Locus 3921

Sequence ID	2L_DroMel_CAF1
Location	11,438,261 – 11,438,394
Length	133
Max. P	0.914473

overview

Window 1

Location	11,438,261 – 11,438,369
Length	108
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	77.71
Mean single sequence MFE	-31.15
Consensus MFE	-17.41
Energy contribution	-17.92
Covariance contribution	0.50
Combinations/Pair	1.33
Mean z-score	-1.68
Structure conservation index	0.56
SVM decision value	0.16
SVM RNA-class probability	0.610119
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11438261 108 - 22407834
---------CAGCCACAU---GGGCUAUCCACCAGUGGUGCAGCCCAUCCAACCGGCCGCACUUAUGCAUCCGCAAUCUUCGCCGGGCUCGCAAUCCCACCUGGAUCACCUGCCCACACC
---------........(---((((.(((((...((((((((((((........((..(((....)))..))((.......)).))))).)))...)))).))))).....))))).... ( -35.00)
>DroVir_CAF1 50071 105 - 1
---------------CAUGCCCGCCUAUCCGCCUGUGGUGCAGCCCAUCCAACCACCAGCAAUCAUGCACGCGCAGUGCUCACCUGGAUCGCAGACCCAUCUGGAUCAGUUGCCGACUCC
---------------..(((((((..........)))).)))................(((((...((((.....)))).......((((.((((....)))))))).)))))....... ( -24.90)
>DroGri_CAF1 72276 106 - 1
--------------AUAUGCCCGGCUAUCCACCGGUGGUGCAACCGAUUCAACCACCAGCAAUAAUGCACGCCCAGUGCUCGCCCGGCUCCCAUUCGCAUCUAGAUCAGCUGCCGACACC
--------------....(((.(((........((((((............)))))).........((((.....))))..))).)))......(((((.((.....)).)).))).... ( -28.80)
>DroSim_CAF1 2050 108 - 1
---------UAGCCACAU---GGGCUAUCCACCAGUGGUGCAGCCCAUCCAACCGGCCGCACUAAUGCAUCCGCAAUCUUCGCCCGGUUCCCAAUCCCACCUAGAUCACCUGCCCACGCC
---------(((((....---.))))).......((((.((((.......((((((.((......(((....))).....)).))))))....(((.......)))...))))))))... ( -28.80)
>DroEre_CAF1 2055 108 - 1
---------CAGCCACAU---GGGCUAUCCGCCAGUGGUGCAGCCCAUCCAACCGGCCGCCCUAAUGCAUCCGCAACCUUCGCCGGGCUCCCAAUCCCACCUGGAUCACCUGCCCACGCC
---------.((((....---.))))........((((.((((...(((((...(((........(((....)))......)))(((........)))...)))))...))))))))... ( -32.74)
>DroYak_CAF1 2056 117 - 1
UCACAGCCACAGCCACAU---GGGCUAUCCGCCAGUGGUGCAGCCCAUCCAGCCGGCCGCCCUAAUGCAUCCGCAACCCUCGCCGGGCUCCCAAUCCCACCUGGAUCACCUGCCCACGCC
....((((.((......)---)))))........((((.((((...((((((..(((........(((....)))......)))(((........)))..))))))...))))))))... ( -36.64)
>consensus
_________CAGCCACAU___GGGCUAUCCACCAGUGGUGCAGCCCAUCCAACCGGCCGCACUAAUGCAUCCGCAAUCCUCGCCGGGCUCCCAAUCCCACCUGGAUCACCUGCCCACGCC
.....................(((((..(((....)))...))))).......(((..((......))..)))...........((((.....((((.....)))).....))))..... (-17.41 = -17.92 +   0.50)

