Locus 3654

Sequence ID	2L_DroMel_CAF1
Location	10,616,428 – 10,616,548
Length	120
Max. P	0.980570

overview

Window 5

Location	10,616,428 – 10,616,548
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	78.32
Mean single sequence MFE	-37.95
Consensus MFE	-18.18
Energy contribution	-18.30
Covariance contribution	0.12
Combinations/Pair	1.27
Mean z-score	-2.36
Structure conservation index	0.48
SVM decision value	0.75
SVM RNA-class probability	0.840272
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10616428 120 + 22407834
UGUCCAAAGUGCCGGCAACACGAGCUACUUAAGCGGAUCUCAUAUAUCCGCGGCUUUACGGCUCAAAUGCGUUAUAAUUCAAGCCCGAAUGCCUGACCGGCCACCUGUUCGUCGGAUAUU
(((((.((((((((......)).)).))))..((((((.......))))))(((.....((((..(((........)))..)))).....))).(((..((.....))..)))))))).. ( -34.40)
>DroPse_CAF1 96223 105 + 1
UGUACCA------GGUAAUCGGAGCCGC--AAACAG---UCGUAUGUCUGCGGCUUUAUGGCUCAAAUGCGUUAUAAUUCAAGCCCGAUUGCCU----GGCCACCUGCUCGACAGACGUU
....(((------(((((((((((((((--(.(((.---.....))).)))))))(((((((.(....).))))))).......))))))))))----))....(((.....)))..... ( -42.00)
>DroEre_CAF1 96662 116 + 1
UGUCCAGAGUGCCGGCAACACGAGCUACUUAAGCGGAUCUCAUAUAUCCGCGGCUUUACGGCUCAAAUGCGUUAUAAUUCAAGCCCGAAUGCCC----GGCCACCUGUUCGUCGGAUAUC
(((((........(....)((((((.......((((((.......))))))(((.....((((..(((........)))..))))((......)----))))....)))))).))))).. ( -33.30)
>DroYak_CAF1 99507 116 + 1
UGUCCAGAGUGCCGGCAACACGAGCUACUUGAGCGGAUCUCAUAUAUCCGCGGCUUUAUGCCUCAAAUGCGUUAUAAUUCAAGCCCGAAUACCU----GGCCACCUGUUCGUCGGAUAUC
......((...(((((((((.(.((...((((((((((.......))))))(((.....)))))))..))............(((.(.....).----)))..).)))).)))))...)) ( -31.80)
>DroAna_CAF1 97970 116 + 1
UGUCGAGCGUAUCCGCGACACGAGCUACUUAAGCUCGUCUCAUAUAUCCGCGGCUUUAUGGCUUAAAUGCGUUAUAAUUCAAGCCCGGAUAG----UCGGCCACCUGUUCGCUGGACAUC
((((.((((.((((((((.(((((((.....))))))).))...((((((.(((((((((((........))))))....))))))))))))----.)))......)).)))).)))).. ( -43.80)
>DroPer_CAF1 98198 105 + 1
UGUACCA------GGUAAUCGGAGCCGC--AAACAG---UCGUAUGUCUGCGGCUUUAUGGCUCAAAUGCGUUAUAAUUCAAGCCCGAUUGCCU----GGCCACCUGCUCGACAGACAUU
(((.(((------(((((((((((((((--(.(((.---.....))).)))))))(((((((.(....).))))))).......))))))))))----))....(((.....)))))).. ( -42.40)
>consensus
UGUCCAAAGUGCCGGCAACACGAGCUACUUAAGCGGAUCUCAUAUAUCCGCGGCUUUAUGGCUCAAAUGCGUUAUAAUUCAAGCCCGAAUGCCU____GGCCACCUGUUCGUCGGACAUC
.............(((.......))).................(((((((.(((((((((((.(....).))))))....)))))((((((((.....))).....))))).))))))). (-18.18 = -18.30 +   0.12)

alignment

secondary structure

dotplot

Window 6

Location	10,616,428 – 10,616,548
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.32
Mean single sequence MFE	-43.07
Consensus MFE	-21.74
Energy contribution	-20.72
Covariance contribution	-1.02
Combinations/Pair	1.31
Mean z-score	-3.01
Structure conservation index	0.50
SVM decision value	1.87
SVM RNA-class probability	0.980570
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10616428 120 - 22407834
AAUAUCCGACGAACAGGUGGCCGGUCAGGCAUUCGGGCUUGAAUUAUAACGCAUUUGAGCCGUAAAGCCGCGGAUAUAUGAGAUCCGCUUAAGUAGCUCGUGUUGCCGGCACUUUGGACA
....(((((......((((.(((((..(((.((..((((..(((........)))..))))..)).)))((((((.......))))))................)))))))))))))).. ( -39.30)
>DroPse_CAF1 96223 105 - 1
AACGUCUGUCGAGCAGGUGGCC----AGGCAAUCGGGCUUGAAUUAUAACGCAUUUGAGCCAUAAAGCCGCAGACAUACGA---CUGUUU--GCGGCUCCGAUUACC------UGGUACA
..(..(((.....)))..)(((----(((.(((((((((..(((........)))..))))....(((((((((((.....---.)))))--)))))).))))).))------))))... ( -49.20)
>DroEre_CAF1 96662 116 - 1
GAUAUCCGACGAACAGGUGGCC----GGGCAUUCGGGCUUGAAUUAUAACGCAUUUGAGCCGUAAAGCCGCGGAUAUAUGAGAUCCGCUUAAGUAGCUCGUGUUGCCGGCACUCUGGACA
....((((.......((..(((----((((.....((((..(((........)))..))))........((((((.......)))))).......))))).))..)).......)))).. ( -39.54)
>DroYak_CAF1 99507 116 - 1
GAUAUCCGACGAACAGGUGGCC----AGGUAUUCGGGCUUGAAUUAUAACGCAUUUGAGGCAUAAAGCCGCGGAUAUAUGAGAUCCGCUCAAGUAGCUCGUGUUGCCGGCACUCUGGACA
..........(..((((((.((----.((((..((((((.............(((((((((.....)))((((((.......))))))))))))))))))...))))))))).)))..). ( -39.01)
>DroAna_CAF1 97970 116 - 1
GAUGUCCAGCGAACAGGUGGCCGA----CUAUCCGGGCUUGAAUUAUAACGCAUUUAAGCCAUAAAGCCGCGGAUAUAUGAGACGAGCUUAAGUAGCUCGUGUCGCGGAUACGCUCGACA
..((((.((((.....(((((((.----.....))(((((((((........))))))))).....)))))........((.(((((((.....))))))).)).......)))).)))) ( -43.60)
>DroPer_CAF1 98198 105 - 1
AAUGUCUGUCGAGCAGGUGGCC----AGGCAAUCGGGCUUGAAUUAUAACGCAUUUGAGCCAUAAAGCCGCAGACAUACGA---CUGUUU--GCGGCUCCGAUUACC------UGGUACA
..(..(((.....)))..)(((----(((.(((((((((..(((........)))..))))....(((((((((((.....---.)))))--)))))).))))).))------))))... ( -47.80)
>consensus
AAUAUCCGACGAACAGGUGGCC____AGGCAUUCGGGCUUGAAUUAUAACGCAUUUGAGCCAUAAAGCCGCGGAUAUAUGAGAUCCGCUUAAGUAGCUCGUGUUGCCGGCACUCUGGACA
.(((((((.((....((..(((.....)))..)).(((((((((........))))))))).......))))))))).........(((.....)))....................... (-21.74 = -20.72 +  -1.02)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:57:53 2006