Locus 3918

Sequence ID	3L_DroMel_CAF1
Location	11,345,193 – 11,345,363
Length	170
Max. P	0.999934

overview

Window 8

Location	11,345,193 – 11,345,307
Length	114
Sequences	3
Columns	114
Reading direction	forward
Mean pairwise identity	90.15
Mean single sequence MFE	-41.15
Consensus MFE	-33.48
Energy contribution	-33.48
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-3.13
Structure conservation index	0.81
SVM decision value	1.15
SVM RNA-class probability	0.923297
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11345193 114 + 23771897
AACUCCGGGAAACCGUAGCUCCUGUCCUCCACUAUCCUGACUAUCCUGUCCGUCCUGCCAGUUAGCCAGUUGGCCAGUUGGCCAUUUGGCUCUUUGGCCGUUUGGCUGUCAGGC
..((.(((....))).)).................((((((......(.(((..(.(((((..((((((.(((((....))))).))))))..))))).)..)))).)))))). ( -46.90)
>DroSec_CAF1 65735 107 + 1
AACUCCGGGAGCUUGCAGCUCCUGUCCUCCACUAUCCUGACUAUCCUAUCCGUCCU-------UGCCAGUUGGCCAGUUGGCCAUUUCGCUGUUUGGCCGUUUGGCUGUCAGGC
.....(((((((.....)))))))...........((((((...............-------.(((((.(((((((..(((......)))..))))))).))))).)))))). ( -40.53)
>DroSim_CAF1 74155 107 + 1
AACUCCGGGAAGCCGCAGCUCCUGUCCUCCACUAUCCUGACUAUCCUAUCCGUCCU-------UGCCAGUUGGCCAGUUGGCCAUUUCGCUGUUUGGCCGUUUGGCUGUCAGGC
.....(((((.((....)))))))...........((((((...............-------.(((((.(((((((..(((......)))..))))))).))))).)))))). ( -36.03)
>consensus
AACUCCGGGAAACCGCAGCUCCUGUCCUCCACUAUCCUGACUAUCCUAUCCGUCCU_______UGCCAGUUGGCCAGUUGGCCAUUUCGCUGUUUGGCCGUUUGGCUGUCAGGC
.....(((((.........)))))...........((((((.......................(((((.(((((((..(((......)))..))))))).))))).)))))). (-33.48 = -33.48 +  -0.00)

