Locus 8618

Sequence ID	X_DroMel_CAF1
Location	21,648,736 – 21,648,836
Length	100
Max. P	0.984251

overview

Window 8

Location	21,648,736 – 21,648,836
Length	100
Sequences	4
Columns	115
Reading direction	forward
Mean pairwise identity	78.54
Mean single sequence MFE	-31.65
Consensus MFE	-26.25
Energy contribution	-25.62
Covariance contribution	-0.62
Combinations/Pair	1.21
Mean z-score	-2.16
Structure conservation index	0.83
SVM decision value	1.97
SVM RNA-class probability	0.984251
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21648736 100 + 22224390
AUCCCAACACGUCAGCAGA-----AUCUGUGUGAUGUGCUUGGGAGGAAAUUUCCAAGCGGCA-AGAUGUGAUAACGAUCGUGUCGCUGAUAUGUA----CUUGGC-----AUAU
.(((((((((((((((((.-----..)))).))))))).))))))(((....))).(((((((-.(((((....)).))).))))))).((((((.----....))-----)))) ( -38.90)
>DroSec_CAF1 360 109 + 1
UCCCCAACACGUCAGCAGA-----AUCUGUGUGAUGUGCUUGGGAGGAAAUUUCCAAGCGGCA-AGAUGUGAUAACGAUUGUGUCGCUGAUAUGUUAGAUAUUAGCAUUAGAUAU
..((((((((((((((((.-----..)))).))))))).))))).(((....)))....((((-.(((((....)).))).))))((((((((.....))))))))......... ( -34.60)
>DroEre_CAF1 267024 97 + 1
UCCCCAACACGUCAGCAGAAUCGAAUCUGUAUAAUGUGCGCGGGGGG-AGUUUCCAAGCGGCAAAGAUGUGAUAAAGAUCGUGUUAUUGAUAUGUA----CA-------------
.((((..(((((..(((((......)))))...)))))...))))((-.....))..(((.(((.((..((((....))))..)).)))...))).----..------------- ( -25.70)
>DroYak_CAF1 79287 98 + 1
UCCCCAACACGUCAGCAGA-----AUCUGUAUGAUGUGCUCGGGGGG-AAUUUCCGAGCGGCA-AGAUGUGAUAAAGAUCGUGUUACUGAUAUGCA----CUUAG------AUGU
(((((..(((((((((((.-----..)))).))))))).....))))-)...((..((..(((-....((((((.......)))))).....))).----))..)------)... ( -27.40)
>consensus
UCCCCAACACGUCAGCAGA_____AUCUGUAUGAUGUGCUCGGGAGG_AAUUUCCAAGCGGCA_AGAUGUGAUAAAGAUCGUGUCACUGAUAUGUA____CUUAG______AUAU
........(((((((((((......))))).))))))(((((((((....))))))))).(((.....((((((.......)))))).....))).................... (-26.25 = -25.62 +  -0.62)

alignment

secondary structure

dotplot

Window 9

Location	21,648,736 – 21,648,836
Length	100
Sequences	4
Columns	115
Reading direction	reverse
Mean pairwise identity	78.54
Mean single sequence MFE	-23.18
Consensus MFE	-19.88
Energy contribution	-19.25
Covariance contribution	-0.62
Combinations/Pair	1.24
Mean z-score	-1.27
Structure conservation index	0.86
SVM decision value	0.20
SVM RNA-class probability	0.631495
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21648736 100 - 22224390
AUAU-----GCCAAG----UACAUAUCAGCGACACGAUCGUUAUCACAUCU-UGCCGCUUGGAAAUUUCCUCCCAAGCACAUCACACAGAU-----UCUGCUGACGUGUUGGGAU
..((-----.(((..----.(((..((((((.((.(((.((....))))).-)).)((((((..........)))))).............-----...)))))..)))))).)) ( -24.20)
>DroSec_CAF1 360 109 - 1
AUAUCUAAUGCUAAUAUCUAACAUAUCAGCGACACAAUCGUUAUCACAUCU-UGCCGCUUGGAAAUUUCCUCCCAAGCACAUCACACAGAU-----UCUGCUGACGUGUUGGGGA
................(((((((..((((((((......))).........-....((((((..........)))))).............-----...)))))..))))))).. ( -26.30)
>DroEre_CAF1 267024 97 - 1
-------------UG----UACAUAUCAAUAACACGAUCUUUAUCACAUCUUUGCCGCUUGGAAACU-CCCCCCGCGCACAUUAUACAGAUUCGAUUCUGCUGACGUGUUGGGGA
-------------..----......((..(((((((.((.............(((((...((.....-))...)).))).......((((......))))..)))))))))..)) ( -19.20)
>DroYak_CAF1 79287 98 - 1
ACAU------CUAAG----UGCAUAUCAGUAACACGAUCUUUAUCACAUCU-UGCCGCUCGGAAAUU-CCCCCCGAGCACAUCAUACAGAU-----UCUGCUGACGUGUUGGGGA
...(------((...----.(((..((((((....(((((.(((.......-((..((((((.....-....)))))).))..))).))))-----).))))))..)))...))) ( -23.00)
>consensus
AUAU______CUAAG____UACAUAUCAGCAACACGAUCGUUAUCACAUCU_UGCCGCUUGGAAAUU_CCCCCCAAGCACAUCACACAGAU_____UCUGCUGACGUGUUGGGGA
.........................((..(((((((.((.................((((((..........))))))........((((......))))..))))))))).)). (-19.88 = -19.25 +  -0.62)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:08:41 2006