Locus 3349

Sequence ID 3L_DroMel_CAF1
Location 9,820,788 – 9,821,078
Length 290
Max. P 0.746557
window5219 window5220 window5221 window5222 window5223

overview

Window 9

Location 9,820,788 – 9,820,907
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 80.59
Mean single sequence MFE -36.30
Consensus MFE -29.83
Energy contribution -29.95
Covariance contribution 0.12
Combinations/Pair 1.10
Mean z-score -1.56
Structure conservation index 0.82
SVM decision value 0.35
SVM RNA-class probability 0.702338
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9820788 119 - 23771897
CAUACACACACACACACACACGCGGUACACCGCCCAGCUGUGUCAACAGGGGCGGAAAACG-GGCGGGGCCAUCCGGUCCUCAGCUUAGAAGGUCUUUUUUUUAAGCUGCAAUUCAUUCU
....................(((.((...((((((..((((....))))))))))...)).-.)))(((((....))))).((((((((((((....))))))))))))........... ( -39.50)
>DroSim_CAF1 118068 110 - 1
CACACACGAACACACACACACGCGGUCCACCGCCCAGCUGUGUCAACAGGGGCGUAAAACGGGGCGGGGCCAUCCGGUCCUCAGCUUAGAAGGCUUUUUUUCAAAGCUAC----------
.......((...........(((((....))((((..((((....))))))))..........)))(((((....)))))))(((((.(((((....))))).)))))..---------- ( -32.50)
>DroEre_CAF1 117757 111 - 1
UACA------CACACACACACGCAGUCCACCGCCCAGCUGUGUCAACAGGGGCGGAAAACGGGGCGGGGCCAUCCGGUCCUCAGUCGAAAAGGCAAUUUUU---AGCAACCACUCAUAUU
....------...........((.((((.((((((..((((....))))))))))......))))((((((....))))))..(((.....))).......---.))............. ( -34.00)
>DroYak_CAF1 127767 109 - 1
CACA--------CACACACACGCAGUCCACCGCCCAGCUGUGUCAACAGGGGCGGAAAACGGGGCGGGGCCAUCCGGUCCUCAGCUGAAAAGGCAACUUUU---AGCUACAACUCAUAUU
....--------........(((.((...((((((..((((....))))))))))...))...)))(((((....)))))..((((((((.(....)))))---))))............ ( -39.20)
>consensus
CACA______CACACACACACGCAGUCCACCGCCCAGCUGUGUCAACAGGGGCGGAAAACGGGGCGGGGCCAUCCGGUCCUCAGCUGAAAAGGCAAUUUUU___AGCUACAACUCAUAUU
....................(((.((...((((((..((((....))))))))))...))...)))(((((....)))))..((((.(((((....)))))...))))............ (-29.83 = -29.95 +   0.12)

alignment

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secondary structure

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Window 0

Location 9,820,907 – 9,821,011
Length 104
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 81.90
Mean single sequence MFE -31.19
Consensus MFE -19.91
Energy contribution -20.71
Covariance contribution 0.80
Combinations/Pair 1.06
Mean z-score -1.71
Structure conservation index 0.64
SVM decision value 0.03
SVM RNA-class probability 0.550268
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9820907 104 + 23771897
----AGUGGGAGGUGAGGCUAUAUAGCUUCGAUUCGCCAUUUGUGUAU------------GUGGCUAUCACCUCGCGACUAUUAUCAAUGGGGUUAUACGUUGCGUAUGUGUGUUGGCAA
----.....(((.(((((((....))))))).)))((((..((..(((------------(..(((((.((((((.((......))..)))))).))).))..))))..))...)))).. ( -34.20)
>DroSec_CAF1 114844 100 + 1
AGUGAGUGGGAGGUGAGGCUAUAU--------UUCGCCAUUUGUGUAU------------GUGGCUAUCACCUCGCGACUAUUAUCAAUGGGGUUAUACGUUGCGUAUGUGUGUUGGCAA
.((.((...(((((((((((((((--------..(((.....))).))------------)))))).)))))))((((((((.(((.....))).))).))))).........)).)).. ( -31.20)
>DroSim_CAF1 118178 96 + 1
----AGUGGGAGGUGAGGCUAUAU--------UUCGCCAUUUGUGUAU------------GUGGCUAUCACCUCGCGACUAUUAUCAAUGGGGUUAUACGUUGCGUAUGUGUGUUGGCAA
----.((.((((((((((((((((--------..(((.....))).))------------)))))).)))))))((((((((.(((.....))).))).)))))..........).)).. ( -30.80)
>DroEre_CAF1 117868 111 + 1
----AGUGAGAGGUGAGGCUUUAG--CUUCGAUUUGCAAUAUGUGUAUGUAUAUAUGUACGUAUCAAUCACCUCGCGACU---AUCAAUGGGGUUAUACGUUGCGUAUGUGUGUUGGCAA
----.(..((...((((((....)--))))).))..)....(((..(..(((((((((((((((.((((.((........---......))))))))))).))))))))))..)..))). ( -31.14)
>DroYak_CAF1 127876 99 + 1
----AGUGGGAGGUGAGGCUAUAG--CUACGAUACCACACAAGUGUGU------------GUAGCAAUCACCUCGCGACU---AUCAAUGGGGUUAUACGUUGCGUAUGUGUGUUGGCAA
----(((.(((((((((((....)--))..(.(((((((....)))).------------))).)..))))))).).)))---.((((((.(..((((((...))))))).))))))... ( -28.60)
>consensus
____AGUGGGAGGUGAGGCUAUAU__CU_CGAUUCGCCAUUUGUGUAU____________GUGGCUAUCACCUCGCGACUAUUAUCAAUGGGGUUAUACGUUGCGUAUGUGUGUUGGCAA
....((((.(((((((((((((............(((.....)))...............)))))).))))))).).)))....((((((.(..((((((...))))))).))))))... (-19.91 = -20.71 +   0.80)

