Locus 1849

Sequence ID	2R_DroMel_CAF1
Location	6,955,896 – 6,956,071
Length	175
Max. P	0.981527

overview

Window 7

Location	6,955,896 – 6,956,016
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.78
Mean single sequence MFE	-41.40
Consensus MFE	-18.02
Energy contribution	-17.83
Covariance contribution	-0.19
Combinations/Pair	1.31
Mean z-score	-2.85
Structure conservation index	0.44
SVM decision value	1.12
SVM RNA-class probability	0.918151
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6955896 120 - 20766785
AUAGCCAGGCCAAAAGCCAAGGCCUUGAAGGUGCCAUCCUCAAUUUGGGUGCAUGCGCCGCAGGCAAAGAAAUUGAGGAUCAAAUUGCCAAGGAAUUCUCCAAUCAAGGCCUGCCACAAU
...((..(((.....))).(((((((((.(((...(((((((((((...(((.(((...))).)))...)))))))))))......)))..(((....)))..)))))))))))...... ( -44.70)
>DroVir_CAF1 90 120 - 1
ACGCCCAGUCCAAAGGCCAACGCCUUAAAGGUGCCAUCCUCUGGCUGGGUGCAGGCGCCACAGGCGAAAAAGUUCAAUAUCAGAUUGCCAAUGAACUCGCCGAUGAGCGCUUGCCAAAGG
..((((((.(((.(((....((((.....))))....))).)))))))))((((((((((..(((((....(((((...............))))))))))..)).))))))))...... ( -50.86)
>DroGri_CAF1 57 120 - 1
ACGCCCAGUCCAAAGGCGAGAGCCUUAAAGGUGCCAUCCUCCUGCUGGGUGCAGGCGCCACAGGCGAAAAAGUUCAAUAUCAAAUUGCCAAUGAAUUCGGCGAUGAGCGCCUGCCACAGA
..(((((((...(((((....)))))..(((......)))...)))))))((((((((((..(.((((...(((((((.....))))..)))...)))).)..)).))))))))...... ( -46.90)
>DroWil_CAF1 57 120 - 1
ACACCCAGACCAAAGGCCAAGGCUUUGAAUGUGCCAUCUUCGAUUUGAGUGCAGGCGCCACAGGCAAAGAAAUUCAAUAUGAAAUUACCCAAAAAUUCACCAAUUAAAGCCUGCCAUAGA
..............(((..(((((((((.((((((.((........))(((....)))....))))......(((.....))).................)).))))))))))))..... ( -24.80)
>DroMoj_CAF1 57 120 - 1
ACACCCAGGCCAAAGGCCAGCGCCUUGAAUGUGCCAUCCUCGGGCUGUGUGCAGGCGCCGCAGGCAAAGAAGUUCAAUAUCAGAUUGCCAAUGAACUCGCCGAUGAGCGCCUGCCAGAGA
...(((.((((...)))).((((.......)))).......)))((.((.((((((((((..(((...((.(((((...............))))))))))..)).)))))))))).)). ( -45.06)
>DroAna_CAF1 21 120 - 1
AUGGCCAGGCCAAAAGCCAGAGCCUUGAAGGUACUAUCCUCCACUUGAGUGCAGGCACCGCAGGCAAAAAAGUUAAGAAUAAGAUUUCCCAGGAAUUCUCCAAUUAGGGCCUGCCAUAAU
(((((.(((((....(((((.(((.....))).))..(((.(((....))).))).......))).......((((.....(((.(((....))).)))....))))))))))))))... ( -36.10)
>consensus
ACACCCAGGCCAAAGGCCAAAGCCUUGAAGGUGCCAUCCUCCAGCUGGGUGCAGGCGCCACAGGCAAAAAAGUUCAAUAUCAAAUUGCCAAUGAAUUCGCCAAUGAGCGCCUGCCACAGA
.....((((...(((((....)))))..(((......)))...)))).(.(((((((((...))).....((((........))))......................)))))))..... (-18.02 = -17.83 +  -0.19)

