Locus 71

Sequence ID 4_DroMel_CAF1
Location 550,255 – 550,415
Length 160
Max. P 0.986628
window114 window115 window116

overview

Window 4

Location 550,255 – 550,375
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 78.59
Mean single sequence MFE -36.64
Consensus MFE -24.08
Energy contribution -22.80
Covariance contribution -1.28
Combinations/Pair 1.35
Mean z-score -2.46
Structure conservation index 0.66
SVM decision value 2.05
SVM RNA-class probability 0.986628
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 550255 120 + 1281640
UGAUGAAUUCAUAACUAUACCAACCAACACGGCUGCCUUGCAGGCUUUCCAAACAGCUGUGGCUGCAGCUGCUCUAGCUGCAGUGCAUCAAAGAUGCGCCGUUAUAAAUCCACCGACACA
.(.((.(((.(((((............((((((((((.....))).........)))))))((((((((((...))))))))))(((((...)))))...))))).))).)).)...... ( -36.70)
>DroPse_CAF1 3756 117 + 1
UGACGACUUCAUGAGUAUACCAACAAACACGGCGGCUCUGCAAGCCUUCCAAACUGCGGUUGCAGCCGCAGCCAUAGCAGCGGUCCAACAACGCUGUAGUGCCAUCAACAUGCCUAG---
.........((((.((......))...((((((((((.....))))........((((((....)))))))))...((((((.........)))))).))).......)))).....--- ( -33.50)
>DroSim_CAF1 1938 120 + 1
UGAUGAGUUUAUAACUAUACCAACCAACACGGCUGCCCUGCAGGCUUUCCAAACAGCUGUGGCUGCAGCUGCUCUAGCUGCCGUGCAUCAAAGAUGCGCUGUUAUAAAUCCACCGAUACA
.(.((..((((((((............((((((((((.....))).........)))))))...(((((((...))))))).(((((((...))))))).))))))))..)).)...... ( -37.40)
>DroEre_CAF1 3374 116 + 1
UGAUGAAUUUAUAAGUAUACCAACCAAUACGGCUGCUCUGCAGGCUUUCCAAACAGCUGUAGCAGCAGCUGCUCUAGCUGCAGUGCAUCAAAGAUGCGCUGCUAUAAAUCCACCGA----
.(.((.(((((((................((((((((((((((.((........)))))))).))))))))........((((((((((...))))))))))))))))).)).)..---- ( -42.10)
>DroPer_CAF1 5378 117 + 1
UGACGACUUCAUGAGUAUACCAACAAACACGGCGGCUCUGCAAGCCUUCCAAACUGCGGUUGCAGCCGCAGCCAUAGCAGCGGUCCAACAACGCUGUAGUGCCAUCAACAUGCCUAG---
.........((((.((......))...((((((((((.....))))........((((((....)))))))))...((((((.........)))))).))).......)))).....--- ( -33.50)
>consensus
UGAUGAAUUCAUAAGUAUACCAACCAACACGGCUGCUCUGCAGGCUUUCCAAACAGCUGUGGCAGCAGCUGCUCUAGCUGCAGUGCAUCAAAGAUGCGCUGCUAUAAAUCCACCGAG___
.(.((.(((.(((.................((..(((.....)))...))...(((((((....)))))))........((((((((((...))))))))))))).))).)).)...... (-24.08 = -22.80 +  -1.28)

