Locus 3152

Sequence ID	2L_DroMel_CAF1
Location	9,013,239 – 9,013,479
Length	240
Max. P	0.726813

overview

Window 8

Location	9,013,239 – 9,013,359
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	88.06
Mean single sequence MFE	-42.73
Consensus MFE	-35.66
Energy contribution	-36.33
Covariance contribution	0.67
Combinations/Pair	1.09
Mean z-score	-1.68
Structure conservation index	0.83
SVM decision value	-0.06
SVM RNA-class probability	0.505340
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9013239 120 + 22407834
ACAUGCUUCAGCACCCGGAGGCAUGGAAACUUCAACAUAUGGAUGACCAUUUUGCCCAGGGUGAUGGCCACCUGCGAGAAGCGAUCGUGGUUCUCGCAAAUGUACGUCAGACCCAUCUCA
.((((((((........))))))))..........((.((((....))))..))....((((((((..((..((((((((.((....)).))))))))..))..))))..))))...... ( -39.60)
>DroSec_CAF1 7163 120 + 1
ACAUGCUUCAGCACCCGGAAGCAUGGAGAUUUCAUCAUUCGAAUGGUCAUUUUGCCCAGGGUGAUGGCCACCCCCGCGAAGCGAUCGUGGGUCUCGCAGAUGUACGAUAGACCCGUCUCA
.((((((((........))))))))(((((............((((((.((((((...(((((.....)))))..)))))).))))))((((((((........)))..)))))))))). ( -46.50)
>DroSim_CAF1 8154 120 + 1
ACACGCUUCAGCACCCGGAAGCAUGGAUACUUCAUCAUUCGGAUGGUCAUUUUGCCCAGGGUGGUGGCCACCCGAGCGAAGCGAUCGUGGGUCUCGCAGAUGUACGAUAGACCCGUCUUA
...((((((.((.....((((........)))).....((((.((((((((..(((...))))))))))).))))))))))))((((((.(((.....))).))))))(((....))).. ( -42.10)
>consensus
ACAUGCUUCAGCACCCGGAAGCAUGGAAACUUCAUCAUUCGGAUGGUCAUUUUGCCCAGGGUGAUGGCCACCCGCGCGAAGCGAUCGUGGGUCUCGCAGAUGUACGAUAGACCCGUCUCA
.((((((((........)))))))).................((((((.((((((...(((((.....)))))..)))))).))))))((((((..(........)..))))))...... (-35.66 = -36.33 +   0.67)

alignment

secondary structure

dotplot

Window 9

Location	9,013,279 – 9,013,399
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	87.22
Mean single sequence MFE	-41.07
Consensus MFE	-32.35
Energy contribution	-32.47
Covariance contribution	0.12
Combinations/Pair	1.13
Mean z-score	-1.99
Structure conservation index	0.79
SVM decision value	0.19
SVM RNA-class probability	0.625214
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9013279 120 - 22407834
AGAUCGCGGCCACUUCAAUCCUUGAGAAGAUACUGCUCGAUGAGAUGGGUCUGACGUACAUUUGCGAGAACCACGAUCGCUUCUCGCAGGUGGCCAUCACCCUGGGCAAAAUGGUCAUCC
.......(((((((((.........))))....((((((..(.((((((.....)...((((((((((((.(......).)))))))))))).))))).)..))))))...))))).... ( -38.70)
>DroSec_CAF1 7203 120 - 1
AGUUUGCGGCCAUCAAAAUCAUUGAGAAGAUACUGCUCAAUGAGACGGGUCUAUCGUACAUCUGCGAGACCCACGAUCGCUUCGCGGGGGUGGCCAUCACCCUGGGCAAAAUGACCAUUC
..((((((((.(((....((((((((.((...)).))))))))...(((((..(((((....))))))))))..))).)))...(.((((((.....)))))).)))))).......... ( -43.00)
>DroSim_CAF1 8194 120 - 1
AGUCUGCGGCCAUCAAAAUCAUUGAGAAGAUACUGCUCAAUAAGACGGGUCUAUCGUACAUCUGCGAGACCCACGAUCGCUUCGCUCGGGUGGCCACCACCCUGGGCAAAAUGACCAUCC
.(((.(((..(.........((((((.((...)).)))))).....(((((..(((((....))))))))))..)..)))...((((((((((...)))))).)))).....)))..... ( -41.50)
>consensus
AGUUUGCGGCCAUCAAAAUCAUUGAGAAGAUACUGCUCAAUGAGACGGGUCUAUCGUACAUCUGCGAGACCCACGAUCGCUUCGCGCGGGUGGCCAUCACCCUGGGCAAAAUGACCAUCC
.....(((((((((....((((((((.((...)).))))))))...((((((..((((....))))))))))................))))))).((.....))))............. (-32.35 = -32.47 +   0.12)

alignment

secondary structure

dotplot

Window 0

Location	9,013,359 – 9,013,479
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	85.00
Mean single sequence MFE	-43.17
Consensus MFE	-31.98
Energy contribution	-31.77
Covariance contribution	-0.21
Combinations/Pair	1.16
Mean z-score	-2.11
Structure conservation index	0.74
SVM decision value	0.41
SVM RNA-class probability	0.726813
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9013359 120 + 22407834
UCGAGCAGUAUCUUCUCAAGGAUUGAAGUGGCCGCGAUCUUGGUCAGCUUCGAUCCCCUGACCAUAUUGGUCAGACAGUGAGGCACGACCUCGCUCCAUAUCAGGAAGAUGAGGACCUCC
..((((..((((((((...(((((((((((((((......)))))).))))))))).((((((.....))))))..(((((((.....)))))))........))))))))..)..))). ( -48.70)
>DroSec_CAF1 7283 120 + 1
UUGAGCAGUAUCUUCUCAAUGAUUUUGAUGGCCGCAAACUUGGUCAGCAUCGAUCCCUUGAGCAUGUUGCUCAGGCAGAGAGGCACGACCUCGGUGGACAGCAAAAAGCUGAUGGCCUCC
(((((((((((...(((((.((((.((.((((((......)))))).))..))))..))))).))))))))))).....(((((.(.((....)).).((((.....))))...))))). ( -40.20)
>DroSim_CAF1 8274 120 + 1
UUGAGCAGUAUCUUCUCAAUGAUUUUGAUGGCCGCAGACUUGGUCAGCUUCGAUCCCUUGAGCAUGUUGCUUAGGCAGAGAGGCACGACCUCGCUGGACAGCAAAAAGCUGAUGGCCUCC
(((((.((...)).))))).......((.((((((((.(((((((.(((((.....(((((((.....)))))))....)))))..))))..(((....)))...)))))).))))))). ( -40.60)
>consensus
UUGAGCAGUAUCUUCUCAAUGAUUUUGAUGGCCGCAAACUUGGUCAGCUUCGAUCCCUUGAGCAUGUUGCUCAGGCAGAGAGGCACGACCUCGCUGGACAGCAAAAAGCUGAUGGCCUCC
(((((.((...)).)))))..........((((........((((.(((((.....(((((((.....)))))))....)))))..))))........((((.....))))..))))... (-31.98 = -31.77 +  -0.21)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:45:35 2006