Locus 7448

Sequence ID 3R_DroMel_CAF1
Location 19,837,125 – 19,837,247
Length 122
Max. P 0.978865
window12042 window12043 window12044

overview

Window 2

Location 19,837,125 – 19,837,215
Length 90
Sequences 5
Columns 101
Reading direction reverse
Mean pairwise identity 84.33
Mean single sequence MFE -35.82
Consensus MFE -26.60
Energy contribution -26.56
Covariance contribution -0.04
Combinations/Pair 1.13
Mean z-score -2.15
Structure conservation index 0.74
SVM decision value 1.00
SVM RNA-class probability 0.898279
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19837125 90 - 27905053
UUGCUUUUCGCUGUCCA--------CUUGGCACGGGGCCAAGGUUCGAGAAUUUGGCUCCCGUGU---GCGUUCAAUCCGUUCAUUUCGUUUGGCAGUGAC
.......((((((.(((--------..(((((((((((((((.........)))))).)))))))---(((.......)))......))..))))))))). ( -33.00)
>DroSec_CAF1 15404 92 - 1
UCGCUACUCGCUGGCCA--------CUUGGCACGGGGCCAAGGUUCGAGAAUUUGGCUCCCGUGCGC-GCGUUCAAUCCGUUCACUUCGUUUGGCAGUGAC
.......((((((.(((--------..(((((((((((((((.........)))))).)))))))(.-(((.......))).)....))..))))))))). ( -36.00)
>DroSim_CAF1 21756 92 - 1
UCGCUACUCGCUGGCCA--------CUUGGCACGGGGCCAAGGUUCGAGAAUUUGGCUCCCGUGCGC-GCGUUCAAUCCGUUCACUUCGUUUGGCAGUGAC
.......((((((.(((--------..(((((((((((((((.........)))))).)))))))(.-(((.......))).)....))..))))))))). ( -36.00)
>DroEre_CAF1 15515 85 - 1
UCGCCUCUAGCUGGCCA--------CUUGGCAUGGGGCCAAGGCUCGUGAAUUUGGCUC-CGUGCU---CGUCCAAUCCAUUC----CGUUUGGCAGUGAC
..(((.......)))((--------((.((((((((((((((.........))))))))-))))))---.(.((((.......----...))))))))).. ( -31.40)
>DroYak_CAF1 15419 97 - 1
UCGCUGCUAGCUGGCCACUUGGCCACUUGGCAUGGGGCCAAGGCUCGUGAAUUUGGCUCCCGUGCUCUCCGUUCAAUCCAUUC----CGUUUGGCAGUGAC
((((((((((((((((....)))))...((((((((((((((.........)))))).)))))))).................----.).)))))))))). ( -42.70)
>consensus
UCGCUACUCGCUGGCCA________CUUGGCACGGGGCCAAGGUUCGAGAAUUUGGCUCCCGUGCGC_GCGUUCAAUCCGUUCA_UUCGUUUGGCAGUGAC
.......((((((................(((((((((((((.........)))))).)))))))............(((..(.....)..))))))))). (-26.60 = -26.56 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 3

Location 19,837,151 – 19,837,247
Length 96
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 76.54
Mean single sequence MFE -36.70
Consensus MFE -15.75
Energy contribution -17.00
Covariance contribution 1.25
Combinations/Pair 1.10
Mean z-score -2.35
Structure conservation index 0.43
SVM decision value 0.83
SVM RNA-class probability 0.861465
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19837151 96 + 27905053
UGAACGC---ACACGGGAGCCAAAUUCUCGAACCUUGGCCCCGUGCCAAG--------UGGACAGCGAAAAGCAAACUUCUGAUGGCCA---CCAGUCGAGUCGUUCAUC
(((((((---.((((((.(((((...........)))))))))))....(--------(((.((..(((........)))...)).)))---).......).)))))).. ( -30.90)
>DroSec_CAF1 15430 98 + 1
UGAACGC-GCGCACGGGAGCCAAAUUCUCGAACCUUGGCCCCGUGCCAAG--------UGGCCAGCGAGUAGCGAACUUCUGAUGGCCA---CCAGUCGAGUCGUUCAUC
((((((.-(((((((((.(((((...........))))))))))))...(--------((((((..((((.....))))....))))))---).......)))))))).. ( -43.10)
>DroSim_CAF1 21782 98 + 1
UGAACGC-GCGCACGGGAGCCAAAUUCUCGAACCUUGGCCCCGUGCCAAG--------UGGCCAGCGAGUAGCGAACUUCUGAUGGCCA---CCAGUCGAGUCGUUCAUC
((((((.-(((((((((.(((((...........))))))))))))...(--------((((((..((((.....))))....))))))---).......)))))))).. ( -43.10)
>DroEre_CAF1 15537 90 + 1
UGGACG---AGCACG-GAGCCAAAUUCACGAGCCUUGGCCCCAUGCCAAG--------UGGCCAGCUAGAGGCGAACUUCUGAUGGCCA---CCAG-----UCGUUCAUC
((((((---((((.(-(.(((((...........))))).)).)))...(--------((((((..((((((....)))))).))))))---)...-----))))))).. ( -38.90)
>DroYak_CAF1 15441 105 + 1
UGAACGGAGAGCACGGGAGCCAAAUUCACGAGCCUUGGCCCCAUGCCAAGUGGCCAAGUGGCCAGCUAGCAGCGAACUUUUGAUGGCCA---CCAGU--AGUCGUUCAUC
(((((((...((..((..((((...(((.(((.((((((.....))))))(((((....)))))((.....))...))).)))))))..---)).))--..))))))).. ( -38.10)
>DroPer_CAF1 30671 86 + 1
UGCAGG------------CCAAAAUCCACGUUCCUUGGCCACUCGCCAAG--------UGC---GCGACAAAUGAACUUUUGAUGGUCAAACCCAGUGGGGCAGU-CACC
(((.((------------(((.......(((.(((((((.....))))))--------.).---))).((((......)))).)))))...(((...))))))..-.... ( -26.10)
>consensus
UGAACGC___GCACGGGAGCCAAAUUCACGAACCUUGGCCCCGUGCCAAG________UGGCCAGCGAGAAGCGAACUUCUGAUGGCCA___CCAGUCGAGUCGUUCAUC
((((((...........................((((((.....))))))........((((((((.....))...(....).)))))).............)))))).. (-15.75 = -17.00 +   1.25)

