Multiple sequence alignment - TraesCS6A01G310400

Loading Multiple Alignment...

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 TraesCS6A01G310400 chr6A 100.000 3082 0 0 1 3082 546598156 546601237 0.000000e+00 5692.0
1 TraesCS6A01G310400 chr6D 89.437 2414 138 56 699 3082 400650566 400652892 0.000000e+00 2937.0
2 TraesCS6A01G310400 chr6D 87.328 363 32 8 2450 2804 400566221 400566577 1.330000e-108 403.0
3 TraesCS6A01G310400 chr6D 84.553 123 8 5 406 518 400650278 400650399 9.030000e-21 111.0
4 TraesCS6A01G310400 chr6D 76.991 113 24 2 48 159 445795263 445795374 2.570000e-06 63.9
5 TraesCS6A01G310400 chr6B 90.265 1130 67 24 1959 3082 599694445 599695537 0.000000e+00 1437.0
6 TraesCS6A01G310400 chr6B 86.261 1281 92 35 699 1945 599693124 599694354 0.000000e+00 1314.0
7 TraesCS6A01G310400 chr6B 85.986 421 44 8 233 650 599692592 599693000 1.310000e-118 436.0
8 TraesCS6A01G310400 chr6B 88.750 240 16 7 2848 3082 267749804 267749571 1.810000e-72 283.0
9 TraesCS6A01G310400 chr6B 92.063 126 6 2 2662 2787 267749936 267749815 1.140000e-39 174.0
10 TraesCS6A01G310400 chr7A 89.540 239 15 6 2848 3082 53341977 53341745 8.360000e-76 294.0
11 TraesCS6A01G310400 chr7A 91.870 123 6 2 2662 2784 53342109 53341991 5.290000e-38 169.0
12 TraesCS6A01G310400 chr7A 90.179 112 11 0 1134 1245 155951991 155952102 2.480000e-31 147.0
13 TraesCS6A01G310400 chr4A 89.121 239 16 5 2848 3082 445280237 445280469 3.890000e-74 289.0
14 TraesCS6A01G310400 chr4A 87.029 239 21 5 2848 3082 110273240 110273472 8.480000e-66 261.0
15 TraesCS6A01G310400 chr4A 93.966 116 3 2 2669 2784 110273115 110273226 4.090000e-39 172.0
16 TraesCS6A01G310400 chr4A 93.966 116 3 2 2669 2784 445280112 445280223 4.090000e-39 172.0
17 TraesCS6A01G310400 chr4A 90.551 127 8 2 2662 2787 167814269 167814146 6.840000e-37 165.0
18 TraesCS6A01G310400 chr4A 79.343 213 26 6 1445 1643 593487571 593487363 1.930000e-27 134.0
19 TraesCS6A01G310400 chr1A 87.866 239 17 8 2848 3082 63974194 63974424 1.410000e-68 270.0
20 TraesCS6A01G310400 chr1A 93.966 116 3 2 2669 2784 63974069 63974180 4.090000e-39 172.0
21 TraesCS6A01G310400 chr5A 87.448 239 20 5 2848 3082 407308669 407308437 1.820000e-67 267.0
22 TraesCS6A01G310400 chr2A 87.712 236 19 6 2848 3079 461740502 461740731 1.820000e-67 267.0
23 TraesCS6A01G310400 chr1B 96.429 112 4 0 1141 1252 727951 728062 5.250000e-43 185.0
24 TraesCS6A01G310400 chr1B 86.806 144 9 5 2855 2993 732158 732296 5.320000e-33 152.0
25 TraesCS6A01G310400 chr7B 82.212 208 25 5 1050 1245 115961879 115962086 5.290000e-38 169.0
26 TraesCS6A01G310400 chr7D 89.286 112 12 0 1134 1245 153972103 153972214 1.150000e-29 141.0
27 TraesCS6A01G310400 chr4B 94.737 38 1 1 1467 1504 104915039 104915003 1.190000e-04 58.4


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 TraesCS6A01G310400 chr6A 546598156 546601237 3081 False 5692.000000 5692 100.000 1 3082 1 chr6A.!!$F1 3081
1 TraesCS6A01G310400 chr6D 400650278 400652892 2614 False 1524.000000 2937 86.995 406 3082 2 chr6D.!!$F3 2676
2 TraesCS6A01G310400 chr6B 599692592 599695537 2945 False 1062.333333 1437 87.504 233 3082 3 chr6B.!!$F1 2849

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
542 547 0.035439 AAATCAGGCGACCGGTTCAT 60.035 50.0 9.42 0.0 0.0 2.57 F
576 581 0.179001 AAACAAAGGGGAGGTCACGG 60.179 55.0 0.00 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1418 1527 0.109597 GTGGTGCAAAGCCTGAATCG 60.110 55.0 0.0 0.0 0.0 3.34 R
2510 2717 0.179192 CCATCATGTCAACAACGCCG 60.179 55.0 0.0 0.0 0.0 6.46 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
17 18 4.597032 TTGGGTGGTTGAGCAAGG 57.403 55.556 0.00 0.00 0.00 3.61
18 19 1.926657 TTGGGTGGTTGAGCAAGGA 59.073 52.632 0.00 0.00 0.00 3.36
19 20 0.178992 TTGGGTGGTTGAGCAAGGAG 60.179 55.000 0.00 0.00 0.00 3.69
20 21 1.352622 TGGGTGGTTGAGCAAGGAGT 61.353 55.000 0.00 0.00 0.00 3.85
21 22 0.890996 GGGTGGTTGAGCAAGGAGTG 60.891 60.000 0.00 0.00 0.00 3.51
37 38 7.087409 CAAGGAGTGCACAATGAATATAACA 57.913 36.000 21.04 0.00 0.00 2.41
38 39 6.683974 AGGAGTGCACAATGAATATAACAC 57.316 37.500 21.04 0.00 0.00 3.32
39 40 5.294306 AGGAGTGCACAATGAATATAACACG 59.706 40.000 21.04 0.00 32.22 4.49
40 41 5.293324 GGAGTGCACAATGAATATAACACGA 59.707 40.000 21.04 0.00 32.22 4.35
41 42 6.183360 GGAGTGCACAATGAATATAACACGAA 60.183 38.462 21.04 0.00 32.22 3.85
42 43 7.139896 AGTGCACAATGAATATAACACGAAA 57.860 32.000 21.04 0.00 32.22 3.46
43 44 7.589395 AGTGCACAATGAATATAACACGAAAA 58.411 30.769 21.04 0.00 32.22 2.29
44 45 8.243426 AGTGCACAATGAATATAACACGAAAAT 58.757 29.630 21.04 0.00 32.22 1.82
45 46 9.497030 GTGCACAATGAATATAACACGAAAATA 57.503 29.630 13.17 0.00 0.00 1.40
58 59 7.899178 AACACGAAAATATATGTCACAGTGA 57.101 32.000 0.00 0.00 0.00 3.41
59 60 7.899178 ACACGAAAATATATGTCACAGTGAA 57.101 32.000 4.32 0.00 0.00 3.18
60 61 8.492673 ACACGAAAATATATGTCACAGTGAAT 57.507 30.769 4.32 4.34 0.00 2.57
61 62 8.390354 ACACGAAAATATATGTCACAGTGAATG 58.610 33.333 4.32 0.00 0.00 2.67
62 63 8.390354 CACGAAAATATATGTCACAGTGAATGT 58.610 33.333 4.32 3.00 45.43 2.71
63 64 9.594478 ACGAAAATATATGTCACAGTGAATGTA 57.406 29.630 4.32 5.01 41.41 2.29
69 70 9.755804 ATATATGTCACAGTGAATGTAGTGAAG 57.244 33.333 4.32 0.00 41.41 3.02
