CGATCATGGAAAAGAGAGGCAAT 59.118 43.478 0.00 0.00 0.00 3.56
232 233 3.273434 CGATCATGGAAAAGAGAGGCAA 58.727 45.455 0.00 0.00 0.00 4.52
233 234 2.910199 CGATCATGGAAAAGAGAGGCA 58.090 47.619 0.00 0.00 0.00 4.75
234 235 1.601430 GCGATCATGGAAAAGAGAGGC 59.399 52.381 0.00 0.00 0.00 4.70
235 236 3.191078 AGCGATCATGGAAAAGAGAGG 57.809 47.619 0.00 0.00 0.00 3.69
236 237 4.186926 TCAAGCGATCATGGAAAAGAGAG 58.813 43.478 0.00 0.00 0.00 3.20
237 238 4.206477 TCAAGCGATCATGGAAAAGAGA 57.794 40.909 0.00 0.00 0.00 3.10
238 239 5.093169 GATCAAGCGATCATGGAAAAGAG 57.907 43.478 0.00 0.00 46.33 2.85
254 255 6.017275 GGGAGAAATTACAGATGCTGATCAAG 60.017 42.308 0.00 0.00 35.18 3.02
255 256 5.824624 GGGAGAAATTACAGATGCTGATCAA 59.175 40.000 0.00 0.00 35.18 2.57
256 257 5.131642 AGGGAGAAATTACAGATGCTGATCA 59.868 40.000 0.82 0.00 35.18 2.92
257 258 5.469421 CAGGGAGAAATTACAGATGCTGATC 59.531 44.000 0.82 0.00 35.18 2.92
258 259 5.374921 CAGGGAGAAATTACAGATGCTGAT 58.625 41.667 0.82 0.00 35.18 2.90
259 260 4.774124 CAGGGAGAAATTACAGATGCTGA 58.226 43.478 0.82 0.00 35.18 4.26
260 261 3.314635 GCAGGGAGAAATTACAGATGCTG 59.685 47.826 0.00 0.00 37.52 4.41
261 262 3.201708 AGCAGGGAGAAATTACAGATGCT 59.798 43.478 0.00 0.00 36.70 3.79
262 263 3.549794 AGCAGGGAGAAATTACAGATGC 58.450 45.455 0.00 0.00 0.00 3.91
263 264 7.814264 ATTTAGCAGGGAGAAATTACAGATG 57.186 36.000 0.00 0.00 0.00 2.90
264 265 9.920946 TTAATTTAGCAGGGAGAAATTACAGAT 57.079 29.630 0.00 0.00 35.70 2.90
265 266 9.747898 TTTAATTTAGCAGGGAGAAATTACAGA 57.252 29.630 0.00 0.00 35.70 3.41
272 273 9.705290 GTTTTCATTTAATTTAGCAGGGAGAAA 57.295 29.630 0.00 0.00 0.00 2.52
273 274 8.311109 GGTTTTCATTTAATTTAGCAGGGAGAA 58.689 33.333 0.00 0.00 0.00 2.87
274 275 7.453126 TGGTTTTCATTTAATTTAGCAGGGAGA 59.547 33.333 0.00 0.00 0.00 3.71
275 276 7.610865 TGGTTTTCATTTAATTTAGCAGGGAG 58.389 34.615 0.00 0.00 0.00 4.30
276 277 7.546250 TGGTTTTCATTTAATTTAGCAGGGA 57.454 32.000 0.00 0.00 0.00 4.20
277 278 6.313658 GCTGGTTTTCATTTAATTTAGCAGGG 59.686 38.462 0.00 0.00 32.11 4.45
278 279 7.099120 AGCTGGTTTTCATTTAATTTAGCAGG 58.901 34.615 0.00 0.00 32.11 4.85
279 280 9.076596 GTAGCTGGTTTTCATTTAATTTAGCAG 57.923 33.333 0.00 0.00 33.96 4.24
280 281 7.753132 CGTAGCTGGTTTTCATTTAATTTAGCA 59.247 33.333 0.00 0.00 0.00 3.49
