Locus 6706

Sequence ID 3L_DroMel_CAF1
Location 17,902,287 – 17,902,422
Length 135
Max. P 0.960705
window10911 window10912 window10913 window10914

overview

Window 1

Location 17,902,287 – 17,902,383
Length 96
Sequences 4
Columns 103
Reading direction forward
Mean pairwise identity 87.23
Mean single sequence MFE -14.45
Consensus MFE -11.02
Energy contribution -11.28
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.54
Structure conservation index 0.76
SVM decision value 0.18
SVM RNA-class probability 0.619375
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17902287 96 + 23771897
CA-------ACUUCUGGCAUAAUUAACUCAAUUAAUGGCAGAGCCAAAAGUCGGCUGAAAAGAAACUCUUAUUUUCUACUCCCUCUCUCUUCUUUUUUUUUUU
..-------...((((.(((((((.....)))).))).))))(((.......))).((((((((.........................))))))))...... ( -13.41)
>DroSec_CAF1 26020 94 + 1
CAAGCAACCACUUCUGGCAUAAUUAACUCAAUUAAUGGCAAAGCCAAAAGUCGGCUGAAAAGAAACUCUUAUUUUCUUCUCCCUCUUCCU-----UU----UC
..(((....((((.((((...(((((.....)))))......)))).))))..)))((.((((((.......)))))).)).........-----..----.. ( -13.90)
>DroSim_CAF1 26289 98 + 1
CAAGCAACCACUUCUGGCAUAAUUAACUCAAUUAAUGGCAAAGCCAAAAGUCGGCUGAAAAGAAACUCUUAUUUUCUUCUCCCUUUUCCU-----UUUUAUUC
..(((....((((.((((...(((((.....)))))......)))).))))..)))((.((((((.......)))))).)).........-----........ ( -13.90)
>DroEre_CAF1 27259 98 + 1
CAAGCCACCACUUCUGGCAUAAUUAACUCAAUUAAUGGCAGAGCCAAAAGUCGGCUGAAAAGAAACUCUUAUUUUCUUCUCCCCCUCGCU-----UUUUAUUC
.((((.......((((.(((((((.....)))).))).))))(((.......))).((.((((((.......)))))).))......)))-----)....... ( -16.60)
>consensus
CAAGCAACCACUUCUGGCAUAAUUAACUCAAUUAAUGGCAAAGCCAAAAGUCGGCUGAAAAGAAACUCUUAUUUUCUUCUCCCUCUCCCU_____UUUUAUUC
.............(((((.(((((.....))))).((((...))))...)))))..((.((((((.......)))))).))...................... (-11.02 = -11.28 +   0.25)

