Locus 1255

Sequence ID 3R_DroMel_CAF1
Location 3,767,052 – 3,767,200
Length 148
Max. P 0.974988
window2044 window2045 window2046 window2047

overview

Window 4

Location 3,767,052 – 3,767,162
Length 110
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 68.19
Mean single sequence MFE -36.74
Consensus MFE -10.93
Energy contribution -11.35
Covariance contribution 0.42
Combinations/Pair 1.25
Mean z-score -2.59
Structure conservation index 0.30
SVM decision value 1.74
SVM RNA-class probability 0.974988
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3767052 110 + 27905053
AGGCGGAAGUUGAAAUUUG-----GAAGUUGGCGUUGACACAGGGGACCCUGUUU--GGUUGGCUGGCAUUCGGUUGGCCAAGUUAAGCUUGUUAAGCUCCGCACGAAAGUCGUUUU
..(((((..((((......-----......(((.((((((((((....)))))((--(((..((((.....))))..)))))))))))))..))))..)))))((....))...... ( -37.94)
>DroPse_CAF1 24381 92 + 1
AGGCGGAAGUUG------------GCAGCUGGGUU----------GCUUUUGCUUUUGCC---UUAGCUUGCCGUUGGCCAAGUUAAGCUUGUUAAGCUUGGCACGAAAGCAGUUUU
((((((((((.(------------(((((...)))----------)))...)))))))))---)..((((..(((..((((((((.((....)).))))))))))).))))...... ( -37.30)
>DroEre_CAF1 20479 110 + 1
AGGCGGAAGGCGGAAGUUG-----GAAGUGGGCUGUGACACAGGGGACCCUGCUU--GGUGGACUGGCAUUCGGUUGGCCAAGUUAAGCUUGUUAAGCUCCGCACGAAAGCCGUUUU
.(((....((((((.(((.-----..((..((((.((((.((((....)))).((--(((.(((((.....))))).)))))))))))))..)).)))))))).)....)))..... ( -45.40)
>DroMoj_CAF1 21945 93 + 1
AGGCGGAUGGCGAAUGGCG-----GAAGUUGGCA---------------AUGCUUAUCCU---UUAGC-UGCUUUUAGCCAAGUUAAGCUUGUUAAGCUUGGCACGAAAGCAGUUUU
....((((((((..((((.-----...))))...---------------.))).))))).---..(((-(((((((.((((((((.((....)).))))))))..)))))))))).. ( -33.80)
>DroAna_CAF1 18797 99 + 1
ACGCGGAAGU----AUAUG-----CCAGUUUGCC--GGCGAAG--AGCUUUGUUU--CCU---UUGGCUUGCUUUUAGCCAAGUUAAGCUUGUUAAGCCUGGCACGAAAGCAGUUUU
..((....))----...((-----(.....((((--(((....--(((...((((--..(---((((((.......)))))))..))))..)))..))).)))).....)))..... ( -29.40)
>DroPer_CAF1 24860 103 + 1
AGGCGGAAGUUCGC-UUUGACAGCGCAGCUGGGUU----------GCUUUUGCUUUUGCC---UUAGCUUGCCGUUGGCCAAGUUAAGCUUGUUAAGCUUGGCACGAAAGCAGUUUU
((((((((((..((-(.....)))(((((...)))----------))....)))))))))---)..((((..(((..((((((((.((....)).))))))))))).))))...... ( -36.60)
>consensus
AGGCGGAAGUUG_AAUUUG_____GAAGUUGGCUU__________GACUUUGCUU__GCU___UUAGCUUGCCGUUGGCCAAGUUAAGCUUGUUAAGCUUGGCACGAAAGCAGUUUU
..((....................((((((((...............................))))).))).....((((((((.((....)).))))))))......))...... (-10.93 = -11.35 +   0.42)

