Multiple sequence alignment - TraesCS3B01G371200

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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 TraesCS3B01G371200 chr3B 100.000 3166 0 0 1 3166 583393936 583390771 0.000000e+00 5847.0
1 TraesCS3B01G371200 chr3B 90.741 216 16 3 1608 1823 763576032 763576243 5.170000e-73 285.0
2 TraesCS3B01G371200 chr3B 87.347 245 24 7 1041 1282 22505977 22505737 1.120000e-69 274.0
3 TraesCS3B01G371200 chr3A 89.694 3105 141 73 161 3166 586423973 586420949 0.000000e+00 3795.0
4 TraesCS3B01G371200 chr3D 90.271 2323 88 49 211 2504 445039040 445036827 0.000000e+00 2911.0
5 TraesCS3B01G371200 chr3D 93.062 663 28 5 2518 3166 445036766 445036108 0.000000e+00 953.0
6 TraesCS3B01G371200 chr3D 87.843 255 23 8 1041 1291 33858870 33858620 3.090000e-75 292.0
7 TraesCS3B01G371200 chrUn 87.843 255 23 8 1041 1291 240676935 240677185 3.090000e-75 292.0
8 TraesCS3B01G371200 chrUn 90.278 216 17 3 1608 1823 162682310 162682521 2.400000e-71 279.0
9 TraesCS3B01G371200 chr2A 90.541 222 17 3 1608 1829 722102192 722101975 1.110000e-74 291.0
10 TraesCS3B01G371200 chr2A 85.714 98 12 2 2423 2519 440365568 440365472 5.590000e-18 102.0
11 TraesCS3B01G371200 chr2A 85.859 99 10 4 2422 2519 700970232 700970137 5.590000e-18 102.0
12 TraesCS3B01G371200 chr7D 87.451 255 23 9 1041 1291 555231877 555231628 5.170000e-73 285.0
13 TraesCS3B01G371200 chr6D 90.741 216 16 3 1608 1823 322697881 322698092 5.170000e-73 285.0
14 TraesCS3B01G371200 chr6D 90.090 222 18 3 1608 1829 384196354 384196137 5.170000e-73 285.0
15 TraesCS3B01G371200 chr6D 84.342 281 29 9 1344 1621 27820131 27819863 8.710000e-66 261.0
16 TraesCS3B01G371200 chr6D 91.463 82 6 1 2439 2519 8138020 8137939 9.280000e-21 111.0
17 TraesCS3B01G371200 chr2D 90.411 219 17 3 1611 1829 614385446 614385232 5.170000e-73 285.0
18 TraesCS3B01G371200 chr2B 90.090 222 17 4 1608 1829 50580978 50580762 1.860000e-72 283.0
19 TraesCS3B01G371200 chr2B 89.655 87 8 1 2434 2519 185812970 185812884 3.340000e-20 110.0
20 TraesCS3B01G371200 chr5D 83.737 289 38 6 1350 1635 519277430 519277712 6.730000e-67 265.0
21 TraesCS3B01G371200 chr5D 89.241 158 17 0 1057 1214 519277258 519277415 6.930000e-47 198.0
22 TraesCS3B01G371200 chr5D 82.051 234 37 5 1354 1586 238066458 238066687 8.960000e-46 195.0
23 TraesCS3B01G371200 chr5A 83.681 288 38 7 1350 1634 645726432 645726713 2.420000e-66 263.0
24 TraesCS3B01G371200 chr5A 82.329 249 39 5 1354 1601 317247921 317247677 8.900000e-51 211.0
25 TraesCS3B01G371200 chr5A 88.679 159 16 2 1057 1214 645726260 645726417 3.220000e-45 193.0
26 TraesCS3B01G371200 chr5B 83.333 288 39 6 1350 1634 653432687 653432968 1.130000e-64 257.0
27 TraesCS3B01G371200 chr5B 81.526 249 41 5 1354 1601 267779038 267778794 1.930000e-47 200.0
28 TraesCS3B01G371200 chr5B 85.535 159 21 2 1057 1214 653432515 653432672 7.030000e-37 165.0
29 TraesCS3B01G371200 chr6B 85.214 257 27 6 1344 1599 51580242 51579996 1.460000e-63 254.0
30 TraesCS3B01G371200 chr6B 88.889 90 8 2 2432 2519 314590345 314590434 3.340000e-20 110.0
31 TraesCS3B01G371200 chr6A 84.411 263 27 8 1344 1604 30191060 30190810 2.440000e-61 246.0
32 TraesCS3B01G371200 chr6A 88.889 90 8 2 2432 2519 352665656 352665745 3.340000e-20 110.0
33 TraesCS3B01G371200 chr1A 82.578 287 36 8 1334 1619 459188156 459187883 1.130000e-59 241.0
34 TraesCS3B01G371200 chr7A 91.566 83 6 1 2438 2519 409866212 409866130 2.580000e-21 113.0
35 TraesCS3B01G371200 chr7A 75.000 232 49 7 1368 1596 512328966 512329191 7.230000e-17 99.0
36 TraesCS3B01G371200 chr7B 80.734 109 21 0 1488 1596 436787462 436787354 5.630000e-13 86.1


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 TraesCS3B01G371200 chr3B 583390771 583393936 3165 True 5847 5847 100.0000 1 3166 1 chr3B.!!$R2 3165
1 TraesCS3B01G371200 chr3A 586420949 586423973 3024 True 3795 3795 89.6940 161 3166 1 chr3A.!!$R1 3005
2 TraesCS3B01G371200 chr3D 445036108 445039040 2932 True 1932 2911 91.6665 211 3166 2 chr3D.!!$R2 2955

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
