Locus 7186

Sequence ID	3L_DroMel_CAF1
Location	19,270,850 – 19,270,993
Length	143
Max. P	0.999721

overview

Window 1

Location	19,270,850 – 19,270,967
Length	117
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	71.03
Mean single sequence MFE	-24.44
Consensus MFE	-9.50
Energy contribution	-12.90
Covariance contribution	3.40
Combinations/Pair	1.08
Mean z-score	-1.94
Structure conservation index	0.39
SVM decision value	0.89
SVM RNA-class probability	0.875182
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19270850 117 + 23771897
UAAAGAAAGUUAAGAAGAGAGAACAUCCGAAAUCAAGAAUGUAGCGGUUUUUCUAUGUAUUCCACCCAUCUCUGGAAUACGUUGAUUACCAAGUCUUUCUUGAUCCUGAGGAUAUUC
....................(((.((((...((((((((.(....(((...((.((((((((((........)))))))))).))..)))....).)))))))).....)))).))) ( -30.10)
>DroSec_CAF1 99637 117 + 1
UGAAGAGUAUUAAGAAGAUAUAACAUCCAAAAUCAAGAAUCUACUGGUUUUAACAUAUAUUCCAGCAAUCUCCGGAAUACGUUGAUUACCAAGUCUUUCUUGAUCCUGAAGAUAUCC
................(((((......((..((((((((...((((((.(((((...((((((..........)))))).)))))..))).)))..))))))))..))...))))). ( -23.60)
>DroSim_CAF1 111066 110 + 1
UAAG-------AAGCAGAGAAGUCAUCCAAAAUCAAGAAUCUAGUGGUUUCAACAUGUAUUCCAGCAAUUUCCGGAAUACGUUGAUUACCAAGUCUUUCUUGAUCCUAAUGAUAUCC
....-------.......((.(((((.....((((((((.....((((.(((((..(((((((..........))))))))))))..)))).....))))))))....))))).)). ( -30.10)
>DroEre_CAF1 103930 90 + 1
UAAAGGAAGUUAAGAAGAGAGAAUAUCCAAAAUCAAGAAUCUAGUGGGUUUUCUAUGUAUUCCG---------------------------AGUAUUUCUUGAUCUAACAGAUAUUC
....................(((((((....((((((((.....((((............))))---------------------------.....))))))))......))))))) ( -15.60)
>DroYak_CAF1 129718 117 + 1
UAAAGGAAGUUGAGAAGAGAAAAUGUCCAACAUUAAGAAUCUACUGGUUUUUCAAUGUAUUCGACGCCUUUCGUAUAUACGCUGAUUACCAAGUAUUUCUUUAUCUUGAAGAUAUUC
.........(..(((((((((((((.....)))).......(((((((...(((.(((((.(((......)))...))))).)))..))).)))).)))))).)))..)........ ( -22.80)
>consensus
UAAAGAAAGUUAAGAAGAGAAAACAUCCAAAAUCAAGAAUCUAGUGGUUUUUCCAUGUAUUCCACCAAUCUCCGGAAUACGUUGAUUACCAAGUCUUUCUUGAUCCUGAAGAUAUUC
........................(((....((((((((.....((((......(((((((((..........))))))))).....)))).....))))))))......))).... ( -9.50 = -12.90 +   3.40)

