Multiple sequence alignment - TraesCS3D01G282100

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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 TraesCS3D01G282100 chr3D 100.000 4148 0 0 1 4148 390077405 390073258 0.000000e+00 7661.0
1 TraesCS3D01G282100 chr3A 94.626 3610 135 33 566 4148 510691843 510688266 0.000000e+00 5537.0
2 TraesCS3D01G282100 chr3A 93.985 133 8 0 14 146 136477424 136477556 7.030000e-48 202.0
3 TraesCS3D01G282100 chr3A 95.349 43 1 1 3141 3183 714070557 714070598 2.680000e-07 67.6
4 TraesCS3D01G282100 chr3B 91.923 2142 117 21 273 2401 507302553 507300455 0.000000e+00 2946.0
5 TraesCS3D01G282100 chr3B 89.905 1684 114 28 2487 4148 507300398 507298749 0.000000e+00 2117.0
6 TraesCS3D01G282100 chr3B 95.588 68 3 0 206 273 507302647 507302580 4.380000e-20 110.0
7 TraesCS3D01G282100 chr2B 96.183 131 5 0 13 143 134488798 134488668 9.030000e-52 215.0
8 TraesCS3D01G282100 chr2B 87.805 164 12 6 14 171 66781166 66781005 7.080000e-43 185.0
9 TraesCS3D01G282100 chrUn 94.030 134 8 0 15 148 93156331 93156464 1.950000e-48 204.0
10 TraesCS3D01G282100 chr7B 94.656 131 7 0 15 145 723351858 723351988 1.950000e-48 204.0
11 TraesCS3D01G282100 chr7B 93.985 133 8 0 9 141 219565143 219565275 7.030000e-48 202.0
12 TraesCS3D01G282100 chr7B 94.615 130 7 0 15 144 401136814 401136685 7.030000e-48 202.0
13 TraesCS3D01G282100 chr6B 95.312 128 6 0 14 141 354257181 354257308 1.950000e-48 204.0
14 TraesCS3D01G282100 chr6B 92.199 141 9 2 3 141 171052240 171052380 9.100000e-47 198.0
15 TraesCS3D01G282100 chr1B 83.824 136 20 2 1349 1483 593837600 593837466 1.210000e-25 128.0
16 TraesCS3D01G282100 chr1A 83.088 136 21 2 1349 1483 534933235 534933101 5.630000e-24 122.0
17 TraesCS3D01G282100 chr1D 85.185 108 16 0 1376 1483 438228754 438228647 1.220000e-20 111.0


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 TraesCS3D01G282100 chr3D 390073258 390077405 4147 True 7661.000000 7661 100.000 1 4148 1 chr3D.!!$R1 4147
1 TraesCS3D01G282100 chr3A 510688266 510691843 3577 True 5537.000000 5537 94.626 566 4148 1 chr3A.!!$R1 3582
2 TraesCS3D01G282100 chr3B 507298749 507302647 3898 True 1724.333333 2946 92.472 206 4148 3 chr3B.!!$R1 3942

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
33 34 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.0 44.66 2.17 F
34 35 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.0 44.66 1.40 F
142 143 0.038744 TTTCGGACGGAGGGAGTACT 59.961 55.000 0.00 0.0 0.00 2.73 F
1293 1330 0.102481 ACTCGTTCGCACTCTTGTGT 59.898 50.000 0.00 0.0 45.44 3.72 F
1386 1431 1.135575 CCGCAACAGATCAAGAAAGCC 60.136 52.381 0.00 0.0 0.00 4.35 F
2805 2883 1.299850 TGTGTCTTGTCGTGAGCCG 60.300 57.895 0.00 0.0 38.13 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1994 2042 0.670162 AATGGCAGCATACGCATTCC 59.330 50.000 0.00 0.00 42.27 3.01 R
2000 2048 2.948093 GCACAAATGGCAGCATACG 58.052 52.632 0.00 0.00 0.00 3.06 R
2035 2083 4.033709 TCACAAACTCCCCATTGGAAAAA 58.966 39.130 3.62 0.00 44.57 1.94 R
2445 2500 0.032540 CCATCCATCATCACGCGAGA 59.967 55.000 15.93 12.19 0.00 4.04 R
2963 3041 0.685097 TAGGCAAAGGACGTGAGCTT 59.315 50.000 0.00 0.00 0.00 3.74 R
4007 4114 2.104253 CCCCAAAATCCCGTCGTCG 61.104 63.158 0.00 0.00 0.00 5.12 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
20 21 2.215942 AGGTGGCATTTTGTACTCCC 57.784 50.000 0.00 0.00 0.00 4.30
21 22 1.710809 AGGTGGCATTTTGTACTCCCT 59.289 47.619 0.00 0.00 0.00 4.20
22 23 2.092323 GGTGGCATTTTGTACTCCCTC 58.908 52.381 0.00 0.00 0.00 4.30
23 24 2.092323 GTGGCATTTTGTACTCCCTCC 58.908 52.381 0.00 0.00 0.00 4.30
24 25 1.339631 TGGCATTTTGTACTCCCTCCG 60.340 52.381 0.00 0.00 0.00 4.63
25 26 1.339727 GGCATTTTGTACTCCCTCCGT 60.340 52.381 0.00 0.00 0.00 4.69
26 27 2.007608 GCATTTTGTACTCCCTCCGTC 58.992 52.381 0.00 0.00 0.00 4.79
27 28 2.629051 CATTTTGTACTCCCTCCGTCC 58.371 52.381 0.00 0.00 0.00 4.79
28 29 0.604578 TTTTGTACTCCCTCCGTCCG 59.395 55.000 0.00 0.00 0.00 4.79
29 30 1.252904 TTTGTACTCCCTCCGTCCGG 61.253 60.000 0.00 0.00 0.00 5.14
30 31 2.141011 TTGTACTCCCTCCGTCCGGA 62.141 60.000 0.00 0.00 42.90 5.14
31 32 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
32 33 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
33 34 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
34 35 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
35 36 1.339097 CTCCCTCCGTCCGGAAATAT 58.661 55.000 5.23 0.00 44.66 1.28
36 37 1.692519 CTCCCTCCGTCCGGAAATATT 59.307 52.381 5.23 0.00 44.66 1.28
37 38 2.104281 CTCCCTCCGTCCGGAAATATTT 59.896 50.000 5.23 0.00 44.66 1.40
38 39 2.158871 TCCCTCCGTCCGGAAATATTTG 60.159 50.000 5.23 0.00 44.66 2.32
39 40 2.420967 CCCTCCGTCCGGAAATATTTGT 60.421 50.000 5.23 0.00 44.66 2.83
40 41 2.870411 CCTCCGTCCGGAAATATTTGTC 59.130 50.000 5.23 0.00 44.66 3.18
41 42 3.527533 CTCCGTCCGGAAATATTTGTCA 58.472 45.455 5.23 0.00 44.66 3.58
42 43 3.264104 TCCGTCCGGAAATATTTGTCAC 58.736 45.455 5.23 0.00 42.05 3.67
43 44 2.353579 CCGTCCGGAAATATTTGTCACC 59.646 50.000 5.23 0.00 37.50 4.02
44 45 3.004171 CGTCCGGAAATATTTGTCACCA 58.996 45.455 5.23 0.00 0.00 4.17
