Multiple sequence alignment - TraesCS7B01G206600

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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 TraesCS7B01G206600 chr7B 100.000 4906 0 0 1 4906 377909702 377904797 0.000000e+00 9060.0
1 TraesCS7B01G206600 chr7B 97.339 902 21 3 4007 4906 6398346 6399246 0.000000e+00 1530.0
2 TraesCS7B01G206600 chr7B 86.792 106 14 0 252 357 589741615 589741510 8.630000e-23 119.0
3 TraesCS7B01G206600 chr7B 85.246 61 8 1 421 480 664982502 664982442 1.470000e-05 62.1
4 TraesCS7B01G206600 chr7A 96.267 3697 81 13 347 4007 432185224 432181549 0.000000e+00 6010.0
5 TraesCS7B01G206600 chr7A 81.517 211 32 5 41 247 547759409 547759202 3.040000e-37 167.0
6 TraesCS7B01G206600 chr7A 81.928 83 12 3 425 505 571740043 571739962 3.170000e-07 67.6
7 TraesCS7B01G206600 chr7D 96.287 2397 61 12 501 2876 383318141 383315752 0.000000e+00 3908.0
8 TraesCS7B01G206600 chr7D 97.461 1142 20 3 2875 4007 383315335 383314194 0.000000e+00 1940.0
9 TraesCS7B01G206600 chr7D 80.337 356 50 11 22 359 383336561 383336208 8.150000e-63 252.0
10 TraesCS7B01G206600 chr7D 82.653 98 15 2 253 350 619817392 619817297 8.750000e-13 86.1
11 TraesCS7B01G206600 chr7D 76.437 174 28 8 352 514 364371109 364371280 1.130000e-11 82.4
12 TraesCS7B01G206600 chr7D 89.831 59 5 1 191 249 613888404 613888461 1.890000e-09 75.0
13 TraesCS7B01G206600 chrUn 97.894 902 17 2 4007 4906 295608306 295609207 0.000000e+00 1559.0
14 TraesCS7B01G206600 chr3B 97.894 902 17 2 4007 4906 5743442 5744343 0.000000e+00 1559.0
15 TraesCS7B01G206600 chr3B 77.253 233 41 9 27 251 758764054 758763826 5.160000e-25 126.0
16 TraesCS7B01G206600 chr5B 97.783 902 18 2 4007 4906 482321522 482320621 0.000000e+00 1554.0
17 TraesCS7B01G206600 chr1B 97.672 902 19 2 4007 4906 351236463 351237364 0.000000e+00 1548.0
18 TraesCS7B01G206600 chr1B 97.450 902 21 2 4007 4906 20831100 20832001 0.000000e+00 1537.0
19 TraesCS7B01G206600 chr4B 97.450 902 21 2 4007 4906 579627305 579628206 0.000000e+00 1537.0
20 TraesCS7B01G206600 chr4B 85.714 56 8 0 193 248 405060367 405060422 5.300000e-05 60.2
21 TraesCS7B01G206600 chr4A 97.228 902 23 2 4007 4906 709885808 709884907 0.000000e+00 1526.0
22 TraesCS7B01G206600 chr4A 97.225 901 21 3 4007 4906 570906515 570905618 0.000000e+00 1522.0
23 TraesCS7B01G206600 chr6B 95.276 127 6 0 1898 2024 40065202 40065328 8.330000e-48 202.0
24 TraesCS7B01G206600 chr2D 95.294 85 4 0 1902 1986 651120317 651120401 8.570000e-28 135.0
25 TraesCS7B01G206600 chr2D 76.190 105 21 4 251 353 567803472 567803574 9.000000e-03 52.8
26 TraesCS7B01G206600 chr3D 78.537 205 41 2 41 244 6170167 6169965 1.110000e-26 132.0
27 TraesCS7B01G206600 chr3D 88.312 77 8 1 185 260 109323816 109323892 1.880000e-14 91.6
28 TraesCS7B01G206600 chr2B 91.358 81 7 0 1903 1983 780252685 780252765 1.440000e-20 111.0
29 TraesCS7B01G206600 chr2B 100.000 29 0 0 41 69 2532048 2532076 2.000000e-03 54.7
30 TraesCS7B01G206600 chr6D 91.176 68 6 0 183 250 291781191 291781258 5.230000e-15 93.5
31 TraesCS7B01G206600 chr6D 100.000 28 0 0 326 353 464684123 464684150 9.000000e-03 52.8
32 TraesCS7B01G206600 chr3A 83.158 95 16 0 259 353 55841683 55841589 2.430000e-13 87.9
33 TraesCS7B01G206600 chr6A 88.571 70 2 2 20 83 103267504 103267435 4.070000e-11 80.5
34 TraesCS7B01G206600 chr4D 88.235 68 7 1 421 487 5921255 5921188 4.070000e-11 80.5
35 TraesCS7B01G206600 chr4D 100.000 29 0 0 223 251 33231203 33231231 2.000000e-03 54.7
36 TraesCS7B01G206600 chr5D 100.000 28 0 0 326 353 393766089 393766062 9.000000e-03 52.8


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 TraesCS7B01G206600 chr7B 377904797 377909702 4905 True 9060 9060 100.000 1 4906 1 chr7B.!!$R1 4905
1 TraesCS7B01G206600 chr7B 6398346 6399246 900 False 1530 1530 97.339 4007 4906 1 chr7B.!!$F1 899
2 TraesCS7B01G206600 chr7A 432181549 432185224 3675 True 6010 6010 96.267 347 4007 1 chr7A.!!$R1 3660
3 TraesCS7B01G206600 chr7D 383314194 383318141 3947 True 2924 3908 96.874 501 4007 2 chr7D.!!$R3 3506
4 TraesCS7B01G206600 chrUn 295608306 295609207 901 False 1559 1559 97.894 4007 4906 1 chrUn.!!$F1 899
5 TraesCS7B01G206600 chr3B 5743442 5744343 901 False 1559 1559 97.894 4007 4906 1 chr3B.!!$F1 899
6 TraesCS7B01G206600 chr5B 482320621 482321522 901 True 1554 1554 97.783 4007 4906 1 chr5B.!!$R1 899
7 TraesCS7B01G206600 chr1B 351236463 351237364 901 False 1548 1548 97.672 4007 4906 1 chr1B.!!$F2 899
8 TraesCS7B01G206600 chr1B 20831100 20832001 901 False 1537 1537 97.450 4007 4906 1 chr1B.!!$F1 899
9 TraesCS7B01G206600 chr4B 579627305 579628206 901 False 1537 1537 97.450 4007 4906 1 chr4B.!!$F2 899
10 TraesCS7B01G206600 chr4A 709884907 709885808 901 True 1526 1526 97.228 4007 4906 1 chr4A.!!$R2 899
11 TraesCS7B01G206600 chr4A 570905618 570906515 897 True 1522 1522 97.225 4007 4906 1 chr4A.!!$R1 899

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 0.107081 TAATTACGACCGCATGGGGG 59.893 55.0 30.26 17.13 41.60 5.40 F
313 314 0.179166 CCGCGACCCAAATGAACATG 60.179 55.0 8.23 0.00 0.00 3.21 F
