Locus 5085

Sequence ID	X_DroMel_CAF1
Location	13,287,275 – 13,287,390
Length	115
Max. P	0.928284

overview

Window 9

Location	13,287,275 – 13,287,390
Length	115
Sequences	4
Columns	118
Reading direction	forward
Mean pairwise identity	81.77
Mean single sequence MFE	-25.72
Consensus MFE	-15.98
Energy contribution	-18.04
Covariance contribution	2.06
Combinations/Pair	1.12
Mean z-score	-2.43
Structure conservation index	0.62
SVM decision value	1.19
SVM RNA-class probability	0.928284
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13287275 115 + 22224390
---AACUAAAUGACGCAUGAUUAACAAACGCUCUGCUGUUCGUUGUCGGAAUUUUUGCGGUAAGUGUUAAAUAUGCUUAUUAAUUAAUGCCGCAAAAUAUCCGCAAAAAUCCAACAAA
---...........((..(((.(((.(((((...)).))).))))))(((..((((((((((...(((((.((....)))))))...))))))))))..))))).............. ( -25.20)
>DroPse_CAF1 44113 115 + 1
AUCAACAACAUGGCGUAUGAUUAGCAUACGCACU--UUUUGUUUGCCGGGAUUCCUGUGGUAAGUGUAAAAUAUAAUUAUUAAUGAAUACCACAAACUAUCCACAAAACU-CAGCAAA
............(((((((.....)))))))...--....((((....((((...(((((((..(((..((((....)))).)))..)))))))....))))...)))).-....... ( -25.00)
>DroSec_CAF1 1929 115 + 1
---AACUAAAUGACGCAUGAUUAACAAACGAUCUGCUGUUCGUCGUCGGGAUUUUUGCGGUAAGUGUUAAAUAUGCUUAUUAAUUAAUGCCGCAAAAUAUCCGCAAAAAUCCAACAAA
---.......(((((.((((.((.((.......)).)).)))))))))(((((((((((((((((((.....))))))).......((........))..))))))))))))...... ( -27.90)
>DroPer_CAF1 43229 115 + 1
AUCAACAACAUGGCGUAUGAUUAACAUACGCACU--UUUUGUUUGCCGGGAUUCCUGUGGUAAGUGUAAAAUAUAAUUAUUAAUGAAUACCACAAACUAUCCACAAAACU-CAGCAAA
............(((((((.....)))))))...--....((((....((((...(((((((..(((..((((....)))).)))..)))))))....))))...)))).-....... ( -24.80)
>consensus
___AACAAAAUGACGCAUGAUUAACAAACGCACU__UGUUCGUUGCCGGGAUUCCUGCGGUAAGUGUAAAAUAUAAUUAUUAAUGAAUACCACAAAAUAUCCACAAAAAU_CAACAAA
............(((((((.....)))))))................(((..((((((((((.......((((....))))......))))))))))..)))................ (-15.98 = -18.04 +   2.06)

alignment

secondary structure

dotplot

Window 0

Location	13,287,275 – 13,287,390
Length	115
Sequences	4
Columns	118
Reading direction	reverse
Mean pairwise identity	81.77
Mean single sequence MFE	-28.09
Consensus MFE	-22.69
Energy contribution	-22.20
Covariance contribution	-0.50
Combinations/Pair	1.26
Mean z-score	-2.00
Structure conservation index	0.81
SVM decision value	1.13
SVM RNA-class probability	0.919555
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13287275 115 - 22224390
UUUGUUGGAUUUUUGCGGAUAUUUUGCGGCAUUAAUUAAUAAGCAUAUUUAACACUUACCGCAAAAAUUCCGACAACGAACAGCAGAGCGUUUGUUAAUCAUGCGUCAUUUAGUU---
(((((((..((.(((((((..((((((((........((((....)))).........))))))))..)))).))).)).)))))))((((.((.....)).)))).........--- ( -27.23)
>DroPse_CAF1 44113 115 - 1
UUUGCUG-AGUUUUGUGGAUAGUUUGUGGUAUUCAUUAAUAAUUAUAUUUUACACUUACCACAGGAAUCCCGGCAAACAAAA--AGUGCGUAUGCUAAUCAUACGCCAUGUUGUUGAU
..(((((-........((((..(((((((((......((((....)))).......))))))))).)))))))))(((((..--.(.(((((((.....))))))))...)))))... ( -29.42)
>DroSec_CAF1 1929 115 - 1
UUUGUUGGAUUUUUGCGGAUAUUUUGCGGCAUUAAUUAAUAAGCAUAUUUAACACUUACCGCAAAAAUCCCGACGACGAACAGCAGAUCGUUUGUUAAUCAUGCGUCAUUUAGUU---
......((((((((((((.((...(((...............)))...........)))))))))))))).((((..((..((((((...))))))..))...))))........--- ( -25.30)
>DroPer_CAF1 43229 115 - 1
UUUGCUG-AGUUUUGUGGAUAGUUUGUGGUAUUCAUUAAUAAUUAUAUUUUACACUUACCACAGGAAUCCCGGCAAACAAAA--AGUGCGUAUGUUAAUCAUACGCCAUGUUGUUGAU
..(((((-........((((..(((((((((......((((....)))).......))))))))).)))))))))(((((..--.(.(((((((.....))))))))...)))))... ( -30.42)
>consensus
UUUGCUG_AGUUUUGCGGAUAGUUUGCGGCAUUAAUUAAUAAGCAUAUUUAACACUUACCACAAAAAUCCCGACAAACAAAA__AGAGCGUAUGUUAAUCAUACGCCAUGUAGUU___
.((((((.........((((.((((((((((......((((....)))).......))))))))))))))))))))...........(((((((.....)))))))............ (-22.69 = -22.20 +  -0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:39:45 2006