Locus 5346

Sequence ID	3L_DroMel_CAF1
Location	14,755,325 – 14,755,466
Length	141
Max. P	0.999504

overview

Window 8

Location	14,755,325 – 14,755,426
Length	101
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	92.87
Mean single sequence MFE	-29.37
Consensus MFE	-21.82
Energy contribution	-22.22
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.32
Structure conservation index	0.74
SVM decision value	0.63
SVM RNA-class probability	0.804847
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14755325 101 + 23771897
GCAAAGGUAACGCAAAAAGAGUGCAAAAGCCCGAAAUGUACGCACAAAUUGGCCAGCAAGUGUACAGCUGGCUGGCUGACUUGCCAUAAACGCGCUGGAAA
((.........))......(((((...((((.(...(((((((................))))))).).))))(((......)))......)))))..... ( -26.49)
>DroSec_CAF1 7277 101 + 1
GCAAAGGUAACGCAAAAAGAGUGCAAAAGCCCGAAAUGUACGCACAAAUUGGCCAGCAAGUGUACAGCUGGCUGGCUGACUUGCCAUAAACGCGCUGUAAA
((.........))....(.(((((...((((.(...(((((((................))))))).).))))(((......)))......))))).)... ( -26.79)
>DroSim_CAF1 7187 101 + 1
GCAAAGGUAACGCAAAAAGAGUGCAAAAGCCCGAAAUGUACGCACAAAUUGGCCAGCAAGUGUACAGCUGGCUGGCUGACUUGCCAUAAACGCGCUGUUAA
((.........))...((.(((((...((((.(...(((((((................))))))).).))))(((......)))......))))).)).. ( -27.69)
>DroEre_CAF1 4633 101 + 1
GCAAAGGUAACGCAGAAAGAGUGCAAAAGUCCGAAAUGGACGCAAAAAUUGGCCAGCAAAUGUACAGCUGGCUGGCUGACUUGCGAUAAAAGCGCUGGAGA
((.........))......(((((....((((.....))))((((...(..((((((....(.....)..))))))..).)))).......)))))..... ( -30.30)
>DroYak_CAF1 11178 101 + 1
GCAAAGGUAACGCAACAAGAGUGCAAAAACCCGAAAGGGACGCAAUAAUUGGCCAGCAAAUGUACAGCUGGCUGGCUGACUUGCGAUAAAUGCGCUGGAUA
((.........))......((((((....(((....))).(((((...(..((((((....(.....)..))))))..).))))).....))))))..... ( -35.60)
>consensus
GCAAAGGUAACGCAAAAAGAGUGCAAAAGCCCGAAAUGUACGCACAAAUUGGCCAGCAAGUGUACAGCUGGCUGGCUGACUUGCCAUAAACGCGCUGGAAA
((.........))......(((((..........................(((((((.........)))))))(((......)))......)))))..... (-21.82 = -22.22 +   0.40)