281 282 8.104222 CGTAGCTGGTTTTCATTTAATTTAGC 57.896 34.615 0.00 0.00 0.00 3.09
324 325 2.552367 TGGTTGGGGTTGGAAGTTTTT 58.448 42.857 0.00 0.00 0.00 1.94
325 326 2.255770 TGGTTGGGGTTGGAAGTTTT 57.744 45.000 0.00 0.00 0.00 2.43
326 327 2.255770 TTGGTTGGGGTTGGAAGTTT 57.744 45.000 0.00 0.00 0.00 2.66
327 328 2.255770 TTTGGTTGGGGTTGGAAGTT 57.744 45.000 0.00 0.00 0.00 2.66
328 329 2.487746 ATTTGGTTGGGGTTGGAAGT 57.512 45.000 0.00 0.00 0.00 3.01
329 330 2.703007 TGAATTTGGTTGGGGTTGGAAG 59.297 45.455 0.00 0.00 0.00 3.46
330 331 2.436173 GTGAATTTGGTTGGGGTTGGAA 59.564 45.455 0.00 0.00 0.00 3.53
422 440 2.829458 GGAGGAGGAGGACGACGG 60.829 72.222 0.00 0.00 0.00 4.79
447 465 2.433491 CCAATCGCGTCCGGAACA 60.433 61.111 5.23 0.00 34.56 3.18
516 534 6.469322 CAGCAAAAAGAAAAGAAAAACGGAG 58.531 36.000 0.00 0.00 0.00 4.63
524 542 3.380004 TCTCGGCAGCAAAAAGAAAAGAA 59.620 39.130 0.00 0.00 0.00 2.52
525 543 2.948979 TCTCGGCAGCAAAAAGAAAAGA 59.051 40.909 0.00 0.00 0.00 2.52
622 640 1.749634 CGAGGACGTCCAAACCTAGAT 59.250 52.381 35.00 12.26 38.89 1.98
656 674 2.110835 TCGCTGCCTTGTGCTTCA 59.889 55.556 0.00 0.00 42.00 3.02
715 733 4.219507 TCGAGATTTCTCCTGATCTATGCC 59.780 45.833 2.08 0.00 39.79 4.40
800 818 2.751436 CGTTGGGATGCAGGTGGG 60.751 66.667 0.00 0.00 0.00 4.61
970 988 0.319727 CTCCTGCATCATCTCCTCGC 60.320 60.000 0.00 0.00 0.00 5.03
1106 1127 1.532868 CTTGGCGAGTCAACTTCTTGG 59.467 52.381 0.00 0.00 0.00 3.61
1230 1251 0.389166 CCGTCTGCACCTCTGTTCTC 60.389 60.000 0.00 0.00 0.00 2.87
1266 1287 4.201891 ACAAGTAGTATCACCTTACGCTCG 60.202 45.833 0.00 0.00 0.00 5.03
1385 1406 0.808125 ACCTTTGCGCGCAATGATAA 59.192 45.000 43.19 30.41 35.70 1.75
1484 1505 4.584638 ACACCCAAAATATGTCCTAGCA 57.415 40.909 0.00 0.00 0.00 3.49
1508 1529 1.119684 AGCCTGTTGGGTTGTTTTCC 58.880 50.000 0.00 0.00 42.12 3.13
1516 1537 1.303888 CAGCATCAGCCTGTTGGGT 60.304 57.895 5.01 0.00 46.37 4.51
1541 1645 0.033601 ACCTTGGTCACCAACAAGCA 60.034 50.000 4.67 0.00 42.01 3.91
1734 2216 2.374184 CCAGAACCAGTTTCACCAACA 58.626 47.619 0.00 0.00 37.93 3.33
1839 2322 0.959372 GAGCAACACTCATGGCAGCT 60.959 55.000 0.00 0.00 45.49 4.24
1872 2355 1.665735 CCAAGCACGGTTTCCATTTCG 60.666 52.381 0.00 0.00 0.00 3.46
2067 3070 7.631377 GCAGCAACCTTCTTCAATATACCAAAT 60.631 37.037 0.00 0.00 0.00 2.32
