Locus 5475

Sequence ID	3R_DroMel_CAF1
Location	14,452,035 – 14,452,155
Length	120
Max. P	0.996916

overview

Window 3

Location	14,452,035 – 14,452,155
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.80
Mean single sequence MFE	-31.24
Consensus MFE	-25.28
Energy contribution	-24.80
Covariance contribution	-0.48
Combinations/Pair	1.11
Mean z-score	-1.52
Structure conservation index	0.81
SVM decision value	0.28
SVM RNA-class probability	0.664948
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14452035 120 + 27905053
GCAAUGUACAUUCACUUUCAAUAGCCAAUGACAUUCACUUGGCCGACAACGGGCAAUUGAUCAGCAGGCCCAGAGCCUGCUGAGCUCCGUAUUAUGGCACCCAUUAAAUGUGAUUCCAUU
..((((.....((((.((.(((.((((...((..(((.(((.(((....))).))).)))(((((((((.....))))))))).....))....))))....))).)).))))...)))) ( -35.10)
>DroSec_CAF1 9232 119 + 1
GCAACGUACAUUCACUUUCAAUAGCCAAUGACAUUCACUUGGCCGACAACGGGCAAUUGAUCAGCAGGCC-GUAGCCCGCUGAGCUCCGCAUUAUGGCACCCAUUAAAUGUGAUUCCAUU
((...((.((((..((......))..))))))..(((.(((.(((....))).))).)))(((((.(((.-...))).)))))))..((((((((((...))))..))))))........ ( -32.10)
>DroSim_CAF1 9811 119 + 1
GCAACGUACAUUCACUUUCAAUAGCCAAUGACAUUCACUUGGCCGACAACGGGCAAUUGAUCAGCAGGCC-GUAGCCCGCUGAGCUCCGUAUUAUGGCACCCAUUAAAUGUGAUUCCAUU
...........((((.((.(((.((((...((..(((.(((.(((....))).))).)))(((((.(((.-...))).))))).....))....))))....))).)).))))....... ( -30.20)
>DroEre_CAF1 9019 119 + 1
GCAACGAACAUUCACUUUCAAUAGCCAAUGACAUUCACUUGCCAGACAACUGGCAAUUGAUCAGCAGGCC-GGCGCCCGCUGAGCUCUGUAUUAUGGCACCCAUUAAAUGCGAUUCCAAU
(((..(((........)))....((((.(((...(((.(((((((....))))))).))))))(((((((-(((....)))).)).))))....))))..........)))......... ( -35.80)
>DroYak_CAF1 10366 119 + 1
GCAACGAACAUUCACUUUCAAUAGCCAAUGACAUUCACUUGGCCGACAACUGGCAAUUGAUCAGCAGCCC-GGAGCCCGCUGAGCUCUGUAUUAUGGUACCCAUUAAAUGCGAUUCCAUU
((...............(((((.((((.((.....)).(((.....))).)))).)))))(((((.((..-...))..)))))))..((((((((((...))))..))))))........ ( -23.00)
>consensus
GCAACGUACAUUCACUUUCAAUAGCCAAUGACAUUCACUUGGCCGACAACGGGCAAUUGAUCAGCAGGCC_GGAGCCCGCUGAGCUCCGUAUUAUGGCACCCAUUAAAUGUGAUUCCAUU
((......((((..((......))..))))....(((.(((.(((....))).))).)))(((((.(((.....))).)))))))..((((((((((...))))..))))))........ (-25.28 = -24.80 +  -0.48)

alignment

secondary structure

dotplot

Window 4

Location	14,452,035 – 14,452,155
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.80
Mean single sequence MFE	-41.30
Consensus MFE	-35.24
Energy contribution	-34.60
Covariance contribution	-0.64
Combinations/Pair	1.14
Mean z-score	-2.38
Structure conservation index	0.85
SVM decision value	2.77
SVM RNA-class probability	0.996916
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14452035 120 - 27905053
AAUGGAAUCACAUUUAAUGGGUGCCAUAAUACGGAGCUCAGCAGGCUCUGGGCCUGCUGAUCAAUUGCCCGUUGUCGGCCAAGUGAAUGUCAUUGGCUAUUGAAAGUGAAUGUACAUUGC
((((...((((...((((((((.((.......)).(.(((((((((.....))))))))).)....))))))))..((((((.((.....)))))))).......)))).....)))).. ( -41.60)
>DroSec_CAF1 9232 119 - 1
AAUGGAAUCACAUUUAAUGGGUGCCAUAAUGCGGAGCUCAGCGGGCUAC-GGCCUGCUGAUCAAUUGCCCGUUGUCGGCCAAGUGAAUGUCAUUGGCUAUUGAAAGUGAAUGUACGUUGC
((((...((((...((((((((((......))...(.(((((((((...-.))))))))).)....))))))))..((((((.((.....)))))))).......)))).....)))).. ( -43.30)
>DroSim_CAF1 9811 119 - 1
AAUGGAAUCACAUUUAAUGGGUGCCAUAAUACGGAGCUCAGCGGGCUAC-GGCCUGCUGAUCAAUUGCCCGUUGUCGGCCAAGUGAAUGUCAUUGGCUAUUGAAAGUGAAUGUACGUUGC
((((...((((...((((((((.((.......)).(.(((((((((...-.))))))))).)....))))))))..((((((.((.....)))))))).......)))).....)))).. ( -43.00)
>DroEre_CAF1 9019 119 - 1
AUUGGAAUCGCAUUUAAUGGGUGCCAUAAUACAGAGCUCAGCGGGCGCC-GGCCUGCUGAUCAAUUGCCAGUUGUCUGGCAAGUGAAUGUCAUUGGCUAUUGAAAGUGAAUGUUCGUUGC
...(((.((((.(((((((...((((....(((....(((((((((...-.)))))))))(((.(((((((....))))))).))).)))...))))))))))).))))...)))..... ( -44.50)
>DroYak_CAF1 10366 119 - 1
AAUGGAAUCGCAUUUAAUGGGUACCAUAAUACAGAGCUCAGCGGGCUCC-GGGCUGCUGAUCAAUUGCCAGUUGUCGGCCAAGUGAAUGUCAUUGGCUAUUGAAAGUGAAUGUUCGUUGC
.((((.(((.(((...)))))).))))......(((((((((((.(...-.).)))))))(((((.((((((.(.((..(....)..)).))))))).)))))........))))..... ( -34.10)
>consensus
AAUGGAAUCACAUUUAAUGGGUGCCAUAAUACGGAGCUCAGCGGGCUCC_GGCCUGCUGAUCAAUUGCCCGUUGUCGGCCAAGUGAAUGUCAUUGGCUAUUGAAAGUGAAUGUACGUUGC
.......((((.((((((((...(((....(((....(((((((((.....)))))))))(((.(((.(((....))).))).))).)))...))))))))))).))))........... (-35.24 = -34.60 +  -0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:55:52 2006