Locus 5642

Sequence ID	X_DroMel_CAF1
Location	14,574,946 – 14,575,096
Length	150
Max. P	0.998682

overview

Window 3

Location	14,574,946 – 14,575,056
Length	110
Sequences	4
Columns	113
Reading direction	forward
Mean pairwise identity	80.86
Mean single sequence MFE	-19.62
Consensus MFE	-12.88
Energy contribution	-13.00
Covariance contribution	0.12
Combinations/Pair	1.12
Mean z-score	-1.66
Structure conservation index	0.66
SVM decision value	0.07
SVM RNA-class probability	0.568096
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14574946 110 + 22224390
AUAGCGCUAACUAAAGCCGCUUGCUGCCCAA-AAACCACAAAAAUAAUACAAAAAAAAAGCCAGUGAGUU-C-GCCAUAAGGCGUUCACACUGAGGCAAAUCAAAUCUAGAUU
...............(((((((.........-.........................))))(((((.(..-(-(((....))))..).))))).)))................ ( -21.98)
>DroSec_CAF1 50433 100 + 1
AUGG------CUUAAGCCGCUUGCUGUCCAAAAAACCACAAAAAUA-----AAAUAAAAGCCAGUGAGUU-C-GCCAUAAGGCGUUCACACUGAGGCAAAUCAAAUCUAGAUU
..((------(....)))(((((((.....................-----.......)))(((((.(..-(-(((....))))..).)))))))))................ ( -23.69)
>DroSim_CAF1 50449 106 + 1
AUAGCGCUAACUUAAGCCGCUUGCUGUCCAAAAAACCACAAAAAUA-----AAAUAAAAGCCAGUGAGUU-G-GCCAUAAGGCGUUCACACUGAGGCAAAUCAAAUCUAGAUU
...............(((((((........................-----......))))(((((.(..-.-(((....)))...).))))).)))................ ( -17.91)
>DroEre_CAF1 44628 94 + 1
--------------AGCCGCUUGCUGUCCAAAAAAA-AGAUAAAUA----AAAAUAAAAGCCAAUGAGUGGCCCCUAAAAGGCAGCCACACUGAGGUAAAUCAAAUCUAGAUU
--------------.(((((((..............-.........----.......))))......(((((.((.....))..))))).....)))................ ( -14.91)
>consensus
AUAG______CUUAAGCCGCUUGCUGUCCAAAAAACCACAAAAAUA_____AAAUAAAAGCCAGUGAGUU_C_GCCAUAAGGCGUUCACACUGAGGCAAAUCAAAUCUAGAUU
...............(((((((...................................))))(((((.(.....(((....)))...).))))).)))................ (-12.88 = -13.00 +   0.12)

alignment

secondary structure

dotplot

Window 4

Location	14,574,985 – 14,575,096
Length	111
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	80.99
Mean single sequence MFE	-22.64
Consensus MFE	-9.72
Energy contribution	-10.12
Covariance contribution	0.40
Combinations/Pair	1.09
Mean z-score	-3.33
Structure conservation index	0.43
SVM decision value	2.11
SVM RNA-class probability	0.988269
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14574985 111 + 22224390
AAAAUAAUACAAAAAAAAAGCCAGUGAGUU-C-GCCAUAAGGCGUUCACACUGAGGCAAAUCAAAUCUAGAUUCCAGAUUCCAGAAUCCAGAUUCCAGAAAUAACCAUUUGCC
.....................(((((.(..-(-(((....))))..).))))).(((((((....(((.((.((..((((....))))..)).)).))).......))))))) ( -27.30)
>DroSec_CAF1 50467 99 + 1
AAAAUA-----AAAUAAAAGCCAGUGAGUU-C-GCCAUAAGGCGUUCACACUGAGGCAAAUCAAAUCUAGAUUCUAGAUUCCAGAAUCC-------AGAAAUAACCAUUUGCC
......-----..........(((((.(..-(-(((....))))..).))))).(((((((....(((.((((((.......)))))).-------))).......))))))) ( -28.10)
>DroSim_CAF1 50489 99 + 1
AAAAUA-----AAAUAAAAGCCAGUGAGUU-G-GCCAUAAGGCGUUCACACUGAGGCAAAUCAAAUCUAGAUUCUAGAUUCCAGAAUCC-------AGAAAUAACCAUUUGCC
......-----..........(((((.(..-.-(((....)))...).))))).(((((((....(((.((((((.......)))))).-------))).......))))))) ( -23.90)
>DroEre_CAF1 44653 95 + 1
UAAAUA----AAAAUAAAAGCCAAUGAGUGGCCCCUAAAAGGCAGCCACACUGAGGUAAAUCAAAUCUAGAUUCCAGAUUC-------C-------AGAAAUAACCAUUUGCC
......----.........((.((((.(((((.((.....))..))))).(((..((.((((.......))))....))..-------)-------)).......)))).)). ( -18.90)
>DroYak_CAF1 46886 88 + 1
----------UAAAUAAAAGCCAAUGAGUU-CCCCCAAAAGGCAGCCACACUGGGGUAAAUCAAAUCUAGAUUCCAGAUUC-------C-------AGAAAUAACCAUUUGCC
----------.........((.((((.(((-.((......)).)))....(((((((.((((.......))))....))))-------)-------)).......)))).)). ( -15.00)
>consensus
AAAAUA_____AAAUAAAAGCCAGUGAGUU_C_GCCAUAAGGCGUUCACACUGAGGCAAAUCAAAUCUAGAUUCCAGAUUCCAGAAUCC_______AGAAAUAACCAUUUGCC
.....................(((((.(.....(((....)))...).))))).(((((((..(((((.......))))).................(.......)))))))) ( -9.72 = -10.12 +   0.40)

