Locus 521

Sequence ID	2R_DroMel_CAF1
Location	2,801,113 – 2,801,228
Length	115
Max. P	0.585852

overview

Window 4

Location	2,801,113 – 2,801,228
Length	115
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	66.69
Mean single sequence MFE	-18.69
Consensus MFE	-9.33
Energy contribution	-9.88
Covariance contribution	0.56
Combinations/Pair	1.18
Mean z-score	-1.40
Structure conservation index	0.50
SVM decision value	0.10
SVM RNA-class probability	0.585852
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2801113 115 + 20766785
CCCUCCAGCAGAUUA-----GUUCUUCGGUUCCCUUUUCACCCAGGCGAUAUGAGAUGCUCCAAGUUCGUAAUCAGCUCACAUGCUGAUCGCCAAUAAUCAAUUUCCAGGUCCAGCUCUU
......(((.((..(-----(..(....)....))..)).....(((((((((((.(......).)))))).(((((......)))))))))).....................)))... ( -23.40)
>DroSec_CAF1 7981 111 + 1
-UUUUAAGCAGAUUA-----GUUAUUCGCUUCCCUUCUCACCCAGACGAUAUGGGAUGCUCCAAGUUCGUAAUCAGCUCACAUGCUGAUCGCCAAUAAUCAAUUUAC---UCCAGCUCUU
-.....((.(((((.-----((((((.((.((((.((((.....)).))...)))).)).........(..((((((......))))))..).)))))).))))).)---)......... ( -24.10)
>DroSim_CAF1 8029 95 + 1
-UUU-AA--------------------GCUUCCCUUCUCACCCAGACUAUAUUGGAUGCUCCAAGUUCGUAAUCAGCUCACAUGCUGAUCGCCAAUAAUCAAUUUAC---UCCAGCUCUU
-...-.(--------------------(((.....................((((.....))))(((.(..((((((......))))))..).)))...........---...))))... ( -17.10)
>DroEre_CAF1 8230 89 + 1
----------------------------UUGCCCUUCUCACCCAGUCGAUAUGGCAUGCUUAAAGCUCGUAAUCAGCUCACAUGCUGAUCGCCAAUAAUCAAUUUAC---UCCAACGUUU
----------------------------...................(((.((((..((.....)).....((((((......)))))).))))...))).......---.......... ( -15.90)
>DroYak_CAF1 7953 88 + 1
----------------------------CUGC-UUUUUCACCCAGUCGAUAUGGGCUGUUUCCAGUUGUUAAUCAGCACACAUGCUGAUCGCCGAAAAUCAAUUUAC---UCCAGCUCUU
----------------------------....-...................((((((.....(((((...(((((((....)))))))..........)))))...---..)))))).. ( -16.12)
>DroAna_CAF1 7819 109 + 1
CUCUCCAGCCACUUCACUCCGUCAUCAGUUUCCCUUCUUGGCU--------UAGCGCGACUCGAGUUCAUAAUCAGCUCACAUGCUGAUCUCUCAUUUUCAAUUAAC---UUAAACGUUU
...............((((.(((....(((..((.....))..--------.)))..)))..)))).....((((((......))))))..................---.......... ( -15.50)
>consensus
_U_U__A____________________GCUUCCCUUCUCACCCAGACGAUAUGGGAUGCUCCAAGUUCGUAAUCAGCUCACAUGCUGAUCGCCAAUAAUCAAUUUAC___UCCAGCUCUU
........................................((((.......)))).............(..((((((......))))))..)............................ ( -9.33 =  -9.88 +   0.56)

alignment

secondary structure

dotplot

Window 5

Location	2,801,113 – 2,801,228
Length	115
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	66.69
Mean single sequence MFE	-25.77
Consensus MFE	-12.43
Energy contribution	-11.74
Covariance contribution	-0.69
Combinations/Pair	1.48
Mean z-score	-1.43
Structure conservation index	0.48
SVM decision value	0.08
SVM RNA-class probability	0.573461
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2801113 115 - 20766785
AAGAGCUGGACCUGGAAAUUGAUUAUUGGCGAUCAGCAUGUGAGCUGAUUACGAACUUGGAGCAUCUCAUAUCGCCUGGGUGAAAAGGGAACCGAAGAAC-----UAAUCUGCUGGAGGG
..........(((.......((((((((..(((((((......))))))).)))..((((....((((...((((....))))...)))).)))).....-----))))).......))) ( -25.14)
>DroSec_CAF1 7981 111 - 1
AAGAGCUGGA---GUAAAUUGAUUAUUGGCGAUCAGCAUGUGAGCUGAUUACGAACUUGGAGCAUCCCAUAUCGUCUGGGUGAGAAGGGAAGCGAAUAAC-----UAAUCUGCUUAAAA-
........((---(((.((((.(((((.(((((((((......))))))).....(((....((.((((.......))))))....)))..)).))))).-----)))).)))))....- ( -29.00)
>DroSim_CAF1 8029 95 - 1
AAGAGCUGGA---GUAAAUUGAUUAUUGGCGAUCAGCAUGUGAGCUGAUUACGAACUUGGAGCAUCCAAUAUAGUCUGGGUGAGAAGGGAAGC--------------------UU-AAA-
..(((((...---............(((..(((((((......))))))).))).(((....((((((........))))))....))).)))--------------------))-...- ( -24.40)
>DroEre_CAF1 8230 89 - 1
AAACGUUGGA---GUAAAUUGAUUAUUGGCGAUCAGCAUGUGAGCUGAUUACGAGCUUUAAGCAUGCCAUAUCGACUGGGUGAGAAGGGCAA----------------------------
....(((...---.....(((((...(((((((((((......)))))))....((.....))..)))).)))))((........)))))..---------------------------- ( -20.80)
>DroYak_CAF1 7953 88 - 1
AAGAGCUGGA---GUAAAUUGAUUUUCGGCGAUCAGCAUGUGUGCUGAUUAACAACUGGAAACAGCCCAUAUCGACUGGGUGAAAAA-GCAG----------------------------
....((((((---(.........)))))))((((((((....)))))))).....(((....)))((((.......)))).......-....---------------------------- ( -25.70)
>DroAna_CAF1 7819 109 - 1
AAACGUUUAA---GUUAAUUGAAAAUGAGAGAUCAGCAUGUGAGCUGAUUAUGAACUCGAGUCGCGCUA--------AGCCAAGAAGGGAAACUGAUGACGGAGUGAAGUGGCUGGAGAG
.(((......---)))..............(((((((......))))))).....(((.((((((..((--------..((.....((....))......))..))..)))))).))).. ( -29.60)
>consensus
AAGAGCUGGA___GUAAAUUGAUUAUUGGCGAUCAGCAUGUGAGCUGAUUACGAACUUGAAGCAUCCCAUAUCGACUGGGUGAGAAGGGAAGC____________________U__A_A_
....(((((................)))))(((((((......))))))).....(((....((.((((.......))))))....)))............................... (-12.43 = -11.74 +  -0.69)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:40:51 2006