Locus 214

Sequence ID	3L_DroMel_CAF1
Location	597,296 – 597,434
Length	138
Max. P	0.999745

overview

Window 4

Location	597,296 – 597,401
Length	105
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	73.04
Mean single sequence MFE	-21.63
Consensus MFE	-14.04
Energy contribution	-15.08
Covariance contribution	1.04
Combinations/Pair	1.06
Mean z-score	-2.32
Structure conservation index	0.65
SVM decision value	2.65
SVM RNA-class probability	0.996096
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 597296 105 + 23771897
---UAAAUUUUACUCAUUAGCCAAGGGAGUACACUUUUUUCGAGAAAAAAUUUCUCAAUGAAUAUCCCGAAGUGCCCUGUUU-UUUCCAGUGCACAAAUGGGACAUUCC
---.......(((((...........)))))..........(((((.....)))))...((((.(((((..((((.(((...-....))).))))...))))).)))). ( -24.90)
>DroSec_CAF1 8652 93 + 1
AGCUAAAUUUUACUUAUAAGA-------------UGUUUACAAGCAAAAAC--CUCAAUGAAUGUCCCGAAGUGCCCUGUUU-UUUUCAGUGCACGAAUGGGACAUUCC
...................((-------------.((((........))))--.))...((((((((((..((((.(((...-....))).))))...)))))))))). ( -27.10)
>DroSim_CAF1 6961 89 + 1
----AAAUUUUACUCAUAAGA-------------AGUUUACAAGCAAAAAC--CUCAAUGAAUGUCGCAAAGUGCCCUGUUU-UUUUCAGUGCACGAAUGGGACAUUCC
----...............((-------------.((((........))))--.))...(((((((.((..((((.(((...-....))).))))...)).))))))). ( -22.90)
>DroEre_CAF1 10497 88 + 1
----CAAUUUUACUCAUAUU--------------UUUGUUCAACCAAAACC--CCCAAUGAAUACCCCGAAGUGCCCCGUUU-UUUCCAGUGCACGAAGGGGACUUUCC
----................--------------..((((((.........--.....))))))((((...(((((..(...-...)..).))))...))))....... ( -15.04)
>DroYak_CAF1 10821 86 + 1
AGCUAAGUUUUACUUAAAG---------------------GAAUCACACCC--GUCAUUGAAUAUCCCAAAGUGGCCUGUUUUUUUCCAGUGCACGAAUGGGACAUUCC
...((((.....))))..(---------------------(........))--......((((.(((((..(((..(((........)))..)))...))))).)))). ( -18.20)
>consensus
___UAAAUUUUACUCAUAAG______________UGUUUACAAGCAAAAAC__CUCAAUGAAUAUCCCGAAGUGCCCUGUUU_UUUCCAGUGCACGAAUGGGACAUUCC
...........................................................((((.(((((..((((.(((........))).))))...))))).)))). (-14.04 = -15.08 +   1.04)

