Locus 7260

Sequence ID	3R_DroMel_CAF1
Location	19,190,176 – 19,190,474
Length	298
Max. P	0.995008

overview

Window 5

Location	19,190,176 – 19,190,283
Length	107
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	79.15
Mean single sequence MFE	-24.78
Consensus MFE	-17.96
Energy contribution	-18.04
Covariance contribution	0.08
Combinations/Pair	1.24
Mean z-score	-1.39
Structure conservation index	0.72
SVM decision value	0.01
SVM RNA-class probability	0.536105
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19190176 107 - 27905053
UGGUUGGAUGGAUUGCAAUGGUAAAGCGGUUGCAUAAUCCCAUGUUAUGCAGUUUUGAAUUGAGCGAGAAAACUUCUUCAAAGCGAAGCGUGUUAAGGGUACAAACA
..(((((((....((((((.(.....).))))))..))))..(((...(((((((((..(((((.(((....))).)))))..)))))).))).......)))))). ( -25.70)
>DroSec_CAF1 2321 96 - 1
UGGUUAAAUGGAUUGCAAUGGUAAAGCAGUUGCAUAAUGCCAUGUUAUGCAGUUGUGAAUUGAGCGAGAAAACUUCUUCAAAGCGAAGCGUGUAA-----------C
..((((.(((..((((.........(((..((((((((.....))))))))..)))...(((((.(((....))).))))).))))..))).)))-----------) ( -23.50)
>DroSim_CAF1 2349 83 - 1
UGGUUGGAUGGAUUGCAAUGGUAAAGCAGUUGCAUAAUGCCAUGUUAUGCAGUUGUGAAUUGAGCGAGAAAACUUCUUCAA-------------A-----------C
..((((.(.....).))))......(((..((((((((.....))))))))..)))...(((((.(((....))).)))))-------------.-----------. ( -17.90)
>DroEre_CAF1 3519 106 - 1
UGGCUGGAUGGAUUGCAAUGUUGAAACAAUUGCAUAAUGCCAUGUUGUGCAGUUGUAAAUUGAGUGAGAAAACUUCUUCGAAGCGAAGCGUGCUAAGGGUACAU-UG
..(((.......((((.........(((((((((((((.....)))))))))))))...(((((.(((....))).))))).)))))))((((.....))))..-.. ( -27.51)
>DroYak_CAF1 6058 96 - 1
UGGUUGGAUGGAUUGCGAUGUUGGAGCAAUUGCAUAAUGCCAUGUUAUGCAGUUGCAAAUUGAGUGAGAAAACUUCUUCGAAGCGCAGCGUGUUAA-----------
......((((..(((((...((((((((((((((((((.....))))))))))))).....((((......)))).)))))..)))))..))))..----------- ( -29.30)
>consensus
UGGUUGGAUGGAUUGCAAUGGUAAAGCAGUUGCAUAAUGCCAUGUUAUGCAGUUGUGAAUUGAGCGAGAAAACUUCUUCAAAGCGAAGCGUGUUAA__________C
............((((.........(((((((((((((.....)))))))))))))...(((((.(((....))).))))).))))..................... (-17.96 = -18.04 +   0.08)

