Locus 145

Sequence ID	2R_DroMel_CAF1
Location	1,406,527 – 1,406,872
Length	345
Max. P	0.999583

overview

Window 7

Location	1,406,527 – 1,406,647
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.00
Mean single sequence MFE	-37.15
Consensus MFE	-35.71
Energy contribution	-35.75
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-2.45
Structure conservation index	0.96
SVM decision value	3.75
SVM RNA-class probability	0.999583
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1406527 120 - 20766785
UUCUUCGGGCAAAGUGCAAUAAAUCAUAAUUUGCUACUUUUUCUAAUGGAUUAUGGACAGUGGCGGCAACAGAAGCCGCAGCAGCAUACUGUUAGAAUCCACUUGGGGAGCUCUUAAGUG
......((((.((((((((...........)))).))))(..((((((((((...((((((((((((.......))))).......)))))))..)))))).))))..)))))....... ( -37.61)
>DroSec_CAF1 32333 120 - 1
UUCUUCGGGCAAAGUGCAAUAAAUCAUAAUUUGCUACUUUUUCUAAUGGAUUAUGGACAGUGGCGGCAACAGAAGCCGCAGCAGCAUACUGUUAGAAUCCACUUGGGGAGCUUUUAAGUG
(((((((((.(((((((((...........)))).)))))......((((((...((((((((((((.......))))).......)))))))..))))))))))))))).......... ( -35.11)
>DroSim_CAF1 37344 120 - 1
UUCUUCGGGCAAAGUGCAAUAAAUCAUAAUUUGCUACUUUUUCUAAUGGAUUAUGGACAGUGGCGGCAACAGAAGCCGCAGAAGCAUACUGUUAGAAUCCACUUGGGGAGCUCUUAAGUG
......((((.((((((((...........)))).))))(..((((((((((...((((((((((((.......))))).......)))))))..)))))).))))..)))))....... ( -37.61)
>DroEre_CAF1 30845 119 - 1
UUCUUCGGGCAAAGUGCAAUAAAUCAUAAUUUGCUACUUUUUCUAAUGGAUUAUGGACAGUGGCGGCAACAGA-GCCGCAGCACCAUACUGUUAGAAUCCACUUGGGGAGCUCUUAAGUG
......((((.((((((((...........)))).))))(..((((((((((...((((((((((((......-))))).......)))))))..)))))).))))..)))))....... ( -38.11)
>DroYak_CAF1 32794 120 - 1
UUCUUGGGGCAAAGUGCAAUAAAUCAUAAUUUGCUACUUUUUCUAAUGGAUUAUGGACAGUGGCGGCAACAGAAGCCACAGCAGCAUACUGUUAGAAUCCACUUGGGGAGCUCUUAAGUG
..((((((((.((((((((...........)))).))))(..((((((((((...((((((((((....)....((....)).)).)))))))..)))))).))))..))).)))))).. ( -37.30)
>consensus
UUCUUCGGGCAAAGUGCAAUAAAUCAUAAUUUGCUACUUUUUCUAAUGGAUUAUGGACAGUGGCGGCAACAGAAGCCGCAGCAGCAUACUGUUAGAAUCCACUUGGGGAGCUCUUAAGUG
......((((.((((((((...........)))).))))(..((((((((((...((((((((((((.......))))).......)))))))..)))))).))))..)))))....... (-35.71 = -35.75 +   0.04)

