Multiple sequence alignment - TraesCS2D01G422700

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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 TraesCS2D01G422700 chr2D 100.000 2495 0 0 1 2495 535753250 535750756 0.000000e+00 4608.0
1 TraesCS2D01G422700 chr2D 84.825 257 37 2 1215 1470 536087376 536087121 8.850000e-65 257.0
2 TraesCS2D01G422700 chr2A 90.336 1728 84 31 232 1916 678832500 678830813 0.000000e+00 2189.0
3 TraesCS2D01G422700 chr2A 89.322 590 38 9 1906 2488 678830629 678830058 0.000000e+00 717.0
4 TraesCS2D01G422700 chr2A 80.645 248 46 2 1224 1470 678898778 678898532 9.110000e-45 191.0
5 TraesCS2D01G422700 chr2B 90.841 1594 89 22 232 1785 637446025 637444449 0.000000e+00 2082.0
6 TraesCS2D01G422700 chr2B 91.457 714 31 9 1786 2489 637444419 637443726 0.000000e+00 953.0
7 TraesCS2D01G422700 chr2B 95.631 206 8 1 2286 2490 637441483 637441278 1.850000e-86 329.0
8 TraesCS2D01G422700 chr2B 80.443 271 51 2 1220 1489 637464623 637464354 3.250000e-49 206.0
9 TraesCS2D01G422700 chr1D 96.364 55 2 0 1337 1391 288906173 288906227 9.500000e-15 91.6


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 TraesCS2D01G422700 chr2D 535750756 535753250 2494 True 4608.000000 4608 100.000 1 2495 1 chr2D.!!$R1 2494
1 TraesCS2D01G422700 chr2A 678830058 678832500 2442 True 1453.000000 2189 89.829 232 2488 2 chr2A.!!$R2 2256
2 TraesCS2D01G422700 chr2B 637441278 637446025 4747 True 1121.333333 2082 92.643 232 2490 3 chr2B.!!$R2 2258

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
159 160 0.035056 GGAGGTGATGTGTCAAGGGG 60.035 60.0 0.0 0.0 35.8 4.79 F
163 164 0.036732 GTGATGTGTCAAGGGGCAGA 59.963 55.0 0.0 0.0 35.8 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1400 1418 0.927537 CACGAGTTTGACGTTCAGCA 59.072 50.0 0.00 0.0 42.07 4.41 R
1936 2217 1.704641 TGACCATATGGAGTCGAGGG 58.295 55.0 28.77 0.0 38.94 4.30 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
21 22 4.708576 TGGGTGATGTAAGTTGTACCAA 57.291 40.909 0.00 0.00 0.00 3.67
22 23 4.647611 TGGGTGATGTAAGTTGTACCAAG 58.352 43.478 0.00 0.00 0.00 3.61
23 24 4.348461 TGGGTGATGTAAGTTGTACCAAGA 59.652 41.667 0.00 0.00 0.00 3.02
24 25 4.694037 GGGTGATGTAAGTTGTACCAAGAC 59.306 45.833 0.00 0.00 0.00 3.01
25 26 5.302360 GGTGATGTAAGTTGTACCAAGACA 58.698 41.667 0.00 0.00 0.00 3.41
26 27 5.761234 GGTGATGTAAGTTGTACCAAGACAA 59.239 40.000 0.00 0.00 36.98 3.18
41 42 9.477484 GTACCAAGACAACAAGTATATATGAGG 57.523 37.037 0.00 0.00 0.00 3.86
42 43 7.509546 ACCAAGACAACAAGTATATATGAGGG 58.490 38.462 0.00 0.00 0.00 4.30
43 44 6.936900 CCAAGACAACAAGTATATATGAGGGG 59.063 42.308 0.00 0.00 0.00 4.79
44 45 6.115448 AGACAACAAGTATATATGAGGGGC 57.885 41.667 0.00 0.00 0.00 5.80
45 46 5.606749 AGACAACAAGTATATATGAGGGGCA 59.393 40.000 0.00 0.00 0.00 5.36
46 47 6.273260 AGACAACAAGTATATATGAGGGGCAT 59.727 38.462 0.00 0.00 41.08 4.40
47 48 6.852404 ACAACAAGTATATATGAGGGGCATT 58.148 36.000 0.00 0.00 38.44 3.56
48 49 6.716628 ACAACAAGTATATATGAGGGGCATTG 59.283 38.462 0.00 0.00 38.44 2.82
49 50 6.702449 ACAAGTATATATGAGGGGCATTGA 57.298 37.500 0.00 0.00 38.44 2.57
50 51 7.276088 ACAAGTATATATGAGGGGCATTGAT 57.724 36.000 0.00 0.00 38.44 2.57
51 52 7.114754 ACAAGTATATATGAGGGGCATTGATG 58.885 38.462 0.00 0.00 38.44 3.07
52 53 6.257994 AGTATATATGAGGGGCATTGATGG 57.742 41.667 0.00 0.00 38.44 3.51
53 54 2.913603 ATATGAGGGGCATTGATGGG 57.086 50.000 0.00 0.00 38.44 4.00
54 55 1.831835 TATGAGGGGCATTGATGGGA 58.168 50.000 0.00 0.00 38.44 4.37
55 56 0.935942 ATGAGGGGCATTGATGGGAA 59.064 50.000 0.00 0.00 31.73 3.97
56 57 0.259647 TGAGGGGCATTGATGGGAAG 59.740 55.000 0.00 0.00 0.00 3.46
57 58 1.075748 AGGGGCATTGATGGGAAGC 60.076 57.895 0.00 0.00 0.00 3.86
58 59 1.381599 GGGGCATTGATGGGAAGCA 60.382 57.895 0.00 0.00 0.00 3.91
59 60 0.761702 GGGGCATTGATGGGAAGCAT 60.762 55.000 0.00 0.00 0.00 3.79
60 61 1.481055 GGGGCATTGATGGGAAGCATA 60.481 52.381 0.00 0.00 0.00 3.14
61 62 2.532843 GGGCATTGATGGGAAGCATAT 58.467 47.619 0.00 0.00 0.00 1.78
62 63 2.901839 GGGCATTGATGGGAAGCATATT 59.098 45.455 0.00 0.00 0.00 1.28
63 64 3.306502 GGGCATTGATGGGAAGCATATTG 60.307 47.826 0.00 0.00 0.00 1.90
64 65 3.575256 GGCATTGATGGGAAGCATATTGA 59.425 43.478 0.00 0.00 0.00 2.57
65 66 4.039488 GGCATTGATGGGAAGCATATTGAA 59.961 41.667 0.00 0.00 0.00 2.69
66 67 4.986659 GCATTGATGGGAAGCATATTGAAC 59.013 41.667 0.00 0.00 0.00 3.18
67 68 5.452216 GCATTGATGGGAAGCATATTGAACA 60.452 40.000 0.00 0.00 0.00 3.18
68 69 6.575267 CATTGATGGGAAGCATATTGAACAA 58.425 36.000 0.00 0.00 0.00 2.83
