Locus 9855

Sequence ID	3R_DroMel_CAF1
Location	26,250,765 – 26,250,886
Length	121
Max. P	0.893992

overview

Window 9

Location	26,250,765 – 26,250,861
Length	96
Sequences	6
Columns	96
Reading direction	forward
Mean pairwise identity	83.33
Mean single sequence MFE	-38.80
Consensus MFE	-25.43
Energy contribution	-26.47
Covariance contribution	1.03
Combinations/Pair	1.19
Mean z-score	-2.54
Structure conservation index	0.66
SVM decision value	0.33
SVM RNA-class probability	0.692434
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26250765 96 + 27905053
GUCUUAUUAAGGGCGUUGACUGGCAACCACGCCUACUCAAUCCGAGUCGGGGUCUCCGUCCGGAUUGAGGCGUGUUAUUUGCCUCACCAGGCAUUA
(((((....)))))((((.....))))((((((...((((((((.(.(((.....))).))))))))))))))).....(((((....)))))... ( -37.70)
>DroSec_CAF1 940 96 + 1
GUCUUAUUAAAGGCGUGGACUGGCAACCACGCCGACUCAAUCCGAGUCGGGGUCUCCGGCCGGAUUGAGGCGUGUUAUUUGCCUCCCCAGGCAUUA
............((.(((...(((((.((((((...((((((((.(((((.....)))))))))))))))))))....)))))...))).)).... ( -45.00)
>DroSim_CAF1 933 96 + 1
GUCUUAUUAAAGGCGUAGACUGGCAACCACGCCGACUCAAUCCGAGUCGGGGUCUCCGGCCGGAUUGAGGCGUGUUAUUUGCCUCCCCAGGCAUUA
(((((....)))))((.....(((((.((((((...((((((((.(((((.....)))))))))))))))))))....))))).......)).... ( -40.30)
>DroEre_CAF1 1020 96 + 1
GGCGUAUCAAAGGCGUGGACUGGCAGCCACGCCUACUCAAUCCGAGUCGGGGUCUCCGGCCGGAUUGGGGCGUGUUAUUUGCCUCACCAGGCAUCA
.((((.....((((((((........)))))))).(((((((((.(((((.....))))))))))))))))))......(((((....)))))... ( -47.10)
>DroYak_CAF1 942 96 + 1
GUCUGAUCAAAGGCGUGGACUGGCAACCACGCCUACUCAAUCCGAGUCGGGGUCUCCGUCCAGAUUGAGGCGUGUUAAUUGCCUCCCCAGGCAUUU
(((((.....((((((((........))))))))..((((((.(.(.(((.....))).)).))))))((((.......))))....))))).... ( -36.20)
>DroAna_CAF1 997 96 + 1
GUCGCAAAAGUGGUGUAGAGUGACAAGCACGGCGGGCCAAUCCAAGACGGGGUCUCCUCCCCGAUUGUGGAGUAGAAAUAGAUUCCUCUGACAUUU
(((((((...((((.(...(((.....)))...).))))........(((((......))))).))))(((((........)))))...))).... ( -26.50)
>consensus
GUCUUAUUAAAGGCGUGGACUGGCAACCACGCCGACUCAAUCCGAGUCGGGGUCUCCGGCCGGAUUGAGGCGUGUUAUUUGCCUCCCCAGGCAUUA
............((.(.(...(((((.((((((...((((((((.(.(((.....))).)))))))))))))))....)))))...).).)).... (-25.43 = -26.47 +   1.03)

