Locus 2530

Sequence ID	X_DroMel_CAF1
Location	6,738,774 – 6,738,894
Length	120
Max. P	0.952317

overview

Window 0

Location	6,738,774 – 6,738,870
Length	96
Sequences	4
Columns	118
Reading direction	forward
Mean pairwise identity	73.69
Mean single sequence MFE	-37.45
Consensus MFE	-24.69
Energy contribution	-25.50
Covariance contribution	0.81
Combinations/Pair	1.04
Mean z-score	-1.46
Structure conservation index	0.66
SVM decision value	0.11
SVM RNA-class probability	0.589127
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6738774 96 + 22224390
CGAUCCGUGUCCAAC---------------------GGACUCCGG-ACUCCGGACUACCGACUCGCGACUCGCAGUUGCUCCCAGCUGAGCUGUCGUCAGCUCAGUCCGGUUGAGUGG
...(((((.....))---------------------))).(((((-...)))))...((.(((((((((.....))))).((..(((((((((....)))))))))..))..)))))) ( -40.90)
>DroSim_CAF1 27687 115 + 1
-GAUCC-UGUCCUACGGACUGCCGACUACGGACUACGGACUACGG-ACUACGGACUACCGACUCGCGACUCCCAGUUGCUCCCAGCUGAGCUGUCGUCAGCUCAGUCCGGUUGAGUGG
-..(((-.((((..(((....))).(....).....))))...))-)...(((....)))(((((((((.....))))).((..(((((((((....)))))))))..))..)))).. ( -42.10)
>DroEre_CAF1 28997 94 + 1
-GAGCC-U---------------------GGACUACCGACUACCG-ACUACCGACUACCCAGUCGCGACUGCCAGUUGCUCCCAGCUGAGCUGUCGUCAGCUCAGUCCGGCUGAGUGG
-.((((-.---------------------(((((.(.(((.....-.....(((((....))))).(((.((((((((....)))))).)).)))))).)...)))))))))...... ( -33.80)
>DroYak_CAF1 34882 90 + 1
-------C---------------------GGACUACGGAGUACCAAACUACCAACUACCGACCCGCGACUCCCAGUUGCUCCCAGCUGAGCUGUCGUCAGCUCAGUCGGUUUGAGUGG
-------.---------------------(((((....))).))...(((((((..((((((..(((((.....))))).......(((((((....)))))))))))))))).)))) ( -33.00)
>consensus
_GAUCC_U_____________________GGACUACGGACUACCG_ACUACCGACUACCGACUCGCGACUCCCAGUUGCUCCCAGCUGAGCUGUCGUCAGCUCAGUCCGGUUGAGUGG
......................................................(((((((((.(((((.....))))).....(((((((((....)))))))))..))))).)))) (-24.69 = -25.50 +   0.81)

alignment

secondary structure

dotplot

Window 1

Location	6,738,793 – 6,738,894
Length	101
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	75.71
Mean single sequence MFE	-36.56
Consensus MFE	-22.84
Energy contribution	-23.24
Covariance contribution	0.40
Combinations/Pair	1.18
Mean z-score	-2.02
Structure conservation index	0.62
SVM decision value	1.42
SVM RNA-class probability	0.952317
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6738793 101 + 22224390
UCCGG-ACUCCGGACUACCGACUCGCGACUCGCAGUUGCUCCCAGCUGAGCUGUCGUCAGCUCAG--UCCGGUUGAGUGGCAGGUCCUGCCCCC-----CAGUUCUC--GC
...((-(((..((.......(((((((((.....))))).((..(((((((((....))))))))--)..))..))))(((((...))))))).-----.)))))..--.. ( -39.70)
>DroSim_CAF1 27725 103 + 1
UACGG-ACUACGGACUACCGACUCGCGACUCCCAGUUGCUCCCAGCUGAGCUGUCGUCAGCUCAG--UCCGGUUGAGUGGCAGGUCCUGCCCCC-----CAGUCCCCCAGC
...((-(((.(((....)))(((((((((.....))))).((..(((((((((....))))))))--)..))..))))(((((...)))))...-----.)))))...... ( -42.60)
>DroEre_CAF1 29014 101 + 1
UACCG-ACUACCGACUACCCAGUCGCGACUGCCAGUUGCUCCCAGCUGAGCUGUCGUCAGCUCAG--UCCGGCUGAGUGGCAGGUCCUGCCCCC-----CAGUUCCC--GC
....(-((..((((((....))))).).((((((.(((((....(((((((((....))))))))--)..))).)).)))))))))(((.....-----))).....--.. ( -37.30)
>DroYak_CAF1 34894 102 + 1
UACCAAACUACCAACUACCGACCCGCGACUCCCAGUUGCUCCCAGCUGAGCUGUCGUCAGCUCAG--UCGGUUUGAGUGGCAGCUCCUGCCCCC-----CAAUUCCC--UC
................((((((..(((((.....))))).......(((((((....))))))))--)))))(((.(.(((((...))))).).-----))).....--.. ( -32.80)
>DroAna_CAF1 28918 88 + 1
--------------------AUUCGCCAGGCUGAGUU-CCCCCAGCUGAGCUGUCGUCAGUUUGGUGUCCAGUUGAGUGGCAGCUCCUGCCCCAGGACCUCCUUCUC--AC
--------------------...(((((((((((...-.(..((((...))))..))))))))))))......((((.((.((.(((((...))))).))))..)))--). ( -30.40)
>consensus
UACCG_ACUACCGACUACCGACUCGCGACUCCCAGUUGCUCCCAGCUGAGCUGUCGUCAGCUCAG__UCCGGUUGAGUGGCAGGUCCUGCCCCC_____CAGUUCCC__GC
....................(((((((((.....)))))......((((((((....)))))))).........))))(((((...))))).................... (-22.84 = -23.24 +   0.40)

