Locus 4832

Sequence ID	2L_DroMel_CAF1
Location	13,756,273 – 13,756,497
Length	224
Max. P	0.997920

overview

Window 6

Location	13,756,273 – 13,756,377
Length	104
Sequences	4
Columns	104
Reading direction	forward
Mean pairwise identity	88.40
Mean single sequence MFE	-31.02
Consensus MFE	-24.15
Energy contribution	-23.78
Covariance contribution	-0.37
Combinations/Pair	1.08
Mean z-score	-3.11
Structure conservation index	0.78
SVM decision value	1.82
SVM RNA-class probability	0.978789
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13756273 104 + 22407834
AAGGAUGGACGGAAGCAUCCAGCUUGUCUUUAUGGCCGUCAAGGAGCGAUGUUCAAGGAAAACUUUCCAGAAUGGCGCCGGCGAGAGGCAAAAAUACAAAAAAA
..(((((..(....))))))...((((((((.((((.((((..((((...))))..((((....))))....))))))))...))))))))............. ( -30.60)
>DroSim_CAF1 21973 102 + 1
AAGGAUGGACGGAAGCAUCCAGCUUGUCUUUAUGGCCGUCAAGGAGCGAUGUUCAAGGAAAACUUUCCAGAAUGGCGGCGGCGAGAGGAAAAAUUAAAAAA--A
..(((((..(....))))))..((((((......(((((((..((((...))))..((((....))))....)))))))))))))................--. ( -29.20)
>DroEre_CAF1 21733 95 + 1
AAGGAUGGACGGAAGCAUCCUGCUUGUCUUUAUGGCCGUCAAGGAGCGAUGUUCAAGGAAAACUUUCCAGAAUGGC---GGCGAGAGGCAAAAA----AU--AA
.((((((..(....)))))))..((((((((...(((((((..((((...))))..((((....))))....))))---))).))))))))...----..--.. ( -33.30)
>DroYak_CAF1 23058 91 + 1
AAGGAUGAACGGAAGUAUCCUGCUCGUCUUUAUGGCCGUCAAGGAGCGAUGUUCAAGGAAAACUUUCCAGAAUGGC---GGCGAGAGGCAAAAA----------
.(((((..((....)))))))....((((((...(((((((..((((...))))..((((....))))....))))---))).)))))).....---------- ( -31.00)
>consensus
AAGGAUGGACGGAAGCAUCCAGCUUGUCUUUAUGGCCGUCAAGGAGCGAUGUUCAAGGAAAACUUUCCAGAAUGGC___GGCGAGAGGCAAAAA____AA___A
..(((((..(....))))))..((((((......((((((...((((...))))..((((....)))).).)))))...))))))................... (-24.15 = -23.78 +  -0.37)

alignment

secondary structure

dotplot

Window 7

Location	13,756,298 – 13,756,417
Length	119
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	77.83
Mean single sequence MFE	-22.48
Consensus MFE	-12.27
Energy contribution	-13.64
Covariance contribution	1.37
Combinations/Pair	1.13
Mean z-score	-1.86
Structure conservation index	0.55
SVM decision value	0.30
SVM RNA-class probability	0.679060
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13756298 119 + 22407834
GUCUUUAUGGCCGUCAAGGAGCGAUGUUCAAGGAAAACUUUCCAGAAUGGCGCCGGCGAGAGGCAAAAAUACAAAAAAAAAAAAGAAUACGAAAAUUGGCACAUAAAAAGUUUUUUAAU
...(((((((((((((..((((...))))..((((....))))....))))(((.......))).................................))).))))))............ ( -23.80)
>DroAna_CAF1 40699 93 + 1
GUCUUUAUGGCUGCCAAGUAGCU---------GCAAACUUU--------GC---GACGGAAGGCAGGAA----GU--AGAACGACAAAAAAAAUAUUGGCAUAUAAAAAGUUUUUUAAU
((((((((..(((((.....(.(---------(((.....)--------))---).)....)))))...----))--)))..)))..(((((((.((.........)).)))))))... ( -15.90)
>DroSim_CAF1 21998 117 + 1
GUCUUUAUGGCCGUCAAGGAGCGAUGUUCAAGGAAAACUUUCCAGAAUGGCGGCGGCGAGAGGAAAAAUUAAAAAA--AAAAAAGAAUAAGAAAAUUGGCACAUAAAAAGUUUUUUAAU
.(((((...(((((((..((((...))))..((((....))))....)))))))..(....)..............--...)))))...((((((((...........))))))))... ( -22.30)
>DroEre_CAF1 21758 110 + 1
GUCUUUAUGGCCGUCAAGGAGCGAUGUUCAAGGAAAACUUUCCAGAAUGGC---GGCGAGAGGCAAAAA----AU--AAAAAAAAAAUAAGAAAAUUGGCACAUAAAAAGUUUUUUAAU
((((((...(((((((..((((...))))..((((....))))....))))---))).)))))).....----..--............((((((((...........))))))))... ( -25.20)
>DroYak_CAF1 23083 99 + 1
GUCUUUAUGGCCGUCAAGGAGCGAUGUUCAAGGAAAACUUUCCAGAAUGGC---GGCGAGAGGCAAAAA-----------------AUAAGAAAAUUGGCACAUAAAAAGUUUUUUAAU
((((((...(((((((..((((...))))..((((....))))....))))---))).)))))).....-----------------...((((((((...........))))))))... ( -25.20)
>consensus
GUCUUUAUGGCCGUCAAGGAGCGAUGUUCAAGGAAAACUUUCCAGAAUGGC___GGCGAGAGGCAAAAA____AA__AAAAAAAGAAUAAGAAAAUUGGCACAUAAAAAGUUUUUUAAU
...(((((((((((((..((((...))))..((((....))))....))))...(.(....).).................................))).))))))............ (-12.27 = -13.64 +   1.37)

