Locus 2268

Sequence ID	3R_DroMel_CAF1
Location	6,428,095 – 6,428,253
Length	158
Max. P	0.999776

overview

Window 1

Location	6,428,095 – 6,428,203
Length	108
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.16
Mean single sequence MFE	-43.32
Consensus MFE	-32.56
Energy contribution	-32.96
Covariance contribution	0.40
Combinations/Pair	1.11
Mean z-score	-3.14
Structure conservation index	0.75
SVM decision value	1.96
SVM RNA-class probability	0.984133
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6428095 108 + 27905053
GAAGUCACAUCGCAUAUUUGUGACAUAUGGCAGCAAGACAUUGUUGAUCUUGCUGCGGC-AUGGGA-----------AGAUGCUGCUGCGGCAACGUAGAUGCUGCUCUUGUCAGCGGGG
...((((((.........)))))).....(((((((((((....)).))))))))).((-.(((.(-----------(((.((..(((((....))))).....)))))).))))).... ( -43.70)
>DroSec_CAF1 191745 108 + 1
GAAGUCACAUCGCAUAUUUGUGACAUAUGGCAGCAAGACAUUGUUGAUCUUGCUGCGGC-AUGGGA-----------AGAAGCUGCUGCGGCAACGUGGAUGCUGCUCUUGUCAGCGGGG
...((((((.........)))))).....(((((((((((....)).))))))))).((-.(((.(-----------((((((..(..((....))..)..)))..)))).))))).... ( -43.00)
>DroSim_CAF1 216977 108 + 1
GAAGUCACAUCGCAUAUUUGUGACAUAUGGCAGCAAGACAUUGUUGAUCUUGCUGCGGC-AUGGGA-----------AGAAGCUGCUGCGGCAACGUGGAUGCUGCUCUUGUCAGCGGGG
...((((((.........)))))).....(((((((((((....)).))))))))).((-.(((.(-----------((((((..(..((....))..)..)))..)))).))))).... ( -43.00)
>DroEre_CAF1 203139 108 + 1
GAAGUCACAUCGCAUAUUUGUGACAUAUGGCAGCAAGACAUUGUUGAUCUGGCUGCGGCAAUGGGA-----------AGAUGUGGCUGCAGCAUCGUAGAUGUUGCUCUUGUCAGCGG-G
..((((((((((((....)))..(((.(.(((((.(((((....)).))).))))).)..)))...-----------.)))))))))((((((((...)))))))).((((....)))-) ( -37.60)
>DroYak_CAF1 196616 118 + 1
GAAGUCACAUCGCAUAUUUGUGACAUAUGGCAGCAAGACAUUGUUGAUCUUGCUGCGGG-AUGGGAUGUGGGAUUUGGGAUGUGG-UGCCGCAUCGUAGAUGUUGCUCUUGUCAGCGGGG
...((((((.........)))))).....(((((((((((....)).)))))))))..(-(..(((.(..(.(((((.((((((.-...)))))).))))).)..))))..))....... ( -49.30)
>consensus
GAAGUCACAUCGCAUAUUUGUGACAUAUGGCAGCAAGACAUUGUUGAUCUUGCUGCGGC_AUGGGA___________AGAUGCUGCUGCGGCAACGUAGAUGCUGCUCUUGUCAGCGGGG
...((((((.........)))))).....(((((((((((....)).))))))))).........................(((((.((((((.......))))))....).)))).... (-32.56 = -32.96 +   0.40)

