Locus 2259

Sequence ID 3R_DroMel_CAF1
Location 6,406,853 – 6,406,983
Length 130
Max. P 0.986226
window3660 window3661 window3662

overview

Window 0

Location 6,406,853 – 6,406,966
Length 113
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 69.38
Mean single sequence MFE -26.48
Consensus MFE -15.80
Energy contribution -16.58
Covariance contribution 0.79
Combinations/Pair 1.52
Mean z-score -2.08
Structure conservation index 0.60
SVM decision value 2.03
SVM RNA-class probability 0.986226
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6406853 113 - 27905053
UAAUAUCUUUCUUUAGGUGUUCAGUAAAA-----UCGGAUUUAUCGAUUAUAGAUUUUCGAAAUUACCUUAAGAGAGCUUUACUACAUUGCUCUCAAUGAUCUUGUAACUUCUAUAAA
.............((((.(((((((((..-----(((((...(((.......))).)))))..)))).....((((((...........))))))........)).))).)))).... ( -20.80)
>DroPse_CAF1 169259 94 - 1
-----ACUCUCUUUAAGUUUUCAUGGAAAUCAAAAC----------------GAUUUCUGGAAUAAUUUCGGGAGAGUUACGAUUAUUUGCAUGGGUUGAACCUGGAACUA---AAAC
-----(((((((..((((((((.((((((((.....----------------))))))))))).)))))..))))))).....(((.((.((.((......)))).)).))---)... ( -23.80)
>DroSec_CAF1 170630 117 - 1
U-AUAUCUUUCUUUAGGGGUUUAGGAAAAUCAAAUCGGAAUUUUCGAUUAUAGAUUUUCGAAACUACCUUAAGAGAGCUUUACUACAUUGCUCUCAACGAUCUUGGAACUUUUAUAAA
(-(((...((((((((((((((..(((((((.(((((((...)))))))...))))))).))))..))))))((((((...........)))))).........))))....)))).. ( -27.80)
>DroSim_CAF1 194780 117 - 1
U-AUAUCUUUCUUUAGGUGGUUAUGAAAAUCGAAUCGGAAUUUUCGAUUAUAGAUUUUCGAAAUGACCUUAAGGGAGCUUUACUACAUUGCUCUCAACGAUCUUGGAACUUUUAUAAA
(-(((...((((..((((.(((.((((((((.(((((((...)))))))...)))))))).))).))))...((((((...........)))))).........))))....)))).. ( -30.60)
>DroEre_CAF1 181854 117 - 1
U-AUUUCCGUCUUUUGGUGUUCAGGAAAAUCGGAUCGGAAUUUUCGAUUAUCGGUUUUUGAAAUGACCUCAAGAGAGCUGUACUCACUUGCUGCCAUUGCUCAUGAACCUUUUAUAAA
.-....(((.....))).......((.(((((((........))))))).))(((((.(((((((.(..((((.(((.....))).))))..).))))..))).)))))......... ( -23.80)
>DroYak_CAF1 174752 117 - 1
U-AUUUCCACCUUUAGGUCUUCUGGAAAAUCGGAUCGGAAUUUUCGAUUAUCGGUUUUUGAAAUGACCUCAAGGGAGUUUUACUAAGCUGCUCGCUUUGAUCCUGGAACAUUUAUUAA
.-..((((.((((.(((((...(.(((((((((((((((...)))))))..)))))))).)...))))).)))).((..(((..((((.....)))))))..)))))).......... ( -32.10)
>consensus
U_AUAUCUUUCUUUAGGUGUUCAGGAAAAUCGAAUCGGAAUUUUCGAUUAUAGAUUUUCGAAAUGACCUCAAGAGAGCUUUACUAAAUUGCUCUCAAUGAUCUUGGAACUUUUAUAAA
......(((((((.(((((.....(((((((.((((((.....))))))...))))))).....))))).)))))))......................................... (-15.80 = -16.58 +   0.79)

