Locus 2602

Sequence ID	2R_DroMel_CAF1
Location	9,179,505 – 9,179,654
Length	149
Max. P	0.823656

overview

Window 7

Location	9,179,505 – 9,179,614
Length	109
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	78.20
Mean single sequence MFE	-30.23
Consensus MFE	-13.31
Energy contribution	-13.07
Covariance contribution	-0.24
Combinations/Pair	1.25
Mean z-score	-2.14
Structure conservation index	0.44
SVM decision value	0.69
SVM RNA-class probability	0.823656
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9179505 109 + 20766785
AGACUACUUGAGUCAAUUUAAAAAGAGA--UUUCUUCGGAACAUAGAAGAGAAC-CCUGUGCCAUCUUUAUUUC--------GGGGUGUUCUAGCCCUUGGGGCGAUUCAAGUGCCUUGG
....((((((((((.........((((.--(((((((........)))))))((-((((..............)--------))))).)))).((((...))))))))))))))...... ( -34.64)
>DroSec_CAF1 63811 116 + 1
AGACUACUUGAGUCAAUUUAAAAAGAGA--UUUCUUCGGUACUUCUAAUAGUAC-CCUGCACCAUCUUUAUAUAUUAUUCUUUAUAUGUUGUAGCCCUUG-GGCGAUUCAAGUGCCUUGG
....((((((((((.........(((((--(......((((((......)))))-).......))))))((((((........))))))....(((....-)))))))))))))...... ( -29.52)
>DroSim_CAF1 56150 110 + 1
AGACUACUUGAGUCAAUUUAAAAAGAUAUAUGUCUUUGGUACUUCUAAUAGUAC-UUUGCACCAUCUUUAUAUC--------AGGGUGUUGUAGCCCUUG-GGCGAUUCAAGUGCCUUGG
....((((((((((.......((((((....))))))((((((......)))))-).((((.((((((......--------)))))).))))(((....-)))))))))))))...... ( -33.30)
>DroEre_CAF1 60595 109 + 1
AGACUACUUGAGUCAAUUUAAAAAGACA--UUUCUUUGUUACACCCAAUAUAGC-CCUGCACUAUCUUUUUAGC--------AGUGUGUUGUAGCCCUUGGGCCCAUUGAAGUGCCUUGG
.((((.....))))........(((.((--((((..((..........((((((-(((((............))--------)).).))))))(((....))).))..)))))).))).. ( -26.20)
>DroYak_CAF1 55006 105 + 1
AGACUACUUGAGUCAGUUCGAAAAGAGC--UUUCUUAGGUACAUCCAAUAGAAUCUAUGCUCUAUCUUCAUA-------------GUGUGGUAGCUCUUGGGGCCAUUCAAGUGCCUUGG
....((((((((..(((((.....))))--)..))))))))...((((.((...(((((((..........)-------------))))))...)).))))((((......).))).... ( -27.50)
>consensus
AGACUACUUGAGUCAAUUUAAAAAGAGA__UUUCUUCGGUACAUCCAAUAGAAC_CCUGCACCAUCUUUAUAUC________AGGGUGUUGUAGCCCUUGGGGCGAUUCAAGUGCCUUGG
.((((.....))))........(((((....))))).(((((...............((((.(((....................))).))))(((.....))).......))))).... (-13.31 = -13.07 +  -0.24)