45 46 3.437395 CGTCCGGAAATATTTGTCACCAA 59.563 43.478 5.23 0.00 0.00 3.67
46 47 4.083217 CGTCCGGAAATATTTGTCACCAAA 60.083 41.667 5.23 0.00 44.27 3.28
47 48 5.563085 CGTCCGGAAATATTTGTCACCAAAA 60.563 40.000 5.23 0.00 43.43 2.44
48 49 6.394809 GTCCGGAAATATTTGTCACCAAAAT 58.605 36.000 5.23 0.00 43.43 1.82
49 50 6.310224 GTCCGGAAATATTTGTCACCAAAATG 59.690 38.462 5.23 0.00 43.43 2.32
50 51 6.209589 TCCGGAAATATTTGTCACCAAAATGA 59.790 34.615 0.00 0.00 43.43 2.57
51 52 6.870965 CCGGAAATATTTGTCACCAAAATGAA 59.129 34.615 5.17 0.00 43.43 2.57
52 53 7.148656 CCGGAAATATTTGTCACCAAAATGAAC 60.149 37.037 5.17 0.00 43.43 3.18
53 54 7.383572 CGGAAATATTTGTCACCAAAATGAACA 59.616 33.333 5.17 0.00 43.43 3.18
54 55 9.050601 GGAAATATTTGTCACCAAAATGAACAA 57.949 29.630 5.17 0.00 43.43 2.83
58 59 6.734104 TTTGTCACCAAAATGAACAAAAGG 57.266 33.333 0.00 0.00 37.62 3.11
59 60 4.764172 TGTCACCAAAATGAACAAAAGGG 58.236 39.130 0.00 0.00 0.00 3.95
60 61 4.126437 GTCACCAAAATGAACAAAAGGGG 58.874 43.478 0.00 0.00 0.00 4.79
61 62 4.033709 TCACCAAAATGAACAAAAGGGGA 58.966 39.130 0.00 0.00 0.00 4.81
62 63 4.657969 TCACCAAAATGAACAAAAGGGGAT 59.342 37.500 0.00 0.00 0.00 3.85
63 64 4.756135 CACCAAAATGAACAAAAGGGGATG 59.244 41.667 0.00 0.00 0.00 3.51
64 65 4.411869 ACCAAAATGAACAAAAGGGGATGT 59.588 37.500 0.00 0.00 0.00 3.06
65 66 5.604650 ACCAAAATGAACAAAAGGGGATGTA 59.395 36.000 0.00 0.00 0.00 2.29
66 67 6.272090 ACCAAAATGAACAAAAGGGGATGTAT 59.728 34.615 0.00 0.00 0.00 2.29
67 68 6.818142 CCAAAATGAACAAAAGGGGATGTATC 59.182 38.462 0.00 0.00 0.00 2.24
68 69 7.310609 CCAAAATGAACAAAAGGGGATGTATCT 60.311 37.037 0.00 0.00 0.00 1.98
69 70 8.748412 CAAAATGAACAAAAGGGGATGTATCTA 58.252 33.333 0.00 0.00 0.00 1.98
70 71 8.525290 AAATGAACAAAAGGGGATGTATCTAG 57.475 34.615 0.00 0.00 0.00 2.43
71 72 6.884472 TGAACAAAAGGGGATGTATCTAGA 57.116 37.500 0.00 0.00 0.00 2.43
72 73 6.650120 TGAACAAAAGGGGATGTATCTAGAC 58.350 40.000 0.00 0.00 0.00 2.59
73 74 5.277857 ACAAAAGGGGATGTATCTAGACG 57.722 43.478 0.00 0.00 0.00 4.18
74 75 4.715297 ACAAAAGGGGATGTATCTAGACGT 59.285 41.667 0.00 0.00 0.00 4.34
75 76 5.895534 ACAAAAGGGGATGTATCTAGACGTA 59.104 40.000 0.00 0.00 0.00 3.57
76 77 6.553852 ACAAAAGGGGATGTATCTAGACGTAT 59.446 38.462 0.00 0.00 0.00 3.06
77 78 7.727186 ACAAAAGGGGATGTATCTAGACGTATA 59.273 37.037 0.00 0.00 0.00 1.47
78 79 8.750298 CAAAAGGGGATGTATCTAGACGTATAT 58.250 37.037 0.00 0.00 0.00 0.86
79 80 8.896722 AAAGGGGATGTATCTAGACGTATATT 57.103 34.615 0.00 0.00 0.00 1.28
80 81 9.986157 AAAGGGGATGTATCTAGACGTATATTA 57.014 33.333 0.00 0.00 0.00 0.98
81 82 9.629878 AAGGGGATGTATCTAGACGTATATTAG 57.370 37.037 0.00 0.00 0.00 1.73
82 83 8.780003 AGGGGATGTATCTAGACGTATATTAGT 58.220 37.037 0.00 0.00 0.00 2.24
83 84 9.406113 GGGGATGTATCTAGACGTATATTAGTT 57.594 37.037 0.00 0.00 0.00 2.24
128 129 8.741101 TTCATTTTGATGACAAGTATTTTCGG 57.259 30.769 0.00 0.00 37.32 4.30
129 130 8.105097 TCATTTTGATGACAAGTATTTTCGGA 57.895 30.769 0.00 0.00 37.32 4.55
130 131 8.020819 TCATTTTGATGACAAGTATTTTCGGAC 58.979 33.333 0.00 0.00 37.32 4.79
131 132 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
132 133 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
133 134 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
134 135 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
135 136 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
136 137 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
137 138 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
138 139 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
139 140 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
140 141 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
141 142 0.890683 TTTTCGGACGGAGGGAGTAC 59.109 55.000 0.00 0.00 0.00 2.73
142 143 0.038744 TTTCGGACGGAGGGAGTACT 59.961 55.000 0.00 0.00 0.00 2.73
143 144 0.038744 TTCGGACGGAGGGAGTACTT 59.961 55.000 0.00 0.00 0.00 2.24
144 145 0.038744 TCGGACGGAGGGAGTACTTT 59.961 55.000 0.00 0.00 0.00 2.66
145 146 0.172803 CGGACGGAGGGAGTACTTTG 59.827 60.000 0.00 0.00 0.00 2.77
146 147 0.108281 GGACGGAGGGAGTACTTTGC 60.108 60.000 0.00 0.00 0.00 3.68
147 148 0.606604 GACGGAGGGAGTACTTTGCA 59.393 55.000 0.00 0.00 0.00 4.08
148 149 0.320697 ACGGAGGGAGTACTTTGCAC 59.679 55.000 0.00 0.00 0.00 4.57
149 150 0.391263 CGGAGGGAGTACTTTGCACC 60.391 60.000 0.00 0.00 0.00 5.01
150 151 0.984995 GGAGGGAGTACTTTGCACCT 59.015 55.000 0.00 0.20 0.00 4.00
151 152 1.066071 GGAGGGAGTACTTTGCACCTC 60.066 57.143 16.63 16.63 42.84 3.85
152 153 1.623811 GAGGGAGTACTTTGCACCTCA 59.376 52.381 18.54 0.00 43.02 3.86
153 154 1.348036 AGGGAGTACTTTGCACCTCAC 59.652 52.381 0.00 0.00 0.00 3.51
154 155 1.071699 GGGAGTACTTTGCACCTCACA 59.928 52.381 0.00 0.00 0.00 3.58
155 156 2.290323 GGGAGTACTTTGCACCTCACAT 60.290 50.000 0.00 0.00 0.00 3.21
156 157 3.003480 GGAGTACTTTGCACCTCACATC 58.997 50.000 0.00 0.00 0.00 3.06
157 158 3.307059 GGAGTACTTTGCACCTCACATCT 60.307 47.826 0.00 0.00 0.00 2.90
158 159 4.319177 GAGTACTTTGCACCTCACATCTT 58.681 43.478 0.00 0.00 0.00 2.40
159 160 4.067896 AGTACTTTGCACCTCACATCTTG 58.932 43.478 0.00 0.00 0.00 3.02
