Locus 2647

Sequence ID	2L_DroMel_CAF1
Location	7,409,093 – 7,409,228
Length	135
Max. P	0.862809

overview

Window 3

Location	7,409,093 – 7,409,188
Length	95
Sequences	6
Columns	97
Reading direction	forward
Mean pairwise identity	76.17
Mean single sequence MFE	-45.18
Consensus MFE	-25.79
Energy contribution	-27.02
Covariance contribution	1.23
Combinations/Pair	1.26
Mean z-score	-1.60
Structure conservation index	0.57
SVM decision value	0.28
SVM RNA-class probability	0.665728
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7409093 95 + 22407834
GUUGUCGUUUGGGGUGCGAUUGCUGGCGCCGCAGCAGGAGCUGUGGUCACGGCGCUCUGGGUGGCGGGAGCACCUGGUG--CAGCAGCCACCGCGGG
....((((...((.(((....((((..((((((((....))))))))..))))((.(..((((.(....)))))..).)--).))).))...)))). ( -48.30)
>DroSec_CAF1 3605 95 + 1
GUUGUCGUUUGGGCUGCGAUUGCUGGCGCCGCAGCGGGAGCUGUGGUCACGGCGCUCUGGGUGGCGGGAGCACCUGGUG--CAGCAGCCACCGCUGG
......((...((((((....((((..((((((((....))))))))..))))((.(..((((.(....)))))..).)--).))))))...))... ( -52.10)
>DroSim_CAF1 3846 95 + 1
GUUGUCGUUUGGGCUGCGAUUGCUGGCGCCGCAGCGGGAGCUGUGGUCACGGCGCUCUGGGUGGCGGGAGCACCUGGUG--CAGCAGCCACCGCUGG
......((...((((((....((((..((((((((....))))))))..))))((.(..((((.(....)))))..).)--).))))))...))... ( -52.10)
>DroEre_CAF1 6000 95 + 1
GUUGUCGUUUGAGGCGCGAUGGCUGGUGCCGUAGCAGGAGCAGUGGUCACAGCGCUUUGGGUGGCGGGAGCACCUGGUG--CUGCGGCCACCACGGG
....((((..(((((((..((((((.((((.......).))).))))))..))))))).((((((.(.(((((...)))--)).).)))))))))). ( -46.20)
>DroYak_CAF1 4139 95 + 1
GUUGUCGUUUGGGGUGCGCUUGCUGCGGCUGUUGCAGGAGCAGUGGUCACGGCGCUUUGAGUGGCGGGAGCACCUGCUG--CUGCAGCCACCGCUGG
..........(.(((((((.....)))...(((((((.(((((((.((.((.(((.....))).)).)).)).))))).--))))))))))).)... ( -42.60)
>DroPer_CAF1 5813 77 + 1
ACCACAGU---------------GGGCGUGGCUGCGGGUGCAGUG---ACGGGGA--UGGGAGGCUGGACCACGGGGAGAACCGCCGGCACCACGGC
......((---------------((.(((.(((((....))))).---)))....--......(((((....(((......)))))))).))))... ( -29.80)
>consensus
GUUGUCGUUUGGGGUGCGAUUGCUGGCGCCGCAGCAGGAGCAGUGGUCACGGCGCUCUGGGUGGCGGGAGCACCUGGUG__CAGCAGCCACCGCGGG
...(((((.......))))).((((..((((((((....))))))))..))))......((((((((.....))((........))))))))..... (-25.79 = -27.02 +   1.23)

alignment

secondary structure

dotplot

Window 4

Location	7,409,093 – 7,409,188
Length	95
Sequences	6
Columns	97
Reading direction	reverse
Mean pairwise identity	76.17
Mean single sequence MFE	-34.42
Consensus MFE	-20.96
Energy contribution	-20.66
Covariance contribution	-0.30
Combinations/Pair	1.41
Mean z-score	-1.71
Structure conservation index	0.61
SVM decision value	0.84
SVM RNA-class probability	0.862809
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7409093 95 - 22407834
CCCGCGGUGGCUGCUG--CACCAGGUGCUCCCGCCACCCAGAGCGCCGUGACCACAGCUCCUGCUGCGGCGCCAGCAAUCGCACCCCAAACGACAAC
...(((((.((((...--.....(((((((..........)))))))(((.((.((((....)))).))))))))).)))))............... ( -37.10)
>DroSec_CAF1 3605 95 - 1
CCAGCGGUGGCUGCUG--CACCAGGUGCUCCCGCCACCCAGAGCGCCGUGACCACAGCUCCCGCUGCGGCGCCAGCAAUCGCAGCCCAAACGACAAC
...(((..((((((((--(....(((((((..........)))))))(((.((.((((....)))).)))))..)))...))))))....)).)... ( -38.60)
>DroSim_CAF1 3846 95 - 1
CCAGCGGUGGCUGCUG--CACCAGGUGCUCCCGCCACCCAGAGCGCCGUGACCACAGCUCCCGCUGCGGCGCCAGCAAUCGCAGCCCAAACGACAAC
...(((..((((((((--(....(((((((..........)))))))(((.((.((((....)))).)))))..)))...))))))....)).)... ( -38.60)
>DroEre_CAF1 6000 95 - 1
CCCGUGGUGGCCGCAG--CACCAGGUGCUCCCGCCACCCAAAGCGCUGUGACCACUGCUCCUGCUACGGCACCAGCCAUCGCGCCUCAAACGACAAC
..(((((((((.(.((--(((...))))).).))))))....((((.(((......(((..(((....)))..)))))).)))).....)))..... ( -35.00)
>DroYak_CAF1 4139 95 - 1
CCAGCGGUGGCUGCAG--CAGCAGGUGCUCCCGCCACUCAAAGCGCCGUGACCACUGCUCCUGCAACAGCCGCAGCAAGCGCACCCCAAACGACAAC
...(((((.(.(((((--.((((((((((............))))))((....)))))).))))).).))))).((....))............... ( -31.90)
>DroPer_CAF1 5813 77 - 1
GCCGUGGUGCCGGCGGUUCUCCCCGUGGUCCAGCCUCCCA--UCCCCGU---CACUGCACCCGCAGCCACGCCC---------------ACUGUGGU
((((..(((..(((((((..((....))...)))).....--.....((---..((((....))))..))))))---------------))..)))) ( -25.30)
>consensus
CCAGCGGUGGCUGCUG__CACCAGGUGCUCCCGCCACCCAGAGCGCCGUGACCACAGCUCCCGCUGCGGCGCCAGCAAUCGCACCCCAAACGACAAC
...(((((((..((((.......((((((............)))))).......))))..))))))).............................. (-20.96 = -20.66 +  -0.30)

