Locus 2371

Sequence ID 3L_DroMel_CAF1
Location 6,641,870 – 6,642,042
Length 172
Max. P 0.981450
window3654 window3655 window3656

overview

Window 4

Location 6,641,870 – 6,641,964
Length 94
Sequences 6
Columns 101
Reading direction forward
Mean pairwise identity 86.78
Mean single sequence MFE -34.55
Consensus MFE -28.19
Energy contribution -28.55
Covariance contribution 0.36
Combinations/Pair 1.20
Mean z-score -2.28
Structure conservation index 0.82
SVM decision value 0.58
SVM RNA-class probability 0.789078
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6641870 94 + 23771897
GCAUUAAUAAGCGGUCAAAGUUUUGAUGGCUUAAUCGAUAU---GGCGACGUCGGCAAC---UUCUGCUCGGCGACCGCAGCGCAUACUGCGGUCAC-CGC
(((....(((((.(((((....))))).)))))...((..(---(.((....)).))..---.))))).(((.((((((((......)))))))).)-)). ( -37.30)
>DroSec_CAF1 18987 94 + 1
GCAUUAAUAAGCGGUCAAAGUUUUGAUGGCUUAAUCGAUAC---GGCGACGUCGGCAAC---UUCUGCUCGGCGACCGCAGCGCAUUCUGCGGUCAC-CGC
.......(((((.(((((....))))).))))).......(---((....(((((((..---...))).))))((((((((......)))))))).)-)). ( -37.00)
>DroSim_CAF1 34973 94 + 1
GCAUUAAUAAGCGGUCAAAGUUUUGAUGGCUUAAUCGAUAC---GGCGACGUCGGCAAC---UUCUGCUCGGCGACCGCAGCGCAUUCUGCGGUCAC-CGC
.......(((((.(((((....))))).))))).......(---((....(((((((..---...))).))))((((((((......)))))))).)-)). ( -37.00)
>DroEre_CAF1 28897 87 + 1
GCAUUAAUAAGCGGUCAAAGUUUUGAUGGCUUAAUCGAUAU---GACGACGUCGGCAAC---UUCUGCUCGGCGACCACAGCGCAUUCUGCGG--------
((.....(((((.(((((....))))).))))).(((....---..)))((((((((..---...))).)))))......))((.....))..-------- ( -25.50)
>DroYak_CAF1 26564 94 + 1
GCAUUAAUAAGCGGUCAAAGUUUUGAUGGCUUAAUCGAUAU---GACGACGUCGGCAAC---UUCUGCUCGGCGACCACAGCGCAUUCUGCGGUCAC-CGC
(((....(((((.(((((....))))).))))).(((((..---......)))))....---...))).(((.((((.(((......))).)))).)-)). ( -30.00)
>DroAna_CAF1 22037 101 + 1
ACAUUAAUAAGCGGUCGAAGUUUUGAUCGUUUAAUCGAUAGGAUGGAGACUCCCGCACUGGAAUUUGUCUGGCGACCGCAGAGCAUUCUGUGGUCGCCCGC
.......(((((((((((....))))))))))).......(((..((...(((......))).))..)))(((((((((((......)))))))))))... ( -40.50)
>consensus
GCAUUAAUAAGCGGUCAAAGUUUUGAUGGCUUAAUCGAUAU___GGCGACGUCGGCAAC___UUCUGCUCGGCGACCGCAGCGCAUUCUGCGGUCAC_CGC
.......(((((.(((((....))))).))))).................(((((((........))).))))((((((((......))))))))...... (-28.19 = -28.55 +   0.36)

alignment

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secondary structure

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dotplot

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Window 5

Location 6,641,926 – 6,642,042
Length 116
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 75.40
Mean single sequence MFE -41.53
Consensus MFE -20.65
Energy contribution -21.90
Covariance contribution 1.25
Combinations/Pair 1.26
Mean z-score -2.40
Structure conservation index 0.50
SVM decision value 1.67
SVM RNA-class probability 0.970915
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6641926 116 + 23771897
-UUCUGCUCGGCGACCGCAGCGCAUACUGCGGUCAC-CGCUCCGGCGCUCAAAAGUAUGCUAGCAUUCUGGUCACGCCGAGCAA-GGAUUAGGUAAUCAGCAC-UUUAAUUGCGAGUAAA
-...(((((((.((((((((......)))))))).)-)((((.((((......((.(((....))).)).....))))))))..-.((((....)))).(((.-......)))))))).. ( -42.90)
>DroSec_CAF1 19043 116 + 1
-UUCUGCUCGGCGACCGCAGCGCAUUCUGCGGUCAC-CGCUCCGGCGCUCAAAAGUAUGCUAGCAUUCUGGUCACGCCGAGCAA-GGAUUAGGUAAUCAGCAC-UUUAAUUGCGAGUAAA
-...(((((((.((((((((......)))))))).)-)((((.((((......((.(((....))).)).....))))))))..-.((((....)))).(((.-......)))))))).. ( -42.30)
>DroSim_CAF1 35029 116 + 1
-UUCUGCUCGGCGACCGCAGCGCAUUCUGCGGUCAC-CGCUCCGGCGCUCAAAAGUAUGCUAGCAUUCUGGUCACGCCGAGCAA-GGAUUAGGUAAUCAGCAC-UUUAAUUGCGAGUAAA
-...(((((((.((((((((......)))))))).)-)((((.((((......((.(((....))).)).....))))))))..-.((((....)))).(((.-......)))))))).. ( -42.30)
>DroEre_CAF1 28953 97 + 1
-UUCUGCUCGGCGACCACAGCGCAUUCUGCGG----------------UGAAAAGUAUGCCAGCAUUCUGGUCAGGACGAGCAA-GGAUUAGGGAAUCAGCAC-UUUAAUUGCAAC----
-...((((((..((((.((.(((.....))).----------------))...((.(((....))).))))))....)))))).-.((((((((........)-))))))).....---- ( -28.00)
>DroYak_CAF1 26620 112 + 1
-UUCUGCUCGGCGACCACAGCGCAUUCUGCGGUCAC-CGCUCCGGCGCUGAAAAGUAUGCCAGCAUUCUGGUCACGACAAGCAA-GGAUUAGGUAAUCAGCGC-UUUAAUUGCCAG----
-...((((.((((((..((((((.....((((...)-)))....))))))....)).))))))))..(((((......((((..-.((((....))))...))-)).....)))))---- ( -37.00)
>DroAna_CAF1 22098 99 + 1
AAUUUGUCUGGCGACCGCAGAGCAUUCUGUGGUCGCCCGCUGCCUGGCUCGCCAGUCUGAU-----------CCGGAGACGGACUGGCUUAGGC-GGCAGGACCUCCAAUU---------
.....(((((((((((((((......))))))))))).(((((((((...(((((((((.(-----------(....)))))))))))))))))-))).))))........--------- ( -56.70)
>consensus
_UUCUGCUCGGCGACCGCAGCGCAUUCUGCGGUCAC_CGCUCCGGCGCUCAAAAGUAUGCUAGCAUUCUGGUCACGACGAGCAA_GGAUUAGGUAAUCAGCAC_UUUAAUUGCGAG____
....((((((.(((((((((......))))))))........................(((((....)))))...).))))))...((((....)))).(((........)))....... (-20.65 = -21.90 +   1.25)