140 141 0.099436 CGCTCATGTTTAAGCAGCCC 59.901 55.0 5.13 0.0 38.45 5.19 F
1653 1769 0.108019 ACCCCAACGTCTTCCAGTTC 59.892 55.0 0.00 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2015 2131 0.036952 AAGTCTGCAGGTCGTCCATG 60.037 55.000 15.13 0.0 35.89 3.66 R
2781 2989 1.135315 CCCACTGTCAATTTCATGGCG 60.135 52.381 0.00 0.0 0.00 5.69 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
22 23 5.088141 CGTGCATATCATGTTCTTTCTCC 57.912 43.478 0.00 0.00 0.00 3.71
23 24 4.571984 CGTGCATATCATGTTCTTTCTCCA 59.428 41.667 0.00 0.00 0.00 3.86
24 25 5.237996 CGTGCATATCATGTTCTTTCTCCAT 59.762 40.000 0.00 0.00 0.00 3.41
25 26 6.238566 CGTGCATATCATGTTCTTTCTCCATT 60.239 38.462 0.00 0.00 0.00 3.16
26 27 7.137426 GTGCATATCATGTTCTTTCTCCATTC 58.863 38.462 0.00 0.00 0.00 2.67
27 28 6.829811 TGCATATCATGTTCTTTCTCCATTCA 59.170 34.615 0.00 0.00 0.00 2.57
28 29 7.137426 GCATATCATGTTCTTTCTCCATTCAC 58.863 38.462 0.00 0.00 0.00 3.18
29 30 7.201758 GCATATCATGTTCTTTCTCCATTCACA 60.202 37.037 0.00 0.00 0.00 3.58
30 31 8.680001 CATATCATGTTCTTTCTCCATTCACAA 58.320 33.333 0.00 0.00 0.00 3.33
31 32 6.957920 TCATGTTCTTTCTCCATTCACAAA 57.042 33.333 0.00 0.00 0.00 2.83
32 33 7.528996 TCATGTTCTTTCTCCATTCACAAAT 57.471 32.000 0.00 0.00 0.00 2.32
33 34 8.634335 TCATGTTCTTTCTCCATTCACAAATA 57.366 30.769 0.00 0.00 0.00 1.40
34 35 9.246670 TCATGTTCTTTCTCCATTCACAAATAT 57.753 29.630 0.00 0.00 0.00 1.28
78 79 6.293698 TCTGAATCAGATGTACATCCAATGG 58.706 40.000 28.26 14.97 35.39 3.16
79 80 4.823442 TGAATCAGATGTACATCCAATGGC 59.177 41.667 28.26 17.79 38.58 4.40
80 81 4.719026 ATCAGATGTACATCCAATGGCT 57.281 40.909 28.26 8.74 38.58 4.75
81 82 4.508551 TCAGATGTACATCCAATGGCTT 57.491 40.909 28.26 8.04 38.58 4.35
82 83 5.628797 TCAGATGTACATCCAATGGCTTA 57.371 39.130 28.26 5.63 38.58 3.09
83 84 6.000246 TCAGATGTACATCCAATGGCTTAA 58.000 37.500 28.26 5.31 38.58 1.85
84 85 6.604171 TCAGATGTACATCCAATGGCTTAAT 58.396 36.000 28.26 6.17 38.58 1.40
85 86 7.744733 TCAGATGTACATCCAATGGCTTAATA 58.255 34.615 28.26 4.07 38.58 0.98
86 87 8.217111 TCAGATGTACATCCAATGGCTTAATAA 58.783 33.333 28.26 3.44 38.58 1.40
87 88 9.017509 CAGATGTACATCCAATGGCTTAATAAT 57.982 33.333 28.26 4.95 38.58 1.28
88 89 9.236006 AGATGTACATCCAATGGCTTAATAATC 57.764 33.333 28.26 2.58 38.58 1.75
89 90 8.938801 ATGTACATCCAATGGCTTAATAATCA 57.061 30.769 1.41 0.00 33.60 2.57
90 91 8.165239 TGTACATCCAATGGCTTAATAATCAC 57.835 34.615 0.00 0.00 33.60 3.06
91 92 7.998383 TGTACATCCAATGGCTTAATAATCACT 59.002 33.333 0.00 0.00 33.60 3.41
92 93 7.902920 ACATCCAATGGCTTAATAATCACTT 57.097 32.000 0.00 0.00 33.60 3.16
93 94 8.995027 ACATCCAATGGCTTAATAATCACTTA 57.005 30.769 0.00 0.00 33.60 2.24
94 95 9.420118 ACATCCAATGGCTTAATAATCACTTAA 57.580 29.630 0.00 0.00 33.60 1.85
111 112 6.548171 TCACTTAATTAAACATAACAGGCGC 58.452 36.000 0.00 0.00 0.00 6.53
112 113 5.451023 CACTTAATTAAACATAACAGGCGCG 59.549 40.000 0.00 0.00 0.00 6.86
113 114 2.468532 ATTAAACATAACAGGCGCGC 57.531 45.000 25.94 25.94 0.00 6.86
114 115 1.444836 TTAAACATAACAGGCGCGCT 58.555 45.000 32.29 14.07 0.00 5.92
115 116 1.444836 TAAACATAACAGGCGCGCTT 58.555 45.000 32.29 23.01 0.00 4.68
116 117 0.109781 AAACATAACAGGCGCGCTTG 60.110 50.000 37.34 37.34 0.00 4.01
117 118 2.277501 CATAACAGGCGCGCTTGC 60.278 61.111 38.59 20.09 0.00 4.01
118 119 2.745884 ATAACAGGCGCGCTTGCA 60.746 55.556 38.59 28.04 39.07 4.08
119 120 2.114670 ATAACAGGCGCGCTTGCAT 61.115 52.632 38.59 29.73 39.07 3.96
120 121 1.656818 ATAACAGGCGCGCTTGCATT 61.657 50.000 38.59 28.57 39.07 3.56
121 122 2.252127 TAACAGGCGCGCTTGCATTC 62.252 55.000 38.59 17.77 39.07 2.67
127 128 2.406401 GCGCTTGCATTCGCTCAT 59.594 55.556 21.07 0.00 46.92 2.90
128 129 1.937846 GCGCTTGCATTCGCTCATG 60.938 57.895 21.07 0.00 46.92 3.07
129 130 1.426621 CGCTTGCATTCGCTCATGT 59.573 52.632 0.00 0.00 39.64 3.21
130 131 0.179181 CGCTTGCATTCGCTCATGTT 60.179 50.000 0.00 0.00 39.64 2.71
131 132 1.730121 CGCTTGCATTCGCTCATGTTT 60.730 47.619 0.00 0.00 39.64 2.83
132 133 2.476018 CGCTTGCATTCGCTCATGTTTA 60.476 45.455 0.00 0.00 39.64 2.01
133 134 3.500982 GCTTGCATTCGCTCATGTTTAA 58.499 40.909 0.00 0.00 39.64 1.52
