Locus 6439

Sequence ID 2R_DroMel_CAF1
Location 20,105,270 – 20,105,396
Length 126
Max. P 0.995544
window10272 window10273 window10274 window10275

overview

Window 2

Location 20,105,270 – 20,105,373
Length 103
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 75.46
Mean single sequence MFE -30.04
Consensus MFE -19.22
Energy contribution -19.27
Covariance contribution 0.06
Combinations/Pair 1.06
Mean z-score -2.85
Structure conservation index 0.64
SVM decision value 2.50
SVM RNA-class probability 0.994637
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20105270 103 + 20766785
AAGUGAACAGUUCUCAA-ACUAAGCUCA-GCA-UUUGCACCGCUUCA-AUCGAGCAUUCCGACGUC---CACUGCC-AGGAUGCAACCAGAAUGCUCCUCUGGAGCCGUAC
(((((...((((.....-....))))..-.))-)))..((.((((((-...((((((((.(.((((---(......-.)))))....).))))))))...)))))).)).. ( -27.40)
>DroPse_CAF1 5655 96 + 1
CUUUUAACCAUUCUCAA-AGUAAGCUUA-GGACUUUGUACUGCUUCAAAUGGAGCAUUCCGAAUGC----AAUGCC-GAU--------GGAAUGCUCUUCUGGAGCCGUUC
..............(((-(((.......-..)))))).((.((((((...(((((((((((...((----...)).-..)--------))))))))))..)))))).)).. ( -28.30)
>DroEre_CAF1 8088 90 + 1
-----AACAGUUCUCAA-ACUAAGCUCA-GCA-UUUGCACCGCUUCA-AUCGAGCAUUCCAACGUC---CACUGGC-GGG--------GGAAUGCUCCUCUGGAGCCGUAC
-----...((((....)-))).......-((.-...))((.((((((-...(((((((((..((((---....)))-)..--------)))))))))...)))))).)).. ( -32.70)
>DroYak_CAF1 8019 99 + 1
AAAUGAACAGUUCUCAA-ACUAAGCUCA-GCA-UUUGCACCGCUUCA-AUCGAGCAUUCCCACGUCAACCACUGGCAGGG--------GGAAUGCUCCUCUGGAGCCGUCC
(((((...((((.....-....))))..-.))-)))..((.((((((-...((((((((((..((((.....))))...)--------)))))))))...)))))).)).. ( -32.80)
>DroAna_CAF1 8567 92 + 1
AUGGCAACAGUUCUCAAAACUAAAAUUAGGCC-UUUGCACAGCUUCA-AUCGAGCAUUCUGACUCC---GA------AGU--------GGAAUGCUCCUCUGGAGCUGUCC
...((((.((..((.............))..)-)))))(((((((((-...(((((((((.(((..---..------)))--------)))))))))...))))))))).. ( -30.72)
>DroPer_CAF1 5662 96 + 1
CUUUUAACCAUUCUCAA-AGUAAGCUUA-GGACUUUGUACUGCUUCAAAUGGAGCAUUCCGAAUGC----AAUGCC-GAU--------GGAAUGCUCUUCUGGAGCCGUUC
..............(((-(((.......-..)))))).((.((((((...(((((((((((...((----...)).-..)--------))))))))))..)))))).)).. ( -28.30)
>consensus
AUGUGAACAGUUCUCAA_ACUAAGCUCA_GCA_UUUGCACCGCUUCA_AUCGAGCAUUCCGACGUC___CACUGCC_GGG________GGAAUGCUCCUCUGGAGCCGUAC
......................................((.((((((....(((((((((............................)))))))))...)))))).)).. (-19.22 = -19.27 +   0.06)