alignment

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secondary structure

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Window 1

Location 9,820,943 – 9,821,051
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.69
Mean single sequence MFE -29.15
Consensus MFE -22.18
Energy contribution -22.58
Covariance contribution 0.40
Combinations/Pair 1.06
Mean z-score -1.69
Structure conservation index 0.76
SVM decision value 0.29
SVM RNA-class probability 0.671327
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9820943 108 + 23771897
UUGUGUAU------------GUGGCUAUCACCUCGCGACUAUUAUCAAUGGGGUUAUACGUUGCGUAUGUGUGUUGGCAAAACAACGCCACUUUUCACAAUCACAAUCGCACAGUUUCAC
(((((...------------(((((...(((..(((((((((.(((.....))).))).))))))...))).((((......)))))))))....))))).................... ( -29.60)
>DroSec_CAF1 114876 108 + 1
UUGUGUAU------------GUGGCUAUCACCUCGCGACUAUUAUCAAUGGGGUUAUACGUUGCGUAUGUGUGUUGGCAAAACAACGCCACUUUUCACAAUCACAAUCGCACAGUUUCAC
(((((...------------(((((...(((..(((((((((.(((.....))).))).))))))...))).((((......)))))))))....))))).................... ( -29.60)
>DroSim_CAF1 118206 108 + 1
UUGUGUAU------------GUGGCUAUCACCUCGCGACUAUUAUCAAUGGGGUUAUACGUUGCGUAUGUGUGUUGGCAAAACAACGCCACUUUUCACAAUCACAAUCGCACAGUUUCAC
(((((...------------(((((...(((..(((((((((.(((.....))).))).))))))...))).((((......)))))))))....))))).................... ( -29.60)
>DroEre_CAF1 117902 117 + 1
AUGUGUAUGUAUAUAUGUACGUAUCAAUCACCUCGCGACU---AUCAAUGGGGUUAUACGUUGCGUAUGUGUGUUGGCAAAACAACGCCACUUUUCACAAUCACAAUCGCACAGACGCAC
.(((((.(((((((((((((((((.((((.((........---......))))))))))).)))))))))((((((......))))))......................))).))))). ( -30.04)
>DroYak_CAF1 127910 105 + 1
AAGUGUGU------------GUAGCAAUCACCUCGCGACU---AUCAAUGGGGUUAUACGUUGCGUAUGUGUGUUGGCAAAACAACGCCACUUUUCACAAUCACAAUCGCAUAGUCGCAC
..(.(.((------------(.......)))).)((((((---((.((((........))))(((..(((((((((((........))))......)))..))))..))))))))))).. ( -26.90)
>consensus
UUGUGUAU____________GUGGCUAUCACCUCGCGACUAUUAUCAAUGGGGUUAUACGUUGCGUAUGUGUGUUGGCAAAACAACGCCACUUUUCACAAUCACAAUCGCACAGUUUCAC
.(((((..............((((((((.((((((.((......))..)))))).))).)))))((...((((.((((........)))).....))))...))....)))))....... (-22.18 = -22.58 +   0.40)

