Locus 3962

Sequence ID	X_DroMel_CAF1
Location	10,519,468 – 10,519,600
Length	132
Max. P	0.998854

overview

Window 9

Location	10,519,468 – 10,519,567
Length	99
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	69.26
Mean single sequence MFE	-27.25
Consensus MFE	-11.89
Energy contribution	-13.42
Covariance contribution	1.53
Combinations/Pair	1.26
Mean z-score	-3.12
Structure conservation index	0.44
SVM decision value	3.25
SVM RNA-class probability	0.998854
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10519468 99 + 22224390
UGCAAUCUCCCAGCUCAGAGCACUGAGCUCUUAGCU------UUCUGGAUCCCAACUCCCUGC-UCC--------------CAACAUUCCGCACUCAUGGGAGCAGACAACCAACCACGU
((..((((...((((.(((((.....))))).))))------....))))..)).....((((-(((--------------((..............))))))))).............. ( -29.94)
>DroSec_CAF1 50977 99 + 1
UGCAGUCUCCCAGCUCAGAGCACUGAGCUCUUAGCU------UUCUGGAUCCCAACUCCCUGC-UCC--------------CAACAUUACGCACUCAUGGGAGCAGACAACCAACCACGU
((..((((...((((.(((((.....))))).))))------....))))..)).....((((-(((--------------((..............))))))))).............. ( -30.24)
>DroSim_CAF1 54507 99 + 1
UGCAAUCUCCCAGCUCAGAGCACUGAGCUCUUAGCU------UUCUGGAUCCCAACUCCCUGC-UCC--------------CAACAUUCCGCACUCAUGGGAGCAGACAACCAACCACGU
((..((((...((((.(((((.....))))).))))------....))))..)).....((((-(((--------------((..............))))))))).............. ( -29.94)
>DroEre_CAF1 52873 100 + 1
UGCAAUCUCCCUGCUCAGAGCUCUGAGCUCUUAGCU------UUCUGCAUCCAAGCUCCCUGCCUGC--------------CACAUUUCCGCACUUAUGAGAGCAAACAACCAACCACGU
((((........(((.(((((.....))))).))).------...)))).....(((((.((..(((--------------.........)))..)).).))))................ ( -19.90)
>DroYak_CAF1 52414 87 + 1
UGCAAUCUCCCAGCUCCGAGCUCCGAGCUCAGAGCU--------------CCAAGCUCUUAG-CUCU--------------UAGCUUUCUGG----AUGGGAGCAGACAAGCAGCCACGU
(((...((((((..((((((((..(((((.(((((.--------------....))))).))-))).--------------.)))))...))----))))))).......)))....... ( -34.20)
>DroAna_CAF1 56618 110 + 1
UGCAA-CUCCCAUCUCCUGACACCCGAAUCUGAAAUCCUUAAUCCUGUAUCCUGAAUCCUCAA-UUCCGACUUGUGCAGCACACUUUUUAGCACUCGUGGGAGCAGCCAACC--------
.((..-((((((((....))....(((..((((((.........((((((.(.((((.....)-))).)....))))))......))))))...)))))))))..)).....-------- ( -19.26)
>consensus
UGCAAUCUCCCAGCUCAGAGCACUGAGCUCUUAGCU______UUCUGGAUCCCAACUCCCUGC_UCC______________CAACAUUCCGCACUCAUGGGAGCAGACAACCAACCACGU
......(((((((((.(((((.....))))).)))...........(((...((......))..)))..............................))))))................. (-11.89 = -13.42 +   1.53)