alignment

secondary structure

dotplot

Window 5

Location	14,574,985 – 14,575,096
Length	111
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	80.99
Mean single sequence MFE	-31.92
Consensus MFE	-17.64
Energy contribution	-18.00
Covariance contribution	0.36
Combinations/Pair	1.11
Mean z-score	-4.10
Structure conservation index	0.55
SVM decision value	3.19
SVM RNA-class probability	0.998682
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14574985 111 - 22224390
GGCAAAUGGUUAUUUCUGGAAUCUGGAUUCUGGAAUCUGGAAUCUAGAUUUGAUUUGCCUCAGUGUGAACGCCUUAUGGC-G-AACUCACUGGCUUUUUUUUUGUAUUAUUUU
(((((...((((..((((((.((..((((....))))..)).))))))..)))))))))((((((.(..((((....)))-)-..).)))))).................... ( -39.10)
>DroSec_CAF1 50467 99 - 1
GGCAAAUGGUUAUUUCU-------GGAUUCUGGAAUCUAGAAUCUAGAUUUGAUUUGCCUCAGUGUGAACGCCUUAUGGC-G-AACUCACUGGCUUUUAUUU-----UAUUUU
(((((...((((..(((-------(((((((((...))))))))))))..)))))))))((((((.(..((((....)))-)-..).)))))).........-----...... ( -38.10)
>DroSim_CAF1 50489 99 - 1
GGCAAAUGGUUAUUUCU-------GGAUUCUGGAAUCUAGAAUCUAGAUUUGAUUUGCCUCAGUGUGAACGCCUUAUGGC-C-AACUCACUGGCUUUUAUUU-----UAUUUU
(((((...((((..(((-------(((((((((...))))))))))))..)))))))))((((((.(...(((....)))-.-..).)))))).........-----...... ( -35.20)
>DroEre_CAF1 44653 95 - 1
GGCAAAUGGUUAUUUCU-------G-------GAAUCUGGAAUCUAGAUUUGAUUUACCUCAGUGUGGCUGCCUUUUAGGGGCCACUCAUUGGCUUUUAUUUU----UAUUUA
(((.((((((((..(((-------(-------((........))))))..))))..........((((((.((.....)))))))).)))).)))........----...... ( -24.10)
>DroYak_CAF1 46886 88 - 1
GGCAAAUGGUUAUUUCU-------G-------GAAUCUGGAAUCUAGAUUUGAUUUACCCCAGUGUGGCUGCCUUUUGGGGG-AACUCAUUGGCUUUUAUUUA----------
(((.((((((((..(((-------(-------((........))))))..))))...((((((...((...))..)))))).-....)))).)))........---------- ( -23.10)
>consensus
GGCAAAUGGUUAUUUCU_______GGAUUCUGGAAUCUGGAAUCUAGAUUUGAUUUGCCUCAGUGUGAACGCCUUAUGGC_G_AACUCACUGGCUUUUAUUU_____UAUUUU
(((((((((.....))................((((((((...)))))))).)))))))((((((.(...(((....))).....).)))))).................... (-17.64 = -18.00 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:53:00 2006