Locus 2375

Sequence ID 2R_DroMel_CAF1
Location 8,611,906 – 8,612,099
Length 193
Max. P 0.999876
window3925 window3926 window3927 window3928 window3929

overview

Window 5

Location 8,611,906 – 8,612,020
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.64
Mean single sequence MFE -43.38
Consensus MFE -35.26
Energy contribution -35.18
Covariance contribution -0.08
Combinations/Pair 1.09
Mean z-score -3.64
Structure conservation index 0.81
SVM decision value 3.25
SVM RNA-class probability 0.998855
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8611906 114 + 20766785
ACUACUUGGCAUUCCAUUGGCAUGCGCCACAUUUCAGAAGGUCCGGCAGGUGUU------UUCCUGCUGAUUUAAAUUAUUUGCAUGCCUUACUGGGGUGUCGAGCCCCCGGCAUAAAUU
.....(((((((((((..((((((((((...........))).(((((((....------..))))))).............)))))))....)))))))))))(((...)))....... ( -42.90)
>DroSec_CAF1 12816 114 + 1
ACUACUUGGCAUUCCAUUGGCAUGCGGCACAUUUCAGAAGGUCCGGCAGGUGUU------UUCCUGCUGAUUUAAAUUAUUUGCAUGCCUUACUGGGGGGCCAUGCCCCCGGCAUAAAUU
.......(((.(((((..((((((((((............)))(((((((....------..))))))).............)))))))....))))).)))(((((...)))))..... ( -40.60)
>DroSim_CAF1 9674 114 + 1
ACUACUUGGCAUUCCAUUGGCAUGCGCCACAUUUCAGAAGGUCCGGCAGGUGUU------UUCCUGCUGAUUUAAAUUAUUUGCAUGCCUUACUGGGGGGCCAUGCCCCCGGCAUAAAUU
.......(((.(((((..((((((((((...........))).(((((((....------..))))))).............)))))))....))))).)))(((((...)))))..... ( -41.40)
>DroEre_CAF1 12146 119 + 1
GCUACUUGGCAUUCCAUUGGCAUGCGCCACAUUGCAGAAAGUCCGGCAGGUGUUUUCGUUUUCCUGCUGAUUUAAAUUAUUUGCAUGCCUUGCUGGGG-GCCAAGCCCCCGGCAUAAAUU
(((....)))........(((((((((......))...(((((.((((((............))))))))))).........))))))).((((((((-((...))))))))))...... ( -48.00)
>DroYak_CAF1 7625 120 + 1
ACUACUUGGCAUUCCAUUGGCAUGCGCCACAUUUCAAAAGGUCCGGCAGGUGUUUUCGUUUUCCUGCUGAUUUAAAUUAUUUGCAUGCCUUGCUGGGGGGCAAAGCCCCCGGCAUAAAUU
......(((....)))..((((((((((...........))).(((((((............))))))).............))))))).(((((((((......)))))))))...... ( -44.00)
>consensus
ACUACUUGGCAUUCCAUUGGCAUGCGCCACAUUUCAGAAGGUCCGGCAGGUGUU______UUCCUGCUGAUUUAAAUUAUUUGCAUGCCUUACUGGGGGGCCAAGCCCCCGGCAUAAAUU
......((((.(((((..((((((((....((((....(((((.((((((............)))))))))))))))....))))))))....))))).)))).(((...)))....... (-35.26 = -35.18 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 6

