Locus 9425

Sequence ID	3R_DroMel_CAF1
Location	24,974,500 – 24,974,682
Length	182
Max. P	0.879754

overview

Window 6

Location	24,974,500 – 24,974,604
Length	104
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	74.63
Mean single sequence MFE	-23.41
Consensus MFE	-10.80
Energy contribution	-12.55
Covariance contribution	1.75
Combinations/Pair	1.00
Mean z-score	-2.49
Structure conservation index	0.46
SVM decision value	0.91
SVM RNA-class probability	0.879754
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24974500 104 + 27905053
AGAAGCAUCAAAAUUCUAGUUUGUUACACU-UUAAAGUCAAA--------AAUUUGC-------CAUCUCAUAUGUUUCUAAAGUUCAGAUUAUGCUUAUGAGCAUAAUUUGAUAGGUUA
((((((((.........(((((...((...-.....))...)--------))))...-------........)))))))).....((((((((((((....))))))))))))....... ( -20.15)
>DroSec_CAF1 1599 105 + 1
AGAAGCAUCUAAAUUUUAGAUUGUUACAUUUUUAAAGUCACA--------AAUUUGC-------AAUCUCAUAUGUUUCUAGCGUUCAGAUUAUGCUUAUGAGCAUAAUUUGAUAGGUUA
((((((((.........(((((((...((((..........)--------)))..))-------)))))...))))))))(((.(((((((((((((....)))))))))))).).))). ( -24.30)
>DroSim_CAF1 1598 105 + 1
AGAAGCAUCUAAAUUUUAGAUUGGUAAAUUUUUAAAGUCAAA--------AAUUUGC-------UAUCUCAUAUGUUUGUAGCAUUCAGAUUAUGCUUAUGAGCAUAAUUUGAUAGGUUA
..(((((((((.....)))).((((((((((((......)))--------)))))))-------)).......))))).((((..((((((((((((....))))))))))))...)))) ( -27.90)
>DroEre_CAF1 1719 116 + 1
AGAAUCACCAAAGUUGCUAAGUGUUGCACU-UUAAAUCUAGAAUUUCACUCAUUUCAGAUUUCUAAUCUCCUAUGUUUCUUAUGCUUA---UAUGCUUAUAAGCAUAGUUUUAAAGGUUA
......((((((((.((........)))))-))((((((.(((..........))))))))).................(((((((((---((....))))))))))).......))).. ( -21.30)
>consensus
AGAAGCAUCAAAAUUUUAGAUUGUUACACU_UUAAAGUCAAA________AAUUUGC_______AAUCUCAUAUGUUUCUAACGUUCAGAUUAUGCUUAUGAGCAUAAUUUGAUAGGUUA
((((((((................................................................)))))))).....((((((((((((....))))))))))))....... (-10.80 = -12.55 +   1.75)

alignment

secondary structure

dotplot

Window 7

Location	24,974,539 – 24,974,644
Length	105
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	81.19
Mean single sequence MFE	-19.80
Consensus MFE	-15.16
Energy contribution	-15.97
Covariance contribution	0.81
Combinations/Pair	1.05
Mean z-score	-1.75
Structure conservation index	0.77
SVM decision value	0.55
SVM RNA-class probability	0.778701
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24974539 105 + 27905053
AA--------AAUUUGC-------CAUCUCAUAUGUUUCUAAAGUUCAGAUUAUGCUUAUGAGCAUAAUUUGAUAGGUUAUCGCCUUUUUUUAACCCUAGUAAUCAAAUUAAAUUAAACG
..--------((((((.-------.....................((((((((((((....))))))))))))..(((((...........)))))........)))))).......... ( -19.10)
>DroSec_CAF1 1639 105 + 1
CA--------AAUUUGC-------AAUCUCAUAUGUUUCUAGCGUUCAGAUUAUGCUUAUGAGCAUAAUUUGAUAGGUUAUCGUCUUUAUUUAACCCUAGUAAUCAAAUUAAAUUAAACG
..--------((((((.-------..........(((.((((...((((((((((((....))))))))))))..(((((...........))))))))).))))))))).......... ( -20.50)
>DroSim_CAF1 1638 105 + 1
AA--------AAUUUGC-------UAUCUCAUAUGUUUGUAGCAUUCAGAUUAUGCUUAUGAGCAUAAUUUGAUAGGUUAUCGUCUUUAUUUAACCCUAGUAAUCAAAUUAAAUUAAACG
..--------....(((-------(((..(....)...)))))).((((((((((((....))))))))))))..(((((...........)))))........................ ( -21.30)
>DroEre_CAF1 1758 117 + 1
GAAUUUCACUCAUUUCAGAUUUCUAAUCUCCUAUGUUUCUUAUGCUUA---UAUGCUUAUAAGCAUAGUUUUAAAGGUUAUCGUCUUUAUUUGACCGCAGUAAUCAAAUUAAAUUAAACG
.................((((.((...............(((((((((---((....))))))))))).......(((((...........)))))..)).))))............... ( -18.30)
>consensus
AA________AAUUUGC_______AAUCUCAUAUGUUUCUAACGUUCAGAUUAUGCUUAUGAGCAUAAUUUGAUAGGUUAUCGUCUUUAUUUAACCCUAGUAAUCAAAUUAAAUUAAACG
..................................((((.......((((((((((((....))))))))))))..(((((...........)))))...................)))). (-15.16 = -15.97 +   0.81)

