Locus 6535

Sequence ID	3L_DroMel_CAF1
Location	17,281,667 – 17,281,825
Length	158
Max. P	0.961072

overview

Window 6

Location	17,281,667 – 17,281,785
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.11
Mean single sequence MFE	-39.28
Consensus MFE	-30.20
Energy contribution	-31.20
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-2.48
Structure conservation index	0.77
SVM decision value	0.70
SVM RNA-class probability	0.825453
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17281667 118 + 23771897
--GCAACAUGUUGCCGGGCAACCGGGCAUAAAUGAGGGGCUUAUCCUAUCGGGCAGCAAAACUUGAGCAAUAAAAUUGCUUUUAUAUGCGAGAGUCUGUGCCGUGGAUGAGCGGGGAAAA
--....(((..((((((....)).))))...)))....((((((((...(((((((....((((..(((((((((....)))))).)))..)))))))).))).))))))))........ ( -41.90)
>DroSec_CAF1 165354 117 + 1
--GCAACAUGUUGCCGGGCAAC-GGGCAUAAAUGAGGAACUUAUCCUAUCGAGCAGCACAACUUGAGCAUUAAAAUUGCUUUUAUAUGCGAGAGUCUGUGCCGUGGAUGAGCGGGGAAAA
--....(((..((((.(....)-.))))...))).....(((((((...((....(((((((((..(((((((((....))))).))))..)))).))))))).)))))))......... ( -36.90)
>DroSim_CAF1 161590 117 + 1
--GCAACAUGUUGCCGGGCAAC-GGGCAUAAAUGGGGGGCUUAUCCUAUCGAGCAGCACAACUUGAGCAAUAAAAUUGCUUUUAUAUGCGAGAGUCUGUGCCGUGGAUGAGCGGGAAAAA
--.(..(((..((((.(....)-.))))...)))..).((((((((...((....(((((((((..(((((((((....)))))).)))..)))).))))))).))))))))........ ( -42.60)
>DroEre_CAF1 168372 117 + 1
--GCAACAUGUUGCCGGGCAAC-GGGCAUAAAUGAGGGGCUUAUCCUAUCGAGCAGCACAACUUGAGCAAUAAAAUUGCUUUUAUAUACGAGAGUCUGUGCCGUGGAUGAGCGGGGAAAA
--....(((..((((.(....)-.))))...)))....((((((((...((....((((((((((((((((...)))))))..........)))).))))))).))))))))........ ( -37.50)
>DroYak_CAF1 173356 119 + 1
CGGCAACAUGUUGCCGGGCAAC-GGGCAUAAAUGAGGGGCUUAUCCUAUCGAGCAGCACAACUUGAGCAAUAAAAUUGCUUUUAUAUACGAGAGUCUGUGCCGUGGAUGAGCGGGGAAAA
......(((..((((.(....)-.))))...)))....((((((((...((....((((((((((((((((...)))))))..........)))).))))))).))))))))........ ( -37.50)
>consensus
__GCAACAUGUUGCCGGGCAAC_GGGCAUAAAUGAGGGGCUUAUCCUAUCGAGCAGCACAACUUGAGCAAUAAAAUUGCUUUUAUAUGCGAGAGUCUGUGCCGUGGAUGAGCGGGGAAAA
...(..(((..((((.........))))...)))..).((((((((...((....(((((((((..(((((((((....)))))).)))..)))).))))))).))))))))........ (-30.20 = -31.20 +   1.00)

alignment

secondary structure

dotplot

Window 7

Location	17,281,705 – 17,281,825
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.50
Mean single sequence MFE	-31.96
Consensus MFE	-28.94
Energy contribution	-29.46
Covariance contribution	0.52
Combinations/Pair	1.06
Mean z-score	-1.64
Structure conservation index	0.91
SVM decision value	1.52
SVM RNA-class probability	0.961072
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17281705 120 + 23771897
UUAUCCUAUCGGGCAGCAAAACUUGAGCAAUAAAAUUGCUUUUAUAUGCGAGAGUCUGUGCCGUGGAUGAGCGGGGAAAAUAGCCUGAAAUAUUCCUGGCAUGCUCAGAUAUACAACCAU
......((((((((.(((......(((((((...))))))).....)))........((((((.(((((..((((........))))...))))).)))))))))).))))......... ( -32.50)
>DroSec_CAF1 165391 120 + 1
UUAUCCUAUCGAGCAGCACAACUUGAGCAUUAAAAUUGCUUUUAUAUGCGAGAGUCUGUGCCGUGGAUGAGCGGGGAAAAUAGCCUGAAAUAUUCCUGGCAUGCUCAGAUAUACAACCAU
......((((((((((((((((((..(((((((((....))))).))))..)))).))))).........((.(((((.((........)).))))).)).))))).))))......... ( -34.80)
>DroSim_CAF1 161627 119 + 1
UUAUCCUAUCGAGCAGCACAACUUGAGCAAUAAAAUUGCUUUUAUAUGCGAGAGUCUGUGCCGUGGAUGAGCGGGAAAAAUAGUC-GAAAUAUUUCUGACAUGCUCAGAUAUACAACCUU
......((((((((((((((((((..(((((((((....)))))).)))..)))).)))))(((......))).........(((-(((....))).))).))))).))))......... ( -30.10)
>DroEre_CAF1 168409 120 + 1
UUAUCCUAUCGAGCAGCACAACUUGAGCAAUAAAAUUGCUUUUAUAUACGAGAGUCUGUGCCGUGGAUGAGCGGGGAAAAUAGCCUGAAAUAUUCCUGGCAUGCUCAGAUAUACAACCAU
......(((((((((((((((((((((((((...)))))))..........)))).))))).........((.(((((.((........)).))))).)).))))).))))......... ( -31.20)
>DroYak_CAF1 173395 120 + 1
UUAUCCUAUCGAGCAGCACAACUUGAGCAAUAAAAUUGCUUUUAUAUACGAGAGUCUGUGCCGUGGAUGAGCGGGGAAAAUAGCCUGAAAUAUUCCUGGCAUGCUCAGAUAUACAACCAU
......(((((((((((((((((((((((((...)))))))..........)))).))))).........((.(((((.((........)).))))).)).))))).))))......... ( -31.20)
>consensus
UUAUCCUAUCGAGCAGCACAACUUGAGCAAUAAAAUUGCUUUUAUAUGCGAGAGUCUGUGCCGUGGAUGAGCGGGGAAAAUAGCCUGAAAUAUUCCUGGCAUGCUCAGAUAUACAACCAU
......((((((((((((((((((..(((((((((....)))))).)))..)))).))))).........((.(((((.((........)).))))).)).))))).))))......... (-28.94 = -29.46 +   0.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:23:22 2006