Locus 3149

Sequence ID	2R_DroMel_CAF1
Location	10,757,382 – 10,757,508
Length	126
Max. P	0.913966

overview

Window 6

Location	10,757,382 – 10,757,475
Length	93
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	77.40
Mean single sequence MFE	-31.29
Consensus MFE	-18.07
Energy contribution	-18.15
Covariance contribution	0.08
Combinations/Pair	1.10
Mean z-score	-1.95
Structure conservation index	0.58
SVM decision value	0.75
SVM RNA-class probability	0.841350
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10757382 93 + 20766785
--------GUUAAAGUUCUUC---AGUGCAGCAUAAUGUGUUUUAAUCGCUGCGACAUGCUGCGC---UUUUGUGCUUACGACCGCAACAUGUUGCAAGUUGGAAUU-------------
--------.....((((((..---..((((((((...(((.......)))((((.......((((---....)))).......))))..))))))))....))))))------------- ( -25.64)
>DroSec_CAF1 23287 103 + 1
--------AUUAAAGUUCUUC---AG--UAGCAUAAGGGUUUUUAAUCGCUGCGACAUGUUGCGC---UUUUGUGCUUACGACCGCAACAUGUUGCA-GUUGGAAUUGUUUAAACCGAAG
--------.........((((---..--...(....)(((((.(((((((((((((((((((((.---..((((....)))).))))))))))))))-))..).))))...))))))))) ( -32.30)
>DroSim_CAF1 22851 95 + 1
--------AUUAAAGUUCUUC---AG--CAGCAUAAGGGUUUUUAAUCGCUGCGACAUGUUGCGC-----------UUACGACCGCAACAUGUUGCA-GUUGGAAUUGUUUAAACCGAAG
--------.........((((---..--...(....)(((((.(((((((((((((((((((((.-----------.......))))))))))))))-))..).))))...))))))))) ( -31.30)
>DroEre_CAF1 21181 114 + 1
GCAUU-UCAUAAAAGUUCUUC---AGUGCUGCAUGAGGGCUUUUCAUCGCUGCGACGUGCUGCGCAACUUUUGUGCUUGCGACCGCAACAUGUUGCA-GUUGGAUUUGUUUAAAGCG-AG
(((..-((..((((((.((((---(........)))))))))))....(((((((((((..(((((.....)))))((((....)))))))))))))-))..))..)))........-.. ( -34.90)
>DroYak_CAF1 21929 119 + 1
GGAUUUUUAUAAAAGUUCUGCAUGAGUGCUGCAUAAGGGGUUUUAAUCGCUGCGACAUGCUGUGCAACUUUUGUGCUUGCGACCGCAACAUGUUGCA-GUUGGAAUUGUUUAAAACGAAG
(((((((....)))))))((((.......))))((((.(((((((...(((((((((((..(..((.....))..)((((....)))))))))))))-))))))))).))))........ ( -32.30)
>consensus
________AUUAAAGUUCUUC___AGUGCAGCAUAAGGGGUUUUAAUCGCUGCGACAUGCUGCGC___UUUUGUGCUUACGACCGCAACAUGUUGCA_GUUGGAAUUGUUUAAACCGAAG
........................................(((((((...(((((((((.((((...................)))).))))))))).)))))))............... (-18.07 = -18.15 +   0.08)

