Locus 609

Sequence ID	3R_DroMel_CAF1
Location	2,260,432 – 2,260,590
Length	158
Max. P	0.990133

overview

Window 6

Location	2,260,432 – 2,260,550
Length	118
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	77.08
Mean single sequence MFE	-28.78
Consensus MFE	-20.37
Energy contribution	-20.85
Covariance contribution	0.48
Combinations/Pair	1.05
Mean z-score	-2.32
Structure conservation index	0.71
SVM decision value	2.20
SVM RNA-class probability	0.990133
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2260432 118 + 27905053
UUCCCCGAAUGAAAAUGGAAAUAUGUCUUUGUGAUUUUCGAUUGCAAGCCGUAAUUUACGAUUGCUGCCCACAAUCGACAACAAAUAUUUUUGGCGGCAGACCGUAAGUUCAAUGUCU
..........((...((((..((((((((((..(((...)))..)))(((((......((((((.......))))))....((((....)))))))))))).))))..))))...)). ( -27.00)
>DroSec_CAF1 51346 105 + 1
UUCCCCUAAUGAAUAUG--AAUAUGCUUUUGUGAUUUUC-----------GUAAUUUACGGUUGCUGCCAACAAUCGACAACGAAUAUUUUUGGCGGCAGACCGUAAGUUCAAUGUCU
.........(((.((((--((.((((....)).)).)))-----------)))((((((((((((((((((.(((((....)))...)).))))))))).))))))))))))...... ( -30.00)
>DroSim_CAF1 49497 104 + 1
UUCCCCUAAUGGAAAUG--AAUAUGCUUUUGUGAUUUUC-----------GUAAUUUACGGUUGCUGCCAACAAUCGACAACGAAUAUUUUUGGCGGC-GACCGUAAGUUCAAUGUCU
........((((((((.--.(((......))).))))))-----------))(((((((((((((((((((.(((((....)))...)).))))))))-)))))))))))........ ( -34.40)
>DroEre_CAF1 49699 102 + 1
--------------AUG--AGUUGGCCUUUGUGAUUUUCGGUUGCAAGUCGUAAUUUACGGUUGCAGCCAACAAUCGACAACAAAUAACUUUGGCAGCAGACCGUAAGUUCAAUGUCU
--------------..(--(((((....((((((((...((((((((.(((((...)))))))))))))...)))).))))....)))))).((((...((.(....).))..)))). ( -28.90)
>DroYak_CAF1 46543 100 + 1
--------------CUC--A-UUUGCCUUUUUGAUUUUCAGUUGUAAGUCGUAAUUUACGGUUGUAGCCAACAAUCGACAACAAAUG-UUUUGGCGACAGACCGUAAGUUCAAUGUCU
--------------...--(-(((((....(((.....)))..)))))).(.(((((((((((((.(((((.....((((.....))-))))))).))).)))))))))))....... ( -23.60)
>consensus
UUCCCC_AAUG_A_AUG__AAUAUGCCUUUGUGAUUUUC__UUG_AAG_CGUAAUUUACGGUUGCUGCCAACAAUCGACAACAAAUAUUUUUGGCGGCAGACCGUAAGUUCAAUGUCU
..................................................(.(((((((((((((((((((...................)))))))).))))))))))))....... (-20.37 = -20.85 +   0.48)

