Locus 7256

Sequence ID	3L_DroMel_CAF1
Location	19,415,813 – 19,415,918
Length	105
Max. P	0.964585

overview

Window 8

Location	19,415,813 – 19,415,918
Length	105
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	83.87
Mean single sequence MFE	-30.22
Consensus MFE	-20.32
Energy contribution	-20.76
Covariance contribution	0.44
Combinations/Pair	1.21
Mean z-score	-1.89
Structure conservation index	0.67
SVM decision value	0.30
SVM RNA-class probability	0.678602
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19415813 105 + 23771897
AAAUUGCACAUGAGCUGCUGU---UGCAUCUUGAUUGCAC-----UUAUCCUGGGUGUACCCAUAAAUGCAUGCAUGAGCAAGGACAUCCUCGUAUGCACAUAAGUAUGCGUU
....((((..((((.(((...---.))).))))..)))).-----......((((....))))..((((((((((((.((((((....)))....))).)))..))))))))) ( -29.70)
>DroSec_CAF1 54548 108 + 1
AAAUGGCACACGAGCUGCAGUAGCUGCAUCUUGAUUGCAC-----UUUUCCUGGGUGUACCCAUAAAUGCAUGCAUGAGCAAGGACAUCCUCGUAUGCACAUAAGUAUGCGUU
..((((....((((.(((((...))))).))))..(((((-----((.....))))))).)))).((((((((((((.((((((....)))....))).)))..))))))))) ( -34.10)
>DroSim_CAF1 55666 108 + 1
AAAUUGCACAUGAGCUGCUGUAGCUGCAUCUUGAUUGCAC-----UUUUCCUGGGUGUACCCAUAAAUGCAUGCAUGAGCAAGGACAUCCUCGUAUGCACAUAAGUAUGCGUU
...((((.(((((((((...)))))((((..((..(((((-----((.....)))))))..))...))))...)))).))))((....)).(((((((......))))))).. ( -31.60)
>DroEre_CAF1 51032 110 + 1
AAAUUAAAUGUGGAUUGCUGU---UGCAUCUCGAUUGCAUCUAGAUUUUCCUGGGUGUACUCAUAAAUGCAUGCAUGAGCAAGGACAUCCUCAUAUGCACGUAAGUAUGCGUU
...........((..(((...---.)))..))((.(((((((((......))))))))).))...((((((((((((.((((((....)))....))).)))..))))))))) ( -31.60)
>DroYak_CAF1 80979 97 + 1
GACUUAAAUGUGAAUUGCUGU---AGCAUCUAGAUUGCAC-----UUUUCCUGUGUGUGCUCAUAAAUGCAUGCAUGAGCAAGGACA--------UGCACGUAAGUAUGUGUU
.......((((...(((((..---.(((.......)))..-----.......((((((((........)))))))).)))))..)))--------)((((((....)))))). ( -24.10)
>consensus
AAAUUGCACAUGAGCUGCUGU___UGCAUCUUGAUUGCAC_____UUUUCCUGGGUGUACCCAUAAAUGCAUGCAUGAGCAAGGACAUCCUCGUAUGCACAUAAGUAUGCGUU
..........((((.(((.......))).))))..................((((....))))..((((((((((((.((((((....)))....))).)))..))))))))) (-20.32 = -20.76 +   0.44)

alignment

secondary structure

dotplot

Window 9

Location	19,415,813 – 19,415,918
Length	105
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	83.87
Mean single sequence MFE	-30.58
Consensus MFE	-21.25
Energy contribution	-21.21
Covariance contribution	-0.04
Combinations/Pair	1.17
Mean z-score	-2.67
Structure conservation index	0.69
SVM decision value	1.57
SVM RNA-class probability	0.964585
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19415813 105 - 23771897
AACGCAUACUUAUGUGCAUACGAGGAUGUCCUUGCUCAUGCAUGCAUUUAUGGGUACACCCAGGAUAA-----GUGCAAUCAAGAUGCA---ACAGCAGCUCAUGUGCAAUUU
...((((....))))(((((.(((..(((..((((((.((..((((((((((((....))))...)))-----)))))..)).)).)))---)..))).))).)))))..... ( -33.30)
>DroSec_CAF1 54548 108 - 1
AACGCAUACUUAUGUGCAUACGAGGAUGUCCUUGCUCAUGCAUGCAUUUAUGGGUACACCCAGGAAAA-----GUGCAAUCAAGAUGCAGCUACUGCAGCUCGUGUGCCAUUU
...........(((.((((((((((((.....(((....)))(((((((.((((....))))....))-----))))))))....(((((...))))).)))))))))))).. ( -36.80)
>DroSim_CAF1 55666 108 - 1
AACGCAUACUUAUGUGCAUACGAGGAUGUCCUUGCUCAUGCAUGCAUUUAUGGGUACACCCAGGAAAA-----GUGCAAUCAAGAUGCAGCUACAGCAGCUCAUGUGCAAUUU
...((((.(((..((((((.(((((....)))))...))))))((((((.((((....))))....))-----))))....)))(((.((((.....)))))))))))..... ( -33.10)
>DroEre_CAF1 51032 110 - 1
AACGCAUACUUACGUGCAUAUGAGGAUGUCCUUGCUCAUGCAUGCAUUUAUGAGUACACCCAGGAAAAUCUAGAUGCAAUCGAGAUGCA---ACAGCAAUCCACAUUUAAUUU
...((((.(((...(((((...(((...((((((((((((........)))))))).....))))...)))..)))))...))))))).---..................... ( -26.40)
>DroYak_CAF1 80979 97 - 1
AACACAUACUUACGUGCA--------UGUCCUUGCUCAUGCAUGCAUUUAUGAGCACACACAGGAAAA-----GUGCAAUCUAGAUGCU---ACAGCAAUUCACAUUUAAGUC
.......(((((..((((--------(.((((((((((((........)))))))).....))))...-----))))).......(((.---...))).........))))). ( -23.30)
>consensus
AACGCAUACUUAUGUGCAUACGAGGAUGUCCUUGCUCAUGCAUGCAUUUAUGGGUACACCCAGGAAAA_____GUGCAAUCAAGAUGCA___ACAGCAGCUCAUGUGCAAUUU
...((((.(((...(((((.........((((((((((((........)))))))).....))))........)))))...)))))))......................... (-21.25 = -21.21 +  -0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:42:23 2006