Locus 897

Sequence ID	3L_DroMel_CAF1
Location	2,712,909 – 2,713,051
Length	142
Max. P	0.802868

overview

Window 8

Location	2,712,909 – 2,713,018
Length	109
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	81.60
Mean single sequence MFE	-36.47
Consensus MFE	-32.22
Energy contribution	-32.58
Covariance contribution	0.36
Combinations/Pair	1.03
Mean z-score	-1.60
Structure conservation index	0.88
SVM decision value	0.62
SVM RNA-class probability	0.802868
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2712909 109 - 23771897
CUAAUUCUAA----------UUUGCAGAGUCGACGCAAAGCGUGGACGGCGGACCUGCAUCGUGGCGUUUAACGCUCGAUCAGGAUCUAAUUGACACGCUCAAGGGCAACUUUCCCAGC
..........----------(((((...(((.((((...)))).))).)))))((((.((((.((((.....)))))))))))).............(((.((((....))))...))) ( -34.40)
>DroVir_CAF1 88057 107 - 1
GUUU-UCU-----------GAUUGCAGAGUCUACGCACAGCGUGGACGGCGGCCCUGCAUCGUGGCGUUUAACGCUCGAUCAGGAUCUUAUUGAUACGCUAAAGGGAAACUUUCCCAGU
....-(((-----------(....))))((((((((...))))))))((((..((((.((((.((((.....))))))))))))(((.....))).))))...((((.....))))... ( -41.70)
>DroGri_CAF1 79083 105 - 1
AUUU--------------UUCUUACAGAGUCUACGCACAGCGUGGACGGCGGCCCUGCAUCGUGGCGUUUAACGCUCGAUCAGGAUCUAAUUGACACGCUCAAGGGUAACUUUCCCAGU
....--------------..........((((((((...))))))))((((..((((.((((.((((.....)))))))))))).((.....))..))))...(((.......)))... ( -35.40)
>DroWil_CAF1 89674 115 - 1
---AUUGUUUGUU-UCUAUUUUUUCAGAGUCUACGCACAGCGUGGAUGGCGGCCCAGCAUCGUGGCGUGUACCGCUCGAUCAGGAUCUAUUAGACACGCUAAAGGGUAAUUUUCCCAGU
---.......((.-((((....(((.((((((((((...))))))))(((((..((((......)).))..)))))...)).))).....)))).))......(((.......)))... ( -29.80)
>DroMoj_CAF1 79619 117 - 1
CUAU-CUU-GUUCGUGUUUUUUUGCAGAGUCUACGCACAGCGUGGACGGCGGCCCUGCAUCGUGGCGUUUAACGCUCGAUCAGGAUCUAAUUGAUACGCUCAAAGGCAACUUUCCCAGU
....-..(-(..((((((..((.((...((((((((...)))))))).))(..((((.((((.((((.....))))))))))))..).))..))))))..))(((....)))....... ( -39.70)
>DroAna_CAF1 73019 112 - 1
CUUAUCCUUU-------UUCAUUGCAGAGUCUACGCACAGCGUGGACGGCGGACCUGCAUCGUGGCGUCUAACGCUCGAUCAGGAUCUUUUUGACACGCUCAAGGGCAACUUCCCCAGC
..........-------......((...((((((((...))))))))((.(((((((.((((.((((.....)))))))))))).............(((....)))....))))).)) ( -37.80)
>consensus
CUUA_UCU__________UUUUUGCAGAGUCUACGCACAGCGUGGACGGCGGCCCUGCAUCGUGGCGUUUAACGCUCGAUCAGGAUCUAAUUGACACGCUCAAGGGCAACUUUCCCAGU
............................((((((((...))))))))((((..((((.((((.((((.....)))))))))))).((.....))..))))...(((.......)))... (-32.22 = -32.58 +   0.36)

alignment

secondary structure

dotplot

Window 9

Location	2,712,949 – 2,713,051
Length	102
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	70.22
Mean single sequence MFE	-21.57
Consensus MFE	-17.60
Energy contribution	-18.10
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-0.31
Structure conservation index	0.82
SVM decision value	0.10
SVM RNA-class probability	0.581496
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2712949 102 - 23771897
AUUUAACUUUUC-----GAA--CCUUUAAAAUUCAAAUUUCUAAU-UCUAA---------UUUGCAGAGUCGACGCAAAGCGUGGACGGCGGACCUGCAUCGUGGCGUUUAACGCUCGA
............-----...--.......................-.....---------..(((((.(((.((((...)))).)))(.....))))))(((.((((.....))))))) ( -21.00)
>DroSec_CAF1 73638 89 - 1
AUUAAACUCUUC-----UAU--CCUUUAAAAU--------------UCUAA---------UUUGCAGAGUCGACGCAAAGCGUGGACGGCGGACCUGCAUCGUGGCUUUUAACGCUCGA
............-----...--...((((((.--------------.(((.---------..(((((.(((.((((...)))).)))(.....))))))...))).))))))....... ( -17.80)
>DroSim_CAF1 71125 89 - 1
AUUUAACUUUUC-----UAU--CCUUUAAAAU--------------UCUAA---------UUUGCAGAGUCGACGCAAAGCGUGGACGGCGGACCUGCAUCGUGGCGUUUAACGCUCGA
............-----...--..........--------------.....---------..(((((.(((.((((...)))).)))(.....))))))(((.((((.....))))))) ( -21.00)
>DroEre_CAF1 80830 94 - 1
------------------------UUAAAAAUUCAAAUUUCUAAU-UCCCAUUCUCCAUUUUUGCAGAGUCGACGCAAAGCGUGGACGGCGGACCUGCAUCGUGGCGUUUAACGCUCGA
------------------------....................(-((((..(((.((....)).)))(((.((((...)))).))))).)))......(((.((((.....))))))) ( -21.10)
>DroYak_CAF1 74430 118 - 1
AUGCAAUAUUUCAGCUUGAAUUUUUUUUAAAUUCCAAUUUCUAAU-UUUAAUUCUUCAUAUUUACAGAGUCGACGCAAAGCGUGGACGGCGGACCUGCAUCGUGGCGUUUAACGCUCGA
.((((....(((.(((.((((((.....))))))...........-......................(((.((((...)))).)))))))))..))))(((.((((.....))))))) ( -24.30)
>DroPer_CAF1 97725 84 - 1
AUCG-------------------------AAAUCGAUUUUCUUUGAUCU-A---------UUUCCAGAGUCUACGCACAGCGUGGACGGAGGACCUGCAUCGUGGCGUUUAACGCUCGA
...(-------------------------((((.((((......)))).-)---------))))....((((((((...))))))))((....))....(((.((((.....))))))) ( -24.20)
>consensus
AUUUAACUUUUC______A___CCUUUAAAAUUC_AAUUUCUAAU_UCUAA_________UUUGCAGAGUCGACGCAAAGCGUGGACGGCGGACCUGCAUCGUGGCGUUUAACGCUCGA
..............................................................(((((.(((.((((...)))).)))(.....))))))(((.((((.....))))))) (-17.60 = -18.10 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:53:52 2006