Locus 5235

Sequence ID 2L_DroMel_CAF1
Location 14,783,699 – 14,783,867
Length 168
Max. P 0.864238
window8333 window8334

overview

Window 3

Location 14,783,699 – 14,783,792
Length 93
Sequences 4
Columns 102
Reading direction forward
Mean pairwise identity 87.74
Mean single sequence MFE -13.95
Consensus MFE -11.40
Energy contribution -11.65
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.63
Structure conservation index 0.82
SVM decision value 0.40
SVM RNA-class probability 0.721527
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14783699 93 + 22407834
CACACACAUACA---------CAUACACUCGCACAGGCACAUCCUUGUGCAUUCAUCAUCAGCCACAUCAUCAUUUAUACAUUGUAUUUGUCUGCCGUUGUU
......((.(((---------.(((((...(((((((......)))))))...........(......).............))))).))).))........ ( -13.00)
>DroSec_CAF1 30058 87 + 1
CACACACA---------------CACACUCGCACAGGCACAUCCUUGUGCAUUCAUCAUCAGCCACAUCAUCAUUUAUACAUUGUAUUUGUCUGACGUUGUU
.....(((---------------.((....(((((((......)))))))........((((.((.((((............)).)).)).)))).))))). ( -13.80)
>DroSim_CAF1 28091 87 + 1
CACACACA---------------CACACUCGCACAGGCACAUCCUUGUGCAUUCAUCAUCAGCCACAUCAUCAUUUAUACAUUGUAUUUGUCUGCCGUUGUU
........---------------.......(((((((......))))))).........((((..((....((..(((.....)))..))..))..)))).. ( -12.60)
>DroEre_CAF1 23215 102 + 1
CACACACACACACACAACACCCAUACGCUGGCACUGGCACAUCCUUGUGCAUUCAUCAUCAGCCACAUCAUCAUUUAUACAUUGUAUUUGUCUGCUGUUGUU
.............((((((..((.(((((((.....(((((....)))))........))))).(((...............)))....)).)).)))))). ( -16.38)
>consensus
CACACACA_______________CACACUCGCACAGGCACAUCCUUGUGCAUUCAUCAUCAGCCACAUCAUCAUUUAUACAUUGUAUUUGUCUGCCGUUGUU
..............................(((((((......))))))).........((((..((....((..(((.....)))..))..))..)))).. (-11.40 = -11.65 +   0.25)

alignment

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secondary structure

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dotplot

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Window 4

Location 14,783,763 – 14,783,867
Length 104
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 88.62
Mean single sequence MFE -22.65
Consensus MFE -19.14
Energy contribution -19.37
Covariance contribution 0.22
Combinations/Pair 1.05
Mean z-score -2.18
Structure conservation index 0.85
SVM decision value 0.84
SVM RNA-class probability 0.864238
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14783763 104 - 22407834
GAUGCAC-UGCCCUAAAUUGGAAACAACAAAUGUCAGCAGUUUUAUGUACUGCGGACC---ACUGGCAGCAGCAGCAAC------AACA------ACGGCAGACAAAUACAAUGUAUAAA
..(((.(-((((.....(((....))).....(((.(((((.......))))).))).---...)))))..)))((...------....------...)).................... ( -24.10)
>DroSec_CAF1 30116 107 - 1
GAUGCAC-UGCCCUAAAUUGGAAACAACAAAUGUCAGCAGUUUUAUGUACUGCAGACCACCACCGGCAGCAGCAACAAC------AACA------ACGUCAGACAAAUACAAUGUAUAAA
..(((.(-((((.....(((....))).....(((.(((((.......))))).))).......)))))..))).....------....------......................... ( -23.50)
>DroSim_CAF1 28149 107 - 1
GAUGCAC-UGCCCUAAAUUGGAAACAACAAAUGUCAGCAGUUUUAUGUACUGCAGACCACCACCGGCAGCAGCAACAAC------AACA------ACGGCAGACAAAUACAAUGUAUAAA
..(((.(-((((.....(((....))).....(((.(((((.......))))).))).......)))))..))).....------....------......................... ( -23.50)
>DroEre_CAF1 23288 104 - 1
GAUGCAC-UGCCCCAAAUUGGAAACAACAAAUGUCAGCAGUUUUAUGUACUGCAGACC---ACCGGCAGCAGCACCAAC------AACA------ACAGCAGACAAAUACAAUGUAUAAA
(.(((.(-((((.....(((....))).....(((.(((((.......))))).))).---...)))))..))).)...------....------......................... ( -23.50)
>DroYak_CAF1 27299 104 - 1
GAUGCAC-UGCCCUAAAUUGGAAACAACAAAUGUCAGCAGUUUUAUGUACUGCAGACC---ACCGGCAGCAGCAACAAC------AACA------GCAGCAGACAAAUACAAUGUAUAAA
..(((.(-((((.....(((....))).....(((.(((((.......))))).))).---...)))))..((......------....------)).)))................... ( -24.10)
>DroAna_CAF1 20082 117 - 1
GCCGCCCGUGUCCCAAAUUGGAAACAACAAAUGUCAGCAGUUUUAUGUACUGCAGACC---GUCAACAGAAACAACAACAGCAACAACAAAAGCUACGCCAGACAAAUACAAUGUAUAAA
.......((((......(((....)))....((((.(((((.......))))).....---..................(((..........)))......)))).)))).......... ( -17.20)
>consensus
GAUGCAC_UGCCCUAAAUUGGAAACAACAAAUGUCAGCAGUUUUAUGUACUGCAGACC___ACCGGCAGCAGCAACAAC______AACA______ACGGCAGACAAAUACAAUGUAUAAA
(.(((...((((.....(((....))).....(((.(((((.......))))).))).......))))...))).)............................................ (-19.14 = -19.37 +   0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:39:21 2006