134 135 3.545078 GCTTGCATTCGCTCATGTTTAAG 59.455 43.478 0.00 0.00 39.64 1.85
135 136 3.135414 TGCATTCGCTCATGTTTAAGC 57.865 42.857 0.00 0.00 39.64 3.09
136 137 2.487372 TGCATTCGCTCATGTTTAAGCA 59.513 40.909 5.13 0.00 38.45 3.91
137 138 3.103738 GCATTCGCTCATGTTTAAGCAG 58.896 45.455 5.13 0.00 38.45 4.24
138 139 2.900122 TTCGCTCATGTTTAAGCAGC 57.100 45.000 5.13 0.00 38.45 5.25
139 140 1.086696 TCGCTCATGTTTAAGCAGCC 58.913 50.000 5.13 0.00 38.45 4.85
140 141 0.099436 CGCTCATGTTTAAGCAGCCC 59.901 55.000 5.13 0.00 38.45 5.19
141 142 0.099436 GCTCATGTTTAAGCAGCCCG 59.901 55.000 0.00 0.00 38.42 6.13
142 143 1.453155 CTCATGTTTAAGCAGCCCGT 58.547 50.000 0.00 0.00 0.00 5.28
143 144 1.131126 CTCATGTTTAAGCAGCCCGTG 59.869 52.381 0.00 0.00 0.00 4.94
144 145 0.171007 CATGTTTAAGCAGCCCGTGG 59.829 55.000 0.00 0.00 0.00 4.94
145 146 0.251165 ATGTTTAAGCAGCCCGTGGT 60.251 50.000 0.00 0.00 39.08 4.16
146 147 0.397187 TGTTTAAGCAGCCCGTGGTA 59.603 50.000 0.00 0.00 35.15 3.25
147 148 1.084289 GTTTAAGCAGCCCGTGGTAG 58.916 55.000 0.00 0.00 35.15 3.18
148 149 0.978151 TTTAAGCAGCCCGTGGTAGA 59.022 50.000 0.00 0.00 35.15 2.59
149 150 0.535335 TTAAGCAGCCCGTGGTAGAG 59.465 55.000 0.00 0.00 35.15 2.43
150 151 1.327690 TAAGCAGCCCGTGGTAGAGG 61.328 60.000 0.00 0.00 35.15 3.69
151 152 3.075005 GCAGCCCGTGGTAGAGGA 61.075 66.667 0.00 0.00 0.00 3.71
152 153 2.435693 GCAGCCCGTGGTAGAGGAT 61.436 63.158 0.00 0.00 0.00 3.24
153 154 1.443407 CAGCCCGTGGTAGAGGATG 59.557 63.158 0.00 0.00 0.00 3.51
154 155 1.762460 AGCCCGTGGTAGAGGATGG 60.762 63.158 0.00 0.00 0.00 3.51
155 156 2.064581 GCCCGTGGTAGAGGATGGT 61.065 63.158 0.00 0.00 0.00 3.55
156 157 1.623542 GCCCGTGGTAGAGGATGGTT 61.624 60.000 0.00 0.00 0.00 3.67
157 158 0.464452 CCCGTGGTAGAGGATGGTTC 59.536 60.000 0.00 0.00 0.00 3.62
158 159 1.191535 CCGTGGTAGAGGATGGTTCA 58.808 55.000 0.00 0.00 0.00 3.18
159 160 1.762957 CCGTGGTAGAGGATGGTTCAT 59.237 52.381 0.00 0.00 0.00 2.57
170 171 4.855340 AGGATGGTTCATATCCACGTTTT 58.145 39.130 6.77 0.00 45.28 2.43
207 212 3.635373 GGATAGGACTTGACGTGGTCATA 59.365 47.826 0.00 0.97 42.40 2.15
209 214 3.526931 AGGACTTGACGTGGTCATATG 57.473 47.619 0.00 0.00 42.40 1.78
240 245 9.554724 CGTTTATATGCTGAAACTAAACAATGT 57.445 29.630 0.00 0.00 33.82 2.71
258 263 5.416952 ACAATGTCATCTTTGAAGGGTCATC 59.583 40.000 0.00 0.00 32.48 2.92
259 264 4.916041 TGTCATCTTTGAAGGGTCATCT 57.084 40.909 0.00 0.00 32.48 2.90
260 265 6.566079 ATGTCATCTTTGAAGGGTCATCTA 57.434 37.500 0.00 0.00 32.48 1.98
261 266 5.734720 TGTCATCTTTGAAGGGTCATCTAC 58.265 41.667 0.00 0.00 32.48 2.59
262 267 5.485353 TGTCATCTTTGAAGGGTCATCTACT 59.515 40.000 0.00 0.00 32.48 2.57
263 268 6.045955 GTCATCTTTGAAGGGTCATCTACTC 58.954 44.000 0.00 0.00 32.48 2.59
264 269 4.720649 TCTTTGAAGGGTCATCTACTCG 57.279 45.455 0.00 0.00 31.85 4.18
265 270 4.087182 TCTTTGAAGGGTCATCTACTCGT 58.913 43.478 0.00 0.00 31.85 4.18
266 271 5.258841 TCTTTGAAGGGTCATCTACTCGTA 58.741 41.667 0.00 0.00 31.85 3.43
293 302 3.503800 TTCTAGCTAGCGTGATCCCTA 57.496 47.619 16.35 0.00 0.00 3.53
357 370 2.568062 TGGAAAACCTTCATGCATGCAT 59.432 40.909 27.46 27.46 37.08 3.96
371 399 3.925238 GCATGCGCGGGTCGTAAG 61.925 66.667 8.83 0.00 41.07 2.34
401 429 3.641906 CCTCATACCTTCCTCCACGTATT 59.358 47.826 0.00 0.00 0.00 1.89
409 440 3.703286 TCCTCCACGTATTACGACATG 57.297 47.619 22.18 10.25 46.05 3.21
412 443 3.316029 CCTCCACGTATTACGACATGGTA 59.684 47.826 22.18 8.94 46.05 3.25
414 445 3.038017 CCACGTATTACGACATGGTACG 58.962 50.000 22.18 2.58 46.05 3.67
435 466 2.125229 CTGCCGCAGCTCACAGAT 60.125 61.111 7.61 0.00 40.80 2.90
436 467 1.142531 CTGCCGCAGCTCACAGATA 59.857 57.895 7.61 0.00 40.80 1.98
437 468 0.875040 CTGCCGCAGCTCACAGATAG 60.875 60.000 7.61 0.00 40.80 2.08
447 478 2.200067 CTCACAGATAGCCAAGAAGCG 58.800 52.381 0.00 0.00 38.01 4.68
489 523 1.135915 CGGATGAGAGGTCCAGAACAG 59.864 57.143 0.00 0.00 35.41 3.16
496 530 2.099405 GAGGTCCAGAACAGAGAGGAG 58.901 57.143 0.00 0.00 0.00 3.69
594 632 2.516225 CGGAAAATCCCTCCCGGC 60.516 66.667 0.00 0.00 38.42 6.13
610 656 2.680913 GGCTGTCGCGCATTTGACT 61.681 57.895 8.75 0.00 36.10 3.41