alignment

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secondary structure

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dotplot

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Window 5

Location 550,255 – 550,375
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 78.59
Mean single sequence MFE -43.06
Consensus MFE -31.12
Energy contribution -30.32
Covariance contribution -0.80
Combinations/Pair 1.25
Mean z-score -2.12
Structure conservation index 0.72
SVM decision value 1.57
SVM RNA-class probability 0.964463
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 550255 120 - 1281640
UGUGUCGGUGGAUUUAUAACGGCGCAUCUUUGAUGCACUGCAGCUAGAGCAGCUGCAGCCACAGCUGUUUGGAAAGCCUGCAAGGCAGCCGUGUUGGUUGGUAUAGUUAUGAAUUCAUCA
......((((((((((((((((((((((...)))))..(((((((.....)))))))))).((((((..(((...(((.....)))..)))...)))))).....)))))))))))))). ( -51.30)
>DroPse_CAF1 3756 117 - 1
---CUAGGCAUGUUGAUGGCACUACAGCGUUGUUGGACCGCUGCUAUGGCUGCGGCUGCAACCGCAGUUUGGAAGGCUUGCAGAGCCGCCGUGUUUGUUGGUAUACUCAUGAAGUCGUCA
---...(((......(((((....(((((.........)))))(((.((((((((......)))))))))))..(((((...)))))))))).((..(.((....)).)..))...))). ( -35.50)
>DroSim_CAF1 1938 120 - 1
UGUAUCGGUGGAUUUAUAACAGCGCAUCUUUGAUGCACGGCAGCUAGAGCAGCUGCAGCCACAGCUGUUUGGAAAGCCUGCAGGGCAGCCGUGUUGGUUGGUAUAGUUAUAAACUCAUCA
......((((..((((((((...(((((...)))))(((((.....(((((((((......))))))))).....(((.....))).))))).............))))))))..)))). ( -45.40)
>DroEre_CAF1 3374 116 - 1
----UCGGUGGAUUUAUAGCAGCGCAUCUUUGAUGCACUGCAGCUAGAGCAGCUGCUGCUACAGCUGUUUGGAAAGCCUGCAGAGCAGCCGUAUUGGUUGGUAUACUUAUAAAUUCAUCA
----..((((((((((((((((.(((((...))))).))))((((((.((.((((((.((.(((((........)).))).)))))))).)).))))))........)))))))))))). ( -47.60)
>DroPer_CAF1 5378 117 - 1
---CUAGGCAUGUUGAUGGCACUACAGCGUUGUUGGACCGCUGCUAUGGCUGCGGCUGCAACCGCAGUUUGGAAGGCUUGCAGAGCCGCCGUGUUUGUUGGUAUACUCAUGAAGUCGUCA
---...(((......(((((....(((((.........)))))(((.((((((((......)))))))))))..(((((...)))))))))).((..(.((....)).)..))...))). ( -35.50)
>consensus
___CUCGGUGGAUUUAUAGCAGCGCAUCUUUGAUGCACCGCAGCUAGAGCAGCUGCUGCAACAGCUGUUUGGAAAGCCUGCAGAGCAGCCGUGUUGGUUGGUAUACUUAUGAAGUCAUCA
......(((((.(((((((....(((((...)))))...((((((.(((((((((......)))))))))....))).)))......((((.......))))....))))))).))))). (-31.12 = -30.32 +  -0.80)

alignment

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secondary structure

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dotplot

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Window 6

Location 550,295 – 550,415
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 70.05
Mean single sequence MFE -33.52
Consensus MFE -21.98
Energy contribution -22.06
Covariance contribution 0.08
Combinations/Pair 1.25
Mean z-score -1.18
Structure conservation index 0.66
SVM decision value 0.09
SVM RNA-class probability 0.580013
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 550295 120 + 1281640
CAGGCUUUCCAAACAGCUGUGGCUGCAGCUGCUCUAGCUGCAGUGCAUCAAAGAUGCGCCGUUAUAAAUCCACCGACACAGGAUACCGUCGAUGAAGACAAGGACUUAGAUACGAAUGUC
..(((................((((((((((...))))))))))(((((...))))))))((..(((.(((.((......)).....(((......)))..))).)))...))....... ( -36.60)
>DroPse_CAF1 3796 108 + 1
CAAGCCUUCCAAACUGCGGUUGCAGCCGCAGCCAUAGCAGCGGUCCAACAACGCUGUAGUGCCAUCAACAUGCCUAG------------AGAAGCAGAUACGGAAAUCGGUCCUUGCAUU
((((((((((...(((((((....))))))).(((.((((((.........)))))).))).........(((....------------....))).....))))...))..)))).... ( -30.10)
>DroSim_CAF1 1978 120 + 1
CAGGCUUUCCAAACAGCUGUGGCUGCAGCUGCUCUAGCUGCCGUGCAUCAAAGAUGCGCUGUUAUAAAUCCACCGAUACAGGAGACCGUCGACGAAGACAAGGACUUAGAUACGAAUGUC
..(((.(((..((((((....((.(((((((...))))))).))(((((...))))))))))).(((.(((.((......)).....(((......)))..))).))).....))).))) ( -35.80)
>DroEre_CAF1 3414 111 + 1
CAGGCUUUCCAAACAGCUGUAGCAGCAGCUGCUCUAGCUGCAGUGCAUCAAAGAUGCGCUGCUAUAAAUCCACCGA---------CCGUCGAGGAAGAUAAGGACAUAGAUACGAAUGUC
.....(((((....(((((.(((((...))))).)))))((((((((((...))))))))))..............---------.......))))).....(((((........))))) ( -35.00)
>DroPer_CAF1 5418 108 + 1
CAAGCCUUCCAAACUGCGGUUGCAGCCGCAGCCAUAGCAGCGGUCCAACAACGCUGUAGUGCCAUCAACAUGCCUAG------------AGAAGCAGAUACGGAAAUCGGUCCUUGCAUU
((((((((((...(((((((....))))))).(((.((((((.........)))))).))).........(((....------------....))).....))))...))..)))).... ( -30.10)
>consensus
CAGGCUUUCCAAACAGCUGUGGCAGCAGCUGCUCUAGCUGCAGUGCAUCAAAGAUGCGCUGCUAUAAAUCCACCGAG________CCGUCGAAGAAGAUAAGGACAUAGAUACGAAUGUC
.......(((...(((((((....)))))))........((((((((((...)))))))))).......................................)))................ (-21.98 = -22.06 +   0.08)

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 09:33:35 2006