Locus 4722

Sequence ID	3L_DroMel_CAF1
Location	13,302,741 – 13,302,876
Length	135
Max. P	0.963259

overview

Window 8

Location	13,302,741 – 13,302,837
Length	96
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	78.77
Mean single sequence MFE	-26.40
Consensus MFE	-15.24
Energy contribution	-16.13
Covariance contribution	0.89
Combinations/Pair	1.08
Mean z-score	-1.63
Structure conservation index	0.58
SVM decision value	0.08
SVM RNA-class probability	0.572956
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13302741 96 - 23771897
UUUUGCAUUUGCAGUUUACUCGGUUAACCGCUUUUCUAGCGGAUUUAACACAUUUC--GGCCUCAGCUGGGC----------GACAACAGAACAGUGGAU-----UGUUUUCG----
..........((((((((((.(((((((((((.....)))))..))))).....((--(.((......)).)----------))........))))))))-----))).....---- ( -26.10)
>DroSim_CAF1 65393 96 - 1
UUUUGCAUUUGCAGUUUACUCGGUUAACCGCUUUUCUAGCGGAUUUAACACAUUUC--GGCCUCAGCUGGGC----------GACAACUGAACAGUGGAU-----UGUUUUUG----
.....((...(((((((((((((((..(((((.....)))))............((--(.((......)).)----------)).))))))...))))))-----)))...))---- ( -28.10)
>DroEre_CAF1 65810 96 - 1
UUUUGCAUUUGCAGUUUACUCGGUUAACCGCGUUUCUAGCGGAUUUAACACAUUUC--GGCCUCAGCCGGGC----------GACAACUGAACAGUGGAU-----UGCUCUUA----
..........(((((((((((((((..((((.......))))...........(((--(((....)))))).----------...))))))...))))))-----))).....---- ( -28.60)
>DroWil_CAF1 82539 95 - 1
UUUUGCAUUUGCAGUUUACUCGGUUAACCGCUUUUAUAGCGGAUUUAACACAUUUUCAGGCCU----UGGGCUCAUAACAUUGACCAAUGCACAGUGGC------------------
.....(((((((((......)(((((((((((.....)))))................((((.----..)))).......))))))..)))).))))..------------------ ( -21.70)
>DroYak_CAF1 70819 96 - 1
UUUUGCAUUUGCAGUUUACUCGGUUAACCGCUUUUCUAGCGGAUUUAACACAUUUC--GGCCUCAGCUGGGC----------GACAACUGAACAGUGGAU-----UGUUUUUG----
.....((...(((((((((((((((..(((((.....)))))............((--(.((......)).)----------)).))))))...))))))-----)))...))---- ( -28.10)
>DroAna_CAF1 61745 97 - 1
UUUUGCAUUU-CAGUUUACUCGGUUAACCGCUUUUAUAGCGGAUUUAGCACAUUUC--AGCCUUGGC----C----------AAUA---CCGUGGUGGAUGUACUGGCUUUUGUGGA
.((..((..(-((((.......((((((((((.....)))))..)))))(((((..--.(((.(((.----.----------....---))).))).))))))))))....))..)) ( -25.80)
>consensus
UUUUGCAUUUGCAGUUUACUCGGUUAACCGCUUUUCUAGCGGAUUUAACACAUUUC__GGCCUCAGCUGGGC__________GACAACUGAACAGUGGAU_____UGUUUUUG____
...(((....)))(((((((..((((((((((.....)))))..)))))..........((((.....)))).....................)))))))................. (-15.24 = -16.13 +   0.89)

alignment

secondary structure

dotplot

Window 9

Location	13,302,767 – 13,302,876
Length	109
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	90.70
Mean single sequence MFE	-38.90
Consensus MFE	-33.52
Energy contribution	-34.80
Covariance contribution	1.28
Combinations/Pair	1.11
Mean z-score	-2.40
Structure conservation index	0.86
SVM decision value	1.55
SVM RNA-class probability	0.963259
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13302767 109 + 23771897
GCCCAGCUGAGGCCGAAAUGUGUUAAAUCCGCUAGAAAAGCGGUUAACCGAGUAAACUGCAAAUGCAAAAUGCGGUUGGUUCACUUCGGUUCGGUGGGGUGACGUCCUG
((((.((((((.(((((..(.(((((..(((((.....)))))))))))(((..(((((((.........)))))))..)))..))))))))))).))))......... ( -39.90)
>DroSec_CAF1 64793 109 + 1
GCCCAGCUGAGGCCGAAAUGUGUUAAAUCCGCUAGAAAAGCGGUUAACCGAGUAAACUGCAAAUGCAAAAUGCGGUUGGUUCACUUCGGCUCGGUGGGGUGAUGUCCUG
((((.((((((.(((((..(.(((((..(((((.....)))))))))))(((..(((((((.........)))))))..)))..))))))))))).))))......... ( -42.30)
>DroSim_CAF1 65419 109 + 1
GCCCAGCUGAGGCCGAAAUGUGUUAAAUCCGCUAGAAAAGCGGUUAACCGAGUAAACUGCAAAUGCAAAAUGCGGUUGGUUCACUUCGGUUCGGUGGGGUGAUGUCCUG
((((.((((((.(((((..(.(((((..(((((.....)))))))))))(((..(((((((.........)))))))..)))..))))))))))).))))......... ( -39.90)
>DroEre_CAF1 65836 109 + 1
GCCCGGCUGAGGCCGAAAUGUGUUAAAUCCGCUAGAAACGCGGUUAACCGAGUAAACUGCAAAUGCAAAAUGCGGUUGGUUCACUUCGGUUCGGUGGGGUGACAUCCUG
((((.((((((.(((((..(.(((((..((((.......))))))))))(((..(((((((.........)))))))..)))..))))))))))).))))......... ( -40.50)
>DroYak_CAF1 70845 109 + 1
GCCCAGCUGAGGCCGAAAUGUGUUAAAUCCGCUAGAAAAGCGGUUAACCGAGUAAACUGCAAAUGCAAAAUGCGGUUGGUUCACUCCGGUUCGGUGGGGUGACGUCCUG
((((.((((((.(((....(.(((((..(((((.....)))))))))))(((..(((((((.........)))))))..)))....))))))))).))))......... ( -37.60)
>DroAna_CAF1 61777 100 + 1
G----GCCAAGGCUGAAAUGUGCUAAAUCCGCUAUAAAAGCGGUUAACCGAGUAAACUG-AAAUGCAAAAUGCGG----UUCAUUUCGGUUCUGCUGGGCUCUUGCCCG
(----((.(..(((((((((.(((....(((((.....)))))................-....((.....))))----).)))))))))..))))((((....)))). ( -33.20)
>consensus
GCCCAGCUGAGGCCGAAAUGUGUUAAAUCCGCUAGAAAAGCGGUUAACCGAGUAAACUGCAAAUGCAAAAUGCGGUUGGUUCACUUCGGUUCGGUGGGGUGACGUCCUG
((((.((((((.(((((..(.(((((..(((((.....)))))))))))(((..(((((((.........)))))))..)))..))))))))))).))))......... (-33.52 = -34.80 +   1.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:31:37 2006