Locus 2056

Sequence ID	3L_DroMel_CAF1
Location	5,663,253 – 5,663,376
Length	123
Max. P	0.671518

overview

Window 5

Location	5,663,253 – 5,663,343
Length	90
Sequences	6
Columns	90
Reading direction	forward
Mean pairwise identity	90.66
Mean single sequence MFE	-26.67
Consensus MFE	-21.56
Energy contribution	-21.78
Covariance contribution	0.22
Combinations/Pair	1.04
Mean z-score	-2.15
Structure conservation index	0.81
SVM decision value	0.17
SVM RNA-class probability	0.614904
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5663253 90 + 23771897
GCUUCAGCAUCAGCUGCAGUGUCCUUGACCGAGUUUAUGUAGAUUUGCAAGGCUUUACACUGCGUGUGUUUGUGGGUUUCUUUCGCCCUG
......(((...(((((((((((((((..(((((((....))))))))))))....)))))))).))...)))((((.......)))).. ( -27.30)
>DroPse_CAF1 36046 89 + 1
G-UUCAGCAUCAGCUGCAGUGUCCUUGACCGAGUUUAUGUAGAUUUGCAAGGCUUUACACUGCUUUCUGCUUUCUUUUUUUUUUGUGCUG
.-..(((((((((..((((((((((((..(((((((....))))))))))))....)))))))...)))...............)))))) ( -25.06)
>DroSim_CAF1 37001 90 + 1
GCUUCAGCAUCAGCUGCAGUGUCCUUGACCGAGUUUAUGUAGAUUUGCAAGGCUUUACACUGCGUGUGUUUGUGGGUUUCUUUCGCCCUG
......(((...(((((((((((((((..(((((((....))))))))))))....)))))))).))...)))((((.......)))).. ( -27.30)
>DroEre_CAF1 39194 90 + 1
GCUUCAGCAUCAGCUGCAGUGUCCUUGACCGAGUUUAUGUAGAUUUGCAAGGCUUUACACUGCGUGUGUUUGUGGGUUUCUUUUGCCCUG
......(((...(((((((((((((((..(((((((....))))))))))))....)))))))).))...)))((((.......)))).. ( -28.00)
>DroYak_CAF1 36657 90 + 1
GCUUCAGCAUCAGCUGCAGUGUCCUUGACCGAGUUUAUGUAGAUUUGCAAGGCUUUACACUGCGUGUGUUUGUGGGUUCCUUUCGCCCUG
......(((...(((((((((((((((..(((((((....))))))))))))....)))))))).))...)))((((.......)))).. ( -27.30)
>DroPer_CAF1 36273 89 + 1
G-UUCAGCAUCAGCUGCAGUGUCCUUGACCGAGUUUAUGUAGAUUUGCAAGGCUUUACACUGCUUUCUGCUUUCUUUUUUUUUUGUGCUG
.-..(((((((((..((((((((((((..(((((((....))))))))))))....)))))))...)))...............)))))) ( -25.06)
>consensus
GCUUCAGCAUCAGCUGCAGUGUCCUUGACCGAGUUUAUGUAGAUUUGCAAGGCUUUACACUGCGUGUGUUUGUGGGUUUCUUUCGCCCUG
.....(((....)))((((((((((((..(((((((....))))))))))))....)))))))..........((((.......)))).. (-21.56 = -21.78 +   0.22)

alignment

secondary structure

dotplot

Window 6

Location	5,663,278 – 5,663,376
Length	98
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	84.38
Mean single sequence MFE	-24.58
Consensus MFE	-19.78
Energy contribution	-20.42
Covariance contribution	0.64
Combinations/Pair	1.05
Mean z-score	-1.64
Structure conservation index	0.80
SVM decision value	0.29
SVM RNA-class probability	0.671518
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5663278 98 - 23771897
AUGUGGGG-AGGGGUGAGGAGUGAACAGGGUAUGCAGGGCGAAAGAAACCCACAAACACACGCAGUGUAAAGCCUUGCAAAUCUACAUAAACUCGGUCA
........-..((.((((..(((....((((.((((((((....(.....)....((((.....))))...)))))))).)))).)))...)))).)). ( -25.40)
>DroSec_CAF1 35939 94 - 1
A-----GCGGUGGGCGGGGGGUGAGCAGGGUAUGCAGGGCGAAAGAAACCCACAAACACACGCAGUGUAAAGCCUUGCAAAUCUACAUAAACUCGGUCA
.-----......(((.(((.(((....((((.((((((((....(.....)....((((.....))))...)))))))).)))).)))...))).))). ( -27.30)
>DroSim_CAF1 37026 93 - 1
A-----GA-AUGGGGGAGGGGUGAGCAGGGUAUGCAGGGCGAAAGAAACCCACAAACACACGCAGUGUAAAGCCUUGCAAAUCUACAUAAACUCGGUCA
.-----((-.((((....((((..(((((((.....((((....)...)))....((((.....))))...)))))))..)))).......)))).)). ( -26.70)
>DroEre_CAF1 39219 80 - 1
-------------------GGGGAGCGGGGUAUGCAGGGCAAAAGAAACCCACAAACACACGCAGUGUAAAGCCUUGCAAAUCUACAUAAACUCGGUCA
-------------------(((.....((((.((((((((....(.....)....((((.....))))...)))))))).)))).......)))..... ( -21.40)
>DroYak_CAF1 36682 80 - 1
-------------------GGGAAGCUGGGUAUGCAGGGCGAAAGGAACCCACAAACACACGCAGUGUAAAGCCUUGCAAAUCUACAUAAACUCGGUCA
-------------------(((....(((((.((((((((....((...))....((((.....))))...)))))))).)))))......)))..... ( -22.10)
>consensus
A_____G____GGG_G_GGGGUGAGCAGGGUAUGCAGGGCGAAAGAAACCCACAAACACACGCAGUGUAAAGCCUUGCAAAUCUACAUAAACUCGGUCA
..................((((.....((((.((((((((....(.....)....((((.....))))...)))))))).))))......))))..... (-19.78 = -20.42 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:21 2006