alignment

secondary structure

dotplot

Window 8

Location	24,974,564 – 24,974,682
Length	118
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	83.43
Mean single sequence MFE	-22.17
Consensus MFE	-14.02
Energy contribution	-16.14
Covariance contribution	2.12
Combinations/Pair	1.10
Mean z-score	-1.92
Structure conservation index	0.63
SVM decision value	0.20
SVM RNA-class probability	0.630361
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24974564 118 - 27905053
AACGAACGUAAGCCAAUUUAAUCUAAUUGAAAGGCAUGCGUUUAAUUUAAUUUGAUUACUAGGGUUAAAAAAAGGCGAUAACCUAUCAAAUUAUGCUCAUAAGCAUAAUCUGAACUUU
...(((((((.(((..((((((...)))))).))).)))))))..................((((((...........)))))).(((.((((((((....)))))))).)))..... ( -26.20)
>DroSec_CAF1 1664 118 - 1
AACGAACUUAAGCCAAUUUAAUCUAAUCGAAAGGCAUGCGUUUAAUUUAAUUUGAUUACUAGGGUUAAAUAAAGACGAUAACCUAUCAAAUUAUGCUCAUAAGCAUAAUCUGAACGCU
...........(((..................)))..(((((((......((((((.....((((((...........))))))))))))(((((((....)))))))..))))))). ( -23.37)
>DroSim_CAF1 1663 118 - 1
AACAAACUCAAGCCAAUUUAAUCUAAUUGAAAGGCAUGCGUUUAAUUUAAUUUGAUUACUAGGGUUAAAUAAAGACGAUAACCUAUCAAAUUAUGCUCAUAAGCAUAAUCUGAAUGCU
...........(((..((((((...)))))).)))..(((((((......((((((.....((((((...........))))))))))))(((((((....)))))))..))))))). ( -23.00)
>DroEre_CAF1 1798 115 - 1
AACGAACCUAAGCCAAUUUAAUCAAUUUGAAAGGCAUGCGUUUAAUUUAAUUUGAUUACUGCGGUCAAAUAAAGACGAUAACCUUUAAAACUAUGCUUAUAAGCAUA---UAAGCAUA
...((.((...(((..(((((.....))))).)))..(((..(((((......))))).)))))))...(((((........)))))....((((((((((....))---)))))))) ( -21.40)
>DroYak_CAF1 1784 102 - 1
AAGAAACUUAAGCCAAUUUAAUCUAAUUGAAAGGUAUGAGUUU-----AAUUUGAUUACUAGGGCUAACUAAA-AUGAUAACCUUUGAAAUUAUGCUUAUGAGCAUG---U-------
..........((((....(((((.(((((((.........)))-----)))).)))))....)))).......-.................((((((....))))))---.------- ( -16.90)
>consensus
AACGAACUUAAGCCAAUUUAAUCUAAUUGAAAGGCAUGCGUUUAAUUUAAUUUGAUUACUAGGGUUAAAUAAAGACGAUAACCUAUCAAAUUAUGCUCAUAAGCAUAAUCUGAACGCU
..........((((....(((((.(((((((((((....))))..))))))).)))))....))))...................(((.((((((((....)))))))).)))..... (-14.02 = -16.14 +   2.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:34:24 2006