Multiple sequence alignment - TraesCS2B01G056800

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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 TraesCS2B01G056800 chr2B 100.000 6255 0 0 1 6255 27706781 27713035 0.000000e+00 11551.0
1 TraesCS2B01G056800 chr2B 84.409 186 14 10 9 182 30587724 30587542 1.080000e-37 169.0
2 TraesCS2B01G056800 chr2B 90.805 87 7 1 5643 5728 551450899 551450813 1.420000e-21 115.0
3 TraesCS2B01G056800 chr2A 94.354 4906 164 52 1367 6200 17616122 17620986 0.000000e+00 7420.0
4 TraesCS2B01G056800 chr2A 92.049 1132 55 13 219 1330 17614633 17615749 0.000000e+00 1559.0
5 TraesCS2B01G056800 chr2A 96.721 61 1 1 6196 6255 17621300 17621360 3.990000e-17 100.0
6 TraesCS2B01G056800 chr2D 95.784 3439 82 27 2788 6201 15588837 15592237 0.000000e+00 5489.0
7 TraesCS2B01G056800 chr2D 92.845 2907 133 28 219 3108 15586372 15589220 0.000000e+00 4146.0
8 TraesCS2B01G056800 chr2D 80.541 185 19 8 4 184 581803667 581803496 6.580000e-25 126.0
9 TraesCS2B01G056800 chr1A 83.146 178 19 6 15 189 311139463 311139294 1.090000e-32 152.0
10 TraesCS2B01G056800 chr4B 89.535 86 8 1 5644 5728 667890562 667890647 2.380000e-19 108.0
11 TraesCS2B01G056800 chr6A 83.333 120 14 4 15 132 305133600 305133715 8.580000e-19 106.0
12 TraesCS2B01G056800 chr6A 86.364 88 9 3 5644 5730 515409133 515409048 6.680000e-15 93.5
13 TraesCS2B01G056800 chr3B 96.774 62 2 0 36 97 494129557 494129496 3.080000e-18 104.0
14 TraesCS2B01G056800 chr5A 86.813 91 9 3 5640 5728 331779590 331779501 1.440000e-16 99.0
15 TraesCS2B01G056800 chr6D 77.249 189 25 12 15 189 362324196 362324380 1.860000e-15 95.3
16 TraesCS2B01G056800 chr6D 80.460 87 8 8 1209 1288 39192251 39192167 2.440000e-04 58.4
17 TraesCS2B01G056800 chr7D 86.364 88 8 4 5643 5728 614282135 614282050 6.680000e-15 93.5
18 TraesCS2B01G056800 chr7A 85.714 91 10 3 5641 5728 232575390 232575480 6.680000e-15 93.5
19 TraesCS2B01G056800 chr1D 85.714 91 7 6 5643 5730 378705162 378705249 2.400000e-14 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 TraesCS2B01G056800 chr2B 27706781 27713035 6254 False 11551.000000 11551 100.000000 1 6255 1 chr2B.!!$F1 6254
1 TraesCS2B01G056800 chr2A 17614633 17621360 6727 False 3026.333333 7420 94.374667 219 6255 3 chr2A.!!$F1 6036
2 TraesCS2B01G056800 chr2D 15586372 15592237 5865 False 4817.500000 5489 94.314500 219 6201 2 chr2D.!!$F1 5982

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
986 994 0.026803 GTCGATTAGGCAAGCAAGCG 59.973 55.000 0.0 0.0 35.03 4.68 F
2559 2927 0.894835 TAATGGAGCGACACAGCAGA 59.105 50.000 0.0 0.0 40.15 4.26 F
2796 3173 0.251297 AACCAGCAATAGCACCAGCA 60.251 50.000 0.0 0.0 45.49 4.41 F
2802 3179 0.322816 CAATAGCACCAGCACCAGGT 60.323 55.000 0.0 0.0 45.49 4.00 F
3963 4418 1.867233 AGTCAAGCACTGCACTTTACG 59.133 47.619 3.3 0.0 32.26 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2777 3154 0.251297 TGCTGGTGCTATTGCTGGTT 60.251 50.000 0.00 0.0 40.48 3.67 R
3875 4318 2.892374 TGGAGCACAGTTCATGTATCG 58.108 47.619 0.00 0.0 41.41 2.92 R
4593 5053 1.073722 CTGTTCTGCTCCTTGGCCA 59.926 57.895 0.00 0.0 0.00 5.36 R
4882 5342 1.605058 GCGCCTGGGAGTTCTCTACA 61.605 60.000 0.00 0.0 0.00 2.74 R
5707 6175 0.035056 ATGCAGAGGCCAGGTGTTAC 60.035 55.000 5.01 0.0 40.13 2.50 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
24 25 7.596749 ATGCTATTTCCGTAATGCATAGTAC 57.403 36.000 0.00 0.00 36.17 2.73
25 26 6.755206 TGCTATTTCCGTAATGCATAGTACT 58.245 36.000 0.00 0.00 30.55 2.73
26 27 7.888424 TGCTATTTCCGTAATGCATAGTACTA 58.112 34.615 4.77 4.77 30.55 1.82
27 28 8.528643 TGCTATTTCCGTAATGCATAGTACTAT 58.471 33.333 9.71 9.71 30.55 2.12
28 29 9.021863 GCTATTTCCGTAATGCATAGTACTATC 57.978 37.037 12.62 8.52 0.00 2.08
34 35 8.188799 TCCGTAATGCATAGTACTATCATAAGC 58.811 37.037 12.62 12.75 0.00 3.09
35 36 8.191446 CCGTAATGCATAGTACTATCATAAGCT 58.809 37.037 12.62 7.22 0.00 3.74
51 52 8.622948 ATCATAAGCTAGTATTTTAGGTTGCC 57.377 34.615 7.52 0.00 40.49 4.52
52 53 7.802117 TCATAAGCTAGTATTTTAGGTTGCCT 58.198 34.615 7.52 0.00 40.49 4.75
53 54 8.272173 TCATAAGCTAGTATTTTAGGTTGCCTT 58.728 33.333 7.52 0.00 40.49 4.35
54 55 9.555727 CATAAGCTAGTATTTTAGGTTGCCTTA 57.444 33.333 7.52 0.00 40.49 2.69
66 67 9.868277 TTTTAGGTTGCCTTATTAATTGACATG 57.132 29.630 0.00 0.00 34.61 3.21
67 68 5.906073 AGGTTGCCTTATTAATTGACATGC 58.094 37.500 0.00 0.00 0.00 4.06
68 69 4.739716 GGTTGCCTTATTAATTGACATGCG 59.260 41.667 0.00 0.00 0.00 4.73
69 70 5.339990 GTTGCCTTATTAATTGACATGCGT 58.660 37.500 0.00 0.00 0.00 5.24
