Locus 944

Sequence ID	3R_DroMel_CAF1
Location	3,124,665 – 3,124,945
Length	280
Max. P	0.999317

overview

Window 7

Location	3,124,665 – 3,124,785
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.33
Mean single sequence MFE	-28.30
Consensus MFE	-25.08
Energy contribution	-25.12
Covariance contribution	0.04
Combinations/Pair	1.04
Mean z-score	-1.46
Structure conservation index	0.89
SVM decision value	0.78
SVM RNA-class probability	0.848911
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3124665 120 - 27905053
CCAAACCAGCCCGGCAUCCCCGCUGAAUGGACUCGUUAGCGAGUCCUGGCGAAACCCAUUUAAAACUUUGCUACACCCGCAUGCUUCUUAAAGGAUAUUCGAAGUUAAUUAAUUUUUAAA
........(((((((......))))...(((((((....))))))).)))(((..((.(((((.....(((.......)))......)))))))...))).................... ( -26.90)
>DroSec_CAF1 356 120 - 1
CCAAACCAGCCCGGCAGCCCCGCUGAAUGGACUCGUUAGCGAGUCCUGGCGAAACCCAUUUAAAACUUUGCUACACCCGCAUGCUUCUUAAAGGAUAUUCGAAGUUAAUUAAUUUUUAAA
........(((((((......))))...(((((((....))))))).)))(((..((.(((((.....(((.......)))......)))))))...))).................... ( -26.90)
>DroSim_CAF1 726 120 - 1
CCAAACCAGCCCGGCAGCCCCGCUGAAUGGACUCGUUAGCGAGUCCUGGCGAAACCCAUUUAAAACUUUGCUACACCCGCAUGCUUCUUAAAGGAUAUUCCAAGUUAAUUAAUUUUUAAA
........(((((((......))))...(((((((....))))))).))).............((((((((.......)))...........((.....))))))).............. ( -26.70)
>DroEre_CAF1 455 119 - 1
CCA-CCCAGCCCGGCAUCCCCGCUGAAUGGACUCGUUAGCGAGUUCUGGCGAAACCCAUUUAAAACUUUGCUACACCCGCAUGGUUCUUAAAGGAUAUUCGAAGUUAAUUAAUUUUUAAA
...-....(((((((......))))...(((((((....))))))).)))(((..((.(((((((((.(((.......))).)))).)))))))...))).................... ( -28.40)
>DroYak_CAF1 581 119 - 1
CCA-CCCUGCCCGGAAUCCCCGCUGAAUGGACUCGUUAGCGAGUCCUGGCGAAAUCCAUUUAAAACUUUGCUACACCCGCAUGGUUCUUAAAGGAUAUUCGAAGUUAAUUAAUUUUUAAA
...-....((((((.....)))......(((((((....))))))).)))(((((((.(((((((((.(((.......))).)))).))))))))).))).................... ( -32.60)
>consensus
CCAAACCAGCCCGGCAUCCCCGCUGAAUGGACUCGUUAGCGAGUCCUGGCGAAACCCAUUUAAAACUUUGCUACACCCGCAUGCUUCUUAAAGGAUAUUCGAAGUUAAUUAAUUUUUAAA
........(((((((......))))...(((((((....))))))).)))(((..((.(((((.....(((.......)))......)))))))...))).................... (-25.08 = -25.12 +   0.04)

