Locus 8186

Sequence ID	3L_DroMel_CAF1
Location	21,535,521 – 21,535,692
Length	171
Max. P	0.747304

overview

Window 4

Location	21,535,521 – 21,535,614
Length	93
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	74.55
Mean single sequence MFE	-25.87
Consensus MFE	-14.60
Energy contribution	-16.16
Covariance contribution	1.56
Combinations/Pair	1.32
Mean z-score	-1.62
Structure conservation index	0.56
SVM decision value	0.47
SVM RNA-class probability	0.747304
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21535521 93 + 23771897
--------GGAUCAGAGUGUAAGA--CCGAUCCGUGUUCAUAUUUGCAUAUUCGCAUAU-CAUAUU----------UAUUAUUUCGCCAGUGC-GGGCGAGAUAAUUCCGAGUCC
--------(((((.(.((.....)--)))))))(..(((.....(((......)))...-......----------.(((((((((((.....-.)))))))))))...)))..) ( -23.00)
>DroPse_CAF1 34519 113 + 1
CUGAUCUGGUGUGAAGGUGCAAGACACAGAUGCAUAUGCAUAUAUAUGUACGUACAUAUGCUUAUUCGUUUACUCCUUUCAUUUCGC-AGUGAUAAAGGAGAUG-UGUAGAAUCU
...(((((((.((......))..)).)))))((((((((((((.(((....))).))))))...........((((((((((.....-.))))..)))))))))-)))....... ( -26.70)
>DroSec_CAF1 6917 93 + 1
--------GGAUCAGAGUGUAAGA--CCGAUCCGUGUGCAUAUUUGCAUACUCGCAUAU-CAUAUU----------UAUUAUUUCGCCAGUGC-GGGCGAGAUAAUUCCGAGUCC
--------(((((.(.((.....)--)))))))(((((((....)))))))........-......----------.(((((((((((.....-.)))))))))))......... ( -29.10)
>DroSim_CAF1 5928 93 + 1
--------GGAUCAGAGUGUAAGA--CCGAUCCGUGUGCAUAUUUGCAUACUCGCAUAU-CAUAUU----------UAUUAUUUCGCCAGUGC-GGGCGAGAUAAUUCCGAGUCC
--------(((((.(.((.....)--)))))))(((((((....)))))))........-......----------.(((((((((((.....-.)))))))))))......... ( -29.10)
>DroEre_CAF1 24808 85 + 1
--------GGAUCACAGUAUAAGA--CCGAUCCGUGCGCAUAUUUGC--------AUAU-CAUAUU----------UAUUAUUUCGCCAGUGC-GGGCGAGAUAAUUCCGAGUCC
--------(((((...........--..)))))(((((......)))--------))..-......----------.(((((((((((.....-.)))))))))))......... ( -22.82)
>DroYak_CAF1 25151 85 + 1
--------GGAUCACAGUAUAAGA--GCGAUCCGUGUGCAUAUUUGC--------AUAU-CAUAUU----------UAUUAGUCCGCCAGUGC-GGGCGAAAUAAUUUCGAGUCC
--------(((((.(.........--).)))))(((((((....)))--------))))-..((((----------(....((((((....))-)))).)))))........... ( -24.50)
>consensus
________GGAUCAGAGUGUAAGA__CCGAUCCGUGUGCAUAUUUGCAUACUCGCAUAU_CAUAUU__________UAUUAUUUCGCCAGUGC_GGGCGAGAUAAUUCCGAGUCC
........(((((...............))))).((((((....))))))...........................(((((((((((.......)))))))))))......... (-14.60 = -16.16 +   1.56)

alignment

secondary structure

dotplot

Window 5

Location	21,535,551 – 21,535,654
Length	103
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	77.27
Mean single sequence MFE	-25.53
Consensus MFE	-16.93
Energy contribution	-17.68
Covariance contribution	0.76
Combinations/Pair	1.29
Mean z-score	-1.27
Structure conservation index	0.66
SVM decision value	0.25
SVM RNA-class probability	0.654864
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21535551 103 - 23771897
CAUGUCUGUGGAAGCGGAAAUGCCUUCCAGCGGAUGCAAAGGACUCGGAAUUAUCUCGCCC-GCACUGGCGAAAUAAUA----------AAUAUG-AUAUGCGAAUAUGCAAAUA
...(((((((((((((....)).)))))).)))))((............(((((.(((((.-.....))))).))))).----------......-((((....))))))..... ( -25.40)
>DroPse_CAF1 34559 103 - 1
----------UGAACGGAAAUGUUUUAGAGUGGAUUUAUAAGAUUCUACA-CAUCUCCUUUAUCACU-GCGAAAUGAAAGGAGUAAACGAAUAAGCAUAUGUACGUACAUAUAUA
----------((.(((...((((((....(((((.((....)).))))).-...(((((((.((...-..))....))))))).........)))))).....))).))...... ( -16.90)
>DroSec_CAF1 6947 103 - 1
CAUGUCUGUGGAAGCGGAAAUGCCUUCCAGCGGAUGCAAAGGACUCGGAAUUAUCUCGCCC-GCACUGGCGAAAUAAUA----------AAUAUG-AUAUGCGAGUAUGCAAAUA
...(((((((((((((....)).)))))).)))))(((....(((((.((((((.(((((.-.....))))).))))).----------......-...).))))).)))..... ( -30.60)
>DroSim_CAF1 5958 103 - 1
CAUGUCUGUGGAAGCGGAAAUGCCUUCCAGCGGAUGCAAAGGACUCGGAAUUAUCUCGCCC-GCACUGGCGAAAUAAUA----------AAUAUG-AUAUGCGAGUAUGCAAAUA
...(((((((((((((....)).)))))).)))))(((....(((((.((((((.(((((.-.....))))).))))).----------......-...).))))).)))..... ( -30.60)
>DroEre_CAF1 24838 95 - 1
CACGUCUGUGGAAGCGGAAAUGCCUUCCAGCGGAUGCAAAGGACUCGGAAUUAUCUCGCCC-GCACUGGCGAAAUAAUA----------AAUAUG-AUAU--------GCAAAUA
..((((((((((((((....)).)))))).)))))).............(((((.(((((.-.....))))).))))).----------......-....--------....... ( -25.20)
>DroYak_CAF1 25181 95 - 1
CACGUCUGUGGAAGCGGAAAUGCCUUCCAGCGGAUGCAAAGGACUCGAAAUUAUUUCGCCC-GCACUGGCGGACUAAUA----------AAUAUG-AUAU--------GCAAAUA
..((((((((((((((....)).)))))).)))))).............((((.((((((.-.....)))))).)))).----------......-....--------....... ( -24.50)
>consensus
CAUGUCUGUGGAAGCGGAAAUGCCUUCCAGCGGAUGCAAAGGACUCGGAAUUAUCUCGCCC_GCACUGGCGAAAUAAUA__________AAUAUG_AUAUGCGAGUAUGCAAAUA
..((((((((((((((....)).)))))).)))))).............(((((.(((((.......))))).)))))..................................... (-16.93 = -17.68 +   0.76)

