Locus 4565

Sequence ID 3R_DroMel_CAF1
Location 12,068,213 – 12,068,561
Length 348
Max. P 0.984000
window7467 window7468 window7469 window7470 window7471

overview

Window 7

Location 12,068,213 – 12,068,326
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.94
Mean single sequence MFE -40.66
Consensus MFE -33.84
Energy contribution -34.92
Covariance contribution 1.08
Combinations/Pair 1.09
Mean z-score -1.46
Structure conservation index 0.83
SVM decision value 0.37
SVM RNA-class probability 0.708308
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12068213 113 + 27905053
-----CUGGGCUAAAAUUGGUGGCUGGCAACGCCACUCGGCCUCACACACAACUGGCAAUGCCCCUGUAUUGUGAUUGUGUUGUGUGUGC--GCUCUCGCUCUCUCCCAGUCAGUCCCAC
-----(((((........((((((.(....))))))).(((..(((((((((((.(((((((....))))))).)....)))))))))).--)))..........))))).......... ( -41.00)
>DroSec_CAF1 4833 107 + 1
-----CUGGGCUAAAAUUGGUGGCUGGCAACGCCGCUCGGCCUCACACACAGCUGGCAAUGCCCCUGUAUUGUGAUUGU------UGUGC--GCUCUCGCUCUCUCCCAGUCAGUUCCAC
-----(((((........((((((.(....))))))).(((..((((.((((.(.(((((((....))))))).)))))------)))).--)))..........))))).......... ( -32.60)
>DroSim_CAF1 5259 113 + 1
-----CUGGACUAAAAUUGGUGGCUGGCAACGCCGCUCGGCCUCACACACAGCUGGCAAUGCCCCUGUAUUGUGAUUGUGUUGUGUGUGC--GCUCUCGCUCUCUCCCAGUCAGUUCCAC
-----.((((((...(((((..(..(((...(((....)))(.(((((((((((.(((((((....))))))).)....)))))))))).--).....)))..)..))))).)).)))). ( -39.20)
>DroEre_CAF1 6774 118 + 1
CUGUGCUGGGUUGAAAUUGGUGGCUGGCAACGCCGCUCGGCCUCACACACAGCUGGCAAUGCCAUGGUAUUGUGAUUGUGUUGGGUGUGC--UCUCUCGCUCUCUCCCAGUCAGUUCCAC
(((.((((((..((....((((((.(....)))))))..((((((.((((((.(.(((((((....))))))).))))))))))).))((--......))))...)))))))))...... ( -43.70)
>DroYak_CAF1 6891 120 + 1
CUGUGCUGGGUUGAAAUUGGUGGCUGGCAACACCGCUCGGCCUCACACACAGCUGGCAAUGCCCCAGUAUUGUGAUUGUGUUGUGUGUGCGCGCUCUCGCUCUCUCCCAGUCAGUCCCAC
(((.((((((..((....(((((.((....))))))).((((.(((((((((((.(((((((....))))))).)....)))))))))).).))).....))...)))))))))...... ( -46.80)
>consensus
_____CUGGGCUAAAAUUGGUGGCUGGCAACGCCGCUCGGCCUCACACACAGCUGGCAAUGCCCCUGUAUUGUGAUUGUGUUGUGUGUGC__GCUCUCGCUCUCUCCCAGUCAGUUCCAC
......((((.....(((((..(..(((...(((....)))..(((((((((((.(((((((....))))))).)....)))))))))).........)))..)..)))))....)))). (-33.84 = -34.92 +   1.08)

