Locus 2830

Sequence ID	3R_DroMel_CAF1
Location	7,579,945 – 7,580,078
Length	133
Max. P	0.998865

overview

Window 3

Location	7,579,945 – 7,580,042
Length	97
Sequences	6
Columns	103
Reading direction	forward
Mean pairwise identity	73.69
Mean single sequence MFE	-22.59
Consensus MFE	-19.07
Energy contribution	-18.52
Covariance contribution	-0.55
Combinations/Pair	1.31
Mean z-score	-3.78
Structure conservation index	0.84
SVM decision value	1.53
SVM RNA-class probability	0.961712
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7579945 97 + 27905053
AUUAUCUUAUUCUCCUCCGUCUGCGCAUCGUUGCGCAUUAU------GGUGAGCUUAGCAAAUUCGCUUUGCUGAGUGUUUUUCUUCAUAUCCAUAUUAUCCA
..............(.((((.((((((....))))))..))------)).).((((((((((.....)))))))))).......................... ( -24.50)
>DroVir_CAF1 5909 88 + 1
AACAUUUC------GAUCUCCUGCGCAUUGUUGCGCAUUGUUGUUGUUGUUGUUGUAGCAAAUUCGCUUUGCUUCGAUUUU---------UCCAUAUUAUCAA
((((...(------(((..(.((((((....))))))..)..)))).))))((((.((((((.....)))))).))))...---------............. ( -19.50)
>DroSim_CAF1 1269 97 + 1
AUUAUUUCAUUCUCCUCCUUCUGCGCAUCGUUGCGCAUUAU------GGUGAGCUUAGCAAAUUCGCUUUGCUGAGUGUUUUUCUUCAUAUCCAUAUUAUCCA
..........((.((......((((((....))))))....------)).))((((((((((.....)))))))))).......................... ( -23.40)
>DroEre_CAF1 1843 97 + 1
AUUAUUCCAUUCUCCUCCUUCUGCGCAUCUUUGCGCAUUAU------GGUGAGCUUAGCAAAUUCGCUUUGCUGAGUUUUUUCCUCCAUAUCCAUUAUAUCCA
.....................((((((....)))))).(((------((.((((((((((((.....))))))))))))......)))))............. ( -26.10)
>DroYak_CAF1 1262 97 + 1
AUUAUCUCAUUCUCCUCCUUCUGCGCAUCUUUGCGCAUUAU------GGUGAGCUUAGCAAAUUCGCUUUGCUGAGUUUUUUCCUCCAAAUCCAUAUUAUCCA
.....................((((((....)))))).(((------((.((((((((((((.....))))))))))))............)))))....... ( -25.02)
>DroMoj_CAF1 5408 85 + 1
AACACGGU------UUUCUCCUGCGCAUCGUUGCGCAUUGUUGUU---GCUUUUGUAGCAAAUUCACUUUGCUUUAUUUUU---------UCCAUAUUAUCAA
.....((.------.......((((((....))))))...(((((---((....)))))))....................---------.)).......... ( -17.00)
>consensus
AUUAUUUCAUUCUCCUCCUUCUGCGCAUCGUUGCGCAUUAU______GGUGAGCUUAGCAAAUUCGCUUUGCUGAGUUUUUU_CU_CAUAUCCAUAUUAUCCA
.....................((((((....))))))...............((((((((((.....)))))))))).......................... (-19.07 = -18.52 +  -0.55)

