Locus 7972

Sequence ID	3L_DroMel_CAF1
Location	21,102,190 – 21,102,430
Length	240
Max. P	0.999958

overview

Window 4

Location	21,102,190 – 21,102,310
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.08
Mean single sequence MFE	-39.48
Consensus MFE	-32.58
Energy contribution	-32.26
Covariance contribution	-0.32
Combinations/Pair	1.11
Mean z-score	-2.42
Structure conservation index	0.83
SVM decision value	2.34
SVM RNA-class probability	0.992684
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21102190 120 - 23771897
GGCCAGGCUCAAAACUUGUGGCUGCAUCGGGCACAAAGCCAACAAUUGCUUUUAAUCCCGGCUGGAGGAUGCUGCCAAAGUGAAAAGUAUACACCAAUUUGGUAGGGUAACCGGUCAAAA
((((..(((....((((.((((.(((((.(((.....)))...............(((.....))).))))).))))))))....)))....(((.....))).((....)))))).... ( -35.40)
>DroSec_CAF1 152452 120 - 1
GGCCAGGCUCAAAACUUGUGGCUGCAUCGGGCACAAAGCCAACAAUUGCUGUUAAUCCGGGCUGGAGGAUGCUGCCACAGUGAAAAUUACACACCAAUUUGGCAGUGUAACCGGUCAAAA
((((.((......(((.(((((.(((((.(((.....)))((((.....))))..(((.....))).))))).)))))))).....((((((.((.....))..)))))))))))).... ( -39.70)
>DroSim_CAF1 59995 120 - 1
GGCCAGGCUCAAAACUUGUGGCUGCAUCGGGCACAAAGCCAACAAUUGCUUUUAAUCCCGGCUGGAGGAUGCUGCCAAAGUGAAAAGUACACACCAAUUUGGCAGUGUAACCGGUCAAAA
(((((.(.........).))))).....(((...(((((........)))))....)))((((((...((((((((((((((.........)))...)))))))))))..)))))).... ( -37.60)
>DroEre_CAF1 74793 119 - 1
GGCCAGGCUCAAAACUUGUGGCUGCAUCGGCCACAGAGCCAACAAUUGCUUUUAAUCCC-GCUGGAGGAUACUGCCAAAGUAAAAAGUACACACAAAUUUGGCAGGGCAGCCGGUCAAUA
((((.(((((......((((((((...))))))))))))).....(((((....(((((-....).)))).((((((((..................)))))))))))))..)))).... ( -42.77)
>DroYak_CAF1 46875 120 - 1
GGCCGGGCUCAAAACUUGUGGCUGCAUCGGCCACAAAGCCAACAAUUGCUUUUAAUCCCGGCUGGAGGAUACUGCCAAAGUGAAAACUACACACCAAUUUGGCAGGGUAGCCGGUCUAAA
((((((.(((.....(((((((((...)))))))))((((...................)))).)))....(((((((((((.........)))...)))))))).....)))))).... ( -41.91)
>consensus
GGCCAGGCUCAAAACUUGUGGCUGCAUCGGGCACAAAGCCAACAAUUGCUUUUAAUCCCGGCUGGAGGAUGCUGCCAAAGUGAAAAGUACACACCAAUUUGGCAGGGUAACCGGUCAAAA
((((.((((......(((((.(((...))).))))))))).....((((.....((((........)))).(((((((((((.........)))...)))))))).))))..)))).... (-32.58 = -32.26 +  -0.32)

