Locus 5531

Sequence ID	2L_DroMel_CAF1
Location	15,793,651 – 15,793,792
Length	141
Max. P	0.937242

overview

Window 4

Location	15,793,651 – 15,793,767
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	76.68
Mean single sequence MFE	-27.44
Consensus MFE	-14.06
Energy contribution	-14.14
Covariance contribution	0.08
Combinations/Pair	1.31
Mean z-score	-2.07
Structure conservation index	0.51
SVM decision value	0.95
SVM RNA-class probability	0.887479
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15793651 116 + 22407834
AUGUUUUCGACUUUUGGUGUCGGAAAUUUAUGUUCCACAAAUAUGUGGCUUUAUUUUUUGGCCACAC-CUUUCUCGGCUUUUUACCUUGUUCCGUAUUACUGUGUG---UAUGGAUAGGA
..(((((((((.......)))))))))................(((((((.........)))))))(-(......)).......(((...(((((((........)---)))))).))). ( -29.70)
>DroSec_CAF1 17475 102 + 1
AUGUUUUCGACUUUUGGCGUCGCAAAUUUAUGUUCCACAAAUAUGUGGCUUUAUUUUUUGGCCACAC-CUUUCACGGCUUUUUACU--------------UGUGUG---UAUGGCUGGGA
..((((.((((.......)))).))))......(((.......(((((((.........))))))).-......(((((...(((.--------------...)))---...)))))))) ( -25.20)
>DroAna_CAF1 16367 113 + 1
AUGUUUUUGACUUUUGGUGUUGAAAAUUUAUGGGCGGCAAAUAUGUGGCUUUGCUUUUUUGCAAUGCUCGCUCUCCGUUUA-------UUUUCAGCUAACUGUGUGACAUAUGGUUAUGA
..................(((((((((..(((((.(((........(((.((((......)))).))).))).)))))..)-------))))))))(((((((((...)))))))))... ( -28.20)
>DroSim_CAF1 8666 101 + 1
AUGUUUUCGACUUUUGGCGUCGGAAAUUUAUGUUCCACAAAUAUGUGGCUUUAUUUUUUGGCCACAC-CUUUCUCGGCUUUUUACU--------------UGUGUG---UAUGGCUGGG-
..(((((((((.......)))))))))................(((((((.........))))))).-....(((((((...(((.--------------...)))---...)))))))- ( -28.50)
>DroEre_CAF1 17994 116 + 1
AUGUUUUCGACUUUUGGCGUCGCAAAUUUAUGGUCCCCAAGUAUGUGGCUUUAUUUUUUGGCCACAC-CUUUCUCGGCCUUGUAUCUCUUUCUAUAUAACUGUAUG---UAUGGUUAGGA
..((((.((((.......)))).))))....((((...(((..(((((((.........))))))).-.)))...)))).......(((..(((((((......))---)))))..))). ( -25.60)
>consensus
AUGUUUUCGACUUUUGGCGUCGCAAAUUUAUGUUCCACAAAUAUGUGGCUUUAUUUUUUGGCCACAC_CUUUCUCGGCUUUUUACC___UU_____U_ACUGUGUG___UAUGGCUAGGA
..(((((((((.......)))))))))................(((((((.........)))))))...................................................... (-14.06 = -14.14 +   0.08)

