Locus 2596

Sequence ID	3L_DroMel_CAF1
Location	7,205,599 – 7,205,797
Length	198
Max. P	0.833617

overview

Window 7

Location	7,205,599 – 7,205,717
Length	118
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	85.41
Mean single sequence MFE	-34.00
Consensus MFE	-24.47
Energy contribution	-25.96
Covariance contribution	1.50
Combinations/Pair	1.10
Mean z-score	-1.55
Structure conservation index	0.72
SVM decision value	0.14
SVM RNA-class probability	0.600791
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7205599 118 + 23771897
CUGCCCUUUGAACUUCACAACCGGGCCACAUUUACACAUUUACAUGGCCA--UCGCGAUAACCAUCUCAACGGCGUUUCUCACCUGAGAAAUGGCCCCGGAUCCGGUGGGCUCCUUUGCG
..((((..((.....))..((((((((................((.((..--..)).))............((((((((((....))))))).)))..)).))))))))))......... ( -32.20)
>DroSec_CAF1 18892 118 + 1
CUGCCCUUUGAACUUCGCAACCGGGCCACAUUUACACAUUUACAUGGCCA--UCGUGAUACCCAUCUCAACGGCGUUUCUCACCUGAGAAAUGACCCCGGAUCCGGCGGUCUCCUUUGCG
...............(((((((((((((................))))).--..(.(((....))).)..))).(((((((....)))))))(((((((....))).))))....))))) ( -33.69)
>DroEre_CAF1 19315 110 + 1
CUGCCCUUUGAACUUCGCACCCGGCCCACAU--------UUACAUGGGCA--ACGCGAUUCCCAUCUCCUCGGCGUUCCUCACCUGAGAAAUGGCCCCGGAUACCGGGGUCUCCUUUUCG
..(((....((...((((.....(((((...--------.....))))).--..))))......)).....)))...........(((((..((((((((...))))))))...))))). ( -35.10)
>DroYak_CAF1 16531 111 + 1
CUGCCCUUUGAACUUCGCACCCGGCCGACAU--------UUACAUGGGCACCACGCGAUACCCAUCUCCACGGCGUUCCUCACCUGAGAAAUGGCCCCGGAU-CCGGGGUCUCCUUUGCG
.(((((..((((..((((.....).)))..)--------)))...)))))...(((((......((((...((.(.....).)).))))...(((((((...-.)))))))....))))) ( -35.00)
>consensus
CUGCCCUUUGAACUUCGCAACCGGCCCACAU________UUACAUGGCCA__ACGCGAUACCCAUCUCAACGGCGUUCCUCACCUGAGAAAUGGCCCCGGAUCCCGGGGUCUCCUUUGCG
..(((....((...((((.....(((((................))))).....))))......)).....)))(((((((....)))))))((((((((...))))))))......... (-24.47 = -25.96 +   1.50)

