Locus 9555

Sequence ID 3R_DroMel_CAF1
Location 25,247,275 – 25,247,397
Length 122
Max. P 0.718089
window15280 window15281 window15282

overview

Window 0

Location 25,247,275 – 25,247,365
Length 90
Sequences 6
Columns 91
Reading direction forward
Mean pairwise identity 82.50
Mean single sequence MFE -22.05
Consensus MFE -15.63
Energy contribution -16.66
Covariance contribution 1.03
Combinations/Pair 1.08
Mean z-score -1.78
Structure conservation index 0.71
SVM decision value 0.26
SVM RNA-class probability 0.659679
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25247275 90 + 27905053
CGCAGAGCUUAUACGCAGCAUAGCAUACUUU-UUUGGGCAGCGUGUUCUCAAAAUGAAGCUGCCCUACCCGCCGCCAUCACCAUCUCCAUU
.((.(.((......((......)).......-...(((((((...(((.......)))))))))).....)))))................ ( -18.90)
>DroSec_CAF1 104536 90 + 1
CGCACAGCUUAUACGCAGCAUAGCAUACUUU-UUUGGGCAGCGCGUUCUCAAAAUGAAGCUGCCCUGCCCGCUGCCAUCUCCAUCUCCAUU
..............(((((...(((......-...(((((((.((((.....))))..))))))))))..)))))................ ( -24.20)
>DroSim_CAF1 106677 90 + 1
CGCACAGCUUAUACGCAGCAUAGCAUACUUU-UUUGGGCAGCGCGUUCUCAAAAUGAAGCUGCCCUGCCCGCUGCCAUCUCCAUCUCCAUU
..............(((((...(((......-...(((((((.((((.....))))..))))))))))..)))))................ ( -24.20)
>DroEre_CAF1 121306 84 + 1
UGCACAGCUUACACGCAGCAUAGCAUACUUU-UUUGGGCAGAGCGUUCCCAAAAUGAAGCUGCCCUGUCCGCUGCCAUCUCCAUC------
....((((..(((.((......)).......-...((((((..((((.....))))...)))))))))..))))...........------ ( -21.60)
>DroYak_CAF1 108796 83 + 1
--CACAGCUUACACGCAGCAUAGCAUACUUUUUUUGGGCAGCGCGUUCCCAAAAUUAAGCUGCCCUGCCCGCUGCCAUCUCCAUC------
--............(((((...(((..........(((((((................))))))))))..)))))..........------ ( -22.69)
>DroAna_CAF1 100478 72 + 1
---GGGGCUUAUACGCGGUGUAGCAUUCUUU-UUUGGGCAGCGCGUACACAAAAUGAAGCUGUCC----------CAUCUCCAUCG-----
---(((((...((((((.(((..((......-..)).))).))))))((.....)).....))))----------)..........----- ( -20.70)
>consensus
CGCACAGCUUAUACGCAGCAUAGCAUACUUU_UUUGGGCAGCGCGUUCUCAAAAUGAAGCUGCCCUGCCCGCUGCCAUCUCCAUCU_____
....((((......((......))...........(((((((................))))))).....))))................. (-15.63 = -16.66 +   1.03)

alignment

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secondary structure

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dotplot

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Window 1

Location 25,247,275 – 25,247,365
Length 90
Sequences 6
Columns 91
Reading direction reverse
Mean pairwise identity 82.50
Mean single sequence MFE -27.25
Consensus MFE -20.13
Energy contribution -21.36
Covariance contribution 1.22
Combinations/Pair 1.11
Mean z-score -1.67
Structure conservation index 0.74
SVM decision value 0.26
SVM RNA-class probability 0.656601
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25247275 90 - 27905053
AAUGGAGAUGGUGAUGGCGGCGGGUAGGGCAGCUUCAUUUUGAGAACACGCUGCCCAAA-AAAGUAUGCUAUGCUGCGUAUAAGCUCUGCG
...((((...(((...((((((....((((((((((.......)))...)))))))...-..((....)).)))))).)))...))))... ( -28.20)
>DroSec_CAF1 104536 90 - 1
AAUGGAGAUGGAGAUGGCAGCGGGCAGGGCAGCUUCAUUUUGAGAACGCGCUGCCCAAA-AAAGUAUGCUAUGCUGCGUAUAAGCUGUGCG
................(((((((((((.((..(((......)))...)).))))))...-...((((((......))))))..)))))... ( -32.10)
>DroSim_CAF1 106677 90 - 1
AAUGGAGAUGGAGAUGGCAGCGGGCAGGGCAGCUUCAUUUUGAGAACGCGCUGCCCAAA-AAAGUAUGCUAUGCUGCGUAUAAGCUGUGCG
................(((((((((((.((..(((......)))...)).))))))...-...((((((......))))))..)))))... ( -32.10)
>DroEre_CAF1 121306 84 - 1
------GAUGGAGAUGGCAGCGGACAGGGCAGCUUCAUUUUGGGAACGCUCUGCCCAAA-AAAGUAUGCUAUGCUGCGUGUAAGCUGUGCA
------..........(((((..(((.(.((((....(((((((.........))))))-).((....))..))))).)))..)))))... ( -25.90)
>DroYak_CAF1 108796 83 - 1
------GAUGGAGAUGGCAGCGGGCAGGGCAGCUUAAUUUUGGGAACGCGCUGCCCAAAAAAAGUAUGCUAUGCUGCGUGUAAGCUGUG--
------..........(((((((((((.((..((((....))))...)).))))))........(((((......)))))...))))).-- ( -30.50)
>DroAna_CAF1 100478 72 - 1
-----CGAUGGAGAUG----------GGACAGCUUCAUUUUGUGUACGCGCUGCCCAAA-AAAGAAUGCUACACCGCGUAUAAGCCCC---
-----.(((((((.((----------...)).)))))))...((((((((.((..((..-......))...)).))))))))......--- ( -14.70)
>consensus
_____AGAUGGAGAUGGCAGCGGGCAGGGCAGCUUCAUUUUGAGAACGCGCUGCCCAAA_AAAGUAUGCUAUGCUGCGUAUAAGCUGUGCG
................(((((.....(((((((................))))))).......((((((......))))))..)))))... (-20.13 = -21.36 +   1.22)

