Locus 1558

Sequence ID	3R_DroMel_CAF1
Location	4,461,340 – 4,461,500
Length	160
Max. P	0.933877

overview

Window 2

Location	4,461,340 – 4,461,460
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.06
Mean single sequence MFE	-42.83
Consensus MFE	-27.31
Energy contribution	-26.63
Covariance contribution	-0.69
Combinations/Pair	1.40
Mean z-score	-1.52
Structure conservation index	0.64
SVM decision value	0.03
SVM RNA-class probability	0.549082
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4461340 120 - 27905053
ACCCAAAUGGUGGCCAAAGCGGCUGGAAAUGAUUGGUAAAGUGCUGCCCAAAGCCUAUUGUUCCAUGGUGAUUUUCACCUCCCUGCAUUUGGGUGUCCUGUUCACGAAAACCACACUGGA
..(((....(((((((((((((..(((......(((..((..(((......)))...))...))).((((.....))))))))))).)))))(((.......))).....))))..))). ( -32.60)
>DroPse_CAF1 15714 120 - 1
GCCCAGUUGGUGGCCCACUUGGCUGCGGCCAGUGGGCGGGCUAAUGGCCAAGGCCUACUGCUCGAUGGUAAUCCUCACCUCGCUCCACUUGGGUUUGCUGUUCACGAAAACCACAUUGGA
((((((.(((.((((((((.(((....))))))))))((((....(((....)))....))))((.(((.......))))).).))).))))))................((.....)). ( -47.00)
>DroSim_CAF1 14749 120 - 1
ACCCAAAUGGUGGCCAAAGCGGCUGGAAAUGAUUGGUCAAGUGCUGGCCAAAGUCUAUUGUUCCAUGGUGAUUUUCACCUCGCUGCAUUUGGGUGUCCUGUUCACGAAAACCACACUGGA
..(((....(((((((((((((((((((..(((((((((.....))))))..))).....))))).((((.....))))..))))).)))))(((.......))).....))))..))). ( -41.90)
>DroEre_CAF1 14263 120 - 1
GCCCCAAUGGUGGCCGAAGCGGCUGGAAUUGGUUGGCCAACUGCUGGCCAAGGCCUAUAGUUCCAUGGUGAUUUUUACCUCGCUGCAUUUGGGUGUGCUGUUCACCAAAACCACACUGGA
...(((...((((.(((((((((((((((((((((((((.....))))))..)))...))))))).(((((...)))))..))))).))))((((.......))))....))))..))). ( -45.50)
>DroYak_CAF1 15836 120 - 1
GCCCAAAUGGUGGCCGAAGCGGCUGGAAAUGAUGGGCCAAGUGCUGGCCAAGGCCUAUAGUUCCAUGGUGAUAUUUACUUCGCUGCAUUUGGGUGUCCUGUUCACCAAAACCACACUGGA
..(((....((((.((((((((((((((...(((((((..(.(....))..)))))))..))))).(((((...)))))..))))).))))((((.......))))....))))..))). ( -40.50)
>DroPer_CAF1 17752 120 - 1
GCCCAGUUGGUGGCCCACUUGGCUACGGCCAGUGGGCGGGCUAAUGGCCAAGGCCUACUGCUCGAUGGUAAUCUUCACCUCGCUCCACUUGGGUCUGCUGUUCACGAAAACCACAUUGGA
((((((.(((.((((((((.(((....))))))))))((((....(((....)))....))))((.(((.......))))).).))).))))))................((.....)). ( -49.50)
>consensus
GCCCAAAUGGUGGCCAAAGCGGCUGGAAAUGAUGGGCCAACUGCUGGCCAAGGCCUAUUGUUCCAUGGUGAUUUUCACCUCGCUGCAUUUGGGUGUCCUGUUCACGAAAACCACACUGGA
(((((((((..((((.....))))((((.((((.(((...............))).))))))))..((((.....))))......)))))))))................((.....)). (-27.31 = -26.63 +  -0.69)

