Locus 526

Sequence ID	3L_DroMel_CAF1
Location	1,551,744 – 1,551,882
Length	138
Max. P	0.957753

overview

Window 8

Location	1,551,744 – 1,551,861
Length	117
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	91.42
Mean single sequence MFE	-32.80
Consensus MFE	-26.68
Energy contribution	-27.30
Covariance contribution	0.62
Combinations/Pair	1.09
Mean z-score	-2.71
Structure conservation index	0.81
SVM decision value	1.48
SVM RNA-class probability	0.957753
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1551744 117 - 23771897
UUCUGCUUCUUCCCGUGGAGAUGCUUCAACAUCAACGACUUCGAAGCAGCAACAACAAC-ACUGCACGGGAGCGAGAAGAAAAACCAAGA-AACUGCUG-GAAACAGUGAAAAUCGGUUA
((((.(((.((((((((.((.((((((...............))))))(......)...-.)).)))))))).))).)))).((((....-....((((-....))))(.....))))). ( -35.76)
>DroSec_CAF1 9452 117 - 1
UUCUGCUUCUUCCCGUGGAGAUGCUUCAACAUCAACGACUUCGAAGCAGCAACAACAAC-ACUGCACGGGAGCAAGAAGAAAAACCAAGA-AACUGCUG-GAAACAGUGAAAAUCGGUUA
((((.(((.((((((((.((.((((((...............))))))(......)...-.)).)))))))).))).)))).((((....-....((((-....))))(.....))))). ( -35.36)
>DroSim_CAF1 9571 117 - 1
UUCUGCUUCUUCCCGUGGAGAUGCUUCAACAUCAACGACUUCGAAGCAGCAACAACAAC-ACUGCACGGGAGCAAGAAGAAAAACCAAGA-AACUGCUG-GAAACAGUGAAAAUCGGUUA
((((.(((.((((((((.((.((((((...............))))))(......)...-.)).)))))))).))).)))).((((....-....((((-....))))(.....))))). ( -35.36)
>DroYak_CAF1 10284 117 - 1
UUCUGCUUCUUCUCGCGGAGAUGCUGCAACA---ACAACUGCGAAGCAGCAACAACAACGACUGCAAGGGAGAGAGAGGAAAAACAAAGAAAACUGCGGGGAAACAGUGAAAUUCAGUCA
..((((((((((((((((.....))))....---....((.(...(((((.........).))))...).)).))))))))......((....))))))(....)............... ( -24.70)
>consensus
UUCUGCUUCUUCCCGUGGAGAUGCUUCAACAUCAACGACUUCGAAGCAGCAACAACAAC_ACUGCACGGGAGCAAGAAGAAAAACCAAGA_AACUGCUG_GAAACAGUGAAAAUCGGUUA
((((.(((.((((((((.((.((((((...............))))))(......).....)).)))))))).))).)))).((((......((((........)))).......)))). (-26.68 = -27.30 +   0.62)