alignment

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secondary structure

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Window 5

Location 3,767,052 – 3,767,162
Length 110
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 68.19
Mean single sequence MFE -25.60
Consensus MFE -8.77
Energy contribution -7.93
Covariance contribution -0.83
Combinations/Pair 1.31
Mean z-score -2.09
Structure conservation index 0.34
SVM decision value 0.91
SVM RNA-class probability 0.879674
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3767052 110 - 27905053
AAAACGACUUUCGUGCGGAGCUUAACAAGCUUAACUUGGCCAACCGAAUGCCAGCCAACC--AAACAGGGUCCCCUGUGUCAACGCCAACUUC-----CAAAUUUCAACUUCCGCCU
...(((.....)))((((((((.....)))......((((.........))))((.....--..(((((....)))))......)).......-----............))))).. ( -23.22)
>DroPse_CAF1 24381 92 - 1
AAAACUGCUUUCGUGCCAAGCUUAACAAGCUUAACUUGGCCAACGGCAAGCUAA---GGCAAAAGCAAAAGC----------AACCCAGCUGC------------CAACUUCCGCCU
......((((((((((((((.((((.....))))))))))..)))).))))..(---(((..(((....(((----------......)))..------------...)))..)))) ( -24.60)
>DroEre_CAF1 20479 110 - 1
AAAACGGCUUUCGUGCGGAGCUUAACAAGCUUAACUUGGCCAACCGAAUGCCAGUCCACC--AAGCAGGGUCCCCUGUGUCACAGCCCACUUC-----CAACUUCCGCCUUCCGCCU
.....(((....(.((((((((.....))).....(((((.........)))))......--..(((((....)))))...............-----.....))))))....))). ( -25.80)
>DroMoj_CAF1 21945 93 - 1
AAAACUGCUUUCGUGCCAAGCUUAACAAGCUUAACUUGGCUAAAAGCA-GCUAA---AGGAUAAGCAU---------------UGCCAACUUC-----CGCCAUUCGCCAUCCGCCU
....(((((((...((((((.((((.....))))))))))..))))))-)....---.((((..((((---------------.((.......-----.)).))..)).)))).... ( -22.40)
>DroAna_CAF1 18797 99 - 1
AAAACUGCUUUCGUGCCAGGCUUAACAAGCUUAACUUGGCUAAAAGCAAGCCAA---AGG--AAACAAAGCU--CUUCGCC--GGCAAACUGG-----CAUAU----ACUUCCGCGU
.....((((....((((.(((......(((((...((((((.......))))))---.(.--...).)))))--....)))--))))....))-----))...----.......... ( -28.70)
>DroPer_CAF1 24860 103 - 1
AAAACUGCUUUCGUGCCAAGCUUAACAAGCUUAACUUGGCCAACGGCAAGCUAA---GGCAAAAGCAAAAGC----------AACCCAGCUGCGCUGUCAAA-GCGAACUUCCGCCU
......((((((((((((((.((((.....))))))))))..)))).))))..(---(((..(((....(((----------......))).((((.....)-)))..)))..)))) ( -28.90)
>consensus
AAAACUGCUUUCGUGCCAAGCUUAACAAGCUUAACUUGGCCAACAGCAAGCCAA___AGC__AAGCAAAGGC__________AAGCCAACUGC_____CAAAUU_CAACUUCCGCCU
............(((..(((((.....)))))...(((((.........)))))..........................................................))).. ( -8.77 =  -7.93 +  -0.83)

alignment

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secondary structure

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Window 6

Location 3,767,087 – 3,767,200
Length 113
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 82.00
Mean single sequence MFE -29.42
Consensus MFE -16.51
Energy contribution -16.43
Covariance contribution -0.08
Combinations/Pair 1.12
Mean z-score -2.53
Structure conservation index 0.56
SVM decision value 0.35
SVM RNA-class probability 0.700039
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3767087 113 + 27905053
CAGGGGACCCUGUUU--GGUUGGCUGGCAUUCGGUUGGCCAAGUUAAGCUUGUUAAGCUCCGCACGAAAGUCGUUUUAAUCUCAAAAUUAAAACGUUUGCAAUUUUCGAGCGACU
((((....))))(((--(((..((((.....))))..))))))...((((.....)))).(((.((((((((((((((((......)))))))))......))))))).)))... ( -37.70)
>DroPse_CAF1 24404 107 + 1
-----GCUUUUGCUUUUGCC---UUAGCUUGCCGUUGGCCAAGUUAAGCUUGUUAAGCUUGGCACGAAAGCAGUUUUAAUCUCAAAAUUAAAACGUUUGCAAUUUUCAGGAGACU
-----.((((((...((((.---..(((.(((..(((((((((((.((....)).)))))))).)))..)))((((((((......))))))))))).))))....))))))... ( -31.00)
>DroGri_CAF1 26504 102 + 1
---------AUGCUUGGCCU---UUAGC-UGCUUUUAGCCAAGUUAAGCUUGUUAAGCUUGGCACGAAAGCAGUUUUAAUCUCAAAAUUAAAACGUUUGUAAUUUACCAGAAACU
---------....((((...---.....-(((((((.((((((((.((....)).))))))))..)))))))((((((((......))))))))............))))..... ( -25.40)
>DroMoj_CAF1 21974 102 + 1
---------AUGCUUAUCCU---UUAGC-UGCUUUUAGCCAAGUUAAGCUUGUUAAGCUUGGCACGAAAGCAGUUUUAAUCUCAAAAUUAAAACGUUUGUAAUUUACCAGCAACU
---------.((((......---.....-(((((((.((((((((.((....)).))))))))..)))))))((((((((......))))))))..............))))... ( -26.20)
>DroAna_CAF1 18826 108 + 1
AAG--AGCUUUGUUU--CCU---UUGGCUUGCUUUUAGCCAAGUUAAGCUUGUUAAGCCUGGCACGAAAGCAGUUUUAAUCUCAAAAUUAAAACGUUUGCAAUUUUCGAGAGACU
...--......((((--(..---((((((.......))))))((((.(((.....))).)))).((((((((((((((((......))))))))...)))...))))).))))). ( -25.20)
>DroPer_CAF1 24894 107 + 1
-----GCUUUUGCUUUUGCC---UUAGCUUGCCGUUGGCCAAGUUAAGCUUGUUAAGCUUGGCACGAAAGCAGUUUUAAUCUCAAAAUUAAAACGUUUGCAAUUUUCAGGAGACU
-----.((((((...((((.---..(((.(((..(((((((((((.((....)).)))))))).)))..)))((((((((......))))))))))).))))....))))))... ( -31.00)
>consensus
_____G__UUUGCUU_UCCU___UUAGCUUGCUGUUAGCCAAGUUAAGCUUGUUAAGCUUGGCACGAAAGCAGUUUUAAUCUCAAAAUUAAAACGUUUGCAAUUUUCAAGAGACU
..........(((........................((((((((.((....)).))))))))....((((.((((((((......))))))))))))))).............. (-16.51 = -16.43 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 7

