Locus 1963

Sequence ID X_DroMel_CAF1
Location 5,379,764 – 5,379,946
Length 182
Max. P 0.995539
window3191 window3192 window3193

overview

Window 1

Location 5,379,764 – 5,379,871
Length 107
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 80.03
Mean single sequence MFE -31.09
Consensus MFE -21.20
Energy contribution -22.70
Covariance contribution 1.50
Combinations/Pair 1.00
Mean z-score -2.48
Structure conservation index 0.68
SVM decision value 2.00
SVM RNA-class probability 0.985197
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5379764 107 - 22224390
GGACAAGGGGGCGUGGCCCCUUCGGUUGCGCCCCAUAAAAA-UGUCCUUCGAACUAUU---CACCCCUUCGUGGCCAUCCCGCCCCCUCUUCUCCCCUUUCCC-----CAUCAGGC
(((.(((((((((..(((.....)))..))))))......(-((.((..((((.....---......)))).)).)))..........))).)))........-----........ ( -31.10)
>DroSec_CAF1 61108 101 - 1
GGACAAGGGGGCGUGGCCCCUUCGGUUGCGCCCCAUAAAAA-UGUCCUUCGAACUAUU---UACCCCUUCCUGGCCAUCGCCC--CCU----UCCCCAAUCCC-----CGCCAGCC
(((((..((((((..(((.....)))..)))))).......-)))))...........---.........(((((........--...----...........-----.))))).. ( -32.50)
>DroSim_CAF1 48068 101 - 1
GGACAAGG-GGCGUGGCCCCUUCGGUUGCGCCCCAUAAAAA-UGUCCUUCGAACUAUU---CACCCCUUCCUGGCCAUCGCCCC-CCU----UCCCCAAUCCC-----CGCCAGCC
(((((.((-((((..(((.....)))..)))))).......-)))))...........---.........(((((.........-...----...........-----.))))).. ( -30.96)
>DroYak_CAF1 53696 107 - 1
-----AGGGGGCGUGGCCCCUUCGGUUGCGCCCCAUAAAAACUGUCCUUCGAACUACUACUCACCUCUUCCUAGACAACCCGACCACG----CCCCCACUCCCGCUGCUGCCCACC
-----.((((((((((.....(((((((......................((........))...(((....)))))).)))))))))----)))))......((....))..... ( -29.80)
>consensus
GGACAAGGGGGCGUGGCCCCUUCGGUUGCGCCCCAUAAAAA_UGUCCUUCGAACUAUU___CACCCCUUCCUGGCCAUCCCCCC_CCU____UCCCCAAUCCC_____CGCCAGCC
(((((..((((((..(((.....)))..))))))........)))))..................................................................... (-21.20 = -22.70 +   1.50)

alignment

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secondary structure

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dotplot

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Window 2

Location 5,379,799 – 5,379,911
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 82.35
Mean single sequence MFE -31.76
Consensus MFE -25.76
Energy contribution -25.96
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.85
Structure conservation index 0.81
SVM decision value 2.59
SVM RNA-class probability 0.995539
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5379799 112 - 22224390
AGAUAAAUCAAAAACCAUUUCCACCAACCGGACACACAGCGGACAAGGGGGCGUGGCCCCUUCGGUUGCGCCCCAUAAAAA-UGUCCUUCGAACUAUU-------CACCCCUUCGUGGCC
....................((((.((..((.........(((((..((((((..(((.....)))..)))))).......-)))))...((.....)-------).))..)).)))).. ( -33.10)
>DroSec_CAF1 61137 107 - 1
---UAAAUCAAAAGCCAUUUCCACCAACCGGACA--AAGCGGACAAGGGGGCGUGGCCCCUUCGGUUGCGCCCCAUAAAAA-UGUCCUUCGAACUAUU-------UACCCCUUCCUGGCC
---..........((((..(((.......)))..--....(((((..((((((..(((.....)))..)))))).......-)))))...........-------..........)))). ( -34.60)
>DroSim_CAF1 48098 106 - 1
---UAAAUCAAAUGCCAUUUCCACCAACCGGACA--AAGCGGACAAGG-GGCGUGGCCCCUUCGGUUGCGCCCCAUAAAAA-UGUCCUUCGAACUAUU-------CACCCCUUCCUGGCC
---..........((((..(((.......)))..--....(((((.((-((((..(((.....)))..)))))).......-)))))...........-------..........)))). ( -32.90)
>DroEre_CAF1 54281 99 - 1
---UAAAUCAAAAGCCAUGUCCAGCAGCCGGACA-----------AAGGGGCGUGGCCCCUUCGGUUGCGCCCCAUAAAAA-UGUCCUGCGAACUACUCACCAUUCACCCCUUC------
---....((....((........)).((.(((((-----------..((((((..(((.....)))..)))))).......-))))).))))......................------ ( -31.10)
>DroYak_CAF1 53732 102 - 1
---UAAAUCAAAAGCCGUUUCCACCAACCGGACA-----------AGGGGGCGUGGCCCCUUCGGUUGCGCCCCAUAAAAACUGUCCUUCGAACUACU----ACUCACCUCUUCCUAGAC
---..........................(((((-----------..((((((..(((.....)))..))))))........)))))...........----.................. ( -27.10)
>consensus
___UAAAUCAAAAGCCAUUUCCACCAACCGGACA___AGCGGACAAGGGGGCGUGGCCCCUUCGGUUGCGCCCCAUAAAAA_UGUCCUUCGAACUAUU_______CACCCCUUCCUGGCC
.............................(((((.............((((((..(((.....)))..))))))........)))))................................. (-25.76 = -25.96 +   0.20)