alignment

secondary structure

dotplot

Window 5

Location	21,102,230 – 21,102,350
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.33
Mean single sequence MFE	-45.01
Consensus MFE	-38.42
Energy contribution	-39.86
Covariance contribution	1.44
Combinations/Pair	1.11
Mean z-score	-2.72
Structure conservation index	0.85
SVM decision value	3.34
SVM RNA-class probability	0.999033
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21102230 120 + 23771897
CUUUGGCAGCAUCCUCCAGCCGGGAUUAAAAGCAAUUGUUGGCUUUGUGCCCGAUGCAGCCACAAGUUUUGAGCCUGGCCAAAUCCGGGCUAUAAUAUCUGUGCCGCUGCCAAGAGGCAA
.(((((((((........((((((....(((((........)))))...))))..)).(.((((..(.((((((((((......))))))).))).)..)))).))))))))))...... ( -45.40)
>DroSec_CAF1 152492 120 + 1
CUGUGGCAGCAUCCUCCAGCCCGGAUUAACAGCAAUUGUUGGCUUUGUGCCCGAUGCAGCCACAAGUUUUGAGCCUGGCCAAAUCCGGGCUAUAAUAUUUGUGCCGCUGCCAAGAGGCAA
..((((((.((......((((((((((....(((.(((..(((.....))))))))).((((...((.....)).))))..))))))))))........))))))))((((....)))). ( -44.64)
>DroSim_CAF1 60035 120 + 1
CUUUGGCAGCAUCCUCCAGCCGGGAUUAAAAGCAAUUGUUGGCUUUGUGCCCGAUGCAGCCACAAGUUUUGAGCCUGGCCAAAUCCGGGCUAUAAUAUUUGUGCCGCUGCCAAGAGGCAA
.(((((((((........((((((....(((((........)))))...))))..)).(.(((((((.((((((((((......))))))).))).))))))).))))))))))...... ( -48.50)
>DroEre_CAF1 74833 119 + 1
CUUUGGCAGUAUCCUCCAGC-GGGAUUAAAAGCAAUUGUUGGCUCUGUGGCCGAUGCAGCCACAAGUUUUGAGCCUGGCCAAAUCUAGGCUGCAAUAUUUGAGCCGCCGCCAAGAGCCAA
.....((...(((((.....-))))).....)).....((((((((.((((....((.((..(((((.((((((((((......))))))).))).))))).)).)).)))))))))))) ( -42.30)
>DroYak_CAF1 46915 120 + 1
CUUUGGCAGUAUCCUCCAGCCGGGAUUAAAAGCAAUUGUUGGCUUUGUGGCCGAUGCAGCCACAAGUUUUGAGCCCGGCCAAAUCUAGGCUGUAAUAUUUGUGCCGCUGCCAAGAGCGAA
.(((((((((........((((((.((((((((........))((((((((.......)))))))))))))).))))))........(((............))))))))))))...... ( -44.20)
>consensus
CUUUGGCAGCAUCCUCCAGCCGGGAUUAAAAGCAAUUGUUGGCUUUGUGCCCGAUGCAGCCACAAGUUUUGAGCCUGGCCAAAUCCGGGCUAUAAUAUUUGUGCCGCUGCCAAGAGGCAA
.(((((((((........((((((....(((((........)))))...))))..)).(.(((((((.((((((((((......))))))).))).))))))).))))))))))...... (-38.42 = -39.86 +   1.44)