160 161 2.936202 ACTTTGCACCTCACATCTTGT 58.064 42.857 0.00 0.00 0.00 3.16
161 162 4.085357 ACTTTGCACCTCACATCTTGTA 57.915 40.909 0.00 0.00 0.00 2.41
162 163 4.067896 ACTTTGCACCTCACATCTTGTAG 58.932 43.478 0.00 0.00 0.00 2.74
163 164 3.769739 TTGCACCTCACATCTTGTAGT 57.230 42.857 0.00 0.00 0.00 2.73
164 165 3.769739 TGCACCTCACATCTTGTAGTT 57.230 42.857 0.00 0.00 0.00 2.24
165 166 4.882842 TGCACCTCACATCTTGTAGTTA 57.117 40.909 0.00 0.00 0.00 2.24
166 167 4.820897 TGCACCTCACATCTTGTAGTTAG 58.179 43.478 0.00 0.00 0.00 2.34
167 168 4.184629 GCACCTCACATCTTGTAGTTAGG 58.815 47.826 0.00 0.00 0.00 2.69
168 169 4.081642 GCACCTCACATCTTGTAGTTAGGA 60.082 45.833 0.00 0.00 0.00 2.94
169 170 5.568825 GCACCTCACATCTTGTAGTTAGGAA 60.569 44.000 0.00 0.00 0.00 3.36
170 171 6.464222 CACCTCACATCTTGTAGTTAGGAAA 58.536 40.000 0.00 0.00 0.00 3.13
171 172 6.591834 CACCTCACATCTTGTAGTTAGGAAAG 59.408 42.308 0.00 0.00 0.00 2.62
172 173 6.497259 ACCTCACATCTTGTAGTTAGGAAAGA 59.503 38.462 0.00 0.00 33.45 2.52
173 174 6.814146 CCTCACATCTTGTAGTTAGGAAAGAC 59.186 42.308 0.00 0.00 31.82 3.01
174 175 7.297936 TCACATCTTGTAGTTAGGAAAGACA 57.702 36.000 0.00 0.00 31.82 3.41
175 176 7.152645 TCACATCTTGTAGTTAGGAAAGACAC 58.847 38.462 0.00 0.00 31.82 3.67
176 177 6.369065 CACATCTTGTAGTTAGGAAAGACACC 59.631 42.308 0.00 0.00 31.82 4.16
177 178 6.042781 ACATCTTGTAGTTAGGAAAGACACCA 59.957 38.462 0.00 0.00 31.82 4.17
178 179 6.681729 TCTTGTAGTTAGGAAAGACACCAT 57.318 37.500 0.00 0.00 0.00 3.55
179 180 6.698380 TCTTGTAGTTAGGAAAGACACCATC 58.302 40.000 0.00 0.00 0.00 3.51
180 181 5.416271 TGTAGTTAGGAAAGACACCATCC 57.584 43.478 0.00 0.00 0.00 3.51
181 182 4.841813 TGTAGTTAGGAAAGACACCATCCA 59.158 41.667 0.00 0.00 35.62 3.41
182 183 5.487488 TGTAGTTAGGAAAGACACCATCCAT 59.513 40.000 0.00 0.00 35.62 3.41
183 184 5.104259 AGTTAGGAAAGACACCATCCATC 57.896 43.478 0.00 0.00 35.62 3.51
184 185 4.536090 AGTTAGGAAAGACACCATCCATCA 59.464 41.667 0.00 0.00 35.62 3.07
185 186 5.192522 AGTTAGGAAAGACACCATCCATCAT 59.807 40.000 0.00 0.00 35.62 2.45
186 187 4.598036 AGGAAAGACACCATCCATCATT 57.402 40.909 0.00 0.00 35.62 2.57
187 188 4.530875 AGGAAAGACACCATCCATCATTC 58.469 43.478 0.00 0.00 35.62 2.67
188 189 3.313526 GGAAAGACACCATCCATCATTCG 59.686 47.826 0.00 0.00 33.30 3.34
189 190 3.912496 AAGACACCATCCATCATTCGA 57.088 42.857 0.00 0.00 0.00 3.71
190 191 4.428294 AAGACACCATCCATCATTCGAT 57.572 40.909 0.00 0.00 0.00 3.59
191 192 4.428294 AGACACCATCCATCATTCGATT 57.572 40.909 0.00 0.00 0.00 3.34
192 193 5.551305 AGACACCATCCATCATTCGATTA 57.449 39.130 0.00 0.00 0.00 1.75
193 194 5.300752 AGACACCATCCATCATTCGATTAC 58.699 41.667 0.00 0.00 0.00 1.89
194 195 5.034852 ACACCATCCATCATTCGATTACA 57.965 39.130 0.00 0.00 0.00 2.41
195 196 5.436175 ACACCATCCATCATTCGATTACAA 58.564 37.500 0.00 0.00 0.00 2.41
196 197 5.885352 ACACCATCCATCATTCGATTACAAA 59.115 36.000 0.00 0.00 0.00 2.83
197 198 6.038603 ACACCATCCATCATTCGATTACAAAG 59.961 38.462 0.00 0.00 0.00 2.77
198 199 6.038603 CACCATCCATCATTCGATTACAAAGT 59.961 38.462 0.00 0.00 0.00 2.66
199 200 6.603201 ACCATCCATCATTCGATTACAAAGTT 59.397 34.615 0.00 0.00 0.00 2.66
200 201 7.773224 ACCATCCATCATTCGATTACAAAGTTA 59.227 33.333 0.00 0.00 0.00 2.24
201 202 8.070171 CCATCCATCATTCGATTACAAAGTTAC 58.930 37.037 0.00 0.00 0.00 2.50
202 203 8.830580 CATCCATCATTCGATTACAAAGTTACT 58.169 33.333 0.00 0.00 0.00 2.24
204 205 9.309516 TCCATCATTCGATTACAAAGTTACTAC 57.690 33.333 0.00 0.00 0.00 2.73
291 319 3.749088 TCATGTCCGTTTGGTGTGAATAC 59.251 43.478 0.00 0.00 36.30 1.89
295 323 4.202233 TGTCCGTTTGGTGTGAATACTGTA 60.202 41.667 0.00 0.00 36.30 2.74
306 334 5.638234 GTGTGAATACTGTAGACCCAAGTTC 59.362 44.000 0.00 0.00 0.00 3.01
325 354 6.690194 AGTTCTGATTATTCACCATGAAGC 57.310 37.500 0.00 0.00 40.05 3.86
329 358 6.182627 TCTGATTATTCACCATGAAGCTTGT 58.817 36.000 2.10 0.00 40.05 3.16
356 387 6.154445 GCTTCCACAATTTGATATGCTATGG 58.846 40.000 2.79 0.00 0.00 2.74
358 389 5.387788 TCCACAATTTGATATGCTATGGCT 58.612 37.500 1.68 0.00 39.59 4.75
359 390 5.242171 TCCACAATTTGATATGCTATGGCTG 59.758 40.000 1.68 0.00 39.59 4.85
365 396 6.964807 TTTGATATGCTATGGCTGTCAAAT 57.035 33.333 17.85 1.20 38.02 2.32
373 404 1.226128 GGCTGTCAAATTCGAGCGC 60.226 57.895 0.00 0.00 31.89 5.92
375 406 1.911293 GCTGTCAAATTCGAGCGCCA 61.911 55.000 2.29 0.00 0.00 5.69
379 410 1.331756 GTCAAATTCGAGCGCCATCAT 59.668 47.619 2.29 0.00 0.00 2.45
380 411 1.599071 TCAAATTCGAGCGCCATCATC 59.401 47.619 2.29 0.00 0.00 2.92
381 412 1.331447 CAAATTCGAGCGCCATCATCA 59.669 47.619 2.29 0.00 0.00 3.07
390 421 3.397482 AGCGCCATCATCAGAAGAATAC 58.603 45.455 2.29 0.00 0.00 1.89
393 424 3.496130 CGCCATCATCAGAAGAATACCAC 59.504 47.826 0.00 0.00 0.00 4.16
401 432 7.851228 TCATCAGAAGAATACCACTTGTACAT 58.149 34.615 0.00 0.00 30.62 2.29
408 439 5.365895 AGAATACCACTTGTACATACTCCCC 59.634 44.000 0.00 0.00 30.62 4.81
424 455 2.202932 CCCGATCTCCGTGGCTTG 60.203 66.667 0.00 0.00 36.31 4.01
425 456 2.202932 CCGATCTCCGTGGCTTGG 60.203 66.667 0.00 0.00 36.31 3.61
426 457 2.721167 CCGATCTCCGTGGCTTGGA 61.721 63.158 0.00 0.00 36.31 3.53
