Locus 6423

Sequence ID	3L_DroMel_CAF1
Location	17,213,307 – 17,213,459
Length	152
Max. P	0.519672

overview

Window 4

Location	17,213,307 – 17,213,424
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.87
Mean single sequence MFE	-38.18
Consensus MFE	-32.04
Energy contribution	-32.28
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-1.27
Structure conservation index	0.84
SVM decision value	-0.03
SVM RNA-class probability	0.519672
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17213307 117 - 23771897
GUUAGUCAAAUGACAGAG---GGCCUCGAGGCGCAUAUGCAAAAUGAAAACUUUGCUCCUGCCGCAGGCCACUCAGCCAACUGCAGAUGUAAGACCAAUGUGUCGUAUGCGCAACGUGGA
....(((....)))....---..((.((..(((((((((((...((.....(((((..((((.(..(((......)))..).))))..)))))..))...)).)))))))))..)).)). ( -36.70)
>DroSec_CAF1 97011 120 - 1
GGUAGUCAAACGACAGAGGAGAGCCGCGAGGCGCAUAUGCAAAAUGAAAACUUUGCUGCUGCCGCAGGCCACUCAGCCAACUGCAGAUGUGAGUCCAAUGUGUCGUAUGCGCAACGUGGA
....(((....))).........(((((..(((((((((((....((..((((((((((....)))(((......)))....))))).))...)).....)).)))))))))..))))). ( -40.30)
>DroSim_CAF1 89489 120 - 1
GGUAGUCAAACGACAGAGGAGGGCCUCGAGGCGCAUAUGCAAAAUGAAAACUUUGCUGCUGCCGCAGGCCACUCAGCCAACUGCAGAUGUGAGUCCAAUGUGUCGUAUGCGCAACGUGGA
(((.(((....))).(((...(((((.(.((((((...(((((.(....).)))))))).))).)))))).))).)))...............((((.(((((.....)))))...)))) ( -39.60)
>DroEre_CAF1 100384 117 - 1
GGUAGUCAAAUGACAGAG---GGCCUCGAGGCGCAUAUGCAAAAUGAAAACUUUGCUGCUGCCGCAGGCCACUCAGCCAACUGCAGAUCCGAGACCAAUGUGUCGUAUGCGCAACGUAGA
(((.(((....))).(((---(((((.(.((((((...(((((.(....).)))))))).))).)))))).))).)))....(((....(((.((....)).)))..))).......... ( -39.70)
>DroYak_CAF1 102563 117 - 1
GGUAGUCAAAUGACAGAG---GGCCUCGAGGCGCAUAUGCAAAAUGAAAACUUUCCUGCUGCCGCAGGCCACUCAGCCAACUGCAGAUUCGAGACCAAUGUGUCGUAUGCGCAACGUAGA
(((.(((....))).(((---(((((((.(((((....)).....(((....)))..)))..)).))))).))).)))....(((....(((.((....)).)))..))).......... ( -34.60)
>consensus
GGUAGUCAAAUGACAGAG___GGCCUCGAGGCGCAUAUGCAAAAUGAAAACUUUGCUGCUGCCGCAGGCCACUCAGCCAACUGCAGAUGUGAGACCAAUGUGUCGUAUGCGCAACGUGGA
....(((....))).........((.((..(((((((((((...((....(((.....((((.(..(((......)))..).))))....)))..))...)).)))))))))..)).)). (-32.04 = -32.28 +   0.24)

alignment

secondary structure

dotplot

Window 5

Location	17,213,347 – 17,213,459
Length	112
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.51
Mean single sequence MFE	-35.68
Consensus MFE	-26.42
Energy contribution	-27.62
Covariance contribution	1.20
Combinations/Pair	1.00
Mean z-score	-1.54
Structure conservation index	0.74
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17213347 112 - 23771897
AACGUGGAUUAAGACCC-----CCCCCGUUCCCAGUUUUGGUUAGUCAAAUGACAGAG---GGCCUCGAGGCGCAUAUGCAAAAUGAAAACUUUGCUCCUGCCGCAGGCCACUCAGCCAA
((((.((..........-----.)).)))).......((((((.(((....))).(((---(((((.(.((((.....(((((.(....).)))))...)))).)))))).))))))))) ( -34.60)
>DroSec_CAF1 97051 120 - 1
AACGUGGAUUAAGACCCCACCCCCCUCGUUCCCAGUUUUGGGUAGUCAAACGACAGAGGAGAGCCGCGAGGCGCAUAUGCAAAAUGAAAACUUUGCUGCUGCCGCAGGCCACUCAGCCAA
...((((................((((...(((......)))..(((....))).))))...(((....)))(((...(((((.(....).))))))))..)))).(((......))).. ( -36.20)
>DroSim_CAF1 89529 120 - 1
AACGUGGAUUAAGACCCCAACCCCCUCGUUCCCAGUUUUGGGUAGUCAAACGACAGAGGAGGGCCUCGAGGCGCAUAUGCAAAAUGAAAACUUUGCUGCUGCCGCAGGCCACUCAGCCAA
...((((.............(((((((...(((......)))..(((....))).)))).)))(((.(.((((((...(((((.(....).)))))))).))).))))))))........ ( -38.40)
>DroEre_CAF1 100424 108 - 1
AACGUGGAUUAAAACCC--------CCGAUCCCAGUU-UGGGUAGUCAAAUGACAGAG---GGCCUCGAGGCGCAUAUGCAAAAUGAAAACUUUGCUGCUGCCGCAGGCCACUCAGCCAA
....(((.........(--------((((.......)-))))..(((....))).(((---(((((.(.((((((...(((((.(....).)))))))).))).)))))).)))..))). ( -36.70)
>DroYak_CAF1 102603 108 - 1
AACGUGGAUUAAAACC---------CCGAUCCGAGUUUUGGGUAGUCAAAUGACAGAG---GGCCUCGAGGCGCAUAUGCAAAAUGAAAACUUUCCUGCUGCCGCAGGCCACUCAGCCAA
(((.((((((......---------..)))))).)))...(((.(((....))).(((---(((((((.(((((....)).....(((....)))..)))..)).))))).))).))).. ( -32.50)
>consensus
AACGUGGAUUAAGACCC_____CCCCCGUUCCCAGUUUUGGGUAGUCAAAUGACAGAG___GGCCUCGAGGCGCAUAUGCAAAAUGAAAACUUUGCUGCUGCCGCAGGCCACUCAGCCAA
....(((.......................(((......)))..(((....))).(((...(((((...((((((...(((((.(....).)))))))).)))..))))).)))..))). (-26.42 = -27.62 +   1.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:18:03 2006