Locus 7319

Sequence ID 2L_DroMel_CAF1
Location 20,467,473 – 20,467,829
Length 356
Max. P 0.873127
window11725 window11726 window11727 window11728

overview

Window 5

Location 20,467,473 – 20,467,589
Length 116
Sequences 3
Columns 116
Reading direction forward
Mean pairwise identity 79.60
Mean single sequence MFE -19.40
Consensus MFE -14.29
Energy contribution -14.30
Covariance contribution 0.01
Combinations/Pair 1.26
Mean z-score -1.51
Structure conservation index 0.74
SVM decision value 0.23
SVM RNA-class probability 0.646528
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20467473 116 + 22407834
UUUAUAGGAGAGUCAAUACGUUUCCAUAUUUUUUCCAAUACUUCGCUCACACUUUUAUGCCACACUUUAAUGUCCUGCGUGUUUUGCAGUGCAUCCGAGCCGGAAAAUAAUUUUUU
......(((((((....)).))))).....((((((........((............))....(((..(((..(((((.....)))))..)))..)))..))))))......... ( -21.90)
>DroSec_CAF1 20428 116 + 1
UUAAUAAAUGAGUCAAUAAUUUUCCAUACUUUUCCCAAUACUUUUCUCACACUUUUAUGCCACACCUUUAUGCUUUGCGUUUUUCGCAGUGCAUCCGAACCGGAAAAUAAUUUUUU
..................(((((((........................((......))..........((((.(((((.....))))).)))).......)))))))........ ( -14.80)
>DroSim_CAF1 22416 103 + 1
UUUAUAAAAGAGUCCAUGGUUUUCCAUAUGUUUUUCAAUACUUUGCUCACACUUUU-------------GUGCUCUGCGUUUUUCGCAGUGCAUCCGAACCGGAAAAUAAUUUUUU
...(((((((.....((((....)))).(((....(((....)))...))))))))-------------))((.(((((.....))))).)).((((...))))............ ( -21.50)
>consensus
UUUAUAAAAGAGUCAAUAAUUUUCCAUAUUUUUUCCAAUACUUUGCUCACACUUUUAUGCCACAC_UU_AUGCUCUGCGUUUUUCGCAGUGCAUCCGAACCGGAAAAUAAUUUUUU
..................(((((((.(((........))).............................((((.(((((.....))))).)))).......)))))))........ (-14.29 = -14.30 +   0.01)

alignment

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secondary structure

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dotplot

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Window 6

Location 20,467,473 – 20,467,589
Length 116
Sequences 3
Columns 116
Reading direction reverse
Mean pairwise identity 79.60
Mean single sequence MFE -23.47
Consensus MFE -14.22
Energy contribution -14.90
Covariance contribution 0.67
Combinations/Pair 1.13
Mean z-score -1.89
Structure conservation index 0.61
SVM decision value 0.15
SVM RNA-class probability 0.605801
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20467473 116 - 22407834
AAAAAAUUAUUUUCCGGCUCGGAUGCACUGCAAAACACGCAGGACAUUAAAGUGUGGCAUAAAAGUGUGAGCGAAGUAUUGGAAAAAAUAUGGAAACGUAUUGACUCUCCUAUAAA
.........((((((((((..((((..((((.......))))..))))..)))((.((((....))))..)).......)))))))((((((....)))))).............. ( -27.90)
>DroSec_CAF1 20428 116 - 1
AAAAAAUUAUUUUCCGGUUCGGAUGCACUGCGAAAAACGCAAAGCAUAAAGGUGUGGCAUAAAAGUGUGAGAAAAGUAUUGGGAAAAGUAUGGAAAAUUAUUGACUCAUUUAUUAA
....(((.((((((((.(((.(((((..((((.....))))..((((....)))).((((....)))).......))))).)))......)))))))).))).............. ( -21.10)
>DroSim_CAF1 22416 103 - 1
AAAAAAUUAUUUUCCGGUUCGGAUGCACUGCGAAAAACGCAGAGCAC-------------AAAAGUGUGAGCAAAGUAUUGAAAAACAUAUGGAAAACCAUGGACUCUUUUAUAAA
......((((.....(((((.(((((.(((((.....))))).((((-------------....)))).......))))).........((((....))))))))).....)))). ( -21.40)
>consensus
AAAAAAUUAUUUUCCGGUUCGGAUGCACUGCGAAAAACGCAGAGCAU_AA_GUGUGGCAUAAAAGUGUGAGCAAAGUAUUGGAAAAAAUAUGGAAAACUAUUGACUCUUUUAUAAA
..........((((((.(((.(((((.(((((.....))))).((((.................)))).......))))).)))......)))))).................... (-14.22 = -14.90 +   0.67)