70 71 4.058124 TGTCACAGTGAATGTAGTGAAGC 58.942 43.478 4.32 0.00 41.41 3.86
71 72 4.058124 GTCACAGTGAATGTAGTGAAGCA 58.942 43.478 4.32 0.00 41.41 3.91
72 73 4.511454 GTCACAGTGAATGTAGTGAAGCAA 59.489 41.667 4.32 0.00 41.41 3.91
73 74 5.007626 GTCACAGTGAATGTAGTGAAGCAAA 59.992 40.000 4.32 0.00 41.41 3.68
74 75 5.764686 TCACAGTGAATGTAGTGAAGCAAAT 59.235 36.000 0.00 0.00 41.41 2.32
75 76 6.073058 TCACAGTGAATGTAGTGAAGCAAATC 60.073 38.462 0.00 0.00 41.41 2.17
76 77 6.000219 ACAGTGAATGTAGTGAAGCAAATCT 59.000 36.000 0.00 0.00 41.60 2.40
77 78 6.072838 ACAGTGAATGTAGTGAAGCAAATCTG 60.073 38.462 0.00 0.00 41.60 2.90
78 79 5.413833 AGTGAATGTAGTGAAGCAAATCTGG 59.586 40.000 0.00 0.00 0.00 3.86
79 80 5.182001 GTGAATGTAGTGAAGCAAATCTGGT 59.818 40.000 0.00 0.00 33.72 4.00
80 81 5.181811 TGAATGTAGTGAAGCAAATCTGGTG 59.818 40.000 0.00 0.00 32.31 4.17
81 82 4.085357 TGTAGTGAAGCAAATCTGGTGT 57.915 40.909 0.00 0.00 32.31 4.16
82 83 4.460263 TGTAGTGAAGCAAATCTGGTGTT 58.540 39.130 0.00 0.00 32.31 3.32
83 84 5.616270 TGTAGTGAAGCAAATCTGGTGTTA 58.384 37.500 0.00 0.00 32.31 2.41
84 85 6.237901 TGTAGTGAAGCAAATCTGGTGTTAT 58.762 36.000 0.00 0.00 32.31 1.89
85 86 7.390823 TGTAGTGAAGCAAATCTGGTGTTATA 58.609 34.615 0.00 0.00 32.31 0.98
86 87 6.992063 AGTGAAGCAAATCTGGTGTTATAG 57.008 37.500 0.00 0.00 32.31 1.31
87 88 6.711277 AGTGAAGCAAATCTGGTGTTATAGA 58.289 36.000 0.00 0.00 32.31 1.98
88 89 7.341805 AGTGAAGCAAATCTGGTGTTATAGAT 58.658 34.615 0.00 0.00 35.25 1.98
89 90 7.281774 AGTGAAGCAAATCTGGTGTTATAGATG 59.718 37.037 0.00 0.00 34.09 2.90
90 91 7.066284 GTGAAGCAAATCTGGTGTTATAGATGT 59.934 37.037 0.00 0.00 34.09 3.06
91 92 7.611467 TGAAGCAAATCTGGTGTTATAGATGTT 59.389 33.333 0.00 0.00 34.09 2.71
92 93 7.325660 AGCAAATCTGGTGTTATAGATGTTG 57.674 36.000 0.00 0.00 34.09 3.33
93 94 6.319658 AGCAAATCTGGTGTTATAGATGTTGG 59.680 38.462 0.00 0.00 34.09 3.77
94 95 6.095440 GCAAATCTGGTGTTATAGATGTTGGT 59.905 38.462 0.00 0.00 34.09 3.67
95 96 7.282224 GCAAATCTGGTGTTATAGATGTTGGTA 59.718 37.037 0.00 0.00 34.09 3.25
96 97 9.342308 CAAATCTGGTGTTATAGATGTTGGTAT 57.658 33.333 0.00 0.00 34.09 2.73
131 132 8.635765 TTGACTTTATCAAGCTTGATTAGGTT 57.364 30.769 39.03 22.94 45.13 3.50
132 133 8.635765 TGACTTTATCAAGCTTGATTAGGTTT 57.364 30.769 39.03 22.64 45.13 3.27
133 134 8.514594 TGACTTTATCAAGCTTGATTAGGTTTG 58.485 33.333 39.03 24.74 45.13 2.93
134 135 8.635765 ACTTTATCAAGCTTGATTAGGTTTGA 57.364 30.769 39.03 20.74 45.13 2.69
135 136 8.734386 ACTTTATCAAGCTTGATTAGGTTTGAG 58.266 33.333 39.03 26.08 45.13 3.02
136 137 8.635765 TTTATCAAGCTTGATTAGGTTTGAGT 57.364 30.769 39.03 18.99 45.13 3.41
137 138 8.635765 TTATCAAGCTTGATTAGGTTTGAGTT 57.364 30.769 39.03 18.81 45.13 3.01
138 139 9.733556 TTATCAAGCTTGATTAGGTTTGAGTTA 57.266 29.630 39.03 18.77 45.13 2.24
139 140 7.672983 TCAAGCTTGATTAGGTTTGAGTTAG 57.327 36.000 25.16 0.00 42.49 2.34
140 141 6.655003 TCAAGCTTGATTAGGTTTGAGTTAGG 59.345 38.462 25.16 0.00 42.49 2.69
141 142 6.374417 AGCTTGATTAGGTTTGAGTTAGGA 57.626 37.500 0.00 0.00 0.00 2.94
142 143 6.174049 AGCTTGATTAGGTTTGAGTTAGGAC 58.826 40.000 0.00 0.00 0.00 3.85
143 144 5.938125 GCTTGATTAGGTTTGAGTTAGGACA 59.062 40.000 0.00 0.00 0.00 4.02
144 145 6.430000 GCTTGATTAGGTTTGAGTTAGGACAA 59.570 38.462 0.00 0.00 0.00 3.18
145 146 7.121315 GCTTGATTAGGTTTGAGTTAGGACAAT 59.879 37.037 0.00 0.00 0.00 2.71
146 147 9.667107 CTTGATTAGGTTTGAGTTAGGACAATA 57.333 33.333 0.00 0.00 0.00 1.90
153 154 9.668497 AGGTTTGAGTTAGGACAATATTAGAAC 57.332 33.333 0.00 0.00 0.00 3.01
154 155 9.668497 GGTTTGAGTTAGGACAATATTAGAACT 57.332 33.333 0.00 0.00 0.00 3.01
164 165 7.550906 AGGACAATATTAGAACTTCAAGTCTGC 59.449 37.037 0.00 0.00 0.00 4.26
165 166 7.334421 GGACAATATTAGAACTTCAAGTCTGCA 59.666 37.037 0.00 0.00 0.00 4.41
166 167 8.621532 ACAATATTAGAACTTCAAGTCTGCAA 57.378 30.769 0.00 0.00 0.00 4.08
167 168 9.236006 ACAATATTAGAACTTCAAGTCTGCAAT 57.764 29.630 0.00 0.00 0.00 3.56
171 172 8.854614 ATTAGAACTTCAAGTCTGCAATTACT 57.145 30.769 0.00 0.00 0.00 2.24
172 173 8.677148 TTAGAACTTCAAGTCTGCAATTACTT 57.323 30.769 0.00 3.56 36.38 2.24
173 174 7.573968 AGAACTTCAAGTCTGCAATTACTTT 57.426 32.000 6.13 0.00 33.72 2.66
174 175 7.420800 AGAACTTCAAGTCTGCAATTACTTTG 58.579 34.615 6.13 3.88 33.72 2.77
175 176 6.076981 ACTTCAAGTCTGCAATTACTTTGG 57.923 37.500 6.13 3.56 33.72 3.28
176 177 5.827797 ACTTCAAGTCTGCAATTACTTTGGA 59.172 36.000 6.13 0.92 33.72 3.53
177 178 6.321181 ACTTCAAGTCTGCAATTACTTTGGAA 59.679 34.615 6.13 7.17 35.02 3.53
178 179 6.899393 TCAAGTCTGCAATTACTTTGGAAT 57.101 33.333 6.13 0.00 35.02 3.01
179 180 6.680810 TCAAGTCTGCAATTACTTTGGAATG 58.319 36.000 6.13 0.00 35.02 2.67
180 181 5.649782 AGTCTGCAATTACTTTGGAATGG 57.350 39.130 0.00 0.00 35.02 3.16
181 182 5.324409 AGTCTGCAATTACTTTGGAATGGA 58.676 37.500 0.00 0.00 35.02 3.41
182 183 5.416952 AGTCTGCAATTACTTTGGAATGGAG 59.583 40.000 0.00 0.00 35.02 3.86
183 184 4.706476 TCTGCAATTACTTTGGAATGGAGG 59.294 41.667 0.00 0.00 35.02 4.30
184 185 3.768757 TGCAATTACTTTGGAATGGAGGG 59.231 43.478 0.00 0.00 35.75 4.30
185 186 4.023291 GCAATTACTTTGGAATGGAGGGA 58.977 43.478 0.00 0.00 35.75 4.20
186 187 4.098501 GCAATTACTTTGGAATGGAGGGAG 59.901 45.833 0.00 0.00 35.75 4.30
187 188 5.264395 CAATTACTTTGGAATGGAGGGAGT 58.736 41.667 0.00 0.00 0.00 3.85
