Locus 738

Sequence ID	3R_DroMel_CAF1
Location	2,630,191 – 2,630,293
Length	102
Max. P	0.661508

overview

Window 8

Location	2,630,191 – 2,630,293
Length	102
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	83.59
Mean single sequence MFE	-38.82
Consensus MFE	-26.47
Energy contribution	-27.97
Covariance contribution	1.50
Combinations/Pair	1.00
Mean z-score	-2.37
Structure conservation index	0.68
SVM decision value	0.27
SVM RNA-class probability	0.661508
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2630191 102 + 27905053
CCUGCCGAGGGCCACACUUGAGGUGCAUUGUUGCACAUAAUUGUGGCUCUGGCCUUG-GCUGCA------CAUUGAUUUAUUUAUGCGGCCGCUCUCCUUUGU---CCCCUG--------
...(((.(((((((((.(((..(((((....))))).))).))))))))))))...(-((((((------...(((.....))))))))))............---......-------- ( -38.70)
>DroPse_CAF1 27220 116 + 1
CCUGCCGAGGGCCACACUUGAGGUGCAUUGUUGCACAUAAUUGUGACUCUGGCCUUGGGCUGCACUACCACAUUGAUUUA----UGCCCGGGAUCUCUUUUGUGUGCUCCUGCCACAGGG
((((..((((..(((((..((((((((....)))))..............(..(((((((....................----.)))))))..).)))..)))))..))).)..)))). ( -39.00)
>DroSim_CAF1 18526 102 + 1
CCUGCCGAGGGCCACACUUGAGGUGCAUUGUUGCACAUAAUUGUGGCUCUGGCCUUG-GCUGCA------CAUUGAUUUAUUUAUGCGGCCGGACUCCUUUGU---CCCCUG--------
...(((.(((((((((.(((..(((((....))))).))).))))))))))))...(-((((((------...(((.....))))))))))((((......))---))....-------- ( -44.30)
>DroEre_CAF1 19963 102 + 1
CCUGCCGAGGGCCACACUUGAGGUGCAUUGUUGCACAUAAUUGUGGCUCUGGCCUUG-GCUGCA------CAUUGAUUUAUUUAUGCGGCCGCUCUCCUUUGU---CCCCGG--------
((.(((.(((((((((.(((..(((((....))))).))).))))))))))))...(-((((((------...(((.....))))))))))............---....))-------- ( -38.90)
>DroYak_CAF1 12429 99 + 1
CCUGCCGAGGGCCACACUUGAGGUGCAUUGUUGCACAUAAUUGCGGCUCUGGCCUUG-GCUGCA------CUUUGAUUUAUUUAUGCGGCCGCUC---UUUGU---CCCCUG--------
...(((.((((((.((.(((..(((((....))))).))).)).)))))))))...(-((((((------...(((.....))))))))))....---.....---......-------- ( -34.80)
>DroPer_CAF1 27333 116 + 1
CCUGCCGAGGGCCACACUUGAGGUGCAUUGUUGCACAUAAUUGUGACUCUGGCCUUGGGCUGCACUACCACAUUGAUUUA----UGCCCGGGAUCUCUUUUGUGUGCUCCUGCCACACGG
...(((.((((.((((.(((..(((((....))))).))).)))).)))))))(((((((....................----.)))))))........(((((((....).)))))). ( -37.20)
>consensus
CCUGCCGAGGGCCACACUUGAGGUGCAUUGUUGCACAUAAUUGUGGCUCUGGCCUUG_GCUGCA______CAUUGAUUUAUUUAUGCGGCCGCUCUCCUUUGU___CCCCUG________
...(((.(((((((((.(((..(((((....))))).))).)))))))))))).....((((((....................)))))).............................. (-26.47 = -27.97 +   1.50)

alignment

secondary structure

dotplot

Window 9

Location	2,630,191 – 2,630,293
Length	102
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	83.59
Mean single sequence MFE	-36.08
Consensus MFE	-22.94
Energy contribution	-22.58
Covariance contribution	-0.36
Combinations/Pair	1.11
Mean z-score	-2.21
Structure conservation index	0.64
SVM decision value	-0.02
SVM RNA-class probability	0.523994
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2630191 102 - 27905053
--------CAGGGG---ACAAAGGAGAGCGGCCGCAUAAAUAAAUCAAUG------UGCAGC-CAAGGCCAGAGCCACAAUUAUGUGCAACAAUGCACCUCAAGUGUGGCCCUCGGCAGG
--------..(...---.)..........(((.(((((..........))------))).))-)...(((((.((((((.....(((((....)))))......)))))).)).)))... ( -35.10)
>DroPse_CAF1 27220 116 - 1
CCCUGUGGCAGGAGCACACAAAAGAGAUCCCGGGCA----UAAAUCAAUGUGGUAGUGCAGCCCAAGGCCAGAGUCACAAUUAUGUGCAACAAUGCACCUCAAGUGUGGCCCUCGGCAGG
.(((((.(.(((.((.((((...(((...((..(((----(......))))))..((((((((...)))....(.((((....))))).....))))))))...)))))))))).))))) ( -36.90)
>DroSim_CAF1 18526 102 - 1
--------CAGGGG---ACAAAGGAGUCCGGCCGCAUAAAUAAAUCAAUG------UGCAGC-CAAGGCCAGAGCCACAAUUAUGUGCAACAAUGCACCUCAAGUGUGGCCCUCGGCAGG
--------....((---((......))))(((.(((((..........))------))).))-)...(((((.((((((.....(((((....)))))......)))))).)).)))... ( -39.10)
>DroEre_CAF1 19963 102 - 1
--------CCGGGG---ACAAAGGAGAGCGGCCGCAUAAAUAAAUCAAUG------UGCAGC-CAAGGCCAGAGCCACAAUUAUGUGCAACAAUGCACCUCAAGUGUGGCCCUCGGCAGG
--------((((((---.....((.....(((.(((((..........))------))).))-)....))...((((((.....(((((....)))))......)))))))))))).... ( -37.10)
>DroYak_CAF1 12429 99 - 1
--------CAGGGG---ACAAA---GAGCGGCCGCAUAAAUAAAUCAAAG------UGCAGC-CAAGGCCAGAGCCGCAAUUAUGUGCAACAAUGCACCUCAAGUGUGGCCCUCGGCAGG
--------..(...---.)...---....(((.((((............)------))).))-)...(((((.((((((.....(((((....)))))......)))))).)).)))... ( -33.70)
>DroPer_CAF1 27333 116 - 1
CCGUGUGGCAGGAGCACACAAAAGAGAUCCCGGGCA----UAAAUCAAUGUGGUAGUGCAGCCCAAGGCCAGAGUCACAAUUAUGUGCAACAAUGCACCUCAAGUGUGGCCCUCGGCAGG
..(((((.......)))))..........((((((.----...(((.....)))......))))...(((((.((((((.....(((((....)))))......)))))).)).))).)) ( -34.60)
>consensus
________CAGGGG___ACAAAGGAGAGCGGCCGCAUAAAUAAAUCAAUG______UGCAGC_CAAGGCCAGAGCCACAAUUAUGUGCAACAAUGCACCUCAAGUGUGGCCCUCGGCAGG
.................................(((....................)))........(((((.((((((.....(((((....)))))......)))))).)).)))... (-22.94 = -22.58 +  -0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:50:43 2006