Locus 10056

Sequence ID 3R_DroMel_CAF1
Location 26,948,417 – 26,948,617
Length 200
Max. P 0.989775
window16015 window16016 window16017 window16018 window16019

overview

Window 5

Location 26,948,417 – 26,948,537
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 86.67
Mean single sequence MFE -40.97
Consensus MFE -30.02
Energy contribution -29.38
Covariance contribution -0.64
Combinations/Pair 1.24
Mean z-score -2.10
Structure conservation index 0.73
SVM decision value 0.75
SVM RNA-class probability 0.839661
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26948417 120 + 27905053
AUAUGAAAGACGGUGGUGUUACCGUAACGCUGUACGAAAGCAAUUUCCAGUUUUUCGGGGGUCAAGCUAUCUCUGCCCAAGGUCAUGCCCAUGACCUUGAUGGCUACAUCCUUGGCCUCC
....(((((((.(..((((((...))))))..)..((((....))))..)))))))((((((((((........((((((((((((....)))))))))..)))......)))))))))) ( -47.54)
>DroSec_CAF1 16083 120 + 1
AUAUGAAAGACAGUGGUGUCACAGAAACGCUGUAUGGAAGCAAUUUCCAGGUUUGCGGGGGUCAAGCUACCUCUGUCCAAGGUCAUGCCCAUGACCUUGAUGGCUACGUCCUUGGCUUCC
.........((((((...((...))..))))))..((((((........((...((((((((......))))))))))((((((((....))))))))((((....))))....)))))) ( -39.80)
>DroSim_CAF1 16138 120 + 1
AUAUGAAAGACAGUGGUGCCACAGAAACGCUGUAUGGAAGCAAUUUCCAGGUUUGCGGGGGUCAAGCUACCUCUGUCCAAGGUCAUGCCCAUGACCUUGAUGGCUACGUCCUUGGCUUCC
.........((((((............))))))..((((((........((...((((((((......))))))))))((((((((....))))))))((((....))))....)))))) ( -39.60)
>DroEre_CAF1 18758 120 + 1
AUAUGAAAUAUGGUGGUGUUAUAGAAGCGCUGUAGUACAGCCAUUUCCAGCUUCGCAGGGGUCAAGCUAUCUCUAUCCAAGGUCAUGCCCAUGACCUUGAUGGCUACAUCCUUGGCUUCC
...........((.(((......(((((((((.....))))........))))).(((((((..(((((((.......((((((((....)))))))))))))))..)))))))))).)) ( -38.51)
>DroYak_CAF1 16583 120 + 1
GUUUGAAAGACGCUGGUGUUAUAGAAGCGCUGUACUAGAGCCAUUUCCAGCUUGGCAGGAUUCAAGCUAUCUGUACCCAAGGUCAUGCCCAUGACCUUGAUGGCCACAUCCUUGGCCUCC
(((((((...((((...........))))((((....((((........)))).))))..)))))))..........(((((((((....)))))))))..(((((......)))))... ( -39.40)
>consensus
AUAUGAAAGACGGUGGUGUUACAGAAACGCUGUACGAAAGCAAUUUCCAGCUUUGCGGGGGUCAAGCUAUCUCUGUCCAAGGUCAUGCCCAUGACCUUGAUGGCUACAUCCUUGGCUUCC
........(((((.(((...((((.....)))).....(((...((((.(.....).))))....)))))).)))))(((((((((....)))))))))..(((((......)))))... (-30.02 = -29.38 +  -0.64)

