Locus 1246

Sequence ID X_DroMel_CAF1
Location 3,710,740 – 3,710,890
Length 150
Max. P 0.989435
window2003 window2004 window2005 window2006

overview

Window 3

Location 3,710,740 – 3,710,857
Length 117
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 90.48
Mean single sequence MFE -28.56
Consensus MFE -23.64
Energy contribution -23.36
Covariance contribution -0.28
Combinations/Pair 1.17
Mean z-score -2.28
Structure conservation index 0.83
SVM decision value 2.16
SVM RNA-class probability 0.989435
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3710740 117 + 22224390
AUCUCCUCUACAUUUCUUUAUCAGUGUCCCACCAGUGAGAAUAUGUCGUUUCAUGGGCUGACUUGGCAAUUAUAC-GCCAAGUACCCAUGUCGAUAGAAAUAAGUACAGCACACAACG
.....((.((((((((....(((.((......)).))).....(((((...((((((...(((((((........-))))))).)))))).))))))))))..))).))......... ( -32.60)
>DroSec_CAF1 2334 117 + 1
AUCUCCUCUACAUUUCUUUAUCAAUGUCCCACCAGUGAGAAUAUGUCGUUUCAUGGACUGACUUGGCAAUUAUAC-GCCAAGUACCCAUGUCGAUAGAAUUAAAUACAACACGCGACG
.((((((..(((((........)))))......)).))))....(((((..(((((....(((((((........-)))))))..)))))((....))..............))))). ( -26.80)
>DroSim_CAF1 2334 117 + 1
AUCUCCUCUACAUUUCUUUAUCAAUGUCCCACCAGUGAGAAUAUGUCGUUUCAUGGACUGACUUGGCAAUUAUAC-GCCAAGUACCCAUGUCGAUAGAAUUAAAUACAACACGCGACG
.((((((..(((((........)))))......)).))))....(((((..(((((....(((((((........-)))))))..)))))((....))..............))))). ( -26.80)
>DroEre_CAF1 2355 118 + 1
AUCUCGUCUACGUUUAUUUAUCGAUGUCCCACCAUUGAGAAUAUGUCGUUUCACGGGCUGACUUGGCAAUUAUACCACCAAGUACCCAUGUCGAUAGAAAUUUAAAAACCACCCGACG
....((((......(((((.((((((......)))))))))))(((((...((.(((...((((((...........)))))).))).)).)))))..................)))) ( -26.50)
>DroYak_CAF1 2352 118 + 1
AUCUCGUCUAUGUUUCUUUAUCGAUGUUCCACCAUUGAGAAUAUGUCGUUUCAUGGGCUGACUUGGCAAUUAUACCCCCAAGUACCCAUGUCGAUAGAAAUUUAUACAACACCCGACG
....((((..((((......((((((......))))))((((.(((((...((((((...((((((...........)))))).)))))).)))))...))))....))))...)))) ( -30.10)
>consensus
AUCUCCUCUACAUUUCUUUAUCAAUGUCCCACCAGUGAGAAUAUGUCGUUUCAUGGGCUGACUUGGCAAUUAUAC_GCCAAGUACCCAUGUCGAUAGAAAUAAAUACAACACCCGACG
.((((((..(((((........)))))......)).))))...(((((...((((((...(((((((.........))))))).)))))).)))))...................... (-23.64 = -23.36 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 4

