Locus 4308

Sequence ID	2L_DroMel_CAF1
Location	12,314,669 – 12,314,806
Length	137
Max. P	0.936730

overview

Window 1

Location	12,314,669 – 12,314,769
Length	100
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	77.52
Mean single sequence MFE	-18.02
Consensus MFE	-12.40
Energy contribution	-12.40
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.40
Structure conservation index	0.69
SVM decision value	0.63
SVM RNA-class probability	0.803992
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12314669 100 - 22407834
UAAUCUUAUUAGCAGUUUGUUGUUCGAACCUAAUCAAUUACCAACGUAAUUACAAACUUUGCUAAUCUGACUCGGUUUCCCCCCAGA-AACGCUUUUCCAG-------------------
...((..(((((((((((((.....((......))((((((....))))))))))))..)))))))..))....(((((......))-)))..........------------------- ( -18.10)
>DroVir_CAF1 168602 99 - 1
UAAUCUUAUUAGCAGUUUGUUGUUCGAACCUAAUCAAUUACCAACGUAAUUACAAACUUUGCUAAUCUGCUUAGCUCACA--GCGCA-CACA------G-A--GCGAAA---------GG
........((((((((((((.....((......))((((((....))))))))))))..))))))((((....((.....--))...-..))------)-)--.(....---------). ( -17.90)
>DroPse_CAF1 203714 109 - 1
UAAUCUUAUUAGCAGUUUGUUGUUCGAACCUAAUCAAUUACCAACGUAAUUACAAACUUUGCUAAUCUGCCUCGGUCUCC--CCCGACAGCGCUACCCAAAAACCAAAA---------GA
...(((((((((((((((((.....((......))((((((....))))))))))))..)))))))..((.((((.....--.))))..))................))---------)) ( -19.30)
>DroGri_CAF1 177291 108 - 1
UAAUCUUAUUAGCAGUUUGUUGUUCGAACCUAAUCAAUUACCAACGUAAUUACAAACUUUGCUAAUCUGCUUAGGUCGCA--ACAGA-UUCA------C-A--UCGAACAGGGCACAGAG
..............((.(.((((((((....((((((((((....)))))).....((..((......))..))......--...))-))..------.-.--)))))))).).)).... ( -19.60)
>DroAna_CAF1 126109 98 - 1
UAAUCUUAUUAGCAGUUUGUUGUUCGAACCUAAUCAAUUACCAACGUAAUUACAAACUUUGCUAAUCUCCCUCGGUUUCC-CCCAGC-AACGAAUUUCC-G-------------------
.......(((((((((((((.....((......))((((((....))))))))))))..)))))))......(((.(((.-......-...)))...))-)------------------- ( -13.90)
>DroPer_CAF1 209195 109 - 1
UAAUCUUAUUAGCAGUUUGUUGUUCGAACCUAAUCAAUUACCAACGUAAUUACAAACUUUGCUAAUCUGCCUCGGUCUCC--CCCGACAGCGCUACCCAAAAACCAAAA---------GA
...(((((((((((((((((.....((......))((((((....))))))))))))..)))))))..((.((((.....--.))))..))................))---------)) ( -19.30)
>consensus
UAAUCUUAUUAGCAGUUUGUUGUUCGAACCUAAUCAAUUACCAACGUAAUUACAAACUUUGCUAAUCUGCCUCGGUCUCC__CCAGA_AACGCU___CC_A___C_AAA_________G_
.......(((((((((((((.....((......))((((((....))))))))))))..)))))))...................................................... (-12.40 = -12.40 +   0.00)

alignment

secondary structure

dotplot

Window 2

Location	12,314,689 – 12,314,806
Length	117
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	92.21
Mean single sequence MFE	-24.75
Consensus MFE	-22.42
Energy contribution	-22.62
Covariance contribution	0.19
Combinations/Pair	1.03
Mean z-score	-1.64
Structure conservation index	0.91
SVM decision value	1.26
SVM RNA-class probability	0.936730
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12314689 117 + 22407834
GGAAACCGAGUCAGAUUAGCAAAGUUUGUAAUUACGUUGGUAAUUGAUUAGGUUCGAACAACAAACUGCUAAUAAGAUUAUUGCAGUUGAGAACAAACCGAGCUGAAAAAACAAA---AG
(....).........(((((...((((((......((((....((((......)))).)))).((((((.((((....))))))))))....))))))...))))).........---.. ( -23.80)
>DroVir_CAF1 168621 119 + 1
UGUGAGCUAAGCAGAUUAGCAAAGUUUGUAAUUACGUUGGUAAUUGAUUAGGUUCGAACAACAAACUGCUAAUAAGAUUAUUGCAGUUGAGAACAAACCGAGCUGAAAAAACAACU-CAA
.....(((((.....)))))...((((((......((((....((((......)))).)))).((((((.((((....))))))))))....)))))).(((.((......)).))-).. ( -26.10)
>DroGri_CAF1 177319 119 + 1
UGCGACCUAAGCAGAUUAGCAAAGUUUGUAAUUACGUUGGUAAUUGAUUAGGUUCGAACAACAAACUGCUAAUAAGAUUAUUGCAGUCGAGAACAAACCGAGCUGAAAAAACAACU-CAA
..((((((((...(((((.(((.((........)).))).)))))..))))).)))........(((((.((((....)))))))))............(((.((......)).))-).. ( -24.70)
>DroEre_CAF1 135206 117 + 1
GGAAACAGCGCCAGAUUAGCAAAGUUUGUAAUUACGUUGGUAAUUGAUUAGGUUCGAACAACAAACUGCUAAUAAGAUUAUUGCAGUUGAGAACAAACCGAGCUGAAAAAACAAA---AG
.....((((((.......))...((((((......((((....((((......)))).)))).((((((.((((....))))))))))....))))))...))))..........---.. ( -24.80)
>DroMoj_CAF1 179368 120 + 1
UGGGCGCUAAGCAGAUUAGCAAAGUUUGUAAUUACGUUGGUAAUUGAUUAGGUUCGAACAACAAACUGCUAAUAAGAUUAUUGCAGUCGAGAGCAAACCGAGCUGAAAAAACAACUUCAG
(.((((((((.....)))))...((((((......((((....((((......)))).))))..(((((.((((....))))))))).....))))))...))).).............. ( -25.30)
>DroAna_CAF1 126127 117 + 1
GGAAACCGAGGGAGAUUAGCAAAGUUUGUAAUUACGUUGGUAAUUGAUUAGGUUCGAACAACAAACUGCUAAUAAGAUUAUUGCAGUUGAGAACAAACCGAGCUGAAAAAACAAA---AA
(....).........(((((...((((((......((((....((((......)))).)))).((((((.((((....))))))))))....))))))...))))).........---.. ( -23.80)
>consensus
GGAAACCGAAGCAGAUUAGCAAAGUUUGUAAUUACGUUGGUAAUUGAUUAGGUUCGAACAACAAACUGCUAAUAAGAUUAUUGCAGUUGAGAACAAACCGAGCUGAAAAAACAAA___AA
...............(((((...((((((......((((....((((......)))).)))).((((((.((((....))))))))))....))))))...))))).............. (-22.42 = -22.62 +   0.19)

