Locus 2618

Sequence ID 2R_DroMel_CAF1
Location 9,229,951 – 9,230,050
Length 99
Max. P 0.854399
window4321 window4322

overview

Window 1

Location 9,229,951 – 9,230,050
Length 99
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 79.72
Mean single sequence MFE -38.32
Consensus MFE -23.71
Energy contribution -24.88
Covariance contribution 1.17
Combinations/Pair 1.25
Mean z-score -1.71
Structure conservation index 0.62
SVM decision value 0.36
SVM RNA-class probability 0.706001
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9229951 99 + 20766785
GGGGAUUGGUAAUGGCUGGCC----GGAGUUGGAGUGGAAAAACCACAGCAUCGCC-GGACGGCCGGCAAACACAUUAGGUGUGGCCAACAACGGCGGCUCCCG
.((((.........((((.((----(..(((((.((((.....))))......(((-((....)))))...(((((...))))).)))))..))))))))))). ( -41.20)
>DroSec_CAF1 123173 93 + 1
GGGGAUUGGU------UGGCC----GGAGCUGGAGUGGAAAAACCACAGCAUCGCC-GGACGGCCGGCAAACACAUUAGGUGUGGCCAACAACGGCGGCUCCUG
((((....((------(((((----(..((((..((......))..))))..)(((-((....)))))..((((.....)))))))))))........)))).. ( -39.40)
>DroSim_CAF1 107872 99 + 1
GGGGAUUGGUAAUGGCUGGCC----GGAGCUGGAGUGGAAAAACCACAGCAUCGCC-GGACGGCCGGCAAACACAUUAGGUGUGGCCAACAACGGCGGCUCCUG
.((((.(.((...(((((.((----((.((((..((......))..))))....))-)).)))))(((..((((.....)))).))).......)).).)))). ( -39.50)
>DroEre_CAF1 108633 99 + 1
GGGGAUUGGUAAUGGCUGGUC----GGAGCUGGAGUGGAAAAACCACAGCAUCGCC-GGCCGGCCGGCAAACACAUUAGGUGUGGCCAACAGCGGCGGCUCCUG
.((((.(.((...((((((((----((.((((..((......))..))))....))-))))))))(((..((((.....)))).))).......)).).)))). ( -43.90)
>DroYak_CAF1 106456 103 + 1
GGGGAUUGGAUCCGGCCAGCCAUUAGGAGCUGGAGUGGAAAAACCACAGCAUCGCC-GGACGGCCGGCAAACACAUUAGGUGUGGCCAGCGACGGCGGCUCCUG
..((.((((......))))))..(((((((....((((.....)))).....((((-(....((.(((..((((.....)))).))).))..)))))))))))) ( -41.70)
>DroPer_CAF1 89642 78 + 1
GGUGGUUGG------------------UGUGGGAAUGGCACAGCCACUGCACUGCUCAGA-----AACACACACAUUAGGUGUGGAUAACA---GCGGCUCUUG
((((((((.------------------(((.......)))))))))))...(((((....-----..(((((.......)))))......)---))))...... ( -24.20)
>consensus
GGGGAUUGGUAAUGGCUGGCC____GGAGCUGGAGUGGAAAAACCACAGCAUCGCC_GGACGGCCGGCAAACACAUUAGGUGUGGCCAACAACGGCGGCUCCUG
..............(((((((....((.((((..((......))..))))....)).....)))))))........((((.((.(((......))).)).)))) (-23.71 = -24.88 +   1.17)

alignment

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secondary structure

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dotplot

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Window 2

Location 9,229,951 – 9,230,050
Length 99
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 79.72
Mean single sequence MFE -35.17
Consensus MFE -21.64
Energy contribution -23.12
Covariance contribution 1.48
Combinations/Pair 1.12
Mean z-score -2.08
Structure conservation index 0.62
SVM decision value 0.80
SVM RNA-class probability 0.854399
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9229951 99 - 20766785
CGGGAGCCGCCGUUGUUGGCCACACCUAAUGUGUUUGCCGGCCGUCC-GGCGAUGCUGUGGUUUUUCCACUCCAACUCC----GGCCAGCCAUUACCAAUCCCC
.((((......((.(((((((((((.....))))(((((((....))-)))))((..((((.....))))..)).....----))))))).))......)))). ( -37.40)
>DroSec_CAF1 123173 93 - 1
CAGGAGCCGCCGUUGUUGGCCACACCUAAUGUGUUUGCCGGCCGUCC-GGCGAUGCUGUGGUUUUUCCACUCCAGCUCC----GGCCA------ACCAAUCCCC
..((((((((((..((((((.((((.....))))..))))))....)-)))).((..((((.....))))..)))))))----((...------.))....... ( -35.90)
>DroSim_CAF1 107872 99 - 1
CAGGAGCCGCCGUUGUUGGCCACACCUAAUGUGUUUGCCGGCCGUCC-GGCGAUGCUGUGGUUUUUCCACUCCAGCUCC----GGCCAGCCAUUACCAAUCCCC
..((((((((((..((((((.((((.....))))..))))))....)-)))).((..((((.....))))..)))))))----((....))............. ( -37.20)
>DroEre_CAF1 108633 99 - 1
CAGGAGCCGCCGCUGUUGGCCACACCUAAUGUGUUUGCCGGCCGGCC-GGCGAUGCUGUGGUUUUUCCACUCCAGCUCC----GACCAGCCAUUACCAAUCCCC
..((((((((((((((((((.((((.....))))..))))).))).)-)))).((..((((.....))))..)))))))----..................... ( -37.40)
>DroYak_CAF1 106456 103 - 1
CAGGAGCCGCCGUCGCUGGCCACACCUAAUGUGUUUGCCGGCCGUCC-GGCGAUGCUGUGGUUUUUCCACUCCAGCUCCUAAUGGCUGGCCGGAUCCAAUCCCC
.(((((((((((..((((((.((((.....))))..))))))....)-)))).((..((((.....))))..))))))))...((....))((((...)))).. ( -41.80)
>DroPer_CAF1 89642 78 - 1
CAAGAGCCGC---UGUUAUCCACACCUAAUGUGUGUGUU-----UCUGAGCAGUGCAGUGGCUGUGCCAUUCCCACA------------------CCAACCACC
....((((((---(((....(((((.....)))))((((-----....))))..)))))))))(((.......))).------------------......... ( -21.30)
>consensus
CAGGAGCCGCCGUUGUUGGCCACACCUAAUGUGUUUGCCGGCCGUCC_GGCGAUGCUGUGGUUUUUCCACUCCAGCUCC____GGCCAGCCAUUACCAAUCCCC
..(((((((((...((((((.((((.....))))..))))))......)))).((..((((.....))))..)))))))......................... (-21.64 = -23.12 +   1.48)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:34:45 2006