alignment

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secondary structure

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Window 8

Location 12,068,326 – 12,068,441
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.74
Mean single sequence MFE -41.70
Consensus MFE -30.50
Energy contribution -32.26
Covariance contribution 1.76
Combinations/Pair 1.03
Mean z-score -1.86
Structure conservation index 0.73
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12068326 115 - 27905053
AGUGCGAGCGAGAACGAUGCA-AC-GCUGUCUCCCUUCCACGACGCGCACUUAUGUAAAAAGCAUUGAAACUGAACGAGUUUCUCGAUAGCAGCGGGGGUGGGAGAGG-GAG--AGAGCG
..((((..((....)).))))-.(-(((.((((((((((((..(.(((((....)).....(((((((((((.....))))..))))).)).))).).))))..))))-)))--).)))) ( -42.30)
>DroSec_CAF1 4940 117 - 1
AGUGCGAGCGAGCACGCUGCAUAC-GCUGUCUCCCUUCCACGACGCGCACUUAUGUAAAAAGCAUUGAAACUGAACGAGUUUCUCGAUAGCAGCGGGGGUGGGAGAGGAGAG--AGAGCG
.((((.((((....)))))))).(-(((.((((((((((((..(.(((((....)).....(((((((((((.....))))..))))).)).))).).))))))).))))).--..)))) ( -45.00)
>DroSim_CAF1 5372 117 - 1
AGUGCGAGCGAGCACUCUGCAUAC-GCUGUCUCCCUUCCACGACGCGCACUUAUGUAAAAAGCAUUGAAACUGAACGAGUUUCUCGAUAGCAGCGGGGGUGGGAGAGUAGAG--AGAGCG
(((((......))))).......(-(((.((((((((((((..(.(((((....)).....(((((((((((.....))))..))))).)).))).).))))))).)..)))--).)))) ( -40.50)
>DroEre_CAF1 6892 117 - 1
AGUGCGAGCGAGCACGCUUCAUACAGCUGUCUCCCUUCCGCGACGCGCACUUAUGUAAAAAGCAUUGAAACCGAACGAGUUUCUCGAAAGCAGCGGGGGUGG-AGAGGAGAG--AGAGCG
.((((......))))..........(((.((((((((((((..(.(((....((((.....)))).((((((....).))))).........))).).))))-).))).)))--).))). ( -40.60)
>DroYak_CAF1 7011 119 - 1
AGUGCGAGCGAGCAAGCUGCAUACAGCUAUCUCCCUCGCGCGACGCGCACUUAUGUAAAAAGCAUUGAAACUGAACGAGUUUCUCGAUAGCAGCGGGGAUGG-UGAGGAGAGAAAGAGCG
.((((.(((......)))))))...(((.((((((((((.(..(((((....((((.....)))).((((((.....))))))......)).)))..)...)-))))).))))...))). ( -40.10)
>consensus
AGUGCGAGCGAGCACGCUGCAUAC_GCUGUCUCCCUUCCACGACGCGCACUUAUGUAAAAAGCAUUGAAACUGAACGAGUUUCUCGAUAGCAGCGGGGGUGGGAGAGGAGAG__AGAGCG
.((((......))))..........(((.((((((((((((..(((((....((((.....)))).((((((.....))))))......)).)))...))))))).))))).....))). (-30.50 = -32.26 +   1.76)

