Locus 661

Sequence ID 3R_DroMel_CAF1
Location 2,430,709 – 2,430,849
Length 140
Max. P 0.688645
window1046 window1047 window1048

overview

Window 6

Location 2,430,709 – 2,430,829
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.75
Mean single sequence MFE -36.95
Consensus MFE -30.21
Energy contribution -31.13
Covariance contribution 0.92
Combinations/Pair 1.09
Mean z-score -1.46
Structure conservation index 0.82
SVM decision value 0.32
SVM RNA-class probability 0.688645
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2430709 120 + 27905053
GCGUUAAAUUUAUGCCAGAAUGCGGCUUCAACGCGCCGCAGUUGCAGCUCCAGCUGCAGAUCCUUUUCAUCCUGAAGCUGCCGUUUCCCCACAUUUGUACAAUGGGUUAAAUGAGAUGGA
((((.......)))).....((((((........)))))).(((((((....))))))).(((.((((((...(((((....)))))((((...........))))....)))))).))) ( -36.50)
>DroSec_CAF1 143447 111 + 1
GCGUUAAAUUUAUGCCAGAAUGCGGCUUCACCGCGCUGCAGUUGCAGCUCCAGCUGCAGAUCCUUUUCAUCCUGAAGCUGCCGUU---------UGGUACAAUGGGUUAAAUGAGAUGGA
.((((.(((((((((((((..(((((((((.....(((((((((......))))))))).............)))))))))..))---------))))...))))))).))))....... ( -36.87)
>DroSim_CAF1 137630 120 + 1
GCGUUAAAUUUAUGCCAGAAUGCGGCUUCACCGCGCUGCAGUUGCAGCUCCAGCUGCAGAUCCUUUUCAUCCUGAAGCUGCCGUUUCCCCACAUUGGUACAAUGGGUUAAAUGAGAUGGA
..............(((....(((((((((.....(((((((((......))))))))).............)))))))))(((((..((.(((((...)))))))..)))))...))). ( -36.57)
>DroEre_CAF1 139255 120 + 1
GCGUUAAAUUUAUGCCAGAAUGCGGCUUCGCCGCGCUGCAGUUGCAACUCGAGCUGCAGAUCCUUUUAAUCCUGAAGCUGCCGUUUUCCCACAUUGGUACAAUGGGUUAAAUGAGACGGA
((((.......))))(((...(((((...))))).((((((((........))))))))............)))...(((((((((..((.(((((...)))))))..))))).).))). ( -35.90)
>DroYak_CAF1 133455 120 + 1
GCGUUAAAUUUAUGCCAGAAUGCGGCUUUACCUCGCUGCAGUUGCAGCUCCAGCUGCAGAUCCUUUUCAUCCUGAAGCUGCCGUUUCCCCACAUUGGUACAAUGGGUUAAAUGAGCUGCA
((((.......)))).....((((((........))))))..(((((((((((((.(((............))).)))))..((((..((.(((((...)))))))..)))))))))))) ( -38.90)
>consensus
GCGUUAAAUUUAUGCCAGAAUGCGGCUUCACCGCGCUGCAGUUGCAGCUCCAGCUGCAGAUCCUUUUCAUCCUGAAGCUGCCGUUUCCCCACAUUGGUACAAUGGGUUAAAUGAGAUGGA
.((((..(((((.(((.....(((((((((.....(((((((((......))))))))).............)))))))))..........(((((...)))))))))))))..)))).. (-30.21 = -31.13 +   0.92)