70 71 6.459024 GGTTGCCTTATTAATTGACATGCGTA 60.459 38.462 0.00 0.00 0.00 4.42
71 72 6.685527 TGCCTTATTAATTGACATGCGTAA 57.314 33.333 0.00 0.00 0.00 3.18
72 73 6.491394 TGCCTTATTAATTGACATGCGTAAC 58.509 36.000 0.00 0.00 0.00 2.50
73 74 6.094186 TGCCTTATTAATTGACATGCGTAACA 59.906 34.615 0.00 0.00 0.00 2.41
74 75 6.413818 GCCTTATTAATTGACATGCGTAACAC 59.586 38.462 0.00 0.00 0.00 3.32
75 76 7.468441 CCTTATTAATTGACATGCGTAACACA 58.532 34.615 0.00 0.00 0.00 3.72
76 77 7.965655 CCTTATTAATTGACATGCGTAACACAA 59.034 33.333 0.00 0.00 0.00 3.33
77 78 9.335891 CTTATTAATTGACATGCGTAACACAAA 57.664 29.630 0.00 0.00 0.00 2.83
78 79 7.795431 ATTAATTGACATGCGTAACACAAAG 57.205 32.000 0.00 0.00 0.00 2.77
79 80 4.829064 ATTGACATGCGTAACACAAAGT 57.171 36.364 0.00 0.00 0.00 2.66
80 81 5.933187 ATTGACATGCGTAACACAAAGTA 57.067 34.783 0.00 0.00 0.00 2.24
81 82 4.983215 TGACATGCGTAACACAAAGTAG 57.017 40.909 0.00 0.00 0.00 2.57
82 83 4.373527 TGACATGCGTAACACAAAGTAGT 58.626 39.130 0.00 0.00 0.00 2.73
83 84 5.530712 TGACATGCGTAACACAAAGTAGTA 58.469 37.500 0.00 0.00 0.00 1.82
84 85 5.403166 TGACATGCGTAACACAAAGTAGTAC 59.597 40.000 0.00 0.00 0.00 2.73
85 86 5.291178 ACATGCGTAACACAAAGTAGTACA 58.709 37.500 2.52 0.00 0.00 2.90
86 87 5.754406 ACATGCGTAACACAAAGTAGTACAA 59.246 36.000 2.52 0.00 0.00 2.41
87 88 5.640218 TGCGTAACACAAAGTAGTACAAC 57.360 39.130 2.52 0.00 0.00 3.32
88 89 5.107824 TGCGTAACACAAAGTAGTACAACA 58.892 37.500 2.52 0.00 0.00 3.33
89 90 5.754406 TGCGTAACACAAAGTAGTACAACAT 59.246 36.000 2.52 0.00 0.00 2.71
90 91 6.258287 TGCGTAACACAAAGTAGTACAACATT 59.742 34.615 2.52 0.00 0.00 2.71
91 92 7.127686 GCGTAACACAAAGTAGTACAACATTT 58.872 34.615 2.52 0.00 0.00 2.32
92 93 8.274939 GCGTAACACAAAGTAGTACAACATTTA 58.725 33.333 2.52 0.00 0.00 1.40
127 128 4.353383 GGTACCACACCTCTCTTTTCTT 57.647 45.455 7.15 0.00 44.79 2.52
128 129 5.479124 GGTACCACACCTCTCTTTTCTTA 57.521 43.478 7.15 0.00 44.79 2.10
129 130 6.051179 GGTACCACACCTCTCTTTTCTTAT 57.949 41.667 7.15 0.00 44.79 1.73
130 131 6.473758 GGTACCACACCTCTCTTTTCTTATT 58.526 40.000 7.15 0.00 44.79 1.40
131 132 6.940867 GGTACCACACCTCTCTTTTCTTATTT 59.059 38.462 7.15 0.00 44.79 1.40
132 133 8.098912 GGTACCACACCTCTCTTTTCTTATTTA 58.901 37.037 7.15 0.00 44.79 1.40
133 134 9.498176 GTACCACACCTCTCTTTTCTTATTTAA 57.502 33.333 0.00 0.00 0.00 1.52
135 136 9.588096 ACCACACCTCTCTTTTCTTATTTAATT 57.412 29.630 0.00 0.00 0.00 1.40
136 137 9.846248 CCACACCTCTCTTTTCTTATTTAATTG 57.154 33.333 0.00 0.00 0.00 2.32
137 138 9.346725 CACACCTCTCTTTTCTTATTTAATTGC 57.653 33.333 0.00 0.00 0.00 3.56
138 139 8.237267 ACACCTCTCTTTTCTTATTTAATTGCG 58.763 33.333 0.00 0.00 0.00 4.85
139 140 8.237267 CACCTCTCTTTTCTTATTTAATTGCGT 58.763 33.333 0.00 0.00 0.00 5.24
140 141 8.237267 ACCTCTCTTTTCTTATTTAATTGCGTG 58.763 33.333 0.00 0.00 0.00 5.34
141 142 8.237267 CCTCTCTTTTCTTATTTAATTGCGTGT 58.763 33.333 0.00 0.00 0.00 4.49
142 143 9.267096 CTCTCTTTTCTTATTTAATTGCGTGTC 57.733 33.333 0.00 0.00 0.00 3.67
143 144 8.779303 TCTCTTTTCTTATTTAATTGCGTGTCA 58.221 29.630 0.00 0.00 0.00 3.58
144 145 8.722342 TCTTTTCTTATTTAATTGCGTGTCAC 57.278 30.769 0.00 0.00 0.00 3.67
145 146 8.346300 TCTTTTCTTATTTAATTGCGTGTCACA 58.654 29.630 3.42 0.00 0.00 3.58
146 147 9.128107 CTTTTCTTATTTAATTGCGTGTCACAT 57.872 29.630 3.42 0.00 0.00 3.21
147 148 8.667987 TTTCTTATTTAATTGCGTGTCACATC 57.332 30.769 3.42 0.00 0.00 3.06
148 149 7.371126 TCTTATTTAATTGCGTGTCACATCA 57.629 32.000 3.42 0.00 0.00 3.07
149 150 7.984391 TCTTATTTAATTGCGTGTCACATCAT 58.016 30.769 3.42 0.00 0.00 2.45
150 151 9.103861 TCTTATTTAATTGCGTGTCACATCATA 57.896 29.630 3.42 0.00 0.00 2.15
151 152 9.715123 CTTATTTAATTGCGTGTCACATCATAA 57.285 29.630 3.42 0.00 0.00 1.90
153 154 8.978564 ATTTAATTGCGTGTCACATCATAAAA 57.021 26.923 3.42 0.00 0.00 1.52
154 155 8.446489 TTTAATTGCGTGTCACATCATAAAAG 57.554 30.769 3.42 0.00 0.00 2.27
155 156 5.878332 ATTGCGTGTCACATCATAAAAGA 57.122 34.783 3.42 0.00 0.00 2.52
156 157 5.681337 TTGCGTGTCACATCATAAAAGAA 57.319 34.783 3.42 0.00 0.00 2.52
157 158 5.878332 TGCGTGTCACATCATAAAAGAAT 57.122 34.783 3.42 0.00 0.00 2.40
158 159 6.252967 TGCGTGTCACATCATAAAAGAATT 57.747 33.333 3.42 0.00 0.00 2.17
159 160 7.371126 TGCGTGTCACATCATAAAAGAATTA 57.629 32.000 3.42 0.00 0.00 1.40
160 161 7.811653 TGCGTGTCACATCATAAAAGAATTAA 58.188 30.769 3.42 0.00 0.00 1.40
161 162 8.458052 TGCGTGTCACATCATAAAAGAATTAAT 58.542 29.630 3.42 0.00 0.00 1.40
162 163 9.289303 GCGTGTCACATCATAAAAGAATTAATT 57.711 29.630 0.00 0.00 0.00 1.40