alignment

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secondary structure

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Window 6

Location 26,948,457 – 26,948,577
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.58
Mean single sequence MFE -42.67
Consensus MFE -33.07
Energy contribution -34.35
Covariance contribution 1.28
Combinations/Pair 1.09
Mean z-score -2.89
Structure conservation index 0.77
SVM decision value 2.18
SVM RNA-class probability 0.989775
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26948457 120 + 27905053
CAAUUUCCAGUUUUUCGGGGGUCAAGCUAUCUCUGCCCAAGGUCAUGCCCAUGACCUUGAUGGCUACAUCCUUGGCCUCCUCGACCGAAGGACUUACGUAGCCCUUGCUAAAUAGUUCCU
................((((((((((........((((((((((((....)))))))))..)))......))))))))))........((((.(((..((((....))))..))).)))) ( -41.84)
>DroSec_CAF1 16123 120 + 1
CAAUUUCCAGGUUUGCGGGGGUCAAGCUACCUCUGUCCAAGGUCAUGCCCAUGACCUUGAUGGCUACGUCCUUGGCUUCCUCGAGCGAAGGACAUACGUAACCCUUGCUGAAUAGUUCAU
..........((((((((((((..(((((........(((((((((....))))))))).)))))..((((((.((((....)))).)))))).......)))))))).))))....... ( -43.30)
>DroSim_CAF1 16178 120 + 1
CAAUUUCCAGGUUUGCGGGGGUCAAGCUACCUCUGUCCAAGGUCAUGCCCAUGACCUUGAUGGCUACGUCCUUGGCUUCCUCGAGCGAAGGACAUACGUAACCCUUGCUGAAUAGUUCAU
..........((((((((((((..(((((........(((((((((....))))))))).)))))..((((((.((((....)))).)))))).......)))))))).))))....... ( -43.30)
>DroEre_CAF1 18798 120 + 1
CCAUUUCCAGCUUCGCAGGGGUCAAGCUAUCUCUAUCCAAGGUCAUGCCCAUGACCUUGAUGGCUACAUCCUUGGCUUCCUCGAGCGAGGGACUUGCGUAGCCCUUGCUGAAUAGUUCCU
.........(((.((.((((((((((......(((((.((((((((....))))))))))))).......)))))).))))))))).(((((((....((((....))))...))))))) ( -44.42)
>DroYak_CAF1 16623 120 + 1
CCAUUUCCAGCUUGGCAGGAUUCAAGCUAUCUGUACCCAAGGUCAUGCCCAUGACCUUGAUGGCCACAUCCUUGGCCUCCUCGAGCGAGGGACACACGUAGCCCUUGGUGAAGAGUUCCU
........(((((((......))))))).(((.(((((((((((((....)))))))))..(((((......)))))(((((....)))))...............)))).)))...... ( -40.50)
>consensus
CAAUUUCCAGCUUUGCGGGGGUCAAGCUAUCUCUGUCCAAGGUCAUGCCCAUGACCUUGAUGGCUACAUCCUUGGCUUCCUCGAGCGAAGGACAUACGUAGCCCUUGCUGAAUAGUUCCU
..............((((((((..((((((.......(((((((((....)))))))))))))))...(((((.((((....)))).)))))........))))))))............ (-33.07 = -34.35 +   1.28)

