Locus 434

Sequence ID	3R_DroMel_CAF1
Location	1,629,976 – 1,630,117
Length	141
Max. P	0.998276

overview

Window 5

Location	1,629,976 – 1,630,085
Length	109
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	81.47
Mean single sequence MFE	-32.18
Consensus MFE	-24.48
Energy contribution	-24.92
Covariance contribution	0.44
Combinations/Pair	1.04
Mean z-score	-1.87
Structure conservation index	0.76
SVM decision value	0.78
SVM RNA-class probability	0.848353
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1629976 109 + 27905053
UUCUAGCUGAUUUGUCAUGUGGAUGUGGAUGUAGUUGUGAAUGUCGAUG--UGUGUGUGGAUGCAAGGAUGCGAGCAUGCAGAAUGCCCACAUGCAAGUGCGGCUGUGUGU
...(((((((((((.(((((((((((.(((((........))))).)))--)((((((...((((....)))).)))))).......)))))))))))).))))))..... ( -35.50)
>DroSec_CAF1 9295 111 + 1
UUCUAGCUGAUUUGUCAUGUGGAUGUGGAUGUAGAUGUGGAUGUAGAUGAGUGUGUGCGGAUGCAGGGAUGCGAGCAUGCAGAAUGCCCACAUGCAAGUGCGGCUGUGUGU
...(((((((((((.(((((((.......((((..((((..((((.((....)).))))..))))....)))).((((.....)))))))))))))))).))))))..... ( -35.60)
>DroSim_CAF1 9299 111 + 1
UUCUAGCUGAUUUGUCAUGUGGAUGUGGAUGUAGAUGUGGAUGUGGAUGAGUGUGUGCGGAUGCAAGGAUGCGAGCAUGCAGAAUGCCCACAUGCAAGUGCGGCUGUGUGU
...(((((((((((.(((((((.......((((....((.((.((.((......)).)).)).))....)))).((((.....)))))))))))))))).))))))..... ( -34.20)
>DroEre_CAF1 9445 85 + 1
UUCUAGCUGAUUUGUCAUGUGGAUGUGGAUGUGGC--------------------------UGCAAGGAUGCCAGCAUGCAGAAUACCCACAUGCAAGUACGCCUGUGUGU
.....((..(((((.(((((((.(((...((((((--------------------------((((....)).)))).))))..))).))))))))))))..))........ ( -26.30)
>DroYak_CAF1 8676 90 + 1
UUCUAGCUGAUUUGUCAUGUGGAUGUGGAUGUAGC---------------------AAGGAUGCAAGGAUGCCAGCAUGCAGAAUGUCCACAAGCAAGUGCGGCUGUGUGU
...((((((((((((..(((((((((...((((((---------------------..(.((......)).)..)).))))..))))))))).)))))).))))))..... ( -29.30)
>consensus
UUCUAGCUGAUUUGUCAUGUGGAUGUGGAUGUAGAUGUG_AUGU_GAUG__UGUGUGCGGAUGCAAGGAUGCGAGCAUGCAGAAUGCCCACAUGCAAGUGCGGCUGUGUGU
...(((((((((((.(((((((........................................(((....)))..((((.....)))))))))))))))).))))))..... (-24.48 = -24.92 +   0.44)

