Locus 1972

Sequence ID	3L_DroMel_CAF1
Location	5,449,324 – 5,449,456
Length	132
Max. P	0.987791

overview

Window 9

Location	5,449,324 – 5,449,426
Length	102
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	75.46
Mean single sequence MFE	-21.26
Consensus MFE	-12.72
Energy contribution	-13.88
Covariance contribution	1.16
Combinations/Pair	1.13
Mean z-score	-1.79
Structure conservation index	0.60
SVM decision value	0.66
SVM RNA-class probability	0.814994
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5449324 102 + 23771897
AUUCGCAGGCAA-----------AAGUCCGCGUUUGCUUUUC-------CACUUUUCUUUUUCUCAGCAGCAAACGGCUGCUCCCCAAUUUGCUGCAGAAAAUGAAAAUUUAAAUUUUUA
...(((.(((..-----------..))).)))..........-------...(((((.((((((..((((((((.((......))...)))))))))))))).)))))............ ( -24.20)
>DroSec_CAF1 10758 102 + 1
UUUCGCAGGCAA-----------AAGUCCGCGUUUGCUUUUC-------CACUUUUCUUUUUCUCAGCAGCAAACGGCUGCUCCCCAAUUUGCUGCAGAAAAUGAAAAUUUAAAUUUUUA
...(((.(((..-----------..))).)))..........-------...(((((.((((((..((((((((.((......))...)))))))))))))).)))))............ ( -24.20)
>DroSim_CAF1 10858 102 + 1
UCUCGCAGGCAA-----------AAGUCCGCGUUUGCUUUUC-------CACUUUUCUUUUUCUCAGCAGCAAACGGCUGCUCCCCAAUUUGCUGCAGAAAAUGAAAAUUUAAAUUUUUA
...(((.(((..-----------..))).)))..........-------...(((((.((((((..((((((((.((......))...)))))))))))))).)))))............ ( -24.20)
>DroEre_CAF1 10507 98 + 1
-----------A-----------AAGUCCGCGUUUGCUUUUCCACAUUCCACUUUUCUUUUUCUCAGCAGCAAACUGCUGCUCCCCAAUUUGCAGCAGAAAAUGAAAAUUUAAAUUUUUA
-----------.-----------........(((((((..............................)))))))((((((..........))))))..((((....))))......... ( -15.21)
>DroMoj_CAF1 1644 96 + 1
CUUUGCGAGCAACUUUAGCCCAGGAGGCGGCAGCUGCU---------------GUUUUUUUUCC-------AAGAGGUU--UUCCCAAUUUGCGGCGGAAAAUGAAAAUUUAAAUUUUUA
.(((((..((((.........((((((((((....)))---------------)))))))....-------....((..--...))...)))).)))))((((....))))......... ( -18.50)
>consensus
UUUCGCAGGCAA___________AAGUCCGCGUUUGCUUUUC_______CACUUUUCUUUUUCUCAGCAGCAAACGGCUGCUCCCCAAUUUGCUGCAGAAAAUGAAAAUUUAAAUUUUUA
.............................((....))...............(((((.((((((..((((((((.((......))...)))))))))))))).)))))............ (-12.72 = -13.88 +   1.16)

