Locus 1933

Sequence ID	2L_DroMel_CAF1
Location	5,237,415 – 5,237,562
Length	147
Max. P	0.884756

overview

Window 3

Location	5,237,415 – 5,237,522
Length	107
Sequences	4
Columns	114
Reading direction	forward
Mean pairwise identity	81.86
Mean single sequence MFE	-31.05
Consensus MFE	-22.17
Energy contribution	-22.48
Covariance contribution	0.31
Combinations/Pair	1.05
Mean z-score	-1.62
Structure conservation index	0.71
SVM decision value	0.17
SVM RNA-class probability	0.617476
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5237415 107 + 22407834
CUGCUCUCGCAAAGAGAG----AGAGAGUAGACGGGAAAAACAUGAGAGCGUGGCGGAAAACGCGAGAAAAUG---CUGGCAGGCGUUUAAAAUCGCGCAACUCACACACUUGC
((((((((.(.......)----.))))))))............((((.((((((((.....)))....(((((---((....))))))).....)))))..))))......... ( -32.40)
>DroSim_CAF1 15578 111 + 1
CUGCUCUCGCAAAGAGAGAGAGAGAGAGUAGUAAGGAAAAACAUGAGAGCGUGGCGGAAAACGCGAGAAAACG---CUAGCAGGCGUUUAAAAUCGCGCAACUCACACACUUGC
((((((((...............))))))))............((((.((((((((.....)))....(((((---((....))))))).....)))))..))))......... ( -32.96)
>DroEre_CAF1 7347 97 + 1
CUGCUCUCGCAG-----------------AGAAAGGAAAAACAUGAGAGCGUGGCGGAAAACGCGAGAGUGCGCUGCUGGCAGGCGUUUAAAAUCGCGCCACUCACACAGUUGC
..(((((((...-----------------..............)))))))((((((.....)))..((((..((.....)).(((((........))))))))).)))...... ( -30.43)
>DroYak_CAF1 16696 108 + 1
CCGCUCUCACGAAGAGA------GAGAGUAGAAAGGAAAAACAUGAGAGCGUGGCGGAAAACGCGAGAGUGAGCUGAUAGCGGGCGUUUAAAAUCGCGCAACUCACACAUUUGC
..((((((((.....).------...........(......).)))))))((((((.....)))..((((..((.....))(.(((........))).).)))).)))...... ( -28.40)
>consensus
CUGCUCUCGCAAAGAGA______GAGAGUAGAAAGGAAAAACAUGAGAGCGUGGCGGAAAACGCGAGAAAACG___CUAGCAGGCGUUUAAAAUCGCGCAACUCACACACUUGC
..(((((((..................................)))))))((((((.....)))(((.....((.....))..((((........))))..))).)))...... (-22.17 = -22.48 +   0.31)

alignment

secondary structure

dotplot

Window 4

Location	5,237,445 – 5,237,562
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.52
Mean single sequence MFE	-36.43
Consensus MFE	-26.64
Energy contribution	-26.68
Covariance contribution	0.04
Combinations/Pair	1.07
Mean z-score	-1.91
Structure conservation index	0.73
SVM decision value	0.16
SVM RNA-class probability	0.612803
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5237445 117 + 22407834
GGAAAAACAUGAGAGCGUGGCGGAAAACGCGAGAAAAUG---CUGGCAGGCGUUUAAAAUCGCGCAACUCACACACUUGCUGGCGUUUAAAAACGCGCGUGAGGUAAAAAUACUCUCUCU
..........((((((((((((.....)))....(((((---(..(((((.((...................)).)))))..)))))).....)))))..(((.........))))))). ( -35.11)
>DroSec_CAF1 14725 117 + 1
GGAAAAACAUGAGAGCGUGGCGGAAAACGCGAGAAAACG---CUAGCAGGCGUUUAAAAUCGCGCAACUCACACACUUGCUGGCGUUUAAAAACGCGCGUGAGGUAGAGAUACUCUCUCU
..........((((((((((((.....)))....(((((---((((((((.((...................)).))))))))))))).....)))))..(((.........))))))). ( -37.91)
>DroSim_CAF1 15612 117 + 1
GGAAAAACAUGAGAGCGUGGCGGAAAACGCGAGAAAACG---CUAGCAGGCGUUUAAAAUCGCGCAACUCACACACUUGCUGGCGUUUAAAAACGCGCGUGAGGUAGAGAUACUCUCUCU
..........((((((((((((.....)))....(((((---((((((((.((...................)).))))))))))))).....)))))..(((.........))))))). ( -37.91)
>DroEre_CAF1 7364 120 + 1
GGAAAAACAUGAGAGCGUGGCGGAAAACGCGAGAGUGCGCUGCUGGCAGGCGUUUAAAAUCGCGCCACUCACACAGUUGCUAGCGUUUAAAAACGCGCGUAAGGUAAAGAUACUCUGUCU
......(((.(((.((((........))))......((((.((((((((((((........)))))(((.....))))))))))(((....)))))))..............)))))).. ( -35.70)
>DroYak_CAF1 16724 120 + 1
GGAAAAACAUGAGAGCGUGGCGGAAAACGCGAGAGUGAGCUGAUAGCGGGCGUUUAAAAUCGCGCAACUCACACAUUUGCUAGCGUUUAAAAACGCGCGUAAGGUAAAUUUACUCUCUCU
.......((((....))))(((.....)))(((((((((...((.(((.((((((.....(((((((.........))))..))).....)))))).)))...))...)))))))))... ( -35.50)
>consensus
GGAAAAACAUGAGAGCGUGGCGGAAAACGCGAGAAAACG___CUAGCAGGCGUUUAAAAUCGCGCAACUCACACACUUGCUGGCGUUUAAAAACGCGCGUGAGGUAAAGAUACUCUCUCU
..........(((((.((((((.....)))(((.....(.......)..((((........))))..))).))).(((((..(((((....)))))..))))).........)))))... (-26.64 = -26.68 +   0.04)

