Locus 4011

Sequence ID	2R_DroMel_CAF1
Location	13,252,019 – 13,252,116
Length	97
Max. P	0.987598

overview

Window 3

Location	13,252,019 – 13,252,116
Length	97
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	79.22
Mean single sequence MFE	-25.71
Consensus MFE	-14.55
Energy contribution	-16.67
Covariance contribution	2.12
Combinations/Pair	1.17
Mean z-score	-2.10
Structure conservation index	0.57
SVM decision value	0.80
SVM RNA-class probability	0.853351
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13252019 97 + 20766785
UCCGCACCCUGGGUUAUGUGGUAGCAGUGGCUAAUUAAUUUAUCACUAGCCUCCGCUGCUGCUCCCUCUUAAUUUUUU--CCCAAAUAA--GCCAGGGCUG
......((((((.(((((..(((((((((((((.............)))))...))))))))..).............--.....))))--.))))))... ( -30.68)
>DroPse_CAF1 5415 88 + 1
GCCGCGAAUUAUAUUAUGUAUUAACAAUGCUUAAUUAAUUUAUCGCCCGUCCCCGCUGCACA---------AGACCAU--CAGAAAUAU--ACCGAAACUA
((.((((((((.((((.((((.....)))).))))))))).............))).))...---------.......--.........--.......... (  -7.61)
>DroSec_CAF1 3623 99 + 1
UCCGCACCCUGGGUUAUGUGCUAGCAGUGGCUAAUUAAUUUAUCACUAGCCUCCGCUGCUGCUCCCUCUUAAUUUUUUUCCCCAAAUAA--GCCAGGGCUG
......((((((.((((..((.(((((((((((.............)))))...)))))))).......................))))--.))))))... ( -27.93)
>DroSim_CAF1 3616 99 + 1
UCCGCACCCUGGGUUAUGUGGUAGCAGUGGCUAAUUAAUUUAUCACUAGCCUCCGCUGCUGCUCCCUCUUAAUUUUUUUCCCCAAAUAA--GCCAGGGCUG
......((((((.(((((..(((((((((((((.............)))))...))))))))..)....................))))--.))))))... ( -30.57)
>DroYak_CAF1 3595 101 + 1
UCCGCACCCUGGGUUAUGUGGUAGCAGUGGCUAAUUAAUUUAUCACCAGCCUCCGCUGCUGCUCCCUCUUAAUUUUUUUUCCCAAAUAAGGGCCAGGGCUG
......((((((.....(..(((((.(.((((...............)))).).)))))..)..................(((......)))))))))... ( -31.76)
>consensus
UCCGCACCCUGGGUUAUGUGGUAGCAGUGGCUAAUUAAUUUAUCACUAGCCUCCGCUGCUGCUCCCUCUUAAUUUUUUU_CCCAAAUAA__GCCAGGGCUG
......((((((.((((..((((((((((((((.............)))))...)))))))))......................))))...))))))... (-14.55 = -16.67 +   2.12)

alignment

secondary structure

dotplot

Window 4

Location	13,252,019 – 13,252,116
Length	97
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	79.22
Mean single sequence MFE	-30.40
Consensus MFE	-22.32
Energy contribution	-23.28
Covariance contribution	0.96
Combinations/Pair	1.26
Mean z-score	-2.43
Structure conservation index	0.73
SVM decision value	2.09
SVM RNA-class probability	0.987598
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13252019 97 - 20766785
CAGCCCUGGC--UUAUUUGGG--AAAAAAUUAAGAGGGAGCAGCAGCGGAGGCUAGUGAUAAAUUAAUUAGCCACUGCUACCACAUAACCCAGGGUGCGGA
..(((((((.--((((.(((.--............(....)...(((((.(((((((.........))))))).))))).))).)))).)))))))..... ( -35.60)
>DroPse_CAF1 5415 88 - 1
UAGUUUCGGU--AUAUUUCUG--AUGGUCU---------UGUGCAGCGGGGACGGGCGAUAAAUUAAUUAAGCAUUGUUAAUACAUAAUAUAAUUCGCGGC
..((..((((--(((((..((--(..((((---------(((((..((....)).)))..........)))).))..)))......))))))..)))..)) ( -12.50)
>DroSec_CAF1 3623 99 - 1
CAGCCCUGGC--UUAUUUGGGGAAAAAAAUUAAGAGGGAGCAGCAGCGGAGGCUAGUGAUAAAUUAAUUAGCCACUGCUAGCACAUAACCCAGGGUGCGGA
..((((((((--((.(((...((......))..))).)))).(((((((.(((((((.........))))))).))))).))........))))))..... ( -33.50)
>DroSim_CAF1 3616 99 - 1
CAGCCCUGGC--UUAUUUGGGGAAAAAAAUUAAGAGGGAGCAGCAGCGGAGGCUAGUGAUAAAUUAAUUAGCCACUGCUACCACAUAACCCAGGGUGCGGA
..(((((((.--((((.(((...............(....)...(((((.(((((((.........))))))).))))).))).)))).)))))))..... ( -35.60)
>DroYak_CAF1 3595 101 - 1
CAGCCCUGGCCCUUAUUUGGGAAAAAAAAUUAAGAGGGAGCAGCAGCGGAGGCUGGUGAUAAAUUAAUUAGCCACUGCUACCACAUAACCCAGGGUGCGGA
..((((((((((((((((........))))...)))))......(((((.(((((((.........))))))).)))))..........)))))))..... ( -34.80)
>consensus
CAGCCCUGGC__UUAUUUGGG_AAAAAAAUUAAGAGGGAGCAGCAGCGGAGGCUAGUGAUAAAUUAAUUAGCCACUGCUACCACAUAACCCAGGGUGCGGA
..(((((((...((((.(((...............(....)...(((((.(((((((.........))))))).))))).))).)))).)))))))..... (-22.32 = -23.28 +   0.96)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:09:39 2006