Locus 6304

Sequence ID	3L_DroMel_CAF1
Location	16,808,838 – 16,809,040
Length	202
Max. P	0.994744

overview

Window 3

Location	16,808,838 – 16,808,946
Length	108
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	70.71
Mean single sequence MFE	-38.68
Consensus MFE	-13.06
Energy contribution	-14.32
Covariance contribution	1.25
Combinations/Pair	1.44
Mean z-score	-1.93
Structure conservation index	0.34
SVM decision value	0.15
SVM RNA-class probability	0.605453
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16808838 108 + 23771897
UGGUGGUAGCAACUUUCCACCGUAUCCCACGGGAUCUAAUGUCGGACCGUACCCCCCGACACCCGCUGGUCCAGCUGGC---GGAUCCGGAUAUCCGGCCUACCCGAAUUU
.(((((..........)))))........((((......((((((..........)))))).((((..(.....)..))---))..((((....))))....))))..... ( -39.80)
>DroVir_CAF1 3297 108 + 1
UAGCGGUGGUAACUUUCCGCCAUAUCCCACUGGUGGCAACUAUAUGCCCUAUCCGGCGACU---GGUGGACCGGCAGGAAACUCCGCCGGCUAUCAGCCCUACAUGAAUUA
....(((((.......)))))......(.((((.((((......))))....)))).).((---(((((.(((((((....))..)))))))))))).............. ( -39.50)
>DroGri_CAF1 3029 111 + 1
UAGCGGUGGUAACUUUCCGCCCUAUCCCACUGGCGGCACUUUCAUGCCAUAUCCAUCGACCAGUGCUGGACCGACUGGUAGUUCAGGCGGAUAUCCGCCGUACAUGAAUUA
..(((((((......((((((....((((((((.((((......))))...((....))))))))..))(((....)))......))))))...))))))).......... ( -38.80)
>DroYak_CAF1 868 108 + 1
UGGUGGCGGCAACUUUCCACCGUAUCCCACAGGAUUCAACUUCGAACCGUAUCCCCCGACACCUGCUGGUCCAGCUGGC---GGAUCCGGCUAUCCGCCGUACAUGAAUUU
.(((((.(....)...)))))((((.(((((((.(((......)))..((........)).)))).))).......(((---((((......)))))))))))........ ( -31.70)
>DroAna_CAF1 1040 111 + 1
UGGUGGCGGCAACUUUCCGCCAUACCCCACUGGCUCCAAUUUCGGACCAUAUCCUCCGGCCGGCAGUGGUCCUGCUGGUCAUGGCGCUGGUUAUCCGCCCUACAUGAAUUU
(((.(((((.((((...((((((.......(((.(((......))))))........(((((((((.....)))))))))))))))..))))..))))))))......... ( -44.70)
>DroPer_CAF1 3768 105 + 1
GAGCGGUGGCAACUUUCCGCCCUAUCCGACAGGUGCUAAUUUCGGACCCUAUCCACCA------GGCGGAUCGGGGGGCAAUGCCGCCGGCUAUCCGCCCUACAUGAAUUU
....(((((((..((.((.(((.(((((...((((..................)))).------..))))).))).)).)))))))))(((.....)))............ ( -37.57)
>consensus
UAGCGGUGGCAACUUUCCGCCAUAUCCCACUGGAGCCAAUUUCGGACCAUAUCCACCGACA___GCUGGACCGGCUGGCAAUGCAGCCGGCUAUCCGCCCUACAUGAAUUU
....(((((.......)))))...........................................(((((...((((((........))))))..)))))............ (-13.06 = -14.32 +   1.25)