alignment

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secondary structure

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dotplot

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Window 3

Location 20,105,270 – 20,105,373
Length 103
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 75.46
Mean single sequence MFE -30.82
Consensus MFE -17.05
Energy contribution -17.11
Covariance contribution 0.06
Combinations/Pair 1.06
Mean z-score -1.74
Structure conservation index 0.55
SVM decision value 0.55
SVM RNA-class probability 0.778629
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20105270 103 - 20766785
GUACGGCUCCAGAGGAGCAUUCUGGUUGCAUCCU-GGCAGUG---GACGUCGGAAUGCUCGAU-UGAAGCGGUGCAAA-UGC-UGAGCUUAGU-UUGAGAACUGUUCACUU
((((.(((.(((..((((((((((...((.(((.-......)---)).))))))))))))..)-)).))).))))...-...-(((((..(((-(....)))))))))... ( -36.00)
>DroPse_CAF1 5655 96 - 1
GAACGGCUCCAGAAGAGCAUUCC--------AUC-GGCAUU----GCAUUCGGAAUGCUCCAUUUGAAGCAGUACAAAGUCC-UAAGCUUACU-UUGAGAAUGGUUAAAAG
.(((.(((.((((.(((((((((--------...-.((...----))....)))))))))..)))).)))....((((((..-.......)))-)))......)))..... ( -25.60)
>DroEre_CAF1 8088 90 - 1
GUACGGCUCCAGAGGAGCAUUCC--------CCC-GCCAGUG---GACGUUGGAAUGCUCGAU-UGAAGCGGUGCAAA-UGC-UGAGCUUAGU-UUGAGAACUGUU-----
((((.(((.(((..(((((((((--------..(-(((...)---).))..)))))))))..)-)).))).))))...-...-......((((-(....)))))..----- ( -31.10)
>DroYak_CAF1 8019 99 - 1
GGACGGCUCCAGAGGAGCAUUCC--------CCCUGCCAGUGGUUGACGUGGGAAUGCUCGAU-UGAAGCGGUGCAAA-UGC-UGAGCUUAGU-UUGAGAACUGUUCAUUU
((((((.((((((.(((((((((--------((..(((...)))....).))))))))))...-..((((...((...-.))-...))))..)-))).)).)))))).... ( -36.60)
>DroAna_CAF1 8567 92 - 1
GGACAGCUCCAGAGGAGCAUUCC--------ACU------UC---GGAGUCAGAAUGCUCGAU-UGAAGCUGUGCAAA-GGCCUAAUUUUAGUUUUGAGAACUGUUGCCAU
(.((((((.(((..((((((((.--------(((------..---..)))..))))))))..)-)).)))))).)...-(((.......((((((...))))))..))).. ( -30.00)
>DroPer_CAF1 5662 96 - 1
GAACGGCUCCAGAAGAGCAUUCC--------AUC-GGCAUU----GCAUUCGGAAUGCUCCAUUUGAAGCAGUACAAAGUCC-UAAGCUUACU-UUGAGAAUGGUUAAAAG
.(((.(((.((((.(((((((((--------...-.((...----))....)))))))))..)))).)))....((((((..-.......)))-)))......)))..... ( -25.60)
>consensus
GAACGGCUCCAGAGGAGCAUUCC________ACC_GGCAGUG___GAAGUCGGAAUGCUCGAU_UGAAGCGGUGCAAA_UGC_UAAGCUUAGU_UUGAGAACUGUUAAAAU
(.((.(((.((...(((((((((............................)))))))))....)).))).)).).................................... (-17.05 = -17.11 +   0.06)

alignment

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secondary structure

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dotplot

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Window 4

Location 20,105,299 – 20,105,396
Length 97
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 72.91
Mean single sequence MFE -30.10
Consensus MFE -20.79
Energy contribution -20.87
Covariance contribution 0.08
Combinations/Pair 1.14
Mean z-score -3.22
Structure conservation index 0.69
SVM decision value 2.59
SVM RNA-class probability 0.995544
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20105299 97 + 20766785
A-UUUGCACCGCUUCA-AUCGAGCAUUCCGACGUCCACUGCCAGGAUGCAACCAGAAUGCUCCUCUGGAGCCGUACAAGCCACGCGAUUCAAUUCAUAC-----
.-((((.((.((((((-...((((((((.(.(((((.......)))))....).))))))))...)))))).)).))))......((......))....----- ( -27.20)
>DroPse_CAF1 5684 95 + 1
ACUUUGUACUGCUUCAAAUGGAGCAUUCCGAAUGC-AAUGCCGAU--------GGAAUGCUCUUCUGGAGCCGUUCAAUUUACGCGUACGCAUAGAAAUGGCAA
.....((((.((((((...(((((((((((...((-...))...)--------))))))))))..))))))(((.......))).))))((.((....)))).. ( -31.10)
>DroSec_CAF1 5721 97 + 1
A-UUUGCACCGCUUCA-AUCGAGCAUUCCGACGUCCACUGCCAGGAUGCUCCCAGAAUGCUCCUCUGGAGCCGUACAAGCCACGCGAUUCAAUUCAUAC-----
.-((((.((.((((((-...((((((((.(((((((.......))))).))...))))))))...)))))).)).))))......((......))....----- ( -29.00)
>DroEre_CAF1 8112 89 + 1
A-UUUGCACCGCUUCA-AUCGAGCAUUCCAACGUCCACUGGCGGG--------GGAAUGCUCCUCUGGAGCCGUACAAGCCACGCGAUUCAAUUCAUAC-----
.-((((.((.((((((-...(((((((((..((((....))))..--------)))))))))...)))))).)).))))......((......))....----- ( -33.30)
>DroAna_CAF1 8598 84 + 1
C-UUUGCACAGCUUCA-AUCGAGCAUUCUGACUCCGA-----AGU--------GGAAUGCUCCUCUGGAGCUGUCCAAUUUACGCGAAUCCAUUCAUAU-----
.-.(((.(((((((((-...(((((((((.(((....-----)))--------)))))))))...))))))))).))).....................----- ( -28.90)
>DroPer_CAF1 5691 95 + 1
ACUUUGUACUGCUUCAAAUGGAGCAUUCCGAAUGC-AAUGCCGAU--------GGAAUGCUCUUCUGGAGCCGUUCAAUUUACGCGUACGCAUAGAAAUGGCAA
.....((((.((((((...(((((((((((...((-...))...)--------))))))))))..))))))(((.......))).))))((.((....)))).. ( -31.10)
>consensus
A_UUUGCACCGCUUCA_AUCGAGCAUUCCGACGUCCACUGCCAGG________GGAAUGCUCCUCUGGAGCCGUACAAGCCACGCGAAUCAAUUCAUAC_____
...(((.((.((((((....(((((((((........((....))........)))))))))...)))))).)).))).......................... (-20.79 = -20.87 +   0.08)