alignment

secondary structure

dotplot

Window 9

Location	14,755,325 – 14,755,426
Length	101
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	92.87
Mean single sequence MFE	-27.36
Consensus MFE	-24.84
Energy contribution	-24.96
Covariance contribution	0.12
Combinations/Pair	1.09
Mean z-score	-1.68
Structure conservation index	0.91
SVM decision value	1.92
SVM RNA-class probability	0.982682
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14755325 101 - 23771897
UUUCCAGCGCGUUUAUGGCAAGUCAGCCAGCCAGCUGUACACUUGCUGGCCAAUUUGUGCGUACAUUUCGGGCUUUUGCACUCUUUUUGCGUUACCUUUGC
.....((((((......(((((..((((.((((((.........)))))).........((.......)))))))))))........))))))........ ( -27.54)
>DroSec_CAF1 7277 101 - 1
UUUACAGCGCGUUUAUGGCAAGUCAGCCAGCCAGCUGUACACUUGCUGGCCAAUUUGUGCGUACAUUUCGGGCUUUUGCACUCUUUUUGCGUUACCUUUGC
.....((((((......(((((..((((.((((((.........)))))).........((.......)))))))))))........))))))........ ( -27.54)
>DroSim_CAF1 7187 101 - 1
UUAACAGCGCGUUUAUGGCAAGUCAGCCAGCCAGCUGUACACUUGCUGGCCAAUUUGUGCGUACAUUUCGGGCUUUUGCACUCUUUUUGCGUUACCUUUGC
.(((((((.((..((((((((((..((((((.((.......)).))))))..)))))).)))).....)).)))...(((.......)))))))....... ( -27.60)
>DroEre_CAF1 4633 101 - 1
UCUCCAGCGCUUUUAUCGCAAGUCAGCCAGCCAGCUGUACAUUUGCUGGCCAAUUUUUGCGUCCAUUUCGGACUUUUGCACUCUUUCUGCGUUACCUUUGC
.....(((((.......(((((.......((((((.........)))))).....)))))((((.....))))...............)))))........ ( -26.50)
>DroYak_CAF1 11178 101 - 1
UAUCCAGCGCAUUUAUCGCAAGUCAGCCAGCCAGCUGUACAUUUGCUGGCCAAUUAUUGCGUCCCUUUCGGGUUUUUGCACUCUUGUUGCGUUACCUUUGC
.....((((((......(((((.......((((((.........)))))).......((((.(((....)))....))))..)))))))))))........ ( -27.60)
>consensus
UUUCCAGCGCGUUUAUGGCAAGUCAGCCAGCCAGCUGUACACUUGCUGGCCAAUUUGUGCGUACAUUUCGGGCUUUUGCACUCUUUUUGCGUUACCUUUGC
.....((((((......(((((..((((.((((((.........)))))).........((.......)))))))))))........))))))........ (-24.84 = -24.96 +   0.12)

alignment

secondary structure

dotplot

Window 0

Location	14,755,357 – 14,755,466
Length	109
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	92.11
Mean single sequence MFE	-39.00
Consensus MFE	-32.78
Energy contribution	-33.30
Covariance contribution	0.52
Combinations/Pair	1.11
Mean z-score	-3.23
Structure conservation index	0.84
SVM decision value	3.66
SVM RNA-class probability	0.999504
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14755357 109 + 23771897
GAAAUGUACGCACAAAUUGGCCAGCAAGUGUACAGCUGGCUGGCUGACUUGCCAUAAACGCGCUGGAAAGGGUUCAGCGCAGUAAAUUUUGCUUGCUGAGCAUGCAAAA
......(((...(((.(..((((((.(((.....))).))))))..).)))........((((((((.....)))))))).)))..((((((.(((...))).)))))) ( -39.60)
>DroSec_CAF1 7309 109 + 1
GAAAUGUACGCACAAAUUGGCCAGCAAGUGUACAGCUGGCUGGCUGACUUGCCAUAAACGCGCUGUAAAGGGUUUAGCGCAGUAAAUGUCGCUUGCUGAGCAUGCAAAA
.........((((.....)(((((((((((.(((....((((((......)))......((((((.........)))))))))...)))))))))))).)).))).... ( -37.90)
>DroSim_CAF1 7219 109 + 1
GAAAUGUACGCACAAAUUGGCCAGCAAGUGUACAGCUGGCUGGCUGACUUGCCAUAAACGCGCUGUUAAGGGUUCAGCGCAGUAAAUGCCGCUUGCUGAGCAUGCAAAA
.........((((.....)(((((((((((....((..((((((......)))......((((((.........)))))))))....))))))))))).)).))).... ( -36.30)
>DroEre_CAF1 4665 109 + 1
GAAAUGGACGCAAAAAUUGGCCAGCAAAUGUACAGCUGGCUGGCUGACUUGCGAUAAAAGCGCUGGAGAAGGUUCAGCGCUGUAAAUGUCGCUUGCUGAGCAUGCAAAA
.........(((......(((((((.........))))))).(((.((..((((((..(((((((((.....))))))))).....))))))..).).))).))).... ( -41.30)
>DroYak_CAF1 11210 109 + 1
GAAAGGGACGCAAUAAUUGGCCAGCAAAUGUACAGCUGGCUGGCUGACUUGCGAUAAAUGCGCUGGAUAAGGUUCAGCGUAGUAAAUGUCGCUUGCUGAGCAUGCAAAA
.........(((......(((((((.........))))))).(((.((..((((((..((((((((((...)))))))))).....))))))..).).))).))).... ( -39.90)
>consensus
GAAAUGUACGCACAAAUUGGCCAGCAAGUGUACAGCUGGCUGGCUGACUUGCCAUAAACGCGCUGGAAAGGGUUCAGCGCAGUAAAUGUCGCUUGCUGAGCAUGCAAAA
.........(((.......(((((((((((..(((((....))))).............((((((((.....)))))))).........))))))))).)).))).... (-32.78 = -33.30 +   0.52)

