Locus 5246

Sequence ID	2L_DroMel_CAF1
Location	14,797,416 – 14,797,574
Length	158
Max. P	0.999530

overview

Window 1

Location	14,797,416 – 14,797,516
Length	100
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	86.37
Mean single sequence MFE	-42.06
Consensus MFE	-34.38
Energy contribution	-34.30
Covariance contribution	-0.08
Combinations/Pair	1.11
Mean z-score	-4.13
Structure conservation index	0.82
SVM decision value	3.69
SVM RNA-class probability	0.999530
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14797416 100 + 22407834
CUCCUU----UAUGUAG----------AUUCAUGAUCGCUGUUCAGCCAUUCGUGAGUCCUUCUCUUGUUUGGGCUUCUGUUGGCAUGGUUGUCAGCAGCCGUGCCAAAGGACU
.(((((----(...(((----------(.((((((..(((....)))...))))))((((..(....)...)))).))))..((((((((((....)))))))))))))))).. ( -38.70)
>DroSec_CAF1 44048 100 + 1
CUCCUU----UAUGUAG----------ACUCAUGAUCGCUGUUCAGCCAUUCGUGAGUCCGUCUCUUGUUUGGGCUUCUGUUGGCAUGGUUGUCAGCAGCCGUGCCAAAGGACU
.(((((----(.....(----------((((((((..(((....)))...))))))))).((((.......)))).......((((((((((....)))))))))))))))).. ( -41.50)
>DroSim_CAF1 44643 100 + 1
CUCCUU----UAUAUAG----------GCUCAUGAUCGCUGUUCAGCCAUUCGUGAGUCCUUCUCUUGUUUGGGCUUCUGUUGGCAUGGUUGUCAGCAGCCGUGCCAAAGGACU
..(((.----.(((.((----------((((((((..(((....)))...))))))).))).....)))..)))..(((.((((((((((((....)))))))))))).))).. ( -41.50)
>DroEre_CAF1 36994 110 + 1
CUCCCC----UAAGCAGUGGUAAUAAAACUGAUGAUCGCUGUGCGGUCAUUCGUGAGUCCUUCUCUGGUUUGGGCCUCUGUUGGCAUGGUUGUCAGCAGCCGUGCCAAAGGACU
....((----(.(((((.(((....((((((((((((((...)))))))))...(((.....))).)))))..))).)))))((((((((((....))))))))))..)))... ( -46.00)
>DroYak_CAF1 39970 114 + 1
CCCCCUACUAUAUGUAGAGGCAAUAAAACUCUCGAUCGCUGUUCAGCCAUUCGUGAGUCCUUCUCUUGUUUGGGCUUCUGUUGGCAUGGUUGUCAGCAGCCGUGCCAAAGGACU
...(((........(((((((......((((.(((..(((....)))...))).))))((..(....)...)))))))))((((((((((((....)))))))))))))))... ( -42.60)
>consensus
CUCCUU____UAUGUAG__________ACUCAUGAUCGCUGUUCAGCCAUUCGUGAGUCCUUCUCUUGUUUGGGCUUCUGUUGGCAUGGUUGUCAGCAGCCGUGCCAAAGGACU
.............................((((((..(((....)))...))))))((((..(((......)))......((((((((((((....)))))))))))).)))). (-34.38 = -34.30 +  -0.08)

