Locus 2141

Sequence ID	3L_DroMel_CAF1
Location	5,832,194 – 5,832,346
Length	152
Max. P	0.939507

overview

Window 1

Location	5,832,194 – 5,832,311
Length	117
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	79.57
Mean single sequence MFE	-24.60
Consensus MFE	-19.67
Energy contribution	-20.50
Covariance contribution	0.83
Combinations/Pair	1.00
Mean z-score	-2.12
Structure conservation index	0.80
SVM decision value	1.30
SVM RNA-class probability	0.939507
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5832194 117 + 23771897
GCAACUCGGAUCGGCGGGACAGCCGGCAGAAAUCACGUUAAGCGCAAUAAAAAGCGCGAAACAUUUUAACGCAUCCCGGCGAUAAAGUAUCUGAAAACAUUGCCCCAGACAAUGUUC-
.....((((((((((......))))...........(((..((((........))))..)))((((((.(((......))).)))))))))))).(((((((.......))))))).- ( -31.80)
>DroVir_CAF1 46715 100 + 1
AGC---------A--GCA-----AAACAGAAAUCACGUUAAGCGCAAUAAAAAGCGCGAAACAUUUUAACGCGUCGCGGCGAUAAAGUAUCUGAAAACAUUGCC-CCGACAAUGUCC-
...---------.--...-----...((((......(((..((((........))))..)))((((((.(((......))).)))))).))))...((((((..-....))))))..- ( -23.90)
>DroGri_CAF1 50897 110 + 1
AGC----GAGCCG--AGAACAGAAAACAGAAAUCACGUUAAGCGCAAUAAAAAGCGCGAAACAUUUUAACGCGUCGAGGCGAUAAAGUAUCUGAAAACAUUGCC-CCGACAAUGUCC-
.((----(....(--(...(........)...))..(((..((((........))))..))).......)))((((.((((((...((........))))))))-.)))).......- ( -25.20)
>DroYak_CAF1 43594 92 + 1
-------------------------GCAGAAAUCACGUUAAGCGCAAUAAAAAGCGCGAAACAUUUUAACGCAUCCCGGCGAUAAAGUAUCUGAAAACAUUGCCCCAGACAAUGUUC-
-------------------------.((((......(((..((((........))))..)))((((((.(((......))).)))))).))))..(((((((.......))))))).- ( -23.80)
>DroAna_CAF1 43060 105 + 1
--AA--CAGAUCCA---UACAGCUGGCUGAAAUCACGUUAAGCUCAAUAAAAAGCGCGAAACAUUUUAACGCAUCCCGGCGAUAAAGUAUCUGAAAACAUUGCCCCAGACAA------
--..--((((((..---((..(((((...............(((........)))(((...........)))...)))))..))..).)))))...................------ ( -17.10)
>DroPer_CAF1 44340 104 + 1
ACA----GGGUC-------CAG--AACAGAAAUCACGUUAAGCGCAAUAAAAAGCGCGAAACAUUUUAACGCAUCUCAGCGAUAAAGUAUCUGAAAACAUUGCC-CAGACAAUGUCCA
...----((...-------...--..((((......(((..((((........))))..)))((((((.(((......))).)))))).))))...((((((..-....)))))))). ( -25.80)
>consensus
A_A____GG_UC_______CAG__AACAGAAAUCACGUUAAGCGCAAUAAAAAGCGCGAAACAUUUUAACGCAUCCCGGCGAUAAAGUAUCUGAAAACAUUGCC_CAGACAAUGUCC_
..........................((((......(((..((((........))))..)))((((((.(((......))).)))))).))))...((((((.......))))))... (-19.67 = -20.50 +   0.83)

