Locus 1078

Sequence ID	2R_DroMel_CAF1
Location	4,372,058 – 4,372,191
Length	133
Max. P	0.990721

overview

Window 0

Location	4,372,058 – 4,372,163
Length	105
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	89.94
Mean single sequence MFE	-41.44
Consensus MFE	-35.24
Energy contribution	-35.72
Covariance contribution	0.48
Combinations/Pair	1.04
Mean z-score	-2.04
Structure conservation index	0.85
SVM decision value	1.91
SVM RNA-class probability	0.982421
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4372058 105 + 20766785
UUCGGCAAGAGCCGACCCACUGUGCCGACUGCUGCGUACUGCGUGCCGCAGUGCCUUCUGCGCUCGCCGAGCCGCCAUUCUCGCCGCUCGGCACCCAUGCCACAU
.(((((....))))).....((((.(((.(((.(.((((((((...)))))))))....))).))(((((((.((.......)).)))))))......).)))). ( -43.00)
>DroSec_CAF1 42720 105 + 1
UCCUGCAAAAACCGACCCACUGUGCCGGCUGCUGCGUACUGCGUGCCGCAGUGCCUUCUGCGCUCGCCGAGCGUCCAUUCUCGCCGCUCGGCACCCAUGCCACAU
....(((..............((((.(((.(((((((((...))).)))))))))....))))..((((((((.(.......).)))))))).....)))..... ( -36.50)
>DroSim_CAF1 42953 105 + 1
UCCUGCGAGAACCGACCCACUGUGCCGGCUGCUGCGUACUGCGUGCCGCAGUGCCUUCUGCGCUCGCCGAGCGUCCAUUCUCGCCGCUCGGCACCCAUGCCACAU
....(((((((..(((.......((((((.((.((((((((((...)))))))).....))))..)))).)))))..))))))).....((((....)))).... ( -39.41)
>DroEre_CAF1 39240 99 + 1
------AAUACCCGACCCACUGUGCCGGCUGCUGCGUACUGCGUGCCGCAGUGCCUUCUGCGCUCGCCGAGCGGCCAUUCUCGCCGCUCGGCACCCAUGCCACAU
------...............((((((((.((.((((((((((...)))))))).....))))..)))(((((((.......))))))))))))........... ( -41.60)
>DroYak_CAF1 41150 99 + 1
------GAUUUCUGGCCCACUGUGCGGGCUGCUGCGUAGUGCUUGCCGCAGUGCCUUUUGCGCUCGCCGAGCGGCCAUUCUCGCCGCUCGGCACCCAUGCCACAU
------......((((.....((((((((.((((((..((....))))))))))))...))))..((((((((((.......))))))))))......))))... ( -46.70)
>consensus
U_C_GCAAGAACCGACCCACUGUGCCGGCUGCUGCGUACUGCGUGCCGCAGUGCCUUCUGCGCUCGCCGAGCGGCCAUUCUCGCCGCUCGGCACCCAUGCCACAU
.....................((((.(((.(((((((((...))).)))))))))....))))..((((((((((.......))))))))))............. (-35.24 = -35.72 +   0.48)