Location 8,611,906 – 8,612,020
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.64
Mean single sequence MFE -38.68
Consensus MFE -34.84
Energy contribution -34.44
Covariance contribution -0.40
Combinations/Pair 1.08
Mean z-score -2.79
Structure conservation index 0.90
SVM decision value 4.34
SVM RNA-class probability 0.999876
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8611906 114 - 20766785
AAUUUAUGCCGGGGGCUCGACACCCCAGUAAGGCAUGCAAAUAAUUUAAAUCAGCAGGAA------AACACCUGCCGGACCUUCUGAAAUGUGGCGCAUGCCAAUGGAAUGCCAAGUAGU
......(((.((((........)))).))).(((((((...............(((((..------....)))))(((.....))).........)))))))..(((....)))...... ( -35.80)
>DroSec_CAF1 12816 114 - 1
AAUUUAUGCCGGGGGCAUGGCCCCCCAGUAAGGCAUGCAAAUAAUUUAAAUCAGCAGGAA------AACACCUGCCGGACCUUCUGAAAUGUGCCGCAUGCCAAUGGAAUGCCAAGUAGU
...((((...((((((...))))))..))))(((((((...............(((((..------....)))))(((.....))).........)))))))..(((....)))...... ( -38.50)
>DroSim_CAF1 9674 114 - 1
AAUUUAUGCCGGGGGCAUGGCCCCCCAGUAAGGCAUGCAAAUAAUUUAAAUCAGCAGGAA------AACACCUGCCGGACCUUCUGAAAUGUGGCGCAUGCCAAUGGAAUGCCAAGUAGU
...((((...((((((...))))))..))))(((((((...............(((((..------....)))))(((.....))).........)))))))..(((....)))...... ( -38.50)
>DroEre_CAF1 12146 119 - 1
AAUUUAUGCCGGGGGCUUGGC-CCCCAGCAAGGCAUGCAAAUAAUUUAAAUCAGCAGGAAAACGAAAACACCUGCCGGACUUUCUGCAAUGUGGCGCAUGCCAAUGGAAUGCCAAGUAGC
......(((.((((((...))-)))).))).(((((((............((.(((((............))))).)).......((......)))))))))..(((....)))...... ( -41.10)
>DroYak_CAF1 7625 120 - 1
AAUUUAUGCCGGGGGCUUUGCCCCCCAGCAAGGCAUGCAAAUAAUUUAAAUCAGCAGGAAAACGAAAACACCUGCCGGACCUUUUGAAAUGUGGCGCAUGCCAAUGGAAUGCCAAGUAGU
......(((.((((((...))))))..))).(((((((..(((.((((((((.(((((............)))))..))...)))))).)))...)))))))..(((....)))...... ( -39.50)
>consensus
AAUUUAUGCCGGGGGCUUGGCCCCCCAGUAAGGCAUGCAAAUAAUUUAAAUCAGCAGGAA______AACACCUGCCGGACCUUCUGAAAUGUGGCGCAUGCCAAUGGAAUGCCAAGUAGU
......(((.((((........)))).))).(((((((...............(((((............)))))(((.....))).........)))))))..(((....)))...... (-34.84 = -34.44 +  -0.40)