alignment

secondary structure

dotplot

Window 6

Location	19,190,216 – 19,190,323
Length	107
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	93.08
Mean single sequence MFE	-22.56
Consensus MFE	-20.26
Energy contribution	-19.58
Covariance contribution	-0.68
Combinations/Pair	1.21
Mean z-score	-1.17
Structure conservation index	0.90
SVM decision value	0.13
SVM RNA-class probability	0.600284
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19190216 107 - 27905053
AAGUCAAUUAAGAGAAAUGAAUUUUCGUAUAUGAACGGAUUGGUUGGAUGGAUUGCAAUGGUAAAGCGGUUGCAUAAUCCCAUGUUAUGCAGUUUUGAAUUGAGCGA
...((((((((((((((.....))))(((((..(((......)))((((....((((((.(.....).))))))..)))).....)))))..))))).))))).... ( -21.80)
>DroSec_CAF1 2350 107 - 1
AAGUCAAUUAAGAGAAAUGAAUUUUCGUAUAUGAACGGAUUGGUUAAAUGGAUUGCAAUGGUAAAGCAGUUGCAUAAUGCCAUGUUAUGCAGUUGUGAAUUGAGCGA
...((((((........(((...(((((......)))))....)))......((((....)))).(((..((((((((.....))))))))..))).)))))).... ( -20.00)
>DroSim_CAF1 2365 107 - 1
AAGUCAAUUAAGAGAAAUGAAUUUUCGUAUAUGAACGGAUUGGUUGGAUGGAUUGCAAUGGUAAAGCAGUUGCAUAAUGCCAUGUUAUGCAGUUGUGAAUUGAGCGA
....(((((..(((((.....)))))((......)).)))))(((.(((...((((....)))).(((..((((((((.....))))))))..)))..))).))).. ( -20.80)
>DroEre_CAF1 3558 107 - 1
AAGUCAAUUAAGAGAAAUGAAUUUUCGUAUAUGAACGGAUUGGCUGGAUGGAUUGCAAUGUUGAAACAAUUGCAUAAUGCCAUGUUGUGCAGUUGUAAAUUGAGUGA
.((((((((..(((((.....)))))((......)).)))))))).......(..(...(((...(((((((((((((.....))))))))))))).)))...)..) ( -24.70)
>DroYak_CAF1 6087 107 - 1
AAGUCAAUUAAGAGAAAUGAAUUUUCGUAUAUGAACGGAUUGGUUGGAUGGAUUGCGAUGUUGGAGCAAUUGCAUAAUGCCAUGUUAUGCAGUUGCAAAUUGAGUGA
.(.((((((..............(((((......)))))...((((.(.....).))))......(((((((((((((.....))))))))))))).)))))).).. ( -25.50)
>consensus
AAGUCAAUUAAGAGAAAUGAAUUUUCGUAUAUGAACGGAUUGGUUGGAUGGAUUGCAAUGGUAAAGCAGUUGCAUAAUGCCAUGUUAUGCAGUUGUGAAUUGAGCGA
...((((((..............(((((......)))))..........................(((((((((((((.....))))))))))))).)))))).... (-20.26 = -19.58 +  -0.68)

alignment

secondary structure

dotplot

Window 7

Location	19,190,283 – 19,190,402
Length	119
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	98.15
Mean single sequence MFE	-30.50
Consensus MFE	-27.27
Energy contribution	-27.13
Covariance contribution	-0.14
Combinations/Pair	1.03
Mean z-score	-2.39
Structure conservation index	0.89
SVM decision value	2.53
SVM RNA-class probability	0.995008
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19190283 119 - 27905053
GUUGCUCAAAAAGCAGCAAAUUUGUUGCCAGAUAUUAAUGUGGCUUUGUAAUUGGUUUUUCU-CAAGUCCAAGUCACGUUAAGUCAAUUAAGAGAAAUGAAUUUUCGUAUAUGAACGGAU
(((.(((.....((((((....))))))..(((.((((((((((((.(...((((......)-)))..).)))))))))))))))......))).))).....(((((......))))). ( -29.20)
>DroSec_CAF1 2417 118 - 1
GUUGCUCAAAAAGCAGCAAAU-UGUUGCCAGAUAUUAAUGUGGCUUUGUAAUUGGUUUUUCU-CAAGUCCAAGUCACGUUAAGUCAAUUAAGAGAAAUGAAUUUUCGUAUAUGAACGGAU
(((.(((.....(((((....-.)))))..(((.((((((((((((.(...((((......)-)))..).)))))))))))))))......))).))).....(((((......))))). ( -28.60)
>DroSim_CAF1 2432 118 - 1
GUUGCUCAAAAAGCAGCAAAU-UGUUGCCAGAUAUUAAUGUGGCUUUGUAAUUGGUUUUUCU-CAAGUCCAAGUCACGUUAAGUCAAUUAAGAGAAAUGAAUUUUCGUAUAUGAACGGAU
(((.(((.....(((((....-.)))))..(((.((((((((((((.(...((((......)-)))..).)))))))))))))))......))).))).....(((((......))))). ( -28.60)
>DroEre_CAF1 3625 118 - 1
GUUGCUCAAAAAGCAGCAAAU-UGUUGCCAGAUAUUAAUGUGGCUUUGUAAUUGGUUUUUCU-CAAGUCCAAGUCACGUUAAGUCAAUUAAGAGAAAUGAAUUUUCGUAUAUGAACGGAU
(((.(((.....(((((....-.)))))..(((.((((((((((((.(...((((......)-)))..).)))))))))))))))......))).))).....(((((......))))). ( -28.60)
>DroYak_CAF1 6154 119 - 1
GUUGCUCAAAAGGCAGCAAAU-UGUUGCCAGAUAUUAAUGUGGCUUUGUAAUUGGUUUUACUCCAAGUCCAAGUCACGUUAAGUCAAUUAAGAGAAAUGAAUUUUCGUAUAUGAACGGAU
(((.(((....((((((....-.)))))).(((.((((((((((((.(...((((.......))))..).)))))))))))))))......))).))).....(((((......))))). ( -35.30)
>DroAna_CAF1 8924 117 - 1
GUUGCUCAAAAGGCAGCAAAU-UGUUGCCAGAUAUUAAUGUGGCUUUGUAAUUGGUUUUUCU-CAAGUCCAAGUCACGUUAAGUCAAUUAAGAGAAAUGAAUUUUCGUAUAUGAACGAA-
(((.(((....((((((....-.)))))).(((.((((((((((((.(...((((......)-)))..).)))))))))))))))......))).))).....(((((......)))))- ( -32.70)
>consensus
GUUGCUCAAAAAGCAGCAAAU_UGUUGCCAGAUAUUAAUGUGGCUUUGUAAUUGGUUUUUCU_CAAGUCCAAGUCACGUUAAGUCAAUUAAGAGAAAUGAAUUUUCGUAUAUGAACGGAU
(((.(((.....((((((....))))))..(((.((((((((((((.(...(((.........)))..).)))))))))))))))......))).))).....(((((......))))). (-27.27 = -27.13 +  -0.14)

