Locus 6593

Sequence ID	3R_DroMel_CAF1
Location	17,347,730 – 17,347,966
Length	236
Max. P	0.966737

overview

Window 3

Location	17,347,730 – 17,347,825
Length	95
Sequences	3
Columns	96
Reading direction	reverse
Mean pairwise identity	81.88
Mean single sequence MFE	-23.83
Consensus MFE	-17.00
Energy contribution	-19.56
Covariance contribution	2.56
Combinations/Pair	1.07
Mean z-score	-1.76
Structure conservation index	0.71
SVM decision value	0.28
SVM RNA-class probability	0.665915
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17347730 95 - 27905053
UAAAGCGACUUGCUGCGAGACCCCUUCAUAAUCUUAUCUUGCAGUCAAGUUUAUCUGGUUC-UCCCAAAUGAGAUAGCGCCGGAAACUGUCUGGAA
....((((((((((((((((................)))))))).))))))(((((.(((.-.....))).))))))).(((((.....))))).. ( -28.69)
>DroSim_CAF1 5635 95 - 1
UAAAGCGACUUGCUGCGAGACCCCUUUCUAAUCUUAUCUUGCAGCCAAGUUUAUCUGGUUC-UCCCAAAUGAGAUAACGCCGGAAACUGUCUGGAA
....((((((((((((((((................)))))))).)))))((((((.(((.-.....))).)))))))))((((.....))))... ( -26.29)
>DroYak_CAF1 7197 83 - 1
UAAAGCGACCUG-------------UUCUAAUCUUAUCUACCAGCCAAGUUUGUCUGGUUGUUCCCAAACGAGAUAACACCGGAUACUGUCUGGAA
............-------------...............((((...(((..(((((((.(((..(......)..)))))))))))))..)))).. ( -16.50)
>consensus
UAAAGCGACUUGCUGCGAGACCCCUUUCUAAUCUUAUCUUGCAGCCAAGUUUAUCUGGUUC_UCCCAAAUGAGAUAACGCCGGAAACUGUCUGGAA
......((((((((((((((................)))))))).))))))(((((.(((.......))).)))))...(((((.....))))).. (-17.00 = -19.56 +   2.56)

alignment

secondary structure

dotplot

Window 4

Location	17,347,825 – 17,347,926
Length	101
Sequences	3
Columns	101
Reading direction	forward
Mean pairwise identity	89.44
Mean single sequence MFE	-30.03
Consensus MFE	-26.94
Energy contribution	-27.83
Covariance contribution	0.89
Combinations/Pair	1.03
Mean z-score	-2.77
Structure conservation index	0.90
SVM decision value	1.60
SVM RNA-class probability	0.966737
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17347825 101 + 27905053
AAAUGCAUGAGCAACUUUUAAACGUGCCACAUAUAAAAGAAUUCCAAGGAUGCACGUAUCCGGCACGUAAAGUGCAAUUGCAUAUUGCUGUUUUUAGCUGC
..(((((...(((.((((...(((((((..........(.....)..(((((....)))))))))))))))))))...)))))...((((....))))... ( -30.40)
>DroSim_CAF1 5730 101 + 1
AAGUGCAUGAGCAACUUUUAAACGUGCCGCACAUAAAAGAAUCCCAAGGAUGCACGUAUCCGGCACGUAAAGUGCAAUUGCACAUUGCUGUUUUUAGCUGC
..(((((...(((.((((...((((((((...(((.....((((...)))).....))).)))))))))))))))...)))))...((((....))))... ( -32.90)
>DroYak_CAF1 7280 101 + 1
AUGUGCUUGUACAACUUUUAAACGUGCCACAUUGAAAAGAAUCCCAAGGAUGCACGUAGCCGGCACGCAAAGUGAUAUUGCACAUUGCUGCUUUUAGCUGC
((((((..(((..(((((....((((((............((((...))))((.....)).)))))).)))))..))).)))))).((.((.....)).)) ( -26.80)
>consensus
AAGUGCAUGAGCAACUUUUAAACGUGCCACAUAUAAAAGAAUCCCAAGGAUGCACGUAUCCGGCACGUAAAGUGCAAUUGCACAUUGCUGUUUUUAGCUGC
..(((((...(((.((((...(((((((..........(.....)..(((((....)))))))))))))))))))...)))))...((((....))))... (-26.94 = -27.83 +   0.89)

