Locus 1045

Sequence ID 2L_DroMel_CAF1
Location 2,927,538 – 2,927,714
Length 176
Max. P 0.996193
window1681 window1682 window1683 window1684

overview

Window 1

Location 2,927,538 – 2,927,648
Length 110
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 81.43
Mean single sequence MFE -11.81
Consensus MFE -11.25
Energy contribution -11.25
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score 0.34
Structure conservation index 0.95
SVM decision value 0.20
SVM RNA-class probability 0.630380
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2927538 110 + 22407834
UGCGCCAGCACUACUCAAGCAAUUCAAUACCAACUCAAUAUUGGCUAACCCAAAAAAUGAAAAAA----------AAGAAAAAGAAUAACAGAAUGAGGGGCCACAAAAAGUUGCAGUUU
(((....)))........((((((......(..((((...((((.....))))....(....)..----------...................))))..)........))))))..... ( -11.94)
>DroSim_CAF1 46929 103 + 1
UGCGCCAGCACUACUCAAGCAAUUCAAUACCAACUCAAUAUUGGCUAACCCAAAA-------AAA----------AAGCAAAAUAAUAACAGAAUGAGGGGCCACAAAAAGUUGCAGUUU
(((....)))....................(((((......((((...(((....-------...----------......................))))))).....)))))...... ( -11.65)
>DroEre_CAF1 46874 108 + 1
UGCGCCAGCAGUACUCAAGCAAUUCAAUACCAACUCAAUAUUGGCUAACCCAAAAAAUUAAAAAAAUACGAAUAAAA------------CAGGAUGAGGGGCCACAAAAAGUUGCAGUUU
(((....)))........((((((......(..((((...((((.....))))...............(........------------..)..))))..)........))))))..... ( -11.84)
>consensus
UGCGCCAGCACUACUCAAGCAAUUCAAUACCAACUCAAUAUUGGCUAACCCAAAAAAU_AAAAAA__________AAG_AAAA_AAUAACAGAAUGAGGGGCCACAAAAAGUUGCAGUUU
(((....)))....................(((((......((((...(((..............................................))))))).....)))))...... (-11.25 = -11.25 +   0.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 2,927,578 – 2,927,688
Length 110
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 81.43
Mean single sequence MFE -22.93
Consensus MFE -22.80
Energy contribution -22.80
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.40
Structure conservation index 0.99
SVM decision value 2.66
SVM RNA-class probability 0.996193
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2927578 110 + 22407834
UUGGCUAACCCAAAAAAUGAAAAAA----------AAGAAAAAGAAUAACAGAAUGAGGGGCCACAAAAAGUUGCAGUUUUCCAGUGACUUUUGGCCAAGUUGAGUGCGGCACAUCAACA
((((((..(((......((......----------..............))......)))......((((((..(.........)..))))))))))))((((((((...))).))))). ( -22.85)
>DroSim_CAF1 46969 103 + 1
UUGGCUAACCCAAAA-------AAA----------AAGCAAAAUAAUAACAGAAUGAGGGGCCACAAAAAGUUGCAGUUUUCCAGUGACUUUUGGCCAAGUUGAGUGCGGCACAUCAACA
((((((..(((....-------...----------......................)))......((((((..(.........)..))))))))))))((((((((...))).))))). ( -23.05)
>DroEre_CAF1 46914 108 + 1
UUGGCUAACCCAAAAAAUUAAAAAAAUACGAAUAAAA------------CAGGAUGAGGGGCCACAAAAAGUUGCAGUUUUCCAGUGACUUUUGGCCAAGUUGAGUGCGGCACGUCAACA
((((((..(((..........................------------........)))......((((((..(.........)..))))))))))))((((((((...))).))))). ( -22.88)
>consensus
UUGGCUAACCCAAAAAAU_AAAAAA__________AAG_AAAA_AAUAACAGAAUGAGGGGCCACAAAAAGUUGCAGUUUUCCAGUGACUUUUGGCCAAGUUGAGUGCGGCACAUCAACA
((((.....))))..............................................(((((...(((((..(.........)..))))))))))..((((((((...))).))))). (-22.80 = -22.80 +   0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 2,927,578 – 2,927,688