alignment

secondary structure

dotplot

Window 5

Location	597,296 – 597,401
Length	105
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	73.04
Mean single sequence MFE	-28.20
Consensus MFE	-20.02
Energy contribution	-20.06
Covariance contribution	0.04
Combinations/Pair	1.19
Mean z-score	-3.26
Structure conservation index	0.71
SVM decision value	3.99
SVM RNA-class probability	0.999745
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 597296 105 - 23771897
GGAAUGUCCCAUUUGUGCACUGGAAA-AAACAGGGCACUUCGGGAUAUUCAUUGAGAAAUUUUUUCUCGAAAAAAGUGUACUCCCUUGGCUAAUGAGUAAAAUUUA---
.(((((((((....((((.(((....-...))).))))...))))))))).(((((((.....)))))))..(((...(((((...........)))))...))).--- ( -32.60)
>DroSec_CAF1 8652 93 - 1
GGAAUGUCCCAUUCGUGCACUGAAAA-AAACAGGGCACUUCGGGACAUUCAUUGAG--GUUUUUGCUUGUAAACA-------------UCUUAUAAGUAAAAUUUAGCU
.(((((((((....((((.(((....-...))).))))...)))))))))......--..((((((((((((...-------------..))))))))))))....... ( -32.40)
>DroSim_CAF1 6961 89 - 1
GGAAUGUCCCAUUCGUGCACUGAAAA-AAACAGGGCACUUUGCGACAUUCAUUGAG--GUUUUUGCUUGUAAACU-------------UCUUAUGAGUAAAAUUU----
.(((((((.((...((((.(((....-...))).))))..)).)))))))......--..(((((((..(((...-------------..)))..)))))))...---- ( -27.00)
>DroEre_CAF1 10497 88 - 1
GGAAAGUCCCCUUCGUGCACUGGAAA-AAACGGGGCACUUCGGGGUAUUCAUUGGG--GGUUUUGGUUGAACAAA--------------AAUAUGAGUAAAAUUG----
.......((((...((((.(((....-...))).))))...))))(((((((....--..(((((......))))--------------)..)))))))......---- ( -23.20)
>DroYak_CAF1 10821 86 - 1
GGAAUGUCCCAUUCGUGCACUGGAAAAAAACAGGCCACUUUGGGAUAUUCAAUGAC--GGGUGUGAUUC---------------------CUUUAAGUAAAACUUAGCU
.((((((((((...(((..(((........)))..)))..))))))))))......--(((......))---------------------).(((((.....))))).. ( -25.80)
>consensus
GGAAUGUCCCAUUCGUGCACUGGAAA_AAACAGGGCACUUCGGGAUAUUCAUUGAG__GUUUUUGCUUGAAAAAA______________CUUAUGAGUAAAAUUUA___
.(((((((((....((((.(((........))).))))...)))))))))........................................................... (-20.02 = -20.06 +   0.04)

alignment

secondary structure

dotplot

Window 6

Location	597,333 – 597,434
Length	101
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	85.52
Mean single sequence MFE	-28.04
Consensus MFE	-20.92
Energy contribution	-20.96
Covariance contribution	0.04
Combinations/Pair	1.14
Mean z-score	-2.41
Structure conservation index	0.75
SVM decision value	1.36
SVM RNA-class probability	0.945960
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 597333 101 - 23771897
UUGGCACACCCACACACCACACACCACACACAUGGAAUGUCCCAUUUGUGCACUGGAAA-AAACAGGGCACUUCGGGAUAUUCAUUGAGAAAUUUUUUCUCG
.(((.....)))......................(((((((((....((((.(((....-...))).))))...)))))))))...(((((.....))))). ( -28.40)
>DroSec_CAF1 8679 92 - 1
UUGGCACACCCACACAC-------CACACACAUGGAAUGUCCCAUUCGUGCACUGAAAA-AAACAGGGCACUUCGGGACAUUCAUUGAG--GUUUUUGCUUG
..((((.(((((.....-------..((....))(((((((((....((((.(((....-...))).))))...)))))))))..)).)--))...)))).. ( -27.80)
>DroSim_CAF1 6984 92 - 1
UUGGCACACCCACACAC-------CACACACAUGGAAUGUCCCAUUCGUGCACUGAAAA-AAACAGGGCACUUUGCGACAUUCAUUGAG--GUUUUUGCUUG
..((((.(((((.....-------..((....))(((((((.((...((((.(((....-...))).))))..)).)))))))..)).)--))...)))).. ( -23.20)
>DroEre_CAF1 10519 92 - 1
UUGGCACACCCACGCAC-------CACACACAUGGAAAGUCCCCUUCGUGCACUGGAAA-AAACGGGGCACUUCGGGGUAUUCAUUGGG--GGUUUUGGUUG
......((.(((...((-------(...((.(((((....((((...((((.(((....-...))).))))...))))..)))))))..--)))..))).)) ( -26.00)
>DroYak_CAF1 10840 93 - 1
UUGGCACACCCACACAC-------CACACACAUGGAAUGUCCCAUUCGUGCACUGGAAAAAAACAGGCCACUUUGGGAUAUUCAAUGAC--GGGUGUGAUUC
.(((.....)))(((((-------(.....(((.((((((((((...(((..(((........)))..)))..)))))))))).)))..--.)))))).... ( -34.80)
>consensus
UUGGCACACCCACACAC_______CACACACAUGGAAUGUCCCAUUCGUGCACUGGAAA_AAACAGGGCACUUCGGGAUAUUCAUUGAG__GUUUUUGCUUG
.(((.....)))..................((..(((((((((....((((.(((........))).))))...)))))))))..))............... (-20.92 = -20.96 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:36:31 2006