Locus 4146

Sequence ID	X_DroMel_CAF1
Location	10,873,658 – 10,873,769
Length	111
Max. P	0.974298

overview

Window 0

Location	10,873,658 – 10,873,769
Length	111
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	92.14
Mean single sequence MFE	-39.03
Consensus MFE	-33.02
Energy contribution	-33.78
Covariance contribution	0.76
Combinations/Pair	1.04
Mean z-score	-1.69
Structure conservation index	0.85
SVM decision value	1.19
SVM RNA-class probability	0.928540
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10873658 111 + 22224390
-UCAUCUUGGCCAGCCACGUCACGCAGCUGGUGAAAAUUUGCUGGCCAGUUGGCCAUCGGGACAACCGAGCAUCAGAUGGCUGACUGGGCAUAUUUUU-UUUCCCCCAACAGC
-......((((((((....((((.......))))......))))))))((..((((((((.....))(.....).))))))..))((((.........-.....))))..... ( -39.74)
>DroSec_CAF1 28408 113 + 1
AUCAUCUUGGCCAGCCACGUCACGCAGCUGGUGAAAAUUUGCUGGCCCGUUGGGCAUCGGGACAACCGAGCAUCAGAUGGCUGACUGGGCAUAUUUUUUUUUCGCCCAACAGC
........(((((((....((((.......))))......))))))).(((((((.((((.....))))((.((((........)))))).............)))))))... ( -42.60)
>DroSim_CAF1 29808 112 + 1
-UCAUCUUGGCCAGCCACGUCACGCAGCUGGUGAAAAUUUGCUGGCCAGUUGGCCAUCGGGACAACCGAGCAUCAGAUGGCUGACUGGGCAUAUUUUUUUUUCGCCCAACAGC
-......((((((((....((((.......))))......))))))))((..((((((((.....))(.....).))))))..))(((((.............)))))..... ( -44.02)
>DroEre_CAF1 4575 107 + 1
-UCAUCUUGGCCAGCCACGUCACGCAGAUGGUGAAAAUUUGCUGGCCAGUUGGCCAACGGGACAUUCGAGCAUCAGAUGGCUGACGGGGCAUAUUU-UUU----CCCAGCGGC
-.(((((((((((((...((((.((((((.......))))))))))..)))))))).(((.....)))......)))))((((..((((.......-..)----)))..)))) ( -36.50)
>DroYak_CAF1 27976 108 + 1
-UCAUCUUGGCCAGCCACGUCACGCAGAUGGUGAAAAUUUGCAGGCCAGUUGGCCAACGGGACAUUCGAGCAUCAGAUGGCUGACUGGGCAUAUUUUUUU----CCCAACGGC
-.(((((((((((((...(((..((((((.......)))))).)))..)))))))).(((.....)))......)))))((((..((((.(........)----)))).)))) ( -32.30)
>consensus
_UCAUCUUGGCCAGCCACGUCACGCAGCUGGUGAAAAUUUGCUGGCCAGUUGGCCAUCGGGACAACCGAGCAUCAGAUGGCUGACUGGGCAUAUUUUUUUUUC_CCCAACAGC
.......((((((((....((((.......))))......))))))))((..((((((((.....))(.....).))))))..)).(((...............)))...... (-33.02 = -33.78 +   0.76)

alignment

secondary structure

dotplot

Window 1

Location	10,873,658 – 10,873,769
Length	111
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	92.14
Mean single sequence MFE	-41.27
Consensus MFE	-32.78
Energy contribution	-34.42
Covariance contribution	1.64
Combinations/Pair	1.03
Mean z-score	-2.36
Structure conservation index	0.79
SVM decision value	1.73
SVM RNA-class probability	0.974298
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10873658 111 - 22224390
GCUGUUGGGGGAAA-AAAAAUAUGCCCAGUCAGCCAUCUGAUGCUCGGUUGUCCCGAUGGCCAACUGGCCAGCAAAUUUUCACCAGCUGCGUGACGUGGCUGGCCAAGAUGA-
(((((((((.....-.........))))).))))(((((..(((((((.....))))(((((....))))))))........(((((..((...))..)))))...))))).- ( -44.34)
>DroSec_CAF1 28408 113 - 1
GCUGUUGGGCGAAAAAAAAAUAUGCCCAGUCAGCCAUCUGAUGCUCGGUUGUCCCGAUGCCCAACGGGCCAGCAAAUUUUCACCAGCUGCGUGACGUGGCUGGCCAAGAUGAU
(((((((((((...........))))))).))))(((((((......((((.((((........)))).))))......)).(((((..((...))..)))))...))))).. ( -44.10)
>DroSim_CAF1 29808 112 - 1
GCUGUUGGGCGAAAAAAAAAUAUGCCCAGUCAGCCAUCUGAUGCUCGGUUGUCCCGAUGGCCAACUGGCCAGCAAAUUUUCACCAGCUGCGUGACGUGGCUGGCCAAGAUGA-
(((((((((((...........))))))).))))(((((..(((((((.....))))(((((....))))))))........(((((..((...))..)))))...))))).- ( -47.80)
>DroEre_CAF1 4575 107 - 1
GCCGCUGGG----AAA-AAAUAUGCCCCGUCAGCCAUCUGAUGCUCGAAUGUCCCGUUGGCCAACUGGCCAGCAAAUUUUCACCAUCUGCGUGACGUGGCUGGCCAAGAUGA-
((((.((((----(..-..((.((...((((((....))))))..)).)).))))).))))((.(((((((((......(((((....).))))....))))))).)).)).- ( -37.60)
>DroYak_CAF1 27976 108 - 1
GCCGUUGGG----AAAAAAAUAUGCCCAGUCAGCCAUCUGAUGCUCGAAUGUCCCGUUGGCCAACUGGCCUGCAAAUUUUCACCAUCUGCGUGACGUGGCUGGCCAAGAUGA-
..(((((((----...........))).(((((((((.(.((((..(.....)..((.((((....)))).))...............)))).).)))))))))...)))).- ( -32.50)
>consensus
GCUGUUGGG_GAAAAAAAAAUAUGCCCAGUCAGCCAUCUGAUGCUCGGUUGUCCCGAUGGCCAACUGGCCAGCAAAUUUUCACCAGCUGCGUGACGUGGCUGGCCAAGAUGA_
(((((((((...............))))).))))(((((..(((.(((.....))).(((((....))))))))........(((((..((...))..)))))...))))).. (-32.78 = -34.42 +   1.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:17:29 2006