alignment

secondary structure

dotplot

Window 0

Location	26,250,765 – 26,250,861
Length	96
Sequences	6
Columns	96
Reading direction	reverse
Mean pairwise identity	83.33
Mean single sequence MFE	-35.63
Consensus MFE	-28.33
Energy contribution	-30.00
Covariance contribution	1.67
Combinations/Pair	1.17
Mean z-score	-2.08
Structure conservation index	0.80
SVM decision value	0.62
SVM RNA-class probability	0.802097
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26250765 96 - 27905053
UAAUGCCUGGUGAGGCAAAUAACACGCCUCAAUCCGGACGGAGACCCCGACUCGGAUUGAGUAGGCGUGGUUGCCAGUCAACGCCCUUAAUAAGAC
........((((.(((((....(((((((((((((((.(((.....))).).))))))))...)))))).)))))......))))........... ( -35.80)
>DroSec_CAF1 940 96 - 1
UAAUGCCUGGGGAGGCAAAUAACACGCCUCAAUCCGGCCGGAGACCCCGACUCGGAUUGAGUCGGCGUGGUUGCCAGUCCACGCCUUUAAUAAGAC
....((.((((..(((((....(((((((((((((((.(((.....))).).))))))))...)))))).)))))..)))).))............ ( -41.60)
>DroSim_CAF1 933 96 - 1
UAAUGCCUGGGGAGGCAAAUAACACGCCUCAAUCCGGCCGGAGACCCCGACUCGGAUUGAGUCGGCGUGGUUGCCAGUCUACGCCUUUAAUAAGAC
....((.((((..(((((....(((((((((((((((.(((.....))).).))))))))...)))))).)))))..)))).))............ ( -39.30)
>DroEre_CAF1 1020 96 - 1
UGAUGCCUGGUGAGGCAAAUAACACGCCCCAAUCCGGCCGGAGACCCCGACUCGGAUUGAGUAGGCGUGGCUGCCAGUCCACGCCUUUGAUACGCC
...(((((....)))))........((..((((((((.(((.....))).).)))))))...(((((((((.....).)))))))).......)). ( -36.20)
>DroYak_CAF1 942 96 - 1
AAAUGCCUGGGGAGGCAAUUAACACGCCUCAAUCUGGACGGAGACCCCGACUCGGAUUGAGUAGGCGUGGUUGCCAGUCCACGCCUUUGAUCAGAC
(((.((.((((..((((((...(((((((((((((((.(((.....))).).))))))))...))))))))))))..)))).)).)))........ ( -38.60)
>DroAna_CAF1 997 96 - 1
AAAUGUCAGAGGAAUCUAUUUCUACUCCACAAUCGGGGAGGAGACCCCGUCUUGGAUUGGCCCGCCGUGCUUGUCACUCUACACCACUUUUGCGAC
....(((((.((((.....))))..((((....(((((......)))))...))))))))).(((.(((..(((......))).)))....))).. ( -22.30)
>consensus
UAAUGCCUGGGGAGGCAAAUAACACGCCUCAAUCCGGCCGGAGACCCCGACUCGGAUUGAGUAGGCGUGGUUGCCAGUCCACGCCUUUAAUAAGAC
....((.((((..(((((....(((((((((((((((.(((.....))).).))))))))...)))))).)))))..)))).))............ (-28.33 = -30.00 +   1.67)

alignment

secondary structure

dotplot

Window 1

Location	26,250,786 – 26,250,886
Length	100
Sequences	6
Columns	100
Reading direction	forward
Mean pairwise identity	81.39
Mean single sequence MFE	-32.39
Consensus MFE	-23.40
Energy contribution	-24.68
Covariance contribution	1.28
Combinations/Pair	1.13
Mean z-score	-2.39
Structure conservation index	0.72
SVM decision value	0.98
SVM RNA-class probability	0.893992
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26250786 100 + 27905053
GGCAACCACGCCUACUCAAUCCGAGUCGGGGUCUCCGUCCGGAUUGAGGCGUGUUAUUUGCCUCACCAGGCAUUAAAAAUUAGAAAAAACGUACUAACCA
((....((((((...((((((((.(.(((.....))).))))))))))))))).....(((((....))))).........................)). ( -33.70)
>DroSec_CAF1 961 99 + 1
GGCAACCACGCCGACUCAAUCCGAGUCGGGGUCUCCGGCCGGAUUGAGGCGUGUUAUUUGCCUCCCCAGGCAUUAAAAAUCAGGAAAAAU-UACUAACCA
((....((((((...((((((((.(((((.....))))))))))))))))))).....(((((....)))))..................-......)). ( -37.00)
>DroSim_CAF1 954 99 + 1
GGCAACCACGCCGACUCAAUCCGAGUCGGGGUCUCCGGCCGGAUUGAGGCGUGUUAUUUGCCUCCCCAGGCAUUAAAAAUCAGGAAAAAU-UACUAACCA
((....((((((...((((((((.(((((.....))))))))))))))))))).....(((((....)))))..................-......)). ( -37.00)
>DroEre_CAF1 1041 99 + 1
GGCAGCCACGCCUACUCAAUCCGAGUCGGGGUCUCCGGCCGGAUUGGGGCGUGUUAUUUGCCUCACCAGGCAUCACAAAACAGGAAAAAU-UACGAUCCA
(((((.(((((((...(((((((.(((((.....)))))))))))))))))))....)))))......((.(((................-...))))). ( -37.01)
>DroYak_CAF1 963 99 + 1
GGCAACCACGCCUACUCAAUCCGAGUCGGGGUCUCCGUCCAGAUUGAGGCGUGUUAAUUGCCUCCCCAGGCAUUUAAAAUAAGAAAGAAG-UACGAUCUA
.((...((((((...((((((.(.(.(((.....))).)).))))))))))))((((.(((((....))))).))))............)-)........ ( -28.80)
>DroAna_CAF1 1018 97 + 1
GACAAGCACGGCGGGCCAAUCCAAGACGGGGUCUCCUCCCCGAUUGUGGAGUAGAAAUAGAUUCCUCUGACAUUUUAAAUCCAUAAAAAUAUUUU---CA
.........((....)).........(((((......))))).(((((((.(((((.((((....))))...)))))..))))))).........---.. ( -20.80)
>consensus
GGCAACCACGCCGACUCAAUCCGAGUCGGGGUCUCCGGCCGGAUUGAGGCGUGUUAUUUGCCUCCCCAGGCAUUAAAAAUCAGGAAAAAU_UACUAACCA
(((((.((((((...((((((((.(.(((.....))).)))))))))))))))....)))))...................................... (-23.40 = -24.68 +   1.28)