alignment

secondary structure

dotplot

Window 8

Location	1,406,567 – 1,406,687
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.17
Mean single sequence MFE	-31.78
Consensus MFE	-29.90
Energy contribution	-29.86
Covariance contribution	-0.04
Combinations/Pair	1.03
Mean z-score	-1.26
Structure conservation index	0.94
SVM decision value	0.27
SVM RNA-class probability	0.661532
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1406567 120 - 20766785
CCAGCGCUCGCACACUUUGUGGCUCUCAUGAAUUUUUCCAUUCUUCGGGCAAAGUGCAAUAAAUCAUAAUUUGCUACUUUUUCUAAUGGAUUAUGGACAGUGGCGGCAACAGAAGCCGCA
....((((.((.(((...)))))((.(((((.....((((((....(((.(((((((((...........)))).))))).)))))))))))))))).))))(((((.......))))). ( -30.50)
>DroSec_CAF1 32373 120 - 1
GCAGCGCUCGCACACUUUGCGGCUCUCAUGAAUUUUUCCAUUCUUCGGGCAAAGUGCAAUAAAUCAUAAUUUGCUACUUUUUCUAAUGGAUUAUGGACAGUGGCGGCAACAGAAGCCGCA
...((((.((((.....))))))((.(((((.....((((((....(((.(((((((((...........)))).))))).))))))))))))))))..)).(((((.......))))). ( -31.90)
>DroSim_CAF1 37384 120 - 1
CCAGCGCUCGCACACUUUGCGGCUCUCAUGAAUUUUUCCAUUCUUCGGGCAAAGUGCAAUAAAUCAUAAUUUGCUACUUUUUCUAAUGGAUUAUGGACAGUGGCGGCAACAGAAGCCGCA
(((..((.((((.....)))))).............((((((....(((.(((((((((...........)))).))))).)))))))))...)))......(((((.......))))). ( -31.90)
>DroEre_CAF1 30885 119 - 1
CCAGCGCUCGCACACUUUGCGGCUCUCAUGAAUUUUUCCAUUCUUCGGGCAAAGUGCAAUAAAUCAUAAUUUGCUACUUUUUCUAAUGGAUUAUGGACAGUGGCGGCAACAGA-GCCGCA
...((....))......((((((((((((((.....((((((....(((.(((((((((...........)))).))))).)))))))))))))).........(....))))-)))))) ( -33.50)
>DroYak_CAF1 32834 120 - 1
CCAGCGCUCGCACACUUUGUGGCUCUCAUGAAUUUUUCCAUUCUUGGGGCAAAGUGCAAUAAAUCAUAAUUUGCUACUUUUUCUAAUGGAUUAUGGACAGUGGCGGCAACAGAAGCCACA
...(((((..(((.....)))((((.((.((((......)))).))))))..)))))......(((((((((..((.......))..)))))))))...(((((..(....)..))))). ( -31.10)
>consensus
CCAGCGCUCGCACACUUUGCGGCUCUCAUGAAUUUUUCCAUUCUUCGGGCAAAGUGCAAUAAAUCAUAAUUUGCUACUUUUUCUAAUGGAUUAUGGACAGUGGCGGCAACAGAAGCCGCA
...((((.((((.....))))))((.(((((.....((((((....(((.(((((((((...........)))).))))).))))))))))))))))..)).(((((.......))))). (-29.90 = -29.86 +  -0.04)

alignment

secondary structure

dotplot

Window 9

Location	1,406,687 – 1,406,795
Length	108
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	74.20
Mean single sequence MFE	-24.04
Consensus MFE	-14.03
Energy contribution	-14.47
Covariance contribution	0.44
Combinations/Pair	1.06
Mean z-score	-1.66
Structure conservation index	0.58
SVM decision value	0.33
SVM RNA-class probability	0.690776
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1406687 108 - 20766785
UUGGUAUGCCACUUUGGAGUUUUUGCCUUCACGACCCCAUGCCCCGUCCUUCUCCAC----------CCCCAUCAC-CCUUCCAUACC-AUCCUGGCUUCAUUUUAGCGGAGCAUACUUU
.(((((((......(((((.......))))).(((..........))).........----------.........-.....))))))-).....(((((........)))))....... ( -16.80)
>DroSec_CAF1 32493 109 - 1
UUUGUAUGCCACUUUGGAGUUUUUGCCUCCACGACCCCAUGCCCCGUCCUCCGCCAC----------CCCCACCGCCCCUUCCAUGCC-AUCCUGGCUUCAUUUCAGCGGAGCAUACUUU
...((((((.....(((((.......)))))..........................----------.....((((.........(((-.....))).........)))).))))))... ( -24.07)
>DroSim_CAF1 37504 119 - 1
UUGGUAUGCCACUUUGGAGUUUUUGCCUCCACGACCCCAUGCCCCGUCCUCCGCCACCCGGGUGCACCCCCACCGCCCCUUCCAUUCC-AUCCUGGCUUCAUUUCAGCGGAGCAUACUUU
..((((((......(((((.......)))))......))))))..((.((((((.....(((.((.........)))))..(((....-....)))..........)))))).))..... ( -29.90)
>DroEre_CAF1 31004 96 - 1
UUCGUAUGCCACUUUGGAGUUUUUGCCCC-----C--------UAGAGCUGCCCGCG----------GUCCCUG-CCCCUCGCAUCGCAGUGCUGGCUUCCAUUCAGCGGAGCAUACUUU
...((((((..(.(((((......(((..-----.--------.((.(((((..(((----------(......-....))))...))))).))))).....))))).)..))))))... ( -27.20)
>DroYak_CAF1 32954 101 - 1
UUCGUAUGCCACAUUGGAGUUUUUGCCUCUACUGC--------CUGUACUUCCCCAU----------GCCCUUU-CCCCUCCCUUUGCAGUCCUGGCUUCAAUUCAGCGGAGCAUACUUU
...((((((..(.(((((......(((...(((((--------..............----------.......-...........)))))...))).....))))).)..))))))... ( -22.25)
>consensus
UUCGUAUGCCACUUUGGAGUUUUUGCCUCCACGACCCCAUGCCCCGUCCUCCCCCAC__________CCCCAUC_CCCCUUCCAUUCC_AUCCUGGCUUCAUUUCAGCGGAGCAUACUUU
...((((((..(.(((((((....(((...................................................................)))...))))))).)..))))))... (-14.03 = -14.47 +   0.44)

