Locus 4324

Sequence ID	3L_DroMel_CAF1
Location	12,706,872 – 12,706,983
Length	111
Max. P	0.765144

overview

Window 2

Location	12,706,872 – 12,706,983
Length	111
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	81.21
Mean single sequence MFE	-26.31
Consensus MFE	-17.96
Energy contribution	-18.88
Covariance contribution	0.92
Combinations/Pair	1.18
Mean z-score	-1.74
Structure conservation index	0.68
SVM decision value	0.32
SVM RNA-class probability	0.688735
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12706872 111 + 23771897
UUUUAGCGGGUAUCCGAACCCGAAUAGCGAUAAU--UGAUCGGAGCAAGUUCCACAAUUUGACAUUUCGAUAUAUUAUCGGAACCGGUUCAACCUGCCUUUGAAAACUUAAA-C
.....((((((....(((((.(.....(((((((--..((((((.((((((....))))))....))))))..)))))))...).))))).))))))...............-. ( -27.20)
>DroSec_CAF1 70174 112 + 1
UUUUAGCGGGUAUCCGAACCCGAACAGCGAUAAU--UGAUGGGAACAAGUUCCACAACUUGAAAUUUCGAUAUAUUAUCGGAACCGGUUCCACCCGCCUUAGAAAAUUUAAAUC
(((((((((((....(((((.(.....(((((((--..((.((((((((((....))))))...)))).))..)))))))...).))))).))))))..))))).......... ( -28.10)
>DroSim_CAF1 68996 112 + 1
UUUUAGCGGGUAUCCGAACCCAAACAGCGAUAAU--UGAUCGGAACAAGUUCCACAACUAGAAAUUUCGAUAUAUUAUCGGAACCGGUUCAACCCGCCUUUGAAAAUUUAAGUC
.....((((((....(((((.......(((((((--..(((((((....(((........))).)))))))..))))))).....))))).))))))................. ( -27.90)
>DroEre_CAF1 73538 114 + 1
AUUUAGCAGGUAUCCGAACCCGUGCACCCGAACCCGUGACCGGAACCAGUUCCACAAGAUUUUAUUUCACUAUUUUAUCGGAACCUGCUUAGCCCGCCUUCGAACAUUUAAAUU
....(((((((.(((((..(((..(((........)))..)))..............((.......)).........))))))))))))......................... ( -24.90)
>DroYak_CAF1 73387 112 + 1
UCUUAGCGAGUAUCCGAACCCGAGUACCGAUAAC--UGAUCGGAACCAGUUCCACAAGCUUUCAUUUCAACCUAUUAUCGGAACCGGUUCAGCCCGCCUUAGAACAUUUAAUUU
(((..(((.(((..((....))..)))((((...--..))))(((((.(((((..........................))))).)))))....)))...)))........... ( -23.47)
>consensus
UUUUAGCGGGUAUCCGAACCCGAACAGCGAUAAU__UGAUCGGAACAAGUUCCACAACUUGAAAUUUCGAUAUAUUAUCGGAACCGGUUCAACCCGCCUUAGAAAAUUUAAAUC
.....((((((....(((((.....................((((....))))...........(((((((.....)))))))..))))).))))))................. (-17.96 = -18.88 +   0.92)

alignment

secondary structure

dotplot

Window 3

Location	12,706,872 – 12,706,983
Length	111
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	81.21
Mean single sequence MFE	-32.27
Consensus MFE	-22.00
Energy contribution	-21.92
Covariance contribution	-0.08
Combinations/Pair	1.23
Mean z-score	-1.85
Structure conservation index	0.68
SVM decision value	0.51
SVM RNA-class probability	0.765144
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12706872 111 - 23771897
G-UUUAAGUUUUCAAAGGCAGGUUGAACCGGUUCCGAUAAUAUAUCGAAAUGUCAAAUUGUGGAACUUGCUCCGAUCA--AUUAUCGCUAUUCGGGUUCGGAUACCCGCUAAAA
.-..............(((.(((((((((.(...(((((((..(((((....)).......(((......))))))..--))))))).....).))))))...))).))).... ( -24.50)
>DroSec_CAF1 70174 112 - 1
GAUUUAAAUUUUCUAAGGCGGGUGGAACCGGUUCCGAUAAUAUAUCGAAAUUUCAAGUUGUGGAACUUGUUCCCAUCA--AUUAUCGCUGUUCGGGUUCGGAUACCCGCUAAAA
................((((((((...((((..((((.........((....)).(((((.((((....))))...))--)))........))))..)))).)))))))).... ( -31.90)
>DroSim_CAF1 68996 112 - 1
GACUUAAAUUUUCAAAGGCGGGUUGAACCGGUUCCGAUAAUAUAUCGAAAUUUCUAGUUGUGGAACUUGUUCCGAUCA--AUUAUCGCUGUUUGGGUUCGGAUACCCGCUAAAA
................(((((((((((((.(..((((((((..((((.(((....((((....)))).))).))))..--)))))))..)..).))))))...))))))).... ( -31.60)
>DroEre_CAF1 73538 114 - 1
AAUUUAAAUGUUCGAAGGCGGGCUAAGCAGGUUCCGAUAAAAUAGUGAAAUAAAAUCUUGUGGAACUGGUUCCGGUCACGGGUUCGGGUGCACGGGUUCGGAUACCUGCUAAAU
.........(((((....)))))..((((((((((((...................((((((.(.((((..(((....)))..)))).).)))))).))))).))))))).... ( -37.15)
>DroYak_CAF1 73387 112 - 1
AAAUUAAAUGUUCUAAGGCGGGCUGAACCGGUUCCGAUAAUAGGUUGAAAUGAAAGCUUGUGGAACUGGUUCCGAUCA--GUUAUCGGUACUCGGGUUCGGAUACUCGCUAAGA
................((((((((((((((((.(((((.(((((((........)))))))..(((((((....))))--)))))))).)))..)))))))...)))))).... ( -36.20)
>consensus
GAUUUAAAUUUUCAAAGGCGGGUUGAACCGGUUCCGAUAAUAUAUCGAAAUGUCAACUUGUGGAACUUGUUCCGAUCA__AUUAUCGCUGUUCGGGUUCGGAUACCCGCUAAAA
................(((.((((((((.((((((.(((((...............))))))))))).))).)))))................((((......))))))).... (-22.00 = -21.92 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:19:37 2006