Locus 6409

Sequence ID X_DroMel_CAF1
Location 16,069,849 – 16,069,943
Length 94
Max. P 0.944871
window10467 window10468

overview

Window 7

Location 16,069,849 – 16,069,943
Length 94
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 76.69
Mean single sequence MFE -30.23
Consensus MFE -17.74
Energy contribution -17.80
Covariance contribution 0.06
Combinations/Pair 1.06
Mean z-score -2.23
Structure conservation index 0.59
SVM decision value 1.35
SVM RNA-class probability 0.944871
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16069849 94 + 22224390
A-------------------AAACUCUAUG------GGGGCGCUUGAAUUUUCCAGGAGC-AAUCCAAGUGCCUCAAAAGGCAAGCGGAUAAAUAAAAAGGCCAUUGAAAAGCCCACCGA
.-------------------........((------(((((((((..(((((((.(((..-..)))...(((((....)))))...))).))))....))))...(....))))).))). ( -27.50)
>DroSec_CAF1 15691 94 + 1
A-------------------AAGCUCAAUG------GGGGCGCUUGAAUUUUCCAGGAGC-AGUCCAAGUGCCUCAAAAGGCAAGCGCAGAAAUAAAAAGGCCAUUGAAAAGCCCACCGA
.-------------------..((((((((------(..(((((((..((((..(((.((-.......)).))).))))..)))))))(....).......)))))))...))....... ( -25.10)
>DroEre_CAF1 15305 99 + 1
AAUGGGUGCGGAG--------AAUACU----------GGGCGGUUGAAUUUUCCAGGAGC-ACUCCAAGUGCCCCAAAAGGCAAGCGGAGAAAUAAAAAGGCCAUUGAA-AGCCCACC-A
....((((.((..--------.....(----------((.(..((...((((((.(((..-..)))...((((......))))...))))))...))..).))).....-..))))))-. ( -29.94)
>DroYak_CAF1 13318 119 + 1
AAAUGCUGCGGAGGGGGGGGAAAUUCUAUGGCGGGGGGAGCGGUUGAGUUUUCCAGGAGCCAGUCCAAGUGCCUCAAGAGGCAAGCGGAGAAAUAAAAAGGCCAUUGAAAAGCCCACC-A
............((...(((...(((.(((((..((..(((......)))..)).........(((...(((((....)))))...)))...........))))).)))...))).))-. ( -38.40)
>consensus
A___________________AAACUCUAUG______GGGGCGCUUGAAUUUUCCAGGAGC_AGUCCAAGUGCCUCAAAAGGCAAGCGGAGAAAUAAAAAGGCCAUUGAAAAGCCCACC_A
.....................................((((..((.(((...((.(((.....)))...((((......))))................))..))).))..))))..... (-17.74 = -17.80 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 16,069,849 – 16,069,943
Length 94
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 76.69
Mean single sequence MFE -27.53
Consensus MFE -19.12
Energy contribution -19.00
Covariance contribution -0.12
Combinations/Pair 1.11
Mean z-score -1.63
Structure conservation index 0.69
SVM decision value 0.42
SVM RNA-class probability 0.727861
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16069849 94 - 22224390
UCGGUGGGCUUUUCAAUGGCCUUUUUAUUUAUCCGCUUGCCUUUUGAGGCACUUGGAUU-GCUCCUGGAAAAUUCAAGCGCCCC------CAUAGAGUUU-------------------U
..((.((((.(((.(((..((.........(((((..(((((....)))))..))))).-......))...))).))).)))))------).........-------------------. ( -26.49)
>DroSec_CAF1 15691 94 - 1
UCGGUGGGCUUUUCAAUGGCCUUUUUAUUUCUGCGCUUGCCUUUUGAGGCACUUGGACU-GCUCCUGGAAAAUUCAAGCGCCCC------CAUUGAGCUU-------------------U
((((((((((.......))))...........((((((((((....)))).((.(((..-..))).)).......))))))...------))))))....-------------------. ( -27.20)
>DroEre_CAF1 15305 99 - 1
U-GGUGGGCU-UUCAAUGGCCUUUUUAUUUCUCCGCUUGCCUUUUGGGGCACUUGGAGU-GCUCCUGGAAAAUUCAACCGCCC----------AGUAUU--------CUCCGCACCCAUU
.-((((((((-......)))).........(((((..(((((....)))))..))))).-....((((.............))----------))....--------.....)))).... ( -27.02)
>DroYak_CAF1 13318 119 - 1
U-GGUGGGCUUUUCAAUGGCCUUUUUAUUUCUCCGCUUGCCUCUUGAGGCACUUGGACUGGCUCCUGGAAAACUCAACCGCUCCCCCCGCCAUAGAAUUUCCCCCCCCUCCGCAGCAUUU
.-((.(((...(((.(((((...........((((..(((((....)))))..))))..(((...(((.....)))...)))......))))).)))...)))))............... ( -29.40)
>consensus
U_GGUGGGCUUUUCAAUGGCCUUUUUAUUUCUCCGCUUGCCUUUUGAGGCACUUGGACU_GCUCCUGGAAAAUUCAACCGCCCC______CAUAGAAUUU___________________U
..((((((((.......))))..........(((...(((((....)))))...(((.....))).))).........))))...................................... (-19.12 = -19.00 +  -0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:13:04 2006