Locus 3472

Sequence ID	X_DroMel_CAF1
Location	9,317,545 – 9,317,662
Length	117
Max. P	0.993762

overview

Window 9

Location	9,317,545 – 9,317,640
Length	95
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	81.15
Mean single sequence MFE	-41.55
Consensus MFE	-26.61
Energy contribution	-27.17
Covariance contribution	0.56
Combinations/Pair	1.17
Mean z-score	-2.28
Structure conservation index	0.64
SVM decision value	0.74
SVM RNA-class probability	0.838615
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9317545 95 + 22224390
-------GCUGAUGGUGGUCGCCAGCGAGAACGCAUUCUGGCCUUGCUGG---GCGGCUUGCGACCAAAUCCGAAUCCAAUGCCCACGGGCGUCGGAUUCAUUUU
-------...(((..(((((((.(((.((((....)))).((((....))---)).))).))))))).))).((((((.(((((....))))).))))))..... ( -43.70)
>DroVir_CAF1 118873 95 + 1
-------GCUGUUGGUGGCGGCCAUCGGGAACGCAUCUUGGCAUUGUUGG---GUGGUUUGCGGCCGCAUCCGAAUCCAAUGCCCACGGGCCUCGGAUUCAUUUU
-------......((..((((((...(.((((.((.((..((...))..)---))))))).)))))))..))((((((...(((....)))...))))))..... ( -38.00)
>DroPse_CAF1 110185 95 + 1
----------GGUCGGGGUCGCCAGCGGGAGCGCAUUUUUGCGUUGUUGGGGGGCGGCUUGCGACCAAACCCGAAUCCAAUGCCCACGGGCGUCGGAUUCAUUUC
----------(((((((((((((..(((.((((((....)))))).)))...)))))))).)))))......((((((.(((((....))))).))))))..... ( -50.80)
>DroGri_CAF1 114225 102 + 1
UAGUGGUGCAGGUGGUGGCGGCCAUCGGGAACGCAUCUUGGCAUUGUUGG---GUGGUUUGCGGCCGCAUCCGAAUCCAAUGCCCACGGGCCUCGGAUUCAUUUU
....((.....(((((.((((((((((....)((......)).......)---)))).)))).)))))..))((((((...(((....)))...))))))..... ( -39.00)
>DroWil_CAF1 110866 95 + 1
-------GCGACUGGUGGCGGCCAACGUGAGCGCAUUUUGGCCUUAUUAG---GUGGCUUACGACCAAAUCCGAAUCCAAUGCCCACGGGCGUCGGAUUCAUUUU
-------((.((((((((.((((((.(((....))).)))))))))))).---)).))..............((((((.(((((....))))).))))))..... ( -37.10)
>DroMoj_CAF1 126011 95 + 1
-------AGUGUUGGUGGGGGCCACCGGGAGCGCUUCUUGGCAUUGUUGG---GAGGUUUGCGGCCGCAUCCGAAUCCAAUGCCCACGGGCGUCGGAUUCAUUUU
-------.((((.(((((...)))))((..((((((((..((...))..)---)))))..))..))))))..((((((.(((((....))))).))))))..... ( -40.70)
>consensus
_______GCUGGUGGUGGCGGCCAGCGGGAACGCAUCUUGGCAUUGUUGG___GUGGCUUGCGACCAAAUCCGAAUCCAAUGCCCACGGGCGUCGGAUUCAUUUU
............((((.((((((...(....)((......)).............))).))).)))).....((((((.(((((....))))).))))))..... (-26.61 = -27.17 +   0.56)

