Locus 2623

Sequence ID	3L_DroMel_CAF1
Location	7,234,649 – 7,235,000
Length	351
Max. P	0.996850

overview

Window 2

Location	7,234,649 – 7,234,769
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.09
Mean single sequence MFE	-26.30
Consensus MFE	-22.34
Energy contribution	-22.94
Covariance contribution	0.60
Combinations/Pair	1.07
Mean z-score	-1.30
Structure conservation index	0.85
SVM decision value	0.18
SVM RNA-class probability	0.620807
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7234649 120 + 23771897
UCAGCCAUCAGAAAUCAGAAAUCGGAGCCAAAACCGGUUGGCAUCAUUGAUUCAAUAAGCAUUCAACUUAGCAUCGAUCUGCGAGUCGAUAGCUGAUUUAUAUAGCACGAAUGCAACCGC
...((.((...(((((((..((((..(((((......)))))..)...(((((..((((.......))))(((......)))))))))))..)))))))..)).)).............. ( -27.80)
>DroSec_CAF1 16218 113 + 1
UCAGCCAUCAG-------AAAUCGAAGUCAAAACCGGUUGGCAUCAUUGAUUCAAUAAGUAUUCAACUUAGCAUCGAUCUGCGACUCGAUAGCUGAUUUAUAUAGCUCGAAUGCAACCGC
...((.(((((-------..(((((.(((..((....)).(((..((((((....(((((.....)))))..)))))).)))))))))))..))))).......((......))....)) ( -24.00)
>DroSim_CAF1 16215 113 + 1
UCAGCCAUCAG-------AAAUCGGAGCCAAAACCGGUUGGCAUCAUUGAUUCAAUAAGCAUUCAACUUAGCAUCGAUCUGCGACUCGAUCGCUGAUUUAUAUAGCUCGAAUGCAACCGC
...........-------....(((.(((((......)))))................((((((...(((..((.((((.((((.....)))).)))).)).)))...))))))..))). ( -25.10)
>DroEre_CAF1 16735 113 + 1
UCAGCAAUCAG-------AAAUCGCAGCCAAAACCGGUUGCCAUCAUUGAUUCAAUAAGCAUUCAACUUAGCAUCGAUCUGCGAAUCGAUCGCUGAUUUAUAUAGCUCGAAUGCAACCGC
...((((((((-------..((.((((((......)))))).))..))))))......((((((((.(((((((((((......)))))).))))).)).........))))))....)) ( -29.70)
>DroYak_CAF1 17770 113 + 1
UCAACAAUCAG-------AAAUCCAAGCCAAAACCGGUUGGCAUCAUUGAUUCAAUAAGCAUUCAACUUAGCAUCGAUCUGCGAGUCGAUCGCUGAUUUAUAUAGCUCGAAUGCAACCGC
.....((((((-------..(((...(((((......)))))......(((((..((((.......))))(((......)))))))))))..))))))......((......))...... ( -24.90)
>consensus
UCAGCCAUCAG_______AAAUCGAAGCCAAAACCGGUUGGCAUCAUUGAUUCAAUAAGCAUUCAACUUAGCAUCGAUCUGCGACUCGAUCGCUGAUUUAUAUAGCUCGAAUGCAACCGC
(((((.(((.................(((((......)))))......(((((..((((.......))))(((......))))))))))).)))))........((......))...... (-22.34 = -22.94 +   0.60)

