Locus 2490

Sequence ID	3L_DroMel_CAF1
Location	6,984,012 – 6,984,239
Length	227
Max. P	0.986777

overview

Window 9

Location	6,984,012 – 6,984,132
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	97.77
Mean single sequence MFE	-29.53
Consensus MFE	-28.81
Energy contribution	-28.37
Covariance contribution	-0.44
Combinations/Pair	1.06
Mean z-score	-1.59
Structure conservation index	0.98
SVM decision value	0.26
SVM RNA-class probability	0.657020
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6984012 120 - 23771897
AAUGACAUCAUUAGGCGCCAAAAACAAACAGCCAUACAAAUUGAACAAUCCCCCCUAAAAGGGGAAUGUGAUUUUCAAGCAUUAUCAUACGAAUUCCUGGCGAUUUUGGUGGCGUGUCUU
((((....))))..((((((....((((..((((..............(((((.......))))).((((((...........))))))........))))...)))).))))))..... ( -30.20)
>DroSec_CAF1 53831 118 - 1
AAUGGCAUCAUUAGGCGCCAAAAACAAACAGCCAUACAAAUUGAACAAUCCCCCC--AAAGGGGAAUGUGAUUUUCAAGCAUUAUCAUACGAAUUCCUGGCGAUUCUGGUGGCGUGUCUU
...(((((((((((.(((((..........((.....(((((..(((.(((((..--...))))).))))))))....))....((....)).....)))))...))))))..))))).. ( -29.20)
>DroSim_CAF1 53601 118 - 1
AAUGGCAUCAUUAGGCGCCAAAAACAAACAGCCAUACAAAUUGAACAAUCCCCCC--AAAGGGGAAUGUGAUUUUCAAGCAUUAUCAUACGAAUUCCUGGCGAUUCUGGUGGCGUGUCUU
...(((((((((((.(((((..........((.....(((((..(((.(((((..--...))))).))))))))....))....((....)).....)))))...))))))..))))).. ( -29.20)
>consensus
AAUGGCAUCAUUAGGCGCCAAAAACAAACAGCCAUACAAAUUGAACAAUCCCCCC__AAAGGGGAAUGUGAUUUUCAAGCAUUAUCAUACGAAUUCCUGGCGAUUCUGGUGGCGUGUCUU
...(((((((((((.(((((..........((.....(((((..(((.(((((.......))))).))))))))....))....((....)).....)))))...))))))..))))).. (-28.81 = -28.37 +  -0.44)

alignment

secondary structure

dotplot

Window 0

Location	6,984,052 – 6,984,172
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	95.25
Mean single sequence MFE	-42.77
Consensus MFE	-40.06
Energy contribution	-40.07
Covariance contribution	0.00
Combinations/Pair	1.05
Mean z-score	-3.34
Structure conservation index	0.94
SVM decision value	2.02
SVM RNA-class probability	0.985842
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6984052 120 + 23771897
GCUUGAAAAUCACAUUCCCCUUUUAGGGGGGAUUGUUCAAUUUGUAUGGCUGUUUGUUUUUGGCGCCUAAUGAUGUCAUUAAGUGGCUGAAGCAGAUUGCCGAACAUGCUAUUUUGAGUC
(((..(((...(((.((((((.....)))))).)))......(((.((((.(((((((((.(.(((.(((((....))))).))).).))))))))).)))).))).....)))..))). ( -43.60)
>DroSec_CAF1 53871 118 + 1
GCUUGAAAAUCACAUUCCCCUUU--GGGGGGAUUGUUCAAUUUGUAUGGCUGUUUGUUUUUGGCGCCUAAUGAUGCCAUUAAGUGGCCGGGGCAGAUUGCCGAACAUGCUGUUUGGAGUC
...........(((.(((((...--..))))).))).((((((((.((((..((((....(((((.(....).))))).))))..))))..))))))))((((((.....)))))).... ( -43.20)
>DroSim_CAF1 53641 118 + 1
GCUUGAAAAUCACAUUCCCCUUU--GGGGGGAUUGUUCAAUUUGUAUGGCUGUUUGUUUUUGGCGCCUAAUGAUGCCAUUAAGUGGCCGCAGCAGAUUGCCGAACAUGCUGUUUGGAGUC
...........(((.(((((...--..))))).))).((((((((.((((..((((....(((((.(....).))))).))))..))))..))))))))((((((.....)))))).... ( -41.50)
>consensus
GCUUGAAAAUCACAUUCCCCUUU__GGGGGGAUUGUUCAAUUUGUAUGGCUGUUUGUUUUUGGCGCCUAAUGAUGCCAUUAAGUGGCCGAAGCAGAUUGCCGAACAUGCUGUUUGGAGUC
((((.(((...(((.((((((.....)))))).)))......(((.((((.(((((((((.(.(((.(((((....))))).))).).))))))))).)))).))).....))).)))). (-40.06 = -40.07 +   0.00)