69 70 6.602410 TTGATGGGAAGCATATTGAACAAA 57.398 33.333 0.00 0.00 0.00 2.83
70 71 6.602410 TGATGGGAAGCATATTGAACAAAA 57.398 33.333 0.00 0.00 0.00 2.44
71 72 7.185318 TGATGGGAAGCATATTGAACAAAAT 57.815 32.000 0.00 0.00 0.00 1.82
72 73 7.622713 TGATGGGAAGCATATTGAACAAAATT 58.377 30.769 0.00 0.00 0.00 1.82
73 74 8.102047 TGATGGGAAGCATATTGAACAAAATTT 58.898 29.630 0.00 0.00 0.00 1.82
74 75 9.598517 GATGGGAAGCATATTGAACAAAATTTA 57.401 29.630 0.00 0.00 0.00 1.40
76 77 9.381033 TGGGAAGCATATTGAACAAAATTTATG 57.619 29.630 0.00 0.00 0.00 1.90
77 78 9.382275 GGGAAGCATATTGAACAAAATTTATGT 57.618 29.630 0.00 0.00 0.00 2.29
81 82 9.723601 AGCATATTGAACAAAATTTATGTTGGT 57.276 25.926 17.63 1.46 40.90 3.67
87 88 8.749841 TGAACAAAATTTATGTTGGTATTCCG 57.250 30.769 17.63 0.00 40.90 4.30
88 89 8.361139 TGAACAAAATTTATGTTGGTATTCCGT 58.639 29.630 17.63 0.00 40.90 4.69
89 90 8.751302 AACAAAATTTATGTTGGTATTCCGTC 57.249 30.769 14.08 0.00 39.43 4.79
90 91 7.317390 ACAAAATTTATGTTGGTATTCCGTCC 58.683 34.615 0.00 0.00 36.30 4.79
91 92 6.459670 AAATTTATGTTGGTATTCCGTCCC 57.540 37.500 0.00 0.00 36.30 4.46
92 93 4.847990 TTTATGTTGGTATTCCGTCCCT 57.152 40.909 0.00 0.00 36.30 4.20
93 94 2.710096 ATGTTGGTATTCCGTCCCTG 57.290 50.000 0.00 0.00 36.30 4.45
94 95 1.354101 TGTTGGTATTCCGTCCCTGT 58.646 50.000 0.00 0.00 36.30 4.00
95 96 1.700739 TGTTGGTATTCCGTCCCTGTT 59.299 47.619 0.00 0.00 36.30 3.16
96 97 2.905085 TGTTGGTATTCCGTCCCTGTTA 59.095 45.455 0.00 0.00 36.30 2.41
97 98 3.520317 TGTTGGTATTCCGTCCCTGTTAT 59.480 43.478 0.00 0.00 36.30 1.89
98 99 4.019141 TGTTGGTATTCCGTCCCTGTTATT 60.019 41.667 0.00 0.00 36.30 1.40
99 100 4.145365 TGGTATTCCGTCCCTGTTATTG 57.855 45.455 0.00 0.00 36.30 1.90
100 101 3.775866 TGGTATTCCGTCCCTGTTATTGA 59.224 43.478 0.00 0.00 36.30 2.57
101 102 4.225492 TGGTATTCCGTCCCTGTTATTGAA 59.775 41.667 0.00 0.00 36.30 2.69
102 103 5.104277 TGGTATTCCGTCCCTGTTATTGAAT 60.104 40.000 0.00 0.00 36.30 2.57
103 104 5.238650 GGTATTCCGTCCCTGTTATTGAATG 59.761 44.000 0.00 0.00 0.00 2.67
104 105 3.992943 TCCGTCCCTGTTATTGAATGT 57.007 42.857 0.00 0.00 0.00 2.71
105 106 4.295141 TCCGTCCCTGTTATTGAATGTT 57.705 40.909 0.00 0.00 0.00 2.71
106 107 4.658063 TCCGTCCCTGTTATTGAATGTTT 58.342 39.130 0.00 0.00 0.00 2.83
107 108 5.074115 TCCGTCCCTGTTATTGAATGTTTT 58.926 37.500 0.00 0.00 0.00 2.43
108 109 5.048364 TCCGTCCCTGTTATTGAATGTTTTG 60.048 40.000 0.00 0.00 0.00 2.44
109 110 5.160641 CGTCCCTGTTATTGAATGTTTTGG 58.839 41.667 0.00 0.00 0.00 3.28
110 111 4.929211 GTCCCTGTTATTGAATGTTTTGGC 59.071 41.667 0.00 0.00 0.00 4.52
111 112 4.837860 TCCCTGTTATTGAATGTTTTGGCT 59.162 37.500 0.00 0.00 0.00 4.75
112 113 5.047377 TCCCTGTTATTGAATGTTTTGGCTC 60.047 40.000 0.00 0.00 0.00 4.70
113 114 5.170748 CCTGTTATTGAATGTTTTGGCTCC 58.829 41.667 0.00 0.00 0.00 4.70
114 115 5.047092 CCTGTTATTGAATGTTTTGGCTCCT 60.047 40.000 0.00 0.00 0.00 3.69
115 116 6.024552 TGTTATTGAATGTTTTGGCTCCTC 57.975 37.500 0.00 0.00 0.00 3.71
116 117 3.855689 ATTGAATGTTTTGGCTCCTCG 57.144 42.857 0.00 0.00 0.00 4.63
117 118 2.559698 TGAATGTTTTGGCTCCTCGA 57.440 45.000 0.00 0.00 0.00 4.04
118 119 3.071874 TGAATGTTTTGGCTCCTCGAT 57.928 42.857 0.00 0.00 0.00 3.59
119 120 3.420893 TGAATGTTTTGGCTCCTCGATT 58.579 40.909 0.00 0.00 0.00 3.34
120 121 3.440173 TGAATGTTTTGGCTCCTCGATTC 59.560 43.478 0.00 0.00 0.00 2.52
121 122 2.559698 TGTTTTGGCTCCTCGATTCA 57.440 45.000 0.00 0.00 0.00 2.57
122 123 2.151202 TGTTTTGGCTCCTCGATTCAC 58.849 47.619 0.00 0.00 0.00 3.18
123 124 1.468914 GTTTTGGCTCCTCGATTCACC 59.531 52.381 0.00 0.00 0.00 4.02
124 125 0.690192 TTTGGCTCCTCGATTCACCA 59.310 50.000 0.00 0.00 0.00 4.17
125 126 0.690192 TTGGCTCCTCGATTCACCAA 59.310 50.000 6.13 6.13 34.91 3.67
126 127 0.250234 TGGCTCCTCGATTCACCAAG 59.750 55.000 0.00 0.00 0.00 3.61
127 128 0.537188 GGCTCCTCGATTCACCAAGA 59.463 55.000 0.00 0.00 0.00 3.02
128 129 1.139853 GGCTCCTCGATTCACCAAGAT 59.860 52.381 0.00 0.00 0.00 2.40
129 130 2.208431 GCTCCTCGATTCACCAAGATG 58.792 52.381 0.00 0.00 0.00 2.90
130 131 2.159043 GCTCCTCGATTCACCAAGATGA 60.159 50.000 0.00 0.00 0.00 2.92
131 132 3.715495 CTCCTCGATTCACCAAGATGAG 58.285 50.000 0.00 0.00 0.00 2.90
132 133 3.365472 TCCTCGATTCACCAAGATGAGA 58.635 45.455 0.00 0.00 0.00 3.27
133 134 3.963374 TCCTCGATTCACCAAGATGAGAT 59.037 43.478 0.00 0.00 0.00 2.75
134 135 4.056740 CCTCGATTCACCAAGATGAGATG 58.943 47.826 0.00 0.00 0.00 2.90
135 136 4.202192 CCTCGATTCACCAAGATGAGATGA 60.202 45.833 0.00 0.00 0.00 2.92
136 137 5.343307 TCGATTCACCAAGATGAGATGAA 57.657 39.130 0.00 0.00 34.03 2.57
