Locus 2025

Sequence ID 2R_DroMel_CAF1
Location 7,635,462 – 7,635,616
Length 154
Max. P 0.929154
window3349 window3350 window3351

overview

Window 9

Location 7,635,462 – 7,635,576
Length 114
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 74.22
Mean single sequence MFE -33.36
Consensus MFE -16.09
Energy contribution -16.78
Covariance contribution 0.69
Combinations/Pair 1.16
Mean z-score -2.14
Structure conservation index 0.48
SVM decision value 0.36
SVM RNA-class probability 0.705373
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7635462 114 + 20766785
CCUUCGUUCCGGCGGGGCAUUUCCCCAGUUCGACUCGAAUU-----UGGGUAAUCCCAUUUAGCUGUC-AUCAGCUGUGGCUCCACUAAUCCCAACAACAGCCGAGGAUUCAAUCACUGA
.....((((((((.(((.(((.(((.((((((...))))))-----.))).))))))....(((((..-..)))))(((....)))..............)))).))))........... ( -33.70)
>DroSec_CAF1 80325 114 + 1
CCUUCGUUCCGGUGGGGCAUUUCCCCAGUUCGACUCGAAUU-----UGGGUAAUCCCAUUUAGCUGUC-AUCAGCUGUGGCUCCUCUAAUCCCAACUACAGCCGAGGAUUCAAUCACUGA
.........((((((((.(((.(((.((((((...))))))-----.))).))))))...((((((..-..))))))((..(((((.................)))))..))..))))). ( -34.83)
>DroYak_CAF1 83373 114 + 1
CCUUCGUGCUGGCGGGGCAUUUCCCCAGUUCGACUCGAAUU-----UGGGUAAUCCCAUUUAGCUGUC-AUCAGCUGUGGCUGCCCUAAUCCCAAGUACACCCGAGGAUUCAAUCACUGA
((((.(((((((.((((((...(((.((((((...))))))-----.))).....((((..(((((..-..))))))))).))))))....)).)))))....))))............. ( -36.50)
>DroAna_CAF1 79980 97 + 1
CCAUCGCU-UGGCGGGGCAUUUCCCAGCUCCAAGCCGAAUAAGGACUUGGUAAUCCCUAUUACCUGUCUAUCUAGUCAGUUUCC---------------------UGAUUGCAUCA-UGA
.....(((-(((((((((........)))))..)))))....((((..((((((....)))))).))))....((((((....)---------------------)))))))....-... ( -28.40)
>consensus
CCUUCGUUCCGGCGGGGCAUUUCCCCAGUUCGACUCGAAUU_____UGGGUAAUCCCAUUUAGCUGUC_AUCAGCUGUGGCUCC_CUAAUCCCAACUACAGCCGAGGAUUCAAUCACUGA
.(((((........(((.(((..((((((((.....))))......)))).))))))...((((((.....)))))).........................)))))............. (-16.09 = -16.78 +   0.69)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 7,635,502 – 7,635,616
Length 114
Sequences 3
Columns 114
Reading direction forward
Mean pairwise identity 91.81
Mean single sequence MFE -33.75
Consensus MFE -32.06
Energy contribution -31.73
Covariance contribution -0.33
Combinations/Pair 1.06
Mean z-score -2.10
Structure conservation index 0.95
SVM decision value 1.20
SVM RNA-class probability 0.929154
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7635502 114 + 20766785
UUGGGUAAUCCCAUUUAGCUGUCAUCAGCUGUGGCUCCACUAAUCCCAACAACAGCCGAGGAUUCAAUCACUGAAUGCACUUUUCACUGGGCUUACCCGGAAUCGCGUUGUGUU
(((((...........(((((....)))))(((....)))....)))))..(((((((((.(((((.....))))).)........(((((....)))))..))).)))))... ( -34.20)
>DroSec_CAF1 80365 114 + 1
UUGGGUAAUCCCAUUUAGCUGUCAUCAGCUGUGGCUCCUCUAAUCCCAACUACAGCCGAGGAUUCAAUCACUGAAUGCACUUUUCACUGGGCUUACCCAGAAUCGCGUUGUGCU
(((((.....((((..(((((....)))))))))..........))))).((((((((((.(((((.....))))).)........(((((....)))))..))).)))))).. ( -34.46)
>DroYak_CAF1 83413 114 + 1
UUGGGUAAUCCCAUUUAGCUGUCAUCAGCUGUGGCUGCCCUAAUCCCAAGUACACCCGAGGAUUCAAUCACUGAAUGCACUUCUCGCUGGGCUUACCCGGAAUCGUUGUGUUAU
..(((((...((((..(((((....))))))))).)))))...........((((.((((.(((((.....))))).)........(((((....)))))..)))..))))... ( -32.60)
>consensus
UUGGGUAAUCCCAUUUAGCUGUCAUCAGCUGUGGCUCCACUAAUCCCAACUACAGCCGAGGAUUCAAUCACUGAAUGCACUUUUCACUGGGCUUACCCGGAAUCGCGUUGUGAU
(((((.....((((..(((((....)))))))))..........)))))..(((((((((.(((((.....))))).)........(((((....)))))..))).)))))... (-32.06 = -31.73 +  -0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 7,635,502 – 7,635,616
Length 114
Sequences 3
Columns 114
Reading direction reverse
Mean pairwise identity 91.81
Mean single sequence MFE -35.87
Consensus MFE -32.38
Energy contribution -31.93
Covariance contribution -0.44
Combinations/Pair 1.03
Mean z-score -1.76
Structure conservation index 0.90
SVM decision value 0.25
SVM RNA-class probability 0.653118
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7635502 114 - 20766785
AACACAACGCGAUUCCGGGUAAGCCCAGUGAAAAGUGCAUUCAGUGAUUGAAUCCUCGGCUGUUGUUGGGAUUAGUGGAGCCACAGCUGAUGACAGCUAAAUGGGAUUACCCAA
................((((((.((((......(((.(((.((((.....(((((.((((....))))))))).(((....))).)))))))...)))...)))).)))))).. ( -36.30)
>DroSec_CAF1 80365 114 - 1
AGCACAACGCGAUUCUGGGUAAGCCCAGUGAAAAGUGCAUUCAGUGAUUGAAUCCUCGGCUGUAGUUGGGAUUAGAGGAGCCACAGCUGAUGACAGCUAAAUGGGAUUACCCAA
.((.....)).....(((((((.((((.......(((..(((.....((.(((((.((((....))))))))).)).))).)))(((((....)))))...)))).))))))). ( -35.00)
>DroYak_CAF1 83413 114 - 1
AUAACACAACGAUUCCGGGUAAGCCCAGCGAGAAGUGCAUUCAGUGAUUGAAUCCUCGGGUGUACUUGGGAUUAGGGCAGCCACAGCUGAUGACAGCUAAAUGGGAUUACCCAA
................((((((((((......((((((((((((.(((...))))).)))))))))).......))))..(((.(((((....)))))...)))..)))))).. ( -36.32)
>consensus
AACACAACGCGAUUCCGGGUAAGCCCAGUGAAAAGUGCAUUCAGUGAUUGAAUCCUCGGCUGUAGUUGGGAUUAGAGGAGCCACAGCUGAUGACAGCUAAAUGGGAUUACCCAA
................((((((.((((.......(((......((.....(((((.((((....)))))))))......)))))(((((....)))))...)))).)))))).. (-32.38 = -31.93 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:19:11 2006