430 461 2.032528 CTCCGTGGCTTGGAGCAA 59.967 61.111 11.70 0.00 45.99 3.91
431 462 2.281484 TCCGTGGCTTGGAGCAAC 60.281 61.111 2.04 0.00 44.75 4.17
439 470 1.576421 CTTGGAGCAACGGAGCAAC 59.424 57.895 4.18 0.00 36.85 4.17
443 474 4.250305 AGCAACGGAGCAACGGGT 62.250 61.111 5.09 0.00 38.39 5.28
445 476 2.388232 GCAACGGAGCAACGGGTAG 61.388 63.158 5.09 0.00 38.39 3.18
474 505 6.761731 CTCTACTAGCTTATTCATGTGCAC 57.238 41.667 10.75 10.75 0.00 4.57
483 514 5.565439 GCTTATTCATGTGCACCATTATCCC 60.565 44.000 15.69 0.00 0.00 3.85
487 518 1.595311 TGTGCACCATTATCCCCTCT 58.405 50.000 15.69 0.00 0.00 3.69
505 536 6.828785 TCCCCTCTAAAAGACTTATTTGCATC 59.171 38.462 0.00 0.00 0.00 3.91
506 537 6.238484 CCCCTCTAAAAGACTTATTTGCATCG 60.238 42.308 0.00 0.00 0.00 3.84
507 538 6.316390 CCCTCTAAAAGACTTATTTGCATCGT 59.684 38.462 0.00 0.00 0.00 3.73
519 550 3.536158 TTGCATCGTGTAACTTGAAGC 57.464 42.857 0.00 0.00 31.75 3.86
544 575 1.530323 AAAGTTATGGCGCCGACTTT 58.470 45.000 32.34 32.34 37.47 2.66
554 585 1.221466 CGCCGACTTTGCTGTCAGAA 61.221 55.000 3.32 0.00 36.82 3.02
566 597 3.565482 TGCTGTCAGAAAAGCCTTGTAAG 59.435 43.478 3.32 0.00 38.71 2.34
573 604 1.523758 AAAGCCTTGTAAGCTCACCG 58.476 50.000 0.00 0.00 40.49 4.94
574 605 0.685097 AAGCCTTGTAAGCTCACCGA 59.315 50.000 0.00 0.00 40.49 4.69
605 638 2.910688 TGTAAGCTATAGGCAGCCAC 57.089 50.000 15.80 0.10 42.84 5.01
698 731 3.330701 ACCAGGCTCACCTCAAGAAATAA 59.669 43.478 0.00 0.00 46.34 1.40
699 732 4.018050 ACCAGGCTCACCTCAAGAAATAAT 60.018 41.667 0.00 0.00 46.34 1.28
700 733 4.337555 CCAGGCTCACCTCAAGAAATAATG 59.662 45.833 0.00 0.00 46.34 1.90
991 1028 0.638242 CGAAACGCGATCGAACATCA 59.362 50.000 26.46 0.00 44.57 3.07
1020 1057 3.071206 GCTCCTCTCCTGTCGCCA 61.071 66.667 0.00 0.00 0.00 5.69
1293 1330 0.102481 ACTCGTTCGCACTCTTGTGT 59.898 50.000 0.00 0.00 45.44 3.72
1294 1331 1.335810 ACTCGTTCGCACTCTTGTGTA 59.664 47.619 0.00 0.00 45.44 2.90
1319 1356 2.280628 CAATCGTCTTTCCCCTGCTAC 58.719 52.381 0.00 0.00 0.00 3.58
1386 1431 1.135575 CCGCAACAGATCAAGAAAGCC 60.136 52.381 0.00 0.00 0.00 4.35
1714 1762 3.384789 TCGATGAGTTTAGCTGCATAGGT 59.615 43.478 1.02 0.00 38.41 3.08
1715 1763 4.583073 TCGATGAGTTTAGCTGCATAGGTA 59.417 41.667 1.02 0.00 35.90 3.08
1716 1764 4.681942 CGATGAGTTTAGCTGCATAGGTAC 59.318 45.833 1.02 0.00 36.68 3.34
1717 1765 5.508153 CGATGAGTTTAGCTGCATAGGTACT 60.508 44.000 1.02 0.00 46.37 2.73
1837 1885 6.636850 CAGGTTGTAAAAACTGTGCTAATGTC 59.363 38.462 2.16 0.00 30.95 3.06
1963 2011 4.560108 GCCCCATGTCTGCATTATTTCATC 60.560 45.833 0.00 0.00 31.99 2.92
1994 2042 3.057596 TCCACTACCGTAACAAACCTACG 60.058 47.826 0.00 0.00 41.39 3.51
2000 2048 3.378959 CGTAACAAACCTACGGAATGC 57.621 47.619 0.00 0.00 38.74 3.56
2035 2083 2.158682 TGTGCCAAACAGTATGAGTGGT 60.159 45.455 0.00 0.00 42.74 4.16
2043 2091 6.406400 CCAAACAGTATGAGTGGTTTTTCCAA 60.406 38.462 0.00 0.00 44.14 3.53
2061 2114 3.009033 TCCAATGGGGAGTTTGTGACTAG 59.991 47.826 0.00 0.00 42.15 2.57
2429 2483 1.842010 CCGGGGGTATCCTCCCTTC 60.842 68.421 0.00 0.00 46.27 3.46
2539 2615 4.389077 CGTCCACCTTCTGAAGTTGTTATC 59.611 45.833 15.72 2.43 0.00 1.75
2546 2623 5.409826 CCTTCTGAAGTTGTTATCACAGACC 59.590 44.000 15.72 0.00 34.79 3.85
2554 2631 4.137116 TGTTATCACAGACCCTATGCAC 57.863 45.455 0.00 0.00 0.00 4.57
2563 2640 4.042934 ACAGACCCTATGCACTTTAAACCT 59.957 41.667 0.00 0.00 0.00 3.50
2565 2642 4.536489 AGACCCTATGCACTTTAAACCTCT 59.464 41.667 0.00 0.00 0.00 3.69
2586 2663 6.591834 CCTCTGTTCATGTAGTAGGTCTTTTG 59.408 42.308 0.00 0.00 0.00 2.44
2592 2669 6.999950 TCATGTAGTAGGTCTTTTGTTAGCA 58.000 36.000 0.00 0.00 0.00 3.49
2711 2789 4.832248 TCTCTGTTCGATACATGGCTTTT 58.168 39.130 0.00 0.00 35.85 2.27
2746 2824 7.972301 ACATATGAAAATCCAGTTTGGGAAAA 58.028 30.769 10.38 0.00 41.12 2.29
2783 2861 7.396540 ACTTCTGATTTTCCACATATCAACC 57.603 36.000 0.00 0.00 0.00 3.77
2786 2864 3.064682 TGATTTTCCACATATCAACCGCG 59.935 43.478 0.00 0.00 0.00 6.46
2798 2876 2.235016 AACCGCGTGTGTCTTGTCG 61.235 57.895 4.92 0.00 0.00 4.35
2805 2883 1.299850 TGTGTCTTGTCGTGAGCCG 60.300 57.895 0.00 0.00 38.13 5.52
2808 2886 2.089349 GTCTTGTCGTGAGCCGCTC 61.089 63.158 13.81 13.81 36.19 5.03
2928 3006 8.370182 AGATACCAAAAGAACGGTAAAACTAGA 58.630 33.333 0.00 0.00 41.03 2.43
2937 3015 9.836076 AAGAACGGTAAAACTAGAATATTTTGC 57.164 29.630 0.00 0.00 31.82 3.68
2940 3018 8.113173 ACGGTAAAACTAGAATATTTTGCCAA 57.887 30.769 17.55 0.00 45.56 4.52
2951 3029 8.496707 AGAATATTTTGCCAATTGTCAATTCC 57.503 30.769 7.87 3.63 0.00 3.01
2963 3041 7.201812 CCAATTGTCAATTCCTCGGATCATTTA 60.202 37.037 7.87 0.00 0.00 1.40
2964 3042 7.880160 ATTGTCAATTCCTCGGATCATTTAA 57.120 32.000 0.00 0.00 0.00 1.52
2966 3044 5.296780 TGTCAATTCCTCGGATCATTTAAGC 59.703 40.000 0.00 0.00 0.00 3.09
2969 3047 4.753516 TTCCTCGGATCATTTAAGCTCA 57.246 40.909 0.00 0.00 0.00 4.26
2971 3049 2.797156 CCTCGGATCATTTAAGCTCACG 59.203 50.000 0.00 0.00 0.00 4.35
2987 3065 1.899814 TCACGTCCTTTGCCTATCTGT 59.100 47.619 0.00 0.00 0.00 3.41
3014 3092 2.322355 ATACTCCTGCTGACATGTGC 57.678 50.000 1.15 1.24 0.00 4.57
3173 3251 1.384409 GAACACGGTCGTTACACATCG 59.616 52.381 0.00 0.00 0.00 3.84