alignment

secondary structure

dotplot

Window 6

Location	21,535,578 – 21,535,692
Length	114
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	82.59
Mean single sequence MFE	-37.80
Consensus MFE	-24.73
Energy contribution	-25.98
Covariance contribution	1.26
Combinations/Pair	1.38
Mean z-score	-1.95
Structure conservation index	0.65
SVM decision value	0.17
SVM RNA-class probability	0.618214
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21535578 114 + 23771897
UUAUUUCGCCAGUGCGGGCGAGAUAAUU---CCGAGUCCUUUGCAUCCGCUGGAAGGCAUUUCCGCUUCCACAGACAUGCAGAUACAUCCUCGGAGGAAACUGGAAUUGCAUAU--GCA
((((((((((......)))))))))).(---(((((...(((((((...((((.((((......)))).).)))..)))))))......))))))(....)......(((....--))) ( -37.40)
>DroSec_CAF1 6974 114 + 1
UUAUUUCGCCAGUGCGGGCGAGAUAAUU---CCGAGUCCUUUGCAUCCGCUGGAAGGCAUUUCCGCUUCCACAGACAUGCAGAUACAUCCUCGGAGGAAACUCGAAUUGCAUAU--GCA
.(((((((((......)))))))))(((---(((((...(((((((...((((.((((......)))).).)))..)))))))......))))(((....)))))))(((....--))) ( -37.90)
>DroSim_CAF1 5985 114 + 1
UUAUUUCGCCAGUGCGGGCGAGAUAAUU---CCGAGUCCUUUGCAUCCGCUGGAAGGCAUUUCCGCUUCCACAGACAUGCAGAUACAUCCUCGGAGGAAACUCGAAUUGCAUAU--GCA
.(((((((((......)))))))))(((---(((((...(((((((...((((.((((......)))).).)))..)))))))......))))(((....)))))))(((....--))) ( -37.90)
>DroEre_CAF1 24857 114 + 1
UUAUUUCGCCAGUGCGGGCGAGAUAAUU---CCGAGUCCUUUGCAUCCGCUGGAAGGCAUUUCCGCUUCCACAGACGUGCAGAUACAUCCUCGGAGGAAACUCGAAUUGCAUAU--GCA
.(((((((((......)))))))))(((---(((((...(((((((...((((.((((......)))).).)))..)))))))......))))(((....)))))))(((....--))) ( -38.20)
>DroYak_CAF1 25200 114 + 1
UUAGUCCGCCAGUGCGGGCGAAAUAAUU---UCGAGUCCUUUGCAUCCGCUGGAAGGCAUUUCCGCUUCCACAGACGUGCAGAUGAAUCCUCGGAGGAAACUCGAAUUGCAUAU--GCA
...((((((....)))))).........---.((((((.(((((((...((((.((((......)))).).)))..))))))).))...))))(((....)))....(((....--))) ( -37.30)
>DroAna_CAF1 6427 107 + 1
UUGUCUUACAUGCGCGGGUGGGGUUGGUAUGUAAAUUUCUGGAUUUCCGCUCGGGGCCAUUUCCGUUUGCACCUA-----------AUCC-GGGGGGAAAUACGAACUGCAUAUGUGCA
..........((((((.(((.((((.((((.....(..(((((((...((.(((((....)))))...))....)-----------))))-))..)...)))).)))).))).)))))) ( -38.10)
>consensus
UUAUUUCGCCAGUGCGGGCGAGAUAAUU___CCGAGUCCUUUGCAUCCGCUGGAAGGCAUUUCCGCUUCCACAGACAUGCAGAUACAUCCUCGGAGGAAACUCGAAUUGCAUAU__GCA
((((((((((......))))))))))......((((...(((((((....((((((.(......))))))).....)))))))......))))(((....)))....(((......))) (-24.73 = -25.98 +   1.26)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:08:55 2006