Locus 1162

Sequence ID	2R_DroMel_CAF1
Location	4,625,496 – 4,625,716
Length	220
Max. P	0.589342

overview

Window 8

Location	4,625,496 – 4,625,616
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.56
Mean single sequence MFE	-33.99
Consensus MFE	-20.17
Energy contribution	-20.32
Covariance contribution	0.14
Combinations/Pair	1.42
Mean z-score	-1.55
Structure conservation index	0.59
SVM decision value	-0.03
SVM RNA-class probability	0.520391
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4625496 120 - 20766785
UCCGGAGUCGUAUAGCGAUGAGUUCCACAUCCAGUACCAACACUUUCUUAGCUUGCUGGAAGUUUUUGCGCUGAAUCCCAGCGAAGAAAACAAAUCCCUGGAUGACAUCGUCAUGUUUGU
..........(((..(((((...((((..(((((((.................))))))).((((((.(((((.....)))))..)))))).......))))...)))))..)))..... ( -31.33)
>DroVir_CAF1 2094 120 - 1
UCCCGAAUCCUACAGCGAUGAGUUUCACACACAAUACGAGCAUUUCCUAAGUCUGCUCGAGAUCUUCGCCCUGAAUCCGGGCGAGGAAAACAAAUCGCUGGACGAGAUCAUAAUGUUUAU
....((.((...(((((((..((((...........((((((...........))))))...(((((((((.......)))))))))))))..)))))))...))..))........... ( -38.90)
>DroGri_CAF1 2150 120 - 1
UCCCGAAUCUUACAGCGAUGAGUUUCACACGCAAUACGAGCAUUUUCUCAGUCUGCUCGAGAUCUUCUCCCUGAAUCCGAGCGAGGAAAACAAAUCGUUGGACGAGAUUUGCAUGUUUAU
...((((((((.(((((((..((((..(.(((.....(((((...........)))))(((.....)))...........))).)..))))..)))))))...))))))))......... ( -33.80)
>DroWil_CAF1 2887 120 - 1
CCCCGAAUCGUAUAGCGAUGAGUUUCACAUCCAGUACCAGCACUUCCUCAGUUUGCUUGGCGUGUUCGCCCUCAAUCCCAGCGAGGAGAACAAAUCGCUGGAUGACAUUGUGAUGUUCAU
....(((.(((...((((((.(...).((((((((.((((((...........))).)))..(((((..((((.........)))).)))))....)))))))).)))))).)))))).. ( -33.40)
>DroMoj_CAF1 2242 120 - 1
UCCUGAGUCCUACAGCGAUGAGUUCCACACGCAAUACGAACAUUUUUUAAGUUUACUUGAAAUCUUUGCCUUAAAUCCGGGCGAGGAAAACAAAUCGUUGGACGAAAUAGUGAUGUUUAU
......((((....(((.((.......)))))...((((.....(((((((....)))))))(((((((((.......))))))))).......)))).)))).(((((....))))).. ( -29.50)
>DroAna_CAF1 2020 120 - 1
CCCAGAGUCGUACAGCGAUGAGUUCCACAUACAGUACCAGCACUUCCUCAGCCUGUUGGAGGUGUUCGCCCUCAAUCCCGGCGAGGAGAAUAAAUCUCUGGACGACAUCGUGAUGUUCAU
....(((((((.(((.(((..((((........((....))...(((((.(((.((((..(((....)))..))))...))))))))))))..))).))).))))).))........... ( -37.00)
>consensus
UCCCGAAUCGUACAGCGAUGAGUUCCACACACAAUACCAGCACUUCCUCAGUCUGCUCGAGAUCUUCGCCCUGAAUCCCAGCGAGGAAAACAAAUCGCUGGACGACAUCGUGAUGUUUAU
.......((...(((((((..((((...........((((((...........))))))...(((((((...........)))))))))))..)))))))...))............... (-20.17 = -20.32 +   0.14)

alignment

secondary structure

dotplot

Window 9

Location	4,625,616 – 4,625,716
Length	100
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	79.50
Mean single sequence MFE	-26.45
Consensus MFE	-22.64
Energy contribution	-22.70
Covariance contribution	0.06
Combinations/Pair	1.27
Mean z-score	-1.05
Structure conservation index	0.86
SVM decision value	0.11
SVM RNA-class probability	0.589342
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4625616 100 - 20766785
--------UCGUAGUUUUUAUACUGUUAUAACGGCUCACCAUGGUGCGGCCCAACAACAACCAGCUGCCGGAGAACCUUCCGCAGUUGCAGAACCUCAUCAAGCGGGA
--------..............(((((.....(((((((....))).))))..........(((((((.((((....))))))))))).............))))).. ( -26.80)
>DroPse_CAF1 2173 89 - 1
--------UCGCAAUUUCU-----------UCGGCUCACCAUGGUGCGGCCCAACAACAAUCAACUGCCGGAGAAUCUUCCGCAGUUACAGAACCUGAUCAAGCGCGA
--------((((.......-----------..(((((((....))).))))...........((((((.((((....)))))))))).................)))) ( -25.30)
>DroEre_CAF1 2130 100 - 1
--------UCGUAGUUUUUAUAUUCUUAAAACGGCUCACUAUGGUGCGGCCCAACAACAACCAGUUGCCGGAGAACCUGCCGCAAUUGCAGAACCUGAUCAAGCGGGA
--------..((.(((((.........)))))(((((((....))).))))..))......(((((((.((........))))))))).....((((......)))). ( -22.50)
>DroYak_CAF1 2136 100 - 1
--------UCGUAGUUAUUAUCCGUUAAGAACGGCUCACCAUGGUGCGGCCUAACAACAACCAGCUGCCGGAGAACCUCCCGCAGUUGCAGAACCUAAUCAAGCGGGA
--------............((((((......(((((((....))).))))..........(((((((.((((...)))).))))))).............)))))). ( -31.60)
>DroAna_CAF1 2140 97 - 1
GAAAUAAGGCGUAAUUUCC-----------CCGGCUCACGAUGGUGCGGCCUAACAAUAAUCAGCUGCCAGAGAACCUGCCGCAGCUGCAGAACCUGAUCAAGCGCGA
........((((.......-----------..(((((((....))).))))..........((((((((((.....)))..)))))))..............)))).. ( -27.20)
>DroPer_CAF1 1993 89 - 1
--------UCGCAAUUUCU-----------UCGGCUCACCAUGGUGCGGCCCAACAACAAUCAACUGCCGGAGAAUCUUCCGCAGUUACAGAACCUGAUCAAGCGCGA
--------((((.......-----------..(((((((....))).))))...........((((((.((((....)))))))))).................)))) ( -25.30)
>consensus
________UCGUAAUUUCU___________ACGGCUCACCAUGGUGCGGCCCAACAACAACCAGCUGCCGGAGAACCUUCCGCAGUUGCAGAACCUGAUCAAGCGCGA
........((((....................(((((((....))).))))..........(((((((.((((...)))).)))))))..............)))).. (-22.64 = -22.70 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:58:00 2006