Locus 1175

Sequence ID	X_DroMel_CAF1
Location	3,498,147 – 3,498,247
Length	100
Max. P	0.995559

overview

Window 2

Location	3,498,147 – 3,498,247
Length	100
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	87.18
Mean single sequence MFE	-28.99
Consensus MFE	-21.29
Energy contribution	-21.57
Covariance contribution	0.28
Combinations/Pair	1.25
Mean z-score	-3.84
Structure conservation index	0.73
SVM decision value	2.59
SVM RNA-class probability	0.995559
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3498147 100 + 22224390
AAUUUAAAUUAAUUGCCAUAGCCGAGCGUACUGUACUUACUG----UACGCACUUUGCUUGGCA---ACAACAGCACGAAUCGAAAUAUUCCUGCAUAUCCUGCAUA
............((((((.(((.((((((((.((....)).)----)))))..)).))))))))---).....(((.((((......)))).)))............ ( -25.10)
>DroSec_CAF1 6765 99 + 1
AAUUUAAAUUAAUUGCCAUAGCCGAGGGGACUGUACUUA-UG----UACGCUCUUCCCUUGGCA---GCAACUGCAGGACCCGAAAUAUUCCUGCAUAUCCUGCAUA
....................((((((((((.(((((...-.)----))))...)))))))))).---(((..(((((((..........))))))).....)))... ( -33.60)
>DroSim_CAF1 7173 96 + 1
AAUUUAAAUUAAUUGCCAUAGCCGAGGGGACUGUACUUA-UG----U---CUCUUCCCUUGGCA---GCAACUGCAGGACCCGAAAUAUUCCUGCAUAUCCUGCAUA
....................((((((((((..(.((...-.)----)---)..)))))))))).---(((..(((((((..........))))))).....)))... ( -30.50)
>DroEre_CAF1 7188 106 + 1
AAUUUAAAUUAAUUGCCAUAGCCAAGGGCACUGUACUUA-UGUAUGUACGUUAUACCCUGGGCAGGACCAACUGCAGAACCCAAAAUAUUCCUGCAUAUCCUGCAUA
.....................(((.(((...(((((...-.....))))).....))))))((((((.....(((((..............)))))..))))))... ( -25.54)
>DroYak_CAF1 4015 99 + 1
AAUUUAAAUUAAUUGCCAUAGCCAAGGGAACUGUACUUA-UG----UACGUUCUUCCCCUGGCA---ACAACUGCAGGACCCAAAAUAUUCCUGCAUAUCCUGCAUA
.............(((....((((.(((((.(((((...-.)----))))...))))).)))).---.....(((((((..........)))))))......))).. ( -30.20)
>consensus
AAUUUAAAUUAAUUGCCAUAGCCGAGGGGACUGUACUUA_UG____UACGCUCUUCCCUUGGCA___ACAACUGCAGGACCCGAAAUAUUCCUGCAUAUCCUGCAUA
.............(((....((((((((((..(.................)..))))))))))..........((((((..........)))))).......))).. (-21.29 = -21.57 +   0.28)

alignment

secondary structure

dotplot

Window 3

Location	3,498,147 – 3,498,247
Length	100
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	87.18
Mean single sequence MFE	-33.52
Consensus MFE	-22.07
Energy contribution	-22.03
Covariance contribution	-0.04
Combinations/Pair	1.22
Mean z-score	-3.43
Structure conservation index	0.66
SVM decision value	1.33
SVM RNA-class probability	0.943380
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3498147 100 - 22224390
UAUGCAGGAUAUGCAGGAAUAUUUCGAUUCGUGCUGUUGU---UGCCAAGCAAAGUGCGUA----CAGUAAGUACAGUACGCUCGGCUAUGGCAAUUAAUUUAAAUU
.......((((.(((.((((......)))).)))))))((---((((((((...(.(((((----(.((....)).)))))).).))).)))))))........... ( -31.60)
>DroSec_CAF1 6765 99 - 1
UAUGCAGGAUAUGCAGGAAUAUUUCGGGUCCUGCAGUUGC---UGCCAAGGGAAGAGCGUA----CA-UAAGUACAGUCCCCUCGGCUAUGGCAAUUAAUUUAAAUU
...(((((((.....(((....)))..)))))))((((((---((((.((((..((..(((----(.-...))))..)))))).)))...))))))).......... ( -32.80)
>DroSim_CAF1 7173 96 - 1
UAUGCAGGAUAUGCAGGAAUAUUUCGGGUCCUGCAGUUGC---UGCCAAGGGAAGAG---A----CA-UAAGUACAGUCCCCUCGGCUAUGGCAAUUAAUUUAAAUU
...(((((((.....(((....)))..)))))))((((((---((((.((((....(---(----(.-........))))))).)))...))))))).......... ( -29.40)
>DroEre_CAF1 7188 106 - 1
UAUGCAGGAUAUGCAGGAAUAUUUUGGGUUCUGCAGUUGGUCCUGCCCAGGGUAUAACGUACAUACA-UAAGUACAGUGCCCUUGGCUAUGGCAAUUAAUUUAAAUU
..((((((((.(((((((..........)))))))....)))))(((.(((((((...((((.....-...)))).))))))).)))....)))............. ( -35.30)
>DroYak_CAF1 4015 99 - 1
UAUGCAGGAUAUGCAGGAAUAUUUUGGGUCCUGCAGUUGU---UGCCAGGGGAAGAACGUA----CA-UAAGUACAGUUCCCUUGGCUAUGGCAAUUAAUUUAAAUU
..((((((((...(((((...))))).))))))))((..(---.((((((((((....(((----(.-...))))..)))))))))).)..)).............. ( -38.50)
>consensus
UAUGCAGGAUAUGCAGGAAUAUUUCGGGUCCUGCAGUUGC___UGCCAAGGGAAGAGCGUA____CA_UAAGUACAGUCCCCUCGGCUAUGGCAAUUAAUUUAAAUU
...(((((((.....(((....)))..)))))))((((((....(((.((((...........................)))).)))....)))))).......... (-22.07 = -22.03 +  -0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:03:03 2006