Locus 3100

Sequence ID	3L_DroMel_CAF1
Location	8,975,694 – 8,975,860
Length	166
Max. P	0.937374

overview

Window 1

Location	8,975,694 – 8,975,784
Length	90
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	70.45
Mean single sequence MFE	-24.49
Consensus MFE	-14.24
Energy contribution	-14.88
Covariance contribution	0.64
Combinations/Pair	1.17
Mean z-score	-1.73
Structure conservation index	0.58
SVM decision value	1.26
SVM RNA-class probability	0.937374
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8975694 90 + 23771897
GAUUUCACCGAGGAGGAGCGCAAGCUGUUCCUAAAGGUAUGUCAUUCA---UAGUUCA-------AGUCAAAUUGGUGCCAC-----UAACCAGCCGAGUUCAAC
(((...(((.(((((.(((....))).)))))...)))..))).....---..(((.(-------(.((...(((((.....-----..)))))..)).)).))) ( -26.70)
>DroPse_CAF1 30503 91 + 1
GACUUUACAGAAGAAGAGCGCAAGCUUUUCCUAAAGGUGAGUACCCGAAAGAAGAUCA-------UGUCUAAG----GCCAUCUCCUUA---AUGCAUAUUCUUU
.((((.((....(((((((....)))))))......))))))........(((((..(-------(((.((((----(......)))))---..))))..))))) ( -23.00)
>DroSec_CAF1 14799 90 + 1
GAUUUCACGGAGGAGGAGCGCAAGCUGUUCCUAAAGGUAAGUCGUUCA---UAGUUCA-------UGUCAAAUUGGUGGCAC-----UAACCAACCGGGUUCAAC
((..((.((((((((.(((....))).)))))...(((.(((.(((..---(((((..-------.....)))))..)))))-----).)))..))))).))... ( -26.90)
>DroSim_CAF1 15445 90 + 1
GAUUUCACGGAGGAGGAGCGCAAGCUGUUCCUAAAGGUAAGUCGUUCA---UAGUUCA-------UGUCAAAUUGGUGCCAC-----UAACCAACCGGGUUCAAC
((..((.((((((((.(((....))).)))))...(((.(((.((...---(((((..-------.....)))))..)).))-----).)))..))))).))... ( -27.30)
>DroEre_CAF1 15158 86 + 1
GAUUUCACGGAGGAGGAGCGUAAGCUGUUCCUAAAGGUAUGUCGUUUA---UAAUUCA-------AGGCAAAUUGGCGCCAC-----U----AACUGAGCACAAC
(((....(..(((((.(((....))).)))))...)....)))(((((---.......-------.(((........)))..-----.----...)))))..... ( -21.84)
>DroYak_CAF1 15693 87 + 1
GACUUCACGGAGGAGGAGCGUAAGCUGUUCCUAAAGGUAUGUCGUUCA---UAACUUUGCUACAUACAUAAAU------AAU-----U----AAUUAAGUAAAAC
.((((..(..(((((.(((....))).)))))...)((((((.((...---.......)).))))))......------...-----.----....))))..... ( -21.20)
>consensus
GAUUUCACGGAGGAGGAGCGCAAGCUGUUCCUAAAGGUAAGUCGUUCA___UAGUUCA_______AGUCAAAUUGGUGCCAC_____UA___AACCGAGUUCAAC
(((....(..(((((.(((....))).)))))...)....))).............................................................. (-14.24 = -14.88 +   0.64)

alignment

secondary structure

dotplot

Window 2

Location	8,975,751 – 8,975,860
Length	109
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	72.58
Mean single sequence MFE	-28.30
Consensus MFE	-17.45
Energy contribution	-16.90
Covariance contribution	-0.55
Combinations/Pair	1.21
Mean z-score	-1.24
Structure conservation index	0.62
SVM decision value	0.17
SVM RNA-class probability	0.614784
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8975751 109 - 23771897
ACGAAUCGAGAAUGGUGGCUCCAGGUGGGCGAAACCCAAAAGCGGCGGCUUUGAGCAGCUGGUGACAAACUGAAAA----GUUGAACUCGGCUGGUUA-----GUGGCACCAAUUUGA
.(((((.......(((.((((....((((.....))))(((((....))))))))).)))((((....(((((..(----((((....)))))..)))-----))..)))).))))). ( -35.00)
>DroPse_CAF1 30563 107 - 1
GCGGAUGGAGAAGGGCGGCUCAAGGUGGGCAAAGCCCAAAAGCGGUGGUUUUGAGCAGCUGGUAACAAACUGUCAA----AAAGAAUAUGCAU---UAAGGAGAUGGC----CUUAGA
............((((.((((.....))))...))))....(((....((((((.(((.((....))..)))))))----))......))).(---(((((......)----))))). ( -28.90)
>DroEre_CAF1 15215 105 - 1
ACGAAUCGAGAAGGGUGGCUCCAGGUGGGCGAAACCCAAAAGCGGAGGCUUUGAGCAGCUAGUAACAAACUGGAAA----GUUGUGCUCAGUU----A-----GUGGCGCCAAUUUGC
......((((...((((((((....((((.....))))(((((....)))))))))((((((((...((((....)----))).)))).))))----.-----....))))..)))). ( -29.70)
>DroYak_CAF1 15757 99 - 1
ACGAAUCGAGAAGGGUGGCUCCAGGUGGGCGAAACCCAAAAGCGGAGGCUUUGAGCAGCUGGUGACAAACUGAAAA----GUUUUACUUAAUU----A-----AUU------AUUUAU
...(((..((..((((.((.((....))))...)))).......((((((((...(((.((....))..))).)))----))))).))..)))----.-----...------...... ( -24.20)
>DroAna_CAF1 14365 100 - 1
GCGAAUGGAGAACGGUGGCUCCAGAUGGGCGAAGCCCAAAAGCGGUGGCUUCGAGCAACUGGUUACAAACUGAAAGAAAAUAUGAA----GUU---UA-----------AGAAUAUGA
............((((....((((.((..((((((((.......).)))))))..)).))))......))))..............----...---..-----------......... ( -23.10)
>DroPer_CAF1 16235 107 - 1
GCGGAUGGAGAAGGGCGGCUCAAGGUGGGCAAAGCCCAAAAGCGGUGGUUUUGAGCAGCUGGUAACAAACUGUCAA----AAAGAAUAUGCAU---UAAGGAGAUGGC----CUUAGA
............((((.((((.....))))...))))....(((....((((((.(((.((....))..)))))))----))......))).(---(((((......)----))))). ( -28.90)
>consensus
ACGAAUCGAGAAGGGUGGCUCCAGGUGGGCGAAACCCAAAAGCGGUGGCUUUGAGCAGCUGGUAACAAACUGAAAA____GAUGAACUUGGUU___UA_____AUGGC____AUUUGA
.............(((.((((....((((.....))))(((((....))))))))).)))(((.....)))............................................... (-17.45 = -16.90 +  -0.55)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:49:30 2006