alignment

secondary structure

dotplot

Window 9

Location	11,345,233 – 11,345,342
Length	109
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	87.58
Mean single sequence MFE	-43.38
Consensus MFE	-39.44
Energy contribution	-39.88
Covariance contribution	0.44
Combinations/Pair	1.13
Mean z-score	-3.72
Structure conservation index	0.91
SVM decision value	4.66
SVM RNA-class probability	0.999934
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11345233 109 + 23771897
-CUAUCCUGUCCGUCCUGCCAGUUAGCCAGUUGGCCAGUUGGCCAUUUGGCUCUUUGGCCGUUUGGCUGUCAGGCAGCUGAAUAAUUUAGCUGCGAUAAUAAGCGGCUGC
-..............(((((...(((((((.(((((((..((((....))))..))))))).)))))))...)))))..........(((((((........))))))). ( -48.30)
>DroSec_CAF1 65775 102 + 1
-CUAUCCUAUCCGUCCU-------UGCCAGUUGGCCAGUUGGCCAUUUCGCUGUUUGGCCGUUUGGCUGUCAGGCAGCUGAAUAAUUUAGCUGCGAUAAUAAGCGGCUGU
-.........((((...-------.(((((.(((((((..(((......)))..))))))).)))))((((..((((((((.....))))))))))))....)))).... ( -38.60)
>DroSim_CAF1 74195 102 + 1
-CUAUCCUAUCCGUCCU-------UGCCAGUUGGCCAGUUGGCCAUUUCGCUGUUUGGCCGUUUGGCUGUCAGGCAGCUGAAUAAUUUAGCUGCGAUAAUAAGCGGCUGU
-.........((((...-------.(((((.(((((((..(((......)))..))))))).)))))((((..((((((((.....))))))))))))....)))).... ( -38.60)
>DroEre_CAF1 70195 108 + 1
--UGUCCUGUCCGUCCUGCUAGUUGGCCAUUUGGCUGUUUGGCCGUUUGGCUGUUUGGCCGUUUGGCUGUCAGGCAGCUGAAUAAUUUAGCUGCGAUAAUAAGCGGCUGC
--......................(((((..(((((....)))))..)))))....(((((((((..((((..((((((((.....)))))))))))).))))))))).. ( -42.60)
>DroYak_CAF1 59333 110 + 1
CCUGUCCUAUCCGUAAUGCUAGUUGGCCAUUUGGCUGUUUGGCCAUUUGGCCAUUUGGCCGUUUGGCUGUCAGGCAGCUGAAUAAUUUAGCCGCGAUAAUAAGCGGCUGU
.................(((((.((((((..(((((....)))))..)))))).))))).(((..((((.....))))..)))....(((((((........))))))). ( -48.80)
>consensus
_CUAUCCUAUCCGUCCUGC_AGUUGGCCAGUUGGCCAGUUGGCCAUUUGGCUGUUUGGCCGUUUGGCUGUCAGGCAGCUGAAUAAUUUAGCUGCGAUAAUAAGCGGCUGU
........................(((((..(((((....)))))..)))))....(((((((((..((((..((((((((.....)))))))))))).))))))))).. (-39.44 = -39.88 +   0.44)

alignment

secondary structure

dotplot

Window 0

Location	11,345,233 – 11,345,342
Length	109
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	87.58
Mean single sequence MFE	-33.24
Consensus MFE	-25.60
Energy contribution	-26.44
Covariance contribution	0.84
Combinations/Pair	1.04
Mean z-score	-2.45
Structure conservation index	0.77
SVM decision value	1.58
SVM RNA-class probability	0.965653
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11345233 109 - 23771897
GCAGCCGCUUAUUAUCGCAGCUAAAUUAUUCAGCUGCCUGACAGCCAAACGGCCAAAGAGCCAAAUGGCCAACUGGCCAACUGGCUAACUGGCAGGACGGACAGGAUAG-
((....))....((((((((((.........))))))(((....((...(.((((...(((((..(((((....)))))..)))))...)))).)...)).))))))).- ( -39.70)
>DroSec_CAF1 65775 102 - 1
ACAGCCGCUUAUUAUCGCAGCUAAAUUAUUCAGCUGCCUGACAGCCAAACGGCCAAACAGCGAAAUGGCCAACUGGCCAACUGGCA-------AGGACGGAUAGGAUAG-
....((((((......((((((.........))))))......((((...(((((....((......))....)))))...)))).-------))).))).........- ( -30.00)
>DroSim_CAF1 74195 102 - 1
ACAGCCGCUUAUUAUCGCAGCUAAAUUAUUCAGCUGCCUGACAGCCAAACGGCCAAACAGCGAAAUGGCCAACUGGCCAACUGGCA-------AGGACGGAUAGGAUAG-
....((((((......((((((.........))))))......((((...(((((....((......))....)))))...)))).-------))).))).........- ( -30.00)
>DroEre_CAF1 70195 108 - 1
GCAGCCGCUUAUUAUCGCAGCUAAAUUAUUCAGCUGCCUGACAGCCAAACGGCCAAACAGCCAAACGGCCAAACAGCCAAAUGGCCAACUAGCAGGACGGACAGGACA--
...(((((((......((((((.........))))))......((((...(((......)))....(((......)))...))))........))).))).)......-- ( -27.90)
>DroYak_CAF1 59333 110 - 1
ACAGCCGCUUAUUAUCGCGGCUAAAUUAUUCAGCUGCCUGACAGCCAAACGGCCAAAUGGCCAAAUGGCCAAACAGCCAAAUGGCCAACUAGCAUUACGGAUAGGACAGG
..((((((........))))))...........(((((((.(.(((....)))....((((((..((((......))))..))))))............).)))).))). ( -38.60)
>consensus
ACAGCCGCUUAUUAUCGCAGCUAAAUUAUUCAGCUGCCUGACAGCCAAACGGCCAAACAGCCAAAUGGCCAACUGGCCAACUGGCAAACU_GCAGGACGGAUAGGAUAG_
....((..........((((((.........))))))(((...(((....)))......((((..(((((....)))))..))))............)))...))..... (-25.60 = -26.44 +   0.84)