188 189 6.423182 CAATTACTTTGGAATGGAGGGAGTA 58.577 40.000 0.00 0.00 0.00 2.59
189 190 5.693769 TTACTTTGGAATGGAGGGAGTAG 57.306 43.478 0.00 0.00 0.00 2.57
190 191 2.239907 ACTTTGGAATGGAGGGAGTAGC 59.760 50.000 0.00 0.00 0.00 3.58
191 192 1.213296 TTGGAATGGAGGGAGTAGCC 58.787 55.000 0.00 0.00 0.00 3.93
203 204 2.760374 GGAGTAGCCCTGAATGATTCG 58.240 52.381 0.18 0.00 0.00 3.34
204 205 2.103263 GGAGTAGCCCTGAATGATTCGT 59.897 50.000 0.18 0.00 0.00 3.85
205 206 3.321111 GGAGTAGCCCTGAATGATTCGTA 59.679 47.826 0.18 0.00 0.00 3.43
206 207 4.021016 GGAGTAGCCCTGAATGATTCGTAT 60.021 45.833 0.18 0.00 0.00 3.06
207 208 5.140747 AGTAGCCCTGAATGATTCGTATC 57.859 43.478 0.18 0.00 0.00 2.24
208 209 4.588951 AGTAGCCCTGAATGATTCGTATCA 59.411 41.667 7.21 7.21 44.52 2.15
209 210 4.422073 AGCCCTGAATGATTCGTATCAA 57.578 40.909 8.88 0.00 43.67 2.57
210 211 4.978099 AGCCCTGAATGATTCGTATCAAT 58.022 39.130 8.88 0.09 43.67 2.57
211 212 5.380043 AGCCCTGAATGATTCGTATCAATT 58.620 37.500 8.88 4.49 43.67 2.32
212 213 6.533730 AGCCCTGAATGATTCGTATCAATTA 58.466 36.000 8.88 0.00 43.67 1.40
213 214 6.998074 AGCCCTGAATGATTCGTATCAATTAA 59.002 34.615 8.88 0.00 43.67 1.40
214 215 7.173907 AGCCCTGAATGATTCGTATCAATTAAG 59.826 37.037 8.88 6.68 43.67 1.85
215 216 7.301054 CCCTGAATGATTCGTATCAATTAAGC 58.699 38.462 8.88 0.00 43.67 3.09
216 217 7.173907 CCCTGAATGATTCGTATCAATTAAGCT 59.826 37.037 8.88 0.00 43.67 3.74
217 218 8.226448 CCTGAATGATTCGTATCAATTAAGCTC 58.774 37.037 8.88 0.00 43.67 4.09
218 219 8.893219 TGAATGATTCGTATCAATTAAGCTCT 57.107 30.769 8.88 0.00 43.67 4.09
219 220 8.982685 TGAATGATTCGTATCAATTAAGCTCTC 58.017 33.333 8.88 0.00 43.67 3.20
220 221 9.202273 GAATGATTCGTATCAATTAAGCTCTCT 57.798 33.333 8.88 0.00 43.67 3.10
221 222 9.553064 AATGATTCGTATCAATTAAGCTCTCTT 57.447 29.630 8.88 0.00 43.67 2.85
222 223 8.948631 TGATTCGTATCAATTAAGCTCTCTTT 57.051 30.769 1.81 0.00 37.83 2.52
223 224 9.383519 TGATTCGTATCAATTAAGCTCTCTTTT 57.616 29.630 1.81 0.00 37.83 2.27
254 255 8.624776 GGAATATCAATTAAGGTCTTGGTTCAG 58.375 37.037 0.00 0.00 0.00 3.02
257 258 6.121776 TCAATTAAGGTCTTGGTTCAGCTA 57.878 37.500 0.00 0.00 0.00 3.32
261 262 8.306761 CAATTAAGGTCTTGGTTCAGCTAAAAT 58.693 33.333 0.00 0.00 0.00 1.82
295 296 8.891671 AAAGCTCTTGATTTGCAATAAGAAAA 57.108 26.923 16.89 0.00 35.59 2.29
328 329 1.760029 GGGAGATCCTGTCCAGAAGAC 59.240 57.143 0.00 0.00 46.51 3.01
356 357 2.100584 CACTCCTAGATGCTCACTGGTC 59.899 54.545 0.00 0.00 0.00 4.02
365 366 0.247736 GCTCACTGGTCGATGAACCT 59.752 55.000 0.00 0.00 40.20 3.50
376 377 4.392138 GGTCGATGAACCTTAAACTCCTTG 59.608 45.833 0.00 0.00 36.32 3.61
391 392 4.652822 ACTCCTTGGATAACTTGGTCAAC 58.347 43.478 0.00 0.00 0.00 3.18
394 395 2.483014 TGGATAACTTGGTCAACCCG 57.517 50.000 0.00 0.00 35.15 5.28
453 458 3.130340 TGGGCCAATTCGAAGCTTAATTC 59.870 43.478 2.13 0.00 0.00 2.17
487 492 2.833533 GCACTTGCTGCCGTGACAA 61.834 57.895 19.20 0.00 40.42 3.18
488 493 1.280746 CACTTGCTGCCGTGACAAG 59.719 57.895 12.16 3.88 44.98 3.16
491 496 4.560743 TGCTGCCGTGACAAGCCA 62.561 61.111 0.00 0.00 0.00 4.75
493 498 2.844451 GCTGCCGTGACAAGCCAAA 61.844 57.895 0.00 0.00 0.00 3.28
494 499 1.008538 CTGCCGTGACAAGCCAAAC 60.009 57.895 0.00 0.00 0.00 2.93
495 500 1.723608 CTGCCGTGACAAGCCAAACA 61.724 55.000 0.00 0.00 0.00 2.83
496 501 1.315981 TGCCGTGACAAGCCAAACAA 61.316 50.000 0.00 0.00 0.00 2.83
497 502 0.594796 GCCGTGACAAGCCAAACAAG 60.595 55.000 0.00 0.00 0.00 3.16
536 541 1.490693 CGGATCAAATCAGGCGACCG 61.491 60.000 0.00 0.00 0.00 4.79
542 547 0.035439 AAATCAGGCGACCGGTTCAT 60.035 50.000 9.42 0.00 0.00 2.57
544 549 2.311688 ATCAGGCGACCGGTTCATCC 62.312 60.000 9.42 7.93 0.00 3.51
575 580 1.687563 AAAACAAAGGGGAGGTCACG 58.312 50.000 0.00 0.00 0.00 4.35
576 581 0.179001 AAACAAAGGGGAGGTCACGG 60.179 55.000 0.00 0.00 0.00 4.94
637 642 3.922240 GCTGTAATTTCGTCCGACAGTAA 59.078 43.478 0.00 0.00 39.75 2.24
638 643 4.201561 GCTGTAATTTCGTCCGACAGTAAC 60.202 45.833 0.00 0.00 39.75 2.50
650 655 5.410439 GTCCGACAGTAACAATAACCAACAT 59.590 40.000 0.00 0.00 0.00 2.71
651 656 5.998981 TCCGACAGTAACAATAACCAACATT 59.001 36.000 0.00 0.00 0.00 2.71
653 658 6.799925 CCGACAGTAACAATAACCAACATTTC 59.200 38.462 0.00 0.00 0.00 2.17
654 659 7.356540 CGACAGTAACAATAACCAACATTTCA 58.643 34.615 0.00 0.00 0.00 2.69
655 660 7.858382 CGACAGTAACAATAACCAACATTTCAA 59.142 33.333 0.00 0.00 0.00 2.69
657 662 9.691362 ACAGTAACAATAACCAACATTTCAATC 57.309 29.630 0.00 0.00 0.00 2.67
658 663 9.689976 CAGTAACAATAACCAACATTTCAATCA 57.310 29.630 0.00 0.00 0.00 2.57
691 711 4.341806 ACATTTCATTCAGCAGAACCAACA 59.658 37.500 0.00 0.00 36.39 3.33
692 712 5.011329 ACATTTCATTCAGCAGAACCAACAT 59.989 36.000 0.00 0.00 36.39 2.71
693 713 5.534207 TTTCATTCAGCAGAACCAACATT 57.466 34.783 0.00 0.00 36.39 2.71
694 714 5.534207 TTCATTCAGCAGAACCAACATTT 57.466 34.783 0.00 0.00 36.39 2.32
697 717 4.998671 TTCAGCAGAACCAACATTTCAA 57.001 36.364 0.00 0.00 0.00 2.69
830 921 2.599578 AGCCAACCAAGCAGCCAG 60.600 61.111 0.00 0.00 0.00 4.85
831 922 4.368543 GCCAACCAAGCAGCCAGC 62.369 66.667 0.00 0.00 46.19 4.85
884 975 0.956633 GACGTATCCGGCCATGACTA 59.043 55.000 2.24 0.00 35.50 2.59
909 1000 3.723348 GTTTCCTCCCACGCGTGC 61.723 66.667 33.17 13.44 0.00 5.34
978 1074 1.577328 CCGCGCATGCCCCTATAAAG 61.577 60.000 13.15 0.00 38.08 1.85
