Locus 3070

Sequence ID	X_DroMel_CAF1
Location	8,203,062 – 8,203,157
Length	95
Max. P	0.961543

overview

Window 1

Location	8,203,062 – 8,203,157
Length	95
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	76.46
Mean single sequence MFE	-29.16
Consensus MFE	-11.88
Energy contribution	-13.92
Covariance contribution	2.04
Combinations/Pair	1.04
Mean z-score	-2.31
Structure conservation index	0.41
SVM decision value	1.53
SVM RNA-class probability	0.961543
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8203062 95 + 22224390
UCGCCU--C-AUCCUUGCGGAGGCCAUUCAGCAUUUCAGCUUCGAUUAAUGUUGCCAAAAAAAAA----CCGGGCAUCUGGGAAGAGCUGAGAUGUCUGGCU------
..((((--(-.........)))))...(((((((((((((((((((....))))...........----((((....))))...))))))))))).))))..------ ( -30.60)
>DroSec_CAF1 105054 87 + 1
UCGCUCCUCAAUCCUUGCGGCGGCCAUUCAGCAUUUCAGCUUCGAUUAAUGUUGCCAAAAAA-------UCG--------------GCUGAGAUGUCUGGCCGUACAA
.(((............)))(((((((....((((((((((..(((((..((....))...))-------)))--------------)))))))))).))))))).... ( -30.80)
>DroSim_CAF1 84899 87 + 1
ACGCUCCUCAAUCCUUGCGGCGGCCAUUCAGCAUUUCAGCUUCGAUUAAUGUUGCCAAAAAA-------UCG--------------GCUGAGAUGUCUGGCCGUACAA
.(((............)))(((((((....((((((((((..(((((..((....))...))-------)))--------------)))))))))).))))))).... ( -31.20)
>DroEre_CAF1 95312 97 + 1
UCACUCCGC-UUCCUUGCGGAGG-CAUUCAGCAUUUCAGCUUCGAUUAAUGUUGCCAAAAA--------UCGGACAGAUAGGAA-AACAGAGAUGUCUGGGCGUAUAA
...((((((-......))))))(-(.(((((((((((.(.(((((((..((....))..))--------)))))).....(...-..).)))))).))))).)).... ( -27.90)
>DroYak_CAF1 95163 105 + 1
UCACUCAUC-AUCCUUGCGGAGG-CAUUCAGCAUUUCGGCUUCGAUUAAUGUUGCCAAAAAAAAAAAAUUGGGGCAGAUAGGAA-AGCAGAGAUGUCUGGGCGUACAA
...(((..(-(....))..)))(-(.(((((((((((.((((...(((...(((((..((........))..))))).)))..)-))).)))))).))))).)).... ( -25.30)
>consensus
UCGCUCCUC_AUCCUUGCGGAGGCCAUUCAGCAUUUCAGCUUCGAUUAAUGUUGCCAAAAAA_______UCGG_CA__U_GGAA_AGCUGAGAUGUCUGGCCGUACAA
...........(((....)))(((((....((((((((((..((((....))))((...............)).............)))))))))).)))))...... (-11.88 = -13.92 +   2.04)

alignment

secondary structure

dotplot

Window 2

Location	8,203,062 – 8,203,157
Length	95
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	76.46
Mean single sequence MFE	-27.82
Consensus MFE	-13.69
Energy contribution	-14.33
Covariance contribution	0.64
Combinations/Pair	1.06
Mean z-score	-1.78
Structure conservation index	0.49
SVM decision value	0.01
SVM RNA-class probability	0.537338
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8203062 95 - 22224390
------AGCCAGACAUCUCAGCUCUUCCCAGAUGCCCGG----UUUUUUUUUGGCAACAUUAAUCGAAGCUGAAAUGCUGAAUGGCCUCCGCAAGGAU-G--AGGCGA
------...(((.(((.((((((((....)))((((..(----......)..))))............))))).))))))....((((((....))).-.--.))).. ( -27.50)
>DroSec_CAF1 105054 87 - 1
UUGUACGGCCAGACAUCUCAGC--------------CGA-------UUUUUUGGCAACAUUAAUCGAAGCUGAAAUGCUGAAUGGCCGCCGCAAGGAUUGAGGAGCGA
((((.((((((..(((.(((((--------------(((-------((...((....))..)))))..))))).))).....))))))((....))........)))) ( -31.50)
>DroSim_CAF1 84899 87 - 1
UUGUACGGCCAGACAUCUCAGC--------------CGA-------UUUUUUGGCAACAUUAAUCGAAGCUGAAAUGCUGAAUGGCCGCCGCAAGGAUUGAGGAGCGU
..((.((((((..(((.(((((--------------(((-------((...((....))..)))))..))))).))).....))))))((....))........)).. ( -31.00)
>DroEre_CAF1 95312 97 - 1
UUAUACGCCCAGACAUCUCUGUU-UUCCUAUCUGUCCGA--------UUUUUGGCAACAUUAAUCGAAGCUGAAAUGCUGAAUG-CCUCCGCAAGGAA-GCGGAGUGA
...(((.(((((.(((.((.(((-(...........(((--------((..((....))..))))))))).)).))))))...(-(.(((....))).-)))).))). ( -27.60)
>DroYak_CAF1 95163 105 - 1
UUGUACGCCCAGACAUCUCUGCU-UUCCUAUCUGCCCCAAUUUUUUUUUUUUGGCAACAUUAAUCGAAGCCGAAAUGCUGAAUG-CCUCCGCAAGGAU-GAUGAGUGA
.....(((.((..((((..(((.-........................(((((((..(.......)..))))))).((.....)-)....)))..)))-).)).))). ( -21.50)
>consensus
UUGUACGGCCAGACAUCUCAGCU_UUCC_A__UG_CCGA_______UUUUUUGGCAACAUUAAUCGAAGCUGAAAUGCUGAAUGGCCUCCGCAAGGAU_GAGGAGCGA
.........(((.(((.((((((........................((..((....))..))....)))))).))))))........((....))............ (-13.69 = -14.33 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:50:15 2006