137 138 5.733676 TCGATTCACCAAGATGAGATGAAA 58.266 37.500 0.00 0.00 33.29 2.69
138 139 6.351711 TCGATTCACCAAGATGAGATGAAAT 58.648 36.000 0.00 0.00 33.29 2.17
139 140 6.481313 TCGATTCACCAAGATGAGATGAAATC 59.519 38.462 0.00 0.00 46.04 2.17
152 153 3.535561 GATGAAATCGGAGGTGATGTGT 58.464 45.455 0.00 0.00 31.13 3.72
153 154 2.972625 TGAAATCGGAGGTGATGTGTC 58.027 47.619 0.00 0.00 0.00 3.67
154 155 2.301583 TGAAATCGGAGGTGATGTGTCA 59.698 45.455 0.00 0.00 0.00 3.58
155 156 3.244387 TGAAATCGGAGGTGATGTGTCAA 60.244 43.478 0.00 0.00 35.80 3.18
156 157 2.680312 ATCGGAGGTGATGTGTCAAG 57.320 50.000 0.00 0.00 35.80 3.02
157 158 0.608130 TCGGAGGTGATGTGTCAAGG 59.392 55.000 0.00 0.00 35.80 3.61
158 159 0.391661 CGGAGGTGATGTGTCAAGGG 60.392 60.000 0.00 0.00 35.80 3.95
159 160 0.035056 GGAGGTGATGTGTCAAGGGG 60.035 60.000 0.00 0.00 35.80 4.79
160 161 0.678048 GAGGTGATGTGTCAAGGGGC 60.678 60.000 0.00 0.00 35.80 5.80
161 162 1.074775 GGTGATGTGTCAAGGGGCA 59.925 57.895 0.00 0.00 35.80 5.36
162 163 0.962356 GGTGATGTGTCAAGGGGCAG 60.962 60.000 0.00 0.00 35.80 4.85
163 164 0.036732 GTGATGTGTCAAGGGGCAGA 59.963 55.000 0.00 0.00 35.80 4.26
164 165 0.770499 TGATGTGTCAAGGGGCAGAA 59.230 50.000 0.00 0.00 0.00 3.02
165 166 1.144708 TGATGTGTCAAGGGGCAGAAA 59.855 47.619 0.00 0.00 0.00 2.52
166 167 2.238521 GATGTGTCAAGGGGCAGAAAA 58.761 47.619 0.00 0.00 0.00 2.29
167 168 2.380064 TGTGTCAAGGGGCAGAAAAT 57.620 45.000 0.00 0.00 0.00 1.82
168 169 2.676748 TGTGTCAAGGGGCAGAAAATT 58.323 42.857 0.00 0.00 0.00 1.82
169 170 2.364970 TGTGTCAAGGGGCAGAAAATTG 59.635 45.455 0.00 0.00 0.00 2.32
170 171 2.627699 GTGTCAAGGGGCAGAAAATTGA 59.372 45.455 0.00 0.00 0.00 2.57
171 172 3.069443 GTGTCAAGGGGCAGAAAATTGAA 59.931 43.478 0.00 0.00 32.13 2.69
172 173 3.321682 TGTCAAGGGGCAGAAAATTGAAG 59.678 43.478 0.00 0.00 32.13 3.02
173 174 3.321968 GTCAAGGGGCAGAAAATTGAAGT 59.678 43.478 0.00 0.00 32.13 3.01
174 175 3.321682 TCAAGGGGCAGAAAATTGAAGTG 59.678 43.478 0.00 0.00 0.00 3.16
175 176 1.620323 AGGGGCAGAAAATTGAAGTGC 59.380 47.619 0.00 0.00 0.00 4.40
176 177 1.669795 GGGGCAGAAAATTGAAGTGCG 60.670 52.381 0.00 0.00 34.86 5.34
177 178 1.669795 GGGCAGAAAATTGAAGTGCGG 60.670 52.381 0.00 0.00 34.86 5.69
178 179 1.000274 GGCAGAAAATTGAAGTGCGGT 60.000 47.619 0.00 0.00 34.86 5.68
179 180 2.227865 GGCAGAAAATTGAAGTGCGGTA 59.772 45.455 0.00 0.00 34.86 4.02
180 181 3.305064 GGCAGAAAATTGAAGTGCGGTAA 60.305 43.478 0.00 0.00 34.86 2.85
181 182 3.668656 GCAGAAAATTGAAGTGCGGTAAC 59.331 43.478 0.00 0.00 0.00 2.50
196 197 3.788434 GGTAACGATGTCAAGTGTGTG 57.212 47.619 0.00 0.00 0.00 3.82
197 198 3.386486 GGTAACGATGTCAAGTGTGTGA 58.614 45.455 0.00 0.00 0.00 3.58
198 199 3.183775 GGTAACGATGTCAAGTGTGTGAC 59.816 47.826 0.00 0.00 46.74 3.67
208 209 4.729086 GTCAAGTGTGTGACGAGATATACG 59.271 45.833 0.00 0.00 38.68 3.06
209 210 3.965292 AGTGTGTGACGAGATATACGG 57.035 47.619 0.00 0.00 34.93 4.02
210 211 2.617308 AGTGTGTGACGAGATATACGGG 59.383 50.000 0.00 0.00 34.93 5.28
211 212 1.951602 TGTGTGACGAGATATACGGGG 59.048 52.381 0.00 0.00 34.93 5.73
212 213 2.224606 GTGTGACGAGATATACGGGGA 58.775 52.381 0.00 0.00 34.93 4.81
213 214 2.031333 GTGTGACGAGATATACGGGGAC 60.031 54.545 0.00 1.89 34.93 4.46
236 237 0.657840 AAAGCGAGTGTGAGTGCAAC 59.342 50.000 0.00 0.00 0.00 4.17
262 263 1.298157 CGCCGAAATCTGAGTTGCCA 61.298 55.000 0.00 0.00 0.00 4.92
269 270 4.083110 CGAAATCTGAGTTGCCACTTCATT 60.083 41.667 0.00 0.00 31.22 2.57
289 293 1.559219 TGATGGATGTCATGGTCCGTT 59.441 47.619 8.27 0.49 37.32 4.44
293 297 1.086696 GATGTCATGGTCCGTTGTGG 58.913 55.000 0.00 0.00 40.09 4.17
294 298 0.960364 ATGTCATGGTCCGTTGTGGC 60.960 55.000 0.00 0.00 37.80 5.01
295 299 2.358125 TCATGGTCCGTTGTGGCG 60.358 61.111 0.00 0.00 37.80 5.69
300 304 2.162754 GGTCCGTTGTGGCGTATCG 61.163 63.158 0.00 0.00 37.80 2.92
336 340 2.335752 GTGCATGCCTAGAGATGATCG 58.664 52.381 16.68 0.00 0.00 3.69
340 344 0.676184 TGCCTAGAGATGATCGGCAC 59.324 55.000 7.54 0.00 45.08 5.01
497 502 9.897744 GTGATCATGTTTTTCTCAGATTAAACA 57.102 29.630 14.58 14.58 42.57 2.83
609 615 2.578679 CGTGCGACGGTTGAAACGA 61.579 57.895 10.61 0.00 38.08 3.85
868 881 2.227968 GACACACGCCATCAGTTCGC 62.228 60.000 0.00 0.00 0.00 4.70
912 925 1.594833 CCTATATAAGCGCGCCCCA 59.405 57.895 30.33 13.99 0.00 4.96
981 999 2.920490 GCTAGAGCACTTCAAACTCGAG 59.080 50.000 11.84 11.84 41.59 4.04
983 1001 1.689273 AGAGCACTTCAAACTCGAGGT 59.311 47.619 18.41 7.47 35.56 3.85
997 1015 1.395826 CGAGGTTAGCTAGCCAGGCT 61.396 60.000 26.35 20.63 43.41 4.58
