Locus 5558

Sequence ID	2R_DroMel_CAF1
Location	17,749,726 – 17,749,817
Length	91
Max. P	0.996341

overview

Window 9

Location	17,749,726 – 17,749,817
Length	91
Sequences	6
Columns	103
Reading direction	forward
Mean pairwise identity	74.71
Mean single sequence MFE	-32.72
Consensus MFE	-16.28
Energy contribution	-16.70
Covariance contribution	0.42
Combinations/Pair	1.19
Mean z-score	-2.93
Structure conservation index	0.50
SVM decision value	2.68
SVM RNA-class probability	0.996341
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17749726 91 + 20766785
UGCUCAUCUCU-CU-UUGCUCUAAUUUUUUCGAUGGGUUAUCUCGCUCUGGCACGAGUCCAUUGGAGUGACAGAGAGGGAGAGAGAGAGCGCU----------
.((((.(((((-((-((.((((.....((((((((((....((((........))))))))))))))......)))))))))))))))))...---------- ( -37.20)
>DroVir_CAF1 25374 97 + 1
UGCUCAUCUUUGCUUUUGCUCAAAAUUUUU--AUGGGUUAUCUCGCUCUGGCACGUUCGUGCAAGAGCAA----AAGGGAAAGAGCGAGAGCUGCCCGACAAU
...........((((((((((.........--..(((....)))(((((.((((....)))).)))))..----........))))))))))........... ( -32.70)
>DroGri_CAF1 24768 94 + 1
UGCUCAUCUUUGCU-UUGCUCAACAUUUUU--AUGGGUUAUCUCGCUCUGGCACGCAAGUGCAAGAGCGA----AAGGGAGAGAGCGAGCACUGCCCGA--AU
(((((.(((((.((-(((((((........--.)))))....(((((((.((((....)))).)))))))----)))).)))))..)))))........--.. ( -38.80)
>DroSec_CAF1 17555 87 + 1
UGCUCAUCUCU-CU-UUGCUCUAAUUUUUU----GGGUUAUCUCGCUCUGGCACGAUUCCAUUGGAGUGACAGAGAGGGAGAGAAAGAGCGUU----------
.((((.(((((-((-((.((((.(((((.(----(((..(((..((....))..)))))))..)))))...)))))))))))))..))))...---------- ( -28.80)
>DroEre_CAF1 18505 91 + 1
UGCUCAUCUCU-CU-UUGCUCUAAUUUUUUCGAUGGGUUAUCUCGCUCUGGCACGAUUCCAUAGCAGUGACAGAGAGGGAGAGAGCGAGCGCU----------
.((((.(((((-((-((.((((............(((....)))(((.(((.......))).)))......)))))))))))))..))))...---------- ( -30.90)
>DroAna_CAF1 17713 87 + 1
UGCUCAUCUCU-CU-GUGCUCUAAUUUUUUCCAUGGGUUAUCUCGCUCUGGCACAACACCAUAAGAGCGAGAGAGAGGGAAAUGGC----GUU----------
.(((..(((((-((-..((((.............))))..(((((((((((.......))...))))))))).)))))))...)))----...---------- ( -27.92)
>consensus
UGCUCAUCUCU_CU_UUGCUCUAAUUUUUU__AUGGGUUAUCUCGCUCUGGCACGAUUCCAUAAGAGCGACAGAGAGGGAGAGAGCGAGCGCU__________
(((((.(((((....((((((.............(((....)))((....))............)))))).....)))))..)))))................ (-16.28 = -16.70 +   0.42)

alignment

secondary structure

dotplot

Window 0

Location	17,749,726 – 17,749,817
Length	91
Sequences	6
Columns	103
Reading direction	reverse
Mean pairwise identity	74.71
Mean single sequence MFE	-28.11
Consensus MFE	-6.53
Energy contribution	-6.03
Covariance contribution	-0.50
Combinations/Pair	1.36
Mean z-score	-2.68
Structure conservation index	0.23
SVM decision value	0.40
SVM RNA-class probability	0.721768
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17749726 91 - 20766785
----------AGCGCUCUCUCUCUCCCUCUCUGUCACUCCAAUGGACUCGUGCCAGAGCGAGAUAACCCAUCGAAAAAAUUAGAGCAA-AG-AGAGAUGAGCA
----------...(((((((((((....(((((........((((.(((((......))))).....)))).........)))))...-))-))))).)))). ( -28.93)
>DroVir_CAF1 25374 97 - 1
AUUGUCGGGCAGCUCUCGCUCUUUCCCUU----UUGCUCUUGCACGAACGUGCCAGAGCGAGAUAACCCAU--AAAAAUUUUGAGCAAAAGCAAAGAUGAGCA
.(..(((((.(((....))).......((----(((((((.((((....)))).)))))))))...)))..--...........((....))...))..)... ( -27.90)
>DroGri_CAF1 24768 94 - 1
AU--UCGGGCAGUGCUCGCUCUCUCCCUU----UCGCUCUUGCACUUGCGUGCCAGAGCGAGAUAACCCAU--AAAAAUGUUGAGCAA-AGCAAAGAUGAGCA
..--..((((...))))(((((((...((----(((((((.((((....)))).)))))))))........--.....((((......-)))).))).)))). ( -32.40)
>DroSec_CAF1 17555 87 - 1
----------AACGCUCUUUCUCUCCCUCUCUGUCACUCCAAUGGAAUCGUGCCAGAGCGAGAUAACCC----AAAAAAUUAGAGCAA-AG-AGAGAUGAGCA
----------...((((..((((((.(.(((((.((((((...)))...))).))))).).(......)----...............-.)-))))).)))). ( -24.00)
>DroEre_CAF1 18505 91 - 1
----------AGCGCUCGCUCUCUCCCUCUCUGUCACUGCUAUGGAAUCGUGCCAGAGCGAGAUAACCCAUCGAAAAAAUUAGAGCAA-AG-AGAGAUGAGCA
----------...(((((((((((....(((((......(.((((.(((.(((....))).)))...)))).).......)))))...-))-)))).))))). ( -27.72)
>DroAna_CAF1 17713 87 - 1
----------AAC----GCCAUUUCCCUCUCUCUCGCUCUUAUGGUGUUGUGCCAGAGCGAGAUAACCCAUGGAAAAAAUUAGAGCAC-AG-AGAGAUGAGCA
----------...----((((((((.((((((((((((((...(((.....))))))))))))...((...)).........)))...-))-.)))))).)). ( -27.70)
>consensus
__________AGCGCUCGCUCUCUCCCUCUCUGUCACUCCUAUGGAAUCGUGCCAGAGCGAGAUAACCCAU__AAAAAAUUAGAGCAA_AG_AGAGAUGAGCA
.....................((((.((((....(((............)))..)))).))))........................................ ( -6.53 =  -6.03 +  -0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:48:38 2006