Locus 5784

Sequence ID	X_DroMel_CAF1
Location	15,012,490 – 15,012,676
Length	186
Max. P	0.939480

overview

Window 5

Location	15,012,490 – 15,012,605
Length	115
Sequences	4
Columns	115
Reading direction	forward
Mean pairwise identity	84.06
Mean single sequence MFE	-50.88
Consensus MFE	-40.09
Energy contribution	-43.53
Covariance contribution	3.44
Combinations/Pair	1.14
Mean z-score	-2.18
Structure conservation index	0.79
SVM decision value	1.28
SVM RNA-class probability	0.939480
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15012490 115 + 22224390
UGCUGCCUGGGCGGCGCCCACAGUGGGUGGUGCUGCGUCAGCGGUGGUGGCGGGGCAAAAGCAGUCGCAUCACCAAUACCACCACUUGGAAAUCGGAGUGCAGGGCAAUACGCCA
.(((((....)))))((((......((((((((((...))))(((((((.(((.((....))..))))))))))...))))))((((.(....).))))...))))......... ( -52.20)
>DroSec_CAF1 30079 115 + 1
UGCUGCCUGGGCGGCGCCCACAGUGGGUGGUGCUGCGCCAGCGCCGGUGGUGGGGCAGAAACAGUCGCACCACCAUUACCACCACUUGGAAAUCGGAGUGCAGGGCAAUACGCCA
.(((((....)))))((((...((((..(((((((...)))))))(((((((.(((.......))).)))))))....))))(((((.(....).)))))..))))......... ( -59.60)
>DroEre_CAF1 31123 115 + 1
UGCUGCCUGGGGGGCGCCUACACUGGGUGGUGCAGCGGAAGCGGCGGUGGUGGGGCAGAAGCAGUCGCACCACCAUUACCACCAUUUGGAAAUCGGAGUGCUGGGCAAUACGCCU
.((.(((.....)))(((((((((.((((((((.((....)).))(((((((.(((.......))).)))))))...)))))).....(....)..)))).))))).....)).. ( -53.30)
>DroYak_CAF1 30995 103 + 1
UGCCGCUUGGGCGGCGCCAACAGUGGGUGGUGCAGCGGCAGC------------ACAGAAGCAGCCACACCACAAUUACCACCAUUUGGAAUUCGGAGUGCAGGGCAAUACGCCC
.(((((....))))).((((..((((((((((....(((.((------------......)).))).)))))).....))))...)))).............((((.....)))) ( -38.40)
>consensus
UGCUGCCUGGGCGGCGCCCACAGUGGGUGGUGCAGCGGCAGCGGCGGUGGUGGGGCAGAAGCAGUCGCACCACCAUUACCACCACUUGGAAAUCGGAGUGCAGGGCAAUACGCCA
.(((((....)))))((((......(((((((((((....)))))(((((((.(((.......))).)))))))...))))))((((.(....).))))...))))......... (-40.09 = -43.53 +   3.44)

