Locus 780

Sequence ID	2L_DroMel_CAF1
Location	2,226,489 – 2,226,615
Length	126
Max. P	0.948026

overview

Window 5

Location	2,226,489 – 2,226,579
Length	90
Sequences	5
Columns	95
Reading direction	forward
Mean pairwise identity	90.48
Mean single sequence MFE	-21.86
Consensus MFE	-18.28
Energy contribution	-19.40
Covariance contribution	1.12
Combinations/Pair	1.11
Mean z-score	-1.29
Structure conservation index	0.84
SVM decision value	-0.01
SVM RNA-class probability	0.527603
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2226489 90 + 22407834
-----CGUUAUCCAACACUUAAGGUCUGGAAAAUUGCCAGUACUGAAAAGUGCGGAAAUCAUGUCACGUCGGAACGUCGACAAAAGACACAAAUA
-----.(((.(((..(((((..(((((((.......)))).)))...))))).))).....((((((((....)))).))))...)))....... ( -22.90)
>DroSec_CAF1 8571 90 + 1
-----CGUUAUCCAACACUUAAGGUCUGGAAAAUUGCCAGUGCUGGAAAAGGCGGAAAGCAUGUCACGUCGGAACGUCGACAAAAGACACAAAUA
-----.(((.(((............((((.......)))).(((......)))))).))).((((..(((((....)))))....))))...... ( -19.90)
>DroSim_CAF1 7586 90 + 1
-----CGUUAUCCAACACUUAAGGUCUGGAAAAUUGCCAGUGCUGGAAAAGGCGGAAAGCAUGUCACGUCGGAACGUCGACAAAAGACACAAAUA
-----.(((.(((............((((.......)))).(((......)))))).))).((((..(((((....)))))....))))...... ( -19.90)
>DroEre_CAF1 7747 95 + 1
CGCAACGUUGUCCAACACUAAGGGUCUGGAAAAUUGCCAGUGCUGGAAAGUGCGGAAAGCAUGUCACGUCGGAACGUCGACAAAAGACACAAAUA
((((.(....((((.((((...(((..........))))))).))))..))))).......((((..(((((....)))))....))))...... ( -22.00)
>DroYak_CAF1 7733 95 + 1
CGCAACGUUUUCCAACACUAAGAGCCUGGAAAAUAGCCAGUGGUGGAAAGUGCGGAAAGCAUGUCACGUCGGAACGUCGACAAAAGACACAAAUA
......(((((((..((((....((((((.......)))..)))....)))).))))))).((((..(((((....)))))....))))...... ( -24.60)
>consensus
_____CGUUAUCCAACACUUAAGGUCUGGAAAAUUGCCAGUGCUGGAAAGUGCGGAAAGCAUGUCACGUCGGAACGUCGACAAAAGACACAAAUA
......(((.(((..(((((..(((((((.......)))).)))...))))).))).))).((((..(((((....)))))....))))...... (-18.28 = -19.40 +   1.12)

