Locus 2451

Sequence ID 3R_DroMel_CAF1
Location 6,779,534 – 6,779,688
Length 154
Max. P 0.999978
window4011 window4012 window4013 window4014

overview

Window 1

Location 6,779,534 – 6,779,648
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.88
Mean single sequence MFE -43.00
Consensus MFE -40.80
Energy contribution -41.24
Covariance contribution 0.44
Combinations/Pair 1.03
Mean z-score -3.51
Structure conservation index 0.95
SVM decision value 5.19
SVM RNA-class probability 0.999978
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6779534 114 + 27905053
CCCGCUAAGCUUUUGUUUGCCUUCGCCAUGCUCCGCUUGGCUUGGUUCCCUUGGUUGUAAAUGCAGUUGCAGUUGCAACUACAUCUGCAGCUGCUUCUGUUAGCGGCUU------ACGCC
.((((((((((.......(((...((((.((...)).))))..)))......))))......((((..(((((((((........)))))))))..))))))))))...------..... ( -40.22)
>DroSec_CAF1 43686 114 + 1
CCCGCUAAGCUUUUGUUUGCCUUCGCCAUGCUCCGCUUGGCUUGGUUCCCGUGGUUGUAAAUGCAGUUGCAGUUGCAGCUACAUCUGCAGCUGCUUCUGUUAGCGGCUU------ACGCC
.((((((((((.......(((...((((.((...)).))))..)))......))))......((((..((((((((((......))))))))))..))))))))))...------..... ( -42.52)
>DroSim_CAF1 47704 114 + 1
CCCGCUAAGCUUUUGUUUGCCUUCGCCAUGCUCCGCUUGGCUUGGUUCCCUUGGUUGUAAAUGCAGUUGCAGUUGCAGCUACAUCUGCAGCUGCUUCUGUUAGCGGCUU------ACGCC
.((((((((((.......(((...((((.((...)).))))..)))......))))......((((..((((((((((......))))))))))..))))))))))...------..... ( -42.52)
>DroEre_CAF1 28752 120 + 1
CCCGCUAAGCUUUUGUUUGCCUUCGCCAUGCUCCGCUUGGCUUGGCUCCCUUGGUUGUAAAUGCAGUUGCAGUUGCAGCUACAUCUGCAGCUGCUUCUGUCAGCGGCUUACGCUUACGCC
...(((((((....((..(((...((((.(((......))).)))).......((((.....((((..((((((((((......))))))))))..)))))))))))..))))))).)). ( -45.70)
>DroYak_CAF1 41099 114 + 1
CCCGCUAAGCUUUUGUUUGCCUUCGCCAUGCUACGCUUGGCUUGGUUCCCUUGGUUGUAAAUGCAGUUGCAGAUGCAGCUACAUCUGCAGCUGCUUCUGUUAGCGGCUU------ACGCC
.((((((((((.......(((...((((.((...)).))))..)))......))))......(((((((((((((......)))))))))))))......))))))...------..... ( -44.02)
>consensus
CCCGCUAAGCUUUUGUUUGCCUUCGCCAUGCUCCGCUUGGCUUGGUUCCCUUGGUUGUAAAUGCAGUUGCAGUUGCAGCUACAUCUGCAGCUGCUUCUGUUAGCGGCUU______ACGCC
.((((((((((.......(((...((((.((...)).))))..)))......))))......((((..((((((((((......))))))))))..)))))))))).............. (-40.80 = -41.24 +   0.44)

