Locus 2897

Sequence ID	3R_DroMel_CAF1
Location	7,775,494 – 7,775,694
Length	200
Max. P	0.996120

overview

Window 1

Location	7,775,494 – 7,775,614
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.00
Mean single sequence MFE	-36.26
Consensus MFE	-31.52
Energy contribution	-31.64
Covariance contribution	0.12
Combinations/Pair	1.07
Mean z-score	-1.27
Structure conservation index	0.87
SVM decision value	0.23
SVM RNA-class probability	0.645890
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7775494 120 - 27905053
UGUGCCCAUGGCCAUGUUGUCCAAGUCCAUGGACGUGGGCAUGCUUGUUGUAGCCCAAAUCGGCGUUUCCGUUUCCACCAGGAAACAUCUCUGCUUGUAGUUCGAAUAUGCUCUUUAAAU
.(((((((((.(((((...........))))).)))))))))((.((((...(((......)))......((((((....))))))..................)))).))......... ( -35.90)
>DroSec_CAF1 72724 120 - 1
UGUGCCCAUGGCCAUGUUGUCCAUGUCCGUGGACGUGGGCGUGCUUGUUGUAGCCCAAAUCGGCGUUUCCAUUUCCACCAGGAAACAUCUCUGCUUGUAGUUCGAAUAUGCUCUUUAAAU
...((((((((.((((.....)))).)))))((..(((((.(((.....))))))))..)))))((((((..........))))))......((.(((.......))).))......... ( -35.30)
>DroSim_CAF1 75967 120 - 1
UGUGCCCAUGGCCAUGUUGUCCGUGCCCGUGGACGUGGGCGUGCUUGUUGUAGCCCAAAUCGGCGUUUCCAUUUCCACCAGGAAACAUCUCUGCUUGUAGUUCGAAUAUGCUCUUUAAAU
...((((((((.((((.....)))).)))))((..(((((.(((.....))))))))..)))))((((((..........))))))......((.(((.......))).))......... ( -34.90)
>DroEre_CAF1 73172 119 - 1
UGUGCCCAUGGCCAUGUUGCCCGUGUCCAUGGACAUGGGCGUGCUUGUUGUAGCCCAAAUCGGCGUUUCCAUUUCCACCAGGAAACAUCUCUGCUU-UAGCUUGAAUAUGUUUUUUGAAU
.(((...((((..((((((((((((((....)))))))))(.(((......))).).....)))))..))))...)))((((((((((.((.((..-..))..))..))))))))))... ( -39.70)
>DroYak_CAF1 73552 120 - 1
UGUGGCCAUGGCCAUGUUGUCCGUGUCCAUGGACGUGGGCAUGCUUGUUGUAACCCAAAUCGGCGUUUCCGUUUCCACCGGGAAACAUCUCUGCUUGUAUCUUGAUUAUGCUUUUAGAAU
.(((((....)))))...((((((....))))))..(((.(((((.(((........))).))))).)))((((((....))))))...((((...((((.......))))...)))).. ( -35.50)
>consensus
UGUGCCCAUGGCCAUGUUGUCCGUGUCCAUGGACGUGGGCGUGCUUGUUGUAGCCCAAAUCGGCGUUUCCAUUUCCACCAGGAAACAUCUCUGCUUGUAGUUCGAAUAUGCUCUUUAAAU
...((((((((.((((.....)))).)))))((..(((((.(((.....))))))))..)))))((((((..........)))))).................................. (-31.52 = -31.64 +   0.12)