alignment

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secondary structure

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dotplot

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Window 2

Location 17,902,287 – 17,902,383
Length 96
Sequences 4
Columns 103
Reading direction reverse
Mean pairwise identity 87.23
Mean single sequence MFE -24.98
Consensus MFE -19.83
Energy contribution -20.82
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.46
Structure conservation index 0.79
SVM decision value 1.52
SVM RNA-class probability 0.960705
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17902287 96 - 23771897
AAAAAAAAAAAGAAGAGAGAGGGAGUAGAAAAUAAGAGUUUCUUUUCAGCCGACUUUUGGCUCUGCCAUUAAUUGAGUUAAUUAUGCCAGAAGU-------UG
...........(((((((((.....((.....))....)))))))))...(((((((((((...((((.....)).)).......)))))))))-------)) ( -21.80)
>DroSec_CAF1 26020 94 - 1
GA----AA-----AGGAAGAGGGAGAAGAAAAUAAGAGUUUCUUUUCAGCCGACUUUUGGCUUUGCCAUUAAUUGAGUUAAUUAUGCCAGAAGUGGUUGCUUG
..----..-----.....(((.(((((((((.......)))))))))((((.(((((((((...((((.....)).)).......))))))))))))).))). ( -25.30)
>DroSim_CAF1 26289 98 - 1
GAAUAAAA-----AGGAAAAGGGAGAAGAAAAUAAGAGUUUCUUUUCAGCCGACUUUUGGCUUUGCCAUUAAUUGAGUUAAUUAUGCCAGAAGUGGUUGCUUG
........-----.....(((.(((((((((.......)))))))))((((.(((((((((...((((.....)).)).......))))))))))))).))). ( -24.90)
>DroEre_CAF1 27259 98 - 1
GAAUAAAA-----AGCGAGGGGGAGAAGAAAAUAAGAGUUUCUUUUCAGCCGACUUUUGGCUCUGCCAUUAAUUGAGUUAAUUAUGCCAGAAGUGGUGGCUUG
.......(-----(((......(((((((((.......))))))))).(((.(((((((((...((((.....)).)).......)))))))))))).)))). ( -27.90)
>consensus
GAAUAAAA_____AGGAAGAGGGAGAAGAAAAUAAGAGUUUCUUUUCAGCCGACUUUUGGCUCUGCCAUUAAUUGAGUUAAUUAUGCCAGAAGUGGUUGCUUG
......................(((((((((.......))))))))).(((.(((((((((...((((.....)).)).......))))))))))))...... (-19.83 = -20.82 +   1.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 17,902,320 – 17,902,422
Length 102
Sequences 4
Columns 103
Reading direction forward
Mean pairwise identity 89.37
Mean single sequence MFE -16.05
Consensus MFE -13.38
Energy contribution -14.12
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -1.43
Structure conservation index 0.83
SVM decision value 0.10
SVM RNA-class probability 0.582116
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17902320 102 + 23771897
GAGCCAAAAGUCGGCUGAAAAGAAACUCUUAUUUUCUACUCCCUCUCUCUUCUUUUUUUUUUUAAGAAUUCUGCAACACUUUCCUUGGCUCCA-AACGCUGAU
(((((((((((..((.(((.(((((.......)))))............(((((.........)))))))).))...))))...)))))))..-......... ( -18.40)
>DroSec_CAF1 26060 94 + 1
AAGCCAAAAGUCGGCUGAAAAGAAACUCUUAUUUUCUUCUCCCUCUUCCU-----UU----UCAAGAAUUCUGCACCACUUUCCUUGGCUCCAAAACGCUGAU
.((((((((((.(((.(((((((((.......)))))).....((((...-----..----..)))).))).)).).))))...))))))............. ( -14.80)
>DroSim_CAF1 26329 98 + 1
AAGCCAAAAGUCGGCUGAAAAGAAACUCUUAUUUUCUUCUCCCUUUUCCU-----UUUUAUUCAAGAAUUCUGCACCACUUUCCUUGGCUCCAAAACGCUGAU
.((((((((((.(((.(((((((((.......))))))..........((-----(.......)))..))).)).).))))...))))))............. ( -13.40)
>DroEre_CAF1 27299 97 + 1
GAGCCAAAAGUCGGCUGAAAAGAAACUCUUAUUUUCUUCUCCCCCUCGCU-----UUUUAUUCAAGAAUUCUGCACCACUUUCCUUGGCUCCA-AGCGCUGAU
(((((((((((.((..((.((((((.......)))))).))..))..((.-----((((.....))))....))...))))...)))))))..-......... ( -17.60)
>consensus
AAGCCAAAAGUCGGCUGAAAAGAAACUCUUAUUUUCUUCUCCCUCUCCCU_____UUUUAUUCAAGAAUUCUGCACCACUUUCCUUGGCUCCA_AACGCUGAU
(((((((((((..((.((.((((((.......)))))).)).......................((....))))...))))...)))))))............ (-13.38 = -14.12 +   0.75)

alignment

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secondary structure

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dotplot

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Window 4

Location 17,902,320 – 17,902,422
Length 102
Sequences 4
Columns 103
Reading direction reverse
Mean pairwise identity 89.37
Mean single sequence MFE -24.50
Consensus MFE -20.48
Energy contribution -20.54
Covariance contribution 0.06
Combinations/Pair 1.11
Mean z-score -1.96
Structure conservation index 0.84
SVM decision value 0.97
SVM RNA-class probability 0.891810
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17902320 102 - 23771897
AUCAGCGUU-UGGAGCCAAGGAAAGUGUUGCAGAAUUCUUAAAAAAAAAAAGAAGAGAGAGGGAGUAGAAAAUAAGAGUUUCUUUUCAGCCGACUUUUGGCUC
.........-..(((((((...((((...((....(((((.........)))))..(((((((((.............))))))))).))..))))))))))) ( -19.82)
>DroSec_CAF1 26060 94 - 1
AUCAGCGUUUUGGAGCCAAGGAAAGUGGUGCAGAAUUCUUGA----AA-----AGGAAGAGGGAGAAGAAAAUAAGAGUUUCUUUUCAGCCGACUUUUGGCUU
............(((((((...((((.(.((....(((((..----..-----)))))....(((((((((.......))))))))).))).))))))))))) ( -26.70)
>DroSim_CAF1 26329 98 - 1
AUCAGCGUUUUGGAGCCAAGGAAAGUGGUGCAGAAUUCUUGAAUAAAA-----AGGAAAAGGGAGAAGAAAAUAAGAGUUUCUUUUCAGCCGACUUUUGGCUU
............(((((((...((((.(.((....(((((........-----)))))....(((((((((.......))))))))).))).))))))))))) ( -25.20)
>DroEre_CAF1 27299 97 - 1
AUCAGCGCU-UGGAGCCAAGGAAAGUGGUGCAGAAUUCUUGAAUAAAA-----AGCGAGGGGGAGAAGAAAAUAAGAGUUUCUUUUCAGCCGACUUUUGGCUC
.........-..(((((((...((((.(.((....((((((.......-----..)))))).(((((((((.......))))))))).))).))))))))))) ( -26.30)
>consensus
AUCAGCGUU_UGGAGCCAAGGAAAGUGGUGCAGAAUUCUUGAAUAAAA_____AGGAAGAGGGAGAAGAAAAUAAGAGUUUCUUUUCAGCCGACUUUUGGCUC
............(((((((...((((.(.((....(((((................))))).(((((((((.......))))))))).))).))))))))))) (-20.48 = -20.54 +   0.06)

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 12:28:07 2006