alignment

secondary structure

dotplot

Window 1

Location	4,372,058 – 4,372,163
Length	105
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	89.94
Mean single sequence MFE	-45.70
Consensus MFE	-38.24
Energy contribution	-38.76
Covariance contribution	0.52
Combinations/Pair	1.11
Mean z-score	-1.52
Structure conservation index	0.84
SVM decision value	0.55
SVM RNA-class probability	0.777698
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4372058 105 - 20766785
AUGUGGCAUGGGUGCCGAGCGGCGAGAAUGGCGGCUCGGCGAGCGCAGAAGGCACUGCGGCACGCAGUACGCAGCAGUCGGCACAGUGGGUCGGCUCUUGCCGAA
.((((((.....((((((((.((.......)).))))))))..(((((......))))))).))))....((((.(((((((.......))))))).)))).... ( -46.70)
>DroSec_CAF1 42720 105 - 1
AUGUGGCAUGGGUGCCGAGCGGCGAGAAUGGACGCUCGGCGAGCGCAGAAGGCACUGCGGCACGCAGUACGCAGCAGCCGGCACAGUGGGUCGGUUUUUGCAGGA
.((((((.....(((((((((...........)))))))))..(((((......))))))).))))....((((.(((((((.......))))))).)))).... ( -45.60)
>DroSim_CAF1 42953 105 - 1
AUGUGGCAUGGGUGCCGAGCGGCGAGAAUGGACGCUCGGCGAGCGCAGAAGGCACUGCGGCACGCAGUACGCAGCAGCCGGCACAGUGGGUCGGUUCUCGCAGGA
...(((((....)))))....((((((((.(((((.((((..((((.....))((((((...)))))).....)).)))))).(....)))).)))))))).... ( -44.60)
>DroEre_CAF1 39240 99 - 1
AUGUGGCAUGGGUGCCGAGCGGCGAGAAUGGCCGCUCGGCGAGCGCAGAAGGCACUGCGGCACGCAGUACGCAGCAGCCGGCACAGUGGGUCGGGUAUU------
((.((((....((((((((((((.......)))))))(((..((((.....))((((((...)))))).....)).)))))))).....)))).))...------ ( -46.40)
>DroYak_CAF1 41150 99 - 1
AUGUGGCAUGGGUGCCGAGCGGCGAGAAUGGCCGCUCGGCGAGCGCAAAAGGCACUGCGGCAAGCACUACGCAGCAGCCCGCACAGUGGGCCAGAAAUC------
.(.((((.((..(((((((((((.......))))))))))).(((.....(((.(((((..........)))))..)))))).))....)))).)....------ ( -45.20)
>consensus
AUGUGGCAUGGGUGCCGAGCGGCGAGAAUGGCCGCUCGGCGAGCGCAGAAGGCACUGCGGCACGCAGUACGCAGCAGCCGGCACAGUGGGUCGGUUAUUGC_G_A
...((((....((((((((((((.......)))))))(((..((((.....))(((((.....))))).....)).)))))))).....))))............ (-38.24 = -38.76 +   0.52)

alignment

secondary structure

dotplot

Window 2

Location	4,372,083 – 4,372,191
Length	108
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	96.02
Mean single sequence MFE	-42.08
Consensus MFE	-38.58
Energy contribution	-39.42
Covariance contribution	0.84
Combinations/Pair	1.03
Mean z-score	-1.80
Structure conservation index	0.92
SVM decision value	2.23
SVM RNA-class probability	0.990721
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4372083 108 + 20766785
CGACUGCUGCGUACUGCGUGCCGCAGUGCCUUCUGCGCUCGCCGAGCCGCCAUUCUCGCCGCUCGGCACCCAUGCCACAUCGCAUCGCCUAUCAUUCUGCACUCGUGG
(((.(((...((((((((...)))))))).....(((...(((((((.((.......)).)))))))....((((......)))))))..........))).)))... ( -38.40)
>DroSec_CAF1 42745 108 + 1
CGGCUGCUGCGUACUGCGUGCCGCAGUGCCUUCUGCGCUCGCCGAGCGUCCAUUCUCGCCGCUCGGCACCCAUGCCACAUCGCAUCGCCUAUCAUUCUGCACUCGUGG
.(((.(.((((....(((((.(((((......)))))...((((((((.(.......).))))))))...))))).....)))).)))).......(..(....)..) ( -39.00)
>DroSim_CAF1 42978 108 + 1
CGGCUGCUGCGUACUGCGUGCCGCAGUGCCUUCUGCGCUCGCCGAGCGUCCAUUCUCGCCGCUCGGCACCCAUGCCACAUCGCAUCGCCUAUCAUUCUGCACUCGUGG
.(((.(.((((....(((((.(((((......)))))...((((((((.(.......).))))))))...))))).....)))).)))).......(..(....)..) ( -39.00)
>DroEre_CAF1 39259 108 + 1
CGGCUGCUGCGUACUGCGUGCCGCAGUGCCUUCUGCGCUCGCCGAGCGGCCAUUCUCGCCGCUCGGCACCCAUGCCACAUCGCAUUGCCCAUCAUUCUGCACUCGUGG
.(((...((((....(((((.(((((......)))))...((((((((((.......))))))))))...))))).....))))..))).......(..(....)..) ( -45.90)
>DroYak_CAF1 41169 108 + 1
GGGCUGCUGCGUAGUGCUUGCCGCAGUGCCUUUUGCGCUCGCCGAGCGGCCAUUCUCGCCGCUCGGCACCCAUGCCACAUCGCAUGGCCCAUCAUUCUGCACUCGUGG
......(..((.(((((.....(.(((((.....))))))((((((((((.......))))))))))..((((((......))))))...........)))))))..) ( -48.10)
>consensus
CGGCUGCUGCGUACUGCGUGCCGCAGUGCCUUCUGCGCUCGCCGAGCGGCCAUUCUCGCCGCUCGGCACCCAUGCCACAUCGCAUCGCCUAUCAUUCUGCACUCGUGG
.(((...((((....(((((.(((((......)))))...((((((((((.......))))))))))...))))).....))))..))).......(..(....)..) (-38.58 = -39.42 +   0.84)