711 762 2.076863 GTCCTCCTCATCCAAACAACG 58.923 52.381 0.00 0.00 0.00 4.10
887 939 0.617820 AGGAGGCGGTATCACAACCT 60.618 55.000 0.00 0.00 37.39 3.50
888 940 0.462047 GGAGGCGGTATCACAACCTG 60.462 60.000 0.00 0.00 37.39 4.00
889 941 1.078426 AGGCGGTATCACAACCTGC 60.078 57.895 0.00 0.00 37.39 4.85
911 973 1.066502 GCCGCCTTTCTCTTCTCTTCT 60.067 52.381 0.00 0.00 0.00 2.85
912 974 2.614229 GCCGCCTTTCTCTTCTCTTCTT 60.614 50.000 0.00 0.00 0.00 2.52
913 975 3.258228 CCGCCTTTCTCTTCTCTTCTTC 58.742 50.000 0.00 0.00 0.00 2.87
914 976 3.056179 CCGCCTTTCTCTTCTCTTCTTCT 60.056 47.826 0.00 0.00 0.00 2.85
915 977 4.562552 CCGCCTTTCTCTTCTCTTCTTCTT 60.563 45.833 0.00 0.00 0.00 2.52
917 979 5.566627 CGCCTTTCTCTTCTCTTCTTCTTCT 60.567 44.000 0.00 0.00 0.00 2.85
918 980 5.869344 GCCTTTCTCTTCTCTTCTTCTTCTC 59.131 44.000 0.00 0.00 0.00 2.87
919 981 6.295292 GCCTTTCTCTTCTCTTCTTCTTCTCT 60.295 42.308 0.00 0.00 0.00 3.10
920 982 7.670364 CCTTTCTCTTCTCTTCTTCTTCTCTT 58.330 38.462 0.00 0.00 0.00 2.85
921 983 7.814587 CCTTTCTCTTCTCTTCTTCTTCTCTTC 59.185 40.741 0.00 0.00 0.00 2.87
924 986 6.434028 TCTCTTCTCTTCTTCTTCTCTTCCAG 59.566 42.308 0.00 0.00 0.00 3.86
930 992 0.321671 TTCTTCTCTTCCAGCACCGG 59.678 55.000 0.00 0.00 0.00 5.28
974 1036 3.636231 TCCAAGGTGGTGGAGCGG 61.636 66.667 0.00 0.00 42.97 5.52
1152 1246 2.435586 CTCTGCAGGAAGGTGGCG 60.436 66.667 15.13 0.00 0.00 5.69
1264 1361 0.621082 CTCTCCCCTCCCCTGTTTTC 59.379 60.000 0.00 0.00 0.00 2.29
1267 1364 0.196118 TCCCCTCCCCTGTTTTCTCT 59.804 55.000 0.00 0.00 0.00 3.10
1274 1371 3.327439 TCCCCTGTTTTCTCTTCTCCTT 58.673 45.455 0.00 0.00 0.00 3.36
1290 1387 2.909662 CTCCTTCTTCCTCCTTCTTGGT 59.090 50.000 0.00 0.00 37.07 3.67
1291 1388 2.639839 TCCTTCTTCCTCCTTCTTGGTG 59.360 50.000 0.00 0.00 37.07 4.17
1310 1422 0.318955 GGTTCAATGTGTGCTGTGCC 60.319 55.000 0.00 0.00 0.00 5.01
1311 1423 0.661187 GTTCAATGTGTGCTGTGCCG 60.661 55.000 0.00 0.00 0.00 5.69
1312 1424 2.405061 TTCAATGTGTGCTGTGCCGC 62.405 55.000 0.00 0.00 0.00 6.53
1313 1425 4.029186 AATGTGTGCTGTGCCGCG 62.029 61.111 0.00 0.00 0.00 6.46
1387 1499 1.000506 GAGTGGTACTTCTTCACGCCA 59.999 52.381 0.00 0.00 36.60 5.69
1456 1568 2.272471 GGCTACTGGAAGGCCACC 59.728 66.667 5.01 9.00 40.52 4.61
1640 1752 1.920351 GATCCCTCAAGGTAACCCCAA 59.080 52.381 0.00 0.00 36.75 4.12
1653 1769 0.108019 ACCCCAACGTCTTCCAGTTC 59.892 55.000 0.00 0.00 0.00 3.01
1680 1796 5.536161 AGTTTGCTCACCAACAATACTGATT 59.464 36.000 0.00 0.00 31.97 2.57
1681 1797 5.627499 TTGCTCACCAACAATACTGATTC 57.373 39.130 0.00 0.00 0.00 2.52
1685 1801 5.503031 GCTCACCAACAATACTGATTCATCG 60.503 44.000 0.00 0.00 0.00 3.84
1715 1831 9.733556 GATACTGAATACTGATCCTTCTCTCTA 57.266 37.037 0.00 0.00 0.00 2.43
1791 1907 3.778954 AGAAGAACAACTGGGAGAAGG 57.221 47.619 0.00 0.00 0.00 3.46
1939 2055 4.436448 GCAGCAGCGCGTCTTCAC 62.436 66.667 8.43 0.00 0.00 3.18
2015 2131 4.329545 TGGTTCACCGGCCTGAGC 62.330 66.667 0.00 0.00 39.43 4.26
2102 2218 3.524606 GACGGCAGCGGCTACCTA 61.525 66.667 16.88 0.00 40.87 3.08
2106 2222 2.722201 GGCAGCGGCTACCTACAGT 61.722 63.158 12.13 0.00 40.87 3.55
2117 2233 2.130272 ACCTACAGTCGATGAGCTCA 57.870 50.000 20.79 20.79 0.00 4.26
2254 2370 9.921637 ACTTTGTTGAACTAGAAAGAGATAGAG 57.078 33.333 11.93 0.00 31.24 2.43
2414 2530 3.947834 CACCAAACTTGTTCTTCTGACCT 59.052 43.478 0.00 0.00 0.00 3.85
2421 2537 5.684704 ACTTGTTCTTCTGACCTTTGATCA 58.315 37.500 0.00 0.00 0.00 2.92
2422 2538 6.122277 ACTTGTTCTTCTGACCTTTGATCAA 58.878 36.000 3.38 3.38 0.00 2.57
2423 2539 6.774656 ACTTGTTCTTCTGACCTTTGATCAAT 59.225 34.615 9.40 0.00 0.00 2.57
2424 2540 6.808008 TGTTCTTCTGACCTTTGATCAATC 57.192 37.500 9.40 4.77 0.00 2.67
2425 2541 6.537355 TGTTCTTCTGACCTTTGATCAATCT 58.463 36.000 9.40 0.00 0.00 2.40
2426 2542 6.429078 TGTTCTTCTGACCTTTGATCAATCTG 59.571 38.462 9.40 8.33 0.00 2.90
2427 2543 6.364568 TCTTCTGACCTTTGATCAATCTGA 57.635 37.500 9.40 10.46 0.00 3.27
2428 2544 6.772605 TCTTCTGACCTTTGATCAATCTGAA 58.227 36.000 19.93 19.93 0.00 3.02
2429 2545 7.226441 TCTTCTGACCTTTGATCAATCTGAAA 58.774 34.615 20.80 13.71 30.13 2.69
2430 2546 6.808008 TCTGACCTTTGATCAATCTGAAAC 57.192 37.500 9.40 0.00 0.00 2.78
