Locus 2798

Sequence ID 2R_DroMel_CAF1
Location 9,745,978 – 9,746,118
Length 140
Max. P 0.861207
window4630 window4631 window4632

overview

Window 0

Location 9,745,978 – 9,746,084
Length 106
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 83.34
Mean single sequence MFE -35.25
Consensus MFE -24.35
Energy contribution -24.88
Covariance contribution 0.53
Combinations/Pair 1.05
Mean z-score -3.19
Structure conservation index 0.69
SVM decision value 0.83
SVM RNA-class probability 0.861207
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9745978 106 + 20766785
-UUAAGUAAAUUGGUUCAGAUAAGAGGGAAAAC-CUUAACACUUACCUCACACUCGGCUCCCUGCUGCGUGUAGAGGUAAUAUGCUUUGCGGCAAUCCUUUGCCCUCU
-....(((((.............((((.....)-))).....(((((((((((.((((.....)))).)))).))))))).....)))))(((((....))))).... ( -33.60)
>DroPse_CAF1 14650 107 + 1
-UUAUAUAUAUAUAAUGAGAUUGAAUGUGAUAUGUUUCCCGCUUACCUCGCACUCGGCACCCUGCUGAGUGUACAGGUAAUAUGCCUUGCGGCAUUCCUUGGCCCGCU
-....((((((...((........))...)))))).....((((((((.(((((((((.....)))))))))..)))))).(((((....)))))..........)). ( -29.40)
>DroSec_CAF1 3723 106 + 1
-UUAGCUAAAUUGGUUCAGGUUAGAGGGAAAAC-CUUUUCCCUUACCUCACACUCGGCUCCCUGCUGCGUGUAGAGGUAAUAUGCCUUUCGGCAAUCCUUUGCCCGCU
-..(((......(((...((..(((((.....)-))))..))(((((((((((.((((.....)))).)))).)))))))...)))....(((((....))))).))) ( -39.90)
>DroSim_CAF1 3716 106 + 1
-UUAGCUAAAUUGGUUCCGAUAAGAGGGAAAAC-CUUUUCACUUACCUCACACUCGGCUCCCUGCUGCGUGUAGAGGUAAUAUGCCUUUCGGCAAUCCUUUGCCCGCU
-..(((......(((......((((((.....)-)))))...(((((((((((.((((.....)))).)))).)))))))...)))....(((((....))))).))) ( -35.90)
>DroEre_CAF1 3619 106 + 1
AUUAAGUAAGUUGGUUCAGCUAAGCG-UAAAAC-CUUUUGCCUUACCUCACACUCGGCUCCCUGCUGCGUGUAGAGGUAAUAGGCCUUGCGGCAAUCCUUUGCCCGCU
.....(((((..((((..((.....)-)..)))-)....((((((((((((((.((((.....)))).)))).))))))..)))))))))(((((....))))).... ( -39.80)
>DroYak_CAF1 3740 106 + 1
UUCAAGUAAAUUGGUUCAGAUAAGCG-UAAAAC-CUUUUGUCGUACCUCACACUCGGCACCCUGCUGCGUGUAGAGGUAAUAAGCCUUGCGGCAAUCCCUUGCCCGCU
............((((..((((((.(-......-).)))))).((((((((((.((((.....)))).)))).))))))...))))..(((((((....))).)))). ( -32.90)
>consensus
_UUAAGUAAAUUGGUUCAGAUAAGAGGGAAAAC_CUUUUCACUUACCUCACACUCGGCUCCCUGCUGCGUGUAGAGGUAAUAUGCCUUGCGGCAAUCCUUUGCCCGCU
..........................................(((((((((((.((((.....)))).)))).)))))))..........(((((....))))).... (-24.35 = -24.88 +   0.53)