alignment

secondary structure

dotplot

Window 7

Location	10,757,382 – 10,757,475
Length	93
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	77.40
Mean single sequence MFE	-24.82
Consensus MFE	-15.49
Energy contribution	-15.65
Covariance contribution	0.16
Combinations/Pair	1.08
Mean z-score	-1.85
Structure conservation index	0.62
SVM decision value	0.72
SVM RNA-class probability	0.833597
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10757382 93 - 20766785
-------------AAUUCCAACUUGCAACAUGUUGCGGUCGUAAGCACAAAA---GCGCAGCAUGUCGCAGCGAUUAAAACACAUUAUGCUGCACU---GAAGAACUUUAAC--------
-------------........(((.(((((((((((((((....).))....---.)))))))))).((((((..(((......)))))))))..)---)))).........-------- ( -22.60)
>DroSec_CAF1 23287 103 - 1
CUUCGGUUUAAACAAUUCCAAC-UGCAACAUGUUGCGGUCGUAAGCACAAAA---GCGCAACAUGUCGCAGCGAUUAAAAACCCUUAUGCUA--CU---GAAGAACUUUAAU--------
(((((((..............(-(((.(((((((((((((....).))....---.)))))))))).))))....(((......)))....)--))---)))).........-------- ( -26.30)
>DroSim_CAF1 22851 95 - 1
CUUCGGUUUAAACAAUUCCAAC-UGCAACAUGUUGCGGUCGUAA-----------GCGCAACAUGUCGCAGCGAUUAAAAACCCUUAUGCUG--CU---GAAGAACUUUAAU--------
(((((((..............(-(((.((((((((((.......-----------.)))))))))).))))....(((......)))....)--))---)))).........-------- ( -27.00)
>DroEre_CAF1 21181 114 - 1
CU-CGCUUUAAACAAAUCCAAC-UGCAACAUGUUGCGGUCGCAAGCACAAAAGUUGCGCAGCACGUCGCAGCGAUGAAAAGCCCUCAUGCAGCACU---GAAGAACUUUUAUGA-AAUGC
..-.(((((......(((...(-(((.((.((((((((.(....))((....))..))))))).)).)))).)))..)))))......(((.((..---(((....)))..)).-..))) ( -23.60)
>DroYak_CAF1 21929 119 - 1
CUUCGUUUUAAACAAUUCCAAC-UGCAACAUGUUGCGGUCGCAAGCACAAAAGUUGCACAGCAUGUCGCAGCGAUUAAAACCCCUUAUGCAGCACUCAUGCAGAACUUUUAUAAAAAUCC
.....................(-((((...((((((((((....).))....(((((((.....)).)))))...............)))))))....)))))................. ( -24.60)
>consensus
CUUCGGUUUAAACAAUUCCAAC_UGCAACAUGUUGCGGUCGUAAGCACAAAA___GCGCAGCAUGUCGCAGCGAUUAAAAACCCUUAUGCUGCACU___GAAGAACUUUAAU________
.......................(((.((((((((((...................)))))))))).))).................................................. (-15.49 = -15.65 +   0.16)

alignment

secondary structure

dotplot

Window 8

Location	10,757,411 – 10,757,508
Length	97
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	79.12
Mean single sequence MFE	-29.06
Consensus MFE	-17.91
Energy contribution	-17.99
Covariance contribution	0.08
Combinations/Pair	1.10
Mean z-score	-2.13
Structure conservation index	0.62
SVM decision value	1.09
SVM RNA-class probability	0.913966
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10757411 97 + 20766785
UUUUAAUCGCUGCGACAUGCUGCGC---UUUUGUGCUUACGACCGCAACAUGUUGCAAGUUGGAAUU-----------------GAAGAUUUCCUAAAAAAUAAACUUAAUAACUAG
(((((...(((((((((((.((((.---..((((....)))).)))).)))))))).))).((((..-----------------......))))))))).................. ( -22.70)
>DroSec_CAF1 23314 113 + 1
UUUUAAUCGCUGCGACAUGUUGCGC---UUUUGUGCUUACGACCGCAACAUGUUGCA-GUUGGAAUUGUUUAAACCGAAGCUCUGAGGAUUUUCGAAAAAAUAAACUUAAUAACUAG
........((((((((((((((((.---..((((....)))).))))))))))))))-)).....((((((....(((((.((....)).)))))...))))))............. ( -32.80)
>DroSim_CAF1 22878 105 + 1
UUUUAAUCGCUGCGACAUGUUGCGC-----------UUACGACCGCAACAUGUUGCA-GUUGGAAUUGUUUAAACCGAAGCUCUGAGGAUUUUCGACAAAAUAAACUUAAUAACUAG
........((((((((((((((((.-----------.......))))))))))))))-)).....((((((....(((((.((....)).)))))...))))))............. ( -31.80)
>DroEre_CAF1 21217 108 + 1
UUUUCAUCGCUGCGACGUGCUGCGCAACUUUUGUGCUUGCGACCGCAACAUGUUGCA-GUUGGAUUUGUUUAAAGCG-AGCUCUGAGGAAUUUCUAAAAAAUAAUCUUGC-------
((((((..(((((((((((..(((((.....)))))((((....)))))))))))))-)).(..(((((.....)))-))..))))))).....................------- ( -30.00)
>DroYak_CAF1 21969 116 + 1
UUUUAAUCGCUGCGACAUGCUGUGCAACUUUUGUGCUUGCGACCGCAACAUGUUGCA-GUUGGAAUUGUUUAAAACGAAGCUCUGGGGAUUUUUUAAAAAAUAUUCUUGUUAAAUAG
.((((((.(((((((((((..(..((.....))..)((((....)))))))))))))-)).(((((..(((((((.....((....))...)))))))....))))).))))))... ( -28.00)
>consensus
UUUUAAUCGCUGCGACAUGCUGCGC___UUUUGUGCUUACGACCGCAACAUGUUGCA_GUUGGAAUUGUUUAAACCGAAGCUCUGAGGAUUUUCUAAAAAAUAAACUUAAUAACUAG
(((((((...(((((((((.((((...................)))).))))))))).))))))).................................................... (-17.91 = -17.99 +   0.08)