alignment

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secondary structure

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dotplot

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Window 2

Location 6,779,534 – 6,779,648
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.88
Mean single sequence MFE -41.72
Consensus MFE -37.18
Energy contribution -36.86
Covariance contribution -0.32
Combinations/Pair 1.07
Mean z-score -3.38
Structure conservation index 0.89
SVM decision value 4.22
SVM RNA-class probability 0.999841
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6779534 114 - 27905053
GGCGU------AAGCCGCUAACAGAAGCAGCUGCAGAUGUAGUUGCAACUGCAACUGCAUUUACAACCAAGGGAACCAAGCCAAGCGGAGCAUGGCGAAGGCAAACAAAAGCUUAGCGGG
(((..------..)))(((......)))..((((((((((((((((....)))))))))))).................((((.((...)).))))..((((........)))).)))). ( -40.70)
>DroSec_CAF1 43686 114 - 1
GGCGU------AAGCCGCUAACAGAAGCAGCUGCAGAUGUAGCUGCAACUGCAACUGCAUUUACAACCACGGGAACCAAGCCAAGCGGAGCAUGGCGAAGGCAAACAAAAGCUUAGCGGG
(((..------..))).....(((..((((((((....))))))))..)))...((((.....................((((.((...)).))))..((((........)))).)))). ( -40.20)
>DroSim_CAF1 47704 114 - 1
GGCGU------AAGCCGCUAACAGAAGCAGCUGCAGAUGUAGCUGCAACUGCAACUGCAUUUACAACCAAGGGAACCAAGCCAAGCGGAGCAUGGCGAAGGCAAACAAAAGCUUAGCGGG
(((..------..))).....(((..((((((((....))))))))..)))...((((.....................((((.((...)).))))..((((........)))).)))). ( -40.20)
>DroEre_CAF1 28752 120 - 1
GGCGUAAGCGUAAGCCGCUGACAGAAGCAGCUGCAGAUGUAGCUGCAACUGCAACUGCAUUUACAACCAAGGGAGCCAAGCCAAGCGGAGCAUGGCGAAGGCAAACAAAAGCUUAGCGGG
.((....)).....((((((((((..((((((((....))))))))..))).....((........((...)).(((..((((.((...)).))))...)))........))))))))). ( -45.50)
>DroYak_CAF1 41099 114 - 1
GGCGU------AAGCCGCUAACAGAAGCAGCUGCAGAUGUAGCUGCAUCUGCAACUGCAUUUACAACCAAGGGAACCAAGCCAAGCGUAGCAUGGCGAAGGCAAACAAAAGCUUAGCGGG
(((..------..))).....((((.((((((((....)))))))).))))...((((.....................((((.((...)).))))..((((........)))).)))). ( -42.00)
>consensus
GGCGU______AAGCCGCUAACAGAAGCAGCUGCAGAUGUAGCUGCAACUGCAACUGCAUUUACAACCAAGGGAACCAAGCCAAGCGGAGCAUGGCGAAGGCAAACAAAAGCUUAGCGGG
..............((((((((((..((((((((....))))))))..)))....(((............((...))..((((.((...)).))))....))).........))))))). (-37.18 = -36.86 +  -0.32)

