Locus 5439

Sequence ID 2R_DroMel_CAF1
Location 17,489,946 – 17,490,222
Length 276
Max. P 0.978534
window8677 window8678 window8679 window8680 window8681

overview

Window 7

Location 17,489,946 – 17,490,063
Length 117
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.78
Mean single sequence MFE -27.62
Consensus MFE -24.49
Energy contribution -24.55
Covariance contribution 0.06
Combinations/Pair 1.04
Mean z-score -1.77
Structure conservation index 0.89
SVM decision value 0.38
SVM RNA-class probability 0.713045
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17489946 117 - 20766785
GACCCACAUUUGUGUGGUUCCCCU-AUUCUGGACUCGCCC--ACCCGCUUUUCCGGGUGUUGAUAACUGUUUUUCCGACCUCCAAAUUCCCCGCAAACUCCUCGGAAAACUUGUCCAUGU
((.(((((....))))).))....-....((((((((..(--(((((......)))))).))).......((((((((.......................))))))))...)))))... ( -29.40)
>DroSec_CAF1 17772 117 - 1
GACCCACAUUUGUGUGGUUCCCCC-AUUCUGGACUCGCCC--ACCCGCUUUUCCGGGUGUUGAUAACUGUUUUUCCGACCUCCAAAUUCCCCGCAAACUCCUCGGAAAACUUGUCCAUGU
((.(((((....))))).))....-....((((((((..(--(((((......)))))).))).......((((((((.......................))))))))...)))))... ( -29.40)
>DroSim_CAF1 30634 117 - 1
GACCCACAUUUGUGUGGUUCCCCC-AUUCUGGACUCGCCC--ACCCGCUUUUCCGUGUGUUGAUAACUGUUUUUCCGACCUCCAAAUUCCCCGCAAACUCCUCGGAAAACUUGUCCAUGU
((.(((((....))))).))....-....((((((((..(--((.((......)).))).))).......((((((((.......................))))))))...)))))... ( -22.30)
>DroYak_CAF1 26808 120 - 1
GACCCACAUUUGUGUGGUUCCCCCCUUUUUGGAUGCGCCCACACCCGCUUUUCCGGGUGUUGAUAACUGUUUUUCCGACCUCCAAAUCCCCCGCAAACUCCUCGGAAAACUUGUCCAUGU
((.(((((....))))).)).........(((((....(.(((((((......))))))).)........((((((((.......................))))))))...)))))... ( -29.40)
>consensus
GACCCACAUUUGUGUGGUUCCCCC_AUUCUGGACUCGCCC__ACCCGCUUUUCCGGGUGUUGAUAACUGUUUUUCCGACCUCCAAAUUCCCCGCAAACUCCUCGGAAAACUUGUCCAUGU
((.(((((....))))).)).........(((((........(((((......)))))............((((((((.......................))))))))...)))))... (-24.49 = -24.55 +   0.06)

alignment

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secondary structure

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Window 8

Location 17,490,063 – 17,490,183
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.67
Mean single sequence MFE -27.68
Consensus MFE -22.20
Energy contribution -23.76
Covariance contribution 1.56
Combinations/Pair 1.03
Mean z-score -1.89
Structure conservation index 0.80
SVM decision value 0.54
SVM RNA-class probability 0.776169
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17490063 120 + 20766785
AAGUUAUUUUCAACACUUAAAAUAAACUCUGCCUCCUCGGCUCGGUUCCUUGCUCUUUGCCAGAAUCCUGGCCAGCAUUUCUUUAGCCGCCCAUUUUCUGGGUCAGUCGCAAACACAGCC
...(((((((........)))))))....(((..(...((((........((((....(((((....))))).)))).......))))(((((.....)))))..)..)))......... ( -26.16)
>DroSec_CAF1 17889 120 + 1
AAGUUAUUUUCAACACUUAAAAUAAACUCAGCUGCCUCGGCUCGGUUCCCUGCUCUUUGCCAGAAUCCUGGCCAGCAUUUCUUUAGCCGCCCAUUUUCUGGGUCAGUCGCAAACACAGCC
...(((((((........))))))).....((((...(((((.((((...((((....(((((....))))).)))).......))))(((((.....))))).)))))......)))). ( -28.10)
>DroSim_CAF1 30751 120 + 1
AAGUUAUUUUCAACACUUAAAAUAAACUCAGCUGCCUCGGCUCGGUUCCUUGCUCUUUGCCAGAAUCCUGGCCAGCAUUUCUUUAGCCGCCCAUUUUCUGGGUCAGUCGCAAACACAGCC
...(((((((........))))))).....((((...(((((.((((...((((....(((((....))))).)))).......))))(((((.....))))).)))))......)))). ( -28.80)
>DroYak_CAF1 26928 106 + 1
AAGUUAUUUUCAACACUUAAAAUAAACUCUGCUGCCUCGGC--------------UUUGCCAGAAUCCUGGCCAGCAUUUCUUUAGCCGCCCAUUUUCUGGGUCAGUCGCAAGCACAGUC
...(((((((........)))))))(((.((((((..((((--------------(..(((((....)))))............))))(((((.....)))))..)..)).)))).))). ( -27.64)
>consensus
AAGUUAUUUUCAACACUUAAAAUAAACUCAGCUGCCUCGGCUCGGUUCCUUGCUCUUUGCCAGAAUCCUGGCCAGCAUUUCUUUAGCCGCCCAUUUUCUGGGUCAGUCGCAAACACAGCC
...(((((((........))))))).....((((....((((........((((....(((((....))))).)))).......))))(((((.....)))))............)))). (-22.20 = -23.76 +   1.56)