alignment

secondary structure

dotplot

Window 8

Location	19,190,323 – 19,190,442
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.65
Mean single sequence MFE	-31.32
Consensus MFE	-28.86
Energy contribution	-28.70
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-2.16
Structure conservation index	0.92
SVM decision value	2.42
SVM RNA-class probability	0.993773
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19190323 119 - 27905053
CUUAAUUAAAAUUUUGGUUGCAUGCCAGGCGCAAAAUUGUGUUGCUCAAAAAGCAGCAAAUUUGUUGCCAGAUAUUAAUGUGGCUUUGUAAUUGGUUUUUCU-CAAGUCCAAGUCACGUU
..............((((.....))))((((((((....(((((((.....)))))))..)))).)))).......((((((((((.(...((((......)-)))..).)))))))))) ( -32.10)
>DroSec_CAF1 2457 118 - 1
CUUAAUUAAAAUUUUGGUUGCAUGCCAGGCGCAAAAUUGUGUUGCUCAAAAAGCAGCAAAU-UGUUGCCAGAUAUUAAUGUGGCUUUGUAAUUGGUUUUUCU-CAAGUCCAAGUCACGUU
..............((((.....))))(((((((.....(((((((.....)))))))..)-)).)))).......((((((((((.(...((((......)-)))..).)))))))))) ( -30.50)
>DroSim_CAF1 2472 118 - 1
CUUAAUUAAAAUUUUGGUUGCAUGCCAGGCGCAAAAUUGUGUUGCUCAAAAAGCAGCAAAU-UGUUGCCAGAUAUUAAUGUGGCUUUGUAAUUGGUUUUUCU-CAAGUCCAAGUCACGUU
..............((((.....))))(((((((.....(((((((.....)))))))..)-)).)))).......((((((((((.(...((((......)-)))..).)))))))))) ( -30.50)
>DroEre_CAF1 3665 118 - 1
CUUAAUUAAAAUUUUGGUUGCAUGCCAGGCGCAAAAUUGUGUUGCUCAAAAAGCAGCAAAU-UGUUGCCAGAUAUUAAUGUGGCUUUGUAAUUGGUUUUUCU-CAAGUCCAAGUCACGUU
..............((((.....))))(((((((.....(((((((.....)))))))..)-)).)))).......((((((((((.(...((((......)-)))..).)))))))))) ( -30.50)
>DroYak_CAF1 6194 119 - 1
CUUAAUUAAAAUUUUGGUUGCAUGCCAGGCGCAAAAUUGUGUUGCUCAAAAGGCAGCAAAU-UGUUGCCAGAUAUUAAUGUGGCUUUGUAAUUGGUUUUACUCCAAGUCCAAGUCACGUU
..............((((.....))))(((((((.....(((((((.....)))))))..)-)).)))).......((((((((((.(...((((.......))))..).)))))))))) ( -33.00)
>consensus
CUUAAUUAAAAUUUUGGUUGCAUGCCAGGCGCAAAAUUGUGUUGCUCAAAAAGCAGCAAAU_UGUUGCCAGAUAUUAAUGUGGCUUUGUAAUUGGUUUUUCU_CAAGUCCAAGUCACGUU
..............((((.....))))((((((......(((((((.....)))))))....)).)))).......((((((((((.(...(((.........)))..).)))))))))) (-28.86 = -28.70 +  -0.16)