alignment

secondary structure

dotplot

Window 3

Location	12,314,689 – 12,314,806
Length	117
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	92.21
Mean single sequence MFE	-24.63
Consensus MFE	-20.12
Energy contribution	-19.90
Covariance contribution	-0.22
Combinations/Pair	1.04
Mean z-score	-2.33
Structure conservation index	0.82
SVM decision value	0.52
SVM RNA-class probability	0.768945
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12314689 117 - 22407834
CU---UUUGUUUUUUCAGCUCGGUUUGUUCUCAACUGCAAUAAUCUUAUUAGCAGUUUGUUGUUCGAACCUAAUCAAUUACCAACGUAAUUACAAACUUUGCUAAUCUGACUCGGUUUCC
..---...(((.....(((..((((((..(.(((((((((((....)))).)))).)))..)..)))))).....((((((....)))))).........))).....)))......... ( -21.00)
>DroVir_CAF1 168621 119 - 1
UUG-AGUUGUUUUUUCAGCUCGGUUUGUUCUCAACUGCAAUAAUCUUAUUAGCAGUUUGUUGUUCGAACCUAAUCAAUUACCAACGUAAUUACAAACUUUGCUAAUCUGCUUAGCUCACA
..(-(((((......))))))((((((..(.(((((((((((....)))).)))).)))..)..)))))).....((((((....)))))).........(((((.....)))))..... ( -28.50)
>DroGri_CAF1 177319 119 - 1
UUG-AGUUGUUUUUUCAGCUCGGUUUGUUCUCGACUGCAAUAAUCUUAUUAGCAGUUUGUUGUUCGAACCUAAUCAAUUACCAACGUAAUUACAAACUUUGCUAAUCUGCUUAGGUCGCA
..(-(((((......))))))((((((..(..((((((((((....)))).))))))....)..)))))).....((((((....)))))).....((..((......))..))...... ( -28.80)
>DroEre_CAF1 135206 117 - 1
CU---UUUGUUUUUUCAGCUCGGUUUGUUCUCAACUGCAAUAAUCUUAUUAGCAGUUUGUUGUUCGAACCUAAUCAAUUACCAACGUAAUUACAAACUUUGCUAAUCUGGCGCUGUUUCC
..---..........((((..((((((..(.(((((((((((....)))).)))).)))..)..)))))).....((((((....)))))).........(((.....)))))))..... ( -24.30)
>DroMoj_CAF1 179368 120 - 1
CUGAAGUUGUUUUUUCAGCUCGGUUUGCUCUCGACUGCAAUAAUCUUAUUAGCAGUUUGUUGUUCGAACCUAAUCAAUUACCAACGUAAUUACAAACUUUGCUAAUCUGCUUAGCGCCCA
((((((......))))))...((((((..(..((((((((((....)))).))))))....)..)))))).....((((((....)))))).........(((((.....)))))..... ( -25.20)
>DroAna_CAF1 126127 117 - 1
UU---UUUGUUUUUUCAGCUCGGUUUGUUCUCAACUGCAAUAAUCUUAUUAGCAGUUUGUUGUUCGAACCUAAUCAAUUACCAACGUAAUUACAAACUUUGCUAAUCUCCCUCGGUUUCC
..---...........(((..((((((..(.(((((((((((....)))).)))).)))..)..)))))).....((((((....)))))).........)))................. ( -20.00)
>consensus
CU___GUUGUUUUUUCAGCUCGGUUUGUUCUCAACUGCAAUAAUCUUAUUAGCAGUUUGUUGUUCGAACCUAAUCAAUUACCAACGUAAUUACAAACUUUGCUAAUCUGCCUAGGUCUCA
................(((..((((((..(..((((((((((....)))).))))))....)..)))))).....((((((....)))))).........)))................. (-20.12 = -19.90 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:14:44 2006