Locus 4037

Sequence ID	2L_DroMel_CAF1
Location	11,698,731 – 11,698,886
Length	155
Max. P	0.738168

overview

Window 9

Location	11,698,731 – 11,698,846
Length	115
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	88.87
Mean single sequence MFE	-33.14
Consensus MFE	-23.80
Energy contribution	-23.80
Covariance contribution	0.00
Combinations/Pair	1.18
Mean z-score	-2.07
Structure conservation index	0.72
SVM decision value	0.44
SVM RNA-class probability	0.738168
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11698731 115 + 22407834
UACAAUGCAUCACCUUAUGAACAUAUCGAGGCAGCUUUAAUGUCAACACCAAAUUUGCCUAAAGAGACUCCUUUCAGCCAGACAGGAUACGGAUGAGCUCUACUUGAGCUCAUGG
............((...........((.((((((.(((..((....))..))).))))))...))...((((.((.....)).))))...))((((((((.....)))))))).. ( -28.30)
>DroSec_CAF1 160204 112 + 1
UACAAUGCAACCCCU---GAACAUAUCGAGGCAGCUUUAAUGUCAACACCGAAUCUGCCUAAAGAGACUCCUGUCAGCCAGACAGGAUACGGAUGAGCUCUACUUGAGCUCAUGG
.............((---(......((.((((((.(((..((....))..))).))))))...))...(((((((.....)))))))..)))((((((((.....)))))))).. ( -36.90)
>DroSim_CAF1 157771 115 + 1
UACAAUGCAACCCCUUAUGAACAUAUCGAGGCAGCUUUAAUGUCAACACCGAAUCUGCCUAAAGAGACUCCUGUCAGCCAGACAGGAUACGGAUGAGCUCUACUUGAGCUCAUGG
............((...........((.((((((.(((..((....))..))).))))))...))...(((((((.....)))))))...))((((((((.....)))))))).. ( -36.60)
>DroEre_CAF1 183107 115 + 1
UUUAAUGCGACCGCUCAUGAACCUAUUGAGACUGCUUUAAUGUCAACACCGAAUCUGCCUAAAGAGGCUCCUUUCAGCAGGACAGGAUACGGAUGAGCUCUACUUGGGCUCGUGG
.((((.(((....((((.........))))..))).))))........(((.((((((((....))))((((......))))..)))).)))((((((((.....)))))))).. ( -32.40)
>DroYak_CAF1 156966 115 + 1
AUCGAUGCAAAGCCUUAUGAACCUAUCGAGACAGCUUUAAUUUCAACACCGAAUCUGACUGAAGAGACUCCUCUCAGGCAGACAGGAUACGGAUGAGCUCUACUUGAGCUCAUGG
.(((....(((((.((.(((.....))).))..)))))..........((...((((.((((.(((....))))))).))))..))...)))((((((((.....)))))))).. ( -31.50)
>consensus
UACAAUGCAACCCCUUAUGAACAUAUCGAGGCAGCUUUAAUGUCAACACCGAAUCUGCCUAAAGAGACUCCUGUCAGCCAGACAGGAUACGGAUGAGCUCUACUUGAGCUCAUGG
.........................(((((((((.(((..((....))..))).))))))........((((.((.....)).))))..)))((((((((.....)))))))).. (-23.80 = -23.80 +   0.00)

alignment

secondary structure

dotplot

Window 0

Location	11,698,771 – 11,698,886
Length	115
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	79.88
Mean single sequence MFE	-35.78
Consensus MFE	-23.01
Energy contribution	-24.77
Covariance contribution	1.75
Combinations/Pair	1.11
Mean z-score	-1.62
Structure conservation index	0.64
SVM decision value	0.35
SVM RNA-class probability	0.701156
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11698771 115 + 22407834
UGUCAACACCAAAUUUGCCUAAAGAGACUCCUUUCAGCCAGACAGGAUACGGAUGAGCUCUACUUGAGCUCAUGGUUAUGCAUCAGCUGCAUUUGCCGGUUCGGCCCAACCUGAG
.............((((.((((((......)))).)).))))((((...(((((((((((.....)))))).((((.(((((.....)))))..)))))))))......)))).. ( -31.40)
>DroSec_CAF1 160241 115 + 1
UGUCAACACCGAAUCUGCCUAAAGAGACUCCUGUCAGCCAGACAGGAUACGGAUGAGCUCUACUUGAGCUCAUGGUUAUGCAUCAGCUGCAUUUGCCGGUUCGGCCCAACCUGGC
.((((...(((..(((......)))...(((((((.....)))))))..)))((((((((.....))))))))(((((((((.....)))))..((((...))))..)))))))) ( -41.00)
>DroSim_CAF1 157811 115 + 1
UGUCAACACCGAAUCUGCCUAAAGAGACUCCUGUCAGCCAGACAGGAUACGGAUGAGCUCUACUUGAGCUCAUGGUUAUGCAUCAGCUGCAUUUGCCGGUUCGGCCCAACCUGGC
.((((...(((..(((......)))...(((((((.....)))))))..)))((((((((.....))))))))(((((((((.....)))))..((((...))))..)))))))) ( -41.00)
>DroEre_CAF1 183147 115 + 1
UGUCAACACCGAAUCUGCCUAAAGAGGCUCCUUUCAGCAGGACAGGAUACGGAUGAGCUCUACUUGGGCUCGUGGUUAUGCAUCAGCUGCAUUUGCCUGCUCGGCCCAGACUGGC
.(((..(((((.((((((((....))))((((......))))..)))).))).)).........(((((.((.(((.(((((.....)))))..)))....)))))))))).... ( -38.00)
>DroYak_CAF1 157006 115 + 1
UUUCAACACCGAAUCUGACUGAAGAGACUCCUCUCAGGCAGACAGGAUACGGAUGAGCUCUACUUGAGCUCAUGGUUAUGCAUCGGUUGCAUUUGCCUGUUCGGCCCAACCUGAC
.............((((.((((.(((....))))))).))))((((...(((((((((((.....))))))..(((.(((((.....)))))..))).)))))......)))).. ( -39.50)
>DroAna_CAF1 164459 87 + 1
------------------------GAAAUCCUUU---ACAGACAGGAUGUGGAUGGCCU-UCGUUCAAUUCAUGGUUAUGCAUCGAUUGCAGUUGCCUGUUUGGCCAAAGUUGGC
------------------------..........---.((((((((((.((((((....-.))))))))))..(((..((((.....))))...)))))))))((((....)))) ( -23.80)
>consensus
UGUCAACACCGAAUCUGCCUAAAGAGACUCCUUUCAGCCAGACAGGAUACGGAUGAGCUCUACUUGAGCUCAUGGUUAUGCAUCAGCUGCAUUUGCCGGUUCGGCCCAACCUGGC
........((((((..............((((.((.....)).)))).....((((((((.....))))))))(((.(((((.....)))))..))).))))))........... (-23.01 = -24.77 +   1.75)