3262 3340 2.117156 CATTTGCTCTCCCGCCCTG 61.117 63.158 0.00 0.00 0.00 4.45
3298 3377 8.882736 TGTTAGCAGTATCTGTAAATCATGTTG 58.117 33.333 0.00 0.00 33.43 3.33
3342 3421 7.684317 TCTGTAAATCACCCATAGGATACAA 57.316 36.000 0.00 0.00 41.41 2.41
3421 3500 3.631144 TCGACGGTGTGTGTAAAAGTAG 58.369 45.455 0.00 0.00 0.00 2.57
3429 3508 6.292168 CGGTGTGTGTAAAAGTAGAGAAACTG 60.292 42.308 0.00 0.00 0.00 3.16
3457 3536 8.757982 AGTGGAATTGTGCATATTCTCTATTT 57.242 30.769 18.33 3.43 33.51 1.40
3471 3573 7.798596 ATTCTCTATTTGCAGATCGAAATGT 57.201 32.000 0.00 0.00 0.00 2.71
3508 3610 7.172361 GGAGATATCATGTGAAACTTAGAAGCC 59.828 40.741 5.32 0.00 38.04 4.35
3529 3631 3.557595 CCACAGGCGAGATGTCTTTATTC 59.442 47.826 0.00 0.00 0.00 1.75
3530 3632 4.183865 CACAGGCGAGATGTCTTTATTCA 58.816 43.478 0.00 0.00 0.00 2.57
3531 3633 4.269603 CACAGGCGAGATGTCTTTATTCAG 59.730 45.833 0.00 0.00 0.00 3.02
3532 3634 4.160439 ACAGGCGAGATGTCTTTATTCAGA 59.840 41.667 0.00 0.00 0.00 3.27
3533 3635 5.163364 ACAGGCGAGATGTCTTTATTCAGAT 60.163 40.000 0.00 0.00 0.00 2.90
3534 3636 6.040955 ACAGGCGAGATGTCTTTATTCAGATA 59.959 38.462 0.00 0.00 0.00 1.98
3535 3637 7.095910 CAGGCGAGATGTCTTTATTCAGATAT 58.904 38.462 0.00 0.00 0.00 1.63
3536 3638 8.246871 CAGGCGAGATGTCTTTATTCAGATATA 58.753 37.037 0.00 0.00 0.00 0.86
3537 3639 8.976353 AGGCGAGATGTCTTTATTCAGATATAT 58.024 33.333 0.00 0.00 0.00 0.86
3538 3640 9.029243 GGCGAGATGTCTTTATTCAGATATATG 57.971 37.037 0.00 0.00 0.00 1.78
3547 3649 8.650490 TCTTTATTCAGATATATGTGTGGAGCA 58.350 33.333 9.50 0.00 0.00 4.26
3548 3650 8.837788 TTTATTCAGATATATGTGTGGAGCAG 57.162 34.615 9.50 0.00 0.00 4.24
3549 3651 4.879197 TCAGATATATGTGTGGAGCAGG 57.121 45.455 9.50 0.00 0.00 4.85
3553 3660 2.742428 ATATGTGTGGAGCAGGCAAT 57.258 45.000 0.00 0.00 0.00 3.56
3559 3666 0.899717 GTGGAGCAGGCAATGGGAAA 60.900 55.000 0.00 0.00 0.00 3.13
3589 3696 5.528320 ACCAAATTGCAAGATTTTGAACTGG 59.472 36.000 20.41 10.21 36.36 4.00
3756 3863 1.591059 CTCGATGCGCTCTTGGAGG 60.591 63.158 9.73 0.00 0.00 4.30
4007 4114 1.215382 GGGCGAAGTGGAATTTGGC 59.785 57.895 0.00 0.00 36.57 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.710809 AGGGAGTACAAAATGCCACCT 59.289 47.619 0.00 0.00 0.00 4.00
2 3 2.092323 GAGGGAGTACAAAATGCCACC 58.908 52.381 0.00 0.00 0.00 4.61
3 4 2.092323 GGAGGGAGTACAAAATGCCAC 58.908 52.381 0.00 0.00 0.00 5.01
4 5 1.339631 CGGAGGGAGTACAAAATGCCA 60.340 52.381 0.00 0.00 0.00 4.92
5 6 1.339727 ACGGAGGGAGTACAAAATGCC 60.340 52.381 0.00 0.00 0.00 4.40
6 7 2.007608 GACGGAGGGAGTACAAAATGC 58.992 52.381 0.00 0.00 0.00 3.56
7 8 2.629051 GGACGGAGGGAGTACAAAATG 58.371 52.381 0.00 0.00 0.00 2.32
8 9 1.206371 CGGACGGAGGGAGTACAAAAT 59.794 52.381 0.00 0.00 0.00 1.82
9 10 0.604578 CGGACGGAGGGAGTACAAAA 59.395 55.000 0.00 0.00 0.00 2.44
10 11 1.252904 CCGGACGGAGGGAGTACAAA 61.253 60.000 4.40 0.00 37.50 2.83
11 12 1.679977 CCGGACGGAGGGAGTACAA 60.680 63.158 4.40 0.00 37.50 2.41
12 13 2.044650 CCGGACGGAGGGAGTACA 60.045 66.667 4.40 0.00 37.50 2.90
13 14 0.967380 TTTCCGGACGGAGGGAGTAC 60.967 60.000 13.64 0.00 46.06 2.73
14 15 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
15 16 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
16 17 1.339097 ATATTTCCGGACGGAGGGAG 58.661 55.000 13.64 0.00 46.06 4.30
17 18 1.797320 AATATTTCCGGACGGAGGGA 58.203 50.000 13.64 4.95 46.06 4.20
18 19 2.218603 CAAATATTTCCGGACGGAGGG 58.781 52.381 13.64 0.00 46.06 4.30
19 20 2.870411 GACAAATATTTCCGGACGGAGG 59.130 50.000 13.64 0.00 46.06 4.30
20 21 3.308866 GTGACAAATATTTCCGGACGGAG 59.691 47.826 13.64 3.15 46.06 4.63
21 22 3.264104 GTGACAAATATTTCCGGACGGA 58.736 45.455 1.83 9.76 43.52 4.69
22 23 2.353579 GGTGACAAATATTTCCGGACGG 59.646 50.000 1.83 3.96 0.00 4.79
23 24 3.004171 TGGTGACAAATATTTCCGGACG 58.996 45.455 1.83 0.00 37.44 4.79
37 38 4.383552 CCCCTTTTGTTCATTTTGGTGACA 60.384 41.667 0.00 0.00 39.83 3.58
38 39 4.126437 CCCCTTTTGTTCATTTTGGTGAC 58.874 43.478 0.00 0.00 0.00 3.67
39 40 4.033709 TCCCCTTTTGTTCATTTTGGTGA 58.966 39.130 0.00 0.00 0.00 4.02
40 41 4.414337 TCCCCTTTTGTTCATTTTGGTG 57.586 40.909 0.00 0.00 0.00 4.17
41 42 4.411869 ACATCCCCTTTTGTTCATTTTGGT 59.588 37.500 0.00 0.00 0.00 3.67
42 43 4.971939 ACATCCCCTTTTGTTCATTTTGG 58.028 39.130 0.00 0.00 0.00 3.28
43 44 7.614494 AGATACATCCCCTTTTGTTCATTTTG 58.386 34.615 0.00 0.00 0.00 2.44
44 45 7.797121 AGATACATCCCCTTTTGTTCATTTT 57.203 32.000 0.00 0.00 0.00 1.82
45 46 8.336235 TCTAGATACATCCCCTTTTGTTCATTT 58.664 33.333 0.00 0.00 0.00 2.32
46 47 7.775561 GTCTAGATACATCCCCTTTTGTTCATT 59.224 37.037 0.00 0.00 0.00 2.57
47 48 7.283329 GTCTAGATACATCCCCTTTTGTTCAT 58.717 38.462 0.00 0.00 0.00 2.57
48 49 6.629515 CGTCTAGATACATCCCCTTTTGTTCA 60.630 42.308 0.00 0.00 0.00 3.18
49 50 5.753921 CGTCTAGATACATCCCCTTTTGTTC 59.246 44.000 0.00 0.00 0.00 3.18
50 51 5.189145 ACGTCTAGATACATCCCCTTTTGTT 59.811 40.000 0.00 0.00 0.00 2.83
51 52 4.715297 ACGTCTAGATACATCCCCTTTTGT 59.285 41.667 0.00 0.00 0.00 2.83
52 53 5.277857 ACGTCTAGATACATCCCCTTTTG 57.722 43.478 0.00 0.00 0.00 2.44
53 54 8.896722 ATATACGTCTAGATACATCCCCTTTT 57.103 34.615 0.00 0.00 0.00 2.27
