Locus 7108

Sequence ID	3R_DroMel_CAF1
Location	18,743,874 – 18,743,984
Length	110
Max. P	0.939977

overview

Window 4

Location	18,743,874 – 18,743,984
Length	110
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	76.68
Mean single sequence MFE	-29.72
Consensus MFE	-12.90
Energy contribution	-13.04
Covariance contribution	0.14
Combinations/Pair	1.13
Mean z-score	-2.42
Structure conservation index	0.43
SVM decision value	0.99
SVM RNA-class probability	0.895307
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18743874 110 + 27905053
C------GCU--GC-AUUUUUGCAUAUCUUGCUGUUUUGUUUGGCAUUUUUAGUGAUUUCACUUAAAUUUUCAUAACAAAAUAUGCACAGUGCGUGCUUG-CAGCUCACUUUUGGCUCAA
.------(((--((-(....(((((....(((((((((((((((...(((.((((....)))).)))...))).))))))))).)))..)))))....))-))))............... ( -31.20)
>DroVir_CAF1 17453 109 + 1
C------GCC--GU-AUAUCUGCAUAUCUGGCAGUUUUGUUUGGCAUUUUUAGUGAUUUCACUUAAAUUUUCAUAACAAAACAUGAAGAGUGCGUGCAUG-CAGCUCGGCUAA-GCUGAG
.------((.--((-((.(.(((((.(((..(((((((((((((...(((.((((....)))).)))...))).)))))))).)).)))))))).).)))-).))(((((...-))))). ( -29.50)
>DroGri_CAF1 3163 116 + 1
GCAUGUUGUU--GUGUUAUUUGCAUAUGAAGCAGUUUUGUUUGGCAUUUUUAGUGAUUUCACUUAAAUUUUCAUAACAAAACAAGAAGAGUACGAGCUUG-UAGCUCGGUUAA-GCUGGG
((.((((..(--((((.....)))))...))))(((((((((((...(((.((((....)))).)))...))).))))))))..........(((((...-..))))).....-)).... ( -28.70)
>DroSec_CAF1 2703 110 + 1
C------GCU--GC-AUUUUUGCAUAUCUGGCUGUUUUGUUUGGCAUUUUUAGUGAUUUCACUUAAAUUUUCAUAACAAAAUAUGCACAGUGCGUGCUUG-CAGCUCACUUUUGGCUCAA
.------(((--((-(.....((((..(((((((((((((((((...(((.((((....)))).)))...))).))))))))).)).)))...)))).))-))))............... ( -32.50)
>DroMoj_CAF1 23672 112 + 1
C------GCCUGGU-GGGCCCGCCCCUUUGAUAGUUUUGUUUGGCAUUUUAAGUGAUUUCACUUAAAUUUUCAUAACAAAACAUGAAGAGUGCGUGCUCGGGCGCUCGUGUAU-GCUGAG
(------((((...-((((.((((.((((.((.(((((((((((...((((((((....))))))))...))).)))))))))))))).).))).)))))))))((((.(...-.))))) ( -36.30)
>DroPer_CAF1 10369 99 + 1
G------ACU--GG-AUUUUUGCAUAUCUUGCCGUUUUGUUUGCCAUU-UUAGUGAUUUCACUUAAAUUUUCAUAACAAAAUAUGCACAGUGCGUGCUUG-CAACAG----------CAG
(------.((--((-((........)))((((.((((((((((..(((-(.((((....)))).))))...)).))))))))..((((.....))))..)-))))))----------).. ( -20.10)
>consensus
C______GCU__GU_AUUUUUGCAUAUCUGGCAGUUUUGUUUGGCAUUUUUAGUGAUUUCACUUAAAUUUUCAUAACAAAACAUGAACAGUGCGUGCUUG_CAGCUCGCUUAU_GCUCAG
....................(((((........(((((((((((...(((.((((....)))).)))...))).)))))))).......))))).......................... (-12.90 = -13.04 +   0.14)

alignment

secondary structure

dotplot

Window 5

Location	18,743,874 – 18,743,984
Length	110
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	76.68
Mean single sequence MFE	-25.85
Consensus MFE	-10.40
Energy contribution	-10.46
Covariance contribution	0.06
Combinations/Pair	1.09
Mean z-score	-2.69
Structure conservation index	0.40
SVM decision value	1.31
SVM RNA-class probability	0.939977
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18743874 110 - 27905053
UUGAGCCAAAAGUGAGCUG-CAAGCACGCACUGUGCAUAUUUUGUUAUGAAAAUUUAAGUGAAAUCACUAAAAAUGCCAAACAAAACAGCAAGAUAUGCAAAAAU-GC--AGC------G
...............((((-((.(((.....)))((((((((((((.......(((.((((....)))).))).((.....))....)))))))))))).....)-))--)))------. ( -27.10)
>DroVir_CAF1 17453 109 - 1
CUCAGC-UUAGCCGAGCUG-CAUGCACGCACUCUUCAUGUUUUGUUAUGAAAAUUUAAGUGAAAUCACUAAAAAUGCCAAACAAAACUGCCAGAUAUGCAGAUAU-AC--GGC------G
......-...(((((.(((-(((((..(((........((((((((.((..(.(((.((((....)))).))).)..)))))))))))))..).)))))))...)-.)--)))------. ( -26.90)
>DroGri_CAF1 3163 116 - 1
CCCAGC-UUAACCGAGCUA-CAAGCUCGUACUCUUCUUGUUUUGUUAUGAAAAUUUAAGUGAAAUCACUAAAAAUGCCAAACAAAACUGCUUCAUAUGCAAAUAACAC--AACAACAUGC
....((-.....(((((..-...)))))........(((((.((((((.....(((.((((....)))).)))..............(((.......))).)))))).--)))))...)) ( -21.10)
>DroSec_CAF1 2703 110 - 1
UUGAGCCAAAAGUGAGCUG-CAAGCACGCACUGUGCAUAUUUUGUUAUGAAAAUUUAAGUGAAAUCACUAAAAAUGCCAAACAAAACAGCCAGAUAUGCAAAAAU-GC--AGC------G
...............((((-((.....((((((.((...(((((((.((..(.(((.((((....)))).))).)..)))))))))..)))))...))).....)-))--)))------. ( -25.30)
>DroMoj_CAF1 23672 112 - 1
CUCAGC-AUACACGAGCGCCCGAGCACGCACUCUUCAUGUUUUGUUAUGAAAAUUUAAGUGAAAUCACUUAAAAUGCCAAACAAAACUAUCAAAGGGGCGGGCCC-ACCAGGC------G
....((-........))(((.(.((.(((.(((((...((((((((.((..(.((((((((....)))))))).)..)))))))))).....)))))))).)).)-....)))------. ( -31.60)
>DroPer_CAF1 10369 99 - 1
CUG----------CUGUUG-CAAGCACGCACUGUGCAUAUUUUGUUAUGAAAAUUUAAGUGAAAUCACUAA-AAUGGCAAACAAAACGGCAAGAUAUGCAAAAAU-CC--AGU------C
.((----------((....-..))))...(((((((((((((((((......((((.((((....)))).)-)))(.....).....))))))))))))).....-.)--)))------. ( -23.10)
>consensus
CUCAGC_AUAACCGAGCUG_CAAGCACGCACUCUGCAUAUUUUGUUAUGAAAAUUUAAGUGAAAUCACUAAAAAUGCCAAACAAAACUGCCAGAUAUGCAAAAAU_AC__AGC______G
...............((......))..(((.........(((((((.((..(.(((.((((....)))).))).)..)))))))))..........)))..................... (-10.40 = -10.46 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:37:31 2006