alignment

secondary structure

dotplot

Window 2

Location	26,250,786 – 26,250,886
Length	100
Sequences	6
Columns	100
Reading direction	reverse
Mean pairwise identity	81.39
Mean single sequence MFE	-31.91
Consensus MFE	-25.05
Energy contribution	-26.33
Covariance contribution	1.28
Combinations/Pair	1.13
Mean z-score	-1.23
Structure conservation index	0.79
SVM decision value	0.06
SVM RNA-class probability	0.563442
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26250786 100 - 27905053
UGGUUAGUACGUUUUUUCUAAUUUUUAAUGCCUGGUGAGGCAAAUAACACGCCUCAAUCCGGACGGAGACCCCGACUCGGAUUGAGUAGGCGUGGUUGCC
.(((....((..................(((((....))))).....(((((((((((((((.(((.....))).).))))))))...)))))))).))) ( -34.80)
>DroSec_CAF1 961 99 - 1
UGGUUAGUA-AUUUUUCCUGAUUUUUAAUGCCUGGGGAGGCAAAUAACACGCCUCAAUCCGGCCGGAGACCCCGACUCGGAUUGAGUCGGCGUGGUUGCC
.........-....(((((..............)))))(((((....(((((((((((((((.(((.....))).).))))))))...)))))).))))) ( -35.64)
>DroSim_CAF1 954 99 - 1
UGGUUAGUA-AUUUUUCCUGAUUUUUAAUGCCUGGGGAGGCAAAUAACACGCCUCAAUCCGGCCGGAGACCCCGACUCGGAUUGAGUCGGCGUGGUUGCC
.........-....(((((..............)))))(((((....(((((((((((((((.(((.....))).).))))))))...)))))).))))) ( -35.64)
>DroEre_CAF1 1041 99 - 1
UGGAUCGUA-AUUUUUCCUGUUUUGUGAUGCCUGGUGAGGCAAAUAACACGCCCCAAUCCGGCCGGAGACCCCGACUCGGAUUGAGUAGGCGUGGCUGCC
.(((.....-.....)))....((((..(((((....))))).))))(((((((((((((((.(((.....))).).))))))).)..))))))...... ( -33.30)
>DroYak_CAF1 963 99 - 1
UAGAUCGUA-CUUCUUUCUUAUUUUAAAUGCCUGGGGAGGCAAUUAACACGCCUCAAUCUGGACGGAGACCCCGACUCGGAUUGAGUAGGCGUGGUUGCC
......(((-.............((((.(((((....))))).))))(((((((((((((((.(((.....))).).))))))))...))))))..))). ( -32.00)
>DroAna_CAF1 1018 97 - 1
UG---AAAAUAUUUUUAUGGAUUUAAAAUGUCAGAGGAAUCUAUUUCUACUCCACAAUCGGGGAGGAGACCCCGUCUUGGAUUGGCCCGCCGUGCUUGUC
..---..........(((((.........(((((.((((.....))))..((((....(((((......)))))...)))))))))...)))))...... ( -20.10)
>consensus
UGGUUAGUA_AUUUUUCCUGAUUUUUAAUGCCUGGGGAGGCAAAUAACACGCCUCAAUCCGGCCGGAGACCCCGACUCGGAUUGAGUAGGCGUGGUUGCC
............................(((((....))))).....(((((((((((((((.(((.....))).).))))))))...))))))...... (-25.05 = -26.33 +   1.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:43:38 2006