54 55 8.896722 AATATACGTCTAGATACATCCCCTTT 57.103 34.615 0.00 0.00 0.00 3.11
55 56 9.629878 CTAATATACGTCTAGATACATCCCCTT 57.370 37.037 0.00 0.00 0.00 3.95
56 57 8.780003 ACTAATATACGTCTAGATACATCCCCT 58.220 37.037 0.00 0.00 0.00 4.79
57 58 8.977267 ACTAATATACGTCTAGATACATCCCC 57.023 38.462 0.00 0.00 0.00 4.81
102 103 9.357652 CCGAAAATACTTGTCATCAAAATGAAT 57.642 29.630 0.00 0.00 43.42 2.57
103 104 8.572185 TCCGAAAATACTTGTCATCAAAATGAA 58.428 29.630 0.00 0.00 43.42 2.57
104 105 8.020819 GTCCGAAAATACTTGTCATCAAAATGA 58.979 33.333 0.00 0.00 39.63 2.57
105 106 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
106 107 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
107 108 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
108 109 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
109 110 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
110 111 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
111 112 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
112 113 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
113 114 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
114 115 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
115 116 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
116 117 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
117 118 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
118 119 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
119 120 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
120 121 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
121 122 1.479730 GTACTCCCTCCGTCCGAAAAT 59.520 52.381 0.00 0.00 0.00 1.82
122 123 0.890683 GTACTCCCTCCGTCCGAAAA 59.109 55.000 0.00 0.00 0.00 2.29
123 124 0.038744 AGTACTCCCTCCGTCCGAAA 59.961 55.000 0.00 0.00 0.00 3.46
124 125 0.038744 AAGTACTCCCTCCGTCCGAA 59.961 55.000 0.00 0.00 0.00 4.30
125 126 0.038744 AAAGTACTCCCTCCGTCCGA 59.961 55.000 0.00 0.00 0.00 4.55
126 127 0.172803 CAAAGTACTCCCTCCGTCCG 59.827 60.000 0.00 0.00 0.00 4.79
127 128 0.108281 GCAAAGTACTCCCTCCGTCC 60.108 60.000 0.00 0.00 0.00 4.79
128 129 0.606604 TGCAAAGTACTCCCTCCGTC 59.393 55.000 0.00 0.00 0.00 4.79
129 130 0.320697 GTGCAAAGTACTCCCTCCGT 59.679 55.000 0.00 0.00 0.00 4.69
130 131 0.391263 GGTGCAAAGTACTCCCTCCG 60.391 60.000 0.00 0.00 0.00 4.63
131 132 0.984995 AGGTGCAAAGTACTCCCTCC 59.015 55.000 0.00 0.00 0.00 4.30
132 133 1.623811 TGAGGTGCAAAGTACTCCCTC 59.376 52.381 8.42 8.42 39.13 4.30
133 134 1.348036 GTGAGGTGCAAAGTACTCCCT 59.652 52.381 0.00 0.00 0.00 4.20
134 135 1.071699 TGTGAGGTGCAAAGTACTCCC 59.928 52.381 0.00 0.00 0.00 4.30
135 136 2.543777 TGTGAGGTGCAAAGTACTCC 57.456 50.000 0.00 0.00 0.00 3.85
136 137 3.931578 AGATGTGAGGTGCAAAGTACTC 58.068 45.455 0.00 0.00 0.00 2.59
137 138 4.067896 CAAGATGTGAGGTGCAAAGTACT 58.932 43.478 0.00 0.00 0.00 2.73
138 139 3.815401 ACAAGATGTGAGGTGCAAAGTAC 59.185 43.478 0.00 0.00 0.00 2.73
139 140 4.085357 ACAAGATGTGAGGTGCAAAGTA 57.915 40.909 0.00 0.00 0.00 2.24
140 141 2.936202 ACAAGATGTGAGGTGCAAAGT 58.064 42.857 0.00 0.00 0.00 2.66
141 142 4.067896 ACTACAAGATGTGAGGTGCAAAG 58.932 43.478 0.00 0.00 0.00 2.77
142 143 4.085357 ACTACAAGATGTGAGGTGCAAA 57.915 40.909 0.00 0.00 0.00 3.68
143 144 3.769739 ACTACAAGATGTGAGGTGCAA 57.230 42.857 0.00 0.00 0.00 4.08
144 145 3.769739 AACTACAAGATGTGAGGTGCA 57.230 42.857 0.00 0.00 0.00 4.57
145 146 4.081642 TCCTAACTACAAGATGTGAGGTGC 60.082 45.833 0.00 0.00 0.00 5.01
146 147 5.661056 TCCTAACTACAAGATGTGAGGTG 57.339 43.478 0.00 0.00 0.00 4.00
147 148 6.497259 TCTTTCCTAACTACAAGATGTGAGGT 59.503 38.462 0.00 0.00 0.00 3.85
148 149 6.814146 GTCTTTCCTAACTACAAGATGTGAGG 59.186 42.308 0.00 0.00 0.00 3.86
149 150 7.329717 GTGTCTTTCCTAACTACAAGATGTGAG 59.670 40.741 0.00 0.00 0.00 3.51
150 151 7.152645 GTGTCTTTCCTAACTACAAGATGTGA 58.847 38.462 0.00 0.00 0.00 3.58
151 152 6.369065 GGTGTCTTTCCTAACTACAAGATGTG 59.631 42.308 0.00 0.00 0.00 3.21
152 153 6.042781 TGGTGTCTTTCCTAACTACAAGATGT 59.957 38.462 0.00 0.00 0.00 3.06
153 154 6.464222 TGGTGTCTTTCCTAACTACAAGATG 58.536 40.000 0.00 0.00 0.00 2.90
154 155 6.681729 TGGTGTCTTTCCTAACTACAAGAT 57.318 37.500 0.00 0.00 0.00 2.40
155 156 6.295688 GGATGGTGTCTTTCCTAACTACAAGA 60.296 42.308 0.00 0.00 0.00 3.02
156 157 5.875359 GGATGGTGTCTTTCCTAACTACAAG 59.125 44.000 0.00 0.00 0.00 3.16
157 158 5.308497 TGGATGGTGTCTTTCCTAACTACAA 59.692 40.000 0.00 0.00 0.00 2.41
158 159 4.841813 TGGATGGTGTCTTTCCTAACTACA 59.158 41.667 0.00 0.00 0.00 2.74
159 160 5.416271 TGGATGGTGTCTTTCCTAACTAC 57.584 43.478 0.00 0.00 0.00 2.73
160 161 5.724370 TGATGGATGGTGTCTTTCCTAACTA 59.276 40.000 0.00 0.00 0.00 2.24
161 162 4.536090 TGATGGATGGTGTCTTTCCTAACT 59.464 41.667 0.00 0.00 0.00 2.24
162 163 4.843728 TGATGGATGGTGTCTTTCCTAAC 58.156 43.478 0.00 0.00 0.00 2.34
163 164 5.715439 ATGATGGATGGTGTCTTTCCTAA 57.285 39.130 0.00 0.00 0.00 2.69
164 165 5.684704 GAATGATGGATGGTGTCTTTCCTA 58.315 41.667 0.00 0.00 0.00 2.94
165 166 4.530875 GAATGATGGATGGTGTCTTTCCT 58.469 43.478 0.00 0.00 0.00 3.36
166 167 3.313526 CGAATGATGGATGGTGTCTTTCC 59.686 47.826 0.00 0.00 0.00 3.13