165 166 9.585099 TGTCACATCATAAAAGAATTAATTGGC 57.415 29.630 5.17 0.00 0.00 4.52
166 167 9.585099 GTCACATCATAAAAGAATTAATTGGCA 57.415 29.630 5.17 0.00 0.00 4.92
169 170 9.048446 ACATCATAAAAGAATTAATTGGCATGC 57.952 29.630 9.90 9.90 0.00 4.06
170 171 9.047371 CATCATAAAAGAATTAATTGGCATGCA 57.953 29.630 21.36 0.00 0.00 3.96
171 172 9.787435 ATCATAAAAGAATTAATTGGCATGCAT 57.213 25.926 21.36 1.70 0.00 3.96
172 173 9.047371 TCATAAAAGAATTAATTGGCATGCATG 57.953 29.630 22.70 22.70 0.00 4.06
173 174 9.047371 CATAAAAGAATTAATTGGCATGCATGA 57.953 29.630 30.64 10.12 0.00 3.07
174 175 9.787435 ATAAAAGAATTAATTGGCATGCATGAT 57.213 25.926 30.64 12.15 0.00 2.45
176 177 8.597662 AAAGAATTAATTGGCATGCATGATAC 57.402 30.769 30.64 18.45 0.00 2.24
177 178 6.694447 AGAATTAATTGGCATGCATGATACC 58.306 36.000 30.64 21.08 0.00 2.73
178 179 6.268158 AGAATTAATTGGCATGCATGATACCA 59.732 34.615 30.64 23.37 0.00 3.25
179 180 3.738830 AATTGGCATGCATGATACCAC 57.261 42.857 30.64 10.90 0.00 4.16
180 181 2.440517 TTGGCATGCATGATACCACT 57.559 45.000 30.64 0.00 0.00 4.00
181 182 2.440517 TGGCATGCATGATACCACTT 57.559 45.000 30.64 0.00 0.00 3.16
182 183 3.574354 TGGCATGCATGATACCACTTA 57.426 42.857 30.64 3.36 0.00 2.24
183 184 4.103013 TGGCATGCATGATACCACTTAT 57.897 40.909 30.64 0.00 0.00 1.73
184 185 4.472496 TGGCATGCATGATACCACTTATT 58.528 39.130 30.64 0.00 0.00 1.40
185 186 5.629125 TGGCATGCATGATACCACTTATTA 58.371 37.500 30.64 1.58 0.00 0.98
186 187 5.473162 TGGCATGCATGATACCACTTATTAC 59.527 40.000 30.64 6.75 0.00 1.89
187 188 5.707298 GGCATGCATGATACCACTTATTACT 59.293 40.000 30.64 0.00 0.00 2.24
188 189 6.128172 GGCATGCATGATACCACTTATTACTC 60.128 42.308 30.64 5.71 0.00 2.59
189 190 6.401474 GCATGCATGATACCACTTATTACTCG 60.401 42.308 30.64 0.00 0.00 4.18
190 191 6.156748 TGCATGATACCACTTATTACTCGT 57.843 37.500 0.00 0.00 0.00 4.18
191 192 6.213677 TGCATGATACCACTTATTACTCGTC 58.786 40.000 0.00 0.00 0.00 4.20
192 193 6.040504 TGCATGATACCACTTATTACTCGTCT 59.959 38.462 0.00 0.00 0.00 4.18
193 194 6.924060 GCATGATACCACTTATTACTCGTCTT 59.076 38.462 0.00 0.00 0.00 3.01
194 195 8.080417 GCATGATACCACTTATTACTCGTCTTA 58.920 37.037 0.00 0.00 0.00 2.10
195 196 9.395707 CATGATACCACTTATTACTCGTCTTAC 57.604 37.037 0.00 0.00 0.00 2.34
196 197 7.934457 TGATACCACTTATTACTCGTCTTACC 58.066 38.462 0.00 0.00 0.00 2.85
197 198 7.557358 TGATACCACTTATTACTCGTCTTACCA 59.443 37.037 0.00 0.00 0.00 3.25
198 199 5.958955 ACCACTTATTACTCGTCTTACCAC 58.041 41.667 0.00 0.00 0.00 4.16
199 200 5.032863 CCACTTATTACTCGTCTTACCACG 58.967 45.833 0.00 0.00 41.36 4.94
200 201 5.163723 CCACTTATTACTCGTCTTACCACGA 60.164 44.000 0.00 0.00 46.42 4.35
201 202 5.736358 CACTTATTACTCGTCTTACCACGAC 59.264 44.000 0.00 0.00 43.79 4.34
202 203 3.772060 ATTACTCGTCTTACCACGACC 57.228 47.619 0.00 0.00 43.79 4.79
203 204 2.183478 TACTCGTCTTACCACGACCA 57.817 50.000 0.00 0.00 43.79 4.02
204 205 0.879765 ACTCGTCTTACCACGACCAG 59.120 55.000 0.00 0.00 43.79 4.00
205 206 0.170561 CTCGTCTTACCACGACCAGG 59.829 60.000 0.00 0.00 43.79 4.45
206 207 1.445582 CGTCTTACCACGACCAGGC 60.446 63.158 0.00 0.00 42.69 4.85
207 208 1.874345 CGTCTTACCACGACCAGGCT 61.874 60.000 0.00 0.00 42.69 4.58
208 209 0.320697 GTCTTACCACGACCAGGCTT 59.679 55.000 0.00 0.00 0.00 4.35
209 210 0.606604 TCTTACCACGACCAGGCTTC 59.393 55.000 0.00 0.00 0.00 3.86
210 211 0.736325 CTTACCACGACCAGGCTTCG 60.736 60.000 7.03 7.03 42.36 3.79
211 212 1.180456 TTACCACGACCAGGCTTCGA 61.180 55.000 14.99 0.00 39.83 3.71
212 213 1.592400 TACCACGACCAGGCTTCGAG 61.592 60.000 14.99 7.26 39.83 4.04
213 214 2.636412 CCACGACCAGGCTTCGAGA 61.636 63.158 14.99 0.00 39.83 4.04
214 215 1.289066 CACGACCAGGCTTCGAGAA 59.711 57.895 14.99 0.00 39.83 2.87
215 216 0.319555 CACGACCAGGCTTCGAGAAA 60.320 55.000 14.99 0.00 39.83 2.52
216 217 0.391597 ACGACCAGGCTTCGAGAAAA 59.608 50.000 14.99 0.00 39.83 2.29
217 218 1.002087 ACGACCAGGCTTCGAGAAAAT 59.998 47.619 14.99 0.00 39.83 1.82
265 266 3.117491 ACATATCTGGTGATTCAGGCG 57.883 47.619 0.00 0.00 35.58 5.52
282 283 0.872021 GCGGTGCCTACATTCGAGAG 60.872 60.000 0.00 0.00 0.00 3.20
287 288 1.277842 TGCCTACATTCGAGAGCCAAA 59.722 47.619 0.00 0.00 0.00 3.28
288 289 1.666189 GCCTACATTCGAGAGCCAAAC 59.334 52.381 0.00 0.00 0.00 2.93
303 304 1.391485 CCAAACGCACGAGAATCAGAG 59.609 52.381 0.00 0.00 33.17 3.35
310 311 2.868044 GCACGAGAATCAGAGTGTGGTT 60.868 50.000 0.00 0.00 36.99 3.67
311 312 2.733552 CACGAGAATCAGAGTGTGGTTG 59.266 50.000 0.00 0.00 33.17 3.77
