Locus 5723

Sequence ID	3L_DroMel_CAF1
Location	15,600,829 – 15,601,027
Length	198
Max. P	0.997669

overview

Window 0

Location	15,600,829 – 15,600,947
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	88.29
Mean single sequence MFE	-26.41
Consensus MFE	-18.28
Energy contribution	-18.72
Covariance contribution	0.44
Combinations/Pair	1.04
Mean z-score	-2.28
Structure conservation index	0.69
SVM decision value	0.45
SVM RNA-class probability	0.739565
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15600829 118 - 23771897
AUGCAAUAAACAUGAAAUAUGCAUGGCCGGAUUAGAAGAACAAUUUCUGAUUGUCCCCGGCGAAAUUGCAACUGGAAAUAAAUCAAAGCCAAACGCAUUAAAGCCAGAAUGC--ACUUUA
.((((((...((((.......))))(((((((((((((.....)))))))).....)))))...))))))..(((.............)))...(((((........)))))--...... ( -26.62)
>DroSec_CAF1 23889 119 - 1
AUGCAAUAAACAUGAAAUAUGCAUGGCCGGAUUAGAAGAACAAUUUCUGAUAGUCGCCGGCGAAAUUGCAACUGGAAAUAAACCAAAGCCAAAUGAAUUAAAGCCAUACUAA-AACUUUU
.((((((...((((.......))))(((((((((..((((....))))..))))..)))))...))))))..(((...(((..((........))..)))...)))......-....... ( -23.40)
>DroSim_CAF1 23803 118 - 1
AUGCAAUAAACAUGAAAUAUGCAUGGCCGGAUUAGAAGAACAAUUUCUGAUAGUCCUCUGCGAAAUUGCAACUGGAAAUAAACCAAAGCCAAAUGCAUUAAAGCCAGACUGC--ACUUUA
.((((.....((((.......))))...((((((..((((....))))..))))))(((((.....((((..(((.............)))..)))).....).)))).)))--)..... ( -25.62)
>DroEre_CAF1 24005 119 - 1
AUGCAAUAAACAUGAAAUAUGCAUGGCCGGAUUAGAAGAACAAUUUCUGAUAGUC-CGGGCAAAAUUGCAACUAGAAAUAAGCCAAAGCGAAGCGUAUUAAAGCCGGACUGGUAAAUAUA
.((((((...((((.......)))).((((((((..((((....))))..)))))-))).....))))))(((((......((....))...((........))....)))))....... ( -30.90)
>DroYak_CAF1 25510 120 - 1
AUGCAAUAAACAUGAAAUAUGCAUGGCCGGAUUAGAAGCACAAUUUCUGAUAGUCUCCGGCAAAAGUGCAACUAGAAAUAUACCAAAGCCGAACGCAUUAAAGCCAGACUGGUAGAUAUU
((((...............(((((.(((((((((((((.....))))))).....))))))....)))))..((....))..............))))....(((.....)))....... ( -25.50)
>consensus
AUGCAAUAAACAUGAAAUAUGCAUGGCCGGAUUAGAAGAACAAUUUCUGAUAGUCCCCGGCGAAAUUGCAACUGGAAAUAAACCAAAGCCAAACGCAUUAAAGCCAGACUGC_AACUUUA
.((((((...((((.......))))(((((((((((((.....)))))))).....)))))...)))))).................................................. (-18.28 = -18.72 +   0.44)

