Locus 325

Sequence ID	2R_DroMel_CAF1
Location	2,130,898 – 2,131,026
Length	128
Max. P	0.871804

overview

Window 2

Location	2,130,898 – 2,131,014
Length	116
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	74.58
Mean single sequence MFE	-46.10
Consensus MFE	-26.34
Energy contribution	-27.52
Covariance contribution	1.17
Combinations/Pair	1.41
Mean z-score	-1.77
Structure conservation index	0.57
SVM decision value	0.87
SVM RNA-class probability	0.871804
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2130898 116 - 20766785
GUCACUUUGGGUGGUUUUCGCGGAUGCUUACGCCGCUGUUGCAUCUGCAGCUUGGCGAUGCUAAGUACCUGCUGAUAGCUGGACACCGUCUCACAACUCGCACUGCGCGAACUA-CU---
.........((((((((.(((((.(((...(((((..(((((....))))).))))).......((.((.((.....)).))))...............)))))))).))))))-))--- ( -40.60)
>DroPse_CAF1 125818 115 - 1
----UCUUGGGCGGUUUGCGGGGGUGCUUGCGACGCUGCUGCAUCUGCAGUUUGGCAAUGCUGAGCACCUGCUGGUAGCUGGACACGGUCCCACUGCUGGCAGUCCUCGAGCUGACC-GU
----.....(((((((((.(((((((((((((..((((((((....)))))..)))..))).))))))))((..((((..((((...))))..))))..))...)).))))))).))-.. ( -55.00)
>DroGri_CAF1 227688 110 - 1
UUUGCUUUGGGCGGUUUUCUUGGAUGUUUGCGUCGCUGUUGCAUUUGCAGCUUGGCAAUGCUGAGCACCUGCUGAUAGCUGGACACGGUGCCGCUGCUUGAAC---------UA-AUUGU
.(((.((..((((((..............((((.((((((((....)))))..))).)))).(.(((((((((.......)).)).))))))))))))..)).---------))-).... ( -33.50)
>DroWil_CAF1 154322 119 - 1
CUAAUCUUGGGCGGUUUACGCGGAUGUUUACGCCUCUGCUGCAUUUGCAGUUUGGCUAUGGUCAGCACCUGUUGGUAGCUCGAAACGGUUUCAUUGCUGGCACUGCGUGAACUG-AUGCU
...........((((((((((((........(((...(((((....)))))..)))....(((((((((....))).....(((.....)))...)))))).))))))))))))-..... ( -44.40)
>DroAna_CAF1 114318 113 - 1
ACCGUUUUGGGUGGCUUGCGGGGGUGCUUGCGGCGUUGCUGCAUCUGCAGUUUGGCGAUGCUGAGCACCUGUUGGUAGCUGGACACAGUUUCGCAGCUGGCGCUGCGCGAACU-------
...((.((.(((.(((.((..(((((((((((.(((((((((....)))))..)))).))).)))))))))).))).))).)).))(((((((((((....)))))).)))))------- ( -48.10)
>DroPer_CAF1 124852 115 - 1
----UCUUGGGCGGUUUGCGGGGGUGCUUGCGACGCUGCUGCAUCUGCAGUUUGGCAAUGCUGAGCACCUGCUGGUAGCUGGACACGGUCCCACUGCUGGCAGUCCUCGAGCUGACC-GU
----.....(((((((((.(((((((((((((..((((((((....)))))..)))..))).))))))))((..((((..((((...))))..))))..))...)).))))))).))-.. ( -55.00)
>consensus
_U__UCUUGGGCGGUUUGCGGGGAUGCUUGCGACGCUGCUGCAUCUGCAGUUUGGCAAUGCUGAGCACCUGCUGGUAGCUGGACACGGUCCCACUGCUGGCACUGCGCGAACUG_CU_GU
...........(((((((.((((.((((((((..((((((((....)))))..)))..))).)))))))(((((((((.(((........))))))))))))..)).)))))))...... (-26.34 = -27.52 +   1.17)

alignment

secondary structure

dotplot

Window 3

Location	2,130,934 – 2,131,026
Length	92
Sequences	6
Columns	102
Reading direction	reverse
Mean pairwise identity	75.25
Mean single sequence MFE	-31.42
Consensus MFE	-22.32
Energy contribution	-21.02
Covariance contribution	-1.30
Combinations/Pair	1.42
Mean z-score	-1.03
Structure conservation index	0.71
SVM decision value	0.35
SVM RNA-class probability	0.702115
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2130934 92 - 20766785
CUCGC----------CGGCGGUGUCACUUUGGGUGGUUUUCGCGGAUGCUUACGCCGCUGUUGCAUCUGCAGCUUGGCGAUGCUAAGUACCUGCUGAUAGCU
.((((----------((((((((((((.....)))......((....))..))))))))(((((....)))))..))))).(((((((....)))..)))). ( -33.80)
>DroPse_CAF1 125857 76 - 1
--------------------------UCUUGGGCGGUUUGCGGGGGUGCUUGCGACGCUGCUGCAUCUGCAGUUUGGCAAUGCUGAGCACCUGCUGGUAGCU
--------------------------.....(((..(..((..(((((((((((..((((((((....)))))..)))..))).))))))))))..)..))) ( -29.40)
>DroEre_CAF1 108429 92 - 1
CUCGC----------CGGCGGUGUCAUUUUGGGUGGUUUUCGCGGAUGCUUACGCCGCUGUUGCAUCUGCAGCUUGGCGAUGCUAAGUACCUGCUGAUAGCU
.((((----------((((((((((((((...(((.....))))))))...))))))))(((((....)))))..))))).(((((((....)))..)))). ( -33.40)
>DroWil_CAF1 154361 102 - 1
CUGGUGAGGAUUGUUAGGUGGCCUAAUCUUGGGCGGUUUACGCGGAUGUUUACGCCUCUGCUGCAUUUGCAGUUUGGCUAUGGUCAGCACCUGUUGGUAGCU
...(((((.(((((((..(.(((((....))))).)..)).)).))).)))))(((...(((((....)))))..))).......((((((....))).))) ( -32.80)
>DroYak_CAF1 110810 92 - 1
CUCGC----------GGGCGGUGUCAUUUUGGGUGGUUUUCGCGGAUGCUUACGCCGCUGUUGCAUCUGCAGCUUGGCAAUGCUAAGUACCUGCUGAUAGCU
...((----------...((((........((((.......((((((((..(((....))).)))))))).(((((((...)))))))))))))))...)). ( -29.70)
>DroPer_CAF1 124891 76 - 1
--------------------------UCUUGGGCGGUUUGCGGGGGUGCUUGCGACGCUGCUGCAUCUGCAGUUUGGCAAUGCUGAGCACCUGCUGGUAGCU
--------------------------.....(((..(..((..(((((((((((..((((((((....)))))..)))..))).))))))))))..)..))) ( -29.40)
>consensus
CUCGC___________GGCGGUGUCAUCUUGGGCGGUUUUCGCGGAUGCUUACGCCGCUGCUGCAUCUGCAGCUUGGCAAUGCUAAGCACCUGCUGAUAGCU
.............................(.(((((.....((((((((..(((....))).)))))))).(((((((...)))))))..))))).)..... (-22.32 = -21.02 +  -1.30)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:35:36 2006