alignment

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secondary structure

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dotplot

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Window 7

Location 8,611,946 – 8,612,059
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.43
Mean single sequence MFE -37.84
Consensus MFE -30.00
Energy contribution -30.28
Covariance contribution 0.28
Combinations/Pair 1.07
Mean z-score -1.96
Structure conservation index 0.79
SVM decision value 1.03
SVM RNA-class probability 0.903294
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8611946 113 + 20766785
GUCCGGCAGGUGUU------UUCCUGCUGAUUUAAAUUAUUUGCAUGCCUUACUGGGGUGUCGAGCCCCCGGCAUAAAUUCC-CCCGCCGGCCAGAAAUUUUAACCAAAGCCAAUUGGCC
...(((((((....------..)))))))..(((((...((((...(((.....(((((.....))))).(((.........-...))))))))))...))))).....(((....))). ( -33.60)
>DroSec_CAF1 12856 113 + 1
GUCCGGCAGGUGUU------UUCCUGCUGAUUUAAAUUAUUUGCAUGCCUUACUGGGGGGCCAUGCCCCCGGCAUAAAUUCC-CCCGCCGGCCAGAAAUUUUAACCAAAGCCAAUUGGCC
...(((((((....------..)))))))..(((((...((((...(((......((((((...))))))(((.........-...))))))))))...))))).....(((....))). ( -37.80)
>DroSim_CAF1 9714 113 + 1
GUCCGGCAGGUGUU------UUCCUGCUGAUUUAAAUUAUUUGCAUGCCUUACUGGGGGGCCAUGCCCCCGGCAUAAAUUCC-CCCGCCGGCCAGAAAUUUUAACCAAAGCCAAUUGGCC
...(((((((....------..)))))))..(((((...((((...(((......((((((...))))))(((.........-...))))))))))...))))).....(((....))). ( -37.80)
>DroEre_CAF1 12186 119 + 1
GUCCGGCAGGUGUUUUCGUUUUCCUGCUGAUUUAAAUUAUUUGCAUGCCUUGCUGGGG-GCCAAGCCCCCGGCAUAAAUUCCCCCCGGCGGCCGCACAUUUUAACCAAAGCCAAUUGGCC
...(((((((............)))))))............(((..(((.((((((((-((...))))))))))......((....)).))).))).............(((....))). ( -40.90)
>DroYak_CAF1 7665 119 + 1
GUCCGGCAGGUGUUUUCGUUUUCCUGCUGAUUUAAAUUAUUUGCAUGCCUUGCUGGGGGGCAAAGCCCCCGGCAUAAAUUCC-CCCGGCGGCCAGAAAUUUUAACCAAAGCCAAUUGGCC
...(((((((............)))))))..(((((...((((...(((..(((((((((....(((...)))......)))-)))))))))))))...))))).....(((....))). ( -39.10)
>consensus
GUCCGGCAGGUGUU______UUCCUGCUGAUUUAAAUUAUUUGCAUGCCUUACUGGGGGGCCAAGCCCCCGGCAUAAAUUCC_CCCGCCGGCCAGAAAUUUUAACCAAAGCCAAUUGGCC
...(((((((............)))))))...............(((((......((((((...)))))))))))..............((((((...((((....))))....)))))) (-30.00 = -30.28 +   0.28)

alignment

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secondary structure

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dotplot

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Window 8

Location 8,611,946 – 8,612,059
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.43
Mean single sequence MFE -38.86
Consensus MFE -31.80
Energy contribution -32.20
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.56
Structure conservation index 0.82
SVM decision value 0.57
SVM RNA-class probability 0.785477
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8611946 113 - 20766785
GGCCAAUUGGCUUUGGUUAAAAUUUCUGGCCGGCGGG-GGAAUUUAUGCCGGGGGCUCGACACCCCAGUAAGGCAUGCAAAUAAUUUAAAUCAGCAGGAA------AACACCUGCCGGAC
((((((......))))))...........((((((((-.......(((((.((((.......)))).....)))))((...............)).....------....)))))))).. ( -36.16)
>DroSec_CAF1 12856 113 - 1
GGCCAAUUGGCUUUGGUUAAAAUUUCUGGCCGGCGGG-GGAAUUUAUGCCGGGGGCAUGGCCCCCCAGUAAGGCAUGCAAAUAAUUUAAAUCAGCAGGAA------AACACCUGCCGGAC
((((((......))))))...........((((((((-.......(((((((((((...))))))......)))))((...............)).....------....)))))))).. ( -39.36)
>DroSim_CAF1 9714 113 - 1
GGCCAAUUGGCUUUGGUUAAAAUUUCUGGCCGGCGGG-GGAAUUUAUGCCGGGGGCAUGGCCCCCCAGUAAGGCAUGCAAAUAAUUUAAAUCAGCAGGAA------AACACCUGCCGGAC
((((((......))))))...........((((((((-.......(((((((((((...))))))......)))))((...............)).....------....)))))))).. ( -39.36)
>DroEre_CAF1 12186 119 - 1
GGCCAAUUGGCUUUGGUUAAAAUGUGCGGCCGCCGGGGGGAAUUUAUGCCGGGGGCUUGGC-CCCCAGCAAGGCAUGCAAAUAAUUUAAAUCAGCAGGAAAACGAAAACACCUGCCGGAC
((((....)))).(((((.((((.(((((((.((....))......(((.((((((...))-)))).))).))).))))....)))).)))))(((((............)))))..... ( -42.40)
>DroYak_CAF1 7665 119 - 1
GGCCAAUUGGCUUUGGUUAAAAUUUCUGGCCGCCGGG-GGAAUUUAUGCCGGGGGCUUUGCCCCCCAGCAAGGCAUGCAAAUAAUUUAAAUCAGCAGGAAAACGAAAACACCUGCCGGAC
(((((.(((((....)))))......))))).(((((-.(((((((((((((((((...))))))......)))))).....)))))...)).(((((............)))))))).. ( -37.00)
>consensus
GGCCAAUUGGCUUUGGUUAAAAUUUCUGGCCGGCGGG_GGAAUUUAUGCCGGGGGCUUGGCCCCCCAGUAAGGCAUGCAAAUAAUUUAAAUCAGCAGGAA______AACACCUGCCGGAC
((((((......))))))...........((((((((.(......(((((.((((.......)))).....)))))((...............)).............).)))))))).. (-31.80 = -32.20 +   0.40)