alignment

secondary structure

dotplot

Window 8

Location	6,955,936 – 6,956,045
Length	109
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	76.46
Mean single sequence MFE	-41.12
Consensus MFE	-25.32
Energy contribution	-24.32
Covariance contribution	-1.00
Combinations/Pair	1.37
Mean z-score	-2.38
Structure conservation index	0.62
SVM decision value	1.89
SVM RNA-class probability	0.981527
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6955936 109 + 20766785
AUCCUCAAUUUCUUUGCCUGCGGCGCAUGCACCCAAAUUGAGGAUGGCACCUUCAAGGCCUUGGCUUUUGGCCUGGCUAUCUUCAUGGCCAUCACGGUGGGUG----------GCUCGU
(((((((((((...(((.(((...))).)))...)))))))))))(.(((((.(.(((((.........)))))((((((....))))))......).)))))----------.).... ( -42.50)
>DroGri_CAF1 97 109 + 1
AUAUUGAACUUUUUCGCCUGUGGCGCCUGCACCCAGCAGGAGGAUGGCACCUUUAAGGCUCUCGCCUUUGGACUGGGCGUCUUCAUGGCCAUUACGGUGAGUG----------GAGUUG
......((((((((((((.(((((..((((.....))))(((((((.(.((...(((((....))))).))....).)))))))...)))))...)))))).)----------))))). ( -42.90)
>DroEre_CAF1 7087 117 + 1
AUCCUCAAUUUCUUUGCCUGCGGUGCAUGCACCCAAAUCGAGGAUGGCACCUUCAAGGCCCUGGCUUUCGGCCUGGCCAUCUUCAUGGCCAUCACGGUGGGU--UCCCCAGGUGCUGUU
((((((.((((...(((.(((...))).)))...)))).))))))(((((((....(((((.(((.....)))(((((((....))))))).......))))--)....)))))))... ( -46.30)
>DroYak_CAF1 65 111 + 1
AUCCUCAACUUCUUUGCCUGCGGUGCAUGCACCCAAGUUGAGGAUGGCACCUUCAAGGCCCUGGCCUUUGGCCUGGCCAUCUUCAUGGCCAUCACGGUGGGUGUUUCCAAU--------
(((((((((((...(((.(((...))).)))...)))))))))))(((((((..(((((....)))))..((((((((((....)))))))....))))))))))......-------- ( -47.20)
>DroMoj_CAF1 97 108 + 1
AUAUUGAACUUCUUUGCCUGCGGCGCCUGCACACAGCCCGAGGAUGGCACAUUCAAGGCGCUGGCCUUUGGCCUGGGUGUCUUCAUGGCCAUUACGGUGAGCA----------AAGCU-
...........(((((((((.(((....)).).))).(((..((((((.(((..((((((((((((...))))..)))))))).))))))))).)))...)))----------)))..- ( -38.70)
>DroAna_CAF1 61 109 + 1
AUUCUUAACUUUUUUGCCUGCGGUGCCUGCACUCAAGUGGAGGAUAGUACCUUCAAGGCUCUGGCUUUUGGCCUGGCCAUUUUCAUGGCUAUAACGGUAAGUU----------UUUUUU
............((((((...((.((((((......))(((((......))))).)))).))(((.....)))(((((((....)))))))....))))))..----------...... ( -29.10)
>consensus
AUCCUCAACUUCUUUGCCUGCGGCGCAUGCACCCAAAUCGAGGAUGGCACCUUCAAGGCCCUGGCCUUUGGCCUGGCCAUCUUCAUGGCCAUCACGGUGAGUG__________GAUCUU
...((((........(((((((.....))))........(((((((((....(((((((....))))).))....)))))))))..)))........)))).................. (-25.32 = -24.32 +  -1.00)

