Locus 2210

Sequence ID 2L_DroMel_CAF1
Location 5,965,881 – 5,966,027
Length 146
Max. P 0.995441
window3554 window3555 window3556

overview

Window 4

Location 5,965,881 – 5,965,989
Length 108
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 76.23
Mean single sequence MFE -27.15
Consensus MFE -12.74
Energy contribution -13.05
Covariance contribution 0.31
Combinations/Pair 1.32
Mean z-score -2.86
Structure conservation index 0.47
SVM decision value 2.14
SVM RNA-class probability 0.988997
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5965881 108 - 22407834
AAUCCUUUCAAUCCUUUCAACAGAGUUCUGGGAGCACCAGCUCCCGCUGCUCCA--ACGCAAAAUGGUAACUUUUUCCAGCGCGUCUUCAAAUUCAACCAGGACGCUGCC
......................((((..(((((((....)))))))..))))..--..(((...(((.........)))..(((((((...........)))))))))). ( -29.80)
>DroPse_CAF1 39260 96 - 1
AAUCCGUUUAAUCCAUUCAACAGAAUUCUGGGCGCUGCAGCUCCCACAACACCUCAGCCCCAAAAG--AAUGGAUUCCAGCGCAUUUUCCAGUUUGAC------------
....((((.(((((((((..(((....)))((.((((.((............)))))).))....)--))))))))..))))................------------ ( -23.30)
>DroSec_CAF1 21911 108 - 1
AAUCCUUUCAAUCCCUUGAACAGAGUUCUGGGAGCACCUGCUCCCGCUGCUCCA--ACGCAAAAUGGUAAUUUUUUCCAGCGCGUCUUCAAAUUCAACCAGGACGCUGCC
......(((((....)))))..((((..(((((((....)))))))..))))..--..(((...(((.........)))..(((((((...........)))))))))). ( -31.30)
>DroSim_CAF1 22028 108 - 1
AAUCCUUUCAAUCCUUUCAACAGAGUUCUGGGAGCACCAGCUCCCGCUGCUCCA--ACGCAAAAUGGUAACUUUUUCCAGCGCGUCUUCAAAUUCAACCAAGACGCUGCC
......................((((..(((((((....)))))))..))))..--..(((...(((.........)))..(((((((...........)))))))))). ( -30.10)
>DroEre_CAF1 26588 108 - 1
AACCCUUUCAAUCCAUUCAACAGAAUUCUGGGAGCACCAGCUCCCAAUCCGCCA--GCACAAAAUGGUCAAUUUUUCCAGCGUGUGUUCAAAUUCAACCAGGACGCUGCC
....................(((..((((((((((....))))))........(--(((((...(((.........)))...))))))...........))))..))).. ( -26.20)
>DroPer_CAF1 38990 96 - 1
AAUCCGUUUAAUCCGUUCAACAGAAUUCUGGGCGCUGCAGCUCCCACAACACCACAGCCCCAAAAG--AAUGGAUUCCAGCGCAUUUUCAAGUUUGAC------------
....((((.(((((((((..(((....)))((.((((.................)))).))....)--))))))))..))))................------------ ( -22.23)
>consensus
AAUCCUUUCAAUCCAUUCAACAGAAUUCUGGGAGCACCAGCUCCCACUGCUCCA__ACGCAAAAUGGUAAUUUUUUCCAGCGCGUCUUCAAAUUCAACCAGGACGCUGCC
......................(((((.(((((((....)))))))..........((((....(((.........)))..)))).....)))))............... (-12.74 = -13.05 +   0.31)