2396 3486 1.209990 AGATTGAGAGCTTCCCTGCAG 59.790 52.381 6.78 6.78 34.99 4.41
2399 3489 2.015587 GCAAGATTGAGAGCTTCCCTG 58.984 52.381 0.00 0.00 26.63 4.45
2403 3493 1.012841 CGGGCAAGATTGAGAGCTTC 58.987 55.000 0.00 0.00 26.63 3.86
2475 3565 3.056313 GCATTTGCGAGTGCCCTCC 62.056 63.158 10.26 0.00 41.78 4.30
2721 3811 1.607612 CACGGGGTTAGGGAGCATT 59.392 57.895 0.00 0.00 0.00 3.56
2908 3998 2.883386 CCATCTTCCAGCCTAGATTTGC 59.117 50.000 0.00 0.00 0.00 3.68
2983 4073 0.179004 ACTTCATCAACGCACCCCAA 60.179 50.000 0.00 0.00 0.00 4.12
3018 4108 1.134461 ACTGATGGCACTGAGAGCATC 60.134 52.381 3.95 5.91 0.00 3.91
3145 4235 7.064674 CAGTCTACACTATATTCGTTCGACTC 58.935 42.308 0.00 0.00 0.00 3.36
3162 4252 1.347378 TGAGCATTGCACCAGTCTACA 59.653 47.619 11.91 0.00 0.00 2.74
3269 4359 3.832704 CATTCCCTATGGCGCGATA 57.167 52.632 12.10 11.80 0.00 2.92
3292 4382 0.329261 CAGATGGCCTTCCTCACCAA 59.671 55.000 14.77 0.00 36.94 3.67
3641 4731 2.203167 CTCTGCATGCCGCCTCAT 60.203 61.111 16.68 0.00 41.33 2.90
3673 4766 2.124942 CGGCTTGCCCCTCTTCTC 60.125 66.667 6.02 0.00 0.00 2.87
3674 4767 4.416738 GCGGCTTGCCCCTCTTCT 62.417 66.667 6.02 0.00 37.76 2.85
3753 4849 3.920841 ACCTTCCTACCTACAAACCCATT 59.079 43.478 0.00 0.00 0.00 3.16
3804 4900 6.902224 AATGCATTCATTCATGTGTGATTG 57.098 33.333 5.99 14.73 38.47 2.67
4026 5123 6.699575 AATTATGAAGCCACAGGTATGTTC 57.300 37.500 0.00 0.00 37.65 3.18
4027 5124 7.480760 AAAATTATGAAGCCACAGGTATGTT 57.519 32.000 0.00 0.00 37.65 2.71
4028 5125 8.766994 ATAAAATTATGAAGCCACAGGTATGT 57.233 30.769 0.00 0.00 41.57 2.29
4113 5210 5.698832 TGATACTGCACAAACAACTTATGC 58.301 37.500 0.00 0.00 36.81 3.14
4116 5213 6.989759 TCTCTTGATACTGCACAAACAACTTA 59.010 34.615 0.00 0.00 0.00 2.24
4159 5256 0.931005 GCCTCGAGCTGAATAAACCG 59.069 55.000 6.99 0.00 38.99 4.44
4291 5497 5.765176 TGCAGCACATAATCTGATAAATGC 58.235 37.500 10.99 9.30 32.26 3.56
4568 7444 5.796935 CGAAATTTGTTGCAGTAGATTGGAG 59.203 40.000 0.00 0.00 0.00 3.86
4570 7446 4.858692 CCGAAATTTGTTGCAGTAGATTGG 59.141 41.667 0.00 0.00 0.00 3.16
4649 7525 7.201591 GCACATGGACATCATATAGTATCTTGC 60.202 40.741 0.00 0.00 34.12 4.01
4740 7616 1.980765 TCAGGATTCAAGGTGAGCACT 59.019 47.619 0.16 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.