Locus 4755

Sequence ID	3L_DroMel_CAF1
Location	13,366,575 – 13,366,734
Length	159
Max. P	0.920269

overview

Window 4

Location	13,366,575 – 13,366,676
Length	101
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	88.42
Mean single sequence MFE	-38.02
Consensus MFE	-31.33
Energy contribution	-32.17
Covariance contribution	0.83
Combinations/Pair	1.09
Mean z-score	-1.97
Structure conservation index	0.82
SVM decision value	0.27
SVM RNA-class probability	0.663569
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13366575 101 + 23771897
--CGGGGUUGAAGACUAAUCUGCAACCUGCAGACUUUAGUCGCUGACACGGCACUCUGUUGGCUUCCGAUUUGGCCAGCGAACUUGGCCAGACUGC------AGCAGUA
--((((((....(((((((((((.....)))))..))))))((((...))))))))))...(((..((.(((((((((.....))))))))).)).------))).... ( -37.10)
>DroSec_CAF1 38178 101 + 1
--CGGGGUUGAAGACUAAUCUGCAACCUGCAGACUUUAGUCGCUGACAUGGCACUCUGUUGGCUUCCGAUUUGGCCAGCGAACUUGGCCAGGCUGC------AGCAGUA
--..........(((((((((((.....)))))..))))))((((...((((....((((((((........))))))))......)))).....)------))).... ( -37.30)
>DroSim_CAF1 38076 101 + 1
--CGGGGUUGAAGACUAAUCUGCAACCUGCAGACUUUAGUCGCUGACAUGGCACUCUGUUGGCUUCCGAUUUGGCCAGCGAACUUGGCCAGGCUGC------AGCAGUA
--..........(((((((((((.....)))))..))))))((((...((((....((((((((........))))))))......)))).....)------))).... ( -37.30)
>DroEre_CAF1 38574 109 + 1
CGGGCGGUUGCAGACUAAUCUGCAACCUGCAGACUUUAGUCGCUGACACGGCACUCUGUUGGCUUCCGAUUUGGCCAGCGAACUUGGCCAGGCUGCGCAAGUAGCAGUA
((((((((((((((....))))))))).)).(((....)))((..(((........)))..))..)))..((((((((.....))))))))(((((....))))).... ( -50.60)
>DroYak_CAF1 39641 103 + 1
CGGUAGGUUGCCGACUAAUCUUCCACCUGCAGACUUUAGUCGCUGACACGGCACUCUGUUGGCUUCCGAUUUGGCCAGCGAACUUGGCCAGGCUGC------AGCAGUA
.((.((((((.....)))))).))..((((((.........((..(((........)))..))......(((((((((.....)))))))))))))------))..... ( -33.00)
>DroAna_CAF1 37960 98 + 1
---GGUGAUGAAGACUAAUCUGCAACUUGCAGAC--UAGUCGUUGACAUGGCACUCUCAUGGCUUCCGAUUUGGCCAGCGAACUUGGCCAAACUGA------UGAUGUC
---(((.((((.(((((.(((((.....))))).--)))))(((.....)))....)))).)))..((.(((((((((.....))))))))).)).------....... ( -32.80)
>consensus
__CGGGGUUGAAGACUAAUCUGCAACCUGCAGACUUUAGUCGCUGACACGGCACUCUGUUGGCUUCCGAUUUGGCCAGCGAACUUGGCCAGGCUGC______AGCAGUA
.....((.....(((((((((((.....)))))..))))))(((((((........)))))))..))...((((((((.....))))))))(((((.......))))). (-31.33 = -32.17 +   0.83)

