Locus 7494

Sequence ID 2L_DroMel_CAF1
Location 20,797,296 – 20,797,441
Length 145
Max. P 0.948752
window12044 window12045 window12046

overview

Window 4

Location 20,797,296 – 20,797,411
Length 115
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 86.24
Mean single sequence MFE -35.18
Consensus MFE -29.30
Energy contribution -30.38
Covariance contribution 1.08
Combinations/Pair 1.03
Mean z-score -1.61
Structure conservation index 0.83
SVM decision value 0.38
SVM RNA-class probability 0.711767
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20797296 115 + 22407834
GCUUAGUUCGUGGCUGAAAUGCAUAUCUGGGUCAGCUGUUGUUUGGCUGUUUGUUCGACUUGCAUAAGCCAGUCCGGCGGCAUGAAAAACCCCCCAUUUCAGCCCCAAACCCAAA-----
.....(((.(.((((((((((.......(((((((((((((.((((((...(((.......)))..))))))..))))))).)))....)))..)))))))))).).))).....----- ( -39.10)
>DroSec_CAF1 20587 115 + 1
GUUUAGUUCGUGGCUGAAAUGCAUAUCUGGGUCAGCUGUUGUUUGGCCGUUUGUUCGACUUGCAUAAGCCAGUCCGGCGGCAUGGAAAACCCCCCAUUUCAGCCCCAAACCCAAA-----
.....(((.(.((((((((((.......(((((((((((((.(((((....(((.......)))...)))))..))))))).))....))))..)))))))))).).))).....----- ( -36.00)
>DroSim_CAF1 24143 109 + 1
GUUUAGUUCGUGGCUGAAAUGCAUAUCUGGGUCAGCUGUUGUUUGGCCGUUUGUUCGACUUGCAUAAGCCAGUCCGGCGGCAUGGAAAACCCCCCAUUUCAGCCCCA------AA-----
.........(.((((((((((.......(((((((((((((.(((((....(((.......)))...)))))..))))))).))....))))..)))))))))).).------..----- ( -35.00)
>DroEre_CAF1 24000 112 + 1
GUUCAGUUCGUGGCUGAAAUGCAUAUCUGGGUCAGCUGUUGUUUGGCCGUUUGUUCGGCUUGCAUAAGCCAGUCCGGCGGCAUG-AAAACCCCCCAUUUCAGCCCCAAACCCA-------
.....(((.(.((((((((((.......(((((((((..(((..(((((......))))).)))...(((.....)))))).))-)...)))..)))))))))).).)))...------- ( -37.00)
>DroYak_CAF1 21545 105 + 1
---CGCUUCGUAGCUAAAAUACAUAUCUGGGUCAGCUGUUGUUUG------------GCUUGCAUAAGCCAGUCCGGCGGCAUGGAAAACCCCCCAUUUUAGCCCCAAACCCAAACCCCC
---.(((....))).............(((((..(((((((.(((------------((((....)))))))..)))))))((((........))))...........)))))....... ( -28.80)
>consensus
GUUUAGUUCGUGGCUGAAAUGCAUAUCUGGGUCAGCUGUUGUUUGGCCGUUUGUUCGACUUGCAUAAGCCAGUCCGGCGGCAUGGAAAACCCCCCAUUUCAGCCCCAAACCCAAA_____
.........(.((((((((((.......(((((((((((((.(((((....(((.......)))...)))))..))))))).))....))))..)))))))))).).............. (-29.30 = -30.38 +   1.08)