351 352 0.321298 GCCGGTTGGAGTTGCTCTTA 60.321 55.0 1.90 0.00 37.49 2.10 F
371 372 0.391597 TTGACAAGGTCAGGTCGTCC 59.608 55.0 0.00 0.00 43.69 4.79 F
423 424 0.594602 TCCGGTGGCGATAATAGTCG 59.405 55.0 0.00 0.00 44.14 4.18 F
1964 1970 0.625849 ATGGTCCATCAAGGGGTGTC 59.374 55.0 0.00 0.00 38.24 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1164 1170 1.202568 GAACGAGACGACGTCGACA 59.797 57.895 41.52 0.00 45.83 4.35 R
1887 1893 1.336702 GCAATTCCGATGTTGCCAACA 60.337 47.619 13.44 13.44 46.94 3.33 R
2240 2261 2.439507 CACCTGTAACCTATCCATGGCT 59.560 50.000 6.96 0.00 0.00 4.75 R
2296 2324 9.772973 TCAGTAGTTATGTTGTTGATTTAGTGT 57.227 29.630 0.00 0.00 0.00 3.55 R
2741 2773 9.722056 GTAGAAATGTAGAATTGCAAATACTGG 57.278 33.333 1.71 0.00 0.00 4.00 R
3957 4432 0.169672 GCGCACTCATCAGCATTGTT 59.830 50.000 0.30 0.00 0.00 2.83 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 2.593436 AGGGTTTTGTGGTCGCCG 60.593 61.111 0.00 0.00 0.00 6.46
18 19 3.666253 GGGTTTTGTGGTCGCCGG 61.666 66.667 0.00 0.00 0.00 6.13
19 20 4.337060 GGTTTTGTGGTCGCCGGC 62.337 66.667 19.07 19.07 0.00 6.13
20 21 4.676586 GTTTTGTGGTCGCCGGCG 62.677 66.667 42.13 42.13 41.35 6.46
21 22 4.912485 TTTTGTGGTCGCCGGCGA 62.912 61.111 45.37 45.37 46.87 5.54
35 36 2.821366 GCGAGGTGGCCAGATGTG 60.821 66.667 5.11 0.00 0.00 3.21
42 43 3.399181 GGCCAGATGTGGACGGGA 61.399 66.667 14.25 0.00 44.19 5.14
43 44 2.966732 GGCCAGATGTGGACGGGAA 61.967 63.158 14.25 0.00 44.19 3.97
44 45 2.876368 GGCCAGATGTGGACGGGAAG 62.876 65.000 14.25 0.00 44.19 3.46
46 47 3.143675 CAGATGTGGACGGGAAGTG 57.856 57.895 0.00 0.00 0.00 3.16
47 48 0.391661 CAGATGTGGACGGGAAGTGG 60.392 60.000 0.00 0.00 0.00 4.00
48 49 0.544357 AGATGTGGACGGGAAGTGGA 60.544 55.000 0.00 0.00 0.00 4.02
49 50 0.541863 GATGTGGACGGGAAGTGGAT 59.458 55.000 0.00 0.00 0.00 3.41
50 51 0.253044 ATGTGGACGGGAAGTGGATG 59.747 55.000 0.00 0.00 0.00 3.51
51 52 0.834261 TGTGGACGGGAAGTGGATGA 60.834 55.000 0.00 0.00 0.00 2.92
52 53 0.108138 GTGGACGGGAAGTGGATGAG 60.108 60.000 0.00 0.00 0.00 2.90
53 54 1.264749 TGGACGGGAAGTGGATGAGG 61.265 60.000 0.00 0.00 0.00 3.86
54 55 1.153349 GACGGGAAGTGGATGAGGC 60.153 63.158 0.00 0.00 0.00 4.70
55 56 2.190578 CGGGAAGTGGATGAGGCC 59.809 66.667 0.00 0.00 0.00 5.19
56 57 2.190578 GGGAAGTGGATGAGGCCG 59.809 66.667 0.00 0.00 0.00 6.13
57 58 2.190578 GGAAGTGGATGAGGCCGG 59.809 66.667 0.00 0.00 0.00 6.13
58 59 2.514824 GAAGTGGATGAGGCCGGC 60.515 66.667 21.18 21.18 0.00 6.13
59 60 4.115199 AAGTGGATGAGGCCGGCC 62.115 66.667 39.29 39.29 0.00 6.13
76 77 4.697756 CCCACCACACGCGTCCAT 62.698 66.667 9.86 0.00 0.00 3.41
77 78 2.668212 CCACCACACGCGTCCATT 60.668 61.111 9.86 0.00 0.00 3.16
78 79 1.374885 CCACCACACGCGTCCATTA 60.375 57.895 9.86 0.00 0.00 1.90
79 80 0.951525 CCACCACACGCGTCCATTAA 60.952 55.000 9.86 0.00 0.00 1.40
80 81 0.869068 CACCACACGCGTCCATTAAA 59.131 50.000 9.86 0.00 0.00 1.52
81 82 1.264557 CACCACACGCGTCCATTAAAA 59.735 47.619 9.86 0.00 0.00 1.52
82 83 1.948145 ACCACACGCGTCCATTAAAAA 59.052 42.857 9.86 0.00 0.00 1.94
83 84 2.031508 ACCACACGCGTCCATTAAAAAG 60.032 45.455 9.86 0.00 0.00 2.27
84 85 2.580589 CACACGCGTCCATTAAAAAGG 58.419 47.619 9.86 0.00 0.00 3.11
85 86 2.224549 CACACGCGTCCATTAAAAAGGA 59.775 45.455 9.86 0.00 0.00 3.36
93 94 2.817258 TCCATTAAAAAGGACTGGCACG 59.183 45.455 0.00 0.00 0.00 5.34
94 95 2.595386 CATTAAAAAGGACTGGCACGC 58.405 47.619 0.00 0.00 0.00 5.34
95 96 0.589223 TTAAAAAGGACTGGCACGCG 59.411 50.000 3.53 3.53 0.00 6.01
96 97 1.231958 TAAAAAGGACTGGCACGCGG 61.232 55.000 12.47 0.00 0.00 6.46
114 115 3.052082 CCTTCCGCACACTGCCAG 61.052 66.667 0.00 0.00 41.12 4.85
115 116 3.052082 CTTCCGCACACTGCCAGG 61.052 66.667 0.00 0.00 41.12 4.45
116 117 3.832237 CTTCCGCACACTGCCAGGT 62.832 63.158 0.00 0.00 41.12 4.00
117 118 4.624364 TCCGCACACTGCCAGGTG 62.624 66.667 8.44 8.44 41.12 4.00
128 129 3.754043 CCAGGTGGGCCCTTGATA 58.246 61.111 25.70 0.00 42.73 2.15
129 130 2.244487 CCAGGTGGGCCCTTGATAT 58.756 57.895 25.70 0.00 42.73 1.63
130 131 0.178981 CCAGGTGGGCCCTTGATATG 60.179 60.000 25.70 12.66 42.73 1.78
131 132 0.552848 CAGGTGGGCCCTTGATATGT 59.447 55.000 25.70 0.00 42.73 2.29
132 133 0.552848 AGGTGGGCCCTTGATATGTG 59.447 55.000 25.70 0.00 42.73 3.21
133 134 0.468029 GGTGGGCCCTTGATATGTGG 60.468 60.000 25.70 0.00 0.00 4.17
134 135 1.109323 GTGGGCCCTTGATATGTGGC 61.109 60.000 25.70 0.00 43.26 5.01
136 137 3.749981 GCCCTTGATATGTGGCCG 58.250 61.111 0.00 0.00 37.94 6.13
137 138 2.555547 GCCCTTGATATGTGGCCGC 61.556 63.158 10.11 10.11 37.94 6.53
138 139 2.253758 CCCTTGATATGTGGCCGCG 61.254 63.158 12.58 0.00 0.00 6.46
139 140 1.523711 CCTTGATATGTGGCCGCGT 60.524 57.895 16.73 16.73 0.00 6.01
140 141 1.095228 CCTTGATATGTGGCCGCGTT 61.095 55.000 17.85 6.56 0.00 4.84
141 142 1.577468 CTTGATATGTGGCCGCGTTA 58.423 50.000 17.85 8.83 0.00 3.18
142 143 1.937223 CTTGATATGTGGCCGCGTTAA 59.063 47.619 17.85 9.06 0.00 2.01
143 144 2.248280 TGATATGTGGCCGCGTTAAT 57.752 45.000 17.85 4.73 0.00 1.40
144 145 2.566913 TGATATGTGGCCGCGTTAATT 58.433 42.857 17.85 0.00 0.00 1.40
145 146 3.729966 TGATATGTGGCCGCGTTAATTA 58.270 40.909 17.85 0.00 0.00 1.40