alignment

secondary structure

dotplot

Window 3

Location	4,372,083 – 4,372,191
Length	108
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	96.02
Mean single sequence MFE	-46.56
Consensus MFE	-42.60
Energy contribution	-43.44
Covariance contribution	0.84
Combinations/Pair	1.03
Mean z-score	-1.62
Structure conservation index	0.91
SVM decision value	1.65
SVM RNA-class probability	0.969976
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4372083 108 - 20766785
CCACGAGUGCAGAAUGAUAGGCGAUGCGAUGUGGCAUGGGUGCCGAGCGGCGAGAAUGGCGGCUCGGCGAGCGCAGAAGGCACUGCGGCACGCAGUACGCAGCAGUCG
...(((.(((....((.....)).((((.((((((.....((((((((.((.......)).))))))))..(((((......))))))).))))...))))))).))) ( -45.00)
>DroSec_CAF1 42745 108 - 1
CCACGAGUGCAGAAUGAUAGGCGAUGCGAUGUGGCAUGGGUGCCGAGCGGCGAGAAUGGACGCUCGGCGAGCGCAGAAGGCACUGCGGCACGCAGUACGCAGCAGCCG
...................(((..((((.((((((.....(((((((((...........)))))))))..(((((......))))))).))))...))))...))). ( -43.70)
>DroSim_CAF1 42978 108 - 1
CCACGAGUGCAGAAUGAUAGGCGAUGCGAUGUGGCAUGGGUGCCGAGCGGCGAGAAUGGACGCUCGGCGAGCGCAGAAGGCACUGCGGCACGCAGUACGCAGCAGCCG
...................(((..((((.((((((.....(((((((((...........)))))))))..(((((......))))))).))))...))))...))). ( -43.70)
>DroEre_CAF1 39259 108 - 1
CCACGAGUGCAGAAUGAUGGGCAAUGCGAUGUGGCAUGGGUGCCGAGCGGCGAGAAUGGCCGCUCGGCGAGCGCAGAAGGCACUGCGGCACGCAGUACGCAGCAGCCG
...................(((..((((.((((((.....(((((((((((.......)))))))))))..(((((......))))))).))))...))))...))). ( -49.00)
>DroYak_CAF1 41169 108 - 1
CCACGAGUGCAGAAUGAUGGGCCAUGCGAUGUGGCAUGGGUGCCGAGCGGCGAGAAUGGCCGCUCGGCGAGCGCAAAAGGCACUGCGGCAAGCACUACGCAGCAGCCC
......((((...........((((((......)))))).(((((((((((.......))))))))))).))))....(((.(((((..........)))))..))). ( -51.40)
>consensus
CCACGAGUGCAGAAUGAUAGGCGAUGCGAUGUGGCAUGGGUGCCGAGCGGCGAGAAUGGCCGCUCGGCGAGCGCAGAAGGCACUGCGGCACGCAGUACGCAGCAGCCG
...................(((..((((.((((((.....(((((((((((.......)))))))))))..(((((......))))))).))))...))))...))). (-42.60 = -43.44 +   0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:51 2006