167 168 4.191544 TCGAATGATGGATGGTGTCTTTC 58.808 43.478 0.00 0.00 0.00 2.62
168 169 4.220693 TCGAATGATGGATGGTGTCTTT 57.779 40.909 0.00 0.00 0.00 2.52
169 170 3.912496 TCGAATGATGGATGGTGTCTT 57.088 42.857 0.00 0.00 0.00 3.01
170 171 4.428294 AATCGAATGATGGATGGTGTCT 57.572 40.909 0.00 0.00 34.24 3.41
171 172 5.056480 TGTAATCGAATGATGGATGGTGTC 58.944 41.667 0.00 0.00 34.24 3.67
172 173 5.034852 TGTAATCGAATGATGGATGGTGT 57.965 39.130 0.00 0.00 34.24 4.16
173 174 6.038603 ACTTTGTAATCGAATGATGGATGGTG 59.961 38.462 0.00 0.00 34.24 4.17
174 175 6.122277 ACTTTGTAATCGAATGATGGATGGT 58.878 36.000 0.00 0.00 34.24 3.55
175 176 6.624352 ACTTTGTAATCGAATGATGGATGG 57.376 37.500 0.00 0.00 34.24 3.51
176 177 8.830580 AGTAACTTTGTAATCGAATGATGGATG 58.169 33.333 0.00 0.00 34.24 3.51
177 178 8.964476 AGTAACTTTGTAATCGAATGATGGAT 57.036 30.769 0.00 0.00 34.24 3.41
178 179 9.309516 GTAGTAACTTTGTAATCGAATGATGGA 57.690 33.333 0.00 0.00 34.24 3.41
179 180 9.314321 AGTAGTAACTTTGTAATCGAATGATGG 57.686 33.333 0.00 0.00 30.19 3.51
250 251 8.861086 GGACATGATCTTTATAGACTTAGTCCA 58.139 37.037 8.96 0.00 39.16 4.02
291 319 7.278868 GTGAATAATCAGAACTTGGGTCTACAG 59.721 40.741 0.00 0.00 35.88 2.74
295 323 5.014123 TGGTGAATAATCAGAACTTGGGTCT 59.986 40.000 0.00 0.00 35.88 3.85
306 334 6.446781 ACAAGCTTCATGGTGAATAATCAG 57.553 37.500 0.00 0.00 35.59 2.90
325 354 7.168637 GCATATCAAATTGTGGAAGCATACAAG 59.831 37.037 0.00 0.00 39.83 3.16
329 358 6.964807 AGCATATCAAATTGTGGAAGCATA 57.035 33.333 0.00 0.00 0.00 3.14
356 387 1.226128 GGCGCTCGAATTTGACAGC 60.226 57.895 7.64 8.45 0.00 4.40
358 389 0.726827 GATGGCGCTCGAATTTGACA 59.273 50.000 7.64 0.00 0.00 3.58
359 390 0.726827 TGATGGCGCTCGAATTTGAC 59.273 50.000 7.64 0.00 0.00 3.18
365 396 0.175531 TTCTGATGATGGCGCTCGAA 59.824 50.000 7.64 2.37 0.00 3.71
373 404 6.118170 ACAAGTGGTATTCTTCTGATGATGG 58.882 40.000 0.00 0.00 0.00 3.51
375 406 7.851228 TGTACAAGTGGTATTCTTCTGATGAT 58.149 34.615 0.00 0.00 33.76 2.45
379 410 8.362464 AGTATGTACAAGTGGTATTCTTCTGA 57.638 34.615 0.00 0.00 33.76 3.27
380 411 7.707035 GGAGTATGTACAAGTGGTATTCTTCTG 59.293 40.741 0.00 0.00 33.76 3.02
381 412 7.147707 GGGAGTATGTACAAGTGGTATTCTTCT 60.148 40.741 0.00 0.00 33.76 2.85
390 421 1.138266 CGGGGGAGTATGTACAAGTGG 59.862 57.143 0.00 0.00 0.00 4.00
393 424 3.231818 AGATCGGGGGAGTATGTACAAG 58.768 50.000 0.00 0.00 0.00 3.16
401 432 1.152819 CACGGAGATCGGGGGAGTA 60.153 63.158 0.00 0.00 44.45 2.59
408 439 2.202932 CCAAGCCACGGAGATCGG 60.203 66.667 0.00 0.00 44.45 4.18
424 455 3.423154 CCGTTGCTCCGTTGCTCC 61.423 66.667 0.00 0.00 0.00 4.70
425 456 2.775032 TACCCGTTGCTCCGTTGCTC 62.775 60.000 0.00 0.00 0.00 4.26
426 457 2.781595 CTACCCGTTGCTCCGTTGCT 62.782 60.000 0.00 0.00 0.00 3.91
427 458 2.357760 TACCCGTTGCTCCGTTGC 60.358 61.111 0.00 0.00 0.00 4.17
428 459 1.005394 ACTACCCGTTGCTCCGTTG 60.005 57.895 0.00 0.00 0.00 4.10
429 460 1.291272 GACTACCCGTTGCTCCGTT 59.709 57.895 0.00 0.00 0.00 4.44
430 461 2.643232 GGACTACCCGTTGCTCCGT 61.643 63.158 0.00 0.00 0.00 4.69
431 462 2.183555 GGACTACCCGTTGCTCCG 59.816 66.667 0.00 0.00 0.00 4.63
460 491 5.047802 GGGGATAATGGTGCACATGAATAAG 60.048 44.000 20.43 0.00 40.44 1.73
465 496 1.852309 AGGGGATAATGGTGCACATGA 59.148 47.619 20.43 4.00 40.44 3.07
474 505 9.868160 AAATAAGTCTTTTAGAGGGGATAATGG 57.132 33.333 0.00 0.00 0.00 3.16
483 514 7.148407 ACACGATGCAAATAAGTCTTTTAGAGG 60.148 37.037 0.00 0.00 0.00 3.69
487 518 8.995220 AGTTACACGATGCAAATAAGTCTTTTA 58.005 29.630 0.00 0.00 0.00 1.52
501 532 2.076863 AGGCTTCAAGTTACACGATGC 58.923 47.619 0.00 4.23 0.00 3.91
505 536 4.545823 TTTCAAGGCTTCAAGTTACACG 57.454 40.909 0.00 0.00 0.00 4.49
506 537 5.891451 ACTTTTCAAGGCTTCAAGTTACAC 58.109 37.500 0.00 0.00 0.00 2.90
507 538 6.524101 AACTTTTCAAGGCTTCAAGTTACA 57.476 33.333 19.75 0.00 36.21 2.41
519 550 1.467374 CGGCGCCATAACTTTTCAAGG 60.467 52.381 28.98 0.00 0.00 3.61
544 575 2.057137 ACAAGGCTTTTCTGACAGCA 57.943 45.000 0.00 0.00 37.81 4.41
554 585 1.071699 TCGGTGAGCTTACAAGGCTTT 59.928 47.619 11.15 0.00 40.40 3.51
595 628 4.502105 TCTTCATTATTGTGGCTGCCTA 57.498 40.909 21.03 6.16 0.00 3.93
991 1028 0.485099 AGAGGAGCCATCGGGTAGAT 59.515 55.000 0.00 0.00 41.01 1.98
1251 1288 4.100963 TGGTCAGAAGCTGAAGAACTTACA 59.899 41.667 0.00 0.00 42.46 2.41
1293 1330 4.022676 GCAGGGGAAAGACGATTGTTTTTA 60.023 41.667 1.70 0.00 33.01 1.52
1294 1331 3.243737 GCAGGGGAAAGACGATTGTTTTT 60.244 43.478 1.29 1.29 35.32 1.94
1319 1356 3.134458 GGAGGAATTGTTATCAGCTCCG 58.866 50.000 0.00 0.00 33.84 4.63
1371 1416 6.360370 TTGTAGTAGGCTTTCTTGATCTGT 57.640 37.500 0.00 0.00 0.00 3.41
1386 1431 3.623060 ACGCCTTCATGCAATTGTAGTAG 59.377 43.478 7.40 1.83 0.00 2.57
1555 1600 4.701651 TCCCTTGCTCATGTTAACTTCATG 59.298 41.667 7.22 2.81 42.53 3.07
1714 1762 8.489676 AGCCATCAGTAGTAGTAGTAGTAGTA 57.510 38.462 0.31 0.00 0.00 1.82
1715 1763 7.377696 AGCCATCAGTAGTAGTAGTAGTAGT 57.622 40.000 0.00 0.00 0.00 2.73
1718 1766 9.723601 GTTATAGCCATCAGTAGTAGTAGTAGT 57.276 37.037 0.00 0.00 0.00 2.73
1719 1767 9.165035 GGTTATAGCCATCAGTAGTAGTAGTAG 57.835 40.741 0.00 0.00 0.00 2.57
