Locus 6847

Sequence ID 3L_DroMel_CAF1
Location 18,363,924 – 18,364,092
Length 168
Max. P 0.903971
window11104 window11105 window11106

overview

Window 4

Location 18,363,924 – 18,364,020
Length 96
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 74.34
Mean single sequence MFE -18.94
Consensus MFE -8.82
Energy contribution -9.49
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.79
Structure conservation index 0.47
SVM decision value 0.10
SVM RNA-class probability 0.584157
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18363924 96 - 23771897
ACUGUACUUCUCGCCGCACACAGUUACAACAAAGGCG------------CUGCCA--C--CAACCUGGCAACAACAACACAACCUCAUAC-AA-----AAACACGCUUGGCAACAGGC
..((((.....((((..................))))------------.(((((--.--.....))))).................)))-).-----......(((((....))))) ( -20.27)
>DroVir_CAF1 84260 106 - 1
ACUGUACUUCUCGCCGCAUACAGUUACAACAAAGGCG------------CGACGAGAACAUAACCUGACAACACACACACACACGCACACAUACUGAGACACCCACUUGGCAACAGGC
.((((..((((((((((.....((....))....)))------------.).))))))...................................(..((.......))..)..)))).. ( -16.10)
>DroSec_CAF1 632 95 - 1
ACUGUACUUCUCGCCGCACACAGUUACAACAAAGGCG------------CUGCCA--A--CAACCUGGCAACAACAACACAACCACAUA--AA-----AAACACGCUUGGCAACAGGC
..(((......((((..................))))------------.(((((--.--.....))))))))................--..-----......(((((....))))) ( -19.47)
>DroEre_CAF1 8194 95 - 1
ACUGUACUUCUCGCCGCACACAGUUACAACAAAGGCG------------CUGCCA--A--CAACCUGGCAACAACAACACAAUCUCAUA--AA-----AAACGCGCUUGGCAACAGGC
..(((......((((..................))))------------.(((((--.--.....))))))))................--..-----......(((((....))))) ( -19.47)
>DroMoj_CAF1 116030 102 - 1
ACUGUACUUCUCGCCGCAUACAGUUACAACAAAGGCG------------CGACGGCGACAG----CGACGCCACACACACACACACAUAUCCAACGAGAGACACGCUUGGCAACAGGC
...((..((((((.........((....))...((((------------((..(....)..----)).))))......................))))))..))(((((....))))) ( -24.90)
>DroAna_CAF1 693 112 - 1
ACUGUACUUCUCACCACAUACAGUUACAACAAAGGCAGCAGCAGCAACCCAGCCA--A--CAACCUGACAACAACAAUUCCCCGUAGUA--UAAAAAAACACACACUUGGCAACAGGC
((((((............))))))(((.((...((..((....))..))(((...--.--....)))................)).)))--..............((((....)))). ( -13.40)
>consensus
ACUGUACUUCUCGCCGCACACAGUUACAACAAAGGCG____________CUGCCA__A__CAACCUGACAACAACAACACAACCUCAUA__AA_____AAACACGCUUGGCAACAGGC
...........((((..................))))...................................................................(((((....))))) ( -8.82 =  -9.49 +   0.67)

alignment

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secondary structure

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dotplot

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Window 5

Location 18,363,956 – 18,364,060
Length 104
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.91
Mean single sequence MFE -34.00
Consensus MFE -20.72
Energy contribution -20.06
Covariance contribution -0.66
Combinations/Pair 1.26
Mean z-score -2.35
Structure conservation index 0.61
SVM decision value 0.15
SVM RNA-class probability 0.605861
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18363956 104 + 23771897
GUGUUGUUGUUGCCAGGUUG--G--UGGCAG------------CGCCUUUGUUGUAACUGUGUGCGGCGAGAAGUACAGUUAGCAUAUUAAUUGUAUUAAAUCGUCGGGGCAUGACAAUC
.(((((((((..((.....)--)--..))))------------)(((((....(((......)))(((((..(((((((((((....)))))))))))...))))))))))..))))... ( -36.50)
>DroVir_CAF1 84298 108 + 1
GUGUGUGUGUUGUCAGGUUAUGUUCUCGUCG------------CGCCUUUGUUGUAACUGUAUGCGGCGAGAAGUACAGUUAGCAUAUUAAUUGUAUUAAAUCGUCGUUGCAUGACAAAC
.........((((((.((.(((.((((((((------------((.....((....))....))))))))))(((((((((((....))))))))))).......))).)).)))))).. ( -31.20)
>DroSec_CAF1 663 104 + 1
GUGUUGUUGUUGCCAGGUUG--U--UGGCAG------------CGCCUUUGUUGUAACUGUGUGCGGCGAGAAGUACAGUUAGCAUAUUAAUUGUAUUAAAUCGUCGGUGCAUGACAAUC
..(((((..(((((((....--)--)))))(------------((((......(((......)))(((((..(((((((((((....)))))))))))...)))))))))))..))))). ( -35.50)
>DroSim_CAF1 662 104 + 1
GUGUUGUUGUUGCCAGGUUG--U--UGGCAG------------CGCCUUUGUUGUAACUGUGUGUGGCGAGAAGUACAGUUAGCAUAUUAAUUGUAUUAAAUCGUCGGUGCAUGACAAUC
..(((((..(((((((....--)--)))))(------------((((.........((.....))(((((..(((((((((((....)))))))))))...)))))))))))..))))). ( -34.20)
>DroMoj_CAF1 116068 104 + 1
GUGUGUGUGGCGUCG----CUGUCGCCGUCG------------CGCCUUUGUUGUAACUGUAUGCGGCGAGAAGUACAGUUAGCAUAUUAAUUGUAUUAAAUCGUCGUCGCAUGACAAAC
..((((((((((...----....))))).))------------)))............(((((((((((((((((((((((((....)))))))))))...)).))))))))).)))... ( -36.80)
>DroAna_CAF1 729 116 + 1
GAAUUGUUGUUGUCAGGUUG--U--UGGCUGGGUUGCUGCUGCUGCCUUUGUUGUAACUGUAUGUGGUGAGAAGUACAGUUAGCAUAUUAAUUGUAUUUAAUCGUCAGGGCAUGACAAAC
...((((..(.(((.(((((--.--..((.((((.((....)).))))..))..))))).....((..((.((((((((((((....))))))))))))..))..)).))))..)))).. ( -29.80)
>consensus
GUGUUGUUGUUGCCAGGUUG__U__UGGCAG____________CGCCUUUGUUGUAACUGUAUGCGGCGAGAAGUACAGUUAGCAUAUUAAUUGUAUUAAAUCGUCGGUGCAUGACAAAC
.....(((((((((((..........(((...............)))..........))).)).((((((..(((((((((((....)))))))))))...))))))......)))))). (-20.72 = -20.06 +  -0.66)

