Locus 4835

Sequence ID	2R_DroMel_CAF1
Location	15,878,983 – 15,879,076
Length	93
Max. P	0.603136

overview

Window 8

Location	15,878,983 – 15,879,076
Length	93
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	83.02
Mean single sequence MFE	-35.58
Consensus MFE	-23.56
Energy contribution	-23.64
Covariance contribution	0.09
Combinations/Pair	1.14
Mean z-score	-1.74
Structure conservation index	0.66
SVM decision value	-0.04
SVM RNA-class probability	0.514881
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15878983 93 + 20766785
G-AAAUCCGGAAU----------------------CCGGGCAUCCGGAUGGCAACCACAGCGGCGACGGCUGCGGCAUAAUAAAUGCGAACAUAACUCUGAUUCUCCGAAUGCUUA
.-....((((...----------------------))))((((.((((..(((......(((((....))))).((((.....))))...........)).)..)))).))))... ( -26.80)
>DroSec_CAF1 16146 109 + 1
G-AAAUCCGGAGUCCG------GGCAUCUGGGCAUCCGGGCAUCCGGAUGGCAACCACAGCGGCGACGGCUGCGGCAUAAUAAAUGCGAACAUAACUCUGAUUCUCCGAAUGCUUA
.-....((((((((((------(....)))))).)))))((((.((((..(((......(((((....))))).((((.....))))...........)).)..)))).))))... ( -39.60)
>DroSim_CAF1 13570 101 + 1
G-AAAAUCGGAGUCCG------GGC--------AUCCGGGCAUCCGGAUGGCAACCACAGCGGCGACGGCUGCGGCAUAAUAAAUGCGAACAUAACUCUGAUUCUCCGAAUGCUUA
(-(.(((((((((...------(.(--------((((((....))))))).).......(((((....))))).((((.....)))).......))))))))).)).......... ( -36.40)
>DroEre_CAF1 13853 114 + 1
G-AAAUCCGGUAUCCAAAAUUCGGAGUCCGG-AAUCCGGGCGUCCGGAUGGCAACCGCAGCGGCGACGGCUGCGGCAUAAUAAAUGCGAACAUAACUCUGAUUCUCCGAAUGCUUA
.-...(((((..(((.......)))..))))-)....((((((.((((..(((..(((((((....).))))))((((.....))))...........)).)..)))).)))))). ( -38.90)
>DroYak_CAF1 16409 116 + 1
CAAAAUCCGGAAUCUGGAAUACGGAAUCCGGGCGUCCGGGCAUCCGGAUGCCAACCGCAGCGGCGACGGCUGCGGCAUAAUAAAUGCGAACAUAACUCUGAUUCUCCGAAUGCUUA
.......((((.((((.....)))).))))(((((((((....)))))))))...(((((((....).))))))((((.....))))(((((......)).)))............ ( -44.20)
>DroAna_CAF1 9327 92 + 1
G-GAAUCCGGAAUCU-----------------------GGCAUCCGGAUGGCAACCACAGCGGCGACGGCUGCGGCAUAAUAAAUGCGAGCAUAACUCUGAUUCUUCGAAUGCUUA
(-(.(((((((....-----------------------....))))))).....))...(((((....))))).((((.....))))((((((...((.((....)))))))))). ( -27.60)
>consensus
G_AAAUCCGGAAUCCG______GG_________AUCCGGGCAUCCGGAUGGCAACCACAGCGGCGACGGCUGCGGCAUAAUAAAUGCGAACAUAACUCUGAUUCUCCGAAUGCUUA
......((((.........................))))((((.((((...........(((((....))))).((((.....)))).................)))).))))... (-23.56 = -23.64 +   0.09)

alignment

secondary structure

dotplot

Window 9

Location	15,878,983 – 15,879,076
Length	93
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	83.02
Mean single sequence MFE	-36.55
Consensus MFE	-27.57
Energy contribution	-28.68
Covariance contribution	1.11
Combinations/Pair	1.03
Mean z-score	-1.60
Structure conservation index	0.75
SVM decision value	0.14
SVM RNA-class probability	0.603136
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15878983 93 - 20766785
UAAGCAUUCGGAGAAUCAGAGUUAUGUUCGCAUUUAUUAUGCCGCAGCCGUCGCCGCUGUGGUUGCCAUCCGGAUGCCCGG----------------------AUUCCGGAUUU-C
...((((((((((((.((......)))))(((........((((((((.......)))))))))))..)))))))))((((----------------------...))))....-. ( -33.80)
>DroSec_CAF1 16146 109 - 1
UAAGCAUUCGGAGAAUCAGAGUUAUGUUCGCAUUUAUUAUGCCGCAGCCGUCGCCGCUGUGGUUGCCAUCCGGAUGCCCGGAUGCCCAGAUGCC------CGGACUCCGGAUUU-C
.....((((((((.....(((.....)))((((((.....((((((((.......))))))))...(((((((....)))))))...)))))).------....))))))))..-. ( -39.50)
>DroSim_CAF1 13570 101 - 1
UAAGCAUUCGGAGAAUCAGAGUUAUGUUCGCAUUUAUUAUGCCGCAGCCGUCGCCGCUGUGGUUGCCAUCCGGAUGCCCGGAU--------GCC------CGGACUCCGAUUUU-C
..........(((((((.(((((......(((........((((((((.......)))))))))))(((((((....))))))--------)..------..))))).))))))-) ( -36.70)
>DroEre_CAF1 13853 114 - 1
UAAGCAUUCGGAGAAUCAGAGUUAUGUUCGCAUUUAUUAUGCCGCAGCCGUCGCCGCUGCGGUUGCCAUCCGGACGCCCGGAUU-CCGGACUCCGAAUUUUGGAUACCGGAUUU-C
...((.(((((((((.((......)))))(((........((((((((.......)))))))))))..)))))).))..(((.(-((((..(((((...)))))..))))).))-) ( -39.80)
>DroYak_CAF1 16409 116 - 1
UAAGCAUUCGGAGAAUCAGAGUUAUGUUCGCAUUUAUUAUGCCGCAGCCGUCGCCGCUGCGGUUGGCAUCCGGAUGCCCGGACGCCCGGAUUCCGUAUUCCAGAUUCCGGAUUUUG
...((((((((((((.((......)))))((.........((((((((.......))))))))..)).)))))))))(((((..(..(((........))).)..)))))...... ( -41.90)
>DroAna_CAF1 9327 92 - 1
UAAGCAUUCGAAGAAUCAGAGUUAUGCUCGCAUUUAUUAUGCCGCAGCCGUCGCCGCUGUGGUUGCCAUCCGGAUGCC-----------------------AGAUUCCGGAUUC-C
...(((............(((.....)))...........((((((((.......))))))))))).(((((((....-----------------------....)))))))..-. ( -27.60)
>consensus
UAAGCAUUCGGAGAAUCAGAGUUAUGUUCGCAUUUAUUAUGCCGCAGCCGUCGCCGCUGUGGUUGCCAUCCGGAUGCCCGGAU_________CC______CGGAUUCCGGAUUU_C
...((((((((((((.((......)))))(((........((((((((.......)))))))))))..)))))))))((((.........................))))...... (-27.57 = -28.68 +   1.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:30:26 2006