alignment

secondary structure

dotplot

Window 0

Location	10,519,468 – 10,519,567
Length	99
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	69.26
Mean single sequence MFE	-36.72
Consensus MFE	-18.14
Energy contribution	-18.78
Covariance contribution	0.64
Combinations/Pair	1.43
Mean z-score	-2.70
Structure conservation index	0.49
SVM decision value	2.83
SVM RNA-class probability	0.997262
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10519468 99 - 22224390
ACGUGGUUGGUUGUCUGCUCCCAUGAGUGCGGAAUGUUG--------------GGA-GCAGGGAGUUGGGAUCCAGAA------AGCUAAGAGCUCAGUGCUCUGAGCUGGGAGAUUGCA
..(..(((..((.((((((((((...((.....))..))--------------)))-))))).))......(((....------((((.(((((.....))))).)))).))))))..). ( -40.20)
>DroSec_CAF1 50977 99 - 1
ACGUGGUUGGUUGUCUGCUCCCAUGAGUGCGUAAUGUUG--------------GGA-GCAGGGAGUUGGGAUCCAGAA------AGCUAAGAGCUCAGUGCUCUGAGCUGGGAGACUGCA
..(..(((..((.((((((((((...((.....))..))--------------)))-))))).))......(((....------((((.(((((.....))))).)))).))))))..). ( -41.50)
>DroSim_CAF1 54507 99 - 1
ACGUGGUUGGUUGUCUGCUCCCAUGAGUGCGGAAUGUUG--------------GGA-GCAGGGAGUUGGGAUCCAGAA------AGCUAAGAGCUCAGUGCUCUGAGCUGGGAGAUUGCA
..(..(((..((.((((((((((...((.....))..))--------------)))-))))).))......(((....------((((.(((((.....))))).)))).))))))..). ( -40.20)
>DroEre_CAF1 52873 100 - 1
ACGUGGUUGGUUGUUUGCUCUCAUAAGUGCGGAAAUGUG--------------GCAGGCAGGGAGCUUGGAUGCAGAA------AGCUAAGAGCUCAGAGCUCUGAGCAGGGAGAUUGCA
...........(((...(((((......((.....((((--------------.(((((.....)))))..))))...------.)).....((((((....)))))).)))))...))) ( -29.30)
>DroYak_CAF1 52414 87 - 1
ACGUGGCUGCUUGUCUGCUCCCAU----CCAGAAAGCUA--------------AGAG-CUAAGAGCUUGG--------------AGCUCUGAGCUCGGAGCUCGGAGCUGGGAGAUUGCA
...(((..((......))..)))(----((....((((.--------------.(((-((..(((((..(--------------....)..)))))..)))))..)))).)))....... ( -37.50)
>DroAna_CAF1 56618 110 - 1
--------GGUUGGCUGCUCCCACGAGUGCUAAAAAGUGUGCUGCACAAGUCGGAA-UUGAGGAUUCAGGAUACAGGAUUAAGGAUUUCAGAUUCGGGUGUCAGGAGAUGGGAG-UUGCA
--------.....((.((((((((..(..((....))..).((((((.((((((((-((...(((((........)))))...)))))).))))...))).)))..).))))))-).)). ( -31.60)
>consensus
ACGUGGUUGGUUGUCUGCUCCCAUGAGUGCGGAAAGUUG______________GGA_GCAGGGAGUUGGGAUCCAGAA______AGCUAAGAGCUCAGUGCUCUGAGCUGGGAGAUUGCA
...........(((...(((((...............................(((..(((....)))...)))..........((((.(((((.....))))).)))))))))...))) (-18.14 = -18.78 +   0.64)

alignment

secondary structure

dotplot

Window 1

Location	10,519,504 – 10,519,600
Length	96
Sequences	5
Columns	104
Reading direction	forward
Mean pairwise identity	80.71
Mean single sequence MFE	-24.44
Consensus MFE	-9.96
Energy contribution	-10.80
Covariance contribution	0.84
Combinations/Pair	1.29
Mean z-score	-3.24
Structure conservation index	0.41
SVM decision value	2.05
SVM RNA-class probability	0.986784
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10519504 96 + 22224390
UUCUGGAUCCCAACUCCCUGC-UCCCAACAUUCCGCACUCAUGGGAGCAGACAACCAACCACGUCACCAAGUCAUCCAGGCAUUCAACCAUAUGC-------CA
...(((((..(.......(((-(((((..............))))))))(((..........))).....)..)))))(((((........))))-------). ( -26.74)
>DroSec_CAF1 51013 103 + 1
UUCUGGAUCCCAACUCCCUGC-UCCCAACAUUACGCACUCAUGGGAGCAGACAACCAACCACGUCACCAAGUCAUCCAGGCAUUCAACCAUAUGCCAUGUGCCA
...(((((..(.......(((-(((((..............))))))))(((..........))).....)..)))))(((((........)))))........ ( -26.74)
>DroSim_CAF1 54543 103 + 1
UUCUGGAUCCCAACUCCCUGC-UCCCAACAUUCCGCACUCAUGGGAGCAGACAACCAACCACGUCACCAAGUCAUCCAGGCAUUCAACCAUAUGCCAUGUGCCA
...(((((..(.......(((-(((((..............))))))))(((..........))).....)..)))))(((((........)))))........ ( -26.74)
>DroEre_CAF1 52909 104 + 1
UUCUGCAUCCAAGCUCCCUGCCUGCCACAUUUCCGCACUUAUGAGAGCAAACAACCAACCACGUCCCCAUGCCAUCCAGGCAUUCAACCAUGUGCCAUGUGCCA
....((((....(((((.((..(((.........)))..)).).))))...........(((((....(((((.....)))))......)))))....)))).. ( -18.60)
>DroYak_CAF1 52450 91 + 1
--------CCAAGCUCUUAG-CUCUUAGCUUUCUGG----AUGGGAGCAGACAAGCAGCCACGUCACCAUGCCAUCCAGGCAUUCAACCAUAUGGCAUGUUCCA
--------....((((((.(-((((((.((....))----.)))))))....))).)))........((((((((...((.......))..))))))))..... ( -23.40)
>consensus
UUCUGGAUCCCAACUCCCUGC_UCCCAACAUUCCGCACUCAUGGGAGCAGACAACCAACCACGUCACCAAGUCAUCCAGGCAUUCAACCAUAUGCCAUGUGCCA
.................((((.(((((..............)))))))))............................(((((........)))))........ ( -9.96 = -10.80 +   0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:12:57 2006