Locus 5498

Sequence ID 3L_DroMel_CAF1
Location 15,079,461 – 15,079,551
Length 90
Max. P 0.981277
window8692 window8693

overview

Window 2

Location 15,079,461 – 15,079,551
Length 90
Sequences 6
Columns 100
Reading direction forward
Mean pairwise identity 75.52
Mean single sequence MFE -26.88
Consensus MFE -12.96
Energy contribution -13.77
Covariance contribution 0.81
Combinations/Pair 1.19
Mean z-score -2.57
Structure conservation index 0.48
SVM decision value 1.88
SVM RNA-class probability 0.981277
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15079461 90 + 23771897
CAG------AAGCCAAGGCAUCUGGAAUUUCAAAAGAAGAGGAAAUAAAUGAUCUACUCAAAUGCUUGGGCAGCAAACUGCCAAAGGG----UAAUUAGA
(((------(.((....)).))))..............(((...............)))...(((((.(((((....)))))...)))----))...... ( -21.26)
>DroSec_CAF1 44481 94 + 1
CAG------AAGCCAAGGCAUCUGGAAUUUCCAAAGAAGAGGAAAUAAAUGAUCUGCUCAAGUGCUUGGGCAGCAAAUUGCCAAAGGGUUCGUGAUUUGA
(((------(.((....)).))))..((((((........)))))).......((((((((....))))))))(((((..(.((....)).)..))))). ( -27.50)
>DroSim_CAF1 57158 94 + 1
CAG------AAGCCAAGGCAUCUGGAAUUUCCAAAGAAGAGGAAAUAAAUGAUCUGCUCAAGUGCUUGGGCAGCAAAUUGCCAAAGGGUUCGUGAUUAGA
..(------((.((..((((..((..((((((........)))))).......((((((((....))))))))))...))))...)).)))......... ( -27.30)
>DroEre_CAF1 46370 89 + 1
CCG------AAUCCAAGACAUCCGUGCUUUCAAAAGAAGAGGAAAUAAAUGACCUGCUCAAAUGCCUGGGCAGCAAACUGCCAAAGGGUUCGUA---A--
.((------(((((......(((...((((.....)))).)))..........(((((((......)))))))............)))))))..---.-- ( -23.90)
>DroYak_CAF1 45985 92 + 1
CGG------AAUCCAAGGCAUCCGUACUUUCAAAGGAAGAGGAAAUAAAUGACCUGCUCAAAUGCCUGGGCAGUAAAUUGCCAAAGGGUUCGUAAUAA--
..(------(((((..(((((((...((((.....)))).)))..........(((((((......))))))).....))))...)))))).......-- ( -27.80)
>DroPer_CAF1 50259 100 + 1
CAGGAACUCCUGCCAAGCAAUCGAAGGAUGUCAGGGGCUACGAAGUGAACGAGCUGCUGAAGUGCUUGGGCAGCAGAUUGCAGAUGGGUUAGAGACUGUU
((((....))))((((((((((....))).((((.((((.((.......)))))).))))..)))))))((((....)))).(((((........))))) ( -33.50)
>consensus
CAG______AAGCCAAGGCAUCUGGAAUUUCAAAAGAAGAGGAAAUAAAUGAUCUGCUCAAAUGCUUGGGCAGCAAAUUGCCAAAGGGUUCGUAAUUAGA
............((..(((((((....((((....)))).)))..........((((((((....)))))))).....))))...))............. (-12.96 = -13.77 +   0.81)

alignment

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secondary structure

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dotplot

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Window 3

Location 15,079,461 – 15,079,551
Length 90
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 75.52
Mean single sequence MFE -24.00
Consensus MFE -10.14
Energy contribution -10.53
Covariance contribution 0.39
Combinations/Pair 1.35
Mean z-score -2.37
Structure conservation index 0.42
SVM decision value 1.07
SVM RNA-class probability 0.911038
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15079461 90 - 23771897
UCUAAUUA----CCCUUUGGCAGUUUGCUGCCCAAGCAUUUGAGUAGAUCAUUUAUUUCCUCUUCUUUUGAAAUUCCAGAUGCCUUGGCUU------CUG
((((.(((----..(((.(((((....))))).)))....))).))))..............(((....)))....((((.((....)).)------))) ( -18.80)
>DroSec_CAF1 44481 94 - 1
UCAAAUCACGAACCCUUUGGCAAUUUGCUGCCCAAGCACUUGAGCAGAUCAUUUAUUUCCUCUUCUUUGGAAAUUCCAGAUGCCUUGGCUU------CUG
.........(((.((...((((.((((((((.(((....))).)))).......((((((........))))))..))))))))..)).))------).. ( -24.30)
>DroSim_CAF1 57158 94 - 1
UCUAAUCACGAACCCUUUGGCAAUUUGCUGCCCAAGCACUUGAGCAGAUCAUUUAUUUCCUCUUCUUUGGAAAUUCCAGAUGCCUUGGCUU------CUG
.........(((.((...((((.((((((((.(((....))).)))).......((((((........))))))..))))))))..)).))------).. ( -24.30)
>DroEre_CAF1 46370 89 - 1
--U---UACGAACCCUUUGGCAGUUUGCUGCCCAGGCAUUUGAGCAGGUCAUUUAUUUCCUCUUCUUUUGAAAGCACGGAUGUCUUGGAUU------CGG
--.---..((((.((...(((((....))))).(((((((((.(((((..........))).(((....))).)).))))))))).)).))------)). ( -27.70)
>DroYak_CAF1 45985 92 - 1
--UUAUUACGAACCCUUUGGCAAUUUACUGCCCAGGCAUUUGAGCAGGUCAUUUAUUUCCUCUUCCUUUGAAAGUACGGAUGCCUUGGAUU------CCG
--.......(((.((...((((......)))).(((((((((.((...(((.................)))..)).))))))))).)).))------).. ( -21.03)
>DroPer_CAF1 50259 100 - 1
AACAGUCUCUAACCCAUCUGCAAUCUGCUGCCCAAGCACUUCAGCAGCUCGUUCACUUCGUAGCCCCUGACAUCCUUCGAUUGCUUGGCAGGAGUUCCUG
..(((.((((...(((...((((((((((.....))))..((((..(((((.......)).)))..))))........)))))).)))..))))...))) ( -27.90)
>consensus
UCUAAUCACGAACCCUUUGGCAAUUUGCUGCCCAAGCACUUGAGCAGAUCAUUUAUUUCCUCUUCUUUGGAAAUUCCAGAUGCCUUGGCUU______CUG
.............((...(((.(((((((((.(((....))).))))...............(((....)))....))))))))..))............ (-10.14 = -10.53 +   0.39)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:51:48 2006