Locus 104

Sequence ID	2R_DroMel_CAF1
Location	1,348,948 – 1,349,141
Length	193
Max. P	0.999568

overview

Window 8

Location	1,348,948 – 1,349,066
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.13
Mean single sequence MFE	-45.05
Consensus MFE	-39.98
Energy contribution	-40.78
Covariance contribution	0.80
Combinations/Pair	1.05
Mean z-score	-2.17
Structure conservation index	0.89
SVM decision value	2.97
SVM RNA-class probability	0.997960
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1348948 118 + 20766785
UGGGCGUGUCUGCGGGGUGUCUGCACAUAUUUAUGAGCAGCGAUGUGCUGCGACGUCGUCCGACGUUGAAUUAAUGAAAUACCUGCCAAGAUUUAUGUGCCAGCUGACUGGCACA--GGG
.......((((((((((((....)))...(((((..(((((.....)))))((((((....))))))......)))))...)))))..))))...((((((((....))))))))--... ( -42.40)
>DroSec_CAF1 67207 120 + 1
UGGGCGUGUCUGCGGGGUGUCUGCACAUAUUUAUGAGCAGCGAUGCGCUGCGACGUCGUCCGACGUUGAAUUAAUGAAAUACCUGCCAAGAUUUAUGUGCCAGCUGACUGGCACACGGGG
.(((((((((.((((.((((((((.(((....))).)))..))))).)))))))).)))))..(((((...))))).....((((..........((((((((....)))))))))))). ( -45.30)
>DroSim_CAF1 45342 120 + 1
UGGGCGUGUCUGCGGGGUGUCUGCACAUAUUUAUGAGCAGCGAUGCGCUGCGACGUCGUCCGACGUUGAAUUAAUGAAAUACCUGCCAAGAUUUAUGUGCCAGCUGACUGGCACACGGGG
.(((((((((.((((.((((((((.(((....))).)))..))))).)))))))).)))))..(((((...))))).....((((..........((((((((....)))))))))))). ( -45.30)
>DroEre_CAF1 47821 118 + 1
UGGGCGUGUCUGCGGGGUGUCUGCACAUAUUUAUGAGCAGUGAUGCGCUGCGACGUCGUCCGACGUGGAAUUAAUGAAAUACCUGCCACGAUUUAUGUGCCAGGUGACUGGCACA--GGG
.(((((((((.((((.((((((((.(((....))).)))..))))).)))))))).)))))..(((((.................))))).....((((((((....))))))))--... ( -52.73)
>DroYak_CAF1 35293 111 + 1
-------GUCUGCGGGGUGUCUGCACAUAUUUAUGAGCAGUGAUGCGGUGCGACGUCGCUUGACGUUGAAAUAAUGAAAUACCUGCCAAGAUUUAUGUGCCAGCUGACUGGCACA--GGG
-------((((((((((((....))).(((((....(((....)))....(((((((....))))))))))))........)))))..))))...((((((((....))))))))--... ( -39.50)
>consensus
UGGGCGUGUCUGCGGGGUGUCUGCACAUAUUUAUGAGCAGCGAUGCGCUGCGACGUCGUCCGACGUUGAAUUAAUGAAAUACCUGCCAAGAUUUAUGUGCCAGCUGACUGGCACA__GGG
.......((((((((((((....)))...(((((..((((((...))))))((((((....))))))......)))))...)))))..))))...((((((((....))))))))..... (-39.98 = -40.78 +   0.80)