alignment

secondary structure

dotplot

Window 1

Location	15,600,867 – 15,600,987
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.92
Mean single sequence MFE	-26.77
Consensus MFE	-22.96
Energy contribution	-22.76
Covariance contribution	-0.20
Combinations/Pair	1.06
Mean z-score	-2.62
Structure conservation index	0.86
SVM decision value	2.91
SVM RNA-class probability	0.997669
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15600867 120 + 23771897
UAUUUCCAGUUGCAAUUUCGCCGGGGACAAUCAGAAAUUGUUCUUCUAAUCCGGCCAUGCAUAUUUCAUGUUUAUUGCAUAUCAUUUACAUUUAAAUUUAUGUAUUGGACUUAUGCUGCC
...........(((.....((((((((((((.....))))))).......)))))...(((((......(((((.((((((..(((((....))))).)))))).))))).)))))))). ( -27.21)
>DroSec_CAF1 23928 120 + 1
UAUUUCCAGUUGCAAUUUCGCCGGCGACUAUCAGAAAUUGUUCUUCUAAUCCGGCCAUGCAUAUUUCAUGUUUAUUGCAUAUCAUUUACAUUUAAAUUUAUGCAUUGGACUUAUGCUGCC
...........(((.....(((((........((((....))))......)))))...(((((......(((((.((((((..(((((....))))).)))))).))))).)))))))). ( -25.64)
>DroSim_CAF1 23841 120 + 1
UAUUUCCAGUUGCAAUUUCGCAGAGGACUAUCAGAAAUUGUUCUUCUAAUCCGGCCAUGCAUAUUUCAUGUUUAUUGCAUAUCAUUUACAUUUAAAUUUAUGCAUUGGACUUAUGCUGCC
.......((..((((((((...((......)).))))))))....)).....(((...(((((......(((((.((((((..(((((....))))).)))))).))))).))))).))) ( -25.90)
>DroEre_CAF1 24045 119 + 1
UAUUUCUAGUUGCAAUUUUGCCCG-GACUAUCAGAAAUUGUUCUUCUAAUCCGGCCAUGCAUAUUUCAUGUUUAUUGCAUAUCAUUUACAUUUAAAUUUAUGCAUUGGACUUAUGCUGCC
...........(((....((.(((-((.((..((((....))))..)).))))).)).(((((......(((((.((((((..(((((....))))).)))))).))))).)))))))). ( -27.20)
>DroYak_CAF1 25550 120 + 1
UAUUUCUAGUUGCACUUUUGCCGGAGACUAUCAGAAAUUGUGCUUCUAAUCCGGCCAUGCAUAUUUCAUGUUUAUUGCAUAUCAUUUACAUUUAAAUUUAUGCAUUGGACUUAUGCUGCC
......(((..(((((((((..(....)...)))))...))))..)))....(((...(((((......(((((.((((((..(((((....))))).)))))).))))).))))).))) ( -27.90)
>consensus
UAUUUCCAGUUGCAAUUUCGCCGGGGACUAUCAGAAAUUGUUCUUCUAAUCCGGCCAUGCAUAUUUCAUGUUUAUUGCAUAUCAUUUACAUUUAAAUUUAUGCAUUGGACUUAUGCUGCC
.......((..((((((((..............))))))))....)).....(((...(((((......(((((.((((((..(((((....))))).)))))).))))).))))).))) (-22.96 = -22.76 +  -0.20)