alignment

secondary structure

dotplot

Window 3

Location	7,234,769 – 7,234,881
Length	112
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.19
Mean single sequence MFE	-21.28
Consensus MFE	-17.02
Energy contribution	-16.74
Covariance contribution	-0.28
Combinations/Pair	1.11
Mean z-score	-1.68
Structure conservation index	0.80
SVM decision value	0.62
SVM RNA-class probability	0.803376
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7234769 112 - 23771897
AUGUCAUCAUCACAUAUAUGUAAUUAAUGUCUCGUGUUGCUUGCACAUUCAUUGCGUGCAAAUUAUACGAAAAAGUAUCCGACAUUCAAACAUUCAGAC--------AUUCAGGCAUUCC
(((((......(((....)))....((((((((((((...((((((.........))))))...))))))....((.....)).............)))--------)))..)))))... ( -20.90)
>DroSec_CAF1 16331 108 - 1
AUGUCAUCAUCACA----UGUAAUUAAUGCCUCGUGUCGCUUGCACAUUCAUUGCGUGCAAAUUAUACGAAAAAGUAUCCGACAUUCAAACAUUCAGAC--------AUUCAGGCAUUCC
..............----.......(((((((.(((((..((((((.........))))))...((((......))))..................)))--------))..))))))).. ( -22.10)
>DroSim_CAF1 16328 108 - 1
AUGUCAUCAUCACA----UGUAAUUAAUGCCUCGUGUCGCUUGCACAUUCAUUGCGUGCAAAUUAUACGAAAAAGUAUCCGACAUUCAAACAUUCAGAC--------AUUCAGGCAUUCC
..............----.......(((((((.(((((..((((((.........))))))...((((......))))..................)))--------))..))))))).. ( -22.10)
>DroEre_CAF1 16848 116 - 1
AUGUCAUCAUCACA----CGUAAUUAAUGCCUCGUGUCGCUUGCACAUUCAUUGCGUGCAUAUUAUACAAAAAAGUAUCCGACAUUCAGACAUUCAAACAUUCAUACACUCAGGCAUUCC
..............----.......(((((((.((((((..(((((.........)))))....((((......)))).))))))...(.....)................))))))).. ( -18.60)
>DroYak_CAF1 17883 116 - 1
AUGUCAUCAUCACA----CGUAAUUAAUGCCUCGUGUCGCUUGCACAUUCAUUGCGUGCAAAUUAUACAAAAAAGUAUCCGACACUCAGACAUUCAGACAGUCAAAGAUUCAGACAUUCC
(((((...(((...----...............((((((.((((((.........))))))...((((......)))).))))))...(((.........)))...)))...)))))... ( -22.70)
>consensus
AUGUCAUCAUCACA____UGUAAUUAAUGCCUCGUGUCGCUUGCACAUUCAUUGCGUGCAAAUUAUACGAAAAAGUAUCCGACAUUCAAACAUUCAGAC________AUUCAGGCAUUCC
(((((......((......))....((((....((((((.((((((.........))))))...((((......)))).)))))).....))))..................)))))... (-17.02 = -16.74 +  -0.28)

alignment

secondary structure

dotplot

Window 4

Location	7,234,801 – 7,234,920
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.86
Mean single sequence MFE	-28.81
Consensus MFE	-26.50
Energy contribution	-25.94
Covariance contribution	-0.56
Combinations/Pair	1.11
Mean z-score	-1.48
Structure conservation index	0.92
SVM decision value	1.42
SVM RNA-class probability	0.952179
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7234801 119 + 23771897
GGAUACUUUUUCGUAUAAUUUGCACGCAAUGAAUGUGCAAGCAACACGAGACAUUAAUUACAUAUAUGUGAUGAUGACAUCACCAUCACCAAGUCAUCUGUUGGUUUGCAGAUU-UCAAU
.(((....((((((....((((((((.......))))))))....))))))................((((((.((....)).))))))...)))((((((......)))))).-..... ( -27.40)
>DroSec_CAF1 16363 115 + 1
GGAUACUUUUUCGUAUAAUUUGCACGCAAUGAAUGUGCAAGCGACACGAGGCAUUAAUUACA----UGUGAUGAUGACAUCACCAUCACCAAGUCAUCUGUCGGCUUGCAGAUU-UCAAU
..((((......))))...(((....)))(((((.(((((((((((.(((((..........----.((((((.((....)).))))))...))).)))))).))))))).).)-))).. ( -28.84)
>DroSim_CAF1 16360 115 + 1
GGAUACUUUUUCGUAUAAUUUGCACGCAAUGAAUGUGCAAGCGACACGAGGCAUUAAUUACA----UGUGAUGAUGACAUCACCAUCACCAAGUCAUCUGCCGGUUUGCAGAUU-UCAAU
.(((....((((((.(..((((((((.......))))))))..).))))))...........----.((((((.((....)).))))))...)))((((((......)))))).-..... ( -28.00)
>DroEre_CAF1 16888 116 + 1
GGAUACUUUUUUGUAUAAUAUGCACGCAAUGAAUGUGCAAGCGACACGAGGCAUUAAUUACG----UGUGAUGAUGACAUCACCAGCACCAAGUCAUCUGUCGGCUUGCAGAUUUUCAAU
..((((......))))..............((((.(((((((((((.(((((.........(----.((((((....)))))))........))).)))))).))))))).))))..... ( -28.93)
>DroYak_CAF1 17923 116 + 1
GGAUACUUUUUUGUAUAAUUUGCACGCAAUGAAUGUGCAAGCGACACGAGGCAUUAAUUACG----UGUGAUGAUGACAUCAUCAUCAGCAAGUCAUCUGUCGGUUUGCAGAUUUUCAAU
..........(((...((((((((((((((((...(((.....(((((............))----)))(((((((....))))))).)))..)))).)).))...))))))))..))). ( -30.90)
>consensus
GGAUACUUUUUCGUAUAAUUUGCACGCAAUGAAUGUGCAAGCGACACGAGGCAUUAAUUACA____UGUGAUGAUGACAUCACCAUCACCAAGUCAUCUGUCGGUUUGCAGAUU_UCAAU
..((((......)))).............(((((.(((((((((((.(((((....((((((....))))))((((.......)))).....))).)))))).))))))).))..))).. (-26.50 = -25.94 +  -0.56)

