Locus 3378

Sequence ID	3L_DroMel_CAF1
Location	9,882,894 – 9,883,011
Length	117
Max. P	0.990056

overview

Window 1

Location	9,882,894 – 9,882,986
Length	92
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	80.10
Mean single sequence MFE	-17.03
Consensus MFE	-9.11
Energy contribution	-10.34
Covariance contribution	1.22
Combinations/Pair	1.05
Mean z-score	-2.19
Structure conservation index	0.54
SVM decision value	0.38
SVM RNA-class probability	0.713847
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9882894 92 - 23771897
AUAUAUGUGUAU-GUGUGUGCAGUGAAAAAUGAUUUAUAAAAAAAA---------AAAUUGAAAAUAAGUGAAUGCAACGGAGCAUCUUU-----UGCGCAUGCAAA
...........(-((((((((((.((....(.((((((........---------.........)))))).).(((......)))))..)-----)))))))))).. ( -16.53)
>DroSec_CAF1 43625 76 - 1
----------------UGUGCAGUGCAAAAUGAUUUAUAAAAA-AA---------AAAUUGAAAAUAAGUGAAUGCAAUGGAGCAUCUUU-----UGCGCAUGCAAA
----------------..(((((((((((((.((((((.....-..---------.........)))))).)((((......)))).)))-----))))).)))).. ( -16.49)
>DroSim_CAF1 45720 83 - 1
---------UAU-GUGUGUGCAGUGCAAAAUGAUUUAUAAAAAAAA---------AAAUUGAAAAUAAGUGAAUGCAAUGGAGCAUCUUU-----UGCGCAUGCAAA
---------...-.....(((((((((((((.((((((........---------.........)))))).)((((......)))).)))-----))))).)))).. ( -16.43)
>DroEre_CAF1 46046 80 - 1
---------UAU-GUGUGUGCAGUGGAAAAUGAUUUAUAAAA---A---------AAAUUGAAAAUAAGUGUAUGCCAUGGAGCAUCUUU-----UGCGCAUGCAAA
---------..(-((((((((((.(((.....((((((....---.---------.........))))))...(((......)))))).)-----)))))))))).. ( -18.24)
>DroYak_CAF1 45116 80 - 1
---------UAU-GUGUGUGCAGUGCAAAAUGAUUUAUACAA---A---------AAAUUGAAAAUAAGUGUAUGCAAUGGAGCAUCUUU-----UGCGCAUGCAAA
---------..(-(((((((((((((...((....((((((.---.---------....(....)....))))))..))...))))....-----)))))))))).. ( -18.20)
>DroPer_CAF1 42266 101 - 1
GUG------UAUCAUAUGUGCAUCGCAAAAUGAGUUAUAAAAAGAAAAAAGUAUUAAAUUGAAAAUAAGUGUAUUCAAAGCAGCUUCUUCUCCUGCGCGCAUGCAAA
...------.........((((((((................................(((((.((....)).))))).((((.........))))))).))))).. ( -16.30)
>consensus
_________UAU_GUGUGUGCAGUGCAAAAUGAUUUAUAAAAA_AA_________AAAUUGAAAAUAAGUGAAUGCAAUGGAGCAUCUUU_____UGCGCAUGCAAA
.............(((((((((..........((((((..........................))))))..((((......)))).........)))))))))... ( -9.11 = -10.34 +   1.22)