alignment

secondary structure

dotplot

Window 1

Location	6,984,052 – 6,984,172
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	95.25
Mean single sequence MFE	-27.55
Consensus MFE	-25.45
Energy contribution	-25.57
Covariance contribution	0.11
Combinations/Pair	1.04
Mean z-score	-1.83
Structure conservation index	0.92
SVM decision value	0.35
SVM RNA-class probability	0.700941
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6984052 120 - 23771897
GACUCAAAAUAGCAUGUUCGGCAAUCUGCUUCAGCCACUUAAUGACAUCAUUAGGCGCCAAAAACAAACAGCCAUACAAAUUGAACAAUCCCCCCUAAAAGGGGAAUGUGAUUUUCAAGC
.....(((((.(((((((((((...........)))...(((((....)))))(((..............))).........))))..(((((.......))))))))).)))))..... ( -25.44)
>DroSec_CAF1 53871 118 - 1
GACUCCAAACAGCAUGUUCGGCAAUCUGCCCCGGCCACUUAAUGGCAUCAUUAGGCGCCAAAAACAAACAGCCAUACAAAUUGAACAAUCCCCCC--AAAGGGGAAUGUGAUUUUCAAGC
...........(((((((((((.....)))..(((..(((((((....))))))).))).......................))))..(((((..--...)))))))))........... ( -28.90)
>DroSim_CAF1 53641 118 - 1
GACUCCAAACAGCAUGUUCGGCAAUCUGCUGCGGCCACUUAAUGGCAUCAUUAGGCGCCAAAAACAAACAGCCAUACAAAUUGAACAAUCCCCCC--AAAGGGGAAUGUGAUUUUCAAGC
...........((.((((((((.....)))).(((..(((((((....))))))).))).......))))))........(((((((.(((((..--...))))).))).....)))).. ( -28.30)
>consensus
GACUCCAAACAGCAUGUUCGGCAAUCUGCUCCGGCCACUUAAUGGCAUCAUUAGGCGCCAAAAACAAACAGCCAUACAAAUUGAACAAUCCCCCC__AAAGGGGAAUGUGAUUUUCAAGC
...........(((((((((((.....)))..(((..(((((((....))))))).))).......................))))..(((((.......)))))))))........... (-25.45 = -25.57 +   0.11)

alignment

secondary structure

dotplot

Window 2

Location	6,984,092 – 6,984,200
Length	108
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	89.69
Mean single sequence MFE	-38.73
Consensus MFE	-35.42
Energy contribution	-35.53
Covariance contribution	0.12
Combinations/Pair	1.08
Mean z-score	-3.32
Structure conservation index	0.91
SVM decision value	2.05
SVM RNA-class probability	0.986777
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6984092 108 + 23771897
UUUGUAUGGCUGUUUGUUUUUGGCGCCUAAUGAUGUCAUUAAGUGGCUGAAGCAGAUUGCCGAACAUGCUAUUUUGAGUCGAAAGACUUUUGGCCAAAUAUGAUGUAA------------
..(((.((((.(((((((((.(.(((.(((((....))))).))).).))))))))).)))).))).((((....(((((....))))).))))..............------------ ( -37.90)
>DroSec_CAF1 53909 119 + 1
UUUGUAUGGCUGUUUGUUUUUGGCGCCUAAUGAUGCCAUUAAGUGGCCGGGGCAGAUUGCCGAACAUGCUGUUUGGAGUCGAAAGACUUUUGGCCAAAUAUGAUGUAA-UGCACAUAUAU
..((((((((.((((((((..(.(((.(((((....))))).))).)..)))))))).)))..((((..(((((((((((....)))).....)))))))..)))).)-))))....... ( -39.80)
>DroSim_CAF1 53679 120 + 1
UUUGUAUGGCUGUUUGUUUUUGGCGCCUAAUGAUGCCAUUAAGUGGCCGCAGCAGAUUGCCGAACAUGCUGUUUGGAGUCGAAAGACUUUUGGCCAAAUAUGAUGUAAGUGCACAUAUAU
..((((((((.(((((((..((((((.(((((....))))).)).)))).))))))).)))..((((..(((((((((((....)))).....)))))))..))))..)))))....... ( -38.50)
>consensus
UUUGUAUGGCUGUUUGUUUUUGGCGCCUAAUGAUGCCAUUAAGUGGCCGAAGCAGAUUGCCGAACAUGCUGUUUGGAGUCGAAAGACUUUUGGCCAAAUAUGAUGUAA_UGCACAUAUAU
......((((.(((((((((.(.(((.(((((....))))).))).).))))))))).)))).((((..(((((((((((....)))).....)))))))..)))).............. (-35.42 = -35.53 +   0.12)

