Locus 3611

Sequence ID	2R_DroMel_CAF1
Location	11,990,712 – 11,990,811
Length	99
Max. P	0.929941

overview

Window 1

Location	11,990,712 – 11,990,811
Length	99
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	75.47
Mean single sequence MFE	-30.97
Consensus MFE	-16.31
Energy contribution	-16.23
Covariance contribution	-0.08
Combinations/Pair	1.35
Mean z-score	-1.94
Structure conservation index	0.53
SVM decision value	0.82
SVM RNA-class probability	0.857997
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11990712 99 + 20766785
GGCGCCAUAAACAGAGCUGCCUGGAAGGCAGUCUUUGAUUAU---AUAACAUAAUGGAUGGGCGAUA-----AUGGGUGGUG------GAGCAUGGUGUGU----UAGGUGUAUGGU
.(((((((((.((((((((((.....))))).))))).))))---.(((((((....(((..(.((.-----.......)).------)..)))..)))))----)))))))..... ( -30.00)
>DroSec_CAF1 41784 102 + 1
GGCGCCAUAAACAGAGCCGCCUG-AAGGCAGUCUUUGAUUAU---AUAACAUAAUGGAUGGGCGAUA-----AUGGGCGGUG------GAGCAUGGUGUGUGUGGUAGGUGUGUGGU
...((((((.((...(((((((.-......((((((.(((((---.....))))).)).))))....-----..))))))).------..((((.....)))).....)).)))))) ( -27.62)
>DroSim_CAF1 45435 102 + 1
GGCGCCAUAAACAGAGCCGCCUG-AAGGCAGUCUUUGAUUAU---AUAACAUAAUGGAUGGGCGAUA-----AUGGGCGGUG------GAGCAUGGUGUGUGUGGUAGGUGUGUGGU
...((((((.((...(((((((.-......((((((.(((((---.....))))).)).))))....-----..))))))).------..((((.....)))).....)).)))))) ( -27.62)
>DroEre_CAF1 42139 96 + 1
AGCGCCAUAAACAGAGCUGCCUG-AAGGCAGUCUUUGAUUAUACCAUAUCAUAAUGGAUGGGCGAUA-----AUGGGUGGCA------GAGCGUGGUG--UG--GGAGGUGU-----
.(((((((((.((((((((((..-..))))).))))).)))).(((((((((....(....((.((.-----....)).)).------...)))))))--))--)..)))))----- ( -34.80)
>DroYak_CAF1 42681 104 + 1
GGCGCCAUAAACAGAGCUGCCUG-AAGGCAGUCUUUGAUUAUACUAUAUCAUAAUGGAUGGGUGAUA-----AUGGGUGGCGGUGCUGGAGCAUGGUGUGUG--CGAGGUGU-----
..((((((...((((((((((..-..))))).)))))......(((((((((.........))))).-----))))))))))(..((...((((.....)))--)..))..)----- ( -35.80)
>DroAna_CAF1 45259 97 + 1
GGCGCCAUAAACAGCGCAGCCCG-CAGGCAGAUUUUGGUUAU---UCAGGAC-UUGGAGGAGCUGUAAAUAUAUGGAUGGCA------GGGGACAGAU--GG--GCGGGCA-----U
.((((........)))).(((((-(............(((((---(((..(.-(((.((...)).))).)...)))))))).------(....)....--..--)))))).-----. ( -30.00)
>consensus
GGCGCCAUAAACAGAGCUGCCUG_AAGGCAGUCUUUGAUUAU___AUAACAUAAUGGAUGGGCGAUA_____AUGGGUGGCG______GAGCAUGGUGUGUG__GUAGGUGU____U
.(((((.........((((((((.......((((((.(((((........))))).)).))))..........)))))))).........((.....))........)))))..... (-16.31 = -16.23 +  -0.08)

alignment

secondary structure

dotplot

Window 2

Location	11,990,712 – 11,990,811
Length	99
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	75.47
Mean single sequence MFE	-18.65
Consensus MFE	-10.89
Energy contribution	-11.62
Covariance contribution	0.72
Combinations/Pair	1.15
Mean z-score	-1.93
Structure conservation index	0.58
SVM decision value	1.20
SVM RNA-class probability	0.929941
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11990712 99 - 20766785
ACCAUACACCUA----ACACACCAUGCUC------CACCACCCAU-----UAUCGCCCAUCCAUUAUGUUAU---AUAAUCAAAGACUGCCUUCCAGGCAGCUCUGUUUAUGGCGCC
............----.............------..........-----...(((((((.....)))....---((((.((.((.(((((.....))))))).)).)))))))).. ( -16.10)
>DroSec_CAF1 41784 102 - 1
ACCACACACCUACCACACACACCAUGCUC------CACCGCCCAU-----UAUCGCCCAUCCAUUAUGUUAU---AUAAUCAAAGACUGCCUU-CAGGCGGCUCUGUUUAUGGCGCC
.........................((..------....))....-----...(((((((.....)))....---((((.((.((.(((((..-..))))))).)).)))))))).. ( -15.60)
>DroSim_CAF1 45435 102 - 1
ACCACACACCUACCACACACACCAUGCUC------CACCGCCCAU-----UAUCGCCCAUCCAUUAUGUUAU---AUAAUCAAAGACUGCCUU-CAGGCGGCUCUGUUUAUGGCGCC
.........................((..------....))....-----...(((((((.....)))....---((((.((.((.(((((..-..))))))).)).)))))))).. ( -15.60)
>DroEre_CAF1 42139 96 - 1
-----ACACCUCC--CA--CACCACGCUC------UGCCACCCAU-----UAUCGCCCAUCCAUUAUGAUAUGGUAUAAUCAAAGACUGCCUU-CAGGCAGCUCUGUUUAUGGCGCU
-----........--..--..........------.(((..((((-----.((((...........)))))))).((((.((.((.(((((..-..))))))).)).)))))))... ( -20.60)
>DroYak_CAF1 42681 104 - 1
-----ACACCUCG--CACACACCAUGCUCCAGCACCGCCACCCAU-----UAUCACCCAUCCAUUAUGAUAUAGUAUAAUCAAAGACUGCCUU-CAGGCAGCUCUGUUUAUGGCGCC
-----.......(--(........(((....)))..(((......-----(((((...........)))))....((((.((.((.(((((..-..))))))).)).))))))))). ( -22.10)
>DroAna_CAF1 45259 97 - 1
A-----UGCCCGC--CC--AUCUGUCCCC------UGCCAUCCAUAUAUUUACAGCUCCUCCAA-GUCCUGA---AUAACCAAAAUCUGCCUG-CGGGCUGCGCUGUUUAUGGCGCC
.-----.((((((--..--....((....------.))........((((((..(((......)-))..)))---)))..............)-))))).(((((......))))). ( -21.90)
>consensus
A____ACACCUAC__CACACACCAUGCUC______CACCACCCAU_____UAUCGCCCAUCCAUUAUGUUAU___AUAAUCAAAGACUGCCUU_CAGGCAGCUCUGUUUAUGGCGCC
.....................................................(((((((.....))).......((((.((.((.(((((.....))))))).)).)))))))).. (-10.89 = -11.62 +   0.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:59:52 2006