146 147 3.495377 TGATATGTGGCCGCGTTAATTAC 59.505 43.478 17.85 0.00 0.00 1.89
158 159 1.600485 GTTAATTACGACCGCATGGGG 59.400 52.381 26.22 26.22 41.60 4.96
159 160 0.107081 TAATTACGACCGCATGGGGG 59.893 55.000 30.26 17.13 41.60 5.40
173 174 2.675423 GGGGGTTTGGCTTCCGAC 60.675 66.667 0.00 0.00 0.00 4.79
174 175 2.114411 GGGGTTTGGCTTCCGACA 59.886 61.111 0.00 0.00 0.00 4.35
175 176 2.265904 GGGGTTTGGCTTCCGACAC 61.266 63.158 0.00 0.00 0.00 3.67
176 177 1.527380 GGGTTTGGCTTCCGACACA 60.527 57.895 0.00 0.00 0.00 3.72
177 178 0.893727 GGGTTTGGCTTCCGACACAT 60.894 55.000 0.00 0.00 0.00 3.21
178 179 0.240945 GGTTTGGCTTCCGACACATG 59.759 55.000 0.00 0.00 0.00 3.21
179 180 0.951558 GTTTGGCTTCCGACACATGT 59.048 50.000 0.00 0.00 0.00 3.21
180 181 2.147958 GTTTGGCTTCCGACACATGTA 58.852 47.619 0.00 0.00 0.00 2.29
181 182 2.550606 GTTTGGCTTCCGACACATGTAA 59.449 45.455 0.00 0.00 0.00 2.41
182 183 2.093306 TGGCTTCCGACACATGTAAG 57.907 50.000 0.00 0.00 0.00 2.34
183 184 1.338674 TGGCTTCCGACACATGTAAGG 60.339 52.381 0.00 2.30 0.00 2.69
184 185 0.727398 GCTTCCGACACATGTAAGGC 59.273 55.000 0.00 0.00 0.00 4.35
185 186 1.369625 CTTCCGACACATGTAAGGCC 58.630 55.000 0.00 0.00 0.00 5.19
186 187 0.390603 TTCCGACACATGTAAGGCCG 60.391 55.000 0.00 0.00 0.00 6.13
187 188 2.461110 CCGACACATGTAAGGCCGC 61.461 63.158 0.00 0.00 0.00 6.53
188 189 2.798501 CGACACATGTAAGGCCGCG 61.799 63.158 0.00 0.00 0.00 6.46
189 190 1.447140 GACACATGTAAGGCCGCGA 60.447 57.895 8.23 0.00 0.00 5.87
190 191 1.693083 GACACATGTAAGGCCGCGAC 61.693 60.000 8.23 0.00 0.00 5.19
191 192 2.508439 ACATGTAAGGCCGCGACG 60.508 61.111 8.23 0.00 0.00 5.12
223 224 3.542742 GCGCGGCGTGTCTACTTC 61.543 66.667 24.46 0.00 0.00 3.01
224 225 3.238241 CGCGGCGTGTCTACTTCG 61.238 66.667 15.36 0.00 0.00 3.79
225 226 2.126580 GCGGCGTGTCTACTTCGT 60.127 61.111 9.37 0.00 0.00 3.85
226 227 2.434134 GCGGCGTGTCTACTTCGTG 61.434 63.158 9.37 0.00 0.00 4.35
227 228 1.081641 CGGCGTGTCTACTTCGTGT 60.082 57.895 0.00 0.00 0.00 4.49
228 229 1.063951 CGGCGTGTCTACTTCGTGTC 61.064 60.000 0.00 0.00 0.00 3.67
229 230 0.731855 GGCGTGTCTACTTCGTGTCC 60.732 60.000 0.00 0.00 0.00 4.02
230 231 1.063951 GCGTGTCTACTTCGTGTCCG 61.064 60.000 0.00 0.00 0.00 4.79
231 232 1.063951 CGTGTCTACTTCGTGTCCGC 61.064 60.000 0.00 0.00 0.00 5.54
232 233 1.063951 GTGTCTACTTCGTGTCCGCG 61.064 60.000 0.00 0.00 0.00 6.46
233 234 2.150837 GTCTACTTCGTGTCCGCGC 61.151 63.158 0.00 0.00 0.00 6.86
234 235 2.879462 CTACTTCGTGTCCGCGCC 60.879 66.667 0.00 0.00 0.00 6.53
235 236 4.764336 TACTTCGTGTCCGCGCCG 62.764 66.667 0.00 0.00 0.00 6.46
248 249 4.520846 CGCCGACGCATTTCAGGC 62.521 66.667 0.00 0.00 44.00 4.85
249 250 4.179579 GCCGACGCATTTCAGGCC 62.180 66.667 0.00 0.00 41.81 5.19
250 251 3.508840 CCGACGCATTTCAGGCCC 61.509 66.667 0.00 0.00 0.00 5.80
251 252 3.864686 CGACGCATTTCAGGCCCG 61.865 66.667 0.00 0.00 0.00 6.13
252 253 2.746277 GACGCATTTCAGGCCCGT 60.746 61.111 0.00 0.00 34.52 5.28
253 254 2.282180 ACGCATTTCAGGCCCGTT 60.282 55.556 0.00 0.00 0.00 4.44
254 255 1.862602 GACGCATTTCAGGCCCGTTT 61.863 55.000 0.00 0.00 31.65 3.60
255 256 1.288752 CGCATTTCAGGCCCGTTTT 59.711 52.632 0.00 0.00 0.00 2.43
256 257 1.008361 CGCATTTCAGGCCCGTTTTG 61.008 55.000 0.00 0.00 0.00 2.44
257 258 0.670239 GCATTTCAGGCCCGTTTTGG 60.670 55.000 0.00 0.00 37.55 3.28
268 269 0.239082 CCGTTTTGGGTTTAGGTCGC 59.761 55.000 0.00 0.00 0.00 5.19
269 270 0.239082 CGTTTTGGGTTTAGGTCGCC 59.761 55.000 0.00 0.00 0.00 5.54
270 271 1.320507 GTTTTGGGTTTAGGTCGCCA 58.679 50.000 0.00 0.00 0.00 5.69
271 272 1.001048 GTTTTGGGTTTAGGTCGCCAC 60.001 52.381 0.00 0.00 0.00 5.01
272 273 0.885596 TTTGGGTTTAGGTCGCCACG 60.886 55.000 0.00 0.00 0.00 4.94
273 274 2.042404 TTGGGTTTAGGTCGCCACGT 62.042 55.000 0.00 0.00 0.00 4.49
274 275 1.301953 GGGTTTAGGTCGCCACGTT 60.302 57.895 0.00 0.00 0.00 3.99
275 276 1.571215 GGGTTTAGGTCGCCACGTTG 61.571 60.000 0.00 0.00 0.00 4.10
276 277 1.571215 GGTTTAGGTCGCCACGTTGG 61.571 60.000 0.00 0.00 41.55 3.77
277 278 1.301874 TTTAGGTCGCCACGTTGGG 60.302 57.895 0.00 0.00 38.19 4.12
288 289 2.663852 CGTTGGGCCGACGTCTTT 60.664 61.111 33.32 0.00 36.60 2.52
289 290 2.943653 GTTGGGCCGACGTCTTTG 59.056 61.111 14.70 3.10 0.00 2.77
290 291 1.890510 GTTGGGCCGACGTCTTTGT 60.891 57.895 14.70 0.00 0.00 2.83
291 292 1.595929 TTGGGCCGACGTCTTTGTC 60.596 57.895 14.70 3.31 35.49 3.18
292 293 2.741211 GGGCCGACGTCTTTGTCC 60.741 66.667 14.70 9.15 35.40 4.02
293 294 3.110178 GGCCGACGTCTTTGTCCG 61.110 66.667 14.70 0.00 35.40 4.79
294 295 3.774702 GCCGACGTCTTTGTCCGC 61.775 66.667 14.70 0.00 36.30 5.54
295 296 3.110178 CCGACGTCTTTGTCCGCC 61.110 66.667 14.70 0.00 35.40 6.13
296 297 3.467119 CGACGTCTTTGTCCGCCG 61.467 66.667 14.70 0.00 35.40 6.46
297 298 3.774702 GACGTCTTTGTCCGCCGC 61.775 66.667 8.70 0.00 32.61 6.53
300 301 3.774702 GTCTTTGTCCGCCGCGAC 61.775 66.667 15.93 11.08 0.00 5.19
309 310 3.427425 CGCCGCGACCCAAATGAA 61.427 61.111 8.23 0.00 0.00 2.57
310 311 2.178273 GCCGCGACCCAAATGAAC 59.822 61.111 8.23 0.00 0.00 3.18
311 312 2.622011 GCCGCGACCCAAATGAACA 61.622 57.895 8.23 0.00 0.00 3.18