alignment

secondary structure

dotplot

Window 5

Location	7,234,801 – 7,234,920
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.86
Mean single sequence MFE	-30.18
Consensus MFE	-26.66
Energy contribution	-27.50
Covariance contribution	0.84
Combinations/Pair	1.03
Mean z-score	-2.11
Structure conservation index	0.88
SVM decision value	2.76
SVM RNA-class probability	0.996850
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7234801 119 - 23771897
AUUGA-AAUCUGCAAACCAACAGAUGACUUGGUGAUGGUGAUGUCAUCAUCACAUAUAUGUAAUUAAUGUCUCGUGUUGCUUGCACAUUCAUUGCGUGCAAAUUAUACGAAAAAGUAUCC
.....-.(((((........))))).((((.(((((((((....)))))))))..................((((((...((((((.........))))))...))))))..)))).... ( -31.40)
>DroSec_CAF1 16363 115 - 1
AUUGA-AAUCUGCAAGCCGACAGAUGACUUGGUGAUGGUGAUGUCAUCAUCACA----UGUAAUUAAUGCCUCGUGUCGCUUGCACAUUCAUUGCGUGCAAAUUAUACGAAAAAGUAUCC
..(((-(...(((((((.((((((.......(((((((((....))))))))).----.(((.....))).)).)))))))))))..))))(((....)))...((((......)))).. ( -31.30)
>DroSim_CAF1 16360 115 - 1
AUUGA-AAUCUGCAAACCGGCAGAUGACUUGGUGAUGGUGAUGUCAUCAUCACA----UGUAAUUAAUGCCUCGUGUCGCUUGCACAUUCAUUGCGUGCAAAUUAUACGAAAAAGUAUCC
.....-.((((((......)))))).((((.(((((((((....))))))))).----.............((((((.(.((((((.........)))))).).))))))..)))).... ( -34.60)
>DroEre_CAF1 16888 116 - 1
AUUGAAAAUCUGCAAGCCGACAGAUGACUUGGUGCUGGUGAUGUCAUCAUCACA----CGUAAUUAAUGCCUCGUGUCGCUUGCACAUUCAUUGCGUGCAUAUUAUACAAAAAAGUAUCC
..((((....(((((((.((((((.(..(((((....((((((....)))))).----....)))))..).)).)))))))))))..)))).............((((......)))).. ( -27.50)
>DroYak_CAF1 17923 116 - 1
AUUGAAAAUCUGCAAACCGACAGAUGACUUGCUGAUGAUGAUGUCAUCAUCACA----CGUAAUUAAUGCCUCGUGUCGCUUGCACAUUCAUUGCGUGCAAAUUAUACAAAAAAGUAUCC
.......(((((........))))).((((((.(((((((....)))))))(((----((............))))).))((((((.........))))))...........)))).... ( -26.10)
>consensus
AUUGA_AAUCUGCAAACCGACAGAUGACUUGGUGAUGGUGAUGUCAUCAUCACA____UGUAAUUAAUGCCUCGUGUCGCUUGCACAUUCAUUGCGUGCAAAUUAUACGAAAAAGUAUCC
.......(((((........))))).((((.(((((((((....)))))))))..................((((((...((((((.........))))))...))))))..)))).... (-26.66 = -27.50 +   0.84)

