Locus 589

Sequence ID 2L_DroMel_CAF1
Location 1,797,109 – 1,797,393
Length 284
Max. P 0.980466
window970 window971 window972 window973

overview

Window 0

Location 1,797,109 – 1,797,209
Length 100
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 74.39
Mean single sequence MFE -23.92
Consensus MFE -14.53
Energy contribution -14.66
Covariance contribution 0.13
Combinations/Pair 1.19
Mean z-score -2.19
Structure conservation index 0.61
SVM decision value 1.86
SVM RNA-class probability 0.980466
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1797109 100 + 22407834
CCCAUUUCCCAUGCUUUCUUUGGAGCGCCACAAAGUAUGCAACACAUGCAGCUGA---------AGCUUCCGCAGAAAGUUUUCUUUUCCCAUUCCCCUUUUCCCUUA-----------C
............(((((((.(((((.((.....(((.((((.....)))))))..---------.))))))).)))))))............................-----------. ( -19.20)
>DroSec_CAF1 4402 100 + 1
CCUAUUUCUCAUGCUUUCUUUGGAGCGCCACAAAGUAUGCAACACAUGCAGCUGA---------AGCUUCAGCAGAAAGUUUUCUUUUCCCAUUCCCCUUUUCCCUUU-----------C
............((((((((((((((.......(((.((((.....)))))))..---------.))))))).)))))))............................-----------. ( -19.90)
>DroPer_CAF1 11137 114 + 1
GCCAUUUUUCAUGCUUUCUUUCGACCGCCGCAAAGCAUGCAACACAUGCAGCUGAGAGCUGGGAAAGUUGAGCGAAAAGUUUGC------CACUCCUCCAUCUCUGAGGGGGGAGAAACC
((.(((((((..((((.(((((..(((((....(((.((((.....)))))))..).)).)))))))..)))))))))))..))------..(((((((.((...)).)))))))..... ( -35.10)
>DroEre_CAF1 6795 99 + 1
CCCAUUUUUCAUGCUUUCUUUGGAGCCCCACAAAGUAUGCAACACAUGCAGCUGA---------AGCU-CCGCAGAAAGUUUUCUUAUCCCGUUCCCCUUUUCCUUUG-----------C
............(((((((.((((((..((....(((((.....)))))...)).---------.)))-))).)))))))............................-----------. ( -21.50)
>consensus
CCCAUUUCUCAUGCUUUCUUUGGAGCGCCACAAAGUAUGCAACACAUGCAGCUGA_________AGCUUCAGCAGAAAGUUUUCUUUUCCCAUUCCCCUUUUCCCUUG___________C
............((((((((((((((.......(((.((((.....)))))))............))))))).)))))))........................................ (-14.53 = -14.66 +   0.13)

alignment

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secondary structure

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Window 1

Location 1,797,209 – 1,797,314
Length 105
Sequences 3
Columns 106
Reading direction forward
Mean pairwise identity 94.95
Mean single sequence MFE -12.90
Consensus MFE -11.50
Energy contribution -11.50
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.92
Structure conservation index 0.89
SVM decision value 0.25
SVM RNA-class probability 0.654035
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1797209 105 + 22407834
UCGCGUUAUAAUAAGUUACGCUUAGCAUUUUCUGUUUU-CCUUUCCGCAAAGUGCAUUUUUCACCUUUUAUCAUUAUUUCUUGGCUCAUUUUCCGAGCUUUUUCCC
..((((.((.....)).))))...(((((((.((....-......)).)))))))...........................(((((.......)))))....... ( -14.80)
>DroSec_CAF1 4502 103 + 1
UCGCUUUAUAAUAAGUUACGCUUAGCAUUUUCUGUUUU-CCU-UCCGCAAAGUGCAUUUUUCACCUUUUAUCAUUAUUUCUU-GCUCAUUUUCCGAGCUUUUUUCC
...........((((.....))))(((((((.((....-...-..)).)))))))...........................-((((.......))))........ ( -11.70)
>DroEre_CAF1 6894 104 + 1
UC-CUUCAUAAUAAGUUACGCUUAGCAUUUUCUGUUUUUCCUUUCCGCAAAGUGCAUUUUUCACCUUUUAUCAUUAUUUCUUGGCUCAUUUUCCGAGCUU-UUCCC
..-........((((.....))))(((((((.((...........)).)))))))...........................(((((.......))))).-..... ( -12.20)
>consensus
UCGCUUUAUAAUAAGUUACGCUUAGCAUUUUCUGUUUU_CCUUUCCGCAAAGUGCAUUUUUCACCUUUUAUCAUUAUUUCUUGGCUCAUUUUCCGAGCUUUUUCCC
...........((((.....))))(((((((.((...........)).)))))))............................((((.......))))........ (-11.50 = -11.50 +   0.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 1,797,248 – 1,797,353
Length 105
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 78.81
Mean single sequence MFE -23.80
Consensus MFE -15.24
Energy contribution -16.55
Covariance contribution 1.31
Combinations/Pair 1.12
Mean z-score -2.40
Structure conservation index 0.64
SVM decision value 1.81
SVM RNA-class probability 0.978446
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1797248 105 + 22407834
CU--------------UUCCGCAAAGUGCAUUUUUCACCUUUUAUCAUUAUUUCUUGGCUCAUUUUCCGAGCUUUUUCCCUACCGAAGUUUCCCGACUUCGU-UCAAGGGGAUGAUGAUU
..--------------....((.....))............((((((((.......(((((.......)))))....((((..(((((((....))))))).-...)))))))))))).. ( -25.80)
>DroSec_CAF1 4541 103 + 1
CU---------------UCCGCAAAGUGCAUUUUUCACCUUUUAUCAUUAUUUCUU-GCUCAUUUUCCGAGCUUUUUUCCUACCGAAGUUUCCCGACUUCGU-UCAAGGGGAUGAUGAUU
..---------------...((.....))..............((((((((..(((-((((.......))))...........(((((((....))))))).-...)))..)))))))). ( -25.00)
>DroPer_CAF1 11289 119 + 1
CUGCCCCUGCCCCCCUCCCUUCUGAGUGCAUUUUUUACCUUUUAUCAUUAUUUGUUCGCACAUUUUCCUUGCUUU-UUCCAAAUGAAGCUUUCCAUCGAGAUGACGCGGGGAUGAUGAUU
....((((((....(((........((((............................)))).........(((((-........)))))........))).....))))))......... ( -20.59)
>DroEre_CAF1 6933 103 + 1
CU--------------UUCCGCAAAGUGCAUUUUUCACCUUUUAUCAUUAUUUCUUGGCUCAUUUUCCGAGCUU-UUCCCUACCGA-GUUUCCCGACUCCGU-UCGAGGGGAUGAUGAUU
..--------------....((.....))............((((((((.......(((((.......))))).-..((((((.((-(((....))))).))-...)))))))))))).. ( -23.80)
>consensus
CU______________UUCCGCAAAGUGCAUUUUUCACCUUUUAUCAUUAUUUCUUGGCUCAUUUUCCGAGCUUUUUCCCUACCGAAGUUUCCCGACUUCGU_UCAAGGGGAUGAUGAUU
...........................................(((((((((((((.((((.......))))...........(((((((....))))))).....))))))))))))). (-15.24 = -16.55 +   1.31)