alignment

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secondary structure

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dotplot

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Window 1

Location 9,745,978 – 9,746,084
Length 106
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 83.34
Mean single sequence MFE -33.38
Consensus MFE -22.59
Energy contribution -23.40
Covariance contribution 0.81
Combinations/Pair 1.14
Mean z-score -2.03
Structure conservation index 0.68
SVM decision value 0.12
SVM RNA-class probability 0.595621
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9745978 106 - 20766785
AGAGGGCAAAGGAUUGCCGCAAAGCAUAUUACCUCUACACGCAGCAGGGAGCCGAGUGUGAGGUAAGUGUUAAG-GUUUUCCCUCUUAUCUGAACCAAUUUACUUAA-
.(((((....(((..(((....(((((.(((((((.((((.(.((.....)).).))))))))))))))))..)-))..))))))))....................- ( -31.40)
>DroPse_CAF1 14650 107 - 1
AGCGGGCCAAGGAAUGCCGCAAGGCAUAUUACCUGUACACUCAGCAGGGUGCCGAGUGCGAGGUAAGCGGGAAACAUAUCACAUUCAAUCUCAUUAUAUAUAUAUAA-
.((..(((.(((.(((((....)))))....)))...(((((.((.....)).)))))...)))..)).(....)................................- ( -30.20)
>DroSec_CAF1 3723 106 - 1
AGCGGGCAAAGGAUUGCCGAAAGGCAUAUUACCUCUACACGCAGCAGGGAGCCGAGUGUGAGGUAAGGGAAAAG-GUUUUCCCUCUAACCUGAACCAAUUUAGCUAA-
(((.((...(((..((((....))))..(((((((.((((.(.((.....)).).)))))))))))((((((..-..)))))).....)))...))......)))..- ( -39.10)
>DroSim_CAF1 3716 106 - 1
AGCGGGCAAAGGAUUGCCGAAAGGCAUAUUACCUCUACACGCAGCAGGGAGCCGAGUGUGAGGUAAGUGAAAAG-GUUUUCCCUCUUAUCGGAACCAAUUUAGCUAA-
(((..((.......((((....))))..(((((((.((((.(.((.....)).).))))))))))))).....(-((..(((........))))))......)))..- ( -33.30)
>DroEre_CAF1 3619 106 - 1
AGCGGGCAAAGGAUUGCCGCAAGGCCUAUUACCUCUACACGCAGCAGGGAGCCGAGUGUGAGGUAAGGCAAAAG-GUUUUA-CGCUUAGCUGAACCAACUUACUUAAU
.((((.(((....)))))))(((((((..((((((.((((.(.((.....)).).))))))))))))))....(-((((..-(.....)..)))))..)))....... ( -36.00)
>DroYak_CAF1 3740 106 - 1
AGCGGGCAAGGGAUUGCCGCAAGGCUUAUUACCUCUACACGCAGCAGGGUGCCGAGUGUGAGGUACGACAAAAG-GUUUUA-CGCUUAUCUGAACCAAUUUACUUGAA
......((((((((((((....)))....((((((.((((.(.((.....)).).))))))))))........(-((((..-.........)))))))))).)))).. ( -30.30)
>consensus
AGCGGGCAAAGGAUUGCCGCAAGGCAUAUUACCUCUACACGCAGCAGGGAGCCGAGUGUGAGGUAAGGGAAAAG_GUUUUACCUCUUAUCUGAACCAAUUUACUUAA_
...((....(((...(((....)))...(((((((.((((.(.((.....)).).)))))))))))......................)))...))............ (-22.59 = -23.40 +   0.81)

alignment

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secondary structure

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dotplot

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Window 2

Location 9,746,012 – 9,746,118
Length 106
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 79.99
Mean single sequence MFE -39.17
Consensus MFE -22.64
Energy contribution -22.70
Covariance contribution 0.06
Combinations/Pair 1.33
Mean z-score -2.02
Structure conservation index 0.58
SVM decision value 0.46
SVM RNA-class probability 0.743264
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9746012 106 + 20766785
UAACACUUACCUCACACUCGGCUCCCUGCUGCGUGUAGAGGUAAUAUGCUUUGCGGCAAUCCUUUGCCCUCUGUAACGCCUGCUGCAGAAAGUGUCUGAAAAAAGA
..(((((((((((((((.((((.....)))).)))).))))).......(((((((((...(.((((.....)))).)..)))))))))))))))........... ( -36.10)
>DroPse_CAF1 14685 105 + 1
UCCCGCUUACCUCGCACUCGGCACCCUGCUGAGUGUACAGGUAAUAUGCCUUGCGGCAUUCCUUGGCCCGCUGCAGGGCCUGAUGCAGGAAGUGUCUGAAGGAGG-
..((..((((((.(((((((((.....)))))))))..)))))).(((((....)))))((((((((((......))))).(((((.....)))))..)))))))- ( -46.30)
>DroWil_CAF1 3790 100 + 1
------CCACCUCACACUCGGCUCCCUGUUGGGUAUACAGAUAAUAGGCCUUGCGGCAAUCCUUUGCCCUUUGCAGAGCCUGUUGAAGGAAGUAUCUGCAAAAUAA
------...(((...(((((((.....))))))).......((((((((.(((((((((....)))))....)))).)))))))).)))................. ( -29.70)
>DroYak_CAF1 3774 105 + 1
UUUGUCGUACCUCACACUCGGCACCCUGCUGCGUGUAGAGGUAAUAAGCCUUGCGGCAAUCCCUUGCCCGCUGUAACGCCUGCUGAAGGAAGUGUCUGAAAAGGA-
.......((((((((((.((((.....)))).)))).)))))).....((((..(((((....)))))((((......(((.....))).))))......)))).- ( -33.60)
>DroAna_CAF1 3946 105 + 1
UCCGGCUCACCUCGCAUUCGGCUCCCUGCUGGGUGUACAGGUAGUAGGCCUUGCGACAGUCCCUGGCCCGUUGUAGCGCCUGCUGCAGGAAGUGUCUGAAAUGGA-
((((.(.(((.(((((((((((.....)))))))))....(((((((((.(((((((.((.....))..))))))).)))))))))..)).)))...)...))))- ( -43.00)
>DroPer_CAF1 13689 105 + 1
UCCCGCUUACCUCGCACUCGGCACCCUGCUGAGUGUACAGGUAAUAUGCCUUGCGGCAUUCCUUGGCCCGCUGCAGGGCCUGAUGCAGGAAGUGUCUGAAGGAGG-
..((..((((((.(((((((((.....)))))))))..)))))).(((((....)))))((((((((((......))))).(((((.....)))))..)))))))- ( -46.30)
>consensus
UCCCGCUUACCUCACACUCGGCACCCUGCUGAGUGUACAGGUAAUAUGCCUUGCGGCAAUCCUUGGCCCGCUGCAGCGCCUGCUGCAGGAAGUGUCUGAAAAAGA_
.......(((((.(((((((((.....)))))))))..)))))....((.(((((((............))))))).))......((((.....))))........ (-22.64 = -22.70 +   0.06)

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 10:39:46 2006