alignment

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secondary structure

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Window 9

Location 12,068,403 – 12,068,521
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.98
Mean single sequence MFE -52.30
Consensus MFE -44.48
Energy contribution -45.60
Covariance contribution 1.12
Combinations/Pair 1.08
Mean z-score -1.98
Structure conservation index 0.85
SVM decision value 1.96
SVM RNA-class probability 0.984000
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12068403 118 + 27905053
UGGAAGGGAGACAGC-GU-UGCAUCGUUCUCGCUCGCACUCACCACGAACGGUGCUCGUACAGGGGUGCAUUUACUUGCGUCUGUGUGCGGGCCUGCCGUUUGGCUGCCUGCUGCCUGCU
.((.(((.((.(((.-((-.((...((........))........(((((((((((((((((.((..(((......)))..)).)))))))))..)))))))))).))))))).))).)) ( -49.20)
>DroSec_CAF1 5018 119 + 1
UGGAAGGGAGACAGC-GUAUGCAGCGUGCUCGCUCGCACUCACCACGAACGGUGCUCGUACAGGGGUGCAUUUACUUGCGUCUGUGUGCGUGGCUGCCGUUUGGCUGCCUGCUGCCUGCU
.....((.((.((((-(...(((((((((......))))......(((((((((((((((((.((..(((......)))..)).)))))).))).))))))))))))).))))).)).)) ( -56.40)
>DroSim_CAF1 5450 119 + 1
UGGAAGGGAGACAGC-GUAUGCAGAGUGCUCGCUCGCACUCACCACGAACGGUGCUCGUACAGGGGUGCAUUUACUUGCGUCUGUGUGCGUGCCUGCCGUUUGGCUGCCUGCUGCCUGCU
.((.(((.((.(((.-(((.((.((((((......))))))....((((((((((.((((((.((..(((......)))..)).)))))).))..)))))))))))))))))).))).)) ( -57.40)
>DroEre_CAF1 6969 119 + 1
CGGAAGGGAGACAGCUGUAUGAAGCGUGCUCGCUCGCACUCAC-UCGCACGGUUCUCGUACAGGGGUGCAUUUACUUGCGUCUGUGUGUGUGCCUACCGUUUGGCUGCCUGCUGCCUGCU
(((.((((((...(((......)))...)))...(((((.(((-.((((.(((....((((....))))....)))))))...))).)))))))).)))...(((........))).... ( -39.90)
>DroYak_CAF1 7090 120 + 1
CGCGAGGGAGAUAGCUGUAUGCAGCUUGCUCGCUCGCACUCGCCACGAACGGUGCUCGUACAGGGGUGCAUUUACUUGCGUCUGUGUGCGUGCCUGCCGUUUGGCUGCCUGCUGCCUGCU
.(((((.(((..(((((....)))))..))).)))))....((((..((((((((.((((((.((..(((......)))..)).)))))).))..)))))))))).....((.....)). ( -58.60)
>consensus
UGGAAGGGAGACAGC_GUAUGCAGCGUGCUCGCUCGCACUCACCACGAACGGUGCUCGUACAGGGGUGCAUUUACUUGCGUCUGUGUGCGUGCCUGCCGUUUGGCUGCCUGCUGCCUGCU
.....((.((.((((.....(((((((((......))))......((((((((((.((((((.((..(((......)))..)).)))))).))..)))))))))))))..)))).)).)) (-44.48 = -45.60 +   1.12)

alignment

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secondary structure

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Window 0

Location 12,068,441 – 12,068,561
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.33
Mean single sequence MFE -44.36
Consensus MFE -41.06
Energy contribution -41.18
Covariance contribution 0.12
Combinations/Pair 1.08
Mean z-score -1.55
Structure conservation index 0.93
SVM decision value 1.52
SVM RNA-class probability 0.960622
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12068441 120 + 27905053
CACCACGAACGGUGCUCGUACAGGGGUGCAUUUACUUGCGUCUGUGUGCGGGCCUGCCGUUUGGCUGCCUGCUGCCUGCUUCUUGAGCGCCGAACGUUUUAUUUGUGAUUUUAGCACGGC
.....(((((((((((((((((.((..(((......)))..)).)))))))))..))))))))...((((((((..(((.....(((((.....))))).....)))....))))).))) ( -47.70)
>DroSec_CAF1 5057 120 + 1
CACCACGAACGGUGCUCGUACAGGGGUGCAUUUACUUGCGUCUGUGUGCGUGGCUGCCGUUUGGCUGCCUGCUGCCUGCUUCUUGAGCGCCGAACGUUUUAUUUGUGAUUUUAGCACGGC
..(((((..(((((((((((((.((..(((......)))..)).)))))..(((.(((....))).))).((.....)).....))))))))..))).......(((.......))))). ( -46.80)
>DroSim_CAF1 5489 120 + 1
CACCACGAACGGUGCUCGUACAGGGGUGCAUUUACUUGCGUCUGUGUGCGUGCCUGCCGUUUGGCUGCCUGCUGCCUGCUUCUUGAGCGCCGAACGUUUUAUUUGUGAUUUUAGCACGGC
.....((((((((((.((((((.((..(((......)))..)).)))))).))..))))))))...((((((((..(((.....(((((.....))))).....)))....))))).))) ( -44.40)
>DroEre_CAF1 7009 119 + 1
CAC-UCGCACGGUUCUCGUACAGGGGUGCAUUUACUUGCGUCUGUGUGUGUGCCUACCGUUUGGCUGCCUGCUGCCUGCUUCUUGAGCGCCGAACGUUUUAUUUGUGAUUUUAGCACGGC
...-(((((.(((...((((((.((..(((......)))..)).)))))).)))...((((((((.(((.((.....)).....).)))))))))).......)))))............ ( -35.50)
>DroYak_CAF1 7130 120 + 1
CGCCACGAACGGUGCUCGUACAGGGGUGCAUUUACUUGCGUCUGUGUGCGUGCCUGCCGUUUGGCUGCCUGCUGCCUGCUUCUUGAGCGCCGAGCGUUUUAUUUGUGAUUUUAGCACGGU
.((((..((((((((.((((((.((..(((......)))..)).)))))).))..)))))))))).((((((((..(((.....((((((...)))))).....)))....))))).))) ( -47.40)
>consensus
CACCACGAACGGUGCUCGUACAGGGGUGCAUUUACUUGCGUCUGUGUGCGUGCCUGCCGUUUGGCUGCCUGCUGCCUGCUUCUUGAGCGCCGAACGUUUUAUUUGUGAUUUUAGCACGGC
.....((((((((((.((((((.((..(((......)))..)).)))))).))..))))))))...((((((((..(((.....(((((.....))))).....)))....))))).))) (-41.06 = -41.18 +   0.12)

