Locus 3818

Sequence ID 3L_DroMel_CAF1
Location 11,010,548 – 11,010,688
Length 140
Max. P 0.997294
window5946 window5947 window5948 window5949

overview

Window 6

Location 11,010,548 – 11,010,656
Length 108
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 73.02
Mean single sequence MFE -21.87
Consensus MFE -12.47
Energy contribution -12.19
Covariance contribution -0.27
Combinations/Pair 1.50
Mean z-score -2.33
Structure conservation index 0.57
SVM decision value 2.19
SVM RNA-class probability 0.990066
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11010548 108 + 23771897
ACUACGA-UACAAAAUCACUUCUACAAGAAUUCUCUAAGUAACCUUAAUGCCACGCCCCCUUCGCACC-----GCCGCAACUCCUUGAGGGCGUGGCACCGACUAAAUCGAAAU
....(((-(........((((.....(((....)))))))........((((((((((.....((...-----...))..(.....).))))))))))........)))).... ( -25.20)
>DroPse_CAF1 155895 89 + 1
ACUACGA-UACAAAAUCACUUCUAGAAGAAUUC-CUAAGUAAGCUUAAUGCCACGUCCGC-----------------------GUGGUGAACAUGGCAUCGACUAAAUCGAAAU
..(((((-(.....))).(((....))).....-....))).(((....((((((....)-----------------------)))))......))).((((.....))))... ( -16.40)
>DroEre_CAF1 144419 107 + 1
ACUACGA-UACAAAAUCACUUCUACAAGAAUUCUCUAAGUAACCUUAAUGCCACGCCCAC-UCGCACC-----AGCACAACUCGUCGAGGGCGUGGCACCGACUAAAUCGAAAU
....(((-(........((((.....(((....)))))))........((((((((((..-(((.((.-----((.....)).)))))))))))))))........)))).... ( -28.10)
>DroMoj_CAF1 160406 91 + 1
ACUACGUUUACAAAAUCACUUUUGGAAGAAUUCUCUAAAUAAAUGUGAUGCCACGAUUAC----------------------UGUUCGUAAUGCGGCAUCGACUAAAUC-AAAU
...((((((((((((....)))))..(((....)))...)))))))((((((.(.(((((----------------------.....)))))).)))))).........-.... ( -19.40)
>DroAna_CAF1 137642 110 + 1
ACUACGA-UACAAAAUCACUUCUACAAGAAUUCUCUAAGUAACCUUAAUGCCGCACCU--UGAGCACUCAAGUUGCACAAGCACUCC-AGGUGUGGCACCGACUAAAUCGAAAU
....(((-(........((((.....(((....)))))))........((((((((((--.(((.........(((....)))))).-))))))))))........)))).... ( -25.70)
>DroPer_CAF1 142231 89 + 1
ACUACGA-UACAAAAUCACUUCUAGAAGAAUUC-CUAAGUAAGCUUAAUGCCACGUCCGC-----------------------GUGGUGAACAUGGCAUCGACUAAAUCGAAAU
..(((((-(.....))).(((....))).....-....))).(((....((((((....)-----------------------)))))......))).((((.....))))... ( -16.40)
>consensus
ACUACGA_UACAAAAUCACUUCUACAAGAAUUCUCUAAGUAACCUUAAUGCCACGCCCAC_______________________GUCGAGAACGUGGCACCGACUAAAUCGAAAU
....((.............................((((....)))).((((((((((..............................)))))))))).))............. (-12.47 = -12.19 +  -0.27)