alignment

secondary structure

dotplot

Window 8

Location	9,179,505 – 9,179,614
Length	109
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	78.20
Mean single sequence MFE	-26.14
Consensus MFE	-14.48
Energy contribution	-15.40
Covariance contribution	0.92
Combinations/Pair	1.19
Mean z-score	-1.74
Structure conservation index	0.55
SVM decision value	-0.01
SVM RNA-class probability	0.528288
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9179505 109 - 20766785
CCAAGGCACUUGAAUCGCCCCAAGGGCUAGAACACCCC--------GAAAUAAAGAUGGCACAGG-GUUCUCUUCUAUGUUCCGAAGAAA--UCUCUUUUUAAAUUGACUCAAGUAGUCU
...((((((((((.((((((...))))..((((.((((--------(.........)))....))-))))(((((........)))))..--..............)).)))))).)))) ( -25.30)
>DroSec_CAF1 63811 116 - 1
CCAAGGCACUUGAAUCGCC-CAAGGGCUACAACAUAUAAAGAAUAAUAUAUAAAGAUGGUGCAGG-GUACUAUUAGAAGUACCGAAGAAA--UCUCUUUUUAAAUUGACUCAAGUAGUCU
...((((((((((.(((((-....))).................(((.((.(((((.(((....(-(((((......))))))......)--))))))).)).))))).)))))).)))) ( -28.30)
>DroSim_CAF1 56150 110 - 1
CCAAGGCACUUGAAUCGCC-CAAGGGCUACAACACCCU--------GAUAUAAAGAUGGUGCAAA-GUACUAUUAGAAGUACCAAAGACAUAUAUCUUUUUAAAUUGACUCAAGUAGUCU
...((((((((((.(((((-....)))...........--------((((((..((((((((...-))))))))....((.......)).))))))..........)).)))))).)))) ( -26.40)
>DroEre_CAF1 60595 109 - 1
CCAAGGCACUUCAAUGGGCCCAAGGGCUACAACACACU--------GCUAAAAAGAUAGUGCAGG-GCUAUAUUGGGUGUAACAAAGAAA--UGUCUUUUUAAAUUGACUCAAGUAGUCU
..((((((.(((..((.((((((.((((......((((--------(((....)).)))))...)-)))...))))))....))..))).--))))))........((((.....)))). ( -27.50)
>DroYak_CAF1 55006 105 - 1
CCAAGGCACUUGAAUGGCCCCAAGAGCUACCACAC-------------UAUGAAGAUAGAGCAUAGAUUCUAUUGGAUGUACCUAAGAAA--GCUCUUUUCGAACUGACUCAAGUAGUCU
...((((((((((..(..(..(((((((......(-------------((((.........))))).((((...((.....))..)))))--))))))...)..)....)))))).)))) ( -23.20)
>consensus
CCAAGGCACUUGAAUCGCCCCAAGGGCUACAACACACU________GAUAUAAAGAUGGUGCAGG_GUUCUAUUAGAUGUACCAAAGAAA__UCUCUUUUUAAAUUGACUCAAGUAGUCU
...((((((((((...(((.....)))...........................((((((((....)))))))).........(((((......)))))..........)))))).)))) (-14.48 = -15.40 +   0.92)

alignment

secondary structure

dotplot

Window 9

Location	9,179,543 – 9,179,654
Length	111
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	78.83
Mean single sequence MFE	-35.19
Consensus MFE	-15.20
Energy contribution	-16.92
Covariance contribution	1.72
Combinations/Pair	1.08
Mean z-score	-1.97
Structure conservation index	0.43
SVM decision value	0.09
SVM RNA-class probability	0.577568
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9179543 111 + 20766785
ACAUAGAAGAGAAC-CCUGUGCCAUCUUUAUUUC--------GGGGUGUUCUAGCCCUUGGGGCGAUUCAAGUGCCUUGGCCCAAUUCUUCGCGAAUGUGGGCUGAGCGAUUCUGUGAUU
.((((((((((.((-((((..............)--------))))).)))).((((...))))........(((.(..(((((((((.....)))).)))))..))))..))))))... ( -39.64)
>DroSec_CAF1 63849 118 + 1
ACUUCUAAUAGUAC-CCUGCACCAUCUUUAUAUAUUAUUCUUUAUAUGUUGUAGCCCUUG-GGCGAUUCAAGUGCCUUGGCCCAAUUCCUCGCGAGAGUGGGCUGAGCGAUUCUGUGAUU
.......((((...-...((((......((((((........))))))(((..(((....-)))....)))))))((..(((((....(((....))))))))..)).....)))).... ( -31.80)
>DroSim_CAF1 56190 110 + 1
ACUUCUAAUAGUAC-UUUGCACCAUCUUUAUAUC--------AGGGUGUUGUAGCCCUUG-GGCGAUUCAAGUGCCUUGGCCCAAUUCCUCGCGAAAGUGGGCUGAGCGAUUCUGUGAUU
..........((((-((((((.((((((......--------)))))).))))(((....-))).....))))))((..(((((.(((.....)))..)))))..))............. ( -32.20)
>DroEre_CAF1 60633 109 + 1
ACACCCAAUAUAGC-CCUGCACUAUCUUUUUAGC--------AGUGUGUUGUAGCCCUUGGGCCCAUUGAAGUGCCUUGGCCCAUUUCUUCGCGAAAGUGGGCUG--CGACGCUGUGAUU
........((((((-...(((((..((....)).--------)))))((((((((((.(((((((((....)))....)))))).......((....))))))))--))))))))))... ( -41.60)
>DroYak_CAF1 55044 105 + 1
ACAUCCAAUAGAAUCUAUGCUCUAUCUUCAUA-------------GUGUGGUAGCUCUUGGGGCCAUUCAAGUGCCUUGGCCCAAUUCUUCGCGUAACUGGGCUG--CGAUUCUGUGAUU
.......((((((((...((.((((....)))-------------).)).(((((((...((((((...........))))))................))))))--))))))))).... ( -30.71)
>consensus
ACAUCCAAUAGAAC_CCUGCACCAUCUUUAUAUC________AGGGUGUUGUAGCCCUUGGGGCGAUUCAAGUGCCUUGGCCCAAUUCUUCGCGAAAGUGGGCUGAGCGAUUCUGUGAUU
...................(((.(((...........................((.((((((....)))))).))(((((((((..((.....))...))))))))).)))...)))... (-15.20 = -16.92 +   1.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:34:13 2006