Locus 791

Sequence ID 2L_DroMel_CAF1
Location 2,262,971 – 2,263,107
Length 136
Max. P 0.996848
window1293 window1294 window1295

overview

Window 3

Location 2,262,971 – 2,263,074
Length 103
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 84.88
Mean single sequence MFE -37.32
Consensus MFE -25.64
Energy contribution -25.32
Covariance contribution -0.32
Combinations/Pair 1.17
Mean z-score -2.15
Structure conservation index 0.69
SVM decision value 0.64
SVM RNA-class probability 0.809459
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2262971 103 + 22407834
----CGGGCGAUUGAUAAGGGGCCUCCAUGUCGGCCAA--CUCGCAUUAUCCAGCUCGAUUCAGUCGGCAAUUAAUGCCACUCCAAUUGCCCGAUUUGCCUGCACCUAC----------
----((((((((((......((((........))))..--...((((((....((.((((...))))))...)))))).....))))))))))................---------- ( -34.70)
>DroSec_CAF1 23518 113 + 1
----CGGGCGUUUGAUAAGCGGCCUCCAUGUCGGCCAA--CUCGCAUUAUCCAGGCCGAUUCAGUCGGCAAUUAAUGCCACUCCAAUUGCCCGAUUUGCCUGCACCUCCGAAGGGGGUA
----((((((.(((......((((........))))..--...((((((.....((((((...))))))...)))))).....))).))))))..........(((.((....))))). ( -42.50)
>DroSim_CAF1 24658 113 + 1
----CGGGCGUUUGAUAAGCGGCCUCCAUGUCGGCCAA--CUCGCAUUAUCCAGCCCGAUUCAGUCGGCAAUUAAUGCCACUCCAAUUGCCCGAUUUGCCUGCACCUCCGAAUGGGGUA
----(((((....(((((((((((........))))..--...)).)))))..)))))....(((.((((.....))))))).....(((((.(((((..........))))).))))) ( -36.50)
>DroEre_CAF1 25228 99 + 1
----CGGGCGUUUGAUAAGCGGCCUCCAUGUUGGCCAA--CUCCCAUUAUCCAGCCCGUUUCAGCCGGCAAUUAAUGGCACUCCAAUUGCCCGAUUUGCCUGUAC--------------
----((((((.(((......((((........))))..--...((((((....(((.((....)).)))...)))))).....))).))))))............-------------- ( -31.90)
>DroYak_CAF1 31542 119 + 1
GUUGCGGGCGUUUGAUAAGCGCCCUCCAUGUGGGCCAACACUCACAUUAUCCAGCCCGAUUCAGGCGGCAAUUAAUGCCACUCCAAUUGCUUGAUUUGCCUGUACCUCGGAAUGAGGUA
.....(((((((.....)))))))...(((((((......)))))))((((((..((((..(((((((((.....))))....(((....)))....)))))....))))..)).)))) ( -41.00)
>consensus
____CGGGCGUUUGAUAAGCGGCCUCCAUGUCGGCCAA__CUCGCAUUAUCCAGCCCGAUUCAGUCGGCAAUUAAUGCCACUCCAAUUGCCCGAUUUGCCUGCACCUCCGAA_G_GGUA
....((((((.(((......((((........)))).......((((((....(.(((.......))))...)))))).....))).)))))).......................... (-25.64 = -25.32 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 4

