Locus 7231

Sequence ID	3R_DroMel_CAF1
Location	19,048,002 – 19,048,141
Length	139
Max. P	0.890260

overview

Window 6

Location	19,048,002 – 19,048,103
Length	101
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	74.37
Mean single sequence MFE	-22.04
Consensus MFE	-11.22
Energy contribution	-12.66
Covariance contribution	1.44
Combinations/Pair	1.14
Mean z-score	-1.69
Structure conservation index	0.51
SVM decision value	0.00
SVM RNA-class probability	0.533890
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19048002 101 + 27905053
---------GACAUGGU----GGCUAUUGCAAUUUUAUGUAGAUAUGGUGUAAGCUUAUAAGCUUUUGACACGUGUCCAUGCAAAUUUUUCAGUUAAUUUGCAUUAGUCAUUUU
---------.....(((----(((((.((((......))))((((((((..(((((....)))))...)).)))))).(((((((((........))))))))))))))))).. ( -25.60)
>DroSec_CAF1 60762 99 + 1
---------GACAUAGU----GGCGAUAGCUAUUUUAUGUAGAUAUGGUGUAAGCUUAUAAGCUUUUGACACGUGUCCAUGCAAAUUUUUCAAUUAAUUUGCAU-AGUAAUU-U
---------.(((((((----(((....)))))..))))).((((((((..(((((....)))))...)).)))))).(((((((((........)))))))))-.......-. ( -26.70)
>DroSim_CAF1 62492 99 + 1
---------GACAUAGU----GGCGAUUGCAAUUUUAUGUAGAUAUGAUGUAAGCUUAUAAGCUUUUGACACGUGUCCAUGCAAAUUUUGCAAUUAAUUUGCAU-AGUAAUU-U
---------.((((((.----.((....))....)))))).((((((.((((((((....)))))...))))))))).(((((((((........)))))))))-.......-. ( -23.40)
>DroEre_CAF1 63778 95 + 1
----UAUUAGAAAUAUUAAGCCGCCUAUA-AAUUUUAUGUAGAUACGGUGUAAGUUUACACGCUUUGUACACGUGUUCA------------AAUUAAUUAGCAU-AGUAAUU-G
----(((((.....(((((((((.(((((-.......)))))...))))....(...(((((.........))))).).------------..))))).....)-))))...-. ( -12.70)
>DroYak_CAF1 64293 112 + 1
UGCAUAUUAUAAAUAUUAAGCCGCGCAGGCUACUUUAUGUAGAUAUAGUGUAAGUUUACAUGCUUUGCACACGUGUCCAUGCAAAUUUUUCAAUUCAUUUGCAU-ACUAACU-U
((((((............((((.....))))....))))))(((((.((((((((......)).))))))..))))).((((((((..........))))))))-.......-. ( -21.79)
>consensus
_________GACAUAGU____GGCGAUUGCAAUUUUAUGUAGAUAUGGUGUAAGCUUAUAAGCUUUUGACACGUGUCCAUGCAAAUUUUUCAAUUAAUUUGCAU_AGUAAUU_U
.........................................((((((.(((((((......))))...))))))))).(((((((((........))))))))).......... (-11.22 = -12.66 +   1.44)