312 313 2.628178 ACGAGAATCAGAGTGTGGTTGA 59.372 45.455 0.00 0.00 33.17 3.18
572 577 4.200092 GAGGTTTCTCTCTCTCTCTCTCC 58.800 52.174 0.00 0.00 37.07 3.71
607 612 0.478072 CCCCATCCATCCGAATTCCA 59.522 55.000 0.00 0.00 0.00 3.53
608 613 1.609208 CCCATCCATCCGAATTCCAC 58.391 55.000 0.00 0.00 0.00 4.02
646 651 2.577059 GACGAACCGCAGATCCCA 59.423 61.111 0.00 0.00 0.00 4.37
649 654 0.035439 ACGAACCGCAGATCCCATTT 60.035 50.000 0.00 0.00 0.00 2.32
656 662 3.131046 ACCGCAGATCCCATTTGATTTTC 59.869 43.478 0.00 0.00 0.00 2.29
725 733 6.464222 CCAAAAGTTTCTAATTTTCTCCCCC 58.536 40.000 0.00 0.00 0.00 5.40
741 749 0.885879 CCCCTTTTCCGTGGCTTAAC 59.114 55.000 0.00 0.00 0.00 2.01
767 775 1.525923 CAGAGGCACCCAGATCCAG 59.474 63.158 0.00 0.00 0.00 3.86
853 861 2.965147 CCACAAGTTTTGGTCCCAAGAT 59.035 45.455 0.00 0.00 37.24 2.40
876 884 1.871080 CGATTTGGGGAGGAGAATCG 58.129 55.000 3.40 3.40 42.97 3.34
930 938 2.285368 TTGAGGTGCCGATCCCCT 60.285 61.111 0.00 0.00 0.00 4.79
932 940 2.444895 GAGGTGCCGATCCCCTCT 60.445 66.667 7.71 0.00 41.31 3.69
986 994 0.026803 GTCGATTAGGCAAGCAAGCG 59.973 55.000 0.00 0.00 35.03 4.68
996 1004 3.012518 GGCAAGCAAGCGGATCATATAT 58.987 45.455 0.00 0.00 34.64 0.86
997 1005 4.080919 AGGCAAGCAAGCGGATCATATATA 60.081 41.667 0.00 0.00 34.64 0.86
1122 1130 2.160417 CGCCATCAGGAAGAACTTGTTC 59.840 50.000 5.44 5.44 36.89 3.18
1125 1133 3.755378 CCATCAGGAAGAACTTGTTCTGG 59.245 47.826 15.61 8.55 36.89 3.86
1126 1134 2.851195 TCAGGAAGAACTTGTTCTGGC 58.149 47.619 15.61 11.08 0.00 4.85
1127 1135 1.882623 CAGGAAGAACTTGTTCTGGCC 59.117 52.381 15.61 17.84 0.00 5.36
1260 1277 2.749280 AGCAAAATGCCTGGCTTAAC 57.251 45.000 21.03 4.65 46.52 2.01
1370 1734 4.434713 TTCCGAGGCTTTTTAGAAATGC 57.565 40.909 0.00 3.50 0.00 3.56
1393 1757 1.548985 CGTCTTTCGTCTATGCGCG 59.451 57.895 0.00 0.00 34.52 6.86
1827 2195 1.078143 AGCACCGAGGAAGGAATGC 60.078 57.895 0.00 0.00 34.58 3.56
1903 2271 4.937015 GCATAATTTTCCTTTGCCACATGT 59.063 37.500 0.00 0.00 0.00 3.21
1913 2281 2.042831 GCCACATGTCTCTGGGCAC 61.043 63.158 16.95 0.00 44.01 5.01
1979 2347 7.901029 TGCCACATTCCAATAATTTCAAACTA 58.099 30.769 0.00 0.00 0.00 2.24
2108 2476 2.051166 GATCGTCCGCTAGCCGTC 60.051 66.667 9.66 0.00 34.38 4.79
2559 2927 0.894835 TAATGGAGCGACACAGCAGA 59.105 50.000 0.00 0.00 40.15 4.26
2674 3042 1.002868 CCTCCACTTCCAGGTGCAG 60.003 63.158 0.00 0.00 36.03 4.41
2743 3120 3.034030 GTGAACCAGCACCAGCAC 58.966 61.111 0.00 0.00 45.49 4.40
2744 3121 2.203337 TGAACCAGCACCAGCACC 60.203 61.111 0.00 0.00 45.49 5.01
2745 3122 2.203337 GAACCAGCACCAGCACCA 60.203 61.111 0.00 0.00 45.49 4.17
2746 3123 2.203394 AACCAGCACCAGCACCAG 60.203 61.111 0.00 0.00 45.49 4.00
2747 3124 3.797507 AACCAGCACCAGCACCAGG 62.798 63.158 0.00 0.00 45.49 4.45
2748 3125 4.275508 CCAGCACCAGCACCAGGT 62.276 66.667 0.00 0.00 45.49 4.00
2753 3130 2.515901 ACCAGCACCAGGTGAACC 59.484 61.111 24.96 5.63 45.95 3.62
2754 3131 2.382770 ACCAGCACCAGGTGAACCA 61.383 57.895 24.96 0.00 45.95 3.67
2785 3162 1.827789 GCACCAGGTGAACCAGCAA 60.828 57.895 24.96 0.00 38.89 3.91
2786 3163 1.181098 GCACCAGGTGAACCAGCAAT 61.181 55.000 24.96 0.00 38.89 3.56
2787 3164 1.886222 GCACCAGGTGAACCAGCAATA 60.886 52.381 24.96 0.00 38.89 1.90
2788 3165 2.086869 CACCAGGTGAACCAGCAATAG 58.913 52.381 15.35 0.00 38.89 1.73
2789 3166 1.098050 CCAGGTGAACCAGCAATAGC 58.902 55.000 1.62 0.00 42.56 2.97
2790 3167 1.614051 CCAGGTGAACCAGCAATAGCA 60.614 52.381 1.62 0.00 45.49 3.49
2791 3168 1.470098 CAGGTGAACCAGCAATAGCAC 59.530 52.381 1.62 0.00 45.49 4.40
2792 3169 0.811281 GGTGAACCAGCAATAGCACC 59.189 55.000 0.00 0.00 45.49 5.01
2793 3170 1.533625 GTGAACCAGCAATAGCACCA 58.466 50.000 0.00 0.00 45.49 4.17
2794 3171 1.470098 GTGAACCAGCAATAGCACCAG 59.530 52.381 0.00 0.00 45.49 4.00
2795 3172 0.453390 GAACCAGCAATAGCACCAGC 59.547 55.000 0.00 0.00 45.49 4.85
2796 3173 0.251297 AACCAGCAATAGCACCAGCA 60.251 50.000 0.00 0.00 45.49 4.41
2797 3174 0.962356 ACCAGCAATAGCACCAGCAC 60.962 55.000 0.00 0.00 45.49 4.40
2798 3175 1.660560 CCAGCAATAGCACCAGCACC 61.661 60.000 0.00 0.00 45.49 5.01
2799 3176 0.961857 CAGCAATAGCACCAGCACCA 60.962 55.000 0.00 0.00 45.49 4.17
2800 3177 0.679002 AGCAATAGCACCAGCACCAG 60.679 55.000 0.00 0.00 45.49 4.00
2801 3178 1.660560 GCAATAGCACCAGCACCAGG 61.661 60.000 0.00 0.00 45.49 4.45
2802 3179 0.322816 CAATAGCACCAGCACCAGGT 60.323 55.000 0.00 0.00 45.49 4.00
2831 3208 2.772191 ACCAGCACCACCACCAGA 60.772 61.111 0.00 0.00 0.00 3.86
3599 4042 6.095432 AGGTTTAATGAGGAGATGATCGAG 57.905 41.667 0.00 0.00 0.00 4.04