alignment

secondary structure

dotplot

Window 1

Location	11,345,271 – 11,345,363
Length	92
Sequences	6
Columns	92
Reading direction	forward
Mean pairwise identity	85.81
Mean single sequence MFE	-35.70
Consensus MFE	-26.80
Energy contribution	-27.53
Covariance contribution	0.74
Combinations/Pair	1.15
Mean z-score	-3.59
Structure conservation index	0.75
SVM decision value	0.99
SVM RNA-class probability	0.895682
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11345271 92 + 23771897
UGGCCAUUUGGCUCUUUGGCCGUUUGGCUGUCAGGCAGCUGAAUAAUUUAGCUGCGAUAAUAAGCGGCUGCAGUGCCAGUGUCCACUGGUUG
(((.((((.(((.((.((((((((((..((((..((((((((.....)))))))))))).)))))))))).)).))))))).)))....... ( -40.70)
>DroSec_CAF1 65806 87 + 1
UGGCCAUUUCGCUGUUUGGCCGUUUGGCUGUCAGGCAGCUGAAUAAUUUAGCUGCGAUAAUAAGCGGCUGUAGUGC-AGUGUCCACUG----
(((.((((.(((((..((((((((((..((((..((((((((.....)))))))))))).))))))))))))))).-)))).)))...---- ( -37.10)
>DroSim_CAF1 74226 87 + 1
UGGCCAUUUCGCUGUUUGGCCGUUUGGCUGUCAGGCAGCUGAAUAAUUUAGCUGCGAUAAUAAGCGGCUGUAGUGC-AGUGUCCACUG----
(((.((((.(((((..((((((((((..((((..((((((((.....)))))))))))).))))))))))))))).-)))).)))...---- ( -37.10)
>DroEre_CAF1 70232 87 + 1
UGGCCGUUUGGCUGUUUGGCCGUUUGGCUGUCAGGCAGCUGAAUAAUUUAGCUGCGAUAAUAAGCGGCUGCAGUGC-AGUGUCCACUG----
.(((((((((.(((..(((((....))))).)))((((((((.....)))))))).....))))))))).(((((.-......)))))---- ( -35.60)
>DroYak_CAF1 59372 91 + 1
UGGCCAUUUGGCCAUUUGGCCGUUUGGCUGUCAGGCAGCUGAAUAAUUUAGCCGCGAUAAUAAGCGGCUGUAGUGC-AGUGUCCACUCGUCC
.(((((..(((((....)))))..)))))....((..((((....((((((((((........))))))).))).)-)))..))........ ( -38.20)
>DroAna_CAF1 57808 71 + 1
------------CAGUUG---GUCCGGCUGUCAGGCUGCUGAAUAAUUUAGCUGCGAUAAUAAGCGGCUGUAGC-C-AGUGUCCACUG----
------------((((.(---(.(((((((((((....))))......(((((((........)))))))))))-)-.).).))))))---- ( -25.50)
>consensus
UGGCCAUUUGGCUGUUUGGCCGUUUGGCUGUCAGGCAGCUGAAUAAUUUAGCUGCGAUAAUAAGCGGCUGUAGUGC_AGUGUCCACUG____
.(((((..........)))))(((((((((.....)))))))))....(((((((........)))))))(((((........))))).... (-26.80 = -27.53 +   0.74)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:09:59 2006