Locus 3622

Sequence ID	X_DroMel_CAF1
Location	9,688,946 – 9,689,085
Length	139
Max. P	0.992964

overview

Window 7

Location	9,688,946 – 9,689,048
Length	102
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	90.70
Mean single sequence MFE	-32.90
Consensus MFE	-26.60
Energy contribution	-27.72
Covariance contribution	1.12
Combinations/Pair	1.14
Mean z-score	-1.94
Structure conservation index	0.81
SVM decision value	1.25
SVM RNA-class probability	0.935929
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9688946 102 + 22224390
GGUUUUCUCAUGCAGUUAACGCCCAGGAUCUGUCCAUAUU--UUGGAUGUCUGAGCAGGAAGC-UUUUUUGUGCGAAUGAGUAUAGCUUCUGCUCGGACUGUGGC
.(((..((.....))..)))((((((.....(((((....--.))))).(((((((((.((((-(.....((((......))))))))))))))))))))).))) ( -36.10)
>DroSec_CAF1 30968 102 + 1
GGUUUUCUCAUGCAGUUAACGCCCAGGAUCUGCCCAUAUU--UUGGGUGUCUGAGCAGGAAGC-UUUUUUGUACGAAUGAGUAUAGCUUCUGCUCGGACUGUGGC
.(((..((.....))..)))((((((.....(((((....--.))))).(((((((((.((((-(.....((((......))))))))))))))))))))).))) ( -38.10)
>DroSim_CAF1 4981 103 + 1
GGUUUUCUCAUGCAGUUAACGCCCAGAAUCUGCCCAUAUU--UUGGGUGUCUGAGCAGGAAGCCUUUUUUGUGCGAAUGAGUAUAGCUUCUGCUCGGACUGUGGC
...........(((((..(((((((((((........)))--))))))))((((((((.((((......(((((......))))))))))))))))))))))... ( -37.30)
>DroEre_CAF1 8479 101 + 1
GCUUUUCUCAUGCAGUUAACGCCCAGGAUUUGGCCAUAUU--UUGGUUGUCUGAGCAGGAAGC-UGUUUUGUGCGAAUGAGUAUAGCUGCU-CUCGGACUGUGGC
((.........)).......((((((.....(((((....--.))))).((((((.((..(((-(((((..(....)..)).)))))).))-))))))))).))) ( -29.00)
>DroYak_CAF1 6105 96 + 1
GCUUUUCUCAUGCAGUUAACGCCCAGGAUCUGCCCAUAUUUUUUGGGUGUCUG--------CC-UUUUUUGUGUGAAUGAGUAUAGCUUCUGCUCGGACUGUGGC
((..(((((((((((..((.((...((((..(((((.......))))))))))--------).-))..))))))))..(((((.......))))))))..))... ( -24.00)
>consensus
GGUUUUCUCAUGCAGUUAACGCCCAGGAUCUGCCCAUAUU__UUGGGUGUCUGAGCAGGAAGC_UUUUUUGUGCGAAUGAGUAUAGCUUCUGCUCGGACUGUGGC
....................((((((.....(((((.......))))).(((((((((.((((......(((((......))))))))))))))))))))).))) (-26.60 = -27.72 +   1.12)