1035 1131 5.349824 AGCTTTTTGTTCGTCTCTTGATC 57.650 39.130 0.00 0.00 0.00 2.92
1044 1140 2.540516 TCGTCTCTTGATCGAGATCGTC 59.459 50.000 24.20 10.17 41.67 4.20
1045 1141 2.542178 CGTCTCTTGATCGAGATCGTCT 59.458 50.000 13.24 0.00 41.67 4.18
1332 1441 1.075050 CCTGGAGGATGGAATGGATGG 59.925 57.143 0.00 0.00 37.39 3.51
1338 1447 3.065940 AGGATGGAATGGATGGATGGAA 58.934 45.455 0.00 0.00 0.00 3.53
1411 1520 6.915349 TGGTTGTGTACATATAGTTTTTGCC 58.085 36.000 0.00 0.00 0.00 4.52
1412 1521 6.025280 GGTTGTGTACATATAGTTTTTGCCG 58.975 40.000 0.00 0.00 0.00 5.69
1413 1522 6.348704 GGTTGTGTACATATAGTTTTTGCCGT 60.349 38.462 0.00 0.00 0.00 5.68
1414 1523 6.804770 TGTGTACATATAGTTTTTGCCGTT 57.195 33.333 0.00 0.00 0.00 4.44
1415 1524 6.833839 TGTGTACATATAGTTTTTGCCGTTC 58.166 36.000 0.00 0.00 0.00 3.95
1418 1527 7.691050 GTGTACATATAGTTTTTGCCGTTCTTC 59.309 37.037 0.00 0.00 0.00 2.87
1427 1536 1.019278 TGCCGTTCTTCGATTCAGGC 61.019 55.000 11.04 11.04 42.86 4.85
1430 1539 2.076863 CCGTTCTTCGATTCAGGCTTT 58.923 47.619 0.00 0.00 42.86 3.51
1446 1555 1.874739 GCTTTGCACCACCACGTAGTA 60.875 52.381 0.00 0.00 41.61 1.82
1447 1556 2.066262 CTTTGCACCACCACGTAGTAG 58.934 52.381 0.00 0.00 41.61 2.57
1450 1559 1.475280 TGCACCACCACGTAGTAGATC 59.525 52.381 0.00 0.00 41.61 2.75
1451 1560 1.475280 GCACCACCACGTAGTAGATCA 59.525 52.381 0.00 0.00 41.61 2.92
1452 1561 2.479730 GCACCACCACGTAGTAGATCAG 60.480 54.545 0.00 0.00 41.61 2.90
1516 1626 2.231478 TCCTTGTGTCCTGTTCTCGATC 59.769 50.000 0.00 0.00 0.00 3.69
1544 1654 5.449588 CCGATGAAATTTGCTGCTGATTAGT 60.450 40.000 0.00 0.00 0.00 2.24
1555 1665 3.585862 TGCTGATTAGTTTCGTCCACTC 58.414 45.455 0.00 0.00 0.00 3.51
1680 1804 1.408340 TCTGAGTAGATGCTGCAGAGC 59.592 52.381 20.43 3.99 46.44 4.09
1804 1929 7.502226 TCCACTTCTGTTTCAACACAAAGATAT 59.498 33.333 13.37 0.00 33.79 1.63
1836 1961 7.232127 ACTGAGAAACTGATGTGGAAATTTCAT 59.768 33.333 19.49 5.59 0.00 2.57
1983 2185 5.675575 GCTGCAGACATTTTTAGAGATGGTG 60.676 44.000 20.43 0.00 0.00 4.17
2021 2223 6.573664 TGTCTAAAATAGTTGCATGCTTGT 57.426 33.333 20.33 5.36 0.00 3.16
2035 2237 4.505566 GCATGCTTGTCCCTCTATATGGAA 60.506 45.833 11.37 0.00 31.03 3.53
2069 2271 7.798982 CGAAAGTTCAACTCAGAAGAATAAACC 59.201 37.037 0.00 0.00 0.00 3.27
2108 2314 1.960689 TGAGATGGTGAACGTCAGTGA 59.039 47.619 0.00 0.00 37.58 3.41
2109 2315 2.029918 TGAGATGGTGAACGTCAGTGAG 60.030 50.000 0.00 0.00 37.58 3.51
2110 2316 1.964223 AGATGGTGAACGTCAGTGAGT 59.036 47.619 0.00 0.00 37.58 3.41
2111 2317 2.029828 AGATGGTGAACGTCAGTGAGTC 60.030 50.000 0.00 0.00 37.58 3.36
2112 2318 1.399714 TGGTGAACGTCAGTGAGTCT 58.600 50.000 0.00 0.00 0.00 3.24
2113 2319 1.067060 TGGTGAACGTCAGTGAGTCTG 59.933 52.381 0.00 0.00 44.85 3.51
2114 2320 1.067212 GGTGAACGTCAGTGAGTCTGT 59.933 52.381 0.00 0.00 43.97 3.41
2115 2321 2.120232 GTGAACGTCAGTGAGTCTGTG 58.880 52.381 0.00 0.00 43.97 3.66
2116 2322 2.021457 TGAACGTCAGTGAGTCTGTGA 58.979 47.619 0.00 0.00 43.97 3.58
2117 2323 2.033424 TGAACGTCAGTGAGTCTGTGAG 59.967 50.000 0.00 0.00 43.97 3.51
2118 2324 1.681538 ACGTCAGTGAGTCTGTGAGT 58.318 50.000 0.00 0.00 43.97 3.41
2119 2325 1.335182 ACGTCAGTGAGTCTGTGAGTG 59.665 52.381 0.00 0.00 43.97 3.51
2205 2411 5.509832 TGATGCTCATAGAAAGCCCATAT 57.490 39.130 0.00 0.00 39.05 1.78
2283 2489 6.605594 TGTAGAGTCACCCAATTTTTCACTTT 59.394 34.615 0.00 0.00 0.00 2.66
2332 2538 7.156000 TCTTCAGTCGTGTACCAATTCATTTA 58.844 34.615 0.00 0.00 0.00 1.40
2333 2539 7.822334 TCTTCAGTCGTGTACCAATTCATTTAT 59.178 33.333 0.00 0.00 0.00 1.40
2334 2540 9.093970 CTTCAGTCGTGTACCAATTCATTTATA 57.906 33.333 0.00 0.00 0.00 0.98
2415 2621 2.472695 TGCACACTGACTAACCATCC 57.527 50.000 0.00 0.00 0.00 3.51
2416 2622 1.977854 TGCACACTGACTAACCATCCT 59.022 47.619 0.00 0.00 0.00 3.24
2417 2623 2.028112 TGCACACTGACTAACCATCCTC 60.028 50.000 0.00 0.00 0.00 3.71
2418 2624 2.234908 GCACACTGACTAACCATCCTCT 59.765 50.000 0.00 0.00 0.00 3.69
2419 2625 3.447586 GCACACTGACTAACCATCCTCTA 59.552 47.826 0.00 0.00 0.00 2.43
2420 2626 4.440802 GCACACTGACTAACCATCCTCTAG 60.441 50.000 0.00 0.00 0.00 2.43
2421 2627 4.098654 CACACTGACTAACCATCCTCTAGG 59.901 50.000 0.00 0.00 0.00 3.02
2455 2661 1.642037 CTGCTTGCCGATGTGGAGTG 61.642 60.000 0.00 0.00 42.00 3.51
2491 2698 1.401931 CGCTGGAAGAACATTGGCAAG 60.402 52.381 5.96 0.50 34.07 4.01
2498 2705 1.202758 AGAACATTGGCAAGGACACGA 60.203 47.619 19.84 0.00 0.00 4.35
2510 2717 4.612939 GCAAGGACACGATTTCACCTAAAC 60.613 45.833 0.00 0.00 0.00 2.01
2512 2719 2.414138 GGACACGATTTCACCTAAACGG 59.586 50.000 0.00 0.00 39.35 4.44
2553 2760 4.267357 TCGTGACTAACAAAGTGCAAAC 57.733 40.909 0.00 0.00 39.07 2.93
2559 2766 5.359576 TGACTAACAAAGTGCAAACCAGATT 59.640 36.000 0.00 0.00 39.07 2.40
2561 2768 6.970484 ACTAACAAAGTGCAAACCAGATTAG 58.030 36.000 0.00 0.00 36.93 1.73
2573 2780 6.514048 GCAAACCAGATTAGTTATGAGCCATC 60.514 42.308 0.00 0.00 0.00 3.51
2575 2782 4.345257 ACCAGATTAGTTATGAGCCATCGT 59.655 41.667 0.00 0.00 0.00 3.73
2577 2784 5.509670 CCAGATTAGTTATGAGCCATCGTCA 60.510 44.000 0.00 0.00 0.00 4.35
2578 2785 6.162079 CAGATTAGTTATGAGCCATCGTCAT 58.838 40.000 0.00 0.00 38.26 3.06
2579 2786 6.309980 CAGATTAGTTATGAGCCATCGTCATC 59.690 42.308 0.00 0.00 36.11 2.92
2581 2788 3.987547 AGTTATGAGCCATCGTCATCTG 58.012 45.455 0.00 0.00 36.11 2.90