alignment

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secondary structure

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dotplot

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Window 5

Location 20,105,299 – 20,105,396
Length 97
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 72.91
Mean single sequence MFE -30.23
Consensus MFE -18.73
Energy contribution -18.73
Covariance contribution -0.00
Combinations/Pair 1.05
Mean z-score -1.89
Structure conservation index 0.62
SVM decision value 1.64
SVM RNA-class probability 0.969125
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20105299 97 - 20766785
-----GUAUGAAUUGAAUCGCGUGGCUUGUACGGCUCCAGAGGAGCAUUCUGGUUGCAUCCUGGCAGUGGACGUCGGAAUGCUCGAU-UGAAGCGGUGCAAA-U
-----.....................((((((.(((.(((..((((((((((...((.(((.......))).))))))))))))..)-)).))).)))))).-. ( -33.20)
>DroPse_CAF1 5684 95 - 1
UUGCCAUUUCUAUGCGUACGCGUAAAUUGAACGGCUCCAGAAGAGCAUUCC--------AUCGGCAUU-GCAUUCGGAAUGCUCCAUUUGAAGCAGUACAAAGU
..........(((((....)))))..(((.((.(((.((((.(((((((((--------....((...-))....)))))))))..)))).))).)).)))... ( -28.30)
>DroSec_CAF1 5721 97 - 1
-----GUAUGAAUUGAAUCGCGUGGCUUGUACGGCUCCAGAGGAGCAUUCUGGGAGCAUCCUGGCAGUGGACGUCGGAAUGCUCGAU-UGAAGCGGUGCAAA-U
-----.....................((((((.(((((((((.....))))))((((((.(((((.......))))).))))))...-...))).)))))).-. ( -33.30)
>DroEre_CAF1 8112 89 - 1
-----GUAUGAAUUGAAUCGCGUGGCUUGUACGGCUCCAGAGGAGCAUUCC--------CCCGCCAGUGGACGUUGGAAUGCUCGAU-UGAAGCGGUGCAAA-U
-----.....................((((((.(((.(((..(((((((((--------..((((...)).))..)))))))))..)-)).))).)))))).-. ( -31.40)
>DroAna_CAF1 8598 84 - 1
-----AUAUGAAUGGAUUCGCGUAAAUUGGACAGCUCCAGAGGAGCAUUCC--------ACU-----UCGGAGUCAGAAUGCUCGAU-UGAAGCUGUGCAAA-G
-----.....................(((.((((((.(((..((((((((.--------(((-----....)))..))))))))..)-)).)))))).))).-. ( -26.90)
>DroPer_CAF1 5691 95 - 1
UUGCCAUUUCUAUGCGUACGCGUAAAUUGAACGGCUCCAGAAGAGCAUUCC--------AUCGGCAUU-GCAUUCGGAAUGCUCCAUUUGAAGCAGUACAAAGU
..........(((((....)))))..(((.((.(((.((((.(((((((((--------....((...-))....)))))))))..)))).))).)).)))... ( -28.30)
>consensus
_____AUAUGAAUGGAAUCGCGUAAAUUGUACGGCUCCAGAGGAGCAUUCC________ACCGGCAGUGGAAGUCGGAAUGCUCGAU_UGAAGCGGUGCAAA_U
..........................(((.((.(((.((...(((((((((........................)))))))))....)).))).)).)))... (-18.73 = -18.73 +  -0.00)

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 12:11:05 2006