alignment

secondary structure

dotplot

Window 2

Location	11,438,301 – 11,438,394
Length	93
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	79.60
Mean single sequence MFE	-38.45
Consensus MFE	-25.56
Energy contribution	-27.15
Covariance contribution	1.59
Combinations/Pair	1.19
Mean z-score	-2.15
Structure conservation index	0.66
SVM decision value	1.10
SVM RNA-class probability	0.914473
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11438301 93 + 22407834
AAGAUUGCGGAUGCAUAAGUGCGGCCGGUUGGAUGGGCUGCACCACUGGUGGAUAGCCC---AUGUGGCUG------------UGACGGUGGUGGUGCGGGGAGCGGU------
...(((((...(((((..((((((((.((...)).))))))))(((((.((.((((((.---....)))))------------)..)).))))))))))....)))))------ ( -39.10)
>DroGri_CAF1 72316 93 + 1
AGCACUGGGCGUGCAUUAUUGCUGGUGGUUGAAUCGGUUGCACCACCGGUGGAUAGCCGGGCAUAU---------------------GGUGGUGCUGCUGGGAGGGAUGAUGAU
.((((.....))))((((((.(((((......)))(((.(((((.(((((.....)))))((....---------------------.))))))).)))...)).))))))... ( -30.90)
>DroSec_CAF1 2091 93 + 1
AAGAUUGCGGAUGCAUUAGUGCGGCCGGUUGGAUGGGCUGCACCACUGGUGGAUAGCCC---AUAUGGCUG------------UGACGGUGGUGGUGCGGGGAGCGGU------
...(((((...(((((((((((((((.((...)).))))))))(((((....((((((.---....)))))------------)..))))).)))))))....)))))------ ( -39.40)
>DroSim_CAF1 2090 93 + 1
AAGAUUGCGGAUGCAUUAGUGCGGCCGGUUGGAUGGGCUGCACCACUGGUGGAUAGCCC---AUGUGGCUA------------UGACGGUGGUGGUGCGGGGAGCGGU------
...(((((...(((((((((((((((.((...)).))))))))(((((....((((((.---....)))))------------)..))))).)))))))....)))))------ ( -39.40)
>DroEre_CAF1 2095 93 + 1
AAGGUUGCGGAUGCAUUAGGGCGGCCGGUUGGAUGGGCUGCACCACUGGCGGAUAGCCC---AUGUGGCUG------------UGGCGGUGGUGAUGCGGGGAGCGGU------
....((((...((((((...((((((.((...)).))))))(((((((.(..((((((.---....)))))------------)).)))))))))))))....)))).------ ( -40.00)
>DroYak_CAF1 2096 105 + 1
AGGGUUGCGGAUGCAUUAGGGCGGCCGGCUGGAUGGGCUGCACCACUGGCGGAUAGCCC---AUGUGGCUGUGGCUGUGACUGUGGCGGUGGUGAUGCGGGGAGCGGU------
.(.((..(.(.(((..(((.(((((((((((.((((((((..((......)).))))))---)).)))))..))))))..)))..))).).)..)).)..........------ ( -41.90)
>consensus
AAGAUUGCGGAUGCAUUAGUGCGGCCGGUUGGAUGGGCUGCACCACUGGUGGAUAGCCC___AUGUGGCUG____________UGACGGUGGUGGUGCGGGGAGCGGU______
...(((((...((((((...((((((.((...)).))))))(((((((.....(((((........)))))...............)))))))))))))....)))))...... (-25.56 = -27.15 +   1.59)

alignment

secondary structure

dotplot

Window 3

Location	11,438,301 – 11,438,394
Length	93
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	79.60
Mean single sequence MFE	-23.55
Consensus MFE	-15.73
Energy contribution	-15.45
Covariance contribution	-0.28
Combinations/Pair	1.21
Mean z-score	-1.91
Structure conservation index	0.67
SVM decision value	0.86
SVM RNA-class probability	0.869751
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11438301 93 - 22407834
------ACCGCUCCCCGCACCACCACCGUCA------------CAGCCACAU---GGGCUAUCCACCAGUGGUGCAGCCCAUCCAACCGGCCGCACUUAUGCAUCCGCAAUCUU
------...((.....(((((((........------------.((((....---.))))........))))))).(((.........))).)).....(((....)))..... ( -24.13)
>DroGri_CAF1 72316 93 - 1
AUCAUCAUCCCUCCCAGCAGCACCACC---------------------AUAUGCCCGGCUAUCCACCGGUGGUGCAACCGAUUCAACCACCAGCAAUAAUGCACGCCCAGUGCU
...............(((((((.....---------------------...)))..(((........((((((............)))))).(((....)))..)))...)))) ( -20.90)
>DroSec_CAF1 2091 93 - 1
------ACCGCUCCCCGCACCACCACCGUCA------------CAGCCAUAU---GGGCUAUCCACCAGUGGUGCAGCCCAUCCAACCGGCCGCACUAAUGCAUCCGCAAUCUU
------...((.....(((((((........------------.((((....---.))))........))))))).(((.........))).)).....(((....)))..... ( -24.13)
>DroSim_CAF1 2090 93 - 1
------ACCGCUCCCCGCACCACCACCGUCA------------UAGCCACAU---GGGCUAUCCACCAGUGGUGCAGCCCAUCCAACCGGCCGCACUAAUGCAUCCGCAAUCUU
------...((.....(((((((.......(------------(((((....---.))))))......))))))).(((.........))).)).....(((....)))..... ( -26.82)
>DroEre_CAF1 2095 93 - 1
------ACCGCUCCCCGCAUCACCACCGCCA------------CAGCCACAU---GGGCUAUCCGCCAGUGGUGCAGCCCAUCCAACCGGCCGCCCUAAUGCAUCCGCAACCUU
------...((.....((((.(((((.((..------------.((((....---.))))....))..)))))((.(((.........))).))....))))....))...... ( -22.10)
>DroYak_CAF1 2096 105 - 1
------ACCGCUCCCCGCAUCACCACCGCCACAGUCACAGCCACAGCCACAU---GGGCUAUCCGCCAGUGGUGCAGCCCAUCCAGCCGGCCGCCCUAAUGCAUCCGCAACCCU
------...((.....((((.......(((...((.......)).((...((---(((((..(((....)))...)))))))...)).))).......))))....))...... ( -23.24)
>consensus
______ACCGCUCCCCGCACCACCACCGUCA____________CAGCCACAU___GGGCUAUCCACCAGUGGUGCAGCCCAUCCAACCGGCCGCACUAAUGCAUCCGCAAUCUU
................((.....................................(((((..(((....)))...)))))........((..((......))..))))...... (-15.73 = -15.45 +  -0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:04:49 2006