Locus 840

Sequence ID	3L_DroMel_CAF1
Location	2,548,923 – 2,549,040
Length	117
Max. P	0.998952

overview

Window 1

Location	2,548,923 – 2,549,040
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	77.25
Mean single sequence MFE	-26.70
Consensus MFE	-19.65
Energy contribution	-20.49
Covariance contribution	0.84
Combinations/Pair	1.06
Mean z-score	-2.37
Structure conservation index	0.74
SVM decision value	2.33
SVM RNA-class probability	0.992514
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2548923 117 + 23771897
AAACAAUCAAUGCAGAGUGCGUUGCCGAAGUUAU--GUGUUAGUUUUAAAUCUGUUAUCAUGAUCUGUUUA-AUCAAAAUGCAUUUCCUCAACGCCCGGCACUUCGGAAACGCACUCCAA
..............(((((((((.(((((((.((--(((((....((((((..(((.....)))..)))))-)....))))))).........((...))))))))).)))))))))... ( -31.20)
>DroSec_CAF1 10931 118 + 1
AAACAAUCAAUGCAGAGUGCGUUGCCGAAGUUAU--GUGUUAGUUUUAAACCUGUUAUCUUGACCUGAUUAUAUCAAAAUGCAUUUCCUUAAGGCCAAGUACUUCGGAAACGCACUCAAA
..............(((((((((.(((((((...--(((.(((........))).)))((((.(((.........................))).)))).))))))).)))))))))... ( -30.71)
>DroSim_CAF1 7835 118 + 1
AAACAAUCAAUGCAGAGUGCGUUGCCGAAAUAAU--GUGUUAGUUUUAAACCUCUUAUCUUGACCUGAUUAUAUCAAAAUGCAUUUCCUUAAGGCCAAGUACUUCGGAAACGCACUCAAG
..............(((((((((.(((((.....--..(((.......))).......((((.(((.........................))).))))...))))).)))))))))... ( -26.51)
>DroEre_CAF1 24667 96 + 1
AAACAAUCAAUGAAGAGUGCGUUCCUGAAGUUAU--AUGUUAGUUCGAAACCAGUUAUCUC------AU-UUAUCAAAAGG---------------CGGAACUUCUGAAACGCACUCCAU
..............(((((((((.(.((((((..--.((((..((..(((..((....)).------.)-))...))..))---------------)).)))))).).)))))))))... ( -22.30)
>DroYak_CAF1 8959 101 + 1
AAACAAUCAAUGCAGAGUGCGUUGCCGAAGUUAUAUAUGUUAGUUUUAAACCAGUUAUCUU------AU-UUAACAAAAAG------------GUUAGGAACUUCUGAAACGCACUCCAA
..............(((((((((.(.((((((....((.((..(.(((((..((....)).------.)-)))).)..)).------------))....)))))).).)))))))))... ( -22.80)
>consensus
AAACAAUCAAUGCAGAGUGCGUUGCCGAAGUUAU__GUGUUAGUUUUAAACCUGUUAUCUUGA_CUGAUUAUAUCAAAAUGCAUUUCCU_AA_GCCAGGAACUUCGGAAACGCACUCCAA
..............(((((((((.((((((((...................................................................)))))))).)))))))))... (-19.65 = -20.49 +   0.84)

alignment

secondary structure

dotplot

Window 2

Location	2,548,923 – 2,549,040
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	77.25
Mean single sequence MFE	-31.37
Consensus MFE	-22.28
Energy contribution	-24.28
Covariance contribution	2.00
Combinations/Pair	1.11
Mean z-score	-2.98
Structure conservation index	0.71
SVM decision value	3.30
SVM RNA-class probability	0.998952
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2548923 117 - 23771897
UUGGAGUGCGUUUCCGAAGUGCCGGGCGUUGAGGAAAUGCAUUUUGAU-UAAACAGAUCAUGAUAACAGAUUUAAAACUAACAC--AUAACUUCGGCAACGCACUCUGCAUUGAUUGUUU
..((((((((((.(((((((....((((((.....)))))(((.((((-(.....))))).)))...................)--...))))))).))))))))))............. ( -36.00)
>DroSec_CAF1 10931 118 - 1
UUUGAGUGCGUUUCCGAAGUACUUGGCCUUAAGGAAAUGCAUUUUGAUAUAAUCAGGUCAAGAUAACAGGUUUAAAACUAACAC--AUAACUUCGGCAACGCACUCUGCAUUGAUUGUUU
...(((((((((.(((((((.((((((((....((((....))))(((...))))))))))).......(((.......)))..--...))))))).))))))))).............. ( -35.50)
>DroSim_CAF1 7835 118 - 1
CUUGAGUGCGUUUCCGAAGUACUUGGCCUUAAGGAAAUGCAUUUUGAUAUAAUCAGGUCAAGAUAAGAGGUUUAAAACUAACAC--AUUAUUUCGGCAACGCACUCUGCAUUGAUUGUUU
...(((((((((.((((((((((((((((....((((....))))(((...))))))))))).......(((.......)))..--..)))))))).))))))))).............. ( -34.20)
>DroEre_CAF1 24667 96 - 1
AUGGAGUGCGUUUCAGAAGUUCCG---------------CCUUUUGAUAA-AU------GAGAUAACUGGUUUCGAACUAACAU--AUAACUUCAGGAACGCACUCUUCAUUGAUUGUUU
..((((((((((((.((((((...---------------...(((((..(-((------.((....)).)))))))).......--..)))))).))))))))))))............. ( -26.46)
>DroYak_CAF1 8959 101 - 1
UUGGAGUGCGUUUCAGAAGUUCCUAAC------------CUUUUUGUUAA-AU------AAGAUAACUGGUUUAAAACUAACAUAUAUAACUUCGGCAACGCACUCUGCAUUGAUUGUUU
..((((((((((.(.((((((......------------.......((((-((------.((....)).)))))).............)))))).).))))))))))............. ( -24.67)
>consensus
UUGGAGUGCGUUUCCGAAGUACCUGGC_UU_AGGAAAUGCAUUUUGAUAUAAUCAG_UCAAGAUAACAGGUUUAAAACUAACAC__AUAACUUCGGCAACGCACUCUGCAUUGAUUGUUU
...(((((((((.(((((((....................((((((((........)))))))).....(((.......))).......))))))).))))))))).............. (-22.28 = -24.28 +   2.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:52:28 2006