alignment

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secondary structure

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dotplot

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Window 2

Location 25,247,296 – 25,247,397
Length 101
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 79.13
Mean single sequence MFE -26.57
Consensus MFE -17.74
Energy contribution -18.77
Covariance contribution 1.03
Combinations/Pair 1.28
Mean z-score -1.47
Structure conservation index 0.67
SVM decision value 0.39
SVM RNA-class probability 0.718089
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25247296 101 + 27905053
AGCAUACUUU-UUUGGGCAGCGUGUUCUCAAAAUGAAGCUGCCCUACCCGCCGCCAUCACCAUCUCCAUUCUCCAAUCUCAUUCUCCGGCGAGGUAGAGCUG
(((.......-...(((((((...(((.......))))))))))(((((((((.................................))))).))))..))). ( -28.61)
>DroSec_CAF1 104557 101 + 1
AGCAUACUUU-UUUGGGCAGCGCGUUCUCAAAAUGAAGCUGCCCUGCCCGCUGCCAUCUCCAUCUCCAUUCUCCAAUCUCAUUCUCCAGCGAGGUGGAGCUG
.(((......-...(((((((.((((.....))))..))))))).......)))((.((((((((((.....................).))))))))).)) ( -28.99)
>DroSim_CAF1 106698 101 + 1
AGCAUACUUU-UUUGGGCAGCGCGUUCUCAAAAUGAAGCUGCCCUGCCCGCUGCCAUCUCCAUCUCCAUUCUCCAAUCUCGUUCUCCGGCGAGGUGGAGCUG
(((.......-...((((((.(((((.((.....))))).)).))))))......................((((.((((((......))))))))))))). ( -31.10)
>DroEre_CAF1 121327 87 + 1
AGCAUACUUU-UUUGGGCAGAGCGUUCCCAAAAUGAAGCUGCCCUGUCCGCUGCCAUCUCCAUC--------------UGAUUCUCCAGCGAGGUGAGGCUG
..........-...((((((..((((.....))))...)))))).....(((..((((((...(--------------((......))).)))))).))).. ( -26.30)
>DroYak_CAF1 108815 88 + 1
AGCAUACUUUUUUUGGGCAGCGCGUUCCCAAAAUUAAGCUGCCCUGCCCGCUGCCAUCUCCAUC--------------UGAUUCUCCACCGAGGUGAAGCUG
..............((((((.(((((..........))).)).))))))(((..((((((....--------------((......))..)))))).))).. ( -23.80)
>DroAna_CAF1 100496 83 + 1
AGCAUUCUUU-UUUGGGCAGCGCGUACACAAAAUGAAGCUGUCC----------CAUCUCCAUCG--------CGAUCUCCGUAUCCAACGACGUGGAGCUA
.((.......-..((((((((.(((.......)))..)))).))----------))........)--------)...(((((..((....))..)))))... ( -20.63)
>consensus
AGCAUACUUU_UUUGGGCAGCGCGUUCUCAAAAUGAAGCUGCCCUGCCCGCUGCCAUCUCCAUCU________CAAUCUCAUUCUCCAGCGAGGUGGAGCUG
(((...........(((((((................))))))).((((((((.................................))))).)))...))). (-17.74 = -18.77 +   1.03)

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 13:37:04 2006