Locus 4846

Sequence ID	2L_DroMel_CAF1
Location	13,770,982 – 13,771,238
Length	256
Max. P	0.999350

overview

Window 8

Location	13,770,982 – 13,771,081
Length	99
Sequences	5
Columns	106
Reading direction	reverse
Mean pairwise identity	75.61
Mean single sequence MFE	-23.76
Consensus MFE	-12.36
Energy contribution	-13.16
Covariance contribution	0.80
Combinations/Pair	1.25
Mean z-score	-1.82
Structure conservation index	0.52
SVM decision value	0.36
SVM RNA-class probability	0.704911
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13770982 99 - 22407834
AAGUCGUGGCCUUAGGUAUGGUCAUACCAAUUAUCGACUAUCGAUAAGAGGCAAUACCGAUUGUUUUGAGAGAAACCGCGAAUAUUUAAGUACCGA--AAA-----
...((((((((((.(((((....)))))..((((((.....)))))))))))..........(((((....))))))))))...............--...----- ( -28.30)
>DroSec_CAF1 33642 92 - 1
AAGUCGUGGCCAUCGGUAUGGUCACACCAAUUAU-------CGAUAACCAGCAAUACCGAUUGUAUUGAGAGGAACCGCGAAUAUUUAAACAUCGG--AAA-----
...((((((..((((((((((.....)))..)))-------))))..((..((((((.....))))))...))..))))))...............--...----- ( -23.80)
>DroSim_CAF1 36665 92 - 1
AAGUCGUGGCCAUCGGUAUGGUCAUACCAAUUAU-------CGAUAACCAGCAAUACCGAUUGUAUUGAGAGGAACCGCAAAUAUUUAAACAUCGG--AAG-----
.....((((..((((((((((.....)))..)))-------))))..((..((((((.....))))))...))..)))).................--...----- ( -20.50)
>DroEre_CAF1 36965 105 - 1
AAGUCGUGGCCGAUGAAAAGGUCAUACUAAAUAUCGACUAUCGAUAAAUGGGAAUAUCGAUUGUAUUCAAAGUAACCGCAAAUAUUUAAUAUUU-UUGGAAUUUCU
.(((.((((((........)))))))))...(((((.....)))))...((((((.((((..(((((..(((((........))))))))))..-)))).)))))) ( -21.80)
>DroYak_CAF1 36694 101 - 1
AAGUCGUGGCCGUUGGUACGGUCAUACCAAUUAUCGACUAUCGAUGAAAGGGAAUAUCGAUUGUAUGCAAAGUAACCGCGAAUAUUAAAUAAUCGUUAGAA-----
...((((((...((((((((((((((((..((((((.....))))))...))..))).)))))))).))).....))))))....................----- ( -24.40)
>consensus
AAGUCGUGGCCAUCGGUAUGGUCAUACCAAUUAUCGACUAUCGAUAAAAGGCAAUACCGAUUGUAUUGAGAGGAACCGCGAAUAUUUAAAAAUCGG__AAA_____
.....((((((((....)))))))).....((((((.....))))))....((((((.....))))))...................................... (-12.36 = -13.16 +   0.80)

alignment

secondary structure

dotplot

Window 9

Location	13,771,081 – 13,771,198
Length	117
Sequences	4
Columns	117
Reading direction	forward
Mean pairwise identity	96.01
Mean single sequence MFE	-31.80
Consensus MFE	-27.77
Energy contribution	-28.15
Covariance contribution	0.38
Combinations/Pair	1.06
Mean z-score	-3.46
Structure conservation index	0.87
SVM decision value	1.33
SVM RNA-class probability	0.943172
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13771081 117 + 22407834
ACCCAGCACCGAAACUCGGAAGAUUUGAAGAAGAAGAAUUGCCAGCAGGGAGACGCAGAAACUACAUUAUAUAUACAAAAUAUAUAGUUUCUAGCGGAAUUUCUGCCAACAAAAGGG
.(((.((.(((.....)))..(((((.........)))))))..((((..(..(((((((((((...(((((.......))))))))))))).)))...)..))))........))) ( -31.70)
>DroSec_CAF1 33734 117 + 1
ACCCAGCACCAAAACUCGGAAGAUUUGAAGAAGAAGAAUUGCCAGCAGGGAGACGCAGAAACUACAUUAUAUAUACAAAAUAUAUAGUUUCUAGCGUAAUUGCUGCCAACACAAGGG
.(((.....((((..((....))))))...........(((.((((((....((((((((((((...(((((.......))))))))))))).))))..)))))).))).....))) ( -32.30)
>DroSim_CAF1 36757 117 + 1
ACCCAGCACCAAAACUCGGAAGAUUUGAAGAAGAAGAAUUGCCAGCAGGGAGACGCAGAAACUACAUUAUAUAUACAAAAUAUAUAGUUUCUAGCGUAAUUGCUGCCAACACAAGGG
.(((.....((((..((....))))))...........(((.((((((....((((((((((((...(((((.......))))))))))))).))))..)))))).))).....))) ( -32.30)
>DroYak_CAF1 36795 117 + 1
ACUCAGCACCAAAACUCGGAAGAUUUGAAGAAGAAGAAUUGCCAGCAGGGAGACGCAGAAACUACAUUAUAUAUACCAAAUAUAUAGUUUCUUGCGGACUUGCUGCCAAAACAAGGG
.(((.....((((..((....))))))...........(((.(((((((....(((((((((((...(((((.......)))))))))))).))))..))))))).))).....))) ( -30.90)
>consensus
ACCCAGCACCAAAACUCGGAAGAUUUGAAGAAGAAGAAUUGCCAGCAGGGAGACGCAGAAACUACAUUAUAUAUACAAAAUAUAUAGUUUCUAGCGGAAUUGCUGCCAACACAAGGG
.(((.....((((..((....))))))...........(((.((((((....((((((((((((...(((((.......))))))))))))).))))..)))))).))).....))) (-27.77 = -28.15 +   0.38)

