Locus 1993

Sequence ID	X_DroMel_CAF1
Location	5,475,930 – 5,476,030
Length	100
Max. P	0.628831

overview

Window 8

Location	5,475,930 – 5,476,030
Length	100
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	74.42
Mean single sequence MFE	-48.27
Consensus MFE	-26.00
Energy contribution	-27.87
Covariance contribution	1.86
Combinations/Pair	1.17
Mean z-score	-1.60
Structure conservation index	0.54
SVM decision value	0.20
SVM RNA-class probability	0.628831
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5475930 100 + 22224390
----------CGGAUGUGGGCGUG---GCAGCGG---AAGCGGAACCGAACCCAUCGACUGGCGCCAGGCUCGGCGGCGCAGCGCUAGAGAGGAUGCGCUGCAGGCCGCCGAAGGG
----------.......((((.((---((.((..---..))((........))..........)))).))))(((((((((((((..........)))))))..))))))...... ( -49.30)
>DroVir_CAF1 9251 101 + 1
GCGG------------UGCCCUCGGCAGCAGCGGGCAACGUUGAGCCGGCCACAUCGACAGGCGUCAGGCUC---GGAGCAGCGCUUGAGAGGAUGCGCUCCAGGCUAUUGAAGGG
....------------..((((((((..(((((.....))))).))))(((.........))).((((((..---(((((.(((..(....)..))))))))..)))..))))))) ( -39.10)
>DroSec_CAF1 1290 100 + 1
----------CGGAUGUGGGCGUG---GCAGCGG---AAGCGGAACCGAACCCAUCGACUGGCGCCAGGCUCGGCGGCGCAGCGCUGGAAAGGAUGCGCUGUAGGCCGCCGAAGGG
----------.......((((.((---((.((..---..))((........))..........)))).))))(((((((((((((..........)))))))..))))))...... ( -47.90)
>DroEre_CAF1 10031 106 + 1
----CGGUGCCGGAUGUGGGCGUG---GCAGCGG---AAGCAGAACCGAACCCAUCGACUGGCGCCAGACUCGGCGGCGCAGCGCUGGAAAGGAUGCGCUGCAGGCCGCCGAAGGG
----.((((((((.((((((..((---(..((..---..))....)))..)))).)).))))))))....(((((((((((((((..........)))))))..)))))))).... ( -61.40)
>DroYak_CAF1 1727 96 + 1
----CA----------CUGGCGUG---GCAGCGG---AAGCGGAACCGAACCCAUCGACUGGCGCCAGGCUCGGCGGCGCAGCGCUGGAGAGGAUGCGCUGCAGGCCGCCGAAGGG
----..----------(((((((.---...((..---..))((........))........)))))))..(((((((((((((((..........)))))))..)))))))).... ( -50.20)
>DroPer_CAF1 1668 98 + 1
----CAGUGGCAGCAGCGGGCAAC---GCCGAGG---AGGCGGA-----CCCCAUCGACUGGCGUCAGACUCGG---GGCAGCGCUGGAUAGGAGUCGCUGGAGGCCGCUGAAGGG
----(((((((..(((((((...(---(((....---.))))..-----.)))...(((....))).(((((.(---..((....))..)..)))))))))...)))))))..... ( -41.70)
>consensus
__________CGGAUGUGGGCGUG___GCAGCGG___AAGCGGAACCGAACCCAUCGACUGGCGCCAGGCUCGGCGGCGCAGCGCUGGAGAGGAUGCGCUGCAGGCCGCCGAAGGG
..............................((.......)).........(((.....(((....)))..(((((((((((((((..........)))))))..)))))))).))) (-26.00 = -27.87 +   1.86)

alignment

secondary structure

dotplot

Window 9

Location	5,475,930 – 5,476,030
Length	100
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	74.42
Mean single sequence MFE	-42.75
Consensus MFE	-24.14
Energy contribution	-26.42
Covariance contribution	2.28
Combinations/Pair	1.04
Mean z-score	-1.43
Structure conservation index	0.56
SVM decision value	-0.00
SVM RNA-class probability	0.531504
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5475930 100 - 22224390
CCCUUCGGCGGCCUGCAGCGCAUCCUCUCUAGCGCUGCGCCGCCGAGCCUGGCGCCAGUCGAUGGGUUCGGUUCCGCUU---CCGCUGC---CACGCCCACAUCCG----------
....((((((((..(((((((..........)))))))))))))))(.(((....))).)(.(((((..(((..((...---.))..))---)..)))))).....---------- ( -44.60)
>DroVir_CAF1 9251 101 - 1
CCCUUCAAUAGCCUGGAGCGCAUCCUCUCAAGCGCUGCUCC---GAGCCUGACGCCUGUCGAUGUGGCCGGCUCAACGUUGCCCGCUGCUGCCGAGGGCA------------CCGC
....(((...((.((((((((............)).)))))---).)).))).((((.(((..(..((.(((........))).))..)...))))))).------------.... ( -34.30)
>DroSec_CAF1 1290 100 - 1
CCCUUCGGCGGCCUACAGCGCAUCCUUUCCAGCGCUGCGCCGCCGAGCCUGGCGCCAGUCGAUGGGUUCGGUUCCGCUU---CCGCUGC---CACGCCCACAUCCG----------
....((((((((...((((((..........)))))).))))))))(.(((....))).)(.(((((..(((..((...---.))..))---)..)))))).....---------- ( -41.30)
>DroEre_CAF1 10031 106 - 1
CCCUUCGGCGGCCUGCAGCGCAUCCUUUCCAGCGCUGCGCCGCCGAGUCUGGCGCCAGUCGAUGGGUUCGGUUCUGCUU---CCGCUGC---CACGCCCACAUCCGGCACCG----
...(((((((((..(((((((..........))))))))))))))))...((.(((.(..(.(((((..(((...((..---..)).))---)..))))))..).))).)).---- ( -52.30)
>DroYak_CAF1 1727 96 - 1
CCCUUCGGCGGCCUGCAGCGCAUCCUCUCCAGCGCUGCGCCGCCGAGCCUGGCGCCAGUCGAUGGGUUCGGUUCCGCUU---CCGCUGC---CACGCCAG----------UG----
...(((((((((..(((((((..........)))))))))))))))).((((((.((((....(((..((....))..)---)))))).---..))))))----------..---- ( -48.10)
>DroPer_CAF1 1668 98 - 1
CCCUUCAGCGGCCUCCAGCGACUCCUAUCCAGCGCUGCC---CCGAGUCUGACGCCAGUCGAUGGGG-----UCCGCCU---CCUCGGC---GUUGCCCGCUGCUGCCACUG----
.....(((.(((...(((((.........((((((((..---..(((.(.(((.(((.....))).)-----)).).))---)..))))---))))..)))))..))).)))---- ( -35.90)
>consensus
CCCUUCGGCGGCCUGCAGCGCAUCCUCUCCAGCGCUGCGCCGCCGAGCCUGGCGCCAGUCGAUGGGUUCGGUUCCGCUU___CCGCUGC___CACGCCCACAUCCG__________
((((((((((((..(((((((..........))))))))))))))))..((((....))))..))).................................................. (-24.14 = -26.42 +   2.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:45 2006