alignment

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secondary structure

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Window 9

Location 17,490,063 – 17,490,183
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.67
Mean single sequence MFE -35.52
Consensus MFE -28.47
Energy contribution -30.03
Covariance contribution 1.56
Combinations/Pair 1.03
Mean z-score -1.89
Structure conservation index 0.80
SVM decision value 0.55
SVM RNA-class probability 0.776784
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17490063 120 - 20766785
GGCUGUGUUUGCGACUGACCCAGAAAAUGGGCGGCUAAAGAAAUGCUGGCCAGGAUUCUGGCAAAGAGCAAGGAACCGAGCCGAGGAGGCAGAGUUUAUUUUAAGUGUUGAAAAUAACUU
((...(.(((((..((...((((((..(((.((((.........)))).)))...))))))...)).))))).).))..(((.....))).(((((.(((((........)))))))))) ( -35.40)
>DroSec_CAF1 17889 120 - 1
GGCUGUGUUUGCGACUGACCCAGAAAAUGGGCGGCUAAAGAAAUGCUGGCCAGGAUUCUGGCAAAGAGCAGGGAACCGAGCCGAGGCAGCUGAGUUUAUUUUAAGUGUUGAAAAUAACUU
((((((............((((.....))))(((((.......((((.(((((....)))))....))))........)))))..))))))(((((.(((((........)))))))))) ( -37.06)
>DroSim_CAF1 30751 120 - 1
GGCUGUGUUUGCGACUGACCCAGAAAAUGGGCGGCUAAAGAAAUGCUGGCCAGGAUUCUGGCAAAGAGCAAGGAACCGAGCCGAGGCAGCUGAGUUUAUUUUAAGUGUUGAAAAUAACUU
((((((.((.(((.(((.((((.....))))))))........((((.(((((....)))))....)))).........)).)).))))))(((((.(((((........)))))))))) ( -36.40)
>DroYak_CAF1 26928 106 - 1
GACUGUGCUUGCGACUGACCCAGAAAAUGGGCGGCUAAAGAAAUGCUGGCCAGGAUUCUGGCAAA--------------GCCGAGGCAGCAGAGUUUAUUUUAAGUGUUGAAAAUAACUU
..((((((((.((.((...((((((..(((.((((.........)))).)))...))))))...)--------------).))))))).)))((((.(((((........))))))))). ( -33.20)
>consensus
GGCUGUGUUUGCGACUGACCCAGAAAAUGGGCGGCUAAAGAAAUGCUGGCCAGGAUUCUGGCAAAGAGCAAGGAACCGAGCCGAGGCAGCAGAGUUUAUUUUAAGUGUUGAAAAUAACUU
.(((((............((((.....))))(((((.......((((.(((((....)))))....))))........)))))..))))).(((((.(((((........)))))))))) (-28.47 = -30.03 +   1.56)