alignment

secondary structure

dotplot

Window 6

Location	21,102,230 – 21,102,350
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.33
Mean single sequence MFE	-42.52
Consensus MFE	-33.51
Energy contribution	-34.15
Covariance contribution	0.64
Combinations/Pair	1.09
Mean z-score	-2.13
Structure conservation index	0.79
SVM decision value	1.16
SVM RNA-class probability	0.924749
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21102230 120 - 23771897
UUGCCUCUUGGCAGCGGCACAGAUAUUAUAGCCCGGAUUUGGCCAGGCUCAAAACUUGUGGCUGCAUCGGGCACAAAGCCAACAAUUGCUUUUAAUCCCGGCUGGAGGAUGCUGCCAAAG
.......(((((((((.(((((.......((((.((......)).))))......))))).((.(((((((...(((((........)))))....))))).)).))..))))))))).. ( -40.42)
>DroSec_CAF1 152492 120 - 1
UUGCCUCUUGGCAGCGGCACAAAUAUUAUAGCCCGGAUUUGGCCAGGCUCAAAACUUGUGGCUGCAUCGGGCACAAAGCCAACAAUUGCUGUUAAUCCGGGCUGGAGGAUGCUGCCACAG
.((((....))))((((((.........(((((((((((......((((......(((((.(((...))).)))))))))((((.....))))))))))))))).....))))))..... ( -45.44)
>DroSim_CAF1 60035 120 - 1
UUGCCUCUUGGCAGCGGCACAAAUAUUAUAGCCCGGAUUUGGCCAGGCUCAAAACUUGUGGCUGCAUCGGGCACAAAGCCAACAAUUGCUUUUAAUCCCGGCUGGAGGAUGCUGCCAAAG
.......(((((((((.(((((.......((((.((......)).))))......))))).((.(((((((...(((((........)))))....))))).)).))..))))))))).. ( -40.72)
>DroEre_CAF1 74833 119 - 1
UUGGCUCUUGGCGGCGGCUCAAAUAUUGCAGCCUAGAUUUGGCCAGGCUCAAAACUUGUGGCUGCAUCGGCCACAGAGCCAACAAUUGCUUUUAAUCCC-GCUGGAGGAUACUGCCAAAG
.......(((((((.(((((.....(((.(((((.(......).))))))))....((((((((...)))))))))))))..............(((((-....).)))).))))))).. ( -42.50)
>DroYak_CAF1 46915 120 - 1
UUCGCUCUUGGCAGCGGCACAAAUAUUACAGCCUAGAUUUGGCCGGGCUCAAAACUUGUGGCUGCAUCGGCCACAAAGCCAACAAUUGCUUUUAAUCCCGGCUGGAGGAUACUGCCAAAG
.......(((((((.(((............)))....((..((((((..........(((((((...)))))))(((((........)))))....))))))..)).....))))))).. ( -43.50)
>consensus
UUGCCUCUUGGCAGCGGCACAAAUAUUAUAGCCCGGAUUUGGCCAGGCUCAAAACUUGUGGCUGCAUCGGGCACAAAGCCAACAAUUGCUUUUAAUCCCGGCUGGAGGAUGCUGCCAAAG
.......(((((((((............(((((.(((((.(((..((((......(((((.(((...))).))))))))).......)))...))))).))))).....))))))))).. (-33.51 = -34.15 +   0.64)

alignment

secondary structure

dotplot

Window 7

Location	21,102,270 – 21,102,390
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.00
Mean single sequence MFE	-40.99
Consensus MFE	-38.50
Energy contribution	-38.34
Covariance contribution	-0.16
Combinations/Pair	1.14
Mean z-score	-2.73
Structure conservation index	0.94
SVM decision value	4.88
SVM RNA-class probability	0.999958
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21102270 120 + 23771897
GGCUUUGUGCCCGAUGCAGCCACAAGUUUUGAGCCUGGCCAAAUCCGGGCUAUAAUAUCUGUGCCGCUGCCAAGAGGCAAGUAAAAAGUGGCAGCAACCAGGACAAUUAGCACAGCCAAA
((((..((((((..(((.(((((..(((...(((((((......)))))))..))).....((((.((....)).))))........))))).)))....)).......))))))))... ( -42.61)
>DroSec_CAF1 152532 120 + 1
GGCUUUGUGCCCGAUGCAGCCACAAGUUUUGAGCCUGGCCAAAUCCGGGCUAUAAUAUUUGUGCCGCUGCCAAGAGGCAAGUAAAAAGUGGCAGCAACCAGGACAAUUAGCACAGCCAAA
((((.(((((((...((((((((((((.((((((((((......))))))).))).)))))))..)))))...).)))..........(((......))).........))).))))... ( -44.00)
>DroSim_CAF1 60075 120 + 1
GGCUUUGUGCCCGAUGCAGCCACAAGUUUUGAGCCUGGCCAAAUCCGGGCUAUAAUAUUUGUGCCGCUGCCAAGAGGCAAGUAAAAAGUGGCAGCAACCAGGACAAUUAGCACAGCCAAA
((((.(((((((...((((((((((((.((((((((((......))))))).))).)))))))..)))))...).)))..........(((......))).........))).))))... ( -44.00)
>DroEre_CAF1 74872 120 + 1
GGCUCUGUGGCCGAUGCAGCCACAAGUUUUGAGCCUGGCCAAAUCUAGGCUGCAAUAUUUGAGCCGCCGCCAAGAGCCAAGUAAAAAGCAACAGCAACUAGGACAAUUAGCACAGCCAAA
((((((.((((....((.((..(((((.((((((((((......))))))).))).))))).)).)).)))))))))).........((....))..((((.....)))).......... ( -37.50)
>DroYak_CAF1 46955 120 + 1
GGCUUUGUGGCCGAUGCAGCCACAAGUUUUGAGCCCGGCCAAAUCUAGGCUGUAAUAUUUGUGCCGCUGCCAAGAGCGAAGUAGAAAGUAACAGCAACUAGGACAAUUAGCACAGCCAAA
((((.((((((((..((...............)).)))))...((((((((((....(((.(((((((......))))..))).)))...)))))..))))).......))).))))... ( -36.86)
>consensus
GGCUUUGUGCCCGAUGCAGCCACAAGUUUUGAGCCUGGCCAAAUCCGGGCUAUAAUAUUUGUGCCGCUGCCAAGAGGCAAGUAAAAAGUGGCAGCAACCAGGACAAUUAGCACAGCCAAA
((((.(((((((...((((((((((((.((((((((((......))))))).))).)))))))..)))))...).))).........((....))..............))).))))... (-38.50 = -38.34 +  -0.16)