alignment

secondary structure

dotplot

Window 8

Location	9,688,971 – 9,689,085
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	86.25
Mean single sequence MFE	-40.34
Consensus MFE	-31.76
Energy contribution	-33.12
Covariance contribution	1.36
Combinations/Pair	1.19
Mean z-score	-2.85
Structure conservation index	0.79
SVM decision value	2.36
SVM RNA-class probability	0.992964
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9688971 114 + 22224390
GGAUCUGUCCAUAUU--UUGGAUGUCUGAGCAGGAAGC-UUUUUUGUGCGAAUGAGUAUAGCUUCUGCUCGGACUGUGGCCACUUCUCAAGUUGAAAAUGAGAGGGUG---CUGCCAUAA
......(((((....--.)))))((((((((((.((((-(.....((((......)))))))))))))))))))(((((((((((((((.........))))).))))---..)))))). ( -45.20)
>DroSec_CAF1 30993 114 + 1
GGAUCUGCCCAUAUU--UUGGGUGUCUGAGCAGGAAGC-UUUUUUGUACGAAUGAGUAUAGCUUCUGCUCGGACUGUGGCUACUGCUCAAGUUGAAAAUGAGAGGGUG---GUGCCACAA
......(((((....--.)))))((((((((((.((((-(.....((((......)))))))))))))))))))((((((.((..(((...............)))..---)))))))). ( -48.86)
>DroSim_CAF1 5006 115 + 1
GAAUCUGCCCAUAUU--UUGGGUGUCUGAGCAGGAAGCCUUUUUUGUGCGAAUGAGUAUAGCUUCUGCUCGGACUGUGGCCACUGCUCAAGUUGAAAAUGAGAGGGUG---GUGCCACAA
......(((((....--.)))))((((((((((.((((......(((((......)))))))))))))))))))((((((.((..(((...............)))..---)))))))). ( -47.86)
>DroEre_CAF1 8504 112 + 1
GGAUUUGGCCAUAUU--UUGGUUGUCUGAGCAGGAAGC-UGUUUUGUGCGAAUGAGUAUAGCUGCU-CUCGGACUGUGGCCACUUCUCAAGAUGAAAAUGACAGGGUG----UGCUAUAU
......(((((....--.)))))(((((((.((..(((-(((((..(....)..)).)))))).))-)))))))(((((((((((.(((.........)))..)))))----.)))))). ( -33.80)
>DroYak_CAF1 6130 111 + 1
GGAUCUGCCCAUAUUUUUUGGGUGUCUG--------CC-UUUUUUGUGUGAAUGAGUAUAGCUUCUGCUCGGACUGUGGCCACUUCUCAAGUUGAAAAUGAGGGGGCGGUGUUGCUAUUG
((((..(((((.......))))))))).--------..-..................(((((..((((((((.(....)))...(((((.........)))))))))))....))))).. ( -26.00)
>consensus
GGAUCUGCCCAUAUU__UUGGGUGUCUGAGCAGGAAGC_UUUUUUGUGCGAAUGAGUAUAGCUUCUGCUCGGACUGUGGCCACUUCUCAAGUUGAAAAUGAGAGGGUG___GUGCCAUAA
......(((((.......)))))((((((((((.((((......(((((......)))))))))))))))))))((((((..(((((((.........)))))))........)))))). (-31.76 = -33.12 +   1.36)

alignment

secondary structure

dotplot

Window 9

Location	9,688,971 – 9,689,085
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	86.25
Mean single sequence MFE	-28.35
Consensus MFE	-16.37
Energy contribution	-18.97
Covariance contribution	2.60
Combinations/Pair	1.07
Mean z-score	-2.56
Structure conservation index	0.58
SVM decision value	-0.04
SVM RNA-class probability	0.515585
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9688971 114 - 22224390
UUAUGGCAG---CACCCUCUCAUUUUCAACUUGAGAAGUGGCCACAGUCCGAGCAGAAGCUAUACUCAUUCGCACAAAAAA-GCUUCCUGCUCAGACAUCCAA--AAUAUGGACAGAUCC
...((((..---(((..(((((.........))))).)))))))..(((.(((((((((((...................)-)))).)))))).))).((((.--....))))....... ( -33.21)
>DroSec_CAF1 30993 114 - 1
UUGUGGCAC---CACCCUCUCAUUUUCAACUUGAGCAGUAGCCACAGUCCGAGCAGAAGCUAUACUCAUUCGUACAAAAAA-GCUUCCUGCUCAGACACCCAA--AAUAUGGGCAGAUCC
.((((((..---.((...((((.........))))..)).))))))(((.(((((((((((.(((......)))......)-)))).)))))).))).((((.--....))))....... ( -34.40)
>DroSim_CAF1 5006 115 - 1
UUGUGGCAC---CACCCUCUCAUUUUCAACUUGAGCAGUGGCCACAGUCCGAGCAGAAGCUAUACUCAUUCGCACAAAAAAGGCUUCCUGCUCAGACACCCAA--AAUAUGGGCAGAUUC
.((((((..---(((...((((.........))))..)))))))))(((.(((((((((((....................))))).)))))).))).((((.--....))))....... ( -36.95)
>DroEre_CAF1 8504 112 - 1
AUAUAGCA----CACCCUGUCAUUUUCAUCUUGAGAAGUGGCCACAGUCCGAG-AGCAGCUAUACUCAUUCGCACAAAACA-GCUUCCUGCUCAGACAACCAA--AAUAUGGCCAAAUCC
........----..........(((((.....))))).((((((..((.((((-((........)))..))).)).....(-((.....)))...........--....))))))..... ( -18.70)
>DroYak_CAF1 6130 111 - 1
CAAUAGCAACACCGCCCCCUCAUUUUCAACUUGAGAAGUGGCCACAGUCCGAGCAGAAGCUAUACUCAUUCACACAAAAAA-GG--------CAGACACCCAAAAAAUAUGGGCAGAUCC
.............(((..((((.........))))..((((....(((...(((....)))..)))...))))........-))--------).....((((.......))))....... ( -18.50)
>consensus
UUAUGGCAC___CACCCUCUCAUUUUCAACUUGAGAAGUGGCCACAGUCCGAGCAGAAGCUAUACUCAUUCGCACAAAAAA_GCUUCCUGCUCAGACACCCAA__AAUAUGGGCAGAUCC
...((((.....(((...((((.........))))..)))))))..(((.((((((((((......................)))).)))))).))).((((.......))))....... (-16.37 = -18.97 +   2.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:03:59 2006