alignment

secondary structure

dotplot

Window 6

Location	15,012,527 – 15,012,642
Length	115
Sequences	4
Columns	115
Reading direction	forward
Mean pairwise identity	84.49
Mean single sequence MFE	-41.50
Consensus MFE	-30.15
Energy contribution	-33.15
Covariance contribution	3.00
Combinations/Pair	1.09
Mean z-score	-1.89
Structure conservation index	0.73
SVM decision value	0.63
SVM RNA-class probability	0.803854
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15012527 115 + 22224390
UCAGCGGUGGUGGCGGGGCAAAAGCAGUCGCAUCACCAAUACCACCACUUGGAAAUCGGAGUGCAGGGCAAUACGCCAACGUUGAUGGAGGCGAGCACCACUAGAGGUGGGAAAC
.....(((((((.(((.((....))..))))))))))....(((((((((.(....).))))...((((....((((..((....))..)))).)).))......)))))..... ( -39.70)
>DroSec_CAF1 30116 115 + 1
CCAGCGCCGGUGGUGGGGCAGAAACAGUCGCACCACCAUUACCACCACUUGGAAAUCGGAGUGCAGGGCAAUACGCCAACGCUGAUGGAGGCAAGCACCACCAGAGAUGGGAAAC
...((((((((((((.(((.......))).)))))))....((.((....))..(((((.((....(((.....))).)).))))))).)))..))....(((....)))..... ( -41.40)
>DroEre_CAF1 31160 115 + 1
GAAGCGGCGGUGGUGGGGCAGAAGCAGUCGCACCACCAUUACCACCAUUUGGAAAUCGGAGUGCUGGGCAAUACGCCUACGCUGAUGGAGGCGAGCACCGCCAGAGGUGGGAAGC
...((..((((((((.(((.......))).)))))))....(((((.(((((....(((..((((((((.....)))).((((......))))))))))))))))))))))..)) ( -50.40)
>DroYak_CAF1 31032 103 + 1
GCAGC------------ACAGAAGCAGCCACACCACAAUUACCACCAUUUGGAAUUCGGAGUGCAGGGCAAUACGCCCACGCUGAUGGAGGCGAGCACCACCAGAGGUGGGAAAC
((.((------------......)).)).............(((((.(((((......(.((((.((((.....)))).((((......)))).))))).))))))))))..... ( -34.50)
>consensus
GCAGCGGCGGUGGUGGGGCAGAAGCAGUCGCACCACCAUUACCACCACUUGGAAAUCGGAGUGCAGGGCAAUACGCCAACGCUGAUGGAGGCGAGCACCACCAGAGGUGGGAAAC
........(((((((.(((.......))).)))))))....(((((.(((((......(.((((..(((.....)))..((((......)))).))))).))))))))))..... (-30.15 = -33.15 +   3.00)

alignment

secondary structure

dotplot

Window 7

Location	15,012,565 – 15,012,676
Length	111
Sequences	4
Columns	117
Reading direction	forward
Mean pairwise identity	86.26
Mean single sequence MFE	-35.35
Consensus MFE	-24.24
Energy contribution	-23.18
Covariance contribution	-1.06
Combinations/Pair	1.28
Mean z-score	-1.42
Structure conservation index	0.69
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15012565 111 + 22224390
AUACCACCACUUGGAAAUCGGAGUGCAGGGCAAUACGCCAACGUUGAUGGAGGCGAGCACCACUAGAGGUGGGAAACAUGCCACAGUGCCCACCA------CUCAGGCACCACCAAA
..........((((......(((((..(((((.....(((.......))).((((..((((......))))(....).))))....)))))..))------))).(....).)))). ( -33.50)
>DroSec_CAF1 30154 111 + 1
UUACCACCACUUGGAAAUCGGAGUGCAGGGCAAUACGCCAACGCUGAUGGAGGCAAGCACCACCAGAGAUGGGAAACAUGCCACAGUGGCCAUCA------CUCAGGCACCACCAAA
...(((.....))).....((.((((..(((.....)))....(((((((.((......)).)))..(((((....)..(((.....))))))).------.))))))))..))... ( -31.90)
>DroEre_CAF1 31198 111 + 1
UUACCACCAUUUGGAAAUCGGAGUGCUGGGCAAUACGCCUACGCUGAUGGAGGCGAGCACCGCCAGAGGUGGGAAGCAUGGAACAGUGGCCACCA------CUCAGGCACCACCAAA
...(((((.(((((....(((..((((((((.....)))).((((......)))))))))))))))))))))...((.((....(((((...)))------)))).))......... ( -36.90)
>DroYak_CAF1 31058 117 + 1
UUACCACCAUUUGGAAUUCGGAGUGCAGGGCAAUACGCCCACGCUGAUGGAGGCGAGCACCACCAGAGGUGGGAAACAUGCAAAAGUGGAUACAGUGGUGCUACAGGCAACAUCAAA
...(((((.(((((......(.((((.((((.....)))).((((......)))).))))).))))))))))......(((....((((.(((....)))))))..)))........ ( -39.10)
>consensus
UUACCACCACUUGGAAAUCGGAGUGCAGGGCAAUACGCCAACGCUGAUGGAGGCGAGCACCACCAGAGGUGGGAAACAUGCAACAGUGGCCACCA______CUCAGGCACCACCAAA
...((..(((((.(....).)))))..)).......(((....(((.(((..(....).))).))).(((((...((........))..)))))...........)))......... (-24.24 = -23.18 +  -1.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:56:19 2006