Locus 3064

Sequence ID	3R_DroMel_CAF1
Location	8,100,083 – 8,100,242
Length	159
Max. P	0.995959

overview

Window 4

Location	8,100,083 – 8,100,202
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.30
Mean single sequence MFE	-46.66
Consensus MFE	-39.56
Energy contribution	-39.40
Covariance contribution	-0.16
Combinations/Pair	1.16
Mean z-score	-2.34
Structure conservation index	0.85
SVM decision value	2.64
SVM RNA-class probability	0.995959
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8100083 119 + 27905053
CUUUGGGCAGCAUUGUGGUUUUGGCAA-UGUGGAAAGCGGUCGGCGAUUGAUGGCUAUCAAUGCCGAUGACUUAUAGCCAGAGUCGCGGACCGAGACUCACAUGAGUCGAGCCAGCCAAA
.....(((.(((((((.......))))-)))((....(((((.((((((..(((((((((.......)))....)))))).)))))).))))).(((((....)))))...)).)))... ( -48.10)
>DroSec_CAF1 51732 120 + 1
CUUUGGGAAGCUUUGUGGUCUUGGCAAGCGUGGAAAGCGGUCGGCGAUUGAUGGCUAUCAAUGCCGAUGACUUAUAGCCAGAGUCGCGGGCCGAGACUCACAUGAGUCGAGCCAGCCAAA
..((((...((((((((((((((((..((((((.(((..((((((.((((((....))))))))))))..)))....)))....)))..)))))))).))))......))))...)))). ( -48.30)
>DroSim_CAF1 23803 119 + 1
CUUUGGGCAGCUUUGUGGUCUUGGCAA-CGUGGAAAGCGGUCGGCGAUUGAUGGCUAUCAAUGCCGAUGACUUAUAGCCGGAGUCGCGGACCGCGACUCACAUGAGUCGAGCCAGCCAAA
.....(((.(((....)))..((((..-........((((((.((((((..(((((((((.......)))....)))))).)))))).))))))(((((....)))))..)))))))... ( -50.00)
>DroEre_CAF1 26824 118 + 1
CUUUGGGCAACUUUGUGGUCUUGGCAA-CGUGGAAAGCGGUCGGCGAU-GAUGGCUAUCAAUGCCGAUGACUUAUAGCCAGAGUCGCAGACCGAGGCGCACAUGAGCAGAGCCAGCCAAA
.....(((..((((((......(....-)((((....(((((.(((((-..(((((((((.......)))....))))))..))))).)))))...).)))....))))))...)))... ( -42.40)
>DroYak_CAF1 20169 119 + 1
CUUUGGGCAACUUUGUGGUCUUGGCAA-CGUGGAAAGCGGUCGGCGAUUGAUGGCUAUCAAUGCCGAUGACUUAUAGCCGGAGUCGCAGACUCAGGCUCACAUGAGUCGAGCCAGCGAAA
.....(((.....(((..(((((....-)).)))..)))((((((.((((((....))))))))))))(((((((((((.(((((...))))).))))...)))))))..)))....... ( -44.50)
>consensus
CUUUGGGCAGCUUUGUGGUCUUGGCAA_CGUGGAAAGCGGUCGGCGAUUGAUGGCUAUCAAUGCCGAUGACUUAUAGCCAGAGUCGCGGACCGAGACUCACAUGAGUCGAGCCAGCCAAA
...............((((..((((............(((((.(((((...(((((((((.......)))....))))))..))))).))))).(((((....)))))..)))))))).. (-39.56 = -39.40 +  -0.16)