1400 1418 1.077265 CCACCATCAAGGCCAAGGT 59.923 57.895 5.01 1.62 43.14 3.50
1493 1511 1.207089 CTCGTTCCAGTGCCCTTCATA 59.793 52.381 0.00 0.00 0.00 2.15
1497 1515 2.952310 GTTCCAGTGCCCTTCATAATCC 59.048 50.000 0.00 0.00 0.00 3.01
1498 1516 2.204463 TCCAGTGCCCTTCATAATCCA 58.796 47.619 0.00 0.00 0.00 3.41
1500 1518 2.092212 CCAGTGCCCTTCATAATCCACT 60.092 50.000 0.00 0.00 34.17 4.00
1501 1519 3.209410 CAGTGCCCTTCATAATCCACTC 58.791 50.000 0.00 0.00 31.75 3.51
1503 1521 2.092429 GTGCCCTTCATAATCCACTCCA 60.092 50.000 0.00 0.00 0.00 3.86
1506 1524 3.668447 CCCTTCATAATCCACTCCATCG 58.332 50.000 0.00 0.00 0.00 3.84
1523 1541 3.191581 CCATCGATCGATTAGCACCTACT 59.808 47.826 27.45 0.31 31.62 2.57
1524 1542 4.395231 CCATCGATCGATTAGCACCTACTA 59.605 45.833 27.45 0.00 31.62 1.82
1525 1543 5.325494 CATCGATCGATTAGCACCTACTAC 58.675 45.833 27.45 0.00 31.62 2.73
1526 1544 4.383173 TCGATCGATTAGCACCTACTACA 58.617 43.478 15.15 0.00 0.00 2.74
1587 1615 0.107508 TGCATGGAGCTAGCACCTTC 60.108 55.000 28.23 18.02 45.94 3.46
1606 1634 5.282510 CCTTCTCAAGGTAAGTACGCATAG 58.717 45.833 0.00 0.00 43.95 2.23
1644 1698 8.352752 ACATGTCATGTGTAATCTGTATAACG 57.647 34.615 17.74 0.00 43.01 3.18
1722 1777 5.444983 TGCGTTGTGTAAATGTGTATCAAC 58.555 37.500 0.00 0.00 0.00 3.18
1725 1780 7.118535 TGCGTTGTGTAAATGTGTATCAACTAT 59.881 33.333 0.00 0.00 33.83 2.12
1726 1781 7.634817 GCGTTGTGTAAATGTGTATCAACTATC 59.365 37.037 0.00 0.00 33.83 2.08
1727 1782 8.652463 CGTTGTGTAAATGTGTATCAACTATCA 58.348 33.333 0.00 0.00 33.83 2.15
1730 1785 9.719355 TGTGTAAATGTGTATCAACTATCAAGT 57.281 29.630 0.00 0.00 37.65 3.16
1736 1791 9.751542 AATGTGTATCAACTATCAAGTACTAGC 57.248 33.333 0.00 0.00 33.75 3.42
1781 1836 9.764870 GCATAATTGCTTATATACATGTGACTG 57.235 33.333 9.11 0.00 45.77 3.51
1784 1839 8.737168 AATTGCTTATATACATGTGACTGTGT 57.263 30.769 9.11 0.49 0.00 3.72
1827 1912 8.629158 TGTGTAGCATTCTTTTTGACAGTTATT 58.371 29.630 0.00 0.00 0.00 1.40
1913 2194 3.151554 AGGAAAATGTTACGACCCCAAC 58.848 45.455 0.00 0.00 0.00 3.77
1924 2205 1.900545 GACCCCAACTCTTCCTCGGG 61.901 65.000 0.00 0.00 36.59 5.14
1936 2217 4.828829 TCTTCCTCGGGATAAAAAGTCAC 58.171 43.478 0.00 0.00 0.00 3.67
1992 2274 1.139853 CCCTTGATAGGCTGGTCTCAC 59.860 57.143 0.00 0.00 40.50 3.51
2014 2297 1.359848 CCAGTCAATGACGCTGGTAC 58.640 55.000 12.07 0.00 43.42 3.34
2055 2338 0.462759 CATCGGGAGCCTCTTTGGAC 60.463 60.000 0.00 0.00 38.35 4.02
2056 2339 1.627297 ATCGGGAGCCTCTTTGGACC 61.627 60.000 0.00 0.00 38.35 4.46
2079 2362 5.593183 GGAACGAAAGAACTACTCCAAAG 57.407 43.478 0.00 0.00 0.00 2.77
2080 2363 5.295152 GGAACGAAAGAACTACTCCAAAGA 58.705 41.667 0.00 0.00 0.00 2.52
2081 2364 5.405873 GGAACGAAAGAACTACTCCAAAGAG 59.594 44.000 0.00 0.00 46.36 2.85
2082 2365 4.884247 ACGAAAGAACTACTCCAAAGAGG 58.116 43.478 0.00 0.00 45.11 3.69
2083 2366 4.587684 ACGAAAGAACTACTCCAAAGAGGA 59.412 41.667 0.00 0.00 45.11 3.71
2186 2469 5.063880 CCTATGGATTGCTACTGGGTAAAC 58.936 45.833 0.00 0.00 0.00 2.01
2187 2470 4.862641 ATGGATTGCTACTGGGTAAACT 57.137 40.909 0.00 0.00 0.00 2.66
2188 2471 4.650972 TGGATTGCTACTGGGTAAACTT 57.349 40.909 0.00 0.00 0.00 2.66
2189 2472 4.585879 TGGATTGCTACTGGGTAAACTTC 58.414 43.478 0.00 0.00 0.00 3.01
2190 2473 4.288626 TGGATTGCTACTGGGTAAACTTCT 59.711 41.667 0.00 0.00 0.00 2.85
2191 2474 5.486063 TGGATTGCTACTGGGTAAACTTCTA 59.514 40.000 0.00 0.00 0.00 2.10
2237 2526 4.928601 TCGTGAATATCTTACGGTCCAAG 58.071 43.478 0.00 0.00 38.29 3.61
2254 2543 1.208293 CAAGGAGGCCCTAGACAAGAC 59.792 57.143 0.00 0.00 43.48 3.01
2457 5192 5.818136 TTCACTTGTTTCTGAAAGGTCTG 57.182 39.130 2.48 0.00 0.00 3.51
2482 5217 6.047511 AGTTGAAGTGCAGATTATCAGTCT 57.952 37.500 0.00 0.00 0.00 3.24
2483 5218 7.175347 AGTTGAAGTGCAGATTATCAGTCTA 57.825 36.000 0.00 0.00 0.00 2.59
2484 5219 7.790027 AGTTGAAGTGCAGATTATCAGTCTAT 58.210 34.615 0.00 0.00 0.00 1.98
2489 5224 9.928236 GAAGTGCAGATTATCAGTCTATTTTTC 57.072 33.333 0.00 0.00 0.00 2.29
2490 5225 9.453572 AAGTGCAGATTATCAGTCTATTTTTCA 57.546 29.630 0.00 0.00 0.00 2.69
2491 5226 9.624373 AGTGCAGATTATCAGTCTATTTTTCAT 57.376 29.630 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 9.477484 CCTCATATATACTTGTTGTCTTGGTAC 57.523 37.037 0.00 0.00 0.00 3.34
16 17 8.647796 CCCTCATATATACTTGTTGTCTTGGTA 58.352 37.037 0.00 0.00 0.00 3.25
17 18 7.420214 CCCCTCATATATACTTGTTGTCTTGGT 60.420 40.741 0.00 0.00 0.00 3.67
18 19 6.936900 CCCCTCATATATACTTGTTGTCTTGG 59.063 42.308 0.00 0.00 0.00 3.61
19 20 6.428159 GCCCCTCATATATACTTGTTGTCTTG 59.572 42.308 0.00 0.00 0.00 3.02
