Locus 680

Sequence ID	3L_DroMel_CAF1
Location	2,016,086 – 2,016,204
Length	118
Max. P	0.794722

overview

Window 7

Location	2,016,086 – 2,016,177
Length	91
Sequences	6
Columns	112
Reading direction	forward
Mean pairwise identity	75.27
Mean single sequence MFE	-34.00
Consensus MFE	-18.75
Energy contribution	-21.28
Covariance contribution	2.53
Combinations/Pair	1.08
Mean z-score	-1.75
Structure conservation index	0.55
SVM decision value	0.60
SVM RNA-class probability	0.794722
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2016086 91 + 23771897
GAACUUCUGG------------GUGGCAAGUGCUCCAAACUGUAGCCAC---AUGCUCAUGAAGGGUGAGCUGCUGGUCCAGGGGAGCAUUGUGGCACAAUUCA------AG
..........------------(((.((((((((((...(((..(((((---(.((((((.....)))))))).)))).))).)))))))).)).)))......------.. ( -35.80)
>DroSec_CAF1 66621 91 + 1
GAACUUCUGC------------GUGGCAAGUGCUCCAAACUGUAGCCAC---AUGCUCAUGAAGGGUGAGCUGCUGGUCCAGGGGAGCAGUGUGGCACAGUUCA------AG
(((((...(.------------((.(((..((((((...(((..(((((---(.((((((.....)))))))).)))).))).)))))).))).)).)))))).------.. ( -37.70)
>DroSim_CAF1 81689 91 + 1
GAACUUCUGC------------GUGGCAAGUGCUCCAAACUGUAGCCAC---AUGCUCAUGAAGGGUGAGCUGCUGGUCCAGGGGAGCAGUGUGGCACAGUUCA------AG
(((((...(.------------((.(((..((((((...(((..(((((---(.((((((.....)))))))).)))).))).)))))).))).)).)))))).------.. ( -37.70)
>DroEre_CAF1 72836 98 + 1
GAACUUUUGC------------CUGGCAAGUGCCCCAAACUGUAGCCACUGUGCGCCCAUGAAGGGUGAGCUGCUGGUCCAGGGGAGCAAUGUGGCAG--UUGAACUGUGGG
..((.(((..------------(((.((..((((((...(((..(((((.((.(((((.....))))).)).).)))).)))))).)))...)).)))--..)))..))... ( -32.30)
>DroYak_CAF1 69380 86 + 1
GAACUUCUGC------------CUGGCAAGUGCUCCAAACUGUAGCCAC---ACGCUCAUGAAGGGUGAGCUGCUGGUCCAGGGGAGCAAUGUGGCAC--A---------AA
.......(((------------(..(((..((((((...(((..(((((---(.((((((.....)))))))).)))).))).)))))).))))))).--.---------.. ( -33.60)
>DroAna_CAF1 64320 92 + 1
UCUCUGUUGCUCCUUCCAGGGUCCUGAAAGUGUUCCAAACUGUAGCAAC---AUGCACAUGAAGGG-----------UCGUGGGGAGGACUGGGCCUGGGUUGA------AG
..........((..((((((.(((....(((.((((........((...---..)).(((((....-----------))))).)))).))))))))))))..))------.. ( -26.90)
>consensus
GAACUUCUGC____________CUGGCAAGUGCUCCAAACUGUAGCCAC___AUGCUCAUGAAGGGUGAGCUGCUGGUCCAGGGGAGCAAUGUGGCACAGUUCA______AG
......................(((.((..((((((...(((..((((......((((((.....))))))...)))).))).))))))...)).))).............. (-18.75 = -21.28 +   2.53)

alignment

secondary structure

dotplot

Window 8

Location	2,016,114 – 2,016,204
Length	90
Sequences	6
Columns	100
Reading direction	reverse
Mean pairwise identity	78.04
Mean single sequence MFE	-18.37
Consensus MFE	-10.67
Energy contribution	-12.45
Covariance contribution	1.78
Combinations/Pair	1.13
Mean z-score	-1.80
Structure conservation index	0.58
SVM decision value	0.52
SVM RNA-class probability	0.766105
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2016114 90 - 23771897
UCC-CCAGUUAUUGUAAUUUACCAUUUCCU------UGAAUUGUGCCACAAUGCUCCCCUGGACCAGCAGCUCACCCUUCAUGAGCAU---GUGGCUACA
...-..........................------.....(((((((((.((((((...)))...)))(((((.......))))).)---))))).))) ( -19.90)
>DroSec_CAF1 66649 90 - 1
UCC-CCAGUUAUCGUAAUUUACCAUUUCCU------UGAACUGUGCCACACUGCUCCCCUGGACCAGCAGCUCACCCUUCAUGAGCAU---GUGGCUACA
...-.(((((.....(((.....)))....------..))))).(((((((((.(((...))).)))..(((((.......))))).)---))))).... ( -22.10)
>DroSim_CAF1 81717 90 - 1
UCC-CCAGUUAUUGUAAUUUACCAUUUCCU------UGAACUGUGCCACACUGCUCCCCUGGACCAGCAGCUCACCCUUCAUGAGCAU---GUGGCUACA
...-.(((((...(.((........)).).------..))))).(((((((((.(((...))).)))..(((((.......))))).)---))))).... ( -22.70)
>DroEre_CAF1 72864 97 - 1
UCU-CCAGUUAUUGUAAUUUACCAUUACCCCACAGUUCAA--CUGCCACAUUGCUCCCCUGGACCAGCAGCUCACCCUUCAUGGGCGCACAGUGGCUACA
...-..(((((((((................)))))..))--))(((((..(((.(((.((((..............)))).))).)))..))))).... ( -20.63)
>DroYak_CAF1 69408 85 - 1
CCU-CCAGUUAUUGUAAUUUACCAAUUCUU---------U--GUGCCACAUUGCUCCCCUGGACCAGCAGCUCACCCUUCAUGAGCGU---GUGGCUACA
...-..........................---------(--(((((((((((((((...)))...)))(((((.......)))))))---))))).))) ( -20.50)
>DroAna_CAF1 64360 79 - 1
UCAAUUCGUUUUUGUAAUUUAAAAU-UCCU------UCAACCCAGGCCCAGUCCUCCCCACGA-----------CCCUUCAUGUGCAU---GUUGCUACA
.....(((((((((.....))))).-....------.......(((......)))....))))-----------.......(((((..---...)).))) (  -4.40)
>consensus
UCC_CCAGUUAUUGUAAUUUACCAUUUCCU______UGAACUGUGCCACACUGCUCCCCUGGACCAGCAGCUCACCCUUCAUGAGCAU___GUGGCUACA
............................................(((((.(((.((.....)).)))..(((((.......))))).....))))).... (-10.67 = -12.45 +   1.78)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:48:20 2006