alignment

secondary structure

dotplot

Window 5

Location	8,100,083 – 8,100,202
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.30
Mean single sequence MFE	-40.84
Consensus MFE	-32.78
Energy contribution	-33.62
Covariance contribution	0.84
Combinations/Pair	1.10
Mean z-score	-2.45
Structure conservation index	0.80
SVM decision value	1.93
SVM RNA-class probability	0.982981
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8100083 119 - 27905053
UUUGGCUGGCUCGACUCAUGUGAGUCUCGGUCCGCGACUCUGGCUAUAAGUCAUCGGCAUUGAUAGCCAUCAAUCGCCGACCGCUUUCCACA-UUGCCAAAACCACAAUGCUGCCCAAAG
(((((..(((..(((((....))))).(((((.((((...(((((((..((.....))....)))))))....)))).))))).........-................)))..))))). ( -38.90)
>DroSec_CAF1 51732 120 - 1
UUUGGCUGGCUCGACUCAUGUGAGUCUCGGCCCGCGACUCUGGCUAUAAGUCAUCGGCAUUGAUAGCCAUCAAUCGCCGACCGCUUUCCACGCUUGCCAAGACCACAAAGCUUCCCAAAG
(((((..((((.......((((.((((.(((..(((....(((....((((..(((((((((((....)))))).)))))..)))).))))))..))).)))))))).))))..))))). ( -43.10)
>DroSim_CAF1 23803 119 - 1
UUUGGCUGGCUCGACUCAUGUGAGUCGCGGUCCGCGACUCCGGCUAUAAGUCAUCGGCAUUGAUAGCCAUCAAUCGCCGACCGCUUUCCACG-UUGCCAAGACCACAAAGCUGCCCAAAG
(((((..((((((((((....)))))).((((.(((((...((....((((..(((((((((((....)))))).)))))..)))).))..)-))))...))))....))))..))))). ( -45.60)
>DroEre_CAF1 26824 118 - 1
UUUGGCUGGCUCUGCUCAUGUGCGCCUCGGUCUGCGACUCUGGCUAUAAGUCAUCGGCAUUGAUAGCCAUC-AUCGCCGACCGCUUUCCACG-UUGCCAAGACCACAAAGUUGCCCAAAG
...(((.(((...((......)))))..((((((((((..(((....((((..(((((..((((....)))-)..)))))..)))).))).)-))))..)))))........)))..... ( -38.70)
>DroYak_CAF1 20169 119 - 1
UUUCGCUGGCUCGACUCAUGUGAGCCUGAGUCUGCGACUCCGGCUAUAAGUCAUCGGCAUUGAUAGCCAUCAAUCGCCGACCGCUUUCCACG-UUGCCAAGACCACAAAGUUGCCCAAAG
......(((..(((((..((((((((.(((((...))))).))))....(((.(((((((((((....)))))).)))))..((........-..))...))))))).))))).)))... ( -37.90)
>consensus
UUUGGCUGGCUCGACUCAUGUGAGUCUCGGUCCGCGACUCUGGCUAUAAGUCAUCGGCAUUGAUAGCCAUCAAUCGCCGACCGCUUUCCACG_UUGCCAAGACCACAAAGCUGCCCAAAG
((((((.(((((.((....))))))).(((((.((((...(((((((..((.....))....)))))))....)))).)))))............))))))................... (-32.78 = -33.62 +   0.84)

alignment

secondary structure

dotplot

Window 6

Location	8,100,122 – 8,100,242
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.50
Mean single sequence MFE	-41.06
Consensus MFE	-37.18
Energy contribution	-37.14
Covariance contribution	-0.04
Combinations/Pair	1.09
Mean z-score	-1.92
Structure conservation index	0.91
SVM decision value	2.48
SVM RNA-class probability	0.994494
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8100122 120 + 27905053
UCGGCGAUUGAUGGCUAUCAAUGCCGAUGACUUAUAGCCAGAGUCGCGGACCGAGACUCACAUGAGUCGAGCCAGCCAAACUGGCAAAUCCAUCCAUCUAUGUGGCACAUUUGACUGCAG
(((((.((((((....))))))))))).(((((.......)))))((((.....(((((....)))))..(((((((.....))).....(((......)))))))........)))).. ( -39.60)
>DroSec_CAF1 51772 120 + 1
UCGGCGAUUGAUGGCUAUCAAUGCCGAUGACUUAUAGCCAGAGUCGCGGGCCGAGACUCACAUGAGUCGAGCCAGCCAAACUGGCAAAUCCAUCCAUCUAUGUGGCACAUUUGACUGCAG
(((((.((((((....))))))))))).(((((.......)))))((((((((.(((((....)))))..(((((.....))))).................)))).(....).)))).. ( -41.50)
>DroSim_CAF1 23842 120 + 1
UCGGCGAUUGAUGGCUAUCAAUGCCGAUGACUUAUAGCCGGAGUCGCGGACCGCGACUCACAUGAGUCGAGCCAGCCAAACUGGCAAAUCCAUCCAUCUAUGUGGCACAUUUGACUGCAG
(((((.((((((....)))))))))))((((((((.(...((((((((...)))))))).))))))))).(((((.....)))))...............((..(((....)).)..)). ( -44.20)
>DroEre_CAF1 26863 119 + 1
UCGGCGAU-GAUGGCUAUCAAUGCCGAUGACUUAUAGCCAGAGUCGCAGACCGAGGCGCACAUGAGCAGAGCCAGCCAAACUGGCAAAUCCAUCCAUCUAUGUGGCACAUUUGACUGCAG
((((((.(-(((....)))).)))))).(((((.......)))))((((.(.((.((.(((((((...(((((((.....))))).......))..)).)))))))...)).).)))).. ( -36.51)
>DroYak_CAF1 20208 120 + 1
UCGGCGAUUGAUGGCUAUCAAUGCCGAUGACUUAUAGCCGGAGUCGCAGACUCAGGCUCACAUGAGUCGAGCCAGCGAAACUGGCAAAUCCAUCCAUCUAUGUGGCACAUUUGACUGCAG
(((((.((((((....)))))))))))((((((((((((.(((((...))))).))))...)))))))).(((((.....)))))...............((..(((....)).)..)). ( -43.50)
>consensus
UCGGCGAUUGAUGGCUAUCAAUGCCGAUGACUUAUAGCCAGAGUCGCGGACCGAGACUCACAUGAGUCGAGCCAGCCAAACUGGCAAAUCCAUCCAUCUAUGUGGCACAUUUGACUGCAG
(((((.((((((....))))))))))).(((((.......)))))((((.....(((((....)))))..(((((.....)))))........((((....)))).........)))).. (-37.18 = -37.14 +  -0.04)