alignment

secondary structure

dotplot

Window 4

Location	16,808,875 – 16,808,980
Length	105
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	84.15
Mean single sequence MFE	-36.45
Consensus MFE	-23.56
Energy contribution	-23.86
Covariance contribution	0.31
Combinations/Pair	1.19
Mean z-score	-2.47
Structure conservation index	0.65
SVM decision value	0.00
SVM RNA-class probability	0.534004
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16808875 105 + 23771897
AAUGUCGGACCGUACCCCCCGACACCCGCUGGUCCAGCUGGC---GGAUCCGGAUAUCCGGCCUACCCGAAUUUCAUACAACCAACCGCCGGUGGGUACCCACCAGCU
..((((((..........))))))...((((((...((((((---((..((((....)))).......(.....)..........))))))))((....)))))))). ( -40.30)
>DroSec_CAF1 991 105 + 1
AACGUCGGACCGUAUCCCCCGACACCCGCUGGUCCAGCUGGU---GGAUCCGGCUAUCCGCCCUACAUGAAUUUCCCACAACCAACCGCCGCUGGGUACCCACCAGCA
...(((((..........)))))....(((((((((((.(((---((....(((.....))).....((.......)).......))))))))))......)))))). ( -36.10)
>DroSim_CAF1 874 105 + 1
AACGUCGGACCGUAUCCCCCGACACCCGCUGGUCCAGCUGGU---GGAUCCGGCUAUCCGCCCUACAUGAAUUUCCCACAACCAACAGCCGGUGGGUACCCACCAGCA
...(((((..........)))))(((....)))...((((((---((....(((.....)))............(((((...(....)...)))))...)))))))). ( -35.30)
>DroEre_CAF1 920 105 + 1
AGCUUCGGACCGUAUCCCCCGACACCCGCUGGUCCAGCCGGC---GGAUCCGGCUAUCAGCCAUACAUGAAUUUCCCGCAACCAACCGCUGGUGGAUACCCACCAGCA
.((.((((..........))))...(((((((.....)))))---))....(((.....)))...............))........((((((((....)))))))). ( -40.20)
>DroYak_CAF1 905 105 + 1
AACUUCGAACCGUAUCCCCCGACACCUGCUGGUCCAGCUGGC---GGAUCCGGCUAUCCGCCGUACAUGAAUUUCCCGCAACCUACAGCGGGUGGUUACCCACCAGCA
...........................((((((......(((---((((......))))))).......(((..(((((........)))))..)))....)))))). ( -33.40)
>DroAna_CAF1 1077 105 + 1
AAUUUCGGACCAUAUCCUCCGGCCGGCAGUGGUCCUGCUGGUCAUGGCGCUGGUUAUCCGCCCUACAUGAAUUUCCCACAACCAU---CCGGUGGCUAUCCACCAGCU
......(((........)))(((((((((.....))))))))).....((((((((.(((((....(((.............)))---..))))).))...)))))). ( -33.42)
>consensus
AACGUCGGACCGUAUCCCCCGACACCCGCUGGUCCAGCUGGC___GGAUCCGGCUAUCCGCCCUACAUGAAUUUCCCACAACCAACCGCCGGUGGGUACCCACCAGCA
....((((((((.................))))))((((((........)))))).............)).................((.(((((....))))).)). (-23.56 = -23.86 +   0.31)