alignment

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secondary structure

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dotplot

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Window 1

Location 6,406,893 – 6,406,983
Length 90
Sequences 5
Columns 95
Reading direction forward
Mean pairwise identity 80.08
Mean single sequence MFE -16.30
Consensus MFE -6.82
Energy contribution -6.90
Covariance contribution 0.08
Combinations/Pair 1.15
Mean z-score -2.09
Structure conservation index 0.42
SVM decision value 0.09
SVM RNA-class probability 0.578815
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6406893 90 + 27905053
GCUCUCUUAAGGUAAUUUCGAAAAUCUAUAAUCGAUAAAUCCGA-----UUUUACUGAACACCUAAAGAAAGAUAUUACUACACUACCAUCCUAA
.((.((((.((((..((...((((((................))-----))))...))..)))).)))).))....................... ( -10.49)
>DroSec_CAF1 170670 92 + 1
GCUCUCUUAAGGUAGUUUCGAAAAUCUAUAAUCGAAAAUUCCGAUUUGAUUUUCCUAAACCCCUAAAGAAAGAUAU-AAUGCACUACCAUCU--G
.((.((((.(((..((((.(((((((...(((((.......))))).)))))))..)))).))).)))).))....-...............--. ( -18.30)
>DroSim_CAF1 194820 94 + 1
GCUCCCUUAAGGUCAUUUCGAAAAUCUAUAAUCGAAAAUUCCGAUUCGAUUUUCAUAACCACCUAAAGAAAGAUAU-ACUGCACUACUAUCCUAA
.((..(((.((((..((..(((((((...(((((.......))))).)))))))..))..)))).)))..))....-.................. ( -15.40)
>DroEre_CAF1 181894 94 + 1
GCUCUCUUGAGGUCAUUUCAAAAACCGAUAAUCGAAAAUUCCGAUCCGAUUUUCCUGAACACCAAAAGACGGAAAU-ACUGCACUAGCAGCCAAA
.((.((((..(((...((((((((.((...((((.......)))).)).))))..)))).)))..)))).))....-.((((....))))..... ( -15.60)
>DroYak_CAF1 174792 94 + 1
ACUCCCUUGAGGUCAUUUCAAAAACCGAUAAUCGAAAAUUCCGAUCCGAUUUUCCAGAAGACCUAAAGGUGGAAAU-ACUGCACUAGUUUCCAAA
....((((.(((((.(((..((((.((...((((.......)))).)).))))..))).))))).))))(((((((-.........))))))).. ( -21.70)
>consensus
GCUCUCUUAAGGUCAUUUCGAAAAUCUAUAAUCGAAAAUUCCGAUCCGAUUUUCCUGAACACCUAAAGAAAGAUAU_ACUGCACUACCAUCCAAA
.((.((((.((((..((...((((......((((.......))))....))))...))..)))).)))).))....................... ( -6.82 =  -6.90 +   0.08)

alignment

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secondary structure

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dotplot

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Window 2

Location 6,406,893 – 6,406,983
Length 90
Sequences 5
Columns 95
Reading direction reverse
Mean pairwise identity 80.08
Mean single sequence MFE -25.06
Consensus MFE -16.18
Energy contribution -16.50
Covariance contribution 0.32
Combinations/Pair 1.41
Mean z-score -2.40
Structure conservation index 0.65
SVM decision value 1.60
SVM RNA-class probability 0.966807
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6406893 90 - 27905053
UUAGGAUGGUAGUGUAGUAAUAUCUUUCUUUAGGUGUUCAGUAAAA-----UCGGAUUUAUCGAUUAUAGAUUUUCGAAAUUACCUUAAGAGAGC
.......................(((((((.(((((....(.((((-----((.((((....))))...))))))).....))))).))))))). ( -16.70)
>DroSec_CAF1 170670 92 - 1
C--AGAUGGUAGUGCAUU-AUAUCUUUCUUUAGGGGUUUAGGAAAAUCAAAUCGGAAUUUUCGAUUAUAGAUUUUCGAAACUACCUUAAGAGAGC
.--.((((......))))-....(((((((.((((((((..(((((((.(((((((...)))))))...))))))).))))).))).))))))). ( -25.30)
>DroSim_CAF1 194820 94 - 1
UUAGGAUAGUAGUGCAGU-AUAUCUUUCUUUAGGUGGUUAUGAAAAUCGAAUCGGAAUUUUCGAUUAUAGAUUUUCGAAAUGACCUUAAGGGAGC
..................-....((..(((.((((.(((.((((((((.(((((((...)))))))...)))))))).))).)))).)))..)). ( -28.10)
>DroEre_CAF1 181894 94 - 1
UUUGGCUGCUAGUGCAGU-AUUUCCGUCUUUUGGUGUUCAGGAAAAUCGGAUCGGAAUUUUCGAUUAUCGGUUUUUGAAAUGACCUCAAGAGAGC
....(((((....)))))-.......((((((((.((.((.(((((((((((((((...)))))))..))))))))....)))).)))))))).. ( -26.50)
>DroYak_CAF1 174792 94 - 1
UUUGGAAACUAGUGCAGU-AUUUCCACCUUUAGGUCUUCUGGAAAAUCGGAUCGGAAUUUUCGAUUAUCGGUUUUUGAAAUGACCUCAAGGGAGU
..((((((((.....)))-..)))))((((.(((((...(.(((((((((((((((...)))))))..)))))))).)...))))).)))).... ( -28.70)
>consensus
UUAGGAUGGUAGUGCAGU_AUAUCUUUCUUUAGGUGUUCAGGAAAAUCGAAUCGGAAUUUUCGAUUAUAGAUUUUCGAAAUGACCUUAAGAGAGC
..((((((............))))))((((.(((((.....(((((((.(((((((...)))))))...))))))).....))))).)))).... (-16.18 = -16.50 +   0.32)

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 10:31:04 2006