alignment

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secondary structure

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dotplot

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Window 6

Location 18,363,983 – 18,364,092
Length 109
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.68
Mean single sequence MFE -32.79
Consensus MFE -20.31
Energy contribution -19.48
Covariance contribution -0.83
Combinations/Pair 1.28
Mean z-score -2.26
Structure conservation index 0.62
SVM decision value 1.03
SVM RNA-class probability 0.903971
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18363983 109 + 23771897
---CGCCUUUGUUGUAACUGUGUGCGGCGAGAAGUACAGUUAGCAUAUUAAUUGUAUUAAAUCGUCGGGGCAUGACAAUCGUUUCUCAUCAAGG--------AGUUCGACAGAGAAAGAC
---...((((((((.((((.(.((.(((((..(((((((((((....)))))))))))...)))))((((.(((.....))).))))..)).).--------))))))))))))...... ( -32.70)
>DroVir_CAF1 84329 112 + 1
---CGCCUUUGUUGUAACUGUAUGCGGCGAGAAGUACAGUUAGCAUAUUAAUUGUAUUAAAUCGUCGUUGCAUGACAAACAUUU-UCAGCACAACGUCUGGAAGGCAAAAAGAGAG----
---.((((((.((((...((((.(((((((..(((((((((((....)))))))))))...)))))))))))..))))......-.((((.....).)))))))))..........---- ( -33.60)
>DroSim_CAF1 689 109 + 1
---CGCCUUUGUUGUAACUGUGUGUGGCGAGAAGUACAGUUAGCAUAUUAAUUGUAUUAAAUCGUCGGUGCAUGACAAUCGUUUUUCACCAAGG--------AGUUCGACAGAGAAAGAC
---...((((((((.((((.(....(((((..(((((((((((....)))))))))))...)))))((((...(((....)))...))))..).--------))))))))))))...... ( -34.30)
>DroYak_CAF1 6605 108 + 1
---CGCCUUUGUUGUAACUGUGUGCGGCGAGAAGUACAGUUAGCAUAUUAAUUGUAUUAAAUCGUCGGAGCAUGACACUCGUUU-UCACCAAGG--------AGUUCGACGGAGAAAGAC
---...((((((((.((((.(.((((((((..(((((((((((....)))))))))))...))))))(((.(((.....))).)-))..)).).--------))))))))))))...... ( -31.60)
>DroMoj_CAF1 116095 112 + 1
---CGCCUUUGUUGUAACUGUAUGCGGCGAGAAGUACAGUUAGCAUAUUAAUUGUAUUAAAUCGUCGUCGCAUGACAAACAUUU-UCAACGCAACGUCUAGAAGGCAAAACAGGAG----
---.(((((((((((...(((((((((((((((((((((((((....)))))))))))...)).))))))))).))).......-.....))))).....))))))..........---- ( -31.86)
>DroAna_CAF1 765 111 + 1
UGCUGCCUUUGUUGUAACUGUAUGUGGUGAGAAGUACAGUUAGCAUAUUAAUUGUAUUUAAUCGUCAGGGCAUGACAAACGGUUUCAGCCCAAG--------UGUUGGACAGAGAAGG-C
....((((((((((.((((((....(((...((((((((((((....)))))))))))).)))((((.....))))..)))))).))))(((..--------...))).....)))))-) ( -32.70)
>consensus
___CGCCUUUGUUGUAACUGUAUGCGGCGAGAAGUACAGUUAGCAUAUUAAUUGUAUUAAAUCGUCGGGGCAUGACAAACGUUU_UCACCAAAG________AGUUCGACAGAGAAAG_C
......(((((((.....(((...((((((..(((((((((((....)))))))))))...))))))..)))((.....))..........................)))))))...... (-20.31 = -19.48 +  -0.83)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:31:13 2006