Locus 4139

Sequence ID	3R_DroMel_CAF1
Location	11,288,877 – 11,288,987
Length	110
Max. P	0.990317

overview

Window 0

Location	11,288,877 – 11,288,987
Length	110
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	73.47
Mean single sequence MFE	-27.81
Consensus MFE	-14.16
Energy contribution	-15.08
Covariance contribution	0.92
Combinations/Pair	1.18
Mean z-score	-1.59
Structure conservation index	0.51
SVM decision value	0.01
SVM RNA-class probability	0.539361
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11288877 110 + 27905053
UAGGAGUGUUCACUGUGCUGCCUUUCCAGCACUCAGUGCC-----CACCGAUUUAGCACUGAGUCGUAAAUGUCGCGCAGGCGCAACACCAUUCUGCAAUCACAAUGCCACAAUC
..((.((((((.((((((.((.(((...(.(((((((((.-----..........))))))))))..))).)).))))))..).)))))((((.((....)).))))))...... ( -31.70)
>DroSec_CAF1 23656 104 + 1
UGGGAGUGUUCACUGCGUAGCCUUUGCAGCACUCAGUGCC-----CACCGAUUUAGCACUGA------AAUGUCGCGCAGGCGCAACACCAUUCUGCAAUCACAAUGCCACAAUC
..((((((.....(((...((((.(((.(((.(((((((.-----..........)))))))------..))).))).)))))))....))))))(((.......)))....... ( -28.90)
>DroSim_CAF1 24293 104 + 1
UGGGAGUGUUCACUGCGCUGCCUUUCCAGCACUCAGUGCC-----CACCGAUUUAGCACUGA------AAUGUCGCGCAGGCGCAACACCAUUCUGCAAUCACAAUGCCACAAUC
(((..((((((.(((((((((.......))).(((((((.-----..........)))))))------......))))))..).)))))((((.((....)).)))))))..... ( -28.90)
>DroEre_CAF1 22724 97 + 1
UAGGAGUUUUCACUGUGCUGCCUUUCCCGCACUCAGUGAC-----CACCGAUUCAGCACUGA------AAUGUCGCGCAGGCGCAACUCCAUUCUGCAAUCACAAUGC-------
..((((((....(((((((((.......))).((((((..-----...........))))))------......))))))....))))))..................------- ( -25.72)
>DroYak_CAF1 23134 95 + 1
UAGGAGUUUUCACUGUGU------UACAGCGCUCAGUGCC-----CACCGAUUUAGCACUGA------AAUGUCGCGCAGGCGCAACUCCAUUCUGCAAUCACAAUGCCACA---
..((((((....((((((------.(((....(((((((.-----..........)))))))------..))).))))))....)))))).....(((.......)))....--- ( -30.20)
>DroMoj_CAF1 29914 96 + 1
--UGACUAUUUACACUGCAUGUUUCACAGUAAUCUUUGGCAAUGGCUAUGAUCAAACACUCG------AUAGCUGCGCAGACGCAACGCCAACAUGCGAUUCAC-----------
--.............(((((((..............((((...((((((((........)).------))))))(((....)))...)))))))))))......----------- ( -21.43)
>consensus
UAGGAGUGUUCACUGUGCUGCCUUUCCAGCACUCAGUGCC_____CACCGAUUUAGCACUGA______AAUGUCGCGCAGGCGCAACACCAUUCUGCAAUCACAAUGCCACA___
..((.((.....((((((..............(((((((................)))))))............)))))).....)).))......................... (-14.16 = -15.08 +   0.92)

alignment

secondary structure

dotplot

Window 1

Location	11,288,877 – 11,288,987
Length	110
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	73.47
Mean single sequence MFE	-36.77
Consensus MFE	-22.82
Energy contribution	-22.93
Covariance contribution	0.12
Combinations/Pair	1.32
Mean z-score	-2.28
Structure conservation index	0.62
SVM decision value	2.21
SVM RNA-class probability	0.990317
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11288877 110 - 27905053
GAUUGUGGCAUUGUGAUUGCAGAAUGGUGUUGCGCCUGCGCGACAUUUACGACUCAGUGCUAAAUCGGUG-----GGCACUGAGUGCUGGAAAGGCAGCACAGUGAACACUCCUA
((.(((..(((((((.((((.....(((((((((....)))))))))....((((((((((.........-----)))))))))).((....))))))))))))).))).))... ( -44.30)
>DroSec_CAF1 23656 104 - 1
GAUUGUGGCAUUGUGAUUGCAGAAUGGUGUUGCGCCUGCGCGACAUU------UCAGUGCUAAAUCGGUG-----GGCACUGAGUGCUGCAAAGGCUACGCAGUGAACACUCCCA
((((.((((((((............(((((((((....)))))))))------.))))))))))))((((-----..(((((.(((((.....))).)).)))))..)))).... ( -40.32)
>DroSim_CAF1 24293 104 - 1
GAUUGUGGCAUUGUGAUUGCAGAAUGGUGUUGCGCCUGCGCGACAUU------UCAGUGCUAAAUCGGUG-----GGCACUGAGUGCUGGAAAGGCAGCGCAGUGAACACUCCCA
((((.((((((((............(((((((((....)))))))))------.))))))))))))((((-----..((((..((((((......))))))))))..)))).... ( -41.12)
>DroEre_CAF1 22724 97 - 1
-------GCAUUGUGAUUGCAGAAUGGAGUUGCGCCUGCGCGACAUU------UCAGUGCUGAAUCGGUG-----GUCACUGAGUGCGGGAAAGGCAGCACAGUGAAAACUCCUA
-------.(((((((.((((........((((((....)))))).((------((..(((....(((((.-----...)))))..))).)))).))))))))))).......... ( -32.90)
>DroYak_CAF1 23134 95 - 1
---UGUGGCAUUGUGAUUGCAGAAUGGAGUUGCGCCUGCGCGACAUU------UCAGUGCUAAAUCGGUG-----GGCACUGAGCGCUGUA------ACACAGUGAAAACUCCUA
---.((..(((((((.((((((......((((((....))))))..(------((((((((.........-----)))))))))..)))))------))))))))...))..... ( -37.60)
>DroMoj_CAF1 29914 96 - 1
-----------GUGAAUCGCAUGUUGGCGUUGCGUCUGCGCAGCUAU------CGAGUGUUUGAUCAUAGCCAUUGCCAAAGAUUACUGUGAAACAUGCAGUGUAAAUAGUCA--
-----------.(((...(((...((((((((((....)))))).((------(((....)))))....)))).))).......((((((.......)))))).......)))-- ( -24.40)
>consensus
___UGUGGCAUUGUGAUUGCAGAAUGGUGUUGCGCCUGCGCGACAUU______UCAGUGCUAAAUCGGUG_____GGCACUGAGUGCUGGAAAGGCAGCACAGUGAACACUCCUA
........(((((((.............((((((....))))))..........((((((....((((((.......)))))))))))).........))))))).......... (-22.82 = -22.93 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:19:11 2006