alignment

secondary structure

dotplot

Window 2

Location	7,775,534 – 7,775,654
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.67
Mean single sequence MFE	-39.94
Consensus MFE	-36.64
Energy contribution	-36.80
Covariance contribution	0.16
Combinations/Pair	1.15
Mean z-score	-1.88
Structure conservation index	0.92
SVM decision value	2.66
SVM RNA-class probability	0.996120
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7775534 120 + 27905053
UGGUGGAAACGGAAACGCCGAUUUGGGCUACAACAAGCAUGCCCACGUCCAUGGACUUGGACAACAUGGCCAUGGGCACAACCAUAAUCACAAUCAGUUCCUGGCGCAGCCCCCACCACC
((((((....((...((((((((((((((......))).((((((.(.(((((...........))))).).))))))...))).))))((.....))....))))...)).)))))).. ( -42.10)
>DroSec_CAF1 72764 120 + 1
UGGUGGAAAUGGAAACGCCGAUUUGGGCUACAACAAGCACGCCCACGUCCACGGACAUGGACAACAUGGCCAUGGGCACAACCAUAAUCACACUCAGUUCCUGGCGCAGCCCCCGCCGCC
.(((((....((...(((((...(((((............))))).(((((.((.((((.....)))).)).)))))........................)))))...))....))))) ( -40.30)
>DroSim_CAF1 76007 120 + 1
UGGUGGAAAUGGAAACGCCGAUUUGGGCUACAACAAGCACGCCCACGUCCACGGGCACGGACAACAUGGCCAUGGGCACAACCAUAAUCACACUCAGUUCCUGGCGCAGCCCCCGCCGCC
.(((((....((...((((((((((((((......)))..(((((((....))(((.((.......))))).)))))....))).))))((.....))....))))...))....))))) ( -38.90)
>DroEre_CAF1 73211 120 + 1
UGGUGGAAAUGGAAACGCCGAUUUGGGCUACAACAAGCACGCCCAUGUCCAUGGACACGGGCAACAUGGCCAUGGGCACAAUCAUAAUCACAAUCAGUUCCUGGCACAGCCCCCGCCGCC
.(((((....(....)........(((((...........((((.((((....)))).))))......((((.((((...................)))).))))..))))))))))... ( -42.41)
>DroYak_CAF1 73592 120 + 1
CGGUGGAAACGGAAACGCCGAUUUGGGUUACAACAAGCAUGCCCACGUCCAUGGACACGGACAACAUGGCCAUGGCCACAACCAUAAUCACAAUCAGUUCCUGGCACAGCCCCCGCCGCC
((((((....((((..((((...(((((............))))).(((....))).))).)....((((....))))...................)))).(((...))).)))))).. ( -36.00)
>consensus
UGGUGGAAAUGGAAACGCCGAUUUGGGCUACAACAAGCACGCCCACGUCCAUGGACACGGACAACAUGGCCAUGGGCACAACCAUAAUCACAAUCAGUUCCUGGCGCAGCCCCCGCCGCC
((((((....(....)((((...(((((............))))).((((((((.((.(.....).)).))))))))........................)))).......)))))).. (-36.64 = -36.80 +   0.16)