alignment

secondary structure

dotplot

Window 8

Location	21,102,270 – 21,102,390
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.00
Mean single sequence MFE	-40.32
Consensus MFE	-34.91
Energy contribution	-33.59
Covariance contribution	-1.32
Combinations/Pair	1.23
Mean z-score	-1.84
Structure conservation index	0.87
SVM decision value	1.84
SVM RNA-class probability	0.979678
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21102270 120 - 23771897
UUUGGCUGUGCUAAUUGUCCUGGUUGCUGCCACUUUUUACUUGCCUCUUGGCAGCGGCACAGAUAUUAUAGCCCGGAUUUGGCCAGGCUCAAAACUUGUGGCUGCAUCGGGCACAAAGCC
...((((.((.........(((((((((((((................)))))))))).)))........(((((.((.((((((.(.........).)))))).))))))).)).)))) ( -41.69)
>DroSec_CAF1 152532 120 - 1
UUUGGCUGUGCUAAUUGUCCUGGUUGCUGCCACUUUUUACUUGCCUCUUGGCAGCGGCACAAAUAUUAUAGCCCGGAUUUGGCCAGGCUCAAAACUUGUGGCUGCAUCGGGCACAAAGCC
...(((((((((...(((((..((((((((((................))))))))))((((.......((((.((......)).))))......))))))..)))...)))))..)))) ( -39.21)
>DroSim_CAF1 60075 120 - 1
UUUGGCUGUGCUAAUUGUCCUGGUUGCUGCCACUUUUUACUUGCCUCUUGGCAGCGGCACAAAUAUUAUAGCCCGGAUUUGGCCAGGCUCAAAACUUGUGGCUGCAUCGGGCACAAAGCC
...(((((((((...(((((..((((((((((................))))))))))((((.......((((.((......)).))))......))))))..)))...)))))..)))) ( -39.21)
>DroEre_CAF1 74872 120 - 1
UUUGGCUGUGCUAAUUGUCCUAGUUGCUGUUGCUUUUUACUUGGCUCUUGGCGGCGGCUCAAAUAUUGCAGCCUAGAUUUGGCCAGGCUCAAAACUUGUGGCUGCAUCGGCCACAGAGCC
..((((((..(((.........(((((((..(((........)))...)))))))((((((.....)).)))))))...))))))(((((......((((((((...))))))))))))) ( -42.80)
>DroYak_CAF1 46955 120 - 1
UUUGGCUGUGCUAAUUGUCCUAGUUGCUGUUACUUUCUACUUCGCUCUUGGCAGCGGCACAAAUAUUACAGCCUAGAUUUGGCCGGGCUCAAAACUUGUGGCUGCAUCGGCCACAAAGCC
...(((((((.((.((((....((((((((((................)))))))))))))).)).)))))))............((((......(((((((((...))))))))))))) ( -38.69)
>consensus
UUUGGCUGUGCUAAUUGUCCUGGUUGCUGCCACUUUUUACUUGCCUCUUGGCAGCGGCACAAAUAUUAUAGCCCGGAUUUGGCCAGGCUCAAAACUUGUGGCUGCAUCGGGCACAAAGCC
...(((((((.((.((((....((((((((((................)))))))))))))).)).)))))))............((((......(((((.(((...))).))))))))) (-34.91 = -33.59 +  -1.32)