20 21 6.101150 TGCCCCTCATATATACTTGTTGTCTT 59.899 38.462 0.00 0.00 0.00 3.01
21 22 5.606749 TGCCCCTCATATATACTTGTTGTCT 59.393 40.000 0.00 0.00 0.00 3.41
22 23 5.865085 TGCCCCTCATATATACTTGTTGTC 58.135 41.667 0.00 0.00 0.00 3.18
23 24 5.904984 TGCCCCTCATATATACTTGTTGT 57.095 39.130 0.00 0.00 0.00 3.32
24 25 6.942005 TCAATGCCCCTCATATATACTTGTTG 59.058 38.462 0.00 0.00 34.33 3.33
25 26 7.090319 TCAATGCCCCTCATATATACTTGTT 57.910 36.000 0.00 0.00 34.33 2.83
26 27 6.702449 TCAATGCCCCTCATATATACTTGT 57.298 37.500 0.00 0.00 34.33 3.16
27 28 6.544931 CCATCAATGCCCCTCATATATACTTG 59.455 42.308 0.00 0.00 34.33 3.16
28 29 6.354213 CCCATCAATGCCCCTCATATATACTT 60.354 42.308 0.00 0.00 34.33 2.24
29 30 5.133322 CCCATCAATGCCCCTCATATATACT 59.867 44.000 0.00 0.00 34.33 2.12
30 31 5.132648 TCCCATCAATGCCCCTCATATATAC 59.867 44.000 0.00 0.00 34.33 1.47
31 32 5.296134 TCCCATCAATGCCCCTCATATATA 58.704 41.667 0.00 0.00 34.33 0.86
32 33 4.121446 TCCCATCAATGCCCCTCATATAT 58.879 43.478 0.00 0.00 34.33 0.86
33 34 3.540493 TCCCATCAATGCCCCTCATATA 58.460 45.455 0.00 0.00 34.33 0.86
34 35 2.361218 TCCCATCAATGCCCCTCATAT 58.639 47.619 0.00 0.00 34.33 1.78
35 36 1.831835 TCCCATCAATGCCCCTCATA 58.168 50.000 0.00 0.00 34.33 2.15
36 37 0.935942 TTCCCATCAATGCCCCTCAT 59.064 50.000 0.00 0.00 36.87 2.90
37 38 0.259647 CTTCCCATCAATGCCCCTCA 59.740 55.000 0.00 0.00 0.00 3.86
38 39 1.111715 GCTTCCCATCAATGCCCCTC 61.112 60.000 0.00 0.00 0.00 4.30
39 40 1.075748 GCTTCCCATCAATGCCCCT 60.076 57.895 0.00 0.00 0.00 4.79
40 41 0.761702 ATGCTTCCCATCAATGCCCC 60.762 55.000 0.00 0.00 0.00 5.80
41 42 1.999648 TATGCTTCCCATCAATGCCC 58.000 50.000 0.00 0.00 35.34 5.36
42 43 3.575256 TCAATATGCTTCCCATCAATGCC 59.425 43.478 0.00 0.00 35.34 4.40
43 44 4.859304 TCAATATGCTTCCCATCAATGC 57.141 40.909 0.00 0.00 35.34 3.56
44 45 6.151663 TGTTCAATATGCTTCCCATCAATG 57.848 37.500 0.00 0.00 35.34 2.82
45 46 6.795144 TTGTTCAATATGCTTCCCATCAAT 57.205 33.333 0.00 0.00 35.34 2.57
46 47 6.602410 TTTGTTCAATATGCTTCCCATCAA 57.398 33.333 0.00 0.00 35.34 2.57
47 48 6.602410 TTTTGTTCAATATGCTTCCCATCA 57.398 33.333 0.00 0.00 35.34 3.07
48 49 8.496707 AAATTTTGTTCAATATGCTTCCCATC 57.503 30.769 0.00 0.00 35.34 3.51
50 51 9.381033 CATAAATTTTGTTCAATATGCTTCCCA 57.619 29.630 0.00 0.00 0.00 4.37
51 52 9.382275 ACATAAATTTTGTTCAATATGCTTCCC 57.618 29.630 0.00 0.00 0.00 3.97
55 56 9.723601 ACCAACATAAATTTTGTTCAATATGCT 57.276 25.926 12.73 0.00 35.18 3.79
61 62 9.197694 CGGAATACCAACATAAATTTTGTTCAA 57.802 29.630 12.73 5.59 35.18 2.69
62 63 8.361139 ACGGAATACCAACATAAATTTTGTTCA 58.639 29.630 12.73 5.59 35.18 3.18
63 64 8.751302 ACGGAATACCAACATAAATTTTGTTC 57.249 30.769 12.73 1.91 35.18 3.18
64 65 7.815549 GGACGGAATACCAACATAAATTTTGTT 59.184 33.333 0.00 4.62 37.79 2.83
65 66 7.317390 GGACGGAATACCAACATAAATTTTGT 58.683 34.615 0.00 0.00 35.59 2.83
66 67 6.754675 GGGACGGAATACCAACATAAATTTTG 59.245 38.462 0.00 0.00 35.59 2.44
67 68 6.666113 AGGGACGGAATACCAACATAAATTTT 59.334 34.615 0.00 0.00 30.58 1.82
68 69 6.096282 CAGGGACGGAATACCAACATAAATTT 59.904 38.462 0.00 0.00 30.58 1.82
69 70 5.592688 CAGGGACGGAATACCAACATAAATT 59.407 40.000 0.00 0.00 30.58 1.82
70 71 5.130350 CAGGGACGGAATACCAACATAAAT 58.870 41.667 0.00 0.00 30.58 1.40
71 72 4.019141 ACAGGGACGGAATACCAACATAAA 60.019 41.667 0.00 0.00 30.58 1.40
72 73 3.520317 ACAGGGACGGAATACCAACATAA 59.480 43.478 0.00 0.00 30.58 1.90
73 74 3.109151 ACAGGGACGGAATACCAACATA 58.891 45.455 0.00 0.00 30.58 2.29
74 75 1.913419 ACAGGGACGGAATACCAACAT 59.087 47.619 0.00 0.00 30.58 2.71
75 76 1.354101 ACAGGGACGGAATACCAACA 58.646 50.000 0.00 0.00 30.58 3.33
76 77 2.484742 AACAGGGACGGAATACCAAC 57.515 50.000 0.00 0.00 30.58 3.77
77 78 4.225492 TCAATAACAGGGACGGAATACCAA 59.775 41.667 0.00 0.00 30.58 3.67
78 79 3.775866 TCAATAACAGGGACGGAATACCA 59.224 43.478 0.00 0.00 30.58 3.25
79 80 4.411256 TCAATAACAGGGACGGAATACC 57.589 45.455 0.00 0.00 0.00 2.73
80 81 5.820947 ACATTCAATAACAGGGACGGAATAC 59.179 40.000 0.00 0.00 0.00 1.89
81 82 5.996644 ACATTCAATAACAGGGACGGAATA 58.003 37.500 0.00 0.00 0.00 1.75
82 83 4.855340 ACATTCAATAACAGGGACGGAAT 58.145 39.130 0.00 0.00 0.00 3.01
83 84 4.295141 ACATTCAATAACAGGGACGGAA 57.705 40.909 0.00 0.00 0.00 4.30
84 85 3.992943 ACATTCAATAACAGGGACGGA 57.007 42.857 0.00 0.00 0.00 4.69
85 86 5.160641 CAAAACATTCAATAACAGGGACGG 58.839 41.667 0.00 0.00 0.00 4.79
86 87 5.160641 CCAAAACATTCAATAACAGGGACG 58.839 41.667 0.00 0.00 0.00 4.79
87 88 4.929211 GCCAAAACATTCAATAACAGGGAC 59.071 41.667 0.00 0.00 0.00 4.46
