Locus 3212

Sequence ID	2R_DroMel_CAF1
Location	10,974,047 – 10,974,152
Length	105
Max. P	0.699051

overview

Window 2

Location	10,974,047 – 10,974,152
Length	105
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	78.15
Mean single sequence MFE	-33.45
Consensus MFE	-25.20
Energy contribution	-24.95
Covariance contribution	-0.25
Combinations/Pair	1.13
Mean z-score	-0.94
Structure conservation index	0.75
SVM decision value	0.08
SVM RNA-class probability	0.573032
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10974047 105 + 20766785
GGGCGUACAACUGCAGCAACAGGAGCUGCAGCAGCAGCGCGGCGGACUGCCGGUGCCCAGCCAAGAUAUAUCUAGUAGCUCAGGUCCGACAA---GUCGCCA------AGUUGC------
..........(((((((.......)))))))..(((((..(((((..((.(((.(((.(((..(((....)))....)))..)))))).)).---.))))).------.)))))------ ( -38.00)
>DroVir_CAF1 111960 108 + 1
GGGCGUCCAAUUGCAGCAACAGGAGCUGCAGCAGCAGCGCGGCGGUCUGCCGGUGCCCACACAAGAUAUCUCUAGUAGCUCAGGUCCGCAAAAAAAAAACCA------AAAAA------A
(((((......))).((.((..(((((((.((....))(((.(((....))).)))..................)))))))..))..))..........)).------.....------. ( -31.30)
>DroGri_CAF1 108491 103 + 1
GGGCGUGCAGCUGCAACAACAGGAGCUGCAGCAACAGCGCGGCGGCCUGCCGGUGCCCCCACAAGAUAUCUCUAGUAGUUCAGGUCCGCAAACAUGAAAU-----------GA------A
((((.((.((((((.....((((.(((((.((....)))))))..))))...(((....)))............)))))))).)))).............-----------..------. ( -34.00)
>DroWil_CAF1 127607 116 + 1
GGGCGUCCAAUUGCAACAACAGGAGCUGCAGCAGCAACGUGGCGGUCUACCAGUGCCCACACAAGAUAUAUCUAGUAGCUCAGGUCCGCCAU---UU-ACCAGCAUUUAAUUGCAAUCAA
.((((.((..(((......)))(((((((.........(((..(((........)))..))).(((....))).))))))).))..))))..---..-....(((......)))...... ( -29.80)
>DroMoj_CAF1 127707 103 + 1
GGGCGUGCAGCUGCAACAACAGGAGCUGCAGCAGCAGCGCGGCGGCCUGCCGGUGCCCACACAAGAUAUCUCUAGUAGUUCAGGUCCGCAAAAAAUUAAC-----------AA------A
((((.((.((((((.......((.(((((....)))))(((.(((....))).))))).....(((....))).)))))))).)))).............-----------..------. ( -36.60)
>DroAna_CAF1 88851 98 + 1
GGGCGUUCAGCUGCAACAACAGGAGCUGCAACAGCAACGCGGAGGGCUGCCGGUGCCCACCCAAGAUAUAUCUAGUAGCUCAGGUCCGACAA---GUCGCC-------------------
.(((((((((((.(.......).))))).)))......((((((((((((.(((....)))..(((....))).)))))))...)))).)..---...)))------------------- ( -31.00)
>consensus
GGGCGUCCAACUGCAACAACAGGAGCUGCAGCAGCAGCGCGGCGGCCUGCCGGUGCCCACACAAGAUAUAUCUAGUAGCUCAGGUCCGCAAA___GUAACC__________AA______A
((((......(((......)))(((((((.........(((.(((....))).))).......(((....))).)))))))..))))................................. (-25.20 = -24.95 +  -0.25)

alignment

secondary structure

dotplot

Window 3

Location	10,974,047 – 10,974,152
Length	105
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.15
Mean single sequence MFE	-39.00
Consensus MFE	-25.01
Energy contribution	-24.93
Covariance contribution	-0.08
Combinations/Pair	1.25
Mean z-score	-1.46
Structure conservation index	0.64
SVM decision value	0.35
SVM RNA-class probability	0.699051
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10974047 105 - 20766785
------GCAACU------UGGCGAC---UUGUCGGACCUGAGCUACUAGAUAUAUCUUGGCUGGGCACCGGCAGUCCGCCGCGCUGCUGCUGCAGCUCCUGUUGCUGCAGUUGUACGCCC
------......------.((((((---(.(((((..((.(((((..(((....)))))))).))..)))))))).))))(((.(((.((((((((.......)))))))).)))))).. ( -47.90)
>DroVir_CAF1 111960 108 - 1
U------UUUUU------UGGUUUUUUUUUUGCGGACCUGAGCUACUAGAGAUAUCUUGUGUGGGCACCGGCAGACCGCCGCGCUGCUGCUGCAGCUCCUGUUGCUGCAAUUGGACGCCC
.------.....------.(((.(((...((((((....(((((((.(((....))).))....(((.((((((.(......))))))).))))))))......))))))..))).))). ( -31.60)
>DroGri_CAF1 108491 103 - 1
U------UC-----------AUUUCAUGUUUGCGGACCUGAACUACUAGAGAUAUCUUGUGGGGGCACCGGCAGGCCGCCGCGCUGUUGCUGCAGCUCCUGUUGUUGCAGCUGCACGCCC
.------..-----------...........((((.((((..((((.(((....))).))))((...))..)))))))).(((.(((.((((((((.......)))))))).)))))).. ( -40.10)
>DroWil_CAF1 127607 116 - 1
UUGAUUGCAAUUAAAUGCUGGU-AA---AUGGCGGACCUGAGCUACUAGAUAUAUCUUGUGUGGGCACUGGUAGACCGCCACGUUGCUGCUGCAGCUCCUGUUGUUGCAAUUGGACGCCC
(..((((((((.....((.((.-..---.(((((((((.(.(((((.(((....)))...)).))).).)))...)))))).(((((....))))).)).)).))))))))..)...... ( -37.00)
>DroMoj_CAF1 127707 103 - 1
U------UU-----------GUUAAUUUUUUGCGGACCUGAACUACUAGAGAUAUCUUGUGUGGGCACCGGCAGGCCGCCGCGCUGCUGCUGCAGCUCCUGUUGUUGCAGCUGCACGCCC
.------..-----------...........((((.((((..((((.(((....)))...)))).......)))))))).(((.(((.((((((((.......)))))))).)))))).. ( -40.30)
>DroAna_CAF1 88851 98 - 1
-------------------GGCGAC---UUGUCGGACCUGAGCUACUAGAUAUAUCUUGGGUGGGCACCGGCAGCCCUCCGCGUUGCUGUUGCAGCUCCUGUUGUUGCAGCUGAACGCCC
-------------------((((..---..(.((((((..((.((.......)).))..)))((((.......)))).))))...(((((.(((((....))))).)))))....)))). ( -37.10)
>consensus
U______UA__________GGUUAC___UUGGCGGACCUGAGCUACUAGAGAUAUCUUGUGUGGGCACCGGCAGACCGCCGCGCUGCUGCUGCAGCUCCUGUUGUUGCAGCUGCACGCCC
...........................................(((.(((....))).))).((((..((((.....))))....(((((.(((((....))))).))))).....)))) (-25.01 = -24.93 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:50:10 2006