alignment

secondary structure

dotplot

Window 5

Location	15,793,651 – 15,793,767
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	76.68
Mean single sequence MFE	-21.00
Consensus MFE	-12.70
Energy contribution	-13.34
Covariance contribution	0.64
Combinations/Pair	1.24
Mean z-score	-2.05
Structure conservation index	0.60
SVM decision value	1.26
SVM RNA-class probability	0.937242
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15793651 116 - 22407834
UCCUAUCCAUA---CACACAGUAAUACGGAACAAGGUAAAAAGCCGAGAAAG-GUGUGGCCAAAAAAUAAAGCCACAUAUUUGUGGAACAUAAAUUUCCGACACCAAAAGUCGAAAACAU
.....((((((---....................(((.....))).......-(((((((...........)))))))...))))))...........((((.......))))....... ( -22.50)
>DroSec_CAF1 17475 102 - 1
UCCCAGCCAUA---CACACA--------------AGUAAAAAGCCGUGAAAG-GUGUGGCCAAAAAAUAAAGCCACAUAUUUGUGGAACAUAAAUUUGCGACGCCAAAAGUCGAAAACAU
.....((((((---(.(((.--------------.((.....)).)))....-)))))))((((........(((((....)))))........))))((((.......))))....... ( -23.39)
>DroAna_CAF1 16367 113 - 1
UCAUAACCAUAUGUCACACAGUUAGCUGAAAA-------UAAACGGAGAGCGAGCAUUGCAAAAAAGCAAAGCCACAUAUUUGCCGCCCAUAAAUUUUCAACACCAAAAGUCAAAAACAU
........................(.((((((-------(....((.(.((((((.((((......)))).)).......))))).)).....))))))).).................. ( -14.21)
>DroSim_CAF1 8666 101 - 1
-CCCAGCCAUA---CACACA--------------AGUAAAAAGCCGAGAAAG-GUGUGGCCAAAAAAUAAAGCCACAUAUUUGUGGAACAUAAAUUUCCGACGCCAAAAGUCGAAAACAU
-..........---..((((--------------((((....(((......)-))(((((...........))))).)))))))).............((((.......))))....... ( -23.30)
>DroEre_CAF1 17994 116 - 1
UCCUAACCAUA---CAUACAGUUAUAUAGAAAGAGAUACAAGGCCGAGAAAG-GUGUGGCCAAAAAAUAAAGCCACAUACUUGGGGACCAUAAAUUUGCGACGCCAAAAGUCGAAAACAU
(((((((....---......))))...................(((((....-(((((((...........))))))).))))))))...........((((.......))))....... ( -21.60)
>consensus
UCCUAACCAUA___CACACAGU_A_____AA___AGUAAAAAGCCGAGAAAG_GUGUGGCCAAAAAAUAAAGCCACAUAUUUGUGGAACAUAAAUUUCCGACGCCAAAAGUCGAAAACAU
...........................................(((...(((.(((((((...........))))))).))).)))............((((.......))))....... (-12.70 = -13.34 +   0.64)

alignment

secondary structure

dotplot

Window 6

Location	15,793,691 – 15,793,792
Length	101
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	67.97
Mean single sequence MFE	-22.88
Consensus MFE	-7.52
Energy contribution	-7.60
Covariance contribution	0.08
Combinations/Pair	1.29
Mean z-score	-1.86
Structure conservation index	0.33
SVM decision value	0.23
SVM RNA-class probability	0.642630
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15793691 101 + 22407834
AUAUGUGGCUUUAUUUUUUGGCCACAC-CUUUCUCGGCUUUUUACCUUGUUCCGUAUUACUGUGUG---UAUGGAUAGGAUAUGAAAUU---GU--------AAGA---UUACCA-UAUA
...(((((((.........)))))))(-(......)).......(((...(((((((........)---)))))).)))(((((.((((---..--------..))---))..))-))). ( -22.50)
>DroSec_CAF1 17515 87 + 1
AUAUGUGGCUUUAUUUUUUGGCCACAC-CUUUCACGGCUUUUUACU--------------UGUGUG---UAUGGCUGGGAUAUGAAAUG---GU--------AAGA---UUACCA-UAUA
...(((((((.........))))))).-..(((.(((((...(((.--------------...)))---...))))))))......(((---((--------(...---.)))))-)... ( -24.30)
>DroAna_CAF1 16407 113 + 1
AUAUGUGGCUUUGCUUUUUUGCAAUGCUCGCUCUCCGUUUA-------UUUUCAGCUAACUGUGUGACAUAUGGUUAUGAUGAUAAGUUUUCGAAGGCUCUAAGGAAUUUUACCUUUAUG
....(((((.((((......)))).)).)))..(((..(((-------((.(((..(((((((((...)))))))))))).)))))((((....)))).....))).............. ( -20.90)
>DroSim_CAF1 8706 86 + 1
AUAUGUGGCUUUAUUUUUUGGCCACAC-CUUUCUCGGCUUUUUACU--------------UGUGUG---UAUGGCUGGG-UAUGAAAUU---GU--------AAGA---UUACCA-UAUA
...(((((((.........))))))).-....(((((((...(((.--------------...)))---...)))))))-((((.((((---..--------..))---))..))-)).. ( -21.10)
>DroEre_CAF1 18034 104 + 1
GUAUGUGGCUUUAUUUUUUGGCCACAC-CUUUCUCGGCCUUGUAUCUCUUUCUAUAUAACUGUAUG---UAUGGUUAGGAUAAGAAUUU---GA--------AAAAAAUGUACCA-UAUA
.(((((((...((((((((((((....-.......))))...((((.((..(((((((......))---)))))..)))))).......---..--------))))))))..)))-)))) ( -25.60)
>consensus
AUAUGUGGCUUUAUUUUUUGGCCACAC_CUUUCUCGGCUUUUUACC___UU_____U_ACUGUGUG___UAUGGCUAGGAUAUGAAAUU___GU________AAGA___UUACCA_UAUA
...(((((((.........))))))).............................................................................................. ( -7.52 =  -7.60 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:46:27 2006