88 89 4.837860 AGCCAAAACATTCAATAACAGGGA 59.162 37.500 0.00 0.00 0.00 4.20
89 90 5.151297 AGCCAAAACATTCAATAACAGGG 57.849 39.130 0.00 0.00 0.00 4.45
90 91 5.047092 AGGAGCCAAAACATTCAATAACAGG 60.047 40.000 0.00 0.00 0.00 4.00
91 92 6.029346 AGGAGCCAAAACATTCAATAACAG 57.971 37.500 0.00 0.00 0.00 3.16
92 93 5.335583 CGAGGAGCCAAAACATTCAATAACA 60.336 40.000 0.00 0.00 0.00 2.41
93 94 5.095490 CGAGGAGCCAAAACATTCAATAAC 58.905 41.667 0.00 0.00 0.00 1.89
94 95 5.007034 TCGAGGAGCCAAAACATTCAATAA 58.993 37.500 0.00 0.00 0.00 1.40
95 96 4.584874 TCGAGGAGCCAAAACATTCAATA 58.415 39.130 0.00 0.00 0.00 1.90
96 97 3.420893 TCGAGGAGCCAAAACATTCAAT 58.579 40.909 0.00 0.00 0.00 2.57
97 98 2.857483 TCGAGGAGCCAAAACATTCAA 58.143 42.857 0.00 0.00 0.00 2.69
98 99 2.559698 TCGAGGAGCCAAAACATTCA 57.440 45.000 0.00 0.00 0.00 2.57
99 100 3.440173 TGAATCGAGGAGCCAAAACATTC 59.560 43.478 0.00 0.00 0.00 2.67
100 101 3.191371 GTGAATCGAGGAGCCAAAACATT 59.809 43.478 0.00 0.00 0.00 2.71
101 102 2.749621 GTGAATCGAGGAGCCAAAACAT 59.250 45.455 0.00 0.00 0.00 2.71
102 103 2.151202 GTGAATCGAGGAGCCAAAACA 58.849 47.619 0.00 0.00 0.00 2.83
103 104 1.468914 GGTGAATCGAGGAGCCAAAAC 59.531 52.381 0.00 0.00 0.00 2.43
104 105 1.073125 TGGTGAATCGAGGAGCCAAAA 59.927 47.619 0.00 0.00 0.00 2.44
105 106 0.690192 TGGTGAATCGAGGAGCCAAA 59.310 50.000 0.00 0.00 0.00 3.28
106 107 0.690192 TTGGTGAATCGAGGAGCCAA 59.310 50.000 9.33 9.33 34.12 4.52
107 108 0.250234 CTTGGTGAATCGAGGAGCCA 59.750 55.000 0.00 0.00 0.00 4.75
108 109 0.537188 TCTTGGTGAATCGAGGAGCC 59.463 55.000 0.00 0.00 0.00 4.70
109 110 2.159043 TCATCTTGGTGAATCGAGGAGC 60.159 50.000 0.00 0.00 0.00 4.70
110 111 3.382865 TCTCATCTTGGTGAATCGAGGAG 59.617 47.826 0.00 0.00 36.10 3.69
111 112 3.365472 TCTCATCTTGGTGAATCGAGGA 58.635 45.455 0.00 0.00 0.00 3.71
112 113 3.808466 TCTCATCTTGGTGAATCGAGG 57.192 47.619 0.00 0.00 0.00 4.63
113 114 4.941657 TCATCTCATCTTGGTGAATCGAG 58.058 43.478 0.00 0.00 0.00 4.04
114 115 5.343307 TTCATCTCATCTTGGTGAATCGA 57.657 39.130 0.00 0.00 0.00 3.59
115 116 6.563567 CGATTTCATCTCATCTTGGTGAATCG 60.564 42.308 0.00 0.00 0.00 3.34
116 117 6.293298 CCGATTTCATCTCATCTTGGTGAATC 60.293 42.308 0.00 0.00 0.00 2.52
117 118 5.530171 CCGATTTCATCTCATCTTGGTGAAT 59.470 40.000 0.00 0.00 0.00 2.57
118 119 4.877823 CCGATTTCATCTCATCTTGGTGAA 59.122 41.667 0.00 0.00 0.00 3.18
119 120 4.162131 TCCGATTTCATCTCATCTTGGTGA 59.838 41.667 0.00 0.00 0.00 4.02
120 121 4.445453 TCCGATTTCATCTCATCTTGGTG 58.555 43.478 0.00 0.00 0.00 4.17
121 122 4.444022 CCTCCGATTTCATCTCATCTTGGT 60.444 45.833 0.00 0.00 0.00 3.67
122 123 4.063689 CCTCCGATTTCATCTCATCTTGG 58.936 47.826 0.00 0.00 0.00 3.61
123 124 4.510711 CACCTCCGATTTCATCTCATCTTG 59.489 45.833 0.00 0.00 0.00 3.02
124 125 4.406972 TCACCTCCGATTTCATCTCATCTT 59.593 41.667 0.00 0.00 0.00 2.40
125 126 3.963374 TCACCTCCGATTTCATCTCATCT 59.037 43.478 0.00 0.00 0.00 2.90
126 127 4.327982 TCACCTCCGATTTCATCTCATC 57.672 45.455 0.00 0.00 0.00 2.92
127 128 4.102210 ACATCACCTCCGATTTCATCTCAT 59.898 41.667 0.00 0.00 0.00 2.90
128 129 3.452264 ACATCACCTCCGATTTCATCTCA 59.548 43.478 0.00 0.00 0.00 3.27
129 130 3.806521 CACATCACCTCCGATTTCATCTC 59.193 47.826 0.00 0.00 0.00 2.75
130 131 3.198635 ACACATCACCTCCGATTTCATCT 59.801 43.478 0.00 0.00 0.00 2.90
131 132 3.535561 ACACATCACCTCCGATTTCATC 58.464 45.455 0.00 0.00 0.00 2.92
132 133 3.055167 TGACACATCACCTCCGATTTCAT 60.055 43.478 0.00 0.00 0.00 2.57
133 134 2.301583 TGACACATCACCTCCGATTTCA 59.698 45.455 0.00 0.00 0.00 2.69
134 135 2.972625 TGACACATCACCTCCGATTTC 58.027 47.619 0.00 0.00 0.00 2.17
135 136 3.338249 CTTGACACATCACCTCCGATTT 58.662 45.455 0.00 0.00 33.38 2.17
136 137 2.355108 CCTTGACACATCACCTCCGATT 60.355 50.000 0.00 0.00 33.38 3.34
137 138 1.208052 CCTTGACACATCACCTCCGAT 59.792 52.381 0.00 0.00 33.38 4.18
138 139 0.608130 CCTTGACACATCACCTCCGA 59.392 55.000 0.00 0.00 33.38 4.55
139 140 0.391661 CCCTTGACACATCACCTCCG 60.392 60.000 0.00 0.00 33.38 4.63
140 141 0.035056 CCCCTTGACACATCACCTCC 60.035 60.000 0.00 0.00 33.38 4.30
141 142 0.678048 GCCCCTTGACACATCACCTC 60.678 60.000 0.00 0.00 33.38 3.85
142 143 1.380302 GCCCCTTGACACATCACCT 59.620 57.895 0.00 0.00 33.38 4.00
143 144 0.962356 CTGCCCCTTGACACATCACC 60.962 60.000 0.00 0.00 33.38 4.02
144 145 0.036732 TCTGCCCCTTGACACATCAC 59.963 55.000 0.00 0.00 33.38 3.06
145 146 0.770499 TTCTGCCCCTTGACACATCA 59.230 50.000 0.00 0.00 0.00 3.07
146 147 1.909700 TTTCTGCCCCTTGACACATC 58.090 50.000 0.00 0.00 0.00 3.06
147 148 2.380064 TTTTCTGCCCCTTGACACAT 57.620 45.000 0.00 0.00 0.00 3.21