alignment

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secondary structure

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dotplot

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Window 4

Location 19,837,151 – 19,837,247
Length 96
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 76.54
Mean single sequence MFE -40.53
Consensus MFE -21.76
Energy contribution -24.93
Covariance contribution 3.17
Combinations/Pair 1.13
Mean z-score -2.53
Structure conservation index 0.54
SVM decision value 1.82
SVM RNA-class probability 0.978865
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19837151 96 - 27905053
GAUGAACGACUCGACUGG---UGGCCAUCAGAAGUUUGCUUUUCGCUGUCCA--------CUUGGCACGGGGCCAAGGUUCGAGAAUUUGGCUCCCGUGU---GCGUUCA
..((((((......(.((---(((.((.((((((....))))).).)).)))--------)).)(((((((((((((.........)))))).)))))))---.)))))) ( -38.00)
>DroSec_CAF1 15430 98 - 1
GAUGAACGACUCGACUGG---UGGCCAUCAGAAGUUCGCUACUCGCUGGCCA--------CUUGGCACGGGGCCAAGGUUCGAGAAUUUGGCUCCCGUGCGC-GCGUUCA
..((((((.(.(..(.((---((((((.(((.((....)).)).).))))))--------)).)(((((((((((((.........)))))).)))))))).-))))))) ( -45.60)
>DroSim_CAF1 21782 98 - 1
GAUGAACGACUCGACUGG---UGGCCAUCAGAAGUUCGCUACUCGCUGGCCA--------CUUGGCACGGGGCCAAGGUUCGAGAAUUUGGCUCCCGUGCGC-GCGUUCA
..((((((.(.(..(.((---((((((.(((.((....)).)).).))))))--------)).)(((((((((((((.........)))))).)))))))).-))))))) ( -45.60)
>DroEre_CAF1 15537 90 - 1
GAUGAACGA-----CUGG---UGGCCAUCAGAAGUUCGCCUCUAGCUGGCCA--------CUUGGCAUGGGGCCAAGGCUCGUGAAUUUGGCUC-CGUGCU---CGUCCA
(((((....-----(.((---((((((.((((.(....).))).).))))))--------)).)(((((((((((((.........))))))))-))))))---)))).. ( -41.80)
>DroYak_CAF1 15441 105 - 1
GAUGAACGACU--ACUGG---UGGCCAUCAAAAGUUCGCUGCUAGCUGGCCACUUGGCCACUUGGCAUGGGGCCAAGGCUCGUGAAUUUGGCUCCCGUGCUCUCCGUUCA
..((((((...--.(.((---((((((......((..((.....))..))....)))))))).)(((((((((((((.........)))))).)))))))....)))))) ( -44.40)
>DroPer_CAF1 30671 86 - 1
GGUG-ACUGCCCCACUGGGUUUGACCAUCAAAAGUUCAUUUGUCGC---GCA--------CUUGGCGAGUGGCCAAGGAACGUGGAUUUUGG------------CCUGCA
(((.-(..((((....)))).).)))......((..((....((((---(..--------((((((.....))))))...)))))....)).------------.))... ( -27.80)
>consensus
GAUGAACGACUCGACUGG___UGGCCAUCAGAAGUUCGCUUCUCGCUGGCCA________CUUGGCACGGGGCCAAGGUUCGAGAAUUUGGCUCCCGUGC___GCGUUCA
..((((((.............((((((.(((.((....)).)).).))))))............(((((((((((((.........)))))).)))))))....)))))) (-21.76 = -24.93 +   3.17)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:46:18 2006