Locus 3585

Sequence ID 2R_DroMel_CAF1
Location 11,932,236 – 11,932,411
Length 175
Max. P 0.723292
window5841 window5842 window5843

overview

Window 1

Location 11,932,236 – 11,932,332
Length 96
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 67.59
Mean single sequence MFE -23.43
Consensus MFE -9.32
Energy contribution -9.52
Covariance contribution 0.19
Combinations/Pair 1.11
Mean z-score -1.65
Structure conservation index 0.40
SVM decision value 0.07
SVM RNA-class probability 0.568673
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11932236 96 + 20766785
--------AAUAAUAU------------GCGCAUAUAUGUAAGUGUAGGCUCUCACCGUUUUCUAUCAGAUACUUGGCCACUUUCACGCCUAUUUUGUAGGCAACUUCAUUGGCCU
--------........------------..((.(((((....))))).)).........................(((((.......((((((...))))))........))))). ( -18.56)
>DroPse_CAF1 39175 92 + 1
AAACCUCUUUUCAUAGAU----------CG--------------GAUGGAGCUUACCAUUGUCAAACAGAUAUUGGGCCACGGCCACGGCAAUGGUGAGGGCCACAUCUUUGGCCU
....((((.(((......----------.)--------------)).))))((((((((((((...(((...)))(((....)))..))))))))))))(((((......))))). ( -35.10)
>DroSec_CAF1 33774 96 + 1
--------AUUAAUAU------------GGGCAUACAUGUAAGUGUAGGCUCUCACCGUUUUCUAUCAGAAACUUGGCCACUUUCACGCCUAUUUUGUAGGCCACUUCAUUGGCCU
--------..(((.((------------((((.(((((....)))))((((......(((((......)))))..))))........)))))).))).((((((......)))))) ( -26.30)
>DroSim_CAF1 31689 98 + 1
--------AUUAAUAAAA----------UGGAUUAUAUGUAAGUGUAGGCUCUCACCGUUUUCUAUCAGAUACUUGGCCACUUUCACGCCUAUUUUGUAGGCCACUUCAUUGGCCU
--------....((((((----------(((..(((((....)))))((((......((((......))))....))))..........)))))))))((((((......)))))) ( -19.90)
>DroEre_CAF1 31042 102 + 1
--------UUAAUUUAAAAAGAUUAUAUAGGAAUAUUG------GUAGGCUCUCACCAUUUUCUAUCAGAUACUUGGCUGCUUUCACGCCGAUUUUAUAGGCCACUUCAUUGGCCU
--------..........((((((..(((((((...((------((........)))).)))))))..))).)))(((((....)).)))........((((((......)))))) ( -21.60)
>DroYak_CAF1 32512 104 + 1
--------UUAAUUUUAAAGGAUUA--UAGGAAUAUAGC--AUAUUGGUCACUCACCGUUUUCUAUCAGAUACUUGGCUGCUUCCACGCCAAUUUUAUAGGCCACCUUAUUGGCCU
--------...............((--(((((..((((.--....((((.....))))....)))).......(((((((....)).))))))))))))(((((......))))). ( -19.10)
>consensus
________AUUAAUAUAA__________AGGAAUAUAUG__AGUGUAGGCUCUCACCGUUUUCUAUCAGAUACUUGGCCACUUUCACGCCUAUUUUGUAGGCCACUUCAUUGGCCU
...........................................................................(((.........)))........((((((......)))))) ( -9.32 =  -9.52 +   0.19)