alignment

secondary structure

dotplot

Window 2

Location	6,428,095 – 6,428,203
Length	108
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.16
Mean single sequence MFE	-33.18
Consensus MFE	-28.50
Energy contribution	-29.38
Covariance contribution	0.88
Combinations/Pair	1.04
Mean z-score	-3.30
Structure conservation index	0.86
SVM decision value	4.05
SVM RNA-class probability	0.999776
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6428095 108 - 27905053
CCCCGCUGACAAGAGCAGCAUCUACGUUGCCGCAGCAGCAUCU-----------UCCCAU-GCCGCAGCAAGAUCAACAAUGUCUUGCUGCCAUAUGUCACAAAUAUGCGAUGUGACUUC
....((((....(.(((((......)))))).)))).((((..-----------....))-)).((((((((((.......)))))))))).....((((((.........))))))... ( -36.20)
>DroSec_CAF1 191745 108 - 1
CCCCGCUGACAAGAGCAGCAUCCACGUUGCCGCAGCAGCUUCU-----------UCCCAU-GCCGCAGCAAGAUCAACAAUGUCUUGCUGCCAUAUGUCACAAAUAUGCGAUGUGACUUC
....((((....(.(((((......))))))....))))....-----------......-...((((((((((.......)))))))))).....((((((.........))))))... ( -34.40)
>DroSim_CAF1 216977 108 - 1
CCCCGCUGACAAGAGCAGCAUCCACGUUGCCGCAGCAGCUUCU-----------UCCCAU-GCCGCAGCAAGAUCAACAAUGUCUUGCUGCCAUAUGUCACAAAUAUGCGAUGUGACUUC
....((((....(.(((((......))))))....))))....-----------......-...((((((((((.......)))))))))).....((((((.........))))))... ( -34.40)
>DroEre_CAF1 203139 108 - 1
C-CCGCUGACAAGAGCAACAUCUACGAUGCUGCAGCCACAUCU-----------UCCCAUUGCCGCAGCCAGAUCAACAAUGUCUUGCUGCCAUAUGUCACAAAUAUGCGAUGUGACUUC
.-..((((.....((((.(......).)))).))))((((((.-----------..........(((((.((((.......)))).)))))(((((.......))))).))))))..... ( -28.70)
>DroYak_CAF1 196616 118 - 1
CCCCGCUGACAAGAGCAACAUCUACGAUGCGGCA-CCACAUCCCAAAUCCCACAUCCCAU-CCCGCAGCAAGAUCAACAAUGUCUUGCUGCCAUAUGUCACAAAUAUGCGAUGUGACUUC
..((((.....(((......))).....))))..-...............((((((....-...((((((((((.......))))))))))(((((.......))))).))))))..... ( -32.20)
>consensus
CCCCGCUGACAAGAGCAGCAUCUACGUUGCCGCAGCAGCAUCU___________UCCCAU_GCCGCAGCAAGAUCAACAAUGUCUUGCUGCCAUAUGUCACAAAUAUGCGAUGUGACUUC
....((((....(.(((((......)))))).))))............................((((((((((.......)))))))))).....((((((.........))))))... (-28.50 = -29.38 +   0.88)

alignment

secondary structure

dotplot

Window 3

Location	6,428,135 – 6,428,243
Length	108
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.86
Mean single sequence MFE	-40.42
Consensus MFE	-31.59
Energy contribution	-32.87
Covariance contribution	1.28
Combinations/Pair	1.03
Mean z-score	-1.71
Structure conservation index	0.78
SVM decision value	0.49
SVM RNA-class probability	0.757965
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6428135 108 + 27905053
UUGUUGAUCUUGCUGCGGC-AUGGGA-----------AGAUGCUGCUGCGGCAACGUAGAUGCUGCUCUUGUCAGCGGGGACUGUAAUUAAGUGCAGACUGCCCCGCUCAUUGAGAAUGU
..((((....(((.(((((-((....-----------..))))))).))).))))((((...))))(((((..(((((((.(((((......)))))....)))))))...))))).... ( -39.70)
>DroSec_CAF1 191785 107 + 1
UUGUUGAUCUUGCUGCGGC-AUGGGA-----------AGAAGCUGCUGCGGCAACGUGGAUGCUGCUCUUGUCAGCGGGGACUGUAAUUAAGUGCAGACUGCCCCGCUCAUUGAGAAUG-
..(((.((.((((((((((-(.(...-----------.....)))))))))))).)).)))....(((..((.(((((((.(((((......)))))....))))))).)).)))....- ( -41.30)
>DroSim_CAF1 217017 107 + 1
UUGUUGAUCUUGCUGCGGC-AUGGGA-----------AGAAGCUGCUGCGGCAACGUGGAUGCUGCUCUUGUCAGCGGGGACUGUAAUUAAGUGCAGACUGCCCCGCUCAUUGAGAAUG-
..(((.((.((((((((((-(.(...-----------.....)))))))))))).)).)))....(((..((.(((((((.(((((......)))))....))))))).)).)))....- ( -41.30)
>DroEre_CAF1 203179 107 + 1
UUGUUGAUCUGGCUGCGGCAAUGGGA-----------AGAUGUGGCUGCAGCAUCGUAGAUGUUGCUCUUGUCAGCGG-GACUGUAAUUAAGUGCAGACUGCCCCGCUCAUUGAGACUG-
......(((((((((((((.(((...-----------...))).))))))))....)))))....(((..((.(((((-(.(((((......))))).....)))))).)).)))....- ( -33.10)
>DroYak_CAF1 196656 117 + 1
UUGUUGAUCUUGCUGCGGG-AUGGGAUGUGGGAUUUGGGAUGUGG-UGCCGCAUCGUAGAUGUUGCUCUUGUCAGCGGGGACUGUAAUUAAGUGCAGACUGCCCCGCUCAUUGAGACCG-
...............((((-(..(((.(..(.(((((.((((((.-...)))))).))))).)..))))..))(((((((.(((((......)))))....)))))))........)))- ( -46.70)
>consensus
UUGUUGAUCUUGCUGCGGC_AUGGGA___________AGAUGCUGCUGCGGCAACGUAGAUGCUGCUCUUGUCAGCGGGGACUGUAAUUAAGUGCAGACUGCCCCGCUCAUUGAGAAUG_
..(((.((.((((((((((.........................)))))))))).)).)))....(((..((.(((((((.(((((......)))))....))))))).)).)))..... (-31.59 = -32.87 +   1.28)

