Locus 6549

Sequence ID	3R_DroMel_CAF1
Location	17,254,052 – 17,254,160
Length	108
Max. P	0.961840

overview

Window 2

Location	17,254,052 – 17,254,160
Length	108
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	92.85
Mean single sequence MFE	-42.60
Consensus MFE	-33.92
Energy contribution	-34.08
Covariance contribution	0.16
Combinations/Pair	1.15
Mean z-score	-2.24
Structure conservation index	0.80
SVM decision value	1.53
SVM RNA-class probability	0.961786
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17254052 108 + 27905053
GCUGGCCAAAUGCAGAGUGCGCUAUACUCCGUGGGGCCGCGGGGUCAGC---GAGGAGUGUUGCUCCGGGGCACGGGGCCAGGCAGAAAAUGCGUUUUUAAAUGGUUUUUA
.((((((...(((......((((..((((((((....)))))))).)))---).((((.....))))...)))...))))))(((.....))).................. ( -43.90)
>DroSec_CAF1 50587 108 + 1
GCUGGCCAAAUGCAGAGUGCGCUAUACGCCGUGGUUCCACGGGGUCAGC---GAGGAGUGUUGCUCCGGGGCAAGGGGCCAGGCAGAAAAUGCGUUUUUAAAUGGUUUUUA
.((((((...(((......((((..((.(((((....))))).)).)))---).((((.....))))...)))...))))))(((.....))).................. ( -42.40)
>DroSim_CAF1 51170 108 + 1
GCUGGCCAAAUGCAGAGUGCGCUAUACGCCGUGGUUCCGCGGGGUCAGC---GAGGAGUGUUGCUCCGGGGCAAGGGGCCAGGCAGAAAAUGCGUUUUUAAAUGGUUUUUA
.((((((...(((......((((..((.(((((....))))).)).)))---).((((.....))))...)))...))))))(((.....))).................. ( -42.00)
>DroEre_CAF1 52528 107 + 1
GCUGGCCAAAUGCAGAGUGCGCUAUACGCUUUGG-GCCGCGGGGUCAGC---GAGGAGUGUUGCUCCGGGGCAAUGGGCCAGGCAGAAAAUGCGUUUUUAAAUGGUUUUUA
.((((((.....(((((((.......))))))).-(((.(((((.((((---(.....)))))))))).)))....))))))(((.....))).................. ( -42.50)
>DroYak_CAF1 73363 110 + 1
GCUGGCUAAAUGCGGAGUGGGCUAUACGCCUUGG-GCCGCGGGGUCAGCAAGGAGGAGUGUUGCUGUGGGGCCAUGGGCCAGGCAGAAAAUGCGUUUUUAAAUGGUUUUUA
(((((((...(((((...((((.....))))...-.))))).)))))))...((((((((((.((((..((((...))))..))))..))))).)))))............ ( -42.20)
>consensus
GCUGGCCAAAUGCAGAGUGCGCUAUACGCCGUGG_GCCGCGGGGUCAGC___GAGGAGUGUUGCUCCGGGGCAAGGGGCCAGGCAGAAAAUGCGUUUUUAAAUGGUUUUUA
.((((((...(((.......(((..((.(((((....))))).)).))).....((((.....))))...)))...))))))(((.....))).................. (-33.92 = -34.08 +   0.16)

alignment

secondary structure

dotplot

Window 3

Location	17,254,052 – 17,254,160
Length	108
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	92.85
Mean single sequence MFE	-31.84
Consensus MFE	-24.66
Energy contribution	-26.06
Covariance contribution	1.40
Combinations/Pair	1.00
Mean z-score	-2.55
Structure conservation index	0.77
SVM decision value	1.53
SVM RNA-class probability	0.961840
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17254052 108 - 27905053
UAAAAACCAUUUAAAAACGCAUUUUCUGCCUGGCCCCGUGCCCCGGAGCAACACUCCUC---GCUGACCCCGCGGCCCCACGGAGUAUAGCGCACUCUGCAUUUGGCCAGC
..................(((.....)))((((((..((((...((((.....)))).(---((((((.(((.(....).))).)).)))))......))))..)))))). ( -34.20)
>DroSec_CAF1 50587 108 - 1
UAAAAACCAUUUAAAAACGCAUUUUCUGCCUGGCCCCUUGCCCCGGAGCAACACUCCUC---GCUGACCCCGUGGAACCACGGCGUAUAGCGCACUCUGCAUUUGGCCAGC
..................(((.....)))((((((...(((...((((.....)))).(---((((((.(((((....))))).)).)))))......)))...)))))). ( -36.60)
>DroSim_CAF1 51170 108 - 1
UAAAAACCAUUUAAAAACGCAUUUUCUGCCUGGCCCCUUGCCCCGGAGCAACACUCCUC---GCUGACCCCGCGGAACCACGGCGUAUAGCGCACUCUGCAUUUGGCCAGC
..................(((.....)))((((((...(((...((((.....)))).(---((((((.(((.(....).))).)).)))))......)))...)))))). ( -32.70)
>DroEre_CAF1 52528 107 - 1
UAAAAACCAUUUAAAAACGCAUUUUCUGCCUGGCCCAUUGCCCCGGAGCAACACUCCUC---GCUGACCCCGCGGC-CCAAAGCGUAUAGCGCACUCUGCAUUUGGCCAGC
..................(((.....)))((((((...(((...((((.....)))).(---((((....(((...-.....)))..)))))......)))...)))))). ( -28.80)
>DroYak_CAF1 73363 110 - 1
UAAAAACCAUUUAAAAACGCAUUUUCUGCCUGGCCCAUGGCCCCACAGCAACACUCCUCCUUGCUGACCCCGCGGC-CCAAGGCGUAUAGCCCACUCCGCAUUUAGCCAGC
..................(((.....)))(((((....((.....((((((.........))))))...))((((.-....(((.....)))....)))).....))))). ( -26.90)
>consensus
UAAAAACCAUUUAAAAACGCAUUUUCUGCCUGGCCCCUUGCCCCGGAGCAACACUCCUC___GCUGACCCCGCGGC_CCACGGCGUAUAGCGCACUCUGCAUUUGGCCAGC
..................(((.....)))((((((...(((...((((.....)))).....((((((.(((.(....).))).)).)))).......)))...)))))). (-24.66 = -26.06 +   1.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:24:15 2006