Locus 2404

Sequence ID	3L_DroMel_CAF1
Location	6,766,001 – 6,766,127
Length	126
Max. P	0.933980

overview

Window 1

Location	6,766,001 – 6,766,115
Length	114
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.43
Mean single sequence MFE	-42.73
Consensus MFE	-27.29
Energy contribution	-27.35
Covariance contribution	0.06
Combinations/Pair	1.16
Mean z-score	-1.67
Structure conservation index	0.64
SVM decision value	0.12
SVM RNA-class probability	0.594430
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6766001 114 - 23771897
UUGAGGGAUGCAGGAGUGGACGCAGCUGCAGCUGAGUUCGACUCCUGGAUUUCUGAUUGCUAGUGGGCCGCCAACUGAUGC---GCCGCUACCGCCGAG---GAUUGCAUAUUCUGUGGG
.(.((..((.(((((((((((.((((....)))).)))).))))))).))..)).)....((((((..(((........))---)))))))((((..((---(((.....))))))))). ( -45.50)
>DroVir_CAF1 40935 96 - 1
UU------GGCAGGAGUGGACGCAGCUGCAGCUGAGUUCGACUCCUGGAUUUCUGAUUGCUAGUGAGCCGCCAAUUGGUGC---GCC---------------GACUGCAUGUUCUGGGGG
..------..(((((((((((.((((....)))).)))).)))))))..(..(.((.(((.(((..((((((....)))).---)).---------------.))))))...)).)..). ( -39.30)
>DroGri_CAF1 38020 96 - 1
UU------UGCAGGAGUGGACGCAGCUGCAGCUGAGUUCGACUCCUGGAUUUCUGAUUGCUAGUGGGCCGCCAACUGAUGC---GCC---------------GACUGCAUGUUCUGGGGA
..------..(((((((((((.((((....)))).)))).)))))))..(..(.((.(((.(((.(((.((........))---)))---------------.))))))...)).)..). ( -39.20)
>DroWil_CAF1 53050 120 - 1
UUAUUGGAUGCAGGAGUUGAUCCGGCUGCAGCUGGAUUCGACUCCUGGAUUUCUGAUUGCUAGUGGGCCGUUAACUGAUGCUGCGCCCCCACCGUUGUGGCUGUUUGCAUGUUCUGGGGG
.(((..(((.((((((((((((((((....)))))).)))))))))).))...((((.(((....))).)))).)..))).....((((((....((..(....)..)).....)))))) ( -46.20)
>DroMoj_CAF1 41185 96 - 1
UU------UGCAGGAGUGGACGCAGCUGCAGCUGAGUUCGACUCCUGGAUUUCUGAUUGCUAGUGAGCCGCCAACUGGUGA---GCC---------------GACUGCAUGUUCUGGGGG
..------..(((((((((((.((((....)))).)))).)))))))..(..(.((.(((.(((..((((((....)))).---)).---------------.))))))...)).)..). ( -39.30)
>DroAna_CAF1 36367 111 - 1
UUGAGGGAUGCAGGAGUGGACGCAGCUGCAGCUGAGUUCGACUCCUGGAUUUCUGAUUGCUAGUGGGCCGCCAACUGGUGC---GCCGCUGCCGCUG------ACUGCAUGUUCUGGGGG
.(.((..((.(((((((((((.((((....)))).)))).))))))).))..)).)....((((((((.(((....)))))---.))))))((.(.(------((.....)))..).)). ( -46.90)
>consensus
UU______UGCAGGAGUGGACGCAGCUGCAGCUGAGUUCGACUCCUGGAUUUCUGAUUGCUAGUGGGCCGCCAACUGAUGC___GCC_______________GACUGCAUGUUCUGGGGG
..........(((((((((((.((((....)))).)))).)))))))..(..(.((.(((.(((.(((((((....))))....)))................))))))...)).)..). (-27.29 = -27.35 +   0.06)

