Locus 6026

Sequence ID	X_DroMel_CAF1
Location	15,475,465 – 15,475,651
Length	186
Max. P	0.857572

overview

Window 3

Location	15,475,465 – 15,475,574
Length	109
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	78.55
Mean single sequence MFE	-31.48
Consensus MFE	-20.06
Energy contribution	-18.86
Covariance contribution	-1.20
Combinations/Pair	1.25
Mean z-score	-1.93
Structure conservation index	0.64
SVM decision value	0.81
SVM RNA-class probability	0.857572
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15475465 109 - 22224390
CAUGGAUUAUGGAUUAUGGAGAUGGCCAUAGUCGGGUUAAGCCCUGCUAAAUGGAAGGAACGGGCCACGCCCACACCGUGAAA-GGAAGGUGUUAUAAAAGCGAUAAUAA
(((((......((((((((......))))))))((((...((((..((........))...))))...))))...)))))...-......((((((.......)))))). ( -31.20)
>DroSec_CAF1 36140 100 - 1
---------UGGAUUAUGGAGAUGGCCAUAGUCGGGUUAAGCCCCGCUAAAUGGAAGGAACGGGCCACGCCCACACCGCGAAA-GGAAGGUGUUAUAAAAGCGAUAAUAA
---------..((((((((......))))))))(((.....)))((((.............((((...))))(((((.(....-)...)))))......))))....... ( -33.30)
>DroSim_CAF1 33853 100 - 1
---------UGGAUUAUGGAGAUGGCCAUAGUCGGGUUAAGCCCUGCUAAAUGGAAGGAACGGGCCACGCCCACACCGCGAAA-GGAAGGUGUUAUAAAAGCGAUAAUAA
---------..((((((((......))))))))((((...((((..((........))...))))...))))(((((.(....-)...)))))................. ( -31.70)
>DroEre_CAF1 37907 82 - 1
----------------------UGGCCAUAGCCGGGCUAAGCCCUGCUAAAUGCGGC---GGGGCCACGCCCA--CCGUGGAG-GGAAGGUGUUAUAAAAGCGAUAAUAA
----------------------.((((...(((((((...)))).((.....)))))---..))))(((((..--((.....)-)...)))))................. ( -31.00)
>DroYak_CAF1 36447 100 - 1
---GGA-GAUGGAG-CUGGUGCUGGUCAUAGCCGGGUUAAGCCCUGUUAAAUGCGGC---GCGGCCACGCCCA--CCGUGGCGGGGAAGGUGUUAUAAAAGCGAUAAUAA
---...-......(-((.((((((....((((.(((.....))).))))....))))---)).((((((....--.)))))).................)))........ ( -30.20)
>consensus
_________UGGAUUAUGGAGAUGGCCAUAGUCGGGUUAAGCCCUGCUAAAUGGAAGGAACGGGCCACGCCCACACCGUGAAA_GGAAGGUGUUAUAAAAGCGAUAAUAA
.......................((((.((((.((((...)))).))))....(......).))))(((((....((.......))..)))))................. (-20.06 = -18.86 +  -1.20)

alignment

secondary structure

dotplot

Window 4

Location	15,475,534 – 15,475,651
Length	117
Sequences	4
Columns	117
Reading direction	reverse
Mean pairwise identity	71.56
Mean single sequence MFE	-27.52
Consensus MFE	-13.64
Energy contribution	-14.20
Covariance contribution	0.56
Combinations/Pair	1.14
Mean z-score	-1.81
Structure conservation index	0.50
SVM decision value	0.04
SVM RNA-class probability	0.554079
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15475534 117 - 22224390
UUGGGAGCAACGGAAGGCGAAGGAGAGGCUGGCACAAUGCAACAGGGAACAUGGAGCAUGGAGCAUGGUGCAUGGUGCAUGGAUUAUGGAUUAUGGAGAUGGCCAUAGUCGGGUUAA
.....(((..(....).(....)....))).((((.(((((.((.....((((...)))).....)).))))).))))...((((((((.((((....))))))))))))....... ( -31.30)
>DroSec_CAF1 36209 91 - 1
-----AGCAGUGGAAGGCGGAGGACAGGCUGGCACAAUGCAACAGGGAACAUGGAGCAU-------GGAGCA--------------UGGAUUAUGGAGAUGGCCAUAGUCGGGUUAA
-----.((.(((..((.(........).))..))).((((..(((....).))..))))-------...)).--------------..((((((((......))))))))....... ( -24.80)
>DroSim_CAF1 33922 98 - 1
-----AGCAGUGGAAGGCGGAGGCCAGGCUGGCACAAUGCAACAGGGAACAUGGAGCAUGGAGCAUGGAGCA--------------UGGAUUAUGGAGAUGGCCAUAGUCGGGUUAA
-----..((((....(((....)))..))))((.(.((((..(((....).))..)))).).))....(((.--------------(.((((((((......)))))))).)))).. ( -27.50)
>DroYak_CAF1 36512 90 - 1
-----AGGCUUGGAAGG-----------CUAGCCACAUGGAACAGGGAACAUGGAUUAUGGAG-AUGGAGCU--------GGA-GAUGGAG-CUGGUGCUGGUCAUAGCCGGGUUAA
-----.(((((((..((-----------((((((.(((((..(((....).))..)))))...-....((((--------...-.....))-)).).)))))))....))))))).. ( -26.50)
>consensus
_____AGCAGUGGAAGGCGGAGGACAGGCUGGCACAAUGCAACAGGGAACAUGGAGCAUGGAG_AUGGAGCA______________UGGAUUAUGGAGAUGGCCAUAGUCGGGUUAA
......((....(..(((.........)))..)...((((..(((....).))..))))..........)).................((((((((......))))))))....... (-13.64 = -14.20 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:02:22 2006