alignment

secondary structure

dotplot

Window 0

Location	9,317,545 – 9,317,640
Length	95
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	81.15
Mean single sequence MFE	-34.70
Consensus MFE	-22.98
Energy contribution	-23.07
Covariance contribution	0.08
Combinations/Pair	1.14
Mean z-score	-2.08
Structure conservation index	0.66
SVM decision value	0.66
SVM RNA-class probability	0.813409
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9317545 95 - 22224390
AAAAUGAAUCCGACGCCCGUGGGCAUUGGAUUCGGAUUUGGUCGCAAGCCGC---CCAGCAAGGCCAGAAUGCGUUCUCGCUGGCGACCACCAUCAGC-------
....(((((((((.(((....))).)))))))))(((.(((((((.(((.((---(......))).((((....)))).))).)))))))..)))...------- ( -39.60)
>DroVir_CAF1 118873 95 - 1
AAAAUGAAUCCGAGGCCCGUGGGCAUUGGAUUCGGAUGCGGCCGCAAACCAC---CCAACAAUGCCAAGAUGCGUUCCCGAUGGCCGCCACCAACAGC-------
.....((((((((.(((....))).))))))))((..(((((((.....)..---.....(((((......)))))......))))))..))......------- ( -33.10)
>DroPse_CAF1 110185 95 - 1
GAAAUGAAUCCGACGCCCGUGGGCAUUGGAUUCGGGUUUGGUCGCAAGCCGCCCCCCAACAACGCAAAAAUGCGCUCCCGCUGGCGACCCCGACC----------
....(((((((((.(((....))).)))))))))((((.((((((.(((.(........)..((((....)))).....))).))))))..))))---------- ( -37.10)
>DroGri_CAF1 114225 102 - 1
AAAAUGAAUCCGAGGCCCGUGGGCAUUGGAUUCGGAUGCGGCCGCAAACCAC---CCAACAAUGCCAAGAUGCGUUCCCGAUGGCCGCCACCACCUGCACCACUA
.....((((((((.(((....))).))))))))((..(((((((.....)..---.....(((((......)))))......))))))..))............. ( -33.10)
>DroWil_CAF1 110866 95 - 1
AAAAUGAAUCCGACGCCCGUGGGCAUUGGAUUCGGAUUUGGUCGUAAGCCAC---CUAAUAAGGCCAAAAUGCGCUCACGUUGGCCGCCACCAGUCGC-------
.....((((((((.(((....))).))))))))((...(((.(....)))).---.......((((((..((....))..))))))....))......------- ( -34.10)
>DroMoj_CAF1 126011 95 - 1
AAAAUGAAUCCGACGCCCGUGGGCAUUGGAUUCGGAUGCGGCCGCAAACCUC---CCAACAAUGCCAAGAAGCGCUCCCGGUGGCCCCCACCAACACU-------
.....((((((((.(((....))).))))))))(((.((((.......))..---........((......))))))).(((((...)))))......------- ( -31.20)
>consensus
AAAAUGAAUCCGACGCCCGUGGGCAUUGGAUUCGGAUGCGGCCGCAAACCAC___CCAACAAUGCCAAAAUGCGCUCCCGAUGGCCGCCACCAACAGC_______
.....((((((((.(((....))).))))))))((...(((((....................((......))(....)...)))))...))............. (-22.98 = -23.07 +   0.08)

alignment

secondary structure

dotplot

Window 1

Location	9,317,563 – 9,317,662
Length	99
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	75.51
Mean single sequence MFE	-42.22
Consensus MFE	-21.90
Energy contribution	-22.32
Covariance contribution	0.42
Combinations/Pair	1.14
Mean z-score	-2.82
Structure conservation index	0.52
SVM decision value	2.42
SVM RNA-class probability	0.993762
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9317563 99 + 22224390
CGAGAACGCAUUCUGGCCUUGCUGG---GCGGCUUGCGACCAAAUCCGAAUCCAAUGCCCACGGGCGUCGGAUUCAUUUUUGGUUCG---UCGGGCG-CU-UCGCUU-------------
...(((.((......((((....))---)).(((((((((((((...((((((.(((((....))))).))))))...))))).)))---.))))))-))-))....------------- ( -42.90)
>DroPse_CAF1 110200 102 + 1
CGGGAGCGCAUUUUUGCGUUGUUGGGGGGCGGCUUGCGACCAAACCCGAAUCCAAUGCCCACGGGCGUCGGAUUCAUUUC-GGUCGG---AAUGUCG-UUCUCGCUC-------------
(((.((((((....)))))).)))(((((((((((.(((((......((((((.(((((....))))).)))))).....-))))).---)).))))-)))))....------------- ( -49.50)
>DroWil_CAF1 110884 102 + 1
CGUGAGCGCAUUUUGGCCUUAUUAG---GUGGCUUACGACCAAAUCCGAAUCCAAUGCCCACGGGCGUCGGAUUCAUUUUGGUUUCCACUUUAGACC-CU-CUUCUU-------------
(((((((.(.....)((((....))---)).)))))))((((((...((((((.(((((....))))).))))))..))))))..............-..-......------------- ( -34.90)
>DroYak_CAF1 98448 101 + 1
CGAGAACGCAUUCUGGCCUUGCUGG---GCGGCUUGCGACCAAAUCCGAAUCCAAUGCCCACGGGCGUCGGAUUCAUUUUUGGUUCGUCGUCGGGCG-CU-UCGCC--------------
(((..(((((..(((.((.....))---.)))..)))(((((((...((((((.(((((....))))).))))))...))))))).))..)))((((-..-.))))-------------- ( -43.90)
>DroMoj_CAF1 126029 100 + 1
CGGGAGCGCUUCUUGGCAUUGUUGG---GAGGUUUGCGGCCGCAUCCGAAUCCAAUGCCCACGGGCGUCGGAUUCAUUUUGGCGUUGUCUUUGGCCA-CU-UGUC---------------
((((.((((((((..((...))..)---)))))..))((((......((((((.(((((....))))).)))))).....(((...)))...)))).-))-))..--------------- ( -39.40)
>DroAna_CAF1 110196 112 + 1
CGGGAACGCAUUCUGGCCUUGUUGG---GCGGCUUGCGACCAAAUCCGAAUCCAAUGCCCACGGGCGUCGGAUUCAUUUUUGGUGAG---UUGGUCCUCU-UUGU-AGUUUUUCUCUCUG
.(((((((((..(((.((.....))---.)))..))))((((((...((((((.(((((....))))).))))))...))))))(((---......))).-....-.....))))).... ( -42.70)
>consensus
CGGGAACGCAUUCUGGCCUUGUUGG___GCGGCUUGCGACCAAAUCCGAAUCCAAUGCCCACGGGCGUCGGAUUCAUUUUUGGUUCG___UUGGGCG_CU_UCGCU______________
......((((....((((..((......)))))))))).........((((((.(((((....))))).))))))............................................. (-21.90 = -22.32 +   0.42)