alignment

secondary structure

dotplot

Window 5

Location	5,237,445 – 5,237,562
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.52
Mean single sequence MFE	-34.74
Consensus MFE	-27.41
Energy contribution	-27.37
Covariance contribution	-0.04
Combinations/Pair	1.03
Mean z-score	-1.91
Structure conservation index	0.79
SVM decision value	0.93
SVM RNA-class probability	0.884756
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5237445 117 - 22407834
AGAGAGAGUAUUUUUACCUCACGCGCGUUUUUAAACGCCAGCAAGUGUGUGAGUUGCGCGAUUUUAAACGCCUGCCAG---CAUUUUCUCGCGUUUUCCGCCACGCUCUCAUGUUUUUCC
...((((((.............(((((((....)))))..))..(((.(((.(..((((((....(((.((......)---).)))..))))))..).)))))))))))).......... ( -32.30)
>DroSec_CAF1 14725 117 - 1
AGAGAGAGUAUCUCUACCUCACGCGCGUUUUUAAACGCCAGCAAGUGUGUGAGUUGCGCGAUUUUAAACGCCUGCUAG---CGUUUUCUCGCGUUUUCCGCCACGCUCUCAUGUUUUUCC
...((((((.............(((((((....)))))..))..(((.(((.(..((((((....((((((......)---)))))..))))))..).)))))))))))).......... ( -38.00)
>DroSim_CAF1 15612 117 - 1
AGAGAGAGUAUCUCUACCUCACGCGCGUUUUUAAACGCCAGCAAGUGUGUGAGUUGCGCGAUUUUAAACGCCUGCUAG---CGUUUUCUCGCGUUUUCCGCCACGCUCUCAUGUUUUUCC
...((((((.............(((((((....)))))..))..(((.(((.(..((((((....((((((......)---)))))..))))))..).)))))))))))).......... ( -38.00)
>DroEre_CAF1 7364 120 - 1
AGACAGAGUAUCUUUACCUUACGCGCGUUUUUAAACGCUAGCAACUGUGUGAGUGGCGCGAUUUUAAACGCCUGCCAGCAGCGCACUCUCGCGUUUUCCGCCACGCUCUCAUGUUUUUCC
((((((((..............(((((((....)))))..))....(((((.(((((((((.......(((.((....))))).....)))))....))))))))).))).))))).... ( -32.60)
>DroYak_CAF1 16724 120 - 1
AGAGAGAGUAAAUUUACCUUACGCGCGUUUUUAAACGCUAGCAAAUGUGUGAGUUGCGCGAUUUUAAACGCCCGCUAUCAGCUCACUCUCGCGUUUUCCGCCACGCUCUCAUGUUUUUCC
...((((((...........(((((((((....)))))........(.((((((((.(((............)))...)))))))).)..))))..........)))))).......... ( -32.80)
>consensus
AGAGAGAGUAUCUUUACCUCACGCGCGUUUUUAAACGCCAGCAAGUGUGUGAGUUGCGCGAUUUUAAACGCCUGCUAG___CGUUUUCUCGCGUUUUCCGCCACGCUCUCAUGUUUUUCC
...((((((........((((((((((((....)))))........)))))))..(((.((....((((((...................)))))))))))...)))))).......... (-27.41 = -27.37 +  -0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:15:16 2006