Locus 4275

Sequence ID	3R_DroMel_CAF1
Location	11,401,915 – 11,402,035
Length	120
Max. P	0.999690

overview

Window 4

Location	11,401,915 – 11,402,035
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.17
Mean single sequence MFE	-29.44
Consensus MFE	-23.90
Energy contribution	-23.62
Covariance contribution	-0.28
Combinations/Pair	1.06
Mean z-score	-1.61
Structure conservation index	0.81
SVM decision value	0.49
SVM RNA-class probability	0.755577
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11401915 120 + 27905053
UUUAUGGUUCAUUUGGUGAGAGAUUUGUUUGUUGUUAUUUGGCUGCGCUUAUUGCACUUAAUGCAGCGUAUCAAAAACGCAGGGGAAAGGAGAAAAUUGGAUUCUUGUAAAAUGAACCUG
.....(((((((((.(..((((.(((.(((((.(((.(((((.(((((((((((....))))).))))))))))))))))))).)))..((.....))...))))..).))))))))).. ( -31.50)
>DroSec_CAF1 149579 120 + 1
UUUAUGGUUCAUUUGGUGAGAGAUUUGUUUGUUGUUAUUUGGCUGCGCUUAUUGCACUUAAUGCAGCGUAUCAAAAACGCAAGGGAAAGGAGAAAAUUGGAUUCUUGUAAAAUGAACCUG
.....(((((((((.(..((((.(((.(((((.(((.(((((.(((((((((((....))))).))))))))))))))))))).)))..((.....))...))))..).))))))))).. ( -31.90)
>DroSim_CAF1 140645 120 + 1
UUUAUGGUUCAUUUGGUGAGAGAUUUGUUUGUUGUUAUUUGGCUGCGCUUAUUGCACUUAAUGCAGCGUAUCAAAAACGCAAGGGAAAGGAGAAAAUUGGAUUCUUGUAAAAUGAACCUG
.....(((((((((.(..((((.(((.(((((.(((.(((((.(((((((((((....))))).))))))))))))))))))).)))..((.....))...))))..).))))))))).. ( -31.90)
>DroEre_CAF1 137656 120 + 1
UUUAUGGUUCAUUUGGUGAGAGAUUUGUUUGUUGUUAUUCGGCUGCACUUAUUGCACUUAAUGCGGCGUAUCAAAAAUGCAAGGGAAAGGAGAAAAUUGGAUUCUUGUAAAAUGAACCUG
.....(((((((((.(..((((.((..(((.((.((.(((.((((((.(((.......)))))))))((((.....))))..))).)).)).)))...)).))))..).))))))))).. ( -30.20)
>DroYak_CAF1 140644 110 + 1
UUUAUGGUUCAUUUGGUGAAAGAUUUGUUUGUUGUUA----------CUUAUUGCACUUAAUGCGGCGUAUCAAAAAUGCGAGGGAAAGGAGAAAAUUGGAUUCUUGUAAAAUGAACCUG
.....(((((((((.....((((.((.(((.((.((.----------(((.(((((.....)))))(((((.....))))).))).)).)).)))....)).))))...))))))))).. ( -21.70)
>consensus
UUUAUGGUUCAUUUGGUGAGAGAUUUGUUUGUUGUUAUUUGGCUGCGCUUAUUGCACUUAAUGCAGCGUAUCAAAAACGCAAGGGAAAGGAGAAAAUUGGAUUCUUGUAAAAUGAACCUG
.....(((((((((.(..((((.((..(((.((.((................((((.....))))((((.......))))......)).)).)))...)).))))..).))))))))).. (-23.90 = -23.62 +  -0.28)

alignment

secondary structure

dotplot

Window 5

Location	11,401,915 – 11,402,035
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.17
Mean single sequence MFE	-22.02
Consensus MFE	-18.98
Energy contribution	-19.62
Covariance contribution	0.64
Combinations/Pair	1.07
Mean z-score	-3.20
Structure conservation index	0.86
SVM decision value	3.90
SVM RNA-class probability	0.999690
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11401915 120 - 27905053
CAGGUUCAUUUUACAAGAAUCCAAUUUUCUCCUUUCCCCUGCGUUUUUGAUACGCUGCAUUAAGUGCAAUAAGCGCAGCCAAAUAACAACAAACAAAUCUCUCACCAAAUGAACCAUAAA
..(((((((((....((((.......))))........(((((((((((...((((......))))))).))))))))............................)))))))))..... ( -25.10)
>DroSec_CAF1 149579 120 - 1
CAGGUUCAUUUUACAAGAAUCCAAUUUUCUCCUUUCCCUUGCGUUUUUGAUACGCUGCAUUAAGUGCAAUAAGCGCAGCCAAAUAACAACAAACAAAUCUCUCACCAAAUGAACCAUAAA
..(((((((((....((((.......))))........(((((((((((...((((......))))))).))))))))............................)))))))))..... ( -23.00)
>DroSim_CAF1 140645 120 - 1
CAGGUUCAUUUUACAAGAAUCCAAUUUUCUCCUUUCCCUUGCGUUUUUGAUACGCUGCAUUAAGUGCAAUAAGCGCAGCCAAAUAACAACAAACAAAUCUCUCACCAAAUGAACCAUAAA
..(((((((((....((((.......))))........(((((((((((...((((......))))))).))))))))............................)))))))))..... ( -23.00)
>DroEre_CAF1 137656 120 - 1
CAGGUUCAUUUUACAAGAAUCCAAUUUUCUCCUUUCCCUUGCAUUUUUGAUACGCCGCAUUAAGUGCAAUAAGUGCAGCCGAAUAACAACAAACAAAUCUCUCACCAAAUGAACCAUAAA
..(((((((((....((((.......))))...(((..(((((((((((.(((..........)))))).))))))))..))).......................)))))))))..... ( -22.00)
>DroYak_CAF1 140644 110 - 1
CAGGUUCAUUUUACAAGAAUCCAAUUUUCUCCUUUCCCUCGCAUUUUUGAUACGCCGCAUUAAGUGCAAUAAG----------UAACAACAAACAAAUCUUUCACCAAAUGAACCAUAAA
..(((((((((....((((.......))))..........((((((.((........))..))))))......----------.......................)))))))))..... ( -17.00)
>consensus
CAGGUUCAUUUUACAAGAAUCCAAUUUUCUCCUUUCCCUUGCGUUUUUGAUACGCUGCAUUAAGUGCAAUAAGCGCAGCCAAAUAACAACAAACAAAUCUCUCACCAAAUGAACCAUAAA
..(((((((((....((((.......))))........(((((((((((.(((..........)))))).))))))))............................)))))))))..... (-18.98 = -19.62 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:24:17 2006