alignment

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secondary structure

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dotplot

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Window 6

Location 6,641,926 – 6,642,042
Length 116
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 75.40
Mean single sequence MFE -41.98
Consensus MFE -23.39
Energy contribution -26.03
Covariance contribution 2.64
Combinations/Pair 1.24
Mean z-score -2.37
Structure conservation index 0.56
SVM decision value 1.89
SVM RNA-class probability 0.981450
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6641926 116 - 23771897
UUUACUCGCAAUUAAA-GUGCUGAUUACCUAAUCC-UUGCUCGGCGUGACCAGAAUGCUAGCAUACUUUUGAGCGCCGGAGCG-GUGACCGCAGUAUGCGCUGCGGUCGCCGAGCAGAA-
................-.((((.............-..(((((((((....((.(((....))).)).....))))).))))(-(((((((((((....)))))))))))).))))...- ( -46.00)
>DroSec_CAF1 19043 116 - 1
UUUACUCGCAAUUAAA-GUGCUGAUUACCUAAUCC-UUGCUCGGCGUGACCAGAAUGCUAGCAUACUUUUGAGCGCCGGAGCG-GUGACCGCAGAAUGCGCUGCGGUCGCCGAGCAGAA-
................-.((((.............-..(((((((((....((.(((....))).)).....))))).))))(-((((((((((......))))))))))).))))...- ( -44.70)
>DroSim_CAF1 35029 116 - 1
UUUACUCGCAAUUAAA-GUGCUGAUUACCUAAUCC-UUGCUCGGCGUGACCAGAAUGCUAGCAUACUUUUGAGCGCCGGAGCG-GUGACCGCAGAAUGCGCUGCGGUCGCCGAGCAGAA-
................-.((((.............-..(((((((((....((.(((....))).)).....))))).))))(-((((((((((......))))))))))).))))...- ( -44.70)
>DroEre_CAF1 28953 97 - 1
----GUUGCAAUUAAA-GUGCUGAUUCCCUAAUCC-UUGCUCGUCCUGACCAGAAUGCUGGCAUACUUUUCA----------------CCGCAGAAUGCGCUGUGGUCGCCGAGCAGAA-
----...(((......-.)))..............-(((((((...((.((((....))))))........(----------------((((((......)))))))...)))))))..- ( -25.30)
>DroYak_CAF1 26620 112 - 1
----CUGGCAAUUAAA-GCGCUGAUUACCUAAUCC-UUGCUUGUCGUGACCAGAAUGCUGGCAUACUUUUCAGCGCCGGAGCG-GUGACCGCAGAAUGCGCUGUGGUCGCCGAGCAGAA-
----((((((....((-(((..((((....)))).-.)))))....)).))))..(((((((............)))....((-((((((((((......))))))))))))))))...- ( -44.30)
>DroAna_CAF1 22098 99 - 1
---------AAUUGGAGGUCCUGCC-GCCUAAGCCAGUCCGUCUCCGG-----------AUCAGACUGGCGAGCCAGGCAGCGGGCGACCACAGAAUGCUCUGCGGUCGCCAGACAAAUU
---------........((((((((-......(((((((.(((....)-----------))..)))))))......)))))..(((((((.((((....)))).))))))).)))..... ( -46.90)
>consensus
____CUCGCAAUUAAA_GUGCUGAUUACCUAAUCC_UUGCUCGGCGUGACCAGAAUGCUAGCAUACUUUUGAGCGCCGGAGCG_GUGACCGCAGAAUGCGCUGCGGUCGCCGAGCAGAA_
.....................................((((((((((....((.(((....))).)).....))))).......((((((((((......)))))))))).))))).... (-23.39 = -26.03 +   2.64)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:30:39 2006