alignment

secondary structure

dotplot

Window 4

Location	6,428,163 – 6,428,253
Length	90
Sequences	5
Columns	106
Reading direction	forward
Mean pairwise identity	81.07
Mean single sequence MFE	-33.14
Consensus MFE	-26.40
Energy contribution	-26.44
Covariance contribution	0.04
Combinations/Pair	1.09
Mean z-score	-1.57
Structure conservation index	0.80
SVM decision value	0.32
SVM RNA-class probability	0.686652
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6428163 90 + 27905053
UGCUGCUGCGGCAACGUAGAUGCUGCUCUUGUCAGCGGGGACUGUAAUUAAGUGCAGACUGCCCCGCUCAUUGAGAAUGUAGAGAGAGAG----------------
.....(((((....)))))...(((((((((..(((((((.(((((......)))))....)))))))...)))))..))))........---------------- ( -32.90)
>DroSec_CAF1 191813 86 + 1
AGCUGCUGCGGCAACGUGGAUGCUGCUCUUGUCAGCGGGGACUGUAAUUAAGUGCAGACUGCCCCGCUCAUUGAGAAUG----GAGAGAG----------------
(((..(..((....))..)..))).(((((...(((((((.(((((......)))))....)))))))(((.....)))----)))))..---------------- ( -33.00)
>DroSim_CAF1 217045 86 + 1
AGCUGCUGCGGCAACGUGGAUGCUGCUCUUGUCAGCGGGGACUGUAAUUAAGUGCAGACUGCCCCGCUCAUUGAGAAUG----GAGAGAG----------------
(((..(..((....))..)..))).(((((...(((((((.(((((......)))))....)))))))(((.....)))----)))))..---------------- ( -33.00)
>DroEre_CAF1 203208 101 + 1
UGUGGCUGCAGCAUCGUAGAUGUUGCUCUUGUCAGCGG-GACUGUAAUUAAGUGCAGACUGCCCCGCUCAUUGAGACUG----GAGAUCGGUAUGGUAUGGUAUUG
..((((.((((((((...))))))))....))))((((-(.(((((......))))).....)))))((((....((((----.....)))).....))))..... ( -29.30)
>DroYak_CAF1 196695 101 + 1
UGUGG-UGCCGCAUCGUAGAUGUUGCUCUUGUCAGCGGGGACUGUAAUUAAGUGCAGACUGCCCCGCUCAUUGAGACCG----GAGAGCGGAAUCGGAUGGUAUGG
.(((.-...)))(((((.(((.((((((((((((((((((.(((((......)))))....)))))))......)))..----)))))))).)))..))))).... ( -37.50)
>consensus
UGCUGCUGCGGCAACGUAGAUGCUGCUCUUGUCAGCGGGGACUGUAAUUAAGUGCAGACUGCCCCGCUCAUUGAGAAUG____GAGAGAG________________
.......((((((.......))))))(((((..(((((((.(((((......)))))....)))))))...))))).............................. (-26.40 = -26.44 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:31:16 2006