Locus 3570

Sequence ID	3R_DroMel_CAF1
Location	9,669,623 – 9,669,841
Length	218
Max. P	0.941239

overview

Window 6

Location	9,669,623 – 9,669,730
Length	107
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	86.64
Mean single sequence MFE	-35.62
Consensus MFE	-33.21
Energy contribution	-33.77
Covariance contribution	0.56
Combinations/Pair	1.03
Mean z-score	-1.88
Structure conservation index	0.93
SVM decision value	1.32
SVM RNA-class probability	0.941239
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9669623 107 + 27905053
UAUAUUUAU-------------AUACGUAGUUAACCACUGUGCGAUGCGUCUUCGUGGAUAAUGCGGCGCUUUGCGAUUUGCAGUUGCAAAGUUUGUCCAAGACGCCAAUGCGAGUGGCG
.........-------------............(((((.((((..((((((...(((((((......((((((((((.....)))))))))))))))))))))))...))))))))).. ( -36.30)
>DroSec_CAF1 61444 107 + 1
UACAUUUAU-------------AUACGUAGUUAACCACGGUGCGAUGCGUCUUUGUGGAUAAUGCGGCGCUUUGCGAUUUGCAGUUGCAAAGUUUGUCCAAGACGCCAAUGCGAGUGGAG
.........-------------............((((..((((..((((((...(((((((......((((((((((.....)))))))))))))))))))))))...)))).)))).. ( -36.20)
>DroSim_CAF1 64336 107 + 1
UAUAUUUAU-------------AUACGUAGUUACCCACUGUGCGAUGCGUCUUCGUGGAUAAUGCGGCGCUUUGCGAUUUGCAGUUGCAAAGUUUGUCCAAGACGCCAAUGCGAGUGGAG
.........-------------............(((((.((((..((((((...(((((((......((((((((((.....)))))))))))))))))))))))...))))))))).. ( -36.80)
>DroYak_CAF1 66425 119 + 1
UAUAUGCAUAAUUUUAAAAGGUAUAACUCCUUAACCACAGUGCGGUGCGUCUUCGUGGAAAAUGCGGCGCUUUGCGGU-UGCAGUUGCAAAGUUUGUCCAAGACGCCAAUGCGAGUGGGA
.................((((.......))))..((((..((((..((((((...((((((((...(((..((((...-.)))).)))...)))).))))))))))...)))).)))).. ( -33.20)
>consensus
UAUAUUUAU_____________AUACGUAGUUAACCACUGUGCGAUGCGUCUUCGUGGAUAAUGCGGCGCUUUGCGAUUUGCAGUUGCAAAGUUUGUCCAAGACGCCAAUGCGAGUGGAG
..................................(((((.((((..((((((...(((((((......((((((((((.....)))))))))))))))))))))))...))))))))).. (-33.21 = -33.77 +   0.56)

alignment

secondary structure

dotplot

Window 7

Location	9,669,623 – 9,669,730
Length	107
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	86.64
Mean single sequence MFE	-27.38
Consensus MFE	-24.27
Energy contribution	-24.52
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.53
Structure conservation index	0.89
SVM decision value	0.38
SVM RNA-class probability	0.713038
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9669623 107 - 27905053
CGCCACUCGCAUUGGCGUCUUGGACAAACUUUGCAACUGCAAAUCGCAAAGCGCCGCAUUAUCCACGAAGACGCAUCGCACAGUGGUUAACUACGUAU-------------AUAAAUAUA
.((((((.((....((((((((((.....(((((....)))))..((........))....))))...))))))...))..))))))...........-------------......... ( -27.70)
>DroSec_CAF1 61444 107 - 1
CUCCACUCGCAUUGGCGUCUUGGACAAACUUUGCAACUGCAAAUCGCAAAGCGCCGCAUUAUCCACAAAGACGCAUCGCACCGUGGUUAACUACGUAU-------------AUAAAUGUA
........(((((.((((((((((.....(((((....)))))..((........))....))))...)))))).......(((((....)))))...-------------...))))). ( -26.40)
>DroSim_CAF1 64336 107 - 1
CUCCACUCGCAUUGGCGUCUUGGACAAACUUUGCAACUGCAAAUCGCAAAGCGCCGCAUUAUCCACGAAGACGCAUCGCACAGUGGGUAACUACGUAU-------------AUAAAUAUA
.((((((.((....((((((((((.....(((((....)))))..((........))....))))...))))))...))..))))))...........-------------......... ( -27.00)
>DroYak_CAF1 66425 119 - 1
UCCCACUCGCAUUGGCGUCUUGGACAAACUUUGCAACUGCA-ACCGCAAAGCGCCGCAUUUUCCACGAAGACGCACCGCACUGUGGUUAAGGAGUUAUACCUUUUAAAAUUAUGCAUAUA
..(((..(((....)))...)))........((((.....(-((((((..(((..((.(((((...))))).))..)))..)))))))((((.......)))).........)))).... ( -28.40)
>consensus
CUCCACUCGCAUUGGCGUCUUGGACAAACUUUGCAACUGCAAAUCGCAAAGCGCCGCAUUAUCCACGAAGACGCAUCGCACAGUGGUUAACUACGUAU_____________AUAAAUAUA
..((((..((....((((((((((.....(((((....)))))..((........))....))))...))))))...))...)))).................................. (-24.27 = -24.52 +   0.25)