2431 2547 6.298361 TCTGACCTTTGATCAATCTGAAACA 58.702 36.000 9.40 3.54 0.00 2.83
2459 2586 2.305858 ACATATACTCCCTCCGTCCC 57.694 55.000 0.00 0.00 0.00 4.46
2466 2593 1.146566 ACTCCCTCCGTCCCGTATTAT 59.853 52.381 0.00 0.00 0.00 1.28
2474 2601 4.435425 TCCGTCCCGTATTATTTGTCTTG 58.565 43.478 0.00 0.00 0.00 3.02
2475 2602 3.558418 CCGTCCCGTATTATTTGTCTTGG 59.442 47.826 0.00 0.00 0.00 3.61
2476 2603 4.435425 CGTCCCGTATTATTTGTCTTGGA 58.565 43.478 0.00 0.00 0.00 3.53
2477 2604 5.054477 CGTCCCGTATTATTTGTCTTGGAT 58.946 41.667 0.00 0.00 0.00 3.41
2478 2605 5.526111 CGTCCCGTATTATTTGTCTTGGATT 59.474 40.000 0.00 0.00 0.00 3.01
2479 2606 6.037830 CGTCCCGTATTATTTGTCTTGGATTT 59.962 38.462 0.00 0.00 0.00 2.17
2480 2607 7.193595 GTCCCGTATTATTTGTCTTGGATTTG 58.806 38.462 0.00 0.00 0.00 2.32
2481 2608 6.887545 TCCCGTATTATTTGTCTTGGATTTGT 59.112 34.615 0.00 0.00 0.00 2.83
2482 2609 7.066525 TCCCGTATTATTTGTCTTGGATTTGTC 59.933 37.037 0.00 0.00 0.00 3.18
2483 2610 7.067008 CCCGTATTATTTGTCTTGGATTTGTCT 59.933 37.037 0.00 0.00 0.00 3.41
2484 2611 9.104965 CCGTATTATTTGTCTTGGATTTGTCTA 57.895 33.333 0.00 0.00 0.00 2.59
2566 2759 7.039853 TCACAGCTGATATTTCATTTTTCACCA 60.040 33.333 23.35 0.00 0.00 4.17
2781 2989 2.036475 TGCAGGCTAGCAGCTATAAGAC 59.964 50.000 25.48 0.00 41.99 3.01
2808 3016 3.181445 TGAAATTGACAGTGGGCACTAGT 60.181 43.478 0.00 0.00 40.20 2.57
2836 3044 2.020694 GCATGGCTCAGTTGGCTGTAT 61.021 52.381 0.00 0.00 43.05 2.29
3110 3319 5.616488 TTATCGTCGGTATGATCGAATCA 57.384 39.130 0.00 0.00 44.55 2.57
3111 3320 3.263602 TCGTCGGTATGATCGAATCAC 57.736 47.619 0.00 0.00 43.01 3.06
3114 3323 3.187842 CGTCGGTATGATCGAATCACCTA 59.812 47.826 0.00 0.00 43.01 3.08
3115 3324 4.474113 GTCGGTATGATCGAATCACCTAC 58.526 47.826 0.00 0.00 43.01 3.18
3147 3356 3.798202 CCTAACTGAAGCCACAGGATAC 58.202 50.000 11.48 0.00 41.59 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.571984 TGGAGAAAGAACATGATATGCACG 59.428 41.667 0.00 0.00 0.00 5.34
1 2 6.630444 ATGGAGAAAGAACATGATATGCAC 57.370 37.500 0.00 0.00 0.00 4.57
2 3 6.829811 TGAATGGAGAAAGAACATGATATGCA 59.170 34.615 0.00 0.00 0.00 3.96
3 4 7.137426 GTGAATGGAGAAAGAACATGATATGC 58.863 38.462 0.00 0.00 0.00 3.14
4 5 8.217131 TGTGAATGGAGAAAGAACATGATATG 57.783 34.615 0.00 0.00 0.00 1.78
5 6 8.812513 TTGTGAATGGAGAAAGAACATGATAT 57.187 30.769 0.00 0.00 0.00 1.63
6 7 8.634335 TTTGTGAATGGAGAAAGAACATGATA 57.366 30.769 0.00 0.00 0.00 2.15
7 8 7.528996 TTTGTGAATGGAGAAAGAACATGAT 57.471 32.000 0.00 0.00 0.00 2.45
8 9 6.957920 TTTGTGAATGGAGAAAGAACATGA 57.042 33.333 0.00 0.00 0.00 3.07
54 55 6.293698 CCATTGGATGTACATCTGATTCAGA 58.706 40.000 29.87 18.29 44.99 3.27
55 56 5.048921 GCCATTGGATGTACATCTGATTCAG 60.049 44.000 29.87 16.34 37.92 3.02
56 57 4.823442 GCCATTGGATGTACATCTGATTCA 59.177 41.667 29.87 18.58 37.92 2.57
57 58 5.068636 AGCCATTGGATGTACATCTGATTC 58.931 41.667 29.87 16.47 37.92 2.52
58 59 5.057843 AGCCATTGGATGTACATCTGATT 57.942 39.130 29.87 13.53 37.92 2.57
59 60 4.719026 AGCCATTGGATGTACATCTGAT 57.281 40.909 29.87 21.58 37.92 2.90
60 61 4.508551 AAGCCATTGGATGTACATCTGA 57.491 40.909 29.87 20.52 37.92 3.27
61 62 6.889301 ATTAAGCCATTGGATGTACATCTG 57.111 37.500 29.87 21.52 37.92 2.90
62 63 9.236006 GATTATTAAGCCATTGGATGTACATCT 57.764 33.333 29.87 12.29 37.92 2.90
63 64 9.013229 TGATTATTAAGCCATTGGATGTACATC 57.987 33.333 24.95 24.95 37.11 3.06
64 65 8.796475 GTGATTATTAAGCCATTGGATGTACAT 58.204 33.333 8.43 8.43 0.00 2.29
65 66 7.998383 AGTGATTATTAAGCCATTGGATGTACA 59.002 33.333 6.95 0.00 0.00 2.90
66 67 8.396272 AGTGATTATTAAGCCATTGGATGTAC 57.604 34.615 6.95 0.00 0.00 2.90
67 68 8.995027 AAGTGATTATTAAGCCATTGGATGTA 57.005 30.769 6.95 0.00 0.00 2.29
68 69 7.902920 AAGTGATTATTAAGCCATTGGATGT 57.097 32.000 6.95 0.00 0.00 3.06
85 86 7.700656 GCGCCTGTTATGTTTAATTAAGTGATT 59.299 33.333 0.00 0.00 0.00 2.57
86 87 7.193595 GCGCCTGTTATGTTTAATTAAGTGAT 58.806 34.615 0.00 0.00 0.00 3.06
87 88 6.548171 GCGCCTGTTATGTTTAATTAAGTGA 58.452 36.000 0.00 0.00 0.00 3.41
88 89 5.451023 CGCGCCTGTTATGTTTAATTAAGTG 59.549 40.000 0.00 0.00 0.00 3.16