312 313 1.933115 GCCGCGACCCAAATGAACAT 61.933 55.000 8.23 0.00 0.00 2.71
313 314 0.179166 CCGCGACCCAAATGAACATG 60.179 55.000 8.23 0.00 0.00 3.21
314 315 0.179166 CGCGACCCAAATGAACATGG 60.179 55.000 0.00 0.00 36.42 3.66
320 321 1.994916 CCAAATGAACATGGGCGAAC 58.005 50.000 0.00 0.00 32.87 3.95
321 322 1.616620 CAAATGAACATGGGCGAACG 58.383 50.000 0.00 0.00 0.00 3.95
322 323 1.198867 CAAATGAACATGGGCGAACGA 59.801 47.619 0.00 0.00 0.00 3.85
323 324 1.529226 AATGAACATGGGCGAACGAA 58.471 45.000 0.00 0.00 0.00 3.85
324 325 1.529226 ATGAACATGGGCGAACGAAA 58.471 45.000 0.00 0.00 0.00 3.46
325 326 1.529226 TGAACATGGGCGAACGAAAT 58.471 45.000 0.00 0.00 0.00 2.17
326 327 1.198867 TGAACATGGGCGAACGAAATG 59.801 47.619 0.00 1.21 0.00 2.32
327 328 0.525761 AACATGGGCGAACGAAATGG 59.474 50.000 0.00 0.00 0.00 3.16
328 329 1.312371 ACATGGGCGAACGAAATGGG 61.312 55.000 0.00 0.00 0.00 4.00
329 330 1.001393 ATGGGCGAACGAAATGGGT 60.001 52.632 0.00 0.00 0.00 4.51
330 331 1.029947 ATGGGCGAACGAAATGGGTC 61.030 55.000 0.00 0.00 0.00 4.46
331 332 2.746803 GGGCGAACGAAATGGGTCG 61.747 63.158 0.00 0.00 46.54 4.79
332 333 2.746803 GGCGAACGAAATGGGTCGG 61.747 63.158 5.06 0.00 45.40 4.79
333 334 2.782615 CGAACGAAATGGGTCGGC 59.217 61.111 0.00 0.00 45.40 5.54
334 335 2.746803 CGAACGAAATGGGTCGGCC 61.747 63.158 0.00 0.00 45.40 6.13
335 336 2.744709 AACGAAATGGGTCGGCCG 60.745 61.111 22.12 22.12 45.40 6.13
336 337 4.770874 ACGAAATGGGTCGGCCGG 62.771 66.667 27.83 8.13 45.40 6.13
337 338 4.770874 CGAAATGGGTCGGCCGGT 62.771 66.667 27.83 3.53 37.37 5.28
338 339 2.360726 GAAATGGGTCGGCCGGTT 60.361 61.111 27.83 9.94 34.97 4.44
339 340 2.675075 AAATGGGTCGGCCGGTTG 60.675 61.111 27.83 0.00 34.97 3.77
340 341 4.733542 AATGGGTCGGCCGGTTGG 62.734 66.667 27.83 0.00 38.77 3.77
344 345 4.324991 GGTCGGCCGGTTGGAGTT 62.325 66.667 27.83 0.00 37.49 3.01
345 346 3.047877 GTCGGCCGGTTGGAGTTG 61.048 66.667 27.83 0.00 37.49 3.16
348 349 3.056328 GGCCGGTTGGAGTTGCTC 61.056 66.667 1.90 0.00 37.49 4.26
349 350 2.032681 GCCGGTTGGAGTTGCTCT 59.967 61.111 1.90 0.00 37.49 4.09
350 351 1.600916 GCCGGTTGGAGTTGCTCTT 60.601 57.895 1.90 0.00 37.49 2.85
351 352 0.321298 GCCGGTTGGAGTTGCTCTTA 60.321 55.000 1.90 0.00 37.49 2.10
352 353 1.679032 GCCGGTTGGAGTTGCTCTTAT 60.679 52.381 1.90 0.00 37.49 1.73
353 354 2.711542 CCGGTTGGAGTTGCTCTTATT 58.288 47.619 0.00 0.00 37.49 1.40
362 363 4.393371 GGAGTTGCTCTTATTGACAAGGTC 59.607 45.833 0.00 0.00 0.00 3.85
366 367 3.327757 TGCTCTTATTGACAAGGTCAGGT 59.672 43.478 0.00 0.00 43.69 4.00
371 372 0.391597 TTGACAAGGTCAGGTCGTCC 59.608 55.000 0.00 0.00 43.69 4.79
372 373 1.292541 GACAAGGTCAGGTCGTCCC 59.707 63.158 0.00 0.00 32.09 4.46
373 374 2.168666 GACAAGGTCAGGTCGTCCCC 62.169 65.000 0.00 0.00 32.09 4.81
377 378 1.454479 GGTCAGGTCGTCCCCGATA 60.454 63.158 0.00 0.00 46.30 2.92
415 416 4.789075 CGTCGTTCCGGTGGCGAT 62.789 66.667 17.22 0.00 37.00 4.58
423 424 0.594602 TCCGGTGGCGATAATAGTCG 59.405 55.000 0.00 0.00 44.14 4.18
432 433 2.542411 GCGATAATAGTCGTTCGGTGGT 60.542 50.000 0.00 0.00 43.27 4.16
435 436 4.556104 CGATAATAGTCGTTCGGTGGTCAT 60.556 45.833 0.00 0.00 36.88 3.06
477 478 9.959749 TTTTATTATGTTTGAGGTGTCTTGTTC 57.040 29.630 0.00 0.00 0.00 3.18
479 480 7.823745 ATTATGTTTGAGGTGTCTTGTTCTT 57.176 32.000 0.00 0.00 0.00 2.52
480 481 5.757850 ATGTTTGAGGTGTCTTGTTCTTC 57.242 39.130 0.00 0.00 0.00 2.87
481 482 4.584874 TGTTTGAGGTGTCTTGTTCTTCA 58.415 39.130 0.00 0.00 0.00 3.02
482 483 5.192927 TGTTTGAGGTGTCTTGTTCTTCAT 58.807 37.500 0.00 0.00 0.00 2.57
483 484 5.066375 TGTTTGAGGTGTCTTGTTCTTCATG 59.934 40.000 0.00 0.00 0.00 3.07
484 485 4.422073 TGAGGTGTCTTGTTCTTCATGT 57.578 40.909 0.00 0.00 0.00 3.21
486 487 4.141733 TGAGGTGTCTTGTTCTTCATGTGA 60.142 41.667 0.00 0.00 0.00 3.58
630 634 1.739562 CGAGCTCAACCACTCCAGC 60.740 63.158 15.40 0.00 0.00 4.85
631 635 1.739562 GAGCTCAACCACTCCAGCG 60.740 63.158 9.40 0.00 36.95 5.18
809 815 3.020984 GTTTGCCGATTTAGGATTGGGA 58.979 45.455 0.00 0.00 0.00 4.37
829 835 4.215399 GGGAATTTGATGAAGTGTGAACGA 59.785 41.667 0.00 0.00 0.00 3.85
830 836 5.147162 GGAATTTGATGAAGTGTGAACGAC 58.853 41.667 0.00 0.00 0.00 4.34
849 855 3.609373 CGACGGCTACAAATTCGAGTTTA 59.391 43.478 5.52 0.00 0.00 2.01
871 877 2.989840 CTCACTGTTCTTGACGTGATCC 59.010 50.000 0.00 0.00 39.35 3.36
879 885 1.692148 TTGACGTGATCCGCGAATGC 61.692 55.000 8.23 0.00 39.94 3.56
1694 1700 4.919754 GTGCTCTTGTTCAACATTTCCATC 59.080 41.667 0.00 0.00 0.00 3.51
1792 1798 2.950309 GAGCTGCATTCTCATGATTGGT 59.050 45.455 1.02 0.00 31.07 3.67
1814 1820 0.752054 ACACAAACCAGCCAATGTGG 59.248 50.000 9.28 0.00 45.65 4.17
1862 1868 2.224314 GCTGAAACTGTACTCCTGTTGC 59.776 50.000 0.00 0.00 35.63 4.17
1887 1893 6.210385 CCTGATATAGAGCACTGTAGAATGGT 59.790 42.308 0.00 0.00 0.00 3.55
1964 1970 0.625849 ATGGTCCATCAAGGGGTGTC 59.374 55.000 0.00 0.00 38.24 3.67
2226 2247 2.789893 GGAAGCATCACTTACGTCGATC 59.210 50.000 0.00 0.00 39.29 3.69
2240 2261 5.471556 ACGTCGATCTCTAGAGGATAGAA 57.528 43.478 19.67 0.00 29.49 2.10
2296 2324 6.689241 CAGTGTGCAGTGTTCGTTTAAAATTA 59.311 34.615 0.00 0.00 0.00 1.40