2582 2789 2.445565 TATGAGCCATCGTCATCTGC 57.554 50.000 0.00 0.00 36.11 4.26
2605 2812 4.161189 CCCATCTGATAGTCAAGTCACAGT 59.839 45.833 0.00 0.00 0.00 3.55
2616 2823 2.684881 CAAGTCACAGTGCATTATCCCC 59.315 50.000 0.00 0.00 0.00 4.81
2645 2856 6.818644 TGCATGTATCTTTTCAGTTACTCTCC 59.181 38.462 0.00 0.00 0.00 3.71
2667 2878 2.639839 ACACCAGAGCTTTACACATCCT 59.360 45.455 0.00 0.00 0.00 3.24
2715 2926 7.170998 TCCAAGTTCAGTCGAGAAGAAAAATAC 59.829 37.037 0.00 0.00 0.00 1.89
2716 2927 7.042051 CCAAGTTCAGTCGAGAAGAAAAATACA 60.042 37.037 0.00 0.00 0.00 2.29
2717 2928 8.499162 CAAGTTCAGTCGAGAAGAAAAATACAT 58.501 33.333 0.00 0.00 0.00 2.29
2718 2929 9.706691 AAGTTCAGTCGAGAAGAAAAATACATA 57.293 29.630 0.00 0.00 0.00 2.29
2785 2999 4.576053 TGTATAGCACCAAGATCACATTGC 59.424 41.667 0.00 0.00 0.00 3.56
2843 3057 6.049955 ACATTACACATACAGTAGCACCTT 57.950 37.500 0.00 0.00 0.00 3.50
2844 3058 7.177832 ACATTACACATACAGTAGCACCTTA 57.822 36.000 0.00 0.00 0.00 2.69
2845 3059 7.039882 ACATTACACATACAGTAGCACCTTAC 58.960 38.462 0.00 0.00 0.00 2.34
2886 3104 4.637534 ACATACAAACTGCAGAGCTAATGG 59.362 41.667 23.35 5.89 0.00 3.16
2990 3213 1.576421 GACCCGCTGCTTGAACTTG 59.424 57.895 0.00 0.00 0.00 3.16
3031 3254 2.747855 GAGCACCGCTTCCTTGGG 60.748 66.667 0.00 0.00 39.88 4.12
3060 3283 2.436824 GTCTCCTTTGCGCCCTCC 60.437 66.667 4.18 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.352622 ACTCCTTGCTCAACCACCCA 61.353 55.000 0.00 0.00 0.00 4.51
2 3 0.890996 CACTCCTTGCTCAACCACCC 60.891 60.000 0.00 0.00 0.00 4.61
3 4 2.633860 CACTCCTTGCTCAACCACC 58.366 57.895 0.00 0.00 0.00 4.61
13 14 6.968904 GTGTTATATTCATTGTGCACTCCTTG 59.031 38.462 19.41 10.08 0.00 3.61
14 15 6.183360 CGTGTTATATTCATTGTGCACTCCTT 60.183 38.462 19.41 0.79 0.00 3.36
15 16 5.294306 CGTGTTATATTCATTGTGCACTCCT 59.706 40.000 19.41 0.00 0.00 3.69
16 17 5.293324 TCGTGTTATATTCATTGTGCACTCC 59.707 40.000 19.41 0.00 0.00 3.85
17 18 6.344572 TCGTGTTATATTCATTGTGCACTC 57.655 37.500 19.41 0.00 0.00 3.51
18 19 6.735678 TTCGTGTTATATTCATTGTGCACT 57.264 33.333 19.41 0.00 0.00 4.40
19 20 7.789341 TTTTCGTGTTATATTCATTGTGCAC 57.211 32.000 10.75 10.75 0.00 4.57
32 33 9.594478 TCACTGTGACATATATTTTCGTGTTAT 57.406 29.630 6.36 0.00 0.00 1.89
33 34 8.989653 TCACTGTGACATATATTTTCGTGTTA 57.010 30.769 6.36 0.00 0.00 2.41
34 35 7.899178 TCACTGTGACATATATTTTCGTGTT 57.101 32.000 6.36 0.00 0.00 3.32
35 36 7.899178 TTCACTGTGACATATATTTTCGTGT 57.101 32.000 10.56 0.00 0.00 4.49
36 37 8.390354 ACATTCACTGTGACATATATTTTCGTG 58.610 33.333 10.56 0.00 36.48 4.35
37 38 8.492673 ACATTCACTGTGACATATATTTTCGT 57.507 30.769 10.56 0.00 36.48 3.85
43 44 9.755804 CTTCACTACATTCACTGTGACATATAT 57.244 33.333 10.56 0.00 38.87 0.86
44 45 7.706607 GCTTCACTACATTCACTGTGACATATA 59.293 37.037 10.56 0.00 38.87 0.86
45 46 6.536582 GCTTCACTACATTCACTGTGACATAT 59.463 38.462 10.56 0.00 38.87 1.78
46 47 5.869344 GCTTCACTACATTCACTGTGACATA 59.131 40.000 10.56 2.66 38.87 2.29
47 48 4.692625 GCTTCACTACATTCACTGTGACAT 59.307 41.667 10.56 4.97 38.87 3.06
48 49 4.058124 GCTTCACTACATTCACTGTGACA 58.942 43.478 10.56 2.70 38.87 3.58
49 50 4.058124 TGCTTCACTACATTCACTGTGAC 58.942 43.478 10.56 0.00 38.87 3.67
50 51 4.335400 TGCTTCACTACATTCACTGTGA 57.665 40.909 6.36 6.36 38.92 3.58
51 52 5.422666 TTTGCTTCACTACATTCACTGTG 57.577 39.130 0.17 0.17 38.92 3.66
52 53 6.000219 AGATTTGCTTCACTACATTCACTGT 59.000 36.000 0.00 0.00 42.13 3.55
53 54 6.312487 CAGATTTGCTTCACTACATTCACTG 58.688 40.000 0.00 0.00 0.00 3.66
54 55 5.413833 CCAGATTTGCTTCACTACATTCACT 59.586 40.000 0.00 0.00 0.00 3.41
55 56 5.182001 ACCAGATTTGCTTCACTACATTCAC 59.818 40.000 0.00 0.00 0.00 3.18
56 57 5.181811 CACCAGATTTGCTTCACTACATTCA 59.818 40.000 0.00 0.00 0.00 2.57
57 58 5.182001 ACACCAGATTTGCTTCACTACATTC 59.818 40.000 0.00 0.00 0.00 2.67
58 59 5.072741 ACACCAGATTTGCTTCACTACATT 58.927 37.500 0.00 0.00 0.00 2.71
59 60 4.655963 ACACCAGATTTGCTTCACTACAT 58.344 39.130 0.00 0.00 0.00 2.29
60 61 4.085357 ACACCAGATTTGCTTCACTACA 57.915 40.909 0.00 0.00 0.00 2.74
61 62 6.743575 ATAACACCAGATTTGCTTCACTAC 57.256 37.500 0.00 0.00 0.00 2.73
62 63 7.847096 TCTATAACACCAGATTTGCTTCACTA 58.153 34.615 0.00 0.00 0.00 2.74
63 64 6.711277 TCTATAACACCAGATTTGCTTCACT 58.289 36.000 0.00 0.00 0.00 3.41
64 65 6.985188 TCTATAACACCAGATTTGCTTCAC 57.015 37.500 0.00 0.00 0.00 3.18
65 66 7.112122 ACATCTATAACACCAGATTTGCTTCA 58.888 34.615 0.00 0.00 28.88 3.02
66 67 7.559590 ACATCTATAACACCAGATTTGCTTC 57.440 36.000 0.00 0.00 28.88 3.86
67 68 7.148018 CCAACATCTATAACACCAGATTTGCTT 60.148 37.037 0.00 0.00 28.88 3.91
68 69 6.319658 CCAACATCTATAACACCAGATTTGCT 59.680 38.462 0.00 0.00 28.88 3.91
69 70 6.095440 ACCAACATCTATAACACCAGATTTGC 59.905 38.462 0.00 0.00 28.88 3.68
70 71 7.630242 ACCAACATCTATAACACCAGATTTG 57.370 36.000 0.00 0.00 28.88 2.32
104 105 9.905713 ACCTAATCAAGCTTGATAAAGTCAATA 57.094 29.630 35.78 22.30 46.60 1.90
105 106 8.814038 ACCTAATCAAGCTTGATAAAGTCAAT 57.186 30.769 35.78 22.37 46.60 2.57
106 107 8.635765 AACCTAATCAAGCTTGATAAAGTCAA 57.364 30.769 35.78 17.21 46.60 3.18
107 108 8.514594 CAAACCTAATCAAGCTTGATAAAGTCA 58.485 33.333 35.78 18.38 46.60 3.41
108 109 8.730680 TCAAACCTAATCAAGCTTGATAAAGTC 58.269 33.333 35.78 0.00 46.60 3.01
