Locus 1514

Sequence ID	2R_DroMel_CAF1
Location	5,733,390 – 5,733,525
Length	135
Max. P	0.556371

overview

Window 1

Location	5,733,390 – 5,733,496
Length	106
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	76.57
Mean single sequence MFE	-16.74
Consensus MFE	-7.63
Energy contribution	-7.38
Covariance contribution	-0.25
Combinations/Pair	1.27
Mean z-score	-1.94
Structure conservation index	0.46
SVM decision value	0.05
SVM RNA-class probability	0.556371
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5733390 106 - 20766785
CAAAGAUACGAAUUGUGUAUGUAACACA-----U--GUGUCAUAAAAAGCG-UACAGCAGGCGAUCAUAAUAAAAUAAAAUGGAAAAGAAACUUGCGAAUUAAAAUUCGCGCGU
....((((((...(((((.....)))))-----)--))))).......(((-(...(((((...((.....................))..)))))((((....)))))))).. ( -20.50)
>DroPse_CAF1 24984 111 - 1
CAAAGAUACAAAUUGUAUAUGUAACAAAAAAUAUGCGAGCAAUAAAGAGAUUCACAAA---AAAGAAUAAUAAAACAAAAUGGAAAAGAAACUUGCGAAUUAAAGCUCGCGCGC
............((((((((..........))))))))((.........((((.....---...))))..........................((((........)))))).. ( -13.60)
>DroSec_CAF1 23904 97 - 1
CAAAGAUACAAAUUGUGUAUGUAACACA-----U--GUGUCAU----------ACAGCAGGCGAUCAUAAUAAAAUAAAAUUGAAAAGAAACUUGCGAAUUAAAAUUCGCGCGU
....((((((...(((((.....)))))-----)--)))))..----------...((......(((..............)))..........((((((....)))))))).. ( -18.94)
>DroYak_CAF1 23895 104 - 1
--AAGAUACAAAUUGUGUAUGUAACACA-----U--GUGUCAUAAAAAGCG-UACAGAAGGGGAUCAUAAUAAAAUAAAAUGGAAAAGAAACUUGCGAAUUAAAAUUCGCGCGU
--..((((((...(((((.....)))))-----)--))))).......(((-(......(((..((.....................))..)))((((((....)))))))))) ( -19.60)
>DroAna_CAF1 26511 102 - 1
CAAAGAUACAAAUUGUGUAUGUAACUGA-----G--CUAUAAAAAAAAGUG-UACAAAAAAAGAUCA----AAAAAGAAAUGAAAAAGAAACUUGCGAAUUUCAAUUCGCAGGC
....(((........(((((...(((..-----.--...........))))-)))).......))).----....................(((((((((....))))))))). ( -15.00)
>DroPer_CAF1 25173 112 - 1
CAAAGAUACAAAUUGUAUAUGUAACAAAAAAUAUGCGAGCAAUAAAGAGAUUCACAAAA--AAAGAAUAAUAAAACAAAAUGGAAAAGAAACUUGCGAAUUAAAGCUCGCGCGC
.....((((.....))))................((((((........(((((.(((..--...............................))).)))))...)))))).... ( -12.81)
>consensus
CAAAGAUACAAAUUGUGUAUGUAACACA_____U__GUGUAAUAAAAAGAG_UACAAAAGGAGAUCAUAAUAAAAUAAAAUGGAAAAGAAACUUGCGAAUUAAAAUUCGCGCGC
.....((((.....))))...........................................................................(((((((....)))))))... ( -7.63 =  -7.38 +  -0.25)

alignment

secondary structure

dotplot

Window 2

Location	5,733,430 – 5,733,525
Length	95
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	75.34
Mean single sequence MFE	-18.48
Consensus MFE	-6.16
Energy contribution	-8.52
Covariance contribution	2.36
Combinations/Pair	1.05
Mean z-score	-2.20
Structure conservation index	0.33
SVM decision value	-0.03
SVM RNA-class probability	0.517448
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5733430 95 - 20766785
UCUUCGCUGCUGCCACAGAUAAA--------AAGAUACAAAGAUACGAAUUGUGUAUGUAACACA-----U--GUGUCAUAAAAAGCG-UACAGCAGGCGAUCAUAAUAAA
...(((((((((..((..((...--------...)).....((((((...(((((.....)))))-----)--))))).........)-).))))).)))).......... ( -20.10)
>DroSec_CAF1 23944 94 - 1
UCUUCGCUGCUGCCACAGAUAAAUAGAUACAAAGAUACAAAGAUACAAAUUGUGUAUGUAACACA-----U--GUGUCAU----------ACAGCAGGCGAUCAUAAUAAA
...(((((((((......((......)).............((((((...(((((.....)))))-----)--)))))..----------.))))).)))).......... ( -20.00)
>DroSim_CAF1 23125 103 - 1
UCUUCGCUGCUGCCACAGAUAAAUAGAUACAAAGAUACAAAGAUACAAAUUGUGUAUGUAACACA-----U--GUGUCAUAAAAAGCG-UACAGCAGGCGAUCAUAAUAAA
...(((((((((..((.........((((((..(.((((...((((.....)))).)))).)...-----)--))))).........)-).))))).)))).......... ( -21.47)
>DroEre_CAF1 23910 96 - 1
UCUUCGCAGCUGCCGCAGAUAAA-------AAAGAUACAAAGAUACAAAUUGUGUAUGUAACACA-----U--GUGUCAUAAAAAGCG-UACAGCAGGCGAUCAUAAUAAA
...((((.((((.(((..((...-------....)).....((((((...(((((.....)))))-----)--))))).......)))-..))))..)))).......... ( -21.80)
>DroYak_CAF1 23935 87 - 1
UCUUCGCUGCUGCCUCAGAUAAA----------------AAGAUACAAAUUGUGUAUGUAACACA-----U--GUGUCAUAAAAAGCG-UACAGAAGGGGAUCAUAAUAAA
(((.((((.(((...))).....----------------..((((((...(((((.....)))))-----)--)))))......))))-...)))................ ( -16.00)
>DroPer_CAF1 25213 90 - 1
UC---GCUC--------GACC--------AAAAUAUACAAAGAUACAAAUUGUAUAUGUAACAAAAAAUAUGCGAGCAAUAAAGAGAUUCACAAAA--AAAGAAUAAUAAA
..---((((--------(...--------...((((((((.........))))))))...............))))).........((((......--...))))...... ( -11.50)
>consensus
UCUUCGCUGCUGCCACAGAUAAA_______AAAGAUACAAAGAUACAAAUUGUGUAUGUAACACA_____U__GUGUCAUAAAAAGCG_UACAGCAGGCGAUCAUAAUAAA
...(((((((((..............................((((.....)))).(((.((((.........)))).)))..........))))).)))).......... ( -6.16 =  -8.52 +   2.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:06:36 2006