alignment

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secondary structure

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Window 2

Location 11,932,236 – 11,932,332
Length 96
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 67.59
Mean single sequence MFE -23.74
Consensus MFE -12.33
Energy contribution -13.17
Covariance contribution 0.83
Combinations/Pair 1.00
Mean z-score -1.48
Structure conservation index 0.52
SVM decision value 0.41
SVM RNA-class probability 0.723292
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11932236 96 - 20766785
AGGCCAAUGAAGUUGCCUACAAAAUAGGCGUGAAAGUGGCCAAGUAUCUGAUAGAAAACGGUGAGAGCCUACACUUACAUAUAUGCGC------------AUAUUAUU--------
.(((((.......((((((.....))))))......)))))((((.((.....))....(((....)))...))))............------------........-------- ( -22.82)
>DroPse_CAF1 39175 92 - 1
AGGCCAAAGAUGUGGCCCUCACCAUUGCCGUGGCCGUGGCCCAAUAUCUGUUUGACAAUGGUAAGCUCCAUC--------------CG----------AUCUAUGAAAAGAGGUUU
(((((...((((..((....(((((((..(.(((....))))....((.....)))))))))..))..))))--------------..----------.(((......)))))))) ( -24.40)
>DroSec_CAF1 33774 96 - 1
AGGCCAAUGAAGUGGCCUACAAAAUAGGCGUGAAAGUGGCCAAGUUUCUGAUAGAAAACGGUGAGAGCCUACACUUACAUGUAUGCCC------------AUAUUAAU--------
((((((......))))))........((((((.(((((......((((.....))))..(((....)))..))))).....)))))).------------........-------- ( -26.80)
>DroSim_CAF1 31689 98 - 1
AGGCCAAUGAAGUGGCCUACAAAAUAGGCGUGAAAGUGGCCAAGUAUCUGAUAGAAAACGGUGAGAGCCUACACUUACAUAUAAUCCA----------UUUUAUUAAU--------
.....((((((((((((((.....)))))(((.(((((........((.....))....(((....)))..))))).)))......))----------)))))))...-------- ( -24.60)
>DroEre_CAF1 31042 102 - 1
AGGCCAAUGAAGUGGCCUAUAAAAUCGGCGUGAAAGCAGCCAAGUAUCUGAUAGAAAAUGGUGAGAGCCUAC------CAAUAUUCCUAUAUAAUCUUUUUAAAUUAA--------
((((((......)))))).(((((..(((((....)).)))..((((..((((......(((....)))...------...))))...)))).....)))))......-------- ( -22.80)
>DroYak_CAF1 32512 104 - 1
AGGCCAAUAAGGUGGCCUAUAAAAUUGGCGUGGAAGCAGCCAAGUAUCUGAUAGAAAACGGUGAGUGACCAAUAU--GCUAUAUUCCUA--UAAUCCUUUAAAAUUAA--------
((((((......))))))......(((((.((....))))))).......((((.....(((.....))).....--.)))).......--.................-------- ( -21.00)
>consensus
AGGCCAAUGAAGUGGCCUACAAAAUAGGCGUGAAAGUGGCCAAGUAUCUGAUAGAAAACGGUGAGAGCCUACACU__CAUAUAUUCCC__________UUAUAUUAAA________
((((((......))))))........(((.........)))..................(((....)))............................................... (-12.33 = -13.17 +   0.83)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,932,294 – 11,932,411
Length 117
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 78.52
Mean single sequence MFE -38.43
Consensus MFE -24.06
Energy contribution -24.40
Covariance contribution 0.34
Combinations/Pair 1.35
Mean z-score -1.43
Structure conservation index 0.63
SVM decision value 0.14
SVM RNA-class probability 0.602444
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11932294 117 + 20766785
CACUUUCACGCCUAUUUUGUAGGCAACUUCAUUGGCCUGCUUCACCAGAGGAUAGAUACGUCCGCUUUGCAUCUCCUCAUUGGUUGGAAAUUCAGCGAGCUCGUGGGCGGCCAAAAG
.........((((((...)))))).......((((((.(((.(((..(((((..(((.((.......)).)))))))).((.(((((....))))).))...))))))))))))... ( -34.60)
>DroSec_CAF1 33832 117 + 1
CACUUUCACGCCUAUUUUGUAGGCCACUUCAUUGGCCUGCUUCACCAGAGGAUAGAUACGUCCACUCUGUAUCUCCUCAUUUGUUGGGAACUCAGCGAGCUCGUGGGCGGCUAAAAG
........(((((((...((((((((......)))))))).......(((((..((((((.......))))))))))).((((((((....))))))))...)))))))........ ( -41.40)
>DroSim_CAF1 31749 117 + 1
CACUUUCACGCCUAUUUUGUAGGCCACUUCAUUGGCCUGCUUCACCAGGGGAUAGAUACGUCCACUCUGUAUCUCCUCAUUUGUUGGGAACUCAGCGAGCUCGUGGGCGGCUAAAAG
........(((((((...((((((((......)))))))).......(((((..((((((.......))))))))))).((((((((....))))))))...)))))))........ ( -40.50)
>DroEre_CAF1 31106 117 + 1
UGCUUUCACGCCGAUUUUAUAGGCCACUUCAUUGGCCUGCUUCACCAGGGGAUAGAUACGUCCACUCUGUAAGUCCUCGUUUGUUGGGAAUUUAGCGAGCUCAUGGGCGCAUAACAG
........((((.((....(((((((......)))))))........((((((...((((.......)))).))))))(((((((((....)))))))))..)).))))........ ( -31.40)
>DroYak_CAF1 32578 117 + 1
UGCUUCCACGCCAAUUUUAUAGGCCACCUUAUUGGCCUCCUUCACCAGGGGAUAGAUCCGUCCACUCUGUAUUUCCUCAUUAGAUGGGAACUUAGCGAGCUCAUGGGCGCACAAAAG
(((.....(((.........((((((......)))))).......((((((((......)))).).)))..(((((((....)).)))))....))).(((....))))))...... ( -28.10)
>DroPer_CAF1 39687 117 + 1
CACGGCCACGGCAAUGGUGAGGGCCACAUCUUUGGCCUCUGUCGCCUUUGGGUAGAUCCUGCCGCUCGCCAUCGCCUCCUCCUCGGGAUAGCCCGCCAAAGUGUGGGCGGCCACCAG
...((((..(((.(((((((((((((......))))).............(((((...))))).)))))))).)))((((....))))..((((((......))))))))))..... ( -54.60)
>consensus
CACUUUCACGCCUAUUUUGUAGGCCACUUCAUUGGCCUGCUUCACCAGGGGAUAGAUACGUCCACUCUGUAUCUCCUCAUUUGUUGGGAACUCAGCGAGCUCGUGGGCGGCCAAAAG
........((((......((((((((......))))))))..(((.((.((((......))))...................(((((....)))))...)).)))))))........ (-24.06 = -24.40 +   0.34)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:59:15 2006