Locus 1463

Sequence ID	2L_DroMel_CAF1
Location	3,873,241 – 3,873,375
Length	134
Max. P	0.957596

overview

Window 3

Location	3,873,241 – 3,873,355
Length	114
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	73.93
Mean single sequence MFE	-35.15
Consensus MFE	-18.42
Energy contribution	-19.45
Covariance contribution	1.03
Combinations/Pair	1.19
Mean z-score	-1.60
Structure conservation index	0.52
SVM decision value	0.12
SVM RNA-class probability	0.593435
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3873241 114 + 22407834
ACUCCUCCAUUUUGGACUUGAAGGGCUCCAUGAUCUCGGGACGCGAGGCGGCCAAAACUUUGGCCGUCGUUCUCUUGCAACCUGAA--GAGCAAUAUCAUGGAUUAGCUAAGUGAU
..(((........))).......(((((((((((((((((..(((((((((((((....))))))))......)))))..)))).)--))......)))))))...)))....... ( -37.80)
>DroPse_CAF1 16029 107 + 1
AUUCCUCCAUUUUGGACUUGAAGGGCUCCACAAUGUCUUCACUGGAGGCAGCCAGUACCUUGGCCUUGGUCCUCUUGAAAACUAAACCAAAGGAUACGCCGAUUAAU---------
..((((....(((((..((.(((((..(((...((((((.....))))))(((((....)))))..)))..))))).))..)))))....)))).............--------- ( -27.30)
>DroEre_CAF1 5068 114 + 1
AUUCCUCCAUUUUGGACUUGAAGGGCUCCAUGAUCUCCGGGCGGGAGGCGGCCAGAACUUUGGCCGUGGUCCUCUUGCAACCUGUA--GGAUGAUUUCAUGGAUUAGCUUAGUGAU
.(((.(((.....)))...)))(((((((((((..((...(((((((((((((((....)))))))....))))))))..((....--))..))..)))))))...))))...... ( -39.90)
>DroYak_CAF1 7353 114 + 1
AUUCCUCCAUUUUGGACUUGAAUGGCUCCAUGAUCUCCGGACGGGAGGCGGCCAACACUUUGGCCGUAGUCCUCUUGCAACCUGAA--GGGGGAUUUCAUGGAUUAGUUAUGUGAU
......((((((.......)))))).(((((((.((((.....))))((((((((....))))))))(((((((((.(.....).)--)))))))))))))))............. ( -40.20)
>DroAna_CAF1 19521 115 + 1
ACUCCUCCAUUUUGGACUUAAAGGGCUCCUGGAUAUCCGGACGCGAGGCGGCCAGCACUUUGGCUGUGGUUCUCUUGUGAUCUAAAU-GGAGGAUAUUUCUUUUUAGGAAACAGUU
..((((((((((.(((....(((((..(((((....)))..(....)((((((((....))))))))))..)))))....)))))))-))))))............(....).... ( -38.40)
>DroPer_CAF1 16492 107 + 1
AUUCCUCCAUUUUGGACUUGAAGGGCUCCACAAUGUCUUCACUGGAGGCAGCCAGUACCUUGGCCUUGGUCCUCUUGAAAACUAAACCAAAGGAUACGCCGAUUAAU---------
..((((....(((((..((.(((((..(((...((((((.....))))))(((((....)))))..)))..))))).))..)))))....)))).............--------- ( -27.30)
>consensus
AUUCCUCCAUUUUGGACUUGAAGGGCUCCAUGAUCUCCGGACGGGAGGCGGCCAGAACUUUGGCCGUGGUCCUCUUGCAACCUAAA__GAAGGAUAUCACGGAUUAG_UAAGUGAU
..((((..(((.((((((.....)).)))).))).......((((((((((((((....)))))))....))))))).............))))...................... (-18.42 = -19.45 +   1.03)

alignment

secondary structure

dotplot

Window 4

Location	3,873,281 – 3,873,375
Length	94
Sequences	6
Columns	97
Reading direction	forward
Mean pairwise identity	72.70
Mean single sequence MFE	-30.27
Consensus MFE	-17.33
Energy contribution	-17.50
Covariance contribution	0.17
Combinations/Pair	1.38
Mean z-score	-1.93
Structure conservation index	0.57
SVM decision value	1.48
SVM RNA-class probability	0.957596
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3873281 94 + 22407834
ACGCGAGGCGGCCAAAACUUUGGCCGUCGUUCUCUUGCAACCUGAA-GAGCAAUAUCAUGGAUUAGCUAAGUGAUGGCAAUGGAA--AUGAUCGCUC
..(((((((((((((....))))))))).((((.((((........-.(((...(((...)))..)))........)))).))))--....)))).. ( -31.23)
>DroSec_CAF1 5671 90 + 1
UCGCGAGGCGGCCAGAACUUUGGCCGUCGUCCUCUUGCAACCUAAA-GGAGAAAACCAUUGA----UUAAGUGAUUGCGAGGGAA--AUGAGCGCUC
..(((.(((((((((....))))))))).(((.(((((((((....-)).......((((..----...)))).)))))))))).--.....))).. ( -34.60)
>DroSim_CAF1 5760 90 + 1
UCGCGAGGCGGCCAGAACUUUGGCCGUCGUCCUCUUGCAACCUAAA-GAAGAAUACCAUUAA----AUAAGUGAUUGCGAAGGAU--AUGAGCGCUC
..(((.(((((((((....)))))))))(((((.((((((.((...-..)).....((((..----...)))).)))))))))))--.....))).. ( -30.10)
>DroEre_CAF1 5108 94 + 1
GCGGGAGGCGGCCAGAACUUUGGCCGUGGUCCUCUUGCAACCUGUA-GGAUGAUUUCAUGGAUUAGCUUAGUGAUUUCGCUGCAA--AUUAGAGCUC
(((((((((((((((....)))))))....))))))))....((((-(..(((..((((.((.....)).))))..)))))))).--.......... ( -31.30)
>DroYak_CAF1 7393 94 + 1
ACGGGAGGCGGCCAACACUUUGGCCGUAGUCCUCUUGCAACCUGAA-GGGGGAUUUCAUGGAUUAGUUAUGUGAUUUCGUUGCAA--AUGAGAACUC
..(((..((((((((....))))))))..)))..((((((((....-))(..(((.(((((.....))))).)))..).))))))--.......... ( -30.80)
>DroAna_CAF1 19561 97 + 1
ACGCGAGGCGGCCAGCACUUUGGCUGUGGUUCUCUUGUGAUCUAAAUGGAGGAUAUUUCUUUUUAGGAAACAGUUUGCUUAAAAAACAAUAUUGUGU
((((((.((((((((....))))))))(((....((((..((((((.((((.....)))).))))))..))))...)))............)))))) ( -23.60)
>consensus
ACGCGAGGCGGCCAGAACUUUGGCCGUCGUCCUCUUGCAACCUAAA_GGAGAAUAUCAUGGAUUAGCUAAGUGAUUGCGAUGGAA__AUGAGCGCUC
((((((.((((((((....)))))))).(((((((............)))))))....................))))))................. (-17.33 = -17.50 +   0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:03:20 2006