alignment

secondary structure

dotplot

Window 3

Location	4,461,380 – 4,461,500
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	78.22
Mean single sequence MFE	-44.64
Consensus MFE	-22.85
Energy contribution	-23.30
Covariance contribution	0.45
Combinations/Pair	1.22
Mean z-score	-2.12
Structure conservation index	0.51
SVM decision value	0.55
SVM RNA-class probability	0.777860
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4461380 120 + 27905053
AGGUGAAAAUCACCAUGGAACAAUAGGCUUUGGGCAGCACUUUACCAAUCAUUUCCAGCCGCUUUGGCCACCAUUUGGGUAACCGCGGCGAUGGCUUCGUGCCAUUCGCCAACUGGAGUC
.((((.....))))...........(((((..(...((...(((((...........(((.....))).........)))))..))(((((((((.....)))).)))))..)..))))) ( -39.35)
>DroPse_CAF1 15754 120 + 1
AGGUGAGGAUUACCAUCGAGCAGUAGGCCUUGGCCAUUAGCCCGCCCACUGGCCGCAGCCAAGUGGGCCACCAACUGGGCAAUCUCGGAGAUGGGUUCAUUCCCAUCGCCAGCUGCAGUC
.(((((...))))).....(((((.(((....)))....((((((((((((((....))).)))))))........))))......((.((((((......)))))).)).))))).... ( -54.60)
>DroSim_CAF1 14789 120 + 1
AGGUGAAAAUCACCAUGGAACAAUAGACUUUGGCCAGCACUUGACCAAUCAUUUCCAGCCGCUUUGGCCACCAUUUGGGUAACCGCGGCGAUGGCUUCGUGCCCAUCGCCAACUGGAGUC
.((((.....))))...........((((.((((((((.((.((.........)).))..))..))))))(((...((....))..(((((((((.....).))))))))...))))))) ( -38.70)
>DroEre_CAF1 14303 120 + 1
AGGUAAAAAUCACCAUGGAACUAUAGGCCUUGGCCAGCAGUUGGCCAACCAAUUCCAGCCGCUUCGGCCACCAUUGGGGCAACCGCGGAGAUGGCUGCGUGCCCAUCGCCAACUGUUGAA
.(((.......)))...........(((....)))((((((((((....((((....((((...))))....))))(((((..(((((......))))))))))...))))))))))... ( -45.70)
>DroYak_CAF1 15876 120 + 1
AAGUAAAUAUCACCAUGGAACUAUAGGCCUUGGCCAGCACUUGGCCCAUCAUUUCCAGCCGCUUCGGCCACCAUUUGGGCAACCGCGGAGAUGGCCGCGUGCCCAUCGCCAACUGUUGUC
..............((((.......(((....))).((((.(((((....((((((.((.((....))........((....))))))))))))))).)))))))).............. ( -39.20)
>DroPer_CAF1 17792 120 + 1
AGGUGAAGAUUACCAUCGAGCAGUAGGCCUUGGCCAUUAGCCCGCCCACUGGCCGUAGCCAAGUGGGCCACCAACUGGGCAAUCUCGGAGAUGGCUUCAUUCCCAUCGCCAGCUGCAGUC
.(((((...))))).....(((((.(((....)))....((((((((((((((....))).)))))))........))))......((.(((((........))))).)).))))).... ( -50.30)
>consensus
AGGUGAAAAUCACCAUGGAACAAUAGGCCUUGGCCAGCACUUGGCCAACCAUUUCCAGCCGCUUCGGCCACCAUUUGGGCAACCGCGGAGAUGGCUUCGUGCCCAUCGCCAACUGCAGUC
.((((.....)))).....((.((((...(((((........................((((....(((........)))....)))).(((((........)))))))))))))).)). (-22.85 = -23.30 +   0.45)