alignment

secondary structure

dotplot

Window 6

Location	7,234,841 – 7,234,960
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.48
Mean single sequence MFE	-31.61
Consensus MFE	-26.30
Energy contribution	-26.06
Covariance contribution	-0.24
Combinations/Pair	1.12
Mean z-score	-1.94
Structure conservation index	0.83
SVM decision value	1.58
SVM RNA-class probability	0.965656
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7234841 119 + 23771897
GCAACACGAGACAUUAAUUACAUAUAUGUGAUGAUGACAUCACCAUCACCAAGUCAUCUGUUGGUUUGCAGAUU-UCAAUUGCAUGCAGUCGCCUCAAAUGUCAGAUGAAAGUUGCAGUU
(((((......................((((((.((....)).))))))....(((((((...(((((..((((-.((......)).))))....)))))..)))))))..))))).... ( -29.90)
>DroSec_CAF1 16403 115 + 1
GCGACACGAGGCAUUAAUUACA----UGUGAUGAUGACAUCACCAUCACCAAGUCAUCUGUCGGCUUGCAGAUU-UCAAUUGCAUACAGUCGCCUCAAAUGUCAGAUGAAAGUUGCAGUU
(((((..(((((..........----.((((((.((....)).)))))).............(((((((((...-....)))))...))))))))).....((....))..))))).... ( -31.20)
>DroSim_CAF1 16400 115 + 1
GCGACACGAGGCAUUAAUUACA----UGUGAUGAUGACAUCACCAUCACCAAGUCAUCUGCCGGUUUGCAGAUU-UCAAUUGCAUACAGUCGCCUCAAAUGUCAGAUGAAAGUUGCAGUU
(((((..(((((..........----.((((((.((....)).))))))...(..((((((......)))))).-.)..............))))).....((....))..))))).... ( -32.50)
>DroEre_CAF1 16928 113 + 1
GCGACACGAGGCAUUAAUUACG----UGUGAUGAUGACAUCACCAGCACCAAGUCAUCUGUCGGCUUGCAGAUUUUCAAUUGCAUACAGU---CUCGAAUGUCAGAUGAAAGUUGCAGUU
(((((.((((((.........(----.((((((....))))))).(((.......((((((......)))))).......))).....))---))))....((....))..))))).... ( -31.04)
>DroYak_CAF1 17963 113 + 1
GCGACACGAGGCAUUAAUUACG----UGUGAUGAUGACAUCAUCAUCAGCAAGUCAUCUGUCGGUUUGCAGAUUUUCAAUUGCAUACAGU---CUCAAAUGUCAGAUGAAAGUUGCAGUU
(((((..(((((..........----..((((((((....))))))))((((...((((((......))))))......)))).....))---))).....((....))..))))).... ( -33.40)
>consensus
GCGACACGAGGCAUUAAUUACA____UGUGAUGAUGACAUCACCAUCACCAAGUCAUCUGUCGGUUUGCAGAUU_UCAAUUGCAUACAGUCGCCUCAAAUGUCAGAUGAAAGUUGCAGUU
(((((..((..(((((.(((((....))))))))))...))............(((((((.((((.(((((........))))).)).(......)...)).)))))))..))))).... (-26.30 = -26.06 +  -0.24)

alignment

secondary structure

dotplot

Window 7

Location	7,234,841 – 7,234,960
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.48
Mean single sequence MFE	-31.50
Consensus MFE	-26.54
Energy contribution	-27.42
Covariance contribution	0.88
Combinations/Pair	1.14
Mean z-score	-1.87
Structure conservation index	0.84
SVM decision value	1.59
SVM RNA-class probability	0.966001
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7234841 119 - 23771897
AACUGCAACUUUCAUCUGACAUUUGAGGCGACUGCAUGCAAUUGA-AAUCUGCAAACCAACAGAUGACUUGGUGAUGGUGAUGUCAUCAUCACAUAUAUGUAAUUAAUGUCUCGUGUUGC
....(((((..(((((((.....((((....)).))((((.....-....))))......)))))))....(((((((((....)))))))))......................))))) ( -31.40)
>DroSec_CAF1 16403 115 - 1
AACUGCAACUUUCAUCUGACAUUUGAGGCGACUGUAUGCAAUUGA-AAUCUGCAAGCCGACAGAUGACUUGGUGAUGGUGAUGUCAUCAUCACA----UGUAAUUAAUGCCUCGUGUCGC
.................(((((..((((((.((((.((((.....-....)))).....))))...((...(((((((((....))))))))).----.))......))))))))))).. ( -34.20)
>DroSim_CAF1 16400 115 - 1
AACUGCAACUUUCAUCUGACAUUUGAGGCGACUGUAUGCAAUUGA-AAUCUGCAAACCGGCAGAUGACUUGGUGAUGGUGAUGUCAUCAUCACA----UGUAAUUAAUGCCUCGUGUCGC
.................(((((..((((((...((.((((.....-.((((((......))))))......(((((((((....))))))))).----))))))...))))))))))).. ( -37.20)
>DroEre_CAF1 16928 113 - 1
AACUGCAACUUUCAUCUGACAUUCGAG---ACUGUAUGCAAUUGAAAAUCUGCAAGCCGACAGAUGACUUGGUGCUGGUGAUGUCAUCAUCACA----CGUAAUUAAUGCCUCGUGUCGC
...((((..(((((..((.(((.((..---..)).)))))..)))))...))))...(((((((.(..(((((....((((((....)))))).----....)))))..).)).))))). ( -25.40)
>DroYak_CAF1 17963 113 - 1
AACUGCAACUUUCAUCUGACAUUUGAG---ACUGUAUGCAAUUGAAAAUCUGCAAACCGACAGAUGACUUGCUGAUGAUGAUGUCAUCAUCACA----CGUAAUUAAUGCCUCGUGUCGC
....((((...((((((((((......---..))).((((..(....)..))))......))))))).)))).(((((((....)))))))(((----((............)))))... ( -29.30)
>consensus
AACUGCAACUUUCAUCUGACAUUUGAGGCGACUGUAUGCAAUUGA_AAUCUGCAAACCGACAGAUGACUUGGUGAUGGUGAUGUCAUCAUCACA____UGUAAUUAAUGCCUCGUGUCGC
.................(((((..(((((..((((.((((..(....)..)))).....))))........(((((((((....)))))))))...............)))))))))).. (-26.54 = -27.42 +   0.88)