alignment

secondary structure

dotplot

Window 3

Location	7,775,534 – 7,775,654
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.67
Mean single sequence MFE	-48.84
Consensus MFE	-43.02
Energy contribution	-42.82
Covariance contribution	-0.20
Combinations/Pair	1.15
Mean z-score	-1.47
Structure conservation index	0.88
SVM decision value	0.98
SVM RNA-class probability	0.894273
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7775534 120 - 27905053
GGUGGUGGGGGCUGCGCCAGGAACUGAUUGUGAUUAUGGUUGUGCCCAUGGCCAUGUUGUCCAAGUCCAUGGACGUGGGCAUGCUUGUUGUAGCCCAAAUCGGCGUUUCCGUUUCCACCA
(((((..(.((..(((((.(((.....(((.(((((((((..(....)..))))))..)))))).)))...((..(((((.(((.....))))))))..)))))))..)).)..))))). ( -52.80)
>DroSec_CAF1 72764 120 - 1
GGCGGCGGGGGCUGCGCCAGGAACUGAGUGUGAUUAUGGUUGUGCCCAUGGCCAUGUUGUCCAUGUCCGUGGACGUGGGCGUGCUUGUUGUAGCCCAAAUCGGCGUUUCCAUUUCCACCA
...((.((((((((((.((((.((..........((((((..(....)..))))))..(((((((((....))))))))))).)))).)))))))).....((.....))....)).)). ( -50.60)
>DroSim_CAF1 76007 120 - 1
GGCGGCGGGGGCUGCGCCAGGAACUGAGUGUGAUUAUGGUUGUGCCCAUGGCCAUGUUGUCCGUGCCCGUGGACGUGGGCGUGCUUGUUGUAGCCCAAAUCGGCGUUUCCAUUUCCACCA
.(.((((.((((.(((((((...))).))))...((((((..(....)..))))))..)))).)))))(((((.(((((..((((.(((........))).))))..))))).))))).. ( -47.40)
>DroEre_CAF1 73211 120 - 1
GGCGGCGGGGGCUGUGCCAGGAACUGAUUGUGAUUAUGAUUGUGCCCAUGGCCAUGUUGCCCGUGUCCAUGGACAUGGGCGUGCUUGUUGUAGCCCAAAUCGGCGUUUCCAUUUCCACCA
...((.((((((((.((((((.((.(((..(....)..)))))..)).))))((.((((((((((((....)))))))))).)).))...)))))).....((.....))....)).)). ( -44.90)
>DroYak_CAF1 73592 120 - 1
GGCGGCGGGGGCUGUGCCAGGAACUGAUUGUGAUUAUGGUUGUGGCCAUGGCCAUGUUGUCCGUGUCCAUGGACGUGGGCAUGCUUGUUGUAACCCAAAUCGGCGUUUCCGUUUCCACCG
((..((((..((...(((....((.....))((((..(((((..((((((.((((...((((((....)))))))))).))))...))..)))))..)))))))))..))))..)).... ( -48.50)
>consensus
GGCGGCGGGGGCUGCGCCAGGAACUGAUUGUGAUUAUGGUUGUGCCCAUGGCCAUGUUGUCCGUGUCCAUGGACGUGGGCGUGCUUGUUGUAGCCCAAAUCGGCGUUUCCAUUUCCACCA
...((.(((((((((..((((.............((((((..(....)..)))))).((((((((((....))))))))))..))))..))))))).....((.....))....)).)). (-43.02 = -42.82 +  -0.20)

alignment

secondary structure

dotplot

Window 4

Location	7,775,574 – 7,775,694
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.08
Mean single sequence MFE	-43.43
Consensus MFE	-33.00
Energy contribution	-33.12
Covariance contribution	0.12
Combinations/Pair	1.10
Mean z-score	-2.19
Structure conservation index	0.76
SVM decision value	0.97
SVM RNA-class probability	0.892427
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7775574 120 + 27905053
GCCCACGUCCAUGGACUUGGACAACAUGGCCAUGGGCACAACCAUAAUCACAAUCAGUUCCUGGCGCAGCCCCCACCACCCCCCACACAUUUUUCACUGCCCUCCGGGGGCGGUCAGGGC
((((..(((((......)))))....(((((((((......))))...........((((((((.((((...........................))))...))))))))))))))))) ( -41.33)
>DroSec_CAF1 72804 120 + 1
GCCCACGUCCACGGACAUGGACAACAUGGCCAUGGGCACAACCAUAAUCACACUCAGUUCCUGGCGCAGCCCCCGCCGCCCCCCACACAUUUUCCAAUGCCCCCGGGCGGCGGUCAGGGC
(((((.(((((.((.((((.....)))).)).)))))............((.....))...))).)).(((((((((((((......((((....)))).....)))))))))...)))) ( -46.10)
>DroSim_CAF1 76047 120 + 1
GCCCACGUCCACGGGCACGGACAACAUGGCCAUGGGCACAACCAUAAUCACACUCAGUUCCUGGCGCAGCCCCCGCCGCCCCCCACACAUUUUCCAAUGCCCCCGGGCGGCGGUCAGGGC
((((........((((..(.....).((((((.((((...................)))).)))).))))))(((((((((......((((....)))).....)))))))))...)))) ( -44.41)
>DroEre_CAF1 73251 120 + 1
GCCCAUGUCCAUGGACACGGGCAACAUGGCCAUGGGCACAAUCAUAAUCACAAUCAGUUCCUGGCACAGCCCCCGCCGCCACACACACAUUUUCCAAUGCCCCCGGGCGGGGGUCAGGGU
(((((((.(((((...........))))).))))))).....................(((((.....((((((((((.....)...((((....))))......)))))))))))))). ( -44.70)
>DroYak_CAF1 73632 120 + 1
GCCCACGUCCAUGGACACGGACAACAUGGCCAUGGCCACAACCAUAAUCACAAUCAGUUCCUGGCACAGCCCCCGCCGCCACCCCCUCAUUUUGCAAUGCCCCCGGGCGGGGGUCAGGGC
((((..(((((.((((..(.....).((((....))))..................)))).))).)).(((((((((............................)))))))))..)))) ( -40.59)
>consensus
GCCCACGUCCAUGGACACGGACAACAUGGCCAUGGGCACAACCAUAAUCACAAUCAGUUCCUGGCGCAGCCCCCGCCGCCCCCCACACAUUUUCCAAUGCCCCCGGGCGGCGGUCAGGGC
((((..((((........))))....(((((..((((....(((.....((.....))...)))....))))...(((((.......((((....))))......))))).))))))))) (-33.00 = -33.12 +   0.12)

