Locus 2069

Sequence ID	3L_DroMel_CAF1
Location	5,689,302 – 5,689,435
Length	133
Max. P	0.923959

overview

Window 5

Location	5,689,302 – 5,689,415
Length	113
Sequences	3
Columns	113
Reading direction	forward
Mean pairwise identity	86.23
Mean single sequence MFE	-22.60
Consensus MFE	-14.71
Energy contribution	-15.04
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.38
Structure conservation index	0.65
SVM decision value	0.11
SVM RNA-class probability	0.588090
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5689302 113 + 23771897
ACACACACACACUUGUAUUUGCAUUGGCAACCUGCAACUGCAACAGCAAAAGCAGCAGCAACAACACGCAACUGCAUCUGCAUCUGCAUCUGCAAAUAAUUGUCAGCUUACUG
..........((...((((((((...(((...((((..(((....)))...((((..((........))..))))...))))..)))...))))))))...)).......... ( -26.10)
>DroEre_CAF1 65469 108 + 1
----ACACAUACUUGCAUUUGCAUUGGCAACCUGCAACUGCAAC-GCAAAAGCAGCAACAACAACACACAACUGAAUCUGCAUCUGCAUCUGCAAAUAAUUGUCAGCUUACUG
----........(((((.(((((..(....).))))).))))).-(((...((((...((............))...))))...)))..((((((....))).)))....... ( -20.00)
>DroYak_CAF1 64055 97 + 1
----ACACGCACUUACAUUUGCAUUGGCAACCUGCAACUGCAAC------------AGCAACAACACGCAACUGCAUCUGCAUCUGCAUCUGCAAAUAAUUGUCAGCUUACUG
----....((((....(((((((...(((...((((..((((..------------.((........))...))))..))))..)))...)))))))....))..))...... ( -21.70)
>consensus
____ACACACACUUGCAUUUGCAUUGGCAACCUGCAACUGCAAC_GCAAAAGCAGCAGCAACAACACGCAACUGCAUCUGCAUCUGCAUCUGCAAAUAAUUGUCAGCUUACUG
................(((((((...(((...((((..((((..............................))))..))))..)))...)))))))................ (-14.71 = -15.04 +   0.33)

alignment

secondary structure

dotplot

Window 6

Location	5,689,302 – 5,689,415
Length	113
Sequences	3
Columns	113
Reading direction	reverse
Mean pairwise identity	86.23
Mean single sequence MFE	-34.00
Consensus MFE	-27.49
Energy contribution	-27.49
Covariance contribution	0.01
Combinations/Pair	1.10
Mean z-score	-2.35
Structure conservation index	0.81
SVM decision value	0.80
SVM RNA-class probability	0.853995
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5689302 113 - 23771897
CAGUAAGCUGACAAUUAUUUGCAGAUGCAGAUGCAGAUGCAGUUGCGUGUUGUUGCUGCUGCUUUUGCUGUUGCAGUUGCAGGUUGCCAAUGCAAAUACAAGUGUGUGUGUGU
..((((.(((.(((((((((((....))))))(((((.(((((.(((......))).))))).)))))......)))))))).))))..(((((.((((....)))).))))) ( -37.80)
>DroEre_CAF1 65469 108 - 1
CAGUAAGCUGACAAUUAUUUGCAGAUGCAGAUGCAGAUUCAGUUGUGUGUUGUUGUUGCUGCUUUUGC-GUUGCAGUUGCAGGUUGCCAAUGCAAAUGCAAGUAUGUGU----
(((....)))(((..((((((((((((((((.((((...(((..........)))...)))).)))))-)))(((...((.....))...)))...))))))))..)))---- ( -31.80)
>DroYak_CAF1 64055 97 - 1
CAGUAAGCUGACAAUUAUUUGCAGAUGCAGAUGCAGAUGCAGUUGCGUGUUGUUGCU------------GUUGCAGUUGCAGGUUGCCAAUGCAAAUGUAAGUGCGUGU----
(((....)))(((..((((((((..((((...((((.((((..((((.((....)).------------..))))..))))..))))...))))..))))))))..)))---- ( -32.40)
>consensus
CAGUAAGCUGACAAUUAUUUGCAGAUGCAGAUGCAGAUGCAGUUGCGUGUUGUUGCUGCUGCUUUUGC_GUUGCAGUUGCAGGUUGCCAAUGCAAAUGCAAGUGUGUGU____
(((....)))(((..((((((((..((((...((((.((((..((((........................))))..))))..))))...))))..))))))))..))).... (-27.49 = -27.49 +   0.01)

