Locus 573

Sequence ID	2R_DroMel_CAF1
Location	2,956,679 – 2,956,799
Length	120
Max. P	0.999302

overview

Window 7

Location	2,956,679 – 2,956,799
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	76.67
Mean single sequence MFE	-29.85
Consensus MFE	-19.89
Energy contribution	-22.32
Covariance contribution	2.44
Combinations/Pair	1.22
Mean z-score	-2.26
Structure conservation index	0.67
SVM decision value	2.03
SVM RNA-class probability	0.986236
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2956679 120 + 20766785
AAUGGAUCAAUACGAGUACGAUUGGGGAGAUCCCAAGGAUCUCUUGAACUUAAAGCCAAAUCUGUGGCAUUCAUAGCUACUGUUAAGUAUCGGAGAUUAUUGGGACACUCCCGAAUAAAA
.......((((.((....))))))(((((.((((((.(((((((.((((((((..........(((((.......)))))..)))))).))))))))).))))))..)))))........ ( -37.80)
>DroSec_CAF1 4005 120 + 1
AAUGGAUCAAUACGAGUACGAUUAGGGAGGUCCCGAAAAUCUCUUCAACUUAAAGCGAAGACUGUGGCAUUCACAACUACAUUAAGGUCUCUGAGAUUAUUGGAACACUCCCGAGUAAAA
................(((.....(((((((.((((.((((((.....(((((.(...((..((((.....)))).)).).)))))......)))))).)))).)).)))))..)))... ( -27.90)
>DroSim_CAF1 4098 120 + 1
AAUGGAUCAAUACGAGUACGAUUGGGGAGGUCCCGAAAAUCUCUUCAACUUAAAGCAGAGUCUGUUGCAUUGAGAGCUACUUUUAAGUUUCUGAGAUUAUUGGAACACUCCCGAAUAAAA
.......((((.((....))))))(((((((.((((.((((((...(((((((((...((.((.((.....)).))))..)))))))))...)))))).)))).)).)))))........ ( -34.40)
>DroEre_CAF1 4264 92 + 1
AAUUGAUCAAUACGA-UACGAUUGGGGAGGACCCGAAAAUCUCUUUAACUUAAAGCAAA---------------------------GUCGCUGAGAUUUUGAGAACACUCCUGAAUAAAA
((((((((.....))-).))))).(((((....(.((((((((....((((......))---------------------------))....))))))))..)....)))))........ ( -19.30)
>consensus
AAUGGAUCAAUACGAGUACGAUUGGGGAGGUCCCGAAAAUCUCUUCAACUUAAAGCAAAGUCUGUGGCAUUCA_AGCUACUUUUAAGUCUCUGAGAUUAUUGGAACACUCCCGAAUAAAA
....................(((.(((((((.((((.((((((....(((((((.......(((((.....))))).....)))))))....)))))).)))).)).))))).))).... (-19.89 = -22.32 +   2.44)

alignment

secondary structure

dotplot

Window 8

Location	2,956,679 – 2,956,799
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	76.67
Mean single sequence MFE	-31.05
Consensus MFE	-20.58
Energy contribution	-20.70
Covariance contribution	0.12
Combinations/Pair	1.23
Mean z-score	-2.85
Structure conservation index	0.66
SVM decision value	3.50
SVM RNA-class probability	0.999302
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2956679 120 - 20766785
UUUUAUUCGGGAGUGUCCCAAUAAUCUCCGAUACUUAACAGUAGCUAUGAAUGCCACAGAUUUGGCUUUAAGUUCAAGAGAUCCUUGGGAUCUCCCCAAUCGUACUCGUAUUGAUCCAUU
........(((((.(((((((..(((((....((((((((.......))...((((......)))).))))))....)))))..))))))))))))((((((....)).))))....... ( -36.10)
>DroSec_CAF1 4005 120 - 1
UUUUACUCGGGAGUGUUCCAAUAAUCUCAGAGACCUUAAUGUAGUUGUGAAUGCCACAGUCUUCGCUUUAAGUUGAAGAGAUUUUCGGGACCUCCCUAAUCGUACUCGUAUUGAUCCAUU
........(((((.(((((...((((((...(((.((((.(((((((((.....))))).))..)).)))))))...))))))...))))))))))((((((....)).))))....... ( -32.20)
>DroSim_CAF1 4098 120 - 1
UUUUAUUCGGGAGUGUUCCAAUAAUCUCAGAAACUUAAAAGUAGCUCUCAAUGCAACAGACUCUGCUUUAAGUUGAAGAGAUUUUCGGGACCUCCCCAAUCGUACUCGUAUUGAUCCAUU
........(((((.(((((...((((((...((((((((.((((.(((.........)))..))))))))))))...))))))...))))))))))((((((....)).))))....... ( -36.00)
>DroEre_CAF1 4264 92 - 1
UUUUAUUCAGGAGUGUUCUCAAAAUCUCAGCGAC---------------------------UUUGCUUUAAGUUAAAGAGAUUUUCGGGUCCUCCCCAAUCGUA-UCGUAUUGAUCAAUU
.........((((.(..((.((((((((...(((---------------------------((......)))))...)))))))).))..))))).((((((..-.)).))))....... ( -19.90)
>consensus
UUUUAUUCGGGAGUGUUCCAAUAAUCUCAGAGACUUAAAAGUAGCU_UGAAUGCCACAGACUUUGCUUUAAGUUGAAGAGAUUUUCGGGACCUCCCCAAUCGUACUCGUAUUGAUCCAUU
........(((((.(((((...((((((............((.((.......)).))....((.((.....)).)).))))))...))))))))))((((((....)).))))....... (-20.58 = -20.70 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:41:56 2006