alignment

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secondary structure

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Window 7

Location 26,948,457 – 26,948,577
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.58
Mean single sequence MFE -42.06
Consensus MFE -34.06
Energy contribution -33.82
Covariance contribution -0.24
Combinations/Pair 1.15
Mean z-score -1.95
Structure conservation index 0.81
SVM decision value 1.23
SVM RNA-class probability 0.933572
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26948457 120 - 27905053
AGGAACUAUUUAGCAAGGGCUACGUAAGUCCUUCGGUCGAGGAGGCCAAGGAUGUAGCCAUCAAGGUCAUGGGCAUGACCUUGGGCAGAGAUAGCUUGACCCCCGAAAAACUGGAAAUUG
.....((((((.((...((((((....((((((.((((.....)))))))))))))))).((((((((((....))))))))))))..))))))........(((......)))...... ( -42.70)
>DroSec_CAF1 16123 120 - 1
AUGAACUAUUCAGCAAGGGUUACGUAUGUCCUUCGCUCGAGGAAGCCAAGGACGUAGCCAUCAAGGUCAUGGGCAUGACCUUGGACAGAGGUAGCUUGACCCCCGCAAACCUGGAAAUUG
............((..((((((.((((((((((.(((......))).)))))))).(((.((((((((((....)))))))))).....))).)).))))))..)).............. ( -40.40)
>DroSim_CAF1 16178 120 - 1
AUGAACUAUUCAGCAAGGGUUACGUAUGUCCUUCGCUCGAGGAAGCCAAGGACGUAGCCAUCAAGGUCAUGGGCAUGACCUUGGACAGAGGUAGCUUGACCCCCGCAAACCUGGAAAUUG
............((..((((((.((((((((((.(((......))).)))))))).(((.((((((((((....)))))))))).....))).)).))))))..)).............. ( -40.40)
>DroEre_CAF1 18798 120 - 1
AGGAACUAUUCAGCAAGGGCUACGCAAGUCCCUCGCUCGAGGAAGCCAAGGAUGUAGCCAUCAAGGUCAUGGGCAUGACCUUGGAUAGAGAUAGCUUGACCCCUGCGAAGCUGGAAAUGG
........((((((..(((..((....)))))((((..(.((((((...((......)).((((((((((....)))))))))).........))))..)))..)))).))))))..... ( -40.10)
>DroYak_CAF1 16623 120 - 1
AGGAACUCUUCACCAAGGGCUACGUGUGUCCCUCGCUCGAGGAGGCCAAGGAUGUGGCCAUCAAGGUCAUGGGCAUGACCUUGGGUACAGAUAGCUUGAAUCCUGCCAAGCUGGAAAUGG
......(((..(((...((((((((.((((((((....)))).)))...).))))))))..(((((((((....))))))))))))..)))(((((((........)))))))....... ( -46.70)
>consensus
AGGAACUAUUCAGCAAGGGCUACGUAUGUCCUUCGCUCGAGGAAGCCAAGGAUGUAGCCAUCAAGGUCAUGGGCAUGACCUUGGACAGAGAUAGCUUGACCCCCGCAAACCUGGAAAUUG
........(((((((((((((((....((((((.(((......))).)))))))))))).((((((((((....))))))))))..........))))............)))))..... (-34.06 = -33.82 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 8

Location 26,948,497 – 26,948,617
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.92
Mean single sequence MFE -41.54
Consensus MFE -33.34
Energy contribution -34.86
Covariance contribution 1.52
Combinations/Pair 1.06
Mean z-score -2.09
Structure conservation index 0.80
SVM decision value 1.45
SVM RNA-class probability 0.955127
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26948497 120 + 27905053
GGUCAUGCCCAUGACCUUGAUGGCUACAUCCUUGGCCUCCUCGACCGAAGGACUUACGUAGCCCUUGCUAAAUAGUUCCUUCUGAAGCAUUUCCAUGGCUGCCCCUGACUUGCGGCCAAU
((((((....))))))..((((....)))).((((((.........((((((.(((..((((....))))..))).))))))....(((..((...((.....)).))..))))))))). ( -39.50)
>DroSec_CAF1 16163 120 + 1
GGUCAUGCCCAUGACCUUGAUGGCUACGUCCUUGGCUUCCUCGAGCGAAGGACAUACGUAACCCUUGCUGAAUAGUUCAUUCUGAAGCAUUUCCAUGGCUGCCCCUGACUUGCGGCCAAU
((((((....))))))...((((....((((((.((((....)))).))))))............((((...(((......))).))))...))))((((((.........))))))... ( -39.90)
>DroSim_CAF1 16218 120 + 1
GGUCAUGCCCAUGACCUUGAUGGCUACGUCCUUGGCUUCCUCGAGCGAAGGACAUACGUAACCCUUGCUGAAUAGUUCAUUCUGAAGCAUUUCCAAGGCUGCCCCUGACUUGCGGCCAAU
((((((....))))))....(((....((((((.((((....)))).))))))............((((...(((......))).))))...))).((((((.........))))))... ( -39.00)
>DroEre_CAF1 18838 120 + 1
GGUCAUGCCCAUGACCUUGAUGGCUACAUCCUUGGCUUCCUCGAGCGAGGGACUUGCGUAGCCCUUGCUGAAUAGUUCCUUCUGAAGCAUUUCCAUGGCCGCCCCUGAUUUGCGGCCAAU
((((((....))))))..((((....))))....(((((.((.((((((((.((.....))))))))))))..((......))))))).......(((((((.........))))))).. ( -44.20)
>DroYak_CAF1 16663 120 + 1
GGUCAUGCCCAUGACCUUGAUGGCCACAUCCUUGGCCUCCUCGAGCGAGGGACACACGUAGCCCUUGGUGAAGAGUUCCUUCUGGAGCAGUUCCAUGGCCGCCCCUGAAUGGCGACCAAU
((((..(.(((((..(((((.(((((......)))))...)))))((((((.(.......)))))))..(((..(((((....)))))..)))))))).)(((.......)))))))... ( -45.10)
>consensus
GGUCAUGCCCAUGACCUUGAUGGCUACAUCCUUGGCUUCCUCGAGCGAAGGACAUACGUAGCCCUUGCUGAAUAGUUCCUUCUGAAGCAUUUCCAUGGCUGCCCCUGACUUGCGGCCAAU
((((((....)))))).....((((((.(((((.((((....)))).))))).....))))))..((((...(((......))).))))......(((((((.........))))))).. (-33.34 = -34.86 +   1.52)