3875 4318 9.458374 CTCCTTTCTAAAATCGACTATCTCTTC 57.542 37.037 0.00 0.00 0.00 2.87
3963 4418 1.867233 AGTCAAGCACTGCACTTTACG 59.133 47.619 3.30 0.00 32.26 3.18
4042 4497 5.283457 TGTTTGTTCCCTTTGGTAATTGG 57.717 39.130 0.00 0.00 0.00 3.16
4882 5342 3.128375 CGCAAGTTGGCCCAGTTT 58.872 55.556 0.00 0.00 0.00 2.66
5191 5651 2.125350 GACCCTCGGCAAGCTCTG 60.125 66.667 0.00 0.00 0.00 3.35
5419 5883 5.242171 TCATTCTGCATTTCACATCACACTT 59.758 36.000 0.00 0.00 0.00 3.16
5430 5894 5.122519 TCACATCACACTTTTGTTAGAGCA 58.877 37.500 0.00 0.00 31.66 4.26
5439 5903 4.463891 ACTTTTGTTAGAGCAATGGGATGG 59.536 41.667 0.00 0.00 0.00 3.51
5442 5906 2.785269 TGTTAGAGCAATGGGATGGGAT 59.215 45.455 0.00 0.00 0.00 3.85
5443 5907 3.152341 GTTAGAGCAATGGGATGGGATG 58.848 50.000 0.00 0.00 0.00 3.51
5444 5908 1.526315 AGAGCAATGGGATGGGATGA 58.474 50.000 0.00 0.00 0.00 2.92
5445 5909 1.854939 AGAGCAATGGGATGGGATGAA 59.145 47.619 0.00 0.00 0.00 2.57
5446 5910 2.158505 AGAGCAATGGGATGGGATGAAG 60.159 50.000 0.00 0.00 0.00 3.02
5447 5911 1.854939 AGCAATGGGATGGGATGAAGA 59.145 47.619 0.00 0.00 0.00 2.87
5714 6182 9.174166 AGGATACAAAATACAATGAGTAACACC 57.826 33.333 0.00 0.00 35.78 4.16
5821 6289 1.420430 ACTCTCTGTTTCCAACCGGA 58.580 50.000 9.46 0.00 40.60 5.14
5837 6305 0.934436 CGGACAACTGCCGCAAAAAG 60.934 55.000 0.00 0.00 42.55 2.27
5840 6308 2.535331 GACAACTGCCGCAAAAAGAAA 58.465 42.857 0.00 0.00 0.00 2.52
5841 6309 2.926838 GACAACTGCCGCAAAAAGAAAA 59.073 40.909 0.00 0.00 0.00 2.29
5842 6310 3.530535 ACAACTGCCGCAAAAAGAAAAT 58.469 36.364 0.00 0.00 0.00 1.82
5843 6311 3.555547 ACAACTGCCGCAAAAAGAAAATC 59.444 39.130 0.00 0.00 0.00 2.17
5844 6312 2.754472 ACTGCCGCAAAAAGAAAATCC 58.246 42.857 0.00 0.00 0.00 3.01
5939 6416 4.274865 GAGTTCAAGTTCAGCTTTTCACG 58.725 43.478 0.00 0.00 34.69 4.35
5978 6456 9.937175 GCAGATTTATTACTACCATTGAGAAAC 57.063 33.333 0.00 0.00 0.00 2.78
6055 6533 8.342725 GTTCTAGAGAACCAACGAGATATTTC 57.657 38.462 10.74 0.00 46.42 2.17
6142 6620 9.939424 GAGAATTATAGGGTAGGGATACTATGT 57.061 37.037 0.00 0.00 33.43 2.29
6175 6653 9.890915 ATTAAGAGATCAGATAGTTACTCCCTT 57.109 33.333 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.386851 AGTACTATGCATTACGGAAATAGCAT 58.613 34.615 18.38 18.38 41.27 3.79
1 2 6.755206 AGTACTATGCATTACGGAAATAGCA 58.245 36.000 3.54 7.79 36.62 3.49
2 3 8.928270 ATAGTACTATGCATTACGGAAATAGC 57.072 34.615 14.71 0.00 0.00 2.97
8 9 8.188799 GCTTATGATAGTACTATGCATTACGGA 58.811 37.037 20.13 5.67 0.00 4.69
9 10 8.191446 AGCTTATGATAGTACTATGCATTACGG 58.809 37.037 20.13 12.59 0.00 4.02
25 26 9.720769 GGCAACCTAAAATACTAGCTTATGATA 57.279 33.333 0.00 0.00 0.00 2.15
26 27 8.440771 AGGCAACCTAAAATACTAGCTTATGAT 58.559 33.333 0.00 0.00 28.47 2.45
27 28 7.802117 AGGCAACCTAAAATACTAGCTTATGA 58.198 34.615 0.00 0.00 28.47 2.15
28 29 8.451908 AAGGCAACCTAAAATACTAGCTTATG 57.548 34.615 0.00 0.00 31.13 1.90
40 41 9.868277 CATGTCAATTAATAAGGCAACCTAAAA 57.132 29.630 0.02 0.00 31.13 1.52
41 42 7.978975 GCATGTCAATTAATAAGGCAACCTAAA 59.021 33.333 0.00 0.00 31.13 1.85
42 43 7.488322 GCATGTCAATTAATAAGGCAACCTAA 58.512 34.615 0.00 0.00 31.13 2.69
43 44 6.238621 CGCATGTCAATTAATAAGGCAACCTA 60.239 38.462 0.00 0.00 31.13 3.08
44 45 5.450412 CGCATGTCAATTAATAAGGCAACCT 60.450 40.000 0.00 0.00 33.87 3.50
45 46 4.739716 CGCATGTCAATTAATAAGGCAACC 59.260 41.667 0.00 0.00 37.17 3.77
46 47 5.339990 ACGCATGTCAATTAATAAGGCAAC 58.660 37.500 0.00 0.00 0.00 4.17
47 48 5.574891 ACGCATGTCAATTAATAAGGCAA 57.425 34.783 0.00 0.00 0.00 4.52
48 49 6.094186 TGTTACGCATGTCAATTAATAAGGCA 59.906 34.615 0.00 0.00 0.00 4.75
49 50 6.413818 GTGTTACGCATGTCAATTAATAAGGC 59.586 38.462 0.00 0.00 0.00 4.35
50 51 7.468441 TGTGTTACGCATGTCAATTAATAAGG 58.532 34.615 0.00 0.00 0.00 2.69
51 52 8.888332 TTGTGTTACGCATGTCAATTAATAAG 57.112 30.769 0.00 0.00 0.00 1.73
52 53 9.335891 CTTTGTGTTACGCATGTCAATTAATAA 57.664 29.630 0.00 0.00 0.00 1.40
53 54 8.508062 ACTTTGTGTTACGCATGTCAATTAATA 58.492 29.630 0.00 0.00 0.00 0.98
54 55 7.367285 ACTTTGTGTTACGCATGTCAATTAAT 58.633 30.769 0.00 0.00 0.00 1.40
55 56 6.730175 ACTTTGTGTTACGCATGTCAATTAA 58.270 32.000 0.00 0.00 0.00 1.40
56 57 6.307031 ACTTTGTGTTACGCATGTCAATTA 57.693 33.333 0.00 0.00 0.00 1.40
57 58 5.181690 ACTTTGTGTTACGCATGTCAATT 57.818 34.783 0.00 0.00 0.00 2.32
58 59 4.829064 ACTTTGTGTTACGCATGTCAAT 57.171 36.364 0.00 0.00 0.00 2.57
59 60 4.812091 ACTACTTTGTGTTACGCATGTCAA 59.188 37.500 0.00 0.00 0.00 3.18
60 61 4.373527 ACTACTTTGTGTTACGCATGTCA 58.626 39.130 0.00 0.00 0.00 3.58