2589 2621 4.899352 ACTACTTTGCCTCTGATGTCTT 57.101 40.909 0.00 0.00 0.00 3.01
2651 2683 1.141858 CTGGACCCAGGGCTTTATCTC 59.858 57.143 4.91 0.00 40.17 2.75
2741 2773 4.187694 CTGGTAGGACTGCTTTCTGATTC 58.812 47.826 0.00 0.00 0.00 2.52
2749 2781 5.649831 GGACTGCTTTCTGATTCCAGTATTT 59.350 40.000 5.10 0.00 41.16 1.40
2812 2844 1.869132 CAGTCGGCATACATGACATGG 59.131 52.381 19.39 3.30 34.77 3.66
3242 3701 6.743575 ATGTGAGCAACTTTATAACTGGTC 57.256 37.500 11.16 11.16 36.95 4.02
3289 3748 3.245048 GGCATGTTTTCTTGTTGAAACGG 59.755 43.478 0.00 0.00 43.55 4.44
3941 4404 5.532406 TGCTTGTAAATGAAAGAGCTTGACT 59.468 36.000 0.00 0.00 0.00 3.41
3952 4427 3.340814 GAGCTTGACTCCTTCCATTGA 57.659 47.619 0.00 0.00 39.75 2.57
3953 4428 3.679389 GAGCTTGACTCCTTCCATTGAA 58.321 45.455 0.00 0.00 39.75 2.69
3954 4429 4.074970 GAGCTTGACTCCTTCCATTGAAA 58.925 43.478 0.00 0.00 39.75 2.69
3955 4430 4.670765 AGCTTGACTCCTTCCATTGAAAT 58.329 39.130 0.00 0.00 0.00 2.17
3956 4431 4.461781 AGCTTGACTCCTTCCATTGAAATG 59.538 41.667 0.00 0.00 36.17 2.32
3957 4432 4.460382 GCTTGACTCCTTCCATTGAAATGA 59.540 41.667 4.58 0.00 38.70 2.57
3958 4433 5.047802 GCTTGACTCCTTCCATTGAAATGAA 60.048 40.000 4.58 0.00 38.70 2.57
3959 4434 5.964958 TGACTCCTTCCATTGAAATGAAC 57.035 39.130 4.58 0.00 38.70 3.18
3960 4435 5.384336 TGACTCCTTCCATTGAAATGAACA 58.616 37.500 4.58 0.00 38.70 3.18
3961 4436 5.832595 TGACTCCTTCCATTGAAATGAACAA 59.167 36.000 4.58 0.00 38.70 2.83
3962 4437 6.494491 TGACTCCTTCCATTGAAATGAACAAT 59.506 34.615 4.58 0.00 38.70 2.71
3976 4451 0.169672 AACAATGCTGATGAGTGCGC 59.830 50.000 0.00 0.00 0.00 6.09
4094 4569 0.753867 ACGGAAAACCGGGCAAAAAT 59.246 45.000 6.32 0.00 37.53 1.82
4095 4570 1.139256 ACGGAAAACCGGGCAAAAATT 59.861 42.857 6.32 0.00 37.53 1.82
4162 4637 1.750682 GCAAAGCCCACCCTTATCGAT 60.751 52.381 2.16 2.16 0.00 3.59
4201 4676 0.104304 AGACAACGCAACTCCGACTT 59.896 50.000 0.00 0.00 0.00 3.01
4286 4762 0.108186 CCTGCAGCCAGTCATCGTAA 60.108 55.000 8.66 0.00 37.38 3.18
4334 4810 2.791158 CGACTCCACAGCAACAAACAAC 60.791 50.000 0.00 0.00 0.00 3.32
4445 4921 4.335647 AAGTCTGGCCGCCACAGG 62.336 66.667 8.43 0.00 36.62 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.666253 CCGGCGACCACAAAACCC 61.666 66.667 9.30 0.00 0.00 4.11
2 3 4.337060 GCCGGCGACCACAAAACC 62.337 66.667 12.58 0.00 0.00 3.27
3 4 4.676586 CGCCGGCGACCACAAAAC 62.677 66.667 44.86 0.00 42.83 2.43
4 5 4.912485 TCGCCGGCGACCACAAAA 62.912 61.111 45.37 23.24 44.01 2.44
18 19 2.821366 CACATCTGGCCACCTCGC 60.821 66.667 0.00 0.00 0.00 5.03
19 20 2.124983 CCACATCTGGCCACCTCG 60.125 66.667 0.00 0.00 0.00 4.63
20 21 1.078143 GTCCACATCTGGCCACCTC 60.078 63.158 0.00 0.00 37.49 3.85
21 22 2.959484 CGTCCACATCTGGCCACCT 61.959 63.158 0.00 0.00 37.49 4.00
22 23 2.436646 CGTCCACATCTGGCCACC 60.437 66.667 0.00 0.00 37.49 4.61
23 24 2.436646 CCGTCCACATCTGGCCAC 60.437 66.667 0.00 0.00 37.49 5.01
24 25 3.716195 CCCGTCCACATCTGGCCA 61.716 66.667 4.71 4.71 37.49 5.36
25 26 2.876368 CTTCCCGTCCACATCTGGCC 62.876 65.000 0.00 0.00 37.49 5.36
26 27 1.450312 CTTCCCGTCCACATCTGGC 60.450 63.158 0.00 0.00 37.49 4.85
27 28 0.391661 CACTTCCCGTCCACATCTGG 60.392 60.000 0.00 0.00 39.23 3.86
28 29 0.391661 CCACTTCCCGTCCACATCTG 60.392 60.000 0.00 0.00 0.00 2.90
29 30 0.544357 TCCACTTCCCGTCCACATCT 60.544 55.000 0.00 0.00 0.00 2.90
30 31 0.541863 ATCCACTTCCCGTCCACATC 59.458 55.000 0.00 0.00 0.00 3.06
31 32 0.253044 CATCCACTTCCCGTCCACAT 59.747 55.000 0.00 0.00 0.00 3.21
32 33 0.834261 TCATCCACTTCCCGTCCACA 60.834 55.000 0.00 0.00 0.00 4.17
33 34 0.108138 CTCATCCACTTCCCGTCCAC 60.108 60.000 0.00 0.00 0.00 4.02
34 35 1.264749 CCTCATCCACTTCCCGTCCA 61.265 60.000 0.00 0.00 0.00 4.02
35 36 1.522569 CCTCATCCACTTCCCGTCC 59.477 63.158 0.00 0.00 0.00 4.79
36 37 1.153349 GCCTCATCCACTTCCCGTC 60.153 63.158 0.00 0.00 0.00 4.79
37 38 2.670148 GGCCTCATCCACTTCCCGT 61.670 63.158 0.00 0.00 0.00 5.28
38 39 2.190578 GGCCTCATCCACTTCCCG 59.809 66.667 0.00 0.00 0.00 5.14
39 40 2.190578 CGGCCTCATCCACTTCCC 59.809 66.667 0.00 0.00 0.00 3.97
40 41 2.190578 CCGGCCTCATCCACTTCC 59.809 66.667 0.00 0.00 0.00 3.46
41 42 2.514824 GCCGGCCTCATCCACTTC 60.515 66.667 18.11 0.00 0.00 3.01
42 43 4.115199 GGCCGGCCTCATCCACTT 62.115 66.667 38.76 0.00 0.00 3.16
59 60 2.789845 TAATGGACGCGTGTGGTGGG 62.790 60.000 20.70 0.00 0.00 4.61
60 61 0.951525 TTAATGGACGCGTGTGGTGG 60.952 55.000 20.70 0.00 0.00 4.61
61 62 0.869068 TTTAATGGACGCGTGTGGTG 59.131 50.000 20.70 0.00 0.00 4.17
62 63 1.595466 TTTTAATGGACGCGTGTGGT 58.405 45.000 20.70 1.15 0.00 4.16
63 64 2.580589 CTTTTTAATGGACGCGTGTGG 58.419 47.619 20.70 0.00 0.00 4.17
64 65 2.224549 TCCTTTTTAATGGACGCGTGTG 59.775 45.455 20.70 0.00 0.00 3.82
65 66 2.224784 GTCCTTTTTAATGGACGCGTGT 59.775 45.455 20.70 0.00 41.50 4.49
66 67 2.846693 GTCCTTTTTAATGGACGCGTG 58.153 47.619 20.70 0.00 41.50 5.34
72 73 2.817258 CGTGCCAGTCCTTTTTAATGGA 59.183 45.455 0.00 0.00 33.96 3.41
73 74 2.671070 GCGTGCCAGTCCTTTTTAATGG 60.671 50.000 0.00 0.00 35.21 3.16
74 75 2.595386 GCGTGCCAGTCCTTTTTAATG 58.405 47.619 0.00 0.00 0.00 1.90