alignment

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secondary structure

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Window 0

Location 17,490,103 – 17,490,222
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.74
Mean single sequence MFE -24.30
Consensus MFE -17.66
Energy contribution -18.98
Covariance contribution 1.31
Combinations/Pair 1.04
Mean z-score -1.90
Structure conservation index 0.73
SVM decision value 0.01
SVM RNA-class probability 0.536771
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17490103 119 + 20766785
CUCGGUUCCUUGCUCUUUGCCAGAAUCCUGGCCAGCAUUUCUUUAGCCGCCCAUUUUCUGGGUCAGUCGCAAACACAGCCCCCCCUUUUCCGACCA-UUUUCCAACCGAAACCCUCUUUG
.((((((...((((....(((((....))))).))))...........(((((.....)))))..((((.(((.............))).))))..-......))))))........... ( -25.12)
>DroSec_CAF1 17929 118 + 1
CUCGGUUCCCUGCUCUUUGCCAGAAUCCUGGCCAGCAUUUCUUUAGCCGCCCAUUUUCUGGGUCAGUCGCAAACACAGCCC-CCCUUUUCCGACCA-UUUUCCAACCGAAACCCUCUUUG
.((((((...((((....(((((....))))).))))...........(((((.....)))))..((((.(((........-....))).))))..-......))))))........... ( -25.10)
>DroSim_CAF1 30791 118 + 1
CUCGGUUCCUUGCUCUUUGCCAGAAUCCUGGCCAGCAUUUCUUUAGCCGCCCAUUUUCUGGGUCAGUCGCAAACACAGCCC-CCCUUUUCCGACCA-UUUUCCAACCGAAACCCUCUUUG
.((((((...((((....(((((....))))).))))...........(((((.....)))))..((((.(((........-....))).))))..-......))))))........... ( -25.20)
>DroYak_CAF1 26968 105 + 1
C--------------UUUGCCAGAAUCCUGGCCAGCAUUUCUUUAGCCGCCCAUUUUCUGGGUCAGUCGCAAGCACAGUCC-CGCUUUUCCGACCACUUUUCCAACCGAAACCCUCUUUG
.--------------...(((((....))))).((..((((.......(((((.....)))))..((((.((((.......-.))))...)))).............))))..))..... ( -21.80)
>consensus
CUCGGUUCCUUGCUCUUUGCCAGAAUCCUGGCCAGCAUUUCUUUAGCCGCCCAUUUUCUGGGUCAGUCGCAAACACAGCCC_CCCUUUUCCGACCA_UUUUCCAACCGAAACCCUCUUUG
.((((((...........(((((....)))))................(((((.....)))))..((((.(((...((......))))).)))).........))))))........... (-17.66 = -18.98 +   1.31)

alignment

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secondary structure

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Window 1

Location 17,490,103 – 17,490,222
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.74
Mean single sequence MFE -36.17
Consensus MFE -31.26
Energy contribution -32.33
Covariance contribution 1.06
Combinations/Pair 1.03
Mean z-score -2.56
Structure conservation index 0.86
SVM decision value 1.82
SVM RNA-class probability 0.978534
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17490103 119 - 20766785
CAAAGAGGGUUUCGGUUGGAAAA-UGGUCGGAAAAGGGGGGGCUGUGUUUGCGACUGACCCAGAAAAUGGGCGGCUAAAGAAAUGCUGGCCAGGAUUCUGGCAAAGAGCAAGGAACCGAG
.......(((((((((((.....-.(((((.(((.((.....))...))).)))))..((((.....))))))))).......((((.(((((....)))))....)))).))))))... ( -37.30)
>DroSec_CAF1 17929 118 - 1
CAAAGAGGGUUUCGGUUGGAAAA-UGGUCGGAAAAGGG-GGGCUGUGUUUGCGACUGACCCAGAAAAUGGGCGGCUAAAGAAAUGCUGGCCAGGAUUCUGGCAAAGAGCAGGGAACCGAG
.......(((((((((((.....-.(((((.(((.((.-...))...))).)))))..((((.....))))))))).......((((.(((((....)))))....)))).))))))... ( -37.10)
>DroSim_CAF1 30791 118 - 1
CAAAGAGGGUUUCGGUUGGAAAA-UGGUCGGAAAAGGG-GGGCUGUGUUUGCGACUGACCCAGAAAAUGGGCGGCUAAAGAAAUGCUGGCCAGGAUUCUGGCAAAGAGCAAGGAACCGAG
.......(((((((((((.....-.(((((.(((.((.-...))...))).)))))..((((.....))))))))).......((((.(((((....)))))....)))).))))))... ( -37.30)
>DroYak_CAF1 26968 105 - 1
CAAAGAGGGUUUCGGUUGGAAAAGUGGUCGGAAAAGCG-GGACUGUGCUUGCGACUGACCCAGAAAAUGGGCGGCUAAAGAAAUGCUGGCCAGGAUUCUGGCAAA--------------G
...........(((((((.((..(..(((.........-.)))..)..)).))))))).((((((..(((.((((.........)))).)))...))))))....--------------. ( -33.00)
>consensus
CAAAGAGGGUUUCGGUUGGAAAA_UGGUCGGAAAAGGG_GGGCUGUGUUUGCGACUGACCCAGAAAAUGGGCGGCUAAAGAAAUGCUGGCCAGGAUUCUGGCAAAGAGCAAGGAACCGAG
.......(((((((((((.(((...((((...........))))...))).))))))).((((((..(((.((((.........)))).)))...))))))............))))... (-31.26 = -32.33 +   1.06)

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 11:44:56 2006