Locus 8022

Sequence ID 3L_DroMel_CAF1
Location 21,137,045 – 21,137,210
Length 165
Max. P 0.973678
window13103 window13104 window13105

overview

Window 3

Location 21,137,045 – 21,137,139
Length 94
Sequences 4
Columns 94
Reading direction reverse
Mean pairwise identity 81.98
Mean single sequence MFE -34.58
Consensus MFE -23.16
Energy contribution -23.97
Covariance contribution 0.81
Combinations/Pair 1.23
Mean z-score -2.35
Structure conservation index 0.67
SVM decision value 1.35
SVM RNA-class probability 0.945127
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21137045 94 - 23771897
GCGCCUGCGCAGCUGCAACAGCUGAUGUUGCUGUUGUUGCUGUUGUUUUGCUGGACAAAAGUACAGCAGCAUGUCGCCCACUAACGUGCAAAUG
((((.((((((((.((((((((.......)))))))).))))).....(((((.((....)).)))))))).).))).(((....)))...... ( -38.20)
>DroSec_CAF1 8249 94 - 1
GCGCCUGCGCAGCUGUAGCAGCUGAUGCUGCUGUUGUUGCUGUUGUUUUGCUGGCCAAAAGUGCAGCAGCAUGUCGCCCACUAACGUGCAAAUG
((((.((((((((..(((((((....)))))))..)))))((((((...(((.......)))))))))))).).))).(((....)))...... ( -36.80)
>DroEre_CAF1 4789 85 - 1
GCGCCUGCGCAGCUGCAGCAGCUGAUGCUGC---------UGUUGUUUUGCUGGCCAAAAGCGCAGCAGCAUGUCGCCCACUUACGUGCAAGUG
((((.(((..(((.((((((((....)))))---------))).))).(((((((.....)).)))))))).).))).(((((......))))) ( -34.90)
>DroYak_CAF1 8329 76 - 1
GCA---------CUGCAGCAGCUGAUGUUGC---------UGUUGUUUUGCUGGCCGAAAGUGCAGCAGCAUGUCGCCCACCUACGUGCAACUG
..(---------(.((((((((....)))))---------))).))..(((((..(....)..)))))((((((.(.....).))))))..... ( -28.40)
>consensus
GCGCCUGCGCAGCUGCAGCAGCUGAUGCUGC_________UGUUGUUUUGCUGGCCAAAAGUGCAGCAGCAUGUCGCCCACUAACGUGCAAAUG
((((....(((((.((((((.....)))))).)))))...(((((((.((((.......)))).)))))))..............))))..... (-23.16 = -23.97 +   0.81)

alignment

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secondary structure

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dotplot

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Window 4

Location 21,137,060 – 21,137,175
Length 115
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 73.93
Mean single sequence MFE -35.66
Consensus MFE -18.15
Energy contribution -21.94
Covariance contribution 3.79
Combinations/Pair 1.19
Mean z-score -2.18
Structure conservation index 0.51
SVM decision value 1.69
SVM RNA-class probability 0.972550
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21137060 115 + 23771897
GGGCGACAUGCUG-CUGUACUUUUGUCCAGCAAAACAACAGCAACAACAGCAACAUCAGCUGUUGCAGCUGCGCAGGCGCCAAAUGCGUAUGCUAAUGUUGGCGGUAAGUUCAUAA
((((....(((((-(((.((....)).))))..((((.((((..(((((((.......)))))))..)))).(((.((((.....)))).)))...))))))))....)))).... ( -41.20)
>DroSec_CAF1 8264 115 + 1
GGGCGACAUGCUG-CUGCACUUUUGGCCAGCAAAACAACAGCAACAACAGCAGCAUCAGCUGCUACAGCUGCGCAGGCGCCAAAUGCGCAUGCUAAUGUUGGCGGUAAGUUCAAAA
((((....(((((-(((..(....)..)))))...((((((((.(...((((((....))))))...).)))(((.((((.....)))).)))...))))))))....)))).... ( -41.10)
>DroEre_CAF1 4804 106 + 1
GGGCGACAUGCUG-CUGCGCUUUUGGCCAGCAAAACAACA---------GCAGCAUCAGCUGCUGCAGCUGCGCAGGCGCCAAAUGCGCAUGCUAAUGUUGGCGGUAAGUUCAAAG
.(.((((((...(-((((((.((((((...........((---------(((((....)))))))..(((.....))))))))).))))).))..)))))).)............. ( -44.30)
>DroYak_CAF1 8344 97 + 1
GGGCGACAUGCUG-CUGCACUUUCGGCCAGCAAAACAACA---------GCAACAUCAGCUGCUGCAG---------UGCCAAAUGGCUAUGCUAAUGUUGGCGGUAAGUUCAAAA
.((((......))-))(.((((.(.(((((((......((---------((.......))))..(((.---------.(((....)))..)))...))))))).).)))).).... ( -30.60)
>DroAna_CAF1 27063 88 + 1
GGGCGG----CUGCCUGCACUUUUAGC---------AACAACAACAACAGCA---CUA------------GCGAGGGCGCCAAAUUCGCAUGCAAAUGGAAGCGGUAAGUUCAAAA
((((((----(.((((((.......))---------.............((.---...------------))..)))))))....((((.(.(....).).))))...)))).... ( -21.10)
>consensus
GGGCGACAUGCUG_CUGCACUUUUGGCCAGCAAAACAACA_CAACAACAGCAACAUCAGCUGCUGCAGCUGCGCAGGCGCCAAAUGCGCAUGCUAAUGUUGGCGGUAAGUUCAAAA
.(((.....)))...((.((((.(.(((((((.................((((((.....))))))(((((((((.........)))))).)))..))))))).).)))).))... (-18.15 = -21.94 +   3.79)

