Locus 6755

Sequence ID	2L_DroMel_CAF1
Location	18,876,615 – 18,876,769
Length	154
Max. P	0.998278

overview

Window 5

Location	18,876,615 – 18,876,711
Length	96
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	89.74
Mean single sequence MFE	-36.85
Consensus MFE	-31.31
Energy contribution	-31.00
Covariance contribution	-0.31
Combinations/Pair	1.08
Mean z-score	-2.82
Structure conservation index	0.85
SVM decision value	1.74
SVM RNA-class probability	0.974823
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18876615 96 + 22407834
CCAGGUGAUGGUUCAUCACCAGCGAUGGCUGUAAUCCAGUUU------------------------GAUUGUGGUUGUGAUUGUGCAACGGUAGCUGGUGAGCCAAAUGGCCACCAAUCU
...((((........((((((((.(..((..(((((......------------------------)))))..))..).((((.....)))).))))))))(((....)))))))..... ( -35.40)
>DroGri_CAF1 249 96 + 1
CCAGGUGAUGAUUCAUCACCAGCGAUGGCUGUAAUCCAGUUU------------------------GAUUGUGAUUGUGGUUGUGCAAUGGUAGCUGGUGAGCCAAAUGGCCACCAAUCU
((((((((((...))))))).((.(..((..(((((((((..------------------------.)))).)))))..))..)))..)))....(((((.(((....)))))))).... ( -38.40)
>DroEre_CAF1 30 96 + 1
CCAGGUGAUGGUUCAUCACCAGCGAUGGCUGUAAUCCAGUUU------------------------GAUUGUGGUUGUGAUUGUGCAACGGUAGCUGGUGAGCCAAAUGGCCACCAAUCU
...((((........((((((((.(..((..(((((......------------------------)))))..))..).((((.....)))).))))))))(((....)))))))..... ( -35.40)
>DroYak_CAF1 108 96 + 1
CCAGGUGAUGGUUCAUCACCAGCGAUGGCUGUAAUCCAGUUU------------------------GAUUGUGGUUGUGAUUGUGCAACGGUAGCUGGUGAGCCAAAUGGCCACCAAUCU
...((((........((((((((.(..((..(((((......------------------------)))))..))..).((((.....)))).))))))))(((....)))))))..... ( -35.40)
>DroMoj_CAF1 30 120 + 1
CCAGGUGAUGAUUCAUCACCAGCGAUGGCUGUAAUCCAGUUUGGCUGUGACUGUGAUUGUGAUUGUGAUUGUGAUUAUGAUUGUGCAAUGGUAGCUGGUGAGCCAAAUGGCCACCAAUCU
...((((........((((((((....((((((((((((((.......))))).))))(..((..((((....))))..))..)...))))).))))))))(((....)))))))..... ( -39.90)
>DroPer_CAF1 30 96 + 1
CCAGGUGAUGGUUCAUCACCAGCGACGGCUGUAAUCCAGUUU------------------------GAUUGUGGUUGUGAUUGUGCAAUGGUAGCUGGUGAGCCAAAUGGCCACCAAUCU
...((((........((((((((.(((((..(((((......------------------------)))))..))))).....(((....)))))))))))(((....)))))))..... ( -36.60)
>consensus
CCAGGUGAUGGUUCAUCACCAGCGAUGGCUGUAAUCCAGUUU________________________GAUUGUGGUUGUGAUUGUGCAACGGUAGCUGGUGAGCCAAAUGGCCACCAAUCU
...((((........((((((((...(((((.....)))))................................(((((......)))))....))))))))(((....)))))))..... (-31.31 = -31.00 +  -0.31)