alignment

secondary structure

dotplot

Window 8

Location	7,205,599 – 7,205,717
Length	118
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	85.41
Mean single sequence MFE	-43.92
Consensus MFE	-32.79
Energy contribution	-32.60
Covariance contribution	-0.19
Combinations/Pair	1.15
Mean z-score	-1.94
Structure conservation index	0.75
SVM decision value	0.72
SVM RNA-class probability	0.833617
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7205599 118 - 23771897
CGCAAAGGAGCCCACCGGAUCCGGGGCCAUUUCUCAGGUGAGAAACGCCGUUGAGAUGGUUAUCGCGA--UGGCCAUGUAAAUGUGUAAAUGUGGCCCGGUUGUGAAGUUCAAAGGGCAG
.........((((.(((....)))(((((((((...((((.....))))...))))))))).((((((--(((((((((..........))))))))..)))))))........)))).. ( -46.80)
>DroSec_CAF1 18892 118 - 1
CGCAAAGGAGACCGCCGGAUCCGGGGUCAUUUCUCAGGUGAGAAACGCCGUUGAGAUGGGUAUCACGA--UGGCCAUGUAAAUGUGUAAAUGUGGCCCGGUUGCGAAGUUCAAAGGGCAG
(((((....((((.(((....)))))))...(((((((((.....))))..)))))(((((..((((.--..(((((....))).))...))))))))).)))))..(((.....))).. ( -39.60)
>DroEre_CAF1 19315 110 - 1
CGAAAAGGAGACCCCGGUAUCCGGGGCCAUUUCUCAGGUGAGGAACGCCGAGGAGAUGGGAAUCGCGU--UGCCCAUGUAA--------AUGUGGGCCGGGUGCGAAGUUCAAAGGGCAG
...........((((((...))))))((((((((..((((.....))))..))))))))...(((((.--.((((((....--------..))))))....))))).(((.....))).. ( -43.60)
>DroYak_CAF1 16531 111 - 1
CGCAAAGGAGACCCCGG-AUCCGGGGCCAUUUCUCAGGUGAGGAACGCCGUGGAGAUGGGUAUCGCGUGGUGCCCAUGUAA--------AUGUCGGCCGGGUGCGAAGUUCAAAGGGCAG
((((..(....)(((((-.((((.(((..((((((....)))))).))).)))).(((((((((....)))))))))....--------.......)))))))))..(((.....))).. ( -45.70)
>consensus
CGCAAAGGAGACCCCCGGAUCCGGGGCCAUUUCUCAGGUGAGAAACGCCGUGGAGAUGGGUAUCGCGA__UGCCCAUGUAA________AUGUGGCCCGGGUGCGAAGUUCAAAGGGCAG
......(((.((....)).)))...(((...((((.((((.....))))...))))((((..((((((...((((((((..........))))))))...))))))..))))...))).. (-32.79 = -32.60 +  -0.19)

alignment

secondary structure

dotplot

Window 9

Location	7,205,677 – 7,205,797
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	92.46
Mean single sequence MFE	-37.40
Consensus MFE	-31.30
Energy contribution	-32.93
Covariance contribution	1.63
Combinations/Pair	1.06
Mean z-score	-1.72
Structure conservation index	0.84
SVM decision value	0.43
SVM RNA-class probability	0.734304
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7205677 120 + 23771897
CACCUGAGAAAUGGCCCCGGAUCCGGUGGGCUCCUUUGCGCUCCGGUUACGUGGGGCUGUGUGGGUCCACAAUUUAUCAUGACACUAAUGAGCGUGAAAUAGGACAAGGUUUAUUAAAUU
.((((.......(.(((((....))).)).)(((((..(((((.(((..(((((.....((((....)))).....)))))..)))...)))))..)...))))..)))).......... ( -37.00)
>DroSec_CAF1 18970 120 + 1
CACCUGAGAAAUGACCCCGGAUCCGGCGGUCUCCUUUGCGCUCCGGUUACGUGGGGCUGUGUGGCUCCACAAUUUAUCAUGACACUAAUGAGCGUGAAAUAGGACAAGGUUUAUUAAAUU
.((((.......(((((((....))).))))(((((..(((((.(....)((((((((....))))))))...................)))))..)...))))..)))).......... ( -41.70)
>DroEre_CAF1 19385 116 + 1
CACCUGAGAAAUGGCCCCGGAUACCGGGGUCUCCUUUUCGCUCCGGUUACGUGA----CUGUGGCUCCACAAUUUAUCAUGACACUAAUGAGCAUGAAAUAGGACAAGGUUUAUUAAAUU
.((((.......((((((((...))))))))((((((((((((.(((..(((((----.((((....)))).....)))))..)))...))))..)))).))))..)))).......... ( -36.60)
>DroYak_CAF1 16603 115 + 1
CACCUGAGAAAUGGCCCCGGAU-CCGGGGUCUCCUUUGCGCUCCGGUUACGUGA----CUGUGGCUCCACAAUUUAUCAUGACACUAAUGAGCAUGAAAUAGGACAAGGUUUAUUAAAUU
.((((.......(((((((...-.)))))))((((.(((((..(((((....))----)))..))...........((((.......)))))))......))))..)))).......... ( -34.30)
>consensus
CACCUGAGAAAUGGCCCCGGAUCCCGGGGUCUCCUUUGCGCUCCGGUUACGUGA____CUGUGGCUCCACAAUUUAUCAUGACACUAAUGAGCAUGAAAUAGGACAAGGUUUAUUAAAUU
.((((.......((((((((...))))))))((((((((((((.(((..(((((.....((((....)))).....)))))..)))...))))))))...))))..)))).......... (-31.30 = -32.93 +   1.63)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:37:00 2006