alignment

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secondary structure

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dotplot

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Window 5

Location 20,797,296 – 20,797,411
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 86.24
Mean single sequence MFE -38.54
Consensus MFE -33.54
Energy contribution -34.36
Covariance contribution 0.82
Combinations/Pair 1.15
Mean z-score -1.95
Structure conservation index 0.87
SVM decision value 1.38
SVM RNA-class probability 0.948752
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20797296 115 - 22407834
-----UUUGGGUUUGGGGCUGAAAUGGGGGGUUUUUCAUGCCGCCGGACUGGCUUAUGCAAGUCGAACAAACAGCCAAACAACAGCUGACCCAGAUAUGCAUUUCAGCCACGAACUAAGC
-----....((((((.((((((((((((.(((.......))).)).((((.((....)).)))).......((((.........))))...........)))))))))).)))))).... ( -41.20)
>DroSec_CAF1 20587 115 - 1
-----UUUGGGUUUGGGGCUGAAAUGGGGGGUUUUCCAUGCCGCCGGACUGGCUUAUGCAAGUCGAACAAACGGCCAAACAACAGCUGACCCAGAUAUGCAUUUCAGCCACGAACUAAAC
-----....((((((.((((((((((((.(((.......))).)).((((.((....)).)))).......((((.........))))...........)))))))))).)))))).... ( -40.50)
>DroSim_CAF1 24143 109 - 1
-----UU------UGGGGCUGAAAUGGGGGGUUUUCCAUGCCGCCGGACUGGCUUAUGCAAGUCGAACAAACGGCCAAACAACAGCUGACCCAGAUAUGCAUUUCAGCCACGAACUAAAC
-----((------((.((((((((((((.(((.......))).)).((((.((....)).)))).......((((.........))))...........)))))))))).))))...... ( -35.60)
>DroEre_CAF1 24000 112 - 1
-------UGGGUUUGGGGCUGAAAUGGGGGGUUUU-CAUGCCGCCGGACUGGCUUAUGCAAGCCGAACAAACGGCCAAACAACAGCUGACCCAGAUAUGCAUUUCAGCCACGAACUGAAC
-------(.((((((.((((((((((((.(((...-...))).))((..(((((..((...((((......))))....))..)))))..)).......)))))))))).)))))).).. ( -43.00)
>DroYak_CAF1 21545 105 - 1
GGGGGUUUGGGUUUGGGGCUAAAAUGGGGGGUUUUCCAUGCCGCCGGACUGGCUUAUGCAAGC------------CAAACAACAGCUGACCCAGAUAUGUAUUUUAGCUACGAAGCG---
..(((((.(((((((((((....((((((....))))))))).)))))))(((((....))))------------).........).)))))..............(((....))).--- ( -32.40)
>consensus
_____UUUGGGUUUGGGGCUGAAAUGGGGGGUUUUCCAUGCCGCCGGACUGGCUUAUGCAAGUCGAACAAACGGCCAAACAACAGCUGACCCAGAUAUGCAUUUCAGCCACGAACUAAAC
.........((((((.((((((((((((.(((.......))).))((..(((((..((...((((......))))....))..)))))..)).......)))))))))).)))))).... (-33.54 = -34.36 +   0.82)

alignment

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secondary structure

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dotplot

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Window 6

Location 20,797,336 – 20,797,441
Length 105
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 82.97
Mean single sequence MFE -22.32
Consensus MFE -15.60
Energy contribution -16.08
Covariance contribution 0.48
Combinations/Pair 1.14
Mean z-score -1.74
Structure conservation index 0.70
SVM decision value 0.24
SVM RNA-class probability 0.648337
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20797336 105 + 22407834
GUUUGGCUGUUUGUUCGACUUGCAUAAGCCAGUCCGGCGGCAUGAAAAACCCCCCAUUUCAGCCCCAAACCCAAA---------------CUCAAACCCAACCCCGUUUUUCAACCCUGC
((((((..((((....((((.((....)).)))).((.(((.(((((.........)))))))))))))))))))---------------)............................. ( -23.70)
>DroSec_CAF1 20627 105 + 1
GUUUGGCCGUUUGUUCGACUUGCAUAAGCCAGUCCGGCGGCAUGGAAAACCCCCCAUUUCAGCCCCAAACCCAAA---------------CUCAAACCCAACCCCGUUUUUCAACCCUGC
((((((..(((((...((((.((....)).)))).(((((.((((........)))).)).))).))))))))))---------------)............................. ( -24.80)
>DroSim_CAF1 24183 99 + 1
GUUUGGCCGUUUGUUCGACUUGCAUAAGCCAGUCCGGCGGCAUGGAAAACCCCCCAUUUCAGCCCCA------AA---------------CUCAAACCCAACCCCGUUUUUCAACCCUGC
((((((..(((((...((((.((....)).)))).(((((.((((........)))).)).))).))------))---------------)))))))....................... ( -22.10)
>DroEre_CAF1 24040 97 + 1
GUUUGGCCGUUUGUUCGGCUUGCAUAAGCCAGUCCGGCGGCAUG-AAAACCCCCCAUUUCAGCCCCAAACCCA----------------------ACCCAACCCCGUAUUUCAACCCUGC
(((((((((..(....(((((....))))).)..))))(((.((-(((........)))))))).)))))...----------------------......................... ( -23.40)
>DroYak_CAF1 21582 108 + 1
GUUUG------------GCUUGCAUAAGCCAGUCCGGCGGCAUGGAAAACCCCCCAUUUUAGCCCCAAACCCAAACCCCCCAAACUCUAACCCAAACCCAACCCCGUAUUUCAACCCUGC
(((((------------(((.((....)).))...((.(((((((........))))....))))).............))))))................................... ( -17.60)
>consensus
GUUUGGCCGUUUGUUCGACUUGCAUAAGCCAGUCCGGCGGCAUGGAAAACCCCCCAUUUCAGCCCCAAACCCAAA_______________CUCAAACCCAACCCCGUUUUUCAACCCUGC
(((((...........((((.((....)).)))).((.(((.(((((.........))))))))))..........................)))))....................... (-15.60 = -16.08 +   0.48)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:38:12 2006