Locus 4279

Sequence ID X_DroMel_CAF1
Location 11,256,150 – 11,256,301
Length 151
Max. P 0.985751
window7034 window7035 window7036

overview

Window 4

Location 11,256,150 – 11,256,264
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 85.81
Mean single sequence MFE -40.63
Consensus MFE -31.86
Energy contribution -31.42
Covariance contribution -0.44
Combinations/Pair 1.08
Mean z-score -1.67
Structure conservation index 0.78
SVM decision value 0.32
SVM RNA-class probability 0.686147
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11256150 114 - 22224390
UGGAGCUGCCGCAAGGAUGCAGGCCAUCUAUGUCCAGUUUGGUCUGCAUCCUGGAGAUCCUUACAUCCUUCAC------CACCUUCGGGGGAUUCUCGUGACCGAAAUGGACCAGGGAAA
.(((.((.((...(((((((((((((.((......))..))))))))))))))))).))).....(((((..(------((..(((((.............))))).)))...))))).. ( -41.92)
>DroSec_CAF1 15528 111 - 1
UGGAGCUGCCGCAAGGAUGCAGGCCAUCUAUGUCCAGCUUGGUCUGCAUCCUGGAGAUCCUUACAUCCUUCA---------CCUUGGAGGGCUCCUCGUAACCGAAAUGGACCAGGGAAA
.(((.((.((...(((((((((((((.((......))..))))))))))))))))).)))............---------(((((((((...))))....((.....))..)))))... ( -39.90)
>DroSim_CAF1 16164 111 - 1
UAGAGCUGCCGCAAGGAUGCAGGCCAUCUAUGUCCAUCUUGGUCUGCAUCCUGGAGAUCCGUACAUCCUUCA---------CCUUGCAGGGCUCCUCGUGACCGAAAUGGACCAGGGAAA
..(((((.(.((((((((((((((((.............))))))))))))(((((...........)))))---------..)))).))))))(((....((.....))....)))... ( -36.72)
>DroEre_CAF1 15300 111 - 1
UGGAGCUGCAGCAAGGAUGCAGGCCAUCUAUGUCCAGUUUGGUCUGCAUCCUGGAGAUCCUCACAUCCUUCACAU---------UGGCCUGCUCCUCGUGGCUGAAAUGGACCAGGGUGA
.(((.((.((....((((((((((((.((......))..)))))))))))))).)).)))...((((((((.(((---------(((((.((.....))))))..))))))..)))))). ( -42.90)
>DroYak_CAF1 15945 120 - 1
CGGAGCCGCAGCAAGGAUGCAGGCCAUCGAUGUCCAGUUUGGUCUGCAUCCUGGAAAUCCUCACAUCCCUCACAUCCCUCACCUUCGAGUGCUCCUCGUGGCCGAAAUGGACCAGGGAAA
.(((.((......(((((((((((((.(........)..)))))))))))))))...))).....(((((....(((.((.((..((((.....)))).))..))...)))..))))).. ( -41.70)
>consensus
UGGAGCUGCCGCAAGGAUGCAGGCCAUCUAUGUCCAGUUUGGUCUGCAUCCUGGAGAUCCUUACAUCCUUCAC________CCUUGGAGGGCUCCUCGUGACCGAAAUGGACCAGGGAAA
..(((..(((...(((((((((((((.............)))))))))))))(((..........))).....................)))..)))....((...........)).... (-31.86 = -31.42 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,256,190 – 11,256,301
Length 111
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 84.23
Mean single sequence MFE -38.50
Consensus MFE -29.16
Energy contribution -29.20
Covariance contribution 0.04
Combinations/Pair 1.21
Mean z-score -1.70
Structure conservation index 0.76
SVM decision value 0.29
SVM RNA-class probability 0.669271
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11256190 111 + 22224390
G------GUGAAGGAUGUAAGGAUCUCCAGGAUGCAGACCAAACUGGACAUAGAUGGCCUGCAUCCUUGCGGCAGCUCCAUUGAUUCCUUUGCCAACACUGACAGC---CCGCAGUCAUC
(------(..(((((..((((((.(((((((((((((.(((..(((....))).))).)))))))))...)).)).))).)))..)))))..)).....((((...---.....)))).. ( -42.10)
>DroSec_CAF1 15567 109 + 1
--------UGAAGGAUGUAAGGAUCUCCAGGAUGCAGACCAAGCUGGACAUAGAUGGCCUGCAUCCUUGCGGCAGCUCCAUUGAUUCCUUCGCCAGCACUGACAAC---CCGCCGUCCUC
--------.((((((..((((((.(((((((((((((.(((..(((....))).))).)))))))))...)).)).))).)))..)))))).........(((...---.....)))... ( -36.60)
>DroSim_CAF1 16203 109 + 1