alignment

secondary structure

dotplot

Window 3

Location	6,984,092 – 6,984,200
Length	108
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	89.69
Mean single sequence MFE	-25.50
Consensus MFE	-20.05
Energy contribution	-20.17
Covariance contribution	0.11
Combinations/Pair	1.04
Mean z-score	-2.42
Structure conservation index	0.79
SVM decision value	0.44
SVM RNA-class probability	0.736341
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6984092 108 - 23771897
------------UUACAUCAUAUUUGGCCAAAAGUCUUUCGACUCAAAAUAGCAUGUUCGGCAAUCUGCUUCAGCCACUUAAUGACAUCAUUAGGCGCCAAAAACAAACAGCCAUACAAA
------------............((((....((((....))))..........((((.(((.....((....))..(((((((....))))))).)))...))))....))))...... ( -20.20)
>DroSec_CAF1 53909 119 - 1
AUAUAUGUGCA-UUACAUCAUAUUUGGCCAAAAGUCUUUCGACUCCAAACAGCAUGUUCGGCAAUCUGCCCCGGCCACUUAAUGGCAUCAUUAGGCGCCAAAAACAAACAGCCAUACAAA
...((((.((.-........((..(((((...((((....))))...............(((.....)))..)))))..)).((((..(....)..))))..........)))))).... ( -27.30)
>DroSim_CAF1 53679 120 - 1
AUAUAUGUGCACUUACAUCAUAUUUGGCCAAAAGUCUUUCGACUCCAAACAGCAUGUUCGGCAAUCUGCUGCGGCCACUUAAUGGCAUCAUUAGGCGCCAAAAACAAACAGCCAUACAAA
...((((.((..........((..(((((...((((....)))).....(((((.(((....))).))))).)))))..)).((((..(....)..))))..........)))))).... ( -29.00)
>consensus
AUAUAUGUGCA_UUACAUCAUAUUUGGCCAAAAGUCUUUCGACUCCAAACAGCAUGUUCGGCAAUCUGCUCCGGCCACUUAAUGGCAUCAUUAGGCGCCAAAAACAAACAGCCAUACAAA
........................((((....((((....))))..........((((.(((.....)))..(((..(((((((....))))))).)))...))))....))))...... (-20.05 = -20.17 +   0.11)

alignment

secondary structure

dotplot

Window 4

Location	6,984,132 – 6,984,239
Length	107
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	86.24
Mean single sequence MFE	-36.80
Consensus MFE	-25.15
Energy contribution	-25.27
Covariance contribution	0.12
Combinations/Pair	1.11
Mean z-score	-3.51
Structure conservation index	0.68
SVM decision value	1.23
SVM RNA-class probability	0.933195
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6984132 107 + 23771897
AAGUGGCUGAAGCAGAUUGCCGAACAUGCUAUUUUGAGUCGAAAGACUUUUGGCCAAAUAUGAUGUAA-------------UGUAGACAGCAGCACAUGAAGUGUGUGUUGUUGGUUUAA
...((((..(((((..((....))..)))).....(((((....))))))..))))............-------------..(((((((((((((((.....)))))))))).))))). ( -34.30)
>DroSec_CAF1 53949 116 + 1
AAGUGGCCGGGGCAGAUUGCCGAACAUGCUGUUUGGAGUCGAAAGACUUUUGGCCAAAUAUGAUGUAA-UGCACAUAUAUUUGUAGAC---AGCACAUGAAGUGUGUGUUGUUGGUUAAA
...(((((.((.((((...((((((.....))))))((((....)))))))).))(((((((.(((..-...))))))))))...(((---(((((((.....))))))))))))))).. ( -39.70)
>DroSim_CAF1 53719 117 + 1
AAGUGGCCGCAGCAGAUUGCCGAACAUGCUGUUUGGAGUCGAAAGACUUUUGGCCAAAUAUGAUGUAAGUGCACAUAUAUUUGUAGAC---AGAACAUGAAGUGUGUGUUGCUGGUUAAA
...(((((((((((.((...(...((((((((((((((((....))))).....((((((((.(((......))))))))))))))))---))..))))..).)).)))))).))))).. ( -36.40)
>consensus
AAGUGGCCGAAGCAGAUUGCCGAACAUGCUGUUUGGAGUCGAAAGACUUUUGGCCAAAUAUGAUGUAA_UGCACAUAUAUUUGUAGAC___AGCACAUGAAGUGUGUGUUGUUGGUUAAA
...(((((((((((..((....))..)))).....(((((....)))))))))))).............................(((...(((((((.....)))))))....)))... (-25.15 = -25.27 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:33:57 2006