Location 3,710,740 – 3,710,857
Length 117
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 90.48
Mean single sequence MFE -33.86
Consensus MFE -24.42
Energy contribution -24.50
Covariance contribution 0.08
Combinations/Pair 1.15
Mean z-score -1.93
Structure conservation index 0.72
SVM decision value 0.17
SVM RNA-class probability 0.617006
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3710740 117 - 22224390
CGUUGUGUGCUGUACUUAUUUCUAUCGACAUGGGUACUUGGC-GUAUAAUUGCCAAGUCAGCCCAUGAAACGACAUAUUCUCACUGGUGGGACACUGAUAAAGAAAUGUAGAGGAGAU
....((.(.((.(((..((((((((((.((((((((((((((-(......))))))))..)))))))...........(((((....)))))...))))..))))))))).)).).)) ( -37.00)
>DroSec_CAF1 2334 117 - 1
CGUCGCGUGUUGUAUUUAAUUCUAUCGACAUGGGUACUUGGC-GUAUAAUUGCCAAGUCAGUCCAUGAAACGACAUAUUCUCACUGGUGGGACAUUGAUAAAGAAAUGUAGAGGAGAU
.(((..(((((((.......((....))((((((.(((((((-(......))))))))...))))))..))))))).(((((.((....))(((((........))))).)))))))) ( -31.30)
>DroSim_CAF1 2334 117 - 1
CGUCGCGUGUUGUAUUUAAUUCUAUCGACAUGGGUACUUGGC-GUAUAAUUGCCAAGUCAGUCCAUGAAACGACAUAUUCUCACUGGUGGGACAUUGAUAAAGAAAUGUAGAGGAGAU
.(((..(((((((.......((....))((((((.(((((((-(......))))))))...))))))..))))))).(((((.((....))(((((........))))).)))))))) ( -31.30)
>DroEre_CAF1 2355 118 - 1
CGUCGGGUGGUUUUUAAAUUUCUAUCGACAUGGGUACUUGGUGGUAUAAUUGCCAAGUCAGCCCGUGAAACGACAUAUUCUCAAUGGUGGGACAUCGAUAAAUAAACGUAGACGAGAU
.(((((((((...........)))))..(((((((((((((..((...))..))))))..)))))))...))))....((((..(((((...)))))..........(....))))). ( -34.50)
>DroYak_CAF1 2352 118 - 1
CGUCGGGUGUUGUAUAAAUUUCUAUCGACAUGGGUACUUGGGGGUAUAAUUGCCAAGUCAGCCCAUGAAACGACAUAUUCUCAAUGGUGGAACAUCGAUAAAGAAACAUAGACGAGAU
((((..(((((.(((..((((((((((.(((((((((((((.(((...))).))))))..)))))))....((.......))..)))))))).))..)))....))))).)))).... ( -35.20)
>consensus
CGUCGCGUGUUGUAUUUAUUUCUAUCGACAUGGGUACUUGGC_GUAUAAUUGCCAAGUCAGCCCAUGAAACGACAUAUUCUCACUGGUGGGACAUUGAUAAAGAAAUGUAGAGGAGAU
.((((.(((((((.......((....))((((((((((((((.((...)).)))))))..)))))))..)))))))..(((((....)))))...))))................... (-24.42 = -24.50 +   0.08)

alignment

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secondary structure

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Window 5

Location 3,710,778 – 3,710,890
Length 112
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.66
Mean single sequence MFE -31.60
Consensus MFE -25.38
Energy contribution -26.22
Covariance contribution 0.84
Combinations/Pair 1.04
Mean z-score -2.12
Structure conservation index 0.80
SVM decision value 1.44
SVM RNA-class probability 0.954469
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3710778 112 + 22224390
GAAUAUGUCGUUUCAUGGGCUGACUUGGCAAUUAUAC-GCCAAGUACCCAUGUCGAUAGAAAUAAGUACAGCACACAACGCCAAAAGAUCUUUGGGUUUUAGGUGCAUUUGAC-------
.....(((((...((((((...(((((((........-))))))).)))))).)))))............((((..(((.(((((.....))))))))....)))).......------- ( -37.70)
>DroSec_CAF1 2372 112 + 1
GAAUAUGUCGUUUCAUGGACUGACUUGGCAAUUAUAC-GCCAAGUACCCAUGUCGAUAGAAUUAAAUACAACACGCGACGCCAAAAGAUCUUUGGGUUUUAGGUGCAUUUGAC-------
.....(((((...(((((....(((((((........-)))))))..))))).)))))...((((((.((...(..(((.(((((.....))))))))...).)).)))))).------- ( -30.90)
>DroSim_CAF1 2372 112 + 1
GAAUAUGUCGUUUCAUGGACUGACUUGGCAAUUAUAC-GCCAAGUACCCAUGUCGAUAGAAUUAAAUACAACACGCGACGCCAAAAGAUCUUUGGGUUUUAGGUGCAUAUGAC-------
.....(((((...(((((....(((((((........-)))))))..))))).)))))..................(.((((..((((((....)))))).))))).......------- ( -29.90)
>DroEre_CAF1 2393 120 + 1
GAAUAUGUCGUUUCACGGGCUGACUUGGCAAUUAUACCACCAAGUACCCAUGUCGAUAGAAAUUUAAAAACCACCCGACGCCAAAAGAUCUUUGGGUUUUAGGUGCAUUUGAACGUACAA
.....(((((...((.(((...((((((...........)))))).))).)).)))))....((((((...((((.(((.(((((.....))))))))...))))..))))))....... ( -28.50)
>DroYak_CAF1 2390 116 + 1
GAAUAUGUCGUUUCAUGGGCUGACUUGGCAAUUAUACCCCCAAGUACCCAUGUCGAUAGAAAUUUAUACAACACCCGACGUCAAAAGAUCUUUAGGUUUUAGGUGCUUUUGGACGU----
.....(((((...((((((...((((((...........)))))).)))))).)))))...................((((((((((((((.........)))).))))).)))))---- ( -31.00)
>consensus
GAAUAUGUCGUUUCAUGGGCUGACUUGGCAAUUAUAC_GCCAAGUACCCAUGUCGAUAGAAAUAAAUACAACACCCGACGCCAAAAGAUCUUUGGGUUUUAGGUGCAUUUGAC_______
.....(((((...((((((...(((((((.........))))))).)))))).)))))....................((((..((((((....)))))).))))............... (-25.38 = -26.22 +   0.84)