alignment

secondary structure

dotplot

Window 0

Location	13,771,081 – 13,771,198
Length	117
Sequences	4
Columns	117
Reading direction	reverse
Mean pairwise identity	96.01
Mean single sequence MFE	-32.27
Consensus MFE	-28.09
Energy contribution	-29.09
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-2.99
Structure conservation index	0.87
SVM decision value	1.32
SVM RNA-class probability	0.942202
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13771081 117 - 22407834
CCCUUUUGUUGGCAGAAAUUCCGCUAGAAACUAUAUAUUUUGUAUAUAUAAUGUAGUUUCUGCGUCUCCCUGCUGGCAAUUCUUCUUCUUCAAAUCUUCCGAGUUUCGGUGCUGGGU
(((..((((..((((......(((.(((((((((((..............)))))))))))))).....))))..))))...................(((.....)))....))). ( -33.64)
>DroSec_CAF1 33734 117 - 1
CCCUUGUGUUGGCAGCAAUUACGCUAGAAACUAUAUAUUUUGUAUAUAUAAUGUAGUUUCUGCGUCUCCCUGCUGGCAAUUCUUCUUCUUCAAAUCUUCCGAGUUUUGGUGCUGGGU
(((...(((..((((.....((((.(((((((((((..............)))))))))))))))....))))..)))...........(((((.((....)).)))))....))). ( -33.44)
>DroSim_CAF1 36757 117 - 1
CCCUUGUGUUGGCAGCAAUUACGCUAGAAACUAUAUAUUUUGUAUAUAUAAUGUAGUUUCUGCGUCUCCCUGCUGGCAAUUCUUCUUCUUCAAAUCUUCCGAGUUUUGGUGCUGGGU
(((...(((..((((.....((((.(((((((((((..............)))))))))))))))....))))..)))...........(((((.((....)).)))))....))). ( -33.44)
>DroYak_CAF1 36795 117 - 1
CCCUUGUUUUGGCAGCAAGUCCGCAAGAAACUAUAUAUUUGGUAUAUAUAAUGUAGUUUCUGCGUCUCCCUGCUGGCAAUUCUUCUUCUUCAAAUCUUCCGAGUUUUGGUGCUGAGU
.....(..(((.(((((((..((((.((((((((((..............)))))))))))))).))...))))).)))..)(((..(.(((((.((....)).))))).)..))). ( -28.54)
>consensus
CCCUUGUGUUGGCAGCAAUUACGCUAGAAACUAUAUAUUUUGUAUAUAUAAUGUAGUUUCUGCGUCUCCCUGCUGGCAAUUCUUCUUCUUCAAAUCUUCCGAGUUUUGGUGCUGGGU
......(((..((((.....((((.(((((((((((..............)))))))))))))))....))))..)))....................((.(((......))).)). (-28.09 = -29.09 +   1.00)