alignment

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secondary structure

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dotplot

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Window 9

Location 26,948,497 – 26,948,617
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.92
Mean single sequence MFE -42.46
Consensus MFE -34.00
Energy contribution -33.60
Covariance contribution -0.40
Combinations/Pair 1.21
Mean z-score -1.54
Structure conservation index 0.80
SVM decision value 0.34
SVM RNA-class probability 0.695707
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26948497 120 - 27905053
AUUGGCCGCAAGUCAGGGGCAGCCAUGGAAAUGCUUCAGAAGGAACUAUUUAGCAAGGGCUACGUAAGUCCUUCGGUCGAGGAGGCCAAGGAUGUAGCCAUCAAGGUCAUGGGCAUGACC
..((((..((.....((((((.(....)...)))))).((((((..(((.((((....)))).)))..))))))((((.....)))).....))..))))....((((((....)))))) ( -44.30)
>DroSec_CAF1 16163 120 - 1
AUUGGCCGCAAGUCAGGGGCAGCCAUGGAAAUGCUUCAGAAUGAACUAUUCAGCAAGGGUUACGUAUGUCCUUCGCUCGAGGAAGCCAAGGACGUAGCCAUCAAGGUCAUGGGCAUGACC
..((((.((......((((((.(....)...)))))).(((((...))))).))..........(((((((((.(((......))).)))))))))))))....((((((....)))))) ( -38.50)
>DroSim_CAF1 16218 120 - 1
AUUGGCCGCAAGUCAGGGGCAGCCUUGGAAAUGCUUCAGAAUGAACUAUUCAGCAAGGGUUACGUAUGUCCUUCGCUCGAGGAAGCCAAGGACGUAGCCAUCAAGGUCAUGGGCAUGACC
..((((.((......((((((.(....)...)))))).(((((...))))).))..........(((((((((.(((......))).)))))))))))))....((((((....)))))) ( -38.50)
>DroEre_CAF1 18838 120 - 1
AUUGGCCGCAAAUCAGGGGCGGCCAUGGAAAUGCUUCAGAAGGAACUAUUCAGCAAGGGCUACGCAAGUCCCUCGCUCGAGGAAGCCAAGGAUGUAGCCAUCAAGGUCAUGGGCAUGACC
..(((((((.........)))))))(((...(((.((....((.....((((((.((((..((....)))))).))).)))....))...)).))).)))....((((((....)))))) ( -42.70)
>DroYak_CAF1 16663 120 - 1
AUUGGUCGCCAUUCAGGGGCGGCCAUGGAACUGCUCCAGAAGGAACUCUUCACCAAGGGCUACGUGUGUCCCUCGCUCGAGGAGGCCAAGGAUGUGGCCAUCAAGGUCAUGGGCAUGACC
..((((((((.......))))))))((((.....))))((((.....))))......((((((((.((((((((....)))).)))...).)))))))).....((((((....)))))) ( -48.30)
>consensus
AUUGGCCGCAAGUCAGGGGCAGCCAUGGAAAUGCUUCAGAAGGAACUAUUCAGCAAGGGCUACGUAUGUCCUUCGCUCGAGGAAGCCAAGGAUGUAGCCAUCAAGGUCAUGGGCAUGACC
.((((..((......((((((.(....)...)))))).((((.....)))).))...((((((....((((((.(((......))).)))))))))))).))))((((((....)))))) (-34.00 = -33.60 +  -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 13:47:56 2006