Locus 5665

Sequence ID	2L_DroMel_CAF1
Location	16,089,093 – 16,089,235
Length	142
Max. P	0.981418

overview

Window 9

Location	16,089,093 – 16,089,183
Length	90
Sequences	6
Columns	102
Reading direction	forward
Mean pairwise identity	82.34
Mean single sequence MFE	-15.30
Consensus MFE	-9.72
Energy contribution	-9.72
Covariance contribution	0.00
Combinations/Pair	1.25
Mean z-score	-1.82
Structure conservation index	0.64
SVM decision value	0.05
SVM RNA-class probability	0.556970
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16089093 90 + 22407834
-----UUUCUUGUUCAAUUUUUAAUGUUCAAUUAAUUGCAUUAAAUUAUGUGCAAAA-------UUAUGCACUUAAAAUGCAAUAAGUUUCCGCCCAUAGAC
-----..(((((..(......((((.....))))((((((((...(((.(((((...-------...))))).)))))))))))........)..)).))). ( -14.60)
>DroVir_CAF1 27626 96 + 1
UGCAUUUUC-CAUUGCACUUUUAAUGUUCAAUUAAUUGCAUUAAAUUAUGUGUAAUACAUAAAUUUAUGUAUUUAAAAUGCACUCCAUUUCG-----UCGAC
((((((((.-..((((((.((((((((..........))))))))....))))))((((((....))))))...))))))))..........-----..... ( -20.20)
>DroPse_CAF1 23596 90 + 1
-----UUUGGUGUUCAAUUUUUAAUGUUCAAUUAAUUGCAUUAAAUUAUGUGCAAAA-------UUAUGCACUUAAAAUGCAAUAAGUUUCAACCUACAGAC
-----...(((....(((((.((((.....))))((((((((...(((.(((((...-------...))))).))))))))))))))))...)))....... ( -16.00)
>DroEre_CAF1 19661 90 + 1
-----UUUCGAGUUCAAUUUUUAAUGUUCAAUUAAUUGCAUUAAAUUAUGUGCAAAA-------UUAUGCACUUAAAAUGCAUUAAGUUUCCGCCCAUAGAC
-----..............((((((((..........))))))))(((((.((.(((-------(((((((.......)))))..)))))..)).))))).. ( -13.30)
>DroAna_CAF1 17768 85 + 1
-----UUUGCAGUUCAAUUUUUAAUGUUCAAUUAAUUGCAUUAAAUUAUGUGCGAAA-------UUAUACACUUAAAAUGCAAUAAGUUUCCGCCUA-----
-----.(((((.......(((((((((..((((..((((((........))))))))-------))..))).)))))))))))..............----- ( -11.71)
>DroPer_CAF1 25588 90 + 1
-----UUUGGUGUUCAAUUUUUAAUGUUCAAUUAAUUGCAUUAAAUUAUGUGCAAAA-------UUAUGCACUUAAAAUGCAAUAAGUUUCAACCUACAGAC
-----...(((....(((((.((((.....))))((((((((...(((.(((((...-------...))))).))))))))))))))))...)))....... ( -16.00)
>consensus
_____UUUCGUGUUCAAUUUUUAAUGUUCAAUUAAUUGCAUUAAAUUAUGUGCAAAA_______UUAUGCACUUAAAAUGCAAUAAGUUUCCGCCUAUAGAC
.............................((((.((((((((...(((.(((((.............))))).))))))))))).))))............. ( -9.72 =  -9.72 +   0.00)