alignment

secondary structure

dotplot

Window 6

Location	1,629,976 – 1,630,085
Length	109
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	81.47
Mean single sequence MFE	-20.32
Consensus MFE	-16.70
Energy contribution	-17.14
Covariance contribution	0.44
Combinations/Pair	1.05
Mean z-score	-2.21
Structure conservation index	0.82
SVM decision value	1.57
SVM RNA-class probability	0.964750
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1629976 109 - 27905053
ACACACAGCCGCACUUGCAUGUGGGCAUUCUGCAUGCUCGCAUCCUUGCAUCCACACACA--CAUCGACAUUCACAACUACAUCCACAUCCACAUGACAAAUCAGCUAGAA
......(((.(...((((((((((((((.....))))..(((....)))...........--...........................))))))).)))..).))).... ( -20.20)
>DroSec_CAF1 9295 111 - 1
ACACACAGCCGCACUUGCAUGUGGGCAUUCUGCAUGCUCGCAUCCCUGCAUCCGCACACACUCAUCUACAUCCACAUCUACAUCCACAUCCACAUGACAAAUCAGCUAGAA
......(((.(...((((((((((((((.....))))..(((....)))........................................))))))).)))..).))).... ( -19.40)
>DroSim_CAF1 9299 111 - 1
ACACACAGCCGCACUUGCAUGUGGGCAUUCUGCAUGCUCGCAUCCUUGCAUCCGCACACACUCAUCCACAUCCACAUCUACAUCCACAUCCACAUGACAAAUCAGCUAGAA
......(((.(...((((((((((((((.....))))..(((....)))........................................))))))).)))..).))).... ( -20.20)
>DroEre_CAF1 9445 85 - 1
ACACACAGGCGUACUUGCAUGUGGGUAUUCUGCAUGCUGGCAUCCUUGCA--------------------------GCCACAUCCACAUCCACAUGACAAAUCAGCUAGAA
.......(((....((((((((((((....((.(((.((((.........--------------------------))))))).)).))))))))).)))....))).... ( -24.30)
>DroYak_CAF1 8676 90 - 1
ACACACAGCCGCACUUGCUUGUGGACAUUCUGCAUGCUGGCAUCCUUGCAUCCUU---------------------GCUACAUCCACAUCCACAUGACAAAUCAGCUAGAA
......(((.((....)).((((((......(((.....(((....))).....)---------------------))....))))))................))).... ( -17.50)
>consensus
ACACACAGCCGCACUUGCAUGUGGGCAUUCUGCAUGCUCGCAUCCUUGCAUCCGCACACA__CAUC_ACAU_CACAGCUACAUCCACAUCCACAUGACAAAUCAGCUAGAA
......(((.(...((((((((((((((.....))))..(((....)))........................................))))))).)))..).))).... (-16.70 = -17.14 +   0.44)

alignment

secondary structure

dotplot

Window 7

Location	1,630,012 – 1,630,117
Length	105
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	78.76
Mean single sequence MFE	-36.94
Consensus MFE	-26.50
Energy contribution	-27.14
Covariance contribution	0.64
Combinations/Pair	1.03
Mean z-score	-1.64
Structure conservation index	0.72
SVM decision value	0.54
SVM RNA-class probability	0.773765
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1630012 105 + 27905053
GUGAAUGUCGAUG--UGUGUGUGGAUGCAAGGAUGCGAGCAUGCAGAAUGCCCACAUGCAAGUGCGGCUGUGUGUGCGCGUGGGC----AUGGCUACGUGCGG----UUGUGUGC
......((((...--(((((((((.((((....)))).((((.....)))))))))))))....)))).....(..((((...((----(((....)))))..----.))))..) ( -37.50)
>DroSec_CAF1 9331 107 + 1
GUGGAUGUAGAUGAGUGUGUGCGGAUGCAGGGAUGCGAGCAUGCAGAAUGCCCACAUGCAAGUGCGGCUGUGUGUGCGCGUGGGC----AUGGCUACGUGCGG----UUGUGUGC
.((.((((((.....(((((((...((((....)))).)))))))..((((((((.((((.(..(....)..).)))).))))))----))..)))))).)).----........ ( -40.90)
>DroSim_CAF1 9335 107 + 1
GUGGAUGUGGAUGAGUGUGUGCGGAUGCAAGGAUGCGAGCAUGCAGAAUGCCCACAUGCAAGUGCGGCUGUGUGUGCGCGUGGGC----AUGGCUACGUGCGG----UUGUGUGC
.((.((((((.....(((((((...((((....)))).)))))))..((((((((.((((.(..(....)..).)))).))))))----))..)))))).)).----........ ( -39.80)
>DroEre_CAF1 9480 82 + 1
-------------------------UGCAAGGAUGCCAGCAUGCAGAAUACCCACAUGCAAGUACGCCUGUGUGUGCGCGUGGGC----AUGGCUACAUGCGG----UUGUGUGC
-------------------------.(((.....(((.(((((.((.((.(((((.((((..(((....)))..)))).))))).----))..)).)))))))----)....))) ( -30.40)
>DroYak_CAF1 8711 95 + 1
--------------------AAGGAUGCAAGGAUGCCAGCAUGCAGAAUGUCCACAAGCAAGUGCGGCUGUGUGUGCGCGUGUGCAUGCAUGGCUACAUGUGGUUGGUUGUGUGC
--------------------......(((....)))..((((((((.....(((((.((....))(((((((((((((....)))))))))))))...)))))....)))))))) ( -36.10)
>consensus
GUG_AUGU_GAUG__UGUGUGCGGAUGCAAGGAUGCGAGCAUGCAGAAUGCCCACAUGCAAGUGCGGCUGUGUGUGCGCGUGGGC____AUGGCUACGUGCGG____UUGUGUGC
..........................(((....)))..((((((((.....(((((((((........)))))))((((((((.(......).))))))))))....)))))))) (-26.50 = -27.14 +   0.64)