alignment

secondary structure

dotplot

Window 5

Location	16,808,912 – 16,809,016
Length	104
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	79.63
Mean single sequence MFE	-36.82
Consensus MFE	-22.42
Energy contribution	-24.17
Covariance contribution	1.75
Combinations/Pair	1.10
Mean z-score	-2.41
Structure conservation index	0.61
SVM decision value	1.16
SVM RNA-class probability	0.924710
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16808912 104 - 23771897
AUUUUUGGAUAAUAAUCUAA--AACUUACAUAUCCCGCAGCUGGUGGGUACCCACCGGCGGUUGGUUGUAUGAAAUUCGGGUAGGCCGGAUAUCCGGAUCC---GCCAG
..((((((((....))))))--))....(((((((.((.((((((((....)))))))).)).))..))))).......((..((((((....)))).)).---.)).. ( -40.60)
>DroSec_CAF1 1028 104 - 1
ACUUUUAGAUUAUAAUCUAC--AACUUACAUAUCCCGCUGCUGGUGGGUACCCAGCGGCGGUUGGUUGUGGGAAAUUCAUGUAGGGCGGAUAGCCGGAUCC---ACCAG
...............(((((--((((........((((((((((.(....)))))))))))..)))))))))............((.((((......))))---.)).. ( -36.40)
>DroSim_CAF1 911 99 - 1
ACUUUU-----AUAAACUAC--AACUUACAUAUCCCGCUGCUGGUGGGUACCCACCGGCUGUUGGUUGUGGGAAAUUCAUGUAGGGCGGAUAGCCGGAUCC---ACCAG
......-----.....((((--(.((((((...((.((.((((((((....)))))))).)).)).)))))).......)))))((.((((......))))---.)).. ( -36.20)
>DroEre_CAF1 957 103 - 1
G-UUUAGGAUUAUGAUCUAC--AACUUACAUAUCCCGCUGCUGGUGGGUAUCCACCAGCGGUUGGUUGCGGGAAAUUCAUGUAUGGCUGAUAGCCGGAUCC---GCCGG
.-....(((((((((.....--..((..((...((.(((((((((((....))))))))))).)).))..))....))))...((((.....)))))))))---..... ( -38.10)
>DroYak_CAF1 942 103 - 1
U-UUUAGGAUUUUGAUCAAC--AACUUACAUAUCCCGCUGCUGGUGGGUAACCACCCGCUGUAGGUUGCGGGAAAUUCAUGUACGGCGGAUAGCCGGAUCC---GCCAG
.-.....(((....)))...--....(((((.((((((.((((((((((....)))))))...))).)))))).....))))).(((((((......))))---))).. ( -38.30)
>DroAna_CAF1 1114 103 - 1
AUACUCCA---AUAAGAUACGAAUCAUACAUAGCCCGCAGCUGGUGGAUAGCCACCGG---AUGGUUGUGGGAAAUUCAUGUAGGGCGGAUAACCAGCGCCAUGACCAG
....(((.---....(((....)))...(((((((.....(((((((....)))))))---..))))))))))...(((((..(.((((....)).)).)))))).... ( -31.30)
>consensus
A_UUUUGGAUUAUAAUCUAC__AACUUACAUAUCCCGCUGCUGGUGGGUACCCACCGGCGGUUGGUUGUGGGAAAUUCAUGUAGGGCGGAUAGCCGGAUCC___ACCAG
........................((((((...((.((.((((((((....)))))))).)).)).))))))............(((.....))).............. (-22.42 = -24.17 +   1.75)

alignment

secondary structure

dotplot

Window 6

Location	16,808,946 – 16,809,040
Length	94
Sequences	6
Columns	101
Reading direction	forward
Mean pairwise identity	71.90
Mean single sequence MFE	-22.67
Consensus MFE	-12.59
Energy contribution	-12.87
Covariance contribution	0.28
Combinations/Pair	1.08
Mean z-score	-1.72
Structure conservation index	0.56
SVM decision value	0.95
SVM RNA-class probability	0.888063
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16808946 94 + 23771897
CAUACAACCAACCGCCGGUGGGUACCCACCAGCUGCGGGAUAUGUAAGUU--UUAGAUUAUUAUCCAAAAAUCGAC--UUCUU---AAUGUUUAAAGCUUA
((((...((..(.((.(((((....))))).)).)..)).))))((((((--((((((.((((.............--....)---))))))))))))))) ( -24.53)
>DroSec_CAF1 1062 94 + 1
CCCACAACCAACCGCCGCUGGGUACCCACCAGCAGCGGGAUAUGUAAGUU--GUAGAUUAUAAUCUAAAAGUCGAC--UUCUU---AAAAUCUGAAGUUUA
...(((((((.((((.(((((.......))))).))))....))...)))--))((((....)))).......(((--(((..---.......)))))).. ( -25.10)
>DroSim_CAF1 945 89 + 1
CCCACAACCAACAGCCGGUGGGUACCCACCAGCAGCGGGAUAUGUAAGUU--GUAGUUUAU-----AAAAGUCGAC--UUCUU---AAAAUCUGAAAUUUA
.......((..(.((.(((((....))))).)).)..)).....((((((--.(((.((.(-----(((((....)--)).))---).)).))).)))))) ( -18.70)
>DroEre_CAF1 991 87 + 1
CCCGCAACCAACCGCUGGUGGAUACCCACCAGCAGCGGGAUAUGUAAGUU--GUAGAUCAUAAUCCUAAA-CCUGC--UUGUU---AUAGU------UUUC
(((((........((((((((....)))))))).)))))...(((((...--((((..............-.))))--...))---)))..------.... ( -25.86)
>DroYak_CAF1 976 87 + 1
CCCGCAACCUACAGCGGGUGGUUACCCACCAGCAGCGGGAUAUGUAAGUU--GUUGAUCAAAAUCCUAAA-ACAGC--UUGUU---AUAGU------UUUC
(((((........((.(((((....))))).)).))))).....((((((--(((..............)-)))))--)))..---.....------.... ( -24.54)
>DroAna_CAF1 1151 91 + 1
CCCACAACCAU---CCGGUGGCUAUCCACCAGCUGCGGGCUAUGUAUGAUUCGUAUCUUAU---UGGAGUAUAGAAUUUUGUUCAUAUAUU-U---GUUUU
...((((...(---(((((((....)))))((.(((((((.......).)))))).))...---.)))(((((((((...)))).))))))-)---))... ( -17.30)
>consensus
CCCACAACCAACCGCCGGUGGGUACCCACCAGCAGCGGGAUAUGUAAGUU__GUAGAUUAUAAUCCAAAA_UCGAC__UUCUU___AAAGU_U___GUUUA
...(((.((..(.((.(((((....))))).)).)..))...)))........................................................ (-12.59 = -12.87 +   0.28)

