Locus 5222

Sequence ID	2L_DroMel_CAF1
Location	14,753,723 – 14,753,874
Length	151
Max. P	0.858727

overview

Window 2

Location	14,753,723 – 14,753,837
Length	114
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	76.73
Mean single sequence MFE	-35.75
Consensus MFE	-22.80
Energy contribution	-21.12
Covariance contribution	-1.68
Combinations/Pair	1.59
Mean z-score	-1.49
Structure conservation index	0.64
SVM decision value	0.54
SVM RNA-class probability	0.775474
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14753723 114 + 22407834
GAGCCUAAGCAGGUUCUUGGAUUUCCUCUCAUCUAGCCGUGGGGACAUUGAGAAUAUUCCGGGCUGCAU------UCAGCUUUUGGAAAAAGGACGGCAUAGUUGCCGUUGCAAUUUCUG
((((((....))))))...(((.(((((.(........).))))).))).((((..((((((((((...------.)))))..)))))....(((((((....))))))).....)))). ( -35.50)
>DroSec_CAF1 17906 113 + 1
GAGCCUAAAAAGGUUCUUGGAUUUCCUCUCAUCUUGCCGUGGGGACAUUGAGAAUAUUCCGAGCUGCAU------GCAGCUU-UGGAAAAAGGACGGCAUAGUUGCUGUUGCAAUUUCUG
((((((....))))))..((....))(((((...((((....)).)).)))))...((((((((((...------.)))).)-)))))....(((((((....))))))).......... ( -36.90)
>DroSim_CAF1 17672 114 + 1
GAGCCUAAGAAGGUUCUUGGAUUUCCUCUCAUCUUGCCGUGGGGACAUUGAGAAUAUUCCGAGCUGCAU------GCAGCUUUUGGAAAAAGGACGGCAUAGUUGCUGUUGCAAUUUCUG
((((((....))))))..(((.....(((((...((((....)).)).)))))....)))((((((...------.))))))..(((((...(((((((....)))))))....))))). ( -36.40)
>DroEre_CAF1 18492 113 + 1
GAGCCUAAGCAGGUUGUUCAAUU-CCGCUUAUCUGGCCGUGGGGACAUUGAAAAUAUAGCGAGUUGCAU------GCGGCUUUUGGUAAGAGGGCGGCAUAGUUGCUGUUGCAAUUUCUG
.......((.(((((((......-((.((((((.((((((((.(((.(((.........)))))).).)------))))))...)))))).))((((((....)))))).))))))))). ( -33.50)
>DroYak_CAF1 20028 112 + 1
GAGCCUAAGCAGGUUGUUGAAUU-CC-UUUAUCUGGCCGUGGGGACAUUGAAAACAUUCCGAGCUGCAU------GCAGCUCUUGGGGAGAGAAAGGCACAGUUGCUGUUGCAAUUUCUG
.(((((....)))))........-((-(((.(((..(((((....)))............((((((...------.))))))..))..))).)))))...((((((....)))))).... ( -31.90)
>DroAna_CAF1 37385 104 + 1
GAGCCUAU-----UUGU-------CC-UUUAGCUA--CUUGGGUGCAUUGAAAAUGUCCCCUGCCACCGAUAUUUGUGUCA-GUGGCAGGGGGAUGUGGCAGUUUCUGUUGCAAUUUCUG
(.(((((.-----..((-------..-....))..--..))))).)...((((...(((((((((((.((((....)))).-))))))))))).((..((((...))))..)).)))).. ( -40.30)
>consensus
GAGCCUAAGCAGGUUCUUGGAUU_CCUCUCAUCUAGCCGUGGGGACAUUGAAAAUAUUCCGAGCUGCAU______GCAGCUUUUGGAAAAAGGACGGCAUAGUUGCUGUUGCAAUUUCUG
.(((((....)))))............(((((......)))))((.((((......(((((((((((........)))))))..))))....(((((((....))))))).)))).)).. (-22.80 = -21.12 +  -1.68)

