Locus 4961

Sequence ID	2L_DroMel_CAF1
Location	14,240,229 – 14,240,372
Length	143
Max. P	0.910806

overview

Window 8

Location	14,240,229 – 14,240,341
Length	112
Sequences	3
Columns	114
Reading direction	forward
Mean pairwise identity	90.59
Mean single sequence MFE	-34.63
Consensus MFE	-29.48
Energy contribution	-29.27
Covariance contribution	-0.22
Combinations/Pair	1.12
Mean z-score	-2.00
Structure conservation index	0.85
SVM decision value	0.29
SVM RNA-class probability	0.669225
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14240229 112 + 22407834
GCAGCGCCAGCACCUCAUCUGGAAUUAAUGAGCUGCUCCUACUGAUGCAUCAUCAGUACAUCGGUAGCCAAA-GGGGGAAGUCUGCCACAUCCCAGAUAAA-GUAUGUAUAUGU
(((((....)).....((((((......((.((((((..((((((((...))))))))....))))))))..-((.((....)).)).....))))))...-...)))...... ( -32.30)
>DroSec_CAF1 72923 113 + 1
GCAGCGC-AGCACCUCAUCUGGAAUUAAUGAGCUGCUACUACUGAUGCAUCAUCAGUACAUCAGUAGCCAAACGGAGGGAGUCUGCUCCAUCCCAGCUAUAUGUAUGUAUGUGU
...((((-((((...(((.(((......((.((((((..((((((((...))))))))....))))))))...(((.((((....)))).)))...))).)))..))).))))) ( -35.30)
>DroSim_CAF1 65157 108 + 1
GCAGCGC-AGCACCUCAUCUGGAAUUAAUGAGCUGCUACUACUGAUGCAUCAUCAGUACAUCAGUAGCCAAA-GGGGGGAGUCUGCUCCAUCCCAGAUAUAU----GUAUGUGU
...((((-((((....((((........((.((((((..((((((((...))))))))....))))))))..-((((((((....)))).))))))))...)----)).))))) ( -36.30)
>consensus
GCAGCGC_AGCACCUCAUCUGGAAUUAAUGAGCUGCUACUACUGAUGCAUCAUCAGUACAUCAGUAGCCAAA_GGGGGGAGUCUGCUCCAUCCCAGAUAUAUGUAUGUAUGUGU
(((((....)).....((((((......((.((((((..((((((((...))))))))....))))))))...((((.(....).))))...)))))).............))) (-29.48 = -29.27 +  -0.22)

alignment

secondary structure

dotplot

Window 9

Location	14,240,229 – 14,240,341
Length	112
Sequences	3
Columns	114
Reading direction	reverse
Mean pairwise identity	90.59
Mean single sequence MFE	-39.83
Consensus MFE	-32.32
Energy contribution	-33.10
Covariance contribution	0.78
Combinations/Pair	1.03
Mean z-score	-3.08
Structure conservation index	0.81
SVM decision value	1.07
SVM RNA-class probability	0.910806
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14240229 112 - 22407834
ACAUAUACAUAC-UUUAUCUGGGAUGUGGCAGACUUCCCCC-UUUGGCUACCGAUGUACUGAUGAUGCAUCAGUAGGAGCAGCUCAUUAAUUCCAGAUGAGGUGCUGGCGCUGC
.......(((((-(((((((((((((((((.(.((((....-.((((...))))..((((((((...))))))))))))).)).)))..))))))))))))))).))....... ( -35.70)
>DroSec_CAF1 72923 113 - 1
ACACAUACAUACAUAUAGCUGGGAUGGAGCAGACUCCCUCCGUUUGGCUACUGAUGUACUGAUGAUGCAUCAGUAGUAGCAGCUCAUUAAUUCCAGAUGAGGUGCU-GCGCUGC
...............((((..(((.((((....)))).))).......(((((((((((....).))))))))))((((((.((((((.......)))))).))))-)))))). ( -42.50)
>DroSim_CAF1 65157 108 - 1
ACACAUAC----AUAUAUCUGGGAUGGAGCAGACUCCCCCC-UUUGGCUACUGAUGUACUGAUGAUGCAUCAGUAGUAGCAGCUCAUUAAUUCCAGAUGAGGUGCU-GCGCUGC
........----........(((..((((....)))).)))-...((((((((((((((....).))))))))))((((((.((((((.......)))))).))))-))))).. ( -41.30)
>consensus
ACACAUACAUACAUAUAUCUGGGAUGGAGCAGACUCCCCCC_UUUGGCUACUGAUGUACUGAUGAUGCAUCAGUAGUAGCAGCUCAUUAAUUCCAGAUGAGGUGCU_GCGCUGC
...............((((((((((.((((......((.......))((((((((((((....).))))))))))).....))))....)))))))))).((((....)))).. (-32.32 = -33.10 +   0.78)