alignment

secondary structure

dotplot

Window 4

Location	4,461,380 – 4,461,500
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.22
Mean single sequence MFE	-49.22
Consensus MFE	-28.61
Energy contribution	-28.95
Covariance contribution	0.34
Combinations/Pair	1.29
Mean z-score	-2.27
Structure conservation index	0.58
SVM decision value	1.23
SVM RNA-class probability	0.933877
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4461380 120 - 27905053
GACUCCAGUUGGCGAAUGGCACGAAGCCAUCGCCGCGGUUACCCAAAUGGUGGCCAAAGCGGCUGGAAAUGAUUGGUAAAGUGCUGCCCAAAGCCUAUUGUUCCAUGGUGAUUUUCACCU
...((((((((((((.((((.....)))))))))(((((((((.....)))))))...)))))))))......(((..((..(((......)))...))...))).((((.....)))). ( -44.90)
>DroPse_CAF1 15754 120 - 1
GACUGCAGCUGGCGAUGGGAAUGAACCCAUCUCCGAGAUUGCCCAGUUGGUGGCCCACUUGGCUGCGGCCAGUGGGCGGGCUAAUGGCCAAGGCCUACUGCUCGAUGGUAAUCCUCACCU
((((((((((((.((((((......)))))).)).)).))))..))))(((((((((((.(((....))))))))))((((....(((....)))....))))............)))). ( -55.90)
>DroSim_CAF1 14789 120 - 1
GACUCCAGUUGGCGAUGGGCACGAAGCCAUCGCCGCGGUUACCCAAAUGGUGGCCAAAGCGGCUGGAAAUGAUUGGUCAAGUGCUGGCCAAAGUCUAUUGUUCCAUGGUGAUUUUCACCU
((((((((((((((((((........))))))))(((((((((.....)))))))...))))))))).....(((((((.....))))))).)))...........((((.....)))). ( -50.70)
>DroEre_CAF1 14303 120 - 1
UUCAACAGUUGGCGAUGGGCACGCAGCCAUCUCCGCGGUUGCCCCAAUGGUGGCCGAAGCGGCUGGAAUUGGUUGGCCAACUGCUGGCCAAGGCCUAUAGUUCCAUGGUGAUUUUUACCU
.........(((..((((((...(((((..((...((((..((.....))..)))).)).)))))...(((((..((.....))..))))).))))))....))).(((((...))))). ( -46.00)
>DroYak_CAF1 15876 120 - 1
GACAACAGUUGGCGAUGGGCACGCGGCCAUCUCCGCGGUUGCCCAAAUGGUGGCCGAAGCGGCUGGAAAUGAUGGGCCAAGUGCUGGCCAAGGCCUAUAGUUCCAUGGUGAUAUUUACUU
..........((.(((((.(....).))))).)).((((..((.....))..))))...((.((((((...(((((((..(.(....))..)))))))..))))).).)).......... ( -42.20)
>DroPer_CAF1 17792 120 - 1
GACUGCAGCUGGCGAUGGGAAUGAAGCCAUCUCCGAGAUUGCCCAGUUGGUGGCCCACUUGGCUACGGCCAGUGGGCGGGCUAAUGGCCAAGGCCUACUGCUCGAUGGUAAUCUUCACCU
((((((((((((.(((((........))))).)).)).))))..))))(((((((((((.(((....))))))))))((((....(((....)))....))))(((....)))..)))). ( -55.60)
>consensus
GACUACAGUUGGCGAUGGGCACGAAGCCAUCUCCGCGGUUGCCCAAAUGGUGGCCAAAGCGGCUGGAAAUGAUGGGCCAACUGCUGGCCAAGGCCUAUUGUUCCAUGGUGAUUUUCACCU
....(((((.((((((((........))))).(((((((((((.....)))))))...))))............(((.........)))...))).))))).....((((.....)))). (-28.61 = -28.95 +   0.34)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:13:30 2006