--------UGAAGGAUGUACGGAUCUCCAGGAUGCAGACCAAGAUGGACAUAGAUGGCCUGCAUCCUUGCGGCAGCUCUAUUGAUUCCUUCGCCAGCACUGACAAC---CCGCAGUCCAA
--------....((((....((....))(((((((((.(((..((....))...))).)))))))))((((((((..((..(((.....)))..))..))).....---))))))))).. ( -33.70)
>DroEre_CAF1 15336 112 + 1
-----AUGUGAAGGAUGUGAGGAUCUCCAGGAUGCAGACCAAACUGGACAUAGAUGGCCUGCAUCCUUGCUGCAGCUCCAUUGAUUCCCUUGCCAUCAGUGGCAAG---CCGCAGUCCUC
-----.............(((((.....(((((((((.(((..(((....))).))).)))))))))..((((.(((((((((((.........))))))))..))---).))))))))) ( -41.50)
>DroYak_CAF1 15985 117 + 1
GAGGGAUGUGAGGGAUGUGAGGAUUUCCAGGAUGCAGACCAAACUGGACAUCGAUGGCCUGCAUCCUUGCUGCGGCUCCGUUGAUUCCCUGGCC---AGUGGCAAGAAACCAAAGUCCUA
..(((((((.(((((.....(((.....(((((((((.(((.............))).))))))))).((....)))))......))))).)).---..(((.......)))..))))). ( -38.62)
>consensus
_______GUGAAGGAUGUAAGGAUCUCCAGGAUGCAGACCAAACUGGACAUAGAUGGCCUGCAUCCUUGCGGCAGCUCCAUUGAUUCCUUCGCCAGCACUGACAAC___CCGCAGUCCUC
.......((((((((..((((((.(((((((((((((.(((.............))).)))))))))...)).)).))).)))..)))))))).......(((...........)))... (-29.16 = -29.20 +   0.04)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,256,190 – 11,256,301
Length 111
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 84.23
Mean single sequence MFE -43.48
Consensus MFE -34.08
Energy contribution -34.60
Covariance contribution 0.52
Combinations/Pair 1.22
Mean z-score -2.62
Structure conservation index 0.78
SVM decision value 2.02
SVM RNA-class probability 0.985751
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11256190 111 - 22224390
GAUGACUGCGG---GCUGUCAGUGUUGGCAAAGGAAUCAAUGGAGCUGCCGCAAGGAUGCAGGCCAUCUAUGUCCAGUUUGGUCUGCAUCCUGGAGAUCCUUACAUCCUUCAC------C
((((..(((.(---((.......))).)))(((((.((......((....)).(((((((((((((.((......))..)))))))))))))...))))))).))))......------. ( -40.20)
>DroSec_CAF1 15567 109 - 1
GAGGACGGCGG---GUUGUCAGUGCUGGCGAAGGAAUCAAUGGAGCUGCCGCAAGGAUGCAGGCCAUCUAUGUCCAGCUUGGUCUGCAUCCUGGAGAUCCUUACAUCCUUCA--------
.......((.(---((.......))).))((((((......(((.((.((...(((((((((((((.((......))..))))))))))))))))).))).....)))))).-------- ( -43.40)
>DroSim_CAF1 16203 109 - 1
UUGGACUGCGG---GUUGUCAGUGCUGGCGAAGGAAUCAAUAGAGCUGCCGCAAGGAUGCAGGCCAUCUAUGUCCAUCUUGGUCUGCAUCCUGGAGAUCCGUACAUCCUUCA--------
..(((.(((((---(((..(..(((.((((......((....))..)))))))(((((((((((((.............))))))))))))))..))))))))..)))....-------- ( -42.82)
>DroEre_CAF1 15336 112 - 1
GAGGACUGCGG---CUUGCCACUGAUGGCAAGGGAAUCAAUGGAGCUGCAGCAAGGAUGCAGGCCAUCUAUGUCCAGUUUGGUCUGCAUCCUGGAGAUCCUCACAUCCUUCACAU-----
(((((((((((---((..(((.((((.........)))).)))))))))))..(((((((((((((.((......))..))))))))))))).....))))).............----- ( -49.60)
>DroYak_CAF1 15985 117 - 1
UAGGACUUUGGUUUCUUGCCACU---GGCCAGGGAAUCAACGGAGCCGCAGCAAGGAUGCAGGCCAUCGAUGUCCAGUUUGGUCUGCAUCCUGGAAAUCCUCACAUCCCUCACAUCCCUC
..(((..(((((((((((((...---)).))))))))))).(((((....)).(((((((((((((.(........)..)))))))))))))((....)).....)))......)))... ( -41.40)
>consensus
GAGGACUGCGG___GUUGUCAGUGCUGGCAAAGGAAUCAAUGGAGCUGCCGCAAGGAUGCAGGCCAUCUAUGUCCAGUUUGGUCUGCAUCCUGGAGAUCCUUACAUCCUUCAC_______
(((((((((((....((((((....)))))).....((....)).))))))..(((((((((((((.............))))))))))))).....))))).................. (-34.08 = -34.60 +   0.52)

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 11:21:05 2006