Locus 1334

Sequence ID	3R_DroMel_CAF1
Location	3,932,970 – 3,933,060
Length	90
Max. P	0.980241

overview

Window 0

Location	3,932,970 – 3,933,060
Length	90
Sequences	5
Columns	106
Reading direction	forward
Mean pairwise identity	66.77
Mean single sequence MFE	-20.08
Consensus MFE	-10.36
Energy contribution	-11.84
Covariance contribution	1.48
Combinations/Pair	1.07
Mean z-score	-2.12
Structure conservation index	0.52
SVM decision value	1.86
SVM RNA-class probability	0.980241
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3932970 90 + 27905053
CAACAACA-----GCGACAA------AAAAAAAACAUAACCAACGUUUCCUGC----CGCGGUGAAAAGUUGGUUGUACUUU-UUUUGAGGCUGUUGCUUUUUUCU
...(((((-----((..(((------(((((....(((((((((.(((((((.----..))).)))).)))))))))..)))-)))))..)))))))......... ( -30.10)
>DroSec_CAF1 1185 84 + 1
CAACAACG----------AA------AAAAAAAACAGAACCAACGUUUCCUGC----CGCGGUGAAAAGUUGGUUGUAUUUUUUUUUGAGAC--UUGCUUUUUUCU
......((----------((------((((((.(((..((((((.(((((((.----..))).)))).))))))))).))))))))))....--............ ( -20.50)
>DroEre_CAF1 1292 100 + 1
CCACAGCGGACAAAAAAAAAAAUAAAACAAAAAACAGAACCAACGUUUCCUGC----CGCGGUGAAAAGUUGGUUGUAUUUUUUUUAGAGGCUGUUGCU--UUUCU
...((((((.....((((((((((...(........)(((((((.(((((((.----..))).)))).))))))).)))))))))).....))))))..--..... ( -22.20)
>DroYak_CAF1 1381 86 + 1
CCACAGA-----AAAUAAAA------AAGAAAAACAGAACCAACGUUUCCUGC----CG---UGAAAAGUUGGUUGUAUAUUUUU--GAGGCUGUUGCUAUUUUCU
....(((-----((((....------..(((((..(.(((((((.(((((...----.)---.)))).))))))).)...)))))--..(((....)))))))))) ( -17.50)
>DroPer_CAF1 993 76 + 1
CAACUACA-----ACUACAG------UGC--CAGCCAACACAACAUUUCCUGCUGCCCGCAGUGAAAAUAUUGUU---UU-U-UUUUG------------UUUUCA
.....(((-----(.....(------((.--.......)))....((((((((.....)))).))))...)))).---..-.-.....------------...... ( -10.10)
>consensus
CAACAACA_____AAUAAAA______AAAAAAAACAGAACCAACGUUUCCUGC____CGCGGUGAAAAGUUGGUUGUAUUUUUUUUUGAGGCUGUUGCU_UUUUCU
.....................................(((((((.((((((((.....)))).)))).)))))))............................... (-10.36 = -11.84 +   1.48)

alignment

secondary structure

dotplot

Window 1

Location	3,932,970 – 3,933,060
Length	90
Sequences	5
Columns	106
Reading direction	reverse
Mean pairwise identity	66.77
Mean single sequence MFE	-21.43
Consensus MFE	-8.41
Energy contribution	-11.34
Covariance contribution	2.93
Combinations/Pair	1.05
Mean z-score	-2.17
Structure conservation index	0.39
SVM decision value	1.37
SVM RNA-class probability	0.947531
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3932970 90 - 27905053
AGAAAAAAGCAACAGCCUCAAAA-AAAGUACAACCAACUUUUCACCGCG----GCAGGAAACGUUGGUUAUGUUUUUUUU------UUGUCGC-----UGUUGUUG
.......(((((((((..(((((-((((.(((((((((.((((.(....----)...)))).))))))..))).))))))------)))..))-----))))))). ( -32.90)
>DroSec_CAF1 1185 84 - 1
AGAAAAAAGCAA--GUCUCAAAAAAAAAUACAACCAACUUUUCACCGCG----GCAGGAAACGUUGGUUCUGUUUUUUUU------UU----------CGUUGUUG
.......(((((--.....(((((((((((.(((((((.((((.(....----)...)))).))))))).))))))))))------).----------..))))). ( -20.20)
>DroEre_CAF1 1292 100 - 1
AGAAA--AGCAACAGCCUCUAAAAAAAAUACAACCAACUUUUCACCGCG----GCAGGAAACGUUGGUUCUGUUUUUUGUUUUAUUUUUUUUUUUGUCCGCUGUGG
.....--....(((((......((((((((.(((((((.((((.(....----)...)))).))))))).)))))))).....................))))).. ( -19.73)
>DroYak_CAF1 1381 86 - 1
AGAAAAUAGCAACAGCCUC--AAAAAUAUACAACCAACUUUUCA---CG----GCAGGAAACGUUGGUUCUGUUUUUCUU------UUUUAUUU-----UCUGUGG
((((((((((....))...--(((((((...(((((((.((((.---(.----...))))).))))))).)))))))...------...)))))-----))).... ( -18.60)
>DroPer_CAF1 993 76 - 1
UGAAAA------------CAAAA-A-AA---AACAAUAUUUUCACUGCGGGCAGCAGGAAAUGUUGUGUUGGCUG--GCA------CUGUAGU-----UGUAGUUG
......------------.....-.-..---.(((((.....((.(((.(((((((.((....)).)))).))).--)))------.))..))-----)))..... ( -15.70)
>consensus
AGAAAA_AGCAACAGCCUCAAAAAAAAAUACAACCAACUUUUCACCGCG____GCAGGAAACGUUGGUUCUGUUUUUUUU______UUGUAGU_____CGUUGUUG
......................((((((((.(((((((.((((...((.....))..)))).))))))).))))))))............................ ( -8.41 = -11.34 +   2.93)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:07:00 2006