alignment

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secondary structure

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Window 2

Location 9,820,943 – 9,821,051
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.69
Mean single sequence MFE -29.56
Consensus MFE -26.78
Energy contribution -26.62
Covariance contribution -0.16
Combinations/Pair 1.03
Mean z-score -1.35
Structure conservation index 0.91
SVM decision value 0.46
SVM RNA-class probability 0.746557
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9820943 108 - 23771897
GUGAAACUGUGCGAUUGUGAUUGUGAAAAGUGGCGUUGUUUUGCCAACACACAUACGCAACGUAUAACCCCAUUGAUAAUAGUCGCGAGGUGAUAGCCAC------------AUACACAA
.......((((...((((((((((....(((((.(((((.((((............))))...))))).)))))....))))))))))(((....)))..------------...)))). ( -28.10)
>DroSec_CAF1 114876 108 - 1
GUGAAACUGUGCGAUUGUGAUUGUGAAAAGUGGCGUUGUUUUGCCAACACACAUACGCAACGUAUAACCCCAUUGAUAAUAGUCGCGAGGUGAUAGCCAC------------AUACACAA
.......((((...((((((((((....(((((.(((((.((((............))))...))))).)))))....))))))))))(((....)))..------------...)))). ( -28.10)
>DroSim_CAF1 118206 108 - 1
GUGAAACUGUGCGAUUGUGAUUGUGAAAAGUGGCGUUGUUUUGCCAACACACAUACGCAACGUAUAACCCCAUUGAUAAUAGUCGCGAGGUGAUAGCCAC------------AUACACAA
.......((((...((((((((((....(((((.(((((.((((............))))...))))).)))))....))))))))))(((....)))..------------...)))). ( -28.10)
>DroEre_CAF1 117902 117 - 1
GUGCGUCUGUGCGAUUGUGAUUGUGAAAAGUGGCGUUGUUUUGCCAACACACAUACGCAACGUAUAACCCCAUUGAU---AGUCGCGAGGUGAUUGAUACGUACAUAUAUACAUACACAU
((((((.((((((.(((((..((((.....(((((......)))))...))))..))))))))))).....((..((---..((....))..))..))))))))................ ( -33.70)
>DroYak_CAF1 127910 105 - 1
GUGCGACUAUGCGAUUGUGAUUGUGAAAAGUGGCGUUGUUUUGCCAACACACAUACGCAACGUAUAACCCCAUUGAU---AGUCGCGAGGUGAUUGCUAC------------ACACACUU
..(((((((((((.(((((..((((.....(((((......)))))...))))..))))))))............))---))))))((((((........------------.))).))) ( -29.80)
>consensus
GUGAAACUGUGCGAUUGUGAUUGUGAAAAGUGGCGUUGUUUUGCCAACACACAUACGCAACGUAUAACCCCAUUGAUAAUAGUCGCGAGGUGAUAGCCAC____________AUACACAA
(((....((((((.(((((..((((.....(((((......)))))...))))..)))))))))))(((.(..((((....)))).).)))........................))).. (-26.78 = -26.62 +  -0.16)

alignment

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secondary structure

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Window 3

Location 9,820,971 – 9,821,078
Length 107
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 83.87
Mean single sequence MFE -29.49
Consensus MFE -24.30
Energy contribution -24.70
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.50
Structure conservation index 0.82
SVM decision value 0.02
SVM RNA-class probability 0.544491
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9820971 107 - 23771897
CAA------------AAAGGCAAAAA-GCGAAGCGUGAGUGUGAAACUGUGCGAUUGUGAUUGUGAAAAGUGGCGUUGUUUUGCCAACACACAUACGCAACGUAUAACCCCAUUGAUAAU
...------------...((......-(((..(((((.(((((..(((.((((((....))))))...)))((((......))))..))))).)))))..)))......))......... ( -29.00)
>DroSec_CAF1 114904 99 - 1
CAA--------------------AAA-GCGAAGCGUGAGUGUGAAACUGUGCGAUUGUGAUUGUGAAAAGUGGCGUUGUUUUGCCAACACACAUACGCAACGUAUAACCCCAUUGAUAAU
...--------------------...-(((..(((((.(((((..(((.((((((....))))))...)))((((......))))..))))).)))))..)))................. ( -27.70)
>DroSim_CAF1 118234 99 - 1
CAA--------------------AAA-GCGAAGCGUGAGUGUGAAACUGUGCGAUUGUGAUUGUGAAAAGUGGCGUUGUUUUGCCAACACACAUACGCAACGUAUAACCCCAUUGAUAAU
...--------------------...-(((..(((((.(((((..(((.((((((....))))))...)))((((......))))..))))).)))))..)))................. ( -27.70)
>DroEre_CAF1 117942 116 - 1
CAGUUUGCUUCUUUCUACGACAAAAA-GCGAAGCGAGAGUGUGCGUCUGUGCGAUUGUGAUUGUGAAAAGUGGCGUUGUUUUGCCAACACACAUACGCAACGUAUAACCCCAUUGAU---
...((((((((...............-..))))))))((((.(.(..((((((.(((((..((((.....(((((......)))))...))))..)))))))))))..))))))...--- ( -30.93)
>DroYak_CAF1 127938 117 - 1
CGGUUUGCUUGUUUCUACGACAAAAAGGCGAAGCGAGAGUGUGCGACUAUGCGAUUGUGAUUGUGAAAAGUGGCGUUGUUUUGCCAACACACAUACGCAACGUAUAACCCCAUUGAU---
((.((((((((((.....))))....)))))).))..((((.(.(..((((((.(((((..((((.....(((((......)))))...))))..)))))))))))..))))))...--- ( -32.10)
>consensus
CAA_____________A_G_CAAAAA_GCGAAGCGUGAGUGUGAAACUGUGCGAUUGUGAUUGUGAAAAGUGGCGUUGUUUUGCCAACACACAUACGCAACGUAUAACCCCAUUGAUAAU
...........................(((..(((((.(((((...((.((((((....))))))...))(((((......))))).))))).)))))..)))................. (-24.30 = -24.70 +   0.40)

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 10:55:44 2006