148 149 2.364970 CAATTTTCTGCCCCTTGACACA 59.635 45.455 0.00 0.00 0.00 3.72
149 150 2.627699 TCAATTTTCTGCCCCTTGACAC 59.372 45.455 0.00 0.00 0.00 3.67
150 151 2.956132 TCAATTTTCTGCCCCTTGACA 58.044 42.857 0.00 0.00 0.00 3.58
151 152 3.321968 ACTTCAATTTTCTGCCCCTTGAC 59.678 43.478 0.00 0.00 0.00 3.18
152 153 3.321682 CACTTCAATTTTCTGCCCCTTGA 59.678 43.478 0.00 0.00 0.00 3.02
153 154 3.656559 CACTTCAATTTTCTGCCCCTTG 58.343 45.455 0.00 0.00 0.00 3.61
154 155 2.037641 GCACTTCAATTTTCTGCCCCTT 59.962 45.455 0.00 0.00 0.00 3.95
155 156 1.620323 GCACTTCAATTTTCTGCCCCT 59.380 47.619 0.00 0.00 0.00 4.79
156 157 1.669795 CGCACTTCAATTTTCTGCCCC 60.670 52.381 0.00 0.00 0.00 5.80
157 158 1.669795 CCGCACTTCAATTTTCTGCCC 60.670 52.381 0.00 0.00 0.00 5.36
158 159 1.000274 ACCGCACTTCAATTTTCTGCC 60.000 47.619 0.00 0.00 0.00 4.85
159 160 2.422276 ACCGCACTTCAATTTTCTGC 57.578 45.000 0.00 0.00 0.00 4.26
160 161 3.906008 CGTTACCGCACTTCAATTTTCTG 59.094 43.478 0.00 0.00 0.00 3.02
161 162 3.810941 TCGTTACCGCACTTCAATTTTCT 59.189 39.130 0.00 0.00 0.00 2.52
162 163 4.136517 TCGTTACCGCACTTCAATTTTC 57.863 40.909 0.00 0.00 0.00 2.29
163 164 4.023536 ACATCGTTACCGCACTTCAATTTT 60.024 37.500 0.00 0.00 0.00 1.82
164 165 3.500680 ACATCGTTACCGCACTTCAATTT 59.499 39.130 0.00 0.00 0.00 1.82
165 166 3.071479 ACATCGTTACCGCACTTCAATT 58.929 40.909 0.00 0.00 0.00 2.32
166 167 2.671396 GACATCGTTACCGCACTTCAAT 59.329 45.455 0.00 0.00 0.00 2.57
167 168 2.063266 GACATCGTTACCGCACTTCAA 58.937 47.619 0.00 0.00 0.00 2.69
168 169 1.000052 TGACATCGTTACCGCACTTCA 60.000 47.619 0.00 0.00 0.00 3.02
169 170 1.705256 TGACATCGTTACCGCACTTC 58.295 50.000 0.00 0.00 0.00 3.01
170 171 2.066262 CTTGACATCGTTACCGCACTT 58.934 47.619 0.00 0.00 0.00 3.16
171 172 1.000506 ACTTGACATCGTTACCGCACT 59.999 47.619 0.00 0.00 0.00 4.40
172 173 1.126113 CACTTGACATCGTTACCGCAC 59.874 52.381 0.00 0.00 0.00 5.34
173 174 1.269883 ACACTTGACATCGTTACCGCA 60.270 47.619 0.00 0.00 0.00 5.69
174 175 1.126113 CACACTTGACATCGTTACCGC 59.874 52.381 0.00 0.00 0.00 5.68
175 176 2.154963 CACACACTTGACATCGTTACCG 59.845 50.000 0.00 0.00 0.00 4.02
176 177 3.183775 GTCACACACTTGACATCGTTACC 59.816 47.826 0.00 0.00 44.62 2.85
177 178 3.121463 CGTCACACACTTGACATCGTTAC 60.121 47.826 4.28 0.00 45.38 2.50
178 179 3.047093 CGTCACACACTTGACATCGTTA 58.953 45.455 4.28 0.00 45.38 3.18
179 180 1.858458 CGTCACACACTTGACATCGTT 59.142 47.619 4.28 0.00 45.38 3.85
180 181 1.066454 TCGTCACACACTTGACATCGT 59.934 47.619 4.28 0.00 45.38 3.73
181 182 1.716050 CTCGTCACACACTTGACATCG 59.284 52.381 4.28 0.00 45.38 3.84
182 183 3.013276 TCTCGTCACACACTTGACATC 57.987 47.619 4.28 0.00 45.38 3.06
183 184 3.667497 ATCTCGTCACACACTTGACAT 57.333 42.857 4.28 0.00 45.38 3.06
184 185 4.783764 ATATCTCGTCACACACTTGACA 57.216 40.909 4.28 0.00 45.38 3.58
185 186 4.729086 CGTATATCTCGTCACACACTTGAC 59.271 45.833 0.00 0.00 42.24 3.18
186 187 4.201881 CCGTATATCTCGTCACACACTTGA 60.202 45.833 0.00 0.00 0.00 3.02
187 188 4.035684 CCGTATATCTCGTCACACACTTG 58.964 47.826 0.00 0.00 0.00 3.16
188 189 3.066342 CCCGTATATCTCGTCACACACTT 59.934 47.826 0.00 0.00 0.00 3.16
189 190 2.617308 CCCGTATATCTCGTCACACACT 59.383 50.000 0.00 0.00 0.00 3.55
190 191 2.287427 CCCCGTATATCTCGTCACACAC 60.287 54.545 0.00 0.00 0.00 3.82
191 192 1.951602 CCCCGTATATCTCGTCACACA 59.048 52.381 0.00 0.00 0.00 3.72
192 193 2.031333 GTCCCCGTATATCTCGTCACAC 60.031 54.545 0.00 0.00 0.00 3.82
193 194 2.224606 GTCCCCGTATATCTCGTCACA 58.775 52.381 0.00 0.00 0.00 3.58
194 195 1.196354 CGTCCCCGTATATCTCGTCAC 59.804 57.143 0.00 0.00 0.00 3.67
195 196 1.516161 CGTCCCCGTATATCTCGTCA 58.484 55.000 0.00 0.00 0.00 4.35
196 197 0.167689 GCGTCCCCGTATATCTCGTC 59.832 60.000 0.00 0.00 36.15 4.20
197 198 0.250640 AGCGTCCCCGTATATCTCGT 60.251 55.000 0.00 0.00 36.15 4.18
198 199 1.730501 TAGCGTCCCCGTATATCTCG 58.269 55.000 0.00 0.00 36.15 4.04
199 200 3.672781 GCTTTAGCGTCCCCGTATATCTC 60.673 52.174 0.00 0.00 36.15 2.75
200 201 2.230750 GCTTTAGCGTCCCCGTATATCT 59.769 50.000 0.00 0.00 36.15 1.98
201 202 2.603953 GCTTTAGCGTCCCCGTATATC 58.396 52.381 0.00 0.00 36.15 1.63
202 203 2.738013 GCTTTAGCGTCCCCGTATAT 57.262 50.000 0.00 0.00 36.15 0.86
214 215 0.440371 GCACTCACACTCGCTTTAGC 59.560 55.000 0.00 0.00 37.78 3.09
215 216 1.783284 TGCACTCACACTCGCTTTAG 58.217 50.000 0.00 0.00 0.00 1.85
216 217 1.864711 GTTGCACTCACACTCGCTTTA 59.135 47.619 0.00 0.00 0.00 1.85
217 218 0.657840 GTTGCACTCACACTCGCTTT 59.342 50.000 0.00 0.00 0.00 3.51