Location 2,263,005 – 2,263,107
Length 102
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 80.85
Mean single sequence MFE -35.87
Consensus MFE -21.37
Energy contribution -23.72
Covariance contribution 2.35
Combinations/Pair 1.15
Mean z-score -3.26
Structure conservation index 0.60
SVM decision value 2.64
SVM RNA-class probability 0.995961
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2263005 102 + 22407834
CUCGCAUUAUCCAGCUCGAUUCAGUCGGCAAUUAAUGCCACUCCAAUUGCCCGAUUUGCCUGCACCUAC------------AUAUCCAGCCAUAUGGCUGGAUUGCGAAAGAAU
.(((((.......((..(....(((((((((((...........))))).))))))..)..))......------------..((((((((....)))))))))))))...... ( -30.60)
>DroSec_CAF1 23552 111 + 1
CUCGCAUUAUCCAGGCCGAUUCAGUCGGCAAUUAAUGCCACUCCAAUUGCCCGAUUUGCCUGCACCUCCGAAGGGGGUAGCAUAU--GGC-AAAUGGCUGGAUUGCGAAAGAAU
.(((((..((((((((((((...)))))).....................((.(((((((((((((.((....))))).)))...--)))-)))))))))))))))))...... ( -44.10)
>DroSim_CAF1 24692 112 + 1
CUCGCAUUAUCCAGCCCGAUUCAGUCGGCAAUUAAUGCCACUCCAAUUGCCCGAUUUGCCUGCACCUCCGAAUGGGGUAGCAUAU--GGCCAAAUGGCUGGAUUGCGAAAGAAU
.(((((..(((((((((((((.(((.((((.....)))))))..)))))....(((((((((((((((.....))))).)))...--)).))))))))))))))))))...... ( -41.20)
>DroEre_CAF1 25262 89 + 1
CUCCCAUUAUCCAGCCCGUUUCAGCCGGCAAUUAAUGGCACUCCAAUUGCCCGAUUUGCCUGUAC---------------C----------AUAUGGCUGGACUGCGAAAGAAU
.........(((((((.......((.(((((.....((((.......))))....))))).))..---------------.----------....)))))))...(....)... ( -26.24)
>DroYak_CAF1 31582 104 + 1
CUCACAUUAUCCAGCCCGAUUCAGGCGGCAAUUAAUGCCACUCCAAUUGCUUGAUUUGCCUGUACCUCGGAAUGAGGUAGC----------AUAUGGCUGGAUGGCGAAAGAAU
......((((((((((.....(((((((((.....))))....(((....)))....)))))((((((.....))))))..----------....))))))))))(....)... ( -37.20)
>consensus
CUCGCAUUAUCCAGCCCGAUUCAGUCGGCAAUUAAUGCCACUCCAAUUGCCCGAUUUGCCUGCACCUCCGAA_G_GGUAGCAUAU___GC_AUAUGGCUGGAUUGCGAAAGAAU
.(((((..((((((((.......((.(((((.....((..........)).....))))).))(((((.....))))).................)))))))))))))...... (-21.37 = -23.72 +   2.35)

alignment

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secondary structure

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dotplot

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Window 5

Location 2,263,005 – 2,263,107
Length 102
Sequences 5
Columns 114
Reading direction reverse
Mean pairwise identity 80.85
Mean single sequence MFE -39.58
Consensus MFE -23.70
Energy contribution -24.62
Covariance contribution 0.92
Combinations/Pair 1.08
Mean z-score -3.35
Structure conservation index 0.60
SVM decision value 2.76
SVM RNA-class probability 0.996848
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2263005 102 - 22407834
AUUCUUUCGCAAUCCAGCCAUAUGGCUGGAUAU------------GUAGGUGCAGGCAAAUCGGGCAAUUGGAGUGGCAUUAAUUGCCGACUGAAUCGAGCUGGAUAAUGCGAG
......(((((((((((((.....(((.(((.(------------((........))).))).)))......(((((((.....)))).))).....).)))))))..))))). ( -35.40)
>DroSec_CAF1 23552 111 - 1
AUUCUUUCGCAAUCCAGCCAUUU-GCC--AUAUGCUACCCCCUUCGGAGGUGCAGGCAAAUCGGGCAAUUGGAGUGGCAUUAAUUGCCGACUGAAUCGGCCUGGAUAAUGCGAG
......(((((((((((((((((-(((--...(((.(((((....)).)))))))))))))..(((((((((.......))))))))).........)).))))))..))))). ( -42.40)
>DroSim_CAF1 24692 112 - 1
AUUCUUUCGCAAUCCAGCCAUUUGGCC--AUAUGCUACCCCAUUCGGAGGUGCAGGCAAAUCGGGCAAUUGGAGUGGCAUUAAUUGCCGACUGAAUCGGGCUGGAUAAUGCGAG
......(((((((((((((.....(((--...(((.(((((....)).)))))))))......(((((((((.......)))))))))..........))))))))..))))). ( -43.30)
>DroEre_CAF1 25262 89 - 1
AUUCUUUCGCAGUCCAGCCAUAU----------G---------------GUACAGGCAAAUCGGGCAAUUGGAGUGCCAUUAAUUGCCGGCUGAAACGGGCUGGAUAAUGGGAG
...((..((..((((((((....----------(---------------((...(((((....((((.......)))).....))))).)))......))))))))..))..)) ( -33.30)
>DroYak_CAF1 31582 104 - 1
AUUCUUUCGCCAUCCAGCCAUAU----------GCUACCUCAUUCCGAGGUACAGGCAAAUCAAGCAAUUGGAGUGGCAUUAAUUGCCGCCUGAAUCGGGCUGGAUAAUGUGAG
......((((.((((((((....----------..((((((.....))))))(((((...((((....))))...((((.....))))))))).....))))))))...)))). ( -43.50)
>consensus
AUUCUUUCGCAAUCCAGCCAUAU_GC___AUAUGCUACC_C_UUCGGAGGUGCAGGCAAAUCGGGCAAUUGGAGUGGCAUUAAUUGCCGACUGAAUCGGGCUGGAUAAUGCGAG
......(((((((((((((.............................(((........))).(((((((((.......)))))))))..........))))))))..))))). (-23.70 = -24.62 +   0.92)

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 09:45:44 2006