alignment

secondary structure

dotplot

Window 4

Location	7,579,945 – 7,580,042
Length	97
Sequences	6
Columns	103
Reading direction	reverse
Mean pairwise identity	73.69
Mean single sequence MFE	-20.60
Consensus MFE	-14.33
Energy contribution	-14.55
Covariance contribution	0.22
Combinations/Pair	1.13
Mean z-score	-2.47
Structure conservation index	0.70
SVM decision value	2.40
SVM RNA-class probability	0.993520
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7579945 97 - 27905053
UGGAUAAUAUGGAUAUGAAGAAAAACACUCAGCAAAGCGAAUUUGCUAAGCUCACC------AUAAUGCGCAACGAUGCGCAGACGGAGGAGAAUAAGAUAAU
...........................((.((((((.....)))))).))(((..(------....((((((....))))))....)..)))........... ( -20.30)
>DroVir_CAF1 5909 88 - 1
UUGAUAAUAUGGA---------AAAAUCGAAGCAAAGCGAAUUUGCUACAACAACAACAACAACAAUGCGCAACAAUGCGCAGGAGAUC------GAAAUGUU
.............---------....((((((((((.....))))))...................((((((....)))))).....))------))...... ( -17.90)
>DroSim_CAF1 1269 97 - 1
UGGAUAAUAUGGAUAUGAAGAAAAACACUCAGCAAAGCGAAUUUGCUAAGCUCACC------AUAAUGCGCAACGAUGCGCAGAAGGAGGAGAAUGAAAUAAU
...........................((.((((((.....)))))).))(((..(------....((((((....))))))....)..)))........... ( -20.30)
>DroEre_CAF1 1843 97 - 1
UGGAUAUAAUGGAUAUGGAGGAAAAAACUCAGCAAAGCGAAUUUGCUAAGCUCACC------AUAAUGCGCAAAGAUGCGCAGAAGGAGGAGAAUGGAAUAAU
.................(((.......)))((((((.....))))))...(((..(------....((((((....))))))....)..)))........... ( -22.20)
>DroYak_CAF1 1262 97 - 1
UGGAUAAUAUGGAUUUGGAGGAAAAAACUCAGCAAAGCGAAUUUGCUAAGCUCACC------AUAAUGCGCAAAGAUGCGCAGAAGGAGGAGAAUGAGAUAAU
...........................(((((((((.....))))))...(((..(------....((((((....))))))....)..)))...)))..... ( -22.70)
>DroMoj_CAF1 5408 85 - 1
UUGAUAAUAUGGA---------AAAAAUAAAGCAAAGUGAAUUUGCUACAAAAGC---AACAACAAUGCGCAACGAUGCGCAGGAGAAA------ACCGUGUU
.....(((((((.---------........((((((.....))))))........---........((((((....)))))).......------.))))))) ( -20.20)
>consensus
UGGAUAAUAUGGAUAUG_AG_AAAAAACUCAGCAAAGCGAAUUUGCUAAGCUCACC______AUAAUGCGCAACGAUGCGCAGAAGGAGGAGAAUGAAAUAAU
...........................(((((((((.....))))))...................((((((....))))))....))).............. (-14.33 = -14.55 +   0.22)

alignment

secondary structure

dotplot

Window 5

Location	7,579,977 – 7,580,078
Length	101
Sequences	6
Columns	101
Reading direction	forward
Mean pairwise identity	90.10
Mean single sequence MFE	-24.52
Consensus MFE	-22.08
Energy contribution	-22.08
Covariance contribution	0.00
Combinations/Pair	1.19
Mean z-score	-3.21
Structure conservation index	0.90
SVM decision value	3.26
SVM RNA-class probability	0.998865
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7579977 101 + 27905053
GCGCAUUAUGGUGAGCUUAGCAAAUUCGCUUUGCUGAGUGUUUUUCUUCAUAUCCAUAUUAUCCAUAAUAAGGUCCUCCCUUAUAUACCCACCGUUAUCGU
(((.((.((((((.((((((((((.....))))))))))............................((((((.....)))))).....)))))).))))) ( -25.60)
>DroSec_CAF1 1294 101 + 1
GCGCAUUAUGGUGAGCUUAGCAAAUUCGCUUUGCUGAGUGUUUUUCUUCAUAUCCAUAUUAUCCAUAAUAAGGUCCUCCCUUAUAUAUCCACCGUUAUCGU
(((.((.((((((.((((((((((.....))))))))))............................((((((.....)))))).....)))))).))))) ( -25.60)
>DroSim_CAF1 1301 101 + 1
GCGCAUUAUGGUGAGCUUAGCAAAUUCGCUUUGCUGAGUGUUUUUCUUCAUAUCCAUAUUAUCCAUAAUAAGGUCCUCCCUUAUAUACCCACCGUUAUCGU
(((.((.((((((.((((((((((.....))))))))))............................((((((.....)))))).....)))))).))))) ( -25.60)
>DroEre_CAF1 1875 101 + 1
GCGCAUUAUGGUGAGCUUAGCAAAUUCGCUUUGCUGAGUUUUUUCCUCCAUAUCCAUUAUAUCCAUAAUAAGGUCAUCCCUUAUAUACCCACCGUUAUCGU
(((.((.(((((((((((((((((.....)))))))))))...........................((((((.....)))))).....)))))).))))) ( -25.70)
>DroYak_CAF1 1294 101 + 1
GCGCAUUAUGGUGAGCUUAGCAAAUUCGCUUUGCUGAGUUUUUUCCUCCAAAUCCAUAUUAUCCAUAAUAAGGUCCUCCCUUAUAUACCCACCGUUAUCGU
(((.((.(((((((((((((((((.....)))))))))))...........................((((((.....)))))).....)))))).))))) ( -25.70)
>DroAna_CAF1 1400 101 + 1
GCGCAUUGUGGUGAGUUUAGCAAAUUCACUUUGCUGGAUUGUUUCCUUUUCUCCCAUAUUAUCCAUAAUAAGCUGCUCCUUUCCAUACUCACCGUUGUCUA
..(((...((((((((..((((((.....))))))(((.....)))........................................)))))))).)))... ( -18.90)
>consensus
GCGCAUUAUGGUGAGCUUAGCAAAUUCGCUUUGCUGAGUGUUUUCCUUCAUAUCCAUAUUAUCCAUAAUAAGGUCCUCCCUUAUAUACCCACCGUUAUCGU
(((.((.((((((.((((((((((.....))))))))))............................((((((.....)))))).....)))))).))))) (-22.08 = -22.08 +   0.00)

