Locus 2389

Sequence ID	3R_DroMel_CAF1
Location	6,743,110 – 6,743,220
Length	110
Max. P	0.992190

overview

Window 9

Location	6,743,110 – 6,743,220
Length	110
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	90.54
Mean single sequence MFE	-34.10
Consensus MFE	-28.47
Energy contribution	-29.03
Covariance contribution	0.56
Combinations/Pair	1.03
Mean z-score	-2.21
Structure conservation index	0.83
SVM decision value	1.28
SVM RNA-class probability	0.939674
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6743110 110 + 27905053
UUUGCAUUAAC-UUUGCAACGGGGUGUGAACAGUGAUUUUGUUGCUAUUGCACAAAUUGCACUGACUGCGUGGAUCUUGUUGU---------UGUUGCAGUUGCCACUGCAGUUGCUAAA
.(((((.....-..)))))...(((.....(((((..(((((.((....)))))))...)))))(((((((((...((((...---------....))))...)))).))))).)))... ( -32.50)
>DroSec_CAF1 7890 109 + 1
UUCGC-UUAAC-UUUGCAACGUGGUGUGAACAGUGAUUUUGUUGCUAUUGCACAAAUUGCACUGACUGCGUGGAUCUUGUUGU---------UGUUGCAGUUGCCACUGCAGUUGCUAAA
.....-.....-...((((((..(((....(((((..(((((.((....)))))))...)))))((((((..(((......))---------)..))))))...)))..).))))).... ( -33.00)
>DroSim_CAF1 12229 109 + 1
UUCGC-UUAAC-UUUGCAACGUGGUGUGAACAGUGAUUUUGUUGCUAUUGCACAAAUUGCACUGACUGCGUGGAUCUUGUUGU---------UGUUGCAGUUGCCACUGCAGUUGCUAAA
.....-.....-...((((((..(((....(((((..(((((.((....)))))))...)))))((((((..(((......))---------)..))))))...)))..).))))).... ( -33.00)
>DroYak_CAF1 3209 117 + 1
UUUGA---AACUUUUGCAACGGAGUGUGAACAGUGAUUUUGUUGCUGUUGCACAAAUUGCAAUGACUGCGUGGAACUUGUUUUUGUUGCUGCUGUUGCAGUUGCCACUGCAGUUGCUAAA
.....---.....((((((.....(((((((((..((...))..))))).))))..)))))).(((((((((((((........)))(((((....)))))..)))).))))))...... ( -37.90)
>consensus
UUCGC_UUAAC_UUUGCAACGGGGUGUGAACAGUGAUUUUGUUGCUAUUGCACAAAUUGCACUGACUGCGUGGAUCUUGUUGU_________UGUUGCAGUUGCCACUGCAGUUGCUAAA
...............(((((((((((....(((((..(((((.((....)))))))...)))))((((((.........................))))))...)))))).))))).... (-28.47 = -29.03 +   0.56)

alignment

secondary structure

dotplot

Window 0

Location	6,743,110 – 6,743,220
Length	110
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	90.54
Mean single sequence MFE	-26.82
Consensus MFE	-24.08
Energy contribution	-24.32
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-2.68
Structure conservation index	0.90
SVM decision value	2.31
SVM RNA-class probability	0.992190
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6743110 110 - 27905053
UUUAGCAACUGCAGUGGCAACUGCAACA---------ACAACAAGAUCCACGCAGUCAGUGCAAUUUGUGCAAUAGCAACAAAAUCACUGUUCACACCCCGUUGCAAA-GUUAAUGCAAA
....(((((((((((....))))))...---------...................(((((...(((((((....)).)))))..)))))..........)))))...-........... ( -25.40)
>DroSec_CAF1 7890 109 - 1
UUUAGCAACUGCAGUGGCAACUGCAACA---------ACAACAAGAUCCACGCAGUCAGUGCAAUUUGUGCAAUAGCAACAAAAUCACUGUUCACACCACGUUGCAAA-GUUAA-GCGAA
....(((((((((((....))))))...---------...................(((((...(((((((....)).)))))..)))))..........)))))...-.....-..... ( -25.40)
>DroSim_CAF1 12229 109 - 1
UUUAGCAACUGCAGUGGCAACUGCAACA---------ACAACAAGAUCCACGCAGUCAGUGCAAUUUGUGCAAUAGCAACAAAAUCACUGUUCACACCACGUUGCAAA-GUUAA-GCGAA
....(((((((((((....))))))...---------...................(((((...(((((((....)).)))))..)))))..........)))))...-.....-..... ( -25.40)
>DroYak_CAF1 3209 117 - 1
UUUAGCAACUGCAGUGGCAACUGCAACAGCAGCAACAAAAACAAGUUCCACGCAGUCAUUGCAAUUUGUGCAACAGCAACAAAAUCACUGUUCACACUCCGUUGCAAAAGUU---UCAAA
....((((((((((((((..((((....)))).(((........))).......)))))))))...((((.(((((...........)))))))))....))))).......---..... ( -31.10)
>consensus
UUUAGCAACUGCAGUGGCAACUGCAACA_________ACAACAAGAUCCACGCAGUCAGUGCAAUUUGUGCAAUAGCAACAAAAUCACUGUUCACACCACGUUGCAAA_GUUAA_GCAAA
....(((((((((((....))))))...............................(((((...(((((((....)).)))))..)))))..........)))))............... (-24.08 = -24.32 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:34:13 2006