alignment

secondary structure

dotplot

Window 7

Location	5,689,335 – 5,689,435
Length	100
Sequences	3
Columns	100
Reading direction	forward
Mean pairwise identity	89.30
Mean single sequence MFE	-22.27
Consensus MFE	-16.53
Energy contribution	-16.87
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-3.00
Structure conservation index	0.74
SVM decision value	0.73
SVM RNA-class probability	0.835028
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5689335 100 + 23771897
GCAACUGCAACAGCAAAAGCAGCAGCAACAACACGCAACUGCAUCUGCAUCUGCAUCUGCAAAUAAUUGUCAGCUUACUGACUCGCAUUCAAUGCAGCAA
(((..((((...(((...((((..((........))..))))...)))...))))..)))........(((((....)))))..((((...))))..... ( -26.30)
>DroEre_CAF1 65498 99 + 1
GCAACUGCAAC-GCAAAAGCAGCAACAACAACACACAACUGAAUCUGCAUCUGCAUCUGCAAAUAAUUGUCAGCUUACUGACUCGCAUUCAACGCAGCAA
....((((...-((....))...................((((..(((...(((....))).......(((((....)))))..)))))))..))))... ( -19.70)
>DroYak_CAF1 64084 88 + 1
GCAACUGCAAC------------AGCAACAACACGCAACUGCAUCUGCAUCUGCAUCUGCAAAUAAUUGUCAGCUUACUGACUCGCAUUCAAUGCAGCAA
(((..(((...------------.))).......((...((((..(((....)))..)))).......(((((....)))))..))......)))..... ( -20.80)
>consensus
GCAACUGCAAC_GCAAAAGCAGCAGCAACAACACGCAACUGCAUCUGCAUCUGCAUCUGCAAAUAAUUGUCAGCUUACUGACUCGCAUUCAAUGCAGCAA
....((((...............................((((..(((....)))..)))).......(((((....)))))...........))))... (-16.53 = -16.87 +   0.33)

alignment

secondary structure

dotplot

Window 8

Location	5,689,335 – 5,689,435
Length	100
Sequences	3
Columns	100
Reading direction	reverse
Mean pairwise identity	89.30
Mean single sequence MFE	-32.77
Consensus MFE	-27.04
Energy contribution	-27.77
Covariance contribution	0.73
Combinations/Pair	1.06
Mean z-score	-2.92
Structure conservation index	0.83
SVM decision value	1.16
SVM RNA-class probability	0.923959
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5689335 100 - 23771897
UUGCUGCAUUGAAUGCGAGUCAGUAAGCUGACAAUUAUUUGCAGAUGCAGAUGCAGAUGCAGUUGCGUGUUGUUGCUGCUGCUUUUGCUGUUGCAGUUGC
...(((((...(((....(((((....))))).)))...))))).(((((..(((((.(((((.(((......))).))))).)))))..)))))..... ( -36.70)
>DroEre_CAF1 65498 99 - 1
UUGCUGCGUUGAAUGCGAGUCAGUAAGCUGACAAUUAUUUGCAGAUGCAGAUGCAGAUUCAGUUGUGUGUUGUUGUUGCUGCUUUUGC-GUUGCAGUUGC
..(((((......((((((((((....)))))......)))))((((((((.((((...(((..........)))...)))).)))))-))))))))... ( -31.20)
>DroYak_CAF1 64084 88 - 1
UUGCUGCAUUGAAUGCGAGUCAGUAAGCUGACAAUUAUUUGCAGAUGCAGAUGCAGAUGCAGUUGCGUGUUGUUGCU------------GUUGCAGUUGC
...(((((((...((((((((((....)))))......))))))))))))..((((.(((((..(((......))).------------.))))).)))) ( -30.40)
>consensus
UUGCUGCAUUGAAUGCGAGUCAGUAAGCUGACAAUUAUUUGCAGAUGCAGAUGCAGAUGCAGUUGCGUGUUGUUGCUGCUGCUUUUGC_GUUGCAGUUGC
..((((((((...(((..(((((....)))))....((((((....))))))))))))))))).....((..((((.((.((....)).)).))))..)) (-27.04 = -27.77 +   0.73)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:42 2006