Locus 6211

Sequence ID	2R_DroMel_CAF1
Location	19,544,723 – 19,544,823
Length	100
Max. P	0.961665

overview

Window 7

Location	19,544,723 – 19,544,823
Length	100
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	77.43
Mean single sequence MFE	-35.06
Consensus MFE	-19.01
Energy contribution	-20.32
Covariance contribution	1.31
Combinations/Pair	1.16
Mean z-score	-2.46
Structure conservation index	0.54
SVM decision value	1.53
SVM RNA-class probability	0.961665
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19544723 100 + 20766785
GUCCGGAGGUGGUUAGUCUGGA----AUGAGAGCUCGAG-------CAUGUUAAAGAAGCCUUCAAUACUCGAUG-UUUG---GAUUCCUACCGGUUGACCACCUCCAUGGAGUG
.((((((((((((((..(.(((----((..(((((((((-------..((((.(((....))).))))))))).)-))).---.)))))....)..)))))))))))..)))... ( -41.90)
>DroSec_CAF1 2753 100 + 1
GUCCGGAGGUGGUUAAUCUGGA----AUGAGAGCUCGAG-------CAUUUUAAAGAAGCCUUGAAUACGCGAUG-UUUG---CAUUCCUACCGGUUGACCACCUCCAUGGAGUG
.(((((((((((((((((.(((----(((..((((((.(-------.((((..(((....))))))).).))).)-))..---))))))....))))))))))))))..)))... ( -41.50)
>DroSim_CAF1 3571 100 + 1
GUCCGGAGGUGGUUAAUCUGGA----AUGAGAGCUCGAG-------CAUGUUAAAGAAGCCUUGAAUACGCGAUG-UUUG---CAUUCCCACCGGUUGACCACCUCCAUGGAGUG
.(((((((((((((((((.(((----(((..(((....(-------(.((((.(((....))).)))).))...)-))..---))))))....))))))))))))))..)))... ( -42.20)
>DroEre_CAF1 2768 99 + 1
GUCCGGAGGUGGUUAGUCUGGA----AUGAGAACUUAGG-------CACGUUAAAGAAGUCAUAAGUACUCG--GUUUUG---GACUCGUACCGGUUGACCACCUCCAUGGAGUG
.(((((((((((((((((..((----(((((.(((((((-------(...........))).))))).))).--))))..---)))(((...))).)))))))))))..)))... ( -38.70)
>DroYak_CAF1 3565 101 + 1
GUCCGGAAGUGGUUAGUCUGGA----AUGAGAGCUCAAG-------CACGUUAAAGAAGGCUCAAAUACUCGAUGUUUUG---GAUUCGUACCGGUUUACCACCUCCAUGGAGUG
.((((((.(((((....((((.----(((((((((....-------(........)..)))))......((((....)))---)..)))).))))...))))).)))..)))... ( -27.90)
>DroPer_CAF1 2194 111 + 1
GACCAGACGUUGUUAAUCUGAGUAGGGGGAAAGGACGAGACAGAGUUAACUUAA----UGUAUAAAUAGUGAAUUUUUUGUGACAAACUUACCUGUUGACCACCUCCAUGGAAUG
.((((((.........)))).)).(((((...((....(((((.((........----..((((((..........))))))........)))))))..)).)))))........ ( -18.17)
>consensus
GUCCGGAGGUGGUUAAUCUGGA____AUGAGAGCUCGAG_______CAUGUUAAAGAAGCCUUAAAUACUCGAUG_UUUG___CAUUCCUACCGGUUGACCACCUCCAUGGAGUG
.(((((((((((((((.((((......(((....))).................................(((....)))...........))))))))))))))))..)))... (-19.01 = -20.32 +   1.31)

alignment

secondary structure

dotplot

Window 8

Location	19,544,723 – 19,544,823
Length	100
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	77.43
Mean single sequence MFE	-28.04
Consensus MFE	-12.79
Energy contribution	-13.99
Covariance contribution	1.20
Combinations/Pair	1.26
Mean z-score	-2.10
Structure conservation index	0.46
SVM decision value	0.23
SVM RNA-class probability	0.644691
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19544723 100 - 20766785
CACUCCAUGGAGGUGGUCAACCGGUAGGAAUC---CAAA-CAUCGAGUAUUGAAGGCUUCUUUAACAUG-------CUCGAGCUCUCAU----UCCAGACUAACCACCUCCGGAC
...(((..(((((((((.....(((.(((((.---....-..(((((((((((((....)))))..)))-------)))))......))----)))..))).)))))))))))). ( -35.52)
>DroSec_CAF1 2753 100 - 1
CACUCCAUGGAGGUGGUCAACCGGUAGGAAUG---CAAA-CAUCGCGUAUUCAAGGCUUCUUUAAAAUG-------CUCGAGCUCUCAU----UCCAGAUUAACCACCUCCGGAC
...(((..(((((((((.((.(....((((((---....-..(((.(((((.(((....)))...))))-------).))).....)))----))).).)).)))))))))))). ( -31.70)
>DroSim_CAF1 3571 100 - 1
CACUCCAUGGAGGUGGUCAACCGGUGGGAAUG---CAAA-CAUCGCGUAUUCAAGGCUUCUUUAACAUG-------CUCGAGCUCUCAU----UCCAGAUUAACCACCUCCGGAC
...(((..(((((((((.((.(....((((((---....-..(((.((((..((((...))))...)))-------).))).....)))----))).).)).)))))))))))). ( -31.60)
>DroEre_CAF1 2768 99 - 1
CACUCCAUGGAGGUGGUCAACCGGUACGAGUC---CAAAAC--CGAGUACUUAUGACUUCUUUAACGUG-------CCUAAGUUCUCAU----UCCAGACUAACCACCUCCGGAC
...(((..(((((((((.....((((((((((---......--...........)))).......))))-------))..(((.((...----...))))).)))))))))))). ( -27.64)
>DroYak_CAF1 3565 101 - 1
CACUCCAUGGAGGUGGUAAACCGGUACGAAUC---CAAAACAUCGAGUAUUUGAGCCUUCUUUAACGUG-------CUUGAGCUCUCAU----UCCAGACUAACCACUUCCGGAC
...(((..(((((((((.....((.......)---)........(((..((..((((.........).)-------))..))..)))..----.........)))))))))))). ( -27.10)
>DroPer_CAF1 2194 111 - 1
CAUUCCAUGGAGGUGGUCAACAGGUAAGUUUGUCACAAAAAAUUCACUAUUUAUACA----UUAAGUUAACUCUGUCUCGUCCUUUCCCCCUACUCAGAUUAACAACGUCUGGUC
........((.((.((.(.((((((.(((((........))))).)).(((((....----.))))).....))))...).))...)).))...((((((.......)))))).. ( -14.70)
>consensus
CACUCCAUGGAGGUGGUCAACCGGUAGGAAUC___CAAA_CAUCGAGUAUUUAAGGCUUCUUUAACAUG_______CUCGAGCUCUCAU____UCCAGACUAACCACCUCCGGAC
...(((..(((((((((..((((((................)))).))......(((((....................)))))..................)))))))))))). (-12.79 = -13.99 +   1.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:05:40 2006