Locus 933

Sequence ID	X_DroMel_CAF1
Location	2,603,709 – 2,603,816
Length	107
Max. P	0.764893

overview

Window 9

Location	2,603,709 – 2,603,799
Length	90
Sequences	6
Columns	94
Reading direction	forward
Mean pairwise identity	78.87
Mean single sequence MFE	-28.41
Consensus MFE	-15.89
Energy contribution	-17.39
Covariance contribution	1.50
Combinations/Pair	1.00
Mean z-score	-1.98
Structure conservation index	0.56
SVM decision value	0.51
SVM RNA-class probability	0.764893
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2603709 90 + 22224390
UCUU---CUUGUCGCAGCGGAUGCUUGGCAUUUAUUGCAGGCGACAAUAUUUUGCUUUGCCCUGCAUCCUCUCAGCGCCUUGGCCCAGC-CCAA
....---...(.(((((.((((((..((((........((((((.......))))))))))..)))))).))..))).)..(((...))-)... ( -25.20)
>DroVir_CAF1 15303 82 + 1
CCUUGUCGCUGGCGCAGCGGAUGCUUGGCAUUUAUUGCAAGCGACAAUAUUUCGCUG---GCUGCAUCAGC--A---A--UG-GAGCAGCAGG-
..((((((((...((((..(((((...)))))..)))).)))))))).......(((---.((((..((..--.---.--))-..))))))).- ( -34.50)
>DroSec_CAF1 11807 89 + 1
UCUU---CUUGUCGCAGCGGAUGCUUGGCAUUUAUUGCAGGCGACAAUAUUUUGCUUUGCCCUGCAUCCUCCCAGCGCCUUGGCCCAGC-CCA-
....---...(.(((.(.((((((..((((........((((((.......))))))))))..)))))).)...))).)..(((...))-)..- ( -23.70)
>DroEre_CAF1 12742 89 + 1
UCUU---CUUGUCGCAGCGGAUGCUUGGCAUUUAUUGCAGGCGACAAUAUUUUGCUUUGCCCUGCAUCCUCUCAGCGCCUUGGCAACGC-CCA-
....---.(((((((((..(((((...)))))..))))(((((.........(((........))).........))))).)))))...-...- ( -25.77)
>DroYak_CAF1 12106 89 + 1
UCUU---CUUGUCGCAGCGGAUGCUUGGCAUUUAUUGCAGGCGACAAUAUUUUGCUUUGCCCUGCAUCCUCUCAGCGCCUUAGCAACGC-CCA-
....---......((((.((((((..((((........((((((.......))))))))))..)))))).))..((......))...))-...- ( -24.00)
>DroMoj_CAF1 19762 85 + 1
CCUUGUCGCUGGCGCAGCGGAUGCUUGGCAUUUAUUGCAAGCGACAAUAUUUCGCUG---GCUGCAUCAGC--AUCGC--UG-GAGCAGCAGG-
..((((((((...((((..(((((...)))))..)))).)))))))).......(((---.((((..((((--...))--))-..))))))).- ( -37.30)
>consensus
UCUU___CUUGUCGCAGCGGAUGCUUGGCAUUUAUUGCAGGCGACAAUAUUUUGCUUUGCCCUGCAUCCUCUCAGCGCCUUGGCAACGC_CCA_
.............((((..(((((...)))))..))))(((((.........(((........))).........))))).............. (-15.89 = -17.39 +   1.50)

