Locus 4708

Sequence ID 3R_DroMel_CAF1
Location 12,368,925 – 12,369,030
Length 105
Max. P 0.834318
window7735 window7736

overview

Window 5

Location 12,368,925 – 12,369,030
Length 105
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 82.92
Mean single sequence MFE -27.25
Consensus MFE -17.35
Energy contribution -18.63
Covariance contribution 1.28
Combinations/Pair 1.07
Mean z-score -1.84
Structure conservation index 0.64
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12368925 105 + 27905053
--GA----------GGGGAGCCAUCAGUCAACAGCGUGUCAGACGCGCGGAAAGUGAAAUGAAAUUCUUAUUUUCAUUUUUUUU-UUUUUUUUUGUUCACUUAUAAGCGCCAAACACU
--..----------..((.((....(((.(((((((((.....)))))((((((.(((((((((.......))))))))).)))-))).....)))).))).....)).))....... ( -24.60)
>DroSec_CAF1 37309 99 + 1
---------------GGGAGCCAUCAGUCAACAGCGUGUCAGACGCGCGGAAAGUGAAAUGAAAUUCUUAUUUUCAUUUUUCCUUUU----UUUGUUCACUUAUAAGCGCCAAACACU
---------------.((.((....(((.(((((((((.....)))))((((((.(((((((((.......)))))))))..)))))----).)))).))).....)).))....... ( -25.30)
>DroSim_CAF1 36612 103 + 1
---------------GGGAGCCAUCAGUCAACAGCGUGUCAGACGCGCGGAAAGUGAAAUGAAAUUCUUAUUUUCAUUUUUCCUUUUUUUUUUUGUUCACUUAUAAGCGCCAAACACU
---------------.((.((....(((.(((((((((.....)))))((((((.(((((((((.......)))))))))..)))))).....)))).))).....)).))....... ( -25.30)
>DroEre_CAF1 37618 110 + 1
GUGGGGGGAGCCAGGGGGAGCCAUCAGUCAACAGCGUGUCAGACGCGCGGAAAGUGAAAUGAAAUUCUUAUUUUCAUUUUUCCA--------CUGUUCACUUAUAAGCGCCAAACACU
(((...((.((...((....))...(((.(((((((((.....)))))(((....(((((((((.......)))))))))))).--------.)))).))).....)).))...))). ( -31.40)
>DroYak_CAF1 33889 97 + 1
GUGG----------GGGGAGCCAUCAGUCAACAGCGUGUCAGACGCGCGGAAAGUGAAAUGAAAUUCUUAUUUUCAUUUUUU-----------UGUUCACUUAUAAGCGCCAAACACU
(((.----------..((.((....(((.(((((((((.....)))))((((((((((((((.....))).)))))))))))-----------)))).))).....)).))...))). ( -26.80)
>DroAna_CAF1 19139 101 + 1
--GG----------CAACAGCCAUCAGUCAACAGCAUGUCAGAUCCGAGGAAAGUGAAAUGAAAUUCUUAUUUUCAUUUUUU-----UCCUCUGGCGCCCAUCUAAGCGCCAAACACU
--((----------(....)))........................(((((((..(((((((((.......)))))))))))-----)))))((((((........))))))...... ( -30.10)
>consensus
__GG__________GGGGAGCCAUCAGUCAACAGCGUGUCAGACGCGCGGAAAGUGAAAUGAAAUUCUUAUUUUCAUUUUUCCU_______UUUGUUCACUUAUAAGCGCCAAACACU
................((.((....(((.(((((((((.....)))))((((((((((((((.....))).)))))))))))...........)))).))).....)).))....... (-17.35 = -18.63 +   1.28)

alignment

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secondary structure

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dotplot

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Window 6

Location 12,368,925 – 12,369,030
Length 105
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 82.92
Mean single sequence MFE -28.67
Consensus MFE -21.63
Energy contribution -22.33
Covariance contribution 0.70
Combinations/Pair 1.03
Mean z-score -2.37
Structure conservation index 0.75
SVM decision value 0.73
SVM RNA-class probability 0.834318
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12368925 105 - 27905053
AGUGUUUGGCGCUUAUAAGUGAACAAAAAAAAA-AAAAAAAAUGAAAAUAAGAAUUUCAUUUCACUUUCCGCGCGUCUGACACGCUGUUGACUGAUGGCUCCCC----------UC--
.(((((.(((((....(((((((..........-.......((((((.......))))))))))))).....))))).)))))((((((....)))))).....----------..-- ( -25.92)
>DroSec_CAF1 37309 99 - 1
AGUGUUUGGCGCUUAUAAGUGAACAAA----AAAAGGAAAAAUGAAAAUAAGAAUUUCAUUUCACUUUCCGCGCGUCUGACACGCUGUUGACUGAUGGCUCCC---------------
.(((((.(((((......(....)...----....((((((((((((.......)))))))....)))))..))))).)))))((((((....))))))....--------------- ( -27.00)
>DroSim_CAF1 36612 103 - 1
AGUGUUUGGCGCUUAUAAGUGAACAAAAAAAAAAAGGAAAAAUGAAAAUAAGAAUUUCAUUUCACUUUCCGCGCGUCUGACACGCUGUUGACUGAUGGCUCCC---------------
.(((((.(((((......(....)...........((((((((((((.......)))))))....)))))..))))).)))))((((((....))))))....--------------- ( -27.00)
>DroEre_CAF1 37618 110 - 1
AGUGUUUGGCGCUUAUAAGUGAACAG--------UGGAAAAAUGAAAAUAAGAAUUUCAUUUCACUUUCCGCGCGUCUGACACGCUGUUGACUGAUGGCUCCCCCUGGCUCCCCCCAC
.(((((.(((((......(....).(--------(((((((((((((.......)))))))....)))))))))))).)))))((((((....))))))......(((......))). ( -31.70)
>DroYak_CAF1 33889 97 - 1
AGUGUUUGGCGCUUAUAAGUGAACA-----------AAAAAAUGAAAAUAAGAAUUUCAUUUCACUUUCCGCGCGUCUGACACGCUGUUGACUGAUGGCUCCCC----------CCAC
.(((((.(((((....(((((((..-----------.....((((((.......))))))))))))).....))))).)))))((((((....)))))).....----------.... ( -26.81)
>DroAna_CAF1 19139 101 - 1
AGUGUUUGGCGCUUAGAUGGGCGCCAGAGGA-----AAAAAAUGAAAAUAAGAAUUUCAUUUCACUUUCCUCGGAUCUGACAUGCUGUUGACUGAUGGCUGUUG----------CC--
......((((((((....))))))))(((((-----((.((((((((.......))))))))...)))))))((....((((.((((((....)))))))))).----------))-- ( -33.60)
>consensus
AGUGUUUGGCGCUUAUAAGUGAACAAA_______AGAAAAAAUGAAAAUAAGAAUUUCAUUUCACUUUCCGCGCGUCUGACACGCUGUUGACUGAUGGCUCCCC__________CC__
.(((((.(((((....((((((..................(((((((.......))))))))))))).....))))).)))))((((((....))))))................... (-21.63 = -22.33 +   0.70)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:37:04 2006