Locus 4903

Sequence ID	3R_DroMel_CAF1
Location	12,883,643 – 12,883,752
Length	109
Max. P	0.881414

overview

Window 5

Location	12,883,643 – 12,883,752
Length	109
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	66.42
Mean single sequence MFE	-30.33
Consensus MFE	-11.22
Energy contribution	-15.78
Covariance contribution	4.56
Combinations/Pair	1.05
Mean z-score	-1.73
Structure conservation index	0.37
SVM decision value	0.19
SVM RNA-class probability	0.627660
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12883643 109 + 27905053
GUUCGAUAGCCUGCGGGAUGGACUGCUCCAGCUCAAACUCCAGCUCCUGUGGCCAGAGUUUGAGUCUGAG------UCAGGGGCAAGGCCACAACAACAACAACAGCCAUCCGUA
...............((((((.((((((..((((((((((..(((.....)))..))))))))))..)))------.))).(((...)))................))))))... ( -38.20)
>DroPse_CAF1 92 85 + 1
AUUCGAUUCCCUACGCGACAGACUGCUGCGGCCCC------------UACUGCCAGAACA----------------ACAGCGGCA--GCCCCAACGCCAACAACUGCCGCCUCCC
..............(((.(((.((((((((((...------------....))).(....----------------.).))))))--).......(....)..))).)))..... ( -18.90)
>DroSec_CAF1 1400 109 + 1
GUUCGAUAGCCUGCGGGAUGGACUGCUCCAGCUCAAACUCCAGCUCCUGUGGCCAGAGUUUGAGUCUGAG------UCAGGGGCAAAGCCACAACAACAACAACAGCCAUCCGUA
...............((((((.((((((..((((((((((..(((.....)))..))))))))))..)))------.))).(((...)))................))))))... ( -38.20)
>DroSim_CAF1 1 92 + 1
-----------------AUGGACUGCUCCAGCUCAAACUCCAGCUCCUGUGGCCAGAGUUUGAGUCUGAG------UCAGGGGCAAAGCCACAACAACAACAACAGCCAUCCGUA
-----------------(((((((((((..((((((((((..(((.....)))..))))))))))..)))------.))).(((...)))...................))))). ( -32.00)
>DroYak_CAF1 1507 115 + 1
GUUCAAUGUCCUGCGCGAUGGACUGCUCCAGCUCAAACUCCAGCUCCUGUGGCCAGAGUUUGAGUCUGAGUCAGAGUCAGGGGCAAAACCACAACAACAACAACAGCCAUCCGUA
...........((((.(((((.((((((..((((((((((..(((.....)))..))))))))))..))).))).((...((......))...))...........))))))))) ( -38.10)
>DroPer_CAF1 192 85 + 1
AUUCGAUUCCCUACGCGACAGACUGCUGCGGCCCU------------UACUGCCAGAACA----------------ACAGCGGCA--GCCCCAACGCCAACAACUCCCGCCUCCC
..............(((...(.((((((((((...------------....))).(....----------------.).))))))--).)....))).................. ( -16.60)
>consensus
GUUCGAUACCCUGCGCGAUGGACUGCUCCAGCUCAAACUCCAGCUCCUGUGGCCAGAGUUUGAGUCUGAG______UCAGGGGCAAAGCCACAACAACAACAACAGCCAUCCGUA
..................(((..((((((.((((((((((..(((.....)))..))))))))))..............))))))...)))........................ (-11.22 = -15.78 +   4.56)

alignment

secondary structure

dotplot

Window 6

Location	12,883,643 – 12,883,752
Length	109
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	66.42
Mean single sequence MFE	-37.93
Consensus MFE	-18.99
Energy contribution	-23.97
Covariance contribution	4.97
Combinations/Pair	1.13
Mean z-score	-1.69
Structure conservation index	0.50
SVM decision value	0.92
SVM RNA-class probability	0.881414
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12883643 109 - 27905053
UACGGAUGGCUGUUGUUGUUGUUGUGGCCUUGCCCCUGA------CUCAGACUCAAACUCUGGCCACAGGAGCUGGAGUUUGAGCUGGAGCAGUCCAUCCCGCAGGCUAUCGAAC
...(((((((((((......((((.(((...))).).))------)((((.(((((((((..(((....).))..)))))))))))))))))).))))))............... ( -42.70)
>DroPse_CAF1 92 85 - 1
GGGAGGCGGCAGUUGUUGGCGUUGGGGC--UGCCGCUGU----------------UGUUCUGGCAGUA------------GGGGCCGCAGCAGUCUGUCGCGUAGGGAAUCGAAU
.....(((((((..(....)((((.(((--(.(..((((----------------(.....)))))..------------).)))).))))...))))))).............. ( -33.00)
>DroSec_CAF1 1400 109 - 1
UACGGAUGGCUGUUGUUGUUGUUGUGGCUUUGCCCCUGA------CUCAGACUCAAACUCUGGCCACAGGAGCUGGAGUUUGAGCUGGAGCAGUCCAUCCCGCAGGCUAUCGAAC
...(((((((((((......((((.(((...))).).))------)((((.(((((((((..(((....).))..)))))))))))))))))).))))))............... ( -42.70)
>DroSim_CAF1 1 92 - 1
UACGGAUGGCUGUUGUUGUUGUUGUGGCUUUGCCCCUGA------CUCAGACUCAAACUCUGGCCACAGGAGCUGGAGUUUGAGCUGGAGCAGUCCAU-----------------
...(((.(((....((..(....)..))...))).(((.------.((((.(((((((((..(((....).))..)))))))))))))..))))))..----------------- ( -37.60)
>DroYak_CAF1 1507 115 - 1
UACGGAUGGCUGUUGUUGUUGUUGUGGUUUUGCCCCUGACUCUGACUCAGACUCAAACUCUGGCCACAGGAGCUGGAGUUUGAGCUGGAGCAGUCCAUCGCGCAGGACAUUGAAC
..((((((((((((((((..((((.((......)).))))..))))((((.(((((((((..(((....).))..)))))))))))))))))).))))).))............. ( -42.80)
>DroPer_CAF1 192 85 - 1
GGGAGGCGGGAGUUGUUGGCGUUGGGGC--UGCCGCUGU----------------UGUUCUGGCAGUA------------AGGGCCGCAGCAGUCUGUCGCGUAGGGAAUCGAAU
....((((((.(((((.(((.((...((--(((((....----------------.....))))))).------------)).))))))))..))))))................ ( -28.80)
>consensus
UACGGAUGGCUGUUGUUGUUGUUGUGGCUUUGCCCCUGA______CUCAGACUCAAACUCUGGCCACAGGAGCUGGAGUUUGAGCUGGAGCAGUCCAUCGCGCAGGCAAUCGAAC
....((((((((((.........(.(((...))).)...........(((.(((((((((((((.......)))))))))))))))).))))).)))))................ (-18.99 = -23.97 +   4.97)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:41:39 2006