Locus 1957

Sequence ID	X_DroMel_CAF1
Location	5,369,986 – 5,370,082
Length	96
Max. P	0.942782

overview

Window 0

Location	5,369,986 – 5,370,082
Length	96
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	69.53
Mean single sequence MFE	-26.06
Consensus MFE	-13.56
Energy contribution	-14.84
Covariance contribution	1.28
Combinations/Pair	1.27
Mean z-score	-1.57
Structure conservation index	0.52
SVM decision value	0.08
SVM RNA-class probability	0.575914
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5369986 96 + 22224390
---AAUGUCGAUUUGAAGCUAUGUAGAGAGACUUUACAUUUGCACGGCAAUUUA--------------------CACAGCAUGUAUUCGACACGAAUCUUUUGUUUUCGACAUUCAACU
---((((((((......((.((((((((...))))))))..))...........--------------------...((((.(.(((((...))))))...)))).))))))))..... ( -19.90)
>DroSec_CAF1 55167 105 + 1
---AAUGUCGAUUUGGAGCUAUGUAGAGGGACUCUACAUGUGCGUGUCAAUUGACAUGUU-----------ACACACUGUAUGCAUUUGACGAGUAUCUUUUGUGUUCGACAUUCGACU
---((((((((......(((((((((((...))))))))).))(((((....)))))...-----------(((((..(.((((.........)))).)..)))))))))))))..... ( -30.20)
>DroSim_CAF1 42116 105 + 1
---AAUGUCGAUUUGGAGCUAUGUAGAGGGACUCUACAUUUGCGCGUCAAUUUACAUGUU-----------ACACACUGUAUGCAUUUGACGAGUAUCUUUUGUGUUCGACAUUCGACU
---...(((((..(.((((.((((((((...)))))))).(((.((((((..((((((..-----------...)).)))).....)))))).)))........)))).)...))))). ( -29.60)
>DroEre_CAF1 48426 118 + 1
UAUAAUGUCGAUUUUGAGCGAUGUAGAGAGACC-UACGUUUGUACUCAAAUUUACAUGUCGCAUACAUUCUACACACAGUAUUCAUUCUACAAGAAUCGUGAGUGUUCGACAAUUUUCC
....((((.((.((((((.(((((((......)-))))))....)))))).))))))((((...(((((((((.....)))...((((.....))))...)))))).))))........ ( -24.70)
>DroYak_CAF1 47396 113 + 1
-----UGUCGAUUUUGAGCGAUGUAGAGCGACCUUACGUUUGCACUUA-AUUUACAUGUCGCACACAUUCUACACGGAGUGUUCAUUCUACACAAAUCUAAAAUGUUCGACAAUUCGUU
-----((((((((((((....(((((((((((..((.(((.......)-)).))...)))))..(((((((....)))))))....))))))....)).))))...))))))....... ( -25.90)
>consensus
___AAUGUCGAUUUGGAGCUAUGUAGAGAGACUCUACAUUUGCACGUCAAUUUACAUGUC___________ACACACAGUAUGCAUUCGACAAGAAUCUUUUGUGUUCGACAUUCGACU
.....((((((......(((((((((((...))))))))).))............................(((((....((((.........))))....)))))))))))....... (-13.56 = -14.84 +   1.28)

alignment

secondary structure

dotplot

Window 1

Location	5,369,986 – 5,370,082
Length	96
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	69.53
Mean single sequence MFE	-26.08
Consensus MFE	-6.93
Energy contribution	-8.33
Covariance contribution	1.40
Combinations/Pair	1.10
Mean z-score	-2.19
Structure conservation index	0.27
SVM decision value	1.33
SVM RNA-class probability	0.942782
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5369986 96 - 22224390
AGUUGAAUGUCGAAAACAAAAGAUUCGUGUCGAAUACAUGCUGUG--------------------UAAAUUGCCGUGCAAAUGUAAAGUCUCUCUACAUAGCUUCAAAUCGACAUU---
.....((((((((.........(((((...)))))....((((((--------------------((....((..(((....)))..)).....))))))))......))))))))--- ( -23.00)
>DroSec_CAF1 55167 105 - 1
AGUCGAAUGUCGAACACAAAAGAUACUCGUCAAAUGCAUACAGUGUGU-----------AACAUGUCAAUUGACACGCACAUGUAGAGUCCCUCUACAUAGCUCCAAAUCGACAUU---
.....((((((((........(((....)))....((.....((((((-----------.....(((....)))))))))((((((((...)))))))).))......))))))))--- ( -28.40)
>DroSim_CAF1 42116 105 - 1
AGUCGAAUGUCGAACACAAAAGAUACUCGUCAAAUGCAUACAGUGUGU-----------AACAUGUAAAUUGACGCGCAAAUGUAGAGUCCCUCUACAUAGCUCCAAAUCGACAUU---
.....((((((((..............((((((.(((((((.....))-----------)...))))..)))))).((..((((((((...)))))))).))......))))))))--- ( -26.40)
>DroEre_CAF1 48426 118 - 1
GGAAAAUUGUCGAACACUCACGAUUCUUGUAGAAUGAAUACUGUGUGUAGAAUGUAUGCGACAUGUAAAUUUGAGUACAAACGUA-GGUCUCUCUACAUCGCUCAAAAUCGACAUUAUA
.......((((((((((.((..((((.........))))..)).))))....((...((((..((((........))))...(((-((....))))).)))).))...))))))..... ( -24.80)
>DroYak_CAF1 47396 113 - 1
AACGAAUUGUCGAACAUUUUAGAUUUGUGUAGAAUGAACACUCCGUGUAGAAUGUGUGCGACAUGUAAAU-UAAGUGCAAACGUAAGGUCGCUCUACAUCGCUCAAAAUCGACA-----
.......((((((((((((((.((..((((.......))))...)).))))))))(.(((((.((((...-....))))..(....)))))).)..............))))))----- ( -27.80)
>consensus
AGUCGAAUGUCGAACACAAAAGAUUCUUGUCGAAUGCAUACUGUGUGU___________AACAUGUAAAUUGACGUGCAAAUGUAAAGUCCCUCUACAUAGCUCCAAAUCGACAUU___
.....((((((((((((...........................))))............................((..(((((.((...)).))))).))......))))))))... ( -6.93 =  -8.33 +   1.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:22:46 2006