alignment

secondary structure

dotplot

Window 2

Location	6,766,035 – 6,766,127
Length	92
Sequences	6
Columns	92
Reading direction	forward
Mean pairwise identity	88.36
Mean single sequence MFE	-25.23
Consensus MFE	-20.94
Energy contribution	-21.05
Covariance contribution	0.11
Combinations/Pair	1.10
Mean z-score	-2.02
Structure conservation index	0.83
SVM decision value	0.41
SVM RNA-class probability	0.724470
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6766035 92 + 23771897
CAUCAGUUGGCGGCCCACUAGCAAUCAGAAAUCCAGGAGUCGAACUCAGCUGCAGCUGCGUCCACUCCUGCAUCCCUCAAUAGUCUAAGCCA
.......((((.....((((......((..((.(((((((.((.(.((((....)))).))).))))))).))..))...))))....)))) ( -25.70)
>DroVir_CAF1 40957 86 + 1
CACCAAUUGGCGGCUCACUAGCAAUCAGAAAUCCAGGAGUCGAACUCAGCUGCAGCUGCGUCCACUCCUGCC------AACAGUCUGCACCA
.......(((.((((....)))...((((....(((((((.((.(.((((....)))).))).)))))))..------.....))))).))) ( -25.00)
>DroPse_CAF1 35556 92 + 1
CACCAGUUGGCGGCUCACUAGCAAUCAGAAAUCCAGGAGUCGAACUCAGCUGCAGCUGCGUCCACUCCUGCAUCCCUCAAUAGUCUAAGCCA
..((....)).((((.((((......((..((.(((((((.((.(.((((....)))).))).))))))).))..))...))))...)))). ( -26.80)
>DroGri_CAF1 38042 86 + 1
CAUCAGUUGGCGGCCCACUAGCAAUCAGAAAUCCAGGAGUCGAACUCAGCUGCAGCUGCGUCCACUCCUGCA------AAUAGUCUGCACCA
.....(((((.......)))))...((((....(((((((.((.(.((((....)))).))).)))))))..------.....))))..... ( -24.30)
>DroWil_CAF1 53090 92 + 1
CAUCAGUUAACGGCCCACUAGCAAUCAGAAAUCCAGGAGUCGAAUCCAGCUGCAGCCGGAUCAACUCCUGCAUCCAAUAAUAGUCUGAGUCA
..(((((((...((......))...........(((((((.((.(((.((....)).))))).)))))))..........))).)))).... ( -22.80)
>DroPer_CAF1 35195 92 + 1
CACCAGUUGGCGGCUCACUAGCAAUCAGAAAUCCAGGAGUCGAACUCAGCUGCAGCUGCGUCCACUCCUGCAUCCCUCAAUAGUCUAAGCCA
..((....)).((((.((((......((..((.(((((((.((.(.((((....)))).))).))))))).))..))...))))...)))). ( -26.80)
>consensus
CACCAGUUGGCGGCCCACUAGCAAUCAGAAAUCCAGGAGUCGAACUCAGCUGCAGCUGCGUCCACUCCUGCAUCCCUCAAUAGUCUAAGCCA
.......((((.((......))...........(((((((.((.(.((((....)))).))).)))))))..................)))) (-20.94 = -21.05 +   0.11)

alignment

secondary structure

dotplot

Window 3

Location	6,766,035 – 6,766,127
Length	92
Sequences	6
Columns	92
Reading direction	reverse
Mean pairwise identity	88.36
Mean single sequence MFE	-37.18
Consensus MFE	-30.08
Energy contribution	-29.53
Covariance contribution	-0.55
Combinations/Pair	1.24
Mean z-score	-3.12
Structure conservation index	0.81
SVM decision value	1.23
SVM RNA-class probability	0.933980
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6766035 92 - 23771897
UGGCUUAGACUAUUGAGGGAUGCAGGAGUGGACGCAGCUGCAGCUGAGUUCGACUCCUGGAUUUCUGAUUGCUAGUGGGCCGCCAACUGAUG
.(((((..((((.(.((..((.(((((((((((.((((....)))).)))).))))))).))..)).)....)))))))))........... ( -38.20)
>DroVir_CAF1 40957 86 - 1
UGGUGCAGACUGUU------GGCAGGAGUGGACGCAGCUGCAGCUGAGUUCGACUCCUGGAUUUCUGAUUGCUAGUGAGCCGCCAAUUGGUG
(((((((((..(((------..(((((((((((.((((....)))).)))).)))))))))).))))...(((....))))))))....... ( -32.80)
>DroPse_CAF1 35556 92 - 1
UGGCUUAGACUAUUGAGGGAUGCAGGAGUGGACGCAGCUGCAGCUGAGUUCGACUCCUGGAUUUCUGAUUGCUAGUGAGCCGCCAACUGGUG
.(((((..((((.(.((..((.(((((((((((.((((....)))).)))).))))))).))..)).)....)))))))))(((....))). ( -41.50)
>DroGri_CAF1 38042 86 - 1
UGGUGCAGACUAUU------UGCAGGAGUGGACGCAGCUGCAGCUGAGUUCGACUCCUGGAUUUCUGAUUGCUAGUGGGCCGCCAACUGAUG
(((((((((.....------(.(((((((((((.((((....)))).)))).))))))).)..))))...(((....))))))))....... ( -32.80)
>DroWil_CAF1 53090 92 - 1
UGACUCAGACUAUUAUUGGAUGCAGGAGUUGAUCCGGCUGCAGCUGGAUUCGACUCCUGGAUUUCUGAUUGCUAGUGGGCCGUUAACUGAUG
....((((.........((((.((((((((((((((((....)))))).)))))))))).)))).((((.(((....))).)))).)))).. ( -36.30)
>DroPer_CAF1 35195 92 - 1
UGGCUUAGACUAUUGAGGGAUGCAGGAGUGGACGCAGCUGCAGCUGAGUUCGACUCCUGGAUUUCUGAUUGCUAGUGAGCCGCCAACUGGUG
.(((((..((((.(.((..((.(((((((((((.((((....)))).)))).))))))).))..)).)....)))))))))(((....))). ( -41.50)
>consensus
UGGCUCAGACUAUUGAGGGAUGCAGGAGUGGACGCAGCUGCAGCUGAGUUCGACUCCUGGAUUUCUGAUUGCUAGUGAGCCGCCAACUGAUG
((((.((((.........(((.(((((((((((.((((....)))).)))).))))))).)))))))...(((....))).))))....... (-30.08 = -29.53 +  -0.55)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:31:33 2006