89 90 5.565695 CGCGCCTGTTATGTTTAATTAAGT 58.434 37.500 0.00 0.00 0.00 2.24
90 91 4.436523 GCGCGCCTGTTATGTTTAATTAAG 59.563 41.667 23.24 0.00 0.00 1.85
91 92 4.095185 AGCGCGCCTGTTATGTTTAATTAA 59.905 37.500 30.33 0.00 0.00 1.40
92 93 3.623960 AGCGCGCCTGTTATGTTTAATTA 59.376 39.130 30.33 0.00 0.00 1.40
93 94 2.422127 AGCGCGCCTGTTATGTTTAATT 59.578 40.909 30.33 0.00 0.00 1.40
94 95 2.014128 AGCGCGCCTGTTATGTTTAAT 58.986 42.857 30.33 0.00 0.00 1.40
95 96 1.444836 AGCGCGCCTGTTATGTTTAA 58.555 45.000 30.33 0.00 0.00 1.52
96 97 1.129624 CAAGCGCGCCTGTTATGTTTA 59.870 47.619 30.33 0.00 0.00 2.01
97 98 0.109781 CAAGCGCGCCTGTTATGTTT 60.110 50.000 30.33 9.30 0.00 2.83
98 99 1.501741 CAAGCGCGCCTGTTATGTT 59.498 52.632 30.33 10.16 0.00 2.71
99 100 3.039202 GCAAGCGCGCCTGTTATGT 62.039 57.895 30.33 2.66 0.00 2.29
100 101 2.277501 GCAAGCGCGCCTGTTATG 60.278 61.111 30.33 17.65 0.00 1.90
101 102 1.656818 AATGCAAGCGCGCCTGTTAT 61.657 50.000 30.33 20.08 42.97 1.89
102 103 2.252127 GAATGCAAGCGCGCCTGTTA 62.252 55.000 30.33 18.67 42.97 2.41
103 104 3.615536 GAATGCAAGCGCGCCTGTT 62.616 57.895 30.33 16.58 42.97 3.16
104 105 4.107051 GAATGCAAGCGCGCCTGT 62.107 61.111 30.33 9.58 42.97 4.00
111 112 0.179181 AACATGAGCGAATGCAAGCG 60.179 50.000 0.00 7.15 46.23 4.68
112 113 1.986698 AAACATGAGCGAATGCAAGC 58.013 45.000 0.00 0.00 46.23 4.01
113 114 3.545078 GCTTAAACATGAGCGAATGCAAG 59.455 43.478 0.00 4.89 46.23 4.01
114 115 3.057666 TGCTTAAACATGAGCGAATGCAA 60.058 39.130 0.00 0.00 46.23 4.08
115 116 2.487372 TGCTTAAACATGAGCGAATGCA 59.513 40.909 0.00 0.00 46.23 3.96
116 117 3.103738 CTGCTTAAACATGAGCGAATGC 58.896 45.455 0.00 0.00 41.75 3.56
117 118 3.103738 GCTGCTTAAACATGAGCGAATG 58.896 45.455 0.00 0.65 41.75 2.67
118 119 2.098117 GGCTGCTTAAACATGAGCGAAT 59.902 45.455 0.00 0.00 41.75 3.34
119 120 1.468520 GGCTGCTTAAACATGAGCGAA 59.531 47.619 0.00 0.00 41.75 4.70
120 121 1.086696 GGCTGCTTAAACATGAGCGA 58.913 50.000 0.00 0.00 41.75 4.93
121 122 0.099436 GGGCTGCTTAAACATGAGCG 59.901 55.000 0.00 0.00 41.75 5.03
122 123 0.099436 CGGGCTGCTTAAACATGAGC 59.901 55.000 0.00 0.00 39.33 4.26
123 124 1.131126 CACGGGCTGCTTAAACATGAG 59.869 52.381 0.00 0.00 0.00 2.90
124 125 1.164411 CACGGGCTGCTTAAACATGA 58.836 50.000 0.00 0.00 0.00 3.07
125 126 0.171007 CCACGGGCTGCTTAAACATG 59.829 55.000 0.00 0.00 0.00 3.21
126 127 0.251165 ACCACGGGCTGCTTAAACAT 60.251 50.000 0.00 0.00 0.00 2.71
127 128 0.397187 TACCACGGGCTGCTTAAACA 59.603 50.000 0.00 0.00 0.00 2.83
128 129 1.084289 CTACCACGGGCTGCTTAAAC 58.916 55.000 0.00 0.00 0.00 2.01
129 130 0.978151 TCTACCACGGGCTGCTTAAA 59.022 50.000 0.00 0.00 0.00 1.52
130 131 0.535335 CTCTACCACGGGCTGCTTAA 59.465 55.000 0.00 0.00 0.00 1.85
131 132 1.327690 CCTCTACCACGGGCTGCTTA 61.328 60.000 0.00 0.00 0.00 3.09
132 133 2.660064 CCTCTACCACGGGCTGCTT 61.660 63.158 0.00 0.00 0.00 3.91
133 134 2.880629 ATCCTCTACCACGGGCTGCT 62.881 60.000 0.00 0.00 0.00 4.24
134 135 2.435693 ATCCTCTACCACGGGCTGC 61.436 63.158 0.00 0.00 0.00 5.25
135 136 1.443407 CATCCTCTACCACGGGCTG 59.557 63.158 0.00 0.00 0.00 4.85
136 137 1.762460 CCATCCTCTACCACGGGCT 60.762 63.158 0.00 0.00 0.00 5.19
137 138 1.623542 AACCATCCTCTACCACGGGC 61.624 60.000 0.00 0.00 0.00 6.13
138 139 0.464452 GAACCATCCTCTACCACGGG 59.536 60.000 0.00 0.00 0.00 5.28
139 140 1.191535 TGAACCATCCTCTACCACGG 58.808 55.000 0.00 0.00 0.00 4.94
140 141 4.322049 GGATATGAACCATCCTCTACCACG 60.322 50.000 0.00 0.00 39.17 4.94
141 142 4.593206 TGGATATGAACCATCCTCTACCAC 59.407 45.833 3.24 0.00 42.21 4.16
142 143 4.593206 GTGGATATGAACCATCCTCTACCA 59.407 45.833 3.24 0.00 42.21 3.25
143 144 4.322049 CGTGGATATGAACCATCCTCTACC 60.322 50.000 3.24 0.00 42.21 3.18
144 145 4.281182 ACGTGGATATGAACCATCCTCTAC 59.719 45.833 0.00 0.00 42.21 2.59
145 146 4.480115 ACGTGGATATGAACCATCCTCTA 58.520 43.478 0.00 0.00 42.21 2.43
146 147 3.309296 ACGTGGATATGAACCATCCTCT 58.691 45.455 0.00 0.00 42.21 3.69
147 148 3.753294 ACGTGGATATGAACCATCCTC 57.247 47.619 0.00 0.00 42.21 3.71
148 149 4.503714 AAACGTGGATATGAACCATCCT 57.496 40.909 0.00 0.00 42.21 3.24