61 62 4.985044 ACTACTTTGTGTTACGCATGTC 57.015 40.909 0.00 0.00 0.00 3.06
62 63 5.291178 TGTACTACTTTGTGTTACGCATGT 58.709 37.500 0.00 5.02 0.00 3.21
63 64 5.832568 TGTACTACTTTGTGTTACGCATG 57.167 39.130 0.00 0.00 0.00 4.06
64 65 5.754406 TGTTGTACTACTTTGTGTTACGCAT 59.246 36.000 8.88 0.00 0.00 4.73
65 66 5.107824 TGTTGTACTACTTTGTGTTACGCA 58.892 37.500 8.88 0.00 0.00 5.24
66 67 5.640218 TGTTGTACTACTTTGTGTTACGC 57.360 39.130 8.88 0.00 0.00 4.42
107 108 7.981102 AAATAAGAAAAGAGAGGTGTGGTAC 57.019 36.000 0.00 0.00 0.00 3.34
109 110 9.588096 AATTAAATAAGAAAAGAGAGGTGTGGT 57.412 29.630 0.00 0.00 0.00 4.16
110 111 9.846248 CAATTAAATAAGAAAAGAGAGGTGTGG 57.154 33.333 0.00 0.00 0.00 4.17
111 112 9.346725 GCAATTAAATAAGAAAAGAGAGGTGTG 57.653 33.333 0.00 0.00 0.00 3.82
112 113 8.237267 CGCAATTAAATAAGAAAAGAGAGGTGT 58.763 33.333 0.00 0.00 0.00 4.16
113 114 8.237267 ACGCAATTAAATAAGAAAAGAGAGGTG 58.763 33.333 0.00 0.00 0.00 4.00
114 115 8.237267 CACGCAATTAAATAAGAAAAGAGAGGT 58.763 33.333 0.00 0.00 0.00 3.85
115 116 8.237267 ACACGCAATTAAATAAGAAAAGAGAGG 58.763 33.333 0.00 0.00 0.00 3.69
116 117 9.267096 GACACGCAATTAAATAAGAAAAGAGAG 57.733 33.333 0.00 0.00 0.00 3.20
117 118 8.779303 TGACACGCAATTAAATAAGAAAAGAGA 58.221 29.630 0.00 0.00 0.00 3.10
118 119 8.840867 GTGACACGCAATTAAATAAGAAAAGAG 58.159 33.333 0.00 0.00 0.00 2.85
119 120 8.346300 TGTGACACGCAATTAAATAAGAAAAGA 58.654 29.630 0.22 0.00 0.00 2.52
120 121 8.500837 TGTGACACGCAATTAAATAAGAAAAG 57.499 30.769 0.22 0.00 0.00 2.27
121 122 9.123709 GATGTGACACGCAATTAAATAAGAAAA 57.876 29.630 0.22 0.00 0.00 2.29
122 123 8.293157 TGATGTGACACGCAATTAAATAAGAAA 58.707 29.630 0.22 0.00 0.00 2.52
123 124 7.811653 TGATGTGACACGCAATTAAATAAGAA 58.188 30.769 0.22 0.00 0.00 2.52
124 125 7.371126 TGATGTGACACGCAATTAAATAAGA 57.629 32.000 0.22 0.00 0.00 2.10
125 126 9.715123 TTATGATGTGACACGCAATTAAATAAG 57.285 29.630 0.22 0.00 0.00 1.73
128 129 8.978564 TTTTATGATGTGACACGCAATTAAAT 57.021 26.923 0.22 0.00 0.00 1.40
129 130 8.293157 TCTTTTATGATGTGACACGCAATTAAA 58.707 29.630 0.22 2.90 0.00 1.52
130 131 7.811653 TCTTTTATGATGTGACACGCAATTAA 58.188 30.769 0.22 0.00 0.00 1.40
131 132 7.371126 TCTTTTATGATGTGACACGCAATTA 57.629 32.000 0.22 0.00 0.00 1.40
132 133 6.252967 TCTTTTATGATGTGACACGCAATT 57.747 33.333 0.22 0.00 0.00 2.32
133 134 5.878332 TCTTTTATGATGTGACACGCAAT 57.122 34.783 0.22 0.00 0.00 3.56
134 135 5.681337 TTCTTTTATGATGTGACACGCAA 57.319 34.783 0.22 0.00 0.00 4.85
135 136 5.878332 ATTCTTTTATGATGTGACACGCA 57.122 34.783 0.22 2.24 0.00 5.24
136 137 8.841444 ATTAATTCTTTTATGATGTGACACGC 57.159 30.769 0.22 0.00 0.00 5.34
139 140 9.585099 GCCAATTAATTCTTTTATGATGTGACA 57.415 29.630 0.00 0.00 0.00 3.58
140 141 9.585099 TGCCAATTAATTCTTTTATGATGTGAC 57.415 29.630 0.00 0.00 0.00 3.67
143 144 9.048446 GCATGCCAATTAATTCTTTTATGATGT 57.952 29.630 6.36 0.00 0.00 3.06
144 145 9.047371 TGCATGCCAATTAATTCTTTTATGATG 57.953 29.630 16.68 0.00 0.00 3.07
145 146 9.787435 ATGCATGCCAATTAATTCTTTTATGAT 57.213 25.926 16.68 0.00 0.00 2.45
146 147 9.047371 CATGCATGCCAATTAATTCTTTTATGA 57.953 29.630 14.93 0.00 0.00 2.15
147 148 9.047371 TCATGCATGCCAATTAATTCTTTTATG 57.953 29.630 22.25 6.21 0.00 1.90
148 149 9.787435 ATCATGCATGCCAATTAATTCTTTTAT 57.213 25.926 22.25 0.87 0.00 1.40
150 151 9.048446 GTATCATGCATGCCAATTAATTCTTTT 57.952 29.630 22.25 0.00 0.00 2.27
151 152 7.658575 GGTATCATGCATGCCAATTAATTCTTT 59.341 33.333 22.25 0.00 37.22 2.52
152 153 7.156673 GGTATCATGCATGCCAATTAATTCTT 58.843 34.615 22.25 0.00 37.22 2.52
153 154 6.268158 TGGTATCATGCATGCCAATTAATTCT 59.732 34.615 22.25 0.00 43.86 2.40
154 155 6.457355 TGGTATCATGCATGCCAATTAATTC 58.543 36.000 22.25 6.14 43.86 2.17
155 156 6.422344 TGGTATCATGCATGCCAATTAATT 57.578 33.333 22.25 0.00 43.86 1.40
162 163 2.440517 AAGTGGTATCATGCATGCCA 57.559 45.000 22.25 19.60 44.57 4.92
163 164 5.707298 AGTAATAAGTGGTATCATGCATGCC 59.293 40.000 22.25 17.22 37.77 4.40
164 165 6.401474 CGAGTAATAAGTGGTATCATGCATGC 60.401 42.308 22.25 11.82 0.00 4.06
165 166 6.646653 ACGAGTAATAAGTGGTATCATGCATG 59.353 38.462 21.07 21.07 0.00 4.06
166 167 6.759272 ACGAGTAATAAGTGGTATCATGCAT 58.241 36.000 0.00 0.00 0.00 3.96
167 168 6.040504 AGACGAGTAATAAGTGGTATCATGCA 59.959 38.462 0.00 0.00 0.00 3.96
168 169 6.448006 AGACGAGTAATAAGTGGTATCATGC 58.552 40.000 0.00 0.00 0.00 4.06
169 170 9.395707 GTAAGACGAGTAATAAGTGGTATCATG 57.604 37.037 0.00 0.00 0.00 3.07
170 171 8.574737 GGTAAGACGAGTAATAAGTGGTATCAT 58.425 37.037 0.00 0.00 0.00 2.45