alignment

secondary structure

dotplot

Window 1

Location	14,755,357 – 14,755,466
Length	109
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	92.11
Mean single sequence MFE	-32.89
Consensus MFE	-28.40
Energy contribution	-28.52
Covariance contribution	0.12
Combinations/Pair	1.12
Mean z-score	-2.56
Structure conservation index	0.86
SVM decision value	3.32
SVM RNA-class probability	0.999005
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14755357 109 - 23771897
UUUUGCAUGCUCAGCAAGCAAAAUUUACUGCGCUGAACCCUUUCCAGCGCGUUUAUGGCAAGUCAGCCAGCCAGCUGUACACUUGCUGGCCAAUUUGUGCGUACAUUUC
((((((.(((...))).))))))......((((((.........))))))...((((((((((..((((((.((.......)).))))))..)))))).))))...... ( -35.70)
>DroSec_CAF1 7309 109 - 1
UUUUGCAUGCUCAGCAAGCGACAUUUACUGCGCUAAACCCUUUACAGCGCGUUUAUGGCAAGUCAGCCAGCCAGCUGUACACUUGCUGGCCAAUUUGUGCGUACAUUUC
..((((.(((...))).))))(((..((.(((((...........)))))))..)))((((((..((((((.((.......)).))))))..))))))........... ( -31.80)
>DroSim_CAF1 7219 109 - 1
UUUUGCAUGCUCAGCAAGCGGCAUUUACUGCGCUGAACCCUUAACAGCGCGUUUAUGGCAAGUCAGCCAGCCAGCUGUACACUUGCUGGCCAAUUUGUGCGUACAUUUC
....((((((.(((((((.(.(((..((.((((((.........))))))))..))).)..((((((......)))).)).)))))))))......))))......... ( -36.60)
>DroEre_CAF1 4665 109 - 1
UUUUGCAUGCUCAGCAAGCGACAUUUACAGCGCUGAACCUUCUCCAGCGCUUUUAUCGCAAGUCAGCCAGCCAGCUGUACAUUUGCUGGCCAAUUUUUGCGUCCAUUUC
....((.(((...))).))(((......(((((((.........)))))))......(((((.......((((((.........)))))).....))))))))...... ( -32.60)
>DroYak_CAF1 11210 109 - 1
UUUUGCAUGCUCAGCAAGCGACAUUUACUACGCUGAACCUUAUCCAGCGCAUUUAUCGCAAGUCAGCCAGCCAGCUGUACAUUUGCUGGCCAAUUAUUGCGUCCCUUUC
....((.(((...))).))(((........(((((.........)))))........((((........((((((.........))))))......)))))))...... ( -27.74)
>consensus
UUUUGCAUGCUCAGCAAGCGACAUUUACUGCGCUGAACCCUUUCCAGCGCGUUUAUGGCAAGUCAGCCAGCCAGCUGUACACUUGCUGGCCAAUUUGUGCGUACAUUUC
....((((((.(((((((..........(((((((.........)))))))..........((((((......)))).)).)))))))))......))))......... (-28.40 = -28.52 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:47:53 2006