Locus 3600

Sequence ID	3R_DroMel_CAF1
Location	9,707,748 – 9,707,899
Length	151
Max. P	0.988679

overview

Window 0

Location	9,707,748 – 9,707,861
Length	113
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	93.10
Mean single sequence MFE	-36.48
Consensus MFE	-30.52
Energy contribution	-31.52
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-2.17
Structure conservation index	0.84
SVM decision value	2.13
SVM RNA-class probability	0.988679
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9707748 113 + 27905053
UUGAGAGUGGUGGGUAUUAUAAUUUCAUUGGGGGCGGAUAAGGCAAUCAAGCCAAACGGUUUGGCUCUCAAAUGACGAGGGU------UUCGGUUUCGGUGGGUGUGUUGCCCGAUUCA
....((((..((((((.((((...((((((..(.((((.........((((((....))))))((((((.......))))))------)))).)..)))))).)))).)))))))))). ( -37.90)
>DroSec_CAF1 31718 117 + 1
UUGA--GUGGUGGGUAUUAUAAUUUCAUUGGGGGCGGAUAAGGCAAUCAAGCCAAACUGUUUGGCUCUCAAAUGAUGAGGGUUUCGGUUUCGGUUUCGGUGGGUGUGUUGCCCGUUUCA
.(((--(...((((((.((((...((((((..(.((.....(((......)))((((((...((((((((.....)))))))).)))))))).)..)))))).)))).)))))).)))) ( -40.20)
>DroSim_CAF1 31446 117 + 1
UUGA--GUGGUGGGUAUUAUAAUUUCAUUGGGGGCGGAUAAGGCAAUCAAGCCAAACUGUUUGGCUCUCAAAUGAUGAGGGUUAUGGUUUCGGUUUCGGUGGGUGUGUUGCCCGUUUCA
.(((--(...((((((.((((...((((((..(.((.....(((......)))(((((...(((((((((.....))))))))).))))))).)..)))))).)))).)))))).)))) ( -38.40)
>DroEre_CAF1 32967 110 + 1
UUGA--GUGGUGGGUAUUAUAAUUUCUUUGGGGGCGGAUAAGGCAAUCAAGCCAAACUGUUUGGCUCUCAAAUGAUGAGGGU------UUCGGUUUCGGUGGGUGUGUUGC-CGUUUUA
....--........................(((((((.(((.(((.....(((((((((...((((((((.....)))))))------).)))))).)))...))).))))-)))))). ( -30.90)
>DroYak_CAF1 32737 111 + 1
UUGA--GUGGUGGGUUUUAUAAUUUCUUUGGGGGCGGAUAAGGCAAUCAAGCCAAACUGUUUGGCUCUCAGAUGAUGAGGGU------UUCGGUUUCGGUGGGUGUGUUGCCCGUUUCA
....--........................(..((((.(((.(((.....(((((((((...((((((((.....)))))))------).)))))).)))...))).))).))))..). ( -35.00)
>consensus
UUGA__GUGGUGGGUAUUAUAAUUUCAUUGGGGGCGGAUAAGGCAAUCAAGCCAAACUGUUUGGCUCUCAAAUGAUGAGGGU______UUCGGUUUCGGUGGGUGUGUUGCCCGUUUCA
..........((((((.((((...((((((..(.((((...(((......)))..........(((((((.....)))))))......)))).)..)))))).)))).))))))..... (-30.52 = -31.52 +   1.00)