alignment

secondary structure

dotplot

Window 9

Location	1,551,782 – 1,551,882
Length	100
Sequences	4
Columns	101
Reading direction	forward
Mean pairwise identity	92.87
Mean single sequence MFE	-34.25
Consensus MFE	-29.23
Energy contribution	-29.23
Covariance contribution	-0.00
Combinations/Pair	1.16
Mean z-score	-1.82
Structure conservation index	0.85
SVM decision value	0.65
SVM RNA-class probability	0.811723
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1551782 100 + 23771897
UCUUCUCGCUCCCGUGCAGU-GUUGUUGUUGCUGCUUCGAAGUCGUUGAUGUUGAAGCAUCUCCACGGGAAGAAGCAGAAGCGAAACGAACGAAGAGGAGA
(((((((((......))..(-(((.(((((.(((((((....((((.(((((....)))))...))))...))))))).)))))))))......))))))) ( -34.60)
>DroSec_CAF1 9490 100 + 1
UCUUCUUGCUCCCGUGCAGU-GUUGUUGUUGCUGCUUCGAAGUCGUUGAUGUUGAAGCAUCUCCACGGGAAGAAGCAGAAGCGAAACGAACGAAGAGGAGA
(((((((((......))..(-(((.(((((.(((((((....((((.(((((....)))))...))))...))))))).)))))))))....))))))).. ( -32.50)
>DroSim_CAF1 9609 100 + 1
UCUUCUUGCUCCCGUGCAGU-GUUGUUGUUGCUGCUUCGAAGUCGUUGAUGUUGAAGCAUCUCCACGGGAAGAAGCAGAAGCGAAACGAACGAAGAGGAGA
(((((((((......))..(-(((.(((((.(((((((....((((.(((((....)))))...))))...))))))).)))))))))....))))))).. ( -32.50)
>DroYak_CAF1 10324 98 + 1
UCCUCUCUCUCCCUUGCAGUCGUUGUUGUUGCUGCUUCGCAGUUGU---UGUUGCAGCAUCUCCGCGAGAAGAAGCAGAAGCGAAACGAGCGAAGAGGAGA
...((((.(((..((((..(((((.(((((.(((((((...(((((---....))))).((((...)))).))))))).)))))))))))))).))))))) ( -37.40)
>consensus
UCUUCUCGCUCCCGUGCAGU_GUUGUUGUUGCUGCUUCGAAGUCGUUGAUGUUGAAGCAUCUCCACGGGAAGAAGCAGAAGCGAAACGAACGAAGAGGAGA
(((((((((......)).((.....(((((.(((((((....((((.(((((....)))))...))))...))))))).))))).....))...))))))) (-29.23 = -29.23 +  -0.00)

alignment

secondary structure

dotplot

Window 0

Location	1,551,782 – 1,551,882
Length	100
Sequences	4
Columns	101
Reading direction	reverse
Mean pairwise identity	92.87
Mean single sequence MFE	-27.80
Consensus MFE	-22.53
Energy contribution	-22.91
Covariance contribution	0.38
Combinations/Pair	1.08
Mean z-score	-1.53
Structure conservation index	0.81
SVM decision value	-0.04
SVM RNA-class probability	0.510804
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1551782 100 - 23771897
UCUCCUCUUCGUUCGUUUCGCUUCUGCUUCUUCCCGUGGAGAUGCUUCAACAUCAACGACUUCGAAGCAGCAACAACAAC-ACUGCACGGGAGCGAGAAGA
.....(((((..((((...((....))....(((((((.((.((((((...............))))))(......)...-.)).)))))))))))))))) ( -27.96)
>DroSec_CAF1 9490 100 - 1
UCUCCUCUUCGUUCGUUUCGCUUCUGCUUCUUCCCGUGGAGAUGCUUCAACAUCAACGACUUCGAAGCAGCAACAACAAC-ACUGCACGGGAGCAAGAAGA
.....(((((.........((....))...((((((((.((.((((((...............))))))(......)...-.)).))))))))...))))) ( -26.16)
>DroSim_CAF1 9609 100 - 1
UCUCCUCUUCGUUCGUUUCGCUUCUGCUUCUUCCCGUGGAGAUGCUUCAACAUCAACGACUUCGAAGCAGCAACAACAAC-ACUGCACGGGAGCAAGAAGA
.....(((((.........((....))...((((((((.((.((((((...............))))))(......)...-.)).))))))))...))))) ( -26.16)
>DroYak_CAF1 10324 98 - 1
UCUCCUCUUCGCUCGUUUCGCUUCUGCUUCUUCUCGCGGAGAUGCUGCAACA---ACAACUGCGAAGCAGCAACAACAACGACUGCAAGGGAGAGAGAGGA
((((((((((.((.((.(((.((((((........)))))).((((((..(.---........)..)))))).......)))..)).)))))))).)))). ( -30.90)
>consensus
UCUCCUCUUCGUUCGUUUCGCUUCUGCUUCUUCCCGUGGAGAUGCUUCAACAUCAACGACUUCGAAGCAGCAACAACAAC_ACUGCACGGGAGCAAGAAGA
.....(((((.........((....))...((((((((.((.((((((...............))))))(......).....)).))))))))...))))) (-22.53 = -22.91 +   0.38)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:44:18 2006