alignment

secondary structure

dotplot

Window 5

Location	13,366,612 – 13,366,706
Length	94
Sequences	6
Columns	100
Reading direction	forward
Mean pairwise identity	85.11
Mean single sequence MFE	-35.82
Consensus MFE	-26.57
Energy contribution	-27.43
Covariance contribution	0.86
Combinations/Pair	1.15
Mean z-score	-2.43
Structure conservation index	0.74
SVM decision value	0.25
SVM RNA-class probability	0.652277
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13366612 94 + 23771897
UCGCUGACACGGCACUCUGUUGGCUUCCGAUUUGGCCAGCGAACUUGGCCAGACUGC------AGCAGUAUUCGUUCUCUUGGCCAAGUCUAGUUAGCUG
..((((((..........(((((((........)))))))((.((((((((((..((------..........))..)).))))))))))..)))))).. ( -35.80)
>DroSec_CAF1 38215 94 + 1
UCGCUGACAUGGCACUCUGUUGGCUUCCGAUUUGGCCAGCGAACUUGGCCAGGCUGC------AGCAGUAUUCGUUCUGUUGGCCAAGUUUAGUUAGCUG
..((((((..........(((((((........)))))))(((((((((((......------.((((........))))))))))))))).)))))).. ( -38.81)
>DroSim_CAF1 38113 94 + 1
UCGCUGACAUGGCACUCUGUUGGCUUCCGAUUUGGCCAGCGAACUUGGCCAGGCUGC------AGCAGUAUUCGUUCUGUUGGCCAAGUUUAGUUAGCCG
..((((((..........(((((((........)))))))(((((((((((......------.((((........))))))))))))))).)))))).. ( -38.41)
>DroEre_CAF1 38613 97 + 1
UCGCUGACACGGCACUCUGUUGGCUUCCGAUUUGGCCAGCGAACUUGGCCAGGCUGCGCAAGUAGCAGUAUUCGUUCUCUUGGCCAAGUCUGAUUAG---
..((..(((........)))..)).((.(((((((((((.((((...((...(((((....))))).))....)))).).)))))))))).))....--- ( -40.10)
>DroYak_CAF1 39680 91 + 1
UCGCUGACACGGCACUCUGUUGGCUUCCGAUUUGGCCAGCGAACUUGGCCAGGCUGC------AGCAGUAUGCGUUCUCUUGGCCACGUCUGAUUAG---
...((((((.(((....((((((((........))))))))....((((((((.(((------(......))))....)))))))).))))).))))--- ( -31.50)
>DroAna_CAF1 37994 91 + 1
UCGUUGACAUGGCACUCUCAUGGCUUCCGAUUUGGCCAGCGAACUUGGCCAAACUGA------UGAUGUCUUGG-GCACUGAGUCAUGUCUGA--AGCAG
..(((((((((((.(.((((.(((.((((.(((((((((.....))))))))).)).------.)).))).)))-)....).))))))))...--))).. ( -30.30)
>consensus
UCGCUGACACGGCACUCUGUUGGCUUCCGAUUUGGCCAGCGAACUUGGCCAGGCUGC______AGCAGUAUUCGUUCUCUUGGCCAAGUCUAAUUAGC_G
..(((.....)))....((((((((........)))))))).(((((((((((((((.......)))))..........))))))))))........... (-26.57 = -27.43 +   0.86)

alignment

secondary structure

dotplot

Window 6

Location	13,366,642 – 13,366,734
Length	92
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	77.29
Mean single sequence MFE	-30.89
Consensus MFE	-17.82
Energy contribution	-17.21
Covariance contribution	-0.61
Combinations/Pair	1.36
Mean z-score	-2.09
Structure conservation index	0.58
SVM decision value	1.13
SVM RNA-class probability	0.920269
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13366642 92 + 23771897
UUUGGCCAGCGAACUUGGCCAGACUGC------AGCAGUA-UUCGUUCUCUUGGCC-------AAGUCUAG--UUAGCUGGUCACUGGUCAA--UGAAAUCUCUACCUGG-
.((((((((.(((((((((((((..((------.......-...))..)).)))))-------))))((((--....)))))).))))))))--................- ( -31.90)
>DroPse_CAF1 14747 105 + 1
UUUGGCCAGCGAACUUGGCCAAACUGU------UGUUGCUUUUUGUUCCAUCAGUCUCGCCCUCAGUCCAGCCUUAGCUGACGUCUGAUUCGUUUCCAAUCUCAACCUCAA
.((((..((((((...(((...((((.------((..((.....))..)).))))...))).((((.(((((....))))..).)))))))))).))))............ ( -27.00)
>DroSec_CAF1 38245 92 + 1
UUUGGCCAGCGAACUUGGCCAGGCUGC------AGCAGUA-UUCGUUCUGUUGGCC-------AAGUUUAG--UUAGCUGGUCACUGGUCAA--UGAAAUCUCUACCUGG-
..(((((((((((((((((((......------.((((..-......)))))))))-------))))))..--...))))))))(.(((...--.((....)).))).).- ( -32.21)
>DroSim_CAF1 38143 92 + 1
UUUGGCCAGCGAACUUGGCCAGGCUGC------AGCAGUA-UUCGUUCUGUUGGCC-------AAGUUUAG--UUAGCCGGUCACUGGUCAA--UGAAAUCUCUACCUGU-
.(((((.((((((((((((((......------.((((..-......)))))))))-------)))))).)--)).)))))..((.(((...--.((....)).))).))- ( -28.21)
>DroEre_CAF1 38643 94 + 1
UUUGGCCAGCGAACUUGGCCAGGCUGCGCAAGUAGCAGUA-UUCGUUCUCUUGGCC-------AAGUCUGA--UUAG----GCACUGGCCAG--UGAAAUCUCUACCUGG-
.((((((((.(.(((((((((((((((....)))))((..-......)).))))))-------))))....--....----.).))))))))--................- ( -36.50)
>DroYak_CAF1 39710 88 + 1
UUUGGCCAGCGAACUUGGCCAGGCUGC------AGCAGUA-UGCGUUCUCUUGGCC-------ACGUCUGA--UUAG----GCACUGGUCAA--UGAAAUCUCUACCUGG-
.((((((((......((((((((.(((------(......-))))....)))))))-------).((((..--..))----)).))))))))--................- ( -29.50)
>consensus
UUUGGCCAGCGAACUUGGCCAGGCUGC______AGCAGUA_UUCGUUCUCUUGGCC_______AAGUCUAG__UUAGCUGGUCACUGGUCAA__UGAAAUCUCUACCUGG_
.((((((((.....))))))))(((((.......)))))......(((..((((((..............................))))))...)))............. (-17.82 = -17.21 +  -0.61)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:32:22 2006