alignment

secondary structure

dotplot

Window 7

Location	16,808,946 – 16,809,040
Length	94
Sequences	6
Columns	101
Reading direction	reverse
Mean pairwise identity	71.90
Mean single sequence MFE	-27.50
Consensus MFE	-19.26
Energy contribution	-20.52
Covariance contribution	1.25
Combinations/Pair	1.11
Mean z-score	-2.53
Structure conservation index	0.70
SVM decision value	2.51
SVM RNA-class probability	0.994744
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16808946 94 - 23771897
UAAGCUUUAAACAUU---AAGAA--GUCGAUUUUUGGAUAAUAAUCUAA--AACUUACAUAUCCCGCAGCUGGUGGGUACCCACCGGCGGUUGGUUGUAUG
...(((((.......---..)))--))....((((((((....))))))--))..((((...((.((.((((((((....)))))))).)).)).)))).. ( -28.50)
>DroSec_CAF1 1062 94 - 1
UAAACUUCAGAUUUU---AAGAA--GUCGACUUUUAGAUUAUAAUCUAC--AACUUACAUAUCCCGCUGCUGGUGGGUACCCAGCGGCGGUUGGUUGUGGG
...(((((.......---..)))--))..................((((--((((........((((((((((.(....)))))))))))..)))))))). ( -30.90)
>DroSim_CAF1 945 89 - 1
UAAAUUUCAGAUUUU---AAGAA--GUCGACUUUU-----AUAAACUAC--AACUUACAUAUCCCGCUGCUGGUGGGUACCCACCGGCUGUUGGUUGUGGG
((((..((.(((((.---...))--)))))..)))-----)....((((--((((.(((.........((((((((....))))))))))).)))))))). ( -29.80)
>DroEre_CAF1 991 87 - 1
GAAA------ACUAU---AACAA--GCAGG-UUUAGGAUUAUGAUCUAC--AACUUACAUAUCCCGCUGCUGGUGGGUAUCCACCAGCGGUUGGUUGCGGG
....------.....---.....--(((((-((..((((....))))..--)))))......((.(((((((((((....))))))))))).))..))... ( -28.80)
>DroYak_CAF1 976 87 - 1
GAAA------ACUAU---AACAA--GCUGU-UUUAGGAUUUUGAUCAAC--AACUUACAUAUCCCGCUGCUGGUGGGUAACCACCCGCUGUAGGUUGCGGG
....------.(((.---(((..--...))-).)))(((....)))...--...........(((((.((((((((((....)))))))...))).))))) ( -24.40)
>DroAna_CAF1 1151 91 - 1
AAAAC---A-AAUAUAUGAACAAAAUUCUAUACUCCA---AUAAGAUACGAAUCAUACAUAGCCCGCAGCUGGUGGAUAGCCACCGG---AUGGUUGUGGG
.....---.-....(((((.....((..(((......---)))..)).....))))).....((((((((((((((....)))))..---..))))))))) ( -22.60)
>consensus
UAAAC___A_ACUAU___AACAA__GUCGA_UUUUGGAUUAUAAUCUAC__AACUUACAUAUCCCGCUGCUGGUGGGUACCCACCGGCGGUUGGUUGUGGG
.....................................................((((((...((.((.((((((((....)))))))).)).)).)))))) (-19.26 = -20.52 +   1.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:15:14 2006