1763 1811 9.620259 AAATCAGAACCCAGTTTAGATAATCTC 57.380 33.333 0.00 0.00 0.00 2.75
1837 1885 4.515191 TCAATCTCGAAAACCTTGGAACAG 59.485 41.667 0.00 0.00 42.39 3.16
1963 2011 4.397103 TGTTACGGTAGTGGACAGATACAG 59.603 45.833 0.00 0.00 0.00 2.74
1994 2042 0.670162 AATGGCAGCATACGCATTCC 59.330 50.000 0.00 0.00 42.27 3.01
2000 2048 2.948093 GCACAAATGGCAGCATACG 58.052 52.632 0.00 0.00 0.00 3.06
2035 2083 4.033709 TCACAAACTCCCCATTGGAAAAA 58.966 39.130 3.62 0.00 44.57 1.94
2043 2091 6.672657 ACTATTACTAGTCACAAACTCCCCAT 59.327 38.462 0.00 0.00 39.55 4.00
2445 2500 0.032540 CCATCCATCATCACGCGAGA 59.967 55.000 15.93 12.19 0.00 4.04
2539 2615 4.156008 GGTTTAAAGTGCATAGGGTCTGTG 59.844 45.833 0.00 0.00 0.00 3.66
2546 2623 5.705441 TGAACAGAGGTTTAAAGTGCATAGG 59.295 40.000 0.00 0.00 37.36 2.57
2554 2631 8.095169 ACCTACTACATGAACAGAGGTTTAAAG 58.905 37.037 0.00 0.00 37.36 1.85
2563 2640 7.062749 ACAAAAGACCTACTACATGAACAGA 57.937 36.000 0.00 0.00 0.00 3.41
2565 2642 7.386848 GCTAACAAAAGACCTACTACATGAACA 59.613 37.037 0.00 0.00 0.00 3.18
2740 2818 9.408648 TCAGAAGTTTATGATCCTAATTTTCCC 57.591 33.333 0.00 0.00 0.00 3.97
2783 2861 1.866171 CTCACGACAAGACACACGCG 61.866 60.000 3.53 3.53 0.00 6.01
2786 2864 2.226269 GGCTCACGACAAGACACAC 58.774 57.895 0.00 0.00 0.00 3.82
2798 2876 1.146358 GACATTACGGAGCGGCTCAC 61.146 60.000 29.33 18.00 31.08 3.51
2805 2883 2.010145 TCTGCAAGACATTACGGAGC 57.990 50.000 0.00 0.00 38.67 4.70
2937 3015 3.947196 TGATCCGAGGAATTGACAATTGG 59.053 43.478 18.00 12.41 0.00 3.16
2940 3018 7.469181 GCTTAAATGATCCGAGGAATTGACAAT 60.469 37.037 0.00 0.00 0.00 2.71
2951 3029 3.448686 ACGTGAGCTTAAATGATCCGAG 58.551 45.455 0.00 0.00 0.00 4.63
2963 3041 0.685097 TAGGCAAAGGACGTGAGCTT 59.315 50.000 0.00 0.00 0.00 3.74
2964 3042 0.905357 ATAGGCAAAGGACGTGAGCT 59.095 50.000 0.00 0.00 0.00 4.09
2966 3044 2.093973 ACAGATAGGCAAAGGACGTGAG 60.094 50.000 0.00 0.00 0.00 3.51
2969 3047 2.038557 ACAACAGATAGGCAAAGGACGT 59.961 45.455 0.00 0.00 0.00 4.34
2971 3049 4.327680 AGAACAACAGATAGGCAAAGGAC 58.672 43.478 0.00 0.00 0.00 3.85
2987 3065 5.738619 TGTCAGCAGGAGTATTAGAACAA 57.261 39.130 0.00 0.00 0.00 2.83
3014 3092 3.808728 TCCTTTGTGTCCTCTTCTGTTG 58.191 45.455 0.00 0.00 0.00 3.33
3173 3251 4.794169 ACGCTTCATAAAACCACACATTC 58.206 39.130 0.00 0.00 0.00 2.67
3262 3340 1.992170 ACTGCTAACACGTCGAATCC 58.008 50.000 0.00 0.00 0.00 3.01
3298 3377 5.036737 CAGATCGGCATCAACCAATTTTAC 58.963 41.667 0.00 0.00 0.00 2.01
3301 3380 3.091545 ACAGATCGGCATCAACCAATTT 58.908 40.909 0.00 0.00 0.00 1.82
3303 3382 2.425143 ACAGATCGGCATCAACCAAT 57.575 45.000 0.00 0.00 0.00 3.16
3308 3387 3.876914 GGTGATTTACAGATCGGCATCAA 59.123 43.478 5.06 0.00 0.00 2.57
3342 3421 8.458573 TGTACACTTGTTTTACATCTGGAATT 57.541 30.769 0.00 0.00 0.00 2.17
3421 3500 4.293415 CACAATTCCACTTGCAGTTTCTC 58.707 43.478 0.00 0.00 0.00 2.87
3429 3508 5.002464 AGAATATGCACAATTCCACTTGC 57.998 39.130 16.30 0.00 34.50 4.01
3457 3536 0.448990 GCTGCACATTTCGATCTGCA 59.551 50.000 5.13 5.13 37.30 4.41
3464 3566 0.725686 CCTCTGAGCTGCACATTTCG 59.274 55.000 1.02 0.00 0.00 3.46
3471 3573 2.954792 TGATATCTCCTCTGAGCTGCA 58.045 47.619 1.02 0.00 38.58 4.41
3508 3610 4.183865 TGAATAAAGACATCTCGCCTGTG 58.816 43.478 0.00 0.00 0.00 3.66
3529 3631 3.244318 TGCCTGCTCCACACATATATCTG 60.244 47.826 0.00 0.00 0.00 2.90
3530 3632 2.974794 TGCCTGCTCCACACATATATCT 59.025 45.455 0.00 0.00 0.00 1.98
3531 3633 3.407424 TGCCTGCTCCACACATATATC 57.593 47.619 0.00 0.00 0.00 1.63
3532 3634 3.862877 TTGCCTGCTCCACACATATAT 57.137 42.857 0.00 0.00 0.00 0.86
3533 3635 3.479489 CATTGCCTGCTCCACACATATA 58.521 45.455 0.00 0.00 0.00 0.86
3534 3636 2.304092 CATTGCCTGCTCCACACATAT 58.696 47.619 0.00 0.00 0.00 1.78
3535 3637 1.682702 CCATTGCCTGCTCCACACATA 60.683 52.381 0.00 0.00 0.00 2.29
3536 3638 0.968901 CCATTGCCTGCTCCACACAT 60.969 55.000 0.00 0.00 0.00 3.21
3537 3639 1.604308 CCATTGCCTGCTCCACACA 60.604 57.895 0.00 0.00 0.00 3.72
3538 3640 2.345760 CCCATTGCCTGCTCCACAC 61.346 63.158 0.00 0.00 0.00 3.82
3540 3642 0.899717 TTTCCCATTGCCTGCTCCAC 60.900 55.000 0.00 0.00 0.00 4.02
3541 3643 0.178938 TTTTCCCATTGCCTGCTCCA 60.179 50.000 0.00 0.00 0.00 3.86
3542 3644 1.137675 GATTTTCCCATTGCCTGCTCC 59.862 52.381 0.00 0.00 0.00 4.70
3543 3645 1.202336 CGATTTTCCCATTGCCTGCTC 60.202 52.381 0.00 0.00 0.00 4.26
3544 3646 0.819582 CGATTTTCCCATTGCCTGCT 59.180 50.000 0.00 0.00 0.00 4.24
3547 3649 2.291282 TGGTACGATTTTCCCATTGCCT 60.291 45.455 0.00 0.00 0.00 4.75
3548 3650 2.096248 TGGTACGATTTTCCCATTGCC 58.904 47.619 0.00 0.00 0.00 4.52
3549 3651 3.859411 TTGGTACGATTTTCCCATTGC 57.141 42.857 0.00 0.00 0.00 3.56
3553 3660 3.574396 TGCAATTTGGTACGATTTTCCCA 59.426 39.130 0.00 0.00 0.00 4.37
3559 3666 7.151308 TCAAAATCTTGCAATTTGGTACGATT 58.849 30.769 18.96 10.90 35.34 3.34
3589 3696 0.107459 GTCAGATGAAGGCCCTCCAC 60.107 60.000 0.00 0.00 33.74 4.02
3756 3863 4.570874 GATCCGGGAAGCAGGGCC 62.571 72.222 0.00 0.00 0.00 5.80
4007 4114 2.104253 CCCCAAAATCCCGTCGTCG 61.104 63.158 0.00 0.00 0.00 5.12


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

AutoCloner maintained by Alex Coulton.