alignment

secondary structure

dotplot

Window 1

Location	9,707,748 – 9,707,861
Length	113
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	93.10
Mean single sequence MFE	-18.10
Consensus MFE	-16.84
Energy contribution	-16.88
Covariance contribution	0.04
Combinations/Pair	1.07
Mean z-score	-1.42
Structure conservation index	0.93
SVM decision value	1.30
SVM RNA-class probability	0.939049
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9707748 113 - 27905053
UGAAUCGGGCAACACACCCACCGAAACCGAA------ACCCUCGUCAUUUGAGAGCCAAACCGUUUGGCUUGAUUGCCUUAUCCGCCCCCAAUGAAAUUAUAAUACCCACCACUCUCAA
......((((...........((((..(((.------....)))...)))).(((((((.....))))))).............))))............................... ( -18.50)
>DroSec_CAF1 31718 117 - 1
UGAAACGGGCAACACACCCACCGAAACCGAAACCGAAACCCUCAUCAUUUGAGAGCCAAACAGUUUGGCUUGAUUGCCUUAUCCGCCCCCAAUGAAAUUAUAAUACCCACCAC--UCAA
......((((..............................((((.....))))((((((.....))))))..............)))).........................--.... ( -18.50)
>DroSim_CAF1 31446 117 - 1
UGAAACGGGCAACACACCCACCGAAACCGAAACCAUAACCCUCAUCAUUUGAGAGCCAAACAGUUUGGCUUGAUUGCCUUAUCCGCCCCCAAUGAAAUUAUAAUACCCACCAC--UCAA
......((((..............................((((.....))))((((((.....))))))..............)))).........................--.... ( -18.50)
>DroEre_CAF1 32967 110 - 1
UAAAACG-GCAACACACCCACCGAAACCGAA------ACCCUCAUCAUUUGAGAGCCAAACAGUUUGGCUUGAUUGCCUUAUCCGCCCCCAAAGAAAUUAUAAUACCCACCAC--UCAA
......(-((((((.................------...((((.....))))((((((.....)))))))).)))))...................................--.... ( -17.30)
>DroYak_CAF1 32737 111 - 1
UGAAACGGGCAACACACCCACCGAAACCGAA------ACCCUCAUCAUCUGAGAGCCAAACAGUUUGGCUUGAUUGCCUUAUCCGCCCCCAAAGAAAUUAUAAAACCCACCAC--UCAA
......((((.....................------...((((.....))))((((((.....))))))..............)))).........................--.... ( -17.70)
>consensus
UGAAACGGGCAACACACCCACCGAAACCGAA______ACCCUCAUCAUUUGAGAGCCAAACAGUUUGGCUUGAUUGCCUUAUCCGCCCCCAAUGAAAUUAUAAUACCCACCAC__UCAA
......((((..............................((((.....))))((((((.....))))))..............))))............................... (-16.84 = -16.88 +   0.04)

alignment

secondary structure

dotplot

Window 2

Location	9,707,787 – 9,707,899
Length	112
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	87.90
Mean single sequence MFE	-32.58
Consensus MFE	-23.72
Energy contribution	-24.08
Covariance contribution	0.36
Combinations/Pair	1.07
Mean z-score	-1.56
Structure conservation index	0.73
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9707787 112 + 27905053
AAGGCAAUCAAGCCAAACGGUUUGGCUCUCAAAUGACGAGGGU------UUCGGUUUCGGUGGGUGUGUUGCCCGAUUCAAUAUUAGAUGGAGUGUUUAUACUGGAGAUGGGGUAUUU
..((((..(..(((((((.(...(((((((.......))))))------).).)))).)))..)..))))((((.((((.....(((((.....))))).....)).)).)))).... ( -27.50)
>DroSec_CAF1 31755 113 + 1
AAGGCAAUCAAGCCAAACUGUUUGGCUCUCAAAUGAUGAGGGUUUCGGUUUCGGUUUCGGUGGGUGUGUUGCCCGUUUCAAUAUUAGAUCGAGUGUUUAUACUGUU-----ACCUUCU
..(((......)))((((((...((((((((.....)))))))).)))))).(((..((((((((.....)))).....((((((......))))))...))))..-----))).... ( -32.50)
>DroSim_CAF1 31483 113 + 1
AAGGCAAUCAAGCCAAACUGUUUGGCUCUCAAAUGAUGAGGGUUAUGGUUUCGGUUUCGGUGGGUGUGUUGCCCGUUUCAAUAUUAGAUGGAGUGUUUAUACUGAU-----ACCAUCU
..((((((((.(((((((((..(((((((((.....)))))))))......)))))).)))...)).))))))............((((((((((....))))...-----.)))))) ( -33.50)
>DroEre_CAF1 33004 106 + 1
AAGGCAAUCAAGCCAAACUGUUUGGCUCUCAAAUGAUGAGGGU------UUCGGUUUCGGUGGGUGUGUUGC-CGUUUUAAUAUUAGAUCGGGUGUUUACACCGAU-----ACCAUCU
..((((((((.(((((((((...((((((((.....)))))))------).)))))).)))...)).)))))-).............(((((.((....)))))))-----....... ( -35.00)
>DroYak_CAF1 32774 106 + 1
AAGGCAAUCAAGCCAAACUGUUUGGCUCUCAGAUGAUGAGGGU------UUCGGUUUCGGUGGGUGUGUUGCCCGUUUCAAUAUUAGAUCGAGU-UUUAUACUGAU-----GCCAUCU
..((((.((..(((((((((...((((((((.....)))))))------).)))))).))).((((((..((.((..((.......)).)).))-..)))))))))-----))).... ( -34.40)
>consensus
AAGGCAAUCAAGCCAAACUGUUUGGCUCUCAAAUGAUGAGGGU______UUCGGUUUCGGUGGGUGUGUUGCCCGUUUCAAUAUUAGAUCGAGUGUUUAUACUGAU_____ACCAUCU
..((((((((.(((((((((....(((((((.....)))))))........)))))).)))...)).))))))..................((((....))))............... (-23.72 = -24.08 +   0.36)