alignment

secondary structure

dotplot

Window 9

Location	21,102,310 – 21,102,430
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.67
Mean single sequence MFE	-36.41
Consensus MFE	-35.27
Energy contribution	-34.27
Covariance contribution	-1.00
Combinations/Pair	1.22
Mean z-score	-1.64
Structure conservation index	0.97
SVM decision value	2.44
SVM RNA-class probability	0.994022
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21102310 120 - 23771897
UGUGCGUUGUCUUGCCAACGGAAACUUAUGGCCCAGCAGUUUUGGCUGUGCUAAUUGUCCUGGUUGCUGCCACUUUUUACUUGCCUCUUGGCAGCGGCACAGAUAUUAUAGCCCGGAUUU
.....((((....((((..(....)...)))).))))((((..(((((((.....((((.((((((((((((................)))))))))).)))))).)))))))..)))). ( -38.59)
>DroSec_CAF1 152572 120 - 1
UGUGCGUUGUCUUGCCAACGGAAACUUAUGGCCCAGCACUUUUGGCUGUGCUAAUUGUCCUGGUUGCUGCCACUUUUUACUUGCCUCUUGGCAGCGGCACAAAUAUUAUAGCCCGGAUUU
.((((........((((..(....)...))))...))))((..(((((((.((.((((....((((((((((................)))))))))))))).)).)))))))..))... ( -36.89)
>DroSim_CAF1 60115 120 - 1
UGUGCGUUGUCUUGCCAACGGAAACUUAUGGCCCAGCACUUUUGGCUGUGCUAAUUGUCCUGGUUGCUGCCACUUUUUACUUGCCUCUUGGCAGCGGCACAAAUAUUAUAGCCCGGAUUU
.((((........((((..(....)...))))...))))((..(((((((.((.((((....((((((((((................)))))))))))))).)).)))))))..))... ( -36.89)
>DroEre_CAF1 74912 120 - 1
UGUGCGUUGUCUUGCCAACGGAAACUUAUGGCCCAGCAGUUUUGGCUGUGCUAAUUGUCCUAGUUGCUGUUGCUUUUUACUUGGCUCUUGGCGGCGGCUCAAAUAUUGCAGCCUAGAUUU
.....((((....((((..(....)...)))).))))(((((.((((((..((.(((....(((((((((((((........)))....))))))))))))).))..)))))).))))). ( -35.20)
>DroYak_CAF1 46995 120 - 1
UGUGCGUUGUCUUGCCAACGGAAACUUAUGGCCCAGCAGUUUUGGCUGUGCUAAUUGUCCUAGUUGCUGUUACUUUCUACUUCGCUCUUGGCAGCGGCACAAAUAUUACAGCCUAGAUUU
.....((((....((((..(....)...)))).))))(((((.(((((((.((.((((....((((((((((................)))))))))))))).)).))))))).))))). ( -34.49)
>consensus
UGUGCGUUGUCUUGCCAACGGAAACUUAUGGCCCAGCAGUUUUGGCUGUGCUAAUUGUCCUGGUUGCUGCCACUUUUUACUUGCCUCUUGGCAGCGGCACAAAUAUUAUAGCCCGGAUUU
.....((((....((((..(....)...)))).))))(((((.(((((((.((.((((....((((((((((................)))))))))))))).)).))))))).))))). (-35.27 = -34.27 +  -1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:02:39 2006