Location 3,767,087 – 3,767,200
Length 113
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 82.00
Mean single sequence MFE -27.07
Consensus MFE -15.91
Energy contribution -16.13
Covariance contribution 0.22
Combinations/Pair 1.13
Mean z-score -2.54
Structure conservation index 0.59
SVM decision value 0.49
SVM RNA-class probability 0.755234
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3767087 113 - 27905053
AGUCGCUCGAAAAUUGCAAACGUUUUAAUUUUGAGAUUAAAACGACUUUCGUGCGGAGCUUAACAAGCUUAACUUGGCCAACCGAAUGCCAGCCAACC--AAACAGGGUCCCCUG
...(((.(((((........((((((((((....))))))))))..))))).)))(((((.....)))))...(((((.............)))))..--...((((....)))) ( -28.32)
>DroPse_CAF1 24404 107 - 1
AGUCUCCUGAAAAUUGCAAACGUUUUAAUUUUGAGAUUAAAACUGCUUUCGUGCCAAGCUUAACAAGCUUAACUUGGCCAACGGCAAGCUAA---GGCAAAAGCAAAAGC-----
...............((....(((((((((....)))))))))((((((..((((.(((((..((((.....))))(((...))))))))..---))))))))))...))----- ( -27.80)
>DroGri_CAF1 26504 102 - 1
AGUUUCUGGUAAAUUACAAACGUUUUAAUUUUGAGAUUAAAACUGCUUUCGUGCCAAGCUUAACAAGCUUAACUUGGCUAAAAGCA-GCUAA---AGGCCAAGCAU---------
.(((..((((...........(((((((((....)))))))))((((((...((((((.((((.....))))))))))..))))))-.....---..)))))))..--------- ( -26.50)
>DroMoj_CAF1 21974 102 - 1
AGUUGCUGGUAAAUUACAAACGUUUUAAUUUUGAGAUUAAAACUGCUUUCGUGCCAAGCUUAACAAGCUUAACUUGGCUAAAAGCA-GCUAA---AGGAUAAGCAU---------
...((((..............(((((((((....)))))))))((((((...((((((.((((.....))))))))))..))))))-.....---......)))).--------- ( -25.20)
>DroAna_CAF1 18826 108 - 1
AGUCUCUCGAAAAUUGCAAACGUUUUAAUUUUGAGAUUAAAACUGCUUUCGUGCCAGGCUUAACAAGCUUAACUUGGCUAAAAGCAAGCCAA---AGG--AAACAAAGCU--CUU
((((((.(((((...(((...(((((((((....))))))))))))))))).)..))))).....(((((...((((((.......))))))---.(.--...).)))))--... ( -26.80)
>DroPer_CAF1 24894 107 - 1
AGUCUCCUGAAAAUUGCAAACGUUUUAAUUUUGAGAUUAAAACUGCUUUCGUGCCAAGCUUAACAAGCUUAACUUGGCCAACGGCAAGCUAA---GGCAAAAGCAAAAGC-----
...............((....(((((((((....)))))))))((((((..((((.(((((..((((.....))))(((...))))))))..---))))))))))...))----- ( -27.80)
>consensus
AGUCUCUCGAAAAUUGCAAACGUUUUAAUUUUGAGAUUAAAACUGCUUUCGUGCCAAGCUUAACAAGCUUAACUUGGCCAAAAGCAAGCUAA___AGCA_AAGCAAA__C_____
.....................(((((((((....)))))))))((((.....((((((.((((.....))))))))))....))))............................. (-15.91 = -16.13 +   0.22)

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 10:04:47 2006