alignment

secondary structure

dotplot

Window 1

Location	11,698,771 – 11,698,886
Length	115
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	79.88
Mean single sequence MFE	-36.97
Consensus MFE	-22.43
Energy contribution	-24.60
Covariance contribution	2.17
Combinations/Pair	1.10
Mean z-score	-1.72
Structure conservation index	0.61
SVM decision value	0.26
SVM RNA-class probability	0.657694
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11698771 115 - 22407834
CUCAGGUUGGGCCGAACCGGCAAAUGCAGCUGAUGCAUAACCAUGAGCUCAAGUAGAGCUCAUCCGUAUCCUGUCUGGCUGAAAGGAGUCUCUUUAGGCAAAUUUGGUGUUGACA
.....((..(((((((.(((...(((((.....)))))....((((((((.....)))))))))))..((((.((.....)).))))((((....))))...)))))).)..)). ( -34.70)
>DroSec_CAF1 160241 115 - 1
GCCAGGUUGGGCCGAACCGGCAAAUGCAGCUGAUGCAUAACCAUGAGCUCAAGUAGAGCUCAUCCGUAUCCUGUCUGGCUGACAGGAGUCUCUUUAGGCAGAUUCGGUGUUGACA
.....((..(((((((.(((...(((((.....)))))....((((((((.....)))))))))))..(((((((.....)))))))((((....))))...)))))).)..)). ( -42.80)
>DroSim_CAF1 157811 115 - 1
GCCAGGUUGGGCCGAACCGGCAAAUGCAGCUGAUGCAUAACCAUGAGCUCAAGUAGAGCUCAUCCGUAUCCUGUCUGGCUGACAGGAGUCUCUUUAGGCAGAUUCGGUGUUGACA
.....((..(((((((.(((...(((((.....)))))....((((((((.....)))))))))))..(((((((.....)))))))((((....))))...)))))).)..)). ( -42.80)
>DroEre_CAF1 183147 115 - 1
GCCAGUCUGGGCCGAGCAGGCAAAUGCAGCUGAUGCAUAACCACGAGCCCAAGUAGAGCUCAUCCGUAUCCUGUCCUGCUGAAAGGAGCCUCUUUAGGCAGAUUCGGUGUUGACA
....(((.(.((((((((((...(((((.....)))))......((((.(.....).))))........))))).(((((.(((((....))))).)))))..))))).).))). ( -38.00)
>DroYak_CAF1 157006 115 - 1
GUCAGGUUGGGCCGAACAGGCAAAUGCAACCGAUGCAUAACCAUGAGCUCAAGUAGAGCUCAUCCGUAUCCUGUCUGCCUGAGAGGAGUCUCUUCAGUCAGAUUCGGUGUUGAAA
....(((((.(((.....)))...((((.....))))))))).(((((((.....)))))))((..((((..(((((.(((((((....))).)))).)))))..))))..)).. ( -41.20)
>DroAna_CAF1 164459 87 - 1
GCCAACUUUGGCCAAACAGGCAACUGCAAUCGAUGCAUAACCAUGAAUUGAACGA-AGGCCAUCCACAUCCUGUCUGU---AAAGGAUUUC------------------------
........(((((...(((....)))...(((((.(((....))).)))))....-.))))).....(((((......---..)))))...------------------------ ( -22.30)
>consensus
GCCAGGUUGGGCCGAACAGGCAAAUGCAGCUGAUGCAUAACCAUGAGCUCAAGUAGAGCUCAUCCGUAUCCUGUCUGGCUGAAAGGAGUCUCUUUAGGCAGAUUCGGUGUUGACA
.......((((((.....)))..(((((.....)))))..)))(((((((.....))))))).(((..((((.((.....)).))))(((......))).....)))........ (-22.43 = -24.60 +   2.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:07:43 2006