109 110 8.635765 TCAAACCTAATCAAGCTTGATAAAGT 57.364 30.769 35.78 28.38 46.60 2.66
110 111 8.734386 ACTCAAACCTAATCAAGCTTGATAAAG 58.266 33.333 35.78 31.62 46.60 1.85
111 112 8.635765 ACTCAAACCTAATCAAGCTTGATAAA 57.364 30.769 35.78 26.26 46.60 1.40
112 113 8.635765 AACTCAAACCTAATCAAGCTTGATAA 57.364 30.769 35.78 15.06 46.60 1.75
113 114 9.383519 CTAACTCAAACCTAATCAAGCTTGATA 57.616 33.333 35.78 23.58 46.60 2.15
115 116 6.655003 CCTAACTCAAACCTAATCAAGCTTGA 59.345 38.462 30.23 30.23 42.14 3.02
116 117 6.655003 TCCTAACTCAAACCTAATCAAGCTTG 59.345 38.462 20.81 20.81 0.00 4.01
117 118 6.655425 GTCCTAACTCAAACCTAATCAAGCTT 59.345 38.462 0.00 0.00 0.00 3.74
118 119 6.174049 GTCCTAACTCAAACCTAATCAAGCT 58.826 40.000 0.00 0.00 0.00 3.74
119 120 5.938125 TGTCCTAACTCAAACCTAATCAAGC 59.062 40.000 0.00 0.00 0.00 4.01
120 121 7.979444 TTGTCCTAACTCAAACCTAATCAAG 57.021 36.000 0.00 0.00 0.00 3.02
127 128 9.668497 GTTCTAATATTGTCCTAACTCAAACCT 57.332 33.333 0.00 0.00 0.00 3.50
128 129 9.668497 AGTTCTAATATTGTCCTAACTCAAACC 57.332 33.333 0.00 0.00 0.00 3.27
138 139 7.550906 GCAGACTTGAAGTTCTAATATTGTCCT 59.449 37.037 0.00 0.00 0.00 3.85
139 140 7.334421 TGCAGACTTGAAGTTCTAATATTGTCC 59.666 37.037 0.00 0.00 0.00 4.02
140 141 8.256611 TGCAGACTTGAAGTTCTAATATTGTC 57.743 34.615 0.00 0.60 0.00 3.18
141 142 8.621532 TTGCAGACTTGAAGTTCTAATATTGT 57.378 30.769 0.00 0.00 0.00 2.71
145 146 9.944376 AGTAATTGCAGACTTGAAGTTCTAATA 57.056 29.630 0.00 0.00 0.00 0.98
146 147 8.854614 AGTAATTGCAGACTTGAAGTTCTAAT 57.145 30.769 0.00 0.00 0.00 1.73
147 148 8.677148 AAGTAATTGCAGACTTGAAGTTCTAA 57.323 30.769 0.00 0.00 34.61 2.10
148 149 8.559536 CAAAGTAATTGCAGACTTGAAGTTCTA 58.440 33.333 0.00 0.00 36.05 2.10
149 150 7.420800 CAAAGTAATTGCAGACTTGAAGTTCT 58.579 34.615 0.00 0.00 36.05 3.01
150 151 6.638468 CCAAAGTAATTGCAGACTTGAAGTTC 59.362 38.462 0.00 0.00 36.05 3.01
151 152 6.321181 TCCAAAGTAATTGCAGACTTGAAGTT 59.679 34.615 0.00 0.00 36.05 2.66
152 153 5.827797 TCCAAAGTAATTGCAGACTTGAAGT 59.172 36.000 0.00 0.00 36.05 3.01
153 154 6.317789 TCCAAAGTAATTGCAGACTTGAAG 57.682 37.500 10.43 0.00 36.05 3.02
154 155 6.707440 TTCCAAAGTAATTGCAGACTTGAA 57.293 33.333 10.43 8.38 36.05 2.69
155 156 6.294675 CCATTCCAAAGTAATTGCAGACTTGA 60.295 38.462 10.43 3.84 36.05 3.02
156 157 5.865552 CCATTCCAAAGTAATTGCAGACTTG 59.134 40.000 10.43 6.26 36.05 3.16
157 158 5.774690 TCCATTCCAAAGTAATTGCAGACTT 59.225 36.000 5.23 5.23 37.73 3.01
158 159 5.324409 TCCATTCCAAAGTAATTGCAGACT 58.676 37.500 0.00 0.00 37.73 3.24
159 160 5.393461 CCTCCATTCCAAAGTAATTGCAGAC 60.393 44.000 0.00 0.00 37.73 3.51
160 161 4.706476 CCTCCATTCCAAAGTAATTGCAGA 59.294 41.667 0.00 0.00 37.73 4.26
161 162 4.142093 CCCTCCATTCCAAAGTAATTGCAG 60.142 45.833 0.00 0.00 37.73 4.41
162 163 3.768757 CCCTCCATTCCAAAGTAATTGCA 59.231 43.478 0.00 0.00 37.73 4.08
163 164 4.023291 TCCCTCCATTCCAAAGTAATTGC 58.977 43.478 0.00 0.00 37.73 3.56
164 165 5.264395 ACTCCCTCCATTCCAAAGTAATTG 58.736 41.667 0.00 0.00 38.84 2.32
165 166 5.536497 ACTCCCTCCATTCCAAAGTAATT 57.464 39.130 0.00 0.00 0.00 1.40
166 167 5.398012 GCTACTCCCTCCATTCCAAAGTAAT 60.398 44.000 0.00 0.00 0.00 1.89
167 168 4.080526 GCTACTCCCTCCATTCCAAAGTAA 60.081 45.833 0.00 0.00 0.00 2.24
168 169 3.454812 GCTACTCCCTCCATTCCAAAGTA 59.545 47.826 0.00 0.00 0.00 2.24
169 170 2.239907 GCTACTCCCTCCATTCCAAAGT 59.760 50.000 0.00 0.00 0.00 2.66
170 171 2.422093 GGCTACTCCCTCCATTCCAAAG 60.422 54.545 0.00 0.00 0.00 2.77
171 172 1.564348 GGCTACTCCCTCCATTCCAAA 59.436 52.381 0.00 0.00 0.00 3.28
172 173 1.213296 GGCTACTCCCTCCATTCCAA 58.787 55.000 0.00 0.00 0.00 3.53
173 174 2.930935 GGCTACTCCCTCCATTCCA 58.069 57.895 0.00 0.00 0.00 3.53
182 183 8.730426 GATACGAATCATTCAGGGCTACTCCC 62.730 50.000 0.00 0.00 42.61 4.30
183 184 2.103263 ACGAATCATTCAGGGCTACTCC 59.897 50.000 0.00 0.00 0.00 3.85
184 185 3.460857 ACGAATCATTCAGGGCTACTC 57.539 47.619 0.00 0.00 0.00 2.59
185 186 4.588951 TGATACGAATCATTCAGGGCTACT 59.411 41.667 0.00 0.00 37.20 2.57
186 187 4.883083 TGATACGAATCATTCAGGGCTAC 58.117 43.478 0.00 0.00 37.20 3.58
187 188 5.545063 TTGATACGAATCATTCAGGGCTA 57.455 39.130 0.00 0.00 41.73 3.93
188 189 4.422073 TTGATACGAATCATTCAGGGCT 57.578 40.909 0.00 0.00 41.73 5.19
189 190 5.695851 AATTGATACGAATCATTCAGGGC 57.304 39.130 0.00 0.00 41.73 5.19
190 191 7.173907 AGCTTAATTGATACGAATCATTCAGGG 59.826 37.037 0.00 0.00 41.73 4.45
191 192 8.092521 AGCTTAATTGATACGAATCATTCAGG 57.907 34.615 0.00 0.00 41.73 3.86
192 193 8.986847 AGAGCTTAATTGATACGAATCATTCAG 58.013 33.333 0.00 0.00 41.73 3.02
193 194 8.893219 AGAGCTTAATTGATACGAATCATTCA 57.107 30.769 0.00 0.00 41.73 2.57
194 195 9.202273 AGAGAGCTTAATTGATACGAATCATTC 57.798 33.333 0.00 0.00 41.73 2.67
195 196 9.553064 AAGAGAGCTTAATTGATACGAATCATT 57.447 29.630 0.00 0.00 35.85 2.57
196 197 9.553064 AAAGAGAGCTTAATTGATACGAATCAT 57.447 29.630 0.00 0.00 36.52 2.45
197 198 8.948631 AAAGAGAGCTTAATTGATACGAATCA 57.051 30.769 0.00 0.00 35.58 2.57
226 227 9.136323 GAACCAAGACCTTAATTGATATTCCAT 57.864 33.333 0.00 0.00 0.00 3.41
227 228 8.112822 TGAACCAAGACCTTAATTGATATTCCA 58.887 33.333 0.00 0.00 0.00 3.53
228 229 8.519799 TGAACCAAGACCTTAATTGATATTCC 57.480 34.615 0.00 0.00 0.00 3.01
229 230 8.131731 GCTGAACCAAGACCTTAATTGATATTC 58.868 37.037 0.00 0.00 0.00 1.75
