Locus 4909

Sequence ID	2R_DroMel_CAF1
Location	16,040,401 – 16,040,495
Length	94
Max. P	0.843590

overview

Window 2

Location	16,040,401 – 16,040,495
Length	94
Sequences	6
Columns	99
Reading direction	forward
Mean pairwise identity	82.67
Mean single sequence MFE	-27.75
Consensus MFE	-22.77
Energy contribution	-23.25
Covariance contribution	0.48
Combinations/Pair	1.15
Mean z-score	-1.94
Structure conservation index	0.82
SVM decision value	0.70
SVM RNA-class probability	0.826685
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16040401 94 + 20766785
AAGCCUGUGU-----UUAGGUGAGCGGCAAGUACUUGCAUAACAUACUUGCAGCCCAAAAGUAAAACAGGACUGGCAACAAUGCCGCAGGAUUGCUGUG
..(((((...-----.)))))..(((((((...(((((......(((((.........)))))..........((((....))))))))).))))))). ( -28.40)
>DroSec_CAF1 95292 94 + 1
AAGCCUGUGU-----UUAGGUGAGCGGCAAGCACUUGCAUAACAUACUUGCAGCCCAAAAGUAAAACAGGACUGGCAACAAUGCCGCAGGAUUGCUGUG
..(((((...-----.)))))..(((((((...(((((......(((((.........)))))..........((((....))))))))).))))))). ( -28.40)
>DroSim_CAF1 98668 94 + 1
AAGCCUGUGU-----UUAGGUGAGCGGCAAGCACUUGCAUAACAUACUUGCAGCCCAAAAGUAAAACAGGACUGGCAACAAUGCCGCAGGAUUGCUGUG
..(((((...-----.)))))..(((((((...(((((......(((((.........)))))..........((((....))))))))).))))))). ( -28.40)
>DroEre_CAF1 101985 88 + 1
AAGCCUGUGC-----UUAGGUGAGCGGCAAGUACUUGCA-----UACUUGCAACC-GAAAGUAAGAGAGGACUGGCAACAAUGCCGCAGGAUUGCUGUG
..(((((...-----.)))))..(((((((...(((((.-----..(((((....-....)))))........((((....))))))))).))))))). ( -30.30)
>DroYak_CAF1 105505 93 + 1
AAGCCUGUGAGUCUGUUAGGUGAGCGGCAAGUACUUGCA-----UACUUGCAGCC-GAAAGUAAAACAGGACUGGCAACAAUGCCGCAGGAUUGCUGUG
...(((((.((((((((......((.(((((((......-----))))))).))(-....)...)))).))))((((....)))))))))......... ( -30.30)
>DroAna_CAF1 105925 81 + 1
AAGCUGGUU--------------GUGGCAGAAACUUAUGUA-UGUACUUUCAGCU-AAAAGUAAAACUGGACUGGCAACAAUGCCACAAGAUUGCUG--
.(((...((--------------((((((....((...((.-..((((((.....-.))))))..)).))..((....)).))))))))....))).-- ( -20.70)
>consensus
AAGCCUGUGU_____UUAGGUGAGCGGCAAGUACUUGCAUA_CAUACUUGCAGCC_AAAAGUAAAACAGGACUGGCAACAAUGCCGCAGGAUUGCUGUG
..(((((.........)))))..(((((((...(((((......(((((.........)))))..........((((....))))))))).))))))). (-22.77 = -23.25 +   0.48)

alignment

secondary structure

dotplot

Window 3

Location	16,040,401 – 16,040,495
Length	94
Sequences	6
Columns	99
Reading direction	reverse
Mean pairwise identity	82.67
Mean single sequence MFE	-27.99
Consensus MFE	-18.90
Energy contribution	-19.93
Covariance contribution	1.03
Combinations/Pair	1.20
Mean z-score	-2.81
Structure conservation index	0.68
SVM decision value	0.76
SVM RNA-class probability	0.843590
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16040401 94 - 20766785
CACAGCAAUCCUGCGGCAUUGUUGCCAGUCCUGUUUUACUUUUGGGCUGCAAGUAUGUUAUGCAAGUACUUGCCGCUCACCUAA-----ACACAGGCUU
....(((....)))((((....))))((.(((((((((....(((((.((((((((.........)))))))).)))))..)))-----).))))))). ( -32.20)
>DroSec_CAF1 95292 94 - 1
CACAGCAAUCCUGCGGCAUUGUUGCCAGUCCUGUUUUACUUUUGGGCUGCAAGUAUGUUAUGCAAGUGCUUGCCGCUCACCUAA-----ACACAGGCUU
....(((....)))((((....))))((.(((((((((....(((((.((((((((.........)))))))).)))))..)))-----).))))))). ( -32.20)
>DroSim_CAF1 98668 94 - 1
CACAGCAAUCCUGCGGCAUUGUUGCCAGUCCUGUUUUACUUUUGGGCUGCAAGUAUGUUAUGCAAGUGCUUGCCGCUCACCUAA-----ACACAGGCUU
....(((....)))((((....))))((.(((((((((....(((((.((((((((.........)))))))).)))))..)))-----).))))))). ( -32.20)
>DroEre_CAF1 101985 88 - 1
CACAGCAAUCCUGCGGCAUUGUUGCCAGUCCUCUCUUACUUUC-GGUUGCAAGUA-----UGCAAGUACUUGCCGCUCACCUAA-----GCACAGGCUU
....(((....)))((((....))))((.(((..((((.....-(((.(((((((-----(....)))))))).)))....)))-----)...))))). ( -24.70)
>DroYak_CAF1 105505 93 - 1
CACAGCAAUCCUGCGGCAUUGUUGCCAGUCCUGUUUUACUUUC-GGCUGCAAGUA-----UGCAAGUACUUGCCGCUCACCUAACAGACUCACAGGCUU
.........((((.((((....))))((((.((((........-(((.(((((((-----(....)))))))).))).....))))))))..))))... ( -29.42)
>DroAna_CAF1 105925 81 - 1
--CAGCAAUCUUGUGGCAUUGUUGCCAGUCCAGUUUUACUUUU-AGCUGAAAGUACA-UACAUAAGUUUCUGCCAC--------------AACCAGCUU
--.(((....(((((((((((....))))...((..(((((((-....)))))))..-.))..........)))))--------------))...))). ( -17.20)
>consensus
CACAGCAAUCCUGCGGCAUUGUUGCCAGUCCUGUUUUACUUUU_GGCUGCAAGUAUG_UAUGCAAGUACUUGCCGCUCACCUAA_____ACACAGGCUU
....(((....)))((((....))))((.(((((..........(((.((((((((.........)))))))).)))..............))))))). (-18.90 = -19.93 +   1.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:31:55 2006