Locus 2126

Sequence ID 2L_DroMel_CAF1
Location 5,734,254 – 5,734,402
Length 148
Max. P 0.976746
window3435 window3436 window3437

overview

Window 5

Location 5,734,254 – 5,734,369
Length 115
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 76.46
Mean single sequence MFE -34.99
Consensus MFE -24.45
Energy contribution -25.45
Covariance contribution 1.00
Combinations/Pair 1.11
Mean z-score -2.12
Structure conservation index 0.70
SVM decision value 1.78
SVM RNA-class probability 0.976746
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5734254 115 + 22407834
AGCGGAGAUGGAGGGAAUGGUGAAGGGUAGCACCAUCACUAGAUCCUGCAGAAACUGCGGCAUGCUCUCCAAAGGCCACAGCAGUCCUGCAAG-AAUUGAAA---AAUAGGUUUCAUAA
.((((.(((((((((..((((((.((......)).))))))....((((((...))))))....))))))....((....)).)))))))...-...(((((---......)))))... ( -35.50)
>DroVir_CAF1 9197 113 + 1
CGCCGAUAUCGAGGGUAUGGUAAAGGGUAGCACCAUUACCAGAUCCUGCAGAAAGCGCGGCAUGCUCUCCAACGGCCACAGCAGACCUAAACAAAAUGC------AUUAAAAAUCCUUA
.((((.....(((((((((((((.((......)).))))).....((((.......)))).))))))))...))))....(((.............)))------.............. ( -29.02)
>DroPse_CAF1 14744 113 + 1
UGCAGAUAUGGAGGGUAUUGUAAAGGGUAAUACCAUCACCAGAUCCUGCAGAAACUGUGGCAUGCUCUCCAGGGGCCACAAUAGACCUAAAAA-UA--CAAAUCAAAAUGGUUU---GA
(((((((.(((..(((((((.......)))))))....))).)).))))).....((((((...(((....))))))))).............-..--((((((.....)))))---). ( -30.40)
>DroYak_CAF1 6363 115 + 1
AGCGGAGAUGGAGGGUAUGGUGAAGGGUAGCACCAUCACUAGGUCCUGCAGGAACUGCGGCAUGCUCUCCAAGGGCCACAGAAGUCCUGCAGG-UAUUCCAA---AUUAGGUUUCAUUA
......(((((((....((((((.((......)).))))))((.(((((((((.(((.(((...((.....)).))).)))...)))))))))-....))..---......))))))). ( -42.10)
>DroAna_CAF1 5571 110 + 1
GGCGGAUAUGGAGGGUAUUGUGAAGGGCAGCACCAUCACUAGGUCCUGCAGGAACUGCGGCAUGCUCUCCAGGGGCCACAAGAGUCCUGAAAA-UA-----G---AAAUGGUUCUGUAG
.(((((..((((((((((.((((.((......)).))))......((((((...)))))).))))))))))((((((....).))))).....-..-----.---.......))))).. ( -37.20)
>DroPer_CAF1 14676 113 + 1
UGCAGAUAUGGAGGGUAUGGUAAAGGGUAAUACCAUCACCAGAUCCUGCAGAAACUGUGGCAUGCUCUCCAGGGGCCACAAUAGGCCUAAAAA-UA--CAAAUCAAAAUUGUUU---GA
..(((((((((((((((((.....((......))...........(..(((...)))..)))))))))))).(((((......))))).....-..--...........)))))---). ( -35.70)
>consensus
AGCGGAUAUGGAGGGUAUGGUAAAGGGUAGCACCAUCACCAGAUCCUGCAGAAACUGCGGCAUGCUCUCCAAGGGCCACAACAGUCCUAAAAA_UA__CAAA___AAAAGGUUUC_UAA
........(((((((((((((((.((......)).))))......((((((...))))))))))))))))).(((.(......).)))............................... (-24.45 = -25.45 +   1.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,734,254 – 5,734,369
Length 115
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 76.46
Mean single sequence MFE -31.00
Consensus MFE -19.95
Energy contribution -18.95
Covariance contribution -1.00
Combinations/Pair 1.35
Mean z-score -1.40
Structure conservation index 0.64
SVM decision value 0.45
SVM RNA-class probability 0.740577
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5734254 115 - 22407834
UUAUGAAACCUAUU---UUUCAAUU-CUUGCAGGACUGCUGUGGCCUUUGGAGAGCAUGCCGCAGUUUCUGCAGGAUCUAGUGAUGGUGCUACCCUUCACCAUUCCCUCCAUCUCCGCU
...(((((......---)))))..(-(((((((((..(((((((((((....)))...))))))))))))))))))....(..((((((........))))))..)............. ( -35.90)
>DroVir_CAF1 9197 113 - 1
UAAGGAUUUUUAAU------GCAUUUUGUUUAGGUCUGCUGUGGCCGUUGGAGAGCAUGCCGCGCUUUCUGCAGGAUCUGGUAAUGGUGCUACCCUUUACCAUACCCUCGAUAUCGGCG
............((------((.((..(....((((......))))..)..)).))))((((.((.....))(((...((((((.((......)).))))))...)))......)))). ( -28.90)
>DroPse_CAF1 14744 113 - 1
UC---AAACCAUUUUGAUUUG--UA-UUUUUAGGUCUAUUGUGGCCCCUGGAGAGCAUGCCACAGUUUCUGCAGGAUCUGGUGAUGGUAUUACCCUUUACAAUACCCUCCAUAUCUGCA