alignment

secondary structure

dotplot

Window 8

Location	9,669,730 – 9,669,841
Length	111
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	82.52
Mean single sequence MFE	-30.10
Consensus MFE	-20.64
Energy contribution	-20.92
Covariance contribution	0.28
Combinations/Pair	1.12
Mean z-score	-1.76
Structure conservation index	0.69
SVM decision value	0.25
SVM RNA-class probability	0.655024
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9669730 111 - 27905053
-------GGGGAUGCGGAGACCUCGAGGCGCAUUCCUGCCACAAAACUGUUGCAAUUAAUUGCAUAAAAGUUCUAAAUUGUCAGCCAGAACCCCGCUCCAAUCCACCCACCAU--ACCGC
-------((((((..((((...((..((((((....))).((((((((..(((((....)))))....)))).....))))..))).))......)))).)))).))......--..... ( -25.90)
>DroSec_CAF1 61551 103 - 1
-------GGGGAUGUGGAGCCCUCGAGCCGCAUUCCUGCCACAAAACUGUUGCAAUUAAUUGCAUAAAAGUUCUAAAUUGUCAGCCAGAACCCCACUCCAAUCCAC----------CCAC
-------((((((((((..(....)..))))))..((((.((((((((..(((((....)))))....)))).....))))..).)))..))))............----------.... ( -23.80)
>DroSim_CAF1 64443 113 - 1
-------GGGGAUGUGGAGCCCUCGAGGCGCAUUCCUGCCACAAAACUGUUGCAAUUAAUUGCAUAAAAGUUCUAAAUUGUCAGCCAGAACCCCGCUCCAACCCACCCACCUCCACCCAC
-------(((....((((((......((((......))))......(((((((((((....((......))....))))).))).)))......)))))).....)))............ ( -28.90)
>DroEre_CAF1 62610 102 - 1
-----ACGGGGAAGUGGAGCCCUCGGGGCACAUUCCAGCCACAAAACUGUUGCAAUUAAUUGCGUAAAAGUUCUAAAUUGUCAGCCAGC-CCCCGCACC--CCCAC----------CAUC
-----..((((..((((.((((...)))).................(((((((((((....((......))....))))).))).))).-..))))..)--)))..----------.... ( -28.40)
>DroYak_CAF1 66544 109 - 1
GGGAGGUGGGGAGGUGGGGCCCUUGGGGCACAUUCCUGCCACAAAACUGUUGCAAUUAAUUGCAUAAAAGUUCUAAAUUGUCAGCCAGC-CCCCGCACCACCCCGC----------CAUC
....(((((((.((((((((...(((((((......))))((((((((..(((((....)))))....)))).....))))...)))))-)))...))).))))))----------)... ( -43.50)
>consensus
_______GGGGAUGUGGAGCCCUCGAGGCGCAUUCCUGCCACAAAACUGUUGCAAUUAAUUGCAUAAAAGUUCUAAAUUGUCAGCCAGAACCCCGCUCCAACCCAC__________CCAC
.......((((.(.(((.........((((......))))((((((((..(((((....)))))....)))).....))))...))).).)))).......................... (-20.64 = -20.92 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:04:30 2006