alignment

secondary structure

dotplot

Window 3

Location	14,753,763 – 14,753,874
Length	111
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	82.34
Mean single sequence MFE	-35.97
Consensus MFE	-23.88
Energy contribution	-22.37
Covariance contribution	-1.52
Combinations/Pair	1.62
Mean z-score	-2.81
Structure conservation index	0.66
SVM decision value	0.82
SVM RNA-class probability	0.858727
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14753763 111 + 22407834
GGGGACAUUGAGAAUAUUCCGGGCUGCAU------UCAGCUUUUGGAAAAAGGACGGCAUAGUUGCCGUUGCAAUUUCUGUUUUGAAAUUGGCUUAUUUACGUA-UUU--UUUAUGCGCC
((.(.(((.(((((((((((((((((...------.)))))..))))..((((((((((....))))))).(((((((......))))))).)))......)))-)))--)).)))).)) ( -35.30)
>DroSec_CAF1 17946 110 + 1
GGGGACAUUGAGAAUAUUCCGAGCUGCAU------GCAGCUU-UGGAAAAAGGACGGCAUAGUUGCUGUUGCAAUUUCUGUUUUGAAAUUGGCUUAUUUACGUA-UUU--UUUAUGCGAA
(....)..((((....((((((((((...------.)))).)-)))))....(((((((....))))))).(((((((......))))))).))))....((((-(..--...))))).. ( -33.90)
>DroSim_CAF1 17712 111 + 1
GGGGACAUUGAGAAUAUUCCGAGCUGCAU------GCAGCUUUUGGAAAAAGGACGGCAUAGUUGCUGUUGCAAUUUCUGUUUUGAAAUUGGCUUAUUUACGUA-UUU--UUUAUGCGCC
((.(.(((.(((((((((((((((((...------.))))))..)))..((((((((((....))))))).(((((((......))))))).)))......)))-)))--)).)))).)) ( -35.40)
>DroEre_CAF1 18531 113 + 1
GGGGACAUUGAAAAUAUAGCGAGUUGCAU------GCGGCUUUUGGUAAGAGGGCGGCAUAGUUGCUGUUGCAAUUUCUGUUUUGUAAUUGGCUUAUUUACGUA-UUUUUUUUCUGCGCC
(.(((....(((((((((((.((((((((------((.((((((.....)))))).))))((((((....))))))........)))))).))).......)))-)))))..))).)... ( -31.91)
>DroYak_CAF1 20066 111 + 1
GGGGACAUUGAAAACAUUCCGAGCUGCAU------GCAGCUCUUGGGGAGAGAAAGGCACAGUUGCUGUUGCAAUUUCUGUUUUGUAAUUGGCUUAUUUACGUA-UUU--UUUCUGCGCC
..(((...((....)).)))((((((...------.))))))..(.((((((((((((.(((((((....(((.....)))...))))))))))).........-)))--))))).)... ( -29.70)
>DroAna_CAF1 37410 117 + 1
GGGUGCAUUGAAAAUGUCCCCUGCCACCGAUAUUUGUGUCA-GUGGCAGGGGGAUGUGGCAGUUUCUGUUGCAAUUUCUGUUUUGAAAUUGGCUUAUUUUGGUCCUUU--UUUAUGCGCC
.(((((((.(((((..(((((((((((.((((....)))).-)))))))))))..(..((((...))))..)((((((......))))))((((......)))).)))--)).))))))) ( -49.60)
>consensus
GGGGACAUUGAAAAUAUUCCGAGCUGCAU______GCAGCUUUUGGAAAAAGGACGGCAUAGUUGCUGUUGCAAUUUCUGUUUUGAAAUUGGCUUAUUUACGUA_UUU__UUUAUGCGCC
(....)..........(((((((((((........)))))))..)))).((((((((((....))))))).(((((((......))))))).)))......................... (-23.88 = -22.37 +  -1.52)

alignment

secondary structure

dotplot

Window 4

Location	14,753,763 – 14,753,874
Length	111
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	82.34
Mean single sequence MFE	-25.14
Consensus MFE	-12.81
Energy contribution	-14.28
Covariance contribution	1.47
Combinations/Pair	1.21
Mean z-score	-2.64
Structure conservation index	0.51
SVM decision value	0.04
SVM RNA-class probability	0.551422
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14753763 111 - 22407834
GGCGCAUAAA--AAA-UACGUAAAUAAGCCAAUUUCAAAACAGAAAUUGCAACGGCAACUAUGCCGUCCUUUUUCCAAAAGCUGA------AUGCAGCCCGGAAUAUUCUCAAUGUCCCC
((.((((...--...-...........((.((((((......)))))))).((((((....)))))).....((((....((((.------...))))..))))........)))).)). ( -25.30)
>DroSec_CAF1 17946 110 - 1
UUCGCAUAAA--AAA-UACGUAAAUAAGCCAAUUUCAAAACAGAAAUUGCAACAGCAACUAUGCCGUCCUUUUUCCA-AAGCUGC------AUGCAGCUCGGAAUAUUCUCAAUGUCCCC
...((((...--...-.(((.......((.((((((......))))))))....(((....)))))).....((((.-.(((((.------...))))).))))........)))).... ( -19.60)
>DroSim_CAF1 17712 111 - 1
GGCGCAUAAA--AAA-UACGUAAAUAAGCCAAUUUCAAAACAGAAAUUGCAACAGCAACUAUGCCGUCCUUUUUCCAAAAGCUGC------AUGCAGCUCGGAAUAUUCUCAAUGUCCCC
((.((((...--...-.(((.......((.((((((......))))))))....(((....)))))).....((((...(((((.------...))))).))))........)))).)). ( -22.40)
>DroEre_CAF1 18531 113 - 1
GGCGCAGAAAAAAAA-UACGUAAAUAAGCCAAUUACAAAACAGAAAUUGCAACAGCAACUAUGCCGCCCUCUUACCAAAAGCCGC------AUGCAACUCGCUAUAUUUUCAAUGUCCCC
((((..(((((....-...((((.........))))......((..((((....)))).(((((.((.............)).))------)))....))......)))))..))))... ( -13.42)
>DroYak_CAF1 20066 111 - 1
GGCGCAGAAA--AAA-UACGUAAAUAAGCCAAUUACAAAACAGAAAUUGCAACAGCAACUGUGCCUUUCUCUCCCCAAGAGCUGC------AUGCAGCUCGGAAUGUUUUCAAUGUCCCC
(((((((...--...-...((((.........))))..........((((....))))))))))).............((((((.------...))))))(((.((....))...))).. ( -28.50)
>DroAna_CAF1 37410 117 - 1
GGCGCAUAAA--AAAGGACCAAAAUAAGCCAAUUUCAAAACAGAAAUUGCAACAGAAACUGCCACAUCCCCCUGCCAC-UGACACAAAUAUCGGUGGCAGGGGACAUUUUCAAUGCACCC
((.((((..(--(((((............(((((((......)))))))............)).....((((((((((-(((........)))))))))))))...))))..)))).)). ( -41.65)
>consensus
GGCGCAUAAA__AAA_UACGUAAAUAAGCCAAUUUCAAAACAGAAAUUGCAACAGCAACUAUGCCGUCCUCUUUCCAAAAGCUGC______AUGCAGCUCGGAAUAUUCUCAAUGUCCCC
((.((((....................((.((((((......))))))))......................((((...((((((........)))))).))))........)))).)). (-12.81 = -14.28 +   1.47)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:39:02 2006