Locus 2723

Sequence ID	3L_DroMel_CAF1
Location	7,610,523 – 7,610,662
Length	139
Max. P	0.531206

overview

Window 5

Location	7,610,523 – 7,610,643
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	86.84
Mean single sequence MFE	-41.03
Consensus MFE	-32.08
Energy contribution	-31.75
Covariance contribution	-0.33
Combinations/Pair	1.27
Mean z-score	-2.03
Structure conservation index	0.78
SVM decision value	-0.01
SVM RNA-class probability	0.529333
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7610523 120 - 23771897
ACUCACUUUUGUAUCUUGGGAUCCAGGCAGCUGAGCUCCUCCAGCUUGGGCAGCUCUAGACUGGAGCCAUGGCACUGCAGAUGGGCAUUCGCCUCCAUGGGCGAGUGCAUGAUGUCCAUG
..................(((((((.(((((..((((.....))))..)((.(((((.....)))))....)).))))...)))((((((((((....)))))))))).....))))... ( -45.60)
>DroVir_CAF1 80979 117 - 1
ACUUACUUUUGUAUUUUUGGUUCCAAACAGCUGAGCUCCUCCAGUUUGGUCAGCUCCAGAUUGGAGGCAUGGCACUGUAGAUGGGCAUUCGCCUCCAUGGGCGAGUGCAU---GUCCAUG
...(((....)))....(((..(((.((((.((....((((((((((((......)))))))))))).....))))))...)))((((((((((....))))))))))..---..))).. ( -45.60)
>DroGri_CAF1 54772 117 - 1
ACUUACUUUUGUAUUUUUGGUUCCAAACAGCUGAGCUCCUCCAGCUUGGUCAGCUCCAUAUUGGAGUCAUGGCACUGGAGAUGAGCAUUGGCCUCCAUGGGCGAGUGCAU---GUCCAUG
...(((....)))..((((....))))..((..(((((((((((....(((((((((.....)))))..)))).))))))..)))).)..))...((((((((......)---))))))) ( -40.20)
>DroWil_CAF1 86970 117 - 1
ACUUACUUUUGUAUUUUUGGUUCCAAACAGCUUAGUUCCUCCAAUUUGGGUAACUCCAGACUGGAGCCAUGGCACUGCAGAUGGGCAUUUGCCUCCAUGGGUGAAUGCAU---UUCCAUA
........(((((..((((....))))..(((......(((((.((((((....)))))).)))))....)))..)))))(((((((((..(((....)))..)))))..---..)))). ( -34.00)
>DroMoj_CAF1 65408 117 - 1
ACUUACUUUUGUAUUUUUGGUUCCAAACAGCUGAGCUCUUCCAGUGUGGUCAGCUCCAGGUUGGACGCAUGGCACUGCAGAUGAGCAUUCGCCUCCAUGGGCGAGUGCAU---GUCCAUG
...(((....)))..(((((........((((((.(.(.......).).))))))))))).((((((((......)))......((((((((((....))))))))))..---))))).. ( -38.50)
>DroAna_CAF1 55650 117 - 1
UCUCACUUUUGUAUUUUCGGUUCCAGGCAGCUCAACUCCUCCAGCUUGGGCAGCUCUAGACUGGAACCAUGGCACUGCAAGUGGGCAUUCGCCUCCAUGGGCGAGUGCAU---GUCUAUG
..((((((..........((((((((((.((((((((.....)).)))))).))......))))))))...((...))))))))((((((((((....))))))))))..---....... ( -42.30)
>consensus
ACUUACUUUUGUAUUUUUGGUUCCAAACAGCUGAGCUCCUCCAGCUUGGGCAGCUCCAGACUGGAGCCAUGGCACUGCAGAUGGGCAUUCGCCUCCAUGGGCGAGUGCAU___GUCCAUG
...........(((((..(((.(((...(((...))).((((((..(((......)))..))))))...))).)))..))))).((((((((((....))))))))))............ (-32.08 = -31.75 +  -0.33)

alignment

secondary structure

dotplot

Window 6

Location	7,610,563 – 7,610,662
Length	99
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	75.70
Mean single sequence MFE	-24.38
Consensus MFE	-17.73
Energy contribution	-17.84
Covariance contribution	0.11
Combinations/Pair	1.22
Mean z-score	-0.82
Structure conservation index	0.73
SVM decision value	-0.00
SVM RNA-class probability	0.531206
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7610563 99 + 23771897
CUGCAGUGCCAUGGCUCCAGUCUAGAGCUGCCCAAGCUGGAGGAGCUCAGCUGCCUGGAUCCCAAGAUACAAAAGUGAGU--UCU-AUCAGCCACACUUAUU---
..(((((.....(((....)))....)))))....(((((.((((((((.((...((.(((....))).))..)))))))--)))-.)))))..........--- ( -29.60)
>DroVir_CAF1 81016 84 + 1
CUACAGUGCCAUGCCUCCAAUCUGGAGCUGACCAAACUGGAGGAGCUCAGCUGUUUGGAACCAAAAAUACAAAAGUAAGU--GCGU-------------------
..(((((......((((((.(.(((......))).).))))))......)))))(((....)))................--....------------------- ( -19.20)
>DroPse_CAF1 60534 98 + 1
CUGCAGUGCCAUGGCUCCAGUCUGGAACUGCCCAAGCUGGAGGAGCUCAGCUGCCUGGACCCCAAAAUACAAAAGUAGGAAAGAA-ACUCU------UUAUCCAU
..(((((.......((((((..(((......)))..)))))).......))))).((((........(((....)))..((((..-...))------)).)))). ( -27.84)
>DroGri_CAF1 54809 81 + 1
CUCCAGUGCCAUGACUCCAAUAUGGAGCUGACCAAGCUGGAGGAGCUCAGCUGUUUGGAACCAAAAAUACAAAAGUAAGU--C----------------------
(((((((.....(.((((.....))))).......)))))))..(((..(((.((((............))))))).)))--.---------------------- ( -19.00)
>DroAna_CAF1 55687 93 + 1
UUGCAGUGCCAUGGUUCCAGUCUAGAGCUGCCCAAGCUGGAGGAGUUGAGCUGCCUGGAACCGAAAAUACAAAAGUGAGA--CCA-AUCCU------UUAUG---
.....(((...(((((((((..(((.(((.(((.....)).).)))....))).)))))))))....))).((((.((..--...-.))))------))...--- ( -22.80)
>DroPer_CAF1 60686 98 + 1
CUGCAGUGCCAUGGCUCCAGUCUGGAACUGCCCAAGCUGGAGGAGCUCAGCUGCCUGGACCCCAAAAUACAAAAGUAGGAAAGAA-ACUCU------UUAUCCAU
..(((((.......((((((..(((......)))..)))))).......))))).((((........(((....)))..((((..-...))------)).)))). ( -27.84)
>consensus
CUGCAGUGCCAUGGCUCCAGUCUGGAGCUGCCCAAGCUGGAGGAGCUCAGCUGCCUGGAACCCAAAAUACAAAAGUAAGA__GCA_A__CU______UUAU____
..(((((.......(((((((.(((......))).))))))).......))))).............(((....)))............................ (-17.73 = -17.84 +   0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:40:16 2006