75 76 1.199097 CGCGTGCCAGTCCTTTTTAAT 59.801 47.619 0.00 0.00 0.00 1.40
76 77 0.589223 CGCGTGCCAGTCCTTTTTAA 59.411 50.000 0.00 0.00 0.00 1.52
77 78 1.231958 CCGCGTGCCAGTCCTTTTTA 61.232 55.000 4.92 0.00 0.00 1.52
78 79 2.551912 CCGCGTGCCAGTCCTTTTT 61.552 57.895 4.92 0.00 0.00 1.94
79 80 2.978010 CCGCGTGCCAGTCCTTTT 60.978 61.111 4.92 0.00 0.00 2.27
97 98 3.052082 CTGGCAGTGTGCGGAAGG 61.052 66.667 6.28 0.00 46.21 3.46
98 99 3.052082 CCTGGCAGTGTGCGGAAG 61.052 66.667 14.43 0.00 46.21 3.46
99 100 3.872603 ACCTGGCAGTGTGCGGAA 61.873 61.111 14.43 0.00 46.21 4.30
100 101 4.624364 CACCTGGCAGTGTGCGGA 62.624 66.667 18.68 0.00 46.21 5.54
114 115 0.468029 CCACATATCAAGGGCCCACC 60.468 60.000 27.56 0.00 40.67 4.61
115 116 1.109323 GCCACATATCAAGGGCCCAC 61.109 60.000 27.56 0.00 40.55 4.61
116 117 1.229927 GCCACATATCAAGGGCCCA 59.770 57.895 27.56 2.74 40.55 5.36
117 118 4.181051 GCCACATATCAAGGGCCC 57.819 61.111 16.46 16.46 40.55 5.80
119 120 2.555547 GCGGCCACATATCAAGGGC 61.556 63.158 2.24 0.00 45.67 5.19
120 121 2.253758 CGCGGCCACATATCAAGGG 61.254 63.158 2.24 0.00 0.00 3.95
121 122 1.095228 AACGCGGCCACATATCAAGG 61.095 55.000 12.47 0.00 0.00 3.61
122 123 1.577468 TAACGCGGCCACATATCAAG 58.423 50.000 12.47 0.00 0.00 3.02
123 124 2.025589 TTAACGCGGCCACATATCAA 57.974 45.000 12.47 0.00 0.00 2.57
124 125 2.248280 ATTAACGCGGCCACATATCA 57.752 45.000 12.47 0.00 0.00 2.15
125 126 3.422603 CGTAATTAACGCGGCCACATATC 60.423 47.826 12.47 0.00 46.10 1.63
126 127 2.477375 CGTAATTAACGCGGCCACATAT 59.523 45.455 12.47 0.00 46.10 1.78
127 128 1.859703 CGTAATTAACGCGGCCACATA 59.140 47.619 12.47 0.00 46.10 2.29
128 129 0.653636 CGTAATTAACGCGGCCACAT 59.346 50.000 12.47 0.00 46.10 3.21
129 130 2.079874 CGTAATTAACGCGGCCACA 58.920 52.632 12.47 0.00 46.10 4.17
130 131 4.959491 CGTAATTAACGCGGCCAC 57.041 55.556 12.47 0.00 46.10 5.01
138 139 1.600485 CCCCATGCGGTCGTAATTAAC 59.400 52.381 0.00 0.00 0.00 2.01
139 140 1.475392 CCCCCATGCGGTCGTAATTAA 60.475 52.381 0.00 0.00 0.00 1.40
140 141 0.107081 CCCCCATGCGGTCGTAATTA 59.893 55.000 0.00 0.00 0.00 1.40
141 142 1.153046 CCCCCATGCGGTCGTAATT 60.153 57.895 0.00 0.00 0.00 1.40
142 143 2.508928 CCCCCATGCGGTCGTAAT 59.491 61.111 0.00 0.00 0.00 1.89
156 157 2.675423 GTCGGAAGCCAAACCCCC 60.675 66.667 0.00 0.00 0.00 5.40
157 158 2.114411 TGTCGGAAGCCAAACCCC 59.886 61.111 0.00 0.00 0.00 4.95
158 159 0.893727 ATGTGTCGGAAGCCAAACCC 60.894 55.000 0.00 0.00 0.00 4.11
159 160 0.240945 CATGTGTCGGAAGCCAAACC 59.759 55.000 0.00 0.00 0.00 3.27
160 161 0.951558 ACATGTGTCGGAAGCCAAAC 59.048 50.000 0.00 0.00 0.00 2.93
161 162 2.552599 TACATGTGTCGGAAGCCAAA 57.447 45.000 9.11 0.00 0.00 3.28
162 163 2.422597 CTTACATGTGTCGGAAGCCAA 58.577 47.619 9.11 0.00 0.00 4.52
163 164 1.338674 CCTTACATGTGTCGGAAGCCA 60.339 52.381 9.11 0.00 0.00 4.75
164 165 1.369625 CCTTACATGTGTCGGAAGCC 58.630 55.000 9.11 0.00 0.00 4.35
165 166 0.727398 GCCTTACATGTGTCGGAAGC 59.273 55.000 9.11 0.00 0.00 3.86
166 167 1.369625 GGCCTTACATGTGTCGGAAG 58.630 55.000 9.11 3.35 0.00 3.46
167 168 0.390603 CGGCCTTACATGTGTCGGAA 60.391 55.000 9.11 0.00 0.00 4.30
168 169 1.216977 CGGCCTTACATGTGTCGGA 59.783 57.895 9.11 0.00 0.00 4.55
169 170 2.461110 GCGGCCTTACATGTGTCGG 61.461 63.158 9.11 7.06 0.00 4.79
170 171 2.798501 CGCGGCCTTACATGTGTCG 61.799 63.158 9.11 6.44 0.00 4.35
171 172 1.447140 TCGCGGCCTTACATGTGTC 60.447 57.895 9.11 0.00 0.00 3.67
172 173 1.740296 GTCGCGGCCTTACATGTGT 60.740 57.895 9.11 0.00 0.00 3.72
173 174 2.798501 CGTCGCGGCCTTACATGTG 61.799 63.158 9.11 0.00 0.00 3.21
174 175 2.508439 CGTCGCGGCCTTACATGT 60.508 61.111 4.51 2.69 0.00 3.21
175 176 3.261951 CCGTCGCGGCCTTACATG 61.262 66.667 4.51 0.00 41.17 3.21
191 192 4.477975 CGCGTCCTCTCGGTGTCC 62.478 72.222 0.00 0.00 0.00 4.02
206 207 3.542742 GAAGTAGACACGCCGCGC 61.543 66.667 13.88 0.00 0.00 6.86
207 208 3.238241 CGAAGTAGACACGCCGCG 61.238 66.667 12.14 12.14 0.00 6.46
208 209 2.126580 ACGAAGTAGACACGCCGC 60.127 61.111 0.00 0.00 41.94 6.53
209 210 1.063951 GACACGAAGTAGACACGCCG 61.064 60.000 0.00 0.00 41.61 6.46
210 211 0.731855 GGACACGAAGTAGACACGCC 60.732 60.000 0.00 0.00 41.61 5.68
211 212 1.063951 CGGACACGAAGTAGACACGC 61.064 60.000 0.00 0.00 41.61 5.34
212 213 1.063951 GCGGACACGAAGTAGACACG 61.064 60.000 0.00 0.00 41.61 4.49
213 214 1.063951 CGCGGACACGAAGTAGACAC 61.064 60.000 0.00 0.00 41.61 3.67
214 215 1.208358 CGCGGACACGAAGTAGACA 59.792 57.895 0.00 0.00 41.61 3.41
215 216 2.150837 GCGCGGACACGAAGTAGAC 61.151 63.158 8.83 0.00 41.61 2.59
216 217 2.177531 GCGCGGACACGAAGTAGA 59.822 61.111 8.83 0.00 41.61 2.59
217 218 2.879462 GGCGCGGACACGAAGTAG 60.879 66.667 8.83 0.00 41.61 2.57
218 219 4.764336 CGGCGCGGACACGAAGTA 62.764 66.667 9.72 0.00 41.61 2.24
231 232 4.520846 GCCTGAAATGCGTCGGCG 62.521 66.667 4.29 4.29 44.10 6.46
232 233 4.179579 GGCCTGAAATGCGTCGGC 62.180 66.667 0.00 0.00 36.84 5.54
233 234 3.508840 GGGCCTGAAATGCGTCGG 61.509 66.667 0.84 0.00 0.00 4.79
234 235 3.864686 CGGGCCTGAAATGCGTCG 61.865 66.667 5.28 0.00 0.00 5.12
235 236 1.862602 AAACGGGCCTGAAATGCGTC 61.863 55.000 21.41 0.00 0.00 5.19