alignment

secondary structure

dotplot

Window 1

Location	13,771,121 – 13,771,238
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	75.80
Mean single sequence MFE	-29.26
Consensus MFE	-15.30
Energy contribution	-17.40
Covariance contribution	2.10
Combinations/Pair	1.21
Mean z-score	-3.03
Structure conservation index	0.52
SVM decision value	3.53
SVM RNA-class probability	0.999350
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13771121 117 + 22407834
GCCAGCAGGGAGACGCAGAAACUACA---UUAUAUAUACAAAAUAUAUAGUUUCUAGCGGAAUUUCUGCCAACAAAAGGGGUCCAGUGGUUACUUCACUAGCACUCCCACACACCACCAA
....((((..(..(((((((((((..---.(((((.......))))))))))))).)))...)..))))........((((((.(((((.....))))).).)).)))............ ( -33.60)
>DroSec_CAF1 33774 117 + 1
GCCAGCAGGGAGACGCAGAAACUACA---UUAUAUAUACAAAAUAUAUAGUUUCUAGCGUAAUUGCUGCCAACACAAGGGGUCCAGUGGUUACUUCACUAGCACUCCCACACACCACCAA
(.((((((....((((((((((((..---.(((((.......))))))))))))).))))..)))))).).......((((((.(((((.....))))).).)).)))............ ( -33.90)
>DroAna_CAF1 56185 93 + 1
---AACCAGAAGA--CAGAAACUAAAAGUUUUAAUAACUAAAAAACACGGU--------------------ACACAAACAGUUUAGUUGUUCC-UAACCAGCACACUUAUAGGCGUCCA-
---........((--(.(((((.....)))))((((((((((.......(.--------------------...)......))))))))))((-((...((....))..)))).)))..- ( -11.52)
>DroSim_CAF1 36797 117 + 1
GCCAGCAGGGAGACGCAGAAACUACA---UUAUAUAUACAAAAUAUAUAGUUUCUAGCGUAAUUGCUGCCAACACAAGGGGUCCAGUGGUUACUUCACUAGCACUCCCACACACCACCAA
(.((((((....((((((((((((..---.(((((.......))))))))))))).))))..)))))).).......((((((.(((((.....))))).).)).)))............ ( -33.90)
>DroYak_CAF1 36835 117 + 1
GCCAGCAGGGAGACGCAGAAACUACA---UUAUAUAUACCAAAUAUAUAGUUUCUUGCGGACUUGCUGCCAAAACAAGGGGUCCAGUGGUUACUUUACCAGCACGUCCAAACACCUCCAA
........((((..((((((((((..---.(((((.......)))))))))))).)))((((.((((.((.......))(((..(((....)))..))))))).))))......)))).. ( -33.40)
>consensus
GCCAGCAGGGAGACGCAGAAACUACA___UUAUAUAUACAAAAUAUAUAGUUUCUAGCGGAAUUGCUGCCAACACAAGGGGUCCAGUGGUUACUUCACUAGCACUCCCACACACCACCAA
....((((.((..(((((((((((.......................)))))))).)))...)).))))........((((((.(((((.....))))).).)).)))............ (-15.30 = -17.40 +   2.10)

alignment

secondary structure

dotplot

Window 2

Location	13,771,121 – 13,771,238
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	75.80
Mean single sequence MFE	-33.39
Consensus MFE	-20.36
Energy contribution	-22.74
Covariance contribution	2.38
Combinations/Pair	1.24
Mean z-score	-1.70
Structure conservation index	0.61
SVM decision value	0.44
SVM RNA-class probability	0.735801
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13771121 117 - 22407834
UUGGUGGUGUGUGGGAGUGCUAGUGAAGUAACCACUGGACCCCUUUUGUUGGCAGAAAUUCCGCUAGAAACUAUAUAUUUUGUAUAUAUAA---UGUAGUUUCUGCGUCUCCCUGCUGGC
..((.(((.(((((...((((.....)))).)))).).)))))....((..((((......(((.(((((((((((..............)---))))))))))))).....))))..)) ( -38.04)
>DroSec_CAF1 33774 117 - 1
UUGGUGGUGUGUGGGAGUGCUAGUGAAGUAACCACUGGACCCCUUGUGUUGGCAGCAAUUACGCUAGAAACUAUAUAUUUUGUAUAUAUAA---UGUAGUUUCUGCGUCUCCCUGCUGGC
..((.(((.(((((...((((.....)))).)))).).)))))....((..((((.....((((.(((((((((((..............)---))))))))))))))....))))..)) ( -39.74)
>DroAna_CAF1 56185 93 - 1
-UGGACGCCUAUAAGUGUGCUGGUUA-GGAACAACUAAACUGUUUGUGU--------------------ACCGUGUUUUUUAGUUAUUAAAACUUUUAGUUUCUG--UCUUCUGGUU---
-.(.((((......)))).).(((((-.(((((.......))))).)).--------------------)))........(((..(((((.....)))))..)))--..........--- ( -13.10)
>DroSim_CAF1 36797 117 - 1
UUGGUGGUGUGUGGGAGUGCUAGUGAAGUAACCACUGGACCCCUUGUGUUGGCAGCAAUUACGCUAGAAACUAUAUAUUUUGUAUAUAUAA---UGUAGUUUCUGCGUCUCCCUGCUGGC
..((.(((.(((((...((((.....)))).)))).).)))))....((..((((.....((((.(((((((((((..............)---))))))))))))))....))))..)) ( -39.74)
>DroYak_CAF1 36835 117 - 1
UUGGAGGUGUUUGGACGUGCUGGUAAAGUAACCACUGGACCCCUUGUUUUGGCAGCAAGUCCGCAAGAAACUAUAUAUUUGGUAUAUAUAA---UGUAGUUUCUGCGUCUCCCUGCUGGC
...((((.(((..(...((((.....))))....)..))).))))...(..((((..((..((((.((((((((((..............)---))))))))))))).))..))))..). ( -36.34)
>consensus
UUGGUGGUGUGUGGGAGUGCUAGUGAAGUAACCACUGGACCCCUUGUGUUGGCAGCAAUUACGCUAGAAACUAUAUAUUUUGUAUAUAUAA___UGUAGUUUCUGCGUCUCCCUGCUGGC
............(((.((.((((((.......)))))))))))....((..((((......(((.((((((((((....((((....))))...))))))))))))).....))))..)) (-20.36 = -22.74 +   2.38)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:29:15 2006