alignment

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secondary structure

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dotplot

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Window 3

Location 5,379,831 – 5,379,946
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 85.80
Mean single sequence MFE -38.86
Consensus MFE -30.96
Energy contribution -31.28
Covariance contribution 0.32
Combinations/Pair 1.09
Mean z-score -2.67
Structure conservation index 0.80
SVM decision value 2.19
SVM RNA-class probability 0.989904
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5379831 115 - 22224390
UCAAAUUCGGUUGGGCAGCCAG-----CAGAAUGUUCGAUAGAUAAAUCAAAAACCAUUUCCACCAACCGGACACACAGCGGACAAGGGGGCGUGGCCCCUUCGGUUGCGCCCCAUAAAA
.....(((((((((((.....)-----).........(((......)))..............)))))))))...............((((((..(((.....)))..))))))...... ( -38.50)
>DroSec_CAF1 61169 109 - 1
UCAAAUUCGGUUGGGCAGCCAG-----CAGAAUGUUCGA----UAAAUCAAAAGCCAUUUCCACCAACCGGACA--AAGCGGACAAGGGGGCGUGGCCCCUUCGGUUGCGCCCCAUAAAA
....((((.(((((....))))-----).))))((((((----....))....((....(((.......)))..--..))))))...((((((..(((.....)))..))))))...... ( -38.00)
>DroSim_CAF1 48130 108 - 1
UCAAAUUCGGCUGGGCAGCCAG-----CAGAAUGUUCGA----UAAAUCAAAUGCCAUUUCCACCAACCGGACA--AAGCGGACAAGG-GGCGUGGCCCCUUCGGUUGCGCCCCAUAAAA
....((((.(((((....))))-----).))))((((((----....))....((....(((.......)))..--..))))))..((-((((..(((.....)))..))))))...... ( -40.40)
>DroEre_CAF1 54314 103 - 1
UCAAUUUCGGUUGGGCGGCCAGC--AGCAGAAUGUUCGA----UAAAUCAAAAGCCAUGUCCAGCAGCCGGACA-----------AAGGGGCGUGGCCCCUUCGGUUGCGCCCCAUAAAA
.....((((((((((((((.(((--(......)))).((----....))....)))..)))))...))))))..-----------..((((((..(((.....)))..))))))...... ( -39.20)
>DroYak_CAF1 53768 105 - 1
UCAAUUUCGGUUGGGCAGCCAGUGGAGUAAAAUGUUCGA----UAAAUCAAAAGCCGUUUCCACCAACCGGACA-----------AGGGGGCGUGGCCCCUUCGGUUGCGCCCCAUAAAA
.....((((((((((...)).((((((.......((.((----....)).))......))))))))))))))..-----------..((((((..(((.....)))..))))))...... ( -38.22)
>consensus
UCAAAUUCGGUUGGGCAGCCAG_____CAGAAUGUUCGA____UAAAUCAAAAGCCAUUUCCACCAACCGGACA___AGCGGACAAGGGGGCGUGGCCCCUUCGGUUGCGCCCCAUAAAA
.....((((((((((((...............)))..((........))..............)))))))))...............((((((..(((.....)))..))))))...... (-30.96 = -31.28 +   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 10:22:57 2006