alignment

secondary structure

dotplot

Window 6

Location	2,226,489 – 2,226,579
Length	90
Sequences	5
Columns	95
Reading direction	reverse
Mean pairwise identity	90.48
Mean single sequence MFE	-25.01
Consensus MFE	-20.72
Energy contribution	-20.44
Covariance contribution	-0.28
Combinations/Pair	1.14
Mean z-score	-1.89
Structure conservation index	0.83
SVM decision value	1.38
SVM RNA-class probability	0.948026
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2226489 90 - 22407834
UAUUUGUGUCUUUUGUCGACGUUCCGACGUGACAUGAUUUCCGCACUUUUCAGUACUGGCAAUUUUCCAGACCUUAAGUGUUGGAUAACG-----
...(..((((...(((((......))))).))))..)..(((((((((....((.((((.......))))))...))))).)))).....----- ( -25.60)
>DroSec_CAF1 8571 90 - 1
UAUUUGUGUCUUUUGUCGACGUUCCGACGUGACAUGCUUUCCGCCUUUUCCAGCACUGGCAAUUUUCCAGACCUUAAGUGUUGGAUAACG-----
.....(((((...(((((......))))).))))).............((((((((((((.........).))...))))))))).....----- ( -22.90)
>DroSim_CAF1 7586 90 - 1
UAUUUGUGUCUUUUGUCGACGUUCCGACGUGACAUGCUUUCCGCCUUUUCCAGCACUGGCAAUUUUCCAGACCUUAAGUGUUGGAUAACG-----
.....(((((...(((((......))))).))))).............((((((((((((.........).))...))))))))).....----- ( -22.90)
>DroEre_CAF1 7747 95 - 1
UAUUUGUGUCUUUUGUCGACGUUCCGACGUGACAUGCUUUCCGCACUUUCCAGCACUGGCAAUUUUCCAGACCCUUAGUGUUGGACAACGUUGCG
.....(((((...(((((......))))).)))))......((((((((((((((((((...............))))))))))).)).).)))) ( -25.96)
>DroYak_CAF1 7733 95 - 1
UAUUUGUGUCUUUUGUCGACGUUCCGACGUGACAUGCUUUCCGCACUUUCCACCACUGGCUAUUUUCCAGGCUCUUAGUGUUGGAAAACGUUGCG
.....(((((...(((((......))))).)))))......((((.((((((.((((((((........))))...)))).))))))....)))) ( -27.70)
>consensus
UAUUUGUGUCUUUUGUCGACGUUCCGACGUGACAUGCUUUCCGCACUUUCCAGCACUGGCAAUUUUCCAGACCUUAAGUGUUGGAUAACG_____
.....(((((...(((((......))))).))))).............((((((((((((.........).))...))))))))).......... (-20.72 = -20.44 +  -0.28)

alignment

secondary structure

dotplot

Window 7

Location	2,226,508 – 2,226,615
Length	107
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	96.64
Mean single sequence MFE	-26.22
Consensus MFE	-23.92
Energy contribution	-25.12
Covariance contribution	1.20
Combinations/Pair	1.00
Mean z-score	-1.26
Structure conservation index	0.91
SVM decision value	0.35
SVM RNA-class probability	0.700884
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2226508 107 + 22407834
UCUGGAAAAUUGCCAGUACUGAAAAGUGCGGAAAUCAUGUCACGUCGGAACGUCGACAAAAGACACAAAUAAUAGGAAAAAGCUUAUUUCGCGCAGGCACUCGCAUA
.((((.......)))).........((((((((....((((..(((((....)))))....)))).......((((......))))))))))))..((....))... ( -23.40)
>DroSec_CAF1 8590 107 + 1
UCUGGAAAAUUGCCAGUGCUGGAAAAGGCGGAAAGCAUGUCACGUCGGAACGUCGACAAAAGACACAAAUAAUAGGAAAAAGCUUAUUUCGCGCAGGCACUCGCAUA
..........(((.((((((.(.....(((((((((.((((..(((((....)))))....))))(........)......)))..)))))).).)))))).))).. ( -26.00)
>DroSim_CAF1 7605 107 + 1
UCUGGAAAAUUGCCAGUGCUGGAAAAGGCGGAAAGCAUGUCACGUCGGAACGUCGACAAAAGACACAAAUAAUAGGAAAAAGCUUAUUUCGCGCAGGCACUCGCAUA
..........(((.((((((.(.....(((((((((.((((..(((((....)))))....))))(........)......)))..)))))).).)))))).))).. ( -26.00)
>DroEre_CAF1 7771 107 + 1
UCUGGAAAAUUGCCAGUGCUGGAAAGUGCGGAAAGCAUGUCACGUCGGAACGUCGACAAAAGACACAAAUAAUAGGAAAAAGCUUAUUUCGCGCAGGCACUCGCAUA
..........(((.((((((.....(((((((((((.((((..(((((....)))))....))))(........)......)))..)))))))).)))))).))).. ( -30.30)
>DroYak_CAF1 7757 107 + 1
CCUGGAAAAUAGCCAGUGGUGGAAAGUGCGGAAAGCAUGUCACGUCGGAACGUCGACAAAAGACACAAAUAAUAGGAAAAAGCUUAUUUCGCGCAGGCACUCGCAUA
..(((.......)))((((((....(((((((((((.((((..(((((....)))))....))))(........)......)))..))))))))...))).)))... ( -25.40)
>consensus
UCUGGAAAAUUGCCAGUGCUGGAAAGUGCGGAAAGCAUGUCACGUCGGAACGUCGACAAAAGACACAAAUAAUAGGAAAAAGCUUAUUUCGCGCAGGCACUCGCAUA
...........((.((((((.....((((((((....((((..(((((....)))))....)))).......((((......)))))))))))).)))))).))... (-23.92 = -25.12 +   1.20)

