Locus 4697

Sequence ID 2L_DroMel_CAF1
Location 13,489,005 – 13,489,157
Length 152
Max. P 0.999306
window7433 window7434 window7435

overview

Window 3

Location 13,489,005 – 13,489,095
Length 90
Sequences 5
Columns 105
Reading direction forward
Mean pairwise identity 80.57
Mean single sequence MFE -19.59
Consensus MFE -11.90
Energy contribution -11.74
Covariance contribution -0.16
Combinations/Pair 1.09
Mean z-score -1.71
Structure conservation index 0.61
SVM decision value -0.02
SVM RNA-class probability 0.521611
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13489005 90 + 22407834
UAAA--------GUAUUAAAGUGUUAUUUUGCCAACAAAAUCAAACAAAUUUGGC--ACGUAUAACUA-----UGCAUACUUUUGGGGCACACUUAGCCUUGAAU
..((--------((((......(((((..((((((...............)))))--)...)))))..-----...))))))(..((((.......))))..).. ( -19.76)
>DroSec_CAF1 87764 97 + 1
UAAA--------GUAAUAAAGUGUUAUUUUGCCAACGAAAUCAAACAAAUUUGGCGCACCUAUUACUAUGGUAUGCAUACUUUUGGGGCAGACUUAGCCUUGAAU
...(--------((((((..((((......(((((...............))))))))).)))))))..((((....))))((..((((.......))))..)). ( -19.76)
>DroSim_CAF1 89342 90 + 1
UAAA--------GUAUUAAAGUGUUAUUUUGCCAACGAAAUCGAACAAAUUUGGC--ACGCAUUACUA-----UGCAUACUUUUGGGGCAGACUUAGCCUUGAAU
..((--------((((....((((((.((((....((....))..))))..))))--))((((....)-----)))))))))(..((((.......))))..).. ( -21.70)
>DroEre_CAF1 92513 90 + 1
------AUAAAAGUAUUAAAGUGAUAUUUUGCCAACGAAAUCAACCAAAUUUGGC----GUAUUACUA-----UGCAUACUUUUGGGGCAGACUUAGCCUUGAAU
------.(((((((((((.((((((((...(((((...............)))))----)))))))).-----)).)))))))))((((.......))))..... ( -21.86)
>DroYak_CAF1 89800 88 + 1
AAAAAAAUAAAAGGAUUGAA----------GCCGACGAAAUCAAACAAAUUUGGC--ACGUAUUACUA-----UGCAUACUUUUGGGGCAGACCUAGCCUUGAAU
....................----------(((((...............)))))--..((((....)-----))).....((..((((.......))))..)). ( -14.86)
>consensus
UAAA________GUAUUAAAGUGUUAUUUUGCCAACGAAAUCAAACAAAUUUGGC__ACGUAUUACUA_____UGCAUACUUUUGGGGCAGACUUAGCCUUGAAU
..............................(((((...............)))))..........................((..((((.......))))..)). (-11.90 = -11.74 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 4

