Locus 3515

Sequence ID	2L_DroMel_CAF1
Location	10,276,853 – 10,277,000
Length	147
Max. P	0.827495

overview

Window 7

Location	10,276,853 – 10,276,970
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.35
Mean single sequence MFE	-29.67
Consensus MFE	-21.91
Energy contribution	-23.03
Covariance contribution	1.12
Combinations/Pair	1.10
Mean z-score	-2.27
Structure conservation index	0.74
SVM decision value	0.70
SVM RNA-class probability	0.827495
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10276853 117 + 22407834
CUUAAAUGUUAAUCU---CCUAAAAUAUGCCUGCAAAAUGCAGGUUUUGUUUAUAAAUAACAAUAGAACUUGCAGCCGUCGUGUCGGCAGACAUGUCUGCGUGCACUCAAAAAAACGAGA
............(((---(........((..((((...(((((((((((((..........)))))))))))))((.(.((((((....)))))).).)).))))..)).......)))) ( -31.06)
>DroSec_CAF1 5010 117 + 1
CUUAAAUGUUAAUCU---CCUAAAAUGUGCCCGCAAAAUGCAGGUUUUGUUUAUAAAUAACAAUAGAACUUGCAGCCGUCGUGUCGACAGACAUGUCUGCGUGCACUCAAAAAAACGAGA
............(((---(.......((((.((((...(((((((((((((..........)))))))))))))...(.((((((....)))))).))))).))))..........)))) ( -34.83)
>DroSim_CAF1 5148 117 + 1
CUUAAAUGUUAAUCU---CCUAAAAUGUGCCCGAAAAAUGCAGGUUUUGUUUAUAAAUAACAAUAGAACUUGCAGCCGUCGUGUCGGCAGACAUGUCUGCGUGCACUCAAAAAAACGAGA
............(((---(.......((((.(......(((((((((((((..........)))))))))))))((.(.((((((....)))))).).))).))))..........)))) ( -31.93)
>DroEre_CAF1 5023 120 + 1
CUUAAAUGUUAAUCUGUUGCUAAAAUGUGACCACGAAACACAGGUUUUGUUUAUAAAUAACAAAAGAACUUGCAGCCGUCGAGUCGGCAGACAUGUCUGAGUGUACUCAAAAAAACGAGA
......(((((....((..(......)..)).(((((((....))))))).......)))))......((((..((((......)))).........((((....))))......)))). ( -24.30)
>DroYak_CAF1 4964 120 + 1
CCUAAAUGUUAAUCUGUUGCUAAAAUGUGCUCACUAAACGCAAGUUUUGUUUAUAAAUCACAAAAGAACUUGCAGCCGUCGAGUCGGCAGACAUGUCUGCGUGCACUCAAAAAAACGAGA
............((((((........((((.(.......(((((((((................))))))))).((((......))))(((....)))..).)))).......))).))) ( -26.25)
>consensus
CUUAAAUGUUAAUCU___CCUAAAAUGUGCCCGCAAAAUGCAGGUUUUGUUUAUAAAUAACAAUAGAACUUGCAGCCGUCGUGUCGGCAGACAUGUCUGCGUGCACUCAAAAAAACGAGA
............(((...........((((.(.......((((((((((((..........)))))))))))).((.(.((((((....)))))).).))).))))...........))) (-21.91 = -23.03 +   1.12)

alignment

secondary structure

dotplot

Window 8

Location	10,276,890 – 10,277,000
Length	110
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	92.73
Mean single sequence MFE	-28.26
Consensus MFE	-21.16
Energy contribution	-22.28
Covariance contribution	1.12
Combinations/Pair	1.10
Mean z-score	-1.68
Structure conservation index	0.75
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10276890 110 + 22407834
CAGGUUUUGUUUAUAAAUAACAAUAGAACUUGCAGCCGUCGUGUCGGCAGACAUGUCUGCGUGCACUCAAAAAAACGAGACAGACCGUUUCAUGGCUUUUUAUCAGAUAG
(((((((((((..........))))))))))).((((((.((((..(((((....)))))..))))..........(((((.....)))))))))))............. ( -30.40)
>DroSec_CAF1 5047 110 + 1
CAGGUUUUGUUUAUAAAUAACAAUAGAACUUGCAGCCGUCGUGUCGACAGACAUGUCUGCGUGCACUCAAAAAAACGAGACAGACCGUUUCAUGGCUAUUUAUCAGAUAG
(((((((((((..........))))))))))).((((((.((((((.((((....)))))).))))..........(((((.....)))))))))))............. ( -29.40)
>DroSim_CAF1 5185 110 + 1
CAGGUUUUGUUUAUAAAUAACAAUAGAACUUGCAGCCGUCGUGUCGGCAGACAUGUCUGCGUGCACUCAAAAAAACGAGACAGACCGUUUCAUGGCUAUUUAUCAGAUAG
(((((((((((..........))))))))))).((((((.((((..(((((....)))))..))))..........(((((.....)))))))))))............. ( -31.00)
>DroEre_CAF1 5063 110 + 1
CAGGUUUUGUUUAUAAAUAACAAAAGAACUUGCAGCCGUCGAGUCGGCAGACAUGUCUGAGUGUACUCAAAAAAACGAGACAGACUGCUUCAUGGUAUUUUAUUAGAUAU
(((((((((((.......))))...)))))))..((((......))))....((((((((.(((.(((........))))))...((((....)))).....)))))))) ( -23.50)
>DroYak_CAF1 5004 110 + 1
CAAGUUUUGUUUAUAAAUCACAAAAGAACUUGCAGCCGUCGAGUCGGCAGACAUGUCUGCGUGCACUCAAAAAAACGAGACAGACGGUUUCAUGUCAGUUUAUAACAUAG
....((((((.........))))))(((((.(((((((((..(((....))).(((((.(((............))))))))))))))....))).)))))......... ( -27.00)
>consensus
CAGGUUUUGUUUAUAAAUAACAAUAGAACUUGCAGCCGUCGUGUCGGCAGACAUGUCUGCGUGCACUCAAAAAAACGAGACAGACCGUUUCAUGGCUAUUUAUCAGAUAG
(((((((((((..........)))))))))))..(((((.((((..(((((....)))))..))))..........(((((.....)))))))))).............. (-21.16 = -22.28 +   1.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:54:17 2006