Locus 2526

Sequence ID 3L_DroMel_CAF1
Location 7,084,210 – 7,084,331
Length 121
Max. P 0.867221
window3922 window3923 window3924

overview

Window 2

Location 7,084,210 – 7,084,309
Length 99
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 81.05
Mean single sequence MFE -30.58
Consensus MFE -20.67
Energy contribution -20.53
Covariance contribution -0.13
Combinations/Pair 1.26
Mean z-score -2.03
Structure conservation index 0.68
SVM decision value 0.69
SVM RNA-class probability 0.822651
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7084210 99 + 23771897
AGU-------------------GGAUUAUCGGAAAUAUCAUGUUAAGUGACGGACGGACGACAAUAAGGCAUAUCGCAAGGAUGUCACUUUGUGAUGUCUGUCCAUUAAUUGCGAAGU
...-------------------......(((.((...((((.....)))).(((((((((((((...(((((.((....)))))))...))))..))))))))).....)).)))... ( -29.30)
>DroSec_CAF1 96584 99 + 1
AGU-------------------GGAUUAUCGGAAAUAUCAUGUUAAGUGACGGACGGACGACAAUAAGGCAUAUCGCAAGGAUGUCACUUUGUGAUGUCUGUCCAUUAAUUGCGAAGU
...-------------------......(((.((...((((.....)))).(((((((((((((...(((((.((....)))))))...))))..))))))))).....)).)))... ( -29.30)
>DroSim_CAF1 129276 99 + 1
AGU-------------------GGAUUAUCGGAAAUAUCAUGUUAAGUGACGGACGGACGACAAUAAGGCAUAUCGCAAGGAUGUCACUUUGUGAUGUCUGUCCAUUAAUUGCGAAGU
...-------------------......(((.((...((((.....)))).(((((((((((((...(((((.((....)))))))...))))..))))))))).....)).)))... ( -29.30)
>DroEre_CAF1 112765 117 + 1
AGUGGAGUCG-GCACUUUGCGGGAAUUAUCGGAAAUAUCAUGUUAAGUGAUGGACGGACGACAAUAAGGCAUAUCGCAAGGAUGUCACUUUGUGAUUUCUGUCCAUUAAUUGCGAAGU
..........-..(((((((((((....)).................(((((((((((..((((...(((((.((....)))))))...))))....))))))))))).))))))))) ( -32.20)
>DroYak_CAF1 112138 118 + 1
AGUUGAGUCGGGCACUUUGCGGGAAUUAUCGGAAAUAUCAUGUUAAGUGACGGACGGACGACAAUAAGGCAUAUCGCAAGGAUGUCACUUUGUGAUGUCUGUCCAUUAAUUGCGAAGU
.............(((((((((...............((((.....)))).(((((((((((((...(((((.((....)))))))...))))..))))))))).....))))))))) ( -35.00)
>DroAna_CAF1 111266 88 + 1
UCU-------------------GGGUUAUCGGAAAUGUCAUGUUCAGUGACG-ACGACUGACAA---------UCGCCAGGACGUCACUUCGCAAUGCCUGUCCAUUAGC-CCGAUGU
..(-------------------((((((..(((...(.(((((..(((((((-....(((....---------....)))..)))))))..)).))).)..)))..))))-))).... ( -28.40)
>consensus
AGU___________________GGAUUAUCGGAAAUAUCAUGUUAAGUGACGGACGGACGACAAUAAGGCAUAUCGCAAGGAUGUCACUUUGUGAUGUCUGUCCAUUAAUUGCGAAGU
.......................(((((..(((.(((((((...((((((((..(...(((............)))...)..)))))))).)))))))...)))..)))))....... (-20.67 = -20.53 +  -0.13)