alignment

secondary structure

dotplot

Window 8

Location	7,234,881 – 7,235,000
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.70
Mean single sequence MFE	-28.05
Consensus MFE	-22.45
Energy contribution	-23.05
Covariance contribution	0.60
Combinations/Pair	1.07
Mean z-score	-1.51
Structure conservation index	0.80
SVM decision value	0.28
SVM RNA-class probability	0.666338
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7234881 119 - 23771897
AAACCAAACCAACUAUUAUGCAGGUACGAAUUAUCCAACCAACUGCAACUUUCAUCUGACAUUUGAGGCGACUGCAUGCAAUUGA-AAUCUGCAAACCAACAGAUGACUUGGUGAUGGUG
..((((.(((((......(((((...................)))))....(((((((.....((((....)).))((((.....-....))))......))))))).)))))..)))). ( -28.21)
>DroSec_CAF1 16439 119 - 1
AAACCAAACCAACCAUUAUGCAGGUACGAAUUAUCCAACCAACUGCAACUUUCAUCUGACAUUUGAGGCGACUGUAUGCAAUUGA-AAUCUGCAAGCCGACAGAUGACUUGGUGAUGGUG
..((((.(((((......(((((...................)))))....(((((((.......((....))((.((((.....-....)))).))...))))))).)))))..)))). ( -28.81)
>DroSim_CAF1 16436 119 - 1
AAACCAAACCAACCAUUAUGCAGGUACGAAUUAUCCAACCAACUGCAACUUUCAUCUGACAUUUGAGGCGACUGUAUGCAAUUGA-AAUCUGCAAACCGGCAGAUGACUUGGUGAUGGUG
...........((((((((.(((((..............(((.((((((..((..((........))..))..)).)))).))).-.((((((......)))))).))))))))))))). ( -30.10)
>DroEre_CAF1 16964 116 - 1
AAACCCAG-CAACUAUUAUGCAGGUACGAACCAACCAGCCAACUGCAACUUUCAUCUGACAUUCGAG---ACUGUAUGCAAUUGAAAAUCUGCAAGCCGACAGAUGACUUGGUGCUGGUG
....((((-((.(((...(((((...................)))))....(((((((....(((.(---.((...((((..(....)..)))))))))))))))))..))))))))).. ( -30.11)
>DroYak_CAF1 17999 116 - 1
AAACCAAG-CAACUAUUAUGCAGGUACGAAAUAUCCAACCAACUGCAACUUUCAUCUGACAUUUGAG---ACUGUAUGCAAUUGAAAAUCUGCAAACCGACAGAUGACUUGCUGAUGAUG
......((-(((......(((((...................)))))....((((((((((......---..))).((((..(....)..))))......))))))).)))))....... ( -23.01)
>consensus
AAACCAAACCAACUAUUAUGCAGGUACGAAUUAUCCAACCAACUGCAACUUUCAUCUGACAUUUGAGGCGACUGUAUGCAAUUGA_AAUCUGCAAACCGACAGAUGACUUGGUGAUGGUG
..((((.(((((......(((((...................)))))....(((((((.......((....))((.((((..(....)..)))).))...))))))).)))))..)))). (-22.45 = -23.05 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:37:54 2006