Locus 1399

Sequence ID	3L_DroMel_CAF1
Location	4,070,175 – 4,070,308
Length	133
Max. P	0.832564

overview

Window 3

Location	4,070,175 – 4,070,286
Length	111
Sequences	4
Columns	111
Reading direction	forward
Mean pairwise identity	87.39
Mean single sequence MFE	-30.62
Consensus MFE	-26.61
Energy contribution	-26.92
Covariance contribution	0.31
Combinations/Pair	1.04
Mean z-score	-1.41
Structure conservation index	0.87
SVM decision value	0.11
SVM RNA-class probability	0.589737
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4070175 111 + 23771897
AGAGUUCCACCCACUCCACUUCCAUUCUUAUCUGACACACGGAGCAGCUGGCGUAGGAUGUUACCACACACUUGGCACUUGGCACUUGGUCCUGCUGCUGCUCCAGCUCCU
.(((((...................((......)).....((((((((....(((((((((....)).((..((.(....).))..))))))))).))))))))))))).. ( -30.50)
>DroSec_CAF1 14364 111 + 1
AGAGUUCCACCCACACCACUCCCAUUCUUAUCUGACACACGGAGCAGCUGGCGGAGGAUGUUACCACACACUUGGCACUUGGCACUUGGUCCUGCUGCUGCUCCAGCUCCU
.(((((...................((......)).....((((((((..((.(((..(((....)))..))).))....((((........))))))))))))))))).. ( -31.50)
>DroSim_CAF1 14501 111 + 1
AGAGUUCCACCCACACCACUCCCAUUCUUAUCUGACACACGGAGCAGCUGGCGGAGGAUGUUACCACACACUUGGCACUUGGCACUUGGUCCUGCUGCUGCUCCAGCUCCU
.(((((...................((......)).....((((((((..((.(((..(((....)))..))).))....((((........))))))))))))))))).. ( -31.50)
>DroEre_CAF1 15270 91 + 1
AGAGUUUCUCCCAC-----------ACUUAUCUGACACACGGAGCAGCUGGCGAAGGAUGUUACCACA---------CUUGGCACUUGGUCCUGCCGCUGCUCCUGCUCCU
.((((........(-----------(......))......((((((((.(((..(((((....(((..---------..)))......)))))))))))))))).)))).. ( -29.00)
>consensus
AGAGUUCCACCCACACCACUCCCAUUCUUAUCUGACACACGGAGCAGCUGGCGGAGGAUGUUACCACACACUUGGCACUUGGCACUUGGUCCUGCUGCUGCUCCAGCUCCU
.(((((...................((......)).....((((((((.(((..(((((....(((.............)))......))))))))))))))))))))).. (-26.61 = -26.92 +   0.31)