alignment

secondary structure

dotplot

Window 7

Location	19,048,002 – 19,048,103
Length	101
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	74.37
Mean single sequence MFE	-18.20
Consensus MFE	-6.48
Energy contribution	-8.52
Covariance contribution	2.04
Combinations/Pair	1.06
Mean z-score	-2.01
Structure conservation index	0.36
SVM decision value	0.96
SVM RNA-class probability	0.890260
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19048002 101 - 27905053
AAAAUGACUAAUGCAAAUUAACUGAAAAAUUUGCAUGGACACGUGUCAAAAGCUUAUAAGCUUACACCAUAUCUACAUAAAAUUGCAAUAGCC----ACCAUGUC---------
.....(((....(((((((........)))))))((((....((((...(((((....))))))))).................((....)).----.)))))))--------- ( -17.80)
>DroSec_CAF1 60762 99 - 1
A-AAUUACU-AUGCAAAUUAAUUGAAAAAUUUGCAUGGACACGUGUCAAAAGCUUAUAAGCUUACACCAUAUCUACAUAAAAUAGCUAUCGCC----ACUAUGUC---------
.-.....((-(((((((((........)))))))))))....((((...(((((....))))))))).......(((((.....((....)).----..))))).--------- ( -20.40)
>DroSim_CAF1 62492 99 - 1
A-AAUUACU-AUGCAAAUUAAUUGCAAAAUUUGCAUGGACACGUGUCAAAAGCUUAUAAGCUUACAUCAUAUCUACAUAAAAUUGCAAUCGCC----ACUAUGUC---------
.-.....((-(((((((((........)))))))))))....(((....(((((....)))))....)))....(((((.....((....)).----..))))).--------- ( -18.80)
>DroEre_CAF1 63778 95 - 1
C-AAUUACU-AUGCUAAUUAAUU------------UGAACACGUGUACAAAGCGUGUAAACUUACACCGUAUCUACAUAAAAUU-UAUAGGCGGCUUAAUAUUUCUAAUA----
.-.((((..-.((((.((.((((------------(..((((((.......))))))...........((....))...)))))-.)).))))...))))..........---- ( -11.60)
>DroYak_CAF1 64293 112 - 1
A-AGUUAGU-AUGCAAAUGAAUUGAAAAAUUUGCAUGGACACGUGUGCAAAGCAUGUAAACUUACACUAUAUCUACAUAAAGUAGCCUGCGCGGCUUAAUAUUUAUAAUAUGCA
(-((((..(-((((....(((((....)))))(((((....))))).....)))))..))))).............(((((..((((.....)))).....)))))........ ( -22.40)
>consensus
A_AAUUACU_AUGCAAAUUAAUUGAAAAAUUUGCAUGGACACGUGUCAAAAGCUUAUAAGCUUACACCAUAUCUACAUAAAAUUGCAAUCGCC____ACUAUGUC_________
..........(((((((((........)))))))))......((((...((((......))))))))............................................... ( -6.48 =  -8.52 +   2.04)

alignment

secondary structure

dotplot

Window 8

Location	19,048,023 – 19,048,141
Length	118
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	82.77
Mean single sequence MFE	-24.47
Consensus MFE	-16.43
Energy contribution	-16.81
Covariance contribution	0.38
Combinations/Pair	1.14
Mean z-score	-1.98
Structure conservation index	0.67
SVM decision value	0.65
SVM RNA-class probability	0.811765
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19048023 118 + 27905053
UUAUGUAGAUAUGGUGUAAGCUUAUAAGCUUUUGACACGUGUCCAUGCAAAUUUUUCAGUUAAUUUGCAUUAGUCAUUUUUUUAACUAGUUCUACAUAACAAAG--UUGAAAUUUGUAUU
.((((((((....(((((((((....)))))...))))(((.(.(((((((((........)))))))))..).))).............))))))))(((((.--......)))))... ( -26.20)
>DroSec_CAF1 60783 118 + 1
UUAUGUAGAUAUGGUGUAAGCUUAUAAGCUUUUGACACGUGUCCAUGCAAAUUUUUCAAUUAAUUUGCAU-AGUAAUU-UGUUAACUAGUUGUACAUAACAAACUUAUGAAAUUGGUAUU
.......((((((((..(((((....)))))...)).)))))).(((((((((........)))))))))-.......-.....(((((((...(((((.....))))).)))))))... ( -25.10)
>DroSim_CAF1 62513 113 + 1
UUAUGUAGAUAUGAUGUAAGCUUAUAAGCUUUUGACACGUGUCCAUGCAAAUUUUGCAAUUAAUUUGCAU-AGUAAUU-UGUUAACUAGUUGUAGUU-----ACAUUUGAAAUUAGUAUU
.......((((((.((((((((....)))))...)))))))))...(((((((.(((((.....))))).-...))))-)))..(((((((.(((..-----....))).)))))))... ( -23.80)
>DroYak_CAF1 64327 117 + 1
UUAUGUAGAUAUAGUGUAAGUUUACAUGCUUUGCACACGUGUCCAUGCAAAUUUUUCAAUUCAUUUGCAU-ACUAACU-UUGCAACUAGUUGUAAAUUACAAACACUUUUAGCU-GUUUA
.....(((....(((((.((((((((.((((((((...((....((((((((..........))))))))-....)).-.)))))..)))))))))))....))))).....))-).... ( -22.80)
>consensus
UUAUGUAGAUAUGGUGUAAGCUUAUAAGCUUUUGACACGUGUCCAUGCAAAUUUUUCAAUUAAUUUGCAU_AGUAAUU_UGUUAACUAGUUGUACAUAACAAACAUUUGAAAUU_GUAUU
.......((((((.(((((((......))))...))))))))).(((((((((........)))))))))..............(((((((...................)))))))... (-16.43 = -16.81 +   0.38)