alignment

secondary structure

dotplot

Window 8

Location	2,226,508 – 2,226,615
Length	107
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	96.64
Mean single sequence MFE	-26.28
Consensus MFE	-24.72
Energy contribution	-24.72
Covariance contribution	0.00
Combinations/Pair	1.07
Mean z-score	-1.18
Structure conservation index	0.94
SVM decision value	0.29
SVM RNA-class probability	0.670508
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2226508 107 - 22407834
UAUGCGAGUGCCUGCGCGAAAUAAGCUUUUUCCUAUUAUUUGUGUCUUUUGUCGACGUUCCGACGUGACAUGAUUUCCGCACUUUUCAGUACUGGCAAUUUUCCAGA
..(((.(((((.((((.(((((.((.......)).......(((((...(((((......))))).))))).))))))))).......))))).))).......... ( -26.00)
>DroSec_CAF1 8590 107 - 1
UAUGCGAGUGCCUGCGCGAAAUAAGCUUUUUCCUAUUAUUUGUGUCUUUUGUCGACGUUCCGACGUGACAUGCUUUCCGCCUUUUCCAGCACUGGCAAUUUUCCAGA
..(((.(((((.((.(((....((((...............(((((...(((((......))))).)))))))))..)))......))))))).))).......... ( -26.56)
>DroSim_CAF1 7605 107 - 1
UAUGCGAGUGCCUGCGCGAAAUAAGCUUUUUCCUAUUAUUUGUGUCUUUUGUCGACGUUCCGACGUGACAUGCUUUCCGCCUUUUCCAGCACUGGCAAUUUUCCAGA
..(((.(((((.((.(((....((((...............(((((...(((((......))))).)))))))))..)))......))))))).))).......... ( -26.56)
>DroEre_CAF1 7771 107 - 1
UAUGCGAGUGCCUGCGCGAAAUAAGCUUUUUCCUAUUAUUUGUGUCUUUUGUCGACGUUCCGACGUGACAUGCUUUCCGCACUUUCCAGCACUGGCAAUUUUCCAGA
..(((.(((((.((((.(((...(((...............(((((...(((((......))))).))))))))))))))).......))))).))).......... ( -27.66)
>DroYak_CAF1 7757 107 - 1
UAUGCGAGUGCCUGCGCGAAAUAAGCUUUUUCCUAUUAUUUGUGUCUUUUGUCGACGUUCCGACGUGACAUGCUUUCCGCACUUUCCACCACUGGCUAUUUUCCAGG
.....((((((..((((.......))...............(((((...(((((......))))).))))))).....)))))).......((((.......)))). ( -24.60)
>consensus
UAUGCGAGUGCCUGCGCGAAAUAAGCUUUUUCCUAUUAUUUGUGUCUUUUGUCGACGUUCCGACGUGACAUGCUUUCCGCACUUUCCAGCACUGGCAAUUUUCCAGA
..(((.(((((..(.(((((((((...........))))))(((((...(((((......))))).)))))......))).)......))))).))).......... (-24.72 = -24.72 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:45:27 2006