alignment

secondary structure

dotplot

Window 0

Location	1,406,755 – 1,406,872
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	78.66
Mean single sequence MFE	-32.37
Consensus MFE	-11.94
Energy contribution	-13.58
Covariance contribution	1.64
Combinations/Pair	1.05
Mean z-score	-2.28
Structure conservation index	0.37
SVM decision value	0.90
SVM RNA-class probability	0.878166
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1406755 117 + 20766785
AUGGGGUCGUGAAGGCAAAAACUCCAAAGUGGCAUACCAAAAUGUAAAACUCUUGUAAUACCCUAGCCACUGU---GGGCCCCUCCAACCGAUGAUUUACCCAGCUUUGGGGCCACCAAA
.((((((..((....))...)))))).((((((.(((......)))..((....)).........))))))..---.((((((.........................))))))...... ( -29.31)
>DroSec_CAF1 32562 120 + 1
AUGGGGUCGUGGAGGCAAAAACUCCAAAGUGGCAUACAAAAAUGUAAAACUCUUGUAAUACCCCAGCCACUGUGCUGGGCCACUCCAACCGCUGAUUUAACCAGCUUUGGGGCCACCAAA
.(((((((.(((((.......))))).((((((.((((....))))................(((((......)))))))))))((((..((((.......)))).)))))))).))).. ( -43.20)
>DroSim_CAF1 37583 120 + 1
AUGGGGUCGUGGAGGCAAAAACUCCAAAGUGGCAUACCAAAAUGUAAAACUCUUGUAAUACCCCAGCCAAUGUGCUGGGCCACUCCAACCGCUGAUUUACCCAGCUUUGGGGCCCCCAAA
..((((((.(((((.......))))).((((((..........(((..((....))..))).(((((......)))))))))))((((..((((.......)))).)))))))))).... ( -44.30)
>DroEre_CAF1 31070 102 + 1
-----G-----GGGGCAAAAACUCCAAAGUGGCAUACGAAAAUGUAAAACUCUUGUAAUACCCCGGCCAGCGU---GGCCCACUCCACCCAG---UUCACCCAGCUUUGGGCC--CCCAA
-----(-----(((((.......(((((((((...((......(((..((....))..)))...((((.....---))))...........)---)....))).)))))))))--))).. ( -31.01)
>DroYak_CAF1 33020 96 + 1
-----GCAGUAGAGGCAAAAACUCCAAUGUGGCAUACGAAAAUGUAAAACUCUUGUAAUACCCUGGCCACUGU---GGCCCACUCCACCCAC-----CAAUCAA-----------CCAAA
-----......(((.......)))....((((..(((((.............))))).......((((.....---))))........))))-----.......-----------..... ( -14.02)
>consensus
AUGGGGUCGUGGAGGCAAAAACUCCAAAGUGGCAUACCAAAAUGUAAAACUCUUGUAAUACCCCAGCCACUGU___GGGCCACUCCAACCGCUGAUUUACCCAGCUUUGGGGCC_CCAAA
.............((......((((((((((((.(((......)))..((....)).........)))........((......)).................)))))))))...))... (-11.94 = -13.58 +   1.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:30:02 2006