236 237 1.460273 AAAACGGGCCTGAAATGCGT 61.460 50.000 21.41 6.89 0.00 5.24
237 238 1.008361 CAAAACGGGCCTGAAATGCG 61.008 55.000 21.41 6.11 0.00 4.73
238 239 0.670239 CCAAAACGGGCCTGAAATGC 60.670 55.000 21.41 0.00 0.00 3.56
239 240 3.512978 CCAAAACGGGCCTGAAATG 57.487 52.632 21.41 13.02 0.00 2.32
249 250 0.239082 GCGACCTAAACCCAAAACGG 59.761 55.000 0.00 0.00 0.00 4.44
250 251 0.239082 GGCGACCTAAACCCAAAACG 59.761 55.000 0.00 0.00 0.00 3.60
251 252 1.001048 GTGGCGACCTAAACCCAAAAC 60.001 52.381 0.00 0.00 0.00 2.43
252 253 1.320507 GTGGCGACCTAAACCCAAAA 58.679 50.000 0.00 0.00 0.00 2.44
253 254 0.885596 CGTGGCGACCTAAACCCAAA 60.886 55.000 0.00 0.00 0.00 3.28
254 255 1.301874 CGTGGCGACCTAAACCCAA 60.302 57.895 0.00 0.00 0.00 4.12
255 256 2.042404 AACGTGGCGACCTAAACCCA 62.042 55.000 0.00 0.00 0.00 4.51
256 257 1.301953 AACGTGGCGACCTAAACCC 60.302 57.895 0.00 0.00 0.00 4.11
257 258 1.571215 CCAACGTGGCGACCTAAACC 61.571 60.000 0.00 0.00 0.00 3.27
258 259 1.571215 CCCAACGTGGCGACCTAAAC 61.571 60.000 0.00 0.00 35.79 2.01
259 260 1.301874 CCCAACGTGGCGACCTAAA 60.302 57.895 0.00 0.00 35.79 1.85
260 261 2.344500 CCCAACGTGGCGACCTAA 59.656 61.111 0.00 0.00 35.79 2.69
261 262 4.382320 GCCCAACGTGGCGACCTA 62.382 66.667 0.57 0.00 42.54 3.08
271 272 2.663852 AAAGACGTCGGCCCAACG 60.664 61.111 20.48 20.48 45.37 4.10
272 273 1.838568 GACAAAGACGTCGGCCCAAC 61.839 60.000 10.46 0.00 0.00 3.77
273 274 1.595929 GACAAAGACGTCGGCCCAA 60.596 57.895 10.46 0.00 0.00 4.12
274 275 2.029964 GACAAAGACGTCGGCCCA 59.970 61.111 10.46 0.00 0.00 5.36
275 276 2.741211 GGACAAAGACGTCGGCCC 60.741 66.667 10.46 2.14 36.73 5.80
276 277 3.110178 CGGACAAAGACGTCGGCC 61.110 66.667 10.46 6.84 36.73 6.13
278 279 3.110178 GGCGGACAAAGACGTCGG 61.110 66.667 10.46 6.64 38.77 4.79
280 281 3.774702 GCGGCGGACAAAGACGTC 61.775 66.667 9.78 7.70 43.06 4.34
283 284 3.774702 GTCGCGGCGGACAAAGAC 61.775 66.667 23.46 7.48 36.91 3.01
292 293 3.427425 TTCATTTGGGTCGCGGCG 61.427 61.111 17.70 17.70 0.00 6.46
293 294 1.933115 ATGTTCATTTGGGTCGCGGC 61.933 55.000 6.13 3.04 0.00 6.53
294 295 0.179166 CATGTTCATTTGGGTCGCGG 60.179 55.000 6.13 0.00 0.00 6.46
295 296 0.179166 CCATGTTCATTTGGGTCGCG 60.179 55.000 0.00 0.00 0.00 5.87
296 297 0.173255 CCCATGTTCATTTGGGTCGC 59.827 55.000 0.00 0.00 46.38 5.19
301 302 1.732077 CGTTCGCCCATGTTCATTTGG 60.732 52.381 0.00 0.00 0.00 3.28
302 303 1.198867 TCGTTCGCCCATGTTCATTTG 59.801 47.619 0.00 0.00 0.00 2.32
303 304 1.529226 TCGTTCGCCCATGTTCATTT 58.471 45.000 0.00 0.00 0.00 2.32
304 305 1.529226 TTCGTTCGCCCATGTTCATT 58.471 45.000 0.00 0.00 0.00 2.57
305 306 1.529226 TTTCGTTCGCCCATGTTCAT 58.471 45.000 0.00 0.00 0.00 2.57
306 307 1.198867 CATTTCGTTCGCCCATGTTCA 59.801 47.619 0.00 0.00 0.00 3.18
307 308 1.467374 CCATTTCGTTCGCCCATGTTC 60.467 52.381 0.00 0.00 0.00 3.18
308 309 0.525761 CCATTTCGTTCGCCCATGTT 59.474 50.000 0.00 0.00 0.00 2.71
309 310 1.312371 CCCATTTCGTTCGCCCATGT 61.312 55.000 0.00 0.00 0.00 3.21
310 311 1.312371 ACCCATTTCGTTCGCCCATG 61.312 55.000 0.00 0.00 0.00 3.66
311 312 1.001393 ACCCATTTCGTTCGCCCAT 60.001 52.632 0.00 0.00 0.00 4.00
312 313 1.673009 GACCCATTTCGTTCGCCCA 60.673 57.895 0.00 0.00 0.00 5.36
313 314 2.746803 CGACCCATTTCGTTCGCCC 61.747 63.158 0.00 0.00 34.16 6.13
314 315 2.746803 CCGACCCATTTCGTTCGCC 61.747 63.158 0.00 0.00 37.29 5.54
315 316 2.782615 CCGACCCATTTCGTTCGC 59.217 61.111 0.00 0.00 37.29 4.70
316 317 2.746803 GGCCGACCCATTTCGTTCG 61.747 63.158 0.00 0.00 37.29 3.95
317 318 2.746803 CGGCCGACCCATTTCGTTC 61.747 63.158 24.07 0.00 37.29 3.95
318 319 2.744709 CGGCCGACCCATTTCGTT 60.745 61.111 24.07 0.00 37.29 3.85
319 320 4.770874 CCGGCCGACCCATTTCGT 62.771 66.667 30.73 0.00 37.29 3.85
320 321 4.770874 ACCGGCCGACCCATTTCG 62.771 66.667 30.73 8.96 38.80 3.46
321 322 2.360726 AACCGGCCGACCCATTTC 60.361 61.111 30.73 0.00 0.00 2.17
322 323 2.675075 CAACCGGCCGACCCATTT 60.675 61.111 30.73 6.49 0.00 2.32
323 324 4.733542 CCAACCGGCCGACCCATT 62.734 66.667 30.73 9.77 0.00 3.16
327 328 4.324991 AACTCCAACCGGCCGACC 62.325 66.667 30.73 0.00 0.00 4.79
328 329 3.047877 CAACTCCAACCGGCCGAC 61.048 66.667 30.73 0.00 0.00 4.79
331 332 3.056328 GAGCAACTCCAACCGGCC 61.056 66.667 0.00 0.00 0.00 6.13
332 333 0.321298 TAAGAGCAACTCCAACCGGC 60.321 55.000 0.00 0.00 0.00 6.13
333 334 2.403252 ATAAGAGCAACTCCAACCGG 57.597 50.000 0.00 0.00 0.00 5.28
334 335 3.125316 GTCAATAAGAGCAACTCCAACCG 59.875 47.826 0.00 0.00 0.00 4.44
335 336 4.072131 TGTCAATAAGAGCAACTCCAACC 58.928 43.478 0.00 0.00 0.00 3.77
336 337 5.335191 CCTTGTCAATAAGAGCAACTCCAAC 60.335 44.000 0.00 0.00 0.00 3.77
337 338 4.761739 CCTTGTCAATAAGAGCAACTCCAA 59.238 41.667 0.00 0.00 0.00 3.53
338 339 4.202461 ACCTTGTCAATAAGAGCAACTCCA 60.202 41.667 0.00 0.00 0.00 3.86
339 340 4.327680 ACCTTGTCAATAAGAGCAACTCC 58.672 43.478 0.00 0.00 0.00 3.85
340 341 4.997395 TGACCTTGTCAATAAGAGCAACTC 59.003 41.667 0.00 0.00 39.78 3.01
341 342 4.973168 TGACCTTGTCAATAAGAGCAACT 58.027 39.130 0.00 0.00 39.78 3.16
342 343 4.154918 CCTGACCTTGTCAATAAGAGCAAC 59.845 45.833 0.00 0.00 42.26 4.17