alignment

secondary structure

dotplot

Window 7

Location	2,260,432 – 2,260,550
Length	118
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	77.08
Mean single sequence MFE	-23.58
Consensus MFE	-18.76
Energy contribution	-18.44
Covariance contribution	-0.32
Combinations/Pair	1.17
Mean z-score	-1.20
Structure conservation index	0.80
SVM decision value	0.41
SVM RNA-class probability	0.726922
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2260432 118 - 27905053
AGACAUUGAACUUACGGUCUGCCGCCAAAAAUAUUUGUUGUCGAUUGUGGGCAGCAAUCGUAAAUUACGGCUUGCAAUCGAAAAUCACAAAGACAUAUUUCCAUUUUCAUUCGGGGAA
..............(((....))).........(((((..(((((((..(((......((((...)))))))..))))))).....)))))......(..((..........))..). ( -24.30)
>DroSec_CAF1 51346 105 - 1
AGACAUUGAACUUACGGUCUGCCGCCAAAAAUAUUCGUUGUCGAUUGUUGGCAGCAACCGUAAAUUAC-----------GAAAAUCACAAAAGCAUAUU--CAUAUUCAUUAGGGGAA
.((...((((.(((((((.(((.(((((......(((....)))...))))).)))))))))).....-----------(.....)...........))--))...)).......... ( -23.00)
>DroSim_CAF1 49497 104 - 1
AGACAUUGAACUUACGGUC-GCCGCCAAAAAUAUUCGUUGUCGAUUGUUGGCAGCAACCGUAAAUUAC-----------GAAAAUCACAAAAGCAUAUU--CAUUUCCAUUAGGGGAA
.....(((((.(((((((.-((.(((((......(((....)))...))))).)).))))))).)).)-----------))..................--..(..((....))..). ( -25.50)
>DroEre_CAF1 49699 102 - 1
AGACAUUGAACUUACGGUCUGCUGCCAAAGUUAUUUGUUGUCGAUUGUUGGCUGCAACCGUAAAUUACGACUUGCAACCGAAAAUCACAAAGGCCAACU--CAU--------------
...............(((((.....((((....))))((((.((((.((((.(((((.((((...))))..))))).)))).)))))))))))))....--...-------------- ( -24.40)
>DroYak_CAF1 46543 100 - 1
AGACAUUGAACUUACGGUCUGUCGCCAAAA-CAUUUGUUGUCGAUUGUUGGCUACAACCGUAAAUUACGACUUACAACUGAAAAUCAAAAAGGCAAA-U--GAG--------------
...((((...((((((((.(((.((((..(-((.(((....))).))))))).))))))))))...............((.....))....)...))-)--)..-------------- ( -20.70)
>consensus
AGACAUUGAACUUACGGUCUGCCGCCAAAAAUAUUUGUUGUCGAUUGUUGGCAGCAACCGUAAAUUACG_CUU_CAA__GAAAAUCACAAAGGCAUAUU__CAU_U_CAUU_GGGGAA
...........(((((((.(((.(((((......(((....)))...))))).))))))))))....................................................... (-18.76 = -18.44 +  -0.32)

alignment

secondary structure

dotplot

Window 8

Location	2,260,471 – 2,260,590
Length	119
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	84.48
Mean single sequence MFE	-31.38
Consensus MFE	-22.99
Energy contribution	-24.31
Covariance contribution	1.32
Combinations/Pair	1.12
Mean z-score	-2.08
Structure conservation index	0.73
SVM decision value	0.83
SVM RNA-class probability	0.861904
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2260471 119 + 27905053
GAUUGCAAGCCGUAAUUUACGAUUGCUGCCCACAAUCGACAACAAAUAUUUUUGGCGGCAGACCGUAAGUUCAAUGUCUGUUAAAUUGGUAUGAUUUGUAUUAUCGCCAACCCUCGGUC
........(((((......((((((.......))))))....((((....))))))))).(((((..((........))......((((((((((....))))).)))))....))))) ( -27.50)
>DroSec_CAF1 51383 108 + 1
-----------GUAAUUUACGGUUGCUGCCAACAAUCGACAACGAAUAUUUUUGGCGGCAGACCGUAAGUUCAAUGUCUGUUAAAUUGGUAUGUUUUGUAUUAUCGCCAACCCUCGGUC
-----------(.(((((((((((((((((((.(((((....)))...)).))))))))).))))))))))).....(((.....((((((((........))).)))))....))).. ( -31.50)
>DroSim_CAF1 49534 107 + 1
-----------GUAAUUUACGGUUGCUGCCAACAAUCGACAACGAAUAUUUUUGGCGGC-GACCGUAAGUUCAAUGUCUGUUAAAUUGGUAUGUUUUGUAUUAUCGCCAAUCCUCGAUC
-----------(.(((((((((((((((((((.(((((....)))...)).))))))))-))))))))))))............(((((((((........))).))))))........ ( -34.70)
>DroEre_CAF1 49722 119 + 1
GGUUGCAAGUCGUAAUUUACGGUUGCAGCCAACAAUCGACAACAAAUAACUUUGGCAGCAGACCGUAAGUUCAAUGUCUGUUAAAUUGGUGUGAUUUGUAUUCCAGCCAACACUCGGUC
((.(((((((((.(((((((((((((.(((((...................))))).))).))))))))))((((.........))))...)))))))))..)).(((.......))). ( -32.01)
>DroYak_CAF1 46565 118 + 1
AGUUGUAAGUCGUAAUUUACGGUUGUAGCCAACAAUCGACAACAAAUG-UUUUGGCGACAGACCGUAAGUUCAAUGUCUGUUAAAUUGGUAUGAUUUGUAUAACCGCUUACAAUCAGUC
.(((((((((.(((((((((((((((.(((((.....((((.....))-))))))).))).))))))))))..........((((((.....))))))....)).)))))))))..... ( -31.20)
>consensus
__UUG_AAG_CGUAAUUUACGGUUGCUGCCAACAAUCGACAACAAAUAUUUUUGGCGGCAGACCGUAAGUUCAAUGUCUGUUAAAUUGGUAUGAUUUGUAUUAUCGCCAACCCUCGGUC
...........(.(((((((((((((((((((...................)))))))).)))))))))))).....(((.....((((((((((....))))).)))))....))).. (-22.99 = -24.31 +   1.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:47:20 2006