alignment

secondary structure

dotplot

Window 2

Location	6,738,793 – 6,738,894
Length	101
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	75.71
Mean single sequence MFE	-43.00
Consensus MFE	-21.96
Energy contribution	-22.28
Covariance contribution	0.32
Combinations/Pair	1.20
Mean z-score	-2.08
Structure conservation index	0.51
SVM decision value	1.11
SVM RNA-class probability	0.916411
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6738793 101 - 22224390
GC--GAGAACUG-----GGGGGCAGGACCUGCCACUCAACCGGA--CUGAGCUGACGACAGCUCAGCUGGGAGCAACUGCGAGUCGCGAGUCGGUAGUCCGGAGU-CCGGA
..--.....(((-----((...(.((((.((((((((..((((.--((((((((....))))))))))))..((.((.....)).)))))).)))))))).)..)-)))). ( -45.50)
>DroSim_CAF1 27725 103 - 1
GCUGGGGGACUG-----GGGGGCAGGACCUGCCACUCAACCGGA--CUGAGCUGACGACAGCUCAGCUGGGAGCAACUGGGAGUCGCGAGUCGGUAGUCCGUAGU-CCGUA
.(..(....)..-----).((((.((((.((((((((..((((.--((((((((....))))))))))))..((.((.....)).)))))).))))))))...))-))... ( -50.80)
>DroEre_CAF1 29014 101 - 1
GC--GGGAACUG-----GGGGGCAGGACCUGCCACUCAGCCGGA--CUGAGCUGACGACAGCUCAGCUGGGAGCAACUGGCAGUCGCGACUGGGUAGUCGGUAGU-CGGUA
((--.....(((-----((.(((((...))))).)))))((((.--((((((((....))))))))))))..)).((((((...(.(((((....))))))..))-)))). ( -47.40)
>DroYak_CAF1 34894 102 - 1
GA--GGGAAUUG-----GGGGGCAGGAGCUGCCACUCAAACCGA--CUGAGCUGACGACAGCUCAGCUGGGAGCAACUGGGAGUCGCGGGUCGGUAGUUGGUAGUUUGGUA
..--.....(((-----((.(((((...))))).)))))(((((--((((.(((.((((..(((((.((....)).))))).))))))).))...)))))))......... ( -38.80)
>DroAna_CAF1 28918 88 - 1
GU--GAGAAGGAGGUCCUGGGGCAGGAGCUGCCACUCAACUGGACACCAAACUGACGACAGCUCAGCUGGGGG-AACUCAGCCUGGCGAAU--------------------
((--.((...(..((((.(((((((...))))).)).....))))..)...)).))....(((..((((((..-..))))))..)))....-------------------- ( -32.50)
>consensus
GC__GGGAACUG_____GGGGGCAGGACCUGCCACUCAACCGGA__CUGAGCUGACGACAGCUCAGCUGGGAGCAACUGGGAGUCGCGAGUCGGUAGUCCGUAGU_CCGUA
....(.((.((......((((((((...))))).)))..((((...((((((((....))))))))))))...........)))).)........................ (-21.96 = -22.28 +   0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:37:00 2006