Locus 1797

Sequence ID	3L_DroMel_CAF1
Location	5,075,316 – 5,075,498
Length	182
Max. P	0.801430

overview

Window 0

Location	5,075,316 – 5,075,418
Length	102
Sequences	4
Columns	105
Reading direction	forward
Mean pairwise identity	93.30
Mean single sequence MFE	-28.40
Consensus MFE	-25.94
Energy contribution	-26.12
Covariance contribution	0.19
Combinations/Pair	1.04
Mean z-score	-1.63
Structure conservation index	0.91
SVM decision value	0.62
SVM RNA-class probability	0.801430
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5075316 102 + 23771897
AACACCGCAGAGCGGCGG---CGGCGGCGGCAACGGCAUCAACAGCAGUAAACAAGCUUCACAUGUGGCAUUUUAUUAAAGUUGAUGCAACUUAAAAUGCAUUUA
..(.((((......))))---.)(((.((....))((((((((...((((((...(((........)))..))))))...)))))))).........)))..... ( -29.00)
>DroSec_CAF1 281719 105 + 1
AACACCGCAGAGCGGCGGCAGCGGCGGCGGCAACGGCAUCAACAGCAGUAAACAAGCUUCACAUGUGGCAUUUUAUUAAAGUUGAUGCAACUUAAAAUGCAUUUA
....((((...((.((....)).)).)))).....((((((((...((((((...(((........)))..))))))...))))))))................. ( -30.30)
>DroSim_CAF1 303007 105 + 1
AACACCGCAGAGCGGCGGCAGCGGCGGCGGCAACGGCAUCAACAGCAGUAAACAAGCUUCACAUGUGGCAUUUUAUUAAAGUUGAUGCAACUUAAAAUGCAUUUA
....((((...((.((....)).)).)))).....((((((((...((((((...(((........)))..))))))...))))))))................. ( -30.30)
>DroEre_CAF1 288763 96 + 1
AACACCGCAGAGCGGCG---------GCAGCGGCGGCAUCAACAGCAGUAAACAAGCUUCACAUGUGGCAUUUUAUUAAAGUUGAUGCAACUUAAAAUGUAUUUA
..(.((((...((....---------)).)))).)((((((((...((((((...(((........)))..))))))...))))))))................. ( -24.00)
>consensus
AACACCGCAGAGCGGCGG___CGGCGGCGGCAACGGCAUCAACAGCAGUAAACAAGCUUCACAUGUGGCAUUUUAUUAAAGUUGAUGCAACUUAAAAUGCAUUUA
......(((..((.((.((....)).)).))....((((((((...((((((...(((........)))..))))))...)))))))).........)))..... (-25.94 = -26.12 +   0.19)

alignment

secondary structure

dotplot

Window 1

Location	5,075,338 – 5,075,458
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.17
Mean single sequence MFE	-30.68
Consensus MFE	-27.34
Energy contribution	-27.18
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-1.27
Structure conservation index	0.89
SVM decision value	0.07
SVM RNA-class probability	0.566956
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5075338 120 + 23771897
GGCGGCAACGGCAUCAACAGCAGUAAACAAGCUUCACAUGUGGCAUUUUAUUAAAGUUGAUGCAACUUAAAAUGCAUUUAAGCCAGAUCCCGGGCUCACAGCUCAAAGAACGUGGCGAAC
.(((....).((((((((...((((((...(((........)))..))))))...))))))))..........))......(((((.((..((((.....))))...)).).)))).... ( -30.60)
>DroSec_CAF1 281744 120 + 1
GGCGGCAACGGCAUCAACAGCAGUAAACAAGCUUCACAUGUGGCAUUUUAUUAAAGUUGAUGCAACUUAAAAUGCAUUUAAGCCAGAUCCCUGGCUCACAGCUCAAAGAACGUGGCGAAC
.((.((....((((((((...((((((...(((........)))..))))))...))))))))..(((.....((.....((((((....))))))....))...)))...)).)).... ( -32.00)
>DroSim_CAF1 303032 120 + 1
GGCGGCAACGGCAUCAACAGCAGUAAACAAGCUUCACAUGUGGCAUUUUAUUAAAGUUGAUGCAACUUAAAAUGCAUUUAAGCCAGAUCCCUGGCUCACAGCUCAAAGAACGUGGCGAAC
.((.((....((((((((...((((((...(((........)))..))))))...))))))))..(((.....((.....((((((....))))))....))...)))...)).)).... ( -32.00)
>DroEre_CAF1 288780 119 + 1
-GCAGCGGCGGCAUCAACAGCAGUAAACAAGCUUCACAUGUGGCAUUUUAUUAAAGUUGAUGCAACUUAAAAUGUAUUUAAGCCAGAUCCCGGGCUCACAGCUCAAAGAACGUGGCGAAC
-...((.(((((((((((...((((((...(((........)))..))))))...))))))))..((((((.....)))))).........((((.....))))......))).)).... ( -30.80)
>DroYak_CAF1 292833 120 + 1
GGCGGCAGCAGCAUCAACAGCAGUAAACAAGCUUCACAUGUGGCAUUUUAUUAAAGUUGAUGCAACUUAAAAUGCAUUUAAGCCAGAUCCCCGGCUCACAGCUCAAAGAACGUGGCGAAC
.((.((....((((((((...((((((...(((........)))..))))))...))))))))..(((.....((.....((((........))))....))...)))...)).)).... ( -28.00)
>consensus
GGCGGCAACGGCAUCAACAGCAGUAAACAAGCUUCACAUGUGGCAUUUUAUUAAAGUUGAUGCAACUUAAAAUGCAUUUAAGCCAGAUCCCGGGCUCACAGCUCAAAGAACGUGGCGAAC
.((.((....((((((((...((((((...(((........)))..))))))...))))))))..(((.....((.....((((........))))....))...)))...)).)).... (-27.34 = -27.18 +  -0.16)