alignment

secondary structure

dotplot

Window 9

Location	19,190,362 – 19,190,474
Length	112
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	94.82
Mean single sequence MFE	-23.12
Consensus MFE	-21.00
Energy contribution	-21.44
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-1.71
Structure conservation index	0.91
SVM decision value	2.01
SVM RNA-class probability	0.985408
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19190362 112 - 27905053
AAAACA--ACCACCCCCAAUAGGAAAAUCAUUUUCUUAAUUAAAAUUUUGGUUGCAUGCCAGGCGCAAAAUUGUGUUGCUCAAAAAGCAGCAAAUUUGUUGCCAGAUAUUAAUG
....((--((((.......(((((((.....)))))))..........)))))).......((((((((....(((((((.....)))))))..)))).))))........... ( -25.13)
>DroSec_CAF1 2496 108 - 1
---ACA--ACCACCCCCAAUAGGAAAAUCAUUUUCUUAAUUAAAAUUUUGGUUGCAUGCCAGGCGCAAAAUUGUGUUGCUCAAAAAGCAGCAAAU-UGUUGCCAGAUAUUAAUG
---.((--((((.......(((((((.....)))))))..........)))))).......(((((((.....(((((((.....)))))))..)-)).))))........... ( -23.53)
>DroSim_CAF1 2511 108 - 1
---ACA--ACCACCCCCAAUAGGAAAAUCAUUUUCUUAAUUAAAAUUUUGGUUGCAUGCCAGGCGCAAAAUUGUGUUGCUCAAAAAGCAGCAAAU-UGUUGCCAGAUAUUAAUG
---.((--((((.......(((((((.....)))))))..........)))))).......(((((((.....(((((((.....)))))))..)-)).))))........... ( -23.53)
>DroEre_CAF1 3704 110 - 1
AAAACA--AGCACCCCCAAUA-CAAAAUGAUUUUCUUAAUUAAAAUUUUGGUUGCAUGCCAGGCGCAAAAUUGUGUUGCUCAAAAAGCAGCAAAU-UGUUGCCAGAUAUUAAUG
......--.(((...((((..-.....(((((.....))))).....)))).)))......(((((((.....(((((((.....)))))))..)-)).))))........... ( -20.50)
>DroYak_CAF1 6234 113 - 1
AAAACACAGCCACCCCCAAUAGCAAAAUGAUUUUCUUAAUUAAAAUUUUGGUUGCAUGCCAGGCGCAAAAUUGUGUUGCUCAAAAGGCAGCAAAU-UGUUGCCAGAUAUUAAUG
..(((((((............((((...((((((.......))))))....)))).(((.....)))...)))))))........((((((....-.))))))........... ( -22.90)
>consensus
AAAACA__ACCACCCCCAAUAGGAAAAUCAUUUUCUUAAUUAAAAUUUUGGUUGCAUGCCAGGCGCAAAAUUGUGUUGCUCAAAAAGCAGCAAAU_UGUUGCCAGAUAUUAAUG
...................(((((((.....)))))))(((((.((((((((.....))))((((((......(((((((.....)))))))....)).)))))))).))))). (-21.00 = -21.44 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:41:30 2006