alignment

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secondary structure

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dotplot

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Window 9

Location 8,611,980 – 8,612,099
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.23
Mean single sequence MFE -38.20
Consensus MFE -32.88
Energy contribution -32.72
Covariance contribution -0.16
Combinations/Pair 1.08
Mean z-score -1.56
Structure conservation index 0.86
SVM decision value 0.89
SVM RNA-class probability 0.875547
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8611980 119 + 20766785
UUGCAUGCCUUACUGGGGUGUCGAGCCCCCGGCAUAAAUUCC-CCCGCCGGCCAGAAAUUUUAACCAAAGCCAAUUGGCCAAGAUAAGAUGUAAUGGUCUUUUAUGGCCCAGUUCGCUGU
..(((.((...((((((((((((......)))))).......-......(((((...((((((.(....(((....)))...).))))))....)))))........))))))..))))) ( -33.50)
>DroSec_CAF1 12890 119 + 1
UUGCAUGCCUUACUGGGGGGCCAUGCCCCCGGCAUAAAUUCC-CCCGCCGGCCAGAAAUUUUAACCAAAGCCAAUUGGCCAAGAUAAGAUGUAAUGGUCUUUUAUGGCCCAGUUCGCUGU
..(((.((...((((((((((...))))))(((.........-...)))(((((...............(((....)))......(((((......)))))...)))))))))..))))) ( -37.40)
>DroSim_CAF1 9748 119 + 1
UUGCAUGCCUUACUGGGGGGCCAUGCCCCCGGCAUAAAUUCC-CCCGCCGGCCAGAAAUUUUAACCAAAGCCAAUUGGCCAAGAUAAGAUGUAAUGGUCUUUUAUGGCCCAGUUCGCUGU
..(((.((...((((((((((...))))))(((.........-...)))(((((...............(((....)))......(((((......)))))...)))))))))..))))) ( -37.40)
>DroEre_CAF1 12226 119 + 1
UUGCAUGCCUUGCUGGGG-GCCAAGCCCCCGGCAUAAAUUCCCCCCGGCGGCCGCACAUUUUAACCAAAGCCAAUUGGCCAAGAUAAGAUGUAAUGGUCUUUUAUGGCCCAGUUCGCUGU
.(((..(((.((((((((-((...))))))))))......((....)).))).)))............(((.(((((((((.((.(((((......))))))).))).)))))).))).. ( -43.00)
>DroYak_CAF1 7705 119 + 1
UUGCAUGCCUUGCUGGGGGGCAAAGCCCCCGGCAUAAAUUCC-CCCGGCGGCCAGAAAUUUUAACCAAAGCCAAUUGGCCAAGAUAAGAUGUAAUGGUCUUUUAUGGCCCAGUUUGCUGU
......(((..(((((((((....(((...)))......)))-)))))))))................(((.(((((((((.((.(((((......))))))).))).)))))).))).. ( -39.70)
>consensus
UUGCAUGCCUUACUGGGGGGCCAAGCCCCCGGCAUAAAUUCC_CCCGCCGGCCAGAAAUUUUAACCAAAGCCAAUUGGCCAAGAUAAGAUGUAAUGGUCUUUUAUGGCCCAGUUCGCUGU
..(((.((...((((((((((...))))))((((((((...........(((((...((((((.(....(((....)))...).))))))....))))).))))).)))))))..))))) (-32.88 = -32.72 +  -0.16)

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 10:28:28 2006