..---..........((((((--..-....)))))).((((((((..((....))...))))))))....((((.((.(((....((((((.........))))))..))).)))))). ( -25.70)
>DroYak_CAF1 6363 115 - 1
UAAUGAAACCUAAU---UUGGAAUA-CCUGCAGGACUUCUGUGGCCCUUGGAGAGCAUGCCGCAGUUCCUGCAGGACCUAGUGAUGGUGCUACCCUUCACCAUACCCUCCAUCUCCGCU
..............---.((((...-(((((((((...(((((((...((.....)).))))))).))))))))).....(((.(((((........))))))))..))))........ ( -40.00)
>DroAna_CAF1 5571 110 - 1
CUACAGAACCAUUU---C-----UA-UUUUCAGGACUCUUGUGGCCCCUGGAGAGCAUGCCGCAGUUCCUGCAGGACCUAGUGAUGGUGCUGCCCUUCACAAUACCCUCCAUAUCCGCC
...(((.((((((.---(-----((-(((((((((...(((((((..((....))...))))))).))))).))))..))).)))))).)))........................... ( -27.50)
>DroPer_CAF1 14676 113 - 1
UC---AAACAAUUUUGAUUUG--UA-UUUUUAGGCCUAUUGUGGCCCCUGGAGAGCAUGCCACAGUUUCUGCAGGAUCUGGUGAUGGUAUUACCCUUUACCAUACCCUCCAUAUCUGCA
((---(((....)))))..((--((-......((((......))))((((.(((((........).)))).))))....((((.(((((........))))))))).........)))) ( -28.00)
>consensus
UAA_GAAACCAAUU___UUUG__UA_UUUUCAGGACUACUGUGGCCCCUGGAGAGCAUGCCGCAGUUUCUGCAGGAUCUAGUGAUGGUGCUACCCUUCACCAUACCCUCCAUAUCCGCA
..............................((((...((((((((...((.....)).)))))))).)))).(((.....((((.((......)).)))).....)))........... (-19.95 = -18.95 +  -1.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,734,294 – 5,734,402
Length 108
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 77.19
Mean single sequence MFE -29.22
Consensus MFE -21.76
Energy contribution -21.35
Covariance contribution -0.41
Combinations/Pair 1.33
Mean z-score -2.16
Structure conservation index 0.74
SVM decision value 1.73
SVM RNA-class probability 0.974472
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5734294 108 - 22407834
GUGGUGUCAAGCUAAUAUUCUUAUCUUUAUAUUUUAUGAAACCUAUU---UUUCAAUUCUUGCAGGACUGCUGUGGCCUUUGGAGAGCAUGCCGCAGUUUCUGCAGGAUCU
..(((.(((....(((((..........)))))...))).)))....---.......((((((((((..(((((((((((....)))...))))))))))))))))))... ( -31.40)
>DroSec_CAF1 10159 108 - 1
GUGUUCUCAAGCUGACUUUCUCAUCUUUAUAUUUUAUGAAACCAAUU---UUUGAAUCAUUGCAGGACUCCUGUGGCCUCUGGAGAGCAUGCCACAGUUUCUGCAGGAUCU
......(((((.(((.....)))..((((((...)))))).......---)))))(((.((((((((...((((((((((....)))...))))))).))))))))))).. ( -25.10)
>DroSim_CAF1 5909 108 - 1
GUGUUCUCAAGCUGAUUUUCUCAUCUACAUAUUUCAUUAAACAAAUU---UUUGAAUCCUUGCAGGACUCCUGUGGCCUCUGGAGAGCAUGCCACAGUUUCUGCAGGAUCU
((((.....((.(((.....))).)))))).................---.....(((((.((((((...((((((((((....)))...))))))).))))))))))).. ( -27.80)
>DroEre_CAF1 6734 108 - 1
GUGUUUACGAGCCAGUUUACACAUUUUCAUAUUUAAUGAAACCCAAU---UUGGAAUACUUGCAGGACUUCUGUGGCCCCUGGAGAGCAUGCCGCAGUUUCUGCAGGACCU
((((..((......))..))))..((((((.....)))))).((...---..))....(((((((((...(((((((..((....))...))))))).))))))))).... ( -33.30)
>DroYak_CAF1 6403 108 - 1
GUGUCCUCCAGCCAGUUUUCCCACAUUCAUAUUUAAUGAAACCUAAU---UUGGAAUACCUGCAGGACUUCUGUGGCCCUUGGAGAGCAUGCCGCAGUUCCUGCAGGACCU
......(((((...((......)).(((((.....))))).......---)))))...(((((((((...(((((((...((.....)).))))))).))))))))).... ( -34.90)
>DroPer_CAF1 14716 106 - 1
GUAAAUGUAAUUUCUUUUCCAAAUUAUCACAUUUC---AAACAAUUUUGAUUUG--UAUUUUUAGGCCUAUUGUGGCCCCUGGAGAGCAUGCCACAGUUUCUGCAGGAUCU
......(((((((.......))))))).(((..((---(((....)))))..))--).......((((......))))((((.(((((........).)))).)))).... ( -22.80)
>consensus
GUGUUCUCAAGCUAAUUUUCUCAUCUUCAUAUUUAAUGAAACCAAUU___UUUGAAUACUUGCAGGACUCCUGUGGCCCCUGGAGAGCAUGCCACAGUUUCUGCAGGAUCU
..........................................................(((((((((...(((((((...((.....)).))))))).))))))))).... (-21.76 = -21.35 +  -0.41)

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 10:20:18 2006