alignment

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secondary structure

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dotplot

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Window 7

Location 2,430,709 – 2,430,829
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.75
Mean single sequence MFE -35.76
Consensus MFE -30.08
Energy contribution -31.00
Covariance contribution 0.92
Combinations/Pair 1.11
Mean z-score -1.25
Structure conservation index 0.84
SVM decision value -0.02
SVM RNA-class probability 0.523031
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2430709 120 - 27905053
UCCAUCUCAUUUAACCCAUUGUACAAAUGUGGGGAAACGGCAGCUUCAGGAUGAAAAGGAUCUGCAGCUGGAGCUGCAACUGCGGCGCGUUGAAGCCGCAUUCUGGCAUAAAUUUAACGC
.(((..........(((((.........)))))(((...((((((((((..((...((...)).)).))))))))))...((((((........)))))))))))).............. ( -37.20)
>DroSec_CAF1 143447 111 - 1
UCCAUCUCAUUUAACCCAUUGUACCA---------AACGGCAGCUUCAGGAUGAAAAGGAUCUGCAGCUGGAGCUGCAACUGCAGCGCGGUGAAGCCGCAUUCUGGCAUAAAUUUAACGC
..........................---------..((((((.(((..........))).)))).((..(((((((....)))))((((.....))))..))..))..........)). ( -31.10)
>DroSim_CAF1 137630 120 - 1
UCCAUCUCAUUUAACCCAUUGUACCAAUGUGGGGAAACGGCAGCUUCAGGAUGAAAAGGAUCUGCAGCUGGAGCUGCAACUGCAGCGCGGUGAAGCCGCAUUCUGGCAUAAAUUUAACGC
(((...((((((..(((((.........)))))(((.(....).))).))))))...)))......((..(((((((....)))))((((.....))))..))..))............. ( -37.80)
>DroEre_CAF1 139255 120 - 1
UCCGUCUCAUUUAACCCAUUGUACCAAUGUGGGAAAACGGCAGCUUCAGGAUUAAAAGGAUCUGCAGCUCGAGUUGCAACUGCAGCGCGGCGAAGCCGCAUUCUGGCAUAAAUUUAACGC
..(((...(((((.(((((.........)))))......((.(((.(((((((.....))))((((((....)))))).))).)))(((((...)))))......)).)))))...))). ( -35.10)
>DroYak_CAF1 133455 120 - 1
UGCAGCUCAUUUAACCCAUUGUACCAAUGUGGGGAAACGGCAGCUUCAGGAUGAAAAGGAUCUGCAGCUGGAGCUGCAACUGCAGCGAGGUAAAGCCGCAUUCUGGCAUAAAUUUAACGC
((((((((......(((((.........))))).......(((((.((((.(....)...)))).)))))))))))))......(((.((.....))((......))..........))) ( -37.60)
>consensus
UCCAUCUCAUUUAACCCAUUGUACCAAUGUGGGGAAACGGCAGCUUCAGGAUGAAAAGGAUCUGCAGCUGGAGCUGCAACUGCAGCGCGGUGAAGCCGCAUUCUGGCAUAAAUUUAACGC
..............(((((.........)))))....((((((.(((..........))).)))).((..(((((((....)))))(((((...)))))..))..))..........)). (-30.08 = -31.00 +   0.92)

alignment

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secondary structure

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dotplot

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Window 8

Location 2,430,749 – 2,430,849
Length 100
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 88.19
Mean single sequence MFE -30.06
Consensus MFE -21.38
Energy contribution -22.46
Covariance contribution 1.08
Combinations/Pair 1.13
Mean z-score -1.67
Structure conservation index 0.71
SVM decision value -0.03
SVM RNA-class probability 0.517100
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2430749 100 - 27905053
UAUA--AGCUGCACCCAGCUUGUCCAUCUCAUUUAACCCAUUGUACAAAUGUGGGGAAACGGCAGCUUCAGGAUGAAAAGGAUCUGCAGCUGGAGCUGCAAC
.(((--(((((....)))))))).............(((((.........)))))......((((((((((..((...((...)).)).))))))))))... ( -31.70)
>DroSec_CAF1 143487 91 - 1
UAUA--AGCUGCCCCUGGCUUGUCCAUCUCAUUUAACCCAUUGUACCA---------AACGGCAGCUUCAGGAUGAAAAGGAUCUGCAGCUGGAGCUGCAAC
.(((--((((......))))))).........................---------....((((((((((..((...((...)).)).))))))))))... ( -23.50)
>DroSim_CAF1 137670 100 - 1
UAUA--AGCUGCCCCCGGCUUGUCCAUCUCAUUUAACCCAUUGUACCAAUGUGGGGAAACGGCAGCUUCAGGAUGAAAAGGAUCUGCAGCUGGAGCUGCAAC
.(((--(((((....)))))))).............(((((((...))))).))(....).((((((((((..((...((...)).)).))))))))))... ( -31.30)
>DroEre_CAF1 139295 102 - 1
CACACCAGCUUAUCCCGGCUUGUCCGUCUCAUUUAACCCAUUGUACCAAUGUGGGAAAACGGCAGCUUCAGGAUUAAAAGGAUCUGCAGCUCGAGUUGCAAC
....((.....((((.((((.(.((((.....((..(((((((...))))).))..)))))))))))...)))).....))...((((((....)))))).. ( -25.50)
>DroYak_CAF1 133495 100 - 1
UAUA--AGCUGGCCCCAGCGUCUGCAGCUCAUUUAACCCAUUGUACCAAUGUGGGGAAACGGCAGCUUCAGGAUGAAAAGGAUCUGCAGCUGGAGCUGCAAC
....--.((((....))))...((((((((......(((((.........))))).......(((((.((((.(....)...)))).))))))))))))).. ( -38.30)
>consensus
UAUA__AGCUGCCCCCGGCUUGUCCAUCUCAUUUAACCCAUUGUACCAAUGUGGGGAAACGGCAGCUUCAGGAUGAAAAGGAUCUGCAGCUGGAGCUGCAAC
.......((((....)))).................(((((.........)))))......((((((((((..((...((...)).)).))))))))))... (-21.38 = -22.46 +   1.08)

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 09:48:39 2006