alignment

secondary structure

dotplot

Window 9

Location	10,757,411 – 10,757,508
Length	97
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	79.12
Mean single sequence MFE	-24.81
Consensus MFE	-15.49
Energy contribution	-15.65
Covariance contribution	0.16
Combinations/Pair	1.08
Mean z-score	-1.73
Structure conservation index	0.62
SVM decision value	0.24
SVM RNA-class probability	0.647575
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10757411 97 - 20766785
CUAGUUAUUAAGUUUAUUUUUUAGGAAAUCUUC-----------------AAUUCCAACUUGCAACAUGUUGCGGUCGUAAGCACAAAA---GCGCAGCAUGUCGCAGCGAUUAAAA
.(((((.................((((......-----------------..))))...((((.(((((((((((((....).))....---.)))))))))).)))).)))))... ( -23.10)
>DroSec_CAF1 23314 113 - 1
CUAGUUAUUAAGUUUAUUUUUUCGAAAAUCCUCAGAGCUUCGGUUUAAACAAUUCCAAC-UGCAACAUGUUGCGGUCGUAAGCACAAAA---GCGCAACAUGUCGCAGCGAUUAAAA
.(((((.....(((((.....(((((..((....))..)))))..)))))........(-(((.(((((((((((((....).))....---.)))))))))).)))).)))))... ( -29.30)
>DroSim_CAF1 22878 105 - 1
CUAGUUAUUAAGUUUAUUUUGUCGAAAAUCCUCAGAGCUUCGGUUUAAACAAUUCCAAC-UGCAACAUGUUGCGGUCGUAA-----------GCGCAACAUGUCGCAGCGAUUAAAA
................(((.((((..........((((....))))............(-(((.((((((((((.......-----------.)))))))))).)))))))).))). ( -29.40)
>DroEre_CAF1 21217 108 - 1
-------GCAAGAUUAUUUUUUAGAAAUUCCUCAGAGCU-CGCUUUAAACAAAUCCAAC-UGCAACAUGUUGCGGUCGCAAGCACAAAAGUUGCGCAGCACGUCGCAGCGAUGAAAA
-------....................(((.((...(((-.(((((....)))....((-(((((....))))))).)).)))......(((((((.....).)))))))).))).. ( -22.20)
>DroYak_CAF1 21969 116 - 1
CUAUUUAACAAGAAUAUUUUUUAAAAAAUCCCCAGAGCUUCGUUUUAAACAAUUCCAAC-UGCAACAUGUUGCGGUCGCAAGCACAAAAGUUGCACAGCAUGUCGCAGCGAUUAAAA
..........................((((......((((((...............((-(((((....))))))))).))))......(((((((.....)).))))))))).... ( -20.06)
>consensus
CUAGUUAUUAAGUUUAUUUUUUAGAAAAUCCUCAGAGCUUCGGUUUAAACAAUUCCAAC_UGCAACAUGUUGCGGUCGUAAGCACAAAA___GCGCAGCAUGUCGCAGCGAUUAAAA
............................................................(((.((((((((((...................)))))))))).))).......... (-15.49 = -15.65 +   0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:48:40 2006