Locus 2561

Sequence ID	2R_DroMel_CAF1
Location	9,077,291 – 9,077,405
Length	114
Max. P	0.998241

overview

Window 7

Location	9,077,291 – 9,077,382
Length	91
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	76.65
Mean single sequence MFE	-24.86
Consensus MFE	-18.44
Energy contribution	-18.28
Covariance contribution	-0.16
Combinations/Pair	1.06
Mean z-score	-1.50
Structure conservation index	0.74
SVM decision value	0.74
SVM RNA-class probability	0.837380
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9077291 91 + 20766785
GAUGCA-------CAUCCAUUGCAU--------------CCAGUGCAACGAAGUGCAACGCCAUCAUUUUUUCCCACAGCCGAGGGCUCUGGGUUAU--------AUUUAACAAAUGCAU
..((((-------(.((..((((((--------------...)))))).)).)))))..((............(((.((((...)))).)))((((.--------...))))....)).. ( -24.00)
>DroSec_CAF1 42207 89 + 1
GUU--A-------CAUUCGUUGCAU--------------CCAGUGCAACCAAGUGCAACGCCAUGGAUCUUUCCCACAGCCGAGGGCUCUGGGUUAU--------AUUUAACAAAUGCAU
(((--.-------((((.(((((((--------------...)))))))..)))).)))....(((((.(..((((.((((...)))).))))..).--------))))).......... ( -23.30)
>DroSim_CAF1 44014 80 + 1
G------------------UUGCAU--------------CCAGUGCAACCAAGUGCAACGCCAUGGAUUUUUCCCACAGCCGAGGGCUCUGGGUUAU--------AUUUAACAAAUGCAU
(------------------((((((--------------...)))))))...(((((......(((((....((((.((((...)))).))))....--------))))).....))))) ( -23.40)
>DroEre_CAF1 49575 98 + 1
AAUGCAUCCAAUGCAUCCGAUGCAU--------------CCAGCGCAGCGAAGUGCAACGCCAUCAGUUUUUCCCACAGCCGAGGGCUCUGGGUUAU--------AUUUAACAAAUGCAU
.((((((...))))))...((((((--------------(((((((......))))...(((.((.(((........))).)).)))..)))((((.--------...))))..)))))) ( -24.70)
>DroYak_CAF1 45356 120 + 1
AAUGCAUCCAAUGCAUCCAAUGCAUCCACUGCAUCCCAUCCAGUGCAGCGAAGUGCAACGCCAUCAGUUUUUCCCACAGCCGAGGGCUCUGGGUUAUAUAUGUAUAUUUAUCAAAUGCAU
.((((((...((((((....(((((.(.((((((........)))))).)..)))))...............((((.((((...)))).))))......)))))).........)))))) ( -28.90)
>consensus
GAUGCA_______CAUCCAUUGCAU______________CCAGUGCAACGAAGUGCAACGCCAUCAAUUUUUCCCACAGCCGAGGGCUCUGGGUUAU________AUUUAACAAAUGCAU
....................(((((.................((((......))))................((((.((((...)))).)))).....................))))). (-18.44 = -18.28 +  -0.16)

alignment

secondary structure

dotplot

Window 8

Location	9,077,291 – 9,077,382
Length	91
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	76.65
Mean single sequence MFE	-33.26
Consensus MFE	-21.72
Energy contribution	-21.56
Covariance contribution	-0.16
Combinations/Pair	1.05
Mean z-score	-2.78
Structure conservation index	0.65
SVM decision value	3.04
SVM RNA-class probability	0.998241
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9077291 91 - 20766785
AUGCAUUUGUUAAAU--------AUAACCCAGAGCCCUCGGCUGUGGGAAAAAAUGAUGGCGUUGCACUUCGUUGCACUGG--------------AUGCAAUGGAUG-------UGCAUC
((((..((((.....--------))))((((.((((...)))).))))...........))))((((((((((((((....--------------.))))))))).)-------)))).. ( -32.40)
>DroSec_CAF1 42207 89 - 1
AUGCAUUUGUUAAAU--------AUAACCCAGAGCCCUCGGCUGUGGGAAAGAUCCAUGGCGUUGCACUUGGUUGCACUGG--------------AUGCAACGAAUG-------U--AAC
.((((((((((....--------....((((.((((...)))).))))....(((((..(((...........)))..)))--------------))..))))))))-------)--).. ( -30.80)
>DroSim_CAF1 44014 80 - 1
AUGCAUUUGUUAAAU--------AUAACCCAGAGCCCUCGGCUGUGGGAAAAAUCCAUGGCGUUGCACUUGGUUGCACUGG--------------AUGCAA------------------C
.(((...........--------....((((.((((...)))).))))....(((((..(((...........)))..)))--------------))))).------------------. ( -24.00)
>DroEre_CAF1 49575 98 - 1
AUGCAUUUGUUAAAU--------AUAACCCAGAGCCCUCGGCUGUGGGAAAAACUGAUGGCGUUGCACUUCGCUGCGCUGG--------------AUGCAUCGGAUGCAUUGGAUGCAUU
((((((((.......--------....((((.((((...)))).))))..........(((((.((.....)).))))).(--------------((((((...))))))))))))))). ( -34.90)
>DroYak_CAF1 45356 120 - 1
AUGCAUUUGAUAAAUAUACAUAUAUAACCCAGAGCCCUCGGCUGUGGGAAAAACUGAUGGCGUUGCACUUCGCUGCACUGGAUGGGAUGCAGUGGAUGCAUUGGAUGCAUUGGAUGCAUU
(((((((..((................((((.((((...)))).))))...........((((((((.(((((((((((.....)).)))))))))))))....))))))..))))))). ( -44.20)
>consensus
AUGCAUUUGUUAAAU________AUAACCCAGAGCCCUCGGCUGUGGGAAAAACUGAUGGCGUUGCACUUCGUUGCACUGG______________AUGCAACGGAUG_______UGCAUC
.(((((.....................((((.((((...)))).))))............((.((((......)))).))...............))))).................... (-21.72 = -21.56 +  -0.16)