alignment

secondary structure

dotplot

Window 6

Location	7,579,977 – 7,580,078
Length	101
Sequences	6
Columns	101
Reading direction	reverse
Mean pairwise identity	90.10
Mean single sequence MFE	-22.75
Consensus MFE	-19.68
Energy contribution	-19.93
Covariance contribution	0.25
Combinations/Pair	1.16
Mean z-score	-1.49
Structure conservation index	0.87
SVM decision value	0.13
SVM RNA-class probability	0.595695
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7579977 101 - 27905053
ACGAUAACGGUGGGUAUAUAAGGGAGGACCUUAUUAUGGAUAAUAUGGAUAUGAAGAAAAACACUCAGCAAAGCGAAUUUGCUAAGCUCACCAUAAUGCGC
........(((((((..((((((.....))))))................................((((((.....))))))..)))))))......... ( -22.30)
>DroSec_CAF1 1294 101 - 1
ACGAUAACGGUGGAUAUAUAAGGGAGGACCUUAUUAUGGAUAAUAUGGAUAUGAAGAAAAACACUCAGCAAAGCGAAUUUGCUAAGCUCACCAUAAUGCGC
........(((((.(((((((((.....))))).)))).........................((.((((((.....)))))).)).)))))......... ( -18.80)
>DroSim_CAF1 1301 101 - 1
ACGAUAACGGUGGGUAUAUAAGGGAGGACCUUAUUAUGGAUAAUAUGGAUAUGAAGAAAAACACUCAGCAAAGCGAAUUUGCUAAGCUCACCAUAAUGCGC
........(((((((..((((((.....))))))................................((((((.....))))))..)))))))......... ( -22.30)
>DroEre_CAF1 1875 101 - 1
ACGAUAACGGUGGGUAUAUAAGGGAUGACCUUAUUAUGGAUAUAAUGGAUAUGGAGGAAAAAACUCAGCAAAGCGAAUUUGCUAAGCUCACCAUAAUGCGC
........(((((((..((((((.....))))))...................(((.......)))((((((.....))))))..)))))))......... ( -24.60)
>DroYak_CAF1 1294 101 - 1
ACGAUAACGGUGGGUAUAUAAGGGAGGACCUUAUUAUGGAUAAUAUGGAUUUGGAGGAAAAAACUCAGCAAAGCGAAUUUGCUAAGCUCACCAUAAUGCGC
........(((((((..((((((.....))))))...................(((.......)))((((((.....))))))..)))))))......... ( -24.60)
>DroAna_CAF1 1400 101 - 1
UAGACAACGGUGAGUAUGGAAAGGAGCAGCUUAUUAUGGAUAAUAUGGGAGAAAAGGAAACAAUCCAGCAAAGUGAAUUUGCUAAACUCACCACAAUGCGC
........(((((((.......(((....(((..(((.....)))...)))....(....)..)))((((((.....))))))..)))))))......... ( -23.90)
>consensus
ACGAUAACGGUGGGUAUAUAAGGGAGGACCUUAUUAUGGAUAAUAUGGAUAUGAAGAAAAAAACUCAGCAAAGCGAAUUUGCUAAGCUCACCAUAAUGCGC
........(((((((..((((((.....))))))................................((((((.....))))))..)))))))......... (-19.68 = -19.93 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:45:43 2006