alignment

secondary structure

dotplot

Window 9

Location	1,348,948 – 1,349,066
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.13
Mean single sequence MFE	-37.10
Consensus MFE	-33.26
Energy contribution	-33.86
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.46
Structure conservation index	0.90
SVM decision value	3.73
SVM RNA-class probability	0.999568
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1348948 118 - 20766785
CCC--UGUGCCAGUCAGCUGGCACAUAAAUCUUGGCAGGUAUUUCAUUAAUUCAACGUCGGACGACGUCGCAGCACAUCGCUGCUCAUAAAUAUGUGCAGACACCCCGCAGACACGCCCA
...--((((((((....)))))))).........(((.((((((..........(((((....))))).(((((.....)))))....)))))).))).........((......))... ( -37.00)
>DroSec_CAF1 67207 120 - 1
CCCCGUGUGCCAGUCAGCUGGCACAUAAAUCUUGGCAGGUAUUUCAUUAAUUCAACGUCGGACGACGUCGCAGCGCAUCGCUGCUCAUAAAUAUGUGCAGACACCCCGCAGACACGCCCA
....(((((((((....)))))))))........(((.((((((..........(((((....))))).((((((...))))))....)))))).))).........((......))... ( -39.50)
>DroSim_CAF1 45342 120 - 1
CCCCGUGUGCCAGUCAGCUGGCACAUAAAUCUUGGCAGGUAUUUCAUUAAUUCAACGUCGGACGACGUCGCAGCGCAUCGCUGCUCAUAAAUAUGUGCAGACACCCCGCAGACACGCCCA
....(((((((((....)))))))))........(((.((((((..........(((((....))))).((((((...))))))....)))))).))).........((......))... ( -39.50)
>DroEre_CAF1 47821 118 - 1
CCC--UGUGCCAGUCACCUGGCACAUAAAUCGUGGCAGGUAUUUCAUUAAUUCCACGUCGGACGACGUCGCAGCGCAUCACUGCUCAUAAAUAUGUGCAGACACCCCGCAGACACGCCCA
...--((((((((....)))))))).....((((((.((.(((.....))).))(((((....))))).)).(((.....((((.(((....))).))))......)))...)))).... ( -37.20)
>DroYak_CAF1 35293 111 - 1
CCC--UGUGCCAGUCAGCUGGCACAUAAAUCUUGGCAGGUAUUUCAUUAUUUCAACGUCAAGCGACGUCGCACCGCAUCACUGCUCAUAAAUAUGUGCAGACACCCCGCAGAC-------
...--((((((((....))))))))....((((((..(((..............(((((....)))))............((((.(((....))).))))..)))))).))).------- ( -32.30)
>consensus
CCC__UGUGCCAGUCAGCUGGCACAUAAAUCUUGGCAGGUAUUUCAUUAAUUCAACGUCGGACGACGUCGCAGCGCAUCGCUGCUCAUAAAUAUGUGCAGACACCCCGCAGACACGCCCA
.....((((((((....)))))))).........(((.((((((..........(((((....))))).(((((.....)))))....)))))).)))...................... (-33.26 = -33.86 +   0.60)

alignment

secondary structure

dotplot

Window 0

Location	1,348,988 – 1,349,101
Length	113
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.52
Mean single sequence MFE	-41.88
Consensus MFE	-29.74
Energy contribution	-31.34
Covariance contribution	1.60
Combinations/Pair	1.00
Mean z-score	-2.16
Structure conservation index	0.71
SVM decision value	0.38
SVM RNA-class probability	0.714407
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1348988 113 + 20766785
CGAUGUGCUGCGACGUCGUCCGACGUUGAAUUAAUGAAAUACCUGCCAAGAUUUAUGUGCCAGCUGACUGGCACA--GGGGAC-----ACACGCGUGAACGGGCGAAGGCGGGAAAAGAA
..........(((((((....))))))).............((((((........((((((((....))))))))--(....)-----...(((.(....).)))..))))))....... ( -40.70)
>DroSec_CAF1 67247 115 + 1
CGAUGCGCUGCGACGUCGUCCGACGUUGAAUUAAUGAAAUACCUGCCAAGAUUUAUGUGCCAGCUGACUGGCACACGGGGGAC-----ACACGCGUGAACGGGCGGGGGAGGGAAAAGAA
.....(.((.(((((((....))))))).............((((((....((..((((((((....))))))))..))(..(-----((....)))..).))))))..)).)....... ( -39.70)
>DroSim_CAF1 45382 115 + 1
CGAUGCGCUGCGACGUCGUCCGACGUUGAAUUAAUGAAAUACCUGCCAAGAUUUAUGUGCCAGCUGACUGGCACACGGGGGAC-----ACACGCGUGAACGGGCGGGGGAGGGAAAAGAA
.....(.((.(((((((....))))))).............((((((....((..((((((((....))))))))..))(..(-----((....)))..).))))))..)).)....... ( -39.70)
>DroEre_CAF1 47861 118 + 1
UGAUGCGCUGCGACGUCGUCCGACGUGGAAUUAAUGAAAUACCUGCCACGAUUUAUGUGCCAGGUGACUGGCACA--GGGGACACCCGACACACGUGGUCGGGCGGAGGAGCGAAAAGAA
.....((((.(....(((((((((..((.(((.....))).))...((((.....((((((((....))))))))--(((....)))......))))))))))))).).))))....... ( -52.30)
>DroYak_CAF1 35326 111 + 1
UGAUGCGGUGCGACGUCGCUUGACGUUGAAAUAAUGAAAUACCUGCCAAGAUUUAUGUGCCAGCUGACUGGCACA--GGGGAC-------ACACGUGAACUGGCGAGGGAGCGAAAAGAA
...(((....(((((((....))))))).............(((((((.(.((((((((((((....))))))).--(....)-------....)))))))))).)))..)))....... ( -37.00)
>consensus
CGAUGCGCUGCGACGUCGUCCGACGUUGAAUUAAUGAAAUACCUGCCAAGAUUUAUGUGCCAGCUGACUGGCACA__GGGGAC_____ACACGCGUGAACGGGCGGGGGAGGGAAAAGAA
..........(((((((....))))))).............((((((........((((((((....))))))))..(....)..................))))))............. (-29.74 = -31.34 +   1.60)