218 219 0.179073 AGTTGCACTCACACTCGCTT 60.179 50.000 0.00 0.00 0.00 4.68
219 220 0.598680 GAGTTGCACTCACACTCGCT 60.599 55.000 10.30 0.00 44.45 4.93
220 221 1.856012 GAGTTGCACTCACACTCGC 59.144 57.895 10.30 0.00 44.45 5.03
228 229 2.558313 GCGGCTTGAGTTGCACTC 59.442 61.111 8.75 8.75 45.26 3.51
229 230 2.980233 GGCGGCTTGAGTTGCACT 60.980 61.111 0.00 0.00 0.00 4.40
230 231 4.389576 CGGCGGCTTGAGTTGCAC 62.390 66.667 7.61 0.00 0.00 4.57
236 237 0.740868 TCAGATTTCGGCGGCTTGAG 60.741 55.000 7.21 0.00 0.00 3.02
262 263 4.863548 ACCATGACATCCATCAATGAAGT 58.136 39.130 0.00 0.00 31.94 3.01
269 270 1.203237 ACGGACCATGACATCCATCA 58.797 50.000 0.00 0.00 34.35 3.07
289 293 4.460683 GCACCCCGATACGCCACA 62.461 66.667 0.00 0.00 0.00 4.17
293 297 2.972505 CCATGCACCCCGATACGC 60.973 66.667 0.00 0.00 0.00 4.42
294 298 1.594293 GTCCATGCACCCCGATACG 60.594 63.158 0.00 0.00 0.00 3.06
295 299 0.180406 AAGTCCATGCACCCCGATAC 59.820 55.000 0.00 0.00 0.00 2.24
300 304 1.978617 CACCAAGTCCATGCACCCC 60.979 63.158 0.00 0.00 0.00 4.95
346 350 0.586802 GACTTCACTGCGGACAAACC 59.413 55.000 0.00 0.00 0.00 3.27
416 421 5.691754 AGAAGATCAATTTTTCACAAACCGC 59.308 36.000 0.00 0.00 0.00 5.68
497 502 5.253330 TGATTAAGGAGAAATTTGCCGTCT 58.747 37.500 0.00 0.00 0.00 4.18
568 573 6.029607 CGTTAGTCGTTACATAGCCTGTTTA 58.970 40.000 0.00 0.00 35.63 2.01
609 615 1.910772 AGACTCTGCCGAGCCAAGT 60.911 57.895 4.89 0.00 41.09 3.16
856 869 3.195698 GACGGGCGAACTGATGGC 61.196 66.667 0.00 0.00 0.00 4.40
905 918 0.678048 AAGAAGATGAAGTGGGGCGC 60.678 55.000 0.00 0.00 0.00 6.53
912 925 3.517500 GGTCTGAGGGAAGAAGATGAAGT 59.482 47.826 0.00 0.00 0.00 3.01
955 973 4.565022 AGTTTGAAGTGCTCTAGCTTCTC 58.435 43.478 3.26 0.00 41.05 2.87
981 999 1.338136 TGGAGCCTGGCTAGCTAACC 61.338 60.000 23.44 17.58 41.75 2.85
983 1001 0.761187 CATGGAGCCTGGCTAGCTAA 59.239 55.000 23.44 5.95 41.75 3.09
1400 1418 0.927537 CACGAGTTTGACGTTCAGCA 59.072 50.000 0.00 0.00 42.07 4.41
1493 1511 4.619394 GCTAATCGATCGATGGAGTGGATT 60.619 45.833 29.99 14.68 34.70 3.01
1497 1515 2.983136 GTGCTAATCGATCGATGGAGTG 59.017 50.000 29.99 18.11 34.70 3.51
1498 1516 2.029828 GGTGCTAATCGATCGATGGAGT 60.030 50.000 29.99 17.18 34.70 3.85
1500 1518 2.239400 AGGTGCTAATCGATCGATGGA 58.761 47.619 29.99 19.67 34.70 3.41
1501 1519 2.732412 AGGTGCTAATCGATCGATGG 57.268 50.000 29.99 24.27 34.70 3.51
1503 1521 5.001874 TGTAGTAGGTGCTAATCGATCGAT 58.998 41.667 24.60 24.60 36.23 3.59
1506 1524 7.142306 TGTATGTAGTAGGTGCTAATCGATC 57.858 40.000 0.00 0.00 0.00 3.69
1587 1615 6.127810 TGTACTATGCGTACTTACCTTGAG 57.872 41.667 0.00 0.00 46.89 3.02
1602 1630 4.155310 CATGTGGCATGCATGTACTATG 57.845 45.455 26.79 22.35 38.96 2.23
1765 1820 8.311109 ACAACTCACACAGTCACATGTATATAA 58.689 33.333 0.00 0.00 32.30 0.98
1776 1831 3.541996 ACATCACAACTCACACAGTCA 57.458 42.857 0.00 0.00 32.30 3.41
1779 1834 2.291465 CCCAACATCACAACTCACACAG 59.709 50.000 0.00 0.00 0.00 3.66
1781 1836 2.033299 CACCCAACATCACAACTCACAC 59.967 50.000 0.00 0.00 0.00 3.82
1782 1837 2.296792 CACCCAACATCACAACTCACA 58.703 47.619 0.00 0.00 0.00 3.58
1783 1838 2.033299 CACACCCAACATCACAACTCAC 59.967 50.000 0.00 0.00 0.00 3.51
1784 1839 2.296792 CACACCCAACATCACAACTCA 58.703 47.619 0.00 0.00 0.00 3.41
1913 2194 4.870991 GTGACTTTTTATCCCGAGGAAGAG 59.129 45.833 0.00 0.00 34.34 2.85
1936 2217 1.704641 TGACCATATGGAGTCGAGGG 58.295 55.000 28.77 0.00 38.94 4.30
1992 2274 2.434884 AGCGTCATTGACTGGCCG 60.435 61.111 14.54 2.53 0.00 6.13
2014 2297 2.791158 GCACGAACGCCAGAAATATTGG 60.791 50.000 0.00 0.00 38.78 3.16
2055 2338 2.029649 TGGAGTAGTTCTTTCGTTCCGG 60.030 50.000 0.00 0.00 0.00 5.14
2056 2339 3.293311 TGGAGTAGTTCTTTCGTTCCG 57.707 47.619 0.00 0.00 0.00 4.30
2078 2361 9.753674 TGGTCATATTTTATGTTTTCTTCCTCT 57.246 29.630 0.00 0.00 0.00 3.69
2186 2469 7.338957 AGCTTTGAGGATTCCAATCTTTAGAAG 59.661 37.037 5.29 0.00 35.73 2.85
2187 2470 7.177878 AGCTTTGAGGATTCCAATCTTTAGAA 58.822 34.615 5.29 0.00 35.73 2.10
2188 2471 6.725364 AGCTTTGAGGATTCCAATCTTTAGA 58.275 36.000 5.29 0.00 35.73 2.10
2189 2472 7.401955 AAGCTTTGAGGATTCCAATCTTTAG 57.598 36.000 5.29 0.00 35.73 1.85
2190 2473 7.781324 AAAGCTTTGAGGATTCCAATCTTTA 57.219 32.000 11.80 0.00 35.73 1.85
2191 2474 6.676990 AAAGCTTTGAGGATTCCAATCTTT 57.323 33.333 11.80 1.96 35.73 2.52
2237 2526 1.276622 TTGTCTTGTCTAGGGCCTCC 58.723 55.000 10.74 0.00 0.00 4.30
2254 2543 6.769341 TCCATATTGTCTCCTGTCATCATTTG 59.231 38.462 0.00 0.00 0.00 2.32
2457 5192 5.181748 ACTGATAATCTGCACTTCAACTCC 58.818 41.667 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.