Locus 3746

Sequence ID	2L_DroMel_CAF1
Location	10,893,225 – 10,893,349
Length	124
Max. P	0.773429

overview

Window 7

Location	10,893,225 – 10,893,328
Length	103
Sequences	6
Columns	104
Reading direction	forward
Mean pairwise identity	89.32
Mean single sequence MFE	-23.18
Consensus MFE	-20.62
Energy contribution	-20.54
Covariance contribution	-0.08
Combinations/Pair	1.14
Mean z-score	-1.55
Structure conservation index	0.89
SVM decision value	0.54
SVM RNA-class probability	0.773429
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10893225 103 + 22407834
-UCCCCAUUGGCCCCCCAAAAAAAAGUGGUAGCAACCGUUAUUCCAGCUUUUGCUUUACCUCAACUUAAUGGCAGCUGCUGUCGUGCUUGAUUACCCAAGUGCC
-......((((....))))......(..(((((..((((((....(((....)))...........))))))..)))))..).(..((((......))))..). ( -23.66)
>DroSec_CAF1 32812 98 + 1
-CCCCCAUUGGCCC-----CCAAAAAUGGUAGCAACCGUUAUUCCAGCUUUUGCUUUACCUCAACUUAAUGGCAGCUGCUGUCGUGCUUGAUUACCCAAGUGCC
-......((((...-----))))..((((((((..((((((....(((....)))...........))))))..)))))))).(..((((......))))..). ( -22.96)
>DroSim_CAF1 33678 103 + 1
-CCCCCAUUGGCCCUCCCCCAAAAAAUGGUAGCAACCGUUAUUCCAGCUUUUGCUUUACCUCAACUUAAUGGCAGCUGCUGUCGUGCUUGAUUACCCAAGUGCC
-......((((.......))))...((((((((..((((((....(((....)))...........))))))..)))))))).(..((((......))))..). ( -23.46)
>DroEre_CAF1 33014 97 + 1
---CCCACUGGCCCC----CAAAAAAUGGUAGCAACCGUUAUUCCAGCUUUUGCUUUACCUCAACUUAAUGGCAGCUGCUGUCGUGCUUGAUUACCCAAGUGCC
---.......((..(----((.....)))..))...........((((..(((((...............)))))..))))..(..((((......))))..). ( -22.06)
>DroYak_CAF1 33765 100 + 1
GCCCCCAUUGGCCCC----CAAAAAAUGGUAGCAACCGUUAUUCCAGCUUUUGCUUUACCUCAACUUAAUGGCAGCUGCUGUCGUGCUUGAUUACCCAAGUGCC
(((......)))...----......((((((((..((((((....(((....)))...........))))))..)))))))).(..((((......))))..). ( -24.66)
>DroAna_CAF1 36190 99 + 1
-AAAAAACAAGAACA----AAAAAAAUGGCUCCUACCGUUAUUGCAGCUUUUGCUUUACCUCAACUUAAUGGCAGCUGCUGUCGUGCUUGAUUACCCAAGUACC
-..............----.....(((((......)))))...(((((..(((((...............)))))..))))).(((((((......))))))). ( -22.26)
>consensus
_CCCCCAUUGGCCCC____CAAAAAAUGGUAGCAACCGUUAUUCCAGCUUUUGCUUUACCUCAACUUAAUGGCAGCUGCUGUCGUGCUUGAUUACCCAAGUGCC
.........................(..(((((..((((((....(((....)))...........))))))..)))))..).(((((((......))))))). (-20.62 = -20.54 +  -0.08)

alignment

secondary structure

dotplot

Window 8

Location	10,893,256 – 10,893,349
Length	93
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.99
Mean single sequence MFE	-19.37
Consensus MFE	-14.44
Energy contribution	-14.58
Covariance contribution	0.14
Combinations/Pair	1.11
Mean z-score	-1.38
Structure conservation index	0.75
SVM decision value	0.43
SVM RNA-class probability	0.734107
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10893256 93 + 22407834
-------CAACCGUUAUUCCAGCUUUUGCUUUACCUCAACUUAAUGGCAGCUGCUGUCGUGCUUGAUUACC-CAAGUGCCACGCCUCUU------------CCGCC----CAUCCA---C
-------....(((.....((((..(((((...............)))))..))))..(..((((......-))))..).)))......------------.....----......---. ( -17.46)
>DroSim_CAF1 33709 93 + 1
-------CAACCGUUAUUCCAGCUUUUGCUUUACCUCAACUUAAUGGCAGCUGCUGUCGUGCUUGAUUACC-CAAGUGCCACGCCUCUU------------CCGCC----CAUCCA---C
-------....(((.....((((..(((((...............)))))..))))..(..((((......-))))..).)))......------------.....----......---. ( -17.46)
>DroEre_CAF1 33039 97 + 1
-------CAACCGUUAUUCCAGCUUUUGCUUUACCUCAACUUAAUGGCAGCUGCUGUCGUGCUUGAUUACC-CAAGUGCCACGCCCCAU------------CCGCCGCCCCUUCCG---C
-------....(((.....((((..(((((...............)))))..))))..(..((((......-))))..).)))......------------...............---. ( -17.46)
>DroWil_CAF1 46764 104 + 1
UUACGUUACUCCGUUACUCCAUCCAAGGCUUUAACUCAACUUAAUGGCAGCUGCUGUCGUGCUUGAUUACCCCGAGUACCACGCCUUCUUUC---------CUGUC----CUUUCC---U
........................(((((................(((((...)))))(((((((.......)))))))...))))).....---------.....----......---. ( -17.90)
>DroYak_CAF1 33793 95 + 1
-------CAACCGUUAUUCCAGCUUUUGCUUUACCUCAACUUAAUGGCAGCUGCUGUCGUGCUUGAUUACC-CAAGUGCCACGCCCCUU------------CCGCAGCCCCAUCC-----
-------.............(((....))).............((((..((((((((.(..((((......-))))..).)))......------------..))))).))))..----- ( -20.40)
>DroAna_CAF1 36217 110 + 1
-------CUACCGUUAUUGCAGCUUUUGCUUUACCUCAACUUAAUGGCAGCUGCUGUCGUGCUUGAUUACC-CAAGUACCACGCCUCCUUUUAGGUGCCUCCCGCCUU--CGUCCUCGCC
-------...........((((((...(((...............))))))))).((.(((((((......-))))))).))((........(((((.....))))).--.......)). ( -25.55)
>consensus
_______CAACCGUUAUUCCAGCUUUUGCUUUACCUCAACUUAAUGGCAGCUGCUGUCGUGCUUGAUUACC_CAAGUGCCACGCCUCUU____________CCGCC____CAUCCA___C
...........(((.....((((..(((((...............)))))..))))..(((((((.......))))))).)))..................................... (-14.44 = -14.58 +   0.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:00:00 2006