Locus 5330

Sequence ID 3R_DroMel_CAF1
Location 13,969,808 – 13,969,911
Length 103
Max. P 0.571271
window8688 window8689

overview

Window 8

Location 13,969,808 – 13,969,911
Length 103
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.59
Mean single sequence MFE -27.67
Consensus MFE -17.47
Energy contribution -17.72
Covariance contribution 0.25
Combinations/Pair 1.14
Mean z-score -1.46
Structure conservation index 0.63
SVM decision value -0.02
SVM RNA-class probability 0.522707
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13969808 103 + 27905053
ACUCGUUACCAAAGCGGGUAACAAAAUGGCUAAAAUGCAUUUGCAACGCUCCAAUGCGUCUGCUUGUG--CUGUGCUGUCUUCUUGCCAUUC------UGCC---------ACAGUCUAC
....((((((......))))))....((((......((((..(((((((......)))).)))..)))--)((.((.........))))...------.)))---------)........ ( -29.40)
>DroSec_CAF1 240346 102 + 1
ACACGUCACCAAAGCGGGUAACAAAAUGGCUAAAAUGCAUUUGCGACGCUCCAGUGCGUCUGCUUGUGCGCUGUGCUGUC---UUGCCAUUC------UGCC---------ACAGUCUAC
...(((.......)))((((....((((((......((((..(((((((......))))).((....)))).))))....---..)))))).------))))---------......... ( -30.00)
>DroSim_CAF1 249658 102 + 1
ACACGUCACCAAAGCGGGUAACAAAAUGGCUAAAAUGCAUUUGCGACGCUCCAGUGCGUCUGCUUGUGCGCUGUGCUGUC---UUGCCAUUC------UGCC---------ACAGUCUAC
...(((.......)))((((....((((((......((((..(((((((......))))).((....)))).))))....---..)))))).------))))---------......... ( -30.00)
>DroEre_CAF1 231841 101 + 1
ACACGUCACCAAAGCGGGUAACAAAAUGGCUAAAAUGCAUUUGCAACGCUCCAAUGCGUCUGCUUGUGCUGUGUGUU-UC---UUGCCAGUC------UGCU---------ACAGUCAAC
....((.(((......))).))....((((..((((((((..(((((((......)))).)))..)))).....)))-).---..))))(.(------((..---------.))).)... ( -24.70)
>DroYak_CAF1 253341 94 + 1
ACACGUCACCAAAGCGGGUAACAAAAUGGCUAAAAUGCAUUUGCAACGCUCGAAUGCGUCUGCUUGUGCAGUGUUUU-AC----------AC------UGUU---------ACAGUCUAG
....((.(((......))).)).....((((.....((((..(((((((......)))).)))..))))((((....-.)----------))------)...---------..))))... ( -25.90)
>DroAna_CAF1 233202 118 + 1
ACACGUCACCAAAGCAAGCUACAAAAUGGCUAAAAUGCAUUUGCAACGCUCCAAUGCGUCUGCUUGUGCUUGGUUCUUUU--UUUCCCAUUUAUUUUUUGCUUUUUAGCUUUCAGCCAUU
..........((((((((.....((((((..((((.((((..(((((((......)))).)))..)))).........))--))..))))))....))))))))...((.....)).... ( -26.00)
>consensus
ACACGUCACCAAAGCGGGUAACAAAAUGGCUAAAAUGCAUUUGCAACGCUCCAAUGCGUCUGCUUGUGCGCUGUGCUGUC___UUGCCAUUC______UGCC_________ACAGUCUAC
....((.(((......))).)).....((((.....((((..(((((((......)))).)))..)))).....((.......................))............))))... (-17.47 = -17.72 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 13,969,808 – 13,969,911
Length 103
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.59
Mean single sequence MFE -30.47
Consensus MFE -19.29
Energy contribution -19.18
Covariance contribution -0.11
Combinations/Pair 1.21
Mean z-score -1.53
Structure conservation index 0.63
SVM decision value 0.08
SVM RNA-class probability 0.571271
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13969808 103 - 27905053
GUAGACUGU---------GGCA------GAAUGGCAAGAAGACAGCACAG--CACAAGCAGACGCAUUGGAGCGUUGCAAAUGCAUUUUAGCCAUUUUGUUACCCGCUUUGGUAACGAGU
.......((---------((((------(((((((.((((..((((...)--)....((((.(((......)))))))...))..)))).)))))))))))))....((((....)))). ( -29.50)
>DroSec_CAF1 240346 102 - 1
GUAGACUGU---------GGCA------GAAUGGCAA---GACAGCACAGCGCACAAGCAGACGCACUGGAGCGUCGCAAAUGCAUUUUAGCCAUUUUGUUACCCGCUUUGGUGACGUGU
..((...((---------((((------(((((((.(---((..(((..((((....)).(((((......)))))))...)))..))).)))))))))))))...))..(....).... ( -35.00)
>DroSim_CAF1 249658 102 - 1
GUAGACUGU---------GGCA------GAAUGGCAA---GACAGCACAGCGCACAAGCAGACGCACUGGAGCGUCGCAAAUGCAUUUUAGCCAUUUUGUUACCCGCUUUGGUGACGUGU
..((...((---------((((------(((((((.(---((..(((..((((....)).(((((......)))))))...)))..))).)))))))))))))...))..(....).... ( -35.00)
>DroEre_CAF1 231841 101 - 1
GUUGACUGU---------AGCA------GACUGGCAA---GA-AACACACAGCACAAGCAGACGCAUUGGAGCGUUGCAAAUGCAUUUUAGCCAUUUUGUUACCCGCUUUGGUGACGUGU
.......((---------((((------((.((((..---(.-....)...(((...((((.(((......)))))))...)))......)))).)))))))).(((....)))...... ( -26.10)
>DroYak_CAF1 253341 94 - 1
CUAGACUGU---------AACA------GU----------GU-AAAACACUGCACAAGCAGACGCAUUCGAGCGUUGCAAAUGCAUUUUAGCCAUUUUGUUACCCGCUUUGGUGACGUGU
(((((.(((---------(.((------((----------(.-....))))).....((((.(((......)))))))...)))).))))).......((((((......)))))).... ( -27.00)
>DroAna_CAF1 233202 118 - 1
AAUGGCUGAAAGCUAAAAAGCAAAAAAUAAAUGGGAAA--AAAAGAACCAAGCACAAGCAGACGCAUUGGAGCGUUGCAAAUGCAUUUUAGCCAUUUUGUAGCUUGCUUUGGUGACGUGU
..(((((....(((....)))..........(((....--.......)))))).)).....((((((..((((((((((((.((......))...))))))))..))))..))).))).. ( -30.20)
>consensus
GUAGACUGU_________AGCA______GAAUGGCAA___GACAGCACAGAGCACAAGCAGACGCAUUGGAGCGUUGCAAAUGCAUUUUAGCCAUUUUGUUACCCGCUUUGGUGACGUGU
...................................................((((..((.(((((......)))))((....))......))......((((((......)))))))))) (-19.29 = -19.18 +  -0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:52:07 2006