alignment

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secondary structure

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Window 1

Location 12,068,441 – 12,068,561
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.33
Mean single sequence MFE -37.10
Consensus MFE -31.36
Energy contribution -32.00
Covariance contribution 0.64
Combinations/Pair 1.03
Mean z-score -1.57
Structure conservation index 0.85
SVM decision value 0.54
SVM RNA-class probability 0.774706
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12068441 120 - 27905053
GCCGUGCUAAAAUCACAAAUAAAACGUUCGGCGCUCAAGAAGCAGGCAGCAGGCAGCCAAACGGCAGGCCCGCACACAGACGCAAGUAAAUGCACCCCUGUACGAGCACCGUUCGUGGUG
((((((.......))).......(((..(((.((((.....(((((..((.(((.(((....)))..))).))...((.((....))...))....)))))..)))).)))..)))))). ( -40.80)
>DroSec_CAF1 5057 120 - 1
GCCGUGCUAAAAUCACAAAUAAAACGUUCGGCGCUCAAGAAGCAGGCAGCAGGCAGCCAAACGGCAGCCACGCACACAGACGCAAGUAAAUGCACCCCUGUACGAGCACCGUUCGUGGUG
((((((.......))).......(((..(((.((((.....(((((.....(((.(((....))).)))..(((.....((....))...)))...)))))..)))).)))..)))))). ( -41.10)
>DroSim_CAF1 5489 120 - 1
GCCGUGCUAAAAUCACAAAUAAAACGUUCGGCGCUCAAGAAGCAGGCAGCAGGCAGCCAAACGGCAGGCACGCACACAGACGCAAGUAAAUGCACCCCUGUACGAGCACCGUUCGUGGUG
((((((.......))).......(((..(((.((((........(((........))).....(((((...(((.....((....))...)))...)))))..)))).)))..)))))). ( -37.80)
>DroEre_CAF1 7009 119 - 1
GCCGUGCUAAAAUCACAAAUAAAACGUUCGGCGCUCAAGAAGCAGGCAGCAGGCAGCCAAACGGUAGGCACACACACAGACGCAAGUAAAUGCACCCCUGUACGAGAACCGUGCGA-GUG
((((((.......)))........((((.((((((.....)))..((.....)).))).))))...)))...(((.((.((....))...))......((((((.....)))))).-))) ( -30.60)
>DroYak_CAF1 7130 120 - 1
ACCGUGCUAAAAUCACAAAUAAAACGCUCGGCGCUCAAGAAGCAGGCAGCAGGCAGCCAAACGGCAGGCACGCACACAGACGCAAGUAAAUGCACCCCUGUACGAGCACCGUUCGUGGCG
.(((((.......))).......(((..(((.((((........(((........))).....(((((...(((.....((....))...)))...)))))..)))).)))..))))).. ( -35.20)
>consensus
GCCGUGCUAAAAUCACAAAUAAAACGUUCGGCGCUCAAGAAGCAGGCAGCAGGCAGCCAAACGGCAGGCACGCACACAGACGCAAGUAAAUGCACCCCUGUACGAGCACCGUUCGUGGUG
((((((.......))).......(((..(((.((((.....(((((..((((.(.(((....))).).)..........((....))...)))...)))))..)))).)))..)))))). (-31.36 = -32.00 +   0.64)

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 11:32:45 2006