149 150 5.576447 AAAAACGTGGATATGAACCATCC 57.424 39.130 0.00 0.00 42.08 3.51
170 171 9.695155 CAAGTCCTATCCCCTATAAAAGAAAAA 57.305 33.333 0.00 0.00 0.00 1.94
178 179 4.831155 CACGTCAAGTCCTATCCCCTATAA 59.169 45.833 0.00 0.00 0.00 0.98
183 184 0.464452 CCACGTCAAGTCCTATCCCC 59.536 60.000 0.00 0.00 0.00 4.81
184 185 1.136500 GACCACGTCAAGTCCTATCCC 59.864 57.143 0.00 0.00 32.09 3.85
185 186 1.822990 TGACCACGTCAAGTCCTATCC 59.177 52.381 7.28 0.00 39.78 2.59
186 187 3.802948 ATGACCACGTCAAGTCCTATC 57.197 47.619 0.00 0.00 45.96 2.08
187 188 4.649674 ACATATGACCACGTCAAGTCCTAT 59.350 41.667 10.38 5.17 45.96 2.57
207 212 5.880332 AGTTTCAGCATATAAACGTGGACAT 59.120 36.000 0.00 0.00 39.90 3.06
209 214 5.796350 AGTTTCAGCATATAAACGTGGAC 57.204 39.130 0.00 0.00 39.90 4.02
222 227 6.882610 AGATGACATTGTTTAGTTTCAGCA 57.117 33.333 0.00 0.00 0.00 4.41
240 245 5.163509 CGAGTAGATGACCCTTCAAAGATGA 60.164 44.000 0.00 0.00 34.61 2.92
357 370 4.789075 GAGCTTACGACCCGCGCA 62.789 66.667 8.75 0.00 46.04 6.09
371 399 2.703007 AGGAAGGTATGAGGACATGAGC 59.297 50.000 0.00 0.00 37.87 4.26
401 429 0.171679 CAGCCACGTACCATGTCGTA 59.828 55.000 7.33 0.00 38.52 3.43
434 465 1.312815 GGATTGCGCTTCTTGGCTAT 58.687 50.000 9.73 0.00 0.00 2.97
435 466 1.089481 CGGATTGCGCTTCTTGGCTA 61.089 55.000 9.73 0.00 0.00 3.93
436 467 2.401766 CGGATTGCGCTTCTTGGCT 61.402 57.895 9.73 0.00 0.00 4.75
437 468 2.100991 CGGATTGCGCTTCTTGGC 59.899 61.111 9.73 0.00 0.00 4.52
470 504 2.430332 CTCTGTTCTGGACCTCTCATCC 59.570 54.545 0.00 0.00 36.70 3.51
594 632 0.792640 AAGAGTCAAATGCGCGACAG 59.207 50.000 12.10 0.05 34.48 3.51
603 649 3.072476 TGAAAGGGACGGAAGAGTCAAAT 59.928 43.478 0.00 0.00 42.62 2.32
610 656 1.677552 GGCTGAAAGGGACGGAAGA 59.322 57.895 0.00 0.00 0.00 2.87
711 762 4.400961 AGCTGCTCGTGGGCTTCC 62.401 66.667 0.00 0.00 31.81 3.46
887 939 1.672356 GAAGAGAAAGGCGGCTGCA 60.672 57.895 21.31 0.00 45.35 4.41
888 940 1.365368 GAGAAGAGAAAGGCGGCTGC 61.365 60.000 14.21 9.72 41.71 5.25
889 941 0.248843 AGAGAAGAGAAAGGCGGCTG 59.751 55.000 14.21 0.00 0.00 4.85
911 973 0.321671 CCGGTGCTGGAAGAGAAGAA 59.678 55.000 0.00 0.00 34.07 2.52
912 974 1.544825 CCCGGTGCTGGAAGAGAAGA 61.545 60.000 0.00 0.00 34.07 2.87
913 975 1.078848 CCCGGTGCTGGAAGAGAAG 60.079 63.158 0.00 0.00 34.07 2.85
914 976 3.068881 CCCGGTGCTGGAAGAGAA 58.931 61.111 0.00 0.00 34.07 2.87
915 977 3.706373 GCCCGGTGCTGGAAGAGA 61.706 66.667 0.00 0.00 34.07 3.10
939 1001 0.601558 GAGAAAAGAAAACCCCGGCC 59.398 55.000 0.00 0.00 0.00 6.13
941 1003 1.989706 TGGAGAAAAGAAAACCCCGG 58.010 50.000 0.00 0.00 0.00 5.73
942 1004 2.296190 CCTTGGAGAAAAGAAAACCCCG 59.704 50.000 0.00 0.00 0.00 5.73
943 1005 3.069586 CACCTTGGAGAAAAGAAAACCCC 59.930 47.826 0.00 0.00 0.00 4.95
944 1006 3.069586 CCACCTTGGAGAAAAGAAAACCC 59.930 47.826 0.00 0.00 40.96 4.11
945 1007 3.704566 ACCACCTTGGAGAAAAGAAAACC 59.295 43.478 0.00 0.00 40.96 3.27
946 1008 4.441495 CCACCACCTTGGAGAAAAGAAAAC 60.441 45.833 0.00 0.00 40.96 2.43
947 1009 3.704061 CCACCACCTTGGAGAAAAGAAAA 59.296 43.478 0.00 0.00 40.96 2.29
948 1010 3.053245 TCCACCACCTTGGAGAAAAGAAA 60.053 43.478 0.00 0.00 41.00 2.52
949 1011 2.512056 TCCACCACCTTGGAGAAAAGAA 59.488 45.455 0.00 0.00 41.00 2.52
950 1012 2.131854 TCCACCACCTTGGAGAAAAGA 58.868 47.619 0.00 0.00 41.00 2.52
994 1064 0.109342 ATTGCCGTCATCATCCTCCC 59.891 55.000 0.00 0.00 0.00 4.30
1264 1361 4.352893 AGAAGGAGGAAGAAGGAGAAGAG 58.647 47.826 0.00 0.00 0.00 2.85
1267 1364 3.584848 CCAAGAAGGAGGAAGAAGGAGAA 59.415 47.826 0.00 0.00 41.22 2.87
1290 1387 0.385029 GCACAGCACACATTGAACCA 59.615 50.000 0.00 0.00 0.00 3.67
1291 1388 0.318955 GGCACAGCACACATTGAACC 60.319 55.000 0.00 0.00 0.00 3.62
1292 1389 0.661187 CGGCACAGCACACATTGAAC 60.661 55.000 0.00 0.00 0.00 3.18
1326 1438 4.072088 CTGCACGAACGAACCCGC 62.072 66.667 0.14 0.00 39.95 6.13
1327 1439 2.355363 TCTGCACGAACGAACCCG 60.355 61.111 0.14 0.00 42.50 5.28
1328 1440 1.006571 TCTCTGCACGAACGAACCC 60.007 57.895 0.14 0.00 0.00 4.11
1329 1441 1.009389 CCTCTCTGCACGAACGAACC 61.009 60.000 0.14 0.00 0.00 3.62
1330 1442 1.009389 CCCTCTCTGCACGAACGAAC 61.009 60.000 0.14 0.00 0.00 3.95