alignment

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secondary structure

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Window 3

Location 6,779,574 – 6,779,688
Length 114
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 84.37
Mean single sequence MFE -37.09
Consensus MFE -27.88
Energy contribution -29.88
Covariance contribution 2.00
Combinations/Pair 1.00
Mean z-score -1.98
Structure conservation index 0.75
SVM decision value 0.16
SVM RNA-class probability 0.614383
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6779574 114 + 27905053
CUUGGUUCCCUUGGUUGUAAAUGCAGUUGCAGUUGCAACUACAUCUGCAGCUGCUUCUGUUAGCGGCUU------ACGCCGGUUUCGAUGCCCCGAUUGGCUACACAUUCACCGCCUCCG
............(((.((.(((((((..(((((((((........)))))))))..))).(((((((..------..)))(((......))).......))))..)))).)).))).... ( -35.30)
>DroSec_CAF1 43726 114 + 1
CUUGGUUCCCGUGGUUGUAAAUGCAGUUGCAGUUGCAGCUACAUCUGCAGCUGCUUCUGUUAGCGGCUU------ACGCCGGUUUCGAUGCCCCGAUUGGCUACACACUCACCGCCUCCG
...((...(.(((..(((....((((..((((((((((......))))))))))..))))(((((((..------..)))(((......))).......)))).)))..))).)...)). ( -40.00)
>DroSim_CAF1 47744 114 + 1
CUUGGUUCCCUUGGUUGUAAAUGCAGUUGCAGUUGCAGCUACAUCUGCAGCUGCUUCUGUUAGCGGCUU------ACGCCGGUUUCGAUGCCCCGAUUGGCUACACACUCACCGCCUCCG
...((......((..(((....((((..((((((((((......))))))))))..))))(((((((..------..)))(((......))).......)))).)))..))......)). ( -36.80)
>DroEre_CAF1 28792 120 + 1
CUUGGCUCCCUUGGUUGUAAAUGCAGUUGCAGUUGCAGCUACAUCUGCAGCUGCUUCUGUCAGCGGCUUACGCUUACGCCGGUUUCGAUGCCUCGAUUGGCUACACAUUCACCGCCUGCG
...(((......(((.((((..((((..((((((((((......))))))))))..))))..(((.....))))))))))(((......(((......))).........)))))).... ( -41.86)
>DroYak_CAF1 41139 104 + 1
CUUGGUUCCCUUGGUUGUAAAUGCAGUUGCAGAUGCAGCUACAUCUGCAGCUGCUUCUGUUAGCGGCUU------ACGCCGGUUUCGAUGCCCCGAUUGGCUACACAUU----------G
.((((..((....((((.....(((((((((((((......)))))))))))))......))))(((..------..)))))..)))).(((......)))........----------. ( -37.10)
>DroAna_CAF1 212 98 + 1
UUUU--UCUC--------------UGUUGCAGUUGCAUUUACAACUGCAGCUGCUUCUGUUAGCGGCUU------ACGCCGGUUUCGGUUCCCCGAUUGGCUACACUUUUCCCGCCCGGA
....--..((--------------((.((((((((......))))))))((((((......))))))..------..(((((..((((....)))))))))...............)))) ( -31.50)
>consensus
CUUGGUUCCCUUGGUUGUAAAUGCAGUUGCAGUUGCAGCUACAUCUGCAGCUGCUUCUGUUAGCGGCUU______ACGCCGGUUUCGAUGCCCCGAUUGGCUACACAUUCACCGCCUCCG
............((((((....((((..((((((((((......))))))))))..))))..)))))).........(((((..(((......))))))))................... (-27.88 = -29.88 +   2.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,779,574 – 6,779,688
Length 114
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 84.37
Mean single sequence MFE -40.88
Consensus MFE -31.46
Energy contribution -33.60
Covariance contribution 2.14
Combinations/Pair 1.16
Mean z-score -3.05
Structure conservation index 0.77
SVM decision value 0.95
SVM RNA-class probability 0.887744
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6779574 114 - 27905053
CGGAGGCGGUGAAUGUGUAGCCAAUCGGGGCAUCGAAACCGGCGU------AAGCCGCUAACAGAAGCAGCUGCAGAUGUAGUUGCAACUGCAACUGCAUUUACAACCAAGGGAACCAAG
....((..((((((((.((((...((((....))))....(((..------..))))))).(((..((((((((....))))))))..))).....))))))))..))............ ( -41.10)
>DroSec_CAF1 43726 114 - 1
CGGAGGCGGUGAGUGUGUAGCCAAUCGGGGCAUCGAAACCGGCGU------AAGCCGCUAACAGAAGCAGCUGCAGAUGUAGCUGCAACUGCAACUGCAUUUACAACCACGGGAACCAAG
((..((..((((((((.((((...((((....))))....(((..------..))))))).(((..((((((((....))))))))..))).....))))))))..)).))......... ( -44.50)
>DroSim_CAF1 47744 114 - 1
CGGAGGCGGUGAGUGUGUAGCCAAUCGGGGCAUCGAAACCGGCGU------AAGCCGCUAACAGAAGCAGCUGCAGAUGUAGCUGCAACUGCAACUGCAUUUACAACCAAGGGAACCAAG
....((..((((((((.((((...((((....))))....(((..------..))))))).(((..((((((((....))))))))..))).....))))))))..))............ ( -43.50)
>DroEre_CAF1 28792 120 - 1
CGCAGGCGGUGAAUGUGUAGCCAAUCGAGGCAUCGAAACCGGCGUAAGCGUAAGCCGCUGACAGAAGCAGCUGCAGAUGUAGCUGCAACUGCAACUGCAUUUACAACCAAGGGAGCCAAG
.(((((((((..((((...(((..((((....))))....)))....))))..)))))((.(((..((((((((....))))))))..))))).))))...................... ( -46.30)
>DroYak_CAF1 41139 104 - 1
C----------AAUGUGUAGCCAAUCGGGGCAUCGAAACCGGCGU------AAGCCGCUAACAGAAGCAGCUGCAGAUGUAGCUGCAUCUGCAACUGCAUUUACAACCAAGGGAACCAAG
.----------....(((((((......))).((.....((((..------..))))......)).((((.(((((((((....))))))))).))))...))))............... ( -36.00)
>DroAna_CAF1 212 98 - 1
UCCGGGCGGGAAAAGUGUAGCCAAUCGGGGAACCGAAACCGGCGU------AAGCCGCUAACAGAAGCAGCUGCAGUUGUAAAUGCAACUGCAACA--------------GAGA--AAAA
(((.....)))...((.((((...((((....))))....(((..------..))))))))).......(.(((((((((....))))))))).).--------------....--.... ( -33.90)
>consensus
CGGAGGCGGUGAAUGUGUAGCCAAUCGGGGCAUCGAAACCGGCGU______AAGCCGCUAACAGAAGCAGCUGCAGAUGUAGCUGCAACUGCAACUGCAUUUACAACCAAGGGAACCAAG
....((..((((((((.((((...((((....))))....(((..........))))))).(((..((((((((....))))))))..))).....))))))))..))............ (-31.46 = -33.60 +   2.14)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:36:38 2006