Locus 6683

Sequence ID 2L_DroMel_CAF1
Location 18,719,806 – 18,719,957
Length 151
Max. P 0.999894
window10661 window10662 window10663

overview

Window 1

Location 18,719,806 – 18,719,917
Length 111
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.11
Mean single sequence MFE -41.46
Consensus MFE -36.90
Energy contribution -37.02
Covariance contribution 0.12
Combinations/Pair 1.07
Mean z-score -3.70
Structure conservation index 0.89
SVM decision value 4.42
SVM RNA-class probability 0.999894
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18719806 111 + 22407834
GAGCCUGCGAUCUAGCGGGCGUUGGAACAAUGGA--------GCUGGGGCCAAAA-AAAGGAAACCUAACUGUAACAUGGCAGGCUACGAGCUCCUUUUUUUGGCCAUAAGCAUGAAAUA
..((((((......))))))..............--------(((..((((((((-((((((.......((((......))))((.....))))))))))))))))...)))........ ( -44.40)
>DroSec_CAF1 12527 111 + 1
GAGCCUGCGAUCUAGCGGGCGUUGGAACAAUGGA--------GCUGGGGCCAAAA-AAAGGAAACCUAACUGUAACAUGGCAGGCUACGAGCUCCUUUUUUUGGCCAUAAGCAUGAAAUA
..((((((......))))))..............--------(((..((((((((-((((((.......((((......))))((.....))))))))))))))))...)))........ ( -44.40)
>DroSim_CAF1 10962 112 + 1
GAGCCUGCGAUCUAGCGGGCGUUGGAACAAUGGA--------GCUGGGGCCAAAAAAAAGGAAACCUAACUGUAACUUGGCAGGCUACGAGCUCCUUUUUUUGGCCAUAAGCAUGAAAUA
..((((((......))))))..............--------(((..(((((((((((.(((.......((((......))))((.....))))))))))))))))...)))........ ( -40.60)
>DroEre_CAF1 12690 111 + 1
GAGCCUGCGAUCUAGCGGGCGUUGGAACAAUGGA--------GCUGGGACCAAAA-AAAGGAAACCUAACUGUAACAUGGCAGGCUACGAGCUCCUUUUUUUGGCCAUAAGCAUGAAAUA
..((((((......))))))..............--------(((.((.((((((-((((((.......((((......))))((.....))))))))))))))))...)))........ ( -40.20)
>DroYak_CAF1 12688 119 + 1
GAGCCUGCGAUCUAGCGGGCGUUGGAACAAUGGAGCUGUGGAGCUGGGGCCAAAA-AAAGGAAACCUAACUGUAACAUGGCAGCCUACGAGCUCCUUUUUUUGGUUAUAAGCAUGAAAUA
..((((((......))))))(((..(((...((((((((((.((((((.((....-...))...))...(........).)))))))).))))))........)))...)))........ ( -37.70)
>consensus
GAGCCUGCGAUCUAGCGGGCGUUGGAACAAUGGA________GCUGGGGCCAAAA_AAAGGAAACCUAACUGUAACAUGGCAGGCUACGAGCUCCUUUUUUUGGCCAUAAGCAUGAAAUA
..((((((......))))))......................(((..((((((((.((((((.......((((......))))((.....))))))))))))))))...)))........ (-36.90 = -37.02 +   0.12)

alignment

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secondary structure

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dotplot

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Window 2

Location 18,719,806 – 18,719,917
Length 111
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.11
Mean single sequence MFE -33.46
Consensus MFE -28.90
Energy contribution -29.18
Covariance contribution 0.28
Combinations/Pair 1.03
Mean z-score -2.46
Structure conservation index 0.86
SVM decision value 2.96
SVM RNA-class probability 0.997917
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18719806 111 - 22407834
UAUUUCAUGCUUAUGGCCAAAAAAAGGAGCUCGUAGCCUGCCAUGUUACAGUUAGGUUUCCUUU-UUUUGGCCCCAGC--------UCCAUUGUUCCAACGCCCGCUAGAUCGCAGGCUC
........(((...(((((((((((((((..(.((((.((........)))))).).)))))))-))))))))..)))--------..............(((.((......)).))).. ( -36.00)
>DroSec_CAF1 12527 111 - 1
UAUUUCAUGCUUAUGGCCAAAAAAAGGAGCUCGUAGCCUGCCAUGUUACAGUUAGGUUUCCUUU-UUUUGGCCCCAGC--------UCCAUUGUUCCAACGCCCGCUAGAUCGCAGGCUC
........(((...(((((((((((((((..(.((((.((........)))))).).)))))))-))))))))..)))--------..............(((.((......)).))).. ( -36.00)
>DroSim_CAF1 10962 112 - 1
UAUUUCAUGCUUAUGGCCAAAAAAAGGAGCUCGUAGCCUGCCAAGUUACAGUUAGGUUUCCUUUUUUUUGGCCCCAGC--------UCCAUUGUUCCAACGCCCGCUAGAUCGCAGGCUC
........(((...(((((((((((((((..(.((((.((........)))))).).)))).)))))))))))..)))--------..............(((.((......)).))).. ( -32.20)
>DroEre_CAF1 12690 111 - 1
UAUUUCAUGCUUAUGGCCAAAAAAAGGAGCUCGUAGCCUGCCAUGUUACAGUUAGGUUUCCUUU-UUUUGGUCCCAGC--------UCCAUUGUUCCAACGCCCGCUAGAUCGCAGGCUC
........(((...(((((((((((((((..(.((((.((........)))))).).)))))))-))))))))..)))--------..............(((.((......)).))).. ( -33.30)
>DroYak_CAF1 12688 119 - 1
UAUUUCAUGCUUAUAACCAAAAAAAGGAGCUCGUAGGCUGCCAUGUUACAGUUAGGUUUCCUUU-UUUUGGCCCCAGCUCCACAGCUCCAUUGUUCCAACGCCCGCUAGAUCGCAGGCUC
........(((.....(((((((((((((..(...(((((........))))).)..)))))))-))))))....)))......................(((.((......)).))).. ( -29.80)
>consensus
UAUUUCAUGCUUAUGGCCAAAAAAAGGAGCUCGUAGCCUGCCAUGUUACAGUUAGGUUUCCUUU_UUUUGGCCCCAGC________UCCAUUGUUCCAACGCCCGCUAGAUCGCAGGCUC
........(((...(((((((((((((((..(.(((.(((........)))))).).))))))).))))))))..)))......................(((.((......)).))).. (-28.90 = -29.18 +   0.28)