alignment

secondary structure

dotplot

Window 8

Location	3,124,705 – 3,124,825
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.33
Mean single sequence MFE	-36.02
Consensus MFE	-32.82
Energy contribution	-32.86
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.42
Structure conservation index	0.91
SVM decision value	0.93
SVM RNA-class probability	0.883482
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3124705 120 - 27905053
CGACGUGUCCAGGCAGAAAGGUUCACCUUGGCUCUCCACCCCAAACCAGCCCGGCAUCCCCGCUGAAUGGACUCGUUAGCGAGUCCUGGCGAAACCCAUUUAAAACUUUGCUACACCCGC
....((((...((((((..((((.....(((....))).....)))).(((((((......))))...(((((((....))))))).)))................)))))))))).... ( -35.20)
>DroSec_CAF1 396 120 - 1
CGACGUGUCCAGGCAGAAAGGUUCACCUUGGCUCUCCACCCCAAACCAGCCCGGCAGCCCCGCUGAAUGGACUCGUUAGCGAGUCCUGGCGAAACCCAUUUAAAACUUUGCUACACCCGC
....((((...((((((..((((.....(((....))).....)))).(((((((......))))...(((((((....))))))).)))................)))))))))).... ( -35.20)
>DroSim_CAF1 766 120 - 1
CGACGUGUCCAGGCAGAAAGGUUCACCUUGGCUCUCCACCCCAAACCAGCCCGGCAGCCCCGCUGAAUGGACUCGUUAGCGAGUCCUGGCGAAACCCAUUUAAAACUUUGCUACACCCGC
....((((...((((((..((((.....(((....))).....)))).(((((((......))))...(((((((....))))))).)))................)))))))))).... ( -35.20)
>DroEre_CAF1 495 119 - 1
CGACGUGUCCAGGCAGAAAGGUUCACCUUGGAUCGCCACCCCA-CCCAGCCCGGCAUCCCCGCUGAAUGGACUCGUUAGCGAGUUCUGGCGAAACCCAUUUAAAACUUUGCUACACCCGC
....((((...((((((((((....))))((.((((((.....-..((((..((....)).))))...(((((((....)))))))))))))...)).........)))))))))).... ( -37.10)
>DroYak_CAF1 621 119 - 1
CGACGUGUCCAGGCAGAAAGGUUCACCUUGGAUCUCCACCCCA-CCCUGCCCGGAAUCCCCGCUGAAUGGACUCGUUAGCGAGUCCUGGCGAAAUCCAUUUAAAACUUUGCUACACCCGC
....((((((.(((((.((((....))))((....))......-..))))).))).....((((....(((((((....))))))).))))......................))).... ( -37.40)
>consensus
CGACGUGUCCAGGCAGAAAGGUUCACCUUGGCUCUCCACCCCAAACCAGCCCGGCAUCCCCGCUGAAUGGACUCGUUAGCGAGUCCUGGCGAAACCCAUUUAAAACUUUGCUACACCCGC
....((((...((((((((((....))))((.((.(((........((((..((....)).))))...(((((((....)))))))))).))...)).........)))))))))).... (-32.82 = -32.86 +   0.04)

alignment

secondary structure

dotplot

Window 9

Location	3,124,825 – 3,124,945
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.95
Mean single sequence MFE	-28.24
Consensus MFE	-24.56
Energy contribution	-24.72
Covariance contribution	0.16
Combinations/Pair	1.04
Mean z-score	-2.64
Structure conservation index	0.87
SVM decision value	3.51
SVM RNA-class probability	0.999317
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3124825 120 + 27905053
UCGUCCUUGGAGACAAUCACUCUCCAUUCAAAACAAUAAUUUCGCUGCUCCUUGAAAAAAAGCGUUGGGAAACUCGCUGGAGCUCAAUGAAAAGCAAAAAGCAAGAGGAAAACAAAGAAA
...((((((((((.......)))))..............(((((..(((((((....)).((((..((....)))))))))))....))))).((.....))..)))))........... ( -29.10)
>DroSec_CAF1 516 119 + 1
UCGUCCUUGGAGACAAUCACUCUCCAUUCAAAACAAUAAUUUCGCUGCUCCUUGAAA-AAAGCGUUGGGAAACUCGCUGGAGCUCAAUGAAAAGCAAAAAGCAAGAGGAAAACAAAGAAA
...((((((((((.......)))))..............(((((..(((((((....-))((((..((....)))))))))))....))))).((.....))..)))))........... ( -29.10)
>DroSim_CAF1 886 120 + 1
UCGUCCUUGGAGACAAUCACUCUCCAUUCAAAACAAUAAUUUCGCUGCUCCUUGAAAAAAAGCGUUGGGAAACUCGCUGGAGCUCAAUGAAAAGCAAAAAGCAAGAGGAAAACAAAGAAA
...((((((((((.......)))))..............(((((..(((((((....)).((((..((....)))))))))))....))))).((.....))..)))))........... ( -29.10)
>DroEre_CAF1 614 112 + 1
UCGUCCUUGGAGACAAUCACUCUCCAUUCAAAACAAUAAUUUCGCUGCUCCUUGAAA-AAACUGCUGGGAAACUCGCUGGAGCUCAAUGAAAG-------GCAGGAGGAAAACAAAGAAA
((.((((((((((.......)))))).............(((((..(((((((....-))...((.((....)).)).)))))....))))).-------..)))).))........... ( -28.70)
>DroYak_CAF1 740 112 + 1
UCGUCCUUGGAGACAAUCACUCUCCAUUCAAAACAAUAAUUUCGCUGCUCCUUGAAA-AAACUGUUGGGAAACUCGCUGGAGCUCAAUGAAAA-------GCAAGAGGAAAACAAAGAAA
...((((((((((.......)))))..............(((((..(((((((....-))...((.((....)).)).)))))....))))).-------....)))))........... ( -25.20)
>consensus
UCGUCCUUGGAGACAAUCACUCUCCAUUCAAAACAAUAAUUUCGCUGCUCCUUGAAA_AAAGCGUUGGGAAACUCGCUGGAGCUCAAUGAAAAGCAAAAAGCAAGAGGAAAACAAAGAAA
...((((((((((.......)))))..............(((((..(((((.........((((..((....)))))))))))....)))))............)))))........... (-24.56 = -24.72 +   0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:56:13 2006