alignment

secondary structure

dotplot

Window 0

Location	2,603,724 – 2,603,816
Length	92
Sequences	5
Columns	93
Reading direction	forward
Mean pairwise identity	83.78
Mean single sequence MFE	-23.51
Consensus MFE	-19.20
Energy contribution	-19.20
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.47
Structure conservation index	0.82
SVM decision value	-0.04
SVM RNA-class probability	0.512456
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2603724 92 + 22224390
GGAUGCUUGGCAUUUAUUGCAGGCGACAAUAUUUUGCUUUGCCCUGCAUCCUCUCAGCGCCUUGGCCCAGC-CCAAACCACCUACCCCGCCCC
((((((..((((........((((((.......))))))))))..)))))).....(((....((......-........)).....)))... ( -21.34)
>DroSec_CAF1 11822 87 + 1
GGAUGCUUGGCAUUUAUUGCAGGCGACAAUAUUUUGCUUUGCCCUGCAUCCUCCCAGCGCCUUGGCCCAGC-CCA-----CCGCCCCGCCCCC
((((((..((((........((((((.......))))))))))..)))))).....(((....(((...))-)..-----.)))......... ( -24.30)
>DroEre_CAF1 12757 87 + 1
GGAUGCUUGGCAUUUAUUGCAGGCGACAAUAUUUUGCUUUGCCCUGCAUCCUCUCAGCGCCUUGGCAACGC-CCA-----CCGCCCCGCCCCU
((((((..((((........((((((.......))))))))))..)))))).....(((....(((.....-...-----..))).))).... ( -24.40)
>DroYak_CAF1 12121 87 + 1
GGAUGCUUGGCAUUUAUUGCAGGCGACAAUAUUUUGCUUUGCCCUGCAUCCUCUCAGCGCCUUAGCAACGC-CCA-----CCGCCCCGCCUUU
((((((..((((........((((((.......))))))))))..)))))).....((((....))...((-...-----..))...)).... ( -21.60)
>DroAna_CAF1 15518 77 + 1
GGAUGCUUGGCAUUUAUUGCAGGCGACAAUAUUUUGCUUUGCCCUGCAUCCU----------UGGGAGCACUCCC-----CCGCACCCUC-CC
((((((..((((........((((((.......))))))))))..)))))).----------.(((.((......-----..)).)))..-.. ( -25.90)
>consensus
GGAUGCUUGGCAUUUAUUGCAGGCGACAAUAUUUUGCUUUGCCCUGCAUCCUCUCAGCGCCUUGGCAACGC_CCA_____CCGCCCCGCCCCC
((((((..((((........((((((.......))))))))))..)))))).......................................... (-19.20 = -19.20 +  -0.00)

alignment

secondary structure

dotplot

Window 1

Location	2,603,724 – 2,603,816
Length	92
Sequences	5
Columns	93
Reading direction	reverse
Mean pairwise identity	83.78
Mean single sequence MFE	-30.70
Consensus MFE	-19.96
Energy contribution	-21.40
Covariance contribution	1.44
Combinations/Pair	1.20
Mean z-score	-1.93
Structure conservation index	0.65
SVM decision value	0.27
SVM RNA-class probability	0.660566
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2603724 92 - 22224390
GGGGCGGGGUAGGUGGUUUGG-GCUGGGCCAAGGCGCUGAGAGGAUGCAGGGCAAAGCAAAAUAUUGUCGCCUGCAAUAAAUGCCAAGCAUCC
..((((..((((((((.((..-(((..(((...(((((....)).)))..)))..)))..)).....))))))))......))))........ ( -32.90)
>DroSec_CAF1 11822 87 - 1
GGGGGCGGGGCGG-----UGG-GCUGGGCCAAGGCGCUGGGAGGAUGCAGGGCAAAGCAAAAUAUUGUCGCCUGCAAUAAAUGCCAAGCAUCC
((..((..((((.-----...-(((..(((...(((((....)).)))..)))..)))....((((((.....))))))..))))..))..)) ( -29.60)
>DroEre_CAF1 12757 87 - 1
AGGGGCGGGGCGG-----UGG-GCGUUGCCAAGGCGCUGAGAGGAUGCAGGGCAAAGCAAAAUAUUGUCGCCUGCAAUAAAUGCCAAGCAUCC
.(((((..(((((-----..(-((((((((...(((((....)).)))..))))).((((....))))))))..)......))))..)).))) ( -33.70)
>DroYak_CAF1 12121 87 - 1
AAAGGCGGGGCGG-----UGG-GCGUUGCUAAGGCGCUGAGAGGAUGCAGGGCAAAGCAAAAUAUUGUCGCCUGCAAUAAAUGCCAAGCAUCC
....((..(((((-----..(-((((((((...(((((....)).)))..))))).((((....))))))))..)......))))..)).... ( -30.20)
>DroAna_CAF1 15518 77 - 1
GG-GAGGGUGCGG-----GGGAGUGCUCCCA----------AGGAUGCAGGGCAAAGCAAAAUAUUGUCGCCUGCAAUAAAUGCCAAGCAUCC
..-..((((((((-----(((....))))).----------....((((((.(...((((....)))).)))))))...........)))))) ( -27.10)
>consensus
GGGGGCGGGGCGG_____UGG_GCGGUGCCAAGGCGCUGAGAGGAUGCAGGGCAAAGCAAAAUAUUGUCGCCUGCAAUAAAUGCCAAGCAUCC
...((((((((...........))))))))............((((((.((((...((((....)))).))))(((.....)))...)))))) (-19.96 = -21.40 +   1.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:57:34 2006