Locus 3269

Sequence ID	3R_DroMel_CAF1
Location	8,727,514 – 8,727,643
Length	129
Max. P	0.974778

overview

Window 9

Location	8,727,514 – 8,727,613
Length	99
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	78.03
Mean single sequence MFE	-28.57
Consensus MFE	-15.66
Energy contribution	-15.38
Covariance contribution	-0.27
Combinations/Pair	1.22
Mean z-score	-2.71
Structure conservation index	0.55
SVM decision value	1.74
SVM RNA-class probability	0.974732
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8727514 99 + 27905053
GUUU----CCUCCUCCACUGAUUGCCGGCUCUU---------GC--CAAAAACGGAUCAAAAGUUAAAUUCCUGUUUGACUUUUCAUUCGAAAAAUUGGAUUUUGCAUUUAGCC
....----.........((((.(((.(((....---------))--).....(((((.(((((((((((....))))))))))).)))))..............))).)))).. ( -24.80)
>DroVir_CAF1 189006 103 + 1
CUGCCGACUG----CUGUUGACUGUUGACUGCUUAGGCA---GC--C--AAACGGAUCAAAAGUUAAACUCAUGUUUGACUUUUCAUUCGAAAAAUUGGAUUUUGCAUUUGGGC
(((((....(----(.((..(...)..)).))...))))---)(--(--((((((((.(((((((((((....))))))))))).)))))((((......))))...))))).. ( -30.80)
>DroPse_CAF1 169493 106 + 1
CUGC----UGUUGACUGCUGAUUGCUGACUGCUUAGGCAGCAGC--C--AAACGGAUCAAAAGUUAAAUUCCUGUUUGACUUUUCAUUCGAAAAAUUGGAUUUUGCAUUUUCCC
....----(((......(..(((((((.((((....))))))))--.--...(((((.(((((((((((....))))))))))).)))))...)))..).....)))....... ( -29.90)
>DroGri_CAF1 155792 106 + 1
CGUUUCACUGU-GAAUGUUGACUGUUGGCUGCUUAGGCA---GC--C--AAACGGAUCAAAAGUUAAGCUCAUGUUUGACUUUUCAUUCGAAAAAUUGGAUUUUGCAUUUGGGC
...((((.((.-.((..(..(...((((((((....)))---))--)--)).(((((.(((((((((((....))))))))))).))))).....)..)..))..))..)))). ( -33.80)
>DroAna_CAF1 144671 96 + 1
GUUC----CC---AACACUGAUUGCUGACUCUU---------GCAGCCAAAACGAAUCAAAAGUUAAAUUCCUGUUUGACUUUUCAUUCGAAAAAUUGGAUUUUGCAUUUAG--
....----((---((........((((.(....---------))))).....(((((.(((((((((((....))))))))))).))))).....)))).............-- ( -22.20)
>DroPer_CAF1 165468 106 + 1
CUGC----UGUUGACUGCUGAUUGCUGACUGCUUAGGCAGCAGC--C--AAACGGAUCAAAAGUUAAAUUCCUGUUUGACUUUUCAUUCGAAAAAUUGGAUUUUGCAUUUUCCC
....----(((......(..(((((((.((((....))))))))--.--...(((((.(((((((((((....))))))))))).)))))...)))..).....)))....... ( -29.90)
>consensus
CUGC____UGU_GACUGCUGAUUGCUGACUGCUUAGGCA___GC__C__AAACGGAUCAAAAGUUAAAUUCCUGUUUGACUUUUCAUUCGAAAAAUUGGAUUUUGCAUUUAGCC
.................((((.(((...........................(((((.(((((((((((....))))))))))).)))))((((......))))))).)))).. (-15.66 = -15.38 +  -0.27)

alignment

secondary structure

dotplot

Window 0

Location	8,727,543 – 8,727,643
Length	100
Sequences	6
Columns	112
Reading direction	forward
Mean pairwise identity	77.23
Mean single sequence MFE	-21.90
Consensus MFE	-14.59
Energy contribution	-14.32
Covariance contribution	-0.28
Combinations/Pair	1.12
Mean z-score	-2.28
Structure conservation index	0.67
SVM decision value	1.74
SVM RNA-class probability	0.974778
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8727543 100 + 27905053
------GC--CAAAAACGGAUCAAAAGUUAAAUUCCUGUUUGACUUUUCAUUCGAAAAAUUGGAUUUUGCAUUUAGCCAGGGAUGCCGAG-GAAAAAGUUUCCGCCCAU---
------..--......(((((.(((((((((((....))))))))))).)))))......(((.....((((((......))))))...(-(((.....))))..))).--- ( -24.00)
>DroVir_CAF1 189039 89 + 1
CA----GC--C--AAACGGAUCAAAAGUUAAACUCAUGUUUGACUUUUCAUUCGAAAAAUUGGAUUUUGCAUUUGGGC--------------AAAAAGUUUUCUGCUAG-CC
.(----((--.--...(((((.(((((((((((....))))))))))).)))))..........((((((......))--------------))))........)))..-.. ( -22.90)
>DroPse_CAF1 169526 101 + 1
CAGC-AGC--C--AAACGGAUCAAAAGUUAAAUUCCUGUUUGACUUUUCAUUCGAAAAAUUGGAUUUUGCAUUUUCCCA------CCGACAGAAAAACUUUCGCCCCACGCC
..((-(.(--(--((.(((((.(((((((((((....))))))))))).))))).....))))....))).........------.(((.((.....)).)))......... ( -19.80)
>DroWil_CAF1 190955 91 + 1
CAACCGGG--C--AAACGGAUCAAAAGUUAAAUUCAUGUUUGACUUUUCAUUCGAAAAAUUGGAUUUUGCAUUUGCCCA----------A-CAAAACUUUUC---UCAC---
.....(((--(--((((((((.(((((((((((....))))))))))).)))))((((......))))...))))))).----------.-...........---....--- ( -23.70)
>DroAna_CAF1 144697 99 + 1
------GCAGCCAAAACGAAUCAAAAGUUAAAUUCCUGUUUGACUUUUCAUUCGAAAAAUUGGAUUUUGCAUUUAG---AGCUUGCCGAC-GAAAAAGUUUCCACCCAC---
------(((.((((..(((((.(((((((((((....))))))))))).))))).....))))....))).....(---(((((......-....))))))........--- ( -21.20)
>DroPer_CAF1 165501 101 + 1
CAGC-AGC--C--AAACGGAUCAAAAGUUAAAUUCCUGUUUGACUUUUCAUUCGAAAAAUUGGAUUUUGCAUUUUCCCA------CCGACAGAAAAACUUUCGCCCCACGCC
..((-(.(--(--((.(((((.(((((((((((....))))))))))).))))).....))))....))).........------.(((.((.....)).)))......... ( -19.80)
>consensus
CA____GC__C__AAACGGAUCAAAAGUUAAAUUCCUGUUUGACUUUUCAUUCGAAAAAUUGGAUUUUGCAUUUACCCA______CCGAC_GAAAAAGUUUCCCCCCAC___
................(((((.(((((((((((....))))))))))).))))).......................................................... (-14.59 = -14.32 +  -0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:57:08 2006