Locus 5861

Sequence ID	2R_DroMel_CAF1
Location	18,532,220 – 18,532,355
Length	135
Max. P	0.913067

overview

Window 1

Location	18,532,220 – 18,532,318
Length	98
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	76.46
Mean single sequence MFE	-21.96
Consensus MFE	-14.76
Energy contribution	-14.98
Covariance contribution	0.22
Combinations/Pair	1.13
Mean z-score	-1.65
Structure conservation index	0.67
SVM decision value	1.09
SVM RNA-class probability	0.913067
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18532220 98 - 20766785
GUCACAAAUUGAGUUAACGCUGCCAAAUUAGCGGCAUGAAUUUAUCGC-UCGGCCA-----ACGGCCAA-----CAACAAAAUCAACUGGCCAAACGCAAAAGCAAAGU--------
.........((((((...(((((.......)))))...))))))..((-(..((..-----..(((((.-----.............)))))....))...))).....-------- ( -21.74)
>DroPse_CAF1 13962 102 - 1
GUCACAAAUUGAGUUAACGCUGCCAAAUUAGCGGCAUGAAUUUAUCGC-UCGGCCA-----ACGGCCAG-----CCACAAAACAAAA---CCA-AUCCGAAACCAAAGCACAACCAC
.......((((.(((...(((((.......)))))...........((-(.((((.-----..))))))-----)..........))---)))-))..................... ( -19.10)
>DroWil_CAF1 17310 100 - 1
GUCACAAAUUGAGUUAACGCUGCCAAAUUAGCAGCAUGAAUUUAUCGCCUUGGUCAGUUAAACAGAGA-------GACAAAGAGAUCCAGGCGAGUGCA--GGCAAAGA--------
(((......((((((...(((((.......)))))...))))))((((((.((((.............-------........)))).)))))).....--))).....-------- ( -25.60)
>DroYak_CAF1 12909 99 - 1
GUCACAAAUUGAGUUAACGCUGCCAAAUUAGCGGCAUGAAUUUAUCGC-UCGGCCA----AACGGCCAA-----CAACAAAAUCAACUGGCCAAACGCAAAAGCAAACG--------
((((......((((....(((((.......)))))..((.....))))-))((((.----...))))..-----.............)))).....((....)).....-------- ( -21.80)
>DroAna_CAF1 11457 98 - 1
GUCACAAAUUGAGUUAACGCUGCCAAAUUAGCGGCAUGAAUUUAUCGC-CCGGCCA-----ACGGCCACUUGGCCAACAAAAGCAAAU---CCGAGGCAGAGCCAAA----------
........(((.(((...(((((.......)))))...........((-((((...-----..((((....))))..(....).....---))).)))..)))))).---------- ( -24.40)
>DroPer_CAF1 12989 102 - 1
GUCACAAAUUGAGUUAACGCUGCCAAAUUAGCGGCAUGAAUUUAUCGC-UCGGCCA-----ACGGCCAG-----CCACAAAACAAAA---CCA-AUCCGAAACCAAAGCACAACCAC
.......((((.(((...(((((.......)))))...........((-(.((((.-----..))))))-----)..........))---)))-))..................... ( -19.10)
>consensus
GUCACAAAUUGAGUUAACGCUGCCAAAUUAGCGGCAUGAAUUUAUCGC_UCGGCCA_____ACGGCCAA_____CAACAAAACCAAAU__CCAAAUGCAAAACCAAAGC________
.........((((((...(((((.......)))))...)))))).......((((........)))).................................................. (-14.76 = -14.98 +   0.22)

alignment

secondary structure

dotplot

Window 2

Location	18,532,252 – 18,532,355
Length	103
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	82.70
Mean single sequence MFE	-29.80
Consensus MFE	-19.50
Energy contribution	-19.50
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.11
Structure conservation index	0.65
SVM decision value	0.25
SVM RNA-class probability	0.654412
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18532252 103 + 20766785
UUG-----UUGGCCGU-----UGG--CCG-A-GCGAUAAAUUCAUGCCGCUAAUUUGGCAGCGUUAACUCAAUUUGUGACCACAAAA-UGCACAAUUUGUCGCUGAUUUUGAUUGCCC--
...-----((((((..-----.))--)))-)-((((((((((..(((((......)))))(((((........((((....))))))-)))..))))))))))...............-- ( -28.30)
>DroVir_CAF1 12180 102 + 1
CUC------CAUUCGU-----UU----GG-A-GCGAUAAAUUUAUGCCGCUAAUUUGGCAGCGUUAACUCAAUUUGUGACCACAAAA-UGCACAAUUUGUCGCGGCUUUUGAUUGCCACA
.((------((.....-----.)----))-)-((((((((((..(((((......)))))(((((........((((....))))))-)))..))))))))))(((........)))... ( -30.30)
>DroGri_CAF1 13236 101 + 1
CUG------CAUUCGU-----UU----AGCG-GCGAUAAAUUUAUGCGGCUAAUUUGGCAGCGUUAACUCAAUUUGUGACCACAAAA-UGCACAAUUUGUCGCGGCUUUUGAUUGCCA--
..(------((.(((.-----..----(((.-((((((((((.((((.(((.....))).)))).....((.(((((....))))).-))...)))))))))).)))..))).)))..-- ( -31.80)
>DroWil_CAF1 17340 108 + 1
UC-------UCUCUGUUUAACUGA--CCA-AGGCGAUAAAUUCAUGCUGCUAAUUUGGCAGCGUUAACUCAAUUUGUGACCACAAAACUGAACAAUUUGUCGCUGAUUUUGAUUGCCU--
..-------...............--...-.(((((((((((.((((((((.....))))))))....(((.(((((....)))))..)))..)))))))))))..............-- ( -25.90)
>DroMoj_CAF1 16292 106 + 1
GUC------CAUUCGU-----UGGUUCAG-A-GCGAUAAAUUUAUGCCGCUAAUUUGGCAGCGUUAACUCAAUUUGUGACCACAAAG-UGCACAAUUUGUCGCGGCUCUUGAUUGCCACA
...------.....((-----.(((((((-(-((..........(((((......)))))(((......(((.(((((((......)-).))))).))).))).)))).)))..))))). ( -27.80)
>DroAna_CAF1 11484 108 + 1
UUGGCCAAGUGGCCGU-----UGG--CCG-G-GCGAUAAAUUCAUGCCGCUAAUUUGGCAGCGUUAACUCAAUUUGUGACCACAAAA-UGCACAAUUUGUCGCUGAUUUUGAUUGCCC--
..((((((.......)-----)))--))(-(-((((((((.((((((((......)))))(((......(((.(((((.(.......-.)))))).))).)))))).))).)))))))-- ( -34.70)
>consensus
UUG______CAUCCGU_____UGG__CCG_A_GCGAUAAAUUCAUGCCGCUAAUUUGGCAGCGUUAACUCAAUUUGUGACCACAAAA_UGCACAAUUUGUCGCGGAUUUUGAUUGCCA__
................................((((((((((.((((.(((.....))).))))........(((((....))))).......))))))))))................. (-19.50 = -19.50 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:56:40 2006