171 172 7.557358 TGGTAAGACGAGTAATAAGTGGTATCA 59.443 37.037 0.00 0.00 0.00 2.15
172 173 7.859875 GTGGTAAGACGAGTAATAAGTGGTATC 59.140 40.741 0.00 0.00 0.00 2.24
173 174 7.467811 CGTGGTAAGACGAGTAATAAGTGGTAT 60.468 40.741 0.00 0.00 42.10 2.73
174 175 6.183360 CGTGGTAAGACGAGTAATAAGTGGTA 60.183 42.308 0.00 0.00 42.10 3.25
175 176 5.392380 CGTGGTAAGACGAGTAATAAGTGGT 60.392 44.000 0.00 0.00 42.10 4.16
176 177 5.032863 CGTGGTAAGACGAGTAATAAGTGG 58.967 45.833 0.00 0.00 42.10 4.00
177 178 5.872635 TCGTGGTAAGACGAGTAATAAGTG 58.127 41.667 0.00 0.00 43.26 3.16
187 188 1.870055 GCCTGGTCGTGGTAAGACGA 61.870 60.000 0.00 0.00 45.84 4.20
188 189 1.445582 GCCTGGTCGTGGTAAGACG 60.446 63.158 0.00 0.00 39.38 4.18
189 190 0.320697 AAGCCTGGTCGTGGTAAGAC 59.679 55.000 0.00 0.00 37.86 3.01
190 191 0.606604 GAAGCCTGGTCGTGGTAAGA 59.393 55.000 0.00 0.00 0.00 2.10
191 192 0.736325 CGAAGCCTGGTCGTGGTAAG 60.736 60.000 0.00 0.00 33.80 2.34
192 193 1.180456 TCGAAGCCTGGTCGTGGTAA 61.180 55.000 6.60 0.00 39.52 2.85
193 194 1.592400 CTCGAAGCCTGGTCGTGGTA 61.592 60.000 6.60 0.00 39.52 3.25
194 195 2.915659 TCGAAGCCTGGTCGTGGT 60.916 61.111 6.60 0.00 39.52 4.16
195 196 2.125912 CTCGAAGCCTGGTCGTGG 60.126 66.667 6.60 0.00 39.52 4.94
196 197 0.319555 TTTCTCGAAGCCTGGTCGTG 60.320 55.000 6.60 4.86 39.52 4.35
197 198 0.391597 TTTTCTCGAAGCCTGGTCGT 59.608 50.000 6.60 0.00 39.52 4.34
198 199 1.394917 CATTTTCTCGAAGCCTGGTCG 59.605 52.381 0.60 0.60 39.88 4.79
199 200 2.427506 ACATTTTCTCGAAGCCTGGTC 58.572 47.619 0.00 0.00 0.00 4.02
200 201 2.568623 ACATTTTCTCGAAGCCTGGT 57.431 45.000 0.00 0.00 0.00 4.00
201 202 3.334691 TGTACATTTTCTCGAAGCCTGG 58.665 45.455 0.00 0.00 0.00 4.45
202 203 5.551760 ATTGTACATTTTCTCGAAGCCTG 57.448 39.130 0.00 0.00 0.00 4.85
203 204 6.575162 AAATTGTACATTTTCTCGAAGCCT 57.425 33.333 9.40 0.00 0.00 4.58
204 205 6.861055 TGAAAATTGTACATTTTCTCGAAGCC 59.139 34.615 26.12 11.91 44.19 4.35
205 206 7.851822 TGAAAATTGTACATTTTCTCGAAGC 57.148 32.000 26.12 12.34 44.19 3.86
206 207 9.398170 ACATGAAAATTGTACATTTTCTCGAAG 57.602 29.630 26.12 18.79 44.19 3.79
236 237 6.896860 TGAATCACCAGATATGTTTCCCAAAT 59.103 34.615 0.00 0.00 33.08 2.32
252 253 2.359850 GCACCGCCTGAATCACCA 60.360 61.111 0.00 0.00 0.00 4.17
253 254 3.134127 GGCACCGCCTGAATCACC 61.134 66.667 0.00 0.00 46.69 4.02
265 266 0.530870 GGCTCTCGAATGTAGGCACC 60.531 60.000 5.71 0.00 35.95 5.01
273 274 0.179215 GTGCGTTTGGCTCTCGAATG 60.179 55.000 0.00 0.00 44.05 2.67
277 278 2.720758 CTCGTGCGTTTGGCTCTCG 61.721 63.158 0.00 0.00 44.05 4.04
278 279 0.944311 TTCTCGTGCGTTTGGCTCTC 60.944 55.000 0.00 0.00 44.05 3.20
282 283 0.179215 CTGATTCTCGTGCGTTTGGC 60.179 55.000 0.00 0.00 43.96 4.52
287 288 0.598562 ACACTCTGATTCTCGTGCGT 59.401 50.000 0.00 0.00 0.00 5.24
288 289 0.987715 CACACTCTGATTCTCGTGCG 59.012 55.000 0.00 0.00 0.00 5.34
303 304 0.242017 GCCATTGCTCTCAACCACAC 59.758 55.000 0.00 0.00 34.60 3.82
607 612 4.241555 GATCCATGCGGCGGGAGT 62.242 66.667 16.67 7.09 36.45 3.85
684 692 1.306642 TGGCGAGAAGAGGACGAGTC 61.307 60.000 0.00 0.00 0.00 3.36
685 693 0.894184 TTGGCGAGAAGAGGACGAGT 60.894 55.000 0.00 0.00 0.00 4.18
686 694 0.243907 TTTGGCGAGAAGAGGACGAG 59.756 55.000 0.00 0.00 0.00 4.18
699 707 5.633601 GGGAGAAAATTAGAAACTTTTGGCG 59.366 40.000 0.00 0.00 0.00 5.69
725 733 0.519961 CGGGTTAAGCCACGGAAAAG 59.480 55.000 22.89 0.74 39.65 2.27
767 775 1.290009 GGTTGCCACCTGTTGATGC 59.710 57.895 0.00 0.00 40.44 3.91
812 820 0.609131 AGGTGATTTGCCCAACCGAG 60.609 55.000 0.00 0.00 0.00 4.63
814 822 1.595093 GGAGGTGATTTGCCCAACCG 61.595 60.000 0.00 0.00 0.00 4.44
853 861 0.617535 TCTCCTCCCCAAATCGCTGA 60.618 55.000 0.00 0.00 0.00 4.26
876 884 1.148759 GCACCGATTCTTCCTCGCTC 61.149 60.000 0.00 0.00 34.84 5.03
930 938 4.113815 CGGCCATTGCTCCCCAGA 62.114 66.667 2.24 0.00 37.74 3.86
986 994 5.012561 GGCCACCTCATCCTATATATGATCC 59.987 48.000 0.00 0.00 33.08 3.36
996 1004 1.457643 CCTCGGCCACCTCATCCTA 60.458 63.158 2.24 0.00 0.00 2.94
997 1005 2.765807 CCTCGGCCACCTCATCCT 60.766 66.667 2.24 0.00 0.00 3.24
1147 1161 2.523412 TATTCGGCTCGGGGGAGG 60.523 66.667 0.00 0.00 0.00 4.30
1253 1270 3.171277 CACAATTAAGCGCAGTTAAGCC 58.829 45.455 11.47 0.00 0.00 4.35
1343 1371 4.261801 TCTAAAAAGCCTCGGAAATCTGG 58.738 43.478 0.00 0.00 0.00 3.86
1391 1755 3.071479 TCATTTTCACCTGGTCTAACGC 58.929 45.455 0.00 0.00 0.00 4.84
1393 1757 5.763204 TCTTGTCATTTTCACCTGGTCTAAC 59.237 40.000 0.00 0.00 0.00 2.34
1471 1839 3.332034 GCAAAAACGCTACTAAGGAGGA 58.668 45.455 0.00 0.00 0.00 3.71