alignment

secondary structure

dotplot

Window 2

Location	9,317,563 – 9,317,662
Length	99
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	75.51
Mean single sequence MFE	-36.62
Consensus MFE	-21.67
Energy contribution	-21.75
Covariance contribution	0.08
Combinations/Pair	1.11
Mean z-score	-2.25
Structure conservation index	0.59
SVM decision value	1.79
SVM RNA-class probability	0.977437
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9317563 99 - 22224390
-------------AAGCGA-AG-CGCCCGA---CGAACCAAAAAUGAAUCCGACGCCCGUGGGCAUUGGAUUCGGAUUUGGUCGCAAGCCGC---CCAGCAAGGCCAGAAUGCGUUCUCG
-------------...(((-((-(((..(.---(((.(((((..(((((((((.(((....))).)))))))))..)))))))))..(((..---.......)))......))))).))) ( -38.30)
>DroPse_CAF1 110200 102 - 1
-------------GAGCGAGAA-CGACAUU---CCGACC-GAAAUGAAUCCGACGCCCGUGGGCAUUGGAUUCGGGUUUGGUCGCAAGCCGCCCCCCAACAACGCAAAAAUGCGCUCCCG
-------------((((.....-((...((---.(((((-(((.(((((((((.(((....))).)))))))))..)))))))).))..))............(((....)))))))... ( -38.60)
>DroWil_CAF1 110884 102 - 1
-------------AAGAAG-AG-GGUCUAAAGUGGAAACCAAAAUGAAUCCGACGCCCGUGGGCAUUGGAUUCGGAUUUGGUCGUAAGCCAC---CUAAUAAGGCCAAAAUGCGCUCACG
-------------......-..-(((((...((((..((((((.(((((((((.(((....))).)))))))))..))))))......))))---......))))).............. ( -34.20)
>DroYak_CAF1 98448 101 - 1
--------------GGCGA-AG-CGCCCGACGACGAACCAAAAAUGAAUCCGACGCCCGUGGGCAUUGGAUUCGGAUUUGGUCGCAAGCCGC---CCAGCAAGGCCAGAAUGCGUUCUCG
--------------((((.-..-))))(((.(((((.(((((..(((((((((.(((....))).)))))))))..)))))))(((..(.((---(......)))..)..)))))).))) ( -41.00)
>DroMoj_CAF1 126029 100 - 1
---------------GACA-AG-UGGCCAAAGACAACGCCAAAAUGAAUCCGACGCCCGUGGGCAUUGGAUUCGGAUGCGGCCGCAAACCUC---CCAACAAUGCCAAGAAGCGCUCCCG
---------------....-.(-(((((...(....)((.....(((((((((.(((....))).)))))))))...)))))))).......---........((......))....... ( -30.90)
>DroAna_CAF1 110196 112 - 1
CAGAGAGAAAAACU-ACAA-AGAGGACCAA---CUCACCAAAAAUGAAUCCGACGCCCGUGGGCAUUGGAUUCGGAUUUGGUCGCAAGCCGC---CCAACAAGGCCAGAAUGCGUUCCCG
....(.(((.....-....-.(((......---)))((((((..(((((((((.(((....))).)))))))))..))))))((((..(.((---(......)))..)..))))))).). ( -36.70)
>consensus
______________AGCGA_AG_CGACCAA___CGAACCAAAAAUGAAUCCGACGCCCGUGGGCAUUGGAUUCGGAUUUGGUCGCAAGCCGC___CCAACAAGGCCAAAAUGCGCUCCCG
.............................................((((((((.(((....))).))))))))((...(((.(....))))....))......((......))....... (-21.67 = -21.75 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:00:14 2006