Locus 1998

Sequence ID	X_DroMel_CAF1
Location	5,498,776 – 5,498,868
Length	92
Max. P	0.509792

overview

Window 4

Location	5,498,776 – 5,498,868
Length	92
Sequences	6
Columns	98
Reading direction	forward
Mean pairwise identity	82.09
Mean single sequence MFE	-43.97
Consensus MFE	-27.96
Energy contribution	-28.15
Covariance contribution	0.19
Combinations/Pair	1.19
Mean z-score	-1.63
Structure conservation index	0.64
SVM decision value	-0.05
SVM RNA-class probability	0.509792
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5498776 92 + 22224390
ACCGGACAGAAGGCCUUUUCCGUAUUGAGGGAUUGCGGCGACAGUGCCCGGAUGGGUGCCU---UCAGUCCA-CAGCU--GCUGUCGCCGCCCUGUUG
....(((((....(((((........)))))...(((((((((((((..((((.((.....---)).)))).-..)).--))))))))))).))))). ( -37.60)
>DroVir_CAF1 38018 98 + 1
ACCGGACAGAAGGCCUUAUCGGUGUUGAGGCUUUGCGGCGACAGCGCCCGGCCGUGGGCCCGUUCCAAUCGGCUGGCUGCGCUGCCGCCGCCCUGUUC
...(((((((((((((((.......)))))))))((((((.(((((((((((((((((.....))))..)))))))..)))))).)))))).)))))) ( -56.80)
>DroGri_CAF1 27032 98 + 1
ACCGGACAGAAGGCCUUGUCAGUGUUGAGGCUAUGCGGCGACAGGGCCCGGCCGGGGGCCCGUUCUAAUCGGCUGGCUGCGCUGCCGCCGCCCUGUUC
...((((((..(((((((.......)))))))..((((((.(((.(((((((((((((....))))...)))))))..)).))).)))))).)))))) ( -47.90)
>DroSim_CAF1 16801 92 + 1
ACCGGACAGAAGGCCUUUUCCGUGUUGAGGGAUUGCGGCGACAGUGCCCGGAUGGGUGCCU---UCAGUCCA-CAGCU--GCUGUCGCCGCCCUGUUG
....(((((....(((((........)))))...(((((((((((((..((((.((.....---)).)))).-..)).--))))))))))).))))). ( -37.60)
>DroYak_CAF1 25197 92 + 1
ACCGGACAGAAGGCCUUCUCCGUAUUGAGGGAUUGCGGCGACAGUGCCCGGUUGGGUACCU---UGAGUCCA-CAGCU--GCUGUCGCCGCCCUGUUG
....(((((....(((((........)))))...(((((((((((....(((((((.((..---...)))).-)))))--))))))))))).))))). ( -39.90)
>DroMoj_CAF1 31712 98 + 1
ACCGGACAGAAGGCCUUCUCGGUGUUGAGGCUCUGCGGCGACAGCGCCCGGCCGUGGGCCCGUUCCAAUCGGCCAGCUACGCUAUCGCCGCCCUGUUC
...((((((.((((((.(........))))).))(((((((.((((.(.(((((((((.....))))..))))).)...)))).))))))).)))))) ( -44.00)
>consensus
ACCGGACAGAAGGCCUUCUCCGUGUUGAGGCAUUGCGGCGACAGUGCCCGGCCGGGGGCCC___CCAAUCCA_CAGCU__GCUGUCGCCGCCCUGUUC
....(((((....((((.........))))....(((((((((((....(((((((.............))..)))))..))))))))))).))))). (-27.96 = -28.15 +   0.19)

alignment

secondary structure

dotplot

Window 5

Location	5,498,776 – 5,498,868
Length	92
Sequences	6
Columns	98
Reading direction	reverse
Mean pairwise identity	82.09
Mean single sequence MFE	-40.02
Consensus MFE	-28.15
Energy contribution	-27.23
Covariance contribution	-0.91
Combinations/Pair	1.20
Mean z-score	-1.31
Structure conservation index	0.70
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5498776 92 - 22224390
CAACAGGGCGGCGACAGC--AGCUG-UGGACUGA---AGGCACCCAUCCGGGCACUGUCGCCGCAAUCCCUCAAUACGGAAAAGGCCUUCUGUCCGGU
.....((((((((((((.--.(((.-((((.((.---.......))))))))).))))))))))...........((((((......))))))))... ( -33.80)
>DroVir_CAF1 38018 98 - 1
GAACAGGGCGGCGGCAGCGCAGCCAGCCGAUUGGAACGGGCCCACGGCCGGGCGCUGUCGCCGCAAAGCCUCAACACCGAUAAGGCCUUCUGUCCGGU
(.((((((((((((((((((..((.((((..(((.......))))))).)))))))))))))))...((((...........))))..))))).)... ( -48.70)
>DroGri_CAF1 27032 98 - 1
GAACAGGGCGGCGGCAGCGCAGCCAGCCGAUUAGAACGGGCCCCCGGCCGGGCCCUGUCGCCGCAUAGCCUCAACACUGACAAGGCCUUCUGUCCGGU
(.((((((((((((((((.......))..........((((((......)))))))))))))))...((((...........))))..))))).)... ( -40.60)
>DroSim_CAF1 16801 92 - 1
CAACAGGGCGGCGACAGC--AGCUG-UGGACUGA---AGGCACCCAUCCGGGCACUGUCGCCGCAAUCCCUCAACACGGAAAAGGCCUUCUGUCCGGU
.....((((((((((((.--.(((.-((((.((.---.......))))))))).))))))))))...........((((((......))))))))... ( -33.90)
>DroYak_CAF1 25197 92 - 1
CAACAGGGCGGCGACAGC--AGCUG-UGGACUCA---AGGUACCCAACCGGGCACUGUCGCCGCAAUCCCUCAAUACGGAGAAGGCCUUCUGUCCGGU
..(((((((((((((((.--.(((.-((....))---.))).(((....)))..)))))))))).....(((......))).......)))))..... ( -31.80)
>DroMoj_CAF1 31712 98 - 1
GAACAGGGCGGCGAUAGCGUAGCUGGCCGAUUGGAACGGGCCCACGGCCGGGCGCUGUCGCCGCAGAGCCUCAACACCGAGAAGGCCUUCUGUCCGGU
(.((((((((((((((((((..(((((((..(((.......)))))))))))))))))))))))((.(((((........).))))))))))).)... ( -51.30)
>consensus
CAACAGGGCGGCGACAGC__AGCUG_CCGACUGA___AGGCACCCAGCCGGGCACUGUCGCCGCAAACCCUCAACACGGAAAAGGCCUUCUGUCCGGU
..(((((((((((((((....(((..(......)....(((.....))).))).))))))))))....(((...........)))...)))))..... (-28.15 = -27.23 +  -0.91)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:51 2006