alignment

secondary structure

dotplot

Window 2

Location	5,075,378 – 5,075,498
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	99.00
Mean single sequence MFE	-27.88
Consensus MFE	-24.76
Energy contribution	-24.60
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-1.59
Structure conservation index	0.89
SVM decision value	0.48
SVM RNA-class probability	0.753055
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5075378 120 + 23771897
UGGCAUUUUAUUAAAGUUGAUGCAACUUAAAAUGCAUUUAAGCCAGAUCCCGGGCUCACAGCUCAAAGAACGUGGCGAACUUUUGCAAUUGUGGGACUAUCAAACAAAACUUUUGCCAAA
(((((.......((((((((((((........))))))......((.((((((((.....)))).....(((..((((....))))...))))))))).........))))))))))).. ( -28.91)
>DroSec_CAF1 281784 120 + 1
UGGCAUUUUAUUAAAGUUGAUGCAACUUAAAAUGCAUUUAAGCCAGAUCCCUGGCUCACAGCUCAAAGAACGUGGCGAACUUUUGCAAUUGUGGGACUAUCAAACAAAACUUUUGCCAAA
(((((.........((((((((((........)))))...((((((....))))))..))))).((((......((((....))))..((((..(.....)..))))..))))))))).. ( -28.90)
>DroSim_CAF1 303072 120 + 1
UGGCAUUUUAUUAAAGUUGAUGCAACUUAAAAUGCAUUUAAGCCAGAUCCCUGGCUCACAGCUCAAAGAACGUGGCGAACUUUUGCAAUUGUGGGACUAUCAAACAAAACUUUUGCCAAA
(((((.........((((((((((........)))))...((((((....))))))..))))).((((......((((....))))..((((..(.....)..))))..))))))))).. ( -28.90)
>DroEre_CAF1 288819 120 + 1
UGGCAUUUUAUUAAAGUUGAUGCAACUUAAAAUGUAUUUAAGCCAGAUCCCGGGCUCACAGCUCAAAGAACGUGGCGAACUUUUGCAAUUGUGGGACUAUCAAACAAAACUUUUGCCAAA
(((((...........((((((...((((((.....)))))).....((((((((.....)))).....(((..((((....))))...))))))).))))))..........))))).. ( -27.70)
>DroYak_CAF1 292873 120 + 1
UGGCAUUUUAUUAAAGUUGAUGCAACUUAAAAUGCAUUUAAGCCAGAUCCCCGGCUCACAGCUCAAAGAACGUGGCGAACUUUUGCAAUUGUGGGACUAUCAAACAAAACUUUUGCCAAA
(((((.......((((((((((((........))))))...(((((.((...(((.....)))....)).).)))).)))))).....((((..(.....)..))))......))))).. ( -25.00)
>consensus
UGGCAUUUUAUUAAAGUUGAUGCAACUUAAAAUGCAUUUAAGCCAGAUCCCGGGCUCACAGCUCAAAGAACGUGGCGAACUUUUGCAAUUGUGGGACUAUCAAACAAAACUUUUGCCAAA
(((((.......((((((((((((........))))))...(((((.((...(((.....)))....)).).)))).)))))).....((((..(.....)..))))......))))).. (-24.76 = -24.60 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:16:47 2006