230 231 7.836183 AGCTGAACCAAGACCTTAATTGATATT 59.164 33.333 0.00 0.00 0.00 1.28
231 232 7.349598 AGCTGAACCAAGACCTTAATTGATAT 58.650 34.615 0.00 0.00 0.00 1.63
232 233 6.721318 AGCTGAACCAAGACCTTAATTGATA 58.279 36.000 0.00 0.00 0.00 2.15
233 234 5.574188 AGCTGAACCAAGACCTTAATTGAT 58.426 37.500 0.00 0.00 0.00 2.57
234 235 4.985538 AGCTGAACCAAGACCTTAATTGA 58.014 39.130 0.00 0.00 0.00 2.57
235 236 6.817765 TTAGCTGAACCAAGACCTTAATTG 57.182 37.500 0.00 0.00 0.00 2.32
236 237 7.833285 TTTTAGCTGAACCAAGACCTTAATT 57.167 32.000 0.00 0.00 0.00 1.40
237 238 9.528489 TTATTTTAGCTGAACCAAGACCTTAAT 57.472 29.630 0.00 0.00 0.00 1.40
238 239 8.927675 TTATTTTAGCTGAACCAAGACCTTAA 57.072 30.769 0.00 0.00 0.00 1.85
239 240 8.927675 TTTATTTTAGCTGAACCAAGACCTTA 57.072 30.769 0.00 0.00 0.00 2.69
269 270 9.979578 TTTTCTTATTGCAAATCAAGAGCTTTA 57.020 25.926 1.71 0.00 38.22 1.85
295 296 3.591079 AGGATCTCCCTTCTTGCTCTTTT 59.409 43.478 0.00 0.00 44.85 2.27
299 300 1.836802 ACAGGATCTCCCTTCTTGCTC 59.163 52.381 0.00 0.00 44.85 4.26
301 302 1.134250 GGACAGGATCTCCCTTCTTGC 60.134 57.143 0.00 0.00 44.85 4.01
319 320 2.599281 TGCCGGTCGTCTTCTGGA 60.599 61.111 1.90 0.00 33.49 3.86
328 329 1.360551 CATCTAGGAGTGCCGGTCG 59.639 63.158 1.90 0.00 39.96 4.79
356 357 4.575885 TCCAAGGAGTTTAAGGTTCATCG 58.424 43.478 0.00 0.00 0.00 3.84
365 366 6.843752 TGACCAAGTTATCCAAGGAGTTTAA 58.156 36.000 0.00 0.00 0.00 1.52
376 377 2.773993 TCGGGTTGACCAAGTTATCC 57.226 50.000 2.12 0.00 40.22 2.59
420 421 1.322538 ATTGGCCCATTTGGAGTCGC 61.323 55.000 0.00 0.00 37.39 5.19
453 458 3.165498 GCCTGTCGTGGCGTTTAG 58.835 61.111 1.71 0.00 43.74 1.85
480 485 0.100325 TGCTTGTTTGGCTTGTCACG 59.900 50.000 0.00 0.00 0.00 4.35
483 488 1.211743 GCTTGCTTGTTTGGCTTGTC 58.788 50.000 0.00 0.00 0.00 3.18
484 489 0.536260 TGCTTGCTTGTTTGGCTTGT 59.464 45.000 0.00 0.00 0.00 3.16
485 490 1.595794 CTTGCTTGCTTGTTTGGCTTG 59.404 47.619 0.00 0.00 0.00 4.01
487 492 0.531311 GCTTGCTTGCTTGTTTGGCT 60.531 50.000 0.00 0.00 0.00 4.75
488 493 1.501337 GGCTTGCTTGCTTGTTTGGC 61.501 55.000 1.96 0.00 0.00 4.52
491 496 1.339291 GAGAGGCTTGCTTGCTTGTTT 59.661 47.619 0.00 0.00 0.00 2.83
493 498 0.110104 AGAGAGGCTTGCTTGCTTGT 59.890 50.000 0.00 0.00 0.00 3.16
494 499 1.068472 CAAGAGAGGCTTGCTTGCTTG 60.068 52.381 14.54 7.22 46.67 4.01
495 500 1.245732 CAAGAGAGGCTTGCTTGCTT 58.754 50.000 14.54 0.00 46.67 3.91
496 501 2.944075 CAAGAGAGGCTTGCTTGCT 58.056 52.632 14.54 0.00 46.67 3.91
518 523 1.160329 CCGGTCGCCTGATTTGATCC 61.160 60.000 0.00 0.00 0.00 3.36
542 547 3.693471 TTTTAGCGGACGGGCGGA 61.693 61.111 0.00 0.00 38.18 5.54
544 549 1.843734 TTTGTTTTAGCGGACGGGCG 61.844 55.000 0.00 0.00 38.18 6.13
556 561 1.687563 CGTGACCTCCCCTTTGTTTT 58.312 50.000 0.00 0.00 0.00 2.43
613 618 0.643820 GTCGGACGAAATTACAGCCG 59.356 55.000 0.00 0.00 40.06 5.52
664 669 6.347696 TGGTTCTGCTGAATGAAATGTTTTT 58.652 32.000 9.40 0.00 34.40 1.94
667 687 5.163426 TGTTGGTTCTGCTGAATGAAATGTT 60.163 36.000 9.40 0.00 34.40 2.71
691 711 1.097547 CCAGCCGCGGAGATTGAAAT 61.098 55.000 33.48 0.00 0.00 2.17
692 712 1.745115 CCAGCCGCGGAGATTGAAA 60.745 57.895 33.48 0.00 0.00 2.69
693 713 2.125147 CCAGCCGCGGAGATTGAA 60.125 61.111 33.48 0.00 0.00 2.69
694 714 2.578163 CTTCCAGCCGCGGAGATTGA 62.578 60.000 33.48 14.30 36.12 2.57
697 717 4.537433 GCTTCCAGCCGCGGAGAT 62.537 66.667 33.48 11.33 36.12 2.75
731 813 2.030562 CGTCCATCCATACGGCCC 59.969 66.667 0.00 0.00 35.51 5.80
772 854 2.549282 CAGTTTTGACCGGCGTCG 59.451 61.111 0.29 0.29 42.37 5.12
814 905 4.368543 GCTGGCTGCTTGGTTGGC 62.369 66.667 9.31 0.00 38.95 4.52
930 1026 1.584495 GGCAACCAATCAACGGGAC 59.416 57.895 0.00 0.00 0.00 4.46
1035 1131 2.123342 GCTCCATCAAAGACGATCTCG 58.877 52.381 0.00 0.00 46.33 4.04
1044 1140 1.808945 AGTTCTTGCGCTCCATCAAAG 59.191 47.619 9.73 1.43 0.00 2.77
1045 1141 1.806542 GAGTTCTTGCGCTCCATCAAA 59.193 47.619 9.73 0.00 0.00 2.69
1302 1410 2.444706 CCTCCAGGGATCAGCCGA 60.445 66.667 0.00 0.00 37.63 5.54
1332 1441 1.337817 CGATCGATCGGCGTTCCATC 61.338 60.000 34.54 13.38 45.93 3.51
1354 1463 0.673644 AGAAACCAACAGATCGGCCG 60.674 55.000 22.12 22.12 0.00 6.13
1408 1517 1.019278 GCCTGAATCGAAGAACGGCA 61.019 55.000 10.12 0.00 43.58 5.69
1409 1518 0.741221 AGCCTGAATCGAAGAACGGC 60.741 55.000 7.71 7.71 43.58 5.68
1411 1520 2.726066 GCAAAGCCTGAATCGAAGAACG 60.726 50.000 0.00 0.00 43.58 3.95
1412 1521 2.226437 TGCAAAGCCTGAATCGAAGAAC 59.774 45.455 0.00 0.00 43.58 3.01
1413 1522 2.226437 GTGCAAAGCCTGAATCGAAGAA 59.774 45.455 0.00 0.00 43.58 2.52
1414 1523 1.806542 GTGCAAAGCCTGAATCGAAGA 59.193 47.619 0.00 0.00 45.75 2.87
1415 1524 1.135575 GGTGCAAAGCCTGAATCGAAG 60.136 52.381 0.00 0.00 0.00 3.79
1418 1527 0.109597 GTGGTGCAAAGCCTGAATCG 60.110 55.000 0.00 0.00 0.00 3.34
1427 1536 2.066262 CTACTACGTGGTGGTGCAAAG 58.934 52.381 15.58 0.00 0.00 2.77
1430 1539 1.475280 GATCTACTACGTGGTGGTGCA 59.525 52.381 15.58 0.00 0.00 4.57
1445 1554 6.428465 AGAGATCTAAAACGATCGCTGATCTA 59.572 38.462 24.68 7.58 45.02 1.98
1446 1555 5.240623 AGAGATCTAAAACGATCGCTGATCT 59.759 40.000 24.80 24.80 45.02 2.75
1447 1556 5.457140 AGAGATCTAAAACGATCGCTGATC 58.543 41.667 16.60 18.42 45.02 2.92
1451 1560 3.067461 AGCAGAGATCTAAAACGATCGCT 59.933 43.478 16.60 0.00 46.81 4.93