alignment

secondary structure

dotplot

Window 0

Location	5,449,324 – 5,449,426
Length	102
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	75.46
Mean single sequence MFE	-26.14
Consensus MFE	-14.32
Energy contribution	-16.40
Covariance contribution	2.08
Combinations/Pair	1.04
Mean z-score	-2.36
Structure conservation index	0.55
SVM decision value	2.09
SVM RNA-class probability	0.987791
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5449324 102 - 23771897
UAAAAAUUUAAAUUUUCAUUUUCUGCAGCAAAUUGGGGAGCAGCCGUUUGCUGCUGAGAAAAAGAAAAGUG-------GAAAAGCAAACGCGGACUU-----------UUGCCUGCGAAU
......(((...(((((.(((((((((((((((.((.......)))))))))))..)))))).)))))...-------))).......(((((.(..-----------..).)))))... ( -29.10)
>DroSec_CAF1 10758 102 - 1
UAAAAAUUUAAAUUUUCAUUUUCUGCAGCAAAUUGGGGAGCAGCCGUUUGCUGCUGAGAAAAAGAAAAGUG-------GAAAAGCAAACGCGGACUU-----------UUGCCUGCGAAA
......(((...(((((.(((((((((((((((.((.......)))))))))))..)))))).)))))...-------))).......(((((.(..-----------..).)))))... ( -29.10)
>DroSim_CAF1 10858 102 - 1
UAAAAAUUUAAAUUUUCAUUUUCUGCAGCAAAUUGGGGAGCAGCCGUUUGCUGCUGAGAAAAAGAAAAGUG-------GAAAAGCAAACGCGGACUU-----------UUGCCUGCGAGA
......(((...(((((.(((((((((((((((.((.......)))))))))))..)))))).)))))...-------))).......(((((.(..-----------..).)))))... ( -29.10)
>DroEre_CAF1 10507 98 - 1
UAAAAAUUUAAAUUUUCAUUUUCUGCUGCAAAUUGGGGAGCAGCAGUUUGCUGCUGAGAAAAAGAAAAGUGGAAUGUGGAAAAGCAAACGCGGACUU-----------U-----------
............(((((((.(((..((.....((......((((((....)))))).....))....))..))).))))))).((....))......-----------.----------- ( -23.60)
>DroMoj_CAF1 1644 96 - 1
UAAAAAUUUAAAUUUUCAUUUUCCGCCGCAAAUUGGGAA--AACCUCUU-------GGAAAAAAAAC---------------AGCAGCUGCCGCCUCCUGGGCUAAAGUUGCUCGCAAAG
..................(((((((........))))))--).((....-------)).........---------------(((((((...(((.....)))...)))))))....... ( -19.80)
>consensus
UAAAAAUUUAAAUUUUCAUUUUCUGCAGCAAAUUGGGGAGCAGCCGUUUGCUGCUGAGAAAAAGAAAAGUG_______GAAAAGCAAACGCGGACUU___________UUGCCUGCGAAA
............(((((.(((((((((((((((.((.......)))))))))))..)))))).)))))...............((....))............................. (-14.32 = -16.40 +   2.08)

alignment

secondary structure

dotplot

Window 1

Location	5,449,353 – 5,449,456
Length	103
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	81.88
Mean single sequence MFE	-28.04
Consensus MFE	-19.20
Energy contribution	-21.36
Covariance contribution	2.16
Combinations/Pair	1.09
Mean z-score	-1.54
Structure conservation index	0.68
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5449353 103 - 23771897
AACUUUCUGGCCAGCCU-GCUCG---------GCGUUGGUUAAAAAUUUAAAUUUUCAUUUUCUGCAGCAAAUUGGGGAGCAGCCGUUUGCUGCUGAGAAAAAGAAAAGUG-------GA
.......((((((((((-....)---------).))))))))..........(((((.(((((((((((((((.((.......)))))))))))..)))))).)))))...-------.. ( -31.30)
>DroSec_CAF1 10787 103 - 1
AACUUUCUGGCCAGCCU-GCUCG---------GCGUUGGUUAAAAAUUUAAAUUUUCAUUUUCUGCAGCAAAUUGGGGAGCAGCCGUUUGCUGCUGAGAAAAAGAAAAGUG-------GA
.......((((((((((-....)---------).))))))))..........(((((.(((((((((((((((.((.......)))))))))))..)))))).)))))...-------.. ( -31.30)
>DroSim_CAF1 10887 103 - 1
AACUUUCUGGCCAGCCU-GCUCG---------GCGUUGGUUAAAAAUUUAAAUUUUCAUUUUCUGCAGCAAAUUGGGGAGCAGCCGUUUGCUGCUGAGAAAAAGAAAAGUG-------GA
.......((((((((((-....)---------).))))))))..........(((((.(((((((((((((((.((.......)))))))))))..)))))).)))))...-------.. ( -31.30)
>DroEre_CAF1 10525 110 - 1
AACUUUCUGGCCAGCCG-GCUCG---------GCGUUGGUUAAAAAUUUAAAUUUUCAUUUUCUGCUGCAAAUUGGGGAGCAGCAGUUUGCUGCUGAGAAAAAGAAAAGUGGAAUGUGGA
.......((((((((((-...))---------))..))))))...((((...(((((.((((((((.((((((((........)))))))).))..)))))).)))))...))))..... ( -30.60)
>DroMoj_CAF1 1682 98 - 1
AACUUUUUGGCAGACUUCGCUCGUCGACGUUUGCGUUGCUUAAAAAUUUAAAUUUUCAUUUUCCGCCGCAAAUUGGGAA--AACCUCUU-------GGAAAAAAAAC-------------
.........((((((.(((.....))).))))))........................(((((((........))))))--).((....-------)).........------------- ( -15.70)
>consensus
AACUUUCUGGCCAGCCU_GCUCG_________GCGUUGGUUAAAAAUUUAAAUUUUCAUUUUCUGCAGCAAAUUGGGGAGCAGCCGUUUGCUGCUGAGAAAAAGAAAAGUG_______GA
.......((((((((...((............))))))))))..........(((((.(((((((((((((((.((.......)))))))))))..)))))).)))))............ (-19.20 = -21.36 +   2.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:21:30 2006