1331 1443 1.289066 CCCTCTCTGCACGAACGAA 59.711 57.895 0.14 0.00 0.00 3.85
1332 1444 2.962569 CCCTCTCTGCACGAACGA 59.037 61.111 0.14 0.00 0.00 3.85
1387 1499 4.729856 GGGTACTTGCGGTCGCGT 62.730 66.667 5.77 6.06 45.51 6.01
1640 1752 0.104304 AACTGCGAACTGGAAGACGT 59.896 50.000 0.00 0.00 38.77 4.34
1680 1796 7.201652 GGATCAGTATTCAGTATCGATCGATGA 60.202 40.741 34.92 24.66 36.17 2.92
1681 1797 6.909895 GGATCAGTATTCAGTATCGATCGATG 59.090 42.308 34.92 22.90 36.17 3.84
1685 1801 8.050778 AGAAGGATCAGTATTCAGTATCGATC 57.949 38.462 0.00 0.00 0.00 3.69
1715 1831 0.664761 GCAATAGCCGCACATCACAT 59.335 50.000 0.00 0.00 33.58 3.21
1791 1907 0.326264 ATGTCCTGCTCCACCTTGAC 59.674 55.000 0.00 0.00 0.00 3.18
1829 1945 1.683441 GTCCATGACCTCCCCGTTT 59.317 57.895 0.00 0.00 0.00 3.60
1868 1984 1.513158 CGTCTGGAAGCTGTCGGAT 59.487 57.895 0.00 0.00 0.00 4.18
1930 2046 2.740714 GCCATGTCCGTGAAGACGC 61.741 63.158 0.00 0.00 44.68 5.19
1933 2049 2.434185 GCGCCATGTCCGTGAAGA 60.434 61.111 0.00 0.00 0.00 2.87
2015 2131 0.036952 AAGTCTGCAGGTCGTCCATG 60.037 55.000 15.13 0.00 35.89 3.66
2036 2152 4.263639 ACCATCTGCCCCATGTTCATATAG 60.264 45.833 0.00 0.00 0.00 1.31
2085 2201 3.524606 TAGGTAGCCGCTGCCGTC 61.525 66.667 20.37 0.00 41.15 4.79
2117 2233 2.507944 GGCCTCATCATCTGCGGT 59.492 61.111 0.00 0.00 31.94 5.68
2249 2365 5.312708 AGAATCATGCCTGGGAAATCTCTAT 59.687 40.000 0.00 0.00 0.00 1.98
2254 2370 3.559069 TCAGAATCATGCCTGGGAAATC 58.441 45.455 0.00 0.00 0.00 2.17
2371 2487 7.279615 TGGTGTTTAGACTTGAGAATTTGAGA 58.720 34.615 0.00 0.00 0.00 3.27
2372 2488 7.496529 TGGTGTTTAGACTTGAGAATTTGAG 57.503 36.000 0.00 0.00 0.00 3.02
2373 2489 7.873719 TTGGTGTTTAGACTTGAGAATTTGA 57.126 32.000 0.00 0.00 0.00 2.69
2374 2490 8.190784 AGTTTGGTGTTTAGACTTGAGAATTTG 58.809 33.333 0.00 0.00 0.00 2.32
2375 2491 8.293699 AGTTTGGTGTTTAGACTTGAGAATTT 57.706 30.769 0.00 0.00 0.00 1.82
2376 2492 7.881775 AGTTTGGTGTTTAGACTTGAGAATT 57.118 32.000 0.00 0.00 0.00 2.17
2377 2493 7.339466 ACAAGTTTGGTGTTTAGACTTGAGAAT 59.661 33.333 18.14 0.00 46.14 2.40
2378 2494 6.657541 ACAAGTTTGGTGTTTAGACTTGAGAA 59.342 34.615 18.14 0.00 46.14 2.87
2424 2540 9.994432 GGAGTATATGTTTCAGATTTGTTTCAG 57.006 33.333 0.00 0.00 0.00 3.02
2425 2541 8.956426 GGGAGTATATGTTTCAGATTTGTTTCA 58.044 33.333 0.00 0.00 0.00 2.69
2426 2542 9.178758 AGGGAGTATATGTTTCAGATTTGTTTC 57.821 33.333 0.00 0.00 0.00 2.78
2427 2543 9.178758 GAGGGAGTATATGTTTCAGATTTGTTT 57.821 33.333 0.00 0.00 0.00 2.83
2428 2544 7.775561 GGAGGGAGTATATGTTTCAGATTTGTT 59.224 37.037 0.00 0.00 0.00 2.83
2429 2545 7.283329 GGAGGGAGTATATGTTTCAGATTTGT 58.717 38.462 0.00 0.00 0.00 2.83
2430 2546 6.425114 CGGAGGGAGTATATGTTTCAGATTTG 59.575 42.308 0.00 0.00 0.00 2.32
2431 2547 6.099845 ACGGAGGGAGTATATGTTTCAGATTT 59.900 38.462 0.00 0.00 0.00 2.17
2466 2593 6.816640 CCGTATCTAGACAAATCCAAGACAAA 59.183 38.462 0.00 0.00 0.00 2.83
2486 2613 9.352191 ACTAAAACTGTCTAGATACATCCGTAT 57.648 33.333 0.00 0.00 41.16 3.06
2487 2614 8.618677 CACTAAAACTGTCTAGATACATCCGTA 58.381 37.037 0.00 0.00 0.00 4.02
2488 2615 7.122353 ACACTAAAACTGTCTAGATACATCCGT 59.878 37.037 0.00 0.00 0.00 4.69
2489 2616 7.481642 ACACTAAAACTGTCTAGATACATCCG 58.518 38.462 0.00 0.00 0.00 4.18
2781 2989 1.135315 CCCACTGTCAATTTCATGGCG 60.135 52.381 0.00 0.00 0.00 5.69
2808 3016 3.011818 CAACTGAGCCATGCTTGTCATA 58.988 45.455 0.00 0.00 39.88 2.15
2836 3044 5.433526 ACAACTTACTTTGGCTGTACAAGA 58.566 37.500 0.00 0.00 0.00 3.02
2846 3054 8.194769 AGTTATGGTGAAAACAACTTACTTTGG 58.805 33.333 0.00 0.00 0.00 3.28
2847 3055 9.019764 CAGTTATGGTGAAAACAACTTACTTTG 57.980 33.333 0.00 0.00 0.00 2.77
2920 3128 3.663995 CCAAAAGATGGTGTTGATGCA 57.336 42.857 0.00 0.00 44.85 3.96
3110 3319 3.204831 AGTTAGGCCTAGTAGCTGTAGGT 59.795 47.826 13.36 8.37 39.56 3.08
3111 3320 3.570550 CAGTTAGGCCTAGTAGCTGTAGG 59.429 52.174 13.36 16.33 40.25 3.18
3114 3323 3.383698 TCAGTTAGGCCTAGTAGCTGT 57.616 47.619 23.08 0.00 0.00 4.40
3115 3324 3.491792 GCTTCAGTTAGGCCTAGTAGCTG 60.492 52.174 13.36 17.95 0.00 4.24


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

AutoCloner maintained by Alex Coulton.