alignment

secondary structure

dotplot

Window 2

Location	5,832,194 – 5,832,311
Length	117
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	79.57
Mean single sequence MFE	-28.93
Consensus MFE	-22.32
Energy contribution	-23.32
Covariance contribution	1.00
Combinations/Pair	1.03
Mean z-score	-1.53
Structure conservation index	0.77
SVM decision value	0.72
SVM RNA-class probability	0.833723
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5832194 117 - 23771897
-GAACAUUGUCUGGGGCAAUGUUUUCAGAUACUUUAUCGCCGGGAUGCGUUAAAAUGUUUCGCGCUUUUUAUUGCGCUUAACGUGAUUUCUGCCGGCUGUCCCGCCGAUCCGAGUUGC
-(((((((((.....)))))))))......((((.((((.(((((((((..((.(((((..((((........))))..)))))..))..))).....)))))).))))..))))... ( -36.20)
>DroVir_CAF1 46715 100 - 1
-GGACAUUGUCGG-GGCAAUGUUUUCAGAUACUUUAUCGCCGCGACGCGUUAAAAUGUUUCGCGCUUUUUAUUGCGCUUAACGUGAUUUCUGUUU-----UGC--U---------GCU
-(((((((((...-.)))))))))...((((...))))((.((((.(((..((.(((((..((((........))))..)))))..))..))).)-----)))--.---------)). ( -28.80)
>DroGri_CAF1 50897 110 - 1
-GGACAUUGUCGG-GGCAAUGUUUUCAGAUACUUUAUCGCCUCGACGCGUUAAAAUGUUUCGCGCUUUUUAUUGCGCUUAACGUGAUUUCUGUUUUCUGUUCU--CGGCUC----GCU
-(((((..(((((-(((..((....))((((...))))))))))))(((((((........((((........))))))))))).............))))).--......----... ( -30.50)
>DroYak_CAF1 43594 92 - 1
-GAACAUUGUCUGGGGCAAUGUUUUCAGAUACUUUAUCGCCGGGAUGCGUUAAAAUGUUUCGCGCUUUUUAUUGCGCUUAACGUGAUUUCUGC-------------------------
-(((((((((.....))))))))).((((...((((.(((......))).))))(((((..((((........))))..)))))....)))).------------------------- ( -26.10)
>DroAna_CAF1 43060 105 - 1
------UUGUCUGGGGCAAUGUUUUCAGAUACUUUAUCGCCGGGAUGCGUUAAAAUGUUUCGCGCUUUUUAUUGAGCUUAACGUGAUUUCAGCCAGCUGUA---UGGAUCUG--UU--
------.((((((..(......)..))))))....(((((.(.((.((((....)))).)).)((((......)))).....)))))..((((((......---)))..)))--..-- ( -22.50)
>DroPer_CAF1 44340 104 - 1
UGGACAUUGUCUG-GGCAAUGUUUUCAGAUACUUUAUCGCUGAGAUGCGUUAAAAUGUUUCGCGCUUUUUAUUGCGCUUAACGUGAUUUCUGUU--CUG-------GACCC----UGU
..((((((((...-.))))))))((((((.((((((.(((......))).))))(((((..((((........))))..))))).......)))--)))-------))...----... ( -29.50)
>consensus
_GGACAUUGUCUG_GGCAAUGUUUUCAGAUACUUUAUCGCCGGGAUGCGUUAAAAUGUUUCGCGCUUUUUAUUGCGCUUAACGUGAUUUCUGCU__CUG_______GA_CC____U_U
.(((((((((.....))))))))).((((...((((.(((......))).))))(((((..((((........))))..)))))....)))).......................... (-22.32 = -23.32 +   1.00)

alignment

secondary structure

dotplot

Window 3

Location	5,832,234 – 5,832,346
Length	112
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	84.54
Mean single sequence MFE	-36.65
Consensus MFE	-24.04
Energy contribution	-25.07
Covariance contribution	1.03
Combinations/Pair	1.09
Mean z-score	-2.49
Structure conservation index	0.66
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5832234 112 - 23771897
AUUCGCGUCGAG--GCUUAGCGCCUUGAAAUCGCCGG----GAACAUUGUCUG--GGGCAAUGUUUUCAGAUACUUUAUCGCCGGGAUGCGUUAAAAUGUUUCGCGCUUUUUAUUGCGCU
...(((.(((((--((.....))))))).(((.((((----(((((((((...--..)))))))))...((((...)))).))))))))))............((((........)))). ( -40.00)
>DroVir_CAF1 46739 106 - 1
AUUCGCGUCGAGGGGCUUAGCGCCCC--AAUU---------GGACAUUGUCGG---GGCAAUGUUUUCAGAUACUUUAUCGCCGCGACGCGUUAAAAUGUUUCGCGCUUUUUAUUGCGCU
...(((((((.(((((.....)))))--....---------(((((((((...---.))))))).....((((...)))).)).)))))))............((((........)))). ( -39.90)
>DroPse_CAF1 44319 115 - 1
AUUCGCGUUGAG--GCUUAGCGCCUGGGAAUGGGCUGUUCUGGACAUUGUCUG---GGCAAUGUUUUCAGAUACUUUAUCGCUGAGAUGCGUUAAAAUGUUUCGCGCUUUUUAUUGCGCU
...((((((..(--((.....((((......)))).((((((((((((((...---.))))))))..)))).))......)))..))))))............((((........)))). ( -37.10)
>DroGri_CAF1 50931 106 - 1
AUUCGCGUCGAGGGGCUUAGCGCCUC--AAUU---------GGACAUUGUCGG---GGCAAUGUUUUCAGAUACUUUAUCGCCUCGACGCGUUAAAAUGUUUCGCGCUUUUUAUUGCGCU
...(((((((((((((.....)))((--....---------(((((((((...---.)))))))))...))..........))))))))))............((((........)))). ( -40.10)
>DroMoj_CAF1 48780 109 - 1
AUUCCCGUCCAGGGGCUUAGCGCCCC--AAUU---------GGACAUUGUCGGUUCGAAAAUGUUUUCAGAUACUUUAUCGCAGCGACGCGUUAAAAUGUUUCGCGCUUUUUAUUGCGCU
......((((((((((.....)))))--...)---------))))...((((.(.(((.((.((........)).)).))).).))))...............((((........)))). ( -33.40)
>DroAna_CAF1 43093 100 - 1
AUUCGCGUUGAG--GCUUAGCGCCUUGGAA----------------UUGUCUG--GGGCAAUGUUUUCAGAUACUUUAUCGCCGGGAUGCGUUAAAAUGUUUCGCGCUUUUUAUUGAGCU
...((((((..(--((.....((((..((.----------------...))..--))))..........((((...)))))))..))))))..............((((......)))). ( -29.40)
>consensus
AUUCGCGUCGAG__GCUUAGCGCCUC__AAUU_________GGACAUUGUCGG___GGCAAUGUUUUCAGAUACUUUAUCGCCGCGACGCGUUAAAAUGUUUCGCGCUUUUUAUUGCGCU
....(((.(((.......(((((..................((((((((((.....))))))))))..(((((.((((.(((......))).)))).))))).))))).....)))))). (-24.04 = -25.07 +   1.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:25:23 2006