Locus 1087

Sequence ID	3R_DroMel_CAF1
Location	3,305,468 – 3,305,602
Length	134
Max. P	0.870866

overview

Window 2

Location	3,305,468 – 3,305,563
Length	95
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	83.10
Mean single sequence MFE	-36.33
Consensus MFE	-27.85
Energy contribution	-27.73
Covariance contribution	-0.13
Combinations/Pair	1.07
Mean z-score	-1.95
Structure conservation index	0.77
SVM decision value	0.87
SVM RNA-class probability	0.870866
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3305468 95 - 27905053
GCUGGUAACACCUGUCAGCAGGUGCAGCCAUCUAGGAUCCUAUCCUUGCUCCCAAGGACGAUG------------GGGGUGAACG-------------GUUGGCUGUAACUUUAUUUCAG
.((((...((((((....))))))((((((.((.((((...))))(..((((((.......))------------))))..)..)-------------).))))))..........)))) ( -34.70)
>DroSec_CAF1 9526 95 - 1
GCUGGCAACACCUGUCAGCAGGUGCAGCCAUCUAGGAUACUAUUCUUGGUCCCAAGGACGAAG------------UGGGUGAACG-------------GUUGGCUGUAACUUUACUUCAG
(((((((.....)))))))(((((((((((.((.(..((((...(((.((((...)))).)))------------..))))..))-------------).))))))).))))........ ( -36.70)
>DroSim_CAF1 13135 95 - 1
GCUGGCAACACCUGUCAGCAGGUGCAGCCAUCUAGGAUCCUAUCCUUGCUCCCAAGGACGAAG------------UGGGUGAACG-------------GUUGGCUGUAACUUUAUUUCAG
(((((((.....)))))))(((((((((((.((.....((((((((((....)))))).....------------)))).....)-------------).))))))).))))........ ( -33.70)
>DroYak_CAF1 19735 120 - 1
GCUGGCAACACCUGUCAGCAGGUGCAGCAAUCUAGGAUCCUAUCCUUGCUCCCAAGGACGCAGGUACGUUUGGUGGGGGAAAACGGUGCCAUCAAGCUGUUGGCUGUAACUUUAUUUCAG
(((((((.....)))))))(((((((((.....(((((...)))))..((((((.(((((......)))))..))))))..((((((........)))))).))))).))))........ ( -40.20)
>consensus
GCUGGCAACACCUGUCAGCAGGUGCAGCCAUCUAGGAUCCUAUCCUUGCUCCCAAGGACGAAG____________GGGGUGAACG_____________GUUGGCUGUAACUUUAUUUCAG
(((((((.....)))))))(((((((((((..(((....)))((((((....))))))..........................................))))))).))))........ (-27.85 = -27.73 +  -0.13)

