Locus 7979

Sequence ID 3R_DroMel_CAF1
Location 21,387,915 – 21,388,023
Length 108
Max. P 0.997012
window12844 window12845

overview

Window 4

Location 21,387,915 – 21,388,023
Length 108
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 72.15
Mean single sequence MFE -30.98
Consensus MFE -12.48
Energy contribution -16.12
Covariance contribution 3.64
Combinations/Pair 1.10
Mean z-score -2.92
Structure conservation index 0.40
SVM decision value 2.78
SVM RNA-class probability 0.997012
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21387915 108 + 27905053
UAUCCCC-----CAU-UUGGGGGCAAAGCGA---ACACUGGCUAUAGA---CUUUUAGGUGCCAGUGUGCAUAAUAUCUCGCCUUCUGGCGGCUUAUCAAAUAUUCACUUAACUUUGCCA
.....((-----(..-..)))(((((((.(.---((((((((..(((.---...)))...)))))))).)...(((..(((((....)))))..)))...............))))))). ( -36.70)
>DroSec_CAF1 82121 107 + 1
UAUGCCC-----CAU-UUGGGGGCA-AGCGA---ACACUGGCUAUAGA---CUUUUAUGUGCCAGUGUACAUAAUAUCCCGCCUUCUGGCGGCUUAUCAAAUAUUCAUUUAACUUUGCCU
..(((((-----(..-...))))))-.((((---(((((((((((((.---...))))).)))))))).....(((..(((((....)))))..))).................)))).. ( -40.00)
>DroSim_CAF1 78669 108 + 1
UAUGCCC-----CAU-UUGGGGGCAAAGCGA---ACACUGGCUAUAGA---CUUUUAGUUGCCAGUGUACAUAAUAUCUCGCCUUCUGGCGGCUUAUCAAAUAUUCAUUUAACUUUGCCU
..(((((-----(..-...))))))(((((.---((((((((....((---(.....))))))))))).).........((((....))))))))......................... ( -36.50)
>DroEre_CAF1 81995 97 + 1
UAUUCCCAUAUCCAUUUUUAGGG------GAUAUAGACU--------------UUUGGGUGCCAGUGUGCAUA---UCUCGCCUUCUGGCGGCUUAUCAAAUAUUCAUUUAACUUUGCCU
(((((((.((........)))))------))))..((..--------------(((((..(((.(....)...---....(((....))))))...)))))...)).............. ( -20.20)
>DroYak_CAF1 81752 116 + 1
UAUCCCCCC-CACAUUUUGGGGGCAAUGAGAUAUAGACUGGAUAUAGAUGAUAUUUGGGUGCCAGUGUGCAUA---ACUCGCCUUCUGGCGGCUUAUCACUUAUUCAUUUAACUUUGCCU
.....((((-((.....)))))).((((((......(((((...(((((...)))))....)))))(((.(((---(..((((....))))..)))))))...))))))........... ( -33.30)
>DroPer_CAF1 123858 89 + 1
UAUCC-G-----CAU-UUAGG--AAAAGAGC---AUUCUGAAUGGAUG---CUUUUGGCAGGCAGUGU----------------UUUGGCGGCUUAUCAAAUAAUCAUUUAACUUCGUUU
..(((-.-----...-...))--).((((((---((((.....)))))---)))))(..((((.((..----------------....)).))))..)...................... ( -19.20)
>consensus
UAUCCCC_____CAU_UUGGGGGCAAAGCGA___ACACUGGCUAUAGA___CUUUUAGGUGCCAGUGUGCAUA___UCUCGCCUUCUGGCGGCUUAUCAAAUAUUCAUUUAACUUUGCCU
....................((((((((......(((((((....................)))))))..........(((((....)))))....................)))))))) (-12.48 = -16.12 +   3.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 21,387,915 – 21,388,023
Length 108
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 72.15
Mean single sequence MFE -29.36
Consensus MFE -12.36
Energy contribution -13.59
Covariance contribution 1.22
Combinations/Pair 1.10
Mean z-score -2.49
Structure conservation index 0.42
SVM decision value 2.03
SVM RNA-class probability 0.986125
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21387915 108 - 27905053
UGGCAAAGUUAAGUGAAUAUUUGAUAAGCCGCCAGAAGGCGAGAUAUUAUGCACACUGGCACCUAAAAG---UCUAUAGCCAGUGU---UCGCUUUGCCCCCAA-AUG-----GGGGAUA
.(((...(((((((....)))))))..))).....(((((((..........((((((((.........---......))))))))---))))))).(((((..-..)-----))))... ( -35.76)
>DroSec_CAF1 82121 107 - 1
AGGCAAAGUUAAAUGAAUAUUUGAUAAGCCGCCAGAAGGCGGGAUAUUAUGUACACUGGCACAUAAAAG---UCUAUAGCCAGUGU---UCGCU-UGCCCCCAA-AUG-----GGGCAUA
((((.................(((((..(((((....)))))..))))).(.((((((((.........---......))))))))---.))))-)(((((...-..)-----))))... ( -37.96)
>DroSim_CAF1 78669 108 - 1
AGGCAAAGUUAAAUGAAUAUUUGAUAAGCCGCCAGAAGGCGAGAUAUUAUGUACACUGGCAACUAAAAG---UCUAUAGCCAGUGU---UCGCUUUGCCCCCAA-AUG-----GGGCAUA
.((((((((............(((((...((((....))))...))))).(.((((((((.........---......))))))))---.)))))))))(((..-..)-----))..... ( -35.76)
>DroEre_CAF1 81995 97 - 1
AGGCAAAGUUAAAUGAAUAUUUGAUAAGCCGCCAGAAGGCGAGA---UAUGCACACUGGCACCCAAA--------------AGUCUAUAUC------CCCUAAAAAUGGAUAUGGGAAUA
.(((...(((((((....)))))))..)))(((((...(((...---..)))...))))).......--------------..((((((((------(.........))))))))).... ( -26.50)
>DroYak_CAF1 81752 116 - 1
AGGCAAAGUUAAAUGAAUAAGUGAUAAGCCGCCAGAAGGCGAGU---UAUGCACACUGGCACCCAAAUAUCAUCUAUAUCCAGUCUAUAUCUCAUUGCCCCCAAAAUGUG-GGGGGGAUA
((((.....((.((((....(((...(((((((....)))).))---)...)))..(((...)))....)))).))......)))).......(((.((((((.....))-)))).))). ( -30.60)
>DroPer_CAF1 123858 89 - 1
AAACGAAGUUAAAUGAUUAUUUGAUAAGCCGCCAAA----------------ACACUGCCUGCCAAAAG---CAUCCAUUCAGAAU---GCUCUUUU--CCUAA-AUG-----C-GGAUA
.......(((((((....)))))))...((((((..----------------....)).........((---(((.(.....).))---))).....--.....-..)-----)-))... (  -9.60)
>consensus
AGGCAAAGUUAAAUGAAUAUUUGAUAAGCCGCCAGAAGGCGAGA___UAUGCACACUGGCACCCAAAAG___UCUAUAGCCAGUGU___UCGCUUUGCCCCCAA_AUG_____GGGGAUA
.(((...(((((((....)))))))..)))(((((...(((........)))...))))).....................................(((.............))).... (-12.36 = -13.59 +   1.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:59:27 2006