alignment

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secondary structure

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dotplot

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Window 3

Location 18,719,840 – 18,719,957
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.28
Mean single sequence MFE -36.14
Consensus MFE -29.20
Energy contribution -29.32
Covariance contribution 0.12
Combinations/Pair 1.06
Mean z-score -2.08
Structure conservation index 0.81
SVM decision value 0.96
SVM RNA-class probability 0.890992
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18719840 117 + 22407834
--GCUGGGGCCAAAA-AAAGGAAACCUAACUGUAACAUGGCAGGCUACGAGCUCCUUUUUUUGGCCAUAAGCAUGAAAUAUUGCGCACAUCCAAAGUGUCCACAUGUCGCUGCGAUCCGC
--((.((((((((((-((((((.......((((......))))((.....))))))))))))))))....(((.(..((((((.((((.......)))).)).))))..))))...)))) ( -38.70)
>DroSec_CAF1 12561 117 + 1
--GCUGGGGCCAAAA-AAAGGAAACCUAACUGUAACAUGGCAGGCUACGAGCUCCUUUUUUUGGCCAUAAGCAUGAAAUAUUGCGCACAUCCAAAGUGUCCACAUGUCGCUGCGAUCCGC
--((.((((((((((-((((((.......((((......))))((.....))))))))))))))))....(((.(..((((((.((((.......)))).)).))))..))))...)))) ( -38.70)
>DroSim_CAF1 10996 118 + 1
--GCUGGGGCCAAAAAAAAGGAAACCUAACUGUAACUUGGCAGGCUACGAGCUCCUUUUUUUGGCCAUAAGCAUGAAAUAUUGCGCACAUCCAAAGUGUCCACAUGUCGCUGCGAUCCGC
--((.(((((((((((((.(((.......((((......))))((.....))))))))))))))))....(((.(..((((((.((((.......)))).)).))))..))))...)))) ( -34.90)
>DroEre_CAF1 12724 117 + 1
--GCUGGGACCAAAA-AAAGGAAACCUAACUGUAACAUGGCAGGCUACGAGCUCCUUUUUUUGGCCAUAAGCAUGAAAUAUUGCGCACAUCCAAAGUGUCCACAUGUCGGAGCGAUCCGC
--(((.((.((((((-((((((.......((((......))))((.....))))))))))))))))...))).....((((((.((((.......)))).)).))))((((....)))). ( -35.70)
>DroYak_CAF1 12728 119 + 1
GAGCUGGGGCCAAAA-AAAGGAAACCUAACUGUAACAUGGCAGCCUACGAGCUCCUUUUUUUGGUUAUAAGCAUGAAAUAUUGCGCACAUCCAAAGUGUCCACAUGUCGGAGCGAUCCGC
..(((..((((((((-((((((.......((((......)))).........))))))))))))))...))).....((((((.((((.......)))).)).))))((((....)))). ( -32.69)
>consensus
__GCUGGGGCCAAAA_AAAGGAAACCUAACUGUAACAUGGCAGGCUACGAGCUCCUUUUUUUGGCCAUAAGCAUGAAAUAUUGCGCACAUCCAAAGUGUCCACAUGUCGCUGCGAUCCGC
..(((..((((((((.((((((.......((((......))))((.....))))))))))))))))...))).(((.....((.((((.......)))).))....)))..(((...))) (-29.20 = -29.32 +   0.12)

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 12:17:19 2006