Length 110
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 81.43
Mean single sequence MFE -18.57
Consensus MFE -18.15
Energy contribution -18.15
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score 0.20
Structure conservation index 0.98
SVM decision value 0.78
SVM RNA-class probability 0.849062
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2927578 110 - 22407834
UGUUGAUGUGCCGCACUCAACUUGGCCAAAAGUCACUGGAAAACUGCAACUUUUUGUGGCCCCUCAUUCUGUUAUUCUUUUUCUU----------UUUUUUCAUUUUUUGGGUUAGCCAA
.(((((.(((...)))))))).((((.....(((((.(((((........))))))))))(((......................----------..............)))...)))). ( -18.42)
>DroSim_CAF1 46969 103 - 1
UGUUGAUGUGCCGCACUCAACUUGGCCAAAAGUCACUGGAAAACUGCAACUUUUUGUGGCCCCUCAUUCUGUUAUUAUUUUGCUU----------UUU-------UUUUGGGUUAGCCAA
.(((((.(((...)))))))).((((.((......(..(((((..((((..(...(((((..........))))).)..))))..----------.))-------)))..).)).)))). ( -18.80)
>DroEre_CAF1 46914 108 - 1
UGUUGACGUGCCGCACUCAACUUGGCCAAAAGUCACUGGAAAACUGCAACUUUUUGUGGCCCCUCAUCCUG------------UUUUAUUCGUAUUUUUUUAAUUUUUUGGGUUAGCCAA
.(((((.(((...)))))))).((((.....(((((.(((((........))))))))))(((........------------..........................)))...)))). ( -18.48)
>consensus
UGUUGAUGUGCCGCACUCAACUUGGCCAAAAGUCACUGGAAAACUGCAACUUUUUGUGGCCCCUCAUUCUGUUAUU_UUUU_CUU__________UUUUUU_AUUUUUUGGGUUAGCCAA
.(((((.(((...)))))))).((((.....(((((.(((((........))))))))))(((..............................................)))...)))). (-18.15 = -18.15 +   0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 2,927,608 – 2,927,714
Length 106
Sequences 3
Columns 114
Reading direction forward
Mean pairwise identity 82.04
Mean single sequence MFE -27.83
Consensus MFE -25.14
Energy contribution -24.70
Covariance contribution -0.44
Combinations/Pair 1.08
Mean z-score -1.09
Structure conservation index 0.90
SVM decision value 0.53
SVM RNA-class probability 0.772135
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2927608 106 + 22407834
AAAGAAUAACAGAAUGAGGGGCCACAAAAAGUUGCAGUUUUCCAGUGACUUUUGGCCAAGUUGAGUGCGGCACAUCAACAGGAUUUCAUUUCGCUCUCUC--------UUUCGC
(((((....(..((((((((((((...(((((..(.........)..))))))))))..((((((((...))).)))))....)))))))..).....))--------)))... ( -27.40)
>DroSim_CAF1 46992 98 + 1
AAAUAAUAACAGAAUGAGGGGCCACAAAAAGUUGCAGUUUUCCAGUGACUUUUGGCCAAGUUGAGUGCGGCACAUCAACAGGAUUUCAUCUCUCUCU----------------C
..........(((..(((((((((...(((((..(.........)..))))))))))..((((((((...))).))))).........))))..)))----------------. ( -26.50)
>DroEre_CAF1 46951 105 + 1
---------CAGGAUGAGGGGCCACAAAAAGUUGCAGUUUUCCAGUGACUUUUGGCCAAGUUGAGUGCGGCACGUCAACAGGAUUUCAUUUCGCUCUCUCUCCCUCCCUCUCGC
---------.(((..(((((((((...(((((..(.........)..)))))))))).....(((.((((...(((.....)))......)))).)))....)))))))..... ( -29.60)
>consensus
AAA_AAUAACAGAAUGAGGGGCCACAAAAAGUUGCAGUUUUCCAGUGACUUUUGGCCAAGUUGAGUGCGGCACAUCAACAGGAUUUCAUUUCGCUCUCUC________U_UCGC
..........(((..(((((((((...(((((..(.........)..))))))))))..((((((((...))).))))).........))))..)))................. (-25.14 = -24.70 +  -0.44)

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 09:51:58 2006