alignment

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secondary structure

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dotplot

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Window 5

Location 21,137,099 – 21,137,210
Length 111
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 73.98
Mean single sequence MFE -32.94
Consensus MFE -17.15
Energy contribution -19.46
Covariance contribution 2.31
Combinations/Pair 1.30
Mean z-score -2.18
Structure conservation index 0.52
SVM decision value 1.72
SVM RNA-class probability 0.973678
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21137099 111 - 23771897
UCACCGAGUGCACGCGCUGUUUGCAUAAAUUAAGCUUAUGAACUUACCGCCAACAUUAGCAUACGCAUUUGGCGCCUGCGCAGCUGCAACAGCUGAUGUUGCUGUUGUUGC
.......(((((.((((((..(((......((((........))))..((........))....)))..)))))).))))).((.((((((((.......)))))))).)) ( -38.20)
>DroSec_CAF1 8303 111 - 1
UCACCGAGUGCACGCGCUAUUUGUAUAAAUUGAGCUUUUGAACUUACCGCCAACAUUAGCAUGCGCAUUUGGCGCCUGCGCAGCUGUAGCAGCUGAUGCUGCUGUUGUUGC
...((((((((.((.((((..(((......((((........))))......))).)))).)).)))))))).......(((((..(((((((....)))))))..))))) ( -38.10)
>DroEre_CAF1 4843 102 - 1
UUACCAAGUGCACGCGCUAUUUGCACAGAUACAGCCUUUGAACUUACCGCCAACAUUAGCAUGCGCAUUUGGCGCCUGCGCAGCUGCAGCAGCUGAUGCUGC---------
.......(((((.((((((..(((.((((.......))))........((........))....)))..)))))).)))))....((((((.....))))))--------- ( -34.20)
>DroYak_CAF1 8383 93 - 1
UUACCGAGUGCCCGCGCUAUUUGCAUAAAUGGAGCUUUUGAACUUACCGCCAACAUUAGCAUAGCCAUUUGGCA---------CUGCAGCAGCUGAUGUUGC---------
......((((((...((.....))..((((((.(((..((.............))..)))....))))))))))---------))((((((.....))))))--------- ( -25.52)
>DroAna_CAF1 27090 95 - 1
UCAGCAAUUGCACGCGCAAUUUGCAUAAUUAAAG-UUUUGAACUUACCGCUUCCAUUUGCAUGCGAAUUUGGCGCCCUCGC------------UAG---UGCUGUUGUUGU
.(((((((.((((....(((((((((.....(((-(.....))))...((........)))))))))))(((((....)))------------)))---))).))))))). ( -28.70)
>consensus
UCACCGAGUGCACGCGCUAUUUGCAUAAAUAAAGCUUUUGAACUUACCGCCAACAUUAGCAUGCGCAUUUGGCGCCUGCGCAGCUGCAGCAGCUGAUGCUGCUGUUGUUG_
.......(((((.((((((..(((.((....(((........)))...((........)).)).)))..)))))).)))))....((((((.....))))))......... (-17.15 = -19.46 +   2.31)

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 13:04:07 2006