Locus 980

Sequence ID 3R_DroMel_CAF1
Location 3,162,417 – 3,162,577
Length 160
Max. P 0.999034
window1578 window1579 window1580

overview

Window 8

Location 3,162,417 – 3,162,537
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 76.18
Mean single sequence MFE -20.46
Consensus MFE -13.68
Energy contribution -14.42
Covariance contribution 0.75
Combinations/Pair 1.18
Mean z-score -1.77
Structure conservation index 0.67
SVM decision value 0.73
SVM RNA-class probability 0.835223
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3162417 120 - 27905053
AAGCGGAAAUAAAGAGGCUCACAGUGUAUUUUGUAGUGUACUGUGAAGUUCUUAAUGCAAUGAAUAAAAAAAAAACACCAAAAAACUUUGAAUAAAAAUUAACUAAAUUACAAUCAACUA
.((..((....(((((..((((((((((((....))))))))))))..))))).........................((((....)))).......................))..)). ( -17.50)
>DroSec_CAF1 10305 118 - 1
AAGCGGAAAUAAAGAGGCUUACAGUGUAUUUUGAAGUGCACUGUGAAGUUCUUAAGACAAUGAAUAGGAAAAA-AC-CCAAAAAACCUUUAAUAAUAAUUAGAUAUAUUAUAAUCAACCA
....((.....(((((..((((((((((((....))))))))))))..))))).......(((...((.....-..-))............((((((........))))))..))).)). ( -22.90)
>DroSim_CAF1 12473 119 - 1
AAGCGGAAAUAAAGAGGCUCACAGUGUAUUUUGUAGUGCACCGUGAAGUUCUUAAGACAAUGAAUAGGAAAAAUAC-UCAAAAAACCUUUAAUAAAAAUUACCUAAAUUAUAAUUACCCA
....((.....(((((..((((.(((((((....))))))).))))..)))))...........((((........-........................))))............)). ( -18.65)
>DroEre_CAF1 2013 107 - 1
AAGCGGAAAUAAAGAGGCUCACAGUGUAUUUUGUACUGCACUGUCAGAACUUUGAGCCAAGCCA------------ACU-AAAAUACUUUAUUAGAAAUAAACUAAGUUGGAUUAAAUCA
.............(((((((((((((((........)))))))).........)))))...(((------------(((-....((.(((((.....))))).))))))))......)). ( -22.80)
>consensus
AAGCGGAAAUAAAGAGGCUCACAGUGUAUUUUGUAGUGCACUGUGAAGUUCUUAAGACAAUGAAUAGGAAAAA_AC_CCAAAAAACCUUUAAUAAAAAUUAACUAAAUUAUAAUCAACCA
...........(((((..((((((((((((....))))))))))))..)))))................................................................... (-13.68 = -14.42 +   0.75)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,162,457 – 3,162,577
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 77.83
Mean single sequence MFE -21.31
Consensus MFE -14.60
Energy contribution -15.44
Covariance contribution 0.84
Combinations/Pair 1.23
Mean z-score -1.78
Structure conservation index 0.69
SVM decision value 0.83
SVM RNA-class probability 0.860797
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3162457 120 + 27905053
UGGUGUUUUUUUUUUAUUCAUUGCAUUAAGAACUUCACAGUACACUACAAAAUACACUGUGAGCCUCUUUAUUUCCGCUUAGAUAAGUUUACUUCAUAAGCGACACUAAAUUAUAUGCCA
((((((.....................((((..((((((((..............))))))))..))))......((((((...(((....)))..))))))))))))............ ( -23.54)
>DroSec_CAF1 10345 118 + 1
UGG-GU-UUUUUCCUAUUCAUUGUCUUAAGAACUUCACAGUGCACUUCAAAAUACACUGUAAGCCUCUUUAUUUCCGCUUAGAUAAGUUUACUUCAUAAGCGACACUAAAUUAUAUGCCA
(((-(.-.....)))).....((((..((((.(((.((((((............)))))))))..)))).......(((((...(((....)))..)))))))))............... ( -21.10)
>DroSim_CAF1 12513 119 + 1
UGA-GUAUUUUUCCUAUUCAUUGUCUUAAGAACUUCACGGUGCACUACAAAAUACACUGUGAGCCUCUUUAUUUCCGCUUAGAUAAGUUUACUUCAUAAGCGACACUAAAUUAUAUGCCA
(((-(((.......)))))).((((..((((..(((((((((............)))))))))..)))).......(((((...(((....)))..)))))))))............... ( -24.90)
>DroEre_CAF1 2053 104 + 1
-AGU------------UGGCUUGGCUCAAAGUUCUGACAGUGCAGUACAAAAUACACUGUGAGCCUCUUUAUUUCCGCUUAGAUAAGUUCACUUC---AGCGACACUAAAUUAUAUGCCA
-...------------((((..(((((.........((((((............)))))))))))..........((((.....(((....))).---))))..............)))) ( -20.50)
>DroYak_CAF1 11801 92 + 1
----------------------------AAGUUUUGACAGUGCACUACAAAGUACACUGCUAGCCUUCUUAUUUCCGCUUAGAUAAGUUCACUUCAUAAGCGACACUAAAUUAUAUGCCA
----------------------------..(((..(.(((((.(((....))).)))))).)))...........((((((...(((....)))..)))))).................. ( -16.50)
>consensus
UGG_GU_UUUUU__UAUUCAUUGUCUUAAGAACUUCACAGUGCACUACAAAAUACACUGUGAGCCUCUUUAUUUCCGCUUAGAUAAGUUUACUUCAUAAGCGACACUAAAUUAUAUGCCA
...........................((((..(((((((((............)))))))))..))))......((((((...(((....)))..)))))).................. (-14.60 = -15.44 +   0.84)