alignment

secondary structure

dotplot

Window 4

Location	4,070,212 – 4,070,308
Length	96
Sequences	4
Columns	98
Reading direction	forward
Mean pairwise identity	90.89
Mean single sequence MFE	-39.10
Consensus MFE	-31.33
Energy contribution	-31.14
Covariance contribution	-0.19
Combinations/Pair	1.04
Mean z-score	-1.97
Structure conservation index	0.80
SVM decision value	0.72
SVM RNA-class probability	0.832564
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4070212 96 + 23771897
CACGGAGCAGCUGGCGUAGGAUGUUACCACACACUUGGCACUUGGCACUUGGUCCUGCUGCUGCUCCAGCUCCU--GCUCCCUGGGCAGGAUCCAAUG
...((((((((....(((((((((....)).((..((.(....).))..))))))))).))))))))...((((--(((.....)))))))....... ( -39.10)
>DroSec_CAF1 14401 96 + 1
CACGGAGCAGCUGGCGGAGGAUGUUACCACACACUUGGCACUUGGCACUUGGUCCUGCUGCUGCUCCAGCUCCU--GCUCCUUGGGCAGGAUCCACUG
...((((((((..((.(((..(((....)))..))).))....((((........))))))))))))...((((--(((.....)))))))....... ( -40.10)
>DroSim_CAF1 14538 96 + 1
CACGGAGCAGCUGGCGGAGGAUGUUACCACACACUUGGCACUUGGCACUUGGUCCUGCUGCUGCUCCAGCUCCU--GCUCCUGGGGCAGGAUCCACUG
...((((((((..((.(((..(((....)))..))).))....((((........))))))))))))...((((--(((.....)))))))....... ( -40.10)
>DroEre_CAF1 15296 89 + 1
CACGGAGCAGCUGGCGAAGGAUGUUACCACA---------CUUGGCACUUGGUCCUGCCGCUGCUCCUGCUCCUUGGCUCCUUGGGCAGGAUCCACUG
...((((((((.(((..(((((....(((..---------..)))......)))))))))))))((((((.((..(....)..))))))))))).... ( -37.10)
>consensus
CACGGAGCAGCUGGCGGAGGAUGUUACCACACACUUGGCACUUGGCACUUGGUCCUGCUGCUGCUCCAGCUCCU__GCUCCUUGGGCAGGAUCCACUG
...((((((((.(((..(((((....(((.............)))......))))))))))))))))...((((..(((.....)))))))....... (-31.33 = -31.14 +  -0.19)

alignment

secondary structure

dotplot

Window 5

Location	4,070,212 – 4,070,308
Length	96
Sequences	4
Columns	98
Reading direction	reverse
Mean pairwise identity	90.89
Mean single sequence MFE	-39.33
Consensus MFE	-30.66
Energy contribution	-30.73
Covariance contribution	0.06
Combinations/Pair	1.00
Mean z-score	-1.95
Structure conservation index	0.78
SVM decision value	0.55
SVM RNA-class probability	0.779839
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4070212 96 - 23771897
CAUUGGAUCCUGCCCAGGGAGC--AGGAGCUGGAGCAGCAGCAGGACCAAGUGCCAAGUGCCAAGUGUGUGGUAACAUCCUACGCCAGCUGCUCCGUG
....((.(((((((....).))--)))).))((((((((.((((((.....(((((.(..(...)..).)))))...))))..))..))))))))... ( -39.20)
>DroSec_CAF1 14401 96 - 1
CAGUGGAUCCUGCCCAAGGAGC--AGGAGCUGGAGCAGCAGCAGGACCAAGUGCCAAGUGCCAAGUGUGUGGUAACAUCCUCCGCCAGCUGCUCCGUG
....((.(((((((....).))--)))).))((((((((.((((((.....(((((.(..(...)..).)))))...))))..))..))))))))... ( -39.20)
>DroSim_CAF1 14538 96 - 1
CAGUGGAUCCUGCCCCAGGAGC--AGGAGCUGGAGCAGCAGCAGGACCAAGUGCCAAGUGCCAAGUGUGUGGUAACAUCCUCCGCCAGCUGCUCCGUG
....((.(((((((....).))--)))).))((((((((.((((((.....(((((.(..(...)..).)))))...))))..))..))))))))... ( -39.20)
>DroEre_CAF1 15296 89 - 1
CAGUGGAUCCUGCCCAAGGAGCCAAGGAGCAGGAGCAGCGGCAGGACCAAGUGCCAAG---------UGUGGUAACAUCCUUCGCCAGCUGCUCCGUG
(..(((.((((.....)))).)))..)....(((((((((((((((.....(((((..---------..)))))...))))..))).))))))))... ( -39.70)
>consensus
CAGUGGAUCCUGCCCAAGGAGC__AGGAGCUGGAGCAGCAGCAGGACCAAGUGCCAAGUGCCAAGUGUGUGGUAACAUCCUCCGCCAGCUGCUCCGUG
.......(((((((....).))..))))...((((((((.((((((.....(((((.(..(...)..).)))))...))))..))..))))))))... (-30.66 = -30.73 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:06:31 2006