343 344 4.202461 ACCTGACCTTGTCAATAAGAGCAA 60.202 41.667 0.00 0.00 42.26 3.91
344 345 3.327757 ACCTGACCTTGTCAATAAGAGCA 59.672 43.478 0.00 0.00 42.26 4.26
345 346 3.935828 GACCTGACCTTGTCAATAAGAGC 59.064 47.826 0.00 0.00 42.26 4.09
346 347 4.177026 CGACCTGACCTTGTCAATAAGAG 58.823 47.826 0.00 0.00 42.26 2.85
347 348 3.576982 ACGACCTGACCTTGTCAATAAGA 59.423 43.478 0.00 0.00 42.26 2.10
348 349 3.926616 ACGACCTGACCTTGTCAATAAG 58.073 45.455 0.00 0.00 42.26 1.73
349 350 3.306502 GGACGACCTGACCTTGTCAATAA 60.307 47.826 0.00 0.00 42.26 1.40
350 351 2.232941 GGACGACCTGACCTTGTCAATA 59.767 50.000 0.00 0.00 42.26 1.90
351 352 1.002087 GGACGACCTGACCTTGTCAAT 59.998 52.381 0.00 0.00 42.26 2.57
352 353 0.391597 GGACGACCTGACCTTGTCAA 59.608 55.000 0.00 0.00 42.26 3.18
353 354 1.469335 GGGACGACCTGACCTTGTCA 61.469 60.000 3.44 0.00 40.50 3.58
372 373 3.680786 TCGCCGCTCCCATATCGG 61.681 66.667 0.00 0.00 45.46 4.18
373 374 2.430921 GTCGCCGCTCCCATATCG 60.431 66.667 0.00 0.00 0.00 2.92
406 407 2.049228 GAACGACTATTATCGCCACCG 58.951 52.381 0.00 0.00 46.22 4.94
409 410 1.677576 ACCGAACGACTATTATCGCCA 59.322 47.619 0.00 0.00 46.22 5.69
415 416 3.181484 CCATGACCACCGAACGACTATTA 60.181 47.826 0.00 0.00 0.00 0.98
575 579 3.416156 AGCAACACCAGATTTTCCTCTC 58.584 45.455 0.00 0.00 0.00 3.20
630 634 2.664851 TTTGGTCGGAGCAGCACG 60.665 61.111 10.06 0.00 0.00 5.34
631 635 2.970974 GCTTTGGTCGGAGCAGCAC 61.971 63.158 14.25 3.78 38.73 4.40
663 668 1.213926 AGGGATCCAGATTGGTTGCTC 59.786 52.381 15.23 0.00 39.03 4.26
809 815 4.319477 CCGTCGTTCACACTTCATCAAATT 60.319 41.667 0.00 0.00 0.00 1.82
829 835 4.563061 AGTAAACTCGAATTTGTAGCCGT 58.437 39.130 1.38 0.00 0.00 5.68
830 836 4.624024 TGAGTAAACTCGAATTTGTAGCCG 59.376 41.667 1.38 0.00 45.72 5.52
849 855 3.553096 GGATCACGTCAAGAACAGTGAGT 60.553 47.826 0.00 0.00 41.36 3.41
879 885 1.790387 GCTCTAACTTGCGCACCTG 59.210 57.895 11.12 6.09 0.00 4.00
1164 1170 1.202568 GAACGAGACGACGTCGACA 59.797 57.895 41.52 0.00 45.83 4.35
1256 1262 1.375908 TCGTTGTCATCCAGCAGCC 60.376 57.895 0.00 0.00 0.00 4.85
1694 1700 4.274459 GGTATGCACTGCAGGAAAATAGAG 59.726 45.833 19.93 0.00 43.65 2.43
1792 1798 3.181471 CCACATTGGCTGGTTTGTGTTTA 60.181 43.478 0.00 0.00 38.19 2.01
1814 1820 9.614792 AGGTAAATCAAGGAATGAACATAGTAC 57.385 33.333 0.00 0.00 42.54 2.73
1862 1868 6.210385 ACCATTCTACAGTGCTCTATATCAGG 59.790 42.308 0.00 0.00 0.00 3.86
1887 1893 1.336702 GCAATTCCGATGTTGCCAACA 60.337 47.619 13.44 13.44 46.94 3.33
1964 1970 4.440525 CCATGTATAGCAACAAAAGGCAGG 60.441 45.833 0.00 0.00 32.02 4.85
2226 2247 4.671831 TCCATGGCTTCTATCCTCTAGAG 58.328 47.826 13.18 13.18 0.00 2.43
2240 2261 2.439507 CACCTGTAACCTATCCATGGCT 59.560 50.000 6.96 0.00 0.00 4.75
2296 2324 9.772973 TCAGTAGTTATGTTGTTGATTTAGTGT 57.227 29.630 0.00 0.00 0.00 3.55
2741 2773 9.722056 GTAGAAATGTAGAATTGCAAATACTGG 57.278 33.333 1.71 0.00 0.00 4.00
2749 2781 7.013274 GCTTATGGGTAGAAATGTAGAATTGCA 59.987 37.037 0.00 0.00 0.00 4.08
2812 2844 0.955919 CAAGTGGTTCTCGAAGGCCC 60.956 60.000 0.00 0.00 0.00 5.80
3242 3701 1.524355 CACTCAACAGACAGCAAGACG 59.476 52.381 0.00 0.00 0.00 4.18
3586 4045 3.044059 GCGCCACTCTTGACCATGC 62.044 63.158 0.00 0.00 0.00 4.06
3686 4149 1.077212 CCATGCCCCAGGAGTGAAG 60.077 63.158 0.00 0.00 0.00 3.02
3911 4374 4.870363 TCTTTCATTTACAAGCAGCCAAC 58.130 39.130 0.00 0.00 0.00 3.77
3915 4378 4.431661 AGCTCTTTCATTTACAAGCAGC 57.568 40.909 0.00 0.00 32.25 5.25
3941 4404 5.246656 AGCATTGTTCATTTCAATGGAAGGA 59.753 36.000 16.62 0.00 46.79 3.36
3949 4424 6.153756 CACTCATCAGCATTGTTCATTTCAA 58.846 36.000 0.00 0.00 0.00 2.69
3952 4427 4.491676 GCACTCATCAGCATTGTTCATTT 58.508 39.130 0.00 0.00 0.00 2.32
3953 4428 3.427098 CGCACTCATCAGCATTGTTCATT 60.427 43.478 0.00 0.00 0.00 2.57
3954 4429 2.096980 CGCACTCATCAGCATTGTTCAT 59.903 45.455 0.00 0.00 0.00 2.57
3955 4430 1.465777 CGCACTCATCAGCATTGTTCA 59.534 47.619 0.00 0.00 0.00 3.18
3956 4431 1.792993 GCGCACTCATCAGCATTGTTC 60.793 52.381 0.30 0.00 0.00 3.18
3957 4432 0.169672 GCGCACTCATCAGCATTGTT 59.830 50.000 0.30 0.00 0.00 2.83
3958 4433 1.651240 GGCGCACTCATCAGCATTGT 61.651 55.000 10.83 0.00 0.00 2.71
3959 4434 1.063649 GGCGCACTCATCAGCATTG 59.936 57.895 10.83 0.00 0.00 2.82
3960 4435 0.750546 ATGGCGCACTCATCAGCATT 60.751 50.000 10.83 0.00 0.00 3.56
3961 4436 0.750546 AATGGCGCACTCATCAGCAT 60.751 50.000 10.83 0.00 0.00 3.79
3962 4437 1.371337 GAATGGCGCACTCATCAGCA 61.371 55.000 10.83 0.00 0.00 4.41
3963 4438 1.094073 AGAATGGCGCACTCATCAGC 61.094 55.000 10.83 0.00 0.00 4.26
3976 4451 5.010922 TCAACATTTTCCTTGGTCAGAATGG 59.989 40.000 0.00 0.00 36.16 3.16
4094 4569 1.134551 GCTTGGCCCTTGTTGTTTCAA 60.135 47.619 0.00 0.00 0.00 2.69
4095 4570 0.463620 GCTTGGCCCTTGTTGTTTCA 59.536 50.000 0.00 0.00 0.00 2.69
4201 4676 3.120792 CGTTCTTTGAGTTCTCCGTCAA 58.879 45.455 0.00 0.00 0.00 3.18
4334 4810 2.203015 CCACGGTATTGCCTCGGG 60.203 66.667 0.00 0.00 34.25 5.14
4445 4921 4.610714 GCGGCCCCGAGAGAATCC 62.611 72.222 11.48 0.00 42.83 3.01


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

AutoCloner maintained by Alex Coulton.