alignment

secondary structure

dotplot

Window 8

Location	13,756,377 – 13,756,497
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	93.61
Mean single sequence MFE	-29.35
Consensus MFE	-26.76
Energy contribution	-26.85
Covariance contribution	0.09
Combinations/Pair	1.09
Mean z-score	-1.45
Structure conservation index	0.91
SVM decision value	1.05
SVM RNA-class probability	0.906192
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13756377 120 + 22407834
AAAAAGAAUACGAAAAUUGGCACAUAAAAAGUUUUUUAAUGAAUGGAAUUAGUGUUUGAGCUGCAGCGACUUUGCUAAAUCGUCCGAGCAUCGCCUCGGAAGUCCACUCAGUGUGCCACU
.................((((((((((((....))))..(((.((((.((((((.....((....)).....))))))....((((((......))))))..)))).))))))))))).. ( -31.20)
>DroSec_CAF1 19967 120 + 1
AAAAAGAAUAAGAAAAUUGGCACAUAAAAAGUUUUUUAAUGAAUGGAAUUAGUGUUUGAGCUGCAGCGACUUUGCUAAAUCGUCCGAGCAUCGCCUCGGAAGUCCACUCAGAGUGCCACU
.................((((((.(((((....))))).(((.((((.((((((.....((....)).....))))))....((((((......))))))..)))).)))..)))))).. ( -30.60)
>DroAna_CAF1 40752 120 + 1
AACGACAAAAAAAAUAUUGGCAUAUAAAAAGUUUUUUAAUGAAUGGAAUUAGUGUUUGAGCUGCACCGACUUUGUUAAAUCGUCCGAGCAGCGUCUCGGAAGUCCACUCAGAGUCCUUCU
...(((..(((((((.((.........)).)))))))..(((.((((............(((((.(.(((...........))).).)))))....(....))))).)))..)))..... ( -22.50)
>DroSim_CAF1 22075 120 + 1
AAAAAGAAUAAGAAAAUUGGCACAUAAAAAGUUUUUUAAUGAAUGGAAUUAGUGUUUGAGCUGCAGCGACUUUGCUAAAUCGUCCGAGCAUCGCCUCGGAAGUCCACUCAGAGUGCCACU
.................((((((.(((((....))))).(((.((((.((((((.....((....)).....))))))....((((((......))))))..)))).)))..)))))).. ( -30.60)
>DroEre_CAF1 21828 120 + 1
AAAAAAAAUAAGAAAAUUGGCACAUAAAAAGUUUUUUAAUGAAUGGAAUUAGUGUUUGAGCUGCAGCGACUUUGCUAAAUCGUCCGAGCAUCGCCUCGGAAGUCCACUCAGAGUGCCACU
.................((((((.(((((....))))).(((.((((.((((((.....((....)).....))))))....((((((......))))))..)))).)))..)))))).. ( -30.60)
>DroYak_CAF1 23149 113 + 1
-------AUAAGAAAAUUGGCACAUAAAAAGUUUUUUAAUGAAUGGAAUUAGUGUUUGAGCUGCAGCGACUUUGCUAAAUCGUCCGAGCAUCGCCUCGGAAGUCCACUCAGAGUGCCACU
-------..........((((((.(((((....))))).(((.((((.((((((.....((....)).....))))))....((((((......))))))..)))).)))..)))))).. ( -30.60)
>consensus
AAAAAGAAUAAGAAAAUUGGCACAUAAAAAGUUUUUUAAUGAAUGGAAUUAGUGUUUGAGCUGCAGCGACUUUGCUAAAUCGUCCGAGCAUCGCCUCGGAAGUCCACUCAGAGUGCCACU
.................((((((.(((((....))))).(((.((((.((((((.....((....)).....))))))....((((((......))))))..)))).)))..)))))).. (-26.76 = -26.85 +   0.09)