alignment

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secondary structure

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dotplot

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Window 5

Location 5,965,917 – 5,966,027
Length 110
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 74.16
Mean single sequence MFE -37.38
Consensus MFE -19.61
Energy contribution -20.45
Covariance contribution 0.84
Combinations/Pair 1.24
Mean z-score -1.62
Structure conservation index 0.52
SVM decision value 0.16
SVM RNA-class probability 0.611662
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5965917 110 + 22407834
AAAGUUACCAUUUUGCGU--UGGAGCAGCGGGAGCUGGUGCUCCCAGAACUCUGUUGAAAGGAUUGAAAGGAUUGAGGGCUCCGAAGGGUCCGAAUGGGUUCAUUCCCAUUC
.......((.(((..(.(--(....((((((((((....))))))((....)))))).)).)...))).)).....((((((....))))))(((((((......))))))) ( -36.90)
>DroPse_CAF1 39284 110 + 1
UCCAUU--CUUUUGGGGCUGAGGUGUUGUGGGAGCUGCAGCGCCCAGAAUUCUGUUGAAUGGAUUAAACGGAUUCAGGCUUCCGAAUGGGCCAAACGGGUUGAGACCCAUUC
((((((--(...((((.(((.(((((((..(...)..))))))))))...))))..)))))))......(((........)))(((((((((((.....))).).))))))) ( -39.90)
>DroSim_CAF1 22064 110 + 1
AAAGUUACCAUUUUGCGU--UGGAGCAGCGGGAGCUGGUGCUCCCAGAACUCUGUUGAAAGGAUUGAAAGGAUUGAGGGCUCCGAAGGGUCCGAAUGGGUUCAUUCCCAUUC
.......((.(((..(.(--(....((((((((((....))))))((....)))))).)).)...))).)).....((((((....))))))(((((((......))))))) ( -36.90)
>DroEre_CAF1 26624 110 + 1
AAAUUGACCAUUUUGUGC--UGGCGGAUUGGGAGCUGGUGCUCCCAGAAUUCUGUUGAAUGGAUUGAAAGGGUUCAGGGCUCCGAAAGGUCCGAAUGGGCUCAUUCCCAUUC
.....((((.(((((.((--(((((((((((((((....))))))))...))))))...((((((.....)))))).)))..))))))))).(((((((......))))))) ( -40.60)
>DroWil_CAF1 39914 105 + 1
AGGAUU--CAUGGUUGGUUGAGGUGUGGUUGGAGCUGGAGCUCCCAGUAUCCGAUUGAAGGGAUUGAAGGGAUUUAGAUUUCCCAAAGCUCCGAAUGGAUUCAAUAC-----
.(((((--(((..(..((((.((((..(..(((((....))))))..))))))))..).((..((...((((........))))..))..))..)))))))).....----- ( -32.00)
>DroPer_CAF1 39014 110 + 1
UCCAUU--CUUUUGGGGCUGUGGUGUUGUGGGAGCUGCAGCGCCCAGAAUUCUGUUGAACGGAUUAAACGGAUUCAGGCUUCCGAAUGGGCCAAACGGGCUCAGACCCAUUC
......--....((((.(((.(((((((..(...)..))))))))))...((((.....)))).....((((........))))..((((((.....))))))..))))... ( -38.00)
>consensus
AAAAUU__CAUUUUGGGC__UGGUGUAGUGGGAGCUGGAGCUCCCAGAAUUCUGUUGAAAGGAUUGAAAGGAUUCAGGGCUCCGAAAGGUCCGAAUGGGUUCAUUCCCAUUC
.....................((......((((((....)))))).((((((.(((....(((((....(((........)))....))))).)))))))))....)).... (-19.61 = -20.45 +   0.84)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,965,917 – 5,966,027
Length 110
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 74.16
Mean single sequence MFE -32.42
Consensus MFE -19.50
Energy contribution -20.62
Covariance contribution 1.11
Combinations/Pair 1.16
Mean z-score -2.68
Structure conservation index 0.60
SVM decision value 2.58
SVM RNA-class probability 0.995441
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5965917 110 - 22407834
GAAUGGGAAUGAACCCAUUCGGACCCUUCGGAGCCCUCAAUCCUUUCAAUCCUUUCAACAGAGUUCUGGGAGCACCAGCUCCCGCUGCUCCA--ACGCAAAAUGGUAACUUU
(((((((......)))))))(((......(((........)))......)))........((((..(((((((....)))))))..))))..--.................. ( -33.70)
>DroPse_CAF1 39284 110 - 1
GAAUGGGUCUCAACCCGUUUGGCCCAUUCGGAAGCCUGAAUCCGUUUAAUCCAUUCAACAGAAUUCUGGGCGCUGCAGCUCCCACAACACCUCAGCCCCAAAAG--AAUGGA
(((((((((...........)))))))))(((........)))......(((((((..(((....)))((.((((.((............)))))).))....)--)))))) ( -35.20)
>DroSim_CAF1 22064 110 - 1
GAAUGGGAAUGAACCCAUUCGGACCCUUCGGAGCCCUCAAUCCUUUCAAUCCUUUCAACAGAGUUCUGGGAGCACCAGCUCCCGCUGCUCCA--ACGCAAAAUGGUAACUUU
(((((((......)))))))(((......(((........)))......)))........((((..(((((((....)))))))..))))..--.................. ( -33.70)
>DroEre_CAF1 26624 110 - 1
GAAUGGGAAUGAGCCCAUUCGGACCUUUCGGAGCCCUGAACCCUUUCAAUCCAUUCAACAGAAUUCUGGGAGCACCAGCUCCCAAUCCGCCA--GCACAAAAUGGUCAAUUU
(((((((......)))))))(((......(((....((((....)))).)))..............(((((((....))))))).)))((((--........))))...... ( -34.40)
>DroWil_CAF1 39914 105 - 1
-----GUAUUGAAUCCAUUCGGAGCUUUGGGAAAUCUAAAUCCCUUCAAUCCCUUCAAUCGGAUACUGGGAGCUCCAGCUCCAACCACACCUCAACCAACCAUG--AAUCCU
-----(.(((((((((....))).....((((........)))).........)))))))((((....(((((....))))).........(((........))--))))). ( -23.20)
>DroPer_CAF1 39014 110 - 1
GAAUGGGUCUGAGCCCGUUUGGCCCAUUCGGAAGCCUGAAUCCGUUUAAUCCGUUCAACAGAAUUCUGGGCGCUGCAGCUCCCACAACACCACAGCCCCAAAAG--AAUGGA
(((((((.(..((....))..))))))))(((........)))......(((((((..(((....)))((.((((.................)))).))....)--)))))) ( -34.33)
>consensus
GAAUGGGAAUGAACCCAUUCGGACCAUUCGGAACCCUGAAUCCUUUCAAUCCAUUCAACAGAAUUCUGGGAGCACCAGCUCCCACUACACCA__ACCCAAAAUG__AAUUUU
(((((((......)))))))((.......(((........))).......................(((((((....))))))).....))..................... (-19.50 = -20.62 +   1.11)

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 10:22:13 2006