Locus 1228

Sequence ID X_DroMel_CAF1
Location 3,660,854 – 3,660,973
Length 119
Max. P 0.997904
window1975 window1976 window1977 window1978

overview

Window 5

Location 3,660,854 – 3,660,955
Length 101
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 70.88
Mean single sequence MFE -28.88
Consensus MFE -15.20
Energy contribution -18.36
Covariance contribution 3.16
Combinations/Pair 1.15
Mean z-score -1.86
Structure conservation index 0.53
SVM decision value 0.99
SVM RNA-class probability 0.896645
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3660854 101 + 22224390
---------CCUUUUGUAAUGCGAUCGCUGCAUUUGU--CCAGCGCCACUUGAGAUGCAUUUUCCGGAAAAUGCGUUCAGCUCAAGUGGUUUGUAGUUGAA---CUUUCCCAUC-----G
---------..........(((((..((((.......--.))))(((((((((((((((((((....)))))))))....)))))))))))))))......---..........-----. ( -30.40)
>DroSec_CAF1 12757 101 + 1
---------CCUUUUGUAAUGCGAUCGCUGCACUUGU--CCAGUGCCACUUGAGAUGCAUUUUCCGGAAAAUGCGUUCAGCUCAAGUGGUUUGUAGUUGAA---CUUUCACAUC-----G
---------.........(((.((((((((((((...--..)))(((((((((((((((((((....)))))))))....))))))))))..)))).))).---...)).))).-----. ( -28.90)
>DroSim_CAF1 17231 101 + 1
AAAUCGAACCCAAUUCAAACUCGAUCGCUGCACUUCC--GCUGGGCCAUU---GUUGCAUUUUCAA-----UUAGC-CCGCUCG-CCGCUUUGUAUUUACAAGGCAUUUACAU-------
..(((((.............))))).((.((......--)).((((....---((((......)))-----)..))-))))...-..(((((((....)))))))........------- ( -20.82)
>DroEre_CAF1 13625 103 + 1
---------CCUUUUGUAAUGCGAUCGCUGCACUUGUGCCCAGCGCCACUUGAGAUGCAUUUUCCGGAAAAUGCGUUAGGCUCAAGUGGCUUGUAGUUGCA---GUUUCCCAUC-----G
---------....(((((((((((..((((((....)))..)))(((((((((((((((((((....)))))))))....))))))))))))))).)))))---).........-----. ( -37.80)
>DroYak_CAF1 13746 94 + 1
---------CC---UGUAAUGCGAUCGCUGCACUUGU--UCAGCGCCACUUGAGAUGCAUUUUCCGGAAAA---------CUCAAGUGGCUUGUAGUUGCC---UUUUCCCAUCGUAUCG
---------..---....(((((((.((((.......--.))))((((((((((...(........)....---------))))))))))...........---.......))))))).. ( -26.50)
>consensus
_________CCUUUUGUAAUGCGAUCGCUGCACUUGU__CCAGCGCCACUUGAGAUGCAUUUUCCGGAAAAUGCGUUCAGCUCAAGUGGUUUGUAGUUGCA___CUUUCCCAUC_____G
..........................((((((...((.....))(((((((((((((((((((....)))))))))....)))))))))).))))))....................... (-15.20 = -18.36 +   3.16)

alignment

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secondary structure

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dotplot

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Window 6

Location 3,660,854 – 3,660,955
Length 101
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 70.88
Mean single sequence MFE -31.41
Consensus MFE -13.22
Energy contribution -17.10
Covariance contribution 3.88
Combinations/Pair 1.07
Mean z-score -2.60
Structure conservation index 0.42
SVM decision value 2.96
SVM RNA-class probability 0.997904
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3660854 101 - 22224390
C-----GAUGGGAAAG---UUCAACUACAAACCACUUGAGCUGAACGCAUUUUCCGGAAAAUGCAUCUCAAGUGGCGCUGG--ACAAAUGCAGCGAUCGCAUUACAAAAGG---------
.-----((((.((...---............(((((((((......(((((((....)))))))..)))))))))(((((.--.......))))).)).))))........--------- ( -30.90)
>DroSec_CAF1 12757 101 - 1
C-----GAUGUGAAAG---UUCAACUACAAACCACUUGAGCUGAACGCAUUUUCCGGAAAAUGCAUCUCAAGUGGCACUGG--ACAAGUGCAGCGAUCGCAUUACAAAAGG---------
.-----(((((((..(---((...........((((((((......(((((((....)))))))..))))))))(((((..--...))))))))..)))))))........--------- ( -32.10)
>DroSim_CAF1 17231 101 - 1
-------AUGUAAAUGCCUUGUAAAUACAAAGCGG-CGAGCGG-GCUAA-----UUGAAAAUGCAAC---AAUGGCCCAGC--GGAAGUGCAGCGAUCGAGUUUGAAUUGGGUUCGAUUU
-------.......(((.((((....)))).)))(-(..((((-((((.-----(((.........)---)))))))).((--....)))).))(((((((..(.....)..))))))). ( -28.00)
>DroEre_CAF1 13625 103 - 1
C-----GAUGGGAAAC---UGCAACUACAAGCCACUUGAGCCUAACGCAUUUUCCGGAAAAUGCAUCUCAAGUGGCGCUGGGCACAAGUGCAGCGAUCGCAUUACAAAAGG---------
.-----((((.((...---...........((((((((((......(((((((....)))))))..))))))))))((((.((....)).))))..)).))))........--------- ( -37.20)
>DroYak_CAF1 13746 94 - 1
CGAUACGAUGGGAAAA---GGCAACUACAAGCCACUUGAG---------UUUUCCGGAAAAUGCAUCUCAAGUGGCGCUGA--ACAAGUGCAGCGAUCGCAUUACA---GG---------
......((((.((..(---(....))....((((((((((---------.................))))))))))((((.--.......))))..)).))))...---..--------- ( -28.83)
>consensus
C_____GAUGGGAAAG___UGCAACUACAAACCACUUGAGCUGAACGCAUUUUCCGGAAAAUGCAUCUCAAGUGGCGCUGG__ACAAGUGCAGCGAUCGCAUUACAAAAGG_________
......((((.((..................(((((((((......(((((((....)))))))..)))))))))(((((..........))))).)).))))................. (-13.22 = -17.10 +   3.88)