alignment

secondary structure

dotplot

Window 6

Location	18,876,615 – 18,876,711
Length	96
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	89.74
Mean single sequence MFE	-28.03
Consensus MFE	-26.66
Energy contribution	-26.35
Covariance contribution	-0.31
Combinations/Pair	1.09
Mean z-score	-2.28
Structure conservation index	0.95
SVM decision value	3.05
SVM RNA-class probability	0.998278
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18876615 96 - 22407834
AGAUUGGUGGCCAUUUGGCUCACCAGCUACCGUUGCACAAUCACAACCACAAUC------------------------AAACUGGAUUACAGCCAUCGCUGGUGAUGAACCAUCACCUGG
.....(((((((....)))((((((((....((((........)))).......------------------------...(((.....))).....))))))))........))))... ( -28.10)
>DroGri_CAF1 249 96 - 1
AGAUUGGUGGCCAUUUGGCUCACCAGCUACCAUUGCACAACCACAAUCACAAUC------------------------AAACUGGAUUACAGCCAUCGCUGGUGAUGAAUCAUCACCUGG
.(((((((((((....))).)))).((.......))........))))......------------------------...(..(....((((....))))((((((...)))))))..) ( -26.50)
>DroEre_CAF1 30 96 - 1
AGAUUGGUGGCCAUUUGGCUCACCAGCUACCGUUGCACAAUCACAACCACAAUC------------------------AAACUGGAUUACAGCCAUCGCUGGUGAUGAACCAUCACCUGG
.....(((((((....)))((((((((....((((........)))).......------------------------...(((.....))).....))))))))........))))... ( -28.10)
>DroYak_CAF1 108 96 - 1
AGAUUGGUGGCCAUUUGGCUCACCAGCUACCGUUGCACAAUCACAACCACAAUC------------------------AAACUGGAUUACAGCCAUCGCUGGUGAUGAACCAUCACCUGG
.....(((((((....)))((((((((....((((........)))).......------------------------...(((.....))).....))))))))........))))... ( -28.10)
>DroMoj_CAF1 30 120 - 1
AGAUUGGUGGCCAUUUGGCUCACCAGCUACCAUUGCACAAUCAUAAUCACAAUCACAAUCACAAUCACAGUCACAGCCAAACUGGAUUACAGCCAUCGCUGGUGAUGAAUCAUCACCUGG
.(((((((((((....))).)))).((.......))..)))).........................(((...((((....(((.....))).....))))((((((...))))))))). ( -30.10)
>DroPer_CAF1 30 96 - 1
AGAUUGGUGGCCAUUUGGCUCACCAGCUACCAUUGCACAAUCACAACCACAAUC------------------------AAACUGGAUUACAGCCGUCGCUGGUGAUGAACCAUCACCUGG
.(((((((((((....))).)))).((.......))..))))....(((.....------------------------...(((.....)))........(((((((...)))))))))) ( -27.30)
>consensus
AGAUUGGUGGCCAUUUGGCUCACCAGCUACCAUUGCACAAUCACAACCACAAUC________________________AAACUGGAUUACAGCCAUCGCUGGUGAUGAACCAUCACCUGG
.....(((((((....)))((((((((....((((........))))..................................(((.....))).....))))))))........))))... (-26.66 = -26.35 +  -0.31)

alignment

secondary structure

dotplot

Window 7

Location	18,876,671 – 18,876,769
Length	98
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	81.52
Mean single sequence MFE	-32.00
Consensus MFE	-23.50
Energy contribution	-23.37
Covariance contribution	-0.14
Combinations/Pair	1.05
Mean z-score	-2.53
Structure conservation index	0.73
SVM decision value	1.06
SVM RNA-class probability	0.908822
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18876671 98 + 22407834
UUGUGCAACGGUAGCUGGUGAGCCAAAUGGCCACCAAUCUCUGCCAUUACCAUAUAUUUGGCUGACAGGA--------CACUCGGCGA-A-GCACACUCGAG-AUA-----------UUU
.(((((...(((((.(((((.(((....))))))))....)))))............((.(((((.....--------...))))).)-)-)))))......-...-----------... ( -32.60)
>DroGri_CAF1 305 108 + 1
UUGUGCAAUGGUAGCUGGUGAGCCAAAUGGCCACCAAUCUCUGCCAUUACCAUAUAUUUGGCUUAUAGACCCCGGCUUAACCACCCAAAA-ACACACUUGUGUGUC-----------UUA
.((((.((((((((.(((((.(((....))))))))....))))))))..))))..(((((.....((.(....))).......))))).-(((((....))))).-----------... ( -30.40)
>DroEre_CAF1 86 98 + 1
UUGUGCAACGGUAGCUGGUGAGCCAAAUGGCCACCAAUCUCUGCCAUUACCAUAUAUUUGGCUGACAGGA--------CACUCGGCGA-A-ACACACUCGAG-AUU-----------UUU
.((((....(((((.(((((.(((....))))))))....)))))...........(((.(((((.....--------...))))).)-)-)))))......-...-----------... ( -28.90)
>DroYak_CAF1 164 98 + 1
UUGUGCAACGGUAGCUGGUGAGCCAAAUGGCCACCAAUCUCUGCCAUUACCAUAUAUUUGGCUGACAGGA--------CACUCGGCGA-A-GCACACUCGAG-AUU-----------UUU
.(((((...(((((.(((((.(((....))))))))....)))))............((.(((((.....--------...))))).)-)-)))))......-...-----------... ( -32.60)
>DroMoj_CAF1 110 102 + 1
UUGUGCAAUGGUAGCUGGUGAGCCAAAUGGCCACCAAUCUCUGCCAUUACCAUAUAUUUGGCUUAUAGAC--CGGC--AACCAACCAA-A-AUACACUUCAG-AUC-----------UUU
...(((((((((((.(((((.(((....))))))))....)))))))).(((......))).........--..))--).........-.-...........-...-----------... ( -26.70)
>DroPer_CAF1 86 109 + 1
UUGUGCAAUGGUAGCUGGUGAGCCAAAUGGCCACCAAUCUCUGCCAUUACCAUAUAUUUGGCUUACAAAA--------CC-CCGGCAA-ACACACACUCGAG-ACGGGGUGGGUGGGUGU
.((((.((((((((.(((((.(((....))))))))....))))))))..))))......((((((...(--------((-(((....-.............-.))))))..)))))).. ( -40.77)
>consensus
UUGUGCAACGGUAGCUGGUGAGCCAAAUGGCCACCAAUCUCUGCCAUUACCAUAUAUUUGGCUGACAGAA________CACCCGGCAA_A_ACACACUCGAG_AUC___________UUU
.((((....(((((.(((((.(((....))))))))....)))))....(((......)))...............................))))........................ (-23.50 = -23.37 +  -0.14)