alignment

secondary structure

dotplot

Window 9

Location	13,756,377 – 13,756,497
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	93.61
Mean single sequence MFE	-30.75
Consensus MFE	-28.52
Energy contribution	-29.18
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-2.17
Structure conservation index	0.93
SVM decision value	2.96
SVM RNA-class probability	0.997920
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13756377 120 - 22407834
AGUGGCACACUGAGUGGACUUCCGAGGCGAUGCUCGGACGAUUUAGCAAAGUCGCUGCAGCUCAAACACUAAUUCCAUUCAUUAAAAAACUUUUUAUGUGCCAAUUUUCGUAUUCUUUUU
..(((((((.((((((((..((((((......))))))((((((....))))))...................)))))))).(((((....))))))))))))................. ( -32.80)
>DroSec_CAF1 19967 120 - 1
AGUGGCACUCUGAGUGGACUUCCGAGGCGAUGCUCGGACGAUUUAGCAAAGUCGCUGCAGCUCAAACACUAAUUCCAUUCAUUAAAAAACUUUUUAUGUGCCAAUUUUCUUAUUCUUUUU
..((((((..((((((((..((((((......))))))((((((....))))))...................)))))))).(((((....))))).))))))................. ( -31.60)
>DroAna_CAF1 40752 120 - 1
AGAAGGACUCUGAGUGGACUUCCGAGACGCUGCUCGGACGAUUUAACAAAGUCGGUGCAGCUCAAACACUAAUUCCAUUCAUUAAAAAACUUUUUAUAUGCCAAUAUUUUUUUUGUCGUU
..((.(((..((((((((..((((((......))))))((((((....))))))...................))))))))..............((((....)))).......))).)) ( -25.30)
>DroSim_CAF1 22075 120 - 1
AGUGGCACUCUGAGUGGACUUCCGAGGCGAUGCUCGGACGAUUUAGCAAAGUCGCUGCAGCUCAAACACUAAUUCCAUUCAUUAAAAAACUUUUUAUGUGCCAAUUUUCUUAUUCUUUUU
..((((((..((((((((..((((((......))))))((((((....))))))...................)))))))).(((((....))))).))))))................. ( -31.60)
>DroEre_CAF1 21828 120 - 1
AGUGGCACUCUGAGUGGACUUCCGAGGCGAUGCUCGGACGAUUUAGCAAAGUCGCUGCAGCUCAAACACUAAUUCCAUUCAUUAAAAAACUUUUUAUGUGCCAAUUUUCUUAUUUUUUUU
..((((((..((((((((..((((((......))))))((((((....))))))...................)))))))).(((((....))))).))))))................. ( -31.60)
>DroYak_CAF1 23149 113 - 1
AGUGGCACUCUGAGUGGACUUCCGAGGCGAUGCUCGGACGAUUUAGCAAAGUCGCUGCAGCUCAAACACUAAUUCCAUUCAUUAAAAAACUUUUUAUGUGCCAAUUUUCUUAU-------
..((((((..((((((((..((((((......))))))((((((....))))))...................)))))))).(((((....))))).))))))..........------- ( -31.60)
>consensus
AGUGGCACUCUGAGUGGACUUCCGAGGCGAUGCUCGGACGAUUUAGCAAAGUCGCUGCAGCUCAAACACUAAUUCCAUUCAUUAAAAAACUUUUUAUGUGCCAAUUUUCUUAUUCUUUUU
..((((((..((((((((..((((((......))))))((((((....))))))...................)))))))).(((((....))))).))))))................. (-28.52 = -29.18 +   0.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:28:44 2006