alignment

secondary structure

dotplot

Window 5

Location	7,409,121 – 7,409,228
Length	107
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	81.36
Mean single sequence MFE	-52.75
Consensus MFE	-36.99
Energy contribution	-36.33
Covariance contribution	-0.66
Combinations/Pair	1.40
Mean z-score	-1.40
Structure conservation index	0.70
SVM decision value	0.12
SVM RNA-class probability	0.592617
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7409121 107 + 22407834
CCGCAGCAGGAGCUGUGGUCACGGCGCUCUGGGUGGCGGGAGCACCUGGUG--CAGCAGCCACCGCGGGCUGUGGAAUGCCCGUGGCACCACCCUUAGCGGGCAAGCCA
..(((.((((.(((((....)))))(((((.(....).))))).)))).))--).((((((......))))))((..(((((((((......))...)))))))..)). ( -54.50)
>DroSec_CAF1 3633 107 + 1
CCGCAGCGGGAGCUGUGGUCACGGCGCUCUGGGUGGCGGGAGCACCUGGUG--CAGCAGCCACCGCUGGCUGAGAAAUGCCCGUGGCACCACCCUUGGCGGGCAAGCCA
(((((((....)))))))....(((((.(..((((.(....)))))..).)--)..((((((....)))))).....(((((((((......))...))))))).))). ( -55.70)
>DroSim_CAF1 3874 107 + 1
CCGCAGCGGGAGCUGUGGUCACGGCGCUCUGGGUGGCGGGAGCACCUGGUG--CAGCAGCCACCGCUGGCUGAGAAAUACCCGUGGCACCACCCUUGGCGGGCAAGCCA
(((((((....)))))))......((((..((((((((((.((((...)))--)..((((((....)))))).......)))).....))))))..))))((....)). ( -52.80)
>DroEre_CAF1 6028 107 + 1
CCGUAGCAGGAGCAGUGGUCACAGCGCUUUGGGUGGCGGGAGCACCUGGUG--CUGCGGCCACCACGGGCUGCUGAAUGCCAGGGGCUCCACCCUUGGCCGGCAAGCCA
.(((.((....)).((((((.(((((((..(((((.(....))))))))))--))).)))))).)))((((((((...((((((((.....)))))))))))).)))). ( -59.60)
>DroYak_CAF1 4167 107 + 1
CUGUUGCAGGAGCAGUGGUCACGGCGCUUUGAGUGGCGGGAGCACCUGCUG--CUGCAGCCACCGCUGGCUGUGGAAUGCCAGUGGCACCACCCUUGGCGGGCAAGCCA
..(((((((.(((((((.((.((.(((.....))).)).)).)).))))).--)))))))..((((((((........)))))))).........((((......)))) ( -53.00)
>DroPer_CAF1 5826 104 + 1
UGGCUGCGGGUGCAGUG---ACGGGGA--UGGGAGGCUGGACCACGGGGAGAACCGCCGGCACCACGGCUGGAGAGAUACCAGCGGGACCACCUUUGGCUGGCACGCCC
.((((((.(((.(((..---..((((.--(((...(((((....(((......)))))))).)))(.(((((.......))))).)..)).)).)))))).))).))). ( -40.90)
>consensus
CCGCAGCAGGAGCAGUGGUCACGGCGCUCUGGGUGGCGGGAGCACCUGGUG__CAGCAGCCACCGCGGGCUGAGAAAUGCCAGUGGCACCACCCUUGGCGGGCAAGCCA
(((((((....)))))))......((((..((((((.((.....)).((((.....(((((......))))).....)))).......))))))..))))((....)). (-36.99 = -36.33 +  -0.66)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:32:45 2006