alignment

secondary structure

dotplot

Window 9

Location	6,955,936 – 6,956,045
Length	109
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	76.46
Mean single sequence MFE	-38.77
Consensus MFE	-24.27
Energy contribution	-26.05
Covariance contribution	1.78
Combinations/Pair	1.08
Mean z-score	-2.33
Structure conservation index	0.63
SVM decision value	1.86
SVM RNA-class probability	0.980169
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6955936 109 - 20766785
ACGAGC----------CACCCACCGUGAUGGCCAUGAAGAUAGCCAGGCCAAAAGCCAAGGCCUUGAAGGUGCCAUCCUCAAUUUGGGUGCAUGCGCCGCAGGCAAAGAAAUUGAGGAU
......----------....((((.....((((.((........))(((.....)))..)))).....))))..(((((((((((...(((.(((...))).)))...))))))))))) ( -36.40)
>DroGri_CAF1 97 109 - 1
CAACUC----------CACUCACCGUAAUGGCCAUGAAGACGCCCAGUCCAAAGGCGAGAGCCUUAAAGGUGCCAUCCUCCUGCUGGGUGCAGGCGCCACAGGCGAAAAAGUUCAAUAU
.((((.----------...((.((....(((((.((....((((((((...(((((....)))))..(((......)))...)))))))))).).))))..)).))...))))...... ( -32.80)
>DroEre_CAF1 7087 117 - 1
AACAGCACCUGGGGA--ACCCACCGUGAUGGCCAUGAAGAUGGCCAGGCCGAAAGCCAGGGCCUUGAAGGUGCCAUCCUCGAUUUGGGUGCAUGCACCGCAGGCAAAGAAAUUGAGGAU
....((((((.(((.--.(((.......(((((((....)))))))((.(....))).))))))...)))))).(((((((((((...(((.(((...))).)))...))))))))))) ( -51.60)
>DroYak_CAF1 65 111 - 1
--------AUUGGAAACACCCACCGUGAUGGCCAUGAAGAUGGCCAGGCCAAAGGCCAGGGCCUUGAAGGUGCCAUCCUCAACUUGGGUGCAUGCACCGCAGGCAAAGAAGUUGAGGAU
--------..((....))..((((((..(((((((....))))))).))..(((((....)))))...))))..(((((((((((...(((.(((...))).)))...))))))))))) ( -48.10)
>DroMoj_CAF1 97 108 - 1
-AGCUU----------UGCUCACCGUAAUGGCCAUGAAGACACCCAGGCCAAAGGCCAGCGCCUUGAAUGUGCCAUCCUCGGGCUGUGUGCAGGCGCCGCAGGCAAAGAAGUUCAAUAU
-..(((----------(((...(((..((((((((.(((.(.(...((((...)))).).).)))..))).)))))...))).(((((.((....)))))))))))))........... ( -35.80)
>DroAna_CAF1 61 109 - 1
AAAAAA----------AACUUACCGUUAUAGCCAUGAAAAUGGCCAGGCCAAAAGCCAGAGCCUUGAAGGUACUAUCCUCCACUUGAGUGCAGGCACCGCAGGCAAAAAAGUUAAGAAU
......----------(((((.........(((((....)))))..(((.....)))...((((....(((.....(((.(((....))).))).)))..))))....)))))...... ( -27.90)
>consensus
AAAAGC__________CACCCACCGUGAUGGCCAUGAAGAUGGCCAGGCCAAAAGCCAGGGCCUUGAAGGUGCCAUCCUCAACUUGGGUGCAGGCACCGCAGGCAAAGAAGUUGAGGAU
............................(((((((....)))))))(((.....)))...((((....((((((((((.......)))))...)))))..))))............... (-24.27 = -26.05 +   1.78)

alignment

secondary structure

dotplot

Window 0

Location	6,955,976 – 6,956,071
Length	95
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	75.56
Mean single sequence MFE	-27.68
Consensus MFE	-19.18
Energy contribution	-18.57
Covariance contribution	-0.61
Combinations/Pair	1.21
Mean z-score	-2.04
Structure conservation index	0.69
SVM decision value	1.82
SVM RNA-class probability	0.978732
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6955976 95 + 20766785
AGGAUGGCACCUUCAAGGCCUUGGCUUUUGGCCUGGCUAUCUUCAUGGCCAUCACGGUGGGUG--------GCUCGUUAAUCU------ACGACAUUAUUCAUACCCAU
..((((((........((((..(((.....))).)))).........))))))...(((((((--------..((((......------)))).........))))))) ( -31.03)
>DroPse_CAF1 137 100 + 1
AGGAUGGCACCUUCAAGGCCUUGGCCUUUGGUCUCUCCAUCUUCAUGGCCAUCACGGUAAGUC--------GCAUAUCAAACAGAAGAUCCAAUCCAAUCAAUACUCA-
.((((((...((((..((((.(((....(((.....)))...))).)))).....((((....--------...)))).....))))..)).))))............- ( -23.60)
>DroSec_CAF1 101 95 + 1
AGGAUGGCACCUUCAAAGCCUUGGCUUUUGGCCUGGCCAUUUUCAUGGCCAUCACGGUGAGUU--------GCUUCUUAAUCU------ACGAAAUUAUUAAUACAUAU
((((.((((.(((....(((..(((.....)))(((((((....)))))))....)))))).)--------))))))).....------.................... ( -24.20)
>DroSim_CAF1 7148 95 + 1
AGGAUGGCACCUUCAAAGCCUUGGCUUUUGGCCUGGCCAUCUUUAUGGCCAUCACGGUGGGUU--------GCUCCUCAACCU------ACGACAUUAUUCAUACGUAU
..((((((.........(((..(((.....))).)))..........))))))((((((((((--------(.....))))))------))((......))...))).. ( -31.71)
>DroYak_CAF1 105 96 + 1
AGGAUGGCACCUUCAAGGCCCUGGCCUUUGGCCUGGCCAUCUUCAUGGCCAUCACGGUGGGUGUUUCCAAU-------AUACU------GCGAUGAUAUUCAUACUCAC
..((((((........((((..((((...)))).)))).........))))))...((((((((....(((-------((.(.------.....)))))).)))))))) ( -31.93)
>DroPer_CAF1 137 100 + 1
AGGAUGGCACCUUCAAGGCCUUGGCCUUUGGUCUCUCCAUCUUCAUGGCCAUCACGGUAAGUC--------GCAUAUCAAACAGAAGAUCCAAUCCAAUCAAUACUCA-
.((((((...((((..((((.(((....(((.....)))...))).)))).....((((....--------...)))).....))))..)).))))............- ( -23.60)
>consensus
AGGAUGGCACCUUCAAGGCCUUGGCCUUUGGCCUGGCCAUCUUCAUGGCCAUCACGGUGAGUC________GCUUAUCAAACU______ACGAUAUUAUUAAUACUCAU
..((((((......(((((....)))))(((.....)))........))))))........................................................ (-19.18 = -18.57 +  -0.61)

