Locus 5537

Sequence ID 2R_DroMel_CAF1
Location 17,686,770 – 17,686,860
Length 90
Max. P 0.855567
window8885 window8886

overview

Window 5

Location 17,686,770 – 17,686,860
Length 90
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 80.16
Mean single sequence MFE -36.60
Consensus MFE -20.23
Energy contribution -24.11
Covariance contribution 3.88
Combinations/Pair 1.12
Mean z-score -1.93
Structure conservation index 0.55
SVM decision value 0.22
SVM RNA-class probability 0.637712
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17686770 90 + 20766785
GCUCUGUG---------------------GCUCAUUCUUUGGCGACGACGAGGAGCAUAAUGACUCGGCUAAAGAUUCAGCACCAUUGCCCACGACUUCGCCAGUGCCUCA---
.....(.(---------------------((.......(((((((.(.((.((.(((...(((.((.......)).))).......))))).)).).))))))).))).).--- ( -24.10)
>DroSec_CAF1 3844 111 + 1
GCUCUGGGAGAAGACGUUGGGGCUAUGGCGCUCAUUCUUUAACGACGACAAGGAGGAUAAUGACUCGGCUAUAGAUUCAGCACCAUUGCCCACGACUUCGCCAGUGCCUCA---
((.((((..((((.(((..((((.((((.(((...(((.((.(..(.....)(((........))).).)).)))...))).)))).))))))).)))).)))).))....--- ( -37.40)
>DroSim_CAF1 871 114 + 1
GCUCUGGGAGAAGACGUUGGGGCUGUGGUGCUCAUUCUUUAACGACGACGAGGAGGAUAAUGACUCGGCUAAAGAUUCAGCACCAUUGCCCACGACUUCGCCAGUGCCUCAGCC
((.((((..((((.(((..((((.((((((((...((((((..(....((((..(.....)..)))).)))))))...)))))))).))))))).)))).)))).))....... ( -46.20)
>DroEre_CAF1 4604 108 + 1
GCUCUGGGAGAAGACGUUGGAUUUCUGGUGCUCAUUCUUUGGCGACCACG---AGCAUAAUGGCUCGGCCAAAGAUUCAGCACCAUCACUCACGACGUCGCCGAUACCUCA---
......((....(((((((((....(((((((...((((((((.....((---(((......)))))))))))))...)))))))....)).))))))).)).........--- ( -43.90)
>DroYak_CAF1 3810 108 + 1
GCUCUGGGAGAAGACGUUGGAUUUCUGGUGCUCAUUCUUUGGCGACCACG---AGCAUAAUUACUCGACUAAAGAUUCAGCACCAUCGCUCACGACUUCGCCAAUACCUCA---
......((.((((.(((.((.....(((((((...(((((((......((---((........)))).)))))))...)))))))...)).))).)))).)).........--- ( -31.40)
>consensus
GCUCUGGGAGAAGACGUUGGAGCUCUGGUGCUCAUUCUUUGGCGACGACGAGGAGCAUAAUGACUCGGCUAAAGAUUCAGCACCAUUGCCCACGACUUCGCCAGUGCCUCA___
((.((((..((((.(((.((.....(((((((...((((((((((...................))).)))))))...)))))))...)).))).)))).)))).))....... (-20.23 = -24.11 +   3.88)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,686,770 – 17,686,860
Length 90
Sequences 5
Columns 114
Reading direction reverse
Mean pairwise identity 80.16
Mean single sequence MFE -38.82
Consensus MFE -23.31
Energy contribution -25.79
Covariance contribution 2.48
Combinations/Pair 1.18
Mean z-score -2.11
Structure conservation index 0.60
SVM decision value 0.81
SVM RNA-class probability 0.855567
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17686770 90 - 20766785
---UGAGGCACUGGCGAAGUCGUGGGCAAUGGUGCUGAAUCUUUAGCCGAGUCAUUAUGCUCCUCGUCGUCGCCAAAGAAUGAGC---------------------CACAGAGC
---((.(((.(((((((.(.((.(((((((((.(((((....)))))....))))..))).)).)).).))))))......).))---------------------).)).... ( -27.00)
>DroSec_CAF1 3844 111 - 1
---UGAGGCACUGGCGAAGUCGUGGGCAAUGGUGCUGAAUCUAUAGCCGAGUCAUUAUCCUCCUUGUCGUCGUUAAAGAAUGAGCGCCAUAGCCCCAACGUCUUCUCCCAGAGC
---....((.((((.((((.(((((((.((((((((.(.(((.((((.(((.((..........)).).)))))).))).).)))))))).))))..))).))))..)))).)) ( -43.40)
>DroSim_CAF1 871 114 - 1
GGCUGAGGCACUGGCGAAGUCGUGGGCAAUGGUGCUGAAUCUUUAGCCGAGUCAUUAUCCUCCUCGUCGUCGUUAAAGAAUGAGCACCACAGCCCCAACGUCUUCUCCCAGAGC
.......((.((((.((((.(((((((..(((((((.(.((((((((((((...........)))).....)))))))).).)))))))..))))..))).))))..)))).)) ( -46.10)
>DroEre_CAF1 4604 108 - 1
---UGAGGUAUCGGCGACGUCGUGAGUGAUGGUGCUGAAUCUUUGGCCGAGCCAUUAUGCU---CGUGGUCGCCAAAGAAUGAGCACCAGAAAUCCAACGUCUUCUCCCAGAGC
---((.((....((.(((((.(.((....(((((((.(.(((((((((((((......)))---)).....)))))))).).)))))))....))).))))).)).)))).... ( -42.20)
>DroYak_CAF1 3810 108 - 1
---UGAGGUAUUGGCGAAGUCGUGAGCGAUGGUGCUGAAUCUUUAGUCGAGUAAUUAUGCU---CGUGGUCGCCAAAGAAUGAGCACCAGAAAUCCAACGUCUUCUCCCAGAGC
---....((.((((.((((.(((((....(((((((.(.(((((.((((((((....))))---)).....)).))))).).)))))))....))..))).))))..)))).)) ( -35.40)
>consensus
___UGAGGCACUGGCGAAGUCGUGGGCAAUGGUGCUGAAUCUUUAGCCGAGUCAUUAUGCUCCUCGUCGUCGCCAAAGAAUGAGCACCAGAAACCCAACGUCUUCUCCCAGAGC
.......((.((((.((((.(((((....(((((((.(.(((((((.(((...................)))))))))).).)))))))....))..))).))))..)))).)) (-23.31 = -25.79 +   2.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:48:14 2006