alignment

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secondary structure

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Window 7

Location 11,010,548 – 11,010,656
Length 108
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 73.02
Mean single sequence MFE -32.47
Consensus MFE -20.67
Energy contribution -19.64
Covariance contribution -1.02
Combinations/Pair 1.37
Mean z-score -3.08
Structure conservation index 0.64
SVM decision value 2.83
SVM RNA-class probability 0.997294
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11010548 108 - 23771897
AUUUCGAUUUAGUCGGUGCCACGCCCUCAAGGAGUUGCGGC-----GGUGCGAAGGGGGCGUGGCAUUAAGGUUACUUAGAGAAUUCUUGUAGAAGUGAUUUUGUA-UCGUAGU
....((((......((((((((((((((......(((((..-----..))))).))))))))))))))((((((((((.(((....)))....))))))))))..)-))).... ( -39.90)
>DroPse_CAF1 155895 89 - 1
AUUUCGAUUUAGUCGAUGCCAUGUUCACCAC-----------------------GCGGACGUGGCAUUAAGCUUACUUAG-GAAUUCUUCUAGAAGUGAUUUUGUA-UCGUAGU
....((((..((((((((((((((((.....-----------------------..))))))))))))..((((...(((-((....))))).))))))))....)-))).... ( -26.40)
>DroEre_CAF1 144419 107 - 1
AUUUCGAUUUAGUCGGUGCCACGCCCUCGACGAGUUGUGCU-----GGUGCGA-GUGGGCGUGGCAUUAAGGUUACUUAGAGAAUUCUUGUAGAAGUGAUUUUGUA-UCGUAGU
....((((......(((((((((((((((((.((.....))-----.)).)))-..))))))))))))((((((((((.(((....)))....))))))))))..)-))).... ( -40.40)
>DroMoj_CAF1 160406 91 - 1
AUUU-GAUUUAGUCGAUGCCGCAUUACGAACA----------------------GUAAUCGUGGCAUCACAUUUAUUUAGAGAAUUCUUCCAAAAGUGAUUUUGUAAACGUAGU
....-......((.(((((((((((((.....----------------------))))).)))))))))).....((((.(((((((((....))).)))))).))))...... ( -23.30)
>DroAna_CAF1 137642 110 - 1
AUUUCGAUUUAGUCGGUGCCACACCU-GGAGUGCUUGUGCAACUUGAGUGCUCA--AGGUGCGGCAUUAAGGUUACUUAGAGAAUUCUUGUAGAAGUGAUUUUGUA-UCGUAGU
....((((......((((((.(((((-.(((..((((.......))))..))).--))))).))))))((((((((((.(((....)))....))))))))))..)-))).... ( -38.40)
>DroPer_CAF1 142231 89 - 1
AUUUCGAUUUAGUCGAUGCCAUGUUCACCAC-----------------------GCGGACGUGGCAUUAAGCUUACUUAG-GAAUUCUUCUAGAAGUGAUUUUGUA-UCGUAGU
....((((..((((((((((((((((.....-----------------------..))))))))))))..((((...(((-((....))))).))))))))....)-))).... ( -26.40)
>consensus
AUUUCGAUUUAGUCGAUGCCACGCCCACAAC_______________________GCGGGCGUGGCAUUAAGGUUACUUAGAGAAUUCUUCUAGAAGUGAUUUUGUA_UCGUAGU
..............((((((((((((..............................))))))))))))....((((.((.(((((((((....))).)))))).))...)))). (-20.67 = -19.64 +  -1.02)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,010,586 – 11,010,688
Length 102
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 82.54
Mean single sequence MFE -28.67
Consensus MFE -21.12
Energy contribution -20.43
Covariance contribution -0.69
Combinations/Pair 1.18
Mean z-score -2.70
Structure conservation index 0.74
SVM decision value 0.92
SVM RNA-class probability 0.882888
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11010586 102 + 23771897
UAACCUUAAUGCCACGCCCCC-UUCGCACC-----GCCGCAACUCCUU---GAGGGCGUGGCACCGACUAAAUCGAAAUACUUUUGUUGUUUGAUUGCUGAUACCCCCCUA
.........((((((((((..-...((...-----...))..(.....---).)))))))))).......(((((((..((....))..)))))))............... ( -26.30)
>DroSec_CAF1 147080 100 + 1
UAACCUUAAUGCCACGCCCCC--UCGCACC-----AACGCAACUCCUC---GGGGGCGUGGCACCGACUAAAUCGAAAUACUUUUGUUGUUUGAUUGCUGAUACCC-GCUA
.........((((((((((((--.......-----.............---)))))))))))).......(((((((..((....))..)))))))((........-)).. ( -31.55)
>DroSim_CAF1 142184 100 + 1
UAACCUUAAUGCCACGCCCCC--UCGCACC-----AACGCAACUCCUC---GGGGGCGUGGCACCGACUAAAUCGAAAUACUUUUGUUGUUUGAUUGCUGAUACCC-CCUA