alignment

secondary structure

dotplot

Window 1

Location	6,955,976 – 6,956,071
Length	95
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	75.56
Mean single sequence MFE	-27.57
Consensus MFE	-18.73
Energy contribution	-18.95
Covariance contribution	0.22
Combinations/Pair	1.17
Mean z-score	-1.13
Structure conservation index	0.68
SVM decision value	0.27
SVM RNA-class probability	0.663534
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6955976 95 - 20766785
AUGGGUAUGAAUAAUGUCGU------AGAUUAACGAGC--------CACCCACCGUGAUGGCCAUGAAGAUAGCCAGGCCAAAAGCCAAGGCCUUGAAGGUGCCAUCCU
.(((((((.....)).((((------......))))..--------.)))))..(.(((((((.(.(((...(((.(((.....)))..)))))).)..).))))))). ( -24.00)
>DroPse_CAF1 137 100 - 1
-UGAGUAUUGAUUGGAUUGGAUCUUCUGUUUGAUAUGC--------GACUUACCGUGAUGGCCAUGAAGAUGGAGAGACCAAAGGCCAAGGCCUUGAAGGUGCCAUCCU
-...((((..(..(((........)))..)..))))((--------(......)))(((((((((....))).....(((.(((((....)))))...))))))))).. ( -26.70)
>DroSec_CAF1 101 95 - 1
AUAUGUAUUAAUAAUUUCGU------AGAUUAAGAAGC--------AACUCACCGUGAUGGCCAUGAAAAUGGCCAGGCCAAAAGCCAAGGCUUUGAAGGUGCCAUCCU
...(((.((..(((((....------.)))))..))))--------)...((((((..(((((((....))))))).))..(((((....)))))...))))....... ( -25.20)
>DroSim_CAF1 7148 95 - 1
AUACGUAUGAAUAAUGUCGU------AGGUUGAGGAGC--------AACCCACCGUGAUGGCCAUAAAGAUGGCCAGGCCAAAAGCCAAGGCUUUGAAGGUGCCAUCCU
.(((((((((......))))------)(((((.....)--------))))...)))).(((((((....)))))))((((.(((((....)))))....).)))..... ( -31.40)
>DroYak_CAF1 105 96 - 1
GUGAGUAUGAAUAUCAUCGC------AGUAU-------AUUGGAAACACCCACCGUGAUGGCCAUGAAGAUGGCCAGGCCAAAGGCCAGGGCCUUGAAGGUGCCAUCCU
.....((((....(((((((------.((..-------..((....))...)).))))))).))))..((((((...(((.(((((....)))))...))))))))).. ( -31.40)
>DroPer_CAF1 137 100 - 1
-UGAGUAUUGAUUGGAUUGGAUCUUCUGUUUGAUAUGC--------GACUUACCGUGAUGGCCAUGAAGAUGGAGAGACCAAAGGCCAAGGCCUUGAAGGUGCCAUCCU
-...((((..(..(((........)))..)..))))((--------(......)))(((((((((....))).....(((.(((((....)))))...))))))))).. ( -26.70)
>consensus
AUGAGUAUGAAUAAUAUCGU______AGUUUGAGAAGC________AACCCACCGUGAUGGCCAUGAAGAUGGCCAGGCCAAAAGCCAAGGCCUUGAAGGUGCCAUCCU
..................................................((((((..(((((((....))))))).))..(((((....)))))...))))....... (-18.73 = -18.95 +   0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:14:43 2006