alignment

secondary structure

dotplot

Window 2

Location	15,600,867 – 15,600,987
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.92
Mean single sequence MFE	-29.38
Consensus MFE	-23.38
Energy contribution	-23.82
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-3.22
Structure conservation index	0.80
SVM decision value	2.02
SVM RNA-class probability	0.985763
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15600867 120 - 23771897
GGCAGCAUAAGUCCAAUACAUAAAUUUAAAUGUAAAUGAUAUGCAAUAAACAUGAAAUAUGCAUGGCCGGAUUAGAAGAACAAUUUCUGAUUGUCCCCGGCGAAAUUGCAACUGGAAAUA
...........((((.(((((........))))).......((((((...((((.......))))(((((((((((((.....)))))))).....)))))...))))))..)))).... ( -28.10)
>DroSec_CAF1 23928 120 - 1
GGCAGCAUAAGUCCAAUGCAUAAAUUUAAAUGUAAAUGAUAUGCAAUAAACAUGAAAUAUGCAUGGCCGGAUUAGAAGAACAAUUUCUGAUAGUCGCCGGCGAAAUUGCAACUGGAAAUA
...........((((.(((((........))))).......((((((...((((.......))))(((((((((..((((....))))..))))..)))))...))))))..)))).... ( -28.50)
>DroSim_CAF1 23841 120 - 1
GGCAGCAUAAGUCCAAUGCAUAAAUUUAAAUGUAAAUGAUAUGCAAUAAACAUGAAAUAUGCAUGGCCGGAUUAGAAGAACAAUUUCUGAUAGUCCUCUGCGAAAUUGCAACUGGAAAUA
(((.(((((..((...((((((.(((((....)))))..))))))........))..)))))...)))((((((..((((....))))..))))))..((((....)))).......... ( -28.20)
>DroEre_CAF1 24045 119 - 1
GGCAGCAUAAGUCCAAUGCAUAAAUUUAAAUGUAAAUGAUAUGCAAUAAACAUGAAAUAUGCAUGGCCGGAUUAGAAGAACAAUUUCUGAUAGUC-CGGGCAAAAUUGCAACUAGAAAUA
.((((((((..((...((((((.(((((....)))))..))))))........))..))))).((.((((((((..((((....))))..)))))-))).))....)))........... ( -33.40)
>DroYak_CAF1 25550 120 - 1
GGCAGCAUAAGUCCAAUGCAUAAAUUUAAAUGUAAAUGAUAUGCAAUAAACAUGAAAUAUGCAUGGCCGGAUUAGAAGCACAAUUUCUGAUAGUCUCCGGCAAAAGUGCAACUAGAAAUA
.((((((((..((...((((((.(((((....)))))..))))))........))..)))))...(((((((((((((.....))))))).....)))))).....)))........... ( -28.70)
>consensus
GGCAGCAUAAGUCCAAUGCAUAAAUUUAAAUGUAAAUGAUAUGCAAUAAACAUGAAAUAUGCAUGGCCGGAUUAGAAGAACAAUUUCUGAUAGUCCCCGGCGAAAUUGCAACUGGAAAUA
.((((((((..((...((((((.(((((....)))))..))))))........))..)))))...(((((((((((((.....)))))))).....))))).....)))........... (-23.38 = -23.82 +   0.44)

alignment

secondary structure

dotplot

Window 3

Location	15,600,907 – 15,601,027
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.67
Mean single sequence MFE	-26.85
Consensus MFE	-24.70
Energy contribution	-24.54
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-2.09
Structure conservation index	0.92
SVM decision value	2.60
SVM RNA-class probability	0.995634
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15600907 120 + 23771897
UUCUUCUAAUCCGGCCAUGCAUAUUUCAUGUUUAUUGCAUAUCAUUUACAUUUAAAUUUAUGUAUUGGACUUAUGCUGCCGAAACGUGAGCAUUUCAUGGACAAUUUCACAGCGAGUAUU
............(.(((((.....(((((((((...(((((((...(((((........)))))...))..))))).....))))))))).....))))).).................. ( -24.20)
>DroSec_CAF1 23968 120 + 1
UUCUUCUAAUCCGGCCAUGCAUAUUUCAUGUUUAUUGCAUAUCAUUUACAUUUAAAUUUAUGCAUUGGACUUAUGCUGCCGAAACGUGAGCAUUUCAUGGACAAUUUCACAGCGAGUAUU
.........((((((...(((((......(((((.((((((..(((((....))))).)))))).))))).))))).)))(((((....)..))))..)))................... ( -25.60)
>DroSim_CAF1 23881 117 + 1
UUCUUCUAAUCCGGCCAUGCAUAUUUCAUGUUUAUUGCAUAUCAUUUACAUUUAAAUUUAUGCAUUGGACUUAUGCUGCCGAAA-GGGAGCAUUUCAUGGACAAU-UCACAG-GAAUAUU
(((((.........(((((..........(((((.((((((..(((((....))))).)))))).)))))..(((((.((....-)).)))))..))))).....-....))-))).... ( -30.87)
>DroEre_CAF1 24084 120 + 1
UUCUUCUAAUCCGGCCAUGCAUAUUUCAUGUUUAUUGCAUAUCAUUUACAUUUAAAUUUAUGCAUUGGACUUAUGCUGCCGAAACGUGAGCAUUUCAUGGACAAUUUCACAGCGAGUAUU
.........((((((...(((((......(((((.((((((..(((((....))))).)))))).))))).))))).)))(((((....)..))))..)))................... ( -25.60)
>DroYak_CAF1 25590 120 + 1
UGCUUCUAAUCCGGCCAUGCAUAUUUCAUGUUUAUUGCAUAUCAUUUACAUUUAAAUUUAUGCAUUGGACUUAUGCUGCCGAAACGUGAGCAUUUCAUGGACAAUUUCACAGCGAGUAUU
(((((((....((((...(((((......(((((.((((((..(((((....))))).)))))).))))).))))).))))...((((((...))))))...........)).))))).. ( -28.00)
>consensus
UUCUUCUAAUCCGGCCAUGCAUAUUUCAUGUUUAUUGCAUAUCAUUUACAUUUAAAUUUAUGCAUUGGACUUAUGCUGCCGAAACGUGAGCAUUUCAUGGACAAUUUCACAGCGAGUAUU
.........((((((...(((((......(((((.((((((..(((((....))))).)))))).))))).))))).)))((((.(....).))))..)))................... (-24.70 = -24.54 +  -0.16)