alignment

secondary structure

dotplot

Window 0

Location	16,089,113 – 16,089,217
Length	104
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	86.43
Mean single sequence MFE	-20.23
Consensus MFE	-15.41
Energy contribution	-15.80
Covariance contribution	0.39
Combinations/Pair	1.08
Mean z-score	-2.43
Structure conservation index	0.76
SVM decision value	0.17
SVM RNA-class probability	0.615325
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16089113 104 + 22407834
GUUCAAUUAAUUGCAUUAAAUUAUGUGCAAAAUUAUGCACUUAAAAUGCAAUAAGUUUCCGCCCAUAGACAAAAUA---CGCACAGAUCAGUGCGCA---AAUGCAUCAA
...........((((((...(((.(((((......))))).)))..(((.....((((........))))......---.((((......)))))))---)))))).... ( -21.90)
>DroPse_CAF1 23616 107 + 1
GUUCAAUUAAUUGCAUUAAAUUAUGUGCAAAAUUAUGCACUUAAAAUGCAAUAAGUUUCAACCUACAGACAGACCUGACCCAACGGAUAAUCGGAAA---UCUGAAUCAA
((((((((.((((((((...(((.(((((......))))).))))))))))).))))........(((......))).......))))..((((...---.))))..... ( -21.00)
>DroSec_CAF1 18127 107 + 1
GUUCAAUUAAUUGCAUUAAAUUAUGUGCAAAAUUAUGCACUUAAAAUGCAAUAAGUUUCCGCCCAUAGACAAAAUA---CGCACAGAUCACUGCGCAUAAAAUGCAUCAA
....((((.((((((((...(((.(((((......))))).))))))))))).))))...................---.((.(((....))).)).............. ( -19.80)
>DroSim_CAF1 18138 107 + 1
GUUCAAUUAAUUGCAUUAAAUUAUGUGCAAAAUUAUGCACUUAAAAUGCAAUAAGUUUCCGCCCAUAGACAAAAUA---CGCACAGAUCACUGCGCAUAAAAUGCAUCAA
....((((.((((((((...(((.(((((......))))).))))))))))).))))...................---.((.(((....))).)).............. ( -19.80)
>DroEre_CAF1 19681 104 + 1
GUUCAAUUAAUUGCAUUAAAUUAUGUGCAAAAUUAUGCACUUAAAAUGCAUUAAGUUUCCGCCCAUAGACAAAAUA---CGCACAGAUCACUGAGCA---AUUGCAUCAA
(((((.(((((.(((((...(((.(((((......))))).)))))))))))))((((........))))......---............))))).---.......... ( -17.70)
>DroPer_CAF1 25608 107 + 1
GUUCAAUUAAUUGCAUUAAAUUAUGUGCAAAAUUAUGCACUUAAAAUGCAAUAAGUUUCAACCUACAGACAGACCUGACCCAACGGAUCAUCGGAAA---UCUGAAUCAA
(((.((((.((((((((...(((.(((((......))))).))))))))))).))))..)))...((((....(((((((....)).)))..))...---))))...... ( -21.20)
>consensus
GUUCAAUUAAUUGCAUUAAAUUAUGUGCAAAAUUAUGCACUUAAAAUGCAAUAAGUUUCCGCCCAUAGACAAAAUA___CGCACAGAUCACUGCGCA___AAUGCAUCAA
....((((.((((((((...(((.(((((......))))).))))))))))).)))).......................((.(((....))).)).............. (-15.41 = -15.80 +   0.39)

alignment

secondary structure

dotplot

Window 1

Location	16,089,145 – 16,089,235
Length	90
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	78.12
Mean single sequence MFE	-27.55
Consensus MFE	-20.33
Energy contribution	-20.83
Covariance contribution	0.50
Combinations/Pair	1.17
Mean z-score	-2.86
Structure conservation index	0.74
SVM decision value	1.89
SVM RNA-class probability	0.981418
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16089145 90 - 22407834
---------------------GUAAA-AACCUGCUCGCUUUUGAUGCAUU---UGCGCACUGAUCUGUGCG---UAUUUUGUCUAUGGGCGGAAACUUAUUGCAUUUUAAGUGCAUAA
---------------------.....-....(((..((((..((((((..---(((((((......)))))---))(((((((....)))))))......))))))..)))))))... ( -27.90)
>DroSec_CAF1 18159 94 - 1
---------------------GUAAAAAACCUGCUCGCUUUUGAUGCAUUUUAUGCGCAGUGAUCUGUGCG---UAUUUUGUCUAUGGGCGGAAACUUAUUGCAUUUUAAGUGCAUAA
---------------------..........(((..((((..((((((...(((((((((....)))))))---))(((((((....)))))))......))))))..)))))))... ( -29.20)
>DroSim_CAF1 18170 94 - 1
---------------------GUAAAAAACCUGCUCGCUUUUGAUGCAUUUUAUGCGCAGUGAUCUGUGCG---UAUUUUGUCUAUGGGCGGAAACUUAUUGCAUUUUAAGUGCAUAA
---------------------..........(((..((((..((((((...(((((((((....)))))))---))(((((((....)))))))......))))))..)))))))... ( -29.20)
>DroEre_CAF1 19713 90 - 1
---------------------GUAAAAAUUA-UGUCGCUUUUGAUGCAAU---UGCUCAGUGAUCUGUGCG---UAUUUUGUCUAUGGGCGGAAACUUAAUGCAUUUUAAGUGCAUAA
---------------------.......(((-((.(((((..((((((..---.((.(((....))).))(---(.(((((((....)))))))))....))))))..)))))))))) ( -27.20)
>DroYak_CAF1 19181 91 - 1
--------------------AGUAAAACCUA-UGUCGCUUUUGAUGCAUU---UGCGCAGUGAUCUGUGCG---UAUUUUGUCUAUGGGCGGAAACUUAUUGCAUUUUAAGUGCAUAA
--------------------.........((-((.(((((..((((((..---.((((((....))))))(---(.(((((((....)))))))))....))))))..))))))))). ( -30.20)
>DroPer_CAF1 25640 114 - 1
CCGAUUCUCCUCCCCUCCACAUUAAAAAAAG-UCUCGCUUUUGAUUCAGA---UUUCCGAUGAUCCGUUGGGUCAGGUCUGUCUGUAGGUUGAAACUUAUUGCAUUUUAAGUGCAUAA
....(((.(((...............(((((-.....)))))....((((---(..((..((((((...))))))))...))))).)))..)))......(((((.....)))))... ( -21.60)
>consensus
_____________________GUAAAAAACC_GCUCGCUUUUGAUGCAUU___UGCGCAGUGAUCUGUGCG___UAUUUUGUCUAUGGGCGGAAACUUAUUGCAUUUUAAGUGCAUAA
...................................(((((..((((((......((((((....))))))......(((((((....)))))))......))))))..)))))..... (-20.33 = -20.83 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:49:43 2006