alignment

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secondary structure

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dotplot

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Window 7

Location 3,660,883 – 3,660,973
Length 90
Sequences 4
Columns 95
Reading direction forward
Mean pairwise identity 85.41
Mean single sequence MFE -25.97
Consensus MFE -21.21
Energy contribution -22.03
Covariance contribution 0.81
Combinations/Pair 1.09
Mean z-score -2.28
Structure conservation index 0.82
SVM decision value 1.47
SVM RNA-class probability 0.956532
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3660883 90 + 22224390
CAGCGCCACUUGAGAUGCAUUUUCCGGAAAAUGCGUUCAGCUCAAGUGGUUUGUAGUUGAACUUUCCCAUC-----GCAUCGCAUAGAAAUUCUC
..(((((((((((((((((((((....)))))))))....)))))))))).(((...((........))..-----)))..))............ ( -25.80)
>DroSec_CAF1 12786 90 + 1
CAGUGCCACUUGAGAUGCAUUUUCCGGAAAAUGCGUUCAGCUCAAGUGGUUUGUAGUUGAACUUUCACAUC-----GCAUCGCAUAUAAAUUCUC
..(((((((((((((((((((((....)))))))))....)))))))))).((..(((((....))).)).-----.))..))............ ( -25.00)
>DroEre_CAF1 13656 90 + 1
CAGCGCCACUUGAGAUGCAUUUUCCGGAAAAUGCGUUAGGCUCAAGUGGCUUGUAGUUGCAGUUUCCCAUC-----GCAGCGCAUAUAAAUUGCC
..(((((((((((((((((((((....)))))))))....)))))))))).....(((((...........-----)))))))............ ( -33.80)
>DroYak_CAF1 13772 86 + 1
CAGCGCCACUUGAGAUGCAUUUUCCGGAAAA---------CUCAAGUGGCUUGUAGUUGCCUUUUCCCAUCGUAUCGCAUCGCAUAUAAAUUGUC
..((((((((((((...(........)....---------)))))))))).....(.(((................))).)))............ ( -19.29)
>consensus
CAGCGCCACUUGAGAUGCAUUUUCCGGAAAAUGCGUUCAGCUCAAGUGGCUUGUAGUUGAACUUUCCCAUC_____GCAUCGCAUAUAAAUUCUC
(((((((((((((((((((((((....)))))))))....)))))))))).....)))).................................... (-21.21 = -22.03 +   0.81)

alignment

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secondary structure

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dotplot

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Window 8

Location 3,660,883 – 3,660,973
Length 90
Sequences 4
Columns 95
Reading direction reverse
Mean pairwise identity 85.41
Mean single sequence MFE -25.46
Consensus MFE -17.08
Energy contribution -18.32
Covariance contribution 1.25
Combinations/Pair 1.00
Mean z-score -1.81
Structure conservation index 0.67
SVM decision value 0.29
SVM RNA-class probability 0.670587
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3660883 90 - 22224390
GAGAAUUUCUAUGCGAUGC-----GAUGGGAAAGUUCAACUACAAACCACUUGAGCUGAACGCAUUUUCCGGAAAAUGCAUCUCAAGUGGCGCUG
(((..(((((((((...))-----.)))))))..))).........(((((((((......(((((((....)))))))..)))))))))..... ( -25.80)
>DroSec_CAF1 12786 90 - 1
GAGAAUUUAUAUGCGAUGC-----GAUGUGAAAGUUCAACUACAAACCACUUGAGCUGAACGCAUUUUCCGGAAAAUGCAUCUCAAGUGGCACUG
(((..(((((((((...))-----.)))))))..))).........(((((((((......(((((((....)))))))..)))))))))..... ( -24.60)
>DroEre_CAF1 13656 90 - 1
GGCAAUUUAUAUGCGCUGC-----GAUGGGAAACUGCAACUACAAGCCACUUGAGCCUAACGCAUUUUCCGGAAAAUGCAUCUCAAGUGGCGCUG
.(((.......)))(((((-----...((....))))).......((((((((((......(((((((....)))))))..)))))))))))).. ( -30.60)
>DroYak_CAF1 13772 86 - 1
GACAAUUUAUAUGCGAUGCGAUACGAUGGGAAAAGGCAACUACAAGCCACUUGAG---------UUUUCCGGAAAAUGCAUCUCAAGUGGCGCUG
.................((..............((....))....((((((((((---------.................)))))))))))).. ( -20.83)
>consensus
GACAAUUUAUAUGCGAUGC_____GAUGGGAAAGUGCAACUACAAACCACUUGAGCUGAACGCAUUUUCCGGAAAAUGCAUCUCAAGUGGCGCUG
.............................................((((((((((......(((((((....)))))))..)))))))))).... (-17.08 = -18.32 +   1.25)

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 10:04:29 2006