alignment

secondary structure

dotplot

Window 8

Location	1,630,012 – 1,630,117
Length	105
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	78.76
Mean single sequence MFE	-29.42
Consensus MFE	-18.86
Energy contribution	-19.30
Covariance contribution	0.44
Combinations/Pair	1.05
Mean z-score	-3.06
Structure conservation index	0.64
SVM decision value	3.05
SVM RNA-class probability	0.998276
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1630012 105 - 27905053
GCACACAA----CCGCACGUAGCCAU----GCCCACGCGCACACACAGCCGCACUUGCAUGUGGGCAUUCUGCAUGCUCGCAUCCUUGCAUCCACACACA--CAUCGACAUUCAC
........----..(((.((((..((----(((((((.((.......)))((....))..)))))))).)))).)))..(((....)))...........--............. ( -28.20)
>DroSec_CAF1 9331 107 - 1
GCACACAA----CCGCACGUAGCCAU----GCCCACGCGCACACACAGCCGCACUUGCAUGUGGGCAUUCUGCAUGCUCGCAUCCCUGCAUCCGCACACACUCAUCUACAUCCAC
((......----..(((.((((..((----(((((((.((.......)))((....))..)))))))).)))).)))..(((....)))....)).................... ( -29.90)
>DroSim_CAF1 9335 107 - 1
GCACACAA----CCGCACGUAGCCAU----GCCCACGCGCACACACAGCCGCACUUGCAUGUGGGCAUUCUGCAUGCUCGCAUCCUUGCAUCCGCACACACUCAUCCACAUCCAC
((......----..(((.((((..((----(((((((.((.......)))((....))..)))))))).)))).)))..(((....)))....)).................... ( -30.70)
>DroEre_CAF1 9480 82 - 1
GCACACAA----CCGCAUGUAGCCAU----GCCCACGCGCACACACAGGCGUACUUGCAUGUGGGUAUUCUGCAUGCUGGCAUCCUUGCA-------------------------
(((.....----((((((((((..((----(((((((.(((...((....))...))).))))))))).)))))))).))......))).------------------------- ( -32.60)
>DroYak_CAF1 8711 95 - 1
GCACACAACCAACCACAUGUAGCCAUGCAUGCACACGCGCACACACAGCCGCACUUGCUUGUGGACAUUCUGCAUGCUGGCAUCCUUGCAUCCUU--------------------
(((.(((..........))).((((.(((((((.....(..((((.(((.......)))))))..)....))))))))))).....)))......-------------------- ( -25.70)
>consensus
GCACACAA____CCGCACGUAGCCAU____GCCCACGCGCACACACAGCCGCACUUGCAUGUGGGCAUUCUGCAUGCUCGCAUCCUUGCAUCCGCACACA__CAUC_ACAU_CAC
..............(((.((((........(((((((.(((..............))).)))))))...)))).)))..(((....))).......................... (-18.86 = -19.30 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:43:06 2006