alignment

secondary structure

dotplot

Window 4

Location	15,600,907 – 15,601,027
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.67
Mean single sequence MFE	-25.84
Consensus MFE	-23.52
Energy contribution	-23.56
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.77
Structure conservation index	0.91
SVM decision value	1.66
SVM RNA-class probability	0.970729
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15600907 120 - 23771897
AAUACUCGCUGUGAAAUUGUCCAUGAAAUGCUCACGUUUCGGCAGCAUAAGUCCAAUACAUAAAUUUAAAUGUAAAUGAUAUGCAAUAAACAUGAAAUAUGCAUGGCCGGAUUAGAAGAA
..(((.....))).....((((..((((((....))))))(((.((((..(((...(((((........)))))...)))))))......((((.......)))))))))))........ ( -24.40)
>DroSec_CAF1 23968 120 - 1
AAUACUCGCUGUGAAAUUGUCCAUGAAAUGCUCACGUUUCGGCAGCAUAAGUCCAAUGCAUAAAUUUAAAUGUAAAUGAUAUGCAAUAAACAUGAAAUAUGCAUGGCCGGAUUAGAAGAA
.....((((((((((((((..(((...)))..)).))))).)))))...(((((..((((((.(((((....)))))..)))))).....((((.......))))...))))).)).... ( -26.20)
>DroSim_CAF1 23881 117 - 1
AAUAUUC-CUGUGA-AUUGUCCAUGAAAUGCUCCC-UUUCGGCAGCAUAAGUCCAAUGCAUAAAUUUAAAUGUAAAUGAUAUGCAAUAAACAUGAAAUAUGCAUGGCCGGAUUAGAAGAA
....(((-.(.(((-.(((.(((((..(((((.((-....)).)))))........((((((.(((((....)))))..))))))................))))).))).))).).))) ( -24.00)
>DroEre_CAF1 24084 120 - 1
AAUACUCGCUGUGAAAUUGUCCAUGAAAUGCUCACGUUUCGGCAGCAUAAGUCCAAUGCAUAAAUUUAAAUGUAAAUGAUAUGCAAUAAACAUGAAAUAUGCAUGGCCGGAUUAGAAGAA
.....((((((((((((((..(((...)))..)).))))).)))))...(((((..((((((.(((((....)))))..)))))).....((((.......))))...))))).)).... ( -26.20)
>DroYak_CAF1 25590 120 - 1
AAUACUCGCUGUGAAAUUGUCCAUGAAAUGCUCACGUUUCGGCAGCAUAAGUCCAAUGCAUAAAUUUAAAUGUAAAUGAUAUGCAAUAAACAUGAAAUAUGCAUGGCCGGAUUAGAAGCA
.......(((........((((..((((((....))))))(((.(((((..((...((((((.(((((....)))))..))))))........))..)))))...)))))))....))). ( -28.40)
>consensus
AAUACUCGCUGUGAAAUUGUCCAUGAAAUGCUCACGUUUCGGCAGCAUAAGUCCAAUGCAUAAAUUUAAAUGUAAAUGAUAUGCAAUAAACAUGAAAUAUGCAUGGCCGGAUUAGAAGAA
..................((((..((((((....))))))(((.((((..(((...(((((........)))))...)))))))......((((.......)))))))))))........ (-23.52 = -23.56 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:57:48 2006