Locus 5665

Sequence ID	2R_DroMel_CAF1
Location	17,971,622 – 17,971,722
Length	100
Max. P	0.997896

overview

Window 6

Location	17,971,622 – 17,971,722
Length	100
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	71.57
Mean single sequence MFE	-29.21
Consensus MFE	-16.41
Energy contribution	-18.50
Covariance contribution	2.09
Combinations/Pair	1.24
Mean z-score	-2.51
Structure conservation index	0.56
SVM decision value	2.96
SVM RNA-class probability	0.997896
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17971622 100 + 20766785
----UCAAUCGAUAGGAUUGGCUGACGGCUGCUCAAAAGCAGCGCUCAUUUGGCUACGAGUCUUUACCUAUAGCUGAUUUACAGCUAAUGCG--------------AUUCC-AUGCUAA
----..(((((.(((((..((((..((((((((....))))))(((.....)))..))))))..).))))((((((.....))))))...))--------------)))..-....... ( -29.30)
>DroSec_CAF1 28781 100 + 1
----UCAAUCGAUAGGGUUGGCUGUCAGCUGCUCAAAAGCAGCGCUCAUUUGGCUAUGAGUCCUUGCCUAUAGCUGAUUUACAGCUAAUGAG--------------AUUUC-AUCCCAA
----..........(((.(((......((((((....)))))).((((((.((((.((((((...((.....)).)))))).))))))))))--------------...))-).))).. ( -32.80)
>DroSim_CAF1 24403 100 + 1
----UCAAUCGAUAGGGUUGGCUGUCAGCUGCUCAAAAGCAGCGCUCAUUUGGCUAUGAGUCUUUGCCUAUAGCUGAUUUACAGCUAAUGAG--------------AUUUU-AUCCCAA
----......((((((((((((.....((((((....))))))((((((......))))))....)))..((((((.....))))))....)--------------)))))-))).... ( -32.80)
>DroEre_CAF1 33195 102 + 1
----UCAAUCGAUACGAUUGGCUGUCAGCUG-----------CGCCCAUUUGGCUAUGAUUCUUAGCUUA--GCUGAUUCAUAGCUUGAAAACCGCACAAAUGGUCAUAUGUUUCCCAA
----......((.(((..(((((((..(.((-----------((.......((((((((...(((((...--))))).)))))))).......)))))..)))))))..))).)).... ( -27.24)
>DroYak_CAF1 33307 97 + 1
AUACUCAAUCGAUAGCUUUGGUUGUCAGCUGCACAAAAGAAGCGCUCAUUUGGCCAUGAGUCUUGGCCUA--AAUGAUUUACAGCUAAAUAA------AA------AUAUG--------
..........((((((....))))))((((((.(.......).))(((((((((((.......))))).)--))))).....))))......------..------.....-------- ( -23.90)
>consensus
____UCAAUCGAUAGGAUUGGCUGUCAGCUGCUCAAAAGCAGCGCUCAUUUGGCUAUGAGUCUUUGCCUAUAGCUGAUUUACAGCUAAUGAG______________AUUUC_AUCCCAA
................(((((((((..(((((......)))))......(((((((((.((....)).)))))))))...))))))))).............................. (-16.41 = -18.50 +   2.09)

alignment

secondary structure

dotplot

Window 7

Location	17,971,622 – 17,971,722
Length	100
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	71.57
Mean single sequence MFE	-28.06
Consensus MFE	-12.91
Energy contribution	-14.96
Covariance contribution	2.05
Combinations/Pair	1.20
Mean z-score	-2.14
Structure conservation index	0.46
SVM decision value	1.65
SVM RNA-class probability	0.969831
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17971622 100 - 20766785
UUAGCAU-GGAAU--------------CGCAUUAGCUGUAAAUCAGCUAUAGGUAAAGACUCGUAGCCAAAUGAGCGCUGCUUUUGAGCAGCCGUCAGCCAAUCCUAUCGAUUGA----
.......-..(((--------------((...((((((.....))))))..(((...(.(((((......))))))((((((....)))))).....)))........)))))..---- ( -27.10)
>DroSec_CAF1 28781 100 - 1
UUGGGAU-GAAAU--------------CUCAUUAGCUGUAAAUCAGCUAUAGGCAAGGACUCAUAGCCAAAUGAGCGCUGCUUUUGAGCAGCUGACAGCCAACCCUAUCGAUUGA----
..(((((-((...--------------.))))((((((.....))))))..(((...(.(((((......))))))((((((....)))))).....)))..)))..........---- ( -31.60)
>DroSim_CAF1 24403 100 - 1
UUGGGAU-AAAAU--------------CUCAUUAGCUGUAAAUCAGCUAUAGGCAAAGACUCAUAGCCAAAUGAGCGCUGCUUUUGAGCAGCUGACAGCCAACCCUAUCGAUUGA----
..(((..-.....--------------.....((((((.....))))))..(((...(.(((((......))))))((((((....)))))).....)))..)))..........---- ( -31.70)
>DroEre_CAF1 33195 102 - 1
UUGGGAAACAUAUGACCAUUUGUGCGGUUUUCAAGCUAUGAAUCAGC--UAAGCUAAGAAUCAUAGCCAAAUGGGCG-----------CAGCUGACAGCCAAUCGUAUCGAUUGA----
...(....).......((.((((((((((.....(((((((.(((((--...)))..)).)))))))......(((.-----------.........)))))))))).))).)).---- ( -24.60)
>DroYak_CAF1 33307 97 - 1
--------CAUAU------UU------UUAUUUAGCUGUAAAUCAUU--UAGGCCAAGACUCAUGGCCAAAUGAGCGCUUCUUUUGUGCAGCUGACAACCAAAGCUAUCGAUUGAGUAU
--------.((((------((------.....(((((.....(((((--(.(((((.......)))))))))))((((.......)))).............)))))......)))))) ( -25.30)
>consensus
UUGGGAU_CAAAU______________CUCAUUAGCUGUAAAUCAGCUAUAGGCAAAGACUCAUAGCCAAAUGAGCGCUGCUUUUGAGCAGCUGACAGCCAACCCUAUCGAUUGA____
................................((((((.....))))))..(((...(.(((((......))))))(((((......))))).....)))................... (-12.91 = -14.96 +   2.05)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:51:20 2006