alignment

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secondary structure

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dotplot

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Window 0

Location 3,162,457 – 3,162,577
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 77.83
Mean single sequence MFE -30.28
Consensus MFE -23.98
Energy contribution -24.50
Covariance contribution 0.52
Combinations/Pair 1.18
Mean z-score -3.16
Structure conservation index 0.79
SVM decision value 3.34
SVM RNA-class probability 0.999034
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3162457 120 - 27905053
UGGCAUAUAAUUUAGUGUCGCUUAUGAAGUAAACUUAUCUAAGCGGAAAUAAAGAGGCUCACAGUGUAUUUUGUAGUGUACUGUGAAGUUCUUAAUGCAAUGAAUAAAAAAAAAACACCA
..((((......((...(((((((..(((....)))...)))))))...))(((((..((((((((((((....))))))))))))..))))).))))...................... ( -28.70)
>DroSec_CAF1 10345 118 - 1
UGGCAUAUAAUUUAGUGUCGCUUAUGAAGUAAACUUAUCUAAGCGGAAAUAAAGAGGCUUACAGUGUAUUUUGAAGUGCACUGUGAAGUUCUUAAGACAAUGAAUAGGAAAAA-AC-CCA
.........(((((.(((((((((..(((....)))...))))).......(((((..((((((((((((....))))))))))))..)))))..)))).))))).((.....-..-)). ( -32.10)
>DroSim_CAF1 12513 119 - 1
UGGCAUAUAAUUUAGUGUCGCUUAUGAAGUAAACUUAUCUAAGCGGAAAUAAAGAGGCUCACAGUGUAUUUUGUAGUGCACCGUGAAGUUCUUAAGACAAUGAAUAGGAAAAAUAC-UCA
.........(((((.(((((((((..(((....)))...))))).......(((((..((((.(((((((....))))))).))))..)))))..)))).)))))...........-... ( -29.40)
>DroEre_CAF1 2053 104 - 1
UGGCAUAUAAUUUAGUGUCGCU---GAAGUGAACUUAUCUAAGCGGAAAUAAAGAGGCUCACAGUGUAUUUUGUACUGCACUGUCAGAACUUUGAGCCAAGCCA------------ACU-
((((......((((...(((((---.(((....))).....)))))...))))..(((((((((((((........)))))))).........)))))..))))------------...- ( -32.60)
>DroYak_CAF1 11801 92 - 1
UGGCAUAUAAUUUAGUGUCGCUUAUGAAGUGAACUUAUCUAAGCGGAAAUAAGAAGGCUAGCAGUGUACUUUGUAGUGCACUGUCAAAACUU----------------------------
((((......((((...(((((((..(((....)))...)))))))...))))...))))((((((((((....))))))))))........---------------------------- ( -28.60)
>consensus
UGGCAUAUAAUUUAGUGUCGCUUAUGAAGUAAACUUAUCUAAGCGGAAAUAAAGAGGCUCACAGUGUAUUUUGUAGUGCACUGUGAAGUUCUUAAGACAAUGAAUA__AAAAA_AC_CCA
..((......((((...(((((((..(((....)))...)))))))...))))...))((((((((((((....)))))))))))).................................. (-23.98 = -24.50 +   0.52)

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 09:57:22 2006