alignment

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secondary structure

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dotplot

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Window 7

Location 20,467,589 – 20,467,709
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.00
Mean single sequence MFE -42.08
Consensus MFE -33.83
Energy contribution -35.08
Covariance contribution 1.25
Combinations/Pair 1.07
Mean z-score -1.74
Structure conservation index 0.80
SVM decision value 0.72
SVM RNA-class probability 0.833168
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20467589 120 - 22407834
AGCUUCGGGCCAAAAAGAGCGACAGCGGCAAAAGAUGCGAAAACUUUUUCGCUGGCAGGCGUAGUAAACGUCAUUUCGCCUGGAGGCGUUUAGCGUUCGGGGGCGUGGCAAGGAGUGCAG
.(((((..((((..........((((((.(((((.........)))))))))))((.(((((.....)))))......((((((.((.....)).)))))).)).))))..))))).... ( -43.30)
>DroSec_CAF1 20544 120 - 1
AGCUCCGGGCCAAAAAGAGCGACAGCGGCAAAAGAUGCGAAAACUUUUUCGCUGGCAGGCGUAGUAAACGUCAUUUCGCCUGGAGGCGUUUAGCGUUCGGGGGCGUGGCAAGGAGUGCAC
.(((((..((((..........((((((.(((((.........)))))))))))((.(((((.....)))))......((((((.((.....)).)))))).)).))))..))))).... ( -46.20)
>DroSim_CAF1 22519 120 - 1
AGCUCCGGGCCAAAAAGAGCGACAGCGGCAAAAGAUGCGAAAACUUUUUCGCUGGCAGGCGUAGUAAACGUCAUUUCGCCUGGAGGCGUUUAGCGUUCGGGGGCGUGGCAAGGAGUGCAC
.(((((..((((..........((((((.(((((.........)))))))))))((.(((((.....)))))......((((((.((.....)).)))))).)).))))..))))).... ( -46.20)
>DroEre_CAF1 22964 120 - 1
AGCUCCGGGCCAAAAAGAGCGACAGCGGCAAAAGAUGCGAAAACUUUUUCGCUGGCAGGCGUAGUAAACGUCAUUUCGCCUGGAGGCGUUUAGCGUGCGGGGGCGUGGCAGGGGAUGCAC
..((((((((.(((....((..((((((.(((((.........))))))))))))).(((((.....))))).))).))))))))((((((.((.((((....))))))...)))))).. ( -42.10)
>DroYak_CAF1 20246 93 - 1
AGCUCCGGGCCAAAAAGAGCGACAGCGGCAAAAGAUGCGAAAACUUUUUCGCUGGCAGGCGUAGUAAACGUCAUUUCGCCUGGAG---------------------------GAAUGCAC
..((((((((.(((....((..((((((.(((((.........))))))))))))).(((((.....))))).))).))))))))---------------------------........ ( -32.60)
>consensus
AGCUCCGGGCCAAAAAGAGCGACAGCGGCAAAAGAUGCGAAAACUUUUUCGCUGGCAGGCGUAGUAAACGUCAUUUCGCCUGGAGGCGUUUAGCGUUCGGGGGCGUGGCAAGGAGUGCAC
..((((((((.(((....((..((((((.(((((.........))))))))))))).(((((.....))))).))).))))))))((((((.(((((....)))))......)))))).. (-33.83 = -35.08 +   1.25)

alignment

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secondary structure

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dotplot

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Window 8

Location 20,467,709 – 20,467,829
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.84
Mean single sequence MFE -35.84
Consensus MFE -30.18
Energy contribution -30.42
Covariance contribution 0.24
Combinations/Pair 1.08
Mean z-score -1.58
Structure conservation index 0.84
SVM decision value 0.88
SVM RNA-class probability 0.873127
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20467709 120 + 22407834
UGGGGUUUGGUCUCUGGGUCUUGGCCAAACUUUAAUGAAAAGUUUUGUUAAAAACUUUUGCUCGCUGGAAAUUUCAACGCUUGAAUGGGUCGCGGUUGGGGAUUUUUCGUGGCGGUGGUG
((((((((((((..........))))))))))))...(((((((((....)))))))))((.(((..(((((..(..(((...........)))....)..)))))..)))))....... ( -35.10)
>DroSec_CAF1 20664 116 + 1
UGGGGUUUGGUCUCUGGGUCUUGGCCAAACUUUAAUGAAAAGUUUUGUUAAAAACUUUUGCUCGCUGGAAAUUUCAACGCUUGAAUGGGUCGCGGUUGGGGAUUUUCCGUCGCGG----G
((((((((((((..........))))))))))))...(((((((((....))))))))).((((((((((((..((((.(.(((.....))).)))))..)..))))))..))))----) ( -36.40)
>DroSim_CAF1 22639 116 + 1
UGGGGUUUGGUCUCUGGGUCUUGGCCAAACUUUAAUGAAAAGUUUUGUUAAAAACUUUUGCUCGCUGGAAAUUUCAACGCUUGAAUGGGUCGCGGUUGGGGAUUUUCCGCGGCGG----G
((((((((((((..........))))))))))))...(((((((((....)))))))))((.(((.((((((..(..(((...........)))....)..)))))).)))))..----. ( -38.40)
>DroEre_CAF1 23084 113 + 1
UGGGGUUUGGUCUCUGGGUCUUGGCCAAACUUUAAUGAAAAGUUUUGUUAAAAACUUUUGCGCGCUGGAAAUUUCAACGCUUGAAUGGGUCGCUGUUGGGGCUUUUCCGCGG-------G
((((((((((((..........))))))))))))...(((((((((....))))))))).(.(((.((((((..((((((...........)).))))..)..)))))))).-------) ( -34.90)
>DroYak_CAF1 20339 113 + 1
UGAGGUUUGGUCUCUGGGUCUUGGCCAAACUUUAAUGAAAAGUUUUGUUAAAAACUUUUGCGCGCUGGAAAUUUCAACGCUUGAAUAGGUCGCUGUUGGGCAUUUUUCGGGG-------C
((((((((((((..........))))))))))))...(((((((((....)))))))))..((.(((((((.((((((((...........)).))))))...))))))).)-------) ( -34.40)
>consensus
UGGGGUUUGGUCUCUGGGUCUUGGCCAAACUUUAAUGAAAAGUUUUGUUAAAAACUUUUGCUCGCUGGAAAUUUCAACGCUUGAAUGGGUCGCGGUUGGGGAUUUUCCGCGGCGG____G
((((((((((((..........))))))))))))...(((((((((....)))))))))((.(((.(((((.((((((((...........)).))))))...))))))))))....... (-30.18 = -30.42 +   0.24)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:33:23 2006