alignment

secondary structure

dotplot

Window 5

Location	7,775,574 – 7,775,694
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.08
Mean single sequence MFE	-56.16
Consensus MFE	-47.20
Energy contribution	-48.80
Covariance contribution	1.60
Combinations/Pair	1.15
Mean z-score	-1.93
Structure conservation index	0.84
SVM decision value	1.65
SVM RNA-class probability	0.969927
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7775574 120 - 27905053
GCCCUGACCGCCCCCGGAGGGCAGUGAAAAAUGUGUGGGGGGUGGUGGGGGCUGCGCCAGGAACUGAUUGUGAUUAUGGUUGUGCCCAUGGCCAUGUUGUCCAAGUCCAUGGACGUGGGC
(((((.(((((((((...(.(((.(....).))).).))))))))).))))).((((((...((.....)).....))).)))(((((((.(((((...........))))).))))))) ( -56.60)
>DroSec_CAF1 72804 120 - 1
GCCCUGACCGCCGCCCGGGGGCAUUGGAAAAUGUGUGGGGGGCGGCGGGGGCUGCGCCAGGAACUGAGUGUGAUUAUGGUUGUGCCCAUGGCCAUGUUGUCCAUGUCCGUGGACGUGGGC
((((...(((((((((..(.(((((....))))).)...))))))))))))).(((((((...))).))))...((((((..(....)..))))))..(((((((((....))))))))) ( -61.40)
>DroSim_CAF1 76047 120 - 1
GCCCUGACCGCCGCCCGGGGGCAUUGGAAAAUGUGUGGGGGGCGGCGGGGGCUGCGCCAGGAACUGAGUGUGAUUAUGGUUGUGCCCAUGGCCAUGUUGUCCGUGCCCGUGGACGUGGGC
((((((.(((((((((..(.(((((....))))).)...)))))))))((((.(((((((...))).))))(((((((((..(....)..))))))..)))...)))).....)).)))) ( -56.60)
>DroEre_CAF1 73251 120 - 1
ACCCUGACCCCCGCCCGGGGGCAUUGGAAAAUGUGUGUGUGGCGGCGGGGGCUGUGCCAGGAACUGAUUGUGAUUAUGAUUGUGCCCAUGGCCAUGUUGCCCGUGUCCAUGGACAUGGGC
.......((((((((((.(.(((((....))))).).)).))))).)))(((((((...((.((.(((..(....)..))))).))))))))).....(((((((((....))))))))) ( -54.70)
>DroYak_CAF1 73632 120 - 1
GCCCUGACCCCCGCCCGGGGGCAUUGCAAAAUGAGGGGGUGGCGGCGGGGGCUGUGCCAGGAACUGAUUGUGAUUAUGGUUGUGGCCAUGGCCAUGUUGUCCGUGUCCAUGGACGUGGGC
(((.(.(((((((((....)))(((....)))..)))))).).)))...((((((((((.((..((((....))))...)).))).))))))).....(((((((((....))))))))) ( -51.50)
>consensus
GCCCUGACCGCCGCCCGGGGGCAUUGGAAAAUGUGUGGGGGGCGGCGGGGGCUGCGCCAGGAACUGAUUGUGAUUAUGGUUGUGCCCAUGGCCAUGUUGUCCGUGUCCAUGGACGUGGGC
.(((((.((((((((((...(((((....))))).)))))))))))))))((((.((((((.((.((((((....))))))))..)).)))))).)).(((((((((....))))))))) (-47.20 = -48.80 +   1.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:47:22 2006