alignment

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secondary structure

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dotplot

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Window 6

Location 3,710,778 – 3,710,890
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.66
Mean single sequence MFE -33.06
Consensus MFE -22.22
Energy contribution -22.62
Covariance contribution 0.40
Combinations/Pair 1.16
Mean z-score -2.68
Structure conservation index 0.67
SVM decision value 0.51
SVM RNA-class probability 0.763062
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3710778 112 - 22224390
-------GUCAAAUGCACCUAAAACCCAAAGAUCUUUUGGCGUUGUGUGCUGUACUUAUUUCUAUCGACAUGGGUACUUGGC-GUAUAAUUGCCAAGUCAGCCCAUGAAACGACAUAUUC
-------(((....((((....(((((((((...)))))).)))..))))..................((((((((((((((-(......))))))))..)))))))....)))...... ( -37.50)
>DroSec_CAF1 2372 112 - 1
-------GUCAAAUGCACCUAAAACCCAAAGAUCUUUUGGCGUCGCGUGUUGUAUUUAAUUCUAUCGACAUGGGUACUUGGC-GUAUAAUUGCCAAGUCAGUCCAUGAAACGACAUAUUC
-------((((((((((.(....((((((((...)))))).)).....).)))))))...........((((((.(((((((-(......))))))))...))))))....)))...... ( -30.70)
>DroSim_CAF1 2372 112 - 1
-------GUCAUAUGCACCUAAAACCCAAAGAUCUUUUGGCGUCGCGUGUUGUAUUUAAUUCUAUCGACAUGGGUACUUGGC-GUAUAAUUGCCAAGUCAGUCCAUGAAACGACAUAUUC
-------(((((((((((((((((..........)))))).)).))))))..................((((((.(((((((-(......))))))))...))))))....)))...... ( -30.40)
>DroEre_CAF1 2393 120 - 1
UUGUACGUUCAAAUGCACCUAAAACCCAAAGAUCUUUUGGCGUCGGGUGGUUUUUAAAUUUCUAUCGACAUGGGUACUUGGUGGUAUAAUUGCCAAGUCAGCCCGUGAAACGACAUAUUC
.(((.((((......(((((...((((((((...)))))).)).)))))...................(((((((((((((..((...))..))))))..))))))).)))))))..... ( -35.90)
>DroYak_CAF1 2390 116 - 1
----ACGUCCAAAAGCACCUAAAACCUAAAGAUCUUUUGACGUCGGGUGUUGUAUAAAUUUCUAUCGACAUGGGUACUUGGGGGUAUAAUUGCCAAGUCAGCCCAUGAAACGACAUAUUC
----(((((.(((((...((.........))..))))))))))...(((((((.......((....))(((((((((((((.(((...))).))))))..)))))))..))))))).... ( -30.80)
>consensus
_______GUCAAAUGCACCUAAAACCCAAAGAUCUUUUGGCGUCGCGUGUUGUAUUUAUUUCUAUCGACAUGGGUACUUGGC_GUAUAAUUGCCAAGUCAGCCCAUGAAACGACAUAUUC
.......(((....((((.....((((((((...)))))).))...))))..................((((((((((((((.((...)).)))))))..)))))))....)))...... (-22.22 = -22.62 +   0.40)

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 10:04:56 2006