alignment

secondary structure

dotplot

Window 7

Location	8,100,122 – 8,100,242
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.50
Mean single sequence MFE	-41.40
Consensus MFE	-34.84
Energy contribution	-35.48
Covariance contribution	0.64
Combinations/Pair	1.07
Mean z-score	-1.47
Structure conservation index	0.84
SVM decision value	0.36
SVM RNA-class probability	0.705275
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8100122 120 - 27905053
CUGCAGUCAAAUGUGCCACAUAGAUGGAUGGAUUUGCCAGUUUGGCUGGCUCGACUCAUGUGAGUCUCGGUCCGCGACUCUGGCUAUAAGUCAUCGGCAUUGAUAGCCAUCAAUCGCCGA
....((((..(((.....))).(.(((((.((...(((((.....)))))..(((((....))))))).)))))))))).((((.....))))(((((((((((....)))))).))))) ( -41.90)
>DroSec_CAF1 51772 120 - 1
CUGCAGUCAAAUGUGCCACAUAGAUGGAUGGAUUUGCCAGUUUGGCUGGCUCGACUCAUGUGAGUCUCGGCCCGCGACUCUGGCUAUAAGUCAUCGGCAUUGAUAGCCAUCAAUCGCCGA
...((..((..((((...))))..))..))((((((((((..(.((.((((.(((((....)))))..)))).)).)..)))))...))))).(((((((((((....)))))).))))) ( -43.80)
>DroSim_CAF1 23842 120 - 1
CUGCAGUCAAAUGUGCCACAUAGAUGGAUGGAUUUGCCAGUUUGGCUGGCUCGACUCAUGUGAGUCGCGGUCCGCGACUCCGGCUAUAAGUCAUCGGCAUUGAUAGCCAUCAAUCGCCGA
...(((((((((...(((......))).(((.....))))))))))))....((((.((((((((((((...))))))))..)).)).)))).(((((((((((....)))))).))))) ( -43.10)
>DroEre_CAF1 26863 119 - 1
CUGCAGUCAAAUGUGCCACAUAGAUGGAUGGAUUUGCCAGUUUGGCUGGCUCUGCUCAUGUGCGCCUCGGUCUGCGACUCUGGCUAUAAGUCAUCGGCAUUGAUAGCCAUC-AUCGCCGA
..((((.(....((((.(((....((..((((...(((((.....)))))))))..)))))))))....).))))((((.........)))).(((((..((((....)))-)..))))) ( -37.90)
>DroYak_CAF1 20208 120 - 1
CUGCAGUCAAAUGUGCCACAUAGAUGGAUGGAUUUGCCAGUUUCGCUGGCUCGACUCAUGUGAGCCUGAGUCUGCGACUCCGGCUAUAAGUCAUCGGCAUUGAUAGCCAUCAAUCGCCGA
.((.((((((((.(((((......))).)).))))(((((.....)))))..))))))....((((.(((((...))))).))))........(((((((((((....)))))).))))) ( -40.30)
>consensus
CUGCAGUCAAAUGUGCCACAUAGAUGGAUGGAUUUGCCAGUUUGGCUGGCUCGACUCAUGUGAGUCUCGGUCCGCGACUCUGGCUAUAAGUCAUCGGCAUUGAUAGCCAUCAAUCGCCGA
...((..((..((((...))))..))..))((((((((((..(.((.((((.(((((....)))))..)))).)).)..)))))...))))).(((((((((((....)))))).))))) (-34.84 = -35.48 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:52:04 2006