Locus 1027

Sequence ID	2R_DroMel_CAF1
Location	4,231,338 – 4,231,450
Length	112
Max. P	0.999317

overview

Window 4

Location	4,231,338 – 4,231,450
Length	112
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	78.61
Mean single sequence MFE	-33.98
Consensus MFE	-24.31
Energy contribution	-25.27
Covariance contribution	0.96
Combinations/Pair	1.20
Mean z-score	-3.24
Structure conservation index	0.72
SVM decision value	3.38
SVM RNA-class probability	0.999118
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4231338 112 + 20766785
-----CCUAUUAAAAGAGUCCUAGAAACCUCGAAGGAUUUAAGAAGGCUAUUUAAGCUUUACUAAAGUAAAGUGGCGAUUUAAAUCUUUUGAGGUCUCUGUAACUCCACCGAUUAUA
-----..........((((..((((.(((((((((((((((((...(((......(((((((....))))))))))..))))))))))))))))).))))..))))........... ( -37.00)
>DroSec_CAF1 833 99 + 1
-----CCUUCUAAGGGAGUCCCAGAAACCUCUAGUGAUUUCAGAAGGCUAUUUUCGC-------------GGUAGCGGUUUAAAUCUGUUGAGGUCUCUGUAACUCCACCGAUUGUA
-----.........(((((..((((.(((((....(((((.(((..((((((.....-------------))))))..))))))))....))))).))))..))))).......... ( -32.70)
>DroSim_CAF1 832 107 + 1
-----CCUUCUAAGGGAGUCCCAGAAACCUCUAGGGAUUUAAGAAGGCUAUUUUCGCUUUACAGA-----AGUAGCGGUUUAAAUCUGUUGAGGUCUCUGUAACUCCGCCGAUUGUA
-----.........(((((..((((.(((((.(.(((((((((...(((((((..(.....)..)-----))))))..))))))))).).))))).))))..))))).......... ( -39.40)
>DroEre_CAF1 840 111 + 1
AAGAACCUUAUAAGGAAGUCCAAGAAACCGCUAGGGAUUUAAGAAAGCUACUUUCGUUU-GCCGA-----AGUAGCGGUUUAAAUCUGUUGCGGUCUUUGUAACUCCCCCGAUUGUA
.............((.(((...(((.(((((.(.(((((((((...((((((((.(...-.).))-----))))))..))))))))).).))))).)))...))).))......... ( -34.20)
>DroYak_CAF1 840 111 + 1
AUGAACCUUUUAAGGAAUUCCCAGAAACCUCUACGGAUUUAAGAAGGCUAAUUUGGCUG-AAUGA-----AGUAGCGGUUUAAAUCUGUUGAGCUCUCUGAAUUUCCCCCGAUUGUA
.............((((....((((...(((.(((((((((((...((((.((((....-..)))-----).))))..))))))))))).)))...))))...)))).......... ( -26.60)
>consensus
_____CCUUCUAAGGGAGUCCCAGAAACCUCUAGGGAUUUAAGAAGGCUAUUUUCGCUU_ACUGA_____AGUAGCGGUUUAAAUCUGUUGAGGUCUCUGUAACUCCACCGAUUGUA
..............(((((..((((.(((((.(.(((((((((...((((((..................))))))..))))))))).).))))).))))..))))).......... (-24.31 = -25.27 +   0.96)

alignment

secondary structure

dotplot

Window 5

Location	4,231,338 – 4,231,450
Length	112
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	78.61
Mean single sequence MFE	-32.56
Consensus MFE	-23.79
Energy contribution	-24.51
Covariance contribution	0.72
Combinations/Pair	1.14
Mean z-score	-3.37
Structure conservation index	0.73
SVM decision value	3.51
SVM RNA-class probability	0.999317
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4231338 112 - 20766785
UAUAAUCGGUGGAGUUACAGAGACCUCAAAAGAUUUAAAUCGCCACUUUACUUUAGUAAAGCUUAAAUAGCCUUCUUAAAUCCUUCGAGGUUUCUAGGACUCUUUUAAUAGG-----
....((..(.((((((..(((((((((.((.(((((((........(((((....)))))(((.....)))....))))))).)).)))))))))..)))))).)..))...----- ( -30.70)
>DroSec_CAF1 833 99 - 1
UACAAUCGGUGGAGUUACAGAGACCUCAACAGAUUUAAACCGCUACC-------------GCGAAAAUAGCCUUCUGAAAUCACUAGAGGUUUCUGGGACUCCCUUAGAAGG-----
.......((.(((((..((((((((((....(((((.....((((..-------------.......))))......)))))....))))))))))..))))))).......----- ( -31.70)
>DroSim_CAF1 832 107 - 1
UACAAUCGGCGGAGUUACAGAGACCUCAACAGAUUUAAACCGCUACU-----UCUGUAAAGCGAAAAUAGCCUUCUUAAAUCCCUAGAGGUUUCUGGGACUCCCUUAGAAGG-----
.......((.(((((..((((((((((....(((((((...((((.(-----(.((.....)).)).))))....)))))))....))))))))))..))))))).......----- ( -35.00)
>DroEre_CAF1 840 111 - 1
UACAAUCGGGGGAGUUACAAAGACCGCAACAGAUUUAAACCGCUACU-----UCGGC-AAACGAAAGUAGCUUUCUUAAAUCCCUAGCGGUUUCUUGGACUUCCUUAUAAGGUUCUU
.......(((((((((.((((((((((....(((((((...((((((-----(((..-...)).)))))))....)))))))....))))))).))))))))))))........... ( -37.40)
>DroYak_CAF1 840 111 - 1
UACAAUCGGGGGAAAUUCAGAGAGCUCAACAGAUUUAAACCGCUACU-----UCAUU-CAGCCAAAUUAGCCUUCUUAAAUCCGUAGAGGUUUCUGGGAAUUCCUUAAAAGGUUCAU
...((((.((((((.((((((((.(((.((.(((((((...((((..-----.....-.........))))....))))))).)).))).))))))))..))))))....))))... ( -27.99)
>consensus
UACAAUCGGGGGAGUUACAGAGACCUCAACAGAUUUAAACCGCUACU_____UCAGU_AAGCGAAAAUAGCCUUCUUAAAUCCCUAGAGGUUUCUGGGACUCCCUUAAAAGG_____
.......((.((((((.((((((((((....(((((((...((((......................))))....)))))))....)))))))))).))))))))............ (-23.79 = -24.51 +   0.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:54:39 2006