alignment

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secondary structure

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dotplot

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Window 3

Location 1,797,274 – 1,797,393
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 87.87
Mean single sequence MFE -28.12
Consensus MFE -19.64
Energy contribution -20.95
Covariance contribution 1.31
Combinations/Pair 1.10
Mean z-score -1.46
Structure conservation index 0.70
SVM decision value -0.05
SVM RNA-class probability 0.506745
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1797274 119 + 22407834
UUUAUCAUUAUUUCUUGGCUCAUUUUCCGAGCUUUUUCCCUACCGAAGUUUCCCGACUUCGU-UCAAGGGGAUGAUGAUUGCUUUGGUCUAUGCAAAGUGUCUCAAUUUGGGUUCAUGUA
.((((((((.......(((((.......)))))....((((..(((((((....))))))).-...))))))))))))((((..........)))).(((.(((.....)))..)))... ( -29.30)
>DroSec_CAF1 4566 118 + 1
UUUAUCAUUAUUUCUU-GCUCAUUUUCCGAGCUUUUUUCCUACCGAAGUUUCCCGACUUCGU-UCAAGGGGAUGAUGAUUGCUUUGGUCUAUGCAAAGUGUCUCAAUUUGGGUUCACGUA
....(((((((..(((-((((.......))))...........(((((((....))))))).-...)))..)))))))((((..........)))).(((.(((.....)))..)))... ( -30.20)
>DroPer_CAF1 11329 119 + 1
UUUAUCAUUAUUUGUUCGCACAUUUUCCUUGCUUU-UUCCAAAUGAAGCUUUCCAUCGAGAUGACGCGGGGAUGAUGAUUGCUUUGGUCUAUGCAAAGUGACUCAAUUUGGGUUCAUGUA
...((((((((((..((((.((((((....(((((-........)))))........))))))..)))))))))))))).((((((.......))))))(((((.....)))))...... ( -25.10)
>DroEre_CAF1 6959 117 + 1
UUUAUCAUUAUUUCUUGGCUCAUUUUCCGAGCUU-UUCCCUACCGA-GUUUCCCGACUCCGU-UCGAGGGGAUGAUGAUUGCUUUGGUCUAUGCAAAGUGUCUCAAUUUGGCUUCAUGUA
.((((((((.......(((((.......))))).-..((((((.((-(((....))))).))-...))))))))))))..((((((.......))))))(((.......)))........ ( -27.90)
>consensus
UUUAUCAUUAUUUCUUGGCUCAUUUUCCGAGCUUUUUCCCUACCGAAGUUUCCCGACUUCGU_UCAAGGGGAUGAUGAUUGCUUUGGUCUAUGCAAAGUGUCUCAAUUUGGGUUCAUGUA
...(((((((((((((.((((.......))))...........(((((((....))))))).....))))))))))))).((((((.......))))))..................... (-19.64 = -20.95 +   1.31)

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 09:40:28 2006