alignment

secondary structure

dotplot

Window 2

Location	9,882,921 – 9,883,011
Length	90
Sequences	5
Columns	95
Reading direction	forward
Mean pairwise identity	71.36
Mean single sequence MFE	-14.13
Consensus MFE	-8.82
Energy contribution	-8.38
Covariance contribution	-0.44
Combinations/Pair	1.44
Mean z-score	-1.84
Structure conservation index	0.62
SVM decision value	1.49
SVM RNA-class probability	0.958244
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9882921 90 + 23771897
CAUUCACUUAUUUUCAAUUUUUUUUUUUAUAAAUCAUUUUUC--ACUGCAC-ACACAUA--CACAUAUAUAGCACAUGUAGUGCAGUGUGGAGUG
..................................(((((..(--(((((((-..((((.--..............)))).))))))))..))))) ( -17.36)
>DroSec_CAF1 43652 70 + 1
CAUUCACUUAUUUUCAAUUUUU-UUUUUAUAAAUCAUUUUGC--ACUGCAC-A---------------------CAUGUAGUGCAGUAUGGAGUG
....(((((...........((-(......))).(((.((((--((((((.-.---------------------..)))))))))).)))))))) ( -16.80)
>DroSim_CAF1 45747 77 + 1
CAUUCACUUAUUUUCAAUUUUUUUUUUUAUAAAUCAUUUUGC--ACUGCAC-ACACAUA---------------CAUGUAGUGCAGUAUGGAGUG
..................................((((((..--(((((((-(((....---------------..))).)))))))..)))))) ( -16.20)
>DroYak_CAF1 45143 77 + 1
CAUACACUUAUUUUCAAUUUU---UUGUAUAAAUCAUUUUGC--ACUGCAC-ACACAUA------------GUACAUGUACUGGAGUAUGAAGUG
.(((((...............---.)))))....((((((..--(((.((.-..((((.------------....))))..)).)))..)))))) (  -9.39)
>DroAna_CAF1 43095 88 + 1
AAUACACUUAUUCGGAAUUUU---UUCUAUAACUUAUUUUGCCCACUAUACUAUAUAUAUAUUUAUAUUCAGC----AUCGUGUAGUUCAGAGUG
....(((((....((((....---))))................(((((((.(((((((....))))).....----)).)))))))...))))) ( -10.90)
>consensus
CAUUCACUUAUUUUCAAUUUUU_UUUUUAUAAAUCAUUUUGC__ACUGCAC_ACACAUA____________G__CAUGUAGUGCAGUAUGGAGUG
..................................(((((((...(((((((.((.......................)).))))))).))))))) ( -8.82 =  -8.38 +  -0.44)

alignment

secondary structure

dotplot

Window 3

Location	9,882,921 – 9,883,011
Length	90
Sequences	5
Columns	95
Reading direction	reverse
Mean pairwise identity	71.36
Mean single sequence MFE	-15.80
Consensus MFE	-6.27
Energy contribution	-7.43
Covariance contribution	1.16
Combinations/Pair	1.15
Mean z-score	-2.34
Structure conservation index	0.40
SVM decision value	2.19
SVM RNA-class probability	0.990056
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9882921 90 - 23771897
CACUCCACACUGCACUACAUGUGCUAUAUAUGUG--UAUGUGU-GUGCAGU--GAAAAAUGAUUUAUAAAAAAAAAAAUUGAAAAUAAGUGAAUG
((((...((((((((((((((..(.......)..--)))))).-)))))))--)......(((((..........))))).......)))).... ( -24.50)
>DroSec_CAF1 43652 70 - 1
CACUCCAUACUGCACUACAUG---------------------U-GUGCAGU--GCAAAAUGAUUUAUAAAAA-AAAAAUUGAAAAUAAGUGAAUG
((((...((((((((......---------------------.-)))))))--)......(((((.......-..))))).......)))).... ( -13.00)
>DroSim_CAF1 45747 77 - 1
CACUCCAUACUGCACUACAUG---------------UAUGUGU-GUGCAGU--GCAAAAUGAUUUAUAAAAAAAAAAAUUGAAAAUAAGUGAAUG
((((...((((((((.((((.---------------...))))-)))))))--)......(((((..........))))).......)))).... ( -15.90)
>DroYak_CAF1 45143 77 - 1
CACUUCAUACUCCAGUACAUGUAC------------UAUGUGU-GUGCAGU--GCAAAAUGAUUUAUACAA---AAAAUUGAAAAUAAGUGUAUG
.....(((((....((((.(((((------------.......-)))))))--))......((((((.(((---....)))...))))))))))) ( -13.40)
>DroAna_CAF1 43095 88 - 1
CACUCUGAACUACACGAU----GCUGAAUAUAAAUAUAUAUAUAGUAUAGUGGGCAAAAUAAGUUAUAGAA---AAAAUUCCGAAUAAGUGUAUU
...((((((((.(((.((----((((.(((((....))))).)))))).))).........)))).)))).---..................... ( -12.20)
>consensus
CACUCCAUACUGCACUACAUG__C____________UAUGUGU_GUGCAGU__GCAAAAUGAUUUAUAAAAA_AAAAAUUGAAAAUAAGUGAAUG
((((....(((((((.((((...................)))).))))))).........(((((..........))))).......)))).... ( -6.27 =  -7.43 +   1.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:56:42 2006