alignment

secondary structure

dotplot

Window 8

Location	18,876,671 – 18,876,769
Length	98
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.52
Mean single sequence MFE	-35.53
Consensus MFE	-26.85
Energy contribution	-26.60
Covariance contribution	-0.25
Combinations/Pair	1.04
Mean z-score	-2.78
Structure conservation index	0.76
SVM decision value	1.23
SVM RNA-class probability	0.933140
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18876671 98 - 22407834
AAA-----------UAU-CUCGAGUGUGC-U-UCGCCGAGUG--------UCCUGUCAGCCAAAUAUAUGGUAAUGGCAGAGAUUGGUGGCCAUUUGGCUCACCAGCUACCGUUGCACAA
...-----------...-......(((((-.-.((...((((--------((((((((((((......))))..)))))).)))((((((((....))).))))))))..))..))))). ( -35.70)
>DroGri_CAF1 305 108 - 1
UAA-----------GACACACAAGUGUGU-UUUUGGGUGGUUAAGCCGGGGUCUAUAAGCCAAAUAUAUGGUAAUGGCAGAGAUUGGUGGCCAUUUGGCUCACCAGCUACCAUUGCACAA
.((-----------((((((....)))))-)))..(((...((..(....)..))...))).......(((((((((...((.(((((((((....))).)))))))).))))))).)). ( -37.10)
>DroEre_CAF1 86 98 - 1
AAA-----------AAU-CUCGAGUGUGU-U-UCGCCGAGUG--------UCCUGUCAGCCAAAUAUAUGGUAAUGGCAGAGAUUGGUGGCCAUUUGGCUCACCAGCUACCGUUGCACAA
...-----------...-......(((((-.-.((...((((--------((((((((((((......))))..)))))).)))((((((((....))).))))))))..))..))))). ( -35.10)
>DroYak_CAF1 164 98 - 1
AAA-----------AAU-CUCGAGUGUGC-U-UCGCCGAGUG--------UCCUGUCAGCCAAAUAUAUGGUAAUGGCAGAGAUUGGUGGCCAUUUGGCUCACCAGCUACCGUUGCACAA
...-----------...-......(((((-.-.((...((((--------((((((((((((......))))..)))))).)))((((((((....))).))))))))..))..))))). ( -35.70)
>DroMoj_CAF1 110 102 - 1
AAA-----------GAU-CUGAAGUGUAU-U-UUGGUUGGUU--GCCG--GUCUAUAAGCCAAAUAUAUGGUAAUGGCAGAGAUUGGUGGCCAUUUGGCUCACCAGCUACCAUUGCACAA
...-----------...-.....(((((.-.-.((((((((.--.(((--((((....((((............))))..)))))))..))))...((((....)))))))).))))).. ( -35.30)
>DroPer_CAF1 86 109 - 1
ACACCCACCCACCCCGU-CUCGAGUGUGUGU-UUGCCGG-GG--------UUUUGUAAGCCAAAUAUAUGGUAAUGGCAGAGAUUGGUGGCCAUUUGGCUCACCAGCUACCAUUGCACAA
..........((((((.-..((((......)-))).)))-))--------).................(((((((((...((.(((((((((....))).)))))))).))))))).)). ( -34.30)
>consensus
AAA___________AAU_CUCGAGUGUGU_U_UCGCCGAGUG________UCCUGUAAGCCAAAUAUAUGGUAAUGGCAGAGAUUGGUGGCCAUUUGGCUCACCAGCUACCAUUGCACAA
.......................((((...............................((((......))))(((((...((.(((((((((....))).)))))))).))))))))).. (-26.85 = -26.60 +  -0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:19:13 2006