alignment

secondary structure

dotplot

Window 9

Location	19,048,023 – 19,048,141
Length	118
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	82.77
Mean single sequence MFE	-24.02
Consensus MFE	-11.94
Energy contribution	-12.50
Covariance contribution	0.56
Combinations/Pair	1.05
Mean z-score	-3.52
Structure conservation index	0.50
SVM decision value	0.86
SVM RNA-class probability	0.867499
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19048023 118 - 27905053
AAUACAAAUUUCAA--CUUUGUUAUGUAGAACUAGUUAAAAAAAUGACUAAUGCAAAUUAACUGAAAAAUUUGCAUGGACACGUGUCAAAAGCUUAUAAGCUUACACCAUAUCUACAUAA
...(((((......--.)))))((((((((..((((((......))))))(((((((((........)))))))))......((((...(((((....)))))))))....)))))))). ( -26.60)
>DroSec_CAF1 60783 118 - 1
AAUACCAAUUUCAUAAGUUUGUUAUGUACAACUAGUUAACA-AAUUACU-AUGCAAAUUAAUUGAAAAAUUUGCAUGGACACGUGUCAAAAGCUUAUAAGCUUACACCAUAUCUACAUAA
...............(((((((((............)))))-)))).((-(((((((((........)))))))))))....((((...(((((....)))))))))............. ( -23.90)
>DroSim_CAF1 62513 113 - 1
AAUACUAAUUUCAAAUGU-----AACUACAACUAGUUAACA-AAUUACU-AUGCAAAUUAAUUGCAAAAUUUGCAUGGACACGUGUCAAAAGCUUAUAAGCUUACAUCAUAUCUACAUAA
.((((..........(((-----(((((....))))).)))-.....((-(((((((((........)))))))))))....))))...(((((....)))))................. ( -20.70)
>DroYak_CAF1 64327 117 - 1
UAAAC-AGCUAAAAGUGUUUGUAAUUUACAACUAGUUGCAA-AGUUAGU-AUGCAAAUGAAUUGAAAAAUUUGCAUGGACACGUGUGCAAAGCAUGUAAACUUACACUAUAUCUACAUAA
.....-.......(((((.(((((((.......)))))))(-((((..(-((((....(((((....)))))(((((....))))).....)))))..))))))))))............ ( -24.90)
>consensus
AAUAC_AAUUUCAAAUGUUUGUUAUGUACAACUAGUUAAAA_AAUUACU_AUGCAAAUUAAUUGAAAAAUUUGCAUGGACACGUGUCAAAAGCUUAUAAGCUUACACCAUAUCUACAUAA
..................................................(((((((((........)))))))))(((...((((...(((((....)))))))))....)))...... (-11.94 = -12.50 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:40:52 2006