alignment

secondary structure

dotplot

Window 2

Location	14,797,442 – 14,797,551
Length	109
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	78.39
Mean single sequence MFE	-42.30
Consensus MFE	-30.14
Energy contribution	-30.94
Covariance contribution	0.80
Combinations/Pair	1.20
Mean z-score	-2.10
Structure conservation index	0.71
SVM decision value	1.53
SVM RNA-class probability	0.961512
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14797442 109 + 22407834
GUUCAGCCAUUCGUGAGUCCU----UCUCUUGUUUGGGCU--UCUGUUGGCAUGGUUGUCAGCAGCCGUGCCAAAGGACUGGUGACUGGAUUCAGCUCGAGGACGAGGACGAGGA
................(((((----(.(((...(((((((--(((.((((((((((((....)))))))))))).)))(.(....).).....)))))))))).))))))..... ( -42.80)
>DroSec_CAF1 44074 103 + 1
GUUCAGCCAUUCGUGAGUCCG----UCUCUUGUUUGGGCU--UCUGUUGGCAUGGUUGUCAGCAGCCGUGCCAAAGGACUGGUGACUGGAUUCAGCUCGAGGACG------AGGA
......(((.(((..((((((----(((.......)))).--....((((((((((((....)))))))))))).)))))..))).)))......((((....))------)).. ( -41.20)
>DroSim_CAF1 44669 109 + 1
GUUCAGCCAUUCGUGAGUCCU----UCUCUUGUUUGGGCU--UCUGUUGGCAUGGUUGUCAGCAGCCGUGCCAAAGGACUGGUGACUGGAUUCAGCUCGAGGACGAGGACGAGGA
................(((((----(.(((...(((((((--(((.((((((((((((....)))))))))))).)))(.(....).).....)))))))))).))))))..... ( -42.80)
>DroYak_CAF1 40010 107 + 1
GUUCAGCCAUUCGUGAGUCCU----UCUCUUGUUUGGGCU--UCUGUUGGCAUGGUUGUCAGCAGCCGUGCCAAAGGACUGGAGUCUGGAUUCAGCUCGAGGACGAGGACGAU--
((((((((...((.(((....----.))).))....))))--((..((((((((((((....)))))))))))).(..((.(((.(((....)))))).))..)))))))...-- ( -44.00)
>DroAna_CAF1 31922 95 + 1
-CCCACUCACGCGGGAGUCACGCUGUCUC-----UGGUCCUCUUUGUUGGCCUGGCUGUCAGCAGCCAUGGCAACGGACCUGAGCCUGGACCCGGCCUGAC--------------
-.....(((.((.((.(((.....(.(((-----.(((((.....((((.((((((((....)))))).))))))))))).))).)..))))).)).))).-------------- ( -40.70)
>consensus
GUUCAGCCAUUCGUGAGUCCU____UCUCUUGUUUGGGCU__UCUGUUGGCAUGGUUGUCAGCAGCCGUGCCAAAGGACUGGUGACUGGAUUCAGCUCGAGGACGAGGACGAGGA
(((...(((.((((.(((((......(((......)))........((((((((((((....)))))))))))).))))).)))).)))....)))................... (-30.14 = -30.94 +   0.80)

alignment

secondary structure

dotplot

Window 3

Location	14,797,478 – 14,797,574
Length	96
Sequences	5
Columns	98
Reading direction	forward
Mean pairwise identity	80.08
Mean single sequence MFE	-34.88
Consensus MFE	-26.27
Energy contribution	-26.23
Covariance contribution	-0.04
Combinations/Pair	1.23
Mean z-score	-1.83
Structure conservation index	0.75
SVM decision value	0.84
SVM RNA-class probability	0.863270
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14797478 96 + 22407834
--UCUGUUGGCAUGGUUGUCAGCAGCCGUGCCAAAGGACUGGUGACUGGAUUCAGCUCGAGGACGAGGACGAGGACAACGACGAGGACCAGAGCACAG
--(((.((((((((((((....)))))))))))).)))(((((..((((.(((..((((....))))..((.(.....)..)).))))))).)).))) ( -36.90)
>DroSec_CAF1 44110 90 + 1
--UCUGUUGGCAUGGUUGUCAGCAGCCGUGCCAAAGGACUGGUGACUGGAUUCAGCUCGAGGACG------AGGACGACGACGAGGACCAGAGCACAG
--(((.((((((((((((....)))))))))))).)))(((((..((((.(((..((((....))------))..((....)).))))))).)).))) ( -36.80)
>DroSim_CAF1 44705 96 + 1
--UCUGUUGGCAUGGUUGUCAGCAGCCGUGCCAAAGGACUGGUGACUGGAUUCAGCUCGAGGACGAGGACGAGGACGACGACGAGGACCAGAGCACAG
--(((.((((((((((((....)))))))))))).)))(((((..((((.(((..((((....))))..((.(.....)..)).))))))).)).))) ( -36.90)
>DroYak_CAF1 40046 93 + 1
--UCUGUUGGCAUGGUUGUCAGCAGCCGUGCCAAAGGACUGGAGUCUGGAUUCAGCUCGAGGACGAGGACGAU---GACGACGAGGACAAGAGCGCAG
--(((.((((((((((((....)))))))))))).)))(((((((....)))).((((..(..(..(..((..---..)).)..)..)..)))).))) ( -35.50)
>DroAna_CAF1 31956 79 + 1
UCUUUGUUGGCCUGGCUGUCAGCAGCCAUGGCAACGGACCUGAGCCUGGACCCGGCCUGAC-------------------UCGAGGACAAGAGCACAG
..(((((((.((((((((....)))))).))))))))).(((.((((...(((((......-------------------))).))...)).)).))) ( -28.30)
>consensus
__UCUGUUGGCAUGGUUGUCAGCAGCCGUGCCAAAGGACUGGUGACUGGAUUCAGCUCGAGGACGAGGACGAGGACGACGACGAGGACCAGAGCACAG
..(((.((((((((((((....)))))))))))).)))((((...(((....)))((((......................))))..))))....... (-26.27 = -26.23 +  -0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:39:39 2006