Locus 6090

Sequence ID	2R_DroMel_CAF1
Location	19,160,622 – 19,160,712
Length	90
Max. P	0.704406

overview

Window 7

Location	19,160,622 – 19,160,712
Length	90
Sequences	6
Columns	96
Reading direction	forward
Mean pairwise identity	80.09
Mean single sequence MFE	-27.40
Consensus MFE	-16.23
Energy contribution	-15.40
Covariance contribution	-0.83
Combinations/Pair	1.35
Mean z-score	-1.81
Structure conservation index	0.59
SVM decision value	0.26
SVM RNA-class probability	0.657553
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19160622 90 + 20766785
------ACCAUCAGACCCACCAUCUGGACAAGUCCGACGACUCGGCCAUUGAGAACUCACCCACCACGUCGACCACCACCGGUGGGUCGGUGGGUC
------.......((((((((....(((....)))((((((..((....(((....)))....))..)))..(((((...)))))))))))))))) ( -35.70)
>DroPse_CAF1 54852 93 + 1
AUCACCACCACCAGAGCCAUCAGCUGGACAAGUCGGAUGACUCGGCCAUCGAAAACUCGCCCAGCACAUCCACCACCACCGC---CUCGGUGGGGC
...............(((....(((((....(((((.....)))))...(((....))).)))))..........((((((.---..))))))))) ( -27.00)
>DroSim_CAF1 45418 92 + 1
----CCACCACCAGACCCACCAUCUGGACAAGUCCGACGACUCGGCCAUUGAGAACUCACCCACCACAUCGACCACCACCGGUGGGUCGGUGGGUC
----...(((((.((((((((...((((....)))).(((...((....(((....)))....))...))).........)))))))))))))... ( -35.00)
>DroWil_CAF1 70369 84 + 1
------AUCAUCAAA---AUCAUUUGGACAAGUCAGAUGACUCGGCCAUUGAGAAUUCGCCAAGCACAUCAACCACCACAGC---AUCGGGGGGCC
------.........---.((((((((.....))))))))...((((.((((......((...))...))))((.((.....---...)))))))) ( -17.20)
>DroAna_CAF1 53575 93 + 1
AUCACCAUCAUCAGAACCACCAGCUGGACAAGUCGGAUGACUCGGCCAUCGAGAACUCGCCCAGCACAUCGAACACCACUGCU---UCAGUGGGAC
......................(((((.(.((((.((((.......))))..).))).).)))))..........((((((..---.))))))... ( -22.50)
>DroPer_CAF1 54867 93 + 1
AUCACCACCACCAGAGCCAUCAGCUGGACAAGUCGGAUGACUCGGCCAUCGAAAACUCGCCCAGCACAUCCACCACCACCGC---CUCGGUGGGGC
...............(((....(((((....(((((.....)))))...(((....))).)))))..........((((((.---..))))))))) ( -27.00)
>consensus
____CCACCACCAGACCCACCAGCUGGACAAGUCGGAUGACUCGGCCAUCGAGAACUCGCCCAGCACAUCGACCACCACCGC___CUCGGUGGGGC
..........((((.........)))).......(((((....((....(((....))))).....)))))....((((((......))))))... (-16.23 = -15.40 +  -0.83)

alignment

secondary structure

dotplot

Window 8

Location	19,160,622 – 19,160,712
Length	90
Sequences	6
Columns	96
Reading direction	reverse
Mean pairwise identity	80.09
Mean single sequence MFE	-38.35
Consensus MFE	-21.87
Energy contribution	-21.57
Covariance contribution	-0.30
Combinations/Pair	1.26
Mean z-score	-2.00
Structure conservation index	0.57
SVM decision value	0.36
SVM RNA-class probability	0.704406
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19160622 90 - 20766785
GACCCACCGACCCACCGGUGGUGGUCGACGUGGUGGGUGAGUUCUCAAUGGCCGAGUCGUCGGACUUGUCCAGAUGGUGGGUCUGAUGGU------
(((((((((((((((((((.(....).)).))))))))..........(((.((((((....)))))).)))..))))))))).......------ ( -44.20)
>DroPse_CAF1 54852 93 - 1
GCCCCACCGAG---GCGGUGGUGGUGGAUGUGCUGGGCGAGUUUUCGAUGGCCGAGUCAUCCGACUUGUCCAGCUGAUGGCUCUGGUGGUGGUGAU
(((((((((..---((.((.(..........((((((((((((...((((((...)))))).))))))))))))).)).))..)))))).)))... ( -43.10)
>DroSim_CAF1 45418 92 - 1
GACCCACCGACCCACCGGUGGUGGUCGAUGUGGUGGGUGAGUUCUCAAUGGCCGAGUCGUCGGACUUGUCCAGAUGGUGGGUCUGGUGGUGG----
..(((((((((((((((.(((.((((((((((((.(.(((....))).).))))...)))).))))...)))..))))))))).))))).).---- ( -44.90)
>DroWil_CAF1 70369 84 - 1
GGCCCCCCGAU---GCUGUGGUGGUUGAUGUGCUUGGCGAAUUCUCAAUGGCCGAGUCAUCUGACUUGUCCAAAUGAU---UUUGAUGAU------
.......(((.---.(..(((.((((((((.(((((((.(........).))))))))))).))))...)))...)..---.))).....------ ( -21.30)
>DroAna_CAF1 53575 93 - 1
GUCCCACUGA---AGCAGUGGUGUUCGAUGUGCUGGGCGAGUUCUCGAUGGCCGAGUCAUCCGACUUGUCCAGCUGGUGGUUCUGAUGAUGGUGAU
(((((((((.---..)))))).(..(.((..((((((((((((...((((((...)))))).))))))))))))..)).)..).)))......... ( -33.50)
>DroPer_CAF1 54867 93 - 1
GCCCCACCGAG---GCGGUGGUGGUGGAUGUGCUGGGCGAGUUUUCGAUGGCCGAGUCAUCCGACUUGUCCAGCUGAUGGCUCUGGUGGUGGUGAU
(((((((((..---((.((.(..........((((((((((((...((((((...)))))).))))))))))))).)).))..)))))).)))... ( -43.10)
>consensus
GACCCACCGAC___GCGGUGGUGGUCGAUGUGCUGGGCGAGUUCUCAAUGGCCGAGUCAUCCGACUUGUCCAGAUGAUGGCUCUGAUGGUGG____
..(((((((......)))))).).((((((.(((.(((.(........).))).))))))))).......(((.........)))........... (-21.87 = -21.57 +  -0.30)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:02:34 2006