Locus 2272

Sequence ID X_DroMel_CAF1
Location 6,154,127 – 6,154,221
Length 94
Max. P 0.999454
window3682 window3683

overview

Window 2

Location 6,154,127 – 6,154,221
Length 94
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 69.89
Mean single sequence MFE -28.40
Consensus MFE -17.83
Energy contribution -18.70
Covariance contribution 0.87
Combinations/Pair 1.17
Mean z-score -1.48
Structure conservation index 0.63
SVM decision value 0.66
SVM RNA-class probability 0.815489
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6154127 94 + 22224390
UAGUCCAACGGAUUCGGCUCUCUUUCGAGAGUGUGUUGGUGUCGAAGUACAGUGAUACCUCGACAGAGUUGAAUACCAGUUAUGACCCAUU---------UAA-----------------
..(((.(((((((((((((((...(((((...((((((.(((......))).))))))))))).)))))))))).)).)))..))).....---------...----------------- ( -28.50)
>DroSec_CAF1 7276 91 + 1
---ACUAACGGGUUCGGCUCUCUUGCGAGAGUGUGUUGGUGUCGAAGUACAGUGAUACCUCGUCAGAGUCGAAGCCCAGUUAUUACCCAUU---------UAA-----------------
---..((((((((((((((((...(((((...((((((.(((......))).))))))))))).))))))).))))).)))).........---------...----------------- ( -31.50)
>DroEre_CAF1 4992 119 + 1
UAGUCCACAGAGUUCGGCUCUCAACUGAGAGUGUGUUGGUGUCGAAGUACAGUGAUUCCUCGUCAAAGUCGAAC-GUAGAUUUUGCACUUUAAAUAUAUUUAAUUGAACUCAAUGGUUUG
....(((..(((((((((((((....))))))(((((((.((((........)))).))..(((((((((....-...))))))).))....))))).......)))))))..))).... ( -31.10)
>DroYak_CAF1 4645 96 + 1
CAGUCCACCGAGUUCGGCUCUCUUCC--GAGUGUGUUGGUGUCGAAGUACAGUGAGCCCUCGCCAAAGUCGAAC-UCAGCUAUUACACAUU---------UAAUUAUU------------
.........(((((((((((((....--))).(((..(((..(........)...)))..)))...))))))))-))..............---------........------------ ( -22.50)
>consensus
UAGUCCAACGAGUUCGGCUCUCUUCCGAGAGUGUGUUGGUGUCGAAGUACAGUGAUACCUCGUCAAAGUCGAAC_CCAGUUAUUACACAUU_________UAA_________________
.........((((((((((((.......(((.((((((.(((......))).)))))))))...)))))))))).))........................................... (-17.83 = -18.70 +   0.87)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 6,154,127 – 6,154,221
Length 94
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 69.89
Mean single sequence MFE -31.22
Consensus MFE -15.12
Energy contribution -16.25
Covariance contribution 1.12
Combinations/Pair 1.17
Mean z-score -3.27
Structure conservation index 0.48
SVM decision value 3.62
SVM RNA-class probability 0.999454
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6154127 94 - 22224390
-----------------UUA---------AAUGGGUCAUAACUGGUAUUCAACUCUGUCGAGGUAUCACUGUACUUCGACACCAACACACUCUCGAAAGAGAGCCGAAUCCGUUGGACUA
-----------------...---------....((((.((((.((.((((.....(((((((((((....)))))))))))........(((((....)))))..)))))))))))))). ( -35.10)
>DroSec_CAF1 7276 91 - 1
-----------------UUA---------AAUGGGUAAUAACUGGGCUUCGACUCUGACGAGGUAUCACUGUACUUCGACACCAACACACUCUCGCAAGAGAGCCGAACCCGUUAGU---
-----------------...---------.........((((.(((.((((.......((((((((....))))))))...........(((((....))))).)))))))))))..--- ( -29.00)
>DroEre_CAF1 4992 119 - 1
CAAACCAUUGAGUUCAAUUAAAUAUAUUUAAAGUGCAAAAUCUAC-GUUCGACUUUGACGAGGAAUCACUGUACUUCGACACCAACACACUCUCAGUUGAGAGCCGAACUCUGUGGACUA
....((((.((((((............(..(((((((...(((.(-(((.......)))).))).....)))))))..)..........(((((....)))))..)))))).)))).... ( -31.00)
>DroYak_CAF1 4645 96 - 1
------------AAUAAUUA---------AAUGUGUAAUAGCUGA-GUUCGACUUUGGCGAGGGCUCACUGUACUUCGACACCAACACACUC--GGAAGAGAGCCGAACUCGGUGGACUG
------------........---------.....((....(((((-(((((.(((((((((((((.....)).)))))...))))....(((--....))))).))))))))))..)).. ( -29.80)
>consensus
_________________UUA_________AAUGGGUAAUAACUGG_GUUCGACUCUGACGAGGUAUCACUGUACUUCGACACCAACACACUCUCGGAAGAGAGCCGAACCCGGUGGACUA
.........................................((((.(((((....((.((((((((....)))))))).))........(((((....))))).)))))...)))).... (-15.12 = -16.25 +   1.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:30:20 2006