alignment

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secondary structure

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dotplot

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Window 3

Location 7,084,210 – 7,084,309
Length 99
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 81.05
Mean single sequence MFE -21.77
Consensus MFE -15.44
Energy contribution -16.08
Covariance contribution 0.64
Combinations/Pair 1.15
Mean z-score -1.30
Structure conservation index 0.71
SVM decision value 0.09
SVM RNA-class probability 0.576295
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7084210 99 - 23771897
ACUUCGCAAUUAAUGGACAGACAUCACAAAGUGACAUCCUUGCGAUAUGCCUUAUUGUCGUCCGUCCGUCACUUAACAUGAUAUUUCCGAUAAUCC-------------------ACU
........((((.((((..((.((((..(((((((......((((((........))))))......)))))))....)))).)))))).))))..-------------------... ( -19.30)
>DroSec_CAF1 96584 99 - 1
ACUUCGCAAUUAAUGGACAGACAUCACAAAGUGACAUCCUUGCGAUAUGCCUUAUUGUCGUCCGUCCGUCACUUAACAUGAUAUUUCCGAUAAUCC-------------------ACU
........((((.((((..((.((((..(((((((......((((((........))))))......)))))))....)))).)))))).))))..-------------------... ( -19.30)
>DroSim_CAF1 129276 99 - 1
ACUUCGCAAUUAAUGGACAGACAUCACAAAGUGACAUCCUUGCGAUAUGCCUUAUUGUCGUCCGUCCGUCACUUAACAUGAUAUUUCCGAUAAUCC-------------------ACU
........((((.((((..((.((((..(((((((......((((((........))))))......)))))))....)))).)))))).))))..-------------------... ( -19.30)
>DroEre_CAF1 112765 117 - 1
ACUUCGCAAUUAAUGGACAGAAAUCACAAAGUGACAUCCUUGCGAUAUGCCUUAUUGUCGUCCGUCCAUCACUUAACAUGAUAUUUCCGAUAAUUCCCGCAAAGUGC-CGACUCCACU
((((.(((((((.((((..((.((((..((((((.......((((((........)))))).......))))))....)))).)))))).)))))...)).))))..-.......... ( -21.24)
>DroYak_CAF1 112138 118 - 1
ACUUCGCAAUUAAUGGACAGACAUCACAAAGUGACAUCCUUGCGAUAUGCCUUAUUGUCGUCCGUCCGUCACUUAACAUGAUAUUUCCGAUAAUUCCCGCAAAGUGCCCGACUCAACU
((((.(((((((.((((..((.((((..(((((((......((((((........))))))......)))))))....)))).)))))).)))))...)).))))............. ( -24.30)
>DroAna_CAF1 111266 88 - 1
ACAUCGG-GCUAAUGGACAGGCAUUGCGAAGUGACGUCCUGGCGA---------UUGUCAGUCGU-CGUCACUGAACAUGACAUUUCCGAUAACCC-------------------AGA
.....((-(.((.((((...((((.....(((((((.((((((..---------..)))))..).-)))))))....))).)...)))).)).)))-------------------... ( -27.20)
>consensus
ACUUCGCAAUUAAUGGACAGACAUCACAAAGUGACAUCCUUGCGAUAUGCCUUAUUGUCGUCCGUCCGUCACUUAACAUGAUAUUUCCGAUAAUCC___________________ACU
........((((.((((..((.((((..(((((((......((((((........))))))......)))))))....)))).)))))).))))........................ (-15.44 = -16.08 +   0.64)

alignment

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secondary structure

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dotplot

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Window 4

Location 7,084,231 – 7,084,331
Length 100
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 79.83
Mean single sequence MFE -32.12
Consensus MFE -22.26
Energy contribution -24.68
Covariance contribution 2.42
Combinations/Pair 1.06
Mean z-score -1.86
Structure conservation index 0.69
SVM decision value 0.85
SVM RNA-class probability 0.867221
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7084231 100 + 23771897
UGUUAAGUGACGGACGGACGACAAUAAGGCAUAUCGCAAGGAUGUCACUUUGUGAUGUCUGUCCAUUAAUUGCGAAGUCGUUGUAUGUGAUUUCAUUAGC------------------
.(((((.....(((((((((((((...(((((.((....)))))))...))))..))))))))).........(((((((.......))))))).)))))------------------ ( -31.50)
>DroSec_CAF1 96605 100 + 1
UGUUAAGUGACGGACGGACGACAAUAAGGCAUAUCGCAAGGAUGUCACUUUGUGAUGUCUGUCCAUUAAUUGCGAAGUCGUUGUAUGUGAUUUCAUUAGC------------------
.(((((.....(((((((((((((...(((((.((....)))))))...))))..))))))))).........(((((((.......))))))).)))))------------------ ( -31.50)
>DroSim_CAF1 129297 100 + 1
UGUUAAGUGACGGACGGACGACAAUAAGGCAUAUCGCAAGGAUGUCACUUUGUGAUGUCUGUCCAUUAAUUGCGAAGUCGUUGUAUGUGAUUUCAUUAGC------------------
.(((((.....(((((((((((((...(((((.((....)))))))...))))..))))))))).........(((((((.......))))))).)))))------------------ ( -31.50)
>DroEre_CAF1 112804 113 + 1
UGUUAAGUGAUGGACGGACGACAAUAAGGCAUAUCGCAAGGAUGUCACUUUGUGAUUUCUGUCCAUUAAUUGCGAAGUCGUUGUAUGUGAUUUCAUUAGCG-----CCUCCGCCGAUC
.......(((((((((((..((((...(((((.((....)))))))...))))....)))))))))))...(((.((.(((((.(((......))))))))-----.)).)))..... ( -34.90)
>DroYak_CAF1 112178 113 + 1
UGUUAAGUGACGGACGGACGACAAUAAGGCAUAUCGCAAGGAUGUCACUUUGUGAUGUCUGUCCAUUAAUUGCGAAGUCGUUGUAUGUGAUUUCAUUAGCG-----CCUCCGUCGAUC
.......(((((((((((((((((...(((((.((....)))))))...))))..))))))))).........(.((.(((((.(((......))))))))-----.)).)))))... ( -34.40)
>DroAna_CAF1 111287 107 + 1
UGUUCAGUGACG-ACGACUGACAA---------UCGCCAGGACGUCACUUCGCAAUGCCUGUCCAUUAGC-CCGAUGUGGUUUCUCCAGAUUCCAUCGGCGGCCCGCCCCAGCCUCCC
(((..(((((((-....(((....---------....)))..)))))))..)))..............((-(.((((..(((......)))..)))))))(((........))).... ( -28.90)
>consensus
UGUUAAGUGACGGACGGACGACAAUAAGGCAUAUCGCAAGGAUGUCACUUUGUGAUGUCUGUCCAUUAAUUGCGAAGUCGUUGUAUGUGAUUUCAUUAGC__________________
.(((((.....(((((((((((((...(((((.((....)))))))...))))..))))))))).........(((((((.......))))))).))))).................. (-22.26 = -24.68 +   2.42)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:34:53 2006