alignment

secondary structure

dotplot

Window 3

Location	9,707,787 – 9,707,899
Length	112
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	87.90
Mean single sequence MFE	-22.57
Consensus MFE	-17.18
Energy contribution	-17.10
Covariance contribution	-0.08
Combinations/Pair	1.12
Mean z-score	-1.53
Structure conservation index	0.76
SVM decision value	0.04
SVM RNA-class probability	0.551866
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9707787 112 - 27905053
AAAUACCCCAUCUCCAGUAUAAACACUCCAUCUAAUAUUGAAUCGGGCAACACACCCACCGAAACCGAA------ACCCUCGUCAUUUGAGAGCCAAACCGUUUGGCUUGAUUGCCUU
..............((((((..............))))))....((((((.........((((..(((.------....)))...)))).(((((((.....)))))))..)))))). ( -18.94)
>DroSec_CAF1 31755 113 - 1
AGAAGGU-----AACAGUAUAAACACUCGAUCUAAUAUUGAAACGGGCAACACACCCACCGAAACCGAAACCGAAACCCUCAUCAUUUGAGAGCCAAACAGUUUGGCUUGAUUGCCUU
..(((((-----((((..........(((...............(((.......)))..((....))....)))....((((.....))))((((((.....)))))))).))))))) ( -22.10)
>DroSim_CAF1 31483 113 - 1
AGAUGGU-----AUCAGUAUAAACACUCCAUCUAAUAUUGAAACGGGCAACACACCCACCGAAACCGAAACCAUAACCCUCAUCAUUUGAGAGCCAAACAGUUUGGCUUGAUUGCCUU
((((((.-----...(((......)))))))))...........((((((((..........................((((.....))))((((((.....)))))))).)))))). ( -24.10)
>DroEre_CAF1 33004 106 - 1
AGAUGGU-----AUCGGUGUAAACACCCGAUCUAAUAUUAAAACG-GCAACACACCCACCGAAACCGAA------ACCCUCAUCAUUUGAGAGCCAAACAGUUUGGCUUGAUUGCCUU
...(((.-----(((((((....)).))))))))..........(-((((((.................------...((((.....))))((((((.....)))))))).))))).. ( -25.60)
>DroYak_CAF1 32774 106 - 1
AGAUGGC-----AUCAGUAUAAA-ACUCGAUCUAAUAUUGAAACGGGCAACACACCCACCGAAACCGAA------ACCCUCAUCAUCUGAGAGCCAAACAGUUUGGCUUGAUUGCCUU
....(((-----(((((......-..(((((.....)))))...(((.......)))............------...........))))(((((((.....)))))))...)))).. ( -22.10)
>consensus
AGAUGGU_____AUCAGUAUAAACACUCGAUCUAAUAUUGAAACGGGCAACACACCCACCGAAACCGAA______ACCCUCAUCAUUUGAGAGCCAAACAGUUUGGCUUGAUUGCCUU
..............((((((..............))))))....((((((((..........................((((.....))))((((((.....)))))))).)))))). (-17.18 = -17.10 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:05:31 2006