.........((((((((((((--.......-----.............---)))))))))))).......(((((((..((....))..)))))))..........-.... ( -31.15)
>DroEre_CAF1 144457 101 + 1
UAACCUUAAUGCCACGCCCAC--UCGCACC-----AGCACAACUCGUC---GAGGGCGUGGCACCGACUAAAUCGAAAUACUUUUGUUGUUUGCUUGCUGAUAUCCCCCUA
((((.....((((((((((..--(((.((.-----((.....)).)))---)))))))))))).(((.....)))..........))))...................... ( -25.70)
>DroYak_CAF1 147640 106 + 1
UAACCUUAAUGCCACGCCCCCCUUAGCACC-----UGCACAACUCCUCAGGGGGGGCGUGGCACCGACUAAAUCGAAAUACUUUUGUUGUUUGUUUGCUGAUAUCCCCCUA
((((.....(((((((((((((...((...-----.))....((....))))))))))))))).(((.....)))..........))))...................... ( -33.30)
>DroAna_CAF1 137680 95 + 1
UAACCUUAAUGCCGCACCU---UGAGCACUCAAGUUGCACAAGCACUC---C-AGGUGUGGCACCGACUAAAUCGAAAUACUUUUGUUGUUUU-UUGCUUUC-----U---
.........((((((((((---.(((.........(((....))))))---.-))))))))))..........(((((.((.......)).))-))).....-----.--- ( -24.00)
>consensus
UAACCUUAAUGCCACGCCCCC__UCGCACC_____AGCACAACUCCUC___GGGGGCGUGGCACCGACUAAAUCGAAAUACUUUUGUUGUUUGAUUGCUGAUACCC_CCUA
((((.....((((((((((..................................)))))))))).(((.....)))..........))))...................... (-21.12 = -20.43 +  -0.69)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,010,586 – 11,010,688
Length 102
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 82.54
Mean single sequence MFE -33.41
Consensus MFE -27.01
Energy contribution -27.17
Covariance contribution 0.15
Combinations/Pair 1.19
Mean z-score -1.98
Structure conservation index 0.81
SVM decision value 0.71
SVM RNA-class probability 0.829446
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11010586 102 - 23771897
UAGGGGGGUAUCAGCAAUCAAACAACAAAAGUAUUUCGAUUUAGUCGGUGCCACGCCCUC---AAGGAGUUGCGGC-----GGUGCGAA-GGGGGCGUGGCAUUAAGGUUA
....(..((((...................))))..).........((((((((((((((---......(((((..-----..))))).-))))))))))))))....... ( -31.71)
>DroSec_CAF1 147080 100 - 1
UAGC-GGGUAUCAGCAAUCAAACAACAAAAGUAUUUCGAUUUAGUCGGUGCCACGCCCCC---GAGGAGUUGCGUU-----GGUGCGA--GGGGGCGUGGCAUUAAGGUUA
..((-........))((((.................((((...))))(((((((((((((---..(.(.(......-----).).)..--)))))))))))))...)))). ( -35.90)
>DroSim_CAF1 142184 100 - 1
UAGG-GGGUAUCAGCAAUCAAACAACAAAAGUAUUUCGAUUUAGUCGGUGCCACGCCCCC---GAGGAGUUGCGUU-----GGUGCGA--GGGGGCGUGGCAUUAAGGUUA
...(-..((((...................))))..).........((((((((((((((---..(.(.(......-----).).)..--))))))))))))))....... ( -34.31)
>DroEre_CAF1 144457 101 - 1
UAGGGGGAUAUCAGCAAGCAAACAACAAAAGUAUUUCGAUUUAGUCGGUGCCACGCCCUC---GACGAGUUGUGCU-----GGUGCGA--GUGGGCGUGGCAUUAAGGUUA
....(..((((...................))))..).........((((((((((((((---(((.((.....))-----.)).)))--..))))))))))))....... ( -31.91)
>DroYak_CAF1 147640 106 - 1
UAGGGGGAUAUCAGCAAACAAACAACAAAAGUAUUUCGAUUUAGUCGGUGCCACGCCCCCCCUGAGGAGUUGUGCA-----GGUGCUAAGGGGGGCGUGGCAUUAAGGUUA
....(..((((...................))))..).........(((((((((((((((...((.(.((....)-----).).))..)))))))))))))))....... ( -37.61)
>DroAna_CAF1 137680 95 - 1
---A-----GAAAGCAA-AAAACAACAAAAGUAUUUCGAUUUAGUCGGUGCCACACCU-G---GAGUGCUUGUGCAACUUGAGUGCUCA---AGGUGCGGCAUUAAGGUUA
---.-----........-.....(((..........((((...))))(((((.(((((-.---(((..((((.......))))..))).---))))).)))))....))). ( -29.00)
>consensus
UAGG_GGGUAUCAGCAAUCAAACAACAAAAGUAUUUCGAUUUAGUCGGUGCCACGCCCCC___GAGGAGUUGCGCU_____GGUGCGA__GGGGGCGUGGCAUUAAGGUUA
.......................(((..........((((...))))(((((((((((((.........((((((.......))))))..)))))))))))))....))). (-27.01 = -27.17 +   0.15)

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 11:07:23 2006