1472 1840 2.418976 GGCAAAAACGCTACTAAGGAGG 59.581 50.000 0.00 0.00 0.00 4.30
1815 2183 0.729690 GAAGTGCGCATTCCTTCCTC 59.270 55.000 22.19 6.19 30.67 3.71
1827 2195 2.154854 TCTGGAGACAAAGAAGTGCG 57.845 50.000 0.00 0.00 42.06 5.34
1894 2262 2.352422 GCCCAGAGACATGTGGCA 59.648 61.111 16.95 0.00 38.56 4.92
1903 2271 0.837691 ATCCTGTGTGTGCCCAGAGA 60.838 55.000 0.00 0.00 0.00 3.10
1913 2281 2.937149 CTCAGCATCTTCATCCTGTGTG 59.063 50.000 0.00 0.00 0.00 3.82
2108 2476 8.606040 TCTTTCCCAAAGAAATTTTTATGCTG 57.394 30.769 0.00 0.00 44.10 4.41
2674 3042 3.909086 GAGGAGGTGGTGGTGCTGC 62.909 68.421 0.00 0.00 0.00 5.25
2741 3118 3.749981 GTGCTGGTTCACCTGGTG 58.250 61.111 20.86 20.86 35.73 4.17
2747 3124 2.555547 GGTGCTGGTGCTGGTTCAC 61.556 63.158 0.00 0.00 40.48 3.18
2748 3125 2.203337 GGTGCTGGTGCTGGTTCA 60.203 61.111 0.00 0.00 40.48 3.18
2749 3126 2.203337 TGGTGCTGGTGCTGGTTC 60.203 61.111 0.00 0.00 40.48 3.62
2750 3127 2.203394 CTGGTGCTGGTGCTGGTT 60.203 61.111 0.00 0.00 40.48 3.67
2751 3128 4.962836 GCTGGTGCTGGTGCTGGT 62.963 66.667 0.00 0.00 40.48 4.00
2752 3129 4.960866 TGCTGGTGCTGGTGCTGG 62.961 66.667 0.00 0.00 40.48 4.85
2753 3130 3.667282 GTGCTGGTGCTGGTGCTG 61.667 66.667 0.00 0.00 40.48 4.41
2754 3131 4.962836 GGTGCTGGTGCTGGTGCT 62.963 66.667 0.00 0.00 40.48 4.40
2777 3154 0.251297 TGCTGGTGCTATTGCTGGTT 60.251 50.000 0.00 0.00 40.48 3.67
2785 3162 1.300963 CACCTGGTGCTGGTGCTAT 59.699 57.895 14.87 0.00 44.09 2.97
2786 3163 2.749682 CACCTGGTGCTGGTGCTA 59.250 61.111 14.87 0.00 44.09 3.49
2790 3167 2.343475 CTGGTTCACCTGGTGCTGGT 62.343 60.000 22.02 0.00 36.11 4.00
2791 3168 1.601759 CTGGTTCACCTGGTGCTGG 60.602 63.158 22.02 6.37 36.82 4.85
2792 3169 1.601759 CCTGGTTCACCTGGTGCTG 60.602 63.158 22.02 11.54 46.49 4.41
2793 3170 2.839098 CCTGGTTCACCTGGTGCT 59.161 61.111 22.02 0.00 46.49 4.40
2798 3175 1.898574 GGTGCACCTGGTTCACCTG 60.899 63.158 32.72 8.23 44.23 4.00
2799 3176 2.343475 CTGGTGCACCTGGTTCACCT 62.343 60.000 36.69 0.00 46.86 4.00
2800 3177 1.898574 CTGGTGCACCTGGTTCACC 60.899 63.158 33.15 33.15 46.91 4.02
2801 3178 2.555547 GCTGGTGCACCTGGTTCAC 61.556 63.158 35.22 19.48 39.41 3.18
2802 3179 2.203337 GCTGGTGCACCTGGTTCA 60.203 61.111 35.22 16.61 39.41 3.18
2803 3180 2.203337 TGCTGGTGCACCTGGTTC 60.203 61.111 35.22 22.94 45.31 3.62
2888 3268 4.338539 GTGCTGCTGCTGGTGCAC 62.339 66.667 17.00 8.80 45.31 4.57
2891 3271 3.667282 GTGGTGCTGCTGCTGGTG 61.667 66.667 17.00 0.00 40.48 4.17
2892 3272 4.962836 GGTGGTGCTGCTGCTGGT 62.963 66.667 17.00 0.00 40.48 4.00
2893 3273 4.960866 TGGTGGTGCTGCTGCTGG 62.961 66.667 17.00 0.00 40.48 4.85
2902 3282 4.204028 ACCTGGTGGTGGTGGTGC 62.204 66.667 0.00 0.00 46.51 5.01
3875 4318 2.892374 TGGAGCACAGTTCATGTATCG 58.108 47.619 0.00 0.00 41.41 2.92
4593 5053 1.073722 CTGTTCTGCTCCTTGGCCA 59.926 57.895 0.00 0.00 0.00 5.36
4882 5342 1.605058 GCGCCTGGGAGTTCTCTACA 61.605 60.000 0.00 0.00 0.00 2.74
5191 5651 2.897350 CCTTGGATCGCGGGCTTC 60.897 66.667 6.13 0.00 0.00 3.86
5419 5883 3.011144 TCCCATCCCATTGCTCTAACAAA 59.989 43.478 0.00 0.00 32.27 2.83
5430 5894 3.822097 GGATCTTCATCCCATCCCATT 57.178 47.619 0.00 0.00 42.91 3.16
5442 5906 2.307768 CTACCTACGCTGGGATCTTCA 58.692 52.381 0.00 0.00 0.00 3.02
5443 5907 1.614413 CCTACCTACGCTGGGATCTTC 59.386 57.143 0.00 0.00 0.00 2.87
5444 5908 1.705873 CCTACCTACGCTGGGATCTT 58.294 55.000 0.00 0.00 0.00 2.40
5445 5909 0.178958 CCCTACCTACGCTGGGATCT 60.179 60.000 0.00 0.00 42.11 2.75
5446 5910 0.469518 ACCCTACCTACGCTGGGATC 60.470 60.000 3.70 0.00 42.11 3.36
5447 5911 0.855598 TACCCTACCTACGCTGGGAT 59.144 55.000 3.70 0.00 42.11 3.85
5707 6175 0.035056 ATGCAGAGGCCAGGTGTTAC 60.035 55.000 5.01 0.00 40.13 2.50
5713 6181 0.394762 TTTGCTATGCAGAGGCCAGG 60.395 55.000 10.92 0.00 40.61 4.45
5714 6182 1.466856 TTTTGCTATGCAGAGGCCAG 58.533 50.000 10.92 0.00 40.61 4.85
5821 6289 2.663826 TTTCTTTTTGCGGCAGTTGT 57.336 40.000 1.67 0.00 0.00 3.32
5966 6444 3.317711 TGCATTGTTCGTTTCTCAATGGT 59.682 39.130 15.50 0.00 44.60 3.55
5978 6456 6.803320 AGAATACTCAAATTGTGCATTGTTCG 59.197 34.615 0.00 0.00 0.00 3.95
6045 6523 2.290641 CCCCCGCAAAAGAAATATCTCG 59.709 50.000 0.00 0.00 33.77 4.04
6055 6533 0.825840 TTGGTTCTCCCCCGCAAAAG 60.826 55.000 0.00 0.00 0.00 2.27
6152 6630 9.890915 ATAAAGGGAGTAACTATCTGATCTCTT 57.109 33.333 0.00 0.00 0.00 2.85
6211 7008 1.589716 GCCCATATGCGGCCATCTTC 61.590 60.000 19.18 0.00 40.78 2.87


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

AutoCloner maintained by Alex Coulton.