Locus 6000

Sequence ID	2L_DroMel_CAF1
Location	16,899,937 – 16,900,078
Length	141
Max. P	0.950991

overview

Window 1

Location	16,899,937 – 16,900,057
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	80.28
Mean single sequence MFE	-40.27
Consensus MFE	-21.10
Energy contribution	-20.97
Covariance contribution	-0.14
Combinations/Pair	1.32
Mean z-score	-2.13
Structure conservation index	0.52
SVM decision value	0.17
SVM RNA-class probability	0.619051
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16899937 120 - 22407834
CUUGAUCUUGGGAUUUCUCUGAAUCUUCUCGUUAUCCAUGGCCUCAGCCAUAAGACAAGCAGCCACUGCCGUUUGUCUCGUGUGCAGAGCCUUCAUCAAUGAUACUAUUUUCAUGGCCAG
...(((..(((((.(((...)))...)))))..)))..(((((...((((..((((((((.((....)).))))))))..)).)).............((((........))))))))). ( -34.10)
>DroVir_CAF1 11682 120 - 1
CUUGAUCUUUGGAUUGCGCUGGAUCUUCUCGUUUUCCAUGGCGUCCGCCAUGAGGCAGGCGGCGACAGCUGUUUGGCGCGUGUGCAGCACCUUCAUAAGGGACACAAUUUUGAUGGCCAG
.........((((..(((..((.....)))))..))))((((((((((((((.(.((((((((....)))))))).).)))).)).....((.....)))))).((....))...)))). ( -39.00)
>DroGri_CAF1 11131 120 - 1
CUUUAUCUUUGGAUUGCGCUGAAUCUUCUCGUUUUCCAUGGCAUCGGCCAUGAGGCAGGCAGCAACAGCUGUUUGCCGUGUGUGCAACACUUUGAGCAGCGAGACUAUUUUAAUGGCCAG
.........(((........((((..((((((((((((((((....)))))).((((((((((....))))))))))((((.....))))...))).)))))))..))))......))). ( -43.74)
>DroWil_CAF1 10280 120 - 1
CUUGAUCUUGGGAUUUCUCUGAAUCUUCUCAUUAUCCAUGGCCUCGGCCAUGAGGCAAGCCGCCACAGCCGUUUGUCGUGUAUGCAAAGCCUUGCAGAGUGACACGAUCUUGAUGGCCAA
...(((..(((((.(((...)))...)))))..)))((((((....)))))).(((.....)))...((((((.(((((((.(((((....))))).....)))))))...))))))... ( -42.40)
>DroMoj_CAF1 10542 120 - 1
CUUUAUCUUUGGGUUUCGCUGAAUUUUCUCAUUCUCCAUGGCAUCUGCCAUGAGGCAGGCAGCAACAGCCGUCUGUCUUGUAUGCAGCACCUUCAUCAGGGAAACAAUUUUCAUGGCUAG
............(((((((((...............((((((....))))))((((((((.((....)).))))))))......)))).(((.....))))))))............... ( -36.00)
>DroAna_CAF1 10355 120 - 1
CUUAAUUUUGGGAUUCCUCUGGAUCUUCUCAUUGUCCAUUGCCUCCGCCAUGAGGCAGGCAGCCACCGCCGUUUGUCUCGUGUGGAGGGCUUUCAUGAGAGCCACUAUUUUGAUGGCCAG
........(((((.(((...)))...))))).((.(((((..((((((.(((((((((((.((....)).)))))))))))))))))((((((....))))))........))))).)). ( -46.40)
>consensus
CUUGAUCUUGGGAUUUCGCUGAAUCUUCUCAUUAUCCAUGGCCUCCGCCAUGAGGCAGGCAGCCACAGCCGUUUGUCGCGUGUGCAGCACCUUCAUCAGGGACACUAUUUUGAUGGCCAG
.................((((...............((((((....)))))).(((((((.((....)).))))))).......))))................................ (-21.10 = -20.97 +  -0.14)