Location 13,489,028 – 13,489,133
Length 105
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 91.37
Mean single sequence MFE -28.16
Consensus MFE -22.95
Energy contribution -23.15
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -3.90
Structure conservation index 0.81
SVM decision value 3.50
SVM RNA-class probability 0.999306
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13489028 105 + 22407834
CCAACAAAAUCAAACAAAUUUGGC--ACGUAUAACUA-----UGCAUACUUUUGGGGCACACUUAGCCUUGAAUUAUUAUUAUAAAGGCCCUUAAAAGUAUGUAUAAAGCCA
....................((((--..(.....)((-----(((((((((((((((........(((((.(((....)))...))))))))))))))))))))))..)))) ( -28.60)
>DroSec_CAF1 87787 112 + 1
CCAACGAAAUCAAACAAAUUUGGCGCACCUAUUACUAUGGUAUGCAUACUUUUGGGGCAGACUUAGCCUUGAAUUAUUAUUAUAAAAGCCCUUAAAAGUAUGUAUAAAGCCA
....................((((....((((....))))((((((((((((((((((...(........)..((((....))))..)))).))))))))))))))..)))) ( -27.70)
>DroSim_CAF1 89365 105 + 1
CCAACGAAAUCGAACAAAUUUGGC--ACGCAUUACUA-----UGCAUACUUUUGGGGCAGACUUAGCCUUGAAUUAUUAUUACAAAGGCCCUUAAAAGUAUGUAUAAAGCCA
....((....))........((((--..(.....)((-----(((((((((((((((........(((((.(((....)))...))))))))))))))))))))))..)))) ( -28.30)
>DroEre_CAF1 92538 103 + 1
CCAACGAAAUCAACCAAAUUUGGC----GUAUUACUA-----UGCAUACUUUUGGGGCAGACUUAGCCUUGAAUUACAAUUAUAAAGGCCCUUAAAAGUAUGUAUAAAGCCA
....................((((----.......((-----(((((((((((((((........(((((.(((....)))...))))))))))))))))))))))..)))) ( -28.10)
>DroYak_CAF1 89821 105 + 1
CCGACGAAAUCAAACAAAUUUGGC--ACGUAUUACUA-----UGCAUACUUUUGGGGCAGACCUAGCCUUGAAUUAUAAUUAAAAAGGCCCUUAAAAGUAUGUAUAAAGCCA
....................((((--..(.....)((-----(((((((((((((((........(((((.(((....)))...))))))))))))))))))))))..)))) ( -28.10)
>consensus
CCAACGAAAUCAAACAAAUUUGGC__ACGUAUUACUA_____UGCAUACUUUUGGGGCAGACUUAGCCUUGAAUUAUUAUUAUAAAGGCCCUUAAAAGUAUGUAUAAAGCCA
....................((((..................(((((((((((((((........(((((.(((....)))...))))))))))))))))))))....)))) (-22.95 = -23.15 +   0.20)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,489,063 – 13,489,157
Length 94
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 80.69
Mean single sequence MFE -24.12
Consensus MFE -19.14
Energy contribution -20.03
Covariance contribution 0.89
Combinations/Pair 1.08
Mean z-score -2.88
Structure conservation index 0.79
SVM decision value 1.47
SVM RNA-class probability 0.956942
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13489063 94 + 22407834
--UGCAUACUUUUGGGGCACACUUAGCCUUGA--AU----UAUUAUUAUAAAGGCCCUUAAAAGUAUGUAUAAAGCCAGU---ACCG------AUAGGUUACACAUUAA--AA
--(((((((((((((((........(((((.(--((----....)))...))))))))))))))))))))........((---(((.------...)).))).......--.. ( -26.00)
>DroSec_CAF1 87827 96 + 1
UAUGCAUACUUUUGGGGCAGACUUAGCCUUGA--AU----UAUUAUUAUAAAAGCCCUUAAAAGUAUGUAUAAAGCCAGU---ACCG------AUAGGUUACACAUUAA--AA
((((((((((((((((((...(........).--.(----(((....))))..)))).))))))))))))))......((---(((.------...)).))).......--.. ( -25.10)
>DroSim_CAF1 89400 94 + 1
--UGCAUACUUUUGGGGCAGACUUAGCCUUGA--AU----UAUUAUUACAAAGGCCCUUAAAAGUAUGUAUAAAGCCAGU---ACCG------AUAGGUUACACAUUAA--AA
--(((((((((((((((........(((((.(--((----....)))...))))))))))))))))))))........((---(((.------...)).))).......--.. ( -26.00)
>DroEre_CAF1 92571 102 + 1
--UGCAUACUUUUGGGGCAGACUUAGCCUUGA--AU----UACAAUUAUAAAGGCCCUUAAAAGUAUGUAUAAAGCCAGU---ACCGAAAAUGCUAGGUUACACAUUAAAAAA
--(((((((((((((((........(((((.(--((----....)))...))))))))))))))))))))...(((((((---(.......)))).))))............. ( -26.80)
>DroYak_CAF1 89856 102 + 1
--UGCAUACUUUUGGGGCAGACCUAGCCUUGA--AU----UAUAAUUAAAAAGGCCCUUAAAAGUAUGUAUAAAGCCAGU---ACCGGAAAUGAUAGGUUACACACUAAAAAA
--(((((((((((((((........(((((.(--((----....)))...))))))))))))))))))))........((---(((..........)).)))........... ( -24.60)
>DroAna_CAF1 152011 103 + 1
--UGCAUACUUUUGGUGAAAAAUUGGGCUUAAGAAUGUCGUA-UGUCUCAAAGACCCUGAAAAGUAUGCUAAAAAAAAGGUCAAUCG------UUAGG-GAUACAUUACAAAA
--.((((((((((((..........(((........)))...-.(((.....)))))..))))))))))..............(((.------.....-)))........... ( -16.20)
>consensus
__UGCAUACUUUUGGGGCAGACUUAGCCUUGA__AU____UAUUAUUAUAAAGGCCCUUAAAAGUAUGUAUAAAGCCAGU___ACCG______AUAGGUUACACAUUAA__AA
..(((((((((((((((........(((((....................))))))))))))))))))))........((...(((..........)))...))......... (-19.14 = -20.03 +   0.89)

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 11:25:00 2006