alignment

secondary structure

dotplot

Window 1

Location	1,349,028 – 1,349,141
Length	113
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.18
Mean single sequence MFE	-28.78
Consensus MFE	-20.30
Energy contribution	-20.86
Covariance contribution	0.56
Combinations/Pair	1.06
Mean z-score	-2.06
Structure conservation index	0.71
SVM decision value	0.27
SVM RNA-class probability	0.661524
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1349028 113 - 20766785
CUAAUAAAACGAUUCAGCACUAUUGCCCUGCAAAAUUAAUUUCUUUUCCCGCCUUCGCCCGUUCACGCGUGU-----GUCCCC--UGUGCCAGUCAGCUGGCACAUAAAUCUUGGCAGGU
................(((....)))(((((..................(((...(((........))).))-----).....--((((((((....)))))))).........))))). ( -28.00)
>DroSec_CAF1 67287 115 - 1
CUAAUAAAACGAUUCAGCACUAUUGCCCUGCAAAAUUAAUUUCUUUUCCCUCCCCCGCCCGUUCACGCGUGU-----GUCCCCCGUGUGCCAGUCAGCUGGCACAUAAAUCUUGGCAGGU
................(((....)))(((((........................(((.(((....))).))-----)......(((((((((....)))))))))........))))). ( -29.50)
>DroSim_CAF1 45422 115 - 1
CUAAUAAAACGAUUCAGCACUAUUGCCCUGCAAAAUUAAUUUCUUUUCCCUCCCCCGCCCGUUCACGCGUGU-----GUCCCCCGUGUGCCAGUCAGCUGGCACAUAAAUCUUGGCAGGU
................(((....)))(((((........................(((.(((....))).))-----)......(((((((((....)))))))))........))))). ( -29.50)
>DroEre_CAF1 47901 118 - 1
CUAAUACGACGUUUCACCACUAUUCCCCCACAAAAUUAAUUUCUUUUCGCUCCUCCGCCCGACCACGUGUGUCGGGUGUCCCC--UGUGCCAGUCACCUGGCACAUAAAUCGUGGCAGGU
........................((.((((........................(((((((((....).)))))))).....--((((((((....))))))))......))))..)). ( -33.80)
>DroYak_CAF1 35366 111 - 1
CUCAUAAAACGAUUCAGCACUAUUCCCCCACAAAAUUAAUUUCUUUUCGCUCCCUCGCCAGUUCACGUGU-------GUCCCC--UGUGCCAGUCAGCUGGCACAUAAAUCUUGGCAGGU
....................................................(((.(((((..((....)-------)..)..--((((((((....)))))))).......))))))). ( -23.10)
>consensus
CUAAUAAAACGAUUCAGCACUAUUGCCCUGCAAAAUUAAUUUCUUUUCCCUCCCCCGCCCGUUCACGCGUGU_____GUCCCC__UGUGCCAGUCAGCUGGCACAUAAAUCUUGGCAGGU
..........................(((((........................(((........)))................((((((((....)))))))).........))))). (-20.30 = -20.86 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:27:19 2006