alignment

secondary structure

dotplot

Window 2

Location	16,899,977 – 16,900,078
Length	101
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	76.42
Mean single sequence MFE	-29.28
Consensus MFE	-19.23
Energy contribution	-19.32
Covariance contribution	0.09
Combinations/Pair	1.38
Mean z-score	-1.11
Structure conservation index	0.66
SVM decision value	-0.04
SVM RNA-class probability	0.514594
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16899977 101 + 22407834
CGAGACAAACGGCAGUGGCUGCUUGUCUUAUGGCUGAGGCCAUGGAUAACGAGAAGAUUCAGAGAAAUCCCAAGAUCAAGAAGGUA----ACAAAAGAGGUAUAA
.(((((((.((((....)))).)))))))(((((....)))))............((((..((....))....)))).........----............... ( -22.50)
>DroPse_CAF1 11891 104 + 1
CGCGGCAGACGGCGGUGGCCGCCUGUCUCAUGGCGGAGGCCUUGGACAAUGAGAAGAUCCAACGGAAUCCCAAGAUCAAGAAGGUGAGGU-CGACAAACGUAUAC
.(.(((((.((((....)))).))))).).(((((((..((((((((........).))))).))..))).....(((......))).))-))............ ( -29.90)
>DroGri_CAF1 11171 104 + 1
CACGGCAAACAGCUGUUGCUGCCUGCCUCAUGGCCGAUGCCAUGGAAAACGAGAAGAUUCAGCGCAAUCCAAAGAUAAAGAAGGUAGGUA-GGAAUGGAGAGUAA
........((..(((((.((((((((((((((((....))))))...........((((......))))............)))))))))-).)))))...)).. ( -30.50)
>DroWil_CAF1 10320 104 + 1
CACGACAAACGGCUGUGGCGGCUUGCCUCAUGGCCGAGGCCAUGGAUAAUGAGAAGAUUCAGAGAAAUCCCAAGAUCAAGAAGGUGAGUU-UGUUAAUUGUGUUC
(((((..((((((....))((((..(((((((((....))))))...........((((..((....))....))))....)))..))))-))))..)))))... ( -30.00)
>DroMoj_CAF1 10582 101 + 1
CAAGACAGACGGCUGUUGCUGCCUGCCUCAUGGCAGAUGCCAUGGAGAAUGAGAAAAUUCAGCGAAACCCAAAGAUAAAGAAGGUGGGUA---AAUGCAGCGUA-
...........(((((...((((..(((((((((....))))))..((((......)))).....................)))..))))---...)))))...- ( -32.90)
>DroPer_CAF1 11909 104 + 1
CGCGGCAGACGGCGGUGGCCGCCUGUCUCAUGGCGGAGGCCUUGGACAAUGAGAAGAUCCAACGGAAUCCCAAGAUCAAGAAGGUGAGGU-CGACAAACGAAUAC
.(.(((((.((((....)))).))))).).(((((((..((((((((........).))))).))..))).....(((......))).))-))............ ( -29.90)
>consensus
CACGACAAACGGCUGUGGCUGCCUGCCUCAUGGCCGAGGCCAUGGACAAUGAGAAGAUUCAGCGAAAUCCCAAGAUCAAGAAGGUGAGUU_CGAAAAAAGUAUAC
...(((((.((((....)))).)))))(((((((....)))))))............................................................ (-19.23 = -19.32 +   0.09)

alignment

secondary structure

dotplot

Window 3

Location	16,899,977 – 16,900,078
Length	101
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	76.42
Mean single sequence MFE	-28.69
Consensus MFE	-20.24
Energy contribution	-19.93
Covariance contribution	-0.30
Combinations/Pair	1.38
Mean z-score	-1.77
Structure conservation index	0.71
SVM decision value	1.41
SVM RNA-class probability	0.950991
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16899977 101 - 22407834
UUAUACCUCUUUUGU----UACCUUCUUGAUCUUGGGAUUUCUCUGAAUCUUCUCGUUAUCCAUGGCCUCAGCCAUAAGACAAGCAGCCACUGCCGUUUGUCUCG
...............----.........(((..(((((.(((...)))...)))))..))).(((((....))))).((((((((.((....)).)))))))).. ( -21.90)
>DroPse_CAF1 11891 104 - 1
GUAUACGUUUGUCG-ACCUCACCUUCUUGAUCUUGGGAUUCCGUUGGAUCUUCUCAUUGUCCAAGGCCUCCGCCAUGAGACAGGCGGCCACCGCCGUCUGCCGCG
.....(((......-..((((.......(((..(((((.(((...)))...)))))..)))...(((....))).)))).((((((((....))))))))..))) ( -30.40)
>DroGri_CAF1 11171 104 - 1
UUACUCUCCAUUCC-UACCUACCUUCUUUAUCUUUGGAUUGCGCUGAAUCUUCUCGUUUUCCAUGGCAUCGGCCAUGAGGCAGGCAGCAACAGCUGUUUGCCGUG
..............-....................(((..(((..((....)).)))..)))(((((....)))))..((((((((((....))))))))))... ( -31.10)
>DroWil_CAF1 10320 104 - 1
GAACACAAUUAACA-AACUCACCUUCUUGAUCUUGGGAUUUCUCUGAAUCUUCUCAUUAUCCAUGGCCUCGGCCAUGAGGCAAGCCGCCACAGCCGUUUGUCGUG
...(((........-.............(((..(((((.(((...)))...)))))..)))((((((....)))))).(((((((.((....)).)))))))))) ( -28.80)
>DroMoj_CAF1 10582 101 - 1
-UACGCUGCAUU---UACCCACCUUCUUUAUCUUUGGGUUUCGCUGAAUUUUCUCAUUCUCCAUGGCAUCUGCCAUGAGGCAGGCAGCAACAGCCGUCUGUCUUG
-......((...---.(((((.............)))))...)).((((......))))..((((((....))))))((((((((.((....)).)))))))).. ( -29.32)
>DroPer_CAF1 11909 104 - 1
GUAUUCGUUUGUCG-ACCUCACCUUCUUGAUCUUGGGAUUCCGUUGGAUCUUCUCAUUGUCCAAGGCCUCCGCCAUGAGACAGGCGGCCACCGCCGUCUGCCGCG
....(((.....))-).((((.......(((..(((((.(((...)))...)))))..)))...(((....))).)))).((((((((....))))))))..... ( -30.60)
>consensus
GUACACGUCUUUCG_AACUCACCUUCUUGAUCUUGGGAUUUCGCUGAAUCUUCUCAUUAUCCAUGGCCUCCGCCAUGAGACAGGCAGCCACAGCCGUCUGCCGCG
...................................((((((....))))))..........((((((....)))))).(((((((.((....)).)))))))... (-20.24 = -19.93 +  -0.30)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:58:35 2006