alignment

secondary structure

dotplot

Window 9

Location	9,077,310 – 9,077,405
Length	95
Sequences	4
Columns	95
Reading direction	forward
Mean pairwise identity	94.39
Mean single sequence MFE	-31.00
Consensus MFE	-27.98
Energy contribution	-28.23
Covariance contribution	0.25
Combinations/Pair	1.12
Mean z-score	-1.65
Structure conservation index	0.90
SVM decision value	0.49
SVM RNA-class probability	0.756202
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9077310 95 + 20766785
CAGUGCAACGAAGUGCAACGCCAUCAUUUUUUCCCACAGCCGAGGGCUCUGGGUUAUAUUUAACAAAUGCAUGAGAGAUUUGGGUGCGCUACGUU
......((((.((((((.(.(((....(((((((((.((((...)))).)))((((....))))........))))))..)))))))))).)))) ( -28.40)
>DroSec_CAF1 42224 95 + 1
CAGUGCAACCAAGUGCAACGCCAUGGAUCUUUCCCACAGCCGAGGGCUCUGGGUUAUAUUUAACAAAUGCAUGAGAGAUUUGGGUGCGCUGCGUU
(((((((.(((.(((......))).(((((((((((.((((...)))).)))((((....))))........))))))))))).))))))).... ( -30.90)
>DroSim_CAF1 44022 95 + 1
CAGUGCAACCAAGUGCAACGCCAUGGAUUUUUCCCACAGCCGAGGGCUCUGGGUUAUAUUUAACAAAUGCAUGAGAGAUUUGGGUGCGCUGCGUU
(((((((.((((((.(....(((((.((((...(((.((((...)))).)))((((....)))))))).)))).).))))))).))))))).... ( -31.60)
>DroEre_CAF1 49601 94 + 1
CAGCGCAGCGAAGUGCAACGCCAUCAGUUUUUCCCACAGCCGAGGGCUCUGGGUUAUAUUUAACAAAUGCAUGAGAGAUUUGGGUGCGCUGCGU-
..((((((((........((((...(((((((((((.((((...)))).)))((((....))))........))))))))..))))))))))))- ( -33.10)
>consensus
CAGUGCAACCAAGUGCAACGCCAUCAAUUUUUCCCACAGCCGAGGGCUCUGGGUUAUAUUUAACAAAUGCAUGAGAGAUUUGGGUGCGCUGCGUU
......((((.((((((.(.(((..(((((((((((.((((...)))).)))((((....))))........)))))))))))))))))).)))) (-27.98 = -28.23 +   0.25)

alignment

secondary structure

dotplot

Window 0

Location	9,077,310 – 9,077,405
Length	95
Sequences	4
Columns	95
Reading direction	reverse
Mean pairwise identity	94.39
Mean single sequence MFE	-28.15
Consensus MFE	-28.09
Energy contribution	-27.90
Covariance contribution	-0.19
Combinations/Pair	1.05
Mean z-score	-1.70
Structure conservation index	1.00
SVM decision value	1.04
SVM RNA-class probability	0.904599
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9077310 95 - 20766785
AACGUAGCGCACCCAAAUCUCUCAUGCAUUUGUUAAAUAUAACCCAGAGCCCUCGGCUGUGGGAAAAAAUGAUGGCGUUGCACUUCGUUGCACUG
...(((((((...((((((......).)))))..........((((.((((...)))).))))...........))))))).............. ( -26.40)
>DroSec_CAF1 42224 95 - 1
AACGCAGCGCACCCAAAUCUCUCAUGCAUUUGUUAAAUAUAACCCAGAGCCCUCGGCUGUGGGAAAGAUCCAUGGCGUUGCACUUGGUUGCACUG
...(((((((...((((((......).)))))..........((((.((((...)))).))))...........))))))).............. ( -28.40)
>DroSim_CAF1 44022 95 - 1
AACGCAGCGCACCCAAAUCUCUCAUGCAUUUGUUAAAUAUAACCCAGAGCCCUCGGCUGUGGGAAAAAUCCAUGGCGUUGCACUUGGUUGCACUG
...(((((((...((((((......).)))))..........((((.((((...)))).))))...........))))))).............. ( -28.40)
>DroEre_CAF1 49601 94 - 1
-ACGCAGCGCACCCAAAUCUCUCAUGCAUUUGUUAAAUAUAACCCAGAGCCCUCGGCUGUGGGAAAAACUGAUGGCGUUGCACUUCGCUGCGCUG
-...((((((...((((((......).)))))..........((((.((((...)))).))))..........((((........)))))))))) ( -29.40)
>consensus
AACGCAGCGCACCCAAAUCUCUCAUGCAUUUGUUAAAUAUAACCCAGAGCCCUCGGCUGUGGGAAAAAUCCAUGGCGUUGCACUUCGUUGCACUG
...(((((((...((((((......).)))))..........((((.((((...)))).))))...........))))))).............. (-28.09 = -27.90 +  -0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:33:09 2006