alignment

secondary structure

dotplot

Window 2

Location	19,270,850 – 19,270,967
Length	117
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	71.03
Mean single sequence MFE	-28.25
Consensus MFE	-16.98
Energy contribution	-19.58
Covariance contribution	2.60
Combinations/Pair	1.33
Mean z-score	-3.01
Structure conservation index	0.60
SVM decision value	3.95
SVM RNA-class probability	0.999721
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19270850 117 - 23771897
GAAUAUCCUCAGGAUCAAGAAAGACUUGGUAAUCAACGUAUUCCAGAGAUGGGUGGAAUACAUAGAAAAACCGCUACAUUCUUGAUUUCGGAUGUUCUCUCUUCUUAACUUUCUUUA
((((((((...((((((((((.(...((((..((...((((((((........))))))))...))...))))...).)))))))))).)))))))).................... ( -31.70)
>DroSec_CAF1 99637 117 - 1
GGAUAUCUUCAGGAUCAAGAAAGACUUGGUAAUCAACGUAUUCCGGAGAUUGCUGGAAUAUAUGUUAAAACCAGUAGAUUCUUGAUUUUGGAUGUUAUAUCUUCUUAAUACUCUUCA
((((((.((((((((((((((..(((.(((....((((((((((((......)))))..)))))))...))))))...))))))))))))))....))))))............... ( -33.10)
>DroSim_CAF1 111066 110 - 1
GGAUAUCAUUAGGAUCAAGAAAGACUUGGUAAUCAACGUAUUCCGGAAAUUGCUGGAAUACAUGUUGAAACCACUAGAUUCUUGAUUUUGGAUGACUUCUCUGCUU-------CUUA
(((..((((((((((((((((.....((((..((((((((((((((......)))))))))..))))).)))).....))))))))))).)))))..)))......-------.... ( -36.30)
>DroEre_CAF1 103930 90 - 1
GAAUAUCUGUUAGAUCAAGAAAUACU---------------------------CGGAAUACAUAGAAAACCCACUAGAUUCUUGAUUUUGGAUAUUCUCUCUUCUUAACUUCCUUUA
((((((((...((((((((((.....---------------------------.((..............))......)))))))))).)))))))).................... ( -17.44)
>DroYak_CAF1 129718 117 - 1
GAAUAUCUUCAAGAUAAAGAAAUACUUGGUAAUCAGCGUAUAUACGAAAGGCGUCGAAUACAUUGAAAAACCAGUAGAUUCUUAAUGUUGGACAUUUUCUCUUCUCAACUUCCUUUA
(((.((.(((((.((.(((((.((((.(((..((((.((((..(((.....)))...)))).))))...)))))))..))))).)).))))).)).))).................. ( -22.70)
>consensus
GAAUAUCUUCAGGAUCAAGAAAGACUUGGUAAUCAACGUAUUCCGGAAAUGGCUGGAAUACAUAGAAAAACCACUAGAUUCUUGAUUUUGGAUGUUCUCUCUUCUUAACUUCCUUUA
((((((((...((((((((((.....((((.......((((((((........))))))))........)))).....)))))))))).)))))))).................... (-16.98 = -19.58 +   2.60)

alignment

secondary structure

dotplot

Window 3

Location	19,270,890 – 19,270,993
Length	103
Sequences	4
Columns	103
Reading direction	reverse
Mean pairwise identity	82.04
Mean single sequence MFE	-25.00
Consensus MFE	-17.64
Energy contribution	-19.82
Covariance contribution	2.19
Combinations/Pair	1.24
Mean z-score	-1.59
Structure conservation index	0.71
SVM decision value	0.10
SVM RNA-class probability	0.584721
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19270890 103 - 23771897
UCUCGGUGGGAAUUGUGUUGGGAGAAGAAUAUCCUCAGGAUCAAGAAAGACUUGGUAAUCAACGUAUUCCAGAGAUGGGUGGAAUACAUAGAAAAACCGCUAC
....(((((.......(((((((........))).....((((((.....))))))...))))((((((((........)))))))).........))))).. ( -27.10)
>DroSec_CAF1 99677 103 - 1
UUUCGGUGGGAAUUUUGUUGGGAGAAGGAUAUCUUCAGGAUCAAGAAAGACUUGGUAAUCAACGUAUUCCGGAGAUUGCUGGAAUAUAUGUUAAAACCAGUAG
....(((...(((...(((((((((......)))))...((((((.....))))))...))))(((((((((......)))))))))..)))...)))..... ( -25.80)
>DroSim_CAF1 111099 103 - 1
UCUCGGUGGCAAUUGUGUUGGGAGAAGGAUAUCAUUAGGAUCAAGAAAGACUUGGUAAUCAACGUAUUCCGGAAAUUGCUGGAAUACAUGUUGAAACCACUAG
....(((..((((...(((((((........))......((((((.....))))))..)))))(((((((((......)))))))))..))))..)))..... ( -28.10)
>DroYak_CAF1 129758 103 - 1
UCUCGGAGGGAAUUAUAUUGCGAGAGGAAUAUCUUCAAGAUAAAGAAAUACUUGGUAAUCAGCGUAUAUACGAAAGGCGUCGAAUACAUUGAAAAACCAGUAG
(((.((((......(((((.(....).))))))))).)))........((((.(((..((((.((((..(((.....)))...)))).))))...))))))). ( -19.00)
>consensus
UCUCGGUGGGAAUUGUGUUGGGAGAAGAAUAUCUUCAGGAUCAAGAAAGACUUGGUAAUCAACGUAUUCCGGAAAUGGCUGGAAUACAUGGAAAAACCACUAG
....(((((.......(((((..((((.....))))...((((((.....))))))..)))))(((((((((......))))))))).........))))).. (-17.64 = -19.82 +   2.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:40:20 2006