1452 1561 3.376540 AGCAGAGATCTAAAACGATCGC 58.623 45.455 16.60 0.00 43.52 4.58
1516 1626 2.032550 AGCAGCAAATTTCATCGGATCG 59.967 45.455 0.00 0.00 0.00 3.69
1544 1654 1.371267 CGAGCGTGAGTGGACGAAA 60.371 57.895 0.00 0.00 42.10 3.46
1642 1766 9.219603 CTACTCAGAATTCAGATAACAAAACCA 57.780 33.333 8.44 0.00 0.00 3.67
1671 1795 1.725557 CCATCACATGGCTCTGCAGC 61.726 60.000 9.47 0.00 44.70 5.25
1780 1905 9.520204 AAATATCTTTGTGTTGAAACAGAAGTG 57.480 29.630 14.20 9.04 42.15 3.16
1804 1929 6.353323 TCCACATCAGTTTCTCAGTGTTAAA 58.647 36.000 0.00 0.00 0.00 1.52
1836 1961 2.223923 CCGTTTGAATTGCCCACAGAAA 60.224 45.455 0.00 0.00 0.00 2.52
1960 2129 5.163683 CCACCATCTCTAAAAATGTCTGCAG 60.164 44.000 7.63 7.63 0.00 4.41
2016 2218 4.689612 TGTTCCATATAGAGGGACAAGC 57.310 45.455 5.80 0.00 41.65 4.01
2021 2223 6.549242 TCGAGTAATGTTCCATATAGAGGGA 58.451 40.000 0.00 0.00 32.35 4.20
2035 2237 6.513180 TCTGAGTTGAACTTTCGAGTAATGT 58.487 36.000 0.00 0.00 0.00 2.71
2044 2246 8.076781 GGGTTTATTCTTCTGAGTTGAACTTTC 58.923 37.037 0.00 0.00 0.00 2.62
2069 2271 4.021104 TCTCAGTAGTTGAATGGTCACTGG 60.021 45.833 0.00 0.00 34.81 4.00
2108 2314 0.969149 TCGGATTGCACTCACAGACT 59.031 50.000 6.38 0.00 0.00 3.24
2109 2315 1.461127 GTTCGGATTGCACTCACAGAC 59.539 52.381 6.38 0.00 0.00 3.51
2110 2316 1.795768 GTTCGGATTGCACTCACAGA 58.204 50.000 6.38 0.00 0.00 3.41
2111 2317 0.439985 CGTTCGGATTGCACTCACAG 59.560 55.000 6.38 0.00 0.00 3.66
2112 2318 0.948623 CCGTTCGGATTGCACTCACA 60.949 55.000 5.19 0.00 0.00 3.58
2113 2319 0.949105 ACCGTTCGGATTGCACTCAC 60.949 55.000 18.28 0.00 0.00 3.51
2114 2320 0.604073 TACCGTTCGGATTGCACTCA 59.396 50.000 18.28 0.00 0.00 3.41
2115 2321 1.717194 TTACCGTTCGGATTGCACTC 58.283 50.000 18.28 0.00 0.00 3.51
2116 2322 2.073816 CTTTACCGTTCGGATTGCACT 58.926 47.619 18.28 0.00 0.00 4.40
2117 2323 1.129811 CCTTTACCGTTCGGATTGCAC 59.870 52.381 18.28 0.00 0.00 4.57
2118 2324 1.002201 TCCTTTACCGTTCGGATTGCA 59.998 47.619 18.28 0.00 0.00 4.08
2119 2325 1.729284 TCCTTTACCGTTCGGATTGC 58.271 50.000 18.28 0.00 0.00 3.56
2239 2445 8.604035 ACTCTACAAGCATTATCATACAAAACG 58.396 33.333 0.00 0.00 0.00 3.60
2298 2504 4.322080 ACACGACTGAAGATGACAGAAA 57.678 40.909 0.00 0.00 38.55 2.52
2332 2538 8.207350 ACTGCTTACATGATTGGGTACTATAT 57.793 34.615 0.00 0.00 0.00 0.86
2333 2539 7.612065 ACTGCTTACATGATTGGGTACTATA 57.388 36.000 0.00 0.00 0.00 1.31
2334 2540 6.500589 ACTGCTTACATGATTGGGTACTAT 57.499 37.500 0.00 0.00 0.00 2.12
2353 2559 1.193203 CTCGTGTGTGACATGAACTGC 59.807 52.381 0.00 0.00 42.90 4.40
2415 2621 2.229792 CTGGACTGCTAGAGCCTAGAG 58.770 57.143 11.96 9.04 41.18 2.43
2416 2622 1.752436 GCTGGACTGCTAGAGCCTAGA 60.752 57.143 11.96 0.00 41.18 2.43
2417 2623 0.673437 GCTGGACTGCTAGAGCCTAG 59.327 60.000 0.00 5.20 41.18 3.02
2418 2624 0.260230 AGCTGGACTGCTAGAGCCTA 59.740 55.000 1.63 0.00 42.10 3.93
2419 2625 1.001503 AGCTGGACTGCTAGAGCCT 59.998 57.895 1.63 0.00 42.10 4.58
2420 2626 1.143620 CAGCTGGACTGCTAGAGCC 59.856 63.158 5.57 0.00 41.98 4.70
2421 2627 4.831698 CAGCTGGACTGCTAGAGC 57.168 61.111 5.57 0.00 41.98 4.09
2444 2650 1.662629 GAGTTGATGCACTCCACATCG 59.337 52.381 0.00 0.00 45.61 3.84
2455 2661 2.289002 CCAGCGAAATAGGAGTTGATGC 59.711 50.000 0.00 0.00 0.00 3.91
2465 2672 4.731773 GCCAATGTTCTTCCAGCGAAATAG 60.732 45.833 0.00 0.00 0.00 1.73
2491 2698 2.414138 CCGTTTAGGTGAAATCGTGTCC 59.586 50.000 0.00 0.00 34.51 4.02
2510 2717 0.179192 CCATCATGTCAACAACGCCG 60.179 55.000 0.00 0.00 0.00 6.46
2512 2719 3.429085 GAATCCATCATGTCAACAACGC 58.571 45.455 0.00 0.00 0.00 4.84
2553 2760 4.887748 ACGATGGCTCATAACTAATCTGG 58.112 43.478 0.00 0.00 0.00 3.86
2559 2766 4.559502 GCAGATGACGATGGCTCATAACTA 60.560 45.833 0.00 0.00 0.00 2.24
2561 2768 2.478134 GCAGATGACGATGGCTCATAAC 59.522 50.000 0.00 0.00 0.00 1.89
2573 2780 2.298446 ACTATCAGATGGGCAGATGACG 59.702 50.000 0.00 0.00 0.00 4.35
2575 2782 3.580039 TGACTATCAGATGGGCAGATGA 58.420 45.455 0.00 0.00 0.00 2.92
2577 2784 3.972638 ACTTGACTATCAGATGGGCAGAT 59.027 43.478 2.03 0.00 27.35 2.90
2578 2785 3.378512 ACTTGACTATCAGATGGGCAGA 58.621 45.455 2.03 0.00 27.35 4.26
2579 2786 3.133542 TGACTTGACTATCAGATGGGCAG 59.866 47.826 2.03 0.61 27.35 4.85
2581 2788 3.118629 TGTGACTTGACTATCAGATGGGC 60.119 47.826 0.00 0.00 0.00 5.36
2582 2789 4.161189 ACTGTGACTTGACTATCAGATGGG 59.839 45.833 0.00 0.00 0.00 4.00
2605 2812 1.614160 TGCAGCAGGGGATAATGCA 59.386 52.632 0.00 0.00 45.01 3.96
2616 2823 4.959596 ACTGAAAAGATACATGCAGCAG 57.040 40.909 0.00 0.00 0.00 4.24
2645 2856 2.744202 GGATGTGTAAAGCTCTGGTGTG 59.256 50.000 0.00 0.00 0.00 3.82
2667 2878 3.082698 GCACTTTGCAAGAATGTCACA 57.917 42.857 0.00 0.00 44.26 3.58
2732 2943 6.151144 GCCACTTCCCGCAGAATAAATAATAT 59.849 38.462 0.00 0.00 32.82 1.28
2785 2999 0.535780 TTCAGTGGCCTTCAGCACTG 60.536 55.000 11.48 11.48 46.50 3.66
2843 3057 2.565834 GTCAACCACTAGGCTTGGAGTA 59.434 50.000 12.14 0.00 39.06 2.59
2844 3058 1.348036 GTCAACCACTAGGCTTGGAGT 59.652 52.381 12.14 0.00 39.06 3.85
2845 3059 1.347707 TGTCAACCACTAGGCTTGGAG 59.652 52.381 12.14 4.51 39.06 3.86
2943 3166 4.390264 GGGAGGTACCATCAGAAATAAGC 58.610 47.826 15.94 0.00 41.20 3.09
3031 3254 1.536943 AAGGAGACGGTGCAGGAGAC 61.537 60.000 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.