alignment

secondary structure

dotplot

Window 0

Location	14,240,266 – 14,240,372
Length	106
Sequences	3
Columns	108
Reading direction	forward
Mean pairwise identity	89.47
Mean single sequence MFE	-31.20
Consensus MFE	-25.04
Energy contribution	-25.60
Covariance contribution	0.56
Combinations/Pair	1.07
Mean z-score	-1.94
Structure conservation index	0.80
SVM decision value	0.02
SVM RNA-class probability	0.542045
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14240266 106 + 22407834
CCUACUGAUGCAUCAUCAGUACAUCGGUAGCCAAA-GGGGGAAGUCUGCCACAUCCCAGAUAAA-GUAUGUAUAUGUAUGUACAUCUUACGCCUUUCGACGUGGCUCC
..((((((((...))))))))....((.(((((..-(..((..(((((........))))).((-(.(((((((....))))))))))....))..)....))))))) ( -31.20)
>DroSec_CAF1 72959 108 + 1
ACUACUGAUGCAUCAUCAGUACAUCAGUAGCCAAACGGAGGGAGUCUGCUCCAUCCCAGCUAUAUGUAUGUAUGUGUAUGUACAUCUUACGCCUUUCGAUGCGGCUCC
.(((((((((.((.....)).)))))))))......(((.((((....)))).))).(((...(((((((((....)))))))))....(((........)))))).. ( -31.40)
>DroSim_CAF1 65193 103 + 1
ACUACUGAUGCAUCAUCAGUACAUCAGUAGCCAAA-GGGGGGAGUCUGCUCCAUCCCAGAUAUAU----GUAUGUGUAUGUACAUCUUACGCCUUUCGAUGCGGCUCC
.(((((((((.((.....)).))))))))).....-((((((((....)))).))))((((.(((----(((....)))))).))))...(((.........)))... ( -31.00)
>consensus
ACUACUGAUGCAUCAUCAGUACAUCAGUAGCCAAA_GGGGGGAGUCUGCUCCAUCCCAGAUAUAUGUAUGUAUGUGUAUGUACAUCUUACGCCUUUCGAUGCGGCUCC
.(((((((((.((.....)).)))))))))......((((((((....)))).))))............(((.((((....))))..)))(((.........)))... (-25.04 = -25.60 +   0.56)

alignment

secondary structure

dotplot

Window 1

Location	14,240,266 – 14,240,372
Length	106
Sequences	3
Columns	108
Reading direction	reverse
Mean pairwise identity	89.47
Mean single sequence MFE	-33.93
Consensus MFE	-26.03
Energy contribution	-25.27
Covariance contribution	-0.77
Combinations/Pair	1.19
Mean z-score	-2.09
Structure conservation index	0.77
SVM decision value	0.02
SVM RNA-class probability	0.545441
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14240266 106 - 22407834
GGAGCCACGUCGAAAGGCGUAAGAUGUACAUACAUAUACAUAC-UUUAUCUGGGAUGUGGCAGACUUCCCCC-UUUGGCUACCGAUGUACUGAUGAUGCAUCAGUAGG
(((((((((((....)))))((((((((........))))).)-)).....((((.((.....)).))))..-...)))).))....((((((((...)))))))).. ( -34.50)
>DroSec_CAF1 72959 108 - 1
GGAGCCGCAUCGAAAGGCGUAAGAUGUACAUACACAUACAUACAUAUAGCUGGGAUGGAGCAGACUCCCUCCGUUUGGCUACUGAUGUACUGAUGAUGCAUCAGUAGU
((((((((.((....)).(((.(((((......)))).).))).....)).))...((((....)))))))).....(((((((((((((....).)))))))))))) ( -34.60)
>DroSim_CAF1 65193 103 - 1
GGAGCCGCAUCGAAAGGCGUAAGAUGUACAUACACAUAC----AUAUAUCUGGGAUGGAGCAGACUCCCCCC-UUUGGCUACUGAUGUACUGAUGAUGCAUCAGUAGU
...(((.........)))...(((((((..((....)).----.)))))))(((..((((....)))).)))-....(((((((((((((....).)))))))))))) ( -32.70)
>consensus
GGAGCCGCAUCGAAAGGCGUAAGAUGUACAUACACAUACAUACAUAUAUCUGGGAUGGAGCAGACUCCCCCC_UUUGGCUACUGAUGUACUGAUGAUGCAUCAGUAGU
(((((((((((...........)))))........................(((..((((....)))).)))....)))).))....((((((((...)))))))).. (-26.03 = -25.27 +  -0.77)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:32:04 2006