alignment

secondary structure

dotplot

Window 5

Location	17,347,825 – 17,347,926
Length	101
Sequences	3
Columns	101
Reading direction	reverse
Mean pairwise identity	89.44
Mean single sequence MFE	-30.23
Consensus MFE	-25.27
Energy contribution	-24.83
Covariance contribution	-0.44
Combinations/Pair	1.14
Mean z-score	-2.46
Structure conservation index	0.84
SVM decision value	0.80
SVM RNA-class probability	0.854578
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17347825 101 - 27905053
GCAGCUAAAAACAGCAAUAUGCAAUUGCACUUUACGUGCCGGAUACGUGCAUCCUUGGAAUUCUUUUAUAUGUGGCACGUUUAAAAGUUGCUCAUGCAUUU
...(((......)))...(((((...((((((((((((((((((......))))..((....)).........)))))))...)))).)))...))))).. ( -26.70)
>DroSim_CAF1 5730 101 - 1
GCAGCUAAAAACAGCAAUGUGCAAUUGCACUUUACGUGCCGGAUACGUGCAUCCUUGGGAUUCUUUUAUGUGCGGCACGUUUAAAAGUUGCUCAUGCACUU
...(((......)))...(((((...(((((((((((((((.(((...(.((((...)))).).....))).))))))))...)))).)))...))))).. ( -33.00)
>DroYak_CAF1 7280 101 - 1
GCAGCUAAAAGCAGCAAUGUGCAAUAUCACUUUGCGUGCCGGCUACGUGCAUCCUUGGGAUUCUUUUCAAUGUGGCACGUUUAAAAGUUGUACAAGCACAU
((.((.....)).)).((((((..(((.(((((((((((((((.....))....(((..(....)..)))..))))))))...))))).)))...)))))) ( -31.00)
>consensus
GCAGCUAAAAACAGCAAUGUGCAAUUGCACUUUACGUGCCGGAUACGUGCAUCCUUGGGAUUCUUUUAUAUGUGGCACGUUUAAAAGUUGCUCAUGCACUU
...(((......)))...(((((...(((((((((((((((....)..((((....((....)).....)))))))))))...)))).)))...))))).. (-25.27 = -24.83 +  -0.44)

alignment

secondary structure

dotplot

Window 6

Location	17,347,846 – 17,347,966
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	90.83
Mean single sequence MFE	-42.27
Consensus MFE	-39.04
Energy contribution	-39.50
Covariance contribution	0.46
Combinations/Pair	1.16
Mean z-score	-2.15
Structure conservation index	0.92
SVM decision value	1.07
SVM RNA-class probability	0.910404
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17347846 120 + 27905053
ACGUGCCACAUAUAAAAGAAUUCCAAGGAUGCACGUAUCCGGCACGUAAAGUGCAAUUGCAUAUUGCUGUUUUUAGCUGCAGCAGUGGGCUGUGUGGGUGCCUUUCAGAUUCGCUGCACA
(((((((..........(.....)..(((((....))))))))))))...(((((...((.(((((((((........))))))))).))...((((((.........))))))))))). ( -40.80)
>DroSim_CAF1 5751 120 + 1
ACGUGCCGCACAUAAAAGAAUCCCAAGGAUGCACGUAUCCGGCACGUAAAGUGCAAUUGCACAUUGCUGUUUUUAGCUGCAGCAGUGGGCGGUGUGGGUGGCUUUCAGAUUCGCUGCACA
..((((.((..((.((((...((((.(((((....))))).((((.....)))).(((((.(((((((((........))))))))).))))).))))...))))...))..)).)))). ( -46.20)
>DroYak_CAF1 7301 120 + 1
ACGUGCCACAUUGAAAAGAAUCCCAAGGAUGCACGUAGCCGGCACGCAAAGUGAUAUUGCACAUUGCUGCUUUUAGCUGCAGUGGUGGGCAAUGUGGGUGGCUUUCAGAUUCGCUGCACA
..((((..(..(....)(((((..((((((.(((((.(((.((..((((.......)))).((((((.((.....)).)))))))).))).))))).))..))))..))))))..)))). ( -39.80)
>consensus
ACGUGCCACAUAUAAAAGAAUCCCAAGGAUGCACGUAUCCGGCACGUAAAGUGCAAUUGCACAUUGCUGUUUUUAGCUGCAGCAGUGGGCAGUGUGGGUGGCUUUCAGAUUCGCUGCACA
(((((((..........(.....)..(((((....))))))))))))...((((((((((.(((((((((........))))))))).)))))((((((.........))))))))))). (-39.04 = -39.50 +   0.46)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:25:24 2006