alignment

secondary structure

dotplot

Window 3

Location	3,305,495 – 3,305,602
Length	107
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	88.69
Mean single sequence MFE	-33.08
Consensus MFE	-29.23
Energy contribution	-30.23
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.58
Structure conservation index	0.88
SVM decision value	0.51
SVM RNA-class probability	0.765733
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3305495 107 + 27905053
ACCCC------------CAUCGUCCUUGGGAGCAAGGAUAGGAUCCUAGAUGGCUGCACCUGCUGACAGGUGUUACCAGCAUUUUGCAUAUGUCUUCC-UCCAUUCCUGGCAACUGAGCA
...((------------((.......)))).((.((((..(((....((((((..(((((((....)))))))..)).((.....))....))))...-)))..)))).))......... ( -34.70)
>DroSec_CAF1 9553 107 + 1
ACCCA------------CUUCGUCCUUGGGACCAAGAAUAGUAUCCUAGAUGGCUGCACCUGCUGACAGGUGUUGCCAGCAUUUUGCAUAUGUCUUCC-UCCAUUUCUGUCAACUGAGCA
.....------------(((.((((...)))).)))..((((....((((((((.(((((((....))))))).))))((.....))...........-......))))...)))).... ( -28.30)
>DroSim_CAF1 13162 107 + 1
ACCCA------------CUUCGUCCUUGGGAGCAAGGAUAGGAUCCUAGAUGGCUGCACCUGCUGACAGGUGUUGCCAGCAUUUUGCAUAUGUCUUCC-UCCAUUUCUGUCAACUGAGCA
.....------------.((((((((((....))))))).(((....(((((((.(((((((....))))))).))).((.....))....))))...-))).............))).. ( -34.70)
>DroYak_CAF1 19775 120 + 1
UCCCCCACCAAACGUACCUGCGUCCUUGGGAGCAAGGAUAGGAUCCUAGAUUGCUGCACCUGCUGACAGGUGUUGCCAGCAUUUUGCAUAUGUCUUCCUUCCAUUUUUGGCAACUGAGCA
...((((....((((....))))...))))(((((...(((....)))..)))))(((((((....)))))(((((((((.....))..(((.........)))...)))))))...)). ( -34.60)
>consensus
ACCCA____________CUUCGUCCUUGGGAGCAAGGAUAGGAUCCUAGAUGGCUGCACCUGCUGACAGGUGUUGCCAGCAUUUUGCAUAUGUCUUCC_UCCAUUUCUGGCAACUGAGCA
.....................(((((((....))))))).(((....(((((((.(((((((....))))))).))).((.....))....))))....))).................. (-29.23 = -30.23 +   1.00)

alignment

secondary structure

dotplot

Window 4

Location	3,305,495 – 3,305,602
Length	107
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	88.69
Mean single sequence MFE	-35.65
Consensus MFE	-27.90
Energy contribution	-28.02
Covariance contribution	0.13
Combinations/Pair	1.07
Mean z-score	-1.60
Structure conservation index	0.78
SVM decision value	0.26
SVM RNA-class probability	0.658561
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3305495 107 - 27905053
UGCUCAGUUGCCAGGAAUGGA-GGAAGACAUAUGCAAAAUGCUGGUAACACCUGUCAGCAGGUGCAGCCAUCUAGGAUCCUAUCCUUGCUCCCAAGGACGAUG------------GGGGU
.((((.((((((((.((((..-......)))........).))))))))(((((....)))))....((((((((....)))((((((....)))))).))))------------))))) ( -35.00)
>DroSec_CAF1 9553 107 - 1
UGCUCAGUUGACAGAAAUGGA-GGAAGACAUAUGCAAAAUGCUGGCAACACCUGUCAGCAGGUGCAGCCAUCUAGGAUACUAUUCUUGGUCCCAAGGACGAAG------------UGGGU
.(((((.((..((..(((((.-..........((((...((((((((.....))))))))..)))).((.....))...)))))..))((((...)))).)).------------))))) ( -32.10)
>DroSim_CAF1 13162 107 - 1
UGCUCAGUUGACAGAAAUGGA-GGAAGACAUAUGCAAAAUGCUGGCAACACCUGUCAGCAGGUGCAGCCAUCUAGGAUCCUAUCCUUGCUCCCAAGGACGAAG------------UGGGU
.(((((.(((.((....)).(-((((((....((((...((((((((.....))))))))..))))....)))....)))).((((((....)))))))))..------------))))) ( -35.00)
>DroYak_CAF1 19775 120 - 1
UGCUCAGUUGCCAAAAAUGGAAGGAAGACAUAUGCAAAAUGCUGGCAACACCUGUCAGCAGGUGCAGCAAUCUAGGAUCCUAUCCUUGCUCCCAAGGACGCAGGUACGUUUGGUGGGGGA
.((......)).......((((((((((....((((...((((((((.....))))))))..))))....)))....)))).)))...((((((.(((((......)))))..)))))). ( -40.50)
>consensus
UGCUCAGUUGACAGAAAUGGA_GGAAGACAUAUGCAAAAUGCUGGCAACACCUGUCAGCAGGUGCAGCCAUCUAGGAUCCUAUCCUUGCUCCCAAGGACGAAG____________GGGGU
.((((.............(((....(((....((((...((((((((.....))))))))..))))....)))....)))..((((((....))))))..................)))) (-27.90 = -28.02 +   0.13)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:00:19 2006